diff --git a/.gitattributes b/.gitattributes index 08ec68de11df88f142f934f21d2bb8ff8bf2540b..825b9efd62ba2a926174a5888b0dc8c30c18a20f 100644 --- a/.gitattributes +++ b/.gitattributes @@ -79,3 +79,95 @@ PMC005xxxxxx_0.jsonl filter=lfs diff=lfs merge=lfs -text PMC006xxxxxx_0.jsonl filter=lfs diff=lfs merge=lfs -text PMC007xxxxxx_0.jsonl filter=lfs diff=lfs merge=lfs -text PMC008xxxxxx_0.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_701.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_702.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_703.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_704.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_705.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_706.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_708.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_709.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_710.jsonl filter=lfs diff=lfs merge=lfs -text 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+PMC_clustering_797.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_798.jsonl filter=lfs diff=lfs merge=lfs -text +PMC_clustering_799.jsonl filter=lfs diff=lfs merge=lfs -text diff --git a/PMC_clustering_700.jsonl b/PMC_clustering_700.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b15027c852ad0964ff52e1b8f1c861385335a5a6 --- /dev/null +++ b/PMC_clustering_700.jsonl @@ -0,0 +1,131 @@ +{"text": "Escherichia coli responsible for intestinal infections in piglets. Phages vB_EcoM_F1, vB_EcoM_FB, vB_EcoS_FP, vB_EcoM_FT, vB_EcoM_SP1, vB_EcoP_SP5M, vB_EcoP_SP7, and vB_EcoS_SP8 were isolated between 2007 and 2018 in the Iberian Peninsula. These viruses span the three tailed phage families, Podoviridae, Siphoviridae, and Myoviridae.We report eight phages infecting enterotoxigenic Escherichia coli responsible for intestinal infections in piglets. Phages vB_EcoM_F1, vB_EcoM_FB, vB_EcoS_FP, vB_EcoM_FT, vB_EcoM_SP1, vB_EcoP_SP5M, vB_EcoP_SP7, and vB_EcoS_SP8 were isolated between 2007 and 2018 in the Iberian Peninsula. These viruses span the three tailed phage families, Podoviridae, Siphoviridae, and Myoviridae.We report eight phages infecting enterotoxigenic Escherichia coli (ETEC) infections cause diarrhea and death among weaning and postweaning piglets in Geneious Prime v2020.1 software .Here, we present eight complete nd Spain . The excnd Spain , isolateisolates were incisolates . DNA wasisolates . Reads wsoftware . Genomicsoftware and compsoftware , tRNAscasoftware , ARAGORNsoftware , and HHpsoftware revealed high homology with several viruses from the nonredundant database . Phages The analyses of these phages\u2019 genomes together with additional studies focused on their fitness can provide new resources to combat ETEC infections.E. coli phage genome sequences are listed in PRJNA646048.The GenBank accession numbers of the"} +{"text": "Our software introduces new visualization technology that enables independent layers of interactivity using Plotly in R, which aids in the exploration of large biological datasets. The bigPint package presents modernized versions of scatterplot matrices, volcano plots, and litre plots through the implementation of layered interactivity. These graphics have detected normalization issues, differential expression designation problems, and common analysis errors in public RNA-sequencing datasets. Researchers can apply bigPint graphics to their data by following recommended pipelines written in reproducible code in the user manual. In this paper, we explain how we achieved the independent layers of interactivity that are behind bigPint graphics. Pseudocode and source code are provided. Computational scientists can leverage our open-source code to expand upon our layered interactive technology and/or apply it in new ways toward other computational biology tasks.Interactive data visualization is imperative in the biological sciences. The development of independent layers of interactivity has been in pursuit in the visualization community. We developed bigPint, a data visualization package available on Bioconductor under the GPL-3 license ( Biological disciplines face the challenge of increasingly large and complex data. One necessary approach toward eliciting information is data visualization. Newer visualization tools incorporate interactive capabilities that allow scientists to extract information more efficiently than static counterparts. In this paper, we introduce technology that allows multiple independent layers of interactive visualization written in open-source code. This technology can be repurposed across various biological problems. Here, we apply this technology to RNA-sequencing data, a popular next-generation sequencing approach that provides snapshots of RNA quantity in biological samples at given moments in time. It can be used to investigate cellular differences between health and disease, cellular changes in response to external stimuli, and additional biological inquiries. RNA-sequencing data is large, noisy, and biased. It requires sophisticated normalization. The most popular open-source RNA-sequencing data analysis software focuses on models, with little emphasis on integrating effective visualization tools. This is despite sound evidence that RNA-sequencing data is most effectively explored using graphical and numerical approaches in a complementary fashion. The software we introduce can make it easier for researchers to use models and visuals in an integrated fashion during RNA-sequencing data analysis. PLOS Computational Biology Software paper.This is a Interactive data visualization is increasingly imperative in the biological sciences . When peInteractive visualization tools for genomic data can have restricted access when only available on certain operating systems and/or when requiring payment \u20135. TheseWe recently developed bigPint, an interactive RNA-sequencing data visualization software package available on Bioconductor. In the current paper, we will now explain the technical innovations and merits of the bigPint package, including new interactive visualization techniques that we believe can be helpful in the development and usage of future biological visualization software.https://lindsayrutter.github.io/bigPint/articles/pipeline). This pipeline uses reproducible code and sample data from the bigPint package, so you can smoothly follow along each line of example code. For additional details, we recommend users to view articles in the Get Started tab on the package website (https://lindsayrutter.github.io/bigPint).For users who would like to immediately try out the package hands-on and apply bigPint graphics to their data, we recommend consulting the example pipeline format and contains the read counts for all genes of interest. The value in row i and column j should indicate how many reads have been assigned to gene i in sample j. This is the same input format required in popular RNA-seq count-based statistical packages, such as DESeq2, edgeR, limma, EBSeq, and BaySeq Editor's specific comments:thank you for your patience while this manuscript was under review, as there was difficulty sourcing appropriately qualified reviewers. Please thoroughly address the comments of both reviewers in your revisions, in particular those focused on software architecture, reliability, and ease of use.Reviewer's Responses to QuestionsComments to the Authors:Please note here if the review is uploaded as an attachment.Reviewer #1: Rutter and Cook discuss their new R package offering data visualization techniques geared towards RNA-seq data. The data visualization techniques make clever use of interactivity to highlight aspects of the data, which enable researchers to identify common analysis errors. While I like the concept of the presented visualization techniques, I am not convinced that this will be a widely applied tool. The tool felt clunky and still produced several errors. I will outline these as well as other issues/suggestions below:1. The authors claim that their software can be used for the exploration of any large biological datasets. However, their choice of plots, in particular the volcanoplot, suggests to me a focus on RNA-seq data. I would suggest the inclusion of another example for a non RNA-seq dataset or making it clear that this package targets RNA-seq data exclusively.https://github.com/dreamRs/shinylogs).2. It is great that all plots are easily downloadable, but for the purpose of replicability it would be great if logs of all user interactions could be provided. This can, for example, be handled with shinylogs ```{r cut_and_paste_from_bit_ly_spmCode, include=FALSE, eval=FALSE}# I have removed this from the review because it uses up too many words...# trust me please, I have cut and pasted it verbatim.```When I run this, a window opens and then closes again. Interesting my datais a Value - not Data in my Global Environment and it says \"NULL (empty)\"Why? Well let's run the data acquisition by itself.Annoyingly this is not a reproducible problem.Sometimes it seems to work but I don't know why.```{r test_data_download, include=TRUE}data <- bigPint:::PKGENVIR$DATAstr(data)```Still NULL, sadly.All the other code examples use the same code to get data in so I'm not going to try them here. I have tried them previously.#### Where else can I go for help?https://www.bioconductor.org/packages/release/bioc/html/bigPint.html].Let's check (Bioconductor)[The page is a good starting point.It has a green build which is a good sign.https://www.bioconductor.org/packages/release/bioc/vignettes/bigPint/inst/doc/bioconductor.R]Check out the (R-script)[Woops! It seems blank. A bit frustrating.https://www.bioconductor.org/packages/release/bioc/vignettes/bigPint/inst/doc/bioconductor.html)[HTML Vignette](https://lindsayrutter.github.%20io/bigPint/)! Woops again!points to website with a [rotten url](Let's go to the Github Repository and see what we can find...https://lindsayrutter.github.io/bigPint/) is in the manuscriptThe [link]data(\"soybean_cn_sub\")soybean_cn_sub <- soybean_cn_subapp <- plotSMApp(data=soybean_cn_sub)if (interactive) {shiny::runApp(app)}```Good new is that the data function works and gives us some data!```{r str_data}str(soybean_cn_sub)```Nice data.frame produced.Bad news is that my interactive plot still won't work!Well actually it does work when I run this again.It is a bit slow and it gives lots of red text:'scatter' objects don't have these attributes: 't2'What happens if I try the```{r try_PKGENVIR$DATA_again}data <- bigPint:::PKGENVIR$DATA```It works! If I do it after I run your App. Wonder why? I'm not going to spend any time working through that at the moment.Now the script above works with lots of error messages.#### Back to square one, can I make the static hex plots```{r static_hex}data(soybean_ir_sub)soybean_ir_sub <- logdata(soybean_ir_sub_metrics)ret <- plotLitrelength(ret)names(ret)[1]ret[[1]]```Answer is Yes! Good and it looks interesting with points highlighted on it.I probably should have started here in the first place but hey...#### I need to try to make the apps work...https://rdrr.io/bioc/bigPint/man/plotVolcanoApp.html]I found some code here: <- logapp <- plotLitreAppif (interactive) {shiny::runApp}```I can see the number of genes in each hexagram if I hover over it - nice.Plot gene works to give orange spots which can be hovered over to identify. However, I'm not sure how I am selecting those genes.I have worked out that it is going through the genes by rank. However, because that information is off the bottom of the screen, it took me a while to realise.I need to watch the video again!https://lindsayrutter.github.io/bigPint/articles/interactive.html]Back to (website)app <- plotSMApp(data=soybean_cn_sub)if (interactive) {shiny::runApp(app)}```This works! Excellent.Selecting hexagrams works.Downloading IDs works.Downloading plots doesn't :-(Need to open in Browser as advised!Could add that as error message?OK so it does work but it produces LOTS of warnings.I wonder why?Warning: 'scatter' objects don't have these attributes: 't2'Lots of repeat of this warning.#### Try plotLitreApp```{r plotSMAapp_again}data(\"soybean_ir_sub\")data(\"soybean_ir_sub_metrics\")soybean_ir_sub_log <- soybean_ir_subsoybean_ir_sub_log <- logapp <- plotLitreAppif (interactive) {shiny::runApp}```#### Try plotPCPApp```{r plotPCPApp}soybean_ir_sub_st = as.data.frame, 1,scale)))soybean_ir_sub_st$ID = as.character(soybean_ir_sub$ID)soybean_ir_sub_st = soybean_ir_sub_stcolnames(soybean_ir_sub_st) = colnames(soybean_ir_sub)nID = which)soybean_ir_sub_st = 0plotGenes = filter %>%select(ID)pcpDat = filterapp <- plotPCPApp(data = pcpDat)if (interactive) {shiny::runApp}```Works!In Browser, I can save images as advised.Nice job.#### Try Volcano app from websitehttps://lindsayrutter.github.io/bigPint/articles/interactive.html#volcano-plot-app) when accessed on 12 Oct 2019.Sadly no code on [website](https://rdrr.io/bioc/bigPint/man/plotVolcanoApp.html] instead as above. Made it work again!Example code from (here) en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8attached base packages:[1] stats graphics grDevices utils datasets methods[7] baseother attached packages:[1] shinycssloaders_0.2.0 Hmisc_4.2-0 Formula_1.2-3[4] survival_2.44-1.1 lattice_0.20-38 RColorBrewer_1.1-2[7] GGally_1.4.0 data.table_1.12.2 dplyr_0.8.3[10] stringr_1.4.0 hexbin_1.27.3 tidyr_1.0.0[13] htmlwidgets_1.5.1 plotly_4.9.0 ggplot2_3.2.1[16] shinydashboard_0.7.1 shiny_1.4.0 bigPint_1.0.0loaded via a namespace (and not attached):[1] Rcpp_1.0.2 assertthat_0.2.1 zeallot_0.1.0[4] digest_0.6.21 mime_0.7 R6_2.4.0[7] plyr_1.8.4 backports_1.1.5 acepack_1.4.1[10] httr_1.4.1 pillar_1.4.2 rlang_0.4.0[13] lazyeval_0.2.2 rstudioapi_0.10 rpart_4.1-15[16] Matrix_1.2-17 checkmate_1.9.4 labeling_0.3[19] splines_3.6.1 foreign_0.8-72 munsell_0.5.0[22] compiler_3.6.1 httpuv_1.5.2 xfun_0.10[25] pkgconfig_2.0.3 base64enc_0.1-3 htmltools_0.4.0[28] nnet_7.3-12 tidyselect_0.2.5 tibble_2.1.3[31] gridExtra_2.3 htmlTable_1.13.2 reshape_0.8.8[34] viridisLite_0.3.0 withr_2.1.2 crayon_1.3.4[37] later_1.0.0 grid_3.6.1 jsonlite_1.6[40] xtable_1.8-4 gtable_0.3.0 lifecycle_0.1.0[43] magrittr_1.5 scales_1.0.0 stringi_1.4.3[46] promises_1.1.0 latticeExtra_0.6-28 ellipsis_0.3.0[49] vctrs_0.2.0 tools_3.6.1 glue_1.3.1[52] purrr_0.3.2 crosstalk_1.0.0 fastmap_1.0.1[55] yaml_2.2.0 colorspace_1.4-1 cluster_2.1.0[58] knitr_1.25**********Have all data underlying the figures and results presented in the manuscript been provided?PLOS Computational Biologydata availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.Large-scale datasets should be made available via a public repository as described in the Reviewer #1: YesReviewer #2: Yes**********what does this mean?). If published, this will include your full peer review and any attached files.PLOS authors have the option to publish the peer review history of their article is very helpful.**********Have all data underlying the figures and results presented in the manuscript been provided?PLOS Computational Biologydata availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.Large-scale datasets should be made available via a public repository as described in the Reviewer #1: Yes**********what does this mean?). If published, this will include your full peer review and any attached files.PLOS authors have the option to publish the peer review history of their article 1223-442824 | ploscompbiol.org | @PLOSCompBiolPLOS Computational Biology | Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom"} +{"text": "R0) of 3.4 in Weifang, and a mean effective reproduction number (t)R that falls below 1 on 4 February. We further estimate the number of infections through time and compare these estimates to confirmed diagnoses by the Weifang Centers for Disease Control. We find that these estimates are consistent with reported cases and there is unlikely to be a large undiagnosed burden of infection over the period we studied.Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given location. Here, we report an analysis of 20 whole SARS- CoV-2 genomes from a single relatively small and geographically constrained outbreak in Weifang, People\u2019s Republic of China. Using Bayesian model-based phylodynamic methods, we estimate a mean basic reproduction number ( These data comprise 20 whole-genome sequences from confirmed COVID-19 cases in Weifang, Shandong Province, People\u2019s Republic of China. The data were collected over the course of several weeks up to 10 February 2020, and overlap with a period of intensifying public health and social distancing measures. These interventions included public health messaging, establishing phone hot-lines, encouraging home isolation for recent visitors from Wuhan (January 23\u201326), optimising triage of suspected cases in hospitals (January 24), travel restrictions (January 26), extending school closures, and establishing \u2018fever clinics\u2019 for consultation and diagnosis (January 27) . In contModel-based phylodynamic methods have been previously used to analyse sequence data from Wuhan and exported international cases . Using aAs of 10 February 2020, 136 suspected cases and 214 close contacts were diagnosed by Weifang Center for Disease Control and Prevention; of these, 38 cases were confirmed positive with SARS-CoV-2. The median age of patients was 36 (range: 6\u201375). Two of twenty patients suffered severe or critical illness.Viral RNA was extracted using the Maxwell 16 Viral Total Nucleic Acid Purification Kit (Promega AS1150) with the magnetic bead method, and the RNeasy Mini Kit (QIAGEN 74104) with the column method. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was carried out using the 2019 novel coronavirus nucleic acid detection kit to confirm the presence of SARS-CoV-2 viral RNA with cycle threshold (Ct) values ranging from 17 to 34, targeting the highly conservative region (ORF1ab/N gene) in the SARS-CoV-2 genome.Concentration of RNA samples was measured by the Qubit RNA HS Assay Kit . The enzyme DNase was used to remove host DNA. The remaining RNA was used to construct the single-stranded circular DNA library with the MGIEasy RNA Library preparation reagent set . Purified RNA was then fragmented. Using these short fragments as templates, random hexamers were used to synthesise the first-strand cDNA and then the second strand. Using the short double-strand DNA, a DNA library was constructed through end repair, adaptor ligation and PCR amplification. PCR products were transformed into a single-strand circular DNA library through DNA-denaturation and circularisation. DNA nanoballs (DNBs) were generated with the single-strand circular DNA library by rolling circle replication. The DNBs were loaded into the flow cell and pair-end 100\u2009bp sequencing was performed on DNBSEQ-T7 platform 8 . Twenty genomes were assembled with length from 26,840 to 29,882 nucleotides.>100\u00d7 average sequencing depth across the SARS-CoV-2 genome were subsampled to achieve 100\u00d7 sequencing depth before being assembled.Total reads were first processed using Kraken v0.10.5 (default parameters) with a self-built database of Coronaviridae genomes to identify Coronaviridae-like reads. To remove low-quality reads, duplications and adaptor contaminations, fastp v0.19.5 (parameters: -q 20-u 20 -n 1 -l 50) and SOAPnuke v1.5.6 (parameters: -l 20 -q 0.2 -E 50 -n 0.02 -5 0 -Q 2 -G -d) were used. The Coronaviridae-like reads of samples with <100\u00d7 average sequencing depth were directly assembled de novo with SPAdes v3.14.0 using default settings. The Coronaviridae-like reads of samples with The 20 Weifang sequences have mean 1.1 per cent N content and are deposited in GISAID (gisaid.org).The phylodynamic model is designed to account for 1, nonlinear epidemic dynamics in Weifang with a realistic course of infection (incubation and infectious periods), 2, variance in transmission rates that can influence epidemic size estimates, and 3, migration of lineages in and out of Weifang.The maximum number of daily confirmed COVID-19 cases occurred on February 5, but it is unknown when the maximum prevalence of infection occurred. To capture a nonlinear decrease in cases following epidemic peak, and to account for a realistic distribution of generation times, we use an extension of the susceptible- exposed-infectious-recovered (SEIR) model for epidJ which has a higher transmission rate (\u03c4 -fold higher) than the I compartment.To estimate total numbers infected, the phylodynamic model must account for epidemiological variables which are known to significantly influence genetic diversity . ForemosJ compartment with probability h,p or otherwise to I. The model is implemented as a system of ordinary differential equations: The variance of the implied offspring distribution is calibrated to give a similar over-dispersion to that of the SARS epidemic. Upon leaving the incubation period, individuals progress to the Y (t)) serves as a source of new infections and is assumed to be growing exponentially (at rate \u03c1) over this time period.The outbreak in Weifang was seeded by multiple lineages imported at various times from the rest of China. We therefore account for location of sampling in our model. Migration is modelled as a bi-directional process with rates proportional to epidemic size in Weifang. The larger reservoir of COVID-19 cases outside of Weifang , \u03b7 is the per-lineage rate of migration out of Weifang, and the total rate of migration in and out of Weifang is \u03b7X.Migration only depends on the size of variables in the Weifang compartment and thus does not influence epidemic dynamics; it will only influence the inferred probability that a lineage resides within Weifang. For compartment \u03b7, \u03b2 and \u03c1 are estimated. Additionally, we estimate initial sizes of Y, E, and S. Initial values of I, J, and R are fixed at 0. Other parameters are fixed based on prior information. We fix 1/\u03b30 = 4.1\u2009days and 1/\u03b31 = 3.8\u2009days and the initial growth rate in cases was approximately 22 per cent per day, consistent with those estimated in other settings and during the early epidemic in Wuhan when Weifang was implementing a variety of public health interventions and contact tracing to limit epidemic spread. Our central estimate of tR drops below 1 on the 4th of February.Effective reproduction number over time is shown in in Wuhan . SamplinAlthough previous studies have shown the significance of realistic modelling for fidelity of phylogenetic inference , our anaIn this analysis, there is a mean of three pairwise differences among sequences from Weifang; the corresponding number among the sequences outside of Weifang is eight.There is correspondingly low confidence in tree topology , and onlThe earliest Weifang sequence was sampled on 25 January from a patient who first showed symptoms on 16 January. These dates cover a similar range as the posterior TMRCA of all Weifang sequences .Our analysis of 20 SARS-CoV-2 genomes has confirmed independent observations regarding the rate of spread and burden of infection in Weifang, China. Surveillance of COVID-19 is rendered difficult by high proportions of illness with mild severity and an unknown proportion of asymptomatic infection . The exttR over time, falling below 1 on 4 February, suggests a slower rate of spread outside of Wuhan and effective control strategies implemented in late January. It is consistent with a previous modelling study of Shandong province is a limitation of this study. However, this represents a significant proportion of the total number of cases reported; there were thirty-eight confirmed cases at the date of the last genetic sample (10 February), rising no further than forty-four from 16 February onwards . DespiteFurther, it is possible that the outbreak observed in Weifang could be due not to community transmission, but rather multiple importations. However, given that we sampled the reference set from a GISAID database downloaded in June, it is reasonable to assume close genetic matches would have been chosen. A maximum-likelihood tree of the entire alignment shows thCommunity transmission is further supported by the fact that cases were identified via contact tracing. This forms another limitation, as it suggests non-random sampling of cases in Weifang. This could lead to an underestimate of the total number of cases in Weifang. However, as a large proportion of reported cases were included in this analysis, the bias is unlikely to be too significant.\u03b2 has a constant value, tR can decrease only as a result of depleting susceptibles. The decrease in tR is therefore a constraint in the model and occurred even when sampling from the prior. Despite this, the genetic data was informative on the value of \u03b2 (and therefore R0), which in turn affects the date at which tR falls below 1. Our analysis demonstrates a reliable mean estimate of R0, with a narrower uncertainty, compared to sampling from the prior. Although other methods which allow for time-varying transmission rate (including other PhyDyn model templates) or models with a piece-wise tR function . Accession numbers for sequences from Weifang: EPI_ISL_413691 EPI_ISL_413693 EPI_ISL_413694, EPI_ISL_413695 EPI_ISL_413696 EPI_ISL_413697, EPI_ISL_413711 EPI_ISL_413729 EPI_ISL_413746, EPI_ISL_413747 EPI_ISL_413748 EPI_ISL_413749, EPI_ISL_413750 EPI_ISL_413751 EPI_ISL_413752, EPI_ISL_413753 EPI_ISL_413761 EPI_ISL_413791, EPI_ISL_413809 EPI_ISL_413692. Accession numbers for sequences from outside of Weifang: EPI_ISL_414380 EPI_ISL_437621 EPI_ISL_429092, EPI_ISL_418327 EPI_ISL_416335 EPI_ISL_413854, EPI_ISL_402121 EPI_ISL_408480 EPI_ISL_418503, EPI_ISL_450196 EPI_ISL_417030 EPI_ISL_424356, EPI_ISL_451351 EPI_ISL_408010 EPI_ISL_430742, EPI_ISL_416366 EPI_ISL_451343 EPI_ISL_416381, EPI_ISL_407988 EPI_ISL_413882 EPI_ISL_413881, EPI_ISL_413879 EPI_ISL_411954 EPI_ISL_417184, EPI_ISL_418992 EPI_ISL_454935 EPI_ISL_414569, EPI_ISL_416570 EPI_ISL_416600 EPI_ISL_413608, EPI_ISL_451347 EPI_ISL_419242 EPI_ISL_414485, EPI_ISL_414005 EPI_ISL_430847 EPI_ISL_415580, EPI_ISL_413595 EPI_ISL_455376 EPI_ISL_417101, EPI_ISL_417168 EPI_ISL_455410 EPI_ISL_424081, EPI_ISL_440461 EPI_ISL_440433 EPI_ISL_455696, EPI_ISL_444577 EPI_ISL_456208 EPI_ISL_434463, EPI_ISL_437264 EPI_ISL_452673 EPI_ISL_437515, EPI_ISL_437185 EPI_ISL_427257 EPI_ISL_432722, EPI_ISL_437704 EPI_ISL_461275 EPI_ISL_403932.Virus Evolution online.veaa102_Supplementary_DataClick here for additional data file."} +{"text": "The data set compiled in this file refers to the Multizone EnergyPlus model, used in the investigations of the research article entitled \"Natural ventilation potential from weather analyses and building simulation\". The technical information regarding the model has been grouped into tables, which include: the general simulation settings, the properties of the building materials, the Airflow Network opening settings used in the annual investigation, in addition to the controls established in the Energy Management System (EMS) for hybrid ventilation system operation. The user behaviour, regarding the living and bedrooms occupancy schedule, is also presented in a graph. This data set is made available to the public to clarify details of the EnergyPlus model and how the hybrid operation was defined. In this way, other researchers can perform an extended analysis of the information. Different configurations/ simulation techniques could be employed based on this available data, so different studies might be compared.\u2022The data presented in this article can assist designers and researchers who deal with the modelling of naturally ventilated buildings, especially with Airflow Network and multizone approach.\u2022The use of Energy Management System (EMS) to model hybrid ventilation operation could be adopted as a reference for further research on naturally ventilated buildings.1The data in this article present the input data regarding the EnergyPlus model used at the investigations addressed in the research paper. General simulation settings are summarised in The model set up is based on consolidated practices used in studies involving INES' experimental houses, and therefore does not use the EnergyPlus database. Since they are originally unoccupied, a classic family occupancy schedule was established, which would represent an extreme/worse possible scenario.Besides, the EnergyPlus input data files (.idf) are available for download in the Mendeley repository 2The controls developed in the Energy Management System (EMS) object for the consolidation of the hybrid behaviour at the annual analyses are presented below. The operation mode was adopted in all occupied zones, exemplified here by the living room zone.The set up enables the following changes: triggering the thermal load calculation at a temperature different from the thermostat; deactivation of the thermal load calculation only after occupancy in a room is null; hybrid control, where the local thermal prognosis is not allowed to occur together with the window opening for natural ventilation in the same time step.All objects in class: energymanagementsystem:sensorEnergyManagementSystem:Sensor,OT_Living, !- NameLiving, !- Output:Variable or Output:Meter Index Key NameZone Operative Temperature; !- Output:Variable or Output:Meter NameEnergyManagementSystem:Sensor,Occ_Living, !- NameLiving_Occ, !- Output:Variable or Output:Meter Index Key NamePeople Occupant Count; !- Output:Variable or Output:Meter NameEnergyManagementSystem:Sensor,Ext_Temp, !- NameEnvironment, !- Output:Variable or Output:Meter Index Key NameSite Outdoor Air Drybulb Temperature; !- Output:Variable or Output:Meter NameEnergyManagementSystem:Sensor,T_Living, !- NameLiving, !- Output:Variable or Output:Meter Index Key NameZone Mean Air Temperature; !- Output:Variable or Output:Meter NameEnergyManagementSystem:Sensor,Heat_Living, !- NameHeat_Living, !- Output:Variable or Output:Meter Index Key NameSchedule Value; !- Output:Variable or Output:Meter NameAll objects in class: energymanagementsystem:ActuatorEnergyManagementSystem:Actuator,HeaterControl_Living, !- NameHeat_Living, !- Actuated Component Unique NameSchedule:Constant, !- Actuated Component TypeSchedule Value; !- Actuated Component Control TypeEnergyManagementSystem:Actuator,NVControl_Living, !- NameNV_Living, !- Actuated Component Unique NameSchedule:Constant, !- Actuated Component TypeSchedule Value; !- Actuated Component Control TypeAll objects in class: energymanagementsystem:programcallingmanagerEnergyManagementSystem:ProgramCallingManager,HybridControl, !- NameBeginTimestepBeforePredictor, !- EnergyPlus Model Calling PointHyb_Living, !- Program Name 1All objects in class: energymanagementsystem:programEnergyManagementSystem:Program,Hyb_Living, !- NameSET Temp_Heat\u202f=\u202fT_Living\u00a0<=\u00a019, !- Program Line 1IF ((Occ_Living > 0) && (Temp_Heat ==1)), !- Program Line 2SET HeaterControl_Living =1, !- A4SET NVControl_Living\u202f=\u202f0,!- A5ELSEIF ((Occ_Living > 0) && (Heat_Living >0)), !- A6SET HeaterControl_Living\u202f=\u202f1, !- A7SET NVControl_Living\u202f=\u202f0,!- A8ELSEIF (Occ_Living > 0), !- A9IF ((Ext_Temp20)), !- A10SET HeaterControl_Living\u202f=\u202f0, !- A11SET NVControl_Living\u202f=\u202f1,!- A12ELSEIF ((Ext_Temp>T_Living) && (Ext_Temp>20)), !- A13SET HeaterControl_Living\u202f=\u202f0, !- A14SET NVControl_Living\u202f=\u202f0,!- A15ELSEIF (Ext_Temp<20), !- A16SET HeaterControl_Living\u202f=\u202f0, !- A17SET NVControl_Living\u202f=\u202f0,!- A18ENDIF, !- A19ELSEIF (Occ_Living\u00a0==\u00a00),!- A20SET HeaterControl_Living\u202f=\u202f0, !- A21SET NVControl_Living\u202f=\u202f0,!- A22ENDIF; !- A23Nayara R. M. Sakiyama: Conceptualization, Methodology, Software, Data-curation, Formal analysis, Investigation, Writing-Original draft preparation; Leonardo Mazzaferro: Software, Visualization, Validation, Writing-Reviewing and Editing; Joyce C. Carlo: Supervision; Timea Bejat: Resources; Harald Garrecht: Project administration.The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article."} +{"text": "Aim: Whole genome and peptide mutation analysis can specify effective vaccine and therapeutics against severe acute respiratory coronavirus-2 (SARS-CoV-2). Materials & methods: Whole genome similarity for Bangladeshi SARS-CoV-2 was determined using ClustalW and BLASTn. Phylogenetic analysis was conducted using neighbor-joining method. Results: 100%\u00a0of isolates in Bangladesh were in the G clade. We found 99.98\u2013100% sequence similarity among Bangladeshi isolates and isolates of England, Greece, USA, Saudi Arabia and India. Deletion of bases at 5\u2032 untranslated region and 3\u2032 untranslated region was detected. Substitution 261 (E\u2192D) at NSP13 and 1109 (F\u2192L) at spike (S) protein were detected. Substitution 377 (D\u2192G) at nucleocapsid with common substitution 614 (D\u2192G) at S were also detected. Conclusion: This study will provide baseline data for development of an effective vaccine or therapeutics against SARS-CoV-2. Coronaviridae), previously named as 2019-novel coronavirus (2019-nCoV), has emerged as a pandemic virus [Betacoronavirus \u2013 SARS-CoV (2003), HCoV NL63 (2004), HKU1 (2005), MERS-CoV (2012)\u00a0\u2013 have been reported to cause human respiratory system infection [A novel species of coronavirus, severe acute respiratory coronavirus-2 (SARS-CoV-2) databases. COVID-19 cases and fatalities data were collected from Worldometers (www.worldometers.info/coronavirus), Johns Hopkins University COVID-19 database (https://coronavirus.jhu.edu/), Epidemiology, Disease Control and Research (www.iedcr.gov.bd/website/) website and Directorate General of Health Services (www.dghs.gov.bd/index.php/bd/) in Bangladesh website. Various environmental data were collected from Bangladesh Meteorological Department (http://live4.bmd.gov.bd/satelite/v/sat_infrared/) and AccuWeather (www.accuweather.com). Each month was divided into four equal weeks (W1\u2013W4) except the last week (W5) contained 3 days in January, 1 day in February, 3 days in March, 2 days in April and 3 days in May, respectively. Appropriate institutional review board approval was taken from Biosafety, Biosecurity and Ethical Committee of Jahangirnagar University for this study. Approval number was BBEC, JU/M 2020/COVID-19/(10)1.Data were collected from different databases. Whole genomes of SARS-CoV-2 were collected from GISAID . Sequence homology was determined using the BLASTn program. Multiple sequence alignment was conducted in BioEdit 7.2.6 using the ClustalW Multiple Alignment algorithm . MutatioPhylogenetic and molecular evolutionary relationship analyses of Bangladeshi SARS-CoV-2 were conducted using the whole genome sequences of the references by the MEGA-X software . PhylogeMexico/CDMX-InDRE|EPI_ISL_412972, Luxembourg/LNS2299410|EPI_ISL_421745, United Arab Emirates/L0881|EPI_ISL_435125, Latvia|EPI_ISL_437090, Saudi Arabia/Jeddah66|EPI_ISL_437755, Saudi Arabia/Jeddah60|EPI_ISL_443182, Singapore/126|EPI_ISL_443218, USA/NY-NYUMC623|EPI_ISL_444740, Chile/Santiago_40|EPI_ISL_445319, Wales/PHWC-2B55B|EPI_ISL_445726, Germany/FFM3|EPI_ISL_447609, Greece/259_31928|EPI_ISL_447651, France/10008DM|EPI_ISL_447697, France/10003SN|EPI_ISL_447719, France/10006HC|EPI_ISL_447727, Greece/54_37163|EPI_ISL_447835, USA/DC-CDC-0019|EPI_ISL_447840, Denmark/ALAB-SSI-899|EPI_ISL_444964, Guangdong/SYSU-IHV|EPI_ISL_444969, Luxembourg/LNS5711030|EPI_ISL_445072, Serbia/Novi Pazar-363|EPI_ISL_445087, Japan/Hu_Kng_19-865|EPI_ISL_445183, Sweden/20-07741|EPI_ISL_445241, Romania/279067|EPI_ISL_445243, Chile/Santiago_80|EPI_ISL_445377, Wales/PHWC-2F065|EPI_ISL_446193, Thailand/Bangkok-0079|EPI_ISL_447020, Romania/279068|EPI_ISL_447054, Georgia/Tb-6598|EPI_ISL_447055, DRC/3653|EPI_ISL_447231, Israel/130710062|EPI_ISL_447469, Spain/Valencia597|EPI_ISL_447519, Spain/Valencia598|EPI_ISL_447520, India/CCMB_J278|EPI_ISL_447565, Australia/QLDID941|EPI_ISL_447594, Germany/FFM7|EPI_ISL_447613, Taiwan/NTU27|EPI_ISL_447621, Greece/238_31927|EPI_ISL_447645, France/10007LJ|EPI_ISL_447725, Greece/55_36015|EPI_ISL_447834, Greece/145_34726|EPI_ISL_447836, Norway/2200|EPI_ISL_447837, India/CCMB_K499|EPI_ISL_447865, Iceland/604|EPI_ISL_424624, Mexico/CDMX-INER_04|EPI_ISL_424626, Czech Republic/IAB20-006-16|EPI_ISL_426581, Uruguay/UY-9|EPI_ISL_426584, Spain/Madrid_H12_2902|EPI_ISL_428701, Russia/Moscow-77620|EPI_ISL_428889, Jordan/SR-036|EPI_ISL_429996, Russia/StPetersburg-RII4917S|EPI_ISL_430070, Beijing/BJ589|EPI_ISL_430738, Argentina/PAIS_A005|EPI_ISL_430797, Greece/150|EPI_ISL_434485, Luxembourg/LNS8258882|EPI_ISL_434491, Myanmar/NIH-4385|EPI_ISL_434709, Vietnam/OUCRU022|EPI_ISL_435303, Spain/Valencia247|EPI_ISL_436342, Russia/Moscow-GCBL3|EPI_ISL_436717, Italy/TE5543|EPI_ISL_436720, Latvia/017|EPI_ISL_437096, Indonesia/JKT-EIJK03|EPI_ISL_437191, Austria/Graz-MUG4|EPI_ISL_437200, Germany/BAV-MVP0062|EPI_ISL_437261, Turkey/HSGM-10232|EPI_ISL_437334, Poland/Wro-02|EPI_ISL_437625, Denmark/ALAB-SSI-137|EPI_ISL_437649, Saudi Arabia/Madinah258|EPI_ISL_437742, USA/WA-UW-6546|EPI_ISL_437860, Greece/246_32206|EPI_ISL_437905, Austria/CeMM0023|EPI_ISL_437913, Japan/Donner9|EPI_ISL_438954, Scotland/EDB3941|EPI_ISL_439666, Northern Ireland/NIRE-FAAED|EPI_ISL_441737, Saudi Arabia/Makkah19|EPI_ISL_443166, Singapore/130|EPI_ISL_443222, France/B5688|EPI_ISL_443293, England/LOND-D5453|EPI_ISL_444222, England/LOND-D606D|EPI_ISL_444272, Australia/QLDID937|EPI_ISL_444611, USA/NY-NYUMC610|EPI_ISL_444727, Wuhan/IVDC-HB-01|EPI_ISL_402119, Wuhan/WH05|EPI_ISL_408978, Cambodia/0012|EPI_ISL_411902, South Korea/SNU01|EPI_ISL_411929, Switzerland/1000477806|EPI_ISL_413024, Italy/UniSR1|EPI_ISL_413489, New Zealand/01|EPI_ISL_413490, South Korea/KUMC03|EPI_ISL_413513, India/1-31|EPI_ISL_413523, USA/CruiseA-24|EPI_ISL_414483, Hong Kong/VM20002582|EPI_ISL_414569, USA/WA-UW75|EPI_ISL_415603, Peru/010|EPI_ISL_415787, Brazil/SPBR-09|EPI_ISL_416031, Brazil/SPBR-10|EPI_ISL_416032, Iceland/242|EPI_ISL_417570, Colombia/Antioquia79256|EPI_ISL_417924, Portugal/PT0021|EPI_ISL_418006, Canada/ON_PHL3802|EPI_ISL_418337, Canada/ON_PHL5710|EPI_ISL_418338, Finland/14M26|EPI_ISL_418406, Germany/NRW-24|EPI_ISL_419541, Georgia/Tb-1352|EPI_ISL_420140, Belgium/ULG-10018|EPI_ISL_421196, Taiwan/NTU11|EPI_ISL_422413 and Netherlands/NA_163|EPI_ISL_422698.Reference sequences of SARS-CoV-2 from 58 countries were used for the phylogenetic analysis. GISAID references are: 2. During 1 February 2020 to 9 June 2020, the minimum temperature average was 20\u00b0C, maximum temperature average was 32.5\u00b0C and mean temperature average was 26.5\u00b0C in Dhaka had been reported from Dhaka, the capital of Bangladesh with an average increase rate of 5973 cases/week and 81 fatalities/week in the country. COVID-19 is increasing relatively slowly in Dhaka, which has a population density of 121,720/miin Dhaka . Along wThe first seven sequenced SARS-CoV-2 in Bangladesh were from the G clade. Compared with 40,000 whole genomes, Bangladeshi SARS-CoV-2 were found to have\u00a0100\u201399.98% sequence similarity with reference sequences. The first sequenced whole genome in Bangladesh, Bangladesh/CHRF had 99.99% sequence similarity with whole genome of SARS-CoV-2 from Germany/FFM3, Sweden/20-07237, USA/NY-NYUMC623, Saudi Arabia/KAUST-Jeddah60, Latvia/011, United Arab Emirates/L0881 and Mexico/CDMX-InDRE_01 . AnotherWhole genomes of the first seven SARS-CoV-2 in Bangladesh were analyzed. The first sequence, CHR|FEPI_ISL_437912, from Bangladesh was 29903 bases in length, sharing the highest similarity with the Wuhan reference sequences (NC_045512/Wuhan-Hu-1) by length. Another six whole genomes, DNAS_CPH_467|EPI_ISL_445213, DNAS_CPH_471|EPI_ISL_445214, DNAS_CPH_427|EPI_ISL_445215, DNAS_CPH_466|EPI_ISL_445216, DNAS_CPH_436|EPI_ISL_445217 and Akbiomed|EPI_ISL_445244, had sequence length of 29642, 29833, 29829, 29828, 29706 and 29823 bases, respectively. CHR|FEPI_ISL_437912 did not have any deletion mutation while the other six isolates had significant deletion at both ends. Furthermore, deletion of the first 25 bases at 5\u2032 untranslated region (UTR) and 40\u201360 bases at 3\u2032 UTR stem loop region were commonly detected in these six isolates. Besides, numbers of deletion mutations were detected in DNAS_CPH_467|EPI_ISL_445213 and DNAS_CPH_436|EPI_ISL_445217 after 27,000 bases. Insertion mutation was detected in only one whole genome, Akbiomed|EPI_ISL_445244, between position 202 and 203. Substitution point mutation was the most common in Bangladeshi SARS-CoV-2. At 5\u2032 UTR, substitution 241 (C\u2192T) was found in all the isolates from Bangladesh. Most frequently detected substitution point mutations at ORF1ab region were 1163 (A\u2192T), 3037 (C\u2192T) and 14408 (C\u2192T) in Bangladeshi SARS-CoV-2. In the spike protein-coding regions, substitution mutation 23403 (A\u2192G) was frequent, while 24887 (T\u2192C) was detected in only DNAS_CPH_427|EPI_ISL_445215. Large number of substitution and deletion were found at ORF7a, ORF7b and ORF8 (27394\u201328259) in DNAS_CPH_436|EPI_ISL_445217. Substitution point mutations 28881 (G\u2192A), 28882 (G\u2192A) and 28883 (G\u2192C) in N protein region were common in most of the Bangladeshi isolates. Large number of substitutions and deletion mutations were also found at N protein (28274\u201329533), ORF10 (29558\u201329674) and 3\u2032 UTR (29675\u201329903) regions in four genomes .In amino acid peptide sequence, significant and rare point mutations were found in Bangladeshi novel coronavirus genomes. At NSP2 protein, 120 (I\u2192F) was detected for the first time in SARS-CoV-2 genome. While at NSP3, 1184 (Q\u2192H) was very rare and detected in Bangladeshi isolates. At NSP6, 3 (V\u2192M) was detected for the first time in DNAS_CPH_467/2020|EPI_ISL_445213 globally. Furthermore, at NSP12, 323 (P\u2192L) was found in all of the Bangladeshi isolates. However, at NSP13, 261 (E\u2192D) was detected in CHRF/EPI_ISL_437912. Spike proteins common mutation 614 (D\u2192G) was present in every isolate from Bangladesh. Of note, 1109 (F\u2192L) at S protein was detected for the first time in DNAS_CPH_471/2020|EPI_ISL_445214 worldwide. At NS3, 172 (G\u2192C) was detected in some of the Bangladeshi isolates. Furthermore, at N protein, 203 (R\u2192K), 204 (G\u2192R) and rare 377 (D\u2192G) were detected in some of isolates .The novel coronavirus has triggered the ongoing COVID-19 pandemic by infecting over 7.2\u00a0million people worldwide ,22. WholThe first seven isolates in Bangladesh were in the G clade. Among the first seven isolates, 57% (four of seven) were detected in male and 43% (three of seven) female. Furthermore, the highest percentage of SARS-CoV-2 in Bangladesh was detected in patients of 21\u201330\u00a0years, followed by 28.6% in 31\u201340\u00a0years, 14.3% in 11\u201320\u00a0years and 14.3% in 41\u201350\u00a0years, respectively. The distribution of gender was similar with previous studies in Europe, China and Asia, but age distribution of COVID-19 patients in Bangladesh was unique ,24.The phylogenetic analysis revealed that the first sequenced SARS-CoV-2 in Bangladesh CHRF|EPI_ISL_437912 was closely related with beta coronavirus from the\u00a0UAE, Latvia, Saudi Arabia, Mexico and the USA and clustered with them. In the BLAST analysis of CHRF|EPI_ISL_437912, this study detected 99.99% sequence similarity with Germany/EPI_ISL_447609, Sweden/EPI_ISL_445231, USA/NY/EPI_ISL_444740, Saudi Arabia/Jeddah60/EPI_ISL_443182, Latvia/EPI_ISL_437090, United Arab Emirates/EPI_ISL_435125 and Mexico/EPI_ISL_412972. This indicates the probable evolutionary linkage of this isolate with European, Middle East and American beta coronaviruses. Another four of these isolates, DNAS_CPH_467|EPI_ISL_445213, DNAS_CPH_471|EPI_ISL_445214, DNAS_CPH_427|EPI_ISL_445215 and DNAS_CPH_436|EPI_ISL_445217 clustered with each other and were closely related with coronavirus of Greece and Spain in the phylogenetic tree. Of note, DNAS_CPH_466|EPI_ISL_445216 clustered with coronavirus of England and Myanmar, and this cluster was closely related with isolates of France and Germany as well. Bangladeshi isolates DNAS_CPH_467|EPI_ISL_445213, DNAS_CPH_471|EPI_ISL_445214 and DNAS_CPH_427|EPI_ISL_445215 shared 99.98% sequence identity with USA/EPI_ISL_447840, Greece/EPI_ISL_447835, Wales/EPI_ISL_445726, Chile/EPI_ISL_445319 and Germany/EPI_ISL_447609 in BLAST analysis. Furthermore, isolate DNAS_CPH_466|EPI_ISL_445216 was found to have 100% sequence similarity with Luxembourg/EPI_ISL_421745 and France/EPI_ISL_447727, while isolate DNAS_CPH_436|EPI_ISL_445217 had 99.99% similarity with USA/EPI_ISL_447840 and Greece/EPI_ISL_447835. Isolate Akbiomed|EPI_ISL_445244 clustered with beta coronavirus of Georgia, Jordan and England in the phylogenetic tree, while shared 99.99% sequence similarity with USA/EPI_ISL_447840, India/EPI_ISL_447554 and India/EPI_ISL_447047 in BLAST. This study detected that Bangladeshi SARS-CoV-2 had significant evolutionary relationships with European, American and Asian SARS-CoV-2.cis-acting elements interaction during the virus replication and RNA synthesis. Besides 5\u2032 UTR (1\u201325) deletion, Akbiomed|EPI_ISL_445244 isolate had a number of point synonymous mutations at SL1, SL5A and SL5B regions with one insertion of G between 202 and 203 base in the SL5A region. Furthermore, substitution point mutation 241 (C\u2192T) was common in all Bangladeshi isolates. Deletion and substitution mutations at SL5A and SL5B of 5\u2032 UTR are involved in altered efficiency of coronavirus replication and infection pattern by changing interaction of the genome with viral nucleocapsid protein (N) and nsp1 protein [cis-acting elements [Whole genome analysis of novel coronavirus is necessary to understand its infectivity, fatality associated with specific variants and to predict any alteration of efficacy of possible drug or vaccine due to target proteins modification of the virus ,26. In w protein . Of noteelements . AlteratIn the protein-coding regions, significant substitution point mutation was detected in Bangladeshi isolates. At ORF1ab (266\u201321555) regions, 1163 (A\u2192T), 3037 (C\u2192T) and 14408 (C\u2192T) were frequent in Bangladeshi isolates. Substitution of isoleucine with phenylalanine at NSP2 120 (I\u2192F) was detected in this study . AnotherSubstitution mutation at 25609 (G\u2192T) of ORF3a was detected in three of the seven isolates. Mutation at ORF3a is most frequent in Europe followed by Asia, Oceania and North America, respectively ,24. AlteSpecific mutations, both deletion and substitution, in Bangladeshi coronavirus isolates were detected at various multiple sites in the genome and in the peptide chain. Of note, several new mutations at ORF1ab regions, specifically in the RdRp and its accessory proteins, will allow the virus to multiply without proof reading that will increase the possibility of accumulating more new mutations in the genome. Furthermore, along with a previous mutation associated with high case fatality, a new mutation at spike protein was also detected that increases the virus\u2019 chance of escaping antibodies or drugs targeting the spike protein. To the best of our knowledge, this is one of the first studies to report phylogenetic and genomic analysis of the first seven sequenced novel coronavirus in Bangladesh. This study reported significant new mutations at important sites in the novel coronavirus genome and antigenic peptide regions. These mutations will affect virus replication strategy and antigenic properties that will ultimately change the virus capability to infect and help the virus to escape from antibodies and drugs. This study will be the baseline database of coronavirus genome analysis that will help to predict effective vaccine and drug targets of coronavirus.In a pandemic like COVID-19, whole genome analysis of the pathogen is important in order to understand the transmission and severity of the disease accurately. With limited resources, the number of whole genome analysis in Bangladesh is lower than in\u00a0other developing countries. This study investigated the total mutation, phylogeny and evolution of the first seven whole genomes of SARS-CoV-2 in Bangladesh. They were closely related with each other and isolates from Germany, the USA, Saudi Arabia, France, Greece and India. Acquisition of unique mutations along with common mutations throughout the genome suggested rapid change of the circulating strains in Bangladesh. This study will provide a baseline to whole genome research of novel coronaviruses in Bangladesh.Approximately 57% (four of seven) severe acute respiratory coronavirus-2 (SARS-CoV-2) isolates were detected in male and 43% (three of seven) in female patients.Approximately 100% Bangladeshi SARS-CoV-2 shared 99.98\u2013100% sequence similarity with isolates of Germany, Sweden, the USA, Saudi Arabia, England, Myanmar and India.Deletion of bases at 5\u2032 untranslated region and 3\u2032 untranslated region in Bangladeshi isolates was specified.New substitution 1109 (F\u2192L) with deadly substitution 614 (D\u2192G) at spike protein was detected.Mutations at RNA-dependent RNA polymerase regions may lead to accumulation of random mutations in the novel coronavirus genome in future."} +{"text": "Dear Editor,Cohesin is a multiprotein complex that not only is essential for cell division but also has key roles in genome organization that underpin its gene regulatory function. Recurrent mutations of genes encoding cohesin subunits occur in myeloid malignancies at 10%\u201312% , and theRUNX1 and ERG genes (RUNX1 and ERG are precociously transcribed in response to phorbol 12-myristate 13-acetate (PMA)-induced megakaryocytic differentiation.Cohesin depletion was previously shown to alter chromatin accessibility and transcription of the RG genes , which eRG genes and founASTAG2-null and BSTAG2-null) defined for K562, CD34+ primary cord blood cells, and CD14+ monocytes , which is only lowly expressed in K562 cells (STAG2-null clones while mRNA was reduced dramatically following 6\u00a0h of treatment (STAG2-null cells (RUNX1/ERG transcription and reduce leukaemic stem cell-associated KIT expression in STAG2 mutant cells.62 cells . Followireatment . Howeverll cells , implyinRUNX1 and ERG, which causes aberrant enhancer-amplified transcription in response to differentiation signals. We show that enhancer suppression using BET inhibitor JQ1 prevents aberrant RUNX1 and ERG signal-induced transcription in STAG2 mutant cells and reduces leukaemic stem cell characteristics of STAG2 mutants.Overall, our results suggest that cohesin-STAG2 depletion de-constrains the chromatin surrounding Antony_et_al_supplementary_material_mjz114Click here for additional data file.Supplementary_Data1_Differential_genes_STAG2nullversus_WT_mjz114Click here for additional data file.Supplementary_Data2_Array_CGH_mjz114Click here for additional data file.Supplementary_Data3_ATAC-seq_differential_STAG2nullA_versus_WT_mjz114Click here for additional data file.Supplementary_Data4_Superenhancers_mjz114Click here for additional data file."} +{"text": "The malignancy potential of the laryngeal lesions are one of the major concerns of the surgeons about choosing the treatment options, forming surgical margins, deciding the follow-up periods. Finding a biomarker to overcome these concerns are ongoing challenges and recently microRNAs (miRNAs) are attributed as possible candidates since they can regulate gene expressions in the human genome. The objective of our study was to investigate their capability as a transformation biomarker for malignant laryngeal lesions.n\u2009=\u200910 in each). miRNA profiling was carried out by quantitative Real-Time polymerase chain reaction (RT-qPCR) and data were analyzed according to fold regulation.We investigated mature miRNA expressions in paraffin-embedded surgical specimens of human laryngeal tissues grouped as benign, premalignant or malignant , 2.72 (p\u2009=\u20090.028) and 3.01 (p\u2009=\u20090.022) fold upregulated respectively in premalignant lesions compared to the benign lesions. Moreover, their expressions were approximately 2.76 fold higher in the malignant group than in the premalignant group compared to the benign group. Besides them, significant 7.57 (p\u2009=\u20090.036), 4.45 (p\u2009=\u20090.045) and 5.98 (p\u2009=\u20090.023) fold upregulations of Hs_miR-21_5p, Hs_miR-218_3p, and Hs_miR-210_3p were noticed in the malignant group but not in the premalignant group when compared to the benign group, respectively.Our results demonstrated that 9 miRNAs were upregulated as the lesions become more malignant. Among them Hs_miR-183_5p, Hs_miR-155_5p, and Hs_miR-106b_3p might be followed as transformation marker, whereas Hs_miR-21_5p, Hs_miR-218_3p, and Hs_miR-210_3p might be a biomarker prone to malignancy.MiRNAs might have important value to help the clinicians for their concerns about the malignancy potentials of the laryngeal lesions. Laryngeal carcinoma is one of the most common malignancies in the head and neck region with a good prognosis when in the early stages . However, has reported significant upregulation and downregulation of 17 (including miR-21) and 9 miRNAs in laryngeal squamous cell carcinoma, particularly [MicroRNAs (miRNA) are endogenous, small, non-coding RNAs that are 21\u201324 nucleotides in length and known to regulate gene expression by silencing target transcripts via complement base-pairing in various pathways including embryogenesis, development, differentiation, and apoptosis . miRNAs icularly . The givHs_miR-21_5p, Hs_miR-106b_3p, Hs_miR-375_5p, Hs_miR-155_5p, Hs_let7a_5p, Hs_miR-210_3p, Hs_miR-425_3p, Hs_miR-183_5p, and Hs_miR-218_3p expressions were investigated within paraffin-embedded specimens that were obtained from patients who underwent surgery because of laryngeal lesions between the years 2012 and 2015. After local ethical committee approval (2014/0196), informed consent was obtained from the patients. The samples were analyzed within 3 groups as benign , premalignant and malignant . Patients who had previous cancer history or had been treated with radiochemotherapy were all excluded. One expert pathologist reviewed 5-\u03bcm sections containing the lesions of interest from the FFPE samples. The sections were transferred to the genetics laboratory in suitable conditions.Here, miRNAs were isolated from the paraffin-embedded tissues of the patients using the miRNeasy FFPE Kit (Qiagen) according to the manufacturer\u2019s protocol. Briefly, xylene and ethanol (%96\u2013100) were used to remove paraffin before total RNA isolation. Next, the pellet was treated with 10\u2009\u03bcl of proteinase K. The fully deparaffinized and lysed laryngeal tumor supernatant was transferred to a new microcentrifuge tube and DNase I was added to eliminate the DNA content. Then, RNeasy MinElute Spin Column (Qiagen) and relevant buffers of the kit were used with subsequent centrifugation and flow-through steps at 8000\u2009g for 15\u2009s. Finally, miRNA-enriched total RNA was eluted with 14\u2009\u03bcl of RNase-free water.cDNAs were randomly primed from 5\u2009\u03bcg of miRNA-enriched total RNA with miScript II Reverse Transcription (Rt) Kit (Qiagen). Briefly, reverse transcription PCR was performed with 4\u2009\u03bcl of 5x miScript HiSpec Buffer, 2\u2009\u03bcl of 10x Nucleic Acid Mix, 1\u2009\u03bcl of miScript Reverse Transcriptase Mix, 8\u2009\u03bcl of RNase-free water and 5\u2009\u03bcl of template RNA, with a total of volume of 20\u2009\u03bcl. The Rt reaction was incubated at 37\u2009\u00b0C for 60\u2009min and 95\u2009\u00b0C for 5\u2009min. The cDNA was then diluted with 200\u2009\u03bcl of nuclease-free water for further use in real-time PCRs.Nine miRNAs covering a variety of miRNA sequences were selected, and mature miRNA expression was determined via quantitative real-time polymerase chain reaction (RT-qPCR) with a QuantiTech SYBR Green PCR Kit (Qiagen) on the Rotor-Gene\u00ae Q instrument using the 2.1.0.9 software. RT-PCR was performed twice for each biological cDNA samples after optimization, including negative and non-template controls.R2 value of 0.9963. The slope of the standard curve was determined to be \u2212\u20093.410, and R2\u2009=\u20090.99630. CT values were exported from the RT-PCR instrument after normalization via the \u2018Dynamic Tube\u2019 and \u2018Slope Correction\u2019 options of the RT-PCR software used. For determining fold change, samples were normalized using housekeeping genes SNORD68, SNORD95 and MIRTC relevant for miRNA studies. Global mean normalization was used for Ct values and calculated concentrations were exported into the Excel spreadsheet, and the average value of duplicate Ct values was converted to quantities for analysis. The quality of expended mature miRNAs was checked via melt curve analyses using SYBR Green. Then, the Ct data were analyzed according to the fold-change (2(\u2212\u0394\u0394CT)) method and converted into fold regulation values using the online miScript miRNA PCR Array Data Analysis Tool (www.qiagen.com). p values under 0.05 were considered statistically significant.The threshold was manually determined as 0.025 in all reactions, and standards were calculated as follows: conc\u2009=\u200910\u02c6 (\u2212\u20090.293*CT\u2009+\u20097.516); and CT values were calculated as follows: CT\u2009=\u2009\u2212\u20093.410*log (conc)\u2009+\u200925.632, with an Patient demographic data were shown in Table\u00a0Fold regulations of the miRNA expressions in premalignant, malignant laryngeal lesions compared to benign lesions were given in Table\u00a0Hs_miR-375_5p, Hs_miR-183_5p, Hs_miR-155_5p, Hs_let-7a_5p, Hs_miR-21_5p and Hs_miR-106b_3p expressions were upregulated; however, in comparison to benign group, only the overexpression of Hs_miR-183_5p, Hs_miR-155_5pandHs_miR-106b_3p were statistically significant. (p\u2009<\u20090.05). The most upregulated miRNA was Hs_miR-183_5p, whereas Hs_miR-155_5p expression represented the lowest fold regulation (less than 2 folds).In the premalignant group Hs_miR-375_5p, Hs_miR-183_5p, Hs_miR-155_5p, Hs_let-7a_5p, Hs_miR-425_3p, Hs_miR-21_5p, Hs_miR-218_3p, Hs_miR-210_3pandHs_miR-106b_3p were all upregulated in the malignant group compared to benign group. However, in addition to significantly upregulated miRNAs in the premalignant group , overexpressions of Hs_miR-218_3p, Hs_miR-210_3p and Hs_miR-21_5p were also statistically significant. (p\u2009<\u20090.05). The most upregulated miRNA was Hs_miR-183_5p, whereas Hs_miR-218_3p was the lowest.Hs_miR-183_5p, Hs_miR-155_5p, and Hs_miR-106b_3p expressions were statistically significant in both premalignant and malignant groups compared to the benign group, whereas Hs_miR-21_5p, Hs_miR-218_3p, and Hs_miR-210_3p expressions were statistically significant only in the malignant group.In other words, Hs_miR-425_3p whereas Hs_miR-106b_3p was the lowest was identified in Caenorhabditis elegans; to date, thousands of miRNAs have been discovered and many more remain unknown [The importance of miRNAs in gene regulation has emerged in recent years. After the first miRNA unknown \u201312. The unknown \u201316. HereHs_miR-106b_3p is another miRNA that targets the 3\u2019UTR of retinoblastoma (RB) gene [RB largely inhibited by miR-106b which further results in the induction of laryngeal carcinoma cells proliferation by deceased control of RB on G1/S transition of the cell cycle [Hs_miR-106b_3p downregulation [Hs_miR-106b_3p and lymph node metastasis, cancer stage in supraglottic laryngeal carcinoma [Hs_miR-106b_3p expressions both in the premalignant and malignant groups, respectively gene and uprell cycle . Though gulation , Sun et arcinoma . In our ly Table . However, Hs_miR-155_5p was also another miRNA that significant 2.72 and 7.75 fold increased expressions were noticed in the premalignant and malignant group compared to the benign group, respectively . Downregulation of the latter has found to induce apoptosis and inhibit cellular proliferation and migration of laryngeal squamous carcinoma cells [EGR1 and PTEN [egulated . There anificant . In our ma cells . Moreoveand PTEN . Hence, , Hs_miR-21_5p upregulations were supposed to be oncogenic for different kinds of tumors [Hs_miR-21_5p would be a prognostic marker in head and neck tumors that is relevant to our results in which the Hs_miR-21_5p was one of the three miRNAs that significantly upregulated solely in the malignant laryngeal tumors group , survival and growth of tumor cells were reduced, and apoptosis was induced [Hs_miR-21_5p [Hs_miR-21_5p expression and 5-year survival rates in the head and neck carcinomas [Hs_miR-21_5p was an oncomir which is overexpressed in laryngeal carcinomas compared to adjacent normal laryngeal tissue [Hs_miR-21_5p expression was 3.45-fold and 7.57-fold increased in the premalignant and malignant group, respectively , a target gene of Hs_miR-218_3p, inhibited migration and invasion in tumor cells [Hs_miR-218_3p could clarify the mechanism of local recurrence and distant metastasis [miR-218 in the HPV-positive group [Hs_miR-218_3p by the E6 oncogene could cause overexpression of LAMB3, which is a target of Hs_miR-218_3p [miR-218 regulated TFF1. Likewise, overexpression of Hs_miR-218_3p in the malignant group might negatively regulate TFF1 in an Erk1/2-dependent manner and promote malignancy as suggested [Hs_miR-218_3p in laryngeal carcinomas. Thus, we believe that unknown factors such as viral infections can affect the results, which should be investigated in larger series.The next miRNA which was significantly overexpressed only in the metastatic group was the or cells . Additiotastasis . Besidesve group . In anotR-218_3p . In oppouggested . HoweverHs_miR-210_3p whether or not it is a tumor suppressor or an oncomir is still ongoing for many tumor types. Apart from that, Gee et al. indicated a correlation between the upregulation of Hs_miR-210_3p and poor prognosis in head and neck tumors by helping the vitality of tumor cells in hypoxic conditions [Hs_miR-210_3p expression was significantly 7.31 fold increased in the malignant group [Hs_miR-375_5p overexpression inhibited cell proliferation, migration, invasion and resulted in increased apoptosis via IGF1R expression [miR-375, increasing levels of miR-375 expression could provide a significant reduction in IGF1R levels and its downstream signaling molecule AKT in laryngeal carcinoma cells [PDK-1 as the target of Hs_miR-375_5p that contributed to AKT activation [Hs_miR-375_5p expression and indicated that the ratio of miR-21/miR-375 had a 94% sensitivity and 94% specificity for distinguishing normal tissue from laryngeal carcinoma tissue [On the other hand, k tumors , 46. Ovell cycle . Also, ipression . Since tma cells . Quaamartivation . Despitea tissue .Hs_miR-106b_3p and Hs_miR-21_5p, while downregulation of Hs_miR-375_5p expression in laryngeal carcinoma tissue compared to adjacent normal tissue [Hs_miR-106b_3p and Hs_miR-21_5p expressions in poor and moderately differentiated laryngeal carcinomas were more upregulated than that in the benign and dysplastic laryngeal tissues [Hs_miR-106b_3p and Hs_miR-21_5p were consistent with our data the downregulation of Hs_miR-375_5p expression particularly in advanced stages than in earlier stages was inconsistent [Apart from that, Yu et al. discovered overexpression of l tissue . Further tissues . Despitensistent . Even thHs_miR-425_3p served as an oncomir and stimulated cell proliferation and inhibited apoptosis [Hs_miR-425_3p upregulation and lymph node metastasis in laryngeal carcinomas [Hs_miR-425_3p expressions were insignificantly increased (Table Hs_let-7a_5p expression was insignificantly 4.12-fold and 10.54-fold upregulated in premalignant and malignant laryngeal tissues when compared to benign laryngeal samples (Table let-7a expression was significantly downregulated in laryngeal squamous cell carcinomas compared to adjacent normal tissues and was significantly further decreased in non-differentiated carcinoma tissues compared with moderately and well-differentiated ones [let-7a expression was insignificantly further upregulated as the tissues became more malignant. (Table let-7a compared with adjacent normal tissues [let-7a could have different impacts on different individuals or that let-7a may not take part in the pathogenesis of all laryngeal carcinomas [Hs_miR-375_5p, Hs_miR-425_3p, and Hs_let-7a_5p.In addition to this, poptosis . Furtherrcinomas . Notwithted ones . In cont tissues . They surcinomas . In the Hs_miR-21_5p, Hs_miR-218_3p, and Hs_miR-210_3p can be a potential biomarker for malignant laryngeal carcinomas. Furthermore, Hs_miR-183_5p, Hs_miR-155_5p, and Hs_miR-106b_3p, each upregulated both in premalignant and malignant groups compared to benign hyperplasia, might have a great value to help physicians to determine the malignancy potential of the laryngeal lesions as the transformation biomarkers upon prognosis.Our study is one of the first to compare the expression levels of several different miRNAs between benign, premalignant and malignant laryngeal lesions with a relatively larger series upon the literature. They indicated that"} +{"text": "HemaSphere. 2020;4:e407), the author made grammar- and style-based corrections to the text as well as to Figure 1. These adjustments have been made and do not affect the outcome of this publication.Since the publication of the article entitled \u201cCytokine Profiling as a Novel Complementary Tool to Predict Prognosis in MPNs?\u201d (https://journals.lww.com/hemasphere/Fulltext/2020/06000/Cytokine_Profiling_as_a_Novel_Complementary_Tool.17.aspxThese additions have been made online:"} +{"text": "Aedes (Tanakius) togoi (Diptera: Culicidae), is found in coastal east Asia in climates ranging from subtropical to subarctic. However, a disjunct population in the Pacific Northwest of North America has an ambiguous heritage. Two potential models explain the presence of Ae. togoi in North America: ancient Beringian dispersal or modern anthropogenic introduction. Genetic studies have thus far proved inconclusive. Here we described the putative ancient distribution of Ae. togoi habitat in east Asia and examined the climatic feasibility of a Beringian introduction into North America using modern distribution records and ecological niche modeling of bioclimatic data from the last interglacial period , the last glacial maximum , and the mid-Holocene (~6000 BP). Our results suggest that suitable climatic conditions existed for Ae. togoi to arrive in North America through natural dispersal as well as to persist there until present times. Furthermore, we find that ancient distributions of suitable Ae. togoi habitat in east Asia may explain the genetic relationships between Ae. togoi populations identified in other studies. These findings indicate the utility of ecological niche modeling as a complementary tool for studying insect phylogeography.The coastal rock pool mosquito, Aedes (Tanakius) togoi , breeds in pools of brackish or salt-water above the high tide level on rocky shorelines and, sporadically, in containers of freshwater further inland and northern Washington, United States dorsalis larvae from the supralittoral coastal rock pools at Caulfield Cove in North Vancouver, BC . Thus, it is possible that Ae. togoi could have gone unnoticed in North America until sometime in the early-to-mid 20th century. in 1907 and firs in 1907 . However in 1907 . Furtheruver, BC has beene. togoi . Aedes d marshes while thAe. togoi: a lineage from temperate and subarctic regions of Japan, China, Taiwan, and other parts of Southeast Asia, a lineage from the subtropical islands of Japan, a lineage from subarctic Japan, and a lineage from Canada . Some data points did not occur on pixels within bioclimatic data due to the irregular shape of coastline or the small size of islands. When this occurred, we relocated data points to the closest 1 km2 raster cell.In the present study, we compiled 86 Asian records and 49 North American records of udy area , personaAe. togoi in Asia, and one for the North Pacific from within Latitude 0\u00b0N to 80\u00b0N and Longitude 95\u00b0E across the Pacific to 100\u00b0W, encompassing all known Ae. togoi populations in Asia and North America and possible unknown populations in the North Pacific. We projected a model from the Asian study area (hereafter referred to as model 1), obtained using Asian Ae. togoi populations, onto the North Pacific study area, following methodology for projecting habitat of invasive species into new areas (Ae. togoi populations (hereafter referred to as model 2), as if it were indigenous. We used WGS84 Mercator projection for maps in the last glacial maximum, and WGS84/PDC Mercator projection for all other maps.We selected two study areas: one from Asia from within Latitude 0\u00b0N to 49\u00b0N and Longitude 94\u00b0E to 157\u00b0E . We also downloaded corresponding sets of variables based on climate conditions from: 1) the last interglacial period at a scale of 1 km2 (2 (2 (Ae. togoi overwintering strategy (Ae. togoi observations (model 1) (Ae. togoi observations (model 2) the 1 km2 m2 and all model 2) , each wiAe. togoi. We used default Maxent settings with and without linear features, and with and without quadratic features, with 1,000 replications, each with 2,000 training iterations, 20% of data points withheld for subsampling, clamping applied, and 10,000 background points. We analyzed results based on extensive presence of predicted suitable habitat on maps calculated from the maximum sensitivity and specificity, a recommended approach for transforming the results of species distribution models into binary presence/absence predictions (PO) of the receiving operator characteristic (ROC). This integral gives a sum between 0 and 1 with a result >0.5 indicative of a model that is more accurate than random, >0.7 representing a useful model, >0.9 representing an excellent model, and a result of 1 indicating a perfect fit (PO of our three best candidate modes as measured by AICc and selected the top performer across both metrics (PO were transformed to a percentage and used as a relative metric of variable importance. We built maps with QGIS version 3.4.3 (https://crc806db.uni-koeln.de/) to add glacial coverage layers where applicable.Maximum entropy niche modeling (Maxent) is a common approach for species habitat modeling . Maxent dictions , as wellfect fit . We comp metrics and 3. Won 3.4.3 , and dowon 3.4.3 from thePO of 0.912 (\u00b10.031) and model 2 has a mean AUCPO of 0.972 (\u00b10.009), both representing models with excellent fits . Consistent with a niche conservatism hypothesis .Mean diurnal range and minimum temperature of the coldest month were important environmental variables in each of our models. In addition, precipitation during the coldest quarter was also critical in model 1, while mean temperature during the warmest quarter was important in model 2. There is evidence that, under certain conditions, temperature fluctuations (rather than absolute temperature) can have negative effects on the development rate and survival of some mosquitoes . With thdes spp. , and ano America . Such pa America and over America . Insulat America and coul dry out , and it survival . This vades spp. . Despitedes spp. , the meades spp. indicatepothesis , this ovAe. togoi into North America can also produce slightly different projections, indicating the inherent uncertainty present in any individual approach , Cook Inlet, the Alexander Archipelago, and the North Coast of British Columbia. We also note a need for Ae. togoi surveillance across its novel predicted range in more heavily surveyed areas, including the Hawaiian Islands and the Mariana Archipelago. To further investigate the origins of Ae. togoi in North America, we propose a combination of survey efforts and population genetic analyses based on mitochondrial and nuclear genome sequencing (Ultimately, our modeling is based on climate data alone and is subject to the realities of limited sampling and, thus, cannot definitely prove or disprove either an anthropogenic introduction or Beringian dispersal for the presence of approach . In futuapproach . Howeverapproach . We propquencing .ieaa035_suppl_Supplementary_Figure_1Click here for additional data file.ieaa035_suppl_Supplementary_Figure_2Click here for additional data file.ieaa035_suppl_Supplementary_Figure_3Click here for additional data file.ieaa035_suppl_Supplementary_Figure_4Click here for additional data file.ieaa035_suppl_Supplementary_Figure_5Click here for additional data file.ieaa035_suppl_Supplementary_Figure_6Click here for additional data file.ieaa035_suppl_Supplementary_Figure_7Click here for additional data file.ieaa035_suppl_Supplementary_Figure_8Click here for additional data file.ieaa035_suppl_Supplementary_Figure_9Click here for additional data file.ieaa035_suppl_Supplementary_Figure_10Click here for additional data file.ieaa035_suppl_Supplementary_Figure_11Click here for additional data file.ieaa035_suppl_Supplementary_Figure_12Click here for additional data file.ieaa035_suppl_Supplementary_Figure_13Click here for additional data file.ieaa035_suppl_Supplementary_Figure_14Click here for additional data file.ieaa035_suppl_Supplementary_Figure_15Click here for additional data file.ieaa035_suppl_Supplementary_Table_1Click here for additional data file.ieaa035_suppl_Supplementary_Table_2Click here for additional data file.ieaa035_suppl_Supplementary_Table_3Click here for additional data file.ieaa035_suppl_Supplementary_Table_4Click here for additional data file.ieaa035_suppl_Supplementary_Table_5Click here for additional data file.ieaa035_suppl_Supplementary_FilesClick here for additional data file."} +{"text": "Capnocytophaga and OTU269_Treponema acted as gatekeepers for both of the two clustered microbiotas. Nine OTUs assigned to seven taxa, i.e., Alloprevotella, Atopobium, Megasphaera, Oribacterium, Prevotella, Stomatobaculum, and Veillonella, were associated with both H7N9 patients with and without secondary bacterial lung infection in Cluster_1. In addition, two groups of healthy cohorts may have potential different susceptibilities to H7N9 infection. These findings suggest that two OP microbial colonization states of H7N9 patients were at different dysbiosis states, which may help determine the health status of H7N9 patients, as well as the susceptibility of healthy subjects to H7N9 infection.The dysbiosis of oropharyngeal (OP) microbiota is associated with multiple diseases, including H7N9 infection. Different OP microbial colonization states may reflect different severities or stages of disease and affect the effectiveness of the treatments. Current study aims to determine the vital bacteria that could possibly drive the OP microbiota in the H7N9 patients to more severe microbial dysbiosis state. The OP microbiotas of 42 H7N9 patients and 30 healthy subjects were analyzed by a series of bioinformatics and statistical analyses. Two clusters of OP microbiotas in H7N9 patients, i.e., Cluster_1_Diseased and Cluster_2_Diseased, were determined at two microbial colonization states by Partition Around Medoids (PAM) clustering analysis, each characterized by distinct operational taxonomic units (OTUs) and functional metabolites. Cluster_1_Diseased was determined at more severe dysbiosis status compared with Cluster_2_Diseased, while OTU143_ Avian influenza has caused great mortalities to human beings and animals during the last two decades \u20134. The hAcinetobacter baumanii, Candida albicans, Flavobacterium indologenes, Klebsiella, Pseudomonas, and Staphylococcus have been isolated from blood, white blood cell, or sputum of H7N9 patients with SBLI (H7N9_SBLI), whereas no bacterium was isolated from those in the H7N9 patients without SBLI (H7N9_NSI) is a usual condition in the H7N9 patients (7N9_NSI) .Atopobium, Eubacterium, Leptotrichia, Oribacterium, Rothia, Solobacterium, and Streptococcus in H7N9_SBLI than H7N9_NSI clustering analysis in order to determine their microbial colonization states. Before PAM clustering, the average silhouette method was used to determine the optimal numbers of clusters for all the OP microbiotas .2 test was performed to compare the numbers of healthy and H7N9 cohorts in the two clusters.Two clusters of OP microbiotas were determined in healthy cohorts and H7N9 cohorts . A Pearson \u03c7t test.Permutation analysis of variance (PERMANOVA) was performed in R software version 3.6.1 with the vegan package to deterLinear discriminant analysis (LDA) effect size (LEfSe) was performed using Kruskal\u2013Wallis test (\u03b1 < 0.05), followed by a Wilcoxon rank-sum test (\u03b1 < 0.05), and a one-against-all strategy for multiclass analysis . It was P values were computed by a permutation step, followed by a bootstrap procedure to merge the P values into one final P value using a method by Brown (Co-occurrence Network (CoNet) analysis was carried out to investigate the co-occurrence and coexclusion of OTUs in Cluster_1_Diseased and Cluster_2_Diseased and to determine the top 10 OTUs with most correlations in the OP bacterial networks of Cluster_1_Diseased and Cluster_2_Diseased. The detailed processes followed the procedures described by Wagner Mackenzie et al. . Brieflyby Brown .Gatekeepers were defined as the phylotypes interacting with different parts of the network to hold together the bacterial community , 27. In The OTUs differentiating the OP microbiotas of H7N9 patients from those of healthy subjects were determined by using the Galaxy implementation of LEfSe run by Huttenhower laboratory .t test. The same data transformation and statistical approach were applied for the comparison of the AIDRs of Cluster_1_Diseased and Cluster_2_Diseased.Dysbiosis ratios of bacterial taxa were associated with different diseases and conditions , 29. In U test was used to compare the abundances of the OTUs associated with H7N9 between Cluster_1_Diseased and Cluster_2_Diseased. The same approach was performed for the comparisons of OTUs associated with healthy cohort between Cluster_1_Diseased and Cluster_2_Diseased. A Pearson \u03c72 test was applied to compare the numbers of OTUs that were associated with H7N9 and more abundant in Cluster_1_Diseased or Cluster_2_Diseased. The same test was carried out for the comparisons of the numbers of OTUs, which were associated with healthy cohort and more abundant in Cluster_1_Diseased or Cluster_2_Diseased.A series of statistical analyses were also performed to help determine the dysbiosis status of the two clusters of OP microbiotas in H7N9 patients. Mann\u2013Whitney The two clustered OP microbiotas in H7N9_NSI (or H7N9_SBLI) were compared to determine whether some OTUs could possibly drive the OP microbiotas to worse microbial dysbiosis state in both H7N9_NSI and H7N9_SBLI.t test, after being transformed in log10 to satisfy the assumptions of normal distribution and equal variance. The same approaches were applied for the comparisons of the AIDRs of H7N9_SBLI cohorts in the two clusters.Avian influenza dysbiosis ratios of H7N9_NSI cohorts in the two clusters were compared by a An LEfSe analysis was applied to determine the OTUs differentiating the two clustered OP microbiotas in H7N9_NSI . The same approach was carried out for determining the OTUs associated with each of the two clustered OP microbiotas in H7N9_SBLI .Similarly, an LEfSe analysis was used to determine the functional metabolites associated with Cluster_1_H7N9_NSI or Cluster_2_H7N9_NSI. The same analysis was used to determine the functional metabolites associated with Cluster_1_H7N9_SBLI or Cluster_2_H7N9_SBLI.The OTUs associated with both Cluster_1_H7N9_NSI and Cluster_1_H7N9_SBLI were determined by an online program Venny diagram version 2.1 . The samt test.Permutation analysis of variance was applied to determine the difference between Cluster_1_Healthy and Cluster_2_Healthy. Avian influenza dysbiosis ratios of Cluster_1_Healthy and Cluster_2_Healthy were transformed in log10 to satisfy the assumptions of normal distribution and equal variance, before being compared by a An LEfSe analysis was applied to determine the OTUs associated with each of the two clustered OP microbiotas in healthy cohorts. The same approach was used for identifying the functional metabolites associated with Cluster_1_Healthy or Cluster_2_Healthy.2 = 9.933, P = 0.002).Silhouette analysis identified two as the most optimal number for clustering all the 72 OP microbiotas . TherefoBacteroidetes, Fusobacteria, and Proteobacteria were more abundant in Cluster_2_Diseased compared with Cluster_1_Diseased, whereas Firmicutes and Saccharibacteria were more abundant in Cluster_1_Diseased than in Cluster_2_Diseased. Nine most abundant orders in the H7N9 patients constituted >90% abundance of all the orders in H7N9 microbiotas, among which Campylobacterales, Clostridiales, Flavobacteriales, Lactobacillales, and Selenomonadales had greater abundances in Cluster_1_Diseased compared with Cluster_2_Diseased, whereas Bacteroidales, Fusobacteriales, Neisseriales, and Pasteurellales were more abundant in Cluster_2_Diseased than in Cluster_1_Diseased.The five most abundant phyla in the OP microbiotas of H7N9 patients accounted for >90% abundance of the OP microbiotas. Among them, R2 = 0.090, P < 0.001). The dissimilarity between Cluster_1_Diseased and Cluster_2_Diseased was relatively high (SIMPER dissimilarity = 64.8%) according to SIMPER results. The similarity within Cluster_1_Diseased (SIMPER average similarity = 38.2%) was lower than that within Cluster_2_Diseased (SIMPER average similarity = 44.1%). Both richness and diversity were similar in Cluster_1_Diseased and Cluster_2_Diseased , but the evenness was significantly higher in Cluster_1_Diseased than in Cluster_2_Diseased .Neisseria) with the largest LDA scores were closely associated with Cluster_1_Diseased and Cluster_2_Diseased, respectively , suggesting a lower AIDR was likely to indicate the dysbiosis of OP microbiotas in H7N9 patients compared with healthy subjects. The AIDR was significantly higher in Cluster_2_Diseased (5.28 \u00b1 1.12 SE) than Cluster_1_Diseased (1.48 \u00b1 0.21 SE) .The LEfSe results showed that 69 OTUs were associated with H7N9, and 22 OTUs were associated with healthy cohort, which were used for the calculations and comparisons of AIDRs in different groups . The heaP < 0.05) .Eleven (of 69) OTUs associated with H7N9 were determined with significantly different abundances between Cluster_1_Dieased and Cluster_2_Diseased . Among tP < 0.02) .Likewise, seven (of 22) OTUs associated with healthy cohort were determined with significantly different abundances between the two clustered H7N9 microbiotas . Among tThese above results consistently suggested that Cluster_2_Diseased were at better dysbiosis status compared with Cluster_1_Diseased.The two bacterial networks of Cluster_1_Diseased and Cluster_2_Diseased were determined by CoNet analysis . None ofCapnocytophaga and OTU269_Treponema were determined as gatekeepers for both Cluster_1_Diseased and Cluster_2_Diseased.Fragmentation results demonstrated a lower fragmentation score in Cluster_2_Diseased than that of Cluster_1_Diseased , suggesting that Cluster_2_Diseased had stronger co-occurrence patterns and greater biotic interactions than Cluster_1_Diseased. A group of nine OTUs was determined to be gatekeepers of Cluster_1_Diseased, and another group of nine OTUs was identified as gatekeepers of Cluster_2_Diseased . OTU143_The two clustered OP microbiotas in H7N9_NSI or H7N9_SBLI were compared to determine the bacteria that could possibly drive the OP microbiotas to more severe microbial dysbiosis state in both H7N9_NSI and H7N9_SBLI.t test, P = 0.001). Likewise, Cluster_2_H7N9_SBLI (4.44 \u00b1 1.76 SE) had a significantly higher AIDR compared with Cluster_1_H7N9_SBLI (1.53 \u00b1 0.30 SE) .Avian influenza dysbiosis ratio was significantly higher in Cluster_2_H7N9_NSI (5.98 \u00b1 1.51 SE) compared with Cluster_1_H7N9_NSI (1.43 \u00b1 0.31 SE) (LEfSe results showed that 33 OTUs were associated with OP microbiotas of H7N9_NSI in Cluster_1 (Cluster_1_H7N9_NSI), and 20 OTUs were associated with OP microbiotas of H7N9_NSI in Cluster_2 (Cluster_2_H7N9_NSI) . A totalLikewise, a total of 20 OTUs were more associated with Cluster_1_H7N9_SBLI, and 41 OTUs were more associated with Cluster_2_H7N9_SBLI . A totalAlloprevotella, Atopobium, Megasphaera, Oribacterium, Prevotella, Stomatobaculum, and Veillonella. Likewise, four OTUs assigned to Alloprevotella or Porphyromonas were associated with both Cluster_2_H7N9_NSI and Cluster_2_H7N9_SBLI associated with both Cluster_1_H7N9_NSI and Cluster_1_H7N9_SBLI , which w7N9_SBLI .In addition, five of the 20 OTUs associated with Cluster_2_H7N9_NSI were also identified being associated with healthy cohort. Likewise, five of 41 OTUs associated with Cluster_2_H7N9_SBLI were also determined being associated with healthy cohort.Dialister was negatively correlated with four other OTUs associated with Cluster_2_H7N9_SBLI . Avian influenza dysbiosis ratio was significantly higher in Cluster_2_Healthy (19.74 \u00b1 3.83 SE) than Cluster_1_Healthy (4.83 \u00b1 1.91 SE) .The PERMANOVA results showed a significant difference between the Cluster_1_Healthy and Cluster_2_Healthy were associated with Cluster_1_Diseased, whereas no Veillonella was associated with Cluster_2_Diseased, suggesting that the increased Veillonella in the OP microbiota could be a source of Veillonella in the gut of H7N9 patients with Cluster_1_Diseased.bacteria . In the controls . In the Capnocytophaga was part of resident OP microbiota in human and could be opportunistic pathogens of extraoral infections , suggesting these phylotypes were likely to cause more severe conditions in H7N9 patients. Some Alloprevotella and Porphyromonas species were determined as opportunistic oral pathogens (Alloprevotella, OTU20_Porphyromonas, OTU26_Porphyromonas, and OTU193_Alloprevotella were associated with both Cluster_2_H7N9_NSI and Cluster_2_H7N9_SBLI, suggesting the four phylotypes were more likely as opportunistic pathogens for inducing H7N9_NSI or H7N9_SBLI.H7N9_NSI . The curathogens \u201364. In tDialister species were associated with some oral diseases, such as periodontal disease, apical periodontitis, and dentinal caries (Dialister was negatively correlated with four OTUs in Cluster_2_H7N9_SBLI, suggesting this phylotype was more likely as pathogenic bacteria and had competitive interactions with some other phylotypes within this OP microbial colonization state. We acknowledge that further studies are needed to confirm it.A few l caries \u201367. AmonMethyl-accepting chemotaxis protein is vital to the cell survival, pathogenesis, and biodegradation . In the Veillonella was more abundant in the gut of H7N9 patients than healthy controls as described above (Veillonella and methyl-accepting chemotaxis protein were determined as the phylotype and functional metabolite most associated with Cluster_1_Healthy, suggesting they were more likely to enhance the greater susceptibility of the healthy subjects to H7N9 infection.Greater AIDR was determined in Cluster_2_Healthy than Cluster_1_Healthy, suggesting the healthy subjects in Cluster_2 could be more tolerant to H7N9 infection than those in Cluster_1. ed above , whereased above . In the Alloprevotella, Atopobium, Megasphaera, Oribacterium, Prevotella, Stomatobaculum, and Veillonella were likely to drive the OP microbiotas to worse microbial dysbiosis state in both H7N9_NSI and H7N9_SBLI. In addition, healthy subjects could have different susceptibilities to H7N9 infection.In conclusion, two OP microbial colonization states were determined in the H7N9 patients, each characterized by distinct phylotypes. Nine phylotypes assigned to PRJNA638222.The raw sequencing data were deposited in NCBI under BioProject accession no. The studies involving human participants were reviewed and approved by The Institutional Review Board and Ethics Committee of the First Affiliated Hospital of Zhejiang University. The patients/participants provided their written informed consent to participate in this study.HZha and LL designed the study. HL and HZhang collected samples and provided the raw sequencing data. HZha, JW, and KC contributed to the data analyses. HZha interpreted the results and drafted the manuscript. HZ, HL, and JW reviewed the manuscript. QW, JL, QL, and YL contributed to the literature search and participate in the study design. All authors approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Supplementary Table 1 and Supplementary Table 2. The expression values given for PDK4 in Supplementary Table 1, ALL_M, CLL_M, AHL_M, CHL_M contrasts were \u22123.90808, 2.10011, \u22124.12057, and \u22124.12057 the correct values are \u22124.1009, 2.07292, \u22124.63904, and 3.05659 same value should appear at the \u201cMax_expression_level\u201d column in HL_node_table in Supplementary Table 2.In the original article, there was a mistake in MT4 given in Supplementary Table 1 for ALL_H, CLL_H, AHL_H, and CHL_H are \u22121.20147, 1.485881, \u22121.19557, and 1.0025, the correct values are \u22123.1675, \u22121.82983, \u22121.35669, and \u22121.84142. To reflect this change, columns \u201cMax_expression_level,\u201d \u201cMax_Tissue,\u201d and \u201cUp/Down\u201d on Supplementary Table 2, \u201cLL_node_table\u201d tab is corrected.Similarly the expression values of The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "This paper presents a novel prototype platform that uses the same LaTeX mark-up language, commonly used to typeset mathematical content, as an input language for modeling optimization problems of various classes. The platform converts the LaTeX model into a formal Algebraic Modeling Language (AML) representation based on Pyomo through a parsing engine written in Python and solves by either via NEOS server or locally installed solvers, using a friendly Graphical User Interface (GUI). The distinct advantages of our approach can be summarized in (i)\u00a0simplification and speed-up of the model design and development process (ii) non-commercial character (iii)\u00a0cross-platform support (iv) easier typo and logic error detection in the description of the models and (v) minimization of working knowledge of programming and AMLs to perform mathematical programming modeling. Overall, this is a presentation of a complete workable scheme on using LaTeX for mathematical programming modeling which assists in furthering our ability to reproduce and replicate scientific work. Mathematical modeling constitutes a rigorous way of inexpensively simulating complex systems\u2019 behavior in order to gain further understanding about the underlying mechanisms and trade-offs. By exploiting mathematical modeling techniques, one may manipulate the system under analysis so as to guarantee its optimal and robust operation.http://www.Pyomo.org/)\u00a0(https://www.python.org/),\u00a0(The dominant computing tool to assist in modeling is the Algebraic Modeling Languages (AMLs)\u00a0. AMLs hamo.org/)\u00a0 for moden.org/),\u00a0 and AMPLn.org/),\u00a0 are the \u2022a strict and specific syntax for the mathematical notation to describe the models; \u2022understand in terms of structural demands;solver interfaces, the bridge between mathematics and what the solver can \u2022a series of available optimization solvers for as many classes of problems as supported with the associated functional interfaces implemented; \u2022explicit data file formats and implementation of the respective import/export mechanisms.vertical abstraction) or extend the embedded functionality . This limited declaration of model components elevates the amount of processing that the platform has to conduct in order to provide equivalent formulations of the input.AMLs provide a level of abstraction, which is higher than the direct approach of generating a model using a programming language. The different levels in the design process of a model are depicted in raction) . The layA systems approach, MOSAIC , has beeLiterate Programming and (ii) the notions of reproducible and replicable research, the fundamental basis of scientific analysis. Literate Programming focuses on generating programs based on logical flow and thinking rather than being limited by the imposing syntactical constraints of a programming language. In essence, we employ a simple mark-up language, LaTeX, to describe a problem and then in turn produce compilable code (Pyomo abstract model) which can be used outside of the presented prototype platform\u2019s framework. Reproducibility and the ability to replicate scientific analysis is crucial and challenging to achieve. As software tools become the vessel to unravel the computational complexity of decision-making, developing open-source software is not necessarily sufficient; the ability for the averagely versed developer to reproduce and replicate scientific work is very important to effectively deliver impact (https://www.coin-or.org/), Science evolves when previous results can be easily replicated.Our work expands upon two axes: (i) the programming paradigm introduced by Donald E. Knuth on Literr impact . To quotvertical abstraction. It therefore strengthens the ability to reproduce and replicate optimization models across literature for further analysis by reducing the demands in working knowledge of AMLs or coding. The key capability is that it parses LaTeX\u00a0formulations of mathematical programs (optimization problems) directly into Pyomo abstract models. The framework then combines the produced abstract model with data provided in the AMPL .dat format (containing parameters and sets) to produce a concrete model. This capability is provided through a graphical interface which accepts LaTeX\u00a0input and AMPL data files, parses a Pyomo model, solves with a selected solver , and returns the optimal solution if feasible, as the output. The aim is not to substitute but to establish a link between those using a higher level of abstraction. Therefore, the platform does not eliminate the use of an AML or the advantages emanating from it.In the endeavor of simplifying the syntactical requirements imposed by AMLs we have developed a prototype platform. This new framework is materializing a level of modeling design that is higher than the AMLs in terms of This is a complete prototype workable scheme to address how LaTeX\u00a0could be used as an input language to perform mathematical programming modeling, and currently supports Linear Programming (LP), Mixed-Integer Linear Programming (MILP) as well as Mixed-Integer Quadratic Programming (MIQP) formulations. Linear Optimization has provThis paper is organized as follows: in \u2018Functionality\u2019, we describe the current functionality supported by the platform at this prototype stage. In \u2018Parser - Execution Engine\u2019, we present the implementation details of the parser. \u2018An illustrative parsing example\u2019 provides a description of an illustrative example. A discussion follows in \u2018Discussion\u2019. Some concluding remarks are drawn in \u2018Conclusion\u2019. Examples of optimization models that were reproduced from scientific papers as well as their corresponding LaTeX\u00a0formulations and Pyomo models can be found in the The set of rules that are admissible to formulate models in this platform are formal LaTeX\u00a0commands and they do not represent in-house modifications. We assume that the model will be in the typical format that optimization programs commonly appear in scientific journals. Therefore, the model must contain the following three main parts and with respect to the correct order as well: 1.the objective function to be optimized (either maximized or minimized); 2.the (sets of) constraints, or else the relationships between the decision variables and coefficients, right-hand side (RHS); 3.the decision variables and their domain space.reads LaTeX\u00a0code and then writes Pyomo abstract models or the code generates code. The resulting .py file is usable outside of the platform\u2019s frame, thus not making the binding and usage of these two necessary after conversion. The main components that we employed for this purpose are the following:We used the programming environment of Python coupled with its modeling library, namely Pyomo. Similar approaches in terms of software selection have been presented for Differential and Algebraic Equations (DAE) modeling and optimization in . By comb \u2022https://www.mathjax.org/) and Google Polymer (https://www.polymer-project.org/);Front-end: HTML, JavaScript, MathJax ( \u2022https://www.djangoproject.com/) and Pyomo.Back-end: Python with Django (https://www.polymer-project.org/). As the main feature of the platform is to allow modeling in LaTeX\u00a0language, we used MathJax as the rendering engine. In this way, the user can see the compiled version of the input model. All of these components form a single suite that works across different computational environments. The front-end is plain but incorporates the necessary functionality for input and output, as well as some solver options. The role of the back-end is to establish the communication between the GUI and the parser with the functions therein. In this way the inputs are being processed inside Python in the background, and the user simply witnesses a seamless working environment without having to understand the black-box parser in detail.In order to increase the effectiveness and user-friendliness of the platform, a Graphical-User Interface (GUI) based on HTML, JavaScript (front-end) and Django as the web-framework (back-end) has been implemented, as shown in The main components of the GUI are: \u2022Abstract model input: The input of the LaTeX\u00a0model, either directly inside the Polymer input text-box or via file upload (a .tex containing the required source LaTeX\u00a0code) \u2022Data files: The input of the data set which follows the abstract definition of the model via uploading the AMPL-format (.dat) data file \u2022Solver options: An array of solver - related options such as: 1.NEOS server job using CPLEX 2.Solve the relaxed LP (if MILP) 3.Select GPLK (built-in) as the optimization solver 4.Select CPLEX (if available) as the optimization solver (currently set to default)The following is an example of a LaTeX\u00a0formulated optimization problem which is ready to use with the platform; the well-known Traveling Salesman Problem (TSP) : \\documeand the raw LaTeX\u00a0code used to generate this was: __________________________________________________________________________________________________________ \u2216\u00a0text\u00a0{\u00a0minimize\u00a0}\u00a0\u2216\u00a0sum\u00a0\u2216\u00a0l\u00a0i\u00a0m\u00a0i\u00a0t\u00a0s\u00a0\u00a0{\u00a0i\u00a0,\u00a0j\u00a0:\u00a0i\u00a0\u2216\u00a0neq\u00a0j\u00a0}\u02c6{}\u00a0\u00a0\u2216\u2216 \u2216\u00a0text\u00a0{\u00a0subject\u00a0to\u00a0:\u00a0}\u2216\u2216 \u2216\u00a0sum\u00a0\u2216\u00a0l\u00a0i\u00a0m\u00a0i\u00a0t\u00a0s\u00a0\u00a0{\u00a0j\u00a0:\u00a0i\u00a0\u2216\u00a0neq\u00a0j\u00a0}\u02c6{}\u00a0\u00a0=\u00a01\u00a0\u2216\u00a0quad\u00a0\u2216\u00a0quad\u00a0\u2216\u00a0f\u00a0o\u00a0r\u00a0a\u00a0l\u00a0l\u00a0i\u00a0\u2216\u2216 \u2216\u00a0sum\u00a0\u2216\u00a0l\u00a0i\u00a0m\u00a0i\u00a0t\u00a0s\u00a0\u00a0{\u00a0i\u00a0:\u00a0i\u00a0\u2216\u00a0neq\u00a0j\u00a0}\u02c6{}\u00a0\u00a0=\u00a01\u00a0\u2216\u00a0quad\u00a0\u2216\u00a0quad\u00a0\u2216\u00a0f\u00a0o\u00a0r\u00a0a\u00a0l\u00a0l\u00a0j\u00a0\u2216\u2216 u\u00a0{\u00a0i\u00a0}\u00a0\u2212\u00a0u\u00a0{\u00a0j\u00a0}\u00a0+\u00a0nx\u00a0{\u00a0i\u00a0,\u00a0j\u00a0}\u00a0\u2216\u00a0leq\u00a0n\u00a0\u2212\u00a01\u00a0\u2216\u00a0quad\u00a0\u2216\u00a0quad\u00a0\u2216\u00a0f\u00a0o\u00a0r\u00a0a\u00a0l\u00a0l\u00a0i\u00a0\u2216\u00a0geq\u00a02\u00a0,\u00a0j\u00a0\u2216\u00a0leq\u00a0|\u00a0j\u00a0|\u22121,\u00a0i \u00a0\u00a0\u00a0\u00a0\u2216neq\u00a0j\u00a0\u2216\u2216 u\u00a0\u2216\u00a0in\u00a0\u00a0\u2216\u00a0mathbb\u00a0Z\u00a0,\u00a0x\u00a0\u2216\u00a0in\u00a0\u00a0\u2216{0\u00a0,1\u2216}\u2216\u2216 ____________________________________________________________________________________________________________ pre-made .tex file which can be uploaded in the corresponding field of the GUI. Either way, the MathJax Engine then renders LaTeX appropriately so the user can see the resulting compiled model live. Subject to syntax-errors, the MathJax engine might or might not render the model eventually, as naturally expected. Empty lines or spaces do not play a role, as well as commented-out lines using the standard notation (the percentage symbol %). The model file always begins with the objective function sense, the function itself, and then the sets of constraints follow, with the variables and their respective type at the end of the file.which is the input for the platform. The user can either input this code directly inside the Google polymer text box or via a parser we define the part of the code (a collection of Python functions) in the back-end side of the platform which is responsible for translating the model written in LaTeX\u00a0to Pyomo, the modeling component of the Python programming language. In order to effectively translate the user model input from LaTeX, we need an array of programming functions to carry out the conversion consistently since preserving the equivalence of the two is implied. The aim of the implementation is to provide minimum loss of generality in the ability to express mathematical notation for different modeling needs.As A detailed description of the implemented scheme is given in .tex model file and the .dat AMPL formatted data file are given, the platform then starts processing the model. The conversion starts by reading the variables of the model and their respective types, and then follows with component identification (locating the occurrence of the variables in each constraint) and their inter-relationships . Additionally, any summation and constraint conditional indexing schemes will be processed separately. Constraint-by-constraint the parser gradually builds the .py Pyomo abstract model file. It then merges through Pyomo the model with its data set and calls the selected solver for optimization.Once the \\quad command). The platform also supports the use of Greek letters. For instance, if a parameter is declared as \u03b1 the platform identifies the symbol, removes the backslash and expects to find alpha in the data-file. This takes place also in the pre-processing stage.A significant amount of pre-processing takes place prior of parsing. The minimum and essential is to first tidy up the input; that is, clear empty lines and spaces, as well as reserved (by the platform) keywords that the user can include but do not play any role in functional parsing , no matter if the initial input was done using the frac environment.The user can also opt-out selectively the constraints by putting regular comments in LaTeX, with the insertion of the percentage symbol (%) in the beginning of each expression. Once done, we attempt to simplify some types of mathematical expressions in order to be able to better process them later on. More specifically, we have two main functions that handle fractions and common factor (distributive expressions) simplifications. For example: This keeps the basic component identification functions intact, since their input is transformed first to the acceptable analytical format. Instead of transforming the parsing functions, we transform the input in the acceptable format. However, the user does not lose either functionality or flexibility, as this takes place in the background. To put it simply, either the user inputs the analytic form of an expression or the compact, the parser is still able to function correctly.To frame the capabilities of the parser, we will now describe how the user can define optimization models in the platform with a given example and the successful parsing to Pyomo. The parser first attempts to split the model into its three major distinct parts: \u2022the objective function \u2022the sets of constraints \u2022the types of the variables definedThese three parts are in a way independent but interconnected as well.string manipulation functions, therefore the use of regular expressions in Python was essential and effective.The parser first attempts to read the variables and their respective domain space (type). The platform is case sensitive since it is based on Pyomo. The processing is done using keywords as identifiers while scanning from the top to the bottom of the manually curated .tex file which contains the abstract model in LaTeX. For the three respective different parts mentioned earlier, the corresponding identifiers are:Reasonably, the focus was on consistency and reliability, rather computational performance mainly due to the lightweight workload of the processing demands in general. In order to do that, the parser uses 1.minimize, maximize}Objective function: { 2.leq, \\geq, =}Sets of constraints: {\\ 3.mathbb , {0,\u00a01}}Variables and their types: {\\.py output model file. Variable types can appear in the following way:This helps separate the processing into sections. Each section is analyzed and passes the information in Pyomo syntax in the \u2022 \\in\u00a0\\mathbb\u00a0R for Real numbers (\u2208\u211d)\u2022 \\in\u00a0\\mathbb\u00a0R_+ for non-negative Real numbers (\u2208\u211d+)\u2022 \\in\u00a0\\mathbb\u00a0R_{*}^{+} for positive Real numbers \u2022 \\in\u00a0\\mathbb\u00a0Z for integers (\u2208\u2124)\u2022 \\in\u00a0\\mathbb\u00a0Z_+ for non-negative integers (\u2208\u2124+)\u2022 \\in\u00a0\\mathbb\u00a0Z_{*}^{+} for positive integers , the parser then creates a list of strings for the names of the variables. This is one of the crucial structures of the parser and utilized alongside the entire run-time of the conversion process. A list of the same length, which holds the types of each respective variable, is also created. The platform in general uses Python lists to store information about variables, index sets, parameters, scalars etc.Our approach for understanding the inter-mathematical relationships between the variables and the parameters relied on exploiting the fundamental characteristics of Linear Programming: \u2022Proportionality \u2022Additivity \u2022Divisibilitydecompose them. By decomposition we define the fragmentation of each mathematical expression at each line of the .tex input model file into the corresponding variables, parameters, summations etc. so as we can process the given information accordingly. A simple graphical example is given in These mathematical relationships can help us understand the structure of the expressions and how to ax to describe coefficient a being multiplied by variable x). In some cases however it is imperative to use the asterisk to decompose a multiplication. For example, say Ds is a parameter and s is also a variable in the same model. There is no possible way to tell whether the expression Ds actually means D*s or if it is about a new parameter altogether, since the parameters are not explicitly defined in the model definition (as in AMLs). Adding to that the fact that for the scalars there is no associated underscore character to identify the parameter as those are not associated with index sets, the task is even more challenging. Therefore, we should write D*s if D is a scalar. As for parameters with index sets, for example Dsisi causes no confusion for the parser because the decomposition based on the underscore character clearly reveals two separate components. In this way, the platform also identifies new parameters. This means that since we know, for instance, that s is a variable but Ds is not, we can dynamically identify Ds on the fly (as we scan the current constraint) as being a parameter which is evidently multiplied with variable s, both having index set i associated with them. However, we need to pay attention on components appearing iteratively in different or in the same sets of constraints; did we have the component already appearing previously in the model again? In that case we do not have to declare it again in the Pyomo model as a new quantity, as that would cause a modeling error.The decomposition with the regular expressions is naturally done via the strings of the possible operators found, that is: addition, subtraction, division , since the asterisk to denote multiplication (\u2217 or \u22c5) is usually omitted in the way we describe the mathematical expressions model. For instance if a set i is identified, the string model.i\u00a0=\u00a0Set(dimen\u00a0=\u00a01) is first written inside the text version of the Pyomo model file, and then on-the-fly executed independently inside the already parsing Python function using the exec command. The execution commands run in a sequential manner. All the different possible cases of relationships between parameters and variables are dynamically identified, and the parser keeps track of the local (per constraint) and global (per model) list of parameters identified while scanning the model in dynamically growing lists.By split function carefully transfers this information intact to the Pyomo model.Dynamic identification of the parameters and index sets is one of the elegant features of the platform, since in most Algebraic Modeling Languages (AMLs) the user explicitly defines the model parameters one-by-one. In our case, this is done in an intelligent automated manner. Another important aspect of the decomposition process is the identification of the constraint type , since the position of the operator is crucial to separate the left and the right hand side of the constraint. This is handled by an independent function. Decomposition also helps identify Quadratic terms. By automatic conversion of the caret symbol to \u2217\u2217 (as this is one of the ways to denote power of a variable in Pyomo language) the Summation terms need to be enclosed inside parentheses (\u22ef), even with a single component. This accelerates identification of the summation terms with clarity and consistency. Summations are in a way very different than processing a simplified mathematical expression in the sense that we impose restrictions on how a summation can be used. First of all, the corresponding function to process summations tries to identify how many summation expressions exist in each constraint at a time. Their respective indexing expressions are extracted and then sent back to the index identification functions to be processed. The assignment of conditional indexing with the corresponding summation is carefully managed. Then, the summation commands for the Pyomo model file are gradually built. Summations can be expressed in the following form, and two different fields can be utilized to exploit conditional indexing (upper and lower brackets): ________________________________________________________________ \u2216sum\u2216\u00a0l\u00a0i\u00a0m\u00a0i\u00a0t\u00a0s\u00a0_\u00a0{p\u00a0:\u00a0\u00a0X_{n\u00a0,\u00a0p}\u00a0=\u00a0\u00a01}\u02c6{} ________________________________________________________________ which then compiles to: p, (that is for p\u00a0=\u00a01:|p|) but only when Xn,p\u00a0=\u00a01 at the same time. If we want to use multiple and stacked summations we can express them in the same way by adding the indexes for which the summation will be generated, as for example:This means that the summation will be executed for all values of _______________________________________________________________________ \u2216\u00a0sum\u00a0\u2216\u00a0l\u00a0i\u00a0m\u00a0i\u00a0t\u00a0s\u00a0_\u00a0{\u00a0i\u00a0,\u00a0j\u00a0}\u02c6{} ________________________________________________________________________ which then compiles to: i,\u00a0j. Dynamic (sparse) sets imposed on constraints can be expressed as:and will run for the full cardinality of sets _____________________________________________________________________________ X\u00a0_{\u00a0i\u00a0,\u00a0j\u00a0}\u00a0=\u00a0Y\u00a0_\u00a0{\u00a0i\u00a0,\u00a0j\u00a0}\u00a0\u2216\u00a0f\u00a0o\u00a0r\u00a0a\u00a0l\u00a0l\u00a0\u00a0\u2216\u00a0in\u00a0\u00a0C\u00a0\u2216\u2216 ______________________________________________________________________________ Xi,j\u00a0=\u00a0Yi,j\u2200\u00a0\u2208\u00a0Cwhich then compiles to: i,\u00a0j) which belong to the dynamic set C. In order to achieve proper and precise processing of summations and conditional indexing, we have built two separate functions assigned for the respective tasks. Since specific conditional indexing schemes can take place both for the generation of an entire constraint or just simply for a summation inside a constraint, two different sub-functions process this portion of information. This is done using the \\forall command at the end of each constraint, which changes how the indexes are being generated for the vertical expansion of the constraints from a specific index set. Concerning summations it is done with the bottom bracket information for horizontal expansion, as we previously saw, for instance, with p:Xn,p\u00a0=\u00a01.This means that the constraint is being generated only for those values of or if a more complex expression is used, the for-loop indexes for the summations are found before the colon symbol (:).A series of challenges arise when processing summations. For instance, which components are inside a summation symbol? A variable that might appear in two different summations at the same constraint can cause confusion. Thus, using a binary list for the full length of variables and parameters present in a constraint we identify the terms which belong to each specific summation. This binary list gets re-initialized for each different summation expression. From the lower bracket of each summation symbol, the parser is expecting to understand the indexes for which the summation is being generated. This is done by either simply stating the indexes in a plain way symbol which then helps understand for which indexes the constraints are being sequentially generated . For instance, \u2200\u00a0\u2208\u00a0C makes sure that the constraint is not generated for all combinations of index sets i,\u00a0j, but only the ones appearing in the sparse set C. The sparse sets are being registered also on the fly, if found either inside summation indexing brackets or in the constraint general indexing (after the \u2200 symbol) by using the keywords \\in, \\notin. The simplest form of constraint indexing is for instance: i and the summation is running for all those values of set j such that i is not equal to j. More advanced cases of constraint conditional indexing are also identified, as long as each expression is separated with the previous one by using a comma. For example in: At the end of each constraint, the parser identifies the \u201c \u2200\u201d\u2019 ( 1.to identify left part (before the operator/reserved keyword/command), 2.the operator and 3.the right-hand part.i\u00a0<\u00a0|i|, the left part is set i, the operator is < and the right-hand part is the cardinality of set i. In this way, by adding a new operator in the acceptable operators list inside the code, we allow expansion of supported expressions in a straightforward manner.For example, in transportation problem: Let us now follow the sequential steps that the parser takes to convert a simple example. Consider the well-known We will now provide in-depth analysis of how each of the main three parts in the model can be processed..tex model file that contains the variable symbols and their respective domains. This is done by trying to identify any of the previously presented reserved keywords specifically for this section. The parser reaches the bottom line by identifying the keyword mathbbR_\u00a0+ in this case. Commas can separate variables belonging to the same domain, and the corresponding parsing function splits the collections of variables of the same domain and processes them separately.The parser first attempts to locate the line of the x. The platform then builds two Python lists with the name of the variables found and their respective types.In this case, the parser identifies the domain and then rewinds back inside the string expression to find the variable symbols. It finds no commas, thus we collect only one variable with the symbol minimize) and tries to identify any involved variables in the objective function. In a different scenario, where not all of the model variables are present in the objective function, a routine identifies one-by-one all the remaining variables and their associated index sets in the block of the given constraint sets.The parser then reads the optimization sense respectively will be analyzed separately. In this case, the upper one is empty, so the lower one contains all the indexes for which the summation has to scale. Separated by commas, a simple extraction gives i,\u00a0j to be used for the Pyomo for-loop in the expression. There is no colon identified inside the lower bracket of the summation, thus no further identification of conditional indexing is required.The parser first attempts to locate any summation symbols. Since this is successful, the contained expression is extracted as split function is then applied on the extracted mathematical expression c_{i,\u00a0j}x_{i,\u00a0j} to begin identification of the involved terms. Since there are no operators we have a list containing only one item; the combined expression. It follows that the underscore characters are used to frame the names of the respective components. It is easy to split on these characters and then create a list to store the pairs of the indexes for each component. Thus, a sub-routine detects the case of having more than just one term in the summation-extracted expression. In this example, c is automatically identified as a parameter because of its associated index set which was identified with the underscore character and since it does not belong to the list of variables.A c, as well as the parameters for the current constraint/objective expression. This helps us clarify which parameters are present in each constraint as well as the set of parameters (unique) for the model thus far, as scanning goes on. Once the parameter c and variable x are identified and registered with their respective index sets, we proceed to read the constraint sets. The parser creates expressions as the ones shown below for this kind of operations:The global list of parameters is then updated by adding ________________________________________________________________________ model\u00a0.\u00a0i\u00a0=\u00a0Set\u00a0(\u00a0dimen\u00a0=1)\u00a0\u2216\u2216 model\u00a0.\u00a0j\u00a0=\u00a0Set\u00a0(\u00a0dimen\u00a0=1)\u00a0\u2216\u2216 model\u00a0.\u00a0c\u00a0=\u00a0Param\u00a0\u00a0\u2216\u2216 model\u00a0.\u00a0x\u00a0=\u00a0Var\u00a0\u00a0\u2216\u2216 ________________________________________________________________________ Since the objective function summation symbol was correctly identified with the respective indexes, the following code is generated and executed: ____________________________________________________________________________________________________________ def\u00a0\u00a0obj\u00a0\u00a0expression\u00a0(\u00a0model\u00a0)\u00a0: \u00a0\u00a0model\u00a0.\u00a0F\u00a0=\u00a0sum\u00a0 \u00a0\u00a0return\u00a0\u00a0model\u00a0.\u00a0F model\u00a0.\u00a0OBJ\u00a0=\u00a0Objective\u00a0 ____________________________________________________________________________________________________________ Since the constraints sets are very similar, for shortness we will only analyze the first one. The parser first locates the constraint type by finding either of the following operators \u2264,\u00a0\u00a0\u2265\u00a0,\u00a0\u00a0=. It then splits the constraint in two parts, left and right across this operator. This is done to carefully identify the position of the constraint type operator for placement into the Pyomo constraint expression later on.a is identified on the fly and since x is already registered as a variable and the parser proceeds to only register the new parameter by generating the following Pyomo expressions:The first component the parser gives is the terms identified raw in the expression __________________________________________________________________________________________ X in the following piece of code:The platform successfully identifies which terms belong to the summation and which do not and separates them carefully. Eventually the \u2200 symbol gives the list of indexes for which the constraints are being generated. This portion of information in the structure of a Pyomo constraint definition goes in replacing _________________________________________________________________________________________ def\u00a0\u00a0axb\u00a0_\u00a0constraint\u00a0_\u00a0\u00a0rule\u00a0_\u00a01\u00a0\u00a0: __________________________________________________________________________________________ and the full resulting function is: __________________________________________________________________________________________ def\u00a0\u00a0axb\u00a0_\u00a0constraint\u00a0_\u00a0rule\u00a0_\u00a01\u00a0\u00a0: \u00a0\u00a0model\u00a0.\u00a0C\u00a0_\u00a01\u00a0=\u00a0sum\u00a0\u00a0<=\u00a0model\u00a0.\u00a0a\u00a0[\u00a0i\u00a0] \u00a0\u00a0return\u00a0\u00a0model\u00a0.\u00a0C\u00a0_\u00a01 model\u00a0.\u00a0AxbConstraint\u00a0_\u00a01\u00a0=\u00a0Constraint\u00a0 __________________________________________________________________________________________ understand almost every different way of writing mathematical models using LaTeX\u00a0is nearly impossible; however, even by framing the way the user could write down the models, there are some challenges to overcome. For instance, the naming policy for the variables and parameters. One would assume that these would cause no problems but usually this happens because even in formal modeling languages, the user states the names and the types of every component of the problem. Starting from the sense of the objective function, to the names and the types of the variables and parameters as well as their respective sizes and the names of the index sets, everything is explicitly defined. This is not the case though in this platform; the parser recognizes the parameters and index sets with no prior given information. This in turn imposes trade-offs in the way we write the mathematical notation. For instance, multiple index sets have to be separated by commas as in xi,j instead of writing xij.Developing a parser that would be able to On the other hand, using symbolic representation of the models in LaTeX\u00a0can enable the user quickly identify errors in the description of the model, the involved variables, parameters or their mathematical relationships therein. This as opposed trying to debug models that have been developed directly in a programming language or in an AML, which would make the detection of such errors or typos more challenging.By scanning a constraint, the parser quickly identifies as mentioned the associated variables. In many cases parameters and variables might have multiple occurrences in the same constraint. This creates a challenging environment to locate the relationships of the parameters and the variables since they appear in multiple locations inside the string expressions and in different ways. On top of this, the name of a parameter can cause identification problems because it might be a sub/super set of the name of another parameter, e.g., parameter AB, and parameter ABC. Therefore naming conflicts are carefully resolved by the platform by meticulously identifying the exact location and occurrences of each term.The CPU time required for each step in the modeling process of the platform can be found in the Supplementary Information. It can be noted that the parser is the least consuming step, which clearly demonstrates the efficiency of the platform. The Pyomo model generation and solver (CPLEX in our measurements) steps and their associated CPU-time are completely outside of the parser\u2019s control. However, it is essential to get an idea of how these timings compare to each other with the addition of this extra higher level of abstraction in the beginning of the modeling process.Challenges also arise in locating which of the terms appearing in a constraint belong to summations, and to which summations; especially when items have multiple occurrences inside a constraint, there needs to be a unique identification so as to include a parameter (or a variable) inside a specific summation or not. We addressed this with the previously introduced binary lists. Then, for each of those summation symbols, the items activated (1) are included in the summation or not (0) and the list is generated for each different summation within the expression.Additionally, another challenge constitutes the extension of the platform to support nonlinear terms, where each term itself can be a combination of various operators and mathematical functions.Finally, it is worth mentioning that the amount of lines/characters to represent a model in LaTeX\u00a0in comparison with the equivalent model in Pyomo is substantially smaller. In this respect, the platform accelerates the modeling development process.left) which would capture more complex mathematical relationships.We presented a platform for rapid model generation using LaTeX\u00a0as the input language for mathematical programming, starting with the classes of LP, MILP and MIQP. The platform is based on Python and parses the input to Pyomo to successfully solve the underlying optimization problems. It uses a simple GUI to facilitate model and data input based on Django as the web-framework. The user can exploit locally installed solvers or redirect to NEOS server. This prototype platform delivers transparency and clarity, speedup of the model design and development process (by significantly reducing the required characters to type the input models) and abstracts the syntax from programming languages and AMLs. It therefore delivers reproducibility and the ability to replicate scientific work in an effective manner from an audience not necessarily versed in coding. Future work could possibly involve expansion to support nonlinear terms as well as differential and algebraic equations, sanity checking and error catching on input, the ability to embed explanatory comments in the input model file which would transfer to the target AML, extending the functionality concerning bounds on the variables as well as adding further support to built-in LaTeX\u00a0commands (such as \u221610.7717/peerj-cs.161/supp-1Supplemental Information 1Click here for additional data file."} +{"text": "HemaSphere. 2020;4:e448), there was an error in the original published title. \u201cLife-threatening\u201d instead appeared as \u201cLife-threating.\u201d The title has now been corrected online:In the article entitled \u201cCoronavirus Disease 2019 in Recipient of Allogeneic Hematopoietic Stem Cell Transplantation: Life-threatening Features Within the Early Post-engraftment Phase\u201d (https://journals.lww.com/hemasphere/Fulltext/2020/08000/Coronavirus_Disease_2019_in_Recipient_of.14.aspx"} +{"text": "Ultrasonic vocalizations (USVs) analysis is a well-recognized tool to investigate animal communication. It can be used for behavioral phenotyping of murine models of different disorders. The USVs are usually recorded with a microphone sensitive to ultrasound frequencies and they are analyzed by specific software. Different calls typologies exist, and each ultrasonic call can be manually classified, but the qualitative analysis is highly time-consuming. Considering this framework, in this work we proposed and evaluated a set of supervised learning methods for automatic USVs classification. This could represent a sustainable procedure to deeply analyze the ultrasonic communication, other than a standardized analysis. We used manually built datasets obtained by segmenting the USVs audio tracks analyzed with the Avisoft software, and then by labelling each of them into 10 representative classes. For the automatic classification task, we designed a Convolutional Neural Network that was trained receiving as input the spectrogram images associated to the segmented audio files. In addition, we also tested some other supervised learning algorithms, such as Support Vector Machine, Random Forest and Multilayer Perceptrons, exploiting informative numerical features extracted from the spectrograms. The performance showed how considering the whole time/frequency information of the spectrogram leads to significantly higher performance than considering a subset of numerical features. In the authors\u2019 opinion, the experimental results may represent a valuable benchmark for future work in this research field. Rodent models are good tools for scientific research because they allow to study and understand the biological mechanisms underlying the different pathologies. Behavioral alterations in animal models offer markers for the symptoms of the human diseases . The stuThe USVs are generally recorded with an ultrasound sensitive microphone and they are analyzed by specific software applications. Each syllable can be classified manually based on specific features, such as frequency, duration, amplitude and general shape. The manual classification provides a detailed characterization, but it is very time-consuming and may be subject to personal interpretation. Even using specific and professional tools, this task usually takes a lot of time and it appears to be only partially automatized. Indeed, it is possible to automatically analyze quantitative parameters , but it is more difficult to evaluate qualitative parameters, such as the different typologies of ultrasonic calls. For these reasons, it could be very interesting to find a method that automatically processes vocalizations starting from the audio tracks. This fundamental and challenging step could speed up the analysis of ultrasonic communication and also provide insight into the meaning of different USVs.ad hoc method for automatic USVs classification on the basis of the well-known USVs classification pattern published by Scattoni and colleagues Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: PartlyReviewer #2: Yes**********2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: NoReviewer #2: Yes**********3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1: NoReviewer #2: No**********4. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1: YesReviewer #2: Yes**********5. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1: The authors developed several classifiers capable of classifying individual vocalizations according to their spectrographicshapes as described by Scattoni et al, 2008. The work employs a quite comprehensive set of machine learning methodsincluding Support Vector Machines(SVM), Random Forests(RF), fully connected and convolutional artificial neural networks .Two-dimensional spectrograms were used as the input data for CNN-based classifiers. For non-convolutional ANN, SVM andRF classifiers the vocalizations were represented as the sets of 16 automatically extracted features.Although the authors made significant effort in optimizing the hyperparameters of SVM and RF classifiers, the set of features chosenrepresenting the vocalizations seems to be inadequate for the task of spectrogram shape classification.It can be hard to differentiate 'chevron' from 'complex' using only overall and marginal max/mean/min values. The confusionmatrices provided in the paper confirm that.The description of the architecture of ANN provided by the authors lacks details. Two convolutional layers onlycan be insufficient for good performance in image classification tasks. The authors don't mention whether they use any ofthe overfitting-prevention techniques such as batch normalization, dropout, weight regularization and data augmentation.The fact that the CNN applied to full spectrograms performs worse than SVM applied to the ambiguous feature setindicates that more effort can be invested in the optimization of CNN architecture and the training protocol.Note also the performances shown by CNNs in much more complex image classification tasks (CIFAR100) andthe RF performance demonstrated by Vogel at al, 2019 solving a similar problem.According to my assessment, the authors need to address the major and minor points listed below.Major1. For statistical confidence, the cross validation technique(e.g. 10-fold) should be applied for model assessment andthe results should be shown together with their confidence intervals2. The feature set used for RF, SVM and non-convolutional ANN input doesn't seem to be adequate for the desired task.The authors should extend the feature set and/or use entire frequency envelope data as the input.3. The architecture of ANNs should employ widely used techniques for overfitting prevention: batch normalization/dropout. It would begood to employ data augmentation to help the CNN perform better. The batch size alsocan be increased to help improve the performance and/or convergence speed.Minor1. SVM OVA approach requires confidence estimation. Which confidence estimation approach was used?2. ANN architecture should be described more thoroughly: convolutional layers kernel sizes, strides, dropout/batch normalization usage,stochastic gradient descent optimizer used, weight initialization strategy.3. The report of Vogel et al, 2019'Quantifying ultrasonic mouse vocalizations using acoustic analysis in asupervised statistical machine learning framework'solving a similar task should be mentioned4. Strain data is not used in the analysis anyhow.It would be interesting to compare the accuracies of two strains' shape prediction results taken separately.Typos96 'can not applies'124 'postnatal (PND)'Reviewer #2: Overview: The authors manually segmented and labeled an impressive number of mouse USVs (48699) according to categories developed by Scattoni and colleagues (2008). A sampling of 1199 USVs per category was used to train several supervised classification algorithms. Support Vector Machines (SVM), Random Forests (RF) and Artificial Neural Networks (ANN), in several configurations. The authors conclude that the best results are obtained by Support Vector Machines with the One-VS-All configuration. However, no method was particularly accurate. Precision, recall, and accuracy fell between %51.4 and 68.5% for all classifiers. I believe the moderate accuracy of the classifiers described in this report are not due to any deficiencies in methodology employed by the authors, rather they are due to the fundamental inaccuracy of human defined USV classification.Main Issues:The original creator of these particular USV categories, Maria Luisa Scattoni, has already published a paper using support vector machines (SVM) and random forests (RF) to categories USVs. They achieved 85% recall. What more does this paper add?https://doi.org/10.1038/s41598-019-44221-3Vogel, A.P., Tsanas, A. & Scattoni, M.L. Quantifying ultrasonic mouse vocalizations using acoustic analysis in a supervised statistical machine learning framework. Sci Rep 9, 8100 (2019). Experimenter derived call categories are generally falling out of favor. Substantial new evidence suggests that USVs don\u2019t categorize neatly into discrete groups, including the data in this paper. SVMs/RFs are capable of much higher accuracy when the training data actually comes from discrete groups with clear separations. The \u201cshort\u201d calls in the present manuscript are a well-defined group and are thus categorized accurately (>90%). But other calls like \u201ccomplex\u201d and \u201ccomposite\u201d are frequently miss-categorized. This likely isn\u2019t a fault of the classifier. Rather, it captures the uncertainty within the human created training data.https://doi.org/10.1101/870311Tim Sainburg, Marvin Thielk, Timothy Q Gentner (2019) Latent space visualization, characterization, and generation of diverse vocal communication signals. bioRxiv 870311; doi: Many methods are now available for un-biased call classification. These categories can then be validated through the behavioral/contextual usage of the calls. Call categories that are used identically during behavior can be collapsed. This method is more sophisticated and ethologically relevant than creating categories based on experimenter visual inspection.https://doi.org/10.1038/s41593-020-0584-zSangiamo, D.T., Warren, M.R. & Neunuebel, J.P. Ultrasonic signals associated with different types of social behavior of mice. Nat Neurosci 23, 411\u2013422 (2020). The training data, code, and finalized classifiers are the most valuable elements of this manuscript, but I did not see any indication that they will be distributed to the field. Without this, the manuscript just describes their internally used classifier with moderate accuracy.Final Thoughts:While there is nothing wrong with the scientific methodology employed in this paper, I would like to see all of the issues above addressed before considering the manuscript for publication.**********what does this mean?). If published, this will include your full peer review and any attached files.6. PLOS authors have the option to publish the peer review history of their article digital diagnostic tool,\u00a0 30 Sep 2020We would like to take this opportunity to sincerely thank the Reviewers for their valuable comments. We have carefully revised our manuscript, taking all the comments and suggestions into consideration.General comments__________________________________________________________________________First, we list the main efforts we have spent to enhance the experimental phase, in accordance with the Reviewers\u2019 recommendations:1) Expansion of the statistical analysis of the results;2) Rerun of the experiments after:a. Extending the standard feature space, for feature-based learning algorithms;b. Improving the Convolutional Neural Network (CNN) architecture by also including pertinent techniques for overfitting prevention;3) Implementation of two new sets of experiments, namely:a. Classification after splitting the dataset into the two genotype-based datasets;b. Classification performed by removing one class.The new experiments have led to an overall improvement in the classification performance, especially when the CNN is used. Of course, the updated results are reported in the new version of the paper. We change the title of the manuscript in \u201cAutomatic classification of mice vocalizations using Machine Learning techniques and Convolutional Neural Networks\u201d, suggesting the importance of use of the Convolutional Neural Networks in our paper.Beyond the experiment aspect, another point that has importantly contributed to the paper revision is related to the work that was suggested by both Reviewers, namely:Vogel, A.P., Tsanas, A. & Scattoni, M.L. Quantifying ultrasonic mouse vocalizations using acoustic analysis in a supervised statistical machine learning framework. Sci Rep 9, 8100 (2019).Accordingly, in the revised paper we discuss the main points that differentiate our work from the above cited paper, which has been properly referenced therein. Furthermore, we want to point out that now we have shifted our attention to the classification method based on CNN architecture, since in the 2019 Scientific Reports paper some traditional machine learning (ML) algorithms were already tested. Consequently, the discussion on the ML techniques results to be more limited with respect to the first submission. This change of focus is also motivated by the fact that the new experiments, carried out in the revision stage, have shown notably superior performance when using CNN as stated above. In addition, as pointed out in the 3) b. item above listed, in order to make the comparison as fair as possible, we have also implemented a further set of experiments, in which the classification has been performed by removing the class harmonic, as done in Vogel\u2019s paper.As a final note, we also mention that we will make both the dataset and the implementation code publicly available.In the following, we reply item by item to the specific Reviewers\u2019 comments.Response to Reviewer #1__________________________________________________________________________Comment 1 (major)\u2022 For statistical confidence, the cross-validation technique (e.g. 10-fold) should be applied for model assessment and the results should be shown together with their confidence intervals.Response: Following this valuable suggestion, we have applied 10-fold cross-validation for model assessment. In the revised paper, we have reported the results as mean \u00b1 standard deviation.__________________________________________________________________________Comment 2 (major) and Comment 3 (minor)\u2022 The feature set used for RF, SVM and non-convolutional ANN input doesn\u2019t seem to be adequate for the desired task. The authors should extend the feature set and/or use entire frequency envelope data as the input.\u2022 The report of Vogel et al, 2019 \u2018Quantifying ultrasonic mouse vocalization using acoustic analysis in a supervised statistical machine learning framework\u2019 solving similar task should be mentioned.Response: The problem expressed in Comment 2 (major) also implicitly deals with Comment3 (minor), therefore we would like to address both the comments in the same answer.We agree with the Reviewer that the results obtained by using the feature set described in the original paper suggest a perfectible ability to generalize the investigated machine learning models. As a matter of fact, we have extended the original feature set by including other features extracted from the spectrograms.The new features selection has been based from the paper suggested by the Reviewer . We have carefully read that report, in which the authors propose an optimal feature subset of 8 acoustic measures for USV classification. They are duration, quart 50 (start), peak freq (stddeventire), peaktopeak, max freq (stddeventire), peak freq (start), peak freq (end) and quart 75 (start). Since 4 of these 8 features are already included in the original feature set, namely, duration, peak freq (start), peak freq (end) and peak freq (stddeventire), we have just added the remaining 4 features, leading to a final feature space formed by 20 features .The new performances outperform the ones referred to the submitted paper, even if the strongest improvement has been obtained by enhancing the CNN architecture, as pointed out in the next response.______________________________________________________________________________Comment 3 (major) and Comment 2 (minor)\u2022 The architecture of ANNs should employ widely used techniques for overfitting prevention: batch normalization/dropout. It would be good to employ data augmentation to help the CNN perform better. The batch size also can be increased to help improve the performance and/or convergence speed.\u2022 ANN architecture should be described more thoroughly: convolutional layers kernel sizes, strides, dropout/batch normalization usage, stochastic gradient descent optimizer used, weight initialization strategy.Response: Regarding the issues detailed in Comment 3 (major), it is undoubtable that overfitting seems to afflict the proposed Convolutional Neural Network (CNN). The previously reported accuracy in training and testing phases are 87.0% and 58.3%, respectively, indicating that our model had some problem to generalize new examples not included in the training dataset.Agreeing with the reviewer suggestions, some techniques for overfitting prevention have been implemented, listed in the following:a. Regularization, i.e., dropout;b. Batch normalization;c. Testing different batch sizes;d. Data augmentation.In order to properly illustrate how we have implemented the just mentioned techniques, it can be helpful to start by describing the CNN architecture, that in turn also answers to Comment 2 (minor). First of all, we want to point out that substantial changes have been applied in the model architecture: indeed, the introduction of methods to prevent overfitting came with an increase of the architecture complexity.The final model is composed by 5 convolutional layers constituted by 32, 64, 64, 128 and 128 filters, respectively. The convolutional layers kernel sizes are 7x7 and 5x5 in the first two layers, and 3x3 in the successive three. The stride is set to 1 for each layer.A max-pooling layer is inserted after each convolutional layer. The pooling size is fixed to 3x3, while the stride is set to 2x2. The tensor is then flattened, and two fully connected layers are inserted, the first of size 1024 with ReLU activation function, and the second of size 10 with Softmax activation function. We mention that the Adam optimization algorithm has been used as stochastic gradient descent optimizer, and that the uniform distribution has been adopted to initialize the network weights. The description of the final CNN architecture has been thoroughly illustrated in the new version of the paper.To prevent overfitting, the strategies that we referred above as a., b., c., and d., have been tested. Dropout, i.e. a., deletes a random sample of the activations during training. Of course, dropout causes information loss, in particular, losing something in the first layer propagates that loss to the whole network. We have designed several configurations, i.e., we have located dropout layers in different positions and tested a range of rates (the fraction of input units to drop), from 0.2 to 0.8. The batch normalization technique (b.) has been similarly evaluated: it helps to coordinate the update of multiple layers in the model. We have experimented batch normalization layers both before and after the activation functions, and in parallel we have considered different batch sizes (c.) in the training phase.In the end, after this thorough hyperparameters optimization/tuning, the best model resulted the one with a dropout layer after each convolutional/max-pooling layer, except the first one, setting the rates to 0.2, 0.3, 0.4 and 0.5. Then, a further dropout layer was added after the first fully-connected layer , and finally batch normalization was included before the Softmax activation function of the last fully-connected layer. The batch size finally adopted is 32. By applying all of these adjustments, the performance of the final CNN architecture has notably improved: indeed, the test accuracy has been enhanced from 58.3% to 78.8%.Here is a final note on data augmentation (d.): given the characteristics of the spectrograms, some image transformations cannot be analyzed, since they would invalidate the ground-truth classification. For example, rotation or horizontal/vertical flipping could lead the network to confuse the upward class with the downward class, and vice-versa. For this reason, and also as suggested by the reviewer, we have increased the dataset by shifting and cropping the spectrogram images at random: however, the experiments have shown that data augmentation does not significantly improve the performance of the model. As with the other points, the discussion on overfitting prevention has been properly argued in the revised paper.______________________________________________________________________________Comment 1 (minor)\u2022 SVM OVA approach requires confidence estimation. Which confidence estimation approach was used? Response: For SVM OVA method, we set a maximum confidence strategy, similar to the weighted voting strategy from OVO systems. So, the output class is taken from the classifier with the largest positive answer. We have reported this detail in the revised version of the paper.______________________________________________________________________________Comment 4 (minor)\u2022 Strain data is not used in the analysis anyhow. It would be interesting to compare the accuracies of two strains' shape prediction results taken separately. Response: We have taken into consideration this valuable suggestion. As a matter of fact, in the revised paper we have included a new set of experiments, by testing the classification methods on the genotype-based datasets taken separately.______________________________________________________________________________Typos\u2022 96 'can not applies' \u2022 124 'postnatal (PND)' Response: We have corrected the typos indicated by the Reviewer.Response to Reviewer #2__________________________________________________________________________Comment 1\u2022 The original creator of these particular USV categories, Maria Luisa Scattoni, has already published a paper using support vector machines (SVM) and random forests (RF) to categories USVs. They achieved 85% recall. What more does this paper add?Vogel, A.P., Tsanas, A. & Scattoni, M.L. Quantifying ultrasonic mouse vocalizations using acoustic analysis in a supervised statistical machine learning framework. Sci Rep 9, 8100 (2019). Response: We have meticulously read the suggested report, and we agree that it is important to shed light on the improvements led by our work with respect to Vogel\u2019s one. We want to focus here on the two main breakthroughs that in our opinion are worthy to be pointed out.First, we made a significant effort to build our dataset. We performed our experiments on 48699 samples, which is a much more sizable dataset than the 225 samples evaluated in the suggested paper. It is well-known that the bigger the sample size is, the more accurate the research results are. That is because larger dataset cardinality allows to better determine the average values of data and reduce potential errors from testing a small number of possible outliers. As a consequence, the statistical analysis becomes more accurate and the margin of error smaller. Given these crucial considerations, we believe that our results benefit from a very effective statistical soundness, and thus that they may represent a further valuable benchmark for future works in this research field. Of course, the dataset will be made publicly available.The second aspect we want to mention is that in our work we explored the classification ability of a Convolutional Neural Network (CNN), extending the analysis beyond traditional machine learning algorithms, such as Support Vector Machine and Random Forest, employed in Vogel\u2019s paper. To the best of the authors\u2019 knowledge, this work is the first to propose a deep learning architecture aimed to classify the ten categories originally introduced in [17]. Furthermore, the CNN model has been notably modified during the revision phase. Accordingly, we have included all of these modifications in the revised paper. In particular, if compared with the original proposed architecture, we have changed the network topology by inserting more convolutional layers and increased the number of the filters composing them, in parallel to have investigated some techniques for overfitting prevention, such as regularization (drop out) and batch normalization (please find more details in the new version of the paper). As a consequence of such improvements, the performance of the final CNN model now achieves an accuracy of 78% on the test dataset, strongly improving the results reported in the original paper (where the test accuracy was 58.3 %).\u2022 Experimenter derived call categories are generally falling out of favor. Substantial new evidence suggests that USVs don\u2019t categorize neatly into discrete groups, including the data in this paper. SVMs/RFs are capable of much higher accuracy when the training data actually comes from discrete groups with clear separations. The \u201cshort\u201d calls in the present manuscript are a well-defined group and are thus categorized accurately (>90%). But other calls like \u201ccomplex\u201d and \u201ccomposite\u201d are frequently miss-categorized. This likely isn\u2019t a fault of the classifier. Rather, it captures the uncertainty within the human created training data.Tim Sainburg, Marvin Thielk, Timothy Q Gentner (2019) Latent space visualization, characterization, and generation of diverse vocal communication signals. bioRxiv 870311.Response: We think that this different perspective is very interesting. We agree that automatic USVs classification into a fixed number of discrete groups is a challenging task, as also suggested by the paper cited in the comment. Indeed, the results reported in the originally submitted paper confirmed the difficulty of distinguishing particular classes, such as complex and composite.Nevertheless, even if manual classification is an undeniably time-consuming activity and also vulnerable to personal interpretation, it can be performed within a more than reasonable margin of error, especially when the general shape of the spectrogram is analyzed.Even acknowledging an intrinsic uncertainty in the human labelling of data, in our work we addressed the problem of designing efficient and accurate machine learning and deep learning models, aimed to automatically classify vocalizations starting from the audio tracks. The performance obtained from the new set of experiments suggests that crucial improvements have been implemented to the originally proposed models. Indeed, the new results show a lesser uncertainty in USVs categorization, indicating that well defined models can actually lead to significant performance even when discrete vocalizations classification is investigated.This discussion has been inserted also in the revised paper, citing the suggested article.______________________________________________________________________________Comment 2\u2022 Many methods are now available for un-biased call classification. These categories can then be validated through the behavioral/contextual usage of the calls. Call categories that are used identically during behavior can be collapsed. This method is more sophisticated and ethologically relevant than creating categories based on experimenter visual inspection.Sangiamo, D.T., Warren, M.R. & Neunuebel, J.P. Ultrasonic signals associated with different types of social behavior of mice. Nat Neurosci 23, 411\u2013422 (2020). doi.org/10.1038/s41593-020-0584-z). This permits to associate distinct vocalizations categories with different types of murine social behavior giving important information to calls meaning. Unfortunately, we do not have these sophisticated instruments to associate behaviors to calls. In addition, we recorded vocalizations emitted by pups and not adults and in pups it is not possible to associate calls to behaviors as done by Sangiamo and colleagues because pups are still very young (first days after birth) and unable to move or perform more complex actions. They still have closed eyes. Finally, we agree with the Reviewer with the idea that it is very interesting to understand the meaning of mice calls and so, in the future, we would like to perform more sophisticated and ethologically relevant analysis on adult mice.Response: In the literature different methods of calls classification exist. We used a method based on experimenter visual inspection referring to papers of Dr. Scattoni cited in our references. This method permits to the operator to classify vocalizations based on features as frequency content, duration, amplitude and general shape. This classification provides a detailed USV characterization, but it says nothing about the meaning of the calls. Recently, new technologies have been developed such as a microphone array system and sound source localization method, to localize and assign USVs to individual mice during a social context 6, 8 ...\" -> \"postnatal day (PND) 6, 8...\"2. Threshold and hold time parameter values used in Avisoft for vocalization extraction should be provided here.Description of the experiments1. 'the first step consisted into' -> 'the first step consisted of'2. 'giving this way a statistical soundness' -> 'ensuring the statistical soundness' ?Features extraction section1. 'identified by the color...' \u00a0-> 'identified by the brightness...'Support vector machines1. 'Maximum confidence strategy was used...' - how the confidence was estimated? SVM provides binary result out of the box, the actual confidence assessment approaches vary.plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.Please submit your revised manuscript by Dec 21 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at Please include the following items when submitting your revised manuscript:A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.An unmarked version of your revised paper without tracked changes. 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If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #1:\u00a0All comments have been addressedReviewer #2:\u00a0All comments have been addressed**********2. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0NoReviewer #2:\u00a0Yes**********5. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0NoReviewer #2:\u00a0Yes**********6. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0Though the authors addressed the points noted in the previous review, the document undergone majorchanges that gave rise to several more major and minor inconsistencies to be addressed.Additionally, for the next review round, I would ask the authors to add line numbers in the documentand to provide the source code for the models described in the paper.Major1. The Random Forests, MP, Stacking NN classification performance results are completely omitted in the paper.SVM performance results are hard to find in the text. At the same time, both RF and SVM are mentioned in the abstract andmultiple times throughout the text. The results of all classifiers mentioned in the paper should be presented in a table.If the resulting accuracy is especially bad and is not worth considering than it should be stated explicitly.Note that the results are compared with the results of RF classifier in Vogel et al, 2019 paper, so the omitting of the RF resultslooks strange.2. 'Data-preprocessing' paragraph. 'This operation prevent imbalanced dataset...' - usually, that is not the mainreason to apply data augmentation when training CNN. To deal with imbalanced data one can just use weighted loss function, asyou mention further in the paragraph. Data augmentation is used mostly to prevent overfitting,generating a potentially infinite, though maybe not diverse enough set of training samples.From your description it is not clear which approach for data augmentationis used for the best-performing CNN: statically generated examples with random crops and shifts,just to balance the source data set,or the on-the-fly generation of randomly altered samples during the training,together/without using loss function weighting?That should be stated explicitly.Additionally, I think that is not necessary to explain that one should not rotate on flip images in that case.'data augmentation' is a general term for generation of pseudo-diverse samples andthat is quite obvious that one should not use the techniques applied for object photographs classification here...3. 'Proposed classification methods' paragraph : you briefly explain the principles of CNN and only after that you startexplaining trivial theory of MP, talking about weights, activation functions and neurons.'Multilayer perceptron' sub-section should go first, since it describes the most basic things on which CNN is based as well.Furthermore, I don't think Fig.2 is worth placing in the paper. That diagram is quite trivial, it occupies half of a pageand is known since 70s. It can be found in any textbook about ANN basics.Why not to use that space to depict the actual architecture of the CNN + ANNs you designed,maybe together with some trained kernel weights visualization or other data?For example, see the figures in our recently published workIvanenko et al, 2020, \"Classifying sex and strain from mouse ultrasonic vocalizations using deep learning\".MinorAbstract1. tested some supervised ... -> tested some other supervised ...2. extracted by the spectrograms -> extracted from the spectrogramsIntroduction1. \"... on such a fixed repertoire of calls typologies\". I think this should be rephrased.May be \"on a predefined set of call types\" ?2. Please cite our paperIvanenko et al, 2020, \"Classifying sex and strain from mouse ultrasonic vocalizations using deep learning\", PLOS CBin the introduction. Though we don't use Scattoni classical vocalization types there, we alsoclassify vocalizations using CNNs basing on their spectrogram shape , thus implementing the 'top-down' approach you mentioned.5. 'Simulation results' - I think the word 'simulation' is misleading here.USV Recording and analysis1. \"postnatal (PND) 6, 8 ...\" -> \"postnatal day (PND) 6, 8...\"2. Threshold and hold time parameter values used in Avisoft for vocalization extraction should be provided here.Description of the experiments1. 'the first step consisted into' -> 'the first step consisted of'2. 'giving this way a statistical soundness' -> 'ensuring the statistical soundness' ?Features extraction section1. 'identified by the color...' -> 'identified by the brightness...'Support vector machines1. 'Maximum confidence strategy was used...' - how the confidence was estimated? SVM provides binary result out of the box,the actual confidence assessment approaches vary.Reviewer #2:\u00a0The authors have made significant efforts to improve their CNN based classification architecture and have at least discussed and considered the theoretical limitations I posed in review. I agree that the scale of the new experiment and improved classification accuracy now expand upon, rather then duplicate, the work of the Scattoni Lab. With the addition of a publicly available dateset and classification CNN, this work now makes a tangible contribution to the field and I recommend it be accepted for publication.**********what does this mean?). If published, this will include your full peer review and any attached files.7. PLOS authors have the option to publish the peer review history of their article digital diagnostic tool,\u00a0 4 Dec 2020We would like to take this opportunity to sincerely thank everyone involved in the review process. We are glad that the adjustments introduced in response to reviewers' comments process have been generally appreciated. The further changes suggested by the reviewer #1 are detailed below.Response to Reviewer #1__________________________________________________________________________Comment 1 (major) The Random Forests, MP, Stacking NN classification performance results are completely omitted in the paper. SVM performance results are hard to find in the text. At the same time, both RF and SVM are mentioned in the abstract and multiple times throughout the text. The results of all classifiers mentioned in the paper should be presented in a table. If the resulting accuracy is especially bad and is not worth considering than it should be stated explicitly.Note that the results are compared with the results of RF classifier in Vogel et al, 2019 paper, so the omitting of the RF results looks strange.Response: As mentioned in the previous response process, in the first revised paper we had moved the focus from the \u201cnumerical features\u201d-based classification techniques, both for distancing our work with respect to Vogel\u2019s paper (as requested by both the reviewers), and also because the new results obtained by using the Convolutional Neural Networks had outperformed the others. Accordingly, we had considered not interesting and redundant the list of all the performance for all the investigated techniques, with that not for that intending to diminish the importance of studying those methods in our work.However, we agree with the reviewer that a table containing the overview of all the results may benefit the completeness of the paper. As a matter of fact, in the new version of the paper, we have inserted such a table in the \u201cPerformance analysis\u201d section. Nonetheless, to streamline the paper, we just report the performance related to the entire mice vocalizations dataset, since the strain-based performances result are similar to the ones obtained for the entire dataset, and so they do not add significant extra information.Finally, the source code has been properly integrated as well.__________________________________________________________________________Comment 2 (major) 'Data-preprocessing' paragraph. 'This operation prevents imbalanced dataset...' - usually, that is not the main reason to apply data augmentation when training CNN. To deal with imbalanced data one can just use weighted loss function, as you mention further in the paragraph. Data augmentation is used mostly to prevent overfitting,generating a potentially infinite, though maybe not diverse enough set of training samples.From your description it is not clear which approach for data augmentationis used for the best-performing CNN: statically generated examples with random crops and shifts, just to balance the source data set, or the on-the-fly generation of randomly altered samples during the training, together/without using loss function weighting? That should be stated explicitly.Additionally, I think that is not necessary to explain that one should not rotate on flip images in that case. 'data augmentation' is a general term for generation of pseudo-diverse samples and that is quite obvious that one should not use the techniques applied for object photographs classification here...Response: Thanks for pointing this out. We take this space to better clarify how data augmentation has been used in our experiments, and we will report these considerations in the new version of the paper.For the CNN design, we have tested data augmentation for both overfitting and imbalanced dataset prevention, separately. In the first case, an offline generation of new examples with random shifts and crops is applied over the entire training dataset; when using data augmentation for this aim, a properly weighted loss function is employed during the training in order to handle the imbalanced dataset problem too. In the second one, data augmentation is performed to balance the source dataset, and so by generating new samples just for the under-represented classes.However, note that data augmentation has been tested in the experimental phase, but it has not been in the end used to obtain the final best-performing CNN model. Indeed, the experimental tests have revealed that just including dropout and batch normalization layers is the most efficient action for overfitting prevention (as reported in the \u201cClassification via CNN\u201d section). Furthermore, the experiments have also provided more uniform accuracy values across the classes when the loss function is properly weighted instead of repopulating the under-represented classes by implementing data augmentation. In conclusion, data augmentation has not been exploited for designing the most-performing CNN architecture.As mentioned before, in the new version of the paper, we have better clarified all these aspects by partially re-writing the former section \u201cData pre-processing\u201d, which is now titled \u201cClass imbalance handling\u201d. Therein, the reviewer will find that all his/her observations above have been properly considered. __________________________________________________________________________Comment 3 (major) 'Proposed classification methods' paragraph: you briefly explain the principles of CNN and only after that you start explaining trivial theory of MP, talking about weights, activation functions and neurons. 'Multilayer perceptron' sub-section should go first, since it describes the most basic things on which CNN is based as well.Furthermore, I don't think Fig.2 is worth placing in the paper. That diagram is quite trivial, it occupies half of a page and is known since 70s. It can be found in any textbook about ANN basics.Why not to use that space to depict the actual architecture of the CNN + ANNs you designed, maybe together with some trained kernel weights visualization or other data? For example, see the figures in our recently published workIvanenko et al, 2020, \"Classifying sex and strain from mouse ultrasonic vocalizations using deep learning\".Response: Thanks for the suggestion. We agree with the reviewer that the paper may be clearer by swapping the \u201cConvolutional Neural Networks\u201d and \u201cMultilayer Perceptron\u201d sub-sections.In the revised version of the paper, we have modified the description of the multilayer perceptrons without the support of Fig. 2. In its place, there is a new figure depicting the entire architecture of the designed CNN; such a figure has been suitably added in \u201cClassification via CNN\u201d section.__________________________________________________________________________Minor (Abstract) tested some supervised ... -> tested some other supervised ... extracted by the spectrograms -> extracted from the spectrogramsResponse: We have revised both the sentences as in 1) and 2).__________________________________________________________________________Minor (Introduction) \"... on such a fixed repertoire of calls typologies\". I think this should be rephrased. May be \"on a predefined set of call types\"? Please cite our paper Ivanenko et al, 2020, \"Classifying sex and strain from mouse ultrasonic vocalizations using deep learning\", PLOS CB in the introduction. Though we don't use Scattoni classical vocalization types there, we also classify vocalizations using CNNs basing on their spectrogram shape , thus implementing the 'top-down' approach you mentioned. 'Simulation results' - I think the word 'simulation' is misleading here.Response: We have revised both the sentences as in 1) and 3). We have also carefully read the paper suggested in 2) and cited it in the introduction while mentioning the top-down approach.__________________________________________________________________________Minor \"postnatal (PND) 6, 8 ...\" -> \"postnatal day (PND) 6, 8...\" Threshold and hold time parameter values used in Avisoft for vocalization extraction should be provided here.Response: We have revised the sentences as in 1) and inserted the requested parameters in the appropriate section as suggested in 2).__________________________________________________________________________Minor (Description of the experiments) 'the first step consisted into' -> 'the first step consisted of' 'giving this way a statistical soundness' -> 'ensuring the statistical soundness'?Response: We have revised both the sentences as in 1) and 2).__________________________________________________________________________Minor (Feature extraction section) identified by the color...' -> 'identified by the brightness...'Response: We have revised the sentences as in 1).__________________________________________________________________________Minor (Support Vector Machines) 'Maximum confidence strategy was used...' - how the confidence was estimated? SVM provides binary result out of the box, the actual confidence assessment approaches vary.Response: The confidence is directly given by the decision function, which is the signed distance between the tested sample and the separating hyperplane. More precisely, the decision function is computed as \u2211_(i\u2208SV)\u2592\u3016y_i \u03b1_i K+b\u3017, where x is the sample to predict; x_i are the support vectors (SV) that construct the hyperplane; b is the intercept; \u03b1_i are the dual coefficients computed in the SVM optimization problem; y_i are the binary labels corresponding to x_i; K=\u03c6(x_i )^T \u03c6(x) is the employed kernel.In the OVA-strategy, we generate 10 classifiers: the first separates class 1 from the remaining ones, the second does the same for class 2, and so on for all 10 classes. The decision function is computed for each class as reported in the previous equation. The classifier that returns the largest positive value identifies the winner class.AttachmentResponse to Reviewers.docxSubmitted filename: Click here for additional data file. 15 Dec 2020Automatic classification of mice vocalizations using Machine Learning techniques and Convolutional Neural NetworksPONE-D-20-09612R2Dear Dr. Premoli,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Please, consider minor edits suggested by one of the reviewers.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Gennady Cymbalyuk, Ph.D.Academic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #1:\u00a0All comments have been addressedReviewer #2:\u00a0All comments have been addressed**********2. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********5. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********6. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0The authors carefully addressed all the comments given in the previous review round. I reccommend acceptance of the paper.Some minor grammar/stylistic/logic errors could be considered:line 391 : generating to -> generating of/forline 432: the CNN architecture has outperformed the other standard features-based methods ->the CNN architecture has outperformed the standard features-based methods (CNN is not a feature-based method in the paper ...)line 455: are arranged on the ten columns -> are arranged in ten columnsline 458 : The values into the matrices are normalized -> the values in the matrices ....line 463, 502: on the x axis there are the predicted labels : \"on x axis there are...\" sounds a bit ungrammatical to me; usually they use something like \"x axis refers to ... \" to describe the meaning of axesline 519: The performance showed that by exploiting the whole time/frequency information of the spectrogramleads to significantly higher performance than considering a subset->The performance showed that the exploiting of the whole time/frequency information of the spectrogramleads to significantly higher performance than considering only a subset of numerical featuresline 525: The final set up on an automatic classification method willdefinitely solve the current main problems in USVs manual classification: long time consuming andoperator-dependent.->The final set up of(?) an automatic classification method willdefinitely solve the current main problems of USVs manual classification: its being a time consuming process andoperator bias.Reviewer #2:\u00a0The authors have done a good job responding to the additional reviewers comments. I recommended to accept the paper in the previous revision.**********what does this mean?). If published, this will include your full peer review and any attached files.7. PLOS authors have the option to publish the peer review history of their article (If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.Yes:\u00a0Aleksandr IvanenkoReviewer #1:\u00a0Yes:\u00a0Kevin CoffeyReviewer #2:\u00a0 7 Jan 2021PONE-D-20-09612R2 Automatic classification of mice vocalizations using Machine Learning techniques and Convolutional Neural Networks Dear Dr. Premoli:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Gennady Cymbalyuk Academic EditorPLOS ONE"} +{"text": "The metabolic tumor volume (MTV) was calculated using a semi-automatic thresholding method and the average tracer uptake within the MTV was converted to a standard uptake value (SUV).When GB was confirmed on T2- and contrast-enhanced T1-weighted MRI, animals were randomized into a treatment group (n = 5) receiving MRI-guided 3D conformal arc micro-irradiation (20 Gy) with concomitant temozolomide, and a sham group (n = 5). Effect of treatment was evaluated by MRI and [18F]FDG PET (SUVmean x MTV) is superior to MTV only. Using (SUVmean x MTV), [18F]FDG PET detects treatment effect starting as soon as day 5 post-therapy, comparable to contrast-enhanced MRI. Importantly, [18F]FDG PET at delayed time intervals (240 min p.i.) was able to detect the treatment effect earlier, starting at day 2 post-irradiation. No significant differences were found at any time point for both the MTV and (SUVmean x MTV) of [18F]FCho PET.To detect treatment response, we found that for [18F]FDG PET were able to detect early treatment responses in GB rats, whereas, in this study this was not possible using [18F]FCho PET. Further comparative studies should corroborate these results and should also include (different) amino acid PET tracers.Both MRI and particularly delayed [ As a result, for newly diagnosed glioblastoma (GB) patients with a good performance status, the standard of care now includes maximal surgical resection followed by combined external beam RT (60 Gy in 30 fractions) and TMZ fluorodeoxyglucose ([18F]FDG), [18F]Fluoroethyltyrosine ([18F]FET), [18F]fluoroazomycin arabinoside ([18F]FAZA), 3,4-dihydroxy-6-[18F]-fluoro-l-phenylalanine ([18F]FDOPA) and [18F]Fluoromethylcholine ([18F]FCho) [18F]FDG and [18F]FET. [18F]FDG PET measures cellular glucose metabolism as a function of the hexokinase enzyme. However, due to its high uptake in normal brain parenchyma, the localization and the delineation of brain tumors is often difficult [18F]FDG and PET acquisition, the so called \u201cdual phase imaging\u201d FDG such as radiolabeled amino acids were developed showing an increased contrast between brain tumors and normal brain tissue. The diagnostic potential of [18F]FET PET in brain tumors is well documented and the RANO working group has recommended amino acid PET as an additional tool in the diagnostic assessment of brain tumors [18F]FET PET compared with MRI and a promising role for the distinction between tumor recurrence and aspecific post-therapeutic changes has been shown [18F]FAZA as a PET tracer may also have clinical relevance because tumor aggressiveness, failure to achieve local tumor control and an increased rate of tumor recurrence are all associated with hypoxia [18F]FAZA PET is that optimal imaging is performed a few hours post-injection and that the degree of hypoxia can theoretically fluctuate, influenced by therapy and the presence of acute versus chronic hypoxia [18F]FCho PET has been shown to be able to distinguish high-grade glioma, brain metastases and benign lesions and to identify the most malignant areas for stereotactic sampling [et al. concluded that [18F]FCho PET was able to differentiate WHO grade IV from grade II and III tumors, whereas MR spectroscopy differentiated grade III/IV from grade II tumors [18F]FCho PET/CT in the intraoperative management or radio-surgical approaches for glioma has been suggested, including intraoperative guidance in conjunction with MR spectroscopy FCho) \u201324. Currifficult , 24. It imaging\u201d \u201327. Alson tumors . Also, aen shown , 30. Hyp hypoxia , 31, 32. hypoxia . Finally hypoxia , 35. Recsampling . Grech-SI tumors . Recentltroscopy , 40, 41.\u00ae, Surrey, UK). Using the F98 GB rat model and the SARRP, we described and validated magnetic resonance imaging (MRI)-guided 3D conformal arc RT with concomitant chemotherapy to bridge the gap between radiation technology in the clinic and preclinical techniques [18F]FDG and [18F]FCho PET, compared to contrast-enhanced MRI, to detect the early effect of combined radiation and TMZ treatment in the F98 GB rat model. In addition, we also investigated which modality is best suited for the early detection of treatment response.Previously, our group used the orthotopic allograft F98 GB rat model to mimic GB treatment in patients. The GB F98 rat model exhibited features of human GB with regard to its aggressiveness, histological appearance and lack of immunogenicity . To enabchniques . In thisThe study was approved by the Ghent University Ethical Committee for animal experiments (ECD 09/23-A). All animals were kept under environmentally controlled conditions with food and water ad libitum. Follow-up of all animals was done by monitoring their body weight, food, water intake and their activity and normal behavior. The method of euthanasia was a lethal dose of pentobarbital sodium (180 mg/kg). Euthanasia was performed prior to the experimental endpoint if a decline of 20% body weight was observed or when the normal behavior severely deteriorated (e.g. lack of grooming).\u00ae) . Full details of the protocol can be found in our previous publications FDG and [18F]FCho. [18F]FDG scans were performed 2, 5, 9 and 12 days after the start of treatment, while [18F]FCho scans were performed 1, 6, 8 and 13 days after the start of treatment. These time points were arbitrarily chosen because, empirically, GB rats survived approximately 14 days after the start of treatment [18F]FDG and [18F]FCho PET scanning was not possible on the same day. An overview of the complete imaging scheme is shown in The assessment of the biological response was evaluated by small animal PET using FDG and 39.55 \u00b1 0.37 [18F]FCho (mean \u00b1 SE) dissolved in 200 \u03bcL saline). The total acquisition time was 20 min for [18F]FCho PET due the fast kinetics of [18F]FCho and 60 min for conventional [18F]FDG PET. In addition, a 30-min [18F]FDG PET scan was acquired 240 min after [18F]FDG administration (delayed imaging). All PET scans were reconstructed into a 200 \u00d7 200 \u00d7 64 matrix by a 2D Maximum Likelihood Expectation Maximization (MLEM) algorithm using 60 iterations and a voxel size of 0.5 \u00d7 0.5 \u00d7 1.157 mm. Identical reconstruction parameters were applied for [18F]FDG and [18F]FCho PET. The dynamically acquired PET data were reconstructed into 6 \u00d7 20 s, 3 \u00d7 1 min, 3 \u00d7 5 min, 2 \u00d7 20 min time frames for [18F]FDG scans and 6 \u00d7 20 s, 3 \u00d7 1 min, 1 \u00d7 5 min, 1 \u00d7 10 min time frames for [18F]FCho scans.Dynamic PET images were acquired in list mode using a dedicated small animal PET scanner . MTV was defined on the last time frame of the dynamic [18F]FDG PET (40\u201360 min post-injection), the delayed [18F]FDG PET (240 min post-injection) and on the last time frame of the dynamic [18F]FCho scan (10\u201320 min post-injection). First, a circular VOI is manually placed over a region with an increased tracer uptake excluding non-specific uptake, such as uptake in the scalp. Within this VOI, MTV was defined as all voxels with an uptake \u2265 60% and \u2265 50% of the maximum uptake for [18F]FDG and [18F]FCho, respectively. The selection of the thresholds was done arbitrarily and based on visual inspection of the [18F]FDG PET scan 40\u201360 min post-injection, the delayed [18F]FDG PET scan 240\u2013270 min post-injection and the [18F]FCho PET scan 10\u201320 min post-injection, see The metabolic tumor volume (MTV) was calculated based on a semi-automatic thresholding method using the PMOD software and (MTV x SUVmean) were calculated and included in the analysis. The TBRmax was defined as the ratio of the SUVmax of the tumor MTV to the SUVmean of the reference VOI located in the contralateral occipital normal brain region.Injected activity was corrected for decay and residual activity in the syringe. In addition to the MTV, the SUV18F]FCho PET were data from [Clinical MRI and PET images used to compare clinical and preclinical [ata from . The scaata from .18F]FCho uptake due to blood\u2013brain barrier (BBB) breakdown, we performed autoradiography and analyzed EB extravasation of a F98 GB rat tumor on day 16 after inoculation, as described in [\u00ae) dissolved in saline at a concentration of 4 mL per kg of body weight was injected intravenously (t = 0 min). [18F]FCho was injected . At t = 60 min, the rat was euthanized, and dissected rat brains were instantly frozen in isopentane (VWR\u00ae) cooled by liquid nitrogen for 2 min followed by 30 min incubation at -20\u00b0C. The brains were then cut into 20 \u03bcm serial sections using a cryostat , with alternating slides for fluorescent staining and hematoxylin and eosin (H&E) stain. The H&E sections were dried prior to fixation in 4% paraformaldehyde. The slices for autoradiography were placed on a Super Resolution storage phosphor screen (in red lighted room) and incubated for 2.5 h. The film was scanned using the PerkinElmer Cyclone Plus (600 dpi). A picture was taken of the frozen brain tissue (Sony\u00ae), and TRITC (tetramethylrhodamine isothiocyanate) fluorescently labeled sections were imaged with a BD pathway 435 automated imaging system (Becton Dickinson) equipped with a 10\u00d7 objective. A montage of 20\u00d715 images provided a complete overview of the brain section. Using the PMOD software, the HE and AR image were manually co-registered and the tumor volume of interest (VOI) was manually drawn on the HE image and transferred to the AR image. The normal brain VOI consists of a 5 x 5 mm square placed in the contralateral normal brain.To evaluate non-specific FDG, at conventional and delayed time point, and for [18F]FCho PET for [18F]FDG (early and delayed) and [18F]FCho PET are shown in To eliminate the influence of the differences in tumor volumes between individual animals, also MTV values were normalized to the MTV pre-therapy. Evolution of the normalized MTV and (SUV18F]FDG PET was significantly different between both groups on day 5 (p = 0.016). Using delayed [18F]FDG PET imaging, significant differences in MTV were present between both groups on day 9 (p = 0.032) and 12 (p = 0.032). No significant MTV differences were found between control and therapy group for [18F]FCho PET at any time point.The MTV on conventional [18F]FDG PET, was significantly different between the control and treated group on day 5 (p = 0.008) post-irradiation using the last time frame of the dynamic PET acquisition. On delayed [18F]FDG PET a significant difference was found on day 2 (p = 0.032), day 9 (p = 0.032) and day 12 (p = 0.016) post-irradiation. No significant differences were found between control and treated group for [18F]FCho PET at any time point.For conventional [18F]FDG, delayed [18F]FDG and [18F]FCho PET. Evolution of the normalized MTV and for [18F]FDG and [18F]FCho PET in a rat receiving control treatment are shown in In 18F]FCho uptake in the F98 GB tumor and very low uptake in normal brain. The background corrected mean tumor-to-mean normal brain ratio was 3,72 and the max tumor-to-mean normal brain ratio was 6.84 shows clearly necrosis in the tumor core, while this is not present in patient (B). However, both show a heterogeneous [18F]FCho uptake ranging from moderate to moderate intense at the invasion front of the tumor and 372.0 MBq (B) injected activity). Low uptake is noted in the normal brain tissue. In the F98 GB rat tumor, no gross central tumor necrosis is seen on contrast-enhanced T1-weighted MRI (C) and increased [18F]FCho uptake is present only in the upper left margin of the tumor . Surrounding extra-cranial organs, such as the salivary glands and the masticatory muscles, show intense [18F]FCho uptake (D). This is clearly visible on the pre-clinical PET, while in humans this uptake is not visible within the axial brain slice. In (B) and (C-D), the leakage pattern of the gadolinium contrast agent on MRI differs strongly from the [18F]FCho uptake pattern. Diffuse leakage of Gd in the entire tumor volume is seen on MRI (C), while a more localized choline uptake is seen in the upper left margin of the tumor just beneath the skull (D).18F]FDG and [18F]FCho PET, a threshold of \u2265 60% and \u2265 50% of the maximum uptake, respectively, was selected based on visual inspection was superior to MTV alone in detecting early treatment effect is also referred to as total lesion glycolysis (TLG), which is a well-known volumetric parameter that enables to capture the glycolytic phenotype and overall tumor burden. In this study, using (SUVmean x MTV), [18F]FDG PET acquired 40\u201360 minutes post-injection, was able to detect treatment response as early as 5 days post-therapy. Similar results were found when evaluating the changes in contrast-enhanced tumor volume on MRI. Importantly, [18F]FDG PET acquired 4 hours post-injection was able to detect the treatment response even earlier, namely at day 2 post-irradiation and [18F]FET PET have been suggested to be better suited than [18F]FDG for brain tumor imaging and monitoring therapy response in brain tumor patients [18F]FCho PET, first introduced for PET imaging of brain tumors by DeGrado et al. Choline PET, a tumor-to-normal-brain ratio (TBR) \u2264 1.4 might predict a longer overall survival in patients with suspected recurrent glioma after treatment [et al. suggested that there was a good correlation between a change in SUVmax of the tumor volume during RT and response [18F]FCho PET study in childhood astrocytic tumors confirmed the added value of [18F]FCho SUVmax and functional MRI apparent diffusion coefficient values to monitor therapy response FCho PET might be able to detect a treatment-induced diminished cell proliferation rate because this choline PET analogue is a substrate for choline kinase, an enzyme commonly overexpressed in malignant lesions involved in the incorporation of choline into phospholipids, which is an essential component of all cell membranes. In cancer, an increased cellular transport and higher expression of choline kinase leads to an increased uptake of radiolabeled choline [18F]FDG, ameliorating the delineation of tumor boundaries [18F]FCho PET compared to state-of-the art conventional MRI using RANO criteria for early therapy response assessment in GB patients. We found that SUV values were not able to predict response, while (SUVmean x MTV) allowed prediction of therapy response one month after the completion of radiation therapy, however, not earlier than changes of tumor volume derived from contrast-enhanced MRI FCho PET between the control and the treatment group. Based on these results, in rats, [18F]FCho PET was not able to detect early combined radiation and chemotherapy effects after the completion of treatment. We can only speculate about an explanation.In this study, we did not find significant differences at any time point for MTV and reached a maximum within a 5-min window following the injection [18F]FCho, several clinical reports performed emission scanning for 15 min, beginning 5\u201310 min after injection of the tracer [18F]FCho uptake by all types of brain lesions was rapid with minimal changes in uptake activity more than 6 min after administration, except for meningiomas [18F]FCho uptake also reached 80% and 90% of the total activity at 3\u00b14 and 7\u00b16 minutes post injection, respectively [18F]FET FET \u201372. Impo[18F]FET , 73, 74.18F]FDG (and particularly acquired 4 hours post-injection) is preferred over [18F]FCho. Further comparative studies should corroborate these results and should also include (different) amino acid PET tracers.Based on a preclinical rat model for GB and multimodal imaging using MRI and PET with two different tracers, to evaluate early treatment response after combined chemo-radiation therapy, we found that both MRI and PET can be used for this purpose. With regard to the choice of PET biomarker, [S1 Fig(TIF)Click here for additional data file. 5 Jan 2021PONE-D-20-36019Assessment of the effect of therapy in a rat model of glioblastoma using [18F]FDG and [18F]FCho PET compared to contrast-enhanced MRI.PLOS ONEDear Dr. Bolcaen,Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE\u2019s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.The article describes the results of a pre-clinical study in a rat model of glioblastoma using [18F]FDG and [18F]FCho PET compared to contrast-enhanced MRI\"\u00a0 for the early detection of treatment response. The objective of the study is interesting and may help future potential applications regard PET imaging in the field of primary brain tumors. However, the paper needs a revision as defined in the section of comments below.plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.Please submit your revised manuscript by Feb 13 2021 11:59PM. 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I agree with the comments of the two reviewers the paper needs a major revision.The results of choline PET and FDG PET have to be discussed carefully because both radiopharmaceutical agents have limited use in this field. For choline PET, despite the biodistribution of the tracer is fast compared to FDG other studies suggest a start acquisition rapidly after injection and a time between 20 and 50 minutes for late imaging in order to have a good balance of T/B ratio. A unique Cho-PET dynamic acquisition 5-20 minutes after the injection may affect negatively the quality of the images. Please discuss in the discussion and eventually in the limitation of the study.I suggest also to report some references missing of recent representative articles on humans: Eg.https://doi.org/10.1007/s40336-020-00398-6- Vetrano, I.G., Laudicella, R. & Alongi, P. Choline PET/CT and intraoperative management of primary brain tumors. New insights for contemporary neurosurgery. Clin Transl Imaging 8, 401\u2013404 (2020). https://doi.org/10.1007/s40336-020-00389-7- Alongi, P., Quartuccio, N., Arnone, A. et al. Brain PET/CT using prostate cancer radiopharmaceutical agents in the evaluation of gliomas. Clin Transl Imaging 8, 433\u2013448 (2020). - Fraioli F, Shankar A, Hargrave D, Hyare H, Gaze MN, Groves AM, Alongi P, Stoneham S, Michopoulou S, Syed R, Bomanji JB. 18F-fluoroethylcholine (18F-Cho) PET/MRI functional parameters in pediatric astrocytic brain tumors. Clin Nucl Med. 2015 Jan;40(1):e40-5. doi: 10.1097/RLU.0000000000000556. PMID: 25188640.Alongi P, Vetrano IG, Fiasconaro E, Alaimo V, Laudicella R, Bellavia M, Rubino F, Bagnato S, Galardi G. Choline-PET/CT in the Differential Diagnosis Between Cystic Glioblastoma and Intraparenchymal Hemorrhage. Curr Radiopharm. 2019;12(1):88-92. doi: 10.2174/1874471011666180817122427. PMID: 30117406.Journal requirements:When submitting your revision, we need you to address these additional requirements.1. 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Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: [Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Partly**********2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0No**********3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********4. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********5. Review Comments to the AuthorReviewer #1:\u00a0In this study, the authors investigated the role of FDG and F-Choline PET compared to MRI for the early detection of treatment response in a glioblastoma rat model obtained with F98 cells. Rats were divided into two groups (control and treated with radiation and Temozolomide) and the response was monitored with MRI and PET with FDG and F-Choline performed at different times points.The text is well organized and methods and results are fully described but there are some points that need to be clarified.Major commentsAbstract1. Line 43, in the abstract authors indicate that F-Choline was performed on day 7 post-treatment but in M&M and in the text is indicated day 8 (line 218).Materials and methods1. Line 231, authors can edit the correct injected dose (mean \u00b1 SE) of FDG and F-Choline because in line 231 authors indicated 37 MBq and in the figure legends authors indicated other specific doses.2. Line 274, the dose of FCho can be edited in MBq, please?3. Lines- 289-292, why these lines are under the paragraph \u201cAutoradiography and Evans Blue (EB) staining\u201d, can authors add another title, please?4. Figure 3, is the same animal? Because the images are different. If not, can authors use the same animal, please?Results5. In table 2 there are only the p-values, can also add the value of each parameter (mean \u00b1 SE), please?6. Figure 4, why FDG MTV values at d2 are so different between control and treated group whereas the volume measured using MRI is closer? The tumor volume of control animals measured using MRI increased along time whereas MTV (both FDG and Choline) remained stable or slight decrease, what is the hypothesis? Authors should discuss.7. On day 9, only 2 control animals performed FDG PET, how is it possible that both MTV and MTV+SUVmean values are significantly different between control and treated group (line 347 and 353)?8. In figure 5 there is represented only a control rat, authors can add a longitudinal figure with a representative treated rat so it is possible compared images of control and treated rats, please?9. Figure 5, what is the color scale for PET ? Can authors also add min and max values on the scale.10. Did authors evaluate post mortem staining for ki67, GFAP, choline kinase?DiscussionEdit discuss on the basis of results (point 6), please.Reviewer #2:\u00a0The authors evaluate the role of FDG-PET and Cho-PET, compared to c.e. MRI, for the early detection of treatment response in murine model of GBM; 5 animals randomizedly received RT plus TMZ, while other 5 no. The treatment effect was evaluated with serial MRI and FDG-PET , and also Cho-PET . The metabolic tumor volume (MTV) was semi-automatically calculatedm and the average tracer uptake within the MTV was converted to a SUV. Using SUVmean x MTV, FDG-PET started to detect treatment's effects at 5 day post-treatment, comparable to c.e. MRI. Moreover, delayed FDG-PET (240 min p.i.) earlier detect such effects (from day 2); on the other hand, no significant differences were found at any time point for both the MTV and (SUVmean x MTV) of Cho-PET. Therefore, the authors concluded that MRI and delayed FDG-PET detect early treatment responses in GB murine model of GBM, whereas these results were not obtained with Cho-PETThe topic is undoubtedly intriguing, but i have some issues:-INTRODUCTIONThe ref 1 is related to 2007 WHO classification; from an epidemiological point of view, it should be better to consider the last CBTRUS report .I suggest also to modify ref. 2 and 3, using a more up-to-date literature reference about glioma management guideline on the diagnosis and treatment of adult astrocytic and oligodendroglial gliomas. Lancet Oncol. 2017 Jun;18(6):e315-e329).Moreover, the study by Stupp in 2005 that showed the role of combined RT-CMT was not the ref n\u00b0 5 but the one published in NEJM :987-96. doi: 10.1056/NEJMoa0433309).It shuld be better to update the references related to the clinical role of ChoPET in brain tumors , due to the increasing interest about such technique.Why the authors selected Cho-PET, instead of [18F]FAZA PET, for example? I think that clarifying the advantages and disadvantages os this choice could increase the informative role of the present work.How where the simple size selected?statistical analysis were performed to selected a population of 10 animals?Finally, the author disclosure a financial support by Lux Luka Foundation, but they must clearly state, according to Journal guidelines, who exactly received fundings, and the role of the sponsor in the study design and analysis.**********what does this mean?). If published, this will include your full peer review and any attached files.6. PLOS authors have the option to publish the peer review history of their article digital diagnostic tool,\u00a0 10 Feb 2021A. Additional Editor Comments:The article describes the results of a pre-clinical study in a rat model of glioblastoma using [18F]FDG and [18F]FCho PET compared to contrast-enhanced MRI\" for the early detection of treatment response. The objective of the study is interesting and may help future potential applications regard PET imaging in the field of primary brain tumors. I agree with the comments of the two reviewers the paper needs a major revision.________________________________________________________________________Comment 1: The results of choline PET and FDG PET have to be discussed carefully because both radiopharmaceutical agents have limited use in this field. For choline PET, despite the biodistribution of the tracer is fast compared to FDG other studies suggest a start acquisition rapidly after injection and a time between 20 and 50 minutes for late imaging in order to have a good balance of T/B ratio. A unique Cho-PET dynamic acquisition 5-20 minutes after the injection may affect negatively the quality of the images. Please discuss in the discussion and eventually in the limitation of the study.The main reason for starting the acquisition early (5\u201310 min) after injection of the tracer is indeed because of the rapid and extensive clearance from the blood after intravenous injection. DeGrado et al. documented that the biodistribution of [18F]FCho changes very slowly after 10-min post-injection (DeGrado TR 2001 and 2002). In 2001, in prostate cancer patients, it was documented that the activity in the prostate reached a maximum within a 5-min window following the injection (DeGrado TR 2001). This was also confirmed by our group investigating the blood kinetics of [18F]FCho in rats, as shown in Figure 8, confirming a fast metabolization with an availability of only 17.5% of intact tracer after 15 min . In multiple clinical reports, emission scanning of the brain was performed for 15 min, beginning 5\u201310 min after injection of the tracer . To confirm this, in a previous publication of our group, we did investigate the optimal timing for imaging brain tumours and other brain lesions with [18F]FCho PET . On the basis of the TACs, PET imaging with [18F]FCho starting within minutes after the administration of the tracer is preferred and uptake by all types of brain lesions was rapid, and minimal changes in uptake activity occurred more than 6 min after the administration of the tracer, except for meningiomas that showed decreasing activity after an early peak . Hence, if discrimination between meningioma and other brain tumours is of concern, both 'early' and 'late' PET imaging could be helpful. Recently, Grkovski M et al. performed a dynamic 40 min [18F]FCho PET in patients with brain metastasis. The percentage of activity due to [18F]FCho in plasma was more stable than in rats: 67\u00b111%, 65\u00b19%, 65\u00b17% and 64\u00b17% at 1, 5, 10 and 30 min after injection. However, intratumor [18F]FCho uptake reached 80% and 90% of the total activity at 3\u00b14 and 7\u00b16 minutes (median 1 and 6 minutes) post injection, respectively (Grkovski M 2020). This confirms other studies that radiolabeled choline uptake is rapid and sustained and appears to reach a plateau faster than [18F]FET (Lohmann P 2015).In contrast with [18F]FDG brain imaging, where dual time point imaging has shown clear advantages to increase the T/B ratio , this is assumed to be less advantageous for [18F]FCho PET since the uptake in normal brain is already low . For the use of [18F]FCho PET for the detection of bone metastasis in prostate cancer patients, delayed imaging is recommended. A significant increase in [18F]FCho accumulation in bone metastases was documented using dual-time-point PET imaging .Based on the above-mentioned we selected a dynamic scan of 20 min for imaging the F98 GB tumor in rats assuming based on the literature that the maximal tumor uptake has been reached by then. Parts of this clarification were added to the discussion: line 567-583.\u25cf Mertens K, Bolcaen J, Ham H, Deblaere K, Van den Broecke C, Boterberg T, De Vos F, Goethals I. The optimal timing for imaging brain tumours and other brain lesions with 18F-labelled fluoromethylcholine: a dynamic positron emission tomography study. Nucl Med Commun. 2012;33:954-9.\u25cf Mertens K, Ham H, Deblaere K, Kalala JP, Van den Broecke C, Slaets D, et al. Distribution patterns of 18F-labelled fluoromethylcholine in normal structures and tumors of the head: a PET/MRI evaluation. Clin Nucl Med. 2012;37:e196-203.\u25cf Mertens K, Acou M, Van Hauwe J, De Ruyck I, Van den Broecke C, Kalala JP, et al. Validation of 18F-FDG PET at conventional and delayed intervals for the discrimination of high-grade from low-grade gliomas: a stereotactic PET and MRI study. Clin Nucl Med. 2013;38:495-500. \u25cf Spence AM, Muzi M, Mankoff DA, O\u2019Sullivan SF, Link JM, Lewellen TK, et al. 18F-FDG PET of gliomas at delayed intervals: improved distinction between tumor and normal gray matter. J Nucl Med. 2004;45:1653-9.\u25cf DeGrado TR, Coleman RE, Wang S, Baldwin SW, Orr MD, Robertson CN, et al. Synthesis and evaluation of 18F-labeled choline as an oncologic tracer for positron emission tomography: initial findings in prostate cancer. Cancer Res 2001;61:110-7.\u25cf DeGrado TR, Reiman RE, Price DT, Wang S, Coleman RE. Pharmacokinetics and radiation dosimetry of 18F-fluorocholine. J Nucl Med. 2002;43:92-6.\u25cf Kwee SA, Wei H, Sesterhenn I, Yun D, Coel MN. Localization of primary prostate cancer with dual-phase 18F-fluorocholine PET. J Nucl Med 2006;47:262-9.\u25cf Kwee SA, Coel MN, Lim J, Ko JP. Combined use of F-18 fluorocholine positron emission tomography and magnetic resonance spectroscopy for brain tumor evaluation. J Neuroimaging. 2004;14:285-9.\u25cf Kwee SA, Ko JP, Jiang CS, Watters MR, Coel MN. Solitary brain lesions enhancing at MR imaging: evaluation with fluorine 18fluorocholine PET. Radiology. 2007;244:557-65.\u25cf Husarik DB, Miralbell R, Dubs M, John H, Giger OT, Gelet A, et al. Evaluation of [(18)F]-choline PET/CT for staging and restaging of prostate cancer. Eur J Nucl Med Mol Imaging. 2008;35:253-63.\u25cf Grkovski M, Kohutek ZA, Sch\u00f6der H, Brennan CW, Tabar VS, Gutin PH, et al. 18F-Fluorocholine PET uptake correlates with pathologic evidence of recurrent tumor after stereotactic radiosurgery for brain metastases. Eur J Nucl Med Mol Imaging. 2020;47:1446-57.\u25cf Schaefferkoetter JD, Wang Z, Stephenson MC, Roy S, Conti M, Eriksson L, et al. Quantitative 18F-fluorocholine positron emission tomography for prostate cancer: correlation between kinetic parameters and Gleason scoring. EJNMMI Res. 2017;7:25.\u25cf Grkovski M, Gharzeddine K, Sawan P, Sch\u00f6der H, Michaud L, Weber WA, et al. 11C-Choline Pharmacokinetics in Recurrent Prostate Cancer. J Nucl Med. 2018;59:1672-8.\u25cf Sutinen E, Nurmi M, Roivainen A, Varpula M, Tolvanen T, Lehikoinen P, et al. Kinetics of [(11)C]choline uptake in prostate cancer: a PET study. Eur J Nucl Med Mol Imaging. 2004;31:317-24.\u25cf Lohmann P, Herzog H, Rota Kops E, Stoffels G, Judov N, Filss C, et al. Dual-time-point O-(2-[(18)F]fluoroethyl)-L-tyrosine PET for grading of cerebral gliomas. Eur Radiol. 2015;25:3017-24. \u25cf Bolcaen J, Lybaert K, Moerman L, Descamps B, Deblaere K, Boterberg T, et al. Kinetic Modeling and Graphical Analysis of 18F-Fluoromethylcholine (FCho), 18F-Fluoroethyltyrosine (FET) and 18F-fluorodeoxyglucose (FDG) PET for the Discrimination between High-grade Glioma and Radiation Necrosis in Rats. PLoS One. 2016;11:e0161845.________________________________________________________________________Comment 2: I suggest also to report some references missing of recent representative articles on humans: Eg.https://doi.org/10.1007/s40336-020-00398-6- Vetrano, I.G., Laudicella, R. & Alongi, P. Choline PET/CT and intraoperative management of primary brain tumors. New insights for contemporary neurosurgery. Clin Transl Imaging 8, 401\u20134 (2020). https://doi.org/10.1007/s40336-020-00389-7- Alongi, P., Quartuccio, N., Arnone, A. et al. Brain PET/CT using prostate cancer radiopharmaceutical agents in the evaluation of gliomas. Clin Transl Imaging 8, 433\u201348 (2020). - Fraioli F, Shankar A, Hargrave D, Hyare H, Gaze MN, Groves AM, Alongi P, Stoneham S, Michopoulou S, Syed R, Bomanji JB. 18F-fluoroethylcholine (18F-Cho) PET/MRI functional parameters in pediatric astrocytic brain tumors. Clin Nucl Med. 2015 Jan;40(1):e40-5. doi: 10.1097/RLU.0000000000000556. PMID: 25188640.-Alongi P, Vetrano IG, Fiasconaro E, Alaimo V, Laudicella R, Bellavia M, Rubino F, Bagnato S, Galardi G. Choline-PET/CT in the Differential Diagnosis Between Cystic Glioblastoma and Intraparenchymal Hemorrhage. Curr Radiopharm. 2019;12(1):88-92. doi: 10.2174/1874471011666180817122427. PMID: 30117406. We agree that these recent references are important and included these in the manuscript. This section was added to the introduction line 150-157:The metabolic information acquired by [18F]FCho PET has been shown to be able to distinguish high-grade glioma, brain metastases and benign lesions and to identify the most malignant areas for stereotactic sampling . Grech-Sollars et al. concluded that [18F]FCho PET was able to differentiate WHO grade IV from grade II and III tumours, whereas MR spectroscopy differentiated grade III/IV from grade II tumours [Grech-Sollars et al. 2019]. Recently, the potential use of [18F]FCho PET/CT in the intraoperative management or radio-surgical approaches for glioma has been suggested, including intraoperative guidance in conjunction with MR spectroscopy .The reference to Fraioli et al. was added in the discussion Line 518 and 523-525: Finally, a [18F]FCho PET study in childhood astrocytic tumors confirmed the added value of [18F]FCho SUVmax and functional MRI apparent diffusion coefficient values to monitor therapy response [Fraioli et al. 2015].Also these recent reference were included in the revised manuscript: - Villena Mart\u00edn M, Pena Pardo FJ, Jim\u00e9nez Arag\u00f3n F, Borras Moreno JM, Garc\u00eda Vicente AM, et al. Metabolic targeting can improve the efficiency of brain tumor biopsies. Semin Oncol. 2020;47:148-54.- Grech-Sollars M, Ordidge KL, Vaqas B, Davies C, Vaja V, Honeyfield L, et al. Imaging and Tissue Biomarkers of Choline Metabolism in Diffuse Adult Glioma: 18F-Fluoromethylcholine PET/CT, Magnetic Resonance Spectroscopy, and Choline Kinase \u03b1. Cancers. 2019;11:1969._______________________________________________________________________B. When submitting your revision, we need you to address these additional requirements.Comment 3: Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found athttps://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf andhttps://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdfUpon submission of the revised manuscript, extra care was taken to meet the PLOS ONE style requirements, including those for file naming. Referring to supplemental materials was adapted and author titels were deleted. 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This content is published under CC BY 4.0 license. To the best of our knowledge, an additional permission request is not required. Please let us know if we understood wrong. We changed the caption to clarify the reuse of the figure (line 589-590). The original figures were uploaded as \u2018other\u2019 in the online submission. ________________________________________________________________________http://journals.plos.org/plosone/s/supporting-information.Comment 5: Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: The guidelines were applied for the supporting information, including an in-text citation: S1 Fig.The name of the supporting information figure was matched with the supporting information captions within the manuscript (line 396). A caption was added at the end of the manuscript, including a title (line 819-820).________________________________________________________________________C. REVIEWER 1In this study, the authors investigated the role of FDG and F-Choline PET compared to MRI for the early detection of treatment response in a glioblastoma rat model obtained with F98 cells. Rats were divided into two groups (control and treated with radiation and Temozolomide) and the response was monitored with MRI and PET with FDG and F-Choline performed at different times points.The text is well organized and methods and results are fully described but there are some points that need to be clarified.Major commentsAbstractComment 1. Line 43, in the abstract authors indicate that F-Choline was performed on day 7 post-treatment but in M&M and in the text is indicated day 8 (line 218).This is indeed an error in the abstract and has been modified (line 52). [18F]FCho PET was performed on day 1-6-8-13 as mentioned in M&M line 247 and in Fig 2, Table 1 and Table 2.________________________________________________________________________Comment 2. Line 231, authors can edit the correct injected dose (mean \u00b1 SE) of FDG and F-Choline because in line 231 authors indicated 37 MBq and in the figure legends authors indicated other specific doses.-4We agree to include the mean injected activity of all [18F]FDG and [18F]FCho scans in the M&M. The mean injected activity for all [18F]FDG scans was 37.89 \u00b1 0.35 MBq and for all [18F]FCho scans it was 39.55 \u00b1 0.37 MBq (mean \u00b1 SE). This was added to the manuscript line 263-264. ________________________________________________________________________Comment 3. Line 274, the dose of FCho can be edited in MBq, please?The activity (0.55 mCi) was changed to MBq at line 313.________________________________________________________________________Comment 4. Lines- 289-292, why these lines are under the paragraph \u201cAutoradiography and Evans Blue (EB) staining\u201d, can authors add another title, please?We agree that these lines do not fit under that paragraph. These lines were moved to lines 302-305. ________________________________________________________________________Comment 5. Figure 3, is the same animal? Because the images are different. If not, can authors use the same animal, please?The axial PET images used in Figure 3 were indeed of 3 different rats. We made a new figure including coronal images of an [18F]FDG (early and late) and a [18F]FCho PET of the same rat with a F98 GB tumor. Different thresholds (\u226540-50-60-70 %) are contoured. The figure legend was adapted (line 294-300). _______________________________________________________________________ResultsComment 6. In table 2 there are only the p-values, can also add the value of each parameter (mean \u00b1 SE), please?The mean \u00b1 SE was added to table 2 (page 13-14).________________________________________________________________________Comment 7. Figure 4, why FDG MTV values at d2 are so different between control and treated group whereas the volume measured using MRI is closer? The tumor volume of control animals measured using MRI increased along time whereas MTV (both FDG and Choline) remained stable or slight decrease, what is the hypothesis? Authors should discuss.The following paragraph has been added to the Discussion (line 503-510):In Figure 4 can be observed that tumor volumes measured using contrast-enhanced MRI clearly increase over time in the control group, while metabolic tumor volumes remain more or less stable and also show larger variability. Our hypothesis is that the fast growing tumors, as observed on MRI, are becoming metabolically more heterogeneous tumors. This results in a more heterogeneous tracer uptake within these tumours (e.g. necrotic core vs. viable tumour proliferation and infiltration), which gives rise to higher variations of the measured MTV-values in the control group and that might also explain why the MTV-values are not increasing over time.In addition (not added to the manuscript):For example, the FDG MTV at day 2 is indeed very different between the control and therapy group whereas the difference of the MRI Gd tumor volume is smaller. When taken a closer look to the data, this can be clarified because 2 rats of the DMSO group showed a 12x increase in FDG MTV between pre-therapy and d2, whereas there was only a 2 to 3 fold increase of the MR Gd volume. The 3 other rats of the DMSO group showed a 2 to 3 fold increase of both the MR Gd volume and FDG MTV between pre-therapy and d2. As a result, the SE-values are higher.________________________________________________________________________Comment 8. On day 9, only 2 control animals performed FDG PET, how is it possible that both MTV and MTV+SUVmean values are significantly different between control and treated group (line 347 and 353)?Thank you for this very valuable comment. After re-checking the data and statistical analysis, we observed a mistake in Table 1. On day 9 FDG PET was performed on 4 control animals and not on 2 control animals. We changed this in the table on page 10 and the total scans included was also changed: line 391.________________________________________________________________________Comment 9. In figure 5 there is represented only a control rat, authors can add a longitudinal figure with a representative treated rat so it is possible compared images of control and treated rats, please?Longitudinal FDG and FCho PET/MRI images of treated rats were added to figure 5. The figure legend was adapted. Mean \u00b1 SE injected activity was added of all FDG and FCho PET scans included in the new figure (see line 424-430).________________________________________________________________________Comment 10. Figure 5, what is the color scale for PET ? Can authors also add min and max values on the scale.The images in Figure 5 were created using the PMOD software and the color scale of the images is in kBq/cc (kBq/mL) before extracting data. Only after VOI (MTV) delineation, the uptake values in kBq/cc were extracted in excel to calculate SUV and TBR values. The contrast range of the images selected in Figure 5 was (0-850 kBq/cc) for early FDG, (0-220 kBq/cc) for delayed FDG and (0-350 kBq/cc) for FCho. These were selected manually to obtain an optimal image of the brain and GB tumor uptake. Hence we prefer not to add the different ranges to the color scale.________________________________________________________________________10. Did authors evaluate post mortem staining for ki67, GFAP, choline kinase?These stainings were not performed in this study. We did make a lot of efforts to optimize IHC for staining the choline transporter (CTL1) to correlate with the [18F]FCho PET uptake. However, after mulitple unsuccesfull attempts, the antibody we purchased seemed to only bind human brain tissue and not rat brain tissue .________________________________________________________________________DiscussionEdit discussion on the basis of results (point 6), please.The following paragraph has been added to the Discussion (line 503-510).D. REVIEWER 2Reviewer #2: The authors evaluate the role of FDG-PET and Cho-PET, compared to c.e. MRI, for the early detection of treatment response in murine model of GBM; 5 animals randomizedly received RT plus TMZ, while other 5 no. The treatment effect was evaluated with serial MRI and FDG-PET , and also Cho-PET . The metabolic tumor volume (MTV) was semi-automatically calculatedm and the average tracer uptake within the MTV was converted to a SUV. Using SUVmean x MTV, FDG-PET started to detect treatment's effects at 5 day post-treatment, comparable to c.e. MRI. Moreover, delayed FDG-PET (240 min p.i.) earlier detect such effects (from day 2); on the other hand, no significant differences were found at any time point for both the MTV and (SUVmean x MTV) of Cho-PET. Therefore, the authors concluded that MRI and delayed FDG-PET detect early treatment responses in GB murine model of GBM, whereas these results were not obtained with Cho-PETThe topic is undoubtedly intriguing, but i have some issues:-INTRODUCTION1. The ref 1 is related to 2007 WHO classification; from an epidemiological point of view, it should be better to consider the last CBTRUS report .Reference 1 was changed to the recent publication of Ostrom et al. We included numbers from this work in the introduction, see line 72-74:\u2018In the US, 84,170 new cases of primary brain and other central nervous system tumors are estimated to be diagnosed in 2021. Glioblastoma (GB) has the highest number of cases of all malignant tumors, with 12,970 cases projected in 2021 [1].\u2019________________________________________________________________________2. I suggest also to modify ref. 2 and 3, using a more up-to-date literature reference about glioma management guideline on the diagnosis and treatment of adult astrocytic and oligodendroglial gliomas. Lancet Oncol. 2017 Jun;18(6):e315-e329).We agree that this is an important and more up to date reference, hence we changed previous references 2 and 3 to Weller et al. 2017_______________________________________________________________________3. Moreover, the study by Stupp in 2005 that showed the role of combined RT-CMT was not the ref n\u00b0 5 but the one published in NEJM :987-96. doi: 10.1056/NEJMoa0433309).Reference 5 was changed to this reference of Stupp et al. from NEJM.________________________________________________________________________4. It should be better to update the references related to the clinical role of ChoPET in brain tumors , due to the increasing interest about such technique.We added more recent references related to the clinical role of ChoPET in brain tumors to the manuscript. An extra section was added to the introduction, see line 150-157. The reference to Fraioli et al. was added in the discussion Line 518 and 523-525. We included the following references:- Vetrano IG, Laudicella R, Alongi P. Choline PET/CT and intraoperative management of primary brain tumors. New insights for contemporary neurosurgery. Clin Transl Imaging. 2020;8:401-4. - Alongi, P, Quartuccio, N, Arnone, A, Kokomani A, Allocca M, Nappi G, et al. Brain PET/CT using prostate cancer radiopharmaceutical agents in the evaluation of gliomas. Clin Transl Imaging. 2020;8:433-48. - Fraioli F, Shankar A, Hargrave D, Hyare H, Gaze MN, Groves AM, et al. 18F-fluoroethylcholine (18F-Cho) PET/MRI functional parameters in pediatric astrocytic brain tumors. Clin Nucl Med. 2015;40:e40-5.- Alongi P, Vetrano IG, Fiasconaro E, Alaimo V, Laudicella R, Bellavia M, et al. Choline-PET/CT in the Differential Diagnosis Between Cystic Glioblastoma and Intraparenchymal Hemorrhage. Curr Radiopharm. 2019;12:88-92. - Villena Mart\u00edn M, Pena Pardo FJ, Jim\u00e9nez Arag\u00f3n F, Borras Moreno JM, Garc\u00eda Vicente AM, et al. Metabolic targeting can improve the efficiency of brain tumor biopsies. Semin Oncol. 2020;47:148-54.- Grech-Sollars M, Ordidge KL, Vaqas B, Davies C, Vaja V, Honeyfield L, et al. Imaging and Tissue Biomarkers of Choline Metabolism in Diffuse Adult Glioma: 18F-Fluoromethylcholine PET/CT, Magnetic Resonance Spectroscopy, and Choline Kinase \u03b1. Cancers. 2019;11:1969.______________________________________________________________5. Why the authors selected Cho-PET, instead of [18F]FAZA PET, for example? I think that clarifying the advantages and disadvantages of this choice could increase the informative role of the present work.For many years, the focus of our research group has been the role of various F-18 labeled PET-tracers in neuro-oncology. In comparison with other PET tracers, FDG and non-FDG tracers alike, [18F]FCho has certain advantages of which a very low uptake in normal white and grey matter of the brain is of major interest because it enhances the contrast between tumour and normal brain tissue. Secondly, it is \u2013 at least in Europe - widely available and it is still the tracer of choice in the management of castration resistant prostate cancer for those centers that do not have access to PSMA PET.Although [18F]FCho PET has been studied for glioma imaging before by other groups, the number of studies is still limited compared to the number of publications on amino acid and hypoxia PET biomarkers.Since hypoxia is associated with tumor aggressiveness, radiation resistance and poor prognosis, it is possible that changes in [18F]FAZA or [18F]FMISO uptake between pre- and post-treatment can be used to monitor treatment response. However, only few studies have been performed. One downside is that the degree of hypoxia can theoretically fluctuate, influenced by therapy and the presence of acute versus chronic hypoxia which can influence the reproducibility of hypoxia PET . In 2013, [18F]FAZA and [18F]FDG uptake in the F98 GB rat model was investigated by Belloli et al., however, not specifically for therapy response assessment. It is also noteworthy that there is no current consensus on which tracer is the best for hypoxia imaging. [18F]FAZA has advantages compared to [18F]FMISO due to better pharmacokinetic properties but [18F]FMISO can cross the blood\u2013brain barrier because of its lipophilic nature while [18F]FAZA and [18F]DiFA can not . Another downside of [18F]FAZA is that imaging is optimal 2-3 hours post-injection (with [18F]FMISO up to 4h), making it less convenient to work with. However, we studied [18F]FET and [18F]FAZA PET in another in vivo study by our group with a focus on the feasibility of PET-guided irradiation . Because hypoxia is directly related to radiation resistance, [18F]FAZA PET could be used to guide an additional boost on hypoxic tumor regions as a strategy to overcome radioresistance and increase therapy effectiveness. [18F]FET has already been studied in depth for imaging glioma, however, tumor-to-normal brain contrast is less optimal compared to [18F]FCho.The underlined parts have been included in the introduction (line 142-144). - Verhoeven J, Bolcaen J, De Meulenaere V, Kersemans K, Descamps B, Donche S, et al. Technical feasibility of [18F]FET and [18F]FAZA PET guided radiotherapy in a F98 glioblastoma rat model. Radiat Oncol. 2019;14(1):89.- Mapelli P, Zerbetto F, Incerti E, Conte GM, Bettinardi V, Fallanca F, et al. 18F-FAZA PET/CT hypoxia imaging of high-grade glioma before and after radiotherapy. Clin Nucl Med 2017;42:e525-26.- Belloli S, Brioschi A, Politi LS, Ronchetti F, Calderoni S, Raccagni I,et al. Characterization of biological features of a rat F98 GBM model: a PET-MRI study with [18F]FAZA and [18F]FDG. Nucl Med Biol. 2013;40:831-40.- Hirata K, Yamaguchi S, Shiga T, Kuge Y, Tamaki N. The Roles of Hypoxia Imaging Using 18F-Fluoromisonidazole Positron Emission Tomography in Glioma Treatment. J Clin Med. 2019;8:1088. - M\u00f6nnich D, Troost EG, Kaanders JH, Oyen WJ, Alber M, Thorwarth D. Modelling and simulation of the influence of acute and chronic hypoxia on [18F]fluoromisonidazole PET imaging. Phys Med Biol. 2012;57:1675-84.________________________________________________________________________6. How where the simple size selected?statistical analysis were performed to selected a population of 10 animals?Using statistical power analysis based on ANOVA using 2 group, 5 repeated measurements, an alpha-value of 0.05, a power of 0.80 and an effect size of 0.4, a total sample size of 10 animals was calculated.________________________________________________________________________7. Finally, the author disclosure a financial support by Lux Luka Foundation, but they must clearly state, according to Journal guidelines, who exactly received fundings, and the role of the sponsor in the study design and analysis.Lux Luka Foundation did indeed support this study financially. Funds were received by Prof. I Goethals and Prof. T Boterberg. The sponsor did not play a role in study design and analysis. The funding source was not included in the Acknowledgements section in the manuscript, according to the Journal\u2019s guidelines. However, this information was added in the cover letter.AttachmentResponse to Reviewers.docxSubmitted filename: Click here for additional data file. 22 Feb 2021Assessment of the effect of therapy in a rat model of glioblastoma using [18F]FDG and [18F]FCho PET compared to contrast-enhanced MRI.PONE-D-20-36019R1Dear Dr. Bolcaen,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Pierpaolo AlongiAcademic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments: 23 Feb 2021PONE-D-20-36019R1 18F]FDG and [18F]FCho PET compared to contrast-enhanced MRI. Assessment of the effect of therapy in a rat model of glioblastoma using [Dear Dr. Bolcaen:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Pierpaolo Alongi Academic EditorPLOS ONE"} +{"text": "There are errors in the Funding Statement. The publisher apologizes for these errors. The correct Funding statement is: This work was supported by Fondazione Celiachia Onlus, Italy, Grant n\u00b0 046_FC_2013."} +{"text": "A step-by-step protocol of how to implement Bayesian multilevel model analysis with social data and how to interpret the result is presented. The article used a dataset regarding religious teachings and behaviors of lying and violence as an example. An analysis is performed using R statistical software and a bayesvl R package, which offers a network-structured model construction and visualization power to diagnose and estimate results. Specifications tableIn social sciences, the persistence of 'stargazing', p-hacking, and HARKing issues has currently led to a severe reproducibility crisis in which 70% of researchers have failed to reproduce the experiments of other scientists The analysis was done using the bayesvl R package (version 0.8.5) in the R statistical software (version 3.6.2) R> data(Legends345)R> data1 <- Legends345R> head(data1)Hereafter, we use one of our latest research studies as an example for performing Bayesian multilevel analysis with social data \u2022\"Lie\": whether the main character lies\u2022\"Viol\": whether the main character employs violence\u2022\"VB\": whether the main characters' behaviors express the value of Buddhism\u2022\"VC\": whether the main characters' behaviors reflect the value of Confucianism\u2022\"VT\": whether the main characters' behaviors express the value of Taoism\u2022\"Int1\": whether there are interventions from the supernatural world\u2022\"Int2\": whether there are interventions from the human world\u2022\"Out\": whether the outcome of a story is favorable for its main charactersEven though there are 25 binary variables, of which only eight variables are employed in this article:First, we establish three different directed acyclic graphs (DAGs), or so-called \"relationship trees,\" from simple to more complex ones, based on the dataset mentioned above.The first and the most straightforward \"relationship tree\" exemplified examines the determinants of the behaviors of lying and violence on the outcome of the main character see .Fig. 1ThR> library(bayesvl)R> model1 <- bayesvlR> model1 <- bvl_addNodeR> model1 <- bvl_addNodeR> model1 <- bvl_addNodeTo construct the \"relationship tree\" in Because the statistical distribution of all employed variables is binomial, we set \"binom\" in the function. Besides binomial distribution, the package also provides various types of statistical distribution for the types of data, namely: normal distribution \u2013 \"norm\", categorical distribution \u2013 \"cat\", Bernoulli distribution \u2013 \"bern\", Student's t-distribution \u2013 \"student\", Poisson distribution \u2013 \"pois\", and so on.R> model1 <- bvl_addArcR> model1 <- bvl_addArcAfter loading all the variables into the \"relationship tree\", the next step is to grant the regression type to the connection between the independent variables \"Lie\" and \"Viol\" and the dependent variable \"O\" by employing the function bvl_addArc. The model can be set as the fixed effect type by adding a \"slope\" into the command:R> bvl_stanPriors(model1)a_O ~ normalb_Viol_O ~ normalb_Lie_O ~ normalIn Bayesian inference, the posterior probability is estimated from a prior probability and a \"likelihood function\" derived from a statistical model for the observed data. Therefore, setting prior distribution is critical before fitting the model. The prior distribution can be determined based on previous empirical findings, researcher's past experience and personal intuition, or expert opinion R> bvl_bnPlot(model1)Since the prior distribution was not set in bvl_addArc, the package automatically set prior distribution of b_Viol_O as default distribution which is normal. Eventually, the function bvl_bnPlot can help produce the graphical network of the constructed model see .R> bvl_bR> summary(model1)Model Info:nodes: 3arcs: 2scores: NAO\u00a0+\u00a0b_Lie_O * Lie\u00a0+\u00a0b_Viol_O * Violformula: O ~ a_Estimates:model is not estimated.To check the structure and mathematical form of the model, one can use the function summary:R> model2 <- bayesvlR> model2 <- bvl_addNodeR> model2 <- bvl_addNodeR> model2 <- bvl_addNodeR> model2 <- bvl_addNodeR> model2 <- bvl_addNodeR> model2 <- bvl_addNodeR> model2 <- bvl_addNodeR> model2 <- bvl_addNodeThe second \"relationship tree\" is designed to estimate the impact of violent behavior and its interaction effect with religious values on the outcome of the main character see . SimilarThe variables \"B_and_Viol\", \"C_and_Viol\", and \"T_and_Viol\" are the interaction variables between the act of violence and the value of Buddhism, Confucianism, and Taoism, respectively. The independent interaction variables, represented by the green nodes, can be subsequently created from two normal independent variables, represented by the blue nodes. Unlike the normal variable \"Viol\" defined as \"binom\", or binomial, the interaction variables are defined as \"trans\", or interaction/transformed. It is noteworthy that the \"trans\" variable does not have a particular distribution but depends on the interaction of two normal variables through applying \" * \" or \"\u00a0+\u00a0\" operator. To standardize, we call normal independent variables as observation data and interaction variables as transformed data from now on.R> model2 <- bvl_addArcR> model2 <- bvl_addArcThe dash-line arrow demonstrates the relation between the transformed data and the observation data see . The valR> model2 <- bvl_addArcR> model2 <- bvl_addArcR> model2 <- bvl_addArcR> model2 <- bvl_addArcThe model can be set as the fixed effect type by adding \"slope\" into the command:a_O ~ normalb_Viol_O ~ normalb_B_and_Viol_O ~ normalb_C_and_Viol_O ~ normalb_T_and_Viol_O ~ normalThe prior distributions of model 2 are also set as default:R> bvl_bnPlot(model2)R> summary(model2)Model Info:nodes: 8arcs: 9scores: NAO\u00a0+\u00a0b_B_and_Viol_O * VB*Viol\u00a0+\u00a0b_C_and_Viol_O * VC*Viol\u00a0+\u00a0b_T_and_Viol_O * Viol*VTformula: O ~ a_Estimates:model is not estimated.Eventually, the function bvl_bnPlot and summary can help produce the graphical network see and the One can create a much more complex model of multilevel regression analysis, while only following a similar procedure with two models mentioned above and employing some additional functions. The primary purpose of the third exemplary \"relationship tree\" is to explore the impacts of lying and violence behaviors, their interaction with religious values, and intervention from the supernatural or human world on the outcome of the main character see .Fig. 5ThInt1_or_Int2\u00a0=\u00a0(Int1\u00a0+\u00a0Int2 > 0 ? 1: 0)To construct the \"relationship tree\" illustrated in R> model3 <- bvl_addNode\", out_type\u00a0=\u00a0\"int\", lower\u00a0=\u00a00, test\u00a0=\u00a0c) fun\u00a0=\u00a0\"({0}> 0 ? 1: 0)\" is equivalent to the conditional algorithm shown above, while out_type stands for the property of the output, such as \"int\" (integer) and \"real\" . The parameter test\u00a0=\u00a0c helps to insert the code computing \u201cfixed predicted outcome\u201d when Int1_or_Int2\u00a0=\u00a00 and Int1_or_Int2\u00a0=\u00a01. The value of transformed data \"Int1_or_Int2\" is defined based on the values of observational data \"Int1\" and \"Int2\" through the mathematical operator \"\u00a0+\u00a0\":R> model3 <- bvl_addArcR> model3 <- bvl_addArcTherefore, the command to create the node of \"Int1_or_Int2\" is augmented as follows:R> model3 <- bvl_addArcR> model3 <- bvl_addArcR> model3 <- bvl_addArc\", \"sigma_ ~ normal\"))+ priors\u00a0=\u00a0For completing the \"relationship tree\" construction, the last step is to connect two observational data \"Lie\" and \"Viol\" as well as other transformed data to the outcome \"O\". Like previous commands, the function bvl_addArc is used, but \"trans\" is replaced by \"slope\" (fixed effect) or \"varint\" (varying intercept), to convert the relationships between \"O\" and other nodes into regression relationships. There are four fundamental types of statistical model integrated in the bayesvl package: fixed-effect model (\"slope\"), varying-intercept model (\"varint\"), varying-slope model (\"varslope\"), and mixed-effect model (\"varpars\").c\", \"sigma_ ~ normal\") into the function bvl_addArc. Similarly, this method can be applied to change the prior distribution of other relationships by using the prefix a0_, b_, or sigma_, depending on the relationship type. Besides normal distribution, other kinds of distribution can also be implemented for setting up prior distribution by replacing \"normal\" by the name of the designated distribution . The prior distribution of each path can be checked by typing:R> bvl_stanPriors(model3)b_B_and_Viol_O ~ normalb_C_and_Viol_O ~ normalb_T_and_Viol_O ~ normalb_Viol_O ~ normalb_B_and_Lie_O ~ normalb_C_and_Lie_O ~ normalb_T_and_Lie_O ~ normalb_Lie_O ~ normala0_Int1_or_Int2 ~ normalsigma_Int1_or_Int2 ~ normalu_Int1_or_Int2 ~ normalThe first and second commands are to create the regression relationships of the outcome with observational and transformed data, respectively, employing a fixed-effect model, while the third command is to create the regression relationship between the outcome and transformed data employing a varying-intercept model. In model 3, the prior distribution of all the paths from observational and transformed nodes to the outcome node is set as default, except for the path from \"Int1_or_Int2\" to \"O\". The prior distributions of the relationship between \"Int1_or_Int2\" and \"O\" is set by adding the code priors\u00a0=\u00a0R> bvl_bnPlot(model3)Eventually, the function bvl_bnPlot can help produce the graphical network of the constructed model see .R> bvl_bR> bvl_formulaB_and_Lie ~ VB*LieR> bvl_formulaInt1_or_Int2 ~ (Int1+Int2 > 0 ? 1: 0)One can also check the mathematical construct of each transformed data in the \"relationship tree\" above by using the function bvl_formula, like the following examples:R> summary(model3)Model Info:nodes: 15arcs: 23scores: NAb_C_and_Viol_O * VC*Viol\u00a0+\u00a0b_T_and_Viol_O * VT*Viol\u00a0+\u00a0b_Viol_O * Viol\u00a0+\u00a0b_B_and_Lie_O * VB*Lie\u00a0+\u00a0b_C_and_Lie_O * VC*Lie\u00a0+\u00a0b_T_and_Lie_O * VT*Lie\u00a0+\u00a0b_Lie_O * Lie\u00a0+\u00a0a_Int1_or_Int2[(Int1+Int2 > 0 ? 1: 0)]formula: O ~ b_B_and_Viol_O * VB*Viol\u00a0+\u00a0To check the structure and mathematical form of the model, one can use the function summary:Estimates: model is not estimated!R> model_string <- bvl_model2Stan(model3)R> cat(model_string)Before fitting the model using MCMC simulation, one needs to generate the Stan code in R. Because the bayesvl package provides an automatic generation of Stan code, one can use the following commands:R> model3 <- bvl_modelFitR> summary(model3)Model Info:nodes: 15arcs: 23scores: NAb_C_and_Viol_O * VC*Viol\u00a0+\u00a0b_T_and_Viol_O *VT*Violformula: O ~ b_B_and_Viol_O * VB*Viol\u00a0+\u00a0b_Viol_O * Viol\u00a0+\u00a0b_B_and_Lie_O * VB*Lie\u00a0+\u00a0b_C_and_Lie_O * VC*Lie\u00a0+\u00a0b_T_and_Lie_O * VT*Lie+ b_Lie_O * Lie\u00a0+\u00a0a_Int1_or_Int2[(Int1+Int2 > 0 ? 1: 0)]+ Estimates:Inference for Stan model: d4bbc50738c6da1b2c8e7cfedb604d80.4 chains, each with iter=5000; warmup=2000; thin=1;post-warmup draws per chain=3000, total post-warmup draws=12,000.The model created from the \"relationship tree\" can be fitted with MCMC simulation using the function bvl_modelFit. The structure of the function bvl_modelFit is partly dissimilar with other currently existent Bayesian analysis packages because it does not require users to construct conventional mathematical relationships among variables as well as set up the prior distribution for each relationship. One only need to input the name of constructed \"relationship tree\", the dataset, and mandatory set-up for MCMC simulation. As the bayesvl package was coded utilizing the No-U-Turn Sampler (NUTS) sampler \u202fThe model is fitted using four chains, each with 5000 iterations of which the first 2000 are for warmup, resulting in a total of 12,000 post-warmup posterior samples. In general, the model's simulated results show a good convergence based on two standard diagnostics of MCMC simulation, n_eff, and Rhat. The n_eff represents the effective sample size, which is the number of iterations needed for effective independent samples W is the within-sequence variance.Where One can aesthetically visualize the convergence diagnostics, posterior distribution, and estimated results. The function bvl_plotTrace can generate the trace plots of the constructed model.R> bvl_plotTrace(model3)R> bvl_plotAcfstx is the sampled value of x at iteration t, T represents the total number of sampled values, and The mathematical formula for the autocorrelation parameter for lag\u00a0=\u00a0L is displayed below:R> bvl_plotGelmans (model3)Measuring how much variance there is between chains relative to how much variance there is within chains is another idea to check the convergence. If the average difference between chains is similar to average difference within chains (when Rhat\u00a0=\u00a01.0), the chains are well convergent. Nevertheless, the relative value might increase (when Rhat > 1.0) and indicates the less convergent tendency between chains, if there appears at least on orphaned or stuck chain R> bvl_plotParams Besides the mean and standard deviation of the posterior distribution summarized in the model fit above, one can visually present the estimated posterior distribution of every variable coefficient through histograms. The visualization can be made using the function bvl_plotParams. We visualize the estimated posterior distribution of every variable in the constructed model in four rows and three columns with the Highest Posterior Distribution Intervals (HPDI) at 89% see . The defR> bvl_plotIntervals)R> bvl_plotDensity)There are also other built-in alternatives to visually present the estimated results after simulation, such as bvl_plotIntervals and bvl_plotDensity. The bvl_plotIntervals function helps visualize the coefficients and their interval, while the bvl_plotDensity function helps plot the posterior probability density of coefficients. The results can be plotted \"all-in-one\" or selectively by both functions. The following commands are to visualize the interval see and the R> bvl_plotDensity2dThe comparison between two different coefficients' distribution of posteriors can be plotted by the following code see :R> bvl_pbayesvl R package for social data analysis also provides the opportunity to construct a \"relationship tree\" among variables intuitively and graphically visualize simulated posterior, especially in the age of Big Data Recently, the reproducibility crisis and the problems of 'stargazing', p-hacking, or HARKing in statistical analysis have required the scientific community to be more rigorous in conducting research and find solutions for the persistent statistical issues. Thus, the method paper proposes Bayesian analysis as a substitution for the conventional frequentist approach. Bayesian statistics have the advantages of treating all unknown quantities probabilistically and incorporating prior knowledge or belief of scientists into the model as an alternative approach for frequentist analysis in social sciences. The usage of the The authors declare that they have no known competing for financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "A second monoclonal antibody\u2014ATA 842\u2014by Atara Biotherapeutics increased muscle mass and strength, as well as insulin sensitivity in old mice over a period of 4\u00a0weekshttps://www.pfizer.com/news/press\u2010release/press\u2010release\u2010detail/pfizer_terminates_domagrozumab_pf_06252616_clinical_studies_for_the_treatment_of_duchenne_muscular_dystrophy). However, in the mouse DMD mdx model, the mouse analogue of domagrozumab\u2014mRK35\u2014significantly increased body weight, muscle weights, grip strength, and ex vivo force production in the extensor digitorum longus (EDL) muscle.Myostatin\u2010targeting antibodies and soluble ActRIIB to block atrophic signalling in skeletal muscle have been studied extensively in animal models and human trials with varying success. In a progeric mouse model, the soluble ActRIIB\u2010Fc improved muscle mass and delayed morbidity.Journal of Cachexia, Sarcopenia and Muscle, Rooks et al.In this issue of the In general, there seems to be no direct relationship between muscle mass and strength,The authors have no conflict of interest regarding the subject of this editorial."} +{"text": "In this article, a Siamese network is applied to the drill wear classification problem. For furniture companies, one of the main problems that occurs during the production process is finding the exact moment when the drill should be replaced. When the drill is not sharp enough, it can result in a poor quality product and therefore generate some financial loss for the company. In various approaches to this problem, usually, three classes are considered: green for a drill that is sharp, red for the opposite, and yellow for a tool that is suspected of being worn out, requiring additional evaluation by a human expert. In the above problem, it is especially important that the green and the red classes not be mistaken, since such errors have the highest probability of generating financial loss for the manufacturer. Most of the solutions analysing this problem are too complex, requiring specialized equipment, high financial investment, or both, without guaranteeing that the obtained results will be satisfactory. In the approach presented in this paper, images of drilled holes are used as the training data for the Siamese network. The presented solution is much simpler in terms of the data collection methodology, does not require a large financial investment for the initial equipment, and can accurately qualify drill wear based on the chosen input. It also takes into consideration additional manufacturer requirements, like no green-red misclassifications, that are usually omitted in existing solutions. Drill wear state recognition belongs to the larger group of problems called tool condition monitoring, which deals with the evaluation of different machine parts\u2019 condition, as well as determining how long they can be used in the production process. Depending on the properties of each tool, as well as the requirements of the final product, different signals can be recorded and later tested using various methods, to obtain the final evaluation. Quite a few procedures in this direction also deal with the main topic of this paper, which is drill wear state recognition. From the manufacturer\u2019s point of view, when the drill starts to become dull, it should be replaced as quickly as possible. Extending the use time of such a tool can result in poor product quality and therefore generate financial loss for the company. Manual evaluation of the drill state is possible and was initially done during the production process, but this is very time consuming, resulting in the prolongation of the entire procedure. A faster and more automated approach was needed, which resulted in extensive research on this subject. For example, one of the existing solutions focuses on measuring tool wear using two approaches: conventional methods and estimation with a customized software combining artificial neural networks and flank wear image recognition . In thisExisting solutions vary greatly in their approach, especially the data collection methodology. As is often the case, especially when it comes to the usage of specialized equipment, the most visible advancements have been made in medicine. For example, in , the autThe solution presented in this paper takes into account different approaches to deep learning in general single-lens reflex digital camera with a 35.9 \u00d7 24.0 mm CMOS image sensor. The entire process was performed in cooperation with the Institute of Wood Sciences and Furniture at Warsaw University of Life Sciences, Poland. For test purposes, a standard CNC vertical machine centre was used. Drilling was performed on a standard, melamine-faced chipboard , which is typically used in the furniture industry. The dimensions of the test piece were 300 \u00d7 35 \u00d7 18 mm. A regular, Faba WP-01 double-blade drill for through drilling equipped with a tungsten carbide tip was used. The drill\u2019s overall length was 70 mm, with a shank length equal to 25 mm, a flute length of 40 mm, a shank diameter of 10 mm, and a 12 mm drill diameter. The clearance angle on the drill face was \u221215.45 degrees. The rake angle was equal to 0 degrees, and the helix angle for the tool used was 15 degrees. The images of the equipment used are presented in The data set used in the current experiments was similar to that in the previous works ,15,16,17Usually, three classes are used in drill wear state recognition: red, green, and yellow. In this case, the obtained samples were divided and labelled manually, using the drill wear rate. For the manual evaluation of the drill state, external corner wear (W(mm)) was adopted as the main condition indicator and was periodically monitored using a standard workshop microscope . Based on the obtained values, three classes for drill wear were selected: green for W < 0.2 mm, yellow for W in the range between 0.2 and 0.35 mm, and red for W > 0.35 mm. Those classes were also used for the drill wear definition in the current, automated approach. In the presented case, the yellow class was used mainly as a buffer for the manufacturer. In the case of the furniture industry, depending on the type of elements produced, different hole qualities can be acceptable. In this case, depending on the manufacturer\u2019s preferences, the yellow class can later be assigned either to the green or red classes in the final production, hence expanding the overall method\u2019s customizability. Example images representing different drill wear classes are presented in The original data set contained significantly more examples for the green class than the remaining two (yellow and red). Since CNN was used as a base network for the presented solution, it was not desirable for the data set to be imbalanced in such a way . To correct this, data augmentation methodologies were used, to ensure an even representation of each class . With the data balanced, the training process should not favour any of the classes. Initial operations performed on the data samples also included resizing each of the images on the fly to a size equal to 64 \u00d7 64 \u00d7 3 pixels. The training input was also normalized by dividing each value by 255, to ensure that they were in the range. Since 5-fold cross-validation was used, the input data were split between the 5 folds, and each of them was additionally divided into two subsets, the first for training and the second one for validation. The structure of each fold is shown in Siamese networks are novel algorithms used in image recognition. The first approaches with this type of procedure focused specifically on face recognition. One of the first applications was a verification system for identifying workers in a building. When it comes to this problem in general, there are two main areas to consider: verification of whether a person in the current image is one stored in a database under a specified ID and recognizing if the person from the input image is one of those stored in the original database. Especially in systems with large amounts of users , accuracy is a very important factor. While having a 99% recognition rate might be acceptable for other applications, it is not the case here. Even if such a system has a 1% error rate, with 100 people in the database, the possibility of not recognizing the current person correctly is still quite high. Additionally, for most cases with face recognition, the algorithm needs to be able to recognize the person while using a single image (the one-shot learning problem). Using CNN for such an approach is not good enough, since firstly, the amount of training data is minimal, and secondly, each time a new person is added to the system, the network would require retraining. This is where the approach used in Siamese networks has the advantage.--f. In that case, if the difference between two images is greater than the set threshold, the person would be classified as different, and as the same in case of this value being below that threshold. In general, it can be described as:To be able to calculate this distance between the input images, both of them are encoded using identical CNN networks. They are then represented as feature vectors instead of the usual classification. In general, what is done at this point is that instead of using the final classifier from the CNN (or other network), the entire process stops at one of the embedding layers . By using this approach, two different, comparable encodings of the images can be obtained, and the distance between them can be measured . The idea of first launching two identical CNN networks to produce feature vectors and secondly using those vectors to calculate the difference measure between images is the basis of the Siamese network architecture .The Siamese network is a good example of a solution that can distinguish between instances of different classes and specifically determine if the image that is provided as the input is the same as the one representing the original class. In terms of face recognition, it would determine if the same person is in the picture. In the case of the solution presented here, with some additional modifications, it should point to which drill wear class the provided example belongs.-\u03b1 is a margin that is enforced between positive and negative pairs-\u03c4 is the set of all possible triplets in the image set and has cardinality N.To train networks used for such recognition, a few steps are required, as well as a definition of the function used to distinguish between positive and negative examples of each class. The presented solution needs to be able to do two things: recognize the same class in two different images and notice that the presented class is different than the one to which it is compared. To achieve that, the following images are required: the first one, containing the element representing a single class , the positive image example, containing the same class , and the negative image, with a different class . When the distance between those images is calculated (from the obtained image representation), the ideal outcome would produce results for which the distance between the images containing the element with the same class is lower than in the case of the images containing elements representing different classes. What is more important for this approach to work accurately is that this distance needs to be significant, reaching at least some predefined margin . The above relation can be described using the following equations:At this point, the loss that needs to be minimized has theAlgorithm 1: Siamese network training.Step 1: Generating the training setfor each input sample do\u2003Using knowledge about the data set to find a set of samples such that each sample \u2003similar to \u2003Pair sample \u2003are similar, end forCombine all the pairs to form the labelled training set.Step 2: Trainingwhile Convergence not reached dofor each pair do\u2003\u2003\u2003if \u2003\u2003if end for\u2003end whileThe margin parameter (\u03b1) is a hyperparameter that needs to be manually adjusted to each classification problem. In the case of the topic described in this paper, one type of positive pair (with label y = 1) and two types of negative pairs were used in that process . Since Siamese networks were originally for the face recognition problem, using a similar approach for the drill wear evaluation considered in this work, some adjustments were required. During the training process, first, the set of examples was created, where each example would contain two samples: anchor and either a positive (P) or a negative (N) example. In this case, instead of a single image that can either be the same or different , a total of three classes were considered. First would be the positive example, with the same class as the anchor. In this case, two negative examples can be generated, containing either of the remaining classes.The approach first divides the entire data set into positive and negative pairs. In the case of negative examples, to increase the diversity of the training set, the class is randomly chosen from the two that are different than the one to which the anchor belongs. Each of the initial images will generate two pairs used for training: one positive, where the anchor is paired with the image of the same class, and one negative, in which the anchor will be paired with an example from a different class. To calculate the distance between the images in consecutive samples, the contrastive loss function is used (see ).Algorithm 2:\u00a0Network training algorithm used for the drill wear recognition\u00a0problem.Create positive and negative pairs:for each of initial D = 3 classes dofor all images in each class do\u2003\u2003\u2003A = current image with index = i\u2003\u2003P = next image from the same class with index = i + 1\u2003\u2003PairPositive = with label = 1\u2003\u2003Randomly choose one of the remaining classes (different than the current one)\u2003\u2003Choose negative image N with index = i\u2003\u2003PairNegative = with label = 0end for\u2003end forCalculate the contrastive loss function:for each created pair do\u2003Contrastive loss = end forReturn classificationAs a base network for the learning process, CNN is used, with three convolutional layers. The detailed structure of the model prepared for the problem chosen as a main topic of this paper is outlined in Listing 1Model: \u201cCNN\u201d_________________________________________________________________Layer (type) Output Shape Param #=================================================================conv2d_1 (Conv2D) 1792_________________________________________________________________activation_1 (Activation) 0_________________________________________________________________max_pooling2d_1 0_________________________________________________________________dropout_1 (Dropout) 0_________________________________________________________________conv2d_2 (Conv2D) 36,928_________________________________________________________________activation_2 (Activation) 0_________________________________________________________________max_pooling2d_2 0_________________________________________________________________dropout_2 (Dropout) 0_________________________________________________________________conv2d_3 (Conv2D) 18,464_________________________________________________________________activation_3 (Activation) 0_________________________________________________________________max_pooling2d_3 0_________________________________________________________________dropout_3 (Dropout) 0_________________________________________________________________flatten_1 (Flatten) 0_________________________________________________________________dense_1 (Dense) 147,584_________________________________________________________________dropout_4 (Dropout) 0_________________________________________________________________dense_2 (Dense) 6450=================================================================Total params: 211,218Trainable params: 211,218Non trainable params: 0_________________________________________________________________During previous experiments ,15,16,17In the current approach, the Siamese network, adjusted to the presented classification problem, was used. To evaluate the obtained results, additional algorithms were implemented, choosing procedures that were successful in previous experiments, but similarly adjusting them to include the new requirement of minimizing the number of misclassifications between the red and green classes.Algorithm 3:\u00a0Accuracy function used for algorithm\u00a0evaluation.\u2003Require: \u2003\u2003Compute classification accuracy with a fixed threshold on image distances\u2003\u2003Return K.mean))\u2003\u2003model.compileDuring the experiments, five-fold cross-validation was used , an early stopping mechanism was used. The patience parameter was used, set at five epochs, meaning that if during that time, there was no improvement to the solution accuracy, the training process was stopped, and the best obtained model was saved. Since the data used during the experiments were stored in a time series manner , it was additionally incorporated in the overall approach, to try and improve the algorithm\u2019s accuracy. Instead of a single image, sets of consecutive images of different lengths were used for the training process. With such an approach, the algorithm should be able to learn how hole edges change, while the drill is steadily dulling. The window parameter was incorporated into the solution, testing sequences of 5, 10, 15, and 20 images, with no window approach used as the baseline . The first solution, which did not use any window, obtained an overall accuracy of 67% , as well as the classification methodology . Since in previous experiments, some of the algorithms were tested and performed well for the overall accuracy parameter, the same algorithms were used for the current comparison. The final set contained the VGG19 pretrained network, 2 ensemble algorithms, the first using 5 and the second using 10 random VGG16 networks, the CNN model trained from scratch, and 5 random initializations of this model. All of those algorithms were trained using the window methodology, starting with no window and finishing at a window size of 20. The accuracy results obtained are presented in Next, the Siamese network approach using different windows was tested, and it achieved the best accuracy results for a window size of 20 (82%). Although for smaller windows, it showed poorer results than some algorithms, it quickly outperformed them for larger windows. While the no window approach produced to many critical errors . Additionally, it is able to accurately distinguish between the red and green classes, with a total number of 37 misclassifications between them (22 red-green and 15 green-red errors). To the best of authors\u2019 knowledge, this is the first application of this methodology to the wood industry. The presented approach is highly adjustable, since in the case of changes in the samples , transfer learning can be used to retrain the previous model for a new application, without the need to start from scratch.To summarize, the presented solution achieved an overall accuracy and misclassification rate that fit into the initial acceptable ranges. With the simplified data collection methodology and low initial costs, it is readily applicable to the actual work environment, with very positive, initial feedback from the manufacturer. Furthermore, the Siamese network approach seems very promising, and while further research is still required, it is believed that additional improvement of both the accuracy and critical error rate is still possible."} +{"text": "Among metrological parameters, average temperature had the strongest correlation (rs = \u22120.675) with the cases. About 82% of Bangladeshi isolates had D614G at spike protein. Both temperature and UV index had strong effects on the frequency of mutations. Among host factors, coinfection is highly associated with frequency of different mutations. This study will give a complete picture of the effects of metrological parameters on COVID-19 cases, fatalities and mutation frequency that will help the authorities to take proper decisions.Coronavirus disease-2019 (COVID-19) has caused the recent pandemic worldwide. Research studies are focused on various factors affecting the pandemic to find effective vaccine or therapeutics against COVID-19. Environmental factors are the important regulators of COVID-19 pandemic. This study aims to determine the impact of weather on the COVID-19 cases, fatalities and frequency of mutations in Bangladesh. The impacts were determined on 1, 7 and 14 days of the case. The study was conducted based on Spearman's correlation coefficients. The highest correlation was found between population density and cases ( Coronaviridae) has triggered the coronavirus 2019 (COVID-19) pandemic worldwide [Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genome of ~30\u00a0000 bases , 2. The The main aim of this study is to analyse the correlation between metrological factors and frequency of mutations in SARS-CoV-2. The second objective of this study is to determine the relationship between host factors and SARS-CoV-2 mutation frequency. The third objective of this study is to investigate the correlation between environmental factors and COVID-19 pandemic in Bangladesh. This study will provide a better insight on the effects of environmental factors on COVID-19 pandemic in Bangladesh.2, Dhaka is the most populous capital in the world. The study period was from 07 March 2020 to 14 August 2020. On 07 March 2020, COVID-19 patients were detected for the first time in Bangladesh and considered as day 1 for the study.This study focused on the correlation of COVID-19 with metrological parameters in eight cities in Bangladesh. This study included Dhaka (23.71\u00b0N to 90.41\u00b0E), Chattogram (22\u00b020\u203206\u2033N to 91\u00b049\u203257\u2033E), Bogura (24\u00b051\u2032N to 89\u00b022\u2032E), Khulna (22\u00b049\u2032N to 89\u00b033\u2032E), Sylhet (24\u00b054\u2032N to 91\u00b052\u2032E) and Mymensingh (24\u00b045\u203214\u2033N to 90\u00b024\u203211\u2033E), Barishal (22\u00b048\u20320\u2033N to 90\u00b030\u20320\u2033E) and Rangpur (25\u00b044\u2032N to 89\u00b015\u2032E). With a population density of 46\u00a0997\u00a0person/kmhttps://covid19bd.idare.io/) and Institute of Epidemiology, Disease Control and Research (https://www.iedcr.gov.bd/website/) in Bangladesh, and cross-confirmed by analysing the data from official websites of WHO (www.who.int), Bing (www.bing.com/covid), Worldometers (www.worldometers.info/coronavirus/) and Johns Hopkins University (https://coronavirus.jhu.edu/). Environmental data including minimum temperature (\u2070C), average temperature (\u00b0C), maximum temperature (\u00b0C), UV index, wind speed (km/h), rain fall (mm), relative humidity (%) were collected from different databases including official website of Bangladesh Meteorological Department (http://live4.bmd.gov.bd/satelite/v/sat_infrared/), meteoblue (www.meteoblue.com), AccuWeather (www.accuweather.com) and WeatherOnline (www.weatheronline.co.uk) during this study. The whole genome of SARS-CoV-2 isolated from Bangladesh and reference genome sequences were collected from the official website of GISAID (https://www.gisaid.org/). Accession number of sequences are: EPI_ISL_437912, EPI_ISL_445213, EPI_ISL_445214, EPI_ISL_445215, EPI_ISL_445216, EPI_ISL_445217, EPI_ISL_445244, EPI_ISL_447590, EPI_ISL_447897, EPI_ISL_447899, EPI_ISL_447904, EPI_ISL_450339, EPI_ISL_450340, EPI_ISL_450340, EPI_ISL_450341, EPI_ISL_450342, EPI_ISL_450343, EPI_ISL_450344, EPI_ISL_450345, EPI_ISL_450839, EPI_ISL_450840, EPI_ISL_450841, EPI_ISL_450842, EPI_ISL_450843, EPI_ISL_455420, EPI_ISL_455458, EPI_ISL_455459, EPI_ISL_458133, EPI_ISL_462090, EPI_ISL_462091, EPI_ISL_462092, EPI_ISL_462093, EPI_ISL_462094, EPI_ISL_462095, EPI_ISL_462096, EPI_ISL_462097, EPI_ISL_462098, EPI_ISL_464159, EPI_ISL_464160, EPI_ISL_464161, EPI_ISL_464162, EPI_ISL_464163, EPI_ISL_464164, EPI_ISL_466626, EPI_ISL_466627, EPI_ISL_466628, EPI_ISL_466629, EPI_ISL_466630, EPI_ISL_466636, EPI_ISL_466637, EPI_ISL_466638, EPI_ISL_466639, EPI_ISL_466644, EPI_ISL_466645, EPI_ISL_466649, EPI_ISL_466650, EPI_ISL_466686, EPI_ISL_466687, EPI_ISL_466688, EPI_ISL_466689, EPI_ISL_466690, EPI_ISL_466691, EPI_ISL_466692, EPI_ISL_466693, EPI_ISL_466694, EPI_ISL_468070-EPI_ISL_468078, EPI_ISL_469285, EPI_ISL_469286, EPI_ISL_469297-EPI_ISL_469300, EPI_ISL_470801, EPI_ISL_475083, EPI_ISL_475084, EPI_ISL_475165-EPI_ISL_475173, EPI_ISL_475238, EPI_ISL_475570, EPI_ISL_475571.The data of COVID-19 cases and fatalities were collected from official websites of the Directorate General of Health Services (DGHS) (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Multiple sequence alignment for the whole genome of Bangladeshi novel coronavirus strains and reference strains (Wuhan/WIV04/2019 and NC_045512/Wuhan-Hu-1) were conducted by using BioEdit 7.2.6 by using the ClustalW Multiple Alignment algorithm. Mutational analysis was performed for specific positions of novel coronavirus whole genome nucleotide sequences and peptide chains.The nucleotide sequences of the whole genome of novel coronaviruses were analysed using Chromas 2.6.5 . Sequence homology was determined by using the BLASTn program (rs) was determined between metrological parameters and COVID-19 cases and fatalities [rs) was determined among environmental factors, host factors and mutation frequency of novel coronaviruses. The association between two variables can be defined using a monotonic function by using Spearman's rank correlation coefficient (rs). The coefficient equation can be written asAll data were analysed using unbiased statistical approach. Spearman's rank correlation coefficient had been reported from Dhaka followed by Chattogram (n\u00a0=\u00a015\u00a0775) Bogura (n\u00a0=\u00a05614), Khulna (n\u00a0=\u00a05039), Sylhet (n\u00a0=\u00a04912) and Mymensingh (n\u00a0=\u00a03078), Barishal (n\u00a0=\u00a02806) and Rangpur (n\u00a0=\u00a01736), respectively , followed by Dhaka (76%), Rangpur (74%) and Khulna (73%), respectively . The higUV is an important metrological factor that affects the transmission and mutation frequency of novel coronaviruses. During this study, the average UV index was recorded between 6.5 and 8 in Bangladesh. The highest average UV index was recorded in Barishal and Bogura followedWind speed has direct effect on the spread of droplet nuclei containing virus particles. The average wind speed was recorded from 3\u00a0km/h to 19\u00a0km/h in this study. During this study, the highest average wind speed was recorded in Chattogram (17\u00a0km/h) followed by Bogura (16\u00a0km/h), Mymensingh (16\u00a0km/h), Khulna (15\u00a0km/h), Dhaka (14\u00a0km/h), Barishal (14\u00a0km/h), Rangpur (13\u00a0km/h) and Sylhet (11\u00a0km/h), respectively .Fig. 6.2) is the most populous city in the world with total population of 21\u00a0006\u00a0000, followed by Khulna (34\u00a0000\u00a0person/km2) with a total population of 1\u00a0122\u00a0000, Chattogram (19\u00a0800\u00a0person/km2) with a total population of 9\u00a0453\u00a0496, Sylhet (19\u00a0865\u00a0person/km2) with a total population of 526\u00a0412, Barishal (10\u00a0524\u00a0person/km2) with a total population of 385\u00a0093, Bogura (7763\u00a0person/km2) with a total population of 540\u00a0000, Mymensingh (5200\u00a0person/km2) with a total population of 476\u00a0543 and Rangpur (4167\u00a0person/km2) with a total population of 15\u00a0665\u00a0000, respectively.Dhaka (46\u00a0997\u00a0person/kmrs\u00a0=\u00a0\u22120.675), followed by average temperature 7 days ago (rs\u00a0=\u00a0\u22120.547), maximum temperature on the day (rs\u00a0=\u00a0\u22120.512) and minimum temperature on the day (rs\u00a0=\u00a0\u22120.486). Maximum temperature on the day had the highest correlation with total fatalities (rs\u00a0=\u00a0\u22120.611). The correlation for both COVID-19 cases and fatalities are negative, which indicates that at lower temperature the number of cases and fatalities increases.Spearman's correlation analysis between metrological and COVID-19 pandemic are presented in rs\u00a0=\u00a00.712) and fatalities (rs\u00a0=\u00a00.678) followed by the total population in every city.Second, relative humidity on the day had the greater correlation with the number of fatalities than case number. The correlation between relative humidity and COVID-19 pandemic reduces with increasing time span. Third, the association between UV index and the number of cases is the highest on the day of the case. Similarly, the correlation between UV index and the number of fatalities was the highest on the day. The correlation of relative humidity and UV index with COVID-19 pandemic was also negative. Fourth, among environmental factors, the average wind speed on the day had the highest correlation with the number of cases. The higher the wind speed was, the more the number of cases and fatalities were. Finally, the total population and population density of a city were highly correlated with the number of cases and fatalities in the city. The population density had the highest correlation with cases (rs\u00a0=\u00a00.611) with average temperature but frequency of rare mutation at spike protein had the highest correlation (rs\u00a0=\u00a00.658) with maximum temperature. Second, UV index was highly correlated with frequencies of all mutational events and the highest correlation was detected (rs\u00a0=\u00a00.678) with rare mutation at ORF1ab. Third, relative humidity had highest correlation (rs\u00a0=\u00a00.389) with frequency of D614G. Fourth, amount of rainfall was also strongly correlated with frequency of D614G. All of the metrological factors were positively related with the frequency of different mutations indicating increased temperature and UV index will favour origin of new mutations in the novel coronavirus. Finally, host factors-coinfection and gender variability were also positively correlated with mutation frequency. Coinfection had the highest association with common mutations at other structural proteins (rs\u00a0=\u00a00.671) . The ageAfter determining the first genome of the novel coronavirus, thousands of mutational events had occurred. Some of the mutations had made the virus more persistent, environmental resistant and more deadly. The first 100 genomes of the novel coronavirus were analysed in this study. Mutations were detected throughout the whole genome. The most common mutation at ORF1ab region were P323L (NSP12) (88%) and I120F (NSP2) (72%) . The mosAmong 100 patients of this study, males were the predominant gender group (63%) followed by female patients (37%). Most of the cases (24%) were detected in the age group 30\u221239 years followed by 19% in 20\u221229 years and 18% in 40\u221249 years, respectively .Fig. 8.rs\u00a0=\u00a0\u22120.486); between maximum temperature and COVID-19 cases (rs\u00a0=\u00a0\u22120.512); between average temperature and COVID-9 cases (rs\u00a0=\u00a0\u22120.675) [et al. [rs\u00a0=\u00a0\u22120.586)/ fatalities (rs\u00a0=\u00a0\u22120.609) [With a moderate transmission rate, COVID-19 pandemic has transmitted throughout the entire world within very short time and continued to infect people , 31, 32.\u00a0\u22120.675) , 34. Fou [et al. did not \u00a0\u22120.609) , 34. Whirs value of COVID-19 cases in China [Previous studies have reported significant correlation of coronaviruses infection with metrological parameters , 35, 36.in China . Furtherin China , 33, 34.in China , 39. Thiin China , 39.rs\u00a0=\u00a00.687) between total population and COVID-19 cases in Turkey. However, this study includes both the total population and population density for COVID-19 cases and fatalities. This study reported stronger correlation between total population and cases (rs\u00a0=\u00a00.645) /fatalities (rs\u00a0=\u00a00.578); between population density and cases (rs\u00a0=\u00a00.712) /fatalities (rs\u00a0=\u00a00.678) than previous study [\u015eahin detectedus study .Mutational events are most important aspects for novel coronavirus infection, transmission and persistence in the host cells. Mutations at spike proteins can create difficulties to develop effective vaccine or therapeutics against novel coronaviruses , 29, 30.rs\u00a0=\u00a00.654), rare mutation (rs\u00a0=\u00a00.598) and at S- D614G (rs\u00a0=\u00a00.611); between maximum temperature and rare mutation at S (rs\u00a0=\u00a00.658). Among other metrological factors, UV index had the highest correlation with frequency of mutations at every site in the genome. Among host factors, coinfections had strong correlation with frequency of mutations at ORF1ab- common mutation (rs\u00a0=\u00a00.485), rare mutation (rs\u00a0=\u00a00.642), at S-D614G (rs\u00a0=\u00a00.644) and common mutation at other protein (rs\u00a0=\u00a00.671). Both age and gender had significant correlation with frequency of mutations at many sites of the genome. As of 18 August 2020 no other study has described the correlation between metrological parameters/host factors and frequency of mutations in novel coronaviruses. However, for other viruses like influenza and Newcastle disease viruses there are reports of environmental and host factors association with the virus mutations [This study determined the correlation between metrological parameters and mutational frequency of novel coronaviruses for the first time. This study included both metrological parameters and host factors to determine correlation with frequency of mutations. Studies have found significant effects of environmental factors and UV radiation on the frequency of mutation of influenza virus and Newcastle disease virus , 43. Thi rs\u00a0=\u00a00.6, at S-D6This study has described the highest correlation between metrological parameters and COVID-19 cases; strong correlation between metrological parameters and COVID-19 fatalities; first time correlation between metrological factors and frequency of mutations in novel coronaviruses; first time correlation between host factors and frequency of mutation. This study also provided the mutation frequency at different sites of novel coronaviruses. A complete picture on the effect of metrological parameters on COVID-19 pandemic and novel coronavirus mutation frequency has been depicted in this study. This study will work as a baseline for the future studies focusing on the environmental and host factors affecting the COVID-19 pandemic. Further, this study will work as a guideline for future studies by containing important information on environmental and host factors impact on mutations of coronaviruses.Other factors like duration of lockdown, mobility of huge number of workers, social and religious gatherings, not using masks, movement of people during vacations, lack of proper detection of COVID-19 patients etc. are significantly affecting the pandemic. If direct contact is not avoided, social distance and personal hygiene are not maintained, environmental factors cannot control the COVID-19 pandemic alone. This study describes high frequency of common and rare mutations in the novel coronavirus genome in Bangladesh. Circulation of these mutants will certainly increase the duration of the pandemic and reduce the effectiveness of vaccine or therapeutics in future. The main limitation of this study is the variation of case number. The actual case and fatality number may vary slightly due to the lack of complete diagnosis of the population. In future, studies including more isolates of viruses, large number of clinical data and environmental data of longer periods can predict more accurate effects of various factors on COVID-19.To the best of our knowledge, this is the first study reporting correlation of environmental factors with COVID-19 pandemic in three time frames in Bangladesh with temperature about 27\u00a0\u00b0C. The strongest correlations between metrological factors and COVID-19 cases/fatalities were specified on the day of cases/fatalities. The highest correlation was detected between population density and cases followed by total population and cases indicating the mobility and crowd are actively increasing the cases and fatalities. For the first time, this study describes the effects of metrological parameters on the frequency of mutation at different sites in novel coronavirus. Both temperature and UV index had strong effects on different mutation events. Among host factors, coinfection also affected different mutations strongly. Including COVID-19 cases, fatalities, mutations, mutation frequency and clinical data this study provides a complete picture of the COVID-19 pandemics and environmental effects on this pandemic. This study will provide useful implications about COVID-19 pandemic and both for policy makers and public to take decision to reduce the health burden of this outbreak."} +{"text": "High-throughput RNA-seq enables comprehensive analysis of the transcriptome for various purposes. However, this technology generally generates massive amounts of sequencing reads with a shorter read length. Consequently, fast, accurate, and flexible tools are needed for assembling raw RNA-seq data into full-length transcripts and quantifying their expression levels. In this protocol, we report TransBorrow, a novel transcriptome assembly software specifically designed for short RNA-seq reads. TransBorrow is employed in conjunction with a splice-aware alignment tool (e.g. Hisat2 and Star) and some other transcriptome assembly tools . The protocol encompasses all necessary steps, starting from downloading and processing raw sequencing data to assembling the full-length transcripts and quantifying their expressed abundances. The execution time of the protocol may vary depending on the sizes of processed datasets and computational platforms. First, create a subdirectory \u201cStar\u201d in your directory and enter it. Next, employ the \u201cwget\u201d command to download the most recent package from the appropriate downloading link address. Subsequently, extract the contents of the downloaded package to obtain the executable file. Lastly, add the path of the Star binary to a directory encompassed within your system\u2019s PATH variable.$ mkdir Star$ cd Starhttps://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz$ wget $ tar -xzf 2.5.3a.tar.gz$ cd STAR-2.5.3a$ echo \u201cexport PATH=$PATH:/mnt/data0/zhaody/Star/STAR-2.5.3a\u201d\u226b\u223c/.bashrc$ source \u223c/.bashrcAn illustration of installing Star is shown as follows.Samtools is a software package designed for processing SAM and BAM format files, which offers a diverse range of command-line utilities for manipulating, converting, and analyzing SAM/BAM files. It enables various tasks such as file format conversion (e.g. SAM to BAM conversion), sorting and indexing SAM/BAM files, assessing coverage and depth of aligned loci, extracting sequences from specific regions, and more .To install Samtools, the following steps can be undertaken. First, create a subdirectory named \u201cSamtools\u201d within your directory. Subsequently, navigate to the \u201cSamtools\u201d directory and use the \u201cwget\u201d command to download the latest package from the appropriate download link address. Afterwards, extract the downloaded package and configure the environment variables for Samtools accordingly. Finally, add the Samtools binary directory to the PATH environment variable in the shell configuration file (see the following illustration)An illustration of installing samtools is shown as follows.$ mkdir Samtools$ cd Samtoolshttps://nchc.dl.sourceforge.net/project/samtools/samtools/1.17/samtools-1.17.tar.bz2$ wget $ tar jxvf samtools-1.17.tar.bz2$ cd samtools-1.17$ ./configure\u2014prefix=/mnt/data0/zhaody/Samtools/samtools-1.17$ make$ make install$ echo \u201cexport PATH=$PATH:/mnt/data0/zhaody/Samtools/samtools-1.17\u201d\u226b\u223c/.bashrc$ source \u223c/.bashrcAfter installing it, you can type the command \u201csamtools\u201d to see the help documentation information.StringTie is an efficient transcriptome assembler, which iteratively extracts the heaviest path from a splice graph, and then estimates the abundance via a network flow algorithm [12].To install StringTie, the following steps can be followed. First, create a subdirectory named \u201cStringTie\u201d within your directory. Next, navigate to the \u201cStringTie\u201d directory and utilize the \u201cwget\u201d command to download the latest package from the appropriate download link address. After downloading, extract the contents of the package to obtain the executable file. Finally, add the path of the StringTie binary directory to the PATH environment variable in the shell configuration file.$ mkdir StringTie$ cd StringTiehttp://ccb.jhu.edu/software/stringtie/dl/stringtie-2.2.1.Linux_x86_64.tar.gz$ wget $ tar -xzvf stringtie-2.2.1.Linux_x86_64.tar.gz$ echo \u201cexport PATH=$PATH:/mnt/data0/zhaody/Stringtie/stringtie-2.2.1.Linux_x86_64\u201d\u226b\u223c/.bashrc$ source \u223c/.bashrcAn illustration of installing StringTie is shown as follows.If you have successfully installed it, you can type the command \u201cstringtie -h\u201d to see the help documentation information.Cufflinks is a software tool specifically designed for analyzing RNA-seq data. It constructs the overlap graph model based on the fragment alignments, and applies a minimum path cover model to search for the transcript-representing paths .To install Cufflinks, the following steps can be undertaken: First, create a subdirectory named \u201cCufflinks\u201d within your directory. Next, navigate to the \u201cCufflinks\u201d directory and use the command \u201cwget\u201d to download the latest package from the appropriate download link address. After downloading the package, extract its contents to obtain the executable file. Finally, add the Cufflinks binary directory to the PATH environment variable in the shell configuration file.$ mkdir Cufflinks$ cd Cufflinkshttp://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz$ wget $ tar -xzvf cufflinks-2.2.1.Linux_x86_64.tar.gz$ echo \u201cexport PATH=$PATH:/mnt/data0/zhaody/Cufflinks/cufflinks-2.2.1.Linux_x86_64\u201d\u226b\u223c/.bashrc$ source \u223c/.bashrcAn illustration of installing Cufflinks is shown as follows.If you have successfully installed it, you can type the command \u201ccufflinks -h\u201d to see the help documentation information.Scallop is a highly efficient transcriptome assembly software designed for the reconstruction of transcripts from RNA-Seq data. It was built upon the standard paradigm of the splice graph, and it decomposed the graphs through optimizing several competing objectives while preserving long-range phasing paths .To install Scallop, the following steps can be followed. First, create a subdirectory named \u201cScallop\u201d within the main directory. Next, navigate to the \u201cScallop\u201d directory and utilize the command \u201cwget\u201d to download the latest package from the appropriate download link address. After downloading, extract the contents of the package to obtain the executable file. Finally, add the Scallop binary directory to the PATH environment variable in the shell configuration file.$ mkdir Scallop$ cd Scallophttps://github.com/Kingsford-Group/scallop/releases/download/v0.10.5/scallop-0.10.5_linux_x86_64$ wget .tar.gz$ tar -xzvf scallop-0.10.5_linux_x86_64.tar.gz$ echo \u201cexport PATH=$PATH:/mnt/data0/zhaody/Scallop/scallop-0.10.5_linux_x86_64\u201d\u226b\u223c/.bashrc$ source \u223c/.bashrcAn illustration of installing Scallop is shown as follows.If you have successfully installed it, you can type the command \u201cscallop -h\u201d to see the help documentation information.boost directory and run \u201c./bootstrap.sh\u201d. Finally, type \u201c./b2 install\u2014prefix=\u201d to install Boost .The Boost library is a highly regarded, portable, and open-source C++ library that is essential for TransBorrow. To install Boost, follow these steps. First, create a subdirectory named \u201cBoost\u201d under your directory. Next, navigate into the \u201cBoost\u201d directory and use the command \u201cwget\u201d to download the latest package from the appropriate download link address. Then, unzip the downloaded package and change to the Please note that the version number and URL provided in your original text may need to be updated. Make sure to use the latest version of Boost and adjust the URL accordingly.$ mkdir Boost$ cd Boosthttps://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/boost_1_82_0.tar.gz$ wget $ tar -xzvf boost_1_82_0.tar.gz$ cd boost_1_82_0$ ./bootstrap.sh$ ./b2 install\u2014prefix=/mnt/data0/zhaody/BoostAn illustration of installing Boost is shown as follows.If the Boost is installed successfully, you can see the \u201clib\u201d and \u201cinclude\u201d directories in YOUR_BOOST_INSTALL_DIRECTORY directory. Take note of the Boost installation directory, because you need to tell the TransBorrow installer where to find Boost later on.TransBorrow is an accurate and efficient transcriptome algorithm, which borrows the assemblies from different assemblers to search for reliable subsequences by building a colored graph from those borrowed assemblies, and employs a newly designed path extension strategy to accurately search for a transcript-representing path cover over each splicing graph .To install TransBorrow, create a subdirectory named TransBorrow under the main directory. After entering the directory, use the command \u201cwget\u201d to download a package from the appropriate download link address and unzip it. In addition, to configure the environment of TransBorrow, change to the \u201cbamtools\u201d directory and make a new directory named \u201cbuild\u201d, then type \u201ccmake\u201d and \u201cmake\u201d to make it install.$ mkdir TransBorrow$ cd TransBorrowhttps://sourceforge.net/projects/transcriptomeassembly/files/TransBorrow/TransBorrow_v.1.3.tar.gz$ wget $ tar -xzvf TransBorrow_v.1.3.tar.gz$ cd TransBorrow_v.1.3$ cd bamtools$ mkdir build$ cd build$ cmake ./$ make$ cd ./An illustration of building bamtools is shown as follows.Assuming the build process finished correctly, you should be able to find the toolkit executable in directory \u201c./bin/\u201d, the Bamtools API Utils libraries \u201c./lib/\u201d, and the Bamtools API headers \u201c./include/\u201d.lib and include directories (absolute path) of both Boost and bamtools to the CMakeLists.txt file located in TransBorrow_v.1.3/src/to configure the installation environment for TransBorrow (see the following illustration for details).Then, add the Please note that the directory structure and file names may vary depending on your specific setup. Adjust the paths and commands accordingly.$ cd src$ vim CMakeList.txtset(BOOST_LIB_DIR/mnt/data0/zhaody/Boost/lib)#setset(BOOST_INCLUDE_DIR/mnt/data0/zhaody/Boost/include)#setset(BAMTOOLS_LIB_DIR/mnt/data0/zhaody/TransBorrow/TransBorrow_v.1.3/bamtools/lib)#set(BAMTOOLS_LIB_DIR/storage/juntaosdu/yuting/bamtools/lib)set(BAMTOOLS_INCLUDE_DIR/mnt/data0/zhaody/TransBorrow/TransBorrow_v.1.3/bamtools/include)#set(BAMTOOLS_INCLUDE_DIR/storage/juntaosdu/yuting/bamtools/include)An illustration of setting the installation environment for TransBorrow is shown as follows.Change to the TransBorrow root directory and make a new directory named \u201cbuild\u201d and change into it, then type \u201ccmake ./src\u201d and \u201cmake\u201d commands for the final installation of TransBorrow.$ cd ../$ mkdir build$ cd build$ cmake ./src$ make$ cd ./src$ makeAn illustration of building TransBorrow is shown as follows.$ cd TransBorrow$ echo \u201cexport PATH=$PATH:/mnt/data0/zhaody/TransBorrow/TransBorrow_v.1.3/build\u201d\u226b\u223c/.bashrc$ source \u223c/.bashrcFinally, add the TransBorrow directory to the PATH environment variable in the shell configuration file. See the following illustration.If you have successfully installed it, you can type the command \u201cTransBorrow -h\u201d to see the help documentation information see .The Gffcompare software is a powerful tool utilized for comparing, merging, annotating, and estimating the accuracy of one or more GFF/GTF files in comparison to reference annotations . To inst$ mkdir Gffcompare$ cd Gffcomparehttp://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.12.6.Linux_x86_64.tar.gz$ wget $ tar -xzvf gffcompare-0.12.6.Linux_x86_64.tar.gz$ echo \u201cexport PATH=$PATH:/mnt/data0/zhaody/Gffcompare/gffcompare-0.12.6.Linux_x86_6\u201d\u226b\u223c/.bashrc$ source \u223c/.bashrcAn illustration of installing Gffcompare is shown as follows.If you have successfully installed it, you can type the command \u201cgffcompare -h\u201d to see the help documentation information.TACO is a tool to reconstruct a consensus transcriptome from multiple RNA-seq data sets. TACO accepts as input a set of GTF files containing transcripts assembled from individual libraries, and it employs a dynamic programming path search strategy in the path graph to reconstruct the transcripts. To install TACO, the following steps should be followed. First, create a subdirectory named \u201cTACO\u201d within the main directory. Subsequently, navigate into the \u201cTACO\u201d folder and utilize the \u201cwget\u201d command to download the latest package from the appropriate download link address. Next, extract the downloaded package to acquire the executable file. Finally, add the TACO binary directory to the PATH environment variable.$ mkdir TACO$ cd TACOhttps://github.com/tacorna/taco/releases/download/v0.7.3/taco-v0.7.3.Linux_x86_64.tar.gz$ wget wget $ tar -xzvf taco-v0.7.3.Linux_x86_64.tar.gz$ echo \u201cexport PATH=$PATH:/mnt/data0/zhaody/TACO/taco-v0.7.3.Linux_x86_64\u201d\u226b\u223c/.bashrc$ source \u223c/.bashrcAn illustration of installing TACO is shown as follows.The RNA-seq data can be downloaded from databases such as the NCBI or the European Bioinformatics Institute (EBI), etc. Alternatively, the researchers can use the RNA-seq data sequenced by themselves. Note that the file format of the input sequencing data must be in FASTA or FASTQ format.RNA-seq technology is mainly categorized into single-end sequencing and paired-end sequencing, based on differences in DNA library preparation during the sequencing process. Single-end sequencing means sequencing only one end of the target DNA/RNA, which requires less sequencing time and cost. In comparison, paired-end sequencing refers to sequencing both ends of the target DNA/RNA, which improves the accuracy of mapping and assembly . AdditioTherefore, the proposed protocol utilized three human RNA-seq data sets based on different types of RNA-seq technology see to demonAn illustration of downloading sequencing data is shown as follows.$ cd Sratoolkit$ prefetch SRR7807492$ cd SRR7807492$ fastq-dump\u2014split-3 SRR7807492.sra$ prefetch ERR3639851$ cd ERR3639851$ fastq-dump\u2014split-3 ERR3639851.sra$ prefetch SRR10611964$ cd SRR10611964$ fastq-dump\u2014split-3 SRR10611964.sra$ mkdir ref_genome$ cd ref_genomehttp://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz$ wget $ gunzip *.gz$ cat *.fa > ref_genome.fa$ rm chr*.faAfter obtaining raw RNA-seq reads, download the human reference genome (the version used in this protocol was hg19) as follows. Create a file named \u201cref_genome\u201d in your home directory and utilize the \u201cwget\u201d command with the appropriate download link address to download the corresponding file. If you complete the downloading, extract the file (see the following illustration for details).The human genome is about 3GB and ensures that you have sufficient storage capacity to accommodate both the downloaded and uncompressed files.In this protocol, all the reference transcripts were set as the ground truth to evaluate the performance of the assemblers. To acquire the reference transcripts, navigate to the \u201cref_genome\u201d directory and employ the \u201cwget\u201d command along with the appropriate downloading link address (see the following illustration for details).$ cd ref_genomehttps://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh37_mapping/gencode.v44lift37.annotation.gtf.gz$ wget $ gunzip gencode.v44lift37.annotation.gtf.gzAn illustration of downloading the reference transcriptome is shown below.Upon successful downloading, you will find three folders named SRR7807492, ERR3639851, and SRR10611964 within the Sratoolkit directory, which store the RNA-seq data in the \u201c.fastq\u201d format The \u201chisat2-build\u201d command generates the reference genome index and is typically followed by the reference genome file in \u201c.fa\u201d format and the desired output file name. The recommended command for this task is as follows.# hisat2-build ref_genome.fa ref_index_genome,ref_genome.fa is the reference genome.where Besides, when utilizing a transcriptome annotation library to aid in building the reference genome index, \u201chisat2-build\u201d requires the use of the \u201c\u2014ss\u201d parameter, which specifies the splice site information of the reference transcripts, and the \u201c\u2014exon\u201d parameter, which denotes the exon information of the reference transcripts. The running command should be as follows.# hisat2-build\u2014ss genome.ss\u2014exon genome.exon ref_genome.fa ref_index_genome,genome.ss and genome.exon can be extracted from a transcriptome annotation file (in GTF format) using the script \u201cextract_splice_sites.py\u201d and \u201cextract_exons.py\u201d provided in the Hisat2 package.where 2) The command \u201chisat2\u201d is utilized for aligning RNA-seq reads to the reference genome. The recommended command is as follows.# hisat2 -p 8\u2014dta -x ref_index_genome -1 reads_1.fastq -2 reads_2.fastq -S test_genome.sam where the parameter \u201c-p\u201d specifies the number of threads running, typically set to be equal to or slightly fewer than the number of available CPU cores. The parameter \u201c\u2014dta\u201d means reporting alignments tailored for transcript assemblers. The parameters \u201c-x\u201d and \u201c-S\u201d provide the indexed reference genome and the name of the output SAM file, respectively. The parameters \u201c-1\u201d and \u201c-2\u201d specify the two paired-end sequencing files in FASTQ format, reads_1.fastq and reads_2.fastq, respectively. If the sequencing data is single-ended, the parameter \u201c-U\u201d is used with the corresponding FASTQ file.The first step of using Hisat2 is to construct an index for the reference genome. Begin by navigating to the Hisat2 directory and employing the \u201cmv\u201d command to relocate the reference genome file from the \u201cref_genome\u201d directory to the current directory. Subsequently, utilize the \u201chisat2-build\u201d command to generate an index for the reference genome. This process will result in the creation of eight files with the \u201c.ht2\u201d suffix. This process of building the index typically takes approximately half an hour (see the following illustration for details).$ cd Hisat2$ mv/mnt/data0/zhaody/ref_genome/ref_genome.fa.$ hisat2-build ref_genome.fa ref_index_genomeAn illustration of the Hisat2 building index is shown below.It is noteworthy that incorporating the annotation information of the transcripts while building the genome index can improve the accuracy of Hisat2 alignment. Utilizing this approach is also an option as follows. Navigate to the Hisat2 directory and employ the \u201cmv\u201d command to relocate the reference genome file and the transcript annotation file from the \u201cref_genome\u201d directory to the current directory. Then, extract splice-site and exon information from the annotation. Proceed by using the \u201chisat2-build\u201d command to construct an index for the reference genome. Finally, eight files will be generated with the \u201c.ht2\u201d suffix. This process of building the index typically takes approximately one hour (see the following illustration for details).$ cd Hisat2$ mv/mnt/data0/zhaody/ref_genome/ref_genome.fa.$ mv/mnt/data0/zhaody/ref_genome/gencode.v44lift37.annotation.gtf.$ extract_splice_sites.py gencode.v44lift37.annotation.gtf >genome.ss$ extract_exons.py gencode.v44lift37.annotation.gtf >genome.exon$ hisat2-build\u2014ss genome.ss\u2014exon genome.exon ref_genome.fa ref_index_genomeAn illustration of the Hisat2 building index using the annotation file is shown below.To align the raw RNA-seq reads to the reference genome, first, navigate to the Hisat2 directory. Then, utilize the \u201cmv\u201d command to relocate the individual \u201c.fastq\u201d files of the three sample datasets from the \u201cSratoolkit\u201d directory to the current directory. Afterward, use the \u201chisat2\u201d command to align the RNA-seq reads from the three sample datasets to the reference genome. Upon completion of the alignment process, you will obtain three mapping files in \u201c.sam\u201d format, with each file corresponding to one of the sample datasets The command \u201cSTAR\u2014runMode genomeGenerate\u201d is utilized for constructing the reference genome index. The recommended command is as follows.# STAR\u2014runThreadN 8\u2014runMode genomeGenerate\u2014genomeDir ./index\u2014genomeFastaFiles ref_genome.fa\u2014sjdbGTFfile reference_Transcripts.gtf\u2014sjdbOverhang readlenth-1where the parameter \u201c\u2014runThreadN\u201d denotes the number of running threads, typically set to be equal to or slightly fewer than the number of CPU cores available. The parameter \u201c\u2014genomeDir\u201d specifies the output directory where the index file is stored. The parameters \u201c\u2014genomeFastaFiles\u201d and \u201c\u2014sjdbGTFfile\u201d indicate the reference genome and reference transcripts respectively. It is generally recommended to set the parameter \u201c\u2014sjdbOverhang\u201d to be the length of sequencing reads minus one.2) The command \u201cSTAR\u201d is employed for aligning RNA-seq reads to the reference genome. The recommended command is as follows:# STAR\u2014runThreadN 8\u2014genomeDir ./index\u2014readFilesIn reads_1.fastq reads_2.fastq\u2014outSAMtype BAM SortedByCoordinatewhere the parameter \u201c\u2014runThreadN\u201d indicates the number of threads running, typically set to be equal to or slightly fewer than the number of available CPU cores. The parameter \u201c\u2014genomeDir\u201d specifies the output directory where the index file is stored. The parameter \u201c\u2014readFilesIn\u201d provides the sequencing reads in FASTQ format, namely reads_1.fastq and reads_2.fastq. The parameter \u201c\u2014outSAMtype BAM SortedByCoordinate\u201d is used to generate a sorted BAM file as the final mapping output, eliminating the need for using Samtools to convert the SAM file to BAM. By default, the final mapping file is saved in the current folder.The first step of using Star is to construct an index for the reference genome. Beginning by entering the Star directory and employing the \u201cmv\u201d command to relocate the reference genome file and the transcript annotation file from the \u201cref_genome\u201d directory to the current directory. Subsequently, utilize the \u201cSTAR\u201d command to generate an index for the reference genome. (see the following illustration for details).$ cd Star$ mv/mnt/data0/zhaody/ref_genome/ref_genome.fa.$ mv/mnt/data0/zhaody/ref_genome/gencode.v44lift37.annotation.gtf.$ STAR\u2014runThreadN 8\u2014runMode genomeGenerate\u2014genomeDir ./index\u2014genomeFastaFiles ref_genome.fa\u2014sjdbGTFfile gencode.v44lift37.annotation.gtf\u2014sjdbOverhang 99An illustration of the Star building index is shown below.To align the raw RNA-seq reads to the reference genome with Star, please navigate to the STAR directory. Then, utilize the \u201cmv\u201d command to relocate the individual \u201c.fastq\u201d files of the three sample datasets from the \u201cSratoolkit\u201d directory to the current directory. Afterward, use the \u201cSTAR\u201d command to align the RNA-seq reads from the three sample datasets to the reference genome. Upon completion of the alignment process, you will obtain three mapping files in \u201cBAM\u201d format, with each file corresponding to one of the sample datasets. By default, the final mapping file is saved in the current folder.$ cd STAR$ mv/mnt/data0/zhaody/Sratoolkit/SRR7807492/SRR7807492_1.fastq.$ mv/mnt/data0/zhaody/Sratoolkit/SRR7807492/SRR7807492_2.fastq.$ mv/mnt/data0/zhaody/Sratoolkit/ERR3639851/ERR3639851.fastq.$ mv/mnt/data0/zhaody/Sratoolkit/SRR10611964/SRR10611964_1.fastq.$ mv/mnt/data0/zhaody/Sratoolkit/SRR10611964/SRR10611964_2.fastq.$ STAR\u2014runThreadN 8\u2014genomeDir ./index\u2014readFilesIn SRR7807492_1.fastq SRR7807492_2.fastq\u2014outSAMtype BAM SortedByCoordinate$ STAR\u2014runThreadN 8\u2014genomeDir ./index\u2014readFilesIn ERR3639851.fastq\u2014outSAMtype BAM SortedByCoordinate$ STAR\u2014runThreadN 8\u2014genomeDir ./index\u2014readFilesIn SRR10611964_1.fastq SRR10611964_2.fastq\u2014outSAMtype BAM SortedByCoordinateAn illustration of Star mapping is shown below.TransBorrow performs transcript assembly by utilizing the alignment of RNA-seq reads to the reference genome, as well as the assemblies generated from other assemblers . In this protocol, we utilize the read alignments generated by Hisat2 to illustrate the entire TransBorrow\u2019s transcript assembly process.# TransBorrow [options] -r -g -b -s It is worth noting that during the TransBorrow assembly process, specific parameters and commands need to be selected according to the data types and your needs to achieve optimal assembly results. The followings are some important parameter descriptions and suggestions for using TransBorrow to assemble transcripts.According to data types, you need to choose the appropriate parameter \u201c-s\u201d, e.g. for the data SRR7807492 that is paired-end and nonstranded, adjust the parameter to \u201c-s unstranded\u201d.The parameter \u201c-c\u201d indicates the minimum coverage of recovered transcripts, which helps to filter out potentially low-confidence transcripts.The parameter \u201c-l\u201d indicates the minimum length (bp) of recovered transcripts. This parameter helps to filter out short transcripts.The parameter \u201c-d\u201d refers to the minimum seed coverage in the path-extensions procedure of the TransBorrow algorithm. The default value for this parameter is typically set to 0. A higher value of min_seed for extension will result in more stringent filtering, potentially excluding low-coverage regions and leading to fewer but more confident assembled transcripts.To run StringTie, begin by navigating to the StringTie directory and moving the three mapping files in BAM format to the current directory. Then, execute the \u201cstringtie\u201d command to conduct the transcript assembly process, the assembled transcripts will be generated in GTF format (see the following illustration). Moreover, it is essential to adjust the parameters according to the provided data types. The recommended command using StringTie is as follows.# stringtie -p 8 -o OutputFile.gtf InputFile.bamIn this command, \u201c-p\u201d specifies the number of threads to be used, which is typically set to be equal to or slightly fewer than the number of available CPU cores. The \u201c-o\u201d parameter specifies the name of the output GTF file, and InputFile.bam indicates the name of the input BAM file. The resulting assembly GTF file will be saved in the current folder.$ cd Stringtie$ mv/mnt/data0/zhaody/Samtools/SRR7807492_genome.bam.$ mv/mnt/data0/zhaody/Samtools/ERR3639851_genome.bam.$ mv/mnt/data0/zhaody/Samtools/SRR10611964_genome.bam.$ stringtie -p 8 -o SRR7807492_genome_stringtie.gtf SRR7807492_genome.bam$ stringtie -p 8 -o ERR3639851_genome_stringtie.gtf ERR3639851_genome.bam$ stringtie -p 8 -o SRR10611964_genome_stringtie.gtf SRR10611964_genome.bamAn illustration of running StringTie with its default sets is shown below.To assemble the transcripts by Cufflinks, navigate to the Cufflinks directory and move the three mapping files in BAM format to the current directory. Subsequently, execute the \u201ccufflinks\u201d command to carry out the transcript assembly, which will generate three GTF files containing the assembled transcripts. It is imperative to adjust the commands accordingly for the provided data types (see the following illustration). The recommended command using Cufflinks is as follows.# cufflinks -p 8 -o OutputFile.gtf InputFile.bam\u2014library-type fr-firststrandIn this command, the \u201c-p\u201d parameter specifies the number of threads to be used, typically matching or slightly lower than the available CPU cores. The \u201c-o\u201d parameter is followed by the desired name for the output GTF file and the name of the input BAM file. The \u201c\u2014library-type fr-firststrand\u201d parameter indicates that the input RNA-seq data were generated using the first-strand cDNA synthesis method. Conversely, the \u201c\u2014library-type rf-secondstrand\u201d parameter would indicate that the input RNA-seq data was generated using the second-strand cDNA synthesis method. The default assumption for input RNA-seq data is nonstranded.$ cd Cufflinks$ mv/mnt/data0/zhaody/Stringtie/SRR7807492_genome.bam.$ mv/mnt/data0/zhaody/Stringtie/ERR3639851_genome.bam.$ mv/mnt/data0/zhaody/Stringtie/SRR10611964_genome.bam.$ cufflinks -p 8 -o SRR7807492_genome_cufflinks.gtf SRR7807492_genome.bam$ cufflinks -p 8 -o ERR3639851_genome_cufflinks.gtf ERR3639851_genome.bam$ cufflinks -p 8 -o SRR10611964_genome_cufflinks.gtf SRR10611964_genome.bam\u2014library-type fr-firststrandAn illustration of running Cufflinks with its default sets is shown below.To assemble the transcripts by Scallop, begin by navigating to the Scallop directory and moving the three mapping files in BAM format to the current directory. Next, execute the \u201cscallop\u201d command to perform transcript assembly, and the assembled transcripts will be generated in GTF format. It is important to note that Scallop requires different parameters to be configured based on the specific data type of the input. Therefore, it is necessary to adjust the commands accordingly for the provided data types. The recommended command using Scallop is as follows.# scallop -i InputFile.bam -o OutputFile.gtf\u2014library-type firstIn this command, the \u201c-i\u201d parameter is followed by the name of the input BAM file, and the \u201c-o\u201d parameter is followed by the desired name for the output GTF file. The \u201c\u2014library-type first\u201d parameter indicates that the input RNA-seq data were generated using the first-strand cDNA synthesis method. Conversely, the \u201c\u2014library-type second\u201d parameter would indicate that the input RNA-seq data were generated using the second-strand cDNA synthesis method. Additionally, the \u201c\u2014library-type unstranded\u201d parameter indicates that the input RNA-seq data are nonstranded. By default, the final assembly GTF file will be saved in the current directory.$ cd Scallop$ mv/mnt/data0/zhaody/Cufflinks/SRR7807492_genome.bam.$ mv/mnt/data0/zhaody/Cufflinks/ERR3639851_genome.bam.$ mv/mnt/data0/zhaody/Cufflinks/SRR10611964_genome.bam.$ scallop -i SRR7807492_genome.bam -o SRR7807492_genome_scallop.gtf\u2014library_type unstranded$ scallop -i ERR3639851_genome.bam -o ERR3639851_genome_scallop.gtf\u2014library_type unstranded$ scallop -i SRR10611964_genome.bam -o SRR10611964_genome_scallop.gtf\u2014library_type firstAn illustration of running Scallop with its default sets is shown below.Besides the alignment file, TransBorrow needs to take as input the transcripts assembled by different transcript assembly tools, which should be merged together first. Create a new directory named \u201cGtf_file\u201d in the home directory to store the merged files. Next, move the nine GTF files to the current directory. Finally, utilize the cat command to merge the three GTF files corresponding to each sample into one file (see the following illustration).$ mkdir Gtf_file$ cd Gtf_file$ mv/mnt/data0/zhaody/Stringtie/SRR7807492_genome_stringtie.gtf.$ mv/mnt/data0/zhaody/Cufflinks/SRR7807492_genome_cufflinks.gtf.$ mv/mnt/data0/zhaody/Scallop/SRR7807492_genome_scallop.gtf.$ cat SRR7807492_genome_stringtie.gtf SRR7807492_genome_cufflinks.gtfSRR7807492_genome_scallop.gtf > combine_SRR7807492.gtfAn illustration of merging the assembled transcripts of different assemblers is shown as follows.To utilize TransBorrow, navigate to the TransBorrow directory and move the mapping BAM files, reference genome FASTA file, and the merged transcripts for each sample to the current directory. Employ the \u201cTransBorrow\u201d command to perform the transcript assembly procedure (see the following illustration for details). It is important to consider that different parameters need to be configured for different types of sample data.The recommended command using TransBorrow is as follows.# TransBorrow -r CombinedInputFile.gtf -b InputFile.bam -g ref_genome.fa -s first -o OutputDirctoryIn this command, the \u201c-r\u201d parameter is followed by the combined transcripts assembled by different tools in GTF format. The \u201c-b\u201d parameter is followed by the name of the input BAM file. The \u201c-g\u201d parameter is followed by the reference genome in FASTA format. The parameter \u201c-s\u201d indicates the type of sequencing data, whether it is stranded or nonstranded, single-ended or paired-ended. In this case, \u201cfirst\u201d indicates that the sequencing data were generated using the first-strand cDNA synthesis method. The \u201c-o\u201d parameter is followed by a directory that stores the temporary files and the final assembled GTF file. Please refer to $ cd TransBorrow$ mv/mnt/data0/zhaody/Gtf_film/combine_SRR7807492.gtf.$ mv/mnt/data0/zhaody/Gtf_film/combine_ERR3639851.gtf.$ mv/mnt/data0/zhaody/Gtf_film/combine_SRR10611964.gtf.$ mv/mnt/data0/zhaody/Scallop/SRR7807492_genome.bam.$ mv/mnt/data0/zhaody/Scallop/ERR3639851_genome.bam.$ mv/mnt/data0/zhaody/Scallop/SRR10611964_genome.bam.$ mv/mnt/data0/zhaody/Hisat2/ref_index_genome.$ TransBorrow -r combine_SRR7807492.gtf -b SRR7807492_genome.bam -g ref_genome.fa -s unstranded -o ./TransBorrow_results/SRR7807492_TransBorrow.gtf -n 3 -t 8$ TransBorrow -r combine_ERR3639851.gtf -b ERR3639851_genome.bam -g ref_genome.fa -s single_unstranded -o ./TransBorrow_results/ERR3639851_TransBorrow.gtf -n 3 -t 8$ TransBorrow -r combine_SRR10611964.gtf -b SRR10611964_genome.bam -g ref_genome.fa -s first -o ./TransBorrow_results/SRR10611964_TransBorrow.gtf -n 3 -t 8An illustration of running TransBorrow is shown as follows.Finally, the results are saved in the directory \u201c./TransBorrow_results/\u201d .To merge the transcripts by TACO, navigate to the TACO directory and move the three assembled GTF files generated by different assemblers to the current directory. Then, add the absolute paths of all GTF files to a TXT file as the input file for TACO. Subsequently, execute the \u201ctaco_run\u201d command to carry out the transcript merging, which will generate a GTF file containing the merged transcripts. The recommended command using TACO is as follows.# taco_run gtf_files.txt\u2014filter-min-expr 0.001 -o TACO_OutDirctory -p 8In this command, the \u201ctaco_run\u201d command specifies the input TXT file. The \u201c-p\u201d parameter specifies the number of threads to be used, typically matching or slightly lower than the available CPU cores. The \u201c-o\u201d parameter is followed by the desired name for the output GTF file. The \u201c\u2014filter-min-expr\u201d parameter is used to filter redundant transcripts to retain only those with expression levels above the specified threshold, and it is recommended here that a setting of 0.001 will provide more flexibility in capturing transcripts with low expression levels.$ cd TACO$ mv/mnt/data0/zhaody/Gtf_file/SRR7807492_genome_stringtie.gtf.$ mv/mnt/data0/zhaody/Gtf_file/SRR7807492_genome_cufflinks.gtf.$ mv/mnt/data0/zhaody/Gtf_file/SRR7807492_genome_scallop.gtf.$ ls -R/mnt/data0/zhaody/TACO/SRR7807492_genome.* > SRR7807492_genome_merge.txt$ ls -R/mnt/data0/zhaody/TACO/ERR3639851_genome.* > ERR3639851_genome_merge.txt$ ls -R/mnt/data0/zhaody/TACO/SRR10611964_genome.* > SRR10611964_genome_merge.txt$ taco_run SRR7807492_genome_merge.txt\u2014filter-min-expr 0.001 -o ./SRR7807492_genome_merge.gtf$ taco_run ERR3639851_genome_merge.txt\u2014filter-min-expr 0.001 -o ./ERR3639851_genome_merge.gtf $ taco_run SRR10611964_genome_merge.txt\u2014filter-min-expr 0.001 -o ./SRR10611964_genome_merge.gtfAn illustration of running TACO with its default sets is shown below.To merge the transcripts by StringTie-merge, navigate to the StringTie directory and move the three assemblies\u2019 GTF file generated by different assemblers to the current directory. Subsequently, execute the \u201cstringtie-merge\u201d command to carry out the transcript merging, which will generate a GTF file containing the merged transcripts. The recommended command using StringTie\u2014merge is as follows.# stringtie\u2014merge stringtie.gtf scallop.gtf cufflinks.gtf -T 0.001 -F 0.001 -o StringTie_merge.gtfIn this command, the \u201c\u2014merge\u201d parameter is followed by three input GTf files. The \u201c-o\u201d parameter is followed by the desired name for the output GTF file. The parameter \u201c-T\u201d and \u201c-F\u201d indicates the minimum TPM and FPKM values of transcripts to be included in the merged results, and a setting of 0.001 is recommended here to allow for more transcripts with lower expression to be merged.$ cd Stringtie$ mv/mnt/data0/zhaody/Gtf_file/SRR7807492_genome_stringtie.gtf.$ mv/mnt/data0/zhaody/Gtf_file/SRR7807492_genome_cufflinks.gtf.$ mv/mnt/data0/zhaody/Gtf_file/SRR7807492_genome_scallop.gtf.$ stringtie\u2014merge SRR7807492_genome_stringtie.gtf SRR7807492_genome_cufflinks.gtf SRR7807492_genome_scallop.gtf -T 0.001 -F 0.001 -o SRR7807492_StringTie_merge.gtf$ stringtie\u2014merge ERR3639851_genome_stringtie.gtf ERR3639851_genome_cufflinks.gtf ERR3639851_genome_scallop.gtf -T 0.001 -F 0.001 -o ERR3639851_StringTie_merge.gtf$ stringtie\u2014merge SRR10611964_genome_stringtie.gtf SRR10611964_genome_cufflinks.gtf SRR10611964_genome_scallop.gtf -T 0.001 -F 0.001 -o SRR10611964_StringTie_merge.gtfAn illustration of running StringTie-merge with its default sets is shown below.In this protocol, we used three RNA-seq data to evaluate the performance of the assembly tools. Two of the latest mapping software, Hisat2 and Star , were emF-score, where the precision is defined as the percentage of the correctly assembled transcripts out of the candidates and recall is defined as the fraction of the correctly recovered transcripts in the ground truth, and F-score is a harmonic mean of recall and precision ) [To evaluate the performance of an assembler, we used the following metrics: the number of correctly assembled transcripts, precision, recall, and recall)) , 22.First, we compared TransBorrow to the alternatives using the data sets with different sequencing library layouts (i.e. single- or paired-end reads), and the data SRR7807492 (paired-end) and ERR3639851 (single-end) were selected as the test data. After comparison, TransBorrow exhibited superior performance in terms of the four aforementioned metrics when compared to other assemblers and SRR10611964 (strand specific). We also compared TransBorrow to other assemblers in terms of the four aforementioned metrics. Once again, TransBorrow exhibited superior performance when compared to other assemblers (see F-score, TransBorrow also reached the highest. These results provide further evidence that TransBorrow outperformed the other compared assemblers in assembling both strand-specific and nonstranded RNA-seq data.In detail, for the correctly assembled transcripts on the nonstranded RNA-seq data SRR7807492 under Hisat2 and Star mappings, TransBorrow demonstrated significant improvement as mentioned above. For the correctly assembled transcripts on the strand-specific RNA-seq data SRR10611964 under the two aligners, TransBorrow detected 11.53% and 8.80% more expressed transcripts than StringTie, 11.08% and 10.83% more than Scallop, 68.04% and 59.81% more than Cufflinks, 22.55% and 20.06% more than StringTie-merge, and 24.78% and 19.06% more than Taco. And, for the precision and As mentioned, various RNA-seq alignment tools were available for the researchers, and Hisat2 and Star are the two most widely used mappers. In order to evaluate the performance of the assemblers under different alignment tools, we used the two different aligners to generate the mapping results of the RNA-seq data. Then we compared TransBorrow to the others using the three data sets SRR7807492, ERR3639851, and SRR10611964, under both Hisat2 and Star mappings. As compared above, TransBorrow consistently demonstrated the best performance in terms of all the aforementioned accuracy metrics regardless of the alignment tools (see Developing accurate and efficient transcript assembly software is crucial for effectively processing large-scale RNA sequencing data. It enables further exploration of the transcriptome and investigations into complex human diseases, such as cancers, which are often associated with aberrant splicing events and expression levels , 24. In TransBorrow incorporates several advantages that contribute to its superior performance. First, it effectively borrows the assembly results of other software to guide its own assembly process, which combines the strengths of multiple tools. Second, TransBorrow integrates the assemblies of other assembles to build a novel graph model, namely color graph, which facilitates efficient extraction of reliable subpaths. Third, TransBorrow constructs the weighted line graph based on the splice graph and the extracted reliable subpaths. Fourth, TransBorrow introduces a new strategy for identifying transcript-representing paths from the weighted line graphs.de novo assemblies, and the relatively complex installation process. In the future, we will definitely tackle these problems.Although we have seen great advantages taken by TransBorrow, the current version of TransBorrow does have several limitations, such as the inability to assemble long reads, incompatible with In conclusion, TransBorrow stands out among existing software by accurately assembling complex raw sequencing data into expressed transcripts. By utilizing TransBorrow, researchers can effectively harness the power of RNA-seq for advanced transcriptome analysis."} +{"text": "An early gastric cancer was found on the gastric body in an 85-year-old man. Subsequently, an endoscopic submucosal dissection (ESD) was performed . AlthouVideo\u20061\u2002Successful clip closure for a delayed perforation after gastric endoscopic submucosal dissection.Delayed perforation after gastric ESD is an extremely rare complication and is often managed surgicallyEndoscopy_UCTN_Code_TTT_1AO_2AG"} +{"text": "Electroacupuncture (EA) is a beneficial physiotherapy approach for addressing neuropsychiatric disorders. Nevertheless, the impact of EA on the gut microbiome in relation to anxiety disorders remains poorly understood.To address this gap, we conducted a study using a chronic restraint stress (CRS) mouse model to investigate the anti-anxiety outcome of EA and its influence on gut microbiota. Our research involved behavioral tests and comprehensive sequencing of full-length 16S rRNA microbiomes.Our findings revealed that CRS led to significant anxiety-like behaviors and an imbalance in the gut microbiota. Specifically, we identified 13 species that exhibited changes associated with anxiety-like behaviors. Furthermore, EA partially alleviated both behaviors related to anxiety and the dysbiosis induced by CRS.In summary, this study sheds light on the alterations in gut microbiota species resulting from CRS treatment and brings new light into the connection between EA\u2019s anti-anxiety effects and the gut microbiota. They affect approximately 12.1% of the global population . These dElectroacupuncture (EA) is a modernized adaptation of traditional Chinese medicine\u2019s acupuncture, a technique known for its significant impact on the nervous, endocrine, and immune systems . EA sharThe gut-brain axis, representing the bidirectional connection between the gut microbiota and the central nervous system (CNS), is a crucial player in regulating emotions and stress. It operates through various mechanisms, including metabolic, neural, hormonal, and immune-mediated pathways . A substIn this context, our current study aimed to investigate how EA treatment impacts the gut microbiome in a murine model of CRS. This is a well-established and widely accepted stress-related anxiety model that reliably induces anxiety-like behavior . Simulta2.2.1.Male C57BL/6 mice, aged 8\u2009weeks and with a weight between 18 and 22 g, were supplied by the Animal Center of Air Force Military Medical University. These mice were group-housed in cages, with each cage accommodating four mice. They had unrestricted access to food and water and were kept in a controlled environment at a temperature of 20\u201325\u00b0C. The cages had wire bottoms, and the mice followed a 12-h light/dark cycle, with lights on from 8:00\u2009a.m. to 8:00\u2009p.m. The research procedures conducted in this study received approval from the Ethics Committee of Xi\u2019an Gaoxin Hospital under the reference number 2023-GXKY-0011. All experiments were conducted in accordance with the guidelines provided in the National Institutes of Health Guide for the Care and Use of Laboratory Animals.2.2.n\u2009=\u20098) and CRS (n\u2009=\u200916). In the CRS group, mice were exposed to CRS for 2\u2009h per day over a continuous 14-day period. This involved placing the mice in conical tubes (50\u2009mL) equipped with airflow holes. In contrast, the Control group mice were transferred from their original cage to an experimental room, delicately managed for 5\u2009min, and then transported back to their holding place 2\u2009h later. This procedure was repeated over the course of 14\u2009days for the EA procedures. Consistent with previous protocols , mice re2.4.The open field chamber used in this study was constructed from white polycarbonate and measured 50\u2009cm\u2009\u00d7\u200950\u2009cm in size. Each mouse was positioned in the middle of the chamber, and their behavior was monitored and recorded for a duration of 5\u2009min. We utilized an overhead video-tracking and analysis system acquired from Top Scan, Clever Sys Inc. (United States) for this purpose. Specifically, we measured the time that mice spent within the central area, which was a 25\u2009cm\u2009\u00d7\u200925\u2009cm square at the center of the chamber, as well as the whole distance they covered during the observation period.2.5.The maze apparatus used in our study, supplied by Dig Behav, Ji Liang Co. Ltd. (China) was comprised of two open arms (each measuring 35\u2009cm\u2009\u00d7\u20096\u2009cm) and two enclosed arms (each measuring 35\u2009cm\u2009\u00d7\u20096\u2009cm), elevated 50\u2009cm over the floor. During the testing phase, mice were initially positioned in the central square of the maze, oriented toward one of the open arms. Their behavior was then observed and recorded for 5\u2009min. We quantified the number of entries into the open arms (entry count) and the duration of placement within the open arms, employing the same monitoring system as used in the OFT. All tests occurred in low light conditions, and the test area was thoroughly sanitized with 30% ethanol after each trial.2.6.http://rdp.cme.msu.edu/. Following the OTU assignment and taxonomy analysis, subsequent analyses including Alpha Diversity Analysis, Linear Discriminant Analysis (LDA), Principal Coordinate Analysis (PCoA), and correlation analysis were performed using the Majorbio cloud platform, which is provided by Majorbio Bio-Pharm Technology Co., Ltd.Each mouse was placed in a metabolic cage between 7:00\u2009a.m. and 11:00\u2009a.m., and fecal samples were collected in sterile cryotubes, and immediately frozen in liquid nitrogen before further analysis. Undefecated mice promote defecation by lifting their tails, ensuring that each mouse collects at least one fecal sample. Genomic DNA was then obtained from these fecal samples using the E.Z.N.A. Stool DNA Kit, manufactured by Omega Bio-Tek, United States . For the2.7.p\u2009<\u20090.05 was deemed statistically significant.Statistical analyses were performed with the GraphPad v.8.0 or SPSS 21.0 software . We first assessed the normal distribution of continuous data using the Shapiro\u2013Wilk test. If the data met the criteria for normal distribution or variance homogeneity, we conducted unpaired t-tests or one-way analysis of variance (ANOVA), and subsequent Bonferroni post-hoc tests for pairwise comparisons. Alternatively, if the data did not meet these criteria, nonparametric tests such as the Wilcoxon rank-sum test or Kruskal-Wallis test were applied. To examine correlations between behaviors and gut microbiota at the species level, we utilized Spearman\u2019s rank correlation coefficient. All significance tests were two-tailed, and a significance level of 3.3.1.t\u2009=\u20090.355, df\u2009=\u200922, p\u2009=\u20090.726; t\u2009=\u20090.443, df\u2009=\u200922, p\u2009=\u20090.662; t\u2009=\u20094.535, df\u2009=\u200922, p < 0.001; t\u2009=\u20092.321, df\u2009=\u200922, p\u2009=\u20090.03; t\u2009=\u20092.654, df\u2009=\u200922, p\u2009=\u20090.015; p\u2009=\u20090.04, r2 =\u20090.258, p =\u20090.001; r2 =\u20090.281, p =\u20090.001; r2 =\u20090.124, p =\u20090.001; No significant difference was observed in the whole distance traveled in the OFT analysis, as illustrated in Muribaculaceae, Streptococcaceae and Burkholderiaceae; genus Duncaniella, unclassified_f_Muribaculaceae, Limosilactobacillus, Mammaliicoccus, Lactococcus, Ralstonia, unclassified_f_Eggerthellaceae and Streptococcus; species Ralstonia_pickettii, Streptococcus_danieliae, unclassified_g_Lactococcus, Limosilactobacillus_reuteri, Mammaliicoccus_sciuri, Odoribacter_laneus, unclassified_f_Muribaculaceae, Duncaniella_freteri, Bacteroides_caecimuris and unclassified_f_Eggerthellaceae were enriched in the Control group. Whereas phylum Candidatus_Melainabacteria; family Bacteroidaceae, Prevotellaceae, unclassified_o_Bacteroidales, unclassified_o_Vampirovibrionales, Clostridiaceae, Eubacteriaceae, unclassified_o_Rhodospirillales and Desulfovibrionaceae; genus unclassified_f_Prevotellaceae, Eubacterium, Muribaculum, Bacteroides, Vampirovibrio, unclassified_o_Bacteroidales, Oscillibacter, Phocea, Sporobacter, Acetatifactor, Phocaeicola, Mailhella, unclassified_o_Rhodospirillales, Anaerotignum, Harryflintia and Clostridium; species Harryflintia_acetispora, Bacteroides_acidifaciens, Bacteroides_uniformis, Phocaeicola_sartorii, Muribaculum_intestinale, unclassified_f_Prevotellaceae, Alistipes_finegoldii, unclassified_o_Bacteroidales, Vampirovibrio_chlorellavorus, unclassified_g_Clostridium, Eubacterium_coprostanoligenes, Acetatifactor_muris, Anaerotruncus_colihominis, Anaerotruncus_rubiinfantis, Oscillibacter_valericigenes, unclassified_g_Oscillibacter, Phocea_massiliensis, Sporobacter_termitidis, unclassified_o_Rhodospirillales, Mailhella_massiliensis and Helicobacter_bilis were enriched in the CRS group.We found distinctions in taxonomic composition between the Control and CRS groups using both LDA with a threshold of LDA\u2009\u2265\u20093 and a significance level of unclassified_o_Bacteroidales, unclassified_g_Christensenella, Odoribacter_splanchnicus, Acutalibacter_muris, Bacteroides_uniformis, Oscillibacter_valericigenes and Acetatifactor_muris; but had a positive correlation with the abundance of Lactobacillus_gasseri, Limosilactobacillus_reuteri, Akkermansia_muciniphila and Ligilactobacillus_murinus. The No. of entries into open arms had a negative correlation with the abundance of Bacteroides_acidifaciens and Eubacterium_coprostanoligenes. The time spent in center had a negative correlation with the abundance of unclassified_g_Anaerotruncus, Phocaeicola_sartorii, unclassified_f_Prevotellaceae, Mailhella_massiliensis, Vampirovibrio_chlorellavorus, Bacteroides_acidifaciens, Bacteroides_uniformis and Acetatifactor_muris; whereas it had a positive correlation with the abundance of unclassified_f_Muribaculaceae, Duncaniella_freteri, Bacteroides_caecimuris and Lactobacillus_gasseri . Notably, the application of EA (CRS\u2009+\u2009EA) partially mitigated the anxiety-like behavior induced by CRS in mice, as indicated by an increase in the time the animals stayed in the center area of the OFT and the open arms of the EPMT when compared to the CRS\u2009+\u2009fEA group (p\u2009<\u20090.05).As depicted in 3.4.r2\u2009=\u20090.131, p\u2009=\u20090.012; r2\u2009=\u20090.112, p\u2009=\u20090.159; r2\u2009=\u20090.108, p\u2009=\u20090.117; Lactobacillaceae, genus Escherichia and Olsenella, species unclassified_g_Lactobacillus, unclassified_g_Olsenella, Escherichia_fergusonii and Lactobacillus_gasseri. Meanwhile, phylum Proteobacteria; family Kiloniellaceae; genus Butyribacter and Aestuariispira; species Parabacteroides_gordonii, Aestuariispira_insulae, Parabacteroides_goldsteinii, Butyribacter_intestini, Bacteroides_uniformis, Eubacterium_coprostanoligenes and Bacteroides_acidifaciens were enriched in the CRS\u2009+\u2009fEA group. Phylum Candidatus_Melainabacteria; family Prevotellaceae and unclassified_o_Vampirovibrionales; genus Faecalimonas, Vampirovibrio and Lachnoclostridium; species Faecalimonas_umbilicata, Vampirovibrio_chlorellavorus and unclassified_g_Lachnoclostridium were enriched in CRS\u2009+\u2009EA group , separation anxiety, selective mutism, specific phobias, social anxiety disorder (SAD), panic disorder, and agoraphobia . The linive mice . Given tEA is an alternative therapeutic approach that combines traditional acupuncture techniques with electrotherapy and is increasingly recognized for its potential in treating neuropsychiatric disorders. A growing body of research has highlighted the beneficial effects of EA, particularly when applied at the \u201cBai hui\u201d (GV20) acupoint. Studies have shown that GV20-based EA can regulate basic fibroblast growth factor (FGF2) in the rat hippocampus , enhanceParasutterella and Bacteroides while decreasing the relative abundances of Dialister, Hungatella, Megasphaera, Barnesiella, Allisonella, Intestinimon and Moryella at the genus level in the treatment of Parkinson\u2019s disease has been well-declared , This in disease . Preclin disease . HoweverOur present study delved into the composition of the gut microbiome in mice subjected to CRS modeling after EA treatment. Similar to other neuromodulation therapies , EA had Lactobacillus_gasseri was more abundant in the Sham group and it was positively correlated with the number of entries into open arms. Conversely, Bacteroides_uniformis was enriched in the CRS\u2009+\u2009fEA group and negatively correlated with the number of entries into open arms and the time the subjects remained in the center. Lactobacillus_gasseri is a probiotic (Bacteroides_uniformis has been associated with the adverse effects of a depressive microbiome on behavior (Eubacterium_coprostanoligenes is a species that has a lipolytic function (Furthermore, our analysis revealed that robiotic whereas behavior . These ffunction . Its abu5.In summary, our findings highlight that CRS leads to pronounced anxiety-like behaviors and disturbances in gut microbiota composition, and these effects can be partially mitigated through EA treatment. We further investigated the specific microbial species associated with anxiety-like behaviors at the species level, identifying 13 species linked to the anxiety-like responses induced by CRS. However, it remains to be explored how longer-duration and varying parameters of EA may impact gut microbiota composition.The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author.The animal study was approved by the research procedures conducted in this study received approval from the Ethics Committee of Xi\u2019an Gaoxin Hospital under the reference number 2023-GXKY-0011. The study was conducted in accordance with the local legislation and institutional requirements.JB: Conceptualization, Investigation, Writing \u2013 original draft. J-QW: Conceptualization, Data curation, Writing \u2013 original draft. QT: Investigation, Writing \u2013 original draft. FX: Formal analysis, Funding acquisition, Writing \u2013 original draft. WZ: Methodology, Writing \u2013 original draft. HH: Conceptualization, Writing \u2013 review & editing."} +{"text": "The metabolic neighborhood of a compound can be defined from a metabolic network and correspond to metabolites to which it is connected through biochemical reactions. With the proposed approach, we suggest more than 35,000 associations between 1,047 overlooked metabolites and 3,288 diseases (or disease families). All these newly inferred associations are freely available on the FORUM ftp server (see information at https://github.com/eMetaboHUB/Forum-LiteraturePropagation).In human health research, metabolic signatures extracted from metabolomics data have a strong added value for stratifying patients and identifying biomarkers. Nevertheless, one of the main challenges is to interpret and relate these lists of discriminant metabolites to pathological mechanisms. This task requires experts to combine their knowledge with information extracted from databases and the scientific literature. However, we show that most compounds (>99%) in the PubChem database lack annotated literature. This dearth of available information can have a direct impact on the interpretation of metabolic signatures, which is often restricted to a subset of significant metabolites. To suggest potential pathological phenotypes related to overlooked metabolites that lack annotated literature, we extend the \u201cguilt-by-association\u201d principle to literature information by using a Bayesian framework. The underlying assumption is that the literature associated with the metabolic neighbors of a compound can provide valuable insights, or an Key Points:Most metabolites have little or no information available in the literature.We propose an original method leveraging information contained in the literature from metabolic neighbors.We provide more than 35000 suggested relations between overlooked metabolites and disease-related concepts.the Matthew effect = P. Under this assumption, for any contributor i, the prior distribution of ip is modeled as a Beta distribution parameterized by mean (\u03bc = P) and sample size (\u03bd):The probability portions . We assuP, a relationship would not be suggested a priori, and the higher \u03bd, the more each contributor i would have to bring new evidence (in) to change this prior belief , is much more sensitive to outlier contributors than LogOdds [LogOdds should be considered a measure of significance and Log2FC as a measure of effect size. Finally, LogOdds and Log2FC can also be computed independently for each contributor i using their associated component in the prior , only the distribution priorf is used to compute LogOdds and Log2FC. In summary, for metabolites without literature, LogOdds and Log2FC are derived from priorf, while for metabolites with literature, they are obtained from postf. For the latter, priorLogOdds and priorLog2FC are computed from the prior distribution priorf and aim to represent the belief of the metabolic neighborhood, without the influence of the compound\u2019s literature.For metabolites mentioned in few articles and with literature available in the neighborhood (2), the behavior of the method is exactly as described above. When the compound Beta(\u03b1(0), \u03b2(0)), and then the posterior distribution is Beta(\u03b1(0), \u03b2(0)) is used, but predictions are automatically discarded.There may be no literature available in the neighborhood of some metabolites. In this case, the prior distribution is simply defined by Since the construction of the prior from the neighborhood\u2019s literature is critical in the proposed method, several diagnostic values are also reported to judge its consistency. Those additional indicators are detailed in Project name: Forum-LiteraturePropagationhttps://github.com/eMetaboHUB/Forum-LiteraturePropagationProject homepage: Operating system(s): Platform independentProgramming language: Python, bash scriptOther requirements: Python 3.7, Pip, CondaLicense: CeCILL 2.1RRID: SCR_023874giad065_GIGA-D-23-00014_Original_SubmissionClick here for additional data file.giad065_GIGA-D-23-00014_Revision_1Click here for additional data file.giad065_GIGA-D-23-00014_Revision_2Click here for additional data file.giad065_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giad065_Response_to_Reviewer_Comments_Revision_1Click here for additional data file.giad065_Reviewer_1_Report_Original_SubmissionBiswapriya Misra -- 2/25/2023 ReviewedClick here for additional data file.giad065_Reviewer_2_Report_Original_SubmissionTara Eicher, M.S. -- 3/3/2023 ReviewedClick here for additional data file.giad065_Reviewer_2_Report_Revision_1Tara Eicher, M.S. -- 6/22/2023 ReviewedClick here for additional data file.giad065_Reviewer_3_Report_Original_SubmissionBrian DeFelice -- 3/15/2023 ReviewedClick here for additional data file.giad065_Reviewer_3_Report_Revision_1Brian DeFelice -- 6/22/2023 ReviewedClick here for additional data file.giad065_Supplemental_FileClick here for additional data file."} +{"text": "This novel device appears to be a promising new method for weight reduction that is fast, feasible, and safe . RandomEndoscopy_UCTN_Code_TTT_1AO_2AN"} +{"text": "To identify sets of genes that exhibit similar expression characteristics, co-expression networks were constructed from transcriptome datasets that were obtained from plant samples at various stages of growth and development or treated with diverse biotic, abiotic, and other environmental stresses. In addition, co-expression network analysis can provide deeper insights into gene regulation when combined with transcriptomics. The coordination and integration of all these complex networks to deduce gene regulation are major challenges for plant biologists. Python and R have emerged as major tools for managing complex scientific data over the past decade. In this study, we describe a reproducible protocol POTFUL (pant co-expression transcription factor regulators), implemented in Python 3, for integrating co-expression and transcription factor target protein networks to infer gene regulation. Drosophila melanogaster, the collective profile of gene expressions in each cell type or tissue does not remain static, since genes are continuously regulating each other ][\u2018GMT\u2019]))# GMT_base/POTFUL-Uncut.gmt# GMT_base/POTFUL-3hpc.gmtf.fig = POT.Plots[Samples[0]][\u2018WGCNA_BarPlot\u2019]fig.show# fig = POT.Plots[Samples[1]][\u2018WGCNA_BarPlot\u2019]fig.show# Using the following Python script, a bar chart of the numbers of the genes in each WGCNA module for each dataset was created a,b:fig Note: The \u201cfig\u201d is a Plotly figure object that can be further modified accordingly to export a publication quality image, as described below:fig.update_layout\u2019,\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0font=dict)fig.update_xaxesfig.update_yaxesfig.write_imagefig.write_imageg.p-value was calculated (hypergeometric test), indicating whether the overlap between the two module gene lists is significant. As the background parameter, the nodes of both co-expression networks that were being compared were used. For assigning significance color codes and significance asterisks, only \u2018Adjusted p-value\u2019 is considered by default. An enrichment analysis of modules was performed of one sample concerning another sample using the following command:POT.WGCNA_Module_EnrichmentUsing Fisher\u2019s exact test, the Note: The results of the module enrichment analysis can be accessed as a Python (Pandas) dataframe using the following command:print(POT.Data[\u201cEnrichment_Dotplot\u201d])h.fig = POT.Plots[\u201cEnrichment_Dotplot\u201d]fig.update_layout)fig.write_imagefig.write_image(POT.OutDir+f\u201d3hpc__UncutEnri_dot.svg\u201d)# Using the following Python command, the enrichment dot plot was generated, and a high-quality image was exported. Every dot in the enrichment dot represents the significance of the enrichment, i.e., green (***), gold (**), and yellow (*). In contrast, the plus (+) symbol represents not significantly enhanced sets.Note: Each WGCNA module of samples on the y-axis (uncut) was compared to samples on the x-axis (3hpc). The order of samples in the \u201cWGCNA_Module_Enrichment\u201d function was changed to do the comparison in the other direction, i.e., (uncut vs. 3hpc) ). Additionally, the \u201cWGCNA_Module_Enrichment\u201d function only accepts two samples.Duration: 5 mina.# UncutPOT.TF_reg# 3hpcPOT.TF_reg(Samples[1])The TF\u2013target pairs that did not belong to the known curated TF\u2013target pairs were filtered out using the following Python command for each sample:Note: We could choose whether to do this step or not. We included this choice to help deal with large numbers of TF\u2013target pairs created by prediction tools like GENI3. The purpose of removing some pairs is to make the analysis smoother, especially when there are many of pairs to go through.b.# UncutPOT.merge_reg_coexp(Samples[0])# 3hpcPOT.merge_reg_coexp(Samples[1])Using the following Python command, the remaining GRN-weighted network was matched with the co-expression network to keep only those pairs that are co-expressed and involved in regulation:Note: The network of node pairs that are co-expressed and are TF\u2013target pairs is called the co-expressed\u2013GRNs.c.# UncutPOT.network_centrality(Samples[0])# 3hpcPOT.network_centrality(Samples[1])Network centrality analysis was performed on the co-expressed\u2013GRN using the following command # 3hpcPOT.generate_graphml_out(Samples[1])The GraphML file was generated, and the network visualized using the following command (see e.# UncutPOT.Graph_vis(Samples[0])POT.Plots[Samples[0]][\u2018Network_Viz\u2019] .show(POT.OutDir+\u2019Uncut.html\u2019)# # 3hpcPOT.Graph_vis(Samples[1])POT.Plots[Samples[1]][\u2018Network_Viz\u2019] .show(POT.OutDir+\u20193hpc.html\u2019)# The CERN was plotted and exported using the following command:f.POT.netowork_overlap# There are 20 nodes overlapping between pair of GraphsPOT.Plots[\u2018Overlap_Network_Viz\u2019].show(\u2018Overlap.html\u2019)# The co-expressed\u2013GRNs of both samples were compared and plotted to check for any overlapping nodes, using the following command:"} +{"text": "Endoscopic resection of duodenal gastrointestinal stromal tumors (GISTs) is challenging with non-negligible complicationsA 59-year-old man was referred for a 2-cm muscle-origin tumor in the duodenal bulb ; the diVideo\u20061\u2002Endoscopic suturing can rescue the defect of endoscopic full-thickness resection for a duodenal gastrointestinal stromal tumor.Endoscopy_UCTN_Code_TTT_1AO_2AC"} +{"text": "Peroral endoscopic myotomy (POEM) is an increasingly adopted strategy for the treatment of Zenker\u2019s diverticulum . The Z-Video\u20061\u2002Peroral endoscopic myotomy for Zenker\u2019s diverticulum without tunneling.After the initial mucosal incision, both submucosal sides of the septum are lifted, with a mixture of hydroxyethyl starch and indigo carmine. Then we proceed to direct myotomy of the septum . The diEndoscopy_UCTN_Code_TTT_1AO_2AGCitation Format10.1055/a-2127-7402.Endoscopy 2023; 55: E946\u2013E948. doi:"} +{"text": "The authors demonstrate that scRNA-seq sample pooling followed by genetics-based separation of individuals is an effective means to identify individual samples in a variety of commonly studied species. Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address these problems is pooling cells from multiple individuals into one sc-seq library. In humans, genotype-based computational separation of pooled sc-seq samples is common. This approach would be instrumental for studying non-isogenic model organisms. We set out to determine whether genotype-based demultiplexing could be more broadly applied among species ranging from zebrafish to non-human primates. Using such non-isogenic species, we benchmark genotype-based demultiplexing of pooled sc-seq datasets against various ground truths. We demonstrate that genotype-based demultiplexing of pooled sc-seq samples can be used with confidence in several non-isogenic model organisms and uncover limitations of this method. Importantly, the only genomic resource required for this approach is sc-seq data and a de novo transcriptome. The incorporation of pooling into sc-seq study designs will decrease cost while simultaneously increasing the reproducibility and experimental options in non-isogenic model organisms. Over the last decade, single-cell RNA sequencing (scRNA-seq) has exploded in popularity as a species agnostic tool for studying gene expression at the level of individual cells . The bigIn fields working with low cell numbers, like developmental biology, pooling of samples from multiple animals with no sample labeling method, or intention of demultiplexing has become a standard practice. This approach lacks advantages of true replicates because there is no way to assess the data for representation of all samples or variation between samples. The inability to demux pooled samples thus lacks the ability to account for replicate variation and perform replicate strengthened differential expression analysis . BecauseMethods for analyzing pooled data and for enabling the demultiplexing of pooled scRNA-seq samples are varied in concept and accuracy and have been recently reviewed . To presIn contrast to these experimental demultiplexing approaches, computational methods have been developed to demultiplex pooled human samples without any labeling regimen using the natural genetic differences between individuals. These approaches detect genetic differences between samples at sites of single-nucleotide polymorphisms (SNPs) and implement demultiplexing based on differential distributions of these SNPs between samples. SNP-based approaches have been benchmarked and shown to be highly effective at separating human samples . RelativIn this project, we set out to learn whether SNP-based demultiplexers work in an array of non-human species. We benchmarked available SNP-based demultiplexing programs and found that most are highly accurate on model organism datasets. We then selected the demultiplexing tool with the broadest potential usability, souporcell , to moreWe first explored the performance of SNP-based demultiplexing methods when applied to a published zebrafish dataset. Two useful resources for applying SNP-based demultiplexing are available for zebrafish, a high-quality genome , and a chttps://github.com/statgen/popscle; After processing each zebrafish scRNA-seq sample individually, we performed in silico pooling of three samples . This syComparison of compute requirements for SNP demuxers.Table S1. To further investigate the demultiplexing accuracy of souporcell, SNP-based cell assignments were assessed for correlations with ground truth animal origin. We found a strong agreement between souporcell assignments and ground truth animal identities . We thenThe presence of doublets in single-cell RNA sequencing is a major confounder. A doublet is a droplet represented by a single-cell barcode that contains more than one cell. In these in silico pools, true doublets can be identified with absolute certainty because we have origin information. When comparing SNP-based demultiplexing results to ground truth, \u201cconfirmed doublets\u201d are cells that were assigned doublets by both the ground truth and demuxer. Furthermore, \u201ccontested doublet\u201d refers to cells in which the experimentally derived ground truth and SNP-based demuxer result disagree about a potential doublet. We thus investigated the doublet detection capacity of souporcell for heterotypic true doublets . Homotypic true doublets created during synthetic pooling were removed, as souporcell relies on intergenotypic doublet detection. We found that souporcell missed almost half of the synthetic heterotypic true doublets in the pooled dataset . The relWe next decided to in silico benchmark these SNP demultiplexers on another potentially inbred population, the African green monkey. The African green monkey is a pre-clinically relevant species, with a published genome and SNP Finally, we also assessed results of SNP-based demultiplexing of synthetically pooled single-nuclei data from axolotl. The axolotl is an example of the type of organism for which scRNA-seq has enabled cell level study of regeneration and immunology for the first time . A genom6 total SNPs and indels . In comparison to the inbred mouse strains, the SNP density of the successfully demultiplexed datasets was higher at 0.34/kb (axolotl), 0.86/kb (African green monkey), and 3.57/kb (zebrafish). Although an exact quantitative analysis of this possible genetic cutoff would be useful, these results imply that a range of 0.2\u20130.34 SNPs/kb may be the minimum required within a sc-seq dataset for SNP-based demultiplexing.Xenopus laevis scRNA-seq data containing eight experimentally pooled samples from three Xenopus transgenic lines that each overexpress a different fluorescent gene Xenopus ly genome .Xenopus transgenic line of origin, the low number of fluorescent gene counts left many cells without sufficient data to make an assignment prediction but no available common SNPs VCF file. We first set out to assess souporcell demux assignments on pooled splenocytes from three transgenic Pleurodeles newts, which express different fluorescent proteins under the same ubiquitous promoter (CAG) . We desier (CAG) .Xenopus analysis, we selected only cells that had sufficient read depth and fluorescent gene detection for benchmarking . The heterogeneity of sample representation in different cell clusters highlights the critical need for demultiplexing of pooled scRNA-seq data (As performed in the hmarking . We founhmarking . The fluhmarking and S8H.hmarking . Furtherseq data . WithoutPleurodeles scRNA-seq data (Xenopus data). Similar to the Xenopus dataset, we attribute these fluorescence-based \u201cnegative\u201d assignments to the low capture of fluorescent gene reads . It is more likely that these large pool experiments occur in non-human samples. Thus, to aid future validations, we provide examples and modified memory-efficient scripts to pool samples and determine accuracy which will aid laboratories\u2019 working in any species to conduct their own benchmarking. In addition, this memory-efficient script allows for pooling without a VCF file, which will be critical for all researchers interested in benchmarking SNP demuxers in organisms without VCF files available. Once upper limits become established, another option to increase throughput would be layered multiplexing, for example, labeling 10 individuals with a CMO, another 10 with a second CMO, and so on. This could be paired with a second SNP-based demultiplexing step and could substantially expand sample throughput.It will also be important to define the upper limit for the number of distinct pooled samples followed by SNP-based demuxing for each organism. In line with this, we obtained assignments when performing SNP-based demultiplexing on a pool of 30 zebrafish samples. However, without a benchmarking assessment from a ground truth derived from a distinct technology, it is uncertain if these results can be trusted. We therefore propose that using SNP-based demultiplexers on large pools needs to be further validated. This can be performed in silico as more single-replicate scRNA-seq datasets become published. Until then, the developers of souporcell indicate that 21 pooled human samples can be demultiplexed and speculate that this could work in up to 40 . Multiple independent programs designed specifically for doublet detection using transcriptomic instead of genotypic information are available for scRNA-seq data including DoubletDetection , we modified the default souporcell pipeline to enable remapping of reads studies will greatly expand single-cell\u2013based discoveries. This will facilitate work in well-known and lesser studied species by lowering the financial and technical hurdles of producing adequately powered single-cell experiments. We predict that both species agnostic and cross-species comparative studies are going to be increasingly fruitful in uncovering biological insights and the application of SNP-based demultiplexing with minimal genomic resources is critical for future research.P. waltl and N. viridescens at Karolinska Institutet and were performed according to local and European ethical permits. N. viridescens and P. waltl were raised in-house. All animals were maintained under standard conditions of 12-h light/12-h darkness at 18\u201324\u00b0C , 20 ml of Yokuchi Bitamin Multivitamin and 10 ml of calcium supplementation into 100 Liters of water). For Pleurodeles and Notophthalmus in the Cellplex experiment, animals were housed in the water as described but modified to only have sea salt, Ektozon, and calcium solution.All experiments were carried out in post-metamorphic 18\u201324\u00b0C . Before P. waltl and processed as individual samples in parallel. All animals were post-metamorphic newts from established transgenic lines close to sexual maturity: one female tgTol2(CAG:Nucbow CAG:Cytbow)Simon were 85%, 98.4%, and 91.6% in eBFP, eGFP, and mCherry animals, respectively. FACS was used to sort for fluorescent-positive cells (Spleens were harvested from three separate length) , one mal11.1 cm) , and fem10.8 cm) . Forcepsve cells . The sam5 cells of GFP+, 4 \u00d7 105 of mCherry+, and 3.15 \u00d7 105 BFP+ were isolated in individual 1.5 ml Eppendorf tubes. GFP and mCherry expression were high, but BFP expression was dim. 500 \u03bcl of each solution was then added to an individual 1.5 ml Eppendorf tube for the fluorescent pool sample were excN. viridescens (4.45 g and 10.6 cm snout-to-tail) and one male N. viridescens (3.55 g and 10.2 cm) were collected, pooled into one tube, and then processed as described in \u201cfluorescence-pooling experiment\u201d excluding FACS cell sorting. The only modification to the above described processing is that cells were kept at room temperature throughout and that cells were resuspended in 0.7X PBS with 0.04% ultrapure BSA.Spleens from one female P. waltl, spleens were removed from animals as described in \u201cfluorescent-pooling experiment\u201d from one adult tgSceI(CAG:loxP-GFP-loxP-Cherry)Simon female (23.5 g and 16.1 cm snout-to-tail length), one male tgSceI(CAG:loxP-GFP-loxP-Cherry)Simon (13.95 g and 15.7 cm) animal. Pleurodeles were processed as individual samples. After the spleen was thoroughly mashed through the pre-wetted 70-\u03bcm nylon filter and the filter being washed with 10 ml of 0.7X PBS, the cells were centrifuged at 300g for 5 min. Splenocytes were resuspended cells in 1 ml of sterile filtered 1X ACK (http://cshprotocols.cshlp.org/content/2014/11/pdb.rec083295.short) to lyse red blood cells. After one minute of lysis, cells were diluted with 10 ml of 0.7X PBS and filtered through a 70-\u03bcm nylon mesh filter and centrifuged at 300g for 5 min. Cells were then resuspended in 0.7X PBS with 0.04% ultrapure BSA.For Notophthalmus sample and the individual Pleurodeles samples were then taken through the 10x Genomics 3\u2032 Cellplex\u2013labeling protocol the only modifications being the use of 0.7X PBS + 0.04% BSA for all wash and resuspension steps. Samples were stained with CM304 , CMO305 , and CMO306 . Samples were manually counted and pooled at equal ratios immediately before loading onto the 10x Genomics Chromium Controller targeting 9,000 cells in total.The pooled Chromium single-cell 3\u2032 kit v3 (10x Genomics) was used according to the manufacturer\u2019s instructions.P. waltl de novo transcriptome from the study of https://figshare.com/articles/dataset/Trinity_Pwal_v2_fasta_gz/7106033/1 and unzipped. The Trinity were downloaded from SRA using prefetch followed by fasterq-dump with flags split-files and include-technical. Files were renamed to 10x FASTQ format and then aligned using Cell Ranger v7.0.0 count to GRCz11 with the corresponding gtf for GRCz11 filtered via Cell Ranger mkgtf for protein_coding genes.FASTQ files from a previously published study (SRA acchttps://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/downloads/NHGRI-1/danRer11/danRer11Tracks/NHGRI1.danRer11.variant.vcf.gz and https://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/downloads/NHGRI-1/danRer11/danRer11Tracks/NHGRI1.danRer11.variant.vcf.gz.tbi (Preprint).To merge bams in silico, a VCF file and tbi index were downloaded from f.gz.tbi and subsf.gz.tbi Preprintexec Demuxafy.sif bcftools filter --include \u201cMAF \u2265 0.05\u201d -Oz --output NHGRI1.maf0.05.danRer11.variant.vcf.gz NHGRI1.danRer11.variant.vcf.gzsingularity exec Demuxafy.sif bcftools sort -Oz NHGRI1.maf0.05.danRer11.variant.vcf.gz -o sorted.NHGRI1.maf0.05.danRer11.variant.vcf.gzsingularity The chromosomes between the vcf and gtf did not match so bcftools annotate --rename-chrs was used to change chromosome names in the VCF using a tab-separated file named chr.conv.txt with the format: chr1 1, chr2 2, etc.exec Demuxafy.sif bcftools annotate --rename-chrs chr.conv.txt sorted.NHGRI1.maf0.05.danRer11.variant.vcf.gz | singularity exec Demuxafy.sif bgzip > rename.sorted.NHGRI1.maf0.05.danRer11.variant.vcf.gzsingularity The sample-specific bam outputs were then merged using Vireo\u2019s synth_pool.py script as follows:python synth_pool.py -s sample1_genome_bam.bam,sample2_genome_bam.bam,sample3_possorted_genome_bam.bam -b sample1/outs/filtered_feature_bc_matrix/barcodes.tsv,sample2/outs/filtered_feature_bc_matrix/barcodes.tsv,sample3/outs/filtered_feature_bc_matrix/barcodes.tsv -d 0.1 -o three_mixed_zf -p 1 -r NHGRI1.maf0.05.danRer11.variant.vcf.gz --randomSEED 50 --nCELL 500.Souporcell was run using souporcell_pipeline.py with inputs: merged BAM output from synth_pool.py, the output barcodes_pool.tsv from synth_pool.py, the genome fasta (Danio_rerio.GRCz11.dna.primary_assembly.fa), N = 3, and vcf file NHGRI1.maf0.05.danRer11.variant.vcf.gz.exec Demuxafy.sif souporcell_pipeline.py -i pooled.bam -b barcodes_pool.tsv -f Danio_rerio.GRCz11.dna.primary_assembly.fa -t 20 -o output -k 3 --common_variants NHGRI1.maf0.05.danRer11.variant.vcf.singularity We found that Freemuxlet failed when using the downloaded VCF file but was successful when inputting the VCF and minimap.bam generated via souporcell when running souporcell without a VCF. This implies that Freemuxlet may be able to be fed a sample-derived VCF . An example of a VCF that worked:exec Demuxafy.sif freebayes -f Danio_rerio.GRCz11.dna.primary_assembly.fa -iXu -C 2 -q 20 -n 3 -E 1 -m 30 -g 100,000 souporcell_minimap_tagged_sorted.bam > zf.freebayes.vcfsingularity exec Demuxafy.sif popscle dsc-pileup --sam pooled.bam--group-list barcodes_pool.tsv --vcf zf.freebayes.vcf --out $FREEMUXLET_OUTDIR/pileupsingularity exec Demuxafy.sif popscle freemuxlet --plp $FREEMUXLET_OUTDIR/pileup --out $FREEMUXLET_OUTDIR/freemuxlet --group-list barcodes_pool.tsv --nsample 3singularity exec Demuxafy.sif bash Freemuxlet_summary.sh $FREEMUXLET_OUTDIR/freemuxlet.clust1.samples.gz > $FREEMUXLET_OUTDIR/freemuxlet_summary.tsvsingularity Then Freemuxlet:\u201c{print $1}\u201d chromosomes.txt | paste -s -d, > chr.list.vireo.txtsingularity exec Demuxafy.sif samtools idxstats pooled.bam > chromosomes.txtawk exec Demuxafy.sif cellsnp-lite -s pooled.bam -b barcodes_pool.tsv -O $OUT_DIR -p 20 --chrom \u201c$(<${DemuxSoupDir}chr.list.vireo.txt)\u201d --minMAF 0.1 --minCOUNT 100 --gzipsingularity exec${DemuxSoupDir}Demuxafy.sif vireo -c $OUT_DIR -o $OUT_DIR -N $N.singularity Vireo:exec Demuxafy.sif samtools view -b -S -q 10 -F 3844 pooled.bam > $SCSPLIT_OUTDIR/filtered_bam.bamsingularity exec Demuxafy.sif samtools rmdupsingularity $SCSPLIT_OUTDIR/filtered_bam.bam$SCSPLIT_OUTDIR/filtered_bam_dedup.bamexec Demuxafy.sif samtools sort -osingularity $SCSPLIT_OUTDIR/filtered_bam_dedup_sorted.bam$SCSPLIT_OUTDIR/filtered_bam_dedup.bamexec Demuxafy.sif samtools indexsingularity $SCSPLIT_OUTDIR/filtered_bam_dedup_sorted.bamexec Demuxafy.sif freebayes -fsingularity Danio_rerio.GRCz11.dna.primary_assembly.fa -iXu -C 2 -q 1$SCSPLIT_OUTDIR/filtered_bam_dedup_sorted.bam >$SCSPLIT_OUTDIR/freebayes_var.vcfexec Demuxafy.sif vcftools --gzvcfsingularity $SCSPLIT_OUTDIR/freebayes_var.vcf --minQ 30 --recode --recode-INFO-all --out $SCSPLIT_OUTDIR/freebayes_var_qual30exec Demuxafy.sif scSplit count -csingularity NHGRI1.maf0.05.danRer11.variant.vcf -v$SCSPLIT_OUTDIR/freebayes_var_qual30.recode.vcf -i$SCSPLIT_OUTDIR/filtered_bam_dedup_sorted.bam -b barcodes_pool.tsv -r$SCSPLIT_OUTDIR/ref_filtered.csv -a $SCSPLIT_OUTDIR/alt_filtered.csv -o $SCSPLIT_OUTDIRexec Demuxafy.sif scSplit run -rsingularity $SCSPLIT_OUTDIR/ref_filtered.csv -a $SCSPLIT_OUTDIR/alt_filtered.csv -n 3 -o $SCSPLIT_OUTDIRexec Demuxafy.sif scSplit genotype -rsingularity $SCSPLIT_OUTDIR/ref_filtered.csv -a $SCSPLIT_OUTDIR/alt_filtered.csv -p $SCSPLIT_OUTDIR/scSplit_P_s_c.csv -o $SCSPLIT_OUTDIRexec Demuxafy.sif bash scSplit_summary.shsingularity $SCSPLIT_OUTDIR/scSplit_result.csv.scSplit:SRR12067711\u2013SRR12067712) using prefetch followed by fasterq-dump with flags split-files and include-technical. Files were renamed to 10x FASTQ format and then aligned using Cell Ranger v7.0.0 count to GRCz11 with the corresponding gtf for GRCz11 filtered via Cell Ranger mkgtf for protein_coding genes. The output possorted_genome_bam.bam and filtered barcodes.tsv file were then used to run souporcell:A previously published dataset of 30 pooled zebrafish embryos was downexec Demuxafy.sif souporcell_pipeline.py -i possorted_genome_bam.bam -b barcodes.tsv -f Danio_rerio.GRCz11.dna.primary_assembly.fa -t $THREADS -o $SOUPORCELL_OUTDIR -k 30 --common_variants NHGRI1.maf0.05.danRer11.variant.vcfsingularity https://github.com/RegenImm-Lab/SNPdemuxPaper.The clusters.tsv file output from souporcell was then used to evaluate cluster distribution of cells. Code for this is the basis for https://sra-pub-src-2.s3.amazonaws.com/SRR13600554/107606_Xen_Pool_BL7_10_14dpa.bam.1) from a previously published publicly available dataset , three blastemas of three siblings , and three samples from three siblings were download directly. SAMtools (https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5057nnn/GSM5057661/suppl/GSM5057661_107606_Xen_Pool_BL7_10_14dpa_barcodes.tsv.gz), X. laevis genome FASTA (https://sra-pub-src-2.s3.amazonaws.com/SRR13600553/Xenbase_v9.2.fa.1), and N = 8. Note: this specific reference includes the plasmid sequences necessary for mapping to fluorescent sequences.The Cell Ranger BAM file ( dataset of fluorSAMtools was usedE-MTAB-11662) labeled \u201creseq\u201d and from samples D_1, L_1, and M_1, three individual animals all run on individual wells on a 10x Genomics chip were downloaded. To make a Cell Ranger reference, the axolotl genome (AmexG_v6.0-DD) was downloaded from https://www.axolotl-omics.org/dl/AmexG_v6.0-DD.fa.gz along with a gtf (AmexT_v47-AmexG_v6.0-DD.gtf) https://www.axolotl-omics.org/dl/AmexT_v47-AmexG_v6.0-DD.gtf.gz, which required the removal of white space for use with Cell Ranger (v7.0.0) mkref. Cell Ranger count was run on each library individually, resulting in three position\u2013sorted BAM files from samples D_1, L_1, and M_1. BAM files were merged using synth_pool.py from Vireo which was filtered using BCFtools v1.11.FASTQ files from a previously published axolotl om Vireo using th\u201cMAF \u2265 0.05\u201d -Oz --output ddMale.common_maf0.05.vcf.gz ddMale_to_AmexGv6.vcf and then sorted:bcftools filter --include bcftools sort -Oz ddMale.common_maf0.05.vcf -o sorted.ddMale.common_maf0.05.vcf.gzBarcodes.tsv files were obtained from filtered outputs of Cell Ranger count for each library. Doublet rate (-d) was set to 0.1 and --randomSEED 50.python synth_pool.py -s /D_1/outs/possorted_genome_bam.bam,/L_1/outs/possorted_genome_bam.bam,/M_1/outs/possorted_genome_bam.bam /D_1/filtered_feature_bc_matrix/barcodes.tsv,/L_1/outs/filtered_feature_bc_matrix/barcodes.tsv,/M_1/outs/filtered_feature_bc_matrix/barcodes.tsv -d 0.1 -o pooled_bam -p 1 -r sorted.ddMale.common_maf0.05.vcf.gz --randomSEED 50.Note: we only expected the troublet portion of souporcell to be capable of detecting heterotypic doublets, so for downstream analysis of this synthetically pooled data, we removed all homotypic doublets.The pooled BAM was indexed using SAMtools index-c which made a .csi index and was renamed to have a .bai file extension for use in souporcell. Souporcell was run using souporcell_pipeline.py with inputs: merged BAM output from synth_pool.py, the output barcodes_pool.tsv from synth_pool.py, the genome fasta (AmexG_v6.0-DD.fa), N = 3, VCF file ddMale.common_maf0.05.vcf.gz, and --skip_remap SKIP_REMAP.exec Demuxafy.sif souporcell_pipeline.py -i pooled.bam -b barcodes_pool.tsv -f AmexG_v6.0-DD.fa -t 20 -o output -k 3 --skip_remap SKIP_REMAP --common_variants ddMale.common_maf0.05.vcfsingularity SRR12507774\u2013SRR12507781), AGM3_Mediastinal Lymph Node (SRR12507790\u2013SRR12507797), AGM5_Mediastinal Lymph Node (SRR12507806\u2013SRR12507813), AGM7_Mediastinal Lymph Node (SRR12507822\u2013SRR12507829), and AGM9_Mediastinal Lymph Node (SRR12507846\u2013SRR12507853). C. aethiops has a robust VCF file available (European Variation Archive: PRJEB7923) that needs to be used in conjunction with genome assembly Chlorocebus_sabeus 1.1 (GCA_000409795.2). This assembly did not have an annotation file available, and we generated a gtf file for this GenBank assembly using minimap2 to create BAMs with these high quality cells. BAMs were subsequently merged using Vireo:Because of low reads/cell in these libraries, we selected barcodes using Seurat with between 1,000 and 2,000 features. These filtered barcode files were used with 10x subset-bam \u201d -Obarcodes_pool.tsv --chrom $VIREO_OUTDIR -p 20 --minMAF 0.1 --minCOUNT 100 --gzipexec Demuxafy.sif vireo -c $VIREO_OUTDIR -o $VIREO_OUTDIR -N 5.singularity And then cellsnp-lite and Vireo were run:exec Demuxafy.sif samtools view -b -S -q 10 -F 3844 pooled.bam > $SCSPLIT_OUTDIR/filtered_bam.bamsingularity exec Demuxafy.sif samtools rmdupsingularity $SCSPLIT_OUTDIR/filtered_bam.bam$SCSPLIT_OUTDIR/filtered_bam_dedup.bamexec Demuxafy.sif samtools sort -osingularity $SCSPLIT_OUTDIR/filtered_bam_dedup_sorted.bam$SCSPLIT_OUTDIR/filtered_bam_dedup.bamexec Demuxafy.sif samtools index $SCSPLIT_OUTDIR/filtered_bam_dedup_sorted.bamsingularity exec Demuxafy.sif freebayes -fsingularity $SCSPLIT_OUTDIR/filtered_bam_dedup_sorted.bam >GCF_000409795.2_Chlorocebus_sabeus_1.1_cds_from_genomic.fna -iXu -C 2 -q 1 $SCSPLIT_OUTDIR/freebayes_var.vcfexec Demuxafy.sif vcftools --gzvcfsingularity $SCSPLIT_OUTDIR/freebayes_var.vcf --minQ 30 --recode --recode-INFO-all --out $SCSPLIT_OUTDIR/freebayes_var_qual30exec Demuxafy.sif scSplit count -csingularity $SCSPLIT_OUTDIR/freebayes_var.vcf -v$SCSPLIT_OUTDIR/freebayes_var_qual30.recode.vcf -i$SCSPLIT_OUTDIR/filtered_bam_dedup_sorted.bam -b barcodes_pool.tsv -r$SCSPLIT_OUTDIR/ref_filtered.csv -a $SCSPLIT_OUTDIR/alt_filtered.csv -o $SCSPLIT_OUTDIRexec Demuxafy.sif scSplit run -rsingularity $SCSPLIT_OUTDIR/ref_filtered.csv -a $SCSPLIT_OUTDIR/alt_filtered.csv -n $N -o $SCSPLIT_OUTDIRexec Demuxafy.sif scSplit genotype -rsingularity $SCSPLIT_OUTDIR/ref_filtered.csv -a $SCSPLIT_OUTDIR/alt_filtered.csv -p $SCSPLIT_OUTDIR/scSplit_P_s_c.csv -o $SCSPLIT_OUTDIRexec Demuxafy.sif bash scSplit_summary.shsingularity $SCSPLIT_OUTDIR/scSplit_result.csvscSplit:Pleurodeles SuperTranscriptome FASTA and gtf files to produce a Cell Ranger compatible reference. Cell Ranger 7.0.0 count command was then used to map and count reads over the transcriptome for the three transgenic animal scRNA-seq dataset.Cell Ranger 7.0.0 mkref command was used with the above listed Preprint) singularity image (image version 1.0.3). The remapping and variant calling stages of souporcell were run externally because of problems with timeouts on the remapping process with the large salamander transcriptome, and issues with the souporcell internal freebayes command failing. The VCF from freebayes was then used in souporcell pipeline with the --skip_remap SKIP_REMAP and--common_variants ${VCF}. Full scripts used for souporcell processes are included below. Summary of souporcell run details can be found in Souporcell -related export\u201c${DemuxSoupDir},${MappingAnalysisDir},${FastaDir}\u201dSINGULARITY_BIND = exec${DemuxSoupDir}Demuxafy.sif renamer.py --bam $BAM --barcodes $BARCODES --out ${OutputName}.fqsingularity exec${DemuxSoupDir}Demuxafy.sif minimap2 -ax splice -I 9 G -t 20 -G50k -k 11 -K 50M -w 15 --sr -A2 -B8 -O12,32 -E2,1 -r200 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g2000 -2K50m --secondary = no ${FASTA}${OutputName}.fq > minimap.samsingularity exec${DemuxSoupDir}Demuxafy.sif retag.py --sam minimap.sam --out minimap_tagged.bamsingularity exec${DemuxSoupDir}Demuxafy.sif samtools sort minimap_tagged.bam > minimap_tagged_sorted.bamsingularity exec${DemuxSoupDir}Demuxafy.sif samtools index minimap_tagged_sorted.bamsingularity #freebayes run:exec${DemuxSoupDir}Demuxafy.sif freebayes -f ${FASTA} -iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 6 minimap_tagged_sorted.bam > free.vcfsingularity #souporcell run.${CurrentAnalysisDir}free.vcfVCF = exec${DemuxSoupDir}Demuxafy.sif souporcell_pipeline.py -i ${CurrentAnalysisDir}minimap_tagged_sorted.bam -b ${BARCODES} -f ${FASTA} -t 20 -o ${OutputName} -k $N --skip_remap SKIP_REMAP --common_variants ${VCF}singularity Pleurodeles and Notophthalmus dataset was then mapped to this dual species index using Cell Ranger 7.0.0 count command. In addition, the Cell Ranger 7.0.0 multi-command was used to assess multiplexing Cellplex information for all cells in the same dataset. For the Cell Ranger multi-command, the following flags were used: . Souporcell demultiplexing was run identically to above on the Pleurodeles only samples but with N = 4, and the relevant FASTQ and dual species reference transcriptome FASTA files.A dual species Cell Ranger 7.0.0 reference was made using the SuperTranscriptomes and corresponding gtf files (described above) from the two species using Cell Ranger mkref command. The two species, four animal, pooled scRNA-seq from SRR15502048, SRR15502052, and SRR15502056 (https://sra-pub-src-1.s3.amazonaws.com/SRR20079758/WT3_possorted_genome_bam.bam.1wget https://sra-pub-src-1.s3.amazonaws.com/SRR20079759/WT2_possorted_genome_bam.bam.1wget https://sra-pub-src-2.s3.amazonaws.com/SRR20079760/WT1_possorted_genome_bam.bam.1.wget C57BL/6 data were downloaded from 15502056 . For DBA15502056 possortehttps://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) and Cell Ranger 7.0.0 count command was then used to map and count reads from each strain and dataset.bamtofastq v1.4.1 was used to generate FASTQ files for subsequent mapping. A Cell Ranger reference was obtained from the 10x Genomics website . To enable more widespread use, we now stabilized memory use throughout the pooling and added an option (--noregionFile) which can pool in the absence of a VCF file. This means that species that do not possess a VCF file can still do the in silico ground truth benchmarking we performed in this study. A pull request has been initiated to propagate the changes to Vireo\u2019s main GitHub repository (https://github.com/single-cell-genetics/vireo/pull/81). The modified version was used to pool the mouse data below. Note: if the pull request is accepted then calling the synth_pool.py script from Vireo\u2019s GitHub repository will in fact be this modified script with new options added. This script can produce identical pooled BAM files to the original.To pool bams, we modified the original synth_pool.py script from Vireo\u2019s GitHub repository which was memory intensive and only allowed for pooling in the presence of a VCF file *100. For Vireo, the \u201cfinal donor size\u201d numbers were used and percentage assigned calculated by ((donor0+donor1+donor2)/unassigned)*100.Vireo and souporcell were run as per the previous species and assignment percentages for souporcell were assessed via awk -F Preprint) singularity container (image version 1.0.3). SNP numbers in each VCF were counted using: grep \u201c##\u201d VCFname | wc -l.A summary figure reviews the computational details used to run souporcell on the above datasets . OverallPleurodeles and dual species datasets, the first two steps of the souporcell pipeline were run separately and then the output from these was introduced back into the souporcell pipeline for completion . Seurat was used to import and analyze single-cell gene expression data for all datasets and to analyze the multiplexing capture data for the dual-species Cellplex (CMO)-labeled dataset.A two part analysis in R and then Python was used to evaluate the efficacy of souporcell demultiplexing for each dataset. Scripts in R (version 4.1.2) primarily using Seurat (version 4.1.0) were usePreprint) and upset plots , and included R version 4.1.2 (2021-11-01).Session info including package numbers for R analyses are embedded in the GitHub page by a demultiplexing method. Cell ID value for each bin was then plotted against average total mapped reads. For datasets including fluorescent transgenic lines, binned data are also colored by the average number of summed mapped fluorescent reads per cell.Bar plots: filtered datasets were subset by the animal or animal group assignment from each demultiplex method being used to benchmark souporcell results. Within those subsets, the total cell quantity of cells assigned to each identity by souporcell was plotted (left plots). Alternatively, within each benchmarking demux result subset, the percentage of cells assigned to each identity by souporcell was calculated by dividing by total cells assigned to that identity by the benchmarking demuxer and multiplied by 100.VCF files were generated from 10x BAMs and the species-specific reference using VCFtools v1.11 with:$GENOME -b bamlist --threads 10 | bcftools call -m -Oz -f GQ --threads 10 -o allsites.vcfbcftools mpileup -f SNP density per kilobase was then calculated using VCFtools v 0.1.15:vcftools --SNPdensity 1000 --gzvcf allsites.vcf.gz\u201c{ total + = $4; count++ } END { print total/count }\u201d out.snpdenThis outputs an out.snpden file, and average SNP density across all sites was calculated using: awk E-MTAB-12186 for three animal pooled Pleurodeles splenocyte scRNA-seq and ArrayExpress accession E-MTAB-12182 for four animal pooled Pleurodeles and Notophthalmus splenocyte scRNA-seq. Code used to analyze the data are present in the Materials and Methods section, in linked Colab notebooks, or via GitHub (https://github.com/RegenImm-Lab/SNPdemuxPaper) All other data used in the study were from previously published works of which accessions are noted in the Materials and Methods section.Data are available on ArrayExpress with accession"} +{"text": "Diabetes is a severe challenge to global public health since it is a leading cause of morbidity, mortality, and rising healthcare costs. 3.0 million Ethiopians, or 4.7% of the population, had diabetes in 2021. Studies on the chronic complications of diabetes in Ethiopia have not been conducted in lower-level healthcare facilities, so the findings from tertiary hospitals do not accurately reflect the issues with chronic diabetes in general hospitals. In addition, there is a lack of information and little research on the complications of chronic diabetes in Ethiopia. The objective of this study was to assess the degree of chronic diabetes complications and associated factors among diabetic patients presenting to general hospitals in the Tigray area in northern Ethiopia.As part of a multi-centre cross-sectional study, 1,158 type 2 diabetes (T2D) patients from 10 general hospitals in the Tigray region were randomly chosen. An interviewer-administered questionnaire, a record review, and an SPSS version 20 analysis were used to collect the data. All continuous data were presented as mean standard deviation (SD), while categorical data were identified by frequencies. Using a multivariable logistic regression model, the factors associated with chronic diabetes complications among T2D diabetic patients were found, and linked factors were declared at p 0.05.Fifty-four of people with diabetes have chronic problems. Hypertension (27%) eye illness, renal disease (19.1%), and hypertension (27%) eye disease were the most common long-term effects of diabetes. Patients with chronic diabetes complications were more likely to be older than 60, taking insulin and an OHGA , having diabetes for more than five years, taking more than four tablets per day , and having high systolic and diastolic blood pressure. Patients with government employment , antiplatelet drug use , and medication for treating dyslipidemia , all had a decreased chance of developing a chronic diabetes problem.At least one chronic diabetic complication was present in more than half of the patients in this study. Chronic diabetes problems were related to patients\u2019 characteristics like age, occupation, diabetes treatment plan, anti-platelet, anti-dyslipidemia medicine, duration of diabetes, high Systolic BP, high Diastolic BP, and pill burden. To avoid complications from occurring, diabetes care professionals and stakeholders must collaborate to establish appropriate methods, especially for individuals who are more likely to experience diabetic complications. Hyperglycemia is a metabolic condition associated with diabetes mellitus . There aDiabetes impacts people\u2019s functional skills and quality of life, leading to severe morbidity and premature mortality, and is one of the top public health concerns in the globe . It negaFor instance, studies on the prevalence of chronic diabetic complications revealed that 96% of patients had hypertension, 46% had peripheral neuropathy, 30% had neuropathy, and 7% had neuropathy encountered impotence and the Information on the prevalence of diabetes-related complications is essential to change diabetes management policies and practices to effectively control the disease. However, studies focusing on such topics are rare in Ethiopia ,20,21 anAlthough very few studies on chronic diabetes complications have been conducted in different parts of the country, there has not been a recent comprehensive study of outpatients in general hospitals. On the other hand, because those studies were conducted in tertiary hospitals, they were unable to provide a precise picture of diabetes complications at a lower level, such as in general hospitals. In addition, those studies were carried out among high-risk individuals, the study population of type 1 and 2 diabetes, assessing only acute complications, microvascular or macrovascular complications, and in some studies data were collected through document review only. Furthermore, it is essential to investigate diabetes complications and their contributing factors regularly to pot evolving patterns and formulate diabetes management strategies. Therefore, this study aimed to identify chronic complications related to diabetes and associated factors in general hospitals in the Tigray region of Northern Ethiopia.A multi-centre cross-sectional study was conducted in the Tigray region from September 2019 to January 2020. Tigray is one of the ten regional states of Ethiopia. The Ethiopian health care system is organized into three-tier: primary, secondary and tertiary levels of care. The primary level of care is provided at a primary hospital, health centre and health post. The Primary Health care Unit (PHCU) is composed of a health centre (HC) and five satellite health posts (HP). These facilities provide service to approximately 25,000 people. A primary hospital provides inpatient and ambulatory service to an average of 100,000 Population and has an inpatient capacity of 25\u201350 beds. A general hospital provides inpatient and ambulatory services to an average of 1,000,000 people. A tertiary hospital serves an average of five million people. It serves as a referral to the general hospital .In 2019/2020, in the Tigray region, there were 2 referral hospitals, 14 general hospitals, 24 primary hospitals, 230 health centres and 741 health posts. There were more than 310 ambulances and a well-established referral system. There were over 750 private health facilities in the private sector, ranging from drug vendors and clinics to general and specialized hospitals. There were more than 25,000 health workforce ranging from health extension workers to specialists and sub-specialists . This stAll type 2 diabetic (T2D) patients admitted to the study hospitals and those who attended diabetic clinics during the data collection period participated in the study. To be involved in the study participants had to be adult.All adult patients aged more than 18 years who were diagnosed to have T2D and had follow-up visits in the study hospitals for \u22651 year. The study did not include patients.All Patients who were pregnant and critically ill.20.535(1\u20130.535)/(0.03)2. 10% of the initial sample size was added for non-response rate and the final sample size was 1,168. Proportional allocation of participants was employed to allocate the sample size among the selected general hospitals based on caseload (The sample size (n) was estimated using a single population proportion formula proposed by Cochran with an caseload .Ten out of fourteen public general hospitals were selected through a simple random sampling technique, and all general hospitals were not included because of budget constraints. Participants were selected using a systematic random sampling method whereby the first patient was selected randomly from the first three by a lottery method, and the next patient was selected every three intervals until the required sample was attained.The data were collected using a pre-tested, interviewer-administered questionnaire that was developed based on relevant literature ,21,31,32The T2D patients attending 10 hospitals during the data collection period were approached by the data collectors, verified for eligibility and then, after informed consent was obtained, data were collected. Data was collected by ten BSc nurses who had either MPH or MSc with multilingual abilities and were supervised by the first and third authors. The type 2 diabetic patients were identified by examining their diagnosis as reported in the medical record. Moreover, clinical and chronic diabetic complications data were extracted from patients\u2019 medical records. The diagnosis of chronic diabetic complication was then confirmed by the physician.To assure data quality, training and orientation of the study were done for the data collectors and supervisors and the questionnaire was pre-tested and checked for its validity and reliability. The pretest of the questionnaire involved 2% of the sample size and it was carried out in Quiha general hospital two weeks before the actual data collection. The questionnaire was revised based on the pre-test results. The questionnaires were checked for completeness and consistency on the daily bases. The data was entered and cleaned, entered in the SPSS version 20 analyses were performed using. A binary logistic regression analysis model was used to identify factors associated with chronic diabetes complications. The Homer-Lemehow goodness-of-fit test was used to check the model fitness and the assumption of a P-value >0.05 was considered a good model fit. Independent variables with p < 0.20 during the bivariate analysis were then included in the multivariable logistic regression for further analysis to control confounding factors. Multicollinearity between independent variables was checked by using the tolerance test and variance inflation factor (VIF). P < 0.05 was considered the cut-off point for reporting an independent variable that shows a statistically significant association with the dependent variable in multivariate analysis. The strength of the association of factors with chronic diabetes complications was demonstrated by computing the adjusted odd ratio (AOR) and its 95% confidence interval (CI).Socio-demographic: age, sex, marital status, religion, ethnicity, educational status, occupation, residence, monthly income (UD), family history of diabetes and BMI.Clinical: diabetes treatment regimen, anti-platelet drug , anti-dyslipidemia drug, glucometer, duration of diabetes, Fasting Blood Glucose (FBG), Systolic Blood Pressure (SBP), Diastolic Blood Pressure (DBP), Pill burden, and high health care cost.Behavioural: adherence to a diabetic diet, saturated fat consumption, vegetable consumption, adherence to diabetic medication, self-blood glucose test, smoking, alcohol consumption, physical activity, and diabetes education.Chronic diabetes complications statusThe data about chronic diabetes complications were extracted from the patient\u2019s chart/medical record. Only chronic complications that developed after the diagnosis of T2D and could be attributed to diabetes were considered in this study.Hypertension: was defined as systolic blood pressure (SBP) \u2265 140 mmHg and/or diastolic blood pressure (DBP) \u2265 90 mmHg, and/or patient on antihypertensive therapy was taken as the hypertensive patient ,36.Coronary artery disease (CAD): The diagnosis criteria for CAD were either a patient with typical anginal pain or equivalent symptoms or an abnormal resting ECG or an asymptomatic patient with the abnormal stress test, either by ECG or echo or a nuclear perfusion imaging test .Peripheral vascular disease: The presence of intermittent claudication and/or an ABI value (< 0.9) in any limb was recorded as peripheral vascular disease .Neuropathy: was diagnosed if a change was found in two or more of the three items hypesthesia or anaesthesia in lower and upper limbs when the patient\u2019s lower limp was evaluated .Eye diseases: Eye diseases such as cataracts, glaucoma and diabetic retinopathy were identified based on the report of the ophthalmologist or optometrist from the dilated eye (fundus photography for retinopathy), and comprehensive eye examination, which was recorded on the patient\u2019s chart .Chronic Kidney disease: was diagnosed based on the presence of urinary albumin, and/or an abnormally high level of serum creatinine (low glomerular filtration rate) .Foot problem: The diagnosis of foot problem was made through foot examination for any abnormalities or all patients were asked about a history of foot ulcer, neuro ischemic foot, or amputation .Follow a healthy diet: consuming vegetables, beans and peas, fruit, whole grain, nut, and seeds, seafood, low-fat milk and milk product, and a moderate amount of lean meat, poultry, and egg ,42.High fat/oil consumption: eat or consume more than 10% of calories from saturated fat, which means more than 20 grams of saturated fat per day ,44.Alcohol consumption: Adult with diabetes who drinks alcohol should do so in moderation (no more than one drink per day for adult women and no more than two drinks per day for adult men). One drink is defined as 12 oz/355ml of beer, 5 oz /148ml glass of wine, or 1.5 oz/44ml of distilled spirit .Physical activity: At least 150 minutes per week of aerobic exercise, plus at least two seasons per week of resistance exercise, are recommended .Ethical approval to conduct the study was obtained from the Institutional Review Board (IRB) of Mekelle University (Ref No. ERC 1370/2019). The study received approval from the Tigray regional health bureau and permission from the Medical Directors of the 10 involved hospitals. The study was conducted following the declaration of Helsinki. Study participants were recruited voluntarily after they were informed about the study and that they can withdraw from the study at any stage thereafter they signed the consent form. All data were kept in a safe and secure place anonymously to ensure confidentiality and only the researchers had access to the data.Overall, a total of 1,168 diabetic individuals were eligible for the study, but only 1,158 of the participant\u2019s questionnaires were fit for final analysis, which makes the response rate 99.14 per cent. Thirty-four per cent of the participants had an age greater than 60 years, with a mean age of 55.9 (D\u00b1 11.9) years. Most of the participants were male (54%), Married (67%), Orthodox Christian (88%), Tigrian ethnicity (96.3%), and urban resident (72.3%). Majority of the participants: 50.5% had no formal education, 80.3% had no family history of diabetes, 29.7% were unemployed, 7.9% had a monthly income of $34.26-$171.16 and 76.5% had a BMI of <25 kg/m2 .Of the total patients included in this study, 78.9%, 11.7%, and 16.8% were taking oral hypoglycemic agent (OHGA), anti-coagulant drug, and anti-dyslipidemia drug respectively. The mean duration of diabetes was 6.3 (D \u00b1 4.6) years and 54.6% of participants had diabetes duration of < 5 years. Of all participants, 10.1% had a glucometer at home, 60.7% had FBG of >130.00 mg/dl, 25.8% had SBP of >149.00 mmHg and 9.0% had DBP of > 90.00 mmHg. From the total participants, 42.7% were taking >4 pills per day, 86.4% had a high health care cost, 69.7% consumed a high amount of saturated fat (>20 g per day), and 68.7% were taking less than the recommended amount of vegetable (<4 serving per week). Of all participants, 90.6% and 50.4% adhered to diabetes medication and a healthy diet. Of the total participants, nine out of ten test their blood glucose once per month, 6.2% ever smoke tobacco product, 12.4% consume more than moderate amount of alcohol (\u22653 drink per day). Moreover, of the total participants, 61.3% were active physically, and 76.5% were attending diabetes education at the time of follow visit .Overall, 54% of participants suffered from at least one chronic complication of diabetes. Among all participants who had the complication, 10.5% had a single complication, 16.9% lived with two and 26.8% with more than two types of complications respectively.Of all types of macrovascular complications, hypertension 27% was the most common but cerebrovascular disease 4.31% was the least common type. Out of all participants who had cerebrovascular complications, 0.3% had TIA and 4% had a history of stroke .The most common type of microvascular complication was ocular disease 22.62% , followed by kidney disease 19.17% and peripheral neuropathy11% respectively. Patients with renal complications consisted of 9% with microalbuminuria,4.0% with macroalbuminuria and 6% with high levels of serum creatinine. Ocular complications included cataracts, retinopathy, diabetes blindness and glaucoma, with magnitudes of 5%, 9%, 1% and 8% respectively. Of the total participant who had a foot disease, 4% had a diabetes-related foot ulcer, 1% had a foot amputation, 3.6% had ischemic pain, 1% had gangrene and 3% had an infection .The Homer-Lemehow goodness-of-fit test was done, and its result showed P = 0.0063, which was considered a good model fit. The odds ratio was calculated for factors found to be associated with chronic diabetes complications among type 2 diabetic patients. After considering all assumptions of binary logistic regression and the p-value (\u2264 0.05) in the bivariate analysis, fifteen variables were identified as candidates for analysis in the multivariable model. In the multivariable logistic regression analysis, nine variables were found to be factors associated with chronic diabetes complications at a 5% level of significance.The odds of a chronic diabetes complication was higher among patients age > 60 years ) than their counterpart, who took insulin and OHA had a higher chance of developing the complication than patients taking insulin injection only, with diabetes duration of \u2265 5 years, were at higher risk to develop the complication than patients with shorter diabetes duration and who took \u22654 pills a day had a greater risk to develop chronic diabetes complication than their counterpart . SimilarThis study aimed to assess the magnitude of chronic diabetes complications and associated factors among diabetic patients attending the general hospitals in the Tigray region, Northern Ethiopia. The overall magnitude of chronic diabetes complications in this study was 54.0% . This is consistent with studies from Bahir Dar, Northwest Ethiopia (54%), and China (52%) ,21. The However, our study showed that 34%, 45% and 77% of the study participants were >60 years of age, with \u2265 5 years of diabetes duration and normal BMI respectively. However, the result of this study is higher than a study in Gurage Zone, Southwest Ethiopia (46%). The probIn this study, 27.28% participants had diabetes-related hypertension which is in line with a study done in Jimma, Ethiopia(25%) . This isIn this study, peripheral vascular disease was seen among 9.13% participants, which is higher than the finding from a survey conducted in Sri Lanka (4.7%) ,58. The Coronary artery disease (CAD)occurred among 3.28% participants in this study, which is lower than studies done in Sri Lanka (11%), Saudi Arabia (23%), Bangladesh (26%), India (8%), Nepal (23%), and Iraq (15%) ,60,62\u201364Of the total participants in this study, 4.31% had a stroke, which is higher than studies done in Libya (1.9%), Saudi Arabia (0.19%), Nepal (1%) and Iraq (0.7%) ,51,54,56Peripheral neuropathy was seen among 11% participants; this finding is almost similar to that of studies conducted in India (11%) and West Ethiopia (10%) ,67. The This result is higher than the result of Saudi Arabia (1.4%) and Iraq (6.5%) ,56. The However, it is lower than the result of Sri Lanka (63%), Southwest Ethiopia (15%), Nepal (15%), Bangladesh (28%), India (19%), Tanzania (29%), and Egypt (22%) ,62,68,69In this study the magnitude of diabetes nephropathy was 19.17% this figure is in line with the study conducted in Ethiopia . Unlike In this study, retinopathy was seen in 9% (95% CI: 7.25\u201310.53) of participants, which is in line with studies conducted in Indonesia (7%), Tunisia (8.1%), Iraq (7.5%), and Ethiopia (10%) ,64,65,69However this result is lower than research findings done in Ethiopia (26%), Sri Lanka (26%), SSA (15%), Nepal (29%), Korea (38%), India (15.4%), Bangladesh (38%), Libya (31%), Tanzania (50%), Sudan (14%), and Egypt 21%) Reviewers' comments:Reviewer's Responses to Questions Comments to the Author1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0PartlyReviewer #2:\u00a0Yes********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0NoReviewer #2:\u00a0No********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0This article can be made simpler for the scientific community with some modifications and clarifications as below.Minor comments1. Consistently use either \u201cTigray\u201d or \u201cTigrai\u201d in the title, author affiliation, study area, and elsewhere.2. Change \u201cnorth Ethiopia / northern Ethiopia\u201d to \u201cNorthern Ethiopia\u201d throughout the manuscript3. Instead of saying \"an institutional-based study,\" say \u201ca multi-center cross-sectional study.\" since the study was conducted in ten public general hospitals.4. It is better to say 54% rather than 54.0%, and 27% rather than 27.0%.5. Throughout the manuscript, apply comma for numbers with more than two digits, like instead of saying 60 000\u2013100 000 people, better to say 60,000-100,000 people.6. Remove double full stops throughout the manuscript7. Since it is an international journal, better to change the income status that you mentioned in Ethiopian birr (ETB) to US dollar using the exchange rate at the date of data collection.8. I recommend you to avoid writing formulas for sample size calculations, it would be better to make it in sentence format the approach you applied for calculating the sample size than writing detailed mathematical equations.9. Remove the Hosmer-Lemeshow goodness-of-fit test result you mentioned in the method section and put it at the result section (particularly at the multivariable regression table), At the method section you have to mention what you have did not what you found.10. Add your response rate in the result section, as your study is a cross-sectional study11. I appreciate writing of the findings of the measure of effect (AOR with its 95% CI), make it consistent in the result section of the manuscript (you mentioned ), re-write it as you have rightly described in the abstract section.12. Avoid P-value if used 95% CI instead of writing like (), remove the P-value and re-write it as , and remove the hyphen (-), rather use comma for writing the 95% CI.13. Check the reference section, the majority of the citations are appropriate, but there are some references citrated in appropriately, check them again using software\u2019s or manually14. Make sure whether your questionnaire has three or four parts, there are inconsistencies in their parts mentioned in the data collection tool and measurement part.Major comments1. Rationale of the study: You mentioned that the previous studies had a critical methodological limitation, which hindered the scientific community to make any conclusion or judgment? How do you know whether the sample size was small, if appropriately calculated even 10 sample size can be enough? There are more than ten similar articles published elsewhere in the country, including in the region, what was the added value of your study? I would suggest you to re-write it again, considering convincible scientific argument.2. Did you assess the risk factors? What you assessed was factors associated with chronic diabetic complications, do you think that we can interchangeably use risk factors and factors associated? Can we assess risk factors using simple, classical cross-sectional study design? I recommend you to consistently use the term factors associated, not risk factors in your manuscript.3. Sample size calculation: It is appreciable that you have used 3% margin of error to maximize the sample size, and your response rate was 94.6%, but after adding 10% non-response rate, the final sample size should be 1,178 not 1,061.4. Rewrite incomplete sentences, as there are many incomplete sentences, check the spelling and grammar issues, please check again the whole manuscript for spelling and grammar issues (use of present or past tense), I am not comfortable with the write-up.Reviewer #2:\u00a0PLOS ONEPONE-D-22-12568Research ArticleMagnitude of Chronic diabetes complication and its associated factors among adultswith type 2 diabetes in Tigray region, northern EthiopiaBy: kalayou kidanu Berhe,Mekelle University College of Health SciencesMekelle, Tigray ETHIOPIADr Hussein Ismail, Reviewer report to PLOS one December 20221. There is a lot of English language errors that need to be corrected, I believe the manuscript needs a professional proofreading before publications. A lot of errors are identified as in the title Chronic .2. Moreover, there are a lot of abbreviation errors, that need to be corrected, e.g., in the abstract Bsc nurses, OHA, \u2026etc. The manuscript has a lot of abbreviation errors as well, e.g., IDF in the abstract.3. Title: Magnitude of Chronic diabetes complication and its associated factors among adultswith type 2 diabetes in Tigray region, northern Ethiopia.The authors stated that they studied 10 general hospitals out of 13 hospitals, and they did not included any referral or primary care centers. So, the selection is based on general hospitals only, there fore it should be mentioned in the title.My suggestion for the title:Magnitude of chronic diabetes complication and its associated factors among diabetic patients attendingthe general hospitals in Tigray region, northern Ethiopia.4. METHODS4.1. Why did not the author include all the 13 general hospitals? I was surprised of taking 10 hospitals and leaving 3 hospitals. Please explain.4.2. Sampling:The methods of sampling were explained efficiently. Although, the author in included p=0.535, (p=proportion of chronic diabetes complications) please include the refence you used that stated the complications proportion as 0.535. Sampling is a step the author did before the research; I am surprised that this proportion used in the sampling was 0.535 is the same as the magnitude of diabetes complications which was the main finding of this study. Please explain.4.3. Regarding the operational definitions, the definition of hypertension the author used was BP> 140/90, I checked the reference used and it was outdated. Reference number 30.30. Muxfeldt ES NAdR, Salles GF, Bloch KV. Demographic and clinical characteristics of hypertensive patients in the internal medicine outpatient clinic of a university hospital in Rio de Janeiro. Sao Paulo Med J Child Adolesc Behav. 2004;122:87-93.My suggestion: please update all the operational definitions according to the updated guidelines or manuscript. Regarding hypertension, you may use the American heart association guidelines 2017 or the European Society of cardiology (ESC) guideline 2018. I recommend the ESC because it agrees with the level of 140/90 that you chose.Moreover, according to guidelines: No caffeine, no smoking, no eating for at least 2 h before measurement. The author stated BP was measured after30 minutes after hot drink as coffee. Please, explain and what is the refence you used?5. RESULTS5.1. The author stated in the results\u2022 \u2022 in which 42.7%, 10.0% and 13.0% had chronic diabetes complicationrespectively.\u2022 had DBP of > 90.00 mmHg in which 6.0%, 32.2% , 19.7% and 6.6%participants had at least one chronic diabetes complication respectively.Suggestion:\u2022 Please specify each complication associated with these numbers.\u2022 Please apply this notion along the whole paper.5.2. Tables: The authors need to put all the abbreviations in the footnote related to each table. Some abbreviations are missing in the footnotes.6. DISCUSSIONThe discussion is well written.7. CONCLUSIONIt highlights the main findings and supported by the study results.8. ReferenceThe authors included a lot of outdated refences. As the refences included:\u2022 Reference 10: 1996\u2022 Reference 22: 1965Suggestion: updating the refences accordingly.Regarding recent refences: Only one reference (number 35) was published 2020.********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Yes:\u00a0Zenawi Hagos Gufue, Adigrat University, EthiopiaReviewer #1:\u00a0Yes:\u00a0Hussein M. Ismail, MD CardiologyReviewer #2:\u00a0**********https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,\u00a0 11 Apr 2023RESPONSE TO REVIEWERS_______________________________________________________________________________________________________Response to Reviewer #1I. Minor comments 1. \u201cTigray\u201d is used consistently instead of \u201cTigrai\u201d in the title, author affiliation, study area, and elsewhere in the manuscript \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.2. \u201cnorth Ethiopia / northern Ethiopia\u201d was changed to \u201c Northern Ethiopia\u201d\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u20263. \"an institutional-based study,\" was replaced by \u201ca multi-center cross-sectional study\u201d\u2026\u2026\u2026\u2026\u2026.4. It was corrected as 54% from 54.0% and as 27% from 27.0% and other similar issues corrected throughout the document as per your suggestion .................................................................................................5. Comma was used for numbers with more than two digits \u2026\u2026\u2026... 6. Double full stops were removed\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026...7. The mentioned Ethiopian birr (ETB) in the Monthly income status section was changed in to US dollar based on average exchange rate of 2019\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026(Page 9)8. The formula for sample size calculation was removed and rewrote in sentence format as per your recommendation and checked using StatCalc for population survey via Epi Info 7.0 software\u2026\u2026\u2026..9. The result of Hosmer-Lemeshow goodness-of-fit test was removed from the method section and placed at the result section (Factors associated with chronic diabetes complication & table3 foot note), \u2026\u2026\u2026.(Page11)10. Result of response rate is included/added in the result section of the manuscript\u2026\u2026\u2026\u2026\u2026\u2026\u2026.........(Page 8)11. The multi variable analysis result was re-wrote as per your recommendation\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026...12. In Abstract & result section P-value was removed and re-wrote as , and the hyphen (-) was removed instead comma was use for writing the 95% CI\u2026\u2026..............................13. In appropriately cited references were checked & corrected via endnote software ...\u2026\u2026\u2026\u2026\u2026\u2026(Page 18-21)14. The questionnaire has four parts, then corrected as \u201c it has four parts\u201d\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.\u2026\u2026\u2026.....(Page 5)_______________________________________________________________________________________________II. Major comments1. Rationale of the study: revised and additional scientific arguments are included \u2026\u2026\u2026\u2026\u2026\u20262. The term \u201cRisk factor\u201d was replaced by \u201cfactors associated\u201d and used consistently throughout the manuscript \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u20263. Sample size calculation: \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026...The required sample size (n) was estimated manually using a single population proportion formula and cheeked using STATCALC for population survey via Epi-info version 7 software with assumptions of 95% CI (z = 1:96), d=0.03, and P=0.535.Therefore the initial sample size was 1061.882 ( ni = (Z1-\u03b1/2)2p (1\u2013p)/d2= (1.96)20.535(1-0.535)/(0.03)2 ). However, a refusal rate of 10% (1061.882*0.1) =106.1882 was added and gives a final sample size of 1,168.0702 , Accordingly10 questioners were excluded because of gross incompleteness and 1,158 participants\u2019 questioner were fit for final analysis which makes response rate of 99.14 % \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026 4. Incomplete sentences were re-wrote, spelling and grammar issues were checked and corrected\u2026 __________________________________________________________________________________________________________________________________________________________________________________Response to Reviewer #2: Title & abstract 1. Gross English language Proofreading was done to correct errors of Spelling, grammar, punctuation and statement construction throughout the manuscript\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026. 2. To avoid confusion with other similar abbreviations the expanded form of the abbreviations were included e.g. IDF , Bsc is corrected as BSc and other abbreviations errors corrected accordingly \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.. 3. Research Title was modified as \u201cMagnitude of chronic diabetes complication and its associated factors among diabetic patients attending the general hospitals in Tigray region, northern Ethiopia\u201d based on your suggestion \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026(page-1)________________________________________________________________________________________________4. Method and materials 4.1 Study Area:: the study was done at 10 general hospitals out of all 14 general hospitals, all general hospitals were not included because of the four hospitals were exclude randomly due to budget constraint / logistic issue\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026...(Page4) 4.2 Sampling: A reference (ref.no 21) for P=0.535, (p=proportion of chronic diabetes complications) was included and this figure is used to calculate the sample size which was done in 2015 which was before our study conducted (2019/20) and taken from a study done at FelegeHiwot referral hospital, Bahardar, Amhara region, Northwest Ethiopia\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026..(Page5)As you mention, by chance the chronic diabetes complication proportion of the study done at FelegeHiwot referral hospital (P=0.535) which we use for sample size calculation is similar to our finding (P=0.54). This could occur because of similarity in socio-demographic characteristics, poor glycemic control as a result of poor adherence to diabetes self-management recommendations\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026 Therefore, the finding of this study But both studies have difference in many things such as sample size , study facility , study area (Amhara region vs. Tigray region) and study period (2015 Vs. 2019/20)\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.... (Page4-6)________________________________________________________________________________________________4.3 Operational definition: 4.3.1 Definition of Hypertension: The reference was updated and replaced by the reference that you recommend \u201cEuropean Society of cardiology (ESC) guideline 2018\u201d \u2026\u2026\u2026\u2026. 4.3.2 Definition of other chronic diabetes complications: all definition/ diagnostic criteria of other chronic diabetes complications were updated according to the updated guidelines or manuscript based on your suggestion\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.4.3.3 Data collection and measurement(BP): the timing of BP measurement related to coffee consumption was revised as 1-2 hours and reference also included \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026................................................................... (Page 6) ___________________________________________________________________________________________5. Result 5.1 Socio-demographic, Clinical and behavioral characteristics: In this section we try to explain the findings based on the cross-tabulation analysis results but as mentioned in your review \u2022 In which 29.4%, 34.0%, 47.1% and 52.4% participants had chronic diabetes complication respectively\u201d\u2022 In which 42.7%, 10.0% and 13.0% had chronic diabetes complication respectively.\u2022 In which 6.0%, 32.2%, 19.7% and 6.6% participants had at least one chronic diabetes complication respectively.Those are findings of overall chronic diabetes complication in terms of socio-demographic, clinical and behavioral characteristics in the cross-tabulation analysis result but we observed such way of explanation may result in confusion for the reader, so to make it clear and simple we prefer to omit/ remove all cross-tabulation findings of chronic diabetes complication from the text explanation of socio-demographic, clinical and behavioral characteristics section but readers can get those findings from the Table 1 & 2 \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026...(Page8-11)5.2 Tables: all the abbreviations related to each table were placed in the footnote\u2026\u2026 6. Discussion: Except English language Proofreading, revision was not done in this section because you mentioned as \u201cThe discussion is well written\u201d7. Conclusion: Revision was not done because you stated as \u201cIt highlights the main findings and supported by the study results\u201d8. Reference: Reference 10: was replaced with updated reference, Reference 22: was replaced with updated reference. Accordingly all references were updated as per your suggestion \u2026\u2026\u2026(Page 18-21)_______________________________________________________________________________________________AttachmentResponse to reviewers.docxSubmitted filename: Click here for additional data file. 16 May 2023
PONE-D-22-12568R1
Magnitude of chronic diabetes complications and its associated factors among diabetic patients attending the general hospitals in Tigray region, Northern Ethiopia
PLOS ONEDear Dr. Berhe,Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE\u2019s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.Please submit your revised manuscript by Jun 30 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at\u00a0
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For instructions see: We look forward to receiving your revised manuscript.Kind regards,Manal S. Fawzy, Ph.D., M.D.Academic EditorPLOS ONEJournal Requirements:Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article\u2019s retracted status in the References list and also include a citation and full reference for the retraction notice.[Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #2:\u00a0All comments have been addressedReviewer #3:\u00a0All comments have been addressed********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2:\u00a0YesReviewer #3:\u00a0Yes********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2:\u00a0YesReviewer #3:\u00a0Yes********** 4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #2:\u00a0YesReviewer #3:\u00a0Yes********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #2:\u00a0NoReviewer #3:\u00a0Yes********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #2:\u00a0First, the manuscript looks much better than the first version, thanks for the authors.Although, I do not think it is ready for publication.The most important is to revise the enligh language again, and the author should submit an offcial proofreading certifcate for the manuscript, if the Editorial Board advise on this regard, it will be very helpful. As I still see lot of English and Grammer mistakes, and the writing way is not quite professional.1. The abstarct/conclusion:Conclusion: In this study, the magnitude of chronic diabetes complication was higher because more than halfof the study participants had at least one complication.I donot understand this statement, the magitude is high than...what?Also, revise the conculsion2. The exclusion and inclusion criteria:The author put bothe the criteria togther, which is confusing. Please specifiy what are the inclusion criteria? and what are the eclusion criteria?3. Diagnosis of chronic diabetes complication:3.1. I suggest using this statment in stead of yoursCoronary artery disease (CAD): The diagnosis criteria for CAD were either a patient with typical anginal pai or equivalentsymptoms and an abnormal resting ECG or an asymptomatic patient with abnormal stress test, either byECG or echo or a nuclear perfusion imaging test .3.2. Peripheral vascuar disease:The peripheral vascular disease defintion, it is advised to limit the ABI to less than 0.9 only, and delete more than 1.33.3. Neuropathyloss of sensitivity is mis nomer, replace with hyposthesia or anasthesia in lower and upper limbsspelling: limp ---> limb.4. Tables:4.1. Yes column: yes is wrongly written. Plz, correct.4.2: The abbreveiations shoud be consistent: if you use SBP for systolic blood pressure, you have to use DBP for diastolic blood pressue, plz be consistent along the whole manuscriptReviewer #3:\u00a0I thank the authors to conduct this interesting study at the local setting.All comments have addressed. No further comment required.********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Yes:\u00a0Hussein M IsmailReviewer #2:\u00a0Yes:\u00a0Mohammed Abdu SeidReviewer #3:\u00a0**********https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,\u00a0 17 Jun 2023RESPONSE TO REVIEWERSResponse to Reviewer #21. Abstract 1.1 Conclusion: revision was made based on your comment and it is revised as \u201cIn this study, more than half participants had at least one chronic diabetes complication\u201d\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026....(Page 2)2. Method 2.1 The exclusion and inclusion criteria: the inclusion criteria and exclusion criteria are separately written under eligibility criteria to avoid confusion\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026...(Page5) 2.2 Diagnosis of chronic diabetes complication2.2.1 Coronary artery disease (CAD): corrected as per your suggestion\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026....... was deleted from the definition, ABI to less than 0.9 only is used \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026..(Page7)2.2.3 Neuropathy: misnomer of loss of sensitivity in the definition replaced with \u201c hyposthesia or anesthesia\u201d in lower and upper limbs & the work limp is corrected as limb\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026...(Page7)3. Results 3.1 The wrongly written the word yes in the column is corrected throughout the tables\u2026\u2026\u20263.2 All abbreviations were written consistently throughout the document \u2026\u2026\u2026...(Page 10-17) 4. Conclusion: corrected as \u201cIn this study, more than half participants had at least one chronic diabetes complication\u201d\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.........(Page15)zainab.karim4@gmail.com) and Prof. Lilian T. Mselle (email: nakutz@yahoo.com ) from MUHAS, Tanzania. Uploaded as Supporting Information file 1 \u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.5. Language editing: Our Manuscript was copyedit for language usage, spelling, and grammar by Zainabu Karim Mohamed from MUHAS, Tanzania :The authors have adequately addressed the concerns raised by the reviewers. Thank youReviewers' comments: 17 Aug 2023PONE-D-22-12568R2 The magnitude of chronic diabetes complications and its associated factors among diabetic patients attending the general hospitals in Tigray region, Northern Ethiopia Dear Dr. Berhe:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofProfessor Manal S. Fawzy Academic EditorPLOS ONE"} +{"text": "Current trends indicate that 63 countries are not on track to achieve the 2030 Sustainable Development Goals (SDG) target of a neonatal mortality rate \u226412 per 1000 live births, with 55 needing to double the annual rate of decline in neonatal mortality to do so . 2017. Available: http://bvsms.saude.gov.br/bvs/publicacoes/atencao_humanizada_metodo_canguru_manual_3ed.pdf. Accessed: 14 March 2023. [in Brasilian]."} +{"text": "An 82-year-old man was admitted for progressively worsening jaundice. Magnetic resonance cholangiopancreatography (MRCP) showed a stenosis of 2\u200acm in length in the common bile duct, with dilatation of the biliary system above . EndoscVideo\u20061\u2002Laser ablation under intraductal cholangioscopic guidance is performed for a cholangiocarcinoma.In recent decades, endoscopic radiofrequency ablation has been introduced into clinical use to palliate unresectable cholangiocarcinomaEndoscopy_UCTN_Code_TTT_1AR_2AF"} +{"text": "Interpretation of noncoding genomic variants is one of the most important challenges in human genetics. Machine learning methods have emerged recently as a powerful tool to solve this problem. State-of-the-art approaches allow prediction of transcriptional and epigenetic effects caused by noncoding mutations. However, these approaches require specific experimental data for training and cannot generalize across cell types where required features were not experimentally measured. We show here that available epigenetic characteristics of human cell types are extremely sparse, limiting those approaches that rely on specific epigenetic input. We propose a new neural network architecture, DeepCT, which can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Furthermore, we show that DeepCT can learn cell type\u2013specific properties, build biologically meaningful vector representations of cell types, and utilize these representations to generate cell type\u2013specific predictions of the effects of noncoding variations in the human genome. Second, some loci become epigenetically bookmarked at the stage of progenitor cells, making these loci unresponsive to trans-factors expressed later in development. See positions in the sequence and at the boInput gradient for each position in the sequence . Since the training dataset mostly contains sequences with a 200-bp intersection, 1 sample contains a target window of another sample. Therefore, there is a consistent increase of importance in the 200-bp intervals. There is also a noticeable drop of gradients centered around the positions in the sequence and at both ends of the input sequence, which reflects the training strategy. We would expect this effect to be alleviated by sampling training data with less consistency in sample overlap size.AP: average precision; bp: base pair; CNN: convolutional neural network; kbp: kilbase pair; MPI: mean feature positional information; SNV: single-nucleotide variant.giad015_GIGA-D-22-00103_Original_SubmissionClick here for additional data file.giad015_GIGA-D-22-00103_Revision_1Click here for additional data file.giad015_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giad015_Reviewer_1_Report_Original_SubmissionFangfang Yan -- 6/6/2022 ReviewedClick here for additional data file.giad015_Reviewer_2_Report_Original_SubmissionYuwen Liu -- 6/27/2022 ReviewedClick here for additional data file.giad015_Reviewer_2_Report_Revision_1Yuwen Liu -- 12/20/2022 ReviewedClick here for additional data file.giad015_Reviewer_3_Report_Original_SubmissionBorbala Mifsud -- 7/4/2022 ReviewedClick here for additional data file.giad015_Supplemental_FileClick here for additional data file."} +{"text": "Here, we present a computational protocol to perform a spatiotemporal reconstruction of an epidemic. We describe steps for using epidemiological data to depict how the epidemic changes over time and for employing clustering analysis to group geographical units that exhibit similar temporal epidemic progression. We then detail procedures for analyzing the temporal and spatial dynamics of the epidemic within each cluster. This protocol has been developed to be used on historical data but could also be applied to modern epidemiological data.For complete details on the use and execution of this protocol, please refer to Galli et\u00a0al. (2023). \u2022Death-based clustering for epidemic reconstruction\u2022Protocol suitable for historical and modern epidemiological data analysis\u2022Spatial dynamics analysis of the epidemic on geographical maps Publisher\u2019s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Here, we present a computational protocol to perform a spatiotemporal reconstruction of an epidemic. We describe steps for using epidemiological data to depict how the epidemic changes over time and for employing clustering analysis to group geographical units that exhibit similar temporal epidemic progression. We then detail procedures for analyzing the temporal and spatial dynamics of the epidemic within each cluster. This protocol has been developed to be used on historical data but could also be applied to modern epidemiological data. The protocol below shows a way for the use of historical data (such as death records) to reconstruct the spatiotemporal evolution of a past epidemic. As an example, we analyzed the information contained in XVII century death registers of the city of Milan to study the spatial and temporal diffusion of a plague epidemic inside the city.This section includes the minimal software and hardware requirements, the installation procedures, as well as the format of the files to be processed throughout this protocol.Timing: 30\u00a0min1.https://cran.r-project.org/ (Note that the protocol has been tested on R version 4.1.3 (2022-03-10)).R is a freely available language and environment for statistical computing and graphics.2.https://www.rstudio.com/.RStudio is a user-friendly integrated development environment for R.Optional: QGIS is a free and open-source geographic information systemhttps://www.qgis.org/en/site/.Timing: 10\u00a0min3.To run this protocol, it is required to previously install the R packages present in the \u201c> install.packages(\u201cname_of_the_package\u201d)Timing: 10\u00a0min\u20131 hYou can follow the protocol using your data or our sample dataset available on GitHub.4.https://github.com/RiccardoND/STAR_protocol_epidemic_reconstruction (GitHub: https://doi.org/10.5281/zenodo.8214153) or directly clone the GitHub repository (\u223c10 Mb), by running the following command on your terminal.You can download our sample dataset from https://github.com/RiccardoND/STAR_protocol_epidemic_reconstruction.> git cloneNote: This repository includes all the data and code necessary to reproduce the protocol. In this dataset, each row contains the total number of \u201ccases\u201d (or deaths) for each cause of death, for each day (or other unit of time) and for each spatial location.5.Format the table to obtain a single case in each row.> df <- read.csv> tab <- data.frame)> tab$count <- NULL> tab$Date <- as.Date(tab$Date)> tab <- tab #sort by dateNote: It is always possible to format your dataset in other ways or add other information, but the protocol must be adjusted accordingly.Note: a version of the dataset\u00a0already formatted as described in this step is available in the file TableS1_formatted.csv.To follow the protocol step-by-step, you must have the data formatted in a dataset in which each row contains a single case. If you have a dataset with cumulative numbers, see below on how to format it properly for the protocol.Timing: 20\u201330\u00a0min1.Prepare the workspace directory. Open RStudio and set the working directory path.> setwd(\"yourpath\")2.Load the dataset of cases/deaths and related information and format it as shown in step 5 of \u201c> head(tab)3.Create a time-series plot that shows the progression of the daily number of deaths for each cause of death (in our case Plague or not plague) .Figure\u00a01> library(ggplot2)>library(tidyverse)> tab %>%\u00a0group_by %>%\u00a0summarize(count\u00a0= n) %>%\u00a0ggplot)\u00a0+\u00a0geom_line(size\u00a0= 0.7)\u00a0+\u00a0geom_point(size\u00a0= 2)\u00a0+\u00a0theme_bw\u00a0+\u00a0scale_color_manual)\u00a0+\u00a0theme,\u00a0\u00a0axis.title.x\u00a0= element_text(size\u00a0= 15),\u00a0\u00a0axis.title.y\u00a0= element_text(size\u00a0= 15))\u00a0+\u00a0labs(y\u00a0= 'Number of Deaths')Note: The plot compares the progression of deaths caused by the disease of interest to deaths related to any other cause: it could show the presence of any kind of seasonality, and the completeness of the dataset. The absence of a signal in the period between 4 and 30 August is due to reasons not related to the analysis.To reconstruct the dynamics of an epidemic, it is helpful to start by plotting the number of deaths (or cases) that occurred at a specific time. In this case, we are going to build a time-series plot with two lines, one for deaths unrelated to the disease of interest, i.e., plague, and one for deaths related to plague. This step allows us to depict the temporal progression of the epidemic in the city and to detect any period with missing data or any other anomaly.Timing: 3\u20134 h4.Load the R packages in the current RStudio session.> library(tidyverse)> library(reshape2)> library(factoextra)> library(ade4)> library(vegan)> library(RColorBrewer)> library(inflection)>library(ggpubr)5.Load the table with one row per case, as shown in step 5 in the \u201c6.a.> tab_1630_peste <- droplevels)> head(tab_1630_peste)filter for the cause of death or disease of interest.b.> t_1630_peste <- as.matrix)build a matrix in which each column is a parish , and each row is a day .c.> days1630\u00a0<- seq(from=as.Date(\"1630-01-01\"), to=as.Date(\"1630-12-31\"), by=1)> absent_days <- as.Date)), origin=\"1970-01-01\")> t_1630_peste_absent <- matrix(ncol=ncol(t_1630_peste), nrow=length(absent_days))> t_1630_peste_absent[is.na(t_1630_peste_absent)] <- 0> row.names(t_1630_peste_absent) <- as.character(absent_days)> t_1630_peste_all <- rbindNote: Select your temporal period of interest. In the example dataset, the cases span the year 1630, thus our range is from the 1st of January 1630 to the 31st of December of the same year.Add to the matrix the days in which there are no recorded plague deaths.d.> t_1630_peste_all_ord <- t_1630_peste_allOrder the table chronologically.e.> peste_cum <- matrix, nrow=0)> for ) {\u00a0tmp <- colSums\u00a0peste_cum <- rbind}> peste_cum <- rbind> row.names(peste_cum) <-row.namescreate a cumulative matrix.f.> peste_cum_norm <- apply x/max(x))Normalize the number of deaths by dividing the number of daily deaths in each parish by the total number of deaths in that parish .g.> peste_cum_norm_m <- melt(peste_cum_norm)> colnames(peste_cum_norm_m) <- )> peste_cum_norm_m$Date <- as.Date(peste_cum_norm_m$Date)> Cumulative_curves <- ggplot)\u00a0+\u00a0geom_line\u00a0+\u00a0theme_bw\u00a0+\u00a0ylab(\"Cumulative relative frequency of plague deaths (%)\")Note: Some parishes may not have enough cases to build a reliable cumulative curve on the selected time range. We can choose a threshold under which the parishes will be excluded from the subsequent analyses. For example, we selected only the parishes with more than one plague death every two weeks during the epidemic.Plot the cumulative relative frequency curves of the parishes plague deaths .> peste_h.Note: The epidemic period is not simply the time between the first and last case, in fact, as in our data, there may be some isolated cases before or after the epidemic. Thus, it is important to analyze the epidemic curve. In our data, the epidemic begins around the middle of March and continues throughout 1630.Calculate the duration of the epidemic. To do so, we have to observe the epidemic curve produced in step 3 to manually determine the starting and ending period of the epidemic.i.> weeks_of_epidemic <- 42> death_count_thr <- weeks_of_epidemic/2#21Calculate the death threshold. To select parishes with more than 1 death every two weeks, we have to look for parishes with more than 21 deaths (week of the epidemics / 2), as explained in Galli et\u00a0al., 2023.j.> parr_sel <- peste_cum\u00a0>\u00a0death_count_thr> peste_cum_norm_sel <- peste_cum_norm> peste_cum_norm_melt <- melt(peste_cum_norm_sel)> colnames(peste_cum_norm_melt) <- c> peste_cum_norm_melt$Date <- as.Date(peste_cum_norm_melt$Date)> cumulative_curves_sel <- ggplot)\u00a0+\u00a0geom_line\u00a0+\u00a0scale_color_manual)\u00a0+\u00a0theme_bw\u00a0+\u00a0ylab(\"Cumulative relative frequency of plague deaths (%)\")Remove parishes with fewer cases than the threshold and plot only the selected cumulative curves .> parr_sBuild the cumulative curves of the plague deaths for each parish .7.Note: To cluster the parishes (or geographic units) in two or more groups, we are going to perform a k-means clustering on the result of the Principal Coordinates Analysis (PCoA) performed on the cumulative curves of plague deaths. In particular, we are going to compare the cumulative curves of the different parishes with each other to generate a distance matrix, which will be subjected to PCoA. Performing a PCoA on the dataset\u00a0allows us to reduce the dimension of our data and to visualize them in two (or three) dimensions. Then we can apply k-means clustering, an unsupervised clustering algorithm that groups a dataset into a specific number of clusters . The k-means algorithm will assign each observation (in our case each parish) to a cluster on the basis of their position on the PCoA space.,a.> dist <- dist(t(peste_cum_norm_sel))Calculate the Euclidean distance matrix between the cumulative curves of the different parishes.b.> pcoa <- cmdscale> plot(pcoa$eig)> pcoa <- cmdscaleNote: First, we must determine the best number of axes for the PCoA analysis on the basis of the eigenvalues. The plot shows that the eigenvalues drastically drop down for the first three dimensions.Perform the Principal Coordinates Analysis (PCoA) and make the scree plot .> pcoa fviz_nbclustNote: We determined the optimal number of clusters in the dataset using a popular cluster validation index: the average silhouette width method.,Determine the optimal number of clusters in which the parishes (or geographic units) can be divided .> fviz_nd.> f <- kmeans> clusters <- as.matrix(f$cluster)> clus <- clustersClusteringPerform the clustering analysis on the basis of the cumulative curves.8.Use the PERMANOVA test to determine if the separation between the clusters is statistically significant.> a <- adonis2> p_value <- a$`Pr(>F)`[1]> p_value[1] 0.0019.Plot the results of the PCoA and the k-means clustering .Figure\u00a06> plot_pcoa <- s.class,\u00a0\u00a0\u00a0col\u00a0= c,\u00a0\u00a0\u00a0cellipse\u00a0= 0,\u00a0\u00a0\u00a0sub\u00a0= paste,\u00a0\u00a0\u00a0xlim\u00a0= c)In this step, we are going to group cases/deaths based on the progression of the epidemic. In particular, we are going to analyze the specific cumulative epidemiological curves of each geographical unit. In the example dataset about the 1630 plague epidemic in Milan, the geographical units are the parishes in which the city was divided and where the person died . Other geographical units can be streets, houses, villages, districts, etc.Timing: 3\u20134 h10.Load the necessary R packages in the current RStudio session.> library(RColorBrewer)> library(inflection)> library(ggpubr)11.Color the cumulative relative frequency curves of plague deaths for each parish on the basis of their clusters .Figure\u00a07> peste_cum_norm_melt <- melt(peste_cum_norm_sel)> colnames(peste_cum_norm_melt) <- c> clusters <- as.matrix(f$cluster)> peste_cum_norm_melt$Date <- as.Date(peste_cum_norm_melt$Date)> peste_cum_norm_melt$Cluster <- as.character(clusters)> Cumulative_curves_sel_clusters <- ggplot)\u00a0+\u00a0geom_line\u00a0+\u00a0scale_color_manual)\u00a0+\u00a0theme_bw\u00a0+\u00a0ylab(\"Cumulative relative frequency of plague deaths (%)\")12.Save a table with the information about the clusters and the corresponding parishes to be used later for further analysis on the clusters.> palette <- c> tab_clusters <- data.frame(Parish\u00a0= row.names(clusters), Cluster\u00a0=\u00a0>\u00a0as.data.frame(clusters)$V1, Color\u00a0= palette[as.matrix(clusters)])> head(tab_clusters)> write.csv13.Note: As an example, we are going to determine: the first plague case for each parish, the inflection points of the cumulative curves, and the date at which the parishes of the two clusters reached 25%, 50%, 75%, and 100% of their total plague deaths.a.> peste_cum_norm_melt_first <- peste_cum_norm_melt> peste_cum_norm_melt_first_nodup <- peste_cum_norm_melt_first> peste_cum_norm_melt_first_nodup <- NULL> colnames(peste_cum_norm_melt_first_nodup) <- cCalculate the dates on which the parishes of the two clusters reached the first plague death.b.> peste_cum_norm_melt_25\u00a0<- peste_cum_norm_melt> peste_cum_norm_melt_25_nodup <- peste_cum_norm_melt_25> peste_cum_norm_melt_25_nodup <- NULL> colnames(peste_cum_norm_melt_25_nodup) <- cCalculate the dates on which the parishes of the two clusters reached 25% of total plague deaths.c.> peste_cum_norm_melt_50\u00a0<- peste_cum_norm_melt> peste_cum_norm_melt_50_nodup <- peste_cum_norm_melt_50> peste_cum_norm_melt_50_nodup <- NULL> colnames(peste_cum_norm_melt_50_nodup) <- cCalculate the dates on which the parishes of the two clusters reached 50% of total plague deaths.d.> peste_cum_norm_melt_75\u00a0<- peste_cum_norm_melt> peste_cum_norm_melt_75_nodup <- peste_cum_norm_melt_75> peste_cum_norm_melt_75_nodup <- NULL> colnames(peste_cum_norm_melt_75_nodup) <- cCalculate the dates on which the parishes of the two clusters reached 75% of total plague deaths.e.> peste_cum_norm_melt_100\u00a0<- peste_cum_norm_melt> peste_cum_norm_melt_100_nodup <- peste_cum_norm_melt_100> peste_cum_norm_melt_100_nodup <- NULL> colnames(peste_cum_norm_melt_100_nodup) <- cCalculate the dates on which the parishes of the two clusters reached 100% of total plague deaths.f.> infl_date_tab <- matrix)> colnames(infl_date_tab) <- c> for (i in 1:ncol(peste_cum_norm)){\u00a0col\u00a0= colnames(peste_cum_norm)[i]\u00a0infl_date <- as.Date(bede(as.numeric(as.Date(row.names(peste_cum_norm))), peste_cum_norm,0)$iplast, origin\u00a0= \"1970-01-01\")\u00a0infl_date_tab <- as.character(infl_date)\u00a0infl_date_tab <- col}Calculate the dates on which the cumulative curves of the parishes of the two clusters change concavity, corresponding to the epidemic peak .g.> all_tab_tmp <- merge> colnames[1:2] <- c> all_tab_tmp1\u00a0<- merge> all_tab_tmp2\u00a0<- merge> all_tab_tmp3\u00a0<- merge> all_tab_tmp4\u00a0<- merge> all_tab <- merge> head> all_tab$Inflection_date <- as.Date> all_tab2\u00a0<- melt)Merge all the data in one table.h.> all_tab2$Cluster <- factor, ordered\u00a0= TRUE)> my_comparisons <- list)> labels <- list#label name of facet> labels <- list> facet_labeller <- function{return}> Clusters_boxplot <- ggboxplot\u00a0+\u00a0scale_fill_manual)\u00a0+\u00a0geom_jitter)\u00a0+\u00a0facet_wrap\u00a0+\u00a0stat_compare_means\u00a0+\u00a0theme(legend.position\u00a0= \"none\")\u00a0+\u00a0ylab( \"Date\")\u00a0+\u00a0theme(strip.text.x\u00a0= element_text(size\u00a0= 8))Plot the results as boxplots and determine if the differences between the two clusters are statistically significant > gps <- read.csv> clusters <- read.csv(\"Clusters.csv\")Load the table with the epidemiological data, the table with the GPS information about the geographic units, in this case, the parishes, and the table with the clusters (see step 12).b.> df2\u00a0<- data.frame)> df3\u00a0<- df2 %>% select(-count)> tab <- left_join> tab$Date <- as.Date(tab$Date)> tab_cluster <- left_join> tab_cluster_2\u00a0<- droplevels))#drop rows without cluster total number of cases in the 2 clusters\u00a0= 7002Produce a summary that integrates all the information for your dataset.c.> tab_cluster_2$Weeks <- as.numeric)> tab_cluster_2$Cluster <- factor)> tab_cluster_3\u00a0<- tab_cluster_2 %>% filter(Death_cause\u00a0== \"Plague\")> cc_clusters <- tab_cluster_3 %>%\u00a0group_by %>%\u00a0summarize(count\u00a0= n) %>%\u00a0ggplot)\u00a0+\u00a0geom_line(size\u00a0= 0.7)\u00a0+\u00a0geom_point(size\u00a0= 2)\u00a0+\u00a0theme_bw\u00a0+\u00a0scale_color_manual)\u00a0+\u00a0theme(axis.title.x\u00a0= element_text(size\u00a0= 12),\u00a0\u00a0axis.title.y\u00a0= element_text(size\u00a0= 12))\u00a0+\u00a0labs(y\u00a0= 'Number of Deaths')Note: The number of color values assigned to the function \u201cscale_fill_manual\u201d must be the same as the number of clusters.Plot the weekly number of plague deaths for each cluster .> tab_clVisualize the epidemiological evolution of the epidemic in the parishes of the two clusters.The parishes, and therefore our cases, have been clustered on the basis of the temporal progression of the epidemic. Now we can analyze what are the differences and similarities between the clusters.Timing: 4 h15.Load the R packages in the current RStudio session.> library(png)> library(grid)16.Produce a summary table that integrates all the information for your dataset (see step 14b).> head(tab_cluster)# A tibble: 6 x 7# Groups: Parish, Cluster, Color, Death_cause, Latitude [6]Note: Latitude and Longitude are the columns used to indicate geographic coordinates.17.Filter the dataset to remove all the parishes without geographic information.> df <- tab_cluster %>% filter(!is.na(Latitude))18.Create a new gray cluster (Cluster \u201c0\u201d) for the unassigned parishes .> df$Cluster[is.na(df$Cluster)] <- 0> df$Color[is.na(df$Color)] <- \"gray\"19.Summarize the number of cases for each parish, cluster, death cause, and coordinates.> df2\u00a0<- df %>% group_by %>%summarize(Count\u00a0= n)> head(df2)# A tibble: 6\u00a0\u00d7\u00a07# Groups: Parish, Cluster, Color, Death_cause, Latitude [6]20.Clean the table removing non-plague-related deaths.> df2$Cluster <- factor,ordered\u00a0= TRUE)> peste_clus_gps <- df2 %>% filter(Death_cause\u00a0== \"Plague\")> peste_clus_gps$Death_cause <- NULL> peste_clus_gps <- peste_clus_gps> peste_clus_gps$Latitude <- as.numeric(peste_clus_gps$Latitude)> peste_clus_gps$Longitude <- as.numeric(peste_clus_gps$Longitude)> peste_clus_gps$Count <- as.numeric(peste_clus_gps$Count)21.png image and transform it into a raster image graphical object.Load your map stored as a > map <- readPNG(\"positron_darker_2023.png\")> map_2_plot <- rasterGrob22.Annotate the GPS coordinates of the four corners of the map image.Note: we can retrieve our base map image from QGIS by cropping the area of interest and annotating the GPS coordinates of the margins of our crop. This is essential to plot the points in their exact location on the map: the map itself needs to be referenced to the real GPS coordinates so that the point can be plotted using the real GPS coordinates available for each parish.> gps_map <-data.frame,\u00a0\u00a0\u00a0Y\u00a0= c,\u00a0\u00a0\u00a0fid\u00a0= c,\u00a0\u00a0\u00a0crop\u00a0= c)> xmin <- gps_map #Bottom Left margin> ymin <- gps_map #Bottom Right margin> xmax <- gps_map #Top Right margin> ymax <- gps_map #Top Right margin23.Find the aspect ratio of the png image and use the \u201czoom\u201d variable to scale the output file size.> img_width <- ncol(map)> img_height <- nrow(map)> aspect_ratio <- img_width/img_height> zoom <- 15Note: With the aspect ratio of the map and a multiplicative factor (zoom variable), it is possible to save the final map image at different sizes maintaining good resolution. The reasonable value of the zoom variable depends greatly on the size (in pixels) and the shape of the initial crop of the map.24.Plotting the parishes over the map according to the GPS coordinate. The size of the points is associated to the number of plague deaths and the color represents the cluster of the parishes.Note: The aspect ratio of the map must be maintained. To do so, we have to fix the width and height of the final plot file. RStudio may automatically plot the map with an incorrect aspect ratio. We strongly recommend saving the png file using the provided commands instead.> p <-ggplot)+\u00a0annotation_custom+\u00a0geom_point)+\u00a0scale_color_manual)+\u00a0labs\u00a0+\u00a0xlim+\u00a0ylim+\u00a0theme_classic+\u00a0theme,\u00a0\u00a0legend.title=element_text(size=zoom/2),\u00a0\u00a0axis.ticks=element_blank,\u00a0\u00a0axis.title.x=element_blank,\u00a0\u00a0axis.title.y=element_blank,\u00a0\u00a0panel.grid.major\u00a0= element_blank,\u00a0\u00a0panel.grid.minor\u00a0= element_blank,\u00a0\u00a0panel.background\u00a0= element_blank,\u00a0\u00a0legend.position\u00a0= c )25.png and scale it using the zoom variable Generate a visualization of the distribution of the parishes of the different clusters on a map using the coordinates and the information about the parishes.Parishes localization on the map of the city of Milan. In blue, parishes of cluster 1; in red, those of cluster 2; in gray, parishes with less than 21 total plague deaths . The size of the points represents the total number of deaths related to the plague experienced by the parish.This protocol has been designed to reconstruct the epidemiological dynamics of an epidemic using the recorded deaths and their geographical location.The first outcome consists of a time-series plot where it is possible to compare the temporal evolution of the epidemics against the incidence of deaths unrelated to the disease of interest .Then, the protocol performs a clustering analysis on the geographical units on the basis of their cumulative relative frequency of plague deaths. The final outcome of this step is the Principal Coordinates Analysis (PCoA) plot, where the parishes have been colored on the basis of the clusters .Once we find the clusters, we can start to analyze the temporal dynamics of the epidemic in each of them; in Lastly, we analyze the spatial dynamics clusters by visualizing the geographical position of the parishes on a map: The clustering analysis used in this protocol does not rely on any kind of geographic information. Although this approach is advantageous when we are dealing with historical data for which geographic information is rarer or imprecise, this approach may be limiting for the analysis of datasets in which this information is available and reliable. In this case, the clustering analysis should consider the implementation of geographic information.In step 5 of \u201cOpen the csv file with a spreadsheet application .In this application, we can easily apply any adjustment and export the spreadsheet as an xlsx or a csv file. The file should be correctly formatted and ready to be imported in R.> df <- read.csvFor xlsx files (Excel format file):> install.packages(\"readxl\")> library(readxl)> df <- read_xlsx(\"TableS1.xlsx\")For csv files, we can import the table in R using the same lines of code in step 5 of \u201cAt step 5 in the \u201c> install.packages(\"vroom\u201d)> library(vroom)> library(tidyverse)> df <- vroom> tab <- as_tibble)> tab$count <- NULL> tab$Date <- as.Date(tab$Date)> tab <- tab #sort by dateWhen a table is too large , the functions \u201cread.csv\u201d (for \u201ccsv files\u201d) or \u201cread.delim\u201d (for tab delimited files) may take too much computational time and RAM to maintain the table in the environment. In this case, the \u201ctibble\u201d class can help reduce time and RAM needed to handle the dataset. Thus, to upload a large table it is better to use another R library such as \u201cvroom\u201d. The following code must be substituted to step 5 of the \u201cAt step 6, parishes name contains spelling errors.> as.matrix(names(table(tab$Parish)))It is possible that the dataset contains spelling errors, or the same parish written in different ways . In these cases, R does not consider them as the same parish. To find possible errors we can list all the parishes and manually check for errors.> tab$Parish <- gsubThen we can correct them using R. As an example, consider a situation in which the parish of \u201cS. Bartolomeo\u201d is written in two different ways: \u201cS. Bartolomeo\u201d and \u201cS. bartolomeo\u201d.In this way we substituted all the cells containing \"S. bartolomeo\" with \"S. Bartolomeo\".At step 7c, the silhouette analysis indicates an optimal number of clusters higher than two.The protocol has been developed on the example dataset in which silhouette analysis finds that two clusters is the optimal number to classify the parishes. For this reason, this protocol can be directly applied only when the two clusters are found to be optimal.Whenever the protocol finds that more than two clusters are needed to describe the dataset, the user should slightly modify the commands to be able to compare the clusters .In the section \u201cGPS information is not always available, particularly when dealing with old datasets that may refer to particular geographic locations that changed names or disappeared over time.The clustering approach applied in this protocol does not rely on any type of geographical information. Thus, you can follow the protocol from step 1 till step 14 without any specific geographic information .Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Riccardo Nodari (This study did not generate new unique reagents."} +{"text": "The software and firmware are designed for Opal Kelly FPGA modules, yet the Python developments are generally useful to organize communication with peripheral chips.We are developing a data acquisition system (DAQ) for real-time feedback that uses FPGA-based control of and acquisition from various electronic chips, or peripherals. Because these peripherals communicate over multiple protocols through an FPGA, we designed pyripherals retains as a dictionary key. When passed the location of the data field, parameterized functions automatically format the data or command as required by the communication interface used by the peripheral. The assembled message is passed to the appropriate hardware controller responsible for low-level communication with the peripheral. In this solution, the addressing, bit indexing, and formatting are handled by pyripherals before the message is sent over the Opal Kelly FrontPanel API to a hardware-level communication controller on an Opal Kelly FPGA for rapid readout of photon return time histograms. Similar to pyripherals, the Python package registerMap = the bit index of the upper end of the data field in the register. Ex. in a 32-bit register where the data field is located in the last 4 bits of the register, Bit Index (High) would be 31.Bit Index (Low) = the bit index of the lower end of the data field in the register. Ex. in a 32-bit register where the data field is located in the last 4 bits of the register, Bit Index (Low) would be 28.pyripherals then reads the spreadsheet, referred to as a register index in the documentation, and returns a dictionary of name-Register pairs using the Register.get_chip_registers static method. The example below retrieves the register index from the table above.\u00bb> MYADC_regs = Register.get_chip_registers(\u2018MyADC\u2019)Register object holds all values from the spreadsheet for the data field it represents. A guide for creating a register index is located in the documentation. An example register is shown below.Each \u00bb> print(MYADC_regs[\u2018RESULT\u2019])0\u00d70[0:11]\u00bb> MYADC_regs[\u2018RESULT\u2019].__dict__{\u2018address\u2019: 0, \u2018default\u2019: 15, \u2018bit_index_high\u2019: 11, \u2018bit_index_low\u2019: 0, \u2018bit_width\u2019: 12}register abstraction of pyripherals allows user code to refer to data fields using only their names. The spreadsheet organization of data fields allows for user-friendly editing and sharing of data field information without the need to change user code. Specific applications include communicating with microcontrollers or development boards like Arduino as well as accessing data using SPI or I2C controllers.The pyripherals uses registers to assemble messages for SPI and a bit_width of 32 that adds 7 to the address every time it is advanced.// bit_width=32 addr_step=7`define MYADC_WRITE_IN_GEN_ADDR 8\u2019h04 WRITE_IN is data from the host computer into the FPGA that is destined for the ADC chip. More information on the syntax and meaning of these lines is available in the endpoint definitions guide.The naming convention for endpoints that contain addresses or bit indices is demonstrated below with curly brackets {} indicating placeholders to be completed by the user. Endpoint directions are from the perspective of the FPGA so Addresses:`define {CHIPNAME}_{ENDPOINT_NAME}{_GEN_ADDR} {hexadecimal address} // bit_width={bit_width} addr_step={addr_step}Bit Indices:`define {CHIPNAME}_{ENDPOINT_NAME}{_GEN_BIT} {decimal bit index} // addr={address or endpoint name} bit_width={bit_width}Note: the above comments must be placed on the same line as the \u2018define. They are split here for readability.create_chips method which instantiates a specified number of chips, incrementing the endpoint addresses and bit indices according to the GEN_ADDR, GEN_BIT, bit_width, and addr_step parameters above.For multiple units of the same chip, each chip class has a endpoint.get_chip_endpoints which returns a dictionary of name-Endpoint pairs. An example using the \u201cMYADC_WRITE_IN\u201d endpoint from earlier is shown below.Once created, the user can read the endpoint definitions file with \u00bb> MYADC_eps = Endpoint.get_chip_endpoints(chip_name=\u2019MYADC\u2019)\u00bb> print(MYADC_eps[\u2018WRITE_IN\u2019])0\u00d74[None:None]\u00bb> MYADC_eps[\u2018WRITE_IN\u2019].__dict__{\u2018address\u2019: 4, \u2018bit_index_low\u2019: None, \u2018bit_index_high\u2019: None, \u2018bit_width\u2019: 32, \u2018gen_bit\u2019: False, \u2018gen_address\u2019: False, \u2018addr_step\u2019: 7}endpoint class in pyripherals extends the capabilities of the Opal Kelly FrontPanel API by automatically linking the Python and Verilog endpoint data with a shared definitions file. With pyripherals, when the user changes the value of an endpoint in the definitions file the change is reflected in both the Python and Verilog code.The pyripherals is available at https://github.com/lucask07/covg_fpga/. It is written for the Opal Kelly XEM7310 FPGA and supports I2C, SPI, and LVDS communication with a DDR for data buffering. An example use of this code is an impedance analyzer using a DAC80508 digital-to-analog converter (Our FPGA code for use with onverter and an Aonverter communichttps://pyripherals.readthedocs.io/en/latest/index.html and the GitHub is available at https://github.com/Ajstros/pyripherals. pyripherals is available for install from pip at https://pypi.org/project/pyripherals/.Documentation is available at pyripherals was developed under an NIH-funded project to create a digital ion channel amplifier at the University of St. Thomas where it is being used to communicate with and control an FPGA-based data acquisition system for real-time feedback."} +{"text": "Endoscopic submucosal dissection (ESD) as a treatment for superficial pharyngeal cancer has been developed and widely accepted by endoscopists in JapanVideo\u20061\u2002A nerve-preserving strategy for endoscopic submucosal dissection of superficial pharyngeal cancers.ESD was performed under general anesthesia. Narrow-band imaging (NBI) and Lugol chromoendoscopy clearly revealed the lesion . We perEndoscopy_UCTN_Code_TTT_1AO_2AG"} +{"text": "A 51-year-old man was referred to our institution with persistent iron deficiency anemia. Initial gastroduodenoscopy and colonoscopy at his local hospital were unremarkable. A subsequent small bowel capsule endoscopy revealed a distal small bowel polyp with evidence of fresh bleeding . A tripDuring intraoperative enteroscopy, an actively bleeding polyp was detected in the distal ileum , and a Video\u20061\u2002The intraoperative enteroscopy procedure.Obscure gastrointestinal bleeding (OGIB) is a challenging condition that accounts for nearly 5\u200a% of all gastrointestinal bleeding casesEndoscopy_UCTN_Code_CCL_1AC_2AC"} +{"text": "These methods thus are hard to apply on real-world datasets (like ImageNet) since there are no such pre-defined attributes in the data environment. The latest works have explored to use semantic-rich knowledge graphs (such as WordNet) to substitute pre-defined attributes. However, these methods encounter a serious \u201crole=\u201cpresentation\u201d>domain shift\u201d problem because such a knowledge graph cannot provide detailed enough semantics to describe fine-grained information. To this end, we propose a semantic-visual shared knowledge graph (SVKG) to enhance the detailed information for zero-shot learning. SVKG represents high-level information by using semantic embedding but describes fine-grained information by using visual features. These visual features can be directly extracted from real-world images to substitute pre-defined attributes. A multi-modals graph convolution network is also proposed to transfer SVKG into graph representations that can be used for downstream zero-shot learning tasks. Experimental results on the real-world datasets without pre-defined attributes demonstrate the effectiveness of our method and show the benefits of the proposed. Our method obtains a +2.8%, +0.5%, and +0.2% increase compared with the state-of-the-art in 2-hops, 3-hops, and all divisions relatively.Almost all existing zero-shot learning methods work only on benchmark datasets ( In recent years, zero-shot learning has attracted widespread attention in computer vision and machine learning areas. It aims to predict new classes that appear during the training process. The base idea of zero-shot learning is to use labeled semantic information to learn a projection between semantic space and visual space. Then, visual samples from new classes can be projected into semantic space to match the attributes to decide the corresponding classifications. In the past five years, a large number of methods for zero-shot learning have been proposed based on this idea \u00a0.etc. Moreover, these datasets are quite small, only tens or hundreds classes and tens of thousands samples, which are far away from real-world data environment, normally tens of thousands classes and millions samples. Thus, existing zero-shot methods are hard to be applied in real-world data environments such as ImageNet which does not provide any pre-defined attributes for any classes.However, these zero-shot learning methods inevitably need to follow a major premise that semantic attributes should be pre-defined and labeled in the datasets. Almost all recent zero-shot learning works are only evaluated on six small benchmark datasets . etc.) to substitute pre-defined attributes in semantics and have better generalization power in semantic representation. However, these GCN-based zero-shot learning methods for image classification on the ImageNet dataset, like GCNZ (etc.) without fine-grained semantics . Thus, the core question becomes \u201ccan a knowledge graph provide fine-grained semantics or even more for zero-shot learning?\u201d.In the past four years, the graph neural network (GNN) has been adopted by zero-shot learning, which makes zero-shot learning tasks applicable in real-world data environments . This isike GCNZ , DGP . At last, a multi-modals GCN network is proposed to embed (SVKG) into graph representations that can be used in zero-shot learning tasks, as showed in Based on the idea, we first scan all the image samples of seen classes in ImageNet-1K to extract parts of visual features for each seen class. Then, WordNet nodes and relations are extracted according to the seen and unseen class labels in ImageNet-1K and embedded as semantic features by a word embedding model. After that, parts of visual features and WordNet semantic features are connected together as a semantic-visual shared knowledge graph , then learn the semantic attribute characteristics of visual objects, and finally judge whether the attribute combinations are satisfied by the visual objects.Attribute-based methods account for the largest proportion of zero-shot learning (ZSL) research since ZSL was first proposed in DAP in 2009 Following the design principles of AwA dataset, a series of benchmark datasets with pre-defined attributes are established today, including AwA2, CUB, SUN, FLO and aPY. Based on these benchmark datasets, ZSL has a blowout development with several milestones.In 2013, with the development of semantic embedding technology, the first milestone of ZSL was the ALE model proposed by In 2017, with the development of deep learning technology in the field of visual computing, the second milestone of ZSL is the SAE model proposed by In 2018, with the remarkable performance of Generative Adversarial Networks (GAN) in imageRecently, some researchers have started to investigate how to mix various types of semantics to address further \u201cdomain shift\u201d issues. For instance, However, the above methods use pre-defined properties as their primary semantic source. As a result, these methods are essentially restricted to benchmark datasets with pre-defined features. The applicability of these methods in real-world environments devoid of pre-defined features is restricted to a small number of cases.Knowledge graph (KG) actually is a third part knowledge base that can provide semantic information for semantic-to-visual transformation in zero-shot learning. Knowledge graph (KG) actually constitutes a third-party knowledge base that can provide semantic information for semantic-to-visual transformation in zero-shot learning. Thus, KG is intuitively considered a substitution for pre-defined attributes. Benefiting from the development of GNN, GCNZ creates However, compared to the pre-defined features in the six benchmark datasets, the knowledge network used in GNN-based approaches providesTo enhance the fine-grained semantic information for existing KG, the latest research tries to apply \u201cvisual knowledge\u201d in zero-shot learning. However, the above methods continue to see visual semantics as auxiliary or augmented semantics. In contrast to them, we want to combine semantic and visual representations into a single common knowledge graph, so-called visual-semantic shared knowledge graph.X\u00a0\u2208\u00a0\u211dN\u00d7F be the word-embedding set for all the nodes in A\u00a0\u2208\u00a0\u211dN\u00d7N be the adjacency matrix transferred from F is the dimensions of the embedding. After, a graph representation model g\u0398 is learned to transfer X to the graph node representation H\u00a0\u2208\u00a0\u211dN\u00d7F\u2032 supervised by Iseen. Here, Iseen\u00a0\u2208\u00a0\u211dN\u00d7F\u2032\u2032 is the seen image feature set extracted by a CNN model. At last, an image classification model Iunseen to the particular class according to the graph node representation H. Here, Iunseen\u00a0\u2208\u00a0\u211dN\u00d7F\u2032\u2032 is the unseen image feature set extracted by a CNN model.Knowledge graph-based Zero-Shot learning uses the knowledge-aided method to learn an image classification model from seen classes to predict unseen classes. First, given a knowledge graph SVKG) is a multi-modal graph that contains both semantic embedding and visual embedding in the same graph. Let X represents the embedding set of the graph nodes with Xs denotes Word-Embedding nodes and Xv represents CNN-Embedding nodes. A represents the edge set while As denotes the edges among Word-Embedding nodes and Av denotes the edges among CNN-Embedding nodes. SVKG is defined in Algorithm 1.Semantic-visual shared knowledge graph ,\u00a0seen\u00a0images Output:\u00a0SV\u00a0KG \u00a01:\u00a0\u00a0Xs\u00a0\u2190\u2212\u00a0Put\u00a0X\u00a0into\u00a0Glove \u00a02:\u00a0\u00a0As\u00a0\u2190\u2212\u00a0Put\u00a0X\u00a0into\u00a0WordNet\u00a0hyponym/hypernym \u00a03:\u00a0\u00a0Xv\u00a0\u2190\u2212\u00a0Put\u00a0seen\u00a0images\u00a0into\u00a0EfficientDet \u00a04:\u00a0\u00a0As\u00a0\u2190\u2212\u00a0Put\u00a0Xv\u00a0connecte\u00a0with\u00a0semantic\u00a0object\u00a0node \u00a05:\u00a0\u00a0X\u2032\u00a0\u2190\u2212\u00a0Xs\u00a0\u222a\u00a0Xv \u00a06:\u00a0\u00a0A\u2032\u00a0\u2190\u2212\u00a0As\u00a0\u222a\u00a0Av \u00a07:\u00a0\u00a0SV\u00a0KG\u00a0\u2190\u2212{\u00a0X\u2032,\u00a0A\u2032\u00a0} \u00a08:\u00a0\u00a0return\u00a0\u00a0SV\u00a0KG \u00a0_______________________________________________________________________________ SVKG, the semantic node set Xs is constructed from WordNet (https://wordnet.princeton.edu/) Noun words and embedded into word features by Glove (https://nlp.stanford.edu/projects/glove/). The edge matrix As is established by WordNet hyponym/hypernym links among these words. The visual node set Xv is obtained by using EfficientDet (etc.) from ImageNet-1k. Then, these visual nodes are connected to their semantic object node by the edge matrix Av . An example of SVKG about bird Finch is presented in In cientDet to detecXs needs to be transferred into semantic-visual shared space H. However, the visual feature space Xv might cause interference during Xs\u27f6H transfer process, leading to a serious over-fitting problem. Empirically, many data augmentation methods have shown to improve the generalization and robustness of the learning model . In SVKGaug, there are two feature modals. One is semantic feature modal {Xs generated from Glove-Embedding. The other is visual feature modal Xv extracted by EfficientDet. Thus, multi-modals graph representation learning is aimed to transfer both Xs and Xv into a semantic-visual shared feature modal H.As explained in the \u2018Problem Definition\u2019 section, knowledge graph Xs and Xv into H, as defined in g\u0398 is a Graph Convolutional Network (GCN) employed from D is the diagonal degree matrix of A matrix, where Di,i). Then, Iunseen is input into the trained classification model to calculate the similarities with all graph features H\u2032. To obtain the predicting result, Resultset records all the similarities between H\u2032 and Iunseen, and the labeli of corresponding In the predicting process, we first use the same Resnet-50 model to extract unseen image feature ________________________________________________________________________________________ Algorithm\u00a02\u00a0Zero-shot\u00a0Predicting\u00a0Process _______________________________________________________________________________________ Input:\u00a0H\u2032,\u00a0Iunseen Output:\u00a0Top-k\u00a0result \u00a01:\u00a0Resultset\u00a0\u2190\u2212{\u2205,\u00a0\u2205} \u00a02:\u00a0for\u00a0H\u2032i\u00a0in\u00a0H\u2032\u00a0do \u00a03:\u00a0\u00a0\u00a0Simi\u00a0\u2190\u2212\u00a0H\u2032i\u00a0\u22c5\u00a0Iunseen \u00a04:\u00a0\u00a0\u00a0lableli\u00a0\u2190\u2212\u00a0findLabel(H\u2032i) \u00a05:\u00a0\u00a0\u00a0Resultset\u00a0\u2190\u2212{Simi,\u00a0lableli} \u00a06:\u00a0end\u00a0for \u00a07:\u00a0Resultset\u00a0\u2190\u2212\u00a0SortBySim(Resultset) \u00a08:\u00a0Resultset\u00a0\u2190\u2212\u00a0Top-k(Resultset) \u00a09:\u00a0return\u00a0\u00a0Resultset \u00a0____________________________________________________________________________________ Iunseen is not used during the whole training process. In the predicting process, the input Iunseen is the first time the model touches the unseen images.It can be observed, the unseen image feature SVKG. At last, extra downstream tasks and observations are discussed.In this section, the datasets and evaluation metrics are introduced first. Then, the implementation details about the model settings are explained. After, the state-of-the-arts comparisons are presented. Then, an ablation study is conducted for the proposed nth jumps to connect to other classes of ImageNet through the relations of a WordNet graph. For example, as showed in The experiments are conducted on ImageNet , which iXv in SVKG, a \u201cDetailed\u201d group which contains four subsets are divided from ImageNet-1K and corresponding parts visual features Xv for all these detailed categories are extracted from their image samples by EfficientDet. In a short, the experiments involve two groups and seven divisions divided by ImageNet. The detailed information for each corresponding division is shown in In order to show the effectiveness of visual feature There, the label rate demonstrates the difficulty of the corresponding division. This is because with the reduction of supervision in semi-supervised manner, there are higher requirements for the generalization and robustness of the model. The performance of corresponding division will also degrade as the supervised label rate decreases. Therefore, the accuracy in widely different divisions can reflect the robustness of the model. As can be seen from The proposed method is evaluated according to Generalized Zero-Shot Learning (GZSL) setting, which is the most challenging evaluation metric for zero-shot learning. In GZSL, all classes, no matter seen or unseen classes, are all considered as the candidate classes in the testing, while the test samples are only from unseen classes. We adopt the same train/test splits and the Top-k Hit Ratio (Hit@k) metric, in accordance with In the model implementations, Resnet-50 is used In this section, all the comparisons conducted in both General and Detailed groups follow the GZSL setting. For General group, DeViSE , ConSE , ConSE2 General group comparisons: From But from Top-2 to Top-20 accuracy evaluations, the latest method CL-DKG surpasses our method. The reason might be the fine-grained features strengthen discrimination ability but weaken, to some extent, the generalization ability of the model. However, it can be seen from Detailed group comparisons: The most significant contribution of the proposed method is that fine-grained visual features are shared with semantic features in the same knowledge graph. Here, Detail comparisons are aimed to show the effects of such shared visual features through some representative categories of ImageNet. It can be seen from From SVKG mainly consists of Xs, Xv and Xaug. Thus, four combinations, \u201cXs\u201d only, \u201cXs+ Xv\u201d, \u201cXs+ Xaug\u201d and \u201cAll\u201d, for ablation study are established. Indeed, \u201cXs\u201d denotes the traditional knowledge graph while \u201cAll\u201d represents the proposed knowledge graph SVKGaug. The experiments are conducted also on the Detailed group to 17.7% (All). The reason is that dog is a well-known category and widely used everywhere. This leads the upstream feature extractor, EfficientDet, to work well and extract more accurate part visual features for SVKG that significantly improves the Top-1 accuracy. A similar phenomenon is also observed in bird and primate categories. The study thus also reveals that the better performance of the upstream feature extractor, the better accuracy the proposed SVKG might achieve. In a short, the study demonstrates the effectiveness of each proposed module in real-world zero-shot learning tasks.As defined in ed group to evaluXs+ Xaug\u201d. The influence of graph augmentation Xaug is weakened after two or three hops, and distant nodes are easy to overfit with the presence of part visual nodes. Therefore, in the long-distance prediction, the overall performance of the model decreases.In the cases from Top-5 to Top-20, the best performance is \u201c For further discussion, we conducted an unseen class search compared with DGP on Detailed group. Some representative results are presented in SVKG graph on dog category. The orange-colored nodes represent seen classes and the blue-colored nodes represent unseen classes. SVKG. Intuitively, SVKG is more structured and order than the graph features of GCNZ and DGP. It can be observed that blue-colored nodes distribute among orange-colored nodes reveals the hidden relationships between seen and unseen classes. This is because the proposed visual features Xv lead the graph representations of SVKG close to real-world dog taxonomy. Unseen class nodes thus are distributed to the most related seen class nodes by the meaning of taxonomy. It obviously alleviates coincidence and proximity during unseen class predicting that improves the performance of zero-shot learning.Meanwhile, t-SNE was used to visualize knowledge graph features for initial graph, GCNZ graph, DGP graph and SVKG with GCNZ graph feature distribution and real image feature distribution, as shown in SVKG is significantly closer to the real image feature distribution than GCNZ. This indicates the feature of SVKG is more close to the real visual feature that is easier to be matched with unseen classes. This also explains why the proposed method achieves the best accuracy on Top-1 and Top-2 unseen class predicting.Moreover, we also compared feature distribution of SVKG) for zero-shot learning on the real-world dataset without needing pre-defined attributes. It combines semantic (from WordNet and Glove embedding) and visual features (extracted from raw images by EfficientDet) together in the same graph. The visual feature provides detailed information for describing fine-grained semantics that alleviates the \u201cDomain-Shift\u201d problem during the semantic-to-visual transformation of zero-shot learning. A novel multi-modal GCN model is also proposed to learn the graph representations of SVKG. After, the graph representations are further used for downstream zero-shot learning tasks in the experiments.In this article, we propose a semantic-visual shared knowledge graph (Experimental results on the real-world dataset demonstrate the effectiveness of our method and illustrate the multi-modal graph guide model generates more discriminative representation. And our method significantly surpasses other methods on Top-1 to Top-5 accuracy evaluations in the bird, snake, primate, and dog categories. Especially, on Top-1 accuracy evaluations, our method even achieves a 2-3 times increase compared with the state-of-the-art.SVKG is only storing fine-grained information in parts of visual features. In the future, we will add color, material, shape, and other relations and associated nodes to the SVKG in order to further increase the model\u2019s performance.The important component of zero-shot learning tasks implemented in real-world environments is still how to reasonably use and construct the knowledge graph. In this paper, the 10.7717/peerj-cs.1260/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj-cs.1260/supp-2Supplemental Information 2Click here for additional data file."} +{"text": "The term \u201cRNA-seq\u201d refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, from single cells, or from single nuclei. The kallisto, bustools, and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples, or both. Additionally, these tools allow gene expression values to be classified as originating from nascent RNA species or mature RNA species, making this workflow amenable to both cell-based and nucleus-based assays. This protocol describes in detail how to use kallisto and bustools in conjunction with a wrapper, kb-python, to preprocess RNA-seq data. While multiple steps are necessary to process input consisting of FASTQ sequencing files, a reference genome FASTA, and a GTF annotation28, to an output of quantifications using kallisto and bustools, these steps are greatly facilitated by the wrapper tool, kb-python. kb-python can extract reference transcriptomes from reference genomes and run kallisto and bustools in workflows optimal for each assay type. The kb-python tool simplifies the running of kallisto and bustools to the extent that all of this can be done in two steps: `kb ref` for generating a kallisto index from an annotated reference genome and `kb count` for mapping and quantification. Thus, kallisto, bustools, and kb-python make RNA-seq preprocessing efficient, modular, flexible, and simple.1The preprocessingindex from a set of sequences, referred to as targets, representing the set of sequences that RNA-seq reads can be mapped to. In a standard analysis, these targets are usually transcript sequences . However, more generally, users can define targets from any sets of sequences they wish to map their sequencing reads against. Since kallisto is a tool that leverages pseudoalignment, the mapping procedure relies on read assignment, such that each read is deemed to be compatible with a certain set of targets, rather than standard alignment. The kallisto index is based on the Bifrost29 implementation of the colored de Bruijn graph30, which enables memory-efficient and rapid read assignment.For RNA-seq read mapping, kallisto builds an kb ref command . The index created by --workflow=nac (nac: nascent and cDNA) contains both the cDNA and the nascent transcripts. The nascent transcript sequences consist of the full gene (both exons and introns). This nac index is suitable for single-nucleus RNA-seq as there exists a high abundance of non-mature transcripts captured in nucleus-based sequencing assays.32 Additionally, this nac index should be used for analyses that require jointly modeling nascent and mature RNA species.38 For both the standard and nac workflows, a user supplies a genome FASTA and GTF annotation, which kb-python uses to extract the relevant sequences. Finally, if one wishes to index a custom set of targets or of k-mers allows specific biotypes to be selected from the GTF file, making possible filtering of entries such as pseudogenes, which can improve read mapping accuracyry usage . It is rkb count command within kb-python enables mapping and quantification of bulk, single-cell, and single-nucleus RNA-seq reads (The eq reads . As diffThe specifications for sequencing assay technology within kb-python are as follows:Technology string: A technology string for a particular type of assay can be supplied via the -x option. The technology string can be used in one of three ways:kb --list) so one can name one of those directly (e.g. one can specify -x 10xv3).Option 1: Several assays are predefined within the software , and the biological sequence that is to be mapped .Strandedness: If a read (or the first read in the case of paired-end reads) is to be mapped in forward orientation, one should specify --strand=forward. If it is to be mapped in reverse orientation, one should specify --strand=reverse. If one does not want to map reads with strand-specificity, then one should specify --strand=unstranded. If a predefined name is used in the technology string -x option (option 1), then kb-python uses a default stranded option for that technology ; otherwise, the default is unstranded. Setting the --strand option explicitly will overrule the default option.Parity: If the technology involves two biological read files that are derived from paired-end sequencing (as is the case with Smartseq243 and Smartseq344 and many bulk RNA sequencing kits), one should specify --parity=paired to perform mapping that takes into account the fact that the reads are paired-end. Otherwise, one can specify --parity=single. If a predefined name is used in the -x technology string option (option 1), then kb-python uses the default parity option for that technology .On list: For single-cell and single-nucleus sequencing assays, barcodes are used to identify each cell or nucleus. The \u201con list\u201d of barcodes represents the known barcode sequences that are included in the assay. Barcodes extracted from the sequencing reads will be error-tolerantly mapped to this list in a process known as barcode error correction. The on list filename can be specified with the -w option in kb count. It can also be obtained by seqspec.40 If an on list is not provided or cannot be found for the given technology, then an on list is created by bustools via the bustools allowlist command which identifies repeating barcodes in sequencing reads. If the technology does not include cell barcodes (as is the case in bulk RNA-seq), the \u201con list\u201d option is irrelevant and no barcode processing occurs which should be the case for assays that don\u2019t include cell/nuclei barcodes . If a predefined name is used in the -x technology string option (option 1), then kb-python uses the default on list option for that technology.--workflow=nac should be used in kb count so that the nascent and mature RNA species are quantified accurately; otherwise that option should be omitted or --workflow=standard (which is the default) can be explicitly specified. For the nac workflow, one obtains three count matrices: 1) nascent, 2) mature, and 3) ambiguous. In most experiments, the plurality of reads will be \u201cambiguous\u201d since they originate from exons, which are present in both nascent RNA and mature RNA. Therefore, it is desirable to generate additional matrices by adding the counts from those three matrices, which users can either do themselves or by using the --sum option.24--sum=total adds all three matrices, --sum=cell adds the mature and ambiguous matrices, and --sum=nucleus adds the nascent and ambiguous matrices. Different matrices may be used for different types of analyses. For example, in single-cell RNA-seq analysis (where most \u201cambiguous\u201d counts are likely of mature RNA origin), jointly modeling the mature+ambiguous count matrix (--sum=cell) with the nascent count matrix permits biophysical modeling of RNA processing.38 In single-nucleus RNA-seq quantification, one might want to use --sum=nucleus to add up the nascent+ambiguous counts. The kb-python, kallisto, and bustools commands for the standard workflow and the nac workflow are shown in If a nac index was generated by kb ref, 48, sleuth49, limma-voom51, and other differential gene expression programs.In addition to single-cell and single-nucleus RNA-seq, kb count can be used for bulk RNA-seq. Bulk RNA-seq generally does not have UMIs or cell barcodes and relies on cDNA mapping. With -x BULK as the technology string, a workflow specific for bulk RNA-seq quantification is executed . This wiTo facilitate multi-sample analysis, artificial unique sample-specific barcodes can be created and stored in the BUS file and the resulting mapping between the artificially generated barcode and the sample ID is outputted. These sample-specific barcodes are 16-bp in length and are also stored in the BUS file. Where there exists both a cell barcode (like in single-cell RNA-seq) and a sample-specific barcode, both sets of barcodes will be outputted so that each entry in the resulting output count matrix can be associated with a particular cell and a particular sample. To utilize the multi-sample workflow, a batch file containing the file names of the FASTQ files must be provided .--dry-run option in kb count outputs the kallisto and bustools commands that will be run without actually running the programs. Also, the --verbose option in kb count is helpful for examining the kallisto and bustools commands that are being run as well as their output.The technical details of how kb count utilizes kallisto and bustools are detailed in the following paragraph. Note that the kallisto bus command within kallisto to produce a BUS file, which stores the read mapping information, and then uses bustools23 commands to process the BUS file. The kallisto bus command maps RNA-seq reads to a kallisto index, and the resultant BUS file stores the mapping information, including the barcode, unique molecular identifier (UMI), and the equivalence class representing the set of transcripts the read is compatible with.23 In certain RNA-seq assays, barcodes and/or UMIs may not be present, and are therefore not considered when processing the BUS file. After the mapping step is complete, the BUS file is sorted via the bustools sort command to facilitate further processing. For single-cell and single-nucleus experiments with multiplexed barcodes in the sequencing reads, an \u201con list\u201d of barcodes, representing the known barcode sequences that are included in the assay, needs to be provided. If an \u201con list\u201d is unavailable, the bustools allowlist command can be used to construct one from a sorted BUS file. The barcodes in the sorted BUS file are error-corrected to the \u201con list\u201d via bustools correct, then the BUS file is sorted again with bustools sort. The final sorted, on list-corrected BUS file is then used to generate quantifications via count matrices through the bustools count command. At any point, a sorted BUS file can be inputted into bustools compress to create a compressed BUS file (a BUSZ file), which can be subsequently decompressed via bustools decompress.52 Other bustools features enable more specialized workflows beyond what is provided by kb-python , one can supply the --cm option for quantification.Gene-level count matrices: In single-cell and single-nucleus RNA-seq, typically a gene-level count matrix is produced by collapsing UMIs to the gene level. Here, the bustools count command is run with the --genecounts option is not provided, and --multimappingis provided to avoid discarding reads or collapsed UMIs that are assigned to multiple genes. If UMIs are not present in the sequencing technology, the --cm option is supplied to perform counting without UMI collapsing. While downstream analyses can be performed on TCCs55, it is more often useful to produce transcript-level abundances from the TCCs for technologies where sequencing reads span the full length of transcripts, such as bulk RNA-seq. In such cases, an expectation-maximization algorithm is typically performed to probabilistically estimate transcript abundances.56 The procedure to generate transcript-level abundance matrices is performed by running the kallisto quant-tcc command on the TCC matrices.Transcript-level count matrices: Transcript-compatibility counts (TCCs) are counts assigned to equivalence classes where each equivalence class is defined by a unique set of transcripts. For producing a matrix of transcript-compatibility counts (TCCs), the 40 provides a specification for the structure of genomic sequencing assays, formatted in a machine-readable YAML file. The specification can be readily inputted into the kallisto bustools workflow for preprocessing reads from a given assay being the matrix columns.Here, the quantification output of the kb count command is described. While the initial step of kb count uses kallisto to produce a BUS file located at output_dir/output.bus, the actual quantification results are located in matrices in subdirectories of output_dir/. All matrices have the extension .mtx and will be in a sparse matrix (Matrix Market) file format with the barcodes (i.e. the cells or samples) being the matrix rows and the genes :The standard workflowcells_x_genes.mtx: The count matrix (in Matrix Market file format); only exonic reads are countedcells_x_genes.barcodes.txt: The barcodes representing the matrix row namescells_x_genes.genes.txt: The gene IDs representing the matrix column namescells_x_genes.genes.names.txt: Same as cells_x_genes.mtx except with gene names instead of gene IDs for the matrix columnscells_x_genes.barcodes.prefix.txt: If sample-specific barcodes are generated in addition to cell barcodes being recorded, then this file will be created and the sample-specific barcodes will be stored here. The lines of this file correspond to the lines in the cells_x_genes.barcodes.txt which contains the cell barcodes (both files will have the same number of lines). The sample-specific barcodes and cell barcodes can be joined together as a unique identifier for downstream analysis.nac workflow: same as the standard workflow except the .mtx files produced are differentcells_x_genes.mature.mtx: The mature RNA count matrixcells_x_genes.ambiguous.mtx: The nascent RNA count matrixcells_x_genes.nascent.mtx: The ambiguous RNA count matrixcells_x_genes.cell.mtx: The mature+ambiguous RNA count matrix (note: this is what is quantified into the count matrix in the standard workflow)cells_x_genes.nucleus.mtx: The nascent+ambiguous RNA count matrixcells_x_genes.total.mtx: The mature+nascent+ambiguous RNA count matrix--tcc option is used.For RNA-seq assays (e.g. bulk RNA-seq or Smartseq2) that profile the full length of transcripts in which case it is desirable to perform transcript-level quantification, the output_dir/counts_unfiltered/ which contains the following files for the standard workflow:The first step to doing transcript-level quantification is to obtain transcript-compatibility counts (TCCs) over equivalence classes (ECs). The TCCs will be outputted into cells_x_tcc.mtx: The count matrix containing the TCCscells_x_tcc.barcodes.txt: The barcodes representing the matrix row namescells_x_tcc.ec.txt: The equivalence classes representing the matrix column names for all transcripts within the equivalence class)output_dir/quant_unfiltered/ directory which contains the following:The --tcc option will additionally produce transcript-level estimated counts which will be placed in the matrix.abundance.mtx: The matrix containing the transcript-level estimated countsmatrix.abundance.tpm.mtx: The matrix containing the TPM-normalized transcript-level abundancesmatrix.efflens.mtx: A matrix that contains the transcript effective lengthsmatrix.fld.tsv: A file with two columns, containing the mean and standard deviation, respectively, of the fragment length distribution used to produce transcript-level abundances and effective lengths for each row of the matrix.matrix.abundance.gene.mtx: A matrix that is the same as the matrix.abundance.mtx matrix except counts are aggregated to gene-levelmatrix.abundance.gene.tpm.mtx: A matrix that is the same as the matrix.abundance.tpm.mtx matrix except TPMs are aggregated to gene-leveltranscripts.txt: The transcript names representing the matrix column names for the transcript-level quantification matricesgenes.txt: The gene IDs representing the matrix column names for the gene-level aggregation quantification matricestranscript_lengths.txt: The transcript names along with their lengthsrow names are the individual samples and will be the same as those in output_dir/counts_unfiltered/cells_x_tcc.barcodes.txt - The output_dir/matrix.cells and output_dir/matrix.sample.barcodes files provide a mapping between the sample name and the sample barcode.*Note: The *Note: The --matrix-to-directories option will output each row of the matrix into a separate subdirectory. In other words, using this option will produce multiple new directories within output_dir/quant_unfiltered/. Each one will be named abundance_{n} . Within each subdirectory, an abundance.tsv text file and abundance.h5 HDF5 file will be created containing the quantifications for that particular sample. These abundance files are identical to the abundance files produced by the original version of kallisto for bulk RNA-seq.60 for downstream processing in python, an anndata61 object needs to be created , the matrices that are loaded in will become much smaller and more efficient to process.A 64-bit computer running either macOS, Windows, or a Linux/Unix operating system.kallisto version 0.50.1 or later (which comes packaged with kb-python)bustools version 0.43.1 or later (which comes packaged with kb-python)kb-python version 0.28.0 or laterPython 3.7 or later (for kb-python version 0.28.0)Bulk, single-cell, or single-nucleus RNA sequencing reads in (possibly gzip) FASTQ format.unfiltered GTF file) and an hour to generate the nac index. For the preprocessing of 800 million Illumina sequencing reads (stored in a single pair of fastq.gz files) produced by single-cell RNA-seq from 10x Genomics, kb count with the nac workflow can take under an hour on 8 threads and under 40 minutes on 16 threads, with an even lower runtime for the standard workflow.The runtime depends on the size of the reference being indexed, the number and length of the sequencing reads being processed, other properties of the dataset being quantified, system hardware, and the number of threads allotted. The kb ref command only needs to be run once to create the index against which reads will be mapped. With 8 threads on a server with x86-64 architecture and 32 Intel Xeon CPUs (E5-2667 v3 @ 3.20GHz), kb ref takes approximately 15 minutes to generate a standard index from the GRCm39 mouse genome file created by kb ref should be the exact file used by kb count when running kb count on that index. All the transcripts in the t2g file must be exactly the same as the transcripts present in the kallisto index. Incompatibilities can lead to unpredictable behavior in the bustools quantification step.31 .dna.toplevel.fa.gz files or the GENCODE67 .primary_assembly.genome.fa.gz files should be used as the reference genome. Use of FASTA files incompatible with the supplied GTF will lead to errors.When using kb ref to generate a kallisto index, a genome FASTA file (not a transcriptome FASTA file) should be supplied along with the genome annotation GTF file. A transcriptome file will automatically be generated by kb ref and be indexed by kallisto. In general, the EnsemblWhen performing multiple kb-python runs simultaneously, a different temporary directory must be specified via the --tmp option for each run. The temporary directory also must not exist beforehand.Finally, one should make sure that the value supplied to the -x technology string option matches the assay from which the sequencing reads were generated.Note: If the technology string begins with a \u2212, for example: \u22121,0,0:0,0,5:0,5,0, one would need to write \u2212x \u201c \u22121,0,0:0,0,5:0,5,0\u201d to avoid the string being misinterpreted as a command-line flag.Here, we describe the procedures to use for mouse samples of paired-end bulk RNA-seq, 10x (version 3) single-cell RNA-seq, and 10x (version 3) single-nucleus RNA-seq.Input:Paired-end unstranded mouse RNA-seq reads (3 samples):sample1_R1.fastq.gz sample1_R2.fastq.gzsample2_R1.fastq.gz sample2_R2.fastq.gzsample3_R1.fastq.gz sample3_R2.fastq.gz1.pip install kb_python2.ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gzwget ftp.ensembl.org/pub/release-108/gtf/mus_musculus/Mus_musculus.GRCm39.108.gtf.gzwget 3.kb ref -i index.idx -g t2g.txt -f1 cdna.fasta \\\u2009\u2009\u2009\u2009Mus_musculus.GRCm39.dna.primary_assembly.fa.gz \\\u2009\u2009\u2009\u2009Mus_musculus.GRCm39.108.gtf.gz4.kb count -x BULK -o output_dir -i index.idx -g t2g.txt \\\u2009\u2009\u2009\u2009--parity=paired --strand=unstranded \\\u2009\u2009\u2009\u2009--tcc --matrix-to-directories \\\u2009\u2009\u2009\u2009sample1_R1.fastq.gz sample1_R2.fastq.gz \\\u2009\u2009\u2009\u2009sample2_R1.fastq.gz sample2_R2.fastq.gz \\\u2009\u2009\u2009\u2009sample3_R1.fastq.gz sample3_R2.fastq.gz5.Output for sample 1:output_dir/quant_unfiltered/abundance_1/abundance.tsvoutput_dir/quant_unfiltered/abundance_1/abundance.gene.tsvoutput_dir/quant_unfiltered/abundance_1/abundance.h5Output for sample 2:output_dir/quant_unfiltered/abundance_2/abundance.tsvoutput_dir/quant_unfiltered/abundance_2/abundance.gene.tsvoutput_dir/quant_unfiltered/abundance_2/abundance.h5Output for sample 3:output_dir/quant_unfiltered/abundance_3/abundance.tsvoutput_dir/quant_unfiltered/abundance_3/abundance.gene.tsvoutput_dir/quant_unfiltered/abundance_3/abundance.h5The abundance.tsv files contain the transcript-level abundances. The abundance.h5 file contains the same information as the abundance.tsv files except in HDF5 format. The abundance.gene.tsv files contain the gene-level abundances (taken by summing up the transcript-level abundances for each gene). These files can be used in downstream differential gene expression programs.Input:10x version 3 single-cell RNA-seq reads: R1.fastq.gz and R2.fastq.gz1.pip install kb_python2.ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gzwget ftp.ensembl.org/pub/release-108/gtf/mus_musculus/Mus_musculus.GRCm39.108.gtf.gzwget 3.kb ref -i index.idx -g t2g.txt -f1 cdna.fasta \\\u2009\u2009\u2009\u2009Mus_musculus.GRCm39.dna.primary_assembly.fa.gz \\\u2009\u2009\u2009\u2009Mus_musculus.GRCm39.108.gtf.gz4.kb count -x 10xv3 -o output_dir -i index.idx -g t2g.txt \\\u2009\u2009\u2009\u2009R1.fastq.gz R2.fastq.gz5.Output:output_dir/counts_unfiltered/cells_x_genes.mtxoutput_dir/counts_unfiltered/cells_x_genes.barcodes.txtoutput_dir/counts_unfiltered/cells_x_genes.genes.txtoutput_dir/counts_unfiltered/cells_x_genes.genes.names.txtThe cells_x_genes.mtx is the count matrix file with the barcodes (the row names) listed in cells_x_genes.barcodes.txt and the gene names (the column names) listed in cells_x_genes.genes.names.txt .Input:10x version 3 single-nucleus RNA-seq reads: R1.fastq.gz and R2.fastq.gz1.pip install kb_python2.ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gzwget ftp.ensembl.org/pub/release-108/gtf/mus_musculus/Mus_musculus.GRCm39.108.gtf.gzwget 3.kb ref --workflow=nac -i index.idx -g t2g.txt \\\u2009\u2009\u2009\u2009-c1 cdna.txt -c2 nascent.txt -f1 cdna.fasta -f2 nascent.fasta \\\u2009\u2009\u2009\u2009Mus_musculus.GRCm39.dna.primary_assembly.fa.gz \\\u2009\u2009\u2009\u2009Mus_musculus.GRCm39.108.gtf.gz4.kb count -x 10xv3 --workflow=nac -o output_dir \\\u2009\u2009\u2009\u2009-i index.idx -g t2g.txt -c1 cdna.txt -c2 nascent.txt \\\u2009\u2009\u2009\u2009--sum=total R1.fastq.gz R2.fastq.gz5.Output:output_dir/counts_unfiltered/cells_x_genes.mature.mtxoutput_dir/counts_unfiltered/cells_x_genes.nascent.mtxoutput_dir/counts_unfiltered/cells_x_genes.ambiguous.mtxoutput_dir/counts_unfiltered/cells_x_genes.cell.mtxoutput_dir/counts_unfiltered/cells_x_genes.nucleus.mtxoutput_dir/counts_unfiltered/cells_x_genes.total.mtxoutput_dir/counts_unfiltered/cells_x_genes.barcodes.txtoutput_dir/counts_unfiltered/cells_x_genes.genes.txtoutput_dir/counts_unfiltered/cells_x_genes.genes.names.txtThis workflow can be used for both single-cell RNA-seq and single-nucleus RNA-seq. Many count matrix files (.mtx files) are generated. For quantification of total RNA present in each cell or nucleus, one would want to use the cells_x_genes.total.mtx. For biophysical models that jointly consider spliced and unspliced transcripts, one may want to use cells_x_genes.cell.mtx (for the \u201cspliced\u201d transcripts) and cells_x_genes.nascent.mtx (for the \u201cunspliced\u201d transcripts).The barcodes (the matrix row names) are listed in cells_x_genes.barcodes.txt and the gene names (the matrix column names) are listed in cells_x_genes.genes.names.txt .There are many ways to extend the standard workflows beyond bulk RNA-seq, 10x single-cell RNA-seq, and 10x single-nucleus RNA-seq. For an additional, extended example that involves preprocessing mouse multiplexed single-nucleus SPLiT-seq RNA-seq data with a filtered mouse genome annotation, see Supplement 1"} +{"text": "In mobile system due to limited space mutual coupling between nearby antenna elements is an issue that distort MIMO antenna performance. Defected ground structure is used to control coupling. The defected ground structure has advantages like ease of fabrication, compact size and high efficiency as compare to other techniques. Less than 30dB coupling is achieved for adjacent elements. The -10 dB impedance bandwidth of 700 MHz is achieved for all radiating elements ranging from 3.3 GHz to 4.1 GHz. The value is about 900MHz for -6dB. The proposed antenna offers good results in terms of fundamental antenna parameters like reflection coefficient, transmission coefficient, maximum gain, total efficiency. The antenna achieved average gain more than 3.8dBi and average radiation efficiency more than 80% for single dual polarized element. The antenna provides sufficient radiation coverage in all sides. The MIMO antenna characteristics like diversity gain (DG), envelope correlation coefficient (ECC), total active reflection coefficient (TARC) and channel capacity are calculated and found according to standards. Furthermore, effect of user on antenna performance in data-mode and talk-mode are studied. Proposed design is fabricated and tested in real time. The measured results shows that proposed design can be used in future smartphones applications. The design is compared with some of the existing work and found to be the best one in many parameters and can be used for commercial use.This manuscript presents high performance dual polarized eight-element multiple input multiple output (MIMO) fifth generation (5G) smartphone antenna. The design consists of four dual-polarized microstrip diamond-ring slot antennas, positioned at corners of printed circuit board (PCB). Cheap Fr-4 dielectric with permittivity 4.3 and thickness of 1.6mm is used as substrate with overall dimension of 150 \u00d7 75 \u00d7 1.6 In modern day, the interest in MIMO wireless communication technology is increased due to key features of MIMO technology like highly improve wireless link reliability, transmission capacity and data rates of wireless system through multi-path transmission and reception . For 5G mm3. The optimized value of the proposed MIMO design is listed in below Here, the design of single element dual-polarized antenna and result analysis of simulated and measured results is discussed. In figure below the configuration of dual-polarized antenna is presented. The aim of the research is the design of a small MIMO antenna that can be easily integrated into a smartphone\u2019s PCB with wide band and having dual polarization capabilities and low mutual coupling. This is accomplished by using microstrip patch antenna with slot in ground plane which increase isolation and wide the antenna bandwidth. Slot antenna is used because of its attractive features like compactness, light wight and ease of fabrication and integration with radio frequency circuits. The width of slot determines operating frequency. The circumference of ring needs to match the dielectric wavelength at the operating frequency as The dual polarization of antenna is achieved by placing radiating elements orthogonal to each other so that they orthogonally polarized. Dual polarization also increase isolation between antenna elements as both elements fed differently. Microstrip feed lines are used for feeding the orthogonal antenna elements. Microstrip feeding techniques offers features like simplicity, miniaturization, low cost, planar compatibility, high integration which is focus of this research. The characteristic impedance (Zo) of microstrip feed line can be calculated as \u03b5eff is given by Where effective height of the feed line can be calculated as The configuration of various structures studied in the designing process of proposed dual polarized antenna alongside with their S-parameter are displayed in Reflection coefficient (S11) of various antenna design parameters like Lf, Wf, Wx and x are demonstrated in The photograph of fabricated prototype of proposed antenna design (single element) and the measured reflection and transmission coefficient are given in Snn) and transmission coefficient (Snm). The figure shows that the suggested antenna design for smart mobile phone exhibits good return loss, wide bandwidth, high isolation, low mutual coupling and polarization diversity. Each of the four dual polarized radiating elements offers comparable performance.Smart phone 8 by 8 antenna design on 75mm by 150 mm PCB is illustrated in The photograph of fabricated prototype of 8 by 8 smart phone antenna is illustrated in The measured and simulated 2D polar plots (E & H-plane) of radiation pattern are compared and illustrated in ith and jth element of m by n MIMO antenna can be determined from antennas S-Matrix using equations ECC, DG, TARC and channel capacity (CC) are some crucial factors that need be taken into account in MIMO antennas to find that MIMO system function properly. ECC between ECC of antenna described about how much radiation pattern of two elements of a MIMO system are independent of each other. If on element is vertically polarized and a near-by second element is horizontally polarized then these elements would have a zero correlation between them. Correspondingly, if one antenna only radiated energy towards the ground and the other antenna element has a radiation pattern towards the sky totally opposite the ECC between these antennas would also be zero. Polarization of the antenna, shape of radiation pattern and relative phase of fields between two elements of a MIMO antenna or taken into consideration when calculating ECC of MIMO system. Envelope correlation coefficient of MIMO system can be calculated using S-matrix via An important parameter for assessing performance of MIMO antenna is TARC. It can be calculated from The detailed comparison of proposed work with already present work in literature is given in Effect of human (users) body tissues on proposed design performance is studied considering three common scenarios i.e., Data mode in which two modes single hand mode (SHM) and dual hand mode (DHM) and talking mode (TM). The placement of mobile phone MIMO antenna in different scenarios is illustrated in For 5G MIMO communications, a mobile phone antenna with dual-polarization capabilities is suggested. The antenna layout includes two-port microstrip feed lines with ground plane diamond slots placed at each of the PCB\u2019s four corners. The antenna elements have a broad bandwidth with a 3.6 GHz center frequency. Antenna performance parameters i.e., S-parameters, Efficiency, maximum realized gain, radiation patterns, DG, ECC, TARC and channel capacity are simulated and adequate results are obtained. Antenna has more than 700 MHz bandwidth and radiation efficiency more than 85% with more than 6 dB gain for MIMO configuration. The antenna has exhibits more than 30dB isolation due to orthogonal placement of adjacent element. ECC one of main MIMO antenna parameters is less than 0.001. The antenna\u2019s performance in talk-mode and data-mode scenarios is examined. Also, the proposed design of smart-phone antenna is fabricated and tested. The experimental results are in decent agreement with simulated one\u2019s with very little variations due to experimental errors. The results showed that the suggested smartphone antenna satisfies the criteria for use in upcoming smart-phones. 28 Apr 2023
PONE-D-23-09968
Dual Polarized 8-port Sub 6 GHz 5G MIMO Antenna for Smart Phone and Portable Wireless Applications
PLOS ONEDear Dr. Muhammad,
\u00a0
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We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide.[Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to Questions Comments to the Author1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Partly********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0N/AReviewer #3:\u00a0N/A********** 3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0No********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0This research work demonstrated and practically implemented a mobile phone antenna with dual-polarization capabilities which is a potential candidate for 5G MIMO communications. The antenna layout includes two-port microstrip feed lines with ground plane diamond slots placed at each of the PCB\u2019s four corners. From this reviewer\u2019s point of view promising results have been achieved and well discussed in the well-organized manuscript. So, the results have been experimentally validated and highlighted by providing a fair comparison with state-of-the-art. Although the concept and idea of this work were found interesting and they seem attractive for the scientific society, authors are requested to carefully address the following comments to improve the quality of the manuscript prior to final recommendation.1) Please add the applied design method of the proposed MIMO antenna to the title.2) Please explain some information about the advantage of the proposed decoupling method in the abstract section.3) Average radiation gain and efficiency can be added to the abstract section.4) Introduction section can be improved by adding more explanations along with proper references. For example, more discussions on 5g MIMO antennas are requested. Also, to realize MIMO antennas, isolation between the radiation elements are very important which need to be discussed. There are various decoupling methods which can be briefly mentioned. Below are helpful suggestions.(i) 5G MIMO antenna\"H-shaped Eight-Element Dual-band MIMO Antenna for Sub-6 GHz 5G Smartphone Applications\", IEEE Access, vol. 10, pp. 85619-85629, 2022.\"An Innovative Antenna Array with High Inter Element Isolation for Sub-6 GHz 5G MIMO Communication Systems\", Scientific Reports, 12, 7907, 2022.\"mmWave Four-Element MIMO Antenna for Future 5G Systems\", Applied Sciences, 12(9), 4280, 2022.\"Uni-Planar MIMO Antenna for Sub-6 GHz 5G Mobile Phone Applications\", Applied Sciences, 12(8), 3746, 2022.\"Multiple Elements MIMO Antenna System with Broadband Operation for 5th Generation Smart Phones\", IEEE Access, vol. 10, pp. 38446-38457, 2022.\u201cNovel MIMO Antenna System for Ultra Wideband Applications\u201d, Applied Sciences, 12(7), 3684, 2022.\u201cA high gain multiband offset MIMO antenna based on a planar log-periodic array for Ku/K-band applications\u201d, Scientific Reports, 12, 4044 (2022).\"A Compact CPW-Fed Ultra-Wideband Multi-Input-Multi-Output (MIMO) Antenna for Wireless Communication Networks,\", IEEE Access, vol. 10, pp. 25278-25289, 2022.\"Printed Closely Spaced Antennas Loaded by Linear Stubs in a MIMO Style for Portable Wireless Electronic Devices\", Electronics, 10(22), 2848, 2021.\"MIMO Antenna System for Modern 5G Handheld Devices with Healthcare and High Rate Delivery\" Sensors, 21(21), 7415, 2021.(ii) Decoupling methods to realize MIMO antennas\"A Comprehensive Survey on \"Various Decoupling Mechanisms with Focus on Metamaterial and Metasurface Principles Applicable to SAR and MIMO Antenna Systems\"\", IEEE Access, vol. 8, pp. 192965-193004, 2020.\u201cStudy on Isolation and Radiation Behaviours of a 34\u00d734 Array-Antennas Based on SIW and Metasurface Properties for Applications in Terahertz Band Over 125-300 GHz\u201d, Optik, International Journal for Light and Electron Optics, Volume 206, March 2020, 163222.\"Isolation Enhancement of Densely Packed Array Antennas with Periodic MTM-Photonic Bandgap for SAR and MIMO Systems\", IET Microwaves, Antennas & Propagation, Volume 14, Issue 3, February 2020, pp. 183 - 188.\"Surface Wave Reduction in Antenna Arrays Using Metasurface Inclusion for MIMO and SAR Systems\", Radio Science, 54, 1067\u20131075, 2019.\"Mutual-Coupling Isolation Using Embedded Metamaterial EM Bandgap Decoupling Slab for Densely Packed Array Antennas\", IEEE Access, vol. 7, pp. 5182\u201351840, April 29, 2019.\"Mutual Coupling Suppression Between Two Closely Placed Microstrip Patches Using EM-Bandgap Metamaterial Fractal Loading\", IEEE Access, vol. 7, Page(s): 23606 \u2013 23614, March 5, 2019.\"Interaction Between Closely Packed Array Antenna Elements Using Metasurface for Applications Such as MIMO Systems and Synthetic Aperture Radars\", Radio Science, Volume53, Issue11, November 2018, Pages 1368-1381.\u201cAntenna Mutual Coupling Suppression Over Wideband Using Embedded Periphery Slot for Antenna Arrays\u201d, Electronics, 2018, 7(9), 198.\u201cStudy on Isolation Improvement Between Closely Packed Patch Antenna Arrays Based on Fractal Metamaterial Electromagnetic Bandgap Structures\u201d, IET Microwaves, Antennas & Propagation, Volume 12, Issue 14, 28 November 2018, p. 2241 \u2013 2247.\u201cMeta-surface Wall Suppression of Mutual Coupling between Microstrip Patch Antenna Arrays for THz-band Applications\u201d, Progress in Electromagnetics Research Letters, Vol. 75, page 105-111, 2018.5) Design process of the proposed single antenna should be elaborated in depth. Please explain why authors have realized diagonal rectangular slots on the back? How were its dimensions optimized?6) Quality of the plots are poor, they need to be improved.7) More discussions on the surface current distributions should be added.8) The feeding mechanism of the MIMO antenna should be explained in detail.9) In comparison table 2 please add the terms \u201capplied design method, radiation gain, and design complexity\u201d as well to make it more comprehensive.10) Please extend the conclusion by adding more numerical results and achievements.11) Reference part needs to be improved as per above mentioned suggestions.Reviewer #2:\u00a01. An 8-port MIMO antenna for smartphone application is proposed.2. Author need top carry out a systematic literature review to establish the technical contribution and need for the proposed work.Please refer below paper for the same: Design and Analysis of Wideband Flexible Self-Isolating MIMO Antennas for Sub-6 GHz 5G and WLAN Smartphone Terminals3. Also authors should refer to some latest sub-6 GHz MIMO antennas and do a thorough comparison to establish the novel contribution:a. Compact wideband four element optically transparent MIMO antenna for mm-wave 5G applicationsb. Multiband hybrid MIMO DRA for Sub\u20106 GHz 5G and WiFi\u20106 applicationsc. Dual-band and dual-polarization CPW Fed MIMO antenna for fifth-generation mobile communications technology at 28 and 38 GHzd. Wideband flexible/transparent connected-ground MIMO antennas for sub-6 GHz 5G and WLAN applications4. Improve the quality of all the figures 5. Show the coordinate axis next to the antenna geometry.6. In Fig 6(a), gain should be in dBi and not dB.7. For such configuration, the number of input ports increases significantly.8. Present selected data in some of the graphs for brevity of data.9. Fig 15 is not at all clear.10. Authors should carry out SAR analysis.Reviewer #3:\u00a0The article \"Dual Polarized 8-port Sub 6 GHz 5G MIMO Antenna for Smart Phone and PortableWireless Applications\" need major revision to process to next level1) The design orientation and associated mathematical formulation is missing in the paper2) Figure captions not given with numbers for review3) For eight ports, the transmission coefficient results shown are of low quality and data in zig zag.4) Human phantom model is used in the work for analysis. I have not found any type SAR readings and related matter.5) The CCL and Diversity Gain and TARC parameters for MIMO was not discussed and presented6) 2D plots with several combinations without any analysis is presented********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1:\u00a0NoReviewer #2:\u00a0NoYes:\u00a0Dr. B T P MadhavReviewer #3:\u00a0**********https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,\u00a0 20 Jun 2023Original Manuscript ID: PONE-D-23-09968Original Article Title: Dual Polarized 8-port Sub 6 GHz 5G MIMO Antenna for Smart Phone and Portable Wireless ApplicationsTo: PLOS ONE EditorRe: We are very thankful to the PLOS ONE journal team and reviewers for such a comprehensive and profound review. We have revised our manuscript in light of their valuable queries and suggestions. We hope our revision has improved the paper quality to a level of reviewers\u2019 satisfaction. The answers to their specific suggestions/queries/comments are given below in detail.Dear Editor,Thank you for allowing a resubmission of our manuscript, with an opportunity to address the reviewers\u2019 comments.We are uploading (a) our point-by-point response to the comments (below) (response to reviewers), (b) an updated manuscript with yellow highlighting indicating changes (Revised Manuscript with Track Changes), and (c) a clean updated manuscript without highlights (Manuscript) (PDF main document).Best regards,Dr. Fazal MuhammadCorresponding Author\u2003Response to Reviewer #1: We would like to thank the reviewer for careful and thorough reading of this manuscript and for the thoughtful comments and constructive suggestions, which help to improve the quality of this manuscript. Our response follows . General Comments: This research work demonstrated and practically implemented a mobile phone antenna with dual-polarization capabilities which is a potential candidate for 5G MIMO communications. The antenna layout includes two-port microstrip feed lines with ground plane diamond slots placed at each of the PCB\u2019s four corners. From this reviewer\u2019s point of view promising results have been achieved and well discussed in the well-organized manuscript. So, the results have been experimentally validated and highlighted by providing a fair comparison with state-of-the-art. Although the concept and idea of this work were found interesting and they seem attractive for the scientific society, authors are requested to carefully address the following comments to improve the quality of the manuscript prior to final recommendation.Reviewer #1 Concerns:1. Please add the applied design method of the proposed MIMO antenna to the title.2. Please explain some information about the advantage of the proposed decoupling method in the abstract section. 3. Average radiation gain and efficiency can be added to the abstract section4. Introduction section can be improved by adding more explanations along with proper references. 5. Design process of the proposed single antenna should be elaborated in depth. Please explain why authors have realized diagonal rectangular slots on the back? How were its dimensions optimized?6. Quality of the plots are poor; they need to be improved.7. More discussions on the surface current distributions should be added.8. The feeding mechanism of the MIMO antenna should be explained in detail.9. In comparison table 2 please add the terms \u201capplied design method, radiation gain, and design complexity\u201d as well to make it more comprehensive.10. Please extend the conclusion by adding more numerical results and achievements.11. Reference part needs to be improved as per above mentioned suggestions.Additional Questions:1. Is the manuscript technically sound, and do the data support the conclusions? Yes2. Has the statistical analysis been performed appropriately and rigorously? Yes3. Have the authors made all data underlying the findings in their manuscript fully available? Yes4. Is the manuscript presented in an intelligible fashion and written in standard English? Yes\u2003Reviewer#1, Concern#1: Please add the applied design method of the proposed MIMO antenna to the title.Author response: Thanks for valuable suggestion, as per respected reviewer we have change the title of our manuscript and added design method to title. Our new title is as under\u201cDual-polarized 8-port sub 6 GHz 5G MIMO diamond-ring slot antenna for smart phone and portable wireless applications\u201d________________________________________Reviewer#1, Concern#2: Please explain some information about the advantage of the proposed decoupling method in the abstract section.Author response: Thank you very much for the valuable suggestions, as per the honorable reviewer suggestions we have added the information about the advantage of the proposed coupling method in the abstract section, as highlight in the revised version of the manuscript.________________________________________Reviewer#1, Concern#3: Average radiation gain and efficiency can be added to the abstract sectionAuthor response: Thanks for the suggestion , the average gain and efficiency are added to abstract section, and highlighted in marked version of manuscript.________________________________________Reviewer#1, Concern#4: Introduction section can be improved by adding more explanations along with proper references.Author response: Thank you very much, as per the honorable suggestion, the introduction section is improved by adding more explanation with proper references, and the changes are highlighted in marked version.________________________________________Reviewer#1, Concern#5: Design process of the proposed single antenna should be elaborated in depth. Please explain why authors have realized diagonal rectangular slots on the back? How were its dimensions optimized?Author response: Thanks for your comment, the design process is elaborated and some mathematical equations are included as shown in revised version. The diagonal slot in ground plane is used to reduce the mutual coupling between antenna elements and increase bandwidth. The dimensions are optimized by doing some parametric study.________________________________________Reviewer#1, Concern#6: Quality of the plots are poor; they need to be improved.Author response: Thanks for very much for the comments , the quality of plots is improved in the revised version and highlighted the revised manuscript.________________________________________Reviewer#1, Concern#7: More discussions on the surface current distributions should be added.Author response: Thank you very much, As per honorable reviewer directions, more discussion on surface currents is added as shown in highlighted version.________________________________________Reviewer#1, Concern#8: The feeding mechanism of the MIMO antenna should be explained in detail.Author response: The feeding mechanism is explained in detail. As the honorable reviewer suggested. Thank you________________________________________Reviewer#1, Concern#9: In comparison table 2 please add the terms \u201capplied design method, radiation gain, and design complexity\u201d as well to make it more comprehensive.Author response: Table 2 is updated as per respected reviewer comment, design method, gain, coupling techniques, and material used columns are added to the table. ________________________________________Reviewer#1, Concern#10: Please extend the conclusion by adding more numerical results and achievements.Author response: Thank you very much, Conclusion is extended by adding more numerical results as per honorable reviewer.________________________________________Reviewer#1, Concern#11: Reference part needs to be improved as per above mentioned suggestions Author response: Reference part is improved according to honorable reviewer suggestion. As highlighted in the references section in the revised version.________________________________________________________________________________\u2003Response to Reviewer #2: We would like to thank the reviewer for careful and thorough reading of this manuscript and for the thoughtful comments and constructive suggestions, which help to improve the quality of this manuscript. Our response follows . General Comments: An 8-port MIMO antenna for smartphone application is proposed.Reviewer #2 Concerns:1. Author needs to carry out a systematic literature review to establish the technical contribution and need for the proposed work. Please refer below paper for the same: Design and Analysis of Wideband Flexible Self-Isolating MIMO Antennas for Sub-6 GHz 5G and WLAN Smartphone Terminals2. Also, authors should refer to some latest sub-6 GHz MIMO antennas and do a thorough comparison to establish the novel contribution.3. Improve the quality of all the figures 4. Show the coordinate axis next to the antenna geometry.5. In Fig 6(a), gain should be in dBi and not dB.6. For such configuration, the number of input ports increases significantly.7. Present selected data in some of the graphs for brevity of data.8. Fig 15 is not at all clear.9. Authors should carry out SAR analysis.Additional Questions:1. Is the manuscript technically sound, and do the data support the conclusions? Yes2. Has the statistical analysis been performed appropriately and rigorously? N/A3. Have the authors made all data underlying the findings in their manuscript fully available? Yes4. Is the manuscript presented in an intelligible fashion and written in standard English? Yes\u2003Reviewer#2, Concern#1: Author needs to carry out a systematic literature review to establish the technical contribution and need for the proposed work.Author response: Thanks for valuable suggestion, as per respected reviewer, the introduction section is improved and a systematic literature review is made with proper references. The changes are highlighted in revised marked version. ________________________________________Reviewer#2, Concern#2: Also, authors should refer to some latest sub-6 GHz MIMO antennas and do a thorough comparison to establish the novel contribution. Author response: Thanks for valuable suggestion, as per respected reviewer some of latest work is referred and compared with the proposed design. The changes are highlighted in revised marked version.________________________________________Reviewer#2, Concern#3: Improve the quality of all the figures Author response: Thank you very much, as per the honorable reviewer comments, the quality of figures is improved.________________________________________Reviewer#2, Concern#4: Show the coordinate axis next to the antenna geometry.Author response: Thank you very much, as per the honorable reviewer, coordinate axis is added next to antenna geometry. See Figure 1 and 9.________________________________________Reviewer#2, Concern#5: In Fig 6(a), gain should be in dBi and not dB.Author response: Thank you very much, as per respected reviewer valuable suggestion, the gain is plotted in dBi instead of dB. See Figure 6(a).________________________________________Reviewer#2, Concern#6: For such configuration, the number of input ports increases significantly.Author response: Thank you very much for the quaries, yes the number of input ports is increased but for 5G the data rate is directly proportional to the number of antenna elements and number of ports. ________________________________________Reviewer#2, Concern#7: Present selected data in some of the graphs for brevity of data.Author response: Thank you very much, as per the honorable reviewer valuable suggestion, some of the symmetrical data has been removed for clarity and brevity of data.________________________________________Reviewer#2, Concern#8: Fig 15 is not at all clear.Author response: Thank you very much for your valuable comment, as per the honorable reviewer suggestion, we have replaced Fig no 15 with a clear one.________________________________________Reviewer#2, Concern#9: Authors should carry out SAR analysis.Author response: Thank you very much for suggestion, as per the honorable review suggestion a detailed SAR analysis is done and the results are presented in revised version. ________________________________________________________________________________\u2003Response to Reviewer #3: We would like to thank the reviewer for careful and thorough reading of this manuscript and for the thoughtful comments and constructive suggestions, which help to improve the quality of this manuscript. Our response follows . General Comments: The article \"Dual Polarized 8-port Sub 6 GHz 5G MIMO Antenna for Smart Phone and Portable Wireless Applications\" need major revision to process to next levelReviewer #3 Concerns:1. The design orientation and associated mathematical formulation is missing in the paper2. Figure captions not given with numbers for review3. For eight ports, the transmission coefficient results shown are of low quality and data in zig zag.4. Human phantom model is used in the work for analysis. I have not found any type SAR readings and related matter.5. The CCL and Diversity Gain and TARC parameters for MIMO was not discussed and presented6. 2D plots with several combinations without any analysis is presentedAdditional Questions:1. Is the manuscript technically sound, and do the data support the conclusions? Partly2. Has the statistical analysis been performed appropriately and rigorously? N/A3. Have the authors made all data underlying the findings in their manuscript fully available? Yes4. Is the manuscript presented in an intelligible fashion and written in standard English? No\u2003Reviewer#3, Concern#1: The design orientation and associated mathematical formulation is missing in the paper.Author response: Thank you very much for bringing our attention to this, as per the honorable reviewer, the mathematical equations are added to the paper.________________________________________Reviewer#3, Concern#2: Figure captions not given with numbers for reviewAuthor response: Sorry for missing this, this time figure captions are added with numbers, Thank you for your comment.________________________________________Reviewer#3, Concern#3: For eight ports, the transmission coefficient results shown are of low quality and data in zig zag.Author response: Thank you very much for the valuable suggestion, as per the honorable reviewer, the quality of plot is improved.________________________________________Reviewer#3, Concern#4: Human phantom model is used in the work for analysis. I have not found any type SAR readings and related matter.Author response: Thank you very much for suggesting SAR analysis, SAR analysis is done and the results are presented in revised version.________________________________________Reviewer#3, Concern#5: The CCL and Diversity Gain and TARC parameters for MIMO was not discussed and presentedAuthor response: Thank you very much for suggesting to add some important MIMO parameters like TARC, DG and channel capacity. The results are calculated and are presented in revised version.________________________________________ Reviewer#3, Concern#6: 2D plots with several combinations without any analysis is presentedAuthor response: Thank you very much for valuable suggestion analysis of 2D plots are added to revised version.________________________________________________________________________________Kind RegardsDr. Fazal Muhammad Corresponding Author 4 Jul 2023Dual Polarized 8-port Sub 6 GHz 5G MIMO Antenna for Smart Phone and Portable Wireless ApplicationsPONE-D-23-09968R1Dear Dr. Muhammad,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Yuan-Fong Chou ChauAcademic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments:Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #1:\u00a0All comments have been addressedReviewer #2:\u00a0All comments have been addressed********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0N/A********** 4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0Appropriate modifications have been applied as per requested to improve the quality of the manuscript to an acceptable level.Reviewer #2:\u00a01. The comments give by the reviewers are addressed and implemented properly.2. The manuscript is good to be published in its present form.********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1:\u00a0NoReviewer #2:\u00a0No********** 18 Jul 2023PONE-D-23-09968R1 Dual-polarized 8-port sub 6 GHz 5G MIMO diamond-ring slotantenna for smart phone and portable wireless applications Dear Dr. Muhammad:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Yuan-Fong Chou Chau Academic EditorPLOS ONE"} +{"text": "Non-coding RNAs (ncRNAs) can control the flux of genetic information; affect RNA stability and play crucial roles in mediating epigenetic modifications. A number of studies have highlighted the potential roles of both virus-encoded and host-encoded ncRNAs in viral infections, transmission and therapeutics. However, the role of an emerging type of non-coding transcript, circular RNA (circRNA) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has not been fully elucidated so far. Moreover, the potential pathogenic role of circRNA-miRNA-mRNA regulatory axis has not been fully explored as yet. The current study aimed to holistically map the regulatory networks driven by SARS-CoV-2 related circRNAs, miRNAs and mRNAs to uncover plausible interactions and interplay amongst them in order to explore possible therapeutic options in SARS-CoV-2 infection. Patient datasets were analyzed systematically in a unified approach to explore circRNA, miRNA, and mRNA expression profiles. CircRNA-miRNA-mRNA network was constructed based on cytokine storm related circRNAs forming a total of 165 circRNA-miRNA-mRNA pairs. This study implies the potential regulatory role of the obtained circRNA-miRNA-mRNA network and proposes that two differentially expressed circRNAs hsa_circ_0080942 and hsa_circ_0080135 might serve as a potential theranostic agents for SARS-CoV-2 infection. Collectively, the results shed light on the functional role of circRNAs as ceRNAs to sponge miRNA and regulate mRNA expression during SARS-CoV-2 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an enveloped RNA virus with a genome size of 29,903 bp, is a highly infectious and pathogenic coronavirus . InitialRecent advances in high-throughput sequencing technologies and computational methods have discovered a substantial number of ncRNA ultimately providing new insights into their role in a range of human diseases , 7. VariOn the other hand, circRNAs, a novel class of ncRNAs have been reported to play crucial role in regulating viral infections and their dysregulation has been implicated in the pathogenesis of various diseases , 18. WhiThe circRNA\u2013miRNA\u2013mRNA regulatory axis has been shown to be of high importance in association with several human diseases including cancers, diabetes, Alzheimer\u2019s disease, and cardiovascular diseases \u201325. ThesThere is an abundance of COVID-19 related transcriptomics studies and data, however, their use is limited by the confounding factors pertaining to each study. In the current study, we have analyzed different datasets in a unified approach which might help in understanding the molecular basis of COVID-19. Moreover, reverse engineering approach was utilized to derive regulatory interactions between circRNAs, miRNAs and mRNAs from gene expression data of SARS-CoV-2 patients. In order to gain better understanding of molecular and immuno-pathological basis, possible regulatory mechanisms of circRNA-miRNA-mRNA axis during SARS-CoV-2 infection were investigated. The circRNA\u2013miRNA\u2013mRNA regulatory network consisting of differentially expressed circRNAs and their downstream miRNAs and target mRNAs have been constructed for SARS CoV-2 related pathogenesis. The circRNAs that may play critical roles in regulating the cytokine storm during SARS-CoV-2 infection were identified. The results from this study revealed some candidate circRNAs that might function as potential theranostic agents in SARS-CoV-2 infection. Moreover, targeting the \"cytokine storm\" using circRNAs might be a feasible therapeutic approach to combat COVID-19 . Togethehttps://www.ncbi.nlm.nih.gov/geo/), a database supported by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) was used to access the microarray and RNA-sequencing datasets that contains circRNA, miRNA and mRNA expression profiles of SARS-CoV-2 infected patients at various stages (https://ngdc.cncb.ac.cn/). As the present study does not involve human subjects and due to free availability of data in the GEO database, neither ethical approval nor informed consent was required.The Gene Expression Omnibus (GEO) ..https://The GSE166552 dataset included 06 samples (03 SARS-CoV-2 positive and 03 controls). The PRJCA002617 dataset included 24 samples (12 SARS-CoV-2 positive and 12 controls). McDonald et al., dataset included 45 samples . The GSE19137 dataset included 21 samples (03 negative and 18 positive for SARS-CoV). Chow et al., dataset included 249 samples (147 SARS-CoV-2 infected samples and 102 controls). Dhar et al., dataset included 2157 samples (including 915 severe COVID-19 patients). Liu et al., dataset contained 40 samples in his study (including 13 severe COVID-19 patients). Farr et al., dataset included 20 samples . Li et al., dataset included 14 samples . Huang et al., dataset comprised of 41 samples (including 13 severe COVID-19 patients). Chi et al., dataset included 70 SARS-CoV-2 infected patients, 04 convalescent cases and 04 healthy controls. Lin et al., dataset included 334 samples in their study (including 23 severe COVID-19 patient samples). Chen et al(b)., dataset included 21 samples (including 11 severe COVID-19 patient samples). Chen et al(c)., dataset study contained 29 samples (including 14 severe COVID-19 patient samples). Blenco Melo et al., included 48 samples (24 SARS-CoV-2 positive samples and 24 negative samples). Del Velle et al., dataset included a total of 1484 samples (1097 positive for SARS-CoV-2 infection and 387 controls). Qin et al., dataset comprised of 452 samples in their study (including 286 severe COVID-19 patient samples). Yang et al., dataset included 50 samples (including 36 severe COVID-19 patient samples).http://www.circbank.cn/) is a comprehensive, publicly available, functionally annotated human circRNAs database containing information of about 140,000 circRNAs from many different sources Please clarify whether this [conference proceeding or publication] was peer-reviewed and formally published. If this work was previously peer-reviewed and published, in the cover letter please provide the reason that this work does not constitute dual publication and should be included in the current manuscript.2. We noted in your submission details that a portion of your manuscript may have been presented or published elsewhere. https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,\u00a0AttachmentManuscript Number PONE D 22 34657.docxSubmitted filename: Click here for additional data file. 23 Feb 2023Response to reviewersDear Editor,We wish to express our appreciation for your in-depth comments, suggestions and corrections, and we would like to convey our sincere thanks for allowing us to improve our manuscript entitled \u201cMapping CircRNA\u2013miRNA\u2013mRNA Regulatory Axis Identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection\u201d. Thank you for your very careful review of our paper. A major revision of the paper has been carried out to take all of weaknesses and limitations identified by the respective reviewers into account. And in the process, we truly hope that the revised manuscript is clear enough to follow.Below is an abridged summary of reviewer\u2019s comments with a detailed response and description of the changes made to the article. Should you find the paper requires further clarification or revision, we most certainly stand ready to do so.Looking forward to your positive responseSincerely,Dr. Faryal Mehwish AwanJournal Requirements:When submitting your revision, we need you to address these additional requirements.Comment # 1Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. ResponseWe have formatted our manuscript according to PLOS ONE\u2019s style. The format has been updated in the revised version of the manuscript as per journal requirements. Comment # 2https://www.ncbi.nlm.nih.gov/gds/) with accession details , , , , , (Demirci and Demirci 2021), , , , , , , , , , , and datasets).] Please clarify whether this [conference proceeding or publication] was peer-reviewed and formally published. If this work was previously peer-reviewed and published, in the cover letter please provide the reason that this work does not constitute dual publication and should be included in the current manuscript. We noted in your submission details that a portion of your manuscript may have been presented or published elsewhere. [All the datasets analyzed during the current study are accessible from the literature as well as from the GEO database repository archives and freely distributes microarray, next-generation sequencing and other forms of high-throughput functional genomics data. Such datasets hold great value for knowledge discovery, particularly when integrated and can potentially bring novel insights into essential questions. The present study has aimed at prioritizing the potential circRNA candidates for a prospective theranostic evaluation via exploring the existing publically available datasets in COVID-19 setting. Public databases have a lot of high throughput data, which greatly helps in revealing the possible disease pathogenesis and identifying potential targets for drug design. Experimental validation of all the discovered associations, let alone all the possible interactions between them, is time-consuming and expensive. In conventional approaches, large experimental screenings are currently used to identify potential leading compounds, but they require significant time and resources. However, one of the lessons learned during the current pandemic is that innovative approaches are required to speed up drug development while increasing its success rate. Since gene expression data are high-dimensional data, an important research aim in the analysis of transcription profiles is the discovery of small subset of biomarkers containing the most discriminant information. Therefore, current study computationally prioritized the data available in the databases for potential SARS-CoV-2 inhibitors by using an integrated approach. A number of recently published research studies have utilized publically available datasets for the prioritization of most promising candidates. Some of these studies are We have added this information in the cover letter to clarify this comment. Comment: 3https://blogs.plos.org/plos/2019/06/looking-good-tips-for-creating-your-plos-figures-graphics/\" https://blogs.plos.org/plos/2019/06/looking-good-tips-for-creating-your-plos-figures-graphics/Please upload a new copy of Figure 7 as the detail is not clear. Please follow the link for more information: ResponseWe agree with your assessment. We have now followed figure graphics requirements for all the figures and have also uploaded a new copy of Figure 7 as \u201cFig7.tif\u201d. Fig 7: Pathway analysis of COVID-19 pathogenesis (KEGG pathway ID: map05171). Highlighted genes are targets of miRNAs and indirect targets of two prioritized circRNAs Comment: 4Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article\u2019s retracted status in the References list and also include a citation and full reference for the retraction notice.ResponseWe have rechecked the whole manuscript for any errors in the references. Corrections have been made and highlighted. Reviewer #1Comments and Suggestions for AuthorsThis is an interesting small study and the authors have collected a unique dataset using cutting edge methodology. The paper is well written and structured.ResponseWe appreciate the positive feedback from the reviewer and would like to thank the respected reviewer for the encouraging assessment and the comments that helped us to improve the manuscript. Comment: 1The following minor issues should be addressed:In introduction section first paragraph author may update number of total people have been infected and death globally with virus SARS-CoV-2 with updated references.ResponseWe agree with your assessment. As per your suggestion, we have updated total number as per World Health Organization report and revised the statement as follows. Currently, >750 million people have been infected globally while >6.8 million people have lost their lives due to COVID-19 .We have updated this information in the revised version of the manuscript.Reviewer #2Comments and Suggestions for AuthorsThe manuscript entitled Mapping CircRNA\u2013miRNA\u2013mRNA Regulatory Axis Identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection can be accepted for publication after few improvementsResponseWe appreciate the positive feedback from the reviewer and would like to thank the respected reviewer for the encouraging assessment and the comments that helped us to improve the manuscript. Comment: 1The author have selected the common circRNAs from circRNA datasets, mRNA datasets, and miRNA datasets. How the author found cicRNAs from mRNAs and miRNAs datasets? The authors are suggested to clearly describe the results in detail rather than superficial writing.Responsehttp://www.circbank.cn/) is a comprehensive, publicly available, functionally annotated human circRNAs database containing information of about 140,000 circRNAs from many different sources . The Users can access information regarding conservation status, miRNA targets as well as protein coding potential of query circRNAs . CircInteractome (https://circinteractome.nia.nih.gov/) is a readily accessible web tool for mapping miRNAs and protein-binding sites on junctions as well as junction-flanking sequences of human circRNAs . RNA Interactome Database, RNAInter v4.0 (http://www.rnainter.org/) is a comprehensive RNA-associated interactome platform containing information of more than 41 million interactions of cellular RNAs in 154 species with evidence from both computational and experimental sources . Selection criteria, threshold and prediction scores for each database were selected on the basis of their previously reported relationship with low false discovery rate and high accuracy in experimental validation studies via PCR and Luciferase assays. The target circRNAs of differentially expressed miRNAs were predicted using different comprehensive databases including CircBank, CircInteractome and RNAInter v4.0 web tools (Table 2). CircBank (http://mirdb.org/), is an integrative, freely accessible, open platform for the prediction of miRNA targets. miRNA-target interactions with scores \u226580.0 were considered relevant, statistically significant and with higher confidence in the interactions whereas miRNA-target interactions with scores \u226480.0 were considered not relevant. By utilizing high-throughput experimental data, miRDB predicts miRNA targets in five species along with integrative analysis of gene ontology (GO) data . miRWalk 2.0 provides information of more than 949 million computationally predicted as well as experimentally validated miRNA-mRNA interactions. In order to ensure reliability and accuracy of forecast results, miRWalk 2.0 incorporates 12 algorithms for prediction including miRWalk, mirbridge, Targetscan, Microt4, PITA, Pictar2, RNAhybrid, RNA22, miRNAMap, miRanda, miRMap and miRDB . Cut-off value with a binding score of > 0.95 was considered as a screening threshold. miRTarBase (https://miRTarBase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/index.php) is a manually curated database containing information of more than 360,000 experimentally validated miRNA-mRNA interactions . miRNA-mRNA interactions have been validated experimentally using microarray, CLIP-seq technology, reporter assays, high through-put sequencing and western blot experiments . All the targets identified via miRTarBase were selected for further analysis. TargetScan v7.0 (http://www.targetscan.org/vert_80/), a flexible web based tool, predicts sequence based effective regulatory targets of miRNAs by incorporating 14 different features . Conservation aggregate score of > 0.80 was considered as selection criteria as this score provides low false discovery rates. An overlap in at least two databases was used as filtering criteria for prioritizing and considering potential candidate targets. Previous comparative studies conducted on miRNA target prediction programs suggested that no program performed consistently superior to all others. Indeed, it has become a common practice for researchers to look at predictions produced by different miRNA-target prediction programs and focus on their intersection which might enhances the performance of analyses as well as improve prediction precision. The differences between algorithms are mostly seen in their respective weaknesses, i.e., the subset of false positives. For that reason, the fundamental motivation to focus selectively on the shared prediction by two algorithms is to eliminate false positives while preserving the vast majority of true positive RNAs. Therefore, conclusively, predictions are much more reliable when two or more prediction algorithms are combined, and the minimal loss of true positives are greatly outweighed by the removal of false positives. Comprehensive analysis of differentially expressed miRNA datasets revealed 38937 target circRNAs. On the other hand, comprehensive analysis of 5109 predicted miRNAs against differentially expressed mRNAs revealed 858423 circRNAs having binding sites for respective miRNAs.For the prediction of potential circRNAs associated with differentially expressed mRNAs, first we predicted miRNAs associated with these mRNA and then circRNAs associated with predicted miRNAs. We used databases including miRDB, miRWalk 2.0, miRTarBase, and TargetScan 7.0 for the prediction of miRNAs associated with respective mRNAs. miRDB . Highlighted genes are targets of miRNAs and indirect targets of two prioritized circRNAs Comment: 3The quality of image needs to be improved as picture is blur and not clearResponseWe agree with your assessment. We have now uploaded a new copy of Figure 7 as \u201cFig7.tif\u201d. In addition we have also updated \u201cTable 4\u201d in tabular text form previously uploaded as a figure due to complexity of data. Fig 7: Pathway analysis of COVID-19 pathogenesis (KEGG pathway ID: map05171). Highlighted genes are targets of miRNAs and indirect targets of two prioritized circRNAs \u2003Table 4: Datasets used for the analysis of SARS-CoV-2 related cytokines Genes Study 1 Study 2 Study 3 Study 4 Study 5 Study 6 Study 7 Study 8 Study 9 Study 10 Study 11 Study 12 up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulated up-regulated down-regulatedIL-1\u03b2 _ _ _ _ _ _ _ _ \u221a _ _ _ \u221a _ _ _ _ _ _ _ \u221a _ _ _IL-2 \u221a _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _ _ _ _ _ _ _ \u221a _IL-4 _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _ _ _ _ _ _ _ \u221a _IL-6 _ _ \u221a _ \u221a _ _ _ \u221a _ \u221a _ \u221a _ \u221a _ \u221a _ \u221a _ \u221a _ \u221a _IL-7 \u221a _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _ _ _IL-8 _ _ _ _ _ _ _ _ \u221a _ \u221a _ _ _ \u221a _ _ _ \u221a _ _ _ _ _IL-10 \u221a _ _ _ \u221a _ _ _ \u221a _ _ _ \u221a _ _ _ _ _ \u221a _ _ _ \u221a _IL-12 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _IL-13 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _IL-17 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _IL-18 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ \u221a _ _ _IL-23 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _IL-33 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ IL-37 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _IL-38 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _TNF-\u03b1 \u221a _ _ _ \u221a _ _ _ \u221a _ \u221a _ \u221a _ \u221a _ _ _ _ _ _ _ \u221a _IFN-\u03b3 _ _ _ _ \u221a _ _ _ _ _ _ _ \u221a _ _ _ _ _ _ _ _ _ \u221a _CCL2 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _ _ _ _ _CXCL6 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _CXCL8 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _ _ _ _ _CXCL10 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _ _ _ _ _ IP-10 \u221a _ _ _ _ _ \u221a _ _ _ _ _ _ _ _ _ _ _ \u221a _ \u221a _ _ _MIP-1A \u221a _ _ _ _ _ \u221a _ _ _ _ _ _ _ _ _ _ _ \u221a _ \u221a _ _ _MIP1-B _ _ _ _ _ _ \u221a _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _PDGF _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _MCP1 \u221a _ _ _ _ _ \u221a _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _ _ _ GM-CSF _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _M-CSF _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ \u221a _ _ _G-CSF \u221a _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ \u221a _ _ _FGF _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _HGF _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \u221a _ _ _TGF-\u03b2 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ We hope that our additions to the manuscript will satisfy the reviewers, and thank both reviewers for their precise and insightful comments, and for the careful attention that they have paid which allowed us to improve the manuscript. We look forward to hearing from you regarding our submission. We would be glad to respond to any further questions and comments that you may have.Reviewer's Responses to QuestionsComments to the Author1. Is the manuscript technically sound, and do the data support the conclusions?Reviewer #1: YesReviewer #2: Yes2. Has the statistical analysis been performed appropriately and rigorously?Reviewer #1: YesReviewer #2: Yes3. Have the authors made all data underlying the findings in their manuscript fully available?Reviewer #1: YesReviewer #2: Yes4. Is the manuscript presented in an intelligible fashion and written in standard English?Reviewer #1: YesReviewer #2: YesReferencesAgarwal, V., et al. (2015) Predicting effective microRNA target sites in mammalian mRNAs, elife, 4, e05005.Blanco-Melo, D., et al. (2020) Imbalanced host response to SARS-CoV-2 drives development of COVID-19, Cell, 181, 1036-1045. e1039.Chen, G., et al. (2020) Clinical and immunological features of severe and moderate coronavirus disease 2019, The Journal of clinical investigation, 130, 2620-2629.Chen, L., et al. (2020) Analysis of clinical features of 29 patients with 2019 novel coronavirus pneumonia, Zhonghua jie he he hu xi za zhi= Zhonghua jiehe he huxi zazhi= Chinese journal of tuberculosis and respiratory diseases, 43, E005-E005.Chi, Y., et al. (2020) Serum cytokine and chemokine profile in relation to the severity of coronavirus disease 2019 in China, The Journal of infectious diseases, 222, 746-754.Dat, V.H.X., et al. (2022) Identification of potential microRNA groups for the diagnosis of hepatocellular carcinoma (HCC) using microarray datasets and bioinformatics tools, Heliyon, 8, e08987.Del Valle, D.M., et al. (2020) An inflammatory cytokine signature predicts COVID-19 severity and survival, Nature medicine, 26, 1636-1643.Dhar, S.K., et al. (2021) IL-6 and IL-10 as predictors of disease severity in COVID-19 patients: results from meta-analysis and regression, Heliyon, 7, e06155.Dudekula, D.B., et al. (2016) CircInteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs, RNA biology, 13, 34-42.Dweep, H. and Gretz, N. (2015) miRWalk2. 0: a comprehensive atlas of microRNA-target interactions, Nature methods, 12, 697-697.Farr, R., et al. (2021) Altered microRNA expression in COVID-19 patients enables identification of SARS-CoV-2 infection.Huang, C., et al. (2020) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China, The lancet, 395, 497-506.Huang, H.-Y., et al. (2020) miRTarBase 2020: updates to the experimentally validated microRNA\u2013target interaction database, Nucleic acids research, 48, D148-D154.Kang, J., et al. (2021) RNAInter v4. 0: RNA interactome repository with redefined confidence scoring system and improved accessibility, Nucleic acids research.Lin, L., et al. (2020) Long-term infection of SARS-CoV-2 changed the body's immune status, Clinical Immunology, 218, 108524.Liu, J., et al. (2020) Longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of SARS-CoV-2 infected patients, EBioMedicine, 55, 102763.Liu, M., et al. (2019) Circbank: a comprehensive database for circRNA with standard nomenclature, RNA biology, 16, 899-905.Pandya, P.H., et al. (2020) Systems biology approach identifies prognostic signatures of poor overall survival and guides the prioritization of novel bet-chk1 combination therapy for osteosarcoma, Cancers, 12, 2426.Qin, C., et al. (2020) Dysregulation of immune response in patients with coronavirus 2019 (COVID-19) in Wuhan, China, Clinical infectious diseases, 71, 762-768.Shams, R., et al. (2020) Identification of potential microRNA panels for pancreatic cancer diagnosis using microarray datasets and bioinformatics methods, Scientific Reports, 10, 7559.Venugopal, P., et al. (2022) Prioritization of microRNA biomarkers for a prospective evaluation in a cohort of myocardial infarction patients based on their mechanistic role using public datasets, Frontiers in Cardiovascular Medicine, 9.Wang, X. (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface, Rna, 14, 1012-1017.Wu, A.T., et al. (2021) Multiomics identification of potential targets for Alzheimer disease and antrocin as a therapeutic candidate, Pharmaceutics, 13, 1555.Yang, Y., et al. (2020) Plasma IP-10 and MCP-3 levels are highly associated with disease severity and predict the progression of COVID-19, Journal of Allergy and Clinical Immunology, 146, 119-127. e114.Zhang, P., et al. (2021) Bioinformatics analysis of candidate genes and pathways related to hepatocellular carcinoma in China: a study based on public databases, Pathology and Oncology Research, 13.AttachmentResponse to reviewers.docxSubmitted filename: Click here for additional data file. 13 Mar 2023Mapping CircRNA\u2013miRNA\u2013mRNA Regulatory Axis Identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infectionPONE-D-22-34657R1Dear Dr. Awan,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. 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For more information, please contact Kind regards,Kanhaiya Singh, Ph.DAcademic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments:Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #2:\u00a0All comments have been addressed********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2:\u00a0Yes********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2:\u00a0Yes********** 4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #2:\u00a0Yes********** 5. 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If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #2:\u00a0No********** 4 Apr 2023PONE-D-22-34657R1 Mapping CircRNA\u2013miRNA\u2013mRNA Regulatory Axis Identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection Dear Dr. Awan:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Kanhaiya Singh Academic EditorPLOS ONE"} +{"text": "K\u03b1 radiation to single-crystal X-ray crystallography and evaluates two different detectors, the Bruker Photon III and the Dectris Eiger2 CdTe, for usage in spherical and aspherical structural models.This paper communicates the first application of MetalJet In K\u03b1 radiation wavelengths for use in X-ray diffraction experiments. The purpose of this paper is to demonstrate the application of indium K\u03b1 radiation in independent-atom model refinement, as well as approaches using aspherical atomic form factors. The results vary greatly depending on the detector employed, as the energy cut-off of the Eiger2 CdTe provides a solution to a unique energy contamination problem of the MetalJet In radiation, which the Photon III detector cannot provide.The MetalJet source makes available new Finally, a C11H10O2S YLID crystal, 5, was used to compare the two detectors and the setup with a second machine using aspherical refinements. The YLID crystal is an established benchmark for IAM refinements but can also be used for benchmarks at low temperatures and Incoatec Helios optics. With the Bruker Photon III detector, gallium contamination was filtered using a palladium foil of 40\u2005\u00b5m thickness. For the Eiger2 CdTe 1M detector, a custom solution within the D8 Venture was implemented. Steering using Diffraction data with silver radiation were collected using a Bruker D8 Venture four-circle diffractometer with an Incoatec I\u03bcS 3.0 Ag source and a Bruker Photon III detector as is.2.3.SAINT was performed using structure factors from periodic projector augmented wave (PAW) density functional theory (DFT) calculations. They employ the SCAN functional is less than half the energy of indium K\u03b1 % for the Eiger2 and 0.44\u2005(4)% for the Photon III detector. The relative percentages are more indicative than the absolute ones, as effects such as scattering cross sections and absorption have been neglected but should be the same for both detectors. Therefore, we could show a very small residual contamination with a slight advantage of the Eiger2 detector. A higher thickness of the palladium attenuator would have solved the problem, but would have led to a lower overall indium intensity.The second, more quantitative, approach used a pseudo-twin refinement of the two sets of reflections to get an impression of the relative strength of the contamination. Cell parameters and orientation and instrument parameters were determined in a first integration with 3.2.Rr.i.m shows the superior performance of the Eiger2 detector for each of the structures studied in this work for both the overall and multiplicity-equivalent data sets.The redundancy-independent merge factor and egross follow the I/\u03c3 indicator of the data collection. Accordingly, we see the superior performance of the agreement with the data collected by the Eiger2 CdTe on the In MetalJet, separated by a significant margin from the I\u03bcS Ag measurement using the Photon III. The In MetalJet measurement on the Photon III shows the highest values and number of undescribed electrons egross for both evaluated methodologies. For the unweighted agreement factor, both Photon III measurements yield the same value for the HAR. However, for the multipole refinement the Photon III In measurement exhibits a higher value than the Photon III measurement using Ag K\u03b1 radiation.The crystallographic quality indicators are very similar for both methods Figs. 3 and 4 \u25b8:wR2 and the goodness of fit (GOF). For the Ag/Photon III and In/Eiger2 data, the performance of these two indicators is basically identical for the HAR, while the multipole refinement shows a slight advantage for the Ag/Photon III. The In/Photon III data show inferior performance for these indicators as well.The conclusion is less clear on the weighted crystallographic agreement factor The Photon III measurements show a higher value in the negative difference electron density for both minima, and also an overall shift in the Henn\u2013Meindl plots. The I\u03bcS Ag data also show a slightly lower maximum in the difference electron density, whereas the In/Photon III data set again exhibits the most pronounced maxima and minima in the difference electron density.The In/Photon III measurement shows a significant jump in the quotient of the sum of observed to the sum of fitted intensities (supporting information) closely follow the Henn\u2013Meindl plots. All refinements show a low level of difference electron density. The indium MetalJet data obtained with the Photon III detector show a noisy overall difference electron density at an isolevel \u00b10.05\u2005e\u2005\u00c5\u22123, with the highest features being located near the heaviest atom, namely the ylid sulfur. At the same time the I\u03bcS 3.0 Ag data with the Photon III show a disposition towards a negative difference electron density, which can be explained by the intensity of the inner data matching less accurately, as observed in the DRKPlot-type plot. In comparison, the difference electron density obtained by the indium MetalJet with the Eiger2 CdTe is much flatter. The visible features at the same low isolevel (\u00b10.05\u2005e\u2005\u00c5\u22123) are limited to the vicinity of the sulfur atom and the oxygen atoms, while also being less strongly expressed at these positions. The resulting difference electron densities of the multipolar refinements are comparable for the three investigations . In the I\u03bcS 3.0 Ag/Photon III data, the increased number of parameters does counteract the overall negative density near the sulfur atom and part, but not all, of the discrepancy is assigned to the density, as investigated in the next section.The difference electron densities of the Hirshfeld atom refinement Fig. 5 and the 3.4.2.et al. ScCoC_eiger, ScCoC_photon, ScPtSi_eiger, ScPtSi_photon, NaWO4_eiger, NaWO4_photon, LAla_eiger, LAla_photon, Ylid_HAR_Ag_Photon, Ylid_HAR_In_Eiger, Ylid_HAR_In_Photon, Ylid_MM_Ag_Photon, Ylid_MM_In_Eiger, Ylid_MM_In_Photon. DOI: 10.1107/S1600576723007215/nb5354ScCoC_eigersup2.hklStructure factors: contains datablock(s) ScCoC_eiger. DOI: 10.1107/S1600576723007215/nb5354ScCoC_photonsup3.hklStructure factors: contains datablock(s) ScCoC_photon. DOI: 10.1107/S1600576723007215/nb5354ScPtSi_eigersup4.hklStructure factors: contains datablock(s) ScPtSi_eiger. DOI: 10.1107/S1600576723007215/nb5354ScPtSi_photonsup5.hklStructure factors: contains datablock(s) ScPtSi_photon. DOI: 10.1107/S1600576723007215/nb5354NaWO4_eigersup6.hklStructure factors: contains datablock(s) NaWO4_eiger. DOI: 10.1107/S1600576723007215/nb5354NaWO4_photonsup7.hklStructure factors: contains datablock(s) NaWO4_photon. DOI: 10.1107/S1600576723007215/nb5354LAla_eigersup8.hklStructure factors: contains datablock(s) LAla_eiger. DOI: 10.1107/S1600576723007215/nb5354LAla_photonsup9.hklStructure factors: contains datablock(s) LAla_photon. DOI: 10.1107/S1600576723007215/nb5354Ylid_HAR_Ag_Photonsup10.hklStructure factors: contains datablock(s) Ylid_HAR_Ag_Photon. DOI: 10.1107/S1600576723007215/nb5354Ylid_HAR_In_Eigersup11.hklStructure factors: contains datablock(s) Ylid_HAR_In_Eiger. DOI: 10.1107/S1600576723007215/nb5354Ylid_HAR_In_Photonsup12.hklStructure factors: contains datablock(s) Ylid_HAR_In_Photon. DOI: 10.1107/S1600576723007215/nb5354Ylid_MM_Ag_Photonsup13.hklStructure factors: contains datablock(s) Ylid_MM_Ag_Photon. DOI: 10.1107/S1600576723007215/nb5354Ylid_MM_In_Eigersup14.hklStructure factors: contains datablock(s) Ylid_MM_In_Eiger. DOI: 10.1107/S1600576723007215/nb5354Ylid_MM_In_Photonsup15.hklStructure factors: contains datablock(s) Ylid_MM_In_Photon. DOI: 10.1107/S1600576723007215/nb5354sup16.pdfAdditional refinement details. DOI:"} +{"text": "HemaSphere. 2023;7(9):e942), a correction is needed for Table 3 and Table 4. Bullet points and subheaders were misaligned, therefore reducing clarity for readers. This has now been adjusted. The journal office apologizes for any inconvenience.Since the publication of the article entitled \u201cMeasurable Residual Disease Testing in Multiple Myeloma Routine Clinical Practice: A Modified Delphi Study\u201d (https://journals.lww.com/hemasphere/fulltext/2023/09000/measurable_residual_disease_testing_in_multiple.12.aspxThe changes have been made online:"} +{"text": "Peroral endoscopic myotomy (POEM) is an increasingly adopted strategy for the treatment of Zenker\u2019s diverticulum . The Z-Video\u20061\u2002Peroral endoscopic myotomy for Zenker\u2019s diverticulum without tunneling.After the initial mucosal incision, both submucosal sides of the septum are lifted, with a mixture of hydroxyethyl starch and indigo carmine. Then we proceed to direct myotomy of the septum . The diEndoscopy_UCTN_Code_TTT_1AO_2AG"} +{"text": "Correction to: Journal of Nuclear Cardiologyhttps://doi.org/10.1007/s12350-022-03164-5The original published Supplementary File I was incorrect and is replaced with the following Supplementary File: \u201c12350_2022_3164_MOESM2_ESM\u201d.The original article has been corrected."} +{"text": "The recruitment process for the position of ECDC Director is handled by the European Commission.\u00a0The deadline for the submission of applications is 26 June 2023, 12:00 noon CEST.For detailed information on the job description, requirements and the application procedure, please visit:https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=OJ%3AJOC_2023_185_A_0001"} +{"text": "Bone mineral content (Z_BMC), fat mass (Z_FM), lean mass (Z_LM), and bone mineral density for the total body (Z_TB) and lumbar spine (Z_L1\u20134) were measured using dual-energy X-ray absorptiometry. Twenty-nine percent of children were vitamin D deficient (25-hydroxyvitaminD level of <20 ng/mL). In winter, low vitamin D intake (P = 0.019) and fewer daylight hours (P = 0.015) were associated with low 25-hydroxyvitaminD level. The 25-hydroxyvitamin D level correlated positively with Z_BMC (P = 0.023), Z_TB (P = 0.018), and Z_L1\u20134 (P = 0.043) independently of sex, puberty, Z_FM, Z_LM, physical activity level, and calcium intake. Z_FM correlated independently with Z_BMC (P< 0.001), Z_TB (P = 0.037), and Z_L1\u20134 (P < 0.001). In conclusion, almost half of peripubertalnonobese children were vitamin D deficient in winter. Considering the beneficial effects of adequate vitamin D status and adiposity on bone health, the current DRI of vitamin D should be upgraded to prevent vitamin D deficiency.The dietary reference intake (DRI) of vitamin D for Korean children wasreduced from 400IU/day in 2005 to 200IU/day in 2010. We evaluated the risk factors for low vitamin D status and itsrelationships with bone health in peripubertalnonobese children living in Seoul or Gyeonggi-do. One hundred children participated in the winter ("} +{"text": "There was an error in the list of accession numbers in Supplementary File S1 in the Supporting Information. Please view the correct version of S1 here: https://dl.dropboxusercontent.com/u/63557304/File_S1_Updated.pdf"} +{"text": "The correct sequences of the primers described in this work are HW_MSchX_F-TGGGTGAAGTAAGTCCAACAG and HW_MSchX_R-TGAAGAACGTATCCAGCCTACA. The amplified fragment corresponds to nucleotides 21227\u201322122 of the human chromosome Xq22.3 (GenBank ID AL390039.10)."} +{"text": "Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth \u2018RNA-puzzle\u2019 competition. These results establish all-atom enumeration as an unusually systematic approach to ab initio protein structure modeling that can leverage high performance computing and physically realistic energy functions to more consistently achieve atomic accuracy.Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. Current approaches, such as the protein local optimization protocol or kinematic inversion closure (KIC) Monte Carlo, involve stages that coarse-grain proteins, simplifying modeling but precluding a systematic search of all-atom configurations. This article introduces an alternative modeling strategy based on a \u2018stepwise ansatz\u2019, recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA) protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include The method has furthermore been successful in blind tests Recently, a conceptually distinct approach to modeling macromolecule structure has arisen from efforts to predict complex RNA structures in all-atom detail Given its advantages over prior RNA modeling approaches and its assurance of complete sampling, stepwise assembly also holds promise for difficult problems in protein structure prediction. This study presents the first application of SWA to proteins, focusing on loop modeling. Protein loop modeling problems arise frequently in comparative modeling, designing new proteins, and solving or refining protein folds with limited crystallographic or NMR data, including weakly populated (\u2018invisible\u2019) states cis-Pro touch turns, loops that thread through tunnels formed by the surrounding protein, and segments of unprecedented length. These cases are solved ab initio by SWA with sub-Angstrom accuracy, albeit at the expense of thousands of CPU-hours per loop. Additional atomic-accuracy results from five blind predictions, including a comparative modeling problem for a protein/RNA complex, give further support to the stepwise ansatz and its Rosetta SWA implementation. Analogous to recent successes of RNA modeling in structural biology To address the conformational sampling bottleneck, this article describes the import of stepwise assembly from RNA modeling to protein loop structure prediction in the Rosetta framework . The res1oyc), an unsolved case in recent studies NHB in 1oyc case). Furthermore, loops make few interactions with the non-polar core, arguably the best modeled region of protein structures 1oyc loop residues , which uses backbone-only hierarchical loop build-up followed by molecular mechanics force field refinement cis proline sampling, and more stringent chain closure. Even in these more extensive calculations , crystallographically observed combinations, and closed loop geometries, sampling each amino acid at sub-Angstrom resolution requires at least tens of backbone conformers (see SI Methods), resulting in at least 1012 backbone torsional combinations for a 12-residue loop. Subsequent side-chain optimization on these backbones would require tens of millions of CPU-hours Most current loop modeling approaches that seek atomic resolution share a seemingly necessary working approximation: an initial search phase using a reduced representation with simplified or no side-chain atoms. Such coarse search phases avoid the complexity and large number of local minima inherent to all-atom representations, but fail to capture non-polar packing interactions and hydrogen bonds involving side-chain atoms, which are pervasive . This protocol has been coded into the Rosetta framework as a stepwise assembly (SWA) algorithm.Recent work in three-dimensional RNA modeling 1oyc loop. For the first five residues implementation was used to carry out structure prediction on a benchmark set of thirty-five protein loops. Twenty of these cases were 12-residue loops used previously to test PLOP and Rosetta approaches First, examining the subset of twenty loops used in prior PLOP and Rosetta studies permitted direct comparison of SWA to these state-of-the-art methods see also . Here, tcis prolines, and reported RMSD for the very lowest energy model.] The high accuracy SWA predictions that were intractable to previous PLOP and/or Rosetta approaches included the 1oyc case described above and 0.89 \u00c5 (best of five lowest energy structures). SWA modeling again outperformed KIC modeling overall, although not by as much as in the first 20-loop benchmark [1.9 \u00c5 (lowest energy) and 0.94 \u00c5 (best of five)]. In 8 of these 15 complex loop tests, SWA returned at least one of five lowest energy models with sub-Angstrom accuracy . High-re12\u2013fold more accessible conformations). However, the stepwise ansatz underlying the SWA method constrains sampling to a subspace that requires only 4-fold more steps to search. For three of the six cases with lengths greater than or equal to 18 residues, the SWA method achieved sub-Angstrom accuracy. Modeling with such accuracy included two 24-residue cases. One involved a mixture of irregular, helix, and strand segments in a bacteriophage head protein . Interestingly, in two of these cases (1arp and 1huw), KIC modeling outperformed SWA modeling in terms of RMSD but gave significantly worse Rosetta energies and not released outside their research group. The closest previously solved structure exhibited low sequence identity to the target ; and analogs of the loop regions either did not exist (loop A) or were different in sequence at all 12 positions (loop B) or at 10 positions (loops C and D) in the homologous structure. The Weis group provided a starting structure with all of these loops and all side-chains removed, and ur cases , includiur cases . In threur cases .2fc3] based on threading with HHPRED and Rosetta 3v7e; As a fifth blind test, SWA models were generated for a loop of protein YbxF This article has presented a strategy for protein structure prediction that achieves atomic accuracy on the majority of loop modeling targets through a systematic all-atom enumeration. Several of these targets were difficult or intractable with prior approaches, despite mainly involving loops excised from crystallographic models, the simplest such puzzles. The main innovation herein is a stepwise ansatz imported from RNA structure modeling. This working hypothesis posits that realistic loop structures are reachable via the residue-by-residue building of partial conformations that are themselves well-stabilized by precise hydrogen bonds and non-polar packing interactions. This ansatz underlies a Rosetta stepwise assembly (SWA) protocol and is supported by tests of the SWA algorithm on forty loop puzzles, including twenty shared with prior loop modeling benchmarks, fifteen more difficult loop cases, and five blind tests. In the majority of cases (32 of 40), including loop puzzles of unprecedented length, all the blind tests, and a comparative model , the SWA method achieved sub-Angstrom accuracy.The stepwise assembly protocol is novel in protein modeling studies: while prior efforts have proposed the build-up of short peptides or lattice models An analogy to lock-picking helps clarify the strengths and limitations of the stepwise assembly method described herein. The main innovation of the protein SWA method is the enumerative sampling of individual residue conformations, which helps guarantee precise fit of the residues' atoms into the surrounding environment. This scenario is a kind of \u2018lock-and-key\u2019 problem but differs from the previous RNA SWA method To unlock a tumbler lock, one \u2018enumeratively samples\u2019 each pin conformation through manipulation with a probing pick, until the boundaries within the pin doublet are aligned with the lock's cylindrical surface . The pinThis analogy clarifies the importance of precise fits between the loop and its surroundings for successful modeling; if such a fit is not possible, the current SWA implementation will give inaccurate solutions. In particular, SWA will have difficulty in problems where the given protein backbone (outside the loop) deviates from its actual conformation. Such scenarios are encountered in comparative modeling and protein design applications. Cases like the community-wide blind trial YbxF above demonstrN residues, the formal size of the conformational space scales exponentially with N; the actual experimental folding times of proteins do not scale so poorly, implying the general existence of folding intermediates or pathways rather than a random walk search N. The resulting efficiency permitted the atomic resolution recovery herein of loops with lengths up to 24 residues, whereas prior work tackled loops no longer than 12 residues tool for uncovering deficiencies in the Rosetta energy function, as in the solvent-exposed loops described above was implemented in C++ in the Rosetta codebase and is available in Rosetta release 3.6, free to academic users at de novo from residue k to residue l, each stage of stepwise assembly involved creating models of the loop with an N-terminal fragment built forward from k\u20131 to residue i and a C-terminal fragment built backward from residue l+1 to j. Each stage could thus be indexed with the two residue positions . The SWA calculation proceeded recursively from stages with short fragments built into the structure towards models with longer fragments, i.e., i increasing from k\u20131 or j decreasing from l+1. This building corresponds to movement from the top-right to the bottom or left, respectively, in A diagram of the entire stepwise assembly (SWA) calculation is given as a directed acyclic graph (DAG) laid out in the style of a dynamic programming matrix in k\u20131, l+1) of the DAG in packer. This pack optimized the rotamers using simulated annealing, after precomputing pairwise energies between all potential side-chain rotamers minimizerThe first step was a \u2018pre-packing\u2019 of the side-chains of the starting model with no loop atoms, corresponding to the top-right corner to (downward arrows in i and \u03c8i) and the previous, adjacent residue , permitting the discovery of configurations in which the dipeptide segment is stabilized by interactions by the new residue without requiring interactions at the previous residue. . For each \u03c6 or \u03c8, the sampling was a grid search from \u2013180\u00b0 to 180\u00b0 in 20\u00b0 increments. To keep only sterically realistic backbones, configurations in which a residue's gave Rosetta ramachandran score greater than 0.8 Rosetta units were discarded. The \u03c9 torsion was assumed to be 180\u00b0 (trans configuration), except for residues that preceded prolines, which were also sampled at 0\u00b0 (cis). The number of backbone combinations varied from tens to several thousand (for segments involving glycine residues and/or residues that preceded proline).The core computation in SWA is the addition of a new residue to a model and enumeration of its backbone conformations. For additions to the i and i\u20131) and their potential neighbors . The side-chain sampling was carried out with the Rosetta rotamer_trials algorithm. The searched side-chain rotamers included those listed in the backbone-dependent Rosetta rotamer library as well as additional rotamers with \u03c71 and \u03c72 shifted by \u00b11 standard deviation from the standard rotamer values. The discreteness of the backbone grid search and rotamer library can penalize favorable side-chain interactions due to minor clashes or slightly imperfect hydrogen bonds. Therefore, the energy function for side-chain optimization was modified from the current standard Rosetta all-atom energy function (score12) to include a lower weight on fa_rep , a higher weight on hbond_sc , and no attenuation of hydrogen bond strength at solvent-exposed residues For each combination of backbone torsion angles, the side-chains of the loop and its surroundings were optimized. Analogous to calculations in protein-protein docking i\u20131 and i . If the RMSD value to any lower energy clusters was less than a fine cutoff (0.10 \u00c5), the model was considered too close to an existing representative and discarded; otherwise the model seeded a new cluster. The lowest energy 400 models after clustering were carried forward to minimization.After enumerative backbone sampling and side-chain optimization, models were clustered as follows. In order of energy, starting with the lowest energy model, the RMSD of each model to all lower energy clusters was computed; this RMSD value was calculated over N, C, C\u03b1, and O atoms at the rebuilt residues minimizerscore12. The models were clustered as described above, and saved to disk.Minimization involved backbone torsions at the sampled residue and torsions \u03c7 for all neighboring side-chains . This torsional optimization was performed with the non-monotone Armijo variant of BFGS minimization in the Rosetta j to the C-terminal loop fragment where 1< (j\u2013I\u20131) <3].For the final stages of SWA assembly, N-terminal and C-terminal fragments were bridged to form continuous loops with ideal backbone bond lengths and angles , and thei+1 was appended to the N-terminal fragment, and other gap residues i+2 to j\u20131 were prepended to the C-terminal fragment. The \u03c6 and \u03c8 torsion angles of the first gap residue i+1 were sampled by grid search as above; and, to attempt chain closure, backbone torsions for \u2018bridge\u2019 residues i+2 up to j\u20131 were subjected to 1000 cycles of cyclic coordinate descent , leading to hundreds of thousands of models. Even larger numbers were generated at the final stage of full-length loop modeling due to the many routes to chain closure. However, these models typically spanned a very large range of energies, and SWA seeks to carry forward only the lowest-energy configurations at each rebuild stage. Thus all models for a given stage were collated, filtered to retain the 4000 lowest energy models, and then reclustered. The clustering followed the procedure described above, except that RMSDs were calculated over the entire rebuilt loop fragments and a clustering RMSD threshold of 0.25 \u00c5 was applied. The 400 lowest energy configurations were carried forward. In the final stage (full-length loop models), models were re-clustered with RMSD threshold 1.0 \u00c5, and the five lowest energy models were taken as the SWA predictions.For a given build-up stage (l+1) is coupled to the loop conformation through the torsion \u03c6l+1. This degree of freedom was not sampled, as \u2018native\u2019 backbone hydrogen atoms were present in the benchmark starting structures. However, for the five blind tests, the hydrogens were not available a priori; they were initially placed in the starting excised structure with Reduce l+1 was not guaranteed to be in its \u2018native\u2019 position, \u03c6l+1 was sampled during build-up of residues l\u20131 and l.In the SWA runs for this study's 35-loop benchmark, some settings in the loop modeling were chosen so as to match prior benchmarks. First, for proteins containing disulfide bonds, these residue-residue pairings were assumed to be known [as in prior work N) with the number of residues N, rather than as O (N2), and is analogous to the recursion used previously for RNA loop modeling N) calculation was carried out first. If the energy gap between the lowest energy model and the second lowest energy model was less than 1 kBT, the calculation was assumed to not have clearly converged on a confident model, and the loop building was repeated with the full O (N2) calculation, except the very long 1rhd and 7cat test cases. Overall, 18 of 40 cases were modeled with the O (N) calculation that some cases could be solved without carrying out the full SWA dynamic programming matrix, but instead by building from the N-terminal side , by building in separate runs from the C-terminal side , and then combining these separate solutions with chain closure to attain final models. This simplified calculation steps with the number of loop residues N (see above) are setup with the same swa_protein_dagman.py script above, but without the last flag \u2013loop_force_Nsquared. For blind tests, the \u03c8 torsion for the starting loop residue and \u03c6 torsion for the ending loop residue were sampled (see above); this was accomplished by omitting the flag -disable_sampling_of_loop_takeoff.Simplified calculations that take O and for post-processing all models available for a given stage by collation into single files and removal of unused files, are available in tools/SWA_protein_python/.Each of the build steps described in protein_build.dag corresponds to a single command line using the Rosetta executable swa_protein_main.An example command-line for pre-packing the 1OYC loop modeling case is:swa_protein_main. -database -rebuild -out:file:silent_struct_type binary -fasta 1oyc.fasta -n_sample 18 -nstruct 400 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weights pack_no_hb_env_dep.wts -in:detect_disulf false -add_peptide_plane -native 1oyc_min.pdb -superimpose_res 1-202 215-399 -fixed_res 1-202 215-399 -calc_rms_res 203-214 -jump_res 1 399 -disable_sampling_of_loop_takeoff -mute all -s1 noloop_1oyc_min.pdb -input_res1 1-202 215-399 -use_packer_instead_of_rotamer_trials -out:file:silent REGION_215_202/START_FROM_START_PDB/region_215_202_sample.outAn example command line that builds residue 206 onto the end of a N-terminal fragment already containing 203\u2013205 is:swa_protein_main. -database -rebuild -out:file:silent_struct_type binary -fasta 1oyc.fasta -n_sample 18 -nstruct 400 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weights pack_no_hb_env_dep.wts -in:detect_disulf false -add_peptide_plane -native 1oyc_min.pdb -superimpose_res 1-202 215-399 -fixed_res 1-202 215-399 -calc_rms_res 203-214 -jump_res 1 399 -disable_sampling_of_loop_takeoff -mute all -silent1 region_215_205_sample.cluster.out -tags1 S_0 -input_res1 1-205 215-399 -sample_res 205 206 -out:file:silent REGION_215_206/START_FROM_REGION_215_205_DENOVO_S_0/region_215_206_sample.outHere, the build is onto the lowest energy model (S_0) available from a previous stage that had rebuilt residues 203\u2013205 from the N-terminal end.An example command line that builds residue 209 onto the N-terminal end of a C-terminal fragment already containing residues 210\u2013214:swa_protein_main. -database -rebuild -out:file:silent_struct_type binary -fasta 1oyc.fasta -n_sample 18 -nstruct 400 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weights pack_no_hb_env_dep.wts -in:detect_disulf false -add_peptide_plane -native 1oyc_min.pdb -superimpose_res 1-202 215-399 -fixed_res 1-202 215-399 -calc_rms_res 203-214 -jump_res 1 399 -disable_sampling_of_loop_takeoff -mute all -silent1 region_210_202_sample.cluster.out -tags1 S_2 -input_res1 1-202 210-399 -sample_res 209 210 -out:file:silent REGION_209_202/START_FROM_REGION_210_202_DENOVO_S_2/region_209_202_sample.outHere, the build is onto the third lowest energy model (S_2) available from a previous stage that had rebuilt residues 210-214 from the C-terminal end.An example command line that takes the lowest energy model from the ensemble that has built up both the N-terminal fragment 203\u2013206 and C-terminal fragment 209\u2013215, samples backbone degrees of freedom at residue 207, and closes the chain by cyclic coordinate descent (CCD) across residues 207 and 208:swa_protein_main. -database -rebuild -out:file:silent_struct_type binary -fasta 1oyc.fasta -n_sample 18 -nstruct 400 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weights pack_no_hb_env_dep.wts -in:detect_disulf false -add_peptide_plane -native 1oyc_min.pdb -superimpose_res 1-202 215-399 -fixed_res 1-202 215-399 -calc_rms_res 203-214 -jump_res 1 399 -disable_sampling_of_loop_takeoff -mute all -silent1 region_209_206_sample.cluster.out -tags1 S_0 -input_res1 1-206 209-399 -sample_res 208 -bridge_res 207 -cutpoint_closed 207 -ccd_close -global_optimize -out:file:silent REGION_207_206/START_FROM_REGION_209_206_CLOSE_LOOP_CCD_S_0/region_207_206_sample.outAn example command line that combines the lowest energy model for N-terminal fragment 203\u2013206 with every model for C-terminal fragment 209\u2013215 and carries out CCD (cyclic coordinate descent) chain closure across 207 and 208:swa_protein_main. \u2013database -rebuild -out:file:silent_struct_type binary -fasta 1oyc.fasta -n_sample 18 -nstruct 400 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weights pack_no_hb_env_dep.wts -in:detect_disulf false -add_peptide_plane -native 1oyc_min.pdb -superimpose_res 1-202 215-399 -fixed_res 1-202 215-399 -calc_rms_res 203-214 -jump_res 1 399 -disable_sampling_of_loop_takeoff -mute all -silent1 region_209_202_sample.cluster.out -tags1 S_0 -input_res1 1-202 209-399 -silent2 region_215_206_sample.cluster.out -input_res2 1-206 215-399 -bridge_res 207 208 -cutpoint_closed 206 -ccd_close -global_optimize -out:file:silent REGION_207_206/START_FROM_REGION_209_202_REGION_215_206_CLOSE_LOOP_CCD_S_0/region_207_206_sample.outAn example command line for clustering the lowest energy 4000 models available for the N-terminal fragment 203\u2013205:swa_protein_main. -cluster_test -silent_read_through_errors -in:file:silent REGION_215_205/start_from_region_215_204_denovo_sample.low4000.out -in:file:silent_struct_type binary -database -cluster:radius 0.25 -calc_rms_res 203-214 -out:file:silent region_215_205_sample.cluster.out -nstruct 400 -score_diff_cut 10.000 -working_res 1-205 215-399de novo models, with the same bond lengths and angles as used in the modeling.To help assess efficiency of conformational sampling, the all-atom Rosetta energies of crystallographic loops were obtained through two strategies. Generally, crystallographic loops contain minor steric clashes that are penalized by the Rosetta energy function, and these conformations need to be subjected to local optimization to permit comparison to idealize application), and the resulting idealized loop conformation was grafted into the same side-chain pre-packed structure as used in the SWA runs above. The loop and all its neighbors were subjected to combinatorial optimization by the packer and then all loop torsions and all side-chain torsions in the loop and surrounding residues were subjected to continuous minimization as above. As above, keeping the backbone outside the loop residue rigorously fixed requires a formal chainbreak within the loop, which remains closed during minimization due to the linear_chainbreak term. For each potential chainbreak location , 20 runs were carried out. The command line used was the following:The first \u2018idealize-and-optimize\u2019 strategy mimicked that from ref. swa_protein_main. \u2013database -rebuild -out:file:silent_struct_type binary -fasta 1oyc.fasta -n_sample 18 -nstruct 400 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weights pack_no_hb_env_dep.wts -in:detect_disulf false -add_peptide_plane -native 1oyc_min.pdb -superimpose_res 1-202 215-399 -fixed_res 1-202 215-399 -calc_rms_res 203-214 -jump_res 1 399 -disable_sampling_of_loop_takeoff -silent1 region_215_202_sample.cluster.out -tags S_0 -input_res1 1-202 215-399 -cutpoint_closed 214 -global_optimize -out:file:silent MINIMIZE_NATIVE/12/1oyc_minimize_native.out -cluster:radius 0.0 -s2 1oyc_min_idealize.pdb -input_res2 202-215 -slice_res2 202-215A second \u2018native SWA\u2019 strategy was used to optimize the loop conformation around the crystallographic loop. In this strategy, the entire SWA calculation after the initial side-chain prepacking was repeated, but at each sampling step, models were only carried forward if their backbone RMSD to the crystallographic loop was less than 2.0 \u00c5. In addition, Rosetta coordinate constraints at loop C\u03b1 atoms were implemented with the following Python script command line:generate_CA_constraints.py 1oyc.pdb \u2013cst_res 203-214 \u2013coord_cst \u2013anchor_res 1 \u2013fade > 1oyc_coordinate2.0.cstThe script is available in tools/SWA_protein_python/. These constraints applied a penalty for each C\u03b1 atom deviating further than 2.0 \u00c5 from the crystallographic position, rising to a maximum of 10.0 kBT for deviations of 4.0 \u00c5; the functional form was a cubic spline with zero derivative at 2.0 \u00c5 and 4.0 \u00c5 (the fade function in Rosetta). These constraints were activated in SWA runs by including flags -rmsd_screen 2.0 and -cst_file 1oyc_coordinate2.0.cst in swa_protein_main command lines above. In all tested loops, the SWA-native strategy gave models within 1.0 \u00c5 C\u03b1 RMSD to the crystallographic loop with lower energies than the idealize-and-optimize strategy ; the SWA-native values are thus reported in To permit comparison of the SWA approach to a prior state-of-the-art method, the KIC (kinematic closure) loop modeling method in Rosetta was repeated on the 20-protein PLOP/Rosetta benchmark. The following command line was used:loopmodel. -database -loops:remodel perturb_kic -loops:refine refine_kic -loops:input_pdb region_FINAL.out.1.pdb -in:file:native 1oyc_min.pdb -loops:loop_file 1oyc.loop -loops:max_kic_build_attempts 10000 -in:file:fullatom -out:file:fullatom -out:prefix 1oyc -out:pdb -ex1 -ex2 -ex1aro -extrachi_cutoff 0 -out:nstruct 1000 -out:file:silent_struct_type binary -out:file:silent 1oyc_kic.out -fix_ca_bond_angles -kic_use_linear_chainbreak -allow_omega_move -sample_omega_at_pre_prolines.The command line is identical to that used previously, except for some additional terms to ensure a fair comparison to the SWA modeling above. The flag -fix_ca_bond_angles retains N\u2013C\u03b1\u2013C bond angles at ideal values defined by Rosetta; sampling these angles did not improve accuracy in prior work The KIC loop modeling method requires an input starting structure with a loop pre-built, and this loop defines the fixed bond lengths and angles used in the run. Rather than using the crystallographic loops Figure S1Energy vs. RMSD plots at intermediate stages of stepwise assembly build-up. Build-up in panels (a) to (k) corresponds to residue-by-residue path in 1oyc loop (residues 203\u2013214). RMSD over all backbone heavy-atoms is shown on x-axis, using the corresponding loop fragments in the crystallographic loop as a reference. In each panel, symbol with black outline marks the specific model that eventually leads to the final lowest energy model in (k).(EPS)Click here for additional data file.Figure S2Energy vs. RMSD summaries of modeling runs for 20-loop PLOP/Rosetta benchmark. Rosetta all-atom energy values and loop C\u03b1 RMSDs are plotted for models from kinematic closure Monte Carlo ; stepwise assembly with O(N) simple calculation (red); stepwise assembly with full O(N2) build-up (pink); crystallographic loops optimized by SWA re-building with constraints (blue); and crystallographic loops optimized by idealizing, re-packing, and continuous minimization (green).(ZIP)Click here for additional data file.Figure S3Energy vs. RMSD summaries of modeling runs for 15 difficult and 5 blind test cases. Rosetta all-atom energy values and loop C\u03b1 RMSDs are plotted for models from models from kinematic closure Monte Carlo ; stepwise assembly with O(N) simple calculation (red); stepwise assembly with full O (N2) build-up (pink); crystallographic loops optimized by SWA re-building with constraints (blue); and crystallographic loops optimized by idealizing, re-packing, and continuous minimization (green). For 3v7e , optimized crystallographic energies are not presented, since loop building was carried out on a comparative model; and energies between KIC and SWA cannot be compared as RNA was not included in the former case.(ZIP)Click here for additional data file.Table S1Comparison of all loop modeling methods in 20-residue PLOP/Rosetta benchmark.(PDF)Click here for additional data file.Table S2Energy comparisons to determine convergence and conformational sampling efficiency.(PDF)Click here for additional data file."} +{"text": "It presently has 115 members. An interesting recent interaction is presented herewith.] serves science well, it does not serve philosophy well at all, for it is not forwarded in its line of enquiry in a fruitful way.But per se. I admire it as the highest form of intellectual enquiry. But it will not do for this highest form to look askance at the obvious that empirical science is producing.Richard, I have no quibbles with philosophy Let me put it a nutshell. Let\u2019s try and answer these questionsPhilosophers are mainly discussing brain functions. How many of them have even a working knowledge of its structure - neuroanatomy, neurophysiology; leave alone its pathology?Tell me why is there no entry \u2018brain\u2019 in any encyclopaedia or dictionary of philosophy? [Correct me if I am wrong.]http://en.wikipedia.org/wiki/Brain] and more specifically \u2018Human Brain\u2019 [see http://en.wikipedia.org/wiki/Human_brain]. There are concepts here that may appear technical, but one can at least start; and what one doesn\u2019t understand one can ask from scientific colleagues in the field of brain biology.How many have even tried to read the entry \u2018brain\u2019 in an encyclopaedia Tell me why is there no entry \u2018brain\u2019 in any encyclopaedia or dictionary of philosophy? [Correct me if I am wrong.][Have you found any that has an entry?]http://en.wikipedia.org/wiki/Brain] and more specifically \u2018Human Brain\u2019 [see http://en.wikipedia.org/wiki/Human_brain]. There are concepts here that may appear technical, but one can at least start; and what one doesn\u2019t understand one can ask from scientific colleagues in the field of brain biology.How many [philosophers] have even tried to read the entry \u2018brain\u2019 in an encyclopaedia Care to opine?Have you made a New Year resolution you will study the brain?Happy New Year.Ajai31 Dec 2010__________________________________________________________________________________________________________________________ wrote:On Fri, 31/12/10, Richard Godwin Sorry, but I still think you don\u2019t make your point. Often discussions of brain functions are accompanied with brain areas or regions, such as primarily the pre-frontal cortex. But if not, then what difference does it make? The brain functions in such and such a way; what difference does it make to point out the pre-frontal cortex and associated regions, such as the amygdala and gray matter? Why should philosophers discuss the anatomy of the brain? If they don\u2019t discuss brain structure, etc., that doesn\u2019t mean they have no knowledge of it, or that they can\u2019t answer questions specific to it. Pathology is important and is mentioned when appropriate, such as the cognitive effects of brain injuries.Almost all philosophers teach and write on \u201cphilosophy of mind.\u201d That covers the brain, especially for physicalists. As to an encyclopaedia, why not look under \u201cmind\u201d, an overall subject including the brain? Or \u201cbiology\u201d, or \u201cphysical\u201d?Perhaps you can explain why any discussion of brain functions requires knowledge of the brain\u2019s structure.Richard.__________________________________________________________________________________________________________________________From: Ajai Singh To: Mind_Brain_Consciousness@yahoogroups.comSent: Thursday, December 30, 2010 5:32 PMI think I replied to that, Richard.\u2018One may say one can very well do thinking without understanding the structure that causes it. I can very well drive a car without understanding its structure. But if I am describing the functions of an entity, I have to know its strucure as well, or at least have a working knowledge. If I am describing the functions of a car, I cannot claim any level of expertise unless I have at least a working knowledge of its structure.about thinking. Hence, they fall in both categories.\u2018Philosophers are not only thinking, they are also talking That is why I am urging my philosopher friends of the second category to get a working knowledge of the brain; and include that in their syllabi, their dictionaries and their encyclopaedias.\u2019Happy New Year.Ajai1 Jan 2011.__________________________________________________________________________________________________________________________From Richard Godwin: meta@rraz.net Date: Sat, 1 Jan 2011 10:12:01 -0700Your car analogy doesn\u2019t work quite well enough. With the car there are so many completely different elements, providing completely different functions (such as \u201cengine\u201d and \u201cwheel\u201d), that the analogy breaks down. There are several identified regions in the brain, and they work neuronal networks through chemical reactions toward any given function. I think philosophers do recognize different regions in the brain, but without scientific knowledge of precisely how those networks perform a task through which regions. But why should that matter? Simply the brain functions through networks of neurons with chemical impulses in different regions of the brain. Shouldn\u2019t that be sufficient for the task of philosophy?Expertise in what? If you mean philosophers should be brain experts, then you might be right. But that is the provenance of science, not philosophy. You want a philosopher also to be a scientist, right? Why?Give us an example how poor philosophical reasoning is caused by lack of knowledge of the precise structure of the brain.I\u2019m just trying to get at the root of your problem. So far, simply you have not made your case.Thank you,Richard.__________________________________________________________________________________________________________________________ wrote:On Sun, 2/1/11, veena garyali I have been following this discussion with great interest. I am not a philosopher but do read a reasonable amount. I tend to agree with Richard. I really do not understand why Ajai is insisting that a philosopher should know the details of brain structure. The fact is that the essential importance of the brain is a given. There can be no thought, feeling or discussion without the brain and that too the human brain. Without being said it is understood. Philosophers focus on what comes after that- different world view, the meaning attributed to certain things, and so much else. Do they need to stipulate in the beginning that they know about the existence of the brain? It is like when you go to testify in the court both attorneys generally agree on the expert\u2019s basic qualifications and they stipulate it without going into details. I am by no means an expert and may be I am missing some deeper meaning, but I fail to see the connection.Veena__________________________________________________________________________________________________________________________ Sunday, 2 January, 2011 20:34 wrote:Ajai Singh Why should philosophers study the brain?I am happy Richard and Veena are unhappy with what is presented until now.Because that lets me proceed with a few observations to clarify why I suggested what I did to my philosophers friends.Let us study a few concepts that have engaged philosophers. To put them in simple terms:Mind-body dualism states the mind is separate from the body.Descartes is credited with stating that mind and body, or consciousness and stuff, interact in the pineal gland.In the mind-body problem, the idealist view is that the mind alone is real.In the problem of personal identity, questions asked are: can a mind animate several bodies? Can several minds animate one body? Can mind exist without a body at all?In Indian thought, manas [roughly translated as mind] is regarded as an internal sense organ.And so on, and so forth.If one has a working knowledge of the brain structure and related functions, one realises that, with regard to each of the points above:Mind is a function of the brain, and brain is not at all separate from the body.The pineal gland is not responsible for any such interaction between physical and mental activity, or mind and body.The idealist view that mind alone is real is really not talking of mind as a function of the brain at all, but as some metaphysical entity. Because if they were to study the brain and its structure and related functions, they would immediately realise that the thought, \u2018The mind alone is real\u2019 is itself a product of their functioning brain, and they would rather say, \u2018My brain functions are surely real, even if there may be doubt whether the external world is real or not\u2019. If their brain were not functioning, they would not come to either conclusion, for whatever they are worth.What are we talking of as \u2018mind\u2019 here? If even an elementary study of brain is done, and if we accept mind to be a collection of brain functions, we would understand the ridiculous nature of these reflections with mind as the focus - the reflection is not at fault, the entity \u2018mind\u2019 as the focus is the culprit.Can a mind animate several bodies, or several minds animate one body? Manas or Mind as an internal sense organ in earlier Indian thought. An organ? If so, it must be present somewhere in the body? One thinks they meant the brain, which was understandably presented as an \u2018internal sense organ\u2019, given the extant nature of their understanding then.A clear understanding of brain structure and related functions makes many of these so called profound problems just evaporate into thin air. And saves precious energies to further more substantial enquiries in the field.That is why I recommend greater need to study the brain in all its nuances - not just its gross structure, but its function, its neurophysiology, its neurochemistry.In fact, if a philosopher/s were to sincerely study all these, and also empathetically study the different reflections on \u2018mind\u2019 and \u2018consciousness\u2019 that philosophers down the centuries have given, in the East and the West, and honestly co-relate them, he would be able to present the most comprehensive understanding of the topic, maybe even a final grand theory that settles matters, once and for all.Also, if a philosopher-scientist were to study and grasp the workings of the brain, and top it up with a comprehensive understanding of the great mass of knowledge that the great masters of thought - philosophers of the East and West - have bequeathed humanity, and co-relate them in a comprehensive manner, a similar grand theory that settles matters would result.When I urge my philosopher friends to study the brain, I do so because I believe they have greater potential to give such a theory. If they continue to live in denial, the scientists are on course, and may pip them to the post.And, of course, if a scientist-philosopher takes it up, and can get over his denial of philosophy because of their often \u2018amorphous\u2019 formulations, he may beat both the philosophers and the scientists to the post too.That is the game, that is the final goal, friends. We are playing for really large stakes.That is why I suggest philosophers plug that loophole in their study - neglecting the brain.And that is why I also now suggest scientists plug their loophole - neglecting the philosophy of mind.And if the two can synergise efforts, the goal can be achieved in half the time.Ready?Happy New Year once again. And kindly once again pardon the long post.Ajai2 Jan 2011Ajai Singh,mensanamonographs@yahoo.co.ukE-mail:"} +{"text": "There was an error in the accession number in Materials and Methods.EBV and KSHV dataset can be found under the Study Accession number: ERP001026.Individual Sample Accessions are as follows:1208_JSC1_SN_KS - ERS0748231212_HBL6_SN_KS - ERS0748241210_JSC1_SN_EB - ERS0748251215_HBL6_SN_EB - ERS074833"} +{"text": "An evaluation of the Bruker SMART X2S for the collection of crystallographic diffraction data, structure solution and refinement is carried out with a variety of materials with different electron densities, presenting some of the successes and challenges of automation in chemical crystallography. An evaluation of the Bruker SMART X2S for the collection of crystallographic diffraction data, structure solution and refinement is carried out with a variety of materials with different electron densities, presenting some of the successes and challenges of automation in chemical crystallography. For the third experiment, the crystal is sufficiently far from the centre of the mount that it is precessing in and out of the beam. Thus, the symmetry-equivalent reflections do not match, the Laue check fails and the larger centred unit cell is not identified. The checkCIF output highlights the missed symmetry, as well as the high R int and final R values, and should alert the nonspecialist to the fact that there is a problem.The first two experiments have similar data, both of which are perfectly acceptable for publication: a slight increase in In summary, the large beam size means that alignment is not as critically important as on other instruments, particularly in the horizontal direction, although for short data collection times and good quality data, it is still important.3.N-cyano-S-benzyl-S-(2-fluorophenyl)sulfilimine, (2), synthesized , (4) and (11) are novel (see the supplementary information for their synthesis). Literature methods were used for the synthesis of (5) . The polarity of compound (9), as evidenced by the Flack \u2013(14) an incorrect structure was obtained. The data quality seems fine, with no evidence of twinning or disorder, so what types of issues have occurred? The errors involve differentiation between atoms that differ by one electron, e.g. N and O atoms are reversed in (12) .Compounds (2)\u2013(14) are anhydrous samples, without any solvent present. The effectiveness of the system for crystals containing more than one compound was investigated: a hydrate, a solvate and a cocrystal, (15)\u2013(17) and (17) were assigned correctly. For (16), a C and an N atom were misassigned, as discussed in \u00a77.13H10OS, was incorrectly input as the sulfoxide, C13H10O2S, and (10), C15H12N2O, was input as C27H22N2O2S. The hydrate (16) and solvate (15) were input as the pure material. The software is robust and coped with an incorrect molecular formula in the majority of cases, with 80% of samples obtaining the correct structure.The effect of inputting the incorrect molecular formula was investigated, since it is necessary to input a formula at the start of the experiment, and in some cases the identity of the crystal may not be known. For example, (5), CThere is one issue that causes inconvenience. The system does not update the CIF and report files with the molecular formula based on the structure obtained, but instead uses the formula input by the user. This requires manual refinement for cases where the submitted formula is different from the structure obtained.8.K\u03b1 source for (2), (8), (11), (12), (16) and (18), which include samples of both good and poor crystal quality. The synthesis of (18), 4-methyl-N-phenylbenzenesulfonamide, has been described by Massah et al. etc. In our experience, those users who are familiar with the checkCIF output after an experienced crystallographer has finalized a crystal structure are asking more questions about the checkCIF output they obtain from the SMART X2S. Novice users are also asking similar questions and some of these questions are about the technique itself. This is a major advantage of the output from the instrument, in that it does seem to be increasing awareness of crystallography among the synthetic chemists.The checkCIF output allows fast diagnosis of any issues in the experiment. Inputting an incorrect formula at the start of the experiment, for example, will immediately become obvious from the checkCIF output because of differences in formula, density APEX2 software suite than the rest of the data set (<5), owing to the beam stop blocking or partially blocking the correct measurement of these reflections in some orientations. This is not unusual for chemical crystallography and omitting these from the latter cycles of refinement would be useful, although it may be better not to do this in a routine manner.In some experiments, In summary, the SMART X2S as an instrument has allowed chemists with no crystallography experience to obtain crystallographic data for novel compounds. The instrument has greatly increased the use of crystallography in the department, with little training required to operate a user-friendly and easy-to-use instrument.supplementary information and have been deposited with the Cambridge Crystallographic Data Centre (CCDC) for the novel crystals (2)\u2013(8), (11) and (14)\u2013(18). [The following computer programs were used in the refinement: APEX2, GIS, SADABS and SAINT (Bruker (2009SHELXS97 and SHELXL97 (Sheldrick, 2008PLATON (Spek, 2009The CIF data (Hall & McMahon, 2006uker 2009, SHELXS910.1107/S0021889810042561/kk5074sup1.cif Crystal structure: contains datablocks Compound_1_Below, Compound_1_Centre, Compound_1_Side, Compound_2_APEX, Compound_2_CCDC, Compound_2_Run_1, Compound_2_Run_2, Compound_2_Run_3, Compound_2_Run_4, Compound_3_CCDC, Compound_3_X2S, Compound_4_CCDC, Compound_4_X2S, Compound_5_CCDC, Compound_5_X2S, Compound_6_CCDC, Compound_6_X2S, Compound_7_CCDC, Compound_7_X2S, Compound_8_APEX, Compound_8_CCDC, Compound_8_X2S, Compound_9_X2S, Compound_10_X2S, Compound_11_APEX, Compound_11_CCDC, Compound_11_X2S, Compound_12_APEX, Compound_12_Manual, Compound_12_X2S, Compound_13_Manual, Compound_13_X2S, Compound_14_CCDC, Compound_14_Manual, Compound_14_X2S, Compound_15_CCDC, Compound_15_Manual, Compound_15_X2S, Compound_16_APEX, Compound_16_CCDC, Compound_16_Manual, Compound_16_X2S, Compound_17_CCDC, Compound_17_X2S, Compound_18_APEX, Compound_18_CCDC, Compound_18_Manual, Compound_18_X2S, global. DOI: 10.1107/S0021889810042561/kk50742_CCDCsup2.hkl Structure factors: contains datablocks 2_CCDC. DOI: 10.1107/S0021889810042561/kk50743_CCDCsup3.hkl Structure factors: contains datablocks 3_CCDC. DOI: 10.1107/S0021889810042561/kk50744_CCDCsup4.hkl Structure factors: contains datablocks 4_CCDC. DOI: 10.1107/S0021889810042561/kk50745_CCDCsup5.hkl Structure factors: contains datablocks 5_CCDC. DOI: 10.1107/S0021889810042561/kk50746_CCDCsup6.hkl Structure factors: contains datablocks 6_CCDC. DOI: 10.1107/S0021889810042561/kk50747_CCDCsup7.hkl Structure factors: contains datablocks 7_CCDC. DOI: 10.1107/S0021889810042561/kk50748_CCDCsup8.hkl Structure factors: contains datablocks 8_CCDC. DOI: 10.1107/S0021889810042561/kk507411_CCDCsup9.hkl Structure factors: contains datablocks 11_CCDC. DOI: 10.1107/S0021889810042561/kk507414_CCDCsup10.hkl Structure factors: contains datablocks 14_CCDC. DOI: 10.1107/S0021889810042561/kk507415_CCDCsup11.hkl Structure factors: contains datablocks 15_CCDC. DOI: 10.1107/S0021889810042561/kk507416_CCDCsup12.hkl Structure factors: contains datablocks 16_CCDC. DOI: 10.1107/S0021889810042561/kk507417_CCDCsup13.hkl Structure factors: contains datablocks 17_CCDC. DOI: 10.1107/S0021889810042561/kk507418_CCDCsup14.hkl Structure factors: contains datablocks 18_CCDC. DOI: 10.1107/S0021889810042561/kk5074sup15.pdf Supplementary material file. DOI: Figures, tables and supplementary information"} +{"text": "A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents Rosetta results for four well-defined test cases: the 20-residue mini-protein Trp cage, an even smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies, several lines of evidence indicate that conformational sampling is not the major bottleneck in modeling these small systems. Instead, approximations and omissions in the Rosetta all-atom energy function currently preclude discriminating experimentally observed conformations from de novo models at atomic resolution. These molecular \u201cpuzzles\u201d should serve as useful model systems for developers wishing to make foundational improvements to this powerful modeling suite. It may seem self-evident that one should start modeling with the very smallest known sequences that take on well-defined 3D structures. For several reasons, such a completely reductionist approach has not been the mainstream strategy in the Rosetta community. First, in early days, most cases of naturally occurring ultra-small proteins were considered irregular and perhaps ill-defined, lacking the clear \u03b1 or \u03b2 secondary structure and hydrophobic cores that are the hallmarks of larger protein domains. Thus, initial Rosetta studies from the mid-1990s focused on 50- to 100- residue protein sequences that formed regular, clearly well-defined structures de novo modeling of short irregular loops and small proteins regularly appear as sub-problems in blind prediction targets and in the design of catalytic sites, conformationally switchable segments, and structured peptides. Predicting the structural features of these small systems and sub-systems \u2013 and even modeling the fine energetic balance between alternative structures \u2013 is no longer something to be avoided but instead a key goal of many Rosetta developers.These historical reasons to avoid small systems are no longer as relevant. First, since the late 1990s, several very small protein systems have been discovered or engineered and then clearly demonstrated to attain precisely defined 3D structures greater than 3 kcal/mol.) Note that the focus herein will be on recovering high-resolution features of the experimental models; thus an acceptable C\u03b1 RMSD should be 1 \u00c5 or lower, comparable to the differences between structures solved in different crystallographic space groups or with different binding partners. Further, the puzzle descriptions include discussion of side-chain conformations deemed experimentally stable and important for each molecule's fold and function.Each of the selected systems has been extensively characterized by numerous experimental structural and energetic methods. In particular, in each case, the free energy associated with the experimental conformation has been measured to be at least 3 kcal/mol more stable than the ensemble of unstructured states at room temperature. community. The Trp cage is a particularly well-characterized mini-protein with a length of 20 residues, engineered by truncating and optimizing exendin-4 from gila monster saliva de novo modeling, on the other hand, fails to solve this problem. While occasionally sampling a near-native conformation, Rosetta's fragment-assembly/all-atom-refinement protocol (\u201cabrelax\u201d) favors a tight cluster of structures with a backbone within 2 \u00c5 C\u03b1 RMSD of the native conformation but with the molecule's central tryptophan side-chain in an incorrect rotamer mini-proteins. The \u03b1-conotoxin GI, isolated from the fish-hunting marine snail de novo modeling (abrelax) gives low energy models that disagree with the crystal structure in all non-helical regions (not shown). The Stepwise Assembly algorithm yields even lower energy models that are still highly discrepant strategies versus StepWise protocols.]Excision of this segment and subsequent Rosetta de novo. than the optimized native models. Thus, at least for these four small puzzles, it is the poor discrimination of the Rosetta all-atom energy function that emerges as the critical problem. In previous studies, the difficulty of conformational sampling for larger problems as well the greater energy gaps attained in those problems likely masked flaws in the Rosetta energy function , these efforts have led to few substantial improvements in benchmarks or actual changes in the main codebase. One potential barrier is that the physics of solvation, H-bonds, and screened electrostatic interactions are strongly coupled to each other, and indeed are reflected in partly unified terms in most other molecular modeling force fields ; this code will be gladly provided to other academic users upon request.We summarize sequences and Rosetta command-lines for each of the four puzzles herein. Most of the calculations in the paper were carried out with Rosetta release 3.2; and all calculations will be implemented in the next Rosetta release. Remaining models were generated with the Rosetta codebase in the Das lab branch (revision number 40197), available to Rosetta developers did not give significantly lower energies. Both of these standard command lines are also executable with Rosetta release 3.2.A total of 20,000 models were generated for both i,j] of the target sequence onto clustered conformational ensembles derived from subfragments and . Each \u201cstep\u201d involves exhaustively sampling \u03c6/\u03c8 in 20\u00b0 increments, repacking side-chains, and minimizing. An example command-line for the step building subfragment Independent modeling runs were carried out with a novel StepWise Assembly (SWA) method. A full benchmark of this method is under preparation. Briefly, the method recursively builds each subfragment [stepwise_protein_test. -database -rebuild -out:file:silent_struct_type binary -fasta 2jof.fasta -n_sample 18 -nstruct 100 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weightspack_no_hb_env_dep.wts -add_peptide_plane -native 2jof.pdb -mute all -silent1 region_4_5_sample.cluster.out -tags1 S_0 -input_res1 4 5 -sample_res 3 4 -out:file:silent REGION_3_5/START_FROM_REGION_4_5_DENOVO_S_0/region_3_5_sample.out [SWA]2 resource. Optimized native conformations were also estimated with the StepWise Assembly method. To ensure a fair comparison, the entire calculation was repeated, but using Rosetta atom-pair constraints (with the Rosetta smoothed step function \u201cfade\u201d) to keep models with inter-residue C\u03b1-C\u03b1 distances within \u00b11 \u00c5 and the tryptophan rotamer in the native conformation. Explicitly, an example command line is:A complete directed acyclic graph (DAG) of the rebuild and clustering steps, along with associated commands in Condor format, was automatically generated by a master Python script. The script and a resulting example DAG are provided via Rosetta protocol capture (see below). The DAG was computed via DAGMAN with the Condor computing platform or with in-house Python scripts on the LSF queuing platform on 200 to 400 cores on Stanford's BioXstepwise_protein_test. -database -rebuild -out:file:silent_struct_type binary -fasta 2jof.fasta -n_sample 18 -nstruct 100 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weightspack_no_hb_env_dep.wts -add_peptide_plane -native 2jof.pdb -mute all -silent1 region_4_5_sample.cluster.out -tags1 S_0 -input_res1 4 5 -sample_res 3 4 -out:file:silent REGION_3_5/START_FROM_REGION_4_5_DENOVO_S_0/region_3_5_sample.out-cst_file 2jof_native_CA_CA_trp.cst [SWA NATIVE]2jof_native_CA_CA_trp.cst is provided by Rosetta protocol capture.and the constraint file ECCNPACGRHYSC. The methods for de novo modeling \u03b1-conotoxin were essentially the same as for Trp cage. However, the following command lines need to be run from the Das lab branch, which disables complications in disulfide input/output and scoring in the Rosetta release 3.2.The modeled sequence was: AbinitioRelax. -database -fasta 1not_.fasta -frag3 aa1not_03_05.200_v1_3 -frag9 aa1not_09_05.200_v1_3 -out:file:silent 1not_abrelax_CST_increase_cycles_no_hb_env_dep.out -out:file:silent_struct_type binary -nstruct 400 -cst_file 1not_native_disulf_CEN.cst -abinitio:relax -cst_fa_file 1not_native_disulf.cst -native 1not.pdb -increase_cycles 10 -score:weights score12_no_hb_env_dep.wts -ex1 -ex2 -extrachi_cutoff 0 [ABRELAX]andrelax. -database -s idealize_1not.pdb -fasta 1not_.fasta -frag3 aa1not_03_05.200_v1_3 -frag9 aa1not_09_05.200_v1_3 -out:file:silent 1not_native_relax.out -out:file:silent_struct_type binary -nstruct 200 -abinitio:relax -cst_fa_file 1not_native_disulf.cst -native 1not.pdb -increase_cycles 10 -score:weights score12.wts -ex1 -ex2 -extrachi_cutoff 0 [NATIVE RELAX]1not_native_disulf.cst; see protocol capture) enforces near-native disulfide bond lengths and angles between residue pairs and ; Rosetta atom-pair constraints are defined, penalizing S\u03b3\u2013S\u03b3 distances outside 1.5\u20132.5 \u00c5 and inter-residue S\u03b3-C\u03b2 distances outside 2.5\u20133.5 \u00c5. For both command-lines, 20,000 models were generated.The constraint file from subfragment are:stepwise_protein_test. -database -rebuild -out:file:silent_struct_type binary -fasta 1not.fasta -n_sample 18 -nstruct 100 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weightspack_no_hb_env_dep.wts -add_peptide_plane -cst_file 1not_native_disulf.cst -native 1not.pdb -mute all -silent1 region_4_5_sample.cluster.out -tags1 S_0 -input_res1 4 5 -sample_res 3 4 -out:file:silent REGION_3_5/START_FROM_REGION_4_5_DENOVO_S_0/region_3_5_sample.out [SWA]stepwise_protein_test. -database -rebuild -out:file:silent_struct_type binary -fasta 1not.fasta -n_sample 18 -nstruct 100 -cluster:radius 0.100 -extrachi_cutoff 0 -ex1 -ex2 -score:weights score12.wts -pack_weightspack_no_hb_env_dep.wts -add_peptide_plane -cst_file 1not_native_disulf_CA_CA.cst -native 1not.pdb -mute all -silent1 region_4_5_sample.cluster.out -tags1 S_0 -input_res1 4 5 -sample_res 3 4 -out:file:silent REGION_3_5/START_FROM_REGION_4_5_DENOVO_S_0/region_3_5_sample.out[SWA NATIVE]VGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG . The Rosetta command-line made use of a recent loop modeling that leverages kinematic loop closure The chymotrypsin inhibitor sequence was the 62-residue truncated sequence from barley seeds: TEWPELVGKSVEEAKKVILQDKPEAQIIVLPloopmodel. -database -loops:remodelperturb_kic -loops:refinerefine_kic -loops:input_pdb 2ci2_min.pdb -in:file:native 2ci2.pdb -loops:loop_file 2ci2_35_45.loop -loops:max_kic_build_attempts 10000 -in:file:fullatom -out:file:fullatom -out:prefix 2ci2 -out:pdb -ex1 -ex2 \u2013extrachi_cutoff 0 -out:nstruct 200 -out:file:silent_struct_type binary -out:file:silent 2ci2_kic_loop35_45.out[KIC]10,000 KIC models were generated. Output files were rescored to generate RMSDs over just the rebuilt loops, using the command line:score. -database -in:file:silent 2ci2_kic_loop35_45.out -native 2ci2.pdb -out:file:scorefile 2ci2_kic_loop35_45.recalculate_rmsd.sc -in:file:silent_struct_type binary -in:file:fullatom -native_exclude_res 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62The optimized native conformation (2ci2_min.pdb) was generated by packing and minimizing side-chains, as described in StepWise Assembly methods were also applied to this case, but could not be directly compared to the KIC results because of difference in which degrees of freedom were optimized . gcuucggc. (Lower-case letters refer to nucleic acids in Rosetta.)The eight-nucleotide modeled RNA sequence, derived from residues 31\u201338 of a ribosomal fragment (PDB: 1F7Y), was:Fragment Assembly of RNA with Full-Atom Refinement rna_denovo. -random_delay 20 -database -fastagcuucggc.fasta -nstruct 200 -out::file::silent gcuucggc.out -minimize_rna -cycles 5000 -mute all -native gcuucggc_RNA.pdb [FARFAR]Optimized native conformations used a similar command line but drew fragments only from the crystallographic model that was the source of the puzzle:rna_denovo. -random_delay 20 -database -fastagcuucggc.fasta -nstruct 200 -out::file::silent gcuucggc_NATIVE.out -minimize_rna -cycles 5000 -mute all -native gcuucggc_RNA.pdb -vall_torsions 1f7y_native.torsions [FARFAR NATIVE]In both cases, 20,000 FARFAR models were generated. The native torsion file was generated by:rna_database. -database -s 1f7y_RNA.pdb -vall_torsions -o 1f7y_native.torsionsi,j] of the target sequence are modeled from clustered conformational ensembles for subfragments and in a recursive manner. Single-residues are enumeratively sampled in 20\u00b0 increments, repacking 2\u2032-OH groups, and minimizing. Here, an ideal Watson-Crick stem was assumed for residues 1\u20132 and 7\u20138, and the UUCG loop 3\u20136 was rebuilt from both ends and connected by CCD loop closure. An example command-line for the basic rebuild step building residue 3 onto the starting stem in either de novo and native-optimization runs are:For RNA modeling cases, StepWise Assembly provides a more efficient sampling method . Analogous to protein cases (A) and (B), sub-fragments [rna_swa_test. -algorithm rna_resample_test -database -fastagcuucggc.fasta -output_virtual -cluster:radius 0.100 -num_pose_kept 100 -score:weights rna_hires_2008.wts -native motif2_1f7y_RNA.pdb -rna_torsion_potential rd2008 -s1 gcgc.pdb -input_res1 1 2 7 8 -out:file:silent REGION_0_1/START_FROM_REGION_0_0/region_0_1_sample.out -sample_res 3[SWA]rna_swa_test. -algorithm rna_resample_test -database -fastagcuucggc.fasta -output_virtual -cluster:radius 0.100 -num_pose_kept 100 -score:weights rna_hires_2008.wts -native motif2_1f7y_RNA.pdb -cst_fileuucg_polar_fade.cst -sampler_native_rmsd_screen -sampler_native_rmsd_screen_cutoff 1.500 -rna_torsion_potential rd2008 -s1 gcgc.pdb -input_res1 1 2 7 8 -out:file:silent REGION_0_1/START_FROM_REGION_0_0/region_0_1_sample.out -sample_res 3[SWA NATIVE]In the latter command-line, a constraint file penalizes conformations in which contacting (within 4 \u00c5) polar heavy atoms are placed beyond 1 \u00c5 from their native distances; the file is provided in the protocol capture (see next).https://svn.rosettacommons.org/source/trunk/RosettaCon2010/protocol_capture/rhiju_four_small_puzzles.All files, including fragments, sequence files (.fasta), native conformations (.pdb), as well as example logs are being provided via \u201cprotocol capture\u201d in the Rosetta Subversion repository: The directory will be gladly provided to readers without access to the repository upon request."} +{"text": "To the Editor: Kala-azar, or visceral leishmaniasis, is a parasitic disease that leads to fever, anemia, and hepatosplenomegaly. Death is the usual outcome when infection is not treated. The majority of infections are caused by the protozoan Leishmania donovani, restricted to India and eastern Africa, but the most widespread are caused by L. infantum, found from People\u2019s Republic of China to the New World, where it infects humans, dogs, and wild canids. All Mediterranean countries are affected by L. infantum, where most patients are co-infected with HIV. Several species of sand flies transmit the disease , possibly by insect eggs or larvae being carried in organic matter.During the 1980s, urban transmission of kala-azar became a major problem in Brazil. More than 3,000 cases are reported annually, and the disease has spread from northeastern Brazil westward to the Amazon region, as well as to the industrialized southeast. Several as yet unproven explanations for the urbanization of kala-azar in Brazil have been proposed are only 3\u20134\u00b0C lower than those of S\u00e3o Borja, Rio Grande do Sul state, the southernmost city where L. longipalpis transmits kala-azar, and even warmer than Chajar\u00ed, Argentina , at the highest southern latitude where this vector is found (Kala-azar has now reached the temperate Brazilian south and Argentina. This spread of the disease warns us of the danger of introduction in other temperate areas. Europe is particularly vulnerable because of the existing natural transmission of orizonte , BraziliL. longipalpis sand flies in Lisbon, the situation could change dramatically, and kala-azar might become a major urban disease in Europe. The International Health Regulations recommends disinfection of aircraft by preflight and blocks-away spraying with pyrethroids (L. longipalpis sand flies was recently described in Brazil (L. longipalpis sand flies, such as minimum temperature tolerance, mechanisms of urban spread, presence in aircraft, and role in inducing more severe disease._______________________________________________________________________________________________________________________________Human kala-azar is less common in Europe, possibly because sand flies there are less anthropophilic. If aircraft introduce anthropophilic"} +{"text": "In Page 6, right column, second paragraph, COG1517 should be COG1571.HVO_2477 should be HVO_2744 and HVO_B0354 should be HVO_B0357.In Table\u2009\u20091, page 7, In Page 8, right column, end of last paragraph, HVO_2477 should be HVO_2744.HVO_B0354 should read VDC2399 H26 \u0394HVO_B0357. In Supplemental Table\u2009\u20091, the entry VDC2399 H26 \u0394HVO_2477 entries should be HVO_2744, and all HVO_B0354 entries should be HVO_B0357.In Supplemental Table\u2009 4, all These corrections do not influence the overall conclusions of this study."} +{"text": "Computational design of protein function involves a search for amino acids with the lowest energy subject to a set of constraints specifying function. In many cases a set of natural protein backbone structures, or \u201cscaffolds\u201d, are searched to find regions where functional sites can be placed, and the identities of the surrounding amino acids are optimized to satisfy functional constraints. Input native protein structures almost invariably have regions that score very poorly with the design force field, and any design based on these unmodified structures may result in mutations away from the native sequence solely as a result of the energetic strain. Because the input structure is already a stable protein, it is desirable to keep the total number of mutations to a minimum and to avoid mutations resulting from poorly-scoring input structures. Here we describe a protocol using cycles of minimization with combined backbone/sidechain restraints that is Pareto-optimal with respect to RMSD to the native structure and energetic strain reduction. The protocol should be broadly useful in the preparation of scaffold libraries for functional site design. There has been recent progress in the computational design of functional proteins and in the prediction of biomolecular interactions across a wide range of problems: ligand-protein Most crystal structures will have regions of high energy as evaluated in Rosetta or other design programs, which will lead to sequence changes in design if they are not addressed. However most minimization protocols will lead to too much deviation from the original wild-type crystal structure. The question is how to properly balance energy minimization with reduction of structural deviation from the starting structure. The concept of optimizing a structure to the energy function in use has a long precedent \u2013 for example the equilibration of structures in molecular dynamics prior to a production run Here we carry out a systematic examination of a number of structure refinement methods, evaluating them for optimality (minimization of Rosetta energy and RMSD from the starting structure simultaneously) and for their influence on subsequent sequence re-design. We found that a combination of harmonic backbone and sidechain coordinate restraints minimizes all-atom RMSD and Rosetta energy together, and reduces the number of sequence changes in subsequent design. Because the restrained relax protocol examined here results in fewer sequence alterations in design, it also minimizes the amount of human intervention required in the overall design process.primum non nocere, or \u201cfirst do no harm\u201d) while also minimizing the Rosetta energy. One possibility in preparing structures for Rosetta is to re-refine the structure using an energy function incorporating standard Rosetta score terms as well as the correspondence to electron density Our goal in evaluating structure minimization protocols was first to minimize RMSD to the native to understand energetic changes effected by the protocol at a residue-by-residue level. The high-energy residues about 5 REU are all moved to lower energy by the protocol; residues in the 1\u20135 REU range are largely moved to lower energy; residues with negative energy remain mostly unchanged . The design protocol on the native places a glutamate at the position 14, in place of native tyrosine . Briefly, these structures were prepared for Rosetta by removal of waters and non-canonical amino acids and preparation of Rosetta parameter files for the ligands. Structure selection is described fully in Niv\u00f3n and Bjelic.The 41 protein monomer sequence recovery set has been described elsewhere min on one core of a mixed Intel-Xeon-L5335-2GHz/AMD-Opteron-2.2GHz cluster and roughly doubling in time for each additional 100 residues.The fast relax protocol in Rosetta is described elsewhere Harmonic coordinate restraints take the form f(x) \u200a=\u200a (d/sd)?2, where d is the distance of the atom from the desired coordinate, and sd is a parameter related to the strength of the restraint. Bounded coordinate restraints take a zero value within WIDTH of the desired coordinate, followed by a small harmonic segment to transition (from WIDTH to WIDTH +0.5*sd) and a linear value of slope set at 1/sd for the rest. Sidechain-sidechain restraint runs have harmonic distance restraints of sd\u200a=\u200a2.0 for all sidechain atom pairs within the specified cutoff distance, and backbone heavy atom harmonic coordinate restraints of sd\u200a=\u200a0.5.Parameter scans were performed with the flags:\u201c-no_optH false -flip_HNQ -use_input_sc -correct -no_his_his_pairE -linmem_ig 10 -nblist_autoupdate true\u201dHarmonic runs added flags \u201c-constrain_relax_to_start_coords -relax:ramp_constraints false -relax:coord_constrain_sidechains -relax:coord_cst_stdev \u201d, where SD ranged from 0.000001 to 5.0Bounded runs added flags \u201c-constrain_relax_to_start_coords -relax:ramp_constraints false -relax:coord_constrain_sidechains -relax:coord_cst_stdev -relax:coord_cst_width \u201d, where SD ranged from 0.1 to 5.0, and WIDTH ranged from 0 to 1.0.Sidechain-sidechain runs added flags \u201c-constrain_relax_to_start_coords-relax:ramp_constraints false -relax:sc_cst_maxdist \u201d where DIST ranged from 3 to 8.Unrestrained runs had no additional flags.RMSD values were computed in pymol with the command \u201calign relaxed and not hydro, reference and not hydro, cycles\u200a=\u200a0\u201d. The median per-residue energy and RMSD of 10 replicates of the relax procedure were taken as the value for that protein, and the mean value across the 51 proteins in the input set were computed for each of the different parameter runs.Design was performed with the Rosetta enzyme design program, using the default parameters from the enzdes scientific test in rosetta (rosetta/rosetta_tests/scientific/biweekly/tests/enzdes_benchmark). Briefly, a design shell of 6 \u00c5, with a 12 \u00c5 shell of repackable residues was used. One cycle of design with a \u201csoft\u201d Lennard Jones repulsive term was followed by one with the standard repulsive term. Extra rotamers were included based on the Dunbrack rotamer distribution, and recent updates to the Rosetta score function were also included \u2013l./inputs/pdb.list\u2013enzdes::detect_design_interface\u2013enzdes::cut1 6.0\u2013enzdes::cut2 8.0\u2013enzdes::cut3 10.0\u2013enzdes::cut4 12.0\u2013enzdes::cst_design\u2013enzdes::design_min_cycles 2\u2013enzdes::cst_min\u2013enzdes::chi_min\u2013ex1\u2013ex2\u2013ex1aro\u2013ex2aro\u2013extrachi_cutoff 1\u2013soft_rep_design\u2013flip_HNQ\u2013correct\u2013no_his_his_pairE\u2013score::hbond_params correct_params\u2013lj_hbond_hdis 1.75\u2013lj_hbond_OH_donor_dis 2.6\u2013dun08 false\u2013nstruct 1\u2013enzdes::no_unconstrained_repack\u2013linmem_ig 10\u2013nblist_autoupdate true\u2013enzdes::lig_packer_weight 1.8\u2013docking::ligand::old_estat true\u2013extra_res_fa inputs/2b3b.params inputs/2ifb.params inputs/1sw1.params inputs/2FQX.params inputs/2p0d.params inputs/2DRI.params inputs/1fby.params inputs/1ZHX.params inputs/2RDE.params inputs/1db1.params inputs/2h6b.params inputs/1z17.params inputs/2FME.params inputs/1y3n.params inputs/1urg.params inputs/1FZQ.params inputs/1y52.params inputs/1POT.params inputs/1XT8.params inputs/2FR3.params inputs/2UYI.params inputs/1USK.params inputs/1n4h.params inputs/2qo4.params inputs/2GM1.params inputs/2rct.params inputs/2HZQ.params inputs/1hsl.params inputs/1A99.params inputs/1uw1.params inputs/1l8b.params inputs/3B50.params inputs/1H6H.params inputs/2Q2Y.params inputs/1hmr.params inputs/1OPB.params inputs/1x7r.params inputs/2Q89.params inputs/1nl5.params inputs/1TYR.params inputs/2e2r.params inputs/1LKE.params inputs/2PFY.params inputs/1wdn.params inputs/1nq7.params inputs/1y2u.params inputs/2ioy.params inputs/1J6Z.params inputs/1RBP.params inputs/1XZX.params inputs/2f5t.params\u2013chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamerVirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitalspro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylatedthr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylatedlys_monomethylated lys_trimethylated lys_acetylated glu_carboxylatedcys_acetylated tyr_diiodinated N_acetylated C_methylamidatedMethylatedProteinCtermFile S1Supporting figures and tables. Table S1. Energy comparison between input and restrained-relax structures. Average over all energy terms for the input set (INPUT) and the set relaxed with sidechain coordinate restraints at sd\u200a=\u200a0.5 (COORD). Values are sorted by the difference in each score term. Energy terms fa_dun (sidechain rotamer probability-based energy) and fa_rep (Lennard-Jones repulsive term) are the largest contributors to lower energy after the relax. Table S2. The top-10 most-improved residues after the relax protocol for 1A99. Score term changes are shown for fa_dun and fa_rep score terms only. INPUT is for the original wild-type crystal structure. COORD is for the coordinate restrained relax structures. Delta is the difference between INPUT and COORD for the specified score term and residue. Table S3. Residue 14 energies for 2ifb.pdb before/after restrained relax and before/after design. Note that after the restrained relax the total energy for residue 14 (\u22121.17) is much lower, even slightly lower than the energy after enzyme design on an unrelaxed input structure (\u22121.14). Figure S1. Per-residue score comparison between an input and restrained-relax structure. Histogram of individual residue Rosetta scores for the putrescine receptor (1A99.pdb) unmodified (blue) and after the coordinate-restrained relax protocol (red), with overlap in purple. Figure S2. Example of improved design after restrained relax. 2ifb position 14 example, native in green, design on the unmodified native in cyan, and design on the restrained-relax native in purple. The wild-type identity at position 14 is mutated from tyrosine to glutamate in the run on an unmodified structure (cyan), but remains the original tyrosine in the run on the restrained-relax structure (purple).(DOCX)Click here for additional data file."} +{"text": "The purpose of the presented study was to trace orthologs of btd in other insects and reconstruct the evolutionary history of the Sp genes within the metazoa.The Sp-family of transcription factors are evolutionarily conserved zinc finger proteins present in many animal species. The orthology of the Sp genes in different animals is unclear and their evolutionary history is therefore controversially discussed. This is especially the case for the Sp gene Tribolium castaneum), a hemimetabolous insect (Oncopeltus fasciatus), primitively wingless hexapods (Folsomia candida and Thermobia domestica), and an amphipod crustacean . We supplemented this data set with data from fully sequenced animal genomes. We performed phylogenetic sequence analysis with the result that all Sp factors fall into three monophyletic clades. These clades are also supported by protein domain structure, gene expression, and chromosomal location. We show that clear orthologs of the D. melanogaster btd gene are present even in the basal insects, and that the Sp5-related genes in the genome sequence of several deuterostomes and the basal metazoans Trichoplax adhaerens and Nematostella vectensis are also orthologs of btd.We isolated Sp genes from representatives of a holometabolous insect (Sp5/btd ortholog, which strongly suggests that btd is not the result of a recent gene duplication, but directly traces back to an ancestral gene already present in the metazoan ancestor.All available data provide strong evidence for an ancestral cluster of three Sp-family genes as well as synteny of this Sp cluster and the Hox cluster. The ancestral Sp gene cluster already contained a Sp1 have been identified in the human genome, and homologous genes have been isolated from several other animal species as well codes for a member of the Sp-family, which represents an important factor for the formation of several head segments and is also involved in the development of the central and peripheral nervous system , Td_Sp1-4 [EMBL: FN562988], Td_Sp5/btd [EMBL: FN562989], Td_Sp6-9 [EMBL: FN562990], Fc_Sp1-4 [EMBL: FN562985], Fc_Sp5/btd [EMBL: FN562986], Fc_Sp6-9 [EMBL: FN562987], Ph_Sp1-4 [EMBL: FN562991], Ph_Sp6-9 [EMBL: FN562992]. BLAST analysis was used to identify the Sp1-4 homologue of D. melanogaster and T. castaneum. Gene specific primers were made to amplify Tc_btd [GenBank: NM_001114320.1], Tc_Sp8 [GenBank: NM_001039420] and Tc_Sp1-4 [GenBank: XM_967159] from T. castaneum cDNA, as well as Dm_btd [GenBank: NM_078545], Dm_D-Sp1 [GenBank: NM_132351] and Dm_CG5669 (Sp1-4) [GenBank: NM_142975] from D. melanogaster cDNA. The sequences of these primers are given in Additional File H. sapiens (Genome Reference Consortium Human Build 37 (GRCh37), Primary_Assembly) , Dm_Btd [GenBank: NP_511100], Dm_D-Sp1 [GenBank: NP_572579], Dps_GA19045 [GenBank: XP_001358829], Dps_GA22354 [GenBank: XP_002134535], Dps_GA12282 [GenBank: XP_001354397], Ag_Sp1-4 [GenBank: NZ_AAAB02008898], Ag_Sp5/Btd [GenBank: NZ_AAAB02008847], Ag Sp6-9 [GenBank: NZ_AAAB01008847]; Nav_Sp1-4 [GenBank: XP_001599101], Nav_Sp5/Btd [GenBank: AAZX01008599], Nav_Sp6-9 [GenBank: XP_001606079], Am_Sp1-4 [GenBank: XP_624316.2], Am_Sp5/Btd [GenBank: XP_001119912], Am_Sp6-9 [GenBank: XP_624528], Bm_Sp1-4 [GenBank: BABH01010251], Bm_Sp5/Btd [GenBank: BABH01024462], Bm_Sp6-9 [GenBank: AADK01002198], Tc_Sp1-4 [GenBank: XP_972252], Tc_Btd [GenBank: NP_001107792], Tc_Sp8 [GenBank: NP_001034509], Of_Sp8/9 [EMBL: FN396612], Nv_Sp1-4 [GenBank: XP_001635004], Nv_Sp5/Btd [GenBank: XP_001635002], Nv_Sp6-9 [GenBank: XP_001634948], Sp_Sp1-4 [GenBank: XR_025838], Sp_Sp5/Btd [GenBank: XP_789110.1], Sp_Sp6-9 [GenBank: XP_793203.2], Hs_Sp1 [GenBank: NP_612482], Hs_Sp2 [GenBank: NP_003101], Hs_Sp3 [GenBank: NP_003102], Hs_Sp4 [GenBank: NP_003103], Hs_Sp5 [GenBank: NP_001003845], Hs_Sp6 [GenBank: NP_954871], Hs_Sp7 [GenBank: NP_690599], Hs_Sp8 [GenBank: NP_874359], Hs_Sp9 [GenBank: NP_001138722], Mm_Sp1 [GenBank: NP_038700], Mm_Sp2 [GenBank: NP_084496], Mm_Sp3 [GenBank: NP_035580], Mm_Sp4 [GenBank: NP_033265], Mm_Sp5 [GenBank: NP_071880], Mm_Sp6 [GenBank: NP_112460], Mm_Sp7 [GenBank: NP_569725], Mm_Sp8 [GenBank: NP_796056], Mm_Sp9 [GenBank: NP_001005343], Dr_Sp1 [GenBank: NP_997827], Dr_Sp2 [GenBank: NP_001093452], Dr_Sp3 [GenBank: NP_001082967], Dr_Sp3-like [GenBank: XP_691096], Dr_Sp4 [GenBank: NP_956418], Dr_Sp5 [GenBank: NP_851304], Dr_Sp5-like [GenBank: NP_919352], Dr_Similar_to_Sp5 [GenBank: XP_001335730], Dr_Sp6 [GenBank: NP_991195], Dr_Sp7 [GenBank: NP_998028], Dr_Sp8 [GenBank: NP_998406], Dr_Sp8-like [GenBank: NP_991113], Dr_Sp9 [GenBank: NP_998125], Gg_Sp1 [GenBank: NP_989935], Gg_Sp2 [GenBank: XP_423405], Gg_Sp3 [GenBank: NP_989934], Gg_Sp4 [GenBank: XP_418708], Gg_Sp5 [GenBank: NP_001038149], Gg_Sp8 [GenBank: AAU04515.1], Gg_Sp9 [GenBank: AAU04516.1], Fr_Sp1 [GenBank: CAAB01000453.1], Fr_Sp2 [GenBank: CAAB01001586.1], Fr_Sp3 [GenBank: CAAB01000508.1], Fr_Sp3-like [GenBank: CAAB01000254.1], Fr_Sp4 [GenBank: CAAB01001019.1], Fr_Sp5 [GenBank: CAAB01001064.1], Fr_Sp5-like [GenBank: CAAB01000006.1], Fr_Sp6 [GenBank: CAAB01004244.1], Fr_Sp7 [GenBank: CAAB01000453.1], Fr_Sp8 [GenBank: CAAB01001019.1], Fr_Sp9 [GenBank: CAAB01000508.1]. In addition, we have provisionally annotated the Sp-family genes of D. pulex, T. adhaerens and B. floridae using the following genomic regions: Dp_Sp1-4 , Dp_Sp5/btd , Dp_Sp6-9 , Ta_Sp1-4 , Ta_Sp5/btd , Ta_Sp6-9 , Bf_Sp1-4 , Bf_Sp5/btd , Bf_Sp6-9 .Click here for fileGenomic locations of Sp genes and Hox genes. This table supplements the schematic overview given in Fig. H. sapiens: Genome Reference Consortium Human Build 37 (GRCh37), Primary_Assembly; D. melanogaster: release 5.10, A. gambiae: AgamP3.3, A. mellifera: Amel_4.0, T. castaneum: Tcas_3.0, D. pulex: JGI-2006-09, N. vectensis: Nematostella vectensis v1.0. The data for the N. vectensis Hox genes can be found in the references given in the table. Alternating shading for different species is used in the table to enhance the legibility of the table. Abbreviations: LG, linkage group; un, unassembled portions of the genome.Click here for fileSequence information about the gene specific primers used in this study. The first column gives the species and the gene. The second column gives the primer sequences in 5' to 3' orientation. The third column gives the length of the cloned fragment resulting from the PCR with the given primers. The fourth column gives the clone ID number. The fifth column gives the polymerase used to transcribe the RNA probe used for in situ hybridizations. The primers for D. melanogaster and T. castaneum have been designed as gene specific pairs using the genome sequence information. For O. fasciatus, T. domestica, F. candida, and P. hawaiensis we first isolated a small fragment of the genes using degenerate primers specified in the Materials and methods section. The gene specific RACE primers were designed on the basis of this sequence information and were used in conjunction with the commercial RACE adaptor primers. The cloned fragment of Ph Sp6-9 resulted from priming of the given primer pair. Abbreviations: Fwd, forward; Rev, reverse.Click here for file"} +{"text": "It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural capability of cancer to adapt dynamically in a Darwinian manner is a primary reason for therapeutic failures. Survival advantages may be induced by cancer therapies and also occur as a result of inherent cell and microenvironmental factors. The selected \"more fit\" clones outmatch their competition and then become dominant in the tumor via propagation of progeny. This clonal expansion leads to relapse, therapeutic resistance and eventually death. The goal of this study is to develop and demonstrate a more detailed clonality approach by utilizing integrative genomics.Patient tumor samples were profiled by Whole Exome Sequencing (WES) and RNA-seq on an Illumina HiSeq 2500 and methylation profiling was performed on the Illumina Infinium 450K array. STAR and the Haplotype Caller were used for RNA-seq processing. Custom approaches were used for the integration of the multi-omic datasets.Reported are major enhancements to CloneViz, which now provides capabilities enabling a formal tumor multi-dimensional clonality analysis by integrating: i) DNA mutations, ii) RNA expressed mutations, and iii) DNA methylation data. RNA and DNA methylation integration were not previously possible, by CloneViz (previous version) or any other clonality method to date. This new approach, named iCloneViz (integrated CloneViz) employs visualization and quantitative methods, revealing an integrative genomic mutational dissection and traceability thru the different layers of molecular structures.The iCloneViz approach can be used for analysis of clonal evolution and mutational dynamics of multi-omic data sets. Revealing tumor clonal complexity in an integrative and quantitative manner facilitates improved mutational characterization, understanding, and therapeutic assignments. It is recognised that cancer is a clonal disease instigated by a single cell and that metastasis is also commenced thru a single cell -3. TumorEvolution is an important scientific concept because it works. It provides a framework to explain changes in biological systems. Cancer is the result of an evolutionary process, but it is destructive, since it involves the loss of mechanisms that are implemented to protect against uncontrolled and undifferentiated growth. Ultimately, natural selection has a harsh reality that worried Darwin, namely, all that seems to matter is reproductive success .MM is a cancer of the bone marrow characterized by a malignant transformation and proliferation of plasma cells . DefinitThere exist an array of computational methods/tools that allow one to characterize various aspects of the clonal architecture of a tumor(s). Each method employs different computational and visualization techniques, and are very briefly described. SciClone allows fClomial is anothAll of the aforementioned referenced methods only make use of a single modality in their characterizations of clonal architecture, namely, DNA-based mutational data, culled from whole genome or whole exome sequencing (WES) experiments. Some methods also attempt to account for the effect of copy number variation on clonal architecture. This is contrasted to the multiple modality datasets employed in the characterization of clonal structure used within iCloneViz. iCloneViz is the only known computational method for inferring clonal architecture, which integrates multiple modality datasets to derive deeper biological meaning. For example, RNA variant calling is performed to detect whether or not a mutation found within the DNA (via a WES or WGS experiment) is detectable within a RNA transcript. Further, if a mutation is found to be present at the RNA level, the expression values associated with the transcript(s) containing the mutation can be quantified and visualized. Finally, DNA methylation data is integrated into the analysis, which could lead to hypotheses regarding methylation suppressing the expression of a tumor suppressor gene (TSG). iCloneViz tracks TSGs both by mutations and epigenetic/methylation events.Presentation) and then later when the cancer recurred . A novel bioinformatic approach named CloneViz .W: WES data in relation W for the patient experiment with the experiment identifier exp_id[i].\u25cf filter_settings: Data structure containing all filter settings including:\u25cf min_vaf: Minimum variant allele frequency (default 4%).\u25cb max_vaf: Maximum variant allele frequency (default 100%).\u25cb min_depth: Minimum read depth (default 20).\u25cb max_depth: Maximum read depth (default 1000).\u25cb min_meth: Minimum methylation percent (default 25%).\u25cb opacity: Opacity of scatter plot points (default 50%).\u25cb show_kg_only: Boolean indicating whether to show only mutations found in the key genes list K .\u25cb default_filter_settings: Default values used for filtering.\u25cf /*******************************************************Name & Purpose: Main, program entry pointInputs: NoneProcessing: Establish main processing loop for iCloneVizOutputs: NoneReturns: NoneAuthors: D. Johann, E. Peterson********************************************************/main{while (window is open){patient_id = display_patient_search;button_selection, exp_id = display_patient_experiments(patient_id);process;}}/*******************************************************Name & Purpose: Display Patient Search, via patient ID display patient meta-dataInputs: noneProcessing: Display patient meta-dataOutputs: NoneReturns: ID of selected patient from MPMDBAuthors: D. Johann, E. Peterson********************************************************/display_patient_search{patient_id = input from user;P;- get / display patient meta-data via relation return patient_id;}/*******************************************************Name & Purpose: Display Patient Experiments, show available experiments for iCloneViz analysisInputs: Patient IDProcessing: Retrieve patient experimental meta-data from MPMDBOutputs: Patient experimental data now in memoryReturns: Array of experiment IDs, Button selection for selected analysis, eg, Genomic Real Estate or Paired Scatter Plot or KDE plus Scatter PlotAuthors: D. Johann, E. Peterson********************************************************/display_patient_experiments(patient_id){P;- get / display all experimental data from database (MPMDB) for patient via relation exp_id = selected experiment ids;return button_selection, exp_id}/*******************************************************Name & Purpose: Process, process data and display visualization based on the user's choice of visualizationInputs: Button selection, & Experiment IDsProcessing: Execute specific function to handle processing based on user's choice of visualizationOutputs: NoneReturns: NoneAuthors: D. Johann, E. Peterson********************************************************/process{if genomic_real_estate(exp_id[0]);else if (button_selection == 'Paired Scatter Plot')paired_scatter_plot(exp_id[0...1]);else if (button_selection == 'KD + Scatter Plot')kd_plus_scatter_plot(exp_id[0]);}/*******************************************************Name & Purpose: Genomic Real Estate, fetch WES-based mutation data, using R.NET to generate R plot and visualizeInputs: Experiment ID of experiment to visualizeProcessing: Using R.NET API, generate plot image and display in windowOutputs: Scatter plot of all mutations by chromosome and variant allele frequency, read depth is encoded by color, see Additional File 2Returns: NoneAuthors: D. Johann, E. Peterson********************************************************/genomic_real_estate(exp_id){W;- execute query to MPMDB to fetch mutation data based on the exp_id and DB relation - establish the R.NET interface and invoke R;- divide x-axis into 24 sections - scale each section by the length of each chromosomew in Wfor each {w along x-axis by position, the y-axis by variant allele frequency, and color by read depth;- plot }- export plot as image file;- return execution to .NET;- display image file in windows form;}/*******************************************************Name & Purpose: Paired Scatter Plot, fetch filter settings and call function to display paired scatter plotInputs: Experiment IDsProcessing: If first time displaying, use default filter settings to display paired plot, otherwise, fetch filter settings from user and display paired plotOutputs: NoneReturns: NoneAuthors: D. Johann, E. Peterson********************************************************/paired_scatter_plot(exp_id){display_paired_scatter_plot;while (window is open){filter_settings = read_filter_toolbar;display_paired_scatter_plot;}}/*******************************************************Name & Purpose: Display Paired Scatter Plot, calculate WES mutations in common and exclusive to each experiment and generate paired scatter plotInputs: Filter settings fetched from user input, and Experiment IDsProcessing: Fetch WES mutations, and using filter settings and referenced equations, calculate mutations in common and exclusive to each experiment; display paired scatter plot with data, see Additional File 3Outputs: A paired scatter plot for each experiment in exp_id array, based on variant allele frequencyReturns: NoneAuthors: D. Johann, E. Peterson********************************************************/display_paired_scatter_plot{// Relational algebra Eq. (9)common = exp_id[0].W \u2229 exp_id[1].W;// Relational algebra Eq. (10)exp0_unique = exp_id[0].W \\ exp_id[1].W;// Relational algebra Eq. (10)exp1_unique = exp_id[1].W \\ exp_id[0].W;K;- label all genes in if (filter_settings.show_kg_only == true)- hide all non-labelled points;- plot common, exp0_unique, and exp1_unique based on DNAllelicFreq using filter-settings;}/*******************************************************Name & Purpose: Read Filter Toolbar, gather user-defined filter settings, and display \"TSG Methylation Table\", \"WES Table\", or \"RNA Table\" if the user so desiresInputs: NoneProcessing: Collect filter settings from user; if the user clicks on \"Filter\" the filter settings are returned and they are used when displaying a desired plot; if the user clicks on \"Show TSG Methylation Table\", \"Show WES Table\", or \"Show RNA Table\", the desired table is displayed using the referenced equationsOutputs: Tables selected if clickedReturns: User-defined filter settingsAuthors: D. Johann, E. Peterson********************************************************/read_filter_toolbar{while (true){filter_settings.min_vaf = user input minimum VAF;filter_settings.max_vaf = user input maximum VAF;filter_settings.min_depth = user input minimum read depth;filter_settings.max_depth = user input maximum read depth;filter_settings.min_meth = user input minimum methylation percent;filter_settings.opacity = user input scatter plot point opacity;filter_settings.show_kg_only = user input show key gene only;if (button_click_filter)return filter_settings;\u00a0\u00a0else if (button_click_show_tsg_methylation_table)- display TGS Methylation Table via Relational algebra Eq. (13);\u00a0\u00a0break;\u00a0\u00a0else if (button_click_show_wes_table)- display WES Table Eq. (11);\u00a0\u00a0break;\u00a0\u00a0else if (button_click_show_rna_table)- display RNA Table Eq. (14);\u00a0\u00a0break;\u00a0\u00a0}return filter_settings;}/*******************************************************Name & Purpose: KD Plus Scatter Plot, call subroutines to process and render data for each of the individual plot areas, as well as, to calculate various metircsInputs: Experiment ID of experiment to visualizeProcessing: Call subroutines to process and render the individual plot areas; call subroutine to calculate various metricsOutputs: NoneReturns: NoneAuthors: D. Johann, E. Peterson********************************************************/kd_plus_scatter_plot(exp_id){display_kd_plot;display_scatter_plot;calculate_metrics;while (window is open){filter_settings = read_filter_toolbar;display_kd_plot;display_scatter_plot;calculate_metrics;}}/*******************************************************Name & Purpose: Display KD Plot, displays the kernel density estimation curve, using the 'ks' R package to calculate an appropriate bandwidthInputs: User-defined filter settings and the experiment ID to be visualizedProcessing: Calculate the KDE for DNA mutations, use R.NET to utilize the 'ks' package Outputs: KD curve, see Figures 1 & 2Returns: NoneAuthors: D. Johann, E. Peterson********************************************************/display_kd_plot{- calculate KDE based on Relational algebra Eq. (11) and Eq. (2) for all mutations in \u0174 and weighted by copy number;- utilize R.NET to call 'hpi' function in the R 'ks', for bandwidth calculation;- display KD plot using filter_settings;}/*******************************************************Name & Purpose: Display Scatter Plot, displays the DNA mutational scatter plot, and tooltip containing RNA expression based info if availableInputs: User-defined filter settings and the experiment ID to be visualizedProcessing: Displays a scatter plot point for each DNA mutation, set each glyph depending on the degree of modality data available, and populate tooltip with RNA expression data if availableOutputs: Mutational scatter plot, see Figures 1 & 2Returns: NoneAuthors: D. Johann, E. Peterson********************************************************/display_scatter_plot{- calculate \u0174 by Relational algebra Eq. (11) using filter_settings;- set glyph for all DNA mutations to be a blue circle and place along a-axis according to variant allele frequency and along y-axis by depthfor each tuple \u0175 in \u0174 having RNA data calculate {- update point glyph, ;- build hover-over tooltip to contain: gene name, transcript(s) ids and FPKM(s) from }- display scatter plot for each mutation in \u0174 with associated tooltip (if RNA data is available);}/*******************************************************Name & Purpose: Calculate Metrics, calculate various metrics for displayInputs: User-defined filter settings and the experiment ID to be visualizedProcessing: Calculate SDI, total number of mutations, and total number of key gene mutations, for the data being visualizedOutputs: Calculated metricsReturns: NoneAuthors: D. Johann, E. Peterson********************************************************/calculate_metrics{- calculate SDI using Eq. (1) and relation \u0174 ) using filter_settings;- calculate total number of mutations in relation \u0174 using filter_settings;K which are found in relation \u0174 using filter_settings;- calculate total number of key genes from - display metrics;}The authors declare that they have no competing interests.DJJ and EAP conceived and designed the study. EAP, MAB, SSC, CJH, NW and DJJ performed experiments and analyses. DJJ and EAP designed the software. EAP, DJJ and MAB implemented the software. DJJ and EAP wrote the manuscript. All authors approved the manuscript.Muti-omic relational integration. Illustration of relations used to integrate multi-omic datasets. The upper-right box (Relations & Attributes) defines all relations and their attributes. The left-most section (iCloneViz DB) lists each dataset and a name / identifier for each. Middle section (Multi-Omic Integration) illustrates the relationships and integration of each dataset using intermediate relations. Each intermediate integration is annotated with the attributes used in each combination. Each intermediate relation is further annotated with the equation used in the manuscript to form the given relation. The final multi-omic \"Integrated Relation\" is shown in the lower right.Click here for fileA corresponds to the Presentation sample and B to Relapse. These provide a general view of the inherent mutational events on a chromosomal basis. The x-axis contains an ordered list of chromosomes , each sized by the number of base pairs (bp) it contains. The y-axis is ordered by variant allele frequency (VAF), and the color scale indicates sequence depth. Each variant is a point in the plot.Genomic mutational overview. A genomic mutational overview of two experiments is computed and displayed. Click here for filePresentation on the x-axis compared to Relapse on y-axis. Both the \u00d7 and y-axes are based on VAF. Variants are colored to indicate whether they are shared or unique. See legend for color assignments.Scatter plot of paired samples. Displayed are variants in the Click here for fileMYC oncogene with mutation showing possible splicing events. Illustrated is a lolliplot diagram of MYC showing the possible missense mutations in the coding region depending on splicing.Click here for fileiCloneViz pseudocode flow diagram. Illustrated is the execution flow of iCloneViz and its associated subroutines. Each subroutine and its formal parameters is represented as a node. Each arc represents a subroutine call from one subroutine to another.Click here for file"} +{"text": "In Thailand, porcine deltacoronavirus (PDCoV) was first identified in November 2015. The virus was isolated from piglets experiencing diarrhea outbreak. Herein, the full-length genome sequence of the Thai PDCoV isolate P23_15_TT_1115 is reported. The results provide a clearer understanding of the molecular characteristics of PDCoV in Thailand. Deltacoronavirus, family Coronaviridae (\u2013\u2013Porcine deltacoronavirus (PDCoV) is an enveloped, single-stranded, positive-sense RNA virus in the genus aviridae \u20133. PDCoVviridae \u2013. The virviridae \u2013\u201310. Cliniridae \u2013\u2013, 11,12. A surveillance study was conducted to identify the PDCoV presence in Thailand that focused on herds with diarrhea outbreak and low mortality. Six intestinal samples were collected from piglets with diarrhea in five herds experiencing diarrhea outbreak. Total RNA was extracted and detected the presence of PDCoV RNA using primers specific to membrane (M) and nucleocapsid (N) genes. PCR positive samples were further investigated. The full-length genome was sequenced using 16 overlapping regions of each genome, cloned in pGEM-T easy vector (Promega), and sequenced in both directions in triplicate according to the previously reported protocol . The 5\u2032\u00a0The full-length genome of the Thai PDCoV isolate P23_15_TT_1115 was characterized. The full-length genome sequence of P23_15_TT_1115 is 25,402 nucleotides (nt) in length. Genome organization of the isolate resembles that of other PDCoV genomes with the following gene order: 5\u2032 untranslated region (UTR), open reading frame 1a/1b (ORF 1a/1b), spike (S), envelope (E), membrane (M), nonstructural protein 6 (Nsp6), nucleocapsid (N), nonstructural protein 7 (Nsp7), 3\u2032 UTR. The lengths of ORF 1a/1b, S, E, M, and N genes are 18,786; 3,477; 249; 651; and 1,026\u00a0nt, respectively. The phylogenetic tree was constructed based on full-length PDCoV genomes of 23 isolates available in GenBank, and phylogenetic analysis demonstrates that the P23_15_TT_1115 isolate belongs to a group separated from PDCoVs reported in both China and the United States.51N) amino acid at position 51, similar to isolates from China.The full-length genome of P23_15_TT_1115 was compared to 23 isolates available in GenBank. P23_15_TT_1115 was more highly homologous to PDCoV isolates from China, with nucleotide and amino acid similarities at 97.2 to 97.8% and 93.0 to 94.0%, respectively. In comparison, P23_15_TT_1115 shares a similarity with isolates from the United States. Moreover, the genetic analysis based on the S gene demonstrated that P23_15_TT_1115 is closely related to China PDCoV with similarities of 95.6 to 96.7% and 95.9 to 98.1% at the nucleotide and amino acid levels, respectively. Twenty-four substitutions at the amino acid level were observed between P23_15_TT_1115 and the isolates from China. Moreover, P23_15_TT_1115 owns a deletion of 1 (The results in this study suggest that P23_15_TT_1115 is a novel isolate, closely related to PDCoV isolates from China. The studies investigating the molecular epidemiology, prevalence, and evolution of PDCoV in Thailand are urgently required.KU984334.The complete genome sequence of P23_15_TT_1115 has been deposited in GenBank under the accession number"} +{"text": "Aspergillusflavus (A. flavus)\u2013peanut pathosystem, development and metabolism of the fungus directly influence aflatoxin contamination. To comprehensively understand the molecular mechanism of A. flavus interaction with peanut, RNA-seq was used for global transcriptome profiling of A. flavus during interaction with resistant and susceptible peanut genotypes. In total, 67.46 Gb of high-quality bases were generated for A. flavus-resistant (af_R) and -susceptible peanut (af_S) at one (T1), three (T2) and seven (T3) days post-inoculation. The uniquely mapped reads to A. flavus reference genome in the libraries of af_R and af_S at T2 and T3 were subjected to further analysis, with more than 72% of all obtained genes expressed in the eight libraries. Comparison of expression levels both af_R vs. af_S and T2 vs. T3 uncovered 1926 differentially expressed genes (DEGs). DEGs associated with mycelial growth, conidial development and aflatoxin biosynthesis were up-regulated in af_S compared with af_R, implying that A. flavus mycelia more easily penetrate and produce much more aflatoxin in susceptible than in resistant peanut. Our results serve as a foundation for understanding the molecular mechanisms of aflatoxin production differences between A. flavus-R and -S peanut, and offer new clues to manage aflatoxin contamination in crops.In the Aspergillusflavus (A. flavus) is a globally distributed filamentous, saprophytic fungus that frequently infects oil-rich seeds of various crop species during pre- and post-harvest, with subsequent production of mycotoxins such as cyclopiazonic acid, aflatrem, and the well-known aflatoxin . Be. Be36]. s so few that theubation) . In eachubation) ; furtherubation) .vs. af_S and T3 vs. T2 were identified using the DESeq R package . Only those genes with the corrected p (q) value < 0.05 were considered to be differentially expressed [A. flavus interaction with R and S peanut (vs. T2 offered insights into the metabolic and regulatory processes in A. flavus during its interaction with the peanut (10(RPKM+1) for the four A. flavus samples of af_R and af_S incubated for three and seven days in comparisons of af_R xpressed . The 179S peanut , while te peanut . To obseven days A. Similavs. af_S_T2), while 1791 DEGs were found between af_R and af_S at T3 (af_R_T3 vs. af_S_T3) and 45 DEGs were obtained between af_S at T3 and at T2 (af_S_T3 vs. af_S_T2), suggesting a markedly higher number of gene expression changes in af_R than in af_S. Eighteen DEGs exhibited common differential expression patterns in comparisons of af_R_T3 vs. af_R_T2 and af_S_T3 vs. af_S_T2 (vs. af_R_T2 were different from those in af_S_T3 vs. af_S_T2.Eleven DEGs were found between af_R and af_S at T2 (af_R_T2 af_S_T3) B. Furthe af_S_T3 B. The ab af_S_T2 C, implyivs. af_S_T2 and af_R_T3 vs. af_S_T3, respectively). The GO functional enrichment analysis of the 1113 (62.14%) DEGs with GO annotation in the af_R_T3 vs. af_S_T3 revealed significantly enriched terms in the biological process and the molecular function categories (vs. af_R_T2 and af_S_T3 vs. af_S_T2), respectively. Of the 263 (55.48%) DEGs with GO annotation in af_R_T3 vs. af_R_T2, only two GO terms (GO: 0003824 and GO: 0016491) in the molecular function category and three in the biological process category were significantly enriched enrichment analysis was performed using the GOseq method in Blast2GO . We firstegories . Catalytenriched . Other tvs. af_S_T2, af_R_T3 vs. af_S_T3, af_R_T3 vs. af_R_T2 and af_S_T3 vs. af_S_T2 were analyzed to identify their associated KEGG metabolic pathways. Consistent with the results of the GO analysis, no KEGG pathways were significantly enriched in DEGs data obtained from af_R_T2 vs. af_S_T2 and af_S_T3 vs. af_S_T2. We found that 14 pathways were significantly enriched in DEGs between af_R_T3 and af_S_T3, including 12 pathways involved in the supply of nutrient and energy for fungal development, biosynthesis of secondary metabolites (afv01110) and peroxisomes (afv04146) .To further investigate the biological functions and interactions of genes, a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted using KEGG Orthology Based Annotation System (KOBAS) . All DEGfv04146) A. Twentyfv04146) B. AlthouA. flavus was significantly changed when the fungus interacted with R and S peanut encoding the alpha-N-arabinofuranosidase was identified in af_S_T3 vs. af_S_T2 and it was up-regulated in this comparison. However, no mycelial growth-related DEGs were observed in neither af_R_T2 vs. af_S_T2 nor af_R_T3 vs. af_R_T2. Concurrently, transcriptions of conidia-specific genes, such as conidial hydrophobin RodA/RolA (AFLA_098380), conidiation-specific proteins and conidial development related genes such as AtfA (AFLA_031340) and PksP (AFLA_00617), were significantly changed to various degrees in different comparisons were up-regulated in af_R_T3 vs. af_R_T2. However, no DEGs involved in conidial development were found in both af_R_T2 vs. af_S_T2 and af_S_T3 vs. af_S_T2.By analyzing gene expression pattern data obtained from deep sequencing, especially those in the list of the 1926 genes that were significantly differentially transcribed , we founS peanut . SeventeS peanut . All 17 parisons . Six of vs. af_S_T2, af_R_T3 vs. af_S_T3, af_R_T3 vs. af_R_T2 and af_S_T3 vs. af_S_T2, respectively. Some of these DEGs were differentially expressed in two or three different comparisons. Additionally, the 54#, 9# and 26# cluster with eight, seven and six DEGs, respectively, were the first three dominant ones in these 36 secondary metabolism gene clusters; while 14 of the 36 clusters only possessed one DEG. The aflatoxin biosynthetic pathway cluster (54#) was most worthy focused on because the carcinogenic, mutagenic aflatoxin has been characterized in A. flavus [vs. af_S_T2, but none were differentially expressed between these two pathosystems. In af_R_T3 vs. af_S_T3, 18 down- and 15 up-regulated genes in 54# cluster were obtained. Interestingly, three genes were significantly down-regulated. Surprisingly, we also identified other two significantly down-regulated genes (AFLA_112820 and AFLA_050450) involved in aflatoxin biosynthesis of the aflatoxin biosynthetic cluster (54#) was significantly enriched in oxidoreductase activity (GO: 0016491). The aflX/ordB gene (AFLA_139160) encoding a monooxygenase participates in aflatoxin biosynthesis [vs. af_R_T2. Interestingly, aflA/fas-2 (AFLA_139380), aflG/avnA (AFLA_139260), aflN/verA (AFLA_139280) and aflP/omtA (AFLA_139210) of the 54# cluster, which were differentially up-regulated in af_R_T3 vs. af_R_T2, were enriched in different biological process and molecular function (GO: 0003824 and GO: 0016491) categories. Similar to the results of the GO analysis, several KEGG pathways were enriched in DEGs between af_R_T3 and af_S_T3 and between af_R_T3 and af_R_T2, whereas no KEGG pathways were significantly enriched in comparisons of af_R_T2 vs. af_S_T2 or af_S_T3 vs. af_S_T2. The biosynthesis of secondary metabolites (afv01110) was significantly enriched in DEGs between af_R_T3 and af_S_T3; moreover, this pathway was enriched in DEGs AFLA_069370, AFLA_070820 and AFLA_116080 in secondary metabolite clusters 24#, 25# and 41#, respectively. The aflatoxin biosynthetic pathway is a complex secondary metabolic process that is regulated and influenced by over 30 genes in the A. flavus genome [vs. af_S_T3 and af_R_T3 vs. af_R_T2, the biosynthesis of secondary metabolites (afv01110) pathway was not found to be enriched in these DEGs. Taken together, these results implied that a greater number of repressed responses took place in af_R compared with af_S, while many more activated responses in af_R than in af_S as the interactive time increased in the A. flavus-peanut pathosystem.The ynthesis . By conts genome ,49. AlthA. flavus than the R, namely, mycelia of A. flavus can much more easily penetrate the S than the R peanut seed.Nutrients are indispensable elements required for the growth and metabolism of all living organisms, including plants and pathogens. For successful infection of the host plant and establishment of disease, fungal pathogens have evolved complex regulatory mechanisms to facilitate penetration, colonization and absorb nutrition for development and metabolisms, meanwhile to protect themselves against host defensive responses ,51,52,53Aspergillus [vs. af_S_T3, five down-regulated DEGs involving in aflatoxin biosynthesis were found. Among them, aflX/ordB (AFLA_139160), aflNa/hypD (AFLA_139270) and aflD/nor-1 (AFLA_139390) belong to the aflatoxin biosynthetic cluster. The oxidoreductase Nor-1 together with NorA and NorB reduce norsolorinic acid, the first stable intermediate in the aflatoxin biosynthesis, to averantin [aflA, aflC, aflG, aflP, aflN and aflCa) in the 54# cluster were up regulated in af_R_T3 compared with af_R_T2. The first step in aflatoxin biosynthesis is the reaction of acetyl-CoA and malonyl-CoA catalyzed by Fas-1/aflB and aflA/Fas-2 to form the starter unit hexanoate [aflG/avnA), monooxygenase (aflN/verA) and O-methyltransferase A (aflP/omtA) enzymatic reactions are respectively involved in the conversion of averantin to 5-hydroxyaverantin, versicolorin A to demethyl-sterigmatocystin and sterigmatocystin to O-methyl sterigmatocystin in aflatoxin biosynthetic pathway [Aflatoxins are biosynthesized through several enzymatic reactions in mycelia of ergillus ,49 and tergillus ,58,59,60verantin . Expressexanoate , followeexanoate . P450 mo pathway ,48. AlthA. flavus, germinate as mycelia to colonize the host plant. The survival ability of A. flavus conidia under severe environmental conditions is stronger than that of mycelia [A. flavus dominantly depends on the dispersal of conidia by air, water and soil movement, rain splash and biotic factors [A. flavus [A. flavus may form conidia in cavities or intercellular spaces of the cotyledon. The formation of conidia in A. flavus requires the concerted activity of numerous signaling proteins and transcription factors [atfA (AFLA_031340) was also down-regulated in af_R_T3 vs. af_S_T3. Interestingly, AtfA, as a bZIP transcription factor, possesses important functions in conidial development [vs. af_R_T2, 5 up-regulated DEGs related to conidial development were obtained, including 4 conidia-specific genes and one conidial yellow-pigment biosynthesis-related gene pksP/alb1 (AFLA_006170). The pksP/alb1 gene encodes a polyketide synthase (PksP) involved in the first step of conidial pigment biosynthesis. PksP catalyzes the reaction of acetyl coenzyme A (acetyl-CoA) andmalonyl-CoA to form the heptaketide naphthopyrone [A. flavus mycelial growth, conidial formation and aflatoxin production during infection and colonization the peanut need to be uncovered in order to paint a complete picture of the interactive mechanism of A. flavus with peanut. This comprehensive transcriptional profiling of A. flavus during interaction with the peanut should advance our fundamental understanding of the various associated genes and major metabolic pathways, thereby providing a direction for further study on the management of aflatoxin contamination in crops.Conidia, the asexual reproductive structure of mycelia . In addi factors . Previou. flavus , with th factors . Transcr factors were sigelopment and stabelopment . Considehopyrone ,68. Our A. flavus during the fungus interaction with the peanut. The research demonstrated that the global transcriptional analysis provided an exhaustive view of genes involved in development of mycelia and asexual spores, controlling of biosynthesis and activities of enzymes, conidial pigments and secondary metabolites processes, which were coordinately influenced in A. flavus by its host peanut (R and S genotypes). The transcriptome comparisons revealed that DEGs associated with mycelial growth and penetration, conidial formation and development, and aflatoxin biosynthesis and accumulation were up-regulated in af_S compared with af_R. This differential transcription may explain why aflatoxin accumulation was much higher in A. flavus-S peanut pathosystem than in A. flavus-R. However, further research is required to determine whether these DEGs are the genes responsible for the difference in aflatoxin accumulation between A. flavus-R and A. flavus-S pathosystems. Further functional exploration of these genes may provide useful information for their future application in the management of aflatoxin contamination in crops.In this study, an RNA-seq approach was employed for the first time to investigate molecular events involved in the development and metabolism of A. flavus was maintained in 20% glycerol at \u221280 \u00b0C at the Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS-OCRI). To prepare the A. flavus inoculation, the stored conidia of AF2202 were cultured on the potato dextrose agar medium for 7 d at 29 \u00b1 1 \u00b0C. The fresh conidia were then collected and suspended in sterile water containing 0.05% Tween-80. The concentration of conidia in the suspension was determined using a hemocytometer [The AF2202 strain of toxigenic A. flavus at post-harvest (6 CFU/mL) was then directly added to 10.0 g of peanut seeds in a sterile Petri plate. The inoculated samples were placed in an incubator and cultured at 29 \u00b1 1 \u00b0C in darkness. After incubation for 1, 3 and 7 d, the A. flavus-colonized seeds were taken out to test aflatoxin content (five replications) by high-performance liquid chromatography [The peanut cultivars Zhonghua 6 and Zhonghua 12 were cultivated and supplied by CAAS-OCRI . The mature seeds of both Zhonghua 6 and Zhonghua 12 are susceptible to seed invasion by -harvest , while ZA. flavus-R and -S peanut pathosystems, the aflatoxin content of these pathosystems was initially tested at the 2nd day after incubation. Aflatoxin content increased at maximum rate between the 3rd and the 4th day, and then remained stable after the 7th day in both peanut cultivars (our unpublished data). Beginning on the 2nd day, the aflatoxin content of the A. flavus-R pathosystem was far lower than that of the A. flavus-S; at its peak, the aflatoxin content of A. flavus-S was over 10-fold that of A. flavus-R. These differences in aflatoxin production between the two pathosystems suggested that the genetic expression of A. flavus was affected by its colonized host peanut. The 1st, 3rd and 7th day as the inflection time points .Although aflatoxin production trends differed between e points in the pA. flavus-peanut pathosystem was isolated using an RNeasy\u00ae Plant Mini kit , according to the manufacturer\u2019s protocol. All RNA samples were treated with RNase-free DNase I. A NanoDrop\u00ae 2000 spectrophotometer , a Qubit\u00aeFluorometer 2.0 and an Agilent 2100 bioanalyzer were used to test the concentration and integrity of RNA samples, and confirm that all RNA samples had an integrity value > 6.5. RNA quality detection, cDNA libraries construction and RNA sequencing were performed at the Novogene Bioinformatics Technology Co. Ltd. according to previously described methods [Total RNA from the methods .Raw data (raw reads) in fastq format were first processed using in-house perl scripts. Clean data (clean reads) were obtained by removing low-quality reads and those containing adapters, poly-N tails from the raw data. The Q20 and Q30 values, GC content, and sequence duplication levels were calculated for the clean data. All downstream analysis used the clean data with high quality. The sequencing data generated in this study have been deposited at the NCBI Short Read Archive database and are accessible through SRA series accession number SRP065525 (BioProject ID: PRJNA300619).A. flavus were downloaded directly from the Ensembl Genomes website [The genome and gene annotation files of website . After c website , paired- website . The ref website . HTSeq ( website .p (q) value < 0.05.Statistical analyses for discovering differentially expressed genes (DEGs) were performed with the DESeq R package . To evaluate the individual effects of the host peanut (Zhonghua 6 and Zhonghua 12) and time points (T1\u2013T3), a multifactorial analysis was conducted using the multi-factor designs method of DESeq . This mep (q) value < 0.05 were considered to be significantly enriched in DEGs. KOBAS software [p (q) value < 0.05 was considered to be significantly enriched in DEGs [GO enrichment analysis of DEGs was implemented using GOseq with a ca, 2014) was used in DEGs ."} +{"text": "Pseudomonas aeruginosa bacteriophage (phage) belonging to the Pbunalikevirus genus of the Myoviridae family of phages. It was isolated from hospital sewage. vB_PaeM_CEB_DP1 is a double-stranded DNA (dsDNA) phage, with a genome of 66,158 bp, containing 89 predicted open reading frames. vB_PaeM_CEB_DP1 is a Pseudomonas aeruginosa PAO1 as the host strain. Its host range was evaluated using a panel of 30 P.\u00a0aeruginosa clinical isolates, and this phage was able to infect approximately 57% of them.The lytic bacteriophage vB_PaeM_CEB_DP1 was isolated from hospital sewage in Portugal using Myoviridae family of phages. Furthermore, the growth parameters determined by the one-step growth experiment showed that phage vB_PaeM_CEB_DP1 has a latent period of ~50\u00a0min, a rise period of ~50\u00a0min, and a burst size of ~70 phages per infected cell.The morphological characterization of phage vB_PaeM_CEB_DP1 was performed by transmission electron microscopy, revealing an icosahedral head of ~70\u00a0nm in diameter and an ~140- \u00d7 18-nm contractile tail. Thus, it was possible to determine that this phage belongs to the The phage genome was sequenced using Roche 454 sequencing procedures at the Plateforme d\u2019analyses of the Institut de Biologie Int\u00e9grative et des Syst\u00e8mes . Shotgun reads were assembled using the gsAssembler module of Newbler v 2.5.3.Pbunalike phages were first annotated using myRAST . Sequence phages . Predicte phages . The tooe phages was usede phages , 6, 7, nThe genome of the phage vB_PaeM_CEB_DP1 consists of 66,158\u00a0bp of dsDNA with a GC content of 55.6%. The whole genome was scanned for CDSs, resulting in 89 predicted genes ranging from 141 bp to 3,111\u00a0bp. Furthermore, 37 of these genes are rightward oriented while 52 are leftward oriented. The initiation codon of 90% of the genes is ATG, while 8% start with GTG and 2% with TTG. According to BLASTP analyses, 68% of the proteins encoded in the genome of vB_PaeM_CEB_DP1 are hypothetical. This study further revealed that this phage has 7 predicted promoters and 12 terminators.Pbunalike genus are reported to encode linear, nonpermuted genomes , KPP12 (94.3%) and vB_PaeM_PAO1_Ab27 (93.1%).The genome of phage vB_PaeM_CEB_DP1 shares high nucleotide identity with other P.\u00a0aeruginosa phage vB_PaeM_CEB_DP1 was deposited in GenBank under the accession number KR869157.The complete genome of the"} +{"text": "The effect of cannabis on emotional processing was investigated using event-related potential paradigms (ERPs). ERPs associated with emotional processing of cannabis users, and non-using controls, were recorded and compared during an implicit and explicit emotional expression recognition and empathy task. Comparisons in P3 component mean amplitudes were made between cannabis users and controls. Results showed a significant decrease in the P3 amplitude in cannabis users compared to controls. Specifically, cannabis users showed reduced P3 amplitudes for implicit compared to explicit processing over centro-parietal sites which reversed, and was enhanced, at fronto-central sites. Cannabis users also showed a decreased P3 to happy faces, with an increase to angry faces, compared to controls. These effects appear to increase with those participants that self-reported the highest levels of cannabis consumption. Those cannabis users with the greatest consumption rates showed the largest P3 deficits for explicit processing and negative emotions. These data suggest that there is a complex relationship between cannabis consumption and emotion processing that appears to be modulated by attention. There are a variety of explanations of how the brain processes emotion emphasizing differing levels at which an explanation is focused. Some approaches emphasize a physiological structural account, others are based on a higher, more \u201ccognitive\u201d level of understanding, with less emphasis on the underlying structures , 2, 3. A9-tetrahydrocannabinol (THC) consumed and participants\u2019 ability to identify emotional expressions in faces showing negative emotions such as fear and anger, but had little effect on faces showing sadness and happiness [The effects of cannabis on cognition and the brain is a rapidly evolving area of investigation which has provided evidence for a complex interaction between physiological and psychological processes. Cannabis consumption elicits both immediate (acute), residual and long-term changes in brain activity, that are manifested throughout the body such as altered appetite and food intake, altered sleep patterns, and changes in measures of executive function and emotional behavior . Crean eappiness . Behavioappiness . In a reappiness . This suBehavioral studies have also linked heavy cannabis use to impairments in emotion processing compared to controls. In a dynamic emotional expression task where participants were asked to identify emotional expressions as faces morphed from open mouthed to an expression, either positive (happy) or negative (fearful) cannabis user\u2019s accuracy and reaction time performance was impaired. Individuals who used cannabis fifteen times a month and more than fifty times in their lifetime showed increased reaction times and decreased accuracy to the faces that became negative .Recent research seeking to clarify the effects of cannabis use on brain structure is mixed. In particular, structural magnetic resonance imaging (MRI) data indicated no significant differences in the amygdala, a critical structure for emotion processing, in both adult and adolescent brains of daily users . HoweverOne approach that can be considered a valuable tool in further investigating the complexity of emotion processing is event related potential (ERP) methodologies. Structural changes in the brain do not always translate to differences in function and behavior. EEG techniques allow us to investigate the relationship between biomarkers (brain mechanisms) of a distributed neural network and associated behavior. This approach is particularly relevant to determine whether or not cannabis use has an effect on the circuitry of the brain when structural differences have not been found.EEG recordings provide information with resolution in the milliseconds. This approach consists of the measurement of the summated firing of neurons in the cortex through electrodes placed on the scalp. When this activity is averaged and time-locked to a specific event , an event-related potential (ERP) is obtained. ERPs provide an indication of the temporal dynamics of cortical activity following that specific event, allowing us to obtain information on the time course of emotion processing. This average is then compared to those obtained for other conditions to examine whether processing of different types of information diverges in time and across electrode sites. Through extensive research some patterns in ERPs associated with cognitive processes have been characterized by ERP components\u2014the amplitude of the waveform at a specific point in time. For example, the P3 or P3 complex component is defined as a change in voltage in a positive direction (increase in amplitude) occurring between 200\u2013400ms on average after stimulus onset .One ERP in particular is of interest to emotion processing and also cannabis use. The P3 complex component has been associated with task-relevant stimulus evaluation and attention allocation and it is has been consistently linked to emotion processing , 19, 20.The exact nature of the P3 and its relationship to emotion is still very much under investigation . HoweverCannabis use has been associated with deficits in the P3 especially pertaining to complex cognitive tasks such as working memory, and selective attention , 31, 32.The consistent P3 pattern exhibited during emotional processing represents an effective means of assessing the effects of cannabis use on neural processing. The P3 has implications for understanding both the short and long-term effects cannabis use has on emotion processing. Despite this the majority of research into the effects of cannabis on emotional expression recognition has focused on either behavioral approaches, for example Ballard et al , or struTo better understand the role of attention on the effects of cannabis in emotion processing our current study uses a paradigm based on Relleke et al and exteIf cannabis use effects emotion processing we would expect to see differences in the P3 to our emotional stimuli for our cannabis user group compared to controls. If attention is also affected by cannabis use, then greater demands on attention, driven by the levels of attentional engagement, elicited by our three processing tasks, implicit, explicit and empathic would also lead to P3 differences.We therefore hypothesize that cannabis users will show a difference in P3 amplitude compared to non-cannabis using controls. This will be further influenced by the type of emotion and task demands.Seventy-three undergraduate students and volunteers recruited from the community provided written consent and self-report of demographic information which is summarized in Undergraduate students who were recruited from the departmental research pool received credit in a Psychology course for their participation. Participants from the local community received no compensation. The study was approved by Colorado State University\u2019s Office of Research Integrity & Compliance Review Office Institutional Review Board (IRB) Protocol ID: 12-3716H.All participants provided written consent and completed a general demographic questionnaire. They were further screened for symptoms of depression and anxiety using the Center for Epidemiological Studies Depression Scale (CES-D) and the After the screening and assessment portion of the study was completed, participants were fitted with a recording EEG cap, detailed below in the EEG acquisition portion of the methods. During the recording, detailed below, participants completed an emotion processing task, presented on a Dell desktop computer at a viewing distance of 30cm using Stim2 software , 41.The emotion processing task required that participants viewed faces depicting positive (happy), neutral, and negative (angry and fearful) emotional expressions, obtained from the Radboud Faces Database . Thirty-After EEG data collection, cannabis use was assessed by self-report using a questionnaire developed specifically for this study; The Recreational Cannabis Use Evaluation (R-CUE). R-CUE was created to better understand the ecology of cannabis use in Colorado\u2019s recreational system of high volume, potency, and variety. Thus, R-CUE consists of questions regarding type of use and method of intake\u2014including use of edibles, concentrates, and transdermal applications\u2014in addition to information about potential current use, relational previous use, and years of use. Based on participants\u2019 responses they were assigned to control or cannabis user groups see . CannabiElectroencephalogram (EEG) was recorded from 25 Ag/AgCl electrodes covering regions of interest (ROI\u2019s) consistent with the measurement of the P3 ERP component and identified based on previous research , 7, 41 in milliseconds, percent correct for sex and emotion identification tasks, and average rated empathy for the empathic task. Participants with over 90% \"no responses\" on any of the three task conditions were excluded from analysis, as were individual trials with RTs faster than 100ms. Repeated measures analyses of variance were performed by cannabis use grouping and emotion for RT, accuracy, and rated empathy scores during each task.t-tests on significant differences with \u03b1 = 0.05 for planned group comparisons and Bonferroni correction for post-hoc tests where appropriate. Eta-squared measures of effect size were reported for all within-group factors, while Cohen's d was reported for between-group effects.EEG was re-referenced offline to the common average and baseline corrected to pre-stimulus interval of 200ms. Artifact rejection was applied using the built in artifact rejection tool in SCAN 4.5 EEG acquisition software . Trials Overall differences in behavioral measures were consistent with differences in ERPs in relation to task, and emotion. This suggests that ERP differences were driven by cannabis exposure and not by differences in responses to emotion or task. A detailed description of the results are as follows.In the emotion processing task we examined the effect of cannabis use grouping and emotional expression on participants\u2019 reaction time (RT) in milliseconds and response scores in a repeated measures analysis of variance see & 3.F = 11.977, p = .001. Emotional expressions did not differ in RT during implicit processing, but they did have a significant effect on RT for explicit and empathic responses. Participants\u2019 responses were the slowest for emotion identification of neutral expressions (angry: t(63) = -8.785, fearful: t(63) = -7.401; all ps < .001), with similar RTs for angry and fearful expressions, t(63) = -1.772, p = .081, and the fastest for happy expressions = -5.120, angry: t(63) = -11.532, fearful: t(63) = -12.379; all ps < .001). Empathic rating scores also differed by emotion, with slower RTs for neutral than angry expressions, t(63) = -2.814, p = .007, and slowest for happy compared to negative expressions (vs. angry: t(63) = -8.785, fearful: t(63) = -7.401, ps < .001), with a similar trend compared to neutral, t(63) = -2.447, p = .017. RTs for fearful expressions during the empathy task did not differ from neutral, t(63) = -1.751, p = .085, or angry expressions, t(63) = -1.735, p = .088.A significant effect of sex on RT for implicit processing was characterized by slower RT for sex identification of female compared to male faces, ps < .05): emotion identification accuracy scores were lowest for angry faces (vs. happy: t(63) = 6.838, p < .001; neutral: t(63) = 3.209, p = .002; fearful: t(63) = 5.933, p<001), lower for neutral than fearful faces (t(63) = -2.700, p = .009), and no other differences for happy faces = 1.149, p = .255; fearful: t(63) = -.849, p = .399). Further, a two-way interaction of emotion by sex indicated greater accuracy for male angry faces than female angry faces, t(63) = 2.965, p = .004, d = .27. The empathy task was characterized by lowest rated ability to empathize for neutral expressions (vs. happy: t(63) = -8.997, angry: t(63) = -5.882, fearful: t(63) = -6.640; all ps < .001), higher ratings for happy than angry expressions, t(63) = 3.733, p < .001, and no other differences for fearful expressions (vs. happy: t(63) = 2.193, p = .032; angry: 2.182, p = .033). A main effect of sex on empathy ratings suggested slightly higher rated ability to empathize with female than male faces, independent of emotion, F = 4.106, p = .047. There were no significant effects of emotion or sex on response scores for implicit trials.A main effect of emotion on response scores was significant for explicit and empathic tasks = 80.518, p = 001, \u03b7p2 = .542 = 3.498, p = .001, Cohen\u2019s d = -.74, fronto-central, t(68) = 3.937, p < .001, d = -.56, and parieto-occipital sites t(62) = 4.201, p < .001, d = -.93, but not at parietal, t(68) = 2.233, p = .029, d = .20, or centro-parietal sites, t(68) = .955, p = .343, d = .56 (see t(65) = -3.992, p < .001, d = .86) and fearful expressions (t(67) = -3.449, p = .001, d = .76), with a similar trend of smaller P3 for angry expressions (t(68) = 2.546, p = .013, d = .58) but no group differences for neutral expressions, t(68) = 2.347, p = .022, d = .63 (see t(62) = 3.289, p = .002, d = .70, and explicit, t(67) = 3.251, p = .002, d = .72, but not empathic processing, t(68) = 2.046, p = .045, d = .51; while right sites showed no group differences (implicit: t(68) = 1.622, p = .109, d = .40, explicit: t(68) = 2.283, p = .026, d = -.40, empathic: t(68) = 2.192, p = .032, d = .55).Cannabis users presented smaller P3 than controls over frontal, .56 see . An intet(69) = -3.151, p = .002. In contrast, P3 at fronto-central sites was enhanced for implicit compared to explicit, t(69) = -2.430, p = .018, and empathic processing, t(69) = -2.430, p = .018 (see t(69) = -3.880, p < .001, and fearful, t(69) = -3.142, p = .002, expressions, with no amplitude differences present for angry, t(69) = -.560, p = .577, or happy expressions, t(69) = .328, p = .744.A main effect of task instructions was characterized over centro-parietal sites as a reduction in P3 during implicit compared to explicit processing of facial expressions, .018 see . Fronto-ps < .01): neutral expressions elicited a larger P3 than fearful = -3.482, p = .001) and angry = -3.055, fronto-central: t(69) = -3.099, parietal: t(69) = -3.578, parieto-occipital: t(69) = 4.540; all ps < .003), but not happy expressions (happy-angry: t(69) = -.766, p = .446; happy-fearful: t(69) = -.954, p = .343; angry-fearful: t(69) = -.133, p = .895). At fronto-central sites, these effects were modulated by a task by emotion interaction, such that during implicit processing, P3 amplitude for happy and angry expressions was reduced compared to neutral expressions (happy: t(69) = -3.436, p = .001; angry: t(69) = -3.296; p = .002), with a trend for fearful compared to neutral (t(69) = -2.807, p = .006), and no differences between emotional expressions (happy-angry: t(69) = -.128, p = .899; happy-fearful: t(69) = -.694, p = .490; angry-fearful: t(69) = -.758, p = .451). Explicit processing presented a similar reduction only for angry expressions compared to neutral, t(69) = -2.730, p = .008, with smaller P3 for happy and fearful expressions compared to neutral approaching significance (happy: t(69) = -2.552, p = .013; fearful: t(69) = -2.387, p = .020), and no other significant differences (happy-angry: t(69) = .089, p = .899; happy-fearful: t(69) = .524, p = .490; angry-fearful: t(69) = 1.150, p = .451). Effects of emotion on P3 for the empathy task were not significant after correction for multiple comparisons, F = 3.352, p = .023. However, there was a trend suggesting smaller P3 for neutral compared to happy expressions, t(69) = 2.322, p = .023, and also a smaller P3 for happy compared to angry expressions, t(69) = -1.328, p = .008, while no other comparisons approached significance.P3 differences between expressions were observed across all but centro-parietal electrode sites (N = 20) and chronic users , and compared P3 amplitudes between the two groups and controls . In this manner, significant group effects for cannabis use were further examined using one-way analyses of variance with follow-up t-tests to explore the possible role of cannabis use frequency in this relationship.To expand on the patterns found in P3 amplitude effects of cannabis use, we examined differences within the cannabis users group based on frequency of use. For this purpose, we divided participants in this group into casual users : frontal = 4.645, p = .013, \u03b7p2 = .122; fronto-central = 5.808, p = .005, \u03b7p2 = .148; parieto-occipital = 4.505, p = .015, \u03b7p2 = .119) with no group effects at parietal, F = 2.868, p = .064, \u03b7p2 = .079, or centro-parietal sites, F = .777, p = .464, \u03b7p2 = .023. However, no comparisons between the three frequency use groups reached significance. Next, we compared mean P3 amplitude between groups at parieto-occipital sites for each emotional expression and found significant effects of reduced P3 amplitude for happy and fearful expressions = 6.121 & 5.416, ps = .004 & .007, \u03b7p2 = .073), but not for neutral, F = 2.887, p = .063, or angry expressions, F = 3.699, p = .030. Specifically, there was a trend for reduced P3 amplitude in both casual and chronic users compared to controls for happy and fearful expressions, with no differences between casual and chronic users and no differences for neutral and angry expressions.For overall P3 amplitudes, group effects remained significant across the same electrode sites responses were affected by explicit and empathic processing in respect to neutral and negative emotions, with angry and fearful faces giving rise to slower RT responses than happy faces in the explicit processing condition. This effect was reversed in the empathy condition where happy faces gave rise to the slowest RT responses. A similar pattern of response was observed in accuracy ratings with angry faces producing the lowest response scores in explicit and empathic processing. There were however no between group differences with cannabis users presenting the same pattern of responses as non-cannabis users. Unlike previous studies we saw aSignificant differences in ERPs were observed for group (cannabis users compared to controls), for task , and for emotion . Specifically, the P3 was significantly reduced in mean amplitude in our emotion processing paradigm for those participants that used cannabis compared to participants who did not. Happy expression eliciting the largest P3, followed by fear and angry expressions in users compared to controls. Differences were further modulated by task: in the implicit and empathic task conditions cannabis had a significant decrease in the P3 compared to controls when processing emotional expression. However when attention was directed in the explicit processing task they have similar P3 responses to emotional expression as controls. When comparing levels of cannabis exposure as a possible factor in our cannabis use group it appears that those who use cannabis casually have greater deficits in emotion processing with a reduced P3 response generally for all emotion conditions. This suggests that possibly increased exposure in our chronic group may have developed compensatory mechanisms to the effects on cannabis on emotion processing. However it is important to acknowledge that acute, residual and long term exposure as well as the specific endocannabinoids and other confounding compounds such as alcohol and tobacco were not specifically controlled for a priori in this study.The dissociation between performance on behavioral measures and corresponding P3 amplitude data are interesting. One possible explanation is that exposure to cannabis alters the way in which the brain allocates resources during emotion processing as measured by the P3 component , 19, 20,Our results are consistent with other studies investigating the effects of cannabis on the P3 as a marker for a number of cognitive processes, especially attention based tasks. Cannabis exposure has been shown to give rise to a marked decrease in the P3 component in a number of attentional tasks both visual and auditory , 32, 33.Task driven differences in the P3 were apparent in our data for both cannabis users and control conditions. With a reduction in the P3 for implicit processing compared to explicit and empathic processing in both groups. This is consistent with previous work by Rellecke et al where implicit and explicit processing of emotional expression gave rise to different patterns of ERP . Our datOur implicit, explicit and empathic tasks were sensitive to cannabis exposure, as marked by a decrease in the P3, which is consistent with the literature indicating that visual , 31 and This suggests that consistent with previous research the effects of cannabis may be more closely tied to attention-based emotional processing rather than emotion processing that is occurring when attention is not directed towards a specific emotion , 31, 32.This has implications for structural accounts of emotion processing . ArguablThe P3 complex also appears to be modulated by the type of emotion being processed with negative emotions having a greater effect on P3 than positive and neutral emotions in our cannabis user group, an effect which is task dependent. This is consistent with the literature showing effects of cannabis on negative emotion , howeverAs previously mentioned frequency of use appears to have an emotion specific effect. Although not significant, the reduction in P3 amplitude to fearful, happy and angry emotional expressions, is greatest in causal users compared to chronic users and controls. This is consistent with Ballard and colleagues who found the effects of cannabis use on emotion processing to be exacerbated for negative but not positive emotions . Follow Ability to empathize, measured as a behavioral response, appears consistent across groups for positive emotions. There was an expected reduction in ability to empathize with neutral expressions in all groups compared to positive and negative valence emotional faces. P3 effects did not reach statistical significance however there was a trend towards a greater P3 response for empathic responses to negative emotions compared to positive and neutral emotions in both groups. Further, while cannabis use was associated with differences in P3 during sex and emotion identification, empathic processing of the same facial expressions resulted in a reduction of these group differences. This supports previous discussion of the role of attention on emotion processing differences in the P3 for cannabis users , 31, 32 One significant limitation of our study was not explicitly controlling for the acute, residual or long term effects of cannabis exposure although the majority of our cannabis users patterns of exposure best fit the residual and long term effects definition. Similarly the inability to control the amount and the type of cannabinoid our sample was exposed to makes our conclusions difficult to evaluate. This is both problematic and yet realistic as recreational cannabis users are unlikely to be able to access this information. Testing of recreational and medical cannabis in Colorado dispensaries for consumers is minimal if not nonexistent at this time. For example, THC content can range from 6\u201312%, to as high as 90%, in concentrates and edibles. We also did not control a priori for exposure to other substances such as alcohol and tobacco use. Although our sample reported minimal exposure to other substances, the residual effects of these substances are well documented to affect cognition, and could be contributing to our results. One particularly interesting point regarding our sample was that they were all using cannabis legally according to Colorado state law. It has become anecdotally apparent that this population tend to restrict their substance exposure to cannabis exclusively. However it should be acknowledged that this is a limitation of our study. As we develop a better understanding of the legal recreational cannabis industry we expect to be able to better address some of these questions.Our data show a significant effect of cannabis use on the P3 in an emotion processing task which was further modulated by task instruction. The P3 amplitude was reduced for negative emotions in our cannabis user group, compared to controls, and this effect was greatest when processing emotional expressions implicitly. There was a trend towards this being a dose dependent relationship with those users self-reporting the greatest exposure to cannabis having larger decrements in P3 amplitude. Attention driven demands on emotion processing appear to be affected by cannabis use as reflected in differences in the P3 amplitude.The Recreational Cannabis Use Evaluation (R-CUE)Cannabis Use Questionnaire:1Age: _________2Are you part of Colorado\u2019s Medical Marijuana Registry (do you own a red card)?aYesbNo3If you answered yes to #2, how many years have you been a member of the registry?aLess than one year (This is my first red card)b1\u20132 yearsc3\u20134 yearsd5\u20137 yearse8\u201310 yearsf10+ years4How many years have you partaken in Cannabis use?aLess than a yearb1\u20132 yearsc3\u20135 yearsd6\u201310 yearse11\u201315 yearsf16\u201320 yearsg20+ years5How many times a week do you use Cannabis (in any form)?aOnce a week: ______bA couple of times a week: ______cA few (3\u20136) times a week:______dDaily: ______e2\u20134 times a day:_____fMore than 4 times a day:______6Which of the following ways do you like to intake cannabis, and which types of Cannabis do you prefer? Check all that apply (and check subcategories to the best of your knowledge/ability):aSmoking Cannabis flower : ______iIndicas (\u201cBody high\u201d): _____iiSativas (\u201cMind high\u201d): _____iiiHybrids: ______1Sativa dominant hybrids: ______2Indica dominant hybrids: ______3True hybrids (50/50 of each): ______bSmoking Cannabis Concentrates (Hashish/\u201dDabs\u201d) ________iType of cannabis in concentrate:1Indica: _______2Sativa: _______3Hybrids: ______aSativa dominant hybrids: ______bIndica dominant hybrids: ______cTrue hybrids (50% of each): ______4Strain specific: _______aIf yes to strain specific hash, list strains that you have used: ________________________________________________________________________________________________________________________________________________iiMethod of THC extraction (the type of Concentrate) Check all that apply:1Solvent based extraction:aButane Honey Oil (BHO): ____bCarbon Dioxide (CO2): ______cQuick Wash Isopropyl Alcohol (QWISO): _____dHexane solvent concentrates: _____ePropane solvent concentrates: ____fEthanol solvent concentrates: _____g\u201cShatter\u201d hash (High purity butane/ethanol extraction): _____2Solvent-less concentrates:aCold Water Extraction (CWE)/Icewax/Solvent-less wax/\u201dgrease\u201d/\u201djewce\u201d: _____bBubble hash: _____cScreen filtered hash (Finger hash/Keif): _____cCannabis Edibles: _______iBaked Edibles: _______iiHard Candy/ Gummy Edibles: ______iiiChocolate Edibles: ____ivDrink based edibles : ______vTinctures: _____1Glycerin based: _____2Ethanol based: _____viCannabis butter (Cannabutter): _____viiOther (Please describe): ____________________________________________________________________________________________________________________________________________________________________________________dDermal Cannabis Application: ______iCannabis skin patches: _____iiCannabis lotions/balms/oils: ______7If you selected any of the flower/concentrate methods of cannabis intake, what smoking devices do you use? aWater-filtration devices:iBong (upright/waterpipe):_____iiBong (gravity):_____iiiBubbler: _____bDry smoking devices:iPipe : ______iiSteamroller: ______iiiJoint: ______ivBlunt:______cVaporizers:iBag vaporizers: ______iiWhip vaporizers: ______iiiPortable/Pen vaporizers:________dDabs:iSpoon dabs:_____iiNail dabs: ______iiiNoodle dabs: ______ivHealth stone dabs: _____vSkillet dabs: _______8In order of preference , what is your preferred form of consuming Cannabis: Cannabis flower/nugget, concentrates/hash, edibles, and topical absorption?1____________________2____________________3____________________4____________________9In order of preference , which is you preferred method(s) of smoking/ingesting Cannabis?1_____________________2_____________________3_____________________4_____________________5_____________________6_____________________7_____________________8_____________________9_____________________10_____________________10In an average month, how much in Cannabis flower/nugget do you smoke?aNone:_____bA gram or less: _______cAn eighth of an ounce (3.5 grams) or less:_____dA quarter of an ounce (7 grams) or less:_____eA half of an ounce (14 grams) or less:_____fAn ounce (28 grams) or less:_____gMore than an ounce: _____hMore than two ounces:_______iMore than a quarter pound (4 ounces):______11In an average month, how much in Cannabis concentrates do you smoke?aNone:______bA gram or less: _______cAn eighth of an ounce (3.5 grams) or less:_____dA quarter of an ounce (7 grams) or less:_____eA half of an ounce (14 grams) or less:_____fAn ounce (28 grams) or less:_____gMore than an ounce: _____12In an average month, how many Cannabis edibles do you consume? .aNone:____bOne edible:____c2\u20134 edibles:______d4\u20138 edibles:______e10\u201320 edibles:______f30+ edibles:________S1 Fig(TIF)Click here for additional data file."} +{"text": "Listeria monocytogenes is responsible for the rare disease listeriosis, which is associated with the consumption of contaminated food products. We report here the complete genome sequences of vB_LmoS_188 and vB_LmoS_293, phages isolated from environmental sources and that have host specificity for L. monocytogenes strains of the 4b and 4e serotypes. Listeria monocytogenes is a Gram-positive facultative anaerobe and the causative agent of listeriosis, a disease associated with the consumption of contaminated food products. Its psychotropic nature, coupled with its ability to persist in the environment and wild mushroom (vB_LmoS_188) samples. The genomes were sequenced by MWG Eurofins on an Illumina MiSeq next-generation sequencing (NGS) system to >100\u00d7 coverage. For each, sequencing yielded approximately 3 million reads, with an average length of 148\u00a0bp and an average quality score of 37. The removal of low-quality reads was undertaken using Trimmomatic (http://www.ebi.ac.uk/interpro).Two vB_LmoS_18 samplesvB_LmoS_23 and wilmmomatic and Artemmomatic , while fListeria bacteriophages , while bacteriophage vB_LmoS_293 is 40,759\u00a0bp in length . PCR analyses confirmed that both genomes contain linear circularly permuted double-stranded DNA (dsDNA) with terminal redundancy. Sixty ORFs were detected in vB_LmoS_188, while 72 ORFs were detected in vB_LmoS_293. The ORFs predominantly begin with the ATG start codon (91.6% in vB_LmoS_188 and 87.5% in vB_LmoS_293). No tRNAs were detected. No function was assigned to 34/60 ORFs detected in vB_LmoS_188 or for 41/72 ORFs in vB_LmoS_293. The genomes are ordered in a modular fashion, consistent with previous observations for iophages . DespiteLP-030-3 . Their sKP399677 (vB_LmoS_188) and KP399678 (vB_LmoS_293).The genome sequences of these two phages have been deposited in GenBank under the accession numbers"} +{"text": "Independent Component analysis (ICA) is a widely used technique for separating signals that have been mixed together. In this manuscript, we propose a novel ICA algorithm using density estimation and maximum likelihood, where the densities of the signals are estimated via p-spline based histogram smoothing and the mixing matrix is simultaneously estimated using an optimization algorithm. The algorithm is exceedingly simple, easy to implement and blind to the underlying distributions of the source signals. To relax the identically distributed assumption in the density function, a modified algorithm is proposed to allow for different density functions on different regions. The performance of the proposed algorithm is evaluated in different simulation settings. For illustration, the algorithm is applied to a research investigation with a large collection of resting state fMRI datasets. The results show that the algorithm successfully recovers the established brain networks. This manuscript puts forward two innovations. Firstly, we demonstrate a fast, likelihood motivated and straightforward method for applying independent components analysis (ICA). Secondly, we propose a parcellation based adjustment when the source signals distribute differently across regions. Our work is routed in the context of understanding human brain networks, and we use functional magnetic resonance imaging (fMRI) data for illustration in this manuscript.We approach our study of fMRI by simultaneously analyzing all voxels. This is in contrast to regional or seed-based approaches is a factor-analytic approach that has been frequently utilized for the analysis of functional neuroimaging data, because of its success in discovering important brain networks in many applications , while Section 5 gives a discussion.The remainder of the paper is organized as follows. Section 2 describes the p-spline based ICA algorithm and considers relaxation of the Xi be a T \u00d7 V matrix for subject i = 1, \u2026, I. In the context of fMRI, T indicates scans while V indicates voxels. Assume the number of ICs is Q. The ICA model specifies Xi = AiS, where Ai is a T \u00d7 Q mixing matrix and S is a Q \u00d7 V matrix of ICs. By assuming common spatial maps across subjects, we can stack the individual matrices in the temporal domain. Let TI \u00d7 V group data matrix, and TI \u00d7 Q group mixing matrix. Spatial group ICA simply specifies the standard modelIndependent component analysis models collected signals as linear weighted combinations of independent sources. Notationally, let X is element of X and define X as row t of X and X as column v. Then, model (1) could be rewritten as We use parentheses to index matrices so that E[X] = \u03bcx = 0 and hence E[S] = \u03bcs = 0. If this assumption were not made, the ICA model would imply X \u2212 \u03bcx = A(S \u2212 \u03bcS), which is exactly an ICA model with a centered data matrix and the ICs having mean 0. Hence, X is demeaned prior to analyses and \u03bcS is assumed to be zero. Similarly, since AS = {A\u2215c} * {cS}, ICs are only identified up to scalar multiplication. Thus, we assume that Var{S} = 1 for q = 1, \u2026, Q and v = 1, \u2026, V.We assume that S \u2aeb S when q \u2260 q\u2032, where \u2aeb implies statistical independence. However, standard variations of ICA also assumes that i.i.d collection, which we also adopt for now. The i.i.d assumption will be relaxed later in the next subsection. As a consequence of these assumptions, X \u2aeb X when v \u2260 v\u2032; yet note that X is not (necessarily) independent of X.ICA gets its name by assuming that Q < TI and Equation (1) is overdetermined. A two-stage dimension reduction is often performed to reduce the computational load and avoid overfitting for v = 1, \u2026, V, and f = , then standard multivariate random variable transformation results imply that the joint density of X isICA estimates n et al. , if fq iv = 1, \u2026, V istherefore the joint log-likelihood including all contributions for fq and B simultaneously. Instead, an iterative optimization is often performed. Specifically, given the current estimate of B at iteration k, say S via \u015ck), density estimation techniques can be used to obtain k.It is generally not possible to solve the joint likelihood for the parameters in ck) < ck) < \u2026 < ck) be equidistant histogram cutpoints, where ck) = \u2212\u03f5 + min \u015ck) and ck) = \u03f5 + max \u015ck). The number \u03f5 is added to avoid numerical boundary effects. Let j = 1, \u2026, J, be the count of values between cutpoints j \u2212 1 and j for row q of \u015ck), ck)] by mk) for j = 1, \u2026, J. We obtain a density estimate via the log-linear model nk) ~ Poisson{\u03bbk)}, where Dk) is a vector of coefficients. To avoid overfitting the B-spline model, and to avoid sensitivity to the degrees of freedom, we choose a large value for the degrees of freedom and put a squared penalty on the coefficients. Let \u03bck) denote the expectation of nk), then the penalized log likelihood takes the form = \u03b2 \u2212 2\u03b2 + \u03b2. The resulting model is then a generalized linear mixed model on the counts. The B-spline basis is evaluated at the midpoint of the cutpoint interval. However, via interpolation, the smoother gives an estimate for all values, thus yielding a continuous function, say where \u03b4 is a parameter controlling the smoothness of the fit, \u0394 denotes the difference operator, \u0394Using generalized linear mixed models to penalize smoothing has become standard practice and is well described in Ruppert et al. . HistogrB) are available in closed form, making gradient- and Hessian-based optimization algorithms easy to implement. This is useful for the stage of the algorithm for obtaining the next iterate of B. Accordingly, we use a Newton-Raphson method to update the mixing matrix. Specifically, let kth iteration, we update B byFurthermore, due to the convenient differentiation properties of B-spline bases and the simple exponential (Poisson) model, the first and second derivatives of B should satisfy the condition that the underlying ICs are the same for all subjects. Following Eloyan et al. ((Bk+1)\u22121. We use the Amari metric between Bk+1)( and Bk) assume that n et al. considerI = 18 ROIs for the whole brain. We assume the signals are i.i.d within region but could be differently distributed across region. Under this assumption, the density function fq can be written as the sum of the region-specific density function, that is,Specifically, we propose to account for the difference in the activity across the brain by allowing different density distribution in different regions. To this end, we adopt the functional parcellation of the brain activity map proposed by Yeo et al. . The parRi denotes the ith ROI, fiq is the density function on Ri. Thus, fiq takes positive values on the ith region and zero elsewhere. The density estimate of fiq can be obtained using the same procedure as proposed in Section 2.2, confined to the ith region. The estimate for fq can be constructed by taking the sum of where The proposed ICA algorithm can be summarized as follows:_______________________________________________________________________________________________________B.Choose an initial value of for the mixing matrix B using the Amari metric.S = BX.Let q, calculate the density function fiq(s) on the ith ROI, i = 1, 2, \u2026, I, using the p-spline based density estimation algorithm.For each IC Get B using the Newton-Raphson method, see Equation (2).Update the mixing matrix Alternate until convergence of _______________________________________________________________________________________________________fq1 = fq2 = \u2026 = fIq, the above algorithm reduces to the algorithm proposed in Section 2.2 assuming i.i.d signals across the entire brain.Note that, in the special case that We conduct simulation studies to evaluate the performance of the proposed ICA algorithm. We consider four settings where data are generated using different distributions. We compare the results of the proposed algorithm with fastICA perform much faster than the likelihood-based algorithms . ~ Weibull, S ~ Gamma, and S ~ Gamma, respectively. Standard Gaussian noises are added to the generated ICs. The mixing matrix is given byIn the first set of simulation studies, we assume there are Figure Q = 2, and we generate the signals based on parcellation. Specifically, we partition the real line into 10 intervals, with cutoffs at the 10th, 20th, 30th, 40th, 50th, 60th, 70th, 80th, and 90th percentiles of the normal distribution. For the first IC, the density function is uniformly distributed within each interval, but the overall shape is approximately normal. For the second IC, the density function follows Laplace distribution within each interval, and the overall shape is approximately normal. The mixing matrix is given byIn the second setting, we assume the number of source signals The boxplots of the spatial correlation and the Amari errors based on 200 replications are summarized in Figure I = 3. The source signals are the same as those in the second setting, and the mixing matrices for the three subjects are given byIn the third setting, we generate multi-subject data with number of subject The simulation results are summarized in Figure In the fourth setting, we generate the ICs and mixing matrices by mimicking signals from real fMRI data. Specifically, we run fastICA on 10 subjects from the NITRC 1000 Connectome dataset to get twenty ICs (networks). Three of the twenty networks are chosen as the true signals, and they are shown in Figure The results indicate that our proposed p-spline based ICA algorithm is successful in recovering signals from real fMRI data.https://www.nitrc.org/projects/fcon_1000/).We apply our proposed algorithm to the 1000 Functional Connectomes Project dataset, which consists of thousands of resting state scans combined across multiple sites with the goal of facilitating discovery and analysis of brain networks , and rerun the ICA algorithm on the dimension reduced dataset. We set R = 15, 20, 30 and Q = 15, 20, 30, respectively. Similarly as in Li et al. , auditory network (0.73), DMN (0.86) and control network (0.84). In addition, the correlations for the major brain networks using R = 20, Q = 30, and R = 20, Q = 20 are as follows: visual network (0.78), auditory network (0.61), DMN (0.88) and control network (0.69). In summary, we find that, although the estimation results depend on the number of components, the major networks appear to be robust against the choices of number of components.As suggested by an anonymous reviewer, we investigate the impact of the dimension of the reduced space on the final results. Specifically, we select different values of i et al. , we findIndependent component analysis is a factor-analytic approach that is commonly used in analyzing fMRI data. In this manuscript, we present a novel and simple ICA algorithm that is fast, likelihood based and straightforward to program. The algorithm is nonparametric, data-driven, and is blind to the particular distribution of the underlying signals. As a byproduct of the algorithm, we obtain the likelihood function of the ICA model which can be used for further statistical inference. It should be noted that, the likelihood function in our algorithm is a profile likelihood, since we are mainly interested in the mixing matrix estimates and the parameters over the spline basis are nuisance parameters. Indeed, one could also study the coefficients on the spline basis in a full likelihood, but this is not the goal of this manuscript, hence the variance of the estimator of the mixing matrix depends on the variance of the nuisance parameters.The proposed algorithm is extended to allow for region specific IC density functions, on the rationale that most signals of interest are reasonably confined to a subset of the entire anatomical brain space (Guo and Pagnoni, Simulation studies show that our proposed algorithm works well in both the simple and complex situations, and it substantially outperforms the existing ICA algorithms when the identically distributed assumption of the source signals is violated. In applying the proposed algorithm to the fMRI data, we choose to account for the difference in brain activities across regions by using the brain parcellation proposed by Yeo et al. . Our datThere are a few directions for future research. Firstly, the test-retest reliability of the intrinsic brain networks is an important issue and has been studied extensively in recent years. For example, Zuo et al. found thThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "A combinatorial synthetic approach is described for the isolation of quaternary cocrystals. The strategy outlines chemical and geometrical modulations in the long-range synthon Aufbau modules (LSAMs) to systematically increase the number of components. A synthetic strategy is outlined whereby a binary cocrystal may be developed in turn into a ternary and finally into a quaternary cocrystal. The strategy hinges on the concept of the long-range synthon Aufbau module (LSAM) which is a large supramolecular synthon containing more than one type of intermolecular interaction. Modulation of these interactions may be possible with the use of additional molecular components so that higher level cocrystals are produced. We report six quaternary cocrystals here. All are obtained as nearly exclusive crystallization products when four appropriate solid compounds are taken together in solution for crystallization. This array is made up of closed TMP\u00b7ORC tetramers consists of discrete synthon B modules that are laterally offset with respect to one another so that there are no C\u2014H\u22ef\u03c0 interactions. Fig. 2et al., 2011This article argues for the synthetic design of complex quaternary solids by systematic selection and fabrication from LSAMs in binary and ternary cocrystals. Fig. 1A , 1,10-phenanthroline (PHEN), 2,2-bisthiophene (22TP), hexamethylbenzene (HMB) and pyrene (PYR) results in stoichiometric ternary cocrystals. The structures of three of them are along predicted lines and they may be considered as being obtained by substitution of the \u2018free\u2019 TMP molecule in Form I of the ORC\u00b7TMP binary with the new aromatic compound Fig. 3. The othA Fig. 4 and the B is constructed exclusively with PHE and the TMP molecules provide cross links via the third \u2018hook\u2019 hydroxy group of the PGL molecule. From MeCN also but under different conditions, we obtained the 2:1:2 Form II which is reminiscent of the ORC\u00b7TMP\u00b7PHE ternary except that PHE is in the \u2018inner\u2019 part of synthon A rather than in the \u2018outer\u2019 part. There was no contamination of either of these ternaries by the \u2018other\u2019 ternary in the crystallization experiments. A priori, it would not be possible to predict which structure one would obtain from MeCN under what conditions. What is important, however, is that there are a number of topologically similar crystal structures available to the system. Which one is actually obtained would seem to depend on the exact experimental conditions used. The system lends itself to high throughput methods. We maintain that we carried out a very large number of crystallization experiments on an entire array of compounds and solvent systems in a combinatorial manner. It is of interest to note that such examples of (pseudo)polymorphism are very rare in three component systems . Let us consider these structures in turn. The 2:1:2:1 ORC\u00b7TMP\u00b7PHE\u00b7HMB structure follows smoothly from the ternary 2:1:2 ORC\u00b7TMP\u00b7PHE in a chemically reasonable manner. In the ternary, one observes \u03c0\u22ef\u03c0 stacking between electron-deficient PHE molecules . In the quaternary, HMB inserts in a classical donor\u2013acceptor fashion (\u223c\u20053.56\u2005\u00c5). Replacement of the electron-rich HMB by PYR and the ditopic PHE by ACR achieves the same result and one obtains the stoichiometric quaternaries 2:1:2:1 ORC\u00b7TMP\u00b7PHE\u00b7PYR and 2:1:2:1 ORC\u00b7TMP\u00b7ACR\u00b7PYR (see section S3). Coming next to PGL, it is not difficult to understand the crystal structure of the quaternary 2:1:1:1 PGL\u00b7TMP.PHE.DPE wherein an infinite synthon A based structure with two ditopic heterocycles is cross linked with DPE. The quaternaries 2:2:1:1 PGL.TMP.PHE.ANT and 2:2:1:1 PGL.TMP.PHE.PYR have very similar structures. Synthon A is constructed with TMP in the \u2018outer\u2019 locations and PHE in the \u2018inner\u2019 location. ANT and PYR intercalate with C\u2014H\u22ef\u03c0 interactions to give a columnar LSAM.In practice, a total of six quaternaries were obtained, three each from ORC and PGL may be found in a ternary cocrystal between say, A, B and C. Similarly, a synthon that is virtual in a three-component system may be seen in a four-component cocrystal. This also implies that proof correction mechanisms exist in the crystallizations, perhaps leading to the specificity of outcome.The results obtained in this work validate the idea of using a supramolecular combinatorial library in the isolation of stoichiometric three- and four-component molecular crystals. We have earlier used this concept to make a single ternary cocrystal global, BS_ORC_TMP, BS_ORC_TMP_Hydrate, BS_PGL_TMP.cif, QS_ORC_TMP_ACR_PYR, QS_ORC_TMP_PHE_HMB, QS_ORC_TMP_PHE_PYR, QS_PGL_TMP_PHE_ANT, QS_PGL_TMP_PHE_DPE, QS_PGL_TMP_PHE_PYR_hydrate, TS_ORC_TMP_22TP, TS_ORC_TMP_ACR, TS_ORC_TMP_HMB, TS_ORC_TMP_PHE, TS_ORC_TMP_PHEN, TS_ORC_TMP_PYR, TS_PGL_TMP_DPE, TS_PGL_TMP_PHE_Form_I, TS_PGL_TMP_PHE_Form_II, TS_PGL_TMP_PYR. DOI: Click here for additional data file.10.1107/S2052252515023957/hi5641sup3.zipCIF files. DOI: 10.1107/S2052252515023957/hi5641sup2.pdfSupporting information. DOI: 1428091, 1428092, 1428093, 1428106, 1428104, 1428105, 1428107, 1428090, 1428108, 1428099, 1428095, 1428098, 1428094, 1428096, 1428097, 1428103, 1428100, 1428101, 1428102CCDC references:"} +{"text": "Supporting Information File Rodrigues_etal_Supporting Information S1 with Track Changes.doc should not appear with the published article. Please view the correct Rodrigues_etal_Supporting Information S1 here.S1 FileSupporting Materials and Methods.(DOC)Click here for additional data file."} +{"text": "A new conceptual data model that addresses the geometric dimensioning and tolerancing concepts of datum systems, datums, datum features, datum targets, and the relationships among these concepts, is presented. Additionally, a portion of a related data model, Part 47 of STEP (ISO 10303-47), is reviewed and a comparison is made between it and the new conceptual data model. NOTE\u2014Though the scope of the DSCDM is limited to the concepts mentioned above, the aim is to provide a foundation upon which more comprehensive GD&T data models may be based.Datum is an entity name and datum refers to the object). Attribute names are printed in italic type . Additionally, permissible values from enumerated data types are printed in all uppercase letters .NOTE\u2014The following conventions are employed throughout the course of this paper. To distinguish between EXPRESS entities and the objects they represent, entity names are printed in bold type and the objects they represent are printed in non-bold type. Furthermore, entity names start with a leading uppercase letter requirements have been exchanged with technical drawings. However, with the advent of computer-aided design, manufacturing, and inspection equipment, the ability to exchange these requirements in a computer-sensible manner has become increasingly more desirable. As \u201ca data model is an effective technique to define the shareable semantics that are essential to the success of data communication in an integrated environment\u201d , a conceElectronic assembly, interconnect and packaging design [\u201cThe first step in data modeling is to define the data requirements\u201d . In regag design . With thMost of the following definitions are from existing drawing-based GD&T standards and associated reference books. These definitions are important, because they explain some of the concepts that are at the foundation of these GD&T standards, and consequently form the basis for the requirements of the DSCDM.Datum: \u201cA theoretically exact point, axis, or plane derived from the true geometric counterpart of a specified datum feature. A datum is the origin from which the location or geometric characteristics of features of a part are established\u201d .Datum Feature: \u201cAn actual feature of a part that is used to establish a datum\u201d .Datum Feature Symbol: \u201cThe symbolic means of indicating a datum feature consists of a capital letter enclosed in a square frame and a leader line extending from the frame to the concerned feature, terminating with a triangle\u201d .Datum System: \u201cA group of two or more separate datums used as a combined reference for a toleranced feature\u201d .Datum Reference Frame: A framework that consists of three mutually perpendicular datum planes, three datum axes (located at the intersection of each pair of datum planes), and a datum point (that is located at the intersection of the three datum planes).Datum Target: \u201cA specified point, line, or area on a part used to establish a datum\u201d .Datum Target Frame: \u201cThe datum targets are indicated by a circular frame divided in two compartments by a horizontal line. The lower compartment is reserved for a letter and a digit. The letter represents the datum feature and the digit the datum target number. The upper compartment is reserved for additional information, such as dimensions of the target area. If there is not sufficient space within the compartment, the information may be placed outside and connected to the appropriate compartment by a leader line\u201d .Feature: \u201cThe general term applied to a physical portion of a part, such as a surface, pin, tab, hole, or slot\u201d . [Feature Control Frame: \u201cThe feature control frame is a rectangular box containing the geometric characteristic symbol and the form, orientation, profile, runout, or location tolerance. If necessary, datum references and modifiers applicable to the feature or the datums are also contained in the box, e.g.\u201d .Feature of Size: \u201cOne cylindrical or spherical surface, or a set of two opposed elements or opposed parallel surfaces, associated with a size dimension\u201d .Least Material Condition (LMC): \u201cThe condition in which a feature of size contains the least amount of material within the stated limits of size\u2014for example, maximum hole diameter, minimum shaft diameter\u201d .least material requirement permits an increase in the stated geometrical tolerance when the concerned feature departs from its least material condition (LMC)\u201d [Least Material Requirement: \u201cThe n (LMC)\u201d .Maximum Material Condition (MMC): \u201cThe condition in which a feature of size contains the maximum amount of material within the stated limits of size\u2014for example, minimum hole diameter, maximum shaft diameter\u201d .maximum material principle is a tolerancing principle which requires that the virtual condition for the toleranced feature(s) and, if indicated, the maximum material condition of perfect form for datum feature(s), shall not be violated\u201d [Maximum Material Principle: \u201cThe iolated\u201d .Regardless of Feature Size (RFS): \u201cThe term used to indicate that a geometric tolerance or datum reference applies at any increment of size of the feature within its size tolerance\u201d .Shape_aspect, Shape_aspect_relationship, Property_definition, and Property_definition_relationship. A review of these entities is presented in STEP integrated generic resources are a series of STEP parts that define resource constructs that are context-independent. The underlying structure of the DSCDM is based on four entities from the STEP integrated generic resources. These entities are Shape_aspect entity of STEP Part 41 [Shape_aspect based entities are the entities based on the Shape_aspect_relationship entity of STEP Part 41. At the bottom of the page are the entities based on the Property_definition entity of STEP Part 41. Note that the DSCDM does not actually contain entities based on the Property_definition_relationship entity of STEP Part 45 [Property_definition based entities are related with attributes that have been included in the Property_definition based entities. For example, instead of specifying a Property_definition_relationship based entity in the DSCDM to relate the Datum_system_definition entity with the Datum_precedence_assignment entity, the relationship between these two entities is established by the assigned_datum_precedences attribute of the Datum_system_definition entity.Property_definition_relationship based entities exist in the DSCDM, they exist in spirit wherever two Property_definition based entities are related.NOTE\u2014While no The DSCDM is presented in the EXPRESS-G diagram shown in Part 41 are at t Part 45 . InsteadShape_aspect based entities are first, followed by the Shape_aspect_relationship based entities, and finally, the Property_definition based entities.The definitions of the entities presented in Datum_system corresponds to a datum system (see Sec. 3 of this paper) that is comprised of one to three datums.Datum_system entity is based on the Shape_aspect entity of STEP Part 41 [NOTE\u2014The Part 41 .NOTE\u2014The definition of datum system as defined in ISO 5459-1981 is given in Sec. 3 of this paper. However, for the purpose of this model, the definition of datum system has been extended so that a datum system may be comprised of a single datum.A datum_usages: The datum_usages attribute specifies a set of one to three Datum_usage_in_datum_systems. Each of the Datum_usage_in_datum_systems in this set corresponds to the usage of a datum in the datum system.defining_definition: The defining_definition attribute specifies the Datum_system_definition that specifies the characteristics of the corresponding datum system .NOTE\u2014On technical drawings, the characteristics of a datum system are typically specified in a feature control frame.EXAMPLE\u2014Both Datum_features specified as the used_datum_feature by the Datum_feature_usage_in_datums that are specified as the datum_feature_usages by the Datums that are specified as the used_datum by the Datum_usage_in_datum_systems that are specified as the datum_usages of the Datum_system, no Datum_feature may be specified more than once.NOTE\u2014WR1 corresponds to the assertion that each datum feature shall not be used more than once in establishing any one datum system.WR1: Of the Datum_targets specified as the used_datum_target by the Datum_target_usage_in_datum_target_sets specified as the datum_target_usages by the Datum_target_sets specified as the used_datum_feature by the Datum_feature_usage_in_datums that are specified as the datum_feature_usages by the Datums that are specified as the used_datum by the Datum_usage_in_datum_systems that are specified as the datum_usages of the Datum_system, no Datum_target may be specified more than once.NOTE\u2014WR2 corresponds to the assertion that each datum target shall not be used more than once in establishing any one datum system.WR2: Of the Datum corresponds to a datum (see Sec. 3 of this paper). A Datum may be either a Simple_datum or a Common_datum.Datum entity is based on the Shape_aspect entity of STEP Part 41 [NOTE\u2014The Part 41 .A datum_feature_usages: The datum_feature_usages attribute specifies a set of zero or more Datum_feature_usage_in_datums. Each of the Datum_feature_usage_in_datums in this set corresponds to the usage of a datum feature in establishing the datum.Simple_datum is a type of Datum that corresponds to a datum that is established from exactly one datum feature.A Simple_datum shall be specified as the used_datum by at least one Datum_usage_in_datum_system.NOTE\u2014WR1 corresponds to the assertion that each simple datum shall be used in at least one datum system.WR1: Each Simple_datum shall specify exactly one Datum_feature_usage_in_simple_datum as its datum_feature_usages.NOTE\u2014WR2 corresponds to the assertion that each simple datum shall be established from exactly one datum feature.WR2: Each Common_datum is a type of Datum that corresponds to a datum that is established from more than one datum feature.NOTE\u2014On technical drawings, a datum that is established from multiple datum features is indicated by placing the identifying letters of the datum features, separated by a dash, within a single compartment in a feature control frame. There is no significance to the order of the datum feature identifying letters within a compartment of the feature control frame.EXAMPLE\u2014The technical drawing presented in A Common_datum shall be specified as the used_datum by at least one Datum_usage_in_datum_system.NOTE\u2014WR1 corresponds to the assertion that each common datum shall be used in at least one datum system.WR1: Each Common_datum shall specify more than one Datum_feature_usage_in_common_datum as its datum_feature_usages.NOTE\u2014WR2 corresponds to the assertion that each common datum shall be established from more than one datum feature.WR2: Each Datum_feature corresponds to a datum feature (see Sec. 3 of this paper). A Datum_feature may be a Datum_target_set.Datum_feature entity is based on the Shape_aspect entity of STEP Part 41 [NOTE\u2014The Part 41 ..NOTE\u2014On technical drawings, a feature is typically identified as a datum feature by means of a datum feature symbol, e.g., NOTE\u2014The concept of datum feature in the DSCDM applies to features that are used to establish one or more datums. Features that may be used as datum features include \u201cpartial\u201d features and datum target sets, as well as \u201ccomplete\u201d and composite features. The concept of datum feature in the DSCDM does not pertain to features in which only a portion of the feature is used to establish one or more datums. \u201cPartial\u201d and composite features are discussed in Sec. 10.2 of this paper.A identification: The identification attribute specifies the string value by which the corresponding datum feature is referred.).NOTE\u2014On technical drawings, each datum feature is referred to by an identifying letter, .WR1: There shall be at most one Datum_target_set is a type of Datum_feature that corresponds to a set of one or more datum targets (see Sec. 3 of this paper).) indicate in which datum target sets the associated datum targets are used.EXAMPLE\u2014There are three datum target sets shown in the technical drawing presented in A datum_target_usages: The datum_target_usages attribute specifies a set of one or more Datum_target_usage_in_datum_target_sets. Each of the Datum_target_usage_in_datum_target_sets in this set corresponds to the usage of a datum target in the datum target set.Datum_target corresponds to a datum target (see Sec. 3 of this paper).Datum_target entity is based on the Shape_aspect entity of STEP Part 41 [NOTE\u2014The Part 41 .NOTE\u2014Datum targets are typically used in situations where it is inappropriate to specify an entire surface as a datum feature.EXAMPLE\u2014There are six datum targets shown in A datum_target_usages: The datum_target_usages attribute specifies a set of one or more Datum_target_usage_in_datum_target_sets. Each of the Datum_target_usage_in_datum_target_sets in this set corresponds to the usage of the datum target in a datum target set.Datum_usage_in_datum_system corresponds to the usage of a datum in a datum system.Datum_usage_in_datum_system entity is based on the Shape_aspect_relationship entity of STEP Part 41 [NOTE\u2014The Part 41 .A comprised_datum_system: The comprised_datum_system attribute specifies the Datum_system that corresponds to the datum system that is either partially or wholly comprised of the corresponding datum.used_datum: The used_datum attribute specifies the Datum that corresponds to the datum that is used in the corresponding datum system.precedence_assignment: The precedence_assignment attribute specifies the Datum_precedence_assignment that corresponds to the specification of the order in which the datum is established within the datum system.comprised_datum_system and used_datum shall be unique within a population of Datum_usage_in_datum_system.NOTE\u2014UR1 corresponds to the assertion that each datum shall not be used more than once in any one datum system.UR1: The combination of Datum specified as the used_datum shall either be a Common_datum or Simple_datum.NOTE\u2013WR1 corresponds to the assertion that each datum that is used in a datum system shall be established from one or more datum features.WR1: The Datum_feature_usage_in_datum_system corresponds to the usage of a datum feature in establishing a datum system.Datum_feature_usage_in_datum_system entity is based on the Shape_aspect_relationship entity of STEP Part 41 [NOTE\u2014The Part 41 .Datum_feature and a Datum_system is indirectly established with a Datum_feature_usage_in_datum, a Datum, and a Datum_usage_in_datum_system. Therefore, a Datum_feature_usage_in_datum_system should not be used unless it is necessary to indicate the application of either the least material requirement or the maximum material principle (see Sec. 3 of this paper) to a datum feature within the context of a datum system. In essence, a Datum_feature_usage_in_datum_system corresponds to a datum feature in the context of a datum system.NOTE\u2014The relationship between a A established_datum_system: The established_datum_system attribute specifies the Datum_system that corresponds to the datum system that is established from the corresponding datum feature.used_datum_feature: The used_datum_feature attribute specifies the Datum_feature that corresponds to the datum feature that is used to establish the corresponding datum system.applied_material_condition_property: The applied_material_condition_property attribute specifies the Datum_feature_material_condition_property that corresponds to the specification of a material condition property that is applied to the datum feature in the context of the datum system.Datum_feature specified as the used_datum_feature shall be specified as the used_datum_feature by a Datum_feature_usage_in_datum that specifies a Datum as the established_datum, and that Datum shall be specified as the used_datum by a Datum_usage_in_datum_system that specifies the same Datum_system as the comprised_datum_system, as is specified as the established_datum_system by the Datum_feature_usage_in_datum_system.NOTE\u2014WR1 corresponds to the assertion that the datum feature shall be used to establish a datum that is used in the datum system.WR1: The Datum_feature_usage_in_datum corresponds to the usage of a datum feature in establishing a datum. A Datum_feature_usage_in_datum is either a Datum_feature_usage_in_simple_datum or a Datum_feature_usage_in_common_datum.Datum_feature_usage_in_datum entity is based on the Shape_aspect_relationship entity of STEP Part 41 [NOTE\u2014The Part 41 .A established_datum: The established_datum attribute specifies the Datum that corresponds to the datum that is established from the corresponding datum feature.used_datum_feature: The used_datum_feature attribute specifies the Datum_feature that corresponds to the datum feature that is used to establish the corresponding datum.Datum_feature_usage_in_simple_datum is a type of Datum_feature_usage_in_datum that corresponds to the usage of a datum feature in establishing a datum that is established from exactly one datum feature.A established_datum: The established_datum attribute specifies the Simple_datum that corresponds to the datum that is established from the corresponding datum feature.Datum_feature specified by the inherited used_datum_feature attribute.NOTE\u2014\u201cThe corresponding datum feature\u201d refers to the datum feature that corresponds to the Datum_feature_usage_in_common_datum is a type of Datum_feature_usage_in_datum that corresponds to the usage of a datum feature in establishing a datum that is established from more than one datum feature.A established_datum: The established_datum attribute specifies the Common_datum that corresponds to the datum that is established, in part, from the corresponding datum feature.Datum_feature specified by the inherited used_datum_feature attribute.NOTE\u2014\u201cThe corresponding datum feature\u201d refers to the datum feature that corresponds to the Datum_target_usage_in_datum_target_set corresponds to the usage of a datum target in a set of datum targets.Datum_target_usage_in_datum_target_set entity is based on the Shape_aspect_relationship entity of STEP Part 41 [NOTE\u2014The Part 41 . symbol in NOTE\u2014On technical drawings, the usage of a datum target in a datum target set is indicated with a datum target frame, e.g., the datum target frame in EXAMPLE\u2014The A comprised_datum_target_set: The comprised_datum_target_set attribute specifies the Datum_target_set that corresponds to the datum target set that is either partially or wholly comprised of the corresponding datum target.datum_target_number: The datum_target_number attribute specifies the integer value by which the corresponding datum target is identified within the corresponding datum target set.NOTE\u2014Datum target numbers are described in 7.1.1 of ISO 5459 . datum target frame of EXAMPLE\u2014The datum target number \u201c1\u201d in the used_datum_target: The used_datum_target attribute specifies the Datum_target that corresponds to a datum target that is used in the corresponding datum target set.used_datum_target and defined_datum_target_set shall be unique within a population of Datum_target_usage_in_datum_target_set.NOTE\u2014UR1 corresponds to the assertion that each datum target shall not be used in any one datum target set more than once.UR1: The combination of datum_target_number and defined_datum_target_set shall be unique within a population of Datum_target_usage_in_datum_target_set.NOTE\u2014UR2 corresponds to the assertion that within a datum target set each datum target shall be identified by a unique datum target number.UR2: The combination of Datum_system_definition corresponds to the specification of the characteristics of a datum system. These characteristics include the order in which the datums are established within the datum system and any material condition properties that are explicitly applied to datum features within the context of the datum system. A Datum_system_definition shall either be a Datum_system_definition_with_material_conditions or a Datum_system_definition_without_material_conditions.Datum_system_definition entity is based on the Property_definition entity of STEP Part 41 [NOTE\u2014The Part 41 .NOTE\u2014On technical drawings, the characteristics of a datum system are typically specified in a feature control frame.A defined_datum_system: The defined_datum_system attribute specifies the Datum_system that corresponds to the datum system the characteristics of which are specified.assigned_datum_precedences: The assigned_datum_precedences attribute specifies a set of one to three Datum_precedence_assignments. Each of the Datum_precedence_assignments in this set corresponds to the specification of the order in which a datum is established within the datum system.Datum_precedence_assignment within the set of Datum_precedence_assignments specified as the assigned_datum_precedences shall specify as its assigned_to a Datum_usage_in_datum_system that specifies as its comprised_datum_system the same Datum_system as specified as the defined_datum_system.NOTE\u2014WR1 corresponds to the assertion that each datum system specification shall only specify the precedence of datums used in the datum system that the specification characterizes.WR1: Each Datum_precedence_assignment that has a name of TERTIARY shall not exist within the set of Datum_precedence_assignments specified as the assigned_datum_precedences unless a Datum_precedence_assignment exists within that set that has a name of SECONDARY.NOTE\u2014WR2 corresponds to the assertion that each datum system specification that specifies a tertiary datum shall also specify a secondary datum.WR2: A Datum_precedence_assignment that has a name of SECONDARY shall not exist within the set of Datum_precedence_assignments specified as the assigned_datum_precedences unless a Datum_precedence_assignment exists within that set that has a name of PRIMARY.NOTE\u2014WR3 corresponds to the assertion that each datum system specification that specifies a secondary datum shall also specify a primary datum.WR3: A Datum_system_definition shall be specified as the referenced_datum_system_definition by at least one Geometric_tolerance_with_specified_datum_systrem or Dimension_with_specified_datum_system.NOTE\u2014WR4 corresponds to the assertion that each datum system specification shall be referenced by at least one geometric tolerance or dimension.WR4: Each Datum_system_definition_with_material_conditions is a type of Datum_system_definition that corresponds to a specification of a datum system that specifies the application of material condition properties to one or more datum features within the context of the datum system.Datum_system_definition_with_material_conditions is specified in a feature control frame that contains either at least one least material requirement symbol that is preceded immediately by a datum feature letter or at least one maximum material principle symbol that is preceded immediately by a datum feature letter, e.g., .NOTE\u2014On technical drawings, a datum system specification that corresponds to a A applied_material_condition_properties: The applied_material_condition_properties attribute specifies a set of one or more Datum_feature_material_condition_propertys. Each of the Datum_feature_material_condition_propertys in this set corresponds to the specification of a material condition property that is explicitly applied to a datum feature within the context of the datum system.Datum_feature_material_condition_property within the set of Datum_feature_material_condition_propertys specified as the applied_material_condition_properties shall specify as its applied_to a Datum_feature_usage_in_datum_system that specifies as its established_datum_system the same Datum_system as specified as the defined_datum_system.NOTE\u2014WR1 corresponds to the assertion that each datum system specification shall only specify material condition properties for datum features used to establish the datum system that the specification characterizes.defined_datum_system attribute referred to in WR1 is inherited from the Datum_system_definition entity of which this entity is a subtype.NOTE\u2014The WR1: Each Datum_system_definition_without_material_conditions is a type of Datum_system_definition that corresponds to a specification of a datum system in which no material condition properties are specified.Datum_system_definition_without_material_conditions is typically specified in a feature control frame that contains neither a least material requirement symbol that is immediately preceded by a datum feature letter nor a maximum material principle symbol that is immediately preceded by a datum feature letter, e.g., .NOTE\u2014In technical drawings, a datum system specification that corresponds to a Datum_system_definition_without_material_conditions could also be specified in a dimension related note; see NOTE\u2014On technical drawings, a datum system specification that corresponds to a A Datum_precedence_assignment corresponds to the specification of the order in which a datum is established within a datum system.Datum_precedence_assignment entity is based on the Property_definition entity of STEP Part 41 [NOTE\u2014The Part 41 .NOTE\u2014On technical drawings, the precedence of a datum within a datum system is typically specified in a feature control frame. The location of the compartment containing the letter(s) corresponding to the datum feature(s) from which the datum is established indicates the assigned precedence. The compartment for the primary datum (if it exists) is immediately to the right of the compartment containing the tolerance value. The compartment for the secondary datum (if it exists) is immediately to the right of the compartment for the primary datum. Lastly, the compartment for the tertiary datum (if it exists) is immediately to the right of the compartment for the secondary datum.EXAMPLE\u2014A assigned_to: The assigned_to attribute specifies a Datum_usage_in_datum_system. In essence, the Datum_usage_in_datum_system corresponds to the datum within the context of the datum system to which the datum precedence is assigned.NOTE\u2014A datum within the context of one datum system may be assigned one precedence, e.g., primary, and the same datum within the context of another datum system may be assigned another precedence, e.g., secondary.EXAMPLE\u2014In name: The name attribute specifies the value of the assigned datum precedence. Valid values for the name are PRIMARY, SECONDARY, and TERTIARY.associate_datum_system_definition: The associate_datum_system_definition attribute specifies the Datum_system_definition that corresponds to the datum system specification to which the datum precedence is associated.name and associate_datum_system_definition shall be unique within a population of Datum_precedence_assignments.NOTE\u2014UR1 corresponds to the assertion that no two datums of a datum system shall have the same precedence.UR1: The combination of Datum_feature_material_condition_property corresponds to the specification of a material condition property that is explicitly applied to a datum feature within the context of a datum system.Datum_feature_material_condition_property entity is based on the Property_definition entity of STEP Part 41 [NOTE\u2014The Part 41 .A applied_to: The applied_to attribute specifies a Datum_feature_usage_in_datum_system. In essence, the Datum_feature_usage_in_datum_system corresponds to the datum feature within the context of the datum system to which the material condition property is applied.least material requirement, and the same datum feature within the context of another datum system may have another material condition property applied, e.g., maximum material principle.NOTE\u2014A datum feature within the context of one datum system may have one material condition property applied, e.g., name: The name attribute specifies the value by which the material condition property is known. Valid values for the name are LEAST_MATERIAL_REQUIREMENT and MAXIMUM_MATERIAL_PRINCIPLE (see Sec. 3 of this paper).Datum_feature_material_condition_property that has a name of LEAST_MATERIAL_REQUIREMENT corresponds to a datum feature letter followed by the symbol in a feature control frame of a technical drawing, e.g., .NOTE\u2014A Datum_feature_material_condition_property that has a name of MAXIMUM_MATERIAL_PRINCIPLE corresponds to a datum feature letter followed by the symbol in a feature control frame of a technical drawing, e.g., .NOTE\u2014A regardless of feature size principle (see Sec. 3 of this paper) shall be in effect in cases where the datum feature is a feature of size (see Sec. 3 of this paper) and a Datum_feature_material_condition_property is not specified.NOTE\u2014It shall be understood that the associate_datum_system_definition: The associate_datum_system_definition attribute specifies the Datum_system_definition_with_material_conditions that corresponds to the datum system specification to which the material condition property is associated.Geometric_tolerance_with_specified_datum_system entity is not completely defined here, as it is not within the scope of this paper. However, the referenced_datum_system_definition attribute of this entity is defined to illustrate how the DSCDM could be tied into a larger GD&T data model.Geometric_tolerance_with_specified_datum_system entity is based on the Property_definition entity of STEP Part 41 [NOTE\u2014The Part 41 .The referenced_datum_system_definition: The referenced_datum_system_definition attribute specifies the Datum_system_definition that corresponds to the datum system specification that is referenced by the geometric tolerance.Dimension_with_specified_datum_system entity is not completely defined here, as it is not within the scope of this paper. However, the referenced_datum_system_definition attribute of this entity is defined to illustrate how the DSCDM could be tied into a larger GD&T data model.Dimension_with_specified_datum_system entity is based on the Property_definition entity of STEP Part 41 [NOTE\u2014The Part 41 .Datum_system_definition entity is associated almost exclusively with geometric tolerances, clause 4.4 of ASME Y 14.5M [Dimension_with_specified_datum_system entity is shown in NOTE\u2014While the data modeled with the EXAMPLE\u2014The three linear dimensions presented in The referenced_datum_system_definition: The referenced_datum_system_definition attribute specifies the Datum_system_definition_without_material_conditions that corresponds to the datum system specification that is referenced by the dimension.Datum_target, Datum_feature, and Datum entities . Additionally, the EXPRESS-G diagram does not show that the Datum_target, Datum_feature, and Datum entities are subtypes of the Shape_aspect entity of STEP Part 41 [A pseudo EXPRESS-G diagram of the datum system related portion of the Part 47 model is presented in Part 41 .NOTE\u2014The actual EXPRESS declarations of these entities have not been included in the definitions given in Tables 1NOTE\u2014The clause and figure numbers specified within Tables 1Geometric_tolerance entity of which the Geometric_tolerance_with_datum_reference entity is a subtype is not shown here, as it is not within the scope of this paper.NOTE\u2014The definition of the The definitions of the entities shown in Tables 1NOTE\u2014The STEP architecture is such that STEP application protocols may specialize entities from the STEP integrated generic resources. However, deficiencies in entities of the type mentioned above will only be passed on to the STEP application protocols that incorporate them.Datum_feature entity from STEP Part 47 will not be able to support multiple use datum features (see Sec. 6.3).EXAMPLE\u2014A STEP application protocol that incorporates the This section discusses the differences between the DSCDM and portions of the model presented in STEP Part 47 that areDatum_system and Datum_system_definition entities of the DSCDM. Two independent comments were submitted against the STEP Part 47 DIS [Datum_reference only made sense in the context of a datum system. Concurring with those comments, the Datum_system and Datum_system_definition entities were incorporated within the DSCDM.One of the main differences between the Part 47 model and the DSCDM is that the Part 47 model has no entities that are equivalent to the t 47 DIS documentidentification attribute is on the Datum_feature entity; in contrast, in the Part 47 model the identification attribute is on the Datum entity. In practice, it is the datum feature to which an identifier is assigned. ASME Y14.5M [identification attribute may seem moot, because if the identification attribute is placed on the Datum entity, the name of the associated datum feature could easily be derived. However, in cases in which a datum is established from more than one datum feature, the Part 47 model produces ambiguous results because it is impossible to determine the name of the datum features from the value of the identification attribute on a Datum. The DSCDM does not have this ambiguity, as the identification attribute is on the Datum_feature entity. feature control frame of the position tolerance in identification attribute of the Datum entity would have a value of \u201cA\u2013B\u201d. However, it would be unclear as to which datum feature is identified as A and which datum feature is identified as B.EXAMPLE\u2014The Datum and Datum_feature entities in the Part 47 model are subtypes of the Shape_aspect entity of STEP Part 41 [name attribute. However, as a Datum_feature corresponds to an actual feature of a part it is likely that the name attribute will not be available for the datum feature identifying letter because it will likely be used for another purpose . Furthermore, as datums are identified solely for GD&T purposes it is likely that the inherited name attribute on the Datum entity would be available, thereby making the identification attribute on the Datum entity not only misplaced but redundant.NOTE\u2014As the Part 41 , they boIn the DSCDM the feature_basis_relationship attribute and WR1 on the Datum_feature entity specify that a Datum_feature shall be related to exactly one Datum. On the other hand, in the DSCDM the inverse datum_feature_usages attribute on the Datum_feature entity constrains the number of Datums that shall be established from a Datum_feature to one or more.). Also, , and ). Furthermore, both datum features A and B are used once again to establish the primary datum (yet another center axis) of the datum system specified by the position tolerance . As the Part 47 model limits the number of datums that may be established from a datum feature to one, this situation cannot be represented with the Part 47 model.EXAMPLE\u2014The technical drawing presented in The Part 47 model fails to account for the fact that a datum feature may be used to establish multiple datums, whereas the DSCDM does account for this fact. In the Part 47 model, the target_basis_relationship attribute and WR1 on the Datum_target entity specify that a Datum_target shall be related to exactly one Datum. On the other hand, the DSCDM does not specify a direct relationship between a Datum_target and a Datum. Instead, in the DSCDM the relationship between a Datum_target and a Datum is specified indirectly via the Datum_target_set entity and the two relationship entities Datum_target_usage_in_datum_target_set and Datum_feature_usage_in_datum. In the DSCDM the constraints on Datum_target and Datum_feature correspond to the assertion that a datum target shall be used in at least one datum target set and because a datum target set is a type of datum feature, the datum target set shall be used to establish at least one datum. The technical drawing presented in and datum target frames is associated with two datum target sets, F and G, each of which is used to establish a separate datum. As the Part 47 model limits the number of datums that may be established from a datum target to one, this situation cannot be represented with the Part 47 model.EXAMPLE\u2014The datum target point in The Part 47 model fails to account for the fact that a datum target may be used to establish multiple datums, whereas the DSCDM does account for this fact. In the Part 47 model the Datum_target_set is a type of Datum_feature. The Part 47 model has no entity that is equivalent to the Datum_target_set entity. Furthermore, the Part 47 model prevents the Datum_feature entity or a specialization of it to serve as a set of datum targets. That is, in the Part 47 model the attributes target_basis_relationship and feature_basis_relationship on the Datum_target and Datum_feature entities, respectively, in association with WR1 on each of these entities, prevent a Datum_target from being related to a Datum_feature via a Shape_aspect_relationship.NOTE\u2014On technical drawings, datum target frames are used to group datum targets into datum target sets., and datum target frames make up datum target set A. Additionally, the two datum target areas (hatched regions are used to indicate datum target areas) that are connected to the and datum target frames constitute datum target set B. Also, the datum target point that is connected to the datum target frame makes up datum target set C.EXAMPLE\u2014In the technical drawing presented in In the DSCDM, a target_id attribute on the Datum_target entity indicates that the use of this attribute is to associate a datum target number with a datum target. However, the placement of this attribute on the Datum_target entity only allows a single datum target number to be associated with a datum target, which is not surprising as the Part 47 model only allows a datum target to be associated with a single datum. On the other hand, in the DSCDM the placement of the datum_target_number attribute on the Datum_target_usage_in_datum_target_set entity permits a different datum target number to be assigned to each usage of a datum target in a datum target set.NOTE\u2014On technical drawings, datum target frames are used to group datum targets into datum target sets. Additionally, datum target frames specify datum target numbers by which the datum targets are identified within the datum target sets.The technical drawing presented in and datum target frames is associated with two datum targets sets, C and G. This datum target is identified by a datum target number of \u201c1\u201d when it is associated with datum target set C and is identified by a datum target number of \u201c2\u201d when it is associated with datum target set G.EXAMPLE\u2014The datum target point in The Part 47 model fails to account for the fact that multiple datum target numbers may be associated with a datum target, whereas the DSCDM does account for this fact. In the Part 47 model, the definition for the A composite datum feature is a datum feature that is composed of other features. Neither the Part 47 model nor the DSCDM have an explicit entity that corresponds to a composite datum feature. However, it is of interest to examine how composite datum features may be represented using these two models.Composite_shape_aspect entity, the intent of which is to group Shape_aspects for a purpose. At first glance this seems like a perfect match\u2014a Shape_aspect that is a Datum_feature as well as a Composite_shape_aspect could represent a composite datum feature. This usage of Composite_shape_aspect is even mentioned in a note in clause 4.4.1 of STEP Part 47 [feature_basis_relationship inverse attribute on the Datum_feature entity requires that a Datum_feature be specified as the relating_shape_aspect by exactly one Shape_aspect_relationship. Conversely, the component_relationships inverse attribute on the Composite_shape_aspect entity requires that a Composite_shape_aspect be specified as the relating_shape_aspect by two or more Shape_aspect_relationships (these Shape_aspect_relationships relate the Composite_shape_aspect with the Shape_aspects from which it is composed). This conflict between the two inverse attributes prohibits a Shape_aspect from being both a Datum_feature and a Composite_shape_aspect. The model presented in STEP Part 47 has a Part 47 submitted against the STEP Part 47 DIS documentThe second difference is that in the Part 47 model the Referenced_modified_datum entity is used to associate modifiers with datums, not datum features. On the other hand, in the DSCDM the Datum_feature_material_condition_property entity is used to associate modifiers with datum features. datum reference letter is somewhat of a misnomer, as a datum reference letter actually refers to a datum feature.NOTE\u2014The term symbol following the letter \u201cA\u201d in the feature control frame associates the maximum material principle with datum feature A. Likewise, the symbol following the letter \u201cB\u201d in the feature control frame associates the maximum material principle with datum feature B.EXAMPLE\u2014In The Part 47 model is inconsistent with ASME Y14.5M [NOTE\u2014While the DSCDM supports the application of different modifiers to the datum features of a common datum, as is permitted in ASME Y14.5M, the author of this paper has been unable to find examples of this situation in standards or reference books. Therefore, it is believed that occurrences of this case are probably extremely limited.One may argue that if modifiers are directly associated with datums, as in the Part 47 model, they are indirectly associated with the datum features that establish those datums. However, this contrivance fails in cases in which the requirements are such that all the datum features from which a common datum is established are not to be associated with the same modifier.Dimension_with_specified_datum_system corresponds to a type of dimension that references a datum system specification. The Part 47 model has no entity that is equivalent to the Dimension_with_specified_datum_system entity.Dimension_with_specified_datum_system entity is not completely defined in this paper, as a discussion of dimensions is outside its scope.NOTE\u2014The NOTE\u2014Clause 4.4 of ASME Y14.5M [EXAMPLE\u2014The technical drawing presented in In the DSCDM the Datum, Datum_feature, and Datum_target entities assert that each datum shall be established from one or more datum features or datum targets, that each datum feature shall be used to establish a single datum, and that each datum target shall be used to establish a single datum. In contrast, the DSCDM only requires that the relationship between the datum feature(s) from which a datum is established be specified for those datums that are used to establish a datum system. That is, for a datum not used to establish a datum system (some datums may just be the origin of one or more dimensions), the DSCDM does not require the corresponding Datum to be related to a Datum_feature via the Datum_feature_usage_in_datum entity.Datum, Datum_feature, and Datum_target entities in the Part 47 model). However, as the DSCDM does not require a Datum to be related to either a Datum_feature or a Datum_system, this situation can be represented using the DSCDM.EXAMPLE\u2014In NOTE\u2014Although the datum planes that are labeled \u201cSecond datum plane\u201d and \u201cThird datum plane\u201d in The Part 47 model cannot be used to represent datums that are not directly established from datum features or datum targets. This is because the attributes and rules on the This paper has presented a data model (the DSCDM) that covers the concepts of datum systems, datums, datum features, and datum targets. Furthermore, for comparison purposes, this paper has presented the datum related portions of the data model given in STEP Part 47 . In pres"} +{"text": "Anopheles mosquitoes were first recognised as the transmitters of human malaria in the late 19th Century and have been subject to a huge amount of research ever since. Yet there is still much that is unknown regarding the ecology, behaviour (collectively \u2018bionomics\u2019) and sometimes even the identity of many of the world\u2019s most prominent disease vectors, much less the within-species variation in their bionomics. Whilst malaria elimination remains an ambitious goal, it is becoming increasingly clear that knowledge of vector behaviour is needed to effectively target control measures. A database of bionomics data for the dominant vector species of malaria worldwide has been compiled from published peer-reviewed literature. The data identification and collation processes are described, together with the geo-positioning and quality control methods. This is the only such dataset in existence and provides a valuable resource to researchers and policy makers in this field. Biting location, biting time and host preference will influence how effectively a mosquito can transmit malaria. In addition, understanding the behaviour of the vector guides how best it can be controlled and the likelihood that a particular intervention measure will be successful2. For example, a night feeding, anthropophilic, endophagic and endophilic mosquito is likely to be a highly effective transmitter of malaria . These same characteristics make this vector an ideal candidate for indoor insecticide-based control such as indoor residual spraying (IRS), which targets mosquitoes that preferentially rest indoors, or long-lasting insecticide-treated nets (LLINs), which target those species attracted to humans indoors at night. On the other hand, a species that is zoophilic, exophagic and exophilic would not be impacted by these control methods , but may be vulnerable to outdoor space spraying or insecticidal zooprophylaxis.The behaviour and life history characteristics of a mosquito vector contribute to the relative importance of the species in terms of human malaria transmission4. It is becoming more widely accepted that simply scaling up existing insecticide based intervention methods is insufficient to tackle increasingly resistant vector populations or to impact existing, control avoiding species5\u20137. Spatially explicit, species-specific behavioural data are needed to populate the emerging transmission models that aim to identify the pathways to achieve elimination4.Increasingly malaria researchers are turning to transmission models to predict the impact of control measures on malaria transmission, to focus limited resources toward the most efficient measures of control and to address residual transmission1, and a brief literature survey of vector bionomics was conducted to accompany a series of papers that mapped the ranges of these species9. The survey did not show the proportion of a species showing a particular trait, but instead the proportion of studies reporting the trait for each species. This highlighted two major points. Firstly, a lack of published spatial datasets describing the ecology or behaviour of even the most dominant malaria vectors, and secondly, how much variation in behaviour exists within individual species. A comprehensive search for spatial bionomics data, incorporating behaviour, parasite infection and transmission potential plus other pertinent parameters was therefore conducted (The dominant vector species (DVS) of Africa, the Americas and the Asia-Pacific region have previously been identifiedonducted .The focus of this publication is to present the results of this work; a global, species-specific, temporally and spatially categorised database of the bionomics of the DVS of human malaria.Bionomics data were abstracted from the published literature detailing research studies that included data on:Vector biology; for example parity and longevity;Vector infection and transmission; for example sporozoite rate and entomological inoculation rate;Human biting rate;Vector host preference (quantifiable measures of anthropo- and zoophily);Human biting preference (quantifiable measures of endo- or exophagy);Human biting activity (preferred time of biting);Resting preference (quantifiable measures of endo- or exophily).Regional datasets were created for Africa, the Americas and the Asia-Pacific region within which all data were attributed to species and location. There is no single standard method for measuring each of the above parameters so full details including mosquito collection date, season and sampling method were recorded, where given.8 (date range of field data: 1985\u20132010). To ensure an up-to-date dataset, additional searches using the DVS specific names as search terms were conducted in PubMed10 and Web of Science11 covering literature published from 2010 to May 2013 for the African DVS and August 2014 for the American and Asia-Pacific DVS. Language restrictions were not placed on these searches. Full text digital copies of all publications were obtained. All articles written in English, French, Portuguese and Spanish were read, and those publications with no useful bionomics data were removed. The decision to only include data collected since 1985 was made to ensure that the dataset reflected the current distribution of the DVS and included specimens identified using more up-to-date identification methods and taxonomy1.Publications detailing occurrence data for the DVS were identified from the MAP DVS databaseAn. gambiae but only relying on morphological identification and with no clear indication whether the specimens were considered An. gambiae species or An. gambiae complex).Each article was searched for relevant bionomics data related to both a given location and to one of the vector species in question. Data were extracted as reported in the source document, with no assumptions made, and only tabulated data or values reported in the text were accepted . When possible, bionomics data for individual sibling species were extracted. However, where there was some ambiguity in the species being reported, they were recorded as the species complex . Where given, we captured full species details, however these use the old molecular form classification. Therefore, consider all mentions of An. gambiae to include An. coluzzii and An. gambiae unless specifically stated otherwise. Our dataset also records the previous classification of chromosomal form, where given. On occasion, despite conducting additional identifications to determine sibling species, authors presented their bionomics data for the species complex, this was also recorded as given.In 2013 the Where possible all data reported in the source for a specific location, time and species are combined on a single data line. For example, this means there may be information relating to a vector population\u2019s host preference, sporozoite infection rate and peak biting time all combined on a single row. However, as not all bionomics parameters were reported by every study this also means that there are blank cells on each row. Blanks cells always represent \u2018no data\u2019.Where given, season was recorded. Due to the high influence of season on mosquito behaviour and abundance, when it was not provided it was calculated from the dates given, either in the source or by searching for information detailing when the rainy and dry seasons normally occurred in the specific location. When season has been calculated this is recorded in a separate column, so that users of the dataset are aware that this was not included in the original data source.For the African dataset a search of the accumulated bionomics library was conducted to identify those authors who were most prolific in publishing pertinent bionomics data. These authors were contacted to ask if they had any further, unpublished data they would be able to contribute. Any unpublished data was added into the dataset as above. Authors were also contacted to clarify details that were unclear or to disaggregate data where the source suggested more detail may have been collected in the study, but had not been presented within the published source. Due to time constraints this step was not carried out for the American and Asia-Pacific datasets.9. All additional sites were georeferenced following the same protocol, fully detailed in Hay et al1. In brief, site location was determined by searching for the site name in online gazetteers or other geolocational resources . Site related contextual information provided in the original reference was used to confirm that the correct site had been identified. Data locations were attributed to area types, including point locations (within 10\u2009km2), wide areas (10\u201325\u2009km2), small polygons (25\u2013100\u2009km2) or large polygons (>100\u2009km2). Single sampling points were identified as point locations. However, data were often reported for several sampling sites combined. In this case, sampling locations were determined as a wide areas, small polygons or large polygons depending on the extent of the sampling area. A single set of coordinates for the most central sampling site of the study are used to define the location of the sampling area, with the area type used to give an indication of the geographic spread of the sampling locations.The majority of sites sampled had previously been geolocated in an earlier study mapping the ranges of the DVSWe define a data record as a data point for a unique site-date-species combination. 13 and the VecNet digital library14. Each survey included in the vector bionomics database has been disaggregated to individual sites , individual dates (if the same site was sampled repeatedly) and individual Anopheles DVS. Values were extracted to a database with the following fields:The three regional databases are publicly available online as comma delimited files (Data Citation 1). The data are also available via the Malaria Atlas Project (MAP) websiteSource_ID. Unique source identifier.Country. Country where the study was conducted.Site. Site name.Lat. Latitude in decimal degrees.Long. Longitude in decimal degrees.Area_type. Point (within 10\u2009km2), wide area (10\u201325\u2009km2), small polygon (25\u2013100\u2009km2) or large polygon (>100\u2009km2).Insecticide_control. Indicates whether insecticide based control methods are in place (previously implemented or implemented as part of the referenced study) at the specified location and time period.T: TRUE.F: FALSE.blank if unknown.Control_type. If \u2018TRUE\u2019 above, details the insecticide control method.ITN: insecticide treated nets.IRS: indoor residual spraying.IT curtains: insecticide treated curtains.Coil: coil.Combination: more than one control method used.?: not stated.Month_start. Survey start month.Month_end. Survey end month.Year_start. Survey start year.Year_end. Survey end year.Season_given. Rainy or dry season at the time of the survey, as indicated in the source.Season_calc. Rainy or dry season at the time of the survey, as derived from information on the general seasonal timings provided from the source or elsewhere.Species. The Anopheles species, species complex or subgroup. Also includes molecular form or chromosomal form if reported.ASSI. Additional species-specific information given in the source and provided as a free text field.Id_1. The method used to identify species.Chromosome banding: banding patterns on chromosomes.Cyto: cytological=cell/chromosomal characteristics.DNA: other DNA probing methods without PCR.M: morphological.Palpal ratio: palpal ratio.PCR: Polymerase Chain Reaction amplification techniques.Polytene chromosome: banding patterns on polytene chromosomes.PCR/DNA: PCR combined with DNA probe.Blank: unknown or unreported identification method.Id_2. The second method used to identify species, using same options as above.Biology_sampling_1. The sampling methods used to collect the specimens detailed in the VECTOR BIOLOGY section. Three methods can be listed. If more than three methods have been used, this is indicated as \u2018t\u2019 in the final column.MBI: Human biting indoorsMBO: Human biting outdoorsMB: Human biting (location not specified)ABI: Animal biting indoorsABO: Animal biting outdoorsAB: Animal biting (location not specified)HRI: House resting indoorsILT: Indoor light trapOLT: Outdoor light trapRO: Resting outdoors RO (pit): Resting outdoors in pitsRO (shelter): Resting outdoors in a shelterRO (ani-shelter): Resting outdoors in an animal shelterWinExit: Window exit trapsHBN: Human baited netABN: Animal baited netOdour-trap: Odour trapTent trap: Tent trapCol. Curtains: Colombian curtains?: Sampling method not specifiedBiology_sampling_2. As \u2018Biology_sampling_1\u2019.Biology_sampling_3. As \u2018Biology_sampling_1\u2019.Biology_sampling_n. \u2018t\u2019 indicates that there are more than three sampling methods.Parity_n. The number of parous females detected from the total number examined.Parity_total. The total number of females examined for parity.Parity_percent. The percentage of parous females in the sample: number of parous females/total number examined*100.Daily_survival_rate_percent. The estimated proportion of female mosquitoes alive on day d that are still alive on day d+1.Fecundity. The number of eggs laid per batch.Gonotrophic_cycle_days. The number of days for a female mosquito to go through the reproduce-feeding cycle.Infection_sampling_1. The sampling methods used to collect the specimens detailed in the VECTOR INFECTION RATE section. Three methods can be listed. If more than three methods have been used, this is indicated as \u2018t\u2019 in the final column. As \u2018Biology_sampling_1\u2019.Infection_sampling_2. As \u2018Infection_sampling_1\u2019.Infection_sampling_3. As \u2018Infection_sampling_1\u2019.Infection_sampling_n. \u2018t\u2019 indicates that there are more than three sampling methods.SR_dissection_n. The number of sporozoite infected females detected by dissection from the total number examined.SR_dissection _total. The total number of females dissected for sporozoites.SR_dissection_percent. The percentage of sporozoite infected females detected by dissection in the sample: number of infected females/total number examined*100.SR_CSP_n. The number of sporozoite infected females detected by circumsporozoite protein (CSP) analysis from the total number examined.SR_CSP_Pf_n. The number of P. falciparum specific sporozoite infected females detected by CSP analysis from the total number examined. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Pv_n. The number of P. vivax (variant not stated or combined) specific sporozoite infected females detected by CSP analysis from the total number examined. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Pv_210_n. The number of P. vivax variant 210 specific sporozoite infected females detected by CSP analysis from the total number examined. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Pv_247_n. The number of P. vivax variant 247 specific sporozoite infected females detected by CSP analysis from the total number examined. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Pm_n. The number of P. malariae specific sporozoite infected females detected by CSP analysis from the total number examined. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Po_n. The number of P. ovale specific sporozoite infected females detected by CSP analysis from the total number examined. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_total. The total number of females analysed for CSP.SR_CSP_percent. The percentage of sporozoite infected females detected by CSP analysis in the sample: number of infected females/total number analysed*100.SR_CSP_Pf_percent. The percentage of P. falciparum specific sporozoite infected females detected by CSP analysis in the sample: number of P. falciparum specific infected females/total number analysed*100. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Pv_percent. The percentage of P. vivax (variant not stated or combined) specific sporozoite infected females detected by CSP analysis in the sample: number of P. vivax specific infected females/total number analysed*100. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Pv_210_percent.The percentage of P. vivax variant 210 specific sporozoite infected females detected by CSP analysis in the sample: number of P. vivax variant 210 specific infected females/total number analysed*100. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Pv_247_percent.The percentage of P. vivax variant 247 specific sporozoite infected females detected by CSP analysis in the sample: number of P. vivax variant 247 specific infected females/total number analysed*100. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Pm_percent. The percentage of P. malariae specific sporozoite infected females detected by CSP analysis in the sample: number of P. malariae specific infected females/total number analysed*100. This field is only included for the Americas and the Asia-Pacific region.SR_CSP_Po_percent. The percentage of P. ovale specific sporozoite infected females detected by CSP analysis in the sample: number of P. ovale specific infected females/total number analysed*100. This field is only included for the Americas and the Asia-Pacific region.Oocyst_n. The number of oocyst infected females detected from the total number examined.Oocyst_total. The total number of females examined for oocysts.Oocyst_percent. The percentage of oocyst infected females detected in the sample: number of infected females/total number examined*100.EIR. The entomological inoculation rate. This is the number of infective bites per person per unit time.EIR_period. The unit of time relating to the EIR.Ext_incubation_period_days. The extrinsic incubation period of the malaria parasite in days.Indoor_HBR_sampling. The sampling method used to collect the mosquitoes from which indoor human biting rate is evaluated. As \u2018Biology_sampling_1\u2019.Indoor HBR. The indoor human biting rate; the number of bites per person per unit time.Outdoor_HBR_sampling. The sampling method used to collect the mosquitoes from which outdoor human biting rate is evaluated. As \u2018Biology_sampling_1\u2019.Outdoor HBR. The outdoor human biting rate; the number of bites per person per unit time.Combined_HBR_sampling_1. The sampling methods used to collect the mosquitoes from which human biting rate is evaluated where data are amalgamated from more than one method . Three methods can be listed. If more than three methods have been used, this is indicated as \u2018t\u2019 in the final column. As \u2018Biology_sampling_1\u2019.Combined_HBR_sampling_2. As \u2018Combined_HBR_sampling_1\u2019.Combined_HBR_sampling_3. As \u2018Combined_HBR_sampling_1\u2019.Combined_HBR_sampling_n. \u2018t\u2019 indicates that there are more than three sampling methods.Combined_HBR. The human biting rate evaluated from the data from amalgamated sampling methods.HBR_unit. The unit time for the HBR data.Indoor_host_sampling. The indoor sampling method used to collect the mosquitoes from which indoor host preference is evaluated. As \u2018Biology_sampling_1\u2019.Indoor_host_n. The number of mosquitoes positively indicating a measure of host preference from the total number collected indoors.Indoor_host_total. The total number of mosquitoes sampled indoors examined for measures of host preference.Indoor host. The measure of host preference from indoor sampled mosquitoes.Outdoor_host_sampling. The outdoor sampling method used to collect the mosquitoes from which outdoor host preference is evaluated. As \u2018Biology_sampling_1\u2019.Outdoor_host_n. The number of mosquitoes positively indicating a measure of host preference from the total number collected outdoors.Outdoor_host_total. The total number of mosquitoes sampled outdoors examined for measures of host preference.Outdoor host. The measure of host preference from outdoor sampled mosquitoes.Combined_host_sampling_1. The sampling methods used to collect the mosquitoes from which host preference is evaluated where data are amalgamated from more than one method, or where the method used is unclear. Three methods can be listed. If more than three methods have been used, this is indicated as \u2018t\u2019 in the final column. As \u2018Biology_sampling_1\u2019.Combined_host_sampling_2. As \u2018Combined_host_sampling_1\u2019.Combined_host_sampling_3. As \u2018Combined_host_sampling_1\u2019.Combined_host_sampling_n. \u2018t\u2019 indicates that there are more than three sampling methods.Combined_host_n. The number of mosquitoes positively indicating a measure of host preference collected by a combination of sampling methods.Combined_host_total. The total number of mosquitoes sampled by a combination of sampling methods, examined for measures of host preference.Combined_host. The measure of host preference from mosquitoes sampled by a combination of methods.Host_unit. Indicates the measure used to identify host preference.HBI (%): Human Blood Index as a percentage.ABI (%): Animal Blood Index as a percentage.HBI : Human Blood Index as a percentage calculated from data given in source.ABI : Animal Blood Index as a percentage calculated from data given in source.AI: \u2018Anthropophilic Index\u2019, a measure of attraction to humans not included above, for example % individuals attracted to human baited trap over total collected in both human and cattle baited trap, calculated from count data.NB. the unit \u2018HBI \u2019 and \u2018ABI \u2019 is where the source provides the raw data needed to calculated HBI or ABI but does not actually present these data. The unit indicates that the calculation has been done here.Other_host_sampling_1. The sampling methods used to collect the mosquitoes from which host preference is evaluated where additional data are presented examining host preference. Three methods can be listed. If more than three methods have been used, this is indicated as \u2018t\u2019 in the final column. As \u2018Biology_sampling_1\u2019.Other_host_sampling_2. As \u2018Other_host_sampling_1\u2019.Other_host_sampling_3. As \u2018Other_host_sampling_1\u2019.Other_host_sampling_n. \u2018t\u2019 indicates that there are more than three sampling methods.Other_host_n. The number of mosquitoes positively indicating a measure of host preference.Other_host_total. The total number of mosquitoes examined for measures of host preference.Other_host. The measure of host preferenceOther_host_unit. As \u2018Host_unit\u2019.Indoor_number_sampling_nights_biting. The sampling effort, in number of \u2018man nights\u2019, to collect the indoor biting data.Indoor_biting_sampling. The sampling method used to collect the indoor mosquitoes from which biting location preference is determined. As \u2018Biology_sampling_1\u2019.Indoor_biting_n. The number of mosquitoes found biting indoors.Indoor_biting_total. The total number of indoor and outdoor biting mosquitoes.Indoor_biting. The percentage or ratio of mosquitoes found biting indoors.Outdoor_number_sampling_nights_biting. The sampling effort, in number of \u2018man nights\u2019, to collect the outdoor biting data.Outdoor_biting_sampling. The sampling method used to collect the outdoor mosquitoes from which biting location preference is determined. As \u2018Biology_sampling_1\u2019.Outdoor_biting_n. The number of mosquitoes found biting outdoors.Outdoor_biting_total. The total number of indoor and outdoor biting mosquitoes.Outdoor_biting. The percentage or ratio of mosquitoes found biting outdoors.Indoor_outdoor_biting_units. Indicates the data unit for the indoor and outdoor biting data.I:O: Indoor to outdoor ratio.%: % biting indoors (or outdoors) given in source.%calc: % biting indoors (or outdoors) calculated from data given in source.NB. the unit \u2018%calc\u2019 is where the source provides the raw data for indoor and outdoor biting densities but does not calculate the percentage indoors/outdoors. The unit indicates that the calculation has been done here.Indoor_number_sampling_nights_biting_activity. The sampling effort, in number of \u2018man nights\u2019, relevant to indoor biting activity data.Indoor_1830_2130. \u2018t\u2019 given here if indoor biting activity peaks in the first quarter of the night, includes dusk biting.Indoor_2130_0030. \u2018t\u2019 given here if indoor biting activity peaks in the second quarter of the night.Indoor_0030_0330. \u2018t\u2019 given here if indoor biting activity peaks in the third quarter of the night.Indoor_0330_0630. \u2018t\u2019 given here if indoor biting activity peaks in the fourth quarter of the night, includes dawn biting.Outdoor_number_sampling_nights_biting_activity. The sampling effort, in number of \u2018man nights\u2019, relevant to outdoor biting activity data.Outdoor_1830_2130. \u2018t\u2019 given here if outdoor biting activity peaks in the first quarter of the night, includes dusk biting.Outdoor_2130_0030. \u2018t\u2019 given here if outdoor biting activity peaks in the second quarter of the night.Outdoor_0030_0330. \u2018t\u2019 given here if outdoor biting activity peaks in the third quarter of the night.Outdoor_0330_0630. \u2018t\u2019 given here if outdoor biting activity peaks in the fourth quarter of the night, includes dawn biting.Combined_number_sampling_nights_biting_activity. The sampling effort, in number of \u2018man nights\u2019, relevant to biting activity data where data are presented for both indoor and outdoor biting combined.Combined_1830_2130. \u2018t\u2019 given here if combined biting activity peaks in the first quarter of the night, includes dusk biting.Combined_2130_0030. \u2018t\u2019 given here if combined biting activity peaks in the second quarter of the night.Combined_0030_0330. \u2018t\u2019 given here if combined biting activity peaks in the third quarter of the night.Combined_0330_0630. \u2018t\u2019 given here if combined biting activity peaks in the fourth quarter of the night, includes dawn biting.Indoor_resting_sampling. Indoor sampling method used to collect the mosquitoes to assess indoor resting behaviour. As \u2018Biology_sampling_1\u2019.Indoor_unfed. Total number of unfed mosquitoes in the sample collected indoors.Indoor_fed. Total number of fed mosquitoes in the sample collected indoors.Indoor_gravid. Total number of gravid mosquitoes in the sample collected indoors.Indoor_total. Total number of mosquitoes in the sample collected indoors, including unfed, fed and gravid females.Outdoor_resting_sampling. Outdoor sampling method used to collect the mosquitoes to assess outdoor resting behaviour. As \u2018Biology_sampling_1\u2019.Outdoor_unfed. Total number of unfed mosquitoes in the sample collected outdoors.Outdoor_fed. Total number of fed mosquitoes in the sample collected outdoors.Outdoor_gravid. Total number of gravid mosquitoes in the sample collected outdoors.Outdoor_total. Total number of mosquitoes in the sample collected outdoors, including unfed, fed and gravid females.Other_resting_sampling. Sampling methods relevant to \u2018other\u2019 data. These columns are used when additional sampling is reported, for example if indoor and outdoor resting mosquitoes are listed in the previous sections, but the source also reports data from a third sampling method such as mosquitoes resting in animal sheds. As \u2018Biology_sampling_1\u2019.Other_unfed. Total number of unfed mosquitoes in the sample collected by additional/\u2018other\u2019 methods.Other_fed. Total number of fed mosquitoes in the sample collected by additional/\u2018other\u2019 methods.Other_gravid. Total number of gravid mosquitoes in the sample collected by additional/\u2018other\u2019 methods.Other_total. Total number of mosquitoes in the sample collected by additional/\u2018other\u2019 methods, including unfed, fed and gravid females.Resting_unit. The unit relating to the indoor, outdoor or other resting data.Count: raw count data.%: percentage.Per man hour: total number collected divided by time spent collecting in hours.Fed:gravid: fed to gravid ratio, total number of fed specimens divided by total number of gravid specimens.Citation. The data source.PubMed_ID. PubMed ID, when available.Bionomics data have been recorded by a large number of researchers, often using different sampling methods and reporting the data using different metrics. Due to the complicated and non-standard nature of the data, all data were reviewed and checked by a second data abstractor. The data were also checked to ensure that recorded values were within the possible ranges (for example between 0 and 100 for parameters recorded as percentages) and that all values had associated units.16 and vector occurrence9 the geolocation coordinates for these sites had already been confirmed. Coordinates were also plotted to ensure that they fall on land and in the correct country.To ensure all locations were accurately geo-located these were again confirmed by a second data abstractor. As many of the data sources identified in this project had previously been included in mapping projects on parasite rateThis is the first time that a comprehensive global database has been compiled of published bionomics data for the DVS of human malaria. The dataset described here will be of value to researchers when assessing the likely impact of vector control measures on malaria transmission and to policy makers when deciding how malaria control resources are allocated. Searching the dataset for data related to a specific DVS, geographic location or bionomic parameter will allow the user to quickly identify the available data, and to link this back to the original data source. In addition, this dataset can be used to identify the current knowledge gaps in the behaviour and life history characteristics of the DVS across their geographic ranges.The published studies did not use consistent units for each of the parameters of interest, and no attempt has been made to standardise the units as part of this work. It is vitally important that the values for each parameter are not treated as single dataset that used a common methodology and unit. Users are strongly advised to examine the sampling methods and units fields provided for each parameter when making use of the data.We will be using these data to test specific hypotheses relating to the DVS of Africa, including the presence of an east-west behavioural cline; whether insecticide control has caused a continent-wide non species-specific shift to exophagy amongst previously endophagic species; whether insecticide control has caused a continent-wide non species-specific shift in biting times amongst night biting species; and whether the DVS are really behaviourally flexible, or if the observed plasticity actually relates to different sub-species or sibling species within a complex.How to cite this article: Massey, N.C. et al. A global bionomic database for the dominant vectors of human malaria. Sci. Data 3:160014 doi: 10.1038/sdata.2016.14 (2016)."} +{"text": "Damastes. Molecular data include the nuclear genes histone H3 (H3) and 28S ribosomal RNA (28S rRNA), mitochondrial genes cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) were sequenced via Sanger sequencing by J.A. Gorneau. Life history data were collected in the field and in the lab by L.S. Rayor and include data on age at sexual maturity, lifespan, social classification, egg sac shape, how the egg sac is attached or carried, retreat location, retreat modification, retreat size relative to adult female body size, approximate mean body mass, and mean cephalothorax width. Morphological data on Deleninae and one Damastes sp. were scored by C.A. Rheims and includes information on the following characters: prosoma , anterior median eye (AME) diameter, AME-AME and PME-PME interdistances), male palp (embolic sclerite (PS), conductor sclerotized base (SB), tegular apophysis (TA), flange (f)) and female epigyne and vulva , spermathecal sacs (SS)). These data were used to clarify relationships among the Australian endemic Deleninae, as well as global patterns in sparassid evolution. The data demonstrate phylogenetic patterns in life history, social evolution, and natural history among the sparassids. These data contribute to future comparative research on sparassid systematics, evolution, and behavior. This data article complements a research article published in Molecular Phylogenetics and Evolution This article on biodiversity and life history data in huntsman spiders (Araneae: Sparassidae) includes the following: molecular data deposited on GenBank for 72 individuals representing 27 species in seven subfamilies, life history and behavioral data on 40 huntsman species from over two decades of observations, and morphological data for 26 species in the subfamily Deleninae as well as an undescribed representative of the genus Specifications Table\u2022While focused molecular investigations and life history datasets are not uncommon, providing an integrated dataset with both molecular and life history data allows for examination of trends in the context of evolution.\u2022These data will be of particular use to arachnologists, evolutionary biologists, systematists, behavioral ecologists, and biogeographers looking to explore trends in comparative social evolution and life history, morphology, and more generally, the evolution of the Sparassidae and Australian endemism.\u2022Molecular data deposited in GenBank will be available for future studies of molecular evolution and phylogenetic analyses, as well as for species-based identification using the barcode gene cytochrome c oxidase subunit I (COI).\u2022Voucher exemplar specimens for molecular, morphological, and behavioral data are deposited in museums for replicability and additional analysis, including sequencing of additional loci in the future.\u2022Morphological and behavioral data will inform individuals designing their own character matrices for members of the Sparassidae, as well as provide a basis from which to designate and define certain life history characteristics.\u2022Long-term datasets presenting total evidence character traits are a rich source for researchers to design their own character matrices for comparative study.1These data present a detailed compilation of molecular, morphological, life history, and behavioral character states for representatives of 37 of the 89 genera of Sparassidae, the eleventh-most speciose spider family, and focus on taxa endemic to Australia. We provide tables including accession numbers for sequences contributed to GenBank, morphological and life history character matrices, and input files and code for each analysis. We also include R code in R Markdown (.Rmd) format for the phylogenetic comparative methods used in Gorneau et\u00a0al. 22.1Primers_and_PCR_protocols.xlsx \u2014 Excel file with information on primers used in this study. C1-N-2776 was used for samples for which the HCO/LCO combination of primers did not amplify adequate DNA. Second sheet of file includes information on PCR protocols used.Voucher_information.xlsx \u2014 Excel file with information on vouchers representing exemplars for the molecular data contributed in this study. Specimens deposited in the National Museum of Natural History arachnology collections.New_data_generated_GenBank.xlsx \u2014 Excel file that corresponds to GenBank_sequences.xlsx \u2014 Excel file with accession numbers for sequences downloaded from GenBank.2.2IQTREE_Sparassidae_10_Nov_2021.phy \u2014 Input file for IQ-TREE inference containing concatenated alignment for all four gene sequences of taxa used in this analysis.IQTREE_partition.nex \u2014 Input NEXUS file for IQ-TREE inference containing details on partitioning of four genes in concatenated dataset IQTREE_Sparassidae_10_Nov_2021.phy.IQTREE_10_Nov_2021.log \u2014 Output .log file for IQ-TREE inference containing details of run progress and models of molecular evolution selected.IQTREE_10_Nov_2021.contree \u2014 Output IQ-TREE phylogeny with results of 10,000 ultrafast bootstrap replicates as nodal support values.2.3RAxML_Sparassidae_10_November.phy.raxml.startTree \u2014 Starting tree as inferred by IQ-TREE. The same tree file as IQTREE_10_Nov_2021.contree.RAxML_22_Nov_2021_partition.txt \u2014 inference containing details on partitioning of four genes in concatenated dataset.RAxML_Sparassidae_10_Nov_2021.phy \u2014 Input file for RAxML inference containing concatenated alignment for all four gene sequences of taxa used in this analysis.RAxML_Sparassidae_10_Nov_2021.raxml.log \u2014 Output .log file for RAxML inference containing details of run progress and models of molecular evolution selected.RAxML_Sparassidae_10_Nov_2021.raxml.bestTree \u2014 Best maximum likelihood tree as inferred by RAxML with bootstrap values as nodal support values.2.4MrBayes_21_Dec_2021.nex \u2014 Input NEXUS file for MrBayes inference with concatenated dataset of four genes, MrBayes block with information about sequence partitions and models used, as well as IQ-TREE phylogeny used as starting tree.MrBayes_21_Dec_2021_stout.txt \u2014 Output file with information on MrBayes run including average standard deviation of split frequencies for duration of run.MrBayes_21_Dec_2021.tre \u2014 Bayesian inference phylogeny output of MrBayes with posterior probability values as nodal support values.2.5Tree_convergence_huntsman.Rmd \u2014 R Markdown file with code to analyze convergence between IQ-TREE inferences and MrBayes and RAxML inferences. Employs the use of the phytools R package.2.6BEAST_28_Jan_2022_mono.xml \u2014 Input file for BEAST 2.6.0 containing information about priors for divergence dating including models of molecular evolution and fossil outgroup calibrations. This file was run independently three times through BEAST to generate three independent .log and files that were then combined into BEAST_28_Jan_2022_combined_runs_123.log in the program LogCombiner.BEAST_28_Jan_2022_combined_runs_123.log \u2014 The combined .log files for the three independent runs of BEAST. Contains information about effective sample sizes to determine the quality of the run in BEAST 2.6.0. Examined using Tracer v.1.7.1BEAST_28_Jan_combined_123_TA_25.tre \u2014 Maximum clade credibility tree from three independent BEAST runs identified by TreeAnnotator, with input merged .trees files from three runs and burn-in percentage 25%. Node heights set at keep target heights.2.7Life_history_data.xlsx \u2014 Excel file containing two spreadsheets: one named Character_States with information about character states for nine life history characters, and one named Character_Matrix with character matrix of life history attributes.lh_matrix.csv \u2014 .csv file with same character matrix from Life_history_data.xlsx Excel file, for use in stochastic character mapping and D-test code in Stochastic_character_mapping_and_D-test_huntsman.Rmd.lifeHistorysubName.csv \u2014 .csv file with substitutions of names from IQ-TREE phylogeny tip labels to names for stochastic character mapping; essentially removes specific identifiers for ease of visualization in Stochastic_character_mapping_and_D-test_huntsman.Rmd code.Stochastic_character_mapping_and_D-test_huntsman.Rmd \u2014 R Markdown file containing code for stochastic character mapping of life history and D-test correlation analysis. Requires the use of the following R packages: corHMM, phylotools, and phytools. Also available on GitHub.Stochastic_character_mapping_model_selection.csv \u2014 .csv file with output of model selection including Akaike information criterion (AIC) values from Stochastic_character_mapping_and_D-test_huntsman.Rmd code among the following models: equal rates (ER), symmetric (SYM), and all rates different (ARD) for all life history characters.D_test_p_values.xlsx \u2014 Excel file with output partitioned by individual sheet showing the p-values of the D-test analysis in a pairwise matrix. The numeric codes for character states correspond to the following file: Life_history_data.xlsx.Stochastic_character_mapping_posterior_probabilities.xlsx \u2014 Posterior probabilities of stochastic character mapping analyses organized by character and then by individual node. Node numbers correspond to Stochastic_character_mapping_w_node_numbers.Stochastic_character_mapping_w_node_numbers.pdf \u2014 PDF file with results of stochastic character mapping analyses with node numbers so Stochastic_character_mapping_posterior_probabilities.xlsx can be consulted to examine specific posterior probabilities for specific life history characters by node.2.8Morphology_data.xlsx \u2014 Excel file with four sheets: Character_States describing the characters and character states in the Character_Matrix sheet; the Character_Matrix sheet, which is the basis for the input file morpho_matrix.csv; Morphological_Vouchers sheet with information on specimens directly examined for morphological character scoring; and Morpohology_From_Literature for species scored with the use of literature, either instead of direct examination or in tandem with direct observation.morpho_matrix.csv \u2014 .csv file of character matrix from Morphology_data.xlsx slightly altered such that the questionable characters were marked as the characters they are likely to be for ease of plotting using the code in Morphology_huntsman.Rmd. The uncertainty was then readded in Adobe Illustrator.morphosubName.csv \u2014 .csv file with substitutions of names from IQ-TREE phylogeny tip labels to names for mapping of morphological data matrix from morpho_matrix.csv; essentially removes the specific identifiers for ease of visualization in Stochastic_character_mapping_and_D-test_huntsman.Rmd code.Morphology_huntsman.Rmd \u2014 R Markdown file containing code for mapping data matrix of morphological data Deleninae\u00a0+\u00a0Damastes. Input files: morpho_matrix.csv, morphosubName.csv, IQTREE_10_Nov_2021.contree. Employs the use of the following packages: corHMM, phylotools, phytools, and RColorBrewer. Also available on GitHub.Male_genitalia.tif \u2013 Male, left palp, ventral view. A: Beregama cordata . B: Delena cancerides Walckenaer, 1837. C: Holconia flindersi Hirst, 1991. D: Isopeda villosa L. Koch, 1875. E: Isopedella leai . F: Neosparassus salacius . G: Pediana regina . H: Typostola barbata . I: Zachria flavicoma L. Koch, 1875. Scale lines: 1 mm. F\u00a0=\u00a0tegular flange; PS\u00a0=\u00a0palpal embolic sclerite; SB\u00a0=\u00a0conductor sclerotized base; TA\u00a0=\u00a0Deleninae tegular apophysisFemale_genitalia.tif \u2013 Female, genitalia. A\u2013B: Delena cancerides Walckenaer, 1837 . C\u2013D: Holconia flindersi Hirst, 1991 . E\u2013F: Isopeda villosa L. Koch, 1875 . G\u2013H: Isopedella conspersa . I\u2013J: Isopedella leai . K\u2013L: Pediana regina . M\u2013N: Typostola barbata . O\u2013P: Zachria flavicoma L. Koch, 1875 . Scale lines: 1 mm. ES\u00a0=\u00a0epigynal sclerite; SS\u00a0=\u00a0spermathecal sac.33.1Gryllodes sigillatus and Acheta domesticus), houseflies (Musca domestica), calliphorid flies , and fruit flies (Drosophila spp.). A table with specimen information and voucher information for exemplars of molecular work is included in the Zenodo dataset (Voucher_information.xlsx). Legs from individuals were stored in ethanol and placed in a -20\u00b0C freezer prior to DNA extraction.Behavior and life history traits for each species were observed in the field and/or laboratory. Spiders were fed a diet of crickets (3.2Primers_and_PCR_protocols.xlsx). PCR products were visualized using gel electrophoresis on a 1% agarose gel with 2 ml of DNA and 2 ml GelRed dye under a BioRad UV transilluminator and imaged using the ImageLab\u2122 software . PCR products were purified using ExoSAP-IT to remove remaining primers and dNTPs. Purified PCR samples were quantified using a Qubit 4 fluorometer and Biotium High Sensitivity AccuGreen dye to determine the quantity of DNA after purification and immediately prior to sequencing. Samples were cycle-sequenced in the forward and reverse directions and diluted based on the DNA concentration for full-service (post-PCR purification) sequencing at the Cornell Genomics Facility .A total of 54 samples were extracted in fall 2019 by JAG using the QIAGEN DNeasy PowerSoil Kit . A single adult leg or whole bodies of immatures were used for DNA extraction. An additional 30 samples were extracted by Dr. Ingi Agnarsson's lab group at the University of Vermont using the QIAGEN DNeasy Tissue Kit . DNA from these extractions was then amplified using polymerase chain reaction (PCR) on a BioRad 96-well C1000 Touch Thermal Cycler for two mitochondrial genes (cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) and two nuclear genes (histone H3 (H3) and 28S ribosomal RNA (28S rRNA). In short, PCR reactions involved 6.5 mL water, 12.5 mL EconoTaq\u00ae PLUS Master Mix , 2.5 mL each of forward and reverse primer (10 mM), and 1 mL of DNA for each 25 mL reaction. The primers used for each gene in this study, and PCR conditions for each gene can be found in the Zenodo dataset (3.3GenBank_sequences.xlsx).In addition, sequences for a total of 201 samples were downloaded from GenBank , Uloborus diversus Marx 1898 ), Oecobius Blackwall 1862 (Oecobiidae), Uroctea durandi ((Latreille 1809); Oecobiidae), Peucetia viridans ((Hentz 1832); Oxyopidae), Dolomedes tenebrosus Hentz 1844 (Pisauridae), Salticus scenicus , Selenops muehlmannorum J\u00e4ger & Praxaysombath 2011 (Selenopidae), and Tibellus chamberlini Gertsch 1933 (Thomisidae). The IQ-TREE inference was used as a starting tree for inferences in RAxML and MrBayes with the concatenated sequences partititioned by gene to see if the tree topologies were comparable Aligned sequences were partitioned and exported from Mesquite in .phy format for analysis in IQ-TREE version 1.6.12 3.6Zamilia aculeopectens Wunderlich 2015 (Oecobiidae) for the node representing Oecobiidae, Oxyopes succini Petrunkevitch 1958 (Oxyopidae) for Oxyopidae\u00a0+\u00a0Pisauridae, Almolinus ligula Wunderlich 2004 for the node containing the outgroups Salticidae\u00a0+\u00a0Thomisidae, and \u2018Selenops\u2019 sp. indet. Wunderlich 1988 (Selenopidae) for the node with outgroups Selenopidae sister to Salticidae\u00a0+\u00a0Thomisidae Zamilia aculeopectens, an exponential distribution was set with an offset of 98.17 and a mean of 0.32. For Oxyopes succini and Almolinus ligula, an exponential distribution was set with an offset of 43.0 my, and a mean of 1.3. For \u2018Selenops\u2019 sp. indet., an exponential distribution was set with an offset of 53.0 my, and a mean of 0.8. As such, these analyses were conducted in accordance with the latest work on fossil calibration of phylogenies by Magalh\u00e3es et\u00a0al. An estimation of divergence time was conducted in BEAST using fossil calibrations recommended for use by Magalh\u00e3es et\u00a0al. 3.7Life_history_data.xlsx).From 2002 \u2013 2021, LSR collected life history and behavioral data from 40 sparassid species, with emphasis on the endemic Australian Deleninae. Data was collected in the field and in her laboratory at Cornell University (USA). Life history variables included: mother-offspring dynamics and sociality, egg sac structure, how the egg sac was attached to the retreat or carried, retreat type, modifications to the retreat, adult female body mass and cephalothorax width, age at sexual maturity, and lifespan. These character states are outlined in the Zenodo dataset , \u2018subsocial\u2019 species dispersed between four \u2013 five weeks (third or fourth instar), \u2018prolonged subsocial\u2019 species remained in mother-offspring groups for five to twelve months prior to dispersing.Three types of egg sacs were observed in the species studied: \u2018plastered\u2019 with a ground sheet silked onto the substrate and the rest of the sac built onto that attached sheet, a \u2018lenticular\u2019 (a relatively flat round disc), and a \u2018spherical\u2019 shape. Egg sacs varied in support structure among the sparassids studied: egg sacs were either \u2018completely adhered\u2019 to the substrate and immobile, \u2018tethered\u2019 by guy-lines of silk and relatively immobile, or actively \u2018carried\u2019 by the adult female under her venter. Adhered egg sacs were only accessible on one side, while tethered and carried egg sacs were relatively accessible on both sides. The spiders in this analysis used retreats under tree \u2018bark\u2019 or in small hollows in trees, \u2018rocks\u2019, in \u2018dead foliage\u2019, in \u2018living foliage\u2019, or in the open without a retreat (\u2018in the open\u2019). Modifications included either \u2018silk bonds\u2019 whch are repeated short silken swaths that bind the bark/rock/leaves together, effectively limiting access to the retreat, or a small \u2018silken cage\u2019 that completely surrounds the female and her egg sac forming a retreat, or \u2018none\u2019 in which there was no silk modification of the retreat.Additionally, parameters of body size , age of female at sexual maturity, and average life span in captivity were collected.3.8To investigate the evolution of life history in the context of phylogeny, the inferred IQ-TREE phylogeny tips were trimmed using the keep.tip function in the R package phytools to the 40 species for which life history data as collected by LSR existed 3.9Damastes were tabulated in a matrix. Character scoring was based on direct examination of available specimens , and when unavailable, from literature Male_genitalia.tif). Female epigynes were dissected and illustrated in ventral and dorsal views. In dorsal view illustrations, the hyaline part of the copulatory ducts was omitted .Relevant morphological data for the endemic Australian Deleninae and This work is consistent with the ethical requirements and standards for publication. This study did not include any human subjects, data collected from social media platforms, or animal experiments requiring approval. The authors have no conflict of interest to disclose.Jacob A. Gorneau: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Software, Validation, Visualization, Writing \u2013 original draft, Writing \u2013 review & editing. Linda S. Rayor: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Writing \u2013 original draft, Writing \u2013 review & editing. Cristina A. Rheims: Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Resources, Supervision, Validation, Writing \u2013 review & editing. Corrie S. Moreau: Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Writing \u2013 review & editing.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "Using genomics, bioinformatics and statistics, herein we demonstrate the effect of statewide and nationwide quarantine on the introduction of SARS-CoV-2 variants of concern (VOC) in Hawai\u2019i. To define the origins of introduced VOC, we analyzed 260 VOC sequences from Hawai\u2019i, and 301,646 VOC sequences worldwide, deposited in the GenBank and global initiative on sharing all influenza data (GISAID), and constructed phylogenetic trees. The trees define the most recent common ancestor as the origin. Further, the multiple sequence alignment used to generate the phylogenetic trees identified the consensus single nucleotide polymorphisms in the VOC genomes. These consensus sequences allow for VOC comparison and identification of mutations of interest in relation to viral immune evasion and host immune activation. Of note is the P71L substitution within the E protein, the protein sensed by TLR2 to produce cytokines, found in the B.1.351 VOC may diminish the efficacy of some vaccines. Based on the phylogenetic trees, the B.1.1.7, B.1.351, B.1.427, and B.1.429 VOC have been introduced in Hawai\u2019i multiple times since December 2020 from several definable geographic regions. From the first worldwide report of VOC in GenBank and GISAID, to the first arrival of VOC in Hawai\u2019i, averages 320 days with quarantine, and 132 days without quarantine. As such, the effect of quarantine is shown to significantly affect the time to arrival of VOC in Hawai\u2019i. Further, the collective 2020 quarantine of 43-states in the United States demonstrates a profound impact in delaying the arrival of VOC in states that did not practice quarantine, such as Utah. Our data demonstrates that at least 76% of all definable SARS-CoV-2 VOC have entered Hawai\u2019i from California, with the B.1.351 variant in Hawai\u2019i originating exclusively from the United Kingdom. These data provide a foundation for policy-makers and public-health officials to apply precision public health genomics to real-world policies such as mandatory screening and quarantine. Hawai\u2019i has experienced unique epidemics within the coronavirus disease 2019 (COVID-19) pandemic, in that Pacific Islanders, which account for 4% of the population, once accounted for nearly 30% of COVID-19 cases Reviewers' comments:Reviewer's Responses to Questions Comments to the Author1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********\u00a0 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********\u00a0 3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********\u00a0 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********\u00a0 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0This paper focuses on analyzing the VOCs that have been found in Hawai\u00ed and performs an analysis of the VOC variants to determine their point of origin. The authors also analyze the case numbers during quarantine and post quarantine in an attempt to demonstrate the efficacy of quarantine in delaying the entry of VOC to Hawai\u00ed, which was, (unsurprisingly) confirmed through analysis and comparison with Utah.The strength of the paper is the thoroughness of the analysis of the genomic data available for the VOCs in Hawaii and the comparison to the VOCs worldwide from banked genomic data. The methods and the analysis of the genomic data is very well presented and explained.What I feel the authors could improve is the background information to help the general reader better understand the significance and impact of the data presented. In particular, I would suggest that the authors rewrite the introduction to describe the general epidemiological trends of COVID infection in Hawai\u00ed, and also provide more details of what is meant by \u2018quarantine\u2019 as this has different guidelines in different countries. This would then provide the readers with a better background heading into the core findings and be able to better appreciate the findings. In the intro line 52 to 63 reads like content better suited to the discussion than the introduction?I would also suggest that in terms of the discussion there are a few other points the authors may wish to briefly mention in the writing and discussion \u2013 it is of course of great epidemiological significance to identify the source of infection to understand the pattern of infection and global spread, however I would argue that the authors assertions (line 467) that the source of infection must be ascertained before steps can be taken may be overstating the case as by that time the case is already in, and it may be more appropriate to argue that understanding the origin of cases may be a reason to look at the processes in that country or in the infection control measures in place in that country for review? With regard to line 367 where the authors have highlighted that the highest number came from California I would suggest inferring some suggestions as to why \u2013 did California have different regulations on COVID control? Or was it because more people entering Hawai\u00ed were from California? Ideas about this then provide more guidance to public health measures at appropriate points in the chain of transmission. In addition, while limiting case numbers is of paramount concern, economic and social considerations also are a factor in deciding on the measure to implement - meaning the data and statistics here are a key consideration, but they are not the only ones.Reviewer #2:\u00a0dear author,this paper is much appreciable and it gives the origin and spread of variants of SARS Cov-2 in different areas.methods should have been simplified with flowchart or something. then it would be easy to reproduce by some other .**********\u00a0 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Yes:\u00a0Priyia PusparajahReviewer #1:\u00a0Reviewer #2:\u00a0No**********https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.
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O\u2019Toole \u00c1, Scher E, Underwood A, Jackson B, Hill V, McCrone J, et al. pangolin: lineage assignment in an emerging pandemic as an epidemiological tool. In: PANGO lineages [Internet]. 2021 [cited 11 Mar 2021]. Available: Has been published since our original submission and has been replaced with:6. O\u2019Toole \u00c1, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution. 2021;7: veab064. doi:10.1093/ve/veab064https://www.R-project.org/16. R Core Team. R: A language and environment for statistical ## computing. [Internet]. Vienna, Austria: R Foundation for Statistical Computing; 2020. Available from: Has been updated to: https://www.R-project.org/16. R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020. Available: 17. Wickham H. ggplot2: Elegant Graphics for Data Analysis. 2nd ed. 2016. Cham: Springer International Publishing\u202f: Imprint: Springer; 2016. 1 p. (Use R!).Has been updated to:https://ggplot2.tidyverse.org17. Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York; 2016. Available from: 28. Scobie H. Update on Emerging SARS-CoV-2 Variants and Vaccine Considerations. 2021 May 12;30.Has been updated to:https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2021-05-12/10-COVID-Scobie-508.pdf28. Scobie H. Update on Emerging SARS-CoV-2 Variants and Vaccine Considerations. 2021 May 12. Available from: 33. Jangra S, Ye C, Rathnasinghe R, Stadlbauer D, PVI study group, Krammer F, et al. The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. Infectious Diseases (except HIV/AIDS); 2021 Jan. doi:10.1101/2021.01.26.21250543Has been published since our original submission and has been replaced with:33. Jangra S, Ye C, Rathnasinghe R, Stadlbauer D, Personalized Virology Initiative study group, Krammer F, et al. SARS-CoV-2 spike E484K mutation reduces antibody neutralisation. Lancet Microbe. 2021;2: e283\u2013e284. doi:10.1016/S2666-5247(21)00068-935. Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, et al. Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. medRxiv. 2021; 2021.03.07.21252647. doi:10.1101/2021.03.07.21252647Has been published since our original submission and has been replaced with:35. Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell. 2021;184: 3426-3437.e8. doi:10.1016/j.cell.2021.04.02536. Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S, et al. The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell (Cambridge). 2020;182: 1284-1294.e9. doi:10.1016/j.cell.2020.07.012Has been updated to:36. Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S, et al. The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell. 2020;182: 1284-1294.e9. doi:10.1016/j.cell.2020.07.01238. Arag\u00f3n TJ, Newsom G. California Department of Public Health - Health Alert: Concerns re: the Use of Bamlanivimab Monotherapy in the Setting of SARS-CoV2 Variants. 2021; 4.Has been updated to:http://publichealth.lacounty.gov/eprp/lahan/alerts/CAHANBamlanivimabandSARSCoV2Variants.pdf38. Arag\u00f3n TJ, Newsom G. California Department of Public Health - Health Alert: Concerns re: the Use of Bamlanivimab Monotherapy in the Setting of SARS-CoV2 Variants. 2021. Available from: The following has been removed due to being revoked:39. Moruf A. Fact Sheet For Health Care Providers Emergency Use Authorization (Eua) Of Bamlanivimab. 2021; 26._________________________________________________________________________[Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.Reviewer #1: YesReviewer #2: Yes2. Has the statistical analysis been performed appropriately and rigorously?Reviewer #1: YesReviewer #2: Yes3. Have the authors made all data underlying the findings in their manuscript fully available?The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.Reviewer #1: YesReviewer #2: Yes4. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1: YesReviewer #2: Yes5. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. _________________________________________________________________________Reviewer 1:Comment 1:Reviewer #1: This paper focuses on analyzing the VOCs that have been found in Hawai\u00ed and performs an analysis of the VOC variants to determine their point of origin. The authors also analyze the case numbers during quarantine and post quarantine in an attempt to demonstrate the efficacy of quarantine in delaying the entry of VOC to Hawai\u00ed, which was, (unsurprisingly) confirmed through analysis and comparison with Utah.The strength of the paper is the thoroughness of the analysis of the genomic data available for the VOCs in Hawaii and the comparison to the VOCs worldwide from banked genomic data. The methods and the analysis of the genomic data is very well presented and explained.Response 1:We thank the reviewer for these comments._________________________________________________________________________Comment 2:What I feel the authors could improve is the background information to help the general reader better understand the significance and impact of the data presented. In particular, I would suggest that the authors rewrite the introduction to describe the general epidemiological trends of COVID infection in Hawai\u00ed, and also provide more details of what is meant by \u2018quarantine\u2019 as this has different guidelines in different countries. This would then provide the readers with a better background heading into the core findings and be able to better appreciate the findings. In the intro line 52 to 63 reads like content better suited to the discussion than the introduction?Response 2:We thank the reviewer for these comments. In the revised manuscript, lines 52 to 63 have been moved to the discussion and we have addressed the remaining comments as follows:\u201cHawaii has experienced unique epidemics within the coronavirus disease 2019 (COVID-19) pandemic, in that Pacific Islanders, which account for 4% of the population, once accounted for nearly 30% of COVID-19 cases.(1) Further, the Japanese population of Hawaii currently accounts for 6% of the population and experiences 15% of COVID-19 cases. White persons, in contrast, account for 37% of the population and 25% of the cases.(2) As such, a heightened need exists to understand SARS-CoV-2 introduction into Hawaii and the effect of public policy measures. Early in the pandemic, in an attempt to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Hawaii, like 42 other states in the United States, implemented a quarantine defined by \u201cStay-at-Home\u201d orders. State-at-Home orders directed residents to stay inside homes except for essential needs and closed operations of non-essential businesses.(3) In addition to this public policy, more than 22,300 SARS-CoV-2 sequences submitted to GISAID and GenBank originate from Hawaii to facilitate further studies.\u201d_________________________________________________________________________Comment 3:I would also suggest that in terms of the discussion there are a few other points the authors may wish to briefly mention in the writing and discussion \u2013 it is of course of great epidemiological significance to identify the source of infection to understand the pattern of infection and global spread, however I would argue that the authors assertions (line 467) that the source of infection must be ascertained before steps can be taken may be overstating the case as by that time the case is already in, and it may be more appropriate to argue that understanding the origin of cases may be a reason to look at the processes in that country or in the infection control measures in place in that country for review? Response 3:We thank the reviewer for this discussion and argument. We have made the statement less assertive and included the reasoning provided in this comment in the revised manuscript as follows: \u201cPolicy-makers should first ascertain the source of the spread before they can control and limit the spread of future VOC. By understanding the source responsible for the highest number of cases, policy-makers can look at interactions between that area and the host area, the policies in that area, identify the reasons for the spread, and address those reasons with appropriate measures both in the present and in future COVID-19 waves.\u201d_________________________________________________________________________Comment 4:With regard to line 367 where the authors have highlighted that the highest number came from California I would suggest inferring some suggestions as to why \u2013 did California have different regulations on COVID control? Or was it because more people entering Hawai\u00ed were from California? Ideas about this then provide more guidance to public health measures at appropriate points in the chain of transmission. In addition, while limiting case numbers is of paramount concern, economic and social considerations also are a factor in deciding on the measure to implement - meaning the data and statistics here are a key consideration, but they are not the only ones.Response 4:We thank the reviewer for this comment and suggestion. We have addressed this in the revised manuscript as follows:In 2020, 27% of all travelers to Hawai\u2019i originated from California, with 53% coming from the West Coast. Further, Hawai\u2019i residents traveled to the West Coast, specifically Las Vegas, Nevada. However, the following is additional information:\u201cFrom the analysis of the SARS-CoV-2 sequence data, a policy-maker could reasonably consider focusing on additional screening, contact tracing, and quarantine efforts among visitors and residents arriving from and traveling to the West Coast of the continental United States. There are several possible reasons for this vast majority of SARS-COV-2 influx from the US West Coast. In 2020, 27% of all travelers to Hawaii originated from California, with 53% coming from the West Coast. California's biggest domestic traveling demographic is in-state travel, meaning that the state likely spreads SARS-CoV-2 efficiently and uniformly within California.(44) Second, Hawaii residents traveling to the West Coast and returning home once infected with the virus. The first case of COVID-19 in Hawaii and the first case of the Delta variant were brought to Hawaii by residents (both vaccinated and unvaccinated) returning from travel .(45\u201347) Additionally, 62% of early cases in Hawaii were in either visitors to Hawaii or returning residents.(47) There are presumably additional factors that participated in the 76% of SARS-CoV-2 VOC attributable to California. Regardless, policymakers must evaluate these possible collective factors and social and economic implications together to determine the appropriate public-policy action.\u201d _________________________________________________________________________Reviewer 2:Reviewer #2: dear author,Comment 1:this paper is much appreciable and it gives the origin and spread of variants of SARS Cov-2 in different areas.Response 1:We thank the reviewer for this comment. _________________________________________________________________________Comment 2:methods should have been simplified with flowchart or something. then it would be easy to reproduce by some other .Response 2:We thank the reviewer for this comment and have added a flowchart as a figure and have uploaded the method to protocols.io. _________________________________________________________________________AttachmentRebuttal_09.26.2022.docxSubmitted filename: Click here for additional data file. 15 Nov 2022Genomic Analysis of SARS-CoV-2 Variants of Concern Circulating in Hawai\u2019i to Facilitate Public-Health PoliciesPONE-D-21-19856R1Dear Dr. Maison,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Ming ZhangAcademic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments: 21 Nov 2022PONE-D-21-19856R1 Genomic Analysis of SARS-CoV-2 Variants of Concern Circulating in Hawai\u2019i to Facilitate Public-Health Policies Dear Dr. Maison:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Ming Zhang Academic EditorPLOS ONE"} +{"text": "Chromatin loops are an essential factor in the structural organization of the genome; however, their detection in Hi-C interaction matrices is a challenging and compute-intensive task. The approach presented here, integrated into the HiCExplorer software, shows a chromatin loop detection algorithm that applies a strict candidate selection based on continuous negative binomial distributions and performs a Wilcoxon rank-sum test to detect enriched Hi-C interactions.HiCExplorer\u2019s loop detection has a high detection rate and accuracy. It is the fastest available CPU implementation and utilizes all threads offered by modern multicore platforms.in situ Hi-C data contain a large amount of noise; achieving better agreement between loop calling algorithms will require cleaner Hi-C data and therefore future improvements to the experimental methods that generate the data.HiCExplorer\u2019s method to detect loops by using a continuous negative binomial function combined with the donut approach from HiCCUPS leads to reliable and fast computation of loops. All the loop-calling algorithms investigated provide differing results, which intersect by HiCCUPS is part of the software Juicer,1 and the implementation requires a general-purpose GPU (GPGPU), which imposes a barrier for users without access to Nvidia GPUs. However, an experimental CPU-based implementation has also been released. Algorithms such as iterative correction and eigenvector decomposition (ICE) ; German Federal Ministry of Education and Research [031 L0101C de.NBI-epi awarded to B.G.]. R.B. was supported by the German Research Foundation (DFG) under Germany\u2019s Excellence Strategy (CIBSS\u2013EXC-2189\u2013Project ID 390939984). We acknowledge support by the Open Access Publication Fund of the University of Freiburg for contributing to the publication fees.J.W. designed and implemented the presented algorithm and wrote the manuscript. R.B. contributed to the manuscript. B.G. contributed to the manuscript.giac061_GIGA-D-21-00069_Original_SubmissionClick here for additional data file.giac061_GIGA-D-21-00069_Revision_1Click here for additional data file.giac061_GIGA-D-21-00069_Revision_2Click here for additional data file.giac061_GIGA-D-21-00069_Revision_3Click here for additional data file.giac061_GIGA-D-21-00069_Revision_4Click here for additional data file.giac061_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giac061_Response_to_Reviewer_Comments_Revision_1Click here for additional data file.giac061_Response_to_Reviewer_Comments_Revision_2Click here for additional data file.giac061_Reviewer_1_Report_Original_SubmissionBorbala Mifsud -- 3/22/2021 ReviewedClick here for additional data file.giac061_Reviewer_1_Report_Revision_1Borbala Mifsud -- 7/5/2021 ReviewedClick here for additional data file.giac061_Reviewer_2_Report_Original_SubmissionFeng Yue -- 4/4/2021 ReviewedClick here for additional data file.giac061_Reviewer_2_Report_Revision_1Feng Yue -- 7/19/2021 ReviewedClick here for additional data file.giac061_Reviewer_3_Report_Revision_2Aleksandra P\u00c4\u2122kowska -- 11/23/2021 ReviewedClick here for additional data file.giac061_Supplemental_FilesClick here for additional data file."} +{"text": "That is, how many changes and options should a sequence script allow before the more efficient choice is to branch out into multiple scripts.\u2022Efforts in Accessible MRI can use the data, acquired using open-source sequences on major commercial scanners, as a reference point for experiments using the same sequences on new hardware.1See 1.11.1.1In the main folder (developer_main_site/IRSE), the sequence implementation is presented in a Jupyter notebook (write_irse_interleaved_split_grad.ipynb). In addition, a developer PDF form (IRSE_DEV_QUALITATIVE.pdf) includes information on the test experiment including sequence parameters, hardware setup, example image, image quality measures, and safety metrics.x'' and \u201cky\u201d. Reconstructed images are included as figures .The simulation information (developer_main_site/IRSE/sim) provides phantom models where the map dimensions are the \u201cx\u201d and \u201cy'' spatial indices and simulated k-space signals with dimensions \u201ckThe acquisition folder (developer_main_site/IRSE/acq) includes the tested sequence file (irse_pypulseq_colab_256_TI150_neg4.4.seq), the randomized slice order (irse_sl_order.mat), and raw data from two repetitions from the same sequence where the data dimensions are \u201csamples\u201d, \u201cchannels\u201d, and \u201creadouts\u201d, in that order. In addition, the acquisition details are listed in a sheet (irse_acq_info.xlsx).In the reconstruction folder (developer_main_site/IRSE/recon), we include the reconstruction script (reconstruct_images.m) as well as the reconstructed images (images_combined.mat) and montage figure (irse_pulseq_montage.png). Image quality metrics (irse_metrics.mat) and ACR test results (ACR_METRICS_IRSE.xlsx) 1.1.2Similar to 1.1.1, we present in the main folder (developer_main_site/TSE) the sequence implementation (write_tse.ipynb) and the developer PDF form (TSE_DEV_QUALITATIVE.pdf). The simulation folder (developer_main_site/TSE/sim) includes equivalent phantoms , simulated images and figures . In addition to the sequence file (tse_ms_TR3000ms_TE50ms_4echoes.seq), the raw data , and the acquisition details (tse_acq_info.xlsx), the acquisition folder (developer_main_site/TSE/acq) also includes the multi-echo phase encoding order (tse_pe_info.mat) with dimensions \u201cnumber of echoes\u201d and \u201cnumber of excitations\u201d. Lastly, the reconstruction folder (developer_main_site/TSE/recon) covers the equivalent files as in 1.1.1 .1.1.31 map and the acquisition details (irse_t1_acq_info.xlsx). Raw data is provided as ten separate files at different Tis .The sequence implementation (write_irse_interleaved_split_grad.ipynb) and documentation PDF (IRSE_DEV_QUANTITATIVE.pdf) are provided like above. Acquisition data (developer_main_site/IRSE_T1_mapping/acq) includes ten sequence files with different inversion times see used to The reconstruction folder (developer_main_site/IRSE_T1_mapping/recon) includes a reconstruction script (reconstruct_T1_mapping_images.m), the original and low-pass filtered reconstructed images , and the montage of all ten filtered images (T1_mapping_images_filtered_montage.png).1 mapping MATLAB code: the function for creating a regression curve following the T1 signal model (createFitT1.m) and the script that takes in filtered images and generates a T1 map (T1Mapping.m). The output map is given in units of seconds in two versions, generated from either the original or the filtered T1 images . The filtered image is shown in a figure after adjusting the display to eliminate the phantom background (T1_map_cleaned.png). Region-Of-Interest (ROI) values for the individual T1 spheres are given in a separate file (t1_by_sphere_filtered.mat).The analysis data (developer_main_site/IRSE_T1_mapping/ana) includes the T1.1.42 mapping (tse_multiecho_NIST_t2_sag.seq), the acquisition details (tse_t2_acq_info.xlsx), and the raw data (T2_mapping_raw_data.mat). In the reconstruction folder, equivalent script, data, and figure are provided of the 23 T2 mapping images, each reconstructed from samples at the same echo number and therefore the same TE . The analysis folder contains analogous mapping scripts , two T2 maps generated from original and filtered data where the latter uses only the 5th to 23rd echoes to best capture the most T2 values imaged, the cleaned T2 map figure (T2_map_cleaned.png), and the ROI statistics (T2_by_sphere_filtered.mat).Similar documentation (TSE_DEV_QUANTITATIVE.pdf) and sequence notebook (write_tse_t2_mapping.ipynb) are included in the main folder (developer_main_site/TSE_T2_mapping). Acquisition data includes the single multi-echo TSE sequence with 23 echoes for variable TE T1.21.2.1The \u201cIRSE_ACR\u201d folder contains the raw data (raw_data_irse_second_site.mat), the image montage (IRSE_images_second_site.png), and the filled user form documenting the steps performed and user feedback (IRSE_USER_QUALITATIVE.pdf).1.2.2The \u201cTSE_ACR\u201d folder contains the equivalent raw data (raw_data_tse_second_site.mat), image figure (TSE_images_second_site.png), and user form (TSE_USER_QUALITATIVE.pdf). It also provides the phase encoding order (pe_info.mat).1.2.31 map as well as the user form (IRSE_USER_QUANTITATIVE.pdf) are included.Eight raw data files are provided for the different TIs . The reconstructed images and T1.2.4Similarly, the raw data (TSE_T2mapping_t2sph_second_site.mat) and reconstructed images (T2_mapping_images_second_site.mat) are included, in addition to the map figure (T2map_second_site.png) and the user form (TSE_USER_QUANTITATIVE.pdf).1.3The folder (documentation_templates) contains the empty developer and user forms for documenting test experiments in the proposed sequence validation framework 22.1Two classic MRI sequences were implemented in the multi-vendor, open-source Pulseq format 2.21/T2 relaxation times, that make up a numerical phantom. When exposed to temporally and spatially varying magnetic fields such as those defined by a pulse sequence program, the isochromat's magnetization vector evolves according to its initial condition, innate parameters, and the external driving fields. A numerical library is used to solve the differential equations. In the end, the detectable signals from the transverse magnetization are added up across all isochromats in a phantom to generate the raw MRI signal.Lower resolution numerical simulation based on the Bloch equations All simulations were performed on a Windows 10 operating system with an Intel(R) Core i7\u20138650\u00a0U CPU. Specific parameters used for the simulation were: FOV\u00a0=\u00a0250\u00a0mm, slice thickness\u00a0=\u00a05\u00a0mm; TR\u00a0=\u00a04500\u00a0ms, TI\u00a0=\u00a0200\u00a0ms, and TE\u00a0=\u00a010\u00a0ms for IRSE; TR\u00a0=\u00a04500\u00a0ms and TE\u00a0=\u00a010\u00a0ms for TSE.2.31/T2 spheres.Experiment parameters are shown in 2.41: 2: 1/T2 maps, small sphere-wise ROIs were manually selected to ensure only interior voxels are used. For each ROI, the mean and standard deviation of T1/T2 values were computed.For each mapping experiment, the corresponding signal equation and Structural Similarity Index Measure (SSIM) 2.5The open-source sar4seq library was used to generate predicted time-averaged RF power and Specific Absorption Rate (SAR) for each sequence ,14. At aOur work did not involve human or other animal subjects and adheres to ethics in publishing standards.Gehua Tong: Formal analysis, Investigation, Methodology, Software, Visualization, Writing \u2013 original draft, Writing \u2013 review & editing. Andreia S. Gaspar: Investigation, Validation, Visualization. Enlin Qian: Methodology, Software. Keerthi Sravan Ravi: Software. John Thomas Vaughan: Writing \u2013 review & editing. Rita G. Nunes: Funding acquisition, Project administration, Resources, Supervision, Validation, Visualization. Sairam Geethanath: Conceptualization, Funding acquisition, Methodology, Project administration, Resources, Software, Supervision, Writing \u2013 review & editing.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "This article provides a pooled cross-sectional sample of Chilean households from 4 survey waves . The data has information on the demographics of the household, labor participation and occupation, savings rates, plus wealth of different sources. The data is available in both Excel and Stata formats. It is an important data for the study of savings, wages, pensions and wealth inequality. The dataset consists of demographics , labor market information , savings rates, and expected wealth components . The dataset includes 33,538 households from the 1997, 2007, 2012 and 2017 waves of the Chilean Family Expenditures Survey. The variables include Household identifier variables and population weights, Demographic variables , Work and income variables, Savings rates and consumption flows variables, Ratios of household wealth as a fraction of permanent household income, Betas for the linear correlation between unemployment risk and income volatility of the different 538 worker types with the aggregate consumption kernel pricing returns and the pension fund returns.Household identifier variables and population weights \u2013hogar \u201chousehold identifier of each EPF wave\u201dfolio_hogar \u201chousehold identifier for the pooled cross-section of all the EPF waves\u201dyear \u201cYear of the EPF Survey wave\u201dfactor_all \u201cexpansion factor (population weight) of the household in the survey\u201did \u201cgroup cluster identifier\u201dDemographic variables \u2013sexo \u201cGender of the household head \u201dedad \u201cage (in years) of the household head\u201deduc \u201ceducation: elementary, secondary, university\u201deduc_ecf \u201cEducation level of the respondent (only 2017 wave)\u201d, with values 1 \u201cElementary education\u201d 2 \u201cSecondary education\u201d 3 \u201cTechnical or Some college\u201d 4 \u201cCollege education\u201d 5 \u201cPost-graduate education\u201docup_female_spouse \u201cfemale partner of the household is employed\u201dcouple_d \u201chousehold has a couple among its members\u201dd_child \u201cdummy for whether the household has a child\u201dnum_sen \u201cdummy for whether the household has a senior citizen (above age 65) among its members\u201dWork and income variables \u2013ILFP \u201cdummy for whether the main income of the household comes from informal employment\u201ddummy_region \u201cdummy for whether the household lives in regions outside of the Metropolitan Capital region\u201dquintile_h \u201chousehold national income quintile\u201dytoth \u201clog of the total household permanent income (monthly)\u201dsd_ln_inc_sect \u201cannual standard deviation of the household labor income\u201dunemp_sect \u201cunemployment risk of the household\u201dSavings rates and consumption flows variables \u2013CBeta \u201cfraction of wealth that should be consumed each year in a standard life cycle model\u201dSRate \u201cratio of the current saving rate in terms of the permanent income\u201dSRatePI \u201cratio of the permanent saving rate in terms of the permanent income\u201daggSRate \u201cratio of the total current saving rate in terms of the permanent income\u201daggSRatePI \u201cratio of the total permanent saving rate in terms of the permanent income\u201dRatios of household wealth as a fraction of permanent household income \u2013Rytoth_c \u201cHousehold income surprise\u201dR_TotalWI_hh \u201cDiscounted total wealth\u201dR_PW2I_hh \u201cDiscounted total pension wealth\u201dR_FE_hh \u201cDiscounted labor earnings wealth\u201dR_PW2I_hh_NoSy \u201cDiscounted contributory pension wealth\u201dR_PW2I_APS \u201cDiscounted solidarity pension wealth\u201dR_PWI_hh_past \u201cDiscounted current contributory pension wealth\u201dR_PWI_hh_NoSy \u201cDiscounted contributory pension wealth\u201dR_FENL_hh \u201cDiscounted non labor earnings wealth\u201dR_FErent \u201cDiscounted rent wealth\u201dR_FEtransfers \u201cDiscounted transfers wealth\u201dR_FEfinassets \u201cDiscounted financial income wealth\u201dBetas for the linear correlation between unemployment risk and income volatility of the different 538 worker types with the aggregate consumption kernel pricing returns and the pension fund returns \u2013BetaPF_unemployed \u201cBeta between the occupational unemployment with the Pension Fund real rate of return\u201dBetaPF_sd_ln_ing_tot_ocup3 \u201cBeta between the occupational income volatility with the Pension Fund real rate of return\u201dBeta_unemployed \u201cBeta between the occupational unemployment with the Consumption Pricing Kernel real rate of return\u201dBeta_sd_ln_ing_tot_ocup3 \u201cBeta between the occupational income volatility with the Consumption Pricing Kernel real rate of return\u201dThis is the list of variables available in the dataset:2The data consists of demographics, labor earnings and risk and a simulation of the future contributory pension wealth plus public solidarity benefits for a sample of Chilean households Madeira . The modEncuesta de Presupuestos Familiares, hence on EPF) between 1997 until 2017. The dynamics of labor force participation, formal versus informal work and unemployment are calibrated from the Chilean Employment Survey , according to 538 workers\u2019 types which are obtained from the multivariate vector of the workers\u2019 sex, age, education, industry and region the raw data of all the EPF and ENE surveys from the website of the Chilean Institute of National Statistics.https://www.ine.cl/estadisticas/sociales/mercado-laboral/ocupacion-y-desocupacion.ENE: https://www.ine.cl/estadisticas/sociales/ingresos-y-gastos/encuesta-de-presupuestos-familiares.EPF:The applied model that was calibrated from the raw data is explained in detail in the online file \u201cMethodology.pdf\u201d. The codes used to create the variables are explained in detail in the file README_JIMF_Codes_Summary.docx and CODES_JIMF.zip includes all the 45 Stata software codes used in the article. These files are publicly available with the data in the repository Mendeley Data.The online file in Mendeley Data CODES_JIMF.zip includes all the software codes with detailed comments on the methods used inside each code. Here I provide a brief summary of those codes. The \u201cM_EPF_analysis.do\u201d do file replicates the analysis of the article, by calling all the algorithms and doing each code in sequenced steps until all the data formatting and analysis is completed.The codes pctile_wgts.do, mean_wgts.do, and linear_reg_impute3.do create conditional group percentiles, mean values and imputations for missing values in the micro survey data.A second set of codes formats the Income and Employment Survey creating unemployment risk and income volatility statistics for 538 worker types for the period 1990 until 2017, with worker types given by gender, education, region, industry of occupation, age, income quintile. These codes include: esi_format.do , panel_esi_allyrs_FLP.do (formats rotating samples between 2 years for the ESI workers in the labor force), panel_esi_ILFP.do , panel_esi_income_growth0.do , layoff_jobfind0.do , income_shock0.do , p_income.do , Consumption_WageVolatility.do : EPF_2017.do, EPF_2017_DurSDurNDur_Tot.do, format_epf_1997.do, format_epf_2007.do, format_epf_2012.do, format_epf_2017.do // It formats the EPF 2017 data with the same variables and formats of other years. The code format_epf_all.do joins all the EPF waves.A fourth set of codes joins the EPF data with the Employment and Income Survey worker type statistics for each of the 538 worker types across survey waves. The codes then estimate past and expected future pension contributions for each worker. This set of codes includes: EPF_labor_risk_vintage.do, EPF_all_LFP_ILFP_FE_PW_PWpast.do, income_potential.do, import_FE_PW_PW_past.do, generate_FE_FENL_PW_PWpast_TW_hh.do, generate_log_Wealth.do, Pension_tope_income.do.A fifth set of codes calibrates the pension system parameters for Chile in previous years, the pension withdrawals , the current policy reforms in 2022, and the counterfactual scenarios for the future reforms. This set of codes includes: Ingreso_bruto.do, Pension_income.do, Pension_PBS.do, Pension_PGU.do, Pension_PBS_2019.do, Pension_PBS_2008.do, Pension_PBS_PASIS.do, Pension_PASIS.do, Pension_Contr_APS_total.do, Pension_Reparto.do, Pension_Future.do, Retiro_AFP.do, PensionReformsFormat.do, predictLS_old_new1.do.The sixth set of codes analyses the data and providing the results in Madeira https://data.mendeley.com/datasets/dyp8yr2sr2/1.All the methods (in Stata do-files), theoretical methodology, and the datasets are published online with the Mendeley Data Madeira : https:/Carlos Madeira: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing \u2013 original draft, Writing \u2013 review & editing, Visualization, Supervision, Project administration, Funding acquisition.The author declares that he has no known competing financial interests or personal relationships which have or could be perceived to have influenced the work reported in this article. I received no funding from any institution besides my employer which is the Central Bank of Chile. Furthermore, there are no patents or impediments to publication, including the timing of publication, with respect to the intellectual property of the article or the associated dataset."} +{"text": "Reproducibility of liquid chromatography separation is limited by retention time drift. As a result, measured signals lack correspondence over replicates of the liquid chromatography\u2013mass spectrometry (LC-MS) experiments. Correction of these errors is named retention time alignment and needs to be performed before further quantitative analysis. Despite the availability of numerous alignment algorithms, their accuracy is limited .We present the Alignstein, an algorithm for LC-MS retention time alignment. It correctly finds correspondence even for swapped signals. To achieve this, we implemented the generalization of the Wasserstein distance to compare multidimensional features without any reduction of the information or dimension of the analyzed data. Moreover, Alignstein by design requires neither a reference sample nor prior signal identification. We validate the algorithm on publicly available benchmark datasets obtaining competitive results. Finally, we show that it can detect the information contained in the tandem mass spectrum by the spatial properties of chromatograms.https://github.com/grzsko/Alignstein.We show that the use of optimal transport effectively overcomes the limitations of existing algorithms for statistical analysis of mass spectrometry datasets. The algorithm\u2019s source code is available at Advances in liquid chromatography\u2013mass spectrometry (LC-MS) have provided a remarkable insight into the functioning of the organisms, ranging from protein level\u00a0, throughOne of these challenges is the correction of errors caused by retention time (RT) drift. It limits the reproducibility of LC separation, which is important for experiments usually acquired in many (even hundreds) replicates. RT drift became a significant obstacle with the emergence of high-performance chromatography (HPLC) and ultra-performance chromatography (UPLC) technologies. For example, nanoflow UPLC column separation takes a relatively long time, usually up to several hours. For these experiments, the elution time of peptides may vary up to 5 minutes\u00a0 or even RT drift can be corrected by the experimental protocol only to a limited extent\u00a0. It may RT drift requires a correction, usually named the RT alignment. It results in the correspondence of signals across runs\u00a0. For exaHere, we present a novel alignment algorithm named Alignstein cf. Fig.\u00a0. It findThis article is organized as follows. First, we characterize Alignstein and analyze how it deals with the swapped signals. Then, we validate the algorithm on publicly available benchmark datasets. Finally, we show the applicability of our approach to detecting corresponding biomarkers in differing samples.RT drift may swap the order of eluting analytes. In the proteomic experiment (cf. Methods), we analyzed that about 3% of all feature pairs are swapped between two chromatograms. Although many of the available algorithms properly align most signals, still they fail to resolve swaps.Most approaches to RT alignment are so-called warping algorithms\u2014for example, OpenMS\u00a0, MetAligm/z and average RT value, ignoring the information of isotopic envelope or feature span over the RT dimension. Without feature spatial characteristics and information of coeluting ions, elution order swaps are practically undetectable\u00a0, including replicates of a sample with 0\u2009\u00b5g/L BaP. For better readability, outliers over 200 seconds are omitted. Most RT differences are not greater than 10 seconds.Supplementary Fig.\u00a0S3. Flow network for finding the optimal feature matching between n features of 1 chromatogram denoted by nodes L1, \u2026, nL and m features from the other chromatogram, denoted by nodes R1, \u2026, mR. Nonzero costs are described by edge labels. The cost between features iL and features jR is equal to the GWD between them. Additional node rT (\u201ctrash\u201d) gives the possibility to not match the feature with cost c. Every edge has capacity equal to 1, except edge between S (source) and rT and edge between rT and T (sink) with capacities equal to max\u2009{0, s \u2212 n} and max\u2009{0, n \u2212 s}, respectively . As a result, we take all matchings .Supplementary Table S1. Detailed results for P1 set in CAAP comparison. P stands for alignment precision, R stands for alignment recall, and F stands for F-score.Supplementary Table S2. Detailed results for P2 set in CAAP comparison. P stands for alignment precision, R stands for alignment recall, and F stands for F-score.m/z: mass-to-charge ratio; RT: retention time; UPLC: ultra-performance liquid chromatography.BaP: benzo[a]pyrene; CAAP: Critical Assessment of Alignment Procedures; C60: fullerene; CID: collision-induced dissociation; DDA: data-dependent acquisition; GWD: generalized Wasserstein distance; HPLC: high-performance liquid chromatography; IR: identification recall; LC-MS: liquid chromatography\u2013mass spectrometry; MS/MS: tandem mass spectrometry; The authors declare that they have no competing interests.G.S. was supported by Polish National Science Center grant number 2019/33/N/ST6/02949. A.G. and B.M. were supported by Polish National Science Center grant number 2018/29/B/ST6/00681.G.S. implemented and verified the algorithm. A.G. conceived the idea of the project and discussed the results. B.M. designed the algorithm and supervised the work. G.S., A.G., and B.M. cowrote the manuscript.giac101_GIGA-D-22-00149_Original_SubmissionClick here for additional data file.giac101_GIGA-D-22-00149_Revision_1Click here for additional data file.giac101_GIGA-D-22-00149_Revision_2Click here for additional data file.giac101_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giac101_Response_to_Reviewer_Comments_Revision_1Click here for additional data file.giac101_Reviewer_1_Report_Original_SubmissionRobbin Bouwmeester -- 6/24/2022 ReviewedClick here for additional data file.giac101_Reviewer_1_Report_Revision_1Robbin Bouwmeester -- 8/25/2022 ReviewedClick here for additional data file.giac101_Reviewer_2_Report_Original_SubmissionKarl Mechtler -- 7/29/2022 ReviewedClick here for additional data file.giac101_Supplemental_FileClick here for additional data file."} +{"text": "Germline genetic variants modulate human immune response. We present analytical pipelines for assessing the contribution of hosts\u2019 genetic background to the immune landscape of solid tumors using harmonized data from more than 9,000 patients in The Cancer Genome Atlas (TCGA). These include protocols for heritability, genome-wide association studies (GWAS), colocalization, and rare variant analyses. These workflows are developed around the structure of TCGA but can be adapted to explore other repositories or in the context of cancer immunotherapy.For complete details on the use and execution of this protocol, please refer to \u2022Pipelines for assessing the contribution of germline genetics on tumor immune contexture\u2022Workflow for data download, processing, assembly, curation, and annotation\u2022Protocols for heritability, GWAS, colocalization, and rare variant analysis\u2022Visualization tools for exploration of the results by iAtlas and PheWeb Publisher\u2019s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Germline genetic variants modulate human immune response. We present analytical pipelines for assessing the contribution of hosts\u2019 genetic background to the immune landscape of solid tumors using harmonized data from more than 9,000 patients in The Cancer Genome Atlas (TCGA). These include protocols for heritability, genome-wide association studies (GWAS), colocalization, and rare variants analysis. These workflows are developed around the structure of TCGA but can be adapted to explore other repositories or in the context of cancer immunotherapy. These protocols describe specific bioinformatic workflows for the analyses of The Cancer Genome Atlas (TCGA) genomic datasets and well-characterized immune traits . HoweverTiming: 1\u20133\u00a0weeks (for step 1)1.To apply for dbGAP, an institutional account is required.2.https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login.Apply for dbGaP authorization to access TCGA and GTEx controlled access data: 3.https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetPdf.cgi?document_name=GeneralAAInstructions.pdf.Prepare a data access request: CRITICAL: Preparing the application is fast, however, the review process of the application can take few weeks and should be considered ahead of time.Authorization from the database of Genotypes and Phenotypes (dbGaP) is necessary to access TCGA germline genetic data (whole exome sequencing (WES) and single nucleotide polymorphism (SNP) array data, including derived imputed SNP data) and Genotype-Tissue Expression (GTEx) genotype data. In addition, download of GTEx summary statistics from the GTEx Google Cloud bucket is a requester-paid download service .b.https://www.cog-genomics.org/plink2.Download and software documentation is available at: PLINK installation.5.a.Install bcftools (1.9 or current version) .b.https://samtools.github.io/bcftools/.Download and software documentation is available at: bcftools installation.6.a.Install GCTA (1.91.2beta or current version) .b.https://cnsgenomics.com/software/gcta.Download and software documentation is available at: Genome-wide Complex Trait Analysis (GCTA) software package installation.7.a.https://www.r-project.org/.Install R (3.5.0 or current version). Download and software documentation is available at: b.https://www.bioconductor.org/.Install Bioconductor (3.7 or current version) . Installc.https://cran.r-project.org/web/packages/snplist/index.html.Install the R package: snplist (0.18.1 or current version) . Installd.https://bioconductor.org/packages/release/data/annotation/html/SNPlocs.Hsapiens.dbSNP144.GRCh37.html.Install the Bioconductor package: SNPlocs.Hsapiens.dbSNP144.GRCh37 (0.99.20 or current version) . Installe.grch37.ensembl.org. Installation instructions and documentation is available at: https://bioconductor.org/packages/release/bioc/html/biomaRt.html.Install the Bioconductor package: biomaRt (2.36.1 or current version) Durinck. Use hosf.https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html.Install the Bioconductor package: GenomicRanges (1.32.7 or current version) . Installg.https://bioconductor.org/packages/release/bioc/html/rtracklayer.html.Install the Bioconductor package: rtracklayer (1.40.6 or current version) . Installh.https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html.Install the Bioconductor package: AnnotationHub (2.12.1 or current version) . Installi.https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v86.html.Install the Bioconductor package: EnsDb.Hsapiens.v86 (2.99.0 or current version) . InstallR/Bioconductor and related packages installation.8.a.http://locuszoom.org/.Install LocusZoom (Genome Build/LD Population: hg19/100 Genomes Nov 2014 EUR) from httLocusZoom installation.9.a.http://zarlab.cs.ucla.edu/tag/ecaviar/.eCAVIAR from htteCAVIAR installation.Note: Indicated software and package versions were used as described in and its binary counterpart BCF.GCTA: Used for heritability analysis. GCTA is one of first and well-established software packages for estimation of the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait allows us to integrate various sources of Linkage Disequilibrium (LD).eCAVIAR: Used for colocalization analysis. eCAVIAR is a commonly used method for colocalization analyses, and, as compared with other methods, has the advantage of modeling the LD .The TCGA quality-controlled genotyping data was imputed to the Haplotype Reference Consortium (HRC) panel . These db.i.Information on composition of genotyping files:\u201cREAD_ME.txt\u201d.ii.File mapping of TCGA Patient ID to corresponding Birdseed genotyping files:\u201cMap_TCGAPatientID_BirdseedFileID.txt\u201d.iii.QC Unimputed Genotyping Data:\u201cREAD_ME_1.txt\u201d .iv.HRC Imputed Genotyping Data:\u201cREAD_ME_4.txt\u201d .Download the open-access files from the \u201cTCGA QC HRC Imputed Genotyping Data used by the AIM AWG from \u201d sectionc.i.To download the controlled access data, follow instructions under the \u201cInstructions for Data Download\u201d for \u201cControlled Access Data\u201d. The necessary manifest files are found under the \u201cData in the GDC\u201d section for \u201cControlled Access Data\u201d.ii.Download the following \u201cQC Unimputed Genotyping Data\u201d files:\u201cQC_Unimputed_plink.zip\u201d .iii.Download the following \u201cHRC Imputed Genotyping Data\u201d files:\u201cHRC imputed genotyping data for chromosome 1 - chr_1.zip\u201d.\u201cHRC imputed genotyping data for chromosome 2 - chr_2.zip\u201d.\u201cHRC imputed genotyping data for chromosome 3 - chr_3.zip\u201d.\u201cHRC imputed genotyping data for chromosome 4 - chr_4.zip\u201d.\u201cHRC imputed genotyping data for chromosome 5 - chr_5.zip\u201d.\u201cHRC imputed genotyping data for chromosome 6 - chr_6.zip\u201d.\u201cHRC imputed genotyping data for chromosome 7 - chr_7.zip\u201d.\u201cHRC imputed genotyping data for chromosome 8 - chr_8.zip\u201d.\u201cHRC imputed genotyping data for chromosome 9 - chr_9.zip\u201d.\u201cHRC imputed genotyping data for chromosome 10 - chr_10.zip\u201d.\u201cHRC imputed genotyping data for chromosome 11 - chr_11.zip\u201d.\u201cHRC imputed genotyping data for chromosome 12 - chr_12.zip\u201d.\u201cHRC imputed genotyping data for chromosome 13 - chr_13.zip\u201d.\u201cHRC imputed genotyping data for chromosome 14 - chr_14.zip\u201d.\u201cHRC imputed genotyping data for chromosome 15 - chr_15.zip\u201d.\u201cHRC imputed genotyping data for chromosome 16 - chr_16.zip\u201d.\u201cHRC imputed genotyping data for chromosome 17 - chr_17.zip\u201d.\u201cHRC imputed genotyping data for chromosome 18 - chr_18.zip\u201d.\u201cHRC imputed genotyping data for chromosome 19 - chr_19.zip\u201d.\u201cHRC imputed genotyping data for chromosome 20 - chr_20.zip\u201d.\u201cHRC imputed genotyping data for chromosome 21 - chr_21.zip\u201d.Note: Please cite format, which is more suitable for Excel.Upload \u201cvep_input.txt\u201d to c.Combine annotations per SNP. VEP provides multiple annotations per SNP. SNPs might map to different genes and could have several biological impacts on nearby genes. Use R script \u201cCombineVEPannotations.R\u201d to combine annotations.d.Example of combined annotations: \u201cCXXC5:synonymous_variant:LOW|CXXC5:upstream_gene_variant:MODIFIER\u201d.Download the Ensembl Variant Effect Predictor\u00a0(VEP) annotation.16.a.https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html#exp_18state.Access the Expanded 18-state model for Build GRCh37/hg19: b.Under \u201cMNEMONICS BED FILES\u201d section, download the archive of all mnemonics bed files: \u201call.mnemonics.bedFiles.tgz\u201d.Download Roadmap Epigenomics Project Epigenomic State Model.Timing: 5\u00a0minThe scripts and code descriptions used in the entirety of this protocol are available at:https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics.17.a.Review all \u201cREADME\u201d files for each section of workflow.b.Ensure all the necessary code has been downloaded.Download or clone the GitHub repository: \u201cTCGA_PanCancer_Immune_Genetics\u201d .a.ReviewOptional: This protocol is designed to work with pre-processed and quality-controlled genotyping data. If users start from raw genotyping data from SNP arrays, please see the companion protocol for quality-control analysis of germline data, stranding and genotype imputation from the University of California, San Francisco (UCSF) Wynton high-performance (HPC) cluster, which currently contains 449 nodes with over 12572 Intel CPU cores and 42 nodes containing a total of 148 NVIDIA GPUs, (2) the original UCSF TIPCC HPC cluster (now C4), which had 8 communal compute nodes and 1 dedicated node, each with 12\u201364 cores , and (3) two additional severs with 32 and 48 CPUs (Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00 GHz), respectively. In the optimization phase, analyses have been performed by different operators and at multiple times to ensure accuracies and reproducibility. As these are shared servers, time might considerably vary in function of the number of nodes available. From a computational point of view, the most time-consuming step is the GWAS . However, file preparation, as well as annotation and curation of the output files is particularly time consuming. An estimated time, considering these manual steps and factoring in some troubleshooting time .20.2\u00a0<\u00a00.5. The imputation R2 is the estimated value of the squared correlation between imputed genotypes and true, unobserved genotypes.a.2 \u2265 0.5.Filter each \u201cchr\u2217.dose.vcf.gz\u201d files and generate \u201cchr\u2217.rsq0.5.dose.vcf.gz\u201d imputed genotype files of SNPs with Rb.Index and generate the corresponding \u201cchr\u2217.rsq0.5.dose.vcf.gz.tbi\u201d files.c.Generate the corresponding filtered \u201cchr\u2217.info.rsq0.5.gz\u201d information files.For each chromosome, filter the HRC imputed genotyping data to exclude SNPs with imputation R21.a.Convert VCF \u201cchr\u2217.rsq0.5.dose.vcf.gz\u201d files to PLINK \u201ctcga_imputed_hrc1.1_rsq0.5_chr\u2217.bed\u201d files.b.Optional: Rename SNP ID names in the HRC imputed dataset with alleles listed in alphabetical order to assist matching with other datasets.Note: This only affects the SNP ID name and not the encoding of the A1 and A2 alleles in PLINK which is maintained.c.Optional: In PLINK, exclude SNPs with MAF\u00a0<\u00a00.005 (--maf).Note: Minor allele frequency (MAF) filtering can be performed at this step to reduce the HRC imputed genotyping data input file size. Alternatively, GWAS analysis can be performed using\u00a0the R2 filtered-HRC imputed genotyping data from \u201cNote: Scripts and code description used in this section are available at: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics.For each chromosome, filter HRC imputed genotyping data to exclude SNPs with minor allele frequency (MAF)\u00a0<\u00a00.005.This section describes the pre-processing steps necessary to use the HRC Imputed Genotyping Data we generated as a general resource for this specific analysis .19.UnzipPre-processing of Imputed Data. The example code in this section were optimized for the high-performance compute environment at UCSF HPC employing Portable Batch System (PBS) job scheduling; consult your system administrator to adapt the provided code to your system.Direct link: Note: \u201cTable\u00a0S1\u201d and \u201cTable\u00a0S2\u201d in the \u201cThe overall disk space needed for the project is 2.67 TB. Breakdown for different data types and analyses are provided below .Table\u00a01DTiming: 1\u00a0day1.a.Curated set of 139 immune traits in TCGA can be downloaded from \u201cTable\u00a0Sb.i.Code to generate gene expression signatures from Amara e and singii.Necessary transformation of immune trait values in TCGA for use in genetic analysis described below are annotated in \u201cTable\u00a0SFor calculation of immune traits in a new dataset, consult methods Prepare curated set immune traits genes.2.Calculate Pearson correlations of continuous values of the 139 immune traits.3.a.Cluster correlation matrix using complete agglomerative hierarchical clustering method and (1-correlation) as distance metric.Generate a correlation heatmap with a hierarchical clustering dendrogram.4.Identify highly correlated blocks (dendrogram clusters) of immune traits to generate immune functional modules.Note: Scripts and code description used in this section are available at: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics.139 immune traits used in the analyses were curated from by selecImmune Traits.Direct link: Timing: 2\u00a0weekshttps://cnsgenomics.com/software/gcta).5.a.Formatted input file of TCGA immune traits is provided in the GitHub rFormat immune trait input file:Heritability analysis on 139 traits is conducted using a mixed-model approach implemented in the genome-wide complex trait analysis (GCTA) software package with the genomic-relatedness-based restricted maximum-likelihood (GREML) method Yang et. This ca6.a.Ancestry assignments for each TCGA individual are provided in \u201cTable\u00a0S1. TCGA Sample List Used in the Analysis\u201d from .b.Formatted input file of TCGA patient barcodes assigned to each genetic ancestry cluster is provided in the GitHub rIdentify genetic ancestry assignment of each individual and create a filtered sample list for each genetic ancestry cluster:\u201cImmune.pheno.139.source.coded.TCGAID.9769.txt\u201d.\u201cTCGAID_Cluster1.EUR.8036.txt\u201d\u201cTCGAID_Cluster2.ASIAN.605.txt\u201d\u201cTCGAID_Cluster3.AFR.904.txt\u201d7.European=7,813, NAfrican=863, NAsian=570, and NAmerican=209 individuals), subset individuals belonging to specified ancestry group from the QC TCGA HRC imputed genotyping data in PLINK (--keep) using ancestry assignments.To conduct heritability analyses within each ancestry subgroup .8.Estimate the genetic relatedness matrix (GRM) from all the autosomal SNPs with MAF\u00a0>\u00a00.01 within each ancestry group using GCTA:gcta64 --bfile [input_filename]--autosome--maf 0.01--make-grm--out [output_filename]--thread-num [numeric_value_number_threads]\u201cqsub_plink_whitelist_geno_mind_unique.indv_chr.auto_hardy.nonriskSNP_maf_uniqueSNP_TCGAID_ancestry.txt\u201d.See script:9.Filter out individuals for relatedness. GCTA removes one of a pair of individuals with estimated relatedness larger than the specified cut-off value (cut-off\u00a0= 0.05):gcta64 --grm [input_filename]--grm-cutoff 0.05--make-grm--out [output_filename]\u201cqsub_gcta_whitelist_geno_mind_unique.indv_chr.auto_hardy.nonriskSNP_maf_uniqueSNP_TCGAID_ancestry_grm.txt\u201d.See script:10.Run GCTA GREML unconstrained to estimate variance explained by SNPs with defined categorical and continuous covariates using the following parameters:gcta64 --reml-no-constrain--grm [input_filename]--pheno [immune_trait_matrix_filename]--mpheno [immune_trait_numeric_index_input_matrix]--covar [categorical_covariates_filename]--qcovar [continuous_covariates_filename]--thread-num [numeric_value_number_threads]--out [output_filename]\u201cqsub_gcta_whitelist_geno_mind_unique.indv_chr.auto_hardy.nonriskSNP_maf_uniqueSNP_TCGAID_ancestry_grm_grm.cutoff.0.05.txt\u201d.CRITICAL: Run heritability analysis unconstrained. This will produce heritability estimates (Vg/Vp) and standard deviations outside the 0\u20131 range.11.From GCTA GREML \u201c.hsq\u201d result file, extract the ratio of genetic variance to phenotypic variance (Vg/Vp), estimate and SE; the LRT p-value and sample size (n)\u00a0for each immune trait.12.a.Annotate each result file with the corresponding immune trait, immune category and immune module .b.Append annotated result files from each immune trait.Concatenate heritability analysis results across all immune traits tested.13.Correct for multiple-hypothesis testing ancestry group by calculating the FDR p-value using the Benjamini-Hochberg adjustment method.14.Optional: Visualize % heritability (Vg/Vp \u2217 100) across all immune traits per ancestry group for exploratory data analysis.Note: Scripts used in this section are available at: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics.See script: \u201cqsub_grm.cutoff.0.05_greml_EUR.ImmunePheno216_CancerTypeSex.covar_PCA.AgeYears.qcovar.txt\u201d.Heritability Analysis. The example code in this section were optimized for the high-performance compute environment at UCSF HPC employing Portable Batch System (PBS) job scheduling; consult your system administrator to adapt the provided code to your system.Direct link: https://www.cri-iatlas.org/), in the \u201cGermline Analysis\u201d module analysis in PLINK in each ancestry cluster (--genome) and filter\u00a0individuals out for relatedness (pihat\u00a0<\u00a00.25). This leaves n=9,603 unrelated individuals in the TCGA cohort in the output file:GWAS were performed on traits that we found to have significant heritability since these would be most likely driven by common genetic variants.16.Recalculate allele frequencies in PLINK for the subset of individuals used in the analysis in PLINK:plink --bed [input_bed_filename]--bim [input_bim_filename]--fam [input_fam_filename]--allow-no-sex--keep-allele-order--keep [GWAS.IBD.ALL.TCGAID.txt]--freq--out [Freq/output_filename]\u201cGWAS.IBD.ALL.TCGAID.txt\u201d.17.Prepare the covariate file:See script: \u201cqsub_plink_freq_GWAS.IBD.ALL.txt\u201d.18.Prepare the phenotype file:\u201ccovar.GWAS.IBD.ALL.txt\u201d.19.Run linear association analysis for each continuous immune traits in PLINK:plink --bed [input_bed_filename]--bim [input_bim_filename]--fam [input_fam_filename]--allow-no-sex--keep-allele-order--keep [GWAS.IBD.ALL.TCGAID.txt]--pheno [Immune.phenotype.33.Set\u2217.GWAS.txt]--all-pheno--covar [covar.GWAS.IBD.ALL.txt]--linear hide-covar--out [output_filename]\u201cImmune.phenotype.33.Set\u2217.GWAS.txt\u201d.20.Run logistic regression on dichotomized discrete immune traits in PLINK by modifying the code in step 19 using the logistic command (--logistic).Note: \u201c.bed\u201d, \u201c.bim\u201d and \u201c.fam\u201d input files are provided separately in the sample code because SNP ID names from the original HRC imputed dataset were renamed with alleles listed in alphabetical order to assist matching with other datasets. This only affects the SNP ID name and not the encoding of the A1 and A2 alleles in PLINK which is maintained.21.\u22128 and suggestive significance at p\u00a0<\u00a01\u00a0\u00d7\u00a010\u22126 in our study.Filter resulting summary statistics from PLINK based on test p-values (P in PLINK). Genome-wide significance was defined at p\u00a0<\u00a05\u00a0\u00d7\u00a010See script: \u201cqsub_plink_linear_GWAS.IBD.ALL_Immune.33.Wolf.Set1.txt\u201d.See script:22.Optional: Visualize results for exploratory data analysis:a.Manhattan plot, plotting GWAS -log10 p-value against the base pair position per chromosome.b.Quantile-quantile plot (Q-Q plot), plotting the quantile distribution of observed p-values for each SNP against expected values from a theoretical \u03c72-distribution; calculate the genomic inflation factor (lamba), the median of the \u03c72 test statistics divided by the expected median of the \u03c72 distribution.Note: Interactive visualization of GWAS from (https://www.cri-iatlas.org/), in the \u201cGermline Analysis\u201d module or using the PheWeb tool (https://pheweb-tcga.qcri.org/) .i.Map the Minimac3 HRC imputation information to the GWAS summary stats using the variant identifier.See script: \u201cr_plotResults_GWAS.IBD.ALL_Immune.33.Set\u2217.r\u201d and \"qsub_r_plotResults_GWAS.IBD.ALL_Immune.33.Set\u2217.txt\".The Minimac3 HRC imputation information for each SNP (extracted from the filtered chr\u2217.info.rsq0.5.gz), including whether SNP was genotyped or imputed (Genotyped), the estimated value of the squared correlation between imputed genotypes and true, unobserved genotypes (Rsq), the average probability of observing the most likely allele for each haplotype , minor allele frequency of the variant in the imputed data (MAF) for the GWAS study set calculated from \u201cc.https://www.rdocumentation.org/packages/BSgenome/versions/1.40.1/topics/SNPlocs-class).i.Transform GWAS results chromosome and base pair position into a GRanges object using the R \u201cGenomicRanges\u201d package.ii.Define the set of SNPs as the \u201cSNPlocs.Hsapiens.dbSNP144.GRCh37\u201d dataset.iii.Overlap the GRanges chromosome and base pair position with the \u201cSNPlocs.Hsapiens.dbSNP144.GRCh37\u201d dataset using the snpsByOverlaps function.iv.Merge annotated data with results file.Note: Not all SNPs have corresponding rsIDs.See script: \u201cr_annotation_SNP.r\".Map the genomic chromosome and base pair position to corresponding SNP rsIDs and IUPAC nucleotide ambiguity codes using the R \u201cSNPlocs.Hsapiens.dbSNP144.GRCh37\u201d package (d.grch37.ensembl.org (https://uswest.ensembl.org/info/data/biomart/index.html).i.Create SNP information table (setSNPTable function) using SNP rsID, chromosome and base pair position.ii.grch37.ensembl.org.Create a gene information table (setGeneTable function) using gene attributes extracted from R \u201cbiomaRt\u201d package using host iii.Find overlaps of the SNP and gene information tables, setting the margin (bp) to the desired distance from SNP of interest (makeGeneSet function).See script: \u201cr_annotation_SNP.r\".The nearest genes to SNP of interest using R \u201csnplist\u201d package to map rsID to gene maps extracted via the R \u201cbiomaRt\u201d package using host e.i.Map the VEP annotation file with:a.24.a.Annotate each summary stat file with the corresponding immune trait, immune category and immune module summary stats across all immune traits tested.25.\u22128). This excludes the HLA locus on chr 6 which spans \u223c3.5 MB.Identify genome-wide significant loci as SNPs within 50 KB region with at least one genome-wide significant SNP (p\u00a0<\u00a05\u00a0\u00d7\u00a010Note: Scripts and code description used in this section are available at: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics.\u201cr_plotResults_GWAS.IBD.ALL_Immune.33.Set\u2217.r\u201d and \"qsub_r_plotResults_GWAS.IBD.ALL_Immune.33.Set\u2217.txt\".Genome-Wide Association Study (GWAS). The example code in this section were optimized for the high-performance compute environment at UCSF HPC employing Portable Batch System (PBS) job scheduling; consult your system administrator to adapt the provided code to your system.Direct link: Timing: 1\u20132\u00a0dayshttps://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html#exp_18state.This section describes the mapping of genome-wide significant and suggestive SNPs to the Roadmap Epigenomics Project Epigenomic Expanded 18-state model which uses 6 marks across 98 epigenomes: 26.a.Import the GWAS suggestive and genome-wide significant SNP result table into R.b.Create a unique data frame of SNP IDs, chromosome and base pair positions.c.Convert into GRanges object using the makeGRangesFromDataFrame function in \u201cGenomicRanges\u201d package.Transform the Immune-Germline GWAS suggestive and genome-wide significant SNPs results table into a GRanges object using the \u201cGenomicRanges\u201d package in R.27.a.Using \u201crtracklayer\u201d package in R, import each epigenome bed file with the annotated Epigenomic Expanded 18-state model.b.At each GRanges SNP chromosome and base pair position, extract the corresponding epigenomic state from each epigenome using the mergeByOverlaps function in \u201cGenomicRanges\u201d package.Iteratively loop and import each Roadmap Epigenomics Project epigenome, and extract epigenomic states that overlap each of the Germline-Immune SNP chromosome and base pair position.28.Map epigenome IDs to corresponding epigenome descriptions of source cell types and tissue types using the \u201cRoadmap.metadata.qc.jul2013.csv\u201d annotation file.29.Annotate epigenetic states with published color schema using \u201cFigureColors.csv\u201d file.30.Manually curate immune-associated epigenomes via cell type or tissue of origin .Note: Scripts and code description used in this section are available at: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics..26.TransEpigenomic Analysis.Direct link: Timing: 1\u00a0weekhttps://gtexportal.org/home/index.html. For the TCGA dataset, the gene expression matrix was downloaded from: https://gdc.cancer.gov/about-data/publications/pancanatlas and analysis was conducted locally.31.a.i.Download gene expression matrix: \u201cEBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv\u201d.ii.https://grch37.ensembl.org/biomart/martview/. Required columns from the \u201cmart_report.txt\u201d output files are: \u201cChromosome\u201d, \u201cStart\u201d, \u201cEnd\u201d, and \u201cGene type\u201d.Download genes\u2019 starts, ends, and types from \u201cbiomaRt\u201d package from iii.Transpose the gene expression matrix. This can be run with R script \u201cOrganizeRNAMatrix.R\u201d.iv.Run association analysis between genome-wide and suggestive SNPs and genes within 1 MB using a linear regression model accounting for genetic ancestry PC1-7, sex, age, and cancer type . This cv.Summarize outcome: results will have the following: chromosome, position, gene name, distance from gene, pan-cancer sample size, pan-cancer effect size, pan-cancer p-value, and then the same information repeated for each cancer type.eQTL.b.i.https://gdc.cancer.gov/about-data/publications/PanCanAtlas-Splicing-2018.Download 5\u2032, 3\u2032, exon skipping, intron retention, and mutually exclusive exon splice events data from ii.Organize the data input and format it for SNP-splicing event association analysis. Use\u00a0\u201cscript PrepareData.sh\u201d. This script keeps the genes that mapped to the most significant SNPs . Example: grep \u2013f ListGenes.txt splice3prime\u00a0>\u00a0Data_3prime. It creates two more files that contain TCGA subject IDs, and splicing event IDs and types. It finally runs an R script \u201cAnalyze.R\u201d that performs association analysis between SNP genotypes and splicing events using linear regression model accounting for genetic ancestry PC1-7, sex, age, and cancer type .iii.Summarize outcome, an output file containing association results as follows: chromosome, position, ensemble ID, gene name, splicing event ID.sQTL.TCGA Analysis.32.a.i.Import the GRanges object of SNP chromosome and base pair positions from 13.ii.Load the chain file \u201cAH14150\u201d for Homo sapiens rRNA hg19 to hg38 from the \u201cAnnotationHub\u201d package in R.iii.Convert SNP chromosome and base pair positions from build GRCh37 to build GRCh38 using the liftOver function in the \u201crtracklayer\u201d package in R.See script: \u201cGWAS.SNPs_liftOver.GRCh38_extended.r\u201d.Convert all GWAS suggestive and genome-wide significant SNP chromosome and base pair positions from build GRCh37 to build GRCh38 to match GTEx annotation.b.i.From each tissue type, extract only GTEx eQTL SNP results that match the GWAS SNP GRCh38 chromosome and base pair position. The output is an R object of GTEx eQTL for suggestively significant variants.See script: \u201cGTEx.eQTL.all.assoc_extract_GWAS.sugg.SNPs.server.r\u201dii.Concatenate filtered GTEx eQTL files from each tissue corresponding to the GWAS suggestively significant variants. Iteratively load, annotate with tissue source, extract GRCh38 chromosome and base pair position from variant ID, and append each file into a single data frame in R.iii.Calculate the false discovery rate (FDR) per variant across all genes and all tissues.iv.Using the GTEx Ensembl IDs, map to gene symbol and Entrez IDs using the \u201cEnsDb.Hsapiens.v86\u201d package in R.v.Merge with Immune-Germline SNP annotation.vi.Extract GTEx eQTL results for variant-gene pairs with an FDR\u00a0<\u00a00.05 in at least one tissue. Exclude the HLA and IL17R locus which are simple eQTLs.vii.Optional: Visualize results by plotting the GTEx eQTL -log10 FDR p-value against the distance from the TSS (\u201ctss_distance\u201d).See scripts: \u201cGTEx.eQTL.all.assoc_processResults_GWAS.sugg.SNPs_extended.r\u201d and \u201cGTEx.eQTL.all.assoc_processResults_GWAS.sugg.SNPs_1mb_extended_plot.r\u201d.eQTL.c.i.From each tissue type, extract only GTEx sQTL SNP results that match the GWAS SNP GRCh38 chromosome and base pair position. The output is an R object of GTEx eQTL for suggestively significant variants.ii.Run the Linux bash script \u201crun_split_sqtl.sh\u201d. Each GTEx sQTL file is very large. This step\u00a0separates the large GTEx sQTL file into a number of small files. The input of this\u00a0script is a list of file names for GTEx sQTL. Each line of this input file is a file name for GTEx sQTL. The script generates a number of small files for each original GTEx sQTL file.iii.Run the R script \u201cr_extract.txt\u201d. This script takes 2 input files. One is an R object for GWAS suggestively significant variants. The other input file is the GTEx sQTL file generated from the previous step. The output is an R object of GTEx sQTL for suggestively significant variants.iv.Concatenate filtered GTEx sQTL files from each tissue corresponding to the GWAS suggestively significant variants. Iteratively load, annotate with tissue source, extract GRCh38 chromosome and base pair position from variant ID, and append each file into a single data frame in R.v.For sQTL, limit analysis to\u00a0+/- 500 KB region. Filter the resulting concatenated GTEx\u00a0sQTL file using the absolute value of the \u201ctss_distance\u201d, set a threshold \u2264 500,000\u00a0bp.vi.Calculate the false discovery rate (FDR) per variant across all genes and all tissues.vii.Using the GTEx Ensembl IDs, map to gene symbol and Entrez IDs using the \u201cEnsDb.Hsapiens.v86\u201d package in R.viii.Merge with Immune-Germline SNP annotation.ix.Extract GTEx sQTL results for variant-gene pairs with an FDR\u00a0<\u00a00.05 in at least one tissue. Exclude the HLA and IL17R locus which are simple eQTLs.x.Optional: Visualize results by plotting the GTEx sQTL -log10 FDR p-value against the distance from the TSS (\u201ctss_distance\u201d).Note: Scripts and code description used in this section are available at: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics.See scripts: \u201cGTEx.sQTL.all.assoc_processResults_GWAS.sugg.SNPs_500kb _extended.r\u201d and \u201cGTEx.sQTL.all.assoc_processResults_GWAS.sugg.SNPs_500kb_extended_plot\u201d.sQTL.GTEx Analysis.This section describes eQTL and sQTL analysis in TCGA and GTEx data. For GTEx data, eQTL/sQTL summary statistics across tissues were downloaded from Expression and splicing quantitative trait locus analysis (eQTLs and sQTL). The example code in this section were optimized for the high-performance compute environment at UCSF HPC employing Portable Batch System (PBS) job scheduling; consult your system administrator to adapt the provided code to your system.Direct link: Timing: 1 Week33.a.Create a file to determine SNP-gene-trait to be tested for colocalization. Run R script \u201cDetermineRegions.R\u201d. This script reads eQTL results and keeps SNP-gene eQTL FDR p\u00a0<\u00a00.1. Output of this script will be a file that contains 5 columns: chromosome, position, gene name, trait, and SNP significance (GW or suggestive).b.For each SNP-gene pair, run eQTL analysis between the SNP and the gene, and also between the 200 extra SNPs centered at the selected SNP and the gene. Use R script \u201cRunEQTL.sh\u201d. This script creates a folder for each SNP-gene pair. It extracts the list of 201 SNPs, calculates LD matrix (plink \u2013bfile EXTRACTED \u2013r square \u2013out EXTRACTED), and performs GWAS and eQTL association analysis using the \u201ceQTL.R\u201d R script. \u201ceQTL.R\u201d script outputs two files: one for GWAS and one for eQTL analysis containing the z-score, beta, and p-value.c.eCAVIAR -o coloc_c1.out -l EXTRACTED.ld -l EXTRACTED.ld -z GWAS.z -z eQTL.z -f 1 -c 1Run eCAVIAR using \u201cRunECAVIAR.sh\u201d script. It calls eCAVIAR as follows:The \u201cGWAS.z\u201d and \u201ceQTL.z\u201d are the z-score produced in the previous step. \u201cEXTRACTED.ld\u201d is a 1-line file that contains the LD between the selected SNP and the 200 SNPs surrounding it (100 SNP to the left and 100 SNPs to the right). The -c flag indicates the number of causal variants assumed in the model . The output that contains the colocalization posterior probability (CLPP) for each SNP is \u201ccoloc_c1.out_col\u201d.d.The same strategy is conducted for sQTL results.TCGA Analysis.34.a.Run the R script \u201cr_match_tcga_gtex.txt\u201d to match the effect allele between GTEx eQTL/sQTL results and TCGA GWAS results. It then calculates Z scores for both GTEx eQTL/sQTL and TCGA GWAS results.b.i.A table for index SNPs. The 1st column should be SNP ID and the 3rd column should be base-pair position in build 38.ii.A list of GTEx eQTL/sQTL results. Each line is the name of a GTEx eQTL/sQTL result. The last part of the file name should be \u201c_rsid.txt\u201d. Each GTEx eQTL/sQTL result file has the following columns: \u201cgene_id\u201d, \u201cvariant_id\u201d, \u201ctss_distance\u201d, \u201cma_samples\u201d, \u201cma_count\u201d, \u201cmaf\u201d, \u201cpval_nominal\u201d, \u201cslope\u201d, and \u201cslope_se\u201d.iii.A PLINK \u201c.bim\u201d file for TCGA genotype data. It has the following columns: chromosome, SNP ID, genetic distance, base-pair position, minor allele, and major allele.iv.A GWAS result file for TCGA. It has the following columns: chr:bp, CHR, SNP ID, BP, A1, A2, Genotyped, Rsq, AvgCall, MAF, Stratified.Freq, NCHROBSTEST, NMISS, BETA, STAT, and P.This R script requires 4 input files:c.i.Z score for GTEx eQTL/sQTL result.ii.Z score for TCGA GWAS result.iii.The list of SNPs in GTEx eQTL/sQTL result.iv.The list of SNPs in TCGA GWAS result.v.The list of SNPs and effect alleles in GTEx eQTL/sQTL result.vi.The list of SNPs and effect alleles in TCGA GWAS result.This R script generates 6 output files:d.Output files iii-vi will be used to generate LD matrix for eCAVIAR. Output files i and ii will be used directly for eCAVIAR.e.i.Run the python script \u201cmake_plink_command_gtex.py\u201d and \u201cmake_plink_command_tcga.py\u201d to generate PLINK commands for GTEx and TCGA separately. The output is a Linux bash file that contains a number of PLINK commands.ii.Run the bash file from steps 34e\u2013i.plink --bfile /wynton/scratch/dhu/gtex_geno/GTEx_WGS_chr11--extract snps_gtex_ENSG00000005801_Nerve_Tibial_ZNF195_rs7951724.txt --make-bed --out temp_gtexplink --bfile temp_gtex --a1-allele snps_alt_gtex_ENSG00000005801_Nerve_Tibial_ZNF195_rs7951724.txt 2 1 --recode A --out Geno_gtex_ENSG00000005801_Nerve_Tibial_ZNF195_rs7951724Example for GTEx:plink --bfile/wynton/scratch/dhu/tcga_geno/tcga_imputed_hrc1.1_noMissnp_b38_chr11 --extract snps_tcga_ENSG00000005801_Nerve_Tibial_ZNF195_rs7951724.txt --make-bed --out temp_tcgaplink --bfile temp_tcga --a1-allele snps_alt_tcga_ENSG00000005801_Nerve_Tibial_ZNF195_rs7951724.txt 2 1 --recode A --out Geno_tcga_ENSG00000005801_Nerve_Tibial_ZNF195_rs7951724Example for TCGA:Run PLINK commands to generate numeric genotype data for GTEx and TCGA for SNPs that were extracted as output files iii and iv from the previous step.f.Run the R scripts \u201cr_cor_gtex.txt\u201d and \u201cr_cor_tcga.txt\u201d to calculate Pearson correlation coefficients for each pair of SNPs in GTEx and TCGA genotype data. There are 2 input files for each R script. The 1st one is the genotype file that was generated from the previous step. The 2nd one is the file with SNP ID and alternate allele. This file was generated as the output file 5 or 6 in the step for running \u201cr_match_tcga_gtex.txt\u201d.g.i.Run the python script \u201cmake_ecaviar.py\u201d to generate commands to run eCAVIAR. The output is a Linux bash script that contains a number of eCAVIAR commands.ii.Run the Linux bash script from steps 34g\u2013i.eCAVIAR -l Cor_tcga_ENSG00000281491_Minor_Salivary_Gland_DNAJB5-AS1_rs72729406.txt -l Cor_gtex_ENSG00000281491_Minor_Salivary_Gland_DNAJB5-AS1_rs72729406.txt -z Result_tcga_ENSG00000281491_Minor_Salivary_Gland_DNAJB5-AS1_rs72729406.txt -z Result_gtex_ENSG00000281491_Minor_Salivary_Gland_DNAJB5-AS1_rs72729406.txt -c 2 -f 1 -o Result_eCAVIAR_c2_ENSG00000281491_Minor_Salivary_Gland_DNAJB5-AS1_rs72729406.txtNote: All programming scripts for GTEx colocalization were run on the UCSF Wynton HPC (https://wynton.ucsf.edu/hpc/) employing Portable Batch System (PBS) job scheduling. An example of script for submitting jobs on the cluster is \u201cqsub_run_plink_gtex.txt\u201d. The command for submitting the job is \u201cqsub_run_plink_gtex.txt\u201d and depends on the setup of the HPC cluster; consult your system administrator to adapt the provided code to your system.Note: Scripts and code description used in this section are available at: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics.Example:Run eCAVIAR assuming 2 causal SNPs.GTEx Analysis.This section describes colocalization analysis performed with eCAVIAR. This analysis was performed using TCGA and GTEx gene expression data. This analysis requires four input files: (1) GWAS summary statistics, (2) eQTL summary statistics, (3) LD matrix computed with GWAS data, and (4) LD matrix computed with genotype data used for eQTL analysis.Colocalization with eCaviar and manual curation of the expanded region.Direct link: Timing: 1\u00a0week35.Download VCF germline file see \u201cke\u201d. Sub-se36.Download annotations of curated Pathogenic and Likely Pathogenic Cancer Predisposition Variants from , which 37.a.Extract unique variants from \u201cTable\u00a0S2\u201d from and writb.bcftools view -r $i PCA.r1.TCGAbarcode.merge.tnSwapCorrected.10389.vcf.gz -O b -o CHR\"$i\".bcf.gzSplit downloaded vcf file per chromosome as follows, where \u201ci\u201d is the chromosome number:c.bcftools norm -Ou -m -any CHR\"$i\".bcf.gz | bcftools norm -Ou -f human_g1k_v37.fasta | |bcftools --missing-to-ref | bcftools annotate -Ob -x ID -I\u00a0+'%CHROM:%POS:-:%ALT' -O z -o CHR\"$i\"_norm.vcf.gzLeft normalize variants:d.bcftools\u00a0+setGT CHR\"$i\"_norm.vcf.gz -O z -o CHR\"$i\"_norm_nomissing.vcf.gz -- -t . -n 0pReplace missing genotypes by homozygous reference:e.plink --vcf CHR\"$i\"_norm_nomissing.vcf.gz --keep-allele-order --vcf-idspace-to _ --const-fid --allow-extra-chr 0 --split-x 2699520 154931044 no-fail --make-bed --out CHR\"$i\"_norm_nomissingConvert vcf files to PLINK formatted files:f.plink --bfile CHR\"$i\"_norm --extract range list_snps.txt --recode A --out OUT$i --allow-no-sexExtract the variant list prepared in step 37a and recode them mutations additively:Annotate per-sample mutations using position information available in \u201cTable\u00a0S2\u201d from .a.Extrac38.Collapse mutations into genes .39.Collapse genes into mutually exclusive pathways , run lib.For phenotypes with skewed distribution, dichotomize values as low vs high , run loPerform pan-cancer analysis.45.a.Repeat steps 44a\u2013b, without including cancer type as covariate.Peform per-cancer analysis.46.Generate outcome summary: exome files related to samples for which all the covariates and at least one immune trait was available should result in a master file of N\u00a0= 9,138 samples. There will be 832 pathogenic/likely pathogenic SNPs/Indels events with at least one copy of rare allele in the whole exome sequencing data, corresponding to 586 distinct pathogenic SNPs/Indels mapping to 99 genes. The regression analysis provides p-values and beta coefficients of the association with immune traits.Note: Scripts and code description used in this section are available at: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics.This section includes a workflow to assess the contribution of rare cancer predisposition variants on different immune traits.Rare Variant Analysis.Direct link: The analysis protocols described above each yield data output files, as described above. Expected output files are summarized here. Data visualization tools enable researchers to explore these results interactively.https://cnsgenomics.com/software/gcta/#GREMLanalysis. The combined results table include the ratio of genetic variance to phenotypic variance (Vg/Vp) estimate and SE; the likelihood-ratio test (LRT) p-value and sample size (n)\u00a0for each immune trait; and the FDR p-value across all immune traits.Output files from GCTA GREML is an .hsq file. For complete description of output variables, see: After conducting heritability analysis across 139 immune traits, we identified 10 immune traits with significant heritability (FDR p\u00a0<\u00a00.05), and 23 other traits with nominally significant heritability (p\u00a0<\u00a00.05) in at least one ancestry group. Within the European ancestry group, 28 traits had at least nominally significant heritability .https://www.cog-genomics.org/plink/1.9/formats#assoc_linear). After optional SNP annotation, addition columns include: the rsID and IUPAC nucleotide ambiguity codes from \u201cSNPlocs.Hsapiens.dbSNP144.GRCh37\u201d; the Genotyped, Rsq, AvgCall, MAF columns from Minimac3 HRC imputation information file; the recalculated MAF for the GWAS samples ; nearest genes to SNP of interest ; VEP annotation.The output from performing GWAS in PLINK consist of .assoc.linear (or .assoc.logistic) files with the following columns: chromosome code (CHR), variant identifier (SNP), base-pair coordinate (BP), allele 1 (A1), allele 2 (A2), test identifier (TEST) number of observations with nonmissing genotype, phenotype, and covariates (NMISS), regression coefficient , t-statistic (STAT) and asymptotic p-value for t-statistic (P). Note, running the PLINK command with parameter --keep-allele-order forces the original A1/A2 allele encoding and A1 should be the minor allele as originally encoded. PLINK output files are further described here: (\u22128) associations at 23 loci for 10 immune traits. We also identified an additional 1,196 suggestive (p\u00a0<\u00a01\u00a0\u00d7\u00a010\u22126) associations for 33 traits .The output table includes all genome-wide and suggestively significant SNPs annotated with the mapped epigenetic state from the Roadmap Epigenomics Project Expanded 18-state model. Each epigenome ID/epigenome represent a column with entries designating the epigenetic state at the SNP chromosome and base pair position .Output files for eQTL will have the following: chromosome, position, gene name, distance from gene, pan-cancer sample size, pan-cancer effect size, pan-cancer p-value, and then the same information repeated for each cancer type.Output file for sQTL will contain association results as follows: chromosome, position, ensemble ID, gene name, splicing event ID.10 QTL p-value of the index SNP and counter SNP, and difference between these values (delta Counter SNP-Index SNP); and the curated expanded range colocalization evidence assessment .Exome files related to samples for which all the covariates and at least one immune trait was available should result in a master file of N\u00a0= 9,138 samples. There will be 832 pathogenic/likely pathogenic SNPs/Indels events with at least one copy of rare allele in the whole exome sequencing data, corresponding to 586 distinct pathogenic SNPs/Indels mapping to 99 genes. The regression analysis provides p-values and beta coefficients of the association with immune traits .https://www.cri-iatlas.org/), in the \"Germline Analysis\" module (https://pheweb-tcga.qcri.org/) was setup to visualize GWAS summary statistics of all tested immune traits is prepopulated with data and results from .The\u00a0CRI iAtlas\u00a0\"Germline\u00a0Analysis\"\u00a0module p-values. The GWAS section provides visualization of significant\u00a0GWAS hits (p\u00a0<\u00a010\u22126), and colocalization results with colocalization posterior probability (CLPP) > 0.01. See tutorial visualizes GWAS summary statistics of all tested immune traits . SNP significance can be also shown for a specific SNP across all tested traits. External resources for SNPs can be accessed from PheWeb .This protocol and related scripts are tailored for the analyses of matched genomic and immune trait datasets in TCGA but can be applied to other datasets with similar structures. The majority of analyzed immune traits are derived from gene expression data and can be adapted to other studies. Code used for the generation of immune traits from gene expression data are provided, and have been previously applied to RNA-sequencing and micrBelow we reported specific limitations related to each step of the protocol.Immune Traits: Immune signatures lack cancer-specific cell type resolution. The majority of immune traits were calculated based on specific gene sets from expression data (RNA-sequencing) from bulk tissue to generate estimates of immune cell activation or abundance using different enrichment or deconvolution techniques. Caution should be exercised when interpreting results in the context of specific tumors or cell types. However, many of these signatures were validated in specific tissues and cancers via FACS sorting or immunohistochemistry/immunofluorescence imaging of immune populations.Many of the immune signatures are highly correlated and not independent measures. Interpretation of results should be considered in context of functional modules defined as clusters of highly correlated signatures. Distribution of immune trait values in the dataset should be considered, and transformation of the data should be performed as needed to approximate a normally distributed set. Traits with a high fraction of zero values should be considered for dichotomization.Heritability Analysis: For heritability estimates run via GCTA GREML, the GCTA FAQ (https://cnsgenomics.com/software/gcta/#FAQ) states that at least 3,160 samples from unrelated individuals are needed to get estimates with standard errors (SEs) down to 0.1 for common SNPs. Only the European ancestry group meets this criterion. Nonetheless, heritability estimates were run in the smaller sized ancestry groups with expectation of large SEs to provide preliminary analyses of immune traits in ancestry groups that are not well studied or sampled.Heritability analysis takes into account only common variants. In this protocol, we used MAF\u00a0>\u00a01% as cut-off. Contribution of rare variants are not accounted for and may explain \u201cmissing\" heritability.GWAS: Linear regression assumes the residuals are normally distributed. Immune traits with skewed distributions were first log10 transformed, those assessed to have close to normal distribution were used as continuous variables. However, some immune traits remained with very skewed distributions due to a high fraction of 0 values, these traits were converted to binary 0 and 1 values based on the median value and logistic regression was performed instead (see \u201cTable\u00a0S2\u201d (able\u00a0S2\u201d ).GWAS was run pan-cancer on the non-hematologic cancers in TCGA which vary in cohort size from 36 (CHOL) to 999 (BRCA). Results may be representative of the most common cancers in TCGA. Post hoc analysis evaluation of associations per cancer (forest plots) can provide insight in the directionality of the betas per cancer and identify potential outliers.2\u00a0\u2265 0.5 and MAF \u2265 0.5% as cut-offs for inclusion. The HRC panel (version 1) consists of 64,976 haplotypes at >39M SNPs constructed from 20 whole genome sequencing studies , per-cancer analysis might reveal additional cancer-specific hits, which might be compared with the ones in the related tissue. Because of the relatively limited number of samples available for each cancer type, per-cancer GWAS and colocalization should be preferentially performed by combining additional cancer-specific sources containing both phenotypic and genotypic data beyond TCGA.Colocalization: Our protocol performed colocalization within a 200 SNP window (+/- 100 from the index SNP). In some cases, we observed that there were SNPs outside of that window that had better association with gene expression but weaker or no association with the immune trait. Therefore, we also performed a manual inspection of the entire locus . We only performed this expanded region analysis of colocalization if there was plausible evidence of colocalization (eCAVIAR CLPP > 0.01) for the 200 SNP window. This expanded region analysis was intended to provide a more stringent criterion.10 p-value of association with the immune trait for each SNP in the region on the X-axis and the negative log10 p-value for association with the relevant gene expression or splicing event . If we found additional SNPs outside of the 200 BP window and they demonstrated a stronger effect for association with gene expression or the sQTL and weaker association with the index SNP, we developed additional criteria for colocalization. If we identified one or more SNPs outside of the window that had a \u2013log10 p-value with expression or splicing that was > 1.5 than the index SNP, we considered that as negative evidence for colocalization. If the SNP(s) with stronger evidence for eQTL or sQTL association had a \u2013log10 p-value that was \u22641.5 compared with the index SNP, we considered the evidence for colocalization as \u201cintermediate.\u201d Finally, if we found no other SNP in the entire region with strong eQTL or sQTL that had a better p-value than the index SNP and the eCAVIAR results gave a posterior probability of colocalization of > 0.01, we considered the evidence to be \u201cstrong.\u201dTo perform these, we plotted the negative logWhile we used this manual second step in addition to eCAVIAR, an alternative approach would have been to use COLOC . This paWithin the TCGA dataset, colocalization was performed on a pan-cancer level. This analysis can be conducted on each cancer type separately, assuming that GWAS and eQTL analyses are also performed for each cancer type separately. Low sample size can be a limiting factor for the per-cancer analysis.Colocalization is based on gene-expression data from TCGA and GTEx\u00a0but can also be performed in different datasets that might be available.Rare Variant Analysis: In this analysis, we focused on variants occurring in cancer-predisposition genes, as previously annotated by . Different aggregation in functional categories might be defined by the users. Heterogeneity of germline calls and batch effect prevented us to run a comprehensive exome-wide analysis as previously defined \u00a0<\u00a00.05%) .Cannot load software or run scripts on the high-performance compute server. Implementation of provided GitHub code produces error see \u201c\u201d.Consult your institution\u2019s IT or compute cluster administrator for proper installation of necessary software including all needed libraries based on the high-performance compute environment. Ensure that the proper software versions, including all libraries and dependencies, are installed. Software implementation may be version specific, the versions used in the protocol are provided to ensure reproducibility.\u2022https://cnsgenomics.com/software/gcta.For troubleshooting of heritability analysis in GCTA GREML, see: \u2022https://www.cog-genomics.org/plink/.For troubleshooting of GWAS in PLINK, see: \u2022https://github.com/CRI-iAtlas/iatlas-app.For issues with installation of CRI iAtlas, see troubleshooting guide on the software website: Provided code should be considered as a guide. Adjust parameters based on cluster capabilities and specifications. Job submission scripts are dependent on the resource allocation management system. E.g., the provided GitHub codes for heritability analysis and GWAS were optimized for the high-performance compute environment at University of California, San Francisco employing Portable Batch System (PBS) job scheduling; consult your system administrator to adapt the provided code to your system.https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020 but the GTEx data were in Build 38 (GRCh38) (see \"https://genome-store.ucsc.edu/) so these two data sets can be compared.We converted the genomic coordinates in TCGA from GRCh37 to GRCh38 using liftOver the SNP in question was not present in the 1000 Genomes Project data which warwsayaman@gmail.com.Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Rosalyn Sayaman, This study did not generate new unique reagents."} +{"text": "Permanent magnet synchronous motors (PMSM) are widely used in industry applications such as home appliances, manufacturing process, high-speed trains, and electric vehicles. Unexpected faults of PMSM are directly related to the significant losses in the engineered systems. The majority of motor faults are bearing fault and stator fault . This article reports vibration and driving current dataset of three-phase PMSM with three different motor powers under eight different severities of stator fault. PMSM conditions including normal, inter-coil short circuit fault, and inter-turn short circuit fault in three motors are demonstrated with different powers of 1.0 kW, 1.5 kW and 3.0 kW, respectively. The PMSMs are operated under the same torque load condition and rotating speed. Dataset is acquired using one integrated electronics piezo-electric (IEPE) based accelerometer and three current transformers (CT) with National Instruments (NI) data acquisition (DAQ) board under international organization for standardization standard (ISO 10816-1:1995). Established dataset can be used to verify newly developed state-of-the-art methods for PMSM stator fault diagnosis. Mendeley Data. DOI: 10.17632/rgn5brrgrn.5 Specifications Table\u00b7 This dataset is acquired from three motors with different powers of 1.0 kW, 1.5 kW, and 3.0 kW, respectively. Two different types of faults including inter-turn short circuits and inter-coil short circuits are seeded. This dataset consists of vibration data which represent the shock of the bearing due to torque unbalance by motor stator faults; and, current data which represent the changes of motor driving power.\u00b7 This dataset is collected according to ISO guideline (ISO 10816-1:1995). Stator faults are artificially seeded using bypassing resistances allocated in inter-coil circuits and inter-turn circuits. Three motors with different powers of 1.0 kW, 1.5 kW, and 3.0 kW are tested under the same experimental setup including rated rotating speed (3000 RPM), rated load condition , sensor location, and their sampling rates .\u00b7 Considering dataset for fault diagnosis often requires large amounts of effort and time consumption, this dataset can provide a useful dataset in the fault diagnosis research field 1This dataset was established for deep learning based motor fault diagnosis research. Unlike other studies, it is very difficult to obtain data in the fault diagnosis research field because it is difficult to apply an actual failure. Therefore, there are many difficulties in training of deep learning algorithm. To solve this problem, we simulated motor stator faults according to the motor power, and obtained vibration and driving current data according to the severity of their faults. This dataset is measured based on mechanical engineering knowledge in accordance with ISO international standards. This dataset used for verification of the deep learning based fault diagnosis method.2Collected dataset consists of vibration and current data acquired from the three PMSMs with different powers of 1.0 kW, 1.5 kW and 3.0 kW. In each motor, total 16 stator faults are seeded with 8 inter-coil circuit faults and 8 inter-turn circuit faults. The motors rotate at a rated rotating speed of 3000 RPM and rated load condition . The collected dataset is stored in technical data management streaming (TDMS) files. TDMS file format can be accessed easily with other data analysis program such as MATLAB 2). The vibration data file includes z-direction of PMSM for inter-turn short circuit and inter-coil short circuit. The description of the vibration files as per operating and health conditions of the motor are provided as follows:1.1000W_0_00_vibration_interturn.tdms: This file includes healthy inter-turn short circuit vibration data in z-direction acquired from the motor whose power is 1.0 kW.2.1000W_2_26_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 2.26 % severity acquired from the motor whose power is 1.0 kW.3.1000W_2_70_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 2.70 % severity acquired from the motor whose power is 1.0 kW.4.1000W_3_35_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 3.35 % severity acquired from the motor whose power is 1.0 kW.5.1000W_4_41_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 4.41 % severity acquired from the motor whose power is 1.0 kW.6.1000W_6_48_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 6.48 % severity acquired from the motor whose power is 1.0 kW.7.1000W_12_17_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 12.17 % severity acquired from the motor whose power is 1.0 kW.8.1000W_21_69_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 21.69 % severity acquired from the motor whose power is 1.0 kW.9.1000W_0_00_vibration_intercoil.tdms: This file includes healthy inter-coil short circuit vibration data in z-direction acquired from the motor whose power is 1.0 kW.10.1000W_0_68_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 0.68 % severity acquired from the motor whose power is 1.0 kW.11.1000W_0_81_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 0.81 % severity acquired from the motor whose power is 1.0 kW.12.1000W_1_01_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 1.01 % severity acquired from the motor whose power is 1.0 kW.131000W_1_34_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 1.34 % severity acquired from the motor whose power is 1.0 kW.14.1000W_2_00_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 2.00 % severity acquired from the motor whose power is 1.0 kW.15.1000W_3_93_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 3.93 % severity acquired from the motor whose power is 1.0 kW.16.1000W_7_56_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 7.56 % severity acquired from the motor whose power is 1.0 kW.17.1500W_0_00_vibration_interturn.tdms: This file includes healthy inter-turn short circuit vibration data in z-direction acquired from the motor whose power is 1.5 kW.18.1500W_1_57_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 1.57 % severity acquired from the motor whose power is 1.5 kW.19.1500W_1_88_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 1.88 % severity acquired from the motor whose power is 1.5 kW.20.1500W_2_34_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 2.34 % severity acquired from the motor whose power is 1.5 kW.21.1500W_3_10_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 3.10 % severity acquired from the motor whose power is 1.5 kW.22.1500W_4_57_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 4.57 % severity acquired from the motor whose power is 1.5 kW.23.1500W_8_74_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 8.74 % severity acquired from the motor whose power is 1.5 kW.24.1500W_16_08_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 16.08 % severity acquired from the motor whose power is 1.5 kW.25.1500W_0_00_vibration_intercoil.tdms: This file includes healthy inter-coil short circuit vibration data in z-direction acquired from the motor whose power is 1.5 kW.26.1500W_4_79_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 4.79 % severity acquired from the motor whose power is 1.5 kW.27.1500W_5_70_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 5.70 % severity acquired from the motor whose power is 1.5 kW.28.1500W_7_02_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 7.02 % severity acquired from the motor whose power is 1.5 kW.29.1500W_9_15_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 9.15 % severity acquired from the motor whose power is 1.5 kW.30.1500W_13_12_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 13.12 % severity acquired from the motor whose power is 1.5 kW.31.1500W_23_20_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 23.20 % severity acquired from the motor whose power is 1.5 kW.32.1500W_37_66_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 37.66 % severity acquired from the motor whose power is 1.5 kW.33.3000W_0_00_vibration_interturn.tdms: This file includes healthy inter-turn short circuit vibration data in z-direction acquired from the motor whose power is 3.0 kW.34.3000W_1_78_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 1.78 % severity acquired from the motor whose power is 3.0 kW.35.3000W_2_13_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 2.13 % severity acquired from the motor whose power is 3.0 kW.36.3000W_2_65_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 2.65 % severity acquired from the motor whose power is 3.0 kW.37.3000W_3_50_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 3.50 % severity acquired from the motor whose power is 3.0 kW.38.3000W_5_16_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 5.16 % severity acquired from the motor whose power is 3.0 kW.39.3000W_9_81_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 9.81 % severity acquired from the motor whose power is 3.0 kW.40.3000W_17_86_vibration_interturn.tdms: This file includes inter-turn short circuit fault vibration data in z-direction with 17.86 % severity acquired from the motor whose power is 3.0 kW.41.3000W_0_00_vibration_intercoil.tdms: This file includes healthy inter-coil short circuit vibration data in z-direction acquired from the motor whose power is 3.0 kW.42.3000W_2_49_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 2.49 % severity acquired from the motor whose power is 3.0 kW.43.3000W_2_98_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 2.98 % severity acquired from the motor whose power is 3.0 kW.44.3000W_3_69_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 3.69 % severity acquired from the motor whose power is 3.0 kW.45.3000W_4_86_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 4.86 % severity acquired from the motor whose power is 3.0 kW.46.3000W_7_12_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 7.12 % severity acquired from the motor whose power is 3.0 kW.47.3000W_13_10_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 13.10 % severity acquired from the motor whose power is 3.0 kW.48.3000W_23_48_vibration_intercoil.tdms: This file includes inter-coil short circuit fault vibration data in z-direction with 23.48 % severity acquired from the motor whose power is 3.0 kW.Vibration data were measured using accelerometer (PCB352C34) and acquired using NI9234 module for 120 seconds with sampling frequency of 25.6 kHz. Each vibration data file contains two columns namely \u2018Time Stamp\u2019, and \u2018amplitude\u2019. The unit of the vibration amplitude is \u2018gravitational constant (g)\u2019 \u2019. The description of the current files as per operating and health conditions of the motor are provided as follows:33.1PMSM testbed was built to measure the vibration and current data of healthy state and faulty states from PMSMs with different powers as shown in 3.2Failure modes of the motor stator can be categorized into: first, the increase of the resistance of the stator (open-like fault); or second, the decrease of the resistance of the stator (short-like fault). In case of open-like fault, a part of the state coil is damaged increasing the stator resistance so that driving current decreased proportional to the resistance change for given input voltage. Hence this type of failure is relatively easy to detect by reading the overall decrease of the current. On the other hand, most of difficult failures come from the second failure mode such that part of stator coil is damaged to have a short-like circuit between turns ; or between coils . These type of short circuit faults introduce a bypassing path of the driving current so that the normal current flowing through the stator coil is reduced by the Kirchhoff's law. As result, the motor experiences reduction of electro-magnetic field in turn the induced torque as well. Considering these types of short circuit faults, we seeded inter-turn short circuit fault and inter-coil short circuit fault controlling the bypass resistances in the short circuits as follows.Rbypass is the bypassing resistance values, and the R is stator resistance values.The smaller the bypass resistance value, the larger driving current flows to the bypass resistance, then the smaller driving current flows through the motor stator due to Kirchhoff's law. In this case, the severity of the motor's fault is regarded as high. Therefore, the fault was representatively seeded by adding a short circuit connecting turns (or coils) using the bypassing resistance to the motor winding as shown in Human Lab., Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea has given the consent that the datasets may be publicly-released as part of this publication. We declare that the manuscript adheres to Ethics in publishing standards and the submitted dataset is the real data recorded in the experiment, and there is no act of stealing other people's data or modifying data.Wonho Jung: Conceptualization, Methodology, Software, Validation, Visualization, Data curation, Writing \u2013 original draft, Writing \u2013 review & editing. Sung-Hyun Yun: Data curation. Yoon-Seop Lim: Investigation. Sungjin Cheong: Investigation. Yong-Hwa Park: Funding acquisition, Writing \u2013 review & editing, Supervision.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "The saccadic pathway involves numerous regions of the brain cortex, the cerebellum and the brainstem. Saccadic movement latency, velocity and precision parameters assess the efficacy of central nervous system (CNS) control over rapid eye movements. Very few disorders which alter the CNS are missed when these parameters are carefully measured using a computer. Pendular tracking assesses the integrity of the oculomotor system in controlling slow eye movements - vulnerable to CNS and vestibular system dysfunctions. Optokinetic nystagmus represents a stereoceptive response which compensates environment movements by psycho-optical inputs.to compare the oculomotricity values found in children with and without learning complaints.prospective study. We included in the study 28 children of both genders, within the age range between 8 and 12 years, with learning disorders (study group) and 15 without (control group). We carried out the fixed and randomized saccadic movement tests, pendular tracking study and optokinetic nystagmus.There was a statistically significant difference between the groups concerning the randomized saccadic movement velocity parameters and in the pendular tracking test.The children with learning disorders presented alterations in some oculomotricity tests when compared to children without complaints. Saccade voluntary control abnormalities have been seen in development disorders such as: dyslexia; learning disorders; hyperactivity and attention deficit. The saccadic pathway involves numerous regions of the brain cortex, cerebellum and brainstem. Latency, velocity and saccadic movement precision parameters assess the central nervous system (CNS) control efficiency over rapid eye movements4Pendular tracking is a test which is strongly affected by the patient's attention span and collaboration. There may be cases of pendular tracking poorly formed in inattentive and non-cooperating patients or even in some elderly individuals, without it meaning a central disorderThe necessary eye movement for reading requires alternate saccade movements and fixation periods. It starts with a saccade that runs for 8 to 10 words mixed with periods of eye fixation and ends with a long saccade in order to start a new lineThe goal of the present study was to compare the eye movement parameters found in children with learning disorders - especially in reading and writing - with children without complaints.QUESTIONNAIRE TEMPLATEChild: ________________________________________________________________Current date: ____/____/ ________Parent/guardian: ________________________________________________________The questionnaire below aims at studying learning difficulties. Please, answer it by checking with a \u00d7 in the option you think correct and fill in the blanks when requested. The data hereby expressed serve research purposes (data computing) and will be kept confidential. It is very important that you return this form to us. The questionnaire must be returned on the day of the medical consultation.Does your child have or has had:Difficulties reading: yes no - Which? _____________________________Difficulties writing: yes no - Which? _____________________________Poor school performance: yes no Repeated a school year (s): yes no Why do you think this happened? ___________________________________________________________________________________________________________________________Problems of attention and concentration at school: yes no The population studied was made up of 43 children of both genders, of age range between 8 and 12 years, being 28 (study group) with diagnosis of learning disorders (reading and writing) and 15 belonging to the control group without any learning disorder. All the children, from both groups, did not wear glasses. We carried out fixed and randomized saccadic movement test, pendular tracking test in the frequencies of 0.20Hz, 0.40Hz and 0.80Hz and optokinetic nystagmus test. Equipment: digital vectonystagmophapher with the VECWIN software, a Neurograff Eletromedicina\u00ae bar of led. The parents/guardians received a questionnaire about learning-related symptoms. The analyses were automatically done by the software. As far as eye movements are concerned, we analyzed the following parameters: accuracy ; velocity ; latency and gain (measure the relationship between eye velocity and the stimulus velocity used in optokinetic and pendular tracking tests)As far as gender is concerned the control and study groups were homogeneous (p= 0.518). The distribution is on In our study we could notice that the mean values found in fixed saccade movements are within normal ranges in digital vectonystagmography in terms of accuracy, latency and velocityChildren with learning disorders have alterations in some eye movement tests when compared to \u201cnormal\u201d healthy children."} +{"text": "The complexity and volume of data associated with population-based cohorts means that generating health-related outcomes can be challenging. Using one such cohort, the UK Biobank\u2014a major open access resource\u2014we present a protocol to efficiently integrate the main dataset and record-level data files, to harmonize and process the data using an R package named \u201cukbpheno\u201d. We describe how to use the package to generate binary phenotypes in a standardized and machine-actionable manner.For complete details on the use and execution of this protocol, please refer to \u2022A protocol to efficiently process UK Biobank phenotypic data\u2022Reproducible and semi-automatic generation of binary health-related phenotypes\u2022Utilities with visualization to aid data exploration and phenotype definition\u2022Example analyses common among genetic epidemiological studies Publisher\u2019s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. The complexity and volume of data associated with population-based cohorts means that generating health-related outcomes can be challenging. Using one such cohort, the UK Biobank\u2014a major open access resource\u2014we present a protocol to efficiently integrate the main dataset and record-level data files, to harmonize and process the data using an R package named \u201cukbpheno\u201d. We describe how to use the package to generate binary phenotypes in a standardized and machine-actionable manner. The UK Biobank is a large-scale population cohort with in-depth collection of phenotypic and genetic data . While ihttps://github.com/niekverw/ukbpheno). The package contains functionalities to harmonize data of various sources in a consistent manner accompanied by structured metadata. To allow interactive exploration, the package contains multiple functionalities to visualize the data and it can be run on typical workstations (high-performance computing cluster is not required). In line with the FAIR principle , it is aIn this protocol, we show how to download and process the data from the UK Biobank as well as to generate health related phenotypes with the use of ukbpheno. More specifically, we utilize the ukbpheno package to first harmonize various data into single episode format and then generate the phenotypes . We thenTiming: 4\u201312 hNote: The UK Biobank data are an open access resource to any bona-fide researchers. The data analyzed in this protocol were obtained through application number 74395. Please refer to the following link to request access to UK Biobank data: https://www.ukbiobank.ac.uk/enable-your-research/apply-for-access.1.a.https://biobank.ctsu.ox.ac.uk/\u223cbbdatan/Accessing_UKB_data_v2.3.pdf) to obtain and decrypt the main dataset from the UK Biobank Data Showcase (Showcase) . Files needed in this step include:i.An MD5 Checksum to verify download .ii.A key file for decryption .iii.Utilities software \u201cukbmd5\u201d and \u201cukbunpack\u201d available on Showcase.Follow the steps in section b.ukbconv ukbxxxxx.enc_ukb docGenerate a metadata file (.html) of the decrypted main dataset (.enc_ukb) using utility \u201cukbconv\u201d (available on Showcase).c.ukbconv ukbxxxxx.enc_ukb rCRITICAL: Do not run the accompanied ukbxxxxx.R script generated at this step. Only the tab separated file (.tab) is required.Generate a tab-separated file (.tab) of the decrypted main dataset (.enc_ukb) using utility \u201cukbconv\u201dDownload and decrypt the main dataset.2.https://biobank.ndph.ox.ac.uk/showcase/).a.Click the \u201cLogin\u201d on the top of the webpage which redirects users to the Access Management System.b.Once logged in, select \u201cProjects\u201d on the left panel of the Access Management System and view the relevant project (\u201cView/Update\u201d).c.i.Once in the Showcase, move to \u201cDownloads\u201d tab on the top of the webpage.ii.In the \u201cDownloads\u201d page, researchers with access to record-level data will see a tab \u201cData Portal\u201d next to the tab \u201cDatasets\u201d.iii.Connect to the record repository in the \u201cData Portal\u201d tab.Inside the project, select the \u201cData\u201d tab to connect the Showcase in \u201clogged-in\u201d mode.d.i.Request access to record-level hospital inpatient data via Field 41259.ii.Request access to record-level primary care data via Field 42038, 42039 and 42040.iii.Request access to record-level death register via Field 40023.Download the complete data tables (.txt) through the \u201cTable\u00a0Download\u201d tab.Obtain the record-level data from Data Portal on Showcase inside an R session.install.packages(\"data.table\")install.packages(\"dplyr\")install.packages(\"ggplot2\")install.packages(\"ggforce\")install.packages(\"tableone\")install.packages(\"survminer\")install.packages(\"MatchIt\")install.packages(\"devtools\")devtools::install_github(\"niekverw/ukbpheno\")library(data.table)library(dplyr)library(ukbpheno)library(ggplot2)library(ggforce)library(tableone)library(survminer)library(\"MatchIt\")There is no hard requirement on R versions for ukbpheno. Results presented in this protocol were produced running with R version 4.0.3 with RStudio version 1.3.959 in a Unix system.Timing: 2\u20138 h1.https://github.com/niekverw/ukbpheno/tree/master/inst/extdata/data.settings.tsv.Download data setting file (data.settings.tsv) to the project directory from 2.https://github.com/niekverw/ukbpheno/tree/master/inst/extdata/definitions_DmRxT2.tsv.Download definition table template to the project directory from 3.a.i.Each code should be separated by a comma.ii.For code systems with hierarchical system (refer to data setting file), it is possible to fill in only the parent codes instead of specifying all codes.iii.Annotations of the codes can be made using curly bracket \u201c\u201d.Optional: We included a shiny app to cross-reference codes between systems using the mapping file provided by UK Biobank. (https://github.com/niekverw/ukbpheno/blob/master/inst/util/shiny.lookup_codes.R). Download the code map file (Excel workbook) provided by the UK Biobank (https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=592): (1) locate the shiny app script and run the shiny app, and (2) visit the address returned in a web browser and use the app. A screenshot of the shiny app can be found in\u00a0For each of code systems e.g., diagnosis codes ICD10 or operation codes OPCS4 as well as codes used in the self-report fields, fill in the corresponding codes in the table.b.i.Fill in field number as Showcase followed by the condition e.g., \u201c6177=3(insulin)\u201dii.iii.Add the corresponding age of diagnosis using \u201c\u201d following the condition e.g., \u201c4041=1[2976]\u201dFill in fields with conditions in the \u201cTS\u201d (touchscreen) column.Fill in one phenotype (such as DmT2) per row. The column \u201cTRAIT\u201d contains the unique identifier of each phenotype which is case sensitive.4.a.\u201cStudy_population\u201d can be used to restrict definition on a subgroup of participants with specific phenotype.b.Participants with phenotypes in \u201cInclude_definition\u201d will be considered to be a case for the composite phenotype.c.Users may use the \u201cExclude_from_cases\u201d and \u201cExclude_from_controls\u201d column to exclude participants with certain phenotype(s) from cases and controls respectively.It is possible to create a composite phenotype, which involves other phenotypes. Composite phenotypes are constructed using four columns in the definition table .a.\u201cStudyNote: For example, a composite phenotype \u201cdiabetes mellitus\u201d may include two phenotypes \u201ctype 1 diabetes\u201d and \u201ctype 2 diabetes\u201d. Alternatively, for the phenotype \u201ctype 2 diabetes\u201d we may want to exclude any cases with also a \u201ctype 1 diabetes\u201d diagnosis.5.a.Trait \u201cDmT2\u201d, \u201cDmT1\u201d and \u201cDmG\u201d contain specific codes for diabetes type 2, type 1 and gestational diabetes respectively;b.\u201cRxDm\u201d defines the antidiabetic medication which is further divided into \u201cRxDmIns\u201d (Insulin) and \u201cRxDmOr\u201d ;c.\u201cDm\u201d captures general codes for diabetes and the remaining definitions are used to differentiate between type 1 and type 2 diabetes within this group.The definition table template \u201cdefinitions_DmRxT2.tsv\u201d contains definitions constructed for the definition of type 2 diabetes in the UK Biobank.Health outcome information from various data sources / data fields within the main dataset is encoded differently. These relationships have been curated and recorded in the data setting file included in the ukbpheno package. For a target phenotype, survey the various data sources/\u00a0data fields on the Showcase and determine the definitions for the target phenotype in\u00a0UK Biobank. An example definition table to define type 2 diabetes is included in the package.\u00a0This example table can be used as a template for users to define their target health outcomes.Timing: 15\u00a0min6.Specify data file paths in R.# The directory with data filespheno_dir <-\"mydata/ukb99999/\"# Main datasetfukbtab <- paste# Metadata filefhtml <- paste# Hospital inpatient datafhesin <- pastefhesin_diag <- pastefhesin_oper <- paste# GP datafgp_clinical <- pastefgp_scripts <- paste# Death registryfdeath_portal <- pastefdeath_cause_portal <- paste# Participant withdrawal listf_withdrawal<-paste7.Specify files paths for the data setting file, the definition table and code maps which are included in the package (extdata/). Alternatively download the files from code repository of ukbpheno hosted at GitHub.# Or download the files fromhttps://github.com/niekverw/ukbpheno/tree/master/inst/extdata/#extdata_dir<-paste0,\"/\")fdefinitions <- paste0fdata_setting <- paste08.Read data setting file. The pre-curated data setting file specifies the characteristics of each data source which are taken into account in the data harmonization process.dfData.settings <- fread(fdata_setting)9.a.i.Code maps include all available codes.The function \u201cread_definition_table\u201d expands parent codes using the code maps and sort out codes relevant for inclusion and exclusion accordingly.b.i.A specific ICD10 code may not exist in the UK Biobank ICD10 code map as this code is not present in the data.ii.There may be typos.The function will also cross-check codes entered in the definition with the code maps and warn users of any non-matching codes e.g.,Run the \u201cread_definition_table\u201d function to process the definition table.dfDefinitions_processed_expanded<-read_defnition_tableOptional: Alternatively download the code maps from the UK Biobank Showcase or create them manually by extracting all unique codes from your data using \u201cget_all_exisiting_codes\u201d which generates flat-form code maps. Adjust the data setting file accordingly.# First input: file path to GP clinical table# Second input: corresponding column names from the .txt file# Third input: output file-pathget_all_exsiting_codes,c)Input files required by the package include data files from UK Biobank including the main dataset, the metadata file and optionally data tables from Data Portal; the completed definition table and data setting file.Timing: 15\u201345\u00a0minAt the harmonization step, we combine all the available data files from various sources and transform them to the format of clinical events to facilitate downstream analyses . For ind10.a.The \u201callow_missing_fields\u201d flag specifies whether field(s) required on the definition table but missing in the main dataset is allowed and ignored. If this flag is set to \u201cFALSE\u201d, the harmonization step will halt in case of any missing field.b.If the participant withdrawal list is provided, records of these individuals will be removed.Load, process and harmonize all data files using harmonized_ukb_data.Note: The function harmonized_ukb_data harmonizes all available data . Additionally, the function will check if all fields required on the definition table are present in the main dataset and inform the user if any field is missing.lst.harmonized.data<-harmonize_ukb_dataNote: Time required to harmonize the data is dependent on size of the files. Factors that should be taken into considerations include number of fields approved for the particular project, number of participants included as well as if record-level primary care data are present.11.View(lst.harmonized.data)a.i.View(lst.harmonized.data$lst.data)Diagnosis codes without associated actual event date will have date of visit to assessment center (such as self-report diabetes) in the \u201ceventdate\u201d column and \u201c0\u201d in the \u201cevent\u201d indicating that the date does not reflect a true event .View definition, the harmonized data tables, the data settings and the individuals to be included (either specified by a vector of participant identifiers or a data-frame containing identifier in the first column and reference dates in the second column).# 1) definition of the target trait \u201cType 2 diabetes\u201dtrait<-\"DmRxT2\"# 2) harmonized data table - lst.harmonized.data# 3) data setting data-frame - dfData.settings# 4) individuals specified via df_reference_date# Here the dates of baseline visit (f.53.0.0) are taken as referencedf_reference_dt_v0<-lst.harmonized.data$dfukb13.lst.DmRxT2.case_control <- get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==trait), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)View(lst.DmRxT2.case_control)a.\u201cdf.casecontrol\u201d is a data.table object of 16 columns providing summary of the diagnosis per participant . Includeb.\u201call_event_dt.Include_in_cases\u201d is data.table object including all event episodes supporting the diagnosis for the cases included .Table\u00a05Cc.\u201call_event_dt.Include_in_cases.summary\u201d is a data.table object with the same format with \u201cdf.casecontrol\u201d but includes only cases (both included and excluded case).Use \u201cget_cases_controls\u201d function to obtain the case/control status. The function returns a list of three data.table objects: \u201cdf.casecontrol\u201d, \u201call_event_dt.Include_in_cases\u201d and \u201call_event_dt.Include_in_cases.summary\u201d .lst.DmRx14.Generate timeline plot to check the relative contribution by various data sources over time . Events DmRxT2_timeline<-plot_disease_timeline_by_source(definition=dfDefinitions_processed_expanded%>%filter(TRAIT==trait),lst.harmonized.data$lst.data,dfData.settings, df_reference_dt_v0$identifiers)DmRxT2_timeline15.Use \u201cmake_upsetplot\u201d to examine the overlaps between the data sources at baseline to gain insight on their relationships .Figure\u00a09upset_plot<-make_upsetplot(definition=dfDefinitions_processed_expanded%>%filter(TRAIT==trait),lst.harmonized.data.gp$lst.data,dfData.settings,df.reference.dates\u00a0= df_reference_dt_v0)upset_plot16.Generate summary descriptions on the events with \u201cget_stats_for_events\u201d. For example, generation of a frequency plot of codes among all events from secondary care may help verify or refine the definition .Figure\u00a01# Extract all hospital admission recordsall_DmRxT2_evnt<-lst.DmRxT2.case_control$all_event_dt.Include_in_casesDmRxT2_hesin_rec<-all_DmRxT2_evnt[grepl ]# Get some descriptive statistics on the records on a code levelhesin_stats<-get_stats_for_events(DmRxT2_hesin_rec)hesin_stats$stats.codes.summary.phesin_stats$stats.codes.summary.p17.Explore secondary care code count by individual .Figure\u00a01# Get some summary statistics on the records on individual levelDmRxT2_rec_cnt<-DmRxT2_hesin_recmax(DmRxT2_rec_cnt$count)median(DmRxT2_rec_cnt$count)mean(DmRxT2_rec_cnt$count)quantile(DmRxT2_rec_cnt$count)# Visualize count with barplot with a zoom-in on count between 0-50ggplot2::ggplot)\u00a0+\u00a0ggplot2::geom_bar(fill=\"#0073C2FF\")\u00a0+ ggplot2::xlab(\"Number fo secondary care record per person\")\u00a0+\u00a0ggplot2::ylab(\"Frequency\")\u00a0+ #theme with white background\u00a0ggplot2::theme_bw\u00a0+ ggplot2::theme(text\u00a0= ggplot2::element_text(size=22),panel.grid.minor\u00a0=ggplot2::element_blank,panel.grid.major\u00a0=ggplot2::element_blank)\u00a0+ ggforce::facet_zoom)18.Generate a timeline of the codes contributing to diagnosis for a particular individual (please replace the identifier if copied from the cell below) .Figure\u00a01# Plot individual time lineplot_individual_timeline19.First identify participants with specific diabetes codes as well as general diabetes code.# Identify individuals with specific DmT2 codeslst.DmT2.case_control<-get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"DmT2\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)# Identify individuals with specific DmT1 codeslst.DmT1.case_control<-get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"DmT1\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)# Identify individuals with DmGlst.DmG.case_control <- get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"DmG\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)# Identify individuals with general diabetes diagnosis codes excl. medicationlst.Dm.case_control <- get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"Dm\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)20.Identify use of different anti-diabetic medications. Find individuals on metformin likely due to\u00a0diseases other than diabetes by cross checking with the list of individuals with diabetes diagnoses.# Identify individuals with metformin uselst.RxMet.case_control <- get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"RxMet\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)#Identify use of insulin/oral diabetic med. excl. metforminlst.RxDmNoMet.case_control <- get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"RxDmNoMet\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)#Identify individuals that are on metformin but no diabetes codes#nor medication other than metforminRxMet_DmUnlikely<-setdiff)21.a.We identify these individuals via set operations of the relevant diagnoses.b.Inspect the records of these individuals for evidence of type 2 diabetes.Cross-examine various diagnoses. For example we want to get individuals with young onset diabetes but did not have records supporting a diagnosis of non-type 2 diabetes. Namely these individuals did not have evidence of type 1 diabetes nor gestational diabetes.# Identify individuals with self-report insulin <12\u00a0months post-diagnosislst.RxDmInsFirstYear.case_control<-get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"RxDmInsFirstYear\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)# Identify young onset self reported diabetes (European origin)lst.SrDmYEw.case_control <- get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"SrDmYEw\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)# identify young onset self reported diabetes (Caribbean African origin)lst.SrDmYSaCa.case_control <- get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==\"SrDmYSaCa\"), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)# Individuals of young onset diabetesind_young_onset<- union# Individuals with evidence of other types of diabetes reportedind_RxInsFirstYear_DmT1_DmG<- union,lst.DmG.case_control$df.casecontrol[Hx==2]$identifier)# Young onset but no DM type 1/ gestational diabetes specific codes nor self report of insulin within first year of diagnosisinds_young_onset_possible_DmT2\u00a0<-setdiff# Check the records of these individualslst.DmRxT2.case_control$all_event_dt.Include_in_cases[identifier %in% inds_young_onset_probable_DmT2]To make the definition of the type 2 diabetes more precise, we may screen and exclude individuals with evidence of other types of diabetes as well as the use of metformin not due to diabetes.Timing: 15\u201330\u00a0min22.Read and process the definition file.# Read the definitions tablefdefinitions <- paste0dfDefinitions_processed_expanded<-read_defnition_table23.a.The metadata provides information such as data type of these fields.b.Extract age at assessment center visit (Field 21003), sex (Field 31), body mass index (Field 21001), glycated hemoglobin level (Field 30750), glucose level (Field 30740), self-report insulin use within the first year of diabetes diagnosis (Field 2986), UK Biobank assessment center visited (Field 54) and Date of attending assessment center (Field 53).Extract only the required fields from the main dataset using read_ukb_tabdata.# Extract clinical variables from the main dataset using read_ukb_tabdata# We need the metadata (.html) file for read_ukb_tabdatadfhtml <- read_ukb_metadata(fhtml)# Rename the identifier column in the metadatadfhtml$field.tab<-\"identifier\"# Age at assessment center visit, sex, BMI, HbA1c, glucose,insulin within 1 year of diagnosis,UK Biobank assessment center location, date of visitbaseline_fields<-c# Extract these variables from main datasetdfukb_baseline <- read_ukb_tabdatagc24.Generate the phenotypes for atrial fibrillation, coronary artery disease, type 2 diabetes, hypertrophic cardiomyopathy, heart failure, hypertension and hyperlipidemia with a loop and merge the phenotype information into one table \u201cdfukb_baseline_pheno\u201d.# The target disease traits we will generate in batchdiseases<-c# Make an output folder to store the resultout_folder<-paste0if(!dir.exists(file.path(out_folder))){dir.create(file.path(out_folder))}df_withdrawal<-fread# remove withdrawn participantsdfukb_baseline_pheno<-dfukb_baseline[! identifier %in% df_withdrawal$V1]# Loop through the traits, including family history of related diseases and the diabetes medication usefor ){print(disease)lst.case_control <- get_cases_controls(definitions=dfDefinitions_processed_expanded %>% filter(TRAIT==disease), lst.harmonized.data$lst.data,dfData.settings, df_reference_date=df_reference_dt_v0)\u00a0# Add the trait to the column namescolnames(lst.case_control$df.casecontrol) <- paste, sep\u00a0= \"_\")\u00a0# Except for participant identifiernames(lst.case_control$df.casecontrol)[names(lst.case_control$df.casecontrol)\u00a0== paste]<-\"identifier\"# Merge these columns with dfukb_baseline_phenodfukb_baseline_pheno<-merge}This session demonstrates how to generate multiple phenotypes and make a clinical characteristics table with these phenotypes, stratified by type 2 diabetes status. An example definition table with the selected cardiometabolic diseases, family history of these diseases and diabetes medication usage is provided in the package. We additionally extract demographic information namely age and sex as well as biomarkers BMI, blood glucose, glycated hemoglobin and self-report insulin use within one year of diabetes diagnosis from the main dataset.Timing: 10\u00a0min25.Select variables to be reported in the clinical characteristics table. Rename the variables in the table to improve readability. Create the clinical characteristics table stratified by type 2 diabetes. Write the clinical characteristic table to a file.# Keep only the variables needed for the tabledfukb_baseline_pheno_fortable1<-dfukb_baseline_pheno# Negative first diagnosis day indicates history while positive indicates follow-up casesdfukb_baseline_pheno_fortable1$DmT2_0_first_diagnosis_years<-(-1\u2217dfukb_baseline_pheno_fortable1$DmT2_0_first_diagnosis_days)/365.25# Rename for readabilitycolnames(dfukb_baseline_pheno_fortable1)<-c# Below the parameters for CreateTableOne# The full variable listvars<-c# The categorical variables on the clinical characteristics tablefactorVars<-setdiff)# Create the clinical characteristic table stratified by type 2 diabetestableOne <- CreateTableOnehist(dfukb_baseline_pheno_fortable1$`Years since type 2 diabetes diagnosis`)tableOnetab1Mat <- print)# Save the table to a CSV filewrite.csv)In the following example analyses, we investigate the characteristics of participants with type 2 diabetes specific codes. We exclude the cases with type 1 diabetes diagnosis codes and we exclude any controls with non-specific diabetes codes .25.SelecTiming: 5\u00a0min26.a.The start time is the date when the participant visited the assessment center;b.Observed time is up to date of event or earliest among date of death and censoring date of hospital inpatient records (last follow up).With time-to-event data as well as the censoring dates for different data sources for different regions, compute the observed time for each participant.# Get death dates from datadeathdt<-unique])# Rename the column and mergecolnames(deathdt)<-cdfukb_baseline_pheno<-merge# HESIN censoring date are different by regions# Use the UK Biobank assessment center location attended by the participantsengland<-cscotland<-cwales<-c# Corresponding censoring datesdfukb_baseline_pheno<-as.Date(\"2021-03-31\")dfukb_baseline_pheno<-as.Date(\"2021-03-31\")dfukb_baseline_pheno<-as.Date(\"2018-02-28\")# Time-to-event/observed time is determined at earliest of date of event, date of death and censoring date of HESIN data (last follow up)# This is already calculated for those who have eventsrange# non-event but died before HESIN censoring datedfukb_baseline_pheno# People censored at last fu# non-event but died after censoring date (HESIN),dfukb_baseline_pheno# non-event and alive by censoring datedfukb_baseline_pheno27.Create the survival object and Kaplan-Meier plot for new onset heart failure stratified by type 2 diabetes status at baseline.#Estimate risk of new onset heart failure by presence/absence of type 2 diabetes at baselinefit<-survival::survfit \u223c DmT2_0_Hx, data\u00a0= dfukb_baseline_pheno[DmT2_0_Hx>0])# summary(fit)# Make Kaplan-Meier plotggsurvplot\",\u00a0censor.size=2,\u00a0palette\u00a0= c,\u00a0conf.int\u00a0= TRUE, # Add confidence interval\u00a0pval\u00a0= TRUE, # Add p-value\u00a0risk.table\u00a0= TRUE, # Add risk table\u00a0risk.table.col\u00a0= \"strata\", # Risk table color by groups\u00a0legend.labs\u00a0= c,\u00a0risk.table.height\u00a0= 0.2)Timing: 5\u00a0min28.To match type 2 diabetes case to control by age, sex and body mass index. We extract those variables and remove individuals with missing values in either the target phenotype or any covariates.######################################### 1:2 case control matching with MatchIt#########################################library(\u201cMatchIt\u201d)# Remove individuals with either missing or excluded phenotype for target phenotype (type 2 diabetes at baseline)df_to_matchit<-dfukb_baseline_pheno[!is.na(DmT2_0_Hx) & DmT2_0_Hx>0]# Pick three covariates age at assessment center visit, sex and BMI for matchingdf_to_matchit<-na.omit])29.Format the coding of the phenotype and name the rows by participant identifier in preparation for the matchit function. Run the matchit function to match 2 controls to each case. Examine the result.# Format the data for the matchit function# Control/case: 1/2 to 0/1df_to_matchit$DmT2_0_Hx<-df_to_matchit$DmT2_0_Hx-1# Name the rowsrownames(df_to_matchit)<-df_to_matchit$identifiercolnames(df_to_matchit)<-c# Run matchitm.dm2<-matchit#Check resultsummary(m.dm2)# Each row in the match.matrix shows identifier of one case with 2 matched controlsm.dm2$match.matrixSometimes it may be desirable to match cases and controls by characteristics such as age and sex\u00a0in certain studies. Here we demonstrate how to further process phenotypes created in ukbpheno to generate matched case-control pairs. We utilize an R package MatchIt for the matching task.After the harmonization step, the user should have in the R workspace the data from both Data Portal (record level data) as well as a subset of the main dataset relevant for the target phenotypes (as specified in the definition table). Users can perform further analyses in R as they see fit .Using our machine with 64 GB RAM (DDR4 2667 MHz) and 10-core processor (Intel Skylake) under an Ubuntu 16 system, it took 12\u00a0min to load and process the main dataset and all record level files. Of which the most time-consuming step was loading the main dataset (six minutes with file size 35.5 GB) followed by the primary care data . The harmonization step was additionally tested on an Ubuntu 16 machine with 16 GB RAM (DDR4 2667 MHz) and 6-core processor (AMD Ryzen 5). It took approximately 45\u00a0minutes to complete on this machine.The \u201cget_cases_controls\u201d function from ukbpheno determines the case/control status for a target phenotype following the inclusion/exclusion criteria outlined in the definition table. Users can extract prevalent as well as incident cases with a specific reference time point. Results presented in this protocol are produced using data downloaded in June 2021, with primary care data for\u00a0around 45% of the UK Biobank cohort available and data censoring dates shown in Following the example definition of \u201cDmRxT2\u201d, users should expect a prevalence of 4.7% at the baseline visit, an estimate close to . AdditioExamining the diabetes diagnoses captured in secondary care system, user should be able to\u00a0obtain similar frequency plots as shown in With the plot_individual_timeline function, user should expect visualization of diagnosis codes\u00a0of\u00a0a selected participant over time. Lastly in the cross-examinations with other types of diabetes and medication, users should expect similar numbers as reported in the prevalence algorithms by Eastwood and colleagues . Users cIn this part users should be able to generate the cardiometabolic phenotypes namely, atrial fibrillation or flutter, coronary artery disease, hypertrophic cardiomyopathy, heart failure, type 2 diabetes, hypertension and hyperlipidemia. Users should also obtain the related phenotypes including family history of diabetes, family history of heart disease, family history of hypertension and the use of diabetes medications. Using our machine with 64 GB RAM (DDR4 2667 MHz) and 10-core processor (Skylake), it took three minutes to process all 12 phenotypes.In this part users should obtain a clinical characteristics table stratified by type 2 diabetes status . The diap<0.0001 in the data analyzed.In the survival analysis on new-onset heart failure (outcome of interest) between participants with or without type 2 diabetes at baseline, user would obtain a Kaplan-Meier plot similar to Following up with the type 2 diabetes phenotype we created, it can be seen that case-control ratio is unbalanced. It can also be seen that the controls were younger, more likely to be female and had lower body mass indices compared to the cases . We usedPhenotyping of a heterogenous resource such as UK Biobank can be challenging due to multiple\u00a0data origins compounded with varying coverage both in terms of time and individuals. In the current protocol we demonstrate how to use the ukbpheno package to define health-related\u00a0outcomes and we presented possible analyses with regard to the phenotyping process.With the ukbpheno package, the case/control status is determined by presence of diagnosis records. In the case of contradictory records, an individual might be classified with theoretically mutually exclusive diagnoses. Ad-hoc analyses would be needed to refine the phenotypes of these individuals should such precision be required.It is also of note that, while the users can assign different weights to different data sources by adjusting minimum instance filter in the setting, it is not possible to directly weight on individual codes which could be important for a certain phenotype. The limitation could be circumvented by an implementation on the definition level (separating the codes in various definitions). It is important to recognize that there is no gold-standard for many of the health-related outcomes. Users should decide on their definitions based on the study questions at hand.Unable to download/decrypt the main dataset (step1).Ensure the most updated project key which is valid for one year after initiation.Unable to download data from Data Portal (step 2).Request the relevant fields listed in step 2 via the UK Biobank Access Management System .Error: Failed to install \u2018ukbpheno\u2019 from GitHub: installation of package \u201cxx\u201d had non-zero exit status (step 5).Installation of the dependent package \u201cxx\u201d was not successful. Find the error message on console, resolve the error and restart the installation. Possible reason of error includes \u201cdependency \u201cxx\u201d is not available (for R version x.x.x) \u201c, which may be solved by specifying the version of package compatible for the corresponding R version.Certain codes are missing after reading in the definition table (step 9).The package drops codes that are not available in data. If a certain code is dropped not due to this reason, check for special characters (accented characters are not recognized) and make sure codes are comma separated.Data processing step fails (step 10).Run \u201cget_all_varnames\u201d with the processed definition table and meta-data file to check if but some required fields are missing in the main dataset. Either remove the missing fields from definition table or allow missing fields in the \u201charmonized_ukb_data\u201d.m.w.yeung@umcg.nl).Further information and requests for resources should be directed to the lead contact, Ming Wai Yeung (This study did not generate new unique reagents."} +{"text": "We announce the coding-complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron strains obtained from Bangladeshi individuals. The Oxford Nanopore Technologies sequencing platform was utilized to generate the genomic data, deploying ARTIC Network-based amplicon sequencing. Coronaviridae, genus Betacoronavirus) variant, known as the Omicron variant (B.1.1.529), was initially reported to the World Health Organization (WHO) on 24 November 2021 (A novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) . To summarize, 3,723,478 reads were generated . A nearly complete genome was obtained for each sample, and the genomic information is provided in https://github.com/cov-lineages/pangolin), followed by visual inspection using CLC Genomics Workbench v21.0 (Qiagen). In comparison with the reference genome (Wuhan Hu-1 [GenBank accession number NC_045512.2]), the spike protein-based signature amino acid variations assigned 22 of the sequences as sublineage BA.5 and 1 as BA.2.75. Genome sequencing has been playing a critical role in COVID-19 responses, because new variants are constantly evolving. Therefore, rapid sequencing and data sharing can contribute to the implementation of quick and informed public health decisions to mitigate COVID-19 consequences.As part of a nationwide coronavirus disease 2019 (COVID-19) surveillance program , nasopharyngeal swab specimens were obtained from routine diagnostic samples from patients across Bangladesh. Reverse transcription -PCR was performed using a commercially available novel coronavirus (2019-nCoV) nucleic acid diagnostic kit . A total of 48 SARS-CoV-2 RT-PCR-positive samples were subjected to sequencing. Viral RNA was extracted from nasopharyngeal swab samples using the QIAamp viral RNA minikit (Qiagen). ARTIC v3 primer-based multiplex PCR amplicons were generated and used as the sequencing libraries . LibrariThe data from this study can be found under GISAID accession numbers EPI_ISL_13439470, EPI_ISL_13439471, EPI_ISL_13439472, EPI_ISL_13439473, EPI_ISL_13439474, EPI_ISL_13439475, EPI_ISL_13439476, EPI_ISL_13439477, EPI_ISL_13439478, EPI_ISL_13439479, EPI_ISL_13439480, EPI_ISL_13439481, EPI_ISL_13574266, EPI_ISL_13574267, EPI_ISL_13574268, EPI_ISL_13574269, EPI_ISL_13439482, EPI_ISL_13574270, EPI_ISL_13574271, EPI_ISL_13439484, EPI_ISL_13439485, EPI_ISL_13439486, and EPI_ISL_14859273. The GenBank accession numbers are listed in"} +{"text": "Patients with dysphagia have impairments in many aspects, and an interdisciplinary approach is fundamental to define diagnosis and treatment. A joint approach in the clinical and videoendoscopy evaluation is paramount.To study the correlation between the clinical assessment (ACD) and the videoendoscopic (VED) assessment of swallowing by classifying the degree of severity and the qualitative/descriptive analyses of the procedures.cross-sectional, descriptive and comparative.held from March to December of 2006, at the Otolaryngology/Dysphagia ward of a hospital in the country side of S\u00e3o Paulo. 30 dysphagic patients with different disorders were assessed by ACD and VED. The data was classified by means of severity scales and qualitative/descriptive analysis.the correlation between severity ACD and VED scales pointed to a statistically significant low agreement (KAPA = 0.4) . The correlation between the qualitative/descriptive analysis pointed to an excellent and statistically significant agreement (KAPA=0.962) (p<0.001) concerning the entire sample.the low agreement between the severity scales point to a need to perform both procedures, reinforcing VED as a doable procedure. The descriptive qualitative analysis pointed to an excellent agreement, and such data reinforces our need to understand swallowing as a process. Multidisciplinary work in dysphagia is a common denominator advocated by researchers and clinicians, since dysphagic patients have losses in the medical, nutritional, physiotherapeutic, physiological and speech arenas, thus needing numerous professionals to serve all of their health care demandsThe most known methods used to assess swallowing are the clinical evaluation of swallowing (CES) and the instrumental tests of video-fluoroendoscopy (VFE) and swallowing video-endoscopy (SVE). CES can not make a definitive diagnosis of dysphagia; however, it is a component which allows us to understand its natureAmong the instrumental tests, VFE has been considered the \u201cgold standard\u201d; however, because of its high cost and scarcity of places where it can be performed, SVE has proven accessible and doable. Swallowing videoendoscopy is a simple test, of low cost and little invasiveness, besides being easily transportable, making it possible to do sequential evaluations in patients with mobility challenges. It allows one to observe the pharyngeal phase of swallowing; it allows the physician to order the patient to perform airway protection maneuvers - so as to help the physician guide the patient regarding a proper diet for these patientsConsidering the importance of SVE in the diagnosis of dysphagia, otorhinolaryngologists gain relevance in the work team, being the professional responsible for performing the exam. The ENT is in charge of interpreting the SVE in its functional and anatomical aspects, and such data is fundamental for diagnosis. The speech therapist can work together with the ENT during the exam, suggesting the assessment of therapeutic strategies.Considering the different functions of each swallowing assessment procedure it is necessary to understand and interpret the different signs and symptoms observed in order to pinpoint the participation of each evaluation procedure and thus establish the approach in cases of dysphagia.To study the correlation between the clinical evaluation (CES) and swallowing video-endoscopy (SVE) by classifying the degree of severity and the qualitative/descriptive analysis of the two evaluation procedures.The present cross-sectional, descriptive and comparative study was approved by the Ethics Committee of the institution under protocol # 796/2005. All the subjects signed the informed consent form.The evaluations were carried out in the dysphagia ward - ENT of a hospital in the country-side of the state of S\u00e3o Paulo between March and December of 2006. This ward is geared specially to patients with neurogenic dysphagia, diagnosed with Parkinson's disease (PD), Amyotrophic Lateral Sclerosis (ALS) and Machado-Joseph Disease (MJD).All the patients were submitted to CES and SVE. After the procedures, the results were discussed with the team, made up by an ENT physician, ENT residents, speech therapists and nutritionists.CES and SVE followed the procedures proposed by the present study (Attachment 1), which was built from the protocols of other authorsThe CES was done in a direct and indirect manner. The indirect one includes interview, structural and sensitive evaluation of the oral cavity and administration of food. The neck was ausculted during rest, during saliva swallowing and before, during and after the swallowing of food. Later on, compensatory maneuvers were studied in order to achieve a safe swallowing.SVE followed the procedures proposed (Attachment 1) and was carried out by an otorhinolaryngologist using the conventional video-endoscopic equipment. The speech therapist participated offering the different food quantities and consistencies to be studied, and also suggesting the evaluation of certain airway protection maneuvers. The exam was recorded in a DVD.The data was analyzed in the following fashion:- Step 1 - CES and SVE analysis by means of classification according to severity scales.The severity scale employed for CES was proposed by Furkim and Silva- Step 2 - Compare the degrees of severity between the CES and SVE scales.- Step 3 - Case-by-case classification according to the qualitative/descriptive analysis, based on the signs and symptoms observed during CES and SVE.The qualitative analysis of the signs observed in the CES and SVE was carried out once the scales did not provide subsidies for the therapeutic planning. The analysis was based on the comparison of the CES and SVE findings according to the criteria presented on The signs listed above make up the assessment protocol presented in the present study - which is descriptive, providing a broad view of the swallowing process and creation of specific treatment plans, since it is possible to identify the alteration shown.Each case had its two assessments (CES and SVE) compared according to the qualitative analysis criteria , and was- Step 4: Comparing the severity degree classification and the qualitative analysis.In order to understand the contribution of each procedure in the evaluation of swallowing we chose to analyze the agreement between the qualitative analysis and the degree of severity, by correlating the scales with the data which were identified in the procedures. After the correlation the data were grouped in the following way:1 - Group in which the CES and SVE severity scale indicated the same degree and the qualitative analysis indicated similar CES and SVE signs;2 - Group in which the severity scales indicated a greater degree by SVE, correlated with cases in which the qualitative analysis indicated a higher SVE degree, correlated with cases in which the qualitative SVE analysis indicated more signs; 3 - cases in which the CES indicated a greater severity in the scale and more data in the qualitative analysis.In order to describe the sample profile according to the study variables, we created frequency tables of the category variables (disease) with absolute (n) and percentage (%) values, and descriptive statistics with position and scatter values of the continuous variable (disease).The statistical analysis used the \u201cThe SAS System for Windows\u201d , version 8.02 software. The agreement analysis among the classifications used the kappa agreement coefficient. Kappa values above 0.75 meant excellent agreement and values between 0.40 and 0.75 meant intermediate agreement, values below 0.40 indicated low agreement among the classifications. The level of significance adopted for the statistical tests was 5% (p<0.05)We studied 30 adult dysphagic patients, 19 men and 11 women. Their mean age was 56 years, varying between 19 and 91 years. They presented different base diagnosis: Parkinson's disease, amyotrophic lateral sclerosis, Machado-Joseph disease, stroke, and four patients with other diagnoses. The correlation among the results from the severity scale classification in each evaluation procedure (step 2) is depicted on KAPA=0.400; CI95%: ; Z=2.74; p=0.006It is possible to see in Graph 1 that the number of agreeing evaluations according to the criteria on the severity scales (same degree of severity in CES and SVE) is not very relevant. The statistical analysis indicated an intermediate/low agreement (KAPA = 0.4) in a significant way (p=0.006). Kappa values below 0.4 indicate low agreement.The results from steps 3 and 4 - descriptive qualitative analysis classification and comparison of these results with the severity degree classification - indicated an agreement in most of the cases studied, as shown on The agreement between the degree of severity and the qualitative analysis indicated excellent degree (Kappa=0.962) in a statistically significant way (P<0.001). Such data reinforces that the qualitative/descriptive analysis proved to be an efficient evaluation method.The subjects in the sample have ages above 50 years, and this can justify the fact that they frequently present neurodegenerative alterations. There is a prevalence of patients with Parkinson's disease and ALS, followed by MJD and Stroke, for being the main population in the ward.According to Table 1, the agreement observed between CES and SVE severity scales was intermediate/low in a statistically significant way. Many studies correlate data found in the CES with findings from objective exams. Mathers-Schmidt and KurlinskiThe correlation of signs observed between CES and SVE, from the qualitative viewpoint is justified by the influence of the oral phase in the pharyngeal phase of swallowingNasal food reflux, which cause is inefficiency or failure of the soft palate muscles, reducing intraoral pressure - which can be seen at CES and SVE. There are correlations between aspiration risk and changes in soft palate movementMotor or sensitive involvement of facial muscles causes alterations to the neuronal information, which is the basis for a proper motor response regarding the food to be ingested. Such involvement may cause an increase in oral transit time, posterior deflection and/or inefficient ejection, resulting in alterations of the pharyngeal phase, especially stasis in the valleculasMultiple swallowing can be seen during CES and in SVE, which happen because of stasis in the oral cavity and vallecula - an inadequate oral phase which causes altered food pushing. Stasis in the pyriform sinuses and posterior pharyngeal walls are also considered alterations to the pharyngeal phase of swallowing, having seen that the mechanism impaired is pharyngeal wall mobility.Throat clearing, cough and alterations in neck auscultation are signs of penetration and/or aspiration seen during CES and can be confirmed by SVE -by the presence of food in the larynx without passing through the vocal folds (penetration) or by the presence of food below the vocal folds (aspiration)International studies comparing the use of neck auscultation, CES and objective exams to predict aspiration indicate that the association of two procedures is safer to find aspiration since the auscultation alone does not guarantee sensitivity to all the altered casesTohara et al.As we observe the data individually, we stress 13 disagreeing cases . In 5 ofWe can argue that in the 8 cases in which SVE showed more data, in two patients we observed stasis which were not suggested in the clinical evaluation, besides aspiration in two and laryngotracheal penetration in four cases.It is important to discuss the clinical evaluation that is not efficient to identify silent penetrations and aspirations, besides being little efficient to detect stasis in difficult places, which can cause late aspirations and inefficient treatment.Of the 30 patients investigated, in 26 who were clinically and vide-ofluoroendoscopically evaluated we noticed that it was not safe to forecast the presence of penetration/aspiration of liquids by the clinical evaluation34. Because of the need for complementary tests, the present study also presents the evaluation roadmap used in order to suggest assessment procedures which may help to better understand the swallowing process and provide complementary information to the clinical-therapeutic rationale of dysphagic patients.Many studies stress the importance of associating the CES and the objective examination in the assessment of swallowing. Such studies suggest that the two procedures are complementary and essential for the diagnosis and treatment planning of dysphagia, leading to the definition of more specific approaches for each patientSwallowing evaluation procedures must try to understand the swallowing process, in other words, the mental cognitive-status behaviorSVE is a highly efficient procedure since it does not require high investments because the equipment utilized is the one ENTs are already used to having, and also in terms of time because the entire test can be performed well under 20 minutes. The SVE also broadens the action scope of otorhinolaryngologists and allows for an interdisciplinary work with speech therapists.1.The severity classification agreement of CES and SVE proved to be intermediate/low, reinforcing the need to perform both assessment procedures.2.The agreement between the correlation of severity degree and qualitative/descriptive analysis severity proved to be excellent, reinforcing the qualitative/descriptive analysis as an efficient assessment method.On-going PhD thesis at the Institute of Language Studies in the field of Neurolinguistics, entitled: \u201cStudy and speech therapy follow up of post-stroke subjects\u201d. Such study is associated to the Neurolinguistics Integrated Project (CNPq: 521773/95-4).ATTACHMENT 1Evaluation RoadmapSwallowing Clinical and Video-endoscopic (SVE) Assessment Protocol (May/07)Exam date: _____ / _____ / _____Patient: ____________________ Reg.#: ____________________ BD: _______________ Age: _____Address: _________________________________________________________________Tel: _________________________ Informer: ___________________________________D.H.: ______________________________________________________________________P.H: ______________________________________________________________________Disease Duration: ____________________________________________________________Medicamentions: ____________________________________________________________Current complaint: ____________________________________________________________Swallowing complaint: Yes_____NoComplaint duration: ____________________________________________________________Prior feeding habits: _______________________________________________________Meal Records (24 hrs): __________________________________________________Usual Weight: __________ Current weight: _______________ Height:__________ BMI:Monthly family income: _________________________ # of family members: __________General health status:Heart disorders: ______________________________________________________________________High blood pressure: ______________________________________________________________________Pulmonary infections: ____________________________________________________________Gastric disorders: _________________________________________________________________Mouth and teeth alterations: ____________________________________________________________Malnutrition: ______________________________________________________________________Dehydration: ______________________________________________________________________Diabetes: (Type) ____________________________________________________________Tracheostomy: Present absentCannula: metal PVC plastic silicone with Cuff WO/cuffMechanical ventilation Present absentNon-invasive ventilation: Mask Nasal Swallowing complaint:Indirect clinical evaluationDirect clinical evaluationSigns of penetration/aspiration:Facial color alteration: ____________________________________________________Respiratory rate alteration: ____________________________________________________2 saturation alteration: ____________________________________________________OManeuvers utilized: ____________________________________________________Swallowing Videoendoscopic Evaluation1.Nasal cavitiesSeptum centered deviated R deviated L Non-obstructive irregularitiesMucosa pale edematous wet atrophicTurbinates normotrophic hypertrophic2.Rhinopharynx:Mucosa pale edematous wet atrophicEustachian tube ostium free obstructed3.Pharynx-soft palate sphincter:Phonation Complete closure Incomplete closure coronal sagittal circular circular with Passavant ringSwallowing Complete closure incomplete closure coronal sagittal circular circular with Passavant ring4.Hypopharynx Tongue base mobility proper altered _______________________Posterior wall mobility proper altered ______________________Vallecula normal lesion saliva stasisEpiglottis normal omega-shape lesion ______________________Arytenoids normal hyperemia edema Interarytenoid region normal hyperemia edemaPyriform recess free obstructed saliva stasis R LSensitivity normal reduced absent5.LarynxVocal folds Ventricular folds mobile normal paresis R L hyperconstriction R L Immobility R L Laryngeal asymmetry yes no arching R L sensitivity to the mechanical stimulus atrophy R L epiglottis normal altered lesion _________________ R L aryepiglottic fold normal altered other ______________________ subglottis normal altered6.Glottic closure complete incomplete consistent inconsistent posterior triangular slit mid-posterior triangular slit anterior spindle-like slit spindle-slit in all the extension hourglass-like slitSwallowing Videoendoscopic Evaluation (SVE)"} +{"text": "The presented method is an adaptation of NeuroKit2 to simplify and automate computation of the various mathematical estimates of heart rate variability (HRV) or similar time series. By default, the present approach accepts as input electrocardiogram's R-R intervals (RRIs) or peak times, i.e., timestamp of each consecutive R peak, but the RRIs or peak times can also stem from other biosensors such as photoplethysmography (PPGs) or represent more general kinds of biological or non-biological time series oscillations. The data may be derived from a single or several sources such as conventional univariate heart rate time series or intermittently weakly coupled fetal and maternal heart rate data. The method describes preprocessing and computation of an output of 124 HRV measures including measures with a dynamic, time-series-specific optimal time delay-based complexity estimation with a user-definable time window length. I also provide an additional layer of HRV estimation looking at the temporal fluctuations of the HRV estimates themselves, an approach not yet widely used in the field, yet showing promise (doi: 10.3389/fphys.2017.01112). To demonstrate the application of the methodology, I present an approach to studying the dynamic relationships between sleep state architecture and multi-dimensional HRV metrics in 31 subjects. NeuroKit2\u2032s documentation is extensive. Here, I attempted to simplify things summarizing all you need to produce the most extensive HRV estimation output available to date as open source and all in one place. The presented Jupyter notebooks allow the user to run HRV analyses quickly and at scale on univariate or multivariate time-series data. I gratefully acknowledge the excellent support from the NeuroKit team. Specifications tableThe methods section is structured as follows. First, following a brief rationale for the method I outline the HRV metrics computed. Second, I describe the implementation in Python. This section contains several elements defining the functions for executing the data loading, preprocessing and feature computation steps followed by data saving; as last step, I provide the code to tie everything together for a single step execution. At last, I present an application of the code to an open-source dataset and conclude with remarks for the broader usage.Heart rate variability (HRV) as a search term on PubMed rendered \u223c55,000 publications as of June 16, 2022. While first studies appeared in 1925, there has been a notable rise in scientific publishing around 1975 with some 400 papers appearing annually as of 2021. This is likely attributable to the steady increase in computational capacity and its access to it along with growing recognition of the HRV physiology and pathophysiology. For example, HRV has been recognized as a biomarker of health and stress in adult and developing organisms reflecting heart-brain interactions and resulting, among other observations, in the phenomenon of heart beat-evoked potentials, a direct reflection of bidirectional brain-heart communication The number of HRV estimates, sometimes also referred to as metrics or biomarkers, has grown as well, now exceeding 100, albeit it is understood that some of these estimates are collinear With the advent of Digital Health and increased utilization of wearable or ambient sensors to capture heart rate and other biological oscillations, the awareness of caveats in HRV analysis in contrast to the traditional electrocardiogram (ECG)-based approach also needs to rise Several toolboxes have been built to collate the existing methodologies in a more accessible format and foster the discovery of new biomarkers of health outcomes based on HRV and other physiological time series In parallel, the ecosystem of Python-based open-source packages for time series processing has also been maturing. One such package stands out in terms of methodological scope, functional depth, rich API and constant updates through a large international community of researchers: NeuroKit2. It is a Python Toolbox for Neurophysiological Signal Processing The presented method is an adaptation of NeuroKit2 to simplify and automate computation of the various mathematical estimates of HRV or similar time series The method describes preprocessing and computation of an output of 124 HRV measures including measures with a dynamic, time-series-specific optimal time delay-based complexity estimation with a user-definable time window length .Table 1HI also provide an additional layer of HRV estimation looking at the temporal fluctuations of the HRV estimates themselves, an approach not yet widely used in the field, yet showing promise.Finally, I present an application of the proposed HRV estimation pipeline to an open-source dataset from PhysioNet acquired in 31 subjects during sleep using Apple Watch and enriched with expert annotation of sleep states ,18,19.How does this methodology add to the existing set of techniques and tools? NeuroKit2\u2032s documentation is extensive. Here, I attempted to simplify things summarizing all the researcher needs to produce the most extensive HRV estimation output available to date as open source and all in one place. The presented Jupyter notebooks allow the user to run HRV analyses quickly and at scale on univariate or multivariate time-series data. I gratefully acknowledge the excellent support from the NeuroKit team.(1)Univariate or multivariate time series input; ingestion, preprocessing and computation of 62 HRV metrics.(2)Standardization of RRI window lengths and RRI duration-specific computation of complexity estimates.(3)Estimation of intra- and inter-individual higher order temporal fluctuations of HRV metrics.(4)Application to a sleep dataset recorded using Apple Watch and expert sleep labeling.The key features of the presented methodology are:The step-by-step approach is as follows.1. Create a dedicated virtual environmentYou may use conda or another environment manager such as pip or Docker. The choice boils down to your preferences and constraints: for example, certain Python packages can only be installed in pip and not in conda. For the proposed approach, I am not aware of any constraints that prevent the user from using conda. Ultimately, using a virtual environment will help you down the road to ensure your Python analytical pipeline keeps on working and does not get broken by unintended package updates and disrupted interdependencies. As an alternative to this conda step, I provide a Docker container here # call conda datanalysis environment!conda init bash!conda activate datanalysis #or use your own preferred venv2. Load the required and recommended packages.import neurokit2 as nkimport pandas as pdimport matplotlib.pyplot as pltimport numpy as npimport osimport scipy.iofrom pathlib import Pathfrom scipy.stats import variationfrom hmmlearn import hmm# load Matlab data filesfrom scipy.io import loadmat3. Import raw peaks.The source may be Matlab files or whatever input data format you may need. In the present example, we load a duo of files: corresponding maternal and fetal peak data. Your use case may differ. For example, you may load just one set of peak data, three or more sets of peak data derived from different ECG channels, an ECG-derived peak times channel and a PPG-derived peak times channel, etc. Simply amend the code accordingly by editing and adding the additional lines for each step as required.In this work, because the focus is on peak times or heart rate time series, an important step is skipped deliberately: the derivation of the peak data from the raw signal. This can be ECG, PPG or otherwise recorded blood pressure fluctuations (pulse). The HRV Task Force recommends checking for the presence of ectopic heartbeats, e.g., premature ventricular contractions (PVCs) ,43. Neur# Import raw peaks from the mat files; adjust to fit your input data formatf_filepath_peaks=Path.cwd/\"raw_peaks/f\" #fetal raw peaks mat files;m_filepath_peaks=Path.cwd/\"raw_peaks/m\" #maternal raw peaks mat files;4. Get ready for batch file processing. a. Create a list of relevant files in directoryf_peaks_files\u00a0=\u00a0[f for f in sorted(f_filepath_peaks.iterdir) #create a list of relevant files in directoryif f.suffix == '.mat']m_peaks_files\u00a0=\u00a0[f for f in sorted(m_filepath_peaks.iterdir) #create a list of relevant files in directoryif f.suffix == '.mat'] b. Read one file at a time using the above list, trim, clean, convert to RRI c. The present syntax is for a specific ECG format; adopt to your use case d. Iterate over i files in the f_ or m_ peaks_files lists and extract the correct peaks channel as numpy arraydef read_mat_file:# Import 5th row of the mat file's peak data which has 1000 Hz sampling rate; you may need to adopt this step as per your data structuref_file_PEAK_raw=loadmat(f_peaks_file)m_file_PEAK_raw=loadmat(m_peaks_file)f_peaks=f_file_PEAK_raw['fetal_Rpeaks'][4] #this is my 5th row ECG-SAVER-extracted peaks channelm_peaks=m_file_PEAK_raw['mother_Rpeaks'][4] #this is my 5th row# Trim trailing zerosf_peaks_trimmed=np.trim_zerosm_peaks_trimmed=np.trim_zeros# Artifact removal [see next section for details]f_clean_peaks=nk.signal_fixpeaks #allow 80\u2013180 bpmm_clean_peaks=nk.signal_fixpeaks #allow 40\u2013150 bpm# Document artifacts from each run as clean_peaks_rri[0]: build a dataframe for each file over all segments# Convert to RRIf_rri\u00a0=\u00a0peaks_to_rrim_rri\u00a0=\u00a0peaks_to_rrireturn f_clean_peaks[1], m_clean_peaks[1], f_rri, m_rri, f_clean_peaks[0], m_clean_peaks[0] e. Proceed with the steps below: HRV compute, save. Cf. final section (10).Convert peaks to RRIs5. Using NeuroKit2\u2019s functions to take the cleaned peaks as input: peaks_to_rri# Some NK functions take RRIs# So use these UDFs borrowed from the NK package: convert peaks to RRI on the cleaned peaks outputdef peaks_to_rri:rri\u00a0=\u00a0np.diff(peaks) / sampling_rate * 1000if interpolate is False:return rrielse:# Minimum sampling rate for interpolationif sampling_rate < 10:sampling_rate\u00a0=\u00a010# Compute length of interpolated heart period signal at requested sampling rate.desired_length\u00a0=\u00a0int(np.rint(peaks[-1]))rri\u00a0=\u00a0signal_interpolate,**kwargs)return rri, sampling_rate6. Artifact correction. a. This is a key step that will influence everything downstream. It is often not reported clearly in the studies. b. Adjust the sampling rate and threshold settings as appropriate for your data. c. Note that we save the logs of artifact correction for audit purposes. Sometimes, you need to know why a certain dataset behaved in the way it did and this documentation can come in handy.# Artifact correction# Integrated into the above UDF red_mat_file, but you may find this useful to adopt elsewhere in your codehttps://neurokit2.readthedocs.io/en/latest/functions.html#neurokit2.signal.signal_fixpeaks# Artifact removal on peaks using Kubios: write into UDF taking trimmed_peaks input# caution: nk.signal_fixpeaks takes peaks, not RRI!# nk.signal_fixpeaks saves the corrected peak locations to the [1] index of the output data sturcture# accessible like so: clean_peaks[1]# Review the settings for fetal versus maternal RRI inputs! Adjust to match your RRI physiology# interval_min \u2013 minimum interval btw peaks | interval_max \u2013 maximum interval btw peaks.f_clean_peaks=nk.signal_fixpeaksm_clean_peaks=nk.signal_fixpeaks# Convert trimmed and cleaned peaks to RRI (using _trimmmed_ raw peaks as input!)rri_clean\u00a0=\u00a0peaks_to_rri7. Compute all HRV metrics segment-wise a. Rather than computing on the entire time series at once and trading the reproducibility as a result , we i. set the segment duration explicitly a priori and ii. Take advantage of the segment-wise estimate of HRV to investigate the higher-order structure of the HRV metrics themselves. b. For complexity estimates, note that we use segment duration-specific estimation of optimal time delay rather than using default settings. This allows us to compute FuzzEn, FuzzEnMSE, FuzzEnRCMSE, cApEn specifically for the optimal time delay. Why select these complexity estimates? It is heuristic. I have found Fuzzy Entropy estimates to be understudied and robust, especially with RRI time series. This is hence worthy of additional attention in future studies deploying complexity estimates. Other time-delay-dependent complexity estimates can be plugged in here, all made available via NeuroKit2 API.# UDF compute_HRV# This UDF computes all [regular and extra non-linear] HRV metrics segment-wise for a filedef compute_HRV:# Regular HRV matrix (from peaks)duration_peaks=peaks[len(peaks)-1] #gives me the duration in samplesdivider=duration_peaks/1000/60/5 #sampling_rate, 5 min window segmentssegment=np.array_split #divide in segments of 5 min; the last segment may be shorter; discard during statistical analysis on HRV metricssegment_df=pd.DataFramefor i in range(len(segment)):segment=nk.hrvsegment_df\u00a0=\u00a0pd.concat# Additional nonlinear HRV metrics from RRIssegment=np.array_split #divide _RRI_ in segments of 5 min; the last segment may be shorter; discard during statistical analysis on HRV metrics#create my dataframe structure to which to append the list as a row in the followingextra_columns=extra_complexity_df=pd.DataFrame(columns=extra_columns)df_length=len(extra_complexity_df)extra_complexity_df_total=pd.DataFrame(columns=extra_columns)for i in range(len(segment)):optimal_complexity_parameters\u00a0=\u00a0nk.complexity_delayextra_complexity_segment_fuzen=nk.entropy_fuzzyextra_complexity_segment_fuzen_mse=nk.complexity_fuzzymseextra_complexity_segment_fuzen_rcmse=nk.complexity_fuzzyrcmseextra_complexity_segment_capen=nk.entropy_approximatesegment_duration=np.sum(segment[i])/1000 #segment duration in seconds#join all individual output floats including values of segment[i] - i.e., for each segment - and its duration in seconds as numpy.sum(segment[1])/1000extra_complexity\u00a0=\u00a0extra_complexity_df.loc[df_length]=extra_complexityextra_complexity_df_total\u00a0=\u00a0pd.concat# simply concatenate both df's horizontally; this scales allowing addition of other df's from bivariate computationsfinal_df=pd.concatreturn final_df #this is per subject with SubjectID output along on the right side8. Compute higher order HRV metrics.Here I made explicit and expanded upon what we attempted first in def compute_basic_stats:# compute mean and variation# assuming \"ts_data\" is where my HRV metric values list is per subjectmean=np.meancoeff_variation=variation# this function works similar to variation but works purely with numpy# cv\u00a0=\u00a0lambda x: np.std(x) / np.mean(x)# First quartile (Q1)Q1\u00a0=\u00a0np.percentile# Third quartile (Q3)Q3\u00a0=\u00a0np.percentile# Interquaritle range (IQR)IQR\u00a0=\u00a0Q3 - Q1midhinge\u00a0=\u00a0(Q3\u00a0+\u00a0Q1)/2quartile_coefficient_dispersion\u00a0=\u00a0(IQR/2)/midhinge# adding entropy estimate; this is experimental!# ts_entropy=nk.entropy_sample(ts_data)# yielding error \"could not broadcast input array from shape into shape (7)\" | the following syntax fixes that and is more elegant in that it estimates optimal delay# optimal_complexity_parameters\u00a0=\u00a0nk.complexity_delay# ts_entropy=nk.entropy_fuzzy# still yielding len errorts_entropy=nk.entropy_shannon(ts_data)basic_stats=, quartile_coefficient_dispersion, ts_entropy]return basic_stats#HMM Modeldef do_hmm(ts_data):#ts_data=numpy.array(data)gm\u00a0=\u00a0hmm.GaussianHMM(n_components=2)gm.fit)hmm_states\u00a0=\u00a0gm.predict)#hmm_states=[states.tolist]print(hmm_states)return hmm_states # next, add _states_ iteratively for all subjects to states_Uber list to spot patterns# deal with last column which is string and needs to be skippeddef skip_last_column(lst):# unpack the list of listsdef Extract(lst):return [item[0] for item in lst]# check for string in the first sublist element_to_check=Extract(lst)[0]return isinstance #return Boolean for presence of string in the sublistdef compute_higher_HRV:# assuming \"final_df\" is the dataframe where the HRV metric values are listed segment-wise per subject# compute basic statshigher_order_basic_stats=for i in range: #last column is the SubjectID string, so skipping it belowmetric=final_df.iloc].values#String skip logic to skip over SubjectID columnif skip_last_column == False:results_temp1=compute_basic_stats,SubjectID)higher_order_basic_stats.append(results_temp1)else:i+=1basic_stats=pd.DataFramecolumns=final_df.columns[0:63] #make sure I don't select the last column which has SubjectIDbasic_stats.index=[columns]basic_stats_final=basic_stats.T #transpose# compute HMM stats: computing on just 7 data points leads to errors in some instances, so omit for now and revisit later when used on longer HRV metrics time series, say, several hours# Estimate HMM probabilities output for a given segmented HRV metric# Then compute basic_stats on this estimate;# Hypothesis: stable tracings will have tight distributions of HMM values and resemble entropy estimates;# This will apply statistically significantly for physiologically stressed (tighter distributions) versus control subjects#higher_order_basic_stats_on_HMM=#for i in range: #last column is the SubjectID string, so removing it# metric=final_df.iloc].values# print)# some HRV metrics have NaNs and the \"do_hmm\" script crashes on those;# Adding logic to skip if NaN is present# a=any(pd.isna(metric)) #checking if _any_ values in HRV metrics list are NaN# b=skip_last_column(metric)# skip_reasons={a:'True', b:'True'}#NaN or string skip logic# if any(skip_reasons):# i+=1# else:# results_hmm_temp2=do_hmm(metric)# print(results_hmm_temp2)# print(type(results_hmm_temp2))# results_stats_hmm_temp=compute_basic_stats #j being the file number; != SubjectID# higher_order_basic_stats_on_HMM.append(results_stats_hmm_temp)#basic_stats_on_HMM=pd.DataFrame#basic_stats_on_HMM.index=[columns]#basic_stats_on_HMM_final=basic_stats_on_HMM.T #transpose#higher_final_df=pd.concathigher_final_df=basic_stats_final #leaving the syntax above for when the data allow HMM analysisreturn higher_final_df #this includes SubjectID9. Save everything.Gather all data from the separate data frames into spreadsheets for further analyses.# Execute the entire analysisFor each file :- call read_mat_file- call compute_HRV- save results to Excel10. Execute the entire pipeline calling the above defined functions# Initialize data structuresf_artifacts_log=m_artifacts_log=Uber_fHRV=Uber_mHRV=Uber_higher_fHRV=Uber_higher_mHRV=i=0# Compute & save into listswhile i<=len(f_peaks_files)-1: #careful - this assumes equal number of fetal and maternal raw files# read the peaks file, trim trailing zeros, artifact correct it, convert to RRIs and return the resultsf_clean_peaks, m_clean_peaks, f_rri, m_rri, f_clean_peaks_artifacts, m_clean_peaks_artifacts=read_mat_filefSubjectID=format(f_peaks_files[i].stem)mSubjectID=format(m_peaks_files[i].stem)f_artifacts_log_i=m_artifacts_log_i=#save artifact processing log from each file starting with its real SubjectIDf_artifacts_log.append(f_artifacts_log_i)m_artifacts_log.append(m_artifacts_log_i)# compute all HRV metricsffinal=compute_HRVmfinal=compute_HRV# update the UBER dfUber_fHRV.appendUber_mHRV.append# compute higher_order HRV metricsfhigher_final=compute_higher_HRVmhigher_final=compute_higher_HRV# update the UBER_higher_dfUber_higher_fHRV.appendUber_higher_mHRV.appendi+=1if i>len(f_peaks_files):breakprint('Computation completed.')# save artifacts logsdf_Uber_f_artifacts\u00a0=\u00a0pd.DataFrame.from_records(f_artifacts_log) #edit the name as neededdf_Uber_m_artifacts\u00a0=\u00a0pd.DataFrame.from_records(m_artifacts_log) #edit the name as neededdf_Uber_f_artifacts.to_exceldf_Uber_m_artifacts.to_excel# save HRV resultsUber_fdf=pd.concat(Uber_fHRV)Uber_fdf.to_excelUber_mdf=pd.concat(Uber_mHRV)Uber_mdf.to_excelUber_higher_fdf=pd.concat(Uber_higher_fHRV)Uber_higher_fdf.to_excelUber_higher_mdf=pd.concat(Uber_higher_mHRV)Uber_higher_mdf.to_excel11. Method validation: Demonstrating the performance of the proposed HRV pipeline in a retrospective analysis of a polysomnography dataset recorded with Apple Watch.date (in seconds since polysomnography start) stage .As validation dataset, the data by Walch et\u00a0al. was used which is available from PhysioNet. The team acquired heart rate data in 31 subjects during sleep using Apple Watch and enriched the data with expert annotation of sleep states ,18,19. T(1)The heart rate data, extracted from the Apple watch, is publicly available.The data were recorded from 31 subjects during sleep, averages 7.3\u00a0h, and comes expertly annotated with sleep state labels.(2)The authors provided a script on GitHub for how to enable such data extraction in the future. This should make such a demonstration particularly relevant for future studies (3)This dataset ties in well with the accompanying publication in the Journal of Biomedical Informatics This dataset is appealing for several reasons for the intended objective of HRV pipeline validation:Interestingly, the presented HRV pipeline yields insights into sleep state dynamics reflected in HRV which I discuss below. The underlying code, based on the presented HRV estimation pipeline, and all generated data can be found on FigShare and DockerHub \u2022The number of HRV metrics was increased from 63 (as per above Jupyter notebook) to 124 HRV metrics, computed on this entire PhysioNet dataset cf. .\u2022Since this is intended as an example only, for ease of computing, I used the entire dataset to compute HRV ; I also set optimization for complexity parameters to default settings for the same reasons. The code is available for those who wish to dive deeper and have the resources to do so.\u2022\u25cbThe code is presented to determine the total duration of each sleep state per recording using the labeled files \u25cbThe saved continuous and averaged SampEn and RMSSD data are provided for the entire cohort, for future analyses \u25cbThe code and the visualizations of each subject's time course are provided for heart rate, SampEn, and sleep state architecture \u25cbR\u00a0=\u00a00.39, p\u00a0=\u00a00.03) or CV RMSSD (R\u00a0=\u00a00.55 and p\u00a0=\u00a00.001), respectively . The findings show again, this time quantitatively across the cohort, a degree of correlation between HRV complexity fluctuations and duration of deep sleep . Note thectively .Fig. 2Sp\u25cbNext, I expanded the scope by assessing and showing the correlations systematically for all subjects, all 124 HRV metrics, and all sleep states [46].FigSample Entropy (SampEn) is reported as an example complexity metric of HRV over time as it changes during sleep along with the traditional linear time-domain metric RMSSD; these are plotted along with the heart rate and sleep state architecture (using the supplied labels). This approach can contribute to studying these relationships systematically and develop open source algorithms to reliably detect sleep states from PPG-derived HRV data.To analyze this dataset, I expanded the presented HRV pipeline further and deployed it in several ways that can be used as a basis for future studies as follows.I suggest the following implications for future work. First, the dataset and the presented findings can be studied further using machine learning tools to derive an optimal HRV metric-based predictor of the NREM states or REM states\u2019 duration. Second, the richness of the temporal fluctuations can be further harnessed for classification and prediction using the code for hidden Markov mechanisms (HMM). I consider this to be out of scope for the present manuscript but provide the necessary code.\u2022https://hub.docker.com/r/mfrasch/hrv-pipeline. The notebook is deposited on GitHub pages (https://martinfrasch.github.io): for viewing online here (https://martinfrasch.github.io/MethodsX%20R1%20HRV%20pipeline%20v4.1.html)All data produced during this analysis has been deposited in FigShare at 10.6084/m9.figshare.20076464 \u2022https://martinfrasch.github.io/MethodsX%20R1%20HRV%20pipeline%20v4.1%20FINAL.ipynb)and as downloadable Jupyter notebook here can be found here (https://chart-studio.plotly.com/\u223cmfrasch/6)12. Data availabilityFinal remarksThe presented HRV computation pipeline in Python using the API of NeuroKit2 package is shown based on the use of the maternal-fetal trans-abdominally derived non-invasive ECG signal followed by maternal and fetal ECG extraction using SAVER algorithm Recent advances in the in silico modeling of physiological systems open avenues for discovery of novel and deeper understanding of the existing HRV metrics The literature indicates a high potential of HRV biomarkers to serve as predictors of important health outcomes such as cardiac or mental health as well as in critical care and disorders of consciousness .The author declares the following financial interests/personal relationships which may be considered as potential competing interests:MGF holds patents on EEG and ECG processing. MGF is founder of and consults for Digital Health companies commercializing predictive potential of physiological time series for human health."} +{"text": "Understanding dysregulation of the eukaryotic initiation factor 4F (eIF4F) complex across tumor types is critical to cancer treatment development. We present\u00a0a protocol and accompanying R package \u201ceIF4F.analysis\u201d. We describe analysis of copy number status, gene abundance and stoichiometry, survival probability, expression covariation, correlating genes, mRNA/protein correlation, and protein co-expression. Using publicly available large multi-omics data, eIF4F.analysis permits computationally derived and statistically powerful inferences regarding initiation factor regulation in human cancers and clinical relevance of protein interactions within the eIF4F complex.For complete details on the use and execution of this protocol, please refer to Wu and Wagner (2021). \u2022An R package to analyze eIF4F dysregulation, using large multi-omics datasets\u2022Detailed steps for software installation, data download, and library initialization\u2022Guidelines for deriving biological and clinical inferences from multiple analyses\u2022Illustrated code structure explains bioinformatics pipeline assembly technique Publisher\u2019s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Understanding dysregulation of the eukaryotic initiation factor 4F (eIF4F) complex across tumor types is critical to cancer treatment development. We present a protocol and accompanying R package \u201ceIF4F.analysis\u201d. We describe analysis of copy number status, gene abundance and stoichiometry, survival probability, expression covariation, correlating genes, mRNA/protein correlation, and protein co-expression. Using publicly available large multi-omics data, eIF4F.analysis permits computationally derived and statistically powerful inferences regarding initiation factor regulation in human cancers and clinical relevance of protein interactions within the eIF4F complex. In complex biological systems, biological processes rely on participation of multiple proteins through their physical and specific functional interactions. Clinical relevance of protein-protein interactions (PPIs) has been traditionally investigated through wet-lab approaches using tissue cultures and animal models, which are often complicated by easily-perturbed cell culture conditions or poor recapitulation of human diseases.in\u00a0vivo gene co-expression and protein interactions has been reported after analyzing large-scale data from multiple species including human.,,The validity of our method derives from the biological requirement for interacting proteins to be simultaneously present within a cell, which implies that synthesis and degradation of interacting proteins ought also to coincide.EIF4F genes and their protein interactions from analysis results. Our innovative computational method can be extended for broader application to reveal the clinical relevance of PPIs in assorted disease conditions, given additional disease-related datasets, custom lists of candidate protein complexes with subunits, and implementation of more association analyses. However, the protocol presented here is narrowly targeted to the production of our eIF4F results.As we previously published,1.Download\u00a0& install R 4.2.1, if not already installed.2.https://www.rstudio.com/products/rstudio/download/).Download\u00a0& install RStudio, if not already installed: )install.packages(\"BiocManager\")> BiocManager::install(version\u00a0= \"3.15\")# install required R packages:> bio_pkgs <- c> BiocManager::install(bio_pkgs)# load required packages> lapplyNote: Except for the \"RCurl,\" \"R.utils,\" and \"utils\" packages that are required for Download.R file, all dependent packages will be installed in the next step. However, installation of all dependent package takes a long time and sometimes gives installation errors related to the setting of individual users. Thus, we recommend users to manually install dependent packages before installing eIF4F.analysis package.CRITICAL: If installation of some dependent packages requires to install or update non-Bioconductor packages, use install.packages for non-Bioconductor packages.The required packages will be automatically installed the first time you run eIF4F.analysis.4.Install eIF4F.analysis package in RStudio.> devtools::install_github5.Load eIF4F.analysis package in RStudio.> libraryInstall the development version of eIF4F.analysis package from GitHub with the following commands:6.Open the terminal and run the following command line to clone our GitHub repository for\u00a0eIF4F.analysis package. This step will store all package files under home directory as \u223c/eIF4F.analysis A.Figure\u00a0https://github.com/a3609640/eIF4F.analysis$ git cloneNote: Installing eIF4F.analysis package in the Linux system is highly recommended.7.Under the \u223c/eIF4F.analysis/Script folder B, there # default directory for data download and output storage> data_file_directory <- Sys.getenv(c(\"DATA_FILE_DIRECTORY\"), unset\u00a0= \"\u223c/eIF4F.analysis/eIF4F_data\")> output_directory <- Sys.getenv(c(\"OUTPUT_DIRECTORY\"), unset\u00a0= \"\u223c/eIF4F.analysis/eIF4F_output\")CRITICAL: By default, Download.R generates root directory paths \u223c/eIF4F.analysis/eIF4F_data and \u223c/eIF4F.analysis/eIF4F_output. These two directory paths are also set inside the package (in Load.R), and the values must agree in both places. The descriptions of the steps that follow assume the use of the default eIF4F_output location.We provide two R scripts in our GitHub repository for users to download datasets and to run eIF4F.analysis package. Users need to clone the package files from GitHub, and set up the directories for input and output files.Timing: 1 h8.Run the Download.R file in RStudio with the following command line.> sourceNote: Download times were observed with a 100 Mbps internet connection. Remote data sources mentioned here may offer limited and lower bandwidth.CRITICAL: By default, user will be able to clone all the scripts and R codes from Github repository, to download datasets, and to store analysis results (by default) under a single folder \u223c/eIF4F.analysis.Execution of Download.R script creates two folders: \u223c/eIF4F.analysis/eIF4F_data and\u00a0\u223c/eIF4F.analysis/eIF4F_output C. Downlo\u2022Software: R version 4.2.1 and RStudio (2022.07.1 build 554).\u2022Operating systems: The package was developed and tested with Linux OS (Pop!_OS 22.04 LTS).CRITICAL: We recommend Linux to run the package.\u2022\u25cbMemory: 48 GB minimum.\u25cbProcessors: tested with Intel Core i7-8700k CPU (6 cores), Intel Core i7-8550U CPU (4 cores).\u25cbDisk space: 30 GB minimum. The total disk space for eIF4F.analysis folder is 26.2 GB, including all downloads and the analysis results.Computer hardware:https://a3609640.github.io/eIF4F.analysis/reference/index.html.The package includes one initiation step, and seven major analysis steps. User can execute each analysis step with one exported function that calls a group of internal functions for data process, data analysis and plotting to achieve a set of analyses. This package organizes all functions related to each analysis step together as one R script under \u223c/eIF4F.analysis/R Analysis.R contains ten exported functions in the package to initialize package and to execute all analyses presented in Wu and Wagner (2021).Timing:\u00a0<\u00a05\u00a0min1.Run the following command line to create the output directories to store the output files.> initialize_dirNote:initialize_dir creates sub-directories under \u223c/eIF4F.analysis/eIF4F_output and stores them as \u201cTCGA_CNV_value.csv\u201d, \u201cTCGA_CNV_sampletype.csv\u201d and \u201cTCGA_CNVratio_sampletype.csv\u201d under the ProcessedData folder.b.i.TCGA_GTEX_RNAseq_sampletype comes from the recomputed RNAseq dataset from both TCGA and GTEx, \"TcgaTargetGtex_RSEM_Hugo_norm_count\", and the annotation dataset \"TcgaTargetGTEX_phenotype.txt\".initialize_RNAseq_data reads the recomputed RNAseq data from both TCGA and GTEx. The implementation details of each operation are within the \u223c/eIF4F.analysis/R/DEG.R file. initialize_RNAseq_data sets one global variable TCGA_GTEX_RNAseq_sampletype for the gene expression analysis (step-3), PCA (step-5) and correlating gene analysis (step-6), and stores TCGA_GTEX_RNAseq_sampletype as \u201cTCGA_GTEX_RNAseq_sampletype.csv\u201d in the ProcessedData folder.c.i.TCGA_RNAseq_OS_sampletype comes from three datasets: the RNAseq dataset \"EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena\", the survival dataset \"Survival_SupplementalTable_S1_20171025_xena_sp\" and the annotation dataset \"TCGA_phenotype_denseDataOnlyDownload.tsv\".initialize_survival_data reads the RNAseq and patient survival data from TCGA.\u00a0The implementation details of this operation are within the \u223c/eIF4F.analysis/R/Survival.R file. This function sets the global variable TCGA_RNAseq_OS_sampletype for survival analysis (step-4), and store TCGA_RNAseq_OS_sampletype as \u201cTCGA_RNAseq_OS_sampletype.csv\u201d inside the ProcessedData folder.d.i.This function sets three global variables for the CCLE data: (1) CCLE_RNAseq contains the\u00a0RNAseq data derived from \"CCLE_expression_full.csv\", (2) CCLE_Anno contains the\u00a0annotation data derived from \"sample_info.csv\", and (3) CCLE_Proteomics contains\u00a0the protein expression level data derived from \"protein_quant_current_normalized.csv\". This function stores CCLE_RNAseq, CCLE_Anno and CCLE_Proteomics as \u201cCCLE_RNAseq.csv\u201d, \u201cCCLE_Anno.csv\u201d, and \u201cCCLE_Proteomics.csv\u201d inside the ProcessedData folder.ii.This function sets two global variables as data frames for the CPTAC LUAD data published in Gillette et\u00a0al. (2020)initialize_proteomics_data reads the proteomics related data from CCLE and CPTAC LUAD, including: proteomics data, annotation data for cancer types, RNAseq data for the correlation analysis on protein RNA levels (step-7 and step-8). The implementation details of this operation are within the \u223c/eIF4F.analysis/R/RNAProCorr.R file.e.i.CPTAC_LUAD_Phos contains the phosphoproteomics data published in Gillette et\u00a0al. (2020)ii.CRITICAL: The first run of data initialization functions creates and stores the processed data from download files. Following runs of the initialization functions will check the existence of processed data files and read them, which take a much shorter time to complete than the first run. CPTAC_LUAD_Clinic_Sampletype contains the annotation data and is derived from\u00a0\"S046_BI_CPTAC3_LUAD_Discovery_Cohort_Clinical_Data_r1_May2019.xlsx\" and \"S046_BI_CPTAC3_LUAD_Discovery_Cohort_Samples_r1_May2019.xlsx\".initialize_phosphoproteomics_data reads phospho-proteomics-related data from CPTAC LUAD, and sets two global variables with data frames for the protein expression\u00a0analysis (step-8). The implementation details of this operation are in the \u223c/eIF4F.analysis/R/Proteomics.R file. This function stores two global variables CPTAC_LUAD_Phos and CPTAC_LUAD_Clinic_Sampletype as \u201cCPTAC_LUAD_Phos.csv\u201d and \u201cCPTAC_LUAD_Clinic_Sampletype.csv\u201d in the ProcessedData folder.Run the following command line to acquire omics datasets from the download data files.Initialization processes rely on three exported functions to define subdirectories for output data, to define the graphic formats (font size and style), and to load data from downloaded data files. The definitions of three initialization functions were stored in \u223c/eIF4F.analysis/R/Load.R.Timing:\u00a0<\u00a01\u00a0minEIF4F genes across TCGA tumors and creates the analysis results both on screen and as pdf files stored in \u223c/eIF4F.analysis/eIF4F_output/CNV folder.4.Run the following command line in RStudio.> EIF4F_CNV_analysisNote:EIF4F_CNV_analysis is a wrapper function of three internal composite functions that take input data frames and call internal functions for analysis. Note:.plot_bargraph_CNV_TCGA takes the data frame TCGA_CNV_sampletype and calculates the frequency of each CNV status for EIF4F genes in all tumors combined from 33 TCGA cancer types. Its output is a stacked bar plot that ranks the EIF4F gene by the frequencies of copy number gain from individual TCGA cancer types. This function produces a CNV ratio boxplot for each gene in individual TCGA cancer types analysis to associate survival probabilities with gene expression. This function takes arbitrary gene expression cutoff, 0.2 for 20% or 0.3 for 30%, to stratify the patient groups based on the top or bottom precents of gene expression within their tumors. This function performs KM analysis on all combined TCGA cancer types regression method. This function can perform survival analyses on all combined TCGA cancer types or individual cancer type such as \u201clung adenocarcinoma\u201d as an argument. The function performs both univariable Cox-PH analysis using a single gene expression as the dependent variable on Timing:\u00a0<\u00a030\u00a0minEIF4F subunits from tumor or healthy samples, and outputs results to the \u223c/eIF4F.analysis/eIF4F_output/COR folder.8.Run the following command line in RStudio.> EIF4F_Corrgene_analysisNote:EIF4F_Corrgene_analysis is a wrapper function to call one internal composite function that takes input data frames and calls internal functions for analysis. Note:.plot_Corr_RNAseq_TCGA_GTEX takes the data frameTCGA_GTEX_RNAseq_sampletype and selects RNAseq data from two sample types: TCGA tumors, or GTEx healthy tissues. This function separately identifies correlating genes (CORs) of EIF4E, EIF4A1, EIF4G1, and EIF4EBP1 from tumor samples or from healthy tissues. The significant CORs for each EIF4F subunit are identified and classified as positive or negative CORs (posCORs and negCORs). This function analyzes the overlap posCORs or negCORs of four EIF4F subunits from tumor samples or healthy tissues as Venn plots datasets, and outputs results to the \u223c/eIF4F.analysis/eIF4F_output/RNApro folder.Timing:\u00a0<\u00a05\u00a0min10.Run the following command line in RStudio.> EIF4F_Proteomics_analysisNote:EIF4F_Proteomics_analysis is a wrapper function to call two internal composite functions that take input data frames and call internal functions for analysis. Note:.plot_scatterplot_protein_LUAD takes the data frame CPTAC_LUAD_Proteomics and selects the proteomics data of tumor samples. It analyzes the correlation between two input proteins across the LUAD tumor samples protein expression in different tumor stages, and outputs results to the \u223c/eIF4F.analysis/eIF4F_output/proteomics folder.All analysis results are produced as plots on screen and as pdf files in output file directories. Examples of results from each analysis step are shown in The execution of this package relies on specific exported functions and does not allow parameter input within the package. However, for each analysis step, the internal composite functions, the required input data frames, and the dependent functions are stored within one R file E. Most ieIF4F.analysis package relies on many dependent packages for data analysis and plotting. Because those dependent packages are widely used for individual applications, their combined usage provides great convenience for users to achieve a thorough understand of eIF4F functions. However, a major limitation of this approach is that incompatibility may occur with future version changes, since those packages are maintained independently of each other.This package aims to provide an easy method to reliably reproduce the results from Wu and Wagner (2021),Attaching package: \u2018eIF4F.analysis\u2019The following objects are masked _by_ \u2018.GlobalEnv\u2019:initialize_data, initialize_dir, initialize_formatError messages during Preparation three: installing and loading eIF4F.analysis.It means that you have objects present in your global environment with the same name as (exported) things in your package. Clean the environment and reload the package.> EIF4F_Corrgene_analysisFailed with error: org.Hs.egPFAM is defunct. Please use select if you need access to PFAM or PROSITE accessions.Note: The object org.Hs.egPFAM has not been not used for any operation in the script, thus this error message does not affect the results of the analyses.While running EIF4F_Corrgene_analysis at step-6: analyze the correlating genes (CORs) of EIF4F subunits, you run into the following error:> library(org.Hs.eg.db)Run the following command to reload the \u201corg.Hs.eg.db\u201d package. If the same error message of defunct org.Hs.egPFAM appears, please reinstall the \"org.Hs.eg.db\" package to the latest version (3.15.0).gerhard_wagner@hms.harvard.edu).Further information and requests for resources should be directed to and will be fulfilled by the lead contact, Gerhard Wagner (This study did not generate new unique reagents."} +{"text": "Lacunicambarus thomai using video surveillance to determine their degree of surface activity and behavioral patterns. Throughout 664 hrs of footage, we observed a surprisingly high amount of activity at the surface of their burrows\u2014both during the day and night. The percentage of time that individual crayfish was observed at the surface ranged from 21% to 69% per individual, with an average of 42.48% of the time spent at the surface across all crayfish. Additionally, we created an ethogram based on six observed behaviors and found that each behavior had a strong circadian effect. For example, we only observed a single observation of foraging on vegetation during the day, whereas 270 observations of this behavior were documented at night. Overall, our results suggest that burrowing crayfishes may exhibit higher levels of surface activity than previously thought. To increase our understanding of burrowing crayfish behaviors ecology, we encourage the continued use of video-recorded observations in the field and the laboratory.Opposed to most crayfish species that inhabit permanent bodies of water, a unique burrowing lifestyle has evolved several times throughout the crayfish phylogeny. Burrowing crayfish are considered to be semi-terrestrial, as they burrow to the groundwater\u2014creating complex burrows that occasionally reach 3 m in depth. Because burrowing crayfishes spend most of their lives within their burrow, we lack a basic understanding of the behavior and natural history of these species. However, recent work suggests that burrowing crayfishes may exhibit a higher level of surface activity than previously thought. In the current study, we conducted a behavioral study of the Little Brown Mudbug, Procambarus clarkii, Procambarus virginalis, Faxonius virilis); all of which inhabit lentic and lotic aquatic environments. Although most crayfish species inhabit surface water systems like streams, lakes, rivers, ponds, and marshes, crayfishes have repeatedly evolved a semi-terrestrial burrowing lifestyle throughout their phylogeny . Although the exact function of these excursions is unknown, it is unclear whether or not L. thomai engages in such behaviors.In summary, based on our preliminary investigation, we found that Further, throughout our study, we did not observe any intra-specific interactions. Again, scattered observations highlight the social behavior of burrowing crayfishes, but interestingly, we did not observe any social behavior throughout the course of our study. Future studies should conduct similar behavioral observations throughout the year and also investigate potential demographic differences in the behaviors we report. By expanding the time frame in which records occur, social interactions of larger foraging excursions may be recorded. Lastly, although our study has shed light on the activity of crayfishes at the surface, much remains unknown about the subsurface behavior of burrowing crayfishes. Additionally, since we discovered that this species displayed easily identifiable postural behaviors, this may allow for automated video analysis of body position, activity, and behaviors. As such, the continued use of burrowing crayfish observations chambers will be S1 File(MP4)Click here for additional data file.S2 File(MP4)Click here for additional data file.S3 File(MP4)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file.S1 Fig(PNG)Click here for additional data file.S2 Fig(PNG)Click here for additional data file.S3 Fig(PNG)Click here for additional data file.S4 Fig(PNG)Click here for additional data file. 3 May 2022
PONE-D-21-39709
On the surface or down below: Field observations reveal a high degree of surface activity in a burrowing crayfish, the Little Brown Mudbug (Lacunicambarus thomai)
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Reviewer #1:\u00a0YesReviewer #2:\u00a0Partly********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0No********** 3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0The authors made an interesting work, continuously filming the surface behavior of crayfish which were thought before to stay mostly or totally in underground burrows. They registered activity both during the day and night along with daily environmental factor variations and analyzed their behavior through the video recordings. While most behavioral studies in crayfish have been done in laboratory settings, this one contributes by rescuing ecological context and opening new perspectives of research. It is mostly well done but there are three general issues to be considered:1) One of the big contributions of this work is to enable discrimination of individual behavior, which is not a simple task in natural observations. Individual data presentations are fine but I suspect that when average analysis are presented, some or most of them are not considering that one individual (#2) with more than double the number of data collection is biasing the results. This can be deduced from some graphs while others do not let us know because description of average calculations are missing in Materials and Methods.2) While behavioral analysis can be made when these crayfish are on surface, nothing can be stated of their underground times. In this sense, it is an error to assign \u201cinactivity\u201d for underground times.3) Discussion needs to be improved.Comments:- Study Site: More basic description is required of the study area around the filming spot, to better explore the results. It is said that most species (tertiary and secondary burrowing crayfish) inhabit lotic and lentic environments but it is not clear how far are the Primary burrowing species of this study from water bodies, for instance. It is said in the Introduction that \u201cLacunicambarus thomai is a burrowing crayfish species with a high propensity to inhabit burrows in marshes, roadside ditches, and flooded fields (38). Populations of L. thomai often live in localized colonies with conspecifics and inhabit burrows that are relatively simple but can nonetheless be up to 1-1.5 m deep \u201d. However, nothing, no information is provided of the specific area where the study took place: proximity from rivers, vegetation types and cover densities, average ranges of daily environmental factor variations, Latitudinal coordinates.- Burrows were selected and filmed. How far is one burrow from the other? Inform the average land area inside which the 6 burrows were located. One individual is associated to each burrow \u2013 is that an assumption or are there evidences that they are solitary? Furthermore, it is said that burrows may have more than one entrance (line 67), how was this issue treated here?- It is said in Statistical Analysis that none of the independent variables were strongly correlated . A representative graph depicting an average 24h variation of environmental factors in the studied season would be informative in Supplemental Material. How was time included in the models, as a categorical or continuous variable? A continuous variable with linear increase (such as a sequence from 0 to 23) would create artificial associations in the model. Please evaluate, based on the statistical parameters found in Table 3, if it is not enough to use a simple model without interaction between time, humidity and temperature to understand the influence of environmental factors on the surface activity. The reason for this question is that the complexity of the best-fit model seems to have inhibited any discussion about the analysis in the end.- The Results section start with \u201cHourly Activity\u201d (which should be \u201cHourly surface activity\u201d) and Figure 4, but there is no explanation as to how this was calculated. It is explained in Statistical Analysis that for an individual to be considered active on surface in one specific hour and day, it needs to be seen in any time point within that hour in that day. Then, how was the group average/percentage calculated taking into account that each contributing individual was registered for a different number of days? Individuals that had more filmed days should not weight more. Finally, Legend Figure 4 needs to inform that averages were calculated taking into account all individuals and all days.An explicit description of calculation should also be added to \u201cpercentage of time spent active throughout daytime\u201d and \u201c proportion of time spent on surface\u201d. In Table 5, how was the \u201cmean duration\u201d of each behavior calculated, taking into account individuals and number of days each individual was filmed?In Figures 5, 6 and 7, it is interesting to show the \u201ccombined\u201d proportions. However, it is biased by individual 2, which was filmed for more days. Could an unbiased calculation be made here?In Figure 8 the number of observations is again biased to individual 2.- Figure 5 and associated text: comparison should be between \u201csurface\u201d and \u201cunderground\u201d, not between \u201cactive\u201d and inactive\u201d because nothing is known about what the crayfish are doing underground. The same for Figure 6: \u201cnighttime on surface\u201d and \u201cdaytime on surface\u201d. In Line 281, replace \u201c active\u201d by \u201con surface\u201d in \u201cThe percentage of time that crayfish were active during the daytime\u201d. In Line 283, \u201cRegarding nighttime activity on surface\u201d. Legend Figure 6: \u201cpercentage of time that each individual crayfish spent on surface during the day and the night\u201d.-- Discussion: In contrast to Bearden et al. (2021), this study brings more information about the behavioral complexity of this particular crayfish species. However, the lengthy discussion is mainly descriptive of results. The authors should explore, for instance, what was found in statistical analysis and how could this be connected to the specificity of the studied environment, to take full advantage of the in situ study. Another suggestion is to take Bearden et al. (2021) as a reference, discuss how the results are constrained by the particular season and microhabitat that was covered in this study.- Humidity was indicated as the most important factor modulating surface appearance in crayfish. This variable, as well as all others were collected from a meteorological station. Any thoughts about the validity of using only macro-environmental measurements in association with behaviors that are restricted to the spatial scale of the entrance of a burrow?- Temperature was shown to be a strong predictor of surface activity. A strong suggestion for future studies is to also consider underground temperature in this analysis. For instance, it has been shown in endothermic subterranean rodents that a combination of external and underground temperatures predict better the episodes of surface emergences . It is reasonable to assume that similar influence is potentially valid for these crayfish.- This crayfish display clear postural signatures that enable behavioral identification through the relative position of body coordinates . This could potentially be used in future automated video analysis of activity patterns.Minor Comments:Fig.2C: view of the cameraLine 248: remove extra \u201cwere\u201dLine 319: \u201cevery single behavior was more likely to occur during day or night compared to another\u201d An alternative could be \u201cdaily phase\u201dTable 4: what does this mean? \u201cthe activity of L. thomai was negatively related to the activity of crayfish.\u201dReviewer #2:\u00a0I understand that behaviour of strictly burrowing crayfish is difficult to study, so the information presented by the authors is surely interesting, and novel. However, the entire manuscript is based on only six individuals that were not even characterized. So, data are very preliminary and should be interpreted more cautiously. Behavioural categories should be also analysed together, considering that are dependent data. I am sorry not to be more positive, but a more specialised journal seems to be more appropriate for the manuscript.Lines 50-52, 109: for the readers it would be interesting to specify that these species are North AmericanLine 67: maybe opening is more suitable than portalLined 128-130: so how many burrows were checked before selecting only six? How about the density of the burrows in the study area?Line 132: crayfish could have been attracted out of the burrows with some baits after the footage to characterize them (for hunt behaviour it is reported they leave the burrow for example)Line 182: were the behavioural data checked for normality?Lines 218-222: those behaviours are dependent each other, so it is better to analyse them together because when crayfish are guarding, for example, they are not feeding or huntingLine 235: please delete during the studyLine 270: please 5 not in italicsI suggest merging Fig 5 and 6 in one figureTable 5: please report all the duration in seconds. Moreover, please change during with duration in the captionTables should be better drafted and presentedLine 343: please correct fiveLine 345: please better rephrase this sentenceLine 356: Loughman et al. 2018 is not present in the bibliography; 46 is Loughman et al. 2015Line 371, 448: please consider that only six individuals were observed, so I suggest being more cautious in this statementLine 381: please do not use intricacies but richness or diversityLine 415: please correct \u201cis required\u201dLine 436: I think it is \u201cuse its claws to push the mud\u201d********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1:\u00a0NoReviewer #2:\u00a0Nohttps://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,\u00a0 18 May 2022Dear Dr. Junhu Dai,Thank you for allowing us the opportunity to revise our manuscript. The comments from the two reviewers were extremely helpful and made the manuscript much stronger. Based on their suggestions, we incorporated most suggestions to our manuscript. Below, you will find a letter detailing how we dealt with each comment of each reviewer. Where applicable, we state what we have changed and the location in which you will find our modifications in our updated manuscript. We address each reviewer comment (C#) in individual answers (A#) to keep everything organized.Reviewer #1: C1: The authors made an interesting work, continuously filming the surface behavior of crayfish which were thought before to stay mostly or totally in underground burrows. They registered activity both during the day and night along with daily environmental factor variations and analyzed their behavior through the video recordings. While most behavioral studies in crayfish have been done in laboratory settings, this one contributes by rescuing ecological context and opening new perspectives of research. It is mostly well done but there are three general issues to be considered:A1: Thank you for the generous comments. We appreciate your suggestions and we have attempted to address all your comments below. ______________________________________________________________________________C2: One of the big contributions of this work is to enable discrimination of individual behavior, which is not a simple task in natural observations. Individual data presentations are fine but I suspect that when average analysis are presented, some or most of them are not considering that one individual (#2) with more than double the number of data collection is biasing the results. This can be deduced from some graphs while others do not let us know because description of average calculations are missing in Materials and Methods.A2: We agree that analyzing behavioral data presents several issues and that this issue can be exacerbated by having an unequal sample size (263 hrs of footage for crayfish 2 vs 40 hours for crayfish 1). This is why we have chosen to present the majority of our results in terms of the percentages and not raw values. Reporting this information in terms of the raw values would certainly bias our results, as you suggest. However, by reporting this information in percentages, we believe that this is the most appropriate way to report our results and adjust for the bias. Furthermore, our manuscript reports relatively few true statistical analyses (and instead opts for more descriptive statistics of what we observed). This aligns with the primary goals of our manuscript\u2014to describe the behavioral diversity of this elusive crayfishes and demonstrate how this new methodology can be lucrative in the field of crustacean behavioral ecology. ______________________________________________________________________________C3: While behavioral analysis can be made when these crayfish are on surface, nothing can be stated of their underground times. In this sense, it is an error to assign \u201cinactivity\u201d for underground times.A3: We agree. Our manuscript can only report of the surface activity, and not any potential underground behaviors. We have altered our language throughout the entire manuscript to account for this comment. We have changed any discussion of \u201cinactivity\u201d to \u201cinactivity at the surface\u201d. ____________________________________________________________________________C4: Discussion needs to be improved.A4: We have taken several of your comments regarding topics that require additional discussion and expanded on them. ______________________________________________________________________________C5: Study Site: More basic description is required of the study area around the filming spot, to better explore the results. It is said that most species (tertiary and secondary burrowing crayfish) inhabit lotic and lentic environments but it is not clear how far are the Primary burrowing species of this study from water bodies, for instance. It is said in the Introduction that \u201cLacunicambarus thomai is a burrowing crayfish species with a high propensity to inhabit burrows in marshes, roadside ditches, and flooded fields (38). Populations of L. thomai often live in localized colonies with conspecifics and inhabit burrows that are relatively simple but can nonetheless be up to 1-1.5 m deep \u201d. However, nothing, no information is provided of the specific area where the study took place: proximity from rivers, vegetation types and cover densities, average ranges of daily environmental factor variations, Latitudinal coordinates.A5: We agree that information on our study site was lacking in the original version of the manuscript. We have now included a detailed description of the location in which we conducted this study (see Lines 127-134). Because our sampling location is on a residential property, we choose to not report exact coordinates. ______________________________________________________________________________C6: Burrows were selected and filmed. How far is one burrow from the other? Inform the average land area inside which the 6 burrows were located. One individual is associated to each burrow \u2013 is that an assumption or are there evidences that they are solitary? Furthermore, it is said that burrows may have more than one entrance (Line 67), how was this issue treated here?A6: We have updated this information within our manuscript. We now provide information regarding how far away one burrow was from one another (Lines 131-132), as well as our assumption that each burrow was occupied by a single crayfish (Lines 141-144). We also clarify how we dealt with the issue with burrows with more than a single entrance (Lines 151-153).______________________________________________________________________________C7: It is said in Statistical Analysis that none of the independent variables were strongly correlated . A representative graph depicting an average 24h variation of environmental factors in the studied season would be informative in Supplemental Material. How was time included in the models, as a categorical or continuous variable? A continuous variable with linear increase (such as a sequence from 0 to 23) would create artificial associations in the model. Please evaluate, based on the statistical parameters found in Table 3, if it is not enough to use a simple model without interaction between time, humidity and temperature to understand the influence of environmental factors on the surface activity. The reason for this question is that the complexity of the best-fit model seems to have inhibited any discussion about the analysis in the end.A7: We have now included 4 new figures in the supplemental materials which display the relevant environmental data during our study period. In the original manuscript, we reported that there were no strong statistical correlations between humidity, temperature, and time (as you mentioned). In our environmental analysis, time was coded as a continuous variable. We tested for the correlations beforehand to potentially deal with any artificial associations that you hint at. However, because of the low correlation values, we decided to proceed with using time as a continuous variable. Furthermore, the fact that time is not a strong predictor of activity (Table 4) suggests that there is no underlying association between these variables.Our best fit model was quite complex, as you note. It was a model with 3 single parameters, and two interaction parameters. This why is we not only conducted a model-selection procedure (results in Table 3), but also the multi-model average procedure (results in Table 4). The results from our full model averaging technique allow us to evaluate all of the models together and construct effect sizes and weights for each of the terms in our model. This is why we come to the conclusion that humidity had the strongest overall effect (Table 4) compared to the other models. We have now included a better discussion of this result in our discussion section (see A14).______________________________________________________________________________C8: The Results section start with \u201cHourly Activity\u201d (which should be \u201cHourly surface activity\u201d) and Figure 4, but there is no explanation as to how this was calculated. It is explained in Statistical Analysis that for an individual to be considered active on surface in one specific hour and day, it needs to be seen in any time point within that hour in that day. Then, how was the group average/percentage calculated taking into account that each contributing individual was registered for a different number of days? Individuals that had more filmed days should not weight more. Finally, Legend Figure 4 needs to inform that averages were calculated taking into account all individuals and all days.A8: We have changed this section to \u201cHourly Surface Activity\u201d as you suggest. We have clarified how this was calculated in the methods sections (Lines 201-209). Again, we report these values in terms of percentages, and not the raw number of hours each crayfish was active to avoid any potential sampling biases as you suggest. We have also updated the legend for Figure 4 to include those averages were calculated by taking into account for all individuals and all days throughout our study. ______________________________________________________________________________C9: An explicit description of calculation should also be added to \u201cpercentage of time spent active throughout daytime\u201d and \u201c proportion of time spent on surface\u201d. In Table 5, how was the \u201cmean duration\u201d of each behavior calculated, taking into account individuals and number of days each individual was filmed?A9: We have updated our methods to also include information as to how we calculated these percentages. By reporting these values in percentages, we avoid any issues based on the number of hours each crayfish was sampled and filmed. We have updated the legend in figure 5 to describe that our mean durations were calculated based on all crayfish. This data is reported to be entirely descriptive in nature, and therefore we believe that reporting such means are the most informative way to describe these different behaviors. ______________________________________________________________________________C10: In Figures 5, 6 and 7, it is interesting to show the \u201ccombined\u201d proportions. However, it is biased by individual 2, which was filmed for more days. Could an unbiased calculation be made here?A10: Reporting our results in terms of percentages is the best way to provide an unbiased calculation for these figures, which are primarily meant to be descriptive and exploratory in nature. If we would have reported the data from the raw amount of time that each behavior/activity was performed, then this would certainly be biased. This is why we chose to reported the data in terms of percentages throughout the manuscript. ______________________________________________________________________________C11: In Figure 8 the number of observations is again biased to individual 2.A11: Yes, Figure 8 is biased based on the increased number of observations from individual 2. This figure are describing trends in whether or not a specific behavior was more or less likely to occur at day versus night. We have included information regarding this issue in our manuscript (Lines 201-203). Anecdotally, if you look at the percentages of all behaviors reported in Fig 5, 6, and 7, there is a similar degree of surface activity/behaviors being exhibited by each crayfish, which implies that this bias may be minimally impacting our results. ______________________________________________________________________________C12: Figure 5 and associated text: comparison should be between \u201csurface\u201d and \u201cunderground\u201d, not between \u201cactive\u201d and inactive\u201d because nothing is known about what the crayfish are doing underground. The same for Figure 6: \u201cnighttime on surface\u201d and \u201cdaytime on surface\u201d. In Line 281, replace \u201c active\u201d by \u201con surface\u201d in \u201cThe percentage of time that crayfish were active during the daytime\u201d. In Line 283, \u201cRegarding nighttime activity on surface\u201d. Legend Figure 6: \u201cpercentage of time that each individual crayfish spent on surface during the day and the night\u201d.A12: You are correct; we do not want to mislead the readers. Now, all of our figures have been accounted for the fact that we are only reporting surface activity and that we cannot comment on underground. Activity. Figures 5 and 6 are now updated accordingly. We have also changed the legend for Figure 6______________________________________________________________________________C13: Discussion: In contrast to Bearden et al. (2021), this study brings more information about the behavioral complexity of this particular crayfish species. However, the lengthy discussion is mainly descriptive of results. The authors should explore, for instance, what was found in statistical analysis and how could this be connected to the specificity of the studied environment, to take full advantage of the in situ study. Another suggestion is to take Bearden et al. (2021) as a reference, discuss how the results are constrained by the particular season and microhabitat that was covered in this study.A13: We agree that we could have expanded on our discussion section. Based on many of your suggestions below we believe that the discussion has significantly improved. ______________________________________________________________________________C14: Humidity was indicated as the most important factor modulating surface appearance in crayfish. This variable, as well as all others were collected from a meteorological station. Any thoughts about the validity of using only macro-environmental measurements in association with behaviors that are restricted to the spatial scale of the entrance of a burrow?A14: We agree that the macro environmental variables that we relate to surface activity are far from ideal for such studies. We have updated our discussion to point this out and suggest that future studies take into account the variables potential micro-environmental influences within and around the burrow entrances (Lines 406-422). ______________________________________________________________________________C15: Temperature was shown to be a strong predictor of surface activity. A strong suggestion for future studies is to also consider underground temperature in this analysis. For instance, it has been shown in endothermic subterranean rodents that a combination of external and underground temperatures predict better the episodes of surface emergences . It is reasonable to assume that similar influence is potentially valid for these crayfish.A15: This is a great suggestion to add to our discussion section. We have now included that looking at the underground temperature variation is a fruitful area for future directions (Lines 416-422). ______________________________________________________________________________C16: This crayfish display clear postural signatures that enable behavioral identification through the relative position of body coordinates . This could potentially be used in future automated video analysis of activity patterns.A16: That is a great suggestion to add the discussion. We have included these postural changes to be used in the identification of automated video analysis in the future (Lines 511-513). ______________________________________________________________________________C17: Fig.2C: view of the cameraA17: We have edited this sentence accordingly.______________________________________________________________________________C18: Line 248: remove extra \u201cwere\u201dA18: We have removed the extra \u201cwere\u201d______________________________________________________________________________C19: Line 319: \u201cevery single behavior was more likely to occur during day or night compared to another\u201d An alternative could be \u201cdaily phase\u201dA19: We believe that the current wording provides for clarity because \u201cdaily phase\u201d may be confused with \u201cday\u201d. ______________________________________________________________________________C20: Table 4: what does this mean? \u201cthe activity of L. thomai was negatively related to the activity of crayfish.\u201dA20: This was a typo and should have read \u201cThus, the activity of L. thomai was negatively related to the degree of environmental humidity.\u201d We have made this change to the Table 4 text. Thank you.______________________________________________________________________________Reviewer #2: C21: I understand that behaviour of strictly burrowing crayfish is difficult to study, so the information presented by the authors is surely interesting, and novel. However, the entire manuscript is based on only six individuals that were not even characterized. So, data are very preliminary and should be interpreted more cautiously. Behavioural categories should be also analysed together, considering that are dependent data. I am sorry not to be more positive, but a more specialised journal seems to be more appropriate for the manuscript.A21: We agree that the fact that our study being only conducted on six individuals is a limitation to our study. Low sample sizes are typical for this type of work, because of the time intensive nature and complexities of naturalistic studies Although this work was only conducted on six individuals (that have unknown demographic information), we believe that the amount and nature of our data is worthy of publication. In the previous and updated versions of our manuscript, we attempt not to overstate our results as they are preliminary and exploratory in nature. Furthermore, although we do not report the demographic data from these crayfishes , there is no data that has alluded to sex differences in burrowing crayfish behavior. We do agree that this is an interesting and important angle for future studies though, so we have included that this information should be investigated in the future (Lines 507-508).Despite these limitations, we still believe that we provide a novel methodology and interesting results (which reviewer 1 highlights) that will be of interest to a wide audience. Because the scope of PLOS ONE is to publish papers based on their scientific validity and methodology, we believe that our study is of interest to an audience outside of smaller, taxonomic focused journals.We respond to the comment on behavioral categories being analyzed together below (see A27).______________________________________________________________________________C22: Lines 50-52, 109: for the readers it would be interesting to specify that these species are North AmericanA22: We have edited Lines 50-52 to clarify that these are North American species (Line 50-51) ______________________________________________________________________________C23: Line 67: maybe opening is more suitable than portalA23: Portal is a term burrowed from the literature on mammalian burrowing behavior and is widely used to refer to crayfish burrow openings. Therefore, we prefer to keep this language consistent with prior published papers. We have included a few examples below. Glon, M. G., Adams, S. B., Loughman, Z. J., Myers, G. A., Taylor, C. A., & Schuster, G. A. (2020). Two new species of burrowing crayfish in the genus Lacunicambarus (Decapoda: Cambaridae) from Alabama and Mississippi. Zootaxa, 4802(3), 401-439.Loughman, Z. J. (2010). Ecology of Cambarus dubius (upland burrowing crayfish) in north-central West Virginia. Southeastern Naturalist, 9(sp3), 217-230.______________________________________________________________________________C24: Lined 128-130: so how many burrows were checked before selecting only six? How about the density of the burrows in the study area?A24: We have now included much more information regarding our study location. Based on the relatively small number of burrows at the study location, we choose to only focus on a small sample size but to collect as much data as possible on each of these adult individuals. ______________________________________________________________________________C25: Line 132: crayfish could have been attracted out of the burrows with some baits after the footage to characterize them (for hunt behaviour it is reported they leave the burrow for example)A25: Yes, that is true. Unfortunately, we did not capture these individuals. We have included information how future studies need to explore how different demographics may exhibit such behaviors differently (lines 50-51). ______________________________________________________________________________C26: Line 182: were the behavioural data checked for normality?A26: Yes, all data and model fits were checked for normality. We have now included this information in the manuscript (Lines 197-199).______________________________________________________________________________C27: Lines 218-222: those behaviours are dependent each other, so it is better to analyse them together because when crayfish are guarding, for example, they are not feeding or huntingA27: This comment highlights the complexities of working with behavioral data, because an organism cannot perform more than a single behavior at once. Therefore, this is why we chose to primarily focus on broad, descriptive statistics throughout our study. Because of the novelty of these findings and the potential impact on our understanding of crustacean behavioral ecology, we believe that this is the proper way to analyze report our data at this stage. ______________________________________________________________________________C28: Line 235: please delete during the studyA28: We have deleted this phrase.______________________________________________________________________________C29: Line 270: please 5 not in italicsA29: We have unitalicized this number.______________________________________________________________________________C30: I suggest merging Fig 5 and 6 in one figureA30: We prefer to keep these figures separate as to avoid confusion between the messages of figure 5 (observed at surface vs. underground) and figure 6 (observed at surface during the day versus observed at surface during the night).______________________________________________________________________________C31: Table 5: please report all the duration in seconds. Moreover, please change during with duration in the captionA31: We have changed the table to report each behavior in. We have changed during to duration as you suggested. ______________________________________________________________________________C32: Tables should be better drafted and presentedA32: Without any comments on the issues of the tables, we are unsure what to change base. ______________________________________________________________________________C33: Line 343: please correct fiveA33: We change made this change. ______________________________________________________________________________C34: Line 345: please better rephrase this sentenceA34: We have rephrased this sentence accordingly (Lines 366-368).______________________________________________________________________________C35: Line 356: Loughman et al. 2018 is not present in the bibliography; 46 is Loughman et al. 2015A35: Thank you for noticing this issue. We meant Loughman et al. 2015 and we have made this change. ______________________________________________________________________________C36: Line 371, 448: please consider that only six individuals were observed, so I suggest being more cautious in this statementA36: We agree that we need to be more cautious with these statements. We have added additional information to these sections based on your comments (see Lines 394-395 and Lines 494-495).______________________________________________________________________________C37: Line 381: please do not use intricacies but richness or diversityA37: We have changed the work intricacies to richness as you have suggested. ______________________________________________________________________________C38: Line 415: please correct \u201cis required\u201dA38: We have changed \u201care required\u201d to \u201cis required\u201d______________________________________________________________________________C39: Line 436: I think it is \u201cuse its claws to push the mud\u201dA39: Thank you for catching this error. We have fixed the typo.Attachmentresponse_to_reviewers_1.docxSubmitted filename: Click here for additional data file. 19 Jul 2022
PONE-D-21-39709R1
On the surface or down below: Field observations reveal a high degree of surface activity in a burrowing crayfish, the Little Brown Mudbug (Lacunicambarus thomai)
PLOS ONEDear Dr. Diehl,Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE\u2019s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.
Since I had difficulties finding a second Reviewer, I decided to review your revised manuscript myself. As you will see, the negative Reviewer of your first submission appreciated your corrections and judged that you contribution is now ready for publication. However, I found some problems that need to be settled before your paper is accepted. The main point concerns difficulties to link the results given in the text with those in the figures. I think that there may be some mistakes. For this reason, please carefully check your Result section. Also, I made several editorial recommendations. You will find all this information in the attached file \"D-21-39709_R1_LFB.pdf\". I appreciated your work and think that it will be a useful contribution to crayfish biology.\u00a0plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.Please submit your revised manuscript by Sep 02 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at\u00a0Please include the following items when submitting your revised manuscript:A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.
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For instructions see: We look forward to receiving your revised manuscript.Kind regards,Louis-Felix Bersier, Ph.D.Academic EditorPLOS ONEJournal Requirements:Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article\u2019s retracted status in the References list and also include a citation and full reference for the retraction notice.Additional Editor Comments:See attached file \"D-21-39709_R1_LFB.pdf\"[Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #2:\u00a0All comments have been addressed********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2:\u00a0Yes********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2:\u00a0Yes********** 4. 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Reviewer #2:\u00a0No**********https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.
While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,\u00a0AttachmentPONE-D-21-39709_R1_LFB.pdfSubmitted filename: Click here for additional data file. 6 Aug 2022Dear Dr. Louis-Felix Bersier, Thank you for allowing us the opportunity to revise our manuscript. Your comments were extremely helpful and made the manuscript much stronger. Based on their suggestions, we incorporated most suggestions to our manuscript. Below, you will find a letter detailing how we dealt with each comment you provided. We address each comment (C#) in individual answers (A#) to keep everything organized.Editor Comments: C1: This level of precision is not necessary. I recommend rounding at unity here (21% to 69%)A1: We have rounded these percentages. ______________________________________________________________________________C2: Could be abridged as \"tertiary-, secondary-, and primary burrowing species\"A2: This is a good suggestion, we have changed the text accordingly.______________________________________________________________________________C3: deleteA3: We have deleted the words \u201cthe setup of\u201d here. ______________________________________________________________________________C4: I guess \"... unable to report ...\"A4: Yes, you are correct. We have edited the text here. ______________________________________________________________________________C5: Meaning not clear to me. If it indicates that this behavior occurs mostly during the night, it should not be part of the description in the table, but should be stated in the results.A5: This statement (more exposed during the night) has been deleted because we agree that it is unclear. We meant to mean that when the crayfish exhibit the guard behavior during the night, they are typically more exposed out of their burrow portal. But we did not quantify this, so we chose to delete it from the text. ______________________________________________________________________________C6: The images are very useful and raise a question since these two behaviors are very similar. As a non-specialist, I would like some words (and possibly a reference) that explain and justify this distinction.A6: After some discussion, we agree with all of your comments regarding our denotation of these behaviors of \u201cguard\u201d and \u201crest\u201d behaviors. We now refer to both of these behaviors as \u201crest\u201d and separate them based on \u201crest-claws open/rest - open\u201d and \u201crest-claws joined/rest \u2013 joined\u201d. Although rest \u2013 closed may represent a guarding behavior, we believe that because this work is preliminary, we are keeping the language simple. The manuscript and figures have been changed accordingly. We believe that this language will properly describes the behaviors of the crayfishes would making any presumptions on the function of the posture. ______________________________________________________________________________C1: There may be an unimodal relationships with these variable, reflecting optima. Did you check for this possibility ?A1: We did check for this, but because there was not as much variation in the environment variables, we did not find any optimum relationship between activity and such environmental variables. ______________________________________________________________________________C1: Personally, I would place the Tables 3 and 4 in the Supporting Information (only a suggestion).A1: We have moved Table 3 and Table 4 to the SI as you have suggested. ______________________________________________________________________________C1: This should be part of the Method section, e.g., on line 216, in the parenthesis \"A1: Thank for noticing this mistake. Yes, the colors on the figure legend should be reversed. in Figure 5. We have fixed this accordingly. Now the numbers and percentages add up correctly. ______________________________________________________________________________C1: Again, I have problem with the values in the text and in Table 5. Crayfish 4 is the only one that foraged during the day. From Table 5, this happened only once, with a total of 360s, which is clearly not equal to 0.34 hr. Please explain.A1: After checking back at our data, you are correct, we mistakenly calculated a larger percentage for the daytime activity of Crayfish 4. This change is now reflected in the manuscript and in the Figure 7, and Table 5. We re-checked the other crayfish as well and the results are correct for them. ______________________________________________________________________________C1: Same remark as for Tables 3 and 4. The results are different but redundant with Fig. 7.A1: We have moved this Table (Table 5) to the SI as you have suggested. ______________________________________________________________________________C1: But Fig. 7 shows the opposite pattern! Table 5 support this.A1: Thank you for catching this error. This was a typo and now correctly states that \u201cThe majority of their time was spent in the relax position during the night, and relaxing was more likely to occur during the night compared to during the day.\u201d______________________________________________________________________________C1: I think that \"proportion\" is more adequate here.A1: We have reworded this to proportion based on your suggestion. ______________________________________________________________________________C1: Again, I would place this Table in the SI, as the main information can be visualized in Fig. 8.A1: We have moved this table to the SI based on your suggestions. ______________________________________________________________________________C1: This relates to my question concerning Fig. 3 (line 183). Does reference 51 separates these two behaviors based on claws' position?A1: See A6. ______________________________________________________________________________C1: At this point, I am uncomfortable with your choice of words (relax and guard) for the two behaviors based on position of claws. Perhaps \"guard - claws open\" and \"guard - claws joined\" may be more appropriate?A1: See A6.______________________________________________________________________________Attachmentresponse_to_reviewers_2.docxSubmitted filename: Click here for additional data file. 11 Aug 2022On the surface or down below: Field observations reveal a high degree of surface activity in a burrowing crayfish, the Little Brown Mudbug (Lacunicambarus thomai)PONE-D-21-39709R2Dear Dr. Diehl,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Louis-Felix Bersier, Ph.D.Academic EditorPLOS ONEAdditional Editor Comments :Thank you for your thorough consideration of my comments. I went through your corrected version and found that it is ready for publication. I just noted a probable mistake on lines 243-244: \"\" rather than \"\". Please check this before submitting your final document.Reviewers' comments: 2 Sep 2022PONE-D-21-39709R2 Lacunicambarus thomai) On the surface or down below: Field observations reveal a high degree of surface activity in a burrowing crayfish, the Little Brown Mudbug (Dear Dr. Diehl:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofProf Louis-Felix Bersier Academic EditorPLOS ONE"} +{"text": "Extractive document summarization (EDS) is usually seen as a sequence labeling task, which extracts sentences from a document one by one to form a summary. However, extracting sentences separately ignores the relationship between the sentences and documents. One solution is to use sentence position information to enhance sentence representation, but this will cause the sentence-leading bias problem, especially in news datasets. In this paper, we propose a novel sentence centrality for the EDS task to address these two problems. The sentence centrality is based on directed graphs, while reflecting the sentence-document relationship, it also reflects the sentence position information in the document. We implicitly strengthen the relevance of sentences and documents by using sentence centrality to enhance sentence representation. Notably, we replaced the sentence position information with sentence centrality to reduce sentence-leading bias without causing model performance degradation. Experiments on the CNN/Daily Mail dataset showed that EDS models with sentence centrality significantly improved compared with baseline models. Automatic document summarization aims to produce a concise summary of a document while preserving its crucial information. Existing summarization methods can be divided into two categories: abstractive and extractive methods. Abstractive methods generate a summary word by word from scratch, and can introduce new words that do not appear in the document . ExtractIn recent years, extractive document summarization (EDS) based on neural networks has achieved great success \u20136. HowevThere is much excellent work based on the first approach. For example, Zhang et al. proposedThe sentence centrality is usually based on undirected graphs and is widely used in unsupervised extractive summarization tasks to identify salient sentences in a document , 14. In Previous work considered sentence centrality as a signal to measure the importance of sentences \u201315. DiffFollowing our intuition mentioned before, we can learn that the sentence centrality is no longer restricted in unsupervised extractive methods. We develop two methods to apply sentence centrality to enhance sentences representation: (1) embedding the sentence centrality directly into the sentence representation output by the encoder; (2) updating the sentence representation indirectly via Graph Attention Network (GAT) . We builThe contributions of our work are as follows:We propose a novel sentence centrality for EDS task and two approaches to use sentence centrality to enhance sentence representation. With the help of the sentence centrality, the relationship between sentences and documents is implicitly strengthened, thus improving the performance of the extractive summarization.We propose to replace sentence position information with sentence centrality, which can reduce the sentence-leading bias in the news dataset caused by position information.The remainder of this article is arranged as follows. We introduce some related topics on the EDS in the section Related Work. In the Method section, we define the EDS and then introduce our sentence centrality-enhanced extractive summarization models. We present the training details, parameter settings and experimental results in the Experiment section. In the Discussion section, we discuss why sentence centrality works. Finally, we conclude our paper in the Conclusion section.To make the paper self-contained, we will introduce some related topics on the EDS and the sentence centrality-based summarization methods.The EDS task aims to extract sentences from the original document to form a summary. The task first encodes the sentences with the help of an encoder to obtain a sentence vector. The sentence vector is then passed through a classification layer to determine whether it should be included in the summary. Nallapati et al ; Zhou etAlthough these methods are effective, they mostly rely on sentence position information to enhance sentence representation. We introduce sentence centrality information in the model and remove sentence position information, which improves model performance and does not cause sentence-leading bias.The sentence centrality is often used to measure the importance of a sentence in unsupervised EDS tasks. In the task, a document is represented as a graph, with nodes representing sentences and edges connecting sentences weighted according to their similarity. TextRank calculatThere are three key differences in our sentence centrality compared to the previous methods. (1) We calculate the centrality of a sentence by counting only the similarity between that sentence and the content that follows it, not the similarity of all other content. (2) The centrality of a sentence is considered a unique property of the associated sentence and document rather than just as a measure of the importance of the sentence. Therefore, we use sentence centrality to strengthen the sentence representation. (3) We applied sentence centrality into the supervised EDS.An essential step in the extractive document summarization task is to obtain sentence embeddings. Traditional sentence embedding methods are based on weighting and averaging words vectors to construct sentences\u2019 vectors. Kedzie et al. averagedTraditional sentence embedding methods are simple and effective. However, extractive document summarization is a document-level task, and the relationship between sentences and documents needs to be considered when obtaining sentence embeddings. Most works , 20, 21 Different from their work, we use sentence center information to enhance sentence representations. Compared to using sentence position information, our methods are able to achieve performance improvements while reducing the sentence lead bias problem.d that contains n sentences, d = {s1, s2, \u2026, sn}, where si = {wi1, wi2, \u2026, wim} is the i-th sentence in the document and wij is the j-th word in the i-th sentence. EDS can be seen as a sequence labeling task 2] to enhHeterogeneous summarization graph (HSG) is an exeij, which are mapped to the multi-dimensional embedding space. The weights of the edge eij are the sum of the sentence centrality and the TF-IDF value of the words, because the types of nodes connected by the edge are different. The modified GAT layer is designed as follows:hi is the hidden state of input node, \u03b1ij refers to the weight of attention between hi and hj. The residual connection is used to avoid gradient vanishing after several iterations. The final sentence representation is:Our modified HSG model is presented in G with word features Xw and sentence node features Xs, the sentence nodes are updated with their neighbor word nodes via the above GAT and feed-forward (FFN) layer:Given a constructed graph We conduct our experiment on the CNN/Daily Mail, XsCNN/Daily Mail is a well-known news dataset for single document extractive summarization, which is split into three parts by Hermann et al. for traiXSum is a one-sentence summary dataset to answer the question \u201cWhat is the article about?\u201d. We conduct experiments on this dataset to study whether sentence centrality-enhanced EDS models are still effective when dealing with dataset with short summaries.We only use the XSum dataset for ablation experiments, as the extraction results on this dataset are few and are insufficient to support our model performance comparison.We limit the sentence length to 50 words calculating sentence centrality. Both models are trained on a single GPU (GeForce RTX 3080).https://github.com/huggingface/pytorch-pretrained-BERT. The model is trained for 40000 steps. The best result on the validation set occurs at step 37000. Adam algorithm is applied for optimizing the loss function. Learning rate schedule is following Vaswani et al. Reviewers' comments:Reviewer's Responses to Questions Comments to the Author1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Partly********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0N/AReviewer #2:\u00a0Yes********** 3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0The manuscript \u201cImproving Extractive Document Summarization with Sentence Centrality\u201d highlights a way to enhance sentence representation for extractive document summarization which in turns boost performance of existing EDS techniques. The paper is well written and contributions are clearly laid out and explained, used methodology is sound. Still some issues are cracking through. The following is a list of items which should be addressed:1. In the introduction, the manuscript references findings of Zheng and Lapata that \u201csimilarity with the previous content will damage centrality\u201d. In the method proposed here, forward edges are removed and only backward edges are considered, but this seems confusing. Why is this the right approach if this tends to damage centrality score?2. Acronym EDS in line 10 is not defined \u2013 please add full text of the meaning.3. The structure of the paper is missing at the end of Introduction.4. While being sufficient example of a graph, figure 1 does not convey idea of degree centrality in a meaningful way. Maybe node size or colour should be varied based on centrality score to reinforce the idea that some sentences are more important than the other.5. In the approach involving heterogeneous graph neural network, edge features were extended with sentence centrality. If sentence centrality is a node characteristic, why is it used to enhance edge features?6. In the equation 6, indices in LHS appear to be duplicated. Equation 7 contains similar problem. Although it may be obvious to knowledgeable reader, terms of the equation 11 should still be defined for rigour, and it should be done for all other equations as well. For example, in equation (1) hi and hi+ are not defined.7. It is not quite clear how is centrality embedding (EmbSCi) is obtained. Specifically, what are the terms on the RHS of the equation 9? If SCi is centrality of sentence i, what is the meaning of the exponents 1 to emb? Furthermore, equation 9 defines EmbSCi as a set of terms SCi, but this seems unusual w.r.t embeddings usually being vectors.8. Please define HSG in line 168.9. Please add short explanation of Trigram Blocking.10. How does table 3 relate to table 1 and table 2? Are these various configurations of input data to SCBERT and SCHSG models from previous tables? If it is indeed so, please make sure it is more clear from the text to prevent any misunderstandings.11. Please cite everything which is not original work presented in the paper, e.g. ROUGE, bert-base-uncased model, and some other instances.12. Please in the appendix define used ROUGE scores.13. \u201cAnalysis\u201d section contains reference to \u201cORACLE summary\u201d, please elaborate some more on what the ORACLE is, how does it work, and cite the relevant paper.14. Consider renaming Analysis Chapter into Discussion and expand it.15. Axes on figure 3 should be appropriately labelled to make the figure stands on it\u2019s own.16. It would be useful to know how the proposed model performs with other similar node-local measures such as selectivity measure. It might be useful as a basis for future work.17. Introduction contains abbreviation \u201cEDT\u201d which is never elaborated or mentioned again. This seems like a very minor typographical error, and presumably was meant to say \"EDS\". In the same vein, \u201cAblation Study\u201d section contains sentence \u201cThe results show that the experimental performance on ROUGE-L, ROUGE-2, ROUGE-L\u201d. Is the first ROUGE-L in line 244 ROUGE-1?18. On several places there is a blank after comma missing.Reviewer #2:\u00a0### Overview and general recommendationThe paper addresses the problem of extractive document summarization. It uses sentence centrality information to enhance sentence representation. This information should reflect the sentence-document relationship and the sentence position information as well. The sentence representation is enhanced in two ways: one is embedded directly into the sentence representation output and the other updates the sentence representation indirectly via a graph attention network.Because of advances in abstractive summarization, the task of extractive document summarization is probably no longer very challenging or interesting for the research field. The paper provides a good method for comparing the impact of sentence position vs. sentence centrality. However, one of the conclusions is not well supported by the experimental results, but overall, this is a very well-written paper with sound methodology, ablations studies, and a well-formulated research question.### Major comments- According to Table 3, the results of different sentence information don't support the conclusion that sentence centrality is a better choice than sentence position. Given that ROUGE is a poor metric, the difference of approximately 0.1 is insignificant.- More ideas for future research could be added to the conclusion.- The related research section could be expanded as well, e.g., adding a section on sentence embeddings, since the paper works on that level of representation.- Some typos should be fixed, and some sentences could be rewritten to make them more clear; Take a look at minor remarks- There is no link to the code repository.### Minor comments- Typo in the caption of Fig. 1, \u201cdocumentt\u201d- Line 176: \u201cusing\u201d \u2192 \u201cuse\u201d- Table 3: \u201csummarizers\u201d \u2192 \u201csummarizer\u201d- Fig. 2: the first sentence should be corrected- Line 244: the first \u201cROUGE-L\u201d should be \u201cROUGE-1\u201d********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1:\u00a0NoReviewer #2:\u00a0Nohttps://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,\u00a0 18 Apr 2022We greatly appreciate the reviewers taking the time to provide constructive comments and helpful suggestions. There is no doubt that the suggestions have significantly raised the quality if the manuscript and have enable us to improve the manuscript. Each suggested revision and comment brought forward by the reviewers was accurately incorporated and considered. We have carefully addressed all the reviewer's concerns. Please see our replies. Changes highlighted in red have been made accordingly in the revised manuscript.Comments to the Author________________________________________1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: PartlyResponse: Thanks for your review. We added experiments to verify the effectiveness of our method. We conducted experiments on XSum dataset. The results demonstrate the superiority of sentence centrality compared to positional information.________________________________________2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes Response: Thank you for agreeing that our analysis is appropriate and rigorous.________________________________________3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. Reviewer #1: Yes Reviewer #2: Yes Response: Thank you for your approval of our data.________________________________________4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: YesResponse: Thank you for your approval.________________________________________Review Comments to the Author________________________________________Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1: The manuscript \u201cImproving Extractive Document Summarization with Sentence Centrality\u201d highlights a way to enhance sentence representation for extractive document summarization which in turns boost performance of existing EDS techniques. The paper is well written and contributions are clearly laid out and explained, used methodology is sound. Still some issues are cracking through. The following is a list of items which should be addressed: 1. In the introduction, the manuscript references findings of Zheng and Lapata that \u201csimilarity with the previous content will damage centrality\u201d. In the method proposed here, forward edges are removed and only backward edges are considered, but this seems confusing. Why is this the right approach if this tends to damage centrality score?Response: We appreciate the reviewer for asking questions about the details of sentence centrality. According to the original paper of Zheng and Lapata, the centrality score of s_i based on the directed graph can be defined as follows:centrality(s_i )=\u03bb_1 \u2211_(ji)e_ij ,where the optimal \u03bb_1 tends to be negative.In our paper, we do not calculate the similarity between the sentence and its previous content of the sentence, which means that we set the weights of forward-looking directed edges \u03bb_1 are equal to 0. We think the descriptions of \u201cforward-looking\u201d and \u201cforward\u201d make our point unclear, so we revised this part of content to convey our idea clearly, in lines 43-45. The description of \u201cInspired by their work, we remove the forward edges of sentences on directed graphs and calculate the sentence centrality based only on the weights of backward edges\u201d is modified by us to \u201cInspired by their work, we calculate the centrality score of a sentence based only on the similarity between the sentence and its following content\u201d.________________________________________2. Acronym EDS in line 10 is not defined \u2013 please add full text of the meaning.Response: We appreciate the reviewer for his/her careful review. We have added the full text of the meaning of EDS in line 10.________________________________________3. The structure of the paper is missing at the end of Introduction.Response: We thank the reviewer for reminding us to describe the structure of our paper, and there is no doubt that this suggestion makes the paper more readable. We have added a description of the paper structure in lines 76-81.________________________________________4. While being sufficient example of a graph, figure 1 does not convey idea of degree centrality in a meaningful way. Maybe node size or colour should be varied based on centrality score to reinforce the idea that some sentences are more important than the other.Response: We thank the reviewer for the helpful suggestions on our figure 1. We now updated the figure 1. we used different colors to indicate different sentences, and used the size of the nodes to indicate the centrality scores. We also increased the number of sentence nodes in order to convey idea our ideas more clearly. ________________________________________5. In the approach involving heterogeneous graph neural network, edge features were extended with sentence centrality. If sentence centrality is a node characteristic, why is it used to enhance edge features?Response: We are grateful to the reviewer for questions about our method. We use sentence centrality to enhance edge features is to modify the graph attention (GAT) layer. In the heterogeneous graph neural network, the sentence representations are updated with their neighbor word nodes via a GAT layer and feed-forward (FFN) layer. The GAT layer is modified by infusing the scalar edge weights e_ij (described in equation 13), which are mapped to the multi-dimensional embedding space. The weights of the edge e_ij are the sum of the sentence centrality and the TF-IDF value of the words, because the types of nodes connected by the edge are different.We added equations and a textual explanation to describe how sentence representations are updated by GAT and FFN in equation 17, equation 18 and lines 228-236. We also do a textual explanation of why we use sentence centrality to enhance edge features in lines 216-221.________________________________________6. In the equation 6, indices in LHS appear to be duplicated. Equation 7 contains similar problem. Although it may be obvious to knowledgeable reader, terms of the equation 11 should still be defined for rigour, and it should be done for all other equations as well. For example, in equation (1) hi and hi+ are not defined.Response: We appreciate the reviewer for his/her careful review and we feel sorry for our lack of rigour. We have corrected equation 6 and equation 7. For terms in the equations that are not strictly defined, we have carefully checked.For equation 1, we defined h_i and h_i^+, and explained the meaning of sim in lines 150-152.For equation 6, we explained the meaning of the term u_ij in line 184.For equation 9 and equation 10, we modified these two equations to make the meaning of \u3016EmbSC\u3017_i clearer. We defined each term in lines 187-192.For equation 11, we define each term of the equation and explain the meaning in lines198-200. ________________________________________7. It is not quite clear how is centrality embedding (EmbSCi) is obtained. Specifically, what are the terms on the RHS of the equation 9? If SCi is centrality of sentence i, what is the meaning of the exponents 1 to emb? Furthermore, equation 9 defines EmbSCi as a set of terms SCi, but this seems unusual w.r.t embeddings usually being vectors.Response: We appreciate the reviewer for his/her careful review. Our definition of equation 9 is not rigorous, leaving our point unclear. We feel sorry for this. We modified the equation 9. Now the equation 9 is:EmbSC_i=W_sc (SC_i ) ,where W_sc is a weight matrix with the weights set to 1. EmbSC_i is the centrality embedding of sentence s_i, which has the same dimension as the sentence embedding.EmbSC_i is obtained by mapping the normalized scalar sentence centrality to the multi-dimensional embedding space. The RHS of the new equation 9 W_sc (SC_i ) means that (SC_i ) is mapped to a higher dimensional space by W_sc. The RHS of our previous equation 9 was trying to convey the same meaning as the new equation 9, but we are sorry that we did not make it clearer. The exponents 1 to emb means that we map sentence centrality to the emb-dimensional space in the previous equation 9. ________________________________________8. Please define HSG in line 168.Response: We thank the reviewer for reminding us to define HSG. We add full text of the meaning HSG in lines 202-204, and give our sentence centrality-enhanced extractive document summarization model based on HSG in Fig.3.________________________________________9. Please add short explanation of Trigram Blocking.Response: We thank the reviewer for reminding us to add short explanation of Trigram Blocking. We added the short explanation of Trigram Blocking in lines 270-273. ________________________________________10. How does table 3 relate to table 1 and table 2? Are these various configurations of input data to SCBERT and SCHSG models from previous tables? If it is indeed so, please make sure it is clearer from the text to prevent any misunderstandings.Response: We thank the reviewer for his/her careful review. All the models in Table 3 are based on the pre-trained language model BERT, where the SCES model is exactly our SCBERT in Table 1. The various configurations of experimental parameters for the SCES model are the same as for the SCBERT model, except that the datasets used are different. We added the relevant description in lines 324-327.________________________________________11. Please cite everything which is not original work presented in the paper, e.g. ROUGE, bert-base-uncased model, and some other instances.Response: We thank the reviewer for his/her careful review. We checked our paper carefully and added citations to the work that needed to be cited.Line 17, we added a reference to transformer.Line 213, we added a reference to Convolutional Neural Network. Line 216, we added a reference to Bidirectional Long and Short-Term Memory.Line 239, we added references to CNN/Daily Mail and XSum datasets.Line 297, we added references to ROUGE.https://github.com/huggingface/pytorch-pretrained-BERT, we put the URL in lines 256-257.\u201cbert-base-uncased model\u201d is published in ________________________________________12. Please in the appendix define used ROUGE scores.Response: We thank the reviewer for reminding us to add the definition of ROUGE scores. We defined the used ROUGE scores in S1 Appendix.________________________________________13. \u201cAnalysis\u201d section contains reference to \u201cORACLE summary\u201d, please elaborate some more on what the ORACLE is, how does it work, and cite the relevant paper.Response: We thank the reviewer for his/her rigorous review. We elaborated the ORACLE summary in lines 353-359, including that what the ORACLE is, how does it work. We also cite the relevant paper.s________________________________________14. Consider renaming Analysis Chapter into Discussion and expand it.Response: We thank the reviewers for the suggestions on the structure of our article.We have renamed Analysis Chapter into Discussion. In this part, we added the content of ORACLE according to your comment 13. We discuss why sentence centrality is a better choice than sentence position information.________________________________________15. Axes on figure 3 should be appropriately labelled to make the figure stands on it\u2019s own.Response: We thank the reviewer for his/her careful review. Since we added a heterogeneous graph model graph, the original figure 3 is now figure 4. The axes on figure 4 are now appropriately labeled.________________________________________16. It would be useful to know how the proposed model performs with other similar node-local measures such as selectivity measure. It might be useful as a basis for future work.Response: We thank the reviewer for his/her constructive suggestion. This suggestion makes us realize that our exploration of sentence centrality needs to go further. We have written this suggestion into future work. Thanks again for the constructive suggestion.________________________________________17. Introduction contains abbreviation \u201cEDT\u201d which is never elaborated or mentioned again. This seems like a very minor typographical error, and presumably was meant to say \"EDS\". In the same vein, \u201cAblation Study\u201d section contains sentence \u201cThe results show that the experimental performance on ROUGE-L, ROUGE-2, ROUGE-L\u201d. Is the first ROUGE-L in line 244 ROUGE-1?Response: We appreciate the reviewer for his/her careful review. \u201cEDT\u201d is a typographical error; we have corrected it in line 41. The first \u201cROUGE-L\u201d is corrected to \u201cROUGE-1\u201d in line 306.________________________________________18. On several places there is a blank after comma missing.Response: We appreciate the reviewer for his/her careful review. We checked our paper carefully and added a blank for commas.We again thank the reviewer for taking the time to review our article. From the review comments, we can feel the rigorous attitude of the reviewers to academics. There is no doubt that the comments of the reviewers make our manuscript more rigorous and clearer. ________________________________________Reviewer #2: ### Overview and general recommendation The paper addresses the problem of extractive document summarization. It uses sentence centrality information to enhance sentence representation. This information should reflect the sentence-document relationship and the sentence position information as well. The sentence representation is enhanced in two ways: one is embedded directly into the sentence representation output and the other updates the sentence representation indirectly via a graph attention network. Because of advances in abstractive summarization, the task of extractive document summarization is probably no longer very challenging or interesting for the research field. The paper provides a good method for comparing the impact of sentence position vs. sentence centrality. However, one of the conclusions is not well supported by the experimental results, but overall, this is a very well-written paper with sound methodology, ablations studies, and a well-formulated research question. ### Major comments - According to Table 3, the results of different sentence information don't support the conclusion that sentence centrality is a better choice than sentence position. Given that ROUGE is a poor metric, the difference of approximately 0.1 is insignificant.Response: We thank the reviewer for pointing out potential limitation in our study. We agree with the reviewer that the superiority of sentence centrality cannot be demonstrated only from the ROUGE scores.In the extractive summarization task, position information is usually used to enhance sentence representation. Although doing so will improve model extraction performance significantly, it will cause sentence-leading bias, especially in news datasets. We present this phenomenon in lines 23-30.we replaced the sentence position information with sentence centrality to reduce sentence-leading bias without causing model performance degradation, which can be seen in the figure 5 and table 3. We added experiments in the news dataset XSum. The experimental results show that the replacement of sentence position information by sentence centrality will not cause model performance degradation.Before reaching the conclusion \"sentence centrality is a better choice than sentence position\", we added a description of the advantages of sentence centrality in reducing sentence leading bias, discussed in the Discussion section.Combining the advantages of sentence centrality in reducing sentence leading bias and experimental results in table 3, we can conclude that sentence centrality information has certain advantages over sentence position information the extractive summarization task.We are grateful to the reviewer for his/her constructive comments, which made our logic more rigorous and greatly improved the quality of our paper. ________________________________________- More ideas for future research could be added to the conclusion.Response: We thank the reviewer for reminding us to expand our future work. We add more ideas in future research, including exploring whether sentence centrality is also effective in other tasks, etc., which are presented in lines 374-381. ________________________________________- The related research section could be expanded as well, e.g., adding a section on sentence embeddings, since the paper works on that level of representation. Response: We thank the reviewer for his/her constructive suggestion. Adding a section on sentence embeddings will make our article more rigorous. We have expanded our related work in lines 113-131.________________________________________- Some typos should be fixed, and some sentences could be rewritten to make them. Take a look at minor remarksResponse: We thank the reviewer for his/her careful review. We have carefully checked our article and corrected errors. We present the modification details in the ### Minor comments section.________________________________________- There is no link to the code repository.Response: We are pleased that the reviewer is interested in our work.https://github.com/GongShuai8210/SCES.The code is released at ________________________________________### Minor comments - Typo in the caption of Fig. 1, \u201cdocumentt\u201d - Line 176: \u201cusing\u201d \u2192 \u201cuse\u201d - Table 3: \u201csummarizers\u201d \u2192 \u201csummarizer\u201d - Fig. 2: the first sentence should be corrected - Line 244: the first \u201cROUGE-L\u201d should be \u201cROUGE-1\u201dResponse: We thank the reviewer for taking the time to review our article carefully. We have corrected the typo now.-Typo in the caption of Fig. 1, \u201cdocumentt\u201d \u2192 \u201cdocument\u201d- Line 213: \u201cusing\u201d has been corrected to \u201cuse\u201d - Table 3: \u201csummarizers\u201d has been corrected to \u201csummarizer\u201d - Fig. 2: the first sentence has been corrected to \u201cEmbSC_i is the centrality embedding of sentence s_i, which is directly embedded in the sentence representation generated by BERT\u201d. - Line 306: the first \u201cROUGE-L\u201d has been corrected to \u201cROUGE-1\u201d.We again thank the reviewer for his/her careful review and constructive suggestions. There is no doubt that the reviewer's suggestions improve the quality of our article.AttachmentResponse to Reviewers.pdfSubmitted filename: Click here for additional data file. 27 Apr 2022Improving Extractive Document Summarization with Sentence CentralityPONE-D-22-05139R1Dear Dr. Gong,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Sanda Martin\u010di\u0107-Ip\u0161i\u0107, PhDAcademic EditorPLOS ONEAdditional Editor Comments :I have reviewed the revised manuscript, responses to reviewer comments, and availability of data and SW. The authors have addressed all reviewer comments and improved the quality of the manuscript. I am pleased to report that the current manuscript revision adequately addresses all issues and meets the required PlosOnNE criteria.Reviewers' comments: 14 Jul 2022PONE-D-22-05139R1 Improving Extractive Document Summarization with Sentence Centrality Dear Dr. Zhu:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Sanda Martin\u010di\u0107-Ip\u0161i\u0107 Academic EditorPLOS ONE"} +{"text": "We report the coding-complete genome sequences of 25 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineage B.1.1.529 Omicron strains obtained from Bangladeshi individuals in samples collected between December 2021 and January 2022. Genomic data were generated by Nanopore sequencing using the amplicon sequencing approach developed by the ARTIC Network. Coronaviridae, genus Betacoronavirus) is a positive-sense single-stranded RNA virus (Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (family NA virus . The mosNA virus .As part of the ongoing SARS-CoV-2 genomic surveillance (protocol IEDCR/IRB/2020/11) by the Institute of Epidemiology, Disease Control, and Research (IEDCR), Bangladesh, two specimens were obtained from individuals who had recently visited Africa and had reported coronavirus disease 2019 (COVID-19) symptoms on return to Bangladesh. These specimens were found to be positive for the SARS-CoV-2 nucleocapsid (N) gene but negative for the S gene by TaqPath COVID-19 Combo reverse transcription (RT)-PCR . Seventeen more SARS-CoV-2-positive specimens from the countrywide SARS-CoV-2 surveillance showed similar results. These specimens were further screened with the TaqMan SARS-CoV-2 mutation panel (Applied Biosystems), which indicated the presence of S:N501Y, one of the signature mutations of the SARS-CoV-2 Omicron variant. This S:N501Y mutation is not present in the S gene of the Delta variant, which was the predominant strain circulating in Bangladesh in the last few months of 2021. Overall, a total of 25 specimens were used as input for genome sequencing using the Oxford Nanopore Technologies sequencing platform. The detailed information for all 25 individuals is presented in https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html). In total, 4,324,431 reads were obtained . Compared to the reference Wuhan Hu-1 genome (GenBank accession number NC_045512.2), the signature amino acid alterations in the spike protein matching the genetic markers of sublineages B1.1.529.1 and B1.1.529.2 were identified. Among the 25 sequences, Pangolin (github.com/cov-lineages/pangolin) assigned 19 sequences to lineage B.1.1.529.1 (BA.1), and six strains were found to be lineage B.1.1.529.2 (BA.2) . Sequencing libraries were prepared using the multiplex PCR amplicon sequencing approach developed by the ARTIC Network , 5. Libr2 (BA.2) . These sThe data from this study can be found under GISAID accession numbers EPI_ISL_7404462, EPI_ISL_7404463, EPI_ISL_8146774, EPI_ISL_8414987, EPI_ISL_8146772, EPI_ISL_8146773, EPI_ISL_8414988, EPI_ISL_8096971, EPI_ISL_8414989, EPI_ISL_8414990, EPI_ISL_8215676, EPI_ISL_8215677, EPI_ISL_8415001, EPI_ISL_8215678, EPI_ISL_8414993, EPI_ISL_8415003, EPI_ISL_8415004, EPI_ISL_8414994, EPI_ISL_8414995, EPI_ISL_9456595, EPI_ISL_9456604, EPI_ISL_9456606, EPI_ISL_9456607, EPI_ISL_9456620, and EPI_ISL_9456621. The Sequence Read Archive (SRA) and GenBank accession numbers are listed in"} +{"text": "Background: To elucidate the potential biological function of hsa_circ_0062270 in the malignant process of melanoma and its potential target.Methods: Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to examine relative level of hsa_circ_0062270 in melanoma tissues and normal skin tissues. The diagnostic and prognostic potentials of hsa_circ_0062270 in melanoma were evaluated. The regulatory effect of hsa_circ_0062270 on the expression of linear transcript Cell division cycle protein 45 (CDC45) was also examined.Results: Hsa_circ_0062270 was up-regulated in melanoma samples and cell lines, which displayed certain diagnostic and prognostic potentials in melanoma. Inhibition of hsa_circ_0062270 attenuated the proliferative, migratory and invasive functions. Hsa_circ_0062270 could stabilize the expression of linear transcript CDC45, and thus participated in the malignant process of melanoma.Conclusion: Hsa_circ_0062270 promotes proliferative, migratory and invasive functions of melanoma cells via stabilizing the linear transcript CDC45. Hsa_circ_0062270 can be used to diagnosis and treatment of melanoma. Melanoma is a highly malignant skin cancer derived from melanocytes. Melanoma accounts for more than 70% of skin cancer deaths . More seCircRNAs are novel noncoding RNAs to be widely analyzed. They are extensively involved in various fields of life sciences . Since cHsa_circ_0062270 is located on chromosome 22: 19496052-19502571, and its gene symbol is CDC45. Evidence has showed that hsa_circ_0062270 is obviously up-regulated in melanoma . A previThe normal skin tissues and melanoma tissues of 50 patients with melanoma in our hospital were selected. The ethics committee of The First People\u2019s Hospital of Lianyungang approved our study. Signed written informed consents were obtained from all participants before the study.2, 37\u00b0C. Cell transfection was performed using Lipofectamine 3,000 as per the protocols. Cell proliferation was determined by EdU .Melanoma cells and normal human epidermal melanocytes (NHEM) were provided by Cell Bank of Type Culture Collection . Cells were cultivated in DMEM containing 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100\u00a0\u03bcg/ml streptomycin at 5% CO\u2212\u0394\u0394Ct. Primers used were shown below: hsa_circ_0062270: Forward: 5\u2032-AGG\u200bATG\u200bGCT\u200bCAG\u200bGGA\u200bCAG\u200bAT-3\u2032, reverse: 5\u2032-AGG\u200bCCA\u200bTGG\u200bTAC\u200bAGC\u200bTTG\u200bTC-3\u2032; CDC45: Forward: 5\u2032-TTC\u200bGTG\u200bTCC\u200bGAT\u200bTTC\u200bCGC\u200bAAA-3\u2032, reverse: 5\u2032-TGG\u200bAAC\u200bCAG\u200bCGT\u200bATA\u200bTTG\u200bCAC-3\u2032; GAPDH: Forward: 5\u2032-CGG\u200bAGT\u200bCAA\u200bCGG\u200bATT\u200bTGG\u200bTCG\u200bTAT-3\u2032, reverse: 5\u2032-AGC\u200bCTT\u200bCTC\u200bCAT\u200bGGT\u200bGGT\u200bGAA\u200bGAC-3\u2032: U6: Forward: 5\u2032-GCT\u200bGAG\u200bGTG\u200bACG\u200bGTC\u200bTCA\u200bAA-3\u2032, reverse: 5\u2032-GCC\u200bTCC\u200bCAG\u200bTTT\u200bCAT\u200bGGA\u200bCA-3\u2032.RNAs isolation was done with TRIzol and were then reversely transcribed into cDNAs. U6 and GAPDH were used as the internal controls with the method of 2A375 cells were exposed to Actinomycin D (3\u00a0\u03bcg/ml). They were collected for isolating total RNAs. Expressions of hsa_circ_0062270 and CDC45 were detected by Quantitative real-time polymerase chain reaction. Cellular RNA (4\u00a0mg) was treated either with RNase R (10\u00a0U/\u03bcg) at 37\u00b0C for 30\u00a0min or not, followed by purification using RNeasy MinElute .Cells were seeded into the top chamber and bottom chamber. After 48-h incubation, cells in the bottom were fixed, dyed in crystal violet and captured. Migratory cells were counted in five randomly selected fields per sample. Invasion assay was conducted using transwell chamber precoated with 100\u00a0\u03bcL of Matrigel . In detail, Matrigel was diluted in serum-free medium at 1:3, which was coated on the top of a chamber.p < 0.05.Data were expressed as mean \u00b1 SD (standard deviation) and they were processed using Statistical Product and Service Solutions (SPSS) 20.0 . Prognostic value of hsa_circ_0062270 in melanoma were evaluated by Kaplan-Meier and receiver operating characteristic (ROC) method, respectively. The correlation between hsa_circ_0062270 and CDC45 levels was assessed through Pearson correlation test. A significant difference was set at p = 0.0234) . Hsa_cir 0.0234) . We furt 0.0234) . RNase R 0.0234) . TherefoTo investigate the effects of hsa_circ_0062270 on melanoma cell proliferation, migration and invasion, cells were treated with hsa_circ_0062270 siRNA. Results indicated that transfection of hsa_circ_0062270 siRNA markedly down-regulated hsa_circ_0062270 level in A375 and A2058 cells . Knockdovia mediating expression levels of their linear transcripts. CDC45 was the linear transcript of hsa_circ_0062270 (Then we focused on the potential target of hsa_circ_0062270 in the regulation of phenotypes of melanoma. CircRNAs are involved in pathological process _0062270 and posi_0062270 . Identic_0062270 . Knockdo_0062270 . It is cTo further elucidate the effects of CDC45 on melanoma phenotypes, we established the overexpression models of CDC45. Transfection of overexpressed plasmid of CDC45 effectively up-regulated CDC45 in A375 and A2058 cells . In melaTo uncover the co-regulation of hsa_circ_0062270 and CDC45, cells were co-transfected using si-CDC45 and overexpressed plasmid of hsa_circ_0062270 . OverexpThe incidence of melanoma is not high, covering 4\u20135% of malignant tumors. Family history, multiple atypical moles and dysplastic moles are risk factors that trigger the carcinogenesis of melanoma . In addiCircRNAs, as a type of emerging noncoding RNAs, have been well concerned because of their unique structure and vital functions . They caIn vitro experiment results illustrated that knockdown of hsa_circ_0062270 remarkably suppressed proliferative, migratory and invasive functions of melanoma cells.We previously found that the expression of hsa_circ_0062270 in melanoma was up-regulated. The diagnostic and prognostic potentials of hsa_circ_0062270 in melanoma were verified through depicting ROC and Kaplan-Meier curves, respectively. Recent studies have demonstrated that circRNAs have an important role in disease progression by mediating expressions of their linear transcripts . Throughin vivo role of hsa_circ_0062270 in melanoma is not explored. Secondly, how hsa_circ_0062270 regulates CDC45 remains unclear. Thirdly, other cell phenotypes of melanoma, including apoptosis, epithelial-mesenchymal transition and cell cycle progression affected by hsa_circ_0062270 are not clear.Collectively, our present study was the first attempt to reveal that hsa_circ_0062270 was up-regulated in melanoma specimens and correlated to its prognosis. Hsa_circ_0062270 stimulated malignant process of melanoma by stabilizing its linear transcript CDC45. Our findings provide a new aspect for developing diagnostic and therapeutic strategies for melanoma. Several limitations of our study should be pointed out. First of all, via stabilizing the linear transcript CDC45. These findings provided strong evidence that hsa_circ_0062270 could be a novel promising therapeutic target used to diagnosis and treatment of melanoma.Hsa_circ_0062270 promotes proliferative, migrative and invasive functions in melanoma cells"} +{"text": "Structural annotation of genetic variants in the context of intermolecular interactions and protein stability can shed light onto mechanisms of disease-related phenotypes. Three-dimensional structures of related proteins in complexes with other proteins, nucleic acids, or ligands enrich such functional interpretation, since intermolecular interactions are well conserved in evolution.We present d-StructMAn, a novel computational method that enables structural annotation of local genetic variants, such as single-nucleotide variants and in-frame indels, and implements it in a highly efficient and user-friendly tool provided as a Docker container. Using d-StructMAn, we annotated several very large sets of human genetic variants, including all variants from ClinVar and all amino acid positions in the human proteome. We were able to provide annotation for more than 46% of positions in the human proteome representing over 60% proteins.d-StructMAn is the first of its kind and a highly efficient tool for structural annotation of protein-coding genetic variation in the context of observed and potential intermolecular interactions. d-StructMAn is readily applicable to proteome-scale datasets and can be an instrumental building machine-learning tool for predicting genotype-to-phenotype relationships. Key PointsA novel bioinformatics tool for structural characterization of genetic variants is presented.Single-nucleotide variants and indels are described with respect to intermolecular interactions in homologous protein complexes.An efficient implementation using a Docker container allows for analysis of large whole proteome-scale datasets.In the age of next-generation sequencing, large-scale genetic diversity within populations became apparent. A single human individual of European ancestry carries around 3 million genetic variants , of whicAlthough most of sequence variants have no functional or pathogenic effect, in some cases, even a single mutation can be disease causing , 6. ExpeOf those tools that employ protein 3D structure to derive various predictive features, several put variants of interest in the context of protein\u2013protein interactions and inteAs far as structural annotation of larger variants is concerned, most methods are developed to annotate single amino acid replacements, and to the best of our knowledge, there is currently no structural annotation pipeline that is able to map indel-type genetic variants to protein 3D structures.In this study, we present d-StructMAn, a new improved implementation of our earlier tool StructMAn , shippedhttps://www.uniprot.org/uniprot/?query=human&fil=proteome%3AUP000005640+AND+organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22&sort=score# ). S.K. was supported by the IMPRS-CS graduate student fellowship and DFG project number 430158625. S.K.S. was partially supported by the UdS-HIPS-Tandem Interdisciplinary Graduate School for Drug Research. O.V.K. was supported by the Klaus Faber Foundation.A.G. devised the method and implemented the core functionality. S.K.S. and S.K. assisted with the method development and implemented the container. V.R. and O.V.K. conceived the project. All authors wrote the manuscript.We would like to thank Anne Tolkmitt, Nadezhda Azbukina, Amit Fenn and Olga Tsoy for testing d-StructMAn.giac086_GIGA-D-22-00032_Original_SubmissionClick here for additional data file.giac086_GIGA-D-22-00032_Revision_1Click here for additional data file.giac086_GIGA-D-22-00032_Revision_2Click here for additional data file.giac086_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giac086_Response_to_Reviewer_Comments_Revision_1Click here for additional data file.giac086_Reviewer_1_Report_Original_SubmissionRoman Laskowski, PhD -- 4/4/2022 ReviewedClick here for additional data file.giac086_Reviewer_1_Report_Revision_1Roman Laskowski, PhD -- 7/14/2022 ReviewedClick here for additional data file.giac086_Reviewer_2_Report_Original_SubmissionEduard Porta Pardo -- 4/5/2022 ReviewedClick here for additional data file.giac086_Reviewer_2_Report_Revision_1Eduard Porta Pardo -- 8/1/2022 ReviewedClick here for additional data file.giac086_Supplemental_FilesClick here for additional data file."} +{"text": "The purpose of this research is to emphasize the importance of mental health and contribute to the overall well-being of humankind by detecting stress. Stress is a state of strain, whether it be mental or physical. It can result from anything that frustrates, incenses, or unnerves you in an event or thinking. Your body\u2019s response to a demand or challenge is stress. Stress affects people on a daily basis. Stress can be regarded as a hidden pandemic. Long-term (chronic) stress results in ongoing activation of the stress response, which wears down the body over time. Symptoms manifest as behavioral, emotional, and physical effects. The most common method involves administering brief self-report questionnaires such as the Perceived Stress Scale. However, self-report questionnaires frequently lack item specificity and validity, and interview-based measures can be time- and money-consuming. In this research, a novel method used to detect human mental stress by processing audio-visual data is proposed. In this paper, the focus is on understanding the use of audio-visual stress identification. Using the cascaded RNN-LSTM strategy, we achieved 91% accuracy on the RAVDESS dataset, classifying eight emotions and eventually stressed and unstressed states. Today, 82 percent of Indians are stressed, as per the Cigna 360 Well-being study . Rising Stress is a condition of mental pressure for individuals facing problems relating to environmental and social well-being which leads to many diseases. It was discovered that academic exams, human relationships, interpersonal difficulties, life transitions, and career choices all contribute to stress. Such stress is commonly associated with psychological, physical, and behavioral issues .According to Lazarus and Folkman (1984), \u201cstress is a mental or physical phenomenon formed through one\u2019s cognitive appraisal of the stimulation and is a result of one\u2019s interaction with the environment\u201d. The existence of stress depends on the existence of the stressor. Feng (1992) and Volpe (2000) defined a stressor as \u201canything that challenges an individual\u2019s adaptability or stimulates an individual\u2019s body or mentality\u201d. Stress can be caused by environmental factors, psychological factors, biological factors, and social factors, as shown in Human stress represents an imbalanced state of an inEmotions are present in almost every decision and moment of our lives. Thus, recognizing emotions awakens interest, since knowing what others feel helps us to interact with them more effectively. Emotions are considered a psychological state . In the It must be considered that emotions are subjective to an individual, i.e., each subject may experience a different emotion in response to the same stimuli. Thus, emotions can be classified into two different models\u2014the discrete model and the dimensional model. The discrete model includes basic emotions such as happiness, sadness, fear, disgust, anger, surprise, and mixed emotions such as motivation , self-awareness , etc. The dimensional model is expressed in terms of two emotions, valence and arousal . The various emotions experienced by a human can be represented through the Plutchik wheel of emotion , as showSeveral researchers have analyzed human stress using basic emotions. It is possible to map emotions with the stress level. Stress can be detected based on emotions obtained from the audio-visual data. Human emotions are expressed in the voice as well as on the face. The emotional state is extracted from the audio-visual data first. Positive emotions such as happiness, joy, love, pride, and pleasure can have a positive effect, such as improving daily work performance, and negative emotions such as anger, terrible, sad and, disgust can have a negative impact on the health of a person. Positive and negative emotions are represented in The valence\u2013arousal space, as illustrated in Our model reached an accuracy of 91% on the \u2018The Ryerson Audio-Visual Database of Emotional Speech and Song (RAVDESS), outperforming some of the previous solutions evaluated in similar conditions. As far as we know, our study also represents the first attempt to combine speech and facial expressions to recognize the eight emotions in RAVDESS and finally conclude on a stressed or relaxed state.The rest of the paper is organized as follows: By outlining some of the difficulties that these systems encountered, we present earlier automatic stress detection techniques here. We describe the stress-inducing stimuli that were employed, how stress was measured, the signals that were gathered, and the machine learning techniques that were applied in these studies.Stress detection from speech signals has many applications. It is used in psychology to monitor the different stress levels of patients with different stress conditions and provide necessary treatments. The safety and security of a system can be established by monitoring the different stress levels of pilots, deep sea divers and military officials undertaking law enforcement. Stress detection is also useful in speaker identification, deception detection and identification of threatening calls in a few cases of crimes . In ordeKevin Tomba et al. worked oSpeech and facial expression are two natural and effective ways of expressing emotions when human beings communicate with each other. During the last two decades, audio-visual emotion recognition integrating speech and facial expression has attracted extensive attention owing to its promising potential applications in human\u2013computer interaction ,28. HoweG. Giannakakis et al. recordedAudio-visual data were not considered for the stress detection, and only audio signals were used. Moreover, the accuracy of the results can be improved. Although there is much research discussing the recognition and analysis of the six basic emotions, i.e., anger, disgust, fear, happiness, sadness, and surprise, considerably less research has focused on stress and anxiety detection from audio visuals, as these states are considered as complex emotions that are linked to basic emotions . The results of emotion state recognition from audio-visual data can be improved using deep learning techniques, which can be further used to detect stress.Overall, this seems to be an interesting area of research, and the analysis of the existing work would help in carrying out future research. To sum up, despite the fact that other works in the literature also performed multimodal emotion recognition on RAVDESS, such as Wang et al. , who useIn the 1990s and 2000s, the face recognition community was dominated by holistic techniques. Faces are represented using holistic approaches utilising the complete facial region. Many of these approaches function by projecting facial photographs into a low-dimensional space that eliminates unimportant features and variances. PCA is one of the most prominent techniques in this field. Deep neural networks trained with extremely huge datasets have lately supplanted older approaches based on hand-crafted features and typical machine learning techniques. Deep face recognition algorithms, which employ hierarchical design to learn discriminative face representation, have significantly enhanced state-of-the-art performance and spawned a multitude of successful real-world applications. Deep learning employs many processing layers to discover data representations with numerous feature extraction levels ,35.Eckman and Friesen created FACS divides the face into 46 action units (AUs), as shown in Almost any anatomically conceivable facial expression can be coded using FACS, which breaks it down into the specific action units (AUs) that give rise to the expression, as shown in OpenFace is a tool intended for computer vision and machine learning researchers, the affective computing community, and people interested in building interactive applications based on facial behavior analysis. OpenFace is the first toolkit capable of facial landmark detection, head pose estimation, facial action unit recognition, and eye-gaze estimation with available source code for both running and training the models. Specifically, OpenFace can identify AUs 1, 2, 4, 5, 6, 7, 9, 10, 12, 14, 15, 17, 20, 23, 25, 26, 28 and 45.There are two ways to categorize AUs: intensity and presence. Presence indicates whether an AU is visible on the face. On a scale of 1 to 5, intensity indicates the degree of AU intensity (min to max). Both of these scores are presented by OpenFace.These two scores are provided by OpenFace. The output file\u2019s column AU01 c encodes 0 as not present and 1 as present for the presence of AU 1. The output file\u2019s column AU01 r has continuous values in the range of 0 (not present), 1 (present at minimum intensity), and 5 (present at maximum intensity) for the intensity of AU 1.Our proposed stress detection framework includes two systems: a speech emotion recognizer and a face emotion recognizer. The outputs of these subsystems were integrated to identify the dominant emotion and eventually result in a stressed or unstressed state. In the current research, we made a point to highlight a novel method of implementing two different algorithms to function better than any single algorithm working individually. The proposed algorithm not only improves the overall accuracy in determining emotions but also is faster than each individual algorithm, as it uses the advantages of each algorithm and eliminates the disadvantages or time-consuming processes of each of them. Further, the work may seem complicated at the first glance; however, the accuracy improvement in the field of mental stress determination is what we are looking for, and our set objectives for the research work are met through the approach.The Ryerson Audio-Visual Database of Emotional Speech and Song (RAVDESS) is licensed under CC BY-NA-SC 4.0. The paper by Livingstone SR and Russo FA (2018) described the construction and validation of the dataset.There are 7356 files in the RAVDESS. Each file was rated ten times for emotional validity, intensity, and authenticity. A group of 247 people who were typical untrained adult research participants from North America provided ratings. The second group of 72 people provided test\u2013retest data. Emotional validity, interrater reliability, and test\u2013retest intra-rater reliability were all reported to be high.The dataset included all 7356 RAVDESS files in their entirety . The three modality formats for each of the 24 actors were audio-only , audio-video , and video-only (no sound). Please take note that Actor 18 did not have any song files.A total of 4948 samples were used for this task. Audio files were extracted from video-audio files using the \u201cmp4 to wav\u201d algorithm. The filenames for each of the 7356 RAVDESS files were distinctive. A seven-part numerical identifier comprised the filename . These codes specified the properties of the stimulus:The filename identifiers used are illustrated in Taking the example of the RAVDESS filename 02-01-06-01-02-01-12.mp4:Video-only (02)Speech (01)Fearful (06)Normal intensity (01)Statement \u201cdogs\u201d (02)1st Repetition (01)12th Actor (12)Female, as the actor ID number is even.ANN and/or CNN have been presented before in the literature, and an accuracy of around 80% has been reported for them. In our literature review, we did not find any individual algorithm which would improve the accuracy of prediction beyond 90%. So, we needed a different approach wherein we combined two relatively less processor-heavy algorithms to work on and improve the accuracy and simultaneously work at a faster rate. However, as rightly pointed out by the reviewer, in our continued plan for our research work, we will make a point to work on ANN- and CNN-based algorithms to either present a comparative analysis or to cascade them as per our intended method to verify their performance for the said cause. Recurrent neural networks (RNNs) have been successfully applied to sequence learning issues such as action identification, scene labeling, and language processing. An RNN has a recurrent connection, unlike feed-forward networks such as convolutional neural networks (CNNs), where the previous hidden state is an input to the subsequent state. An enhanced RNN, or sequential network, called a long short-term memory network, allows information to endure. It is capable of resolving the RNN\u2019s vanishing gradient issue. Persistent memory is achieved via a recurrent neural network or RNN. Let us imagine that when reading a book or viewing a movie, you are aware of what happened in the preceding scene or chapter. RNNs function similarly; they retain the knowledge from the past and apply it to process the data at hand. Due to their inability to remember long-term dependencies, RNNs have this drawback. Long-term dependency issues are specifically avoided when designing LSTMs.In our case, RNN is used to classify data of facial landmark position with respect to time for visual data analysis and to classify the pitch of different frequencies of the audio signal with respect to time to determine the emotions.Speech and facial expressions are used to detect users\u2019 emotional states. These modalities are combined by employing two independent models connected by a novel approach. By merging the information from aural and visual modalities, audio-visual emotion identification is vital for the human\u2013machine interaction system. We propose a cascaded RNN-LSTM approach for audio-visual emotion recognition through correlation analysis. The emotions will finally be categorized as a stressed mental state or a relaxed mental state. We use the RAVDESS dataset for the verification of the proposed algorithm.The flowgraph for stress recognition using speech signals is shown in Our deep learning model contains two individual input streams, i.e., the audio network processing audio signals with the cascaded RNN-LSTM model, and the visual network processing visual data with the hybrid RNN-LSTM model. The flowchart for the algorithm is in In the proposed algorithm, audio files are extracted from the video files and processed separately. Librosa is used to process audio files while OpenFace is used to process video files. Overall, 66% of samples are used for training purposes, while the rest are used for testing the algorithm. In the algorithm, RNN and LSTM work parallelly to improve the speed of the feature extraction process. Audio signals need 20 neurons in the LSTM network while video signals need 40 neurons due to their signal processing requirements. MFCC is used as a filter for feature extraction. Dropout layers are used to prevent data from overfitting. Max pooling with convolution creates the final 8 required labels from the features. A dense sigmoid function is used for the final classification of the output with 10 neurons each. The separate outputs of both audio and video files are compared on a common platform to improve the accuracy by matching the missing labels. The following emotions are predicted in this model: \u201cneutral\u201d: \u201c01\u201d, \u201ccalm\u201d: \u201c02\u201d, \u201chappy\u201d: \u201c03\u201d, \u201csad\u201d: \u201c04\u201d, \u201cangry\u201d: \u201c05\u201d, \u201cfearful\u201d: \u201c06\u201d, \u201cdisgust\u201d: \u201c07\u201d, \u201csurprised\u201d: \u201c08\u201d. Finally, 8 emotions are classified into 2 mental states\u2014stressed and relaxed. First of all, we chose the method of comparing both audio and video files to avoid any misrepresentation of emotions due to the use of only one kind of file. In a scenario where the classification of both files is different, the average sum of scores of each signal will determine the probability of the inclination of the signals to a particular emotion. However, such a scenario has not yet occurred in our work, and hence the algorithm has not yet been validated.We used the Jupyter interface to run the program. LibROSA, a python package, was used for music and audio analysis, while the OpenFace package was used for facial motion tracking.We plotted the signal from a random file with audio and facial recognition separated as shown in Two facial recognition examples are illustrated in NumPy array was created for extracting Mel-frequency cepstral coefficients (MFCCs), while the classes for prediction were extracted from the name of the file.To apply the cascaded RNN-LSTM method effectively, we need to expand the dimensions of our array, adding a third one using the NumPy \u201cexpand_dims\u201d feature.Layer (type) Output Shape Param #=================================================================conv1d_1 (Conv1D) 768_________________________________________________________________activation_1 (Activation) 0_________________________________________________________________dropout_1 (Dropout) 0.1_________________________________________________________________max_pooling1d_1 0_________________________________________________________________conv1d_2 (Conv1D) 82,048_________________________________________________________________activation_2 (Activation) 0_______________________________________________________________dropout_2 (Dropout) 0.5_________________________________________________________________flatten_1 (Flatten) 0_________________________________________________________________dense_1 (Dense) 6410_________________________________________________________________activation_3 (Activation) 0=================================================================Total params: 89,226Trainable params: 89,226Non-trainable params: 0The model loss of epochs based on training and test data is shown in the To understand the errors of the top solution, we extracted the confusion matrix of the SVM, LSTM, and RNN-LSTM approaches with an accuracy of 76%, 82%, and 91%, respectively. The confusion matrix displayed in the The proposed algorithm is compared with the conventional ones and the performance analysis is presented the Final Output:1633/1633 [==============================]\u20140s 125s/stepAccuracy: 91.00%The existing work was focused on either audio or facial images. In audio-visual data, the separate output of audio and video files was compared on a common platform to improve accuracy by matching the missing labels. In order to enhance the accuracy further, we increased the dimensions of the dataset, as LSTM works better with more data. The accuracy for prediction for the proposed algorithm for the RAVDESS dataset is 91%.Only image-based classification may give polarized results in cases where the image under processing lacks the overall gesture being conveyed. Moreover, using audio and visual signals will help to improve the emotion classification accuracy, which is needed to determine whether the algorithm further needs to be fully developed for the medical determination of mental stress. Although we used well-established packages for our work, we made several changes to the algorithm to make it work and provide novelty. The changes in the algorithm include cascading or the parallel operation of algorithms , the addition of dropout layers to adjust the blank values and to avoid overfitting of the data, and processing of both audio and video files to compare and improve classification accuracy. We would like to state that this method of implementing the algorithm has never been reported in the literature before.Detecting stress is essential before it turns chronic and leads to health issues. The current paper suggests that audio-visual data have the potential to detect stress. In our society, stress is becoming a major concern, and modern employment challenges such as heavy workloads and the need to adjust to ongoing change only make the situation worse. In addition to severe financial losses in businesses, people are experiencing health issues related to excessive amounts of stress. Therefore, it is crucial to regularly check your stress levels to detect stress in its preliminary stages and prevent harmful long-term consequences. The necessity for individuals to handle chronic stress gave rise to the concept of stress detection. The accuracy of the cascaded RNN-LSTM approach for the RAVDESS dataset is 91%. The obtained results are 15\u201320% better than those of other conventional algorithms. The proposed method is an excellent starting point to work towards mental health by detecting stress and improving one\u2019s quality of life.The evaluation of the test results showed that the successful detection of stress is achieved, although further improvements and extensions can be made. The implementation of this system can be improved by using more efficient data structures and software to reduce delays and achieve real-time requirements."} +{"text": "Although wildfires are an important ecological process in forested regions worldwide, they can cause significant economic damage and frequently create widespread health impacts. We propose a network optimization approach to plan wildfire fuel treatments that minimize the risk of fire spread in forested landscapes under an upper bound for total treated area. We used simulation modeling to estimate the probability of fire spread between pairs of forest sites and formulated a modified Critical Node Detection (CND) model that uses these estimated probabilities to find a pattern of fuel reduction treatments that minimizes the likely spread of fires across a landscape. We also present a problem formulation that includes control of the size and spatial contiguity of fuel treatments. We demonstrate the approach with a case study in Kootenay National Park, British Columbia, Canada, where we investigated prescribed burn options for reducing the risk of wildfire spread in the park area. Our results provide new insights into cost-effective planning to mitigate wildfire risk in forest landscapes. The approach should be applicable to other ecosystems with frequent wildfires. Wildfires, while being a natural ecosystem process in many biomes, can pose significant economic and social threat to human communities in forested regions \u20133. Land Preventive fuel treatments, such as prescribed burns or strategic thinning of forest stands, are intended to decrease the probability of fire spread and reduce fire severity and, consequently, the damage to human infrastructure. While there is a consensus that a substantial reduction of flammable biomass will reduce fire spread and severity, factors such as the location, size, maintenance, and use in fire operations may undermine fuel-treatment effectiveness ,6. If efOptimization has been widely used to support decisions about fire prevention and suppression \u201320. SeveSeveral of the proposed models minimized connectivity between forest patches with high wildfire risk as a way to reduce fire spread potential in a landscape . Minas aIn this paper, we employ a directional metric that quantifies the probability of fires spreading between a pair of locations in a landscape to solve a fuel treatment problem: allocating a set of prescribed burns to minimize the chance that wildfires will spread through the landscape, subject to an upper bound on the total treated area of prescribed burning or similar fuel reduction treatments (henceforth referred to as \u201cprescribed burning\u201d). For each pair of forest patches, we estimate the probability that a fire ignited in one patch will spread to another. We incorporate this metric into a modified Critical Node Detection (CND) problem \u201339, whicA forest landscape can be thought of as a connected network of flammable patches (nodes), where the connecting arcs (edges) depict possible vectors of fire spread between adjacent patches. To minimize the possibility of fires spreading widely across the area, the manager allocates a set of treatments (prescribed burns) among the nodes. Treating a node helps reduce fire intensity to the pA popular strategy for solving this problem is to reduce the connectivity between nodes with flammable fuels in the landscape network. This strategy can be implemented by solving a CND problem, which finds the key nodes in a network whose removal maximally degrades the connectivity of the network according to a chosen metric \u201338,43\u201345G = be a graph with a set of N nodes (vertices) and a set of edges E, E \u2282 N\u00d7N and there is a path connecting i and j, i.e., when nodes i and j are in the same connected component . The graph obtained after a removal of R critical nodes is a subgraph(s) of G composed of the set of remaining nodes, N \\ R after removal of al nodes ,37. BeloO(|N|2) constraints and is more efficient than the original CND problem formulation with triangular inequalities . Constraints . Set \u0398i denotes adjacent nodes j (including node 0) that can pass flow to node i, while set \u0398i+ denotes adjacent nodes k that can receive flow from i. Constraint (ij is not selected and constraint (ij if no flow occurs between nodes i and j in step t. Constraint (i from other nodes (including node 0) over T steps comes through no more than one arc. This guarantees no overlap between the node selections in different steps t. Constraint and zero otherwise. Constraint ensures straints \u201312 ensurnstraint ensures nstraint ensures nstraint specifienstraint specifienstraint ensures T planned burns. The time to find a feasible solution can be reduced by replacing objective t\u2019 includstraints and 7) t\u2019 inclut\u2019 to account for a cumulative reduction of fire spread potential after each period. This makes problem 3 combinatorically harder than problem 2. To reduce the solving time, we used the problem 2 solutions to initialize problem 3. We first solved problem 3 with constraint (B), i.e.:\u03c7i denotes the values of decision variable xi in problem 2 solution. Under constraint from i to j because the spread probability value pij only defines the likelihood that a fire which is ignited in location i will spread to location j and does not require specification of how the fire might spread from i to j. Evaluating the presence of a path connecting nodes i and j is handled by the CND model constraints ..i,j in tpij between node pairs ij in landscape N. Fire simulation models generate stochastic ignition events and plausible perimeters of fires spreading from the ignition locations from the solution with T = 3 as a warm start, and so on until we solved the model for a desired number of steps. We then used the set of decision variables from the last solution to warm start the full problem. Problem 3 was initialized from problem 2 solutions in similar fashion. The model was run for 72 hours or until reaching an optimality gap of 0.5%, whichever came first. The model was composed in the General Algebraic Modeling System Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********4. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********5. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0General comments:Your work is interesting and, for the most part, well-presented. I find no major flaws in your analysis that warrant revision to the methods, but there are a few sections of the paper that could be improved to clarify your assumptions and methods. I\u2019ll highlight my main critiques here, followed by specific recommendations.First, I suggest you revisit the abstract to make sure it aligns with what you accomplished. Specific notes follow.Fire behavior is a general term that includes spread but also intensity, duration, and type. In most cases, I think it would be clearer to say something like burn probability or spread likelihood instead in this paper.Does the problem 3 formulation with time add value to your analysis? As you point out, you do not actually remodel the fire spread probabilities. My personal view is that there is little value planning far in advance in fire-prone landscapes because stochastic wildfire activity will alter the priorities for subsequent periods more than the treatments. If you are interested, other researchers have examined the effects of uncertainty in fire occurrence using two stage models solved with backwards induction:Konoshima M, Montgomery CA, Albers HJ, Arthur JL (2008) Spatial-endogenous fire risk and efficient fuel management and timber harvest. Land Economics 84(3), 449-468.Konoshima M, Albers HJ, Montgomery CA, Arthur JL (2010) Optimal spatial patterns of fuel management and timber harvest with fire risk. Canadian Journal of Forest Research 40, 95-108.These should probably be cited in the discussion when discussing multiple planning periods. I\u2019m surprised you advocate for problem 3 formulation in the discussion given that you say it produced similar results as problem 2 but with added complexity. Why?If you had more space, I would recommend you compare your method to something simple and widely used, such as Finney\u2019s treatment optimization method or specific patterns of fuel treatments. When you start to describe the contexts that your problem 3 can be applied in , I start to wonder if you really diverge from a plan that interrupts the major spread paths of an anticipated problem fire scenario.Finney MA (2004) Chapter 9, Landscape fi re simulation and fuel treatment optimization. In: J.L. Hayes, A.A. Ager, J.R. Barbour, (tech. eds). Methods for integrated modeling of landscape change: Interior Northwest Landscape Analysis System. PNW-GTR-610. p 117-131.Finney MA (2001) Design of regular landscape fuel treatment patterns for modifying fire growth and behavior. Forest Science 47(2), 219-228.Specific comments:Lines 40-42: It is fair to point out that resources to mitigate wildfire risk are limited, and it is therefore important to prioritize, but there are many tools to assist forest managers in planning fuel treatments. I suggest dropping the focus on limited tools here. Whether the tools are used by managers is another issue.Line 42: I suggest replacing \u201cinterdiction\u201d with common language since you felt the need to define it in the paper.Line 43: Did you really cover consequences in this work? I didn\u2019t see an effects analysis here.Lines 44-45: How about \u201cWe used simulation modeling to estimate the likelihood of fire spread between forest network nodes and we\u2026\u201dLine 46: fuel treatment ALLOCATION problemLines 64-68: Yes. Costs tend to rise with fire sizes, but rising suppression costs are often attributed to the expansion of human values into wildlands. It would be less controversial if you focused this statement only on the challenge of suppressing fires in rugged landscapes.Lines 69-70: I think it is appropriate to at least mention that not all forestry and fire scientists agree that fuel treatments will reduce fire spread. Your Agee reference on shaded fuelbreaks includes discussion of this. Agee and Skinner (2005) and Reinhardt et al. (2008) argue strongly that most fuel treatments are, or should be, aimed at reducing fire intensity and severity.Lines 70-72: Is the saving costs statement supported by these citations? It was a modeling study, but the Thompson et al. (2013) \u2018Quantifying the Potential Impacts of Fuel Treatments on Wildfire Suppression Costs\u2019 article provides the clearest estimates of how fuel treatments could reduce costs via their effects on fire sizes.Lines 76-77: Again, I think it is appropriate to acknowledge that some of these models were aimed at reducing the severity of effects instead of large fire spread.Lines 115-116: I would drop the subscripts here and save them for the methods.Lines 127-130: Again, I think you should temper this statement to make it clear that it is more of an assumption supported by rules of thumb than a clear conclusion of the research. It is also prudent to acknowledge that fuel treatments do not generally achieve 100% protection, especially in the case of extreme weather. The Kalies and Kent (2016) review on fuel treatment effectiveness may be worth mentioning here.Line 134: You already introduced the CND abbreviation.Line 156-157: Would it not be simpler to introduce the model as area limited since you don\u2019t account for variable costs? I see the future value of accounting for this, but it adds slight confusion to the paper. For example, you describe the model as having an upper bound for Rx fire area in the abstract and introduction.Lines 183-185: And fire suppression?Line 197: \u201cdepict well\u201d to \u201crepresent\u201d?Line 234: \u201cConsecutively\u201d or \u201cconsequently\u201d?Lines 313-314: I do not think it is a good idea to use T and t for both steps in problem 2 and time periods in problem 3. I suggest changing a different letter for the steps in problem 2 to avoid confusion.Lines 405-407: Rephrase for clarity.Lines 437-442: You should clarify exactly how the information you mention was used. Were treatments limited to a particular vegetation type? Did you use the ignition probability, but not spread probability components of Burn P3? Is this later what you refer to as prioritizing on ignitions?Lines 443-452: This is where it would help to know the difference between T steps and T time periods.Lines 464-474: As noted in my general comments, this is an important enough change in methods that you should clarify which results it applies to and describe it fully in the methods section instead of supplementary material referenced from the results.Lines 488-489: \u201cignoring spatial contiguity rules\u201d? or \u201cignoring the simulated connectivity measures\u201d?Line 494: Suggest changing fire behavior to fire spread.Lines 520-525: Why is this scenario suddenly popping up in the results? This should be introduced earlier with justification for what it tells you. Prescribed fires likely reduce ignition risk for a short period after treatment, but this will not last long as fuels reaccumulate. Reducing ignitions with rules and enforcement may require different methods in some landscapes.Lines 579-582: I\u2019m confused about what scenarios are being compared here.Lines 598-611: I\u2019m wondering how much the small/large fire size tradeoff that is important at this site pertains to the use of probability vs. binary fireshed weighting versus the specific pattern of fire sizes and occurrence on your landscape? What do you think you would find on a landscape with high probability of fire spread from less frequent but large fires?Lines 615-619: Did the approximation you made to get at spread paths within fires really \u201caddress\u201d the problem? I don\u2019t have a brilliant solution to do better without complicating the simulation. I would be tempering my language here to reflect that some approximations were made to prototype a model framework.Line 625: With a shortest path approximation\u2026Figure 3: You should probably include a scale bar and north arrow in the study site panel.Reviewer #2:\u00a0GENERAL COMMENTThe manuscript entitled \u201cDetecting critical nodes in forest landscape networks to reduce wildfire spread\u201d aims to propose a modeling approach to optimize preventive fuel treatments for minimizing the wildfire spread likelihood and consequences. The methodological approach presented in this manuscript was tested in a study area located in Kootenay National Park, British Columbia (Canada).Overall, I do think the work is interesting and has the potential to provide insights and methods for future studies or analysis that would investigate the potential effects of spatial locations of fuel treatments on wildfire spread, while considering the maximization of the benefit/cost ratio. The present study could also provide relevant information for policy makers and stakeholders to adapt or improve future management plans and strategies in Canada as well as in other areas.https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/03-5210; Davies et al. 2015, http://dx.doi.org/10.1071/WF15055; Salis et al. 2018, https://www.sciencedirect.com/science/article/pii/S0301479718301191; Prichard et al. 2020 https://pubmed.ncbi.nlm.nih.gov/32086976/ doi:10.3390/f6062148). This is a shortcoming that can be improved.The Introduction section is well written and provides a generally good overview of the works that investigated this topic. I only have a remark. The authors limit the Introduction section focusing on previous works carried out in forest areas and using prescribed burnings, while the applicability of the approach they propose could be expanded also to semiarid or rural areas, as well as to fuel management strategies different than prescribed fires . Even if manuscripts published in Plos One can be any length, there is need to reduce this part and omit some redundant sentences. Some specific points to improve this section will be provided in later rows.The Results are in my opinion fine. I would suggest making some improvements in Figures 3 and 4.The Discussion section needs to be improved, as the comparison between the results and approach presented in this work are not compared with those obtained in other similar works.In the end, the manuscript is overall of good quality and well-written, but should be improved by reducing the length of the text and improving the quality of the discussion sections.SPECIFIC COMMENTShttps://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/03-5210; Davies et al. 2015, http://dx.doi.org/10.1071/WF15055; Salis et al. 2018, https://www.sciencedirect.com/science/article/pii/S0301479718301191; Prichard et al. 2020 https://pubmed.ncbi.nlm.nih.gov/32086976/ doi:10.3390/f6062148).Introduction: The Introduction section seem too much focused on works carried out in forest areas and application of prescribed burnings, while the approach proposed in this study could be expanded also to semiarid or rural areas, as well as to fuel management strategies different than prescribed fires L399-402: Considering that no information is provided on crown fire and spot fire settings, I suppose the authors applied Burn-P3 model to simulate surface fire spread. In case the authors simulated crown fires and spot fires, I would recommend including more details on this.L408-410: Please include a table, in the Supplementary data, to summarize the main input data used for fire simulations L435-439: Problems 1-4 related to the critical nodes detection (CND) were introduced in the first equations, several pages before this part. I would recommend helping readers and clarifying that these problems refer to the first equations and the detection of critical nodes.L533: Starting a sentence with \u201cRecall that\u201d might be inappropriate, please checkL613-666: The Discussion section summarizes relatively well the principles and generalizations from results as well as the significance of results. On the other hand, it does not discuss the results and methods presented in this work in relation to those of others. This is a limitation, so I recommend improving the Discussion in this sense.Figures 3-4: Please include the scale bar.**********what does this mean?). If published, this will include your full peer review and any attached files.6. PLOS authors have the option to publish the peer review history of their article digital diagnostic tool,\u00a0 5 Aug 2021PONE-D-21-15640 \u201cDETECTING CRITICAL NODES IN FOREST LANDSCAPE NETWORKS TO REDUCE WILDFIRE SPREAD\u201d \u2013 A Reply to Reviewers\u2019 Comments.Academic Editor\u2019s comments:Both reviewers have indicated that the manuscript requires revisions to the Discussion, specifically that you should compare your method against existing methods to show the improvements or disadvantages.We have added text comparing our technique with some previously proposed treatment methods.One common strategy is to treat sites with the highest likelihoods of ignition . However, this strategy does not optimally reduce the risk of spread of escaped fires nor does it address the uncertainty of determining the sites with the highest fire ignition potential. By comparison, our probabilistic fireshed strategy compartmentalizes regions with high ignition potential, thus providing a hedge against the possibility of fires escaping to spread elsewhere.Several other fuel treatment strategies have used site-specific priority weights. Minas et al. (2015) linked site treatment and deployment resources to minimize the number of sites covered by these activities. Each site was assigned a weight by ignition probability and the value under risk if a fire originating in that site is not contained by the initial response. Rachmawati et al. (2015) focused on rapid fuel accumulation after treatment and used site-based combinations of vegetation type and age since fire to find an optimal multi-period sequence of fuel treatments. Wei (2012) applied optimization of fuel treatment at a very small scale (7x7 rows) without embedding a fire simulation model but examined the geometry of the treated areas. Finney et al. proposed the assessment of fuel treatments by dividing the landscape into rectangular strips oriented normal to the predominant wind directions. Then, fire growth was simulated, starting with the strip farthest upwind, to identify key fire spread routes and their intersections with the potential treatment areas. The process was repeated after moving each strip in the direction of the wind to impact downwind travel routes and subsequent treatment areas. This method finds fuel treatment configurations for a set of likely fire spread routes but overlooks the combinatorial aspects when allocating multiple treatments under a limited budget. Another network-based approach aimed to minimize the connectivity between sites with high fuel loads . Pais et al. (2021) used a network flow model to control the spatial contiguity of the treated area and prioritized treatments using a site-based fire risk metric . The DPV metric assigns treatment priority ranks to sites by modeling fire propagation through a forest landscape as a tree graph and accounts for the potential of a fire ignited at a given site to burn other sites. In contrast, our model makes decisions using the fire spread probabilities between pairs of locations, which enables control based on the presence of possible fire spread paths between these locations. ______________________________________________________Reviewer 2 has indicated that the length of the methods should be reduced, but expects additions around describing the study area and Burn-P3 parameterization.We wanted to note that the Methods section includes the formulation and description of the Critical Node Detection model. The new model formulation is a result on its own but, in keeping with tradition, is presented in the Methods section. This explains the larger-than-normal section size. We believe that the CND model requires a detailed description to understand its principles, and so keeping the larger section size felt justified. However, the fire behaviour simulation model was already published previously in Reimer at al. (2019), so we have only included a brief summary of this model in the main text and moved the description of the its parameters to Supplement S1.______________________________________________________ Reviewer 1 has offered some specific suggestions for improvements in the methods section and the authors should consider moving some text to supplementary materials as suggested by Reviewer 2. Though I found the methods to be a lot to wade through, much of it is necessary in my mind.We agree that much of the descriptive material in the Methods section is necessary to understand how the model works. To reduce the section size, we have moved a portion of text describing the Burn-P3 model and a table with the model parameters to Supplement S1.______________________________________________________ 2. We note that Figure 3 in your submission contain map images which may be copyrighted. <\u2026>We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission:Figure 3 is our own design. While it resembles the figure from Reimer et al. (2019), it was created in GIS from scratch using Burn-P3 inputs and data layers in the public domain, and therefore does not require permission to publish.______________________________________________________ Reviewer\u2019s 1 comments:Reviewer #1: General comments:First, I suggest you revisit the abstract to make sure it aligns with what you accomplished. Specific notes follow.We have edited the abstract to make it more succinct.______________________________________________________Fire behavior is a general term that includes spread but also intensity, duration, and type. In most cases, I think it would be clearer to say something like burn probability or spread likelihood instead in this paper.We have used fire spread in the text to avoid confusion. ______________________________________________________Does the problem 3 formulation with time add value to your analysis? As you point out, you do not actually remodel the fire spread probabilities. My personal view is that there is little value planning far in advance in fire-prone landscapes because stochastic wildfire activity will alter the priorities for subsequent periods more than the treatments.We agree with the reviewer about there being little value to long-term planning in fire-prone landscapes and perceive our approach as a short-term planning tool. Nevertheless, even short-term treatments are typically implemented in a stepwise fashion over a defined time period. The idea behind the problem 3 formulation is to account for the cumulative nature of multi-step planning per se; that is, the actions taken in the first step have the most impact on the system and may thus affect the actions taken in the subsequent steps. The primary difference between the problem 2 and 3 formulations is that the problem 3 formulation allocates the treatments with the greatest impact on fire spread probabilities first, followed by less impactful treatments. We have edited the text to make this point clearer.______________________________________________________If you are interested, other researchers have examined the effects of uncertainty in fire occurrence using two stage models solved with backwards induction:Konoshima M, Montgomery CA, Albers HJ, Arthur JL (2008) Spatial-endogenous fire risk and efficient fuel management and timber harvest. Land Economics 84(3), 449-468.Konoshima M, Albers HJ, Montgomery CA, Arthur JL (2010) Optimal spatial patterns of fuel management and timber harvest with fire risk. Canadian Journal of Forest Research 40, 95-108.These should probably be cited in the discussion when discussing multiple planning periods. The suggested references and a brief section of text referring to two-stage models have been added to the Introduction section:Konoshima et al. integrated a fire simulation model into a two-period stochastic dynamic model to find spatial allocations of timber harvest and fuel management in the face of spatially endogenous fire risk. Their approach used a fire simulation model to enumerate all possible fire occurrence patterns in all plausible treatment decisions and considered the trade-offs between fire risk, timber harvest value and fuel treatment cost.______________________________________________________I\u2019m surprised you advocate for problem 3 formulation in the discussion given that you say it produced similar results as problem 2 but with added complexity. Why?Problems 2 and 3 produced similar spatial results but different allocation of treatments in time. Problem 3 helps find the optimal sequence of treatments , whereas problem 2 does not address the issue of optimal timing because it solves only one CND network for an entire planning horizon. In a sense, problem 3 is more realistic because it provides guidance to forest managers about a stepwise implementation of the fuel reduction strategy.______________________________________________________If you had more space, I would recommend you compare your method to something simple and widely used, such as Finney\u2019s treatment optimization method or specific patterns of fuel treatments. When you start to describe the contexts that your problem 3 can be applied in , I start to wonder if you really diverge from a plan that interrupts the major spread paths of an anticipated problem fire scenario.Finney MA (2004) Chapter 9, Landscape fire simulation and fuel treatment optimization. In: J.L. Hayes, A.A. Ager, J.R. Barbour, (tech. eds). Methods for integrated modeling of landscape change: Interior Northwest Landscape Analysis System. PNW-GTR-610. p 117-131.Finney MA (2001) Design of regular landscape fuel treatment patterns for modifying fire growth and behavior. Forest Science 47(2), 219-228.The only limitation for problem 3 is high numerical complexity. The model can be applied to larger landscapes at a coarser spatial resolution. We have added a brief discussion comparing our approach with other methods \u2013 see our reply to the first comment from the Academic Editor.______________________________________________________ Specific comments:Lines 40-42: It is fair to point out that resources to mitigate wildfire risk are limited, and it is therefore important to prioritize, but there are many tools to assist forest managers in planning fuel treatments. I suggest dropping the focus on limited tools here. Whether the tools are used by managers is another issue.The text discussing limited tools has been dropped following the reviewer\u2019s suggestion.______________________________________________________ Line 42: I suggest replacing \u201cinterdiction\u201d with common language since you felt the need to define it in the paper.We have dropped the mention of interdiction \u2013 critical node detection is already a good description of the approach.______________________________________________________ Line 43: Did you really cover consequences in this work? I didn\u2019t see an effects analysis here.Yes \u2013 essentially, this is what the CND formulation in problems 1-3 does.______________________________________________________ Lines 44-45: How about \u201cWe used simulation modeling to estimate the likelihood of fire spread between forest network nodes and we\u2026\u201dThe text has been edited as suggested by the reviewer.______________________________________________________Line 46: fuel treatment ALLOCATION problemThis text fragment was deleted.______________________________________________________ Lines 64-68: Yes. Costs tend to rise with fire sizes, but rising suppression costs are often attributed to the expansion of human values into wildlands. It would be less controversial if you focused this statement only on the challenge of suppressing fires in rugged landscapes.We have edited the text to focus the statement on managing fires in rugged landscapes.______________________________________________________Lines 69-70: I think it is appropriate to at least mention that not all forestry and fire scientists agree that fuel treatments will reduce fire spread. Your Agee reference on shaded fuelbreaks includes discussion of this. Agee and Skinner (2005) and Reinhardt et al. (2008) argue strongly that most fuel treatments are, or should be, aimed at reducing fire intensity and severity.We agree with the reviewer that the focus should not entirely be placed on spread and have added references to fire severity. Although limiting fire spread defines the proposed strategies, we should have better acknowledged the benefits of fuel treatments in reducing fire intensity and severity with respect to the intended purpose of the fuel treatments. In addition to the probability of fire spread, our approach could incorporate other fire behaviour parameters (such as fire intensity) in conjunction with spread as long as such data could be generated with the fire simulation models. We added some explanatory text about this to the Discussion. ______________________________________________________Lines 70-72: Is the saving costs statement supported by these citations? It was a modeling study, but the Thompson et al. (2013) \u2018Quantifying the Potential Impacts of Fuel Treatments on Wildfire Suppression Costs\u2019 article provides the clearest estimates of how fuel treatments could reduce costs via their effects on fire sizes.We have added text referring to Thompson et al. (2013) as the reviewer suggested.______________________________________________________ Lines 76-77: Again, I think it is appropriate to acknowledge that some of these models were aimed at reducing the severity of effects instead of large fire spread.We have added text acknowledging that some models were also designed to reduce the severity of future fires in the landscape. ______________________________________________________ Lines 115-116: I would drop the subscripts here and save them for the methods.Done.______________________________________________________ Lines 127-130: Again, I think you should temper this statement to make it clear that it is more of an assumption supported by rules of thumb than a clear conclusion of the research. It is also prudent to acknowledge that fuel treatments do not generally achieve 100% protection, especially in the case of extreme weather. The Kalies and Kent (2016) review on fuel treatment effectiveness may be worth mentioning here.The statement has been edited to make clear that this assumption is a simplification and we acknowledge that fuel treatments are not usually 100% effective. A citation to Kalies and Kent (2016) has been added to the text.______________________________________________________ Line 134: You already introduced the CND abbreviation.Dropped.______________________________________________________ Line 156-157: Would it not be simpler to introduce the model as area limited since you don\u2019t account for variable costs? I see the future value of accounting for this, but it adds slight confusion to the paper. For example, you describe the model as having an upper bound for Rx fire area in the abstract and introduction.We have replaced the budget limit with a treatment area limit as suggested by the reviewer.______________________________________________________ Lines 183-185: And fire suppression?Edited.______________________________________________________ Line 197: \u201cdepict well\u201d to \u201crepresent\u201d?Edited______________________________________________________ Line 234: \u201cConsecutively\u201d or \u201cconsequently\u201d?Consequently.______________________________________________________ Lines 313-314: I do not think it is a good idea to use T and t for both steps in problem 2 and time periods in problem 3. I suggest changing a different letter for the steps in problem 2 to avoid confusion.We have denoted time periods and the full timespan in problem 3 as t\u2019 and T\u2019, respectively, while keeping t (a planning step) and T for problem 2. We opted to use the same letter to highlight the analogies between the problem 2 and problem 3 formulations.______________________________________________________ Lines 405-407: Rephrase for clarity.The sentence was deleted.______________________________________________________ Lines 437-442: You should clarify exactly how the information you mention was used. Were treatments limited to a particular vegetation type? Did you use the ignition probability, but not spread probability components of Burn P3? Is this later what you refer to as prioritizing on ignitions?No \u2013 this scenario only used a binary map of flammable / non-flammable land cover types and the flammable land classes were expected to support the spread of fires. Comparatively, the scenarios using fire behaviour information utilized fire spread probabilities pij calculated with the fire simulation model.The only scenario that used ignition probabilities instead of pij values was the solution that allocated treatments to minimize the ignition probability in Fig 8. We have edited the text to make this clearer.______________________________________________________Lines 443-452: This is where it would help to know the difference between T steps and T time periods.We have changed the notation for time periods in the problem 3 formulation to t\u2019 (and the notation for the full timespan to T\u2019) where appropriate. ______________________________________________________ Lines 464-474: As noted in my general comments, this is an important enough change in methods that you should clarify which results it applies to and describe it fully in the methods section instead of supplementary material referenced from the results.The calculation of the wij values is not related to the CND model per se \u2013 these values were used only to map the fire spread hotspots between multiple pairs of locations. Direct mapping of pij arcs makes the map cluttered and difficult to read. The new mapping procedure of fire spread probabilities is a novelty on its own and could help better understand the fire spread patterns in complex landscapes. The full description of the wij mapping procedure is beyond the scope of the current study \u2013 this is the focus of another manuscript. The text provides only basic description germane to understanding the fire spread probability maps. The text has been edited to make this aspect clearer.______________________________________________________ Lines 488-489: \u201cignoring spatial contiguity rules\u201d? or \u201cignoring the simulated connectivity measures\u201d?Ignoring spatial contiguity constraints for prescribed treatments \u2013 the sentence has been edited.______________________________________________________ Line 494: Suggest changing fire behavior to fire spread.Edited.______________________________________________________Lines 520-525: Why is this scenario suddenly popping up in the results? This should be introduced earlier with justification for what it tells you. Prescribed fires likely reduce ignition risk for a short period after treatment, but this will not last long as fuels reaccumulate. Reducing ignitions with rules and enforcement may require different methods in some landscapes.We have introduced a scenario minimizing ignition probabilities in the Methods section, after the description of the scenario based on land cover information only. In our case, we have only done a basic comparison of methods with the same treatment area. Implementing a practical enforcement scenario that reduces the probability of ignitions would require adapting both the CND and ignition-minimizing scenarios to the current practical standards and is considered as a theme for another manuscript.______________________________________________________Lines 579-582: I\u2019m confused about what scenarios are being compared here.These sentences were dropped to avoid confusion.______________________________________________________ Lines 598-611: I\u2019m wondering how much the small/large fire size tradeoff that is important at this site pertains to the use of probability vs. binary fireshed weighting versus the specific pattern of fire sizes and occurrence on your landscape? What do you think you would find on a landscape with high probability of fire spread from less frequent but large fires?Given that the model behaviour depends on the spatial configuration of fire spread patterns in the landscape, this question may best be answered by testing the CND model on real landscapes with high probabilities of large fires . This could be the focus of future work. To target a particular range of fire sizes, the pij value for each pair of locations i and j could be adjusted in the objective equation by a user-defined coefficient based on the distance between i and j. This would make the approach adaptable to other fire regime conditions and management objectives. The extent of this adaptability to different fire regimes will be examined in further studies.______________________________________________________Lines 615-619: Did the approximation you made to get at spread paths within fires really \u201caddress\u201d the problem? I don\u2019t have a brilliant solution to do better without complicating the simulation. I would be tempering my language here to reflect that some approximations were made to prototype a model framework.We did not use approximation to calculate the pij probabilities of fire spread between pairs of locations. As shown in Supplement 1, the pij calculations used raw fire simulation model outputs . A pij value only defines the probability that a fire ignited in location i will spread to location j, but does not specify how exactly the fire could spread from i to j; in short, the CND model does not require exact specification of the fire spread paths between i and j. In our study, we have used the ignition points and perimeters of the simulated fires, but did not track specific (and possibly dynamic) fire spread paths within individual fires. Tracking daily or hourly fire spread within individual fire perimeters could potentially refine the pij values, particularly for long spread distances, but would require a more sophisticated fire simulation model that can output the expansion of individual fires on an hourly or daily basis. This would require updating the Burn-P3 simulation model and could be a topic for future research.______________________________________________________Line 625: With a shortest path approximation\u2026No, there is no shortest path approximation in the calculation of the pij values. The pij values were calculated directly from raw fire simulation model outputs . The CND model only needs to know the probability that a fire ignited in location i will spread to location j and does not require specification of a spread path from i to j. Accounting for the presence of a path connecting a pair of locations i and j is handled by the CND model constraints (3) and (4). Note that we did use a shortest path approximation to calculate the wij values, but this metric is not used in the CND model and was utilized only for mapping the fire spread patterns.______________________________________________________ Figure 3: You should probably include a scale bar and north arrow in the study site panel.We have added a scale bar and north arrow to Figure 3.______________________________________________________ Reviewer\u2019s 2 comments: https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/03-5210; Davies et al. 2015, http://dx.doi.org/10.1071/WF15055; Salis et al. 2018, https://www.sciencedirect.com/science/article/pii/S0301479718301191; Prichard et al. 2020 https://pubmed.ncbi.nlm.nih.gov/32086976/ doi:10.3390/f6062148). This is a shortcoming that can be improved.The Introduction section is well written and provides a generally good overview of the works that investigated this topic. I only have a remark. The authors limit the Introduction section focusing on previous works carried out in forest areas and using prescribed burnings, while the applicability of the approach they propose could be expanded also to semiarid or rural areas, as well as to fuel management strategies different than prescribed fires . Even if manuscripts published in Plos One can be any length, there is need to reduce this part and omit some redundant sentences. Some specific points to improve this section will be provided in later rows.We wanted to note that the methods section includes the formulation and description of the new Critical Node Detection model. The model formulation represents a new result on its own but is traditionally presented in the Methods section. The model formulation also required detailed explanations to understand its principles. Nevertheless, we have edited the Methods section, reducing textual descriptions wherever possible, eliminating redundancies and moving a portion of the Burn-P3 fire model description to Supplement S1.______________________________________________________ The Discussion section needs to be improved, as the comparison between the results and approach presented in this work are not compared with those obtained in other similar works.We have also added a short discussion describing the other treatment strategies \u2013 see our reply to the first comment from the Academic Editor.______________________________________________________Specific comments:https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/03-5210; Davies et al. 2015, http://dx.doi.org/10.1071/WF15055; Salis et al. 2018, https://www.sciencedirect.com/science/article/pii/S0301479718301191; Prichard et al. 2020 https://pubmed.ncbi.nlm.nih.gov/32086976/ doi:10.3390/f6062148).Introduction: The Introduction section seem too much focused on works carried out in forest areas and application of prescribed burnings, while the approach proposed in this study could be expanded also to semiarid or rural areas, as well as to fuel management strategies different than prescribed fires .______________________________________________________L386-389: Please include the size of the study area, as well as the total size of the modeling domain .The study area corresponds to the size of the modelling domain (approximately 834 km2). The network included both a core area and a buffer area. We have noted the size of the study area in the text.______________________________________________________L399-402: Considering that no information is provided on crown fire and spot fire settings, I suppose the authors applied Burn-P3 model to simulate surface fire spread. In case the authors simulated crown fires and spot fires, I would recommend including more details on this.We\u2019ve added the following text explaining how Burn-P3 simulates fires: Burn-P3 fully implements the crown fire scheme of the Canadian Fire Behaviour Prediction System (FBP), modelling surface fires as well as the transition to crown fires (and the rate of crown fire spread itself). We have also provided a short Burn-P3 summary in the online Supplement S1 along with the key model parameters: The critical weather conditions under which the transition from surface to crown fire occurs are dependent on the fuel type. While spot fires are not discretely modelled within the FBP System, the empirical rate of spread equations are based on wildfire observation data for high-intensity crown fires, thus effectively incorporating the role of spot fires and ember transport into the rate of spread models.______________________________________________________ L408-410: Please include a table, in the Supplementary data, to summarize the main input data used for fire simulations .We have added a short summary and a table summarizing the main inputs for Burn-P3 simulations to online Supplement S1.______________________________________________________L435-439: Problems 1-4 related to the critical nodes detection (CND) were introduced in the first equations, several pages before this part. I would recommend helping readers and clarifying that these problems refer to the first equations and the detection of critical nodes.We have edited the text naming problems 1-3.______________________________________________________L533: Starting a sentence with \u201cRecall that\u201d might be inappropriate, please checkRemoved.______________________________________________________L613-666: The Discussion section summarizes relatively well the principles and generalizations from results as well as the significance of results. On the other hand, it does not discuss the results and methods presented in this work in relation to those of others. This is a limitation, so I recommend improving the Discussion in this sense.We have added text relating the presented method to other planning fuel treatment methods to Discussion section \u2013 see our reply to the first comment from the Academic Editor. To avoid repetitions and keep the size of the manuscript reasonable we have compared our approach with the most common methods that use site-based fire hazard metrics.______________________________________________________ Figures 3-4: Please include the scale bar.We have added scale bars to Figures 3 and 4.Attachmentresponse_to_comments_v2.docSubmitted filename: Click here for additional data file. 1 Sep 2021PONE-D-21-15640R1DETECTING CRITICAL NODES IN FOREST LANDSCAPE NETWORKS TO REDUCE WILDFIRE SPREADPLOS ONEDear Dr. Yemshanov,Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE\u2019s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.Reviewer 1 has expressed that the manuscript can be accepted pending some minor revisions.\u00a0Reviewer 2 was unavailable to review the revision, so I reviewed the authors\u2019 revisions based on the reviewer\u2019s comments and found that all issues have been adequately addressed.\u00a0Lines\u00a0326-328, \u201cIn general, long-term planning in fire-prone landscapes has little utility because stochastic wildfire activity may override the long-term treatment plans.\u201d is very poor phrasing and inaccurate. Long term planning is a hallmark of forest management generally and there is good work being undertaken at a range of temporal scales that\u00a0specifically\u00a0address stochasticity in fire regimes. There is no need for this baseless claim and it should be removed.plosone@plos.org. 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For instructions see:\u00a0We look forward to receiving your revised manuscript.Kind regards,Paul Pickell, Ph.D.Academic EditorPLOS ONEJournal Requirements:Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article\u2019s retracted status in the References list and also include a citation and full reference for the retraction notice.[Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #1:\u00a0(No Response)**********2. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0Yes**********3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0Yes**********4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0Yes**********5. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0Yes**********6. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0I am pleased with the revisions. Thank you for clarifying your methods and for explaining where you think the multi-year planning scenario adds value. I still think the method of defining spread probabilities between nodes using the shortest paths from ignition points to perimeters should be framed as an approximation, but this is not central to your work, and the detailed spread paths may not matter much if the \u201cnodes\u201d are large.A few minor writing suggestions:L49-51: I would edit this sentence as: \u201cOur results provide new insights into cost-effective planning to mitigate wildfire risk in forest landscapes. The approach should be applicable to other ecosystems with frequent wildfires.\u201dL64: Drop \u201cin places\u201d?L78: \u201cfuel treatments\u201d instead of \u201cfuel treatment measures\u201dL132: Drop \u201carea\u201dL430-436: Are these sentences necessary after you simplified to an area/node count limit?**********what does this mean?). If published, this will include your full peer review and any attached files.7. PLOS authors have the option to publish the peer review history of their article digital diagnostic tool,\u00a0 3 Sep 2021Manuscript PONE-D-21-15640R1 \u201cDETECTING CRITICAL NODES IN FOREST LANDSCAPE NETWORKS TO REDUCE WILDFIRE SPREAD\u201d \u2013 A Reply to Reviewers\u2019 Comments:Academic Editor:Lines 326-328, \u201cIn general, long-term planning in fire-prone landscapes has little utility because stochastic wildfire activity may override the long-term treatment plans.\u201d is very poor phrasing and inaccurate. Long term planning is a hallmark of forest management generally and there is good work being undertaken at a range of temporal scales that specifically address stochasticity in fire regimes. There is no need for this baseless claim and it should be removed.We deleted this text as suggested by the Editor.__________________________________Reviewer #1: I am pleased with the revisions. Thank you for clarifying your methods and for explaining where you think the multi-year planning scenario adds value. I still think the method of defining spread probabilities between nodes using the shortest paths from ignition points to perimeters should be framed as an approximation, but this is not central to your work, and the detailed spread paths may not matter much if the \u201cnodes\u201d are large.We want to clarify that the calculation of fire spread probabilities pij between pairs of nodes (which were used in our optimization model) did not involve a shortest path approximation. Recall that the spread probability value pij depicts the likelihood that a fire ignited in node i spreads to node j without indication of how the fire might spread from i to j. Information about the ignition locations came from the geographic coordinates for individual fires simulated by the Burn-P3 model, and then we used the perimeters of the simulated fires to identify the locations j to which a particular fire ignited in i could spread.The only place where we utilized a shortest path approximation was in the calculation of the spread probabilities wij between adjacent nodes for visualizing the fire spread patterns. For each simulated fire, we used the shortest path approximation to project the possible fire spread path (with the probability pij) between locations i and j over the network of arcs connecting the adjacent nodes. This map only served to illustrate the fire spread patterns and was not used in optimization modelling. We have edited two sections of the main text, \u201cCalculating the fire spread probabilities pij\u201d and \u201cMapping the fire spread probabilities\u201d, as well as Supplement S4 to make this aspect clearer.__________________________________A few minor writing suggestions:L49-51: I would edit this sentence as: \u201cOur results provide new insights into cost-effective planning to mitigate wildfire risk in forest landscapes. The approach should be applicable to other ecosystems with frequent wildfires.\u201dEdited as the reviewer suggested.__________________________________L64: Drop \u201cin places\u201d?Dropped.__________________________________L78: \u201cfuel treatments\u201d instead of \u201cfuel treatment measures\u201dCorrected.__________________________________L132: Drop \u201carea\u201dDropped.__________________________________L430-436: Are these sentences necessary after you simplified to an area/node count limit?These sentences provide background about why we simplified the budget calculations to an area/node count limit and so should stay in the text. Note that the budget constraint [2] would require a variable cost component if the site treatments were solely managed by ground crews, in which case the total treatment cost would depend on the time required to access the treatment sites (which could be a function of complex terrain and proximity to roads).Attachmentresponse_to_comments_Sept_v2.docSubmitted filename: Click here for additional data file. 17 Sep 2021DETECTING CRITICAL NODES IN FOREST LANDSCAPE NETWORKS TO REDUCE WILDFIRE SPREADPONE-D-21-15640R2Dear Dr. Yemshanov,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Paul Pickell, Ph.D.Academic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments: 21 Sep 2021PONE-D-21-15640R2 DETECTING CRITICAL NODES IN FOREST LANDSCAPE NETWORKS TO REDUCE WILDFIRE SPREAD Dear Dr. Yemshanov:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Paul Pickell Academic EditorPLOS ONE"} +{"text": "MSTN) negatively regulates muscle development and positively regulates metabolism through various pathways. Although MSTN function in cattle has been widely studied, the changes in the gut microbiota due to MSTN mutation, which contribute to host health by regulating its metabolism, remain unclear. Here, high-throughput sequencing of the 16S rRNA gene was conducted to analyze the gut microbiota of wild-type (WT) and MSTN mutant (MT) cattle. A total of 925 operational taxonomic units (OTUs) were obtained, which were classified into 11 phyla and 168 genera. Alpha diversity results showed no significant differences between MT and WT cattle. Beta diversity analyses suggested that the microbial composition of WT and MT cattle was different. Three dominant phyla and 21 dominant genera were identified. The most abundant bacterial genus had a significant relationship with the host metabolism. Moreover, various bacteria beneficial for health were found in the intestines of MT cattle. Analysis of the correlation between dominant gut bacteria and serum metabolic factors affected by MSTN mutation indicated that MSTN mutation affected the metabolism mainly by three metabolism-related bacteria, Ruminococcaceae_UCG-013, Clostridium_sensu_stricto_1, and Ruminococcaceae_UCG-010. This study provides further insight into MSTN mutation regulating the host metabolism by gut microbes and provides evidence for the safety of gene-edited animals.Myostatin ( Yellow cattle are a characteristic resource of China, having 52 breeds, of which Qinchuan, Luxi, Nanyang, Jinnan, and Yanbian cattle have been domesticated and bred for thousands of years. They contain rich genetic resources and have rough feeding tolerance, strong stress resistance ability, strong adaptability, and tender meat. However, due to their long-term use as service cattle, common defects in these cattle, such as slow growth rate, underdeveloped rear-drive, slow fattening, weight gain, and low carcass production, cannot meet the requirements of international beef cattle.MSTN), a member of the transforming growth factor \u03b2 (TGF-\u03b2) superfamily, is highly expressed in skeletal muscle tissue and negatively regulates muscle growth _coprostanoligenes_group, Clostridium_sensu_stricto_1, uncultured_bacterium_f_Ruminococcaceae, Ruminococcaceae_UCG-014, uncultured_bacterium_f_Muribaculaceae, Alistipes, Prevotellaceae_UCG-003, uncultured_bacterium_o_Mollicutes_RF39, Ruminococcaceae_UCG-013, dgA-11_gut_group, Bacteroides, uncultured_bacterium_f_Lachnospiraceae, Prevotellaceae_UCG-004, uncultured_bacterium_o_Clostridiales, uncultured_bacterium_f_p-2534-18B5_gut_group, and uminococcaceae_UCG-009 in WT cattle (1.23 \u00b1 0.16%); however, its relative abundance in MT cattle was <1% (0.80 \u00b1 0.05%).The bacterial composition of the samples was analyzed at the genus level. A total of 168 bacterial genera from the six fecal samples were identified, of which 21 showed an average relative abundance above 1%. These were _UCG-009 . The domMSTN mutation affects the gut bacterial communities of the cattle. Substantial differences were observed in gut flora between WT and MT cattle. At the genus level, the presence of Caproiciproducens, Erysipelatoclostridium, Prevotellaceae_Ga6A1_group, uncultured_bacterium_f_Bifidobacteriaceae, uncultured_bacterium_o_Clostridiales, uncultured_bacterium_f_Erysipelotrichaceae, Acetanaerobacterium, Aeriscardovia, Candidatus_Saccharimonas, Bifidobacterium, Sphingomonas, and Rikenellaceae_RC9_gut_group were substantially higher in MT cattle than in WT cattle. However the presence of Ruminococcaceae_UCG-013, Clostridium_sensu_stricto_1, Solibacillus, Lysinibacillus, Ruminococcaceae_UCG-009, Family_XIII_AD3011_group, Paraclostridium, Blautia, Porphyromonas, uncultured_bacterium_f_Christensenellaceae, Terrisporobacter, Pseudoflavonifractor, XBB1006, Paeniclostridium, Ruminococcaceae_UCG-004, [Eubacterium]_nodatum_group, and uncultured_bacterium_o_Rhodospirillales were substantially lower in MT cattle than in WT cattle (p < 0.05).The gut microbiota composition of WT and MT cattle was analyzed to identify whether T cattle (LDA > 2The functions of the bacteria with significant abundance (>1% in each group) of the MT and WT cattle were predicted using the KEGG database. The primary functions of these bacteria were related to metabolism . SeveralClostridium_sensu_stricto_1 and Ruminococcaceae_UCG-009 (p < 0.05) were significantly positively correlated to AST. Clostridium_sensu_stricto_1 (p < 0.05) showed a significant positive relationship with ALT. Clostridium_sensu_stricto_1, Rikenellaceae_RC9_gut_group, Ruminococcaceae_UCG-013, and Ruminococcaceae_UCG-009 (p < 0.05) were significantly correlated to AMY, of which Rikenellaceae_RC9_gut_group was negatively correlated, whereas the others were positively correlated. Rikenellaceae_RC9_gut_group, Ruminococcaceae_UCG-009, and Ruminococcaceae_UCG-013 (p < 0.05) were significantly related to LDHL, of which Rikenellaceae_RC9_gut_group was negatively correlated, whereas the others were positively correlated. Rikenellaceae_RC9_gut_group, Ruminococcaceae_UCG-013, and Ruminococcaceae_UCG-009 (p < 0.05) were significantly related to LACT, of which Rikenellaceae_RC9_gut_group were negatively correlated, and the others were positively correlated.The relevance between microbial species abundances and serum biochemical indicators was examined to identify marker species linking microbiota and serum biochemical indicators. Spearman\u2019s rank correlation coefficients between abundant microbial species (>1% in each group) and serum biochemical indicators of the MT and WT cattle were determined . ClostriMSTN, a TGF-\u03b2 superfamily member, functions as a negative regulator during muscle growth in many species [MSTN expression for achieving muscle-improved animals [MSTN knockout animals have developed skeletal muscle development. Continued in-depth study of regulation mechanisms has shown that MSTN regulates the metabolism of the host, including muscle development, fat metabolism [ species \u20136. There animals \u201325. To otabolism , glucosetabolism , 9, bonetabolism , and othMSTN mutation was discussed. This study provides a research basis for evaluating the health status of MT cattle intestinal microflora and the effect of MSTN mutation on the gut microbial composition.The bacterial microbiota in the host plays vital roles in the energy and nutrition metabolism, reproduction, and immune homeostasis of the host . ConcernMSTN mutation had no significant influence on the richness and diversity of gut microbiota, which is consistent with the results on the MT pigs [MSTN mutation influenced the gut microbiota.The diversity and richness of the observed OTUs showed no significant difference between the fecal samples of MT and WT cattle, indicating that the MT pigs . NMDS baMSTN mutation promoted fat metabolism and inhibited its formation as reported before [MSTN mutations can regulate metabolism by regulating changes in the gut flora community.At the phylum level, 11 phyla in the six fecal samples were identified, and Firmicutes, Bacteroidetes, and Tenericutes showed an average relative abundance above 1%. Firmicutes and Bacteroidetes were core microbiota of both MT and WT cattle, which is consistent with the results on MT pigs . Previoud before . In otheRuminococcaceae_UCG-005 [Ruminococcaceae_UCG-014, Ruminococcaceae_UCG-010, Ruminococcaceae_UCG-013, uncultured_bacterium_o_Mollicutes_RF39 [uncultured_bacterium_o_Clostridiales [Ruminococcaceae_UCG-005, Rummeliibacillus [uncultured_bacterium_f_Ruminococcaceae, and Prevotellaceae_UCG-004 [Bacteroides, associated with human diseases, such as colorectal inflammation [Bacteroides are a commonly occurring flora in the living environment of animals [At the genus level, 168 genera in the six fecal samples were identified, of which 21 showed an average relative abundance above 1%. Most of them were related to metabolism by function prediction, of which some were butyrate-producing gut bacteria, such as _UCG-005 , Ruminoctes_RF39 , and uncridiales ; others bacillus , uncultu_UCG-004 . These bammation , were ob animals , indicatCaproiciproducens [Acetanaerobacterium [Sphingomonas [uncultured_bacterium_f_Bifidobacteriaceae [Aeriscardovia [Bifidobacterium [MSTN mutation leads to a decrease in fat content and an increase in the lean meat rate, which enhances the metabolism efficiency and reduces type 2 diabetes risk [Pseudoflavonifractor, a type 2 diabetes-related flora, was decreased in MT cattle, indicating that MSTN can regulate metabolism by regulating intestinal flora. Some flora associated with intestinal inflammation was increased in MT cattle, such as Erysipelatoclostridium [Prevotellaceae_Ga6A1_group [Candidatus_Saccharimonas [Paraclostridium, Porphyromonas, Terrisporobacter, and Paeniclostridium. Therefore, in this study, the effect of MSTN mutation on intestinal inflammation could not be determined. The results in MT pigs showed that MSTN mutation leads to a relative reduction in the inflammatory response [The abundance of some bacteria was significantly higher in MT cattle than those in WT cattle. Most of the abundant bacteria such as roducens , Acetanaacterium , and Sphngomonas are relaeriaceae , Aeriscacardovia , and Bifacterium , which pacterium , and ourtes risk . In our stridium , PrevoteA1_group , and Canarimonas , whereasresponse ; howeverMSTN mutation was correlated with serum metabolic factors. All serum biochemical factors were related to enhanced metabolism, indicating that MSTN mutation leads to increased metabolism, which was consistent with a previous study [Rikenellaceae_RC9_gut_group was positively correlated with HFD-induced \u201charmful indicators\u201d and negatively correlated with \u201cbeneficial indicators\u201d [Rikenellaceae_RC9_gut_group was negatively correlated with AMY, LDHL, and LACT, suggesting that MSTN mutation was negatively correlated with HFD-induced \u201charmful indicators\u201d and positively correlated with \u201cbeneficial indicators.\u201d In addition, Clostridium_sensu_stricto_1 was positively correlated with AST, ALT, and AMY, Ruminococcaceae_UCG-013 was positively correlated with AMY, LDHL, and LACT, and Ruminococcaceae_UCG-010 was positively correlated with AST, AMY, LDHL, and LACT. The three abovementioned bacteria were all indicators for improving metabolic intensity [MSTN mutation and indicates that MSTN mutation mainly affected the metabolism by regulating these three bacteria.In this study, we found that us study . Previouicators\u201d . In our ntensity , which iMSTN mutation had no remarkable influence on the diversity and richness of the gut microbiota in Luxi cattle. However, MSTN mutation influenced the composition of gut microbiota. The most abundant bacterial genus had a significant relationship with host metabolism. Moreover, the abundance of microorganisms beneficial for the health in the intestine of MT cattle was higher than in the WT cattle. Analysis of the correlation between bacteria and serum metabolic factors affected by MSTN mutation indicated that MSTN mutation affected the metabolism mainly by three metabolism-related bacterial, Ruminococcaceae_UCG-013, Clostridium_sensu_stricto_1, and Ruminococcaceae_UCG-010. The findings of this study provide further insight into MSTN mutation regulating host metabolism via gut microbes and theoretical evidence for the connection between MSTN and gut microbes. In addition, this study demonstrates a novel way to evaluate the safety of gene-edited animals.In this study, high-throughput sequencing of the 16S rRNA gene was performed to analyze fecal samples of WT and MT cattle. S1 Fig(DOCX)Click here for additional data file.S1 Appendix(GZ)Click here for additional data file.S2 Appendix(GZ)Click here for additional data file.S3 Appendix(GZ)Click here for additional data file.S4 Appendix(GZ)Click here for additional data file.S5 Appendix(GZ)Click here for additional data file.S6 Appendix(GZ)Click here for additional data file.S7 Appendix(GZ)Click here for additional data file.S8 Appendix(GZ)Click here for additional data file.S9 Appendix(GZ)Click here for additional data file.S10 Appendix(GZ)Click here for additional data file.S11 Appendix(GZ)Click here for additional data file.S12 Appendix(GZ)Click here for additional data file.S1 Raw images(PDF)Click here for additional data file."} +{"text": "Molecular design and evaluation for drug development and chemical safety assessment have been advanced by quantitative structure\u2013activity relationship (QSAR) using artificial intelligence techniques, such as deep learning (DL). Previously, we have reported the high performance of prediction models molecular initiation events (MIEs) on the adverse toxicological outcome using a DL-based QSAR method, called DeepSnap-DL. This method can extract feature values from images generated on a three-dimensional (3D)-chemical structure as a novel QSAR analytical system. However, there is room for improvement of this system\u2019s time-consumption. Therefore, in this study, we constructed an improved DeepSnap-DL system by combining the processes of generating an image from a 3D-chemical structure, DL using the image as input data, and statistical calculation of prediction-performance. Consequently, we obtained that the three prediction models of agonists or antagonists of MIEs achieved high prediction-performance by optimizing the parameters of DeepSnap, such as the angle used in the depiction of the image of a 3D-chemical structure, data-split, and hyperparameters in DL. The improved DeepSnap-DL system will be a powerful tool for computer-aided molecular design as a novel QSAR system. Quantitative structure\u2013activity relationship (QSAR) models can reduce the time and cost of molecular screening through mathematical prediction models of regression or classification of properties and activities of a chemical compound based on their chemical structure and statistically significant corresponding physicochemical/toxicological properties with other methods such as homology modeling, molecular docking, and molecular dynamics (MD) simulation ,32,33,34receiver operating characteristic area under the curve (ROC_AUC) of the prediction models for 59 MIE targets in validation, test, and foldout datasets indicated 0.818 \u00b1 0.056, 0.803 \u00b1 0.063, and 0.792 \u00b1 0.076, respectively [A DL-based QSAR system, called DeepSnap-DL, was reported to capture molecular features from molecular images photographed on a 3D-chemical structure . In the ectively . Furtherectively .transforming growth factor (TGF)-beta/Smad (PubChem assay AID:1347032_TGF_beta_ant), and thyrotropin-releasing hormone receptor (PubChem assay AID:1347030_TRHR_ago), by optimizing parameters in the DeepSnap-DL system. According to the previously reported MIE molecules, agonist, or antagonist prediction models in the three MIE molecules constructed using the modified DeepSnap-DL with Python showed that it would be essential tools in a novel QSAR system in computer-aided molecular design.In this study, we used the modified DeepSnap-DL with Python and basic DeepSnap-DL with DIGITS systems to construct prediction models in three of MIEs, glucocorticoid receptor (PubChem assay AID:720725_GR_ant), To analyze the influence of different angles on the snapshot generation of DeepSnap_Python and DeepSnap_DIGITS as 256 \u00d7 256 pixel PNG files, we used 31 and 23 from 65\u00b0, 65\u00b0, 65\u00b0 to 350\u00b0, 350\u00b0, 350\u00b0 in Python and from 70\u00b0, 70\u00b0, 70\u00b0 to 345\u00b0, 345\u00b0, 345\u00b0 in DIGITS of 720725_GR_ant, 15 and 17 from 95\u00b0, 95\u00b0, 95\u00b0 to 325\u00b0, 325\u00b0, 325\u00b0 in Python and from 95\u00b0, 95\u00b0, 95\u00b0 to 355\u00b0, 355\u00b0, 355\u00b0 in DIGITS of 1347030_TRHR_ago, 16 and 16 from 75\u00b0, 75\u00b0, 75\u00b0 to 350\u00b0, 350\u00b0, 350\u00b0 in Python and from 75\u00b0, 75\u00b0, 75\u00b0 to 350\u00b0, 350\u00b0 350\u00b0 in DIGITS of 1347032_TGF_beta_ant, different angles . AdditioAs results, DeepSnap_Python and DeepSnap_DIGITS in the three MIE targets achieved the following prediction-performance. The mean ROC_AUC, BAC, MCC, and Acc values in the valid dataset were 0.832 \u00b1 0.048 for ROC_AUC_Python in 720725_GR_ant, 0.856 \u00b1 0.029 for ROC_AUC_DIGITS in 720725_GR_ant, 0.875 \u00b1 0.031 for ROC_AUC_Python in 1347030_TRHR_ago, 0.886 \u00b1 0.028 for ROC_AUC_DIGITS in 1347030_TRHR_ago, 0.879 \u00b1 0.015 for ROC_AUC_Python in 1347032_TGF_beta_ant, 0.907 \u00b1 0.020 for ROC_AUC_DIGITS in 1347032_TGF_beta_ant, 0.762 \u00b1 0.044 for BAC_Python in 720725_GR_ant, 0.791 \u00b1 0.023 for BAC_DIGITS in 720725_GR_ant, 0.811 \u00b1 0.032 for BAC_Python in 1347030_TRHR_ago, 0.829 \u00b1 0.023 for BAC_DIGITS in 1347030_TRHR_ago, 0.805 \u00b1 0.015 for BAC_Python in 1347032_TGF_beta_ant, 0.849 \u00b1 0.030 for BAC_DIGITS in 1347032_TGF_beta_ant, 0.248 \u00b1 0.065 for MCC_Python in 720725_GR_ant, 0.282 \u00b1 0.030 for MCC_DIGITS in 720725_GR_ant, 0.141 \u00b1 0.017 for MCC_Python in 1347030_TRHR_ago, 0.155 \u00b1 0.022 for MCC_DIGITS in 1347030_TRHR_ago, 0.309 \u00b1 0.025 for MCC_Python in 1347032_TGF_beta_ant, 0.384 \u00b1 0.044 for MCC_DIGITS in 1347032_TGF_beta_ant, and 0.790 \u00b1 0.058 for Acc_Python in 720725_GR_ant, 0.812 \u00b1 0.044 for Acc_DIGITS in 720725_GR_ant, 0.781 \u00b1 0.030 for Acc_Python in 1347030_TRHR_ago, 0.769 \u00b1 0.060 for Acc_DIGITS in 1347030_TRHR_ago, 0.770 \u00b1 0.029 for Acc_Python in 1347032_TGF_beta_ant, 0.833 \u00b1 0.033 for Acc in 1347032_TGF_beta_ant, respectively .The highThe highest prediction performance values of PR_AUC on the valid dataset for the angles and data-split ratios were 0.660 at 176\u00b0 and train:valid:test = 7:1:2 in AID:720725_GR_ant, 0.194 at 176\u00b0 and train:valid:test = 3:1:2 in 1347030_TRHR_ago, and 0.453 at 176\u00b0 and train:valid:test = 3:1:1 in 1347032_TGF_beta_ant ; Table 3These findings suggested that image augmentation is effectively worked. It has been reported that even though a small number of images was used, the DL can classify by increasing the number of images with the addition of artificial operations, such as movement, rotation, enlargement/reduction, and inversion to the original images ,56. In aHowever, since the image will be similar to the original image, the risk of overfitting, i.e., a decrease in the performance on the test dataset due to the prediction model fitting to match into the training dataset, cannot be ruled ,66,67,68To investigate the effect of hyperparameters in DeepSnap-DL with Python system on prediction-performance values of the three MIE targets, we optimized 39 LRs from 0.004 to 0.0000001 in 720725_GR_ant, 24 LRs from 0.007 to 0.000001 in 1347030_TRHR_ago, and 38 LRs from 0.002 to 0.000001 in 1347032_TGF_beta_ant using the valid dataset . The meaDeepSnap_Python in the three MIE targets achieved the following prediction-performance values of loss, PR_AUC, and F. The mean loss values on the train and valid datasets were 0.215 \u00b1 0.231 for loss_train in 720725_GR_ant and 0.263 \u00b1 0.186 for loss_valid in 720725_GR_ant, 0.098 \u00b1 0.062 for loss_train in AID: 1347030_TRHR_ago and 0.122 \u00b1 0.058 for loss_valid in 1347030_TRHR_ago, 0.125 \u00b1 0.110 for loss_train in 1347032_TGF_beta_ant and 0.236 \u00b1 0.062 for loss_valid in 1347032_TGF_beta_ant , Table 4Furthermore, the lowest prediction-performance values of loss on the train and valid datasets for the LRs were 0.022 at 0.00003 and 0.124 at 0.00003 in 720725_GR_ant, 0.020 at 0.00002 and 0.066 at 0.0008 in 1347030_TRHR_ago, 0.038 at 0.00003 and 0.170 at 0.000021 in 1347032_TGF_beta_ant , Table 4Finally, to investigate the effect of BS in the improved DeepSnap-DL with Python system on prediction-performance values, we optimized 84 BSs from 2 to 300 in 720725_GR_ant, 13 LRs from 2 to 26 in 1347030_TRHR_ago, and 37 LRs from 2 to 80 in 1347032_TGF_beta_ant using the valid dataset . The meaThe highest prediction-performance values of ROC_AUC on the test dataset for BS were 0.983 at 125 in 720725_GR_ant, 0.934 at 14 in 1347030_TRHR_ago, 0.925 at 28 in 1347032_TGF_beta_ant , Table 5Additionally, DeepSnap_Python in the three MIE targets achieved the following prediction-performance values of loss, PR_AUC, and F. The mean loss values on the train and test datasets were 0.045 \u00b1 0.033 for loss_train in 720725_GR_ant and 0.119 \u00b1 0.025 for loss_test in 720725_GR_ant, 0.322 \u00b1 0.013 for loss_train in 1347030_TRHR_ago and 0.314 \u00b1 0.022 for loss_test in 1347030_TRHR_ago, 0.097 \u00b1 0.047 for loss_train in 1347032_TGF_beta_ant and 0.203 \u00b1 0.023 for loss_test in 1347032_TGF_beta_ant , Table 5As a method often used to improve the generalization performance of DL, LR decay, meaning to lower LR in places where learning has progressed to some extent, is known to improve accuracy sharply . HoweverIt was previously reported that BS and LR are proportional, whereas BS and momentum coefficient are inversely proportional . It is cThese findings are expected to lead to drug development from the estimation and identification of new ligands for nuclear receptors.The datasets of three MIE targets, including antagonists of the glucocorticoid receptor (PubChem assay AID:720725_GR_ant), TGF-beta/Smad (PubChem assay AID:1347032_TGF_beta_ant), and agonist of the thyrotropin-releasing hormone receptor (PubChem assay AID:1347030_TRHR_ago) for the chemical structures in SMILES format and the corresponding agonist or antagonist scores defined as Pubchem_activity_scores from the Tox21 10K library in the PubChem database housing quantitative high-throughput assays to identify small molecule agonists and antagonists for MIEs, as previously reported, were downloaded ,52,53,54https://www.mn-am.com/products/corina, accessed on 25 January 2022) was used to determine a suitable form of each chemical structure. The 3D chemical structures of the compounds from SDF files were depicted as 3D ball-and-stick models with different colors corresponding to different atoms by a Jmol, an open-source Java viewer software for 3D molecular modeling of chemical structures [x-, y-, and z-axes saved as 256 \u00d7 256-pixel resolution PNG files (RGB) and split into three train, valid, and test datasets, as previously reported [We applied the SMILES format for 3D conformational import to generate the 3D chemical database with rotatable torsion and saved it as a structure data file (SDF) using molecular operating environment (MOE) 2018 scientific applications . Then, the external program, CORINA classic software , were divided into the train, valid, and test datasets. Additionally, the external test dataset is permanently fixed. TensorFlow and Keras on CentOS Linux 7.3.1611 with the CNN GoogLeNet were used all 2D PNG images produced by the DeepSnap-DL-Python system for training and fine-tuning the prediction models. Background colors in the images were changed to the color values in PyMOL, where a force field, which is a set of parameters for the bond lengths, angles, torsional parameters, electrostatic properties, and van der Waals interactions, uses the Merck Molecular Force Field (MMFF) [The improved DeepSnap-DL-Python system used a new 3D conformational import application, called SMILES_TO_SDF, to produce the SDF files from the SMILES format. We used PyMOL, an open-source molecular visualization system written in the Python programming language , to obtain high-quality 3D molecular modeling of chemical structures with 3D ball-and-stick models with different colors corresponding to different atoms. The 3D chemical structures can produce different images depending on the direction. They are captured automatically by DeepSnap as snapshots with user-defined angle increments with respect to the d (MMFF) .x, y, and z axes. The prediction models of the three MIE targets were constructed using these images of the 3D chemicals as input data for the DIGITS-based DL. Another system that is modified DeepSnap-DL by TensorFlow and Keras with Python was used. The SMILES format was used for a new 3D application, called SMILES_TO_SDF, to produce high-quality 3D molecular modeling of the chemical structures saved as a chemical database in SDF format. 2D PNG images produced from the SDF file were produced by DeepSnap, and the prediction models were constructed using these images as input data by DL with TensorFlow and Keras, called DeepSnap-DL-Python.Next, using the structural information for these chemicals derived from the SMILES format, the 3D chemical structure per compound with \u201crotatable torsions\u201d was depicted using MOE application software program, and optimized to generate a single low energy conformation using CORINA classic software. These 3D chemical structures were saved in SDF format as a database file. Then, molecular images were generated as snapshots of the 3D structure from the SDF file using the DeepSnap method at different angles along the \u00ae Pro. 14 , as previously reported [x-, y-, and z-axes directions for one molecule. Classification performance was evaluated based on a confusion matrix defined by the cutoff value (\u03b8) from the Youden\u2019s Index (YI) as follows [k is the diagnostic categories, wj \u2208 .We analyzed the probability of the prediction results using the prediction model with the lowest minimum loss in valid value among 30 examined echoes using the DeepSnap-DL-DIGITS method. We used the medians of each predicted value as representative values for target molecules using statistical analysis software JMPreported ,51,52, b follows ,78,79:YIHowever, the DeepSnap-DL-Python system automatically obtains the probability of prediction results with the lowest minimum loss_valid value among 30 examined epochs, which are the numbers of repeats for one training dataset modulated by early stopping. Additionally, the performance of each model was automatically calculated in terms of the metrics: ROC_AUC, precision recall_AUC (PR_AUC), balanced accuracy (BAC), F, Matthew\u2019s correlation coefficient (MCC), accuracy (Acc), and loss. These performance metrics are defined as follows. Here TP, FN, TN, and FP denote true positive, false negative, true negative, and false positive, respectively.To determine the optimal cutoff point for the definition of TP, FN, TN, and FP, we adopted a method for maximizing the sensitivity (1\u2014specificity), called YI. This index has a value ranging from 0 to 1, where 1 represents the maximum effectiveness, and 0 represents the minimum effectiveness. Additionally, the area under the curve (AUC) for the receiver operating characteristics (ROC) is given byf, j iterates over the true points, Np is the number of true points, T is the number of thresholds, and prect is the precision at threshold t. For broader cases, let prec0 = prec1, and precT = 0 [Here, ROC_AUC denotes AUC recT = 0 . The PR recT = 0 ,54. ThisIn this study, we constructed prediction models for antagonists of the glucocorticoid receptor, TGF-beta/Smad, and agonist of the thyrotropin-releasing hormone receptor using the classic DeepSnap-DL system with DIGITS and improved DeepSnap-DL system with TensorFlow and Keras using the Tox21 10k library. We performed high-throughput and decreased computational costs using the improved DeepSnap-DL system by optimizing the parameters in DeepSnap. Consequently, we obtained that the improved DeepSnap-DL system would be a powerful advanced QSAR system on toxicological and biochemical/cheminformatic fields."} +{"text": "In response to COVID-19, the Government of Ethiopia has been taking a series of policy actions beyond public health initiatives alone. Therefore, this study was aimed to assess the applicability of basic preventive measures of the pandemic COVID-19 and associated factors among the residents of Guraghe Zone from 18th to 29th September, 2020. Systematic random sampling method was applied among the predetermined 634 samples. Variables which had p-value less than 0.25 in bivariate analysis were considered as candidate for multivariable logistic regression model. P-value <0.05 was used as a cutoff point to determine statistical significance in multiple logistic regressions for the final model.Community based cross sectional study was conducted at Guraghe Zone from 18In this study, 17.7% of the respondents apply the basic preventive measures towards the prevention of the pandemic COVID-19. In addition, being rural resident , being studied grade 1\u20138 , being a farmer , currently not married , having family size 1-3, have no diagnosed medical illness and having poor knowledge were factors which are statistically significant in multivariable logistic regression model.Despite the application of preventive measures and vaccine delivery, the applicability of the pandemic COVID-19 preventive measures was too low, which indicate that the Zone is at risk for the infection. Rural residents, those who have lower educational level, farmers, non-marrieds, those who have lower family size, those who have diagnosed medical illnesses and those who have poor knowledge were prone to the infection with the pandemic COVID-19 due to the lower practice of applying the basic preventive measures. In addition, awareness creation should be in practice at all levels of the community especially lower educational classes and rural residents. The pandemic of coronavirus disease 2019 (COVID-19) started in December 2019 in Wuhan, China Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0No**********2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0NoReviewer #2:\u00a0YesReviewer #3:\u00a0No**********3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********4. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0NoReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********5. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a01. The manuscript has a lot of typo errors grammatical, spelling, punctuation, and consistency in word usage like; COVID-19, COVID-2019 and COVID 19, Guraghe zone and Gurage zone, dyed instead of died.2. High knowledge: If the respondent answers 11 of the 14 knowledge assessment questions correctly (10). What if the respondent answer 12, 13, and 14 of 14 knowledge assessment questions correctly????3. Moderate knowledge: If the respondent answers nine of the 14 knowledge assessment questions correctly (10). What if the respondent answers 10 of 14 knowledge assessment questions correctly????4. Poor or low knowledge: If the respondent responds below nine knowledge assessment questions correctly (10).5. Good knowledge: If the respondent responds above nine knowledge assessment questions correctly6. How did you measure attitude is not operationalized7. The maximum total score ranged from 0\u201313, with a higher score indicating better knowledge about COVID-19. How can it be the maximum score of 13 if one individual answers all 14 questions correctly the maximum score will be 14? So, how do you justify it?8. Data were cleaned, edited, coded, and entered into Epi-data version 3.1 and exported to SPSS version 25 for Windows. How can you cleaned, edited, and coded before data entry?9. Television is not social media?10. How do you manage the multicollinearity between being a rural residence and a lower educational level?11. Should supply the basic preventive measures such as mask and sanitizers for financially poor individuals: You didn\u2019t assess the availability of these preventive accessories so how can you recommend.12. Those independent variables that had p-value less than 0.25 in bivariate analysis were entered in to the multivariable logistic regressions model. What is your justification to use 0.25 as cut off points?Reviewer #2:\u00a0In this manuscript, the authors conducted a community based cross-sectional study to assess The applicability of basic preventive measures of the pandemic COVID-19 and associated factors among residents in Guraghe Zone. The study is well written, is easy to follow and covers a hot topic, but some issues should be improved before publication.Comments1.The study is well thought off. I believed that the topic and the content of the manuscript was different. So, it will be advisable to modify the title like KAP2.In the method section, replace Method by Method and material3.There are many language mistakes, please revisit the manuscript for correction.4. Reference for your operational definition?5.Please give some explanations about the current availability of the vaccine6.Please complete all necessary information on the title of each Table7. Discussion section: Will be useful to the reader to add some interesting recent literature about the updates against COVID-19 outbreak and related tools to counteract the same8.Used very few reference, which results poor interpretation of your result, please use the following reference 9.Conclusion Section: The paragraph requires a general revision to eliminate redundant sentences and please refine and don\u2019t repeat it in the abstract part.Reviewer #3:\u00a0major3 why use design effect 1.5? , is there scientifically recommended to use design effect 1.5minor1, there is sentence and paragraph without reference on introduction part2, study are description part, please use recent data not more than 5 years3, the sampling procedure is multistage , it is better represent graphically that makes easily understand to readers4. on table 5 there is missing data , please incorporate this data5, it is better to exclude those data are not significant on multi-variate regression6, please include the p-value for those factors that are significant at multi-variant**********what does this mean?). If published, this will include your full peer review and any attached files.6. PLOS authors have the option to publish the peer review history of their article digital diagnostic tool,\u00a0AttachmentPONE-D-21-05518_reviewer comment.pdfSubmitted filename: Click here for additional data file. 16 Apr 2021Response to the Reviewers1. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.Reviewer #1: YesReviewer #2: YesReviewer #3: NoResponse; Thank you and certain revision were made.________________________________________2. Has the statistical analysis been performed appropriately and rigorously?Reviewer #1: NoReviewer #2: YesReviewer #3: NoResponse: Thank you and it was revised in detail.________________________________________3. Have the authors made all data underlying the findings in their manuscript fully available?The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.Reviewer #1: YesReviewer #2: YesReviewer #3: YesResponse: Thank you________________________________________4. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1: NoReviewer #2: YesReviewer #3: YesResponse: Thank you and it was revised by a language expert. ________________________________________5. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Response: It was revised and we have responded point by point for each raised concerns and corrected as highlighted in the revised version.Reviewer #1: 1. The manuscript has a lot of typo errors grammatical, spelling, punctuation, and consistency in word usage like; COVID-19, COVID-2019 and COVID 19, Guraghe zone and Gurage zone, dyed instead of died.\u2022 Response: Thank you. All the inconsistencies were resolved and the whole manuscript was revised by language expert. ________________________________________2. High knowledge: If the respondent answers 11 of the 14 knowledge assessment questions correctly (10). What if the respondent answer 12, 13, and 14 of 14 knowledge assessment questions correctly????Response: Thank you and it was revised and it was to mean at least 11 of the 14 assessment questions. ________________________________________3. Moderate knowledge: If the respondent answers nine of the 14 knowledge assessment questions correctly (10). What if the respondent answers 10 of 14 knowledge assessment questions correctly????\u2022 Response: It was revised and which was to mean at least nine of the knowledge assessment questions. ________________________________________4. Poor knowledge: If the respondent responds below nine knowledge assessment questions correctly (10).\u2022 Response: It was revised as:- \u201cPoor knowledge: If the respondent responds < 8 knowledge assessment questions correctly\u201d. ________________________________________5. Good knowledge: If the respondent responds above nine knowledge assessment questions correctly\u2022 Response: It was revised as: - \u201cGood knowledge: If the respondent responds > 9 knowledge assessment questions correctly\u201d.________________________________________6. How did you measure attitude is not operationalized\u2022 Response: It was mentioned at the end of data collection tool and procedure but no we have stated at the subtitle, operational definition. ________________________________________7. The maximum total score ranged from 0\u201313, with a higher score indicating better knowledge about COVID-19. How can it be the maximum score of 13 if one individual answers all 14 questions correctly the maximum score will be 14? So, how do you justify it?\u2022 Response: Thank you. It was a typing error, which was to mean 14. If a respondent answers all the knowledge assessment questions correctly, stated as scored 14 of the 14 questions. ________________________________________8. Data were cleaned, edited, coded, and entered into Epi-data version 3.1 and exported to SPSS version 25 for Windows. How can you cleaned, edited, and coded before data entry?Response: The statement was rephrased and stated as:- \u201cData were entered into Epi-data version 3.1 and exported to SPSS version 25 for Windows, then cleaned, edited, coded and exploratory data analysis was carried out to check the levels of missing values, presence of influential outliers, multi-co linearity\u201d.________________________________________9. Television is not social media?Response: It was revised and which was to mean mass media.________________________________________10. How do you manage the multicollinearity between being a rural residence and a lower educational level?Response: All the variables were checked for multicholinearity but multicholinearity was not existed. Therefore; no any management is required unless multicholinearity was observed. ________________________________________11. Should supply the basic preventive measures such as mask and sanitizers for financially poor individuals: You didn\u2019t assess the availability of these preventive accessories so how can you recommend.Response: It was missed during manuscript preparation and incorporated now. This study was conducted as a baseline for further studies and for conducting community service across the study area. This study was presented within the university and community service was delivered through delivering the sanitizers, mask and health information dissemination. ________________________________________12. Those independent variables that had p-value less than 0.25 in bivariate analysis were entered in to the multivariable logistic regressions model. What is your justification to use 0.25 as cut off points?Response: In this study, we had used 12 independent variables. If we had sufficient variables, we can minimize the cutoff point but if the number of variables were not much we can increase the cutoff point. In addition; increasing the cutoff point will keep the marginally significant variables. Therefore; we have used the cutoff point 0.25 to select the candidate variable for multivariable analysis. ________________________________________Reviewer #2: In this manuscript, the authors conducted a community based cross-sectional study to assess The applicability of basic preventive measures of the pandemic COVID-19 and associated factors among residents in Guraghe Zone. The study is well written, is easy to follow and covers a hot topic, but some issues should be improved before publication.1) The study is well thought off. I believed that the topic and the content of the manuscript was different. So, it will be advisable to modify the title like KAPResponse: It was not aimed to investigate the knowledge and attitude but both of them were independent variables. They were described and as independent factors associated with the applicability of the basic preventive measures of COVID-19. As you have seen in the introduction part, it was focused to show the gap in the applicability of the basic preventive measures. In addition, as you have seen the outcome variable is the applicability of the basic preventive measures of the pandemic COVID-19, not KAP. ________________________________________2) In the method section, replace Method by Method and materialResponse: It was replaced accordingly.________________________________________3) There are many language mistakes, please revisit the manuscript for correction.Response: The whole manuscript was revised by a language expert. ________________________________________4) Reference for your operational definition?Response: Thank you all the operational definitions were cited. ________________________________________5) Please give some explanations about the current availability of the vaccineResponse; It was incorporated at the introduction section.________________________________________6) Please complete all necessary information on the title of each TableResponse: Thank you. It was revised and all the necessary information was incorporated. ________________________________________7) Discussion section: Will be useful to the reader to add some interesting recent literature about the updates against COVID-19 outbreak and related tools to counteract the sameResponse: Certain updated recent articles were cited. ________________________________________8) Used very few reference, which results poor interpretation of your result, please use the following reference Response: Thank you. All of them were cited. ________________________________________9) Conclusion Section: The paragraph requires a general revision to eliminate redundant sentences and please refine and don\u2019t repeat it in the abstract part.Response: The conclusion was revised and certain amendments were made.________________________________________Response to Reviewer #3Why use design effect 1.5? , is there scientifically recommended to use design effect 1.5\u2022 Response: Design effect is determined by the researcher in considering the heterogeneity of the population. Most researchers use design effect 2 but it is possible to use also 1.5. We have decided to use it 1.5 in considering, the heterogeneity of the populations and the cost that we have afford. ________________________________________Minor1. There is sentence and paragraph without reference on introduction partResponse: Thank you. All the statements were cited. ________________________________________2. On table 5 there is missing data , please incorporate this dataResponse: It was not a missing data, which was for the variables which were not statistically significant in multivariable analysis but to resolve this, we have the table in to two (table 5 & 6). ________________________________________3. It is better to exclude those data are not significant on multi-variate regressionResponse: It was revised and removed. ________________________________________4. Please include the p-value for those factors that are significant at multi-variantResponse: Thank you, it was included. ________________________________________AttachmentResponse to reviewers.docxSubmitted filename: Click here for additional data file. 15 Jun 2021PONE-D-21-05518R1The applicability of basic preventive measures of the pandemic COVID-19 and associated factors among residents in Guraghe ZonePLOS ONEDear Dr. Dessu,Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE\u2019s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.Please address second reviewer concern and rephrase sentences in the abstract and conclusion to minimize repetition.\u00a0plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.Please submit your revised manuscript by Jul 30 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at Please include the following items when submitting your revised manuscript:A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). 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Read more information on sharing protocols at\u00a0https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see:\u00a0We look forward to receiving your revised manuscript.Kind regards,Enamul KabirAcademic EditorPLOS ONEJournal Requirements:Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article\u2019s retracted status in the References list and also include a citation and full reference for the retraction notice.[Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #1:\u00a0All comments have been addressedReviewer #2:\u00a0All comments have been addressedReviewer #3:\u00a0All comments have been addressed**********2. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********5. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********6. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0Line space in abstract part is not consistent. So make it consistent the line space for the conclusion part is not consistent with the other parts`Reviewer #2:\u00a0The author addresses all comments, however, still they did not understood one of my comment regarding redundancy of sentence the conclusion in both the abstract and main body. Therefore, please rephrase and rewrite the conclusion to minimize repetitionReviewer #3:\u00a0(No Response)**********what does this mean?). If published, this will include your full peer review and any attached files.7. PLOS authors have the option to publish the peer review history of their article digital diagnostic tool,\u00a0 15 Jun 2021Both concdrns were addressed and corrected.AttachmentResponse to reviewers.docxSubmitted filename: Click here for additional data file. 21 Jul 2021PONE-D-21-05518R2The applicability of basic preventive measures of the pandemic COVID-19 and associated factors among residents in Guraghe ZonePLOS ONEDear Dr. Dessu,Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE\u2019s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.One of the reviewers raised some minor issues those need to be fixed before taking final decision.plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.Please submit your revised manuscript by Sep 04 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at Please include the following items when submitting your revised manuscript:A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.An unmarked version of your revised paper without tracked changes. 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For instructions see:\u00a0We look forward to receiving your revised manuscript.Kind regards,Enamul KabirAcademic EditorPLOS ONEJournal Requirements:Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article\u2019s retracted status in the References list and also include a citation and full reference for the retraction notice.Additional Editor Comments (if provided):[Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #1:\u00a0All comments have been addressedReviewer #2:\u00a0All comments have been addressedReviewer #3:\u00a0All comments have been addressed**********2. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********5. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0YesReviewer #3:\u00a0Yes**********6. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0CommentsThe authors have carefully addressed almost all the issues raised by reviewers in the first review process. However, the additional comments below should be addressed to enhance the quality of the paper.On Abstract, data processing and analysis, and result session better to address these comments which are highlighted in the main manuscript:\u2022 P-value \u22640.05 better to change <0.05\u2022 All prevalence, proportion, and magnitude are better to be in one decimal point including its confidence intervals. For instance, 21.9% of the respondents have good knowledge, 94.2% had a favorable attitude, and 17.7% apply basic preventive measures \u2026\u2026\u2026\u2026\u2022 The odds ratio and its respective confidence interval better to be in two decimal points. For example, \u2022 As a principle; the prevalence, proportion, magnitude, odds, and its respective confidence interval should have a similar decimal points which means one decimal point for prevalence, proportion, and magnitude and two decimal points for odds.\u2022 All the recommendations have no owner it doesn\u2019t tell anything about for whom you are going to recommend. So, it is better to indicate the specific stakeholders for each of your recommendations.Reviewer #2:\u00a0The author addressed all comments provided by me and all other reviewers. Therefore, I confirmed that it is accepted.Reviewer #3:\u00a0the author addressed all comments adequately and proper statically analysis and technically good and I recommend for publication**********what does this mean?). If published, this will include your full peer review and any attached files.7. PLOS authors have the option to publish the peer review history of their article digital diagnostic tool,\u00a0AttachmentPONE-D-21-05518_R2 with comments.pdfSubmitted filename: Click here for additional data file.AttachmentComments to Autor.docxSubmitted filename: Click here for additional data file. 22 Jul 2021Response to reviewers\u2022 P-value \u22640.05 better to change <0.05 Response: It was revised and corrected as \u201cP-value <0.05 was used as a cutoff point to determine statistical significance in multiple logistic regressions for the final model\u201d. \u2022 All prevalence, proportion, and magnitude are better to be in one decimal point including its confidence intervals. For instance, 21.9% of the respondents have good knowledge, 94.2% had a favorable attitude, and 17.7% apply basic preventive measures \u2026\u2026\u2026\u2026Response: It was revised and corrected all over the manuscript as:- \u201cIn this study, 17.7% of the respondents apply the basic preventive measures towards the prevention of the pandemic COVID-19\u201d. \u2022 The odds ratio and its respective confidence interval better to be in two decimal points. For example, o Response: It was revised and corrected as:- \u201cIn addition, being rural resident , being studied grade 1-8 , being a farmer , currently not married , having family size 1-3, have no diagnosed medical illness and having poor knowledge were factors which are statistically significant in multivariable logistic regression model\u201d.\u2022 As a principle; the prevalence, proportion, magnitude, odds, and its respective confidence interval should have a similar decimal points which means one decimal point for prevalence, proportion, and magnitude and two decimal points for odds. o Response: It was revised and corrected as per your recommendations.\u2022 All the recommendations have no owner it doesn\u2019t tell anything about for whom you are going to recommend. So, it is better to indicate the specific stakeholders for each of your recommendations.o Response: It was revised and the recommendations were given for the specific bodies.AttachmentResponse to reviewers.docxSubmitted filename: Click here for additional data file. 11 Aug 2021The applicability of basic preventive measures of the pandemic COVID-19 and associated factors among residents in Guraghe ZonePONE-D-21-05518R3Dear Dr. Dessu,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Enamul KabirAcademic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #1:\u00a0All comments have been addressedReviewer #2:\u00a0All comments have been addressed**********2. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified.The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********5. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes**********6. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0All comments have been addressed; The language, typographic errors, analysis, and overall the paper addressed scientific writeup formats. And all my concerns are addressed and it is fit to be accepted for possible publication.Reviewer #2:\u00a0All comments are well addressed and incorporated in the main body of the manuscript. So, please do not submit again more for revision**********what does this mean?). If published, this will include your full peer review and any attached files.7. PLOS authors have the option to publish the peer review history of their article (If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? 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If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Enamul Kabir Academic EditorPLOS ONE"} +{"text": "Nature Communications 10.1038/s41467-021-25534-2, published online 6 September 2021.Correction to: In the original PDF version of this Article, there was an error in the code within the 'Methods' subsection \u2018scETM software\u2019. The original text read:\u201cfrom scETM import scETM,UnsupervisedTrainermodel = scETMtrainer = UnsupervisedTrainertrainer.trainmodel.get_all_embeddings_and_nll(adata)\u201dThe correct format is:\u201cfrom scETM import scETM, UnsupervisedTrainermodel = scETMtrainer = UnsupervisedTrainertrainer.trainmodel.get_all_embeddings_and_nll(adata)\u201dThis has been corrected in the PDF version of the Article; the HTML version was correct at the time of publication."} +{"text": "Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome.Cassava differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in <2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding.Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity. Manihot esculenta, NCBI:txid3983) genome has a haploid genome size \u223c750 Mb dCTP) probes. DNA was extracted from individual clones using Nucleobond Xtra midi kit (Macherey-Nagel) and used for PacBio library preparation by the French Plant Genomic Resources Center (CNRGV) of the French National Research Institute for Agriculture, Food and Environment (INRAE). PacBio sequencing was performed on the Sequel II system with a movie time of 30 hours with 120-min pre-extension step by Gentyane Genomic Platform (INRAE). Circular consensus sequence (CCS) reads per BAC clone were generated using SMRT Analysis Software SMRT Link v9.0.0 and FastQ Screen v0.11.1 , respectively. The technical quality of PacBio raw data was checked using the \u201cQC module\u201d in the PacBio SMRT Analysis Software SMRT Link version 8.0 . Iso-Seq reads were clustered into high-quality transcripts using the \u201cIso-Seq Analysis\u201d Application in PacBio SMRT Analysis Software (SMRT Link v10.1.0.119588). The technical quality of Hi-C data was checked using HiCUP v0.8.0 [The technical quality and potential sample contamination in Illumina PE reads were evaluated using FastQC v0.11.8 .k-mers in the Illumina PE reads using Preqc in SGA v0.10.15 [Genome complexities such as repeat content and the level of heterozygosity were evaluated with _001982) ,54. Anal_001982) , cassavaRRID:SCR_016089) [RRID:SCR_021069) [RRID:SCR_015880) [PacBio CLR reads were assembled using Falcon in pb-as_016089) , hifiasm_021069) , and HiCRRID:SCR_001228) [k-mer\u2013based method Merqury (v1.1) [Assembly statistics were collected using QUAST v4.5 . NG50 [5_001228) was calck-mer analysis results were first used to compute false duplication rates, where k-mers that appeared more than twice in each haploid assembly were used to identify artificial duplications. PacBio CLR reads were then aligned to each haploid genome and the coverage was analyzed using Asset software [For evaluation of structural accuracy, Merqury software . AssemblRRID:SCR_015008) completeness of single-copy orthologs discovered in plants (Viridiplantae Odb10) [RRID:SCR_018550) [Functional completeness was measured using BUSCO v5 , and alie Odb10) were dowe Odb10) . Referen_018550) . The \u201cas_018550) were cal_018550) .RRID:SCR_011919) [Two sets of haplotype-resolved, phased contig (haplotig) assemblies were generated using hifiasm (v0.15.3) with a combination of HiFi reads and PE Hi-C reads. Haplotigs were first validated against the high-density genetic map of cassava , which c_011919) . For eacRRID:SCR_021171) [Hi-C reads were mapped back to each set of haplotigs independently using the Arima mapping pipeline and were_021171) was used_021171) . Given tRRID:SCR_015027), with dependency on TRF (v4.09) [RRID:SCR_021170) [RRID:SCR_014653) [RRID:SCR_012954) [RRID:SCR_016120) [RRID:SCR_017623) [RRID:SCR_011811) [RRID:SCR_007105) [Starting with the assembly of all resolved alleles , repeat elements were predicted using RepeatModeler v2.0.1 , RECON v_021170) , RepeatS_014653) , and Rep_016120) , LTR_Ret_017623) , Ninja (_017623) , MAFFT v_011811) , and CD-_007105) . Among t_007105) , and eacGenome annotation was first performed by transferring reference gene models from AM560 v8.1 to TME204 haplotype assemblies using liftoff (v1.6.1) . Findingab initio gene prediction was performed using AUGUSTUS [RRID:SCR_006646). Predicted protein sequences were compared against AM560 v8.1 protein sequences and Uniprot/Swiss-Prot (release 2021_03) using blastp v2.10.1+ and InterPro using InterProScan v5.52\u201386.0 . The best protein matches from AM560 v8.1, Uniprot/Swiss-Prot, and InterPro, plus Gene Ontology (GO) terms and pathways, were used to functionally annotate predicted genes.Complementary to the transferred reference gene models, _008417) with expRRID:SCR_016582) [RRID:SCR_015687) [2|FC| >\u00a02 and adjusted P < 0.00001.Transcripts annotated in TME204 H1 and H2 were pooled and de-duplicated using cd-hit-est (v4.8.1) to gener_015687) as thoseRRID:SCR_001598) comparison of H1 and H2 transcripts. A unique, bi-directional best-matched transcript pair was considered as allele A and B. Expression values for bi-allelic transcripts were a subset from the master quantification table including all resolved alleles. ASE was determined using the same package DEseq2, with adjusted P < 0.05.\u00a0ASE transcripts overlapped between tissues and haplotypes were analyzed using upsetR [For ASE, bi-allelic transcripts were identified by reciprocal blastn (v2.10.0) [For alignment-based sequence similarity analysis, the cassava reference genome AM560 v8.0 was first disassembled into contig sequences using the utility function \u201csplit_scaffold\u201d in IDBA (v1.1.3) . Each se_018171) , which r_018171) and Asse_018171) for idenRRID:SCR_018550) [For SV analysis using HiFi reads, TME204 HiFi reads were aligned to reference contigs of AM560 and TME204 haplotigs using minimap2 v2.15r905 . SVs wer_018550) . Summary_018550) .For chromosome-level comparisons, the alignment-free method smash++ (v20.04) was usedPan-genomes were constructed using minigraph (v0.15-r426) . Large SRRID:SCR_014798) [P-value cut-off set to 0.00001. The only exception was for the 141 homozygous DETs, where the P-value cut-off was set to 0.001. GO annotation of the ab initio predicted gene models were used as the background gene set.For all selected gene sets, GO enrichment analysis was performed using topGO v2.44.0 ,90 with MZ959795, MZ959796, MZ959797, and MZ959798. All supporting data and materials are available in the GigaScience GigaDB database [Raw sequencing read data from PacBio and Illumina (Hi-C and shotgun) underlying this article are available in the European Nucleotide Archive (ENA) database and can be accessed with accession No. PRJEB43673 (or ERP127652 as the secondary accession number in ENA). Assembled genome sequences of TME204 H1 and H2 are available in the NCBI database and can be accessed with accession No. PRJNA758616 and PRJNA758615, respectively. Assembled BAC clone sequences are available in the NCBI GenBank database and can be accessed with accession Nos. database .ASE: allele-specific expression; BAC: bacterial artificial chromosome; BP: biological process; bp: base pairs; CCS: circular consensus sequence; CDS: coding sequence; CLR: continuous long reads; CMD: Cassava Mosaic Diseases; CPU: central processing unit; DE: differentially expressed/differential expression; DET: differentially expressed transcript; ENA: European Nucleotide Archive; GO: gene ontology; HiFi: high-fidelity; HMW: high molecular weight; Indel: insertion and deletion; IPA: Improved Phased Assembler; kb: kilobase pairs; Mb: megabase pairs; MF: molecular function; NCBI: National Center for Biotechnology Information; numt's: nuclear mitochondrial pseudogene regions; PacBio: Pacific Biosciences; PE: paired-end; QV: quality value; RAM: root apical meristem; SAM: shoot apical meristem; SMRT: Single Molecule Real-Time; SNP: single-nucleotide polymorphism; SV: structural variation; TPM: transcript per million; VGP: the Vertebrate Genome Project.The cassava TME204 cultivar used in our study was obtained by ETH Zurich from the International Institute of Tropical Agriculture (IITA) in Nigeria in 2003 prior to the implementation of the International Treaty on Plant Genetic Resources for Food and Agriculture . TME204 The authors declare that they have no competing interests.This work was supported by the Bill & Melinda Gates Foundation (INV-008213), ETH Zurich, and the Functional Genomics Center Zurich (FGCZ). D.P. is funded by national funds through FCT under the Institutional Call to Scientific Employment Stimulus (reference CEECINST/00026/2018). W.G. is supported by a Yushan Scholarship of the Ministry of Education in Taiwan.W.Q., Y.L., A.P., R.S., and W.G. designed the study. Y.L. and C.C. prepared DNA and RNA samples for sequencing. A.P., S.G., and A.B. prepared CLR, HiFi, and Iso-Seq libraries and performed PacBio sequencing. Y.L., N.R., E.P., S.V., and M.F. generated the BAC sequences. W.Q., Y.L., P.S., D.P., and W.G. analyzed data. W.Q., Y.L., A.P., A.B., P.S., and W.G. wrote the manuscript. All authors reviewed the final manuscript before submission.giac028_GIGA-D-21-00333_Original_SubmissionClick here for additional data file.giac028_GIGA-D-21-00333_Revision_1Click here for additional data file.giac028_GIGA-D-21-00333_Revision_2Click here for additional data file.giac028_GIGA-D-21-00333_Revision_3Click here for additional data file.giac028_Response_to_Reviewer_Comments_Revision_1Click here for additional data file.giac028_Response_to_Reviewer_Comments_Revision_2Click here for additional data file.giac028_Response_to_Reviewer_Comments_Revision_3Click here for additional data file.giac028_Reviewer_1_Report_Original_SubmissionZehong Ding -- 11/11/2021 ReviewedClick here for additional data file.giac028_Reviewer_1_Report_Revision_1Zehong Ding -- 1/16/2022 ReviewedClick here for additional data file.giac028_Reviewer_2_Report_Original_SubmissionC Robin Buell -- 11/17/2021 ReviewedClick here for additional data file.giac028_Reviewer_2_Report_Revision_1C Robin Buell -- 1/16/2022 ReviewedClick here for additional data file.giac028_Supplemental_FileClick here for additional data file."} +{"text": "With the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the acquisition of novel mutations in existing lineages, the need to implement methods capable of monitoring viral dynamics arises. We report the emergence and spread of a new SARS-CoV-2 variant within the B.1.575 lineage, containing the E484K mutation in the spike protein (named B.1.575.2), in a region in northern Spain in May and June 2021. SARS-CoV-2-positive samples with cycle threshold values of \u226430 were selected to screen for presumptive variants using the TaqPath coronavirus disease 2019 (COVID-19) reverse transcription (RT)-PCR kit and the TaqMan SARS-CoV-2 mutation panel. Confirmation of variants was performed by whole-genome sequencing. Of the 200 samples belonging to the B.1.575 lineage, 194 (97%) corresponded to the B.1.575.2 sublineage, which was related to the presence of the E484K mutation. Of 197 cases registered in the Global Initiative on Sharing Avian Influenza Data (GISAID) EpiCoV database as lineage B.1.575.2, 194 (99.5%) were identified in Pamplona, Spain. This report emphasizes the importance of complementing surveillance of SARS-CoV-2 with sequencing for the rapid control of emerging viral variants. During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, several variants that were catalogued as variants of concern (VOCs) or variants of interest (VOIs) by the European Centre for Disease Prevention and Control have emerged in different countries. As of 23 June 2021, the four important lineages with evident impact on transmissibility, severity, and immunity are lineages B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and P.1 (Gamma) 14. LineagThe lineage B.1.575 emerged in the United States, and since its emergence two new sublineages have been identified. The B.1.575.1 sublineage was classified in the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineage system as a Spanish sublineage of B.1.575 with spike mutations P681H, S494P, and T716I, and the B.1.575.2 sublineage, whose main characteristic is the presence of the E484K spike mutation, also originated in Spain screening and whole-genome sequencing.TC) value of \u226430. Occasionally, targeted samples are also included according to epidemiological criteria.The Microbiology Department of the Complejo Hospitalario de Navarra, which is located in Pamplona, the capital city of Navarra, Spain , is the reference laboratory of the public health system for SARS-CoV-2. Upper respiratory specimens for SARS-CoV-2 detection are routinely collected at hospitals and primary care centers and processed by commercial RT-qPCR methods. Since the end of 2020, when variant B.1.1.7 became predominant in the United Kingdom, prospective sample-based surveillance has been conducted in our community to identify novel emerging SARS-CoV-2 variants. A two-step laboratory procedure includes all positive SARS-CoV-2 samples from hospital patients and community settings with a cycle threshold (Screening of presumptive SARS-CoV-2 variants carrying the \u0394H69/\u0394V70 deletion was performed using the TaqPath coronavirus disease 2019 (COVID-19) RT-PCR kit , following the manufacturer\u2019s instructions. Then, all samples of non-B.1.1.7 variants were subjected to a second RT-qPCR assay with the TaqMan SARS-CoV-2 mutation panel (Thermo Fisher Scientific). At that time, we customized the TaqMan assay to detect SARS-CoV-2 spike protein with the N501Y, E484K, K417N, and K417T mutations. All samples were sequenced.https://www.gisaid.org), Nextstrain (https://nextstrain.org), and the PANGO lineage system (https://cov-lineages.org) on the Illumina NovaSeq 6000 system located in the public company NASERTIC, following the manufacturer\u2019s instructions. The viral lineage classifications were performed with the Global Initiative on Sharing Avian Influenza Data (GISAID) EpiCoV database (ges.org) \u201311.http://gisaid.org) under accession numbers EPI_ISL_2510533, EPI_ISL_2510585 to EPI_ISL_2510589, EPI_ISL_2510592, EPI_ISL_2516620, EPI_ISL_2516686 to EPI_ISL_2516689, EPI_ISL_2516691, EPI_ISL_2516698 to EPI_ISL_2516704, EPI_ISL_2516709, EPI_ISL_2516710 to EPI_ISL_2516715, EPI_ISL_2516717 to EPI_ISL_2516721, EPI_ISL_2516723, EPI_ISL_2516724, EPI_ISL_2516726 to EPI_ISL_2516728, EPI_ISL_2516731, EPI_ISL_2516732, EPI_ISL_2516734 to EPI_ISL_2516749, EPI_ISL_2516753, EPI_ISL_2516754, EPI_ISL_2516756, EPI_ISL_2516757, EPI_ISL_2516759 to EPI_ISL_2516761, EPI_ISL_2516855 to EPI_ISL_2516857, EPI_ISL_2516861 to EPI_ISL_2516877, EPI_ISL_2516879, EPI_ISL_2516881, EPI_ISL_2516934, EPI_ISL_2516937 to EPI_ISL_2516940, EPI_ISL_2934576 to EPI_ISL_2934590, EPI_ISL_2934594, EPI_ISL_2934597, EPI_ISL_2934599 to EPI_ISL_2934603, EPI_ISL_2934617 to EPI_ISL_2934623, EPI_ISL_2934625, EPI_ISL_2934626, EPI_ISL_2934629 to EPI_ISL_2934635, EPI_ISL_2934638 to EPI_ISL_2934640, EPI_ISL_2934642, EPI_ISL_2934645 to EPI_ISL_2934651, EPI_ISL_2934656 to EPI_ISL_2934659, EPI_ISL_2934661, EPI_ISL_2934662, EPI_ISL_2934665 to EPI_ISL_2934669, EPI_ISL_2934672, EPI_ISL_2934673, EPI_ISL_2934676 to EPI_ISL_2934681, EPI_ISL_2934684 to EPI_ISL_2934686, EPI_ISL_2934699, EPI_ISL_2934703 to EPI_ISL_2934722, EPI_ISL_2934728 to EPI_ISL_2934730, EPI_ISL_2934844, EPI_ISL_2934846 to EPI_ISL_2934848, EPI_ISL_2934852, EPI_ISL_2934853, EPI_ISL_2934897, EPI_ISL_2934905, EPI_ISL_2934906, EPI_ISL_2934910, and EPI_ISL_2934917 (B.1.575.2), EPI_ISL_1392993 and EPI_ISL_1393347 (B.1.575.1), and EPI_ISL_1622537, EPI_ISL_1622538, EPI_ISL_1622541, and EPI_ISL_1622850 (B.1.575).All genomes generated in this work were deposited in the GISAID EpiCoV database related to the B.1.575 lineage, i.e., 4 (2%) B.1.575, 2 (1%) B.1.575.1, and 194 (97%) B.1.575.2. Among the common substitutions present in these lineages, four occurred in the spike protein . All samThe first case with the B.1.575 lineage to be identified in Pamplona dates back to 20 January 2021; after that date, no other case was identified until 15 March 2021, when three isolates showing mutations common to the B.1.575 lineage were recorded. Between week 20 and week 26 of 2021, we identified 194 cases with lineage B.1.575, which had acquired another S mutation, E484K, classified in the GISAID EpiCoV and Pangolin databases as representing sublineage B.1.575.2. The first case with the B.1.575.2 lineage was identified in a sample isolated on 19 May 2021 (week 20 of 2021); the number of cases grew to 48 cases in weeks 23 and 24 and declined suddenly at the end of June due to the emergence of the Delta (B.1.617.2) variant . This vaTo determine the distribution of the SARS-CoV-2 B.1.575 lineage, we searched in the GISAID EpiCoV and PANGO lineage databases. From May to July, the lineage and sublineages of B.1.575 have increased exponentially in different countries. The B.1.575 lineage was predominant in the United States (90%), while the B.1.575.1 and B.1.575.2 sublineages dominated in Spain .The B.1.575.2 sublineage was predominant in Navarra, since 99.5% of the cases (194/197 cases) registered in the GISAID EpiCoV database were identified in this region. In contrast, we did not identify any genomes of the B.1.575 or B.1.575.1 lineage carrying the E484K mutation.In this study, we observed the emergence of lineage B.1.575.2 with the spike E484K mutation, circulating in Pamplona in association with an outbreak. Pamplona is a small city located in the north of Spain, near France, and it could serve as a spread model for other cities in the world. The new lineage displayed a low prevalence (4.10%) among SARS-CoV-2 genomes analyzed between 23 March 2020 and 30 June 2021. Still, it was already dispersed in our city and represented 97% of the B.1.575 sequences detected during that period. The E484K mutation is considered one of the most important substitutions associated with reduced antibody neutralization potency and efficacy of the SARS-CoV-2 vaccine \u201315. The \u20131\u2013Screening PCR is a useful tool for detecting mutations, mainly because of its rapidity. Future identification with this method, including new mutations characteristic of the lineage, could serve as a rapid method of variant identification. However, whole-genome sequencing remains the gold standard technique for pandemic control.To our knowledge, this is the first study that describes the emergence of the lineage B.1.575.2. This genetic variant includes a mutation in the spike protein (E484K). This SARS-CoV-2 genetic variant was discovered in Pamplona in association with an outbreak, demonstrating the importance of genetic sequencing, especially for new community outbreaks.This brief report emphasizes the importance of exhaustive surveillance for circulating variants of SARS-CoV-2, to reduce community transmission, to assess the COVID-19 vaccine effectiveness, and to prevent the emergence of more transmissible variants that could further increase the severity of the epidemic in the country."} +{"text": "G3 Genes|Genomes|Genetics, 2021, 11(3)., DOI: https://doi.org/10.1093/g3journal/jkaa029https://doi.org/10.25387/g3.12813299\u201d. This should have been \u201chttps://figshare.com/articles/figure/Supplemental_Material_for_Shweta_Basargekar_and_Ratnaparkhi_2020/12813299?file=25392737\u201d. This has now been corrected online.When this paper first published, in the data availability section, the location of supplementary data was erroneously given as \u201cfigshare DOI:"} +{"text": "This protocol tracks engaged transcription complexes across functional genomic regions demonstrated in human K562 erythroleukemia cells.Nascent RNA-sequencing tracks transcription at nucleotide resolution. The genomic distribution of engaged transcription complexes, in turn, uncovers functional genomic regions. Here, we provide analytical steps to (1) identify transcribed regulatory elements For complete details on the use and execution of this protocol, please refer to \u2022de novo genome-wideIdentification of transcribed regulatory elements \u2022Quantification of engaged transcription complexes at functional genomic regions\u2022Measuring distribution of transcription regulators across the functional genomic regions\u2022Revealing functional genomic regions from nascent transcription data de novo genome-wide, (2) quantify engaged transcription complexes at enhancers, promoter-proximal regions, divergent transcripts, gene bodies, and termination windows, and (3) measure distribution of transcription machineries and regulatory proteins across functional genomic regions. This protocol tracks engaged transcription complexes across functional genomic regions demonstrated in human K562 erythroleukemia cells.Nascent RNA-sequencing tracks transcription at nucleotide resolution. The genomic distribution of engaged transcription complexes, in turn, uncovers functional genomic regions. Here, we provide analytical steps to (1) identify transcribed regulatory elements Transcription is a fundamental process in every organism, and its coordination defines RNA synthesis in the cell. A plethora of transcription factors, cofactors, chromatin remodelers and RNA-processing complexes orchestrate the process of RNA synthesis complexes, and the three-dimensional architecture of the linear DNA molecules for PRO-seq have been reported. Here, we begin with sequenced and mapped PRO-seq reads in bed format (https://www.ncbi.nlm.nih.gov/geo/) using accession code GSE181161.Wet-lab protocols and compd format B and strd format C. The bed format C and unrd format , remappehttp://hgdownload.soe.ucsc.edu/goldenPath/. Here, the human hg38 file (2020-08-17) is downloaded in step 4 using wget (https://www.gnu.org/software/wget/).We derive functional genomic regions from the profile of active transcription and the refGene-annotated coordinates of gene transcripts. The refGene list of transcripts can be downloaded from the UCSC genome golden path: de novo using the pattern of divergent transcription (via the web interface (https://django.dreg.scigap.org/) or installed locally (https://github.com/Danko-Lab/dREG). For broad accessibility, the web-based tool is used here. Unnormalized bigWig files are generally provided with PRO-seq data. If needed, the code below converts a bed file reporting the whole read (https://www.encodeproject.org/software/bedgraphtobigwig/). The required chrSizes.txt file is a two-column data frame that contains the chromosome names and the sizes , obtainable for the appropriate genome from http://hgdownload.cse.ucsc.edu/goldenpath/.awk \u2018$6\u00a0== \"+\"\u2019 PROseq.bed | genomeCoverageBed -i stdin -3 -bg -g chrSizes.txt > PROseq_pl.bedgraphawk \u2018$6\u00a0== \"-\"\u2019 PROseq.bed | genomeCoverageBed -i stdin -3 -bg -g chrSizes.txt > PROseq_temp.bedgraphawk \u2018{$4=$4\u2217-1; print}\u2019 PROseq_temp.bedgraph > PROseq_mn.bedgraphbedgraphToBigWig PROseq_pl.bedgraph chrSizes.txt PROseq_pl.bigWigbedgraphToBigWig PROseq_mn.bedgraph chrSizes.txt PROseq_mn.bigWigEnhancers can be identified cription . In thiscription . dREG inole read C. One ofhttps://github.com/Vihervaara/ChIP-seq_analyses).Regulatory proteins coordinate every step of transcription. In this protocol, the functional genomic regions are first identified and color-coded to show enhancer regions in green, sites of divergent transcription (div) in purple, promoter-proximal regions (pp) in orange, gene body (gb) in black, region around CPS in light blue and termination window (tw) in pink A and 3B.https://www.r-project.org) and coordinates of functional genomic regions are compared to active sites of nascent transcription using bedtools ((https://bedtools.readthedocs.io/en/latest/).The data-analyses reported here are conducted in the command line environment of the Apple OS X operating system. Lists of genomic coordinates are processed in R de novo A. Subseqde novo A. Sites de novo . For simvia GitHub .Enhancer coordinates reported here are the dREG-identified sites of divergent transcription that do not overlap with any annotated promoter of a gene. Active genes, instead, are further divided into distinct regions B. A browTiming: 1\u20133 hThis section identifies transcribed regulatory elements in the investigated cell line and condition.1.https://django.dreg.scigap.org/. Log in.a.Choose dREG peak calling.b.plus strand file to the correct box.Upload the unnormalized 3\u2032-coverage bigWig c.minus strand file to the correct box.Upload the unnormalized 3\u2032-coverage bigWig plus strand and -1 for the minus strand).Please note that the bigWig files need to be unnormalized to describe your run and press Launch. The run time depends on the size of the file and available processing capacity, commonly ranging 1\u20133h.Create an account at 2.When the run is complete, download the prefix.dREG.peak.full.bed.gz file and gunzip it.3.Move the downloaded file to the working directory and rename it to a simpler form:mv \u223c/Downloads/K562_hg38.dREG.peak.full.bed\u00a0/pathToWorkingDirectory/dREGcalls_hg38_K562.bedTiming: 30\u00a0minThese steps (4\u20136) divide genes into functional regions.4.Download RefGene datafile, gunzip it and open it in R.http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gzwget -c -O hg38.refGene.txt.gz\u00a0gunzip hg38.refGene.txt.gzRrefGene\u00a0= read.table#gives the number of rows and columns in the refGene dataframedim(refGene)\u00a0#shows the first six rows of the dataframehead(refGene)\u00a0\u00a0#shows information on each dimensionstr(refGene)\u00a05.Name the refGene columns and remove unnecessary columns and chromosome entries.names(refGene)\u00a0=c#maintains chromosomes 1-22, X, Y and M.refGene\u00a0= refGene\u00a0\u00a0#drops the extra levels removed above.refGene$chr\u00a0= factor(refGene$chr)\u00a0\u00a0refGene\u00a0= refGene#look at the dataframe againhead(refGene)\u00a0\u00a06.Generate coordinates of functional regions for every annotated gene transcript.### Subset the genes based on the strand:refGene_pl\u00a0= subsetrefGene_mn\u00a0= subsetplus strand:### Genes on the # TSSrefGene_pl$TSS\u00a0= refGene_pl$txStart\u00a0# CPSrefGene_pl$CPS\u00a0= refGene_pl$txEnd\u00a0\u00a0# region of divergent transcriptionrefGene_pl$DIVs\u00a0= refGene_pl$txStart-750\u00a0refGene_pl$DIVe\u00a0= refGene_pl$txStart-251# promoter-proximal regionrefGene_pl$PPs\u00a0= refGene_pl$TSS-250\u00a0\u00a0refGene_pl$PPe\u00a0= refGene_pl$TSS+249# genebodyrefGene_pl$GBs\u00a0= refGene_pl$TSS+250\u00a0\u00a0refGene_pl$GBe\u00a0= refGene_pl$CPS-501# CPS regionrefGene_pl$CPSs\u00a0= refGene_pl$CPS-500\u00a0\u00a0refGene_pl$CPSe\u00a0= refGene_pl$CPS+499# termination windowrefGene_pl$TWs\u00a0= refGene_pl$CPS+500\u00a0\u00a0refGene_pl$TWe\u00a0= refGene_pl$CPS+10499minus strand:#### Genes on the # TSSrefGene_mn$TSS\u00a0= refGene_mn$txEnd\u00a0\u00a0# CPSrefGene_mn$CPS\u00a0= refGene_mn$txStart\u00a0\u00a0# divergent transcription regionrefGene_mn$DIVs\u00a0= refGene_mn$txEnd+251\u00a0\u00a0refGene_mn$DIVe\u00a0= refGene_mn$txEnd+750# promoter-proximal regionrefGene_mn$PPs\u00a0= refGene_mn$TSS-249\u00a0\u00a0refGene_mn$PPe\u00a0= refGene_mn$TSS+250# genebodyrefGene_mn$GBs\u00a0= refGene_mn$CPS+501\u00a0\u00a0refGene_mn$GBe\u00a0= refGene_mn$TSS-250# CPS regionrefGene_mn$CPSs\u00a0= refGene_mn$CPS-499\u00a0\u00a0refGene_mn$CPSe\u00a0= refGene_mn$CPS+500# termination windowrefGene_mn$TWs\u00a0= refGene_mn$CPS-10499\u00a0\u00a0refGene_mn$TWe\u00a0= refGene_mn$CPS-500#### combine the data of plus and minus stands:refGene\u00a0= rbindrefGene$promC1\u00a0= refGene$TSS-500refGene$promC2\u00a0= refGene$TSS+500#### generate data files:write.tablewrite.table], file=\"hg38_refGenes_TSSpm500.txt\", col.names=F, row.names=F, quote=F, sep=\"\\t\")save.image\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0# saves the above entries in the Rq\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0# exits Ry\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0# answers \u2018yes\u2019 for saving the workspace imageIn the RefGene data file, the \u2018txStart\u2019 is smaller than the same transcript\u2019s \u2018txEnd\u2019. This is convenient when working with the coordinates of genes, but it leads to different columns reporting different functional sites depending on whether the plus or the minus strand encodes the gene. For example, the annotated TSS for genes on the plus strand is reported as txStart, while the TSS for genes on the minus strand is reported as txEnd. In the following steps, we add a column \u2018TSS\u2019 that reports the annotated TSS for each transcript. We then output a file that reports a 1000-nt window around the TSS. These windows of 1000 nt are intersected with the coordinates of dREG-identified sites of divergent transcription in step 7 to identify genes with active transcription and distal sites of divergent transcription, i.e., enhancers. We also obtain transcript-specific coordinates of promoter-proximal region (PP), divergent transcription (DIV), gene body (GB), CPS, and termination window (TW) according to the scheme in https://github.com/Vihervaara/functionalGenomicRegions).Please note that an R script comprising the steps from reading the refGene file in step 4 to the end of step 6 is provided in GitHub 9.Generate a new data frame in R that contains only actively transcribed genes. In essence, the \u2018refGene\u2019 data frame generated in step 6 is reduced here to contain only gene transcripts which initiate transcription. The \u2018txID\u2019 column contains an individual identification code for each transcript variant.refGeneAct\u00a0= subset10.Write files that contain the coordinates of promoter-proximal and divergent transcription regions. These coordinates were generated in step 6.write.table], file=\"ppPolII.txt\", col.names=F, row.names=F, quote=F, sep=\"\\t\")write.table], file=\"divTx.txt\", col.names=F, row.names=F, quote=F, sep=\"\\t\")11.Remove short genes before generating files with the gene body coordinates. This stage is needed to omit gene transcripts, where, due to shortness of the gene, the gene body would overlap with the promoter-proximal region (stretching to\u00a0+500 from TSS) and CPS (starting from \u2212500 from CPS) windows.shortGenes\u00a0= subsetrefGeneAct_\u00a0= subset#in K562 cells mapped against hg38, 351 active genes are removed at this stage.12.Write the files for the CPSs, gene body coordinates and transcription windows.write.table], file=\"CPS.txt\", col.names=F, row.names=F, quote=F, sep=\"\\t\")write.table], file=\"TW.txt\", col.names=F, row.names=F, quote=F, sep=\"\\t\")refGeneAct_\u00a0= subset #ensuring no negative gene body lengths remain.write.table], file=\"geneBody.txt\", col.names=F, row.names=F, quote=F, sep=\"\\t\")save.imageqyOf note: In the RefGen for hg38 file, short genes constitute 3,575 transcripts. Of these, only 351 genes were uniquely mappable, identified as \u2018Active\u2019 and, therefore, removed from our list of active gene transcripts in K562 cells.The steps 8\u201312 can also be run via an R script provided in GitHub .Timing: 20\u00a0minIn steps 13 and 14, active sites of transcription are allocated to individual functional genomic regions. The active sites of transcription are derived from the nascent transcription sequencing data.13.a.echo retaining 3prime most coordinate of the bed file\u00a0awk \u2018$6\u00a0== \"+\"\u2019 PROseq_K562_hg38.bed > tempPL.bed\u00a0awk \u2018$6\u00a0== \"-\"\u2019 PROseq_K562_hg38.bed > tempMN.bedSplit the file based on the strand of the mapped readb.\u00a0awk \u2018{$2\u00a0= $3; print}\u2019 tempPL.bed > tempPL_3p.bed\u00a0awk \u2018{$3\u00a0= $2; print}\u2019 tempMN.bed > tempMN_3p.bedActive site of transcription (3\u2032-most nt) is the coordinate given in the third column of plus strand reads and the second column for minus strand reads. In this step, the active site of transcription (single nt) will be placed both to the second and the third column.c.\u00a0cat tempPL_3p.bed tempMN_3p.bed | tr \u2018 \u2018 \u2018\\t\u2018 > temp_3p.bed\u00a0sortBed -i temp_3p.bed > PROseq_K562_hg38_3pnt.bed\u00a0rm \u2217temp\u2217The reads from plus and minus strands are combined, the data is converted to tab-delimited, and the reads sorted based on genomic coordinates. Intermediary files are removed.Generate a bed file that only contains the 3\u2032-nucleotide (active site of transcription) of each read B. In the14.Intersect the coordinates of nascent transcription with the coordinates of functional genomic regions.Note: To allocate each engaged Pol II complex only once, we use the -u option in the bedtools intersect command and sequentially allocate the coordinates of active transcription to the distinct genomic categories. In each round, two different files are generated: File 1 retains active sites that localize to the given functional category (options -u and -wa). File 2 reports the active sites that do not localize to the given functional category (controlled with option -v). The file 2 will be used in the subsequent round to ensure that each engaged Pol II is allocated only to one genomic region. The order of the intersections is: i) promoter-proximal regions, ii) sites of divergent transcription, iii) enhancers, iv) CPSs, v) gene bodies, and vi) termination windows. In this order, promoter-associated Pol II molecules are not counted into enhancer transcription. Furthermore, transcription at intragenic enhancers is allocated to enhancers instead of gene bodies. Finally, termination windows can be relatively short or extend over several kilobases are allocated to distinct functional\u00a0categories.Timing: 10\u00a0minThe code in step 15 calculates engaged Pol II molecules in each category of functional genomic regions . Engaged Pol II that does not occur in any of the categories is indicated as unannotated. Step 15 further analyses the distribution of engaged Pol II across the functional genomic regions in the dataset. Here, we only have a single sample and, therefore, focus on the distribution (proportions) of active sites across the genomic regions. With PRO-seq data, a normalization factor that accounts for differences in data handling and sequencing depth can be computed. Detailed description of normalization factors is out of the scope of this study. In brief, invariant whole-genome spike-in from a distinct organism can be added to all samples before the run-on reaction. This equal amount of foreign chromatin provides a count of nascent transcription against which the samples can be normalized . If desired, the color-code for each category of functional genomic regions can be adjusted here by changing the rgb values.awk -F \u2018\\t\u2019 -v OFS=\u2018\\t\u2019 \u2018{ $(NF+1)\u00a0=\"243,132,0\"; print }\u2019 ppPolCounts.tmp > ppPolCounts.bedawk -F \u2018\\t\u2019 -v OFS=\u2018\\t\u2019 \u2018{ $(NF+1)\u00a0=\"178,59,212\"; print }\u2019 ppDivCounts.tmp > ppDivCounts.bedawk -F \u2018\\t\u2019 -v OFS=\u2018\\t\u2019 \u2018{ $(NF+1)\u00a0=\"115,212,122\"; print }\u2019 enhancerCounts.tmp > enhancerCounts.bedawk -F \u2018\\t\u2019 -v OFS=\u2018\\t\u2019 \u2018{ $(NF+1)\u00a0=\"0,0,0\"; print }\u2019 geneBodyCounts.tmp > geneBodyCounts.bedawk -F \u2018\\t\u2019 -v OFS=\u2018\\t\u2019 \u2018{ $(NF+1)\u00a0=\"103,200,249\"; print }\u2019 CPSCounts.tmp > CPSCounts.bedawk -F \u2018\\t\u2019 -v OFS=\u2018\\t\u2019 \u2018{ $(NF+1)\u00a0=\"255,54,98\"; print }\u2019 TerminationWinCounts.tmp > TerminationWinCounts.bed18.Combine the files. Add an extra column \".\" to obtain a genome browser compatible bed file for visualization.cat ppPolCounts.bed ppDivCounts.bed enhancerCounts.bed geneBodyCounts.bed CPSCounts.bed TerminationWinCounts.bed > catRegions.tempawk -F \u2018\\t\u2019 -v OFS=\u2018\\t\u2019 \u2018{ $(NF+1)\u00a0=\".\"; print }\u2019 catRegions.temp > catRegions2.temp19.Reorganize the columns and add a header track.awk \u2018{print $1 \"\\t\" $2 \"\\t\" $3 \"\\t\" $7 \"\\t\" $5 \"\\t\" $6 \"\\t\" $2 \"\\t\" $3 \"\\t\" $8}\u2019 catRegions2.temp > catRegions3.tempawk \u2018!seen++\u2019 catRegions3.temp | sortBed > catRegions4.temptouch headerLine.txtecho track name=\"functional_genomic_regions\" itemRgb=\"On\" >> headerLine.txtcat headerLine.txt catRegions4.temp > functionalGenomicRegions.bedrm \u2217.temprm headerLine.txtNote: As mentioned above, the number of engaged Pol II complexes at the distinct genomic regions generated in this protocol originates from raw read counts of the data. This count depends on the sequencing depth. To get a normalized count of engaged Pol II, the column 4 (reporting raw count) in the \u2019functionalGenomicregions.bed\u2019 file can be multiplied with a normalization factor.The generated \u2019functionalGenomicregions.bed\u2019 file can be read in genome browsers to show the identified functional genomic regions as well as the count of engaged Pol II at each indicated region . As starting material, please use a file that reports the summit coordinate of each peak, named with '_summits.bed', for example: K562_TBP_summits.bed, K562_GATA1_summits.bed, K562_CTCF_summits.bed, K562_H3K36me3_summits.bed .Obtain or generate datasets of interest. Place them in the folder of your working directory. Here, we used TBP, GATA1, CTCF, H3K36me3, NELFe, p300 and RAD21 ChIP-seq data . We remab.for x in the code below.\u00a0In the loop, the ${x} will be replaced with the factor name, one listed factor after another.The peak summits for each given chromatin-associated factor are intersected with the\u00a0distinct genomic regions. The strategy described in step 14 is used to ensure that each identified enrichment of a factor at the genome (peak) is counted once. For efficiency, we use a loop function that takes one bed file of mapped peak summits at a time. To define which datasets are analyzed in the loop function, please place names of factors in quotation marks, separated by a space, after the c.Run the code below using the factors of your choice. Please, ensure that the files are placed in the correct folder (working directory) and that the file names correspond to the names in the code. The files listing the coordinates of functional genomic regions were generated in steps 1\u201312.Count genome-associating factors at distinct functional genomic regions.for x in \"TBP\" \"GATA1\" \"CTCF\" \"H3K36me3\"do## Factor-derived reads at promoter-proximal regionsbedtools intersect -u -wa -a K562_${x}_summits.bed -b ppPolII.txt > ${x}_K562_ppPolII.bedbedtools intersect -v -a K562_${x}_summits.bed -b ppPolII.txt > ${x}_ppRemoved.bed## Factor-derived reads at the sites of divergent transcriptionbedtools intersect -u -wa -a ${x}_ppRemoved.bed -b divTx.txt > ${x}_K562_ppDiv.bedbedtools intersect -v -a ${x}_ppRemoved.bed -b divTx.txt > ${x}_ppdivRemoved.bed## Factor-derived reads at enhancersbedtools intersect -u -wa -a ${x}_ppdivRemoved.bed -b enhancers.bed > ${x}_K562_enhancers.bedbedtools intersect -v -a ${x}_ppdivRemoved.bed -b enhancers.bed > ${x}_ppdivEnhRemoved.bed## Factor-derived reads at CPSbedtools intersect -u -wa -a ${x}_ppdivEnhRemoved.bed -b CPS.txt > ${x}_K562_CPS.bedbedtools intersect -v -a ${x}_ppdivEnhRemoved.bed -b CPS.txt > ${x}_ppdivEnhCPSRemoved.bed## Factor-derived reads at GBbedtools intersect -u -wa -a ${x}_ppdivEnhCPSRemoved.bed -b geneBody.txt > ${x}_K562_GB.bedbedtools intersect -v -a ${x}_ppdivEnhCPSRemoved.bed -b geneBody.txt > ${x}_ppdivEnhCPSgbRemoved.bed## Factor-derived reads at termination windowsbedtools intersect -u -wa -a ${x}_ppdivEnhCPSgbRemoved.bed -b TW.txt > ${x}_K562_TW.bedbedtools intersect -v -a ${x}_ppdivEnhCPSgbRemoved.bed -b TW.txt > ${x}_K562_noGene_noEnh.bedrm \u2217Removed.beddone21.a.script Factor_counts_at_functional_regions.txtInitiate the script that collects factor counts at the functional genomic regions.b.Plot the counts of rows in each intersected bed file.c.control\u00a0+ D in the terminal window.Terminate the log script by pressing Plot the counts of chromatin-associated factors at distinct categories of functional regions.22.The file \u2018Factor_peaks_at_functional_regions.txt\u2019 reports the number of ChIP-seq peaks at each functional category. ined see E and 4C.functional_genomic_regions.bed file, each block represents the coordinates of an individual functional genomic region. The block color codes for the category of the region . In UBET2 and PPP1R12B genes are shown, and two intergenic enhancer candidates identified on the longer isoform of PPP1R12B. Furthermore, the protocol counts engaged Pol II complexes that localize to each identified functional genomic region. The raw count of active sites of transcription is given in column 4 of the functional_genomic_regions.bed file, appearing above the color-coded block when visualized in a genome browser (HBE1 gene to the region\u2019s upstream locus control element (LCR). In PRO-seq used here :https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)\"/bin/bash -c \"$. Likewise, the names of the files in the scripts should be updated to match the user-specific input files.Please find the code as shell and R script files in the GitHub repository viher@kth.se).Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Anniina Vihervaara (This study did not generate new unique reagents."} +{"text": "Escherichia coli (EHEC) isolates of serotype O157:H7 are serious foodborne zoonotic pathogens and prime targets for biocontrol using bacteriophages. We report on the complete genome sequences of 11 novel lytic bacteriophages, representing three viral genera, isolated from cattle in Hungary that target E. coli O157 strains.Enterohemorrhagic Escherichia coli (EHEC) isolates of serotype O157:H7 are serious foodborne zoonotic pathogens and prime targets for biocontrol using bacteriophages. We report on the complete genome sequences of 11 novel lytic bacteriophages, representing three viral genera, isolated from cattle in Hungary that target E. coli O157 strains.Enterohemorrhagic Escherichia coli (EHEC) strains, particularly of the O157:H7 serotype, are serious foodborne zoonotic pathogens, and several phages which show effective lysis of these have previously been characterized , and atypical pathotypes isolated earlier in Hungary, as well , FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and Trimmomatic , genome sizes of 166,440 and 166,441\u2009bp, respectively, and a GC content of 35.4%. Phages vb_EcoM_bov10K2, vb_EcoM_bov11CS3, vb_EcoM_bov22_2, and vb_EcoM_bov25_3 are rV5-like phages belonging to the Vequintavirus genus of the Vequintavirinae subfamily, having a >96% nucleotide identity to the type phage rV5 (DQ832317.1). Their genome sizes were between 135,960 and 135,961\u2009bp, with a 43.7% GC content. Phages vb_EcoS_bov11C2, vb_EcoS_bov15_1, vb_EcoS_bov16_1, vb_EcoS_bov22_1, and vb_EcoS_bov25_1D represent HK578-like phages, officially the Dhillonvirus genus from the Siphoviridae family, with 86% genome coverage and >90% nucleotide identity to phage HK578 (JQ086375.1). Their genome sizes were between 44,612 and 44,747\u2009bp, and their GC content was 54.5%.Phages vb_EcoM_bov9_1 and vb_EcoM_bov10K1 proved to be T4-like phages, representing the Phages within the same genus were very uniform. The T4-like phages differed in only a 1-bp gap. Of the rV5-like phages, vb_EcoM_bov10K2, vb_EcoM_bov11CS3, and vb_EcoM_bov25_3 were 100% identical except for a 1-bp gap, while vb_EcoM_bov22_2 differed from them in only 2 single nucleotide polymorphisms (SNPs). The dhillonviruses differed at most by 11 SNPs, with a gap of 30 or 89\u2009bp. The genome of vb_EcoS_bov22_1 was assembled as a partial genome sequence, with a different start position compared to the other dhillonviruses.MT884006 through MT884015 and MT951623.The nucleotide sequences of the phages are deposited in GenBank under the accession numbers"} +{"text": "X + Y, are classic and important problems. Here, a new algorithm is presented, which generates the top k values of the form Selection and sorting the Cartesian sum, Note that this problem definition is presented w.l.o.g.; X and Y need not share the same length. Top-k is important to practical applications, such as selecting the most abundant k isotopologue peaks from a compound (k is \u2208 \u03a9(n + k), because loading the vectors is \u2208 \u0398(n) and returning the minimal k values is \u2208 \u0398(k).Given two vectors of length compound . Top-k ik can be solved trivially in n2 values of the form Xi + Yj. By using median-of-medians (O(n2) steps by generating all n2 values and performing k-selection on them.Top--medians , this cakth minimum value from X + Y in In 1982, Frederickson & Johnson introduced a method reminiscent of median-of-medians ; their m)) steps .k smallest elements from a min-heap in O(k), assuming the heap has already been built solves top-k in O(n + k). The tree data structure in Frederickson\u2019s method can be combined with a combinatoric heap to compute the kth smallest value from X + Y.Frederickson subsequently published a second algorithm, which finds the en built . Combinikth smallest value . Then, as tuple is popped from soft heap, lower-quality tuples are inserted into the soft heap. These lower-quality tuples of areKaplan et al. described an alternative method for selecting the st value ; that mest value . By heapXi + Yj , this scheme progresses in row-major order, thereby avoiding a tuple being added multiple times.In the matrix kth smallest value from X + Y, the best k values are popped from the soft heap. Even though only the minimal k values are desired, \u201ccorruption\u201d in the soft heap means that the soft heap will not always pop the minimal value; however, as a result, soft heaps can run faster than the t \u00b7 \u03b5, where t is the number of insertions into the soft heap thus far. Thus, instead of popping k items values, which must include the minimal k values, are popped. These values are post-processed to retrieve the minimal k values via linear time one-dimensional selection .To compute the election . For conk in O(n + k) steps; this is because computing the kth smallest value from X + Y pops the minimal k values from the soft heap.Note that the Kaplan et al. method easily solves top-X + Y. LOHs are stricter than heaps but not as strict as sorting: Heaps guarantee only that Xi \u2264 Xchildren(i), but do not guarantee any ordering between one child of Xi, a, and the child of the sibling of a. Sorting is stricter still, but sorting n values cannot be done faster than Xu)( = Xu). The size of these layers starts with |X(1)| = 1 and grows exponentially such that u children from layer u + 1, this can be seen as a more constrained form of the heap; however, unlike sorting, for any constant \u03b1 > 1, LOHs can be constructed \u2208 O(n) by performing iterative linear time one-dimensional selection, iteratively selecting and removing the largest layer until all layers have been partitioned. For example, 8,1,6,4,5,3,2 can be LOHified with \u03b1 = 2 into an LOH with three layers by first selecting the largest 4 values on the entire list , removing them, and then selecting the largest 2 values from the remaining 3 values .This paper uses layer-ordered heaps (LOHs) to produ\u03b1 LOHs has been necessary to demonstrate that for k values from X1 + X2 + \u22ef + Xm (where each Xi has length n) in \u03b1 is not trivial when X(1)| = |X(2)| = \u22ef = 1, indicating a sorting, which implies a runtime \u2208 \u03a9(nlog(n)) . Furthernlog(n)) .python implementation of a LOH is shown in listing 1.A k presented here makes extensive use of LOHs. It is simple to implement, does not rely on anything more complicated than linear time one-dimensional selection . Due to its simplicity and contiguous memory access, it has a fast performance in practice.The new, optimal algorithm for solving top-The algorithm presented is broken into phases. An illustration of these phases is provided in X and Y. This is performed by using linear time one-dimensional selection to iteratively remove the largest remaining layer both Xu)( and Yv)( are layers of their respective LOHs.Now layer products of the form Xu)( and Yv). The algorithm proceeds by popping the lexicographically minimum tuple from H. W.l.o.g., there is no guaranteed ordering of the form Xu)( + Yv)( \u2264 Xu(+ 1) + Yv)( + Yv) > min(Xu(+ 1) + Yv); however, lexicographically, H only after \u230a\u230b has been popped from H. Note that for this reason and to break ties where layer products contain identical values, are included in the tuple. \u2308\u2309 tuples do not insert any new tuples into H when they\u2019re popped.Binary heap u,v)\u2309 is popped from H, the index is appended to list q and the size of the layer product |Xu)( + Yv)(| = |Xu)(|\u00b7|Yv) appended to list q. s\u2032 is the total number of elements in each of these layer products appended to q during phase 2.Any remaining tuple in q are generated. A linear time one-dimensional k-selection is performed on these values and returned.The values from every element in each layer product in q must contain the minimal k values in X + Y. Thus, by performing one-dimensional k-selection on those values in phase 3, the minimal k values in X + Y are found.Lemma 2.4 proves that at termination all layer products found in Lemma 2.1.If > 1) and 1) must previously have been popped from H.Proof. There is a chain of pops and insertions backwards from u, v = 1, the lemma is true.When both u = 1 this chain is of the form W.l.o.g. if H increment either row or column, something of the form H before inserting a = u, then a < u, then from the insertion of H, until H must contain something of the form H. Because there are a finite number of these a' and they are not revisited, before Otherwise, both Lemma 2.2If .Proof. Inserting 1) and 1). These pops will insert will therefore be popped before Lemma 2.3All tuples will be visited in ascending order as they are popped from H.Proof. Let H and let a < u, b \u2264 v, or w.l.o.g. a < u, b > v. In the former case, H until In the latter case, lemma 2.1 says that H, H, then H. Each Ordering on popping with H until Identical reasoning also shows that \u25a1Thus, all tuples are popped in ascending order. Lemma 2.4At the end of phase 2, the layer products whose indices are found in q contain the minimal k values.Proof. Let be the layer product that first makes s\u2265 k. There are at least k values of X + Y that are q at the end of phase 1 can only be improved by trading some value for a smaller value, and thus require a new value 1 and v\u2032>1. By lemma 2.3, minimum and maximum layer products are popped in ascending order. By the layer ordering property of X and Y, \u25a1Lemma 2.6s, the number of elements in all layer products appended to q in phase 1, is \u2208 O(k).Proof. is the layer product whose inclusion during phase 1 in q achieves s \u2265 k; therefore, . This happens when H.If k = 1, popping .k > 1, then at least one layer index is >1: u > 1 or v > 1. W.l.o.g., let u > 1. By lemma 2.1, popping H requires previously popping Xu)( + Yv)(|\u2208 O(|Xu(\u22121) + Yv)(|). |Xu(\u22121) + Yv)( + Yv)( + Yv)(|\u2208 O(k). s \u2208 O(k). \u25a1If Lemma 2.7s\u2032, the total number of elements in all layer products appended to q in phase 2, \u2208 O(k).Proof. Each layer product appended to q in phase 2 has had u\u2032 = 1 or v\u2032 = 1 or u\u2032 > 1 and v\u2032 > 1. Each matches exactly one layer product . Because s, the count of all elements whose layer products were inserted into q in phase 1, includes Xu\u2032)( + Yv\u2032)( (the latter is appended to q during phase 2). By exponential growth of layers in X and Y, Xu\u2032(\u22121) + Yv\u2032(\u22121)| values were included in s during phase 1, and thus the total number of elements in all such layer products is \u2264 s. Thus the sum of sizes of all layer products with u\u2032 > 1 and v\u2032 > 1 that are appended to q during phase 2 is asymptotically \u2264 \u03b12\u00b7 s.First consider when u\u2032 = 1 or v\u2032 = 1, the number of elements in all layer products must be \u2208 O(n): u\u2032 = 1 or v\u2032 = 1 are \u2208 O(k):When either u\u2032>1, H only when H at any time. Furthermore, popping H requires previously popping H: layer ordering on X implies max(Xu\u2032(\u22121)) \u2264 min (Xu\u2032) and |Y(1)| = 1 implies min(Y(1)) = max(Y(1)), and so H and counted in s. By the exponential growth of layers, the contribution of all such u\u2032 > 1, v\u2032 = 1 will be u\u2032 > 1, v\u2032 = 1 or u\u2032 = 1, v\u2032 > 1 will be \u2248 \u2264 2 \u03b1 \u00b7 s.W.l.o.g. for u\u2032 = v\u2032 = 1, the layer product contains 1 element.When s\u2032, the total number of elements found in layer products appended to q during phase 2, has s\u2032\u2208 O(k). \u25a1Therefore, Theorem 2.8The total runtime of the algorithm is \u2208 O(n + k).Proof. For any constant \u03b1 > 1, LOHification of X and Y runs in linear time, and so phase 0 runs \u2208 O(n).\u03b1(n); therefore, the total number of layer products is 2\u03b1(n) elements, because each layer product may be inserted as both orO(n) runtime of phase 0.The total number of layers in each LOH is \u2248 logs\u2208 O(k). Likewise, lemma 2.7 shows that s\u2032\u2208 O(k). The number of elements in all layer products in q during phase 3 is s + s\u2032\u2208 O(k). Thus, the number of elements on which the one-dimensional selection is performed will be k-selection in phase 3 is \u2208 O(k).Lemma 2.6 shows that O(n + k + k + k) = O(n + k). \u25a1The total runtime of all phases \u2208 O(n2log(n) + k) method (chosen for reference because it is the easiest method to implement and because of the fast runtime constant on python\u2019s built-in sorting routine), the soft heap-based method from Kaplan et al., and the LOH-based method in this paper are shown in Runtimes of the naive kth best value Xi + Yj occurs. It is somewhat reminiscent of skip lists ). But unlike soft heaps, LOHs can be constructed easily using only an implementation of median-of-medians .The algorithm can be thought of as \u201czooming out\u201d as it pans through the layer products, thereby passing the value threshold at which the ip lists ; howeverk appears in the runtime formula. This is significant because the layer products in q at the end of phase 2 could be returned in their compressed form . The total runtime of phases 0\u20132 is \u2208 O(n). It may be possible to recursively perform X + Y selection on layer products Xu)( + Yv).Phase 3 is the only part of the algorithm in which X and Y are extended on the fly or where several subsequent selections are performed), whereas listing 2 could be adapted to those uses.As noted in theorem 2.8, even fully sorting all of the minimum and maximum layer products would be Phase 0 (which performs LOHification) is the slowest part of the presented python implementation; it would benefit from having a practically faster implementation to perform LOHify.The fast practical performance is partially due to the algorithm\u2019s simplicity and partially due to the contiguous nature of LOHs. Online data structures like soft heap are less easily suited to contiguous access, because they support efficient removal and therefore move pointers to memory rather than moving the contents of the memory.\u03b1 affects performance through the cost of LOHifying and the amount by which the number of generated values overshoots the k minimum values wanted: when \u03b1 \u2248 1, LOHify effectively sorts X and Y, but generates few extra values; k-selection.The choice of k values from X + Y. The new optimal algorithm presented here is faster in practice than the existing soft heap-based optimal algorithm.LOHs can be constructed in linear time and used to produce a theoretically optimal algorithm for selecting the minimal Listing 1.LayerOrderedHeap.py: A class for LOHifying, retrieving layers, and the minimum and maximum value in a layer.# https://stackoverflow.com/questions/10806303/python-implementation-of-median-of-medians-algorithmdef median_of_medians_select: # returns j-th smallest value:if len(L) < 10:L.sortreturn L[j]S = lIndex = 0while lIndex+5 < len(L)-1:S.append(L[lIndex:lIndex+5])lIndex += 5S.append(L[lIndex:])Meds = for subList in S:Meds.append-1)/2)))med = median_of_medians_select-1)/2))L1 = L2 = L3 = for i in L:if i < med:L1.append(i)elif i > med:L3.append(i)else:L2.append(i)if j < len(L1):return median_of_medians_selectelif j < len(L2) + len(L1):return L2[0]else:return median_of_medians_select-len(L2))def partition:n = len(array)right_n = n - left_n# median_of_medians_select argument is index, not size:max_value_in_left = median_of_medians_selectleft = right = for i in range(n):if array[i] < max_value_in_left:left.append(array[i])elif array[i] > max_value_in_left:right.append(array[i])num_at_threshold_in_left = left_n - len(left)left.extendnum_at_threshold_in_right = right_n - len(right)right.extendreturn left, rightdef layer_order_heapify_alpha_eq_2(array):n = len(array)if n == 0:return if n == 1:return arraynew_layer_size = 1layer_sizes = remaining_n = nwhile remaining_n > 0:if remaining_n >= new_layer_size:layer_sizes.append(new_layer_size)else:layer_sizes.append(remaining_n)remaining_n -= new_layer_sizenew_layer_size *= 2result = for i,ls in enumerate(layer_sizes[::-1]):small_vals,large_vals = partition - ls)array = small_valsresult.appendreturn result[::-1]class LayerOrderedHeap:def __init__:self._layers = layer_order_heapify_alpha_eq_2(array)self._min_in_layers = [ min(layer) for layer in self._layers ]self._max_in_layers = [ max(layer) for layer in self._layers ]#self._verifydef __len__(self):return len(self._layers)def _verify(self):for i in range(len(self)-1):assert(self.max(i) <= self.min(i+1))def __getitem__:return self._layers[layer_num]def min:assert( layer_num < len(self) )return self._min_in_layers[layer_num]def max:assert( layer_num < len(self) )return self._max_in_layers[layer_num]def __str__(self):return str(self._layers)Listing 2.CartesianSumSelection.py: A class for efficiently performing selection on X + Y in \u0398(n + k) steps.from LayerOrderedHeap import *import heapqclass CartesianSumSelection:def _min_tuple:# True for min corner, False for max cornerreturn (self._loh_a.min(i) + self._loh_b.min(j), , False)def _max_tuple:# True for min corner, False for max cornerreturn (self._loh_a.max(i) + self._loh_b.max(j), , True)def _in_bounds:return i < len(self._loh_a) and j < len(self._loh_b)def _insert_min_if_in_bounds:if not self._in_bounds:returnif not in self._hull_set:heapq.heappush)self._hull_set.add )def _insert_max_if_in_bounds:if not self._in_bounds:returnif not in self._hull_set:heapq.heappush)self._hull_set.add )def __init__:self._loh_a = LayerOrderedHeap(array_a)self._loh_b = LayerOrderedHeap(array_b)self._hull_heap = [ self._min_tuple ]# False for min:self._hull_set = { }self._num_elements_popped = 0self._layer_products_considered = self._full_cartesian_product_size = len(array_a) * len(array_b)def _pop_next_layer_product(self):result = heapq.heappop(self._hull_heap)val, , is_max = resultself._hull_set.remove )if not is_max:# when min corner is popped, push their own max and neighboring minsself._insert_min_if_in_boundsself._insert_min_if_in_boundsself._insert_max_if_in_boundselse:# when max corner is popped, do not pushself._num_elements_popped += len(self._loh_a[i]) * len(self._loh_b[j])self._layer_products_considered.append )return resultdef select:assert( k <= self._full_cartesian_product_size )while self._num_elements_popped < k:self._pop_next_layer_product# also consider all layer products still in hullfor val, , is_max in self._hull_heap:if is_max:self._num_elements_popped += len(self._loh_a[i]) * len(self._loh_b[j])self._layer_products_considered.append )# generate: values in layer products# Note: this is not always necessary, and could lead to a potentially large speedup.candidates = for val_b in self._loh_b[j] ]print / k) )k_small_vals, large_vals = partitionreturn k_small_valsListing 3.SimplifiedCartesianSumSelection.py: A simplified implementation of Listing 2. This implementation is slower when k \u226a n2; however, it has the same asymptotic runtime for any n and k: \u0398(n + k).from LayerOrderedHeap import *class SimplifiedCartesianSumSelection:def _min_tuple:# True for min corner, False for max cornerreturn (self._loh_a.min(i) + self._loh_b.min(j), , False)def _max_tuple:# True for min corner, False for max cornerreturn (self._loh_a.max(i) + self._loh_b.max(j), , True)def __init__:self._loh_a = LayerOrderedHeap(array_a)self._loh_b = LayerOrderedHeap(array_b)self._full_cartesian_product_size = len(array_a) * len(array_b)self._sorted_corners = sorted for i in range(len(self._loh_a)) for j in range(len(self._loh_b))] + [self._max_tuple for i in range(len(self._loh_a)) for j in range(len(self._loh_b))])def select:assert( k <= self._full_cartesian_product_size )candidates = index_in_sorted = 0num_elements_with_max_corner_popped = 0while num_elements_with_max_corner_popped < k:val, , is_max = self._sorted_corners[index_in_sorted]new_candidates = [ v_a+v_b for v_a in self._loh_a[i] for v_b in self._loh_b[j] ]if is_max:num_elements_with_max_corner_popped += len(new_candidates)else:# Min corners will be popped before corresponding max corner;# this gets a superset of what is needed (just as in phase 2)candidates.extend(new_candidates)index_in_sorted += 1print / k) )k_small_vals, large_vals = partitionreturn k_small_vals"} +{"text": "With the development of distributed generation and the corresponding importance of the P.V. (photovoltaic) system, it is desired to operate a P.V. system efficiently and reliably. To ensure such an operation, a monitoring system is required to diagnose the health of the system. This paper aims to analyze a P.V. system under various operating conditions to identify parameters\u2013derived from the I-V (current-voltage) characteristics of the P.V. system\u2013that could serve as electrical signatures to various faulty operations and facilitate in devising a monitoring algorithm for the system. A model-based approach has been adopted to represent a P.V. system, using a one-diode model of a practical P.V. cell, developed in MATLAB/Simulink. The modelled system comprises two arrays, while each array has two panels in series. It was simulated for various operating conditions: healthy condition represented by STC (Standard Testing Condition), O.C. (open-circuited), soiling, P.S. , H.S. (panels hotspots) and P.D. (panels degradation) conditions. For the analysis of I-V curves under these conditions, six derived parameters were selected: Vte , MCPF (maximum current point factor), Ri (currents ratio), S (slope), and Dv and Di . Using these parameters, data of the actual system under various conditions were compared with its model-generated data for healthy operating conditions. Thresholds were set for each parameter\u2019s value to mark normal operation range. It was observed that almost each considered fault creates a unique combination of sensitive parameters whose values exceeds the pre-defined thresholds, creating an electrical signature that will appear only when the corresponding conditions on the system are achieved. Based on these signatures, an algorithm has been proposed in this study which aims to identify and classify the considered faults. In comparison to other such studies, this work has been focused on those sensitive parameters for faults identification which shows greater sensitivity and contribute more to creation of unique sets of sensitive parameters for considered faults. Energy\u2014being the necessity for economic development\u2014has played an essential role in making up current-day civilization. The living standards of a country can be judged from energy consumption per person living there . Owing tNevertheless, like any other process, a P.V. system operation is vulnerable to certain limitations and faults . These lThe methodology opted in this work, to monitor a P.V. system against various contingent situations, belongs to electrical methods. It relies on the analysis of the I-V characteristics of the P.V. plant, using a model-based approach. By comparing these characteristics of an actual system with its modelled system with help of derived parameters from it, system\u2019s health could be inferenced. Such an approach has been opted in this work using One-diode model with improved parameters for modelling a P.V. system, as it is uncomplicated and accurate enough to represent a practical P.V. plant operation . The modsh) and series (Rs) resistances account for the losses in a practical P.V. cell operation. The equation that describes the One-diode model is given by Eq is charge on an electron, K.B. (1.38065\u00d710\u221223 J/K) is Boltzmann constant and A is the diode ideality factor of a P.V. cell. For several cells connected in series (Ns), to make a panel/module, the equation becomes,While observing Eq , Io is tWhere asIo, is given by Eq and short-circuit current (Iscn) at STC. Eq , and Tn (in Kelvin) represents the temperature of the panel at STC. These equations can be solved using data from the P.V. panels manufacturer datasheet along with irradiance and temperature values for any operating condition. Literature study reveals that a pyranometer at the panel\u2019s surface can estimate the irradiance very well, while temperature of the panels can be estimated using the empirical formula in Reviewers' comments:Reviewer's Responses to Questions Comments to the Author1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0PartlyReviewer #2:\u00a0Yes********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0I Don't KnowReviewer #2:\u00a0Yes********** 3. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a01. There are places in the article that do not indicate which equation to cite, such as the paragraph above Equation 7.2. What does P.S. (3.1) mean in the descriptive paragraph of Figure 6?3. In the analysis of Figure 6, it is mentioned that four different regions can be set for values beyond the predefined thresholds, but it is not clearly described what the four regions are and how to define the boundary between the four regions.4. Appropriately add some relevant descriptions on how to determine the threshold range.5. Add some comparisons with other scholars' work on electrical methods.6. Further elaborate on the specific advantages or innovations of this method.Reviewer #2:\u00a01. The introduction of this submission should be improved further. The key differences between your work and previous studies should be clarified. A point-to-point way is recommended to state the main contributions.2. PV modeling section is very traditional, and this reviewer suggests this section can be shorten properly.3. The writing style of this work likes a technical report, but not a scientific paper.4. A comparison of your method and other work should be carried out.5. Most of the figures have poor quality, such as, lacking of unit.********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1:\u00a0NoReviewer #2:\u00a0Nohttps://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at\u00a0figures@plos.org. Please note that Supporting Information files do not need this step.While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,\u00a0 26 Sep 2021Editor\u2019s comments,Comments to the AuthorThank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE\u2019s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. We look forward to receiving your revised manuscript.1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found athttps://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdfAuthor\u2019s response: The corresponding author, on behalf of all the co-authors, would like to thank the editor for the positive feedback and encouragement. The revised version of the manuscript has been updated according to the guidelines provided by the PLOS ONE style requirements. ________________________________________2. Thank you for stating the following financial disclosure: Author\u2019s response: The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.________________________________________a) Please clarify the sources of funding for your study. List the grants or organizations that supported your study, including funding received from your institution. Author\u2019s response: No funding or any financial grant has been received for conducting this study. ________________________________________b) State what role the funders took in the study. If the funders had no role in your study, please state:Author\u2019s response: The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript________________________________________c) If any authors received a salary from any of your funders, please state which authors and which funders.Author\u2019s response: The authors received no specific funding for this work. ________________________________________http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. 3. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see In your revised cover letter, please address the following prompts:a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail and who has imposed them . Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent.Author\u2019s response: There are no ethical restrictions on sharing a de-identified data set. ________________________________________http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories.b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of acceptable repositories, please see Author\u2019s response: The data set is uploaded in the review as a Supporting Information file. ________________________________________4. Please amend your list of authors on the manuscript to ensure that each author is linked to an affiliation.Author\u2019s response: The list of authors is provided with affiliation in the given order, which is requested to be considered in the revised version of the manuscript. i. Muhammad Adnan Khan1, Affiliation: Research Associate, Center for Advanced Studies in Energy University of Engineering and Technology, Phase 5, opposite to Sui Northern Gas Pipeline office, Postal address 25000, Peshawar. ii. Khalid Khan2* Affiliation: Research Associate, Center for Advanced Studies in Energy University of Engineering and Technology, Phase 5, opposite to Sui Northern Gas Pipeline office, Postal address 25000, Peshawar.iii. Adnan Daud Khan3*Affiliation: Dean Faculty Renewable Energy, Center for Advanced Studies in Energy University of Engineering and Technology, Phase 5, opposite to Sui Northern Gas Pipeline office, Postal address 25000, Peshawar.iv. Zubair Ahmad Khan4Affiliation: Professor at Department of Mechatronics, University of Engineering and Technology, Phase 5, opposite to Sui Northern Gas Pipeline office, Postal address 25000, Peshawar.v. Shahbaz Khan5Affiliation: Lab Engineer at Department of Mechatronics, University of Engineering and Technology, Phase 5, opposite to Sui Northern Gas Pipeline office, Postal address 25000, Peshawar.vi. Muhammad Rizwan Siddiqui6Lecturer at Capital University of Science and technology (CUST), Islamabad Expressway, Kahuta\u060c Road Zone-V Sihala, Islamabad, Islamabad Capital Territory.________________________________________5. PLOS authors have the option to publish the peer review history of their article. If published, this will include your full peer review and any attached files.Author\u2019s response: The authors agree to publish the review history of the article.________________________________________Please carefully address the comments of two reviewers to improve your paper.Editor\u2019s comments,Concern #1:Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.Reviewer #1: PartlyAuthor response: The authors appreciate the positive remarks of the reviewer #1 and would like to reflect on any particular section of the manuscript to improve its quality, if highlighted by the reviewer. Reviewer #2: YesAuthor response: The authors appreciate the positive response of the reviewer #2.________________________________________Concern #2:Has the statistical analysis been performed appropriately and rigorously?Reviewer #1: I Don't KnowAuthor response: The authors would be happy to elaborate further on the techniques used in the article, provided specific questions are asked to be addressed. Reviewer #2: YesAuthor response: The authors appreciate the feedback of the reviewer #2.________________________________________Concern #3:Have the authors made all data underlying the findings in their manuscript fully available?The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g., participant privacy or use of data from a third party\u2014those must be specified.Reviewer #1: YesAuthor response: The authors appreciate the positive feedback of the reviewer #1.Reviewer #2: YesAuthor response: The authors appreciate the positive feedback of the reviewer #2.________________________________________Concern #4:Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1: YesAuthor response: The authors appreciate the positive feedback of the reviewer #1.Reviewer #2: YesAuthor response: The authors appreciate the positive response of the reviewer #2.________________________________________5. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1: 1. There are places in the article that do not indicate which equation to cite, such as the paragraph above Equation 7.Author\u2019s response: The author appreciates reviewer #1 comment on this issue, as it was mistakenly left by author in the earlier draft. This mistake has been rectified and all equations are numbered properly as well as cited properly in the new draft. Equations after correction are highlighted yellow in the new draft.________________________________________2. What does P.S. (3.1) mean in the descriptive paragraph of Figure 6?Author\u2019s response: This question has been answered more properly and the issue has been addressed in the new draft in the last paragraph of methodology section, being highlighted in yellow there. Hope this will answer reviewer\u2019s question.________________________________________3. In the analysis of Figure 6, it is mentioned that four different regions can be set for values beyond the predefined thresholds, but it is not clearly described what the four regions are and how to define the boundary between the four regions.Author\u2019s response: To answer this question, a brief description has been added to the new draft just below fig. (6), in highlighted text. This description has elaborated, in a brief way, on threshold levels and how they were selected. Furthermore, all the four regions regarding \u201cVte\u201d are described and the boundaries between them are clearly defined in that. However, the focus of this paper is on checking the sensitivity of parameters that could serve in creating electrical signatures. Hence, it was found that Vte does the job by responding to various operating conditions in ways different enough from each other to differentiate between faults, which description tells clearly.________________________________________4. Appropriately add some relevant descriptions on how to determine the threshold range.Author\u2019s response: This question has already been answered in question 3. Apart from that, threshold levels are defined more clearly in first paragraph of Methodology section, text highlighted in yellow. Hope that will answer the question.________________________________________5. Add some comparisons with other scholars' work on electrical methods.Author\u2019s response: A comparison with other scholars\u2019 work has been made at the end of results and discussions section. Highlighted in yellow.________________________________________6. Further elaborate on the specific advantages or innovations of this method.Author\u2019s response: It has been answered in the same description where comparison with other scholars\u2019 work has been made, as stated above.________________________________________Reviewer #2: 1. The introduction of this submission should be improved further. The key differences between your work and previous studies should be clarified. A point-to-point way is recommended to state the main contributions.Author\u2019s response: The paper has been reviewed by the author after reviewers\u2019 comments and the content has been improved. Hope it will satisfy the reviewer.________________________________________2. PV modelling section is very traditional, and this reviewer suggests this section can be shortened properly.Author\u2019s response: Author appreciate reviewer\u2019s comment on PV modelling. In response, it is stated that PV modelling contains equations for modelling the related text to describe the terms used in model equations. No extra content has been added and author has aimed to contain modelling section in as small portion as possible.________________________________________3. The writing style of this work likes a technical report, but not a scientific paper.Author\u2019s response: Paper has been revised with minor changes as per reviewers\u2019 comments. Hopefully the new draft resembles more like paper.________________________________________ 4. A comparison of your method and other work should be carried out.Author\u2019s response: Done at the end of Results and Discussion chapter.________________________________________ 5. Most of the figures have poor quality, such as, lacking unit.Author\u2019s response: This issue has been addressed in the new draft, where care has been taken while generating new figures for the paper.AttachmentResponse to Reviewers.docxSubmitted filename: Click here for additional data file. 17 Nov 2021A model-based approach for detecting and identifying faults on the D.C. side of a P.V. system using electrical signatures from I-V characteristicsPONE-D-21-20995R1Dear Dr. Khan,We\u2019re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you\u2019ll receive an e-mail detailing the required amendments. When these have been addressed, you\u2019ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at onepress@plos.org.If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they\u2019ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact Kind regards,Lei Chen, Ph.D.Academic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments:Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the \u201cComments to the Author\u201d section, enter your conflict of interest statement in the \u201cConfidential to Editor\u201d section, and submit your \"Accept\" recommendation.Reviewer #1:\u00a0All comments have been addressedReviewer #2:\u00a0All comments have been addressed********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data\u2014e.g. participant privacy or use of data from a third party\u2014those must be specified. The Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1:\u00a0YesReviewer #2:\u00a0Yes********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1:\u00a0(No Response)Reviewer #2:\u00a0(No Response)********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.If you choose \u201cno\u201d, your identity will remain anonymous but your review may still be made public.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1:\u00a0NoReviewer #2:\u00a0No 23 Dec 2021PONE-D-21-20995R1 A model-based approach for detecting and identifying faults on the D.C. side of a P.V. system using electrical signatures from I-V characteristics Dear Dr. Khan:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofProfessor Lei Chen Academic EditorPLOS ONE"} +{"text": "Mycobacterium smegmatis mc2 155 Siphoviridae temperate phages with 52,935 and 41,876 base pairs in genome length, respectively. HarryOW belongs to the A1 subcluster and Peeb to the G1 subcluster. They were isolated and annotated by students from the SUNY Old Westbury Science and Technology Entry Program.HarryOW and Peeb are Mycobacterium smegmatis mc2 155 Siphoviridae temperate phages with 52,935 and 41,876 base pairs in genome length, respectively. HarryOW belongs to the A1 subcluster and Peeb to the G1 subcluster. They were isolated and annotated by students from the SUNY Old Westbury Science and Technology Entry Program.HarryOW and Peeb are Mycobacterium smegmatis mc2 155 following two cycles of purification and amplification in 7H9 top agar at 37\u00b0C . Isolation was done by enrichment with at 37\u00b0C 1). DNA. DNAMyco at 37\u00b0C . The rawhttp://cobamide2.bio.pitt.edu/computer.htm), and gene prediction tools GLIMMER v3.0 with whom it shares 94.32% gene content and 58 gene phams. The integration cassette genes of Peeb are SEA_PEEB_32, a tyrosine integrase; SEA_PEEB_33, an immunity repressor; and SEA_PEEB_34, an excise. SEA_PEEB_32 and SEA_PEEB_33 are the only two genes in the Peeb genome coded on the reverse strand. SEA_PEEB_54 is a mycobacteriophage mobile element 1 (MPME1) found in other members of this gene pham and of this cluster , a GC content of 66.6%, 62 genes, and an 11-bp 3\u2032 sticky overhang terminus. A total of 23 of the 62 genes are of known function. Peeb is 99% genetically identical to Schiebel (GenBank accession no. cluster .NC_052461), sharing 80.02% gene content similarity and 74 phams. As in many of the A cluster phages, the immunity repressor SEA_HARRYOW_76 is not located adjacent to the serine integrase SEA_HARRYOW_37, and the DNA primase has two overlapping reading frames, namely, SEA_HARRYOW_54 and SEA_HARRYOW_55. One of the three minor tail protein genes, SEA_HARRYOW_6, is located in the left arm of the genome, upstream of the lysin A SEA_HARRYOW_10, lysin B SEA_HARRYOW_11, and the terminase SEA_HARRYOW_12. The other two minor tail protein genes, namely, SEA_HARRYOW_26 and SEA_HARRYOW_28, are located after the tape measure gene SEA_HARRYOW_25.HarryOW is an A1 cluster mycobacteriophage with 52,935 bp, a GC content of 63.8%, 94 genes, and an 11-bp 3\u2032 sticky overhang terminus. A total of 35 of the 94 genes are of known function. Forty genes are on the forward strand, mostly on the left arm of the genome, except for genes SEA_HARRYOW_90, SEA_HARRYOW_91, and SEA_HARRYOW_93. HarryOW is 98% genetically identical to Rutherferd (GenBank accession no. The genome sequences for Peeb and HarryOW have been deposited in GenBank and the Sequence Read Archive see ."} +{"text": "Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Furthermore, a high-quality reference genome allows for precise functional annotation of gene regulatory elements. The rapid advances in genome assembly algorithms and emergence of sequencing technologies with increasingly long reads provide the opportunity for an improved de novo assembly of the sheep reference genome.The domestic sheep (Short-read Illumina (55\u00d7 coverage), long-read Pacific Biosciences (75\u00d7 coverage), and Hi-C data from this ewe retrieved from public databases were combined with an additional 50\u00d7 coverage of Oxford Nanopore data and assembled with canu v1.9. The assembled contigs were scaffolded using Hi-C data with Salsa v2.2, gaps filled with PBsuitev15.8.24, and polished with Nanopolish v0.12.5. After duplicate contig removal with PurgeDups v1.0.1, chromosomes were oriented and polished with 2 rounds of a pipeline that consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly is 2.63 Gb in length and has improved continuity (contig NG50 of 43.18 Mb), with a 19- and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies.The ARS-UI_Ramb_v2.0 assembly is a substantial improvement in contiguity that will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits in sheep. Ovis aries) is a globally important livestock species raised for a variety of purposes including meat, wool, and milk. Domestication likely occurred in multiple events \u223c11,000 years ago [The domestic sheep , is based on a combination of Pacific Biosciences RSII WGS long-read and Illumina short-read sequencing. It has an improved contig NG50 of 2.9 megabases (Mb) and is generally regarded as the official reference assembly for global sheep research.Genome research in sheep holds promise to improve efficiency and sustainability of production and reduce the environmental effects of animal agriculture . The firde novo assembly of the same Rambouillet ewe used for Oar_rambouillet_v1.0, based on \u223c50\u00d7 coverage of nanopore reads (N50 47 kb)\u00a0and\u00a075\u00d7 coverage Pacific Biosciences (PacBio) reads (N50 13 kb).\u00a0The\u00a0new assembly, ARS-UI_Ramb_v2.0, offers a 15-fold improvement in contiguity and increased accuracy, providing a basis for regulatory element annotation in the FAANG project and facilitating the discovery of biological mechanisms that influence traits important in global sheep research and production.The continued maturation of long-read sequencing technologies provided an opportunity to improve upon the sheep reference genome assembly. Because most of the proposed FAANG annotation assays had already been performed on the Rambouillet ewe, lung tissue from the same animal was chosen for DNA extraction. This allowed the use of existing long-read data to supplement new, longer-read, Oxford Nanopore PromethION sequencing. We report a The full-blood Rambouillet ewe used for this genome assembly . The final aqueous phase was transferred to a 50-mL conical tube and the DNA precipitated with 2\u00a0mL of 5 M\u00a0ammonium acetate and 15\u00a0mL of ice-cold 100% ethanol. The DNA was pulled from the alcohol using a Pasteur pipet \u201chook\u201d and placed in 10\u00a0mL of cold 70% ethanol to wash the pellet. The ethanol was poured off and the DNA pellet dried for 20\u201330 minutes, then dissolved in a dark drawer at room temperature for 48 hours in 1\u00a0mL of 10 mM\u00a0Tris-Cl pH 8.5. Library preparation for Oxford Nanopore long-read sequencing was performed with an LSK-109 template preparation kit as recommended by the manufacturer with modifications as described by Logsdon [DNA was extracted from \u223c50\u00a0mg of lung tissue using phenol:chloroform-based method as described . Briefly Logsdon . The lig Logsdon . Fastq fSequence data used in the previous Oar_rambouillet_v1.0 assembly were retrieved from the SRA listed under project number PRJNA414087 . PacBio RRID:SCR_015880) through the trimmed reads stage of assembly. Parameters for contig construction were set as \u201cbatOptions = -dg 4 -db 4 -mo 1000\u201d [Contigs were assembled with Oxford Nanopore and PacBio reads generated as described above using canu v1.8 [Two Hi-C datasets from liver tissue from 2 different library preparations were retrieved as described above. The Hi-C reads were first aligned to the polished contigs using the Arima Genomics mapping pipeline . This pi_006646) . Salsa v_006646) .The Hi-C reads were aligned to the scaffolded assembly with the Arima Genomics mapping pipeline and then processed with PretextMap to visually evaluate the scaffolds as a contact map in PretextView . The scaRRID:SCR_016157) [RRID:SCR_012954) [RRID:SCR_010761) [RRID:SCR_005227) [k-mer consequences of variant calls and filters unsupported variants.Gap filling was completed with pbsuite v15.8.24 using both the PacBio and Oxford Nanopore reads. Nanopolish v0.12.5 with the_016157) was used_016157) . The chr_012954) . The mit_010761) variant _005227) , which ePRJEB35292, specifically under SRA run numbers ERR3665717 (skin), ERR3728435 , ERR3650379 (pituitary), ERR3665711 (lymph node mesenteric), and ERR3650373 (abomasum pylorus). Reads were trimmed with Trim Galore v0.6.4 [RNA sequencing data were generated from 5 tissues including skin, thalamus, pituitary, lymph node (mesenteric), and abomasum pylorus collected from the animal used to assemble the reference genome. Details regarding the RNA isolation protocol, library preparation, and sequencing as well as the raw data can be found in GenBank under BioProject e v0.6.4 and alige v0.6.4 . Indels e v0.6.4 .The annotation for ARS-UI_Ramb_v2.0, NCBI Ovis aries Annotation Release 104, is available in RefSeq and other NCBI genome resources .Here we also provide a liftover of the annotation for Oar_rambouillet_v1.0 onto ARS-UI_Ramb_v2.0. The annotation used for the liftover was NCBI v103 GCF_002742125.1_Oar_rambouillet_v1.0_genomic.fna.gz. The GFF3 format gene annotation file was prepared for processing using liftOff v1.5.2 [RRID:SCR_016582) [PRJNA414087 and PRJEB35292) to estimate transcript-level expression for every tissue as transcript per million mapped reads (TPM) and compared across the 3 annotations.To compare the breakdown of transcripts captured by the 3 annotations , we generated transcript expression estimates using Kallisto v0.44.0 . For theGCF_016772045.1, and statistics of contigs and scaffolds following initial polishing, scaffolding with Hi-C data, and manual editing, gap-filling, and final polishing, are shown in Table\u00a0The 4 flow cells of PromethION data produced 136 Gb of WGS sequence (\u223c51\u00d7 coverage) in reads having a read N50 of 47\u00a0kb. The initial generation of contigs used this data as well as 198.1 Gb of RSII data with a read N50 of 12.9\u00a0kb. The ARS-UI_Ramb_v2.0 assembly was submitted to NCBI GenBank under accession number The Themis-ASM pipeline was implk-mer\u2013based quality value and error rates improved with ARS-UI_Ramb_v2.0 compared with Oar_rambouillet_v1.0 and Oar_v4.0. This is also reflected in the proportion of complete assembly based on k-mers (merCompleteness), which is similar between ARS-UI_Ramb_v2.0 and Oar_rambouillet_v1.0 and both are higher than Oar_v4.0. Furthermore, the single-nucletide polymorphism (SNP) and indel quality value (baseQV) were greatest overall in ARS-UI_Ramb_v2.0 (41.84), followed by Oar_rambouillet_v1.0 (40.69) and Oar_v4.0 (32.40). The percentage of short reads not mapped to the genome was \u22641% in all 3 assemblies.The RRID:SCR_015008) v5.2.2 scores with the cetartiodactyla_odb10 dataset and metaeuk gene predictor [The completeness of ARS-UI_Ramb_v2.0 was evaluated by examining the presence or absence of evolutionarily conserved genes in each assembly using BUSCO in the ARS-UI_Ramb_v2.0 assembly were characterized and compared with Oar_rambouillet_v1.0 by mapping 150\u00a0bp paired-end RNA-seq data from skin, thalamus, pituitary, lymph node (mesenteric), and abomasum pylorus generated from the same animal used to assemble the reference genome Table . In all The ARS-UI_Ramb_v2.0 annotation represents a substantial improvement over the annotation on Oar_rambouillet_v1.0. For example, for ARS-UI_Ramb_v2.0 16,500 coding genes have an ortholog to human , and the BUSCO scores demonstrate that 99.1% of the gene models (cetartiodactyla_odb10) are complete in the new annotation versus 98.8% in the previous one. The annotation for ARS-UI_Ramb_v2.0 includes Iso-Sequencing for 8 tissues to improve contiguity of gene models, and CAGE sequencing for 56 tissues to define transcription start sites, that were not used to annotate Oar_rambouillet_v1.0.Using Kallisto we compared the number of expressed transcripts, for the RNA-Seq dataset of 61 tissue samples from Benz2616, across the 3 annotations . There was a considerable increase in the number of transcripts captured by the annotation for ARS-UI_Ramb_v2.0 60,064) relative to Oar_Rambouillet_v1.0 42,058) and the liftover annotation (Ramb1LO2) lifting over the annotation for Oar_Rambouillet_v1.0 onto ARS-UI_Ramb_v2.0. According to the annotation report provided by NCBI , 70% of The ARS-UI_Ramb_v2.0 genome assembly serves as a reference for genetic investigation of traits important in sheep research and production across the world. This genome is assembled from the same animal used in the Ovine FAANG Project, which provides a high-quality basis for epigenetic annotation to serve the international sheep genomics community and scientific community at large.https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Ovis_aries/104/. Ovis aries Annotation Release 104 is also available in RefSeq and other NCBI genome resources [The datasets supporting the results of this article are available in the RefSeq repository, GCF_016772045.1, and in the GigaScience Database . RNA seqesources .Supplementary File 1. Annotation lifted over from Oar_rambouillet_v1.0 to ARS-UI_Ramb_v2.0.Supplementary File 2. RNA file from annotation lift over.Supplementary File 3. Scripts from annotation lift over.giab096_GIGA-D-21-00165_Original_SubmissionClick here for additional data file.giab096_GIGA-D-21-00165_Revision_1Click here for additional data file.giab096_GIGA-D-21-00165_Revision_2Click here for additional data file.giab096_Response_to_Reviewer_Comments_Revision_1Click here for additional data file.giab096_Reviewer_1_Report_Original_SubmissionAaron Shafer -- 8/30/2021 ReviewedClick here for additional data file.giab096_Reviewer_2_Report_Original_SubmissionElizabeth Ross -- 10/10/2021 ReviewedClick here for additional data file.giab096_Supplemental_FilesClick here for additional data file.bp: base pairs; BUSCO: Benchmarking Universal Single-Copy Orthologs; CAGE: cap analysis gene expression; EDTA: ethylenediaminetetraacetic acid; FAANG: Ovine Functional Annotation of Animal Genomes; Gb: gigabase pairs; kb: kilobase pairs; Mb: megabase pairs; NCBI: National Center for Biotechnology Information; PacBio: Pacific Biosciences; SDS: sodium dodecyl sulfate; SNP: single-nucletide polymorphism; USDA: United States Department of Agriculture; WGS: whole-genome shotgun.Funding was provided by Agriculture and Food Research Initiative Competitive grants from the USDA National Institute of Food and Agriculture supporting improvements of the sheep genomes (2013\u201367015-21228) and FAANG activities . Additional funding was received from the International Sheep Genome Consortium (217201191442) and infrastructure support from a grant to R. Gibbs from the NIH NHGRI Large-Scale Sequencing Program (U54 HG003273).D.M.B. was supported by appropriated USDA CRIS project 5090\u201331000-026\u201300-D. T.P.L.S. was supported by appropriated USDA CRIS Project 3040\u201331000-100\u201300D. B.D.R. was supported by appropriated USDA CRIS Project 8042\u201331000-001\u201300-D. The USDA does not endorse any products or services. Mentioning of trade names is for information purposes only. The USDA is an equal opportunity employer.B.M.M., T.P.L.S., D.M.B., and B.D.R. conceptualized the study. B.M.M., N.E.C., M.P.H., and T.P.L.S. selected the animal and collected samples. K.W. and S.C.M. facilitated the generation of RSII, short-read, and Hi-C data. T.P.L.S. facilitated the nanopore long-read data generation. K.M.D., D.M.B., T.P.L.S., B.M.M., and B.D.R. performed the genome assembly, scaffolding, RNA-sequencing alignment, polishing, and quality control. M.S. and E.L.C. contributed the section describing the LiftOff annotation and comparative analysis of transcript expression estimates for the 3 annotations. K.M.D., D.M.B., T.P.L.S., B.M.M., and B.D.R. generated tables and figures and drafted the manuscript. K.M.D., D.M.B., K.W., S.C.M., N.E.C., T.P.L.S., B.M.M., and B.D.R. edited the manuscript. All authors contributed to the article and approved the final version.The authors have no conflicts of interest."} +{"text": "Single-cell RNA sequencing has led to unprecedented levels of data complexity. Although several computational platforms are available, performing data analyses for multiple datasets remains a significant challenge. Here, we provide a comprehensive analytical protocol to interrogate multiple datasets on SingCellaR, an analysis package in R. This tool can be applied to general single-cell transcriptome analyses. We demonstrate steps for data analyses and visualization using bespoke pipelines, in conjunction with existing analysis tools to study human hematopoietic stem and progenitor cells.For complete details on the use and execution of this protocol, please refer to \u2022SingCellaR is an open-source analysis tool for single-cell RNA sequencing data\u2022SingCellaR facilitates various analyses, including data integration and comparison\u2022Step-by-step analysis and visualization using SingCellaR for human hematopoietic cells Single-cell RNA sequencing has led to unprecedented levels of data complexity. Although several computational platforms are available, performing data analyses for multiple datasets remains a significant challenge. Here, we provide a comprehensive analytical protocol to interrogate multiple datasets on SingCellaR, an analysis package in R. This tool can be applied to general single-cell transcriptome analyses. We demonstrate steps for data analyses and visualization using bespoke pipelines, in conjunction with existing analysis tools to study human hematopoietic stem and progenitor cells. This protocol describes a method for analyzing single-cell RNA sequencing (scRNA-seq) datasets using an R package called SingCellaR. In addition to standard functions , similar to those performed by available R and Python analysis tools like Seurat , MonocleSingCellaR supports multiple modalities for visualization, including tSNE, UMAP, force-directed graph (FDG) in two- or three-dimensional embeddings, diffusion maps, violin and bubble plots, and heatmaps. Cells can be identified on these plots according to user-defined parameters, such as\u00a0cluster, donor, tissue of origin, disease state, etc., by accessing relevant information from\u00a0the\u00a0SingCellaR object. Multiple signature gene scores can also be superimposed on the same embeddings. For example, visualization of sets of canonical genes used to distinguish different blood cell lineages can help exploration of the cell types contained within a dataset independently of cell clustering algorithms. To annotate cell types and states, SingCellaR uses gene set enrichment analysis to calculate enrichment scores for user-defined, curated gene sets. This system can be used alongside manual inspection for canonical marker genes, or other\u00a0existing algorithms .We recently demonstrated the utility of the SingCellaR pipeline in a study of human hematopoiesis. Studying the site- and stage-specific changes of normal hematopoiesis over human development is crucial to understanding the origin of disorders that tend to emerge at specific ages. We analyzed scRNA-seq datasets from hematopoietic stem and progenitor cells (HSPCs) from five different tissues sampled across four stages of the human lifetime . This stHere we present a comprehensive protocol for the analytical pipeline demonstrating step-by-step data analysis and visualization as employed in the recent publication . We coveTiming: 5\u201310\u00a0minIn this protocol, we use scRNA-seq datasets of hematopoietic stem and progenitor cells (HSPCs) from human tissues across different developmental stages, including early fetal liver (eFL), matched fetal liver (FL) and bone marrow (FBM) isolated from the same fetuses, pediatric bone\u00a0marrow (PBM), and adult bone marrow (ABM). Here, human fetal liver samples from first\u00a0and second trimester are referred to eFL and FL respectively. Table\u00a0S1 in \u00a0shows thhttps://doi.org/10.5281/zenodo.5879071. Zenodo (https://zenodo.org/) is an open and citable repository for sharing curation and publication of data and software from research outputs, regardless of data format, size, and access restrictions or license.We have provided pre-processed datasets and available gene sets on Zenodo: 1.cellranger pipeline outputs of samples from different tissues: the file \u2018cellranger_output.zip\u2019 is a zipped folder containing the cellranger pipeline results of 9 samples ;2.human signature gene sets that are used in this protocol;3.codes (Code.zip) used in this protocol;4.generated R objects from this protocol.The compiled datasets consist of:https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) contains analysis pipelines used to align sequencing reads to the reference genome, generate feature-barcode matrices, and perform other downstream analyses. We performed cellranger count as described in https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count to obtain feature-barcode matrices for each library. The outputs of the pipeline include a Matrix Market file of gene expression (matrix.mtx.gz), cell barcode (barcodes.tsv.gz) and gene metadata (features.tsv.gz) files.) {>\u00a0install.packages(\"devtools\")> }> if(!require(BiocManager)) {>\u00a0install.packages(\"BiocManager\")> }> devtools::install_githubCRITICAL: We tested SingCellaR installation on macOS Mojave and Catalina, and Windows 10.Before we begin, the user has to install SingCellaR and other dependency packages. R packages are hosted across multiple repositories, namely Comprehensive R Archive Network (CRAN), Bioconductor, and Github. For a brief introduction, CRAN is the R central software repository for the latest and previous versions of the R distribution and packages. Bioconductor is the R repository to facilitate R packages developed for biological data analysis. GitHub is a commercial repository that hosts services for individuals and teams for software version control and collaboration. The R functions \u2018install.packages\u2019, \u2018BiocManager::install\u2019, and \u2018devtools::install_github\u2019 will be used to install packages from CRAN, Bioconductor, and Github, respectively. Prior to installation, the function \u2018if(!require(\"package_name\"))\u2019 will be used to check if the package has already been installed on a computer, and installation will proceed for packages not yet installed on the computer.2.a.> library(reticulate)> conda_create> py_install> py_installModules required for the force-directed graph analysis.b.> py_installCRITICAL: We tested the fa2 python module for the force-directed graph analysis using Python versions 2.7, 3.6 and 3.8. Using Conda environment is recommended in conjunction with reticulate package. Conda (https://docs.conda.io/en/latest/) is a virtual environment management system for Python. With Conda, the user can create, remove, and update environments that have different versions of Python packages installed in them. This flexibility is especially helpful on devices in which the user does not have administrative privileges to install Python packages on the device and compile version control for specific packages.Module required for doublet removal using Scrublet.Install required python modules by running the following R code:3.a.> if(!require(harmony)) {>\u00a0install.packages(\"harmony\")> }harmony \u2013 required for data integration using Harmony method .> if(!reb.> if(!require(AUCell)) {>\u00a0BiocManager::install(\"AUCell\")> }AUCell \u2013 required for computing AUCell scores with specified gene signatures .> if) {>\u00a0install.packages> }> if(!require(doRNG)) {>\u00a0install.packages(\"doRNG\")> }doParallel and doRNG \u2013 required for parallel processing in AUCell analysis.d.> if(!require(DAseq)) {>\u00a0devtools::install_github(\"KlugerLab/DAseq\")> }DAseq \u2013 required for the analysis of differential abundance .> if(!ree.> if(!require(destiny)) {>\u00a0BiocManager::install(\"destiny\")}destiny \u2013 required for the trajectory analysis using diffusion map .> ifNote: The destiny package is not available for Bioconductor version 3.13. The user can install this package from GitHub.> install_githubOptional: SingCellaR supports multiple dataset integration and batch correction methods including Scanorama Seurat CCA/RPCA \u2013 required for the data integration.i.> install.packages(\"rliger\")rliger \u2013 required for the data integration.j.> if )\u00a0install.packages(\"BiocManager\")> BiocManager::install(\"sva\")ComBat \u2013 required for the batch removal.k.> if )\u00a0install.packages(\"BiocManager\")> BiocManager::install(\"limma\")Limma \u2013 required for the batch removal.Install required R packages by running the following R code:R version 4 or higher is required with other R packages, as shown in the Timing: 10\u201315\u00a0min for each sample, depending on the number of cells being analyzed4.Load SingCellaR package into R environment:> library(SingCellaR)> setwd(\"./SingCellaR_objects\")Note: \u2018./SingCellaR_objects\u2019 is a local folder for this analysis. The user can change the folder name to a suitable file path in a local computer or server.5.Create SingCellaR object. SingCellaR object is an extension of the SingleCellExperiment (periment object f> data_matrices_dir<-\"./cellranger_output/eFL1/\"> eFL_1<-new(\"SingCellaR\")> eFL_1@dir_path_10x_matrix<-data_matrices_dir> eFL_1@sample_uniq_id<-\"eFL_1\"> load_matrices_from_cellranger> eFL_1This step creates a SingCellaR object for each sample and performs quality control (QC) to identify\u00a0cells that qualify for further downstream analyses. We demonstrate the selection process\u00a0of high-quality cells using multiple QC plots, data normalization, and identifying highly variable genes. The process starts from reading in the input files for each sample generated directly from the cellranger pipeline. Here, we show an early fetal liver (eFL_1) dataset as an example.CRITICAL: The \u2018cellranger.version\u2019 parameter is required to be compatible with the cellranger pipeline output file. The cellranger output file \u2018features.tsv.gz\u2019 for gene features is generated from Cell Ranger version 3 and above, whereas version 2 of Cell Ranger creates the file \u2018genes.tsv.gz\u2019.6.Create cell metadata. Cell metadata will be created. Rows represent cells and columns represent variables. Variables computed in this step include the number of UMIs and detected genes per cell, and percentage of mitochondrial gene expression for each cell.> process_cells_annotationa.mito_genes_start_with: Gene names starting with \u2018MT-\u2019 are used as a set of mitochondrial genes for human and \u2018mt-\u2019 for mouse samples.Note: The cell metadata can be accessed using the function \u2018get_cells_annotation(eFL_1)\u2019 or eFL_1@meta.data. The user can manually add additional information to the columns of the cell metadata.The following parameter is required:7.Visualize QC matrices. QC matrices computed in step 6 can be explored using the plotting functions:a.> plot_cells_annotationHistogram A.> plot_b.> plot_cells_annotationBoxplot B.> plot_c.> plot_UMIs_vs_Detected_genes(eFL_1)Plot of the number of UMIs versus the number of detected genes per cell C.> plot_Now the SingCellaR object \u2013 eFL_1 is created.8.Annotate cell quality, identify expressed genes, and assign cell and gene status into metadata. After visualizing QC matrices in step 7, the user can specify filtering parameters using the observed number of UMIs and detected genes per cell, and percentage of mitochondrial gene expression. The function \u2018filter_cells_and_genes\u2019 assigns a new column named IsPassed that will be added into the cell metadata. Cells that pass QC will be annotated as TRUE. Expressed genes will be identified in this step and the column named IsExpress will be added into the gene metadata. Genes expressed above and below the user-defined threshold will be annotated as TRUE or FALSE. Although all original cells and genes are retained in the metadata and gene expression matrix in this step, these annotations will be used to subset cells and expressed genes for further downstream analyses. The number of cells passing QC thresholds will be shown on the R console after running the following code:> filter_cells_and_genesa.min_UMIs: The lower threshold for UMI counts, above which cells are annotated as high-quality. To be used in conjunction with max_UMIs argument. Default value is 1,000.b.max_UMIs: The upper threshold for UMI counts, below which cells are annotated as high-quality. To be used in conjunction with min_UMIs argument. Default value is 30,000.c.min_detected_genes: The lower threshold for the number of expressed genes, above which cells are annotated as high-quality. To be used in conjunction with max_detected_genes argument. Default value is 1,000.d.max_detected_genes: The upper threshold for the number of expressed genes, below which cells are annotated as high-quality. To be used in conjunction with min_detected_genes argument. Default value is 8,000.e.genes_with_expressing_cells: The lower threshold for the number of cells in which a gene is expressed (UMI >=1), above which, the gene will be annotated as expressed. Default value is\u00a010.f.isRemovedDoublets: If set to TRUE (default), doublets will be removed prior to downstream analyses.Note: Parameters used for filtering out cells with low quality can be varied across tissues and organs from different datasets. For example, the percentage threshold for mitochondrial gene expression, \u2018max_percent_mito\u2019 can be set higher for liver tissues The following parameters are described:9.Normalize UMI counts. SingCellaR scales UMI counts by normalizing each library size to 10,000 or mean library size.> normalize_UMIsThe following parameter is required:use.scaled.factor: When set to TRUE, the gene expression values will be multiplied by 10,000 (by default) and normalized against the library size of each cell. The user can change the scale factor value using the scale.factor parameter. If set to FALSE, the function will use the mean of library size across all cells as the scale factor.CRITICAL: Using use.scaled.factor=TRUE is recommended for 10\u00d7 genomics data. The user should consider specifying use.scaled.factor=FALSE for scRNA-seq data generated from plate-based protocols, e.g., Smart-seq2 as the fitting method for gene expression and coefficient of variation to identify highly variable genes. The GLM is suitable for modeling log-normal data from a sparse normalized gene expression matrix. A column named IsVarGenes is added to the gene metadata and genes identified as highly variable are annotated as TRUE, while all other genes are annotated as FALSE. The number of genes used to fit in the model and the number of identified variable genes will be shown after running the following code:> get_variable_genes_by_fitting_GLM_modela.mean_expr_cutoff: The mean normalized expression value, above which, the genes are identified as highly variable. Default value is 0.1.b.disp_zscore_cutoff: The dispersion of z-score, above which, the genes are identified as highly variable. Default value is 0.1.Note: In this step, we used lower cut-off values to increase the number of detected highly variable genes per sample for the downstream analyses.The following parameters are required:11.Save the R object for further analyses.> save12.Repeat the analyses for the rest of samples. R codes are available at Zenodo: https://doi.org/10.5281/zenodo.5879071.Pause point: The user can pause the analysis after pre-processing each sample.Timing: 15\u201330\u00a0min for each group, 1\u20132\u00a0h for all stages13.Load SingCellaR package.> library(SingCellaR)14.Integrate pre-processed biological replicates. The user will initialize the integrated SingCellaR class object \u2018SingCellaR_Int\u2019 and assign a unique identifier prior to merging two datasets using the \u2018preprocess_integration\u2019 function.> eFL <- new(\"SingCellaR_Int\")> eFL@dir_path_SingCellR_object_files<-\"./\"> eFL@SingCellR_object_files=c> preprocess_integration(eFL)> eFL15.Annotate cell quality and expressed genes. Filtering process has been already performed separately for each sample (see step 8), therefore the filtering parameters for this step will be set to include all cells. From the filtering output below, all cells will be retained, after running the following code:> filter_cells_and_genes16.Normalize and scale UMI counts.> normalize_UMIsNote: See step 9 for details of required parameters.17.Regress out confounding factors. The normalized and scaled gene expression values from step 16 will be adjusted by regressing out cell-to-cell variation in gene expression values due to confounding factors . To this end, SingCellaR implements the \u2018lmFit\u2019 function from the R package limma ge limma , SingCela.residualModelFormulaStr: The formula format used to regress out confounding factors. The names of variables defined have to be the same as the column names of the cell metadata.Note: The user can change the residualModelFormulaStr parameter and perform the following steps down to step 23 to explore the effect on cell clustering by specifying different sets of confounding factors. For example, the user can set residualModelFormulaStr\u00a0= \"\u223cUMI_count+percent_mito\" to compare with residualModelFormulaStr\u00a0= \"\u223cUMI_count+percent_mito+sampleID\" to explore the effect of sample.The following parameter is required:18.Identify highly variable genes. The number of genes used for fitting the GLM model and the number of highly variable genes will be identified after running the following code:> get_variable_genes_by_fitting_GLM_modelNote: See step 10 for details of required parameters.19.Remove selected genes. Here, we remove mitochondrial and ribosomal genes from highly variable genes identified from step 18 to avoid the skewed effect of ribosomal and mitochondrial gene expression in downstream analyses. The number of genes that are excluded will be shown after running the following code:> remove_unwanted_genes_from_variable_gene_set)Note: The human.ribosomal-mitochondrial.genes.gmt file can be downloaded from Zenodo: https://doi.org/10.5281/zenodo.5879071 under the folder Human_genesets.20.Visualize highly variable genes A.Figure\u00a0> plot_variable_genes(eFL)21.Perform principal component analysis (PCA). To interpret the relationship across single cells, dimensionality reduction methods are required to reduce high dimensionality data to the visualizable two- or three-dimensional space. In PCA, the reduced dimensional space is represented by principal components. The top PCs will capture most of the variance of the dataset. Here, we perform linear dimensionality reduction using PCA and then bring forward the most informative PCs for further nonlinear dimensionality reduction to visualize cells in a two-dimensional space. To this end, highly variable genes identified from steps 18\u201319 and visualized in step 20 will be used for PCA using the \u2018runPCA\u2019 function, a wrapper function for the \u2018irlba\u2019 function from the irlba package (http://bwlewis.github.io/irlba/).> SingCellaR::runPCAa.use.components: The number of principal components (PCs) to estimate. Default value is 50.b.use.regressout.data: If set to TRUE (default), the adjusted gene expression values from step 17 will be used.The following parameters are required:22.Visualize principal components. The elbow plot is used to determine the number of PCs to be included for further dimensionality reduction analyses 23.Perform nonlinear dimensionality reduction analyses. Running nonlinear dimension reduction on all highly variable genes requires high computational resources and processing time. Hence, using identified PCs from step 22 for nonlinear dimension reduction analysis is a standard technique for scRNA-seq analysis. Nonlinear dimension reduction analysis is suitable for capturing cellular heterogeneity (https://cran.r-project.org/web/packages/uwot/). Based on the elbow plot shown in step 22, we select the first 30 PCs for UMAP analysis.> SingCellaR::runUMAPogeneity . Here, wogeneity by runnia.dim_reduction_method: The method name for the linear dimension reduction.b.n.dims.use: The number of selected PCs as determined in step 22.c.n.neighbors: The number of neighboring cells used for manifold approximation. Default value is 30.d.uwot.metric: The distance metric name. Default is \u2018cosine\u2019.Note: The user can also apply the t-Distributed Stochastic Neighbor Embedding (tSNE) approach using the \u2018runTSNE\u2019 function. The reduced dimension coordinates for UMAP and tSNE can be accessed using functions \u2018get_umap.result\u2019 and \u2018get_tsne.result\u2019 respectively.The following parameters are required:24.Visualize cell lineages on low dimensional space. To explore whether the cells in each lineage are clustered in close proximity, we will visualize the UMAP result with the expression of multi-lineage gene sets using the \u2018plot_umap_label_by_multiple_gene_sets\u2019 function ,\u00a0custom_color\u00a0= c,\u00a0isNormalizedByHouseKeeping\u00a0= F,\u00a0point.size\u00a0= 1)function C. Here, a.gmt.file: Path to the file containing the gene signatures in GMT format.b.show_gene_sets: The names of the gene signatures to plot on UMAP.c.custom_color: The color assignment to each signature specified in \u2018show_gene_sets\u2019.d.isNormalisedByHouseKeeping: When set to TRUE (default), the gene expression values of the individual genes of each gene signature specified will be normalized by the housekeeping genes. The housekeeping genes are defined as the top 100 genes with the highest total gene expression values across all cells.e.point.size: Size of the data points on UMAP plot. Default value is 2.Note: Lineage gene sets (human.signature.genes.v1.gmt) are available at Zenodo: https://doi.org/10.5281/zenodo.5879071 under Human_genesets folder and from original publication is used for cell clustering.> identifyClustersa.n.dims.use: The number of PCs to use. Default number is 30.b.dim_reduction_method: The dimensionality reduction analysis name.c.n.neighbors: The number of neighboring cells. This number may be the same as specified in step 23 if UMAP is used. Default number is 30.d.knn.metric: The distance metric, \u2018euclidean\u2019 is used by default. Another option is \u2018cosine\u2019.Note: The cluster metadata for each cell can be accessed using the \u2018get_cluster\u2019 function.The following parameters are required:26.Visualize clusters on low dimensional space. Louvain clusters can be shown on UMAP using the \u2018plot_umap_label_by_clusters\u2019 function function D.> plot_a.show_method: The clustering detection name used as in step 25.b.mark.clusters: If set to TRUE (default) , cluster identifiers will be shown on the plot.The following parameters are required:27.Identify cluster-specific genes. The user can identify marker genes, which are particularly expressed in each cluster using the \u2018findMarkerGenes\u2019 function. Differentially expressed gene analysis between one cluster against all other clusters is performed using the nonparametric Wilcoxon test on normalized expression values for the comparison of expression level and Fisher\u2019s exact test for the comparison of expressing cell frequency . This process is iterated for each cluster against all other clusters, therefore the processing time in this step is dependent on the number of cells and clusters. By default, the minimum log2 fold change \u2018min.log2FC\u2019 parameter is set to 0.5 and the minimum fraction of expressing cells in each cluster \u2018min.expFraction\u2019 parameter is set to 0.3.> findMarkerGenesrequency . P-valuea.cluster.type: The clustering detection method used in step 25.The following parameter is required:28.Save R object for further analyses.> save29.Repeat the integration process for all biological replicates of FL, FBM, and PBM samples. There is only one sample for ABM. Therefore, data integration is not required for this sample at this step. All R codes provided for each integration are available at Zenodo: https://doi.org/10.5281/zenodo.5879071.Pause point: The user can pause the analysis after integrating the biological replicates for each developmental stage and save the results in multiple SingCellaR objects.This step integrates the individual R objects from pre-processed biological or technical replicates generated from step 12. Here, we illustrate the integration of two early fetal liver samples collected from two donors .13.Load Timing: 2\u20133 hThe aim of integrating all samples is to assess the existence of batch or donor-specific effects that are confounding factors contributing to differences in gene expression profile across samples. Examples of batch effect include differences in library preparation methods, sequencing batch, and donor or sample ID . If the 30.Load SingCellaR package.> library(SingCellaR)31.Initialize the SingCellaR_Int object and merge datasets generated from step 29.> Human_HSPC <- new(\"SingCellaR_Int\")> Human_HSPC@dir_path_SingCellR_object_files<-\"./\"> Human_HSPC@SingCellR_object_files=c> preprocess_integration(Human_HSPC)> Human_HSPC32.Annotate cell quality. Input parameters for integrated samples have been set to include all cells. The user should observe that there are no cells being filtered out after running the following code:> filter_cells_and_genes33.Incorporate donor and sequencing batch information into cell metadata. This information is required to perform the batch correction.> meta.data <- read.delim> Human_HSPC@meta.data<- meta.dataGeneral examples of data integration include integrating samples from healthy donors and patients and from> head(Human_HSPC@meta.data)34.Normalize and scale UMI counts.> normalize_UMIs35.Identify highly variable genes.> get_variable_genes_by_fitting_GLM_model36.Remove ribosomal and mitochondrial genes.> remove_unwanted_genes_from_variable_gene_set)37.Visualize highly variable genes.> plot_variable_genes(Human_HSPC)38.Run PCA.> SingCellaR::runPCA39.Visualize principal components. Based on the elbow plot, the first 40 PCs will be used for data integration.> plot_PCA_Elbowplot(Human_HSPC)40.Integrate data using Supervised Harmony. We introduce Supervised Harmony, a method for data integration implemented in SingCellaR. Supervised Harmony can be performed using the \u2018runSupervised_Harmony\u2019 function. This method is an adaptation of Harmony method ,\u00a0\u00a0\u00a0\u00a0n.dims.use\u00a0= 40,\u00a0\u00a0\u00a0\u00a0hcl.height.cutoff\u00a0= 0.3,\u00a0\u00a0\u00a0\u00a0harmony.max.iter\u00a0= 20,\u00a0\u00a0\u00a0\u00a0n.seed\u00a0= 6)y method . More dey method . Here, sa.covariates: The name(s) of the covariate(s) specified as batch effect to be adjusted. The names should be the same as the column names of the cell metadata.b.n.dims.use: The number of PCs as determined from step 39 to be used in this step.c.hcl.height.cutoff: The cutree cut-off value for hierarchical clustering. Default value is 0.25.d.harmony.max.iter: The maximum number of rounds to run harmony. Default value is 10.e.n.seed: The random seed number generator. Default value is 1.CRITICAL: Before running Supervised Harmony method, the \u2018findMarkerGenes\u2019 function must be performed for each developmental stage analysis (see step 27). The seed number (random number generator) and software version can vary across different devices. Hence, the user may notice variations in the rotation of the plots and clusters, which can be verified and visualized using lineage genes (see step 24).The following parameters are required:41.Nonlinear dimension reduction analysis.> SingCellaR::runUMAPUpdated meta.data can be checked by running:> supervised_harmony.UMAP<-get_umap.result(Human_HSPC)> saveRDS42.Integrate data using Harmony. SingCellaR also implements a wrapper function for Harmony integration method (> library(harmony)> SingCellaR::runHarmony,\u00a0\u00a0\u00a0\u00a0\u00a0n.dims.use\u00a0= 40,\u00a0\u00a0\u00a0\u00a0\u00a0harmony.max.iter\u00a0= 20,\u00a0\u00a0\u00a0\u00a0\u00a0n.seed\u00a0= 6)n method . Harmonya.covariates: The name(s) of the covariate(s) specified as batch effect to be adjusted. The names should be the same as the column names of the cell metadata.b.n.dims.use: The number of PCs as determined from step 39 to be used in this step.c.harmony.max.iter: The maximum number of rounds to run harmony. Default value is 10.d.n.seed: The random seed number generator. Default value is 1.> SingCellaR::runUMAP> harmony.UMAP<-get_umap.result(Human_HSPC)> saveRDSThe UMAP analysis result from Harmony integration will be saved. This UMAP object contains cell metadata and UMAP coordinates that will be used to compare with the results from other integrative methods.The following parameters are required:43.Integrate data using Seurat. SingCellaR implements two wrapper functions for Seurat integration . Due to the fast integration of using RPCA, in this protocol, we will demonstrate the function \u2018runSeuratIntegration_with_rpca\u2019 as an example. However, the user should try Seurat CCA to make a comparison of the integrative results. The user can find how to use the function \u2018runSeuratIntegration\u2019 from SingCellaR\u2019s vignette. After the integration, the UMAP analysis from Seurat RPCA integration will be performed to obtain the embedding.> library(Seurat)> meta.data<-get_cells_annotation(Human_HSPC)> rownames(meta.data)<-meta.data$Cell> SingCellaR::runSeuratIntegration_with_rpcaegration . First, a.Seurat.metadata: The cell metadata.b.n.dims.use: The number of PCs as determined from step 39 to be used in this step.c.Seurat.split.by: The indicated feature name found in the cell metadata for splitting samples for integration.d.Use.SingCellaR.varGenes: If set to TRUE, the highly variable genes identified by SingCellaR will be used. If set to FALSE, the highly variable genes will be identified using Seurat. Default value is FALSE.> SingCellaR::runUMAP> Seurat_rpca.UMAP<-get_umap.result(Human_HSPC)> saveRDSNext, the UMAP analysis from Seurat RPCA integration will be performed and saved. This UMAP object will be used to compare with the results from other integrative methods.The following parameters are required:44.Integrate data using Scanorama. SingCellaR implements a wrapper function for Scanorama integration (egration . Scanora> runScanorama(Human_HSPC)> runPCA> SingCellaR::runUMAP> Scanorama.UMAP<-get_umap.result(Human_HSPC)> saveRDS45.Integrate data using Limma batch correction method. To perform Limma analysis > runPCA> SingCellaR::runUMAP> Limma.UMAP<-get_umap.result(Human_HSPC)> saveRDS46.Assign a cell type to single cells using the AUCell analysis. In this step, we will perform AUCell analysis (> library(AUCell)> exprMatrix <- get_umi_count(Human_HSPC)> human_HSPCs_cells_rankings <- AUCell_buildRankingsanalysis with seva.exprMat: The raw expression count matrix. This can be retrieved from the SingCellaR object using the \u2018get_umi_count\u2019 function.b.nCores: The number of cores to use for parallel processing. The maximum number of cores is dependent on the user\u2019s device. Default value is 1.c.plotStats: If set to TRUE (default), the expression statistics will be summarized and plotted in the histogram and boxplots.Note: This step may be time-consuming. The user is advised to save the output of this step using the following code:> save> human_HSPCs.AUCells.score <- Run_AUCellNext, the AUCell analysis will be performed using the \u2018Run_AUCell\u2019 function.The following parameters are required:d.AUCell_buildRankings.file: The input file name from the AUCell rankings.e.geneSets.gmt.file: The GMT file name that contains gene sets.> SingCellaR::runUMAP>plot_umap_label_by_AUCell_score,Human_HSPC.AUCells.Score,AUCell_cutoff=0.15,point.size\u00a0= 0.5)To explore the AUCell scores on UMAP plots, the user can run UMAP analysis using different types of integrative methods. This step is to identify the AUCell cut-off score for a particular cell type. The example below shows the \u2018plot_umap_label_by_AUCell_score\u2019 function that will be used to plot the myeloid AUCell scores A.> SingC> Human_HSPC.CellType<-Human_HSPC.AUCells.Score> Human_HSPC.CellType$CellType<-\"\"> Human_HSPC.CellType$CellType[Human_HSPC.CellType$HSPC_MPP >0.2]<-\"HSC_MPP\"> Human_HSPC.CellType$CellType[Human_HSPC.CellType$Erythroid >0.15]<-\"Erythroid\"> Human_HSPC.CellType$CellType[Human_HSPC.CellType$Myeloid >0.15]<-\"Myeloid\"> Human_HSPC.CellType$CellType[Human_HSPC.CellType$Lymphoid >0.15]<-\"Lymphoid\"> Human_HSPC.CellType$CellType[Human_HSPC.CellType$Megakaryocyte >0.15]<-\"Megakaryocyte\"> Human_HSPC.CellType$CellType[Human_HSPC.CellType$Eosinophil_Basophil_Mast >0.15]<-\"Eo_Ba_Mast\"> Human_HSPC.CellType$CellType[Human_HSPC.CellType$Endothelial_cells\u00a0>\u00a00.15]<-\"Endothelial_cell\"Next, cells with high AUCell scores for each cell type will be assigned.> table(Human_HSPC.CellType$CellType)> saveRDSThe user can explore the number of cells with high AUCell scores for each cell type using the function below and the Human_HSPC.CellType data frame object will be saved for use as the reference to perform benchmarking explained in the next step.The following parameters are required:The UMAP analysis result from Supervised Harmony integration will be saved. This UMAP object will be used to compare with the results from other integrative methods (see steps below).47.Benchmark distinct integrative methods using LISI and kBET methods. Next, we assess whether single cells with identified cell types derived from the AUCell analysis are clustered well across covariate variables . SingCellaR provides the wrapper functions for a Local Inverse Simpson\u2019s Index (LISI) (k-nearest-neighbor batch-effect test (kBET) (> library(lisi)> reference.celltypes<-\"Human_HSPC.CellType_from_AUC_High.rds\"> integrative.umaps<-c> method.names<-c> runLISIx (LISI) and k-net (kBET) to measut (kBET) B.> libraa.lisi_label1: The covariate variable name of interest such as batch or donor. Default value is donor.b.lisi_label2: The variable name that represents ground truth or high AUC score cell type. Default value is CellType.c.reference.celltype.rds.file: The RDS file name that contains cell type information.d.integrative.umap.rds.files: The RDS file names that contain UMAP coordinate information generated by different integrative methods.e.integrative.method.names: The integrative method names that represent in the same order as in integrative.umap.rds.files.f.IsShowPlot: If set to TRUE (default), the iLISI and cLISI scores will be plotted.> library(kBET)> reference.celltypes<-\"Human_HSPC.CellType_from_AUC_High.rds\"> integrative.umaps<-c> method.names<-c>kBET_result<-runKBETSecond, the \u2018runKBET\u2019 function is performed as shown below. This function will calculate kBET scores across different integrative methods and return a data frame that can be used for plotting.The following parameters are required:g.Covariate_variable_name: The covariate variable name of interest such as batch or donor. Default value is donor.h.reference.celltype.rds.file: The RDS file name that contains cell type information.i.integrative.umap.rds.files: The RDS file names that contain UMAP coordinate information generated by different integrative methods.j.integrative.method.names: The integrative method names that represent in the same order as in integrative.umap.rds.files.k.n.sample: The downsample size of data points used in kBET analysis. Default value is 1,000.Note: This step may be time-consuming, depending on the number of cells downsampled for kBET analysis.> level_order <- factor)> ggplot)\u00a0+\u00a0\u00a0+ geom_boxplot+theme_classic+theme(axis.title.x=element_blank)Next, kBET scores across integrative methods will be plotted using the \u2018ggplot\u2019 function C.> levelIn this step, we illustrate how to benchmark integrative results generated from different methods using the wrapper functions for LISI and kBET analyses implemented in SingCellaR. We show the objective measurement of integration for each method using iLISI and cLISI scores B and kBEThe following parameters are required:48.Visualize selected features and cell lineages on low dimensional space. Here, we will assess whether the data integration was performed successfully. To this end, we annotate the UMAP by sample ID, donor type, sequencing batch, and lineage signature genes. After running the following codes, we observe that cells are clustered by cell lineage, while sample ID, donor type and sequencing batch effects are successfully corrected. These indicate that data integration and batch correction was effective in eliminating batch effect, while enabling functionally related cell to be clustered in close proximity.a.> plot_umap_label_by_a_feature_of_interestAnnotate UMAP plot by sample ID A.> plot_b.> plot_umap_label_by_a_feature_of_interestAnnotate UMAP plot by donor B.> plot_c.> plot_umap_label_by_a_feature_of_interestAnnotate UMAP plot by sequencing batch C.> plot_i.feature: The feature to annotate on UMAP plot. The feature name should match the column name of the cell metadata.ii.point.size: Size of the data points on UMAP. Default value is 1.iii.mark.feature: If set to TRUE (default), the feature name will be shown on the plot.The following parameters are required:d.> plot_umap_label_by_multiple_gene_sets,\u00a0custom_color\u00a0= c,\u00a0isNormalizedByHouseKeeping\u00a0= F,\u00a0point.size\u00a0= 1)Annotate UMAP plot by lineages genes D.> plot_49.Detect and assign clusters.> identifyClustersNote: Information in this step and the required parameters have been detailed in step 25 with the additional \u2018integrative_method\u2019 parameter specified to indicate the data integration and batch correction method used in step 40.50.Visualize clusters on low dimensional space. A.Figure\u00a0> plot_umap_label_by_clusters51.Identify cluster-specific genes. This step will perform differential gene expression analysis to identify marker genes per each cluster.> findMarkerGenesNote: See details in step 27. This step will take time to run on the fully integrated datasets depending on the number of cells and identified clusters.52.Save the integrated R object for further analyses.> savePause point: The user can save the integrative SingCellaR_Int object for further downstream analyses.Timing: 1.5\u20132 hhttps://doi.org/10.5281/zenodo.5879071 in GMT file format and are also available in Table\u00a0S3 from the original publication (53.Load the SingCellaR package.> library(SingCellaR)54.Load the integrated R object generated from step 52.> load(file\u00a0= \"./Human_HSPC_All.SingCellaR.rdata\")55.Generate the pre-ranked genes. For each cluster, differential gene expression analysis is performed erformed against a.cluster.type: The clustering method name.b.fishers_exact_test: The cut-off p-value. Default value is 0.1.c.min.expFraction: The fraction of expressing cells, above which, the gene will be included for GSEA. Default value is 0.01.d.min.log2FC: The log2 fold change, above which, the gene will be included for GSEA. Default value is 0.1.Note: The processing time of this step depends on the number of cells and clusters. The user is advised to save the output of this step using the following code:> saveThe following parameter is required:56.Perform GSEA. For each cluster, the ranked genes are subjected to GSEA to assess the enrichment for all curated hematopoietic gene sets.> fgsea_Results <- Run_fGSEA_for_multiple_comparisonsa.GSEAPrerankedGenes_list: The object containing the ranked genes for each cluster generated from step 55.b.gmt.file: Curated gene sets in GMT file format.Note: Here, we curated gene sets encompassing 75 hematopoietic signatures, but the user can also generate other customized gene sets in GMT file format as the input for GSEA. Each line of the GMT file represents one gene set. Specifically, the first column represents the name of the gene set, the second column represents the description of the gene set,\u00a0and the third column onwards represents the genes that constitute the gene set, whereby\u00a0each column represents one gene. The GMT file should be saved in tab-delimited format.The following parameters are required:57.Visualize GSEA results. A heatmap is used to observe and compare enrichment scores of each gene set (rows) across all clusters (columns). This visualization allows the user to annotate a cell type identity and cell states to each cluster based on the degree of enrichment of the curated gene sets. ne sets. B.> plot_a.isApplyCutoff: If set to TRUE, only the normalized enrichment scores (NES) of gene sets with adjusted P-values below the user-defined values in \u2018adjusted_pval\u2019 argument will be displayed on the heatmap. Default is FALSE.b.use_pvalues_for_clustering: If set to TRUE (default), the -log10 will be used instead of NES to cluster rows and/or columns.c.show_NES_score: If set to TRUE (default), NES will be displayed on the heatmap.d.fontsize_row: The font size of the gene set names along the rows of the heatmap. Default value is 5.e.adjusted_pval: The value, below which, NES will be displayed on the heatmap. The default value is 0.25.f.show_only_NES_positive_score: If set to TRUE, only NES\u00a0>\u00a00 will be displayed on the heatmap. Default is FALSE.g.format.digits: The number of significant digits to be used for numeric display on the heatmap. Default value is 2.h.clustering_method: The clustering method for clustering the rows and/or columns. Default is \"complete\".i.clustering_distance_rows: The distance metric to use when clustering the rows. Default is \"euclidean\".j.clustering_distance_cols: The distance metric to use when clustering the columns. Default is \"euclidean\".k.show_text_for_ns: If set to TRUE (default), non-significant (ns) NES will be displayed on the heatmap.The following parameters are required:58.Visualize selected canonical marker genes using UMAP. One or more individual genes can be plotted on UMAP using the \u2018plot_umap_label_by_genes\u2019 function )# Myeloid progenitor> plot_umap_label_by_genes)# Erythroid progenitor> plot_umap_label_by_genes)# Megakaryocytic progenitor> plot_umap_label_by_genes)# B lymphoid progenitor> plot_umap_label_by_genes)# Dendritic precursor> plot_umap_label_by_genes)# Eosinophil/Basophil/Mast progenitor> plot_umap_label_by_genes)# Endothelial cells> plot_umap_label_by_genes)function A.# HSC/Ma.gene_list: A vector of one or more gene names to plot.The following parameter is required:The aim of cell type annotation is to assign a cell type identity to each cluster. The expression of selected marker genes can be visualized and explored across the different clusters, either using UMAP, dotplot, heatmap, or violin plots . Neverthlication .53.Load 59.Visualize selected canonical marker genes using bubble plot > plot_bubble_for_genes_per_clusterble plot B. One ora.cluster.type: The clustering method name used to identify and assign the cell clusters.b.gene_list: A vector of one or more gene names to plot.c.show.percent: If set to TRUE, the percentage of expressing cells for respective genes in each cluster are displayed on the dotplot. Default is FALSE.The following parameters are required:60.Visualize identified marker genes for each cluster using heatmap. One or more individual genes can be plotted using a heatmap with the \u2018plot_heatmap_for_marker_genes\u2019 function. Each gene is represented on each row of the output.> plot_heatmap_for_marker_genesa.cluster.type: The name of the clustering method used to identify and assign the cell clusters.b.n.TopGenes: The number of top genes for each cluster to plot. Default value is 5.The following parameters are required:61.Export top marker genes for each cluster. The top marker genes with statistical analysis results can be exported to the text file format.> export_marker_genes_to_tablea.cluster.type: The clustering method name used to identify and assign the cell clusters.b.n.TopGenes: The number of top genes for each cluster. Default value is 5.c.min.log2FC: The log2FC value, above which, genes will be included. Default value is 0.5.d.min.expFraction: The fraction of expressing cells, above which, genes will be included. Default value is 0.3.e.write.to.file: The file path to be exported.The following parameters are required:Timing: 2\u20133 h62.Load SingCellaR and required R packages. Here, the user can load the integrated R object saved from step 52.> library(SingCellaR)> library(AUCell)> library(ggplot2)> library(DAseq)> source('./utilis.R')63.Load the integrated R object generated from step 52.> load(file\u00a0= \"./Human_HSPC_All.SingCellaR.rdata\")64.Build AUCell gene rankings. The user will have to create the ranked gene list using the function \u2018AUCell_buildRankings\u2019 implemented in AUCell package.> set.seed(2021)> exprMatrix <- get_umi_count(Human_HSPC)> human_HSPCs_cells_rankings <- AUCell_buildRankingsa.exprMat: The raw expression count matrix. This can be retrieved from the SingCellaR object using the \u2018get_umi_count\u2019 function.b.nCores: The number of cores to use for parallel processing. The maximum number of cores is dependent on the user\u2019s device. Default value is 1.c.plotStats: If set to TRUE (default), the expression statistics will be summarized and plotted in the histogram and boxplots.Note: This step may be time-consuming. The user is advised to save the output of this step using the following code:> saveThe following parameters are required:65.Calculate AUCell scores. AUCell scores for each cell will be computed using the ranked genes from the previous step for the provided hematopoietic gene sets.> set.seed(2021)> human_HSPCs.AUCells.score <- Run_AUCellOptional: The user is advised to save the AUCell scores for further analysis.> save66.Visualize AUCell scores. The user can visualize AUCell scores for a given gene signature on specific clusters on the UMAP embedding. Here, we will use HSC/MPP gene signature on cluster 1 as an example example A. We obsa.AUCell_gene_set_name: The name of the gene signature to plot. The signature name specified here must be the same as the gene signature name in the GMT file provided in step 65.b.AUCell_score: The R object created from computing AUCell scores in step 65.c.selected.limited.clusters: Cells in selected cluster IDs will be displayed with the AUCell scores.d.IsLimitedAUCscoreByClusters: If set to TRUE, the AUCell scores will only be displayed for selected clusters as specified using the \u2018selected.limited.clusters\u2019 argument. Default is FALSE.e.AUCell_cutoff: The AUCell score threshold, above which, the scores will be displayed. The higher the score threshold, the more stringent the threshold. Default is 0.Note: AUCell cutoff score is arbitrary. To explore the AUCell cutoff score for each gene signature, the user can plot the score distribution using ggplot2 and manually explore the suitable threshold.The following parameters are required:67.Differential abundance testing. We use DAseq ,\u00a0\u00a0\u00a0\u00a0labels.2\u00a0= c,\u00a0\u00a0\u00a0\u00a0path\u00a0= \"./\",\u00a0\u00a0\u00a0\u00a0outputname\u00a0= \"eFL_vs_FL.pdf\")se DAseq to perfose DAseq B as an ea.groupA and groupB: The group names for integrated samples or an individual sample name.b.labels.1 and labels.2: The sample IDs of groupA and groupB, respectively.c.path: The folder path to save the output file.d.outputname: The output file name.The following parameters are required:The user can calculate the enrichment of specific gene sets assigned for an individual cell. We incorporated AUCell score analysis into SinTiming: 1\u20131.5 hFrom the annotation of cell types assigned in the cell type annotation steps, the user can further investigate the direction of cellular differentiation trajectories. The user can trace immature to more differentiated cell populations and understand the functional relationship between different cell populations in terms of cellular maturity. It is noteworthy that current trajectory analysis requires the user to identify the starting point (immature cell state), in this case, HSC/MPP. Hence, the cell annotations inferred from previous steps will be helpful to infer the primitive cell clusters. SingCellaR supports two approaches of trajectory analysis, namely force-directed graph (FDG) and diff68.Load SingCellaR package.> library(SingCellaR)69.Load the integrated R object generated from step 52.> load(file\u00a0= \"./Human_HSPC_All.SingCellaR.rdata\")70.Run force-directed graph analysis. The user can use the \u2018runFA2_ForceDirectedGraph\u2019 function to build the force-directed graph layout (embeddings). The layout can be annotated using various features, including cell lineage signature genes. Here, we use the Supervised harmony embeddings to generate force-directed graph layout.> runFA2_ForceDirectedGrapha.useIntegrativeEmbeddings: If set to TRUE, the data integration or batch correction embeddings will be used in conjunction with \u2018integrative_method\u2019 argument. Default is FALSE.b.integrative_method: The data integration or batch correction method name.c.knn.metric: The distance metric.d.n.dims.use: The number of PCs from \u2018integrative_method\u2019. If \u2018useIntegrativeEmbedding\u2019 is set to FALSE, the PCA analysis result is used. Default value is 30.e.n.neighbors: The number of neighboring cells.f.n.seed: The random number generator. Default value is 1.g.fa2_n_iter: The number of iterations for analyzing the \u2018networkx\u2019 graph. Default value is 1,000.The following parameters are required:71.> plot_forceDirectedGraph_label_by_clustersVisualize trajectories by Louvain clustering A.> plot_a.show_method: The clustering method name.The following parameter is required:72.> plot_forceDirectedGraph_label_by_multiple_gene_sets,\u00a0\u00a0custom_color\u00a0= c,\u00a0\u00a0isNormalizedByHouseKeeping\u00a0= F,\u00a0edge.size=0,\u00a0edge.color\u00a0= \"#FFFFFF\",\u00a0vertex.size\u00a0= 0.2,\u00a0showEdge\u00a0= F,\u00a0showLegend\u00a0= T)Visualize trajectories by using multiple lineages gene sets B.> plot_a.gmt.file: Path to the file containing the gene signatures in GMT format.b.show_gene_sets: The vector of gene signature names to show on the plot. The names must be the same names as found in the \u2018gmt.file\u2019.c.custom_color: The assigned colors for gene signatures in \u2018show_gene_set\u2019.d.isNormalizedByHouseKeeping: When set to TRUE (default), the gene expression values of each gene signature specified will be normalized by the housekeeping genes. The housekeeping genes are defined as the top 100 genes with the highest total gene expression values across all cells.e.edge.size: The size of the edges connecting the nodes. Default value is 0.2.f.edge.color: The color of the edges. Default color is gray.g.vertex.size: The size of the nodes. Default value is 1.5.h.showEdge: When set to TRUE (default), the edges will be displayed.i.showLegend: When set to TRUE (default), the legend will be displayed.The following parameters are required:73.Load SingCellaR and destiny R packages.> library(SingCellaR)> library(destiny)74.Load the integrated R object generated from step 52.> load(file\u00a0= \"./Human_HSPC_All.SingCellaR.rdata\")75.Run diffusion map analysis. The user can use the \u2018runDiffusionMap\u2019 function to generate the diffusion map layout (embeddings). The layout can be annotated using various features, including cell lineage signature genes. We will use the Supervised harmony embeddings to generate the diffusion map layout.> runDiffusionMapa.useIntegrativeEmbeddings: If set to TRUE, the data integration or batch correction embeddings will be used in conjunction with \u2018integrative_method\u2019 argument. Default is FALSE.b.integrative_method: The data integration or batch correction method name.c.n.dims.use: The number of PCs from \u2018integrative_method\u2019. If \u2018useIntegrativeEmbedding\u2019 is set to FALSE, the PCA result will be used. Default value is 30.d.n.seed: The random number generator. Default value is 1.The following parameters are required:76.> plot_diffusionmap_label_by_clustersVisualize trajectories by Louvain clustering C.> plot_a.show_method: The clustering method name.The following parameter is required:77.> plot_diffusionmap_label_by_multiple_gene_sets,\u00a0\u00a0custom_color\u00a0= c,\u00a0\u00a0isNormalizedByHouseKeeping\u00a0= F)Visualize trajectories by multiple lineages genes D.> plot_a.gmt.file: Path to the file containing the gene signatures in GMT format.b.show_gene_sets: The vector names of gene signatures to show in the plot. The names must be the same names as found in the gmt.file.c.custom_color: The assigned colors for gene signatures in \u2018show_gene_set\u2019.d.isNormalizedByHouseKeeping: When set to TRUE (default), the gene expression values of the individual genes of each gene signature specified will be normalized by the housekeeping genes. The housekeeping genes are defined as the top 100 genes with the highest total gene expression values across all cells.The following parameters are required:78.Load SingCellaR and required R packages.> library(SingCellaR)> library(monocle3)> library(ggplot2)> library(ComplexHeatmap)> library(circlize)> library(RColorBrewer)> source('./utilis.R')79.Load the integrated R object generated from step 52.> load(file\u00a0= \"./Human_HSPC_All.SingCellaR.rdata\")80.Prepare input files for Monocle3. The required objects include the expression matrix of raw counts, cell cluster metadata, and gene metadata.# Expression matrix> cells.used <- Human_HSPC@sc.clusters$Cell> umi <- get_umi_count(Human_HSPC)> used.umi <- umi> expression_matrix <- used.umi> dim(expression_matrix) # check the dimension of object# Cell cluster metadata> cell_metadata <- Human_HSPC@sc.clusters> rownames(cell_metadata) <- cell_metadata$Cell# Gene metadata> gene_annotation <- as.data.frame(rownames(used.umi))> colnames(gene_annotation) <- \"gene_short_name\"> rownames(gene_annotation) <- gene_annotation$gene_short_name81.Create Monocle3 object.> cds <- new_cell_data_set82.Integrate Monocle3 and SingCellaR results. Monocle3 normalizes the raw gene counts, and then performs PCA. The user can run the default workflow as suggested by Monocle3 tutorial. In this step, we will replace Monocle3\u2019s UMAP embeddings and add cluster information derived from the SingCellaR object.# Pre-process Monocle3 object> cds <- preprocess_cds> cds <- align_cds(cds)# Substitute Monocle3's embeddings with SingCellaR's embeddings> embeddings <-\u00a0>Human_HSPC@SupervisedHarmony.embeddings> cds@int_colData@listData$reducedDims$Aligned <- embeddings# Nonlinear dimension reduction> cds <- reduce_dimension# Identify and assign clusters> cds <- cluster_cells# Substitute Monocle3's UMAP embeddings with SingCellaR's embedding> newcds<- cds # change monocle3 objects name> SingCellaR.umap <-,c]> Human_HSPC@umap.result> rownames(umap) <- umap$Cell> umap$Cell <- NULL> newcds@int_colData$reducedDims$UMAP <- umap# Substitute Monocle3's cluster identity with SingCellaR's cluster identity> anno.clusters <- Human_HSPC@sc.clusters$louvain_cluster> names(anno.clusters) <- Human_HSPC@sc.clusters$Cell> newcds@clusters$UMAP$clusters <- anno.clusters83.Generate trajectory graph and order cells by pseudotime. To learn the cell differentiation trajectories, the user will use the \u2018learn_graph\u2019 function provided by Monocle3. By default, Monocle3 uses a 'self-defined' node to perform the pseudotime analysis. Thus, the user will need to define the root node, i.e., the most immature cluster. To identify the root node, the user can use the \u2018get_earliest_principal_node\u2019 function. Based on the previous analyses, the user can select \u2018cl1\u2019, the HSC/MPP cluster, as the starting point of the trajectory.> newcds <- learn_graph(newcds)# Apply function to retrieve root node> root.nodes <- get_earliest_principal_node# Order cells by pseudotime relative to root node> newcds <- order_cells# Save R object> save84.Visualize trajectory paths on UMAP 85.Visualize pseudotime on UMAP 86.Visualize pseudotime on SingCellaR FDG ,]> fa2\u00a0<- Human_HSPC@fa2_graph.layout> fa2.used <- fa2# Extract the pseudotime information> new_data <- data.frame)> new_data$Cell <- rownames(new_data)> new_data <- new_data# Integrate pseudotime with FDG embeddings> fa2.used <- fa2.used> colnames(fa2.used) <- c> fa2.dat <- cbind# Plot FDG> ggplot)\u00a0+\u00a0geom_point)\u00a0+\u00a0scale_color_viridis_c+\u00a0theme_classic\u00a0+\u00a0xlab(\"FDG1\")\u00a0+\u00a0ylab(\"FDG2\")87.Visualize the expression of selected genes along the paths. We plot erythroid lineage genes as the example.a.# Retrieve UMAP coordinates and annotate with cluster information> sc.clusters <-Human_HSPC@sc.clusters> umap.results <- Human_HSPC@umap.result> umap.results <- merge### Add developmental stage information> umap.results$stage[umap.results$sampleID %in% c]<- \"eFL\"> umap.results$stage[umap.results$sampleID %in% c(\"1_ABM_1\")]<- \"ABM\"> umap.results$stage[umap.results$sampleID %in% c]<- \"FL\"> umap.results$stage[umap.results$sampleID %in% c]<- \"FBM\"> umap.results$stage[umap.results$sampleID %in% c]<- \"PBM\"Add developmental stages information to the metadata.b.> Ery.path <- cDefine the path for the erythroid lineage based on the FDG, diffusion map, and Monocle3. We selected the path \u2018cl1-cl7-cl12-cl3\u2019 for the erythroid lineage.c.> umap.results.Ery <- umap.results> cells.eFL <- umap.results.Ery$Cell[umap.results.Ery$stage\u00a0== \"eFL\"]> cells.FL <- umap.results.Ery$Cell[umap.results.Ery$stage\u00a0== \"FL\"]> cells.FBM <- umap.results.Ery$Cell[umap.results.Ery$stage\u00a0== \"FBM\"]> cells.PBM <- umap.results.Ery$Cell[umap.results.Ery$stage\u00a0== \"PBM\"]> cells.ABM <- umap.results.Ery$Cell[umap.results.Ery$stage\u00a0== \"ABM\"]Extract cells from the erythroid trajectory for all stages.d.> genes.E <- c> matrix <- newcds@assays@data$counts> pt.matrix<-\u00a0matrix),order(pseudotime(newcds))]Extract genes known to be involved in the erythroid trajectory based on the pseudotime.e.> pt.matrix.eFL <- ExtractMatrix> pt.matrix.FL <- ExtractMatrix> pt.matrix.FBM <- ExtractMatrix> pt.matrix.PBM <- ExtractMatrix> pt.matrix.ABM <- ExtractMatrixExtract gene expression matrix for each group of cells.f.> ht1\u00a0<- plot_development_heatmap> ht2\u00a0<- plot_development_heatmap> ht3\u00a0<- plot_development_heatmap> ht4\u00a0<- plot_development_heatmap> ht5\u00a0<- plot_development_heatmap> ht.full <- ht1+ht2+ht3+ht4+ht5> ht.fullPlot gene expression heatmap along the path of the different developmental stages H.> ht1\u00a0 Ery.eFL <- ExtractCells(selected.cells\u00a0= cells.eFL)> Ery.FL <- ExtractCells(selected.cells\u00a0= cells.FL)> Ery.FBM <- ExtractCells(selected.cells\u00a0= cells.FBM)> Ery.PBM <- ExtractCells(selected.cells\u00a0= cells.PBM)> Ery.ABM <- ExtractCells(selected.cells\u00a0= cells.ABM)> matrix <- newcds@assays@data$counts> matrix.total <-Matrix::colSums(matrix)> norm.matrix <-(t(t(matrix)/matrix.total))\u221710000> expr.eFL <- norm.matrix> expr.eFL <- reshape2::melt(as.matrix(expr.eFL))> colnames(expr.eFL) <- c> expr.eFL$Stage <- \"eFL\"> expr.FL <- norm.matrix> expr.FL <- reshape2::melt(as.matrix(expr.FL))> colnames(expr.FL) <- c> expr.FL$Stage <- \"FL\"> expr.FBM <- norm.matrix> expr.FBM <- reshape2::melt(as.matrix(expr.FBM))> colnames(expr.FBM) <- c> expr.FBM$Stage <- \"FBM\"> expr.PaedBM <- norm.matrix> expr.PaedBM <- reshape2::melt(as.matrix(expr.PaedBM))> colnames(expr.PaedBM) <- c> expr.PaedBM$Stage <- \"PBM\"> expr.AdultBM <- norm.matrix> expr.AdultBM <- reshape2::melt(as.matrix(expr.AdultBM))> colnames(expr.AdultBM) <- c> expr.AdultBM$Stage <- \"ABM\"> expr.Ery <- rbindExtract gene expression from downsampled cells along the path from different developmental stages and pseudotime from \u2018newcds\u2019 object from step 83.h.> pseudotime <- as.data.frame(pseudotime(newcds))> colnames(pseudotime) <- \"pseudotime\"> pseudotime$Cell <- rownames(pseudotime)> pseudotime$pseudotime[pseudotime$pseudotime %in% \"Inf\"] <- 0> pseudotime <- pseudotimeExtract the pseudotime information from Monocle3 results.i.> expr.Ery <- mergeMerge gene expression data with pseudotime analysis results.j.> plot_genes> plot_genesVisualize selected erythroid gene expression along the path I.> plot_The step-by-step protocols describe an analysis pipeline used in a recent publication . Here, wSingCellaR requires signature gene sets to perform the cell type annotation analysis. Thus, the user would have to compile and curate customized gene sets for the relevant system of interest. In this protocol, we provide 75 gene sets curated from previous studies relevant to hematopoiesis. SingCellaR still lacks 'automatic object transformation' to interact with other existing packages, such as Seurat. However, SingCellaR uses the SingleCellExperiment object, the standard object for storing single-cell experimental data in R. Therefore, the gene expression matrix and cell metadata can be extracted simply from the SingleCellExperiment object. This issue will be improved when SingCellaR is updated to the next version to support more interactions with other packages and ensure compatibility with relevant R packages incorporated in SingCellaR.The user may encounter the following error when executing the function \u2018runFA2_ForceDirectedGraph\u2019:Error in runFA2_ForceDirectedGraphThere are two potentially problems: the fa2 package is not installed; and the R environmental path for FA2 module in python is not found by R.FA2 installation.The fa2 package can be installed as suggested in the Note: The fa2 package is not compatible with python 3.9 or higher versions.Conda environment is recommended by using \u2018conda_create\u2019 function after loading the reticulate package.python version configuration.### Set the python version into R environment.use_python(\"/miniconda3/envs/r-reticulate/bin/python\")Note: The user must change the python path as shown here to Conda-specific path found in the user\u2019s computer.### Open \u2018\u223c/.Renviron\u2019 in the terminal and add the following code:RETICULATE_PATH=\"/miniconda3/envs/r-reticulate/bin/python\"### Restart R session and then use below code to check:Sys.which(\"python\")\"/miniconda3/envs/r-reticulate/bin/python\" should be shown on the console.The user can use the following code to configure the python path:https://rstudio.github.io/reticulate/articles/versions.html.The user can refer to Python version configuration tutorial in the reticulate R package found in this URL: The user may find this error when performing the runScanorama(Human_HSPC) function:\u201cError in runScanorama(Human_HSPC) : The scanorama python module is not installed!. Please install using pip \u201dThe scanorama package can be installed as suggested in the SingCellaR installation section. The Python environment configuration can be found in Problem 1.UMAP/FDG plots may show different rotations from this protocol. This is caused by different software versions for generating plots and the seed number setting.This can be solved by setting a seed number (n.seed parameter) found in runUMAP and runFA2_ForceDirectedGraph functions.The user may encounter running time and memory issues when performing the AUCell_buildRankings function for a large-scale dataset.The user can use the alternative function named \u2018Build_AUCell_Rankings_Fast\u2019 to speed up running time and use less memory for ranking gene expression for each cell.The kBET score is used to benchmark the integration results from different integrative methods. The user may encounter slightly different kBET scores from this protocol. This is due to the different seed number settings and the number of subsampling cells for kBET analysis. More running time and memory will be used if the user sets the high number of the downsample size in kBET analysis.This issue can be solved by setting the seed number prior to running kBET using the \u2018set.seed\u2019 function. The user can subsample and fix the number of cells for the kBET analysis using the n.sample parameter described in the \u2018runKBET\u2019 function.supat.thongjuea@imm.ox.ac.uk).Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Supat Thongjuea (This study did not generate new unique reagents."} +{"text": "Scientific Reportshttps://doi.org/10.1038/s41598-021-95102-7, published online 04 August 2021Correction to: The Code availability section in the original version of this Article was incomplete.\u201cCodes will be uploaded soon to [Insert URL].\u201dnow reads:https://github.com/kyuchoi/graph_neural_network_suicide_prediction\u201d\u201cThe codes are available at\u00a0The original Article has been corrected."} +{"text": "Scientific Reports 10.1038/s41598-021-02943-3, published online 08 December 2021Correction to: The original version of this Article contained an error in the link in the Code Availability section where,https://github.com/sblabbioinformatics/BG4_CUT_and_Tag_sc.\u201d\u201cScripts and general codes for G4-CUT&Tag data analysis are available at now reads:https://github.com/sblab-bioinformatics/BG4_CUT_and_Tag_sc.\u201d\u201cScripts and general codes for G4-CUT&Tag data analysis are available at The original Article has been corrected."} +{"text": "This article describes a method for creating applications for cluster computing systems using the parallel BSF-skeleton based on the original BSF (Bulk Synchronous Farm) model of parallel computations developed by the author earlier. This model uses the master/slave paradigm. The main advantage of the BSF model is that it allows to estimate the scalability of a parallel algorithm before its implementation. Another important feature of the BSF model is the representation of problem data in the form of lists that greatly simplifies the logic of building applications. The BSF-skeleton is designed for creating parallel programs in C++ using the MPI library. The scope of the BSF-skeleton is iterative numerical algorithms of high computational complexity. The BSF-skeleton has the following distinctive features.\u2022 The BSF-skeleton completely encapsulates all aspects that are associated with parallelizing a program.\u2022 The BSF-skeleton allows error-free compilation at all stages of application development.\u2022 The BSF-skeleton supports OpenMP programming model and workflows. Specifications Tablefarm skeleton based on the master/slave paradigm. The farm skeleton and the master/slave paradigm are discussed in a large number of papers model of parallel computations Map and Reducef to each element of list i denotes the iteration number; i-th approximation ; A is the list of elements of a certain set x is the current approximation) that maps the set B is a list of elements of the set A; A parallel skeleton is a programming construct, which abstracts a pattern of parallel computation and interaction i. Step 3 calculates the list B by applying the higher-order function Compute that calculates the next approximation s of the higher-order function Reduce. Step 6 increases the iteration counter i by one. Step 7 checks a termination criteria by invocating the Boolean user function StopCond, which takes two parameters: the new approximation StopCond returns true, the algorithm outputs Step 1 reads input data of the problem and an initial approximation. Step 2 assigns the zero value to the iteration counter A into K sublists of equal length . In the steps 3 and 4, the master process is idle. In Step 5, all worker processes send the partial foldings Reduce over the list of partial foldings Compute that calculates the next approximation; checks the termination criteria by using the Boolean user function StopCond and assigns its result to the Boolean variable exit. In the steps 6-9, the worker processes are idle. In Step 10, the master process sends the exit value to all worker processes. If the exit value is false, the master process and worker processes go to the next iteration, otherwise the master processes outputs the result and the computation stops. Note that, in the Steps 2 and 10, all processes perform the implicit global synchronization.The result is the parallel BSF\u201d prefix contain problem-independent code and are not subject to changes by the user; files with the \u201cProblem\u201d prefix are intended for filling in problem-dependent parts of the program by the user. Descriptions of all source code files are given in The BSF-skeleton is a compilable but not executable set of files. This set is divided into two groups: files with the \u201cinclude is shown in The dependency graph of the source code files by the directive #Problem-bsfParameters.h. They are used in the BSF-Code.cpp and should be set by the user. All these parameters are presented in The BSF-skeleton parameters are declared as macroses in the file Problem-bsfTypes.h. They are used in the BSF-Code.cpp and should be set by the user. All these types are presented in The predefined problem-depended BSF types are declared as data structures in the file reduceCounter. This extended reduce-list is presented by the pointer BD_extendedReduceList declared in the BSF-Data.h. When performing the Reduce function (see BC_ProcessExtendedReduceList in Section \u201cKey problem-independent functions (prefix BC_)\u201d), the elements that have this field equal to zero are ignored. For elements where reduceCounter is not zero, the values of the reduceCounter are added together. By default, the function BC_WorkerMap (see Section \u201cKey problem-independent functions (prefix BC_)\u201d) sets the reduceCounter to 1. The user can set the value of this field to 0 by setting the parameter *success of the function PC_bsf_MapF to 0.The BSF-skeleton appends to each element of the reduce-list the additional integer field called BSF-SkeletonVariables.h. The user can exploit these variables for the sake of debugging, tracing, and non-standard implementing . The user should not change the values of these variables. All skeleton variables are presented in The skeleton variables are declared in the file The skeleton functions are divided into two groups:BC_ that have implemented in the file BSF-Code.cpp; problem-dependent functions (predefined BSF functions) with the prefix PC_bsf_ that have declared in the file Problem-Code.cpp.1) problem-independent functions with the prefix BC_. The user also cannot change function headers with the prefix PC_bsf_ but must write an implementation of these functions. The body of a predefined BSF function cannot include calls of problem-independent functions with the prefix BC_. The hierarchy of the key function calls is presented in The user cannot change the headers and bodies of the functions with the prefix BSF-Code.cpp. Descriptions of some key problem-independent functions are presented in The implementations of all problem-independent functions can be found in the file PC_bsf_ declared in Problem-bsfCode.cpp. The user must implement all these functions. An instruction is presented in Section \u201cStep-by-step instruction\u201d. An example is presented in Section \u201cExample of using the BSF-skeleton\u201d.This section contains detailed descriptions of the predefined problem-dependent BSF functions with the prefix PC_bsf_CopyParameterPT_bsf_parameter_T (see Section \u201cError! Reference source not found.\u201d).Copies all order parameters from the in-structure to the out-structure. The order parameters are declared in the predefined problem-depended BSF type Syntaxvoid PC_bsf_CopyParameter;In parameters parameterInThe structure from which parameters are copied.Out parameters parameterOutPThe pointer to the structure to which parameters are copied.PC_bsf_InitProblem-Data.h.Initializes the problem-depended variables and data structures defined in Syntaxvoid PC_bsf_Init(bool* success);Out parameters*successfalse if the initialization failed. The default value is true.Must be set to PC_bsf_IterOutputOutputs intermediate results of the current iteration.Syntaxvoid PC_bsf_IterOutput;void PC_bsf_IterOutput_1;PC_bsf_IterOutput_2;void PC_bsf_IterOutput_3;In parameters reduceResultReduce function. reduceCounterPointer to the structure that contains the result of executing the reduceCounter (see Section \u201cExtended reduce-list\u201d).The number of summed .The functions PC_bsf_JobDispatcherThis function is used to organize the workflow (see Section \u201cWorkflow support\u201d) and is executed by the master process before starting each iteration. It implements a state machine that switches from one state to another. If you do not need the workflow support, then you should use the empty implementation of this function.Syntaxvoid PC_bsf_JobDispatcher;In|out parameters parameterPC_bsf_ProcessResults_1, PC_bsf_ProcessResults_2 and PC_bsf_ProcessResults_3.The pointer to the structure containing the parameters of the next iteration. This structure may be also modified by the functions Out parameters*jobThis variable must be assigned the number of the next action (job).*exittrue. The default value is false.If the stop condition holds, then this variable must be assigned RemarksBSF_sv_parameter is not allowed in the implementation of this function.Important: The use of the structure PC_bsf_JobDispatcher is invocated after the invocation of function PC_bsf_ProcessResults_1, PC_bsf_ProcessResults_2 or PC_bsf_ProcessResults_3.The function PC_bsf_MapFMap. To implement the PC_bsf_MapF function, we can use the problem-dependent variables and data structures defined in the file Problem-Data.h, and the structure BSF_sv_parameter of the type PT_bsf_parameter_T defined in Problem-bsfTypes.h.Implements the function that is applied to the map-list elements when performing the higher-order function Syntaxvoid PC_bsf_MapF;void PC_bsf_MapF_1;void PC_bsf_MapF_2;void PC_bsf_MapF_3;In parameters mapElemThe pointer to the structure that is the current element of the map-list.Out parameters reduceElemThe pointer to the structure that is the corresponding reduce-list element to be calculated.*successfalse if the corresponding reduce-list element must be ignored when the Reduce function will be executed. The default value is true.Must be set to RemarksPC_bsf_MapF_1, PC_bsf_MapF_2 and PC_bsf_MapF_3 are used to organize a workflow .The functions PC_bsf_ParametersOutputOutputs parameters of the problem before starting the iterative process.Syntaxvoid PC_bsf_ParametersOutput(PT_bsf_parameter_T parameter);In parameters parameterThe structure containing the parameters of the problem.PC_bsf_ProblemOutputOutputs the results of solving the problem.Syntaxvoid PC_bsf_ProblemOutput;void PC_bsf_ProblemOutput_1;void PC_bsf_ProblemOutput_2;void PC_bsf_ProblemOutput_3;In parameters reduceResultReduce. parameterThe pointer to the structure that is the result of executing the higher-order function The structure containing the parameters of the final iteration.RemarksThe functions PC_bsf_ProblemOutput_1, PC_bsf_ProblemOutput_2 and PC_bsf_ProblemOutput_3 are used to organize a workflow .PC_bsf_ProcessResultsProcesses the results of the current iteration: computes the order parameters for the next iteration and checks the stop condition.Syntaxvoid PC_bsf_ProcessResults;void PC_bsf_ProcessResults_1;void PC_bsf_ProcessResults_2;void PC_bsf_ProcessResults_3;In parameters reduceResultReduce. reduceCounterThe pointer to the structure that is the result of executing the higher-order function reduceCounter (see Section \u201cExtended reduce-list\u201d).The number of summed , then this variable must be assigned the number of the next action (job). Otherwise, this parameter is not used.*exittrue. The default value is false.If the stop condition holds, then this variable must be assigned RemarksBSF_sv_parameter is not allowed in the implementations of these functions.Important: The use of the structure PC_bsf_ProcessResults_1, PC_bsf_ProcessResults_2 and PC_bsf_ProcessResults_3 are used to organize a workflow .The functions PC_bsf_ReduceFImplements the operation Syntaxvoid PC_bsf_ReduceF;void PC_bsf_ReduceF_1;void PC_bsf_ReduceF_2;void PC_bsf_ReduceF_3;In parameters xThe pointer to the structure that presents the first term. yThe pointer to the structure that presents the second term.Out parameters zThe pointer to the structure that presents the result of the operation.RemarksPC_bsf_ReduceF_1, PC_bsf_ReduceF_2 and PC_bsf_ReduceF_3 are used to organize a workflow .The functions PC_bsf_SetInitParameterPT_bsf_parameter_T (see Section \u201cError! Reference source not found.\u201d).Sets initial order parameters for the workers in the first iteration. These order parameters are declared in the predefined problem-depended BSF type Syntaxvoid PC_bsf_SetInitParameter(PT_bsf_parameter_T* parameter);Out parameters parameterThe pointer to the structure that the initial parameters should be assigned to.PC_bsf_SetListSizeSets the length of the list.Syntaxvoid PC_bsf_SetListSize(int* listSize);Out parameters*listSizeMust be assigned a positive integer that specifies the length of the list.RemarksThe list size should be greater than or equal to the number of workers.PC_bsf_SetMapListElemi.Initializes the map-list element with the number Syntaxvoid PC_bsf_SetMapListElem;In parameterselemThe pointer to the map-list element.iThe ordinal number of the specified element.RemarksImportant: The numbering of elements in the list begins from zero.PC_bsfAssignAddressOffsetBSF_sv_addressOffset (see Section \u201cSkeleton variables\u201d).Assigns the number of the first element of the map-sublist to the skeleton variables Syntax void PC_bsfAssignAddressOffset;In parameters valueNon-negative integer value.RemarksImportant: The user should not use this function.PC_bsfAssignIterCounterBSF_sv_iterCounter (see Section \u201cSkeleton variables\u201d).Assigns the number of the first element of the map-sublist to the skeleton variables Syntax void PC_bsfAssignIterCounter;In parameters valueNon-negative integer value.RemarksImportant: The user should not use this function.PC_bsfAssignJobCaseBSF_sv_jobCase (see Section \u201cSkeleton variables\u201d).Assigns the number of the current activity (job) in workflow to the skeleton variables Syntax void PC_bsfAssignJobCase;In parameters valueNon-negative integer value.RemarksImportant: The user should not use this function.PC_bsfAssignMpiMasterBSF_sv_mpiMaster (see Section \u201cSkeleton variables\u201d).Assigns the rank of the master MPI process to the skeleton variables Syntax void PC_bsfAssignMpiMaster;In parameters valueNon-negative integer value.RemarksImportant: The user should not use this function.PC_bsfAssignMpiRankBSF_sv_mpiRank (see Section \u201cSkeleton variables\u201d).Assigns the rank of current MPI process to the skeleton variables Syntax void PC_bsfAssignMpiRank;In parameters valueNon-negative integer value.RemarksImportant: The user should not use this function.PC_bsfAssignNumberInSublistBSF_sv_numberInSublist (see Section \u201cSkeleton variables\u201d).Assigns the number of the current element in the map-sublist to the skeleton variables Syntax void PC_bsfAssignNumberInSublist;In parameters valueNon-negative integer value.RemarksImportant: The user should not use this function.PC_bsfAssignNumOfWorkersBSF_sv_numOfWorkers (see Section \u201cSkeleton variables\u201d).Assigns the total number of the worker processes to the skeleton variables Syntax void PC_bsfAssignNumOfWorkers;In parameters valueNon-negative integer value.RemarksImportant: The user should not use this function.PC_bsfAssignParameterBSF_sv_parameter (see Section \u201cSkeleton variables\u201d).Assigns the order parameters to the structure Syntax void PC_bsfAssignParameter(PT_bsf_parameter_T parameter);In parameters parameterThe structure from which the order parameters are taken.RemarksImportant: The user should not use this function.PC_bsfAssignSublistLengthBSF_sv_sublistLength (see Section \u201cSkeleton variables\u201d).Assigns the length of the current map-sublist to the skeleton variables Syntax void PC_bsfAssignSublistLength;In parameters valueNon-negative integer value.RemarksImportant: The user should not use this function.Step-by-step instructionThis section contains step-by-step instructions on how to use the BSF-skeleton to quickly create a parallel program. Starting from Step 2, we strongly recommend compiling the program after adding each language construction.Step 1. First of all, we must represent our algorithm in the form of operations on lists using the higher-order functions Map and Reduce . For example: typedef PT_point_T[PP_N]; // Point in n-Dimensional SpaceStep 4. In the file Problem-bsfTypes.h, implement the predefined BSF types. If we do not use a workflow then we do not have to implement the types PT_bsf_reduceElem_T_1, PT_bsf_reduceElem_T_2, PT_bsf_reduceElem_T_3, but we can't delete these empty structures. For example:struct PT_bsf_parameter_T {PT_point_T approximation; // Current approximation};struct PT_bsf_mapElem_T {int columnNo; // Column number in matrix Alpha};struct PT_bsf_reduceElem_T {double column[PP_N]; // Column of intermediate matrix};struct PT_bsf_reduceElem_T_1 {};struct PT_bsf_reduceElem_T_2 {};struct PT_bsf_reduceElem_T_3 {};Step 5. In the file Problem-Data.h, define the problem-dependent variables and data structures. For example: static double PD_A[PP_N][PP_N]; // Coefficients of equationsStep 6. In the file Problem-bsfCode.cpp, implement the predefined problem-dependent BSF functions (see Section \u201cPredefined problem-dependent BSF functions (prefix PC_bsf_)\u201d) in the suggested order. To implement these functions, the user can write additional problem (user) functions in the Problem-bsfCode.cpp. The prototypes of these problem functions must be included in the Problem-Forwards.h.Step 7. In the file Problem-bsfCode.cpp, we can configure the BSF-skeleton parameters (see Section \u201cBSF-skeleton parameters\u201d).Build and run the solution in the MPI environment.Jacobi methodIn this section, we show how to use the BSF-skeleton to implement the iterative Jacobi method as an example. The It is assumed that Let us define the vector Step 1. Step 2. Step 3. If Step 4. Step 5. Stop.diagonal dominance of the matrix In the Jacobi method, an arbitrary vector j-th column of matrix Let us represent the Jacobi method in the form of algorithm on lists. Let n. For any vector j-th column of the matrix C by the j-th coordinate of the vector x. The BSF-implementation of the Jacobi method presented as C entered in line 1 is implicitly used to calculate the values of the function Let https://github.com/leonid-sokolinsky/BSF-Jacobi. Additional examples of using the BSF-skeleton can be found on GitHub at the following links:\u2022https://github.com/leonid-sokolinsky/BSF-LPP-Generator;\u2022https://github.com/leonid-sokolinsky/BSF-LPP-Validator;\u2022https://github.com/leonid-sokolinsky/BSF-gravity;\u2022https://github.com/leonid-sokolinsky/BSF-Cimmino;\u2022https://github.com/leonid-sokolinsky/NSLP-Quest.The source code of the BSF-Jacobi algorithm, implemented by using the BSF-skeleton, is freely available on Github at Problem-bsfTypes.h. All jobs have the same type of map list elements. To organize the workflow, we need to follow these steps:The BSF-skeleton supports workflows. A workflow consists of orchestrated and repeatable activities (jobs). The BSF-skeleton supports up to four different jobs. The starting job is always numbered 0 (omitted in the source codes). The other jobs have sequential numbers 1, ..., 3. Each job has its own type of reduce-list elements defined in the file Problem-bsfParameters.h, redefine the macros PP_BSF_MAX_JOB_CASE specifying the largest number of a job. For example, if the total job quantity is 3, the number to be assigned to PP_BSF_MAX_JOB_CASE must be 2.In the file Problem-bsfTypes.h, define the types of reduce-list elements for all jobs whose sequential numbers are less than or equal to PP_BSF_MAX_JOB_CASE.In the file Problem-bsfCode.cpp, implement the functions PC_bsf_MapF[_*], PC_bsf_ReduceF[_*], PC_bsf_ProcessResults[_*], PC_bsf_ProblemOutput[_*] and PC_bsf_IterOutput[_*] for all jobs whose sequential numbers are less than or equal to PP_BSF_MAX_JOB_CASE. The functions PC_bsf_ProblemOutput[_*] should assign the parameter *nextJob a sequential number of the next job (possibly the same).In the file PC_bsd_JobDispatcher to manage these states. An example of a solution using the BSF-skeleton with the workflow support is freely available on Github at https://github.com/leonid-sokolinsky/Apex-methodIf the number of workflow states is greater than the number of jobs, you can use the function BC_WorkerMap) using the #pragma omp parallel for. This support is disabled by default. To enable this support, we must define the macros PP_SF_OMP in the file Problem-bsfParameters.h. Using the macros PP_BSF_NUM_THREADS, we can specify the number of threads to use in the parallel for. By default, all available threads are used.The BSF-skeleton supports a parallelization of the map-list processing cycle in the worker processes .Some numerical algorithms can be implemented naturally using the function https://github.com/leonid-sokolinsky/BSF-skeleton.Supplementary material: The source code of the BSF-skeleton is freely available on Github at The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "Present-day and ancient population genomic studies from different study organisms have rapidly become accessible to diverse research groups worldwide. Unfortunately, as datasets and analyses become more complex, researchers with less computational experience often miss their chance to analyze their own data. We introduce FrAnTK, a user-friendly toolkit for computation and visualization of allele frequency-based statistics in ancient and present-day genome variation datasets. We provide fast, memory-efficient tools that allow the user to go from sequencing data to complex exploratory analyses and visual representations with minimal data manipulation. Its simple usage and low computational requirements make FrAnTK ideal for users that are less familiar with computer programming carrying out large-scale population studies. Our wrapper scripts make it possible to run this kind of analysis with a single command and support average pairwise distances, 3f, 4f, \u201cbasic\u201d D and enhanced D-statistics. In addition, we include wrapper scripts for computing admixture/contamination-corrected 4f-statistics over a range of admixture/contamination proportions and minor allele count-stratified D-statistics over a specified range of minor allele counts.To supplement the scripts for computing single statistics, we provide multi-threaded wrappers for automated computation of multiple related statistics . A commoe.g., The wrapper scripts also provide automated plotting functionality, which allows users to create visual representations of classical exploratory analyses e.g., . For evepostmortem damage-related error , R and perl and depend only on standard tools and libraries that are commonly present in Unix-like setups in the field of population genomics: plink R librarf- and other site-statistics are available, e.g., popstats , which we distributed over 20 threads (Intel Xeon Gold 2.10\u2009GHz CPU). Using the qpDstat (v712) program from admixtools, the task was completed in 5.1\u2009h, with a peak memory usage of \u223c520\u2009GB (\u223c26\u2009GB per thread). Using the automated D-statistic wrapper in FrAnTK (autoDwfixed.R), the task was completed in 2.2\u2009h, with a peak memory usage of \u223c5.8\u2009GB (\u223c287\u2009MB per thread). We attribute these gains to two key features: (1) precomputing the allele frequencies to speed up subsequent computation and (2) processing one site at a time instead of loading the whole dataset onto memory. In this example, the admixtools-based approach would require the user to prepare a set of input files and distribute the parallel processes across different threads. Once all processes have run, the user would have to parse separate results and use a custom script for visualizing the results. By contrast, by using FrAnTK, the user can go from the initial data to a visual representation of the results by running two one-line commands.To assess the performance of our toolkit, we computed a number of statistics on a whole-genome reference dataset using FrAnTK and admixtools . We use the HGDP SNP array dataset to compute the 51 possible 3f-statistics of the form 3f, where X represents all the populations in the HGDP SNP array dataset. This run was completed in \u223c20\u2009s.Using the merged data, we can explore the broad genetic affinities of the low-depth Mal'ta genome. We use the frantk autof3wfixed \\ freqpref=HGDP_hg19_genotypes_f_WithBam h1\u2009=\u2009MalTa \\target=Yoruba catfile=HGDP_hg19_genotypes_cat \\legfile=HGDP_hg19_genotypes_leg nthr\u2009=\u200940autof3wfixed.R will output the plot shown in HGDP_hg19_genotypes_cat and HGDP_hg19_genotypes_leg files, which we supply through the catfile and legfile options. These results replicate the finding in (autoDwfixed.R wrapper (with 40 threads) to compute all possible D-statistics of the form D, where X represents all the populations in the HGDP dataset, including the Mal'ta individual. This run was completed in \u223c20\u2009s.frantk autoDwfixed \\ freqpref=HGDP_hg19_genotypes_f_WithBam \\ h1=Karitiana \\h2=Han h4=Yoruba \\ catfile=HGDP_hg19_genotypes_cat \\legfile=HGDP_hg19_genotypes_leg nthr=40autoDwfixed.R will output the plot shown in D deviated significantly from D\u2009=\u20090 (Z\u223c14.9). This pattern is most likely due to shared ancestry between the Mal'ta individual and present-day French . This procedure was completed in \u223c30\u2009s.We can use the t format . First, echo \"SanMbutiPygmyYorubaMandenkaPapuanMelanesianHanDaiFrenchItalianSardinianOrcadianMalTaKaritianaSurui\" > poi\u2003frantk Freqs2Treemix \\ freqpref=HGDP_hg19_genotypes_f_WithBam \\tmpref=hgdp_malta_tm popsofint=poiFinally, we run treemix following the parameters in #Compute the number of SNPs that should be included in each autosomal 5\u2009Mb-block.a=`zcat hgdp_malta_tm_ALL_tm.gz | wc -l`nsnps=`echo \"5000000/(2881033286/\"$a\")\u201d | bc`\u2003#Run treemix with 0 and 1 migrationstreemix -i hgdp_malta_tm_ALL_tm.gz -o tm_ALL_res_0mig -k \"$nsnps\" -noss \\-global -root San -m 0 -seed012345treemix -i hgdp_malta_tm_ALL_tm.gz -o tm_ALL_res_1mig -k \"$nsnps\" -noss \\-global -root San -m 1 -seed112345Treemix admixture graphs in FrAnTK is a toolkit that streamlines a set of common analyses that rely on allele frequency-based statistics, and makes them accessible to users that are less familiar with computer programming. We reduce memory and computing times by precomputing allele frequencies, thus allowing researchers to explore their own datasets with reduced computational resource requirements. Notably, the automated wrappers and plotting functionality in FrAnTK allow the user to carry out complex exploratory analyses and produce publication-ready visual representations with single-line commands and minimal data manipulation. Thus, we consider an appropriate protocol would comprise an initial exploration using the tools in FrAnTK, followed by the application of model-based strategies such as those implemented in qpWave and qpGraph (FrAnTK and its documentation are freely available in github.com/morenomayar/FrAnTK.G3 online.jkab357_Supplementary_DataClick here for additional data file."} +{"text": "Emerging evidence suggested that circular RNAs (circRNAs) play critical roles in cervical cancer (CC) progression. However, the roles and molecular mechanisms of hsa_circ_0007364 in the tumorigenesis of CC remain unclear. In the present study, we used bioinformatics analysis and a series of experimental analysis to characterize a novel circRNA, hsa_circ_0007364 was up-regulated and associated with advanced clinical features in CC patients. Hsa_circ_0007364 inhibition notably suppressed the proliferation and invasion abilities of CC cells in vitro and reduced tumor growth in vivo. Moreover, hsa_circ_0007364 was uncovered to sponge miR-101-5p. Additionally, methionine adenosyltransferase II alpha (MAT2A) was verified as a target gene of miR-101-5p, and its downregulation reversed the inhibitory effects of hsa_circ_0007364 knockdown on CC progression. Therefore, we suggested that hsa_circ_0007364 might serve as an oncogenic circRNA in CC progression by regulating the miR-101-5p/MAT2A axis, which provides a potential therapeutic target to the treatment.Research highlightshsa_circ_0007364 was upregulated in CChsa_circ_0007364 promoted CC cell progressionhsa_circ_0007364/miR-101-5p/MAT2A axis in CC In 2012 there were an estimated 530,000 CC cases and about 275,000 CC deaths . Thus, nin vitro. Hu et al. , h, hP <\u00a00.circRNAs ), and hscircRNAs ).Figure Assessment of hsa_circ_0007364 expression in CC revealed that hsa_circ_0007364 is remarkably upregulated in GSE102686 and GSE113696 datasets ,b). And 3.2.in vitro . CCK-8 in vitro ,g). More(in vivo ). Togeth3.3.Previous studies have shown that circRNAs can \u2018sponge\u2019 miRNAs in CC cells . To esta3.4.To elucidate the mechanism of miR-101-5p activity in CC cells, we predicted its targets using TargetScan, Starbase, miRTarBase and mircode and identified MAT2A as a possible target for miR-101-5p \u2013c). Dualin vitro . Similain vitro ,f). Take3.5.Next, we examined whether hsa_circ_0007364 functions as a molecular sponge against miR-101-5p to regulate MAT2A expression. RT-qPCR analysis revealed that hsa_circ_0007364 deficiency resulted in reduced MAT2A expression, while miR-101-5p suppression reversed this effect ,b). Resc4.Cervical cancer (CC) is one of the commonest malignancies globally . MountinMultiple studies show that circRNAs participate in tumorigenesis by sponging miRNAs ,29. PredMiRNAs modulate various cellular processes via their molecular targets . A searc5.In summary, we found that hsa_circ_0007364 is overexpressed in CC, and may enhance the proliferative and invasion capacity of CC cells by interacting with the miR-101-5p/MAT2A axis. Our findings highlight this axis as a potential therapeutic target against CC."} +{"text": "Germline Variants (GVs) are effective in predicting cancer risk and may be relevant in predicting patient outcomes. Here we provide a bioinformatic pipeline to identify GVs from the TCGA lower grade glioma cohort in Genomics Data Commons. We integrate paired whole exome sequences from normal and tumor samples and RNA sequences from tumor samples to determine a patient\u2019s GV status. We then identify the subset of GVs that are predictive of patient outcomes by Cox regression.For complete details on the use and execution of this protocol, please refer to \u2022Integration of whole-exome and RNA sequences to determine Germline Variants (GVs)\u2022Whole-exome and RNA sequences from tumors resolve low coverage issue in normal samples\u2022High correlation of GV allele frequencies between patient data and the GnomAD database\u2022GVs predict patient cancer outcome Germline Variants (GVs) are effective in predicting cancer risk and may be relevant in predicting patient outcomes. Here we provide a bioinformatic pipeline to identify GVs from the TCGA lower grade glioma cohort in Genomics Data Commons. We integrate paired whole exome sequences from normal and tumor samples and RNA sequences from tumor samples to determine a patient\u2019s GV status. We then identify the subset of GVs that are predictive of patient outcomes by Cox regression. Timing: 5\u00a0minThe scripts and test data sets required to run this protocol are available on the GitHub repositoryhttps://github.com/ds21uab/STAR_protocols_GV_calling.git.1.Open the Linux command-line interface. Copy and paste the command below to clone protocol directory from the GitHub repository:>git clonehttps://github.com/ds21uab/STAR_protocols_GV_calling.gitTiming: 1\u00a0min2.a.>pwdTo determine the exact location of the \u2018STAR_protocols_GV_calling\u2019 directory using command-line, type command pwd from the directory where \u201cSTAR_protocols_GV_calling\u201d is locatedThe output should look something like thisThe output of the pwd command shows that user is in the project directory, which is in the /home/dsahu/ directory.b.>nano \u223c/.bash_profileOpen and edit the bash profile using your favorite text editorc.>export protocol_dir=\"/home/dsahu/project\"Add the output of the pwd command to the last line.d.Press \u2018control\u2019\u00a0+ \u2018x\u2019 key to exit. You will be prompted to save the file. Press \u2018Y\u2019 for Yes to save the changes and \u2018enter\u2019.e.>source \u223c/.bash_profileActivate the changes in the bash_profileSave path for the \u2018STAR_protocols_GV_calling\u2019 directory in a local or online Linux cluster.Timing: 1\u00a0min3.Navigate to STAR_protocols_GV_calling directory.>cd STAR_protocols_GV_calling/4.Navigate to \u2018scripts\u2019 directory and set executable permission to all the scripts executable using the following command>cd scripts/>chmod\u00a0+x \u2217This protocol describes a computational approach that is based on several Linux-based software including gdc-client, SAMtools , BCFtoolTiming: 20\u00a0min5.https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files/.a.>cd data/reference_data/HSapiens/hg38/>tar xvzf GRCh38.d1.vd1.fa.tar.gzUnzip and place the reference human genome FASTA sequence in the \u2018/data/reference_data/HSapiens/hg38/\u2019 directory.b.>module load samtools/1.12SAMtools should be loaded in the system PATH. We used the command below to load samtools in our online Linux cluster.c.>samtools faidx GRCh38.d1.vd1.faIndex the FASTA sequence.Navigate to \u2018data\u2019 directory with three subdirectories \u2018BAM\u2019, \u2018reference_data\u2019 and \u2018samples\u2019. The reference_data directory contains gene annotation BED file from the GENCODE database. Download GDC reference genome (hg38) FASTA sequence (GRCh38.d1.vd1.fa.tar.gz) from 6.a.Download BAM files using the following commandNavigate to \u2018BAM\u2019 directory and download BAM files for wxs-normal samples, wxs-tumor samples, and rnaseq-tumor samples from the provided manifest files and place them in their respective directory. A GDC token is required to download BAMs from the GDC database.>cd STAR_protocols_GV_calling/data/BAM/wxs-normal/>gdc-client download -m gdc_manifest_wxs-normal.txt -t token.txt>cd STAR_protocols_GV_calling/data/BAM/wxs-tumor/>gdc-client download -m gdc_manifest_wxs-tumor.txt -t token.txt>cd STAR_protocols_GV_calling/data/BAM/rnaseq-tumor/>gdc-client download -m gdc_manifest_rnaseq-tumor.txt -t token.txtThis protocol requires whole-exome-sequences from the normal samples , whole-exome-sequences from the tumor samples (wxs-tumor) and RNA-sequences from the tumor samples (rnaseq-tumor) from The Cancer Genome Atlas (TCGA) patients available in the Genomics Data Commons (GDC) data portal . The aliTiming: 1\u00a0min7.a.>cd data/BAM/wxs-normal/>find $(pwd) -type d | awk '!/logs/' | sed '1d'\u00a0>\u00a0input.listRun the following command from the directory that contains only folders of BAM files and do not contain other information except previous logs. For example, let us create an input.list for wxs-normal BAMs.b.>mv input.list wxs-normal_input.listRename the input.list as you wish.Variant calling using VarDictJava requires an input.list that contain path to folders of BAM files. Prepare an input list for wxs-normal, wxs-tumor and rnaseq-tumor data types, separately.8.The default output for this protocol is within the following directory.>cd STAR_protocols_GV_calling/analysis/\u2022data.table (v.1.14.0)\u2022dplyr (v1.0.6)\u2022forcats (v0.5.1)\u2022stringr (v1.4.0)\u2022purrr (v0.3.4)\u2022readr (v1.4.0)\u2022tidyr (v1.1.3)\u2022tibble (v3.1.2)\u2022ggplot2 (v3.3.3)\u2022Tidyverse (v.1.3.1)\u2022survival (v3.2-13) R software and required R packages: While newer versions of some of these packages are available, this protocol was developed with R v4.0.3, RStudio v4.1.1, and the following versions of R packages:\u2022Operating system: GNU/Linux\u2022Memory: 100 GB (memory requirement depends on size of the dataset)\u2022Processors: 1 required, 5 recommendedHardware Recommendations:The script in this protocol follows Simple Linux Utility for Resource Management (SLURM)-based schema and requires submission of the job to an online Linux cluster. The steps discussed below\u00a0loop over each BAM file or the downstream output files that were generated. Therefore, it is easier to submit similar jobs as job arrays, which will create a number of independent jobs (corresponding to the defined number of tasks) and execute them simultaneously. It is common to load pre-installed software as an environmental module available on the Linux cluster. User needs to load the relevant modules on their cluster. This protocol expects that R, VarDictJava, SAMtools and BCFtools are installed on your local or online Linux cluster and loaded in the system PATH.Note: Run parts 1-5 separately for wxs-normal samples, wxs-tumor samples, and rnaseq-tumor samples.A typical workflow to call germline variants from the wxs-normal samples, wxs-tumor samples, and rnaseq-tumor samples (the three \u2018data types\u2019 in this protocol) requires six parts. The first part is variant calling using VarDictJava. The second part is the preprocessing of VCFs and extraction of genotype status of each variant for each sample. We then perform union of all the unique variants from all three data types. The third part is to calculate the sequencing coverage of the union of unique variants. The fourth part is to merge genotype status file and sequencing coverage file of each sample to determine the status of each variant after correction for low sequence coverage. The variant status at positions with fewer than ten reads for a given sample is changed to unknown. The fifth part is to combine variant status file from each sample to create a large multi-sample VCF file. Finally, in the sixth part, at positions at which variant status is listed as unknown in the wxs-normal samples (because of low sequence coverage) we will insert variant calls made from the corresponding wxs-tumor samples. If the variant status is still unknown in a normal sample but is called in the corresponding rnaseq-tumor sample, then the rnaseq-derived variant is inserted to create the final combined wxs-rnaseq variant call set.Timing: 2\u00a0h 1.a.>nano VariantCallingFrom_VarDict.shNavigate to \u2018scripts\u2019 directory and open VariantCallingFrom_VarDict.sh script in your favorite text editor.b.>#SBATCH\u00a0-N 1 ##number of nodes>#SBATCH\u00a0--cpus-per-task=5 ##number of cpus per task>#SBATCH\u00a0-mem=100Gb ##memory requested per node in GB>#SBATCH\u00a0-t 02:00:00 ##time limit hrs:min:sec>#SBATCH\u00a0-p partition ##partition requested in the cluster>#SBATCH\u00a0-A account ## account to be charged>#SBATCH\u00a0-e slurm-%j.err ##standard error>#SBATCH\u00a0-output slurm-%j.out ##standard output>#SBATCH\u00a0-array=1-5 ##number of array jobs is from 1 to 5Note: Set the number of nodes, number of cpus, requested memory, and time in the job script according to the number of samples to be processed and resources available on the user online Linux cluster. The numbers designating the array jobs correspond to the numbers of the jobs in the input list.As the script in this protocol follows SLURM based schema. The structure of the job script is described below.c.>input_list=\"$protocol_dir/STAR_protocols_GV_calling/data/BAM/wxs\u00a0-normal/wxs-normal_input.list\"As different data types are processed, set the path in the script to the input list that corresponds to the data type See . For exad.>cd STAR_protocols_GV_calling/analysis/VCFs_from_VarDict/The default output for this step is stored in the following directory.e.>mkdir wxs-normal>mkdir wxs-tumor>mkdir rnaseq-tumorUser should create directory \u2018wxs-normal\u2019, \u2018wxs-tumor\u2019, and \u2018rnaseq-tumor\u2019 in the \u2018VCFs_from_VarDict\u2019 directory to store VCFs for respective data types.f.>out_VCF=\"$protocol_dir/STAR_protocols_GV_calling/analysis/VCFs_fr\u00a0om_VarDict/wxs-normal\"Set output path in the script accordingly See . For exag.>sbatch$protocol_dir/STAR_protocols_GV_calling/scripts/VariantCallingFrom_VarDict.shRun script using the following commandh.i.>#PBS -k o ##keep the job output>#PBS -N JobName ## name of the job>#PBS -l nodes=1 ##number of nodes>#PBS -l ncpus=5 ## number of cpus>#PBS -l mem=100Gb ## memory requested per node in Gb>#PBS -l walltime=02:00:00 ## time limit hrs:min:sec>#PBS -q queue ##partition requested in the cluster>#PBS -e torque-%j.err ##standard error>#PBS -o torque-%j.out ##standard output>#PBS -t 1-5 ##number of array jobs is from 1 to 5Change the structure of the job script in the VariantCallingFrom_VarDict.sh as described belowii.>qsub$protocol_dir/STAR_protocols_GV_calling/scripts/VariantCallingFrom_VarDict.shRun script using the following commandIf the user online Linux cluster supports Terascale Open-source Resource and QUEue Manager (TORQUE) system,Variant calling on wxs-normal BAMs, wxs-tumor BAMs, and rnaseq-tumor BAMs using VarDictJava. The settings were set as default except for requiring mapping quality greater than 30, base quality greater than 25, a minimum of 3 reads supporting a variant, minimum allele frequency of 5%, no structural variant calling, and the removal of duplicate reads.Timing: 30\u00a0min2.a.>cd STAR_protocols_GV_calling/analysis/PASS_variants/The default output for this step is stored in the following directory.b.>mkdir wxs-normal>mkdir wxs-tumor>mkdir rnaseq-tumorUser should create directory for each data type in the \u2018PASS_variants\u2019 directory to store outputs for respective data type.c.>nano extract_pass_variants.sh>out_VCF=\"$protocol_dir/STAR_protocols_GV_calling/analysis/PASS_va\u00a0riants/wxs-normal\"Set output path in the extract_pass_variants.sh script for each data type accordingly. For example, let\u2019s set the output path to store indexed passed variants for wxs-normal samplesd.>$protocol_dir/STAR_protocols_GV_calling/scripts/extract_pass_variants.shRun the script from the directory where VCFs from VarDictJava are located.Index VCF file and extract variants that received a PASS (shown in the \u201cfilter\u201d column) in the indexed VCF file.3.Remove header section from VCFs. Run the script from the directory where indexed pass variants are located.>$protocol_dir/STAR_protocols_GV_calling/scripts/remove_header_VCF.sh4.Extract unique variants from all the passed variants VCF files. Run script from the directory where VCF files without header are located. This script will output allVCF_variants.txt file , and unique_variants.txt file . User may rename the unique_variants.txt for each data type accordingly.>$protocol_dir/STAR_protocols_GV_calling/scripts/extract_uniqueVariants.shNote: This bash script extract_uniqueVariants.sh includes R script extract_uniqueVariants.R. See \u2018Potential 5.a.>cd STAR_protocols_GV_calling/analysis/genotype_status/The default output for this step is in the following directory.b.>mkdir wxs-normal>mkdir wxs-tumor>mkdir rnaseq-tumorUser should create separate directory in the \u2018genotype_status\u2019 directory to store outputs for each data types.c.>nano extract_genotype_from_passedVariants.sh>out_VCF=\"$protocol_dir/STAR_protocols_GV_calling/analysis/genotyp\u00a0e_status/wxs-normal\"Set output path in the extract_genotype_from_passedVariants.sh script for each data type. For example, set output path for wxs-normal samplesd.>$protocol_dir/STAR_protocols_GV_calling/scripts/extract_genotype_from_passedVariants.shRun script from the indexed passed variants VCFs directoryExtract genotype status for each variant from each sample. Here, we extract chromosome, position, reference allele, observed alternate allele, mutation status, total depth, and variant depth of each variant from each VCF file.6.a.>library (data.table)Load required R packageb.>wxs_normal=fread>wxs_tumor=fread>rnaseq_tumor=freadLoad data in Rc.>wxs_normal <- setDF >wxs_tumor <- setDF (wxs_tumor)>rnaseq_tumor <- setDF (rnaseq_tumor)Convert data.table to data.framed.>variant_list\u00a0= listConvert into liste.>union_variants= Reduce merge, by.y\u00a0= c, all.x=TRUE, all.y=TRUE),\u00a0\u00a0variant_list)Merge list based on chromosome, position, reference allele, and alternate allelef.>drop <- c>union_variants<-union_variantsDrop unwanted columnsg.>fwriteSave union variants in the analysis directoryh.>quitTerminate the current R session. User will be prompted to save the workspace. Please type \u2018no\u2019 if you wish not to save the workspace.i.>mv union_wxs_rnaseq_variants.txt union_wxs_rnaseq_variants.bedNow we are outside R. Convert the union_wxs_rnaseq_variants.txt file into .bed file in the Linux command lineMerge unique variants obtained from the wxs-normal, wxs-tumor and rnaseq-tumor data type by chromosome, position, reference allele and observed alternate allele. Here, we will keep the union of unique variants obtained from all the three data types and save them as union_wxs_rnaseq_variants.bed file. User can use R to merge the unique variants obtained from the three data typesTiming: 2 h7.a.>cd STAR_protocols_GV_calling/analysis/variant_coverageThe default output for this step is in the following directory.b.>mkdir wxs-normal>mkdir wxs-tumor>mkdir rnaseq-tumorUser should create separate directory for each data type in the \u2018variant_coverage\u2019 directory to store output for each data type.c.>nano UnionVariantCoverageFrom_Samtools_depth.sh>out_depth=\"$protocol_dir/STAR_protocols_GV_calling/analysis/varia\u00a0\u00a0\u00a0nt_coverage/wxs-normal\"Set output path in the script accordingly. For example, set output path for wxs-normal samplesd.>sbatch$protocol_dir/STAR_protocols_GV_calling/scripts/UnionVariantCoverageFrom_Samtools_depth.shCRITICAL: union_wxs_rnaseq_variants.bed file and input.list that contain the location of the BAM files are required as input files. Set path of input files in the script. Set array jobs with number of jobs in the input list.Run the script using the following commandIn this step, we will calculate the sequencing coverage of union variants (listed in the union_wxs_rnaseq_variants.bed file) on all BAMs requiring mapping quality greater than 30.Timing: 5\u00a0min8.a.Input files: prepare a tab separated input_genotype_samdepth.txt file as shown in b.>cd STAR_protocols_GV_calling/analysis/variant_statusThe default output for this step is in the following directory.c.>mkdir wxs-normal>mkdir wxs-tumor>mkdir rnaseq-tumorUser should create separate directory for each data type in the \u2018variant_status\u2019 directory to save output for each data type.d.>STAR_protocols_GV_calling/analysis/variant_status/wxs-normal/Set path in the out_filename column in the input_genotype_samdepth.txt file to save results for each data type. For example, set output path for wxs-normal samplese.Place the input_genotype_samdepth.txt file in the analysis directory.f.>sbatch$protocol_dir/STAR_protocols_GV_calling/scripts/determineVariantStatus.shNote: The bash script determineVariantStatus.sh includes R script determineVariantStatus.R. Set array jobs with number of jobs in the input list.Run the script using the following commands from the analysis folder.Determine status of each variant using the genotype status and sequencing coverage of each variant in each sample. The variant status at positions fewer than ten reads for a given patient is changed to unknown. If the sequencing coverage of the variant is more than ten reads and no alternate allele is reported for that variant, then the status of that given variant is changed to Homozygous reference.Timing: 1 h9.a.>cd STAR_protocols_GV_calling/analysis/combined_variant_statusThe default output for this step is in the following directory.b.>mkdir wxs-normal>mkdir wxs-tumor>mkdir rnaseq-tumorUser should create a separate directory in the \u2018combined_variant_status\u2019 to save output for each data type.c.>sbatch$protocol_dir/STAR_protocols_GV_calling/scripts/combineAllSamplesVariantStatus.shCRITICAL: The bash script combineAllSamplesVariantStatus.sh includes the R script combineAllSamplesVariantStatus.R. In the R script set full path for input files and the output path where combined variants from all samples to be saved. The memory and time may vary based on the number of samples to be processed.Run the script using the following commandsCombine variant status file of each sample to create a multi-sample VCF which stores the variant status from all the samples.10.>file=combinedVariantStatusFromAllSamples.txt>head -1 $file\u00a0>\u00a0header.txt>sed '1d' $file\u00a0>\u00a0combined_variants_without_header.txt>split -d -l 50000 combined_variants_without_header.txt -a 4 \u2013\u00a0additional-suffix=.txt segment_The script above outputs a large table which contains variant status from all the samples. However, we need to do a bit of legwork to get our data into reasonable shape. First, the combined variants status file contains millions of variants, and it will take too much of memory and time for data pre-processing. Therefore, we will first split the large-combined variant status file into chunks of small files keeping the same number of columns but split based on fixed number of rows. In this file, each line corresponds to one variant.a.-d #add numeric suffix to split fileb.-l #number of lines in each of the smaller filesc.-a #suffix lengthd.--additional-suffixe.segment_ #split file prefixWith the above commands we did the following:11.Prepare input list for pre-processing>find $(pwd) -type f -name \"segment\u2217\"\u00a0>\u00a0input.txt>sort -V input.txt\u00a0>\u00a0input.list12.a.Input files: input.list and header.txt fileb.Output files: processed combined variant status file for each split filec.>sbatch$protocol_dir/STAR_protocols_GV_calling/scripts/processCombinedVariants.shNote: The bash script processCombinedVariants.sh includes R script processCombinedVariants.R. Set array jobs with number of jobs in the input list.Run script from the folder where input.list and header.txt is storedThe pre-processing step takes each split file from the input.list and first removes the unwanted columns. Then for each variant it extracts the chromosome, base-position, the reference allele, the observed alternate allele and the variant status for each sample. From the fifth column onwards, the column names change to the respective sample names from TCGA. Modify the script if you have different sample names.13.Once preprocessing of each split file is finished, the next step is to merge them. Run the command below from the command line interface>awk 'NR\u00a0== 1 || FNR\u00a0>\u00a01' processed_CombinedVariants_\u2217.txt >processed_CombinedVariantsFromAllSamples.txt14.Remove variants which are either unknown or Homozygous reference across all samples from the processed_CombinedVariantsFromAllSamples.txt file. Run the script below from the directory where the processed_CombinedVariantsFromAllSamples.txt file is located. The script will output the processed_CombinedPotentialSNPs.txt file.>Rscript$protocol_dir/STAR_protocols_GV_calling/scripts/extractPotentialSNPsFromCombinedVariants.RTiming: 40\u00a0min15.a.i.processed_CombinedPotentialSNPs.txt file obtained for wxs-normal, wxs-tumor and rnaseq-tumor data types.ii.Patient list with Case_ID and Sample_Barcode. If a matched tumor /normal sample have whole exome sequencing and associated RNA sequencing file, then the different datasets from the patient will have the same Case_ID. Prepare separate patient list for wxs-normal, wxs-tumor and rnaseq tumor samples. Set the column names of each file as suggested:\u00a0wxs-normal: Case_ID and normal\u00a0wxs-tumor: Case_ID and tumor\u00a0rnaseq-tumor: Case_ID and rnaseqInput files:b.>cd STAR_protocols_GV_calling/data/samplesPatient list for this protocol is provided in the sample directory and can be accessed by the following commandc.>sbatch$protocol_dir/STAR_protocols_GV_calling/scripts/fillUnknownVariantsInNormalSamples.shCRITICAL: The bash script fillUnknownVariantInNormalSamples.sh includes R script fillUnknownVariantInNormalSamples.R. Set full path for the patient files and the processed_CombinedPotentialSNPs.txt file in the script.Run the script using the following command. Run the script from the analysis folder.d.i.combined_normal_unknown_filled.txtii.combined_normal_unknown_filled_arranged.txtiii.final_merged_wxs_rnaseq_variants.txt iv.final_variantsForAnnovar.txt The output from step six includes four filesThe goal of this step is to insert variant status at positions listed as unknown in the wxs-normal sample from the corresponding tumor sample. If the variant status is still unknown in the normal sample, then we will insert variant status of the rnaseq-derived variant from the corresponding rnaseq-tumor sample. This step will allow us to create a final combined wxs-rnaseq variant call set.16.Use Annovar software to perform functional annotation of germline variants such as in which gene the variant is located, whether variant is in the exonic, intronic, UTR, promoter, or splicing region of a gene or is in the intergenic region.17.Use Annovar to determine the allele frequencies of germline variants in whole-genome sequencing data from various ethnic populations such as listed in the GnomAD database.18.Calculate the allele frequency of the germline variant in this study using the following formula:19.Calculate the correlation of the allele frequencies in the four variant call sets with each other and with the allele frequency from GnomAD using GGally R package. In our study, the allele frequencies in the combined data set from \u223c500 patients gave a correlation coefficient of >0.9 with the allele frequencies in GnomAD.20.Determine whether the germline variant calls separate patients based on self-reported race using the PLINK software.21.Determine the genetic linkage between germline variants at different loci by performing Linkage Disequilibrium analysis.22.a.>libraryLoad required R packageb.i.Homozygous_ref: 0ii.Heterozygous: 1iii.Homozygous_alt: 2Variant genotype is encoded as character vector. Model genotype in ordinal scalec.>labels <- variant_genotypeSave variant genotype for each patientd.>data <- read.csvDownload the survival data to the working directory see and loade.>Risk_survival= survfit\u223c labels,\u00a0\u00a0data=data)>pvalue_Risk_survival= survdiff\u223c\u00a0\u00a0\u00a0labels, data=data, rho=0)>p.val= 1 - pchisq - 1)Survival analysisf.>par, cex.axis=1, cex.lab=1, cex.main=1,font.axis=1, font.lab=1, par(font=1))>plot, col=c,mark.time=TRUE, xlab=\"Follow up in months\", ylab=\"Overallsurvival\", lwd=1)>text))Plot the Kaplan-Meier curves >par \u223c labels\u00a0+ Age\u00a0+\u00a0Percent_aneuploidy\u00a0+ Histology\u00a0+ Grade\u00a0+\u00a0IDH_status\u00a0+ Mutation_count\u00a0+ Chr7gainORChr10loss\u00a0+ MGMT_promoter_status\u00a0+ Chr1OR19q_codeletion\u00a0+\u00a0Treatment_site\u00a0+ PC3, data=data)>summary(variant.cox)Principal component 3 (PC3)Multivariate Cox regression analysis : ConvertDetermine for a given germline variant whether there is a significant difference in survival outcome in the minor allele compared to the reference major allele . Here, we have compared the overall survival outcome between LGG patients (n=507) with different rs1131397 (Chr1-154965759-G-C) genotypes. See 23.The output for multivariate Cox regression analysis includes coefficient, hazard ratio, z-score and p value for each variant. As multiple variants are tested, it is important to correct the p values after Cox regression. In our study, 196,022 variants were tested. False discovery was performed through Bonferroni Correction.24.Determine whether a given germline variant is predictive of increase or decrease in tumor mutation burden and responsiveness to immune checkpoint chemotherapy .25.For germline variants that are significantly associated with a phenotype , determine whether the variant is associated with differences in gene expression of nearby genes by performing expression quantitative trait loci (eQTLs) analysis. For more details on other downstream analyses that can be performed with germline variants, please refer to .In the previous steps, we have identified germline variants from the whole-exome sequences and rna-sequences in the TCGA-LGG cohort. Several downstream analyses can be performed to evaluate the quality and clinical relevance of the identified germline variants.This protocol presents instructions to integrate the whole-exome sequencing datasets from normal and tumor samples and RNA sequencing dataset from the tumor samples of the TCGA-LGG cohort to determine the germline variants.Germline variants from the TCGA datasets are typically called in wxs-normal blood samples. This approach captures exonic region of the genome, allowing one to find the variants within genes. However, sequence (and variants) outside the exonic region, such as the promoters, introns, intron-exon boundaries and UTRs are also captured as a byproduct of whole-exome capture and are present in wxs data . In thisThere were some choices we made in our protocol that may be changed by a user. We use a minimal sequencing coverage threshold of 10 before a variant status is called because that gives us enough confidence that if a variant was present at that locus, it should have been sampled by then (and sampled at least 3 times). This is an arbitrary threshold and other users can set other thresholds if they so desire, but one has to balance the need for finding sufficient patients with a minor allele with the need to be 100% confident that the variant call is correct. In addition, we have a filter that a minimum of three reads should support the reported variant, and this too can be changed by the user. Note that we also removed reads that may have come from PCR duplicates, so that only one read with the identical start position is kept among all the duplicates. Finally, we turned off the calling of structural variants in this analysis so that no insertions, deletions, duplications, inversions, or large copy number variations were called.Our method has the benefit of determining the genotype status of a variant with low sequencing coverage in wxs-normal sample, by taking the genotype status of that variant from the corresponding wxs-tumor sample, where the variant at that position may be supported with higher sequencing coverage. However, if we are still unable to determine the genotype status, we insert the genotype status from the rnaseq counterparts. This method has not significantly affected the accuracy of the variant call in our study because the allele frequency calculated from the rnaseq tumor datasets were significantly positively correlated (r\u00a0>\u00a00.98) with the allele frequencies from the wxs-normal, wxs-tumor and combined-wxs-rnaseq variant call set. Importantly, allele frequencies in our study were significantly positively correlated with the allele frequency of germline variants listed in the population gnomAD database, supporting the reliability of our calls. Specifically, the allele frequency in GnomAD correlated (Pearson\u2019s correlation coefficient) with wxs-normal variant set (r\u00a0>\u00a00.963), wxs-tumor variant set (r\u00a0>\u00a00.964), rnaseq-tumor variant set (r\u00a0>\u00a00.937) and combined-wxs-rnaseq variant set (r\u00a0>\u00a00.947) .Once the genotype status for each variant in each patient is identified, the user can check the survival outcome of minor allele compared to major allele for each variant. The Kaplan-Meier survival analysis for the three genotype in variaThis protocol performs variant calling, pre-processing VCFs, calculating sequencing coverage, determining variant status, merging variant status from multi-samples, determining genotype of variant with low sequencing coverage from the respective wxs-normal, wxs-tumor and rnaseq-tumor BAM files. As these calculations are computationally intensive, we recommend running the protocol on a high-performance cluster. The memory and number of CPUs required to run each step See may varyhttps://gdc.cancer.gov/access-data/obtaining-access-controlled-data.A token is required for downloading controlled test dataset See from theDownloading GDC datasets and germline variant calling consumes considerable amount of time and computational resources. We recommend processing a small number of wxs and rnaseq BAM files to guide the computational resources requirement for the future analyses. This protocol requires user to modify the time needed in the job script for each step accordingly.This protocol follows SLURM based schema and requires knowledge of the bash and R scripting language. Newer users may need to learn some basic Linux commands such as ls, echo, cd, rm, mv, mkdir, find, nano, awk, sed, grep, pwd, bash, and sbatch used in this protocol to execute it fully.A common warning may be displayed for the bam index: BAM index file is older than BAM file (corresponding protocol step: >samtools index \u2217.bamIt is a warning message for bam index file. It can be ignored if you are sure that the index file is up to date. You can create the more recent index file of the bam file using the command below and the warning message should go away.A common error may be displayed: These module(s) or extension(s) exist but cannot be loaded as requested \u00a0<\u00a0value: \u2018names\u2019 attribute must be the same length as the vector and Anindya Dutta (duttaa@uab.edu).Further information and requests for resources should be directed to and will be fulfilled by the technical and lead contacts, Divya Sahu (This study did not generate new unique reagents."} +{"text": "This study aimed to assess the predictive ability of 18F-FDG PET/CT radiomic features for MYCN, 1p and 11q abnormalities in NB.One hundred and twenty-two pediatric patients with NB were retrospectively enrolled. Significant features by multivariable logistic regression were retained to establish a clinical model (C_model), which included clinical characteristics. 18F-FDG PET/CT radiomic features were extracted by Computational Environment for Radiological Research. The least absolute shrinkage and selection operator (LASSO) regression was used to select radiomic features and build models (R-model). The predictive performance of models constructed by clinical characteristic (C_model), radiomic signature (R_model), and their combinations (CR_model) were compared using receiver operating curves (ROCs). Nomograms based on the radiomic score (rad-score) and clinical parameters were developed.n = 86) and a test set (n = 36). Accordingly, 6, 8, and 7 radiomic features were selected to establish R_models for predicting MYCN, 1p and 11q status. The R_models showed a strong power for identifying these aberrations, with area under ROC curves (AUCs) of 0.96, 0.89, and 0.89 in the training set and 0.92, 0.85, and 0.84 in the test set. When combining clinical characteristics and radiomic signature, the AUCs increased to 0.98, 0.91, and 0.93 in the training set and 0.96, 0.88, and 0.89 in the test set. The CR_models had the greatest performance for MYCN, 1p and 11q predictions (P < 0.05).The patients were classified into a training set (The pre-therapy 18F-FDG PET/CT radiomics is able to predict MYCN amplification and 1p and 11 aberrations in pediatric NB, thus aiding tumor stage, risk stratification and disease management in the clinical practice. Neuroblastoma (NB), the most common extracranial solid pediatric tumor, accounts for about 8\u201310% of all childhood cancer and 12\u201315% of childhood cancer mortality . It is t123I-Metaiodobenzylguanidine (123I-MIBG) scintigraphy is a standard practice in the diagnosis of NB in the diagnosis and follow-up of NB patients. 18F-FDG PET imaging has been reported to be equal or superior to 123I-MIBG scan for delineating NB disease extent in the chest, abdomen, and pelvis pathologically confirmed NB; (2) age \u2264 18 years at diagnosis; (3) complete PET/CT imaging data; (4) complete clinical information; (5) no cancer therapy before PET/CT imaging; (6) complete MYCN amplification and 1p and 11q aberrations data. Subsequently, 17 cases were excluded because of unavailable MYCN, 1p and 11q information, and 122 patients were included in this study. These patients were randomly divided into training set and test set with a ratio of 7:3. This retrospective study was approved by Institutional Review Board of our hospital and the requirement of written informed consent was waived.MYCN amplification and 1p and 11q aberrations were determined using FISH from paraffin-embedded tissue obtained by biopsy or surgery at initial diagnosis according to the previously published method . AccordiPatient gender, age, neuron-specific enolase (NSE), serum ferritin (SF), lactate dehydrogenase (LDH), vanillylmandelic acid (VMA), homovanillic acid (HVA), maximum tumor diameter (MTD) in Ultrasound, and MTD in CT and/or MRI.All patients underwent whole body scan on the PET/CT scanner in accordance with EANM guidelines , 20 and Univariate analysis was performed to compare the differences in clinical characteristics. Based on the selected characteristics, a clinical model (C-model) was established.n = 18), shape features (n = 14), gray level co-occurrence matrix (GLCM) features (n = 24), gray level run length matrix (GLRLM) features (n = 16), gray level size zone matrix (GLSZM) features (n = 16), neighboring gray tone difference matrix (NGTDM) features (n = 5), and gray level dependence matrix (GLDM) features (n = 14) were extracted from the original and the pre-processed images. The following methods were used in the imaging processing: wavelet filtering, square, square root, logarithm, exponential and gradient filtering were obtained to assess the reliability of variables using the features extracted from the two sets of ROIs portrayed separately by two different nuclear medicine physicians in 24 out of the 122 patients with NB after 2 months. Because of imbalanced datasets, synthetic minority oversampling technique (SMOTE) was used to improve random oversampling in the training set. Least absolute shrinkage and selection operator (LASSO) was applied for variable selection and regularization in the training set. Predictive R_models were built by logistic regression and the radiomic score (rad-score) for each patient was computed based on the selected radiomic features. Additionally, the selected clinical characteristics combined with radiomics features were used to construct the combination model (CR_model). All models were built and trained in the training set, and the prediction performance was evaluated in the training and test sets. Ten-fold cross-validation was applied to prevent model overfitting in the training process. Receiver operating characteristic (ROC) curve and area under curve (AUC) were employed for the evaluation of the diagnostic performance in the training and test sets.www.python.org) and R . The Python packages of \u201csklearn,\u201d \u201cnumpy,\u201d and \u201cpandas\u201d were used for LASSO binary logistic regression and ROC curve; the \u201cscipy\u201d was for analyzing statistical properties; the \u201cimblearn\u201d was for SMOTE. The R package \u201crms\u201d was employed to create nomograms. The t-test or Mann-Whitney U-test was applied for univariate analysis, and p < 0.05 with a 95% confidence interval was considered as statistical significance. AUC-ROC curve was calculated for evaluating the diagnostic performance of models. AUC ranging from 0.5 to 1.0 is commonly used as a measure of classifier performance. A value of 0.5 is equal to random guessing, while 1.0 means a perfect classifier.Statistical analyses were performed with Python . Between 1p-positive and negative cases, NSE, LDH, VMA, MTD in Ultrasound and MTD in CT/MRI were distinct (All p < 0.05). Between 11q-positive and negative cases, age, SF, LDH, VMA, and HVA were distinct (All p < 0.05) .The total of 2,632 radiomic features were extracted from PET/CT images using pyradiomics. After assessing the robustness, 1,623 out of 2,632 features retained for model building, with intraclass correlation coefficients (ICC) > 0.75. In respect of C-model constructed by logistic regression and trained in the training set, 4 clinical characteristics were selected for MYCN prediction, with 3 characteristics for 1p prediction and 3 characteristics for 11q prediction. As for R_model (radiomics signature) establishment, 6 radiomic features were chosen for MYCN prediction, with 8 features for 1p prediction and 7 features for 11q prediction .In regard to CR_model construction, eight features were chosen for MYCN prediction, which included 4 clinical characteristics and 2 PET, 2 CT features , 3. ElevRad-scores were calculated by the following formula:Rad_score_MYCN = \u22122.6446+ 0.17750 \u00d7 PET_wavelet-LLH_glszm_GrayLevelNonUniformity+ 0.88251 \u00d7 PET_wavelet-HHH_glszm_SizeZoneNonUniformity\u2013 0.00069 \u00d7 CT_exponential_glrlm_LongRunEmphasis\u2013 0.02217 \u00d7 CT_wavelet-HHL_firstorder_MaximumRad_score_1p = 2.9612\u2013 115.24 \u00d7 PET_squareroot_ngtdm_Contrast\u2013 0.29673 \u00d7 PET_logarithm_firstorder_Minimum+ 0.04218 \u00d7 PET_wavelet-LLH_glrlm_LongRunLowGrayLevelEmphasis+ 2.1217 \u00d7 PET_wavelet-HHH_glszm_SmallAreaHighGrayLevelEmphasis\u2013 5.5262 \u00d7 PET_wavelet-HHH_glszm_LowGrayLevelZoneEmphasis\u2013 5.1213 \u00d7 CT_exponential_glszm_SmallAreaEmphasisRad_score_11q = \u22122217.3\u2013 147.63 \u00d7 PET_wavelet-LHL_gldm_DependenceNonUniformityNormalized\u2013 0.41560 \u00d7 CT_wavelet-LLL_glrlm_RunVariance\u2013 0.59915 \u00d7 CT_wavelet-LHL_firstorder_Median+ 58.736 \u00d7 CT_wavelet-LHL_glcm_Imc1\u2013 14.536 \u00d7 CT_wavelet-HLL_glrlm_LowGrayLevelRunEmphasis+ 2232.9 \u00d7 CT_wavelet-HHH_firstorder_Entropy.p-values of radiomic features are shown in p < 0.001). NB with MYCN, 1p and 11q positive had higher Rad-score than those with negative in both the training and test sets.The Nomogram score (Nomo_score) was calculated by the following formula :Nomo_score_MYCN = \u22120.7569 + 0.0064 \u00d7 LDH + 2.4857 \u00d7 Rad_score_MYCNNomo_score_1p = \u22120.5175 + 0.0017 \u00d7 LDH + 1.0476 \u00d7 Rad_score_1pNomo_score_11q = \u22120.3897 \u2013 0.0020 \u00d7 LDH + 0.0088 \u00d7 SF + 1.6657 \u00d7 Rad_score_11qThe nomogram was created based on the training set, which represented individualized prediction and visualized proportion of each factor .To evaluate the performance in predicting MYCN, 1p and 11q status, C_model, R_model and CR_model were compared. The predictive abilities of models were shown in 18F-FDG PET/CT-based radiomics had an extremely important role in predicting MYCN amplification and 1p and 11q aberrations. In particular, CR_model was suggested to be the best model for the prediction of MYCN, 1p and 11q status with the largest AUCs in the training and test sets.Considering the well-established role of MYCN, 1p and 11q abnormalities in the prognosis of NB, identifying these events are crucial for risk stratification. This study provided three distinct forms of predictive models for identifying MYCN and chromosomal abnormalities in a non-invasive way, demonstrating that pre-therapy Recently, clinical variables (such as LDH and SF) have been demonstrated to be prognostic biomarkers in large-scale studies, which suggested to reconsider utilizing LDH and SF as NB risk stratification factors , 23. In In this study, radiomic features were selected to construct CR_model for predicting MYCN, 1p and 11q abnormalities, including: PET_wavelet-LLH_glszm_GrayLevelNonUniformity, PET_wavelet-HHH_glszm_SizeZoneNonUniformity, CT_exponential_glrlm_LongRunEmphasis, CT_wavelet-HHL_firstorder_Maximum, PET_squareroot_ngtdm_Contrast, PET_logarithm_firstorder_Minimum, PET_wavelet-LLH_glrlm_LongRunLowGrayLevelEmphasis, PET_wavelet-HHH_glszm_SmallAreaHighGrayLevelEmphasis, PET_wavelet-HHH_glszm_LowGrayLevelZoneEmphasis, CT_exponential_glszm_SmallAreaEmphasis, PET_wavelet-LHL_gldm_DependenceNonUniformityNormalized, CT_wavelet-LLL_glrlm_RunVariance, CT_wavelet-LHL_firstorder_Median, CT_wavelet-LHL_glcm_Imc1, CT_wavelet-HLL_glrlm_LowGrayLevelRunEmphasis, and CT_wavelet-HHH_firstorder_Entropy. The majority of these features (12/16) were not derived from the primary image but from wavelet decomposition images, possibly because wavelet transformed features contained high-order information that may be more helpful for MYCN, 1p and 11q prediction. Previous studies have revealed the potential value of wavelet features in histologic subtype prediction and prognostic assessment , 26. In 123I-MIBG scan is the most frequently used imaging modality and is regarded as standard of care in patients with NB. In comparison with 18F-FDG PET/CT, 123I-MIBG scan is carried out over 2 days and the image quality is less ideal that could post a challenge to inexperienced physicians the status of MYCN, 1p and 11q can be used for risk stratification, therapy selection, therapy response monitor and prognosis prediction.The potential clinical significance of the present study included: (1) radiomics based on pre-therapy This study had limitations. Small size cohort from single center may influence the generalized ability, sensitivity and specify of the predictive models. Therefore, prospective larger cohort from multi-center is necessary to validate the results and improve the reliability of models for MYCN, 1p and 11q predictions in NB.The models developed by the pre-therapy 18F-FDG PET/CT radiomic signature and clinical parameters are able to predict MYCN amplification and 1p and 11 aberrations in pediatric NB, thus risk stratification, disease management and guiding personalized malignancy therapy in the clinical practice.The original contributions presented in the study are included in the article/The studies involving human participants were reviewed and approved by Beijing Friendship Hospital, Capital Medical University. Written informed consent from the participants' legal guardian/next of kin was not required to participate in this study in accordance with the national legislation and the institutional requirements.LQ, SY, and SZ made substantial contributions to study design, image acquisition, data analysis and interpretation, and new software creation in this work. SZ, HQ, WW, YK, LL, JL, and HZ contributed writing and/or revising the manuscript. JY and JL approved all versions to be published and were responsible for all aspects of this study. All authors contributed to the article and approved the submitted version.This study was supported by Capital Health Development Research Project (No. 2020-2-2025), National Natural Science Foundation of China , and National Key Research and Development Plan (No. 2020YFC0122000).LL was employed by the company Sinounion Medical Technology (Beijing) Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "The Carbon Ore Resources Database (CORD) is a working collection of 399 data files associated with carbon ore resources in the United States. The collection includes spatial/non-spatial, filtered, processed, and secondary data files with original data acquisition efforts focused on domestic coal resources. All data were acquired via open-source, online sources from a combination of 18 national, state, and university entities. Datasets are categorized to represent aspects of carbon ore resources, to include: Geochemistry, Geology, Infrastructure, and Samples. Geospatial datasets are summarized and analyzed by record and dataset density or the number of records or datasets per 400 square kilometer grid cells. Additionally, the \u201cCORD Platform,\u201d an ArcGIS Online geospatial dashboard web application, enables users to interact and query with CORD datasets. The CORD provides a single database and location for data-driven analytical needs associated with the utilization of carbon ore resources. Specifications TableValue of the Data\u2022The Carbon Ore Resources Database (CORD) enables broader understanding and data-driven analyses of in-situ-, supply chain-, and consumer- based carbon resources, by providing a single location to efficiently access carbon ore resource datasets for a range of applications and end users. The systematized database organizes carbon ore data so it can easily be retrieved and analyzed.\u2022Increased accessibility to systematized carbon ore resource datasets benefits research and development scientists, analysts, developers, economists, and engineers from various organizations. These entities include coal mining companies; power plant operators; government agencies; non-governmental organizations (NGOs); and natural resource managers.\u2022Access to integrated, comprehensive carbon ore resource data are necessary for a range of applications, including optimizing coal production and deliveries to existing and new markets; mitigating the impacts of coal ash disposal, acid mine drainage, and greenhouse gas emissions; increase beneficial use of coal and coal by-products; and extraction of specific coal sources for carbon-based products and rare earth elements.\u2022Broader applications include decision support for carbon management and policy, identifying opportunities for the development of coal and carbon management technologies.\u2022Geospatial datasets within the CORD facilitate mapping and analysis using GIS (Geographic Information Systems) software.1https://edx.netl.doe.gov/dataset/cord) as two separate zipped folders, one in a geodatabase format and the other in a folder file structure.The Carbon Ore Resources Database (CORD) is a collection of 399 individual data files associated with carbon ore resources. The original data acquisition efforts focused on coal resources in the United States. Supplementary File 1 provides descriptions for each individual data file organized by category. Supplementary File 2 lists each file by name, category, data type (secondary or processed), coal filter field , data format type , spatial (raster), or table), available formats, source organization, link to the data download source, and publication citation (if available). The CORD can be downloaded from the NETL's Energy Data eXchange website The \u201cInfrastructure network\u201d category consists of nine processed data files and 90,634 records associated with coal resource infrastructure . CurrentThe \u201cSamples integrated\u201d category consists of two processed data files and 64,776 records associated with coal samples . This inThe \u201cSamples original\u201d category consists of 17 processed and secondary data files and 36,216 records associated with coal samples . This in\u2022Samples_All (tab \u201cSamples_All\u201d)\u2022Coal_Delivery_Pathways_2011_2016 \u2022Coal_Mine_Deliveries_2011_2016 \u2022Coal_Mine_Production_2011_2016 \u2022Coal_Source_Regions_Production_Deliveries_2011_2016 \u2022Power_Plant_ByProductsType_2011_2016 (tab \u201cPowerPlant_ByProdType_2011_2016\u201d)\u2022Power_Plant_Consumption_2011_2016 (tab \u201cPowerPlant_Cons_2011_2016\u201d)\u2022Power_Plant_Deliveries_and_ByProducts_2011_2016 (tab \u201cPowerPlant_Del_ByProd_2011_2016\u201d)\u2022Power_Plant_Deliveries_by_Coal_Source_Region_2011_2016 (tab \u201cPowerPlant_Del_by_CSR_2011_2016\u201d)\u2022Power_Plant_Stockpiles_2011_2016 (tab \u201cPowerPlant_Stock_2011_2016\u201d)A data dictionary (field names and descriptions) is provided in an Excel workbook for datasets that required additional processing and integration steps (Supplementary File 3), where each tab refers the following 10 datasets:\u2022CORD_Data_Script1.py - This script takes an input folder path with CSV files and exports the files into a new folder with updated and modified attribute names.\u2022CORD_Data_Script2.py - This script takes an input folder path with CSV files and exports the combined files into a new folder with an updated schema and all empty rows removed.\u2022CORD_Field_map.csv - This CSV file provides the Mapping of the input data fields to the output data fields for the data conversion script CORD_Data_Script1.py.\u2022CORD_Schema_combined.csv - This CSV file contains the combined schema for the data that is converted from multiple input CSV files to a single output CSV. It is used with the CORD_Data_Script2.py python script.Additionally, two python scripts and two CSV files associated with field mapping of the \u201cSamples_All\u201d table are provided in Supplementary File 4:2All data processing was performed using ESRI's ArcGIS ArcMap 10.7 software Secondary data files that did not require any processing were directly imported into the database. If data required filtering for explicit coal records, the field name used to filter the records was recorded Supplementary File 2, within the \u201cCoal_filter_field\u201d. Files labelled as \u201cprocessed\u201d in Supplementary File 2, required additional modification before including into the database. These data files include those in the \u201cInfrastructure network\u201d, \u201cSamples original\u201d, and \u201cSamples integrated\u201d categories. Each processed data file involves a unique method before integrating into the CORD. These methods are described by category and for each processed data file as necessary:Infrastructure network:Coal_Source_Regions_Production_Deliveries_2011_2016: This dataset was created from the original secondary data file \u201cCoal_fields_USGS\u201d https://www.eia.gov/coal/data/browser/). This North Appalachian Basin Region was further split to separate the Pennsylvania Anthracite Region. In total, 109 separate coal source regions were developed. Coal production and delivery quantities information from 2011 through 2016 were added by spatially joining (point features closest to each region) and summing values from the \u201cCoal_Mine_Production_2011_2016\u201d and \u201cCoal_Mine_Deliveries_2011_2016\u201d, respectively.Coal_Delivery_Pathways_2011_2016: This dataset was extracted from the \u201cPage 5 Fuel Receipts and Costs\u201d tab in the EIA-923 excel files Coal_Mine_Deliveries_2011_2016: This dataset was created from the \u201cCoal_Delivery_Pathways_2011_2016\u201d dataset, by dissolving on the MSHA unique identifying number, latitude, and longitude fields to obtain a single unique record for each mine. Delivery quantities were aggregated and summed for each and all years, including total delivery count from each mine. Point features were then created to represent individual mines. To obtain the name of the coal source region associated with each mine , the \u201cCoal_Source_Region_2011_2016\u201d dataset was spatially joined to the mine point features . The mine point features were then joined to the \u201cCoal_Delivery_Pathways_2011_2016\u201d dataset\u201d by a temporary \u201cDelivery_ID\u201d field (deleted after join), to obtain the coal source region names within the deliveries dataset.Coal_Mine_Production_2011_2016: This was extracted from the EIA-7A excel files Power_Plant_Deliveries_by_Coal_Source_Region_2011_2016: This dataset was extracted from the \u201cCoal_Delivery_Pathways_2011_2016\u201ddataset. First, the \u201cCoal_Delivery_Pathways_2011_2016\u201d dataset was dissolved on the unique identifying number for power plants (\u201cPlant_code\u201d) and \u201cCoal_Source_Region\u201d fields to obtain a single unique record for each unique combination of power plant and coal source region. Delivery quantities were aggregated and summed for each and all years. The \u201cCoal_Source_Region\u201d field was then pivoted to add fields for coal delivery quantity totals for each unique combination of region and year. Point features were then created to represent individual power plants.Power_Plant_Deliveries_and_ByProducts_2011_2016: This dataset was extracted from the \u201cCoal_Delivery_Pathways_2011_2016\u201d dataset and the \u201c8A Annual Byproduct Disposition\u201d tab in the EIA-923 excel files Power_Plant_Consumption_2011_2016: This dataset was extracted from the \u201cPage 1 Generation and Fuel Data\u201d tab within the EIA-923 excel files Power_Plant_Stockpiles_2011_2016: This dataset was extracted from the \u201cPage 2 Coal Stocks Data\u201d tab within the EIA-923 excel files Power_Plant_ByProductsType_2011_2016: This dataset was extracted from the \u201c8A Annual Byproduct Disposition\u201d tab in the EIA-923 excel files disposition type]_2011_2016\u201d) and overall total .Samples original:AK_Coal_samples_AGDB_USGS: The original data were extracted from the \u201cMain\u201d, \u201cChemistry\u201d, and \u201cParameters\u201d tables within the Alaska Geochemical Database (geodatabase format) AK_Holitina_Basin_Coal_samples_ADGGS: The original data were filtered for the term \u201ccoal\u201d from the \u201cri2015\u20133-rock-eval-toc\u201d CSV file AK_Jarvis_creek_coal_samples_ADGGS: The original data were extracted from the \u201cpir2018\u20132-jarvis-creek-coal-proximate-analysis\u201d, \u201cpir2018\u20132-jarvis-creek-coal-ultimate-analysis\u201d, and \u201cpir2018\u20132-jarvis-creek-coal-rock-eval-ro-toc\u201d CSV files AR_Coal_samples_AGS: The original data were copied from \u201chttps://www.geology.arkansas.gov/energy/coal-in-arkansas.html under the \u201cChemical Analysis\u201d heading. The entire table was pasted into an excel spreadsheet, converted to a CSV and file geodatabase table.Coal_Ash_samples_NETL: The original data were extracted from the \u201cResults (whole Sample Conc.)\u201d and \u201cResults (Ash Based Conc.)\u201d tables or tabs within the \u201ccollected-samples-spreadsheet-v051515\u201d excel file Coal_CCP_samples_USGS: The original data Coal_samples_NaCQI_USGS: The original data were extracted from the \u201cDescriptive data\u201d, \u201cOxide analyses\u201d, \u201cWhole Coal \u2013 Remnant moisture\u201d, \u201cWhole Coal \u2013 Dry basis\u201d, and \u201cProximate-Ultimate analyses\u201d tables or tabs within the \u201cNaCQI\u201d excel file Coal_samples_NGDB_USGS: The original data were extracted from the \u201cGEODATA\u201d, \u201cNAA\u201d, \u201cOTHER\u201d, and \u201cUNKNOWN\u201d dbf files from the National Geochemical Database for Rocks Coal_samples_PSU_Energy_Institute_Coal_Bank: The original data were downloaded from the PSU Energy Institute Coal Sample Bank COALQUAL_USGS: The original data were extracted from the \u201cCOALQUAL\u201d point feature class, \u201cOxide\u201d, \u201cProximate_Ultimate\u201d, and \u201cTrace_Elements\u201d and file geodatabase tables within the \u201cCOALQUAL\u201d geodatabase Fly_Ash_Samples_Taggart: The original data were downloaded from the supplementary data associated with the Taggart et\u00a0al. (2016) journal publication IL_Coal_quality_samples_ISGS: The original data was directly converted from the \u201ccoal-quality-nonconf\u201d excel file IN_Coal_quality_samples_DB_IGWS: The dataset KY_Coal_quality_samples_KGS: The original data were extracted from the \u201cborehole_12,182,019_19,372\u201d, \u201cphysicalPropsAnaly\u201d, \u201cproximateAnaly\u201d, \u201cultimateAnaly\u201d, \u201cwholeTraceAnaly\u201d, and \u201cashTraceAnaly\u201d excel files from the KGS. All but the 2 \u201cTraceAnaly\u201d tables were joined using the \u201csample_number\u201d field and saved out into a single CSV file OK_Coal_quality_samples_OGS: The original data were extracted from the \u201cData-Coal-Analytical-Header\u201d and \u201cData-Coal-Analytical-Data\u201d excel files from the OGS PRB_Trace_elements_Stratigraphy_USGS: The original data was directly converted from the \u201cwaptg\u201d shapefile WY_Coal_samples_WSGS: The original data was extracted from the \u201cAppendix 1\u201d, \u201cAppendix 2\u201d, \u201cAppendix 3\u201d tabs within the \u201cri-71-ap\u201d excel file from the WSGS Samples integrated:Samples_All: This working dataset was created by manually mapping the fields within the \u201cSamples original\u201d datasets (CSV files) to a new single table schema (Supplementary File 4) in Excel. With the field mapping complete, the new table (CSV file) was populated with the new schema using several python scripts (Supplementary File 4). The resulting CSV file was converted into a file geodatabase table. Additionally, fields with all null values were deleted from the table.Samples_spatial: This working dataset was created by converting the available latitude and longitude coordinates from the \u201cSamples_All\u201d dataset to a point feature class .The authors declare that the work described is original and has not been submitted elsewhere for publication. No conflict of interest exists in this submission.Devin Justman: Methodology, Software, Investigation, Data curation, Writing \u2013 original draft, Visualization. Michael Sabbatino: Software, Data curation, Methodology, Writing \u2013 review & editing. Scott Montross: Conceptualization, Writing \u2013 review & editing. Scott Pantaleone: Writing \u2013 review & editing. Andrew Bean: Writing \u2013 review & editing. Kelly Rose: Conceptualization, Supervision, Project administration, Funding acquisition. Randal B. Thomas: Conceptualization, Supervision, Writing \u2013 review & editing.The authors declare that they have no known competing financial interests or personal relationships which have or could be perceived to have influenced the work reported in this article."} +{"text": "Periophthalmus modestus, is one of the mudskippers, which are the largest group of amphibious teleost fishes, which are uniquely adapted to live on mudflats. Because mudskippers can survive on land for extended periods by breathing through their skin and through the lining of the mouth and throat, they were evaluated as a model for the evolutionary sea-land transition of Devonian protoamphibians, ancestors of all present tetrapods.The shuttles hoppfish (mudskipper), Ab initio and homology-based gene prediction identified 30,505 genes, of which 94% had homology to the 14 Actinopterygii transcriptomes and 89% and 85% to Pfam familes and InterPro domains, respectively. Comparative genomics with 15 Actinopterygii species identified 59,448 gene families of which 12% were only in P. modestus.A total of 39.6, 80.2, 52.9, and 33.3 Gb of Illumina, Pacific Biosciences, 10X linked, and Hi-C data, respectively, was assembled into 1,419 scaffolds with an N50 length of 33 Mb and BUSCO score of 96.6%. The assembly covered 117% of the estimated genome size (729 Mb) and included 23 pseudo-chromosomes anchored by a Hi-C contact map, which corresponded to the top 23 longest scaffolds above 20 Mb and close to the estimated one. Of the genome, 43.8% were various repetitive elements such as DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. We present the high quality of the first genome assembly and gene annotation of the shuttles hoppfish. It will provide a valuable resource for further studies on sea-land transition, bimodal respiration, nitrogen excretion, osmoregulation, thermoregulation, vision, and mechanoreception. Mudskippers are of the subfamily Oxudercinae and the family Oxudercidae, which was recently separated from the family Gobiidae\u00a0, and theBoleophthalmus pectinirostris is useful as a draft genome.The family Oxudercidae has 10 genera and 42 species in FishBase. Among them, 4 species have been sequenced for the draft genome\u00a0[Periophthalmus modestus using Pacific Biosciences (PacBio) long-read, Illumina short-read, 10X linked read, and Hi-C sequencing. P. modestus\u00a0[P. modestus can reach a length of 10 cm , in May 2018. Total DNA was isolated from the muscle of P. modestus using the DNeasy Blood & Tissue kit , following the manufacturer\u2019s protocol.RRID:SCR_018059) with the same PCR primer set. The sequence data were edited and aligned using the ATGC 4.0 software .For species identification, the mitochondrial DNA cytochrome b gene barcode region was amplified using PCR as described in . The PCROrgans of specimens collected in July 2019 were manually dissected for eye, brain, liver, gut, muscle, and fin tissues, and total RNA was extracted from the dissected organs using the RNeasy Mini Kit . The RNA preparation was repeated 3 times, and then 3-replicate RNA samples were mixed and processed for RNA sequencing (RNA-seq) and isoform sequencing (Iso-seq).RRID:SCR_016386). For long-read sequencing, a 20-kb SMRTbell library was prepared and sequenced on a PacBio Sequel using 11 cells. To increase continuity in the genome assembly, we further produced linked reads and Hi-C reads. For linked-read sequencing, a 10X Chromium genome v2 library was constructed and sequenced on an Illumna NovaSeq 6000 instrument. For long-range scaffolding, a Dovetail Hi-C library was prepared with Dovetail Hi-C Library kit and sequenced on an Illumina NovaSeq 6000 instrument .For short-read sequencing, a paired-end library with insert sizes of 550\u00a0bp was constructed using Illumina TruSeq DNA Nano Prep Kit and sequenced on an Illumina HiSeq 4000 instrument . For PacBio Iso-seq, 3 libraries of length 1\u20132, 2\u20133, and 3\u20136\u00a0kb were prepared from polyadenylated RNA according to the PacBio Iso-seq protocol . Six SMRT cells were run on a PacBio RS II system .For RNA-seq, paired-end libraries with insert size of 150\u00a0bp were prepared with the Truseq mRNA Prep kit from total messenger RNA (mRNA), which was subsequently sequenced on an Illumina HiSeq 2500 \u00a0[RRID:SCR_005491)\u00a0[RRID:SCR_017014)\u00a0[Trimmomatic \u00a0 was used_005491)\u00a0 generateRRID:SCR_018550)\u00a0[RRID:SCR_017642)\u00a0[RRID:SCR_018550) using PacBio long reads, and further polished using Pilon \u00a0[RRID:SCR_010910)\u00a0[RRID:SCR_007936) and PCR duplicates were marked using Novosort\u00a0[RRID:SCR_001228)\u00a0[RRID:SCR_015008)\u00a0[RRID:SCR_021173)\u00a0[MiniASM\u00a0 assemble_018550)\u00a0 using Pa_017642)\u00a0 with the_014731)\u00a0 with the_010910)\u00a0 using Il_010910)\u00a0. Dovetai_010910)\u00a0 linked tNovosort\u00a0. Then Hi_001228)\u00a0 accessed_021173)\u00a0 purged hRRID:SCR_012954)\u00a0[de novo library built by RepeatModeler \u00a0[RRID:SCR_021169)\u00a0[Repeats were predicted in 3 ways. Tandem Repeats Finder\u00a0 identifi_012954)\u00a0 identifi_015027)\u00a0 and withde novo, RNA-based and homology-based methods to carry out protein-coding gene prediction. For the de novo and RNA-based gene prediction, Illumina RNA-seq and PacBio Iso-seq datasets were used to generate 2 hint files. Tophat \u00a0[RRID:SCR_008992)\u00a0[RRID:SCR_008417)\u00a0[RRID:SCR_018964)\u00a0[RRID:SCR_015661)\u00a0[RRID:SCR_008417). GeneMark-ET predicts genes with unsupervised training, whereas AUGUSTUS predicts genes with supervised training based on intron and protein hints.We combined _013035)\u00a0 aligned _013035)\u00a0 correcte_008417)\u00a0 generate_018964)\u00a0 predicte_015661)\u00a0 and AUGUP. modestus was aligned against the genes of 14 Actinopterygii genomes (RRID:SCR_011980) using TBLASTN \u00a0[RRID:SCR_020951)\u00a0[RRID:SCR_016088)\u00a0[ab initio prediction only when there was no conflict. Then the merged genes were removed if their coding sequences contained premature stop codons or were not supported by hints. InterProScan \u00a0[RRID:SCR_007701)\u00a0[RRID:SCR_004726)\u00a0[RRID:SCR_003352)\u00a0[RRID:SCR_003412)\u00a0[RRID:SCR_006969)\u00a0[RRID:SCR_003457)\u00a0[RRID:SCR_007952)\u00a0[RRID:SCR_005493)\u00a0[For the homology-based gene prediction, the assembly of genomes and vert_011822)\u00a0 with an _020951)\u00a0 clustere_016088)\u00a0. Finally_005829)\u00a0 annotate_007701)\u00a0, Pfam (P_004726)\u00a0, PIRSF (_003352)\u00a0, PRINTS _006969)\u00a0, PROSITE_003457)\u00a0, SUPERFA_007952)\u00a0, and TIGRRID:SCR_011809)\u00a0[RRID:SCR_017075)\u00a0[RRID:SCR_010835)\u00a0[To predict non-coding genes, Infernal \u00a0, RNAmmer_017075)\u00a0, and tRN_010835)\u00a0 were useRRID:SCR_007839)\u00a0[RRID:SCR_002811) enrichment was performed using the Fisher exact test and false discovery rate correction to identify functionally enriched GO terms among gene families relative to the \u201cgenome background,\u201d as annotated by Pfam.Chromeister\u00a0 performe_007839)\u00a0 identifiRRID:SCR_011812)\u00a0[RRID:SCR_017334)\u00a0[RRID:SCR_006086)\u00a0[RRID:SCR_000667)\u00a0[RRID:SCR_005983)\u00a0[For phylogenetic analysis and divergence time estimation, MUSCLE \u00a0 aligned _017334)\u00a0 filtered_006086)\u00a0 construc_000667)\u00a0 calculat_005983)\u00a0 with thehttp://www.ncbi.nlm.nih.gov/) showed >99% sequence identity to P. modestus (GenBank accession No. DQ901364.1), 89% to Periophthalmus argentilineatus (AP019359.1), and 85% to Periophthalmus barbarus (KF415633.1).Comparison of cytochrome b sequences against the NCBI GenBank database of Illumina, PacBio, 10X linked, and Hi-C data, respectively, for genome sequencing . The genP. modestus with 16 Actinopterygii species for repeats with 25 types . RNAmmerP. modestus and Periophthalmus magnuspinnatus had the lowest score, meaning the closest pair. The second and third lowest score corresponded to the pair of Boleophthalmus pectinirostris with P. magnuspinnatus and P. modestus, respectively. Note that the scores of Danio rerio and Lepisosteus oculatus with the others were >0.99 because of the evolutionary distances.The 17 Actinopterygii genomes were comAstatotilapia calliptera, Anabas testudineus, B. pectinirostris, D. rerio, Esox lucius, Gastersteus aculeatus, Kryptolebias marmoratus, Lates calcarifer, L. oculatus, Oryzias latipes, P. magnuspinnatus, P. modestus, Scophthalmus maximus, Tetraodon nigroviridis, and Takifugu rubireps, respectively. As shown in Fig.\u00a0P. modestus had more families than the others and the number of common families in \u226513 species were dominant. The unique gene families of P. modestus were enriched in negative regulation of RNA metabolic and biosynthetic process, nucleic acid-templated, transcription DNA-templated, nucleobase-containing, biosynthetic process, and cellular macromolecule , respectively.All genomes had 281 single-copy orthologous gene families, which were used to construct a phylogenetic tree and estimate divergence time. The TimeTree database\u00a0 was usedP. modestus with its common ancestor were 411 and 225, while those of P. magnuspinnatus, the closest genome, were 257 and 442, respectively .J.H.C. and Y.Y. conceived the concept; H.Y.S., S.J., and S.H.J. collected and classified the sample; J.H.C. and Y.Y. designed the experiments; J.Y.Y., S.H.B., Y.Y., and J.H.C. analyzed the genomic data; S.H.B. and Y.Y. deposited the data into NCBI; and H.Y.S., Y.Y., and J.H.C. wrote the manuscript. All authors reviewed the manuscript.giab089_GIGA-D-21-00233_Original_SubmissionClick here for additional data file.giab089_GIGA-D-21-00233_Revision_1Click here for additional data file.giab089_GIGA-D-21-00233_Revision_2Click here for additional data file.giab089_GIGA-D-21-00233_Revision_3Click here for additional data file.giab089_Response_to_Reviewer_Comments_Revision_2Click here for additional data file.giab089_Reviewer_1_Report_Original_SubmissionJiang Hu -- 9/1/2021 ReviewedClick here for additional data file.giab089_Reviewer_2_Report_Original_SubmissionYunyun Lv -- 9/7/2021 ReviewedClick here for additional data file.giab089_Reviewer_2_Report_Revision_1Yunyun Lv -- 11/9/2021 ReviewedClick here for additional data file.giab089_Supplemental_Figures_and_TablesClick here for additional data file."} +{"text": "This also falsely reduces PVPI and GEF. One of these studies suggested a correction formula for femoral venous access that markedly reduced the bias for GEDV. Consequently, the last PiCCO-algorithm requires information about the CVC, and correction for femoral access has been shown. However, two recent studies demonstrated inconsistencies of the last PiCCO algorithm using incorrected GEDV for PVPI, but corrected GEDV for GEF. Nevertheless, these studies were based on mathematical analyses of data displayed in a total of 15 patients equipped with only a femoral, but not with a jugular CVC.Transpulmonary thermodilution (TPTD) is used to derive cardiac output CO, global end-diastolic volume GEDV and extravascular lung water EVLW. To facilitate interpretation of these data, several ratios have been developed, including pulmonary vascular permeability index (defined as EVLW/(0.25*GEDV)) and global ejection fraction ((4*stroke volume)/GEDV). PVPI and GEF have been associated to the aetiology of pulmonary oedema and systolic cardiac function, respectively. Several studies demonstrated that the use of Therefore, this study compared PVPI_fem and GEF_fem derived from femoral TPTD to values derived from jugular indicator injection in 25 patients with both jugular and femoral CVCs.54 datasets in 25 patients were recorded. Each dataset consisted of three triplicate TPTDs using the jugular venous access as the gold standard and the femoral access with (PVPI_fem_cor) and without (PVPI_fem_uncor) information about the femoral indicator injection to evaluate, if correction for femoral GEDV pertains to PVPI_fem and GEF_fem.PVPI_fem_uncor was significantly lower than PVPI_jug . Similarly, PVPI_fem_cor was significantly lower than PVPI_jug . This is explained by the finding that PVPI_fem_uncor was not different to PVPI_fem_cor . This clearly suggests that correction for femoral CVC does not pertain to PVPI.GEF_fem_uncor was significantly lower than GEF_jug . By contrast, GEF_fem_cor was not different to GEF_jug . Furthermore, GEF_fem_cor was significantly higher than GEF_fem_uncor . This finding emphasizes that an appropriate correction for femoral CVC is applied to GEF_fem_cor.2/821mL/m2; 129%). This further emphasizes that GEF, but not PVPI is corrected in case of femoral indicator injection.The extent of the correction for GEF and the relation of PVPI_jug/PVPI_fem_uncor are in the same range as the ratio of GEDVI_fem_uncor/GEDVI_fem_cor (1056ml/mFemoral indicator injection for TPTD results in significantly lower values for PVPI and GEF. While the last PiCCO algorithm appropriately corrects GEF, the correction is not applied to PVPI. Therefore, GEF-values can be used in case of femoral CVC, but PVPI-values are substantially underestimated. PVPI_fem_uncor_form was calculated by multiplying PVPI_fem_uncor with the ratio 0.25*GEDVuncorrected/0.25*GEDVcorrected.PVPI_fem_uncor_form was corrected using the formula suggested for correction of femoral indicator injection derived GEDVI: GEDVI(TIF)Click here for additional data file.S2 Fig(TIF)Click here for additional data file."} +{"text": "Scientific Reports7: Article number: 4362310.1038/srep43623; published online: 03022017; updated: 05042017This Article contains errors in Reference 11 which was incorrectly given as:http://www.who.int/influenza/human_animal_interface/faq_H7N9/en/ (2014).World Health Organisation. Frequently Asked Questions on human infection caused by the avian influenza A(H7N9) virus. URL The correct reference is listed below:http://www.who.int/influenza/human_animal_interface/virology_laboratories_and_vaccines/influenza_virus_infections_humans_feb14.pdf (2014).World Health Organisation. Influenza virus infections in humans (February 2014). URL"} +{"text": "Podoviridae family and vB_KpnM_BIS47 of the Myoviridae family, which act against animal-pathogenic Klebsiella pneumoniae strains, were isolated from sewage plants in Poland. They possess double-stranded DNA genomes of 41,697\u00a0bp, 41,335\u00a0bp, 40,605\u00a0bp, and 147,443\u00a0bp, respectively.Four lytic phages, vB_KpnP_BIS33, vB_KpnP_IL33, and vB_KpnP_PRA33 of the Klebsiella pneumoniae is a facultative anaerobic Gram-negative bacterium that causes a wide range of diseases in humans and in domestic and farm animals. As a pathogen, it can acquire resistance to carbapenems, which are often considered to be drugs of last resort (K.\u00a0pneumoniae infections might be phage therapy. Lytic bacteriophages (phages) and/or their gene products, such as lysins, can easily be used as therapeutic agents against bacteria, as they are host specific and generally show no side effects.t resort . One proKlebsiella phages, vB_KpnP_BIS33, vB_KpnP_IL33, vB_KpnP_PRA33, and vB_KpnM_BIS47, were isolated by a standard enrichment method , I\u0142awa (IL33), and Prabuty (PRA33) in Poland. Genomic DNA from the phages was isolated with a modified phenol-chloroform extraction method were identified also for putative homing endonuclease, helicase, DNA ligase, and DNA polymerase. Additionally, CDSs for terminase, head-tail connector protein, collar protein, putative tail tubular proteins, and tail fiber protein were found. Bacteriophages vB_KpnP_BIS33 and vB_KpnP_IL33 possess their own RNA polymerase, suggesting that they are related to phage T7. The CDSs for holin and therapeutically desired endolysin were detected in all four genomes. Lysogenization genes, such as site-specific integrases and repressors, were not identified in any of the four genomes. Additionally, genome annotation of vB_KpnM_BIS47 revealed 18 tRNA genes.Whole-genome sequence alignments with BLASTn and moleNucleotide sequence accession numbers are shown in"} +{"text": "ACS Synthetic Biology abstracts (Volumes 1 to 6 and Volume 7 issue 1) was performed as well as extraction from the following databases: Bionemo v6.0 [1], RegTransbase r20120406 [2], RegulonDB v9.0 [3], RegPrecise v4.0 [4] and Sigmol v20180122 [5].The aim of this dataset is to identify and collect compounds that are known for being detectable by a living cell, through the action of a genetically encoded biosensor and is centred on bacterial transcription factors. Such a dataset should open the possibility to consider a wide range of applications in synthetic biology. The reader will find in this dataset the name of the compounds, their InChI (molecular structure), the publication where the detection was reported, the organism in which this was detected or engineered, the type of detection and experiment that was performed as well as the name of the biosensor. A comment field is also provided that explains why the compound was included in the dataset, based on quotes from the reference publication or the database it was extracted from. Manual curation of Specifications TableValue of the data\u2022This dataset provides a basis for the development of new biosensing circuits for synthetic biology and metabolic engineering applications, e.g. the design of whole-cell biosensor, high-throughput screening experiments, dynamic regulation of metabolic pathways, transcription factor engineering or creation of sensing-enabling pathways.\u2022This dataset provides a unique source of a broad number of compounds that can be detected and acted upon by a cell, increasing the possibility of orthogonal circuit design from the few usual compounds used in those applications.\u2022The manually curated section provides information on where the biosensor has been first reported and successfully used, enabling the reader to select trustworthy information for his application of choice.\u2022Detectable compounds can be searched by both by name and chemical similarity.\u2022This dataset is an update of [10.6084/m9.figshare.3144715.v1].1ACS Synthetic Biology abstracts (Volumes 1 to 6 and Volume 7 issue 1) was performed as well as extraction from the following databases: Bionemo v6.0 The aim of this dataset is to identify and collect compounds that are known for being detectable by a living cell, through the action of a genetically encoded biosensor and is centred on bacterial transcription factors. The dataset should allow the synthetic biology community to consider a wide range of applications. The reader will find in this dataset the name of the compounds, their InChI (molecular structure), the publication where the detection was reported, the organism in which this was detected or engineered, the type of detection and experiment that was performed as well as the name of the biosensor. A comment field is also provided that explains why the compound was included in the dataset, based on quotes from the reference publication or the database it was extracted from. Manual curation of This dataset is available online on GitHub to allow for further updates as well as community contributions.2\u2022Manual curation of ACS Synthetic Biology (Volume 1\u20136 and Volume 7 issue 1):ACS Synthetic Biology (Volume 1\u20136 and Volume 7 issue 1) were read and information relevant to this dataset was extracted from those abstracts. The aim of this manual curation was to establish a list of detectable compounds whose detection method was already successfully implemented in a synthetic circuit, providing a good basis for further implementation for synthetic biologists.All abstracts of \u2022Bionemo v6.0The SQL request used to create this dataset is:SELECT DISTINCT substrate.id_substrate, minesota_code, name FROM substrateINNER JOIN complex_substrate ON complex_substrate.id_substrate=substrate.id_substrateINNER JOIN complex ON complex.id_complex=complex_substrate.id_complexWHERE activity='REG';\u2022RegTransbase r20120406The SQL request used to create this dataset is:SELECT DISTINCT a.pmid, e.name, r.nameFROM regulator2effectors AS reINNER JOIN exp2effectors AS ee ON ee.effector_guid=re.effector_guidINNER JOIN dict_effectors AS e ON e.effector_guid=ee.effector_guidINNER JOIN regulators AS r ON r.regulator_guid=re.regulator_guidINNER JOIN articles AS a ON a.art_guid=ee.art_guidORDER BY e.name;RegTransbase was not maintained anymore at the time of writing of this manuscript.\u2022RegulonDB v9.0The SQL request used to create this dataset is:SELECT c.conformation_id, c.final_state, e.effector_id, e.effector_name, tf.transcription_factor_id, tf.transcription_factor_name, p.reference_id, xdb.external_db_nameFROM effector AS eINNER JOIN conformation_effector_link AS mm_ce ON mm_ce.effector_id=e.effector_idLEFT JOIN conformation AS c ON c.conformation_id=mm_ce.conformation_idLEFT JOIN transcription_factor AS tf ON tf.transcription_factor_id=c.transcription_factor_idLEFT JOIN object_ev_method_pub_link AS x ON x.object_id=c.conformation_id OR x.object_id=tf.transcription_factor_id OR x.object_id=e.effector_idLEFT JOIN publication AS p ON p.publication_id=x.publication_idLEFT JOIN external_db AS xdb ON xdb.external_db_id=p.external_db_idWHERE c.interaction_type IS Null OR c.interaction_type!='Covalent';\u2022RegPrecise v4.0The RegPrecise website was accessed (version v4.0) and all relevant data was extracted from the effector pages of the website.\u2022Sigmol v20170216Quorum Sensing Signaling Molecule page. In the \u201cdetected by\u201d column, we provide the class of signaling compounds the compound belongs to. The comment field reads \u2018Extracted from Sigmol v20170216 \u2013 Uniq_QSSM_\u201cnumber\u201d\u2019.Sigmol was accessed on 16/02/2017 and all effector data was retrieved from the unique 2.1In in vivo, unspecified or other), as well as the repartition of Biosensor type in the full dataset and the manually curated dataset from ACS Synthetic Biology."} +{"text": "The URL at the end of the Materials and Methods section directing readers to download the data is incorrect.https://figshare.com/articles/Survey_of_biologist_s_computational_needs/4643641The correct URL is:"} +{"text": "Gene set enrichment analysis is a popular approach for prioritising the biological processes perturbed in genomic datasets. The Bioconductor project hosts over 80 software packages capable of gene set analysis. Most of these packages search for enriched signatures amongst differentially regulated genes to reveal higher level biological themes that may be missed when focusing only on evidence from individual genes. With so many different methods on offer, choosing the best algorithm and visualization approach can be challenging. The EGSEA package solves this problem by combining results from up to 12 prominent gene set testing algorithms to obtain a consensus ranking of biologically relevant results.This workflow demonstrates how EGSEA can extend limma-based differential expression analyses for RNA-seq and microarray data using experiments that profile 3 distinct cell populations important for studying the origins of breast cancer. Following data normalization and set-up of an appropriate linear model for differential expression analysis, EGSEA builds gene signature specific indexes that link a wide range of mouse or human gene set collections obtained from MSigDB, GeneSetDB and KEGG to the gene expression data being investigated. EGSEA is then configured and the ensemble enrichment analysis run, returning an object that can be queried using several S4 methods for ranking gene sets and visualizing results via heatmaps, KEGG pathway views, GO graphs, scatter plots and bar plots.\u00a0Finally, an HTML report that combines these displays can fast-track the sharing of results with collaborators, and thus expedite downstream biological validation.\u00a0EGSEA is simple to use and can be easily integrated with existing gene expression analysis pipelines for both human and mouse data. In an effort to unify these computational methods and knowledge-bases, theEGSEA R/Bioconductor package was developed. EGSEA, which stands forEnsemble of Gene Set Enrichment Analyses5 combines the results from multiple algorithms to arrive at a consensus gene set ranking to identify biological themes and pathways perturbed in an experiment. EGSEA calculates seven statistics to combine the individual gene set statistics of base GSE methods to rank biologically relevant gene sets. The current version of theEGSEA package6 utilizes the analysis results of up to twelve prominent GSE algorithms that include:ora7,globaltest8,plage9,safe10,zscore11,gage12,ssgsea13,padog14,gsva15,camera16,roast17 andfry17. Theora,gage,camera andgsva methods depend on acompetitive null hypothesis which assumes the genes in a set do not have a stronger association with the experimental condition compared to randomly chosen genes outside the set. The remaining eight methods are based on aself-contained null hypothesis that only considers genes within a set and again assumes that they have no association with the experimental condition.Gene set enrichment analysis allows researchers to efficiently extract biological insights from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of gene set enrichment (GSE) analysis methods released through the Bioconductor projectEGSEAdata package that includes more than 25,000 gene sets for human and mouse organised according to their database sources and c1\u2013c7) that explore different biological themes ranging from very broad through to more specialised ones focusing on cancer and immunology (c7). The other main sources are GeneSetDB3 and KEGG4 which have similar collections focusing on different biological characteristics 18 that consists of 3 cell populations and Mature Luminal (ML)) sorted from the mammary glands of female virgin mice. Triplicate RNA samples from each population were obtained in 3 batches and sequenced on an Illumina HiSeq 2000 using a 100 base-pair single-ended protocol. Raw sequence reads from the fastq files were aligned to the mouse reference genome (mm10) using theRsubread package19. Next, gene-level counts were obtained usingfeatureCounts20 based onRsubread\u2019s built-inmm10 RefSeq-based annotation. The raw data along with further information on experimental design and sample preparation can be downloaded from the Gene Expression Omnibus using GEO Series accession number GSE63310 and will be preprocessed according to the RNA-seq workflow published by Lawet al. (2016)21.The first experiment analysed in this workflow is an RNA-seq dataset from Sheridanet al. (2010)22 and is the microarray equivalent of the RNA-seq dataset mentioned above. The same 3 populations , LP and ML) were sorted from mouse mammary glands via flow cytometry. Total RNA from 5 replicates of each cell population were hybridised onto 3 Illumina MouseWG-6 v2 BeadChips. The intensity files and chip annotation file available in Illumina\u2019s proprietary formats (IDAT and BGX respectively) can be downloaded fromhttp://bioinf.wehi.edu.au/EGSEA/arraydata.zip. The raw data from this experiment is also available from GEO under Series accession number GSE19446.The second experiment analysed in this workflow comes from Limet al. (2016) which performs a differential gene expression analysis on this data set using the Bioconductor packagesedgeR23,limma24 andGlimma25 with gene annotation from theMus.musculus package26. Thelimma package offers a well-developed suite of statistical methods for dealing with differential expression for both microarray and RNA-seq datasets and will be used in the analyses of both datasets presented in this workflow.Our RNA-seq analysis follows on directly from the workflow of Lawhttp://bioinf.wehi.edu.au/EGSEA/mam.rnaseq.rdata. The code below loads the preprocessed count matrix from Lawet al. (2016), performs TMM normalisation27 on the raw counts, and calculates voom weights for use in comparisons of gene expression between Basal and LP, Basal and ML, and LP and ML populations.To get started with this analysis, download the R data file from> library(limma)> library(edgeR)> load(\"mam.rnaseq.rdata\")> names(mam.rnaseq.data)[1] \"samples\" \"counts\" \"genes\"> dim(mam.rnaseq.data)[1] 14165 9> x = calcNormFactors> design = model.matrix(~0+x$samples$group+x$samples$lane)> colnames(design) = gsub)> colnames(design) = gsub)> head(design) Basal LP ML L006 L008\t 1 0 1 0 0 0\t 2 0 0 1 0 0\t 3 1 0 0 0 0\t 4 1 0 0 1 0\t 5 0 0 1 1 0\t 6 0 1 0 1 0\t > contr.matrix = makeContrasts)> head(contr.matrix) Contrasts Levels BasalvsLP BasalvsML LPvsML\t Basal\t 1\t 1\t 0\t LP\t -1\t 0\t 1\t ML\t 0\t -1\t-1\t L006\t 0\t 0\t 0\t L008\t 0\t 0\t 0 voom function28 from thelimma package converts counts to log-counts-per-million (log-cpm) and calculates observation-level precision weights. Thevoom object (v) contains normalized log-cpm values and gene information used by all of the methods in the EGSEA analysis below. The precisionweights stored withinv are also used by thecamera,roast andfry gene set testing methods.The> v = voom > names(v) [1] \"genes\" \"targets\" \"E\" \"weights\" \"design\" et al. (2016), as a detailed explanation of these steps is beyond the scope of this article.For further information on preprocessing see Lawvoom object (v), a design matrix (design) and an optional contrasts matrix (contr.matrix). The design matrix describes how the samples in the experiment relate to the coefficients estimated by the linear model29. The contrasts matrix then compares two or more of these coefficients to allow relative assessment of differential expression. Base methods that utilize linear models such as those fromlimma andGSVA make use of the design and contrasts matrices directly. For methods that do not support linear models, these two matrices are used to extract the group information for each comparison.The EGSEA algorithm makes use of theEGSEAdata includes more than 25,000 gene sets organized in collections depending on their database sources. Summary information about the gene set collections available inEGSEAdata can be displayed as follows:The package> library(EGSEAdata)> egsea.data(\"mouse\")The following databases are available in EGSEAdata for Mus musculus: Database name: KEGG PathwaysVersion: NADownload/update date: 07 March 2017Data source: gage::kegg.gsetsSupported species: human, mouse, ratGene set collections: Signaling, Metabolism, DiseaseRelated data objects: kegg.pathwaysNumber of gene sets in each collection for Mus musculus :Signaling: 132Metabolism: 89Disease: 67 Database name: Molecular Signatures Database (MSigDB)Version: 5.2Download/update date: 07 March 2017Data source: http://software.broadinstitute.org/gseaSupported species: human, mouseGene set collections: h, c1, c2, c3, c4, c5, c6, c7Related data objects: msigdb, Mm.H, Mm.c2, Mm.c3, Mm.c4, Mm.c5, Mm.c6, Mm.c7Number of gene sets in each collection for Mus musculus :h Hallmark Signatures: 50c2 Curated Gene Sets: 4729c3 Motif Gene Sets: 836c4 Computational Gene Sets: 858c5 GO Gene Sets: 6166c6 Oncogenic Signatures: 189c7 Immunologic Signatures: 4872 Database name: GeneSetDB DatabaseVersion: NADownload/update date: 15 January 2016Data source: http://www.genesetdb.auckland.ac.nz/Supported species: human, mouse, ratGene set collections: gsdbdis, gsdbgo, gsdbdrug, gsdbpath, gsdbregRelated data objects: gsetdb.human, gsetdb.mouse, gsetdb.ratNumber of gene sets in each collection for Mus musculus :GeneSetDB Drug/Chemical: 6019GeneSetDB Disease/Phenotype: 5077GeneSetDB Gene Ontology: 2202GeneSetDB Pathway: 1444GeneSetDB Gene Regulation: 201 Type ? to get a specific informationabout it, e.g., ?kegg.pathways. ?) command, for instance?Mm.c2 will return more information on the mouse version of the c2 collection from MSigDB. The above information can be returned as a list:As the output above suggests, users can obtain help on any of the collections using the standard R help > names(info)[1] \"kegg\" \"msigdb\" \"gsetdb\"> info$msigdb$info$collections[1] \"h\" \"c1\" \"c2\" \"c3\" \"c4\" \"c5\" \"c6\" \"c7\" EGSEA package, the KEGG pathways, c2 (curated gene sets) and c5 (Gene Ontology gene sets) collections from the MSigDB database are selected. Next, an index is built for each gene set collection using the EGSEA indexing functions to link the genes in the different gene set collections to the rows of our RNA-seq gene expression matrix. Indexes for the c2 and c5 collections from MSigDB and for the KEGG pathways are built using thebuildIdx function which relies on Entrez gene IDs as its key. In theEGSEAdata gene set collections, Entrez IDs are used as they are widely adopted by the different source databases and tend to be more consistent and robust since there is one identifier per gene in a gene set. It is also relatively easy to convert other gene IDs into Entrez IDs.To highlight the capabilities of the> library(EGSEA)> gs.annots = buildIdx, go.part = TRUE)[1] \"Loading MSigDB Gene Sets ... \"[1] \"Loaded gene sets for the collection c2 ...\"[1] \"Indexed the collection c2 ...\"[1] \"Created annotation for the collection c2 ...\"[1] \"Loaded gene sets for the collection c5 ...\"[1] \"Indexed the collection c5 ...\"[1] \"Created annotation for the collection c5 ...\"MSigDB c5 gene set collection has been partitioned intoc5BP, c5CC, c5MF[1] \"Building KEGG pathways annotation object ... \"> names(gs.annots)[1] \"c2\" \"c5BP\" \"c5CC\" \"c5MF\" \"kegg\" summary,show andgetSetByName (orgetSetByID) can be invoked on an object of classGSCollectionIndex, which stores all of the relevant gene set information, as follows:To obtain additional information on the gene set collection indexes, including the total number of gene sets, the version number and date of last revision, the methods> class(gs.annots$c2)[1] \"GSCollectionIndex\"attr[1] \"EGSEA\"> summary(gs.annots$c2)c2 Curated Gene Sets (c2): 4726 gene sets - Version: 5.2, Update date: 07 March 2017> show(gs.annots$c2)An object of class \"GSCollectionIndex\"Number of gene sets: 4726Annotation columns: ID, GeneSet, BroadUrl, Description, PubMedID, NumGenes, ContributorTotal number of indexing genes: 14165Species: Mus musculusCollection name: c2 Curated Gene SetsCollection unique label: c2Database version: 5.2Database update date: 07 March 2017> s = getSetByNameID: M13072GeneSet: SMID_BREAST_CANCER_LUMINAL_A_DNBroadUrl: http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_A_DN.htmlDescription: Genes down-regulated in the luminal A subtype of breast cancer.PubMedID: 18451135NumGenes: 23/24Contributor: Jessica Robertson> class(s)[1] \"list\"> names(s)[1] \"SMID_BREAST_CANCER_LUMINAL_A_DN\"> names(s$SMID_BREAST_CANCER_LUMINAL_A_DN)[1] \"ID\" \"GeneSet\" \"BroadUrl\" \"Description\" \"PubMedID\"[6] \"NumGenes\" \"Contributor\" GSCollectionIndex store for each gene set the Entrez gene IDs in the slotoriginal, the indexes in the slotidx and additional annotation for each set in the slotanno.Objects of class> slotNames(gs.annots$c2)[1] \"original\" \"idx\" \"anno\" \"featureIDs\" \"species\"[6] \"name\" \"label\" \"version\" \"date\" buildCustomIdx,buildGMTIdx,buildKEGGIdx,buildMSigDBIdx andbuildGeneSetDBIdx can be also used to build gene set collection indexes. The functionsbuildCustomIdx andbuildGMTIdx were written to allow users to run EGSEA on gene set collections that may have been curated within a lab or downloaded from public databases and allow use of gene identifiers other than Entrez IDs. Example databases include, ENCODE Gene Set Hub (available fromhttps://sourceforge.net/projects/encodegenesethub/), which is a growing resource of gene sets derived from high quality ENCODE profiling experiments encompassing hundreds of DNase hypersensitivity, histone modification and transcription factor binding experiments30. Other resources include PathwayCommons (http://www.pathwaycommons.org/)31 and theKEGGREST32 package that provides access to up-to-date KEGG pathways across many species.Other EGSEA functions such asgenes data.frame of thevoom object as follows:Before an EGSEA test is carried out, a few parameters need to be specified. First, a mapping between Entrez IDs and Gene Symbols is created for use by the visualization procedures. This mapping can be extracted from the> colnames(v$genes)[1] \"ENTREZID\" \"SYMBOL\" \"CHR\"> symbolsMap = v$genes> colnames(symbolsMap) = c> symbolsMap = as.character baseMethods in the code below), which determines the individual algorithms that are used in the ensemble testing. The supported base methods can be listed using the functionegsea.base as follows:Another important parameter in EGSEA is the list of base GSE methods , which can be listed as follows:Since each base method generates different> egsea.combine[1] \"fisher\" \"wilkinson\" \"average\" \"logitp\" \"sump\" \"sumz\"[7] \"votep\" \"median\" Finally, the sorting of EGSEA results plays an essential role in identifying relevant gene sets. Any of EGSEA\u2019s combined scores or the rankings from individual base methods can be used for sorting the results.> egsea.sort [1] \"p.value\" \"p.adj\" \"vote.rank\" \"avg.rank\" \"med.rank\" [6] \"min.pvalue\" \"min.rank\" \"avg.logfc\" \"avg.logfc.dir\" \"direction\"[11] \"significance\" \"camera\" \"roast\" \"safe\" \"gage\"[16] \"padog\" \"plage\" \"zscore\" \"gsva\" \"ssgsea\"[21] \"globaltest\" \"ora\" \"fry\" p.adj is the default option for sorting EGSEA results for convenience, we recommend the use of eithermed.rank orvote.rank because they efficiently utilize the rankings of individual methods and tend to produce fewer false positives5.Althoughegsea function that takes avoom object, a contrasts matrix, collections of gene sets and other run parameters as follows:Next, the EGSEA analysis is performed using the> gsa = egseaEGSEA analysis has started##------ Fri Jun 16 09:49:11 2017 ------##Log fold changes are estimated using limma package ...limma DE analysis is carried out ...Number of used cores has changed to 3in order to avoid CPU overloading.EGSEA is running on the provided data and c2 collectionEGSEA is running on the provided data and c5BP collectionEGSEA is running on the provided data and c5CC collectionEGSEA is running on the provided data and c5MF collectionEGSEA is running on the provided data and kegg collection##------ Fri Jun 16 09:57:56 2017 ------##EGSEA analysis took 525.812 seconds.EGSEA analysis has completed contrasts argument. If this parameter isNULL, all pairwise comparisons based onv$targets$group are created, assuming thatgroup is the primary factor in the design matrix. Likewise, all the coefficients of the primary factor are used if the design matrix has an intercept.In situations where the design matrix includes an intercept, a vector of integers that specify the columns of the design matrix to test using EGSEA can be passed to theEGSEA is implemented with parallel computing features enabled using theparallel package33 at both the method-level and experimental contrast-level. The running time of the EGSEA test depends on the base methods selected and whether report generation is enabled or not. The latter significantly increases the run time, particularly if the argumentdisplay.top is assigned a large value (> 20) and/or a large number of gene set collections are selected. EGSEA reporting functionality generates set-level plots for the top gene sets as well as collection-level plots.EGSEA package also has a function namedegsea.cnt, that can perform the EGSEA test using an RNA-seq count matrix rather than avoom object, a function namedegsea.ora, that can perform over-representation analysis with EGSEA reporting capabilities using only a vector of gene IDs, and theegsea.ma function that can perform EGSEA testing using a microarray expression matrix as shown later in the workflow.TheClasses used to manage the results. The output of the functionsegsea,egsea.cnt,egsea.ora andegsea.ma is an S4 object of classEGSEAResults. Several S4 methods can be invoked to query this object. For example, an overview of the EGSEA analysis can be displayed using theshow method as follows:> show(gsa)An object of class \"EGSEAResults\"Total number of genes: 14165Total number of samples: 9Contrasts: BasalvsLP, BasalvsML, LPvsMLBase GSE methods: camera (limma:3.32.2), safe (safe:3.16.0), gage (gage:2.26.0), padog (PADOG:1.18.0), plage (GSVA:1.24.1), zscore (GSVA:1.24.1), gsva (GSVA:1.24.1), ssgsea (GSVA:1.24.1),P-values combining method: wilkinsonSorting statistic: med.rankOrganism: Mus musculusHTML report generated: NoTested gene set collections:c2 Curated Gene Sets (c2): 4726 gene sets - Version: 5.2, Update date: 07 March 2017c5 GO Gene Sets (BP) (c5BP): 4653 gene sets - Version: 5.2, Update date: 07 March 2017c5 GO Gene Sets (CC) (c5CC): 584 gene sets - Version: 5.2, Update date: 07 March 2017c5 GO Gene Sets (MF) (c5MF): 928 gene sets - Version: 5.2, Update date: 07 March 2017KEGG Pathways (kegg): 287 gene sets - Version: NA, Update date: 07 March 2017EGSEA version: 1.5.2EGSEAdata version: 1.4.0Use summary(object) and topSets to explore this object. p-values derived from different GSE algorithms, the sorting statistic used and the size of each gene set collection. Note that the gene set collections are identified using the labels that appear in parentheses (e.g.c2) in the output ofshow.This command displays the number of genes and samples that were included in the analysis, the experimental contrasts, base GSE methods, the method used to combine theGetting top ranked gene sets. A summary of the top 10 gene sets in each collection for each contrast in addition to the EGSEA comparative analysis can be displayed using the S4 methodsummary as follows:> summary(gsa)**** Top 10 gene sets in the c2 Curated Gene Sets collection ****** Contrast BasalvsLP **LIM_MAMMARY_STEM_CELL_DN | LIM_MAMMARY_LUMINAL_PROGENITOR_UPMONTERO_THYROID_CANCER_POOR_SURVIVAL_UP | SMID_BREAST_CANCER_LUMINAL_A_DNNAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP | REACTOME_LATENT_INFECTION_OF_HOMO_SAPIENS...REACTOME_TRANSFERRIN_ENDOCYTOSIS_AND_RECYCLING | FARMER_BREAST_CANCER_CLUSTER_2KEGG_EPITHELIAL_CELL_SIGNALING_... | LANDIS_BREAST_CANCER_PROGRESSION_UP ** Contrast BasalvsML **LIM_MAMMARY_STEM_CELL_DN | LIM_MAMMARY_STEM_CELL_UPLIM_MAMMARY_LUMINAL_MATURE_DN | PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DNNAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP | LIM_MAMMARY_LUMINAL_MATURE_UPCHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP | RICKMAN_HEAD_AND_NECK_CANCER_AYAGUE_PRETUMOR_DRUG_RESISTANCE_DN | BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN ** Contrast LPvsML **LIM_MAMMARY_LUMINAL_MATURE_UP | LIM_MAMMARY_LUMINAL_MATURE_DNPHONG_TNF_RESPONSE_VIA_P38_PARTIAL | WOTTON_RUNX_TARGETS_UPWANG_MLL_TARGETS | PHONG_TNF_TARGETS_DNREACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS | CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DNGERHOLD_RESPONSE_TO_TZD_DN | DURAND_STROMA_S_UP ** Comparison analysis **LIM_MAMMARY_LUMINAL_MATURE_DN | LIM_MAMMARY_STEM_CELL_DNNAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP | LIM_MAMMARY_LUMINAL_MATURE_UPCOLDREN_GEFITINIB_RESISTANCE_DN | LIM_MAMMARY_STEM_CELL_UPCHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP | LIM_MAMMARY_LUMINAL_PROGENITOR_UPBERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN | MIKKELSEN_IPS_WITH_HCP_H3K27ME3 **** Top 10 gene sets in the c5 GO Gene Sets (BP) collection ****** Contrast BasalvsLP **GO_SYNAPSE_ORGANIZATION | GO_IRON_ION_TRANSPORTGO_CALCIUM_INDEPENDENT_CELL_CELL_ADHESION_VIA_PLASMA_MEMBRANE_CELL_ADHESION_MOLECULES | GO_PH_REDUCTIONGO_HOMOPHILIC_CELL_ADHESION_VIA_PLASMA_MEMBRANE_ADHESION_MOLECULES | GO_VACUOLAR_ACIDIFICATIONGO_FERRIC_IRON_TRANSPORT | GO_TRIVALENT_INORGANIC_CATION_TRANSPORTGO_NEURON_PROJECTION_GUIDANCE | GO_MESONEPHROS_DEVELOPMENT ** Contrast BasalvsML **GO_FERRIC_IRON_TRANSPORT | GO_TRIVALENT_INORGANIC_CATION_TRANSPORTGO_IRON_ION_TRANSPORT | GO_NEURON_PROJECTION_GUIDANCEGO_GLIAL_CELL_MIGRATION | GO_SPINAL_CORD_DEVELOPMENTGO_REGULATION_OF_SYNAPSE_ORGANIZATION | GO_ACTION_POTENTIALGO_MESONEPHROS_DEVELOPMENT | GO_NEGATIVE_REGULATION_OF_SMOOTH_MUSCLE_CELL_MIGRATION ** Contrast LPvsML **GO_NEGATIVE_REGULATION_OF_NECROTIC_CELL_DEATH | GO_PARTURITIONGO_RESPONSE_TO_VITAMIN_D | GO_GPI_ANCHOR_METABOLIC_PROCESSGO_REGULATION_OF_BLOOD_PRESSURE | GO_DETECTION_OF_MOLECULE_OF_BACTERIAL_ORIGINGO_CELL_SUBSTRATE_ADHESION | GO_PROTEIN_TRANSPORT_ALONG_MICROTUBULEGO_INTRACILIARY_TRANSPORT | GO_CELLULAR_RESPONSE_TO_VITAMIN ** Comparison analysis **GO_IRON_ION_TRANSPORT | GO_FERRIC_IRON_TRANSPORTGO_TRIVALENT_INORGANIC_CATION_TRANSPORT | GO_NEURON_PROJECTION_GUIDANCEGO_MESONEPHROS_DEVELOPMENT | GO_SYNAPSE_ORGANIZATIONGO_REGULATION_OF_SYNAPSE_ORGANIZATION | GO_MEMBRANE_DEPOLARIZATION_DURING_CARDIAC_MUSCLE_CELL_ACTION_POTENTIALGO_HOMOPHILIC_CELL_ADHESION_VIA_PLASMA_MEMBRANE_ADHESION_MOLECULES | GO_NEGATIVE_REGULATION_OF_SMOOTH_MUSCLE_CELL_MIGRATION **** Top 10 gene sets in the c5 GO Gene Sets (CC) collection ****** Contrast BasalvsLP **GO_PROTON_TRANSPORTING_V_TYPE_ATPASE_COMPLEX | GO_VACUOLAR_PROTON_TRANSPORTING_V_TYPE_ATPASE_COMPLEXGO_MICROTUBULE_END | GO_MICROTUBULE_PLUS_ENDGO_ACTIN_FILAMENT_BUNDLE | GO_CELL_CELL_ADHERENS_JUNCTIONGO_NEUROMUSCULAR_JUNCTION | GO_AP_TYPE_MEMBRANE_COAT_ADAPTOR_COMPLEXGO_INTERMEDIATE_FILAMENT | GO_CONDENSED_NUCLEAR_CHROMOSOME_CENTROMERIC_REGION ** Contrast BasalvsML **GO_FILOPODIUM_MEMBRANE | GO_LATE_ENDOSOME_MEMBRANEGO_PROTON_TRANSPORTING_V_TYPE_ATPASE_COMPLEX | GO_NEUROMUSCULAR_JUNCTIONGO_COATED_MEMBRANE | GO_ACTIN_FILAMENT_BUNDLEGO_CLATHRIN_COAT | GO_AP_TYPE_MEMBRANE_COAT_ADAPTOR_COMPLEXGO_CLATHRIN_ADAPTOR_COMPLEX | GO_CONTRACTILE_FIBER ** Contrast LPvsML **GO_CILIARY_TRANSITION_ZONE | GO_TCTN_B9D_COMPLEXGO_NUCLEAR_NUCLEOSOME | GO_INTRINSIC_COMPONENT_OF_ORGANELLE_MEMBRANEGO_ENDOPLASMIC_RETICULUM_QUALITY_CONTROL_COMPARTMENT | GO_KERATIN_FILAMENTGO_PROTEASOME_COMPLEX | GO_CILIARY_BASAL_BODYGO_PROTEASOME_CORE_COMPLEX | GO_CORNIFIED_ENVELOPE ** Comparison analysis **GO_PROTON_TRANSPORTING_V_TYPE_ATPASE_COMPLEX | GO_ACTIN_FILAMENT_BUNDLEGO_NEUROMUSCULAR_JUNCTION | GO_AP_TYPE_MEMBRANE_COAT_ADAPTOR_COMPLEXGO_CONTRACTILE_FIBER | GO_INTERMEDIATE_FILAMENTGO_LATE_ENDOSOME_MEMBRANE | GO_CLATHRIN_VESICLE_COATGO_ENDOPLASMIC_RETICULUM_QUALITY_CONTROL_COMPARTMENT | GO_MICROTUBULE_END **** Top 10 gene sets in the c5 GO Gene Sets (MF) collection ****** Contrast BasalvsLP **GO_HYDROGEN_EXPORTING_ATPASE_ACTIVITY | GO_SIGNALING_PATTERN_RECOGNITION_RECEPTOR_ACTIVITYGO_LIPID_TRANSPORTER_ACTIVITY | GO_TRIGLYCERIDE_LIPASE_ACTIVITYGO_AMINE_BINDING | GO_STRUCTURAL_CONSTITUENT_OF_MUSCLEGO_NEUROPEPTIDE_RECEPTOR_ACTIVITY | GO_WIDE_PORE_CHANNEL_ACTIVITYGO_CATION_TRANSPORTING_ATPASE_ACTIVITY | GO_LIPASE_ACTIVITY ** Contrast BasalvsML **GO_G_PROTEIN_COUPLED_RECEPTOR_ACTIVITY | GO_TRANSMEMBRANE_RECEPTOR_PROTEIN_KINASE_ACTIVITYGO_STRUCTURAL_CONSTITUENT_OF_MUSCLE | GO_VOLTAGE_GATED_SODIUM_CHANNEL_ACTIVITYGO_CORECEPTOR_ACTIVITY | GO_TRANSMEMBRANE_RECEPTOR_PROTEIN_TYROSINE_KINASE_ACTIVITYGO_LIPID_TRANSPORTER_ACTIVITY | GO_SULFOTRANSFERASE_ACTIVITYGO_CATION_TRANSPORTING_ATPASE_ACTIVITY | GO_PEPTIDE_RECEPTOR_ACTIVITY ** Contrast LPvsML **GO_MANNOSE_BINDING | GO_PHOSPHORIC_DIESTER_HYDROLASE_ACTIVITYGO_BETA_1_3_GALACTOSYLTRANSFERASE_ACTIVITY | GO_COMPLEMENT_BINDINGGO_ALDEHYDE_DEHYDROGENASE_NAD_ACTIVITY | GO_MANNOSIDASE_ACTIVITYGO_LIGASE_ACTIVITY_FORMING_CARBON_NITROGEN_BONDS | GO_CARBOHYDRATE_PHOSPHATASE_ACTIVITYGO_LIPASE_ACTIVITY | GO_PEPTIDE_RECEPTOR_ACTIVITY ** Comparison analysis **GO_STRUCTURAL_CONSTITUENT_OF_MUSCLE | GO_LIPID_TRANSPORTER_ACTIVITYGO_CATION_TRANSPORTING_ATPASE_ACTIVITY | GO_CHEMOREPELLENT_ACTIVITYGO_HEPARAN_SULFATE_PROTEOGLYCAN_BINDING | GO_TRANSMEMBRANE_RECEPTOR_PROTEIN_TYROSINE_KINASE_ACTIVITYGO_LIPASE_ACTIVITY | GO_PEPTIDE_RECEPTOR_ACTIVITYGO_CORECEPTOR_ACTIVITY | GO_TRANSMEMBRANE_RECEPTOR_PROTEIN_KINASE_ACTIVITY **** Top 10 gene sets in the KEGG Pathways collection ****** Contrast BasalvsLP **Collecting duct acid secretion | alpha-Linolenic acid metabolismSynaptic vesicle cycle | Hepatitis CVascular smooth muscle contraction | Rheumatoid arthritiscGMP-PKG signaling pathway | Axon guidanceProgesterone-mediated oocyte maturation | Arrhythmogenic right ventricular cardiomyopathy (ARVC) ** Contrast BasalvsML **Collecting duct acid secretion | Synaptic vesicle cycleOther glycan degradation | Axon guidanceArrhythmogenic right ventricular cardiomyopathy (ARVC) | Glycerophospholipid metabolismLysosome | Vascular smooth muscle contractionProtein digestion and absorption | Oxytocin signaling pathway ** Contrast LPvsML **Glycosylphosphatidylinositol(GPI)-anchor biosynthesis | Histidine metabolismDrug metabolism - cytochrome P450 | PI3K-Akt signaling pathwayProteasome | Sulfur metabolismRenin-angiotensin system | Nitrogen metabolismTyrosine metabolism | Systemic lupus erythematosus ** Comparison analysis **Collecting duct acid secretion | Synaptic vesicle cycleVascular smooth muscle contraction | Axon guidanceArrhythmogenic right ventricular cardiomyopathy (ARVC) | Oxytocin signaling pathwayLysosome | Adrenergic signaling in cardiomyocytesLinoleic acid metabolism | cGMP-PKG signaling pathway comparative analysis allows researchers to estimate the significance of a gene set across multiple experimental contrasts. This analysis helps in the identification of biological processes that are perturbed in multiple experimental conditions simultaneously. This experiment is the RNA-seq equivalent of Limet al. (2010)22, who used Illumina microarrays to study the same cell populations (see later), so it is reassuring to observe theLIM gene signatures derived from this experiment amongst the top ranked c2 gene signatures in both the individual contrasts and comparative results.EGSEA\u2019sN sets in each collection and contrast using the methodtopSets. For example, the top 10 gene sets in the c2 collection for the comparative analysis can be retrieved as follows:Another way of exploring the EGSEA results is to retrieve the top ranked> topSets Extracting the top gene sets of the collection c2 Curated Gene Sets for the contrast comparison Sorted by med.rank [1] \"LIM_MAMMARY_LUMINAL_MATURE_DN\" [2] \"LIM_MAMMARY_STEM_CELL_DN\" [3] \"NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP\" [4] \"LIM_MAMMARY_LUMINAL_MATURE_UP\" [5] \"COLDREN_GEFITINIB_RESISTANCE_DN\" [6] \"LIM_MAMMARY_STEM_CELL_UP\" [7] \"CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP\" [8] \"LIM_MAMMARY_LUMINAL_PROGENITOR_UP\" [9] \"BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN\" [10] \"MIKKELSEN_IPS_WITH_HCP_H3K27ME3\" med.rank as selected whenegsea was invoked above. When the argumentnames.only is set toFALSE, additional information is displayed for each gene set including gene set annotation, the EGSEA scores and the individual rankings by each base method. As expected, gene sets retrieved by EGSEA included theLIM gene sets22 that were derived from microarray profiles of analagous mammary cell populations as well as those derived from populations with similar origin (sets 7 and 9) and behaviour or characteristics (sets 5 and 10).The gene sets are ordered based on theirtopSets can be used to search for gene sets of interest based on different EGSEA scores as well as the rankings of individual methods. For example, the ranking of the sixLIM gene sets from the c2 collection can be displayed based on themed.rank as follows:Next,> t = topSets> t p.adj Rank med.rank vote.rankLIM_MAMMARY_LUMINAL_MATURE_DN 1.646053e-29 1 36 5LIM_MAMMARY_STEM_CELL_DN 6.082053e-43 2 37 5LIM_MAMMARY_LUMINAL_MATURE_UP 2.469061e-22 4 92 5LIM_MAMMARY_STEM_CELL_UP 3.154132e-103 6 134 5LIM_MAMMARY_LUMINAL_PROGENITOR_UP 3.871536e-30 8 180 5LIM_MAMMARY_LUMINAL_PROGENITOR_DN 2.033005e-06 178 636 115 LIM gene sets are ranked in the top 10 by EGSEA, the values shown in the median rank (med.rank) column indicate that individual methods can assign much lower ranks to these sets. EGSEA\u2019s prioritisation of these gene sets demonstrates the benefit of an ensemble approach.While five of theSimilarly, we can find the top 10 pathways in the KEGG collection from the ensemble analysis for the Basal versus LP contrast and the comparative analysis as follows:> topSets Extracting the top gene sets of the collection KEGG Pathways for the contrast BasalvsLP Sorted by med.rank [1] \"Collecting duct acid secretion\" \"alpha-Linolenic acid metabolism\" [3] \"Synaptic vesicle cycle\" \"Hepatitis C\" [5] \"Vascular smooth muscle contraction\" \"Rheumatoid arthritis\" [7] \"cGMP-PKG signaling pathway\" \"Axon guidance\" [9] \"Progesterone-mediated oocyte maturation\" \"Arrhythmogenic right ventricular cardiomyopathy (ARVC)\" > topSets Extracting the top gene sets of the collection KEGG Pathways for the contrast comparison Sorted by med.rank [1] \"Collecting duct acid secretion\" \"Synaptic vesicle cycle\" [3] \"Vascular smooth muscle contraction\" \"Axon guidance\" [5] \"Arrhythmogenic right ventricular cardiomyopathy (ARVC)\" \"Oxytocin signaling pathway\" [7] \"Lysosome\" \"Adrenergic signaling in cardiomyocytes\" [9] \"Linoleic acid metabolism\" \"cGMP-PKG signaling pathway\" Vascular smooth muscle contraction andOxytocin signalling pathway) and milk production and secretion from luminal lineage cells .EGSEA highlights many pathways with known importance in the mammary gland such as those associated with distinct roles in lactation like basal cell contraction Generating heatmap for LIM_MAMMARY_STEM_CELL_UP from the collectionc2 Curated Gene Sets and for the contrast comparison> plotHeatmapGenerating heatmap for LIM_MAMMARY_STEM_CELL_DN from the collectionc2 Curated Gene Sets and for the contrast comparison plotHeatmap, thegene.set value must match the name returned from thetopSets method. The rows of the heatmap represent the genes in the set and the columns represent the experimental contrasts. The heatmap colour-scale ranges from down-regulated (blue) to up-regulated (red) while the row labels (Gene symbols) are coloured in green when the genes are statistically significant in the DE analysis (i.e. FDR\u2264 0.05 in at least one contrast). Heatmaps can be generated for individual comparisons by changing thecontrast argument ofplotHeatmap. TheplotHeatmap method also generates a CSV file that includes the DE analysis results fromlimma::topTable for all expressed genes in the selected gene set and for each contrast (in the case ofcontrast = \"comparison\"). This file can be used to create customised plots using other R/Bioconductor packages.When usingplotPathway method which uses functionality from thepathview package36. For example, the third KEGG signalling pathway retrieved for the contrastBasalvsLP isVascular smooth muscle contraction and can be visualized as follows:In addition to heatmaps, pathway maps can be generated for the KEGG gene sets using the> plotPathwayGenerating pathway map for Vascular smooth muscle contraction from the collectionKEGG Pathways and for the contrast BasalvsLP limma DE analysis Generating pathway map for Vascular smooth muscle contraction from the collectionKEGG Pathways and for the contrast comparison The comparative pathway map shows the log-fold-changes for each gene in each contrast by dividing the gene nodes on the map into multiple columns, one for each contrast .Visualizing results at the experiment level. SinceEGSEA combines the results from multiple gene set testing methods, it can be interesting to compare how different base methods rank a given gene set collection for a selected contrast. TheplotMethods command generates a multi-dimensional scaling (MDS) plot for the ranking of gene sets across all the base methods used (self-contained versuscompetitive).ds used . Methods> plotMethodsGenerating MDS plot for the collectionc2 Curated Gene Sets and for the contrast BasalvsLP> plotMethodsGenerating MDS plot for the collectionc5BP GO Gene Sets and for the contrast BasalvsLP plotSummary method.The significance of each gene set in a given collection for a selected contrast can be visualized using EGSEA\u2019s> plotSummaryGenerating Summary plots for the collectionKEGG Pathways and for the contrast LPvsML 10 (X-axis) and the average absolute log fold-change of the set genes (Y-axis). The sets that appear towards the top-right corner of this plot are most likely to be biologically relevant. EGSEA generates two types of summary plots: the directional summary plot (sort.by argument). The bubble size is based on the EGSEAsignificance score in the former plot and the gene set size in the latter. For example, the summary plots of the KEGG pathways for the LP vs ML contrast show few significant pathways Generating Summary plots for the collectionc2 Curated Gene Sets and for the contrast LPvsML x.cutoff can be used to focus in on the significant gene sets rather than plotting the entire gene set collection, for example Generating Summary plots for the collectionc2 Curated Gene Sets and for the contrast LPvsML plotSummary method as follows:Comparative summary plots can be also generated to compare the significance of gene sets between two contrasts, for example, the comparison between Basal vs LP and Basal vs ML shows th> plotSummary,+ file.name = \"summary_kegg_1vs2\")Generating Summary plots for the collectionKEGG Pathways and for the comparison BasalvsLP vs BasalvsML plotSummary method has two useful parameters: (i)use.names that can be used to display gene set names instead of gene set IDs and (ii)interactive that can be used to generate an interactive version of this plot.TheEGSEA utilizes functionality from thetopGO package37 to generate GO graphs for the significant biological processes (BPs), cellular compartments (CCs) and molecular functions (MFs). TheplotGOGraph method can generate such a display (The c5 collection of MSigDB and the Gene Ontology collection of GeneSetDB contain Gene Ontology (GO) terms. These collections are meant to be non-redundant, containing only a small subset of the entire GO and visualizing how these terms are related to each other can be informative.display as follo> plotGOGraphGenerating GO Graphs for the collection c5 GO Gene Sets (BP) and for the contrast BasalvsLP based on the med.rank> plotGOGraphGenerating GO Graphs for the collection c5 GO Gene Sets (CC) and for the contrast BasalvsLP based on the med.rank sort.by, which in this instance was taken asmed.rank by default since this was selected when EGSEA was invoked. The top five most significant GO terms are highlighted by default in each GO category . More terms can be displayed by changing the value of the parameternoSig. However, this might generate very complicated and unresolved graphs. The colour of the nodes varies between red (most significant) and yellow (least significant). The values of thesort.by scoring function are scaled between 0 and 1 to generate these graphs.The GO graphs are coloured based on the values of the argumentbar plot. The methodplotBars can be used to generate a bar plot for the topN gene sets in an individual collection for a particular contrast or from a comparative analysis across multiple contrasts. For example, the top 20 gene sets of the comparative analysis carried out on the c2 collection of MSigDB can be visualized in abar plot Generating a bar plot for the collection c2 Curated Gene Sets and the contrast comparison 10(p.ad j) values are plotted for the top 20 gene sets selected and ordered based on thesort.by parameter. The parametersbar.vals,number andsort.by ofplotBars can be changed to customize thebar plot.The colour of the bars is based on the regulation direction of the gene sets, i.e., red for up-regulated, blue for down-regulated and purple for neutral regulation . By default, the \u2212 logsummary heatmap can be a useful visualization. The methodplotSummaryHeatmaps generates a heatmap of the topN gene sets in the comparative analysis across all experimental conditions Generating summary heatmap for the collection c2 Curated Gene Setssort.by: med.rank, hm.vals: avg.logfc.dir, show.vals:> plotSummaryHeatmapGenerating summary heatmap for the collection KEGG Pathwayssort.by: med.rank, hm.vals: avg.logfc.dir, show.vals: EGSEAResults object using thelimmaTopTable method.We find the heatmap view at both the gene set and summary level and the summary level bar plots to be useful summaries to include in publications to highlight the gene set testing results. The top differentially expressed genes from each contrast can be accessed from the> t = limmaTopTable> head(t) ENTREZID SYMBOL CHR logFC AveExpr t P.Value adj.P.Val B19253 19253 Ptpn18 1 -5.63 4.13 -34.5 5.87e-10 9.62e-07 13.216324 16324 Inhbb 1 -4.79 6.46 -33.2 7.99e-10 9.62e-07 13.353624 53624 Cldn7 11 -5.51 6.30 -40.2 1.75e-10 9.62e-07 14.5218518 218518 Marveld2 13 -5.14 4.93 -34.8 5.56e-10 9.62e-07 13.512759 12759 Clu 14 -5.44 8.86 -41.0 1.52e-10 9.62e-07 14.770350 70350 Basp1 15 -6.07 5.25 -34.3 6.22e-10 9.62e-07 13.3 Creating an HTML report of the results. To generate an EGSEA HTML report for this dataset, you can either setreport=TRUE when you invokeegsea or use the S4 methodgenerateReport as follows:> generateReportEGSEA HTML report is being generated ... http://bioinf.wehi.edu.au/EGSEA/mam-rnaseq-egsea-report/index.html (DT package (https://CRAN.R-project.org/package=DT) and summary plots fromplotly (https://CRAN.R-project.org/package=plotly) are integrated into the report usinghtmlwidgets (https://CRAN.R-project.org/package=htmlwidgets) and can be added by settinginteractive = TRUE in the command above. This option significantly increases both the run time and size of the final report due to the large number of gene sets in most collections.The EGSEA report generated for this dataset is available online atex.html . The HTMThis example completes our overview of EGSEA\u2019s gene set testing and plotting capabilities for RNA-seq data. Readers can refer to the EGSEA vignette or individual help pages for further details on each of the above methods and classes.et al. (2010)22 and is the microarray equivalent of the RNA-seq data analysed above. Support for microarray data is a new feature in EGSEA, and in this example, we show an express route for analysis according to the steps shown inThe second dataset analysed in this workflow comes from Limhttp://bioinf.wehi.edu.au/EGSEA/arraydata.zip into the current working directory. Illumina BeadArray data can be read in directly using thereadIDAT andreadBGX functions from theilluminaio package38. However, a more convenient way is via theread.idat function inlimma which uses theseilluminaio functions and outputs the data as anEListRaw object for further processing.To analyse this dataset, we begin by unzipping the files downloaded from> library(limma)> targets = read.delim> data = read.idat(as.character(targets$File),+ bgxfile=\"GPL6887_MouseWG-6_V2_0_R0_11278593_A.bgx\",+ annotation=c)Reading manifest file GPL6887_MouseWG-6_V2_0_R0_11278593_A.bgx ... Done 4481850214_B_Grn.idat ... Done 4481850214_C_Grn.idat ... Done 4481850214_D_Grn.idat ... Done 4481850214_F_Grn.idat ... Done 4481850187_A_Grn.idat ... Done 4481850187_B_Grn.idat ... Done 4481850187_D_Grn.idat ... Done 4481850187_E_Grn.idat ... Done 4481850187_F_Grn.idat ... Done 4466975058_A_Grn.idat ... Done 4466975058_B_Grn.idat ... Done 4466975058_C_Grn.idat ... Done 4466975058_D_Grn.idat ... Done 4466975058_E_Grn.idat ... Done 4466975058_F_Grn.idat ... DoneFinished reading data.> data$other$Detection = detectionPValues(data)> data$targets = targets> colnames(data) = targets$Sample neqc function inlimma is used to carry outnormexp background correction and quantile normalisation on the raw intensity values using negative control probes39. This is followed by log2-transformation of the normalised intensity values and removal of the control probes.Next the> data = neqc(data) p-value of less than 0.05 in at least 5 samples (the number of samples within each group). We next remove genes without a valid Entrez ID and in cases where there are multiple probes targeting different isoforms of the same gene, select the probe with highest average expression as the representative one to use in the EGSEA analysis. This leaves 7,123 probes for further analysis.We then filter out probes that are consistently non-expressed or lowly expressed throughout all samples as they are uninformative in downstream analysis. Our threshold for expression requires probes to have a detection> table(targets$Celltype)Basal LP ML 5 5 5> keep.exprs = rowSums(data$other$Detection<0.05)>=5> table(keep.exprs)keep.exprsFALSE TRUE23638 21643> data = data> dim(data)[1] 21643 15> head(data$genes) Probe_Id Array_Address_Id Entrez_Gene_ID Symbol Chromosome3 ILMN_1219601 2030280 C920011N12Rik4 ILMN_1252621 1980164 101142 2700050P07Rik 66 ILMN_3162407 6220026 Zfp367 ILMN_2514723 2030072 1110067B18Rik8 ILMN_2692952 6040743 329831 4833436C18Rik 49 ILMN_1257952 7160091 B930060K05Rik> sum(is.na(data$genes$Entrez_Gene_ID))[1] 11535> data1 = data> dim(data1)[1] 10108 15> ord = order(lmFit(data1)$Amean, decreasing=TRUE)> ids2keep = data1$genes$Array_Address_Id[ord][!duplicated(data1$genes$Entrez_Gene_ID[ord])]> data1 = data1> dim(data1)[1] 7123 15> expr = data1$E> group = as.factor(data1$targets$Celltype)> probe.annot = data1$genes> head(probe.annot)> head(probe.annot) Array_Address_Id Entrez_Gene_ID Symbol39513 4120224 20102 Rps4x9062 2260576 22143 Tuba1b15308 5720202 12192 Zfp36l139894 1470600 11947 Atp5b24709 2710477 20088 Rps249872 1580471 228033 Atp5g3 29 and contrasts matrix to look for differences between the Basal and LP, Basal and ML and LP and ML populations. A batch term is included in the linear model to account for differences in expression that are attributable to the day the experiment was run.As before, we need to set up an appropriate linear model> head(data1$targets) File Sample Celltype Time Experiment2-2 4481850214_B_Grn.idat 2-2 ML At1 13-3 4481850214_C_Grn.idat 3-3 LP At1 14-4 4481850214_D_Grn.idat 4-4 Basal At1 16-7 4481850214_F_Grn.idat 6-7 ML At2 17-8 4481850187_A_Grn.idat 7-8 LP At2 18-9 4481850187_B_Grn.idat 8-9 Basal At2 1> experiment = as.character(data1$targets$Experiment)> design = model.matrix(~0 + group + experiment)> colnames(design) = gsub)> design Basal LP ML experiment21 0 0 1 02 0 1 0 03 1 0 0 04 0 0 1 05 0 1 0 06 1 0 0 07 0 0 1 08 0 1 0 09 1 0 0 010 0 0 1 111 0 1 0 112 1 0 0 113 1 0 0 114 0 0 1 115 0 1 0 1attr[1] 1 1 1 2attrattr$group[1] \"contr.treatment\" attr$experiment[1] \"contr.treatment\" > contr.matrix = makeContrasts)> contr.matrix ContrastsLevels BasalvsLP BasalvsML LPvsML Basal 1 1 0 LP -1 0 1 ML 0 -1 -1 experiment2 0 0 0 EGSEAdata package and build indexes based on Entrez IDs that link between the genes in each signature and the rows of our expression matrix.We next extract the mouse c2, c5 and KEGG gene signature collections from the> library(EGSEA)> library(EGSEAdata)> gs.annots = buildIdx, go.part = TRUE)[1] \"Loading MSigDB Gene Sets ... \"[1] \"Loaded gene sets for the collection c2 ...\"[1] \"Indexed the collection c2 ...\"[1] \"Created annotation for the collection c2 ...\"[1] \"Loaded gene sets for the collection c5 ...\"[1] \"Indexed the collection c5 ...\"[1] \"Created annotation for the collection c5 ...\"MSigDB c5 gene set collection has been partitioned intoc5BP, c5CC, c5MF[1] \"Building KEGG pathways annotation object ... \"> names(gs.annots)[1] \"c2\" \"c5BP\" \"c5CC\" \"c5MF\" \"kegg\" egsea.ma. Gene sets were again prioritised by their median rank across the 11 methods.The same 11 base methods used previously in the RNA-seq analysis were selected for the ensemble testing of the microarray data using the function> baseMethods = egsea.base[-2]> baseMethods [1] \"camera\" \"safe\" \"gage\" \"padog\" \"plage\" \"zscore\" [7] \"gsva\" \"ssgsea\" \"globaltest\" \"ora\" \"fry\">> gsam = egsea.maEGSEA analysis has started##------ Tue Jun 20 14:27:32 2017 ------##Log fold changes are estimated using limma package ...limma DE analysis is carried out ...Number of used cores has changed to 3in order to avoid CPU overloading.EGSEA is running on the provided data and c2 collectionEGSEA is running on the provided data and c5BP collectionEGSEA is running on the provided data and c5CC collectionEGSEA is running on the provided data and c5MF collectionEGSEA is running on the provided data and kegg collection##------ Tue Jun 20 14:33:37 2017 ------##EGSEA analysis took 365.359 seconds.EGSEA analysis has completed generateReport function. We complete our analysis by displaying the top ranked sets for the c2 collection from a comparative analysis across all contrasts.An HTML report that includes each of the gene set level and summary level plots shown individually for the RNA-seq analysis was then created using the> generateReportEGSEA HTML report is being generated ...> topSets Sorted by med.rank [1] \"LIM_MAMMARY_STEM_CELL_UP\" [2] \"LIM_MAMMARY_LUMINAL_MATURE_DN\" [3] \"LIM_MAMMARY_STEM_CELL_DN\" [4] \"CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN\" [5] \"LIU_PROSTATE_CANCER_DN\" http://bioinf.wehi.edu.au/EGSEA/mam-ma-egsea-report/index.html. Reanalysis of this data retrieves similar c2 gene sets to those identified by analysis of RNA-seq data. These included theLIM gene signatures as well as those derived from populations with similar cellular origin (set 4).The EGSEA report generated for this dataset is available online atEGSEA package to combine the results obtained from different gene signature databases across multiple GSE methods to find an ensemble solution. A key benefit of an EGSEA analysis is the detailed and comprehensive HTML report that can be shared with collaborators to help them interpret their data. This report includes tables prioritising gene signatures according to the user specified analysis options, and both gene set specific and summary graphics, each of which can be generated individually using specific R commands. The approach taken by EGSEA is facilitated by the diverse range of gene set testing algorithms and plotting capabilities available within Bioconductor. EGSEA has been tailored to suit a limma-based differential expression analysis which continues to be a very popular and flexible platform for transcriptomic data. Analysts who choose an individual GSE algorithm to prioritise their results rather than an ensemble solution can still benefit from EGSEA\u2019s comprehensive reporting capability.In this workflow article, we have demonstrated how to use theEGSEA123 workflow package available from Bioconductor:https://www.bioconductor.org/help/workflows/EGSEA123.Code to perform this analysis can be found in thehttps://github.com/mritchie/EGSEA123.Latest source code is available at:https://doi.org/10.5281/zenodo.104343640.Archived source code as at the time of publication is available at:Software license: Artistic License 2.0. GSEA analysis methods do not all produce same results. Score-based gene set analysis methods like the Broad Institute GSEA tool are considered to perform better than normal Fisher\u2019s exact test . But analysts often use methods they know to be less than ideal in order to reduce complexity and save time. So it is good to have a unified interface for GSEA analyses with R \u2013 it helps save programming time and reduces complexity. In addition EGSEA is a unique method that combines up to 12 gene set analysis methods into a single score. Independent test also corroborate that the tool using the 12 has more specificity and good sensitivity compared to using some of the tests alone. The EGSEA 1-2-3 workflow is easy to use and generate good-quality figures with the ggplot2 R package. So9me of the figures are novel compared to other packages e.g., scatter plots designed to compare different contrasts. It is also very useful that the tool can be applied to multiple contrasts at a time, although if there are too many contrasts then the number of plots becomes unwieldly . Some more technical comments: The results object is very complicated for retrieving individual method analysis results . I quite like the \"biobroom\" Bioconductor package that does \"tidy\" data frames from limma results objects. All in all a very useful package both for automating the running of lots of methods at the same time and of course for the \"ensemble\" method. \u00a0It is recommended to be considered to be part of a standard bioinformatics workflow.We have read this submission. We believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. EGSEA is a new gene set analysis tool that combines results from multiple individual tools in R as to yield better results. The authors have published EGSEA methodology previously. This paper focuses on the practical analysis workflow based on EGSEA with specific examples. As EGSEA is a compound and complicated analysis procedure, this work serves as a valuable guidance for the users to make full use of this tool. I\u2019ve gone through the workflow line by line, it seems to work well. However, authors can improve their work by addressing the following issues.There should be an R code script which includes all source code and concise comments like the one in company with the vignette in any Bioconductor package. It would be much easy for the users/reviewers to try the example code. It is not convenient to follow the code in this manuscript, the code need to be edit to remove the prompt symbols (> or +) at each line when copying/pasting.It takes too long to run the egsea analysis example on modest machine. It is advisable to show a lesser example in the workflow with only one gene set collection like kegg and just a few base methods like: gsa = egseaThe rank of the gsa results shown following the t = topSets(..) line is confusing. The p.adj for the top 1 gene set is not the smallest, actually much bigger than top 2, 6 and 8. Presumably, the gene sets are ranked by med.rank instead of p.adj here. However, the opposite was described in the text above near the egsea.sort line: \u201cAlthough p.adj is the default option for sorting EGSEA results for convenience, ...\u201dIn addition, there is big difference between the final rank and med.rank (e.g. 1 vs 36). This may suggest inconsistent results came from different base methods. This may also be due to the large number of gene sets being tested. Again, using a smaller gene set collection and a few base methods could make the ranking more consistent.All visualization functions, i.e. plotHeatmap, plotPathway, plotGOGraph, plotMethods, plotSummary and plotBars share largely the same set of arguments, they can have a unified wrapper function like plot.gsa with an extra argument type to specify the plot type.Functions plotPathway, plotGOGraph are wrapper functions for those in the pathview and topGO package as the author noted in the text. It would be good to explicit show some message like \u201ccalling plotting function from pathview or topGO package etc\u201d, just like the message when running egsea.http://bioinf.wehi.edu.au/EGSEA/mam-rnaseq-egsea-report/index.html.HTML report of the results is a very valuable feature for the users. However, the code can run a long time, it would be helpful to add some progress reminder message to generateReport function like egsea. BTW, the KEGG Pathway graphs are not shown properly in the report example at \u00a0I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. 1, and this article gives a well-written walk-through of how to use the packages.This F1000 software tool article describes the EGSEA package that incorporates many different gene set testing methods from various packages and also allows access to a wide array of gene sets from different databases through the accompanying EGSEAdata package. These packages will enable researchers to conveniently test many different methods and incorporate their results to get more robust biological insightshttp://www.genome.jp/kegg/catalog/org_list.html) and GO terms are readily available for 19 species using BioC's pre-built OrgDB packages and\u00a0hundreds of other through AnnotationHub. It is unclear whether EGSEA functions buildCustomIdx and buildGMTIdx that were \"written to allow users to run EGSEA on gene set collections that may have been curated within a lab or downloaded from public databases and allow use of gene identifiers other than Entrez IDs\" can be used to run EGSEA on additional species. If so, this should be clearly stated in both the Abstract and in the body of the article, plus an example given on how to use\u00a0buildCustomIdx for another species. If there is some reason that EGSEA cannot currently extend to other species, this should be acknowledged as a limitation and future versions should strive to allow this .\u00a0 The biggest limitation I see it that EGSEA is focused only on\u00a0human and mouse data (and rat? The article does not list rat but the help page for\u00a0buildIdx lists rat as one of the species). I understand that many of the gene set collections like\u00a0MSigDB and\u00a0GeneSetDB are only available for human/mouse, but KEGG currently lists 429 Eukaryotic organisms :\u00a0 EXPR must be a length 1 vectorhttps://support.bioconductor.org/p/103640/#103748)\u00a0\u00a0and got a speedy reply from the author. It hopefully will be resolved soon, although there is a concern of why the error was not found on another Windows machine.\u00a0 However, I reported this error to\u00a0the support site 2 prior to running EGSEA.I am concerned that as demonstrated in this paper, EGSEA seems to take the place of standard limma differential expression analysis, in that the model fitting takes place within the\u00a0egsea function. Certain gene set testing functions do need the individual expression values and not just the fitted values in an MArrayLM object but given the computational time (8 min as shown in the article code block\u00a0and 19 min on my own computer) you should never run egsea without first assessing the model fit on your own!\u00a0Ideally the egsea function could be written to accept MArrayLM, or at least the article should clearly state that users should have first assessed the validity of the model fit through the usual workflow of LawI also wonder why there are different interfaces for voom-based analysis and microarray data given that both use EList objects. I understand that the voom weights need to be used internally, but limma's lmFit function handles both without trouble, although it was originally coded for microarray data and the voom functionality came later. Even if there needs to be a separate function\u00a0egsea.ma for non-voom, non-count data, it should still accept an EList object so that the user does not have to pull out the expression data and\u00a0the grouping info.Back to the computational time required, there are several vague references to removing the roast method \"to save time\" and that the report generation \"significantly\" increases run time. it would be nice to have an example of the time required to run roast and\u00a0the report generation for the\u00a0computational architecture that created the article.\u00a0 Other issues to address before approval:I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. package. \u00a0EGSEA is an ensemble-like method recently published1 by the authors of this workflow that allows the user to simultaneously apply\u00a0different GSEA algorithms on a high-throughput molecular profiling data set, by combining p-values associated with each algorithm using classical meta-analysis approaches such as the Fisher's method.This article describes a gene set enrichment analysis\u00a0(GSEA) workflow for the \"Ensembl of GSEA\"\u00a0(EGSEA) R/Bioconductor software Because the statistical methodology is already described in detail in the corresponding publication, the present software tool article focuses on showing a step-by-step workflow with EGSEA. However, the vignette of the software package already provides a very detailed description about how to use EGSEA through its 39 pages. Therefore, it would be useful for the interested reader to find upfront when he/she should be consulting the vignette and when he/she should be consulting this workflow. Besides this introductory aspects, the following issues should be addressed before approval:The code given in the article breaks, at least in my computer, more concretely, at this line: gsa = egsea EGSEA analysis has started ##------ Mon Nov 27 12:37:42 2017 ------## Log fold changes are estimated using limma package ... limma DE analysis is carried out ... Number of used cores has changed to 4 in order to avoid CPU overloading. EGSEA is running on the provided data and c2 collection .......camera*....safe*...gage*.padog*....gsva*..fry*...plage*...globaltest*...zscore*...ora*...ssgsea* \u00a0 Error in temp.results[[baseGSEA]][[i]] : \u00a0 incorrect number of dimensions while running it with the latest release version 1.6.0. This is strange since the package builds and runs the vignette without problems. So, this might be related to the different sample data sets. A possible hint may come from the fact that the 'buildIdx' call is not returning the expected class of object, according to the workflow: class(gs.annots$s2) ## [1] \"NULL\" summary(gs.annots$s2) ## Length \u00a0Class \u00a0 Mode\u00a0 ## \u00a0 \u00a0 \u00a00 \u00a0 NULL \u00a0 NULL\u00a0The workflow contains a rather high amount of code, often with a non-trivial use of externally instantiated objects and nested calls to functions. It would be helpful for the interested reader to be able to easily copy and paste the instructions, but the fact that R commands are given with the R shell '>' and '+' symbols makes it less easy. A non-expert user may even copy those characters and get an error. I would recommend removing those characters from the illustrated code, just as it happens with the vignette.The workflow assumes that the user has a 'DGEList' object with gene metadata including the mapping between Entrez identifiers' and HGNC symbols. This is a rather unrealistic assumption and I would recommend that the workflow starts building that object from scratch and showing how to build that table of gene metadata. Below I also describe other issues\u00a0that I would recommend to be considered in future versions of the software but which I do not consider them to be required for approval of this article:The so-called \"summary plot\" shows the -log10 p-value on the x-axis and average absolute log fold-change of the set genes on the y-axis. Because this is in a way analogous to a rotated volcano plot, I would suggest to use the same arrangement of axes as in the volcano plot, which is a rather standardized display of significance and magnitude of the effects of interest.package, in which data structures are defined to store and access gene sets and collections of gene sets of different kinds. A salient feature of that infrastructure is the possibility to seamlessly map gene identifiers of different kinds. This would\u00a0simplify and improve the user experience of EGSEA since mapping between genes coded with a particular kind of identifier, and gene sets defined with another kind, is one of the most common tasks in a GSEA-like analysis.One of the key features of the Bioconductor project, to which the EGSEA package is contributing to, is enabling software interoperability through sharing the use of common data structures across different software packages. \u00a0Using specialized data structures, where analogous ones have been already designed by the Bioconductor core team or by a wider community of developers, locks the user into that package and limits the possibilities of using it as a building block in other more complex workflows. I'm making this comment because I have the impression that the EGSEA package would benefit of using the infrastructure provided by the Bioconductor GSEABase \u00a0I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above."} +{"text": "Alatina alata as \u201copsins\u201d in Fig.\u00a0After publication of our article , it was A. alata \u201c7 transmembrane receptor (rhodopsin family)\u201d GPCRs revealed only two likely opsins (comp71410 and comp74136) based on the alignment of their conserved lysine (K), for retinal binding, with that of the bovine rhodopsin reference protein. Therefore, all mention of A. alata \u201copsin\u201d expression in the original article should be interpreted as \u201crhodopsin family GPCR\u201d expression, except when referencing the two putative opsins: comp71410 and comp74136 . In light of these new findings, Fig.\u00a0A. alata opsin ORFs. The gene tree reconstructions (.tre file) and corresponding alignment are available at: https://figshare.com/articles/Supplemental_Information_for_A_new_transcriptome_and_transcriptome_profiling_of_adult_and_larval_tissue_in_the_box_jellyfish_Alatina_alata_an_emerging_modelfor_studying_venom_vision_and_sex/3471425.More stringent analysis of the A. alata opsin diversity is less broad than previously suggested does not impact the overall conclusions of our paper regarding opsin expression. Our updated findings still suggest that A. alata opsin is most abundant in the rhopalium, but also expressed in planulae, which have eyes spots, as well as in extra-ocular tissue types in the medusa, suggesting the presence of yet undescribed photoreceptors. Additional non-opsin rhodopsin family GPCRs (n\u2009=\u200931), whose specific identities await further analyses, are expressed in both the A. alata medusa samples and planulae. Previously we touched on the apparent diversity of A. alata rhodopsin family GPCRs, based on the fact that some of our BLAST hits for those sequences corresponded to non-opsin GPCRs , while others corresponded to various opsin types .The discovery that"} +{"text": "Eukaryotic genome assembly remains a challenge in part due to the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematodes are parasites and some represent a serious threat to human health. There is a pressing need for better molecular characterization of animal and plant parasitic nematodes. The advent of long-read DNA sequencing methods offers the promise of resolving complex genomes.Nippostrongylus brasiliensis as a test case, applying improved base-calling algorithms and assembly methods, we demonstrate the feasibility of de novo genome assembly matching current community standards using only MinION long reads. In doing so, we uncovered an unexpected diversity of very long and complex DNA sequences repeated throughout the N. brasiliensis genome, including massive tandem repeats of tRNA genes.Using Base-calling and assembly methods have improved sufficiently that de novo genome assembly of large complex genomes is possible using only long reads. The method has the added advantage of preserving haplotypic variants and so has the potential to be used in population analyses.The online version of this article (10.1186/s12915-017-0473-4) contains supplementary material, which is available to authorized users. Necator americanus and Ancylostoma duodenale continue to be a major global health problem. Next-generation sequencing (NGS) techniques open the door to molecular epidemiological monitoring of nematode and helminth parasites in endemic areas. Such studies are, however, hampered by the heterogeneous nature of parasite populations and by the intrinsically complex genome structures of nematodes -based approach using RNA-seq data gave a marginally higher complement of USCO genes, we used this gene set for further analyses. In addition to an elevated proportion of fragmented USCOs (see below), we also noted a high proportion of duplicated USCOs. Inspection revealed that some of these were bona fide lineage-specific expansions. For example, the analysis uncovered three distinct loci encoding isoforms of fructose 1,6-bisphosphatase (PFAM: PF00316), as predicted also from the WTSI assembly. Pairs of USCOs were also found on homologous contigs. There were four such examples in the 12 heterozygous branch subgraphs alone; this presumably reflects haplotypic variants.While generating a complete high-quality annotation was beyond the scope of this study, we made use of expert knowledge regarding carbohydrate-active enzymes (CAZymes) to provide a complementary insight into the predicted genes compared to the WTSI set . Of the N. brasiliensis, attempts are made to maintain genotypic diversity in the population. The assembly that we produced reflects this. Surgical transplantation of single adult parasitic worms has very recently been shown to be feasible, allowing controlled matings and the establishment of inbred lines _??????); do echo ${x}; read_fast5_basecaller.py -t 6 -i ${x} -s called_${x} -o fastq -c r94_450bps_linear.cfg; doneIllumina reads for the WTSI genome assembly were retrieved from the Sequence Read Archive (accession ERR063640). These reads were processed into k-mer counts using Jellyfish v2.2.6 , and thejellyfish count -C --bf-size 20G -t 6 -s 2G -m 21 <(zcat ERR063640_1P.fastq.gz) <(zcat ERR063640_2P.fastq.gz) -o ERR063640_mer_counts.jfjellyfish histo ERR063640_mer_counts.jf > ERR063640_mer_counts.histoUsing the FASTQ files, rather than just reads from the called pass bin, allowed a maximum amount of sequence information to be recovered. Reads were trimmed by 65\u00a0bp at each end to exclude adapters (see below), then Canu v1.5 was run with default parameters. The estimated genome size was 205\u00a0Mb as determined using GenomeScope (qb.cshl.edu/genomescope/) and the WTSI Illumina reads. Long-read sequencing of a heterogeneous population would be expected to generate a longer genome size due to the separation of haplotypes. We, therefore, made a conservative estimate of 300\u00a0Mb. The assumed genome size alters how many reads are selected for the final Canu assembly. If the coverage of corrected reads is greater than 40\u00d7, then only the longest reads are used (up to 40\u00d7 coverage). In our case, the coverage was below 40\u00d7 regardless of what parameters were used, so it would not be expected to alter the outcome. Within Canu, assembly parameters are adjusted when read counts are below 20\u00d7 (e.g. corMinCoverage\u2009=\u20090) as previously described :## trim readspv called_[CFED]_*_albacore_1.1.0.fq.gz | zcat | ~/scripts/fastx-fetch.pl -t 65 | gzip > called_CFED_65bptrim_albacore_1.1.0.fq.gz## run Canu~/install/canu/canu-1.5/Linux-amd64/bin/canu -nanopore-raw called_CFED_65bptrim_albacore_1.1.0.fq.gz -p Nb_ONTCFED_65bpTrim_t1 -d Nb_ONTCFED_65bpTrim_t1 genomeSize=300\u00a0MBowtie2 was used in local mode to map RNA-seq reads to the assembled genome contigs:bowtie2 -p 10 --local -x Nb_ONTCFED_65bpTrim_t1.contigs.fasta -1 ../1563-all_R1_trimmed.fastq.gz -2 ../1563-all_R2_trimmed.fastq.gz | samtools sort > 1563_vs_uncorrected_NOCFED.bamPilon was used to correct based on the RNA-seq mapping to the genome, with structural reassembly disabled (in case it collapsed introns):java -Xmx40G -jar ~/install/pilon/pilon-1.22.jar --genome Nb_ONTCFED_65bpTrim_t1.contigs.fasta --frags 1563_vs_uncorrected_NOCFED.bam --fix snps,indels --output BT2Pilon_NOCFED --gapmargin 1 --mingap 10000000 --threads 10 --changes 2>BT2Pilon_NOCFED.stderr.txt 1>BT2Pilon_NOCFED.stdout.txtContigs that were entirely composed of homopolymer sequences were identified using grep and removed from the assembly:## identify homopolymer (and binary division-rich) regionspv BT2Pilon_NOCFED.fasta | ~/scripts/fastx-hplength.pl > hplength_BT2Pilon_NOCFED.txtpv BT2Pilon_NOCFED.fasta | ~/scripts/fastx-hplength.pl -mode YR > hplength_YR_BT2Pilon_NOCFED.txtpv BT2Pilon_NOCFED.fasta | ~/scripts/fastx-hplength.pl -mode SW > hplength_SW_BT2Pilon_NOCFED.txtpv BT2Pilon_NOCFED.fasta | ~/scripts/fastx-hplength.pl -mode MK > hplength_MK_BT2Pilon_NOCFED.txt## example grep hunt for repeated sequencecat BT2Pilon_NOCFED.fasta | grep -e '^[AT]\\{80\\}' -e '^>' | grep --no-group-separator -B 1 '^[AT]\\{80\\}' | ~/scripts/fastx-length.pl## exclude contigs and sort by length~/scripts/fastx-fetch.pl -v tig00010453 tig00024413 tig00024414 tig00023947 | ~/scripts/fastx-sort.pl -l > Nb_ONTCFED_65bpTrim_t1.contigs.hpcleaned.fastaThis produced the final assembly described in the paper. At this stage, we had an assembled genome, but validation of the genome was difficult. We decided to carry out a draft genome-guided transcriptome assembly with Trinity. To evaluate the completeness of the genome, we focused on expressed genes and used a set of Illumina RNA-seq reads to perform a genome-guided transcriptome assembly using Trinity.The RNA-seq reads were remapped to the corrected assembly for genome-guided Trinity:bowtie2 -p 10 -t --local --score-min G,20,8 -p 10 -x BT2Pilon_NOCFED_hpcleaned.fasta --rf -X 15000 -1../1563-all_R1_trimmed.fastq.gz -2 < 2>bowtie2_1563_vs_BNOCFED_hp.summary.txt | samtools sort > bowtie2_1563_vs_BNOCFED_hp.bam## Trinity assembly; assume introns can be up to 15\u00a0kb in length~/install/trinity/trinityrnaseq-Trinity-v2.4.0/Trinity --CPU 10 --genome_guided_bam bowtie2_1563_vs_BNOCFED_hp.bam --genome_guided_max_intron 15000 --max_memory 40G --SS_lib_type RF --output trinity_BNOCFEDThe assembly that Trinity generated had similar completeness (as measured by BUSCO) to a de novo assembly generated using the same RNA-seq reads (see Table\u00a0https://www.ebi.ac.uk/ena/data/view/ERS1809079), where details of the samples can be found.Our RNA-seq data is publicly available from the European Nucleotide Archive of the European Bioinformatics Institute were usThe RNA-seq reads were mapped to the Trinity-generated transcripts using Salmon:## create Salmon index~/install/salmon/Salmon-0.8.2_linux_x86_64/bin/salmon index -t Trinity-BNOCFED.fasta -i Trinity-BNOCFED.fasta.sai## quantify transcript coverage with Salmon~/install/salmon/Salmon-0.8.2_linux_x86_64/bin/salmon quant -i Trinity-BNOCFED.fasta.sai -1 ../../1563-all_R1_trimmed.fastq.gz -2 ../../1563-all_R2_trimmed.fastq.gz -p 10 -o quant/1563-all_quant -l AThe expression of BUSCO genes was used to set a credible signal cutoff -db missing_busco_list_intersectionBUSCO_nematodes.fasta -outfmt 6 -evalue 1e-3 > BLAST_NOCFED_vs_BUSCO_missing_intersection.tsvHits for the same contig/USCO combination were merged using a custom script, and sequence extracted from the assembly to cover the entire matched region: > BLAST_NOCFED_vs_BUSCO_missing_intersection.fastahttp://onecodex.com). Reads that mapped to any DNA in the OneCodex database were excluded from the read set:DNA extracted from a single adult worm was amplified using a Qiagen Midi RepliG kit. Raw reads and called FASTQ files were obtained from ONT following sequencing. Reads were filtered to exclude those from contaminating DNA using OneCodex ((zcat OneCodex_RefSeq_132394.fastq.gz.results.tsv.gz | awk '{if($3 == 0){print $1}}'; zcat OneCodex_OCD_132394.fastq.gz.results.tsv.gz | awk '{if($3 == 0){print $1}}') | sort | uniq -d | gzip > OCunmapped_names_132394.txt.gzpv 132394.fastq.gz | zcat | ~/scripts/fastx-fetch.pl -i OCunmapped_names_132394.txt.gz | ~/scripts/fastx-fetch.pl -v -i ONTmapped_names_132394.txt.gz | gzip > OCunmapped_ONTunmapped_132394.fastq.gzFiltered reads from the WGA sample were called using Albacore 1.1.0:read_fast5_basecaller.py -o fastq -i A_132394 -t 10 -s called_A_132394 -c r94_450bps_linear.cfgReads with a length of greater than 10\u00a0k were extracted for subsequent analysis:pv called_A_132394_albacore_1.1.0.fq.gz | zcat | ~/scripts/fastx-fetch.pl --min 10000 | gzip > 10k_called_A_132394_albacore_1.1.0.fq.gzTo define the region of raw nanopore sequences for adapter exclusion, the >10\u00a0k reads were mapped to 50\u00a0M reads that had been generated by WTSI and that had been used for the existing WTSI assembly:bowtie2 -p 10 --no-unal --no-mixed --local -x 10k_called_A_132394_albacore_1.1.0.fa -1 <(pv ~/bioinf/MIMR-2017-Jan-01-GBIS/GLG/ONT/aws/Sampled_50M_ERR063640.R1.fq.gz | zcat) -2 ~/bioinf/MIMR-2017-Jan-01-GBIS/GLG/ONT/aws/Sampled_50M_ERR063640.R2.fq.gz | samtools sort > WTSI_Sampled_50M_vs_10k_called_A_132394.bam## find position of first mapped Illumina read for each nanopore readpv WTSI_Sampled_50M_vs_10k_called_A_132394.bam | samtools view - | awk '{print $3,$4}' | sort -k 1,1 -k 2,2n | sort -u -k 1,1 | gzip > firstHit_WTSI_Sampled_50M_vs_10k_called_A_132394.txt.gz## determine position of last mapped Illumina readpv WTSI_Sampled_50M_vs_10k_called_A_132394.bam | samtools view - | awk '{print $3,$4}' | sort -k 1,1 -k 2,2rn | sort -u -k 1,1 | gzip > lastHit_WTSI_Sampled_50M_vs_10k_called_A_132394.txt.gz## count positions of first readszcat firstHit_WTSI_Sampled_50M_vs_10k_called_A_132394.txt.gz | awk '{print $2}' | sort -n | uniq -c | gzip > firstBase_counts_WTSI_Sampled_50M_vs_10k_called_A_132394.txt.gzWhen we mapped the 5' ends of Illumina reads to the start of nanopore reads with Bowtie2, there was a common register shift of 28\u201332 bases, corresponding to the presence of adapter sequences in the nanopore reads. Reads were conservatively trimmed by 65 bases at each end to exclude adapters:pv called_A_132394_albacore_1.1.0.fq.gz | zcat | ~/scripts/fastx-fetch.pl --min 1130 --max 1000000 | \\~/scripts/fastx-fetch.pl -t 65 | gzip > 65bpTrim_called_A_132394_albacore_1.1.0.fq.gzCanu v1.5 was used to assemble the trimmed reads. The assembly was done in stages (with an assembly at each stage) to determine whether or not particular stages were redundant for the assembly:## attempt assembly-only with Canu v1.5~/install/canu/canu-1.5/Linux-amd64/bin/canu -assemble -nanopore-raw 65bpTrim_called_A_132394_albacore_1.1.0.fq.gz -p Nb_ONTA_65bpTrim_t1 -dNb_ONTA_65bpTrim_t1 genomeSize=300\u00a0M## attempt assembly + correction~/install/canu/canu-1.5/Linux-amd64/bin/canu -assemble -nanopore-corrected 65bpTrim_called_A_132394_albacore_1.1.0.fq.gz -p Nb_ONTA_65bpTrim_t2 -d Nb_ONTA_65bpTrim_t2 -correct genomeSize=300\u00a0M## attempt stringent trim with corrected reads~/install/canu/canu-1.5/Linux-amd64/bin/canu -trim-assemble -p Nb_ONTA_65bpTrim_t3 -d Nb_ONTA_65bpTrim_t3 genomeSize=300\u00a0M -nanopore-corrected Nb_ONTA_65bpTrim_t2/Nb_ONTA_65bpTrim_t2.correctedReads.fasta.gz -trim-assemble trimReadsOverlap=500 trimReadsCoverage=5 obtErrorRate=0.25An alternative, less-stringent overlap was also attempted (with trimReadsCoverage = 2), but resulted in a less complete assembly. The results of an analysis surrounding the different assemblies suggested that the default Canu assembly process of correction, trimming, then assembly produced the best outcome, namely the WGA assembly presented in Table\u00a0Canu includes a step of normalization, reducing the shortest reads, if coverage is over a predefined threshold, but that normalization threshold was not triggered for our assembly. We did not attempt a k-mer-based normalization, since this would not resolve the incomplete genome sequence coverage. Selective amplification combined with random sampling by the sequencer means that poorly amplified regions were unlikely to be present in the sequenced reads. We did notice that an assembly combining both WGA and unamplified DNA samples produced a more fragmented genome, which is why a combined assembly is not presented here. It is possible that k-mer normalization of the WGA reads might improve such a hybrid assembly.Additional file 1: Table S1.Detailed comparative sequence analysis and genome assembly statistics. (DOCX 12 kb)Additional file 2: Figure S1.Dot plots of all-against all sequence comparisons between the five most compressible VeCTR regions, based on minimum-distance alignments using LAST-align, created using LAST-dotplot. The names of the corresponding contigs and the coordinates of the plotted regions are indicated for each VeCTR and their unique flanking sequences. The longest of these five VeCTRs corresponds to 147 repeats of tRNA-Trp followed by 114\u00a0bp of non-conserved sequence, while the shortest contains 90 copies of tRNA-Ser with 80\u00a0bp of non-conserved sequence. (PDF 69 kb)Additional file 3: Figure S2.a Venn diagram showing the overlap for USCOs flagged as missing in the analysis of three genome assemblies (Uncorrected (Canu only), Nanopolish and Trinity [genome-guided]; see Table\u00a0b,d) and the sequence alignment, generated using Muscle, with the predicted N. brasiliensis protein sequence extracted from the tblastn alignment . For both N. brasiliensis sequences, note the presence of stop codons (*) in the sequence; these will confound BUSCO analysis. (PDF 398 kb)Potential orthologs of missing USCOs. Additional file 4: Table S2.BLAST hits for missing USCOs (see Excel file). (XLSX 78 kb)Additional file 5: Table S3.CAZy analysis (see Excel file). (XLSX 265 kb)Additional file 6: Figure S3.Distribution of read lengths for whole-genome amplified (WGA) DNA. Comparison of the distribution of read lengths for amplified DNA (WGA) and unamplified DNA extracted by method 1 see Fig.\u00a0."} +{"text": "However, tools for integrating an assembled transcriptome with reference annotation are lacking.RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing.Necklace is a software pipeline that runs genome-guided and Necklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts, which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data are mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods. Despite the increasing number of species with a sequenced genome, the vast majority of reference genomes are incomplete. They may contain gaps, have unplaced assembly scaffolds, and be poorly annotated. The na\u00efve approach to analyzing RNA sequencing (RNA-seq) on species with a genome would follow the same procedure as for model organisms, i.e., align reads the genome and count reads overlapping annotated genes, then test for differential expression based on gene counts . Howeverde novo assembly y \u2190 DGEList(counts = counts)Genes with a counts per million (cpm) less than or equal to 0.5 in fewer than four samples were filtered out and the libraries normalized.keep \u2190 rowSums(cpm(y) > 0.5) > = 4y \u2190 yy \u2190 calcNormFactors(y)We then estimated the dispersion and looked for differential expression with an FDR <0.05:y \u2190 estimateDispfit \u2190 glmFitqlf \u2190 glmLRTis.de \u2190 decideTestsProject name: NecklaceRRID:SCR_016103Scicrunch https://github.com/Oshlack/necklace/wikiProject home page: Operating systems: LinuxProgramming language: Groovy and C/C++Other requirements: Java 1.8License: GPL 3.0GigaScience GigaDB repository [An archival snapshot of the code is available in the pository .bp: base pair; cpm: counts per million; FDR: false discovery rate; RNA-seq: RNA sequencing.GIGA-D-17-00354.pdfClick here for additional data file.GIGA-D-17-00354_R1.pdfClick here for additional data file.GIGA-D-17-00354_R2.pdfClick here for additional data file.Response_to_Reviewer_Comments_Original_Submission.pdfClick here for additional data file.Response_to_Reviewer_Comments_Revision_1.pdfClick here for additional data file.Reviewer_1_Report_ -- Li Song1/12/2018 ReviewedClick here for additional data file.Reviewer_1_Report_(Revision_1) -- Li Song3/25/2018 ReviewedClick here for additional data file.Reviewer_2_Report_ -- Mickael Orgeur1/16/2018 ReviewedClick here for additional data file.Reviewer_2_Report_(Revision_1) -- Mickael Orgeur3/21/2018 ReviewedClick here for additional data file."} +{"text": "Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E.\u00a0amylovora bacteriophages. Erwinia amylovora is a Gram-negative facultative anaerobic rod-shaped bacterium and the causative agent of fire blight and sequenced using 454 pyrosequencing or Illumina HiSeq 2500 sequencing . Contigs were assembled using Newbler version 2.9 and Consed and otheThe 19 phages fell into five distinct clusters according to genomic analysis. The first group included the jumbo myoviruses vB_EamM_Deimos-Minion, vB_EamM_RAY, vB_EamM_Simmy50, and vB_EamM_Special G, which share a minimum of 97.2% average nucleotide identity to one another. The second group included two jumbo myoviruses, vB_EamM_RisingSun and vB_EamM_Joad, which differ by only two putative gene products. The third group included diverse jumbo myoviruses vB_EamM_Caitlin, vB_EamM_ChrisDB, vB_EamM_EarlPhillipIV, vB_EamM_Huxley, vB_EamM_Kwan, vB_EamM_Machina, vB_EamM_Parshik, vB_EamM_Phobos, and vB_EamM_Stratton, which share a minimum of 50.5% average nucleotide identity. An additional jumbo myovirus, vB_EamM_Yoloswag, did not have any close phage relatives. Podovirus phages vB_EamP_Frozen, vB_EamP_Gutmeister, and vB_EamP_Rexella share at least 97.2% average nucleotide identity. The four jumbo myovirus groups package DNA by headful packaging based on homology of their putative terminase genes to the phiKZ terminase and GepaErwinia bacteriophages are listed in GenBank accession numbers for the 19"} +{"text": "Evidence has shown that physical activity may attenuate the negative physical, psychological and functional effects of treatment in women diagnosed with breast cancer. Physical activity levels also decline substantially during and after completion of treatment for cancer, highlighting the importance of strategies to promote participation in regular physical activity in this population. Oncologists and surgeons may serve as an influential source of motivation to be physically activity in cancer patients, by conveying the importance of a healthy lifestyle. The primary purpose of the present study was to investigate whether oncologists and surgeons routinely discuss physical activity with their breast cancer patients and to investigate the nature of any information/advice provided during consultations. A secondary aim was to examine whether physically active oncologists and surgeons were more likely to provide advice about physical activity to patients, than inactive oncologists and surgeons. A brief postal questionnaire was sent to 710 consultant breast cancer oncologists and surgeons throughout the UK and 102 responded (response rate = 14.4%). Of responders, most (55.9%) did not routinely discuss physical activity with their patients. Amongst oncologists/surgeons (clinicians) who did offer advice, most focussed on discussing the benefits of physical activity for physical and functional health gains and for facilitating weight control and maintenance. A number of clinicians indicated they advised patients that physical activity may decrease risk of recurrence and improve survival, despite the lack of evidence from RCTs to support this suggestion. There was no significant association between the physical activity status of oncologists/surgeons and the likelihood that they discussed physical activity with patients. Educational strategies aimed at encouraging clinicians to promote physical activity in consultations need to be targeted widely amongst the cancer clinician community. Evidence from RCTs has shown that physical activity may attenuate the negative effects of cancer treatment in women diagnosed with breast cancer ,2. RatesOncologists and surgeons may serve as an important source of motivation by encouraging patients to be physically active and by conveying the importance of a healthy lifestyle after cancer diagnosis. Oncologists have also been found to have a favourable attitude towards promoting exercise with cancer patients ,6. In adStudies ,6 conducAs part of the development procedures for a RCT of the effects of physical activity on breast outcome, a brief anonymous postal questionnaire (see Appendix 1) was sent (one mailing with no reminders) to 710 consultants registered with the Cancer Research UK Clinical Trials Unit database and comprised of 332 surgeons, 255 clinical oncologists and 84 medical oncologists (clinicians). Clinicians were asked to report whether they routinely provided advice to patients about physical activity during consultations and to indicate the nature and context of any advice provided. An open comment section was included in the questionnaire where clinicians were given the opportunity to provide written details of the advice they gave to patients. Clinicians were also asked to indicate who they believed would be the most suitable health professional to deliver physical activity intervention/advice to breast cancer patients . In addition, the questionnaire also included items to assess clinicians' age, gender, medical speciality and the amount of moderate intensity physical activity that they typically achieved per week.A total of 102 breast cancer consultants working across 65 sites in the UK responded to the study questionnaire (response rate = 14.4%). The majority of responders were from district hospitals (56%) and worked in specialist cancer centres (63%). Most respondents were aged 40\u201350 years (n = 44) or 50\u201360 years (n = 37). Of responders, 44.1% (n = 45) routinely gave advice to their patients about physical activity. Walking was the most commonly advocated type of activity although advice relating to the duration and intensity of physical activity that patients were encouraged to achieve varied considerably [see additional file]. The nature of the advice provided can be broadly categorised into five main themes; benefits for recurrence and mortality, benefits for weight control and management, benefits for physical and functional health, benefits of active healthy living and general comments about physical activity prescription [see additional file Chi-squared analysis showed that oncologists were significantly (p < 0.01) more likely to give patients advice about physical activity than surgeons (n = 36/60: 60.0% versus n = 9/38: 23.7%). Relatively few clinicians (36.5%: n = 33/85) were themselves meeting current public health recommendations for physical activity of at least 150 minutes of moderate intensity physical activity per week. Chi-squared analysis indicated no relationship between physical activity status and whether clinicians promoted physical activity with their patients (yes or no). Clinicians felt nurses (50%: n = 51) and physiotherapists (33.3%: n = 34) were the most suitable health professionals to deliver physical activity interventions to breast cancer patients; 11.8% indicated 'other health professional' in response to this question (e.g. fitness instructor). Only 1.9% (n = 2) of clinicians felt oncologists were the most suitable person to deliver physical activity interventions and no respondents indicated that surgeons were suitable.This study found that about 44% of clinicians gave advice to their patients about physical activity. This finding is consistent with previous research conducteOncologists were much more likely to promote physical activity with their patients than surgeons; this might be because oncologists have greater levels of contact with patients during follow-up and/or because they see patients at the completion of treatment and give formal advice on prevention of relapse. In contrast, surgeons see patients during active treatment when advice about physical activity may not be as appropriate. These findings also serve to highlight differences in practice between clinicians of different sub-specialities and help to identify where the greatest need for training might lie. Results are also in broad agreement with a previous study which foAmongst clinicians who did offer physical activity advice, most focussed on the physical and functional benefits that it can provide and its role in facilitating weight maintenance. It was interesting to note that many clinicians discussed physical activity with patients in the context that participation may decrease their risk of recurrence and improve survival. Currently there is only epidemiological evidence to support an association between physical activity and mortality from breast cancer and RCTs are still required to confirm any potential survival benefit.About a third of clinicians were meeting the current public health recommendations for physical activity per week, which is similar to rates found for the general population in the UK . Those cThis study should be interpreted in the context of several limitations. The response rate was low and those who did respond may not be representative of all oncologists and surgeons. Larger studies may be better positioned to explore these issues more precisely. However, responses were obtained from male and female clinicians of different ages located at sixty-five sites throughout the UK and this should serve to increase the generalisability of the findings. It is anticipated that responders were more likely to have some interest in physical activity than non-responders and therefore these findings may represent a 'best case scenario' regarding current practice of cancer clinicians.To the best of our knowledge this is the first study of its kind to take place in the UK and to provide information about both the qualitative and quantitative nature of the physical activity advice given to patients by oncologists and surgeons. Previous studies from North America have focussed on oncologists and less is known about the practice of cancer surgeons in relation to physical activity; the present study addresses this gap in the literature.Many clinicians discuss physical activity with their patients but a large proportion do not. Few clinicians felt that they were best placed to offer patients advice about physical activity and this may explain why many do not do so. Greater efforts need to be made to educate cancer clinicians in the UK about physical activity so that patients are routinely advised about the health benefits that participation might provide both during and after active treatment for breast cancer.RCTs: randomised controlled trials; UK: United Kingdom.The authors declare that they have no competing interests.AJD drafted the manuscript and conducted the analyses. SJB coordinated the study, helped to draft the manuscript and contributed to data analysis. All authors participated in conceptualisation and design of the questionnaire study. All authors read and approved the final version of the manuscript.1) Indicate your profession:Clinical Oncologist \u25a1 Medical Oncologist \u25a1 Surgeon \u25a12) Would you normally give patients advice regarding exercise? No \u25a1 Yes \u25a1If yes, briefly describe the advice you would give below:_____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________3) Who would you consider most suitable to deliver an exercise intervention?Research Nurse \u25a1 Physiotherapist \u25a1Surgeon \u25a1 Oncologist \u25a1Other \u25a1 please specify:_____________________________4) We would be grateful if you could provide the following optional information about yourselfa) What is your gender? Female \u25a1 Male \u25a1b) What is your age range in years? < 30 \u25a1 30\u201340 \u25a1 40\u201350 \u25a1 50\u201360 \u25a1 > 60 \u25a1c) In a typical week how many times, and for how long, do you participate in moderate intensity exercise Number of times per week: _____________Average time per session: _____________ minutesAdvice given to breast cancer patients by consultant oncologists and surgeons in the UK. This information provided an overview of the type of advice given to breast cancer patients by consultant oncologists and surgeons.Click here for file"} +{"text": "All instances of the symbols \"t_ant_clear\" and \"t_syn_clear\" relating to Figures 4 and S2 should instead read \"N_ant_double\" and \"N_syn_double\" respectively. Similarly, all instances of \"sigma_syn/sigma_ant\" relating to Figures S2 and S3 should read \"N_ant_double/N_syn_double.\""} +{"text": "Escherichia coli bacteriophage vB_EcoP_PR_Kaz2018, isolated from a water sample. vB_EcoP_PR_Kaz2018 is a linear double-stranded DNA T7-like podophage with a genome of 39,704\u2009bp containing 45 predicted open reading frames (ORFs).Here, we describe the complete genome sequence of the Escherichia coli bacteriophage vB_EcoP_PR_Kaz2018, isolated from a water sample. vB_EcoP_PR_Kaz2018 is a linear double-stranded DNA T7-like podophage with a genome of 39,704\u2009bp containing 45 predicted open reading frames (ORFs).Here, we describe the complete genome sequence of the Escherichia coli bacteriophage vB_EcoP_PR_Kaz2018 was isolated from a water sample and is capable of infecting encapsulated Escherichia coli expressing the K1 capsular antigen, a major causative agent of neonatal septicemia, sepsis, and meningitis . The DNA library was prepared using the Nextera XT DNA sample preparation kit (Illumina). Whole-genome sequencing was performed with an Illumina MiSeq sequencing platform. Low-quality reads were filtered and adapters trimmed with Trimmomatic (Enterobacter phage K1F (GenBank accession number AM084414), with 100% query coverage and 95.28% identity; Escherichia phage LM33_P1 (LT594300), with 86% query coverage and 95.22% identity; Escherichia phage PE3-1 (KJ748011), with 85% query coverage and 95.13% identity; and Escherichia phage YZ1 (MG845865), with 84% query coverage and 94.73% identity.The genomic DNA was extracted from the phage lysate of the mmomatic from themmomatic . As a remmomatic . The avemmomatic , 6. The mmomatic , 8, nameE. coli.The complete genome of phage vB_EcoP_PR_Kaz2018 is a linear double-stranded DNA (dsDNA) of 39,704\u2009bp, with 178-bp-long terminal repeats. The GC content of the genome was 49.8%. Gene prediction was done using GeneMark and PHAST . A totalEscherichia phage vB_EcoP_PR_Kaz2018 was deposited in GenBank under the accession number MN510331. Raw sequence reads are available under BioProject accession number PRJNA574554.The complete genome sequence of the"} +{"text": "Although the de\u00a0novo transcriptome assembly of non-model organisms has been on the rise recently and new tools are frequently developing, there is still a knowledge gap about which assembly software should be used to build a comprehensive de\u00a0novo assembly.In recent years, massively parallel complementary DNA sequencing (RNA sequencing [RNA-Seq]) has emerged as a fast, cost-effective, and robust technology to study entire transcriptomes in various manners. In particular, for non-model organisms and in the absence of an appropriate reference genome, RNA-Seq is used to reconstruct the transcriptome de\u00a0novo assembly tools are applied to 9 RNA-Seq data sets spanning different kingdoms of life. Overall, we built >200 single assemblies and evaluated their performance on a combination of 20 biological-based and reference-free metrics. Our study is accompanied by a comprehensive and extensible Electronic Supplement that summarizes all data sets, assembly execution instructions, and evaluation results. Trinity, SPAdes, and Trans-ABySS, followed by Bridger and SOAPdenovo-Trans, generally outperformed the other tools compared. Moreover, we observed species-specific differences in the performance of each assembler. No tool delivered the best results for all data sets.Here, we present a large-scale comparative study in which 10 de\u00a0novo transcriptome assembly.We recommend a careful choice and normalization of evaluation metrics to select the best assembling results as a critical step in the reconstruction of a comprehensive Even though a reference genome is available, it is still recommended to complement a gene expression study by a de\u00a0novo transcriptome assembly to identify transcripts that have been missed by the genome assembly process or are just not appropriately annotated\u00a0) has established itself as a powerful technique to understand versatile molecular mechanisms and to address various biological questions\u00a0. In partnnotated\u00a0.At first glance, the transcriptome assembly process seems similar to genome assembly, but actually, there are fundamental differences and various challenges. On the one hand, some transcripts might have a shallow expression level, while others are highly expressed\u00a0,4,6. Espde\u00a0novo transcriptome assembly of non-model organisms has been on the rise recently, and new tools are frequently developed. Now there is a knowledge gap: which assembly software and parameter settings should be used to construct a good assembly? In addition, there is no consensus about which metrics should be used to evaluate the quality of multiple de\u00a0novo transcriptome assemblies.The de\u00a0novo transcriptome assembly\u00a0\u00a0) are staupported\u00a0.IDBA-Tran (v1.1.1), a novel assembly tool that claims to be more robust regarding uneven expression levels in RNA-Seq data\u00a0 64-bit). Of course, how easily a tool can be installed and executed depends heavily on the machine used, the server setup, and how familiar the user is with the programing language the tool is based on. Nevertheless, it should be the goal of each publicly available piece of software to be as user-friendly as possible. Therefore, we collected our experiences during the installation and execution of each assembler to share our observations Table\u00a0.Electronic Supplement publicly available at www.rna.uni-jena.de/supplements/assembly\u00a0[doi.org/10.17605/OSF.IO/5ZDX4\u00a0[BUSCO and TransRate as well as other results are also archived in the GigaScience GigaDB respository\u00a0[A comprehensive assembly\u00a0 accompanIO/5ZDX4\u00a0. AdditioS1Supplementary Table : Data sets and preprocessing.S2Supplementary Table : Assembly tools.S3Supplementary Files : Executed assembly commands.S4Supplementary Figures : HISAT2 re-mapping rate.S5Supplementary Figures : rnaQUAST statistics.S6Supplementary Tables : TransRate.S7Supplementary Figures : ExN50.S8Supplementary Figures : BUSCO.S9Supplementary Tables : DETONATE.S10Supplementary Tables : Selected main metrics.S11Supplementary Figures : Runtime and memory consumption.S12Supplementary Figures : -normalized scores per data set and metric.GIGA-D-18-00307_Original_Submission.pdfClick here for additional data file.GIGA-D-18-00307_Revision_1.pdfClick here for additional data file.GIGA-D-18-00307_Revision_2.pdfClick here for additional data file.GIGA-D-18-00307_Revision_3.pdfClick here for additional data file.Response_to_Reviewer_Comments_Original_Submission.pdfClick here for additional data file.Response_to_Reviewer_Comments_Revision_1.pdfClick here for additional data file.Response_to_Reviewer_Comments_Revision_2.pdfClick here for additional data file.Reviewer_1_Report_Original_Submission -- Andrey D. Prjibelski, M.Sc.9/26/2018 ReviewedClick here for additional data file.Reviewer_1_Report_Revision_1 -- Andrey D. Prjibelski, M.Sc.2/7/2019 ReviewedClick here for additional data file.Reviewer_2_Report_Original_Submission -- Brian Haas9/27/2018 ReviewedClick here for additional data file.Reviewer_2_Report_Revision_1 -- Brian Haas1/27/2019 ReviewedClick here for additional data file.Homo sapiens; KC: k-mer compression; MK: multiple k-mer; MS: metric score; nt: nucleotides; OMS: overall metric score; RNA-Seq: RNA sequencing.BUSCO: benchmarked universal single-copy orthologs; Chr1: chromosome 1; EBOV: Ebola virus; HSA: The authors declare that they have no competing interests.This work has been funded by the German Research Foundation (DFG) projects Collaborative Research Center/Transregio 124\u2014\u201cPathogenic fungi and their human host: Networks of Interaction,\u201d subproject B5; DFG SPP-1596\u2014\u201cEcology and species barriers in emerging viral diseases\u201d; and CRC 1076 \u201cAquaDiva\u201d, subproject A06.M.M. conceived the research idea. M.H. designed the project, performed calculations and analysis, interpreted the data, and wrote the main manuscript. M.M. contributed in discussions and in proofreading the final manuscript. This work is part of the doctoral thesis of M.H. All authors read and approved the final manuscript."} +{"text": "The gene LsWRKY (Lsat_1_v5_gn_6_12161) incorrectly did not appear in"} +{"text": "Helicobacter pylori causes gastric cancer in 1\u20132% of cases but is also beneficial for protection against allergies and gastroesophageal diseases. An estimated 85% of H. pylori\u2013colonized individuals experience no detrimental effects. To study the mechanisms promoting host tolerance to the bacterium in the gastrointestinal mucosa and systemic regulatory effects, we investigated the dynamics of immunoregulatory mechanisms triggered by H. pylori using a high-performance computing\u2013driven ENteric Immunity SImulator multiscale model. Immune responses were simulated by integrating an agent-based model, ordinary, and partial differential equations.In silico validation showed that colonization with H. pylori decreased with a decrease in epithelial cell proliferation, which was linked to regulatory macrophages and tolerogenic dendritic cells.The outputs were analyzed using 2 sequential stages: the first used a partial rank correlation coefficient regression\u2013based and the second a metamodel-based global sensitivity analysis. The influential parameters screened from the first stage were selected to be varied for the second stage. The outputs from both stages were combined as a training dataset to build a spatiotemporal metamodel. The Sobol indices measured time-varying impact of input parameters during initiation, peak, and chronic phases of infection. The study identified epithelial cell proliferation and epithelial cell death as key parameters that control infection outcomes. H. pylori infection identified epithelial cell proliferation as a key factor for successful colonization of the gastric niche and highlighted the role of tolerogenic dendritic cells and regulatory macrophages in modulating the host responses and shaping infection outcomes.The hybrid model of The outputs from the first stage (152 \u00d7 20 runs) and second stage (115 \u00d7 20 runs) were combined to provide the training data to build a spatiotemporal metamodel. For the second-stage analyses, we utilized a metamodeling-based approach. Metamodels are surrogate models that can be used as a substitute for the simulation model , cov[M], ..., cov[M]T, that contains spatial covariance between the k design points and a given prediction point kxk covariance matrix of the vector of simulation errors associated with the vector of point estimates k is the kx 1 vector of ones and Similar as in Ankenman et al. , shown in et al. , the besequation :(4)\\docn et al. is givenTo implement the metamodeling approach as described above, the unknown model parameters are estimated through maximizing the log-likelihood function. The underlying standard assumption is that .g., see and 45]\\document.g., see is used To determine the effect of input variables on the output, we employed the variance decomposition method. These methods involve the decomposition of the variance of the output as a sum of the variance produced by each input parameter .Second-stage analysis, and the Sobol\u2019 indices were computed as described in were shown to have positive influence on the resident macrophage cells, whereas the T-cell type transition parameters [p_iTregtoTh17 = (0.3\u20130.4) and p_Th17toiTreg = (0.1\u20130.2)] showed a negative impact on the resident macrophages. Similarly, we performed the PRCC analysis for all the cell populations under consideration during the infection (not shown).Global sensitivity analysis) were selected to be varied for the second-stage design. All the selected inputs are shown in The significant parameters (marked in blue bars) obtained from the SA of the output from the first-stage design of experiments , using the mlegp package in R obtained. The diagnostic plots denote the black circles, which are the cross-validated prediction. Cross-validation is in the sense that for predictions made at design point x, all observations at design point x are removed from the training set. The lower panel represents the residual plots for the cell populations: (a) H. pylori, (b) resident macrophages, (c) monocyte-derived macrophages in the LP, and (d) tolerogenic DCs in the GLN compartment.ABM: agent-based model; DC: dendritic cell; ENISI MSM: Enteric Immunity Simulator multiscale modeling; GLN: gastric lymph node; GP: Gaussian process; HPC: high-performance computing; IFN-\u03b3: interferon \u03b3; IL: interleukin; iTreg: induced regulatory T; KO: knockout: LP: lamina propria; LSODA: Livermore Solver for Ordinary Differential Equations; ODE: ordinary differential equation; PDE: partial differential equation; PPAR\u03b3: peroxisome proliferator-activated receptor \u03b3; PRCC: partial rank correlation coefficient; RRID: research identification initiative ID; SA: sensitivity analysis; SRCC: Spearman rank correlation coefficient; STAT3: signal transducer and activator of transcription 3; TGF-\u03b2: transforming growth factor \u03b2; Th: T helper; Treg: regulatory T; WT: wild type.The authors declare that they have no competing interests.www.nimml.org). The funding body had no role in the design of the study, data collection, analysis, interpretation of data, and writing of the manuscript.This work was supported by the Defense Threat Reduction Agency (DTRA) grant HDTRA1\u201318-1\u20130008 to J.B.R. and R.H. and funds from the Nutritional Immunology and Molecular Medicine Laboratory (H. pylori experimental data. J.B.R., V.A., and R.H. supervised the project. J.B.R. and R.H. edited the manuscript. J.B.R., A.L., N.T.J., S.H., V.A., X.C., and R.H. participated in discussions on the model and results. All authors provided critical feedback on the project.M.V., R.H., and J.B.R. formulated the model, implemented, performed the simulations, analyzed model-generated outputs, made the figures, and wrote the manuscript. M.V., A.L., J.B.R., R.H., and S.H. formulated the model. S.H., A.L., and V.A. implemented the code architecture and benchmarked the parallel version of the hybrid model. X.C. and M.V. wrote the codes for global sensitivity analysis and generated the design matrices. N.T.J. generated macrophage and giz062_GIGA-D-18-00435_Original_SubmissionClick here for additional data file.giz062_GIGA-D-18-00435_Revision_1Click here for additional data file.giz062_GIGA-D-18-00435_Revision_2Click here for additional data file.giz062_GIGA-D-18-00435_Revision_3Click here for additional data file.giz062_GIGA-D-18-00435_Revision_4Click here for additional data file.giz062_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giz062_Response_to_Reviewer_Comments_Revision_1Click here for additional data file.giz062_Response_to_Reviewer_Comments_Revision_2Click here for additional data file.giz062_Response_to_Reviewer_Comments_Revision_3Click here for additional data file.giz062_Reviewer_1_Report_Original_SubmissionChang Gong -- 12/9/2018 ReviewedClick here for additional data file.giz062_Reviewer_1_Report_Revision_1Chang Gong -- 1/28/2019 ReviewedClick here for additional data file.giz062_Reviewer_2_Report_Original_SubmissionElsje Pienaar -- 12/17/2018 ReviewedClick here for additional data file.giz062_Reviewer_2_Report_Revision_1Elsje Pienaar -- 1/31/2019 ReviewedClick here for additional data file.giz062_Reviewer_2_Report_Revision_2Elsje Pienaar -- 2/18/2019 ReviewedClick here for additional data file.giz062_Reviewer_3_Report_Revision_2Paul Macklin, Ph.D. -- 2/25/2019 ReviewedClick here for additional data file.giz062_Reviewer_3_Report_Revision_3Paul Macklin, Ph.D. -- 3/21/2019 ReviewedClick here for additional data file.giz062_Reviewer_3_Report_Revision_4Paul Macklin, Ph.D. -- 4/7/2019 ReviewedClick here for additional data file.giz062_Supplement_FilesClick here for additional data file."} +{"text": "Diabetes is a significant health concern with more than 30 million Americans living with diabetes. Onset of diabetes increases the risk for various complications, including kidney disease, myocardial infractions, heart failure, stroke, retinopathy, and liver disease. In this paper, we study and predict the onset of these complications using a network-based approach by identifying fast and slow progressors. That is, given a patient\u2019s diagnosis of diabetes, we predict the likelihood of developing one or more of the possible complications, and which patients will develop complications quickly. This combination of \"if a complication will be developed\u201d with \u201dhow fast it will be developed\u201d can aid the physician in developing better diabetes management program for a given patient. Diabetes is a significant public health concern in the United States. According to the Center for Disease Control (CDC), in 2015 it was estimated that 30.3 million people have diabetes, with 23.1 million cases diagnosed and 7.2 million undiagnosed . 90 to 9To achieve the objective of predictability of onset of complications, we first represent a patient\u2019s disease history as a network based on what happens in the second year after a diabetes diagnosis. Genetic determinants and other independent accelerating factors of the complications of diabetes clearly The proposed network developed in this study will not only provide a useful modeling construct but also a mechanism for visualizing disease complications. The use of networks to understand disease progression has been studied before, such as in Alzheimer\u2019s and hearWe use a large data set comprising of Type 2 Diabetes patients in Indiana, collected over 20 years obtained through the Regenstrief Institute. This data includes both diagnosis codes taken from the International Statistical Classification of Diseases and Related Health Problems, Ninth Revision and Tenth Revision, and clinical laboratory test results. Researchers have had success using ICD codes to predict future disease states . We creaPredicting diabetic complications is incredibly challenging due to the inequality of healthcare consumption and the speed at which patients receive diagnoses. In our work, we posit that by establishing appropriate thresholds and choosing balanced populations, we can ensure that even patients who infrequently visit their physician can still benefit from our models.The Regenstrief Institute created one of the earliest electronic medical record systems in 1972 to support research and continues to handle the research use of the INPC (Indiana Network for Patient Care) database . With thIn a collaboration of Indiana Biosciences Research Institute, Regenstrief Institute, and industrial partners, a primary data set of type 2 diabetes mellitus (T2DM) patients was created. Using inclusion criteria of one T2D diagnosis code OR a laboratory glycated hemoglobin HbA1C) test results \u2265\u20096.5% OR at least one Medi-Span-defined anti-diabetes medication where the patients were \u2265\u200918 years of age on date of first inclusion criteria. Using this criteria, a primary T2DM cohort of 805,867 individuals was identified from INPC over 20 years (1995-2015). The demographics, diagnosis codes, medical procedures, prescriptions, and results from clinical laboratory tests were extracted for these individuals. This exC test reTo clean this T2DM data set, the extracted INPC data placed on a secure Amazon Web Services (AWS) server. This large T2DM dataset across 20 years was multi-modal and there were many missing parameters across the records, as well as inconsistency in the measurements identified by error codes or per-patient longitudinal analysis or out of range values. In addition, we had to take into account the correction of features that were reported for quality control (QC) checks. To that end, we implemented a comprehensive a data cleaning framework to normalize the features, remove bad or missing values, and have consistent units of measure was done using PySpark. The feature values were normalized and extreme values were identified and filtered on minimum and maximum values ever measured for a parameter. Additionally, if any values were +/- 2 standard deviations from the median, they were filtered. Also, we looked for more than two distribution patterns in the data where potentially two different units of measure were applied to the same variable, which could indicate a problem with poor previous data integration. After this extensive effort to clean all the issues from this \"real-world\" captured data set from INPC, an \"analysis-ready\" data set was created for the modeling. An overview of the size of the different data tables is given in Table\u00a0Type 2 diabetes mellitus - ICD9/ICD10 codes 249, 250, 357.2, 362.[01-07], 366.41, E10, E11Kidney disease - ICD9/ICD10 codes 584, 586, 585, 403, 404, 581, 583, 588, N18, N17, N19, I12, I13, N04, N05, N08, N25, 593Liver disease - ICD9/ICD10 codes 571, 572, 573, K76, K75Heart failure - defined as ICD9/ICD10 codes 428, I50Myocardial infarction - ICD9/ICD10 codes 410, 412, I21Stroke - ICD9/ICD10 codes 435, G45, 430, 431, I60, I61, 432, I62, 436, 433, 434Retinopathy - ICD9/ICD10 codes 362, H35We use the following to categorize primary T2DM diagnoses and complications: We further sample to create the following data about patients: patient diagnosis, which contains all the diagnoses codes (ICD-9/ICD-10) received by a patient, demographics, which contains age, gender, and race/ethnicity information, and clinical variables, which contains metabolic measurements taken while at the doctor\u2019s office. Header files for the diagnosis table is given in Table\u00a0We detail the network construction in Algorithm 1, and network pruning in Algorithm 2. We retain a listing of the edges and nodes that represent the fast paths to diabetic complications, along with the nodes that result in the largest information gain.There are three primary data sources that we use to build our models: patient demographic data, which remains constant throughout the duration of the study and is represented by nodes at the beginning of the network at time zero; patient diagnosis, which contains all the diagnoses that occur over the course of a patient\u2019s visit with a doctor or healthcare provider; and clinical variables, which contain all the available measurements and laboratories tests available in the patient\u2019s health records as contained in INPC.We tested the following clinical variables and grouped them into quartiles, which were included in the clinical variables file: non high-density lipoprotein cholesterol (Non-HDL C), low-density lipoprotien (LDL) high-density lipoprotein (HDL) ratio, thyroid-stimulating hormone (TSH), fibrosis-4 (Fib 4) index, total cholesterol, low-density lipoprotein cholesterol (LDL C), high-density lipoprotein cholesterol (HDL C), cholesterol ratio, total bilirubin, basophil platlet count (PC), monocyte count, aspartate transaminase to platelet ratio index (APRI), neutrophil count, albumin, alkaline phosphatase (ALP), aspartate transaminase (AST) alanine transaminase (ALT) ratio. eosinophil PC, protein, HbA1C, ALT, estimated glomerular filtration rate (eGFR), AST, lymphocyte PC, calcium, red blood PC, platelet count, mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), glucose, blood urea nitrogen (BUN), chloride, creatinine, and carbon dioxide (CO2).Additionally included in the clinical variables file were the following variables, pre-processed into normal and abnormal statuses: weight classification, HDL C, high serum creatinine, high urine glucose, hyperglycemia, hypertension, hypertriglyceridemia, impaired fasting glycemia (IFG), impaired glucose tolerance (IGT), LDL C, and triglycerides. Finally, we also quartile the age of the patients so that we have large groups to test on. Then every piece of information in a patient history is linked all other nodes, thus creating a heterogeneous network. An example of the network is given in Fig.\u00a0After building the network, we prune it by discarding any edges that do not contain statistically significant differences between the fast and slow progressors as defined by using a two-proportion Z test score.To determine if a patient is a slow or fast progressor, the nodes and edges of the sub-network that match the patient\u2019s medical history are traversed and their individual probability of developing a complication is computed. We assume that the node and edge weights, corresponding to the percentages of patients who suffer from that complication that are contained by that node or edge, are equally likely and statistically independent. These weights are multiplied together to get the probability of being a fast progressor. To decrease noise, we experimentally concluded that the weights, or percent likelihood of developing the specific complication of diabetes, corresponding to the top 12 most significant edges and nodes are used as determined by the two-proportion Z-test. In other words, for each individual patient, we only used the most significant parts of their individual network to predict whether or not that patient was a fast or slow progressor. The average AUC values from each of these experiments is shown in Table\u00a0w0,...,wn correspond to the n most significant edge and node weights as determined by the two-proportion Z-test, where n\u226412. Remove wh from the computation, which corresponds to the lowest probability of developing the complication. Let The method to compute the probability that an individual will be a fast or slow progressor is: Let Only information in patient history that occurred in the second year following a Type 2 diabetes diagnosis is considered. Healthy patients survive longer than sickly ones, so if we extend our analysis for too long after a diabetes diagnosis, the data will become biased towards healthy patients. Patients tend to move and change doctors, and analyzing what occurs in the second year after the diagnosis will ensure that many patients are still in the system. We can see in Fig.\u00a0Diagnoses are truncated to the first three digits of the ICD-9 or ICD-10 code to remove the disease subtypes and only focus on the primary diagnoses.All nodes that are not shared by at least one percent of the population are removed.All patients that have received less than five diagnoses or more than twice the median amount of diagnoses are removed. This assists with biases introduced by individuals having an excessive medical history or too few observations.The cleaned dataset is sampled to ensure that our fast and slow progressors have the same number of patients.The significance on the edges is computed and any edges that do not test for a two-proportion z-test with 95 percent confidence are removed.Fast progressors are defined as patients who develop a complication of diabetes faster than 75 percent of the population. All patients from our dataset who develop the complication before being diagnosed with diabetes, or up to one year afterwards are removed.Slow progressors are defined as patients who develop a complication of diabetes slower than 75 percent of the population. Everyone retained in our network is eventually diagnosed with the complication which assists in making sure the datasets are balanced and with limited bias.Every node and every edge is given a Z-score, which corresponds to the likelihood of a significant difference between fast and slow progressors. Every node and edge will be given the percent likelihood that a patient who has the condition given in the node, or combination of conditions as represented by an edge, will be a fast or slow progressor.We only consider new diagnoses that occur after a diabetes diagnosis. We do not consider diagnoses or lab values that occurred before the type 2 diabetes diagnosis. Incorporating past values might be included in future work. Our test set contained 20 percent of our patients. The percent likelihood of their complication development was computed against the patient network generated from the 80 percent training set. We queried the large network for nodes and edges corresponding to an individual patient\u2019s disease history. Because all the edges that failed to show a significant difference between the fast and slow progressors were pruned, the sub-network might be disconnected. The top five conditions that lead to each complication by percentage of fast progressors and Z-score are given in Table\u00a0The results for these predictions of fast progressors for onset of these various diabetic complications are shown in Table\u00a0Diabetic complications are often correlated with one another, which might reflect the generalized damage that the body has taken from a micro and macrovascular perspective . Others Many of the top confidence nodes are shared between different complications. Correlations between the fast and slow progressors are given in Table\u00a0In our future work, we would like to examine the false positives and identify what causes them to not develop complications immediately, even though their diagnosis history and lab results identify them as fast progressors. This will inform health management strategies \u2013 lifestyle, behavioral or environmental factors \u2013 in addition to the medication to manage diabetes. We believe this analysis should help enable recommendations for diabetic patients to limit development of complications.Given a patient\u2019s disease history and lab results, we can predict their likelihood of developing complications from diabetes. We also show what disease diagnoses or lab results (from our heterogeneous network or graph) are most likely to lead to specific diabetic complications. We reaffirm that diabetes is a complicated disease. It continues to be important for diabetic patients to manage their disease and be aware of the complications. The diagnoses graphs can help illuminate health problems faced by many patients and what might be the best course of disease management. Not managing complications, especially for fast progressors, can cause rapid development of uncontrolled diabetes, from which it is hard to recover. Moreover, disease diagnoses graphs can also be a useful tool for physicians to understand the effects of co-morbid conditions, and personalize a wellness and disease management plan. This can lead to an improvement in both individual and population health outcomes.Below is a list of data columns included in the clinical variables file: STUDYID, AGE, DAYS_VIS_INDEX, GENDER, INDEX_AGE, angiotensin converting enzyme (ace), acetaminophen, acetone, act, albumin, albumin_creatinine_ratio, albumin_globulin_ratio, alcohol_pc, aldolase, aldosterone, alp, alp_bone_isoenzyme, alpha_1_antitrypsin, alpha_1_globulin, alpha_2_globulin, alpha_tocopherol, alt, ammonia, amylase, anion_gap, aorta_sinuses_diam, aortic_root_diam, aov_peak_pressure, aov_peak_velocity, apri, arterial_diastolic_bp, ast, ast_alt_ratio, antithrombin iii (atiii), band count (cnt), band_pc, bard_score, base_excess, basophil_count, basophil_pc, beta2_microglobulin, beta_globulin, beta_hydroxybutyrate, bicarbonate, blast_count, blast_pc, body mass index (bmi), body_surface_area, bun, bun_cr, bun_post_dialysis, bun_pre_dialysis, complement 3 (c3), complement 4 (c4), c_peptide, calciferol, calcium, calcium_albumin, carboxyhemoglobin, cyclic citrullinated peptide (ccp), cluster of differentiation (cd) 2_t_cells, cd3_t_cells, cd4_cd8_ratio, cd4_helper_t, cd4_t_cells, cd8_supprs_t_cells, cd8_t_cells, carcinoembryonic antigen (cea), cell_count, chloride, cholecalciferol, cholesterol_ratio, creatine kinase (ck)_bb), ck_index, ck_mb, ck_mb_tot, ck_mm, ck_total, chronic kidney disease (ckd)_stage, co2, colony_count, conjugated_bilirubin, cortisol, creatinine, creatinine_ck, creatinine_clear, c-reactive protein (crp), central venous pressure (cvp), d_dimer, (dehydroepiandrosterone) dhea_s, diabetic_nephropathy_status, diabetic_status, diastolic_bp, diastolic_bp_standing, direct_bilirubin, epstein-barr (ebv)_antibody, eGFR, eosinophil_count, eosinophil_pc, esr, estradiol_unconjugated, estrogen, factor_viii_activity, fasting_glucose, forced expiratory flow (fef)25_75, ferritin, fib_4_index, fibrinogen, fraction of inspired oxygen (fio2), folate, free_lambda, fructosamine, follicle-stimulationg hormone (fsh), gamma-glutamyl transpeptidase (ggt), globulin, glucose, glucose_gtt_1h, glucose_gtt_1hr_ob, glucose_gtt_2h, glucose_gtt_3h, glucose_gtt_pp, hba1c, hdl_c, hdl_c_status, hdl_ cholesterol (chol), hdl_ldl, height, hepatitis (hepb)_ab, hemoglobin (hgb), hemoglobin a2 (hgb_a2), high_serum_creatinine_status, high_urine_glucose_status, histamine, homeostatic model assessment of beta cell function (homa_b), homeostatic model assessment of insulin resistance (homa_ir), homocysteine, hyperglycemia_status, hypertension_status, hypertriglyceridemia_status, ifg_status, immunoglobulin a (iga), immunoglobulin e (ige), insulin-like growth factor 1 (igf_1), immunoglobulin g (igg), immunoglobulin m (igm), igt_status, immature_granulocytes_pc, indirect_bilirubin, insulin, iron, interventricular septum (ivs)_thickness, left atrium (la)_diameter, lactate, lactate_dehydrogenase, lactic acid dehydrogenase (ldh)_1, ldh_2, ldh_3, ldh_4, ldh_5, ldl_c, ldl_c_status, ldl_hdl_ratio, lh, lipase, lipoprotein (lpa), left ventricle (lv)_mass, lv_stroke_volume, lv_systolic_volume, left ventricular outflow tract (lvot)_peak_gradient, lvot_peak_velocity, left ventricular posterior wall (lvpw)_thickness_diastolic, lymphocyte_atypical, lymphocyte_count, lymphocyte_pc, lymphocyte_reactive, lymphocyte_variant, lymphotycte cerebrospinal fluid (csf), macrophage_pc, map, mch, mcv, mean_arterial_pressure, mean_glucose_bld_ghb_test, mesothelial_cells_pc, metamyelocytes_count, metamyelocytes_pc, methemoglobin, methemoglobin_pc, mixed_mono_count, mixed_mono_pc, monocyte_count, monocyte_csf_pc, monocyte_pc, myelocyte_count, myelocyte_pc, nafld_fibrosis_score, neutrophil_count, neutrophil_pc, non_hdl_c, nucleated red blood cells (nrbc)_count, nrbc_pc, nrbc_white blood cell (wbc), N-terminal pro b-type natriuretic peptide (nt_probnp), nucleated_cell_count, oxygen (o2), oxyhemoglobin_pc, p_wave_offset, p_wave_onset, partial pressure of carbon dioxide (pco2), ph, phosphorus, platelet_count, partial pressure of oxygen (po2), poly_count, poly_pc, potassium, pr_interval, pre_diabetic_status, progesterone_17_OH, promyelocytes_count, prostate_free, prostrate_total, protein, pulse, qt_corrected, quantitative insulin-sensitivity check index (quicki), red blood cell distribution width (rdw), red_blood_cell_count_csf, red_blood_pc, renal_exocrine pancreatic insufficiency (epi)_cells, respiratory_rate, selenium, serum_osmolality, smudge_cell_count, sodium, systolic_bp, systolic_bp_standing, triiodothyronine (t3)_free, t3_total, thyroxine (t4)_free, t4_total, t_wave_axis, t_wave_offset, temperature, testosterone_free, testosterone_total, total iron binding capacity (tibc), total_bilirubin, total_cholesterol, triglyceride_hdl_ratio, triglycerides, triglycerides_status, troponin, troponin_2h, tsh, urine albumin-to-creatinine ratio (uacr), unconjugated_billirubin, uric_acid, urine_albumin, urine_ascorbate, urine_bacteria, urine_billirubin, urine_cast, urine_chloride, urine_cortisol_free, urine_creatinine, urine_creatinine_24, urine_crystals, urine_epithelial_cells, urine_gamma_globulin, urine_glucose, urine_granular_cast, urine_hgb, urine_hyaline_cast, urine_ketones, urine_microalbumin, urine_microalbumin_24, urine_microalbumin_creatinine_ratio, urine_microalbumin_creatinine_ratio_24, urine_potassium, urine_protein, urine_protein_24, urine_protein_creatinine_ratio, urine_red blood cells (rbc), urine_specific gravity (sp_grav), urine_squaous_epithelial (epi)_cells, urine_trans_epi_cells, urine_urea_nitrogen, urine_urobilinogen, urine_waxy_cast, vitamin (vit)_a, vit_b1, vit_b12, vit_d2, vit_25-hydroxyvitamin d2(d2_25_oh), very low-density lipoprotein (vldl), vldl_c, waist_circumference, wbc_count, wbc_count_csf, weight, weight_classification, zinc, CARDIOVASCULAR, NEPHROPATHY, LIVER, OUTCOME"} +{"text": "Scientific Reports 10.1038/s41598-019-52700-w, published online 12 November 2019Correction to: In this Article, there is a typographical error in the Data availability section, where:https://gin.gnode.org/USZ_NCH/Scalp_EEG_HFO.\u201d\u201cThe EEG data and HFO markings are freely available at should read:https://gin.g-node.org/USZ_NCH/Scalp_EEG_HFO.\u201d\u201cThe EEG data and HFO markings are freely available at"} diff --git a/PMC_clustering_701.jsonl b/PMC_clustering_701.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..d866cb3549f522289eb8d852446465c6af3c3d06 --- /dev/null +++ b/PMC_clustering_701.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e489bb655d3801c7d521bacf8774e5c21a7b9ad404462b6bbcf057e3d323a7b8 +size 58742908 diff --git a/PMC_clustering_702.jsonl b/PMC_clustering_702.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..e051ccbbe037cd3f6bd883813664e0f3b9844be7 --- /dev/null +++ b/PMC_clustering_702.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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0000000000000000000000000000000000000000..4ad20c6fd6af56fba80a4df6f681bb19c889c83a --- /dev/null +++ b/PMC_clustering_705.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:498e778586344107330049da63c1901512263993cd55983543efed9807831c37 +size 13264565 diff --git a/PMC_clustering_706.jsonl b/PMC_clustering_706.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..64b3a92e0c9e5690cc6a7a768d56aa64f13eeb5b --- /dev/null +++ b/PMC_clustering_706.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cdbf2c112618ae4122968a4d62007e9c698d7be0657d41858f93858975242e60 +size 28615866 diff --git a/PMC_clustering_707.jsonl b/PMC_clustering_707.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..2f53c1e38d1a16d7e0ccb990d43b6ec65c161306 --- /dev/null +++ b/PMC_clustering_707.jsonl @@ -0,0 +1,433 @@ +{"text": "The eleventh author's name is spelled incorrectly. The correct name is: Lenard I. Lesser."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Anne A. Dowton."} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: Mona M.F. Ganem."} +{"text": "The fourth author\u2019s name appears incorrectly. The correct name is: Alex M. Downs."} +{"text": "The eleventh author\u2019s middle initial is incorrect. The correct name is: Rayaz A. Malik."} +{"text": "The eighth author\u2019s middle initial is incorrect. The correct name is: Judith D. Cohn."} +{"text": "TVST.I thank Dr. Van Gelder for his editorial"} +{"text": "The sixth author's name is spelled incorrectly. The correct name is: Binyam Minuye."} +{"text": "The twelfth author\u2019s name is spelled incorrectly. The correct name is: Letzibeth Mendez-Rivera."} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: Kazuhiro Tokuda."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is Carlo Geraldo Fraga."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Solomon Weldegebreal Asgedom."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Hengrui Xing."} +{"text": "The fourth author's first name is spelled incorrectly. The correct name is: Braden Gammon."} +{"text": "The thirteenth author's name is spelled incorrectly. The correct name is: Jonathan E. Shaw"} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: Kris Carlyon."} +{"text": "The ninth author's name is spelled incorrectly. The correct name is: Mayte Villalba."} +{"text": "The third author\u2019s name is spelled incorrectly. The correct name is: Sarah J. Stednitz"} +{"text": "The ninth author's middle initial is incorrect. The correct name is: Alex H. Wei"} +{"text": "The correct corresponding author is Emily Slesinger. Emily Slesinger's email address is:"} +{"text": "The ninth author's initials are indexed incorrectly in PubMed. The correct initials are: Perera MTPR."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Annemieke Aartsma-Rus"} +{"text": "The fifteenth author's initials are indexed incorrectly in PubMed. The correct initials are: Fischer TK."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Augustine Ajuogu. The publisher apologizes for the error."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Marel Gonzalez Medina."} +{"text": "The eighth author\u2019s initials are indexed incorrectly in PubMed. The correct initials are: Sousa-Neto MD."} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: Liz Hasseld"} +{"text": "The correct name is Laure Abensur Vuillaume. The correct indexing in PubMed should read Abensur Vuillaume L.The 8"} +{"text": "The twelfth author\u2019s name is spelled incorrectly. The correct name is: Olivia Biermann."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Louise T. Day."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Keibun Liu."} +{"text": "The 14th author\u2019s name is spelled incorrectly. The correct name is: Ioannis Vogindroukas."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Nancy Van Damme."} +{"text": "The correct name is: Javier Prados Chica.The 15"} +{"text": "We appreciate Wakolbinger-Habel and Muschitz\u2019s comment . The goa"} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Yosuke Inaba"} +{"text": "Massanat. The correct name is Y. Masannat.This error has been corrected."} +{"text": "The ninth author\u2019s name is incorrect. The correct name is: Jacques David.The tenth author\u2019s name is incorrect. The correct name is: Florian Fort.The eleventh author\u2019s name is incorrect. The correct name is: H\u00e9l\u00e8ne Fr\u00e9ville.The twelfth author\u2019s name is incorrect. The correct name is: Cyrille Violle."} +{"text": "The thirteenth author\u2019s initials are indexed incorrectly in PubMed. The correct initials are: Fraga de Abreu VH."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Om Prakash Singh."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Sherik-fa Anang."} +{"text": "The second author\u2019s first name is spelled incorrectly. The correct name is: Jeffrey Pruet."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Eric Allison Philot."} +{"text": "The fifteenth author\u2019s name is spelled incorrectly. The correct name is: Alexandre Tremeau-Bravard.valitutto@ecohealthalliance.org.There is an error in the corresponding author\u2019s email address. The correct email address is:"} +{"text": "Stephen Meltzer's middle initial was omitted in the published article. His name should be: Stephen J. Meltzer."} +{"text": "The second author's name was spelled incorrectly. The correct name is: Mohammad J. Najafzadeh."} +{"text": "The third author\u2019s name was spelled incorrectly. The correct name is Zhanzhi Liu."} +{"text": "The seventh author's name was spelled incorrectly. The correct name is: Massimo Milione"} +{"text": "The final author's name was spelled incorrectly. The correct name is: Ana Maria Oliveira Battastini."} +{"text": "The fifteenth author's name was listed incorrectly. The correct name is: Ramasamy Santhanam"} +{"text": "The first author's name was spelled incorrectly. The correct name is: Han-Li Huang."} +{"text": "The first author's name is misspelled. The correct first author name is: Mar\u00eda Fabiana Laguna"} +{"text": "The ninth author's name was spelled incorrectly. The correct name is: Ninet Sinaii."} +{"text": "The second author's name was spelled incorrectly. The correct name is: Lingshu Wang."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Kenneth Briley Jr."} +{"text": "The fifth author's name was spelled incorrectly. The correct name is: Francesca Walker."} +{"text": "The seventh author's last name is misspelled. The author's correct full name is Esther D. Quakkelaar."} +{"text": "The eleventh author's last name was spelled incorrectly. The correct name is: Thomas Duhen."} +{"text": "There was an error in the eighth author's name. Jianxin Lu is correct."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Manica Balasegaram."} +{"text": "The sixth author's name is misspelled. It should read Bayeh Abera"} +{"text": "There was an error in the third author's name. Michel Toth Kamimura is correct."} +{"text": "The ninth author's name was spelled incorrectly. The correct name is: Stephen D. Larson."} +{"text": "The name of the twelfth author should be: Martin P. Grobusch"} +{"text": "The name of the eighth author is spelled incorrectly. The correct name is: Hitendra R. H. Patel."} +{"text": "The second author's name is misspelled. The correct spelling is: Micheal S. Allen"} +{"text": "The second author's name was spelled incorrectly in the author byline.The correct name is: Yunrong Li."} +{"text": "The name of the seventh author was given incorrectly. The correct name is: Jonathan H. Epstein."} +{"text": "There was a spelling error in the fifteenth author's name. The correct spelling is: Daniel Healy."} +{"text": "The sixth author's name was spelled incorrectly. The correct name is: Philippe Le Bouteiller."} +{"text": "The last author's name was spelled incorrectly. The correct name is: Malaria Genomic Epidemiology Network"} +{"text": "There was an error in the seventh author's name. The author's correct name is Ruth Khalili Friedman. The author's contributions were: Analyzed the data: RKF."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct spelling is: Manica Balasegaram."} +{"text": "There was a spelling error in the fifth author's name. The correct spelling is Sharanjot Saini."} +{"text": "The first author's name is spelled incorrectly. The correct name is: Priyadarsini Kumar."} +{"text": "The 13th author's name is spelled incorrectly. The correct name is: Dax A. Hoffman."} +{"text": "There was an error in the tenth author's name. Guo-Chang Fan is correct."} +{"text": "The eleventh author's name was incorrectly reported. The correct name is: Mary Edyth Wilson."} +{"text": "The aeglected . The bet"} +{"text": "The first author's name was spelled incorrectly. The correct name is: Sang Ok Song"} +{"text": "The 14th author's name is incorrect. The correct name is: Beat A. Imhof"} +{"text": "There was a spelling error in the fifteenth author's name. The correct spelling is Liviana Da Dalt."} +{"text": "The name of the fourth author is incorrect. The correct name is: Octavio Hern\u00e1ndez-Perera."} +{"text": "The correct name of the eleventh author is: Olaf S. Andersen"} +{"text": "The middle initial of fourth author's name was missing. The correct name is Belinda S Cowling."} +{"text": "The sixth author's name was spelled incorrectly. The correct name is: Yingxiu Huang"} +{"text": "The name of the seventh author was given incorrectly. The correct name is: Mark Aspinall-O'Dea."} +{"text": "The fifth author's name was misspelled. The correct name is: Syed Mian."} +{"text": "The sixth author's name was spelled incorrectly. The correct name is: Chrissa Kioussi."} +{"text": "The sixth author name was spelled incorrectly. The correct name is: Emil Egecioglu."} +{"text": "The name of the first author was missing a middle initial.The correct name is: Christina S. Faherty"} +{"text": "The 7th author's name is misspelled. The correct 7th author's name is: Javid I. Dasti"} +{"text": "There was a typographical error in the antepenultimate author's name. The correct spelling is Sarah Derrett."} +{"text": "The third to last author's name was spelled incorrectly. The correct name is: Joel L. Vanneste."} +{"text": "The fourth author's name was spelled incorrectly. The correct name is: Qiyong Gong."} +{"text": "The name of the sixth author was spelled incorrectly. The correct name is: Jos\u00e9 Vitor B. Fasoli."} +{"text": "The eighth author's name was spelled incorrectly. The correct name is: Jennifer L. Gnerlich."} +{"text": "The correct spelling of the 12th author's name is: Xin-Xin Yan"} +{"text": "The correct name is: Tommaso A. Dragani.The name of the 12"} +{"text": "The 12th author's last name is misspelled. The correct author name is: Antje Hutschenreuther."} +{"text": "The eighth author's name was spelled incorrectly. The correct name is: Xiaokai Li."} +{"text": "The name of the fourth author is incorrect. The correct name is: Malgorzata Marja\u0144ska."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is Erol Bakkalbasi."} +{"text": "The ninth and tenth author's names were spelled incorrectly. The correct names are: Sudha Chaturvedi and Vishnu Chaturvedi."} +{"text": "The ninth author's name was spelled incorrectly.The correct name is: Linchun Fu."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Jean-Christophe Grenier."} +{"text": "The seventh author's name was spelled incorrectly. The correct name is: Antonio Di Pietro."} +{"text": "The second author's name was spelled incorrectly. The correct name is: Jeffrey J. DeStefano."} +{"text": "The fifth author's name was spelled incorrectly. The correct name is: Young-Hag Koh."} +{"text": "The twelfth author's name was spelled incorrectly. The correct name is: Derek Amoako."} +{"text": "The sixth author's name was spelled incorrectly. The correct name is: Elizabeth Selvin."} +{"text": "The third author's name was spelled incorrectly.The correct name is: Jinyang He."} +{"text": "There was an error in the last author's name. Suzette A. Priola is correct."} +{"text": "The seventh author's name was spelled incorrectly. The correct name is: Shyam S. Mohapatra."} +{"text": "The name of the sixth author was given incorrectly. The correct name is: Sergio Encarnaci\u00f3n-Guevara. The correct abbreviation in Contributions is: SEG."} +{"text": "The eighth author's name was spelled incorrectly. The correct name is: Veronica Montserrat."} +{"text": "The correct spelling of the 7th author's name is: Petra J. Pouwels."} +{"text": "The 7th author's name is misspelled. The correct spelling is: \"Jin-Hua Chen\""} +{"text": "The thirteenth author's name was spelled incorrectly. The correct name is David M. Kemeny."} +{"text": "The sixth author's name is incorrect. The correct name is: Edward C. Holmes."} +{"text": "The second author's name was spelled incorrectly. The correct name is: Juhwan Oh."} +{"text": "The eighteenth author's name was incomplete. The complete name is: Stephen W. Scherer."} +{"text": "There was a typographical error in the sixth author's name. The correct spelling is Yigeremu Abebe."} +{"text": "There was a spelling error in the sixth author's name. The correct spelling is Ousmane Faye."} +{"text": "The tenth author's name was spelled incorrectly. The correct name is: Saw Yen Ow."} +{"text": "The first author's name was spelled incorrectly. The correct name is: Mohammad Jubair."} +{"text": "The 7th author's name is misspelled. The correct spelling is: Bedrich L. Eckhardt"} +{"text": "Author 'George Bonanno' should be listed as 'George A. Bonanno'."} +{"text": "The first author's name is incorrectly referenced in the citation. The correct citation is: Tekola Ayele F."} +{"text": "The third author's name was spelled incorrectly. The correct name is: Xingkun Jin."} +{"text": "The 11th author's name was entered incorrectly. The correct name is: Julio Viera"} +{"text": "The seventh author\u2019s name is incorrectly spelled. The correct name is Yi Zhao."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Avril Monahan."} +{"text": "The seventh author\u2019s name is incorrect. The correct name is: Mingzhao Zhu."} +{"text": "The fourth author's name is spelled incorrectly. The correct name is: Frederik Gohde. The citation remains the same."} +{"text": "The author\u2019s name is spelled incorrectly. The correct name is: Lauren A. Richardson. The updated article citation is below."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Viviane Grazielle da Silva."} +{"text": "There is an error in the byline. The third author\u2019s name is spelled incorrectly. The correct name should be: Kathryn E Ackerman."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Jose M. Garcia-Manteiga."} +{"text": "The ninth author\u2019s name appears incorrectly. The correct name is: Mohammad Obaidul Hoque."} +{"text": "The second author\u2019s name is misspelled. The correct name is: Cheng-Yi Xia."} +{"text": "The tenth author's name is spelled incorrectly. The correct name is: Marja L. Mikkola."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Renato Anghinah. The publisher apologizes for the error."} +{"text": "The thirteenth author\u2019s name is spelled incorrectly. The correct name is: Ymkje Stienstra."} +{"text": "We thank Dr. Barnett for his kind comments . We agre"} +{"text": "The Data Availability statement is incorrect. The correct statement is: All relevant data are available via NCBI's Gene Expression Omnibus (GEO) (accession number GSE73984)."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Ling Fu."} +{"text": "The thirteenth author\u2019s name is spelled incorrectly. The correct name is Carlos G. Grijalva. The publisher apologizes for this error."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Xu Wen Ng."} +{"text": "The tenth author\u2019s name is spelled incorrectly. The correct name is: Omar M.A. El-Agnaf."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Marcia Regina von Zeska Kress."} +{"text": "The eighth author\u2019s name is missing the middle initial. The correct name is Mohammad S. Yousef."} +{"text": "The fifteenth author\u2019s name is spelled incorrectly. The correct name is: Daniel H. Paris"} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Sarah K. Wendel. The publisher apologizes for the error."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Jinzhi He."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct spelling is: Shaym Sundar."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Claudio Maruottolo."} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: Chhatra B. Kunwar."} +{"text": "The correct name is: Ma\u2019en Obeidat.The 37"} +{"text": "The third author's name is spelled incorrectly. The correct name is: Eunjoo Lee. The publisher apologizes for the error."} +{"text": "The third author\u2019s name in the author byline is incorrect. The correct name is Aloysious Arvinthan. The article citation remains correct."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Maeli Dal-Pai-Silva. The publisher apologizes for the error."} +{"text": "The fifth author's name is spelled incorrectly. The correct name is: Tomonori Nochi."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Piroon Jenjaroenpun."} +{"text": "IJMS [The authors wish to change IJMS . Figure"} +{"text": "The fifteenth author\u2019s name is spelled incorrectly. The correct name is: Peter D. Kwong."} +{"text": "The eleventh author\u2019s name is spelled incorrectly. The correct name is: Piergiuseppe De Berardinis."} +{"text": "The eighteenth author\u2019s name is incorrectly spelled. The correct name is George S. Vlachos."} +{"text": "The tenth author\u2019s name is spelled incorrectly. The correct name is: Olle Ljungqvist."} +{"text": "The eighth author's name was spelled incorrectly upon publication of this paper. The correct name is Ronen Marmorstein."} +{"text": "The seventh author\u2019s first name is spelled incorrectly. The correct name is: Bryan Kim."} +{"text": "The tenth author\u2019s name is misspelled. The correct name is: Sean C. Murphy."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Rashmi S. Hegde."} +{"text": "The first author\u2019s surname is spelled incorrectly. The correct name is Teresa K. Attwood."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Pamela Fischer-Posovszky"} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct spelling is: Yi Jing."} +{"text": "Zhouli Wang is not a corresponding author. The corresponding author is Dr. Tianli Yue ("} +{"text": "The third author's name is spelled incorrectly. The correct name is: Takehiro Shinohara."} +{"text": "The correct name is: Eric D\u2019Ortenzio.The 103"} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: H. Marike Boezen."} +{"text": "The correct name is Massimiliano Berretta.The 15"} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Chong Dong."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Janet L. Rader."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Rasa Izadnegahdar."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Francisco Rodriguez-Valera."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Beatriz Eugenia Ferro."} +{"text": "The last author's name is spelled incorrectly. The correct name is: Jos\u00e9 Mar\u00eda Pego-Reigosa."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is Hiroaki Anada."} +{"text": "The third author\u2019s name is misspelled. The correct name is: Yi-Ju Shen. The publisher apologizes for the error."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: D. Michiel Pegtel."} +{"text": "The twenty-first author\u2019s name is misspelled. The correct name is: A. Alonso Aguirre."} +{"text": "The thirteenth author\u2019s name is spelled incorrectly. The correct name is: Julija Baginskaite."} +{"text": "The ninth author's middle initials are missing. The correct name is: Kristina E. M. Persson."} +{"text": "The fifth author\u2019s name is spelled incorrectly. The correct name is: Yun-Dun Shen."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Christian Milani."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Yehia Mechref."} +{"text": "The tenth author\u2019s last name is omitted. The correct name is: Rose Q. Do."} +{"text": "The first author\u2019s name is spelled incorrectly. The correct name is: Alparslan Asan."} +{"text": "The seventh author\u2019s name is incorrect. The correct name is Appolinaire Djikeng."} +{"text": "Theisen-Kunde's and Dr. Brinkmann's names were originally presented incorrectly. The article has since been corrected online.In the article \u201cSelective Retina Therapy in Patients With Chronic Central Serous Chorioretinopathy: A Pilot Study\u201d,"} +{"text": "The fifth author\u2019s name is incorrect. The correct name is: Phoebe Hodges."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Sudipto Ganguly"} +{"text": "The seventeenth author's name is spelled incorrectly. The correct name is: Marta G. Murreddu."} +{"text": "The first author\u2019s name is spelled incorrectly. The correct name is: Wei-Ping Luo."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Victoria Vickerstaff."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Erika Olmedo-Vicente."} +{"text": "The fifth author's name is spelled incorrectly. The correct name is: Fergal O'Gara. The publisher apologizes for this error."} +{"text": "The eighth author\u2019s name is misspelled. The correct name is: Richard G. Brown."} +{"text": "The second author\u2019s name is incorrectly spelled. The correct name is: Arto J. Pesola."} +{"text": "The third author\u2019s name is spelled incorrectly. The correct name is: B.A. Wallace."} +{"text": "There is an error in the seventh author\u2019s name. The middle initial was omitted. The correct name is: Thomas S. Lisse."} +{"text": "The size of the cloth targets used is incorrect. The correct size is: 0.0625 m"} +{"text": "The third author's name is spelled incorrectly. The correct name is Xiuquan Ma."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Claudine J. C. Lamoth. The publisher apologizes for the error."} +{"text": "The tenth author\u2019s last name is improperly indicated. The correct name is: Jean de Dieu Tapsoba. The correct abbreviation is: Tapsoba JD."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Michael S. Magee."} +{"text": "The third author's name is spelled incorrectly. The correct name is: Nicholas Thomas."} +{"text": "Kotb's and Dr. Lotfi's MD degreeswere originally omitted. The article has been corrected online.In the article \u201cPediatric Online Evidence-Based Medicine Assignment Is a NovelEffective Enjoyable Undergraduate Medical Teaching Tool: A SQUIRE CompliantStudy,"} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Rong-Yu Liu. The correct initials in the Author Contributions are RYL."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Rukmini Bhardwaj."} +{"text": "The ninth author\u2019s first and last names are incorrectly switched. The correct name is: Stefania Tommasi."} +{"text": "The third author\u2019s name is spelled incorrectly. The correct name is: Weiqing Han."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Seung Hwan Chung."} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: Bart H. Bijnens."} +{"text": "The eleventh author's name is misspelled. The correct spelling is: Edward D. Chan."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Sean R. Bollinger."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is Zhimin Wang."} +{"text": "The twenty-second author\u2019s name is spelled incorrectly. The correct name is: Chihiro Nishiura."} +{"text": "The formatting and spelling of the last Author\u2019s name is incorrect. The correct name is: Maurine A. Leverstein-van Hall."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Qingbin Song. The citation is correct."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Janet S. Rader."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Pilar Aparicio."} +{"text": "The tenth author's name is spelled incorrectly. The correct name is: Stephanie L. Swift."} +{"text": "The ninth author\u2019s name is incorrect. The correct name is: Humberto E. Bohorquez."} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: Robin P Shook."} +{"text": "The thirteenth author\u2019s name is spelled incorrectly. The correct name is: Ronaldo A. P. Nagem."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Yung-Fu Chang."} +{"text": "The ninth author's name is spelled incorrectly. The correct name is: Robert F. Foronjy."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Birgitt Sch\u00fcle."} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: Elena H. Martinez-Lapiscina."} +{"text": "The eleventh author\u2019s name is spelled incorrectly. The correct spelling is: Martine Daujat-Chavanieu."} +{"text": "The thirteenth author\u2019s name is spelled incorrectly. The correct name is: Thomas M. Gill."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Chin Hua Chia."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Jing Shen."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Carlo Dallocchio."} +{"text": "The tenth author\u2019s name is incorrectly spelled. The publisher apologizes for the error. The correct name is: JS Mehta."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Valeria Cavalcanti Rolla."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Antoinette am Zehnhoff-Dinnesen. The publisher apologizes for the error."} +{"text": "The formatting of the last Author\u2019s name is incorrect. The correct name is: Maurine A. Leverstein-van Hall."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Kouji Banno."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Georg Karpel-Massler. The publisher apologizes for this error."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Shanta S. Ramsaran."} +{"text": "The middle initial of the tenth author\u2019s name is missing. The correct name is: Pablo A. Manavella."} +{"text": "The last author\u2019s name is spelled incorrectly. The correct name is: Giorgio Tamburlini."} +{"text": "The correct corresponding author is Dr. Shuyang Zhang ("} +{"text": "The eighth\u2019s author name is spelled incorrectly. The correct name is: Ming Pei."} +{"text": "The eleventh author's name is spelled incorrectly. The correct name is: Jung Mook Lyu."} +{"text": "The correct name is: Andreas D. Flouris.The 12"} +{"text": "The second author\u2019s name is spelling incorrectly. The correct name is: Jinfeng Wu."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Yen-Lin Liu."} +{"text": "The seventh author\u2019s initials are indexed incorrectly in PubMed. The correct initials are: Mediano MFF."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Aklilu Habte.The publisher apologizes for the error."} +{"text": "The tenth author\u2019s name is spelled incorrectly. The correct name is: Adriana P. Vicentini."} +{"text": "The last author\u2019s name is spelled incorrectly. The correct name is: Jinpeng Zhang."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Bradley P. Nicholson."} +{"text": "The tenth author\u2019s initials are indexed incorrectly in PubMed. The correct initials are: Peichoto ME."} +{"text": "The publisher apologizes for the error.The second author\u2019s name is spelled incorrectly. The corr"} +{"text": "The first author\u2019s name is spelled incorrectly. The correct name is: Wai Chung Yeong."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Eduardo Luis Hettwer Giehl."} +{"text": "The twelfth author\u2019s name is spelled incorrectly. The correct name is: Allison Tong.The publisher apologizes for the error."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: David Jean Simon."} +{"text": "The tenth author\u2019s name is indexed incorrectly in PubMed. The name should be indexed as: Ribeiro ALP."} +{"text": "The eleventh author\u2019s name is spelled incorrectly. The correct name is: David McIlwain."} +{"text": "Elena Bellotti's family name is correct as reflected here.The original article was corrected."} +{"text": "The last author\u2019s name is incorrect. The correct name is: Kay Choong See. The author\u2019s initials are also indexed incorrectly in PubMed. The correct initials are: See KC."} +{"text": "The fourteenth author\u2019s name is spelled incorrectly. The correct name is: Karla Mar\u00eda Tamez-Torres."} +{"text": "The original article contained errors in Md. Rafiul Biswas's and Farida Mohsen's names which have since been corrected."} +{"text": "The last author\u2019s name is spelled incorrectly. The correct name is: Mekuriaw Alemayehu."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Neelakantan T Vasudevan."} +{"text": "The sixth author\u2019s first name is incorrect. The correct name is Anthony Morton."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Ioannis Orfanos."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Jos\u00e9 R. Figueiredo. The publisher apologizes for the error."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Sarah Wozniak."} +{"text": "The thirteenth author\u2019s name is spelled incorrectly. The correct name is: D. Woodrow Benson."} +{"text": "The thirteenth author\u2019s name is spelled incorrectly. The correct name is: Florence Canoui-Poitrine."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Katarzyna Czabanowska."} +{"text": "The twenty-eighth author\u2019s name is spelled incorrectly. The correct name is: Weiming Xia. The publisher apologizes for the error."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Thomas P. Gumpel."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Vinay Devadanam."} +{"text": "The ninth author\u2019s name is incorrect. The correct name is: Jung Keun Lee."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Luis Del Valle.The author\u2019s initials are also indexed incorrectly in PubMed. The correct initials are: Del Valle L."} +{"text": "The twelfth author\u2019s name is spelled incorrectly. The correct name is: Joseph Hinds."} +{"text": "The spret al. ."} +{"text": "The fourteenth author\u2019s name is spelled incorrectly. The correct name is: Nikos Vasilakis."} +{"text": "The twelfth author\u2019s name is spelled incorrectly. The correct name is: Er\u00e9ndira M. Quintana Morales. The publisher apologizes for the error."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Zhe-Chen Li."} +{"text": "The sixth author\u2019s first name is spelled incorrectly. It should read On Chen. The publisher apologizes for the error."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Derek A. Oldridge."} +{"text": "The seventh author\u2019s name is incorrect. The correct name is: Neva Girotto. The publisher apologizes for the error."} +{"text": "The eleventh author\u2019s name is spelled incorrectly. The correct name is: Svetlana Zhdanova."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Sarah Hoskinson."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Muhammad Khurram Khan."} +{"text": "The fourth author\u2019s name is spelled incorrectly in the byline and Funding section. The correct name is: Antony S. Tin."} +{"text": "The fourth author\u2019s name is incorrect. The correct name is: Kok Weng Ng."} +{"text": "The eighth author's name is spelled incorrectly. The correct name is: G\u00f6ran Dellgren."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Myung-Whan Suh."} +{"text": "The seventh author's name appears incorrectly. The correct name is: Maria Bujnowska-Fedak."} +{"text": "The twelfth author's name is incorrect. The correct name is: Mario R. Romano."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is Appalanaidu Sasapu."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Jeonghyung Kim."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Salma A. Al-Karmi."} +{"text": "The last author\u2019s name is incorrect. The correct name is: Awang Bulgiba."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Giliane S. Souza."} +{"text": "The 13th author\u2019s name is incorrect in the published article. The correct name is: Amber A. van der Heijden."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Michael Gyngell."} +{"text": "The seventh author's name appears incorrectly in the published article. The correct name is: Bernhard K. Kr\u00e4mer."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Benjamin T. Galloway."} +{"text": "The tenth author\u2019s name is spelled incorrectly. The correct name is: Graeme Keith Hart."} +{"text": "The ninth author's name is spelled incorrectly. The correct name is: Philippe Travers."} +{"text": "The second author's name appears incorrectly. The correct name is: Sofie V. Hellsten."} +{"text": "The third author\u2019s name is spelled incorrectly. The correct name is: Evangelos Giannitsis."} +{"text": "The seventh author\u2019s name is incorrect. The correct name is: Sandrine McKay-Chopin."} +{"text": "The ninth author\u2019s middle initial is missing. The correct name is: Jonathan H. Epstein."} +{"text": "The third author\u2019s name is incorrect. The correct name is: Amarpreet Sabharwal."} +{"text": "The middle initial of the seventh author's name is omitted. The correct name is: Dominik M. Meinel."} +{"text": "The seventh author\u2019s name is spelled incorrected. The correct name is: Veriko Mirtskhulava."} +{"text": "The first author\u2019s name is incorrect. The correct name is: Jakub Lubi\u0144ski."} +{"text": "The eleventh author\u2019s name is incorrect. The correct name is: Luis Fonseca-Ornelas."} +{"text": "The eleventh author's name is listed incorrectly. The correct name is: Mohiuddin."} +{"text": "The fourth author\u2019s first name is spelled incorrectly. The correct name is: Thorsten Dohrmann."} +{"text": "The tenth author\u2019s name is spelled incorrectly. The correct name is: Ryan C. Gimple."} +{"text": "The final author's name is incorrect. The correct name is: Carmen Navarro. The publisher apologizes for the error."} +{"text": "Tc01_g000020.The original version of the manuscript containe"} +{"text": "The fourteenth author's name is spelled incorrectly. The correct name is: Irva Hertz-Picciotto."} +{"text": "The first author's name is spelled incorrectly. The correct name is: Gajenthiran Sinnathamby."} +{"text": "The tenth author\u2019s name appears incorrectly. The correct name is Kurt R. Stenmark. The eleventh author\u2019s name appears incorrectly. The correct name is Paul W. Buehler."} +{"text": "The fourteenth author's name is spelled incorrectly. The correct name is: Kazunori Tomono. The publisher apologizes for this error."} +{"text": "The tenth author\u2019s name is spelled incorrectly. The correct name is: Geerten P. van Nieuw Amerongen."} +{"text": "The authors are retracting this article . After p"} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Melkizedeck T. Leshabari."} +{"text": "The eleventh author\u2019s name is spelled incorrectly. The correct name is: Yoshiro Okubo."} +{"text": "The seventh author\u2019s name is spelled incorrectly. The correct name is: Bahar Yetkin-Arik."} +{"text": "The fifteenth author's name is spelled incorrectly. The correct name is: Rachel B. Caligiorne."} +{"text": "The second author\u2019s name is spelled incorrectly. The correct name is: Zipei Feng."} +{"text": "The eleventh author's name appears incorrectly. The correct name is: Eleonore Susanne Victoria de Sonnaville. The publisher apologizes for the error."} +{"text": "The fourth author\u2019s name is incorrect. The correct name is: Natalie Sofia Ramirez-Ochoa."} +{"text": "The ninth author's name is spelled incorrectly. The correct name is: Richard Marlink."} +{"text": "The thirty-third author's name is spelled incorrectly. The correct name is: Jadranka Serti\u0107"} +{"text": "The ninth author's name is spelled incorrectly. The correct name is: Grace Ragi."} +{"text": "The eleventh author\u2019s name is spelled incorrectly. The correct name is: Jonathan Barasch."} +{"text": "There are two errors in the author list. The seventh author\u2019s name is incorrect. The correct name is Erin M. Scherer. The twentieth author\u2019s name is incorrect. The correct name is Denise A. Galloway."} +{"text": "The middle initial of the last author's name was omitted. The correct name is: Arup K. Indra."} +{"text": "The fourth author's name is spelled incorrectly. The correct name is: Andreas Hoenger."} +{"text": "The seventh author's name was incorrect. The correct name is Margarita Zayas."} +{"text": "The seventh author's name was spelled incorrectly. It should read: Andreas Podbielski."} +{"text": "The second author's name is spelled incorrectly. The correct spelling is Ha-Won Jeong. The co-contribution is still valid."} +{"text": "The seventh author's name was spelled incorrectly. The correct name is: Jens Hollunder."} +{"text": "The 10th author's name is misspelled. The correct name is Raymond Diadhiou."} +{"text": "The ninth author's name was misspelled. The correct name is: Jerzy Ostrowski."} +{"text": "The twelfth author's name appears incorrectly. It should read: Dominique Bonnefont-Rousselot."} +{"text": "The twelfth author's name was spelled incorrectly. It should read: J\u00fcrgen Schrezenmeir."} +{"text": "The eighth author's name is incorrect. The correct name is: Shashikant Kulkarni."} +{"text": "The last author's name was incomplete. The correct name is: David E. MacHugh."} +{"text": "The sixth author's name was spelled incorrectly. The correct name is: Bastien Kaniewski."} +{"text": "The seventh author's name is incorrect. The correct name should be: Pier Leopoldo Capecchi."} +{"text": "The eighth author's name was displayed incorrectly. It should be: Christian T. Bautista."} +{"text": "The eighth author's name was incomplete. The correct name is: Pedro A. Moreno."} +{"text": "The eighth author's name was misspelled. The correct name is: Loyce M. A. Okedi."} +{"text": "The eighth author's name appears incorrectly. It should be: Shoji Ito"} +{"text": "The fourth author's name was spelled incorrectly. The correct name is: Wing-Kin Sung."} +{"text": "The eighth author's name appears incorrectly. The correct name is: Alfred H. Schinkel."} +{"text": "The seventh author's name was spelled incorrectly. It should read: Hidde L. Ploegh."} +{"text": "The fourth author's name appears incorrectly. It should be spelled: Roland Leclercq"} +{"text": "Doratonotus megalepis. The species name in figure 124 is incorrect. The correct species name is"} +{"text": "The last author's name was spelled incorrectly. The correct name is: Sasithon Pukrittayakamee."} +{"text": "The first author's name is incorrect in the citation. The correct citation is Del Giacco L."} +{"text": "The 7th author's middle initial was inadvertently omitted. The correct name is: James G. Khan."} +{"text": "The eighth author's name is incorrect. The correct name is: Flair J. Carrilho."} +{"text": "The fifth author's name was spelled incorrectly. The correct name is: Amy Hye Won Jeon."} +{"text": "The first author's name is incorrect in the article citation. It should appear as: Lee JM."} +{"text": "The second author's name is misspelled. The correct name is Isaac S. Kohane."} +{"text": "The seventh author's name appears incorrectly. It should be: Geoffrey S. Ginsburg"} +{"text": "The first author's name was spelled incorrectly. It should read: Amit Bhardwaj. This also affects the article's citation."} +{"text": "The seventh author's name was spelled incorrectly. The correct name is: Keith Satterley."} +{"text": "The 12th author's name was incorrect as published. The correct name is A. Jennifer Morton."} +{"text": "The eighth author's name should read: Joshua D. Nosanchuk. The first and second authors should not have been attributed equal contribution to the research."} +{"text": "In 'Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining' ["} +{"text": "The 12th author's name was spelled incorrectly. It should read: Karl Dykema."} +{"text": "The first author's name in the article citation was incorrectly written. The correct name is \"Shio MT.\""} +{"text": "The tenth author's initials are indexed incorrectly in PubMed. The correct initials are: Bragazzi NL."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Youn-Goo Kang.The seventh author\u2019s name is spelled incorrectly. The correct name is: Ah-Ram Kim."} +{"text": "The first author's name was erroneously entered backwards (Romagna Alexander). The correct name is Alexander Romagna. The manuscript has been updated to reflect this change."} +{"text": "The tenth author's name is spelled incorrectly. The correct name is: Vladim\u00edr \u0160ubr."} +{"text": "The third author\u2019s name is spelled incorrectly. The correct name is: Philipp Sippl."} +{"text": "Please see: Editor's Note"} +{"text": "The tenth author's name is spelled incorrectly. The correct name is: Yu Kanesaki."} +{"text": "The twenty-second author's name is spelled incorrectly. The correct name is: Regan Williams.There is also an error in"} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Paul H. Hayashi."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Johan Sundstr\u00f6m."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Kathryn Moseley."} +{"text": "The correct corresponding author is Ching Li. Dr. Li\u2019s email address is:"} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Guoying Wang."} +{"text": "The second author's name is spelled incorrectly. The correct name is: Qianchuan He."} +{"text": "The first author's name should be written as Sul A Lee. The publisher apologizes for the error."} +{"text": "The ninth author's name is spelled incorrectly. The correct name is: Florian Rieder."} +{"text": "The ninth author\u2019s name is missing the middle initial. The correct name is: Stanley L. Liauw."} +{"text": "The tenth author's name is spelled incorrectly. The correct name is: W. Ian Lipkin."} +{"text": "The last author's name is indexed incorrectly in PubMed. The correct name is: Ruiz JR."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Terrence A. Barrett."} +{"text": "The second author's name is spelled incorrectly. The correct name is: Iasmin Mayumi Enokida."} +{"text": "The sixth author\u2019s name is spelled incorrectly. The correct name is: Ying-Hsia Chu."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct name is: Amir Emtiazjoo."} +{"text": "The last author\u2019s name is spelled incorrectly. The correct name is: Jeroen B. J. Smeets.In the Funding statement, the last author\u2019s name is spelled incorrectly. The correct name is Jeroen Smeets."} +{"text": "The thirteenth author\u2019s name is spelled incorrectly. The correct name is: Chanthalakeo Vixay."} +{"text": "The ninth author's initials are indexed incorrectly in PubMed. The correct initials are: Benn CS."} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Ilaria Callegari."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Sara Sella."} +{"text": "The middle initial of the eighth author is incorrectly omitted. The eighth author\u2019s correct name is: James P. Duffy."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Ariel E. Feldstein"} +{"text": "The eighth author\u2019s middle initials are missing. The correct name is: Virginie J. M. Verhoeven."} +{"text": "The tenth author's name is spelled incorrectly. The correct name is: Duminda Wijeysundera."} +{"text": "The seventh author\u2019s name is incorrect. The correct name is: Nicole Piera Palomba."} +{"text": "The correct corresponding author is Apar Kishor Ganti. Dr. Ganti's email address is:"} +{"text": "The third author\u2019s name is spelled incorrectly. The correct name is: Jacqueline Roseleur."} +{"text": "The fourth author\u2019s name is spelled incorrectly. The correct name is: Eva Rodriguez-Carrasco."} +{"text": "The fifth author\u2019s first name is incorrect. The correct name is: Marilyn Nyanduko."} +{"text": "The third author's name is spelled incorrectly. The correct name is: Matthew T. Boots."} +{"text": "The eighth author\u2019s name is spelled incorrectly. The correct spelling is: Longhuan Ma."} +{"text": "The publisher apologizes for this error. Dr. Eltokhi\u2019s email address is:"} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Maur\u00edcio L. Barreto"} +{"text": "The ninth author\u2019s name is spelled incorrectly. The correct name is: Matitiahu Berkovitch."} +{"text": "The authors regret making a spelling error in Carmen Blanco\u2010Aparicio's name. The spelling is herewith corrected."} +{"text": "The tenth author\u2019s name is incorrect. The correct name is Raghavan Parthasarathy."} diff --git a/PMC_clustering_708.jsonl b/PMC_clustering_708.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..14a8d0b598476e6118db2be97bcf6a97256ad7c6 --- /dev/null +++ b/PMC_clustering_708.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3a9fb3815fcc18bcfd504d56a3b648ac998b1e279ba980ecc66fc0a11f349d85 +size 55967885 diff --git a/PMC_clustering_709.jsonl b/PMC_clustering_709.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..bf41a8bf4595d9328169517a78992bf085db6b15 --- /dev/null +++ b/PMC_clustering_709.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f420458d79172d5ba92f1ad0d0dde5c9260ca51fc171fc69466e83070d151757 +size 105495349 diff --git a/PMC_clustering_710.jsonl b/PMC_clustering_710.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..c2b583464a37c3b5f45180f6a0a750239e71ab4f --- /dev/null +++ b/PMC_clustering_710.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e752c0a14617d9059f420079126db58280e2a34d0bbcfcc33b49a359b3ff4ce1 +size 86498590 diff --git a/PMC_clustering_711.jsonl b/PMC_clustering_711.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..3f81fd27a4faaf203a817921e207a0667c25619d --- /dev/null +++ b/PMC_clustering_711.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a09e693eb9cd2c014738877bdcccbed23aee155e1c3c1ddd0561bd945a3c9150 +size 72738133 diff --git a/PMC_clustering_712.jsonl b/PMC_clustering_712.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..25455ff4169cf8261e1aea50296d06a8a6c0ba88 --- /dev/null +++ b/PMC_clustering_712.jsonl @@ -0,0 +1,506 @@ +{"text": "Greene, PhD1; Kevin Guerra, MPH1; Mary Huynh, PhD1; Christina Hwang, MPH1; Maryam Iqbal, MPH1; Jillian Jessup, MPH1; Jillian Knorr, MPH1; 1;Ramona Lall, PhD Julia Latash, MPH1; Ellen Lee, MD1; Kristen Lee, MPH1; Wenhui Li, PhD1; Robert Mathes, MPH1; Emily McGibbon, MPH1; Natasha McIntosh1; Matthew Montesano, MPH1; Miranda S. Moore, MPH1; Kenya Murray, MPH1; Stephanie Ngai, MPH1; Marc Paladini, MPH1; Rachel Paneth-Pollak, MD1; Hilary Parton, MPH1; Eric Peterson, MPH1; Renee Pouchet, MHA1; Jyotsna Ramachandran, MPH1; Kathleen Reilly, PhD1; Jennifer Sanderson Slutsker, MPH1; Gretchen Van Wye, PhD1; Amanda Wahnich, MPH1; Ann Winters, MD1; Marcelle Layton, MD1; Lucretia Jones, DrPH1; Vasudha Reddy, MPH1; Anne Fine, MD1.\u201dIn the report \u201cCOVID-19 Outbreak \u2014 New York City, February 29\u2013June 1, 2020,\u201d on p. 1725, the list of authors should have read \u201cCorinne N. Thompson, PhDThe affiliation for Dr. Lall is New York City Department of Health and Mental Hygiene, Long Island City, New York."} +{"text": "Sleep disturbances are associated with increased risk of migraine, however the extent of shared underlying biology and the direction of causal relationships between these traits is unclear. Delineating causality between sleep patterns and migraine may offer new pathophysiologic insights and inform subsequent intervention studies. Here, we used genetic approaches to test for shared genetic influences between sleep patterns and migraine, and to test whether habitual sleep patterns may be causal risk factors for migraine and vice versa.n\u00a0\u2265\u00a0237,627), and migraine from the International Headache Genetics Consortium . We then tested for potential causal effects between sleep traits and migraine using bidirectional, two\u2010sample Mendelian randomization.To quantify genetic overlap, we performed genome\u2010wide genetic correlation analyses using genome\u2010wide association studies of nine sleep traits in the UK Biobank (P\u00a0<\u00a010\u221231) and difficulty awakening . Mendelian randomization analyses provided evidence for potential causal effects of difficulty awakening on risk of migraine , and nominal evidence that liability to insomnia symptoms increased the risk of migraine . In contrast, there was minimal evidence for an effect of migraine liability on sleep patterns or disturbances.Seven sleep traits demonstrated genetic overlap with migraine, including insomnia symptoms (rg\u00a0=\u00a00.29, These data support a shared genetic basis between several sleep traits and migraine, and support potential causal effects of difficulty awakening and insomnia symptoms on migraine risk. Treatment of sleep disturbances may therefore be a promising clinical intervention in the management of migraine. Migraine is a debilitating and highly prevalent chronic pain condition that is a leading contributor to disability worldwide.Causality can be investigated using Mendelian randomization (MR).n\u00a0\u2264\u00a0452,071) and migrainen\u00a0=\u00a0375,752) now provides an opportunity to test shared genetic predisposition and causal effects. Here, we leveraged cross\u2010trait LD Score regressionThe availability of large\u2010scale genome\u2010wide association studies (GWAS) for sleep traitsGenetic associations for sleep traits were obtained from publishedn\u00a0=\u00a020,395) and 27 population\u2010based cohorts . Characteristics of each of the contributing cohorts have been previously described.We obtained genetic associations with migraine from the largest available meta\u2010analysis of genome\u2010wide association studies (GWAS) of migraine conducted by the International Headache Genetics Consortium (IHGC).We calculated genome\u2010wide genetic correlations (rg) using cross\u2010trait LD Score regression with precomputed LD scoresThe design of our MR analysis is shown in Figure\u00a0MR provides strong evidence for causality under the following assumptionsP values less than these corrected alpha thresholds were considered to represent significant evidence for causal effects, and P\u00a0<\u00a00.05 was considered to represent nominal evidence for a causal effect. Analyses were performed using the LDSC software,The Bonferonni\u2010adjusted threshold for MR analyses accounted for 14 forward and reverse MR tests . The IGHC migraine GWAS summary statistics including data from 23andMe were provided under a Data Transfer Agreement by 23andMe.P\u00a0<\u00a00.007; Table\u00a0P\u00a0=\u00a01.87\u00a0\u00d7\u00a010\u221232), with weaker correlations between migraine and short sleep duration , difficulty awakening , and daytime napping . There was no evidence for a genetic correlation between migraine and morning diurnal preference or snoring .As sleep disturbances are comorbid with migraine and are also heritable, we first tested if the traits have shared genetic influences using cross\u2010trait LD score regression.P\u00a0=\u00a00.002). There was also nominal evidence for an effect of liability to insomnia symptoms on migraine . Removing weakly correlated SNPs (using a stricter clumping threshold of r2\u00a0<\u00a00.001 vs. r2\u00a0<\u00a00.01) yielded nearly identical effect estimates for insomnia and for difficulty awakening . MR estimates were null for the effect of all other sleep traits on migraine susceptibility .We first tested whether results were consistent when using a genetic instrument for insomnia symptoms developed from a meta\u2010analysis of the UK Biobank and 23andme studies . The effects of insomnia symptoms and difficulty awakening on migraine were consistent when excluding variants associated at genome\u2010wide significance with other sleep traits, and in multivariable MR modeling pleiotropic effects on both exposures on migraine susceptibility, suggesting that effects of insomnia symptoms on migraine are not driven by pleiotropic effects of the variants on RLS , with consistent estimates across sensitivity analyses gene may simultaneously cause familial migraine and advanced sleep phase syndrome,We found evidence f shared genetic influences between several sleep traits and migraine, with the strongest genetic correlation found with insomnia symptoms (rg\u00a0=\u00a00.29). With the exception of a previously reported genetic correlation of migraine with MDD of 0.32, the magnitude of genetic overlap between insomnia and migraine was greater than that reported for most other common disease traits in the UK Biobankn\u00a0=\u00a01,331,010; 3%) and that the genetic instrument for insomnia is strong (F\u2010statistic\u00a0>\u00a010).P\u00a0=\u00a00.02) for migraine after 11\u00a0years of follow up.Mendelian randomization analyses suggested a causal effect of insomnia symptoms on migraine, adding support to findings from prospective epidemiologic studies.Relative to insomnia, less is known about the phenomenon of difficulty awakening, which in some settings is referred to as sleep inertia.There was minimal evidence for an effect of migraine on any of the sleep patterns or disturbances. While longitudinal epidemiologic studies lasting up to 11\u00a0years have suggested potential effects of migraine on insomnia risk,There are several potential pathways by which sleep quality or insomnia symptoms may influence migraine susceptibility. Cortical excitability, a potential mechanism of migraine pathophysiology,We acknowledge limitations to this work. First, although we incorporated sensitivity analyses for horizontal pleiotropy, we cannot fully exclude the influence of this potential bias. Second, MR power calculators are not currently designed for ordinal or binary exposures, so we focused on interpretation of the confidence intervals to determine whether the bounds contained clinically relevant effects. Third, single, self\u2010reported questions are less reliable for phenotyping than validated scales or physician\u2010diagnosed insomnia, which were unavailable in UKB. Fourth, the known common variant contributions to migraine primarily reflect the genetic architecture of migraine without aura (MO), which is the most prevalent form of migraine.The genetic determinants of sleep and migraine are partly overlapping. Sleep disturbances may causally influence migraine etiology, and are promising targets for the treatment of migraine.ID and RS conceived and designed the study with input from all coauthors. RS and DC provided the data. ID and YG analyzed the data. ID drafted the initial manuscript. RS, AV, YG, and DC provided critical feedback to the manuscript and approved the final version. ID and RS are the guarantors. The corresponding authors attest that all listed authors meet authorship criteria and that no others meeting the criteria have been omitted.31\u221234, Verneri Anttila32,33,35, Bendik S. Winsvold36\u221238, Priit Palta39, Tonu Esko32,40,41, Tune H. Pers32,41\u221243, Kai\u2010How Farh32,35,44, Ester Cuenca\u2010Leon31\u221233,45, Mikko Muona39,46\u221248, Nicholas A. Furlotte30, Tobias Kurth49,9, Andres Ingason10, George McMahon50, Lannie Ligthart51, Gisela M. Terwindt52, Mikko Kallela53, Tobias M. Freilinger54,55, Caroline Ran56, Scott G. Gordon22, Anine H. Stam52, Stacy Steinberg10, Guntram Borck57, Markku Koiranen58, Lydia Quaye59, Hieab H. H. Adams6,61, Terho Lehtim\u00e4ki62, Antti\u2010Pekka Sarin39, Juho Wedenoja63, David A. Hinds30, Julie E. Buring9,64, Markus Sch\u00fcrks65, Paul M. Ridker9,64, Maria Gudlaug Hrafnsdottir66, Hreinn Stefansson10, Susan M. Ring50, Jouke\u2010Jan Hottenga51, Brenda W. J. H. Penninx67, Markus F\u00e4rkkil\u00e453, Ville Artto53, Mari Kaunisto39, Salli Veps\u00e4l\u00e4inen53, Rainer Malik55, Andrew C. Heath68, Pamela A. F. Madden68, Nicholas G. Martin22, Grant W. Montgomery8, Mitja I. Kurki31\u221233,39,69, Mart Kals40, Reedik M\u00e4gi40, Kalle P\u00e4rn40, Eija H\u00e4m\u00e4l\u00e4inen39, Hailiang Huang32,33,35, Andrea E. Byrnes32,33,35, Lude Franke70, Jie Huang34, Evie Stergiakouli50, Phil H. Lee31\u221233, Cynthia Sandor71, Caleb Webber71, Zameel Cader72,73, Bertram Muller\u2010Myhsok74,75, Stefan Schreiber76, Thomas Meitinger77,78, Johan G. Eriksson79,8, Veikko Salomaa80, Kauko Heikkil\u00e481, Elizabeth Loehrer60,82, Andre G. Uitterlinden83, Albert Hofman60, Cornelia M. van Duijn60, Lynn Cherkas59, Linda M. Pedersen36, Audun Stubhaug84,85, Christopher S. Nielsen84,86, Minna M\u00e4nnikk\u00f658, Evelin Mihailov40, Lili Milani40, Hartmut G\u00f6bel87, Ann\u2010Louise Esserlind88, Anne Francke Christensen88, Thomas Folkmann Hansen89, Thomas Werge90,91,7, Jaakko Kaprio39,63,92, Arpo J. Aromaa80, Olli Raitakari93,94, M. Arfan Ikram60,61,95, Tim Spector59, Marjo\u2010Riitta J\u00e4rvelin58,96\u221298, Andres Metspalu40, Christian Kubisch99, David P. Strachan100, Michel D. Ferrari52, Andrea C. Belin56, Martin Dichgans55,75, Maija Wessman39,46, Arn M. J. M. van den Maagdenberg52,101, John\u2010Anker Zwart36\u221238, Dorret I. Boomsma51, George Davey Smith50, Kari Stefansson10,102, Nicholas Eriksson30, Mark J. Daly32,33,35, Benjamin M. Neale32,33,35, Jes Olesen88, Daniel I. Chasman9, Dale R. Nyholt1, Aarno Palotie31\u221235,103.Padhraig Gormley1School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia. 2Department of Epidemiology and Cancer Control, St. Jude Children\u2019s Research Hospital, Memphis, Tennessee 38105, USA. 323andMe, Inc., 899 W. Evelyn Avenue, Mountain View, California 94041, USA. 4School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom. 5Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 950\u20102181, Japan. 6Department of Biomedicine \u2010 Human Genetics, Aarhus University, DK\u20108000 Aarhus, Denmark. 7iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, DK\u20102100 Copenhagen, Denmark. 8Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia. 9Divisions of Preventive Medicine, Department of Medicine, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA, USA. 10deCODE Genetics/Amgen, 101 Reykjavik, Iceland. 11Department of Biostatistics, University of Liverpool, Liverpool L69 3GL, UK. 12Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.13KULeuven, Department of Development and Regeneration, Organ systems, 3000 Leuven, Belgium. 14Department of Obstetrics and Gynaecology, Leuven University Fertility Centre, University Hospital Leuven, 3000 Leuven, Belgium. 15Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA. 16Channing Division of Network Medicine, Department of Medicine, Brigham and Women\u2019s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA. 17Division of Preventive Medicine, Brigham and Women\u2019s Hospital, Boston, Massachusetts 02215, USA. 18Institute of Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA. 19Vanderbilt Genetics Institute, Division of Epidemiology, Institute of Medicine and Public Health, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA. 20Cognitive Science Department, University of California, San Diego, La Jolla, California 92093, USA. 21Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, DK\u20102100 Copenhagen, Denmark. 22Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia. 23Endometriosis CaRe Centre, Nuffield Dept of Obstetrics & Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK. 24Center for Integrative Medical Sciences, RIKEN, Yokohama 230\u20100045, Japan. 25Institute of Medical Sciences, The University of Tokyo, Tokyo 108\u20108639, Japan. 26Department of Obstetrics and Gynecology, Landspitali University Hospital, 101 Reykjavik, Iceland. 27Faculty of Medicine, School of Health Sciences, University of Iceland, 101 Reykjavik, Iceland. 28Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Institute of Medicine and Public Health, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA. 29Global Medical Affairs Fertility, Research and Development, Merck KGaA, Darmstadt, Germany. 3023andMe, Inc., 899 W. Evelyn Avenue, Mountain View, California 94041, USA. 31Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. 32Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. 33Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. 34Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK. 35Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. 36FORMI, Oslo University Hospital, Oslo, Norway. 37Department of Neurology, Oslo University Hospital, Oslo, Norway. 38Institute of Clinical Medicine, University of Oslo, Oslo, Norway. 39Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland. 40Estonian Genome Center, University of Tartu, Tartu, Estonia. 41Division of Endocrinology, Boston Children\u2019s Hospital, Boston, Massachusetts, USA. 42Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark. 43Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. 44Illumina, San Diego, California, USA. 45Pediatric Neurology, Vall d\u2019Hebron Research Institute, Barcelona, Spain. 46Folkh\u00e4lsan Institute of Genetics, Helsinki, Finland. 47Neuroscience Center, University of Helsinki, Helsinki, Finland. 48Molecular Neurology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. 49Institute of Public Health, Charit\u00e9\u2013Universit\u00e4tsmedizin Berlin, Berlin, Germany. 50Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK. 51Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands. 52Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands. 53Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland. 54Department of Neurology and Epileptology, Hertie\u2010Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany. 55Institute for Stroke and Dementia Research, Klinikum der Universit\u00e4t M\u00fcnchen, Ludwig\u2010Maximilians\u2010Universit\u00e4t M\u00fcnchen, Munich, Germany. 56Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden. 57Institute of Human Genetics, Ulm University, Ulm, Germany. 58Center for Life Course Epidemiology and Systems Medicine, University of Oulu, Oulu, Finland. 59Department of Twin Research and Genetic Epidemiology, King\u2019s College London, London, UK. 60Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands. 61Department of Radiology, Erasmus University Medical Center, Rotterdam, the Netherlands. 62Department of Clinical Chemistry, Fimlab Laboratories, School of Medicine, University of Tampere, Tampere, Finland. 63Department of Public Health, University of Helsinki, Helsinki, Finland. 64Harvard Medical School, Boston, Massachusetts, USA. 65Department of Neurology, University Duisburg\u2013Essen, Essen, Germany. 66Landspitali University Hospital, Reykjavik, Iceland. 67Department of Psychiatry, VU University Medical Centre, Amsterdam, the Netherlands. 68Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA. 69Department of Neurosurgery, NeuroCenter, Kuopio University Hospital, Kuopio, Finland. 70Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands. 71MRC Functional Genomics Unit, Department of Physiology, Anatomy & Genetics, Oxford University, Oxford, UK. 72Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK. 73Oxford Headache Centre, John Radcliffe Hospital, Oxford, UK. 74Max Planck Institute of Psychiatry, Munich, Germany. 75Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. 76Institute of Clinical Molecular Biology, Christian Albrechts University, Kiel, Germany. 77Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany. 78Institute of Human Genetics, Technische Universit\u00e4t M\u00fcnchen, Munich, Germany. 79Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland. 80National Institute for Health and Welfare, Helsinki, Finland. 81Institute of Clinical Medicine, University of Helsinki, Helsinki, Finland. 82Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. 83Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands. 84Department of Pain Management and Research, Oslo University Hospital, Oslo, Norway. 85Medical Faculty, University of Oslo, Oslo, Norway. 86Department of Ageing and Health, Norwegian Institute of Public Health, Oslo, Norway. 87Kiel Pain and Headache Center, Kiel, Germany. 88Danish Headache Center, Department of Neurology, Rigshospitalet, Glostrup Hospital, University of Copenhagen, Copenhagen, Denmark. 89Institute of Biological Psychiatry, Mental Health Center Sct. Hans, University of Copenhagen, Roskilde, Denmark. 90Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Copenhagen, Denmark. 91Institute of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Copenhagen, Copenhagen, Denmark. 92Department of Health, National Institute for Health and Welfare, Helsinki, Finland. 93Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland. 94Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland. 95Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands. 96Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPE) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK. 97Biocenter Oulu, University of Oulu, Oulu, Finland. 98Unit of Primary Care, Oulu University Hospital, Oulu, Finland. 99Institute of Human Genetics, University Medical Center Hamburg\u2010Eppendorf, Hamburg, Germany. 100Population Health Research Institute, St George\u2019s, University of London, London, UK. 101Department of Human Genetics, Leiden University Medical Centre, Leiden, the Net herlands. 102Faculty of Medicine, University of Iceland, Reykjavik, Iceland.\u00a0103Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA.The authors declare no conflicts of interest.Data S1. Supplementary Methods.Table S1. Summary of GWAS and genetic instruments used in MR analysis.Table S2. UK Biobank questions answered by participants at the baseline visit to ascertain sleep outcomes.Table S3. Variants used in genetic instruments for sleep exposures.Table S4. Validation of approach to selecting genetic instrumental variables for insomnia symptoms by comparison with lead variants identified in the insomnia symptoms GWAS.Table S5. Variants used in the IHGC migraine genetic instrument .Table S6. Mendelian randomization heterogeneity and pleiotropy test results for significant effects identified in inverse\u2010variance weighted analysis.Table S7. Variants removed in GSMR HEIDI filtering.Table S8. MR estimates for the effect of migraine liability on binary sleep exposures, reported as odds ratios.Table S9. MR sensitivity analyses for the effect of migraine liability on napping.Figure S1. Forest plot of two\u2010sample Mendelian randomization sensitivity analyses for the effect of difficulty awakening and liability to insomnia symptoms on risk of migraine .Figure S2. Leave\u2010one\u2010out plot for MR Egger effect of liability to insomnia symptoms on risk of migraine.Figure S3. Leave\u2010one\u2010out plot for MR Egger effect of difficulty awakening on risk of migraine.Figure S4. Leave\u2010one\u2010out MR estimates for the effect of difficulty awakening on risk of migraine.Figure S5. Leave\u2010one\u2010out MR estimates for the effect of insomnia symptoms on risk of migraine.Click here for additional data file."} +{"text": "Following publication of the original article , we were1,\u2020, Yujia Zhao2,\u2020, Qinqin Wei2, Ye Zhao2, Qiyi Yi2,*Lei Lv1Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230031, Anhui, People\u2019s Republic of China.2Teaching and Research Section of Nuclear Medicine, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, People\u2019s Republic of China."} +{"text": "In \u201cAddressing Implementation Challenges to Digital Care Delivery for Adults With Multiple Chronic Conditions: Stakeholder Feedback in a Randomized Controlled Trial\u201d :e23498) the authors noted one error.In the originally published article, the affiliation for author Kevin L Kraemer:Center for Research on Health Care, Division of General Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United Stateswas inadvertently removed and replaced by the affiliation:Department of Psychiatry, College of Medicine-Tucson, University of Arizona, Tuscon, AZ, United StatesIn the originally published article, the full list of authors and affiliations was listed as follows:1, MPH, PhD; Sarah Markwardt1, MID; Shannon M Kearney1, CPH, MPH, DrPH; Jordan F Karp2, MD; Kevin L Kraemer2, MD; Margaret J Park3, MDiv; Paul Freund4, MEd; Andrew Watson5, FACS, M. Litt, MD; James Schuster1, MBA, MD; Ellen Beckjord1, PhD, MPHKelly Williams1UPMC Center for High-Value Health Care, Insurance Services Division, UPMC, Pittsburgh, PA, United States2Department of Psychiatry, College of Medicine-Tucson, University of Arizona, Tuscon, AZ, United States3Community Wellness Consultancy, Pittsburgh, PA, United States4Consumer Action Response Team of Allegheny County, NAMI Keystone Pennsylvania, Pittsburgh, PA, United States5Department of Surgery, UPMC, Pittsburgh, PA, United StatesThis has been corrected to:1, PhD, MPH; Sarah Markwardt1, MID; Shannon M Kearney1, DrPH, MPH,\u00a0CPH; Jordan F Karp2, MD; Kevin L Kraemer3, MD; Margaret J Park4, MDiv; Paul Freund5, MEd; Andrew Watson6, FACS, MLitt, MD; James Schuster1, MBA, MD; Ellen Beckjord1, PhD, MPHKelly Williams1UPMC Center for High-Value Health Care, Insurance Services Division, UPMC, Pittsburgh, PA, United States2Department of Psychiatry, College of Medicine-Tucson, University of Arizona, Tucson, AZ, United States3Center for Research on Health Care, Division of General Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States4Community Wellness Consultancy, Pittsburgh, PA, United States5Consumer Action Response Team of Allegheny County, NAMI Keystone Pennsylvania, Pittsburgh, PA, United States6Department of Surgery, UPMC, Pittsburgh, PA, United StatesThe correction will appear in the online version of the paper on the JMIR Publications website on February 26, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "There are errors in the author affiliations. The publisher apologizes for the errors. The correct affiliations are as follows:1, Ma\u0142gorzata Niesiob\u0119dzka1, Janusz Surzykiewicz2,3Karol Konaszewski1 Faculty of Education, University of Bialystok, Bialystok, Poland, 2 Faculty of Philosophy and Education, Katholische Universit\u00e4t Eichst\u00e4tt-Ingolstadt, Germany, 3 Faculty of Education, Cardinal Stefan Wyszynski University in Warsaw, Poland."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Chiara Masetti2, Gaia Messana3, Riccardo Muglia1,3, Nicola Pugliese2,3, Roberto Ceriani2, Ana Lleo de Nalda2,3, Lorenza Rimassa3,4, Guido Torzilli5,6, Dario Poretti1, Felice D\u2019Antuono1, Letterio Salvatore Politi3,4, Vittorio Pedicini1, Alessio Aghemo2,3Ezio Lanza1 Humanitas Clinical and Research Center\u2013IRCCS\u2014Division of Interventional Radiology, Department of Radiology, via Manzoni 56, 20089 Rozzano (Mi)\u2013Italy 2 Humanitas Clinical and Research Center\u2013IRCCS\u2014Division of Internal Medicine and Hepatology, Department of Gastroenterology, via Manzoni 56, 20089 Rozzano (Mi)\u2013Italy 3 Humanitas University, Department of Biomedical Sciences, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele\u2013Milan, Italy 4 Humanitas Clinical and Research Center\u2013IRCCS\u2014Medical Oncology and Hematology Unit, Humanitas Cancer Center, via Manzoni 56, 20089 Rozzano (Mi)\u2013Italy 5 Humanitas Clinical and Research Center\u2013IRCCS\u2014Division of Hepatobiliary & General Surgery, Department of Surgery, via Manzoni 56, 20089 Rozzano (Mi)\u2013Italy 6 Humanitas Clinical and Research Center\u2013IRCCS\u2014Department of Radiology via Manzoni 56, 20089 Rozzano (Mi)\u2013Italy"} +{"text": "In \u201cEvaluation of a Mobile App to Enhance Relational Awareness and Change During Cognitive Analytic Therapy: Mixed Methods Case Series\u201d :e19888) the authors noted one error.The paper was inadvertently published with an incorrect list of affiliations. The original paper listed the authors and affiliations as follows:1, BSc, MSc, D Clin; Katherine Easton2, BSc, MRes, PhD; Martin Cooper3, BA, MSc; Abigail Millings2, BSc, PhD; Melanie Simmonds-Buckley2, BSc, PhD; Glenys Parry2, BA, PhDStephen Kellett1Sheffield Health & Social Care NHS Foundation Trust, Clinical Psychology Unit, University of Sheffield, Sheffield, United Kingdom2Catalyse, UK, Sheffield, United Kingdom3Software Engineering, Graphics and Multimedia; Sheffield Hallam University, Sheffield, United KingdomThe corrected affiliations are as follows:1, BSc, MSc, D Clin; Katherine Easton2, BSc, MRes, PhD; Martin Cooper3, BA, MSc; Abigail Millings2, BSc, PhD; Melanie Simmonds-Buckley2, BSc, PhD; Glenys Parry4, BA, PhDStephen Kellett1Sheffield Health & Social Care NHS Foundation Trust, University of Sheffield, Sheffield, United Kingdom2University of Sheffield, Sheffield, United Kingdom3Sheffield Hallam University, Sheffield, United Kingdom4Catalyse, Sheffield, United KingdomThe correction will appear in the online version of the paper on the JMIR Publications website on January 15, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "Therefore, the correct author affliations for this article should have been presented as follows:1,2, CHUIZHENG MENG2, ZHONGMIN JIANG1. DIEGO GONZALEZ-RIVAS3, JUNFEN RUAN2, WEI XU2, CHUANPING LIU2, LEI ZHANG2, GUOGANG GAO2, GE YU2, HEZHI TENG2 and JIN JU2SHANLEI WANG1Department of Thoracic Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250000; 2Department of Thoracic Surgery, Weihai Municipal Hospital, Weihai, Shandong 264200, P.R. China; 3Department of Thoracic Surgery and Minimally Invasive Thoracic Surgery Unit (UCTMI), 15008 Coru\u00f1a, SpainThe authors apologize for this oversight on their part, and for any inconvenience caused."} +{"text": "In , the infThe below information,1, Xueren Thong, MM1, Wengang Zhu, MM1, Yu Chen, BS1, Longze Zhou, MM1, Xiangheng Dai, MM1, Junjian Liao, MM1, Zhong Li, MM3, Konghe Hu, MD1, Kangsheng Bei, BS1, Yinghui Xiong, BS1, Yongyu Hu, BS1, Qinfu Zhao, BS2, Zhouxing Zhu; BS2, Yanli Yu, BS1, Qiang Wu, MD1, Xinhua Xi, MM1.Yongzheng Bao, MD1Department of Spinal Surgery, Nanfang Hospital, Southern Medical University, Guangzhou and2Department of Orthopedic Surgery, Lechang People's Hospital, Shaoguan and3Department of Spine Surgery, Jingmen Second People's Hospital Jingmen, China.should be corrected as:1, Xueren Zhong MM1, Wengang Zhu MM1, Yu Chen BS1, Longze Zhou MM1, Xiangheng Dai MM2, Junjian Liao MM1, Zhong Li MM3, Konghe Hu MD1, Kangsheng Bei BS1, Yinghui Xiong BS1, Yongyu Hu BS1, Qinfu Zhao BS4, Zhouxing Zhu BS4, Yanli Yu BS1, Qiang Wu MD1\u203b, Xinhua Xi MM1\u203bYongzheng Bao MD1Department of Spine Surgery, Yuebei People's Hospital Affiliated to Shantou University Medical College, Shaoguan City, Guangdong Province, China, 512026.2Department of Spinal Surgery, Nanfang Hospital, Southern Medical University, Guangzhou City, Guangdong Province, China, 510515.3Department of Spine Surgery, Jingmen Second People's Hospital, Jingmen City, Hubei Province, China, 448000.4Department of Orthopedic Surgery, Lechang People's Hospital, Shaoguan City, Guangdong Province, China, 512200.Co\u2010first authors: Yongzheng Bao, Xueren Zhong.sgwuqiang@sina.com; Xinhua Xi, 56249042@qq.comCorresponding author: Qiang Wu, E\u2010mail: The publisher apologizes for these errors and any convenience these may have caused."} +{"text": "Correction to: BMC Psychiatry 20, 379 (2020)https://doi.org/10.1186/s12888-020-02784-wFollowing the publication of the original article , the autYuchen Ying1,2,3\u2020, Liemin Ruan3\u2020, Fanqian Kong4, Binbin Zhu5, Yunxin Ji3 and Zhongze Lou3*2. Ningbo College of Health Sciences, Ningbo, Zhejiang 315,010, P.R. China.3. Department of Psychosomatic Medicine, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, 59 Liuting Street, Haishu District, Ningbo, Zhejiang 315,211, P.R. China.The author group has been updated above and the original article has been"} +{"text": "Correction to: Mol Med (2018) 24:22https://doi.org/10.1186/s10020-018-0026-5Following publication of the original article (Heikal et al. Correct:1Brighton and Sussex Medical School Department of Clinical and experimental investigation, University of Sussex, Falmer East Sussex, Brighton BN1 9PS, UK3Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt"} +{"text": "By Kalliopi Domvri, Konstantinos Porpodis, Panagiota Zisi, ApostolosApostolopoulos, Angeliki Cheva, Theodora Papamitsou, Despoina Papakosta, TheodorosKontakiotisTobacco Induced Diseases, Volume 18, Issue March, Pages 1-8Publish date: 24 March 2020DOI:https://doi.org/10.18332/tid/118718In the original article, in the first page, in the authors list, the superscriptsindicating the authors\u2019 affiliations were mistakenly given as follows:1,2, Konstantinos Porpodis1,2,Panagiota Zisi1,2, ApostolosApostolopoulos1,2, Angeliki Cheva3, TheodoraPapamitsou4, Despoina Papakosta1,2, TheodorosKontakiotis1,2Kalliopi DomvriThe superscripts in the original manuscript are now corrected:1, Konstantinos Porpodis1, PanagiotaZisi1, Apostolos Apostolopoulos1, Angeliki Cheva2,Theodora Papamitsou3, Despoina Papakosta1, TheodorosKontakiotis1Kalliopi Domvri1Department of Respiratory Medicine, Aristotle University of Thessaloniki,George Papanikolaou Hospital, Thessaloniki, Greece2Laboratory of Pathology, Medical School, Aristotle University ofThessaloniki, Thessaloniki, Greece3Laboratory of Histology-Embryology, Aristotle University of Thessaloniki,Thessaloniki, Greece"} +{"text": "A new oncolytic Vaccinia virus augments antitumor immune responses to prevent tumor recurrence and metastasis after surgery. J ImmunoTher Cancer 2020;8:e000415. doi: 10.1136/jitc-2019-000415Ahmed J, Chard LS, Yuan M, In this article, the author Joel Schwartz was incorrectly linked to affiliation 3 twice and authors Nicholas Lemoine and Yaohe Wang should be linked to affiliation 2 in addition to affiliation 1. The correct author and affiliation list are shown below:1 Louisa S Chard,1 Ming Yuan,1 Jiwei Wang,2 Anwen Howells,1 Yuenan Li,2 Haoze Li,2 Zhongxian Zhang,2 Shuangshuang Lu,2 Dongling Gao,2 Pengju Wang,2 Yongchao Chu,2 Chadwan Al Yaghchi,1 Joel Schwartz,3 Ghassan Alusi,1 Nicholas Lemoine,1,2 Yaohe Wang1,2Jahangir Ahmed,1Centre for Biomarkers & Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK2National Centre for International Research in Cell and Gene Therapy, Zhengzhou University, Zhengzhou, Henan, China3University of Illinois at Chicago, Chicago, Illinois, USA"} +{"text": "Correction to: BMC Complement Med Ther 21, 28 (2021)https://doi.org/10.1186/s12906-021-03203-7Following publication of the original article , the autThe updated author affiliations should be:1*, Hussam Aly Sayed Murad1,2, Hossam Mohammed Abdallah3,4 and Ali M. El-Halawany3,4Misbahuddin Rafeeq1 Department of Pharmacology, Faculty of Medicine, King Abdulaziz University (KAU), Rabigh Campus, Jeddah 21,589, Saudi Arabia.2 Department of Pharmacology, Faculty of Medicine, Ain Shams University, Cairo 11,562, Egypt.3 Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, KAU, Jeddah 21,589, Saudi Arabia.4 Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11,562, Egypt.The original article has been"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1.3, Gerd Jomrich1,3, Dietmar Tamandl2, Michael Gnant3, Martin Schindl1,3, Klaus Sahora1,3Elisabeth S. Gruber1 Division of General Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria, 2 Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria, 3 Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, 2, 3*, Vyacheslav Buko4,5, Alfred Lautwein1, Radovan Dvorsky6,7, Elena Belonovskaya4, Oksana Lukivskaya4, Elena Naruta4, Siarhei Kirko4, Viktor Andreev8, Dominik Buckert1,9, Sebastian Bergler1, Christian Renz1, Edith Schneider10, Florian Kuchenbauer10,11, Mukesh Kumar12, Cagatay G\u00fcnes12, Berthold B\u00fcchele13, Thomas Simmet13, Dieter M\u00fcller-Enoch1, Thomas Wirth1, Thomas Haehner1Torsten Diesinger1 Institute of Physiological Chemistry, Ulm University, Ulm, Germany, 2 Department of Internal Medicine, Neu-Ulm Hospital, Neu-Ulm, Germany, 3 Chair of Biochemistry and Molecular Medicine, Witten/Herdecke University, Witten, Germany, 4 Division of Biochemical Pharmacology, Institute of Biochemistry of Biologically Active Substances, Grodno, Belarus, 5 Department of Biotechnology, University of Medical Sciences, Bialystok, Poland, 6 Institute of Biochemistry and Molecular Biology II, Medizinische Fakult\u00e4t der Heinrich-Heine-Universit\u00e4t D\u00fcsseldorf, D\u00fcsseldorf, Germany, 7 Max Planck Institute of Molecular Physiology, Dortmund, Germany, 8 Department of Medical Biology and Genetics, Grodno State Medical University, Grodno, Belarus, 9 Department of Internal Medicine II, University Hospital Ulm, Ulm, Germany, 10 Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany, 11 University of British Columbia, Terry Fox Laboratory, Vancouver, Canada, 12 Department of Urology, University Hospital Ulm, Ulm, Germany, 13 Institute of Pharmacology of Natural Products and Clinical Pharmacology, University Ulm, Ulm, GermanyThe publisher apologizes for the error."} +{"text": "Journal of Experimental Botany, Advance Access publication: 27 April 2020, doi: 10.1093/jxb/eraa131In the above article, the author list has been corrected to:1,2, Wei Wei3, Zhongqi Fan3, Xiaodan Zhao4, Yiping Zhang1, Yuan Jing1, Benzhong Zhu1, Hongliang Zhu1, Wei Shan3, Jianye Chen3, Donald Grierson2,5, Yunbo Luo1, Tomislav Jemri\u0107\u200a6, Cai-Zhong Jiang7,8 and Da-Qi Fu1,*Ying GaoCo-author Cai-Zhong Jiang was initially omitted from the above article. This has now been corrected. Cai-Zhong Jiang\u2019s affiliations are as follows:7Department of Plant Sciences, University of California, Davis, CA 95616, USA8Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA 95616, USA"} +{"text": "This article has been corrected: After carefully repeating certain experiments and reviewing old research records, we\u2019ve uncovered evidence that PD0325901 and RAD001 doses used for in vivo experiments, in Watson et al., 2014, were lower than intended. We found that in contrast to the original paper, Everolimus (Selleckchem S1120) and PD0325901 (Selleckchem S1036) were only tolerated in young mice at much lower concentrations than originally reported. Likely due to dilution errors, the mice in the original draft received significantly reduced amounts of drug. New dose escalation studies showed that the mice could tolerate 5mg/kg RAD001 thrice weekly and 0.5mg/kg PD0325901 thrice weekly as monotherapies or in combination. As monotherapies, both RAD001 and PD0325901 slightly extended the survival of genetically engineered mice with peripheral nerve sheath tumors . Ten control mice were injected with DMSO and PBS vehicles. As seen in in vivo effects of PD0325901, RAD001 and combined treatment are much stronger than first reported. Overall, the conclusions and trends drawn from the original paper have not changed substantially. That being said, when the correct doses were given, the in vivo data was much more robust and displayed an extraordinary increase in longevity. Our in vitro data verified what had been previously seen in pharmacodynamics in the Watson et al paper, showing dose dependent decreases in phosphorylated ERK with corresponding increases in phosphorylated AKT. Together these data draw much more impactful and profound conclusions while still holding true to the originally published trends.In addition, the author list for this paper has been updated. The revised author list is shown below:1,2,3,4,*, Bryant J. Keller1,2,3,4,*, Kyle A. Williams1,2,3,4, Namrata N. Damle1,2,3,4, Samuel J. Finnerty1,2,3,4, Leah K. Anderson1,2, Andrew D. Greeley1,2, Vincent W. Keng1,2,3,4,10, Eric P. Rahrmann1,2,3,4, Amanda L. Halfond5, Natasha M. Powell4, Margaret H. Collins8, Tilat Rizvi8, Christopher L. Moertel6, Nancy Ratner7,9, and David A. Largaespada1,2,3,4,6Adrienne L. Watson1Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA2Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA3Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA4Brain Tumor Program, University of Minnesota, Minneapolis, MN, USA5Health and Natural Sciences Department, University of Minnesota, Minneapolis, MN, USA6Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA7Division of Experimental Hematology and Cancer Biology, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA.8Division of Pathology and Laboratory Medicine, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA9Department of Pediatrics, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA10Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong*These two authors contributed equally to this work1502-1514. https://doi.org/10.18632/oncotarget.1609Original article: Oncotarget. 2014; 5:1502\u20131514."} +{"text": "In: Xiaochu Yu, Zixing Wang, Yubing Shen, Zhong Liu, Hongjie Wang, Shumei Zhang, et al. Population-based projections of blood supply and demand, China, 2017-2036. Bull World Health Organ. 2020 Jan 1;98(1):10\u201318On page 14, Figure 5, should read as follows:"} +{"text": "There is an error in the title of the paper . The tit1\u00a0Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, BioMeditech and Tays Cancer Center, Tampere University Hospital, P.O. Box 553, 33101 Tampere, Finland2\u00a0Predictive Medicine and Data Analytics Lab, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O. Box 553, 33101 Tampere, FinlandIn addition, the first affiliation \u201cMolecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, BioMeditech and Tays Cancer Center, Tampere University Hospital, P.O. Box 553, 33101 Tampere, Finland\u201d should be split into two:Thus, the original affiliation orders 2\u20138 should be changed to 3\u20139, respectively. The correct version is listed below:1,2, Aliyu Musa 3, Akshaya Murugesan 1,2,4, Jo\u00e3o R. Vale 5,6, Carlos A. M. Afonso 6, Saravanan Konda Mani 7, Olli Yli-Harja 8,9, Nuno R. Candeias 5,* and Meenakshisundaram Kandhavelu 1,2,*Anisha Viswanathan 1\u00a0Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University and BioMeditech, P.O. Box 553, 33101 Tampere, Finland2\u00a0Tays Cancer Center, Tampere University Hospital, 33520 Tampere, Finland3\u00a0Predictive Medicine and Data Analytics Lab, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O. Box 553, 33101 Tampere, Finland4\u00a0Department of Biotechnology, Lady Doak College, Madurai 625002, India5\u00a0Faculty of Engineering and Natural Sciences, Tampere University, 33101 Tampere, Finland6\u00a0Instituto de Investiga\u00e7\u00e3o do Medicamento (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal7\u00a0Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China8\u00a0Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O. Box 553, 33101 Tampere, Finland9\u00a0Institute for Systems Biology, 1441N 34th Street, Seattle, WA 98103-8904, USAWe apologize for this error and state that the scientific conclusions are unaffected. The original article has been updated."} +{"text": "Correction to: J Exp Clin Cancer Res 39, 76 (2020)https://doi.org/10.1186/s13046-020-01578-yFollowing publication of the original article , the autThe incorrect author\u2019s affiliation is:1,2,3\u2020, Ting Long2,3\u2020, Yidan Ma2,3, Jiaxian Zhu2,3, Lingfang Gao 2,3, Yan Zhong 2,3, Xia Wang 1,2,3, Xiaoyan Wang 1,2,3, Zuguo Li 4,5,6*Zhiyan Hu1 Department of Pathology, Shenzhen Hospital of Southern Medical University, Shenzhen, China.2 Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.3 Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.4 Guangdong Provincial Key Laboratory of Molecular tumor Pathology, Guangzhou, China.5 Department of Pathology, School of Basic Medical Sciences, Southern Medical University,6 Guangdong Provincial Key Laboratory of Molecular tumor Pathology, Guangzhou, China.The correct author\u2019s affiliation is:2,3,4\u2020, Ting Long3,4\u2020, Yidan Ma3,4, Jiaxian Zhu3,4, Lingfang Gao3,4, Yan Zhong3,4, Xia Wang2,3,4, Xiaoyan Wang2,3,4 and Zuguo Li1,3,4*Zhiyan Hu1 Department of Pathology, Shenzhen Hospital of Southern Medical University, Shenzhen, China.2 Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.3 Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.4 Guangdong Provincial Key Laboratory of Molecular tumor Pathology, Guangzhou, China.The author group has been updated above and the original article has been"} +{"text": "Therefore, the affiliations for this paper should have appeared as follows:1, PENG-FEI GUO1, ZHAO MA2, CHENG CHANG2, QING-NAN MENG1, YA GAO1, IMRAN KHAN1, XIAO-BO WANG1 and ZHENG-JUN CUI1RONG-QIANG YANG1Department of Burn and Repair Reconstruction Surgery, The First Affiliated Hospital of Zhengzhou University; 2The School of Basic Medical Science of Zhengzhou University, Zhengzhou, Henan 450052, P.R. ChinaThe authors regret that these errors with the author affiliations were not noticed prior to the publication of their paper, and apologize for any inconvenience caused."} +{"text": "In the byline, some affiliation numbers are attributed incorrectly to some authors. The byline and affiliation list should read:1*, Anne Stevenson2, Sreeja S. Kalapurakkel3, Charlotte Hanlon4, Soraya Seedat5, Boniface Harerimana6,7, Bonginkosi Chiliza8, and Karestan C. Koenen9Lauren C. Ng1 Department of Psychology, University of California Los Angeles, Los Angeles, California, United States of America, 2 Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America, 3 Duke University Global Health Institute, Durham, North Carolina, United States of America, 4 Centre for Global Mental Health, Health Service and Population Research, Department Institute of Psychiatry, Psychology and Neuroscience King\u2019s College, London, United Kingdom, 5 Department of Psychiatry, Stellenbosch University, Cape Town, South Africa, 6 Faculty of Health Sciences, Western University, London, Ontario, Canada, 7 College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda, 8 Department of Psychiatry, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa, 9 Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, E. Gnuchikh1,2,3, S. Bazhenov1,6, M. Bermeshev4, V. Pevgov1, V. Samoilov4, S. Shorunov4, A. Maksimov4, L. Yaguzhinsky1,5, I. Manukhov1,6,7A. Kessenikh1 Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia, 2 State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Centre \u201cKurchatov Institute\u201d, Kurchatov Genomic Center, Moscow, Russia, 3 NRC \u201cKurchatov Institute\u201d, Moscow, Russia, 4 Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia, 5 AN Belozersky Res Inst Physicochem Biol, Moscow MV Lomonosov State Univ, Moscow, Russia, 6 HSE University, Moscow, Russia, 7 Federal Research Center of Biological Systems and Agro-technologies of RAS, Orenburg, Russia."} +{"text": "Correction to: Pediatr Rheumatol Online J (2019) 17:66https://doi.org/10.1186/s12969-019-0345-2Following publication of the original article , we haveIvan Foeldvari1*\u2020, Jens Klotsche2,3\u2020, Gabriele Simonini4, Clive Edelsten5, Sheila T. Angeles-Han6, Regitze Bangsgaard7,Joke de Boer8, Gabriele Brumm9, Rosa Bou Torrent10,21, Tamas Constantin11, Cinzia DeLibero12, Jesus Diaz23,24,Valeria Maria Gerloni13, Margarida Guedes14, Arnd Heiligenhaus15, Kaisu Kotaniemi16, Sanna Leinonen16,Kirsten Minden2,17, Vasco Miranda18, Elisabetta Miserocchi19, Susan Nielsen7, Martina Niewerth2, Irene Pontikaki13,Carmen Garcia de Vicuna10, Carla Zilhao14, Steven Yeh20, Jordi Anton10,21,22"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1,2,3, Alice Valentini5,6, Noor Kamal Khan3, Christian Miquel5, Pierre Taberlet5, Jon E. Swenson2,4Muhammad Ali Nawaz1 Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan, 2 Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, Norway, 3 Himalayan Wildlife Foundation, Islamabad, Pakistan, 4 Norwegian Institute for Nature Research, Trondheim, Norway, 5 Laboratoire d\u2019Ecologie Alpine, Universite\u00b4 Joseph Fourier, France, 6 Dipartimento di Ecologia e Sviluppo Economico Sostenibile, Universit\u00e0 degli Studi della Tuscia, Viterbo, Italy."} +{"text": "Cell Prolif., 2020, 53, e12808Potential role of two novel agonists of thyroid hormone receptor\u2010\u03b2 on liver regeneration1, Marta Anna Kowalik1, Lavinia Cabras1, Massimiliano Runfola2, Simona Sestito3, Cristina Migliore4,5, Silvia Giordano4,5, Grazia Chiellini3, Simona Rapposelli2, Amedeo Columbano1Andrea Perra11Department of Biomedical Sciences, Unit of Oncology and Molecular Pathology, University of Cagliari, Cagliari, Italy2Department of Pharmacy, University of Pisa, Pisa, Italy3Department of Pathology, University of Pisa, Pisa, Italy4Department of Oncology, University of Turin, Turin, Italy5Candiolo Cancer Institute, FPO\u2010IRCCS, Candiolo, ItalyThe authors would like to draw the reader's attention to the below errors:\u2018Candiolo Cancer Institute, FPO\u2010IRCCS, Candiolo, Italy\u2019, which was already corrected in the above list of affiliations.Affiliation 5 was erroneously written in the published version of the article. The correct affiliation is The authors would like to apologize for any inconvenience caused."} +{"text": "Additional affiliations for the first and tenth authors are missing. The correct affiliations are as follows:1,2,3, Ho-Hsiung Chang1, Jui-Che Chang1, Hsiang-Chia Lu4, Tan-Tung Wang4, Duen-Wei Hsu5, Yuh Tzean1, An-Po Cheng1, Yi-Shu Chiu1 and Hsin-Hung Yeh1,2,4,6Li Chang1 Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan, 2 Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan, 3 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan, 4 Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan, 5 Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan, 6 Biotechnology Center, National Chung Hsing University, Taichung, Taiwan."} +{"text": "This article has been corrected: The authors requested to add missing affiliation of corresponding author Chih-Yang Huang. This correction does not change the content of the publication. The correct list of authors and affiliations is provided below:1,*, Wei-Wen Kuo2,*, Rathinasamy Baskaran3, Chia-Hua Kuo4, Yun-An Chen2, William Shao-Tsu Chen5, Tsung-Jung Ho6, Cecilia Hsuan Day7, B. Mahalakshmi8, Chih-Yang Huang9,10,11,12,13Jing-Ying Lin1Department of Medical Imaging and Radiological Science, Central Taiwan University of Science and Technology, Taichung, Taiwan2Department of Biological Science and Technology, China Medical University, Taichung, Taiwan3Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan4Laboratory of Exercise Biochemistry, University of Taipei, Taipei, Taiwan5Division of Addictive Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Tzu Chi University, Hualien, Taiwan6Department of Chinese Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Tzu Chi University, Hualien, Taiwan7Department of Nursing, MeiHo University, Pingtung, Taiwan8Institute of Research and Development, Duy Tan University, Da Nang, Vietnam9Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan10Center of General Education, Buddhist Tzu Chi Medical Foundation, Tzu Chi University of Science and Technology, Hualien, Taiwan11Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan12Department of Biotechnology, Asia University, Taichung, Taiwan13Cardiovascular and Mitochondrial Related Disease Research Center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Tzu Chi University of Science and Technology, Hualien, Taiwan*Equal contribution . https://doi.org/10.18632/aging.103046Original article: Aging. 2020; 12:6852\u20136864."} +{"text": "Correction to: BMC Immunol (2021) 22:3https://doi.org/10.1186/s12865-020-00396-3It was highlighted that the original article containeIncorrect1 and Jingjing Luo2,3Weigang Xiu1 Department of Thoracic Oncology and State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China. 2 Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China. 3 Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, PR China.Correct1,2,3 and Jingjing Luo1,2Weigang Xiu1 Department of Laboratory Medicine, West China Second University Hospital, Sichuan University. 2 Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education. 3 Department of Thoracic Oncology and State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Karin Orsel1, Wendy Hutchins2, Layne G. Adams3, Kimberlee Beckmen4, John E. Blake5, Sylvia L. Checkley1, Tracy Davison6, Juliette Di Francesco1, Brett Elkin6, Lisa-Marie Leclerc7, Angela Schneider1, Matilde Tomaselli1,8, Susan J. Kutz1Fabien Mavrot1 Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada 2 Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada 3 US Geological Survey, Alaska Science Center, Anchorage, Alaska, USA 4 Alaska Department of Fish and Game, Fairbanks, Alaska, USA 5 University of Fairbanks, Fairbanks, Alaska, USA 6 Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada 7 Government of Nunavut, Kugluktuk, Nunavut, Canada 8 Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada"} +{"text": "The first affiliation is missing for the first author. Monika S\u0142upecka-Ziemilska\u2019s first affiliation is: Department of Human Epigenetics, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland.The correct affiliations are as follows:1,2, Paulina Szczurek3, Maria Boryczka2, Ma\u0142gorzata Gajewska4, Piotr Wychowa\u0144ski5, Atsukazu Kuwahara6, Ikuo Kato7, \u017baneta Dzi\u0119gelewska4, Jaros\u0142aw Woli\u0144ski2Monika S\u0142upecka-Ziemilska1 Department of Human Epigenetics, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland, 2 Department of Animal Physiology, Polish Academy of Sciences, The Kielanowski Institute of Animal Physiology and Nutrition, Jab\u0142onna, Poland, 3 Department of Animal Nutrition and Feed Sciences, National Research Institute of Animal Production, Balice, Poland, 4 Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland, 5 Department of Dental Surgery, Medical University of Warsaw, Warsaw, Poland, 6 Laboratory of Physiology, Institute for Environmental Sciences & Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan, 7 Department of Medical Biochemistry, Kobe Pharmaceutical University, Kobe, Japan."} +{"text": "This article has been corrected: The authors requested to remove affiliation 1 for Na Li.The correct affiliation is given below:1,*, Na Li2,*, Fangzhou Chen1, Ruoxuan Hei1, Junxia Gu1, Yaojuan Lu3, Lichun Sun4, Qiping Zheng1,3Qian Wang1Department of Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China2Department of Blood Transfusion, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China3Shenzhen Academy of Peptide Targeting Technology at Pingshan, and Shenzhen Tyercan Bio-pharm Co., Ltd., Shenzhen 518118, China4Department of Medicine, School of Medicine, Tulane Health Sciences Center, New Orleans, LA 70112, USA*Equal contribution . https://doi.org/10.18632/aging.103190Original article: Aging. 2020; 12:8669\u20138679."} +{"text": "In the editorial \u201c50 Years of Children\u2019s HeartLink and the Partnerships in Brazil\u201d, with DOI code 10.21470/1678-9741-2019-0426, published in the Brazilian Journal of Cardiovascular Surgery, in edition 35.2, pages IV to VI, 2020:In the original version the information was:1, MD, PhD; Valdester Cavalcante Junior2, MD, PhD; Marcelo Biscegli Jatene3, MD, PhD; Andreas Tsakistos4, MD, PhD; Bistra Zheleva4, MD, PhDUlisses CrotiThe correct information is:1, MD, PhD; Valdester Cavalcante Pinto Junior2, MD, PhD; Marcelo Biscegli Jatene3, MD, PhD; Andreas Tsakistos4, MD, PhD; Bistra Zheleva4, MD, PhDUlisses Alexandre Croti"} +{"text": "Correction: BMC Plant Biol (2020) 20:478https://doi.org/10.1186/s12870-020-02705-9CorrectionIn the original publication of this article the auth1\u2020, Jianbin Liu1\u2020, Di Wu1, Ying Liu1, Weijian Cen1, Shaokui Wang3, Rongbai Li1,2* and Jijing Luo1*Baiyang Yu1. College of Life Science and Technology , Guangxi University, Nanning 530004, China2. Agriculture College, Guangxi University, Nanning 530004, China3. Agriculture College, South China Agricultural University, Guangzhou 510642, ChinaThe original publication has been corrected."} +{"text": "Regarding the paper \u201cWeight gain among treatment\u2010na\u00efve persons with HIV starting integrase inhibitors compared to non\u2010nucleoside reverse transcriptase inhibitors or protease inhibitors in a large observational cohort in the United States and Canada\u201d by Kassem Bourgi, Cathy A Jenkins, Peter F Rebeiro, Frank Palella, Richard D Moore, Keri N Altoff, John Gill, Charles S Rabkin, Stephen J Gange, Michael A Horberg, Joseph Margolick, Jun Li, Cherise Wong, Amanda Willig, Viviane D Lima, Heidi Crane, Jennifer Thorne, Michael Silverberg, Gregory Kirk, William C Mathews, Timothy R Sterling, Jordan Lake and, John R Koethe for the North American AIDS Cohort Collaboration on Research and Design (NA\u2010ACCORD)Journal of the International AIDS Society, Citation: Journal of the International AIDS Society 2020, 23: 25484. https://doi.org/10.1002/jia2.25484Published in the The author name, \u201cKeri N Altoff\u201d was misspelt and should have been corrected to \u201cKeri N Althoff\u201d.Bryan Shepherd was omitted and should have been added to the list of authors.The authors noticed the following errors in the author byline and should have been corrected.The author byline should have read:1,2, Cathy A. Jenkins1, Peter F. Rebeiro1, Bryan E. Shepherd1, Frank Palella3, Richard D. Moore4, Keri N. Althoff4, John Gill5, Charles S. Rabkin6, Stephen J. Gange4, Michael A. Horberg7, Joseph Margolick4, Jun Li8, Cherise Wong4, Amanda Willig9, Viviane D. Lima10, Heidi Crane11, Jennifer Thorne4, Michael J. Silverberg12, Gregory Kirk4, William Christopher Mathews13, Timothy R. Sterling1, Jordan Lake14 and John R. Koethe1,15,\u00a7 for the North American AIDS Cohort Collaboration on Research and Design (NA\u2010ACCORD)Kassem Bourgi1Vanderbilt University Medical Center, Nashville, Tennessee, USA; 2Indiana University School of Medicine, Indianapolis, Indiana, USA; 3Northwestern University Feinberg School of Medicine, Chicago, IL, USA; 4Johns Hopkins University, Baltimore, Maryland, USA; 5University of Calgary, Calgary, Alberta, Canada; 6National Cancer Institute, Bethesda, Maryland, USA; 7Mid\u2010Atlantic Permanente Research Institute, Kaiser Permanente Mid\u2010Atlantic States, Rockville, Maryland, USA; 8Centers for Disease Control and Prevention, Atlanta, Georgia, USA; 9University of Alabama at Birmingham, Birmingham, Alabama, USA; 10University of British Columbia, Vancouver, British Columbia, Canada; 11University of Washington, Seattle, Washington, USA; 12Kaiser Permanente Division of Research, Kaiser Permanente Northern California, Oakland, California, USA; 13University of California San Diego, San Diego, California, USA; 14University of Texas Health Science Center at Houston, Houston, Texas, USA; 15Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USAThis article has been corrected online."} +{"text": "In , the aff3.Giuseppe M. C. Rosano3Centre for Clinical and Basic Research, Department of Medical Sciences, IRCCS San Raffaele Pisana, Rome, Italy."} +{"text": "The information for affiliations 1 and 2 is switched. The correct affiliations are as follows:1, Roberta Ascrizzi2, Marco Martinelli1, Silvia Gonzali1, Lorenzo Mariotti3, Laura Pistelli3, Guido Flamini2, Pierdomenico Perata1Claudia Kiferle1 PlantLab, Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, 56127 Pisa, Italy 2 Department of Pharmacy, University of Pisa, 56126 Pisa, Italy 3 Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy"} +{"text": "There are errors in the correction published on October 5, 2020. The publisher apologizes for the error. The correct text is:The ninth author's name is spelled incorrectly. The correct name is: Suliman Mohammad Alghanem. Additionally, the affiliation for the ninth author is incorrect. The correct affiliations are as follows:1, Muhammad Amjad Bashir2, Muneeba Haider3, Najeeba Haider3, Khalid Ali Khan4,5,6, Hamed A. Ghramh4,5,6, Mohammad Javed Ansari7, \u00c7etin Mutlu8, Suliman Mohammad Alghanem9Haider Karar1 Mango Research Institute, Multan, Pakistan, 2 Department of Plant Protection faculty of Agricultural Sciences, Ghazi University Dera Ghazi Khan Punjab, Dera Ghazi Khan, Pakistan, 3 Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan, 4 Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia, 5 Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, Abha, Saudi Arabia, 6 Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia, 7 Department of Botany, Hindu College Moradabad, Moradabad, Uttar Pradesh, India, 8 Department of Plant Protection, Harran University, \u015eanl\u0131urfa, Turkey, 9 Biology Department, Faculty of Science, Tabuk University, Tabuk, Saudi Arabia"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1,2, Jie Liang3, ZiYu Qu2, FangYun Yang2, ZhengYin Liao2, HongFeng Gou2Biao Yang1 Department of Gastroenterology, West China Hospital, West China Medical School, Sichuan University, Chengdu, P.R. China, 2 Department of Abdominal Oncology, West China Hospital, West China Medical School, Sichuan University, Chengdu, P.R. China, 3 School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, P.R. China."} +{"text": "Correction to: Chiropr Man Therap 29, 9 (2021)https://doi.org/10.1186/s12998-021-00363-8Following publication of the original article , we were3. Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, Hong Kong.4. Faculty of Rehabilitation Medicine, University of Alberts, Edmonton, Canada.5. AECC University College, Bournemouth, UK.6. Faculty of Medicine, Memorial University of Newfoundland, St. John\u2019s, NL, Canada.7. Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.8. Department of Chiropractic, Macquarie University, Sydney, Australia.9. Division of Research and Innovation, Canadian Memorial Chiropractic College, Toronto, Canada.10. Department of Chiropractic, Universit\u00e9 du Qu\u00e9bec \u00e0 Trois-Rivi\u00e8res, Trois-Rivi\u00e8res, Qu\u00e9bec, Canada.11. School of Psychology, University of Southampton, Southampton, UK.12. Research Institute, Parker University, Dallas, TX, USA.Originally published affiliations:3. Faculty of Rehabilitation Medicine, University of Alberts, Edmonton, Canada.4. AECC University College, Bournemouth, UK.5. Faculty of Medicine, Memorial University of Newfoundland, St. John\u2019s NL, Canada.6. Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.7. Department of Chiropractic, Macquarie University, Sydney, Australia.8. Division of Research and Innovation, Canadian Memorial Chiropractic College, Toronto, Canada.9. Department of Chiropractic, Universit\u00e9 du Qu\u00e9bec \u00e0 Trois-Rivi\u00e8res, Trois-Rivi\u00e8res, Qu\u00e9bec, Canada.10. Schoolof Psychology, University of Southampton, UK.11. Research Institute, Parker University, Dallas, Texas, United States.12. Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong.Corrected affiliations:The original article has been corrected."} +{"text": "During submission the author name Andreas Link was unfortunately omitted. The correct author list reads as follows:1,2, Davor Vukadinovic1, Andreas Link1, Sebastian Ewen1, Felix Mahfoud1Bruno Scheller1Internal Medicine III, Cardiology, Angiology and Intensive Care Medicine, Saarland University Hospital, Saarland University, Homburg, Saar, Germany2Clinical and Experimental Interventional Cardiology, University of Saarland, Homburg, Saar, Germany"} +{"text": "Correction to: BMC Complement Altern Med 19, 182 (2019)https://doi.org/10.1186/s12906-019-2575-8Following publication of the original article , the autTayyaba Afsar1,2*, Suhail Razak2*, Ali Almajwal2, Maria Shabbir1,3 and Muhammad Rashid Khan11 Quaid I Azam Univ, Fac Biol Sci, Dept Biochem, Islamabad, Pakistan. 2 King Saud Univ, Dept Community Hlth Sci, Coll Appl Med Sci, Riyadh, Saudi Arabia.3 NUST, Atta ur Rahman Sch Appl Biosci, Islamabad, Pakistan."} +{"text": "The authors wish to make the following changes to this paper .The affiliation numbers of the authors Che-Hsuan Lin, Long-Sheng Lu, and Dean Wu are not correct in the original published version. The original version is1,2,3,4,5, Che-Hsuan Lin 6,7, Hui-Yu Lin 1,8, Chia-Hao Kuei 1,9, Jing-Quan Zheng 1,10, Yuan-Hung Wang 1,11, Long-Sheng Lu 12, Fei-Peng Lee 13,14, Chaur-Jong Hu 1,2, Dean Wu 1,3,4,5,15,* and Yuan-Feng Lin 1,16,*Hsun-Hua Lee 1\u00a0kaorulei@yahoo.com.tw (H.-H.L.); candycarol0227@gmail.com (H.-Y.L.); pplay1028@gmail.com (C.-H.K.); 16044@s.tmu.edu.tw (J.-Q.Z.); d508091002@tmu.edu.tw (Y.-H.W.); chaurjongh@tmu.edu.tw (C.-J.H.)Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; 2\u00a0Department of Neurology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan3\u00a0Dizziness and Balance Disorder Center, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan4\u00a0Department of Neurology, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan5\u00a0Taipei Neuroscience Institute, Taipei Medical University, New Taipei City 23561, Taiwan6\u00a0cloudfrank@gmail.comGraduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; 7\u00a0Department of Otolaryngology, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan8\u00a0Breast Center, Department of General Surgery, Cardinal Tien Hospital, Xindian District, New Taipei City 231, Taiwan9\u00a0Urology, Division of Surgery, Cardinal Tien Hospital, Xindian District, New Taipei City 231, Taiwan10\u00a0Department of Critical Care Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan11\u00a0Department of Medical Research, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan12\u00a0lslu@tmu.edu.twDepartment of Radiation Oncology, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan; 13\u00a0fplee@tmu.edu.twDepartment of Otolaryngology, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; 14\u00a0Department of Otolaryngology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan15\u00a0Sleep Center, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan16\u00a0Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 116, TaiwanAnd should be replaced with1,2,3,4,5, Che-Hsuan Lin 6,7,8, Hui-Yu Lin 1,9, Chia-Hao Kuei 1,10, Jing-Quan Zheng 1,11, Yuan-Hung Wang 1,12, Long-Sheng Lu 13,14, Fei-Peng Lee 8,15, Chaur-Jong Hu 1,2, Dean Wu 1,2,4,5,16,* and Yuan-Feng Lin 1,17,*Hsun-Hua Lee 1\u00a0kaorulei@yahoo.com.tw (H.-H.L.); candycarol0227@gmail.com (H.-Y.L.); pplay1028@gmail.com (C.-H.K.); 16044@s.tmu.edu.tw (J.-Q.Z.); d508091002@tmu.edu.tw (Y.-H.W.); chaurjongh@tmu.edu.tw (C.-J.H.)Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; 2\u00a0Department of Neurology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan3\u00a0Dizziness and Balance Disorder Center, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan4\u00a0Department of Neurology, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan5\u00a0Taipei Neuroscience Institute, Taipei Medical University, New Taipei City 23561, Taiwan6\u00a0cloudfrank@gmail.comGraduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; 7\u00a0Department of Otolaryngology, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan8\u00a0fplee@tmu.edu.twDepartment of Otolaryngology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; 9\u00a0Breast Center, Department of General Surgery, Cardinal Tien Hospital, Xindian District, New Taipei City 231, Taiwan10\u00a0Urology, Division of Surgery, Cardinal Tien Hospital, Xindian District, New Taipei City 231, Taiwan11\u00a0Department of Critical Care Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan12\u00a0Department of Medical Research, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan13\u00a0lslu@tmu.edu.twDepartment of Radiation Oncology, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan; 14\u00a0Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan15\u00a0Department of Otolaryngology, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan16\u00a0Sleep Center, Shuang-Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan17\u00a0Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 116, TaiwanThe order of affiliations has been adjusted to make sure they appear in numerical order.The authors apologize for any inconvenience brought to the readers by these changes. These changes do not affect the scientific results. The manuscript will be updated, and the original will remain online on the article webpage."} +{"text": "The correct affiliations are as follows: Wen-Pei Wu1 Department of Diagnostic Radiology, Changhua Christian Hospital, Changhua, Taiwan, 2 School of Medicine, Kaohusiung Medical University, Kaohsiung, Taiwan, 3 Department of Pathology, Taichung Veterans General Hospital, Taichung, Taiwan, 4 School of Medicine, Chung Shan Medical University, Taichung, Taiwan, 5 Department of Medical Technology, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli, Taiwan, 6 Division of General Surgery, Department of Surgery, Changhua Christian Hospital, Changhua, Taiwan, 7 Comprehensive Breast Cancer Center, Department of Surgery, Changhua Christian Hospital, Changhua, Taiwan, 8 Division of Breast Surgery, Department of Surgery, Changi General Hospital, Singapore, 9 Endoscopic & Oncoplastic Breast Surgery Center, Department of Surgery, Changhua Christian Hospital, Changhua, Taiwan, 10 School of Medicine, National Yang Ming University, Taipei, TaiwanThe publisher apologizes for the errors."} +{"text": "Scientific Reports 10.1038/s41598-020-74220-8, published online 15 October 2020Correction to: This Article contained an error in the labelling of Supplementary Movie files.Supplementary Movies 11, 1, 2, 3, 4, 5, 6, 7, 8, 9 and 10 were incorrectly published as Supplementary Videos 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and 11, respectively.This has now been corrected in the HTML; the PDF version of the paper was correct from the time of publication."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Fiaz Ahmad2, Farman Ullah1, Usman Habib3, Saeed Nawaz1, Mohsin Iqbal4*, Ajmal Farooq5Muhammad Abid1 Department of Electrical Engineering, COMSATS Institute of Information Technology, Attock, Pakistan, 2 Department of Electrical & Computer Engineering, Air University, Islamabad, Pakistan, 3 Department of Computer Science, National University of Computer & Emerging Sciences, Islamabad, Pakistan, 4 Department of Electrical Engineering, Sarhad University of Science & IT, Peshawar, Pakistan 5 Department of Electrical Engineering, National University of Computer & Emerging Sciences, Islamabad, Pakistan,"} +{"text": "Nature Communications 10.1038/s41467-019-11642-7, published online 15 August 2019.Correction to: The original version of this Article omitted from the author list the 11th author \u2018Giovanna Peruzzi\u2019, who is from the \u2018Istituto Italiano di Tecnologia, Center for Life Nano Science@Sapienza, Viale Regina Elena 291, 00161, Rome, Italy\u2019. Consequently, the new author list and affiliations is as follows;1,2,7, Luca Digiacomo1,7, Daniela Pozzi1, Sara Palchetti1, Elisabetta Vulpis1, Anna Laura Capriotti3, Riccardo Zenezini Chiozzi3, Aldo Lagan\u00e03, Heinz Amenitsch4, Laura Masuelli5, Giovanna Peruzzi2, Morteza Mahmoudi6, Isabella Screpanti1, Alessandra Zingoni1 & Giulio Caracciolo1\u201cFrancesca Giulimondi1Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy. 2Istituto Italiano di Tecnologia, Center for Life Nano Science@Sapienza, Viale Regina Elena 291, 00161, Rome, Italy. 3Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy. 4Institute of inorganic Chemistry, Graz University of Technology, Stremayerg 6/IV, 8010 Graz, Austria. 5Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy. 6Precision Health Program, Michigan State University, East Lansing, MI 48823, USA. 7These authors contributed equally: Francesca Giulimondi, Luca Digiacomo. Correspondence and requests for materials should be addressed to M.M. (email: mahmou22@msu.edu) or to G.C. (email: giulio.caracciolo@uniroma1.it)\u201dThis has been corrected in both the PDF and HTML versions of the Article."} +{"text": "There are errors in the author affiliations. The publisher apologizes for the error. The correct affiliations are as follows:1 Peter Nydahl2, Manfred Blobner3, Rolf Dubb4, Silke Filipovic5, Arnold Kaltwasser6, Bernhard Ulm3, Stefan J. Schaller3,7Carsten Hermes1 CCRN, Bonn, Germany, 2 Nursing Research, Department of Anesthesiology and Intensive Care Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany, 3 Department of Anesthesiology and Intensive Care, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany, 4 Academy of District Clinics Reutlingen, Reutlingen, Germany, 5 Department of Physiotherapy, University Hospital of Giessen and Marburg, Marburg, Germany, 6 Academy of District Clinics Reutlingen, Reutlingen, Germany, 7 Department of Anesthesiology and Operative Intensive Care Medicine, Charit\u00e9 \u2013Universit\u00e4tsmedizin Berlin, Berlin, GermanyThere are duplicates in the references section. References 7 refers to the same source as reference 12, and reference 8 refers to the same source as reference 31."} +{"text": "Correction to: J Exp Clin Cancer Res 39, 212 (2020)https://doi.org/10.1186/s13046-020-01718-4Following publication of the original article , the autThe updated author affiliations should be:Jian Li1,2,3\u2020, Danli Ye1,2\u2020, Peng Shen4\u2020, Xiaorong Liu1,2, Peirong Zhou1,2, Guifang Zhu1,2, Yangwei Xu1,2, Yun Fu1,2,3, Xuanqi Li 1, Jingbo Sun1,2, Jia Xu5, Qingling Zhang1*1Department of Pathology, Guangdong Provincial People\u2019s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510000, Guangdong Province, People\u2019s Republic of China.2Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou 510282, Guangdong Province, People\u2019s Republic of China.3Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People\u2019s Republic of China.4Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, People\u2019s Republic of China.5Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.The original article has been updated."} +{"text": "In an articleCorrect authors and their affiliations are listed below1,2 | Dan Yan1 | Yina Wang1 | Wei Shi1 | Tianshu Liu1 | Chongqiang Zhao1,3 | Shengqi Huo1 | Jialin Duan1 | Jingwen Tao1 | Maocai Zhai1 | Pengcheng Luo1 | Junyi Guo1 | Lei Tian1 | Lulu Mageta1 | David Jou4 | Cuntai Zhang5 | Chenglong Li6 | Jiayuh Lin7 | Jiagao Lv1 | Sheng Li1 | Li Lin1Haiyan Ma1Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China2Division of Cardiology, Departments of Internal Medicine, First People's Hospital of ShangQiu, Shangqiu, China3Division of Cardiology, Tianjin First Center Hospital, Tianjin, China4Center for Childhood Cancer, Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, College of Medicine, The Ohio State University, Columbus, OH, USA5Departments of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China6Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA7Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USAThe authors apologize for the errors."} +{"text": "Therefore, the correct details for this article are as follows:In Zarei et al. , the aut1, Fatemeh Nasimi2, Hassanali Abedi3, Najmeh Sadeghi4Safar Zarei1Department of Physiology, Faculty of Medicine, Jahrom University of Medical Sciences, Jahrom, Iran2Department of Intensive Neonatal Care Nursing, Faculty of Nursing, Jahrom University of Medical Sciences, Jahrom, Iran3Research Center for Non\u2010Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran4Sirjan School of Medical Sciences, Sirjan, IranThe authors apologize for this error."} +{"text": "Correction to: Mol Med (2018) 24:51https://doi.org/10.1186/s10020-018-0052-3Following publication of the original article (Gyetvai et al. Correct:1Department of Clinical and Experimental Medicine, Brighton & Sussex Medical School, Brighton BN1 9PS, UK2Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt"} +{"text": "Correction to: BMC Health Serv Res (2020) 20:415https://doi.org/10.1186/s12913-020-05199-1Following the publication of the original article , it was The correct figures have been included in this correction, and the original article has been corrected.The author affiliations need to be revised as below and the original article has been corrected.1, Mackenzie Naert2, Benjamin Andama3, Rae Dong2, David Edelman1, Carol Horowitz2, Peninah Kiptoo3, Simon Manyara3, Winnie Matelong3, Esther Matini3, Violet Naanyu4, Sarah Nyariki3, Sonak Pastakia5, Thomas Valente6, Valentin Fuster2, Gerald S. Bloomfield1, Jemima Kamano4, and Rajesh Vedanthan7*Claudia L. Leung"} +{"text": "Scientific Reports 10.1038/s41598-018-28023-7, published online 25 June 2018Correction to: The original version of this Article contained an error in Affiliation 6, which was incorrectly given as \u2018Department of Internal Medicine and Bioregulatory Science, Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi, Fukuoka, 812-8582, Japan\u2019. The correct affiliation is listed below:Department of Internal Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-8582, Japan.Additionally, in the Supplementary Information file originally published with this Article, Affiliation 2 was incorrectly given as \u2018Department of Medical Science, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku, Tokyo 160-8402, Japan\u2019. The correct affiliation is listed below:Institute of Medical Science, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo, 160-8402, JapanThese errors have now been corrected in the HTML and PDF versions of the article, alongside the Supplementary information file."} +{"text": "Correction to: Pilot Feasibility Stud 6, 170 (2020)https://doi.org/10.1186/s40814-020-00719-6Following publication of the original article , the aut1. School of Psychology, Western Sydney University, Sydney, Australia2. School of Psychiatry, University of New South Wales, Sydney, AustraliaThe original article has been corrected."} +{"text": "In Results, Volume 10, issue 6, e02512-19, 2019,"} +{"text": "Masiello1; Sujata Joshi, MSPH2; Adrian E. Dominguez, MS3; Amy Poel, MPH3; Crisandra M. Wilkie, MPH3; Jonathan M. Bressler, MPH4; Joseph McLaughlin, MD4; Jennifer Kraszewski, MS5; Kenneth K. Komatsu, MPH6; Xandy Peterson Pompa, MPH6; Megan Jespersen, MPH7; Gillian Richardson, MPH7; Nicholas Lehnertz, MD8; Pamela LeMaster, PhD8; Britney Rust, MPH9; Alison Keyser Metobo, MPH10; Brooke Doman, MPH11; David Casey, MA12; Jessica Kumar, DO12; Alyssa L. Rowell, MA12; Tracy K. Miller, PhD13; Mike Mannell, MPH14; Ozair Naqvi, MS14; Aaron M. Wendelboe, PhD14; Richard Leman, MD15; Joshua L. Clayton, PhD16; Bree Barbeau, MPH17; Samantha K. Rice, MPH18; 18Samantha J.H. Rolland, PhD; Victoria Warren-Mears, PhD2; Abigail Echo-Hawk, MA3; Andria Apostolou, PhD19; Michael Landen, MD1.In the report \u201cCOVID-19 Mortality Among American Indian and Alaska Native Persons \u2014 14 States, January\u2013June 2020,\u201d on page 1853, the list of authors should have read \u201cJessica Arrazola, DrPHThe affiliation for Samantha J.H. Rolland is Washington State Department of Health."} +{"text": "Correction to: BMC Psychiatry 20, 200 (2020)https://doi.org/10.1186/s12888-020-02524-0Following publication of the original article , the autRagnar Urheim3, Tom Palmstierna3,2, Knut Rypdal3, Rolf Gjestad3, Mette Senneseth3,43.Centre for Research and Education in Forensic Psychiatry, Haukeland University Hospital, Bergen, Norway4.Western Norway University of Applied SciencesThe author group has been updated above and the original article has been"} +{"text": "Correction: BMC Trials 24, 641 (2023)https://doi.org/10.1186/s13063-023-07636-yFollowing publication of the original article , we haveOriginally published: Pecqueux Mathieu, Distler Marius, Weitz J\u00fcrgen and Kahlert Christoph. Correct name tagging: Mathieu Pecqueux, Marius Distler, J\u00fcrgen Weitz, Christoph KahlertAlso, there were originally five author affiliations declared for authors 1, 2, 3, 6, 7, 8, 9 and 10:1 Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Fetscherstrasse 74, Dresden 01307, Germany. 2 National Center for Tumor Diseases (NCT/UCC), Dresden, Germany. 3 German Cancer Research Center (DKFZ), Heidelberg, Germany. 4 Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Dresden, Germany. 5 Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany.Affiliations 2\u20135 were all condensed under affiliation 2.The original article has been corrected."} +{"text": "Cellular & Molecular Immunology 10.1038/s41423-023-00986-2, published online 01 March 2023Correction to: 1Institute of Immunology, Third Military Medical University, Chongqing, China. 2Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, China. 3Shanghai Public Health Clinical Center, Fudan University, Shanghai, China\u2019 but should have been \u20181Shanghai Public Health Clinical Center, Fudan University, Shanghai, China. 2Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, China. 3Institute of Immunology, Third Military Medical University, Chongqing, China.\u2019 While the author should be accordingly changed from Qiao Liu1,2,3,8, Ling Ran1,8, Zhengliang Yue1,8, Xingxing Su1, Lisha Wang1, Shuqiong Wen4, Shun Lei1, Xiaofan Yang5, Yan Zhang6, Jianjun Hu1, Jianfang Tang1, Zhirong Li1, Li Hu1, Bo Zhu2, Lifan Xu1,*, Lilin Ye1,** and Qizhao Huang7,*** to \u201cQiao Liu1,2,3,8, Ling Ran3,8, Zhengliang Yue3,8, Xingxing Su3, Lisha Wang3, Shuqiong Wen4, Shun Lei3, Xiaofan Yang5, Yan Zhang6, Jianjun Hu3, Jianfang Tang3, Zhirong Li3, Li Hu3, Bo Zhu2, Lifan Xu3,*, Lilin Ye3,** and Qizhao Huang7,***\u201dIn this article, the affiliation details were incorrectly given as \u2018The original article has been corrected."} +{"text": "Cell Death & Differentiation 10.1038/s41418-023-01122-3, published online 04 February 2023Correction to: The original version of this article contained a mistake. When preparing the revised version of this paper the authors omitted a new co-author by mistake. The correct authorship list should be: Zilu Wang1,2; Huimin Hu1,2; Luuk Heitink1,2; Kelly Rogers1,2; Yue Y0u1,2; Tao Tan1,2; Connie Li Wai Suen1,2; Alex Garnham1,2; Hao Chen1,2; Elizabeth Lieschke1,2; Sarah T Diepstraten1,2; Catherine Chang1; Tianwei Chen1,2; Diane Moujalled1,2; Kate Sutherland1,2; Guillaume Lssene1,2,3; Oliver M Sieber1,2; Jane Visvader1,2; Gemma L Kelly1,2,4 and Andreas Strasser1,2,4.1 The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia, 2 Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia3 Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, VIC 3052, Australia4 These authors jointly supervised this work: Gemma LKelly, Andreas Strasser. gkelly@wehi.edu.au; strasser@wehi.edu.auThe original article has been corrected."} +{"text": "Correction to: Stefania et al. Respiratory Research (2023) 24:21710.1186/s12931-023-02516-0Following publication of the original article , the autThe given name and family name of all authors name were erroneously transposed.1\u2020, Castelli Germana1\u2020, Blacon\u00e0 Giovanna2, Bruno Sabina Maria2, Sette Giovanni1, Pigliucci Riccardo1, Villella Valeria Rachela3,4, Esposito Speranza3,4, Zollo Immacolata3,4, Spadaro Francesca5, De Maria Ruggero6,7, Biffoni Mauro1, Cimino Giuseppe8, Amato Felice3,4, Lucarelli Marco2,9\u2020 and Eramo Adriana1*\u2020The incorrect author name is: Lo Cicero Stefania1\u2020, Germana Castelli1\u2020, Giovanna Blacon\u00e02, Sabina Maria Bruno2, Giovanni Sette1, Riccardo Pigliucci1, Valeria Rachela Villella3,4, Speranza Esposito3,4, Immacolata Zollo3,4, Francesca Spadaro5, Ruggero De Maria6,7, Mauro Biffoni1, Giuseppe Cimino8, Felice Amato3,4, Marco Lucarelli2,9 and Adriana Eramo1*The correct author name is: Stefania Lo CiceroThe author group has been updated above and the original article has been"} +{"text": "Correction: BMC Trials 24, 594 (2023)https://doi.org/ 10.1186/s13063-023-07600-wOriginally published affiliations:Following publication of the original article , we haveFiras Abu Akar, MD [1] Giorgio Cannone, MD [2] Mahmoud Ismail, MD [3] Marcelo Jim\u00e9nez, MD [4] Marko Kostic, MD [5] Calvin S.H. Ng, MD [6] Reinhold Perkmann, MD Elena Priscindaro, MD [7] Lorenzo Spaggiari, MD Paula Ugalde, MD [8]1 Department of Cardiothoracic Surgery, Al-Makassed Charitable Society Hospital, East Jerusalem, Palestine.2 Department of Vascular and Thoracic Surgery, Regional Hospital, Bolzano, Italy.3 Klinikum Ernst von Bergmann, Potsdam, Germany.4 Department of Thoracic Surgery, Salamanca University Hospital, Salamanca, Spain.5 Clinic for Thoracic Surgery, University Clinical Center of Serbia, University of Belgrade, Belgrade, Serbia.6 The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.7 Department of Thoracic Surgery, UZ Leuven, Belgium.Corrected affiliations:8 Division of Thoracic and Cardiac Surgery Brigham and Women\u2019s Hospital, Harvard University, USA.Firas Abu Akar, MD [4], Giorgio Cannone, MD [1], Mahmoud Ismail, MD [5], Marcelo Jim\u00e9nez, MD [6], Marko Kostic, MD [7], Calvin S.H. Ng, MD [8], Elena Priscindaro, MD [9], Lorenzo Spaggiari, MD , Reinhold Perkmann, MD [1], Paula Ugalde, MD [11]1 Department of Vascular and Thoracic Surgery, Regional Hospital, Bolzano, Italy.2 Department of Visceral, Thoracic and Vascular Surgery, University of Marburg, Marburg, Germany.3 Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Milan, Italy.4 Department of Cardiothoracic Surgery, Al-Makassed Charitable Society Hospital, East Jerusalem, Palestine.5 Klinikum Ernst von Bergmann, Potsdam, Germany.6 Department of Thoracic Surgery, Salamanca University Hospital, Salamanca, Spain.7 Clinic for Thoracic Surgery, University Clinical Center of Serbia, University of Belgrade, Belgrade, Serbia.8 The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.9 Department of Thoracic Surgery, UZ Leuven, Belgium.10 Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.11 Division of Thoracic and Cardiac Surgery Brigham and Women\u2019s Hospital. Harvard University. USA.The original article has been corrected."} +{"text": "The ORCID iD for Stephan C. Sch\u00fcrer is as follows: 0000-0001-7180-0978The first author, Derek J. Essegian, is incorrectly noted as the corresponding author. The correct corresponding author is Stephan C. Sch\u00fcrer (There are errors in the author affiliations. The correct affiliations are as follows:1, Valery Chavez 2, Rabia Khurshid 1, Jaime R. Merchan 2,3, Stephan C. Sch\u00fcrer *,1,3,4Derek J. Essegian 1 Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL, USA.2 Department of Medicine, University of Miami, Miami, FL, USA.3 Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.4 Institute for Data Science & Computing, University of Miami, Miami, FL, USA."} +{"text": "There is an error in the affiliations for the first author. Specifically, #3 was included in error and should not have been indicated. The correct affiliations are as follows:1,2,3*, Khorshed Alam1,2, Jeff Dunn1,4,5, Jeff Gow1,2,6Rashidul Alam Mahumud1 Health Economics and Policy Research, Centre for Health, Informatics and Economic Research, University of Southern Queensland, Toowoomba, Queensland, Australia, 2 School of Commerce, University of Southern Queensland, Toowoomba, Queensland, Australia, 3 Health and Epidemiology Research, Department of Statistics, Rajshahi, Bangladesh, 4 Cancer Research Centre, Cancer Council Queensland, Fortitude Valley, Queensland, Australia, 5 Prostate Cancer Foundation of Australia, St Leonards, New South Wales, Australia, 6 School of Accounting, Economics and Finance, University of KwaZulu-Natal, Durban, South Africarashed.mahumud@usq.edu.au.Additionally, there was an error in the corresponding author\u2019s listed email addresses. Correspondence regarding this article should only be sent to the following email address:"} +{"text": "In the published article, there was an error in the author list. The corrected author list appears below.Ping Chen 1\u2020, Haolin Song 2\u2020, Wei Xu 3\u2020, Jin Guo4, Jianfei Wang5, Juhong Zhou5, Xiang Kang5, Chaolei Jin6, Yubo Cai7,8,9, Zixuan Feng4, Hainv Gao1, Fengmin Lu10,11*, Lanjuan Li7,8,9*The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.In the published article, there was an error in affiliation(s). Instead of1State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,2National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,3Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,4Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China,5Hepatology Institute, Peking University People\u2019s Hospital, Beijing, China,6Department of Infectious Diseases, Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China,7College of Medicine, Zhejiang University, Hangzhou, China,8College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China,9Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China,10Research and Development Division, Oriomics Biotech Inc, Hangzhou, China,11Infection and Immunity Institute and Translational Medical Center of Huaihe Hospital, Henan University, Kaifeng, China,it should be1Department of Infectious Diseases, Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China,2College of Medicine, Zhejiang University, Hangzhou, China,3College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China,4Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China,5Research and Development Division, Oriomics Biotech Inc, Hangzhou, China,6Infection and Immunity Institute and Translational Medical Center of Huaihe Hospital, Henan University, Kaifeng, China,7State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,8National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,9Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,10Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China,11Hepatology Institute, Peking University People\u2019s Hospital, Beijing, ChinaThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Incorrect Affiliation2Jinhua Prefecture-level Center for Disease Control and Prevention, Jinhua, China, 3Department of TB Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China, 4Department of Immunization Program, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China, 5Department of Public Health Emergency Response, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China, 6Yiwu County-level Center for Disease Control and Prevention, Jinhua, China\u201d, it should be, \u201c2Yiwu County-level Center for Disease Control and Prevention, Jinhua, China, 3Jinhua Prefecture-level Center for Disease Control and Prevention, Jinhua, China, 4Department of TB Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China, 5Department of Immunization Program, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China, 6Department of Public Health Emergency Response, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China\u201d.In the published article, there was an error in affiliations 2, 3, 4, 5, and 6. The affiliations were incorrectly written as, \u201cIncorrect Author Name1\u2020, Liu Shelan1\u2020, Zhu Liebo2\u2020, Wang Fengying2\u2020, Wu Kunyang3, He Hanqing4, Qi Xiaohua5, Pang Zhifeng2, Dong Xuanjun6, Gong Zhenyu1* and Yu Min7*. The correct spellings are Mingyu Luo1\u2020, Shelan Liu1\u2020, Liebo Zhu2\u2020, Fengying Wang3\u2020, Kunyang Wu4, Hanqing He5, Xiaohua Qi6, Zhifeng Pang3, Xuanjun Dong2, Zhenyu Gong1* and Min Yu7*.In the published article, the authors' names were incorrectly written as Luo MingyuThe authors apologize for these errors and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Correction: Journal of Orthopaedic Surgery and Research (2023) 18:368https://doi.org/10.1186/s13018-023-03848-9Following publication of the original article , the aut1+, Xiuyu Qin2+, Jiani Wang3, Wangzhe Yang2, Junjun Bai2, Jia Lv2*Jian Li1Department of Orthopaedics, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China2Department of Orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, China3Department of Paediatric Medicine, Shanxi Medical University, Taiyuan, 030001, ChinaThe original article has been corrected."} +{"text": "Leukemia 10.1038/s41375-022-01620-2, published online 22 June 2022Correction to: Dr Ritsuro Suzuki, Department of Hematology & Oncology, Shimane University School of Medicine, Shimane, Japan, was regrettably omitted from the main author list;Dr Arianna Di Napoli, Department of Clinical and Molecular Medicine, Sapienza University, School of Medicine and Psychology, Sant\u2019Andrea Hospital, Rome, Italy, was incorrectly included as a contributor in the author contribution list, and instead should be a coauthor in the main author list;Dr Luis M. Allende, a contributor in the author contribution list, was assigned with an incorrect affiliation, and the correct affiliation is 70 Immunology Department, Hospital 12 de Octubre, imas12, Madrid, Spain;Dr Aanchal Kakkar, a contributor in the author contribution list, was assigned with an incorrect affiliation, and the correct affiliation is Pathology, All India Institute of Medical Sciences, New Delhi, India.At the time of original publication, there was an incomplete listing of contributing authors and their institutions. This revision corrects those omissions.The above errors have been corrected, and the corrected list of the authors and contributors and their affiliations are as follows.1, Catalina Amador2, Ioannis Anagnostopoulos3, Ayoma D. Attygalle4, Iguaracyra Barreto de Oliveira Araujo5, Emilio Berti6, Govind Bhagat7, Anita Maria Borges8, Daniel Boyer9, Mariarita Calaminici10, Amy Chadburn11, John K.C. Chan12, Wah Cheuk12, Wee-Joo Chng13, John K. Choi14, Shih-Sung Chuang15, Sarah E. Coupland16, Magdalena Czader17, Sandeep S. Dave18, Daphne de Jong19, Arianna Di Napoli,20 Ming-Qing Du21*, Kojo S. Elenitoba-Johnson22, Judith Ferry23*, Julia Geyer11, Dita Gratzinger24, Joan Guitart25, Sumeet Gujral26, Marian Harris27, Christine J. Harrison28, Sylvia Hartmann29, Andreas Hochhaus30, Patty M. Jansen31, Kennosuke Karube32, Werner Kempf33, Joseph Khoury34, Hiroshi Kimura35, Wolfram Klapper36, Alexandra E. Kovach37, Shaji Kumar38, Alexander J. Lazar39, Stefano Lazzi40, Lorenzo Leoncini40, Nelson Leung41, Vasiliki Leventaki42, Xiao-Qiu Li43, Megan S. Lim22, Wei-Ping Liu44, Abner Louissaint Jr.23, Andrea Marcogliese45, L. Jeffrey Medeiros34, Michael Michal46, Roberto N. Miranda34, Christina Mitteldorf47, Santiago Montes-Moreno48, William Morice49, Valentina Nardi23, Kikkeri N. Naresh50, Yasodha Natkunam24, Siok-Bian Ng51, Ilske Oschlies36, German Ott52*, Marie Parrens53, Melissa Pulitzer54, S. Vincent Rajkumar55, Andrew C. Rawstron56, Karen Rech49, Andreas Rosenwald3, Jonathan Said57, Cl\u00e9mentine Sarkozy58, Shahin Sayed59, Caner Saygin60, Anna Schuh61, William Sewell62, Reiner Siebert63*, Aliyah R. Sohani23, Ritsuro Suzuki64, Reuben Tooze65, Alexandra Traverse-Glehen66, Francisco Vega34, Beatrice Vergier67, Ashutosh D. Wechalekar68, Brent Wood37, Luc Xerri69, Wenbin Xiao54Rita Alaggio1Pathology Unit, Department of Laboratories, Bambino Gesu Children\u2019s Hospital, IRCCS, Rome, Italy;2Department of Pathology, University of Miami, Miami, FL, USA;3Institute of Pathology, Julius-Maximilians-Universit\u00e4t W\u00fcrzburg, W\u00fcrzburg, Germany;4Department of Histopathology, Royal Marsden Hospital, London, UK;5Department of Pathology, Federal University of Bahia (UFBA), Salvador, Brazil;6University of Milan, Fondazione C\u00e0 Granda, IRCCS, Ospedale Maggiore Policlinico, Milan, Italy;7Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA;8Division of Histopathology, SL Raheja Hospital, Mumbai, India;9Department of Pathology, University of Michigan, Ann Arbor, MI, USA;10Centre for Haemato-Oncology, Barts Cancer institute, QMUL and SIHMDS Barts Health NHS Trust, London, UK;11Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA;12Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong;13National University Cancer Institute, Singapore, Singapore;14Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA15Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan;16Liverpool Clinical Laboratories, Liverpool University Hospitals Foundation Trust, Liverpool, UK;17Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA;18Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, NC, USA19Amsterdam UMC, location Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands;20Department of Clinical and Molecular Medicine, Sapienza University, School of Medicine and Psychology, Sant\u2019 Andrea Hospital, Rome, Italy;21Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK;22Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA;23Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA;24Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA;25Department. of Dermatology, Northwestern University Feinberg Medical School, Chicago, IL, USA;26Department of Pathology, Tata Memorial Hospital, Mumbai, India;27Department of Pathology, Boston Children\u2019s Hospital, Boston, MA, USA;28Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK;29Dr. Senckenberg Institute of Pathology, Goethe University Frankfurt, Frankfurt am Main, Germany;30Hematology/Oncology, Universit\u00e4tsklinikum Jena, Jena, Germany;31Leiden University Medical Center, Department of Pathology, Leiden, The Netherlands;32Department of Pathology and Laboratory Medicine, Nagoya, Japan;33Kempf und Pfaltz Histologische Diagnostik Zurich, and Department of Dermatology, University Hospital Zurich, Zurich, Switzerland;34Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;35Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan;36Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, University of Kiel, Kiel, Germany;37Department of Pathology and Laboratory Medicine, Children\u2019s Hospital Los Angeles, Los Angeles, CA, USA;38Division of Hematology, Mayo Clinic, Rochester, MN, USA;39Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;40Department of Medical Biotechnology, University of Siena, Siena, Italy;41Division of Nephrology and Hypertension, Division of Hematology, Mayo Clinic, Rochester, MN, USA;42Department of Pathology, Medical College of Wisconsin and Children\u2019s Wisconsin, Milwaukee, WI, USA;43Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, PR China;44Department of Pathology, West-China Hospital, Sichuan University, Chengdu, PR China;45Department of Pathology & Immunology, Baylor College of Medicine and Texas Children\u2019s Hospital, Houston, TX, USA;46Department of Pathology, Charles University in Prague, Faculty of Medicine in Plzen, Plzen, Czech Republic;47Department of Dermatology, Venereology and Allergology, University Medical Center G\u00f6ttingen, G\u00f6ttingen, Germany;48Anatomic Pathology Department and Translational Hematopathology Lab, Valdecilla/IDIVAL University Hospital, Santander, Spain;49Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA;50Section of Pathology, Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA;51Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore;52Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany;53Department of Pathology, Bordeaux University Hospital, Bordeaux, France;54Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA;55Division of Hematology, Mayo Clinic, Rochester, Minnesota, Rochester, MN, USA;56HMDS, Leeds Cancer Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK;57Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA;58Institut Curie, Hematology department, Saint Cloud, France;59Department of Pathology\u2014Aga Khan University Hospital\u2014Nairobi, Nairobi, Kenya;60Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA;61Department of Oncology, University of Oxford, Oxford, UK;62Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, Australia;63Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany;64Department of Hematology & Oncology, Shimane University School of Medicine, Shimane, Japan;65Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK;66Hospices Civils de Lyon/Department of Pathology/Universit\u00e9 Lyon 1/Centre International de Recherche en Infectiologie (CIRI) INSERM U1111\u2014CNRS UMR5308, Lyon, France;67Department of Pathology, Hopital Haut-L\u00e9v\u00eaque, CHU Bordeaux, Pessac, France;68National Amyloidosis Centre, University College London, London, UK;69Department of Pathology, Institut Paoli-Calmettes and Aix-Marseille University, Marseille, France;AUTHOR CONTRIBUTIONSJK and AJL are standing members of the WHO Classification of Tumours editorial board. RA, JKCC, WJC, SEC, SSD, DDJ, MQD, JF, SG, AH, MSL, KNN, GO, SS, AS, WS, RSi and BW are expert members of the Haematolymphoid Tumours 5th edition blue book editorial board. CA, IA, ADA, IBOA, EB, GB, AMB, DB, MC, AC, WC, JKC, SSC, MC, AND, KSEJ, JG, DG, JG, MH, CJH, SH, PMJ, KK, WK, HK, WK, AEK, SK, SL, LL, NL, VL,XQL, WPL, ALj, AM, LJM, MM, RNM, CM, SMM, WM, VN, YN, SBN, IO, MP, MP, SVJ, ACR, KR, AR, JS, CS, CS, ARS, RSu, RT, ATG, FV, BV, ADW, LX and WX contributed as responsible authors in the book. All authors and editors contributed to discussions on the content of the book chapters. All listed authors edited and approved the manuscript.The following colleagues are acknowledged for their expert contributions as authors in the WHO Classification of Haematolymphoid Tumours blue book on lymphoid topics, mesenchymal lesions specific to lymph node and spleen, and germline predisposition syndromes associated with the lymphoid neoplasms. Their affiliations were provided as given in the International Agency for Research on Cancer (IARC) databases. Where authors are identified as personnel of IARC/World Health Organization, the authors alone are responsible for the views expressed in this article, and they do not necessarily represent the decisions, policy, or views of the International Agency for Research on Cancer/World Health Organization.70, Yassmine Akkari71, Luis M. Allende72, Katsuyuki Aozasa73, Iguaracyra Araujo74, Luca Arcaini75, Kirit M. Ardeshna76, Naoko Asano77, Andishe Attarbaschi78, Chris M. Bacon28, Sharon Louise Barrans56, Tracy Batchelor79, Maxime Battistella80, Linda B. Baughn49, Amir Behdad81, Sigbj\u00f8rn Berentsen82, Giada Bianchi83, Jacob Bledsoe27, Peter Borchmann84, Mark Bower85, Barbara Buldini86, Jan Andreas Burger87, Birgit Burkhardt88, Ryan D. Cassaday89, Giovanni Cazzaniga90, Nadine Cerf-Bensussan91, Ethel Cesarman11, Mammen Chandy92, Jennifer R. Chapman93, Bj\u00f6rn Chapuy94, Xueyan Chen95, Chee Leong Cheng96, Carlos Chiattone97, Nicholas Chiorazzi98, Lucy B. Cook99, Wendy A. Cooper100, Gregory Philip Corboy101, Andrew John Cowan89, Immacolata Cozzolino102, Ian A Cree103, Emanuele S.G. d\u2019Amore104, Andrew John Davies105, Martina Deckert106, Jan Delabie107, Elizabeth G. Demicco107, Vikram Deshpande23, Arjan Diepstra108, Daan Dierickx109, Kieron Dunleavy110, Barbara Eichhorst111, Daisuke Ennishi112, David C. Fajgenbaum113, Pedro Farinha114, Carlos Fern\u00e1ndez de Larrea115, Kevin E. Fisher45, Jude Fitzgibbon116, Melina Flanagan117, Jonathan Fromm95, Juan F. Garcia118, William Robert Geddie107, Morie Gertz38, Ajay Gopal89, Satish Gopal119, Patricia Theresa Greipp49, Alejandro Gru120, Ritu Gupta121, Martin-Leo Hansmann122, Konnie M. Hebeda123, Klaus Herfarth124, Marco Herling125, Olivier Hermine126, Khe Hoang-Xuan127, Jennelle Hodge128, Shimin Hu34, Yuhua Huang129, Yin Pun Hung23, Stephen Hunger130, Hiroto Inaba131, Hiroshi Inagaki132, Javeed Iqbal133, Kenji Ishitsuka134, Noriko Iwaki135, Keiji Iwatsuki136, Nitin Jain87, Yoon Kyung Jeon137, Marshall Kadin138, Sachiko Kaji139, Aanchal Kakkar121, Anastasios Karadimitris140, Keisuke Kataoka141, Seiichi Kato142, Marie Jos\u00e9 Kersten143, Rhett P. Ketterling49, Ji Eun Kim144, Christian P. Kratz145, Robert Kridel146, Sigurdur Kristinsson147, Ralf K\u00fcppers148, Isinsu Kuzu149, Yok-Lam Kwong150, Ann Lacasce151, Laurence Lamant-Rochaix152, Thierry Lamy153, Ola Landgren154, Siddhartha Laskar155, William Bradlyn Laskin156, Georg Lenz157, Shaoying Li34, Gan Di Li44, Pei Lin34, Franco Locatelli158, Robert Brian Lorsbach159, Izidore Lossos154, Thomas P. Jr Loughran160, William R. Macon49, Joseph J. Maleszewski49, Pankaj Malhotra161, Teresa Marafioti162, Dai Maruyama163, Alexander Marx164, Sam M. Mbulaiteye165, Veronique Meignin80, Ester Mejstrikova166, Pamela Michelow167, Markku Miettinen168, Rodney R. Miles169, Hiroaki Miyoshi170, Thierry Jo Molina171, Manuela Mollejo172, Shuji Momose173, Tetsuya Mori174, William G. Morice49, Bertrand Nadel175, Hirokazu Nagai176, Motoo Nagane177, Reena Nair92, Naoya Nakamura178, Atsuko Nakazawa179, Samih Nasr49, Andrew Gordon Nicholson180, Alina Nicolae181, Robert Shigeo Ohgami182, Naoki Oishi183, Timothy S. Olson130, Nicolas Ortonne184, Bruno Paiva185, Qiang Pan-Hammarstr\u00f6m186, Mayur Parihar187, Marco Paulli188, Andrea Petersen189, Jennifer Picarsic190, Alessandro Pileri191, Nicola Pimpinelli192, Jose A Plaza193, Karen R. Rabin194, Markus Raderer195, Kanti Rai196, Ulla Randen197, Huilan Rao129, Alistair Robson198, Rosemary Rochford199, Richard Rosenquist200, Davide Rossi201, Esther D. Rossi202, Simon Rule203, Grzegorz Rymkiewicz204, Elena Sabattini205, Vaskar Saha206, Mamiko Sakata-Yanagimoto207, Christian A. Sander208, J. Martin Sangueza209, Omar P. Sang\u00fceza210, Marco Santucci211, Yasuharu Sato212, Akira Satou142, Kristian Theo Schafernak213, Fernando Schmitt214, Gianpietro Semenzato215, Manju Sengar92, Tait Shanafelt216, Kazuyuki Shimada217, Graham W. Slack114, Susan Slager218, Riccardo Soffietti219, David A. Solomon182, Kostas Stamatopoulos220, Christian Steidl221, Stephan Stilgenbauer222, Narittee Sukswai223, Kengo Takeuchi224, Giovanni Tallini225, Junichi Tamaru226, Soo-Yong Tan51, Prashant Tembhare227, Enrico Tiacci228, Yoshiki Tokura229, Olivier Tournilhac230, Steven Treon231, Lorenz Truemper232, Kunihiro Tsukasaki233, Frits van Rhee234, Abraham Varghese235, Maarten H. Vermeer236, Philippe Vielh237, Brian Walker238, Michael Wang239, Huan-You Wang240, Zhe Wang241, Takashi Watanabe242, Oliver Weigert243, David Weinstock244, Sean J. Whittaker245, Rein Willemze236, Wilhelm Woessmann246, Catherine J. Wu244, Motoko Yamaguchi247, Hidetaka Yamamoto248, Daisuke Yamashita249, Shenmiao Yang250, David T Yang251, Takahiko Yasuda252, Wei-Hua Yin253, Yoh Zen254, Sha Zhao44, Wei-Li Zhao255Norah Olubunmi Akinola70Haematology and Immunology, Obafemi Awolowo University, Ile Ife, Nigeria;71Cytogenetics and Molecular Pathology, Legacy Health, Portland, OR, USA;72Immunology Department, Hospital 12 de Octubre, imas12, Madrid, Spain;73Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan;74Pathology and Forensic Medicine, Federal University of Bahia, Salvador, Bahia, Brazil;75Fondazione IRCCS Policlinico San Matteo and Departement of Molecular Medicine, University of Pavia, University of Pavia, Pavia, Italy;76Cancer Division, University College London Hospitals, London, UK;77Molecular Diagnostics, Nagano Prefectural Shinshu Medical Center, Suzaka, Japan;78Pediatric Hematology and Oncology, St. Anna Children\u2019s Hospital, Vienna, Austria;79Department of Neurology, Brigham and Women\u2019s Hospital, Boston MA, USA;80Pathology Department, H\u00f4pital Saint Louis, AP-HP Universit\u00e9 Paris, Paris, France;81Department of Pathology, Northwestern University, Chicago, IL, USA;82Department of Research and Innovation, Helse Fonna Hospital Trust, Haugesund, Norway;83Division of Hematology, Department of Medicine, Brigham and Women\u2019s Hospital, Boston MA, USA;841st Dept of Internal Medicine, University Hospital of Cologne, Cologne, Germany;85National Centre for HIV Malignancy, Chelsea & Westminster Hospital, London, UK;86Maternal and Child\u2019s Health Department, University of Padova, Padova, Italy;87Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;88Pediatric Hematology, Oncology and BMT, University Hospital Muenster, Muenster, Germany;89Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA;90Pediatrics and Medical Genetics, Univ Milan Bicocca\u2014Centro Ricerca Tettamanti, Barzano, Italy;91Laboratory Intestinal Immunity, Institut Imagine-Inserm U1183, Universit\u00e9 de Paris, Paris, France;92Clinical Hematology & Medical Oncology, Tata Medical Center, Kolkata, India;93Pathology and Laboratory Medicine, University of Miami, Miami, FL, USA;94Hematology, Oncology and Tumor Immunology, Charit\u00e9, University Medical Center Berlin, Berlin, Germany;95Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA;96Anatomical Pathology, Singapore General Hospital, Singapore, Singapore;97Hematology and Oncology, Santa Casa Midical School, Sao Paulo, Brazil;98Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, Manhasset, NY, USA;99Department of Haematology, Imperial College Healthcare NHS Trust, London, UK;100Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, NSW Health Pathology, Camperdown, NSW, Australia;101Department of Haematology, Pathology Queensland, Herston, QLD, Australia;102Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania \u201cL. Vanvitelli\u201d, Naples, Italy103Evidence Synthesis and Classification Branch, International Agency for Research on Cancer, Lyon, France;104UOC di Anatomia Patologica, Ospedale San Bortolo, Vicenza, Italy;105Cancer Sciences Unit, University of Southampton, Southampton, UK;106Department of Neuropathology, University Hospital of Cologne, Cologne, Germany;107Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, ON, Canada;108Pathology and Laboratory Medicine, University Medical Center Groningen, Groningen, The Netherlands;109Department of Hematology, University Hospitals Leuven, Leuven, Belgium;110Hematology and Oncology, Lombardi Cancer Center, Georgetown University, Washington, DC, USA;111Department I for Internal Medicine and Center for Integrated Oncology Aachen, Bonn, Cologne, Duesseldorf, University of Cologne, Cologne, Germany;112Department of Hematology and Oncology, Okayama University Hospital, Okayama, Japan;113Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA;114Department of Pathology, BC Cancer Agency, Vancouver, BC, Canada;115Amyloidosis and Myeloma Unit, Department of Hematology, Hospital Cl\u00ednic of Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain;116Genomics and Computational Biology, Queen Mary University of London, London, UK;117Department of Pathology, West Virginia University School of Medicine, Morgantown, WV, USA;118Department of Pathology, MD Anderson Cancer Center Madrid, Madrid, Spain;119Center for Global Health, National Cancer Institute, Rockville, MD, USA;120Pathology & Dermatology, University of Virginia, Charlottesville, VA, USA;121Laboratory Oncology, All India Institute of Medical Sciences, Delhi, New Delhi, India;122Consultation Center for Hematopathology, Institute of Pathology and Molecular Pathology, Wuppertal, Germany;123Department of Pathology, The Radboud University Medical Center, Nijmegen, The Netherlands;124Radiation Oncology, University Hospital Heidelberg, Heidelberg, Germany;125Hematology, Cellular Therapy, Hemostaseology, University of Leipzig, Leipzig, Germany;126Hematology and Laboratory of Physiopathology and Treatment of Hematological Disorders, Necker Hospital, APHP, INSERM U1163, Imagine, Paris University, Paris, France;127Neuro-oncology, H\u00f4pital Universitaire Piti\u00e9 Salp\u00eatri\u00e8re, Paris, France;128Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA;129Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China;130Division of Oncology, Department of Pediatrics, Children\u2019s Hospital of Philadelphia, Philadelphia, PA, USA;131Department of Oncology, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA;132Department of Pathology and Molecular Diagnostics, Nagoya City University, Nagoya, Japan;133Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA;134Department of Hematology and Rheumatology, Kagoshima University, Kagoshima, Japan;135Department of Hematology, National Cancer Center Hospital, Tsukiji, Chuo-ku, Tokyo, Japan;136Departments of Dermatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan;137Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea;138Department of Pathology and Laboratory Medicine, Brown University Alpert School of Medicine, Providence, RI, USA;139Department of Pathology, Japanese Red Cross Narita Hospital, Narita, Chiba, Japan;140Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK;141Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan;142Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan;143Department of Hematology, Amsterdam University Medical Centers, Amsterdam, The Netherlands;144Department of Pathology, Seoul National University SNU SMG Boramae Hospital, Seoul, South Korea;145Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany;146Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre\u2014UHN, Toronto, ON, Canada;147Faculty of Medicine, University of Iceland, Reykjavik, Iceland;148Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany;149Department of Pathology, University of Ankara, School of Medicine, Ankara, Turkey;150Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong;151Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA;152Departement of Pathology, Institut Universitaire du cancer Toulouse Oncopole, Toulouse, France;153Department of Hematology, Rennes University Hospital, Rennes, France;154Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA;155Radiation Oncology, Tata Memorial Centre, Mumbai, India;156Department of Pathology, Yale School of Medicine, New Haven, CT, USA;157Department of Hematology, Oncology and Pneumology, University Hospital M\u00fcnster, M\u00fcnster, Germany;158Pediatric Hematology/Oncology, Cell and Gene Therapy, Bambino Ges\u00f9 Children\u2019s Hospital, Rome, Italy;159Division of Pathology, Cincinnati Children\u2019s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA;160Hematology/Oncology, University of Virginia, Charlottesville, VA, USA;161Clinical Hematology and Medical Oncology, Postgraduate Institute of Medical Education and Research, Chandigarh, India;162Department of Cellular Pathology, University College Hospital London, London, UK;163Hematology Oncology, Cancer Institute Hospital of Japanese Foundation of Cancer Research, Tokyo, Japan;164Department of Pathology, University Medical Centre Mannheim, Mannheim, Germany;165Infections and Immunoepidemiology Branch, DCEG, National Cancer Institute, Rockville, MD, USA;166Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, University Hospital Motol, Prague, The Czech Republic;167Department of Anatomical Pathology, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa;168Laboratory of Pathology, National Cancer Institute/NIH, Bethesda, MD, USA;169Department of Pathology, University of Utah, Salt Lake City, UT, USA;170Department of Pathology, Kurume University, School of Medicine, Kurume, Japan;171Department of Pathology, AP-HP, H\u00f4pital Necker-Enfants Malades and Robert Debr\u00e9, Universit\u00e9 de Paris, Paris, France;172Department of Pathology, Hospital Universitario de Toledo, Toledo, Spain;173Department of Pathology, Saitama Medical University, Saitama Medical Center, Kawagoe, Japan;174Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan;175Centre d\u2019Immunologie de Marseille-Luminy, Inserm CNRS AMU, Marseille, France;176Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan;177Department of Neurosurgery, Kyorin University Faculty of Medicine, Tokyo, Japan;178Department of Pathology, Tokai University School of Medicine, Isehara, Japan;179Clinical Research, Saitama Children\u2019s Medical Center, Saitama, Japan;180Department of Histopathology, Royal Brompton & Harefield NHS Foundation Trust, London, UK;181Department of Pathology, Hautepierre, University Hospital Strasbourg, Strasbourg, France;182Department of Pathology, University of California San Francisco, San Francisco, CA, USA;183Department of Pathology, University of Yamanashi, Chuo, Yamanashi, Japan;184Department of Pathology, AP-HP, Hopitaux Universitaires Henri-Mondor, Creteil, France;185Hemato-Oncology, Clinica Universidad de Navarra, Pamplona, Spain;186Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden;187Lab Haematology/Cytogenetics & Molecular Genetics, Tata Medical Center, Kolkata, India;188Pathology Unit, Department of Molecular Medicine, University of Pavia, Pavia, Italy;189Pediatric Development and Rehab, Genetics Division, Legacy Health/Randall Children\u2019s Hospital and Washington State University Elson S. Floyd College of Medicine, Portland, OR, USA;190Department of Pathology, Cincinnati Childrens Hospital Medical Center, Cincinnati, OH, USA;191Experimental, Diagnostic and Specialty Medicine Department, Dermatology Unit, Bologna, Italy;192Health Sciences, University of Florence Medical School, Florence, Italy;193Pathology and Dermatology, The Ohio State University Medical Center, Columbus, OH, USA;194Baylor College of Medicine, Texas Children\u2019s Cancer Center, Houston, TX, USA;195Internal Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria;196Department of Medicine, Northwell Health Cancer Institute, New Hyde Park, NY, USA;197Department of Pathology, Akershus University Hospital/University of Oslo, L\u00f8renskog, Norway;198Departamento de Diagnostico Laboratorial, IPOLFG\u2014Servico de Anatomia Patologica, Lisboa, Portugal;199Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA;200Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden;201Department of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland;202Department of Anatomic Pathology and Histology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy;203Department of Haematology, Plymouth University Medical School, Plymouth, UK;204Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland;205Haematopathology, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy;206Paediatric Haematology and Oncology, Tata Translational Cancer Research Centre, Kolkata, India;207Department of Hematology, University of Tsukuba, Ibaraki, Japan;208Department of Dermatology, Asklepios Klinik St. Georg, Hamburg, Germany;209Pathology and Dermatology, Hospital Obrero Nro 1 CNS, Hospital General, La Paz, Spain;210Dept of Pathology and Dermatology, Wake Forest University, School of Medicine Medical Center Boulevard, Winston-Salem, NC, USA;211Department of Health Sciences, Division of Histopathology and Molecular Diagnostics, University of Florence School of Human Health Sciences, Firenze, Italy;212Department of Pathology, Okayama University Graduate School of Health Sciences, Okayama, Japan;213Pathology and Laboratory Medicine, Phoenix Children\u2019s Hospital, Phoenix, AZ, USA;214Molecular Pathology Unit, Medical Faculty, Porto University, Porto, Portugal;215Department of Hematology, Veneto Institute of Molecular Medicine, University of Padua, Padova, Italy;216Department of Medicine, Division of Hematology, Stanford University, Palo Alto, CA, USA;217Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan;218Medicine and Quality Health Sciences, Mayo Clinic, Rochester, MN, USA;219Department of Neuro-Oncology, University of Turin and City of Health and Science Hospital, Turin, Italy;220Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece;221Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada;222Comprehensive Cancer Center Ulm (CCCU), Ulm University, Ulm, Germany;223Department of Pathology, Chulalongkorn University, Bangkok, Thailand;224Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan;225Department of Pathology, Policlinico S.Orsola-Malpighi, Bologna, Italy;226Pathology, Biomedical and Sciences, Saitama Medical Center, Saitama Medical University, Kawagoe, Japan;227Hematopathology Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India;228Department of Medicine and Surgery, Institute of Hematology and Center for Hemato-Oncology Research, Perugia, Italy;229Allergic Disease Research Center, Chutoen General Medical Center, Kakegawa, Japan;230Hematology and Cell Therapy, CHU de Clermont-Ferrand, Clermont-Ferrand, France;231Department of Medicine, Harvard Medical School, Boston, MA, USA;232Hematology and Medical Oncology, Universit\u00e4tsmedizin G\u00f6ttingen, G\u00f6ttingen, Germany;233Department of Hematology, International Medical Center, Saitama Medical University, Hidaka, Japan;234Myeloma Center, UAMS Winthrop P. Rockefeller Cancer Institute, Little Rock, AR, USA;235Department of Haematology, Little Flower Hospital and Research Centre, Angamaly, India;236Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands;237Department of Pathology, Medipath and American Hospital of Paris, Paris, France;238Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA;239Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA;240Department of Pathology, University of California San Diego, San Diego, CA, USA;241Department of Pathology, Fourth Military Medical University, Xi\u2019an, PR China;242Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Japan;243Medical Department III, Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany;244Medical Oncology, Dana-Farber Cancer Institute and Havard Medical School, Boston, MA, USA;245School of Basic and Medical Biosciences KCL, St. John\u2019s Institute of Dermatology, London, UK;246Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;247Department of Hematological Malignancies, Mie University Graduate School of Medicine, Tsu, Japan;248Anatomic Pathology, Kyushu University, Fukuoka, Japan;249Department of Pathology, Kobe City Medical Center General Hospital, Kobe, Japan;250Department of Hematology, Peking University Peoples\u2019 Hospital, Peking Institute of Hematology, Beijing, PR China;251Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA;252Advanced Diagnosis, Nagoya Medical Center, Nagoya, Japan;253Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, PR China;254Institute of Liver Studies, King\u2019s College Hospital, London, UK;255National Center of Translational Medicine, Institute of Hematology, Shanghai, PR China."} +{"text": "Food Science and Nutrition, 11, 3621\u20133630. https://doi.org/10.1002/fsn3.3360Imran, A., Shehzadi, U., Islam, F., Afzaal, M., Ali, R., Ali, Y. A., Chauhan, A., Biswas, S., Khurshid, S., Usman, I., Hussain, G., Zahra, S. M., Shah, M. A., & Rasool, A. (2023). Bacteriophages and food safety: An updated overview. The following affiliations were erroneously missing for Mohd Asif Shah: School of Business, Woxsen University, Kamkole, Sadasivpet, Hyderabad, Telangana, India; Division of Research and Development, Lovely Professional University, Phagwara, Punjab, India; and School of Engineering and Technology, Sharda University, Greater Noida, India.The corrected affiliations appear here:1 | Umber Shehzadi1 | Fakhar Islam1,2 | Muhammad Afzaal1 | Rehman Ali1 | Yuosra Amer Ali3 | Anamika Chauhan4,5 | Sunanda Biswas6 | Sadaf Khurshid1 | Ifrah Usman1 | Ghulam Hussain7 | Syeda Mahvish Zahra8,9 | Mohd Asif Shah10,11,12 | Adil Rasool13Ali Imran1Department of Food Sciences, Government College University, Faisalabad, Pakistan2Department of Clinical Nutrition, NUR International University, Lahore, Pakistan3Department of Food Sciences, College of Agriculture and Forestry, University of Mosul, Mosul, Iraq4Department of Home Science, Chaman Lal Mahavidyalaya Landhora, Haridwar, India5Sri Dev Suman University, Tehri, India6Department of Food & Nutrition, Acharya Prafulla Chandra College, Kolkata, India7Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan8Department of Environmental Design, Health and Nutritional Sciences, Allama Iqbal Open University, Islamabad, Pakistan9Institute of Food Science and Nutrition, University of Sargodha, Sargodha, Pakistan10University Centre for Research & Development, University School of Business, Chandigarh University, Gharuan, Mohali, Punjab, India11School of Business, Woxsen University, Kamkole, Sadasivpet, Hyderabad, Telangana, India12Division of Research and Development, Lovely Professional University, Phagwara, Punjab, India13Department of Management, Bakhtar University, Kabul, Afghanistan"} +{"text": "Scientific Reportshttps://doi.org/10.1038/s41598-023-32271-7, published online 30 March 2023Correction to: The original version of this Article contained errors in the Affiliations.Affiliation 2 was incorrectly given as \u2018Medical Imaging, Physics and Technology, University of Oulu, 90029 Oulu, Finland\u2019. The correct affiliation is listed below.Diagnostics, Medical Research Center, Oulu University Hospital, 90029 Oulu, Finland.Affiliation 7 was incorrectly given as \u2018MRC, Oulu University Hospital, 90029 Oulu, Finland\u2019. The correct affiliation is listed below.Biocenter Oulu, University of Oulu, 90014 Oulu, Finland.Additionally, affiliation 3 was omitted from Zalan Rajna and affiliations 3 and 7 were omitted from Vesa Kiviniemi.Finally, Janne Kananen was incorrectly affiliated with \u2018Clinical Neurophysiology, Oulu University Hospital, 90029 OYS, Oulu, Finland\u2019 and Johanna Annunen and Hanna Ansakorpi were incorrectly affiliated with \u2018Research Unit of Clinical Neuroscience, Neurology, University of Oulu, 90029 Oulu, Finland.\u2019The corrected affiliations are as follows:1,3*, Mia Suhonen2,3*, Zalan Rajna1,3, Youssef Hosni1,3, Janne Kananen2,3,4, Johanna Annunen5,6, Hanna Ansakorpi5, Vesa Korhonen2,3, Tapio Sepp\u00e4nen1, Vesa Kiviniemi2,3,7*Ahmed Elabasy1Center for Machine Vision and Signal Analysis, University of Oulu, 90014 Oulu, Finland.2Diagnostics, Medical Research Center, Oulu University Hospital, 90029 Oulu, Finland.3Oulu Functional NeuroImaging, Research Unit of Health Science and Technology, University of Oulu, 90029 Oulu, Finland.4Clinical Neurophysiology, Research Unit of Health Science and Technology, University of Oulu, 90029 Oulu, Finland.5Research Unit of Clinical Neuroscience, Neurology, University of Oulu, 90029 Oulu, Finland.6Neurocenter (Member of ERN EpiCARE), Medical Research Center, Oulu University Hospital, 90029 Oulu, Finland.7Biocenter Oulu, University of Oulu, 90014 Oulu, Finland.The original Article has been corrected."} +{"text": "JAMIA Open, Volume 6, Issue 2, July 2023, https://doi.org/10.1093/jamiaopen/ooad025This is a correction to: Roberto Casale and others, Predicting risk of metastases and recurrence in soft-tissue sarcomas via Radiomics and Formal Methods, 1, Giulia Varriano2, Antonella Santone2, Carmelo Messina3,5, Chiara Casale4, Salvatore Gitto3,5, Luca Maria Sconfienza3,5, Maria Antonietta Bali1, and Luca Brunese2\u201d instead of: \u201cRoberto Casale1, Giulia Varriano2, Antonella Santone2, Carmelo Messina3, Chiara Casale4, Salvatore Gitto5, Luca Maria Sconfienza5, Maria Antonietta Bali1, and Luca Brunese2\u201d.In the originally published version of this manuscript, affiliations were incomplete\u00a0for the fourth, sixth and seventh authors. These should read: \u201cRoberto CasaleThe emendations have been made in the article."} +{"text": "There is an error in the affiliations for the first author. Specifically, #3 was included in error and should not have been indicated. The correct affiliations are as follows:1,2,3,4*, Khorshed Alam1,2, Syed Afroz Keramat1,2,5, Gail M. Ormsby6, Jeff Dunn1,7,8, Jeff Gow1,2,9Rashidul Alam Mahumud1 Health Economics and Policy Research, Centre for Health Research, University of Southern Queensland, Toowoomba, Queensland, Australia, 2 School of Commerce, University of Southern Queensland, Toowoomba, Queensland, Australia, 3 School of Social Sciences, Western Sydney University, Penrith, Australia, 4 Translational Health Research Institute, Western Sydney University, Penrith, Australia, 5 Economics Discipline, School of Social Science, University of Khulna, Khulna, Bangladesh, 6 School of Health and Wellbeing, University of Southern Queensland, Toowoomba, Queensland, Australia, 7 Cancer Research Centre, Cancer Council Queensland, Fortitude Valley, Queensland, Australia, 8 Prostate Cancer Foundation of Australia, St Leonards, NSW, Australia, 9 School of Accounting, Economics and Finance, University of KwaZulu-Natal, Durban, South Africarashed.mahumud@usq.edu.au.Additionally, there was an error in the corresponding author\u2019s listed email addresses. Correspondence regarding this article should only be sent to the following email address:"} +{"text": "DOI: 10.20945/2359-3997000000126Arch Endocrinol Metab. 2019;63(2):121-7Where you read:1, A. Seval Ozgu-Erdinc1, Burcu Kisa1, Rahime Bedir Findik1, Canan Yilmaz1, Yasemin Tasci1Hatice Kansu-Celik1 University of Health Sciences, Zekai Tahir Burak Health Practice Research Center, Ankara, TurkeyShould read:1, A. Seval Ozgu-Erdinc1, Burcu Kisa1, Rahime Bedir Findik1, Canan Yilmaz2, Yasemin Tasci1Hatice Kansu-Celik1 University of Health Sciences, Zekai Tahir Burak Health Practice Research Center, Ankara, Turkey2Gazi University Faculty of Medicine, Department of Medical Biochemistry, Ankara, Turkey"} +{"text": "The development of machine learning in bariatric surgery By Enodien B, Taha-Mehlitz S, Saad B, Nasser M, Frey DM and Taha A. (2023) Front. Surg. 10:1102711. doi: 10.3389/fsurg.2023.1102711A Corrigendum on Incorrect AffiliationIn the published article, there was an error in affiliations associated with Dr. Anas Taha and Dr. Daniel M. Frey.The incorrect affiliations are:1, Stephanie Taha-Mehlitz2, Baraa Saad3, Maya Nasser3, Daniel M. Frey4, Anas Taha2,4Bassey Enodien1Department of Surgery, GZO-Hospital, Wetzikon, Switzerland.2Clarunis, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital, Basel, Switzerland.3School of Medicine, St. George\u2019s University of London, London, United Kingdom.4Department of Biomedical Engineering, Faculty of Medicine, University of Basel, Allschwil, Switzerland.The correct affiliations are:1, Stephanie Taha-Mehlitz2, Baraa Saad3, Maya Nasser3, Daniel M. Frey1, Anas Taha1,4Bassey Enodien1Department of Surgery, GZO-Hospital, Wetzikon, Switzerland.2Clarunis, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital, Basel, Switzerland.3School of Medicine, St. George\u2019s University of London, London, United Kingdom.4Department of Biomedical Engineering, Faculty of Medicine, University of Basel, Allschwil, Switzerland.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "There is an error in the affiliations for the first author. Specifically, #3 was included in error and should not have been indicated. The correct affiliations are as follows:1,2,3*, Khorshed Alam1,2, Jeff Dunn1,4,5, Jeff Gow1,2,61 Health Economics and Policy Research, Centre for Health, Informatics and Economic Research, University of Southern Queensland, Toowoomba, Queensland, Australia, 2 School of Commerce, University of Southern Queensland, Toowoomba, QLD Australia, 3 Health and Epidemiology Research, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh, 4 Cancer Research Centre, Cancer Council Queensland, Fortitude Valley, QLD, Australia, 5 Prostate Cancer Foundation of Australia, St Leonards NSW, Australia, 6 School of Accounting, Economics and Finance, University of KwaZulu-Natal, Durban, South AfricaRashidul Alam Mahumudrashed.mahumud@usq.edu.au.Additionally, there was an error in the corresponding author\u2019s listed email addresses. Correspondence regarding this article should only be sent to the following email address:"} +{"text": "BMC Geriatrics (2023) 23:54810.1186/s12877-023-04259-5After publication of this article , the aut1, Sahar Khoshravesh2,3, Erfan Ayubi4,5, Akram Karimi Shahanjarini5, Samane Shirahmadi6 and Parshang Faghih Solaymani5* Saeid Bashirian1Autism Spectrum Disorders Research Center, Hamadan University of Medical Sciences, Hamadan, Iran2Department of Community Health Nursing, School of Nursing and Midwifery, Hamadan University of Medical Sciences, Hamadan, Iran3Chronic Diseases (Home Care) Research Center, Hamadan University of Medical Sciences, Hamadan, Iran4Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran5Social Determinants of Health Research Center, Hamadan University of Medical Sciences, Hamadan, Iran6Department of Community Oral Health, School of Dentistry, Dental Research Center, Hamadan University of Medical Sciences, Hamadan, IranThe original article has been"} +{"text": "Correction: Ann Clin Microbiol Antimicrob (2023) 22:2110.1186/s12941-023-00573-3Following publication of the original article , the autRawan Taha (1)Ola Kader (1)Sherine Shawky (1)Shahinda Rezk (2)1: Microbiology Department, Medical Research Institute, Alexandria University, Egypt.2: Lecturer of Molecular and Diagnostic Microbiology, Microbiology Department, Medical Research Institute, Alexandria University, 165 Horreya Avenue, Hadara, Alexandria, Egypt.The original article has been corrected."} +{"text": "Correction to: European Journal of Applied Physiology 10.1007/s00421-023-05210-7The original version of this article unfortunately contained a mistake. Affiliation details for Author Thomas A. W. Paulson were incorrectly given1British Paralympic Association, London, UK3UK athletics, Birmingham, UKbut should have been2Sport Exercise and Health Sciences, The Peter Harrison Centre for Disability Sport, Loughborough University, Loughborough, UK3UK athletics, Birmingham, UK"} +{"text": "Correction to: Psychopharmacologyhttps://doi.org/10.1007/s00213-022-06191-9After publication of this paper, the authors inadvertently excluded Dr. Pagano Zottola from the list of authors and that the journal Psychopharmacology has no responsibility for the omission.All authors agree to correct the list of authors as follows:Antonio C. Pagano Zottola4,5,7, Valeria Orr\u00f93, Valentina Serra3, Edoardo Fiorillo3, Paola Fadda1,6, Giovanni Marsicano4,5,Maria Antonietta De Luca1Giulia Margiani#,1, Maria Paola Castelli #,1, Nicholas Pintori1, Roberto Frau1,2, Maria Grazia Ennas1, 4 INSERM, U1215 NeuroCentre Magendie, Bordeaux, France5 University of Bordeaux, Bordeaux, France7 Institut de Biochimie et G\u00e9n\u00e9tique Cellulaires, UMR 5095, Bordeaux FranceThe original article has been corrected."} +{"text": "Cell Death Discovery 10.1038/s41420-023-01465-3, published online 17 May 2023Correction to: In this article the author order was given erroneously. It should be read:1,2,3,4#, Lingfei Li4#, Qiong Zhang1,2#, Yongqing He4, Yao Huang1,2,3, Junhui Zhang5, Dongxia Zhang1,2, Yuesheng Huang6, Xia Lei4*, Jiongyu Hu2,7*, Gaoxing Luo1,2*Yanhai FengAffiliations.1Institute of Burn Research, Southwest Hospital, Third Military Medical University , Chongqing, China;2State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University , Chongqing, China;3Army 953 Hospital, Shigatse Branch of Xinqiao Hospital, Third Military Medical University , Shigatse, China;4Department of Dermatology, Daping Hospital, Third Military Medical University , Chongqing, China;5Department of Geriatric Oncology, Department of Palliative care, Department of Clinical nutrition, Chongqing University Cancer Hospital, Chongqing, China;6Department of Wound Repair, Institute of Wound Repair and Regeneration Medicine, Southern University of Science and Technology Hospital, Southern University of Science and Technology School of Medicine, Shenzhen, China;7Endocrinology Department, Southwest Hospital, Third Military Medical University , Chongqing, China;The original article has been corrected."} +{"text": "The order of the affiliations is incorrect. Please view the correct affiliation order here:1,2, Anas A. Al-Nabulsi2, Asma\u2019 O. Taybeh2, Leila Cheikh Ismail1, Sheima T. Saleh1Tareq M. Osaili1 Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, P. O. Box 27272 Sharjah, United Arab Emirates, 2 Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan."} +{"text": "In the published article, there was an error in affiliations 4, 5, 6, 7. Instead of:4Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia, 5Department of Theriogenology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt, 6Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China, 7Animal Production Department, Faculty of Agriculture, Assuit University, Asyut, Egypt\u201d\u201cThe affiliation numbers of these authors should be:4, Amin A. Al-Doaiss4, Yasser Sabry Mostafa4, Ahmed Ezzat Ahmed4,5 and Mohamed Abdelrahman6,7\u201d\u201cFatimah A. Al-SaeedAnd affiliations 4, 5, 6 and 7 should be:4Biology Department, College of Science, King Khalid University, Saudi Arabia, 5Department of Theriogenology, Obstetrics, and Artificial Insemination, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt, 6Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China, 7Animal Production Department, Faculty of Agriculture, Assiut University, Asyut, Egypt\u201d\u201cThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Correction to: Clinical rheumatologyhttps://doi.org/10.1007/s10067-023-06659-9The affiliations in the published version of the attached above article was incorrectly designated to the authors. The correct presentation are as follows:Fangfang Chen1, Yitian Lang3, Shikai Geng1, Xiaodong Wang1, Liangjing Lu1, Shuang Ye1, Le Zhang1,2, Ting Li11 Department of Rheumatology, Ren Ji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People\u2019s Republic of China\u00a02 Department of Pharmacy, Ren Ji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China\u00a03 Department of Pharmacy, Huangpu Branch, Shanghai Ninth People\u2019s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaThe original article has been corrected."} +{"text": "The above abstract [1] published with a duplication of Yulia A. Levites Strekalova\u2019s name in the author list, which appeared as \u201cYulia A. Levites.\u201d This has been removed.Additionally, the correct author affiliations were missing. The correct author list and subsequent affiliations should appear as follows:1*, Akshita Gupta2*, Jamie L. Fermin1*, Samuel P. Border3, Sanjay Jain4, John E. Tomaszewski5, Yulia A. Levites Strekalova6+, and Pinaki Sarder7+Myles Joshua T. Tan1Department of Electrical & Computer Engineering, University of Florida, 2Department of Health Outcomes & Biomedical Informatics, University of Florida, 3J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 4Division of Nephrology, Washington University School of Medicine in St. Louis, 5Department of Pathology and Anatomical Sciences, University at Buffalo, 6Department of Health Services Research, Management & Policy, University of Florida, 7Division of Nephrology, Hypertension & Renal Transplantation, University of Florida+Co-corresponding*Equal contribution, The original abstract has been corrected online to rectify these errors."} +{"text": "Correction: Journal of Translational Medicine (2023) 21:209 10.1186/s12967-023-04053-2Following publication of the original article , we have1Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, Seongnam 13620, Korea:\u00a0Jinho Kim\u20201, Heetak Lee1,3.2Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, Korea:\u00a0Hyunjung Kim\u20202, Min-Seok Lee2, Sun Shim Choi2*."} +{"text": "Scientific Reports 10.1038/s41598-023-30713-w, published online 03 March 2023Correction to: The original version of this Article contained errors in the Results section, under the subheading \u2018Research characteristics\u2019,13,14,15,16,17,18,19, while 2 studies were based on cerebrospinal fluid12,21. Eight studies reported the expression levels of HMBG1 in children with FS and children with fever but no FS12,14,15,16,17,18,19,20,21, including 6 results based on serum and 2 results based on cerebrospinal fluid.\u201d\u201cFive studies were based on peripheral blood resultsnow reads:13,14,15,16,17,18,19, while 2 studies were based on cerebrospinal fluid12,20. Eight studies reported the expression levels of HMBG1 in children with FS and children with fever but no FS12,14,15,16,17,18,19,20, including 6 results based on serum and 2 results based on cerebrospinal fluid.\u201d\u201cSeven studies were based on peripheral blood resultsThe original Article has been corrected."} +{"text": "GigaScience, Volume 12, 2023, giad023, https://doi.org/10.1093/gigascience/giad023.This is a correction to: Jinghui Zheng, Xiaobo Wang, Tong Feng, Saif ur Rehman, Xiuying Yan, Huiquan Shan, Xiaocong Ma, Weiguan Zhou, Wenhua Xu, Liying Lu, Jiasheng Liu, Xier Luo, Kuiqing Cui, Chaobin Qin, Weihua Chen, Jun Yu, Zhipeng Li, Jue Ruan, Qingyou Liu, Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes, In the originally published version of this manuscript, there were errors in Fig. 3.Extraneous \u201cCount\u201d legends from sections D and E are removed and the Figure should read:instead of:There were also emendations needed in the affiliations list and enumeration in authorlist. These should read:1,2,\u2020, Xiaobo Wang3,\u2020, Tong Feng3,5,\u2020, Saif ur Rehman3, Xiuying Yan3, Huiquan Shan3, Xiaocong Ma2, Weiguan Zhou6, Wenhua Xu2, Liying Lu2, Jiasheng Liu2, Xier Luo1,4, Kuiqing Cui1,3, Chaobin Qin3,Weihua Chen5, Jun Yu6, Zhipeng Li3, Jue Ruan4,* and Qingyou Liu1,3,*\"Jinghui Zheng1Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528,225, China2Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530,011, China3State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530,004, China4Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518,120, China5Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology,Wuhan, Hubei 430,074, China6Biological Institute of Guangxi Academy of Sciences, Nanning 530,007, China7CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100,101, China\"instead of:1,\u2020, Xiaobo Wang2,3,\u2020, Tong Feng2,3,\u2020, Saif ur Rehman2, Xiuying Yan2, Huiquan Shan2, Xiaocong Ma1, Weiguan Zhou4, Wenhua Xu1, Liying Lu1, Jiasheng Liu1, Xier Luo2,3, Kuiqing Cui2, Chaobin Qin2, Weihua Chen5, Jun Yu6, Zhipeng Li2, Jue Ruan3,* and Qingyou Liu7,*\"Jinghui Zheng1Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530,011, China2State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530,004, China3Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518,120, China4Biological Institute of Guangxi Academy of Sciences, Nanning 530,007, China5Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430,074, China6CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100,101, China7Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528,225, China\".These changes have been made in the article."} +{"text": "In the published article, there was an error in affiliation 2. Instead of \u201cChina-DRIs Expert Committee on Human Milk Composition, Beijing, China\u201d, it should be \u201cChina-DRIs Research Group on Human Milk Composition, Beijing, China.\u201dIn the published article, there was an error regarding the affiliations for Huanmei Zhang, Xiangnan Ren, and Jianqiang Lai. As well as having affiliation(s) 2, 3, they should also have Key Laboratory of Human Milk Science, Chinese Center for Disease Control and Prevention, Beijing, China.In the published article, there was an error in the author list, and author Yuexin Yang was erroneously excluded. The corrected author list appears below.1,2\u2020, Xianyun Wang1\u2020, Kuo Liu1, Huanmei Zhang2,3,4, Xiangnan Ren2,3,4, Ai Zhao2,5, Yuexin Yang2,3, Jianqiang Lai2,3,4* and Rong Xiao1*Yuandi XiIn the published article, there was an error in the Funding statement. A source of funding was missed from the statement. The correct Funding statement appears below."} +{"text": "In the published article, there was an error in the author list, and author Antonio Inserra was erroneously excluded. The corrected author list, affiliations and author contributions appears below.1,2*\u2020, Nige Netzband3\u2020, WaiFung Tsang4, Merlin Davies2, Antonio Inserra5, Matthew Butler4, James J. H. Rucker4, Lu\u00eds Fernando T\u00f3foli6, Emma Louise Dempster2, Allan H. Young1 and Celia J. A. Morgan2Simon G. D. Ruffell1Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London & South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Beckenham, United Kingdom, 2College of Life and Environmental Sciences, Washington Singer Laboratories, University of Exeter, Exeter, United Kingdom, 3Department of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom, 4Kings College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom, 5Neurobiological Psychiatry Unit, Department of Psychiatry, McGill University, Montreal, QC, Canada, 6Interdisciplinary Cooperation for Ayahuasca Research and Outreach (ICARO), University of Campinas, S\u00e3o Paulo, BrazilSR, AI, and CM: conceptualization. SR, NN, WT, and CM: methodology. SR and NN: data collection. WT and MB: data analysis. SR, NN, and WT: writing\u2014original draft preparation. SR, NN, WT, MB, LT, AY, and CM: writing\u2014review and editing. MD and ED: epigenetic analysis. JR, LT, ED, AY, and CM: supervision. All authors contributed to the article and approved the submitted version.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "An additional affiliation is missing for the second author. Konstantinos Rounis is also affiliated with: Laboratory of Translational Oncology, Medical School, University of Crete.1,2, Konstantinos Rounis1,3,4, Alexandros-Pantelis Tsigkas5, Alexandra Georgiou5, Nikolaos Galanakis6, George Tsakonas3,7, Simon Ekman3,7, Chara Papadaki4, Alexia Monastirioti4, Meropi Kontogianni5, Ioannis Gioulbasanis8, Dimitris Mavroudis1,4, Sofia Agelaki1,4The correct affiliations are as follows: Dimitrios Makrakis1 Department of Medical Oncology, University General Hospital, Heraklion, Crete, Greece, 2 Jacobi Medical Center, Albert Einstein College of Medicine, The Bronx, NY, United States of America, 3 Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden, 4 Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Greece, 5 Department of Nutrition & Dietetics, School of Health Sciences and Education, Harokopio University, Athens, Greece, 6 Department of Medical Imaging, University General Hospital, Heraklion, Crete, Greece, 7 Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden, 8 Department of Medical Oncology, Animus Kyanus Stavros General Clinic, Larissa, Greece"} +{"text": "Human Brain Mapping, 44(4), 1476\u20131495. https://doi.org/10.1002/hbm.26137Zyuzin, J., Combs, D., Melrose, J., Kodaverdian, N., Leather, C., Carrillo, J. D., Monterosso, J. R., & Brocas, I. (2023). The neural correlates of value representation: From single items to bundles. In the published version of the article, James Melrose, Niree Kodaverdian, Calvin Leather, and Juan D. Carrillo were missing from the author list. The corrected authorship appears below. The online version of this article has been corrected accordingly.1, Dalton Combs1, James Melrose2, Niree Kodaverdian3, Calvin Leather2, Juan D. Carrillo2, John R. Monterosso4, Isabelle Brocas2Jekaterina Zyuzin1University of Southern California, Los Angeles, California, USA.2Department of Economics, University of Southern California, Los Angeles, California, USA.3Argyros School of Business and Economics, Chapman University, Orange, California, USA.4Department of Psychology, University of Southern California, Los Angeles, California, USA."} +{"text": "Cell Death Discovery 10.1038/s41420-022-01294-w, published online 04 February 2023Correction to: The original version of this article contained errors in the author affiliations. The correct affiliations can be found below. The original article has been corrected.1,2,6, Yuxin Zan1,6, Yingying Huang1,6, Xiaoyun Peng1,6, Shinan Ma1, Ji Ren1, Xiao Li1, Lin Wei1, Xiaoli Wang1, Yahong Yuan1, Junming Tang1, Zhongqun Zhan3, Zhixiao Wang1,4, Yan Ding1,5Yi WangAff 1 Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, ChinaAff 2 Cardiovascular Department, Yiyang people\u2019s hospital, Yiyang, Hunan, 413000Aff 3 Department of Cardiology, University of Chinese Academy of Sciences-Shenzhen Hospital, Shenzhen 518107, ChinaAff 4 Cardiovascular Department, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, ChinaAff 5 Hubei Clinical Research Center for Umbilical cord blood hematopoietic stem cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China6 These authors contributed equallyCorresponding Authors:Yan Ding, E-mail: 20090990@hbmu.edu.cn;Zhixiao Wang, E-mail: zhixiaowang@whu.edu.cn;Zhan Zhongqun, E-mail: zzqun21@yahoo.com.cn"} +{"text": "Affiliations 1, 2, 3. Instead of \u201cJieru Wang1,2,3, Jiajia Suo1, Ruizhi Yang1, Cheng-Long Zhang2,3, Xiaopeng Li2,3, Zhipeng Han2,3, Wen Zhou2,3, Shudong Liu2,3,* and Qinghua Gao1,2,3,*; 1Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China; 2Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China; 3Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China,\u201d it should be \u201cJieru Wang1,2, Jiajia Suo1, Ruizhi Yang1, Cheng-long Zhang3,4, Xiaopeng Li3,4, Zhipeng Han3,4, Wen Zhou3,4, Shudong Liu2,3,4,* and Qinghua Gao2,3,4,*; 1College of Life Science and Technology, Tarim University, Alar, Xinjian, China; 2Key Laboratory of Utilization of Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, Xinjiang, China; 3College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China; 4Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, Xinjiang, China.\u201dIn the published article, there was an error in Conflict of interest statement. Instead of \u201cThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\u201d it should be \u201cAuthors C-lZ, XL, ZH, WZ, SL, and QG were employed by Xinjiang Production and Construction Corps.Furthermore, there was an error in the The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\u201dThe authors apologize for these errors and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "In the published article, there was an error in the author list, and author \u201cMirja Krause\u201d was erroneously excluded. The corrected author list and author contributions section are appears below.1, 2*, Rebecca Lim3, 4, Mirja Krause3, 4, Siow T. Chan3, 4, Hannah McDonald3, 4, Poh-Yi Gan5, 6, Shenpeng R. Zhang7, Liz J. Barreto Arce7, Jason Vuong1, 2, Tharani Thirugnanachandran1, 2, Benjamin Clissold1, 2, John Ly1, 2, Shaloo Singhal1, 2, Marie Veronic Hervet1, 2, Hyun Ah Kim7, Grant R. Drummond7, Euan M. Wallace4, 8, Henry Ma1, 2 and Christopher G. Sobey7*\u201d\u201cThanh G. PhanTP, HMa, RL, EW, and CS designed the trial protocol and were major contributors in the writing of the manuscript. JV performed image analysis. TT, BC, JL, and SS recruited patients and performed clinical assessments. RL, MK, SC, and HMc prepared cells for administration to patients. MH administered cell infusions and collected the patient data. P-YG, SZ, LB, and HK performed the analyses of blood samples for inflammatory markers. CS and GD analyzed the data. All authors contributed to the article and approved the submitted version.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Correction: BMC Cardiovascular Disorders 23, 136 (2023)https://doi.org/10.1186/s12872-023-03153-7Following publication of the original article , in this1*, Greta \u017diubryt\u01171,2, Nojus Jodka1 and Ram\u016bnas Unikas1Mindaugas Barauskas1Department of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania2Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, LithuaniaThe original article has been corrected."} +{"text": "The author list for this article was incomplete - the correct author list should be:1,2, Kenn Chi Ndi1, Lionel Tabola1, Esther Dina Bell3, Vanessa Mouaye2, Pelagie Douanla1, Nasser Nsangou1, Glenda Nkeng1, Carmen Vanvolkenburgh4, Bonaventure Dzekem4, Prisca Adejumo5, Olutosin Awolude6, Toyin Aniagwu7, Dezheng Huo4, Paul Ndom1,2 and Olufunmilayo Olopade3Berthe Sabine Esson Mapoko1Department of Internal Medicine and Specialties, Faculty of Medicine and Biomedical Sciences, The University of Yaound\u00e9 I, Yaound\u00e9 99322, Cameroon2National Cancer Control Committee, Yaound\u00e9 99322, Cameroon3Department of Clinical Sciences, Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala 99322, Cameroon4Center for Global Health, University of Chicago Medical Center, Chicago, IL 60637, USA5Department of Nursing, College of Medicine, University of Ibadan, Ibadan 200284, Nigeria6Department of Obstetrics and Gynaecology, University College Hospital, Ibadan 200284, Nigeria7School of Occupational Health Nursing, University College Hospital, Ibadan 200212, NigeriaThe acknowledgments section should be replaced by the following text:Thanks to persons not listed as co-authors but who contributed to this work, especially the Chicago, Nigerian and Cameroonian teams.The authors provided contributions in: conception and design, final approval, accountable for all aspects of the work."} +{"text": "The publisher apologises that upon publication of He Q-Q, Rui J-W, Zhang L, Tao Y, Wu J-J, Mace R, Ji T (2022) the affiliation for author Ting Ji was incorrectly listed and they were not noted as a corresponding author. The correct affiliations are listed as below:1, Jun-Wen Rui1, Li Zhang1, Yi Tao2, Jia-Jia Wu3, Ruth Mace4 and Ting Ji2Qiao-Qiao He1College of Life Science, Shenyang Normal University, Shenyang, Liaoning 110034, China,2Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China,3Life Science, Lanzhou University, Tianshui Rd, Chengguan Qu, Lanzhou, Gansu Province, 730000, China and4Department of Anthropology, University College London, London WC1H 0BW, UKThe correct corresponding author list is listed as below:r.mace@ucl.ac.uk, jiting@ioz.ac.cnCorresponding author: The online version of this article has been updated."} +{"text": "JCI Insight. 2022;7(21):e159751. https://doi.org/10.1172/jci.insight.159751Original citation: JCI Insight. 2023;8(10):e171762. https://doi.org/10.1172/jci.insight.171762Citation for this corrigendum: Author contributions section. The correct author and affiliations lists and sentence from the Author contributions section are below. The HTML and PDF versions have been updated online.Jorge Romo-Tena\u2019s name was inadvertently omitted from the author list and 1,2,3 Zewen K. Tuong,1,2,4 Kevin W. Loudon,1,2 Eduardo Pati\u00f1o-Mart\u00ednez,3 John R. Ferdinand,1,2 Ana\u00efs Portet,1,2 Jorge Romo-Tena,3 Kathleen R. Bashant,3 Emeline Thevenon,5 Francesca Rucci,5 Thomas Hoyler,5 Tobias Junt,5 Mariana J. Kaplan,3 Richard M. Siegel,3,5 Menna R. Clatworthy1,2,4Nathan Richoz,1Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom. 2Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom. 3National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA. 4Cellular Genetics Programme, Wellcome Sanger Institute, Hinxton, United Kingdom. 5Novartis Institutes for BioMedical Research, Basel, Switzerland.Conducting experiments was contributed by NR, KWL, EPM, JRF, AP, and JRT."} +{"text": "In the published article, there was an error in the affiliations. Instead of six, there are only five affiliations. The original affiliation 2 has been removed. The correct affiliations are listed below:Instead of1,2, Yan-Dong Tang 3, Guoqing Zhan 4, Chenhe Su 5, Chunfu Zheng 2, 6Huifang Zhu 1Neonatal/Pediatric Intensive Care Unit, Children\u2019s Medical Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.\u201c2Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.3State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.4Department of Infectious Disease, Renmin Hospital, Hubei University of Medicine, Shiyan, China.5The Wistar Institute, Philadelphia, PA, United States.6Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.\u201d,it should be1, Yan-Dong Tang 2, Guoqing Zhan 3, Chenhe Su 4, Chunfu Zheng 5Huifang Zhu 1Neonatal/Pediatric Intensive Care Unit, Children\u2019s Medical Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.\u201c2State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.3Department of Infectious Disease, Renmin Hospital, Hubei University of Medicine, Shiyan, China.4 The Wistar Institute, Philadelphia, PA, United States.5Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.\u201dThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "AMP\u2010activated protein kinase \u03b11 phosphorylates PHD2 to maintain systemic iron homeostasis. Clin Transl Med. 2022 May;12(5):e854. In the originally published article by Cheng Wang et\u00a0al. (2022), Ming\u2010hui Zou, Georgia State University, was not properly included as the corresponding author. Related grants from NIH which were not properly acknowledged in the initial version of this article. The corrected authorship and acknowledgements are as the followings:1,2,3,4,*, Wencheng Zhang5, Wenjing Xu1, Zhaoyu Liu6, Kai Huang1,2,*, Ming\u2010Hui Zou4,*Cheng Wang1Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China2Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China3Department of Rheumatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China4Center for Molecular and Translational Medicine, Georgia State University, Atlanta, Georgia, USA5Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China6Department of Cardiology, Sun Yat\u2010sen Memorial Hospital, Sun Yat\u2010sen University, Guangzhou, ChinaThe author apologizes for this error."} +{"text": "Correction: BMC Neurosci 24, 9 (2023)10.1186/s12868-023-00777-5Following publication of the original article [1], the authors reported that the order of affiliations was inverted. The corrected affiliations are the following:1Affiliated Hospital of Zunyi Medical University, 149 Dalian Road, Huichuan District, 563,000, Zunyi, Guizhou, China.2Zunyi Medical University, 6 Xuefu West Road, Xinpu New District, 563,000, Zunyi, Guizhou, ChinaThe original article has been"} +{"text": "Evaluation of changes to work patterns in multidisciplinary cancer team meetings due to the COVID\u201019 pandemic: A national mixed\u2010 method survey study. Cancer Med. 2023;12:8729\u20138741. doi:In the originally published article, the fourth author's name had been misspelled as \u201cPhilip Rowland.\u201d It is now corrected to \u201cPhilip Rolland.\u201dThe updated author byline and affiliations are mentioned below:1Tayana Soukup | 2David Winters | 1Kia\u2010Chong Chua | 3,4Philip Rolland | 3Jacqueline Moneke | 5Ted A. Skolarus | 6Rasiah Bharathan | 7,8Leanne Harling | 9Anish Bali | 9Viren Asher | 10Tasha Gandamihardja | 1Nick Sevdalis | 2James S. A. Green | 2,11,12Benjamin W. Lamb1Institute of Psychiatry, Psychology, and Neuroscience, Health Service and Population Research Department, King's College London, London, UK2Department of Urology, Barts Health, NHS Trust, London, UK3Department of Urology, Cambridge, University Hospital NHS Trust, London, UK4Gloucestershire Hospitals NHS Foundation Trust, Cheltenham, UK5Dow Division of Health Services, Research, Department of Urology, University of Michigan, Center for Clinical Management Research, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan, USA6University Hospitals of Leicester NHS, Trust, Leicester, UK7Department of Surgery and Cancer, Imperial College London, London, UK8School of Cancer and Pharmaceutical Science, Kings College London, London, UK9Gynaecology Cancer Centre, University Hospitals of Derby & Burton, Derby, UK10Chelmsford Breast Unit, Broomfield Hospital, Chelmsford, UK11Bart's Cancer Institute, Queen Mary, University of London, London, UK12Department of Urology, University London College Hospitals, London, UKWe apologize for this error."} +{"text": "Parahololepidella Pettibone, 1969 is a polynoid genus commensal with the antipatharian genus Tanacetipathes Opresko, 2001. These scale worms are elongate with numerous segments and small elytra. To date, the only other known polynoid associated with Tanacetipathes is Antipathipolyeunoa Pettibone, 1991. By re-examining the holotype of Antipathipolyeunoa, we have identified several overlooked characters that no longer distinguish this genus from Parahololepidella. Based on the presence of chaetae on the tentacular segment and elytral irregularity on posterior segments, we propose synonymizing Antipathipolyeunoa with Parahololepidella. Polynoidae Kinberg, 1856 scale worms are one of the most diverse groups of Annelida found in association with other organisms and elytra, elytra irregularly arranged posteriorly with different numbers on right and left sides, tentacular segment (segment 1) with chaetae, neuropodia with a digitiform subacicular process, and slightly hooked neurochaetae thicker than notochaetae from West Africa, was originally reported as a free-living species inhabiting mucous tubes incrusted with sand grains and shell fragments. Parahololepidellagreeffi from the syntypes and newly collected topotypes from S\u00e3o Tom\u00e9 and Pr\u00edncipe (Gulf of Guinea), finding specimens living in association with the antipatharian Tanacetipathescf.spinescens and not free-living as originally thought [as Antipathes] in Barbados without chaetae, neuropodia with projecting subacicular process, and falcate neurochaetae stouter than notochaetae. Antipathipolyeunoa closely resembled Polyeunoa , and elytral irregularities are present in the posterior region of all three paratypes. The lack of elytral variation in the holotype suggests that this condition may have been overlooked because it is the only specimen complete with dorsal cirri and elytra still attached.Upon re-examination of the holotype (USNM 80097) and the three paratypes (USNM 136587) of Parahololepidella and Antipathipolyeunoa. Therefore, we propose the synonymy of Antipathipolyeunoa with Parahololepidella and accordingly include Antipathipolyeunoanuttingi as a member of Parahololepidella; providing an updated systematic account for Parahololepidella as well as additional morphological details for Parahololepidellanuttingi comb. nov.Based on the presence of chaetae on the tentacular segment and the irregularities in the posterior segments found in the type material, we conclude that no significant differences exist between the monotypic genera Aphroditiformia Levinsen, 1883Suborder Polynoidae Kinberg, 1856Family Taxon classificationAnimaliaPhyllodocidaPolynoidae\ufeffPettibone, 196996221E9E-4D7D-58CA-9A80-7CCD543BC2B5ParahololepidellaHololepidellagreeffi Augener, 1918, by original designation].\u2014 Pettibone, 1969: 54 . Pettibone, 1991: 715 [type species: Parahololepidella (ZHM 5692) were examined and illustrated by Pettibone for her 1969 revision of Hololepidella, and subsequently re-examined by Parahololepidellagreeffi (NNMN 24481 and MNCN 16.01/13708). Only original notes and illustrations by Pettibone were examined herein.The type specimens of Parahololepidella now includes two species commensal with the antipatharian genus Tanacetipathes Opresko, 2001. Both Parahololepidella species show cryptic coloration patterns and are found nestled along the stems of the coral branches.Taxon classificationAnimaliaPhyllodocidaPolynoidae\ufeffcomb. nov.E274653B-2D98-5C90-AA2F-70614B0FC839Antipathipolyeunoanuttingi Pettibone, 1991: 716\u2013719, figs 1, 2.Holotype. Barbados \u25cf 1; Sta. 65, off Payne\u2019s Bay Church; 91 m; 1918; collector CC Nutting; Barbados-Antigua Expedition; on Antipathestanacetum (now Tanacetipathes); USNM 80097. Paratypes. Venezuela \u25cf 3; Sta. 736, W of Tortuga Island; 10.95, \u221265.8667; 69\u2013155 m; 22 July 1968; R/V Pillsbury; on Antipathestanacetum (now Tanacetipathes); USNM 136587.(based on the holotype). Body with numerous segments, >80 consist of one posteriorly incomplete specimen, two additional anterior ends, and several middle and posterior fragments. It was only possible to trace one of the two shorter anterior fragments to their respective remaining body fragments. Longest anterior paratype fragment, 24.5 mm long, 2 mm wide excluding chaetae, 85 segments. Reconstructed paratype, 25 mm long, 2.3 mm wide excluding chaetae, 102 segments. Shortest anterior paratype fragment, 5.7 mm long, 1.5 mm wide excluding chaetae, 25 segments.Pigmentation is present in all specimens, present along the midline of the dorsum, with wider bands of pigment present in the paratypes Fig. . AdditioParatype 1.R: 2, 4, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 26, 29, 32, 33, 35, 37, 38, 41, 43, 45, 47, 49, 52, 54, 56, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85L: 2, 4, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 26, 29, 32, 34, 36, 38, 41, 43, 45, 47, 49, 51, 53, 55, 56, 58, 59, 60, 62, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85Paratype 2.R: 2, 4, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 26, 29, 32, 34, 36, 38, 40, 42, 44, 46, 47, 50, 52, 54, 56, 58, 60, 62, 64, 66, 86, 70, 72, 74, 76, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102.L: 2, 4, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 26, 29, 32, 33, 35, 37, 39, 41, 43, 45, 47, 49, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102.The current diagnosis mostly agrees with that of Parahololepidellanuttingi comb. nov. is very similar to P.greeffi, but can be differentiated as follows. In P.nuttingi, the dorsal cirrophores are shorter than the notopodium in middle segments, whereas in P.greeffi, the dorsal cirrophores surpass the notopodium , whereas in P.greeffi, the tooth-like structures are larger when present, giving them almost a bidentate appearance. P.greeffi (ZMH 5692) were artifacts due to poor preservation and dehydration over time. However, given that similar structures were found in all specimens of P.nuttingi, we feel that this character is valid and illustrates the importance of detailed microscopical examination and reexamination.dium see , fig. 1G"} +{"text": "Due to a production error, there was an error in the author affiliations as published. During the production process, affiliations 2 and 3 were conflated, resulting in the following erroneous affiliation list being published:1,*, Aleksandra Boba1,2, Bartosz Kozak1, Dariusz Sztafrowski3, Jan Widu\u0142a2, Jan Szopa1,2 and Marta Preisner1Kamil Kostyn1Department of Genetics, Plant Breeding & Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland2Faculty of Electrical Engineering, Wroclaw University of Science and Technology, Wroclaw, Poland3Faculty of Biotechnology, University of Wroclaw, Wroclaw, PolandThe corrected author affiliation information appears below:1,*, Aleksandra Boba1,3, Bartosz Kozak1, Dariusz Sztafrowski2, Jan Widu\u0142a3, Jan Szopa1,3 and Marta Preisner1\u201cKamil Kostyn1Department of Genetics, Plant Breeding & Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland2Faculty of Electrical Engineering, Wroclaw University of Science and Technology, Wroclaw, Poland3Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland\u201dThe publisher apologizes for this mistake. The original version of this article has been updated."} +{"text": "Shepherd21, Julie Hunter22, Kishore Kumar23, Melina Ellis24, Miguel E. Renter\u00eda25, Sulev Koks26, Alexander Zimprich27, Artur F. Schumacher-Schuh28, Carlos Rieder29, Paula Saffie Awad30, Vitor Tumas31, Sarah Camargos32, Edward A. Fon33, Oury Monchi34, Ted Fon35, Benjamin Pizarro Galleguillos36, Marcelo Miranda37, Maria Leonor Bustamante38, Patricio Olguin36, Pedro Chana39, Beisha Tang40, Huifang Shang41, Jifeng Guo42, Piu Chan43, Wei Luo44, Gonzalo Arboleda45, Jorge Orozco46, Marlene Jimenez del Rio47, Alvaro Hernandez48, Mohamed Salama49, Walaa A. Kamel50, Yared Z. Zewde51, Alexis Brice52, Jean-Christophe Corvol53, Ana Westenberger54, Anastasia Illarionova55, Brit Mollenhauer56, Christine Klein54, Eva-Juliane Vollstedt54, Franziska Hopfner57, G\u00fcnter H\u00f6glinger58, Harutyun Madoev54, Joanne Trinh54, Johanna Junker54, Katja Lohmann54, Lara M. Lange59, Manu Sharma60, Sergio Groppa61, Thomas Gasser60, Zih-Hua Fang62, Albert Akpalu63, Georgia Xiromerisiou64, Georgios Hadjigorgiou64, Ioannis Dagklis65, Ioannis Tarnanas66, Leonidas Stefanis67, Maria Stamelou68, Efthymios Dadiotis64, Alex Medina69, Germaine Hiu-Fai Chan70, Nancy Ip71, Nelson Yuk-Fai Cheung70, Phillip Chan71, Xiaopu Zhou71, Asha Kishore72, Divya KP73, Pramod Pal74, Prashanth Lingappa Kukkle75, Roopa Rajan76, Rupam Borgohain77, Mehri Salari78, Andrea Quattrone79, Enza Maria Valente80, Lucilla Parnetti81, Micol Avenali80, Tommaso Schirinzi82, Manabu Funayama83, Nobutaka Hattori84, Tomotaka Shiraishi85, Altynay Karimova86, Gulnaz Kaishibayeva86, Cholpon Shambetova87, Rejko Kr\u00fcger88, Ai Huey Tan89, Azlina Ahmad-Annuar89, Mohamed Ibrahim Norlinah90, Nor Azian Abdul Murad91, Norlinah Mohamed Ibrahim92, Shahrul Azmin92, Shen-Yang Lim89, Wael Mohamed93, Yi Wen Tay89, Daniel Martinez-Ramirez94, Mayela Rodriguez-Violante95, Paula Reyes-P\u00e9rez96, Bayasgalan Tserensodnom97, Rajeev Ojha98, Tim J. Anderson99, Toni L. Pitcher99, Arinola Sanyaolu100, Njideka Okubadejo100, Oluwadamilola Ojo101, Jan O. Aasly102, Lasse Pihlstr\u00f8m103, Manuela Tan103, Shoaib Ur-Rehman104, Mario Cornejo-Olivas105, Maria Leila Doquenia106, Raymond Rosales106, Angel Vinuela107, Elena Iakovenko108, Bashayer Al Mubarak109, Muhammad Umair110, Eng-King Tan111, Jia Nee Foo112, Ferzana Amod113, Jonathan Carr114, Soraya Bardien115, Beomseok Jeon116, Yun Joong Kim117, Esther Cubo118, Ignacio Alvarez119, Janet Hoenicka120, Katrin Beyer121, Maria Teresa Peri\u00f1an122, Pau Pastor123, Sarah El-Sadig124, Christiane Zweier125, Krack Paul125, Chin-Hsien Lin126, Hsiu-Chuan Wu127, Pin-Jui Kung128, Ruey-Meei Wu126, Serena Wu129, Yihru Wu127, Rim Amouri130, Samia Ben Sassi131, A. Nazl Ba\u015fak132, Gencer Genc133, \u00d6zg\u00fcr \u00d6ztop \u00c7akmak132, Sibel Ertan132, Alastair Noyce134, Alejandro Mart\u00ednez-Carrasco135, Anette Schrag135, Anthony Schapira135, Camille Carroll136, Claire Bale137, Donald Grosset138, Eleanor J. Stafford135, Henry Houlden135, Huw R. Morris135, John Hardy135, Kin Ying Mok139, Mie Rizig135, Nicholas Wood135, Nigel Williams140, Olaitan Okunoye135, Patrick Alfryn Lewis141, Rauan Kaiyrzhanov135, Rimona Weil135, Seth Love142, Simon Stott143, Simona Jasaitye135, Sumit Dey134, Vida Obese135, Alberto Espay144, Alyssa O\u2019Grady145, Andrew B. Singleton146, Andrew K. Sobering147, Bernadette Siddiqi145, Bradford Casey145, Brian Fiske145, Cabell Jonas148, Carlos Cruchaga149, Caroline B. Pantazis150, Charisse Comart145, Claire Wegel151, Cornelis Blauwendraat150, Dan Vitale150, Deborah Hall152, Dena Hernandez150, Ejaz Shiamim153, Ekemini Riley154, Faraz Faghri150, Geidy E. Serrano155, Hampton Leonard156, Hirotaka Iwaki157, Honglei Chen158, Ignacio F. Mata159, Ignacio Juan Keller Sarmiento160, Jared Williamson153, Jonggeol Jeff Kim150, Joseph Jankovic161, Joshua Shulman162, Justin C. Solle145, Kaileigh Murphy145, Karen Nuytemans163, Karl Kieburtz164, Katerina Markopoulou165, Kenneth Marek166, Kristin S. Levine157, Lana M. Chahine167, Laurel Screven146, Lauren Ruffrage168, Lisa Shulman169, Luca Marsili144, Maggie Kuhl145, Marissa Dean168, Mary B. Makarious150, Mathew Koretsky150, Miguel Inca-Martinez159, Mike A. Nalls150, Naomi Louie145, Niccol\u00f2 Emanuele Mencacci160, Roger Albin170, Roy Alcalay171, Ruth Walker172, Sara Bandres-Ciga150, Sohini Chowdhury145, Sonya Dumanis173, Steven Lubbe160, Tao Xie174, Tatiana Foroud175, Thomas Beach176, Todd Sherer145, Yeajin Song150, Duan Nguyen177, Toan Nguyen177, Masharip Atadzhanov178.Emilia M. Gatto18Sanatorio de la Trinidad Mitre- INEBA, Buenos Aires, Argentina, 19Hospital JM Ramos Mejia, Buenos Aires, Argentina, 20Somnus Neurology Clinic, Yerevan, Armenia, 21Neuroscience Research Australia, Sydney, NSW, Australia, 22ANZAC Research Institute, Concord, NSW, Australia, 23Garvan Institute of Medical Research and Concord Repatriation General Hospital, Darlinghurst, NSW, Australia, 24Concord Hospital, Concord, NSW, Australia, 25QIMR Berghofer Medical Research Institute, Herston, QL, Australia, 26Murdoch University, Perth, Australia, 27Medical University Vienna Austria, Vienna, Austria, 28Universidade Federal do Rio Grande do Sul / Hospital de Cl\u00ednicas de Porto Alegre, Porto Alegre, Brazil, 29Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil, 30Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil, 31University of S\u00e3o Paulo, S\u00e3o Paulo, Brazil, 32Universidade Federal de Minas Gerais, Belo Horizonte, Brazil, 33Montreal Neurological Institute, Montreal, QC, Canada, 34Institut universitaire de g\u00e9riatrie de Montr\u00e9al, Montreal, QC, Canada, 35McGill University, Montreal, QC, Canada, 36Universidad de Chile, Santiago, Chile, 37Fundaci\u00f3n Diagnosis, Santiago, Chile, 38Faculty of Medicine Universidad de Chile, Santiago, Chile, 39CETRAM, Santiago, Chile, 40Central South University, Changsha, China, 41West China Hospital Sichuan University, Chengdu, China, 42Xiangya Hospital, Changsha, China, 43Capital Medical University, Beijing, China, 44Zhejiang University, Hangzhou, China, 45Universidad Nacional de Colombia, Bogot\u00e1, Colombia, 46Fundaci\u00f3n Valle del Lili, Santiago De Cali, Colombia, 47University of Antioquia, Medellin, Colombia, 48University of Costa Rica, San Jose, Costa Rica, 49The American University in Cairo, Cairo, Egypt, 50Beni-Suef University, Beni Suef, Egypt, 51Addis Ababa University, Addis Ababa, Ethiopia, 52Paris Brain Institute, Paris, France, 53Sorbonne Universit\u00e9, Paris, France, 54University of L\u00fcbeck, L\u00fcbeck, Germany, 55Deutsches Zentrum f\u00fcr Neurodegenerative Erkrankungen, G\u00f6ttingen, Germany, 56University Medical Center G\u00f6ttingen, G\u00f6ttingen, Germany, 57University Hospital, LMU Munich, Munich, Germany, 58Hannover Medical School, Hannover, Germany, 59University of L\u00fcbeck and University Medical Center Schleswig-Holstein, L\u00fcbeck, Germany, 60University of Tubingen, T\u00fcbingen, Germany, 61University of Mainz, Mainz, Germany, 62The German Center for Neurodegenerative Diseases, G\u00f6ttingen, Germany, 63University of Ghana Medical School, Accra, Ghana, 64University of Thessaly, Volos, Greece, 65Aristotle University of Thessaloniki, Thessaloniki, Greece, 66Ionian University, Corfu, Greece, 67Biomedical research Foundation of the Academy of Athens, Athens, Greece, 68Diagnostic and Therapeutic Centre HYGEIA Hospital, Marousi, Greece, 69Hospital San Felipe, Tegucigalpa, Honduras, 70Queen Elizabeth Hospital, Kowloon, Hong Kong, 71The Hong Kong University of Science and Technology, Kowloon, Hong Kong, 72Aster Medcity, Kochi, India, 73Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India, 74National Institute of Mental Health & Neurosciences, Bengaluru, India, 75Manipal Hospital, Delhi, India, 76All India Institute of Medical Sciences, Delhi, India, 77Nizam\u2019s Institute Of Medical Sciences, Hyderabad, India, 78Shahid Beheshti University of Medical Science, Tehran, Iran, 79Magna Gr\u00e6cia University of Catanzaro, Catanzaro, Italy, 80University of Pavia, Pavia, Italy, 81University of Perugia, Perugia, Italy, 82University of Rome Tor Vergata, Rome, Italy, 83Juntendo University, Tokyo, Japan, 84Juntendo University faculty of medicine, Tokyo, Japan, 85Jikei University School of Medicine, Tokyo, Japan, 86Institute of Neurology and Neurorehabilitation, Almaty, Kazakhstan, 87Kyrgyz State Medical Academy, Bishkek, Kyrgyzstan, 88University of Luxembourg, Luxembourg, Luxembourg, 89University of Malaya, Kuala Lumpur, Malaysia, 90Universiti Kebangsaan Malaysia, Selangor, Malaysia, 91UKM Medical Molecular Biology Institute, Kuala Lumpur, Malaysia, 92Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia, 93International Islamic University, Kuala Lumpur, Malaysia, 94Tecnologico de Monterrey, Monterrey, Mexico, 95Instituto Nacional de Neurologia y Neurocirugia, Mexico City, Mexico, 96Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico, 97Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia, 98Tribhuvan University, Kirtipur, Nepal, 99University of Otago, Dunedin, New Zealand, 100University of Lagos, Lagos, Nigeria, 101College of Medicine of the University of Lagos, Lagos, Nigeria, 102Norwegian University of Science and Technology, Trondheim, Norway, 103Oslo University Hospital, Oslo, Norway, 104University of Science and Technology Bannu, Bannu, Pakistan, 105Instituto Nacional de Ciencias Neurologicas, Lima, Peru, 106Metropolitan Medical Center, Manila, Philippines, 107University of Puerto Rico, San Juan, Puerto Rico, 108Research Center of Neurology, Moscow, Russia, 109King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia, 110King Abdullah International Medical Research Center, Jeddah, Saudi Arabia, 111National Neuroscience Institute, Singapore, Singapore, 112Nanyang Technological University, Singapore, Singapore, 113University of KwaZulu-Natal, Durban, South Africa, 114University of Stellenbosch, Stellenbosch, South Africa, 115Stellenbosch University, Stellenbosch, South Africa, 116Seoul National University Hospital, Seoul, South Korea, 117Yongin Severance Hospital, Seoul, South Korea, 118Hospital Universitario Burgos, Burgos, Spain, 119University Hospital Mutua Terrassa, Barcelona, Spain, 120Institut de Recerca Sant Joan de Deu, Barcelona, Spain, 121Research Institute Germans Trias i Pujol, Barcelona, Spain, 122Instituto de Biomedicina de Sevilla, Seville, Spain, 123University Hospital Germans Trias i Pujol, Barcelona, Spain, 124Faculty of medicine university of Khartoum, Khartoum, Sudan, 125Inselspital Bern, University of Bern, Bern, Switzerland, 126National Taiwan University Hospital, Taipei City, Taiwan, 127Chang Gung Memorial Hospital, Taoyuan City, Taiwan, 128National Taiwan University, Taipei City, Taiwan, 129Chang Gung University, Taoyuan City, Taiwan, 130National Institute Mongi Ben Hamida of Neurology, Tunis, Tunisia, 131Mongi Ben Hmida National Institute of Neurology, Tunis, Tunisia, 132Ko\u00e7 University, Istanbul, Turkey, 133Sisli Etfal Training and Research Hospital, Istanbul, Turkey, 134Queen Mary University of London, London, United Kingdom, 135University College London, London, United Kingdom, 136University of Plymouth, Plymouth, United Kingdom, 137Parkinson\u2019s UK, London, United Kingdom, 138University of Glasgow, Glasgow, United Kingdom, 139Univeristy College London, London, United Kingdom, 140Cardiff University, Cardiff, United Kingdom, 141Royal Veterinary College University of London, London, United Kingdom, 142University of Bristol, Bristol, United Kingdom, 143Cure Parkinson\u2019s, London, United Kingdom, 144University of Cincinnati, Cincinnati, OH, USA, 145The Michael J. Fox Foundation for Parkinson\u2019s Research, New York, NY, USA, 146National Institute on Aging, Bethesda, MD, USA, 147Augusta University / University of Georgia Medical Partnership, Augusta, GA, USA, 148Mid-Atlantic Permanente Medical Group, Bethesda, MD, USA, 149Washington University, St. Louis, MO, USA, 150National Institutes of Health, Bethesda, MD, USA, 151Indiana University, Bloomington, IN, USA, 152Rush University, Chicago, IL, USA, 153Kaiser Permanente, Oakland, CA, USA, 154Coalition for Aligning Science, Washington, WA, USA, 155Banner Sun Health Research Institute, Sun City, AZ, USA, 156National Institute on Aging/National Institutes of Health, Bethesda, MD, USA, 157Data Tecnica International, Washington, WA, USA, 158Michigan State University, East Lansing, MI, USA, 159Cleveland Clinic, Cleveland, OH, USA, 160Northwestern University, Evanston, IL, USA, 161Baylor College of Medicine, Houston, TX, USA, 162Baylor College of Medicine / Texas Children\u2019s Hospital, Houston, TX, USA, 163University of Miami Miller School of Medicine, Miami, FL, USA, 164Beth Israel Deaconess Medical Center, Boston, MA, USA, 165North Shore University Health System, Chicago, IL, USA, 166Institute for Neurodegenerative Disorders, New Haven, CT, USA, 167University of Pittsburgh, Pittsburgh, PA, USA, 168University of Alabama at Birmingham, Birmingham, AL, USA, 169University of Maryland, Baltimore, MD, USA, 170Universit of Michigan, Ann Arbor, MI, USA, 171Columbia University, New York, NY, USA, 172James J. Peters Veterans Affairs Medical Center, New York, NY, USA, 173Aligning Science Across Parkinson\u2019s, Washington, WA, USA, 174University of Chicago, Chicago, IL, USA, 175Indiana University School of Medicine, Indianapolis, IN, USA, 176Sun Health Research Institution, Sun City, AZ, USA, 177Hue University, Hu\u1ebf, Vietnam, 178University of Zambia, Lusaka, Zambia."} +{"text": "The above abstract published with mistakes in some author names and affiliations. Some authors names were not included in the author list at all.The correct list of authors and their affiliations is as follows:1, A Jo Chien2, Rachel C Jankowitz3, Mark JM Magbanua4, Jason A Mouabbi5, Rebecca A Shatsky6, Julia Levine7 and Rita A Mukhtar8Harriet T Rothschild1School of Medicine, University of California, San Francisco, 2Department of Medicine, University of California, San Francisco, 3Department of Medicine, University of Pennsylvania, 4Department of Laboratory Medicine, University of California, San Francisco, 5Department of Breast Medical Oncology, MD Anderson Cancer Center, 6Department of Medicine, University of California, San Diego, 7Lobular Breast Cancer Alliance and 8Department of Surgery, University of California, San FranciscoThe original abstract has been corrected online to rectify these errors."} +{"text": "Correction to: Child and Adolescent Psychiatry and Mental Health (2023) 17:45 10.1186/s13034-023-00596-wAn earlier version of the eIn Abstract section, the numbers 11, 10, 13 and 1 should be replaced by 10, 12, 11 and 2 respectively.In Findings section , the numbers 50 and 37 should be replaced by 67 and 52 respectively.In the same section , numbers 14, 14, 29 and 15 should be replaced by 26, 19, 44 and 32 respectively.In Work-family Conflict section , the numbers 37, 18, 18 and 1 should be replaced by 52, 27, 23 and 2 respectively.In Direction of Work-family Conflict section , numbers 13, 11, 11, 7 and 6 should be replaced by 27, 9, 12, 18 and 9 respectively.In Work-family Conflict and Specific Outcomes the numbers 10, 10, 7, 3, 3, 7, 13, 8 and 1 should be replaced by 15, 22, 8, 6, 11, 10, 11, 6 and 2 respectively.In Role of Parental Sex section , the numbers 22, 8, 7, 10, 1, 7, 4, and 4 should be replaced by 24, 11, 17, 0, 11, 6 and 5 respectively. The interpretation changes here, as the proportion of positive associations is higher for mothers.In Mediation Effects section the numbers 11, 3, 9, 2, and 3 should be replaced by 19, 5, 14, 5 and 5 respectively.In Discussion section , the number 37 should be replaced by 52."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1,2,3, John Humphrey Amuasi2,3,4,5, Evie Prokesh1, Alexis Beyuo6, Chrisantus Danaah Dari7, Sofanne J. Ravensbergen1, Melvin Katey Agbogbatey2,8, Austin Gideon Adobasom Anane2,4, Kabiru Mohammed Abass9, David G Lalloo10, J\u00f6rg Blessmann8, Benno Kreuels5,8, Ymkje Stienstra1,10Leslie Mawuli AglanuAffiliations1 University Medical Centre Groningen, Department of Internal Medicine/Infectious Diseases, University of Groningen, Groningen, The Netherlands2 Global Health and Infectious Diseases Research Group, Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana3 Research Group Global One Health, Department of Implementation Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany4 Department of Global Health, School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana5 Division for Tropical Medicine, Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany6 Department of Development Studies, Simon Diedong Dombo University of Business and Integrated Development Studies, Upper West Region, Wa, Ghana7 Regional Health Directorate, Ghana Health Service, Upper West Region, Wa, Ghana8 Research Group Snakebite Envenoming, Department of Implementation Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany9 Presbyterian Hospital, Agogo, Ashanti Region, Ghana10 Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom"} +{"text": "In the above article, an error was made in the author affiliations, which had been listed as:1, Yuqian Dai2, Qi Wang1, Jie Yang3, Xiang Chen1, Ting\u2010Ting Liu3, Jie Liu1,3*Binlu Deng1Southwest Medical University, Luzhou, China2School of Medicine, St. George's University, St. George, Grenada3Department of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China1Department of Neurology, the Affiliated Hospital of Southwest Medical University, Luzhou, China.\u201dThe affiliation to Southwest Medical University should be changed to:\u201cWe apologize for this error."} +{"text": "This article has been corrected: The affiliation of Dr. Shu-Feng Zhou has been clarified. This work was started in Dr. Shu-Feng Zhou's laboratory in 2013, when he was at the University of South Florida. However, he left that position in 2016 and was not affiliated with USF at the time of the article's publication. His current affiliation is the College of Chemical Engineering, Huaqiao University, Xiamen 361021, China. The corrected authors affiliations are listed below.1,2,3,4,5, Qing Li6,8, Cheng-xiong Xu6,8, Zhi-Wei Zhou7, Guan-Bin Song7, Cheng-Bin Hu9, Fang Wen2, Han-Lin Yang2, Lei Nie2, Xing Zhao3, Jun Tan4, Shu-Feng Zhou5,10, Zhi-Xu He3,11Dan Zi1Department of Obstetrics and Gynecology, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou, China2Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China3Key Laboratory of Adult Stem Cell Transformation Research, Chinese Academy of Medical Sciences/Stem Cell and Tissue Engineering Research Center, Guizhou Medical University, Guiyang 550004, China4Key Laboratory of Endemic and Ethnic Diseases and Key Laboratory of Molecular Biology, Ministry of Education, Guizhou Medical University, Guiyang 550004, China5Former affiliation: Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL 33612, USA6Cancer Center, Daping Hospital and Research Institute of Surgery, The Third Military Medical University, Yuzhong 40042, Chongqing, China7Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA8Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China9Department of Computer Science and Engineering, University of South Florida, Tampa, FL 33620, USA10Current affiliation: Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian, China11Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China"} +{"text": "Correction to: Military Medical Research (2023) 10:8 10.1186/s40779-023-00443-1Following publication of the original article , it was 1 The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People\u2019s Hospital, Quzhou 324000, Zhejiang, China2 Istituto Italiano di Tecnologia, Centre for Materials Interfaces, Pontedera 56025, ItalyThe original paper has been updated."} +{"text": "JCO Glob Oncol10.1200/GO.22.57000) was published online May 5, 2022, with errors.The meeting abstract by Sanga et al entitled \u201cCommunity Awareness About Pediatric Cancer in Tanzania\u201d (4Kilimanjaro Christian Medical University College, Moshi, Tanzania5Kilimanjaro Christian Medical Center, Moshi, TanzaniaIn the affiliation list, the following should have been included:3 should have been Elizabeth Msoka, MSc3,4,5. The remaining author affiliations should have been Shabani Rajabu, MA6; Francis Karia, MBA, MSc-PH7; Hillary Sued, BS6; Kathryn Pollak, PhD8; and Kristin Schroeder, MD, MPH8 and the full affiliation list updated to:In the author list, `Elizabeth Msoka, MSc1National Institute of Medical Research\u2014Lake Zone, Dar-es-Salaam, Tanzania2National Institute of Medical Research Headquarters, Dar-es-Salaam, Tanzania3Kilimanjaro Clinical Research Institute, Moshi, Tanzania4Kilimanjaro Christian Medical University College, Moshi, Tanzania5Kilimanjaro Christian Medical Center, Moshi, Tanzania6Bugando Medical Center, Mwanza, Tanzania7Duke Clinical Research Institute, Durham, NC8Duke University Medical Center, Durham, NCThis has been corrected as of July 5, 2022. The authors apologize for the errors."} +{"text": "Scientific Reportshttps://doi.org/10.1038/s41598-023-36914-7, published online 18 June 2023Correction to: The original version of this Article contained an error in Affiliations 1 and 4.Affiliation 1\u201cGraduate School of Human Life Design, Tokyo University, 1-7-11 Akabanedai, Kita-Ku 115-8650, Tokyo, Japan.\u201dnow reads:\u201cGraduate School of Human Life Design, Toyo University, 1-7-11 Akabanedai, Kita-Ku 115-8650, Tokyo, Japan.\u201dAnd Affiliation 4\u201cGraduate School of Health and Sports Science, Tokyo University, Tokyo, Japan.\u201dnow reads:\u201cGraduate School of Health and Sports Science, Toyo University, Tokyo, Japan.\u201dThe original Article has been corrected."} +{"text": "Correction: BioMedical Engineering OnLine (2023) 22:17 https://doi.org/10.1186/s12938-022-01049-9Following publication of the original article , the aff1, Tianyou Zhang2, Liying Lin3, Fenghua Long4, Hongyu Guo4* and Li Han4,5*Zefeng Liu1Department of Radiology, Tianjin Medical University General Hospital, Tianjin 300052, People\u2019s Republic of China2First Central Clinical College, Tianjin Medical University, 22 Qixiangtai Road, Heping District, Tianjin 300070, People\u2019s Republic of China3Department of Radiology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300041, People\u2019s Republic of China4School of Medical Imaging, Tianjin Medical University, 9\u2011307, Guangdong Rd. #1, Hexi, Tianjin 300203, People\u2019s Republic of China5Department of Radiology, University of Michigan, Ann Arbor, Michigan 48109, USAThe original article has been corrected."} +{"text": "Correction: BMC Plant Biol23, 527 (2023)https://doi.org/10.1186/s12870-023-04557-5Following publication of the original article , author Chang Liu1,2\u2020, Mengya Cheng1,3\u2020, Chao Ma4, Junfeng Chen1 and Hexin Tan1,2,5*1Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University , Shanghai, China2Department of Pharmacy, Shanghai Fourth People\u2019s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China3School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China4Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China5 Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, ChinaFurthermore, the font\u2019s style and size of texts in the images of all figures are updated to be consistent. The correct Figs."} +{"text": "Author Debmalya Barh was omitted from the original submission. The full list of authors and affiliations can be found below:1Edward Hill2 David Han1Pierre Dumouchel3Najim Dehak4Thomas Quatieri5Charles Moehs6Marlene Oscar-Berman7John Giordano8Thomas Simpatico13Debmalya Barh7,8,9,10,11,12,13Kenneth Blum1 Department of Software and Information Technology Engineering, \u00c9cole de Technologie Sup\u00e9rieure - Universit\u00e9 du Qu\u00e9bec, Montr\u00e9al, Qu\u00e9bec, Canada2 Department of Management Science and Statistics, University of Texas at San Antonio, San Antonio, Texas, United States of America3 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America4 Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, Massachusetts, United States of America5 Occupational Medicine Associates, Watertown, New York, United States of America6 Departments of Psychiatry, Neurology, and Anatomy and Neurobiology, Boston University School of Medicine, and Boston Veteran Affaires Healthcare System, Boston, Massachusetts, United States of America7 G & G Holistic Health Care Services, LLC., North Miami Beach, Florida, United States of America8 Global Integrated Services Unit University of Vermont Center for Clinical and Translational Science, College of Medicine, Burlington, Vermont, United States of America9 Department of Psychiatry and McKnight Brain Institute, University of Florida, College of Medicine, Gainesville, Florida, United States of America10 Dominion Diagnostics, LLC, North Kingstown, Rhode Island, United States of America11 Department of Clinical Neurology, Path Foundation New York, New York, United States of America12 Department of Addiction Research and Therapy, Malibu Beach Recovery Center, Malibu Beach, California, United States of America13 Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India"} +{"text": "Published 4 June 2013Gutierrez-Arcelus M, Lappalainen T, Montgomery SB, Buil A, Ongen H, Yurovsky A, Bryois J, Giger T, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Padioleau I, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. 2013. Passive and active DNA methylation and the interplay with genetic variation in gene regulation. The affiliations for Stephen B Montgomery were incorrect, and there were errors in affiliations 1 and 2. The correct author affiliations are:1,2,3, Tuuli Lappalainen1,2,3, Stephen B Montgomery1,4, Alfonso Buil1,2,3, Halit Ongen1,2,3, Alisa Yurovsky1,2,3, Julien Bryois1,2,3, Thomas Giger1,2, Luciana Romano1,2,3, Alexandra Planchon1,2,3, Emilie Falconnet1,2, Deborah Bielser1,2, Maryline Gagnebin1,2, Ismael Padioleau1,2,3, Christelle Borel1,2, Audrey Letourneau1,2, Periklis Makrythanasis1,2, Michel Guipponi1,2, Corinne Gehrig1,2, Stylianos E Antonarakis1,2, Emmanouil T Dermitzakis1,2,3Maria Gutierrez-Arcelus1Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; 2Institute of Genetics and Genomics in Geneva, Geneva, Switzerland; 3Swiss Institute of Bioinformatics, Geneva, Switzerland; 4Departments of Pathology and Genetics, Stanford University, Stanford, United StatesThe article has been corrected accordingly."} +{"text": "The author affiliations are not in the correct order. Affiliation 1 and affiliation 2 should be switched. The full, correct list of authors and affiliations can be found below.1,2\u262fHuaijie Hao2,3\u262fWenjia Hui2Peng Liu2Qingyu Lv2Xiaotao Zeng2Hua Jiang2,4Yanzi Wang2,5Xin Zheng2Yuling Zheng3*Jianchun Li1*Xuyu Zhou2*Yongqiang Jiang 1 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China 2 State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China 3 Department of Traditional Chinese Medicine Pharmacology, Shenyang Pharmaceutical University, Shenyang, China 4 Department of Pharmacy, Jiangsu Provincial Xuzhou Pharmaceutical Vocational College, Xuzhou, China 5 Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China* E-mail: jiangyq@nic.bmi.ac.cn (YJ); zhouxy@im.ac.cn (X. Zhou); lijianchun0317@sina.com.cn (JL)\u262f These two authors contributed equally to this work."} +{"text": "There were errors in the author affiliations. The affiliations should appear as shown here:1#, So-Young Jun2#, Bo-Young Yoon2, Saemee Song1, Kangseok Lee1*, Nam-Chul Ha2*Minho Lee1 Department of Life Science, Chung-Ang University, Seoul, Republic of Korea, 2 Department of Manufacturing Pharmacy, College of Pharmacy, Research Institute for Drug Development, Pusan National University, Busan, Republic of Korea"} +{"text": "Published 13 December 2012Ragunathan K, Liu C, Ha T. 2012. RecA filament sliding on DNA facilitates homology search. The author affiliations for Kaushik Ragunathan and Taekjip Ha were incorrect. The correct author affiliations are:1,2,3\u2020a, Cheng Liu4\u2020b, Taekjip Ha1,2,3,4,5*Kaushik Ragunathan1Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States2Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States3Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States4Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States5Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States\u2020aDepartment of Cell Biology, Harvard Medical School, Boston, United States; \u2020bCenter for Research Computing, University of Notre Dame, Notre Dame, United StatesPresent address: The article has been corrected accordingly."} +{"text": "Zookeys 51: 17\u201332, doi: 10.3897/zookeys.51.457), the below text:In the paper of Wu and Zhou (Jie Wu 1,\u2020, Hong-Zhang Zhou 2,\u20211\tKey Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichenxi Rd., Chaoyang District, Beijing 100101, P. R. China2\tShanghai Entomological Museum, Chinese Academy of Sciences, 300 Fenglin Rd., Xuhui District, Shanghai 200032, P. R. Chinashould read:Jie Wu 1,2,\u2020, Hong-Zhang Zhou 1,\u20211\tKey Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichenxi Rd., Chaoyang District, Beijing 100101, P. R. China2\tShanghai Entomological Museum, Chinese Academy of Sciences, 300 Fenglin Rd., Xuhui District, Shanghai 200032, P. R. China"} +{"text": "There were errors in the author affiliations. The correct versions of the affiliations are available below:2,5\u262f, Ryan M. B. Hoffman1,2\u262f, Anat Burger2,3, Patricio O. Craig1,2, Elizabeth A. Komives1, Peter G. Wolynes2,4*Nicholas P. Schafer1 Chemistry/Biochemistry, University of California San Diego, La Jolla, California, United States of America,2 Center for Theoretical Biological Physics, University of California, San Diego and Rice University, La Jolla, CA and Houston, TX, USA3 Physics, University of California San Diego, La Jolla, California, United States of America,4 Chemistry, Rice University, Houston, Texas, United States of America,5 Physics and Astronomy, Rice University, Houston, Texas, United States of AmericaIn numerous occasions in the References section, the author name \"Wolnes P\" should have been \"Wolynes PG\"."} +{"text": "Lie-Cun Gao was not included in the author byline. Please view the correct author order, affiliations, and citation here:1,4#, Liu-Cun Gao2#, Ya-Bo Yan1,3#, Zi-Xiang Wu1, Tian-Xia Qiu3, Ee-Chon Teo3, Wei Lei1*Wei Qi1 Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi\u2019an, China, 2 State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi\u2019an, China, 3 School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 4 Surgery Department of 520th Hospital of PLA, Mian yang, ChinaQi W, Gao L-C, Yan Y-B, Wu Z-X, Qiu T-X, Teo E-C, et al. (2012) Finite Element Study of the Mechanical Response in Spinal Cord during the Thoracolumbar Burst Fracture. PLoS ONE 7(9): e41397. doi:10.1371/journal.pone.0041397"} +{"text": "There is an additional error in the affiliations. The correct affiliations are:Zhen Qu1,Lanzhi Li1,2, Junyuan Luo3, Peng Wang3, Sibin Yu3, Tongmin Mou3*, Xingfei Zheng1,Zhongli Hu1*1 State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China,2 Hunan Provincial Key Laboratory for Biology and Control of Plant Disease and Insect Pests, College of Bio-Safety Science and Technology, Hunan Agricultural University, Changsha, China,3 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China."} +{"text": "There was an error in the author byline. The correct author list and affiliations are:1, Melissa D. Landis1, David J. Tweardy2,Jenny C. Chang1Bhuvanesh Dave1 The Methodist Cancer Center, Houston, Texas, United States of America,2 Department of Infectious Diseases, Departments of Molecular & Cellular Biology andRadiology, Baylor College of Medicine, Houston, Texas, United States of America"} +{"text": "The order of authors is incorrect. Please view the correct author order, order of affiliations and Citation below:1, Pengcheng Liu 1, Li Wei 2, Jinshen Wang 2, Jin Qi 2, Shengmei Feng 2, Lianfu Deng 2Ming Cai1 Department of Orthopaedics, Shanghai Tenth People\u2019s Hospital, Tongji University School of Medicine, Shanghai, China2 Shanghai Institute of Traumatology and Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Ruijin Hospital, Jiao Tong University School of Medicine, Shanghai, ChinaCai M, Liu P, Wei L, Wang J, Qi J, et al. (2014) Atp6v1c1 May Regulate Filament Actin Arrangement in Breast Cancer Cells. PLoS ONE 9(1): e84833. doi:10.1371/journal.pone.0084833"} +{"text": "There were errors in the author affiliations. The correct affiliations are as follows:1,2, Chao-sheng He3, Ming Liu1,2Mian Xie1 China State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China2 Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China3 Southern Medical University, Guangzhou, China"} +{"text": "Several authors were not included in the author byline. Please see the correct list of authors, affiliations, and citation here:Mary Elizabeth Wilson1*, Felipe Fregni2, Maria Amelia de S.M.Veras3, Jason Dyett4, Amie Shei5, Guilherme Sousa Ribeiro6, John David7, Marcia C. Castro1, Aluisio Cotrim Segurado8, Albert Icksang Ko9, Mitermayer G. Reis101 Department of Global Health and Population, Harvard School of Public Health, Boston, Massachusetts, United States of America, 2 Harvard Medical School; Spaulding Rehabilitation Hospital and Massachusetts General Hospital, Boston, Massachusetts, United States of America, 3 Department of Social Medicine, School of Medical Sciences, Santa Casa do S\u00e3o Paulo, S\u00e3o Paulo, Brazil, 4 Brazil Office, David Rockefeller Center for Latin American Studies at Harvard, S\u00e3o Paulo, Brazil, 5 Harvard University Ph.D. Program in Health Policy, Cambridge, Massachusetts, United States of America, 6 Instituto de Saude Coletva, Universidade Federal da Bahia and Fundacao Oswaldo Cruz, Salvador, Bahia, Brazil, 7 Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America, 8 Department of Infectious Diseases, School of Medicine, University of S\u00e3o Paulo, S\u00e3o Paulo, Brazil 9 Yale School of Public Health, Epidemiology of Microbial Disease Division, New Haven, Connecticut, United States of America, 10 Funda\u00e7\u00e3o Oswaldo Cruz, Salvador, Bahia, Brazil; Escola Bahiana de Medicina e Sa\u00fade P\u00fablica and Faculdade de Medicina da Bahia, Federal University of Bahia, Salvador, Bahia, BrazilWilson ME, Fregni F, Veras MASM, Dyett J, Shei A (2011) Collaborative Teaching and Learning: A Model for Building Capacity and Partnerships to Address NTDs. PLoS Negl Trop Dis 5(3): e939. doi:10.1371/journal.pntd.0000939"} +{"text": "The names of the fourth and fifth authors are incorrectly merged. Please view the correct list of authors, affiliations and Citation below:1*, Md Amir Hossain3, Mahtab Uddin Hassan3, Sophie Osbourne1, Katherine Langan1, Abu Sayeed3, Mohammed Rezaul Karim3, Rasheda Samad3, Shyamanga Borooah4,Bal Dhillon4, Nicholas P. J. Day1,2, Arjen M. Dondorp1,2, Richard J. Maude1,2,4Rapeephan R. Maude1 Mahidol-Oxford Tropical Medicine Research Unit, Rajthewi, Bangkok, Thailand2 Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom3 Chittagong Medical College Hospital, Chittagong, Bangladesh4 College of Medicine and Veterinary Medicine, University of Edinburgh,Edinburgh, United KingdomMaude RR, Amir Hossain M, Hassan MU, Osbourne S, Langan K, et al. (2013) Transorbital Sonographic Evaluation of Normal Optic Nerve Sheath Diameter in Healthy Volunteers in Bangladesh. PLoS ONE 8(12): e81013. doi:10.1371/journal.pone.0081013"} +{"text": "There were errors in the author affiliations. The affiliations should appear as shown here:1*, Nada El Husseini2, Cody A. Chastain3, Michael S. Lee4, Charles Poole1, Til St\u00fcrmer1, Jonathan J. Juliano5, David J. Weber1,5, John R. Perfect2Emily W. Bratton1 Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 2 Department of Medicine, Duke University, Durham, North Carolina, United States of America, 3 Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America, 4 Department of Medicine, Brigham and Women\u2019s Hospital, Boston, Massachusetts, United States of America, 5 Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America"} +{"text": "Four authors were erroneously excluded from the author list.1,2,4*, Steven R. Meikle1,2, Hong Zhou3, Yu Zheng3, Julie M. Blair3,6, Marcus Seibel3, Colin R. Dunstan3,5, Richard B. Banati1,2,4.The correct byline is: Winnie Wai-Ying KamThe correct affiliations are:1 Discipline of Medical Radiation Sciences, Faculty of Health Sciences, University of Sydney, Cumberland, New South Wales, Australia,2 Ramaciotti Imaging Center, Brain and Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia,3 Bone Research Program, Anzac Research Institute, University of Sydney, Concord, New South Wales, Australia,4 Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales, Australia,5 School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, Camperdown, New South Wales, Australia,6 Department of Medical Affairs, Amgen Australia Ptv. Ltd., Macquarie Park, New South Wales, Australia.The correct citation is: Kam WW-Y, Meikle SR, Zhou H, Zheng Y, Blair JM, et al. (2012) The 18 kDa Translocator Protein Expression in the Bone of Normal, Osteoprotegerin or Low Calcium Diet Treated Mice. PLoS ONE 7(1): e30623. doi:10.1371/journal.pone.0030623The correct author contributions are: Conceived and designed the experiments: WW-YK SRM MS CRD RBB. Performed the experiments: WW-YK SRM HZ YZ JMB CRD. Analyzed the data: WW-YK SRM HZ YZ JMB CRD RBB. Contributed reagents/materials/analysis tools: SRM HZ YZ JMB CRD RBB. Wrote the paper: WW-YK."} +{"text": "The authors wish to add R\u00e9mi Mounier as the 4th author in the byline. The updated byline is: Herv\u00e9 Pournot1,2, Fran\u00e7ois Bieuzen1*, Julien Louis2, R\u00e9mi Mounier4, Jean-Robert Fillard3, Etienne Barbiche5, Christophe Hausswirth1The updated Affiliations are: 1 Research Department, National Institute of Sport, Expertise and Performance (INSEP), Paris, France, 2 Laboratory of Physiological Adaptations, Motor Performance and Health (EA 3837), Faculty of Sport Sciences of Nice-Sophia Antipolis, Nice, France, 3 Medical Department, National Institute of Sport, Expertise and Performance (INSEP), Paris, France, 4 Capbreton, France, 5 Inserm U1016, Institut Cochin, Paris, FranceThe updated citation is: Pournot H, Bieuzen F, Louis J, Mounier R, Fillard J-R, et al. (2011) Time-Course of Changes in Inflammatory Response after Whole-Body Cryotherapy Multi Exposures following Severe Exercise. PLoS ONE 6(7): e22748. doi:10.1371/journal.pone.0022748In addition to the other authors's contributions, R\u00e9mi Mounier's roles were: Conceived and designed the experiments, Performed the experiments, Analyzed the data, Contributed reagents/materials/analysis tools, and Wrote the manuscript"} +{"text": "There were errors in the author affiliations. The correct affiliations are:1, Steven M. Abel1, Arup K. Chakraborty1,2,3,4*Woo Chung1 Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America,2 Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America,3 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America,4 Ragon Institute of MGH, MIT, and Harvard, Charlestown, Massachusetts, United States of America"} +{"text": "In the byline, the author order is incorrect. Please see the correct author order, order of affiliations and Citation below.1, Yang Liu2, Fang Zhou2, Guirong Wang1, Chunju An1Dongxu Shen1 Department of Entomology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, China2 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, ChinaOstrinia furnacalis against Entomopathogenic Fungi by RNA-Seq Analysis. PLoS ONE 9(1): e86436. doi:10.1371/journal.pone.0086436Citation: Shen D, Liu Y, Zhou F, Wang G, An C (2014) Identification of Immunity-Related Genes in"} +{"text": "There were errors in the published affiliations. The correct affiliations are:1,2 Hong-Zhe Zhang1,2 Longzhe Guo3Jong-Min Kim4 Moo Hyun Kim1,2Sung-Whan Kim1 Regional Clinical Trial Center, Dong-A University Hospital, Busan, South Korea2 Department of Cardiology, College of Medicine , Dong-A University, Busan , SouthKorea3 Department of Cardiology, The Forth Hospital of Harbin Medical University, Harbin,China4 Department of Anatomy and & Cell Biology and Mitochondria Hub Regulation Center,College of Medicine, Dong-A University, Busan, South Korea"} +{"text": "The Acknowledgments section is missing author and affiliation information about the H. B. C. Study Team. The following is the list of authors and their affiliations:The HBC study team includes: Ms. Riyo Takabayashi 1, Yukiko Suzuki 1, Yumeno Kugizaki 1, Hiroko Muraki 1, Yui Seno 1, Emiko Kawai 1,2, Noriko Kodera 1, Emi Higashimoto 1, Atsuko Nakamura 1, Eriko Sato 1, Drs. Naohiro Kanayama 3, Hiroaki Itoh 3, Chie Shimmura 1, Yujin K. Kuroda 1, Shun Takahashi 1,2, Tsuruko Mori 1,2, Keiko Iwata 1,2, Yosuke Kameno 1,4, Yujiro Yoshihara 1,4, Shu Takagai 4, Tomoyasu Wakuda 4, Kiyokazu Takebayashi 4, Daisuke Kurita 4, Masayoshi Kawai 4, Shiro Suda 1, Genichi Sugihara 1, Kyoko Nakaizumi 1, Koichi Hirano 5, Yusaku Endoh 5, Teruhiko Suzuki 5, Toshirou Sugiyama 2,6, and Masatsugu Tsujii 1,2,7.1 Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu, Japan,2 United Graduate School of Child Development, Hamamatsu University School of Medicine, Hamamatsu, Japan,3 Department of Obstetrics and Gynaecology, Hamamatsu University School of Medicine, Hamamatsu, Japan,4 Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan,5 Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan,6 Department of Child Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan,7 Faculty of Modern Sociology, Chukyo University, Nagoya, Japan"} +{"text": "Please view the correct author order, affiliations, and citation here: Jing Wang1 Department of Orthodontics, College of Stomatology, Forth Military Medical University, Xin Cheng District, Xi\u2019an, China2 Department of Urological, General Hospital of People\u2019s Liberation Army, Hai Dian District, Beijing, China3 Department of Pathology and Experimental Medicine, 306 Hospital of PLA, Chao Yang District, Beijing, China4 Department of Stomatology, 306 Hospital of PLA, Chao Yang District, Beijing, China.Wang J, Zhu Q, Song S, Shi L, Ma C, et al. (2013) Temporal Expression of Pelp1 during Proliferation and Osteogenic Differentiation of Rat Bone Marrow Mesenchymal Stem Cells. PLoS ONE 8(10): e75477. doi:10.1371/journal.pone.0075477."} +{"text": "P value should be 0.68, not 0.034, on page 8, column 1, paragraph 2, line 12. None of these corrections affect any of the conclusions drawn.The country name mentioned before reference [14] on page 5, column 2, line 3, should be the United Kingdom, not Australia. Also, the"} +{"text": "The affiliations for the 1st, 8th, 9th, and 10th authors were not indicated. The complete author list and affiliations are:Junyan Feng, Lu Lu(1), Cong Hua(1), Ling Qin(1), Pingwei Zhao(1), Juan Wang(1), Ye Wang(1), Wanyu Li(2), Xiaodong Shi(2), Yanfang Jiang(1) Department of Central Laboratory, the Second Part of First Hospital, Jilin University, Changchun, China(2) Department of Hepatology, First Hospital, Jilin University, Changchun, China"} +{"text": "We noticed an error that the name of a key contributor, Dr. Yu Wu, was left out from the author list. The corrected author list and the affiliations are the following.1, Luye Mu2, Yao Lu1, Jonathan J. Chen1, Yu Wu1, Kara Brower1,3 and Rong Fan1,4*Minsuk Kwak1Department of Biomedical Engineering, Yale University, New Haven, CT, USA2Department of Electrical Engineering, Yale University, New Haven, CT, USA3Isoplexis Inc., New Haven, CT, USA4Yale Comprehensive Cancer Center, New Haven, CT, USA"} +{"text": "Department of Clinical Neuroimaging, Integrative Brain Imaging Center, National Center for Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan was missing from the affiliation list. The corrected affiliations are:Yuki Motomura,1,2,3 Shingo Kitamura,1 Kentaro Oba,1,2 Yuri Terasawa,1,2 Minori Enomoto,1 Yasuko Katayose,1 Akiko Hida,1 Yoshiya Moriguchi,1,2 Shigekazu Higuchi,4 and Kazuo Mishima1,2,*1 Department of Psychophysiology, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan2 Department of Clinical Neuroimaging, Integrative Brain Imaging Center, National Center for Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan3 Graduate School of Integrated Frontier Science, Kyushu University 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Japan4 Faculty of Design, Kyushu University 4-9-1 Shiobaru, Minami-ku, Fukuoka, JapanUniversity of Pennsylvania School of Medicine, United States of America"} +{"text": "We report the complete genomic sequences of an avian orthoreovirus, strain GuangxiR1, isolated from a chicken flock in Guangxi Province, southern China, in 2000. Phylogenetic analyses suggest that the strain is closely related to the S1133 strain, which is associated with tenosynovitis, but is far different from strain AVS-B, which is associated with runting-stunting syndrome in broilers. Orthoreovirus, family Reoviridae (Avian orthoreovirus (ARV) is the etiological agent of viral arthritis, runting-stunting syndrome, and tenosynovitis in chickens, causing significant economic losses in the poultry industry , 2. Aviaoviridae . The genoviridae . These soviridae , 6, 7. Toviridae .The avian orthoreovirus strain GuangxiR1, which caused paralysis and hock joints in commercial broilers, was isolated from Guangxi, southern China, in 2000 , 10. TheThe complete genome of GuangxiR1 is 23,494\u00a0bp. The full lengths of the L1, L2, L3, M1, M2, M3, S1, S2, S3, and S4 segments are 3,959, 3,830, 3,907, 2,283, 2,158, 1,996, 1,643, 1,324, 1,202, and 1,192 nucleotides, respectively. The deduced lengths of the structural and nonstructural proteins \u03bba, \u03bbB, \u03bbC, \u03bcA, \u03bcB, \u03bcNS, \u03c3C, \u03c3A, \u03c3B, and \u03c3NS are 1,293, 1,259, 1,285, 732, 676, 635, 326, 416, 367, and 367\u00a0amino acids, respectively. The \u03c3C protein, involved in the induction of apoptosis, is coded by the S1 segment. Amino\u00a0acid comparative analyses indicated that \u03c3C shares the highest sequence homology (98.2%) with that from the S1133 strain, associated with tenosynovitis (GenBank accession no. AF330703), but only 48.5% with that from the AVS-B strain, associated with runting-stunting syndrome in broilers (GenBank accession no. FR694197). These data are useful for analyses of the epidemiology and evolutionary characteristics of avian orthoreovirus GuangxiR1.KC183743 to KC183752 correspond to L1, L2, L3, M1, M2, M3, S1, S2, S3, and S4, respectively.The complete genome sequences of GuangxiR1 are available in GenBank. The accession no."} +{"text": "The affiliations for Dr. J\u00f6rg Schorer are incorrect. The full, correct author byline and affiliations are as follows:1,3, Nick Wattie2, Joseph R. Baker2J\u00f6rg Schorer1 Institute of Sport and Exercise Sciences, University of Muenster, M\u00fcnster, Germany, 2 School of Kinesiology and Health Science, York University, Toronto, Canada, 3 Institute for Sport Science, University of Oldenburg, Oldenburg, Germany"} +{"text": "Author Zhongdao Li is missing an affiliation. The complete byline and affiliations are:Zhongdao Li1,2,3, Jikai Wen4, Yaning Lin5, Shihua Wang5, Peng Xue2, Zhiping Zhang1, Ying Zhou2, Xiao Wang6, Li Sui6, Li-Jun Bi2*, Xian-En Zhang1*1 State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China,2 National Laboratory of Biomacromolecules and Proteomics Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,3 Graduate School, Chinese Academy of Sciences, Beijing, China,4 School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK,5 College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China,6 Department of Nuclear Physics, China Institute of Atomic Energy, Beijing, China"} +{"text": "Author Francesco Viola was omitted from the author byline. The full, correct list of authors and affiliations is as follows:1Federico Ricci2Giovanni Staurenghi3Tiziana Lepre1Filippo Missiroli3Stefania Zampatti3Raffaella Cascella3Paola Borgiani3Luigi Tonino Marsella4Chiara Maria Eandi7Francesco Viola1Andrea Cusumano5,6Giuseppe Novelli3Emiliano Giardina1 UOSD Patologia retinica Fondazione PTV \"Policlinico Tor Vergata\", Rome, Italy2 Eye Clinic, Department of Clinical Science \"Luigi Sacco\", Sacco Hospital, University ofMilan, Milan, Italy3 Department of Biomedicine and Prevention, Centre of Excellence for Genomic Risk Assessment in Multifactorial and Complex Diseases, School of Medicine, University of Rome \"Tor Vergata\", Rome, Italy4 Department of Clinical Physiopathology, Eye Clinic, University of Torino, Turin, Italy5 National Agency of Evaluation of Universities and Research (ANVUR), Rome, Italy6 S. Pietro Fatebenefratelli Hospital, Rome, Italy7 UO Oculistica Fondazione IRCCS C\u00e0 Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy"} +{"text": "There are multiple errors in the order and affiliations of multiple authors. Please see the correct author order and list of affiliations below.1, Paolo Verderio2, Sara Pizzamiglio2, Carmela Nici3, Maria Valeria Maiorana3, Alessio Naccarati1,4, Ludmila Vodickova5,6, Veronika Vymetalkova5,6, Silvia Veneroni7, Maria Grazia Daidone7, Fernando Ravagnani8, Tiziana Bianchi9, EPICOLON Consortium\u00b6, Luis Bujanda10, Angel Carracedo11, Antoni Castells12, Clara Ruiz-Ponte11, Hans Morreau13, Kimberley Howarth14, Angela Jones14, Sergi Castellv\u00ed-Bel12, Li Li15, Ian Tomlinson14, Tom Van Wezel13, Pavel Vodicka4,5, Paolo Radice16, Paolo Peterlongo3Barbara PardiniGenomic Variation in Human Populations and Complex Diseases Unit, Human Genetics Foundation, Turin, Italy.Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.Molecular and Genetic Epidemiology Unit, Human Genetics Foundation, Turin, Italy.Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic.First Medical Faculty, Charles University, Prague, Czech Republic.Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.Immunohematology and Transfusion Medicine Service, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.Associazione Italiana Volontari Sangue (AVIS) Comunale Milano, Milan, Italy.Gastroenterology Department, Hospital Donostia, Networked Biomedical Research Centre for Hepatic and Digestive Diseases (CIBEREHD), Basque Country University, San Sebasti\u00e1n, Spain.Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Cl\u00ednico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain.Department of Gastroenterology, Hospital Cl\u00ednic, Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Hep\u00e1ticas y Digestivas (CIBEREHD), Institut d\u2019Investigacions Biom\u00e8diques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain.Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.Molecular and Population Genetics Laboratory and NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.Department of Family Medicine and Community Health and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America.Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.\u00b6 Please see the Acknowledgments for a full list of authors comprising the EPICOLON Consortium and their respective affiliations.In addition, there are multiple errors in"} +{"text": "Two authors, Adam R. Karpf, and Smith A. James, were inadvertently omitted from the by-lineand Author Contributions section. The correct author byline is: Foluso O. Ademuyiwa 1*, WiamBshara 2, Kristopher Attwood 3, Carl Morrison 2, Stephen B. Edge 4, Adam R. Karpf 5, SmithA. James 5, Christine B. Ambrosone 6, Tracey L. O\u2019Connor 1, Ellis G. Levine 1, AnthonyMiliotto 7, Erika Ritter 8, Gerd Ritter 8, Sacha Gnjatic 8, Kunle Odunsi 7.The correct affiliation list is: 1 Department of Medicine, Roswell Park Cancer Institute,Buffalo, New York, United States of America, 2 Department of Pathology, Roswell Park CancerInstitute, Buffalo, New York, United States of America, 3 Department of Biostatistics,Roswell Park Cancer Institute, Buffalo, New York, United States of America, 4 Department ofSurgical Oncology, Roswell Park Cancer Institute, Buffalo, New York, United States ofAmerica, 5 Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute,Buffalo, New York, United States of America 6 Department of Cancer Prevention and Control,Roswell Park Cancer Institute, Buffalo, New York, United States of America, 7 Department ofGynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, United States ofAmerica, 8 Ludwig Institute for Cancer Research Ltd. New York Branch of Human CancerImmunology, Memorial Sloan Kettering Cancer Center, New York, New York, United States ofAmericaAuthor contributions are: ARK Conceived and designed the experiments, performed theexperiments, analyzed the data, contributed reagents/materials/analysis tools, and wrote thepaper. SAJ performed the experiments, analyzed the data, and wrote the paper"} +{"text": "There were errors in the published affiliations. The correct affiliations are:1*, Patrick L. Gurian1, Yin Huang1, Charles N. Haas1Tao Hong1. Department of Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, Pennsylvania, United States of America"} +{"text": "There were errors in Tables 1, 4, 5, 6, 9, and 10. The pattern of results remained unchanged. The corrected tables can be viewed here:"} +{"text": "There are errors in the affiliations. The correct affiliations are listed below.1*, Marlene Sinclair1, George Kernohan1, Evie McCrum-Gardner2, John Keller3Janine Stockdale1 Institute of Nursing and Health Research, University of Ulster, Belfast, Northern Ireland, 2 Clinical Research Support Centre, Belfast, Northern Ireland, 3 Instructional Systems Faculty, Florida State University, Tallahassee, Florida, United States of Americadj.stockdale@ulster.ac.uk* E-mail:"} +{"text": "There were errors in multiple affiliations for multiple authors. Please see the following correct list of authors and affiliations:1,2*,Jintanat Ananworanich, 3,4,5,6, Melissa Agsalda 6, Napapon Sailasuta 7, Thep Chalermchai 3, Alexandra Schuetz 8, Cecilia Shikuma 6, Chin-Yuan Liang 6, Supunee Jirajariyavej 9, Pasiri Sithinamsuwan 10, Somporn Tipsuk 3, David B. Clifford 11, Robert Paul 12, James L. K. Fletcher 3, Mary A. Marovich 13, Bonnie M. Slike 14, Victor DeGruttola 15, Bruce Shiramizu 6Victor G. Valcour 1. Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA USA2. Division of Geriatric Medicine, Department of Medicine, University of California, San Francisco CA, USA3. SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand4. HIV-NAT, Thai Red Cross AIDS Research Center, Bangkok, Thailand5. Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand6. Hawaii Center for AIDS, University of Hawaii, Honolulu HI USA7. Huntington Medical Research Institutes, Pasadena CA USA8. Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand9. Taksin Hospital, Bangkok, Thailand10. Division of Neurology, Department of Medicine, Phramongkutklao Hospital, Bangkok, Thailand11. Department of Neurology, Washington University, St. Louis MO USA12. Department of Psychology, University of Missouri, St. Louis MO, USA13. Division of AIDS, National Institute of Allergy and Infection Diseases of the National Institutes of Health, Bethesda MD, USA14. US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring MD, USA15. Department of Biostatistics, Harvard School of Public Health, Boston MA, USA"} +{"text": "After publication of this work , we note1Department of Infectious Diseases, Qilu Hospital, Shandong University, Wenhua Xi Road 107, Jinan 250012, Shandong Province, China. 2Department of Laboratory Sciences, School of Public Health, Shandong University, Wenhua Xi Road 107, Jinan 250012, Shandong Province, China. 3Cryo Medicine Laboratory, Qilu Hospital, Shandong University, Wenhua Xi Road 107, Jinan 250012, Shandong Province, China. 4Department of Peripheral Vascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Wenhua Xi Road 42, Jinan 250011, Shandong Province, China. 5Laboratory for Tumor Immunity and Traditional Chinese Drug Immunity, Institute of Basic Medicine, Shandong Academy of Medical Science, Jingshi Road 89, Jinan 250062, Shandong Province, China."} +{"text": "Journal of Environmental Health Science and Engineering 2013, 11:41. doi:10.1186/2052-336X-11-41After publication of this article , we notiAuthors1*, Mohammad Reza Mehrasebi2, Mehran Mohammadian Fazli2, Ali Assadi2Mansour Baziar*Corresponding author1Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Science, Tehran, Iran2Department of Environmental Health, Faculty of Health, Zanjan University of Medical Sciences, Zanjan, Iran"} +{"text": "There were multiple errors in the affiliations of multiple authors. The affiliations should appear as shown here:1,2, Chloe A. Teasdale1,2,3, Chunhui Wang1,2, Maria Lahuerta1,2,3, Harriet Nuwagaba-Biribonwoha1,2, Edwin Tayebwa1, Eugenie Ingabire1, Pacifique Ingabire4, Ruben Sahabo1, Peter Twyman1,5, Elaine J. Abrams1,2,3 for the Identifying Optimal Models for HIV Care in Rwanda CollaborationVeronicah Mugisha 1 International Center for AIDS Care and Treatment Programs-Columbia University, Mailman School of Public Health, New York, New York, United States of America, 2 Identifying Optimal Models of HIV Care in Africa Study, International Center for AIDS Care and Treatment Programs-Columbia University, New York, New York, United States of America, 3 Department of Epidemiology, Columbia University, New York, New York, United States of America, 4 Ministry of Health Rwanda, Kigali, Rwanda, 5 Keep a Child Alive Foundation, New York, New York, United States of America"} +{"text": "Affiliations numbers 1 and 2 for the first and fourth authors were given incorrectly.The correct citations are: 1, Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India; 2, Centre for Genetic Disorders, Banaras Hindu University, Varanasi, Uttar Pradesh, India."} +{"text": "Author Fabian Fu\u03b2er's name is misspelled. The correct spelling is: Fabian Fu\u00dferThere was an error in the list of author affiliations. The full, correct list of authors and affiliations is as follows:1,5*, Laurence O'Dwyer5, Alina Jurcoane6, Viola Oertel-Kn\u00f6chel5, Christian Kn\u00f6chel5, David Prvulovic5, Felipe Sudo1, Carlos Eduardo Alves1, Letice Valente1, Denise Moreira3,4, Fabian Fu\u00dfer5, Tarik Karakaya5, Johannes Pantel7, Eliasz Engelhardt1,2, Jerson Laks1Gilberto Sousa Alves1 Alzheimer's Disease Center - Institute of Psychiatry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil2 Cognitive and Behavior Neurology Unit - Institute of Neurology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil3 Radiology Service - Instituto de Neurologia Deolindo Couto, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil4 Procard\u00edaco Hospital, Rio de Janeiro, Brazil5 Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe-University, Frankfurt am Main, Germany6 Institute for Neuroradiology, Goethe-University, Frankfurt am Main, Germany7 Institute of General Practice, Geriatric Medicine, Goethe-University, Frankfurt am Main, Germany*E-mail: gsalves123@hotmail.com"} +{"text": "The affiliations were missing information. The authors and correct affiliations are:\"Md. Tabish Rehman2#, Punyatirtha Dey1#, Md. Imtaiyaz Hassan2, Faizan Ahmad2, Janendra K. Batra1*\" \"1 Immunochemistry Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India, 2 Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India\""} +{"text": "The information for references 1 and 2 are incorrect. The correct information is:1. Department of Pharmacology, Universit\u00e9 de Sherbrooke, Sherbrooke, Quebec, Canada2. Department of Nuclear Medicine and Radiobiology, Universit\u00e9 de Sherbrooke, Sherbrooke, Quebec, Canada"} +{"text": "After publication of this work , we noteGuoyi Wu(1), Nan Lin(2), Linan Xu(3), Bo Liu(1) and Mark A. Feitelson(4)1 Department of General Surgery, the lingnan Hospital, the Third Affiliated Hospital, Sun Yat-Sen University, GuangZhou 510630, PR China2 Department of Hepatobiliary Surgery, the Third Affiliated Hospital, Sun Yat-Sen University, GuangZhou, 510630, PR China3 Department of Gynecology and Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, GuangZhou 510089, PR China4 Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USAThe pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2407/14/216/prepub"} +{"text": "There was an error in affiliations 1, 3, and 4. The correct affiliations are:1 INRA , UMR1253 Science et Technologie du Lait et de l'OEuf, Rennes, France,3 INRA , CIRM-BIA, UMR1253 Science et Technologie du Lait et de l'OEuf, Rennes, France,4 INRA , UMR518 Math\u00e9matiques et Informatique Appliqu\u00e9es, Paris, France"} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:1*, Zoe Morrison1, Dipak Kalra2, Aziz Sheikh1Kathrin Cresswell1 eHealth Research Group, Centre for Population Health Sciences, The University of Edinburgh, Edinburgh, United Kingdom, 2 Centre for Health Informatics and Multi-professional Education, University College London, London, United KingdomCresswell K, Morrison Z, Kalra D, Sheikh A (2012) \u201cThere Are Too Many, but Never Enough\": Qualitative Case Study Investigating Routine Coding of Clinical Information in Depression. PLoS ONE 7(8): e43831. doi:10.1371/journal.pone.0043831"} +{"text": "Affiliations for multiple authors are incorrect. Please view the list of authors with the correctly indicated list of affiliations below:1, Meng-Xiong Tang1,2, Yun Ti1, Zhi-Hao Wang1,3, Jia Wang1, Wen-Yuan Ding1, Hua Wang1, Yun Zhang1, Wei Zhang1, Ming Zhong1* Lu Han1 Key Laboratory of Cardiovascular Remodeling and Function Research Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Ji\u2019nan, People\u2019s Republic of China2 Department of Emergency, Qilu Hospital of Shandong University, Ji\u2019nan, People\u2019s Republic of China3 Department of Geriatric Medicine, Qilu Hospital of Shandong University, Ji\u2019nan, People\u2019s Republic of China"} +{"text": "The affiliations for three of the authors, Mirjana Maletic-Savatic, Juan M. Encinas, and Amanda Sierra, are listed incorrectly in the original article. Dr. Maletic-Savatic is not affiliated with Centre de recherche du CHU de Qu\u00e9bec, but rather Baylor College of Medicine. Dr. Encinas is not affiliated with Baylor College of Medicine, but rather Ikerbasque Foundation. Dr. Sierra is not affiliated with Baylor College of Medicine, but rather Ikerbasque Foundation. The complete list of authors with the correct affiliations is listed below:1,2\u262f, Sol Beccari1,2\u262f, Irune Diaz-Aparicio1,2\u262f, Agnes Nadjar3, Sophie Lay\u00e93, Quentin Leyrolle3, Diego G\u00f3mez-Nicola4, Mar\u00eda Domercq1,2, Alberto P\u00e9rez-Samart\u00edn1,2, V\u00edctor S\u00e1nchez-Zafra1,2, I\u00f1aki Paris1,2, Jorge Valero1,2,5, Julie C. Savage6,7, Chin-Wai Hui6,7, Marie-\u00c8ve Tremblay6,7, Juan J. P. Deudero8, Amy L. Brewster8, Anne E. Anderson8, Laura Zaldumbide9, Lara Galbarriatu9, Ainhoa Marinas9, Maria dM. Vivanco10, Carlos Matute1,2, Mirjana Maletic-Savatic8, Juan M. Encinas1,2,5, Amanda Sierra1,2,5*Oihane Abiega1 Achucarro Basque Center for Neuroscience, Bizkaia Science and Technology Park, Zamudio, Spain,2 University of the Basque Country, Leioa, Spain,3 Universit\u00e9 Bordeaux Segalen, Bordeaux, France,4 Centre for Biological Sciences, University of Southampton, Southampton, United Kingdom,5 Ikerbasque Foundation, Bilbao, Spain,6 Centre de recherche du CHU de Qu\u00e9bec, Axe Neurosciences, Qu\u00e9bec, Canada,7 Universit\u00e9 Laval, D\u00e9partement de m\u00e9decine mol\u00e9culaire, Qu\u00e9bec, Canada,8 Baylor College of Medicine, The Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital, Houston, Texas, United States of America,9 University Hospital of Cruces, Bilbao, Spain,10 CIC BioGUNE, Derio, Spain\u262f OA, SB, and IDA contributed equally to this work.a.sierra@ikerbasque.org*"} +{"text": "The individuals who comprise the Geographical Variability of Bacteremia Study Group should be included in the author byline instead of the Acknowledgements. The authors and their affiliations are listed below.Rodolfo E. Quir\u00f3s, Division of Infectious Diseases, Prevention and Infection Control Service, Hospital Universitario Austral, Buenos Aires, ArgentinaViviana Vilches, Laboratory of Microbiology, Hospital Universitario Austral, Buenos Aires, ArgentinaTony M. Korman, Monash Infectious Diseases, Monash Health, Clayton, AustraliaSpyros Miyakis, The Wollongong Hospital, Wollongong, AustraliaCraig S. Boutlis, The Wollongong Hospital, Wollongong, AustraliaAlistair B. Reid, The Wollongong Hospital, Wollongong, AustraliaAna Cristina Gales, Laborat\u00f3rio Especial de Microbiologia Cl\u00ednica, Division of Infectious Diseases, Universidade Federal de S\u00e3o Paulo, S\u00e3o Paulo, BrazilLygia Schandert, Laborat\u00f3rio Especial de Microbiologia Cl\u00ednica, Division of Infectious Diseases, Universidade Federal de S\u00e3o Paulo, S\u00e3o Paulo, BrazilRafael Affini, Laborat\u00f3rio Especial de Microbiologia Cl\u00ednica, Division of Infectious Diseases, Universidade Federal de S\u00e3o Paulo, S\u00e3o Paulo, BrazilAntonia Machado Oliveira, Laborat\u00f3rio Especial de Microbiologia Cl\u00ednica, Division of Infectious Diseases, Universidade Federal de S\u00e3o Paulo, S\u00e3o Paulo, BrazilAlexandre R. Marra, Hospital Israelita Albert Einstein, S\u00e3o Paulo, BrazilLuis Fernando Aranha Camargo, Hospital Israelita Albert Einstein, S\u00e3o Paulo, BrazilMichael B. Edmond, Virginia Commonwealth University Medical Center, VCU Medical Center, Richmond, VirginiaLuci Correa, Hospital Israelita Albert Einstein and Hospital do Rim e Hipertensao, S\u00e3o Paulo, BrazilTeresa Cristina Teixeira Sukiennik, Hospital Santa Casa de Porto Alegre, Porto Alegre, Rio Grande do Sul, BrazilPaulo Renato Petersen Behar, Hospital Conceicao, Porto Alegre, Rio Grande do Sul, BrazilEvelyne Gir\u00e3o, Hospital Walter Cantidio, Fortaleza, Ceara, BrazilCarla Guerra, Hospital de Diadema, S\u00e3o Paulo, BrazilCarlos Brites, Hospital Espanhol, Salvador, Bahia, BrazilMarta Antunes de Souza, Hospital das Clinicas de Goiania, Goiania, Goias, BrazilAllison J. McGeer, Mt. Sinai Hospital, Toronto, ON, CanadaStephanie Smith, Division of Infectious Diseases, University of Alberta, Edmonton, Alberta, CanadaAmani A. El Kholy, Clinical Pathology Department, Faculty of Medicine, Cairo University (Kasr Al Ainy), Dar Al Fouad Hospital, Cairo, EgyptGeorge Plakias, Hygeia General Hospital, Marousi, Athens, GreeceEvelina Tacconelli, Division Infectious Diseases, Internal Medicine, T\u00fcbingen University Hospital, T\u00fcbingeneveHitoshi Honda, Department of Infection Prevention, Tokyo Metropolitan Tama Medical Center, Tokyo, JapanJan Kluytmans, Amphia Hospital Breda, Laboratory for Microbiology and Infection Control, NetherlandsAnucha Apisarnthanarak, Division of Infectious Diseases, Thammasat University Hospital, Pratumthani, ThailandMohamad G. Fakih, Infection Prevention and Control Department, St John Hospital and Medical Center, Grosse Pointe Woods, MichiganJonas Marschall, Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, SwitzerlandAnthony J. Russo, Barnes Jewish Hospital, St Louis, Missouri"} +{"text": "In the article Web-based evaluation of experts' opinions on impacted maxillary caninesforced eruption using CBCT, published at Dental Press Journal of Orthodontics, 20(2):90-99,on page 90, where it was written:1, Nasrin Farhadian1, VahidMollabashi2, Faezeh Yousefi3Amirfarhang Miresmaeili1Associate professor, Hamadan University of Medical Science, School ofDentistry, Department of Orthodontics, Hamadan, Iran.2Assistant professor, Hamadan University of Medical Science, School ofDentistry, Department of Orthodontics, Hamadan, Iran.3Associate professor, Hamadan University of Medical Science, School ofDentistry, Department of Dento-maxillofacial radiology, Hamadan, Iran.It should be written:1, Ib Leth Neilsen2, MasoudVarshosaz3, Nasrin Farhadian4, Vahid Mollabashi5, AbbasMoghymbeigi6, Faezeh Yousefi7Amirfarhang Miresmaeili1Associate professor of Orthodontics department, School of Dentistry, HamadanUniversity of Medical Science, Hamadan, Iran.2Professor of Orthodontics, University of California, San Francisco, USA.3Assistant Professor of Dentomaxillofacial Radiology department, School ofDentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran.4Associate professor of Orthodontics department, School of Dentistry, HamadanUniversity of Medical Science, Hamadan, Iran.5Assistant professor of Orthodontics department, School of Dentistry, HamadanUniversity of Medical Science, Hamadan, Iran.6Associate professor of Biostatistics and Epidemiology department, School ofPublic Health, Hamadan University of Medical Sciences, Hamadan, Iran.7Assistant professor of Dentomaxillofacial Radiology department, School ofDentistry, Hamadan University of Medical Science, Hamadan, Iran."} +{"text": "There is an error in the author affiliations for this article. Please refer to the correct author affiliations below:1,2,3, Guang-yan Zhong 2,3*, Jian-qiang Yue 4, Run-ting Yang 1, Chong Li 1, Yue-jia Li 2,3, Yun Zhong 2,3, Xuan Wang 1, Bo Jiang 2,3, Ji-wu Zeng 2,3, Li Zhang 2,3, Shu-tang Yan 1, Xue-jun Bei 1, Dong-guo Zhou 4Bo Wu 1 College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China2 Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China3 Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China4 Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China"} +{"text": "There are errors in the author affiliations. The publisher apologizes for the error. The affiliations should appear as shown here:1, Kerri A. Nottage2, Elliott W. Cole1, Jane S. Hankins2, James G. Gurney1,3Vikki G. Nolan1 Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA, 2 Department of Hematology, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA, 3 Department of Epidemiology and Cancer Control, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA."} +{"text": "Maria Teresa Neves-Petersen is affiliated with: 2 BioPhotonics Group, Department of Nanomedicine, International Iberian Nanotechnology Laboratory (INL), Braga, Portugal and 7 Department of Clinical Medicine, Aalborg University, S\u00f8ndre Skovvej 15, 9000 Aalborg, Denmark.An affiliation for the 7"} +{"text": "The fourteenth author\u2019s name is spelled incorrectly. The correct name is: Yaacov R. LawrenceAdditionally, there are errors in the author affiliations. The affiliations should appear as shown here:1,2, Liron Tuval-Kochen2,3, David Castel3,4, Itai Moshe1, Inbal Mazal2, Osher Cohen5, Camila Avivi6, Kineret Rosenblatt6, Sarit Aviel-Ronen6, Ginette Schiby6, Joachim Yahalom7, Ninette Amariglio2,8, Raphael Pfeffer2, Yaacov R. Lawrence2,3, Amos Toren1,2, Gideon Rechavi2,3, Shoshana Paglin2Michal Yalon1 Department of Pediatric Hematology-Oncology, Safra Children's Hospital, Sheba Medical Center Ramat-Gan 52621, Israel2 Cancer Research Center, Sheba Medical Center, Ramat-Gan 52621, Israel3 Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel4 Neufeld Cardiac Research Institute, Sheba Medical Center, Ramat-Gan 52621, Israel5 Department of Surgery, Sheba Medical Center, Ramat-Gan 52621, Israel6 Department of Pathology, Sheba Medical Center, Ramat-Gan 52621, Israel7 Department of Radiation Oncology, Memorial Sloan Kettering, NYC 10021, USA8 The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israelhttp://ec.europa.eu/research/mariecurieactions/ Grant # PCIG10-GA-2011-303795 (Y.L.), Chaya and Kadish Shermeister endowment , the estate of Miss HARAN ESTER of blessed memory through Keren Izvonot, Israel Ministry of Health (S.P.) and the Bencuya Family Foundation . The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Finally, there are errors in the funding section. The complete, correct Funding Statement is:"} +{"text": "Lupton from the original publication of the paper \u2018PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins\u2019. The authorship list should have read as follows:1, Jeremy Nagel1, Steve Androulakis2, Christopher J. Lupton1, Jiangning Song1,3,*, and Ashley M. Buckle1,*Chen Li1Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, 2Monash Bioinformatics Platform, Monash University, Melbourne, Vic. 3800, Australia, and 3National Engineering Laboratory of Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China"} +{"text": "Please view the correct author order and affiliations here: Wanshuai Li1 The Department of Cardiothoracic Surgery, No. 2 People's Hospital of Changzhou, 29 Xinglong Xiang, Changzhou, Jiangsu, 213004, China, 2 Changzhou GoPath Diagnostic Laboratory Co. Ltd, 801 Changwuzhong Road, Changzhou, Jiangsu, 213164, China, 3 GoPath Laboratories LLC, 1351 Barclay Blvd, Buffalo Grove, Illinois, 60089, United States of America"} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:1, Yan Cao2, Zhan Gao1, Zhonghua Ou1, Yajing Wang1, Jianbin Qiu2, Yizhi Zheng1Yulin Tang1 Shenzhen Key Laboratory of Microbial and Gene Engineering, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People\u2019s Republic of China2 The Key Laboratory for Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People\u2019s Republic of ChinaTang Y, Cao Y, Gao Z, Ou Z, Wang Y, et al. (2014) Expression of a Vacuole-Localized BURP-Domain Protein from Soybean (SALI3-2) Enhances Tolerance to Cadmium and Copper Stresses. PLoS ONE 9(6): e98830. doi:10.1371/journal.pone.0098830"} +{"text": "Short CommunicationIsolation of Fucosyltransferase-Producing Bacteria from Marine Environments1,2, Munetoyo Toda3, Toshiki Mine1, Hiroshi Nakada2, and Takeshi Yamamoto1*Hitomi Kajiwara1Glycotechnology Business Unit, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438\u20130802, Japan;2Intellectual Property Center, Legal Division, Japan Tobacco Inc., 2\u20131, Toranomon 2-chome, Minato-ku, Tokyo, 105\u20138422, Japan; and3Department of Biotechnology, Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, Kyoto 603\u20138555, JapanVolume 27, no. 4, Page 515\u2013518, 2012711119) of the 16S rRNA gene of DOT-118-2 showed the highest similality, over 98%, to the DNA sequence of the 16S rRNA gene from Polaribacter sp. S-6 (accession number DQ978987)\u2019.Page 517, \u2018A partial DNA sequence (accession number: AB"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Elena Longhi1,2, Nadia Bolognini1,3, Irene Senna1,4, Paolo Tagliabue5, Viola Macchi Cassia1, Chiara Turati1Margaret Addabbo1 Department of Psychology and NeuroMi, Milan Center for Neuroscience, University of Milan-Bicocca, Piazza Ateneo Nuovo 1 (U6), 20126, Milano, Italy, 2 Research Department of Clinical, Educational and Health Psychology, University College London, London, United Kingdom, 3 Laboratory of Neuropsychology, Istituto Auxologico Italiano, Milano, Italy, 4 Cognitive Neuroscience Department and Cognitive Interaction Technology-Center of Excellence, Bielefeld University, Bielefeld, Germany, 5 Neonatology and Intensive Care Unit, MBBM Foundation, San Gerardo Hospital, 20900, Monza, Italy."} +{"text": "The third affiliation for the authors was omitted. Please refer to the complete affiliations below:1,2,3 Jie Xiang 1,3 Jie Zhou 1,3 Zhiwei Li1,3 Zhenhua Hu1,3 Chung Mau Lo,2* Weilin Wang1,3*Jun Zheng 1Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China2Department of Surgery, The University of Hong Kong, Hong Kong3Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang, China."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Hamid Rez Khankeh2, Hussain Fekrazad1*, Mohammad Kamali5, Hassan Rafiey1, Pooria Sarrami Foroushani3, Kevin Rowell4, Shokoufeh Ahmadi6Fardin Alipour1 Department of Social Work, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran2 Department of Health in Emergency and Disaster and Nursing, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran. Department of Clinical Science and Education, Karoliska Institutet, Stockholm, Sweden3 University of New South Wales, Sydney, Australia4 Department of Psychology and Counseling, University of Central Arkansas, Conway, Arkansas, USA5 Department of Rehabilitation Management, Medical University of Iran, Tehran, Iran6 Department of Health in Emergency and Disaster, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran*hamid.khankeh@ki.seAlipour F, Khankeh HR, Fekrazad H, Kamali M, Rafiey H, Sarrami Foroushani P, Rowell K, Ahmadi S. Challenges for Resuming Normal Life After Earthquake: A Qualitative Study on Rural Areas of Iran. PLOS Currents Disasters. 2014 Oct 17. Edition 1. doi: 10.1371/currents.dis.b4e84b942500e2f8f260f3471b7ee815.View Article"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, RouhAllah Vahabpour1, Mohammad Reza Aghasadeghi1, Syed Mehdi Sadat1, Nader Howaizi2, Ehsan Mostafavi4, Ali Eslamifar3, Vida Fallahian3Pooneh Rahimi1 Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran, 2 WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran, 3 Department of Vaccination, Rabies post-exposure prophylaxis, Pasteur Institute of Iran, Tehran, Iran, 4 Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran."} +{"text": "The authors\u2019 first and last names are switched. Please view the correct author list, affiliations, and citation here:1,2, Ruiming Han1, Yinjing Wan3, Bo Liu1,4, Xiaoyan Tang2, Bin Liang2, Guoxiang Wang1Wenlin Wang1 Jiangsu Key Laboratory of Environmental Change and Ecological Construction, College of Geographical Science, Nanjing Normal University, Nanjing, China2 Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing, China3 Jiangsu Environmental Engineering Consulting Center, Nanjing, China4 School of Geography Science, Nantong University, Nantong, ChinaAcorus calamus. PLoS ONE 9(5): e98457. doi:10.1371/journal.pone.0098457Wang WL, Han RM, Wan YJ, Liu B, Tang XY et al. (2014) Spatio-Temporal Patterns in Rhizosphere Oxygen Profiles in the Emergent Plant Species"} +{"text": "There is an error in the Affiliations. Affiliations 1, 2, and 3 should list \u201cJinling Hospital\u201d rather than \u201cJingling Hospital.\u201d The affiliations should appear as shown here:2, ZhaoRong Shi3, Zhen Wang2, Zhibing Liu1, Xinhu Wu2, Zetian Shen2, Bing Li2, Yong Song3, Xixu Zhu2*Jing Li1 Jinling Hospital, Department of Radiotherapy Center, Nanjing University School of Medicine, Nanjing, China2 Jinling Hospital, Department of Radiotherapy Center, Nanjing, China3 Jinling Hospital, Nanjing, China"} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:1, Li Zhang2, Deng-Shu Wu1, Xiao-Yu Yuan1, Yan-Hui Yu1, Xie-Lan Zhao1, Fang-Ping Chen1, Hui Zeng1Fang-Fang Huang1 Department of Hematology, Xiang Ya Hospital, Central South University, Changsha, Hunan, China2 Department of Hematology, West China Hospital, Si Chuan University, Chengdu, Sichuan, ChinaHuang F-F, Zhang L, Wu D-S, Yuan X-Y, Yu Y-H, et al. (2014) PTEN Regulates BCRP/ABCG2 and the Side Population through the PI3K/Akt Pathway in Chronic Myeloid Leukemia. PLoS ONE 9(3): e88298. doi:10.1371/journal.pone.0088298"} +{"text": "The authors are listed out of order. The publisher apologizes for the error. Please view the correct author order, affiliations, and citation here:1, Natalie J. Thatcher2\u00a4, Richard Hammersley3, Alan S. Rigby4, Fraser L Courts1, Alexandros Pechlivanis5, Nigel J. Gooderham5, Elaine Holmes5, Carel W. le Roux6, Stephen L. Atkin7Thozhukat Sathyapalan1 Academic Endocrinology, Diabetes and Metabolism, Hull York Medical School, University of Hull, Hull, United Kingdom,2 Food Standards Agency, London, United Kingdom,3 Department of Psychology, University of Hull, Hull, United Kingdom,4 Department of Academic Cardiology, University of Hull, Hull, United Kingdom,5 Faculty of Medicine, Imperial College, London, United Kingdom,6 Diabetes Complications Research Centre, Conway Institute, University College Dublin, Belfield, Ireland,7 Weill Cornell Medical College Qatar, Education City PO Box 24144, Doha, Qatar10.1371/journal.pone.0116212Sathyapalan T, Thatcher NJ, Hammersley R, Rigby AS, Courts FL, Pechlivanis A, et al. (2015) Aspartame Sensitivity? A Double Blind Randomised Crossover Study. PLoS ONE 10(3): e0116212. doi:"} +{"text": "The first and second author affiliations are switched. The affiliations should appear as shown here:1, 2, Ziyan Wu1, Shulan Zhang1, Si Chen1, Ping Li1, Jing Li1, Chunwei Cao1, Bin Liu2, Fengchun Zhang1, Yongzhe Li1Yuan Li1 Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China,2 Department of Rheumatology, The Affiliated Hospital of Qingdao University, China"} +{"text": "The authors are listed out of order. The publisher apologizes for this error. Please view the correct author order, affiliations, and citation here:1,2\u262f, Zhuling Yu1\u262f, Deren Hou1*, Lin Zhou3, Yanyao Deng1, Mi Tian1, Xialu Feng1Wei Li1Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China 2Department of Nerve medical center, The First Hospital of Changsha, Changsha, China 3Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, China\u262fThese authors contributed equally to this work10.1371/journal.pone.0125186Li W, Yu Z, Hou D, Zhou L, Deng Y, Tian M, et al. (2015) Relationship between Adiponectin Gene Polymorphisms and Late-Onset Alzheimer\u2019s Disease. PLoS ONE 10(4): e0125186. doi:"} +{"text": "Maria Teresa Neves-Petersen is affiliated with: 2 BioPhotonics Group, Department of Nanomedicine, International Iberian Nanotechnology Laboratory (INL), Braga, Portugal and 6 Department of Clinical Medicine, Aalborg University, S\u00f8ndre Skovvej 15, 9000 Aalborg, Denmark.An affiliation for the 6"} +{"text": "There are errors in the author affiliations. The correct affiliations should appear as shown here:1, Nathalie E. Holz1, Arlette F. Buchmann1, Dorothea Blomeyer1, Michael M. Plichta2, Isabella Wolf1,3, Sarah Baumeister1, Andreas Meyer-Lindenberg2, Tobias Banaschewski1, Daniel Brandeis1,4,5,6\u262f, Manfred Laucht1,7\u262f*Regina Boecker1 Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany,2 Department of Psychiatry and Psychotherapy, Central Institute of Mental Health Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany,3 Department of Neuroimaging, Central Institute of Mental Health Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany,4 Department of Child and Adolescent Psychiatry, University of Zurich, Zurich, Switzerland,5 Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland,6 Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland,7 Department of Psychology, University of Potsdam, Potsdam, Germanymanfred.laucht@zi-mannheim.de* Email: \u262f These authors contributed equally to this work."} +{"text": "The correct order is: Li-zhao Chen 1,2,#, Xiang-yun Li 1,3,#, Hong Huang 1, Wei Xing 1, Wei Guo 1, Jing He 3, Zhi-ya Sun 3, An-xiong Luo 3, Hua-ping Liang 1, Jing Hu 5, Zheng-guo Wang 4,*, Yun-sheng Xu 6,*, Xiang Xu 1,3,*The 111First department, State Key Laboratory of Trauma, Burn and Combined Injury, Research Institute of Surgery and Daping Hospital, Third Military Medical University, Chongqing, China2Department of Neurosurgery, Research Institute of Surgery and Daping Hospital, Third Military Medical University, Chongqing, China3Cell-based Biotherapy Center, Research Institute of Surgery and Daping Hospital, Third Military Medical University, Chongqing, China4Fourth department, State Key Laboratory of Trauma, Burn and Combined Injury, Research Institute of Surgery and Daping Hospital, Third Military Medical University, Chongqing, China5Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.6Department of Dermatology, First Affiliated Hospital of Wenzhou Medical College, Wenzhou Zhejiang, China#These authors contributed equally to this work.*These authors are co-corresponding authors"} +{"text": "Following publication of our article , it has 1,2, Olivier Bourron 3, Cees Vemeer 4, Elke Theuwissen 4, Elke Magdeleyns 4, Carole Elodie Aubert 3, Michel Brazier 1, Romuald Mentaverri 1, Agnes Hartemann 3, and Ziad A. Massy 1,5Sophie Liabeuf We apologize for any inconvenience this has caused."} +{"text": "Among these genes, FOS and PTGS2 have been previously reported to be involved in BP-related processes; the others are novel. The top BP signature genes in aggregate explain 5%\u20139% of inter-individual variance in BP. Of note, rs3184504 in SH2B3, which was also reported in GWAS to be associated with BP, was found to be a trans regulator of the expression of 6 of the transcripts we found to be associated with BP . Gene set enrichment analysis suggested that the BP-related global gene expression changes include genes involved in inflammatory response and apoptosis pathways. Our study provides new insights into molecular mechanisms underlying BP regulation, and suggests novel transcriptomic markers for the treatment and prevention of hypertension.Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not receiving antihypertensive drug treatment. We identified 34 genes that were differentially expressed in relation to BP GWAS has been the identification of common DNA sequence variants associated with the phenotype; this approach provides only one dimension of molecular information about BP. While it is a critical dimension, analyzing DNA variation alone is not sufficient for achieving an understanding of the multidimensional complexity of BP physiology. The top loci identified by GWAS explain only about 1 percent of inter-individual BP variability. In this study, we performed a meta-analysis of gene expression profiles in relation to BP and hypertension in 7017 individuals from six studies. We identified 34 differentially expressed genes for BP, and discovered that the top BP signature genes explain 5%\u20139% of BP variability. We further linked BP gene expression signature genes with BP GWAS results by integrating expression associated SNPs (eSNPs) and discovered that one of the top BP loci from GWAS, rs3184504 in Systolic and diastolic blood pressure (SBP and DBP) are complex physiological traits that are affected by the interplay of multiple genetic and environmental factors. Hypertension (HTN) is a critical risk factor for stroke, renal failure, heart failure, and coronary heart disease . Genome-Alterations in gene expression may mediate the effects of genetic variants on phenotype variability. We hypothesized that characterizing gene expression signatures of BP would reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. We additionally hypothesized that by integrating gene expression profiling with genetic variants associated with altered gene expression (eSNPs or eQTLs) and with BP GWAS results, we would be able to characterize the genetic architecture of gene expression effects on BP regulation.Several previous studies have examined the association of global gene expression with BP ,5 or HTNTable 1. The mean age varied across the cohorts as did the proportion of individuals with hypertension .After excluding individuals receiving anti-hypertensive treatment, the eligible sample size was 7017 . Clinical characteristics of participants from the four studies are presented in p<0.05, we identified 73, 31, and 8 genes that were differentially expressed in relation to SBP, DBP, and HTN, respectively in the FHS, which used an Affymetrix array for expression profiling, and 6, 1, and 1 genes in the meta-analysis of the 5 cohorts that used an Illumina array (Illumina cohorts): EGCUT, RS, InCHIANTI, KORA F4 and SHIP-TREND (S1 Table). For each differentially expressed BP gene in the FHS or in the Illumina cohorts, we attempted replication in the other group. At a replication p<0.05 (Bonferroni corrected), 13 unique genes that were identified in the FHS were replicated in the Illumina cohorts, including 10 for SBP , 5 for DBP , and 2 for HTN (GZMB and MYADM) (Table 2). Each of the unique BP signature genes in the Illumina cohorts, 6 for SBP , 1 for DBP (BHLHE40) and 1 for HTN (SLC31A2), replicated in the FHS. All 6 Illumina cohorts BP signature genes that replicated in the FHS were among the 13 FHS BP signature genes that replicated in the Illumina cohorts. The BP signature genes identified in the FHS showed enrichment in the Illumina cohorts at pi1 = 0.88, 0.75, and 0.99 for SBP, DBP, and HTN respectively in aggregate explained 5.3% of DBP phenotypic variance in the Illumina cohorts. These results suggest that in contrast to common genetic variants identified by BP GWAS, which explain in aggregate only about 1% of inter-individual BP variation , EGCUT [GSE48348], RS [GSE33828], InCHIANTI [GSE48152], KORA F4 [E-MTAB-1708] and SHIP-TREND [GSE36382]). The details of sample collection, microarrays, and data processing and normalization in each cohort are provided in the S2 Text.RNA was isolated from whole blood samples that were collected in PaxGene tubes in FHS, RS, InCHIANTI, KORA F4 and SHIP-TREND, and in Blood RNA Tubes in EGCUT. Gene expression in the FHS samples used the Affymetrix Exon Array ST 1.0. EGCUT, RS, InCHANTI, KORA F4, and SHIP-TREND used the Illumina HT12v3 or HT12v4 (RS) array. Raw data from gene expression profiling are available online in the FHS samples (Set 1) and attempted replication in the meta-analysis results from the Illumina cohorts . Replication was established at Bonferroni corrected p = 0.05, correcting for the number of pre-selected BP signatures genes in the discovery set. We computed the pi1 value to estimate the enrichment of significant p values in the replication set (the Illumina cohorts) for BP signatures identified in the discovery set (the FHS) by utilizing the R package Qvalue based on the overlap of FHS and illumina cohort interrogated gene sets).We performed meta-analysis of the five Illumina cohorts (for discovery and replication purposes), and then performed meta-analysis of all six cohorts. An inverse variance weighted meta-analysis was conducted using fixed-effects or random-effects models by the ) method was usedTo estimate the proportion of variances in SBP or DBP explained by a group of differentially expressed BP signature genes , we used the following two models:Full model:Null model:The proportion of variance in BP attributable to the group of differentially expressed BP signature genes . A cis-eQTL was defined as an eQTL within 1 megabase (MB) flanking the gene. Other eQTLs were defined as trans-eQTLs. We combined the eQTL list generated in the FHS with the eQTLs generated by meta-analysis of seven other studies (n = 5300) that were also based on whole blood expression[SNPs associated with altered gene expression (i.e. eQTLs) were identified using genome-wide genotype and gene expression data in all available FHS samples (n = 5257) at FDR<0.1 Gon\u00e7alo Abecasis, Murielle Bochud, Mark Caulfield (co-chair), Aravinda Chakravarti, Dan Chasman, Georg Ehret (co-chair), Paul Elliott, Andrew Johnson, Louise Wain, Martin Larson, Daniel Levy (co-chair), Patricia Munroe (co-chair), Christopher Newton-Cheh (co-chair), Paul O'Reilly, Walter Palmas, Bruce Psaty, Kenneth Rice, Albert Smith, Harold Snider, Martin Tobin, Cornelia Van Duijn, Germaine Verwoert.Members1,2,3, Patricia B. Munroe4, Kenneth M. Rice5, Murielle Bochud2, Andrew D. Johnson6,7, Daniel I. Chasman8,9, Albert V. Smith10,11, Martin D. Tobin12, Germaine C. Verwoert13,14,15, Shih-Jen Hwang6,16,7, Vasyl Pihur1, Peter Vollenweider17, Paul F. O'Reilly18, Najaf Amin13, Jennifer L Bragg-Gresham19, Alexander Teumer20, Nicole L. Glazer21, Lenore Launer22, Jing Hua Zhao23, Yurii Aulchenko13, Simon Heath24, Siim S\u00f5ber25, Afshin Parsa26, Jian'an Luan23, Pankaj Arora27, Abbas Dehghan13,14,15, Feng Zhang28, Gavin Lucas29, Andrew A. Hicks30, Anne U. Jackson31, John F Peden32, Toshiko Tanaka33, Sarah H. Wild34, Igor Rudan35,36, Wilmar Igl37, Yuri Milaneschi33, Alex N. Parker38, Cristiano Fava39,40, John C. Chambers18,41, Ervin R. Fox42, Meena Kumari43, Min Jin Go44, Pim van der Harst45, Wen Hong Linda Kao46, Marketa Sj\u00f6gren39, D. G. Vinay47, Myriam Alexander48, Yasuharu Tabara49, Sue Shaw-Hawkins4, Peter H. Whincup50, Yongmei Liu51, Gang Shi52, Johanna Kuusisto53, Bamidele Tayo54, Mark Seielstad55,56, Xueling Sim57, Khanh-Dung Hoang Nguyen1, Terho Lehtim\u00e4ki58, Giuseppe Matullo59,60, Ying Wu61, Tom R. Gaunt62, N. Charlotte Onland-Moret63,64, Matthew N. Cooper65, Carl G.P. Platou66, Elin Org25, Rebecca Hardy67, Santosh Dahgam68, Jutta Palmen69, Veronique Vitart70, Peter S. Braund71,72, Tatiana Kuznetsova73, Cuno S.P.M. Uiterwaal63, Adebowale Adeyemo74, Walter Palmas75, Harry Campbell35, Barbara Ludwig76, Maciej Tomaszewski71,72, Ioanna Tzoulaki77,78, Nicholette D. Palmer79, CARDIoGRAM consortium80, CKDGen Consortium80, KidneyGen Consortium80, EchoGen consortium80, CHARGE-HF consortium80, Thor Aspelund10,11, Melissa Garcia22, Yen-Pei C. Chang26, Jeffrey R. O'Connell26, Nanette I. Steinle26, Diederick E. Grobbee63, Dan E. Arking1, Sharon L. Kardia81, Alanna C. Morrison82, Dena Hernandez83, Samer Najjar84,85, Wendy L. McArdle86, David Hadley50,87, Morris J. Brown88, John M. Connell89, Aroon D. Hingorani90, Ian N.M. Day62, Debbie A. Lawlor62, John P. Beilby91,92, Robert W. Lawrence65, Robert Clarke93, Rory Collins93, Jemma C Hopewell93, Halit Ongen32, Albert W. Dreisbach42, Yali Li94, J H. Young95, Joshua C. Bis21, Mika K\u00e4h\u00f6nen96, Jorma Viikari97, Linda S. Adair98, Nanette R. Lee99, Ming-Huei Chen100, Matthias Olden101,102, Cristian Pattaro30, Judith A. Hoffman Bolton103, Anna K\u00f6ttgen104,103, Sven Bergmann105,106, Vincent Mooser107, Nish Chaturvedi108, Timothy M. Frayling109, Muhammad Islam110, Tazeen H. Jafar110, Jeanette Erdmann111, Smita R. Kulkarni112, Stefan R. Bornstein76, J\u00fcrgen Gr\u00e4ssler76, Leif Groop113,114, Benjamin F. Voight115, Johannes Kettunen116,126, Philip Howard117, Andrew Taylor43, Simonetta Guarrera60, Fulvio Ricceri59,60, Valur Emilsson118, Andrew Plump118, In\u00eas Barroso119,120, Kay-Tee Khaw48, Alan B. Weder121, Steven C. Hunt122, Yan V. Sun81, Richard N. Bergman123, Francis S. Collins124, Lori L. Bonnycastle124, Laura J. Scott31, Heather M. Stringham31, Leena Peltonen119,125,126,127, Markus Perola125, Erkki Vartiainen125, Stefan-Martin Brand128,129, Jan A. Staessen73, Thomas J. Wang6,130, Paul R. Burton12,72, Maria Soler Artigas12, Yanbin Dong131, Harold Snieder132,131, Xiaoling Wang131, Haidong Zhu131, Kurt K. Lohman133, Megan E. Rudock51, Susan R Heckbert134,135, Nicholas L Smith134,136,135, Kerri L Wiggins137, Ayo Doumatey74, Daniel Shriner74, Gudrun Veldre25,138, Margus Viigimaa139,140, Sanjay Kinra141, Dorairajan Prabhakaran142, Vikal Tripathy142, Carl D. Langefeld79, Annika Rosengren143, Dag S. Thelle144, Anna Maria Corsi145, Andrew Singleton83, Terrence Forrester146, Gina Hilton1, Colin A. McKenzie146, Tunde Salako147, Naoharu Iwai148, Yoshikuni Kita149, Toshio Ogihara150, Takayoshi Ohkubo149,151, Tomonori Okamura148, Hirotsugu Ueshima152, Satoshi Umemura153, Susana Eyheramendy154, Thomas Meitinger155,156, H.-Erich Wichmann157,158,159, Yoon Shin Cho44, Hyung-Lae Kim44, Jong-Young Lee44, James Scott160, Joban S. Sehmi160,41, Weihua Zhang18, Bo Hedblad39, Peter Nilsson39, George Davey Smith62, Andrew Wong67, Narisu Narisu124, Alena Stan\u010d\u00e1kov\u00e153, Leslie J. Raffel161, Jie Yao161, Sekar Kathiresan162,27, Chris O'Donnell163,27,9, Stephen M. Schwartz134, M. Arfan Ikram13,15, W. T. Longstreth Jr.164, Thomas H. Mosley165, Sudha Seshadri166, Nick R.G. Shrine12, Louise V. Wain12, Mario A. Morken124, Amy J. Swift124, Jaana Laitinen167, Inga Prokopenko51,168, Paavo Zitting169, Jackie A. Cooper69, Steve E. Humphries69, John Danesh48, Asif Rasheed170, Anuj Goel32, Anders Hamsten171, Hugh Watkins32, Stephan J.L. Bakker172, Wiek H. van Gilst45, Charles S. Janipalli47, K. Radha Mani47, Chittaranjan S. Yajnik112, Albert Hofman13, Francesco U.S. Mattace-Raso13,14, Ben A. Oostra173, Ayse Demirkan13, Aaron Isaacs13, Fernando Rivadeneira13,14, Edward G Lakatta174, Marco Orru175,176, Angelo Scuteri174, Mika Ala-Korpela177,178,179, Antti J Kangas177, Leo-Pekka Lyytik\u00e4inen58, Pasi Soininen177,178, Taru Tukiainen180,181,177, Peter W\u00fcrtz177,18,180, Rick Twee-Hee Ong56,57,182, Marcus D\u00f6rr183, Heyo K. Kroemer184, Uwe V\u00f6lker20, Henry V\u00f6lzke185, Pilar Galan186, Serge Hercberg186, Mark Lathrop24, Diana Zelenika24, Panos Deloukas119, Massimo Mangino28, Tim D. Spector28, Guangju Zhai28, James F. Meschia187, Michael A. Nalls83, Pankaj Sharma188, Janos Terzic189, M. J. Kranthi Kumar47, Matthew Denniff71, Ewa Zukowska-Szczechowska190, Lynne E. Wagenknecht79, F. Gerald R. Fowkes191, Fadi J. Charchar192, Peter E.H. Schwarz193, Caroline Hayward70, Xiuqing Guo161, Charles Rotimi74, Michiel L. Bots63, Eva Brand194, Nilesh J. Samani71,72, Ozren Polasek195, Philippa J. Talmud69, Fredrik Nyberg68,196, Diana Kuh67, Maris Laan25, Kristian Hveem66, Lyle J. Palmer197,198, Yvonne T. van der Schouw63, Juan P. Casas199, Karen L. Mohlke61, Paolo Vineis200,60, Olli Raitakari201, Santhi K. Ganesh202, Tien Y. Wong203,204, E Shyong Tai205,57,206, Richard S. Cooper54, Markku Laakso53, Dabeeru C. Rao207, Tamara B. Harris22, Richard W. Morris208, Anna F. Dominiczak209, Mika Kivimaki210, Michael G. Marmot210, Tetsuro Miki49, Danish Saleheen170,48, Giriraj R. Chandak47, Josef Coresh211, Gerjan Navis212, Veikko Salomaa125, Bok-Ghee Han44, Xiaofeng Zhu94, Jaspal S. Kooner160,41, Olle Melander39, Paul M Ridker8,213,9, Stefania Bandinelli214, Ulf B. Gyllensten37, Alan F. Wright70, James F. Wilson34, Luigi Ferrucci33, Martin Farrall32, Jaakko Tuomilehto215,216,217,218, Peter P. Pramstaller30,219, Roberto Elosua29,220, Nicole Soranzo119,28, Eric J.G. Sijbrands13,14, David Altshuler221,115, Ruth J.F. Loos23, Alan R. Shuldiner26,222, Christian Gieger157, Pierre Meneton223, Andre G. Uitterlinden13,14,15, Nicholas J. Wareham23, Vilmundur Gudnason10,11, Jerome I. Rotter161, Rainer Rettig224, Manuela Uda175, David P. Strachan50, Jacqueline C.M. Witteman13,15, Anna-Liisa Hartikainen225, Jacques S. Beckmann105,226, Eric Boerwinkle227, Ramachandran S. Vasan6,228, Michael Boehnke31, Martin G. Larson6,229, Marjo-Riitta J\u00e4rvelin18,230,231,232,233, Bruce M. Psaty21,135*, Gon\u00e7alo R Abecasis19*, Aravinda Chakravarti1, Paul Elliott18,233*, Cornelia M. van Duijn13,234*, Christopher Newton-Cheh27,115, Daniel Levy6,16,7, Mark J. Caulfield4, Toby Johnson4Georg B. EhretAffiliationsCenter for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USAInstitute of Social and Preventive Medicine (IUMSP), Centre Hospitalier Universitaire Vaudois and University of Lausanne, Bugnon 17, 1005 Lausanne, SwitzerlandCardiology, Department of Specialties of Internal Medicine, Geneva University Hospital, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 14, SwitzerlandClinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UKDepartment of Biostatistics, University of Washington, Seattle, WA, USAFramingham Heart Study, Framingham, MA, USANational Heart Lung, and Blood Institute, Bethesda, MD, USADivision of Preventive Medicine, Brigham and Women's Hospital, 900 Commonwealth Avenue East, Boston MA 02215, USAHarvard Medical School, Boston, MA, USAIcelandic Heart Association, Kopavogur, IcelandUniversity of Iceland, Reykajvik, IcelandDepartment of Health Sciences, University of Leicester, University Rd, Leicester LE1 7RH, UKDepartment of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The NetherlandsDepartment of Internal Medicine, Erasmus Medical Center, Rotterdam, The NetherlandsNetherlands Consortium for Healthy Aging (NCHA), Netherland Genome Initiative (NGI), The NetherlandsCenter for Population Studies, National Heart Lung, and Blood Institute, Bethesda, MD, USADepartment of Internal Medicine, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, SwitzerlandDepartment of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UKCenter for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48103, USAInterfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, 17487 Greifswald, GermanyCardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USALaboratory of Epidemiology, Demography, Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USAMRC Epidemiology Unit, Institute of Metabolic Science, Cambridge CB2 0QQ, UKCentre National de G\u00e9notypage, Commissariat \u00e0 L'Energie Atomique, Institut de G\u00e9nomique, Evry, FranceInstitute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, EstoniaUniversity of Maryland School of Medicine, Baltimore, MD, USA, 21201, USACenter for Human Genetic Research, Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, 02114, USADepartment of Twin Research & Genetic Epidemiology, King's College London, UKCardiovascular Epidemiology and Genetics, Institut Municipal d'Investigacio Medica, Barcelona Biomedical Research Park, 88 Doctor Aiguader, 08003 Barcelona, SpainInstitute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy\u2014Affiliated Institute of the University of L\u00fcbeck, GermanyDepartment of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USADepartment of Cardiovascular Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UKClinical Research Branch, National Institute on Aging, Baltimore MD 21250, USACentre for Population Health Sciences, University of Edinburgh, EH89AG, UKCentre for Population Health Sciences and Institute of Genetics and Molecular Medicine, College of Medicine and Vet Medicine, University of Edinburgh, EH8 9AG, UKCroatian Centre for Global Health, University of Split, CroatiaDepartment of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, SwedenAmgen, 1 Kendall Square, Building 100, Cambridge, MA 02139, USADepartment of Clinical Sciences, Lund University, Malm\u00f6, SwedenDepartment of Medicine, University of Verona, ItalyEaling Hospital, London, UB1 3HJ, UKDepartment of Medicine, University of Mississippi Medical Center, USAGenetic Epidemiology Group, Epidemiology and Public Health, UCL, London, WC1E 6BT, UKCenter for Genome Science, National Institute of Health, Seoul, KoreaDepartment of Cardiology, University Medical Center Groningen, University of Groningen, The NetherlandsDepartments of Epidemiology and Medicine, Johns Hopkins University, Baltimore MD, USACentre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Uppal Road, Hyderabad 500 007, IndiaDepartment of Public Health and Primary Care, University of Cambridge, CB1 8RN, UKDepartment of Basic Medical Research and Education, and Department of Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, 791-0295, JapanDivision of Community Health Sciences, St George's University of London, London, SW17 0RE, UKEpidemiology & Prevention, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USADivision of Biostatistics and Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USADepartment of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, FinlandDepartment of Preventive Medicine and Epidemiology, Loyola University Medical School, Maywood, IL, USADepartment of Laboratory Medicine & Institute of Human Genetics, University of California San Francisco, 513 Parnassus Ave. San Francisco CA 94143, USAGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, SingaporeCentre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, SingaporeDepartment of Clinical Chemistry, University of Tampere and Tampere University Hospital, Tampere, 33521, FinlandDepartment of Genetics, Biology and Biochemistry, University of Torino, Via Santena 19, 10126, Torino, ItalyHuman Genetics Foundation (HUGEF), Via Nizza 52, 10126, Torino, ItalyDepartment of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USAMRC Centre for Causal Analyses in Translational Epidemiology, School of Social & Community Medicine, University of Bristol, Bristol BS8 2BN, UKJulius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The NetherlandsComplex Genetics Section, Department of Medical Genetics\u2014DBG, University Medical Center Utrecht, 3508 GA Utrecht, The NetherlandsCentre for Genetic Epidemiology and Biostatistics, University of Western Australia, Crawley, WA, AustraliaHUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, 7600 Levanger, NorwayMRC Unit for Lifelong Health & Ageing, London, WC1B 5JU, UKOccupational and Environmental Medicine, Department of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, SwedenCentre for Cardiovascular Genetics, University College London, London WC1E 6JF, UKMRC Human Genetics Unit and Institute of Genetics and Molecular Medicine, Edinburgh, EH2, UKDepartment of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, LE3 9QP, UKLeicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, LE3 9QP, UKStudies Coordinating Centre, Division of Hypertension and Cardiac Rehabilitation, Department of Cardiovascular Diseases, University of Leuven, Campus Sint Rafa\u00ebl, Kapucijnenvoer 35, Block D, Box 7001, 3000 Leuven, BelgiumCenter for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USAColumbia University, NY, USADepartment of Medicine III, Medical Faculty Carl Gustav Carus at the Technical University of Dresden, 01307 Dresden, GermanyEpidemiology and Biostatistics, School of Public Health, Imperial College, London, W2 1PG, UKClinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, GreeceWake Forest University Health Sciences, Winston-Salem, NC 27157, USAA list of consortium members is supplied in the Supplementary MaterialsDepartment of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USADivision of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas at Houston Health Science Center, 12 Herman Pressler, Suite 453E, Houston, TX 77030, USALaboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USALaboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, NIH, Baltimore, Maryland, USAWashington Hospital Center, Division of Cardiology, Washington DC, USAALSPAC Laboratory, University of Bristol, Bristol, BS8 2BN, UKPediatric Epidemiology Center, University of South Florida, Tampa, FL, USAClinical Pharmacology Unit, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, UKUniversity of Dundee, Ninewells Hospital &Medical School, Dundee, DD1 9SY, UKGenetic Epidemiology Group, Department of Epidemiology and Public Health, UCL, London WC1E 6BT, UKPathology and Laboratory Medicine, University of Western Australia, Crawley, WA, AustraliaMolecular Genetics, PathWest Laboratory Medicine, Nedlands, WA, AustraliaClinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, OX3 7LF, UKDepartment of Epidemiology and Biostatistics, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USADepartment of Medicine, Johns Hopkins University, Baltimore, USADepartment of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, 33521, FinlandDepartment of Medicine, University of Turku and Turku University Hospital, Turku, 20521, FinlandDepartment of Nutrition, University of North Carolina, Chapel Hill, NC, 27599, USAOffice of Population Studies Foundation, University of San Carlos, Talamban, Cebu City 6000, PhilippinesDepartment of Neurology and Framingham Heart Study, Boston University School of Medicine, Boston, MA, 02118, USADepartment of Internal Medicine II, University Medical Center Regensburg, 93053 Regensburg, GermanyDepartment of Epidemiology and Preventive Medicine, University Medical Center Regensburg, 93053 Regensburg, GermanyDepartment of Epidemiology, Johns Hopkins University, Baltimore MD, USARenal Division, University Hospital Freiburg, GermanyD\u00e9partement de G\u00e9n\u00e9tique M\u00e9dicale, Universit\u00e9 de Lausanne, 1015 Lausanne, SwitzerlandSwiss Institute of Bioinformatics, 1015 Lausanne, SwitzerlandDivision of Genetics, GlaxoSmithKline, Philadelphia, Pennsylvania 19101, USAInternational Centre for Circulatory Health, National Heart & Lung Institute, Imperial College, London, UKGenetics of Complex Traits, Peninsula Medical School, University of Exeter, UKDepartment of Community Health Sciences & Department of Medicine, Aga Khan University, Karachi, PakistanMedizinische Klinik II, Universit\u00e4t zu L\u00fcbeck, L\u00fcbeck, GermanyDiabetes Unit, KEM Hospital and Research Centre, Rasta Peth, Pune-411011, Maharashtra, IndiaDepartment of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital, Malm\u00f6, SwedenLund University, Malm\u00f6 20502, SwedenProgram in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02139, USADepartment of Chronic Disease Prevention, National Institute for Health and Welfare, FIN-00251 Helsinki, FinlandWilliam Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UKMerck Research Laboratory, 126 East Lincoln Avenue, Rahway, NJ 07065, USAWellcome Trust Sanger Institute, Hinxton, CB10 1SA, UKUniversity of Cambridge Metabolic Research Labs, Institute of Metabolic Science Addenbrooke's Hospital, CB2 OQQ, Cambridge, UKDivision of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USACardiovascular Genetics, University of Utah School of Medicine, Salt Lake City, UT, USADepartment of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USANational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892,USANational Institute for Health and Welfare, 00271 Helsinki, FinlandFIMM, Institute for Molecular Medicine, Finland, Biomedicum, P.O. Box 104, 00251 Helsinki, FinlandBroad Institute, Cambridge, Massachusetts 02142, USALeibniz-Institute for Arteriosclerosis Research, Department of Molecular Genetics of Cardiovascular Disease, University of M\u00fcnster, M\u00fcnster, GermanyMedical Faculty of the Westfalian Wilhelms University Muenster, Department of Molecular Genetics of Cardiovascular Disease, University of Muenster, Muenster, GermanyDivision of Cardiology, Massachusetts General Hospital, Boston, MA, USAGeorgia Prevention Institute, Department of Pediatrics, Medical College of Georgia, Augusta, GA, USAUnit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The NetherlandsDepartment of Biostatical Sciences, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USADepartment of Epidemiology, University of Washington, Seattle, WA, 98195, USAGroup Health Research Institute, Group Health Cooperative, Seattle, WA, USASeattle Epidemiologic Research and Information Center, Veterans Health Administration Office of Research & Development, Seattle, WA 98108, USADepartment of Medicine, University of Washington, 98195, USADepartment of Cardiology, University of Tartu, L. Puusepa 8, 51014 Tartu, EstoniaTallinn University of Technology, Institute of Biomedical Engineering, Ehitajate tee 5, 19086 Tallinn, EstoniaCentre of Cardiology, North Estonia Medical Centre, S\u00fctiste tee 19, 13419 Tallinn, EstoniaDivision of Non-communicable disease Epidemiology, The London School of Hygiene and Tropical Medicine London, Keppel Street, London WC1E 7HT, UKSouth Asia Network for Chronic Disease, Public Health Foundation of India, C-1/52, SDA, New Delhi 100016, IndiaDepartment of Emergency and Cardiovascular Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 41685 Gothenburg, SwedenDepartment of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, NorwayTuscany Regional Health Agency, Florence, ItalyTropical Medicine Research Institute, University of the West Indies, Mona, Kingston, JamaicaUniversity of Ibadan, Ibadan, NigeriaDepartment of Genomic Medicine, and Department of Preventive Cardiology, National Cerebral and Cardiovascular Research Center, Suita, 565-8565, JapanDepartment of Health Science, Shiga University of Medical Science, Otsu, 520-2192, JapanDepartment of Geriatric Medicine, Osaka University Graduate School of Medicine, Suita, 565-0871, JapanTohoku University Graduate School of Pharmaceutical Sciences and Medicine, Sendai, 980-8578, JapanLifestyle-related Disease Prevention Center, Shiga University of Medical Science, Otsu, 520-2192, JapanDepartment of Medical Science and Cardiorenal Medicine, Yokohama City University School of Medicine, Yokohama, 236-0004, JapanDepartment of Statistics, Pontificia Universidad Catolica de Chile, Vicu\u00f1a Mackena 4860, Santiago, ChileInstitute of Human Genetics, Helmholtz Zentrum Munich, German Research Centre for Environmental Health, 85764 Neuherberg, GermanyInstitute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, GermanyInstitute of Epidemiology, Helmholtz Zentrum Munich, German Research Centre for Environmental Health, 85764 Neuherberg, GermanyChair of Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universit\u00e4t, 81377 Munich, GermanyKlinikum Grosshadern, 81377 Munich, GermanyNational Heart and Lung Institute, Imperial College London, London, UK, W12 0HS, UKMedical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USAMedical Population Genetics, Broad Institute of Harvard and MIT, 5 Cambridge Center, Cambridge MA 02142, USANational Heart, Lung and Blood Institute and its Framingham Heart Study, 73 Mount Wayte Ave., Suite #2, Framingham, MA 01702, USADepartment of Neurology and Medicine, University of Washington, Seattle, USADepartment of Medicine (Geriatrics), University of Mississippi Medical Center, Jackson, MS, USADepartment of Neurology, Boston University School of Medicine, USAFinnish Institute of Occupational Health, Finnish Institute of Occupational Health, Aapistie 1, 90220 Oulu, FinlandWellcome Trust Centre for Human Genetics, University of Oxford, UKLapland Central Hospital, Department of Physiatrics, Box 8041, 96101 Rovaniemi, FinlandCenter for Non-Communicable Diseases Karachi, PakistanAtherosclerosis Research Unit, Department of Medicine, Karolinska Institute, Stockholm, SwedenDepartment of Internal Medicine, University Medical Center Groningen, University of Groningen, The NetherlandsDepartment of Medical Genetics, Erasmus Medical Center, Rotterdam, The NetherlandsGerontology Research Center, National Institute on Aging, Baltimore, MD 21224, USAIstituto di Neurogenetica e Neurofarmacologia, Consiglio Nazionale delle Ricerche, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, ItalyUnita`Operativa Semplice Cardiologia, Divisione di Medicina, Presidio Ospedaliero Santa Barbara, Iglesias, ItalyComputational Medicine Research Group, Institute of Clinical Medicine, University of Oulu and Biocenter Oulu, 90014 University of Oulu, Oulu, FinlandNMR Metabonomics Laboratory, Department of Biosciences, University of Eastern Finland, 70211 Kuopio, FinlandDepartment of Internal Medicine and Biocenter Oulu, Clinical Research Center, 90014 University of Oulu, Oulu, FinlandInstitute for Molecular Medicine Finland FIMM, 00014 University of Helsinki, Helsinki, FinlandDepartment of Biomedical Engineering and Computational Science, School of Science and Technology, Aalto University, 00076 Aalto, Espoo, FinlandNUS Graduate School for Integrative Sciences & Engineering (NGS) Centre for Life Sciences (CeLS), Singapore, 117456, SingaporeDepartment of Internal Medicine B, Ernst-Moritz-Arndt-University Greifswald, 17487 Greifswald, GermanyInstitute of Pharmacology, Ernst-Moritz-Arndt-University Greifswald, 17487 Greifswald, GermanyInstitute for Community Medicine, Ernst-Moritz-Arndt-University Greifswald, 17487 Greifswald, GermanyU557 Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, U1125 Institut National de la Recherche Agronomique, Universit\u00e9 Paris 13, Bobigny, FranceDepartment of Neurology, Mayo Clinic, Jacksonville, FL, USAImperial College Cerebrovascular Unit (ICCRU), Imperial College, London, W6 8RF, UKFaculty of Medicine, University of Split, CroatiaDepartment of Internal Medicine, Diabetology, and Nephrology, Medical University of Silesia, 41-800, Zabrze, PolandPublic Health Sciences section, Division of Community Health Sciences, University of Edinburgh, Medical School, Teviot Place, Edinburgh, EH8 9AG, UKSchool of Science and Engineering, University of Ballarat, 3353 Ballarat, AustraliaPrevention and Care of Diabetes, Department of Medicine III, Medical Faculty Carl Gustav Carus at the Technical University of Dresden, 01307 Dresden, GermanyUniversity Hospital M\u00fcnster, Internal Medicine D, M\u00fcnster, GermanyDepartment of Medical Statistics, Epidemiology and Medical Informatics, Andrija Stampar School of Public Health, University of Zagreb, CroatiaAstraZeneca R&D, 431 83 M\u00f6lndal, SwedenGenetic Epidemiology & Biostatistics Platform, Ontario Institute for Cancer Research, TorontoSamuel Lunenfeld Institute for Medical Research, University of Toronto, CanadaFaculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, UKDepartment of Epidemiology and Public Health, Imperial College, Norfolk Place London W2 1PG, UKResearch Centre of Applied and Preventive Cardiovascular Medicine, University of Turku and the Department of Clinical Physiology, Turku University Hospital, Turku, 20521, FinlandDepartment of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan Medical Center, Ann Arbor, Michigan, USASingapore Eye Research Institute, Singapore, 168751, SingaporeDepartment of Ophthalmology, National University of Singapore, Singapore, 119074, SingaporeDepartment of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, SingaporeDuke-National University of Singapore Graduate Medical School, Singapore, 169857, SingaporeDivision of Biostatistics, Washington University School of Medicine, Saint Louis, MO, 63110, USADepartment of Primary Care & Population Health, UCL, London, UK, NW3 2PF, UKBHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UKEpidemiology Public Health, UCL, London, UK, WC1E 6BT, UKDepartments of Epidemiology, Biostatistics, and Medicine, Johns Hopkins University, Baltimore MD, USADivision of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, The NetherlandsDivision of Cardiology, Brigham and Women's Hospital, 900 Commonwealth Avenue East, Boston MA 02215, USAGeriatric Rehabilitation Unit, Azienda Sanitaria Firenze (ASF), Florence, ItalyNational Institute for Health and Welfare, Diabetes Prevention Unit, 00271 Helsinki, FinlandHjelt Institute, Department of Public Health, University of Helsinki, 00014 Helsinki, FinlandSouth Ostrobothnia Central Hospital, 60220 Sein\u00e4joki, FinlandRed RECAVA Grupo RD06/0014/0015, Hospital Universitario La Paz, 28046 Madrid, SpainDepartment of Neurology, General Central Hospital, 39100 Bolzano, ItalyCIBER Epidemiolog\u00eda y Salud P\u00fablica, 08003 BarcelonaDepartment of Medicine and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USAGeriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD, USAU872 Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, Centre de Recherche des Cordeliers, Paris, FranceInstitute of Physiology, Ernst-Moritz-Arndt-University Greifswald, 17487 Greifswald, GermanyInstitute of Clinical Medicine/Obstetrics and Gynecology, University of Oulu, FinlandService of Medical Genetics, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, SwitzerlandHuman Genetics Center, 1200 Hermann Pressler, Suite E447 Houston, TX 77030, USADivision of Epidemiology and Prevention, Boston University School of Medicine, Boston, MA, USADepartment of Mathematics, Boston University, Boston, MA, USAInstitute of Health Sciences, University of Oulu, BOX 5000, 90014 University of Oulu, FinlandBiocenter Oulu, University of Oulu, BOX 5000, 90014 University of Oulu, FinlandNational Institute for Health and Welfare, Box 310, 90101 Oulu, FinlandMRC-HPA Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UKCentre of Medical Systems Biology (CMSB 1\u20132), NGI Erasmus Medical Center, Rotterdam, The NetherlandsS1 Figp<0.05 (corrected for 7717 genes). And finally, we cross-analyzed the BP signature genes with blood eQTLs as well as with BP GWAS results to identify the BP signature genes having BP GWAS eQTLs.At first, we identified BP differentially expressed genes in six cohorts respectively. Second, we conducted a meta-analysis of the Illumina cohorts . Third, for discovery and replication purpose, we replicated the BP signature genes identified in the FHS cohort in the Illumina cohorts. And in turn, we replicated the BP signature genes identified in Illumina cohorts in FHS cohort. Fourth, we conducted a meta-analysis in the six cohorts and reported the BP signature genes passing Bonferroni corrected (TIF)Click here for additional data file.S2 FigA) SBP; B) DBP; C) HTN. The x-axis is the effect size of meta-analysis and the y-axis is the \u2212log10 transformed p values.(TIF)Click here for additional data file.S3 FigThe numbers in the Heatmap indicate Pearson correlations between pairs of genes.(TIF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.S6 Table(XLSX)Click here for additional data file.S1 Text(DOCX)Click here for additional data file.S2 Text(DOCX)Click here for additional data file."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Pengfei Song3, Dan Zou4, Xuesong Hu2, Shancen Zhao2,5, Shengjie Gao2,6, Fei Ling1Minfeng Chen1 School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China, 2 BGI-Shenzhen, Shenzhen, 518083, China, 3 The fourth people\u2019s hospital of Shenzhen , Shenzhen, 518033, China, 4 School of Computer, National University of Defense Technology, Changsha, 410073, China, 5 State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China, 6 Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Roberto D\u2019Alessandro3, Francesca Bianco1, Valerio Carelli2,3, Giovanna Cenacchi2, Antonio D. Pinna1, Massimo Del Gaudio1, Rita Rinaldi4, Vincenzo Stanghellini1, Loris Pironi1, Kerry Rhoden1, Vitaliano Tugnoli2, Carlo Casali5, and Roberto De Giorgio1Elisa Boschetti1 Department of Surgical and Medical Sciences, University of Bologna, Bologna, Italy, 2 Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy, 3 IRCCS Institute of Neurological Sciences, Bologna, Italy, 4 Neurology Unit, St. Orsola-Malpighi Hospital, Bologna, Italy, 5 Department of Medico-Surgical Sciences and Biotechnologies, University \u2018La Sapienza\u2019, Rome, Italy"} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:1\u262f, Hong Wang1\u262f, Jiangbei Cao1, Changtian Li2, Weidong Mi1*, Li Yang3, Fang Guo1, Xianwang Wang4, Tie Yang3Changsheng Zhang1 Anesthesia and Operation Center, Chinese PLA General Hospital, Beijing, 100853, China, 2 Department of Ultrasound, The Southern Building, Chinese PLA General Hospital, Beijing, 100853, China, 3 Department of Radiology, Chinese PLA General Hospital, Beijing, 100853, China, 4 Department of Anesthesia, The 309th hospital of Chinese PLA, Beijing, 100096, China\u262f These authors contributed equally to this work.plamzk@126.com* 10.1371/journal.pone.0123177Zhang C, Wang H, Cao J, Li C, Mi W, Yang L, et al. (2015) Measurement and Analysis of the Tracheobronchial Tree in Chinese Population Using Computed Tomography. PLoS ONE 10(4): e0123177. doi:"} +{"text": "The authors are listed out of order. The publisher apologizes for the error. Please view the correct author order, affiliations, and citation here:1,2,4, Alain Vaguet3, N.K Yadav6, B. Lefebvre3, A. Cebeillac3,4, B.N. Nagpal5, Eric Daud\u00e93,4, Richard E. Paul1,2Olivier Telle1 Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 8204 G\u00e9ographie-cit\u00e9s, Paris, France, 2 Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Paris, France, 3 Centre National de la Recherche Scientifique, Unit\u00e9 Mixte de la de Recherche 6266, IDEES, Rouen, France, 4 Centre de Sciences Humaines, Delhi, India, 5 National Institute of Malaria Research, Delhi, India, 6 Municipal Corporation of Delhi, Delhi, India10.1371/journal.pone.0146539Telle O, Vaguet A, Yadav NK, Lefebvre B, Cebeillac A, Nagpal BN, et al. (2016) The Spread of Dengue in an Endemic Urban Milieu\u2013The Case of Delhi, India. PLoS ONE 11(1): e0146539. doi:In the Author Contributions section, Richard E. Paul (RP) should be listed as one of the persons who contributed reagents/materials/analysis tools."} +{"text": "There are several errors in the author affiliations. The first, fourth, and fifth authors are also affiliated with: Research and Development Office, VA Pacific Islands Health Care System, Honolulu, Hawaii. The affiliations should appear as shown here:1,2,3,4, Brian J. Morris1,5, John S. Grove1,6, Helen Petrovitch1,2,3,4, Webster Ross1,2,3,4, Kamal H. Masaki1,3, Beatriz Rodriguez1,3,6,7, Randi Chen1, Timothy A. Donlon1,8, D. Craig Willcox1,3,9, Bradley J. Willcox1,2,3,7Qimei He1 Honolulu Heart Program/Honolulu-Asia Aging Study, Physicians\u2019 Office Tower, Kuakini Medical Center, Honolulu, Hawaii, United States of America2 Pacific Health Research and Education Institute, Honolulu, Hawaii3 Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, United States of America4 Research and Development Office, VA Pacific Islands Health Care System, Honolulu, Hawaii5 School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia6 Department of Public Health, University of Hawaii at Manoa, Honolulu, Hawaii7 Instituto Tecnologico de Monterrey, Monterrey, Mexico8 Department of Research, Kuakini Medical Center, Honolulu, Hawaii, United States of America9 Department of Human Welfare, Okinawa University, Ginowan, Okinawa, JapanThe following information is missing from the Funding section: This study was supported by Kuakini Medical Center.FOXO3 Genetic Association Study,\u201d the first sentence should read \u201cLater (in 2007), a subset of 615 subjects who participated in Exam 4 were chosen for a genetic association study of single nucleotide polymorphisms (SNPs) of FOXO3 and longevity, as reported previously [19].\u201dIn the Materials and Methods section, under the title \u201cSubjects for In"} +{"text": "Author list for the article \u201cGenome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis\u201d should be as follows:1,2*, Francesca Cavaciocchi1,3, Ana Lleo4, Cristina Cheroni5, Raffaele De Francesco5, Simone A. Lombardi1, Maria De Santis1,3, Francesca Meda1, Maria Gabriella Raimondo1, Chiara Crotti1, Marco Folci1, Luca Zammataro1, Marlyn J. Mayo6, Nancy Bach7, Shinji Shimoda8, Stuart C. Gordon9, Monica Miozzo10,11, Pietro Invernizzi4, Mauro Podda1, Rossana Scavelli5, Michelle R. Martin12, Michael F. Seldin13,14, Janine M. LaSalle12, and M. Eric Gershwin2Carlo Selmi1Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center, Milan, Italy2Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis, Davis, CA, USA3BIOMETRA Department, University of Milan, Milan, Italy4Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Milan, Italy5National Institute of Molecular Genetics (INGM), Milan, Italy6University of Texas Southwestern, Dallas, TX, USA7Mt. Sinai University, New York, NY, USA8Clinical Research Center, National Nagasaki Medical Center, Nagasaki, Japan9Henry Ford Hospital, Detroit, MI, USA10Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy11Division of Pathology, Fondazione IRCCS C\u00e0 Granda Ospedale Maggiore Policlinico, Milan, Italy12Genome Center and M.I.N.D. Institute, University of California at Davis, Davis, CA, USA13Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA, USA14Department of Internal Medicine, University of California at Davis, Davis, CA, USAThe original article has been updated.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "After publication of this work , we note1*, Vassilis Golfinopoulos1, Amelie Deleporte1, Marianne Paesmans2, Hazem El Mansy1, Camilo Garcia3, Marc Peeters4, Lieven Annemans5, Caroline Vandeputte1, Marion Maetens1, Marc Van den Eynde6, Rapha\u00ebl Mar\u00e9chal10, Ivan Borbath6, Damien Dresse7, Ghislain Houbiers8, Michael Fried9, Ahmad Awada1, Martine Piccart1, Jean-Luc Van Laethem10 and Patrick Flamen3Alain HendliszAH, PM, VG Contribution to protocol writing, Manuscript design, Setting-up the trial, Writing manuscript; HEM, AD, CV, MM, MVDE, RM, Writing manuscript; CG, PF, Contribution to protocol writing, Manuscript design, Setting-up the trial, Writing manuscript, Coordination of PET imaging network; PM, AA, MP, Contribution to protocol writing, Setting-up the trial; JVL, Contribution to protocol writing, Setting-up the trial, Writing manuscript. All authors read and approved the final manuscript."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1; Anam Parand, PhD1; Bruno Rigole, MSc2; Angus Thomson, PhD2; Marisa Miraldo, PhD3; Charles Vincent, PhD4; Nick Sevdalis, PhD1Ana Wheelock, MSc1Faculty of Medicine, Imperial College London, London, UK; 2Sanofi Pasteur, Lyon, France; 3Imperial College Business School, London, UK; 4Department of Experimental Psychology, University of Oxford, Oxford, UK"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Jin Young Lee1,2, Hyung-Sik Kim1,3, In-Sun Hong4,5, Soon Won Choi1,2, Yoojin Seo1,2, Insung Kang1,2, Jae-Jun Kim1,2, Byung-Chul Lee1,2, SeungHee Lee1,2,3, Andreas Kurtz1,2,6, Kwang-Won Seo1,2,3 and Kyung-Sun Kang1,2,Kyung-Rok Yu1 Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, South Korea2 Research Institute for Veterinary Medicine, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea3 Institute for Stem Cell and Regenerative Medicine in Kangstem Biotech, Biotechnology Incubating Center, Seoul National University, Seoul 151-742, Korea4 Department of Molecular Medicine, Gachon University, Incheon, Republic of Korea5 Lee Gil Ya Cancer and Diabetes Institute, Incheon, Republic of Korea6 Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany"} +{"text": "There are errors in the author affiliations in the XML version of the article. The publisher apologizes for these errors. The affiliations should appear as shown here:1,2,3,4, Adina Coroiu1, Laura Copeland1, Carlos Gomez-Garibello1, Cornelia Albani5, Markus Zenger5,6*, Elmar Br\u00e4hler5,7Annett K\u00f6rner1 Department of Educational and Counselling Psychology, McGill University, Montreal, Canada, 2 Department of Oncology, McGill University, Montreal, Canada, 3 Louise-Granofsky-Psychosocial Oncology Program, Segal Cancer Centre, Jewish General Hospital, Montreal, Canada, 4 Psychosocial Oncology Program, McGill University Health Centre, Montreal, Canada, 5 University of Leipzig, Department of Medical Psychology and Medical Sociology, Leipzig, Germany, 6 Faculty of Applied Human Studies, University of Applied Sciences Magdeburg and Stendal, Stendal, Germany, 7 Department of Psychosomatic Medicine and Psychotherapy, Universal Medical Center Mainz, Mainz, Germany."} +{"text": "Bratschi2,3, Gerd Pluschke2,3, Alphonse Um Boock8There are errors in the author affiliations. The affiliations should appear as shown here: Earnest Njih Tabah1 National Yaws, Leishmaniasis, Leprosy and Buruli ulcer Control Programme, Ministry of Public Health, Yaounde, Cameroon, 2 Swiss Tropical and Public Health Institute, Basel; University of Basel, Basel, Switzerland, 3 The University of Basel, Basel, Switzerland, 4 Faculty of Medicine and Biomedical Sciences, The University of Yaounde 1, Yaounde, Cameroon, 5 Department of Public Health and Hygiene, Faculty of Health Sciences, University of Buea, Cameroon, 6 Department of Operational Research in Health, Ministry of Public Health, Yaounde, Cameroon, 7 Department of Neurology, Central Hospital, Yaounde, Cameroon, 8 Regional Bureau for Africa of the FAIRMED Foundation, Yaounde, Cameroon."} +{"text": "Nucl. Acids Res. (2014) Jan;42(Database issue):D677\u201384. doi: 10.1093/nar/gkt1203.Author Tomer Altman was accidently omitted from the list of authors of the above article. The full list of authors and affiliations is provided below.The authors apologize to the readers and publisher for any inconvenience this may have caused.1, Gavin Sherlock2, Deborah A. Siegele3, Suzanne A. Aleksander1, 4Tomer Altman, Catherine A. Ball2, Janos Demeter2, Sushanth Gouni1, Timothy A. Holland4, Peter D. Karp4, John E. Lewis1, Nathan M. Liles1, Brenley K. McIntosh1, Huaiyu Mi5, Anushya Muruganujan5, Farrell Wymore2 and Paul D. Thomas5James C. Hu1Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA2Department of Genetics, Stanford University, Stanford, CA 94305, USA3Department of Biology, Texas A&M University, College Station, TX, 77843, USA4Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA5Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USAPresent address: Tomer Altman, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA"} +{"text": "Corrigendum to: Ariga T, Toita T, Kato S, et al. Treatment outcomes of patients with FIGO Stage I/II uterine cervical cancer treated with definitive radiotherapy: a multi-institutional retrospective research study. J Radiat Res 2015 Sep; 56(5): 841\u20138.In the article \u201cTreatment outcomes of patients with FIGO Stage I/II uterine cervical cancer treated with definitive radiotherapy: a multi-institutional retrospective research study.\u201d, the affiliation of two authors, i.e. of Dr. Shingo Kato and Dr. Teruki Teshima were incomplete.The full and correct affiliations are follows:1, Takafumi Toita1*, Shingo Kato2,21, Tomoko Kazumoto3, Masaki Kubozono4, Sunao Tokumaru5, Hidehiro Eto6, Tetsuo Nishimura7, Yuzuru Niibe8, Kensei Nakata9, Yuko Kaneyasu10,22, Takeshi Nonoshita11, Takashi Uno12, Tatsuya Ohno13, Hiromitsu Iwata14, Yoko Harima15, Hitoshi Wada16, Kenji Yoshida17, Hiromichi Gomi18, Hodaka Numasaki19, Teruki Teshima19,23, Shogo Yamada4 and Takashi Nakano20Takuro Ariga1Department of Radiology, Graduate School of Medical Science, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa, 903\u20130215, Japan2Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba, Japan3Department of Radiation Oncology, Saitama Cancer Center, Saitama, Japan4Department of Radiation Oncology, Tohoku University School of Medicine, Sendai, Japan5Department of Radiology, Saga University, Saga, Japan6Department of Radiology, Kurume University Hospital, Fukuoka, Japan7Division of Radiation Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan8Department of Radiology and Radiation Oncology, Kitasato University School of Medicine, Kanagawa, Japan9Department of Radiology, Sapporo Medical University, Sapporo, Japan10Department of Radiation Oncology, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan11Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan12Department of Diagnostic Radiology and Radiation Oncology, Chiba University Graduate School of Medicine, Chiba, Japan13Gunma University Heavy Ion Medical Center, Gunma University, Gunma, Japan14Department of Radiation Oncology, Nagoya Proton Therapy Center, Nagoya City West Medical Center, Aichi, Japan15Department of Radiology, Takii Hospital, Kansai Medical University, Osaka, Japan16Department of Radiation Oncology, Miyagi Cancer Center, Miyagi, Japan17Division of Radiation Oncology, Kobe University Graduate School of Medicine, Hyogo, Japan18Department of Radiation Oncology, St Marianna University, School of Medicine, Kanagawa, Japan19Department of Medical Physics and Engineering, Osaka University Graduate School of Medicine, Osaka, Japan20Department of Radiation Oncology, Gunma University Graduate School of Medicine, Gunma, Japan21Department of Radiation Oncology, Saitama Medical University International Medical Center, Saitama, Japan22Department of Radiation Oncology, National Hospital Organization, Fukuyama Medical Center, Hiroshima, Japan23 Department of Radiation Oncology, Osaka Medical Center for Cancer and Cardiovascular Disease, Osaka, Japan*Corresponding author. Department of Radiology, Graduate School of Medical Science, University of the Ryukyus, 207 Uehara, Nishihara-choWe sincerely apologize for this inconvenience."} +{"text": "In the original article the list1,4*, Martin I Sigurdsson1, Sverrir Hardarson2, Vigdis Petursdottir2, Eirikur Jonsson1, Gudmundur V Einarsson1 and Tomas Gudbjartsson1,3Johann P Ingimarsson1Departments Urology and Surgery, Landspitali University Hospital2Department of Pathology, Landspitali University Hospital3University of Iceland, Faculty of Medicine, Reykjavik, Iceland4Dartmouth-Hitchcock Medical Center, Lebanon, New HampshireWe would like to apologize for this error and for any inconvenience this may have caused."} +{"text": "Here by, authors declare that the corrected authors list and affiliations are:1; Mohammad Javad Hosseini 2,*; Morteza Izadi 3; Abbas Mahmoodzadeh Poornaki 1; Javid Sadraei 4; Behzad Einollahi 5; Mohammad Reza Rezaimanesh 6; Ozra Bagheri 2; Jahangir Abdi 7Babak Rezavand 1 Department of Parasitology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, IR Iran2 Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran3 Health Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran4 Department of Parasitology, Medical School, Tarbiat Modares University, Tehran, IR Iran5 Nephrology and Urology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran6 Department of Laboratory Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, IR Iran7 Department of Parasitology, School of Medicine, Ilam University of Medical Sciences, Ilam, IR IranSincerely YoursMohammad Reza Rezaimanesh"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2,4, Fei Pan5, Guangchao Li3, Jingjing Li2,4Enhui He1 Nankai University School of Medicine, Tianjin, China, 2 Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, China, 3 School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China, 4 Beijing Friendship Hospital, affiliated with Capital Medical University, Beijing, China, 5 Department of Gastroenterology and Hepatology, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, China."} +{"text": "Erratum to: Neth Heart J (2016)DOI 10.1007/s12471-015-0797-zIn the version of the article originally published online, the members of the DANARA study group were appended to the list of authors. The author line should have read:1; Yannick J.H.J. Taverne, MD2; Charlotte Houck, Msc1; Marco G\u00f6tte, MD, PhD3; Bianca J.J.M. Brundel, PhD4,5; Reinder Evertz, MD6; Maarten Witsenburg, MD, PhD1; Jolien W. Roos-Hesselink, MD, PhD1; Ad J.J.C. Bogers, MD, PhD2; Natasja M.S. de Groot, MD, PhD1; DANARA Study InvestigatorsChristophe P. Teuwen, MD7; Tanwier T.T.K. Ramdjan, MSc1; Wim A. Helbing, MD, PhD8; Janneke A.E. Kammeraad, MD, PhD8; H.G. Reinhart Dorman, MD9; Jurren M. van Opstal, MD, PhD10; Thelma C. Konings, MD11; Joris W.J. Vriend, MD, PhD3; Pepijn van der Voort, MD12;Collaborators: Sander G. Molhoek, MD, PhD1Dept of Cardiology, Erasmus University Medical Center, Rotterdam, The Netherlands; 2Dept of Cardio-Thoracic Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands; 3Dept of Cardiology, Haga Hospital, The Hague, The Netherlands; 4Dept of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, Groningen, The Netherlands; 5Dept of Physiology, Institute of Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands; 6Dept of Cardiology, University Medical Center St. Radboud, Nijmegen, The Netherlands; 7Dept of Cardiology, Amphia Hospital, Breda, The Netherlands; 8Dept of Pediatrics, Division of Pediatric Cardiology, Erasmus Medical Center \u2013 Sophia Children\u2019s Hospital, Rotterdam, The Netherlands; 9Dept of Cardiology, Bravis Hospital, Rosendaal, The Netherlands; 10Dept of Cardiology, Medisch Spectrum Twente, Enschede, The Netherlands; 11Dept of Cardiology, VU University Medical Center, Amsterdam, The Netherlands; 12Dept of Cardiology, Catharina Hospital, Eindhoven, The Netherlands;"} +{"text": "Aging (Albany NY) 2015; 7(9): 629-647.PMCID: PMC 4600622 PMID: 26363853In this Article, the additional author Aine Brigette Henley is added to this manuscript:http://www.impactaging.com/papers/v7/n9/pdf/100790.pdf. The updated authors\u2019 list with affiliations is provided here:1, Jose Luis Venero2, Ryota Iwasawa1, Mohammed-khair Hankir3, Sunniyat Rahman1, Aine Brigette Henley4, Alan Boobis1, and Nabil Hajji1Aleksandra Dabrowska1 Imperial College London, Centre for Pharmacology and Therapeutics, Department of Medicine, London, United Kingdom;2 Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Facultad de Farmacia, Universidad de Sevilla, C/Prof. Garc\u00eda Gonz\u00e1lez, Sevilla, Spain;3 Integrated Research and Treatment Centre for Adiposity Diseases, Department of Medicine, University of Leipzig, Leipzig, Germany:4 Research Centre for Optimal Health, Faculty of Science and Technology, University of Westminster, London, United Kingdom"} +{"text": "In conjunction with the development of a bidirectional scattering metrology project, a large number of papers pertaining to the theory and measurement of bidirectional scattering from optical surfaces were collected and categorized. This collection includes papers that deal with various aspects of the bidirectional scattering distribution function (BSDF), its measurement, interpretation, use, and implications. Each paper is classified in one or more subject categories on the basis of its technical content. The subject categories are included just to serve as a key to the most salient characteristics of each paper cited. Because of the interest in this field, this bibliography is being published as a service to the public. The bidirectional scattering distribution function (BSDF) radiometrically characterizes the scatter of optical radiation from a surface as a function of the angular positions of the incident and scattered beams. By definition, it is the ratio of the scattered radiance to the incident irradiance: the unit is inverse steradian. The term bidirectional reflectance distribution function (BRDF) is used when specifically referring to reflected scatter. Likewise, bidirectional transmittance distribution function (BTDF) refers to scatter transmitted through a material.The bidirectional characterization of elastic scatter from surfaces is a property that is required for the evaluation of elements contained within larger systems that need minimal or controlled scattered light. The need for this information is readily seen in applications such as ring laser gyroscopes and telescopes. This type of information is also requisite for characterization of materials intended for use in temperature control where thermal radiation must be modelled or in imaging applications where stray light must be suppressed. It may also be used to assist the acceptance/rejection process in optical manufacturing settings.The present state of most of the facilities measuring this quantity needs to be upgraded to support new and more stringent requirements as well as recent strides in the production of high-quality optics.There is a lack of uniformity throughout the community for physical standards which can ascertain the accuracy of BSDF measurements (paper 91). The NIST Bidirectional Scattering Metrology Project is currently developing an instrument which will later serve to develop standard reference materials as well as a standard measurement technique.In conjunction with the development of this BSDF instrument, a large number of papers pertaining to the theory and measurement of bidirectional scattering from optical surfaces were collected and categorized. This collection includes papers that deal with various aspects of the BSDF, its measurement, interpretation, use, and implications.Each paper is classified in one or more subject categories on the basis of its technical content. The subject categories are included just to serve as a key to the most salient characteristics of each paper cited. In the literature, there is a bibliography (paper 117) of papers published prior to 1975 that relate to scattering from surfaces. Building upon that bibliography, this bibliography includes papers related to BSDF published since that time to the present. Neither the category classification list nor the list of papers is complete. There were two selection criteria used to determine whether a paper should be included in this bibliography: the paper was used during certain phases of the NIST project development and/or it was regarded as relevant and important to the field. However, inclusion or omission from the list does not necessarily imply endorsement or reproval, respectively. This systematized bibliography is sufficiently extensive to be of significant help to workers in the field, and particularly to those just beginning to work in it. For further breadth of information, the reader is suggested to review the conference proceedings from the Society of Photo-Optical Instrumentation Engineers (SPIE) that focus on scattering from surfaces; some papers from each of these are cited here.As an aid to identifying papers related to a certain field, each of the papers is listed under each category in which it has been classified. Due to the wide interdisciplinary nature of optical scattering metrology, some topics had to be grouped together so that the list would not become unmanageable. The subject categories are coded and used as follows:The optical design of a system determines the aberrations that will be present \u2013 assuming accurate alignment\u2013and their magnitudes. The calculation of these aberrations and their effect on the measurement of BSDF are addressed in the following papers: 3,96,102,159,160.Many different instruments are described in the literature. A sampling of these apparatus overviews is contained in the following papers: 4,12,31,41,51,52,63,65,66,76,77,79,83,84,87,89,90,93,94,95,103,111,112,132,113,118,120,122,128,129,136,137,138,140,145,146,151,159,160,161,166,168,169.Techniques for calibration and/or error analysis include reference methods and absolute methods. Specific details concerning calibration and the philosophy of calibration are discussed in these papers: 23,33,34,83,89,108,145,158.The use of laser sources in BSDF instruments is very common. Coherence becomes a critical property of these sources in diffuse BSDF metrology. The following papers address the property as it pertains to radiometry in general and to BSDF metrology in particular: 3,8,37,39,40,49,59,61,63,73,80,97,98,101,125,126.Design criteria and plans or layouts of components or subsystems of BSDF instruments are separated out and described in detail. These subsystems include source, sample manipulation, receiver, attenuation, apertures, etc: 3,10,11,21,22,27,28,29,31,35,41,51,52,60,66,68,69,71,76,85,86,87,89,90,93,94,95,108,112,132,118,119,124,128,130,136,141,142,156,157,159,160,162,163,166,168,170.Truncation of optical beams by apertures cause diffraction and thereby affect the instrument signature of BSDF instruments. This effect is discussed in the following papers: 3,49,69,70,72,89,96,139,159,160.These articles include experimental results in the form of tabulated data or graphs from a variety of different types of measurements. Some of these include data from actual BSDF scans on particular material samples while others give interpretive results highlighting instrument capabilities. Still other papers give profilometry data that yield topographic information. The particular type of experimental data given within each paper should be obvious from the title of the paper: 4,5,7,9,13,15,16,17,18,20,22,24,25,26,28,29,30,32,35,36,38,40,41,42,44,46,48,52,53,54,57,59,64,67,73,76,78,79,83,88,91,92,94,99,100,101,103,104,109,110,111,132,113,114,115,119,120,121,122,123,127,128,129,130,131,133,134,135,138,139,140,142,143,145,147,149,151,152,154,158,161,165,167,168,169,170.The background measurement of the noise equivalent BSDF, or the instrument signature, limits an instrument to the measurement of samples that have a BSDF larger than the NEBSDF. Specific instrument profiles or signatures are displayed in some of the following papers. The other papers address general concerns in obtaining and improving the signature of an instrument: 4,12,36,76,77,85,86,90,120,124,130,136,137,139,141,151,159,160,162,164,166,168,171.Particular optical materials and/or coatings are identified and experimental BSDF data are given for each of these in the following papers: 2,7,9,13,16,17,22,24,25,28,29,32,35,42,48,52,53,64,67,76,78,83,92,94,99,100,104,109,110,113,114,115,121,122,123,129,130,131,133,135,138,145,149158,162,165,Polarization control, theory, and associated problems are examined: 5,6,23,24,25,59,79,95,144,147,167.Various types of mechanical and optical surface profiling techniques are described and/or compared against optical scattering predictions of surface finish : 1,2,17,20,30,39,43,44,46,54,56,57,59,65,88,91,100,109,111,134,137,140,150,151.The following papers describe techniques used for, or problems in, referencing BSDF measurements, thereby assigning a level of confidence to the accuracy of the measurement: 33,53,83,91,92,108,130,145,158,164.Control, or suppression, of geometrically stray light is examined in this group of papers. Included in these are some papers which evaluate baffling materials with BRDF data: 18,22,27,28,29,42,50,58,60,69,71,78,87,90,113,123,146,149,156,157,163,170.Below is a list of papers that are outstanding in their fields and provide comprehensive coverage of a well-defined topic within BSDF metrology: 19,24,45,46,65,74,76,77,81,82,89,91,92,105,106,107,108,117,130,140,148,171.Among the theoretical questions explored throughout these papers are: basic definition of BSDF, scattering theory of surfaces, mathematical treatment of surfaces, subsurface contributions to scatter, inverse scattering problem, and scaling of BSDF with respect to angle of incidence and wave-length: 1,3,5,6,7,8,12,14,15,16,17,18,20,23,26,37,38,39,40,43,44,45,46,47,49,55,56,57,58,59,61,62,69,70,71,72,74,75,77,79,80,81,82,90,94,96,97,98,101,103,105,106,107,108,109,110,111,116,120,124,125,126,129,131,134,139,144,146,147,148,150,152,153,154,155,156,157,161,162,167,170.Surface roughness and sample isotropy, homogeneity, and cleanliness are all topographic contributions to optical scatter. These topics as well as some subsurface contributions are treated in the following papers: 1,2,4,9,14,15,16,17,18,19,20,30,38,39,40,43,44,45,46,47,54,55,56,57,62,74,75,88,100,109,110,111,116,120,121,125,127,134,135,139,142,144,147,150,152,153,154,155,161,162,167,169.Issues related to the bidirectional transmittance distribution function, BTDF, are considered in these papers: 52,103,122,126."} +{"text": "Author list for the article \u201cRag defects and thymic stroma: lessons from animal models\u201d should be as follows:1,2, Pietro Luigi Poliani3, Luigi Daniele Notarangelo4, Fabio Grassi5, and Anna Villa1,2*Veronica Marrella1Milan Unit, Institute of Genetics and Biomedic Research, National Research Council, Milan, Italy2Istituto Clinico Humanitas, Istituto di Ricovero e Cura a Carattere Scientifico, Rozzano, Italy3Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy4Division of Immunology, Boston Children\u2019s Hospital, Boston, MA, USA5Institute for Research in Biomedicine, Bellinzona, SwitzerlandThe original article has been updated.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "In Volume 93, Issue 8, August 2015, page 541, equation (3) should read:"} +{"text": "Aging (Albany NY) 2015; 7(3): 167-176.PMCID: PMC4394728 PMID: 25960543In this Article, the additional affiliation is added for Arie Budovsky, a co-author of this manuscript:http://www.impactaging.com/papers/v7/n3/pdf/100726.pdf. The additional affiliation 4 is provided here:1, Dimitri Toren1, Klemens Vierlinger2, Manuela Hofner2, Christa Nohammer2, Marco Chilosi3, Arie Budovsky1,4, and Vadim E. Fraifeld1Hagai Yanai1The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel2AIT - Austrian Institute of Technology, ATU14703506, Vienna, Austria3Department of Pathology, University of Verona, Verona, Italy4Judea Regional Research and Development Center, Carmel, Israel"} +{"text": "Unfortunately, the original version of this article containe1, Lee, R T.2, Kingstone, T.2, Singh, S.3, Shah, P R.2, Edwards, S5., Roberts, L.4Soundy, A.1School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, Birmingham B15 2TT, UK2Integrated Medicine Department, Freshwinds Charity, Prospect Hall, 12 College Walk, Selly Oak, Birmingham B29 6LE, UK3Department of Gastroenterology, Consultant in Gastroenterology, Good Hope Hospital, Sutton Coldfield, UK4Primary Care Clinical Sciences, School of Health and Population Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK5Healer Member of The Healing Trust, UK"} +{"text": "The UK IBD Genetics Consortium is listed out of order in the author list. The correct order is:1\u2021 *, Benjamin Lehne1,2\u2021, Kristina Stone1, James C. Lee3, Kirstin Taylor1, Jo Knight1,4,5, Efterpi Papouli6, Muddassar M. Mirza6, Michael A. Simpson1, Sarah L. Spain1, Grace Lu7, Franca Fraternali7, Suzannah J. Bumpstead8, Emma Gray8, Ariella Amar1, Hannah Bye1, Peter Green1, UK IBD Genetics Consortium\u00b6, Guy Chung-Faye9, Bu\u2019Hussain Hayee9, Richard Pollok10, Jack Satsangi11, Miles Parkes3, Jeffrey C. Barrett8, John C. Mansfield12, Jeremy Sanderson13, Cathryn M. Lewis1, Michael E. Weale1\u2021, Thomas Schlitt1\u2021, Christopher G. Mathew1,14\u2021Natalie J. Prescott1 Department of Medical and Molecular Genetics, Kings College London, Guy\u2019s Hospital, London, United Kingdom, 2 Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom, 3 Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom, 4 Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada, 5 Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada, 6 NIHR GSTFT/KCL Comprehensive Biomedical Research Centre Genomics Core Facility, King\u2019s College London School of Medicine, Guy\u2019s Hospital, London, United Kingdom, 7 Randall Division of Cell and Molecular Biophysics, King\u2019s College London, Guy\u2019s Campus, London, United Kingdom, 8 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, 9 Department of Gastroenterology, King\u2019s College Hospital NHS Foundation Trust, Denmark Hill, London, United Kingdom, 10 Gastroenterology and Hepatology, St George\u2019s Healthcare NHS Trust, Tooting, London, United Kingdom, 11 Gastrointestinal Unit, Molecular Medicine Centre, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom, 12 Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom, 13 Guy\u2019s & St Thomas\u2019 NHS Foundation Trust, St Thomas\u2019 Hospital, Department of Gastroenterology, London, United Kingdom, 14 Division of Medical Biochemistry, University of Cape Town, Cape Town, South Africa\u2021 NJP and BL contributed equally to this work. MEW, TS, and CGM also contributed equally to this work.\u00b6 Membership of the UK IBD Genetics Consortium is listed in the Acknowledgments.natalie.prescott@kcl.ac.uk* E-mail:"} +{"text": "There are errors in the author affiliations for Chung-Ho Chang and Chih-Pin Chuu. The correct author affiliations are shown here:1\u262f, Hui-Ping Lin2\u262f, Shih Sheng Jiang2, Ching-Yu Lin3, Junichi Fukuchi1,4, Richard A. Hiipakka1, Chi-Jung Chung5, Tzu-Min Chan6,7, Shutsung Liao1, Chung-Ho Chang3, Chih-Pin Chuu3,8,9,10*John M. Kokontis1The Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, U.S.A. 2National Institute of Cancer Research, National Health Research Institutes, Miaoli County, Taiwan 3Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan 4Pharmaceuticals and Medical Devises Agency, Tokyo, Japan 5Department of Health Risk Management, China Medical University, Taichung City, Taiwan 6Department of Medical Education and Research, China Medical University Beigang Hospital, Yunlin, Taiwan 7Department of Medical Education and Research, Tainan Municipal An-Nan Hospital-China Medical University, Tainan, Taiwan 8Graduate Institute of Basic Medical Science, China Medical University, Taichung City, Taiwan 9Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, Taichung City, Taiwan 10Ph.D. program in Environmental and Occupational Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwancpchuu@nhri.org.tw* Email: These authors contributed equally to this work."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Farah Sakri1, Atiqah Mokhsin1, Thuhairah Rahman1,2,5, Nadzimah Mohd Nasir1,2, Suraya Abdul-Razak3, Mazapuspavina Md Yasin3, Aletza Mohd Ismail1,2, Zaliha Ismail4, Hapizah Nawawi1,2,5Wan Nor Hanis Wan Ahmad1 Centre for Pathology Diagnostic and Research Laboratories (CPDRL), 2 Cluster for Pathology and Laboratory Medicine, 3 Primary Care Medicine Discipline, 4 Population Health and Preventive Medicine Discipline, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Sungai Buloh, Selangor, Malaysia, 5 Institute for Pathology, Laboratory and Forensic Medicine (I-PPerForM), UniversitiTeknologi MARA (UiTM), Selayang Campus, Selayang, Selangor"} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:1, Ji-an Chen1, Lin Liu2, Da-hua Wang1, Wen-juan Fu1, Ling-qiao Wang1, Jiao-hua Luo1, Liang Zhang1, Yao Tan1, Zhi-qun Qiu1, Yu-jing Huang1, Wei-qun Shu1*Hui Zeng1 Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P. R. China2The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of AmericaZeng H, Chen J-a, Liu L, Wang D-h, Fu W-j, et al. (2014) Experimental Comparison of the Reproductive Outcomes and Early Development of the Offspring of Rats Given Five Common Types of Drinking Water. PLoS ONE 9(10): e108955. doi:10.1371/journal.pone.0108955"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Christopher P. Morris1, Marc P. H\u00fcbner1,2, and Edward Mitre1Ellen Mueller Fox1Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20815; 2Institute for Medical Microbiology, Immunology, and Parasitology, University Hospital Bonn, 53105 Bonn, German"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Amy L. Cole3, Taha Hirbod4, Lyle McKinnon5, Terry B. Ball1,2,7, Garrett R. Westmacott6, Joshua Kimani7, Frank Plummer1,2,6,7, Alexander M. Cole3, Adam Burgener1,2,4, Kristina Broliden4Kenzie D. M. Birse1 National Laboratory for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada, 2 Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, 3 Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, United States of America, 4 Unit of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden, 5 Centre for the AIDS Programme of Research In South Africa, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Congella, South Africa, 6 National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada, 7 Department of Medical Microbiology, Kenyatta National Hospital, University of Nairobi, Nairobi, Kenya"} +{"text": "AbstractBaetiscf.nubecularis Eaton, 1898 and Rhithrogena from the diaphana group were recorded. Ephemeracf.parnassiana Demoulin, 1958, the species previously recorded only from Greece, was also recorded.Knowledge of the mayfly biodiversity in the Balkan Peninsula is still far from complete. Compared to the neighbouring countries, the mayfly fauna in Croatia is very poorly known. Situated at the crossroads of central and Mediterranean Europe and the Balkan Peninsula, Croatia is divided into two ecoregions: Dinaric western Balkan and Pannonian lowland. Mayflies were sampled between 2003 and 2013 at 171 sites, and a total of 66 species was recorded. Combined with the literature data, the Croatian mayfly fauna reached a total of 79 taxa. Of these, 29 species were recorded for the first time in Croatia while 15 species were not previously recorded in Dinaric western Balkan ecoregion. Based on the mayfly assemblage, sampling sites were first structured by ecoregion and then by habitat type. In comparison with the surrounding countries, the Croatian mayfly fauna is the most similar to the Hungarian and Bosnian fauna. Some morphologically interesting taxa such as Ephemeroptera) have a worldwide distribution, being absent only from Arctic region, Antarctica and some remote oceanic islands . The results of field studies were then combined with the literature data given in PageBreakCroatia is a relatively small country situated at the crossroads of Central and Mediterranean Europe and Balkan Peninsula, and is divided into two ecoregions: Dinaric western Balkan (ER5) and Pannonian lowland ER11) . Specime1 . SpeciThe list of the 171 sampling site names with number codes (site ID), altitude, latitude and longitude is presented in Table PageBreakPageBreakPageBreakPageBreakPageBreakBaetidae and cerci, necessary for the species identification, were fixed in Euparal and examined under a microscope. Adult specimens were mostly identified by the imaginal male genitalia. The collected material (larvae and adult specimens) was identified using Mayflies were sampled in every season at 34 sites, while at the remainder of sites, sampling was usually performed only once between April and September. Specimens were stored in 80% ethanol and identified in the lab using a stereomicroscope and microscope. A reference collection was made by preparing permanent slide mounts of identified species. Larvae were treated with 10% KOH and 99% acetic acid to remove all muscle parts. Mouth parts, legs, gills, thorax, abdomen, paraproct plate in All recorded specimens were included in the Croatian mayfly species list. Data for the sites with the same sampling effort were statistically analysed using the PRIMER 6 software package . As suchBaetis Leach, 1815 and Ecdyonurus Eaton, 1868 both with 11 species. Baetisrhodani and Serratellaignita were the most widely distributed species, present in 83 and 76 sampling sites, respectively. Fourteen species were recorded at only one sampling site: Cloeonsimile Eaton, 1870, Procloeonnana , Caenispusilla Nav\u00e0s, 1913, Ephemeracf.parnassiana Demoulin, 1958, Leptophlebiavespertina , Ecdyonurusvitoshensis Jacob & Braasch, 1984, Ecdyonuruszelleri , Electrogenamazedonica , Heptageniacoerulans Rostock, 1878, Heptageniaflava Rostock, 1878, Heptagenialongicauda , Rhithrogenairidina , Rhithrogenagr.diaphana and Rhithrogenasemicolorata .In total, 79 mayfly taxa Table were recPageBreakPageBreakPageBreakwere recorded in both the Black and Adriatic Sea Basins, while 25 species were recorded only for Black Sea basin and 11 species only for Adriatic Sea basin were present in both ecoregions. A total of 50 species was recorded as present only in the Dinaric western Balkan ecoregion (ER5) and 48 only in the Pannonian lowland ecoregion (ER11) Table . Nearly The S\u00f8rensen Index of Similarity indicated the Croatian mayfly fauna had the greatest similarity with the Hungarian assemblage Table .For the distribution data, the following format was used: \u201cLiterature data\u201d were mainly taken from \u25cf New records for the Croatian mayfly fauna\u25a0 Only adults recordedPageBreakI. Ametropodidae Bengtsson, 1913Ametropusfragilis Albarda, 18781. Literature data: Drava River, Donji Miholjac Metreletusbalcanicus 3. Literature data: Bauernfeind and Sold\u00e1n (2012)Baetidae Leach, 1815III. Alainitesmuticus 4. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 79, 80\u25a0, 82, 84, 85, 86 5. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 13, 15, 57, 63Baetisbuceratus Eaton, 1870 \u25cf6. New records: 2, 36Baetisfuscatus 7. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 5, 7, 8, 10, 18, 19, 26, 29, 31, 32, 35, 36, 40, 56, 60, 61, 62Baetisliebenauae Kefferm\u00fcller, 1974 \u25cf8. New records: 1, 2, 9, 10, 35, 36, 37, 62, 98, 109, 110, 111, 112, 113, 122, 128, 131, 134, 139, 140, 141, 143, 151, 152, 153, 162, 171Baetislutheri M\u00fcller-Liebenau, 19679. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 7, 18, 19, 35, 61, 62, 103, 116, 141, 142, 146, 147, 150, 157Baetismelanonyx \u25cf10. New records: 115, 117, 120, 146, 147, 156, 157, 158, 159, 160, 161, 162, 163Baetiscf.nubecularis Eaton, 1898 \u25cf11. Literature data with new records: 79, 80, 81, 82, 83, 84, 85, 86, 87 12. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 79, 80, 81, 82, 83, 84, 85, 87, 88 New records: 7, 26Baetistricolor Tshernova, 1928 \u25cf14. New records: 20, 43, 44Baetisvernus Curtis, 1834 \u25cf15. New records: 7, 9, 10, 36, 38, 53, 54, 76Baetopustenellus \u25cf16. New records: 19, 64, 94Nigrobaetisniger \u25cf17. Literature data with new records: 138New records: 15, 36, 38, 93, 103, 109, 110, 128, 131Centroptilumluteolum 18. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 84, 85, 86, 87, 88, 89, 90, 91, 92 19. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 1, 5, 20, 24, 35, 37, 39, 41, 43, 44, 45, 46, 47, 60, 67, 78, 101, 103, 104, 105, 121, 125, 127, 128, 129, 152Cloeonsimile Eaton, 187020. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 125Procloeonbifidum 21. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 6, 19, 20, 28, 29, 31, 32, 40, 41, 42, 44, 47, 62, 68, 69, 71, 115, 121, 141PageBreakProcloeonnana \u25cf22. New records: 68Procloeonpennulatum 23. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 84, 85, 86 26. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 86, 87, 89, 90, 91, 92 New records: 8, 9, 10, 18, 26, 27, 28, 31, 32, 35, 40, 41, 54, 61, 68, 71, 115, 140, 141, 142, 143Caenispusilla Nav\u00e0s, 1913 \u25cf28. New records: 62Caenisrivulorum Eaton, 1884 \u25cf29. New records: 40, 41Caenisrobusta Eaton, 1884 \u25cf30. New records: 1, 24, 39, 47Ephemerellidae Klap\u00e1lek, 1909V. Ephemerellamucronata \u25cf31. New records: 14, 134, 139, 163Serratellaignita 32. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 83, 84, 85, 86, 88 PageBreakNew records: 1, 7, 8, 9, 10, 12, 17, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 48, 49, 53, 46, 58, 59, 60, 61, 62, 64, 65, 66, 68, 69, 73, 76, 98, 99, 100, 103, 108, 109, 110, 113, 114, 115, 116, 117, 118, 119, 121, 122, 129, 134, 137, 138, 139, 140, 141, 142, 143, 144, 146, 147, 148, 150, 153, 157, 158, 159, 162, 163, 171Torleyamajor 33. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 84, 86 Literature data with new records: 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92 Ephemeralineata Eaton, 187036. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 106, 107, 108, 109, 110, 118, 119, 122, 137, 138, 139, 140, 141, 142, 143, 147Ephemeracf.parnassiana Demoulin, 1958 \u25cf37. New records: 98Ephemeravulgata Linnaeus, 175838. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 11, 54, 55, 59, 100, 125, 128, 154, 164Ephemerazettana Kimmins, 1937 \u25cf \u25a039. New records: 102, 118, 134, 136, 138, 141, 142, 154, 155Heptageniidae Needham, 1901VII. Ecdyonurusaurantiacus 40. Literature data: Bauernfeind and Sold\u00e1n (2012)Ecdyonurusdispar 41. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 61, 63, 66, 68, 69PageBreakEcdyonurusinsignis 42. Literature data: Cetina River, between Podgrade and Slime Ecdyonurusstarmachi Sowa, 1971 \u25cf45. New records: 13, 14, 26, 53, 103, 120Ecdyonurussubmontanus Landa, 1969 \u25cf46. Literature data with new records: 82, 83 New records: 95, 99, 118, 119, 120Ecdyonurusvenosus 48. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 97\u25a0, 99, 100, 109, 110, 112, 118, 119, 120, 137, 138, 139, 141, 148, 150, 162Ecdyonurusvitoshensis Jacob & Braasch, 198449. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 12Ecdyonuruszelleri \u25cf50. New records: 53Electrogenaaffinis \u25cf51. New records: 68, 69, 70Electrogenalateralis 52. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 86 \u25cf53. New records: 128PageBreakElectrogenaujhelyii \u25cf54. New records: 11, 13, 16, 24, 50, 93Epeorusassimilis Eaton, 188555. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 4, 13, 94, 97\u25a0, 98, 99, 115, 116, 117, 120, 135\u25a0, 137, 138, 141, 142, 146, 147, 156Heptageniacoerulans Rostock, 187856. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 18Heptageniaflava Rostock, 187857. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 167Heptagenialongicauda \u25cf58. New records: 63Heptageniasulphurea 59. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 7, 8, 18, 21, 40, 42Kageroniafuscogrisea 60. Literature data: Bauernfeind and Sold\u00e1n (2012)Rhithrogenabraaschi Jacob, 1974 \u25cf61. Literature data with new records: 79, 80, 81, 82, 83, 85 Rhithrogenairidina \u25cf64. New records: 27Rhithrogenasemicolorata 65. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 53PageBreakLeptophlebiidae Banks, 1900VIII. Choroterpespicteti 66. Literature data: Bauernfeind and Sold\u00e1n (2012)Habroleptoidesconfusa Sartori and Jacob, 198667. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 22, 120, 158Habrophlebiafusca 68. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 27, 28, 30, 35, 38, 48, 59, 69, 70, 131, 168, 169Habrophlebialauta Eaton, 188469. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 82, 83, 85, 90 \u25cf70. Literature data with new records: 90, 91 71. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 79, 83, 84, 85, 86, 87, 88 73. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 26, 27, 32Palingeniidae Albarda, 1888X. Palingenialongicauda 74. Literature data: Bauernfeind and Sold\u00e1n (2012)Polymitarcyidae Banks, 1900XI. Ephoronvirgo 75. Literature data: Bauernfeind and Sold\u00e1n (2012)PageBreakPotamanthidae Albarda, 1888XII. Potamanthusluteus 76. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 7, 8, 9, 10, 18, 35, 36, 37, 40Siphlonuridae Ulmer, 1920 (1888)XIII. Siphlonurusarmatus 77. Literature data: Bauernfeind and Sold\u00e1n (2012)Siphlonuruscroaticus Ulmer, 192078. Literature data: Bauernfeind and Sold\u00e1n (2012)Literature data with new records: 82, 83, 85, 87 79. Literature data: Bauernfeind and Sold\u00e1n (2012)New records: 26, 27, 30, 73, 76PageBreakmayfly assemblage, sampling sites were mainly structured first by ecoregion and then by habitat type. Species richness at the sampling sites and diversity indices are presented in Table The majority of the Croatian mayfly species were found to be associated with rivers and streams Table . Among tThe SIMPER analysis between sites within the same habitat type showed an average similarity ranging from 35.1% for the Pannonian lowland rivers to 57.3% for the springs , patchy central European as well as southern (e.g. Ephemerazettana) and Balkan distribution were recorded in Croatia. Additionally, 15 taxa were found that were not previously recorded in the Dinaric western Balkan ecoregion: Baetiscf.nubecularis, Procloeonnana, Caenisbeskidensis, Ephemeracf.parnassiana, Ecdyonurusmacani, Ecdyonurussubmontanus, Ecdyonurustorrentis, Electrogenaaffinis, Electrogenamazedonica, Electrogenaujhelyii, Heptagenialongicauda, Rhithrogenabraaschi, Habroleptiodesconfusa, Leptophlebiavespertina and Paraleptophlebiawerneri . Thus, reliable identification cannot be distinguished at this time. Comparison with other Balkan Rhithrogenadiaphana group species and further detailed studied are required. A similar case is recorded for the Baetisalpinus group , which presents the morphological characteristics that are intermediate between Baetisalpinus and Baetisnubecularis. Interestingly, the species is only recorded in high numbers , as well as to determine the presence of the thirteen species listed in the literature which were not confirmed in this study . The rare or unconfirmed presence of most of these species is likely due to the lack of seasonal sampling. It is possible that they were present at some sampling sites included in this study, but at a very young instar or even egg stage, and as such were overlooked. Additionally, some species might have PageBreakbecome extinct from the Croatian rivers, such as Palingenialongicauda, which at present likely only inhabits the Danube River and Tisza River in Hungary, Slovakia and Ukraine or a wide range of habitat type preferences grouped together with the tufa-barriers . Howeveron (ER5) . This ison (ER5) . It had on (ER5) . This ison, 1881 .Baetisvardarensis Ikonomov, 1962, Rhithrogenapicteti Sowa, 1971, Leptophlebiamarginata , Ephemerellanotata Eaton, 1887, Caenisluctuosa ) but were not yet recorded, due to the lack of systematic sampling in all seasons, future studies should include seasonal sampling PageBreakof a higher number of sites and habitat types. Additionally, the main focus should be on the eastern lowland part of the country, where a lower number of sites was visited during this study.As expected, this study revealed a higher number of mayfly taxa inhabiting Croatian freshwater habitats than known from the previous literature. As two of the most similar mayfly assemblages of the neighbouring countries have several taxa that could also inhabit Croatian habitats . Considering these species were recorded from a small number of sites in this study, they could be considered rare. Future studies on the taxonomic status, ecological features and detailed distribution of these species is necessary.In the present study, some interesting taxa with restricted European and local distributions were recorded (e.g. Baetisliebenauae was recorded on larger karstic rivers, a different habitat type than previously known, more detailed information on its preferences at the microhabitat scale and water physico-chemical properties should be investigated.Additionally, as"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Meiying Xu2, 4*, Yuming Zhong2,4, Yongqiang Yang3, Fanrong Chen3, Jun Guo2,4Yingli Lian1. School of Biological Science & Engineering, South China University of Technology, Guangzhou, 510006, China.2. Guangdong Provincial Key Laboratory of Microbial Culture Collection, Guangdong Institute of Microbiology, Guangzhou, 510070, China.3. Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.4. State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, China."} +{"text": "One affiliation for the second author is not indicated. Emily Bennitt is also affiliated with: Okavango Research Institute, University of Botswana, Private Bag 285, Maun, Botswana. The affiliations should appear as shown here:1, Emily Bennitt1,2, Stuart E. Newson3, Charlotte Packman1, William J. Browne4, Stephen Harris1, Gareth Jones1*, Emma Stone1Matt R. K. Zeale1 School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom, 2 Okavango Research Institute, University of Botswana, Private Bag 285, Maun, Botswana, 3 British Trust for Ornithology, The Nunnery, Thetford, Norfolk, IP24 2PU, United Kingdom, 4 Graduate School of Education, and Centre for Multilevel Modelling, University of Bristol, 2 Priory Road, Bristol, BS8 1TX, United Kingdom"} +{"text": "Unfortunately, the original version of this article containe1,2*, TD Thomsen1, JW Larsen1 and J Markvart3HI Jensen* Corresponding author: Hanne Irene Jensen, Hanne.Irene.Jensen@rsyd.dk1 Kolding Hospital, part of Lillebaelt Hospital, Kolding, Denmark2 Institute of Regional Health Research, University of Southern Denmark3 Danish Building Research Institute/Aalborg University, Copenhagen, Denmark"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,3, Peter Zeidman3, Peter Smittenaar3, Rick A. Adams3, Fiona McNab2,3, Robb B. Rutledge3, Raymond J. Dolan3Harriet R. Brown1 Oxford Centre for Human Brain Activity, University of Oxford, Oxford, United Kingdom, 2 School of Psychology, University of Birmingham, Birmingham, United Kingdom, 3 Wellcome Trust Centre for Neuroimaging, University College London, London, United Kingdom"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Philip W. Boyd2, Christina M. McGraw3,4, Christopher D. Hepburn7, Conrad A. Pilditch5, Jaz N. Morris1, Abigail M. Smith7, Catriona L. Hurd1,6Christopher E. Cornwall1 Department of Botany, University of Otago, Dunedin, New Zealand, 2 National Institute for Water and Atmospheric research (NIWA) Centre of Physical and Chemical Oceanography, Dunedin, New Zealand, 3 School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts, United States of America, 4 School of Science and Technology, University of New England, Armidale, Australia, 5 Department of Biological Sciences, University of Waikato, Hamilton, New Zealand, 6 Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia, 7 Department of Marine Sciences, University of Otago, Dunedin, New Zealand"} +{"text": "In Volume 93, Issue 5, May 2015, page 360,"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2,3, Sophie Le Coeur2,4,6,, Billy Amzal2,7, Lily Ingsrisawang1, Patrinee Traisathit8, Nicole Ngo-Giang-Huong2,4,5, Kenneth McIntosh9,10, Tim R. Cressey2,4,5, Suraphan Sangsawang11, Boonsong Rawangban12, Prateep Kanjanavikai13, Jean-Marc Tr\u00e9luyer14,15,16,, Gonzague Jourdain2,4,5, Marc Lallemant2 and Sa\u00efk Urien14,15,16Patumrat Sripan1 Department of Statistics, Faculty of Science, Kasetsart University, Bangkok, Thailand, 2 Institut de recherche pour le d\u00e9veloppement (IRD) UMI 174-PHPT, Marseille, France, 3 Ecole Doctorale de Sant\u00e9 Publique, Universit\u00e9 Paris-Sud, Paris, France, 4 Department of Medical Technology, Faculty of Associated Medical Science, Chiang Mai University, Chiang Mai, Thailand, 5 Harvard School of Public Health, Boston, MA, United States of America, 6 Institut d'Etudes D\u00e9mographiques, Paris, France, 7 LASER Analytica, London, United Kingdom, 8 Department of Statistics, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand, 9 Boston Children's Hospital, Boston, MA, United States of America, 10 Department of Pediatrics, Harvard Medical School, Boston, MA, United States of America, 11 Health Promotion Center Region 10, Chiang Mai, Thailand, 12 Nopparat Rajathanee Hospital, Bangkok, Thailand, 13 Banglamung Hospital, Chonburi, Thailand, 14 EAU08 Universit\u00e9 Paris Descartes, Sorbonne Paris Cit\u00e9, Paris, France, 15 Unit\u00e9 de Recherche Clinique, AP-HP, H\u00f4pital Tarnier, Paris, France, 16 CIC1419 INSERM, Cochin-Necker, Paris, France."} +{"text": "The authors are listed out of order, and the first three authors, Ning Hung, Li-Yu Hu, and Cheng-Che Shen, should be noted as contributing equally to this work. Please view the correct author order, affiliations, and citation here:2\u00b6, Li-Yu Hu1\u00b6, Cheng-Che Shen3,4, Yu-Wen Hu2,5,6, Chiu-Mei Yeh7, Chung-Jen Teng2,6,8, Ai-Seon Kuan2, San-Chi Chen9, Tzeng-Ji Chen2,7, Chia-Jen Liu2,6,9*Ning Hung1 Department of Psychiatry, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, 2 School of Medicine, National Yang-Ming University, Taipei, Taiwan, 3 Department of Psychiatry, Chiayi Branch, Taichung Veterans General Hospital, Chiayi, Taiwan, 4 Department of information management, National Chung-Cheng University, Chiayi, Taiwan, 5 Cancer Center, Taipei Veterans General Hospital, Taipei, Taiwan, 6 Institute of Public Health, National Yang-Ming University, Taipei, Taiwan, 7 Department of Family Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, 8 Division of Oncology and Hematology, Department of Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan, 9 Division of Hematology and Oncology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan\u00b6These authors contributed equally to this work.*Corresponding authorpures1000@yahoo.com.twE-mail:"} +{"text": "The revised Volume 6, issue 3, doi:"} +{"text": "There is an error in the affiliations for the seventh author. Sabine Cevoli should not be affiliated with Affiliation 7, Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), University of Bologna, Bologna, Italy. The full, correct list of authors and affiliations is given below.1,2, Giorgio Binelli3, Raffaella Fabbri4,5, Maria L. Valentino6,7, Rossella Vicenti4,5, Maria Macciocca4,5, Sabina Cevoli6, Agostino Baruzzi6,7, Salvatore DiMauro1, Valerio Carelli6,7*Francesco Pallotti1 Department of Neurology, Columbia University, New York City, New York, United States of America2 Dipartimento di Scienze Chirurgiche e Morfologiche, University of Insubria, Varese, Italy3 Dipartimento di Scienze Teoriche e Applicate, University of Insubria, Varese, Italy4 Unit\u00e0 Operativa di Ginecologia e Fisiopatologia della Riproduzione Umana, Ospedale S.Orsola-Malpighi, University of Bologna, Bologna, Italy5 Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), University of Bologna, Bologna, Italy6 IRCCS Istituto delle Scienze Neurologiche di Bologna, Ospedale Bellaria, Bologna, Italy7 Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), University of Bologna, Bologna, Italyvalerio.carelli@unibo.it* E-mail:"} +{"text": "There is an error in the affiliation for authors Ying Zhang, Yanrong Lv, and Haidong Gao. The first affiliation should be listed as the Department of Breast Surgery, QiLu Hospital of Shandong University, Jinan, China. The updated list can be viewed below:1, Yanrong Lv1, Yongyang Zhang2, Haidong Gao1*Ying Zhang1 Department of Breast Surgery, QiLu Hospital of Shandong University, Jinan, China2 Emergency Department, Shandong Jining No.1 People\u2019s Hospital, Jining, Chinahaidongao@163.com* E-mail:"} +{"text": "Santanu Chakraborty, Department of Radiology, University of Ottawa, Department of Medical Imaging, The Ottawa Hospital, 1053 Carling Avenue, Ottawa, ON K1Y 4E9, Canada. Phone: (613) 737 8571; Fax: (613) 761 4476; E-mail:"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:Hashem Koohy 1,2, Thomas A. Down 1, Mikhail Spivakov 1, Tim Hubbard 21 The Babraham Institute, Babraham Research Campus, Cambridge United Kingdom2 Wellcome Trust Sanger Institute, Wellcome Trust Research Campus, Cambridge, United Kingdom."} +{"text": "Enterococcus faecalis were isolated from copper fed pigs in Denmark. These Gram-positive bacteria within the genus Enterococcus are able to survive a variety of physical and chemical challenges by the acquisition of diverse genetic elements. The genome of strains S1, S12, S17, S18, S19 and S32 contained 2,615, 2,769, 2,625, 2,804, 2,853 and 2,935 protein-coding genes, with 41, 42, 27, 42, 32 and 44 genes encoding antibiotic and metal resistance, respectively. Differences between Cu resistant and sensitive E. faecalis strains, and possible co-transfer of Cu and antibiotic resistance determinants were detected through comparative genome analysis.Six strains of Copper is an essential trace element with an ubiquitous cellular distribution and performs several biological functions . It servEnterococci belong to the gastrointestinal flora of humans and animals, and have been known for more than a century for their pathogenicity to humans, causing urinary tract and surgical wound infections, bacteraemia and endocarditis . R. REnteropathogen , 14], a, aEnteroablished , 16]. H. HEnterofaecalis . Herein,E. faecalis ATCC 29212 and E. faecalis SFL with a high bootstrap value (100\u00a0%). All the E. faecalis are in a distinct branch with the other enterococci, such as E. casseliflavus , E. faecium , E. hirae and the another pig gut Firmicute, that is Streptococcus equinus NCDO 1037 method implemented in MEGA version 6.0. The resultant tree topologies were evaluated by bootstrap analyses with 1,000 random samplings. Phylogenetic analysis based on 16S rRNA gene sequences showed that the six strains clustered together with E. faecalis is a Gram-positive, oval-shaped, and often highly pathogenic bacterium classified as a member of the genus Enterococcus were isolated from Cu-fed pigs as part of the Danish Integrated Antimicrobial Resistance Monitoring (DANMAP) surveillance program to to28] toE. faecalis strains S1, S12, S17, S18, S19 and S32 resulted in 156, 162, 240, 84, 172 and 200 fold coverage of the genomes, respectively. The draft genome sizes were 2,762,808, 2,896,725, 2,786,673, 2,888,656, 2,969,229 and 3,037,709\u00a0bp in length, with an average GC content of 37.6, 37.4, 37.5, 37.4, 37.2 and 37.2\u00a0%, respectively, and comprises 2,615; 2,769; 2,625; 2,804; 2,853 and 2,935 protein coding sequences, respectively. Of the protein coding genes, 2,002; 2,006; 1,949; 2,001; 2,058 and 2,073 were genes with function predictions, with 41, 42, 27, 42, 32 and 44 genes responsible for antibiotics and toxic compounds resistant, respectively. There are 52 (4 rRNA genes and 48 tRNA genes), 54 (3 rRNA genes and 51 tRNA genes), 48 (3 rRNA genes and 45 tRNA genes), 52 (4 rRNA genes and 48 tRNA genes), 53 (3 rRNA genes and 50 tRNA genes) and 55 (5 rRNA genes and 50 tRNA genes) RNA genes for strains S1, S12, S17, S18, S19 and S32, respectively. The properties and statistics for the genome are summarized in Table\u00a0Whole genome sequencing of copYZAB, encoding a Cu resistance determinant and vancomycin (vanA) ..tetM in MDR: Multidrug-resistantThe authors declare that they have no competing interests.SZ drafted the manuscript, performed laboratory experiments, and analyzed the data. DW and YW performed the comparative genome analysis. HH, FA and HA sequenced, assembled, and annotated the genome. YZ revised the manuscript. CR organized the study and revised the manuscript. All authors read and approved the final manuscript."} +{"text": "Drs. Difei Wang, Lin An, and Robinder Gauba are not included in the author byline. Please view the corrected author byline here:1,2,3, Maki Nishida1, Michael Harris1, Shruti Rao1, Amrita K. Cheema2,4, Kirandeep Gill2, Difei Wang1,2, Lin An1, Robinder Gauba1, Haeri Seol5, Lauren P. Morgenroth5, Erik Henricson6, Craig McDonald6, Jean K. Mah7, Paula R. Clemens8,9, Eric P. Hoffman5, Yetrib Hathout5, Subha Madhavan1,2Simina M. Boca1 Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, United States of America,2 Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America,3 Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC, United States of America,4 Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America,5 Children\u2019s National Medical Center and the George Washington University, Washington, DC, United States of America,6 Department of Physical Medicine and Rehabilitation, University of California Davis, School of Medicine, Davis, California, United States of America,7 Department of Pediatrics, University of Calgary, Alberta Children\u2019s Hospital, Calgary, Alberta, Canada,8 Neurology Service, Department of Veteran Affairs Medical Center, Pittsburgh, Pennsylvania, United States of America,9 Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of AmericaThe contributions of Dr. Wang, Dr. An, and Dr. Gauba are as follows: Contributed reagents/materials/analysis tools."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Jonathan Selleslagh1,3, Elsa Breton1, Khalef Rabhi1, Vincent Cornille1, Mahmoud Bacha1, Eric Lecuyer4, Rachid Amara1Achwak Benazza1 Universit\u00e9 du littoral, UMR 8187 LOG, F-62930 Wimereux, France, 2 Universit\u00e9 Badji Mokhtar, Laboratoire d\u2019Ecobiologie Milieux Marins et Littoraux, Annaba, Algeria, 3 Universit\u00e9 de Bordeaux, CNRS, UMR 5805 EPOC, Station Marine d\u2019Arcachon, place du Docteur Peyneau, F-33120 Arcachon, France, 4 CNRS, UMR 8187 LOG, F-62930 Wimereux, France"} +{"text": "This addendum supplies corrected statements and proofs of an error by author. Hear by, authors declare that The correct authors list and affiliations are:1,2, Mohsen Mobini-Dehkordi 1,2,*, Behnaz Saffar 1,2Fahimeh Afzal-Javan 1 Department of Genetics, Faculty of Science, University of Shahrekord, Shahrekord, IR Iran2 Research Institute of Biotechnology, University of Shahrekord, Shahrekord, IR IranMohsen Mobini-Dehkordi"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2,3; Shuguang Wei 2; Hongsheng Gui 2; Zuyi Yuan 1,3; Shengbin Li 1,2Zhe Zhang 1 Key Laboratory of Environment and Gene Related to Diseases, Ministry of Education, College of Medicine, Xi\u2019an Jiaotong University, Shaanxi, China2 The Key Laboratory of National Ministry of Health for Forensic Sciences, College of Medicine and Forensics, Xi\u2019an Jiaotong University, Shaanxi, China3 Department of Cardiovascular Medicine, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Shaanxi, China."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Daniel A. Brenner2, James M. McCabe3, Mark Dela Cruz4, Brian Long5, Venkata A. Narla4, Joseph Park6, Ameya Kulkarni7, Elizabeth Sinclair5, Stephen Y. Chan6, Suzaynn F. Schick8, Namita Malik8, Peter Ganz4, Priscilla Y. Hsue4Stephen W. Waldo1 Currently, Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, 2 Currently, Division of Cardiovascular Medicine, Stanford University Medical Center, Stanford, CA, 3 Currently, Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA 4 Division of Cardiology and the Center of Excellence in Vascular Research, San Francisco General Hospital, University of California, San Francisco, CA, 5 Division of Experimental Medicine, University of California, San Francisco, CA, 6 Division of Cardiovascular Medicine, Brigham and Women\u2019s Hospital, Boston, MA, 7 Currently, Division of Cardiology, Mid-Atlantic Permanente Medical Group, 8 Division of Occupational and Environmental Medicine, University of California, San Francisco, CAAdditionally, the following information is missing from the Funding section: Schick SF and Malik N were supported by the University of California Tobacco-Related Disease Research Program (20PT-0184)."} +{"text": "SAH is acute cerebrovascular event associated high mortality and tendency to cause dependence, accompanied by multiple medical complications. These patients must be admitted to an intensive care unit and be cared for by a multidisciplinary experienced team.Analysis of epidemiology, complications and critical care management of SAH patients admitted in five neurocritical care units.Multicenter, prospective and observational study. Including SAH admissions in ICU over 2014. Variables analized: epidemiological, cause of SAH, if aneurysmal SAH: aneurysm location and size, repair treatment; complications, ICU and hospital lenght of stay and morbidity .Sample size: 127 patients. Epidemiology data: age 60,46 years , 54,33% women and risk factors: HBP 40,16%, dyslipidemia 22,05% and DM 6,30%. Severity scales: Hunt-Hess V: 23,62%, IV 13,39%; Fisher IV: 65,87 %, III 16,67 %; WFNS V: 22,83 %, IV 18,90%. Cause of SAH: 70,97% aneurysmal, 4,03% arteriovenous malformation (AVM) and 25% other. Aneurysm location: anterior comunicant 27,27%; posterior 21,21 %; middle cerebral artery 26,26 %. Aneurysmal sack diameter: small (< 15 mm) 67,05 %, large 22,73% and giant (>25 mm) 10,23%. Repair treatment: surgical 20,63%, endovascular (EVT) 39,68 % and conservative 39,68 %. Time admission-repairment: 3,5 days , median 1 day (IQR 1). Complications: vasospasm 20,47 %, rebleeding 12,7%, delayed cerebral ischemia (DCI) 26,19%, hydrocephalus 31,75 %, seizures 7,14 %, ventriculitis 6,35% , heart complications 15,87% and sodium disorders 20,47% . Invasive monitoring: ICP 22,40% and PtiO2 6,60%. Median of length of stay: ICU 5 days (IQR 14) and hospital 15,5 days (IQR 22). Morbidity-GOS scale: 1 (death)= 23,39 % ; 2 = 3,23 %; 3 = 8,06 %; 4: 12,90%; 5: 52,42%.The most common cause of SAH is cerebral aneurysm rupture with high Fisher. In this study the endovascular and conservative treatment are the same frequency greater than surgical. Maybe the severity of clinical presentation and high variability in the election of treatment among centers could influence. Time admission-repairment was near to recommendations. Results about complications and GOS scale are similar to the literature."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Xinling Liang2,1, Shuangxin Liu1, Zhiming Ye1, Yuanhan Chen1, Wenjian Wang1, Ruizhao Li1, Lixia Xu1, Zhonglin Feng1, Wei Shi1Zhilian Li1 Department of Nephrology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China, 5100802 Southern Medical University, Guangzhou, China, 510515"} +{"text": "Jabbar1, Xin Cao1, Alexandar Tzankov3, Carlo Visco4, Lalitha Nagarajan5, Qinging Cai1, Santiago Montes-Moreno6, Yuji An1, Karen Dybkaer7, April Chiu8, Attilio Orazi9, Youli Zu10, Govind Bhagat11, Kristy L. Richards12, Eric D. Hsi13, William WL. Choi14, J. Han van Krieken15, Jooryung Huh16, Maurilio Ponzoni17, Andr\u00e9s J.M. Ferreri17, Xiaoying Zhao18, Michael B. M\u00f8ller19, John P. Farnen20, Jane N. Winter21, Miguel A. Piris6, Roberto N. Miranda1, L. Jeffrey Medeiros1, and Ken H. Young1,22*Zijun Y. Xu-Monette1 Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA2 Peking University Cancer Hospital and Institute, Beijing, China3 University Hospital, Basel, Switzerland4 San Bortolo Hospital, Vicenza, Italy5 Department of Genetics and Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA6 Hospital Universitario Marques de Valdecilla, Santander, Spain7 Aalborg University Hospital, Aalborg, Denmark8 Memorial Sloan-Kettering Cancer Center, New York, NY, USA9 Weill Medical College of Cornell University, New York, NY, USA10 The Methodist Hospital, Houston, TX, USA11 Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA12 University of North Carolina School of Medicine, Chapel Hill, NC, USA13 Cleveland Clinic, Cleveland, OH, USA14 University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China15 Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands16 San Medical Center, Ulsan University College of Medicine, Seoul, Korea17 San Raffaele H. Scientific Institute, Milan, Italy18 Zhejiang University School of Medicine, Second University Hospital, Hangzhou, China19 Odense University Hospital, Odense, Denmark20 Gundersen Lutheran Health System, La Crosse, WI, USA21 Feinberg School of Medicine, Northwestern University, Chicago, IL, USA22 The University of Texas School of Medicine, Graduate School of Biomedical Sciences, Houston, Texas, USA* These authors have equal contributions to this work."} +{"text": "The fifth author\u2019s name is spelled incorrectly. The correct name is: Grigorios Dimitriadis.Additionally, there are errors in the author affiliations. The affiliations should appear as shown here:1,2, Herbert Peremans2, Norizham Abdul Razak3, Edouard Verstraelen4, Greg Dimitriadis4Dieter Vanderelst1 School of Biological Sciences, Bristol University, Bristol, UK, 2 Department of Engineering Management, Active Perception Lab, University of Antwerp, Antwerp, Belgium, 3 School of Aerospace Engineering, Engineering Campus, Universiti Sains Malaysia, 14300 Nibong Tebal, Seberang Perai Selatan, Pulau Pinang, Malaysia, 4 Aerospace and Mechanical Engineering Department, University of Li\u00e8ge, Li\u00e8ge, Belgium."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2,4,5, Ying Li1,2,4,5, Yingke Zhang1,2,4,5, Lin Zhang1,2,4,5, Zilian Wang3, Xuzhi Zhang1,2,4,5, Lian Gui1,2,4,5, Junqi Huang1,2,4,5*.Yiming Qi1 Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China, 2 Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China, 3 Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China, 4 Key Laboratory of Tropical Diseases Control, Ministry of Education, Guangzhou, PR China, 5 Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR Chinahttp://isis.nsfc.gov.cn; Natural Science Foundation of Guangdong Province http://gdsf.gdstc.gov.cn; Guangdong Province Scientific Technology Project http://www.gdstc.gov.cn; Guangzhou City Scientific Technology Project http://apply.gysi.gov.cn; The Fundamental Research Funds for the Central Universities (no. 10YKPY31) http://mso.sysu.edu.cn; Guangdong Provicial Key Laboratory Construction Projection on Organ Donation and Transplant Immunology (no.2013A061401007) http://www.gdstc.gov.cn. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.2. There are errors in the Funding section. The correct funding information is as follows: This work was supported by the National Natural Science Foundation of China (no.30872350 and no.31370870)"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Adam D. Kennedy2, Fotinos Panagakos1, William Devizio1, Harsh M. Trivedi1, Thomas J\u00f6nsson2, Lining Guo2, Shannon Cervi3, Frank A. Scannapieco3*Virginia M. Barnes1 Colgate Palmolive Technology Center, Piscataway, NJ, United States of America2 Metabolon, Durham, NC, United States of America3 Department of Oral Biology, School of Dental Medicine, University at Buffalo, State University of New York, Buffalo, NY, United States of America"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Paulina C. Drohomyrecky4, Stephen D. S. McCarthy1,2, Danila Leontyev1, Xue-Zhong Ma1, Donald R. Branch1,2,3*\u262f, Shannon E. Dunn3,4,5*\u262fCarlyn A. Figueiredo1 Centre for Innovation, Canadian Blood Services, 67 College Toronto, Toronto, Ontario, Canada,2 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada,3 Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada,4 Department of Immunology, University of Toronto, Toronto, Ontario, Canada,5 Women\u2019s College Research Institute, Toronto, Ontario, Canada* Email: don.branch@utoronto.ca (DRB); sdunn@uhnresearch.ca (SED)These authors contributed equally to this work."} +{"text": "K. Ullas Karanth is incorrectly listed as being affiliated with the Nicholas School of Environment, Duke University, Durham, North Carolina, United States of America, in place of Krithi K Karanth, who is affiliated with the Nicholas School of Environment, Duke University. The publisher apologizes for this error.1,2*, Krithi K. Karanth2,3,5, Devcharan Jathanna2, N. Samba Kumar2,4, K. Ullas Karanth2,3The correct affiliation is: Arjun Srivathsa1 Post-Graduate Programme in Wildlife Biology and Conservation, Wildlife Conservation Society, India Program, National Centre for Biological Sciences , Bangalore, India,2 Centre for Wildlife Studies, Bangalore, India,3 Wildlife Conservation Society, Bronx, New York, United States of America,4 Wildlife Conservation Society, India Program, Bangalore, India,5 Nicholas School of Environment, Duke University, Durham, North Carolina, United States of America"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Feng Shi2, Gang Li2, Drew Fralick3,4, Ting Shen1, Meihui Qiu1, Jun Liu5, Kaida Jiang6, Dinggang Shen2,7, Yiru Fang1Daihui Peng1 Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China, 2 Department of Radiology and BRIC, University of North Carolina, Chapel Hill, North Carolina, United States of America, 3 Suicide Research and Prevention Center, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China, 4 Palo Alto University, Palo Alto, California, United States of America, 5 The Fifth People\u2019s Hospital of Shanghai, Fudan University, Shanghai, China, 6 Huashan Hospital, Fudan University, Shanghai, China 7 Department of Brain and Cognitive Engineering, Korea University, Seoul, Republic of Korea"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Xiao-Tong Li1, Xiao Zhao1, Xun-Li Liu1, Kazuho Ikeo2, Takashi Gojobori2,3, Qing-Xin Liu1Qi Yu1 Laboratory of Developmental Genetics, Shandong Agricultural University, Tai\u2019an, Shandong, China, 2 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka, Japan, 3 Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering, KAUST (King Abdullah University of Science and Technology), Thuwal, Saudi Arabia"} +{"text": "There are multiple errors in the author byline. Please see the correct author byline here.1, Masanari Watanabe1, Katsuyuki Tomita2, Hiroyuki Sano3, Akira Yamasaki1, Eiji Shimizu1Jun Kurai1 Department of Respiratory Medicine and Rheumatology, Tottori University Faculty of Medicine, Yonago, Tottori, Japan,2 Department of Respiratory Medicine, Yonago Medical Center, Yonago, Tottori, Japan,3 Department of Respiratory Medicine and Allergology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, JapanThe correct citation is: Kurai J, Watanabe M, Tomita K, Hiroyuki S, Yamasaki A, et al. (2014) Influence of Asian Dust Particles on Immune Adjuvant Effects and Airway Inflammation in Asthma Model Mice. PLoS ONE 9(11): e111831. doi:10.1371/journal.pone.0111831"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Rebecca Vile1, Lisa A. Osborne2, Michela Romano3, Roberto Truzoli3Phil Reed1 Swansea University, Swansea, United Kingdom, 2 Abertawe Bro Morgannwg University Health Board, Swansea, United Kingdom, 3 Universit\u00e0 degli Studi di Milano, Milan, Italy.There is an error in"} +{"text": "Unfortunately, the original version of this article containe1*, Sascha K\u00f6pke2, Jane Noyes3, Jackie Chandler4Gabriele Meyer1Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, D-06112 Halle , Germany2University of L\u00fcbeck, Germany3Bangor University, UK4Cochrane Collaboration, Oxford, UKCorrespondence: Gabriele Meyer \u2013 Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, D-06112 Halle , Germany"} +{"text": "The order of author affiliations is listed incorrectly. Division of Medical Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China should appear first. The correct list of affiliations is below.2, Jian Sa1,2, Ping-Shou Zhong2, Yuehua Cui,1,2 *Tao He1 Division of Medical Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China2 Department of Statistics and Probability, Michigan State University, East Lansing, Michigan, United States of Americacui@stt.msu.edu* E-mail:"} +{"text": "This corrigendum supplies corrected statements and proofs of an error by author. Hear by, authors declare that The correct authors list and affiliations are:1,*, Saeede Pishghadam 2, Fatemeh Mollaamine 3 Mohammad Reza Zand Monfared 3Ramesh Ahmadi 1 Department of Physiology, Qom Branch, Islamic Azad University, Qom, IR Iran2 Department Of Biology, Qom branch, Islamic Azad University, Qom, IR Iran3Department of chemistry, Qom branch, Islamic Azad university, Qom, IR Iran"} +{"text": "In the original publication affiliations 1 and 3 were published incorrectly and the correct affiliations are given in this Correction.1 Department of Radiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Ki-taku, Okayama, 700\u20138558, Japan.3 Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700\u20138558, Japan."} +{"text": "This article has been corrected: The authors changed the order of the affiliations 1 and 2 and added new affiliation to the first author due to the job transfer. The new affiliations are presented below.1,2,*, Rong-Bin Liang1,*, San-Hua Xu1,*, Yi-Cong Pan1, Qiu-Yu Li1, Hui-Ye Shu1, Min\u00a0Kang1, Pin Yin1, Li-Juan Zhang1, Yi Shao1Yun-Qing Luo1Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Medical Imaging Research Institute, Nanchang 330006, Jiangxi, PR China2Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Jiangxi Province Ocular Disease Clinical Research Center, Nanchang 330006, Jiangxi, PR China*Equal contribution"} +{"text": "In the recent article by Gong et al.\u00a0, the sec1, Joash Bryan Adajar2, L\u00e9a Tessier3, Shuai Li1, Leno Guzman4, Ying Chen4, Long Qi1,5,*Hao Gong1College of Engineering, South China Agricultural University, Guangzhou, China2Department of Civil Engineering, University of Manitoba, Winnipeg, Manitoba, Canada3Department of Biological Science, University of Manitoba, Winnipeg, Manitoba, Canada4Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada5Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, ChinaThe authors apologize for this error."} +{"text": "Communications Biology 10.1038/s42003-021-02787-7, published online 19 November 2021.Correction to: An oversight was committed in neglecting to include several Malian co-authors who conducted the clinical study and provided samples for the study in the list of authors. This has now been corrected in the PDF and HTML versions of the Article.Corrected list of authors and affiliations:1, Justin Y.A. Doritchamou1, Bergeline C. Nguemwo Tentokam1, Robert D. Morrison1, Matthew V. Cowles1, Martin Burkhardt1, Rui Ma1, Almahamoudou Mahamar2, Oumar Attaher2, Bacary S. Diarra2, Moussa Traore2, Alassane Dicko2, Niraj H. Tolia1, Michal Fried1, Patrick E. Duffy1Jonathan P. Renn1 Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.2 Malaria Research and Training Center, University of Sciences, Techniques, and Technologies of Bamako, Bamako, Mali."} +{"text": "Twelve children with a median age of 2.9 (1.0\u20136.8) years had a mean left ventricular ejection fraction of 28% (22\u201332%) and myocarditis was confirmed by endomyocardial biopsy. Patients with primary immunodeficiency were excluded from the study. Four patients underwent implantation of a ventricular assist device and subsequent heart transplantation. Genetic analysis of the 12 families revealed an (L)P variant in the CMP gene in 8/12 index patients explaining DCM. Screening of recessive immune disorder genes identified a heterozygous (L)P variant in 3/12 index patients. This study supports the genetic impact of CMP genes for pediatric myocarditis with the DCM phenotype. Piloting the idea that additional immune-related genetic defects promote myocarditis suggests that the presence of heterozygous variants in these genes needs further investigation. Altered cilium function might play an additional role in inducing inflammation in the context of CMP.Myocarditis is an inflammatory disease of the heart. Pediatric myocarditis with the dilated cardiomyopathy (DCM) phenotype may be caused by likely pathogenic or pathogenic genetic variants [(L)P] in cardiomyopathy (CMP) genes. Systematic analysis of immune disorder gene defects has not been performed so far. We analyzed 12 patients with biopsy-proven myocarditis and the DCM phenotype together with their parents using whole-exome sequencing (WES). The WES data were filtered for rare pathogenic variants in CMP ( Myocarditis is an inflammatory entity of the myocardium that may lead to severe heart failure . In the Myocarditis arises mostly from infectious causes, less frequently from (auto)immunological predisposition, or drug toxicity . Viral iRecently, we showed that pediatric myocarditis with the DCM phenotype is due to pathogenic or likely pathogenic genetic variants [(L)P] in CMP disease genes . In thisTLR3 and IFN-\u03b1/\u03b2 associated genes. Homozygous variants in CMP disease genes such as desmoplakin (DSP) and troponin I3 (TNNI3) were identified in pediatric patients with myocarditis [DSP and TNNI3 was replicated in several studies involving children or adults with myocarditis [TTN-tv), filamin C (FLNC), and DSP, which are CMP disease-related genes, in a cohort of adult lymphocytic myocarditis cases [HLA-DRB4) with idiopathic DCM [IL12RB1) variants and the TLR3 p.Pro554Ser variant as genetic susceptibility factors for myocarditis [The potential role of genetic factors in immune disorder genes was assessed in pediatric patients with acute myocarditis . Howevercarditis . The cricarditis ,22,23,24is cases . A seminthic DCM . Single-carditis ,28. AltoClinical data from patients below 18 years of age with suspected myocarditis were extracted from medical records at the Pediatric Cardiology Departments of the Charit\u00e9-Universit\u00e4tsmedizin Berlin, the German Heart Center Berlin, and the Heart- and Diabetescenter NRW, Bad Oeynhausen, Germany between January 2010 and April 2021. Starting in 2013, six patients were also enrolled in MYKKE, a prospective multicenter registry for suspected myocarditis . The online database of the MYKKE registry includes patients\u2019 clinical data and is hosted by the Competence Network for Congenital Heart Defects, Germany [The inclusion criteria of index patients were the following: Biopsy-proven myocarditis and present DCM phenotype at admission, as previously described before . PatientCategorical variables were summarized by frequencies and percentages. For continuous measures, data were presented as median values with the interquartile range (IQR). Pearson\u2019s chi-square test and Fisher\u2019s exact test were used to compare dichotomous variables. For the comparison of independent groups, the Mann\u2013Whitney U and Kruskal\u2013Wallis tests were applied. A probability value of <0.05 was considered statistically significant. Data were analyzed using IBM Corp. Released 2017, IBM SPSS Statistics for Windows, Version 25.0. .n = 12). All biopsies were analyzed histopathologically and immunohistologically as previously described and by quantitative polymerase chain reaction (qPCR) for myocardial detection of viral RNA/DNA by one specialized center for Cardiopathology [Endomyocardial biopsies (EMB) were taken according to the clinical routine from the left, right, or both ventricles as a diagnostic approach or transmural specimen during VAD implantation from all patients (Germany) ,29,30. HGermany) ,32.For NGS analysis, DNA was isolated from peripheral blood and quality checked with Qubit and Bioanalyzer . Whole-ehttps://gnomad.broadinstitute.org/; accessed on 1 April 2021, Broad Institute, Cambridge, MA, USA) [https://blueprintgenetics.com; accessed on 1 April 2021, Blueprint Genetics, Espoo, FIN) [Alignment of WES raw data sets and variant calling was performed using the GRCh37 (hs37d5.fa) reference genome . BrieflyMA, USA) . We evalMA, USA) ,36 and 6oo, FIN) ,39.ALMS1, ANKRD1, BAG3, BRAF, CALR3, CAV3, CBL, COX15, CRYAB, CSRP3, DES, DMD , TBX20, TCAP, TGFB3, TMEM43, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR, VCL. Genes given in regular format were considered disease-causing only with autosomal dominant (AD) inheritance. Genes in bold were considered disease-causing only with autosomal recessive (AR) inheritance.Variants in the following genes were bioinformatically evaluated and classified: ABCB7 , CFTR, CHD7, CHEK2, CIB1, CIITA, CLCN7, CLEC7A, CLPB, CLU, COG6, COLEC11, COPA, CORO1A, CPT2, CR2, CREBBP, CRP, CSF2RA , XLCSF2RB, CSF3R, CTC1, CTLA4, CTNNBL1, CTPS1, CTSC, CXCR2, CXCR4, CYBA, CYBB , XLCYP27A1, DBR1, DCLRE1B, DCLRE1C, DDX11, DDX41, DDX58, DEF6, DGAT1, DGKE, DHFR, DKC1 , CYCS, XL), DNAAF1, DNAAF2, DNAAF3, DNAAF5, DNAH1, DNAH11, DNAH5, DNAH9, DNAI1, DNAI2, DNAJC21, DNAL1, DNASE1L3, DNASE2, DNMT3B, DOCK2, DOCK8, DRC1, DTNBP1, EFL1, EIF2AK3, ELANE, EP300, EPCAM, EPG5, EPO, ERCC2, ERCC3, ERCC4, ERCC6L2, ETV6, EXTL3, FAAP100, FAAP24, FADD, FANCA, FANCB , FPR1, G6PC3, G6PD , XLGAS2L2, GAS8, GATA1 , XLGBA, GFI1, GFI1B, GINS1, GLRX5, GNE, GP1BA, GP1BB, GP9, GTF2H5, GUCY2C, HAVCR2, HAX1, HELLS, HMOX1, HNRNPK, HOXA11, HPS1, HPS3, HPS4, HPS5, HPS6, HRAS, HSPA9, HYDIN, HYOU1, ICOS, ICOSLG, IFIH1, IFNAR1, IFNAR2, IFNGR1, IFNGR2, IGLL1, IKBKB, IKZF1, IL10, IL10RA, IL10RB, IL12B, IL12RB1, IL12RB2, IL17F, IL17RA, IL17RC, IL18BP, IL1RN, IL21, IL21R, IL23R, IL2RA, IL2RB, IL2RG , GATA2, XLIL36RN, IL6R, IL6ST, IL7R, INO80, INVS, IRAK1, IRAK4, IRF2BP2, IRF3, IRF4, IRF7, IRF8, IRF9, ISG15, ITCH, ITGA2, ITGA2B, ITGB2, ITGB3, ITK, JAGN1, JAK1, JAK2, JAK3, KDM1A, KDM6A , XLLAMTOR2, LAT, LCK, LCT, LIG1, LIG4, LIPA, LPIN2, LRBA, LRRC6, LRRC8A, LYST, LZTR1, MAD2L2, MAGT1 , KIF23, KLF1, KMT2A, KMT2D, KRAS, XLMALT1, MAN2B1, MANBA, MAP2K1, MAP2K2, MAP3K14, MAP3K8, MASP1, MASP2, MASTL, MAT2A, MBL2, MCIDAS, MCM4, MECOM, MEFV, MLH1, MLPH, MOGS, MPL, MPO, MRAS, MS4A1, MSH2, MSH6, MSN , XLMTHFD1, MVK, MYD88, MYH9, MYO5A, MYO5B, MYSM1, NAF1, NBAS, NBEAL2, NBN, NCF1, NCF2, NCF4, NCKAP1L, NCSTN, NEUROG3, NF1, NFAT5, NFE2L2, NFIL3, NFKB1, NFKB2, NFKBIA, NHEJ1, NHP2, NLRC4, NLRP1, NLRP12, NLRP3, NME8, NOD2, NOP10, NRAS, NSMCE2, NSMCE3, NUP214, OAS1, OFD1 , XLORAI1, OSTM1, OTUD6B, OTULIN, PALB2, PARN, PAX5, PEPD, PGM3, PIGA , XLPIH1D3 , XLPIK3R1, PLCG2, PLEKHM1, PLG, PMM2, PMS2, PNP, POLA1 , PIK3CD, XLPOLD1, POLD2, POLE, POLE2, POLR3A, POLR3C, POLR3F, POMP, POT1, PPP1CB, PRF1, PRG4, PRKACG, PRKCD, PRKDC, PSEN1, PSENEN, PSMB8, PSMG2, PSTPIP1, PTEN, PTPN11, PTPRC, PTX3, PUS1, RAB27A, RAC2, RAD50, RAD51, RAD51C, RAF1, RAG1, RAG2, RANBP2, RAP1A, RAP1B, RASA2, RASGRP1, RBCK1, RBM8A, RECQL4, REL, RELA, RELB, RFWD3, RFX5, RFXANK, RFXAP, RHOH, RIPK1, RIT1, RMRP, RNASEH2A, RNASEH2B, RNASEH2C, RNF168, RNF31, RNU4ATAC, RORC, RPGR , XLRPL10 , XLRRAS, RSPH1, RSPH3, RSPH4A, RSPH9, RTEL1, RUNX1, SAMD9, SAMD9L, SAMHD1, SAR1B, SBDS, SBF2, SEC23B, SEC61A1, SEMA3E, SERPING1, SH2D1A , RPL11, RPL15, RPL18, RPL19, RPL26, RPL27, RPL31, RPL35A, RPL36, RPL5, RPL9, RPS10, RPS14, RPS15, RPS15A, RPS19, RPS24, RPS26, RPS27, RPS27A, RPS28, RPS29, RPS7, RPSA, XLSH3KBP1 , SH3BP2, XLSI, SKIV2L, SLC10A2, SLC19A2, SLC25A38, SLC26A3, SLC29A3, SLC35A1, SLC35C1, SLC37A4, SLC39A4, SLC39A7, SLC46A1, SLC5A1, SLC7A7, SLC9A3, SLFN14, SLX4, SMARCAL1, SMARCD2, SNX10, SOS1, SOS2, SP110, SPAG1, SPINK5, SPINT2, SPPL2A, SPRED1, SRC, SRP54, SRP72, STAT1, STAT2, STAT3, STAT5B, STIM1, STK36, STK4, STX11, STX3, STXBP2, STXBP3, TAP1, TAP2, TAPBP, TASP1, TAFAZZIN , SHOC2, XLTCIRG1, TCN2, TERC, TERF2, TERF2IP, TERT, TFRC, TGFB1, TGFBR1, TGFBR2, THBD, THPO, THRA, THRB, TICAM1, TINF2, TIRAP, TLR3, TMC6, TMC8, TMEM173, TNFAIP3, TNFRSF11A, TNFRSF13B, TNFRSF13C, TNFRSF1A, TNFRSF4, TNFRSF9, TNFSF11, TNFSF12, TOP2B, TP53, TPP2, TRAC, TRADD, TRAF3, TRAF3IP2, TREX1, TRIM22, TRNT1, TSR2 , TBK1, TBX1, TCF3, XLTTC37, TTC7A, TUBB1, TYK2, UBE2T, UNC119, UNC13D, UNC93B1, UNG, USB1, USP18, VPS13B, VPS45, VSIG4 , XLVTN, WAS , XLWDR1, WIPF1, WRAP53, XIAP , XLXRCC2, ZAP70, ZBTB24, ZCCHC8, ZMYND10, ZNF341), . Genes given in regular format were considered disease-causing only with AD inheritance. Genes in bold were considered disease-causing only with AR inheritance. Genes in underlined bold were considered disease-causing with AD or AR inheritance. Genes with X-linked (XL) inheritance are indicated.Variants in the following genes were bioinformatically evaluated and classified: https://www.ncbi.nlm.nih.gov/clinvar/submitters/506935/ . The filter criteria for the 89 CMP disease genes included the following variants: Missense, protein length changing, splice effects in either genetic status . The filter criteria for the 631 immune disease genes included the following variants: Missense only when annotated in ClinVar as (L)P variant or appear homo-/hemizygous, protein length changing, splice effects in either genetic status . The following variant types were assessed: Single nucleotide variants (SNV), insertion/deletion (indel), and multi-nucleotide variants (MNV). Variant annotation occurred according to Ensembl , Hinxton Cambridge, UK).All filtered genetic variants were classified as pathogenic (P), likely pathogenic (LP), or a variant of uncertain significance (VUS) according to the guidelines of the American College of Medical Genetics and Genomics (ACMG) ,41. The DSP, BAG3, and TNNI3 only. For TTN-tv, we did not apply PVS1. The ACMG terms PM5 or PS1 were activated when published LP/P variants occurred at the same amino acid position or amino acid exchange, respectively. PS3 was applied when database evidence, e.g., PubMed , Ensembl , UniProt , or ClinVar , provided a clear pathological impact of the variant. PM1 was used when variants in proximity affected the functional domain or LP/P variants accumulated close to the analyzed variant. The ACMG term PM2 was activated at a gnomAD MAF < 0.0001. PM4 was applied for protein-length-changing variants due to coding sequence changes. PM6 was activated when a de novo variant was detected without confirmation of paternity and maternity. PP3 was activated when in silico prediction tools, e.g., MT2 , Berlin, Germany) or Provean , provided a negative impact of the variant. For classification, the National Center for Biotechnology (NCBI) database ClinVar was applied. Missense variants in TTN were not evaluated. The impact of TTN length-changing variants was validated according to the splice pattern displayed at cardiodb , Imperial College London, London, UK) [de novo mutation or segregation. The Combined Annotation-Dependent Depletion (CADD) score was calculated for all variants [Variant classification was performed according to ACMG guidelines . The terdon, UK) . GeneticGermany) . The CADn = 12) and both parents (n = 24). The index patients had a median age of 1.6 (0.8\u20138.0) years, including five males and seven females . Most of these patients had low viral loads (n = 5). Eleven patients underwent implantation of a ventricular assist device (VAD) and nine patients subsequently received HTx; none died. One patient could be weaned from VAD. This patient had moderate viral myocardial PVB19 levels.We enrolled 12 families including the pediatric index patient , inherited in trans from the mother and father, likely explains the clinical phenotype composed of skeletal myopathy and DCM [TTN p.Y8199* is annotated as (L)P variant (VCV000223326). All these (L)P variants have a CADD value > 23. Three (L)P variants appeared de novo, and one was homozygous (TNNC1) p.G34S , TNNI3 p.E182Q , TNNI3 p.L49Q , and TTN p.Y8199 * . The high yield of CMP causative (L)P variants reflects the severe clinical stage of the analyzed pediatric cohort.Genetic analysis of the 12 families revealed an (L)P variant in a CMP gene in 8/12 index patients related to DCM , Table 2 and DCM . From thmozygous . Four (LDNAH11) p.R2051*, FA complementation group C (FANCC) p.R548*, and sperm-associated antigen 1 (SPAG1) p.Q672* (FANCC), primary ciliary dyskinesis 7 (DNAH11), and primary ciliary dyskinesis 28 (SPAG1) so far. Within the 12 families, three variants were found in FANCC and FA complementation group M (FANCM) that were associated with Fanconi anemia and spermatogenic failure, respectively. Considering the molecular function of the immune disease genes, we observe an accumulation of variants in genes directly or indirectly associated with ciliary transport: Coiled-coil domain containing 40 (CCDC40), dynein axonemal heavy chain 9 (DNAH9), DNAH11, PIH1 domain-containing protein 3 (PIH1D3), and SPAG1. Further analysis excluded another missense variant in trans of the same gene for all filtered 15 immune gene variants. This dismisses compound heterozygosity for these genes. The CMP variant TTN p.Y8199* was maternally inherited in the index patient of family #1, while both immune-related variants originate from the father P variant in an immune disorder gene in 3/12 index patients. More specifically, genetic analysis of 631 immune disease genes yielded at least a VUS in nine patients and no genetic immune variant in three patients . Overall p.Q672* . Of notee father . WhetherMYH7, TNNC1, TNNI3, ryanodine receptor 2 (RYR2) but also TTN-tv, which is expected in a DCM cohort [Using a family-based approach, this study provides further evidence that pediatric myocarditis with the DCM phenotype can be genetically caused by the mutation of established CMP disease genes. The spectrum of (L)P variants found in this study comprises missense variants in M cohort ,45. ThusM cohort . The eleFANCC), primary ciliary dyskinesis 7 (DNAH11), and primary ciliary dyskinesis 28 (SPAG1). Due to limitations of the ACMG guidelines and ClinVar annotations, these (L)P variants in recessive genes cannot be classified as pathogenic in the heterozygous state. Importantly, these patients had no obvious signs of Fanconi anemia or primary ciliary dyskinesis. Interpretation of these variants is hampered by a lack of knowledge about mild clinical signs in the heterozygous genotype. The heterozygous variant FANCC, c.1642C > T, p.R548* is discussed as a low penetrance risk allele for breast cancer [We piloted the idea that additional immune-related genetic defects promote inflammation. Heterozygous truncation variants with high CADD scores in immune-related genes were detected in 6/12 index patients and may have led to partial immunological dysfunction. Of note, this study did not identify genetic alterations in a single gene or isolated functional complex, indicating that myocarditis may be associated with several immune pathway defects. Three variants in immune genes were categorized in ClinVar as (L)P in association with the AR inheritance mode for Fanconi anemia, complementation group C disease genes typically with AR inheritance; PIH1D3 follows X-linked recessive (XLR) inheritance [CCDC40, DNAH9, DNAH11, PIH1D3, and SPAG1 have not been described. In immune cells, the immunological synapse serves as a molecular interface between the antigen-presenting cell and the interacting, activated lymphocyte [CCDC40, DNAH9, DNAH11, PIH1D3, and SPAG1 gene function with the immunological synapse has been identified so far. Moreover, all five genes are highly expressed in the respiratory system, primarily suggesting a role in respiratory epithelial function [Considering the immune-related genes, this study found genetic variants in genes such as unctions . More imeritance . Most frmphocyte . From a mphocyte . No assofunction ,51,52,53function . Furtherfunction . TogetheThe interpretation of immune disease gene variants is limited due to the incomplete understanding of the clinical impact after monoallelic deactivation; a significant proportion of immune diseases are inherited recessively. Our genetic analysis approach assessed small genetic variation within or close to coding regions but did not test for other genomic alterations such as deep intronic or copy number variants. Currently, most of the exonic missense variants in immune disease genes are not interpretable due to a lack of knowledge. The study has an explorative character and requires complementation with further families and genetic burden analysis to solicit or reject the findings from the current analysis.This study supports the idea that pediatric myocarditis with the DCM phenotype may be caused by the mutation of known CMP genes. Piloting the idea that additional immune-related genetic defects promote inflammation revealed truncation and (L)P variants in immune disease genes. These variants were present in the monoallelic, heterozygous state. Expanded analysis of individuals with pediatric myocarditis and the DCM phenotype will identify immune-related genetic factors predisposing one to myocardial inflammation."} +{"text": "In the manuscript \u201cHIV, syphilis, hepatitis B and C in key populations: results of a 10-year cross-sectional study, Southern Brazil\u201d, DOI number: 10.31744/einstein_journal/2022AO6934, published at einstein (S\u00e3o Paulo). 2022;20:eAO6934, page 1, abstract results:Stated:A total of 67,448 samples were analyzed, 9,086 of these tested positive, 3,633 (56%) for HIV, 4,978 (77%) for syphilis, 340 (5%) for hepatitis C virus (HCV), and 135 (2%) for hepatitis B virus (HBV).It should be read:A total of 9,086 samples were positive across all samples tested, and yielded 3,633 (5%) for HIV, 4,978 (10%) for syphilis, 340 (1%) for hepatitis C virus (HCV), and 135 (<1%) for hepatitis B virus (HBV)."} +{"text": "Instead of \u201cYu-tian Cao1. The First Clinical Medical College of Nanjing University of Chinese Medicine, Nanjing, China2. Department of Endocrinology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China1,2, Kai-yu Zhang2, Jing Sun1,2, Yan Lou1, Tian-su Lv2, Xinyi Yang1,2, Wen-hui Zhang1,2, Jiang-yi Yu1, Qi-biao Wu3 and Xi-qiao Zhou1*3. State Key Laboratory of Quality Research in Chinese Medicines and Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao, Macao SAR, China\u201d, it should be \u201cYu-tian Cao1. Department of Endocrinology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China2. The First Clinical Medical College of Nanjing University of Chinese Medicine, Nanjing, China3. State Key Laboratory of Quality Research in Chinese Medicines and Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao, Macao SAR, China\u201d.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "In this article, the affiliation details of all the authors were incorrectly assigned. The correct affiliations are given in this correction:Correct order of author affiliations and notation as followed:1\u2020, Lingqi Wang1,3\u2020, Zhongwu Guo4, Tao Zhang1 and Ping Zhang2*Jiang Zhu1Medical Laboratory Technology College, Daqing Campus of Harbin Medical University, Daqing 163319, Heilongjiang, China.2International School of Public Health and One Health, Hainan Medical University, Haikou 571199, Hainan, China.3Department of Laboratory Diagnosis, The fifth Affiliated Hospital of Harbin Medical University, Daqing 163319, Heilongjiang, China.4General Surgery, Daqing Oil General Hospital, Daqing 163319, Heilongjiang, China.The original article has been"} +{"text": "Correction to: BMC Oral Health (2022) 22:481 10.1186/s12903-022-02501-xIn this article, the affiliation details for the author Zhancheng Gao were incorrectly given as \u201cDepartment of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China\u201d and \u201cDepartment of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China\u201d but should have been only \u201cDepartment of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China\u201d.The revised affiliations are given below:1, Wenyi Yu2, Guangyao Li3, Yukun He2, Zhiming Shi4, Jing Wu1, Xinqian Ma2, Yu Zhu3, Lili Zhao2, Siqin Liu5, Yue Wei6, Jianbo Xue2, Shuming Guo1* and Zhancheng Gao2*Zhixia Zhang1Nursing Department, Linfen Central Hospital, 041000 Shanxi, Shanxi, China2Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital, Beijing, China3Science and Education Department, Linfen Central Hospital, Hainan, Shanxi, China4Cardiology Department, Linfen Central Hospital, Hainan, Shanxi, China5The Stomatology College of Binzhou Medical University, Yantai, Shandong, China6Nursing College of Shanxi Medical University, Shanxi, China"} +{"text": "Clinical and Experimental Immunology, 2022, uxac019, https://doi.org/10.1093/cei/uxac019This is a correction to: Meiping Chen, Yijun Ge, Wanmi Lin, Haiping Ying, Wen Zhang, Xuechan Yu, Chunlin Li, Chao Cao, Clinical features and nasal inflammation in asthma and allergic rhinitis, In the originally published version of this manuscript, the affiliation indicators were out of order. The correct affiliations are as follows:1,2, Yijun Ge1,2, Wanmi Lin1, Haiping Ying1, Wen Zhang1, Xuechan Yu2, Chunlin Li3,* and Chao Cao1,*Meiping Chen1Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China2School of Medicine, Ningbo University, Ningbo, China3Department of Otorhinolaryngology-Head and Neck Surgery, Ningbo First Hospital, Ningbo, ChinaThis error has been corrected (online)."} +{"text": "The publisher apologises that upon publication of this article the authors affiliations were not correctly assigned to the authors.The correct listing is as below:1, Min Zhao1,3, Qianying Wu1, Chenyi Ma1, Xiangdong Du2, Xinchuan Lu2, Qiufang Jia2, Chuanwei Li2*Jing Lu1.Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China2.Suzhou Guangji Hospital, Affiliated Guangji Hospital of Soochow University, Suzhou, Jiangsu, China3.Shanghai Key Laboratory of Psychotic Disorders, Shanghai, ChinaThe online version of this article has been updated."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Muhammad Matloob2, Rongji Dai1 *, Yulin Deng1, Kifayat Ullah3, Ihsan Ullah Kakar4, Ghulam Khaliq5, Muhammad Umer4, Zhoaib Ahmed Bhutto4, Sarfarz Ali Fazlani4, Muhammad Zubair MehboobMohib Ullah Kakar1 Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology (BIT), Beijing, PR China, 2 Department of Biomedical Engineering, National University of Science and Technology (NUST), Islamabad, Pakistan, 3 Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan, 4 Faculty of Veterinary and Animal Sciences, Lasbela University of Agriculture, Water and Marine Sciences (LUAWMS), Uthal, Balochistan, 5 Department of Horticulture, Lasbela University of Agriculture, Water and Marine Sciences (LUAWMS), Uthal, Balochistan, 6 Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan."} +{"text": "In the published article, there was an error in affiliation 3, 4, 5. Instead of \u201c3 Reproductive Immunology Research Center, Avicenna Research Institute (ARI), Tehran, Iran, 4 Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium, 5 Breast Cancer Research Center, Motamed Cancer Institute, Tehran, Iran\u201d, it should be \u201c3 Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran, 4 Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran, 5 Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran\u201d.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Similar to other causes of acute respiratory distress syndrome, coronavirus disease 2019 (COVID\u201019) is characterized by the aberrant expression of vascular injury biomarkers. We present the first report that circulating plasma bone morphogenetic proteins (BMPs), BMP9 and pBMP10, involved in vascular protection, are reduced in hospitalized patients with COVID\u201019. The rapid spread of a severe acute respiratory syndrome coronavirus (SARS\u2010CoV\u20102), first identified in 2019, led to a major worldwide public health crisis. For many individuals, coronavirus disease 2019 (COVID\u201019) led to no or mild symptoms. However, for some patients, severe COVID\u201019 resulted in respiratory failure, admission to intensive care, the requirement for mechanical ventilation, and death. According to the World Health Organization (WHO), infection with SARS\u2010CoV\u20102 was observed in over 600 million individuals worldwide and accounted for more than 6 million deaths by October 2022.Originally, SARS\u2010CoV\u20102 was reported to directly infect pulmonary endothelial cells (ECs) via the angiotensin\u2010converting enzyme 2\u00a0receptors with sustained infection\u00a0resulting in the destruction of ECs and vascular leak, causing tissue edema and thromboinflammation.n\u2009=\u200929) were recruited through the University of Cambridge COVID\u201019 asymptomatic screening program. Recruitment of inpatients at Cambridge University Hospital NHS Foundation Trust and controls was undertaken by the NIHR Cambridge Clinical Research Facility Outreach Team and the NIHR BioResource research nurse team. Ethical approval was provided by the East of England\u2014Cambridge Central Research Ethics Committee (REC ref. no.: 17/EE/0025 for the NIHR BioResource Research Tissue Bank). Structured electronic health record data were extracted from the EpiCov Database specifically created to support COVID\u201019 relevant monitoring and research. The EpiCov database is regulated under NHS Research Ethics Committee (REC) permission (ref. no.: 20/EE/0270). Patients with COVID\u201019 were recruited at or soon after admission to the hospital\u00a0and were divided into two categories of clinical severity based upon the WHO clinical progression scalen\u2009=\u200949); and 7, 8, 9\u2009=\u2009hospitalized with severe disease requiring assisted ventilation (n\u2009=\u200922) upon study enrollment and plasma samples were processed on the same day as receipt. Acellular banked plasma aliquots were stored at \u221280\u00b0C. A stock aliquot per participant was then defrosted and subaliquoted for this study, meaning the plasma provided had one freeze\u2013thaw cycle. Enzyme\u2010linked immunosorbent assays (ELISAs) for BMP9 and pBMP10 were conducted as previously described.We confirmed many of the vascular injury and proangiogenesis markers previously reported to be associated with disease severity and mortality in COVID\u201019. First, SAA\u00a0and CRP\u00a0were significantly elevated in all patients with COVID\u201019 patients compared to ventilated patients and healthy controls Figure\u00a0. SimilarThis is the first report that circulating concentrations of BMP9 and pBMP10 are decreased during COVID\u201019. This is perhaps unsurprising given the association of inflammation and vascular dysfunction with BMP9 and pBMP10. In fact, BMP9 and pBMP10 have been shown to inhibit chemokine (C\u2013C motif) ligand 2\u00a0secretion by vascular ECs, while endogenous circulating BMP9 is elevated in inflammation.Interestingly, plasma concentrations did not correlate with disease severity as individuals who required mechanical ventilation had similar plasma concentrations to control subjects. The principal limitations of our study are the small number of patients recruited into the ventilated cohort\u00a0and the lack of longitudinal follow\u2010up. Upon examination of the COVID\u201019 medications prescribed, we discovered that all ventilated patients were administered dexamethasone for significantly longer before study enrollment than those individuals requiring noninvasive oxygen therapy Figure\u00a0. SuccessFurthermore, due to the nature of patient recruitment, we also observed that several individuals in both the nonventilated and ventilated groups were not enrolled in the study until 7 days after hospital admission. Interestingly, plasma BMP9 concentrations were decreased in patients recruited within 7 days of hospital admission, when compared to those recruited after 7 days Figure\u00a0. We therBenjamin J. Dunmore designed, performed, and analyzed the experiments, and wrote the manuscript; Paul D. Upton performed the ELISAs and contributed to writing the manuscript; Kate Auckland analyzed clinical data; R. J. Samant analyzed clinical data; CITIID\u2010NIHR BioResource COVID\u201019 Collaboration enrolled patients, collected/processed samples, and analyzed clinical data. The EpiCov database collated electronic health record data. Paul A. Lyons devised and supervised the collection and processing of COVID\u201019 samples. Kenneth G. C.\u00a0Smith devised and supervised the collection and processing of COVID\u201019 samples. Stefan\u00a0Gr\u00e4f devised and supervised the collation of electronic health records and supervised the analysis of clinical data. Charlotte Summers supervised the analysis of clinical data and wrote the manuscript. Nicholas W. Morrell devised the study and wrote the manuscript.2,6, John Bradley1,3,6,10,14, Patrick Chinnery3,22,23, Daniel Cooper10, 24, Gordon Dougan2,6, Ian Goodfellow7, Ravindra Gupta2,6,12,15, Nathalie Kingston3,4, Paul J. Lehner2,6,12, Paul A. Lyons2,6, Nicholas J. Matheson2,6,12,26, Caroline Saunders9, Kenneth G. C. Smith2,6, Charlotte Summers6,11,25, James Thaventhiran18, M. Estee Torok 6,12,13, Mark R. Toshner6,8,25, Michael P. Weekes2,6,12,27, Gisele Alvio9, Sharon Baker9, Areti Bermperi9, Karen Brookes9, Ashlea Bucke, Jo Calder, Laura Canna, Cherry Crucusio, Isabel Cruz9, Ranalie de Jesus9, Katie Dempsey9, Giovanni Di Stephano9, Jason Domingo9, Anne Elmer9, Julie Harris, Sarah Hewitt, Heather Jones9, Sherly Jose9, Jane Kennet, Yvonne King,, Jenny Kourampa9, Emily Li, Caroline McMahon9, Anne Meadows, Vivien Mendoza9, Criona O'Brien, Charmain Ocaya9, Ciro Pasquale9, Marlyn Perales9, Jane Price, Rebecca Rastall, Carla Ribeiro9, Jane Rowlands, Valentina Ruffolo, Hugo Tordesillas, Phoebe Vargas9, Bensi Vergese9, Laura Watson9, Jieniean Worsley9, Julie\u2010Ann Zerrudo9, Laura Bergamashi2,6, Ariana Betancourt, Georgie Bower, Ben Bullman, Chiara Cossetti, Aloka De Sa, Benjamin J. Dunmore6,29, Maddie Epping, Stuart Fawke, Stefan Gr\u00e4f 3,6,29, Richard Grenfell, Andrew Hinch, Josh Hodgson, Christopher Huang, Oisin Huhn, Kelvin Hunter2,6, Isobel Jarvis, Emma Jones, Ma\u0161a Josipovi\u0107, Ekaterina Legchenko, Daniel Lewis, Joe Marsden, Jennifer Martin, Federica Mescia2,6, Ciara O'Donnell, Ommar Omarjee, Marianne Perera, Linda Pointon, Nicole Pond, Nathan Richoz, Nika Romashova, Natalia Savinykh, Rahul Sharma, Joy Shih, Mateusz Strezlecki, Rachel Sutcliffe, Tobias Tilly, Zhen Tong, Carmen Treacy, Lori Turner, Jennifer Wood, Marta Wylot, John Allison3,4, Heather Biggs3,17, John R. Bradley1,3,6,10,14, Helen Butcher3,5, Daniela Caputo3,5, Matt Chandler3,5, Patrick Chinnery3,22,23, Debbie Clapham\u2010Riley3,5, Eleanor Dewhurst3,5, Christian Fernandez3, Anita Furlong3,5, Barbara Graves3,5, Jennifer Gray3,5, Sabine Hein3,5, Tasmin Ivers3,5, Emma Le Gresley3,5, Rachel Linger3,5, Mary Kasanicki3,10, Rebecca King3,5, Nathalie Kingston3,4, Sarah Meloy3,5, Alexei Moulton3,5, Francesca Muldoon3,5, Nigel Ovington3,4, Sofia Papadia3,5, Christopher J. Penkett3,4, Isabel Phelan3,5, Venkatesh Ranganath3,4, Roxana Paraschiv3,4, Abigail Sage3,5, Jennifer Sambrook3,4, Ingrid Scholtes3,5, Katherine Schon3,16,17, Hannah Stark3,5, Kathleen E. Stirrups3,4, Paul Townsend3,4, Neil Walker3,4, Jennifer Webster3,5, Mayurun Selvan28, Petra, Polgarova11, Sarah L. Caddy2,6, Laura G. Caller19,20, Yasmin Chaudhry7, Martin D. Curran21, Theresa Feltwell6, Stewart Fuller19, Iliana Georgana7, Grant Hall7, William L. Hamilton6,12,13, Myra Hosmillo7, Charlotte J. Houldcroft6, Rhys Izuagbe7, Aminu S. Jahun7, Fahad A. Khokhar2,6, Anna G. Kovalenko7, Luke W. Meredith7, Surendra Parmar21, Malte L. Pinckert7, Anna Yakovleva7, Emily C. Horner18, Lucy Booth18, Alexander Ferreira18, Rebecca Boston18, Robert Hughes18, Juan Carlos Yam Puc18, Nonantzin Beristain\u2010Covarrubias18, Maria Rust18, Thevinya Gurugama18, Lihinya Gurugama18, Thomas Mulroney18, Sarah Spencer18, Zhaleh Hosseini18, Kate Williamson18, Neda Farahi6,29Stephen Baker1NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK2Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK3NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK4Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK5Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK6Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK7Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK8Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK9Cambridge Clinical Research Centre, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK10Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK11Intensive Care Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK12Department of Infectious Diseases, Addenbrooke's Hospital, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK13Department of Microbiology, Addenbrooke's Hospital, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK14Department of Renal Medicine, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK15Africa Health Research Institute, Durban, South Africa16Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK17Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK18MRC Toxicology Unit, Gleeson Building, Tennis Court Road, Cambridge, UK19University of Cambridge, Cambridge, UK20The Francis Crick Institute, London, UK21Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK22Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK23Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge, UK24Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia25Heart and Lung Research Institute, Cambridge Biomedical Campus, Cambridge, UK26NHS Blood and Transplant, Cambridge, UK27Cambridge Institute for Medical Research, Biomedical Campus, Hills Rd, Cambridge UK28Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK29Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK1, Helen Street1, Adam Loveday1, Habeebat Ibraheem1, Jacob Letowski1, Peter Driscoll1, Afzal Chaudhry1, Mark Sharpley2, Guilherme Balzana2, Wojciech J. Turek2, Stuart J. Rankin2, Paul Calleja2, Nicholas S. Gleadall1,3,4, Connor Rochford1,3,4, John R. Bradley1,3,4, Willem H. Ouwehand1,3,4, Stefan Gr\u00e4f1,3,4Vince Taylor1Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK2Research Computing Service, University of Cambridge, Cambridge, UK3NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK4University of Cambridge, Cambridge, UKPaul D. Upton is a founder of, and scientific advisor to, Morphogen\u2010IX Ltd. Nicholas W. Morrell is a founder and CEO of Morphogen\u2010IX Ltd. Paul D. Upton and Nicholas W. Morrell have published US (US10336800) and EU (EP3166628B1) patents entitled: \u201cTherapeutic Use of Bone Morphogenetic Proteins.\u201d The remaining authors declare no conflicts of interest.The ethics for this study were approved by the Cambridge Central Research Ethics Committee and the NHS Research Ethics Committee. All patients provided informed written consent."} +{"text": "Evaluation and management of systemic corticosteroids-induced ocular hypertension in children with non-Hodgkin lymphoma By Chang Y, Zhang Y, Cui Z, Jin X, Zhao Y, Liang L and Chang J. (2022) Front. Pediatr. 10: 982224. doi: 10.3389/fped.2022.982224A corrigendum on Original version of affiliation(s)(the correct version of the affiliation(s):1,2\u2020, YuTong Zhang1\u2020, Zhihua Cui3, Xianmei Jin1,Yitian Chang1, Lingling Liang3 and Jian Chang1*Yufei Zhao1Department of Pediatric Oncology, The First Hospital of Jilin University, Changchun, China,2Department of Ophthalmology, The Second Hospital of Dalian Medical University, Dalian, China,3Department of Ophthalmology, The First Hospital of Jilin University, Changchun, China)Incorrect AffiliationIn the published article, there was an error in the order of affiliations 1 and 2. The corrected affiliation list appears below.1\u2020, YuTong Zhang2\u2020, Zhihua Cui3, Xianmei Jin2, Yufei Zhao2, Lingling Liang3 and Jian Chang2*Yitian Chang1Department of Ophthalmology, The Second Hospital of Dalian Medical University, Dalian, China,2Department of Pediatric Oncology, The First Hospital of Jilin University, Changchun, China\u201d, it should be \u201cYitian Chang1,2\u2020, YuTong Zhang1\u2020, Zhihua Cui3, Xianmei Jin1, Yufei Zhao1, Lingling Liang3 and Jian Chang1*1Department of Pediatric Oncology, The First Hospital of Jilin University, Changchun, China,2Department of Ophthalmology, The Second Hospital of Dalian Medical University, Dalian, China,\u201d.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Correction: BMC Geriatr 22, 685 (2022)https://doi.org/10.1186/s12877-022-03367-yAfter publication of this article , the autMeng Mao1,4, Lei-yuan Wang2, Lan-yue Zhu3, Fei Wang2, Ying Ding2, Jian-hua Tong2, Jie Sun3, Qiang Sun1,4, Mu-huo Ji21Department of Anesthesiology, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.2Department of Anesthesiology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.3Department of Anesthesiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China.4Jiangsu Province Key Laboratory of Oral Diseases. Nanjing, China.The original article has been"} +{"text": "Page 5, Volume 9, no. 2, e01185-21, 2021, Correction of this figure does not change the conclusions of this paper."} +{"text": "Glycobiology, cwab013, doi: https://doi.org/10.1093/glycob/cwab013.1,2, Matthew P. Campbell3, Nathan Edwards3, Leyla Jael Castro4, Frederique Lisacek5, Julien Mariethoz6, Tamiko Ono7, Rene Ranzinger8, Daisuke Shinmachi9 and Kiyoko F. Aoki-Kinoshita10Issaku Yamada2Research Depertment, The Noguchi Institute, 1-9-7 Kaga, Itabashi, Tokyo 173-0003, Japan, 3Institute for Glycomics, Griffith University at Gold Coast, Southport, QLD 4215, Australia, 4Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, D.C. 20007, USA, 5ZB MED Information Centre for Life Sciences, Gleueler Str. 60, 50931 Cologne, Germany, 6Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Computer Science Department, University of Geneva, route de Drize 7, CH \u2013 1227 Geneva Switzerland, and also Section of Biology, University of Geneva, Geneva, Switzerland, 7Proteome Informatics Group, SIB Swiss Institute of Bio informatics, 7 Route de Drize, 1227 Geneva, Switzerland, 8Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan, 9Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA, 10R&D Department, SparqLite LLC., 1615-22 Ishikawamachi, Hachioji, Tokyo 192-0032, Japan, and 11Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan1To whom correspondence should be addressed: Tel: +81-3-5944-3214; Fax: +81-3-3961-4071; e-mail: issaku@noguchi.or.jp.They should have read:1,2, Matthew P. Campbell3, Nathan Edwards4, Leyla Jael Castro5, Frederique Lisacek6, Julien Mariethoz7, Tamiko Ono8, Rene Ranzinger9, Daisuke Shinmachi10 and Kiyoko F. Aoki-Kinoshita11Issaku Yamada2Research Depertment, The Noguchi Institute, 1-9-7 Kaga, Itabashi, Tokyo 173-0003, Japan, 3Institute for Glycomics, Griffith University at Gold Coast, Southport, QLD 4215, Australia, 4Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, D.C. 20007, USA, 5ZB MED Information Centre for Life Sciences, Gleueler Str. 60, 50931 Cologne, Germany, 6Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Computer Science Department, University of Geneva, route de Drize 7, CH \u2013 1227 Geneva Switzerland, and also Section of Biology, University of Geneva, Geneva, Switzerland, 7Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland, 8Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan, 9Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA, 10R&D Department, SparqLite LLC., 1615-22 Ishikawamachi, Hachioji, Tokyo 192-0032, Japan, and 11Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan1To whom correspondence should be addressed: Tel: +81-3-5944-3214; Fax: +81-3-3961-4071; e-mail: issaku@noguchi.or.jp.The paper has now been corrected online."} +{"text": "In the published article, there was an error in affiliation(s)1,2\u2020, Zihan Zhou1\u2020, Zehui Yu2\u2020, Manli He2, Lvqin He2, Zhengzhong Luo1, Wudian Xiao2, Qian Yang2, Fangfang Zhao1, Weiyao Li1, Liuhong Shen1, Jianhong Han2, Suizhong Cao1, Zhicai Zuo1, Junliang Deng1, Qigui Yan2, Zhihua Ren2, Mingde Zhao2* and Shumin Yu1*\u201d, it should be \u201cCongwei Gu1,2\u2020, Zihan Zhou1\u2020, Zehui Yu2\u2020, Manli He2, Lvqin He2, Zhengzhong Luo1, Wudian Xiao2, Qian Yang2, Fangfang Zhao1, Weiyao Li1, Liuhong Shen1, Jianhong Han2, Suizhong Cao1, Zhicai Zuo1, Junliang Deng1, Qigui Yan1, Zhihua Ren1, Mingde Zhao2* and Shumin Yu1*\u201d.Due to our error, affiliation of two authors, Qigui Yan and Zhihua Ren, were incorrectly labeled as \u201cLaboratory Animal Centre, Southwest Medical University, Luzhou, China\u201d. The correct affiliation of the two authors is \u201cCollege of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China\u201d. Instead of \u201cCongwei GuWe apologize for our mistake. We stated this does not change the scientific conclusions of the article in any way. The original article has been updated.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "In \u201cAn Alternative to the Light Touch Digital Health Remote Study: The Stress and Recovery in Frontline COVID-19 Health Care Workers Study\u201d :e32165), the authors noted one error.In the originally published article, author Shazia Rangwala's name was inadvertently not included in the list of authors. They have been added as the 7th author and with the first affiliation. The list of authors and affiliations now appears as follows:1,2, PhD; Emma Karlin1, MPH; Alexandria Alfarano3, MA; Alexa Brooks1, MSc, RD; Carol Chapman1, MPH; Rachelle Desille1, BA; Shazia Rangwala1, MPH; Daniel R Karlin1,4,5, MA, MD; Hoora Emami6, BA; Nancy Fugate Woods7, BSN, PhD, FAAN; Adrien Boch8, MSc; Luca Foschini8, PhD; Mackenzie Wildman8, PhD; Francesca Cormack9,10, PhD; Nick Taptiklis9, BA; Abhishek Pratap11,12,13,14, PhD; Marzyeh Ghassemi12,15,16, PhD; Anna Goldenberg12,17,18,19, PhD; Sujay Nagaraj12,17, BSc; Elaine Walsh7, PhD, RN, PMHCNS-BC; Stress and Recovery Participants1; Stephen Friend1,2, MD, PhDSarah M Goodday14YouandMe, Seattle, WA, United States2Department of Psychiatry, University of Oxford, Oxford, United Kingdom3Nationwide Children's Hospital, Columbus, OH, United States4MindMed, New York, NY, United States5Tufts University School of Medicine, Boston, MA, United States6Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada7School of Nursing, University of Washington, Seattle, WA, United States8Evidation Health Inc, San Mateo, CA, United States9Cambridge Cognition, Cambridge, United Kingdom10Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom11Krembil Center for Neuroinformatics, Center for Addiction and Mental Health, Toronto, ON, Canada12Vector Institute, Toronto, ON, Canada13University of Washington, Seattle, WA, United States14King's College London, London, United Kingdom15Institute for Medical Engineering and Science, MIT, Cambridge, MA, United States16Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, United States17The Hospital for Sick Children, Toronto, ON, Canada18Department of Computer Science, University of Toronto, Toronto, ON, Canada19Canadian Institute for Advanced Research, Toronto, ON, CanadaThe correction will appear in the online version of the paper on the JMIR Publications website on April 18, 2022, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "Due to a production error, the list of affiliations used for the authors was incorrect. The correct affiliations list is shown below.1,2,\u2020, Xiaoqin Zhang3,\u2020, Yaqing Ou4,\u2020, Maoyu Liu1,2,\u2020, Dongke Yu1,2, Zhiheng Song5, Lihong Niu6,*, Lijuan Zhang1,2,* and Jianyou Shi1,2,*Lu Chen1Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People\u2019s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China2Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China3Department of Critical Care Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People\u2019s Hospital, Affiliated Hospital of University of Electronic Science and Technology of China, Chengdu, Sichuan, China4Department of Pharmacy, The Affiliated Chengdu 363 Hospital of Southwest Medical University, Chengdu, Sichuan, China5Suzhou University of Science and Technology, Suzhou, Jiangsu, China, 6 Institute of Laboratory Animal Sciences, Academy of Medical Sciences and Sichuan Provincial People\u2019s Hospital, Chengdu, Sichuan, ChinaThe publisher apologizes for this mistake. The original version of this article has been updated."} +{"text": "Following publication of the original article , the autIt currently reads:2Department of Medical Oncology, University General Hospital of Heraklion, 1352 PO BOX, 711 10 Heraklion, Crete, GreeceIt should read:1Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, 71003 Heraklion, Crete, Greece2Department of Medical Oncology, University General Hospital of Heraklion, 1352 PO BOX, 711 10 Heraklion, Crete, GreeceThe original article has been"} +{"text": "Correction to: Theoretical and Applied Genetics 10.1007/s00122-022-04222-9The order of author list has been incorrectly published in the original publication. The complete correct order of author list is given below.2,3, Liping Sun2, Siqi Jiang1,3, Honglei Ren5, Rujian Sun3, Zhongyan Wei3, Huilong Hong3,8, Xiaoyan Luan5, Jun Wang6, Xiaobo Wang4, Donghe Xu7, Wenbin Li8, Changhong Guo1, Lijuan Qiu3.Bingfu GuoThe original article has been corrected."} +{"text": "In the published article, there was an error in the author list, and authors Youngae Lee and Jang-Hee Oh were erroneously not annotated as co-first authors. The corrected author list appears below.1,2,3\u2020, Jang-Hee Oh1,2,3\u2020, Na Li1,2,3,4, Hyun-Jae Jang5, Kyung-Seop Ahn5, Sei-Ryang Oh5, Dong Hun Lee1,2,3 and Jin Ho Chung1,2,3,4*Youngae Lee\u2020 These authors have contributed equally to this work.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "The authors wish to make the following corrections in the original paper .Electrical and Computer Engineering Department, Queen\u2019s University, Kingston, ON K7L 3N6, CanadaElectronics and Electrical Communication Engineering Department, Tanta University, Tanta 31512, EgyptProfound Positioning Inc., Calgary, AB T2P 3G3, CanadaElectrical and Computer Engineering Department, Mississippi State University, Starkville, MS 39762, USAThe affiliation, Electrical and Computer Engineering Department, Royal Military College of Canada, Kingston, ON K7K 7B4, Canada, has been added to the third author Aboelmagd Noureldin. Consequently, all affiliation information has been updated from the following:toElectrical and Computer Engineering Department, Queen\u2019s University, Kingston, ON K7L 3N6, CanadaElectronics and Electrical Communication Engineering Department, Tanta University, Tanta 31512, EgyptProfound Positioning Inc., Calgary, AB T2P 3G3, CanadaElectrical and Computer Engineering Department, Royal Military College of Canada, Kingston, ON K7K 7B4, CanadaElectrical and Computer Engineering Department, Mississippi State University, Starkville, MS 39762, USAThe authors apologize for any inconvenience caused and state that the scientific conclusions are unaffected. The original article has been updated."} +{"text": "In the published article , there w1,2,*, Sofia Xenaki 1, Konstantinos Lasithiotakis 1, Alexandros Chrysos 1,3, Marilena Kampa 2, George Notas 2,4,* and Emmanuel Chrysos 1Anna Daskalaki 1\u2003Department of General Surgery, University Hospital of Heraklion, 715 00 Heraklion, Greece2\u2003Laboratory of Experimental Endocrinology, Department of Laboratory Medicine, University of Crete School of Medicine, 715 00 Giofirakia, Greece3\u2003Department of General, Visceral and Transplantation Surgery, University Clinic RWTH Aachen, 52074 Aachen, Germany4\u2003Department of Emergency Medicine, University Hospital of Heraklion, 715 00 Heraklion, Greece*\u2003Correspondence: daskalaki.a@hotmail.com (A.D.); gnotas@uoc.gr (G.N.); Tel.: +30-28-1039-2416 (A.D.); +30-28-1039-4556 (G.N.)The authors apologize for any inconvenience caused and confirm that the scientific conclusions are unaffected by this change. This correction was approved by the Academic Editor. The original publication has also been updated."} +{"text": "We are extremely grateful to the following members of the medical profession from Pakistan and Overseas for sparing their precious time to review the manuscript during the year, 2021.Peshawar 7Aatik Arsh, USA 1Abdul Hannan, Faisalabad 1Abdul Haque, Saudi Arabia 2Abdul Qadeer Memon, Karachi 4Abdul Razaque Shaikh, Saudi Arabia 1Abdul Samad Khan, Turkey 1Abdullah AlAlwani, Turkey 1Abdullah Boyuk, Karachi 1Abid Saleem, Islamabad 1Abida Shaheen, Multan 2Abrar Ahmed Javed, TM Khan 2Abrar A. Wagan, Lahore 1Afifa Ehsan, Lahore 1Afshan Shahid, UK 1Afzal Javed, Saudi Arabia 1Ahmed Bader, Turkey 2Ahmet Balik, Turkey 1Ahmet Sarici, UK 1Ahsan Mukhtar, Peshawar 2Ahsan Sethi, Bahawalpur 1Ajwad Farogh, Turkey 1Ali Dogan, Turkey 1Ali Eser, Lahore 2Ali Madeeh Hashmi, Islamabad 1Alia Halim, Rawalpindi 2Aliya Hisam, Karachi 4Ambreen Usmani, Karachi 1Ambrin Fatima, Lahore 2Amina Ahmad, Lahore 1Amjad Hussain Wyne, Lahore 1Ammar Anwer, USA 3Ammara Mushtaq, Karachi 2Anisuddin Bhatti, Rawalpindi 1Anjum Jalal, China 1An-Jun Li, Canada 2Anmol Shahid, Lahore 1Ansa Rabia, Turkey 1Arif Emre, Karachi 1Arshad Hasan, Peshawar 1Arshad Hussain, Karachi 1Ashraf Ganatra, USA 1Asim Shah, Kohat 1Asmat Shaheen, Turkey 1Asude Aksoy, Iran 3Ata Mahmoodpoor, Lahore 1Atia ur Rehman, Lahore 2Attia Bari, Sudan 1Awad M. Ahmed, Kuwait 1Ayman F. Alshayji, Karachi 2Azhar Rashid, Lahore 1Aziz Fatima, Karachi 5Bader F. Zuberi, Lahore 1Bisma Ejaz, India 1Bobby Joseph, Turkey 1Burak Acikel, Bahawalpur 1Bushra Sher Zaman, China 1Chen-li Zhang, China 1Chong-Chao Yan, China 3Chun-guo Wang, China 1Chunying Zhu, Turkey 1Cihan Heybeli, Islamabad 1Col. Ch. Aqeel Safdar, Rawalpindi 1Dilshad Ahmed Khan, USA 1Donald Hathaway III, Karachi 4Ejaz Ahmed Vohra, Saudi Arabia 1Elfadil Abass, Turkey 1Enes Uyar, Turkey 1Ertan Mert, Turkey 1Esengul Unguder, Turkey 1Esra Atilgan, Karachi 1Fahd Haroon, Saudi Arabia 1Fahim Vohra, Lahore 6Faisal Nazeer Hussain, Islamabad 1Faiza Hassan, Karachi 4Faraz Shafiq, Lahore 1Farhat Nadeem, Lahore 1Farzana Ashraf, Wah Cantt 2Fatima Aamir Khan, Lahore 1Fatima Ali, Lahore 1Fatima Naumeri, Peshawar 1Fazal I Wahid, Karachi 1Fazal-ur-Rehman, USA 1Fizza S. Gillani, Multan 1Furhan Iqbal, Karachi 2Ghulam Asghar Channa, Quetta 3Ghulam Sarwar Pirkani, Egypt 6Gohar Wajid, China 1Guojin Zuo, Turkey 2Gurkan Ozturk, Karachi 3H.R. Ahmad, Turkey 1Haci Yusuf Gunes, London 1Hadred Matheos, China 2Hai-bo Li, USA 1Haider Ghazanfar, Saudi Arabia 1Haitham Osman, Turkey 1Handan Inonu Koseoglu, Karachi 1Haroon Tayyab, Saudi Arabia 5Hasan Ejaz, Brazil 2Henrico Badaoui Strazzi Sahyon, China 3Hongmei Zhao, China 2Hongwei Zhang, China 2Hong-xun Cui, China 2Hong-ya Li, China 1Hong-zhen Zhang, China 2Huan-rong Feng, China 1Huaxiang Xia, China 2Huiling Xue, China 3Huiyi Ye, UAE 4Huma Mamun Mahmud, Rawalpindi 1Huma Mushtaq, Islamabad 10Humaira Zafar, Turkey 1Ibrahim Bashan, UAE 1Iftikhar Ahmad Jan, Turkey 1Ilhami Berber, Lahore 1Imran Ijaz Haider, Karachi 4Imtiaz Khalid, Karachi 2Iqbal A. Muhammad Khyani, Multan 1Irfan Ullah, Karachi 2Jahanara Ainuddin, Multan 1Jamal Hafeez, China 2Jiang Zheng, China 1Jian-zhou Tong, China 1Jiaywei Tsauo, China 1Jinghui Dong, China 3Jingqin Liu, China 1Jinsheng Wang, USA 1John Outland, USA 1Joseph Bosco, China 1Jun-kai Xu, Islamabad 1Kaleem Ullah Toori, Saudi Arabia 3Kamran Hafeez, UK 1Kamran Hafeez, Saudi Arabia 1Kamran Sattar, UK 1Khalid Ansari, Karachi 2Khalid Mahmood, Spain 1Khalid Saeed Khan, Karachi 1Khemchand N Moorani, Greece 1Kostatinos Sergis, USA 1Kyung-Rae Kim, Rawalpindi 5Laima Alam, China 1Lei Li, China 1Liang Hong, Multan 2Liaqat Ali Rao, China 1Lin Li, China 1Lina Peng, China 1Li-na Shang, China 1Ling Zhang, China 1Ling-ling Li, China 2Li-ping Du, China 1Liu Jingqin, Rawalpindi 2Lubna Meraj, Lahore 4M Akbar Chaudhry, Malaysia 1M Ibrahim Hasan, Karachi 2M Kamran, Lahore 1M Naeem Afzal, Lahore 2M Perwaiz Iqbal, Karachi 1M Yahya Noori, Multan 4M Yasir Khan, Karachi 1M. Amir, Gujranwala 2M. Asim Mehboob, Lahore 1M. Aslam, Islamabad 1M. Azeem Aslam, Lahore 1M. Faheem Afzal, Multan 1M. Imran, Karachi 3M. Kamran, Saudi Arabia 1M. Mujahid Khan, Lahore 1M. Naeem Afzal, R'pindi 5Maj. Gen. M. Aslam, Islamabad 1Mansoor Khan, Lahore 1Maryam Gul Agha, Karachi 1Masood Ahmad Sheikh, Karachi 1Masood Jawaid, Islamabad 1Mazhar Malik, Karachi 1Mazhar ul Hasan, Malaysia 2Md. Abdus Salam, Hyderabad 5Meharunnissa Khaskheli, Turkey 1Mehmet Adam, Turkey 1Mehmet Ferdi Kinci, China 1Mingyue Liu, Turkey 1Miray Cetinkaya, Islamabad 1Misbah Durrani, Egypt 1Mohamed Awad Mohamed Ismail, USA 1Mohsin Ali, Egypt 1Mostafa Kamel Al Fouly, Karachi 2Mozaffar Rahim Hingorjo, Lahore 1M. Abubakar, Bahawalpur 1M. Farooq, Islamabad 1Muhammad, Multan 1M. Shahid, Karachi 1Mujeeb Ur Rehman, Peshawar 4Mujeeb Ur Rehman, Saudi Arabia 2Mukhtiar Baig, Muzaffarabad 1Mulazim Hussain Bukhari, Hyderabad 4Munawar Alam Ansari, Karachi 9Musarrat Riaz, Karachi 2Mustafa Naseem, China 4Na Cui, Karachi 3Nadeem Ahmad, Islamabad 1Nadeem Iqbal, Turkey 1Narin Yildirim, Karachi 1Naseer Ahmed, Peshawar 1Naseer Ahmed, Karachi 1Nasim Karim, Islamabad 3Nasir Khokhar, Lahore 1Nauman Tarif, Karachi 2Nausheen Hayat, Lahore 1Naveed Ashraf, Oman 1Nawal Al Mashaikhi, Lahore 6Nazish Imran, Karachi 2Nazli Hossain, Faisalabad 4Noor-i-Kiran Haris, Turkey 1Nureddin Yuzkat, UK 2Paul Sharpe, China 1Ping Wang, China 1Qian Sun, China 2Quanjin Si, Karachi 1Rabia Arshad, Islamabad 6Ramesh Kumar, Denmark 1Raner Lashom, Multan 6Rashida Parveen, Islamabad 3Rehan A. Khan, Karachi 1Rehman Siddiqui, Karachi 2Riffat Jaleel, Karachi 1Rizwan Jouhar, Lahore 1Romeeza Tahir, China 1Rongrong Ren, Lahore 1Roquyya Gul, Karachi 4Rubina Naqvi, Turkey 1Ruhsan Muduroglu, Karachi 5Saba Sohail, Turkey 1Sabri Selcuk Atamanalp, Lahore 1Sadaf Iftikhar, Saudi Arabia 1Sadananda Acharya, Karachi 1Sadia Fatima, Karachi 1Saera Suhail Kidwai, Okara 4S. Nasir Mansoor, Norway 4Sahrai Saeed, Karachi 3Saima Askari, Islamabad 1Sajid Malik, Multan 4Sajid Rashid, Islamabad 1Salman A. Tipu, Lahore 1Samara Siddique, Hyderabad 3Sameen Afzal Junejo, Rawalpindi 1Sami Saeed, Rawalpindi 1Sana Jalil, Saudi Arabia 3Seema Bibi Qureshi, Turkey 1Senol Demircan, Turkey 1Servet Karagul, Turkey 1Sevgi Ozcan, Islamabad 3SH Waqar, Karachi 1Shabeen Naz Masood, UK 2Shabih H Zaidi, Lahore 1Shah Jahan, Lahore 1Shahid Hameed, Lahore 6Shahid Sarwar, Quetta 1Shahzeb Ahmed Satti, Ireland 3Shankar Lal, China 2Shanshan Cai, China 1Shanshan Zhu, China 1Shao-hui Zhang, Karachi 7Shaukat Ali Jawaid, Islamabad 1Shazia Qayyum, Lahore 2Shehnoor Azhar, Multan 1Shoaib Saleem, China 1Shouguo Fang, China 1Shuli Li, Karachi 2Sohail A. Khan, Nigeria 2Stephen Onwere, Saudi Arabia 6Sultan A. Alshoabi, Saudi Arabia 2Sultan Ayoub Meo, Peshawar 1S.Kaleem Ur Rahman, UAE 3S. Mamun Mahmud, Multan 2S. Najam Hyder, Lahore 3S. Nazim H. Bokhari, Saudi Arabia 1S. Rashid Habib, Karachi 2S. Riazul Hasan, Lahore 1S. Rizwan ul Ahsan Jilani, Karachi 1S. Wasim Akhtar, Hyderabad 7S. Zulfiquar Ali Shah, Rawalpindi 1S. Hanaa Fatima, S. Kauser Ali, Karachi 1Peshawar 1Tahira Nishtar, Karachi 1Tahira Perveen Umer, China 1Tao Gu, Saudi Arabia 1Tareef S. Daqqaq, Karachi 3Tariq Mahmood, Tariq Wahab Khanzada, Oman 1Lahore 1Tariq Waqar, Lahore 4Tayyaba Gul Malik, Lahore 2Tayyiba Wasim, China 1Ting-ting Li, Multan 1Ubaid Ullah, Islamabad 1Usman Anwer Bhatti, Peshawar 4Usman Mahboob, Rawalpindi 1Uzma Abdullah, USA 1Uzma Z. Khan, USA 1Veoler Martine, Australia 1Waheed Khan, Karachi 12Wajid Jawaid, Lahore 1Waqas Sami, Canada 2Waqas Tahir, Karachi 5Waris Qidwai, Multan 1Wasim Sattar, China 3Wei Geng, China 1Wei Wang, China 1Xiang-ju Zhuge, China 1Xian-yi Liu, China 1Xiao Zhang, China 1Xiao-fang Li, China 2Xiaoguang Yu, China 1Xin Li, China 2Xin-xin Zhang, China 1Xinyu Yang, China 2Xiuhua Dai, China 1Yanfeng Guo, China 1Yang Liu, Karachi 1Yaqoob Ahmedani, China 1Yihui Wang, China 4Ying Hu, Germany 6Younis Abdelwahab Skaik, China 2Yuanda Zhang, China 1Yuanfu Wei, China 2Yu-kun Luo, China 1Yundai Chen, Turkey 1Yusuf Taha Gullu, China 1Yu-Xi Xie, Peshawar 1Zafar Iqbal, Lahore 1Zahid Kamal, China 2Zheng Zhang, China 1Zhen-yu Cui, China 1Zhihong Li, China 1Zhiqiang Ren, China 2Zhi-Yong Bu, UK 1Ziauddin Shaikh, Peshawar 1Zilli Huma, Australia 1Zohaib Akram, Sialkot 1Zoya Zahid Ch,"} +{"text": "Due to a production error, a previously published Erratum introducThere was an error regarding the affiliations for Helen Dimitriou. As well as having affiliation 1, they should also have \u201cLaboratory of Child Health, School of Medicine, University of Crete, Heraklion, Greece.\u201dThere was also an error in the affiliation of Angelos Pappas. Instead of \u201cDepartment of Pediatrics, University Hospital, School of Medicine, University of Crete, Heraklion, Greece,\u201d they should have \u201cDiabetic Center, Venizeleion General Hospital of Heraklion, Crete, Greece.\u201dThere was an error in the affiliations for Chrysoula Perdikogianni and Emmanouil Galanakis. As well as having affiliation 1, they should also have \u201cDepartment of Pediatrics, University Hospital, School of Medicine, University of Crete, Heraklion, Greece.\u201dThe corrected affiliations are as follows:1,2, Helen Dimitriou1,3*, Angelos Pappas4, Chrysoula Perdikogianni1,5, Emmanouil K. Symvoulakis6, Emmanouil Galanakis1,5 and Christos Lionis1,6Georgios Galanos1 Postgraduate Program \u201cVaccines and Prevention of Infectious Diseases,\u201d School of Medicine, University of Crete, Heraklion, Greece2 Health Center of Arkalohori, 7th Health District of Crete, Crete, Greece3 Laboratory of Child Health, School of Medicine, University of Crete, Heraklion, Greece4 Diabetic Center, Venizeleion General Hospital of Heraklion, Crete, Greece5 Department of Pediatrics, University Hospital, School of Medicine, University of Crete, Heraklion, Greece6 Clinic of Social and Family Medicine, School of Medicine, University of Crete, Heraklion, GreeceThe publisher apologizes for this mistake. The original version of this article has been updated."} +{"text": "Following publication of the original article , the ord1,2,3, Jiaqi Li1,3, Yun Luo1,3, Wei Zhang1,3*Jiaxun Jiao1Department of Spinal Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang 050051, People\u2019s Republic of China.2Department of Spinal Surgery, Harrison International Peace Hospital, Hengshui 053000, Hebei, People\u2019s Republic of China.3The Key Laboratory of Orthopedic Biomechanics of Hebei Province, The Third Hospital of Hebei Medical University, Shijiazhuang 050051, People\u2019s Republic of China.All authors agree to these corrections and apologize for the inconvenience caused.The original article has been revised."} +{"text": "The authors wish to make the following changes to their paper . Original:1,2, Ming-Jen Cheng 3,*, Tzong-Huei Lee 4, Yueh-Hsiung Kuo 5,6,7,* and Chao-Tsen Lu 5Jih-Jung Chen 1\u2003Department of Pharmacy, School of Pharmaceutical Sciences, National Yang Ming Chiao Tung University (NYCU), Taipei 112, Taiwan2\u2003Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404, Taiwan3\u2003Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute (FIRDI), Hsinchu 300, Taiwan4\u2003Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan5\u2003Department of Chemistry, National Taiwan University, Taipei 106, Taiwan6\u2003Department of Biotechnology, Asia University, Taichung 413, Taiwan7\u2003Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Pharmacy, China Medical University, Taichung 404, Taiwan*\u2003Correspondence: chengfirdi@gmail.com (M.-J.C.); yhkuo800@gmail.com (Y.-H.K.)To be replaced with:1,2,\u2020, Ming-Jen Cheng 3, Tzong-Huei Lee 4, Yueh-Hsiung Kuo 5,6,7,8,* and Chao-Tsen Lu 5,\u2020Jih-Jung Chen 1\u2003Department of Pharmacy, School of Pharmaceutical Sciences, National Yang Ming Chiao Tung University (NYCU), Taipei 112, Taiwan2\u2003Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404, Taiwan3\u2003Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute (FIRDI), Hsinchu 300, Taiwan4\u2003Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan5\u2003Department of Chemistry, National Taiwan University, Taipei 106, Taiwan6\u2003Department of Biotechnology, Asia University, Taichung 413, Taiwan7\u2003Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Pharmacy, China Medical University, Taichung 404, Taiwan8\u2003Chinese Medicine Research Center, China Medical University, Taichung 404, Taiwan*\u2003Correspondence: kuoyh@mail.cmu.edu.tw\u2020\u2003These authors contributed equally to this work."} +{"text": "There are errors in the author affiliations. The publisher apologizes for the errors. The correct affiliations are as follows:1, Asmaa Ali2,6, Ayman Mohamed Maaly3, Mohamed Anwar Mahgoub4, Hany Hassan Ziady5, Eman Anwar Sultan5Ahmed Samir Abdelhafiz1 Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt, 2 Department of Pulmonary Medicine, Abbassia Chest Hospital, MOH, Cairo, Egypt, 3 Department of Anaesthesia and Surgical Intensive Care, Faculty of Medicine, Alexandria University, Alexandria, Egypt, 4 Department of Microbiology, High Institute of Public Health, Alexandria University, Alexandria, Egypt, 5 Department of Community Medicine, Faculty of Medicine, Alexandria University, Alexandria, Egypt, 6 Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China"} +{"text": "Communications Biology 10.1038/s42003-022-03321-z, published online 19 April 2022.Correction to: The original versions of this article and the\u00a01,2,9, Lionel Thollon3, Fran\u00e7ois Marchal1, Cinzia Fornai4,5,8, Nicole M. Webb4,6,7,9 & Martin Haeusler4,9Pierre Fr\u00e9mondi\u00e8re1 UMR 7268 ADES, Aix Marseille University, EFS, CNRS, 51 boulevard Pierre Dramard, 13344 Marseille cedex 15, France.2 Aix Marseille University, School of Midwifery, Faculty of Medical and Paramedical Sciences, 51 boulevard Pierre Dramard, 13344 Marseille cedex 15, France.3 Aix Marseille University, UMRT24, 51 boulevard Pierre Dramard, 13344 Marseille cedex 15, France.4 Institute of Evolutionary Medicine, University of Z\u00fcrich, Winterthurerstrasse 190, 8057 Z\u00fcrich, Switzerland.5 Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.6 Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.7 Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute of Archaeological Sciences, Eberhard Karls University of T\u00fcbingen, R\u00fcmelinstrasse 23, 72070 T\u00fcbingen, Germany.8 Present address: Vienna School of Interdisciplinary Dentistry\u2014VieSID, Wasserzeile 35, 3400 Klosterneuburg, Austria.9 These authors contributed equally: Pierre Fr\u00e9mondi\u00e8re, Nicole M. Webb, Martin Haeusler.This error has been corrected in the HTML and PDF versions of the Article, along with the\u00a01,2,10, Lionel Thollon3, Fran\u00e7ois Marchal1, Cinzia Fornai4,5,6,9, Nicole M. Webb4,7,8,10 & Martin Haeusler 4,10Pierre Fr\u00e9mondi\u00e8re1 UMR 7268 ADES, Aix Marseille University, EFS, CNRS, 51 boulevard Pierre Dramard, 13344 Marseille cedex 15, France.2 Aix Marseille University, School of Midwifery, Faculty of Medical and Paramedical Sciences, 51 boulevard Pierre Dramard, 13344 Marseille cedex 15, France.3 Aix Marseille University, UMRT24, 51 boulevard Pierre Dramard, 13344 Marseille cedex 15, France.4 Institute of Evolutionary Medicine, University of Z\u00fcrich, Winterthurerstrasse 190, 8057 Z\u00fcrich, Switzerland.5 Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.6 Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.7 Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.8 Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute of Archaeological Sciences, Eberhard Karls University of T\u00fcbingen, R\u00fcmelinstrasse 23, 72070 T\u00fcbingen, Germany.9 Present address: Vienna School of Interdisciplinary Dentistry\u2014VieSID, Wasserzeile 35, 3400 Klosterneuburg, Austria.10 These authors contributed equally: Pierre Fr\u00e9mondi\u00e8re, Nicole M. Webb, Martin Haeusler.Updated Supplementary Information"} +{"text": "There are errors in the author affiliations. The order of affiliations 1 and 2 are incorrect. The correct affiliations are as follows:1,2, Davaalkham Jagdagsuren2, Batbaatar Gunchin1, Tsogtsaikhan Sandag1Solongo Bayarsaikhan1 Department of Immunology, School of Biomedicine, [2 AIDS/ STI Research and Surveillance Division, National Center for Communicable Diseases, MoH, Ulaanbaatar, Mongolia."} +{"text": "Correction: Skeletal Muscle 9, 20 (2019)https://doi.org/10.1186/s13395-019-0205-2Following publication of the original article , the aut1Guangdong Provincial Key Laboratory of Medical Biomechanics, Department of Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou"} +{"text": "Correction: Journal of Translational Medicine (2022) 20:537 10.1186/s12967-022-03750-8Following publication of the original article , we have1, Yiwei Guo1, Yao Chen1, Xinya Wang1, Qiuting Xu1, and Yu Zhang2, Lina Quan1*Chuiming Jia"} +{"text": "In this article, the affiliations of all the authors were inadvertently swapped. The correct affiliations are listed below:Saleem Abdulrab1,2*, Nawras Mostafa1, Sadeq Ali Al\u2011Maweri3, Hisham Abada4, Esam Halboub5,6 and Hatem A. Alhadainy71 Um Salal Health Centre, Primary Health Care Corporation, Doha, Qatar.2 Department of Restorative Dentistry, Faculty of Dentistry, University of Western Cape, Cape Town, South Africa.3 College of Dental Medicine, QU Health, Qatar University, Doha, Qatar.4 Department of Endodontics, Faculty of Oral and Dental Medicine, Kafrelsheikh University, Kafr El\u2011Sheikh, Egypt.5 Department of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Kingdom of Saudi Arabia.6 Department of Oral Medicine, Oral Pathology and Oral Radiology, Faculty of Dentistry, Sana\u2019a University, Sanaa, Yemen.7 Department of Endodontics, College of Dentistry, University of Tanta, Tanta, Egypt.The original article has been corrected."} +{"text": "In the original article, there was an error in the affiliations.1, 2, Hua Zhang1, 3, 4, Panpan Xiong1, 2, Huixia Jia1, 2 and Maoxian He1, 3, 4*\u201d it should be \u201cGaoyou Yao1, 2, 3, Hua Zhang1, 2, 4, Panpan Xiong1, 3, Huixia Jia1, 3 and Maoxian He1, 2, 4*\u201dInstead of \u201cGaoyou Yao1 CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China2 Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China3 College of Marine Science, University of Chinese Academy of Sciences, Beijing, China4 Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, ChinaThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Correction: BMC Cancer 22, 1-12 (2022)https://doi.org/10.1186/s12885-022-09655-5Following publication of the original article , the autProfessor Quan-lin Guan is affiliated to Lanzhou University\u00a0First Hospital, and Professor Tao Gong is affiliated to HeBei General Hospital. The following is the correct format:Qian-wen Luo1; Shan Gao2; Xiao Lv3; Si-jia Li2; Bo-fang Wang4; Qing-qing Han2; Yun-peng Wang4; Quan-lin Guan 5*; Tao Gong2*1 The First Clinical Academy of Lanzhou University, Lanzhou , Gansu 730000, China2 Department of Gland Surgery, HeBei General Hospital, Shijiazhuang, HeBei 050051, China3 Department of Cardiovascular Medicine, People's Hospital of Dongxihu District, Wuhan, Hubei 430040, China4 The Second Clinical Academy of Lanzhou University, Lanzhou 730000, Gansu, China5 Department of surgical oncology, The Lanzhou University First Hospital, Lanzhou, Gansu 730030, China"} +{"text": "Affiliation 12 should not appear and Author Qingyun Lu should be affiliated with affiliation 1. Affiliation and author list should appear, respectively, as follows:In the original article, there was an error with \u201c1 Department of Epidemiology, School of Public Health, Nantong University, Nantong, China2 Department of Nutrition and Dietetics, School of Allied Health Sciences, University of Health and Allied Sciences, Ho, Ghana3 Diettherapy Department, Ho Teaching Hospital, Ho, Ghana4 Department of Midwifery, School of Nursing and Midwifery, University of Health and Allied Sciences, Ho, Ghana5 Obstetrics and Gynaecology Department, Saint (ST) Dominic Hospital, Akwatia, Ghana6 Ashaiman Municipal Health Directorate, Ashaiman, Ghana7 Community Health Department, Evangelical Presbyterian Mimi Clinic, Adaklu, Ghana8 Maternity Department, Madina Polyclinic Kekele, Madina, Ghana9 Maternity Department, Ga South Municipal Hospital, Waija, Ghana10 Maternity Department, Eastern Regional Hospital, Koforidua, Ghana11 Department of Community Health Nursing, Nurses Training College, Ho, Ghana\u201d1, 2, 3, Comfort Agbadja4, Cynthia Sekyere Bruku4, 5, Vivian Kumordzi4, 6, Jessica Dzigbordi Tuglo4, 7, Leticia Atiah Asaaba4, 8, Mercy Agyei4, 9, Cynthia Boakye4, 10, Sylvia Mawusinu Sakre11 and Qingyun Lu1*\u201d\u201cLawrence Sena TugloThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Marie L. Manguette1,2, Thomas Breuer2,3, Milou Groenenberg2, Richard J. Parnell4, Claudia Stephan5,6,7, Emma J. Stokes4, Martha M. Robbins1Andrew M. Robbins1 Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany, 2 Mbeli Bai Study, Wildlife Conservation Society Congo Program, B.P. 14537, Brazzaville, Congo, 3 World Wide Fund for Nature, Reinhardtstrasse 18, 10117 Berlin, Germany, 4 Wildlife Conservation Society, Global Conservation Program, 2300 Southern Boulevard, Bronx, NY, 10460, USA, 5 Wildlife Conservation Society\u2013Congo Program, Republic of Congo, 6 Nouabal\u00e9-Ndoki Foundation, Republic of Congo, 7 Division of Developmental Biology, Friedrich-Alexander University Erlangen, Germany. The publisher apologizes for the errors."} +{"text": "Due to a production error, the order of affiliations entered incorrectly in the published version, this meant that for authors HD, AP, CP, ES, and CL, affiliations were inaccurate.In the original version, the author affiliations appeared thus:1,2, Helen Dimitriou1,4*, Angelos Pappas5, Chrysoula Perdikogianni1,3, Emmanouil K. Symvoulakis3, Emmanouil Galanakis1,3 and Christos Lionis1,6Georgios Galanos1Postgraduate Program \u201cVaccines and Prevention of Infectious Diseases\u201d, School of Medicine, University of Crete, Heraklion, Greece, 2Health Center of Arkalohori, 7th Health District of Crete, Crete, Greece, 3Laboratory of Child Health, School of Medicine, University of Crete, Heraklion, Greece, 4Diabetic Center, Venizeleion General Hospital of Heraklion, Crete, Greece, 5Department of Pediatrics, University Hospital, School of Medicine, University of Crete, Heraklion, Greece, 6Clinic of Social and Family Medicine, School of Medicine, University of Crete, Heraklion, GreeceThe corrected version appears thus:1,2, Helen Dimitriou1,3*, Angelos Pappas4, Chrysoula Perdikogianni1,5, Emmanouil K. Symvoulakis6, Emmanouil Galanakis1,5 and Christos Lionis1,6Georgios Galanos1Postgraduate Program \u201cVaccines and Prevention of Infectious Diseases\u201d, School of Medicine, University of Crete, Heraklion, Greece, 2Health Center of Arkalohori, 7th Health District of Crete, Crete, Greece, 3Diabetic Center, Venizeleion General Hospital of Heraklion, Crete, Greece, 4Department of Pediatrics, University Hospital, School of Medicine, University of Crete, Heraklion, Greece, 5Laboratory of Child Health, School of Medicine, University of Crete, Heraklion, Greece, 6Clinic of Social and Family Medicine, School of Medicine, University of Crete, Heraklion, GreeceThe publisher apologizes for this mistake. The original version of this article has been updated."} +{"text": "Phil. Trans. R. Soc. B 378, 2021442. (Published online 28 November 2022) (https://doi.org/10.1098/rstb.2021.0442)A correction is required to the author list and contributions statement for \u2018Repercussions of patrilocal residence on mothers\u2019 social support networks among Tsimane forager\u2013farmers\u2019. All of our authors consent to the addition of the author, Amanda Veile. The updated list is as follows:1,2,\u2020, Sarah Alami1,3,\u2020, Thomas S. Kraft4, Helen Davis5, Ann E. Caldwell6, Paul Hooper2,7, Lisa McAllister8, Sarah Mulville9, Amanda Veile10, Christopher von Rueden11, Benjamin Trumble12, Jonathan Stieglitz13, Michael Gurven3 and Hillard Kaplan2Edmond Seabright1School of Collective Intelligence, Mohammed 6 Polytechnic University, Ben Guerir 43150, Morocco2Department of Anthropology, University of New Mexico, Albuquerque, NM 87106, USA3Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA 93106, USA4Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA5Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 01451, USA6Division of Endocrinology, Metabolism and Diabetes, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80217, USA7Economic Science Institute, Chapman University, Orange, CA 92866, USA8Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA9Institute of Agriculture, University of Tennessee, Knoxville, TN 37996, USA10Department of Anthropology, Purdue University, West Lafayette, IN, USA11Jepson School of Leadership Studies, University of Richmond, Richmond, VA 23173, USA12Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287-1701, USA13Institute for Advanced Study in Toulouse, Toulouse 1 Capitol University, Toulouse 31080, France\u2020These authors contributed equally to this study.Corrected Authors\u2019 contributions:E.S.: conceptualization, data curation, formal analysis, methodology, visualization, writing\u2014original draft, writing\u2014review and editing; S.A.: conceptualization, data curation, formal analysis, methodology, visualization, writing\u2014original draft, writing\u2014review and editing; T.S.K.: data curation, methodology, writing\u2014review and editing; H.D.: data curation, investigation, writing\u2014review and editing; A.E.C.: investigation, writing\u2014review and editing; P.H.: investigation, writing\u2014review and editing; L.M.: investigation, writing\u2014review and editing; S.M.: investigation, writing\u2014review and editing; A.V.: data curation; C.v.R.: investigation, writing\u2014review and editing; B.T.: investigation, writing\u2014review and editing; J.S.: investigation, writing\u2014review and editing; M.G.: conceptualization, funding acquisition, investigation, methodology, supervision, writing\u2014review and editing; H.K.: conceptualization, funding acquisition, methodology, supervision, writing\u2014review and editing.All authors gave final approval for publication and agreed to be held accountable for the work performed therein.This has been corrected on the publisher's website."} +{"text": "February 14, 2022, Mathias L. Heltberg\u2019s and Hussein N. Awada\u2019s affiliations were listed incorrectly. Mathias L. Heltberg\u2019s affiliations are Laboratoire de Physique, \u00c9cole Normale Sup\u00e9rieure, 75231 Paris Cedex 05, France; and Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark. Hussein N. Awada\u2019s affiliations are Section of Surgical Pathophysiology, University Hospital Copenhagen, 2200 Copenhagen, Denmark; and Department of Anesthesiology, University Hospital Copenhagen, 2200 Copenhagen, Denmark. The article has been corrected online, and the correct author affiliations appear below.In the article, \u201cBiophysical Modeling of Dopaminergic Denervation Landscapes in the Striatum Reveals New Therapeutic Strategy,\u201d by Mathias L. Heltberg, Hussein N. Awada, Alessandra Lucchetti, Mogens H. Jensen, Jakob K. Dreyer, and Rune N. Rasmussen, which was published online 1,2 Hussein N. Awada,3,4 Alessandra Lucchetti,2 Mogens H. Jensen,2 Jakob K. Dreyer,5,6 and Rune N. Rasmussen7Mathias L. Heltberg,1Laboratoire de Physique, \u00c9cole Normale Sup\u00e9rieure, 75231 Paris Cedex 05, France, 2Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, 3Section of Surgical Pathophysiology, University Hospital Copenhagen, 2200 Copenhagen, Denmark, 4Department of Anesthesiology, University Hospital Copenhagen, 2200 Copenhagen, Denmark, 5Department of Neuroscience, University of Copenhagen, 2200 Copenhagen, Denmark, 6Department of Bioinformatics, H Lundbeck A/S, 2500 Valby, Denmark, and 7Center for Translational Neuromedicine, University of Copenhagen, 2200 Copenhagen, Denmark"} +{"text": "Following publication of the original article , in this1\u2020, Shasha Chen1\u2020, Xue Yang2\u2020, Mingfei Li1, Wei Li3, Xiaochun Zhang1*, Daxin Zhou1*, Yat-Yin Lam4* and Junbo Ge1Qinchun Jin1Department of Cardiology, Zhongshan Hospital, Shanghai Institute of Car\u2011diovascular Disease, Fudan University, 180 Fenglin Road, 200032 Shanghai, China. 2Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai, China. 3Department of Echocardiology, Zhongshan Hospital, Fudan University, Shanghai, China. 4Division of Cardiology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, SAR, China.The original article has been corrected."} +{"text": "In the published article, there was an error in the order of the affiliations. The original list read:1, Barna Budai2,*, Erika Hitre3, Attila Pat\u00f3cs2,4,5 and Tam\u00e1s Mersich1N\u00e1ndor Polk1Departmet of Visceral Surgery, National Institute of Oncology, Budapest, Hungary2Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary3Medical Oncology and Clinical Pharmacology \u201cB\u201d Department, National Institute of Oncology, Budapest, Hungary4Clinical Central Laboratory, National Institute of Oncology, Budapest, Hungary5Department of Laboratory Medicine, Semmelweis University, Budapest, HungaryThe corrected list is:2, Barna Budai3,*, Erika Hitre4, Attila Pat\u00f3cs1,3,5,* and Tam\u00e1s Mersich2N\u00e1ndor Polk1Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary2Departmet of Visceral Surgery, National Institute of Oncology, Budapest, Hungary3Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary4Medical Oncology and Clinical Pharmacology \u201cB\u201d Department, National Institute of Oncology, Budapest, Hungary5Clinical Central Laboratory, National Institute of Oncology, Budapest, HungaryA new corresponding author has been included. The correct correspondence footnote is:budai.barna@oncol.hu; Attila Pat\u00f3cs, patocs.attila@med.semmelweis-univ.hu*Correspondence: Barna Budai, The authors apologize for these errors and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "The authors of Moledina et al. have supCo\u2010authors \u201cGinetta Salvalaggio, Gary Bloch, David Ponka, Tim Aubrey, Claire Kendall\u201d have been added.Correct author group and affiliations are:1, Olivia Magwood2, Eric Agbata3, Jui\u2010Hsia Hung4, Ammar Saad5, Kednapa Thavorn6, Ginetta Salvalaggio8, Gary Bloch9, David Ponka7, Tim Aubrey10, Claire Kendall7, Kevin Pottie7Aliza Moledina1Faculty of Medicine, University of Ottawa, Ottawa, Canada2C.T. Lamont Primary Health Care Research Centre, Bruyere Research Institute, Ottawa, Canada3School of Epidemiology, Public Health and Preventive Medicine, Bruyere Research Institute, Ottawa, Canada4School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Canada5Department of Epidemiology, C.T. Lamont Primary Care Research Centre, Bruyere Research Institute, University of Ottawa, Ottawa, Canada6Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Canada7Family Medicine, University of Ottawa, Ottawa, Canada8University of Alberta, Alberta, Canada9Department of Family Medicine, University of Toronto, Toronto, Canada10School of Psychology & Centre for Research on Educational and Community Services, University of Ottawa, Ottawa, Canadahttps://doi.org/10.1002/cl2.1154. The authors apologise for the error.The original version is also corrected and can be found on the below link:"} +{"text": "The correct affiliations are as follows: Chih-Sheng Lai1 Division of Plastic and Reconstructive Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan, 2 College of Medicine, National Chung Hsing University, Taichung, Taiwan, 3 Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, 4 Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, 5 School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, 6 PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, 7 Core Laboratory of Antibody Generation and Research, Taipei Medical University, Taipei, Taiwan, 8 Department of Emergency Medicine, Tri-Service General Hospital, Taipei, Taiwan, 9 School of Medicine, National Defense Medical Center, Taipei, Taiwan, 10 Psychiatry Department, Chiayi Branch, Taichung Veterans General Hospital, Chiayi, Taiwan, 11 Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, 12 Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, 13 Department of Emergency Medicine, E-Da Hospital and I-Shou University, Kaohsiung, Taiwan, 14 The School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung, Taiwan, 15 Taichung Wildlife Conservation Group, Taichung, Taiwan, 16 Division of Traumatology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, 17 Green Nature Experience, New Taipei, Taiwan, 18 Show Chwan Memorial Hospital, Changhua, Taiwan"} +{"text": "Due to a production error, the affiliation of LL was erroneously omitted. The correct author list and affiliation list appear below:1\u2020*, Shengfu Liu2\u2020, Liying Luo3\u2020, Zhong Wu1, Shan Lu4*, Zhiqiang Guan5* and Kun Tao2*Zhiyuan Guan1Department of Orthopedics, The Shanghai Tenth People\u2019s Hospital of Tongji University, Shanghai, China2Nanjing Medical University, Nanjing, China3The Department of Ophthalmology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China4Department of Nursing, Xuzhou Municipal Hospital Affiliated with Xuzhou Medical University, Jiangsu, China5Department of Dermatology, Xuzhou Municipal Hospital Affiliated with Xuzhou Medical University, Xuzhou, Jiangsu, ChinaThe publisher apologizes for this mistake. The original version of this article has been updated."} +{"text": "In the published article, there was an error in the author list, and author Marlies J. W. Peeters was erroneously omitted. The corrected author list appears below.1, Morten Orebo Holmstr\u00f6m1, Pia Aehnlich1, Anne Rahbech1, Marlies J. W. Peeters1, Aneta Radziwon-Balicka1, Carlos Zamora2, Tobias Wirenfeldt Klausen1, Vibe Skov3, Lasse Kj\u00e6r3, Christina Ellervik4-6, Daniel El Fassi4,7, Silvia Vidal2, Hans Carl Hasselbalch3, Mads Hald Andersen1,8 and Per thor Straten*1,8Ana Micaela Carnaz Sim\u00f5es1Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Herlev University Hospital, Herlev, Denmark.2 IIB-Sant Pau- Institut Rec. Hospital de la Santa Creu i Sant Pau, Barcelona, Spain3Department of Hematology, Zealand University Hospital, Roskilde, Denmark.4Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.5Department of Laboratory Medicine, Boston Children\u2019s Hospital, Harvard Medical School, Boston, MA, United States.6Department of Data and Innovation Support, Region Zealand, Sor\u00f8, Denmark.7Department of Hematology, Rigshospitalet University Hospital, Copenhagen, Denmark8Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1*, Karolina Filipska2, Marlena Puchowska1, Katarzyna Piec1, Filip Jask\u00f3lski1, Robert \u015alusarz2Adam Wi\u015bniewski1 Department of Neurology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toru\u0144, Bydgoszcz, Poland,Laboratory for Experimental Biotechnology, Laboratory for Experimental Biotechnology, 2Laboratory for Experimental Biotechnology, Laboratory for Experimental Biotechnology,Department of Neurological and Neurosurgical Nursing, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toru\u0144, Bydgoszcz, Poland."} +{"text": "Due to a production error, there was a mistake in the author list order and affiliations two and three as published. The correct author list and affiliation list are as follows:1, 2, 3*, Boris Sokolov3, Marc Albert Tasse4, Erdenebileg Jamballuu4, Michael Schachner5 and Anneli Kaasa2Michael Minkov1 Varna University of Management, Sofia, Bulgaria2 University of Tartu, Tartu, Estonia3 Ronald Inglehart Laboratory for Comparative Social Research, National Research University Higher School of Economics, Moscow, Russia4 SICA, Ulaanbaatar, Mongolia5 Vrije Universiteit, Amsterdam, NetherlandsThe publisher apologizes for this mistake. The original version of this article has been updated."} +{"text": "Health Policy and Planning, 2022; czac098, https://doi.org/10.1093/heapol/czac098This is a correction to: Anita Musiega, Benjamin Tsofa, Lizah Nyawira, Rebecca G Njuguna, Joshua Munywoki, Kara Hanson, Andrew Mulwa, Sassy Molyneux, Isabel Maina, Charles Normand, Julie Jemutai, Edwine Barasa, Examining the influence of budget execution processes on the efficiency of county health systems in Kenya, In the originally published version of this manuscript, authors\u2019 affiliations were incorrect. The correct affiliations are as follows:1,2,*, Benjamin Tsofa3, Lizah Nyawira1, Rebecca G Njuguna1, Joshua Munywoki1, Kara Hanson4, Andrew Mulwa5, Sassy Molyneux3, Isabel Maina6, Charles Normand7, Julie Jemutai1 and Edwine Barasa1,2,8Anita Musiega1 Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, 197 Lenana Place, Lenana Road, P.O Box 43\u2009460\u201300100, Nairobi, Kenya2 Institute of Healthcare Management, Strathmore Business School, Strathmore University, Ole Sangale Road, P.O. Box 59\u2009857\u201300200, Madaraka, Nairobi, Kenya3 Health Systems and Research Ethics Department, KEMRI-Wellcome Trust Research Programme, P.O Box 230\u20138010, Kilifi, Kenya4 Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK5 Directorate of Medical Services, Preventive and Promotive Health, Ministry of Health, Afya House, Cathedral Road, P.O. Box 30\u2009016\u201300100, Nairobi, Kenya6 Health Financing Department, Ministry of Health, Afya House, Cathedral Road, P.O. Box 30\u2009016\u201300100, Nairobi, Kenya7 Centre for Health Policy and Management, Trinity College, The University of Dublin, Dublin, Ireland8 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, The Peter Medawar Building for Pathogen Research, South Parks Road, Oxon, Oxford OX1 3SY, UKThese errors have now been corrected."} +{"text": "In the published article, there was an error in the author list. The authors Nana Ai, Wei Ge, and Chu-Xia Deng were erroneously excluded. The corrected author list appears below.1,2,3, Nana Ai4, Shigao Huang1, Cheng Jiang5, Muhammad Jameel Mughal1, Wei Ge4, Guanyu Wang2,5* and Chu-Xia Deng1*\u201d.\u201cFuqiang XingThe affiliations list, author contributions, and acknowledgements statements were updated to reflect the addition of these authors."} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:1, Santanu Samanta1, Josh Strauss2, John Eley2, Michael Creed3, Tami Kingsbury3, Paul N. Staats4, Binny Bhandary1, Minjie Chen1, Tijana Dukic1, Sanjit Roy1, Javed Mahmood1, Zeljko Vujaskovic1, Hem D. Shukla1Dominic Leiser1 Division of Translational Radiation Sciences (DTRS), Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, United States of America, 2 Department of Radiation Oncology, School of Medicine, Vanderbilt University, Nashville, TN, United States of America, 3 Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, United States of America, 4 Department of Pathology, University of Maryland, School of Medicine, Baltimore, MD, United States of America.https://doi.org/10.1371/journal.pone.0258951.Leiser D, Samanta S, Strauss J, Eley J, Creed M, Kingsbury T, et al. (2021) Role of caveolin-1 as a biomarker for radiation resistance and tumor aggression in lung cancer. PLoS ONE 16(11): e0258951."} +{"text": "Correction: Tropical Medicine and Health (2018) 46:32 10.1186/s41182-018-0115-8Following publication of the original article , the autThe original author affiliations were:1 Parasitology Research Division, Department of Medical Research (DMR), No. 5 Ziwaka Road, Yangon 11191, Myanmar.2 DMR, Yangon, Myanmar.3 National Malaria Control Program, Department of Public Health (DoPH), Yangon, Myanmar.4 Parasitology Research Division, DMR, Yangon, Myanmar.5 Epidemiology Research Division, DMR, Yangon, Myanmar.6 Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Nakhon Pathom, Thailand.The correct author affiliations have been updated in this Correction.The original article has been"} +{"text": "In \u201cThe Effects of a Virtual Reality\u2013Based Training Program for Adolescents With Disruptive Behavior Problems on Cognitive Distortions and Treatment Motivation: Protocol for a Multiple Baseline Single-Case Experimental Design\u201d :e33555) the authors noted an error.Child and Adolescent Psychiatry, Amsterdam UMC Location University of Amsterdam) was inadvertently omitted. The corrected list of authors and their affiliations now appear as follows:In the originally published article, one of the affiliations of author Ram\u00f3n J L Lindauer (1,2,3, MSc; Arne Popma1,3,4, MD, PhD; Ram\u00f3n J L Lindauer3,4,5, MD, PhD; Levi van Dam2,6, PhDRen\u00e9e E Klein Schaarsberg1Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands2Dutch Innovation Network for Societal Youth Challenges, Garage2020, Amsterdam, Netherlands3Mental Health, Amsterdam Public Health, Amsterdam, Netherlands4Academic Center for Child and Adolescent Psychiatry, Levvel, Amsterdam, Netherlands5Child and Adolescent Psychiatry, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands6Department of Child Development and Education, University of Amsterdam, Amsterdam, NetherlandsThe correction will appear in the online version of the paper on the JMIR Publications website on May 27, 2022, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "In the originally published version of this manuscript, there were errors in the details and enumeration for authors' affiliations. These should read:1, Susan van Erp1, Kim Wolzak1, Axel Behrens2, Gennadij Raivich3, Joost Verhaagen1,4\u201cMatthew R J Mason1 Laboratory for Regeneration of Sensorimotor Systems, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, Amsterdam 1105BA, The Netherlands2 Cancer Stem Cell Laboratory, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; Convergence Science Centre, Imperial College, London, SW7 2BU, UK3 UCL Institute for Women's Health, Maternal and Fetal Medicine, Perinatal Brain Repair Group, London WC1E 6HX, UK4 Center for Neurogenomics and Cognition Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands\u201d instead of1, Susan van Erp1, Kim Wolzak1, Axel Behrens1,2,3, Gennadij Raivich3 and Joost Verhaagen1,4\u201cMatthew R.J. Mason1 Cancer Stem Cell Laboratory, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK2 Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK3 Convergence Science Centre, Imperial College, London, SW7 2BU, UK4 Center for Neurogenomics and Cognition Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands\u201d. These errors have now been corrected in the article online."} +{"text": "Correction to: Journal of Patient-Reported Outcomes 5, 47 (2021)https://doi.org/10.1186/s41687-021-00326-wFollowing publication of the original article , the autThe current authors and affiliations lists read:P. K. M\u00f8ller1,2, H. Pappot3,4, U. Bernchou2,5, T. Schytte2,6, K. B. Dieperink1,2 and Pia Krause M\u00f8ller7*Department of Oncology, Odense University Hospital, AgeCare, Academy of Geriatric Cancer Research, Odense University Hospital, Odense, Denmark. 2 Department of Clinical Research, University of Southern Denmark, Odense, Denmark. 3 Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark. 4 Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. 5 Laboratory of Radiation Physics, Odense University Hospital, Odense, Denmark. 6 Department of Oncology, Odense University Hospital, Odense, Denmark. 7 Odense University Hospital, Research Unit of Oncology, Kl\u00f8verv\u00e6nget 19, 5000 Odense C, DenmarkThe correct authors and affiliations lists should readP. K. M\u00f8ller1,2, H. Pappot3,4, U. Bernchou2,5, T. Schytte2,6, K. B. Dieperink1,2Department of Oncology, Odense University Hospital, AgeCare, Academy of Geriatric Cancer Research, Odense University Hospital, Odense, Denmark. 2 Department of Clinical Research, University of Southern Denmark, Odense, Denmark. 3 Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark. 4 Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. 5 Laboratory of Radiation Physics, Odense University Hospital, Odense, Denmark. 6 Department of Oncology, Odense University Hospital, Odense, Denmark.The author group has been updated above and the original article has been"} +{"text": "A Correction to this paper has been published: https://doi.org/10.1038/s41421-021-00267-0 Cell Discovery (2020) 6:96Correction to: 10.1038/s41421-020-00235-0 Published online 22 December 20201, there was an omission in author affiliations. \u201cUniversity of the Chinese Academy of Sciences, Beijing 100049, China\u201d needs to be added to the affiliation of Yuan Sun, Qingxing Wang, Xiaming Jiang and Gengfu Xiao as the author\u2019s second affiliation. The correct information is as follows. This correction does not affect the description of the results or the conclusion of this work. Lei-Ke Zhang1, Yuan Sun1,2, Haolong Zeng3, Qingxing Wang1,2, Xiaming Jiang1,2, Wei-Juan Shang1, Yan Wu1, Shufen Li1, Yu-Lan Zhang1, Zhao-Nian Hao4, Hongbo Chen5, Runming Jin5, Wei Liu6, Hao Li6, Ke Peng1, Gengfu Xiao1,2. 1State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei 430071, China. 2University of the Chinese Academy of Sciences, Beijing 100049, China. 3Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China. 4Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China. 5Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China. 6Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, ChinaWe apologize for the mistake of the author affiliation information. In the initial published version of this article"} +{"text": "Due to a production error, \u201cShiyu Shang\u201d was not included as an author in the published article. The corrected affiliations appear below.1, Xian-shu Gao1*, Zishen Wang2, Xiaomei Li1, Xi Cao1, Chenghao Jia1, Mu Xie1, Feng Lyu1, Shiyu Shang3 and Xuanfeng Ding4*Peilin Liu1 Department of Radiation Oncology, Peking University First Hospital, Beijing, China, 2 Department of Radiation Oncology, Hebei Yizhou Tumor Hospital, Zhuozhou, China, 3 Department of Oncology, Hebei North University, Shijiazhuang, China,4 Department of Radiation Oncology, Beaumont Health, Proton Beam Therapy Center, Royal Oak, MI, United StatesThe corrected Author Contributions Statement appears below.\u201cStudy conception and design: X-SG, XD, and PLL. Data acquisition: MX, ZW, FL, SYS, and CHJ. Data and statistical analysis: PL and XD. Drafting of the manuscript: PL, XC, and XML. Critical editorial and writing contributions: XD, X-SG, and XC. All authors contributed to the article and approved the submitted version.\u201dAdditionally, author Xi Cao was mistakenly captured as Cao Xi. This error has now been corrected.The publisher apologizes for these mistakes.\u00a0The original version of this article has been updated."} +{"text": "Correction to: Rice 14, 59 (2021)https://doi.org/10.1186/s12284-021-00504-wIt was highlighted that in the original article (Liu et al. Incorrect AffiliationsXinxin Liu1\u2020, Hualong Liu2\u2020, Yuanye Zhang3\u2020, Mingliang He4,5, Rongtian Li3, Wei Meng1, Zhenyu Wang4, Xiufeng Li4* and Qingyun Bu4*1College of Life Science, Northeast Forestry University, 150081 Harbin, China.2College of Life Science, Heilongjiang University, 150080 Harbin, China.3Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, 150081 Harbin, China.4Rice Research Institute, College of Agriculture, Northeast Agricultural University, 150030 Harbin, China.5University of Chinese Academy of Sciences, Beijing 100049, China."} +{"text": "Scientific Reports 10.1038/s41598-018-23014-0, published online 16 March 2018Correction to: The original version of this Article contained a repeated error in Affiliations 1,2,3,4 and 5 where \u201cKangbuk Samsung Hospital\u201d was incorrectly given as the Organisational name.The correct affiliations are listed below:Affiliation 1Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South KoreaAffiliation 2Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul, South KoreaAffiliation 3Center for Clinical Epidemiology, Samsung Medical Center, Sungkyunkwan University, Seoul, South KoreaAffiliation 4Center for Health Promotion, Samsung Medical Center, Seoul, South KoreaAffiliation 5Department of Clinical Pharmacology and Therapeutics, Samsung Medical Center, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul, South KoreaThe original Article has been corrected."} +{"text": "There is an error in the order of author affiliations. The publisher apologizes for the error. The correct order is:2*, Sara Connolly3\u00b6, Stefan Fuchs1\u00b6, Channah Herschberg4\u00b6, Brigitte Schels1,5\u00b6Claartje J. Vinkenburg1 Institute for Employment Research, IAB, Nuremberg, Germany, 2 Independent expert, Amsterdam, the Netherlands, affiliated with VU Amsterdam, 3 Norwich Business School, University of East Anglia, Norwich, United Kingdom, 4 Institute for Management Research, Radboud University, Nijmegen, the Netherlands, 5 Friedrich-Alexander University of Erlangen-Nuremberg, Nuremberg, Germany* Corresponding author\u00b6 Corresponding author is principal investigator, all other authors appear in alphabetical order, and made equal contributions to data collection, data analysis, and writing"} +{"text": "Correction to: BMC Pregnancy Childbirth 21, 510 (2021)https://doi.org/10.1186/s12884-021-03992-2Following publication of the original article , it was 1\u2020; Un Suk Jung 2\u2020; Ho Yeon Kim 1; Soo Bin Lee3; Minjeong Kim 1; Ki-Hoon Ahn 1; Sung Won Han 3; Soon-Cheol Hong1; Hai-Joong Kim 1; Younghan Kim 4*\u2020; Min-Jeong Oh 1*\u2020Geum Joon Cho 1Department of Obstetrics and Gynecology, Korea University College of Medicine, Seoul, Republic of Korea2Department of Obstetrics and Gynecology, Hanyang University Guri Hospital, College of Medicine, Hanyang University, Seoul, Republic of Korea3School of Industrial Management Engineering, Korea University, Seoul, Republic of Korea4Deparment of Obstetrics and Gynecology, Severance Hospital, Yonsei University Health System, Seoul, Republic of KoreaThe original article has been"} +{"text": "Correction to: Scientific Reports 10.1038/s41598-020-77671-1, published online 01 December 2020The original version of this Article omitted affiliations for Marcus R. Makowski. The correct affiliations are listed belowDepartment of Radiology, Charit\u00e9, Charit\u00e9platz 1, Berlin, GermanyDepartment of Radiology, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, GermanyKing\u2019s College London, School of Biomedical Engineering and Imaging Sciences, United Kingdom, St Thomas\u2019 Hospital Westminster Bridge Road, London, SE1 7EH, UKThe original Article has been corrected."} +{"text": "CpG\u2010related SNPs in the MS4A region have a dose\u2010dependent effect on risk of late\u2013onset Alzheimer disease. Aging Cell. 2019; 18:e12964. In the article \u201cCpG\u2010related SNPs in the MS4A region have a dose\u2010dependent effect on risk of late\u2013onset Alzheimer disease,\u201d the authors would like to add co\u2010authors with corresponding affiliations due to the summary statistics in manuscript replication that they have contributed. Hence, the author byline and affiliation section should appear as:1,2, Gyungah R. Jun 1,3,4, Jaeyoon Chung 1, Xiaoling Zhang 1,3, Brian W. Kunkle 5, Adam C. Naj 6,7, Li\u2010San Wang7, Charles C. White 8,9, Benjamin Grenier\u2010Boley10, Philippe Amouyel10, Jean\u2010Charles Lambert10, The European Alzheimer\u2019s Disease Initiative, Rebecca Sims11,12, Alfredo Ramirez13,14, Julie Williams11,12, Genetic and Environmental Risk in AD Consortium, Joshua C. Bis15, Cornelia M. van Duijn16,17, Sudha Seshadri18,19, Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium, David A Bennett 20, Philip L. De Jager 2,8,9, Alzheimer\u2019s Disease Genetics Consortium, Richard Mayeux 21, Jonathan L. Haines 22, Margaret A. Pericak\u2010Vance 5, Gerard D. Schellenberg 7, Lindsay A. Farrer 1,3,4,23,24, Kathryn L. Lunetta 3Yiyi Ma 1 Department of Medicine , Boston University School of Medicine, Boston, Massachusetts.2 Center for Translational & Computational Neuroimmunology, Multiple Sclerosis Clinical Care and Research Center, Division of Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, New York.3 Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.4 Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts.5 John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida.6 Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.7 Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.8 Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's, Boston, Massachusetts.9 Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.10 Univ. Lille, Inserm, Centre Hosp. Univ Lille, Institut Pasteur de Lille, UMR1167 \u2010 Labex DISTALZ \u2010 RID\u2010AGE \u2010 Risk factors and molecular determinants of aging\u2010related diseases, Epidemiology and Public Health Department, F\u201059000 Lille, France11 Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK.12 UK Dementia Research Institute at Cardiff, Cardiff University, Cardiff, UK.13 Department for Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany.14 Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany.15 Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA16 Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands.17 Nuffield Department of Population Health, Oxford University, Oxford, United Kingdom.18 The Glenn Biggs Institute for Alzheimer\u2019s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX 78229 USA19 Boston University School of Medicine and the Framingham Heart Study, Boston, MA 02118 USA20 Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois.21 Department of Neurology and Sergievsky Center, Columbia University, New York, New York.22 Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland Ohio.23 Department of Neurology, Boston University School of Medicine, Boston, Massachusetts.24 Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts.On the other hand, the statement below should be added after the last sentence in the funding information section.Infrastructure for the CHARGE Consortium is supported in part by the National Heart, Lung, and Blood Institute grant HL105756. This work is also supported by the grant AG049505 and AG054076.Then, the sentence below should be the last entry in the author\u2019s contribution section.BG\u2010B, PA, J\u2010C L, AR, JW, JCB, CMvD, SS contributed summary statistics for replication.Furthermore, the following sections should be included to \u201cAppendix 1\u201d:Members of the European Alzheimer\u2019s Disease Initiative1,, Vincent Chouraki1, Diana Zelenika2, Yoichiro Kamatani3, Marie\u2010Th\u00e9r\u00e8se Bihoreau3, Florence Pasquier4, Olivier Hanon5, Dominique Campion6, Claudine Berr7, Vincent Deramecourt4, Luc Letenneur8, Kristel Sleegers9,10, Nathalie Fi\u00e9vet1, Lina Keller12, Pascale Barberger\u2010Gateau8, Carole Dufouil8, David Wallon6, Jordi Clarimon13,14, Alberti Lleo13,14, Paola Boss\u00f915, Gianfranco Spalletta15, Sandro Sorbi16,17, Florentino Sanchez Garcia18, Maria Candida Deniz Naranjo18, Paolo Bosco19, Daniela Galimberti20, Michelangelo Mancuso21, Patrizia Mecocci22, Maria Del Zompo23, Alberto Pilotto24, Maria Bullido25,26,27, Francesco Panza28, Paolo Caffarra29,30, Benedetta Nacmias16,17, Lars Lannfelt97, Martin Ingelsson31, Victoria Alvarez32, Cristina Razquin33, Pau Pastor33,34, Ignacio Mateo35, Onofre Combarros34, Hilkka Soininen36,37, Laura Fratiglioni38,39, Karolien Bettens9,10, Alexis Brice40,41Didier Hannequin6, Karen Ritchie7,42, Mikko Hiltunen36,37, Jean\u2010Fran\u00e7ois Dartigues8,43, Christophe Tzourio8, Caroline Graff39,44, Mark Lathrop22,3,45, Christine Van Broeckhoven9,10.C\u00e9line Bellenguez1Univ. Lille, Inserm, Institut Pasteur de Lille, UMR1167 \u2010 Labex DISTALZ \u2010 RID\u2010AGE \u2010 Risk factors and molecular determinants of aging\u2010related diseases, Epidemiology and Public Health Department, F\u201059000 Lille, France; 2Centre National de Genotypage, Institut Genomique, Commissariat \u00e0 l'\u00e9nergie Atomique, Evry, France; 3Fondation Jean Dausset, CEPH, Paris, France; 4Univ. Lille, Inserm, Centre Hosp. Univ Lille, Lille, 59000, France; 5University Paris Descartes, Sorbonne Paris V; Broca Hospital, Geriatrics department; Paris, France; 6CNR\u2010MAJ; Inserm, U1079; Rouen University Hospital; 76031 France, Rouen, France ; 7Inserm, U1061; Faculty of Medicine; H\u00f4pital La Colombi\u00e8re; Montpellier, France; 8Inserm, U897; Victor Segalen University; F\u201033076, Bordeaux, France; 9Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium; 10Department of Molecular Genetics, VIB, Laboratory of Neurogenetics, Institute Born\u2010Bunge, University of Antwerp, Antwerp, Belgium; 12Aging Reasearch Center, Dept Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden; 13Neurology Department. IIB Sant Pau. Sant Pau Hospital. Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain; 14Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Barcelona, Spain; 15Clinical and Behavioral Neurology, Fondazione Santa Lucia, Roma, Italy; 16NEUROFARBA Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy; 17Centro di Ricerca, Trasferimento e Alta Formazione DENOTHE, University of Florence, Florence, Italy; 18Department of Immunology, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain; 19IRCCS Associazione Oasi Maria SS, Troina, Italy; 20University of Milan, Fondazione C\u00e0 Granda, IRCCS Ospedale Policlinico, Milan, Italy; 21Neurological Clinic, University of Pisa, Italy; 22Section of Gerontology and Geriatrics, Department of Clinical and Experimental Medicine, University of Perugia, Perugia, Italy; 23Section of Neuroscience and Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy; 24Gerontology and Geriatrics Research Laboratory, I.R.C.C.S. Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy; 25Centro de Biolog\u00eda Molecular Severo Ochoa (CSIC\u2010UAM); Madrid, Spain; 26Centro de Investigaci\u00f3n Biom\u00e9dica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain; 27Instituto de Investigaci\u00f3n Sanitaria \u201cHospital la Paz\u201d (IdIPaz), Madrid, Spain; 28Departement of Geriatrics,Center for Aging Brain ,University of Bari, Bari, Italy; 29Department of Neuroscience\u2010University of Parma, Parma, Italy; 30Center for Cognitive Disorders AUSL, Parma, Italy; 31Dept. of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden; 32Genetica molecular\u2010Huca\u2010Oviedo, Oviedo, Spain; 33Neurogenetics Laboratory, Division of Neurosciences, Center for Applied Medical Research, University of Navarra School of Medicine, Pamplona, Spain; 34CIBERNED, Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Spain; 35Neurology Service and CIBERNED, \"Marqu\u00e9s de Valdecilla\" University Hospital (University of Cantabria and IFIMAV), Santander, Spain; 36Institute of Clinical Medicine \u2010 Neurology, University of Eastern Finland, Kuopio, 70211 Finland; 37Department of Neurology, Kuopio University Hospital, FIN\u201070211 Kuopio, Finland; 38Aging Reasearch Center, Dept Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden; 39Dept Geriatric Medicine, Genetics Unit, Karolinska University Hospital Huddinge, S\u201014186 Stockholm; 40INSERM UMR_S975\u2010CNRS UMR 7225, Universit\u00e9 Pierre et Marie Curie, Centre de recherche de l'Institut du Cerveau et de la Mo\u00eblle \u00e9pini\u00e8re\u2010CRICM, H\u00f4pital de la Salp\u00eatri\u00e8re, Paris France; 41AP\u2010HP, H\u00f4pital de la Piti\u00e9\u2010Salp\u00eatri\u00e8re, Paris, France; 42Imperial College, London ; 43Centre de M\u00e9moire de Ressources et de Recherche de Bordeaux, CHU de Bordeaux, Bordeaux, France; 44Karolinska Institutet, Dept Neurobiology, Care Sciences and Society, KIADRC, Novum floor 5, S14186 Stockholm, Sweden; 45McGill University and G\u00e9nome Qu\u00e9bec Innovation Centre, Montreal, CanadaMembers of the Genetic and Environmental Risk in AD Consortium1, Rebecca Sims2, Nicola Denning2, Charlene Thomas2, Amy Gerrish3, Melanie L Dunstan4, Paul Hollingworth5, Jade Chapman6, Alexandra Stretton6, Angharad Morgan6, Patrick G Kehoe7, Christopher Medway8, Jenny Lord8, James Turton8, Nigel M Hooper9, Emma Vardy10, Jason D Warren11, Jonathan M Schott11, James Uphill12, Natalie Ryan13, Martin Rossor11,13, Yoav Ben\u2010Shlomo14, Daniilidou Makrina15, Olymbia Gkatzima15, Michelle Lupton16, Maria Koutroumani15, Despoina Avramidou15, Antonia Germanou15, Frank Jessen17\u201019, Steffi Riedel\u2010Heller20, Martin Dichgans21,22, Reiner Heun18, Heike K\u00f6lsch18, Britta Sch\u00fcrmann18, Christine Herold23, Andr\u00e9 Lacour23, Dmitriy Drichel24, Per Hoffmann25\u201027, Johannes Kornhuber28, Wei Gu29, Thomas Feulner30, Hendrik van den Bussche31, Brian Lawlor32,33, Aoibhinn Lynch32,33, David Mann34, A David Smith35, Donald Warden35, Gordon Wilcock36, Isabella Heuser37, Jens Wiltfang38\u201040, Lutz Fr\u00f6lich41, Michael H\u00fcll42, Kevin Mayo43, Gill Livingston44, Nicholas J Bass44, Hugh Gurling45, Andrew McQuillin44, Rhian Gwilliam46, Panagiotis Deloukas47, Ammar Al\u2010Chalabi48, Christopher E Shaw48,49, Andrew B Singleton50, Rita Guerreiro51, Karl\u2010Heinz J\u00f6ckel52, Norman Klopp53, H\u2010Erich Wichmann54\u201056, Dennis W Dickson57, Neill R Graff\u2010Radford57, Li Ma57, Gina Bisceglio57, Elizabeth Fisher58, Nick Warner59, Stuart Pickering\u2010Brown60, David Craig61, Peter Passmore61, Bernadette McGuinness61, Janet A Johnston61, Stephen Todd61, Seth Love62, David C Rubinsztein63, Peter St George\u2010Hyslop64\u201066, Nick C Fox67, John S K Kauwe68, John Hardy69, John Collinge70, Minerva M Carrasquillo71, Amanda J Myers72, Alfredo Ramirez73\u201075, Simon Lovestone76, Carlos Cruchaga77,78, Clive Holmes79, Karen Ritchie80, Wolfgang Maier81,82; Tim Becker81,83, Susanne Moebus84, Kevin Morgan85, Kristelle Brown85, Markus M N\u00f6then86, John Gallacher87, Anthony Bayer87, John F Powell88, Petroula Proitsi88, Carol Brayne89, Michael Gill90,91, Fiona Matthews92, Simon Mead93, Robert Clarke94, Alison M Goate95, Michael J Owen2, Michael C O'Donovan2, Lesley Jones2, Peter A Holmans2, Valentina Escott\u2010Price2, Julie Williams96.Denise Harold1School of Biotechnology, Dublin City University, Dublin 9, Ireland; 2Division of Psychological Medicine and Clinial Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, UK; 3West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK; 4Kennedy Institute of Rheumatology (NDORMS), University of Oxford, UK; 5Department of Psychology and Counselling, Cardiff and Vale University Health board, UK; 6Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, UK; 7Bristol Medical School, University of Bristol, Southmead Hospital, Bristol, UK; 8Institute of Genetics, Queens Medical Centre, University of Nottingham, Nottingham, UK; 9Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; 10Institute for Ageing and Health, Newcastle University, Biomedical Research Building, Campus for Ageing and Vitality, Newcastle upon Tyne; 11Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; 12Department of Neurodegenerative Disease, MRC Prion Unit at UCL, Institute of Prion Diseases, London, UK; 13MRC Prion Unit at UCL, Institute of Prion Diseases, London; 14Population Health Sciences, Bristol Medical School, University of Bristol; 15Aristotle University of Thessaloniki, Despere 3, Thessaloniki, 54621, Greece; 16King\u2019s College London, Institute of Psychiatry, Department of Neuroscience, De Crespigny Park, Denmark Hill, London, UK; 17German Center for Neurodegenerative Diseases (DZNE), 53175, Bonn, Germany; 18Department of Psychiatry and Psychotherapy, University of Bonn, 53127, Bonn, Germany; 19Department of Psychiatry and Psychotherapy, University of Cologne, 50937 Cologne, Germany; 20Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, 04103 Leipzig, Germany; 21Institute for Stroke and Dementia Research, Klinikum der Universit\u00e4t M\u00fcnchen, Munich, Germany; 22German Center for Neurodegenerative Diseases , Munich, 80336, Germany; 23Deutsches Zentrum f\u00fcr Neurodegenerative Erkrankungen , Bonn, Germany; 24Cologne Center for Genomics, University of Cologne, Cologne, Germany; 25Institute of Human Genetics, University of Bonn, Bonn, Germany; 26Department of Genomics, Life & Brain Center, University of Bonn, 53127, Bonn, Germany; 27Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, CH\u20104058, Basel, Switzerland; 28Department of Psychiatry and Psychotherapy, University of Erlangen\u2010Nuremberg, Germany; 29Department of Psychiatry and Psychotherapy, University Hospital, Saarland, Germany; 30Dept. Of Psychiatry, University Hospital, Saarland; 31Institute of Primary Medical Care, University Medical Center Hamburg\u2010Eppendorf, Germany; 32Mercer's Institute for Research on Ageing, St James' Hospital, Dublin; 33James Hospital and Trinity College, Dublin, Ireland; 34Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK; 35OPTIMA, Oxford University, Dept of Pharmacology, Mansfield Rd, Oxford OX1 3QT; 36Formerly Director of The Oxford Project To Investigate Memory and Ageing, Nuffield Department of Clinical Neurosciences, University of Oxford, West Wing, John Radcliffe Hospital, Oxford. OX3 9DJ; 37Department of Psychiatry, Charit\u00e9 Berlin, Germany; 38Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Germany; 39German Center for Neurodegenerative Diseases (DZNE), 37075 Goettingen, Germany; 40iBiMED, Medical Sciences Department, University of Aveiro, Aveiro, Portugal; 41Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Germany; 42Department of Psychiatry, University of Frankfurt am Main, Frankfurt am Main, Germany; 43Departments of Psychiatry, Neurology and Genetics, Washington University School of Medicine, St Louis, MO 63110, US.; 44Division of Psychiatry, University College London, UK; 45Department of Mental Health Sciences, University College London, UK; 46LGC, Unit 1\u20102 Trident Ind Est, Pindar Rd, Hoddesdon, Herts, EN11 0WZ; 47The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.; 48Kings College London, Institute of Psychiatry, Psychology and Neuroscience, UK; 49UK Dementia Research Institute at King's College London, UK; 50Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; 51LaboratoryofNeurogenetics,NationalInstituteonAging,NationalInstitutesofHealth,Bethesda,MD,20892, USA; 52Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg\u2010Essen, Hufelandstr; 53Institute of Epidemiology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, Neuherberg, Germany; 54Helmholtz Center Munich, Institute of Epidemiology, Neuherberg; 55Ludwig\u2010Maximilians University Chair of Epidemiology, Munich, Germany; 56Joint Biobank Munich and KORA Biobank; 57Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, 32224, USA; 58Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; 59Somerset Partnership NHS Trust, Somerset, UK; 60Institute of Brain, Behaviour and Mental Health, Faculty of Human and Medical Sciences, University of Manchester, Manchester, UK; 61Ageing Group, Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, UK; 62Bristol Medical School, University of Bristol, Southmead Hospital, Bristol, UK; 63Cambridge Institute for Medical Research and UK Dementia Research Institute, University of Cambridge, Cambridge, UK; 64Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; 65Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; 66Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, Ontario, Canada; 67Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; 68Department of Biology, Brigham Young University, Provo, Utah, USA; 69Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK; 70Department of Neurodegenerative Disease, MRC Prion Unit at UCL, Institute of Prion Diseases, London, UK; 71Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA; 72Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, Florida, USA; 73Department of Psychiatry and Psychotherapy, University Hospital Cologne, Cologne, Germany; 74Department for Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany; 75Institute of Human Genetics, University of Bonn, Bonn, Germany; 76Department of Psychiatry, University of Oxford, Oxford, UK; 77Department of Psychiatry, Washington University School of Medicine, St. Louis Missouri, USA; 78Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of Medicine, St. Louis, Missouri, USA; 79Division of Clinical Neurosciences, School of Medicine, University of Southampton, Southampton, UK; 80Faculty of Medicine, Imperial College, St. Mary's Hospital, London, UK; 81German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; 82Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany; 83Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany; 84Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg\u2010Essen, Hufelandstr, 55, D\u201045147 Essen, Germany; 85Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, UK; 86Institute of Human Genetics, Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany; 87Institute of Primary Care and Public Health, Cardiff University, Neuadd Meirionnydd, University Hospital of Wales, Heath Park, Cardiff UK; 88Institute of Psychiatry, King's College London, Denmark Hill, London, UK; 89Institute of Public Health, University of Cambridge, Cambridge, UK; 90Mercer's Institute for Research on Ageing, St James' Hospital, Dublin; 91James Hospital and Trinity College, Dublin, Ireland; 92MRC Biostatistics Unit, Cambridge, UK; 93MRC Prion Unit, Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK; 94Oxford Healthy Aging Project (OHAP), Clinical Trial Service Unit, University of Oxford, Oxford, UK; 95Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine, Mount Sinai, New York; 96UK Dementia Research Institute\u00a0at Cardiff, Cardiff University, CF24 4HQ.Members of the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium1, Sven J. van der Lee2, Johanna Jakobsdottir3, Sonia Moreno\u2010Grau4,5, Yuning Chen6, Shahzad Ahmad7, Merce Boada4,5, Annette L. Fitzpatrick8,9, Albert V. Smith10,11, Xueqiu Jian12, Seung\u2010Hoan Choi4, Hieab H. Adams7, Jennifer A. Brody1, Gudny Eiriksdottir3, Thor Aspelund3,13, Edith Hofer14,25, Chloe Sarnowski6, Charles C. White16, Dina Vojinovic2, L.Adrienne Cupples6,17, Jayanadra J. Himali6,17,18, Adela Orellana4, Melissa E. Garcia19, Honghuang Lin20, Hata Comic21, Gena Roschupkin7, Shuo Li6, Isabel Hern\u00e1ndez4,5, Qiong Yang6, Alexa S. Beiser6,17,18, Lluis Tarraga4,5, Thomas H. Mosley22, WT Longstreth9,23, Jr, Fernando Rivadeneira7,24,25, Eric Boerwinkle26,27, Jerome I. Rotter28, Andre G. Uitterlinden7,24,25, Itziar de Rojas4,5, In\u00e9s Quintela29, \u00c1ngel Carracedo29, Luis M. Real30, Yasaman Saba31, Oscar L. Lopez32\u201034, Myriam Fornage35, Najaf Amin7, Lenore J. Launer19, M. Arfan Ikram7,36,37, Helena Schmidt14,31, Reinhold Schmidt14, Anita L. DeStefano6,18, Vilmundur Gudnason3,11, Bruce M. Psaty1,9,38,39, Agustin Ruiz4,5, Cornelia M. van Duijn7,40, Sudha Seshadri41,42.Joshua C. Bis1Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA; 2Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, 3015CN the Netherlands; 3Icelandic Heart Association, Kopavogur, Iceland; 4Research Center and Memory Clinic of Fundaci\u00f3 ACE, Institut Catal\u00e0 de Neuroci\u00e8ncies Aplicades\u2010Universitat Internacional de Catalunya, Barcelona, Spain; 5Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain; 6Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; 7Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands; 8Department of Family Medicine, University of Washington, Seattle, WA, USA; 9Department of Epidemiology, University of Washington, Seattle, WA, USA; 10Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; 11Faculty of Medicine, University of Iceland, Reykjavik, Iceland; 12Brown Foundation Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA; 13Centre for Public Health, University of Iceland, Reykjavik, Iceland; 14Clinical Division of Neurogeriatrics, Department of Neurology, Medical University Graz, Graz, Austria; 15Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria; 16Program in Medical and Population\u00a0Genetics, Broad Institute, Cambridge, MA, USA; 17Framingham Heart Study, Framingham, MA, USA; 18Department of Neurology, Boston University School of Medicine, Boston, MA, USA; 19Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD, USA; 20Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA; 21Brain Center Rudolf Magnus, Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands; 21Departments of Medicine, Geriatrics, Gerontology and Neurology, University of Mississippi Medical Center, Jackson, MS, USA; 23Department of Neurology, University of Washington, Seattle, WA, USA;24Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands; 25Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands; 26School of Public Health, Human\u00a0Genetics\u00a0Center, University of Texas Health Science Center at Houston, Houston, TX, USA; 27Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; 28Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles BioMedical Research Institute at Harbor\u2010UCLA Medical Center, Torrance, CA, USA;29Grupo de Medicina Xenomica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado, Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Raras, Santiago de Compostela, Spain; 30Unidad Cl\u00ednica de Enfermedades Infecciosas y Microbiolog\u00eda, Hospital Universitario de Valme, Sevilla, Spain; 31Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University Graz, Graz, Austria; 32Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA; 33Alzheimer's Disease Research Center, University of Pittsburgh, Pittsburgh, PA, USA; 34Department of Neurology, University of Pittsburgh, Pittsburgh, PA, US;35Brown Foundation Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA; 36Department of Neurology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; 37Departments of Radiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; 38Department of Health Services, University of Washington, Seattle, WA, USA; 39Kaiser Permanente, Washington Health Research Institute, Seattle, WA, USA; 40Nuffield Department of Population Health, Oxford University, Oxford, United Kingdo; 41The Glenn Biggs Institute for Alzheimer\u2019s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX 78229 USA; 42Boston University School of Medicine and the Framingham Heart Study, Boston, MA 02118 USA.The authors would like to apologize for the inconvenience caused."} +{"text": "Linum usitatissimum L.) plants. Linseed is used for obtaining seeds, while fiber flax is used for fiber production. We aimed to identify the genes associated with the flax plant type, which could be important for the formation of agronomically valuable traits. A search for polymorphisms was performed in genes involved in the biosynthesis of cell wall components, lignans, fatty acids, and ion transport based on genome sequencing data for 191 flax varieties. For 143 of the 424 studied genes , one or more polymorphisms had a strong correlation with the flax type. Based on the transcriptome sequencing data, we evaluated the expression levels for each flax type-associated gene in a wide range of tissues and suggested genes that are important for the formation of linseed or fiber flax traits. Such genes were probably subjected to the selection press and can determine not only the traits of seeds and stems but also the characteristics of the root system or resistance to stresses at a particular stage of development, which indirectly affects the ability of flax plants to produce seeds or fiber.As a result of the breeding process, there are two main types of flax ( Linum usitatissimum L.) is traditionally grown for obtaining fiber from stems and oil from seeds [Flax ,25. Chro4CLs encode 4-coumarate:CoA ligases; C3\u2032Hs encode p-coumarate 3-hydroxylases; C4Hs encode cinammate 4-hydroxylases; CADs encode cinnamyl alcohol dehydrogenases; CCRs encode cinnamoyl CoA reductases; CCoAOMTs encode affeoyl CoA 3-O-methyltransferases; COMTs encode caffeate/5-hydroxyferulate O-methyl-transferases; F5Hs encode 5-hydroxylases; HCTs encode hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferases; and PALs encode phenylalanine ammonia-lyases) [CTLs encode chitinase-like proteins; BGALs encode \u03b2-galactosidase-like proteins; TUBs encode tubulins; CESAs encode cellulose synthases; RGLs encode rhamnogalacturonan lyases; and ACTs encode actins) [DIRs encode dirigent proteins; PLRs encode pinoresinol\u2013lariciresinol reductases; and UGTs encode UDP-glycosyltransferases) [FADs encode fatty acid desaturases and SADs encode stearoyl-ACP desaturases) [ABCs encode ATP binding cassette transporters and HMAs encode heavy metal-associated proteins) [In addition, studies have identified and characterized particular gene families that likely participate in flax plant processes, including those involved in the biosynthesis of lignin (-lyases) ,56 and o actins) ,62,63,64ferases) ,66,67,68turases) ,70,71,72roteins) . However4CL, C3\u2032H, C4H, CAD, CCR, CCoAOMT, COMT, F5H, HCT, and PAL), 35 CTL genes, 40 BGAL genes, 206 ABC and HMA genes, 9 lignan biosynthesis genes , 21 TUB genes, 16 CESA genes, 10 RGL genes, 6 fatty acid biosynthesis genes (FAD and SAD), and 15 ACT genes) based on genome sequencing data for 191 flax varieties (79 fiber flax and 112 linseed varieties) from the NCBI database (PRJNA590636 and PRJNA478805). The results are presented in In the present work, we focused our attention on genes that are important for cell wall formation, because these genes are crucial for the determination of flax stem traits; genes involved in the biosynthesis of lignans and fatty acids, the content of which is an important characteristic of seeds; and ABC transporter and heavy metal\u2013associated genes, which participate in numerous processes in flax plants. We performed a search for polymorphisms among 424 genes are presented in For lignin-related genes, we identified 2703 polymorphisms; for ABCG11, F5H8, ABCH10, CTL9, HMA6, F5H7, ABCG68, 4CL5, ABCG47, and ABCG16 value \u2265 0.4 or \u2264\u22120.4 with flax type (s \u2265 0.6 or \u2264\u22120.6): PAL1, PAL3, BGAL30, ABCB40, ABCB42, ABCB45, ABCB47, ABCC4, ABCG8, ABCG79, ABCH1, HMA12, PLR1, and CESA1-B. These genes could play an important role in the formation of traits specific to linseed or fiber flax and are of particular interest for further analysis.For the identification of genes potentially associated with flax type, correlation analysis between variant allele frequency (VAF) values and belonging of a variety to a linseed or fiber flax group was performed. For 143 of the 424 studied genes, one or more polymorphisms had a Spearman\u2019s correlation coefficient (rlax type . Data ons \u2265 0.4 or \u2264\u22120.4) with flax type varied significantly between the studied groups of genes. For groups of BGAL genes and ABC plus HMA genes, a significant proportion (about 40%) of the studied genes had FTA polymorphisms. In groups of CESA, TUB, CTL, and RGL genes and genes involved in lignin synthesis, about 20\u201331% of the studied genes had polymorphisms with a strong correlation with flax type. In groups of fatty acid and lignan synthesis genes, fewer than 20% of the studied genes had FTA polymorphisms, while in the ACT group, there were no such genes. In general, these results were in concordance with those observed in the cluster analysis described above; the more polymorphisms with a high correlation coefficient in a group, the clearer the flax type-associated clusters formed for this group.The proportion of genes with polymorphisms with a strong correlation with the focus on genes with polymorphisms with a strong correlation with flax type. The following types of flax tissues were included in the analysis: roots and shoots of seedlings, leaves, flowers, and stems of adult plants , capsule4CL1, 4CL4, 4CL5, C4H3, C4H4, CAD1A, CAD1B, CAD4A, CAD4B, CAD7, CCR11, CCR4, CCoAOMT5, COMT2, COMT3, F5H1, F5H7, PAL1, and PAL3 had polymorphisms with a strong correlation (rs \u2265 0.4 or \u2264\u22120.4) with flax type. For the majority of these genes, higher expression levels were observed in seedling roots, sXYL, and capsules. Within this group of genes, PAL1 and PAL3 had polymorphisms with a very strong correlation (rs \u2265 0.6 or \u2264\u22120.6) with flax type (1 and 2 polymorphisms respectively). PAL1 was predominantly expressed in sXYL and could be associated with lignin synthesis in flax stems, while PAL3 was predominantly expressed in seedling roots and could be associated with the root traits important for the formation of a particular flax plant type. We performed clustering based on the VAF of PAL1 and PAL3; however, we did not reveal a clear enough association of clusters with flax type and result in cinnamic acid formation [PAL is one of the key players in lignin synthesis [PAL results in a reduction in the lignin content and a change in the lignin composition in Arabidopsis thaliana [Medicago sativa [Populus trichocarpa [Nicotiana tabacum [Among the genes related to lignin synthesis, lax type . This coormation . PAL is ynthesis , and dowthaliana , Medicago sativa Populus chocarpa , and Nic tabacum ,81.s \u2265 0.4 or \u2264\u22120.4) with flax type among the lignin synthesis genes was identified for 4CL1. This gene was expressed more highly in seedling roots and sXYL than in other analyzed tissues. A cluster of predominantly linseed varieties and a cluster of predominantly fiber flax varieties were observed in the dendrogram based on the VAF of 4CL1 of FTA polymorphisms. This gene was mostly expressed in seedling roots and sXYL. A cluster of predominantly linseed varieties, a cluster of predominantly fiber flax varieties, and a mixed cluster were observed based on the VAF of C4H4 , while 4CL genes, which encode 4-coumarate:CoA ligases, are responsible for the formation of p-coumaroyl CoA from p\u2013coumaric acid [C4Hs and 4CLs along with PALs play an important role in lignin formation; the downregulation of C4Hs and 4CLs was reported to decrease the lignin content [The highest number (32) of polymorphisms with a strong correlation of the thirteen studied had polymorphisms with a strong correlation (rs \u2265 0.4 or \u2264\u22120.4) with flax type. These five genes had increased expression levels in seedling roots; in addition, CAD1A and CAD1B were also highly expressed in sXYL, while CAD4A was also highly expressed in stems; these genes are of the most interest because they could be involved in the determination of the lignin content in flax stems. Among these three genes, clustering based on the VAF of CAD1B had the greatest concordance with flax type of polymorphisms with flax type was observed for CESA1-B, CESA3-A, CESA4, and CESA8-A (from one to two polymorphisms). These genes had increased expression levels in sXYL, and CESA1-B was also highly expressed in seedling roots. For CESA1-B, one polymorphism had a very strong correlation (rs = \u22120.63) with flax type. Clustering based on the VAF of CESA1-B revealed a cluster of predominantly linseed varieties and a mixed cluster with flax type were identified for CTL1, CTL10, CTL13, CTL18, CTL2, CTL22, CTL23, CTL24, CTL26, CTL35, and CTL4. The expression profiles of these genes in different tissues were quite dissimilar: CTL1, CTL2, and CTL23 had increased expression levels in sXYL; CTL23, CTL24, CTL26, CTL22, and CTL4 in capsules; CTL13 and CTL4 in seedling roots; and CTL10 in leaves and flowers. Meanwhile, the expression of CTL35 and CTL18 was low in all analyzed tissues (CPM < 10 in each sample). The greatest number of FTA polymorphisms was revealed for CTL1 and CTL18. In clustering based on the VAF of CTL1, a small cluster of predominantly linseed varieties and a large mixed cluster were observed of polymorphisms with flax type was revealed for Alfa_TUB2, Beta_TUB13, Beta_TUB3, Beta_TUB6, and Beta_TUB7. All of these genes had increased expression levels in seedling roots and stem tissues. Several of these genes were also highly expressed in other tissue types, but there was a significant variation in such tissue types between genes. The greatest number (8) of FTA polymorphisms was identified for Beta_TUB3, and clustering based on the VAF of this gene had a relatively high concordance with flax type with flax type (the number of such polymorphisms varied from 1 to 25). The expression profiles of these genes also varied; however, most genes had the highest expression levels in leaves, flowers, iFIB, and tFIB. BGAL40 had the highest number (25) of FTA polymorphisms, and clustering of varieties based on the VAF of this gene was in high concordance with the division of varieties into fiber flax and linseed with flax type were revealed, and the highest expression level of this gene was observed in flowers. However, clustering based on the VAF of BGAL30 did not show clear enough differentiation of clusters according to flax type . RGL1_B was predominantly expressed in sXYL, while the expression of RGL4_B was higher in leaves, flowers, and capsules; however, the expression level of this gene was also significant in all other studied tissues. It is known that rhamnogalacturonan lyases are involved in the modification of cell wall polysaccharides [RGL1_B plays role in the modification of cell wall polysaccharides in xylem tissues [RGL1_B could also indicate a role for this gene in flax cell wall formation and its importance for stem traits of fiber flax.Among rhamnogalacturonan lyases-encoding genes, ackbone) . Transcrackbone) ,57. BasePLR1 had many FTA polymorphisms. This gene was predominantly expressed in capsules, and clustering based on the VAF of PLR1 revealed clear enough differentiation of clusters according to flax type (s = 0.64) with flax type. It was shown that PLRs are important for the synthesis of the major lignan in flax seeds, secoisolariciresinol diglucoside (SDG) [PLR1 in the flax plant stress response was revealed [PLR1 could be due to its importance for the formation of a linseed trait, the lignan content. However, the difference in linseed and fiber flax based on PLR1 polymorphisms could also be associated with the role of this gene in the formation of other characteristics, which are important for a particular flax type, namely, stress response.For genes related to lignan synthesis, lax type . In addide (SDG) ,99. SDG de (SDG) . PLR1 code (SDG) ,100,101.revealed . Thus, aFAD2A, encoding fatty acid desaturases 2, had one polymorphism associated with flax type (rs = \u22120.44). The expression of FAD2A was higher in capsules and embryo than in other analyzed tissues, and clustering had some concordance with flax type, but it was poor enough with flax type, and the number of such polymorphisms per gene varied from 1 to 39. The expression profiles of these genes in the studied tissues were very different, but in general, most genes had the highest expression levels in seedling roots. For ABCA1, ABCA7, ABCB42, ABCB47, ABCG71, and ABCG80 genes with a high number (27\u201339) of FTA polymorphisms, VAF clustering revealed a linseed cluster, whose size varied from gene to gene, while the rest clusters were not clear enough differentiated according to flax type with flax type were identified, and the expression profiles of these genes in the studied flax tissues varied greatly. The highest expression level of ABCG79 was revealed in leaves and seedling shoots; ABCB42 in seedling roots; ABCH1 in leaves, capsules, seedling shoots, iFIB, and tFIB; ABCB40 in flowers; ABCB45 in seedling roots and sXYL; HMA12 in sXYL; ABCG8 in seedling shoots; and ABCC4 in iFIB. ABC transporters are essential components of plant cell membranes and are involved in numerous processes, including growth and development, nutrition, and responses to abiotic and biotic stresses [Lus10016125 gene with flax type. Among our analyzed groups of genes, the group of ABC and HMA genes had one of the highest proportions of genes with FTA polymorphisms (40%). As the functions of ABC and HMA genes vary and their expression profiles were diverse between flax tissues, they could be involved in the determination of traits of different organs of flax plants, which ultimately define features that are important for linseed or fiber flax.Within the studied ABC transporter and heavy metal-associated genes, 83 genes had polymorphisms with a strong correlation is probn et al. . In the Linseed and fiber flax differ not only in the characteristics of plant parts that are key for agricultural use, namely, the seeds and stems, but also in the anatomy and morphology of the roots , as well as the consumption of nutrients in different periods of plant development , the requirements for the content of nutrients in soil , and the ability to grow under unfavorable conditions . TherefoVarious approaches are used for the identification of genetic markers or genes associated with important flax plant characteristics. Linkage mapping and association mapping/genome-wide association studies (GWAS) have allowed scientists to identify quantitative trait loci (QTL) and quantitative trait nucleotides (QTN) associated with seed yield and quality traits, fiber traits, agronomic traits, disease resistance, and abiotic stress response in flax ,115,116.L. usitatissimum genome assembly GCA_000224295.2 (ASM22429v2) by BWA-MEM 0.7.17 [http://broadinstitute.github.io/picard/, accessed on 27 October 2021). Next, duplicated reads were marked with MarkDuplicatesWithMateCigar (picard-tools). Finally, variant calling was performed by freeBayes 1.3.2 [4CL1, 4CL2, 4CL3, 4CL4, 4CL5, 4CL6, 4CL7, 4CL8, 4CL9, C3\u2032H1, C3\u2032H2, C3\u2032H3, C4H1, C4H2, C4H3, C4H4, C4H5, CAD1A, CAD1B, CAD2A, CAD2B, CAD3A, CAD3B, CAD4A, CAD4B, CAD5A, CAD5B, CAD6, CAD7, CAD8, CCoAOMT1, CCoAOMT2, CCoAOMT3, CCoAOMT4, CCoAOMT5, CCR1, CCR10, CCR11, CCR12, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, COMT1, COMT2, COMT3, F5H1, F5H2, F5H3, F5H4, F5H5, F5H6, F5H7, F5H8, HCT1, HCT2, HCT3, HCT4, HCT5, PAL1, PAL2, and PAL3; 35 genes encoding chitinase-like proteins\u2014CTL1, CTL10, CTL11, CTL12, CTL13, CTL14, CTL16, CTL17, CTL18, CTL19, CTL2, CTL20, CTL21, CTL22, CTL23, CTL24, CTL25, CTL26, CTL27, CTL28, CTL29, CTL3, CTL30, CTL31, CTL32, CTL33, CTL35, CTL36, CTL37, CTL4, CTL5, CTL6, CTL7, CTL8, and CTL9; 40 genes encoding \u03b2-galactosidases\u2014BGAL1, BGAL10, BGAL11, BGAL12, BGAL13, BGAL14, BGAL16, BGAL18, BGAL19, BGAL2, BGAL20, BGAL21, BGAL22, BGAL23, BGAL24, BGAL25, BGAL26, BGAL27, BGAL28, BGAL29, BGAL3, BGAL30, BGAL31, BGAL32, BGAL33, BGAL34, BGAL35, BGAL36, BGAL37, BGAL38, BGAL39, BGAL4, BGAL40, BGAL41, BGAL42, BGAL43, BGAL6, BGAL7, BGAL8, and BGAL9; 206 genes encoding ABC transporters and heavy metal\u2013associated genes\u2014ABCA1, ABCA2, ABCA3, ABCA4, ABCA5, ABCA6, ABCA7, ABCA8, ABCB1, ABCB10, ABCB11, ABCB12, ABCB13, ABCB14, ABCB15, ABCB16, ABCB17, ABCB18, ABCB19, ABCB2, ABCB20, ABCB21, ABCB22, ABCB23, ABCB24, ABCB25, ABCB26, ABCB27, ABCB28, ABCB29, ABCB3, ABCB30, ABCB31, ABCB32, ABCB33, ABCB34, ABCB35, ABCB36, ABCB37, ABCB38, ABCB39, ABCB4, ABCB40, ABCB41, ABCB42, ABCB43, ABCB44, ABCB45, ABCB46, ABCB47, ABCB48, ABCB5, ABCB6, ABCB7, ABCB8, ABCB9, ABCC1, ABCC10, ABCC11, ABCC12, ABCC13, ABCC14, ABCC15, ABCC16, ABCC17, ABCC18, ABCC19, ABCC2, ABCC3, ABCC4, ABCC5, ABCC6, ABCC7, ABCC8, ABCC9, ABCD1, ABCD2, ABCD3, ABCD4, ABCD5, ABCE1, ABCE2, ABCF1, ABCF2, ABCF3, ABCF4, ABCF5, ABCF6, ABCF7, ABCF8, ABCF9, ABCG1, ABCG11, ABCG12, ABCG13, ABCG14, ABCG16, ABCG17, ABCG18, ABCG19, ABCG2, ABCG20, ABCG21, ABCG22, ABCG23, ABCG24, ABCG25, ABCG26, ABCG27, ABCG28, ABCG29, ABCG3, ABCG30, ABCG31, ABCG32, ABCG33, ABCG34, ABCG35, ABCG36, ABCG37, ABCG38, ABCG39, ABCG4, ABCG40, ABCG41, ABCG42, ABCG43, ABCG44, ABCG45, ABCG46, ABCG47, ABCG48, ABCG49, ABCG5, ABCG50, ABCG51, ABCG52, ABCG53, ABCG54, ABCG55, ABCG56, ABCG57, ABCG58, ABCG59, ABCG6, ABCG60, ABCG61, ABCG62, ABCG63, ABCG64, ABCG65, ABCG66, ABCG67, ABCG68, ABCG69, ABCG7, ABCG70, ABCG71, ABCG72, ABCG73, ABCG74, ABCG75, ABCG76, ABCG77, ABCG78, ABCG79, ABCG8, ABCG80, ABCG81, ABCG82, ABCG83, ABCG84, ABCG85, ABCG9, ABCH1, ABCH10, ABCH11, ABCH12, ABCH13, ABCH14, ABCH15, ABCH16, ABCH17, ABCH18, ABCH19, ABCH2, ABCH20, ABCH21, ABCH22, ABCH3, ABCH4, ABCH5, ABCH6, ABCH7, ABCH8, HMA1, HMA10, HMA11, HMA12, HMA2, HMA3, HMA4, HMA6, HMA7, HMA8, and HMA9; 9 genes related to lignan synthesis\u2014DIR1, DIR2, DIR3, DIR4, DIR5, DIR6, PLR1, PLR2, and UGT74S1; 21 genes encoding tubulins\u2014Alfa_TUB1, Alfa_TUB2, Alfa_TUB3, Alfa_TUB4, Alfa_TUB5, Alfa_TUB6, Beta_TUB1, Beta_TUB10, Beta_TUB11, Beta_TUB12, Beta_TUB13, Beta_TUB2, Beta_TUB3, Beta_TUB4, Beta_TUB5, Beta_TUB6, Beta_TUB7, Beta_TUB8, Beta_TUB9, Gamma_Tub1, and Gamma_Tub2; 16 genes encoding cellulose synthases\u2014CESA1-A, CESA1-B, CESA3-A, CESA3-B, CESA3-C, CESA4, CESA6-A, CESA6-B, CESA6-C, CESA6-D, CESA6-E, CESA6-F, CESA7-A, CESA7-B, CESA8-A, and CESA8-B; 10 genes encoding rhamnogalacturonate lyases\u2014RGL1_B, RGL2, RGL3_A, RGL3_B, RGL4_A, RGL4_B, RGL6_A, RGL6_B, RGL7_A, and RGL7_B; 6 genes related to fatty acid synthesis\u2014FAD2A, FAD2B, FAD3A, FAD3B, SAD1, and SAD2; and 15 genes encoding actins\u2014Act1, Act10, Act11, Act12, Act13, Act14, Act15, Act2, Act3, Act4, Act5, Act6, Act7, Act8, and Act9. Data for gene sequences/genome coordinates were obtained from the literature [For association analysis between allele variants and flax type (fiber flax or linseed), we used Illumina whole-genome sequencing (WGS) data from two NCBI BioProjects: PRJNA590636 , we performed hierarchical clustering of varieties using Ward\u2019s minimum variance method (\u2018ward.D2\u2019 in R 3.6.2).Next, we performed correlation analysis between the VAF values and whether a variety belonged to linseed or fiber flax. Spearman\u2019s, Pearson\u2019s, and Kendall\u2019s correlation coefficients and For gene expression analysis, we used NCBI BioProjects PRJNA475325 , PRJNA63L. usitatissimum genome assembly GCA_000224295.2 (ASM22429v2) with splice-aware STAR 2.7.2b mapper [In total, 69 samples were included in the analysis. To eliminate mapping bias, reads from all samples were cropped to the minimal length across all samples (86 nt) with Trimmomatic. When paired-end read data were available, only forward read data were used. Next, reads were mapped to the reference b mapper . Since tThe derived BAM files were sorted with samtools 1.10 and reordered, and read groups were assigned with picard-tools. Then, reads that contained Ns in their CIGAR field were split with SplitNCigarReads from GATK 4.2.2.0 . Next, r"} +{"text": "Scientific Reports 10.1038/s41598-021-99760-5, published online 12 October 2021Correction to: ADAMTS4, ADRA1D, APLNR, AQP1, CD44, DUOX1, KLK6, LRP2, NEFH, NEUROD1, PVALB, SNCG, SYT2, TDO2, and TNC were not underlined.The original version of this Article contained a formatting error in Table 2 where the Genes LIPG, PTGIS, ADAMST18, HLA-DQB1, and HLA-DRB5 were not underlined.In addition, in Table 4, the Gene names The original version of the Article has been corrected."} +{"text": "The co-authors and their affiliations are omitted in the published article.The correct list of author names and their affiliations are copied below:1, Mostafa Qaraqei2, Rahma Algadeeb3, Hassan Faqeehi4, Abdulrahman Al-Matary1,*Kumail AlGadeeb1. Neonatology department, Maternity and children hospital, Alhasa, Saudi Arabia2. Neonatology department, King Fahad Medical city, Riyadh, Saudi Arabia3. Postgraduate center for preventive medicine, Alhasa, Saudi Arabia4. Department of Nephrology, Children\u2019s hospital, King Fahad Medical City, Riyadh, Saudi Arabia*Corresponding author, amatary@yahoo.comThe original article has been corrected."} +{"text": "Clostridium perfringens food poisoning in psychiatric patients. S Afr J Psychiatr. 2019;25(0):a1339. https://doi.org/10.4102/sajpsychiatry.v25i0.1339, there was an error in the affiliations. Instead of:In the published article, Bamford C, Milligan P, Kaliski S. Dangers of \u2018Authors:1,2,3Colleen Bamford4,6Peter Milligan5,6Sean KaliskiAffiliations:1Medical Microbiologist, Pathcare, East London, South Africa2National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa3Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa4Department of Psychiatry, Ngwelezana Hospital, Empangeni, South Africa5Forensic Mental Health Service, Valkenberg Hospital, Cape Town, South Afria6Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa\u2019,It should be:\u2018Authors:1,2Colleen Bamford3,4Peter Milligan4,5Sean KaliskiAffiliations:1National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa2Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa3Acute services, Valkenberg Hospital, Cape Town, South Africa4Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa5Forensic Mental Health Service, Valkenberg Hospital, Cape Town, South Africa\u2019.The authors apologise for this error. The correction does not change the study\u2019s findings of significance or overall interpretation of the study\u2019s results or the scientific conclusions of the article in any way."} +{"text": "In \u201cPredicting Antituberculosis Drug\u2013Induced Liver Injury Using an Interpretable Machine Learning Method: Model Development and Validation Study\u201d :e29226) two corrections were made.Daihai He was listed as the corresponding author. The corresponding author has been changed to Shengyuan Liu and the corrected details are as follows:1. In the originally published article, author Corresponding Author:Shengyuan Liu, PhDDepartment of Tuberculosis ControlShenzhen Nanshan Center for Chronic Disease ControlNanshan DistrictHua Ming Road No 7Shenzhen, 518000ChinaPhone: 86 13543301395Email: jfk@sznsmby.comXiaoli Dong, Ka Hing Wong, and Wing Tak Wong, the affiliation was originally listed as follows:2. For authors 2, PhD; Ka Hing Wong2, PhD; Wing Tak Wong2Xiaoli DongDepartment of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, ChinaThis has been corrected to:5,6, PhD; Ka Hing Wong5,6, PhD; Wing Tak Wong5,6Xiaoli Dong5Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong, China6Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, ChinaThe complete author information and affiliations in the corrected article are listed below.1*, BSc; Zian Zhuang2,3,4*, BSc; Xiaoli Dong5,6, PhD; Ka Hing Wong5,6, PhD; Wing Tak Wong5,6, PhD; Jian Wang1, BSc; Daihai He2,4, PhD; Shengyuan Liu1, PhDTao Zhong1Department of Tuberculosis Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China2Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China3Department of Biostatistics, University of California, Los Angeles, CA, United States4Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China5Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong, China6Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China* these authors contributed equallyThe correction will appear in the online version of the paper on the JMIR Publications website on August 13, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1*, Mark McConnell1, Jake Gockley2, Mary H. Young1, Adam Rosenthal3, Frank Schmitz1, David J. Reiss1, Phil Farmer4, Daisy V. Alapat4, Amrit Singh4, Cody Ashby4, Michael Bauer4, Yan Ren1, Kelsie Smith1, Suzana S. Couto5, Frits van Rhee4, Faith Davies4, Maurizio Zangari4, Nathan Petty4, Robert Z. Orlowski6, Madhav V. Dhodapkar7, Wilbert B. Copeland1, Brian Fox1, Antje Hoering3, Alison Fitch1, Katie Newhall1, Bart Barlogie8, Matthew W. B. Trotter9, Robert M. Hershberg10, Brian A. Walker4, Andrew P. Dervan1, Alexander V. Ratushny1\u2021*, Gareth J. Morgan4\u2021*Samuel A. Danziger1 Bristol Myers Squibb, Seattle, Washington, United States of America2 Sage Bionetworks, Seattle, Washington, United States of America3 Cancer Research and Biostatistics, Seattle, Washington, United States of America4 Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America5 Genmab, Princeton, New Jersey, United States of America6 The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America7 Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America8 Department of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America9 BMS Center for Innovation and Translational Research Europe (CITRE), Seville, Spain10 Frazier Life Sciences, Seattle, Washington, United States of America"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1,2, Rie Nishitani1, Akiyoshi Shimura3,4, Ayano Takeuchi2, Mamoru Touko1, Takashi Kato5, Sahoko Chiba1, Keiko Ashidate1, Nobuo Ishiwata1, Tomoyasu Ichijo1, Masataka Sasabe1Yoshiki Ishibashi1 Department of Internal Medicine, Kudanzaka Hospital, Company Overview of Federation of National Public Service Personnel Mutual Aid Associations, 1-6-12, Kudan-minami, Chiyoda-ku, Tokyo, 102\u20130074 Japan, 2 Department of Preventive Medicine and Public Health, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160\u20138582 Japan, 3 Department of Psychiatry, Tokyo Medical University, 6-7-1 Nishi-shinjuku, Shinjuku-ku, Tokyo, 160\u20130023 Japan, 4 Department of Sleep and Psychiatry, Kanno Hospital, 28\u20131 Honcho, Wako-shi, Saitama, 351\u20130114 Japan, 5 Department of pharmacy, Kudanzaka Hospital, Company Overview of Federation of National Public Service Personnel Mutual Aid Associations, 1-6-12, Kudan-minami, Chiyoda-ku, Tokyo, 102\u20130074 Japan."} +{"text": "In \u201cThe Good Food for Learning Universal Curriculum-Integrated Healthy School Lunch Intervention: Protocol for a Two-Year Matched Control Pre-Post and Case Study\u201d :e30899), one error was noted.In the originally published paper, one author, Sylvana Tu, was not included in the list of authors. Sylvana Tu has now been included in the authorship list between authors Sinikka Elliott and Brent Hills. Sylvana Tu's author affiliation has also been added as follows:Saskatchewan Population Health Evaluation and Research Unit, University of Saskatchewan, Saskatoon, SK, CanadaThis affiliation has been added as affiliation 9 in the corrected paper, and the remaining affiliations have been renumbered accordingly.The full list of authorship and affiliations was as follows in the originally published paper:1, PhD; Jennifer Black2, PhD; Nazeem Muhajarine1, PhD; Wanda Martin3, PhD; Jason Gilliland4, PhD; Janet McVittie5, PhD; Sara Kirk6, PhD; Hannah Wittman2, PhD; Amin Mousavi7, PhD; Sinikka Elliott8, PhD; Brent Hills9, MEd; Gordon Androsoff10, MSc; Debbie Field11, MA; Brit Macdonald12, BA; Chelsea Belt13, MSc; Hassan Vatanparast14, PhDRachel Engler-Stringer1Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada2Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada3College of Nursing, University of Saskatchewan, Saskatoon, SK, Canada4Western University, London, ON, Canada5Department of Educational Foundations, College of Education, University of Saskatchewan, Saskatoon, SK, Canada6School of Health and Human Performance, Dalhousie University, Halifax, NS, Canada7Department of Educational Psychology and Special Education, College of Education, University of Saskatchewan, Saskatoon, SK, Canada8Department of Sociology, University of British Columbia, Vancouver, BC, Canada9Saskatoon Public Schools Division, Saskatoon, SK, Canada10CHEP Good Food Inc, Saskatoon, SK, Canada11Coalition for Healthy School Food, Food Secure Canada, Montreal, QC, Canada12Little Green Thumbs Program, Agriculture in the Classroom, Saskatoon, SK, Canada13Health Promotion Department, Saskatchewan Health Authority, Saskatoon, SK, Canada14College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, CanadaThis has been corrected to:1, PhD; Jennifer Black2, PhD; Nazeem Muhajarine1, PhD; Wanda Martin3, PhD; Jason Gilliland4,PhD; Janet McVittie5, PhD; Sara Kirk6, PhD; Hannah Wittman2, PhD; Amin Mousavi7, PhD; Sinikka Elliott8, PhD; Sylvana Tu9, MPH; Brent Hills10, MEd; Gordon Androsoff11, MSc; Debbie Field12, MA; Brit Macdonald13, BA; Chelsea Belt14, MSc; Hassan Vatanparast15, PhDRachel Engler-Stringer1Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada2Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada3College of Nursing, University of Saskatchewan, Saskatoon, SK, Canada4Western University, London, ON, Canada5Department of Educational Foundations, College of Education, University of Saskatchewan, Saskatoon, SK, Canada6School of Health and Human Performance, Dalhousie University, Halifax, NS, Canada7Department of Educational Psychology and Special Education, College of Education, University of Saskatchewan, Saskatoon, SK, Canada8Department of Sociology, University of British Columbia, Vancouver, BC, Canada9Saskatchewan Population Health Evaluation and Research Unit, University of Saskatchewan, Saskatoon, SK, Canada10Saskatoon Public Schools Division, Saskatoon, SK, Canada11CHEP Good Food Inc, Saskatoon, SK, Canada12Coalition for Healthy School Food, Food Secure Canada, Montreal, QC, Canada13Little Green Thumbs Program, Agriculture in the Classroom, Saskatoon, SK, Canada14Health Promotion Department, Saskatchewan Health Authority, Saskatoon, SK, Canada15College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, CanadaThe correction will appear in the online version of the paper on the JMIR Publications website on November 3, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "Instead of \u201c8 School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Malaysia, 9 Department of Chemical and Materials Engineering, National Central University, Taoyuan City, Taiwan, 10 R&D Center for Membrane Technology, Chung Yuan Christian University, Taoyuan City, Taiwan, 11 Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Chennai, India.\u201d It should be \u201c8 Sultan Idris Education University, Tanjong Malim, Malaysia, 9 School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Malaysia, 10 Department of Chemical and Materials Engineering, National Central University, Taoyuan City, Taiwan, 11 R&D Center for Membrane Technology, Chung Yuan Christian University, Taoyuan City, Taiwan, 12 Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Chennai, India.\u201dIn the published article, there was an error in affiliations for Mahendran Maniam, Antony V. Samrot, Akon Higuchi and S. Suresh Kumar. Instead of having affiliations \u201cMahendran Maniam7, Antony V. Samrot8, Akon Higuchi9,10 and S. Suresh Kumar 1,11*\u201d it should be \u201cMahendran Maniam8, Antony V. Samrot9, Akon Higuchi10,11 and S. Suresh Kumar1,12*.\u201dIn the published article, there was an error regarding the The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1,2, Min Jin Jin4, Jang-Kyu Lee3, Hee-Song Kim1, Hyung-Ki Ji1, Ki-Pyoung Kim1, Myoung-Ho Hyun2, Hyeon-Gi Hong1,2Sue Hyun Jung1 Division of Forensic Psychology, National Forensic Service, Wonju-si, Gangwon-do, Republic of Korea, 2 Department of Psychology, Chung-Ang University, Seoul, Republic of Korea, 3 Institute of Forensic Psychiatry Ministry of Justice, Gongju-si, Chungcheongnam-do, Republic of Korea, 4 Institute of General Education, Kongju National University, Gongju, Republic of Korea."} +{"text": "In \u201cAssociation Between Improvement in Baseline Mood and Long-Term Use of a Mindfulness and Meditation App: Observational Study\u201d :e12617) the authors noted one error.In the originally published paper, author Paul Wehner's name was inadvertently not included in the list of authors, and the full list of authors and affiliations appeared as follows:1*, BSc; Jamison M McCorrison2,3*, BSc; Susan Smalley4, PhD; Jamie Price5, JD; Jim Grady5, BA; Julie Campistron5, MBA; Nicholas J Schork1,3,6,7, PhDArgus J Athanas1Department of Biomedical Informatics, University of California San Diego, San Diego, CA, United States2Department of Bioinformatics and Systems Biology, University of California San Diego, San Diego, CA, United States3J Craig Venter Institute, San Diego, CA, United States4Department of Psychiatry, University of California Los Angeles, Los Angeles, CA, United States5Stop, Breathe & Think, Los Angeles, CA, United States6The Translational Genomics Research Institute (TGen), Department of Quantitative Medicine, Phoenix, AZ, United States7The City of Hope/Translational Genomics Research Institute IMPACT Center, Duarte, CA, United States*these authors contributed equallyThe corrected list of authors and affiliations is as follows:1*, BSc; Jamison M McCorrison2,3*, BSc; Susan Smalley4, PhD; Jamie Price5, JD; Jim Grady5, BA; Paul Wehner6, BA; Julie Campistron5, MBA; Nicholas J Schork1,3,7,8, PhDArgus J Athanas1Department of Biomedical Informatics, University of California San Diego, San Diego, CA, United States2Department of Bioinformatics and Systems Biology, University of California San Diego, San Diego, CA, United States3J Craig Venter Institute, San Diego, CA, United States4Department of Psychiatry, University of California Los Angeles, Los Angeles, CA, United States5Stop, Breathe & Think, Los Angeles, CA, United States6Positive Place Inc, The Villages, FL, United States7The Translational Genomics Research Institute (TGen), Department of Quantitative Medicine, Phoenix, AZ, United States8The City of Hope/Translational Genomics Research Institute IMPACT Center, Duarte, CA, United States*these authors contributed equallyThe correction will appear in the online version of the paper on the JMIR Publications website on June 30, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "In \u201cData Sharing Goals for Nonprofit Funders of Clinical Trials\u201d :e23011) the authors noted two errors.In the originally published manuscript, Lynn Matrisian was the last author listed in the order of authorship. This has been corrected to place Lynn Matrisian fifteenth in the order of authorship, after Mary Jane Marchisotto and before Elizabeth Myers. Author affiliations have been renumbered accordingly.As well, the affiliation for Mary Jane Marchisotto has been corrected from:MJM Advisory, LLC, McLean, VA, United Statesto:MJM Advisory, LLC, New York, NY, United StatesThe complete list of authors and affiliations in the originally published paper was as follows:1, MSc, PhD; Mad Price Ball2, PhD; Marc Boutin3, JD; Abby Bronson4, MBA; David T Dexter5, PhD; Rebecca A English6, MPH; Patricia Furlong7, BSN; Andrew D Goodman8, MD; Cynthia Grossman9, PhD; Adrian F Hernandez10, MD, MHS; Jennifer E Hinners11, MPH, MD; Lynn Hudson12, PhD; Annie Kennedy7, BSc; Mary Jane Marchisotto13, MBA; Elizabeth Myers14, PhD; W Benjamin Nowell15, PhD; Brian A Nosek16, PhD; Todd Sherer17, PhD; Carolyn Shore6, PhD; Ida Sim18, PhD, MD; Luba Smolensky17, BA; Christopher Williams19, MSc; Julie Wood20, BA; Sharon F Terry21, MA, LhD; Lynn Matrisian22, PhD, MBATimothy Coetzee1National Multiple Sclerosis Society, Cherry Hill, NJ, United States2Open Humans Foundation, San Diego, CA, United States3Novartis, Basel, Switzerland4Edgewise Therapeutics, Boulder, CO, United States5Parkinson\u2019s UK, London, United Kingdom6National Academies of Sciences, Engineering, and Medicine, Washington, DC, United States7Parent Project Muscular Dystrophy, Bethesda, MD, United States8Department of Neurology, University of Rochester Medical Center, Rochester, NY, United States9Biogen, Cambridge, MA, United States10Duke University School of Medicine, Durham, NC, United States11Bison Ink, Washington, DC, United States12Critical Path Institute, Tucson, AZ, United States13MJM Advisory, LLC, McLean, VA, United States14Doris Duke Charitable Foundation, New York, NY, United States15Global Healthy Living Foundation, Upper Nyack, NY, United States16Center for Open Science, Charlottesville, VA, United States17The Michael J Fox Foundation for Parkinson\u2019s Research, New York, NY, United States18Department of Medicine, University of California San Francisco, San Francisco, CA, United States19Multiple Myeloma Research Foundation, Norwalk, CT, United States20Vivli, Columbia, MO, United States21Genetic Alliance, Washington, DC, United States22Pancreatic Cancer Action Network, Washington, DC, United StatesThe complete list of authors and affiliations in the corrected paper is as follows:1, MSc, PhD; Mad Price Ball2, PhD; Marc Boutin3, JD; Abby Bronson4, MBA; David T Dexter5, PhD; Rebecca A English6, MPH; Patricia Furlong7, BSN; Andrew D Goodman8, MD; Cynthia Grossman9, PhD; Adrian F Hernandez10, MD, MHS; Jennifer E Hinners11, MPH, MD; Lynn Hudson12, PhD; Annie Kennedy7, BSc; Mary Jane Marchisotto13, MBA; Lynn Matrisian14, PhD, MBA; Elizabeth Myers15, PhD; W Benjamin Nowell16, PhD; Brian A Nosek17, PhD; Todd Sherer18, PhD; Carolyn Shore6, PhD; Ida Sim19, PhD, MD; Luba Smolensky18, BA; Christopher Williams20, MSc; Julie Wood21, BA; Sharon F Terry22, MA, LhDTimothy Coetzee1National Multiple Sclerosis Society, Cherry Hill, NJ, United States2Open Humans Foundation, San Diego, CA, United States3Novartis, Basel, Switzerland4Edgewise Therapeutics, Boulder, CO, United States5Parkinson\u2019s UK, London, United Kingdom6National Academies of Sciences, Engineering, and Medicine, Washington, DC, United States7Parent Project Muscular Dystrophy, Bethesda, MD, United States8Department of Neurology, University of Rochester Medical Center, Rochester, NY, United States9Biogen, Cambridge, MA, United States10Duke University School of Medicine, Durham, NC, United States11Bison Ink, Washington, DC, United States12Critical Path Institute, Tucson, AZ, United States13MJM Advisory, LLC, New York, NY, United States14Pancreatic Cancer Action Network, Washington, DC, United States15Doris Duke Charitable Foundation, New York, NY, United States16Global Healthy Living Foundation, Upper Nyack, NY, United States17Center for Open Science, Charlottesville, VA, United States18The Michael J Fox Foundation for Parkinson\u2019s Research, New York, NY, United States19Department of Medicine, University of California San Francisco, San Francisco, CA, United States20Multiple Myeloma Research Foundation, Norwalk, CT, United States21Vivli, Columbia, MO, United States22Genetic Alliance, Washington, DC, United StatesThe correction will appear in the online version of the paper on the JMIR Publications website on June 30, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "Correction to: BMC Anesthesiol 21, 75 (2021)https://doi.org/10.1186/s12871-021-01296-81 Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China2 Department of Anaesthesiology, Fujian Provincial Hospital, Fuzhou, China3 Fujian Emergency Medical Center, Fuzhou, ChinaFollowing publication of the original article , the aut"} +{"text": "Owing to a production error, several authors were linked to the wrong affiliations in the article as originally published, as follows:1\u2020, Yu Zang2\u2020, Shuai Shang1,3, Shuo Liang1, Meiling Zhu1, Ying Wang1,4* and Xuexi Tang1,4*Jun Chen1 College of Marine Life Sciences, Ocean University of China, Qingdao, China2 College of Biological and Environmental Engineering, Binzhou University, Binzhou, China3 Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China4 Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, ChinaThe correct presentation of the authors and their affiliations is as follows:1\u2020, Yu Zang3\u2020, Shuai Shang1,4, Shuo Liang1, Meiling Zhu1, Ying Wang1,2*, Xuexi Tang1,2*Jun Chen1 College of Marine Life Sciences, Ocean University of China, Qingdao, China2 Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China3 Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China4 College of Biological and Environmental Engineering, Binzhou University, Binzhou, ChinaThe publisher apologizes for this mistake. The original article has been updated."} +{"text": "Scientific Reports 10.1038/s41598-020-71876-0, published online 23 September 2020Correction to: The original version of this Article contained an error in Affiliation 1 and 4, which were incorrectly given as \u2018LRIT, URAC No 29, Rabat IT Center, Mohammed V University, Rabat, Morocco \u2018and \u2018FLSH, Mohammed V University, 10500 Rabat, Morocco\u2019.The correct affiliations are listed below:Affiliation 1LRIT, URAC No 29, Rabat IT Center, Mohammed V University in Rabat, Rabat, MoroccoAffiliation 4FLSH, Mohammed V University in Rabat, Rabat, Morocco"} +{"text": "In Volume 12, issue 5, e01192-21, 2021,"} +{"text": "In \u201cTracking and Monitoring Mood Stability of Patients With Major Depressive Disorder by Machine Learning Models Using Passive Digital Data: Prospective Naturalistic Multicenter Study\u201d :e24365) the authors noted three errors.1. In the originally published manuscript, there was no equal contribution footnote for authors Ran Bai and Le Xiao. This has been corrected to note that the authors contributed equally to the manuscript.2. The affiliation for authors Le Xiao, Xuequan Zhu, Nanxi Li, Lei Feng, Gang Wang was incorrectly listed as follows in the original publication:Beijing Anding Hospital, Capital Medical University, Beijing, ChinaThis has been corrected to the following:The National Clinical Research Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China3. The original order of authors was as follows:1,2, MS; Le Xiao3, PhD, MD; Yu Guo4, MEng; Xuequan Zhu3, MA; Nanxi Li3, MD; Yashen Wang2, PhD; Qinqin Chen2, PhD; Lei Feng3, PhD, MD; Yinghua Wang2, PhD; Xiangyi Yu2, MS; Haiyong Xie1,2, PhD; Gang Wang1,3, PhD, MDRan Bai1Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China2National Engineering Laboratory for Risk Perception and Prevention, Beijing, China3Beijing Anding Hospital, Capital Medical University, Beijing, China4Beijing University of Posts and Telecommunications, Beijing, ChinaIn the corrected version of the manuscript, Chunxue Wang, Yongdong Hu, and Zhandong Liu have been added as coauthors for their contribution to the design of protocol and data collection. All authors agree with the addition and new order of authors. The revised order of authors is as follows:1,2*, MS; Le Xiao3*, PhD, MD; Yu Guo4, MEng; Xuequan Zhu3, MA; Nanxi Li3, MD; Yashen Wang2, PhD; Qinqin Chen2, PhD; Lei Feng3, PhD, MD; Yinghua Wang2, PhD; Xiangyi Yu2, MS; Chunxue Wang5, MD, PhD; Yongdong Hu6, MD, PhD; Zhandong Liu7, MD; Haiyong Xie1,2, PhD; Gang Wang1,3, PhD, MDRan Bai1Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China2National Engineering Laboratory for Risk Perception and Prevention, Beijing, China3The National Clinical Research Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China4Beijing University of Posts and Telecommunications, Beijing, China5Department of Neuropsychiatry and Clinical Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China6Department of Psychological Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China7Department of Neurology, Medical Health Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China*these authors contributed equallyThe correction will appear in the online version of the paper on the JMIR Publications website on June 17, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "This article has been corrected: The authors requested to remove the first and last affiliations. This correction does not change the content of the publication. The correct list of authors and affiliations is provided below:1,*, Qing Lin2,3,4,5,*, Shuai Chen6,7,*, Lixiang Sun1,*, Qingjie Chen8, Kehui Yi2,9, Zhi Li1, Qilin Ma2,3,4,5,&, Chi-Meng Tzeng1Wen-Qing Huang1Translational Medicine Research Center (TMRC), School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China2Department of Neurology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China3Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China4School of Medicine, Xiamen University, Xiamen, Fujian, China5The First Clinical College of Fujian Medical University, Fuzhou, Fujian, China6Department of Otolaryngology-Head and Neck Surgery, Xiamen Key Laboratory of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China7Chen Zhi-nan Academician Workstation, Institute of Basic and Translational Medicine, Xi\u2019an Medical University, Xi\u2019an, Shanxi, China8Department of Nuclear Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China9Department of Neurology, Zhongshan Xiamen Hospital, Fudan University, Xiamen, Fujian, China*Equal contribution"} +{"text": "Cell Death & Disease 10.1038/s41419-022-04617-y, published online 25 February 2022Correction to: The original version of this article unfortunately contained errors in the affiliations. The correct affiliations should be as follows: Fengying Du1,2,6, Lipan Peng1,6, Qiang Wang3, Kangdi Dong1, Wenting Pei4, Hongqing Zhuo1, Tao Xu1, Changqing Jing1, Leping Li1 and Jizhun Zhang1,51Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.2Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.3Personnel Office, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.4Hematology and Oncology, Qilu Children\u2019s Hospital of Shandong University, Jinan, Shandong, China.5Center for Post-doctoral Studies, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.6These authors contributed equally: Fengying Du and Lipan Peng. The original article has been corrected."} +{"text": "After publication of the original article , the aut1,7, Laura Libera2,7, Enrico Berrino1,3,7, Nora Sahnane4,7, Anna Maria Chiaravalli4,7, Cristiana Laudi5, Mattia Berselli6,7, Anna Sapino1,3, Fausto Sessa2,7, Tiziana Venesio1,7*\u2020 and Daniela Furlan2,7\u2020Carla Debernardi1Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy. 2Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy. 3Department of Medical Sciences, University of Torino, Torino, Italy. 4Pathology Unit, ASST Sette Laghi, Varese, Italy. 5Gastroenterology, Candiolo Cancer Institute, Candiolo, Italy. 6Surgical Oncology and Minimally Invasive Unit, Department of Surgery, ASST Sette Laghi, Varese, Italy. 7Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy.The correct affiliation is:1, Laura Libera2,7, Enrico Berrino1,3, Nora Sahnane4,7, Anna Maria Chiaravalli4,7, Cristiana Laudi5, Mattia Berselli6,7, Anna Sapino1,3, Fausto Sessa2,7, Tiziana Venesio1,*\u2020, Daniela Furlan2,7\u2020Carla Debernardi1Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy. 2Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy. 3Department of Medical Sciences, University of Torino, Torino, Italy. 4Pathology Unit, ASST Sette Laghi, Varese, Italy. 5Gastroenterology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy. 6Surgical Oncology and Minimally Invasive Unit, Department of Surgery, ASST Sette Laghi, Varese, Italy. 7Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy.The author group has been updated above and the original article has been"} +{"text": "R. Soc. Open Sci. 4, 160806. (Published 22 February 2017). (doi:10.1098/rsos.160806)The author affiliations should read as follows. The original paper has now been updated.1,*, Oscar T. Giles1, Jelena Havelka1, Sumaya Ali3, Peter R. Culmer2, Richard M. Wilkie1 and Mark Mon-Williams1,4,5Amanda H. Waterman1School of Psychology, and2School of Mechanical Engineering, University of Leeds, Leeds LS2 9JT, UK3The Public Authority for Applied Education and Training, PO Box 23778, Safat 22081, Kuwait4Bradford Institute of Health Research, Temple Bank House, Bradford Royal Infirmary, Duckworth Lane, Bradford BD9 6RJ, UK5Bradford Norwegian Centre for Vision, The University of South-East Norway, H\u00f8gskolen i S\u00f8r\u00f8st-Norge, Postboks 235, 3606 Kongsberg, Norway*Corresponding author"} +{"text": "The authors regret to inform that part of the methodology related to the description of the determination of dioxins, PCBs, and PBDEs in the published paper is outdated. This also relates to the description of some of the certified control materials (CRM) and internal control materials and 3 usThe authors would like to apologise for any inconvenience caused.[40]): 2,3,7,8-TCDD; 1,2,3,7,8-PeCDD; 1,2,3,4,7,8-HxCDD; 1,2,3,6,7,8-HxCDD; 1,2,3,7,8,9-HxCDD; 1,2,3,4,6,7,8-HpCDD; OCDD; 2,3,7,8-TCDF; 1,2,3,7,8-PeCDF; 2,3,4,7,8-PeCDF; 1,2,3,4,7,8-HxCDF; 1,2,3,6,7,8-HxCDF; 1,2,3,7,8,9-HxCDF; 2,3,4,6,7,8-HxCDF; 1,2,3,4,6,7,8-HpCDF; 1,2,3,4,7,8,9-HpCDF, and OCDF. The dioxin-like PCBs analysed were also those assigned WHO-TEFs\u00a0[42]: non-ortho PCBs; CB 77, 81, 126, and 169, and the mono-ortho PCBs; CB 105, 114, 118, 123, 156, 157, 167, and 189. Indicator PCBs include the non-dioxin-like CB 28, 52, 101, 138, 153, and 180 . An extra non-dioxin-like PCB, CB-31, was included from 2020. For PBDEs, the tri-hepta BDEs 28, 47, 49, 66, 99, 100, 119, 138 153, 154, and 183 were analysed, and the tri-hepta BDEs 35, 71, 75, 85, and 118 were reported from 2020. The octa-deka PBDEs BDE 196, 197, 206, 207 and 209, were also reported from 2020. Often PBDE results are presented as sum PBDE7 .Samples were analysed for the 17 PCDD/F congeners which have been assigned Toxic Equivalency Factors (TEFs) by the World Health Organization ). The analytes were extracted with hexane by an accelerated solvent extractor under elevated pressure and temperature and concentrated using Turbovap II . The sample extracts were purified using high performance clean-up columns , on an automated GO-6HT system . PBDEs, ndl-PCBs, and mono-ortho-PCBs were collected in one fraction, whereas PCDD/Fs and non-ortho PCBs were collected in a second fraction. Furthermore, solvent exchange and adding of recovery standards were executed by automated liquid handling .PCDD/F and non-ortho-PCB analysis was performed by high-resolution gas chromatography/high resolution mass spectrometry (HRGC-HRMS) , equipped with a fused silica capillary column .Ndl-PCBs, mono-ortho-PCBs and tri-hepta PBDEs were analysed by gas chromatography/tandem mass spectrometry (GC-MS/MS) , equipped with a low bleed proprietary phased column .Octa-deka PBDEs were analysed by negative chemical ionisation GC/MS , equipped with a fused silica capillary column .[44]. Mono-ortho PCBs, ndl-PCBs, and tri-hepta PBDEs were quantified using eight-point calibration curves. Okta-deka PBDEs were quantified using five-point calibration curves weighted 1/S2.Quantification of congeners was performed according to the isotope dilution/internal standard method using relative response factors (RRs) or response factors (RFs) determined from calibration curves. For quantification of PCDD/Fs and non-ortho PCBs, a five-point calibration curve was used, according to the US EPA 1613 and 1668 method\u00a0[45]. Concentrations below the LOQ were reported as the LOQ (upper bound LOQ) to avoid underestimation of the risk.Final quantified PCCD/F and DL-PCB values are expressed as pg WHO-TEQ/g wet weight using the WHO-TEFs from 2005 according to EU legislation"} +{"text": "Correction to: Egypt J Radiol Nucl Med 52, 114 (2021)https://doi.org/10.1186/s43055-021-00493-2Following publication of the original article , the autAhmed M. Magdy1*, Mohammad A. Saad1, Ahmed F. El Khateeb2, Mona I. Ahmed3 and Dina H. Gamal El-Din41Radiology department, Faculty of Medicine, Fayoum University.2Department of critical care, Faculty of Medicine, Fayoum University.3Department of chest disease and tuberculosis, Faculty of Medicine, Fayoum University.4Radiology department, Faculty of Medicine, Cairo University.The author group has been updated above and the original article has been"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Zbigniew Trzaskoma2, Dominik Sitarski3, Bart\u0142omiej Gromu\u01423, Ireneusz Haponiuk1, Dariusz Czaprowski4Paulina Ewertowska1 Department of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland, 2 Faculty of Rehabilitation, J\u00f3zef Pi\u0142sudski University of Physical Education, Warsaw, Poland, 3 Department of Health Sciences, Olsztyn University, Olsztyn, Poland, 4 Physiotherapy Unit, Department of Health Sciences, Poznan University of Medical Sciences, Poznan, Poland."} +{"text": "The correct affiliations appear below:Due to a production error, there was a mistake in 1,2*, Jesper Alfraeus1,2, Elin Good1,2,3, Jan Engvall1,2,4, Ebo de Muinck1,2,3 and Petter Dyverfeldt1,2Magnus Ziegler1 Division of Cardiovascular Medicine, Department of Health, Medicine and Caring Sciences, Link\u00f6ping University, Link\u00f6ping, Sweden2 Center for Medical Image Science and Visualization (CMIV), Link\u00f6ping University, Link\u00f6ping, Sweden3 Department of Cardiology, Department of Health, Medicine and Caring Sciences, Link\u00f6ping University, Link\u00f6ping, Sweden4 Department of Clinical Physiology, Department of Health, Medicine and Caring Sciences, Link\u00f6ping University, Link\u00f6ping, Swedenmagnus.ziegler@liu.se*Correspondence: Magnus Ziegler, The publisher apologizes for these mistakes. The original article has been updated."} +{"text": "In the report, \u201cCharacteristics and Clinical Outcomes of Children and Adolescents Aged <18 Years Hospitalized with COVID-19 \u2014 Six Hospitals, United States, July\u2013August 2021,\u201d on page 1766, the list of authors should have read,1,2; Megan E. Gerdes, MPH1; Dallas S. Shi, MD, PhD1,2; Rewa Choudhary, MD1,2; Theresa M. Dulski, MD1,2; Sophia Hsu, MSN, MPH1; Osatohamwen I. Idubor, MD1; Bryant J. Webber, MD1,2; Arthur M. Wendel, MD1; Nickolas T. Agathis, MD1,2; Kristi Anderson, MD1; Tricia Boyles, MHA1; Sophia K. Chiu, MD1; Eleanor S. Click, MD, PhD1; Juliana Da Silva, MD1; Hannah Dupont, MPH1; Mary Evans, MD1; Jeremy A.W. Gold, MD1; Julia Haston, MD1,2; Pamela Logan, MD1; Susan A. Maloney, MD1; Marisol Martinez, PharmD1; Pavithra Natarajan, BMBS1; Kevin B. Spicer, MD, PhD1; Mark Swancutt, MD1; Valerie A. Stevens1; Jessica Brown, PhD1; Gyan Chandra, MBA1; Megan Light, MPH1; Frederick E. Barr, MD3; Jessica Snowden, MD3; Larry K. Kociolek, MD4; Matthew McHugh, MPH4; David Wessel, MD5; Joelle N. Simpson, MD5; Kathleen C. Gorman, MSN5; Kristen A. Breslin, MD5; Roberta L. DeBiasi, MD5; Aaron Thompson, MD6,7; Mark W. Kline, MD6,7; 8,10Julie A. Boom, MD; 9,10Ila R. Singh, MD, PhD; Michael Dowlin9; 11Mark Wietecha, MS, MBA; Beth Schweitzer, MS1; Sapna Bamrah Morris, MD1; Emily H. Koumans, MD1; Jean Y. Ko, PhD1; Anne A. Kimball, MD1,*; David A. Siegel, MD1,*\u201d\u201cValentine Wanga, PhDIn addition, on page 1771, the list of author affiliations should have read,\u201c1CDC COVID-19 Emergency Response Team; 2Epidemic Intelligence Service, CDC; 3Arkansas Children\u2019s, Little Rock, Arkansas; 4Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; 5Children\u2019s National Hospital, Washington, DC; 6Children\u2019s Hospital New Orleans, New Orleans, Louisiana; 7Tulane University School of Medicine and LSU Health, New Orleans, Louisiana; 8Department of Pediatrics, Baylor College of Medicine, Houston, Texas; 9Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; 10Texas Children\u2019s Hospital, Houston, Texas; 11Children\u2019s Hospital Association, Washington, DC.\u201d"} +{"text": "Blood Cancer Journal 10.1038/s41408-021-00468-6, published online 19 April 2021Correction to: After the publication of the original article, the author list was updated as given here:1, Gudmar Thorleifsson2, Aitzkoa Lopez de Lapuente Portilla1, Abhishek Niroula1,3, Molly Went4, Malte Thodberg1, Maroulio Pertesi1, Ram Ajore1, Caterina Cafaro1, Pall I. Olason2, Lilja Stefansdottir2, G. Bragi Walters2, Gisli H. Halldorsson2, Ingemar Turesson5, Martin F. Kaiser4, Asta F\u00f6rsti6, Hartmut Goldschmidt7, Kari Hemminki6, Niels Weinhold8, Niels Abildgaard9, Niels Frost Andersen10, Ulf-Henrik Mellqvist11, Anders Waage12, Annette Juul-Vangsted13, Unnur Thorsteinsdottir2,14, Markus Hansson1,5, Richard Houlston4, Thorunn Rafnar2, Kari Stefansson2,14, Bj\u00f6rn Nilsson1,3Laura Duran-Lozano1Hematology and Transfusion Medicine, Department of Laboratory Medicine, 221 84 Lund, Sweden. 2deCODE genetics, Sturlugata 8, IS-101 Reykjavik, Iceland. 3Broad Institute, 415 Main Street, Cambridge MA 02124, USA. 4Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, United Kingdom. 5Hematology Clinic, Lund University Hospital, 221 85 Lund, Sweden. 6German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany. 7Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany, 8Department of Internal Medicine V, University Hospital of Heidelberg, 69120 Heidelberg, Germany. 9Hematology Research Unit, Department of Clinical Research, University of Southern Denmark and Department of Hematology, Odense University Hospital, Denmark. 10Department of Haematology, Aarhus University Hospital, 8200 Aarhus N, Denmark. 11S\u00f6dra \u00c4lvsborgs Sjukhus Bor\u00e5s, Sweden. 12Institute of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Department of Hematology, and Biobank1, St Olavs hospital, Trondheim, Norway. 13Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.14Faculty of Medicine, University of Iceland, Reykjavik, Iceland."} +{"text": "Cell Discovery (2021) 7:92Correction to: 10.1038/s41421-021-00304-y Published online 12 October 20211, we made an error in the authors affiliations. We apologize for any inconvenience that it may have caused.In the original publication of this CorrespondenceNow we provided a corrected version here about the affiliations of all authors here.1,3,4,5,6, Yanhui Liang1,3,4,5, Jianping Zhao2, Yuan Li2, Shixue Gou1,3,4,5, Min Zheng2, Juanjuan Zhou1,4,5, Quanjun Zhang1,4,5, Jidong Mi2 and Liangxue Lai1,4,5Xiaomin Wang1CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China2Beijing SINOGENE Biotechnology Co., Ltd, Beijing, 102200, China3University of Chinese Academy of Sciences, Beijing, 100049, China4Bioland Laboratory , Guangzhou, 510005, China5Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China6Current address: School of Life Sciences, Westlake University, Shilongshan Road No. 18, Cloud Town, Xihu District, Hangzhou, Zhejiang 310024, ChinaThese authors contributed equally: Xiaomin Wang, Yanhui Liang, Jianping Zhao.Correspondence: Jidong Mi (jidong-m@sinogene.com.cn) or Liangxue Lai (lai_liangxue@gibh.ac.cn)"} +{"text": "Cell Death and DiseaseCorrection to: 10.1038/s41419-021-03796-4 published online 22 May 20211, Yuan Huang2, Yuchao Zhang3, Xiangtai Zeng4, Mei Yan3, Zhongsheng Xia3, Dongming Lai3The original version of this article unfortunately contained a mistake in the affiliations. We apologize for the error. The original article has been corrected. The correct affiliations are: Yixin Tong1Department of Tongji Medical College of Huazhong University, 1095 Jiefang Dadao, Wuhan, Hubei Province, China.2Department of Endoscopy Center, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Xuhui, Shanghai, China.3Department of Gastrointestinal Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, 107 Yanjiang West Road, Guangzhou, Guangdong Province, China.4Department of The First Affiliated Hospital, Gannan Medical University, 23 Qingnian Road, Zhanggong District, Ganzhou, Jiangxi Province, China."} +{"text": "The report \u201cGenomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants \u2014 United States, June 2021\u2013January 2022\u201d contained several errors.1,2,*; Philip Shirk, PhD1,*; Molly K. Steele, PhD1; Prabasaj Paul, PhD1; Clinton R. Paden, PhD1; Betsy Cadwell, MSPH1; Heather E. Reese, PhD1; Yutaka Aoki, PhD1; Norman Hassell, MS1; 1,3; Nicholas A. Kovacs, PhD1,4; Jonathan G. Gerhart, MS5; Han JiaJason Caravas, PhD1,6; Ng, PhDXiao-yu Zheng, PhD1,7; 1; Reina Chau, MS1; Roxana Cintron, MS1; Peter W. Cook, PhD1; Christopher A. Gulvik, PhD1; Dakota Howard1; Yunho Jang, PhD1; Kristen Knipe, MS1; Kristine A. Lacek, MS1; Kara A. Moser, PhD8; Adrian C. Paskey, PhD1; Benjamin L. Rambo-Martin, PhD1; Roopa R. Nagilla, MS7; Adam C. Retchless, PhD1; Matthew W. Schmerer, PhD1; Sandra Seby, MS1; Samuel S. Shepard, PhD1; Richard A. Stanton, PhD1; Thomas J. Stark, PhD1; Anna Uehara, PhD1; Yvette Unoarumhi, MS1,4; Meghan L. Bentz1; Alex Burgin1; Mark Burroughs1; Morgan L. Davis, MS1,5; Matthew W. Keller, PhD1; Lisa M. Keong7; Shoshona S. Le1; Justin S. Lee, DVM, PhD1; Joseph C. Madden Jr, PhD1; Sarah Nobles, MS1; D. Collins Owuor, PhD1; Jasmine Padilla1,5; Mili Sheth, PhD1; Malania M. Wilson, MS, MBA1;Andrew Beck, PhD Sarah Talarico, PhD1; Jessica C. Chen, PhD1; M. Steven Oberste, PhD1; Dhwani Batra, MS, MBA1; Laura K. McMullan, PhD1; Alison Laufer Halpin, PhD1; Summer E. Galloway, PhD1; Duncan R. MacCannell, PhD3; Rebecca Kondor, PhD1; John Barnes, PhD1; Adam MacNeil, PhD1; Benjamin J. Silk, PhD1; Vivien G. Dugan, PhD1; Heather M. Scobie, PhD1; David E. Wentworth, PhD1.\u201dOn page 206, the list of authors should have read, \u201cAnastasia S. Lambrou, PhDEric Chirtel, Victoria Caban Figueroa, Tymeckia Kendall, Garrett Longmire, Brian Mann, Nicole Patterson, Catherine Smith, Erica Sula, Subblakshmi Voleti, Jonathan Zhong.\u201dOn pages 210\u201311 the acknowledgments should have read, \u201c1CDC COVID-19 Emergency Response Team; 2Epidemic Intelligence Service, CDC; 3Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, CDC; 4Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee; 5ASRT6Eagle Global Scientific, LLC, San Antonio, Texas;Inc., Smyrna, Georgia; 7General Dynamics Information Technology, Inc., Falls Church, Virginia; 8Goldbelt C6, LLC, Chesapeake, Virginia.\u201dOn page 211, the author affiliations should have read, \u201cAll authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed."} +{"text": "Correction to: J Exp Clin Cancer Res 40, 300 (2021)https://doi.org/10.1186/s13046-021-02104-4Following publication of the original article , an erro\u201cLee Jia designed, wrote and supervised the study. Xiaobo Yu, Jie Wang, Huayi Peng, Qing Shi performed all experiments. Yusheng Lu, Shuhui Li, Jian Liu, Haiyan Dong, and Vladimir Katanaev participated in data analyses, or technology consultations.\u201dFurthermore, author affiliations and their corresponding affiliation details are updated to:1\u2020, Xiaobo Yu2\u2020, Huayi Peng3\u2020, Yusheng Lu1, Shuhui Li2, Qing Shi2, Jian Liu2, Haiyan Dong4, Vladimir Katanaev1,5 and Lee Jia1,*Jie Wang1College of Materials and Chemical Engineering, Minjiang University, 350108 Fuzhou, China.2Cancer Metastasis Alert and Prevention Center, College of Chemistry; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, 350108 Fuzhou, P.R. China.3Fujian Provincial Key Laboratory of Inspection and Quarantine Technology Research/ Technology Center of Fuzhou Customs, 350108 Fuzhou, China.4 Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, 350108 Fuzhou, China.5Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.The correction does not have any effect on the results or conclusions of the paper. The original article has been corrected."} +{"text": "Nature Communications 10.1038/s41467-021-24510-0, published online 13 July 2021.Correction to: The author affiliation was missing for the first author (Jiaqi Tang) which resulted in the affiliation list being reordered as follows:Jiaqi Tang1,2,5, Xiang Wang2,5, Jiaxu Zhang2,5, Jing Wang3, Wanjian Yin3, Dong-Sheng Li4 & Tao Wu1,*1 College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou 510632, China.2 College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.3 College of Energy, Soochow University, Suzhou 215006, China.4 College of Materials and Chemical Engineering, Hubei Provincial Collaborative Innovation Centre for New Energy Microgrid, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China Three Gorges University, Yichang 443002, China.5 These authors contributed equally: Jiaqi Tang, Xiang Wang, Jiaxu Zhang* Correspondence and requests for materials should be addressed to T.W. (wutao@jnu.edu.cn).These errors have been corrected in the PDF and HTML versions of the Article."} +{"text": "Correction to: BMC Complement Med Ther 21, 83 (2021)10.1186/s12906-021-03246-wFollowing publication of the original article , the aut1,2, Mohammad-Reza Rashidi3, Maryam Akbarzadeh2,4, Ahad Bazmani5,6, Mostafa Mostafazadeh1,2, Saba Nikanfar1,2, Zohre Zibaei1,6, Reza Rahbarghazi3,7,8*\u2020 and Mohammad Nouri3,7*\u2020Sanya Haiaty1Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.2Department of Biochemistry and Clinical Laboratories, Tabriz University of Medical Sciences, Tabriz, Iran.3Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.4Department of Biochemistry, Erasmus University Medical Center, Rotterdam, the Netherlands.5Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University Of Mashhad, Mashhad, Iran.6Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.7Stem Cell Research Center, Tabriz University of Medical Sciences, Imam Reza St., Golgasht St, Tabriz, Iran.8Departmnt of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.The incorrect author name is: Ahad BazmanyThe correct author name is: Ahad BazmaniAcknowledgmentsWe special thanks to the Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences for their assistance in the progression of my thesis.The original article has been"} +{"text": "In the published article, there was an error in the affiliations of all the authors. Instead of:1, Rui Zhou2, Dong Liu3, Min Cui4, Ke Yu5, Hai Yang1, Ling Li1, Juan Liu1, Yang Chen1, Wenjuan Hong6, Jie Huang6, Congguo Wang6, Jingjing Ma6 and Huadong Zhou6*Zeyan Peng1 Department of Neurology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China2 Department of Neurology, Army Medical Center of PLA, Chongqing, China3 Southwest Hospital, Army Medical University, Chongqing, China4 State Key Laboratory of Trauma, Army Medical Center of PLA, Chongqing, China5 Department of Neurology, The General Hospital of Central Theater Command, Wuhan, China6 Department of Neurology, The General Hospital of Western Theater Command, Chengdu, ChinaIt should be:1, 2, Rui Zhou3, Dong Liu4, Min Cui5, Ke Yu6, Hai Yang2, Ling Li2, Juan Liu2, Yang Chen2, Wenjuan Hong1, Jie Huang1, Congguo Wang1, Jingjing Ma1, Huadong Zhou1*Zeyan Peng1Department of Neurology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China2 Department of Neurology, Army Medical Center of PLA, Chongqing, China3 Southwest Hospital, Army Medical University, Chongqing, China4 State Key Laboratory of Trauma, Army Medical Center of PLA, Chongqing, China5 Department of Neurology, The General Hospital of Central Theater Command, Wuhan, China6 Department of Neurology, The General Hospital of Western Theater Command, Chengdu, ChinaThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Carmela Serio1, Davide Tamagnini2, Marina Melchionna1, Alessandro Mondanaro1,3, Mirko Di Febbraro4, Antonio Profico5, Paolo Piras6,7, Filippo Barattolo1, Pasquale Raia1Silvia Castiglione1 Dipartimento di Scienze della Terra, dell\u2019Ambiente e delle Risorse, University of Naples Federico II, Napoli, Italy 2 Dipartimento di Biologia e Biotecnologie \u201cCharles Darwin\u201d, Sapienza Universit\u00e0 di Roma, Rome, Italy 3 Dipartimento di Scienze della Terra, University of Florence, Firenze, Italy 4 Dipartimento di Bioscienze e Territorio, University of Molise, Pesche, Isernia, Italy 5 Dipartimento di Biologia Ambientale, Sapienza Universit\u00e0 di Roma, Rome, Italy 6 Dipartimento di Ingegneria Strutturale e Geotecnica, Sapienza Universit\u00e0 di Roma, Rome, Italy 7 Dipartimento di Scienze Cardiovascolari, Respiratorie, Nefrologiche, Anestesiologiche e Geriatriche, Sapienza Universit\u00e0 di Roma, Rome, Italy"} +{"text": "Labels in Volume 13, issue 1, e03252-21, 2021,"} +{"text": "There are errors in the author affiliations. The publisher apologizes for these errors. The correct affiliations are as follows:1,2,3,8, Jose Maria Gutierrez Lopez4, M Cristina Reinoso del Rio4, Antonio M Saez Romero5, Francisco Giles Guzman1, Geraldine Finlayson1,2,8*, Francisco Giles Pacheco1, David Abulafia6, Stewart Finlayson1,2,7, Richard P Jennings8, Joaquin Rodriguez Vidal9Clive Finlayson1 The Gibraltar National Museum, Gibraltar, 2 The University of Gibraltar, Gibraltar Museum Campus, Gibraltar, 3 Department of Anthropology, University of Toronto, Canada, 4 Museo Hist\u00f3rico Municipal de Villamart\u00edn, C\u00e1diz, Spain, 5 Department of Prehistory and Archaeology, University of Seville, Spain, 6 Gonville and Caius College, Cambridge University, United Kingdom, 7 Department of Life Sciences, Anglia Ruskin University, Cambridge, United Kingdom, 8 School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom, 9 Department of Earth Sciences and CIPHCN-Heritage Centre, Campus del Carmen, University of Huelva, Huelva, Spain."} +{"text": "There was a change in the author names in the published article. The new list should read:1,2, Vanessa T. Devine3, Denise E. Morris1, Karen L. Osman1, Rebecca A. Gladstone4, Stephen D. Bentley4, Saul N. Faust1,5, Stuart C. Clarke1,2,6David W. Cleary1Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.2NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.3Northern Ireland Centre for Stratified Medicine and Clinical Translational Research Innovation Centre, Londonderry, UK.4Pathogen Genomics, Wellcome Trust Sanger Institute, UK.5NIHR Southampton Clinical Research Facility, University Hospital Southampton Foundation NHS Trust, Southampton, UK.6Global Health Research Institute, University of Southampton, Southampton, UK."} +{"text": "In \u201cYouths\u2019 and Parents\u2019 Experiences and Perceived Effects of Internet-Based Cognitive Behavioral Therapy for Anxiety Disorders in Primary Care: Mixed Methods Study\u201d :e26842) the authors noted one error.In the originally published manuscript, some affiliations were missing for first author Josefine Lotten Lilja. Only affiliation 1 was listed for this author, but all 3 affiliations on the paper should have been listed for this author.The full list of authors and affiliations was originally published as follows:1*, PhD; Mirna Rupcic Ljustina1, PsyM; Linnea Nissling1,2,3*, PsyM; Anna Caroline Larsson1*, PsyM; Sandra Weineland1,2,3*, PhDJosefine Lotten Lilja1Research, Development, Education and Innovation, Primary Health Care, Region V\u00e4stra G\u00f6taland, G\u00f6teborg, Sweden2Department of Psychology, University of Gothenburg, Gothenburg, Sweden3General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden*these authors contributed equallyThe list of authors and affiliations has been corrected as follows:1,2,3*, PhD; Mirna Rupcic Ljustina1, PsyM; Linnea Nissling1,2,3*, PsyM; Anna Caroline Larsson1*, PsyM; Sandra Weineland1,2,3*, PhDJosefine Lotten Lilja1Research, Development, Education and Innovation, Primary Health Care, Region V\u00e4stra G\u00f6taland, G\u00f6teborg, Sweden2Department of Psychology, University of Gothenburg, Gothenburg, Sweden3General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden*these authors contributed equallyThe correction will appear in the online version of the paper on the JMIR Publications website on December 2, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "Correction to: BMC Plant Biol 22, 117 (2022)https://doi.org/10.1186/s12870-022-03500-4Following publication of the original article , authors1 College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China.2 State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.1,2\u2020.Furthermore, author, Qi Ai has been added to affiliation 2. The final affiliation for Qi Ai would be Qi AiThe original article has been corrected."} +{"text": "Xiaoyu Zhang1, Xiaoqin He1, Yue Li1, Yangtao Xu1, Wenliang Chen1, Xin Liu1, Xinyao Hu1, Ximing Xu1. Instead of \u201c1Wuhan University, Wuhan, China\u201d it should be 1Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China. In addition, incorrect affiliation was included for Lin Xiong2. Instead of \u201c2Renmin Hospital of Wuhan University, Wuhan, China\u201d it should be 2Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China.In the published article, incorrect affiliation was included for The authors apologize for these errors and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Correction to: BMC Public Health 21, 2092 (2021)https://doi.org/10.1186/s12889-021-12050-7After publication of the original article the auth1 Institute for Medical Information Processing, Biometry and Epidemiology, TU M\u00fcnchen, Marchioninistrasse 17, 80336 Munich, Germany.2 Institute for Medical Information Processing, Biometry and Epidemiology, LMU Munich Marchioninistrasse 17, 80336 Munich, Germany.3 Munich School of Management and Munich Center of Health Sciences, LMU Munich, Munich, Germany.4 Pettenkofer School of Public Health, Munich, Germany.5 Institute of Health Economics and Health Care Management, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health (GmbH), Ingolst\u00e4dter Landstra\u00dfe 1, 85764 Neuherberg, Germany.The original affiliations were published as:1 Department of Sport and Health Sciences, Technical University of Munich Georg-Brauchle-Ring 60/62 80992 Munich, Germany2 Institute for Medical Information Processing, Biometry and Epidemiology, LMU Munich Marchioninistrasse 17 80336 Munich, Germany3 Pettenkofer School of Public Health Munich, Germany4 Munich School of Management and Munich Center of Health Sciences, LMU Munich, Munich, Germany5 Institute of Health Economics and Health Care Management, Helmholtz Zentrum M\u00fcnchenResearch Center for Environmental Health (GmbH) Ingolst\u00e4dter Landstra\u00dfe 1 85764 Neuherberg, GermanyThe correction affiliations are:The original article has been updated."} +{"text": "Due to a production error, there was an error in the order of the authors. The EVAN group should be listed as the 8th author.The publisher also wishes to correct the affiliations for Nathalie Godart. The city for affiliation 7 was also corrected to Paris. The corrected author and affiliation lists appear below.1,2,3\u2020, Agathe Raynal4\u2020, Lama Mattar5, Christophe Lalanne6, France Hirot7,8, Caroline Huas7,9, Jeanne Duclos10,11, EVHAN group, Sylvie Berthoz8,12\u2021 and Nathalie Godart7,8,9,13*\u2021Elise Riquin1 Department of Child and Adolescent Psychiatry, Centre Hospitalier Universitaire d'Angers [Angers University Hospital], Angers, France2 Laboratory of Psychology, LPPL EA4638, University of Angers, Angers, France3 Adolescent and Young Adult University Hospital Department of the Health Foundation of Students of France, Centre Pierre Daguet, Sabl\u00e9-sur-Sarthe, France4 Department of Child and Adolescent Psychiatry, CH du Rouvray-CHU de Rouen, Rouen, France5 Nutrition Division, Department of Natural Sciences, School of Arts and Sciences-Lebanese American University, Beirut, Lebanon6 Universit\u00e9 Paris Diderot [Paris Diderot University], Paris Sorbonne Cit\u00e9, Paris, France7 CESP, Univ. Paris-Sud, UVSQ, INSERM U 1178, Universit\u00e9 Paris-Saclay [Paris-Saclay University], Paris, France8 Department of Psychiatry for Adolescents and Young Adults, Institut Mutualiste Montsouris, Paris, France9 Adolescent and Young Adult University Hospital Department of the Health Foundation of Students of France, Paris, France10 Univ. Lille, CNRS, CHU Lille, UMR 9193\u2014SCALab\u2014Cognitive and Affective Sciences, Lille, France11 H\u00f4pital Saint Vincent de Paul, GHICL, D\u00e9partement de Psychiatrie, Paris, France12 Univ. Bordeaux INCIA CNRS UMR 5287, Bordeaux, France13 UFR des Sciences de la Sant\u00e9 Simone Veil [Simone Veil Health Science Training and Research Unit], Universit\u00e9 de Versailles Saint-Quentin-en-Yvelines [Versailles Saint-Quentin-en-Yvelines University], Versailles, FranceThe publisher apologizes for this mistake. The original article has been updated."} +{"text": "Due to a production error, there were errors in the affiliations in the originally published article. Instead of1,2,3, Juhua Liu4, Caihong Jia4, Wei Hu4, Shun Song1,2,3*, Biyu Xu4* and Zhiqiang Jin4*\u201cYi Xu1Key Laboratory of Genetic Improvement of Bananas, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China2Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China3Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, China4Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China\u201d,the affiliations should have been presented as1,3,4, Juhua Liu2, Caihong Jia2, Wei Hu2, Shun Song1,3,4*, Biyu Xu2* and Zhiqiang Jin2*\u201cYi Xu1Key Laboratory of Genetic Improvement of Bananas, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China2Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China3Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China4Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, China\u201d.The publisher apologizes for this mistake. The original article has been updated."} +{"text": "Cell Death and Disease 10.1038/s41419-021-04016-9, published online 27 July 2021Correction to: The original version of this article unfortunately contained a mistake. Due to a typesetting error the affiliations were incorrect. We apologize for the mistake. The correct affiliations are:Zhong-xin Jiang1, 2, 3, \u2020, Yi-ning Wang2, \u2020, Zi-yuan Li2, \u2020, Zhi-hui Dai4, \u2020, Yi He2, Kun Chu2, Jia-yi Gu2, Yi-Xuan Ji2, Ning-xia Sun2,*, Fu Yang4,*, Wen Li1, 2,*Affiliations:1 Center for Reproductive Medicine and Fertility Preservation Program, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030 Shanghai, China2 The Center of Reproductive Medicine, Shanghai Changzheng Hospital, Naval Medical University, 200003 Shanghai, China3 Obstetrics and Gynecology Department, The 1st Naval hospital of Southern Theater Command, 4 The Department of Medical Genetics, Naval Medical University, 200433 Shanghai, China524005 Guangdong, China\u2020These authors contributed equally.* Corresponding author.In addition, there was a misspelling in the footnote of Figure 1C: form should be changed to from. The original article has been corrected."} +{"text": "In the original publication an error1 Biomedical Imaging Research Institute, Cedars Sinai Medical Center, Los Angeles, CA2 Department of Radiology, Zhongshan Hospital, Fudan University; Shanghai, 200032, China7 Department of Medical Imaging, Shanghai Medical School, Fudan University and Shanghai Institute of Medical Imaging, Shanghai, 200032, ChinaIncorrect affiliations:1 Biomedical Imaging Research Institute, Cedars Sinai Medical Center, Los Angeles, CA2 Department of Radiology, Zhongshan Hospital, Fudan University; Shanghai, 200032, China3 Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China.Correct affiliations:"} +{"text": "Scientific Reports 10.1038/s41598-021-84995-z, published online 31 March 2021Correction to: The original version of this Article contained errors in the author list as a previous version of the author list was erroneously published.The order of author names was incorrect. Chien-An Sun, Chen Lin, and Hung-Che Lin were omitted from the author list. In addition, Yu-Jia Chang was omitted as an equally contributing author. The original author list and affiliations appear below.1,2,3,4,16, Huan-Ming Hsu5,6,16, Chi-Wen Chang7,8,16, Yuan-Kuei Li9,7,16, Yu-Jia Chang10,16, Jyh-Cherng Yu5, Chien-Ting Chen1, Chen-En Jian1, Meng-Chiung Lin12, Kang-Hua Chen7,11, Ming-Hao Kuo13, Chia-Shiang Cheng14, Ya-Ting Chang15, Yi-Syuan Wu14, Hao-Yi Wu15, Ya-Ting Yang15, Je-Ming Hu5 & Yu-Tien Chang1,2Chi-Ming Chu1Division of Biostatistics and Informatics, Department of Epidemiology, School of Public Health, National Defense Medical Center, No. 161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan. 2Big Data Research Center, Fu-Jen Catholic University, New Taipei City, Taiwan. 3Department of Public Health, China Medical University, Taichung City, Taiwan. 4Department of Healthcare Administration and Medical Informatics College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan. 5Division of General Surgery, Department of Surgery, TriService General Hospital, National Defense Medical Center, Taipei, Taiwan. 6Department of Surgery, Songshan Branch of Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan. 7School of Nursing, College of Medicine, Chang Gung University, Taoyuan, Taiwan. 8Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan. 9Division of Colorectal Surgery, Department of Surgery, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan. 10Cancer Research Center and Translational Laboratory, Department of Medical Research, Taipei Medical University Hospital, Taipei, Taiwan. 11Department of Nursing, Chang Gung Memorial Hospital, TaoYuan, Taiwan. 12Division of Gastroenterology, Department of Medicine, Taichung Armed Forces General Hospital, Taichung, Taiwan. 13Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan. 14Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan. 15School of Public Health, National Defense Medical Center, Taipei, Taiwan. 16These authors contributed equally: Yuan-Kuei Li, Huan-Ming Hsu, Meng-Chiung Lin, Chi-Wen Chang, and Chi-Ming Chu.The original Article has been corrected."} +{"text": "Bender1, 2, Andrea Th\u00fcrmer3, Guido Werner1, 2 and Birgit Strommenger1, 2*In the published article, there was an error in affiliations. Instead of \u201cRobert E. Weber1 Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany2 Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany3 Methodology and Research Infrastructure, Bioinformatics, Robert Koch-Institute, Berlin, Germany\u201d, it should be1, Stephan Fuchs2, Franziska Layer1, Anna Sommer1, Jennifer K. Bender1, Andrea Th\u00fcrmer3, Guido Werner1 and Birgit Strommenger1\u201cRobert E. Weber1 Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany2 Methodology and Research Infrastructure, Bioinformatics, Robert Koch-Institute, Berlin, Germany3 Methodology and Research Infrastructure, Genome Sequencing, Robert Koch-Institute, Berlin, Germany\u201dThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "In \u201cText Messaging Versus Email Messaging to Support Patients With Major Depressive Disorder: Protocol for a Randomized Hybrid Type II Effectiveness-Implementation Trial\u201d :e29495) the authors noted two errors.1. In the originally published paper, author affiliations 1 and 2 were numbered incorrectly. The numbering of these affiliations has been switched in the corrected paper.2. The equal contribution symbol '*' for author Felix Osiogo has been removed.The complete list of authorship and affiliations was originally published as follows:1*, BSc, MSc; Reham Shalaby1*, MD; Ejemai Eboreime1, MD, PhD; Adegboyega Sapara1, PhD, FRCPC; Nnamdi Nkire1, MD, MBBS, DHSM, DCP, FRAMI; Rajan Chawla1, MBBS, CCT, MSC, MRCPsych; Chidi Chima1, MBBS, MPH, PhD; Michael Achor1, MD, MSC, FRCPC; Felix Osiogo1*, FRCPC, FWACS, CCT-UK, MBBS; Pierre Chue1, MD, DABPN, MRCPsych, FRCPC; Andrew J Greenshaw1, PhD, FRSA; Vincent Israel Agyapong1,2, MD, PhD, FRCPC, FRCPsychMedard Kofi Adu1Department of Psychiatry, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada2Department of Psychiatry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada*these authors contributed equallyThis has been corrected to the following:1*, BSc, MSc; Reham Shalaby1*, MD; Ejemai Eboreime1, MD, PhD; Adegboyega Sapara1, PhD, FRCPC; Nnamdi Nkire1, MD, MBBS, DHSM, DCP, FRAMI; Rajan Chawla1, MBBS, CCT, MSC, MRCPsych; Chidi Chima1, MBBS, MPH, PhD; Michael Achor1, MD, MSC, FRCPC; Felix Osiogo1, FRCPC, FWACS, CCT-UK, MBBS; Pierre Chue1, MD, DABPN, MRCPsych, FRCPC; Andrew J Greenshaw1, PhD, FRSA; Vincent Israel Agyapong1,2, MD, PhD, FRCPC, FRCPsychMedard Kofi Adu1Department of Psychiatry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada2Department of Psychiatry, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada*these authors contributed equallyThe correction will appear in the online version of the paper on the JMIR Publications website on November 5, 2021, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:1,2*, Nguyen Minh Tam1*, Vo Tam3, Huynh Van Minh3, Nguyen Phuong Hoa4, Stefan Heytens5, Anselme Derese5, Dirk Devroey2Ho Anh Hien1 Department of Family Medicine, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam2 Department of Family Medicine and Chronic Care, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium3 Department of Internal Medicine, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam4 Department of Family Medicine, Hanoi Medical University, Hanoi, Vietnam5 Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium"} +{"text": "In \u201cRehabilitation Needs, Service Provision, and Costs in the First Year Following Traumatic Injuries: Protocol for a Prospective Cohort Study\u201d :e25980), several errors were noted in author affiliations.1. In the originally published paper, author affiliations 1 and 3 were the same. Therefore, \u201cOslo University Hospital HF\u201d has been corrected to \u201cOslo University Hospital\u201d in this affiliation for the following authors: Helene Lundgaard Soberg, Mari S Rasmusssen, Torgeir Hellstr\u00f8m, Nada Andelic. The remaining affiliations have been renumbered as necessary.2. For Audny Anke, the originally published author affiliation was:Department of Cardiothoracic and Vascular Surgery, University Hospital of North Norway, Troms\u00f8, NorwayThis has been corrected to the following:Faculty of Health Sciences, Department of Clinical Medicine, University of Troms\u00f8, The Arctic University of Norway, Troms\u00f8, NorwayThe following new affiliation has also been added for this author:Institute of Health and Society, Research Centre for Habilitation and Rehabilitation Models & Services (CHARM), Faculty of Medicine, University3. For Eline Aas, the originally published author affiliation was:Department of Health Management and Health Economics, Institute for Health and Society, University of Oslo, Oslo, NorwayThis has been corrected to:Department of Health Management and Health Economics, Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo, Norway4. For Marianne L\u00f8vstad, the originally published author affiliation was:Department of Psychology, University of Oslo, Oslo, NorwayThis has been corrected to the following:Department of Psychology, Faculty of Social Sciences, University of Oslo, Oslo, Norway5. For Kristian Bartnes, the originally published author affiliation was:Institute of Clinical Medicine, University of Troms\u00f8, The Arctic University of Norway, Troms\u00f8, NorwayThis has been corrected to the following:Faculty of Health Sciences, Department of Clinical Medicine, University of Troms\u00f8, The Arctic University of Norway, Troms\u00f8, Norway 6. For Christoph Sch\u00e4fer, the originally published author affiliation was:Department of Cardiothoracic and Vascular Surgery, University Hospital of North Norway, Troms\u00f8, NorwayThis has been corrected to the following:Faculty of Health Sciences, Department of Clinical Medicine, University of Troms\u00f8, The Arctic University of Norway, Troms\u00f8, NorwayThe following new affiliation has also been added for this author:Department of Physical Medicine and Rehabilitation, Oslo University Hospital, Oslo, NorwayIn the originally published paper, the complete listing of authors and affiliations was as follows:1,2*, PhD; H\u00e5kon \u00d8greid Moksnes 3,4*, MD; Audny Anke 5,6, MD, PhD; Olav R\u00f8ise 7,8, MD, PhD; Cecilie R\u00f8e 3,7, MD, PhD; Eline Aas 9, PhD; Unni Sveen 2,3, PhD; Christine Gaarder 7,10, MD, PhD; P\u00e5l Aksel N\u00e6ss 7,10, MD, PhD; Eirik Helseth 7,11, MD, PhD; Hilde Margrete Dahl 7,12, MD, PhD; Frank Becker 7,13, MD, PhD; Marianne L\u00f8vstad 13,14, PhD; Kristian Bartnes 6,15, MD, PhD; Christoph Sch\u00e4fer 5,6, MD; Mari S Rasmussen 1,4, MSc; Paul Perrin 16, PhD; Juan Lu 17, MD, PhD; Torgeir Hellstr\u00f8m 1, MD, PhD; Nada Andelic 1,4*, MD, PhDHelene Lundgaard Soberg 1Department of Physical Medicine and Rehabilitation, Oslo University Hospital HF, Oslo, Norway 2Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway 3Department of Physical Medicine and Rehabilitation, Oslo University Hospital, Oslo, Norway4Institute of Health and Society, Research Centre for Habilitation and Rehabilitation Models & Services (CHARM), Faculty of Medicine, University of Oslo, Oslo, Norway5Department of Rehabilitation, University Hospital of North Norway, Troms\u00f8, Norway6Department of Cardiothoracic and Vascular Surgery, University Hospital of North Norway, Troms\u00f8, Norway7Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway8Division of Orthopaedic Surgery, Oslo University Hospital, Oslo, Norway 9Department of Health Management and Health Economics, Institute for Health and Society, University of Oslo, Oslo, Norway10Department of Traumatology, Oslo University Hospital, Oslo, Norway11Department of Neurosurgery, Oslo University Hospital, Oslo, Norway12Department of Child Neurology, Oslo University Hospital, Oslo, Norway13Sunnaas Rehabilitation Hospital, Nesoddtangen, Norway14Department of Psychology, University of Oslo, Oslo, Norway15Institute of Clinical Medicine, University of Troms\u00f8, The Arctic University of Norway, Troms\u00f8, Norway16Departments of Psychology and Physical Medicine and Rehabilitation, Virginia Commonwealth University, Richmond, VA, United States17Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States*these authors contributed equallyCorresponding Author:Helene Lundgaard Soberg, PhDDepartment of Physical Medicine and RehabilitationOslo University Hospital HFPO Box 4956 NydalenOslo, N-0424NorwayPhone: 47 951009637Email: h.l.soberg@medisin.uio.noThe complete corrected list of authors and affiliations is as follows:1,2*, PhD; H\u00e5kon \u00d8greid Moksnes 1,3*, MD; Audny Anke 3,4,5, MD, PhD; Olav R\u00f8ise 6,7, MD, PhD; Cecilie R\u00f8e 1,7, MD, PhD; Eline Aas 8, PhD; Unni Sveen 1,2, PhD; Christine Gaarder 7,9, MD, PhD; P\u00e5l Aksel N\u00e6ss 7,9,MD, PhD; Eirik Helseth 7,10 MD, PhD; Hilde Margrete Dahl 7,11, MD, PhD; Frank Becker 7.12, MD, PhD; Marianne L\u00f8vstad 12,13, PhD; Kristian Bartnes 5,14, MD, PhD; Christoph Sch\u00e4fer 1,4,5, MD; Mari S Rasmussen 1,3, MSc; Paul Perrin 15, PhD; Juan Lu 16, MD, PhD; Torgeir Hellstr\u00f8m 1, MD, PhD; Nada Andelic 1,3*, MD, PhDHelene Lundgaard Soberg 1Department of Physical Medicine and Rehabilitation, Oslo University Hospital, Oslo, Norway2Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway3Institute of Health and Society, Research Centre for Habilitation and Rehabilitation Models & Services (CHARM), Faculty of Medicine, University of Oslo, Oslo, Norway4Department of Rehabilitation, University Hospital of North Norway, Troms\u00f8, Norway5Faculty of Health Sciences, Department of Clinical Medicine, University of Troms\u00f8, The Arctic University of Norway, Troms\u00f8, Norway6Division of Orthopaedic Surgery, Oslo University Hospital, Oslo, Norway7Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway8Department of Health Management and Health Economics, Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo, Norway9Department of Traumatology, Oslo University Hospital, Oslo, Norway10Department of Neurosurgery, Oslo University Hospital, Oslo, Norway11Department of Child Neurology, Oslo University Hospital, Oslo, Norway12Sunnaas Rehabilitation Hospital, Nesoddtangen, Norway13Department of Psychology, Faculty of Social Sciences, University of Oslo, Oslo, Norway14Department of Cardiothoracic and Vascular Surgery, University Hospital of North Norway, Troms\u00f8, Norway15Departments of Psychology and Physical Medicine and Rehabilitation, Virginia Commonwealth University, Richmond, VA, United States16Division of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, Richmond, VA, United States*these authors contributed equallyCorresponding Author:Helene Lundgaard Soberg, PhDDepartment of Physical Medicine and RehabilitationOslo University HospitalPO Box 4956 NydalenOslo, N-0424NorwayPhone: 47 951009637Email: h.l.soberg@medisin.uio.noThe correction will appear in the online version of the paper on the JMIR Publications website on March 23, 2022, together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories."} +{"text": "Erratum for Volume 12, no. 3, e00560-21, 2021, In"} +{"text": "In the manuscript \u201cNeurocognitive study of school performance among Moroccan high schoolstudents: The role of working memory\u201d, DOI: 10.1590/1980-57642018dn13-020013, publishedin the Dement Neuropsychol. 2019;13(2):232-237, on page 232.Where it reads:1, Ahmed Ahami1, Khaoula Mammad1Aziz Eloirdi1Team of Clinical Neuroscience, Cognitive and Health, Laboratory of Biologyand Health, Faculty of Science, IbnTofail University, BP. 133, Kenitra, Morocco.It should read:1, Ahmed Ahami2, Khaoula Mammad2Aziz Eloirdi1Team of Clinical Neuroscience, Cognitive and Health, Laboratory of Biologyand Health, Faculty of Science, IbnTofail University, BP. 133, Kenitra, Morocco and theHassan First University, Sports Science Institute, Settat, Marroco.2Team of Clinical Neuroscience, Cognitive and Health, Laboratory of Biologyand Health, Faculty of Science, IbnTofail University, BP. 133, Kenitra, Morocco."} +{"text": "The article by Liu et al. was publThe author affiliation is shown as:\u201cYulan Liu, Jun Yu, Xinrui Wang, Jicheng Dong\u201dPsychiatric Department, Qingdao Mental Health Center, Qingdao University, Qingdao City, ChinaThis should have appeared as:1, Jun Yu2, Xinrui Wang1, Jicheng Dong1\u201d\u201cYulan Liu1Psychiatric Department, Qingdao Mental Health Center, Qingdao University, Qingdao City, China2Psychiatric Department, Laizhou Glory Solider's Hospital in Yantai City, Laizhou, 261400, China"} +{"text": "Correction to:Experimental and Molecular Medicine10.1038/s12276-019-0336-x published online 28 November 2019After online publication of this article, the authors noticed an error in the Affiliation section.The correct statement of this article should have read as below.\u201cTwo of authors\u2019 affiliations was misprinted. Authors' affiliations list should be corrected as follows:1,2, Eunjeong Seo1, Jin Won Kim1, Hyung Wook Kim2,10, Hong Lim Kim3, Kyuryung Kim4,5, Tae-Min Kim4,5, Ji Hyeon Ju6, Ivan G. Gomez7, Kohei Uchimura8, Benjamin D. Humphreys8, Chul Woo Yang2, Jae Yeon Lee9, Jin Kim1, Dong Woo Cho9,*, Benjamin S. Freedman7,* and Yong Kyun Kim1,2,10,*Sun Ah Nam1Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea2Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea3Integrative Research Support Center, College of Medicine, The Catholic University of Korea, Seoul, Korea4Cancer Research Institute, College of Medicine, The Catholic University of Korea and Department of Medical Informatics, College of Medicine, The Catholic University of Korea5Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea6Catholic iPSC Research Center, and Division of Rheumatology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea7Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.8Division of Nephrology, Department of Medicine, and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA9Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, South Korea10Department of Internal Medicine, College of Medicine, The Catholic University of Korea, St. Vincent\u2019s Hospital, Suwon, Korea\u201dThe authors apologize for any inconvenience caused."} +{"text": "Following publication of the original article , the autPeng Cheng1, 2*, Jianwei Xie1, Zhiyong Liu1, Jian Wang2*1Department of Neurology, Second Naval Hospital of Southern Theater Command , Sanya 572000, China.2Institute of Neurosciences, Fourth Military Medical University, Xi\u2019an 7110032, China.The affiliations has been updated above and the original article has been"} +{"text": "Following publication of the original article , the autIncorrect2 Translational Oncology, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, GermanyBenedikt Brors affiliations\u20141,2,5Correct2 Division of Translational Medical Oncology, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, GermanyBenedikt Brors affiliations\u20141,5"} +{"text": "Kull61, E. Mel\u00e9n61, M. Wickman62, G. De Vries63, M. van Eerd63, I. Agache64, I. J. Ansotegui65, S. Bosnic\u2010Anticevich66E. Eller60Odense Research Center for Anaphylaxis, ORCA, Dept. Dermatology and Allergy Center, Odense University hospital, Denmark.61Department of Clinical Science and Education, S\u00f6dersjukhuset, Karolinska Institutet, Sach's Children and Youth Hospital, S\u00f6dersjukhuset, Sweden.62Centre for Clinical Research S\u00f6rmland, Uppsala University, Eskilstuna, Sweden.63Peercode BV, Geldermalsen, The Netherlands.64Transylvania University Brasov, Brasov, Romania.65Department of Allergy and Immunology, Hospital Quir\u00f3nsalud Bizkaia, Erandio, Spain.66Quality Use of Respiratory Medicine Group, Woolcock Institute of Medical Research, The University of Sydney, and Sydney Local Health District, Sydney, NSW, Australia."} +{"text": "After publication of the original article , an erroThe correct affiliations list is given below:1,*, Marina Kazimi2, Philipp K\u00f6rner2, Thomas Attin2 and Florian Just Wegehaupt2.Blend Hamza1Clinic of Orthodontics and Pediatric Dentistry, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland;2Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zurich, Switzerland.The original article has been corrected."} +{"text": "The correct spelling is **Hesham Sadek**.An author name was incorrectly spelled as **Incorrect version**1,2\u2020, Uday Chintapula1,2\u2020, Aneetta E. Kuriakose1,2, Samantha Laboy1, Thuy Thi Dang Truong1, LeNaiya A. Kydd1, Justyn Jaworski1, Zui Pan3, Hashem Sadek2, Kytai T. Nguyen1,2* and Juhyun Lee1,2*Victoria L. Messerschmidt1 Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States2 Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States3 College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, TX, United States**CORRECT version**1,2\u2020, Uday Chintapula1,2\u2020, Aneetta E. Kuriakose1,2, Samantha Laboy1, Thuy Thi Dang Truong1, LeNaiya A. Kydd1, Justyn Jaworski1, Zui Pan3, Hesham Sadek2, Kytai T. Nguyen1,2* and Juhyun Lee1,2*Victoria L. Messerschmidt1 Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States2 Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States3 College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, TX, United StatesThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "After publication of the original article , it was The updated figures Figs. , 2, 3, 4"} +{"text": "PLoS Medicine, volume 3, issue 7: DOI: 10.1371/journal.pmed.0030228In In Table 1, column 3, last row, the value 113,919 is incorrect; it should be 117,964."} +{"text": "There are errors in the author affiliations. Affiliation 1 and affiliation 3 should not be separated. The affiliations should appear as shown here:1,2, Yaling Jing1,2, Qiang Wen1,2, Xianping Ding1,2, Tao Wang1,2, Xuemei Mu1,2, Yuwei Chenzhang1,2, Man Cao1,2Zuyi Chen1 Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China, 2 Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China."} +{"text": "Present: Due to an error made during submission of the revised manuscript, Dr. Chi-Jung Liang's name was spelled incorrectly.Corrected: The correct author list for this manuscript is provided below. Authors sincerely apologize for this oversight.38029-45. doi: 10.18632/oncotarget.5703.Original article: Oncotarget. 2015; 6(35): 1,*, Wei-Hsin Lin1,2,*, Yi-Wen Chang1,*, Kuo-Chen Wei3, Chi-Jung Liang1, Shin-Cheh Chen4 and Jia-Lin Lee1,5Ying-Jhen Su1 Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan2 Department of Orthopedics, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan3 Department of Neurosurgery, Chang-Gung Memorial Hospital, Linkou, Taiwan4 Department of Surgery, Chang-Gung Memorial Hospital, Linkou, Taiwan5 Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan* These authors have contributed equally to this work"} +{"text": "We carried out a tridimensional, axial, coronal and sagittal reconstruction Figures . During -5,7,9 traction or manual reduction,,4,7,9 with the use of analgesic, physiotherapy,9 or surgery.,7,9Correct diagnosis is crucial for adequate management. Treatment can be conservative using immobilization,"} +{"text": "The order of affiliations for all authors is incorrect. Please see the author list, with the correctly ordered affiliations indicated, and the correctly ordered list of affiliations below.2,3, Xingchang Zhang1,2, Qing Zhen2,3, Fengpeng Han1,2.Mingming Li1 State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling 712100, PR China2 Institute of Soil and Water Conservation\uff0cChinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, PR China 3 University of Chinese Academy of Sciences, Beijing 100049, PR China"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Jana Z\u00e1rubov\u00e12, Barbora Mikulov\u00e12,3,4, Elena Filov\u00e12, Ji\u0159ina B\u00e1rtov\u00e15, Lucie Ba\u010d\u00e1kov\u00e12, Eduard Brynda1Ond\u0159ej Kaplan1 Institute of Macromolecular Chemistry, Czech Academy of Sciences, CZ-162 06, Prague, Czech Republic, 2 Institute of Physiology, Czech Academy of Sciences, CZ-142 20, Prague, Czech Republic, 3 Institute of Microbiology, Czech Academy of Sciences, CZ-142 20, Prague, Czech Republic, 4 Faculty of Science, Charles University in Prague, CZ-128 40, Prague, Czech Republic, 5 School of Dental Medicine, General University Hospital in Prague, CZ-128 08, Prague, Czech Republic"} +{"text": "This article has been corrected: The correct author affiliations are given below:Xin-Xing Zhu1,2,*, Ya-Wei Yan1,2,*, Demeng Chen3, Chun-Zhi Ai1, Xifeng Lu4, Shan-Shan Xu1, Shan Jiang1, Gen-Shen Zhong5, Dong-Bao Chen6and Yi-Zhou Jiang11 Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China2 Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China3 School of Dentistry, University of California, Los Angeles, CA, USA4 Department of Physiology, Center for Diabetes, Obesity and Metabolism, Shenzhen University Health Science Center, Shenzhen University, Shenzhen, Guangdong, China5 Henan Key Laboratory of Neural Regeneration and Repairment, The First affiliated Hospital of Xinxiang Medical University, Weihui, Henan, China6 Department of Obstetrics and Gynecology, University of California, Irvine, CA, USA* These authors contributed equally to this workhttps://doi.org/10.18632/oncotarget.11538Original article: Oncotarget. 2016; 7:63561-63570."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Mong-Liang Lu2,3, Ming-Chyi Huang1,2, Po-Yu Chen1,4, Yen-Kuang Lin5, Shih-Ku Lin1,2, Chun-Hsin Chen2,3Chih-Chiang Chiu1 Department of Psychiatry, Taipei City Psychiatric Center, Taipei City Hospital, Taipei, Taiwan, 2 Department of Psychiatry, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, 3 Department of Psychiatry, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan, 4 Graduate Institute of Medical Science, School of Medicine, Taipei Medical University, Taipei, Taiwan, 5 Biostatistics Center, Taipei Medical University, Taipei, Taiwan"} +{"text": "An affiliation for the first author was incorrectly omitted. The affiliations should appear as shown here:1,2,3, Hai Gu3, Weiqing Ning4, Hua Zhou5, Hengjin Dong1*Hua You1 Center for Health Policy Studies, School of Medicine, Zhejiang University, Hangzhou, China2 Department of Social Medicine and Health Education, School of Public Health, Nanjing Medical University, Nanjing, China,3 Center for Health Management and Care Security Policy Research, School of Government, Nanjing University, Nanjing, China,4 Department of Women Health Care, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China,5 Department of Child Health Care, Maternal and Child Health Hospital of Changzhou, Changzhou, Jiangsu, China"} +{"text": "Mycobacterium kansasii is a nontuberculous mycobacterial (NTM) pathogen, frequently isolated from clinical samples and responsible for a large part of NTM infections in the human population. Here, we report the draft genome sequences of 12 M.\u00a0kansasii strains isolated from clinical and host-associated sources from the Netherlands, Germany, and Poland. Mycobacterium kansasii is one of the most significant nontuberculous mycobacterial (NTM) pathogens recovered from clinical specimens and is responsible for a large part of NTM infections in the human population adds more complexity to the clinical and epidemiological relevance of M.\u00a0kansasii isolations. Of the M.\u00a0kansasii subtypes, type I has been isolated most frequently from human sources and involved in the causation of NTM disease . The total lengths of the contigs for each genome, along with some basic clinical data regarding the strains, are presented in A total of 1,261,159, 1,274,864, 1,348,130, 1,609,452, 1,549,556, 1,498,034, 1,616,934, 1,386,880, 1,714,844, 1,390,906, 1,207,915, and 1,151,718 reads were obtained for strains NLA001000927, NLA001001166, NLA001001128, NLA001000449, NLA001000521, ATCC 25221, B11073207, B11063838, 7728, 6200, 7744, and 2193, respectively. The draft genomes of genotype I strains were M.\u00a0kansasii strains reported here are provided in The accession numbers of the draft genome sequences of the"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,4, Maria Viladrosa1,2,4, Pilar J\u00fcrschik1,4, Teresa Botigu\u00e91,4, Carmen Nu\u00edn1,4, Olga Masot1,4, Raquel Laved\u00e1n3Ana Laved\u00e1n1 Department of Nursing and Physiotherapy, University of Lleida, Lleida, Spain, 2 University Hospital Arnau de Vilanova, Lleida, Spain, 3 University Clinical Hospital Lozano Blesa, Zaragoza, Spain, 4 Health Care Research Group (GRECS), Biomedical Research Institute of Lleida, Spain."} +{"text": "The affiliation for the 25th author is incorrect. Matti Ristola is not affiliated with #19 but with #17 Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland. Please see the full, correct byline and affiliations below.1*, Chris Wymant1,2, Marion Cornelissen3, Astrid Gall4\u00a4, Margreet Bakker3, Daniela Bezemer5, Matthew Hall2, Mariska Hillebregt5, Swee Hoe Ong4, Jan Albert6,7, Norbert Bannert8, Jacques Fellay9,10, Katrien Fransen11, Annabelle J. Gourlay12, M. Kate Grabowski13, Barbara Gunsenheimer-Bartmeyer14, Huldrych F. G\u00fcnthard15,16, Pia Kivel\u00e4 17, Roger Kouyos15,16, Oliver Laeyendecker18, Kirsi Liitsola19, Laurence Meyer20, Kholoud Porter12, Matti Ristola17, Ard van Sighem5, Guido Vanham21, Ben Berkhout3, Paul Kellam22,23, Peter Reiss5,24, Christophe Fraser 1,2*, BEEHIVE collaboration\u00b6Fran\u00e7ois Blanquart1 Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom, 2 Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, 3 Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands, 4 Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom, 5 Stichting HIV Monitoring, Amsterdam, the Netherlands, 6 Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden, 7 Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden, 8 Division for HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany, 9 School of Life Sciences, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne, Lausanne, Switzerland, 10 Swiss Institute of Bioinformatics, Lausanne, Switzerland, 11 HIV/STI reference laboratory, WHO collaborating centre, Institute of Tropical Medicine, Department of Clinical Science, Antwerpen, Belgium, 12 Department of Infection and Population Health, University College London, London, United Kingdom, 13 Department of Epidemiology, John Hopkins University, Baltimore, Maryland, United States of America, 14 Department of Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany, 15 Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland, 16 Institute of Medical Virology, University of Zurich, Zurich, Switzerland, 17 Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland, 18 Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America, 19 Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland, 20 INSERM CESP U1018, Universit\u00e9 Paris Sud, Universit\u00e9 Paris Saclay, APHP, Service de Sant\u00e9 Publique, H\u00f4pital de Bic\u00eatre, Le Kremlin-Bic\u00eatre, France, 21 Virology Unit, Immunovirology Research Pole, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerpen, Belgium, 22 Kymab Ltd, Cambridge, United Kingdom, 23 Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom, 24 Department of Global Health, Academic Medical Center, Amsterdam, the Netherlands\u00a4 Current address: Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom\u00b6 Membership of the BEEHIVE collaboration is provided in the Acknowledgments.f.blanquart@imperial.ac.uk (FB); christophe.fraser@bdi.ox.ac.uk (CF)*"} +{"text": "Following publication of the original article it was b1,2,7*, Andrea Peloso1,2, Barbara Vischioni3, Denis Panizza3, Maria Rosaria Fiore3, Piero Fossati4, Viviana Vitolo3, Alberto Iannalfi3, Mario Ciocca3, Silvia Brugnatelli5, Tommaso Dominioni1,2, Dario Bugada6, Marcello Maestri1,2, Mario Alessiani1,2, Francesca Valvo3, Roberto Orecchia3,4 and Paolo Dionigi1,2Lorenzo CobianchiThis has now been updated on the BioMed Central website."} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2,3, Amin Doosti-Irani2,3, Ali Sanjari Moghaddam4, Mohadeseh Sani5, Milad Nazarzadeh6, Ehsan Mostafavi2,7*Erfan Ayubi1 Department of Epidemiology, School of Public Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran, 2 Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran, 3 Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran, 4 School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran, 5 School of Medicine, Zabol University of Medical Sciences, Zabol, Iran, 6 The collaboration center of meta-analysis research (ccMETA), Iranian Research Center on Healthy Aging, Sabzevar University of Medical Sciences, Sabzevar, Iran, 7 Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, IranThere are errors in the Corresponding Author\u2019s email address. The publisher apologizes for the error.The email address should appear as shown here:mostafavi@pasteur.ac.ir, mostafaviehsan@gmail.com*"} +{"text": "Tapia MD, Sow SO, Lyke KE, et al. Use of ChAd3-EBO-Z Ebola virus vaccine in Malian and US adults, and boosting of Malian adults with MVA-BN-Filo: a phase 1, single-blind, randomised trial, a phase 1b, open-label and double-blind, dose-escalation trial, and a nested, randomised, double-blind, placebo-controlled trial. Lancet Infect Dis 16: 31\u2013422016; \u2014In the lower panel of figure 2A, the y axis read 0, 1, 10, 100, 100, 1000, and 10\u2008000, whereas it should have read 0, 1, 10, 100, 1000, 10\u20080000, and 100\u2008000. The correction has been made online as of Dec 14, 2015, and the print version is correct."} +{"text": "The affiliations should appear as shown here: Teik Hwa Ong1 School of Postgraduate Studies, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia, 2 Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia, 3 School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia, 4 School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia.*Current address: School of Pharmacy, Taylors University, Selangor, Malaysia"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Chia-Kwung Fan3,4, Hong-Jeng Yu5, Chia-Chang Wu1,2, Kuan-Chou Chen1,2, Shih-Ping Liu5, Po-Ching Cheng3,4Chen-Hsun Ho1 Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, 2 Department of Urology, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan, 3 Department of Molecular Parasitology and Tropical Diseases, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, 4 Center for International Tropical Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, 5 Department of Urology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan"} +{"text": "Correction to:Cell Death and Disease (2017) 8, e2682; doi:10.1038/cddis.2017.100; published online 16 March 2017In the version of this article originally published, the following affiliation for Sang Chul Lee was incorrectly listed as 3 instead of 1.The correct affiliations are listed below:1,2,5, Seon-Jin Lee1,2,5, Hee Jun Cho1, Yun Sun Park1, Jong-Tae Kim1, Suk Ran Yoon1, Sang Chul Lee1, Jong-Seok Lim3, Bo-Yeon Kim4, Yong-Kyung Choe1 and Hee Gu Lee1,2Byung Moo Oh1Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea2Department of Biomolecular Science, University of Science and Technology (UST), Daejeon, Republic of Korea3Department of Biological Sciences, Sookmyung Women\u2019s University, Seoul, Republic of Korea4World Class Institute, Korea Research Institute of Bioscience and Biotechnology, Ochang, Republic of Korea5These authors contributed equally to this work.The corrected article appears online together with this erratum."} +{"text": "Present: Due to an error during submission of the revised manuscript, Dr. Jean Soulier's name was omitted from the author list.Corrected: Correct author list for this article is available below: Authors sincerely apologize for this oversight.13069-81. doi: 10.18632/oncotarget.7541.Original article: Oncotarget. 2016; 7(11): 1,2,3, Mariana Varna4,5,6, Jean-Paul Feugeas3,7, Aur\u00e9lie Sadoux1, Saliha Yahiaoui1, Marie-Pierre Podgorniak8, Geoffroy Leclert1, Sarra Mazouz Dorval3,9, Nicolas Dumaz1,3, Jean Soulier10,11, Anne Janin4,5,12, Samia Mourah1,3,8,* and C\u00e9leste Lebb\u00e91,2,3,*Julie Delyon1 INSERM UMR_S976, Paris, F-75010, France2 AP-HP, H\u00f4pital Saint-Louis, Department of Dermatology, Paris, F-75010, France3 Universit\u00e9 Paris-Diderot, Sorbonne Paris Cit\u00e9, Paris, F-75013, France4 INSERM UMR_S1165, Paris, F-75010, France5 Universit\u00e9 Paris-Diderot, Department of Pathology, UMR_S1165, Paris, F-75010, France6 UMR CNRS 8612, Institut Galien-UFR de Pharmacie, Universit\u00e9 de Paris-Sud, Ch\u00e2tenay-Malabry, F-92290, France7 INSERM UMR_1137, Paris, F-75010, France8 AP-HP, H\u00f4pital Saint-Louis, Laboratoire de Pharmacologie Biologique, Paris, F-75010, France9 AP-HP, H\u00f4pital Saint-Louis, Department of Plastic, Reconstructive and Esthetic Surgery, Paris, F-75010, France10 AP-HP, H\u00f4pital Saint-Louis, Department of Biological Hematology, Paris, F-75010, France11 Institute of Hematology (IUH), University Paris-Diderot, Paris, F-75010, France12 AP-HP, H\u00f4pital Saint-Louis, Department of Pathology, Paris, F-75010, France* These authors have contributed equally to this work"} +{"text": "The affiliation order is incorrect. The affiliations should appear as shown here:1,2, Xinping Li1, Wei Xie2Zhenhua Liu1 College of Bioresources Chemical and Materials Engineering, Shanxi University of Science and Technology, Xi\u2019an, Shanxi Province P. R. China, 2 School of Chemical Engineering, Wuzhou University, Wuzhou, Guangxi Province P. R. ChinaThe publisher apologizes for the error."} +{"text": "Friday, May 19 Room 5, Nagoya Congress Center [Bldg.1 4F Reception Hall (East)]Friday, May 19 Room 6, Nagoya Congress Center [Bldg.1 4F Reception Hall (West)]Friday, May 19 Room 6, Nagoya Congress Center [Bldg.1 4F Reception Hall (West)]Saturday, May 20 Room 5, Nagoya Congress Center [Bldg.1 4F Reception Hall (East)]Saturday, May 20 Room 6, Nagoya Congress Center [Bldg.1 4F Reception Hall (West)]Friday, May 19 Poster Room, Nagoya Congress Center [Underground carpark]Friday, May 19 Poster Room, Nagoya Congress Center [Underground carpark]Friday, May 19 Poster Room, Nagoya Congress Center [Underground carpark]Friday, May 19 Poster Room, Nagoya ter [Underground carpark]Friday, May 19 Poster Room, Nagoya Congress Center [Underground carpark]Friday, May 19 Poster Room, Nagoya Congress Center [Underground carpark]Friday, May 19 Poster Room, Nagoya Congress Center [Underground carpark]Friday, May 19 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]Saturday, May 20 Poster Room, Nagoya Congress Center [Underground carpark]"} +{"text": "Present: Due to an error made during submission of the revised manuscript, Dr. Giovanni Gravina's name was spelled incorrectly.Correct: The correct author list for this manuscript is provided below. Authors sincerely apologize for this oversight.5383-400. doi: 10.18632/oncotarget.6579.Original article: Oncotarget. 2016; 7(5):1,2,*, Giovanni Luca Gravina1,*, Xiaoming Ju2, Antonella Vetuschi1, Roberta Sferra1, Mathew C. Casimiro2, Simona Pompili1, Claudio Festuccia1, Alessandro Colapietro1, Eugenio Gaudio3, Ernesto Di Cesare1, Vincenzo Tombolini4, Richard G. Pestell2Francesco Marampon1 University of L'Aquila, Department of Biotechnological and Applied Clinical Sciences, L'Aquila, Italy2 Department of Cancer Biology, Medical Oncology and Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA3 Department of Human Anatomy, \u201cLa Sapienza\u201d University of Rome, Rome, Italy4 Department of Radiotherapy, Policlinico Umberto I \u201cSapienza\u201d University of Rome, Rome, Italy* These authors contributed equally to this work"} +{"text": "After publication of the original article , it cameAffiliation 1 incorrectly contained \u2018Clinical Research Unit\u2019, and the postcode was incorrect. Affiliation 5 was mistakenly included as \u2018Department of Medicine, Obesity Research & Management, University of Alberta\u2019.In addition, in the list of authors, Jeffrey A. Johnson should be affiliated to institutions 2 and 5, and Arya. A. Sharma should have been affiliation to institutions 3 and 5.The list of authors and affiliations is correct in this erratum. The \u2018Author details\u2019 section of the article should have read as follows:Author details1Department of Family Medicine, University of Alberta, Edmonton, AB, Canada T6G 2T4. 2School of Public Health, University of Alberta, Edmonton, AB, Canada T6G 2E3. 3Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1. 4Department of Anthropology, University of Alberta, Edmonton, AB, CanadaT6G 2H4. 5Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada T6G 2T9."} +{"text": "Emilie Dugast should be included in the author byline. She should be listed as sixth author.There are errors in the author affiliations. The affiliations should appear as shown here:1,2,3, Pauline Blery2,3,4, Micha\u00ebl Henoux1,2,3, J\u00e9r\u00f4me Guicheux2,3, Pierre Weiss2,3,4, Emilie Dugast5,6, Sophie Brouard5,6, Olivier Malard1,2,3, Florent Espitalier1,2,3Guillaume Michel1 Service d'O.R.L. et de chirurgie cervico-faciale, Centre Hospitalier Universitaire, Nantes, France, 2 INSERM, UMRS 791, LIOAD, Universit\u00e9 de Nantes, Nantes, France, 3 PHU4 OTONN, Centre Hospitalier Universitaire, Nantes, France, 4 Service d'Odontologie Restauratrice et Chirurgicale, Centre Hospitalier Universitaire, Nantes, France, 5 INSERM UMR 1064, ITUN, Universit\u00e9 de Nantes, Nantes, France, 6 Laboratoire d'immunologie (CIMNA), Centre Hospitalier Universitaire, Nantes, Francehttps://doi.org/10.1371/journal.pone.0178060The correct citation is: Michel G, Blery P, Henoux M, Guicheux J, Weiss P, Dugast E, et al. (2017) Bone marrow cell extract promotes the regeneration of irradiated bone. PLoS ONE 12(5): e0178060."} +{"text": "J Investig Med High Impact Case Rep. 2017;5(1):1-2. doi:10.1177/2324709616689106.Timlin H, Machireddy K, Petri M. Low Level of Haptoglobin in Lupus. The affiliation of second author, Kirthi Machireddy, is incorrect. The correct author byline and affiliations are given below.1, Kirthi Machireddy2, and Michelle Petri, MD, MPH1Homa Timlin, MD, MSc1Johns Hopkins University, Baltimore, MD, USA2University of the Sciences, Philadelphia, PA, USA"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Alireza Majdi1, Sarah K. McCann2, Javad Mahmoudi1, Manouchehr S. Vafaee1,3,4, Malcolm R. Macleod5Saeed Sadigh-Eteghad1 Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran, 2 Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom, 3 Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark, 4 Department of Psychiatry, Clinical Institute, University of Southern Denmark, Odense, Denmark, 5 Department of Clinical Neurosciences, The University of Edinburgh, Edinburgh, United Kingdom."} +{"text": "Martha L. Wall is not included in the author byline. She should be listed as the second author and is affiliated with the Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, United States of America. The contributions of this author are as follows: Analyzed the data.Please view the correct author byline, affiliations, and citation here:1, Martha L. Wall2, D. Emerson Ridley1, Freyja D. James3, Curtis C. Hughey1, E. Patrick Donahue3, Benoit Viollet4,5,6, Marc Foretz4,5,6, Jamey D. Young1,2, David H. Wasserman1,3Clinton M. Hasenour1 Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America, 2 Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, United States of America, 3 Mouse Metabolic Phenotyping Center, Vanderbilt University, Nashville, Tennessee, United States of America, 4 Inserm, U1016, Institut Cochin, Paris, France, 5 CNRS, UMR 8104, Paris, France, 6 Universit\u00e9 Paris Descartes, Sorborne Paris Cit\u00e9, Paris, Francehttps://doi.org/10.1371/journal.pone.0170382Hasenour CM, Wall ML, Ridley DE, James FD, Hughey CC, Donahue EP, et al. (2017) Liver AMP-Activated Protein Kinase Is Unnecessary for Gluconeogenesis but Protects Energy State during Nutrient Deprivation. PLoS ONE 12(1): e0170382."} +{"text": "The potential superior benefits of adaptive deep brain stimulation (aDBS) approachesBecause aDBS administration was never systematically assessed during prolonged stimulation sessions in more ecologic conditions, we tested unilateral aDBS delivered for 2 hours, with specific focus on the concurrent administration of levodopa treatment, in freely moving parkinsonian patients.We therefore randomly administered aDBS and cDBS through an external wearable prototypeF1,9 = 0.2, P > .05). When the patient was under the effect of both levodopa and DBS (stimON/medON), we observed a similar improvement on global motor symptoms regardless to the type of DBS . Throughout the entire experiment, we did not observe any serious adverse event specifically linked to DBS.The clinical scores were not significantly different between the 2 experimental sessions at baseline Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy2Department of Electronics, Computer Science and Systems, University of Bologna, Cesena, Italy3Department of Engineering and Architecture, University of Trieste, Trieste, Italy4Unit of Clinical Neurophysiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy5Dino Ferrari Center, Neuroscience Section, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy6Department of Neuroscience \u201cRita Levi Montalcini,\u201d University of Turin, Turin, Italy7Unit of Stereotactic Functional and Neuroendoscopic Neurosurgery, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy8Department of Health Sciences, University of Milan & Ospedale San Paolo, Milan, ItalyManuela Rosa, PhD,1) Research project: A. Conception, B. Organization, C. Execution; 2) Statistical Analysis: A. Design, B. Execution, C. Review and Critique; 3) Manuscript: A. Writing of the first draft, B. Review and Critique.M.R.: 1B, 1C, 2B, 3AM.A.: 1B, 1C, 2C, 3BSM: 1B, 2A, 2C, 3AF.C.: 1BG.A.: 1BA.D.F.: 1CL.L.: 3BE.S.: 3AA.M.: 2CM.L.: 1CP.M.R.: 1C, 3BA.P.: 1BAP and SM were consultant for Newronika srl in the last 12 months"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Jiaxin Chen1, Guibing He1Chuqian Chen1 Department of Psychology and Behavioral Sciences, Zhejiang University, Hangzhou, P.R. China, 2 Department of Social Work and Social Administration, the University of Hong Kong, Pokfulam, Hong Kong, SAR, P.R. China."} +{"text": "Present: Due to an error made during manuscript preparation, one of Dr. Ashraf Khalil's affiliations was omitted from the final version of the article.Corrected: The correct affiliation list for this manuscript is provided below. Publisher sincerely apologizes for this oversight.27674-87. doi: 10.18632/oncotarget.4876.Original article: Oncotarget. 2015; 6(29): 1,2,*, Seth M. Dever1,2,*, Nisha Gnawali1, Ashraf Khalil1,7, Amrita Sule1,2, Sarah E. Golding1, Elizabeth Rosenberg1, Aarthi Narayanan3, Kylene KehnHall3, Bo Xu4, Lawrence F. Povirk5, Kristoffer Valerie1,2,6Jason M. Beckta1 Department of Radiation Oncology, Virginia Commonwealth University, Richmond, VA, USA2 Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, USA3 National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, USA4 Cancer Research Department, Southern Research Institute, Birmingham, AL, USA5 Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA6 Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA7 Department of Biochemistry, National Liver Institute, Menoufiya University, Egypt* These authors have contributed equally to this work"} +{"text": "The author list in the original publication should h1,2, Pengfei Wang2, Han Xia2, Chuanzhi Zhao2, Lei Hou2, Changsheng Li2, Chao Gao1, Xingjun Wang1,2* and Shuzhen Zhao2*Ye ZhangThe author affiliations should have been as follows:1 School of Life Sciences, Shandong University, Jinan, Shandong 250100, People\u2019s Republic of China2 Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People\u2019s Republic of China"} +{"text": "This article unfortunThe author list was previously incorrectly presented as:1, Hend Fakhri NourEldin1, Heba Abusamra1, Nada Salem1, Elham Alhathli1, Joel Dudley2, Max Sanderford3, Laura B. Scheinfeldt3,4 and Sudhir Kumar1,3,4*Sajjad Karim1Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia. 2Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA. 3Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA. 4Department of Biology, Temple University, Philadelphia, PA 19122, USA."} +{"text": "State Laws Prohibiting Sales to Minors and Indoor Use of Electronic Nicotine Delivery Systems \u2014 United States, November 2014,\u201d on page 1149, in Figure 2, \u201cStates with and without laws prohibiting smoking and use of electronic nicotine delivery systems (ENDS) in indoor areas of private worksites, restaurants, and bars \u2014 United States, November 30, 2014,\u201d DC was incorrectly shaded. DC should have been shaded to indicate \u201cProhibits indoor smoking only.\u201dIn the report, \u201cAirport Exit and Entry Screening for Ebola \u2014 August\u2013November 10, 2014,\u201d on page 1165, in the Figure \u201cNumber of travelers arriving from Guinea, Liberia, and Sierra Leone who were screened for Ebola at U.S. airports, by state and county of destination \u2014 October 11\u2013November 10, 2014,\u201d for Minnesota, the numeral 82 should have been included in the outline for the number of travelers to that state.In the report, \u201cClinical Inquiries Regarding Ebola Virus Disease Received by CDC \u2014 United States, July 9\u2013November 15, 2014,\u201d errors occurred in the list of authors and their affiliations. Those should read as follows:In the report, \u201c1,2,3, Elissa Meites, MD2,4, Kathleen E. Fullerton, MPH2,5, Ute Str\u00f6her, PhD2,6, Luis Lowe, MS, MPH2,7, Mark Rayfield, PhD2,8, Dianna M. Blau, DVM, PhD2,6, Barbara Knust, DVM2,6, Jacqueline Gindler, MD2,9, Chris Van Beneden, MD2,10, Stephanie R. Bialek, MD2,11, Paul Mead, MD2,12, Alexandra M. Oster, MD2,13 (Author affiliations at end of text)Mateusz P. Karwowski, MD1Epidemic Intelligence Service, CDC; 2Epidemiology/Laboratory Task Force, 2014 Ebola Response Team, CDC; 3Division of Environmental Hazards and Health Effects, National Center for Environmental Health, CDC; 4Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, CDC; 5Division of Health Informatics and Surveillance, Center for Surveillance, Epidemiology, and Laboratory Services, CDC; 6Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, CDC; 7Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, CDC; 8Division of Global Disease Detection and Emergency Response, Center for Global Health, CDC; 9Global Immunization Division, Center for Global Health, CDC; 10Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, CDC; 11Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, CDC; 12Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC; 13Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, CDC (Corresponding author: Mateusz (Matt) P. Karwowski, ydh4@cdc.gov, 770-488-4397)"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Pei-Fang Su2, Kuan-Ya Chen2, Tung-Hee Tie3, Hsu-Cheng Ke3, Hau Chen3, Yu-Chi Su3, Yu-Chen Su3, Huang-Tz Ou4,5,6Meng-Hsing Wu1 Department of Obstetrics and Gynecology, College of Medicine and Hospital, National Cheng Kung University, Tainan, Taiwan, 2 Department of Statistics, National Cheng Kung University, Tainan, Taiwan, 3 School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan, 4 Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan, 5 Department of Pharmacy, College of Medicine, National Cheng Kung University, Tainan, Taiwan, 6 Department of Pharmacy, National Cheng Kung University Hospital, Tainan, Taiwan."} +{"text": "Present: Due to an error made by the authors while submitting a revision, Dr. Tuan Zea Tan was omitted from the list of authors.Corrected: Correct author list can be found below. Authors sincerely apologize for this oversight.39050-61. doi: 10.18632/oncotarget.5176.Original article: Oncotarget. 2015; 6(36): 1, Xiaoliang Qiu1, Hong Zhi Ma1, Miranda Yeung1, Shweta Aras1, Ivana de la Serna1, Fahd Al-Mulla2, Tuan Zea Tan3, Jean Paul Thiery3,4, Robert Trumbly1, Fan Xuan5, Hongjuan Cui5 and Kam C. Yeung1Ila Datar1 Department of Biochemistry and Cancer Biology, University of Toledo, College of Medicine, Health Science Campus, Toledo, OH, USA2 Kuwait University, Faculty of Medicine, Safat, Kuwait3 Cancer Science Institute of Singapore National University of Singapore, Center for Translational Medicine, Singapore, Singapore4 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore5 State Key Laboratory Of Silkworm Genome Biology, Chongqing, China"} +{"text": "In the original publication are erroIncorrect affiliation 4:Guangdong Provincial Center for Skin Diseases and Sexually Transmitted Infections Control, No. 2 Lujing Road, Guangzhou, China, 510095.Correct affiliation 4:Guangdong Provincial Center for Skin Diseases and Sexually Transmitted Infections Control Center, Dermatology Hospital, Southern Medical University, No. 2 Lujing Road, Guangzhou, China, 510095.Incorrect author affiliation:15, Dianmin Kang15Meizhen LiaoCorrect author affiliation:16, Dianmin Kang16Meizhen LiaoMissing affiliation 16:Shandong Provincial Center for Disease Control and Prevention, Jinan, China"} +{"text": "There were errors in the author affiliations. The affiliations should appear as shown here:1,2, Tai-Ho Hung3, Yen-Ho Wang4, Chii-Wann Lin1, Pei-Yi Wang2, Chun-Yen Lee2, Szu-Fu Chen2,5*Chien-Cheng Chen1 Institute of Biomedical Engineering, National Taiwan University Taipei, Taiwan, Republic of China, 2 Department of Physical Medicine & Rehabilitation, Cheng Hsin General Hospital, Taipei, Taiwan, Republic of China, 3 Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Taipei and College of Medicine, Chang Gung University, Taipei, Taiwan, Republic of China, 4 Department of Physical Medicine & Rehabilitation, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan, Republic of China, 5 Departments of Physiology and Biophysics, National Defense Medical Center, Taipei, Taiwan, Republic of China"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1,2, Li Zhang1,2, Xinfang Wang1,2, Qing L\u00fc1,2, Lin He1,2, Jing Wang1,2, Bin Wang1,2, Ling Li1,2, Li Yuan1,2, Jinfeng Liu1,2, Shuping Ge1,2,3, Mingxing Xie1,2Yali Yang1 Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China, 2 Hubei Province Key Laboratory of Molecular Imaging, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China, 3 The Heart Center, St. Christopher's Hospital for Children and Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America"} +{"text": "The ninth author's name is incorrect. The correct name is: Yutaka Suzuki.In the Funding section, the first grant number from JSPS KAKENHI is listed incorrectly. The correct grant number is: 26292020.There are errors in the author affiliations. The affiliations should appear as shown here:1,2,3, Magdi El-Sayed2, Shusei Sato3, Hideki Hirakawa4, Shin-ichi Ito1, Keisuke Tanaka5, Yoko Mine6, Nobuo Sugiyama6, Yutaka Suzuki7, Naoki Yamauchi1, Masayoshi Shigyo1Mostafa Abdelrahman1 College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi-City, Yamaguchi, Japan, 2 Botany Department, Faculty of Science, Aswan University, Aswan, Egypt, 3 Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai-City, Miyagi, Japan, 4 Kazusa DNA Research Institute, Kisarazu-City, Chiba, Japan, 5 NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-Ku, Tokyo, Japan, 6 Department of Agriculture, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi-City, Kanagawa, Japan, 7 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-City, Chiba, Japan"} +{"text": "AbstractRaptobaetopustenellus, Caenisluctuosa and Caenisrivulorum are recorded as new to the fauna of Mongolia, and there are new distribution records for Ameletusmontanus, Baetis (Acentrella) lapponica, Baetissibiricus, Baetis (Labiobaetis) attrebatinus, Centroptilumluteolum, Procloeonpennulatum, Ephemerellaaurivillii, Serratellasetigera, Ephemerasachalinensis, Ecdyonurus (Afronurus) abracadabrus, Cinygmulakurenzovi, Ecdyonurus (Afghanurus) vicinus and Epeorus (Belovius) pellucidus from the Mongolian Altai region. Baetisvernus and Ephemerellaaurivillii are the most frequently encountered species in this region.Streams in the Mongolian Altai Mountains are mostly fed from glaciers and are extreme conditions for mayflies because of high elevation, low temperatures and low annual precipitation. Previous information about mayflies of Western Mongolia is scarce, but with this study a total of 38 species belonging to 26 genera and subgenera and 8 families of mayflies has been recorded in the Mongolian Altai region. Study material was entirely imagos and collected from 78 sites during expeditions led by the Mongolian Aquatic Insect Survey in 2008, 2009 and 2010. Baetismongolicus tricolor by Early studies of the mayfly fauna from the Mongolian region date to 1940 by Kinji Imanishi , althougMost of the area of Western Mongolia is highly elevated, mostly dominated by the Mongolian Altai Mountains, which have permanent glacial snow at the highest points. The average altitude of the Mongolian Altai Mountains is about 3200\u20133500 m a.s.l. The air temperature of the warmest month in Mongolian Altai Mountains is 12.3 \u00b0C in the higher areas and 21.1 \u00b0C in the lower areas of the region . Thus, fCentral Asian Internal Watershed (CAIW) . Uvs nuur (\u201cnuur\u201d refers to lake in Mongolian) is the largest lake in Mongolia, with a drainage basin of 70712 km2. In addition to these there are several smaller freshwater and saltwater lakes (Uureg nuur) in the basin of Western Mongolia, namely Khovd, Bayan-Olgiy and Uvs. We collected a total of 2180 adult specimens from 78 sites and Caenisrivulorum Eaton, 1884 are new to the fauna of Mongolia, and there are new distribution records in Western Mongolia for 13 species: Ameletusmontanus Imanishi, 1930, Baetis (Acentrella) lapponica Bengtsson, 1912, PageBreakBaetis (Acentrella) sibiricus Kazlauskas, 1963, Baetis (Labiobaetis) attrebatinus Eaton, 1870, Centroptilumluteolum , Procloeonpennulatum , Ephemerellaaurivillii Bengtsson, 1909, Serratellasetigera , Ephemerasachalinensis Matsumura, 1911, Ecdyonurus (Afronurus) abracadabrus , Cinygmulakurenzovi , Ecdyonurus (Afghanurus) vicinus Demoulin, 1964, and Epeorus (Belovius) pellucidus . The following species list gives the specific localities where a species was found as site number (#), and Figure A total of 38 species, belonging to 26 genera and subgenera and 8 families of mayflies, are recorded in this study area lapponica Bengtsson, 1912 - # 31, 51, 59- * Baetis (Acentrella) sp. 1 - # 1, 2, 4, 24, 27, 31, 33, 43, 47, 53, 56, 63, 65, 72, 77- Baetis (Acentrella) sibiricus Kazlauskas, 1963 - # 3, 16, 34, 35, 49, 50- * Baetis (Labiobaetis) attrebatinus Eaton, 1870 - # 47, 70- * Baetisvernus Curtis, 1834 - # 2, 3, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 29, 32, 35, 37, 38, 40, 45, 51, 52, 53, 56, 59, 61, 62, 63, 71- Baetis sp. 1 - # 1, 3, 15, 18, 24, 41, 60, 62, 65, 66, 68- Baetopus sp. 1 - # 60, 64- Centroptilumluteolum - # 31, 37, 39- * Procloeonpennulatum - # 59, 60, 61, 64, 66- * Procloeon sp. 1 - # 13- Pseudocentroptilum sp. 1 - # 3, 22, 43, 48, 57- Pseudocloeon sp. 1 - # 8, 16, 17- Raptobaetopustenellus Albadra, 1878 - # 57, 61, 63, 67, 71- ** CaenidaeCaenisluctuosa - # 16, 53- ** Caenisrivulorum Eaton, 1884 - # 13- ** Caenisrobusta Eaton, 1884 - # 53, 58- EphemerellidaeDrunellatriacanhta - # 23, 41- Ephemerellaaurivillii Bengtsson, 1909 - # 5, 6, 16, 19, 28, 31, 33, 35, 36, 37, 38, 41, 65, 67, 68, 70, 71, 73, 75- * Ephemerellamucronata - # 3, 38- Ephemerellanuda Tshernova, 1949 - # 1, 3, 10, 11, 29, 30, 40, 53, 65, 66- Ephemerella sp. 1 - # 30, 60- Serratellaignita - # 24, 43, 45, 54, 59, 61, 63, 66, 76- Serratellasetigera - # 43- * Uracanthellapunctisetae Matsumura, 1931 - # 33, 37, 38, 39, 40, 41, 42, 43- EphemeridaeEphemerasachalinensis Matsumura, 1911 - # 43- * PageBreakHeptageniidaeCinygmulacava - # 6, 17, 18, 19, 23, 31, 36, 65, 68, 69, 70, 73, 74, 75- Cinygmulakurenzovi - # 4, 63- * Ecdyonurus (Afghanurus) vicinus Demoulin, 1964 - # 18, 20, 22, 24, 45, 46, 47, 61, 65, 66, 72, 77, 78- * Ecdyonurus (Afronurus) abracadabrus - # 43- * Epeorus (Belovius) pellucidus - # 3, 33, 36, 39, 40, 41, 42, 43, 47, 61- * Epeorus sp. 1 - # 19- Heptageniaflava Rostock, 1878 - # 53, 54, 60- Heptageniasulphurea - # 3, 53- Rhithrogenalepnevae Brodsky, 1930 - # 2, 3, 24, 39, 40, 41, 42, 43, 44, 60, 78- Rhithrogenasibirica Brodsky, 1930 - # 4, 19, 31, 32, 38, 55, 64, 67, 73- PolymitarcyidaeEphoronnigridorsum - # 53- SiphlonuridaeSiphlonuruslacustris Eaton, 1970 - # 12, 14, 56, 57, 71, 75, 78- Caenisrobusta, Baetis (Acentrella) sibiricus and Rhithrogenalepnevae, were found along both lotic and lentic habitats. Only two species, Procloeon sp. and Caenisrivulorum, were recorded from a lake (# 13- Khoton nuur). Five species were taken around cold springs although none was found exclusively along this habitat.Of the 38 species recorded as adults, 36 occurred along streams and rivers. Three species, Baetisvernus, which was recorded from 34 of the 78 sites sp. 1 and Cinygmulacava were found at 19, 15, and 14 different sites, respectively. In contrast, seven species were recorded as adults only at one site: Serratellasetigera (site # 43), Ephoronnigridorsum (site # 53), Ephemerasachalinensis (site # 43), Epeorus sp. 1 (site # 19), Ecdyonurus (Afronurus) abracadabrus (site # 43), Procloeon sp. 1 (site # 13), and Caenisrivulorum (site # 13). The remaining species occurred at between two to 13 sites.The most frequently encountered species was Taxa richness at rivers and lakes varied between one and 16 Figure . The higEphemeroptera fauna of Western Mongolia comprise more than one-third of the total species recorded for the country. In addition, three new species were recorded for Mongolia for the first time, Raptobaetopustenellus, Caenisluctuosa and Caenisrivulorum. Raptobaetopustenellus is a Transpalaearctic to Eastern Palaearctic (lower Ob' River and basin in Siberia to Primoriye region) lapponica, Baetis (Acentrella) sibiricus, Baetis (Labiobaetis) attrebatinus, Centroptilumluteolum, Procloeonpennulatum, Ephemerellaaurivillii, Serratellasetigera, Ephemerasachalinensis, Ecdyonurus (Afronurus) abracadabrus, Cinygmulakurenzovi, Ecdyonurus (Afghanurus) vicinus and Epeorus (Belovius) pellucidus are new to Western Mongolia. Of these, Baetis (Labiobaetis) attrebatinus, Procloeonpennulatum, Ephemerasachalinensis, Ecdyonurus (Afronurus) abracadabrus and Ecdyonurus (Afghanurus) vicinus were recently recorded in Mongolia for the first time by Baetis (Acentrella) lapponica has been recorded previously in Mongolia (Baetis (Acentrella) lapponica in Western Mongolia, based on adult specimens confirms the species occurrence in Mongolia and brings the Mongolian mayfly fauna to 100 species.Our study shows that the region) . Caenish Africa . Caenisan fauna . AmeletuMongolia in the SMongolia due to iCaenisrobusta, Baetis (Acentrella) sibiricus and Rhithrogenalepnevae were sampled around both lotic and lentic habitats. Caenisrobusta was collected near a river (Khovd Gol) and also a brackish lake (Shaazgai nuur). Baetis (Acentrella) sibiricus and Rhithrogenalepnevae were found at more lotic habitats rather than lentic habitats. Procloeon sp. and Caenisrivulorum were recorded only in Lake Khoton. Larvae of Caenisrivulorum were previPageBreakously recorded in lakes with stony substrate as well as rivers at variable elevations between 200\u2013500 m a.s.l. in Europe abracadabrus, and Caenisrivulorum were found only at a single sampling site. Ephoronnigridorsum and Ephemerasachalinensis are both burrowing mayflies preferring larger and lowland rivers (Serratellasetigera and Ecdyonurus (Afronurus) abracadabrus, both found only at Bulgan Gol ."} +{"text": "The authors sincerely apologize for this error.PRESENT LIST:1, Anat Geiger-Maor1, Eithan Galun1, Hagai Amsalem2, Jacob Rachmilewitz1Avital Guedj1Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel2Department of Obstetrics and Gynecology, Hadassah University Hospital-Mount Scopus, Jerusalem, IsraelUPDATED LIST:1, Anat Geiger-Maor1, Hadar Benyamini2, Yaval Nevo2, Sharona Elgavish2, Eithan Galun1, Hagai Amsalem3, Jacob Rachmilewitz1Avital Guedj1Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel2Bioinformatics Unit, of the I-CORE Computation Center, the Hebrew University and Hadassah Hebrew University Medical Center, Jerusalem, Israel3Department of Obstetrics and Gynecology, Hadassah University Hospital-Mount Scopus, Jerusalem, Israel"} +{"text": "There were errors in affiliations and missing affiliations for multiple authors. Please see the list of authors with the correct indications of affiliations, as well as the correct list of affiliations, below:Inmaculada Bautista-Casta\u00f1o1,2, Patricia Henriquez-Sanchez1,2, NestorAleman-Perez1, Jose J. Garcia-Salvador1, Alicia Gonzalez-Quesada1,Jose A. Garc\u0131a-Hernandez3, Luis Serra-Majem1,21 Department of Clinical Sciences, University of Las Palmas de GranCanaria, Las Palmas de Gran Canaria, Spain, 2 Biomedical ResearchCenter Network on Obesity and Nutrition (CIBERobn) Physiopathology ofObesity and Nutrition, Institute of Health Carlos III, Madrid, Spain 3Gynecology and Obstetrics Department, Maternal & Child UniversityHospital of Gran Canaria, Las Palmas de Gran Canaria, Spain"} +{"text": "The author David P. Price was not included as an author in the published article. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way.The revised author list:1, 2, Peter M. Piermarini3, Carlos J. Esquivel3, David P. Price4, Hannah E. Drumm1, Faye D. Schilkey5, and Immo A. Hansen1, 2, 4, 6Yiyi Li1 Department of Biology, New Mexico State University, Las Cruces, NM, United States2 Department of Computer Science, New Mexico State University, Las Cruces, NM, United States3 Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States4 Molecular Biology Program, New Mexico State University, Las Cruces, NM, United States5 National Center for Genome Resources, Santa Fe, NM, United States6 Institute of Applied Biosciences, New Mexico State University, Las Cruces, NM, United StatesPerformed the experiments: DP, HD, FS, and YL; Analyzed the data: DP, YL, PP, FS, and CE; Wrote the paper: IH, PP, FS, CE, DP; Edited the manuscript: YL, PP, CE, FS, and IH.The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Scientific Reports7:533; doi:10.1038/s41598-017-00558-1; Article published online 03 April 2017In the original version of this Article, Hojatollah Vali was incorrectly affiliated to \u2018Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA\u2019 The correct affiliations for this author are listed below:Facility for Electron Microscopy Research, McGill University, 3640 University Street, Montreal, Quebec, H3A 0C7, Canada.Department of Anatomy & Cell Biology, McGill University, 3640 University Street, Montreal, Quebec\ufeff,\ufeff H3A 0C7, Canada.This error has now been corrected in the PDF and HTML versions of this Article."} +{"text": "In the Material and Methods section, the concentrations for glyburide, AFN1252, and A22 are incorrect. The concentrations for glyburide, AFN1252, and A22 should be 300 micromolar, 12 micromolar, and 100 micromolar, respectively."} +{"text": "Present: Due to an omission on the part of the author, the affiliations of the first author are incomplete.Corrected: Additional affiliation information for the first author is listed below. The authors sincerely apologize for this error.11397-11411. doi: 10.18632/oncotarget.7242.Original article: Oncotarget. 2016; 7(10):PRESENT LIST:1, Jamie Sui-Lam Kwok2, Pui-Wah Choi1, Minghua Liu2, Junzheng Yang1, Margit Singh1, Shu-Kay Ng4, William R. Welch5, Michael G. Muto1, Stephen KW Tsui2, Stephen P. Sugrue3, Ross S. Berkowitz1, Shu-Wing Ng1Yanli Zhang1 Laboratory of Gynecologic Oncology, Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA2 School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong3 Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA4 School of Medicine and Menzies Health Institute Queensland, Griffith University, Meadowbrook, Australia5 Department of Pathology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA, USAUPDATED LIST:1,6, Jamie Sui-Lam Kwok2, Pui-Wah Choi1, Minghua Liu2, Junzheng Yang1, Margit Singh1, Shu-Kay Ng4, William R. Welch5, Michael G. Muto1, Stephen KW Tsui2, Stephen P. Sugrue3, Ross S. Berkowitz1, Shu-Wing Ng1Yanli Zhang1 Laboratory of Gynecologic Oncology, Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA2 School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong3 Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA4 School of Medicine and Menzies Health Institute Queensland, Griffith University, Meadowbrook, Australia5 Department of Pathology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA, USA6 Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China"} +{"text": "This article has been corrected: The correct author names and affiliations are given below:1,3, Keiji Nihei1, Katsuyuki Karasawa1, Takeshi Sawada1, Fumiaki Koizumi1, Shigeo Yamaguchi2, Shunsuke Kato2, Hidehiro Hojo3, Atsushi Motegi3, Katsuya Tsuchihara3 and Tetsuo Akimoto3Shun-Ichiro Kageyama1 Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Bunkyo-ku, Tokyo 113-8677, Japan2 Juntendo University Main Hospital, Tokyo 113-8431, Japan3 National Cancer Center Hospital East, Kashiwa, Chiba 277-8577, Japan19368-19378. https://doi.org/10.18632/oncotarget.25053Original article: Oncotarget. 2018; 9:"} +{"text": "The publisher failed to include the following affiliation for Vadim V. Nikulin:Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, GermanyThe original article has been updated as follows:1, Mona Irrmischer2, Emilia Winnebeck3, Maria Fissler3, Julia M. Huntenburg3, Titus A. Schroeter3, Malek Bajbouj1, Klaus Linkenkaer-Hansen2, Vadim V. Nikulin4,5,6*\u2020 and Thorsten Barnhofer3\u2020Matti G\u00e4rtner1Department of Psychiatry and Psychotherapy, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany2Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, Netherlands3Dahlem Center for Neuroimaging of Emotions, Freie Universit\u00e4t Berlin, Berlin, Germany4Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany5Department of Neurology and Clinical Neurophysiology, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany6Center for Cognition and Decision Making, National Research University Higher School of Economics, Moscow, Russia"} +{"text": "The affiliations should appear as shown here: Kaitai Liu1 Department of Radiation Oncology, Lihuili Hospital, Ningbo Medical Center, Ningbo, China, 2 Department of Thoracic Surgery, Lihuili Hospital, Ningbo Medical Center, Ningbo, China, 3 Department of Respiratory Medicine, The Second Hospital of Yinzhou, Ningbo, China, 4 Department of Respiratory Medicine, Lihuili Hospital, Ningbo Medical Center, Ningbo, China."} +{"text": "Intracellular growth of Mycobacterium tuberculosis after macrophage cell death leads to serial killing of host cells. Published 28, January 2017Dr Emily B Wong and Dr Moosa Suleman were accidentally left out as co-authors on the work in the originally published version of the article. Their contribution was obtaining and transferring to us bronchoalveolar lavage clinical samples that contained alveolar macrophages. These cells were utilized in Figure 7D, blue line. The corrected list of authors and their affiliations is below:1,2, Mikael Boulle1,2,3, Yashica Ganga1, Chanelle Mc Arthur1,2, Steven Skroch1,2, Lance Oom1,2, Oana Catinas1, Kelly Pillay1,2, Myshnee Naicker1, Sanisha Rampersad1,2, Colisile Mathonsi1,2, Jessica Hunter1,2, Emily B Wong1,4, Moosa Suleman5,6, Gopalkrishna Sreejit1, Alexander S Pym1, Gila Lustig1, Alex Sigal1,2,3*Deeqa Mahamed1KwaZulu-Natal Research Institute for TB-HIV, Durban, South Africa; 2University of KwaZulu-Natal, Durban, South Africa; 3Max Planck Institute for Infection Biology, Berlin, Germany; 4Division of Infectious Diseases, Massachusetts General Hospital, Boston, United States; 5Department of Pulmonology and Critical Care, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; 6Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Durban, South Africa*Corresponding authorAdditional information for Dr Emily B Wong:Funding:Burroughs-Wellcome Fund / American Society of Tropical Medicine and Hygiene fellowshipNational Institutes of Health K08 AI118538In addition, we accidentally omitted that Kelly Pillay was funded by a Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE) fellowship.The article has been corrected accordingly."} +{"text": "The correct names are provided and replaced online which is mentioned as under:1, Yoona Choi1,*, Ji-Hye Lee2, Da-El Jang3 and Sanghee Kim4Sung Hae Kim1College of Nursing, Graduate School, Yonsei University, Seoul, Korea2College of Nursing, Graduate School, Yonsei University, Samsung Medical Center, Seoul, Korea3College of Nursing, Graduate School, Yonsei University, Severance hospital, Seoul, Korea4College of Nursing, Mo-Im Kim Nursing Research Institute, Yonsei University, Seoul, KoreaThe original names was: 1, Yoona Choil1*, Ji-Hye Lee2, Da-El Jang3, Sanghee Kim1Sung Hae Kim"} +{"text": "Open Biol.6, 160080. (doi:10.1098/rsob.160080)The correct affiliation for this author is as follows:2,3,4,8Mireille Vasseur-Cognet1Universit\u00e9 Paris 13, Laboratoire d'Ethologie Exp\u00e9rimentale et Compar\u00e9e, EA4443, 93430 Villetaneuse, France2UMR IRD 242, UPEC, CNRS 7618, UPMC 113, INRA 1392, PARIS 7 113, Institut d'Ecologie et des Sciences de l'Environnement de Paris, 93140 Bondy, France3Sorbonne Paris Cit\u00e9, Paris, France4Sorbonne Universit\u00e9s, Paris, France5Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague, Czech Republic6Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark7Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, Unit\u00e9 1016, Institut Cochin, 75014 Paris, France8Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, Paris, France"} +{"text": "Present: The author's affiliations are listed incorrectly.Correct: The proper affiliations are listed below.Yan-Liang Qu1,*, Jun Liu2,*, Li-Xin Zhang1, Chun-Min Wu1, Ai-Jie Chu1, Bao-Lei Wen1, Chao Ma1, Xu-yan Yan1, Xin Zhang1, De-Ming Wang1, Xin Lv2, Shu-Jian Hou31 Department of Anesthesiology, No. 401 Hospital of PLA, Qingdao 266071, Shandong, China2 Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China3 Department of Hand Surgery, No. 401 Hospital of PLA, Qingdao 266071, Shandong, Chinahttps://doi.org/10.18632/oncotarget.14595Original article: Oncotarget. 2017; 8:11614-11620."} +{"text": "There are errors in the author affiliations. The affiliation \u201cDepartment of Experimental Biomedicine and Clinical Neuroscience, University of Palermo, Palermo, Italy\u201d was added for Francesca Rappa. The affiliation \u201cCentro Studi Fegato (CSF)-Liver Research Center, Fondazione Italiana Fegato, Trieste, Italy\u201d was removed for Manlio Vinciguerra. The affiliations should appear as shown here.1\u262f, Hong Seok Shim1\u262f, Kyung Hwa Kim1\u262f, Manlio Vinciguerra2,3, Francesca Rappa5,6, Min Wei1, Sebastian Brandhorst1, Francesco Cappello5,6, Hamed Mirzaei1, Changhan Lee1, Valter D. Longo1,7*Stefano Di Biase1 Longevity Institute, Leonard Davis School of Gerontology and Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America, 2 Institute for Liver and Digestive Health, Royal Free Hospital, University College London (UCL), London, United Kingdom, 3 Center for Translational Medicine (CTM), International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, Czech Republic, 4 Centro Studi Fegato (CSF)-Liver Research Center, Fondazione Italiana Fegato, Trieste, Italy, 5 Euro-Mediterranean Institute of Science and Technology, Palermo, Italy, 6 Department of Experimental Biomedicine and Clinical Neuroscience, University of Palermo, Palermo, Italy, 7 IFOM, FIRC Institute of Molecular Oncology, Milano, Italy\u262f These authors contributed equally to this work.vlongo@usc.edu*"} +{"text": "Following publication of the original article it was b1Guang\u2019anmen Hospital, China Academy of Chinese Medical Sciences, No.5 Beixiange Street, Xicheng District, Beijing 100053, China2Graduate School, Beijing University of Chinese Medicine, No.11 Beisanhuan East Road, Chaoyang District, Beijing 100029, ChinaHowever, the corrected sequence should appear as:1Graduate School, Beijing University of Chinese Medicine, No.11 Beisanhuan East Road, Chaoyang District, Beijing, 100029 China2Guang\u2019anmen Hospital, China Academy of Chinese Medical Sciences, No.5 Beixiange Street, Xicheng District, Beijing, 100053 ChinaPlease also note that based on this new sequence, the author affiliations should also be updated to the following:1,2, Yongmei Liu2 and Jie Wang2*Jiangquan Liao"} +{"text": "This article unfortunThe author list was previously incorrectly presented as:1*, Jennifer D. Churchill1, Jonathan L. King1, Monika Stoljarova1,2, Harrell Gill-King3, Mourad Assidi4, Muhammad Abu-Elmagd4, Abdelbaset Buhmeida4 and Bruce Budowle1,4*Angie D. Ambers1Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North, Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA. 2Institute of Gene Technology, Department of Molecular Diagnostics, Tallinn University of Technology, Akadeemia tee 15A-604, Tallinn 12618, Estonia. 3Department of Biological Sciences, Laboratory of Forensic Anthropology, Center for Human Identification, University of North Texas, 1511\u00a0W. Sycamore, Denton, TX, USA. 4Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia."} +{"text": "Following publication of the original article it was b1,2, Manal F. El-Khadragy1,2,3, Reem A. Alajmi1, Mohamed S. Othman4,5, Amira A. Bauomy3,6, Shaimaa R. Ibrahim7 and Ahmed E. Abdel Moneim3*Ebtesam M. Al-Olayan1Chair vaccines research of infectious diseases, Faculty of Science, King Saud University, Riyadh, and KSA2Department of Zoology, Faculty of Science, King Saud University, Riyadh, KSA3Department of Zoology and Entomology, Faculty of Science, University of Helwan, Cairo, Egypt4Faculty of Preparatory year, University of Hail, Hail, KSA5Faculty of Biotechnology, October University for Modern Science and Arts (MSA), Giza, Egypt6Laboratory Sciences Dept., College of Science and Arts, Qassim University, Al-Rass, KSA7Molecular Drug Evaluation Department, National Organization for Drug Control & Research (NODCAR), Giza, EgyptPlease also note that the Acknowledgements section should be updated to the following: \u201cThe authors extend their appreciation to the Deanship of Scientific Research at King Saud University for funding the work through the research group project No. RGPVPP-074\u201d."} +{"text": "Copyright: Yang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Present: The affiliation information is incorrect.Correct: The proper affiliations appear below.15420-15430. https://doi.org/10.18632/oncotarget.14331Original article: Oncotarget. 2017; 8:Ru Yang1,*, Yingzi Zhang2,*, Lin Wang3,*, Ji Hu4, Jian Wen1, Leixi Xue1, Mei Tang1, Zhichun Liu1, Jinxiang Fu51 Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Jiangsu, China2 Department of Orthopaedics, The Second Affiliated Hospital of Soochow University, Jiangsu, China3 Department of Laboratory Medicine, The First Affiliated Hospital of Soochow University, Jiangsu, China4 Department of Endocrinology, The Second Affiliated Hospital of Soochow University, Jiangsu, China5 Department of Hematology, The Second Affiliated Hospital of Soochow University, Jiangsu, China"} +{"text": "Correction to: Cell Death Dis. 8, e2979 (2017); 10.1038/cddis.2017.374; published online 10th August 2017Following publication of the article, the authors spotted errors in the affiliations and footnote on page 1. They should read as follows:,1,2,6, B\u00e9ryl Laplace-Builh\u00e91,6, Jana Travnickova2, Patricia Luz-Crawford1,3, Gautier Tejedor1, Georges Lutfalla2, Karima Kissa2, Christian Jorgensen1,4,5 and Farida Djouad*,1,5Mai Nguyen-Chi*1IRMB, INSERM, University of Montpellier, Montpellier, France; 2DIMNP, CNRS, University of Montpellier, Montpellier, France; 3Laboratorio de Immunologia Celular y Molecular, Facultad de Medicina, Universidad de Los Andes, Santiago, Chile; 4Clinical Unit for Osteoarticular Diseases and Department for Biotherapy, CHU Lapeyronie, Montpellier, France. 5,6These authors contributed equally to this work.\u00a0* Correspondence to Mai Nguyen-Chi (mai.nguyen-chi@univ-montp2.fr) and Farida Djouad (farida.djouad@inserm.fr)"} +{"text": "In the Funding section, one of the grant numbers from Taipei Medical University-Shuang Ho Hospital, Ministry of Health and Welfare is missing. The correct grant numbers are 105-SHH-HCP-06 and 106TMU-SHH-05.1,2, Jau-Yih Tsauo1, Dun-Jen Hsiao3, Tsan-Hon Liou2,4,5, Shih-Wei Huang2,5,6, Li-Fong Lin2,7. 1 School and Graduate Institute of Physical Therapy, College of Medicine, National Taiwan University, Taipei, Taiwan, 2 Department of Physical Medicine and Rehabilitation, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan, 3 College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwanm, 4 Graduate Institute of Injury Prevention and control, Taipei Medical University, Taipei, Taiwan, 5 Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, 6 Graduate Institute of Sports Science, National Taiwan Sport University, Taoyuan, Taiwan 7 School of Gerontology Health Management, College of Nursing, Taipei Medical University, Taipei, Taiwan.There are errors in the author affiliations. The affiliations should appear as shown here: Chun-De Liao"} +{"text": "Drs. Thorsten Buch, and Ari Waisman were not included in the Author byline. They should be listed as the sixth and seventh authors, respectively. Please view the full author list and affiliations here:1, Hiep Le1, Christopher Vollmers1, Sheena Racheal Keding1, Nobushige Tanaka1\u00a4, Thorsten Buch2, Ari Waisman3, Christian Schmedt4, Timothy Jegla5, Satchidananda Panda1*Megumi Hatori1 The Salk Institute for Biological Studies, La Jolla, California, United States of America2 Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland3 I.Medizinische Klinik und Poliklinik, Johannes Gutenberg-Universit\u00e4t Mainz, Mainz, Germany4 Genomics Institute of Novartis Research Foundation, San Diego, California, United States of America5 Department of Cell Biology and Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, California, United States of America * To whom correspondence should be addressed. E-mail: satchin@salk.edu \u00a4 Current address: Kyorin University, Tokyo, Japan"} +{"text": "Dr. Tuncay Delibasi was not included in the author byline. He should be listed as the fourth author. This also affects the article's citation. Please view the corrected author byline, affiliations, and citation here:1,2, Talin Babikian3, Robert Asarnow3, Tuncay Delibasi4, Karin Esposito1, Halil K. Erol1, Ma-Li Wong1, Julio Licinio1*Gilberto J. Paz-Filho1 Department of Psychiatry and Behavioral Sciences, Center for Pharmacogenomics, University of Miami MillerSchool of Medicine, Miami, Florida, United States of America; 2 SEMPR \u2013 Servi\u00e7o de Endocrinologia e Metabologiada UFPR, Curitiba, Parana, Brazil; 3 Department of Psychiatry and Biobehavioral Sciences, David Geffen School ofMedicine at University of California Los Angeles, Los Angeles, California, United States of America; 4 Department ofEndocrinology and Metabolism, Ankara Numune Education and Research Hospital, Ankara, Turkey* E-mail: jlicinio@med.miami.eduCitation: Paz-Filho GJ, Babikian T, Asarnow R, Delibasi T, Esposito K, et al. (2008) Leptin Replacement Improves Cognitive Development. PLoS ONE 3(8): e3098. doi:10.1371/journal.pone.0003098"} +{"text": "Dr. Christos C. Zouboulis was not included in the author byline. He should be listed as the fourth author. Please view the corrected author list, affiliations, and citation here:1,2, Yu-Tsueng Liu3, Cheng-Po Huang2,3, Christos C. Zouboulis4, Richard L. Gallo1,2, Chun-Ming Huang1,2,3,5*Teruaki Nakatsuji1 Division of Dermatology, Department of Medicine, University of California San Diego, San Diego, California, United States of America 2 Veterans Affairs (VA) San Diego Healthcare Center, San Diego, California, United States of America 3 Moores Cancer Center, University of California San Diego, San Diego, California, United States of America 4 Departments of Dermatology, Venerology, Allergology, and Immunology, Dessau Medical Center, Dessau, Germany 5 La Jolla Institute for Molecular Medicine, San Diego, California, United States of America * To whom correspondence should be addressed. E-mail: chunming@ucsd.edu P. acnes: Implication for New Treatment of Acne Vulgaris. PLoS ONE 3(2): e1551. doi:10.1371/journal.pone.0001551 Nakatsuji T, Liu Y-T, Huang C-P, Zouboulis CC, Gallo RL, et al. (2008) Vaccination Targeting a Surface Sialidase of"} +{"text": "Correction to: British Journal of Cancer (2004) 90: 844\u2013852. doi:10.1038/sj.bjc.6601602Owing to an author error, the author affiliations in the above paper were shown incorrectly. The correct affiliations are given below:1, M Toyota1,2, H Ikeda3, T Tokino2 and K Imai1Y Morimoto1First Department of Internal Medicine, Cancer Research Institute, Sapporo Medical University, Sapporo 060-8543, Japan; 2Department of Molecular Biology, Cancer Research Institute, Sapporo Medical University, Sapporo 060-8543, Japan; 3Department of Pathology, Sapporo Medical University, Sapporo 060-8543, Japan"} +{"text": "Dr. Aruna Panda was not included in the Author Byline. She should be listed as the eighth author. Please view the corrected author byline, with affiliations here:1, Wing-Pui Kong1, Chih-Jen Wei1, Zhi-Yong Yang1, Martha Nason1, Darrel Styles2, Louis J. DeTolla4, Aruna Panda4, Erin M. Sorrell3, Haichen Song3, Hongquan Wan3, Gloria C. Ramirez-Nieto3, Daniel Perez3, Gary J. Nabel1Srinivas Rao1 Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America, 2 United States Department of Agriculture, Animal and Plant Health Inspection Service, Riverdale, Maryland, United States of America, 3 College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America, 4 Comparative Medicine, University of Maryland Baltimore, Baltimore, Maryland, United States of America"} +{"text": "Correction to: British Journal of Cancer (2009) 100, 311\u2013314; doi:10.1038/sj.bjc.6604858On correction of the above article, the affiliations of some of the authors were incorrectly presented. The correct affiliations are as follows:1,2,7, A van Helvoort1,7, JM Argil\u00e9s3, S van Tuijl1, K Arts1, M Gorselink4, A Laviano5, D Kegler1, HP Haagsman6 and EM van der Beek1K van Norren1Danone Research \u2013 Centre for Specialised Nutrition (formerly known as Numico Research), Wageningen, The Netherlands; 2Nutrition and Pharmacology Group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands; 3Cancer Research Group, Facultat de Biologia, Departament de Bioqu\u00edmica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain; 4Center for Innovative Consumer Studies, Wageningen UR, Wageningen, The Netherlands; 5Department of Clinical Medicine, University La Sapienza, Rome, Italy; 6Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands7These authors contributed equally to this work."} +{"text": "Correction to: British Journal of Cancer (2008) 99, 294\u2013304; doi:10.1038/sj.bjc.6604459On correction of the above article, the affiliations of some of the authors were incorrectly presented. The correct affiliations are as follows:1,2, CD Riffkin1, MM Lovric3, T Mikeska4, A Dobrovic4,5, JA Maxwell6, HS Friedman6, KJ Drummond7, AH Kaye7, HK Gan8, TG Johns8 and CJ Hawkins*,1,2,3DM Ashley1Children's Cancer Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville 3052, Australia; 2Department of Paediatrics, University of Melbourne, Parkville 3010, Australia; 3Department of Biochemistry, La Trobe University, Bundoora 3086, Australia; 4Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria 8006, Australia; 5Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia; 6Department of Surgery, Duke University Medical Center, Durham 27710, USA; 7Department of Surgery, University of Melbourne, The Royal Melbourne Hospital, Parkville 3050, Australia; 8Oncogenic Signalling Laboratory and Tumor Targeting Program, Ludwig Institute for Cancer Research, Heidelberg 3084, Australia"} +{"text": "The published Figures 2, 3, 4, and 5 are illegible. Please see the corrected figures here: Figure 2, Figure 3, Figure 4, Figure 5,"} +{"text": "Page 22; Column 2; Authors:1, John E Grantmyre2Anmar M Nassir1Department of Surgery, Um Al-Qura University, Makkah, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia2Department of Urology, Dalhousie University, Queen Elizabeth II Health Sciences Center, Halifax NS, CanadaShould read as1, John E Grantmyre2, Rekha Gupta3Anmar M Nassir1Department of Surgery, Um Al-Qura University, Makkah, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia2Department of Urology, Dalhousie University, Queen Elizabeth II Health Sciences Center, Halifax NS, Canada3Department of Pathology, Dalhousie University, Queen Elizabeth II Health Sciences Center, Halifax NS, Canada"} +{"text": "Affiliations 2 and 3 were switched. Affiliation 2 should be Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia. Affiliation 3 should be Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia."} +{"text": "A comma was omitted between the names of authors nine and ten, so the two authors appear to be one. Rainer Dietz is author number nine, with affiliations 1, 2, and 3. Ingo Morano is author number ten, with affiliation number 1. The author byline and affiliations should appear as shown here:1 Maximilian G. Posch,2,3 Natalia Alenina,1 Santhosh K. Ghadge,1 Bettina Erdmann,1 Elena Popova,1 Andreas Perrot,2,3 Christian Geier,2,3 Rainer Dietz,1,2,3 Ingo Morano,1 Michael Bader,1 and Cemil \u00d6zcelik1,2,3Anna N. Panek,1 Department of Cardiovascular and Metabolic Disease Research, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 2 Experimental and Clinical Research Center (ECRC) at the Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3 Department of Cardiology, Charit\u00e9-Universit\u00e4tsmedizin, Campus Virchow Klinikum, Berlin, Germany"} +{"text": "Ehrlich et al. [Environ Health Perspect 116:1689\u20131693 (2008)], Kambis Atefie was inadvertently omitted from the list of authors. The correct list of authors and affiliations is as follows:In the article by 1 Armen K. Nersesyan,1 Kambis Atefie,1 Christine Hoelzl,1 Franziska Ferk,1 Julia Bichler,1 Eva Valic,2 Andreas Schaffer,3 Rolf Schulte-Hermann,1 Michael Fenech,4 Karl-Heinz Wagner,5 and Siegfried Knasm\u00fcller1Veronika A. Ehrlich,1Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria; 2Austrian Workers Compensation Board, Vienna, Austria; 3Department of Medicine II, Medical University of Vienna, Vienna, Austria; 4Commonwealth Scientific and Industrial Research Organisation, Human Nutrition, Adelaide, Australia; 5Department of Nutritional Sciences, University of Vienna, AustriaThe authors apologize for the error."} +{"text": "There was an error in the author affiliations. The correct affiliations should appear as shown here:1, Frederick E. Grine2,3,4, Mark F. Teaford5Peter S. Ungar1 Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, United Statesof America, 2 Department of Anthropology, Stony Brook University, StonyBrook, New York, United States of America, 3 Department of Anatomical Sciences, StonyBrook University, Stony Brook, New York, United States of America, 4 LeverhulmeCenter for Human Evolutionary Studies, The University of Cambridge, Cambridge, UnitedKingdom, 5 Center for Functional Anatomy and Evolution, The Johns HopkinsUniversity School of Medicine, Baltimore, Maryland, United States of America"} +{"text": "The correct affiliations are:Bente Vilming Elgaaen 1,2*, Kari Bente Foss Haug 3#, Junbai Wang 4#, Ole Kristoffer Olstad 3, Dario Fortunati 3, Mathias Onsrud 2,5, Anne Cathrine Staff 2,5, Torill Sauer 4,5, Kaare M. Gautvik 3,51 Department of Gynaecological Oncology, Oslo University Hospital, OsloNorway**2 Department of Gynaecology, Oslo University Hospital, Oslo, Norway3 Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway4 Department of Pathology, Oslo University Hospital, Oslo, Norway5 Faculty of Medicine, University of Oslo, Oslo, Norway*corresponding author# These authors contributed equally to this work.**Current address."} +{"text": "The Authors are listed out of order. Please view the correct author order, affiliations, and citation here:1, Kai Zhao2, Li-Min Guo1, Lan-Juan Li3, Qin Xie4, Hong Ren5, Ji-Ming Zhang6, Min Xu7, Hui-Fen Wang8, Wen-Xiang Huang9, Xue-Fan Bai10, Jun-Qi Niu11, Pei Liu12, Xin-Yue Chen13, Xin-Liang Shen2, Zheng-Hong Yuan14, Xuan-Yi Wang14,15, Yu- Mei Wen14Dao-Zhen Xu1 Ditan Hospital, Beijing, China, 2 Beijing Institute of Vaccine and Biological Products, Beijing, China, 3 First affiliated hospital, Zhejiang University, Hangzhou, Zhejiang Province, China, 4 Rui-Jin Hospital, Shanghai Jiaotong University, Shanghai, China, 5 Second affiliated hospital, Chongqing Medical University, Chongqing, China, 6 Hua-Shan Hospital, Fudan University, Shanghai, China, 7 Guangzhou Eighth Hospital, Guangzhou, Guangdong Province, China, 8 302 Military Hospital, Beijing, China, 9 First affiliated hospital, Chongqing Medical University, Chongqing, China, 10 Tangdu Hospital, Fourth Military Medical University, Xi\u2019an, Shanxi Province, China, 11 First affiliated hospital, Jilin University, Changchun, Jilin Province, China, 12 Second hospital affiliated to China Medical University, Shenyang, Liaoning Province, China, 13 You-An Hospital, Capital Medical University, Beijing, China, 14 Key Laboratory Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai, China, 15 Institute of Biological Sciences, Fudan University, Shanghai, ChinaXu D-Z, Zhao K, Guo L-M, Li L-J, Xie Q, et al. (2008) A Randomized Controlled Phase IIb Trial of Antigen-Antibody Immunogenic Complex Therapeutic Vaccine in Chronic Hepatitis B Patients. PLoS ONE 3(7): e2565. doi:10.1371/journal.pone.0002565"} +{"text": "Correction to: British Journal of Cancer (2009) 99, 713\u2013722. doi: 10.1038/sj.bjc.6604905During correction of the above manuscript, the second affiliation of the lead author (Klaske van Norren) was omitted. The full affiliations are now shown below.*,1,5, D Kegler1, JM Argil\u00e9s2, Y Luiking1, M Gorselink3, A Laviano4, K Arts6, J Faber1, H Jansen1, EM van der Beek1 and A van Helvoort1K Van Norren1Danone Research \u2013 Centre for Specialised Nutrition (formerly known as Numico Research), Wageningen, The Netherlands; 2Cancer Research Group, Departament de Bioqu\u00edmica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Spain; 3Center for Innovative Consumer Studies, Wageningen UR, The Netherlands; 4Department of Clinical Medicine, University La Sapienza, Rome, Italy; 5Nutrition and Pharmacology Group, Division of Human Nutrition, Wageningen University, The Netherlands; 6Former employee of Numico Research, Danone Research \u2013 Centre for Specialised Nutrition (formerly known as Numico Research), Wageningen, The Netherlands"} +{"text": "This article has been corrected: During production, the affiliations for this article were listed incorrectly. The proper affiliations are shown below.1,*, Quan-Ning Chen3,*, Xi-Qiang Liu4,*, Xiao-Ming Wang5, Qi-Meng Chang6, Qi Pan2, Lu Wang2 and Yi-Lin Wang2Li-Chao Xu1 Department of Interventional Radiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China2 Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China3 Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China4 Department of Hepatobiliary-Pancreatic Surgery, Hangzhou, 310014, China5 Department of Hepatobiliary Surgery, Yi Ji-shan Hospital, Wan Nan Medical College, Wuhu, 241000, China6 Department of General Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, China# These authors contributed equally to this work56168-56173. https://doi.org/10.18632/oncotarget.17040Original article: Oncotarget. 2017; 8:"} +{"text": "This article has been corrected: The correct order of author affiliations is given below:Hyunchul Jung1,4,*, Hae Yong Yoo2,*, Seung Ho Lee2,*, Sohyun Shin3, Sang Cheol Kim4, Sejoon Lee4, Je-Gun Joung4, Jae-Yong Nam2,4, Daeun Ryu2,4, Jae Won Yun4,5, Jung Kyoon Choi1, Ambarnil Ghosh5, Kyeong Kyu Kim5, Seok Jin Kim6, Won Seog Kim6, Woong-Yang Park1and Young Hyeh Ko31 Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea2 Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea3 Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea4 Samsung Genome Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea5 Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea6 Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea* These authors have contributed equally to this workhttps://doi.org/10.18632/oncotarget.14928Original article: Oncotarget. 2017; 8:17038-17049."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Carola Dreier2, Colin Vullioud1, G\u00fclsah Gabriel2,3, Alex D. Greenwood1,4, Hans-Peter Grossart5,6Daniela Numberger1 Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany, 2 Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany, 3 University of Veterinary Medicine Hannover, Foundation, Hannover, Germany, 4 Freie Universit\u00e4t Berlin, Department of Veterinary Medicine, Institute for Virology, Berlin, Germany, 5 Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany, 6 University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1,2,3, Jian Dong1,2,3, Jianbin Bi1,2,3, Ruhai Bai4, Jia Zhang1,2,3, Zheng Wu3, Yi Lv1,2,3, Xufeng Zhang1,2,3, Rongqian Wu1,2Zhaoqing Du1 Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, First Affiliated Hospital of Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi Province, China, 2 Institute of Advanced Surgical Technology and Engineering, First Affiliated Hospital of Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi Province, China, 3 Department of Hepatobiliary Surgery, First Affiliated Hospital of Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi Province, China, 4 Department of Epidemiology and Biostatistics, Xi\u2019an Jiaotong University School of Public Health, Xi\u2019an, Shaanxi Province, China."} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:1, Marc Suhrcke2,3, Karen Bloor1, Shehzad Ali1,4Darius Erlangga1 Department of Health Sciences, University of York, York, England, United Kingdom, 2 Centre of Health Economics, University of York, York, England, United Kingdom, 3 Luxembourg Institute of Socio-economic Research (LISER), Luxembourg, 4 Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canadahttps://doi.org/10.1371/journal.pone.0219731Erlangga D, Suhrcke M, Bloor K, Ali S (2019) The impact of public health insurance on health care utilisation, financial protection and health status in low- and middle-income countries: A systematic review. PLoS ONE 14(8): e0219731."} +{"text": "There was a change in the author names in the published article. The new list should read:1, Johanna J. Kenyon2, Mohammad Hamidian3 , Mark B. Schultz4, Derek J. Pickard5, Gordon Dougan5, Ruth M. Hall3Kathryn E. Holt1, Department of Biochemistry & Molecular Biology, The University of Melbourne, Royal Parade, Parkville, Victoria, Australia2, School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia3, School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia4, Centre for Systems Genomics, The University of Melbourne, Parkville, Victoria, Australia5, Wellcome Sanger Trust Institute, Hinxton, Cambridge, UKThe author apologizes for any inconvenience caused."} +{"text": "Scientific Reports 10.1038/s41598-018-20341-0, published online 07 February 2018Correction to: The original version of this Article contained errors.Affiliation 2 was incorrectly given as \u2018School of Environmental Science, University of Guelph, Guelph, N1G 2W1, Canada\u2019. The correct affiliation is listed below:School of Environmental Sciences, University of Guelph, Guelph, N1G 2W1, CanadaAn affiliation for Vivek A. Thampi was omitted. The correct affiliations for Vivek A. Thampi are listed below:Department of Applied Mathematics, University of Waterloo, Waterloo, N2L 3G1, CanadaSchool of Environmental Sciences, University of Guelph, Guelph, N1G 2W1, CanadaChris T. Bauch was incorrectly affiliated with \u2018School of Environmental Sciences, University of Guelph, Guelph, N1G 2W1, Canada\u2019. The correct affiliation is \u2018Department of Applied Mathematics, University of Waterloo, Waterloo, N2L 3G1, Canada\u2019.Madhur Anand was incorrectly affiliated with \u2018Department of Applied Mathematics, University of Waterloo, Waterloo, N2L 3G1, Canada\u2019. The correct affiliation is \u2018School of Environmental Sciences, University of Guelph, Guelph, N1G 2W1, Canada\u2019.In addition, the email addresses for Chris T. Bauch and Madhur Anand, were incorrectly listed as manand@uogelph.ca and cbauch@uwaterloo.ca respectively.These errors have now been corrected in the PDF and HTML versions of the Article."} +{"text": "Anasplatyrhynchos appears incorrectly in the title, citation, and first sentence of the second paragraph of the Introduction section. The correct word is Anas platyrhynchos.The word 1,2, Lihong Gu3, Haopeng Yu4, Xuefei Jiang5, Yunsheng Zhang2, Xiaohui Zhang6, Guang Rong1, Zhengkui Zhou2, Kyle M. Schachtschneider7, Shuisheng Hou2There are errors in the author affiliations. The correct affiliations are as follows: Tieshan Xu1 Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, P.R. China, 2 Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China, 3 Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Science, Haikou, P.R. China, 4 West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, P.R. China, 5 Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, P.R. China, 6 College of Animal Science, Henan University of Science and Technology, Luoyang P. R. China, 7 Department of Radiology, University of Illinois at Chicago, Chicago, Illinois, United States of America"} +{"text": "The authors are listed out of order. Please view the correct author order, affiliations, and citation here:\u00b6*1, Arik Cheshin\u00b62, Dana Harari3, Shira Agasi4, Hadar Moriah4, Hanna Admi5, Anat Rafaeli4Dorit Efrat-Treister1 Department of Management, Ben-Gurion University of the Negev, Beersheba, Israel, 2 Department of Human Services, University of Haifa, Haifa, Israel, 3 Scheller College of Business, Georgia Institute of Technology, Atlanta, United States, 4 Faculty of Industrial Engineering and Management, Technion-Israel Institute of Technology, Haifa, Israel, 5 Department of Nursing, The Max Stern Yezreel Valley College, Yezreel Valley, Israelhttps://doi.org/10.1371/journal.pone.0218184Efrat-Treister D, Cheshin A, Harari D, Agasi S, Moriah H, Admi H, et al. (2019) How psychology might alleviate violence in queues: Perceived future wait and perceived load moderate violence against service providers. PLoS ONE 14(6): e0218184."} +{"text": "There are errors in the author affiliations. The correct affiliations are:1,2, Doris Patricia Maldonado3, Anna Hevia4, Marina Hoashi4, Paola Frattaroli4, Valentina Montacutti4, Adriana Heguy5, Igor Dolgalev5, Maricruz Mojica6, Gregorio Iraola1,7, Maria G. Dominguez-Bello4,8Carlos Robello1 Institut Pasteur de Montevideo, Montevideo, Uruguay, 2 Facultad de Medicina, Universidad de la Rep\u00fablica, Uruguay, 3 Universidad Andina Sim\u00f3n Bol\u00edvar, Sucre, Bolivia, 4 Division of Translational Medicine, New York University School of Medicine, New York, NY, United States of America, 5 Genome Technology Center, New York University Langone Medical Center, New York, NY, United States of America, 6 University San Francisco Javier de Chuquisaca, Sucre, Bolivia, 7 Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile, 8 Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States of America."} +{"text": "Correction to: J Exp Clin Cancer Reshttps://jeccr.biomedcentral.com/articles/10.1186/s13046-019-1213-0In the original publication of this article , the autThe correct version is:1, Bin Zhou1, Li Liu1, Fu Yang2, Carly Conran3, Yuan Ji4, Jinlin Hou1 and Deke Jiang1*Haoming Mai1State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, GuangZhou 510515, China2Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China3University of Illinois College of Medicine, Chicago, IL 60612, USA4Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA"} +{"text": "Correction to: J Exp Clin Cancer Res (2019) 38: 6https://doi.org/10.1186/s13046-018-1003-0In the publication of this article , there iThe corrected correspondence author order and author affiliation information is as given hereafter:1,2, Xiliang Cong1, Hongyu Gao1, Xiuwen Lan1, Zhiguo Li1, Wenpeng Wang3, Shubin Song1, Yimin Wang1, Chunfeng Li1, Hongfeng Zhang1, Yuzhou Zhao2* and Yingwei Xue1*Sen Li1 Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, 150 Ha Ping Road, Harbin 150081, China.2 Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, 127 Dong Ming Road, Zhengzhou 450008, China.3 Department of Gynecologic Oncology, Cancer Hospital Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China."} +{"text": "Katarzyna Nowomiejska was omitted in this publication by mistake. The correct information is provided below. The authors declare that this correction does not change the results or conclusions of this paper. The authors sincerely apologize for this error.1, Antonio Longo1, Teresio Avitabile1, Andrea Russo1, Matteo Fallico1, Vincenza Bonfiglio1, Mario Damiano Toro1,3, Robert Rejdak3, Katarzyna Nowomiejska3, Paolo Murabito1, Claudio Furino2, Michele Reibaldi1Niccol\u00f2 Castellino1Policlinico Gaspare Rodolico-University of Catania, Catania, Italy2Eye Clinic, University of Bari, Bari, Italy33Department of General Ophthalmology, Medical University in Lublin, Lublin, Poland"} +{"text": "There are errors in the author affiliations. The publisher apologizes for the errors. The correct affiliations are as follows:1,2, Stephanie Hilz3,4, Andrew Grimson3, Peter N. Schlegel1, Anne E. Jedlicka5, William W. Wright6Darius A. Paduch1 Department of Urology, Weill Cornell Medical College, New York, NY, United States of America, 2 Consulting Research Services, Inc, North Bergen, N.J., United States of America, 3 Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America, 4 Department of Neurological Surgery, University of California, San Francisco, California, United States of America, 5 Genomic Analysis and Sequencing Core Facility, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America, 6 Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America."} +{"text": "Cervical Epidural Steroid Injection: Parasagittal versus Midline Approach in Patients with Unilateral Cervical Radicular Pain; A Randomized Clinical Trial.\u201d [1 Payman Dadkhah,1 Mehrdad Taheri,1 Ebrahim Golmakani,1,2 Kasra Dehghan,1 Rouhollah Valizadeh.3\u201d. The affiliations are also corrected as follow: \u201c1Pain Management Fellowship, Department of Anesthesiology, Anesthesiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2Department of Anesthesiology, Mashhad University of Medical Sciences, Mashhad, Iran; 3Department of Epidemiology, Student Research Committee, Iran University of Medical Sciences, Tehran, Iran\u201d. The article was corrected online. In the original investigation entitled \u201c Trial.\u201d which wa"} +{"text": "Nature. Communications.; 10.1038/s41467-018-06327-6, published online 20 Sep 2018.Correction to: In the original HTML version of this Article, the affiliation details for Hirosuke Shiura were incorrectly given as: \u2018Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan; Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan; Present address: Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan\u2019. The correct affiliations are: \u2018Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan\u2019.Also, in the original HTML version of this Article, the affiliation details for Hidetoshi Hasuwa were incorrectly given as: \u2018Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan\u2019. The correct affiliations are: \u2018Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan; Present address: Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582, Japan\u2019.Additionally, in the original HTML version of this Article, the affiliation details for Takashi Kohda were incorrectly given as: \u2018Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan; Present address: Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582, Japan\u2019. The correct affiliations are: \u2018Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan; Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan\u2019.These have now been corrected in the HTML version of the Article."} +{"text": "Glob PedHea. 2017;4. doi:10.1177/2333794X17744947Azevedo L, Jay A, Lorenzana A, et al. Case Report of an Adolescent Male With UnexplainedPancytopenia: GATA2-Associated Bone Marrow Failure and Genetic Testing. Global Pediatric Health, withthe second author, Rofida Nofal, omitted.The above article was published in volume 4 of Dr. Rofida Nofal wrote the case report section; including patient history, physical examfindings, work up, case progression and follow up, as well as contribution to thebackground.The final authorship for the article is:1*, Rofida Nofal, MD, MS2, Allison Jay,MD1*, Adonis Lorenzana, MD1, Sioban Keel, MD3, Roshini S.Abraham, PhD4 , Marshall Horwitz, MD, PhD3, Michelle van Hee,BS4 , and Hadi Sawaf, MD1Lauren Azevedo, MS, DO1St John Providence Children\u2019s Hospital, Detroit, MI, USA2UCSF Beniof Children\u2019s Hospital, Oakland, CA, USA3University of Washington, Seattle, WA, USA4Mayo Clinic, Rochester, MN, USA* These authors contributed to the case report equally.The revised Acknowledgments section follows:AcknowledgmentsGenetic testing for the patient was graciously performed at University of Washington underthe direction of Dr Marshall Horwitz, Dr Sioban Keel, and Dr Mary-Claire King, and at the MayoClinic in Dr Roshini Abraham\u2019s laboratory. The authors also wish to thank Dr Rofida Nofal forresearch into the background of GATA2."} +{"text": "In the published article, there was an error in the affiliation order and numbering. The corrected affiliation order and numbering should be as follows:1,2*, Haakon R. Hol3,4, Susanne S. Hernes4,5, Linda Chang6,7,8, Thomas Ernst6,7,8, Andreas Engvig9, Knut J\u00f8rgen Bjuland10, Bengt-Ove Madsen5, Elisabeth M. S. Lindland3,11,12, Anne-Brita Knapskog13, Ingun D. Ulstein13, Trine E. E. Lona14, Jon Skranes1,2 and Gro C. C. L\u00f8haugen2\u201d\u201cMarianne M. FlakThere was also an error regarding the affiliations for Professor Linda Chang. As well as having affiliation 6, they should also have \u201cDepartment of Diagnostic Radiology and Nuclear Medicine, and Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, United States\u201d and \u201cDepartment of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States\u201dAdditionally, there was also an error regarding the affiliation of Professor Thomas Ernst. As well as having affiliation 6, they should also have \u201cDepartment of Diagnostic Radiology and Nuclear Medicine, and Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, United States\u201d and \u201cDepartment of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States\u201dThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "M. Pawley1, Sarah L. Dwyer1, Catherine Lea1, Gabriela Tezanos-Pinto1Affiliations 1 and 2 are listed out of order. The affiliations should appear as shown here: Krista Hupman1 Coastal-Marine Research Group, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand, 2 National Institute of Water and Atmospheric Research, 301 Evans Bay Parade, Wellington, 6021, New Zealand, 3 Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States of America"} +{"text": "The author list, affiliations and contact information of this paper are revi1,2,3,\u2020, Ying-Qian Liu 4,\u2020, Liu-Meng Yang 1, Rui-Rui Wang 1, Wei Pang 1 , Shi-Wu Chen 4 Xuan Tian 4,* and Yong-Tang Zheng 1,*Yu-Ye Li 1 Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China2 Graduate School of the Chinese Academy of Sciences, Beijing 100039, China3 The First Affiliated Hospital of Kunming Medical College, Kunming, Yunnan 650032, China4 State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China\u2020 These authors contributed equally to this work.zhengyt@mail.kiz.ac.cn (Y-T.Z.); xuant@lzu.edu.cn (X.T.); Tel./Fax: +86 871 5195684 (Y.-T.Z).* Authors to whom correspondence should be addressed; E-Mail:"} +{"text": "The authors are listed out of order. Please view the correct author order,affiliations, and citation here:1,2, Uri Obolski3, Luiz Carlos JuniorAlcantara4, Maricelia M. de Lima4, Elizabeth A.Ashley5,6, Frank Smithuis5,6,7, Peter Horby7,Richard J. Maude6,7,8,9, Zaw Lin10, Aye Mon MonKyaw10, Jos\u00e9 Louren\u00e7o3Pablo Noel Perez-Guzman1 Department of Global Health and Tropical Medicine, University of Oxford, UK; 2Department of Infectious Disease Epidemiology, Imperial College, London, UK; 3Department of Zoology, University of Oxford, UK; 4 Laboratory of Haematology,Genetics and Computational Biology, FIOCRUZ, Brazil; 5 Myanmar-Oxford ClinicalResearch Unit, Yangon; 6 Centre for Tropical Medicine and Global Health, NuffieldDepartment of Medicine, University of Oxford, UK; 7 Nuffield Department of Medicine,University of Oxford, UK; 8 Mahidol-Oxford Tropical Medicine Research Unit, Facultyof Tropical Medicine, Mahidol University,Thailand; 9 Harvard TH Chan School ofPublic Health, Harvard University, Boston, USA; 10 Myanmar Ministry of Health andSports, Naypyidaw, MyanmarPerez-Guzman PN, Obolski U, Carlos Junior Alcantara L, de Lima MM, Ashley EA,Smithuis F, Horby P, Maude RJ, Lin Z, Kyaw AMM, Louren\u00e7o J. Measuring Mosquito-borneViral Suitability in Myanmar and Implications for Local Zika Virus Transmission.PLOS Currents Outbreaks. 2018 Sep 28 . Edition 1. doi:10.1371/currents.outbreaks.7a6c64436a3085ebba37e5329ba169e6.Perez-Guzman PN, Carlos Junior Alcantara L, Obolski U, de Lima MM, Ashley EA,Smithuis F, Horby P, Maude RJ, Lin Z, Kyaw AMM, Louren\u00e7o J. Measuring Mosquito-borneViral Suitability in Myanmar and Implications for Local Zika Virus Transmission.PLOS Currents Outbreaks. 2018 Sep 28 . Edition 1. doi:10.1371/currents.outbreaks.7a6c64436a3085ebba37e5329ba169e6."} +{"text": "The correct names are: Whitney E. Purtha and Paolo S. Manzanillo. The correct citation is: Hao Y, Purtha WE, Cortesio C, Rui H, Gu Y, Chen H, et al. (2018) Crystal structures of human procathepsin H. PLoS ONE 13(7): e0200374. 1,2, Whitney E. Purtha3, Christa Cortesio4, Huan Rui1, Yan Gu4, Hao Chen4, E. Allen Sickmier1, Paolo S. Manzanillo3, Xin Huang1There are errors in the author affiliations. The correct affiliations are as follows: Yue Hao1 Department of Molecular Engineering, Amgen Discovery Research, 360 Binney Street, Cambridge, MA 02142, USA, 2 Amgen Postdoctoral Fellow Program, 360 Binney Street, Cambridge, MA 02142, USA, 3 Department of Inflammation and Oncology, Amgen Discovery Research, 1120 Veteran Boulevard, South San Francisco, CA 94080, USA, 4 Department of Protein Technologies, Amgen Discovery Research, 360 Binney Street, Cambridge, MA 02142, USA"} +{"text": "The missing author (D Stampoulis) is included below in the proper order and affiliation. The authors would like to apologise for any inconvenience caused.In issue 36 of Mitochondrion, an author was excluded from the article Topical Coenzyme Q10 demonstrates mitochondrial-mediated neuroprotection in a rodent model of ocular hypertension1, Tian K1, Pahlitzsch M1, Brenton J1, Ravindran N1, Stampoulis D4, Butt G1, Malaguarnera G1, Normando EM2, Guo L1, Cordeiro MF3Davis BM1Department of Visual Neuroscience, UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom2Department of Visual Neuroscience, UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom3Department of Visual Neuroscience, UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom; Western Eye Hospital, Imperial College London, United Kingdom. Electronic address: m.cordeiro@ucl.ac.uk4Department of Cell Biology, UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Getiye Dejenu Kibret2, and Cheru Tesema Leshargie2Birtukan Aklog Yihun1 Debre Markos Referral Hospital, Debre Marko, Ethiopia, 2 College of Health Science, Debre Markos University, Debre Marko, Ethiopia."} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1, Brian Crudge2, Thona Lim2, David O\u2019Connor1,3,4, Vichet Roth2, Matt Hunt2, Jenny Anne Glikman1Elizabeth Oneita Davis1 San Diego Zoo Institute for Conservation Research, Escondido, CA, USA, 2 Free the Bears, Phnom Penh, Cambodia, 3 National Geographic Partners, NW, Washington DC, USA, 4 The Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany."} +{"text": "Bioscience Reports (2019) 39(4), BSR20190231; https://doi.org/10.1042/BSR20190231After detailed discussion, the authors of the published article have decided to change the order of their authorship listing. The agreed authorship listing is as follows:1, Binbin Tang2, Xiping Zhang1, Hongjian Yang1, Enqi Qiao1, Xiangming He1 and Feijiang Yu3Dehong Zou1Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China; 2Second Outpatient Department of Traditional Chinese Internal Medicine, Tongde Hospital of Zhejiang Province, Hangzhou 310012, Zhejiang Province, China; 3Medical Records Room, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, ChinaIn addition, Dehong Zou, Binbin Tang and Xiping Zhang should no longer be considered co-first authors."} +{"text": "Correction to:Cell Death and Disease (2018)9:102710.1038/s41419-018-1036-5published online 09 October 2018The correct ordering and designations for corresponding/first authors are as follows:1,2*, Mingyue Zhu3, Qiaoyun Wang3, Yuli Hou4, Lei Li5, Honglei Weng6, Yan Zhao4, Dexi Chen1,2, Junli Guo3, Huiguo Ding#5, Mengsen Li#3Shanshan Wang1Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China2Beijing Precision Medicine and Transformation Engineering Technology Research Center of Hepatitis and Liver Cancer, Beijing, China3Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, China4Clinical Laboratory Center, Beijing Youan Hospital, Capital Medical University, Beijing, China5Department of Gastrointestinal and Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China6Molecular Hepatology, University of Heidelberg, University Medical Center Mannheim, 68167 Mannheim, Germany*First author# Corresponding author."} +{"text": "Correction to: J Immunother Cancer10.1186/s40425-018-0412-0Following publication of the original article , the autIn this Correction the authors are listed with their correct affiliations below.1, Chrystia M Zobniw2, Van A Trinh2, Junsheng Ma3, Roland L Bassett Jr3, Noha Abdel-Wahab4,5, Jaime Anderson2, Jennifer E Davis6, Jocelyn Joseph2, Marc Uemura1, Ali Noman7, Hamzah Abu-Sbeih7, Cassian Yee1, Rodabe Amaria1, Sapna Patel1, Hussein Tawbi1, Isabella C Glitza1, Michael A Davies1, Michael K Wong1, Scott Woodman1, Wen-Jen Hwu1, Patrick Hwu1, Yinghong Wang7 and Adi Diab1Daniel H Johnson1Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA2Division of Pharmacy, Clinical Section, The University of Texas MD Anderson Cancer Center, Houston, TX, USA3Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA4Section of Rheumatology and Clinical Immunology, Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA5Department of Rheumatology and Rehabilitation, Faculty of Medicine, Assiut University Hospitals, Assiut, Egypt6Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA7Department of Gastroenterology, Hepatology, and Nutrition, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA"} +{"text": "There are errors in the author affiliations. The affiliations should appear as shown here:1, Ester Orsini1, Isabella Zironi2,6,7, Lorenzo Isolan3,8, AlessandraCappellini4, Stefania Rapino5,7, Agostino Tartari3, Domiziano Mostacci3, Giorgio Cucchi3, Alberto Maria Martelli1, Marco Sumini3,6, Gastone Castellani2,6,7Francesca Buontempo1 University of Bologna, Department of Biomedical and Neuromotor Sciences, Bologna, Italy, 2 University of Bologna, Department of Physics and Astronomy, Bologna, Italy, 3 University of Bologna, Department of Industrial Engineering, Bologna, Italy, 4 University of Cassino and Southern Lazio, Department of Human Social and Health Sciences, Cassino, Italy, 5 University of Bologna, Department of Chemistry \u201cG. Ciamician\u201d, Bologna, Italy, 6 National Institute for Nuclear Physics (INFN), Bologna, Italy, 7 Interdepartmental Centre \u201cL. Galvani\u201d (CIG) for integrated studies of bioinformatics, biophysics and biocomplexity, Bologna, Italy, 8 European Institute of Oncology and Monzino Cardiac Center Foundation (IEO-CCM), Milano, Italy.In the Funding section, the grant from the funder INFN ETHICS 2015 is incorrectly attributed to Dr. Giorgio Cucchi. The correct attribution is to Gastone Castellani. The publisher apologizes for the errors."} +{"text": "The seventh author's name is spelled incorrectly. The correct name is: Hang-Korng Ea.1,2,3, Ant\u00f3nio Camacho4, Agn\u00e8s Ostertag5, Martine Cohen-Solal5, I. Jorge Pinto6, Gra\u00e7a Porto6,7,8, Hang-Korng Ea5, M. Leonor Cancela2,3,9.There are errors in the author affiliations. The correct affiliations are as follows: M\u00e1rcio Sim\u00e3o1 PhD Program in Biomedical Sciences, Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal, 2 Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal, 3 Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal, 4 Department of Orthopedics, Hospital de Cascais, Alcabideche, Portugal, 5 Inserm U1132/ BIOSCAR, and Universit\u00e9 Paris 7 Denis Diderot, H\u00f4pital Lariboisi\u00e8re, Paris, France, 6 Basic and Clinical Research on Iron Biology, Institute for Molecular and Cell Biology (IBMC) and I3S \u2013Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, University of Porto, Porto, Portugal, 7 Pathology and Molecular Immunology Department, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal, 8 Hematology Service, Hospital de Santo Ant\u00f3nio, Centro Hospitalar do Porto, Porto, Portugal, 9 Algarve Biomedical Center, University of Algarve, Campus de Gambelas, 8005\u2013139, Faro, Portugal."} +{"text": "There are multiple errors in the author byline. Please view the correct author order, affiliations, and citation here:1,2, Zahi Aizer2, Rephael Mohr1,2, Nahum Nesher1,2, Amir Kremer1,2, Yosef Paz1,2, Nadav Taih1,2, Yanai Ben-Gal1,2Dmitry Pevni1 Department of Cardiothoracic Surgery Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel, 2 Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israelhttps://doi.org/10.1371/journal.pone.0201227.Pevni D, Aizer Z, Mohr R, Nesher N, Kremer A, Paz Y, et al. (2018) Are two internal thoracic grafts better than one in patients with chronic obstructive lung disease? Analysis of 387 cases between 1996\u20132011. PLoS ONE 13(8): e0201227."} +{"text": "Day care (DC) provides a break in daily care as a support strategy for family caregivers (FC) of people with dementia (PwD).to analyze the support strategies used by the DC for FC, their methodological and theoretical models, as well as the respective benefits for FC burden, coping strategies and quality of life.a systematic review following the Prisma methodology was performed on PubMed, PsycInfo, Scopus and SciELO electronic databases in August, 2018. The search keywords were \u201cday care\u201d, \u201cdementia\u201d or Alzheimer disease, \u201ccaregiver\u201d, \u201cquality of life\u201d and \u201cpsychological adaptation\u201d.twenty-one studies were included. No randomized controlled trials were found. The provision of education, counseling and support, access to information, the professionals' expertise and the quality of their relationship with DC users were highlighted by caregivers. Compared to standard programs centering on PwD, the integrated program focused on PwD and FC activities showed increased feelings of competence and self-confidence of FC to postpone institutionalization. Heterogeneity in the structure and organization of the DC programs, intervention strategies and theoretical basis was observed.Integrated programs are a promising approach that addresses the needs and demands of PwD and their FC in a multidimensional manner. Studies published from 1998 and 2017 were included. The search keywords included the following MeSH terms: \u201cday care\u201d [MeSH} or (care day) or and \u201cdementia\u201d [MeSH] or Alzheimer disease [MeSH] or (Alzheimer's disease) or (Alzheimer type dementia) and \u201ccaregiver\u201d [MeSH] or (family caregiver) or (carers) and \u201cquality of life\u201d [MeSH] or and \u201cadaptation, psychological\u201d [MeSH] or (coping behavior) or (coping skills). A manual search was also performed by revising the reference of all papers selected. The inclusion criteria were: 1. cross-sectional or longitudinal studies, 2. randomized or nonrandomized, 3. with or without a control group, 4. studies on day care for people with dementia with caregiver outcomes, 5. reports written in English or Portuguese.The exclusion criteria were: 1. Participants with other pathologies; 2. Other community or outpatient care settings; 3. Evaluation of specific therapeutics ; 4. Evaluation of instruments; 5. Literature reviews; 6. Other languages; 7. Studies without full text; 8. Outcomes focused on the PWD; 9. Books, dissertations and theses; 10. Public health policies and epidemiological studies.,The articles were evaluated using the quality score metrics proposed by the Mixed Methods Assessment (MMAT),20Two authors (VLRM and MCND) screened titles and abstracts to identify eligible papers. We excluded all studies that clearly did not meet all inclusion criteria or that met at least one of the exclusion criteria. Subsequently, two authors (VLRM and MATB) independently reviewed the full publications of the remaining papers and held consensus meetings to discuss any disagreement and to reach a consensus about inclusion. When necessary, a third co-author of this paper (RLS) clarified study eligibility.The articles were reviewed considering the research procedures and the configuration of DC, the program, its objectives, therapeutic proposals and theoretical basis.The initial database searches retrieved 587 articles; 82 were found on PsycINFO, 301 on Scopus, 202 were identified on PubMed and 2 on SciELO. All the authors reviewed the selected documents to reach a consensus.After duplicates were removed (n=274), 299 studies not meeting inclusion criteria were excluded, and fourteen studies were selected for inclusion in this systematic review. Seven further studies were identified by manually searching the references in the selected articles. Twenty-one papers had been selected by the end of this search process . A flow Place. Ten out of the twenty-one studies were conducted in the USA,22-32-Sample. Nineteen studies included FC of both genders, 22-24,26,28-25,22-24,26,28,31-39,25,29,30,40,Study design. No randomized controlled trials were found. Six descriptive qualitative studies23,24,32,35,36,37,23,24,32,22,25,27,28,30,31,33,34,40,26,29,38,22,25,27,30,31,40,28,33,Caregivers' outcomes. In the study by de Jong et al.,-26,28-31,33-36,38-22,25,30,31,33,40,25,38,23-25,22-25,24,33,28,23,24,30,26,35,23,24,35,Seventeen studies observed a reduction in time spent on care activities and in exposure to primary stressors,22Mossello et al.Kwork et al.,27,28,36-26,36,38,The observation of improvement in self-esteem and well-being, quality of life and health status, associated with increased social stimulation of the PwD resulted in a secondary benefit for FC health and quality of life.24,28,33,34,A delay in institutionalization was associated with improved health of the dyad and in their quality of relationships.27G\u00fastafsd\u00f3ttir,35,38,The last benefit of the DC for the FC was the sharing of care with professionals, the information exchange and reflection on the case, and proposing care strategies.32,33,28,33,33,The three articles that studied the benefits of an integrated approach compared to standard care offered to PwD only, observed a significant decrease in FC suffering over PwD behavioral problems,28The characteristics of the selected studies are shown in Sources of subsidy. Different sources of subsidy for DC were reported. Rokstad et al.32-26,29,38,23,24,27,28,30,35,37,39,Structure. Twelve articles provided no information about the structure of the DC.23-25,27,28,30,35-39,22,26,29,31-34,40,22,28,32,36,40,22,28,40,29,36,Program. Eleven studies did not describe the activities offered.23-25,27,28,30,31,35,37,39,36,22,26,29,32,33,34,38,-27,30-32,35,36,39,29,Twelve articles made no mention of whether the DC offered caregiver support programs.23,Dr\u00f5es et al.33Gitlin et al.Objectives and therapeutic proposals. The DC proposes to offer significant activities,36,22,29,32,36,26,28,32-34,36,38,36,26,28,32-34,36,38,22,33,34,36,40,28,28,33,22,36,Theoretical basis. Only four studies reported the theoretical basis of the support program offered to FC. Dr\u00f5es et al.33,43,The structure, objectives and theoretical basis of the DC are depicted in -7,4-6,Historically, the DC, as a strategy for supporting FC, was originally intended to offer a break in caregiving tasks, and to maintain or improve the health and quality of life of the PwD-FC dyad. This concept of service was inspired by studies on the burden and coping strategies of family caregivers and the impact on their quality of life.2,29,31-34,36,38,41,2,6,22,2,6,22,The need for support, together with the benefits outlined, has justified investment from different actors, such as governments, statutory, third sector organizations, health insurance and assistance, universities, private institutions and families.25,25,27,30,31,40,32,35,26,Quantitative approaches with controls to evaluate the impact of this care22,24,27,30,25,35,37,22-37,39-There was methodological heterogeneity in the characteristics of the FC samples and in the assessments used. This diversity hinders comparison among studies and their outcomes. For example, case studies with controls compared the days of DC treatment to the days when the PwD was cared for at home,23,26,29-34,40,7,9,28,32,35,36,3,9,28,32,35,36,Attendance frequency varied from one to five times a week and the number of hours from four to eight hours per day.22-25,27,30,31,35,37,39,26,32,22,28,29,33,34,37,38,40-The diversity of the intervention designs impacts the results of the studies.23,26,28,32-34,36,38,26,35,36,38,40,46-46-The two approaches, including the caregivers in the service or otherwise, identified different protocols of activities aimed at PwD. Programs of recreational activities with an emphasis on socialization and well-being,36,38,32,35,36,The results concerning the impact of activities on behavioral changes were contradictory. Zarit et al.36,34,22,28,29,33,34,37,22,28,29,33,34,22,28,33,34,33,34,22,28,37,22,28,33,34,22,28,33,34,37,22,28,32-36,28,33,Different approaches to FC were observed. In one study, the DC program offered informal counselling,28,43,43,43,With regard to theoretical background, the adaptation coping model adopted by the MCS was briefly described in the two articles by Dr\u00f5es et al.33The stress process model of Pearlin et al.The person-centered approach was cited as the recommended theoretical axis to guide the care model of the DC.These approaches are offered as theoretical references for care delivery and are part of the set of psychosocial models used in the field of Psychogeriatrics.The possible influence of socioeconomic and cultural differences between the samples studied calls for caution in the interpretation of results. Likewise, the lack of standardization in the configuration of DC hampers comparison of results. In addition. the conception of DC as a rest service, restricts the understanding of its therapeutic role as a treatment and rehabilitation device for PwD, and a source of guidance and support for FC.Most of the studies failed to describe the strategies of interaction, support and guidance for FC, and did not explain the theoretical framework that conceptually defines the services model and its therapeutic goals. The lack of a detailed description limits the interpretation of the congruence of results in relation to objectives proposed and intervention programs.In conclusion, The reduction in daily exposure of the FC to primary stressors promoted a rest period and contributed to the continuity of the family living together with the PwD, delaying institutionalization. The DC appears to be a promising technology for reducing FC burden, thereby improving their health and quality of life.Integrated programs that cater for the needs of the PwD and their FC represent a promising approach that meets their needs and demands in a multidimensional manner. The DC is a technology that aims to promote health, prevent disease and also provide treatment through interventions that minimize burden and enable long-term care. However, there is a lack of integrative approaches that articulate the contribution of different complementary theories and guide comprehensive and cost-effective intervention programs."} +{"text": "Cuicui Wang to the list of authors. Cuicui Wang was omitted in this publication by mistake. The correct authors' list is provided below. The authors declare that this correction does not change the results or conclusions of this paper. The authors sincerely apologize for this error.1, Elena Colicino2, Jincheng Shen3, Allan C. Just2, Jamaji C. Nwanaji-Enwerem4, Cuicui Wang4, Brent Coull5, Xihong Lin5, Pantel Vokonas6, Yinan Zheng7, Lifang Hou7, Joel Schwartz4, Andrea A. Baccarelli1Xu Gao1Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA2Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA3Department of Population Health Sciences, University of Utah, School of Medicine, Salt Lake City, UT 84132, USA4Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA5Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA6Veterans Affairs Normative Aging Study, Veterans Affairs Boston Healthcare System, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA7Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1,2, Lian-Yu Chen1,3, Hsing-Cheng Liu1,4,5, Chi-Shin Wu6, Shu-Yu Yang1,7, Chun-Hung Pan1,8, Shang-Ying Tsai4,5, Chiao-Chicy Chen4,5,9, Chian-Jue Kuo1,4,5Wen-Yin Chen1 Taipei City Psychiatric Centre, Taipei City Hospital, Taipei, Taiwan, 2 Graduate Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health, Taipei, Taiwan, 3 Department of Psychiatry, National Cheng Kung University, Tainan, Taiwan, 4 Department of Psychiatry, School of Medicine, College of Medicine, Taipei Medical University, 5 Psychiatric Research Center, Taipei Medical University Hospital, Taipei, Taiwan, 6 Department of Psychiatry, National Taiwan University Hospital, Taipei, Taiwan, 7 Graduate Institute of Clinical Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, 8 Department of Psychology, National Chengchi University, Taipei, Taiwan, 9 Department of Psychiatry, Mackay Memorial Hospital, Taipei, Taiwan and Department of Psychiatry, Mackay Medical College, Taipei, Taiwan."} +{"text": "Correction to: Cell Death & Disease10.1038/s41419-019-1589-y published online 01 May 2019After publication of this article, the authors found some mistakes in the author information. The correct list of author information should be as following:1,2, Xiying Hou1, Xueqiao Wang3, Yinfeng Shi1, Liuqing Xu1, Xiaoqing Zheng3, Na Liu1, Andong Qiu3, Shougang Zhuang1,4Jun Ni1Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China2Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China3School of Life Sciences and Technology, Tongji University, China4Department of Medicine, Rhode Island Hospital and Brown University School of Medicine, Providence, RI, USACorrespondence: Shougang Zhuang (szhuang@lifespan.org)1Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China4Department of Medicine, Rhode Island Hospital and Brown University School of Medicine, Providence, RI, USAThis has been corrected in both the PDF and HTML versions of the Article."} +{"text": "Longzuan Tongbi Formula (LZTB) is an effective proved prescription in Zhuang medicine for treating active rheumatoid arthritis (RA). However, its active ingredients, underlying targets, and pharmacological mechanism are still not clear in treating RA. We have applied network pharmacology to study LZTB and found that 8 herbs in LZTB and 67 compounds in the 8 herbs are involved in the regulation of RA-related genes; we have conducted pathway analysis of overlapping genes and found that 7 herbs participate in the regulations of 24 pathways associated with RA and that 5 herbs in the 7 herbs and 25 compounds in the 5 herbs participate in the regulation of hsa05323 (rheumatoid arthritis). The results indicated that all herbs in LZTB and some compounds in those herbs participate in the treatment of RA; 25 compounds are main active ingredients and hsa05323 (rheumatoid arthritis) is the major pathway in the treatment of RA. We have also found that three pathways might have some effect on the treatment of RA. Toddalia asiatica (TA), Kadsura coccinea (KC), Alangium chinense (AC), Sinomenium acutum (SA), Bauhinia championii (BC), Spatholobus suberectus (SS), Zanthoxylum nitidum (ZN), and Ficus hirta Vahl (FHV). Clinical studies have shown that LZTB can significantly reduce RA patients' erythrocyte sedimentation rate, and that it has a good therapeutic effect on improving RA patients' morning stiffness and joint pain [Rheumatoid arthritis (RA) is a chronic, systemic, and autoimmune disease. It can lead to irreversible joint destruction and deformity, seriously affecting people's quality of life . Diseaseint pain . HoweverCompound preparations in traditional medicine can act on multiple targets through multicomponent reaction, play an indispensable role in core pathways in diseases, and help achieve the purpose of treating diseases . Much athttp://bionet.ncpsb.org/batman-tcm/) was used to predict targets of LZTB for RA. On this platform, drug similarity is used to predict underlying drug targets. Its core idea is to calculate drug similarity and rank potential drug-target interactions by comparing potential and known drug-target interactions [ Ficus hirta Vahl (FHV) as major compound information (PubChem_ID: the details are described in BATMAN-TCM platform (ractions . On BATMDisGeNET (http://www.disgenet.org) database was applied to acquire RA targets .RA targets were acquired through DisGeNET, Gene_IDs of targets were input into String , speciesTargets of LZTB were acquired through BATMAN-TCM and text retrieval, and herb-compound target network was constructed through Cytoscape3.6.1.Draw Venn Diagram (http://bioinformatics.psb.ugent.be/webtools/Venn/) was applied online to find the intersection of LZTB targets acquired through BATMAN-TCM and RA targets acquired through DisGeNET. Cytoscape3.6.1 was applied to construct LZTB-RA interaction network.In large protein-protein interaction (PPI) networks, topological modules or clusters are defined as the regions where molecular complexes are densely connected , 17, andIn the field of biology, GO analysis is widely used to analyze the functions of genes . It is m p value in enrichment analysis. Target analysis was based on the enrichment analysis of functional items to investigate the potential biological functions and involved biological pathways. The technology roadmap is described in In this study, the ClusterProfiler package of R3.5.0 was adopThere are 1,254 nodes and 11,181 edges in the RA target PPI network. The closer the nodes are to red and the larger the nodes are, the higher the degree of freedom they have. This demonstrates that these genes are closely related to other genes in the network, suggesting that these genes may play an important role in RA. Pathogenic factors may directly influence RA-related genes or indirectly influence RA-related genes by affecting these genes, thereby affecting the development of RA, which suggests that these genes may be the key or central genes. The top 10 proteins with the highest degree of freedom are PIK3CA, APP, MAPK1, TP53, JUN, PTPN11, RAC1, RELA, SRC, and MAPK3. The respective degrees of freedom are 164, 132, 122, 118, 115, 111, 104, 103, 103, and 103. The details are described in Five clusters were found after RA target network was analyzed through MCODE (K-Core=10). This demonstrates that these clusters may be the most relevant to RA in studies at present. The details are described in The biological process (BP) enrichment analysis (p=0.05) of 5 clusters was conducted, and we found the following.Cluster 1 contains 394 biological processes of which those associated with RA mainly include regulation of chemotaxis in immune cells, immune cell migration, angiogenesis, apoptosis, enzyme activity, and immune responses. The details are described in Cluster 2 contains 1,392 biological processes of which those associated with RA mainly include regulation of immune cell migration, chemotaxis in immune cells, cell secretion, biosynthesis of tumor necrosis factor (TNF), enzyme activity, hormone secretion, ossification, apoptosis signaling pathway, immune responses, and phagocytosis. The details are described in Cluster 3 contains 847 biological processes of which those associated with RA mainly include regulation of TNF-mediated signaling pathway, immune cell activation, immune responses, immune cell proliferation, and Wnt signaling pathways. The details are described in Cluster 4 contains 443 biological processes of which those associated with RA mainly include regulation of immune cell activation, inflammatory cell proliferation, and apoptosis signaling pathway. The details are described in p=0.05) was carried out, and 24 pathways associated with RA were found. The details are described in Cluster 5 contains 486 biological processes of which those associated with RA mainly include regulation of immune cell activation, inflammatory cell proliferation, immune responses, and apoptosis. The details are described in In the aforementioned biological processes, regulation of immune responses, immune cell activation, and immune cell proliferation contributes to RA through joint damage caused by boosting immune responses and promoting inflammatory responses; regulation of inflammatory cell proliferation promotes RA through direct joint damage; dysregulation of apoptosis and phagocytosis promotes RA by giving rise to the dysplasia of angiogenesis and provides nutrition pathways for cell hyperplasia, which aggravates the development of RA; abnormal ossification of joints contributes significantly to the joint deformity of RA patients.In the aforementioned pathways, Th17 cell differentiation, IL-17 signaling pathway, and Chemokine signaling pathway participate in the pathological process of RA through inflammatory response; TNF signaling pathway, NF-kappa B signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, apoptosis, apoptosis-multiple species, and phagosome participate in the pathological process of RA by influencing the apoptosis, proliferation, inflammatory response, and autophagy of synovial cells; osteoclast differentiation and AMPK signaling pathway participate in the pathological process of RA by leading to joint deformity through the damage of joint cartilage and bone; Toll-like receptor signaling pathway, Th1 and Th2 cell differentiation, T cell receptor signaling pathway, TGF-beta signaling pathway, and B cell receptor signaling pathway participate in the pathological process of RA by regulating innate and adaptive immunity and influencing the proliferation of synovioblast and pathological angiogenesis; Jak-STAT signaling pathway, FoxO signaling pathway, HIF-1 signaling pathway, and cAMP signaling pathway play an important role in the proliferation and apoptosis of synovial cells, osteocyte differentiation, and immunoregulation as they accept the activation of inflammatory factors and transmit signals to the corresponding targets; rheumatoid arthritis signaling pathway exhibits the pathological process of RA in many aspects, including abnormal activation of immune system, abnormal inflammatory response, abnormal proliferation of synovial cells, pannus formation, and osteoclast differentiation. p value set at 0.05, 74 known compounds in LZTB and 2,987 target genes were retrieved. For Toddalia asiatica (TA), there are 13 compounds and 441 target genes: Chelidimerine (TA-1), Citronellol (TA-2), Isopinocamphone (TA-3), Mexolide (TA-4), Diosphenol (TA-5), Eugenol (TA-6), Alpha-Pinene (TA-7), Oxychelerythrine (TA-8), Tohogenol (TA-9), Robustine (TA-10), Skimmianine (TA-11), Citronellyl Acetate (TA-12), and Eugenol Methyl Ether (TA-13); for Kadsura coccinea (KC), there is 1 compound and 20 target genes: Schisantherin L (KC-1); for Zanthoxylum nitidum (ZN) there is 1 compound and 11 target genes: Oxynitidine (ZN-1); for Bauhinia championii (BC), there are 3 compounds and 24 target genes: Sinensetin (BC-1), 5,7,3\u2032,4\u2032,5\u2032-Pentamethoxyflavone (BC-2), and 5,6,7,3\u2032,4\u2032,5\u2032-Hexamethoxyflavone (BC-3); for Sinomenium acutum (SA), there are 15 compounds and 397 target genes: Stepholidine (SA-1), Magnoflorine (SA-2), Stepharine (SA-3), Dispegatrine (SA-4), Disinomenine (SA-5), Isosinomenine (SA-6), Michelalbine (SA-7), Magnograndiolide (SA-8), Michelenolide (SA-9), Sinactine (SA-10), Tuduranine (SA-11), Stigmasterol (SA-12), Sinomontanine D (SA-13), Gamma-sitosterol (SA-14), and Sinomenine (SA-15); for Spatholobus suberectus (SS), there are 16 compounds and 361 target genes: Licochalcone A (SS-1), Isoliquiritigenin (SS-2), Biochanin A (SS-3), Genistein (SS-4), Vestitol (SS-5), Afrormosin (SS-6), Isosativan (SS-7), Daidzein (SS-7), Formononetin (SS-8), Calycosin (SS-9), Prunetin (SS-10), Campesterol (SS-11), Stigmasterol (SS-12), Odoratin (SS-13), Pendulone (SS-14), and Medicagol (SS-15); for Alangium chinense (AC), there is 1 compound and 71 target genes: (+-)-Anabasine (AC-1); and for Ficus hirta Vahl (FHV), there are 24 compounds and 1,662 target genes: Palmitic acid (FHV-1), Meranzin hydrate (FHV-2), Quercetin (FHV-3), Oleic acid (FHV-4), Luteolin (FHV-5), Bergapten (FHV-6), Umbelliferone (FHV-7), Kaempferol (FHV-8), Sitosterol (FHV-9), Ethyl acetate (FHV-10), Methyleugenol (FHV-11), Narigenin (FHV-12), Hesperidin (FHV-13), p-hydroxybenzoic acid (FHV-14), Tricin (FHV-15), Acacetin (FHV-16), 1,2-benzenedicarboxylic acid, bis(2-methylpropyl) ester (FHV-17), \u03b1-amyrin acetate (FHV-18), Physcion (FHV-19), Cyclomorusin (FHV-20), Linoleic acid (FHV-21), \u03b2-amyrin acetate (FHV-22), Apigenin (FHV-23), and 4-hydroxy-3-methoxybenzoic acid (FHV-24). The details are described in With cutoff set at 10,The aforementioned results indicate that 8 herbs in LZTB and 67 compounds in the 8 herbs possibly are the material bases that play a key pharmacological role.After the intersection process, we found there is an overlap between 8 herbs in LZTB and RA. Toddalia asiatica (TA) have overlapping genes with RA: Citronellol (TA-2): SHBG, RET, ALDH1A2, ESR1, RHO, GATA3, ALDH1A1, CACNA1S, PGR, VCAM1, ALDH1A3, LRAT, AR; Isopinocamphone (TA-3): AR; Mexolide (TA-4): IL5, TNF, MUC2, RNASE3, NFKB1; Diosphenol (TA-5): ANXA1, ADORA2A, GRIK4, FADS2, NR3C1, CYP19A1, TH, TNF, PTGS2, ESR1, PARK2, TRPV1, TNFSF11, FOS, PGR, CYP17A1, NFKB1, HSD11B1, PTGS1, AR, PDE4A; Eugenol (TA-6): ALOX5, CNR1, CNR2, SEC14L2, NR1I2; Alpha-Pinene (TA-7): EDN1, IGF1, LEP, APOE, FAS, ALDH1A2, ASPA, MIP, ESR1, PPARD, SCGB1A1, FADD, KCNA3, ALDH1A1, PGR, CYP17A1, ALDH1A3, CAT, IL1B, SPARC, LRAT; Oxychelerythrine (TA-8): ADRA1A, PTGS2, ADRA2B, PTGS1; Tohogenol (TA-9): VDR, AR; Robustine (TA-10): ALOX5, FGF1, CHGA, PTPN2, CNR1, ABCB1, SOAT1, ABCG2, CNR2, SOCS1, SEC14L2, SERPINE1, NR1I2, TTPA, CCL3; Skimmianine (TA-11): MTNR1B, MTNR1A; Citronellyl Acetate (TA-12): ESR1, ADRA2B, PGR, AR; Eugenol Methyl Ether (TA-13): CNR1, CNR2.Specifically, 12 compounds in Kadsura coccinea (KC) has 1 overlapping gene with RA: Schisantherin L (KC-1): TOP2B.One compound in Alangium chinense (AC) has overlapping genes with RA: (+)-Anabasine (AC-1): CXCR4, PTK2B, HRH4, ADORA2A, ADRA1A, CYP19A1, TACR2, CHAT, ADRB2, LILRB1, ADRA2B, ADRB3, HTR2A.One compound in Zanthoxylum nitidum (ZN) has overlapping genes with RA: Oxynitidine (ZN-1): ADRA1A, PTGS2, ADRA2B, PTGS1.One compound in Bauhinia championii (BC) have overlapping genes with RA: Sinensetin (BC-1): IL5, TNF, MUC2, RNASE3, NFKB1; 5,7,3\u2032,4\u2032,5\u2032-Pentamethoxyflavone (BC-2): IL5, TNF, MUC2, RNASE3, NFKB; 5,6,7,3\u2032,4\u2032,5\u2032-Hexamethoxyflavone (BC-3): IL5, TNF, MUC2, RNASE3, NFKB1.Three compounds in Spatholobus suberectus (SS) have overlapping genes with RA: Licochalcone A (SS-1): HSD17B1, CNR1, PDE3A, SOAT1, CNR2; Isoliquiritigenin (SS-2): HSD17B1, ALOX5, PPARG, PTGS2, ESR1, CFTR, PTGS1; Biochanin A (CS-3): ALOX5, CNR1, SOAT1, CNR2, SEC14L2, NR1I2; Genistein (SS-4): HSD17B1, ESR1, CACNA1S, PGR, NR1I2, AR, ESR2; Vestitol (SS-5): ALOX5, FGF1, CHGA, PTPN2, CNR1, ABCB1, SOAT1, ABCG2, CNR2, SOCS1, SEC14L2, SERPINE1, NR1I2, TTPA, CCL3; Afrormosin (SS-6): ALOX5, CNR1, SOAT1, CNR2, SEC14L2, NR1I2; Isosativan (SS-7): ALOX5, FGF1, CHGA, PTPN2, CNR1, ABCB1, SOAT1, ABCG2, CNR2, SOCS1, SEC14L2, SERPINE1, NR1I2, TTPA, CCL3; Formononetin (SS-9): ALOX5, CNR1, SOAT1, CNR2, SEC14L2, NR1I2; Calycosin (SS-10): ALOX5, CNR1, SOAT1, CNR2, SEC14L2, NR1I2; Prunetin (SS-11):ALOX5, CNR1, SOAT1, CNR2, SEC14L2, NR1I2; Campesterol (SS-12): ANXA1, NR3C1, ESR1, VDR, PGR, AR; Stigmasterol (SS-13): EDN1, IGF1, LEP, APOE, FAS, ALDH1A2, ASPA, MIP, ESR1, PPARD, SCGB1A1, FADD, KCNA3, ALDH1A1, PGR, CYP17A1, ALDH1A3, CAT, IL1B, SPARC, LRAT; Odoratin (SS-14): ALOX5, CNR1, SOAT1, CNR2, SEC14L2, NR1I2; Pendulone (SS-15): ADRA1A, CNR1, SOAT1, CNR2, ADRA2B.Fourteen compounds in Sinomenium acutum (SA) have overlapping genes with RA: Stepholidine (SA-1): NCF4, RAC1, RAC2, NCF2, NCF1, ESR1, ADRA2B, CYBB, HTR2A, ESR2; Magnoflorine (SA-2): ALOX5, ADRA2B, SEC14L2, HTR2A, NR1I2; Dispegatrine (SA-4): ADRA2B, HTR2A; Disinomenine (SA-5): SHH, ESR1, CREB1, TLR4, HTR2A, ESR2; Isosinomenine (SA-6): SHH, ESR1, CREB1, TLR4, HTR2A, ESR2; Michelalbine (SA-7): NFATC1, NPPB, ADORA2A, ADRA1A, SELE, TNF, ADRB2, VEGFA, ADRA2B, IL2, FOS, ATF2, HIF1A, VCAM1, ADRB3, HTR2A, JUN, HBA1; Magnograndiolide (SA-8): ATP1A1, ITGB2, HMGCR, AR, ITGAL; Michelenolide (SA-9): ADRA1A; Sinactine (SA-10): NCF4, RAC1, ELANE, RAC2, HRH4, NCF2, ADRA1A, SLC22A1, NCF1, ADRA2B, CYBB, TLR4, HTR2A; Tuduranine (SA-11): ADRA2B, HTR2A; Stigmasterol (SA-12): EDN1, IGF1, LEP, APOE, FAS, ALDH1A2, ASPA, MIP, ESR1, PPARD, SCGB1A1, FADD, KCNA3, ALDH1A1, PGR, CYP17A1, ALDH1A3, CAT, IL1B, SPARC, LRAT; Sinomontanine D (SA-13): UGCG, GAA, PADI4; Gamma-Sitosterol (SA-14): CALB1, KL, NR3C1, GC, ESR1, VDR, PML, PGR, CYP17A1, NFKB1, AR, SNAI2, BAX; Sinomenine (SA-15): ESR1, ESR2.Fourteen compounds in Ficus hirta Vahl (FHV) have overlapping genes with RA: palmitic acid (FHV-1): BTG2, EDN1, IGF1, PAK1, SOD2, FGFR1, MTNR1B, NR4A2, F2RL1, EDNRA, GHRL, CNTN2, ADRA1A, LXN, TACR2, F2, PTGS2, BMP2, TAC1, PDE4D, SNCA, NR4A3, PARK2, HYAL2, EPHB1, TRPV1, INS, CRHR1, LPAR3, GDNF, CRH, IL10, CHD7, TYK2, F2R, STRA6, TACR3, ALDH1A3, CAT, ADAM17, ADRB3, ADM, UCN3, CAV2, IL1B, HTR2A, CX3CR1, P2RX7, GNA12, PTEN, PTK2B, RAB3GAP1, CLN8, MECP2, ARHGEF7, NOS1, PTPN11, NPPB, YWHAE, BDKRB2, ADORA2A, CHGA, DLL1, CRHR2, CNR1, FABP3, CDK6, TH, VIM, EDNRB, CDC42, ARRB1, ADRB2, ADA, PARP1, CD34, INHBA, LILRB1, ADRA2B, S1PR1, FOS, MDK, IGF1R, HPRT1, HIF1A, XBP1, GFAP, CREBRF, CDK5, MAP2K1, PTGS1, LPAR1, GHSR; quercetin (FHV-3)ADRA2B, HTR2A; oleic acid (FHV-4): IGF1, ANXA1, NOS1, SHBG, ABCA1, BDKRB2, SCD5, PPARG, ALOX15, RARB, RET, FADS2, ALDH1A2, MAPK9, PTPN2, NR3C1, FABP3, TNF, ABCC2, ITGAV, APOA2, PTGS2, FGF4, GPRC5A, ESR1, SNCA, S100A8, IL13, PTGER4, TRPV1, VDR, PPARD, IHH, FASLG, INS, RARA, SERPINH1, PPARA, GATA3, NAMPT, PTGER2, SP1, JUNB, FGF2, ALDH1A1, SLC3A2, GDF5, PGR, RARG, ALDH1A3, IL1B, PTGS1, PPARGC1B, AR, NOTCH1, CYR61, S100A9, ADIPOQ; bergapten (FHV-6): RARB, TNF, VDR, RARA, RARG; umbelliferone (FHV-7): SOD2, SOD3, SOD1; kaempferol (FHV-8): HSD17B1; sitosterol (FHV-9): COX5A, CALB1, ABCA1, KL, COX8A, ABCB1, NR3C1, GC, ABCC2, COX1, ESR1, SOAT1, VDR, HMGCR, PML, PLA2G1B, ANPEP, PGR, CYP17A1, COX2, AKT1, NFKB1, ABCC8, AR, SNAI2, BAX, ITGAL; ethyl acetate (FHV-10): HSD17B1, PF4, BDKRB2, ARHGEF2, HDAC9, TH, EGLN1, SULT2A1, CDC42, CDH11, WNT10B, GPT, CCL2, SHMT1, CYP1A2, IL10, EDA, SLC16A4, SLC16A3, CCL5, SLC25A12, HDAC1, SIRT1, P4HB, DHODH, SLC52A2; methyleugenol (FHV-11): MTNR1B, DNMT3B, FOLR1, AURKA, DHFR, ABCC2, MPO, CALR, HOXA5, ESR1, TYMS, PDE3A, FOLR2, CALM2, MTNR1A, SHMT1, HYAL2, DNMT1, HIF1A, CALM3, CDKN1A, IL1B, HTR2A, GAS6, ATIC, CALM1, PDE4A; p-hydroxybenzoic acid (FHV-12): ANXA1, ALOX5, AKR1B10, ABCA1, BDKRB2, PPARG, ALOX15, MAPK9, PTPN2, TPMT, FABP3, TNF, MPO, ITGAV, CHUK, APOA2, PTGS2, SNCA, S100A8, IL13, INS, PPARA, NAMPT, PLA2G1B, IKBKB, IFNG, IKBKE, SERPINE1, IL1B, PTGS1, S100A9, ADIPOQ; tricin (FHV-13): ALOX5, CNR1, SOAT1, CNR2, SEC14L2, NR1I2; acacetin (FHV-14): ALOX5, ADORA2A, CNR1, NR3C1, ESR1, SOAT1, CNR2, SEC14L2, NR1I2, HBA1; 1,2-benzenedicarboxylic acid, bis(2-methylpropyl) ester (FHV-15): NFKB2, EDNRA, CRP, PTGS2, CHKA, SLC5A7, ADRA2B, IKBKB, TP53, NFKB1, NFKBIA, PTGS1, RPS6KA3; \u03b1-amyrin acetate (FHV-16): NR3C1, CYP19A1, ESR1, ADRA2B, PGR, AR; physcion (FHV-17): CNR1, PTGS2, ESR1, SOAT1, CNR2, PTGS1; cyclomorusin (FHV-18): CNR1, CNR2; linoleic acid (FHV-19): IGF1, ANXA1, NOS1, PCYT1A, SHBG, ABCA1, BDKRB2, SCD5, PPARG, ALOX15, RARB, RET, FADS2, ALDH1A2, MAPK9, PTPN2, NR3C1, FABP3, TNF, ABCC2, ITGAV, APOA2, PTGS2, FGF4, GPRC5A, SNCA, S100A8, IL13, PTGER4, TRPV1, VDR, PPARD, IHH, FASLG, INS, RARA, SERPINH1, PPARA, GATA3, NAMPT, PTGER2, SP1, JUNB, FGF2, ALDH1A1, SLC3A2, GDF5, RARG, ALDH1A3, IL1B, HSD11B1, PTGS1, PPARGC1B, AR, NOTCH1, CYR61, S100A9, ADIPOQ; narigenin (FHV-20): HSD17B1, SUMO1, ALOX5, C3, CNR1, ESR1, SOAT1, CNR2, SEC14L2, AKT1, NR1I2, ESR2; \u03b2-amyrin acetate (FHV-21): NR3C1, CYP19A1, ESR1, ADRA2B, PGR, AR; hesperidin (FHV-23): ESR1, ADRB2, SOAT1, VDR, HTR2A, NR1I2, ESR2; 4-hydroxy-3-methoxybenzoic acid (FHV-24): ANXA1, FOXP3, ABCA1, BDKRB2, PPARG, ALOX15, RARB, MAPK9, MAPK14, TNF, ITGAV, PTGS2, FGF4, SNCA, VDR, IHH, INS, RARA, SERPINH1, PPARA, NAMPT, FGF2, GDF5, RARG, TP53, GCG, PTGS1, CDKN2A, ABCC8, NOTCH1, CYR61, ADIPOQ. The details are described in Twenty-one compounds inThe aforementioned results suggest that LZTB has intervention effects on RA as the 8 herbs in LZTB can have effects on RA through multiple compounds and targets.We obtained 3 clusters after conducting clustering analysis for LZTB target-RA target network (K-core=2). The details are described in Toddalia asiatica (TA), Bauhinia championii (BC), Sinomenium acutum (SA), and Alangium chinense (AC). It indicates that the 8 compounds in the 4 aforementioned Zhuang herbs play an important role in the treatment of RA.Cluster 1 contains 4 compounds: BC-1, BC-2, BC-3, and TA-4; cluster 2 contains 2 compounds: A-10 and AC-1; cluster 3 contains 2 compounds: SA-14 and TA-2. Three clusters contain 8 compounds and 4 Zhuang herbs:Cluster 1 contains 3 genes: MUC2, IL5, and RNASE3; cluster 2 contains 2 genes: HTR2A and ARA2B; and cluster 3 contains 2 genes: AR and PGR. It indicates that the 7 aforementioned genes are key to the treatment of RA with LZTB.p=0.05) showed that cluster 1 contains 20 biological processes of which those associated with RA mainly include regulation of immunoglobulin secretion, immune responses, and B cell proliferation. The details are described in p=0.05), 24 pathways associated with RA were found, and 7 herbs in LZTB participate in the regulations of pathways. The details are described in The GO enrichment analysis of the aforementioned clusters indicated that it is directly associated with RA. TA-4, TA-5, TA-7, TA-10, BC-1, BC-2, BC-3, SA-5, SA-6, SA-7, SA-8, SA-10, SA-12, SS-5, SS-7, SS-13,FHV-1, FHV-4, FHV-6, FHV-9, FHV-10, FHV-11, FHV-12, FHV-19, and FHV-24 are effective compounds in LZTB that directly intervene with RA pathways, and 13 genes are involved: CCL2, CCL3, CCL5, FOS, IFNG, IL1B, ITGAL, ITGB2, JUN, TLR4, TNF, TNFSF11, and VEGFA. The details are described in TRP channels are a group of nonselective cation channels throughout the body, and they are Ca 2 + permeable. TRP channels consist of more than 30 members that are divided into 7 subfamilies: TRPC, TRPV, TRPM, TRPA, TRPP, TRPML, and TRPN . Accordi\u03b1, PPAR-\u03b2, and PPAR-\u03b3. PPAR-\u03b3 is more closely related to RA. According to research, the expression of PPAR-\u03b3 can be detected in synovial cells involved in rheumatoid arthritis. PPAR-\u03b3 agonists can inhibit the hyperplasia of synovial cells and induce their apoptosis [\u03b3 agonists can inhibit the generation of key mediators in RA from macrophages, including IL-1\u03b2, IL-6, and TNF-\u03b1 [PPARs (peroxisome proliferation-activated receptors) are ligand-activated transcription factors, comprising of the following three subtypes: PPAR-poptosis , 37. In nd TNF-\u03b1 . In conc\u03b1) are released into articular cavity. Then, the activated PI3K in synovioblasts transmits signal to Akt. Regulating multiple transcription factors, the activated Akt helps with cell survival by inhibiting the expression of apoptosis gene and the activity of proapoptotic protein (Bad) and enhancing the expression of antiapoptotic gene [Serine/threonine-protein kinase mTOR belongs to the PIKK (phosphoinostitide-3-kinase-related kinase) family, and it plays a key role in regulating cell growth, proliferation and survival. In RA-related mTOR signaling pathways, PI3K/Akt/mTOR signaling pathway is actively studied . In the , NF\u2014\u03baB) . Akt act, NF\u2014\u03baB) . In summIn conclusion, the three aforementioned signaling pathways of LZTB possibly act on RA.Currently, conventional synthetic disease-modifying antirheumatic drugs remain the first choice for clinical treatment in RA. We found in this study that some compounds in LZTB are directly involved in the regulation of RA pathways and that they possibly are major compounds in LZTB for the treatment of RA, for example, Mexolide, Diosphenol, Alpha-Pinene, Robustine, Sinensetin, 5,7,3\u2032,4\u2032,5\u2032-Pentamethoxyflavone, 5,6,7,3\u2032,4\u2032,5\u2032-Hexamethoxyflavone, Stepholidine, Magnoflorine, Dispegatrine, Disinomenine, Isosinomenine, Michelalbine, Magnograndiolide, Michelenolide, Sinactine, Tuduranine, Stigmasterol, Vestitol, Daidzein, Odoratin, Palmitic acid, Oleic acid, Bergapten, Sitosterol, Ethylacetate, Methyleugenol, Narigenin, Physcion, and 4-hydroxy-3-methoxybenzoicacid. In this study, we applied network-based computational methods to predict and expound the molecular synergy of LZTB for RA. It will provide new ideas for further research on ethnopharmacology, Chinese medicinal herbs and ethnic compounds. The targets, clusters, biological processes, and pathways associated with RA were discovered through this study. LZTB target-RA target network exhibited the effective chemical compounds, potential pharmacology, and molecular mechanism of LZTB for treating RA and also justified the composition of LZTB."} +{"text": "Correction to: Arthritis Res Therhttps://doi.org/10.1186/s13075-017-1399-5Following publication of the original article , the aut1Centre for Prognostic Studies in the Rheumatic Diseases, Toronto Western Hospital, University of Toronto, 1-412, 399 Bathurst Street, Toronto, ON M5T 2S8, Canada.8Department of Rheumatology, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel."} +{"text": "Therefore, the authors\u2019 names and affiliations for this paper should have been presented as follows:1, AYMAN G. MUSTAFA2,4, AMAL ABU OMAR2, AHMED N. AL.DWAIRI1, MOHAMMAD A. ALQUDAH1, MONA S. NAZZAL1, MAHMOUD A. ALFAQIH1, and RAMI A. AL.HADER3OTHMAN A. AL.SHBOUL1Physiology and Biochemistry, and 2Anatomy, Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110; 3Department of Physiology and Biochemistry, Princess Basma Teaching Hospital, Faculty of Medicine, Jordan University of Science and Technology, Irbid 21110, JordanDepartments of Correspondence to: Dr Othman A. Al-Shboul, Department of Physiology and Biochemistry, Faculty of Medicine, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, JordanE.mail: oashboul@just.edu.joPresent address: 4Department of Basic Medical Sciences, College of Medicine, Qatar University, Doha, QatarThe authors regret this oversight in terms of their author affiliations, and apologize for any inconvenience caused."} +{"text": "This article has been corrected: During production, the 4th affiliation was mistakenly added to the name of the last author, Dr. Andrew S. Moore. The proper affiliation information is shown below.5755-5767. https://doi.org/10.18632/oncotarget.27206Original article: Oncotarget. 2019; 10:5755\u20135767. 1,4,*, Christine R.C. Zhang1,4,*, Alexandre S. Cristino1,6, John P. Grady1,5, J. Lynn Fink1 and Andrew S. Moore1,2,3Amanda M. Smith1The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Australia2Oncology Services Group, Queensland Children\u2019s Hospital, South Brisbane, Australia3Child Health Research Centre, The University of Queensland, South Brisbane, Australia4Current address: Washington University in Saint Louis, Saint Louis, Missouri, United States of America5Current address: Garvan Institute of Medical Research, Darlinghurst, Australia6Current address: Griffith Institute for Drug Discovery, Brisbane Innovation Park, Nathan, Australia*These authors contributed equally to this work"} +{"text": "O. Box LG 25, Legon, Ghana 2\u00a0Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P. O. Box LG 25, Legon, Ghana3\u00a0West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, P. O. Box LG 25, Legon, GhanaThe name of country in affiliations provided was: 1 Department of Biomedical Engineering, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 25, Legon2 Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P. O. Box LG 25, Legon3 West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, P. O. Box LG 25, Legon"} +{"text": "Lipoprotein glomerulopathy (LPG) is an uncommon cause of nephrotic syndromeand/or kidney failure. At microscopy, LPG is characterized by the presence oflipoprotein thrombi in dilated glomerular capillaries due to different ApoEmutations. ApoE gene is located on chromosome 19q13.2, and can be identified inalmost all serum lipoproteins. ApoE works as a protective factor inatherosclerosis due its interaction with receptor-mediated lipoprotein clearanceand cholesterol receptor. Most common polymorphisms include ApoE2/2, ApoE3/2,ApoE3/3, ApoE4/2, ApoE4/3, and ApoE4/4. All age-groups can be affected by LPG,with a discrete male predominance. Compromised patients typically revealdyslipidemia, type III hyperlipoproteinemia, and proteinuria. LPG treatmentincludes fenofibrate, antilipidemic drugs, steroids, LDL aphaeresis, plasmaexchange, antiplatelet drugs, anticoagulants, urokinase, and renaltransplantation. Recurrence in kidney graft suggests a pathogenic component(s)of extraglomerular humoral complex resulting from abnormal lipoproteinmetabolism and presumably associated to ApoE. The compromisedglomeruli exhibit ectatic capillary lumina occupied by lipoprotein thrombi.1,4,5,7,12,13,14,15,The first case of LPG described in English literature was by Saito et al, whoreported a patient with resistant nephritic syndrome and accumulation of lipiddroplets in glomeruli loops.1,3,4,7,8,3,4,5,7,12,15,18,1,4,5,9,19,21,22,23,4,7,8,19,25,26,27,13,15,17,19,20,23,29,ApoE is a fundamental component of lipid and lipoprotein metabolism byfunctioning as the ligand for receptor-mediated catabolism of chylomicrons, someHDLs, and VLDLs. ApoE is present in almost all serum lipoproteins and acts as aprotective factor in atherosclerosis due its interaction with receptor-mediatedlipoprotein clearance and cholesterol receptor.1,19,([21]) Matsunaga etal.Arg25Cys is a common mutation of ApoE gene and is known as ApoE Kyoto.12cis or in trans) that can inducedifferent levels of expression of the mutant vs the wild-type allele ; b) an uncommonmutation or a polymorphism in another gene possibly associated to the fullphenotypic expression of LPG; and c) epigenetic processes related to theregulation of a mutant gene.Chen at al.,7,8,19,21,39,19,21,34,41,3,8,13,14,15,17,21,28,19,21,34,41,The most common mutation is the Sendai form, which is characterized by asubstitution of proline for arginine-145. ApoE Sendai can break the\u03b1-helical structure of ApoE in the low-density lipoproteinreceptor-binding domain and modify the ApoE protein that are deposited inglomeruli thrombi and mesangium.2,5,6,9,2,7,9,19,22,4,6,15,23,26,30,1,7,10,11,15,16,22,28,4,6,7,9,23,27,1,9,11,15,17,32,The characteristic histologic finding of LPG is the presence of large glomerulidue to ectatic capillary loops, which are occupied with lipoprotein thrombi. The glo1,5,8,15,21,25,5,8,15,21,25,32,45,Associated to histological findings, proteinuria, dyslipidemia, and increasedserum apolipoproteins levels are also hallmarks of LPG. The patients exhibittype III hyperlipoproteinemia and progress to nephritic syndrome in most cases.All age groups can be affected in LPG, with a discrete male predominance.1,8,18,21,32,35,39,41,4,21,32,35,MODENA mutation that wastreated successfully with low-density lipoprotein-apheresis with the Heparininduced extracorporeal lipoprotein precipitation system. Heparin-inducedextracorporeal low-density lipoprotein (LDL) precipitation (HELP) is a selectiveand careful apheresis procedure. Through the application of heparin and loweringthe pH value, lipoproteins and fibrinogen are reduced by 50-60%. In addition,adhesion molecules , which play a key role in thedevelopment and progression of atherosclerosis are also markedly reduced.Many reports describe various therapies such as LDL aphaeresis, plasma exchange,renal transplantation, steroids, antiplatelets, anticoagulants, ACEI, ARB,urokinase, and antilipidemic drugs.4,4,8,12,21,32,1,4,8,12,21,32,35,Although all these treatments determine some benefits to LPG patients, not allpatients respond the same way. A point to be further analyzed is theheterogeneity of the disease and the type of mutation involved. Most mutations,including ApoE Sendai, associated with LPG locate around the receptor-bindingdomain for LDL cholesterol and reduce the receptor-binding activity. Patientsfrequently have accompanying hyperlipidemia. Moreover, several patients withApoE Kyoto or ApoE5 mutations, which locate far from receptor binding sites, arenot complicated with hyperlipidemia. Those mutations indicate that ApoE mutantscausing LPG do not damage glomeruli via hyperlipidemia but might injureglomeruli directly by forming aggregated deposits of lipoproteins that have highaffinity or low clearance in glomeruli.1,21,Since half of the patients with LPG might eventually develop end-stage renaldisease, kidney transplantation should be considered in these patients. However,the long-term outcome of kidney transplantation in patients with LPG remainsuncertain. All of five kidney transplants reported in the literature had LPGrelapse, which were confirmed by renal graft biopsy within 2 years aftertransplantation. It seems that LPG recurrence in a transplanted kidney isinevitable, which is also associated with poor prognosis.12"} +{"text": "There are errors in the author affiliations. The correct affiliations are as follows:1,2, Mary Grace Tan2, Woei Bing Poon2Lay Ong Tan1 Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 2 Department of Neonatal & Developmental Medicine, Singapore General Hospital, Singapore."} +{"text": "In the published article, there was an error in affiliations 1 and 2.1, Guohong Wang1,2, Zhengyuan Zhai1, Pengyu Zhou1 and Yanling Hao1,2*Instead of \u201cXiayin Ma1 Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, China Agricultural University, Beijing, China2 The Innovation Centre of Food Nutrition and Human Health (Beijing), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China,\u201d1,2, Guohong Wang1,2, Zhengyuan Zhai1,2, Pengyu Zhou2 and Yanling Hao1,2*it should be \u201cXiayin Ma1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China2 Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, China Agricultural University, Beijing, China.\u201dThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "This article has been corrected: The correct author information and affiliations are given below:1, Boris Gole1,2, Laurent Chatre3,4, Paul Walther5, Enrico Calzia6, Anja Palmer7, J. Christof M. Gebhardt7, Miria Ricchetti3,4 and Lisa Wiesm\u00fcller1Rahel Stefanie Wiehe1 Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany2 Present address: Centre for Human Molecular Genetics and Pharmacogenomics, Medical Faculty, University of Maribor, Maribor, SI-2000, Slovenia3 Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France4 Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France5 Central Facility for Electron Microscopy, Ulm University, Ulm, 89081, Germany6 Institute of Anesthesiological Pathophysiology and Process Engineering, Ulm University Hospital, Ulm, 89081, Germany7 Institute of Biophysics, Ulm University, Ulm, 89081, Germanyhttps://doi.org/10.18632/oncotarget.24822Original article: Oncotarget. 2018; 9:18309-18326."} +{"text": "Int J Epidemiol 2013;42:1754-1771, doi:10.1093/ije/dyt198During the preparation of this article, owing to an administrative oversight between the collaborating institutions, we omitted Dr Dermot Maher from the author list. Dr Maher was involved in the early phases of the General Population Cohort (GPC) Study, data from which were used in the individual-level participant data analyses in this manuscript. His role included contributing to the GPC study protocol development, management of initial research ethics application for the GPC, and organisation of initial field programmes at MRC/UVRI Uganda Research Unit on AIDS.As a result, we request that Dr Maher is included in the author list. This results in the following correction:1,2 Deepti Gurdasani,1,2 Johanna Riha,1,2 Kenneth Ekoru,1,2,3 Gershim Asiki,3 Billy N Mayanja,33Dermot Maher, Naomi S Levitt,4 Nigel J Crowther,5 Moffat Nyirenda,6 Marina Njelekela,7 Kaushik Ramaiya,8 Ousman Nyan,9 Olanisun O Adewole,10 Kathryn Anastos,11 Livio Azzoni,12 W Henry Boom,13 Caterina Compostella,14 Joel A Dave,15 Halima Dawood,16 Christian Erikstrup,17 Carla M Fourie,18 Henrik Friis,19 Annamarie Kruger,20 John A Idoko,21 Chris T Longenecker,22 Suzanne Mbondi,23 Japheth E Mukaya,24 Eugene Mutimura,11 Chiratidzo E Ndhlovu,25 George Praygod,26 Eric W Pefura Yone,27 Mar Pujades-Rodriguez,28,29 Nyagosya Range,26 Mahmoud U Sani,30 Aletta E Schutte,18 Karen Sliwa,31 Phyllis C Tien,32 Este H Vorster,33 Corinna Walsh,34 Rutendo Zinyama,35 Fredirick Mashili,7 Eugene Sobngwi,36,37 Clement Adebamowo,38,39 Anatoli Kamali,3 Janet Seeley,3 Elizabeth H Young,1,2 Liam Smeeth,40 Ayesha A Motala,41 Pontiano Kaleebu,3 Manjinder S Sandhu1,2* and on behalf of the African Partnership for Chronic Disease Research (APCDR).David G Dillon,1Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge, UK,2Genetic Epidemiology Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK,3MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda,4Division of Diabetic Medicine and Endocrinology, Department of Medicine, University of Cape Town, Cape Town, South Africa; Chronic Diseases Initiative in Africa,5Department of Chemical Pathology, National Health Laboratory Service, University of the Witwatersrand Medical School, Johannesburg, South Africa,6Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi,7Department of Physiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania,8Department of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania,9Royal Victoria Teaching Hospital, School of Medicine, University of The Gambia, Banjul, The Gambia,10Department of Medicine, Obafemi Awolowo University, Ile Ife, Nigeria,11Women\u2019s Equity in Access to Care &Treatment, Kigali, Rwanda,12HIV-1 Immunopathogenesis Laboratory, Wistar Institute, Philadelphia, PA,13Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University, Cleveland, OH,14Department of Medical and Surgical Sciences, University of Padua, Padua, Italy,15Division of Diabetic Medicine and Endocrinology, Department of Medicine, University of Cape Town, Cape Town, South Africa,16Infectious Diseases Unit, Department of Medicine, Grey\u2019s Hospital, Pietermaritzburg, South Africa,17Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark,18HART (Hypertension in Africa Research Team), North-West University, Potchefstroom, South Africa,19Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark,20Africa Unit for Transdisciplinary Health Research (AUTHeR), North-West University, Potchefstroom, South Africa,21Department of Medicine, Jos University Teaching Hospital, Jos, Nigeria,22University Hospitals Case Medical Center, Cleveland, OH,23German Development Cooperation (GTZ), Yaounde, Cameroon,24Department of Medicine, Makerere University, Kampala, Uganda,25Clinical Epidemiology Resource Training Centre, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe,26National Institute for Medical Research, Dar es Salaam, Tanzania,27Chest Unit of Jamot Hospital, Yaounde, Cameroon,28Epicentre, M\u00e9decins Sans Frontie`res, Paris, France,29Clinical Epidemiology Group, Department of Epidemiology and Public Health, University College London, London, UK,30Cardiology Unit, Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria,31Soweto Cardiovascular Research Unit, Chris Hani Baragwanath Hospital, University of the Witwatersrand, Johannesburg, South Africa,32Department of Medicine, University of California, San Francisco, CA, 33Faculty of Health Sciences, North-West University, Potchefstroom, South Africa,34Department of Nutrition and Dietetics, University of the Free State, Bloemfontein, South Africa,35Medical Research Council of Zimbabwe, Department of Medical Laboratory Sciences, University of Zimbabwe, Harare, Zimbabwe,36Faculty of Medicine and Biomedical Sciences, University of Yaounde 1, Yaounde, Cameroon,37Institute of Health and Society, University of Newcastle, Newcastle, UK,38Institute of Human Virology, Abuja, Nigeria,39Department of Epidemiology and Public Health, Institute of Human Virology and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD,40Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK41Department of Diabetes and Endocrinology, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africams23@sanger.ac.uk*Corresponding author. International Health Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. E-mail: We apologise for this oversight."} +{"text": "Correction to:Cell Death & Disease10.1038/s41419-018-0970-6, published online 17 September 2018Following publication of this article, the authors realized that there were 1) errors made in the author affiliations and that 2) a typo in a grant number needed to be corrected. The corrected author affiliations and grant numbers are listed below. We apologize for the inconvenience.1,2, Jih-Yang Ko3, Yu-Shan Chen1,2, Huei-Ching Ke1,2, Shin-Long Wu1,2, Chung-Wen Kuo1,2, Feng-Sheng Wang1,2,41) Wei-Shiung Lian1 Core Laboratory for Phenomics and Diagnostic, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan2 Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan3 Department of Orthopedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan4 Graduate Institute of Clinical Medical Science, Chang Gung University College of Medicine, Kaohsiung, Taiwan2) In the Acknowledgements section, grant numberCMRPG8H00112 is incorrect. The correct grant number is CMRPG8H0111.This has been corrected in both the PDF and HTML versions of the Article."} +{"text": "Scientific Reports 10.1038/s41598-018-22296-8, published online 07 March 2018Correction to: The original version of this Article contained errors. Affiliations 1 and 3 were incorrectly given as \u2018National Oceanography Centre, Southampton, SO14 3ZH, United Kingdom\u2019 and \u2018University of Oxford, Department of Zoology, Oxford, OX2 6GG, United Kingdom\u2019 respectively. In addition, an affiliation was omitted, which is now listed as Affiliation 5.Furthermore, the authors of this manuscript were incorrectly affiliated. Lissette Victorero was incorrectly affiliated with \u2018National Oceanography Centre, Southampton, SO14 3ZH, United Kingdom\u2019. Katleen Robert was incorrectly affiliated with \u2018National Oceanography Centre, Southampton, SO14 3ZH, United Kingdom\u2019. Laura F. Robinson was incorrectly affiliated with \u2018University of Oxford, Department of Zoology, Oxford, OX2 6GG, United Kingdom\u2019. Michelle L. Taylor was incorrectly affiliated with \u2018University of Bristol, School of Earth Sciences, Bristol, BS8 1RJ, United Kingdom\u2019. Veerle A.I. Huvenne was incorrectly affiliated with \u2018University of Southampton, Ocean and Earth Science, Southampton, SO14 3ZH, United Kingdom\u2019.The correct affiliations list and affiliated authors are given below.Affiliation 1:National Oceanography Centre, University of Southampton Waterfront Campus, Southampton, SO14 3ZH, United KingdomLissette VictoreroKatleen RobertVeerle A.I. HuvenneAffiliation 2:University of Southampton, Ocean and Earth Science, Southampton, SO14 3ZH, United KingdomLissette VictoreroAffiliation 3:Fisheries and Marine Institute of Memorial University, St. John\u2019s, NL A1C 5R3, CanadaKatleen RobertAffiliation 4:University of Bristol, School of Earth Sciences, Bristol, BS8 1RJ, United KingdomLaura F. RobinsonAffiliation 5:University of Essex, School of Biological Sciences, Colchester, CO4 3SQ, United KingdomMichelle L. TaylorThese errors have now been corrected in the PDF and HTML versions of the paper, and in the accompanying Supplementary information file."} +{"text": "Brain, awy358, https://doi.org/10.1093/brain/awy358.Peter Rudge, Zane Jaunmuktane, Harpreet Hyare, Matthew Ellis, Martin Koltzenburg, John Collinge, Sebastian Brandner, Simon Mead. Early neurophysiological biomarkers and spinal cord pathology in inherited prion disease. The authors would like to apologise for two of the authors' affiliations being listed incorrectly in the original manuscript, they are listed correctly below:1,2 and Simon Mead1,2John Collinge1 National Prion Clinic, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust (UCLH), London, UK 2 MRC Prion Unit at UCL, Institute of Prion Diseases, 33 Cleveland St. London, W1W 7FF, UKThe manuscript has been corrected online."} +{"text": "The affiliations should be as follows:In \u201cControl of the HIV-1 Load Varies by Viral Subtype in a Large Cohort of African Adults With Incident HIV-1 Infection\u201d by Matt A. Price et al [J Infect Dis 2019; 9,15,16,17, Paramesh Chetty,1,14Vinodh A. Edward,1International AIDS Vaccine Initiative, New York, New York;9Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut;14School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, and15Advancing Care and Treatment for TB/HIV, South African Medical Research Council, Johannesburg, and16Desmond Tutu HIV Foundation, Cape Town, South Africa17Advancing Care and Treatment for TB/HIV, South African Medical Research Council, Johannesburg."} diff --git a/PMC_clustering_713.jsonl b/PMC_clustering_713.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..69ae9e5b760541d7c06045c650bed061f4ce8858 --- /dev/null +++ b/PMC_clustering_713.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:23d99d925e89e82ebd94d35a10da492f63823729ef2110309fd4214c5de761a7 +size 90112664 diff --git a/PMC_clustering_714.jsonl b/PMC_clustering_714.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..f1a9ad4a24a23d06f180ba6d9a6bbebad73f12f0 --- /dev/null +++ b/PMC_clustering_714.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7324189d75ab5e1d5d08fe5cdd3367deecc15fbbd61ecc843a91c5216f0be15a +size 36805523 diff --git a/PMC_clustering_715.jsonl b/PMC_clustering_715.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..092990c3a0d40763a1a0669e1902b73dbc8b124d --- /dev/null +++ b/PMC_clustering_715.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:57fecab9018822d7458715caa3154c446e83caa9b1e4901352f2a1f449ac55a8 +size 29701212 diff --git a/PMC_clustering_716.jsonl b/PMC_clustering_716.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..e165aa041c6ca68b18556d600671027ac5debe0e --- /dev/null +++ b/PMC_clustering_716.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:226e6d753725b88fec1ba044bae9cc1526e050663acfad6dfd8c1af0e75035fb +size 25070027 diff --git a/PMC_clustering_717.jsonl b/PMC_clustering_717.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..8ff2c1ca99512549324f7d483027c002b7aa7286 --- /dev/null +++ b/PMC_clustering_717.jsonl @@ -0,0 +1,511 @@ +{"text": "This case report highlights the clinical efficacy of endoscopic transpapillary drainage for gallbladder perforation in a high\u2010risk surgical patient with a history of steroid treatment for interstitial pneumonia. The usefulness of endoscopic transpapillary gallbladder drainage in high\u2010risk surgical patients with acute cholecystitis has not been established. In difficult cases of emergent surgery, such as described here, endoscopic transpapillary drainage is a promising method to manage gallbladder perforation and acute cholecystitis recurrence. A 74\u2010year\u2010old woman who had been treated with prednisolone for interstitial pneumonia was referred to our department because of complaints of severe abdominal pain and high fever. Physical examination revealed tenderness in the right upper quadrant with positive Murphy's sign. Blood tests showed elevated white blood cell count and C\u2010reactive protein level. Computed tomography (CT) revealed an enlarged gallbladder with pericholecystic inflammation Fig. ; therefoThe standard treatment for perforated cholecystitis is emergent cholecystectomy.Video Clip S1 Successful treatment with endoscopic transpapillary drainage for gallbladder perforation.Click here for additional data file."} +{"text": "Erythroblastic islands (EBIs) were first described by Marcel Bessis in 1958 .We found a picturesque erythroblastic island with a central macrophage encircled by a garland of erythroid cells in the bEarly descriptions of EBIs did not receive much attention because of their infrequent occurrence in BMA due to their distortion during smear preparation . Some re"} +{"text": "In the Acknowledgement Section, the author wrote ``Hyogo Prefectural Particle Beam Medical Care Center'', but it should be ``Hyogo Ion Beam Medical Center''. This has now been corrected. The author apologizes for this error."} +{"text": "The original version of this article did not include Kyung-Won Hong's affiliation with Theragen Etex Bio Institute or Jongpill Choi's affiliation with Thermo Fisher Scientific Solutions, and incorrectly stated that Hyo-Jeong Ban was affiliated with both Theragen Etex and Thermo Fisher. These errors have now been corrected."} +{"text": "Fixpoint logics have recently been drawing attention as common foundations for automated program verification. We formalize fold/unfold transformations for fixpoint logic formulas and show how they can be used to enhance a recent fixpoint-logic approach to automated program verification, including automated verification of relational and temporal properties. We have implemented the transformations in a tool and confirmed its effectiveness through experiments."} +{"text": "A robust body of literature has found birdirectional associations between sleep quality and marital quality in couple relationships . Additionally, dyadic research shows that differences in couples\u2019 bed time routines and habits is associated with mental health outcomes , however the literature has not connected them with other marital processes that are mutable and clinically relevant. Attachment theory provides a clinically relevant framework that captures both interpersonal marital processes such as relationship conflict as well intrapersonal processes of individual emotional safety\u2014essentially individuals\u2019 personal strategies to balance closeness and distance in a relationship . The two main attachment styles related to sleep processes are attachment avoidance and attachment anxiety . Utilizing data from 234 couple dyads, we investigated if differences in partners\u2019 bed times is associated with conflict frequency and attachment avoidance using a structural equation modeling approach. We controlled for a number of important factors and tested our hypothesized model against two plausible alternative models. Results revealed that greater difference in partners\u2019 bed times was associated with higher conflict frequency for both husbands and wives through higher men\u2019s attachment avoidance. Our findings highlight previous research on matched vs. unmatched couples on sleep routines, habits, and chronotypes but highlight mutable and clinically relevant constructs for intervention. Implications for health promotion and marital therapy will be discussed."} +{"text": "There is an error in the title of the paper . The autChange the title from \u201cCryopreserved Human Natural Killer Cells Exhibit Potent Antitumor Efficacy against Orthotopic Pancreatic Cancer through Efficient Tumor-Homing and Cytolytic Ability (Running Title: Cryopreserved NK Cells Exhibit Antitumor Effect)\u201d to \u201cCryopreserved Human Natural Killer Cells Exhibit Potent Antitumor Efficacy against Orthotopic Pancreatic Cancer through Efficient Tumor-Homing and Cytolytic Ability\u201d. We apologize for this error and state that the scientific conclusions are unaffected. The original article has been updated."} +{"text": "Neighborhood experiences may have a cumulative effect on cognitive health outcomes across the lifespan. We investigated independent and combined associations between current and retrospective childhood neighborhoods and daily cognitive function in 209 adults who participated in a 14-day ecological momentary assessment study. Participants reported perceptions of their current neighborhood and the neighborhood they lived in at age 5; including neighborhood cohesion, safety, violence, and physical conditions. Greater current neighborhood violence was independently associated with poorer spatial working memory. Childhood neighborhood violence was not significantly associated with performance. The interaction between current and childhood neighborhood ratings was significant: individuals who reported greater childhood neighborhood violence, but lower current violence had better performance than those who experienced consistently high or low neighborhood violence. Effects for other neighborhood domains were not significant. Results indicate that neighborhood influences on cognition in adulthood may be moderated by childhood neighborhood experiences."} +{"text": "Mesenchymal stem/stromal cells (MSCs) are considered a relevant therapeutic product for various clinical applications. They have generated great interest as cell therapies for a range of inflammatory and autoimmune conditions . Residin"} +{"text": "We describe a patient with incidental endobronchial synchronous hamartoma and typical carcinoid with different management strategy. We describe a patient with incidental endobronchial synchronous hamartoma and typical carcinoid and the management strategy. A 49\u2010year\u2010old woman was admitted to our hospital due to paroxysmal dry cough and mild dyspnoea. She was treated with inhaled steroid and bronchodilator for asthma. On contrast\u2010enhanced chest computed tomography (CT) scan, a solid endobronchial lesion totally occluding the right upper bronchus and an incidental triangular\u2010shaped lesion on intermedius bronchus were shown Fig. . FibrobrAppropriate written informed consent was obtained for publication of this case report and accompanying images."} +{"text": "The kinematics of the right ventricle (RV) are not well understood due to its thin wall and asymmetric geometry . Cine dith order Polynomial functions. Lagrangian strain taken tangential to the midwall (Ett) was computed from both the left ventricle (LV) and RV motion trajectories [In accordance with protocols approved by the UCT Research Ethics Committee, 3 confirmed, 6 suspected ARVC cases and 4 normal volunteers were scanned using cine DENSE. ARVC diagnosis was based on standard clinical criteria . DisplacExample basal slice cine DENSE magnitude images and corresponding end systolic tangential strain maps are shown for a normal volunteer Figure and a coPreliminary results indicate that cine DENSE CMR is useful in detecting abnormal myocardial strain in ARVC. Due to improved SNR and motion properties, cine DENSE using spiral data acquisition may impr"} +{"text": "In order to elucidate the mechanism showing false\u2010positive MIBG examination in RCC, further accumulation will be desirable.Chromophobe RCC oncocytic variant is an extremely rare renal neoplasm and there are such previously reported six cases.The author declares no conflict of interest."} +{"text": "GSA COVID-19 Task Force members worked with organizational leaders and special interest groups to ascertain areas where further research about COVID-19 and older adults would be helpful. The responses were compiled into a single document to create a research agenda. Processes to share the agenda with federal agencies and partners will be shared."} +{"text": "The effective use of radiofrequency thermal energy for the palliative relief of cervical facet pain has been known for decades . The radAs illustrated by the following images obtained from a single cadaveric specimen, a simple process yields precise \u201ctrue\u201d lateral imaging during cannula positioning . First,"} +{"text": "To the Editor: We would like to retract our article Novel Orthobunyavirus Causing Severe Kidney Disease in Broiler Chickens, Malaysia, 2014\u20132017 from the June 2019 issue of Emerging Infectious Diseases ("} +{"text": "After publication of the original article , the autThe incorrect author name is:Marlene J.Le BerThe correct author name is:Marlene JanzenLe BerThe original article has been corrected."} +{"text": "Najafi has published a letter about our published article regarding the comparison of SORT maneuver versus a conventional technique of neck flexion lateral pressure (NFLP) for nasogastric tube (NGT) insertion in ICU admitted patients . He mentHe also mentioned SORT maneuver as an ideal technique for NGT insertion in critically ill patients with COVID-19. As this technique considers anatomical characteristics, it can be an ideal option for health care workers who are familiar with this technique and airway anatomy. Moreover, every physician/nurses should notice the fact that NGT insertion is an aerosol producing technique and every one should consider full protection during its insertion with every technique . So, SOR"} +{"text": "Two infants aged 11 and 5 months consulted for eczematous plaques on the nape. Their parents reported that the lesions had developed over previous erythematous stains. Both cases corresponded to eczematous changes over nevus simplex, known as Meyerson phenomenon .Meyerson phenomenon is defined as a spontaneous eczematous reaction within an overlying skin lesion. This phenomenon was first reported in melanocytic lesions ; however"} +{"text": "The original publication of Healey et al. containeThe full correct title is \u201cCAEP Position Statement \u2013 Management of devastating brain injuries in the emergency department: Enhancing neuroprognostication and maintaining the opportunity for organ and tissue donation.\u201dThe publisher regrets this error. The original article has been updated."} +{"text": "This manuscript has been updated in order to amended incorrect affiliation indices for several authors. The publisher apologies for any confusion caused."} +{"text": "Due to a production error, the Data Availability Statement was not included in the article. The Data Availability Statement appears below. The publisher apologizes for this mistake.\u201c16S rRNA gene sequencing data and metatranscriptome data were submitted to the European Nucleotide Archive (ENA) with the accession number PRJEB15104.\u201dThe original article has been updated."} +{"text": "Androglossini is one of four tribes recognized within a neotropical parrot subfamily Arinae. The tribe includes 10 genera of which Pionus is represented by eight species. However, its evolutionary diversification and relationship with other Androglossini members are still unclear. Depending on studied molecular markers, Pionus is closely related with Amazona genus or two monotypic genera Alipiopsitta and Graydidascalus or the clade in which Amazona genus is sister to Alipiopsitta and Graydidascalus. Therefore, we sequenced Pionus menstruus menstruus mitogenome to gain molecular data appropriate for future studies to resolve these discrepancies obtained in various phylogenetic analyses published so far. Arinae subfamily, in which four tribes were recognized was absolutely typical for other P. menstruus menstruus individuals, we proved its taxonomic affiliation in phylogenetic analyses of nd2 sequences including all available Pionus taxa with confirmed geographic origins. The obtained tree (rubrigularis and reichenowi.The sequence of ned tree revealed"} +{"text": "These values should have appeared as means with standard deviations instead of medians with interquartile ranges and means with 95% confidence intervals. This article has been corrected. In the Original Investigation titled \u201cComparison of Office-Based Physician Participation in Medicaid Managed Care and Health Insurance Exchange Plans in the Same US Geographic Markets,\u201d"} +{"text": "Older adults frequently experience daily stressors and are at increased risk of adverse health consequences. Emerging studies have focused on factors that may buffer older adults\u2019 well-being and strengthen their resilience to stress. This symposium adds to this burgeoning literature and presents studies that identify a wide range of such stress-buffering factors, including individual characteristics and daily social and emotional experiences. Huo et al. considered older adults\u2019 empathy and found that more empathic individuals tended to use constructive strategies but not destructive strategies when coping with interpersonal tensions. When daily tensions occurred, more empathic individuals were also better at maintaining their mood. Kim et al. showed that older adults\u2019 marital status influenced their irritable encounters with grown children. Although irritable encounters were associated with increased daily negative mood, this link varied by parents\u2019 marital status. Hong et al. assessed the link between daily stressors and negative affect among older adults with varying levels of loneliness. They found that positive interpersonal encounters were particularly protective for lonely older adults\u2019 daily affect. Leger et al. further examined the buffering effects of trait level and same-day positive emotions during times of stress. Higher trait and same-day levels of positive emotions reduced negative emotions on the day following a stressor. Together, findings might inform future interventions aimed at increasing the daily experience of older adults. Dr. Hoppmann will serve as the Discussant and summarize the theoretical and methodological contributions of these studies. She will discuss challenges in this field and directions for future research."} +{"text": "The paper shares the same ethical approval number and trial registration as an article previously published in Plos One. After investigation, it was determined that authors did not receive proper ethics approval and did not register the trial for the study published in Medicine.The article \u201cCONSORT-epidural dexmedetomidine improves gastrointestinal motility after laparoscopic colonic resection compared with morphine\u201d,"} +{"text": "While affordable housing typically describes housing costs that fall within 30 percent of total income, older adult spending systematically differs from younger cohorts. For instance, budgets may skew away from mortgages and towards home modifications while medical or personal care expenses can drive monthly costs. This research uses the Health and Retirement Study (HRS) to explore various older adult housing cost burden measures and identify their relative advantages. Measures of cost burden are applied to HRS respondents and different cost burdened groups are defined. The welfare of each group is then assessed using metrics such as unmet need and caregiver stress. Findings suggest that traditional cost burden measures identify many vulnerable older adults. However, other measures of cost burden can highlight older adults who are disproportionately impacted by medical cost. This research should help professionals better align the metric that defines their target population members with their policy area."} +{"text": "Merging digital technologies with neuropsychological testing allows for collection of novel metrics that may reveal early, subtle differences in cognitive functioning. We examined whether digital pen metrics from the Clock Drawing Test (CDT) differentiate healthy agers from spouses and individuals by APOE genotype. We used generalized estimating equations adjusted for sociodemographics, familial longevity, and APOE genotype. Among 1974 participants with correct clocks (mean age 71\u00b110 years), familial longevity was associated with better cognitive processing whereas the e4 allele was associated with smaller clock diameter and longer latencies. The e2 allele was negatively associated with total time and latencies. Therefore, digital metrics captured differences in cognitive processing among individuals with correct clocks and thus may be more sensitive than traditional scores. Additionally, familial longevity may confer cognitive advantages that are distinct from the risk/protection afforded by APOE genotype."} +{"text": "Subjective age bias suggests that middle-aged and older adults feel relative younger, whereas adolescents and young adults often feel older than their chronological age. However, we still know very little about its social conditions and consequences across the life span particularly within the work domain. Across three studies , we show that feeling older (among younger adults) and younger (among older adults) is triggered by undesirable age stereotypes concerning competence and status of young and later adulthood and desirable age stereotypes of midlife. We further demonstrate that feeling relatively older among young adults and younger among older adults increases individuals\u2019 self-perceived competence at work and predicts proactive behavior such as speaking up. We discuss subjective age bias as socially-mediated phenomenon and how it affects behavior at work across the life span."} +{"text": "A recent paper comparedA recent review on ML methods in a clinical epidemiological context shows that benefits of ML tend to arise in biased comparisons . In the"} +{"text": "China*Contributed equallyThe authors regret their oversight in this regard, and apologize for any inconvenience caused."} +{"text": "We will present the implementation approach used to evaluate a novel mobile health exercise intervention designed to improve older adult\u2019s fitness and brain health. A randomized controlled trial design evaluated if the use of mHealth strategies improved walking speed in real world environments to help participants achieve current physical activity guidelines. Cognitively healthy older adults were randomized to a 12-week, unsupervised, exercise prescription condition or to a healthy aging education condition. Participants used a heart rate tracker programmed to provide haptic feedback when they fell outside of their prescribed heart rate target during an exercise session. Participant\u2019s perceptions regarding the mHealth technology device, as well as their feedback regarding the privacy of their data when using mHealth devices will be presented. Recommendations to improve the design of future mHealth exercise trials will be discussed."} +{"text": "He was 0%-34%) .(2). This case showed two important issues: harlequin syndrome may be caused by tumors and patients with harlequin syndrome may exhibit cardiac sympathetic hyperactivity.Although no report has described the cardiac sympathetic function of harlequin syndrome, our patient likely presented with cardiac sympathetic hyperactivity, as indicated by the increased washout rate NoneYT wrote the manuscript. KS supervised all procedures.This manuscript is a case report.Informed consent was obtained from the patient."} +{"text": "Subgroup analyses assess whether a given effect measure differs according to baseline characteristics . In geneNEJM, a review of the last 100 randomized trials reporting subgroup analyses was performed were performed using data from SPRINT and PARAMeta-epidemiological studies suggest that relative effects are generally more constant across baseline risk as compared to absolute effects \u20136. Some Additional file 1."} +{"text": "In this paper, we demonstrate our independent replication of the original experimental results. We implemented Statistical model checking uses Monte Carlo simulation to analyse stochastic formal models. It avoids state space explosion, but requires rare event simulation techniques to efficiently estimate very low probabilities. One such technique is"} +{"text": "Positive affect is beneficial for regulating negative emotional responses to stressful events. Yet, few studies have examined if positive affect may attenuate negative affect the following day. We examined how both trait positive affect and state positive affect are associated with next day stressor-related negative emotions. Participants from the National Study of Daily Experiences II (NSDE II) and the Midlife in the United States survey (MIDUS II) answered questions about stressors and emotion across eight days. People high on trait positive affect reported less negative affect the day following a stressor. On days when people experienced a stressor and higher than average state positive affect, they experienced less negative emotion the following day. This held true regardless of whether people were high or low on trait positive affect. Positive affect can help explain both who and when people will have attenuated emotional responses to stressful events."} +{"text": "The current study investigated older parents\u2019 practices and plans to support their own autonomous lives with/without children\u2019s living assistance and how these parents negotiate autonomous lives with their adult children among three racial/ethnic groups. The study participants were older parents who resided in the Southern California who were recruited through local senior centers . Content analysis revealed that Caucasian American parents supported their autonomous lives by using friend networks and professional caregivers rather than depending on their children. Parents with Mexican origin emphasized that their children well took care of them and there were no conflicts with their children. Filipino parents planned to migrate to the Philippines where professional services were affordable so that they would not rely on their children\u2019s care. Similarities and differences in older parents\u2019 need among different racial/ethnic groups will be discussed."} +{"text": "In the original article, there was an error. Sentences include misinformation.**CURRENT LIMITATIONSAND FUTURE DIRECTIONS**, **Sensor Configuration ofTwo Different Devices**, **FirstParagraph**A correction has been made to ORIGINAL SENTENCES\u201cHowever, because light leakage from an fNIRS system can contaminate EEG signals, it is necessary to block this leakage when combining the two devices. One study (Koo et al., CORRECTED AS FOLLOWS\u201cOne study (Koo et al., The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Nezu et al. reported a case of mucinous urethral adenocarcinoma in which targetable EGFR amplification led to successful treatment with erlotinib.Mucinous urethral adenocarcinoma has no standard treatment approach. The authors suggested that erlotinib might be effective because epidermal growth factor receptor (EGFR) immunostaining was strongly positive in this case. Bryce The authors declare no conflict of interest."} +{"text": "The differential diagnosis of scrotal masses includes testicular cancer. Serum parameters can be helpful in distinguishing a scrotal mass from testicular cancer, but a testicular biopsy is currently required to completely rule out malignancy. Kimura The periductal distribution of granulomas might cause ductal compression or Leydig cell damage.The authors declare no conflict of interest."} +{"text": "Although the majority of our cohort were rescanned at 3-6 months after the index event, some patients were scanned up to a year later. Reduced myocardial manganese uptake was apparent irrespective of the time period of the second scan . We agreAlthough possible, we believe it is unlikely that absent manganese uptake would occur if we had imaged our patients earlier in the hyperacute phase. Many patients had completely akinetic left ventricular segments but continued to have demonstrable uptake . We believe that absent uptake would be more indicative of a completely infarcted or fibrosed myocardium which is not the case for patients with takotsubo syndrome.A recent ischaemia reperfusion animal model reported that manganese-enhanced magnetic resonance imaging is an early biomarker of final infarct size after permanent coronary occlusion . Spath eWe believe that reduced myocardial manganese uptake reflects abnormal myocardial calcium handling rather than ischemia per se. We excluded patients with obstructive coronary disease although we cannot exclude a contribution of ischemia from microvascular dysfunction or impaired vasoreactivity. Our previous studies have demonstrated reduced manganese uptake patients with acute myocardial infarction, chronic myocardial ischaemia, and those with cardiac risk factors as well as those with dilated cardiomyopathy . HoweverWe demonstrated elevated T1 and T2 values in remote myocardium of patients with takotsubo syndrome reflecting myocardial edema. Due to the nature of quantifying manganese uptake, we captured only a single short-axis slice ["} +{"text": "The use of thermal radiofrequency (RF) energy to destroy medial branch nerves innervating specific lumbar facet joints for the palliative relief of chronic low back pain has been described extensively . PreciseA \u201ctrue\u201d lateral fluoroscopic imaging technique has been proposed for confirmation of correct cannula placement before initiation of destructive thermal energy . Each luThe use of the proposed features for \u201ctrue\u201d lateral lumbar imaging may enhance thermal RF lumbar medial branch neurotomy technique, as the final position of the RF cannula in relation to its target structures is more accurately visualized at each segment."} +{"text": "A 34 year old female presented with upper abdominal pain and nausea. Her medical history included alcoholic chronic pancreatitis. Computed tomography angiography revealed a gastroduodenal artery pseudoaneurysm with a portal fistula associated with chronic pancreatitis. Angiography showed an eccentric sac measuring 26 x 38 mm (asterisk) with a small fistula to the portal vein (red arrow). Front and back door embolisation was performed using Amplatzer Vascular Plugs , excluding the pseudoaneurysm while preserving the anterior pancreaticoduodenal artery and common hepatic artery arising from the superior mesenteric artery. The patient was asymptomatic one month after the procedure."} +{"text": "The retraction has been agreed following an investigation into concerns raised by a third party, which revealed inappropriate duplications between this and previously published articles [The above article, published online on 28 June 2019 in Wiley Online Library ("} +{"text": "PLOS ONE Editors retract this article [The article because article . These cZL and JS did not agree with the retraction. All other authors either did not respond directly or could not be reached."} +{"text": "PLOS Biology found fluctuations increased parasite transmission instead, highlighting questions about how climate change will impact infectious diseases.Theory predicts that temperature fluctuations should reduce performance near an organism\u2019s thermal optimum. A new study in Theory predicts that temperature fluctuations should reduce performance near an organism\u2019s thermal optimum. This Primer explores a new study in PLOS Biology showing that fluctuations increased parasite transmission instead, highlighting questions about how climate change will impact infectious diseases. PLOS Biology by Krichel and colleagues . How. How2]. Fluctuations around a mean temperature\u2014an inherent part of most natural environments\u2014add yet another layer of complexity to predicting organismal performance and species interactions across temperature gradients. It is generally infeasible to conduct experiments with treatments at enough relevant combinations of mean temperature and fluctuation size. Thus, ideally there would be a modeling approach that could accurately predict organismal performance and ecological outcomes in fluctuating environments based on performance observed in constant temperatures. Nonlinear averaging is a commonly used method that asOrdospora colligata that infects freshwater zooplankton Daphnia magna) responds unimodally to constant temperatures [In their recent paper, Krichel and colleagues investigeratures . Thus, neratures . Few otheratures ,11), alteratures . Observaeratures ).Ordospora-Daphnia disease system used consistent \u201cdaily\u201d fluctuations that changed the temperature each hour (So what could possibly be driving the disparity between theoretical predictions and empirical results in this case? One potential answer is acclimation, which allows organisms to maintain high levels of performance in variable environments. The temperature variability hypothesis suggests that parasites can gain an advantage in fluctuating thermal environments because they are smaller than their hosts and therefore can acclimate faster to changing temperatures . This hyOverall, the study by Krichel and colleagues demonstr"} +{"text": "Due to a production error, the contributions of authors Rim Diab and Federica Pilotto were not included in the author contributions in the published article. The corrected Author Contributions Statement appears below.\u201cSS wrote the review with equal contributions from FP and RD. FP designed all figures. All authors read and approved the submitted version.\u201dThe publisher apologizes for this mistake. The original article has been updated."} +{"text": "Catatonia due to cerebrovascular stroke is a rare condition that needs further observation and research.To review the opinions of psychotic disorders experts worldwide as to this issue based on evidence and clinical experience and to consider strategies for future investigations.This case shows a 64 years old female who suddenly developed wish for isolation, followed 10 days later by discontinuity of ideas, hallucinatory behavior and food refusal. She had verbal and physical aggression due to a fixed belief that family members are conspiring somehow to harm her.On examination she was mute with waxy flexibility and negativism. Extensor plantar reflex was evident. MRI Brain showed small vessel disease and right basal ganglia acute ischemic infarction. On IV midazolam 7.5 mg, patient\u2019s mutism, negativism and waxy flexibility improved. Lower limb Venous Duplex revealed acute right popliteal and left soleal veins thrombosis. CT angiography showed Bilateral pulmonary embolism with no pulmonary infarction. D dimer was positive.Early diagnosis and intervention improves outcome if psychiatric teams gives attention and has enough awareness with warning symptoms and prompt necessary interventions.None Declared"} +{"text": "An omission to the funding section of the original article was made in error. The following sentence has been added: \u201cOpen access funding was provided by ETH Zurich.\u201dThe original article has been updated."} +{"text": "This is a peer-review report submitted for the paper \u201cLeft Ventricular Outflow Tract Obstruction in Patients Treated With Milrinone for Cerebral Vasospasm: Case Report and Literature Review.\u201dThis paper deals wiThe rationale for radioembolization of aneurysms needs to be elaborated.The probable differential diagnosis of stunned myocardium syndrome in the acute phase needs to be mentioned."} +{"text": "PLOS ONE Editors retract this article [The article because BX, CZ, and SJ either did not respond directly or could not be reached. KK responded but expressed neither agreement nor disagreement with the editorial decision."} +{"text": "Helsinki, FI: ECHA.).\u2019These details have been corrected only in this correction notice to preserve the published version of record."} +{"text": "Pregnant women with depression face complicated treatment decisions, either because of the risk associated with not treating depression or because of the risks associated with antidepressant use. Approximately 1 in 5 women experience depressive symptoms during pregnancy. This information suggests that many women may take an antidepressant at some time during pregnancy. Once pregnant women initiate antidepressant prescription pharmacotherapy, medication treatment persistence plays an important role in managing depression, yet little is known regarding antidepressant use behavior in pregnant women.To determine antenatal antidepressant treatment nonpersistence and associated factors in low-income, insured pregnant women.We identified eligible pregnant women (\u226518 years) diagnosed with major depression who initiated antidepressant medications during pregnancy from South Carolina Medicaid claims data (2004-2009). Our main outcome measure was treatment nonpersistence to antidepressant therapy during pregnancy. We defined treatment nonpersistence to antidepressant pharmacotherapy as having a gap between 2 consecutive prescriptions lasting at least 15 days during pregnancy. We applied a proportional hazards model to identify predictors associated with the risk for antidepressant nonpersistence during pregnancy.Of 804 pregnant women meeting study criteria, nearly 45% of this cohort did not continue to use antidepressant pharmacotherapy, showing a gap \u226515 days between 2 prescriptions, after initiating antidepressant therapy during pregnancy. Women reporting nonwhite race were 36% more likely to show a gap in antidepressant medication use during pregnancy than white women. Women with a history of antidepressant use before pregnancy were 44% more likely to discontinue the antidepressant therapy during pregnancy.Treatment persistence to antidepressant medications was poor during pregnancy in low-income, insured pregnant women. Individualized treatment might be considered to reduce the risks of untreated depression and antenatal antidepressant use in vulnerable women."} +{"text": "Next, local anesthetic is injected and a shallow incision (scoring) is made around the tumor borders with a scalpel . CarefulThe technique is most helpful where both the tumor appears clinically well defined and additionally where there are risk factors for epidermal shearing, such as significant actinic damage or corticosteroid exposure causing atrophic skin, or thin periocular or genital skin. While tactile feedback of the curettage technique is important, sclerotic tumors have notoriously needed a sharp debulk. This technique provides tumor delineation via curettage and avoids excessive epidermal shearing which can unnecessarily enlarge the Mohs defect.None disclosed."} +{"text": "With this notice, Frontiers states its awareness of serious allegations surrounding the institutional review board Centro Internacional de Vacunas cited in this article. These allegations are being investigated in line with COPE guidelines. The situation will be updated as soon as the investigation is complete."} +{"text": "Corrections to percentages, point estimates, and confidence intervals did not affect the study findings or conclusions. This article was corrected online.In the original investigation titled \u201cEvaluation of Potentially Avoidable Acute Care Utilization Among Patients Insured by Medicare Advantage vs Traditional Medicare,\u201d"} +{"text": "PLOS ONE Editors retract this article [The article because article and Fig article . These cAll authors either did not respond directly or could not be reached."} +{"text": "After the publication, we realizedthat the clinical trial name mentioned in the \u201cPatient Samples\u201dsection is not correct. The \u201cPatient Samples\u201d sectionshould read as below:From the prospective radical prostatectomydatabase maintainedby Dr. Kryvenko, we obtained patient samples from treatment na\u00efveand salvage radical prostatectomies with preoperative neoadjuvantandrogen deprivation therapy or chemotherapy. All tissue samples submittedto the research lab were deidentified. An arbitrary identifier wasassigned to each specimen so that all recipients were blinded to informationthat identifies or could be used to identify the donor subject fromwhom the material was obtained."} +{"text": "Endoscopic resection of giant pedunculated colorectal polyps (PCPs) with large heads and thick stalks can be technically difficult with conventional snare polypectomy and involves the risk of clinically significant bleedingA safe therapeutic strategy is used to resect a giant pedunculated colorectal polyp with a thick stalk.Video 1A 61-year-old man underwent colonoscopy for intermittent hematochezia for 3 months; the results revealed a giant PCP in the sigmoid colon that was almost completely blocking the lumen . ComputPlanned treatment strategies are essential in the prevention of intraoperative complications associated with giant PCPs with thick stalks.Endoscopy_UCTN_Code_TTT_1AQ_2AD"} +{"text": "I agree with the authors that oldhamite could have been involved as a transient phase in important geological processes [Oldhamite . ThisConflict of interest statement. None declared."} +{"text": "With this notice, Frontiers states its awareness of serious allegations surrounding the institutional review board Centro Internacional de Vacunas cited in this article. These allegations are being investigated in line with COPE guidelines. The situation will be updated as soon as the investigation is complete."} +{"text": "In this fourth session of our motivational interviewing workshop, we will go from theory to practice through simple and direct examples from clinical practice. The participants will be able to watch previously filmed clinical cases and participate in role plays, where they can practice using different motivational interviewing techniques that they had learned before.None Declared"} +{"text": "This is a peer-review report submitted for the paper \u201cExploring the Reasons for Low Cataract Surgery Uptake Among Patients Detected in a Community Outreach Program in Cameroon: Focused Ethnographic Mixed Methods Study.\u201dDear Authors,Thank you very much for this interesting paper about caKind regards!"} +{"text": "The Editorial Board has retracted this article. After publication concerns were raised aboutthe data reported for this study. The authors provided the raw data which was examined by twoindependent experts who concluded that the data contain serious anomalies. The Editorial Boardtherefore no longer has confidence in the results presented."} +{"text": "PLOS ONE Editors retract this article [The article because article , and Fig article . These cAll authors either did not respond directly or could not be reached."} +{"text": "Inflammatory processes related to vascular damage may have key biomarkers and pathways that correlate with infiltrating immune cells and systemic autoimmune diseases are dominant in women . As is wne cells . Since tne cells . Last bune cells . FurtherThe author confirms being the sole contributor of this work and has approved it for publication."} +{"text": "With this notice, Frontiers states its awareness of serious allegations surrounding the institutional review board Centro Internacional de Vacunas cited in this article. These allegations are being investigated in line with COPE guidelines. The situation will be updated as soon as the investigation is complete."} +{"text": "This should read \"Abdul K Qadree\" instead of \"Abdul K Qadri\". This is emended in the article.This error has been corrected (online)."} +{"text": "Initiatives to harmonise clinical research methods have been primarily focused on Caucasian populations, neglecting underrepresented populations.The authors declare no conflicts of interest."} +{"text": "Crohn's disease (CD), a chronic inflammatory bowel disease (IBD), is an ongoing clinical challenge. Tight disease monitoring is increasingly recognized as a key strategy to achieve optimal disease control.The authors have no conflicts of interest to declare."} +{"text": "Designing biological sequences is an important challenge that requiressatisfying complex constraints and thus is a natural problem to address withdeep generative modeling. Diffusion generative models have achievedconsiderable success in many applications. Score-based generative stochasticdifferential equations (SDE) model is a continuous-time diffusion modelframework that enjoys many benefits, but the originally proposed SDEs are notnaturally designed for modeling discrete data. To develop generative SDE modelsfor discrete data such as biological sequences, here we introduce a diffusionprocess defined in the probability simplex space with stationary distributionbeing the Dirichlet distribution. This makes diffusion in continuous spacenatural for modeling discrete data. We refer to this approach as Dirchletdiffusion score model. We demonstrate that this technique can generate samplesthat satisfy hard constraints using a Sudoku generation task. This generativemodel can also solve Sudoku, including hard puzzles, without additionaltraining. Finally, we applied this approach to develop the first human promoterDNA sequence design model and showed that designed sequences share similarproperties with natural promoter sequences."} +{"text": "Shared decision making (SDM) has found its way into mental health care to a limited extent only, and especially \u201cchallenging\u201d patients do not benefit from this approach. In this lecture we will describe barriers to shared decision making among mental health professionals and among patients. Integrative approaches will be presented that meet the needs of patients and mental health staff when aiming at implementing SDM in acute mental health settings. Finally, best practice examples will illustrate that SDM actually can be implemented in the very acute settings/treatment phases and yields positive results.None Declared"} +{"text": "PLOS ONE Editors retract this article [The article because article , and bet article and Fig article , 3. ThesAll authors either did not respond directly or could not be reached."} +{"text": "An omission to the funding section of the original article was made in error. The following sentence has been added: \u201cOpen access funding was provided by ETH Zurich.\u201dThe original article has been updated."} +{"text": "An omission to the funding section of the original article was made in error. The following sentence has been added: \u201cOpen access funding was provided by ETH Zurich.\u201dThe original article has been updated."} +{"text": "Unavoidable flaring in downstream oil industry causes pollutant emission in large amounts which is potentially harmful to nearby cities or farms. Hence one must manage exhaust toxic gases to raise enough in atmosphere or redirect from such places. Since Kirkuk refinery in north Iraq is next-door to agricultural farms on west yet to residential areas on east optimizing its layout for flare stacks is something acute. In this work we wrote codes in MATLAB software to simulate incomplete rather than complete oxidation as well as pollutant generation reactions. Then we made use of FLEUENT software to simulate pollutant propagation in Kirkuk oil purifier complex yet also farther to city as well as farms with respect to seasonal air currents on lowest troposphere layer. Finally, we set neural network approach to train on simulation data thereafter to unify outcomes to turn into a fast technique for layout optimization. Results show that optimization process efficiency relies on air current velocities as well as its direction. At intermediate air flow rates optimum layout includes only a selective portion of existent flare stacks. Outcomes also illustrate that heuristic techniques that have stronger local search such as particle swarm or artificial immune system can improve flare layout in seasons with intermediate air currents here summer plus early months in autumn while approaches with weak local search like Monte Carlo are more appropriate in winter for which we have no or low air flows in Kirkuk governorate. It was shown that air pollutant emission is firmly dependent on flue gas flow rate rather than airflow velocity as well as distance from flare stacks1. Alameddine et al.2 made use of an industrial complex air pollutant dispersion model to estimate sulfur oxide concentrations in a power distillation plant in an industrial area. It was shown that whenever flare stacks have different heights or in situations with low or no air currents more contaminants emit in near environment2. Yassin et al.3 set tunnel apparatus to simulate pollutant dispersion in a residential area in Japan under various air flow conditions. Outcomes show that under low or no air flow condition pollutant diffusion was high in comparison to situations with high air currents3. Lee4 developed several codes in FORTRAN language to simulate pollutants emission via diffusion on an uneven surface under turbulent condition. Outcomes display that local pollutant mass fractions are highly sensitive to location of pollution source as well as existent structures4. Nazirdoust et al.5 made use of FLUENT software to simulate pollutant dispersion in residential areas with tall structures. Results show that the windy face of constructions is has less pollutant mass fractions yet structure heights are effective on pollutant propagation5. Perez-Roa et al.6 set artificial neural network to train on several pollutant measurement data plus simulation results thereafter made use of this intelligent network to trace 6. Kahforoshan et al.7 developed codes in MATLAB software to study to what extent factors like flare height or air conditions can affect pollutant emission in an industrial area in Africa. It was shown that forecasts from simulations were in nice agreement with experimental information on 7. Edokpa et al.8 did several sensitivity analyses on parameters like air flow velocity rather than direction in Niger delta of Nigeria via employing a commercial simulator. It was shown that higher air flow velocity as well as lower sour gas flow rate causes higher pollutant concentrations near the flare rather than farther locations8. Alkaim et al.9 set data mining technique down with optimization algorithms which relies on multivariate adaptive regression technique to achieve optimal gas flaring rate with respect to costs. It was shown that this approach was very fast yet powerful since it applies integration function9. Fawole et al.10 did an study to discover to what extent stack height or gas composition influences pollutant emission in the Niger delta. Outcomes illustrate that the density of fuel has reverse relation with zero level pollutants concentration while authors propose using a taller flare stack in lieu of a shorter one10. Zoeir et al.11 wrote several codes in MATLAB software to model complete rather than incomplete oxidation reaction then to minimize pollutants in flue gases. Outcomes illustrate that there is specific value for excess air for which mass fractions of air contaminants namely 11. Baroutian et al.12 made use of Gaussian plume model to forecast pollutant dispersion from cement plant to residential areas of Kerman city in southeastern Iran thereafter did a comparison with real data that came from measurements. Since predictions via Gaussian plume model were in nice agreement with data it was a proof that this approach is rational elsewhere under low air currents12. Abiye et al.13 set sensors to measure air pollutants in an iron recycling factory that uses fossil fuels as main energy source thereafter made estimations via plume dispersion simulation in other places for which sensors did not exist. Sensitivity analyses to air temperature in addition to net radiation illustrate that that locations with intermediate distance from the scrap-iron recycling factory were most prone to the impacts of the gaseous releases from the factory\u2019s operations13. Ismail et al.14 wrote several computer programs to simulate incomplete rather than complete oxidations in addition to pollutant generation reactions for 14.In 2010 ten countries were at fault for 72% of total sour gas flares internationally. Top four countries were Russia (27%) then Nigeria (11%) thereafter Iran (8%) yet at last Iraq (7%). Data from Satellites show that overall gas flaring fell to about 80% in recent few years. The most significant reductions in terms of volume were made in Russia (up to 40%) then Nigeria (up to 29%). One can expect Iraq to run up the list in next few years. Kirkuk refinery as largest oil complex in northern Iraq emits more than 70\u00a0million Main novelties of this study in comparison to other works in the literature are that here we employ heuristic optimization techniques to detect monthly optimal flare layout in Kirkuk governorate. Here we concern not only the air currents in lowest troposphere layer yet also simulate pollutant migration through an upper layer with powerful air currents that do not sense earth\u2019s features. In addition to that we develop an intelligent technique namely neural network to rapidly forecast optimum layout for any specific daily air current without requiring to perform computational dynamics. Moreover, we do several sensitivity analyses on factors like air flow air flow characteristics or sour gas flow rates to investigate to what extent each optimization algorithm is efficient.In this section we firstly explain our industrial case study in northern Iraq with further details on stack locations in addition to average sour gas composition. Then we report information on local seasonal rather than permanent air currents that are taken from NASA online site Fig.\u00a0. To coinTo speak on data, one must firstly explain the case study for which we want to optimize flare stack layout. Kirkuk refinery meets residential areas on its east to south east as well as farms on west. Both areas suffer from air pollutants in high concentration due to their proximity if air currents in troposphere cannot effectively carry contaminants away. Pollutant emission with high mass fractions in Kirkuk city causes several diseases such as stroke or cancer in society thus directly affects lives. This is while high pollutant concentrations in plantations or farms indirectly influence fauna with taint on crops. Our further data is on locations of flare stacks that are currently set in place in Kirkuk refinery limits. In order to represent locations, we use global positioning system that employs geographical factors namely latitudinal values for distances from equator line in addition to longitudinal values for distances from prime meridian line as well as altitudinal amounts for height from free sea level. Here mainly due to economical purposes we perform optimization computations on existent flares via changing they\u2019re on or off status rather than excess air to detect layouts that minimize pollutant mass fraction in two target areas. Certainly, one can even consider potential to place new stacks in refinery limits which surely increases capital investments. Further details on flare positions plus their current status is shown in Table To discuss seasonal local air currents in Kirkuk governorate we use data from NASA online site that not only includes surface air currents yet also explains air flow velocities in higher troposphere layers. Information tells us that during early spring in lowest troposphere layer we see no or extremely low air currents while after two- or three-months seasonal air flows start to rush from northwest. In summer we have powerful flows with high velocities from north to south for 2\u00a0months after that air currents weaken for 1\u00a0month. In autumn delicate air currents direct from northeast to southwest. Finally in winter air currents slow down to reach trivial velocities prior to spring. This is while in upper troposphere layers air flows are not so much relevant to seasons. In contrast there we have extremely powerful air currents that are always from west to east. If one wants to explain why air flows near the surface are so uncertain the answer lies under local topological features such as mountain or plateaus.Since provincial hills or valleys are always there, we can expect local air currents to do not undergo significant yearly changes. Anyway, daily currents may not exactly follow this algorithm due to impermanent reasons such as unusual temperature profiles or other factors. Here we introduce two exemplar air current maps for April rather than June as shown in Fig.\u00a0Since Kirkuk complex is the largest oil clarifier unit in northern Iraq it vents large amounts of sour gas each year. Corrosive components in streamline prior to oxidation reaction are Further details on sour gas compositions are shown in Table To compute the amount of greenhouse gases as well as air pollutants that emit from flare stacks, we simulate fuel oxidation reaction to attain flue gas composition. Each hydrocarbon component within inlet sour gaseous phase participates in an exothermic reaction which in the presence of enough excess air will go through complete oxidation that yields only Conversely in situations with less than enough oxidant hydrocarbon components go through incomplete oxidation that produces One must calculate enthalpy changes relevant to each fuel component from thermodynamics that concerns difference in free energy that determines whether reaction is exothermic or not. Conversely reaction rates for reactants come from kinetics via considering especial orders yet constants for each fuel component within its cremation. Enthalpy values for all hydrocarbon components are negative which exhibits exothermic oxidations whereas also reaction rates show their instant conversion. Conversely While slow spontaneous conversion of nitric oxide to nitrogen dioxide takes place in small amounts according to exothermic equation of form:It is noticeable that the overall Sour flares intake In order to perform reaction calculations, one has two alternatives. First way is to write an independent program or apply a convenient software for such purpose. Next option is to do oxidation calculations in the same software that performs computational dynamics. Here we chose to develop an in-house MATLAB program that gives us flame temperature as well as flue gas composition with respect to excess air as shown in Fig.\u00a0In this step we know flame temperature for each flare in addition to information on flue gas composition for all existent stacks with known locations. Now is the time to simulate pollutant dispersion from Kirkuk refinery to its environs namely adjacent city on east as well as farms on west. To do this one must employ computational dynamics that unites mass with energy conservation equations to predict flow specifications in systems. For this purpose, we use GAMBIT software that designs structures in accompaniment with Fluent software that employs dominant laws to do computational dynamics. In this section we develop a three-dimensional prototype that simulates to what extent air contaminant can reach residential area or agricultural farms. Main reason to use spatial geometry rather than two dimensional areal models is that we want to know how each pollutant component lowers its height when cools down in environment. In addition to that since here we have several flare stacks at once one cannot use vertical cross section geometry in this study. Therefore, we prepare three dimensional prototypes that considers not only refinery limits yet urban regions on Kirkuk city as well as next door agricultural farms as shown in Fig.\u00a0All our simulations in this case study undergo steady state condition since times to turn on or off flares are extremely small in comparison to operation times. By applying computational dynamics, we appraise average concentration for each contaminant component namely Monte Carlo technique relies on fortuitous sampling from solution space in overall scale which is here statuses of flares. Two crucial issues that appear in applying this technique are weak local search as well as requirement for massive random tries to detect an optimal solution. This is while genetic algorithm starts with an initial random try to set flare statuses thereafter evaluates target functions to select top candidates among all initial tries. Process continues with changing statuses for one next-door flare stack from layout that comes from previous step. Genetic algorithm improves layout with advancing local search rather than overall that may result premature solutions. Particle swarm optimization randomly places set values for flare statuses in each layout to discover most valuable layout via evaluating pollutant concentrations. This metaheuristic technique defines a velocity vector for each flare stack with respect to its status in interim optimal layout that updates after each try.In last step of our computations, we made use of neural network approach to unify monthly information that came from search in our case study for optimal layout. This approach is a pure mathematical therefore fast technique which exactly relates intake factors to outlet results. Since neural network neglects all the previous conceptual laws it is most useful in solution spaces with unknown governing equations. Here we use seasonal air direction rather than average monthly velocities as two most significant inputs. Beside them we also import excess air for each flare that computes flame temperature together with statuses of flare stacks in each optimal layout. One can expect more accurate outcomes with less intake parameters yet respectively more train or test instances. Here we employ 80% of exemplar data taken from monthly searches as train data while leaving 20% for test. Finally, we employ this intelligent network to perform sensitivity analyses on mean air flow velocity rather than its direction in addition to total intake volumetric flow rate.In this section firstly we verify our outcomes against routine pattern for which all flares are inline. In order to do this, we draw seasonal pollutant concentrations in two target regions namely city on east as well as farms on west. Thereafter we illustrate two exemplar optimal layouts for two specific circumstances for local seasonal air currents. After that we explore to what extent each search algorithm optimizes alive flare pattern as iterations go on. Farther in this section we perform several sensitivity analyses over air current velocity rather than direction as well as intake sour gas flow rate via applying neural network approach.In order to verify our outcomes on optimal flare layouts most correct way is to evaluate pollutant concentrations in target areas versus normal situations in which all flares work. For an easy comparison one can report an average value for each air pollutant in residential area as well as farms. Two main air contaminants that show high amounts are Outcomes illustrate that whenever currents are in route to our two target areas their consequences on pollutant mass fractions for optimal flare layout deviates significantly from normal flare pattern. For example, in summer that seasonal air currents are from northwest to southeast applying optimization algorithms seriously improves process performance that cause crucial reduction in pollutant emission in Kirkuk city. In another case we have autumn in which weaker air currents flow from Kirkuk refinery to farms on west. Here one can see smaller yet still important difference among pollutant mass fractions when optimal flares are inline versus normal pattern whenever all flare stacks work. Conversely during spring or winter season that we have trivial or no air flows in Kirkuk governorate air contaminants in two target areas due to sour gas flares are insignificant. In such circumstances pollutants freely arise in atmosphere to reach higher troposphere air layers with larger velocities. Surely for more accurate forecasts one can advise to concern temperature inversion for winter season which we did not include in our computations. Anyway, in slow or no air flows not only pollutant diagrams are smaller yet also difference of outcomes for two scenarios namely normal minus optimal flare layouts is unimportant. Here we schematically display two exemplar monthly optimal flare layouts for April as well as June in Kirkuk refinery as shown in Fig.\u00a0Graphical results on optimum layout in April illustrate that more than 90% of existent stacks participates in sour gas oxidation. This is while in June when we have air flows direct to residential areas refinery must turn on only carefully chosen stacks up to 60% to reduce pollutant mass fractions. To discuss optimum layout for alive flares in June one can say that specific flares that sets down nearer to Kirkuk city push up pollutant gases that come from other flares. Alive stacks in optimal layout let to freely carry unequal sour gas volumetric flow rates more than minimum yet less than maximum values that flare stack can work. In addition to that each flare can have its own excess air thus specific flame temperature. One can see schematic flare layout as shown in Fig.\u00a0At low or no air flow conditions optimization process works almost similar we mean more accurate flare stack locations attains at higher iterations except that here genetic algorithm plus artificial immune system that have strong local search impressively refine flare layout at fewer tries. In addition to that such algorithms more accurately discover optimal flare layout after achieving convergence. This is while Monte Carlo or particle swarm optimization fail to compete the two other optimization approaches from convergence viewpoint. One can look at Fig.\u00a0From flow direction point of view whenever air currents are from Kirkuk refinery to target areas namely city on east as well as farms on west pollutant mass fractions are high yet optimization process is effective. Conversely whenever seasonal air flows are not in direction of target areas low mass fractions appear thus one do not require any optimization process. In order to speak on results for sour gas volumes one can tell that at situations with high intake flow rates search for an optimal flare layout is more crucial that when refinery vents less sour gas. For further details on our analyses see Table Either pollutant mass fractions in target areas or optimization process efficiency rely on air current velocities as well as its direction. At no or low air flows or when air velocities are extremely high optimum layout includes almost all existent flares.Heuristic techniques that have stronger local search such as particle swarm or artificial immune system can improve flare layout in seasons with intermediate air currents here summer plus early months in autumn accurately at less iteration.Optimization approaches which express weak local search like Monte Carlo help to detect optimal layout for flare stacks in circumstances with low or no air currents. These approaches are more appropriate in winter or spring for which we have low or no air flows in lowest troposphere layer in Kirkuk governorate.Fast simulation approaches such as neural network is several times faster than full computational dynamics specially when working with large volume data whereas convergence times are almost same when working with small volume data.Several key findings from present article are as follows:"} +{"text": "In malignant pleural mesothelioma patients, pleural effusion may improve during the course of the disease. Pleural effusion with nodular shadows bordering the pleura should be followed up even if the pleural effusion improves. In malignant pleural mesothelioma patients, pleural effusion may improve during the course of the disease. Pleural effusion with nodular shadows bordering the pleura should be followed up even if the pleural effusion improves. A 69\u2010year\u2010old, male patient visited our hospital 4\u2009years ago after a chest x\u2010ray found a right pleural effusion during a physical review Figure\u00a0. He had In the advanced stages of malignant pleural mesothelioma, pleural effusion may occasionally improve when tumour cells cause adhesion of the pleura.Sayaka Nishida and Kazutoshi Toriyama collected the clinical data and drafted the original manuscript. Makiko Yomota and Yukio Hosomi were in charge of patient care, obtained informed consent from the patient and revised the original manuscript. All authors have confirmed the final manuscript and agreed to publication.None declared.The authors declare that appropriate written informed consent was obtained for the publication of this manuscript and accompanying images."} +{"text": "Dear Editor,\u201cSharing microphotographs of histopathological or cytological cases via WhatsApp is a very easy and fast method to obtain a second opinion in pathology practice and also to discuss difficult cases (We read the publication named \u201cUsefulness of WhatsApp for Discussing Difficult Cases in Pathology Practice: A Moroccan Experience.\u201d with great interest . Bennanilt cases .\u201d We woult cases . Neverthlt cases . Protectlt cases . Crane alt cases . The dev"} +{"text": "Redo mitral valve surgery using resternotomy after coronary artery bypass grafting (CABG) is challenging as previous CABG with patent internal thoracic artery (ITA) poses a risk of injury due to dense adhesion. It is paramount to have alternative method to minimize this risk.: We report a case of redo mitral and tricuspid valve repair via right thoracotomy under hypothermia and systemic potassium administration with axillary artery cannulation in a patient after CABG with patent bilateral ITA grafts crossing over the sternum. Herein, critical dissection around the aorta and functioning ITA grafts was avoided by performing the procedure under systemic hypothermia via thoracotomy. Furthermore, considering the presence of atheroma in the aorta, the axillary artery was used as a perfusion route to prevent stroke events. Postoperative course was uneventful and echocardiography demonstrated preserved cardiac function.Performing axillary artery cannulation and right thoracotomy under hypothermic cardiac arrest with systemic hyperkalemia without clamping the patent bilateral ITAs and aorta allowed us to perform redo mitral valve surgery after CABG without major postoperative cardiac or cerebral complications. Mitral valve surgery in patients with a history of coronary artery bypass grafting (CABG) can be challenging for cardiac surgeons. As patent internal thoracic artery (ITA) graft injury during reoperation via resternotomy in the setting of dense adhesion is often fatal, it is essential to establish an alternative protocol to minimize potential injury to ITA grafts. Previous studies have reported that redo mitral valve surgery can be safely performed via right thoracotomy without clamping ITAs under hypothermic cardiac arrest after initial CABG with patent ITA grafts . Here, wA 77-year-old woman who had undergone CABG with bilateral ITAs 6 years ago, with right ITA to left anterior descending artery and left ITA to obtuse marginal artery, presented to our hospital with symptoms of heart failure and was diagnosed with severe mitral and tricuspid regurgitation Fig.\u00a0a\u2013c. EchoThoracotomy rather than resternotomy was performed because the patent ITA graft crossed over the sternum Fig.\u00a0a, c. An The optimal strategy for myocardial protection during reoperative cardiac surgery after initial CABG with patent ITA graft remains controversial. Some researchers believe that ITA dissection and clamping should be avoided as the risk of ITA injury outweighs the benefits of identifying and controlling the ITA graft ; conversThe right minithoracotomy approach provides an excellent operative view of the mitral valve without requiring the dissection of the adhesion and ITA grafts after CABG with median sternotomy. Evidence also shows that redo mitral surgery via the right thoracotomy reduces mortality as well as shorter hospital stay compared with remedian sternotomy .Owing to the antegrade perfusion of the brain, axillary artery cannulation is more effective than femoral artery cannulation in protecting the brain and preventing stroke events during aortic surgeries requiring hypothermic circulatory arrest . Also, SIn this case, the combination of axillary artery cannulation and right thoracotomy under hypothermic cardiac arrest with systemic hyperkalemia without clamping the patent bilateral ITAs and aorta enabled safe surgery without major postoperative cardiac or cerebral complications in a patient with atheromatous aorta and previous CABG with patent bilateral ITAs."} +{"text": "Chronic wound infection has become a major healthcare burden globally. The colonized microbiome features and correlation between bacteria and fungi have not been listed.In this study, we enrolled 38 acute wound infection and 28 chronic wound infection patients. The wound swabs sampling at admission were tested by metagenomic next-generation sequencing. Microbial community characteristics in wound infection patients and bacteria-fungi correlations in chronic wound infection patients were analyse after filtering background organisms.We found that wound microbiome in chronic wound infection patients had higher abundance of Pseudomonas aeruginosa than that in acute wound patients. Meanwhile, microbes with high relative abundant in chronic infection wounds were less significantly association with plasma inflammation factors compared with those in acute infection wounds. Finally, we investigated the association between fungi and bacteria in chronic infection patients and found that relative abundance of Pseudomonas aeruginosa was negatively associated with that of Candida albicans.Our metagenomic sequencing results of wound supported that Pseudomonas aeruginosa may be the biomarker of chronic wound infection and have interaction with candida albicans.All Authors: No reported disclosures"} +{"text": "Most metacarpal fractures produce a flexion deformity and often minimal shortening. Reduction can frequently be achieved by exerting pressure on the metacarpal head from the palmar aspect, either directly or using the proximal phalanx as a piston. The main issue with the closed technique is maintaining the reduced position in a plaster cast once moulding is complete, thereby commonly necessitating surgical stabilisation. We describe a novel and useful technique that maintains the reduction in the intrinsic plus (Edinburgh) position with the wrist at 20\u201330\u00ba of extension .Figure First, a Tubigrip\u2122 elasticated tubular bandage is applied. An Actimove\u00ae Alufoam aluminium finger splint is bent into the intrinsic plus position and applied to the volar aspect of the hand and forearm, bridging the fractured metacarpals. The fracture is then reduced as described above. An Actimove\u00ae Manus Eco wrist brace is applied snuggly over this. The injured metacarpal fingers are buddied up to the Actimove\u00ae Alufoam aluminium finger splint with tape. Finally, a Hospicrepe\u00ae Type II cotton cr\u00eape bandage is applied to prevent the patient interfering with the splint .Figure This technique allows bony union without the need for changing immobilisation materials throughout the fracture healing process, thus enabling continuous stabilisation through conservative management."} +{"text": "Authors David Abraham and Kithiganahalli Narayanaswamy Balaji should not have been attributed equal contributions to the article. Shalu Verma-Kumar is the only first author."} +{"text": "Footwear is an effective biomechanical solution to lower extremity joint problems. Variable stiffness shoe (VSS) is designed. It has been proved to reduce knee internal abduction moment . This he15 female and 15 male subjects walked in 2 conditions: VSS and Control. VSS had a lateral sole 1.6 times stiffer than medial (Figure Increased posterior force during running and stop jumping Table ensured The study demonstrated great potential of VSS in improving sports achievement and protecting knee. Outsole configuration can be further modified by varying outsole stiffness along anteroposterior axis for better performance and protection."} +{"text": "Patients who are critically injured with imminent cardiac arrest may require immediate thoracotomy as an integral component of their initial resuscitation in the emergency department. Fluid resuscitation can be difficult owing to a shutdown state. A simple method for fluid delivery in patients requiring emergency department clamshell thoracotomy entails the insertion of a large bore venous catheter directly into the right atrium at its appendage and using it for fluid resuscitation . This me"} +{"text": "Sensors recently [We found that the affiliation of author Vasu Chakravarthy was incorrect in our paper published in recently . Therefo"} +{"text": "In Figure 4, the results labelled TTM should be labelled DLM and vice versa. Please view the correct figure here: ."} +{"text": "The soft tissue injury associated with Pilon fractures is significant. Fixation using minimally invasive techniques allows for early ankle mobilisation while protecting the soft tissue envelope. Ligamentotaxis using an ankle distractor is a non-invasive reduction technique that protects the soft tissue and maintains access for minimally invasive fixation. The patient is positioned supine with a bolster under the knee. The sterile Guhl Non-Invasive Ankle Distractor is applied and attached to the table using an extension bar under the drapes. Traction is applied. An upturned bowl under the calcaneus avoids sag."} +{"text": "Pharmacophore models play an essential role in drug discovery. Generating pharmacophore models which encode accurate molecular recognition features are highly dependent on properly defined annotations. Simplistic or ill-defined pharmacophore annotations which do not capture subtle electronic or geometric effects lead to many inaccuracies. SMARTS patterns which are often used to specify annotation \"rules\" are subject to such inaccuracies.The application of Extended Huckel Theory (EHT) to pharmacophore annotations compensates for deficiencies observed in \"rule\" based methods by taking into account electron withdrawal and resonance effects and treating these effects in a consistent manner independent of structural depiction. The application of the EHT approach will be further described and discussed through a number of case studies."} +{"text": "There is a typographical error in the funding statement. Grant NS060885 is incorrectly published as NS06885."} +{"text": "Dear Editor,There is an important point related to temporomandibular joint (TMJ) injuries and derangement due to trauma from dental extractions by dental students. This subject should be an utmost cause for concern for dentists and dental practitioners. Because if not treated it may become chronic. This issue has been noted by many researchers in academic dental training centers worldwide. The results of many studies in this field have shown surprisingly high prevalence rates of TMJ injuries 50-63 %) after extracting mandibular teeth by dental students . About 6 % after"} +{"text": "After the publication of this work , we becaTranscript derived fragments (TDFs) from Puccinia striiformis f. sp. tritici infected wheat leaves with altered expression patterns and their closest matches in the GenBank database.Click here for file"} +{"text": "Older patients with stroke to either hemisphere had a higher frequency of deficits in the verbal working memory task compared to older TIA patients. Additionally, the deficits in older stroke patients were mainly in retrieval time while the deficits in younger stroke patients were mainly in accuracy. These data suggest that bihemispheric activity is necessary for older adults to successfully perform a verbal working memory task.Functional imaging studies consistently find that older adults recruit bilateral brain regions in cognitive tasks that are strongly lateralized in younger adults, a characterization known as the Hemispheric Asymmetry Reduction in Older Adults model. While functional imaging displays what brain areas are active during tasks, it cannot demonstrate what brain regions are necessary for task performance. We used behavioral data from acute stroke patients to test the hypothesis that older adults need both hemispheres for a verbal working memory task that is predominantly left-lateralized in younger adults. Right-handed younger (age \u2265 50,"} +{"text": "Whole blood experiments suggest that cardiopulmonary bypass (CPB) causes red blood cell (RBC) trauma and changes in deformability that may contribute to postoperative microcirculatory dysfunction. We used a novel fluctuation microscopy technique to quantify the effects of CPB on RBC elasticity at a cellular level.We collected blood samples from elective cardiac surgery patients pre (at induction) and post CPB. Thermal fluctuations of individual RBCs were recorded using a high-frame-rate camera allowing a complete analysis of RBC shape variation over time. Mean elasticity of the cell membrane was then quantified for each sample collected.Fifteen patients were recruited. Table RBC thermal fluctuation analysis quanties the impact of CPB on erythrocyte membrane elasticity. We clearly identified two separate RBC elasticity responses to CPB. This finding is contrary to traditional flow measurement techniques that suggest CPB impairs whole blood flow and reduces RBC deformability."} +{"text": "Author Soon Gyu Hong should have been noted as a Corresponding Author, with the email address polypore@kopri.re.kr"} +{"text": "Heart valve injuries due to non-penetrating blunt thoracic trauma are rare with aortic valve being the most vulnerable. Tricuspid valve injury resulting in severe regurgitation is unusual after blunt chest trauma. Two major issues for the management of traumatic tricuspid regurgitation are timing and type of the operation. Valve repair is naturally the first choice but valve replacement may be required in severely destructed valves with good surgical outcomes.A 61 years old man who suffered a car accident was admitted to emergency department with multiple traumas. He had costal fractures, bilateral pneumothorax and left femur fracture. Chest auscultation revealed 3/6\u00b0 systolic murmur. Transthoracic echocardiography demonstrated chordal ruptures for anteroseptal leaflet, causing severe tricuspid regurgitation. He was hospitalized in the intensive care unit. Chest tubes were inserted for pneumothorax with orthopedical retraction applied for left femur fracture. He did not develop any symptoms related to severe tricuspid regurgitation and valve surgery was postponed to full recovery of other system injuries. Three months later he was scheduled for elective tricuspid surgery. Median sternotomy and standard aorto-bicaval cannulation was performed. Tricuspid valve was severely destructed with multiple leaflet lacerations, chordae and papillary muscle ruptures. Tricuspid repair was not possible and valve replacement with 31mm bioprosthesis was performed.Intensive care unit and subsequent ward follow up was uneventful. He was discharged at postoperative 6th day. His nine months follow up revealed an asymptomatic patient with a functional capacity of NYHA 1.Although rare, heart valve injuries may occur following blunt thoracic trauma. Transthoracic echocardiography is a must for evaluating such patients. Surgery if necessary can then be planned either urgent or electively according to each patient situation."} +{"text": "This work presents a simulator that facilitates dynamic neural field (DNF) calculations obeying models of the typeinvolving axonal finite transmission speed c. The underlying numerical computation method utilizesThe simulator consists of a window where one can choose DNF parameters and the output format. The parameter window Figure consistsThe options for output include text based notifications and graphical visualization in 3 dimensions Figure . These o"} +{"text": "Lens epithelial cells are well coupled by conneTo further test this hypothesis, we have been developing methods to quantitatively measure the permeation of relevant second messengers such as cAMP through gap junction channels."} +{"text": "The article Hendra Virus Outbreak with Novel Clinical Features, Australia contained several errors related to specific case descriptions and spillover events. The article has been corrected online"} +{"text": "The term \"moderate-intermediate\" has been incorrectly printed without a hyphen in multiple places through the article. It should have a hyphen."} +{"text": "Several errors were introduced in the preparation of this article for publication.The word \"connexin\" has been incorrectly substituted by \"connection\" throughout the article."} +{"text": "The bottom set of graphs in Figure 2 was labelled incorrectly. It should read UKRAGG rather than WTCCC. Please download the correct file here:"} +{"text": "The CONSORT checklist and trial protocol that accompany this study were erroneously omitted during the production process. Please view the files here:Click here for additional data file.Click here for additional data file."} +{"text": "Dear Editor,I thank Chowdhury for the Pleomorphic adenoma arising from an ectopic lacrimal gland is a rarity. The literature search did not yield any results of recurrent pleomorphic adenoma arising from an ectopic lacrimal gland."} +{"text": "There was an error in the Author Contributions. LZL SLN SP XZ TRO conceived and designed the experiments."} +{"text": "Removal of broken locking bolts requires careful planning. The following tips facilitate the procedure and reduce operation time.Positioning the patient supine without traction allows optimal adduction. Early screw removal will leave the nail rotationally unstable; apply the jig beforehand. If direct palpation is not possible, access the end cap by a guided drill . Use scr"} +{"text": "Efforts to develop congenital heart surgery programs are numerous but few view the concomitant development of interventional cardiology as a critical component of these efforts.A case series describing perioperative complications of the first Fontan procedures performed in a developing congenital heart surgery program.Two patients underwent the first Fontan palliations while participating in a development program for congenital heart surgery. Both presented at 32-33 months of age with baseline oxygen saturations of 82-84%. Patient 1 underwent an extracardiac Fontan with a GoreTex conduit larger than the IVC due to limited supplies. Postoperatively, the patient decompensated to a low cardiac output state with elevated Fontan pressures and significant edema that did not resolve despite fenestration creation. Catheterization demonstrated inferior conduit anastomotic stenosis and right pulmonary artery (RPA) obstruction by compression. Angioplasty of the extracardiac conduit distal anastomosis and RPA stent implant reduced Fontan pressures. The patient was extubated in 3 days and discharged home at 21 days. Patient 2 underwent a lateral tunnel Fontan and extubated 2 hours after surgery, but developed desaturation and low cardiac output within 24 hours. Catheterization revealed elevated Fontan pressures and a large SVC to pulmonary vein collateral. After coil embolization, the patient slightly improved, but underwent subsequent catheterization several days later where an Amplatzer duct occluder was used to obstruct significant antegrade flow through a previously banded pulmonary valve resulting in acute clinical improvement.Availability of interventional cardiology allowed early intervention to perioperative complications, reducing the need for repeat surgery and facilitating good clinical outcomes. Development of combined congenital heart surgery and interventional cardiology programs can be of great benefit for patients."} +{"text": "Many insects manage their foraging behaviors or prey detection based on resource information. Their brain system should encode the resource location efficiently. Honeybees remember the nectar source location and communicate with their colleagues using their own dance language . Desert"} +{"text": "Migraine end epilepsy have common pathophysiologic mechanisms and share essential and defining attributes which distinguish them from other common neurological disorders. They are both characterized by paroxysmal symptoms and are, therefore, episodic disorders. Occipital lobe to be the brain structures most responsible for development of migraine and occipital lobe epilepsies Both are characterized by visual symptoms followed by headache and other autonomic symptoms. Recognition of headache as an epileptic manifestation per se still represents a challenge.This study included consecutive 89 patients with IEH= ictal epileptic headache,at our hospital and our diagnostical department \u2013 MRI and EEG.EEG recordings high voltage rhythmic 11-12 Hz activity with intermingled spikes over the right TO regions. Other \u2013high voltage theta activity intermingled with sharp waves over occipital region. And third bilateral SWC.Brain MRI showed secondary brain lesion in the right TPO region with restricted diffusion in the right occipital region.IEH be used to classify the events in wich headache represent the only ictal epileptic feature These rare cases should be classified as autonomic epilepsy."} +{"text": "Dear Editor,We read with great interest the recent published outstanding article in your esteemed journal by Rostami et al. entitledThe impact of gender on quality of life (QoL) has remained a challenge yet. Although Rostami and coworkers showed tAlthough Rostami et al. showed nWe agree that QoL in HD patients are poorer than normal population. It seems that besides preparing these patients for kidney transplantation and treatment of biochemical disorders, HD patients counseling can improve QoL. Abraham and coworkers conducte"} +{"text": "The equal contributions statement was omitted. Dajun Liu, Luping Huang and Yanlin Wang contributed equally to the manuscript."} +{"text": "Takayasu arteritis is an idiopathic chronic inflammatory disease affecting frequently the aorta-big arteries and may cause stenosis, occlusion or aneursymatic degeneration. Coarctation or aneurysm formation may be seen due to aortitis. We present a patient with severe aortic regurgitation and ascending aorta dilatation we treated surgically.A 38 years old man with diagnose of Takayasu arteritis was admitted to our hospital with chest pain. Echocardiography revealed severe aortic regurgitation + ascending aorta dilatation. Computed tomographic angiography showed ascending aorta was 44 mm. He was scheduled for elective cardiac operation. His medication was adjusted as Addison protocol for operation. Axillary artery cannulation and median sternotomy was performed. Ascending aorta was aneursymatic up to truncus brachiocephalicus. Coronary ostia were prepared as buttons. Aortic valve and ascending aorta was resected and replaced with a valved conduit including a 25 # St Jude mechanical prosthetic valve and 30 mm Dacron tube graft. The left and the right coronary ostia were anastomosed on the Dacron tube graft. Bentall procedure was completed with the distal anastomosis of Dacron graft strengthened with Teflon strip to aorta beyond truncus cephalicus. Cardiopulmonary bypass was terminated without inotropic support.Intensive care unit and hospital follow-up was uneventful. He was discharged with low dose corticosteroids at postoperative sixth day. Although surgical therapies for patients with chronic vasculitis may be challenging due to chronic inflammatory influences on vessels, a meticulous approach with supporting the anastomosis with additive surgical materials may improve surgical success.Although surgery in Takayasu arteritis is known to be complicated because of vessel structure due to chronic inflammation. A radical and elaborate approach may ease an uneventful operation when surgery is mandatory."} +{"text": "Not all tumor cells are created equal when it comes to telomere biology. Tumor cells that do not express telomerase appear to utilize a telomerase-independent process to maintain telomere length, known as ALT for alternative lengthening of telomeres . Althoug"} +{"text": "Lentiviral entry to quiescent lymphocytes represents a 'time bomb' waiting for cellular activation to spread infection. In order to undergo immune activation T cells interact with dendritic cells presenting peptide:MHC complexes 'sampling' them to look for agonist peptides and receiving survival signals from self peptides. This makes the dendritic cell:T cell interaction an ideal checkpoint to contain lentiviral infection of quiescent lypmhocytes.We have used replication defective lentiviral vectors expressing reporter genes and/or HIV proteins to study the innate immune response to lentiviral infection in vitro using primary mouse and human cells and in vivo in B6 mice. We have used flow cytometry and PCR to quantify the infection rates in various culture and adoptive transfer conditions to identify conditions where successful viral infection is inhibited.Activating T cells exposed to dendritic cells display inhibited lentiviral vector infection compared to activated control cells. This infection reduction is mediated by dendritic cell:T cell contact. Dendritic cell mediated inhibition of infection reduces over time as cells become fully activated and proliferate. When using lentiviral vectors similar results are seen in primary human T cells in culture. However when replication defective vectors expressing HIV proteins are used to infect T cells de novo expression of HIV proteins in the host cell prevents DC mediated inhibition. We have gone on to use knockout mice to assess the role of established innate immune sensing pathways in DC mediated inhibition but have not yet identified the molecular sensor mediating this phenomenon.The inhibition of productive T cell infection by lentiviral vectors caused by contact with dendritic cells represents a previously undescribed innate immune response which we have called DC mediated inhibition. The successful lentiviral pathogen HIV overcomes DC mediated inhibition enhancing its replication and obscuring this immune response."} +{"text": "The equal contributions designation was inadvertently omitted. Brooks B. Pond and Shankar Sadasivan contributed equally to this manuscript."} +{"text": "The requirement to wear gloves when caring for patients on contact precautions may cause personnel to neglect hand hygiene before aseptic procedures, thereby increasing infection transmission.The aim of this study was to assess the compliance with hand hygiene before and after eliminating mandatory glove use for patients on contact precaution at our institution.We assessed hand hygiene compliance of HCW taking care of 50 adult patients colonized with MDR microorganisms before (2009) and six months after (2012) eliminating the mandatory wearing of gloves. This policy change was implemented by our infection control team and communicated to all hospital floors. Along with this policy change, we routinely provided hand hygiene training to HCW on all floors. Hand hygiene observation was performed by two trained infection control nurses during routine care using a standardized questionnaire.after patient contact remained high . During the same period, we observed a smaller increase in hand hygiene compliance for the entire hospital .We observed 426 hand hygiene indications before the policy change and 492 six months after policy change. Compared to 2009, we observed a significantly higher compliance with hand hygiene in patients colonized with MDR microorganism in 2012 . In particular, compliance improved before performing invasive procedures: , and before patient contact . Hand hygiene compliance Eliminating mandatory glove use in contact with isolated patients increased hand hygiene compliance, particularly before invasive procedures and before patient contacts. Glove use may cause healthcare workers to bypass hand hygiene. The potential impact on the risk of MDR organism transmission should be determined next.None declared."} +{"text": "These days cochlear implantation is the accepted modality to rehabilitate deafened people. Meningitis is still a life threatening disease which may lead to deafness due to sole disease or secondary to ototoxic drugs used to stop the disaster . Sepsis The cornerstone to rehabilitate deaf victims is cochlear implantation. Time to perform bilateral implantation is a challenging issue. Cochlear obliterance after bacterial meningitis enhances electrode insertion and efficiency. This case report confirms the idea of bilateral cochlear implantation as early as possible.In Sep 2010 a 4 month girl was brought to our cochlear implant centre after discharging from another hospital with deafness after proven pneumococcal meningitis. She took Imipenem\u00ae and Vancomycin\u00ae during hospital course without harsh on kidney, liver or blood. There was not any familial history of deafness or proven history of TORCH infection. TEOAE after birth was passed but new TEOAE after meningitis was failed and ABR could not detect any wave at 90 dB Hearing Level. Second ABR two months later was same as before. Her family accepted the suggestion for cochlear implantation and she was taken to operating room just three months after meningitis recovery. Unfortunately family found for CI was restricted to do bilateral implantation at that time. One year later when family could prepare for second ear surgery new CT scan revealed ossification and near complete obliteration of cochlea .Now her Although our patient\u2019s general health condition and hearing and speech rehabilitation is favorable, she might have lost the chance to have bilateral hearing . Some da"} +{"text": "The letter \"m,\" used as an abbreviation of \"meter,\" appears incorrectly throughout the manuscript. The correct abbreviation should be \"um,\" to indicate micrometer(s)."} +{"text": "A frequent hypothesis in theoretical neuroscience is that cognitive entities are represented and processed by attracting states of the underlying neural system . For insUsing state space reconstruction theorems and statintrinsic dimensionality which is relevant to the animal\u2019s arm choices could be computed [Results showed cognitive-epoch-specific neural ensemble states in ACC computed . Results"} +{"text": "There was a typographical error in the first sentence in the second paragraph under the \"Population dynamics on RNA neutral networks\" heading. \"limi\" should be \"limit\"."} +{"text": "We report a case of a young patient presenting concomitant pulmonary artery embolism and an intra-aortic thrombus occluding the left subclavian artery due to a patent foramen ovale. This patient was treated under short circulatory arrest and unilateral cerebral perfusion allowing aortic and pulmonary embolectomy and closure of the small PFO. Follow up was uneventful so this case shows a successful treatment of a massive paradoxical aortic embolism and pulmonary embolism. Complete preoperative imaging is necessary to choose the safest cannulation option."} +{"text": "The striatum forms the main input structure to the Basal Ganglia (BG), a subcortical structure involved in the selection and reinforcement learning of action sequences. It is 90% composed of medium spiny neurons (MSNs) which inhibit each other through collaterals, receive excitatory projections from cortex and are the only cells projecting outside the striatum. Because of its inhibitory structure the MSN network is often thought to act selectively, transmitting the most active cortical inputs downstream in the BG while suppressing others. However studies show that local MSN network connections are too sparse and weak to perform global selection and their function remains puzzling. Here we suggest that rather than generating a static stimulus dependent activity pattern the MSN network is optimized to generate stimulus dependent dynamical population activity patterns for extended time periods after variations in cortical excitation. Indeed MSNs form cell assemblies whose population firing rates vary coherently on slow behaviourally relevant timescales . Further"} +{"text": "Cutaneous leishmaniasis is an endemic disease of Iran. Unfortunately, there is no definite treatment for this disease.Leishmaniasis scars are usually depressed and atrophic. Patients affected by these scars usually have psychosocial and cosmetic complains."} +{"text": "Allrgic reaction to natural rubber latex have increased during past 10 years especially among health worker and patients with high exposure to latex allergen. Latex allergy is associsted with clinical or serological cross reactivity to plant derived food allergcn especially tropical fruit for example avocado bannana chestnut kiwi papaya potato and peaches. In this study on health worker among 580 participants 104(17.9 %) who were positive to latex skin prick test.Of 464 patients with negative skin prick test to latex are have 12 patiets with positive skin prick test to kiwi and in 197 patiens with positive skin prick test to latex 7 patients had positive skin prick test to kiwi( p<0.05). In this study difference of sensivity to banana and potato in both groups were not significant according to this study kiwi hypersensivity is important problem among health worker with sensivity to latex.latex Allergy -kiwi \u2013 skin prick test"} +{"text": "Equal contribution was unassigned. Tini Garske and Hongjie Yu contributed equally to this work."} +{"text": "Recent advances in reproductive medicine havecreated a demand for more accurate and safe imaging modalities before assisted reproductive treatment (ART) . GradualThe aim of this article is to evaluate a communicated uterus through 3D image, while to compare this result with quite similar images of thispatient with hysterosalpingography .Thepati"} +{"text": "Sir,Nanobiotechnology is the assembling of biological molecules into 1\u2013100 nm dimensions. These dimensions can be the diameter of nanodimension artificial cells or particles; membranes with nanodimension thickness or nanotubules with nanodimension diameter. Past exp"} +{"text": "Recent studies suggest that the functional organization of brain networks is altered in patients with severe disorders of consciousness (DOC), including coma . A betteThe major findings are summarized in Figure"} +{"text": "The equal contributions statement was omitted. Virginie Lvovschi and Laurent Arnaud contributed equally to this work."} +{"text": "The last sentence of the section \"Total Circulating Leukocytes\" should have cited reference 8 instead of 51.The correct sentence should read: However, bats typically rewarm to euthermia more rapidly than other hibernators and may have arousal bouts under 90 minutes [8] making it difficult to predict changes in circulating leukocytes given the extent to which they differ from other taxa."} +{"text": "Standard Titanium Elastic Nail fixation requires a 2.5mm drilled entry point at the base of the metacarpal. This can damage soft tissues including the extensor tendon and also risks breaching the volar cortex. We recommend opening the dorsal metacarpal cortex with a curved artery clip . Initial"} +{"text": "Although apoplexy and cystic formation are common inside the pituitary adenoma and hemorrhage with different times of occurrence as revealed by magnetic resonance imaging sequences can be seen within a pituitary macroadenoma, a classic saccular aneurysm and its association with carotid artery haven\u2019t been yet reported. A 52 years old woman was referred for visual loss and headache accompanied by pituitary adenoma. She has no particular past medical history was operated her huge pituitary macroadenoma was resected by endoscopic endonasal transsphenoidal surgery.During surgery we encountered a tough saccular mass and checking imaging brought the conjecture of a thrombosed aneurysm. By careful dissection and use of intranasal Doppler sonography its association with left internal carotid was revealed. After coagulation of its main branch that was probably a tumor feeder aneurysm resected totally and we proceed for further tumor removal.Up to our knowledge and review of the related literatures it is the first time that intra adenoma thrombosed aneurysm is reported. Intra adenoma thrombosed aneurysm, Classic saccular aneurysm, Case report, Doppler Sonography"} +{"text": "There is an error in the article title, which is missing the word \"binding\". The title should instead read:\"Therapeutic Efficacy of Antibodies Lacking Fc\u03b3 Receptor Binding against Lethal Dengue Virus Infection Is Due to Neutralizing Potency and Blocking of Enhancing Antibodies\""} +{"text": "Magnetic resonance imaging (MRI) is a highly advanced and sophisticated imaging modality for cardiac motion assessment and quantitative analysis. The myocardial tagging techniques have seen wide applications for cardiac deformation analysis . A rotation motion phantom and a healthy volunteer were imaged using OCSPAMM. First row in Figure We have proposed a new tagging sequence and cardiac deformation can be extracted from OCSPAMM tagged images. The images results showed good tag persistence and motion field verified the effectiveness of cardiac deformation analysis from OCSPAMM tagging technique."} +{"text": "Although rare, popliteal artery aneurysms form the majority of peripheral arterial aneurysms and are generally asymptomatic. They usually cause embolic events such as extremity ischemia. In this paper, we present a patient successfully treated with endovascular stent grafting for bilateral popliteal artery aneurysm.A 67-year-old woman presented to our clinic with pain at the back of bilateral knee joints. Physical examination showed manually palpable distal arterial pulses and a pulsatile mass at bilateral popliteal fossae. Arterial Doppler ultrasonography revealed bilateral popliteal arterial aneurysms. Multislice computerized tomography showed an aneurysm starting from distal femoral artery and involving entire popliteal artery at the left side and aneurysmal dilatation in both popliteal artery and proximal segment of the anterior tibial artery at the right side. Screening tests failed to show any additional aneurysms at other sites.Both popliteal artery and right tibial artery aneurysms were successfully treated with stent grafts at one month interval. The patient was discharged with full recovery after an uneventful postoperative course.Management of popliteal artery aneurysms are very important because the complications threaten both limb and life."} +{"text": "Increasing alcohol consumption among older individuals in the UK is a public health concern. Although brief interventions (BIs) can effectively reduce heavy drinking in older age groups generally, social and contextual factors may influence implementation and effectiveness. Identities offer a useful theoretical concept to explain why the potential for public health messages to reduce rates of heavy drinking in this sector has not been realised, and can inform preventive approaches. A qualitative study explored older people\u2019s reasoning about drinking in later life and how this interacted with health concerns, to inform future, targeted prevention in this group. A diverse sample of older adults in North East England (ages 51-90) participated in interviews and three focus groups (participants n=27). Data were analysed using grounded theory and discursive psychology methods. Older adults portrayed drinking less alcohol as an appropriate response if one experienced impaired health. However continued heavy drinking could be presented as normal behaviour for someone experiencing relative wellbeing in later life, or if ill health was construed as unrelated to alcohol consumption. When talking about alcohol use older people oriented strongly towards opposed identities of normal or problematic drinker, defined by propriety rather than health considerations. These identities were flexible in older people\u2019s talk since they could be applied to either moderate or heavy drinking. Older people displayed scepticism about health advice on alcohol when avoiding stigmatised identity as a drinker. Findings indicate that older UK adults do not recognise unhealthy drinking as distinct from dependent drinking, and are highly sensitive to stigma when discussing alcohol consumption. Preventive strategies should encourage older people\u2019s identification of heavy drinking as neither healthy nor synonymous with dependence. BIs for heavy drinkers in later life should be tailored to address lay reasoning that is resistant to recognition of health risks."} +{"text": "A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded,"} +{"text": "Decision makers commit the sunk cost fallacy when they are influenced by previous investments instead of estimated future returns . As resoWe tested the extent to which rats are influenced by previous investment and expected future gains in a naturalistic foraging context. Rats foraged for food on a circular path outfitted with three equidistant feeder sites. Each feeder was associated with a delay that remained fixed within a session. Six sets of delays were chosen to create six session types, across which the opportunity cost of time varied. We computed the optimal strategy for each session type following the prey selection model of foraging theory . Each feWe tested several possible explanations for rats\u2019 behavior on this task, including satisficing , operantA to model subjects\u2019 reluctance to skip feeder sites. Subjects\u2019 unwillingness to abandon sites varied across session types, indicating energetic expenditure cannot fully account for their suboptimal behavior. Interestingly, we found that A correlated positively with opportunity cost. These data suggest that rats\u2019 decisions are influenced by sunk costs, and that the investment they track likely incorporates both energetic costs and the reinforcement statistics of the environment.The sunk cost effect predicts that as investment in a option increases, willingness to abandon that option decreases. Running between feeder locations entails an energetic investment that could bias subjects towards waiting out long delays despite the resulting decrease in reward rate. We fit an aversion parameter"} +{"text": "Traditionally, excision of forehead lipomas is performed via a transverse incision camouflaged in a forehead crease. This approach necessarily violates the frontalis, under which these lipomas reside.The border of the lipoma is marked ; dots anWhile similar results can be achieved with liposuction"} +{"text": "Salamanders typically use a traveling wave of body curvature during swimming, and a standing wave during terrestrial stepping. This pattern is reflected in EMG recordings . A previThe model suggests that salamanders can modulate their intersegmental coordination by modulating the stiffness of their trunk musculature. Salamanders are known to stiffen their trunk during walking. In the"} +{"text": "Operative treatment of comminuted, osteoporotic distal fibula fractures is challenging due to poor bone stock. Conventional plates provide inadequate fixation. We describe treatment using the Proximal Humeral Interlocking System (PHILOS) plate . Following adequate exposure and reduction of the fracture, the PHILOS plate applied to the fibula in an inverted position. Proximal plate fixation using a compression screw is followed by distal fixation using locking screws. An image intensifier ensures satisfactory screw length. The PHILOS fixation is strong and provides angular stability. This technique has been used successfully in three patients with osteoporotic fibula fractures . The pla"} +{"text": "Stochastic gradient ascent learning exploits correlations of parameter variations with overall success of a system. This algorithmic idea has been related to neuronal network learning by postulating eligibility traces at synapses, which make them selectable for synaptic changes depending on later reward signals ( and 2]))2]). For"} +{"text": "Severe sepsis has a high mortality and high healthcare costs. Rapid recognition and treatment can save lives but requires a coordinated response . HospitaPatients admitted to any critical care unit with a primary admission diagnosis of infection were screened for severe sepsis. The pre-ICU care of patients who met the criteria was then audited against the Surviving Sepsis Guidelines . Time zeSince November 2011 we have provided feedback on over 300 severe sepsis cases. Antibiotic administration in <1 hour has risen from 35% to 75% (Figure Individualised feedback on sepsis care has led to substantial improvements in guideline compliance."} +{"text": "The Basal Ganglia represent subcortical structures that have a crucial role in determining when a given motor program should be selected and called into action . The inpWe simultaneously recorded local field potentials (LFPs) in the cortex and striatum in order to determine how striatum processes cortical neuronal avalanches. Cortical neuronal avalanches represent activity clusters with a cluster size distribution that follows a power law with exponent -1.5 . To unde"} +{"text": "Computation in the brain is often thought of as being carried out solely by neurons without regards to their supporting cells. Recent work suggests that astrocytes may play a role alongside neurons in information processing. We investigated what types of spatio-temporal patterning can be supported for such a network. Namely the astrocyte networks contained both fast speed direct connections, representing gap junction coupling, and slower speed extracellular connections, representing local ATP diffusion or changes in local potassium concentration. We investigated what spatio-temporal dynamics results from the interplay between these two processes. We observed each process individually drive network activity and saw competition between the local and direct connections."} +{"text": "A 63 year old male had a sudden episode of cardiac arrest during travel. He was resuscitated and cardioverted successfully with a semi-automatic defibrillator. The first ECG showed atrial fibrillation with inferior Q waves and he spontaneously reverted to sinus rhythm over the next few hours. The patient had been asymptomatic up to the episode of cardiac arrest and referred no prior history of ischemic heart disease. An acute ischemic event was ruled out because there was neither ST segment elevation on the surface electrocardiogram nor cardiac enzyme elevation. An echocardiogram showed localized inferior akinesia and preserved left ventricular ejection fraction. While being monitored over the next 2 days we documented recurrent episodes of supraventricular tachycardia (SVT) that converted to sinus rhythm after carotid sinus massage. On three occasions these episodes of SVT degenerated to syncopal polymorphic ventricular tachycardia (VT) that had to be cardioverted . The patThis case illustrates the unusual case of a supraventricular tachycardia degenerating to VT in a patient with ischemic heart disease. Tachycardia-induced tachycardia is a rare condition. Cases have been described of AVNRT coincident with right ventricular outflow tract tachycardia or with left ventricular tachycardia . In some"} +{"text": "Borrelia burgdorferi sensu lato species in ticks presented in the article was originally developed and published by Sjoerd Rijpkema and colleagues [This article has beenlleagues . The aut"} +{"text": "The cox1 accession number for Kenya on page 6 (\"JQ397340\") is incorrect. The correct accession number is \"JQ397370.\" Additionally, this line is incorrectly printed twice.The correct Supporting Information, Table 1 can be viewed here: Click here for additional data file."} +{"text": "The accession numbers were not provided in the manuscript text. Genome regions containing open reading frames for genes and proteins identified in this study have been deposited at NCBI with accessions JQ677126-JQ677134."} +{"text": "Cataglyphis fortis) and honeybees can return their home after foraging. Desert ants choose a direct path to return home after a long journey, and it is believed that they use path integration approach. Path integration process needs internal integrator to accumulate their traveled distance and direction to estimate the homing vector. Biologists showed that Cataglyphis fortis uses a step integrator as an odometer [Many insects including desert ants (odometer . The patodometer showed todometer found thodometer proposedodometer showed a"} +{"text": "DNA damage elicits a cellular signaling response that initiates cell cycle arrest and DNA repair. The metabolic response to DNA damage is largely unknown. Here we report a novel metabolic response to genotoxic stress. DNA damage triggers a critical block in the uptake of glutamine, a mitochondrial substrate essential for cellular proliferation. Sirtuins regulate both cellular metabolism and stress responses. We found mitochondrial SIRT4 is involved in the metabolic response to DNA damage. These results suggest that the metabolic adaptation is important for cellular DNA damage response."} +{"text": "Deepwater Horizon oil spill.The Natural Resources Defense Council reports the FDA underestimated seafood consumption by Gulf Coast residents in developing their June 2010 protocol for determining safe seafood levels of toxic PAHs following the BP On 1\u20132 February 2011 the Federal Bed Bug Workgroup will sponsor the second national bedbug summit in Washington, DC.USGS researchers used a chemical mass-balance model to show that coal tar pavement sealants were the chief source of PAHs flowing into 40 U.S. urban lakes.Ford Motor Company recently announced its 2012 Ford Focus models will use carpet backing and soundproofing materials made from recycled cotton denim.4\u201cGreenwashing\u201d is the term for ads and labels that promise more environmental benefit than they deliver."} +{"text": "One classic explanation is that mechanisms like neuronal adaptation underlie the switching phenomenon . On the We use Deep Boltzmann Machines (DBMs) as models of cortical processing . DBMs arHere, we make this connection explicit. Using a DBM model that has learned to represent toy images of unambiguous cubes, we show how a sampling algorithm similar to can be u"} +{"text": "Traditional whole blood experiments suggest that sepsis causes abnormal red blood cell (RBC) deformability. To investigate this at the cellular level, we employed a novel biophysical method to observe individual RBC membrane mechanics in patients with septic shock.We collected blood samples from patients with septic shock until either death or day 5 of admission. Thermal influctuations of individual RBCs were recorded allowing a complete analysis of RBC shape variation over time. Mean elasticity of the cell membrane was then quantified for each sample collected.We recruited nine patients with septic shock. Table RBC thermal fluctuation analysis allows variations in RBC elasticity during sepsis to be quantified at a cellular level. We could not identify any specific trend between sepsis severity and erythrocyte elasticity. Cells demonstrated both increases and decreases in fluctuation independent of SOFA score. This is contrary to current evidence that suggests RBC deformability is reduced during sepsis."} +{"text": "Various techniques for quadriceps tendon repair have been described with biomechanical studies suggesting greater failure threshold with longitudinally placed drill holes.\u00ae Director\u2122 Drill Guide , the desired entry and exit locations for drill holes are selected on the patella (\u00ae (Smith & Nephew) cannulated drill bit. The free ends of suture are passed through the eyes of the 2.4mm drill tip passing pins (Satisfactory hold is achieved in the quadriceps tendon with sutures. Using the Acufex patella . Three t patella . Each paing pins and pulling pins . The repThe ability to drill parallel longitudinal transpatellar bone tunnels accurately freehand avoiding the articular surface while maintaining accurate exit points can pose a technical challenge. Coupled with difficulties encountered in passing the sutures through the tunnels, this can result in prolonged operative time with an associated increase in morbidity and needless frustration for the operating surgeon. The technique described here overcomes these difficulties while achieving gold standard repair."} +{"text": "Chemists working in biomolecular application projects are usually looking at many related molecules . For a convenient visual analysis of this data it is essential that differences between molecules are easily detectable. This can be quite difficult if structural similarities are not taken into account while creating molecule structure diagrams. We present a method for generating globally aligned structure diagrams for two molecules following IUPAC standards . Using a"} +{"text": "Hand hygiene is a simple yet often omitted gesture to prevent pathogen transmission and healthcare-associated infections. Training healthcare workers in hand hygiene is a key element in any multifaceted promotion strategy. Physicians are notoriously known for their underperformance in this field. We sought to design a natural immersive environment to improve physicians\u2019 hand hygiene performance.We inserted filmed sequences based on a plot of two physicians interacting with different patients during ward rounds into an interactive computer interface allowing the physician 'gamer' to decide where to use hand hygiene and disposable gloves. Hand hygiene being a very repetitive and often subconsciously executed task, virtual immersion might increase learning and improve long-term retention. Thus, we used both an emotionally engaging but also distracting plot to create role identity and simulate mental load typical for medical activity on the ward. Design features were refined through individual think-aloud protocols and target group testing. Immediate feedback messages and a result tracking mechanism were added.The design specifications could all be met. The resulting application proofed equally suitable for the training of hand hygiene observers. Computing the user\u2019s results allows for benchmarking.A serious game was successfully launched immersing the \u2018gamer\u2019 into the real-life challenge of hand hygiene. Post-launch evaluation and clinical effectiveness have to be performed in a next step.None declared."} +{"text": "Motor neurons are frequently overlooked as critical contributors to the programming of motor output except where they directly play a role in central pattern generators (CPGs). Leech heart motor neurons have been shown to contribute significant phase shifts to the rhythmic motor patterns they produce -3, altho"} +{"text": "Bone cysts are commonly found when preparing the acetabulum during a total hip replacement . We descThe Exeter\u2122 plug trials used to measure cement restrictors can be employed to pack bone graft into cysts. They are supplied in diameters from 6mm to 20mm and allow the surgeon to choose the appropriate sized plug trial to fit the bone cyst for optimal impaction. The long T-handle allows this technique to also be applied in overweight patients with deeply located acetabuli."} +{"text": "The equal contributions designation was incorrectly assigned. Clarisse A. Roth and Melanie Busch-Dienstfertig should be noted as having contributed equally to this work."} +{"text": "Pancreatic ductal adenocarcinoma (PDAC) has a dismal survival rate. Patients are diagnosed at either a local invasive or metastatic stage, but will ultimately dye within five years after diagnosis. This dismal prognosis is first the result of a late diagnosis. Symptoms appear when the primary tumor has already spread out and specific diagnosis tools such as imaging techniques or biomarkers enabling the detection of early lesions are not available yet. Dissemination to distant organs occurs early, as revealed by using mouse models that spontaneously develop PDAC and reproducibly recapitulate both preneoplastic and neoplastic changes observed during human PDAC . Such gein-cellulo activation of the chemotherapeutic drug gemcitabine are eagerly awaited.Laval and al. report t"} +{"text": "Suturing incisions deep inside the nose can be difficult and knot tying risks \u2018cheese wiring\u2019 the skin of the nasal vestibule. We have found using a Jobson Horne ring probe useful . This in"} +{"text": "Distal femoral replacement is becoming an increasingly common procedure for patients with distal femoral fractures above a total knee arthroplasty and as revision knee arthroplasty becomes more complex.The senior author sites a corkscrew device transversely across the remaining bone of the femoral condyles inside the femoral prosthesis. The device is routinely used for removing the femoral head during hemiarthroplasty for fractured neck of femur. This provides excellent purchase on the fragment. The distal fragment may then be manipulated effectively to peel the distal femur out of its soft tissue envelope.Distal femoral replacement is a challenging procedure that may require extensive operative time."} +{"text": "The following information disclosure by the author was omitted from the article: \"Raj K. Batra is an inventor on a relevant patent application PCT/US2013/050712 entitled METHODS OF BIOMARKER VALIDATION AND TARGET DISCOVERY filed in July 2013.This patent application does not alter the authors' adherence to all the Plos ONE policies on sharing data and materials. Therefore all materials presented in the manuscript will be freely available to the scientific community although not for commercial purposes.\u201d"} +{"text": "K-wires may be used to maintain fracture reduction for several weeks in orthopaedic surgery. Exposed sharp ends are a potential risk to the surgeon and patient. Covering the exposed wire end with a 1ml syringe gasket (black bung located at plunger tip) provides secure protection . This is"} +{"text": "To the Editor: Martina et al. reported that domestic cats and ferrets are susceptible to infection by severe acute respiratory syndrome (SARS)\u2013associated coronavirus (SARS-CoV) isolated from a patient infected with SARS. These infected animals could efficiently transmit the virus to uninfected animals housed with them ("} +{"text": "After publication of the original article , the autThe association between gender and malaria knowledge score was wrongly reported. The correct interpretation of multiple linear regression analysis is that female workers displayed poor malaria knowledge scores when compared to males.The Results section should therefore have read as follows:Multiple linear regression analysis (Table\u00a05) showed that female construction-site workers displayed poor malaria knowledge scores when compared to males. Workers who reported suffering from malaria within 1\u00a0year and those who preferred allopathic/modern medicine displayed higher knowledge scores."} +{"text": "We read with great interest the pilot study on fracture risk in 46 critically ill patients by Rawal and colleagues . Bone mi"} +{"text": "The development of technologies that enable bioactive molecules with low membrane permeability to effectively penetrate biological membranes is one of the greatest challenges in the pharmaceutical field. The HIV-1 transactivating transcriptor (TAT) peptide is one of the most widely used molecular beacons for drug delivery. Cationic antimicrobial peptides have received increasing attention due to their broad spectrum activities and ability to combat multi drug resistant microbes. Our aim is to develop cationic cell penetrating peptide nanoparticles which could efficiently deliver antimicrobial agents against infectious diseases.The cationic TAT peptides were synthesized by Fmoc solid phase peptide synthesis and were purified by semi preparative RP-HPLC. The molecular mass of peptides was confirmed by MALDI TOF-MS. The purified peptides were modified into self assembled nanoparticles (micelles) and structural characterization was done by a particle size analyzer and TEM. The antimicrobial activity evaluation was done against both Gram positive and Gram negative bacterial strains.We have designed and synthesized arginine and lysine rich cationic TAT peptides and modified them into nanoparticles. These nanoparticles were structurally and functionally characterized. Some analogues of these nanoparticles cargoes showed significant antimicrobial activity against Gram positive and negative bacterial strains especially those cause brain infections with low MIC values. These were shown relatively low haemolysis.The findings of this study revealed the improved antimicrobial activity of modified cationic TAT peptide nanoparticles against different bacterial strains. This could revolutionize in the field of chemotherapy and can be efficiently used to treat brain infections and other diseases."} +{"text": "Dear Editor,Foreign body aspiration FBA) is a common problem among children or infants. Nearly 85% of all FB aspiration occurs in childhood. Common organic aspirated materials include nuts and seeds while inorganic materials include plastic pieces or parts of toys . In adulA is a coWhile wearing turban using their two hands to fix the headscarf, some women prefer to hold the pins between their lips . Actions"} +{"text": "Myelin is a membrane characterized by high lipid content to facilitate impulse propagation. Changes in myelin fatty acid (FA) composition have been associated with peripheral neuropathy , but the"} +{"text": "Neurons in the hippocampal formation exhibit a variety of spatially tuned firing patterns. The mechanisms by which these different patterns emerge are not fully resolved, although competing computational models exist for several of them. Here we present a new model that can generate all observed spatial firing patterns by a single mechanism. The model consists of a feedforward network with a single output neuron. Its essential ingredients are i) spatially tuned excitatory and inhibitory inputs and ii) interacting excitatory and inhibitory Hebbian plasticity. The inhibitory plasticity homeostatically controls the output firing rate by balancing excitation and inhibition . We showIn conclusion, we propose a feedforward network model that generates all known spatial firing patterns in the hippocampal formation through a single self-organizing mechanism."} +{"text": "Congenital anomalies which do not cause functional or cosmetic problems are usually incidentally identified at diagnostic researches or surgical explorations.Our case was 54 year-old male patient. He had cerebral ischemic attack a year ago and amaurosis fugax 2 months ago, in his medical history.Patient's coronary angiography and selective arcus aortography revealed 50% stenosis at left main coronary artery and serious three-vessel disease. Cardiology and Cardiovascular surgery council decided that ulcerous lesion at left carotid artery has priority. Patient underwent coronary revascularization three weeks after left carotid endarterectomy.Under general anesthesia, median sternotomy was performed. LIMA graft preparation and great saphenous vein preparation from right lower extremity were maintained together. Three separate accessory saphenous veins were visualized below knee level. The medial one was thin but other two had optimal diameter. For reducing incision length and surgical wound size, both accessory saphenous veins were prepared by controlled saline infusion and collaterals were ligated. Three coronary arteries were successfully revascularized. The patient recovered uneventfully. Patient is still followed up by our outpatient clinic.As in our case, latent congenital anomalies are usually incidentally identified at surgical explorations. Sometimes this situation may be altered for patient's advantage and be beneficial for patient even by reducing tissue damage.Written informed consent was obtained from the patient for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal"} +{"text": "FindZebra.com is a tool for generating hypotheses about rare disease diagnosis. It uses freely available high quality curated information on rare diseases and open source information retrieval software (Apache Lucene Solr) tailored to the problem. FindZebra is intended primarily for physicians and other professionals concerned with diagnosis of rare diseases. Our benchmarking against several search tools (Google search, PubMed and symptoms ,2. Our f"} +{"text": "The authors would like to correct The authors confirm that these changes do not alter their findings. The authors have provided raw, uncropped blots as Supporting Information.S1 FigOriginal unmodified blots used for the assembly of (TIF)Click here for additional data file."} +{"text": "Greater Occipital Nerve (GON) and Multiple Cranial Nerve (MCN) blocks using local anaesthetics and corticosteroids have been used to treat various headache syndromes including Trigeminal Autonomic Cephalgias (TAC). We report cases where low cortisol levels have been seen in patients with TAC treated with GON/MCN blocks that included triamcinolone.We report four cases of adrenal suppression in TAC patients treated with GON/MCN blocks.The cases were collected retrospectively from a specialist headache clinic. Pituitary function tests prior to GON/MCN blocks were undertaken as part of their routine work up for TAC. Cortisol levels were repeated in the patients reported here due to varied nonspecific medical complaints.Our cases include a 25 year old female with TAC who reported weight loss and leg pain following three MCN blocks in three weeks. Cortisol levels were found to be low on two separate occasions.Another case is a 33 year old female treated with MCN blocks for TAC who was found to have low cortisol; the patient\u2019s cortisol also failed to respond adequately to synthetic ACTH.We aim to present another two patients, under ongoing investigation, who have had low cortisol levels associated with GON/MCN blocks for TACs.Whilst adrenal suppression is a known side effect of steroid use, it has not been widely described in patients treated with GON/MCN blocks. These cases suggest that professionals using local nerve blocks containing steroids should be cautious of the potential for adrenal suppression, particularly when used on a repeated basis.No conflict of interest."} +{"text": "Traumatic cerebral venous sinus injuries are usually managed conservatively, however sinus thrombosis and obstruction can result in refractory intracranial hypertension.We retrospectively analysed CT venograms performed on 29 patients who had sustained a skull fracture that crossed a venous sinus at a London Major Trauma Centre.18 of the 29 patients studied had either venous sinus thrombosis (14) or significant sinus caliber compromise (+/- thrombosis). Three mechanisms of sinus injury were noted in this group (Figure CT Venography should be considered in patients with fractures overlying a venous sinus especially in cases with refractory or disproportionate intracranial hypertension or headache out of keeping with imaging appearances. We demonstrate different types of injury and management options."} +{"text": "Recently, novel image processing and analysis software named TiQuant has been published that allows for reconstruction and quantification of biological tissue from common confocal laser scans . TiQuan"} +{"text": "This erratum supplies corrected statements and proofs of an error made during publishing process.Hereby, Publisher declares that the corrected email address of the corresponding author is: editor@hepatmon.comPublishing Corporation."} +{"text": "The rapid shallow breathing index (RSBI) is considered a good parameter to predict mechanical ventilator liberation. We hypothesized that the RSBI provides no benefit when clinical readiness criteria are met.Adults with acute respiratory who required MV for more than 24 hours, excluding COPD, were assessed daily as a liberation protocol Figure . During P = 0.43).Analysis of 120 cases with clinical characteristics as presented in Table The inclusion of RSBI in our standard mechanical ventilator liberation protocol for patients who met the clinical readiness criteria did not significantly increase the success rate of mechanical ventilator liberation."} +{"text": "We are interested in explaining neuronal network development through visualizations that summarize trends in large data. We utilized previously-recorded spiking patterns of embryonic rat cortex cells grown on multielectrode arrays . We pres"} +{"text": "The authors would like to correct The authors confirm that these changes do not alter their findings. The authors have provided raw, uncropped blots as Supporting Information.S1 Fig(TIF)Click here for additional data file."} +{"text": "Overlapping immune signatures are observed among cancers with a better prognostic connotation and those with an increased likelihood to respond to immunotherapeutic approaches ,2. Such"} +{"text": "Penicillium marneffei can cause a fatal systemic mycosis in patients infected with the HIV. Infections are endemic in the tropical regions of southeast Asia. Here, we report the genome sequences of the type strains of P.\u00a0marneffei and its avirulent near relative, Talaromyces stipitatus. Penicillium marneffei is the third most prevalent opportunistic infectious microbe of HIV positive patients in northern Thailand and is associated with a high mortality rate master record accession number is ABAR00000000. The annotated genome sequence of T.\u00a0stipitatus ATCC10500 has been deposited under accession number EQ962652 and EQ963471. The WGS master record accession number is ABAS00000000.The annotated genome sequence of"} +{"text": "Peanut allergy is increasing Food allergy has a huge impact on Quality of Life for the patients and their families. Allergy is seldom reported as emergencies from Commercial Airlines but many peanut allergic patients\u2019 reports symptoms during air flight by ingestion of peanuts but mostly by inhalation.Many peanut allergic patients avoid travelling by airplane. The risk for reaction is controversial.From opening peanut bags and stirring in peanut bowl. No severe reaction was observed. 23 children were tested. Nine patients had a mild reaction like itching of skin, eyes or mouth or urticaria. Three patients received treatment with antihistamine and one with oral steroid. Only one had objectively observed symptoms.Air travel seems to be safe with only risk of mild symptoms in peanut allergic patient even when peanuts are served during flight."} +{"text": "Hereditary Cancer in Clinical Practice would like to thank all our reviewers who have contributed to the journal in 2015.The editors of Hereditary Cancer in Clinical Practice. We look forward to your continued support in 2016.Without the participation of skilful reviewers, no academic journal could succeed, and we are grateful to the committed individuals who have given their time and expertise to the peer review of manuscripts for Stefan AretzGermanyGabriela BaloghArgentinaElizabeth BancroftUKMorgan ButrickUSABerta CamposSpainJohn V ConaglenNew ZealandCezary CybulskiPolandTadeusz DebniakPolandPawel DomagalaPolandThilo DorkGermanyDagmara DymerskaPolandD Gareth EvansUKThomas HansenDenmarkShirley HodgsonUKFrans HogervorstNetherlandsEvgeny ImyanitovRussiaArvids IrmejsLatviaAnna JakubowskaPolandWojciech Klu\u017aniakPolandKristina Lagerstedt RobinsonSwedenMarcin LenerPolandAnnika LindblomSwedenFinlay MacraeAustraliaDiptasri MandalUSAAlexandra MartinsFranceCliff MeldrumAustraliaJanusz MenkiszakPolandCaterina MianItalyPal MollerNorwaySteven NarodCanadaJan OosterwijkNetherlandsCarmen Radecki BreitkopfUSAMalgorzata Stawicka NielacnaPolandBente Talseth-PalmerAustraliaAmanda TolandUSAAnnemieke van der HoutNetherlandsRob van der LuijtNetherlandsMichelle Wong-BrownAustraliaXingnan ZhengUSA"} +{"text": "Subarachnoid hemorrhage (SAH) is a serious neurological condition. Common cause of SAH is vascular origin. Gnathostomiasis is also a common disease in Thailand and may cause SAH.This study aimed to find clinical differences between SAH caused by both causes.This was a retrospective study and collected data from medical charts of patients diagnosed as SAH at Srinagarind Hospital during 2009 and 2011. SAH caused by vascular causes diagnosed by cerebral angiogram, while cerebral gnathostomiasis diagnosed by negative cerebral angiogram with positive gnathostoma antibody. Clinical features between both groups were compared by descriptive statistics.There were 18 patients in vascular group and 10 patients in gnathostomiasis group. Most variables between both groups were comparable except cerebrospinal fluid glucose/plasma glucose. This ratio in gnathostomiasis group was significantly higher than vascular group .Cerebrospinal fluid glucose/plasma glucose ratio was significantly higher in SAH patients caused by gnathostomiasis than vascular group.No conflict of interest."} +{"text": "The sentence should read as follows: \u201cDespite consistent guidelines by three national organizations recommending against routine screening for cervical cancer posthysterectomy, the proportion of women aged"} +{"text": "There are different possible temporal associations between epileptic seizures andheadache attacks wich have given rise to uncleare or controversal terminologies. Migraine endepilepsy have common pathophysichologic mechanisms and share essential anddefining attributes which distinguish them from other common neurologicaldisorders. They are both characterized by paroxysmal symptoms and episodic disorders. Occipital lobe to be thebrain structures most responsible for development of migraine and occipitallobe epilepsies Both are characterized by visual symptoms followed by headacheand other autonomic symptoms. Recognition of headache as an epilepticmanifestation per se still represents a challenge.The classification of the international league AgainstEpilepsy does not refer to this type of disorder, while the International Classification of headache Disorderdefines kinds of association _ migraine triggered seizures hemicrania epilepticaand post ictal headache.Epileptic headache or ictal epileptic headache is anepileptic manifestation per se, with onset and cessation if isolated ,coinciding with EE patern of an epileptic seizures EH maybe followed by other epleptic i manifestation /motor/ sensory/ autonomic/.Hemicrania epileptica is very rare variant . Post ictalor pre ictal headache _ when headache is followed during or short time aftertypical epi seizures Migraine attac maybe with or without aura, and seizures triggerring role is stole a subjectdebate.No conflict of interest."} +{"text": "Dyslexics are diagnosed for their poor reading skills. Yet, they characteristically also suffer from poor verbal memory, and often from poor auditory skills. We now hypothesize that dyslexia can be understood computationally as a deficit in integrating prior information with noisy observations. To test this hypothesis we analyzed performance in two tones pitch discrimination task using a two-parameter computational model. One parameter captures the internal noise in representing the current event and the other captures the impact of recently acquired prior information . We foun"} +{"text": "Dear Editor,I read with interest the article by Bayrami et al., reporting the predictive ability of drug use for subjects with attention deficit hyperactivity disorder (ADHD) symptoms . The tar"} +{"text": "Bleeding has always been an alarming clinical symptom in all human societies, and physicians have had varying degrees of success in diagnosing and treating bleeding patients . Because"} +{"text": "We read with great interest the review by Scholzel et al. , about cCould these abnormalities play a role in recurrent pulmonary hypertension after pulmonary endarterectomy?"} +{"text": "Brucellosis is a common zoonotic infection caused by bacterial genus brucella. Brucellosis is an old disease known by various names including undulant fever or Mediterranean fever. This is one of the infectious diseases transmissible between animals and humans. Brucella bacteria multiply inside the body in some ways like swallowing, breathing, contact between damaged skin and slinked fetus or amniotic fluid of septic animals , 2. This"} +{"text": "Errors were introduced to The authors confirm that these changes do not alter their findings. The authors have provided raw, uncropped blots as Supporting Information.S1 File(PPTX)Click here for additional data file."} +{"text": "Pleura effusion in post cardiac surgery is the one of problems in management of cardiac surgery patients. Large amounts of pleura effusion may affect the recovery period requiring a longer hospital stay. Early diagnosis and quantification of pleural effusion is important to be ideal postoperative adequate treatment. Ultrasound shows better sensitivity and reliability for diagnosis pleural effusion than physic diagnostic and X-ray. Ultrasound can be repeated serially at bedside without any radiation risk. Procedure perform under ultrasound guided showed a reduction of complication rate.We report 60 patients with pleural effusion after cardiac surgery. We perform tapping of fluid under guiding ultrasound. Before procedure we calculate amount of pleural effusion and make decision where site of needle will inserted. Regarding the literature we make intraclavicula line as a guided. Tapping procedure will perform if fluid more than 450 cc. Tapping procedure use abbocate needle no 14 or 16fr. Amount of perithoracosistesis fluid is almost same with fluid prediction of before +/- 50 cc, depend on body weight and size of heart if pleural effusion on left thorax. There are not complications after the procedure. Patient experiences were feel convenient and with minimal pain. After procedure patients can complete mobilization and if indication to discharge patients can discharge directly.our experience show the ultrasound guided procedure for tapping pleura effusion easy to do, make patient convenient, safe and shorten hospitalization after cardiac surgery."} +{"text": "The immunosuppressive tumor microenvironment perturbs numerous immune regulatory networks and usurps host antitumor immunity. We discovered that tumor interferes with host hematopoietic Notch system in lung cancer patients . The res"} +{"text": "Contrary to ThyA, ThyX generates tetrahydrofolate rather than dihydrofolate upon catalysis and therefore does not require high dihydrofolate reductase activity to provide sufficient levels of tetrahydrofolate . Assumiack thyA . Consequpossible .thyX compared to what was observed for the two closely related Peruvian control strains \u201325. Alth\u2013"} +{"text": "Inflammatory Breast Cancer (IBC) is the most aggressive and highly metastatic form of breast cancer -3. In a Transcriptomic data from 197 breast tumours were used for this analysis (GEO GSE23720) . All tumWe provide evidence that NFAT5 transcription factor could constitute a novel IBC biomarker that could help to identify the most aggressive forms of BC into routine clinical practice."} +{"text": "An inexpensive and readily available material for practising tendon repair sutures is dental rolls. Two dental rolls secured to a table and placed longitudinally opposite each other can simulate the cut ends of a tendon . The siz"} +{"text": "Clinically, late preterm infants have more apnea and periodic breathing than term infants and immature coordination of sucking, swallowing and breathing often delay their ability to feed without episodes of bradycardia, desaturation and even apnea [Late preterm infants have been called \u201cgreat imposters\u201d because en apnea .Clinical data indicate that late preterm are also predisposed to wheezing in infancy and early childhood although not exposed to excessive supplemental oxygen or ventilator support . Exposur"} +{"text": "Characterizing neural spiking covariability is essential for understanding the collective activity of neural populations. Recent experiments have provided evidence of statistical dependencies among groups of neurons beyond that expected by the firing rates and pairwise correlations alone -3. These"} +{"text": "In the published articlePembrolizumab has not yet received FDA approval for NSCLC patients. In October 2014 pembrolizumab received FDA breakthrough therapy designation for lung cancer treatment supported by data from a phase Ib trial in previously treated NSCLC patientsThe authors apologize for the errors and for any confusion it may have caused."} +{"text": "JH-/- mouse that had been exposed to prion infectivity containing aerosols, can be seen here. The authors also wish to clarify that the original blots for Figs The authors would like to correct Figs The corrected versions of Figs S1 FileIndividual blots at various exposure times are shown.(TIF)Click here for additional data file.S2 FileIndividual blots at various exposure times are shown.(TIF)Click here for additional data file."} +{"text": "The UBIOPRED study (Unbiased BIOmarkers for the Prediction of REspiratory Diseases) is a longitudinal asthma research study. It will identify phenotype/\u2019omic handprints to improve our understanding of severe asthma and identify potential targets for new pharmacotherapies.The aim of this poster is to illustrate how the research team successfully recruited and retained the Southampton portion of the paediatric UBIOPRED cohort using an acronymic approach.A simple acronym was developed by the NIHR Southampton Wellcome Trust Clinical Research Facility (WTCRF) nurses to enable successful recruitment and retention of participants:Approach \u2013Participants were usually approached during their outpatients\u2019 appointment. This ensured neutral ground, so the study could be discussed with their consultant.\u2022 Belief \u2013 The research nurses believed in UBIOPRED, which instilled confidence when discussing the study with potential recruits.\u2022 Commitment \u2013 Retention was only possible through the commitment of participants and nurses. Study visits were coincided with clinic appointments whenever possible to reduce inconvenience.\u2022 Dedication \u2013 The research nurses went to great lengths to ensure the participants\u2019 needs were met.\u2022 Experience \u2013 The participants\u2019 research experience needed to be positive to ensure retention. Participants were supported if they had anxieties and were never pressurised to undertake research procedures.\u2022 Fun \u2013Age appropriate fun was key to each study appointment.\u2022 The final recruitment figures for the UBIOPRED paediatric cohort at Southampton exceeded the target set figure . At presUsing an ABCDEF approach, the children\u2019s asthma and allergy research nurses have exceeded their recruitment target and successfully followed up participants on the UBIOPRED study."} +{"text": "Drosophila brains were taken from confocal laser scanning microscope [Quantitative analysis of neurons is a very important issue in neural science especially after numerous three-dimensional neural images in croscope . Howevercroscope and moducroscope methods"} +{"text": "Critical Care reported that plasma [Two recent studies published in t plasma and urint plasma levels oThe investigators assessed NGAL elimination during continuous venovenous hemofiltration and hemoThese membranes are increasingly applied for hemofiltration in critically ill patients . Thus, i"} +{"text": "Columba livia) and humans in formally identical choice tasks where all outcomes were learned from experience. Both species were more risk seeking for larger rewards than for smaller ones. The data suggest that the largest and smallest rewards experienced are overweighted in risky choice. This observed bias towards extreme outcomes represents a key step towards a consilience of these two disparate literatures, identifying common features that drive risky choice across phyla.Whereas humans are risk averse for monetary gains, other animals can be risk seeking for food rewards, especially when faced with variable delays or under significant deprivation. A key difference between these findings is that humans are often explicitly told about the risky options, whereas non-human animals must learn about them from their own experience. We tested pigeons ( Collapsed across the final two blocks and Natural Sciences and Engineering Research Council (NSERC) of Canada.This study was financially supported by the"} +{"text": "Following publication of the original article in Stem Cell Research & Therapy , we woulThe corrected title reads: Retinoic acid receptor signaling preserves tendon stem cell characteristics and prevents spontaneous differentiation in vitro.The original article has been updated with the corrected title. The publisher apologizes for the inconvenience this may have caused."} +{"text": "Esophageal strictures commonly complicate radiation therapy for neck and thoracic malignancies. We here report a case of radiation induced stricture esophagus and illustrate the classical barium esophagogram in this condition. 58 year old male with past history of carcinoma esophagus treated with radiotherapy had presented with recurrence of dysphagia. Dysphagia was insidious in onset and was predominantly for solids than liquids. Physical examination was normal except for gross emaciation. Hemogram and routine biochemical panel were within normal limits. Barium swallow revealed significant mid-esophageal luminal narrowing with significant contrast pooling above. Upper gastrointestinal endoscopy revealed luminal narrowing at 25cms from the incisors; it was not possible to negotiate through the stricture. At endoscopy mucosa appeared normal except for minimal erythema. Mucosal biopsies revealed only normal stratified squamous epithelium and no evidence of neoplasm. Contrast computed tomography revealed no evidence of tumor recurrence or metastasis or lymphadenopathy. Patient was managed with serial dilatation with Savary Guillard dilators. Patient improved with treatment and is currently able to take oral feeds. Stricture is commonly reported to develop in 2-3 weeks to 4-8 months after radiation exposure, though late presentations also can occur. In patients presenting with dysphagia following radiotherapy for carcinoma esophagus it is always important to rule out residual or recurrent neoplasm with endoscopy and imaging. Esophageal dilatation with or without stenting is the current treatment of choice."} +{"text": "Dear Sir,,Skin stapling devices are widely used to secure skin graft because they are easy to use and useful\u2014especially for large grafting areas. They can save operating time and improve graft taking.3"} +{"text": "Homeostatic regulation of neuronal firing rates has been reliably observed in response to chronic manipulation of neural activity. From such experiments a variety of putative homeostatic mechanisms have been reported, including compensatory changes for several synapse types . Unfortu"} +{"text": "Combination of metformin and garlic extract may ameliorate diabetic nephropathy.et al. further attests our results and those published by previous investigators which garlic extract protects against tubular injury by restoring the biochemical alterations and modulation of oxidative stress on the tubules have been completely observed by the author.None."} +{"text": "Potential kidney protective effects of metformin, might have synergistic effect with some other antioxidants such as medicinal plants.et al. observed that gentamicin-induced renal tubular injury is ameliorated by metformin have been completely observed by the authors.None."} +{"text": "A central pattern generator (CPG) is a population of neurons producing rhythmic or repetitive behavior without requiring rhythmic input to the population. Turtles are observed to produce several rhythmic motor patterns in response to stimuli, in particular rostral scratch and pocket scratch (see Figure"} +{"text": "This project helps address concerns about reproducibility by providing unique searchable identifiers, or Research Resource Identifiers (RRIDs), for critical reagents and tools. RRIDs link readers to external resources and enable search engines to return all papers utilizing a particular antibody, organism, or tool. Using RRIDs, authors can easily track all papers using various antibodies and assess how well the antibody works in different scenarios. eNeuro joins other neuroscience publications currently employing RRIDs. A complete listing of journals utilizing RRIDs can be found in Google Scholar or PubMed. This initiative is completely voluntary for eNeuro authors. RRIDs offer an important means for ensuring reproducible methods and providing critical data to help researchers identify suitable reagents and tools. We encourage all eNeuro authors to participate."} +{"text": "The publisher apologizes for this error.The corresponding author indication is incorrect. The correct corresponding author is Martijn Timmermans ("} +{"text": "Her correct title is associate professor.EHP regrets the error."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Digital conversational agents (DCAs) have become extraordinarily ubiquitous. Researchers envision the prospects of using DCAs to monitor health among older adults. However, older adults show hesitation to engage with DCAs. It is possible older adults prefer receiving human assistance rather than getting help from a machine. Another potential explanation is that communicative cues of DCAs such as voice need to be further optimized to invoke behavioral engagement. To understand how DCAs can better support older adults, we develop an experiment with three scenarios in which an agent shares active aging information. We manipulate the agent\u2019s voice in terms of age . We investigate how the interplay of agent categories and intragenerational/intergenerational voice cues affect older adult participants\u2019 evaluation of information and intention to adopt DCAs. Our study will contribute to DCAs design for older clients."} +{"text": "PLOS ONE Editors retract this article [The article because RS, ATKZ, and AMES did not agree with the retraction. MRY and HMS either did not respond directly or could not be reached."} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "PLOS ONE Editors retract this article [The article because KAB, SF, and EAR did not agree with the retraction. HAF responded but expressed neither agreement nor disagreement with the editorial decision. All other authors either did not respond directly or could not be reached."} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Antidepressant withdrawal manic states are rare and controversial phenomena. The underlying pathophysiology and the clinical implications have not been thoroughly discussed in the literature.We aimed to review reports of antidepressant discontinuation manic states and to discuss the different hypothetical pathophysiological changes underlying this phenomenon. We also argued in favor of its inclusion in the bipolar spectrum.We searched Pubmed using the key words: \u2018antidepressant withdrawal\u2019 or \u2018antidepressant discontinuation\u2019 plus \u2018mania\u2019 or \u2018hypomania\u2019 from January 2008 until January 2018.Twenty-nine cases of antidepressant discontinuation manic states were identified. Hypotheses involve the implication of Catecholamines, Acetylcholine and Serotonin in the pathophysiology of this paradoxical phenomenon. The search for red flags for bipolar disorder in these case reports revealed psychiatric histories in favor of a bipolar spectrum disorder in 12 individuals while five were already known to have bipolar disorder.Antidepressant discontinuation mania should be considered on the bipolar spectrum.No significant relationships."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Psychiatric emergency visits have been associated to several climate variables. However, the influence of relative humidity has been not well stablished.The analyse the influence of relative humidity on emergency care visits.Daily urgency visits were extracted from electronic medical records of Hospital Universitario La Paz from 1st January 2019 to 31st December 2019. Relative humidity data (%) was obtained from a local climate station. A negative binomial multivariate regression model was performed with relative humidity, weekday and month as covariates.Relative humidity was not associated with number of psychiatric emergency department visits Relative humidity did not influence emergency help seeking for patients suffering from suicidal phenomenaNo significant relationships."} +{"text": "Systemic mastocytosis is a neoplastic proliferation of mast cells that most frequently involves cutaneous sites. Mastocytosis involves various extracutaneous sites, but the lymph node is rare. We present an interesting image of systemic mastocytosis in the lymph node with marked eosinophilia. It is a rare subtype of systemic mastocytosis requiring high suspicion levels for the correct diagnosis."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Suicidal seeking help seeking behaviour has with associated with seasonal pattern that reflect an array of psychosocial factors. Its understanding is paramount for improving psychiatric emergency care.Our aim was to analyse weekly and monthly seasonality on emergency department visits due to autolytic phenomenaDaily urgency visits from suicidal phenomena (including suicide attempt and ideation) were extracted from electronic medical records of Hospital Universitario La Paz from 1st January 2019 to 31st December 2019. A poisson multivariate model was performed with day of the week and month as covariates. Predictive margins were estimatedPsychiatric emergency visits due to suicidal phenomena were less frequent in Saturday and Sunday (1.8 visits per day) than weekdays (2.5 visits per day). Peaks were observed in February and September, being April and May the months with fewer visitsA weekly season pattern was observed with less psychiatric emergency visits due to suicidal phenomena during weekends. They picked during colder months and were less frequent during spring timeNo significant relationships."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "The authors have retracted this article. Following publication, errors were identified affecting Figs.\u00a04 and 6. The values of mean total chlorophyll concentration in control plants and individual leaves reported in the article were several fold higher than those from other reports. Moreover, the chlorophyll a/b ratios of control plants presented in Fig.\u00a04c were also much higher than reported values for tree seedlings. The authors believe these discrepancies are due to technical errors and intend to submit a revised manuscript which will undergo peer review. All authors agree with this retraction."} +{"text": "HoweverClinical trials of inactivated vaccines report antigen\u2010specific humoural and cellular immune responses and protective efficacy against pandemics caused by the Wuhan strain.In conclusion, all of these data support the conclusion that boosting previously inactivated vaccine\u2010immunized individuals with an mRNA vaccine is a promising strategy for increasing population\u2010level immunity against the rising pandemic caused by variants.The authors declare no competing interests.Supporting InformationClick here for additional data file."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Pathogens Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Many observational studies have documented that hyperglycemia frequently occurs among patients hospitalized with the acute coronary syndrome (ACS) and without diabetes mellitus . Epidemi"} +{"text": "A middle aged adult with a nearly 3\u2010year history of stage III follicular lymphoma experienced progressive abdominal pain and distention\u00a0before collapsing suddenly. The patient was resuscitated and underwent emergency laparotomy that showed copious intraperitoneal blood originating from a rupture of a markedly enlarged spleen. Despite splenectomy, hemostasis could not be achieved and the patient was pronounced deceased.The resected spleen was diffusely enlarged and disrupted by a large irregular laceration (Figure\u00a0Low\u2010grade follicular lymphoma is typically clinically indolent and minimally symptomatic. Atraumatic splenic rupture secondary to massive splenomegaly in follicular lymphoma is uncommon but can be fatal even with urgent medical intervention. Close monitoring for ongoing or rapid splenic enlargement and appropriate patient education may therefore be warranted in patients with follicular lymphoma.MX wrote the manuscript. CO, DL, and JR edited and revised the manuscript. All authors performed the pathologic assessment on the case reported.The authors declare no conflict of interest."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Older adults in the U.S. are increasingly using cannabis as a method to manage pain. Some studies have linked increased cannabis use with an increase in prescription opioid use while others have suggested that older adults may be using cannabis as a way reduce/replace opioids. From April 2018 - January 2019 we conducted 12 focus groups throughout Illinois with 82 cannabis users aged 60+. To examine the relationship between cannabis and opioid use we used an inductive thematic analysis to code and theme the focus group transcripts. We found three themes 1) medical culture around opioids influences cannabis use; 2) past negative experiences with opioids influences cannabis use, and 3) aversion to ever trying opioids out of fear of an anticipated harm that may be brought about by opioid use such as overdose. In this session we present these findings and discuss cannabis use relative to opioids by older adults."} +{"text": "Swallowed rice cake (mochi) without chewing retained in the stomach intactly. We successfully treated the hardened mochi without surgery. Eye\u2010catching images showed as many as 10 intact mochi in the stomach and endoscopic crushing procedure. Misconception that gastric acid can dissolve rice cake (mochi) leads to retention of mochi in the stomach. Although mochi is soft in a hot soup dish, it can get much harder in the stomach temperature. Swallowed mochi without chewing can be resolved only by endoscopic procedure. Abdominal computed tomography (CT) revealed multilayer arc\u2010like high\u2010density objects in the stomach Figure\u00a0, which rAlthough airway obstruction by mochi is well recognized, a gastro\u2010intestinal foreign body associated with mochi is poorly recognized because of its rarity. Retained mochi can cause severe gastric ulcer which possibly leads to gastric perforation. Accordingly, retained mochi requires an endoscopic procedure as soon as possible.All authors contributed significantly toward the completion of this case report.The authors declare no conflict of interest.None.Written informed consent was obtained from the patient to publish this report in accordance with the journal's patient consent policy."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Visual agnosia was noticed after blood pressure oscillations, during immunoglobulin therapy for suspected autoimmune encephalitis. Brain magnetic resonanbce imaging scans before and after visual agnosia are presented in"} +{"text": "Akiskal proposed the bipolar spectrum concept with the aim of including those patients with atypical depressive presentations and mood temperaments. Also Koukopoulos accepted this proposal in those patients with poor response to antidepressants or highly recurrent course. Concretely bipolar disorder type IV was defined as clinical depression based on a lifelong hyperthymic temperament. Some years after DSM-III several experts in bipolar disorder continued in this work line even though DSM-IV and most recent DSM-V not considered to include this concept as a new diagnostic category.To present a theoretical and practical review about bipolar spectrum and its relationship with hyperthymic traits.We carry out a literature review about bipolar spectrum, accompanied by the clinical description of one patient with major depressive disorder and hyperthymic traits base.45 years old female referred to our outpatient mental health service after episode of voluntary drug overdose. She presented long evolution depressive symptoms with onset in postpartum. She reported a previous depressive episode 9 years ago with good response to fluoxetine. Hyperthimic traits were described but no history of manic symptoms. An erratic evolution was observed with various antidepressant treatment and finally improved adding mood stabilizer.We must propose to consider the diagnosis of bipolar spectrum in order to treat effectively patients with major depression dissorder and hyperthymic temperament in absence of manic symptoms.No significant relationships."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the The journal has been informed that corresponding author CD is deceased."} +{"text": "Following publication of the original article 1], there is formatting error in Tables , there iThe original article has been corrected."} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Suicidal phenomena help seeking depends on a broad array of factors, which include climatic variables. Our aim was to analyse the effect of precipitation with help seeking in patients suffering from suicidal behaviourOur aim was to analyse the effect of precipitation with help seeking in patients suffering from suicidal behaviourDaily urgency visits from suicidal phenomena (including suicide attempt and ideation) were extracted from electronic medical records of Hospital Universitario La Paz from 1st January 2019 to 31st December 2019. Precipitation data (measured as accumulated litres per square meter) was obtained from a local climate station. Spearman correlation was estimatedThe Spearman correlation coefficient was 0.04(p = 0.48)Precipitation did not influence help seeking for patients affected by suicidal phenomenaNo significant relationships."} +{"text": "Psychiatric emergency visits have with associated with seasonal pattern that reflect psychosocial factors. Its knowledge could proving valuable insight about help seeking behaviour of patiens suffering with mental illness.Our aim was to analyse weekly and monthly seasonalityDaily urgency visits were extracted from electronic medical records of Hospital Universitario La Paz from 1st January 2019 to 31st December 2019. A poisson multivariate model was performed with day of the week and month as covariates. Predictive margins were estimatedPsychiatric emergency visits were less frequent in Saturday and Sunday (5.5 visits per day) than weekdays (7.5 visits per day). Not differences were observed among months.A weekly season pattern was observed with less psychiatric emergency visits during weekends.No significant relationships."} +{"text": "These should have been given as 3358 participants excluded and 1549 without data in the CHARLS 2014 survey. This article has been corrected.1In the Original Investigation titled \u201cAdverse Childhood Experiences and Subsequent Chronic Diseases Among Middle-aged or Older Adults in China and Associations With Demographic and Socioeconomic Characteristics,\u201d"} +{"text": "We thank Dr. Mraz for insightful comments that provide additional context to the findings in our study, in particular bringing to the forefront studies in other B cell malignancies including chronic lymphocytic leukemia (CLL) . As poin"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the The journal has been informed that third author CD is deceased."} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "The 7th author name has been incorrectly published in the original publication. The complete correct name should read as follows Dinesh Kumar ChellappanThe original article has been corrected."} +{"text": "However, I believe it is worthwhile to discuss possible treatment options for patients whose lives are at grave risk in the COVID-19 era."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Following publication, the publisher has uncovered conclusive evidence that false identities were used as peer reviewers for this article. These reviewers were not suggested by the authors. These peer reviewers have now been removed.This article is currently under post publication assessment. This expression of concern has been posted while Frontiers awaits the outcome of this assessment and will then be updated accordingly."} +{"text": "She had dull aching pain in the leg with slight swelling. Thephysical examination of her leg revealed swelling and mildly painful movement withlimitation. The radiological study revealed multiple diffuse lytic areas withsurrounding sclerosis distal to the tibia extending from the metaphysis to the diaphysisand pathological fracture . Magneti"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "We sought to provide an overview of the literature on decision aid interventions for family caregivers of older adults with advanced dementia regarding decision-making around tube feeding. The process was guided by Arksey and O\u2019Malley\u2019s methodological framework. Six publications reporting on four unique decision aid interventions were included. All the interventions targeted caregivers of older adults with advanced dementia. Three of decision aids were culturally adapted from existing ones. The Ottawa Decision Support Framework and the International Patient Decision Aid Standards Framework were used in these studies. Interventions aimed to improve decision-making regarding tube feeding for caregivers through static delivery methods. Caregivers rated these decisions as helpful and acceptable. Reduction in decisional conflict and increase in knowledge were consistently found among dementia caregivers, but no intervention effects were found on preferences for use of tube feeding. Culturally adapted decision aids effectively improve decision-making regarding tube feeding among the target population."} +{"text": "Breast core biopsies show a diffuse sheet of neoplastic cells with round nuclear contour, open chromatin, eccentric nuclei with distinct nucleolus and relatively abundant eosinophilic cytoplasm Figure\u00a0, immunogThe authors declare that they have no conflict of interest.The authors received no specific funding for this work.This case followed the University Health Nerwork and patients' ethics."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "PLOS ONE Editors retract this article [The article because SS either did not respond directly or could not be reached. KM and MUS responded but expressed neither agreement nor disagreement with the editorial decision. ASA, KGR, and MH did not agree with the retraction."} +{"text": "Despite significant and urgent mental health needs among low-income homebound older adults, the existing mental health service systems\u2019 reach for these older adults is almost nonexistent. Given the current and projected geriatric mental health workforce shortages, innovative approaches are needed to better serve these underserved older adults. This presentation will focus on a series of randomized clinical trials that tested acceptable and feasible mental health service delivery models for homebound older adults who are served by aging service network agencies that provide hot meals and case management. Findings from the real-world effectiveness trials of tele-delivered behavioral activation treatment for depression and loneliness by bachelor\u2019s-level lay counselors who are embedded in aging service agencies will be shared. Ways to promote a wider adoption of scalable and sustainable mental health service delivery models for homebound older adults will be discussed."} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "To ensure autististic prisoners are understood and receive necessary support in custodial environment.Prison healthcare staff and discipline staff jointly trained about autism and how it is best managed in prison setting.Promotion re-education aids for prisons visually and verbally.Prison staff as autistic champions.Accessible autistic spectrum lead in healthcare team to coordinate need.priority that prison becomes autism accredited by national autistic society in progress.There is increase of prisoners with neurodevelopmental disorders and ensuring their needs met in prison and this is CAT A challenging prison environment."} +{"text": "Since the discovery of vitamin D a century ago, a great number of metabolites, analogs, hybrids and nonsteroidal VDR ligands have been developed. An enormous effort has been made to synthesize compounds which present beneficial properties while attaining lower calcium serum levels than calcitriol. This structural review covers VDR ligands published to date. KK-052 serves as a valuable compound for interrogating SREBP/SCAP in vivo and may represent an unprecedented translational opportunity for synthetic vitamin D analogs.1746) , was fouA century has passed since vitamin D was discovered. The structural diversity achieved among vitamin D receptor ligands . Seeing as vitamin D plays a ubiquitous role in human physiology, VDR ligands have been found to cure or ameliorate the symptoms of various diseases. It is disheartening to note that for more than twenty years no drug based on a VDR ligand has been placed on the market because the structural diversity achieved in the VDR ligands might encode new therapies for other illness different than the calcium\u2013phosphorous homeostasis."} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "PLOS ONE Editors retract this article [The article because AMAS agreed with the retraction. MR, SA, SAA and MA either did not respond directly or could not be reached. MFA and MJA did not agree with the retraction."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the First author ST has informed the journal that corresponding author CD is deceased."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Following publication, the publisher has uncovered conclusive evidence that false identities were used as peer reviewers for this article. These reviewers were not suggested by the authors. These peer reviewers have now been removed.This article is currently under post publication assessment. This expression of concern has been posted while Frontiers awaits the outcome of this assessment and will then be updated accordingly."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Usually, superior vena cava (SVC) entrance block is confirmed when SVC potentials disappear during sinus rhythm. We present a case of pseudo SVC entrance block during sinus rhythm, which was uncovered by continuous atrial pacing. Under coronary sinus pacing, SVC potentials disappeared by adding RF application at the anterolateral side catheter ablation including pulmonary vein isolation (PVI) and superior vena cava (SVC) isolation. After completing the PVI, we proceeded with empiric SVC isolation because he had a long SVC sleeve.Figure\u00a0. Under e Figure\u00a0. Circumfe Figure\u00a0 to elimiThis case indicated that a careful investigation should be performed to confirm the SVC entrance block. Recently, a novel method for SVC isolation utilizing intrinsic conduction block area has been conceived.These results indicated that the intrinsic conduction block area of the RA\u2010SVC junction could present persistent conduction by atrial pacing even after achieving the SVC entrance block during sinus rhythm. Therefore, the SVC entrance block during sinus rhythm might not be enough to confirm the true SVC entrance block. The sinus node has been reported to be located on the epicardial side of the terminal crest and insulated by the transitional cells, and sinus impulse exits from the node via the multiple preferential pathways.This case illustrated a risk of misdiagnosing with superior vena cava entrance block when omitting RF applications at the intrinsic conduction block area close to the sinus node. Confirming the SVC entrance block both during sinus rhythm and continuous atrial pacing away from the sinus node might be necessary in the situation.Authors declare no conflict of interests for this article.N/A ."} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS Genetics Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Following publication, the publisher has uncovered conclusive evidence that false identities were used as peer reviewers for this article. These reviewers were not suggested by the authors. These peer reviewers have now been removed.This article is currently under post publication assessment. This expression of concern has been posted while Frontiers awaits the outcome of this assessment and will then be updated accordingly."} +{"text": "Although rates of major depressive disorder are lower among older adults, depressive symptoms are a common presentation for aging individuals in medical settings. Unique challenges arise when treating depressive symptoms co-occurring with brain health concerns in older adults with a complex medical history. This presentation reviews how cognitive behavioral interventions for later-life depression are relevant for mental health practitioners who work in primary care and general medical settings. Specific clinical and multicultural considerations will be highlighted to support clinicians and interdisciplinary teams to work effectively with older adults who have co-existing depressive symptoms and cognitive concerns."} +{"text": "This article has beenPLOS Neglected Tropical Diseases Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "PLOS ONE Editors retract this article [The article , 2 becauSB and MH did not agree with the retraction. MZuH and FM either did not respond directly or could not be reached."} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "This article has beenPLOS ONE Editors issue this Expression of Concern.PLOS will be investigating these concerns in accordance with COPE guidance and journal policies. Meanwhile, the"} +{"text": "Guided by Lyons and Lee\u2019s (2018) Dyadic Theory of Illness Management, the current study explored covariation in dyadic health management behaviors within a sample of seventeen older African American married couples . We also examined if spouses agreed on how they took care of each other\u2019s health and whether these patterns changed after couples participated in a health-focused intervention together. Prior to beginning a 12-week walking plus resistance training exercise intervention, spouses completed questionnaires asking them to list the common things they did to help take care of their partner\u2019s health as well as what their partner did for them. Thirteen couples completed these questionnaires post-intervention. Data from both waves were analyzed using thematic analysis . Five health management behaviors domains were identified . Although both partners reported encouraging healthier diets and exercise, wives also reported promoting other health management behaviors. Couples had greater congruence in their appraisals of wives\u2019 health management behaviors compared to husbands\u2019, as wives recognized many things husbands did to take care of them that husbands did not report themselves. Patterns appeared stable over time. Findings suggest the incongruence in couples\u2019 health management behaviors represented complementary efforts to support each other and revealed that husbands may be underestimating how much care they are providing to their wives. A promising method for addressing health disparities in this population may involve capitalizing on this clear investment that older African American couples have in each other\u2019s health."} +{"text": "Endoscopic scissors have the advantage of preventing potential complications associated with thermal and mechanical damage to surrounding structuresA middle-aged man presented to the emergency department with abdominal pain for the past eight days. He disclosed that he had ingested a long plastic tube trapped with a silk line after drinking two years ago. Physical examination was normal, as was his routine blood test. Computed tomography scans showed multiple tubular objects in the stomach and duodenum . GastroVideo\u20061\u2002Endoscopic scissors for removal of plastic tubes trapped with silk lines.We highlight the role of endoscopic scissors in cutting through silk line in this challenging case, which prevented further surgical removal of the foreign bodies. Endoscopic scissors, originally designed for cutting the nasobiliary duct in vivoEndoscopy_UCTN_Code_TTT_1AO_2AL"} +{"text": "The effect of subjective views of aging (VoA) on health outcomes is well established, yet this effect was rarely examined among older adults undergoing hospitalization or rehabilitation. Moreover, the additive effect of healthcare personnel\u2019s ageist attitudes on treatment outcomes is unknown. Accordingly, these effects were examined within older adults hospitalized for osteoporotic fractures \u2013 a frequent late-life condition with cardinal functional implications. Study 1 found that feeling younger at admission predicted better rehabilitation outcomes. The reverse effect of functional independence at admission on subjective age at discharge was non-significant. Study 2 replicated these findings with additional VoA indices, and further demonstrated that rehabilitation outcomes were better when occupational and physical therapists reported low levels of ageist attitudes. Findings suggest that successful rehabilitation may be promoted by reducing negative VoA among patients as well as healthcare personnel."} +{"text": "PLOS ONE Editors retract this article [The article because ABG and MAA did not agree with the retraction. JL and ME responded but expressed neither agreement nor disagreement with the editorial decision. RMA and SMA either did not respond directly or could not be reached."} +{"text": "Rhodnius brethesi appears incorrectly throughout the article due to misidentification during the breeding process. The correct species name verified by genotyping is Rhodnius neglectus, which lives also in sylvatic areas (such as the Cerrado (savanna) region in Central Brazil) and nests on several species of palm trees. Both species share many similarities.The species name"} +{"text": "As the pandemic caused widespread disruption across the world, studies suggested younger adults were faring more poorly than other adults. We hypothesized that younger adults might possess fewer emotion regulation resources and skills, accounting for their greater distress. In a national sample of 1528 adults, we examined how baseline resources predicted distress five weeks later, when states began initial reopenings. Younger adults reported greater distress and less social support, mindfulness, and emotion regulation skills than did middle aged and older adults.. Controlling for stress exposure, younger adults\u2019 distress was predicted by impulsivity and lack of perceived strategies while middle-aged and older adults\u2019 distress was predicted by acceptance of negative emotions; perceived social support was related to lower distress for both groups but mindfulness was unrelated. Results suggest that emotion regulation skills are a promising prevention and intervention focus."} +{"text": "In the original version of this article, the given and family names were incorrectly structured.The correct given and family names should be:Tobias ZrzavyAlice WielandnerLukas HaiderSophie BartschFritz LeutmezerThomas BergerKarl Heinz NenningAlexander RauscherPaulus RommerGregor KasprianThe original article has been corrected."} +{"text": "To the editor,We appreciate very much your comment about our paper published recently in Int Braz J Urol . In respThe Authors"} +{"text": "Introduction: Many studies have investigated the risk factors associated with progression from mild cognitive impairment (MCI) to cognitive impairment, while it is unclear which lifestyle factors are associated with cognitive recovery among those who have mild cognitive impairment. Methods: The study includes 7,422 participants above 65 years old with MCI from The Chinese Longitudinal Healthy Longevity Survey (CLHLS). Cox regression analysis was adopted to investigate the association between cognitive recovery and selected lifestyle factors. LASSO was applied to select the variables. Results: Daily consumption of fresh fruits is associated with higher possibility of cognitive recovery while daily consumption of meat show opposite influence . Smoking and alcohol consumption are both negatively associated with cognitive recovery. Daily engagement in reading , housework as well as mahjong and other card games are associated with higher possibility of cognitive recovery. Conclusion: This study has identified important modifiable lifestyle factors associated with natural cognitive recovery from MCI. The findings have considerable implications for dementia prevention."} +{"text": "Following publication of the original article [1], the authors flagged that the author name Fabiana Trentacosti had been erroneously spelled as Fabiana Trenatacosti.The published article has since been corrected.The authors apologize for any inconvenience caused."} +{"text": "These images have now been replaced with equivalent images from the same experiment, but that have not been published previously.While selecting representative images for publication from the same time-lapse experiment, the authors mistakenly selected images they had published previously"} +{"text": "Following publication of the original article [1], the authors identified an error in the author name of SeyedAhmad SeyedAlinaghi and in the author name of Mohammad\u2011Mehdi Mehrabi Nejad.The incorrect author name is: Seyed Ahmad SeyedalinaghiThe correct author name is: SeyedAhmad SeyedAlinaghiThe incorrect author name is: Mohammad-Mehdi MehrabinejadThe correct author name is: Mohammad\u2011Mehdi Mehrabi NejadThe original article has been corrected."} +{"text": "Booker and Christopher L. Haga should have been denoted as equally contributing authors. The original article has been corrected."} +{"text": "Sustainability in livestock production systems will play a critical role in reaching the Sustainable Development Goals developed by the United Nations . Globall"} +{"text": "The original version of this article unfortunately contained a mistake. Author name Titus Watrin was incorrectly written as Titus Vatrin."} +{"text": "Excessive light exposure before bedtime can disrupt one\u2019s circadian rhythm and can lead to poor sleep. The purpose of this study was to describe the relationship between evening light exposure and subjective sleep measures in people living with dementia (PLWD). We conducted secondary data analysis using the baseline data from Healthy Patterns Clinical Trial (N=137). We used Actiwatch Spectrum Plus to collect light data over three consecutive days. We defined evening light exposure as the average white light intensity for 4 hours before sleep. Sleep measures included Epworth Sleepiness Scale and PROMIS Sleep-Related Impairment. We used univariate regression analysis. We found that that greater evening intensity of light exposure was associated with higher daytime sleepiness and more sleep impairment . The results of our study suggest that exposure to bright light during evening can disturb nighttime sleep and increase daytime sleepiness in PLWD."} +{"text": "Authors would like to update below as article note which was missed out in original publication. The original article has been corrected.Haoming Ma and Guo Yu contributed equally to this manuscript."} +{"text": "When this paper was originally published, Valerio DiNicola was originally missing as the fourth author. This has now been corrected online."} +{"text": "The development of brain metastases from primary cancer profoundly impacts patient prognosis. Up to one quarter of lung cancers develop brain metastases and subsequent median overall survival is one year. Although clinical factors do not reliably predict brain metastasis development, DNA methylation signatures have been recently shown to predict outcomes in other cancers. It is hypothesized that DNA methylation signatures predicting brain metastasis development from lung cancer will be identified. This work may allow for treatment strategies that prevent brain metastasis development in high risk lung cancer patients.DNA methylation profiling was undertaken on N=124 lung adenocarcinoma patients. In a randomly selected 70% training cohort, differentially methylated CpG sites between patients developing and not developing brain metastases were identified and used to build a generalized boosted regression model. Patients in the independent 30% testing cohort were assigned brain metastasis risk scores by the model.Brain metastases developed in 49/124 (39.5%) of patients and 2.3K CpG sites were significantly differentially methylated between patients developing and not developing metastases. Methylation-based brain metastasis risk scores predicted time to brain metastasis development in the testing cohort . A multivariate cox analysis assessing tumor size and nodal positivity together with methylation scores as covariates identified methylation scores as the only independent predictor of brain metastasis development in the testing cohort .DNA methylation signatures in lung adenocarcinomas predict brain metastasis development independently from the non-metastatic components of cancer stage. Future work developing a comprehensive nomogram utilizing methylation scores together with clinical factors to determine patient specific risk values may aid in treatment decisions and patient prognosis counselling."} +{"text": "As the mainstay of curative treatment for esophageal cancer, surgery increases survival but entails impaired health-related quality of life (HRQL).The current Swedish nationwide longitudinal studyStudies elucidating potential effective interventions to improve postoperative HRQL are warranted. It might be worth examining whether increasing dispositional optimism could improve postoperative HRQL. Identifying the potential modifiable mediators between dispositional optimism and HRQL may also be valuable because some potential mediators such as coping strategy and social support may be easier to be\u00a0modified than dispositional optimism. In addition, interventions to prevent or relieve psychological distress may also help improve HRQL after esophageal cancer surgery.5"} +{"text": "This paper consists of a clinical image of a complex developmental anomaly that is usually diagnosed prenatally or during childhood. Its detection in adult life is very rare, as happened in the present case. Surgical biopsy was performed, demonstrating cavities covered with respiratory epithelium exhibiting mucinous cell hyperplasia, consistent with a type 1 congenital pulmonary airway malformation (CPAM) scan showed right apical and middle lobe polylobulated consolidations (Figure\u00a0None declared.The authors declare that appropriate written informed consent was obtained for the publication of this manuscript and accompanying images."} +{"text": "Physical examination of her wrist revealed swelling and mildly painful movement with minimal limitation. The patient was living in a region endemic for hydatid disease. A radiological study revealed soft tissue swelling of the wrist with no bone erosion or calcification . Magneti"} +{"text": "Research has shown cognitive ability in older age is associated with activity engagement, but little is known about what psychological mechanisms are linking the two constructs. This study investigates an emotional pathway, in which affective states mediate the temporal associations between momentary working memory and momentary activities in older age. We examined data from 153 healthy older adults aged 65 to 91 who completed a smartphone-based ambulatory assessment survey seven times a day over 15 days. In each assessment point, participants reported their momentary activities and affective states and took a working memory task. Initial results suggest that during an approximate time period of six hours , working memory performance influences subsequent likelihood of social activity engagement. Moreover, positive affect mediates this temporal association. Results will be discussed in the context of cognitive aging research."} +{"text": "DOI: 10.1039/C3RA23176CCorrection for \u2018Nanochannel conduction in piezoelectric polymeric membrane using swift heavy ions and nanoclay\u2019 by Karun Kumar Jana This correction does not alter the conclusions presented in this The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers."} +{"text": "Research suggests that marital quality may buffer the impact of sensory impairments in later life, and that marital quality relates to cognitive functioning. This study explored how marital quality moderated links between sensory impairments and cognitive functioning. We used data from 723 paired marital dyads from two cohorts in the NHATS and NSOC studies across three-year periods . Growth curve models of executive functioning indicated that marital quality moderated effects of both hearing and vision impairment on changes in cognitive functioning longitudinally. Specifically, higher marital quality was associated with higher executive functioning across time. Results suggested no improvement in executive functioning among those with average or lower marital quality. Although cognition declines with advanced age and with sensory impairments, results suggest that older adults with higher marital quality may improve in some aspects of cognition longitudinally."} +{"text": "Ureteral stent catheterization is a common procedure in urological practice. Although ureteral stents have undergone notable technological advancements in the past few decades, numerous side effects exist and affect the patient physically and psychologically.In this case report, a ureteral stent for cutaneous ureterostomy was changed every month. One paper showed that the catheter\u2010free rate was 70%\u201380% for cutaneous ureterostomy.In this case report, the author changed the ureteral stent without fluoroscopy. Sometimes, experienced urologists change a ureteral stent without fluoroscopy. A recent paper regarding the techniques and tips for ureteral stent placement demonstrated that a ureteral stent is changed under fluoroscopy and retrograde pyelography.So far, 30 reports about the knotting stent have been reported.The authors declare no conflict of interest."} +{"text": "The original article contained two errors whereby both equation 1 and supplementary files were presented incorrectly.The original article has since been updated to correct these errors ."} +{"text": "In The authors have provided a corrected version of In the Results subsection \u2018Lack of statistical power suggests spurious evidence for silent representations of unattended memories,\u2019 sentence 9 should be removed. The correct sentence series is:We found that unattended memories could be robustly decoded during the whole delay and in particular immediately before pinging from high-decoding sessions, while discarded memories could not (both p>0.45,"} +{"text": "When this paper first published online, the author name Rei Mastueda was incorrect. It should have been Rei Matsueda. This has now been corrected online."} +{"text": "In our previous report, deep invasion in urothelial carcinoma within a pyelocalyceal diverticulum was discussed.The author declares no conflict of interest."} +{"text": "Tricuspid valvectomy occasionally might be a temporizing bridge treatment in extremely ill and hemodynamically unstable patients who are prepared for eventual tricuspid valve repair/replacement.65.See Article page Three decades ago, tricuspid valvectomy was the last resort in certain cases of infective endocarditis associated with septic shock in patients with mostly intravenous illicit drug addiction. Excision of infected tricuspid valve is well known to all the cardiac surgeons. The topic is perhaps timely, as recreational drug use has become an alarming national epidemic. In the recent years, the feasibility of tricuspid valve repair or tricuspid valve replacement has been compared with the valve excision option."} +{"text": "Hypothetical mechanisms in the development of mixed tumors have been described.Methotrexate (MTX)\u2010associated lymphoproliferative disorders (LPDs) can be considered in patients undergoing long\u2010term MTX treatment, because these patients have a relatively high risk of lymphoma.The authors declare no conflict of interest."} +{"text": "Lower pre-chemotherapy night time cortisol excretion predicted more severe cisplatin induced nausea and vomiting in 42 ovarian cancer patients receiving ondansetron as a single antiemetic agent. Dexamethasone administration added to the antiemetic effect of ondansetron principally in patients who had low excretion of cortisol."} +{"text": "Dr. Levine's comments are greaThe patient presented in the case study had an The modern dual chamber detection algorithms have significantly improved specificity for ventricular arrhythmia detection. I am in total agreement with Dr. Levine regarding the programming of monitoring zones in the early post implant period. When done correctly, such programming can provide a great deal of information on arrhythmia characteristics and accuracy ofdiscrimination algorithms."} +{"text": "Objective: To determine the rate of positive group B streptococcus (GBS) cultures at 35\u201337 weeks gestationin women who have first trimester asymptomatic GBS bacteriuria.Methods: Pregnant women with asymptomatic first trimester GBS bacteriuria had genital cultures for GBSperformed at 35\u201337 weeks gestational age. Serotyping was performed by the standard Lancefield capillaryprecipitin method.Results: Fifty-three women with positive urine cultures had genital cultures performed at 35\u201337 weeks. Sixteenof the 53 third trimester vaginal cultures were positive for GBS.Five of eight (63%) of the women with typable urine serotypes had the same typable serotype in the thirdtrimester genital culture.Conclusion: Genital tract cultures at 35\u201337 weeks for GBS correlate poorly with first trimester asymptomatic GBSbacteriuria. Recommendations for GBS prophylaxis in labor in women who have first trimester asymptomaticGBS bacteriuria should be investigated further and reconsidered."} +{"text": "Seven out of 18 assessable patients (39%) responded with minimal toxicity. Endocrine studies demonstrated that the drug produced significant initial falls in oestradiol and oestrone levels, but that these levels rose toward pretreatment levels as the study progressed. Sex hormone binding globulin (SHBG) levels gradually fell during the study suggesting that the drug has a minor degree of androgenic activity albeit of no clinical significance. There was a transient reduction of adrenal steroid levels, which remained however within the normal range. There were no symptoms of adrenal insufficiency."} +{"text": "This very encouraging article is basedI recently reported that many detained psychiatric inpatients had not been fully investigated to exclude organic causes of their seeming first episode of schizophrenic-like psychosis .These authors state that their patients had DSM-IV\u2013diagnosed schizophrenia, which excludes organic causation. What investigations did they do to ensure that their clinical sample had no organic precipitants?"} +{"text": "Incorporation of cytotoxic drugs into microspheres reduces but does not eliminate systemic toxicity. The extent of liver to lung shunt was measured in 26 patients with colorectal liver metastasis. Liver to lung shunting correlated with proportion of liver replacement but did not exceed 4.4% and therefore is unlikely to cause systemic toxicity."} +{"text": "Sixteen patients with advanced and recurrent malignant salivary gland tumours were admitted to a randomised trial and the response assessed. Seven patients received Epirubicin/5-Fluorouracil and none of these patients responded. Nine patients received Cisplatinum and only one patient had a partial response. The trial suggests that chemotherapy has no place in the treatment of advanced salivary gland malignant tumours."} +{"text": "Premorbid personality characteristics could have a pathoplastic effect on behavioral symptoms and personality changes related to neurodegenerative diseases. Patients with personality disorders, in particular of the dramatic cluster, may present functional frontolimbic abnormalities. May these neurobiological vulnerabilities linked to a premorbid personality disorder predispose or represent a risk factor to subsequently develop a neurodegenerative disorder? Are subjects with personality disorders more at risk to develop a dementia than mentally healthy subjects? This topic is discussed presenting the clinical case of a patient who suffered of a probable Narcissistic Personality Disorder and subsequently developed a clinically diagnosed Frontotemporal Dementia."} +{"text": "Patients with transient ischemic stroke and patients with non-cortical stroke did not have significant deficits in working memory in either modality.Functional imaging studies indicate that the left hemisphere mediates verbal working memory, while the right hemisphere mediates both verbal and spatial working memory. We evaluated acute stroke patients with working memory tests and imaging to identify whether unilateral dysfunction causes deficits in spatial and/or verbal working memory deficits. While left cortical stroke patients had verbal working memory impairments ("} +{"text": "Robotic technology for use in surgery has advanced considerably in the past 10 years. This has become particularly apparent in urology where robotic-assisted radical prostatectomy using the da Vinci surgical system has become very popular. The use of robotic assistance for benign urological procedures is less well documented. This article considers the current robotic technology and reviews the situation with regard to robotic surgery for benign urological conditions."} +{"text": "It is acceptable to interpret that metformin has three different responsibilities including: blood glucose regulatory effect, renal tubular cell protection by acting as an effective antioxidant and finally protective effect on diabetic nephropathy through saving the podocytes. Hence, diabetic patients may benefit from all of these three distinct ameliorative effects. et al. found that gentamicin-induced kidney tubular damage is attenuated by metformin have been completely observed by the authors.None declared."} +{"text": "Minimally invasive urological procedures have gained in popularity and replaced open surgery in various urological procedures. Although considered minimally invasive, these procedures are not free from complications, and life-threatening hemorrhage may occur. Herein we describe 3 case series of patients who underwent minimally invasive urological surgeries that were complicated with bleeding. In all 3 patients we used super selective angiographic embolization to stop hemorrhage. Minimally invasive urological surgeries carry the risk of hemorrhage, and patients should be informed about this possibility. In hemodynnmic stable patients endovascular embolization allowed bleeding cessation with maximal preservation of the bleeding kidney tissue."} +{"text": "While increased renal venous and direct renal parenchymal pressure may cause renal insufficiency, there are no prior reports of hypersplenism secondary to chronic lymphocytic leukemia (CLL) doing so. This first report of massive splenomegaly leading to marked compression of the left kidney associated with renal insufficiency that resolved after splenectomy illustrates that profound extrinsic renal compression from splenomegaly may significantly compromise left renal function and splenectomy should be considered in this situation."} +{"text": "The authors regret that Kenneth Mellits\u2019 middle initial was listed incorrectly in their paper. The correct initial appears above.The authors would like to apologise for any inconvenience caused."} +{"text": "Anosognosia for cortical blindness, also called Anton\u2019s syndrome, is a rare neurological disorder usually following bilateral lesions to occipital cortices. Neuropsychological, morphological and functional neuroimaging (SPECT and fMRI) findings are reported in a patient who incurred Anton\u2019s syndrome after an ischaemic lesion confined to the left occipital lobe involving the corpus callosum. The present case study suggests that Anton's syndrome may also follow from lesions disconnecting the occipital cortices."} +{"text": "Numerous studies have shown a correlation between high autoantibody titers and subsequent autoimmune disease in patients with psychiatric disorders compared to healthy individuals. In this study we used a targeted affinity proteomics approach to investigate these autoantibody repertoires. We therefore obtained serum samples from patients diagnosed with various psychiatric disorders and compared these with samples of healthy volunteers. Additionally we used our approach to identify autoantibodies in post mortem brain tissue from patients diagnosed with schizophrenia.In this study we utilized a well characterized cohort of patients with psychiatric disorder to study the autoantibody repertoire. From this sample set we analysed more than 600 serum in a first discovery approach. Based on the in-house screening and previous external published studies of autoantibodies within psychiatry we selected a set of 231 protein fragments from the Human Protein Atlas with a length of roughly 80 amino acids. With this selected panel we screened additional 130 post mortem brain tissue samples. Autoantibody profiling was performed using suspension bead array technology and IgG reactivity was measured in patients and controls.Our findings could indicate altered immune response in patients with psychiatric disorders compared to healthy controls. In our study we identified potential predictive autoimmune signatures. Those were presented with higher IgG reactivity in patients compared to healthy control samples.With our approach we were able to profile autoantibody repertoires in patients with psychiatric disorders. Additionally, we were able to use our approach to profile brain tissue using a multiplexed affinity proteomics approach. By further validating these putative autoimmunity targets, we could gain insights into the autoantigens associated to chronical mental illnesses."} +{"text": "The antibiotic name amoxicillin appears incorrectly throughout the article. The correct antibiotic name is amoxicillin-clavulanate.The antibiotic name amoxicillin appears incorrectly in Tables The antibiotic name amoxicillin appears incorrectly in"} +{"text": "Pathological laughter is an uncommon symptom usually caused by bilateral, diffuse cerebral lesions. It has rarely been reported in association with isolated cerebral lesions. Midbrain involvement causing pathological laughter is extremely unusual. We describe three patients who developed pathological laughter after midbrain and pontine-midbrain infarction. In two patients a small infarction in the left paramedian midbrain was detected, whereas the third one sustained a massive bilateral pontine infarction extending to the midbrain. Laughter heralded stroke by one day in one patient and occurred as a delayed phenomenon three months after stroke in another. Pathological laughter ceased within a few days in two patients and was still present at a two year follow-up in the patient with delayed-onset laughter. Pathological laughter can herald midbrain infarction or follow stroke either shortly after onset of symptoms or as a delayed phenomenon. Furthermore, small unilateral midbrain infarctions can cause this rare complication."} +{"text": "In Sectipovirus . Thus, mThe authors apologize for any inconvenience this may have caused. The changes do not significantly affect the scientific results however rectify the taxonomic inaccuracies."} +{"text": "In our discussion we erronThe observed difference in costs per average CAP patients can be partly explained by the younger cohort in the Spoorenberg et al. study (m"} +{"text": "The assessment of male patients with lower urinary tract symptoms presents a common urological request and prostatic surgery places heavy demands on Health Service resources. Sixty male patients attended a urine flow clinic during their preliminary clinical assessment, to identify those with objective evidence of bladder outflow obstruction. Nineteen were shown to have a reduced urine flow rate and of these 13 proceeded to prostatectomy. The clinic has a useful role as a screening investigation."} +{"text": "We describe a technique for protecting and cooling soft tissues while using cement in bony defects. Internal fixation using cement to augment neoplastic lesions is a recognised technique but the resulting exothermic reaction risks the surrounding tissues. We have used a surgical glove partially filled with water to protect volar structures of the wrist while cementing a distal radial lesion . Through"} +{"text": "We report a case of spontaneous superior pole renal artery dissection in a healthy forty-one year old man. Spontaneous renal artery dissection is a rare event occurring in patients with hypertension or renovascular disease such as fibromuscular dysplasia. This case demonstrates the importance of maintaining renovascular accidents as part of the differential diagnosis of abdominal pain."} +{"text": "Arterial spin labeling of the heart has been shown to estimate myocardial perfusion and perfusion reserve at a single short-axis slice for coronary artery disease assessment. However, current spatial labeling methods suffer from transit delay effects when imaging is extended to more than a single slice. Velocity selective (VS) labeling is a promising alternative that does not suffer from transit delay effects.Eight healthy volunteers were scanned using a 3T GE Signa Excite HD scanner with an 8-channel cardiac coil. Myocardial ASL measurements were made at a single short axis slice using both VSASL and conventional flow alternating inversion recovery (FAIR) ASL as a reference. VS labeling was performed using an adiabatic BIR4 pulse with bipolar gradients as shown in Figure Figure We have successfully labeled coronary blood based on velocity and demonstrated that VSASL is sensitive to myocardial perfusion. We believe that VSASL has the potential to become a more sensitive labeling scheme than spatial labeling sequences because of its insensitivity to transit delay and because it is inherently compatible with whole heart coverage."} +{"text": "Corrigendum:After publication, the authors noticed that five authors\u2019 names were listed incorrectly. The author list and author contributions have been amended so that: Xuan Hong Sun is now listed as Hongxuan Sun. Wen Ya Liu is now listed as Yawen Liu. Qin Ya Yu is now listed as Yaqin Yu. Feng Xu Huang is now listed as Xufeng Huang. Yang Xiang Zhang is now listed as Xiangyang Zhang."} +{"text": "Pruritus was assessed in plaque psoriasis, atopic eczema and acne vulgaris using visual analogue scales. The results demonstrate that itch is a common and frequently troublesome symptom in plaque psoriasis. This observation should be more widely recognised in textbooks and publications."} +{"text": "The originally published Figure 6 had several mis-drawn structures with charges in incorrect locations. These errors have been corrected in the new version see ."} +{"text": "Acquired stuttering is a disorder of the fluency of speech. The mechanism underlying stuttering is unknown. It may occur after bilateral and unilateral cortical or subcortical brain damage. We report two cases who had stuttering resulting from left parietal infarction."} +{"text": "An 8 years old girl suffers from strabismus since her first months of life. Her visual acuity was very low and could only see fingers moving in her left eye. Her left eye fundus showed a chorioretinal scar in the macula due to congenital toxoplasmosis. The biological findings proved the diagnosis of congenital toxoplasmosis. Functional prognosis of macular scars is very dark."} +{"text": "The supernumerary kidney is an accessory organ with its own blood supply and collecting system. It is a very rare type of congenital renal anomaly with fewer than 100 cases reported since firstly described at 1656 . It may We aimed to present a rare case of supernumerary fused and malrotated kidney. Thirty-seven year-old woman was admitted to our clinic with left flank pain. CT scan demonstrated multiple calculi in the left kidney and supernumerary fused kidney and 2. TGrieshammer and colleagues showed that mutant mice lacking either SLIT2 or its receptor ROBO2 develop supernumerary ureteric buds that are correlated with abnormal maintenance of Gdnf expression in anterior metanephric mesenchyme . The SLI"} +{"text": "Diabetes mellitus are rising rapidly in worldwide despite advancing diabetes modalities and services. Many researches are in charge to provide unique healthcare system for diabetic condition management.Diabetes mellitus are rising rapidly in worldwide despite advancing diabetic modalities and services. This is depicted by a recent study were conducted to improve presented services for diabetic children . In thisSimilarly, a cross sectional study was conducted between April 2008 and January 2009 have been completely observed by authors.None."} +{"text": "An unexpected diagnosis of metastatic RCC after excision biopsy of a skin nodule can bring uncertainty. A case of isolated scalp metastasis from undiagnosed RCC was noted and a review of the literature was undertaken to aid management. RCCs often present with distant disease involving multiple organ systems. Single metastasis to the scalp region without other organ involvement is uncommon. Cytoreductive nephrectomy and limited metastectomy offer survival advantage in physically fit patients with RCC."} +{"text": "CT imaging. This case also highlights the need for immunohistochemical analysis of unusual tumor deposits facilitating appropriate treatment.Colonic metastases from lung cancer are rare . Presentation of an abdominal mass in the setting of a new lung cancer diagnosis should prompt complete evaluation including endoscopic and CT imaging confirmed a colonic lesion during staging investigations of a 56\u2010year\u2010old female smoker with lung adenocarcinoma and mediastinal lymphadenopathy Fig.\u00a0. ImmunohGF: drafted submission and submitted case report for publication. EO: performed literature review and assisted with drafting of submission. MF: obtained and prepared radiology and endoscopic images for case report. CR: is respiratory physician responsible for diagnosing and managing patient's lung adenocarcinoma. FB: is pathologist who reported on colonic biopsy samples and who obtained pathology slides contained in this case report. KB: is general surgeon responsible for investigating patient's colonic lesion through performing colonoscopy and obtaining colonic biopsy samples, assisted with drafting of submission and literature review.None declared."} +{"text": "Segmental testicular infarction is a rare entity with fewer than 40 cases documented in the literature. It frequently mimics an acute scrotum presenting with pain and swelling. Difficulty distinguishing benign from malignant lesions on imaging has led to radical orchiectomy in the past. With improvements in imaging, this condition may be treated more conservatively. We present the first case of bilateral segmental testicular infarction and discuss management options."} +{"text": "Conventional management of acute left sided colonic obstruction employs some form of proximal colostomy. Intraoperative antegrade colonic irrigation relieves proximal faecal loading and may permit safer primary resection and anastomosis. The results of a pilot study are presented, and are shown to be favourable."} +{"text": "This error appears only in PDF versions downloaded on or before January 31, 2018. Rockefeller University Press apologizes for this regrettable error."} +{"text": "A survey was carried out of three hundred general practice patients who were questioned about recurrent abdominal pain or discomfort and other related symptoms. Patients who responded positively to the questionnaire fell into three main groups.Twenty two patients (7%) were found to have previously diagnosed irritable bowel syndrome. A further twenty patients (7%) had similar symptoms but had not sought medical help for them. Finally there were twenty eight (9%) patients with abdominal pain due to miscellaneous organic diseases.Age-sex matched controls were selected from the two hundred and thirty patients who responded negatively to assess the rate of consultation and the rate of prescribing benzodiazepines and antidepressants."} +{"text": "We present a female patient who developed mucosal and skin hyperpigmentation due to metastatic malignant melanoma. Diffuse cutaneus melanosis is a rare entity that complicates a small percentage of metastatic melanomas, confering a fatal prognosis. We discuss briefly the current evidence on pathogenesis of melanosis arising from metastatic melanoma."} +{"text": "An English speaking women developed a French accent, without any aphasic syndromes, in conjunction with multiple left sided cranial nerve deficits, temporally related to cranial trauma. Extensive testing with multimodality magnetic resonance imaging, cerebrospinal fluid and laboratory analysis was unremarkable. She was followed over a 3 year period during which her French accent resolved as did the majority of her multiple unilateral cranial neuropathies. The neurological diagnoses included a foreign accent syndrome attributed to a reversible Garcin syndrome."} +{"text": "In patients with no history of trauma, nasal leakage is often overlooked. In our case, we diagnosed it accurately and successfully cured this patient with a transnasal transsphenoidal neuroendoscopic surgery approach."} +{"text": "Fibrous dysplasia (FD) is a benign fibroosseous bone disorder. It has poliostotic and monostotic patterns. Monostotic FD is frequently asymptomatic and is usually discovered incidentally by radiologic imaging performed for other reasons. Bone scintigraphy is valuable for identifying disease extent. Craniofacial FD (CFD) is a form of the disease where lesions are limited to contiguous bones of the craniofacial skeleton. We presented a case with monostotic CFD who was detected incidentally on bone scintigraphy single-photon emission computed tomography/computerized tomography while being investigated for inflammatory arthropaties."} +{"text": "KX757840 was listed incorrectly in Puumala Virus in Bank Voles, Lithuania . The article has been corrected online ("} +{"text": "We describe four patients with relapsing remitting multiple sclerosis (RRMS) who experienced a relapse with acute onset of painful sensations. Pain sensations disappeared in two of them and markedly reduced in the other ones after repeat application of intrathecal triamcinolone acetonide (TCA) following a prior unsuccessful treatment with intravenous steroids. TCA administration was well tolerated and no serious side effects occurred. Repeated intrathecal TCA injection may provide a substantial benefit in RRMS patients with acute onset of pain due to an inflammatory lesion within the spinal cord."} +{"text": "Hantavirus pulmonary syndrome (HPS) occurs in most infections with Sin Nombre virus and other North American hantaviruses. We report five cases of acute hantavirus infection that did not fit the HPS case definition. The patients had characteristic prodromal symptoms without severe pulmonary involvement. These cases suggest that surveillance for HPS may need to be expanded."} +{"text": "Dear Editor,In their recent article entitled 'Temporary ectropion therapy by adhesive taping: a case study', Drs Schrom and Habermann 'propose a simple method to correct temporary ectropion in facial palsy by applying an adhesive strip' . The aut"} +{"text": "Ontologies are becoming increasingly important for the efficient storage, retrievaland mining of biological data. The description of phenotypes using ontologies is aparticularly complex problem. We outline a schema that can be used to describephenotypes by combining orthologous axiomatic ontologies. We also describe tools forstoring, browsing and searching such complex ontologies. Central to this approach isthat assays (protocols for measuring phenotypic characters) describe what has beenmeasured as well as how this was done, allowing assays to link individual organisms toontologies describing phenotypes. We have evaluated this approach by automaticallyannotating data on 600 000 mutant mice phenotypes using the SHIRPA protocol. Webelieve this approach will enable the flexible, extensible and detailed description ofphenotypes from any organism."} +{"text": "A case of a 70 year old man who was found to have an extrahepatic portal vein aneurysm during an evaluation for hematuria is reported. Extrahepatic portal vein aneurysms are rare with only twenty cases reported in the literature. Typically, patients present with hemorrhage requiring surgical exploration or the aneurysm is discovered during evaluation of another abdominal process. Management includes careful follow-up in the asymptomatic patient without underlying liver disease or portal hypertension."} +{"text": "Human immunodeficiency virus (HIV) is a diploid virus: each virion carries two complete RNA genomic strands. Homologous recombination can occur when a cell is coinfected with two different but related strains. Naturally occurring recombinant HIV strains have been found in infected patients in regions of the world where multiple genotypic variants cocirculate. One recombinant HIV strain has spread rapidly to millions of persons in Southeast Asia. Recombination is a mechanism whereby high level and multidrug-resistant strains may be generated in individual treated patients. Recombination also poses theoretical problems for the development of a safe HIV vaccine. Certain features of HIV replication, such as syncytium formation and transactivation, may be best understood as components of a sexual reproductive cycle. Recombination may be an important HIV evolutionary strategy."} +{"text": "Techniques are described for hapten attachment to the cell membranes of mouse tumour cells. Dinitrophenylation and tyrosylation could be achieved without substantial loss of viability as measured by dye exclusion. In addition hapten coated tumour cells were capable of initiating new tumour formation in syngeneic hosts. Pre-immunization of recipient mice with hapten coated tumour cells did not increase their resistance to tumour formation upon subsequent challenge with graded doses of untreated tumour cells."} +{"text": "The resultsshow that the complexes retain Keggin structure. The complexes exhibit antitumoral activity in vitro as shown by MTT experiment.Six new compounds [(CpTi)X, Cp=\u03cb"} +{"text": "Fibrolamellar hepatocellular carcinoma (FHCC) is avariant of hepatocellular carcinoma, which mainly affectsa young age group and carries a relatively goodprognosis. It is widely accepted that aggressive curativeresection is still the best option for FHCC. Wereport here a case of successful arterialisation of theportal vein with an aortoportal jump graft for portalvein thrombosis, which developed postoperatively inan already comprised portal vein with tumour invasionfollowing an extensive liver resection for FHCC."} +{"text": "Therapeutic nuclear medicine is less advanced but can provide significant benefits provided the radionuclide is accurately targetted.Radiometals are the mainstay of both diagnostic and therapeutic nuclear medicine because the choice of radionuclide is primarily dictated by nuclear decay characteristics rather than chemistry."} +{"text": "A patient is described with a synchronous intraluminal squamous cell carcinoma of theleft upper lobe carina. He refused photodynamic therapy after sleeve lobectomy of theright upper lobe. The intraluminal tumor was treated with fiberoptic bronchoscopicelectrosurgery. Complete remission was achieved, at the moment already for 36 months."} +{"text": "Hypersensitivity pneumonitis (HP) in workers exposed to metal removal fluids (MRFs) is increasing. This study supports the hypothesis that aerosolized mycobacteria colonizing the MRFs likely cause the disease. Three case studies of HP outbreaks among metal workers showed potentially high exposures to a rare and newly proposed Mycobacterium species. Retrospective review of samples submitted to our laboratory showed an association between presence of mycobacteria and HP."} +{"text": "To the Editor: Enterohemorrhagic Escherichia coli (EHEC) can cause severe hemorrhagic colitis characterized by gastrointestinal symptoms and bloody diarrhea as well as hemolytic uremic syndrome domestic animals such as cats ("} +{"text": "Diffuse biliary papillomatosis is a rare bile duct tumour. We report a case of multiple biliarypapillomatosis treated surgically with a transhepatic stent. Diffuse biliary papillomatosis involving intra and extrahepatic bile ducts is extremely rare. It isregarded as having low grade malignant potential. In this report a case of diffuse biliary papillomatosiswith obstructive jaundice is presented."} +{"text": "Arias et al in the article 'A narrow QRS complex tachycardia with an apparently concentric retrograde atrial activation sequence' describe a case with spontaneous intra atrial block along the mitral isthmus to explain the change in atrial activation . This ph"} +{"text": "Several compoundsexhibit excellent antitumour activities. in vivo screening also gave very promising results.An overview of the"} +{"text": "A case of fibrous histiocytoma of low grade malignancy arising from the uncinate lobe of the pancreas isreported. This is an unusual site for these extremely rare tumours. Survival up to 4 years has been achievedin our patient following surgical resection."} +{"text": "The present study investigates the prognostic value of immunohistochemically detected cathepsin D expression in endometrial adenocarcinoma. Patients with surgically treated endometrial adenocarcinoma FIGO stages I-III and consecutive irradiation therapy were included in the study. When we performed immunohistochemistry to detect cathepsin D in 115 tissue specimens 35 cases showed a positive reaction. In the univariate analysis cathepsin D expression showed significant prognostic value for overall survival . In the multivariate analysis with established prognostic parameters we found an independent prognostic value for cathepsin D . Immunohistochemical detection of cathepsin D could aid in predicting prognosis and planning therapy for patients with endometrial adenocarcinoma."} +{"text": "We present a case of giant cavernous hemangioma ofthe liver with disseminated intravascular coagulopathy(Kasabach\u2013Merritt syndrome) which wascured by enucleation. The 51 year old womanpresented with increased abdominal girth and easybruisability. Workup elsewhere revealed a massivehepatic hemangioma and she was started on radiationtherapy to the lesion and offered an orthotopicliver transplant. After careful preoperative preparation,we felt that resection was possible and sheunderwent a successful enucleation. The operationand postoperative course were complicated bybleeding but she recovered and remains well infollowup after 6 months. All coagulation parametershave returned to normal. Enucleation shouldbe considered the treatment of choice for hepatichemangiomas, including those presenting withKasabach\u2013Merritt syndrome. The benefits of enucleationas compared to liver transplantation forthese lesions are discussed."} +{"text": "Leucocyte migration inhibition by autologous breast tumour cell fractions was mediated by a soluble factor synthesized and released by mononuclear leucocytes and active against migrating granulocytes. This mechanism is similar to that previously described in respect to cell-mediated sensitivity to microbial antigens. Alternative mechanisms involving directly reactive granulocytes or cytophilic antibodies were rarely operative in the migration tests."} +{"text": "The presence of soft tissue edema around a malignant musculoskeletal neoplasm can interfere with accurate local tumorstaging at magnetic resonance imaging. This article discusses and illustrates such edema, emphasizing means for avoidingmisinterpretation of edema and subsequent overstaging."} +{"text": "Indirect evidence suggests that cancer anorexia is associated with specific aversions to macronutrients. To investigate this, patients with cancer anorexia and hospitalized control subjects devised 3-day menus comprising foods that they wished to eat. These foods were then provided for 3 days and the intakes of each food carefully measured. As expected, patients with cancer anorexia consumed substantially less energy than hospitalized control subjects . However, macronutrient composition was consistently maintained in the patients with cancer anorexia. These data argue against cancer anorexia representing a state of macronutrient aversion."} +{"text": "Isolated bile duct injuries after blunt abdominal trauma are rare. Surgery is the usual mode of treatment. We report a patient with a right hepatic duct injury following blunt abdominal trauma who was managed successfully by endoscopic papillotomy."} +{"text": "The survival of 64 consecutive patients with disseminated midgut carcinoid tumours was compared in a retrospective study with that of 25 consecutive patients with sporadic malignant endocrine pancreatic tumours treated according to similar surgical principles. The presence of hepatic metastases implied a worse prognosis in neuroendocrine tumours of pancreatic rather than midgut origin. This infers that these tumour types must be separated when treatments are evaluated. \u00a9 1999 Cancer Research Campaign"} +{"text": "Pulmonary lymphangitis carcinomatosa is an unusalcause of death in a young adult. This case describesan apparently healthy young woman who presentedwith severe acute pancreatitis, which is a recognizedcomplication of a choledochal cyst. Autopsy examinationrevealed advanced malignancy with poorlydifferentiated adenocarcinoma penetrating the wallof the choledochal cyst and metastatic adenocarcinomain the lymph nodes, lungs and kidneys. Thiscase emphasises the unusual presentation of acholedochal cyst with acute pancreatitis and theaggressive nature of malignancy associated with thiscongenital anomaly."} +{"text": "Background: Disseminated coccidiomycosis during pregnancy can lead to both maternal and neonatal mortality. Placentitis is an uncommon sequelae and its effect on placental function remains speculative. The present report describes our management of such a case and describes serial umbilical artery velocimetry of an affected placenta. Case: A pregnant woman with coccidioidal placentitis confirmed histologically was treated with systemic and intrathecal amphotericin B starting at 28 weeks gestation. Serial umbilical artery velocimetry revealed that all systolic/diastolic ratios remained normal, and a normal infant was delivered at term. Conclusion: Coccidioidal placentitis was successfully treated with amphotericin B; serial umbilical artery velocimetry monitoring exhibited no abnormalities and, along with other reassuring fetal parameters, allowed continuation of the pregnancy to term."} +{"text": "Peliosis hepatis is defined as the appearance ofblood filled lakes in the hepatic parenchyma. It hasbeen associated with various pharmacologicalagents and infections. Treatment has been primarilysymptomatic and includes discontinuation of offendingmedications, partial hepatectomy or occasionallyliver transplantation. We report a 58 yearold white female on hormone replacement therapywho developed symptomatic peliosis hepatis andunderwent successful superselective hepatic arteryembolization with control of bleeding."} +{"text": "Famciclovir is an antiviral with efficacy and safety comparable to aciclovir, but famciclovir's more favorable pharmacokinetic profile enables a less frequent dosing regimen. Future trials will likely determine famciclovir's role in the suppression of HBV."} +{"text": "A method has been devised to calculate breast volumes from mammograms. This has been applied to mammograms from 42 women with breast cancer and 42 age-matched normal controls. No difference in breast volumes was noted."} +{"text": "The only curative treatment for proximal bile duct cancer with involvement of both main hepatic ducts isliver transplantation. Most patients do not fulfill the requirements for liver transplantation. Ourtreatment strategy in appropriate cases is palliative tumor resection and reconstruction of the biliarypassage by sutureless bilioenteric anastomosis. We have treated 12 patients, 5 in combination withintraluminal and percutaneous radiotherapy. Our results indicate that this strategy leads to effectivepalliation in some cases provided that only microscopic residual tumor is left in-situ. Our survival timescompare favourably with survival after liver transplantation."} +{"text": "Cholesterol gallstone disease is extremely common. Three major stages are recognized for stoneformation, namely bile that becomes supersaturated with cholesterol, cholesterol nucleation leading tocrystal formation and finally retention of the crystals in the gallbladder resulting in stone formation.Supersaturation is common but nucleation into crystals probably requires protein nucleating factors.Impaired motility of the gallbladder causes crystal retention and is probably very important in stoneformation."} +{"text": "Yanrui Li is incorrectly listed as a corresponding author for this manuscript. Instead, Yanrui Li should be listed as having contributed equally with Jincheng Li and Stefan Donath."} +{"text": "A 29 year old morbidly obese patient suffered injury to his common bile duct during cholecystectomy.Subsequent access to the biliary tree was obtained by using a long heavy gauge needle afterfirst opacifying the system with contrast injection through a nasobiliary tube. It is now twenty sixmonths after initial percutaneous biliary drainage placement and eighteen months after removalof all biliary access. The patient is asymptomatic and has normal liver function tests. Thistechnique can be useful in morbidly obese patients who are at increased risk from surgical repairof biliary duct injuries."} +{"text": "A novel method of repeated hepatic dearterialization was evaluated in five patients with multiplemetastases from gastric cancer in both hepatic lobes. After gastrectomy with extensive lymph nodedissection (R2/3), all patients underwent implantation of a vascular occluder around the hepaticartery. Cannulation of the hepatic artery was added for later chemotherapy. The hepatic artery wasoccluded repeatedly for 1 hour twice daily in combination with intrahepatic infusion of anticancerdrugs for as long as possible. Three of five patients demonstrated marked tumour regression withunexpectedly long survival .Carcinoembryonic antigen (CEA) levels decreased to almost normal in four patients who had initiallyhigh levels. The present experiences seems to indicate that long survival can be hoped for in patientswith advanced gastric cancer with unresectable liver metastases."} +{"text": "Because the author Christos C. Zouboulis was added to the author byline after publication, the Author Contributions section does not correctly reflect the new authorship. There should be an additional section which reads: Contributed reagents/materials/analysis tools: CCZ"} +{"text": "We report a case of a pigmented gallstone which formed around a surgical staple in the bile duct. Thestone was removed and retrieved endoscopically. A brief review of bile duct foreign bodies andgallstones is presented."} +{"text": "Computed tomography and sonography allowed excellent preoperative assessmentbut to attempt a distinction between the histological variants may be hazardous. Two tumourswere only autopsy findings and 5 patients underwent laparotomy. It is confirmed that potentiallymalignant mucinous cystadenomas and cytadenocarcinomas should be resected whenever possible;serous cystadenomas are always benign and should therefore be resected only when the diagnosis isdoubtful or if they cause symptoms.Cystic neoplasms of the pancreas are rare and their diagnosis and treatment can be difficult. This reportdetails 7 patients who had histologically proven serous cystadenoma"} +{"text": "PLoS Medicine Editors discuss what role food aid should play in addressing the global childhood malnutrition crisis.The The Economist made the case that childhood hunger and malnutrition have a far greater impact upon child health than was previously thought emergency\u201d . The rea"} +{"text": "Cultured rat liver cells induced a strong antibody response in syngeneic rats, directed against foetal calf serum components which were incorporated into the liver cell surface from the cell-culture medium. This antibody could be removed by absorption with liver cells or glutaraldehyde-fixed foetal calf serum. It is possible that the antigenic cross-reactivity observed in earlier studies with cultured cells treated with carcinogens could be due to this foetal calf serum component."} +{"text": "Fludarabine is a comparatively new drug for the treatment of low-grade lymphoid malignancy. This report describes five cases of unusual neurological illnesses occurring after treatment with fludarabine. These suggest that caution should be exercised in patients receiving fludarabine who develop neurological abnormalities, with prompt investigation and if necessary cessation of the drug."} +{"text": "The paper describes the development of periodic modules used for the peptide synthesis of hydroxamic acid. A powder conveyor using the principle of positive weighing distribution is described. Purification is provided using automatic filtration and a liquid\u2014 liquid extraction module separation device. Device quality is improved using failure mode and effects analysis."} +{"text": "Sir,I read with great interest the case reported by Drs Saini and Khurana titled \"Chronic relapsing inflammatory optic neuropathy\". I do rea24This is why steroid sparing agents should be strongly considered for the management of this condition."} +{"text": "We investigated two fatal cases of invasive Haemophilus influenzae type b (Hib) infection in a community nursing home in western Sydney, Australia. Two elderly women had lived in the same room, and the onset of their illness was 5 days apart. Hib isolates from blood cultures showed identical profiles by pulsed field gel electrophoresis. These findings suggest that Hib infection was transmitted within this nursing home. Serious Hib disease may be underrecognized in this setting. Continued surveillance and serotyping of invasive H. influenzae disease is essential for identifying groups at increasing risk that may benefit from immunization against Hib."} +{"text": "Gastrointestinal hemorrhage due to splenic artery aneurysm pancreatic duct fistula in chronic pancreatitisis rare. It is, however, important to diagnose this condition particularly in patients having chronicpancreatitis, since it may result in a life-threatening situation. The diagnosis is usually difficult toestablish and it may take repeated admissions for intermittent gastrointestinal bleeding until the realsource is recognized. Clinical attacks of epigastric pain followed by GI-bleeding 30\u201340 minutes later arecharacteristic. Occasionally these attacks are followed by transient jaundice. The present case reportdescribes this rare complication and reviews the current literature."} +{"text": "There is a wide array of endoscopic lithotriptors presently available. Each of these hasits own advantages and disadvantages. No single lithotriptor is suitable for all applicationsand none can meet the goal of fragmenting all calculi while remaining harmless totissue."} +{"text": "Subcutaneous growth of immunogenic chemically induced rat sarcomata and a hepatoma was restricted when cells were injected into syngeneic animals in admixture with MER. Rats rejecting mixed inocula were immune to further challenge with the same tumour. Growth of a chemically induced mammary carcinoma which lacks detectable immunogenicity was suppressed when low cell inocula were injected in admixture with MER or intact BCG organisms, although animals were not immune to re-challenge. These studies indicate that clinically MER may be a suitable alternative to BCG for contact suppression of tumour growth or incorporation into tumour cell:adjuvant vaccines for active immunotherapy."} +{"text": "We describe two unusual cases in sheep of subclinical mastitis caused by Streptococcus parasanguinis. This bacterium has been associated with the development of experimental endocarditis; its presence at relatively high concentrations in apparently healthy sheep milk may pose a health risk in persons with predisposing heart lesions."} +{"text": "There was an error in the published title of this manuscript. The correct title is: \"Citral Sensing by Transient Receptor Potential Channels in Dorsal Root Ganglion Neurons.\""} +{"text": "The publisher wishes to note that the \"Accept\" date on this article reflects the \"Production Accept\" date. This article was accepted by the editor on 16 April 2010, while its companion article Cryptococcal Cell Morphology Affects Host Cell Interactions and Pathogenicity. PLoS Pathog 6(6):"} +{"text": "Sir,et al. on cardiac Candida krusei infection presenting as a right ventricular mass with great interest.[et al. have mentioned that necrotizing enterocolitis and disseminated fungal infection result in an adverse outcome as was seen in their case.[Candida krusei infection is difficult to treat. Majority of the reported cases with hematogenous spread have died[I read the report by Patted interest. Patted eeir case. Indeed, have died Basic anhave died In the chave died Intravenhave died"} +{"text": "Nosocomial viral respiratory infections cause considerable illness and death on pediatric wards. Common causes of these infections include respiratory syncytial virus and influenza. Although primarily a community pathogen, rhinovirus also occasionally results in hospitalization and serious sequelae. This article reviews effective infection control interventions for these three pathogens, as well as ongoing controversies."} +{"text": "A simple liquid culture technique has been used to study peripheral blood from patients with acute myelogenous leukaemia. Evidence is presented that cells from morphologically identical types of leukaemia have differing capacity for \"differentiation\" from free floating blast cells into plastic-adherent phagocytic, trypsin-resistant macrophage-like cells with Fc and C3 receptors. Preliminary analysis suggests that patients whose cells have the greatest capacity for \"differentiation\" have a better chance of achieving complete remission."} +{"text": "A 65 year old patient with polycystic liver disease presented with obstructive jaundice thought to be a cholangiocarcinoma. Subsequent investigations demonstrated a large cyst compressing the confluence of the hepatic ducts. Percutaneous decompression of the biliary tree led to a complication necessitating surgery. Treatment options for symptomatic polycystic liver disease are reviewed."} +{"text": "Sir,Anastomotic stricture following complex esophageal and urethral anastomosis is often a distressing problem. Transanastomotic stenting and postoperative dilatation appears to be a useful adjunct in the management of this problem. Combined antegrade and retrograde dilatation is a very useful technique for difficult strictures.\u20133 We hav"} +{"text": "The benefits of laparoscopic trainers in the improvement of laparoscopic surgical skills are well established. Unfortunately simulators and trainers are expensive and sparsely available in surgical departments. Home built laparoscopic trainers on much smaller budgets have been described. The base"} +{"text": "Because two authors were added to the author byline, the Author Contributions do not correctly reflect the new authorship. The \"Conceived and designed the experiments\" statement should now include the following: SF EG MG JYG. The \"Performed the experiments\" statement should now include the following: SC SF EG JYG."} +{"text": "Controlled vocabularies are common within bioinformatics resources. They can be used togive a summary of the knowledge held about a particular entity. They are also used toconstrain values given for particular attributes of an entity. This helps create a sharedunderstanding of a domain and aids increased precision and recall during querying ofresources. Ontologies can also provide such facilities, but can also enhance their utility.Controlled vocabularies are often simply lists of words, but may be viewed as a kind ofontology. Ideally ontologies are structurally enriched with relationships between termswithin the vocabulary. Use of such rich forms of vocabularies in database annotation couldenhance those resources usability by both humans and computers. The representation ofthe knowledge content of biological resources in a computationally accessible form opensthe prospect of greater support for a biologist investigating new data."} +{"text": "This effect we have shown to be solely in the 19s fraction after Sephadex G-200 separation.Cell-free lymph from immunized rats was shown to be cytotoxic to the tumour cells This 19s fraction conferred partial protection to tumour bearing mice when given shortly after transplantation, but had negligible effect against late well established tumour."} +{"text": "Dr. Schweitzer submitted this article to BMC MThe pre-publication history for this paper can be accessed here:"} +{"text": "Adult CBA mice thymectomized, treated with antilymphocytic globulin (ALG) and inoculated with human leprosy organisms were accidentally infected with polyoma virus and all developed tumours. After cessation of ALG administration, some animals were given spleen cells from syngeneic donors immunized with polyoma virus; none developed tumours. Similar results were obtained in mice deliberately infected with polyoma virus but not with leprosy organisms. Passive transfer of antibody before but not after virus inoculation prevented tumour formation in immunosuppressed recipients. Virus infection in thymectomized, lethally irradiated and bone marrow reconstituted mice resulted in only a very low incidence of tumours. These results emphasize the role of immunological surveillance in preventing polyoma tumour formation under natural conditions."} +{"text": "A prolonged ascitic leak through abdominal drains is a source of postoperative complications and ofprolonged postoperative hospital stay after liver resection for hepatocellular carcinoma (HCC) incirrhotic patients. Therefore we elected to abstain from routine abdominal drainage in the last 14resections in cirrhotic livers. A significantly smaller number of patients had postoperative complicationsfollowing liver resections without drainage (7%) than historical controls with abdominal drainage . The number of complications related to ascites was significantly greater in patients withabdominal drainage (76%) than without . Postoperative hospital stay was also significantlylonger following resections with abdominal drainage (19 \u00b1 4 days) than in patients without . The long postoperative hospital stay in patients with abdominal drainage wasrelated to ascitic discharge for a mean period of 13 \u00b1 10 days. No clinically significant accumulationof ascites was noted in patients without drainage. A more frequent utilization of hepatic vascular inflowocclusion did not account for the better results in the group of patients without drainage. These resultssuggest that routine abdominal drainage should not be used following liver resection for HCC incirrhotic patients. This appears to be another of the technical details improving postoperative resultsin these patients."} +{"text": "A 51 year old lady with chronic active hepatitis presented with massive lower gastrointestinal tract bleeding. Angiography demonstrated a solitary varix in the caecum which was found at laparotomy to be entering the bowel wall at the site ofadhesions from a previous appendicectomy. The portal pressure was found to be raised.Aright hemicolectomy stopped the blood loss, but she subsequently died ofliver failure. Solitary colonic varicesassociated with adhesions are extremely rare and their optimal management has not been established."} +{"text": "Increasing experience with major hepatic resections has stimulated the development of improvedresectional techniques and tools. A new high velocity water jet dissector is reported which offerssignificant advances over previously developed ultrasonic and low pressure water jet machines. It hasbeen successfully used in 8 major hepatic resections with minimal blood loss, excellent visibility andwithout complications. The dissector is also of value in the exposure of intrahepatic bile ducts for biliaryentericanastomosis."} +{"text": "The concentration of circulating ferritin was measured in 250 normal adult women and 229 women presenting with early breast cancer. Ferritin concentrations are higher in cancer patients than in normal women. Patients with an intial circulating ferritin concentration above 200 mug/1 have a higher tumour recurrence rate during the subsequent 4 years."} +{"text": "Idarubicin is a highly lipophilic anthracycline and appears effective against tumours resistant to conventional anthracyclines. Confocal microscopy demonstrates predominantly cytoplasmic idarubicin accumulation. This distribution is unaltered by resistance status or the resistance reversing agent verapamil. Our results contrast with studies on conventional anthracyclines and suggest that nuclear accumulation may not be a prerequisite for anthracycline cytotoxicity."} +{"text": "A randomized cross-over clinical and endoscopic evaluation of 85 Ugandan patients showed that esophageal candidiasis in AIDS patients with oral candidiasis could be managed without endoscopy and biopsies. Oral lesions, especially when accompanied by esophageal symptoms, were sufficient for diagnosis. Miconazole was more effective than nystatin in treating esophageal candidiasis and could be a valid alternative to more expensive azolic drugs in developing countries."} +{"text": "Thirteen patients underwent hepatic cryotherapyand synchronous colonic resection. Two of the ninepatients developed hepatic abscess \u2013 this is a rarecomplication of cryotherapy alone."} +{"text": "Ziprasidone, an atypical antipsychotic, widely in use because of its better side effect profile. Recently some researchers have raised doubts about their association with sudden cardiac death. Here the authors present such a case report with Ziprasidone in a Schizophrenic patient and it is being suggested that psychiatrist must remain vigilant about cardiac harmful effects with newer antipsychotics for the better care of patient."} +{"text": "Coturnix coturnix Japonica) by intra-testicular injections of 3% zinc chloride solution during a period of testicular growth artificially stimulated by increased photoperiod. These tumours resemble those previously induced by similar methods in domestic fow1 and have histological features in common with spontaneous testicular teratomas in man.Teratomas have been induced in Japanese quail ("} +{"text": "We describe a case of giant cavernous haemangioma of the liver with disseminated intravascular coagulopathy (Kasabach-Merritt syndrome) which was cured by orthotopic liver transplant.A 47 year old man presented with bleeding and tender massive hepatomegaly after tooth extraction. Investigations showed disseminated intravascular coagulopathy and a giant hepatic haemangioma involving both lobes of the liver. Initial treatment failed to resolve the coagulopathy and liver resection was attempted. At laparotomy the turnout was unresectable and the only option for cure was to offer a liver transplantation. The orthotopic liver transplant was performed 20 days after initial laparotomy. Subsequently, all coagulation parameters returned to normal and the patient remains well after 12 months. Orthotopic liver transplant can be considered for giant hepatic haemangioma with Kasabach-Merritt syndrome when resection is necessary and a partial hepatectomy is not technically feasible."} +{"text": "Hepatic angiomyolipomas are rare benign tumours. First reported by Ishak in 1976. Since then, theworld literature showed only 32 cases including 8 autopsy findings. In this paper a retrospective analysisof the published data will be presented and the first report ofthe preoperative colour doppler andintraoperative sonography appearances will also be described."} +{"text": "Drug therapy may be effective in controlling symptoms but thefrequent coexistence of endometriosis and the lack of controlledstudies make their efficacy difficult to quantify. Danazol IUD hasbeen shown to reduce symptoms. Conservative surgery involvingendomyometrial ablation, laparoscopic myometrialelectrocoagulation or excision has proven to be effective in morethan 50% of patients, although follow up has been restrictedto three years. Arterial uterine artery embolization is a newtechnique which may be tried before considering hysterectomy.Hysterectomy may still be necessary in severe cases ofadenomyosis."} +{"text": "Our results suggest thatthe additional signals provided by costimulatory ligands are not required for TCR-mediatedpositive selection, although other ancillary signals provided by thymic epithelial cells maybe involved.We have investigated the possibility that the costimulatory signals required for activation ofmature T cells also play a role in providing differentiation signals for positive selectionduring T-cell development. We show that purified MHC Class II"} +{"text": "ICRF 159 and Triton WR 1339 have been examined for their ability to suppress subcutaneous growth and pulmonary metastases from a transplanted rat epithelioma. Neither compound influenced subcutaneous tumour development or reduced the propensity to metastasize when administered in regimens reported to suppress pulmonary, lymph node or intracerebral metastases in other experimental system."} +{"text": "Splenic arteriovenous fistula is a rare but curable cause of portal hypertension. This report describes apatient with such a disorder, presenting with bleeding esophageal varices and ascites. It emphasises theimportance of performing selective catheterization of the celiac and superior mesenteric artery in allpatients with signs of portal hypertension without evidence of chronic liver disease. Etiopathology andmanagement are discussed."} +{"text": "Percutaneous endoscopic gastrostomy (PEG) has been widely accepted for patients who haveno swallowing ability but have an intact gut. Its clinical application is mainly for nutritionalsupport and decompression of the intestine in patients with bowel obstruction. In this paper, wereport external pancreatic juice drainage through a percutaneous endoscopic drainage tube ina patient with postoperative pancreatic juice leakage. Soon after this procedure, pancreaticjuice leakage subsided. This procedure was minimally invasive for the patient and may be anew application of PEG to maintain the good quality of life (QOL) in a patient with pancreaticjuice leakage."} +{"text": "An immunoadsorbent technique is described whereby tumour-specific antibodies may be isolated. Extracts from normal human lung tissue were pooled and bound to cyanogen bromide activated Sepharose 4B. Antisera raised in rabbits to a variety of extracts from human bronchogenic carcinoma were passed through these immunoadsorbent columns to yield antisera specific for tumour-associated antigens as demonstrated by immunodiffusion and immunoelectrophoresis."} +{"text": "Factors other than antimicrobial activity of soaps and antiseptic agents used for hand hygiene by health personnel play a role in compliance with recommendations. Hand hygiene products differ considerably in acceptance by hospital personnel. If switching from a nonmedicated soap to an antiseptic agent or increased use of an existing antiseptic agent for hand hygiene prevented a few more infections per year, additional expenditures for antiseptic agents would be offset by cost savings."} +{"text": "In panels A and B of Figure 2, the legend symbols have been switched. Filled squares should represent Alkaline CFGE and filled triangles should represent Neutral CFGE. Please view the correct figure here:"} +{"text": "We report a case of fulminant supraglottitis with dramatic external cervical swelling due to associated cellulitis. Blood cultures were positive for Neisseria meningitidis. The patient recovered completely after emergency fiberoptic intubation and appropriate antibiotic therapy. We summarize five other cases of meningococcal supraglottitis, all reported since 1995, and discuss possible pathophysiologic mechanisms."} +{"text": "Gene regulatory networks are a major focus of interest in molecular biology. Acrucial question is how complex regulatory systems are encoded and controlled by thegenome. Three recent publications have raised the question of what can be learnedabout gene regulatory networks from microarray experiments on gene deletionmutants. Using this indirect approach, topological features such as connectivity andmodularity have been studied."} +{"text": "Expert opinion backed by an evidence base of limited quantity and quality would suggest that dismembered pyeloplasty using an open or laparoscopic approach represents optimum treatment for patients with primary PUJ obstruction. For thos"} +{"text": "This contraction caused deformation of neighbouring cells leading to a heterogeneous strain field throughout the monolayer. Quantification of the strain fields in the monolayer using digital image correlation revealed local strains much higher than threshold values typically reported to stimulate extracellular bone matrix productionin vitro. This use of point targeting with femtosecond pulse lasers could provide a new method for stimulating cell activity in orthopaedic tissue engineering.A study demonstrating how ultrafast laser radiation stimulates osteoblasts is presented. The study employed a custom made optical system that allowed for simultaneous confocal cell imaging and targeted femtosecond pulse laser irradiation. When femtosecond laser light wasfocused onto a single cell, a rise in intracellular Ca"} +{"text": "Shared authorship was inadvertently omitted for the first two authors. Yuehui Wang and Sarbani Ghoshal should be listed as co-first authors on this article."} +{"text": "Our preliminary results suggest that laparoscopiccholecystectomy is of clinical benefit as compared to classic cholecystectomy since it reduces the surgicaltrauma, limiting weight loss and shortening the hospital stay.Twelve selected patients undergoing cholecystectomy were operated in a prospective randomised studyby laparoscopy (CO"} +{"text": "Dear Editor,et al.,[We read with interest the article by Panda et al., wherein 3F8 gas exchange and postoperative prone positioning. This prevents recurrent macular detachment, which is common in this condition.Fibrin glue has exciting intraoperative applications during vitreoretinal surgeries as well. It has been found to not have any toxic effects on retinal function or structure in a rabbit model. The intr3Fibrin glue has also been used to stabilize keratoprosthetic devices during vitreoretinal surgeries."} +{"text": "The retrospective analysis of 250 breast cancer patients with disseminated disease provided evidence that the increase in CA 125 serum levels in these patients was caused by lung metastases or pleural effusions. Seven patients with lung metastases and pleural involvement had elevated CA 125 levels, while in four patients with lung metastases but without pleural effusions CA 125 levels remained normal. In patients with only bone or liver metastases CA 125 levels were usually not elevated. If these results are confirmed, CA 125 would be the first tumour marker in breast cancer whose levels could be associated with one single site of metastases."} +{"text": "BR6 female mice treated with a mixture of hormones, developed mammary tumours earlier than untreated virgin animals. Implantation of ectopic pituitaries also increased tumour incidence and reduced the age at which tumours first appeared. This effect was obtained even in the absence of ovaries. Neither hormone treatment nor ectopic pituitaries succeeded in producing tumours as early as they appear in breeding females."} +{"text": "Four persons became ill with trichinellosis after eating meat from a wild boar hunted in Camargue, France. Nonencapsulated larvae of Trichinella pseudospiralis were detected in meat and muscle biopsy specimens. The diagnoses were confirmed by molecular typing. Surveillance for the emerging T. pseudospiralis should be expanded."} +{"text": "There is conflicting evidence concerning the effects of portal hypertension on the gastric mucosa. Thispaper summarises the histological and haemodynamic alterations which are present in both human andexperimental portal hypertension. Despite the fact that histological studies suggests that the gastricmucosa is an oedematous plethoric structure in portal hypertension, haemodynamic studies show thatgastric mucosal blood glow is at least maintained if not increased in portal hypertension. The term\u201cactive\u201d rather than \u201cpassive\u201d congestion is a more appropriate description of the basic change presentin the gastric mucosa in portal hypertension."} +{"text": "Benigncomplications were equally frequent in both Groups,although additional sedation was more common inthe sclerotherapy Group. We concluded that bothtreatments are equally effective in the eradication ofoesophageal varices, although banding ligation isbetter tolerated by the patient and probably faster.Endoscopic sclerotherapy and banding ligation arethe two preferred methods to treat oesophagealvariceal bleeding. There are many reports dealingwith such treatment in cirrhotic patients but we do notknow how good they are to treat varices secondary toother forms of portal hypertension. Schistosomiaismansoni is the main cause of portal hypertension andoesophageal varices in Brazil. We performed aprospective randomised study to compare: 1) theefficacy of both treatments in eradicating oesophagealvarices, and 2) complications secondary to bothtreatments. Forty patients were divided in twoGroups. Both sclerotherapy and banding ligationwere performed until variceal eradication. There wereno severe complications. Variceal eradication wasfaster obtained with banding ligation than sclerotherapyalthough there was no statistical difference (meannumber of sessions 3.05"} +{"text": "A questionnaire was sent to 53 patients who had undergone an upper gastrointestinalendoscopy under total intravenous anaesthesia (TIVA) using intermittent Propofol. All of thepatients would accept the same technique again. Out of 20 patients who had previously had theprocedure performed under Diazepam sedation, 18 preferred the use of Propofol.This technique can only be used with an anaesthetist present."} +{"text": "Granulosa cell tumors are rare benign tumors which may be found throughout the body. Rare cases areisolated within the biliary tree. If completely resected, surgical excision is curative.\t\tA case of biliary duct granulosa cell tumor is presented with review of the world\u2019s literature on thistopic."} +{"text": "Salmonella typhi have been well documented. There are onlytwo previous case reports of intrauterine infection with non-typhoidal species. This paper presents athird case of maternal septicemia followed by neonatal sepsis with Salmonella heidelberg.Maternal and neonatal infections with"} +{"text": "We propose a denoising algorithm for medical images based on acombination of the total variation minimization scheme and thewavelet scheme. We show that our scheme offers effective noiseremoval in real noisy medical images while maintaining sharpnessof objects. More importantly, this scheme allows us to implementan effective automatic stopping time criterion."} +{"text": "Survival following major juxtahepatic venous injury is rare in blunt liver trauma despite the use ofintracaval shunting. Prolonged liver arterial inflow control, total hepatic venous isolation and lobectomywithout shunting was used in a patient to repair a combined vena caval and hepatic venous injury afterblunt liver injury. An extended period of normothermic hepatic ischemia was tolerated. Earlyrecognition of retrohepatic venous injury and temporary liver packing to control bleeding and correcthypovolemia are essential before caval occlusion. Hepatic vascular isolation without shunting is aneffective simple alternative technique allowing major venous repair in complex liver trauma."} +{"text": "Mycobacterium butyricum gave better transplant immunity to tumour cell challenge than tumour extracts alone. Mice immunized with Mycobacterium butyricum alone prior to challenge with tumour cells, did not show any significant difference in the incidence of tumours from control mice.Transplant immunity to adenovirus 12-induced tumour cells was demonstrated in CBA mice which had been previously immunized with extracts of homologous tumour cells. Immunization of mice with tumour cell extract together with heat-killed"} +{"text": "The relative efficacies of cytotoxic chemotherapy regimens in the treatment of advanced breast cancer are generally assessed by comparing response rates in randomised trials. Treatment attempts to prolong survival but trials rarely demonstrate a statistically significant survival advantage: it has been argued that chemotherapy does not prolong survival. The correlation between response rates and survival has been examined by reviewing 79 comparisons between arms with unequal response rates in 50 published trials of chemotherapy in advanced breast cancer. In 73% of comparisons the group with the higher response rate also demonstrated the longer median survival (P less than 0.001). Weighted linear regression showed a statistically significant relationship between relative response rates and survival (P less than 0.001). The number of patients in a comparison did not influence this relationship."} +{"text": "Serum retinol levels were determined by a fluorometric method in patients with colorectal cancer or polyps and those with inflammatory bowel disease. Serum retinol levels in patients with benign or malignant colorectal polyps and stage B cancer (modified Dukes' classification) were similar to those found in controls. By contrast, serum retinol levels were significantly lower in patients with Dukes' stage C or D. Among cancer patients that were followed after surgical treatment serum retinol levels did not differ significantly from those found in controls. Patients who died of metastases during follow-up possessed very low serum retinol levels. These findings suggest that a decreased serum retinol level in cancer patients is a consequence rather than a precursor of the neoplastic process. Furthermore, this study suggests that the marked decrease in serum retinol level might be an indicator of poor prognosis in colorectal cancer patients after surgery."} +{"text": "Acute acalculous cholecystitis may develop in patients suffering from necrotizing pancreatitis.Conversely, acute pancreatitis may complicate acute gallbladder disease. We present a case that lendssupport to the existence of another possibility: gallbladder necrosis caused by direct extension of thenecrotizing pancreatitic process."} +{"text": "We present a case of adult hepatoblastoma. This young female presented with severe acutecholangitis. Preoperative diagnosis was common bile duct (CBD) obstruction with portal veinthrombosis. On exploration she had a tumor mass in the CBD. The unusual features of this caseare discussed in this report."} +{"text": "Life course perspectives suggest that the consequences of being mothers\u2019 favorite children will vary, depending on the expectations associated with that status at different points in mothers\u2019 lives. We propose that maternal favoritism predicts depressive symptoms only when mothers are older and at greater risk of facing losses for which favored children perceive they should provide additional emotional support. To address this question we used mixed-methods panel data collected from 479 adult children as part of the Within-Family Differences Study. Multi-level regression analyses revealed that perceiving oneself as the child most emotionally close to the mother did not predict depressive symptoms for daughters or sons at T1, but was a predictor of daughters\u2019 depressive symptoms at T2. Qualitative analyses revealed that by T2, favored daughters had begun perceiving themselves as emotional caregivers when mothers faced age-related losses, whereas favored sons did not hold these role perceptions at either wave."} +{"text": "Following publication of the original article , the autThe names appeared on the article as follows:Ippoliti RobertoFalavigna GretaMontani FlorianaRizzi SilviaThey correct names are as follows:Roberto IppolitiGreta FalavignaFloriana MontaniSilvia Rizzi"} +{"text": "Initials were used instead of full author names in the above mentioned article.Cambridge University Press apologises for this error, which has since been rectified."} +{"text": "It was highlighted that the original article was missDetails as to simulationsSupporting Information.docxPython scripts for running analysisUtilities.zipThis Correction article includes the missing Additional files Additional file 2. Simulations details.Additional file 3. Python scripts for running analysis."} +{"text": "In recent years, several studies have addressed the positive effects of levosimendan upon renal function. We sought to summarize the recent findings in order to understand by which mechanism levosimendan is improving renal function. In acute decompensated heart failure, levosimendan has an immediate renoprotective effect by increasing renal blood flow (RBF) through selective renal arterial and venous vasodilation . In a re"} +{"text": "In recent years evidence has accumulated that genes involved in circadian clock control play a role as tumor suppressors. Strong evidence has been presented by Broadberry and colleagues who published an article about disrupted circadian clocks in breast cancer (Broadberry et al., 2018; Grundy"} +{"text": "The human liver consists of approximately one million liver lobules, which are known to show metabolic zonation . It wilThe author declares no conflict of interest."} +{"text": "Flotation through a slightly hyperosmotic discontinuous gradient iodixanol achieves a much higher recovery of islets of an improved viability than the customary method using sedimentation on to a diatrizoate/polysaccharide barrier. Flotation techniques achieve an enhanced separation of the islets from any residual digestive enzymes and from acinar cells. The method has been extended to human pancreas."} +{"text": "To evaluate the impact of early life racial discrimination (ELRD) on mental health among Black adults. Data were from the Nashville Stress and Health Study (n=618). OLS regression models examined the relationship between ELRD and adult psychological distress; logistic regression estimated the probability of past-year major depressive disorder (MDD). We also assessed whether ELRD moderated the relationship between adult discrimination and mental health. Childhood and adolescent ELRD were associated with adult distress. Individuals who experienced childhood ERLD had 88% lower odds of adult MDD than individuals with no ELRD. Significant interaction analyses showed that ELRD was generally protective against adult discrimination. While ELRD importantly shapes distress and MDD among Black adults, patterns vary by outcome. Results indicate that adult distress and MDD develop through cumulative adversity processes that are further influenced by sensitive periods in the life course."} +{"text": "Dear Editor,The study by Kurtz et al. shed ligThe mixed methods study highlighted that students found writing questions a beneficial tool . HoweverMaximum benefit from these devised questions would require questions to cover universally challenging themes identified by students. As question authors have researched their difficult topic in detail, relevant information found should be included alongside answers. Students benefit from collaborative reviews so may aIn addition to concerns about time spent writing questions, there may be limitations with different question styles. Imperial College School of Medicine regularly tests students with Single Best Answer questions (SBAs) rather than MCQs. SBAs are an excellent tool to consider similar differentials and focus on the most likely and \u2018best\u2019 option. However, developing these questions is difficult and students may have insufficient knowledge to consider which option is first-line and appropriate plausible detractors . HoweverTo conclude, as highlighted by Kurtz et al , creatin"} +{"text": "A surgical procedure may lead to unusual and unexpected clinical scenario. Good medical practice should always keep it in mind. So, a broken sternal steel wire was the rare cause of massive emphysema. A surgical procedure may lead to unusual and unexpected clinical scenario. Good medical practice should always keep it in mind. So, a broken sternal steel wire was the rare cause of massive emphysema. Robicsek closure is frequently used to restore sternal integrity after wound complications. We report an unusual case of massive subcutaneous emphysema following Robicsek closure that required urgent surgical revision.A 71\u2010year\u2010old diabetic woman, with a recent history of coronary artery bypass graft using the left internal mammary artery, was re\u2010admitted two weeks after surgery for aseptic sternal wound dehiscence and treated using the Robicsek technique.Postoperative chest X\u2010ray had shown the integrity of the Robicsek closure Figure A. SeveraNatalia Pavone and Federico Cammertoni: wrote the paper. Massimo Massetti and Piergiorgio Bruno: supervised the paper. Giovanni Alfonso Chiariello e Giovanni Graziano: collected data and images."} +{"text": "China*Contributed equallyThe authors regret their oversight in this regard, and apologize for any inconvenience caused."} +{"text": "The literature documents mixed findings regarding how helping others influences individuals\u2019 mental and physical health. We assessed various types of support that older adults offered and examined how helping others was associated with older adults\u2019 daily mood and physical activity. This study utilized data from the Daily Experiences and Well-being Study, where 293 participants aged 65+ reported on their helping behaviors and mood at the end of each day across 5 days. Participants also wore Actical accelerometers to track physical activity. Multilevel models revealed that older adults reported greater negative mood and less physical activity on days when they provided emotional support. Yet, giving advice was associated with increased positive mood that day. Moreover, older adults spent less time being sedentary on days when they offered practical help. This study offers insights into psychological and health consequences of helping others by examining older adults\u2019 everyday lives."} +{"text": "This paper describes data of post-release mitigation strategy and its effect for chemical process. The data in this paper is associated with the article entitled \u201cDamage reduction strategies against chemical accidents by using a mitigation barrier in Korean chemical risk management\u201d. The data includes computational fluid dynamics (CFD) simulation result for vapor cloud explosion accident scenarios. Simulations with suggested mitigation strategy and without the mitigation strategy were conducted. The data is expected to good reference for developing chemical plant mitigation plan. VCE accident is also important consideration for developing chemical accident mitigation strategy. The article entitled \u201cDamage reduction strategies against chemical accidents by using a mitigation barrier in Korean chemical risk management\u201d 22.1Simulation conditions for column are shown in The explosion accident occurs when composition of xylene is within LFL and UFL. 2.2With the developed VCE scenario, explosion simulation is conducted. Two simulation is shown in this study. One is explosion simulation without the mitigation barrier, the other is explosion simulation with the mitigation barrier."} +{"text": "The literature links social integration to better physical health, but little research asks how contact with diverse social partners influences older adults\u2019 physical activity in a daily context. We examined this link using the Daily Experiences and Well-being Study and explored whether this link varied by gender. The sample included 175 older women and 138 older men who reported their contact with close partners and not-close partners throughout each day across 5 days. Participants also wore Actical accelerometers to track physical activity. Multilevel models revealed significant gender differences. Older men had reduced physical activity when having contact with close partners, whereas older women maintained physical activity during such contact. Both older men and women had increased physical activity when having contact with not-close partners, but this link was stronger for men. This study advances our understanding of gender differences in older adults\u2019 social experiences and well-being."} +{"text": "Next generation sequencing has provided important insight into genome dynamics during cancer progression, reflected in consecutive acquisition of mutations and chromosomal aberrations and expansion of particular cancer subclones based on a distinctive genomic profile . Alongsi"} +{"text": "Each of these factors may impact on CT prevalence among those tested in GP surgeries or GUM clinics.White and Lewis comment"} +{"text": "The Funding statement is incorrect. The correct Funding statement is as follows: Rodoniki Athanasiadou was partially supported by RiskEcon\u00ae Lab for Decision Metrics @ Courant Institute of Mathematical Sciences NYU."} +{"text": "Following publication of the original article , the autIncorrect name in the original article:\u2003Antoninus Obinna Ezekwu.Correct name:\u2003Antoninus Obinna Ezeukwu.The original article has been corrected."} +{"text": "Complete immunization against hepatitis A requires 2 doses of a monovalent vaccine or 3 doses of a combined hepatitis A and hepatitis B vaccine; approximately 90% of vaccinated persons achieve protective antibody levels after a single dose of either product occurred among persons with HIV infection, six of whom had received a partial or complete vaccination series before acute HAV infection . All sixPrevious vaccination for hepatitis did not reliably provide protection among some persons with HIV infection. Approximately half of the patients with HAV and HIV infections were previously vaccinated. The Advisory Committee on Immunization Practices does not currently address specific PEP considerations for persons with HIV infection who have been fully vaccinated against hepatitis A ("} +{"text": "We read the paper by Oliveira C et al. The authors' findings regarding maternal position contradict much published studies, which demonstrate that compared to the left lateral position, a supine maternal position results in reduced maternal cardiac output"} +{"text": "Cold Spring Harbor Molecular Case Studies, we have included the first publication or request a custom report from ClinGen , which will also highlight variants in which the submitter has an outlier interpretation compared to other submitters (Cold Spring Harbor Molecular Case Studies.Clinical laboratories can obtain reports of their variant interpretation differences from the ClinVar Miner website (bmitters . Studiesbmitters . We encoThe author has declared no competing interest."} +{"text": "This case illustrates surgical technique for wide neck aneurysm clipping in a rotated complex and how to manage intraoperative aneurysm rupture while maintaining hemostasis . This case is a presentation of one possible approach for repair of an unruptured rotated anterior communicating artery aneurysm.This video was deemed IRB exempt by the Institutional Review Board (IRB) as it is considered a case report, which does not require IRB approval or patient consent. All ethical rules and guidelines were followed.None declared.OC: performed the procedure and provided video narration. GG: performed critical video editing and preparation for publication.\u00a0Click here for additional data file."} +{"text": "A rare case of benign peritoneal strumosis was screened for driver mutations in genes relevant to currently approved cancer therapies. Therefore, three formalin fixed paraffin embedded issue sections were screened with the GeneReader Actionable Insights NGS panel for the occurrence of driver mutations. Several mutations were identified in drug-targetable genes, such as ALK, EGFR, and BRAF. The majority of identified mutations were single nucleotide variant, but also a insertion/deletion mutation was identified. The presented dataset is the first NGS dataset available from a patient with benign peritoneal strumosis. Specifications TableValue of the data\u2022The knowledge on molecular alterations occurring in benign peritoneal strumosis is limited, the present data extent this limited knowledge.\u2022The presented data could trigger further (multicenter) studies on benign strumosis.\u2022The data show that no benign peritoneal strumosis can occur without \u201cclassical\u201d targetable mutations.1A dataset obtained by next generation sequencing of drug-targetable genes of a clinical case with benign peritoneal strumosis is presented. Benign peritoneal strumosis is a clinical condition that is rarely observed The dataset was obtained from histologically confirmed formalin fixed paraffin embedded tissue samples of a 33 year old Caucasian woman with benign peritoneal strumosis. To date there were no datasets available that reported the mutational landscape of drug-targetable genes in clinical cases of benign peritoneal strumosis.We identified several mutations that to date are classified as mutations with uncertain pathogenic role . In part2In order to identify putative therapy targets and to further characterize this rare clinical condition we have performed a Next Generation Sequencing (NGS) analyses using the GeneReader Actionable Insights panel as recently described"} +{"text": "Not all complications from transradial access can be prevented, even with diligent patient selection and preprocedure planning. This brief visual report offers technical suggestions to reverse knots and kinks encountered during catheter manipulation for endovascular transradial cerebral procedures. Not all complications from transradial access can be prevented, even with diligent patient selection and preprocedure planning. This brief visual report offers technical suggestions to reverse knots and kinks encountered during catheter manipulation for endovascular transradial cerebral procedures. A growing body of evidence supports the adoption of transradial artery access in cerebral interventions due to reduced rates of complications, bleeding, and improved patient satisfaction when compared to transfemoral approaches.None declared.All three authors were operators in these cases and assisted in manuscript and image preparation."} +{"text": "Dear Editor:We thank Rahman and Ireen for their interest in our recent publication . Indeed,"} +{"text": "Corrigendum: A previous version of this article contained a wrong affiliation of Kamal Niaz. Please refer only to these revised affiliations which are corrected accordingly."} +{"text": "NMR spectroscopic studies revealed that the glycoconjugate consists of two diastereomers of -open mono-adducts. The electronic properties were characterized using Vis/NIR absorption spectroscopy and electrochemical measurements. This study demonstrates that glycosylidene carbene is useful to incorporate carbohydrate moieties onto endohedral metallofullerene surfaces.Endohedral metallofullerene glycoconjugates were synthesized under mild conditions by carbene addition using appropriate glycosylidene-derived diazirine with La We believe that this work paves the way for development of functionalized EMFs for biological and pharmacological applications.The results of this study demonstrate clearly that addition of electrophilic carbene is a powerful means to functionalize EMFs. The glycosilydene carbene generated"} +{"text": "Drosophila. We review what is known about how cells translate an unknown signal into asymmetric cytoskeletal reorganization. We then discuss how the vertebrate processes of convergent extension and cochlear hair-cell development may relate to Drosophila PCP signaling.Epithelial cells and other groups of cells acquire a polarity orthogonal to their apical\u2013basal axes, referred to as Planar Cell Polarity (PCP). The process by which these cells become polarized requires a signaling pathway using Frizzled as a receptor. Responding cells sense cues from their environment that provide directional information, and they translate this information into cellular asymmetry. Most of what is known about PCP derives from studies in the fruit fly,"} +{"text": "Hearing care services for older adults with hearing aids are underutilized and are not covered by the Medicare program. Little information exists to the value of hearing care services for older adults with hearing aids. Using the Medicare Current Beneficiary Survey 2013, we conducted a cross-sectional analysis of the impact of hearing care services use on Medicare spending among those with hearing aids. Older Medicare beneficiaries with hearing aids that received hearing care services in the previous 12 months were propensity score matched to those who did not receive services. Average annual Medicare spending was $8196 (CI:$6670-$9723) among Medicare beneficiaries who used hearing care services and $10,709 (CI:$8878-12541) among matched controls. Spending differences were driven by higher skilled nursing facility and home health spending among matched controls. Increasing access to hearing care services among Medicare beneficiaries with hearing aids may provide value to the health care system and Medicare program."} +{"text": "The eighth author\u2019s name was entered into the submission system incorrectly and therefore was indexed incorrectly on PubMed. The correct name is Mohammad Hassan Murad. The correct indexing in PubMed should read Murad MH."} +{"text": "Following publication of the original article [1], an error in one of the author names was reported. In this Correction the incorrect and correct author name is listed. The original article has been updated.Woo Wan KimIncorrect author name upon publication:Soo Wan KimThe correct author name:"} +{"text": "The top blot shown in The supplemental PDF has been corrected. These errors appear only in PDF versions downloaded on or before March 8, 2019."} +{"text": "China*Contributed equallyThe authors regret their oversight in this regard, and apologize for any inconvenience caused."} +{"text": "Studies suggest conversation improves cognitive skills among older adults. While contact with family members is common in late life, contact with friends and acquaintances is relatively less frequent. Yet, we know little about how often older adults engage in conversation when they have contact with different social partners. This study used data from the Daily Experiences and Well-being Study to investigate how older adults talk with different social partners on a daily basis. Participants (N = 303) completed an initial interview about their social partners and reported on their contact with each social partner in ecological momentary assessments every 3 hours across 5 to 6 days. Participants also wore Electronically Activated Recorders (EAR), which captured snippets of their daily conversation. Findings revealed that contact with family members occurred most often, with less frequent contact with other social partners , and then friends. Multilevel models also revealed that participants talked more when they had contact with their friends than when they had contact with family members or other social partners. Results from these multiple methods suggest that daily contact with friends could potentially encourage conversation that may facilitate cognitive functioning among older adults."} +{"text": "Xu et al. conclude that changes in gut microbiota in neurocritically ill patients seem to have an impact on their mortality . We woulXu also suggested that critical illness could lead to microbial translocation, potentially explaining the association between specific pathogens and mortality . Another"} diff --git a/PMC_clustering_718.jsonl b/PMC_clustering_718.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..fd641cee3c59965b36e60ad98aeba93c7d7085ea --- /dev/null +++ b/PMC_clustering_718.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1716e3f6d0c711273942945353b5002bce60d1cf850d541889dde57eec6c2911 +size 60868449 diff --git a/PMC_clustering_719.jsonl b/PMC_clustering_719.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..5677c6ddb44e78fd98a3b779f167340cdc2db745 --- /dev/null +++ b/PMC_clustering_719.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0a183772c6ac66f34fa6c5636325133bd7db90e9eb992fcb2be46be726ce479d +size 17372018 diff --git a/PMC_clustering_720.jsonl b/PMC_clustering_720.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..1cb55c63c794157a75d5530b95ae00dafa73dd30 --- /dev/null +++ b/PMC_clustering_720.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a515ff212b9b08a5cfd5925329fd5777224f55677dbe72db814b2ae59c90c0d9 +size 65766134 diff --git a/PMC_clustering_721.jsonl b/PMC_clustering_721.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..6c06f3cd1668fe756bdc001bffda74bca9deb9f1 --- /dev/null +++ b/PMC_clustering_721.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:52417c9765e2b0f515735b3a5b14e652cdb54496b3d30f2fd6e7358bdf507ada +size 47197363 diff --git a/PMC_clustering_722.jsonl b/PMC_clustering_722.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..302cb8a4d7859d0013c1c0cda4cdea9d57c29a11 --- /dev/null +++ b/PMC_clustering_722.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:63d0843ab0e432d0206d2e3ce19b093a4bc74c9b1586282d4c37817282f7bc78 +size 34108902 diff --git a/PMC_clustering_723.jsonl b/PMC_clustering_723.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..0a5e4cb93d4352ca97d17277a32f6442c8d49e6b --- /dev/null +++ b/PMC_clustering_723.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2f187e1e689efa1f3b4f49c4a03fa0621b6cd7d9c70d918875b5cae985cdbe4c +size 72411681 diff --git a/PMC_clustering_724.jsonl b/PMC_clustering_724.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..45dca2794f9dd9ea0ddfe51abf22027a21f3dfc2 --- /dev/null +++ b/PMC_clustering_724.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f8fcf45c333708a9a542cdcf056a5366620b2c003644b64c4ca69bb9035efbab +size 107054648 diff --git a/PMC_clustering_725.jsonl b/PMC_clustering_725.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..516657095246bae05c76d380733cc76dd48a846b --- /dev/null +++ b/PMC_clustering_725.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:75b6fab9041b8dd5cf292c96292b785ecd9defd0263addfa53a2e28a3b75be3b +size 101747394 diff --git a/PMC_clustering_726.jsonl b/PMC_clustering_726.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..2e9ca1a0ddeeb0b83bbe074035cdc3e5bd28782a --- /dev/null +++ b/PMC_clustering_726.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fa011abc78e8482dabf30563c8bfb407929c28b1141396d0d045ef451cb25b01 +size 68386094 diff --git a/PMC_clustering_727.jsonl b/PMC_clustering_727.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..d18d137b824e63a89cdbbe7ae71dbe40b0057f76 --- /dev/null +++ b/PMC_clustering_727.jsonl @@ -0,0 +1,1246 @@ +{"text": "P=0.015), T stage (P=0.006), lymph node metastasis (P=0.028) and the worst prognosis of PC patients (P=0.004). Meanwhile, a positive relationship between FAM172A and E-cadherin (E-cad) was observed in clinical samples, which contributed to the better prognosis of PC patients (P=0.014). FAM172A silencing induced EMT in both AsPC-1 and BxPC-3 cells, including inducing the increase of Vimentin, MMP9 and pERK and the decrease of E-cad and \u03b2-catenin expression, stimulating EMT-like cell morphology and enhancing cell invasion and migration in PC cells. However, MEK1 inhibitor PD98059 reversed FAM172A silencing-enhanced EMT in PC cells. We conclude that FAM172A inhibits EMT of PC cells via ERK-MAPK signaling.FAM172A, as a newly discovered gene, is little known in cancer development, especially in pancreatic cancer (PC). We investigated the potential role and molecular mechanism of FAM172A in epithelial to mesenchymal transition (EMT) in both human clinical samples and PC cells. FAM172A was downregulated in human PC tissues compared with that in non-cancerous pancreas cells by immunohistochemistry and qRT-PCR. FAM172A expression was negatively associated with tumor size ( Summary: FAM172A inhibits EMT in pancreatic cancer via specifically regulating ERK-MAPK signaling. Pancreatic cancer (PC), as a deadly malignancy, ranks as the fourth leading cancer-related cause of death in Europe . It is aFamily with sequence similarity 172 member A (FAM172A), cloned from human aortic tissues, is subsequently observed in human endothelial and vascular smooth muscle cells, and macrophages . HoweverThe ERK-MAPK signaling plays a significant role in regulating cell proliferation, differentiation, survival, migration senescence and apoptosis via transmitting signals from cell surface receptors . ERK-MAPP<0.01) (P=0.002) A. In mosP<0.01) B, and viP<0.01) C. SpearmP=0.002) .Fig. 1.P=0.015), T stage (P=0.006), lymph node metastasis (P=0.028), but had no relationship with age, gender, tumor location, differentiation, vascular invasion and preoperative CA199 level in PC patients (P>0.05) (P=0.003) (P=0.159) (P=0.014) (P=0.020) (Chi-squared test showed that FAM172A was negatively associated with tumor size ((P>0.05) . PatientP=0.003) D. ThoughP=0.159) E, patienP=0.014) F. In mulP=0.020) .Table\u00a02.P=0.002) A. Both FP=0.002) B,C. The in vitro.AsPC-1 and BxPC-3 cells with high FAM172A expression were used for FAM172A silencing experiments. FAM172A protein expression in the FAM172AsiRNA group was much lower than that in the siRNAcontrol group in both cell lines . FAM172APD98059 was identified as a highly selective inhibitor of MEK1 activation and the MAP kinase cascade . PD98059In addition, FAM172AsiRNA transfected AsPC-1 and BxPC-3 cells presented EMT-like cell morphology: most cells lost their epithelial properties of tight junction, and presented a spindle-shaped and fibroblast-like morphology . Howeverin vitro was significantly reversed by MEK1 inhibitor PD98059. PD98059 also inhibited FAM172A silencing-induced EMT like cell morphology and cell invasiveness. Previous studies have shown that FAM172A promotes the proliferation of papillary thyroid carcinoma cells via p38/MAPK signaling , which were cultured in the recommended growth media with 10% FBS .IHC was performed as described previously ,b. BriefAs described previously , whole-cell lysates of PC cells were put into 12% SDS-polyacrylamide gels, transferred to PVDF membrane and incubated with primary FAM172A , E-cadherin , \u03b2-catenin , N-cadherin , Vimentin , MMP9 , and \u03b1-Smooth muscle actin , pERK , ERK and GAPDH antibodies overnight. Then membranes were incubated with secondary antibodies (Proteintech) at room temperature and were visualized with the ECL machine . PC cells were pretreated with 20\u2005\u00b5M of MEK1 inhibitor PD98059 for 2\u2005h before western blotting. The experiment was repeated three times.As described previously , qRT-PCRThe FAM172AsiRNA sequences were: sense: 5\u2032-GCCACTGAGAGTGAACCAAAG -3\u2032, which were synthesized from GenePharma company . siRNA transfections (20\u2005\u00b5M) were mixed with Oligofectamine 3000 for transient transfection following the manufacturer\u2019s instructions.As described previously , FAM172ABriefly, FAM172AsiRNA and siRNAcontrol transfected AsPC-1 and BxPC-3 cells (pretreated with 20\u2005\u00b5M of PD98059 for 2\u2005h only once) was seeded onto 8.0-\u00b5M pore size membrane inserts coated with matrigel in 24-well plates with FBS-free growth media. Growth media plus 10% FBS was added to the bottom wells as a chemoattractant. 24\u2005h later, cells that moved to the underside of the inserts were stained with Crystal Violet Hydrate . The migratory cells were counted in five random fields per well. Results were expressed as cells migrated per field and repeated three times. The transwell assay was performed in a similar way without matrigel.in vitro were described as means\u00b1s.e. (standard deviation) and were compared via t-test. P-value is presented as follow: *P<0.05; **P<0.01.Under SPSS software 20.0 , paired nonparametric test, chi-squared test and spearman correlation test were used for IHC assays, respectively. The log-rank test and Cox's regression was used to evaluate the postoperative survival time of PC patients. Western blotting, qRT-PCR and transwell assays"} +{"text": "The present study evaluates the protective effects of myricitrin and its solid lipid nanoparticle (SLN) on diabetic nephropathy (DN) induced by streptozotocin-nicotinamide (STZ-NA) in mice. In this experimental study, 108 adult male NMRI mice were divided into 9 groups: control, vehicle, diabetes, diabetes + myricitrin 1, 3, and 10 mg/kg and, diabetes + SLN containing myricitrin 1, 3, and 10 mg/kg. After the experimental period, the plasma and tissue samples were collected for experimental, histopathological, real-time PCR and apoptosis assessments. Total antioxidant capacity, catalase, glomerular filtration rate, plasma level of albumin, urine (BUN) and, creatinine (Cr) levels decreased, and the kidney weight, intake/output, malondialdehyde, plasma level of BUN and Cr, urine level of sodium, potassium, albumin and glucose, fractional excretions of sodium and potassium, transforming growth factor-\u03b2 (TGF-\u03b2) and nuclear factor kappa B (NF-\u03baB) gene expression, red blood cell accumulation and infiltration of inflammatory cells, and kidney apoptosis increased in untreated diabetic mice compared to the control group, and administration of myricitrin and its SLN recovered all of these changes. Ultimately, myricitrin and its SLN administration improved DN changes by reducing oxidative stress and increasing antioxidant enzymes level, and these effects were more prominent in the SLN-administered mice. Myrica cerifera (Diabetic nephropathy (DN), known as a kidney progressive disease is characterized by persistent albuminuria, progressive decrease in glomerular filtration rate (GFR) and increases in plasma level of creatinine (Cr). This disease occurs in 45 % of diabetic patients . The rencerifera . Oral bicerifera . Solid lcerifera . Streptocerifera . Howevercerifera . So, basChemicals and experimental kitsUnited Kingdom) assay kits, blood urea nitrogen (BUN), Cr, albumin, glucose assay kits , RNeasy Mini Kit , cDNA Synthesis Kit, Sybergreen , TGF-\u03b2 and NF-\u03bab, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) primers , TUNEL assay kit , Proteinase K .Myricitrin (Purity 98 %) , Citrate buffer, Tween 80 , Streptozotocin , Nicotinamide, Hematoxylin, Eosin, , Ketamine/Xylazine , phosphate-buffered saline (PBS) , Iran), malondiadehyde (MDA), total oxidant capacity (TAC), catalase (CAT) , superoxide dismutase (SOD) and encapsulation efficiency (EE %) were assessed in that study .Animalsad libitum. After one-week acclimatization of mice, T2DM induced by intraperitoneal injection of STZ (65 mg/kg) and NA (120 mg/kg) (dissolved in a citrate buffer (pH: 4.5) and normal saline, respectively) with 15 min interval. Mice with fasting blood glucose above 200 mg/dl were considered as diabetic and entered the study at 3 days after STZ-NA administration mice (25-30 g) were obtained from the Ahvaz Jundishapur University of Medical Sciences (AJUMS) animal facility and, treated in accordance with the principles and guidelines on animal care of AJUMS as reviewed by an ethics committee (IR.AJUMS.REC.1395.136) and kept at a 20 \u00b0C \u00b1 4 \u00b0C temperature with a 12 hr / 12 hr light and dark cycle. They received tap water and commercial chow Group I: ControlGroup II: Vehicle solvents)Group III: DiabetesGroups IV, V and, VI: Diabetes in addition to administration of Myricitrin 1, 3, and 10 mg/kg, respectively.Groups VII, VIII and, IX: Diabetes in addition to administration of SLN containing myricitrin 1, 3, and 10 mg/kg, respectively injected anesthetized mice. Then, plasma samples were prepared by blood samples centrifuging at 3500 rpm for 20 min. Following that, the kidney of all animals was separated for histological, gene expression, and apoptosis assessment. The plasma and kidney samples were maintained at \u221280 \u00b0C until the laboratory measurements were performed . Experimental measurementsThe kidney homogenate was prepared using Sharma and Singh method. In brief, the separated kidney slab on the dry ice pack, homogenized in 1/5 (w/v) PBS (pH: 7.4) with a Teflon homogenizer, and centrifuged at 2000 rpm for 10 min. Finally, the supernatant was used to measure the levels of lipid peroxidation (MDA) and antioxidant defense variables by specific commercial kits .Plasma and urine level of the BUN, Cr, albumin, sodium (Na), potassium (K) and, urine level of glucose were measured by using an Autoanalyzer electrolyte analyzer devices and biochemical assay kits . Also, GFR, and fractional excretion of sodium and potassium were assessed by the following formula: GFR= Urine Cr \u00d7 Urine volume / Plasma Cr; FE Na= (Urine Na \u00d7 Plasma Cr / Plasma Na \u00d7 Urine Cr) \u00d7 100; FE K= (Urine K \u00d7 Plasma Cr / Plasma K \u00d7 Urine Cr) \u00d7 100 .Gene expression assessment-\u0394\u0394CT). The sequences of forward and reverse primer for TGF-\u03b2, NF-\u03bab, and GAPDH genes are presented in Real-time PCR method was used for gene expression measurement in the present study. In brief, total RNA and cDNA were purified and synthesized from the kidney by the RNeasy mini kit and Reverse Transcriptase kit, respectively according to their instructions . Real-tiHistopathological and apoptosis assessmentsIn Situ Cell Death Detection Kit, POD, and the dark brown stained nucleus was included as dead cells. The index of apoptosis was measured in 3 randomly slides/animal and ten fields for each slide as a percentage of TUNEL-positive cells and hematoxylin and eosin (H&E) staining method. Then, seven microscopic slides of tissue sections (5 to 7 \u00b5m) were assessed and read using blind method. Apoptosis assessment was carried out by TUNEL staining according to the labeling of DNA strand breaks by administration of ve cells .Statisticspost hoc least significant difference (LSD) tests. Moreover, the data were represented as the mean\u00b1standard error of the mean (SEM), and the statistically significant differences were considered at P<0.05.The obtained results were statistically analyzed by SPSS software (version 16) with one-way analysis of variance (ANOVA) and The role of myricitrin and its SLN on kidney weight and intake/outputP<0.01) compared to the control and decreased in the groups II (P<0.01), IX (P<0.05), and others (P<0.01) versus diabetes group. The water and food intake showed a significant increase in diabetic mice when compared to control . The water intake decreased in groups IV, V (P<0.05), and others (P<0.01) compared to the diabetes group. Food intake assessment showed a similar effect in the groups II, IV, V, VI (P<0.01), VII, VIII, and IX (P<0.001) compared to diabetes group. The urinary volume of untreated diabetic mice increased significantly (P<0.01). Further, the urine output decreased in groups IX (P<0.001) and others (P<0.01) versus diabetes group.As shown in Lipid peroxidation and antioxidant enzymes level in the kidneyP<0.01). This factor of lipid peroxidation reduced in the groups II (P<0.05), IV, V (P<0.01), VI, and VII (P<0.01) versus diabetes group (P<0.05) and group VI (P<0.01), and increased in groups V (P<0.01), VIII (P<0.05), and IX (P<0.001) in comparison with control. Further, this variable increased in groups II (P<0.05), IV (P<0.01), V (P<0.001), VII (P<0.01), VIII and IX (P<0.001) compared to untreated diabetic mice (P<0.001), groups IV (P<0.01), VI (P<0.001), VIII and IX (P<0.05) when compared to control, but this variable increased in groups II (P<0.001), IV (P<0.05), V (P<0.001), VII, VIII (P<0.01), and IX (P<0.01) versus diabetes group . This variable increased in the groups II (P<0.01), VIII (P<0.001), and others (P<0.05) versus diabetes group. Plasma level of BUN increased in diabetes (P<0.001) and groups IV (P<0.001), V (P<0.01), VI (P<0.05), and VII (P<0.01) compared to the control. Also, this factor decreased in the groups II (P<0.001), IV (P<0.01), and others (P<0.001) compared to untreated diabetic mice. Plasma Cr level showed a significant increase in diabetes and groups IV, V, VI, and IX in comparison with the control group (P<0.001). This variable decreased in the groups II (P<0.001), IV, V (P<0.05), VIII, and IX (P<0.001) versus diabetes group. Plasma level of albumin reduced in all experimental groups except group II versus the control (P<0.001). Moreover, this factor increased in the groups II (P<0.001), V, and VIII (P<0.05) when compared to the diabetes group (P<0.001). Further, this variable increased in the groups IV, VII (P<0.01), and others (P<0.001) versus diabetes group (P<0.01) and groups VI and IX (P<0.001) compared to the control group. Also, this factor increased in the groups II, IV, V, VII, and VIII (P<0.01) when compared to diabetes group (P<0.001) and groups IV, V (P<0.01), VI (P<0.001), VII (P<0.01), VIII (P<0.01), and IX (P<0.001) versus the control group. Moreover, urine albumin level decreased in the groups II (P<0.001), V, and VIII (P<0.01) when compared to untreated diabetic mice compared to the control. Also, this variable decreased in all groups (P<0.01) except IV and VII versus the diabetes group. The urine K level increased in diabetes compared to control (P<0.01). Also, this factor decreased in the groups II (P<0.01), IV, V (P<0.05), VI (P<0.001), VII (P<0.05), VIII (P<0.01), and IX (P<0.001) when compared to diabetes group. FE Na showed a remarkable increase in diabetes (P<0.001) and groups IV (P<0.05), VI (P<0.001) and, IX (P<0.01) versus to the control group. Further, this variable reduced in the groups II (P<0.001), IV (P<0.01), V (P<0.001), VII, VIII (P < 0.001) and, IX (P<0.05) compared to the diabetes. The results of FE K indicated a significant increase in diabetes (P<0.001) and groups IV, V (P<0.05), VI (P<0.01), and IX (P<0.01) in comparison with the control group. Moreover, FE K decreased in the groups VI (P<0.01) and others (P<0.001) when compared to the diabetes group and groups V (P<0.01), VI (P<0.001), VIII (P<0.05), and IX (P<0.001) compared to the control group. Also, TGF-\u03b2 gene expression decreased in the groups II (P<0.001), IV (P<0.001), V (P<0.01), VII, and VIII (P<0.001), and increased in the group IX (P<0.001) when compared to the diabetes group . NF-\u03bab gene expression showed a remarkable increase in diabetes (P<0.001) and groups VIII (P<0.01) and IX (P<0.001) versus the control group. This variable decreased in the groups II (P<0.001), IV (P<0.001), V (P<0.01), VII (P<0.001), and VIII (P<0.001) compared to the diabetes group .The gene expression of TGF-\u03b2 increased in diabetes (Effect of myricitrin and its SLN on the kidney histopathology and apoptosisP<0.001) and groups IV (P<0.01), V (P<0.05), VI (P<0.001), VII (P<0.05), and IX (P<0.01) when compared to the control. Furthermore, this variable decreased in the groups II (P<0.001), IV, V (P<0.001), VI (P<0.05), VII, VIII, and IX (P<0.001) compared to the diabetes group accumulation and infiltration of inflammatory cells in diabetes group compared to the control group. These alterations decreased in the groups II and others treated groups versus diabetes group, and this decreasing effect was more obvious in the groups VII and VIII . The reses group .et al. demonstrated an increase in kidney weight of type 2 diabetic rats due to renal enlargement, hypertrophy, and hyperfunctioning, and treatment with silymarin as a plant-derived antioxidant improved kidney weight (The present study showed that polyphagia, polydipsia, and polyuria occurred in untreated diabetic mice, and myricitrin and its SLN administration improved these disorders. The present results indicated that the kidney weight increased in diabetic mice and administration of myricitrin and its SLN recovered this alteration. Consists with this result Sheela y weight . When thy weight . TherefoT2DM increases ROS production and attenuates free radical scavenging molecules such as antioxidant enzymes. Free radicals induce basement membrane damage and lead to altering the membrane fluidity, ion transports and increased urinary albumin excretion . It seemMurraya paniculata ameliorated kidney dysfunctions of DN in diabetic rats through reducing oxidative stress and increasing antioxidant enzymes level (Urinary albumin excretion, hypoalbuminemia, elevated BUN, serum Cr, urine glucose, and decreased GFR levels occurred in DN, which may be related to T2DM and formation of free radicals . The enhes level . MoreoveGlomerular damage may accelerate tubulointerstitial injury by multiple pathways such as tubular chemokine expression that results in inflammatory cell infiltration in DN . AbnormaThe obtained results indicated that T2DM induced by STZ-NA causes to DN, kidney apoptosis and, inflammation via the increasing lipid peroxidation and decreasing antioxidant defense. Moreover, administration of myricitrin and its SLN in low and moderated doses improved all of the DN changes through reducing oxidative stress and increasing antioxidant enzymes level, and these effects were more potent in the SLN-administered diabetic mice."} +{"text": "Brachycephalus sulfuratus was recently described from southeastern and southern Brazil. In its description, the authors overlooked previous records of flea toads that had been identified as \u201cBrachycephalus sp. nov.\u201d and B. hermogenesi occurring in the same regions, which could suggest the possibility of up to three flea toads coexisting in southern Brazil. In addition, B. sulfuratus is characterized by substantial phenotypic variability, to an extent that compromises its current diagnosis with respect to its congener B. hermogenesi. Therefore, the current state-of-affairs regarding the geographical distribution of these two species and the identification of previously known populations is hitherto uncertain. Our goals are to reassess previous records of flea toads attributable to B. hermogenesi, B. sulfuratus and \u201cBrachycephalus sp. nov.\u201d, considering the description of B. sulfuratus, and to review the diagnosis of B. sulfuratus.The flea toad B. hermogenesi, B. sulfuratus, or to a potentially undescribed species from southeastern and southern Brazil was based either on the analysis of morphology or on their advertisement calls. These analyses include our independent examinations of specimens and, when not possible, examinations of published descriptions. To allow for a consistent comparison of advertisement calls between B. hermogenesi and B. sulfuratus, we made recordings of both species, including in the type locality of the former.A critical analysis of the species identity of flea toad specimens attributable to B. sulfuratus in relation to B. hermogenesi vary intraspecifically. Live individuals with ventral yellow spots correspond to B. sulfuratus; individuals without yellow spots can be either B. sulfuratus or B. hermogenesi. In preservative, they are indistinguishable. Previous records of Brachycephalus sp. nov. correspond to B. sulfuratus. We propose that the reduced number of notes per call and the presence of only isolated notes in the call of B. sulfuratus, as opposed to a high number of notes per call with isolated notes and note groups in the call of B. hermogenesi, as the only diagnostic characters between them. Regarding their distributions and based in our assessment, only B. sulfuratus occurs in southern Brazil, without any overlap with B. hermogenesi. There is a narrow gap between the distributions of these species around the southeast of the city of S\u00e3o Paulo. Our revision also revealed that some records previously attributed to B. hermogenesi in Rio de Janeiro and north S\u00e3o Paulo represent a distinct, unidentified flea toad that is not B. sulfuratus. Both species occur side by side in Corcovado, S\u00e3o Paulo, a locality from where five paratypes of B. hermogenesi were obtained. Biogeographic events that might have led to vicariance between B. hermogenesi and B. sulfuratus are discussed.We found that morphological and call characters originally proposed as diagnostic for Brachycephalus Fitzinger, 1826 includes 36 small diurnal anuran species that live in the leaf litter across the Brazilian Atlantic Rainforest , municipality of Guaraque\u00e7aba, in the northern coast of Paran\u00e1 . Third, if the unidentified species of B. sulfuratus, there could be a single species of flea toad in southern Brazil (B. sulfuratus).The absence of a nomenclatural review of records of flea toads in southern Brazil can be evidenced by the fact that a single location in Santa Catarina, called Castelo dos Bugres, was recorded as harboring specimens identified as \u201c nov. 1\u201d , or Bracs sp. 1. and B. smogenesi , Brachycalus sp. and B. slfuratus . Second, records were assp. nov.\u201d , leadingBrachycephalus sp. nov. 1\u201d , Curitiba, Paran\u00e1, Brazil, Cole\u00e7\u00e3o Herpetol\u00f3gica do Departamento de Zoologia (DZUP), Universidade Federal do Paran\u00e1, Curitiba, Paran\u00e1, Brazil, and Museu de Hist\u00f3ria Natural (ZUEC), Universidade Estadual de Campinas, Campinas, S\u00e3o Paulo, Brazil. The sound collection analyzed include MHCNI, Xeno-Canto sound collection (www.xeno-canto.org), and Fonoteca Neotropical Jacques Vielliard .The critical analysis of the species identity of specimens attributable to B. sulfuratus .The analyses began by the assessment of the original diagnosis of lfuratus . We lookB. sulfuratus and B. hermogenesi, we noticed that the calls of B. hermogenesi described by B. hermogenesi and digital devices, with Sennheiser ME 66 and ME 67 microphones. Analogical recordings were digitized at 44.1 kHz and 16 bit using Raven Pro 1.4 . Digital recordings were made equally with sampling frequency rate of 44.1 kHz and 16-bit resolution. We analyzed calls under note-centered approach , as BornB. sulfuratus and B. hermogenesi, vouchered with specimens collected and deposited in the MHNCI. Collection permits were issued by ICMBIO . Geographical coordinates are based on the WGS84 datum. Elevations for literature records and author\u2019s records were obtained from Google Earth, after plotting the location point It \u201cdiffers from\u2026 B. hermogenesi\u2026 by having (in life) yellow blotches on the ventral surfaces of the throat, chest, arms, and forearms\u201d . The inverted v-shaped mark can be absent in individuals of B. sulfuratus \u201d .\u201dorearms\u201d : 43, 50;genesi\u2026\u201d : 43, 50;ogenesi\u201d : 50. SpeCatarina have revCatarina . Moreove compare . Additio pulex)\u201d : 50. Als pulex)\u201d : 46. Fin pulex)\u201d : 50: \u201cThB. sulfuratus from B. hermogenesi. However, for identification purposes, we considered individuals with yellow spots on their ventral side as B. sulfuratus, whereas individuals without yellow spots could be either B. sulfuratus or B. hermogenesi. It is important to note that specimens with yellow spots of B. sulfuratus must be observed in life because in the preservative the change in color prevents separate them in relation to specimens of B. hermogenesi.Currently, there are no unique morphological character that could differentiate either live or preserved specimens for B. sB. sulfuratus the following parameters of the advertisement call: \u201cadvertisement call long, composed of a set of 4\u20137 high-frequency notes (6.2\u20137.2 kHz) repeated regularly.\u201d In the section \u201cComparisons with other species\u201d, B. hermogenesi is the most similar to the new species (B. sulfuratus), being quite similar in frequency (dominant frequency = 6.8 kHz), which are the highest recorded for the genus. However, the advertisement call of B. hermogenesi can be simple or composed of 2\u20137 shorter notes with 1\u20133 pulses is within the range of B. sulfuratus (6.2\u20137.2).In addition to morphological characters, 3 pulses .\u201d In sumB. hermogenesi call can be simple or composed and the presence of \u201cattenuated notes\u201d with only isolated notes of B. sulfuratus, while in B. hermogenesi the advertisement call has a high number of notes (\u226524) with the presence of isolated notes and note groups . One of these records involves \u201cB. hermogenesi\u201d from the municipality of Piedade, state of S\u00e3o Paulo, of HQ435682.1 and HQ435709.1; B. sulfuratus, which was placed on the tree together with a specimen from the Municipality of Barra do Turvo, in an early-diverging branch of the B. sulfuratus clade on the tree , also examined by us, collected in the state of Paran\u00e1, that was first identified as \u201c nov. 1\u201d , \u201cBrachys sp. 1\u201d , and, fifuratus\u201d ). There part.), two localities previously considered as occurrence of B. hermogenesi . The phylogenetic analysis revealed that the specimen from Municipality of Paraibuna is indeed B. hermogenesi with distinct durations (= transliteration size) related to the number of notes in the call. This diagnosis between B. sulfuratus and B. hermogenesi is only feasible under the note-centered approach. Considering their calls under the call-centered approach, there would be no diagnosis to be proposed between them at this moment, because each note would represent a call , consolidate the benefit of the note-centered approach over the call-centered approach in describing calls of species of this genus , for example, from the B. ephippium group, which includes most species from the state of S\u00e3o Paulo to the north up to Esp\u00edrito Santo and Minas Gerais.The advertisement calls of ix group , 2018a, B. hermogenesi in southern Brazil and the presence of B. sulfuratus as far north as the east of S\u00e3o Paulo city, only 25 km in straight line from the southernmost site of a confirmed record of B. hermogenesi since 2009, focusing on their distribution, ecology and conservation , on the border between the municipalities of Jaragu\u00e1 do Sul and Massaranduba, where we described B. albolineatus . In the studies . In the studies and snak studies .Brachycephalus toads and Scytalopus birds of S\u00e3o Paulo, Paran\u00e1, and Santa Catarina originated less than 2\u20135 million years ago and Mesozoic, respectively and Eleoscytalopus indigoticus , and calls of B. hermogenesi in N\u00facleo Santa Virg\u00ednea, Parque Estadual da Serra do Mar, municipality of S\u00e3o Luiz do Paraitinga, S\u00e3o Paulo, can be heard in a recording of E. indigoticus at Corcovado, S\u00e3o Paulo, is the only confirmed case of sympatry between species of Brachycephalus in the same group. Other cases of sympatry include Brachycephalus from distinct groups . RIO DE JANEIRO: Trilha do Corisco, municipality of Paraty MHNCI 206\u201312. S\u00c3O PAULO: Corcovado, municipality of Ubatuba MHNCI 193\u2013205.10.7717/peerj.10983/supp-1Supplemental Information 1Abbreviation: NA = not available.Click here for additional data file.10.7717/peerj.10983/supp-2Supplemental Information 2MHNCI 124 Brachycephalus sulfuratus near Jurupara dam voucher MHNCI 10791 or MHNCI 10792 29 set 2016 MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-3Supplemental Information 3MHNCI 124 Brachycephalus sulfuratus near Jurupara dam voucher MHNCI 10791 or MHNCI 10792 29 set 2016 MRBornschein cutted.Click here for additional data file.10.7717/peerj.10983/supp-4Supplemental Information 4MHNCI 125 Brachycephalus sulfuratus near Jurupara dam not collected 29 set 2016 MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-5Supplemental Information 5MHNCI 126 Brachycephalus sulfuratus Nucleo Itutinga Piloes ind 1 not collected 08 out 2016 MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-6Supplemental Information 6MHNCI 127 Brachycephalus sulfuratus Nucleo Itutinga Piloes ind 2 not collected 08 out 2016 MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-7Supplemental Information 7MHNCI 128 Brachycephalus sulfuratus Biquinha not collected 18 set 2016 MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-8Supplemental Information 8MHNCI 129 Brachycephalus sulfuratus Serra Agua Limpa MHNCI 11583 26 out 2011 MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-9Supplemental Information 9MHNCI 130 Brachycephalus sulfuratus Serra do Guarau not collected 22 out 2016 MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-10Supplemental Information 10MHNCI 131 Brachycephalus sulfuratus Caratuval near Parque Estadual Lauraceas MHNCI 11571 L Correa.Click here for additional data file.10.7717/peerj.10983/supp-11Supplemental Information 11MHNCI 132 Brachycephalus sulfuratus Caratuval Parque Estadual Lauraceas not collected 18 dez 2010 L Correa.Click here for additional data file.10.7717/peerj.10983/supp-12Supplemental Information 12MHNCI 133 Brachycephalus sulfuratus Reserva Particular do Patrimonio Natural Salto Morato not collected 10 marco 2016 MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-13Supplemental Information 13MHNCI 134 Brachycephalus sulfuratus Fazenda Thalia not collected MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-14Supplemental Information 14MHNCI 135 Brachycephalus sulfuratus Truticultura not collected MRBornschein.Click here for additional data file.10.7717/peerj.10983/supp-15Supplemental Information 15MHNCI 136 Brachycephalus sulfuratus Morro Garuva not collected 02 nov 2016 Andre Confetti.Click here for additional data file.10.7717/peerj.10983/supp-16Supplemental Information 16MHNCI 137 Brachycephalus sulfuratus Morro do Garraf\u00e3o not collected LFRibeiro.Click here for additional data file.10.7717/peerj.10983/supp-17Supplemental Information 17MHNCI 165 000107 0122S4 Brachy hermogenesi Corcovado specimen one two starting notes lost without interruption.Click here for additional data file.10.7717/peerj.10983/supp-18Supplemental Information 18MHNCI 168 190330 05 Brachy hermogenesi ind 03 Boraceia 30 marco 2019 MRB.Click here for additional data file.10.7717/peerj.10983/supp-19Supplemental Information 19MHNCI 169 190330 06 Brachy hermogenesi ind 04 Boraceia 30 marco 2019 MRB.Click here for additional data file.10.7717/peerj.10983/supp-20Supplemental Information 20MHNCI 172 BLR00061 Brachy hemogenesi Picinguaba ind 01 ex 01 sem detalhes 13 dez 2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-21Supplemental Information 21MHNCI 173 BLR00062 B hermogenesi Picinguaba ind2 ex1 4 notas perdidas 13dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-22Supplemental Information 22MHNCI 174 BLR00064 B hermogenesi Picinguaba ind3 6 notas perdidas 13dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-23Supplemental Information 23MHNCI 175 BLR00065 B hermogenesi Picinguaba ind1ex2 tudo 13 dez 2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-24Supplemental Information 24MHNCI 176 BLR00067 B hermogenesi Picinguaba ind1ex3 tudo ind4ex1 3 perdidas 13dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-25Supplemental Information 25MHNCI 177 BLR00068 B hermogenesi_Picinguaba ind2 ex2 tudo 05cm 13 dez 2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-26Supplemental Information 26MHNCI 178 BLR00069 B hermogenesi Picinguaba ind3 ex2 5 notas perdidas 13 dez 2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-27Supplemental Information 27MHNCI 179 BLR00070 B hermogenesi Picinguaba ind 04 ex 02 13 dez 2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-28Supplemental Information 28MHNCI 180 BLR00071 B hermogenesi Picinguaba ind 03 ex 03 sem detalhes 13 dez 2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-29Supplemental Information 29MHNCI 181 BLR00072 B hermogenesi Picinguaba ind3 ex4 perdeu uma nota 13 dez 2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-30Supplemental Information 30MHNCI 182 BLR00073 B hermogenesi Picinguaba ind2 ex3 soh o final do canto 13 dez 2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-31Supplemental Information 31MHNCI 183 BLR00076 B hermogenesi Picinguaba ind4ex3 tudo 5-20cm distancia 13dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-32Supplemental Information 32MHNCI 184 000106 0115S4 Brachy hermogenesi Picinguaba specimen one several starting notes lost without interruption.Click here for additional data file.10.7717/peerj.10983/supp-33Supplemental Information 33MHNCI 185 000106 0117S4 Brachy hermogenesi Picinguaba specimen two two starting notes lost without interruption.Click here for additional data file.10.7717/peerj.10983/supp-34Supplemental Information 34MHNCI 186 000106 0119S4 Brachy hermogenesi Picinguaba specimen three one starting notes lost without interruption.Click here for additional data file.10.7717/peerj.10983/supp-35Supplemental Information 35MHNCI 187 000106 0120S4 Brachy hermogenesi Picinguaba specimen four several starting notes lost without interruption.Click here for additional data file.10.7717/peerj.10983/supp-36Supplemental Information 36MHNCI 213 080409 02 B hermogenesi ind1 muito perdido ruim Paranapiacaba MRB.Click here for additional data file.10.7717/peerj.10983/supp-37Supplemental Information 37MHNCI_188_000103_0135S4_Brachy hermogenesi Trilha do Ipiranga ind 1 e unknown starting notes with interruption.Click here for additional data file.10.7717/peerj.10983/supp-38Supplemental Information 38MHNCI 189 000103 0137S4 Brachy hermogenesi Trilha do Ipiranga ind 2 three starting notes lost.Click here for additional data file.10.7717/peerj.10983/supp-39Supplemental Information 39MHNCI 190 000103 0140S4 Brachy hermogenesi Trilha do Ipiranga ind 3 three starting notes lost.Click here for additional data file.10.7717/peerj.10983/supp-40Supplemental Information 40MHNCI 191 000103 0141S4 Brachy hermogenesi Trilha do Ipiranga ind 4 four starting notes lost.Click here for additional data file.10.7717/peerj.10983/supp-41Supplemental Information 41MHNCI 193 BLR00084 Brachy sp ind1 parte final Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-42Supplemental Information 42MHNCI 194 BLR00085 Brachy sp ind2 2m Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-43Supplemental Information 43MHNC 195 BLR00086 Brachy sp ind3 perdeu notas 20cm Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-44Supplemental Information 44MHNCI 196 BLR00087 Brachy sp ind4ex1 perdeu 3 notas 30-100cm Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-45Supplemental Information 45MHNCI 197 BLR00089 Brachy sp ind5 soh final Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-46Supplemental Information 46MHNCI 198 BLR00091 Brachy sp ind6ex1 4 notas perdidas 10-50cm Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-47Supplemental Information 47MHNCI 199 BLR00092 Brachy sp ind6ex2 soh final 50-80cm Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-48Supplemental Information 48MHNCI 200 BLR00093 Brachy sp ind4ex2 perdeu 7 notas 20cm Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-49Supplemental Information 49MHNCI 201 BLR00094 Brachy sp ind7 perdeu 4 notas 20-100cm Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-50Supplemental Information 50MHNCI 202 BLR00095 Brachy sp ind8 perdeu 6 notas Corcovado 18dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-51Supplemental Information 51MHNCI 203 000102 0129S4 Brachycephalus sp ind1 Corcovado two starting notes lost.Click here for additional data file.10.7717/peerj.10983/supp-52Supplemental Information 52MHNCI 204 000102 0130S4 Brachycephalus sp ind2 Corcovado two starting notes lost.Click here for additional data file.10.7717/peerj.10983/supp-53Supplemental Information 53MHNCI 205 000102 0132S4 Brachycephalus sp ind4 ind5 Corcovado two starting notes lost.Click here for additional data file.10.7717/peerj.10983/supp-54Supplemental Information 54MHNCI 211 000104 0113S4 Brachycephalus sp ind1 Trilha do Corisco several starting notes lost.Click here for additional data file.10.7717/peerj.10983/supp-55Supplemental Information 55MHNCI 212 000104 0114S4 Brachycephalus sp ind2 Trilha do Corisco several starting notes lost.Click here for additional data file.10.7717/peerj.10983/supp-56Supplemental Information 56MHNCI 206 BLR00053 Brachycephalus sp Trilha do Corisco ind1 perdeu inicio 40 cm 12dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-57Supplemental Information 57MHNCI 207 BLR00054 Brachycephalus sp Trilha do Corisco ind2 perdeu inicio 12dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-58Supplemental Information 58MHNCI 208 BLR00055 Brachycephalus sp Trilha do Corisco ind3 microfone flutuou 12dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-59Supplemental Information 59MHNCI 209 BLR00056 Brachycephalus sp Trilha do Corisco ind4 20-60 cm 12dez2017 MRB.Click here for additional data file.10.7717/peerj.10983/supp-60Supplemental Information 60MHNCI 217 190206 05 Brachycephalus sp mais B sulfuratus Serra do Pico MRB 6fev2019.Click here for additional data file.10.7717/peerj.10983/supp-61Supplemental Information 61MHNC 218 BLR00165 Brachy sp mais Brachy sulfuratus Torre Embratel MRB n\u00e3o coletado.Click here for additional data file.10.7717/peerj.10983/supp-62Supplemental Information 62MHNCI 219 200123 0448S4 Brachycephalus sulfuratus Entroncamento Teba 20 cm from microphone LFR JAN-2020.Click here for additional data file.10.7717/peerj.10983/supp-63Supplemental Information 63MHNCI 220 Brachycephalus sulfuratus Morro do Canal 150 cm from microphone LFRibeiro JAN-2017.Click here for additional data file.10.7717/peerj.10983/supp-64Supplemental Information 64MHNCI 221 161115 02 Brachycephalus sulfuratus Monte Crista 100 cm from microphone Luiz Fernando Ribeiro NOV-2016.Click here for additional data file.10.7717/peerj.10983/supp-65Supplemental Information 65Brachycephalus hermogenesi ind1 parte do canto Morro do Cantagalo-Caraguatatuba LC.MHNCI 222 180802 08 Click here for additional data file.10.7717/peerj.10983/supp-66Supplemental Information 66Brachycephalus hermogenesi ind2 parte do canto Morro do Cantagalo-Caraguatatuba LC.MHNCI 223 180802 09 Click here for additional data file."} +{"text": "Pancreatic ductal adenocarcinoma (PDAC) is a fatal malignant neoplasm. It is necessary to improve the understanding of the underlying molecular mechanisms and identify the key genes and signaling pathways involved in PDAC.GSE28735, GSE62165, and GSE91035 were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified by integrated bioinformatics analysis, including protein\u2013protein interaction (PPI) network, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The PPI network was established using the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. GO functional annotation and KEGG pathway analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. Hub genes were validated via the Gene Expression Profiling Interactive Analysis tool (GEPIA) and the Human Protein Atlas (HPA) website.The microarray datasets FN1, COL1A1, COL3A1, BGN, POSTN, FBN1, COL5A2, COL12A1, THBS2, COL6A3, VCAN, CDH11, MMP14, LTBP1, IGFBP5, ALB, CXCL12, FAP, MATN3, and COL8A1. These genes were validated using The Cancer Genome Atlas (TCGA) and Genotype\u2013Tissue Expression (GTEx) databases, and the encoded proteins were subsequently validated using the HPA website. The GO analysis results showed that the most significantly enriched biological process, cellular component, and molecular function terms among the 20 hub genes were cell adhesion, proteinaceous extracellular matrix, and calcium ion binding, respectively. The KEGG pathway analysis showed that the 20 hub genes were mainly enriched in ECM\u2013receptor interaction, focal adhesion, PI3K-Akt signaling pathway, and protein digestion and absorption. These findings indicated that FBN1 and COL8A1 appear to be involved in the progression of PDAC. Moreover, patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the expression levels of COL12A1 and MMP14 were correlated with a poor prognosis in PDAC patients (p\u00a0<\u00a00.05).A total of 263 DEGs (167 upregulated and 96 downregulated) were common to the three datasets. We used STRING and Cytoscape software to establish the PPI network and then identified key modules. From the PPI network, 225 nodes and 803 edges were selected. The most significant module, which comprised 11 DEGs, was identified using the Molecular Complex Detection plugin. The top 20 hub genes, which were filtered by the CytoHubba plugin, comprised MMP14 and COL12A1 is associated with poor overall survival, and these might be a combination of prognostic biomarkers in PDAC.The results demonstrated that upregulation of Pancreatic ductal adenocarcinoma (PDAC) is the most common malignant tumor of the pancreas and is a lethal malignancy with poor prognosis, which is in part due to its rapid progression and the lack of diagnostic and therapeutic targets. In 2018, pancreatic cancer (PC) ranked 11th among the most common cancers, with 458,918 new cases and 432,242 deaths due to PC worldwide . Recent KRAS and biological pathways linked to various malignant tumors. Therefore, microarray techniques are promising and efficient ways to identify candidate biomarkers involved in the pathogenesis of PDAC. The purpose of our study was to determine significant DEGs and pathways implicated in PDAC by integrated bioinformatics analysis and to provide novel insights into the progression, diagnosis, and therapeutic targets of PDAC.https://www.ncbi.nlm.nih.gov/geo/) is a public repository of high-throughput gene expression genomics datasets is an online analysis tool that is based on the R programming language and can be used to identify DEGs that differentiate between cancer and normal samples in a GEO series is an online application that can be used to assess DEG-encoded proteins and protein\u2013protein interaction (PPI) networks is a public online bioinformatics database (p\u00a0<\u00a00.05. We performed enrichment of the GO terms and KEGG pathways for the candidate DEGs using DAVID.The Gene Ontology (GO) is used to perform enrichment analysis, which covers the cellular component (CC), biological process (BP), and molecular function (MF), of the selected genes . The Kyodatabase that conhttp://gepia.cancer-pku.cn/) is used to perform functions such as survival analysis, the detection of similar genes, and correlation analysis to clarify the relationships between diseases and DEGs database and the Genotype\u2013Tissue Expression (GTEx) database, the Gene Expression Profiling Interactive Analysis tool website on the basis of spatial proteomics data and quantitative transcriptomics data (RNA-Seq) obtained from immunohistochemical analysis of tissue microarrays.The expression of proteins encoded by the PDAC candidate genes was validated using the Human Protein Atlas Functional and pathway enrichment analyses were accomplished using DAVID. GO analysis showed that the most significant module was mainly enriched in cell adhesion, extracellular matrix structural constituent, and proteinaceous extracellular matrix Table 2Table 2. COL12A1 and MMP14 were correlated with an unfavorable prognosis in PDAC patients (p\u00a0<\u00a00.05) (p\u00a0>\u00a00.05).Patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the high expression levels of \u00a0<\u00a00.05) . The oveFN1, COL1A1, COL3A1, BGN, POSTN, FBN1, COL5A2, COL12A1, THBS2, COL6A3, VCAN, CDH11, MMP14, LTBP1, IGFBP5, FAP, MATN3, and COL8A1 were significantly overexpressed in PDAC tissues in comparison with normal pancreatic tissues, whereas ALB was underexpressed in PDAC tissues (p\u00a0<\u00a00.05) .To ensure the reliability of the identification of the top 20 hub genes, we validated these via the GEPIA using TCGA and GTEx databases. Boxplots of the hub genes associated with PDAC were downloaded from the GEPIA. The results demonstrated that \u00a0<\u00a00.05) . CXCL12 COL5A2, IGFBP5, and MATN3 are reported on the HPA website, and expression profiles of the other 17 genes in PDAC clinical specimens are shown in We obtained the expression levels of proteins encoded by the 20 hub genes associated with PDAC from the HPA website. No data for proteins encoded by FN1, MMP14, COL12A1, COL3A1, COL1A1, POSTN, VCAN, LTBP1, FBN1, and FAP were upregulated in PDAC tissues in comparison with normal tissues, with only ALB being downregulated in PDAC tissues. COL6A3, COL8A1, CDH11, and CXCL12 were not expressed in either PDAC tissues or normal tissues, and BGN and THBS2 were overexpressed in both cancer and normal tissues.The protein expressions of GSE28735, GSE62165, and GSE91035. The main findings deduced from the studies used to compile GSE28735 were that dipeptidase 1 and a unique set of free fatty acids played roles in the development, progression, and prognosis of PC and might be potential targets in PDAC (GSE62165 found that hepatocyte nuclear factor (HNF)-1 \u03b1 and HNF-1 \u03b2 seem to be good candidates as tumor suppressors in PDAC . Ca2+ is a ubiquitous and versatile second messenger involved in the regulation of numerous cellular functions, including gene transcription, vesicular trafficking, and cytoskeletal rearrangements and enhances the production of type I collagen by increasing transforming growth factor- \u03b2 signaling are a family of calcium- and zinc-dependent membrane-anchored or secreted endopeptidases that are overexpressed in various diseases, including breast cancer . MMP14 i of PDAC . Moreoveasive PC , and MMPasive PC . Type I al cells , and COLignaling . Ottaviac tissue . These fCOL1A1, COL3A1, COL5A2, COL6A3, FN1, and THBS2, were significantly associated with ECM\u2013receptor interactions, focal adhesion, and the phosphatidylinositol-3-kinase\u2013protein kinase B (PI3K-Akt) signaling pathway. In addition, collagen-encoding genes, including COL1A1, COL3A1, and COL5A2, were also enriched in protein digestion and absorption and platelet activation.The KEGG pathway analysis showed that six hub genes, namely, COL1A1 and COL3A1 were significantly downregulated in PC (p <0.0001) after treatment with gemcitabine in combination with EC359 . As we hFBN1 and COL8A1 appear to be involved in the progression of PDAC. FBN1 encodes a structural component of the microfibrils of the ECM that have diameters of 10\u201312 nm, which impart both regulatory and structural properties to load-bearing connective tissues and the related enriched functions or pathways, which regulate the progression and metastatic invasion of PDAC, as well as overall survival. The results demonstrate that the upregulation of MMP14 and COL12A1 in PDAC is closely associated with poor overall survival, that these might be a potential combination of prognostic biomarkers in patients with PDAC, and that FBN1 and COL8A1 might be biomarkers of PDAC. In brief, our study increases the understanding of the potential critical genes and related pathways that participate in the pathogenesis of PDAC.In conclusion, we screened the top 20 hub genes (10.7717/peerj.10419/supp-1File S1Click here for additional data file.10.7717/peerj.10419/supp-2Table S1Click here for additional data file.10.7717/peerj.10419/supp-3Supplemental Information 3Click here for additional data file.10.7717/peerj.10419/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.10419/supp-5Supplemental Information 5Click here for additional data file.10.7717/peerj.10419/supp-6Supplemental Information 6Click here for additional data file.10.7717/peerj.10419/supp-7Supplemental Information 7Click here for additional data file.10.7717/peerj.10419/supp-8Supplemental Information 8Click here for additional data file.10.7717/peerj.10419/supp-9Supplemental Information 9Click here for additional data file.10.7717/peerj.10419/supp-10Supplemental 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In this cross-sectional study we examined the relationships between FOF and factors associated with fall-risk such as gait quality, cognition, and walking-confidence. Using baseline data from older adult participants in a randomized exercise trial , we quantified the following outcome measure for (1) gait quality: harmonic ratio (smoothness) and time-frequency spatiotemporal variables from triaxial accelerometry during 6 minute walk; gait speed, step-time CoV (variability) and walk-ratio (step-length/cadence) on an instrumented walkway; (2) cognition: Trails A and B (3) walking-confidence: Gait efficacy Scale. Mann Whitney U-tests indicated individuals without FOF had better gait quality (p<0.05): greater smoothness (2.38\u00b1.58 vs 1.14\u00b1.73), speed (1.10\u00b1.15 vs 1.04\u00b1.17 m/s) and walk-ratio (.56\u00b1.07 vs .53\u00b1.08 cm/steps/min), lower step-time CoV (3.72\u00b11.24 vs 4.17\u00b11.66), and greater walking-confidence (89\u00b111 vs 79\u00b113). A random forest classifier predicted FOF with 64% (gait only) and 70% accuracy; Gini-index based ranking indicated gait quality direction, walking speed) were consistently important variables. Linear Support Vector Machine learning yielded accuracies of 60% (only gait) and 68% : smoothness V, mediolateral frequency bandwidth, gait speed among top 4 ranked variables in both models, and walking-confidence in the additional measures model; smoothness-V the highest weighted coefficient (-0.52). Based on these findings, interventions targeted for gait quality and walking-confidence may be important to overcome FOF and reduce fall risks."} +{"text": "Staphylococcus aureus (MRSA), there have been few studies focused on the molecular characterization of methicillin-susceptible Staphylococcus aureus (MSSA). In this cross-sectional study, 85 MSSA isolates were characterized by antimicrobial susceptibility testing, virulence genes analysis, accessory gene regulator (agr) typing, and S. aureus protein A locus (spa) typing.Compared to methicillin-resistant agr types detected in tested strains were mainly type I (76.5%), II (12.9%), and III (10.6%). Of 85 MSSA examined isolates, 48 (56.5%) isolates were toxinogenic with 27 producing pvl (31.8%) and 21 tst (24.7%). The findings of the study show a high genetic diversity in MSSA strains warranting continued surveillance to provide critical insights into control and treatment of MSSA infections.In present study, 9 different clonal complexes namely CC8-MSSA-t037 (22.4%), CC8-MSSA-t008 (11.8%), CC7-MSSA-t091 and CC30-MSSA-t021 (each 9.4%), CC8-MSSA-t037 (8.3%), CC398-MSSA-t034 (7.1%), CC22-MSSA-t005 (5.9%), CC5-MSSA-t002 and CC15-MSSA-t084 (each 4.7%), CC22-MSSA-t790 and CC59-MSSA-t437 (each 3.5%), CC22-MSSA-t1869, CC5-MSSA-t045, and CC45-MSSA-t015 (each 2.3%), CC30-MSSA-t318 and CC15-MSSA-t491 (each 1.2%) were found. Staphylococcus aureus is a common hospital- and community-acquired pathogen [S. aureus strain diversity appears to differ by geographic region, there has been a dramatic increase in the prevalence of S. aureus strains associated with human infections around the world and this appears to be especially true for methicillin-susceptible Staphylococcus aureus (MSSA) [S. aureus infections [pathogen . It is rpathogen . Althougs (MSSA) \u20135. MSSA s (MSSA) , 6. Comps (MSSA) . Antimicfections , 8. Knowfections , 10. AltS. aureus isolates phenotypically by using standard microbiological techniques. Polymerase chain reaction (PCR) assay targeting the S. aureus-specific nuc gene was applied to verify the isolates [S. aureus isolates susceptible to cefoxitin disc in a disc diffusion assay using established methods (CLSI 2018) and negative for the presence of mecA gene by PCR were considered as MSSA strains [Eighty-five MSSA isolates were obtained from hospitalized patients at four hospitals affiliated to Shahid Beheshti University of Medical Sciences during an 9-month collection period from March 2019 to November 2019. This study protocol was approved by the Ethics Committee of the Shahid Beheshti University of Medical Sciences in Tehran, Iran (IR. SBMU. MSP.REC. 1398. 774). Furthermore, we confirmed isolates , 12. TheS. aureus ATCC 25923, ATCC 43300, and ATCC 29213 strains.In present study, Kirby\u2013Bauer disk diffusion method was applied to determine the antimicrobial susceptibility of isolates based on the clinical and laboratory standards institute (CLSI) criteria (CLSI 2018). The antimicrobial agents included penicillin, teicoplanin, gentamicin, kanamycin, amikacin, tobramycin, clindamycin, erythromycin, tetracycline, linezolid, rifampicin, mupirocin, ciprofloxacin, quinupristin\u2013dalfopristin, and trimethoprim\u2013sulfamethoxazole . The minimal inhibitory concentrations (MIC) values of vancomycin was evaluated by broth microdilution method. Susceptibility test was quality controlled by using eta, and etb), Panton-Valentine leukotoxin gene (pvl), and toxic shock syndrome toxin (tsst-1) by PCR assay [S. aureus ATCC49775 and toxin positive S. aureus\u00a0strains obtained from our previous were used as reference strains [S. aureus strain ATCC 25923 were also used as negative control.Genomic DNA was isolated using the phenol\u2013chloroform extraction method. All of the isolates were screened for virulence encoding genes namely: exfoliative toxin genes (CR assay \u201314. The agr type detection using primer set comprising a common forward primer (Pan) and reverse primers specific to each agr group [agr types were identified by comparing the banding patterns of isolates to RN6390 (agr type I), RN6607 (agr type II), RN8465 (agr type III), RN4550 (agr type IV), and RN6911 (negative control), as reference strains. PCR amplification was used for spa typing as described previously [spa gene amplified by PCR with forward (5\u2032-AGACGATCCTTCGGTGAGC-3\u2032) and reverse (5\u2032-GCTTTTGCAATGTCATTTACTG-3\u2032) primers. The purified PCR products were sequenced and then edited. The Ridom SpaServer database (http://www.spaserver.ridom.de) was applied to determine the spa type of each isolate. Each set of PCR reactions include a spa-type t008 isolate from our previous study as positive control sample (14), and a reaction mixture containing no template DNA as a control for possible false positive results.Multiplex PCR was performed for gr group . agr typeviously . In thispvl (31.8%) and 21 tst (24.7%).The sources of isolates included: skin and soft tissue wounds (44.7%), purulent exudates from wounds or abscesses 17.7%), urine (14.1%), blood (11.8%), sputum (8.2%), and other body fluids (3.5%). Out of 85 MSSA isolates, 29 isolates were obtained from hospital H1 (34.1%), 25 isolates from hospital H2 (29.4%), 20 isolates from hospital H3 (23.5%), and 11 isolates from hospital H4 (13%). Among 85 MSSA isolates tested, the highest rate of resistance was detected for penicillin (74.1%), and gentamicin (54.1%). , II (12.9%), and III (10.6%). spa results showed 16 types corresponding to nine clonal complexes (CCs), namely CC8 (42.3%), CC22 (11.8%), CC30 (10.6%), CC7 (9.4%), CC5 (7.1%), CC398 (7.1%), CC15 (5.9%), CC59 (3.5%), and CC45 (2.3%). spa type t037 was the most common spa type identified among 85 MSSA isolates, with a frequency of 22.3%, followed by t008 (11.8%), t021 and t091 (each 9.4%), t030 (8.2%), t034 (7%), t005 (5.9%), t084 and t002 (each 4.7%), t790 and t437 (each 3.5%), t1869, t045, and t015 (each 2.4%), t318 and t491 (each 1.2%) (Table\u00a05%), II 1.9%, and Inducible clindamycin resistance was observed in CC8-MSSA-t037 (n\u2009=\u20095), CC30-MSSA-t021 (n\u2009=\u20094) CC8-MSSA-t008 (n\u2009=\u20093) isolates; while constitutive resistance phenotype was observed in CC8-MSSA-t037 (n\u2009=\u20098), CC8-MSSA-t030 (n\u2009=\u20093), CC-MSSA-t034 (n\u2009=\u20094), CC-MSSA-t091 (n\u2009=\u20095), CC-MSSA-t045 (n\u2009=\u20094), CC-MSSA-t005 (n\u2009=\u20094), and CC-MSSA-t790 (n\u2009=\u20091) isolates. Detailed results of the genotype distribution are presented in Table\u00a0spa types among MSSA isolates. We detected CC8 in 42.3% of isolates. Although multi-resistant CC8 was previously reported as one of the main international CCs of MRSA, the predominance of the CC8-MSSA clone has previously been reported in Europe [Infection with MSSA as the most common pathogen in hospitalized patients is becoming increasingly problematic globally and requires special attention . As presn Europe and Afrin Europe , 19. We n Europe , Irelandn Europe , and Nign Europe . We confn Europe , 21. As n Europe .We noted a relatively low prevalence of CC7 (9.4%), CC5 (7.1%), CC398 (7.1%), CC15 (5.9%), CC59 (3.5%), and CC45 (2.3%) in our study. A study conducted in China during the 4-year period indicated that CC22-t309 26.0%), CC188-t189 (5.1%), CC796-t796 (4.8%), CC121-t435 (4.8%), and CC398-t571 (3.6%) were the most dominant clones among MSSA isolates . They de.0%, CC18pvl encoding gene. Prevalence PVL positive MSSA strains has varied among studies from different geographic regions including China (34.4%) [Present results demonstrated that out of the 85 tested MSSA, 27 isolates 31.8%) carried 1.8% carr 34.4%) , Ireland (34.4%) , Colombi.4% , Ire (34.4%) , Russia (34.4%) . In a re (34.4%) . However (34.4%) , 19. In (34.4%) , 26, 28, (34.4%) .tst positive. This reported rate was different from the earlier studies in Africa (7%) [tst gene were associated with CC8-MSSA-t037 (11.8%), CC8-MSSA-t0307 (5.9%), CC22-MSSA-t790 (3.5%), and CC59-MSSA-t437 (3.5%) clones. A multicenter study\u00a0from china reported that 4.0% of MSSA isolates carried tst\u00a0gene which belonged to CC5 clone [tst-positive MSSA was distributed into four STs and the majority of them belonged to CC30 clone [tst encoding gene among S. aureus clinical isolates (21.3%) [tst were significantly higher in MSSA isolates in comparison to MRSA isolates (18.1% vs. 11.6%) [tst-positive MSSA clones seems geographically different and CC8 may represent a newly emerging clone in Iran.In our strain collection, 24.7% of isolates were ica (7%) , China (ica (7%) and Turkica (7%) . Contrarica (7%) , 31 whicC5 clone . A recenSSA-t037 .8%, CC8- (21.3%) . In a st. 11.6%) . Overallagr genotypes are strictly associated with the clonal lineages [agr type I, as the most predominant type (76.4%), was associated with CC8, CC22, CC7, CC45, CC398, and CC59 isolates. In line with our results, Croes et al. demonstrated that CC7, CC8, CC22, CC25 and CC45 clonal lineages harbored agr I [agr type I (68.8%), followed by agr III (18.7%), and agr IV (12.5%) among MSSA isolates [According to the evidence, the lineages , 35. In ant type 6.4%, wasOur research had some limitations. Firstly, present work lacks detailed clinical information about the patients, Secondly, our samples were not collected consecutively. Thirdly, whole genome sequencing technique was not applied in the present work due to some of technical limitations."} +{"text": "The results showed that a HSD, salt gene overexpression and dFOXO knockdown significantly reduced climbing endurance, climbing index, survival, dFOXO expression and SOD activity level, and increased malondialdehyde level in aging flies. Inversely, in a HSD aging flies, endurance exercise and dFOXO overexpression significantly increased their climbing ability, lifespan and antioxidant capacity, but they did not significantly change the salt gene expression. Overall, current results indicated that a HSD accelerated the age-related decline of climbing capacity and mortality via upregulating salt expression and inhibiting the dFOXO/SOD pathway. Increased dFOXO/SOD pathway activity played a key role in mediating endurance exercise resistance to the low salt tolerance-induced impairment of climbing capacity and longevity in aging Drosophila.A high-salt diet (HSD) is a major cause of many chronic and age-related defects such as myocardial hypertrophy, locomotor impairment and mortality. Exercise training can efficiently prevent and treat many chronic and age-related diseases. However, it remains unclear whether endurance exercise can resist HSD-induced impairment of climbing capacity and longevity in aging individuals. In our study, flies were given exercise training and fed a HSD from 1-week old to 5-weeks old. Overexpression or knockdown of This article has an associated First Person interview with the first author of the paper. Summary: Increased dFOXO/SOD pathway activity played a key role in mediating endurance exercise resistance to the salt tolerance-induced impairment of climbing capacity and longevity in aging Drosophila. Sodium chloride from dietary salt supplies essential electrolytes to the human body, and it plays a vital role in maintaining the stability of the intracellular and extracellular environments . DespiteExercise training is an efficient strategy for the prevention and treatment of many chronic diseases caused by diet or aging such as myocardial hypertrophy, hypertension and obesity . For exaDrosophila melanogaster provides significant practical advantages over other model systems to study the molecular mechanisms of exercise training, nutrition and aging, which include developed exercise and diet programs, a short lifespan (2\u20133\u2005months), low genetic redundancy compared with mammals, and a plethora of tools available to easily manipulate gene expression , but a 2%-SD had no remarkable influence on CI (P>0.05) , a 4%-SD and an 8%-SD significantly reduced the climbing fatigue time (CFT) (ctively) B. In 3-wctively) C. In 5-wctively) D. In addctively) E\u2013H. Nextctively) I. In 1-w(P>0.05) J. In 3-wctively) J. In 5-wctively) J. These Drosophila. In this experiment, the results showed that a 2%-SD significantly reduced the lifespan of Drosophila (P<0.05), and a 4%-SD and an 8%-SD acutely reduced lifespan of flies K. These Drosophila (P>0.05) (P>0.05) (P>0.05) , and senility significantly decreased their CI (P<0.01) (P<0.05), and senility significantly decreased their CI (P<0.01) (P<0.05), but the CI of 4%-SD and 5-week-old flies did not change significantly after exercise training (P>0.05), and senility significantly decreased their CI (P<0.01) (P>0.05), and senility significantly decreased their CI (P<0.01) (P<0.05) (P>0.05) A\u2013C, but (P>0.05) D. Furthectively) E\u2013G, but (P>0.05) H. Moreovctively) I,J, and (P>0.05) K,L. The (P<0.01) M. In 2%-(P<0.01) N. In 2%-(P<0.01) O. The CI(P<0.01) P. What i(P<0.05) Q,U, but (P>0.05) V,W. ThesD. melanogaster , and the expression of Salt gene of 2%-SD flies, 4%-SD flies and 8%-SD flies did not change significantly after exercise training (P>0.05) (dFOXO gene (P<0.01), and exercise training significantly increased the dFOXO gene expression in the 0%-SD flies, 2%-SD flies and 4%-SD flies , but dFOXO gene expression of the 8%-SD flies did not change significantly after exercise training (P>0.05) (P<0.01), and exercise training significantly increased the SOD level of the 0%-SD flies, 2%-SD flies and 4%-SD flies , but the SOD level of the 8%-SD flies did not change significantly after exercise training (P>0.05) , and exercise training significantly decreased the MDA level of the 0%-SD flies, 2%-SD flies and 4%-SD flies (P<0.05), but the MDA level of the 8%-SD flies did not change significantly after exercise training (P>0.05) A. In add(P>0.05) B. Moreov(P>0.05) C. Finall(P>0.05) D. These FOXO is associated with an increase in the expression of SOD and SOD activity , exercise training significantly increased the CFT (P<0.05) , exercise training significantly increased the CFT (P<0.05) , exercise training could not be said to significantly increase the CFT (P>0.05) , but exercise training significantly increased the CI (P<0.05) , but exercise training significantly increased the CI (P<0.01) , but exercise training significantly increased the CI (P<0.01) , but exercise training significantly increased lifespan (P<0.05) A. In 3-w(P<0.05) B. Howeve(P>0.05) C. Next, (P<0.01) D. In 1-w(P<0.05) E. In 3-w(P<0.01) E. In 5-w(P<0.01) E. Moreov(P<0.05) F,G. ThesSalt gene (P<0.01), but exercise training did not significantly decrease the expression of the Salt gene (P>0.05) , but exercise training significantly increased the expression of dFOXO gene (P<0.05) , but exercise training significantly increased the SOD level (P<0.01) , but exercise training significantly increased the MDA level (P<0.01) H. In add(P<0.05) I. Moreov(P<0.01) J. Finall(P<0.01) K. These salt gene knockdown can improve salt tolerance, and it can increase the survival of a HSD fly , and a HSD also did not significantly reduce the CFT (P>0.05) , and a HSD also did not significantly reduce the CI (P>0.05) , and a HSD also did not significantly reduce the lifespan (P>0.05) , but a HSD did not significantly increased the salt gene expression (P>0.05) A\u2013C. In s(P<0.01) D. Howeve(P>0.05) E. What i(P>0.05) F,G, whic(P>0.05) . Next, t(P>0.05) H. Finall(P>0.05) I\u2013K. ThesSalt gene function takes part in regulating salt tolerance, and downstream it regulates antioxidant function, climbing capacity and aging.Two principal classes of manipulation are usually employed to study gene function. Loss-of-function (LOF) approaches attempt to eliminate gene function partially or completely. Gain-of-function (GOF) approaches attempt to obtain functional information by creating conditions where the gene is excessively or ectopically expressed or its function exaggerated . In thisdFOXO gene expression was also changed by UAS/Gal4 system in flies, and their CFT, CI and lifespan were measured.In animals, it has been identified that a HSD increases the oxidative stress and causes cell damage . In fliedFOXO gene overexpression significantly increased the CFT (P<0.05), and it significantly increased the CFT in HSD 1-week-old flies (P<0.001) (dFOXO gene overexpression significantly increased the CFT (P<0.05), and it also significantly increased the CFT in HSD 3-week-old flies (P<0.001) (dFOXO gene overexpression significantly increased the CFT (P<0.05), and it also significantly increased the CFT in HSD 5-week-old flies (P<0.01) (dFOXO gene significantly increased the CI (P<0.05), and it also significantly increased the CI in HSD 1-week-old flies (P<0.05) (dFOXO gene significantly increased the CI (P<0.05), and it also significantly increased the CI in HSD 3-week-old flies (P<0.01) (dFOXO gene significantly increased the CI (P<0.01), and it also significantly increased the CI in HSD 5-week-old flies (P<0.01) (dFOXO gene significantly increased the lifespan of flies (P<0.05), and it also significantly increased the lifespan of HSD flies (P<0.01) A. In 3-wP<0.001) B. In 5-w(P<0.01) C. Moreov(P<0.01) D. In 1-w(P<0.05) E. In 3-w(P<0.01) E. In 5-w(P<0.01) E. Furthe(P<0.01) F,G. ThesdFOXO gene (P<0.01), it also significantly increase the dFOXO gene expression in HSD flies (P<0.01) , and it also significantly did not change the salt gene expression in HSD flies (P>0.05) (dFOXO gene significantly increased the SOD level (P<0.01), and it also significantly increased the SOD level in HSD flies (P<0.01) (dFOXO gene significantly decreased the MDA level (P<0.01), and it also significantly increased the MDA level in HSD flies (P<0.01) I. In add(P>0.05) H. Howeve(P<0.01) J. Finall(P<0.01) K. These dFOXO gene knockdown significantly decreased the CFT and CI in flies , and a HSD aggravated the lifespan reduction in dFOXO gene knockdown flies (P<0.01) , but a HSD significantly increased the salt gene expression in dFOXO gene knockdown flies (P<0.01) (dFOXO gene RNAi significantly decreased the dFOXO gene expression (P<0.01), and a HSD aggravated dFOXO gene expression reduction in dFOXO gene knockdown flies (P<0.01) (dFOXO gene knockdown significantly decreased the SOD activity level (P<0.01), and a HSD aggravated SOD activity level reduction in dFOXO gene knockdown flies (P<0.01) (dFOXO gene knockdown significantly increased the MDA level (P<0.01), and a HSD aggravated MDA level increase in dFOXO gene knockdown flies (P<0.01) A\u2013E, and P<0.001) A\u2013E. More(P<0.01) F,G. Howe(P<0.01) H. Next, (P<0.01) I. Simila(P<0.01) J. Finall(P<0.01) K. TherefdFOXO gene function is closely to lifespan in flies. For instance, the dFOXO overexpression decreased mortality and increased lifespan of flies via reducing oxidative stress, and the dFOXO is required both for transcriptional changes that mark the fly's dietary history and for nutritional programming of lifespan by excess dietary sugar . The UAS-salt-overexpression flies , the UAS-dFOXO-overexpression flies , and the arm-gal4 flies were obtained from the Bloomington Stock Center. The UAS-salt-knockdown flies and the UAS-dFOXO-knockdown flies were obtained from the Vienna Drosophila Resource Center .The KO saltmir-1014-KO\u2019 and \u2018arm-gal4>w*; TI /total dead numbers. Sample sizes were 200\u2013210 flies per group method. Ten fresh-frozen flies were converted to homogenates in a homogenizer filled with 1\u2005ml PBS (pH 7.2\u20137.4). The homogenates were centrifuged at 4\u00b0C for 15\u2005min with a speed of 2000\u2005r/min. The supernatant was mixed with the reagents supplied in an MDA Assay Kit and incubated at 95\u00b0C for 40\u2005min. After cooling at room temperature, the mixture was centrifuged at 4000\u2005The total SOD activity in flies was determined using the hydroxylamine method. Ten fresh-frozen flies were converted to homogenates in a homogenizer filled with 1\u2005ml PBS (PH7.2\u20137.4). The homogenates were centrifuged at 4\u00b0C for 15\u2005min with a speed of 2000\u2005r/min. The supernatant was mixed with the reagents supplied in a SOD Assay Kit . The mixture was incubated at room temperature for 10\u2005min, and the absorbance of the compound was then measured at 550\u2005nm. All operations were according to the manufacturer's instructions. Each preparation was tested in triplicate. SOD activity was expressed as U/ml. All assays were repeated three times.salt were as follows: F: 5\u2032-TTAATCGCAGGCGCGTCAGTG-3\u2032; R: 5\u2032-GGACGAGACCACCGTGTTAATCAG-3\u2032. Primer sequences of dFOXO were as follows: F: 5\u2032-AACAACAGCAGCATCAGCAG-3\u2032; R: 5\u2032-CTGAACCCGAGCATTCAGAT-3\u2032. Primer sequences of Rp49 were as follows: F:5\u2032-CTAAGCTGTCGCACAAATGG-3\u2032; R:5\u2032-AACTTCTTGAATCCGGTGGG-3\u2032.About ten flies were homogenized in Trizol. First, 10\u2005\u03bcg of the total RNA was purified by organic solvent extraction from the Trizol . The purified RNA was treated with DNase I and used to produce oligo dT-primed cDNAs , which were then used as templates for quantitative real-time PCR. The rp49 gene was used as an internal reference for normalizing the quantity of total RNAs. Real-time PCR was performed with SYBR green using an ABI7300 Real time PCR Instrument (Applied Biosystems), with three biological replicates. Expression of the various genes was determined by the comparative CT method . Primer sequences of dFOXO overexpression on flies. Using a non-parametric followed by a log-rank test for analyzing survival and time to fatigue. Analyses were performed using the Statistical Package for the Social Sciences (SPSS) version 16.0 for Windows , with statistical significance set at P<0.05. Data are represented as means\u00b1s.e.m.The one-way ANOVA with LSD tests were used to identify differences among the relevant groups. A two-way ANOVA was used to analyze the effects of a HSD and"} +{"text": "Correction to: Glob Health Res Policy (2020) 5:54https://doi.org/10.1186/s41256-020-00183-yAfter publication of this article , it is nThe correct reference 7 is below:Wang X, Yu Y, Hu Y, Yu C. COVID-19 analysis and forecast based on exponential smoothing model in Hubei Province. J Public Health Prev Med. 2020;31(1):1\u20134. (in Chinese)The original article has been updated."} +{"text": "Correction to: Mol Cancer (2019) 18:126https://doi.org/10.1186/s12943-019-1054-7After publication of the article , the autThe correct figures are updated below.Fig.3i and jFig.4hAdditional file 3: Figure S2d"} +{"text": "Candidatus Dehalogenimonas etheniformans\u201d strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.9% and harbors 50 putative reductive dehalogenase genes.\u201c Candidatus Dehalogenimonas etheniformans\u201d strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.9% and harbors 50 putative reductive dehalogenase genes.\u201c Dehalogenimonas are obligate organohalide-respiring bacteria implicated in the turnover of naturally occurring and anthropogenic chlorinated compounds in anoxic environments . Paired-end sequencing (2\u2009\u00d7\u2009150\u2009bp) was performed using a NovaSeq PE150 flow cell . The sequence reads were trimmed and filtered (https://github.com/lh3/readfq), resulting in 4,073,240 high-quality reads. Assembly using NanoPore raw long reads and Illumina short reads was performed using Unicycler version 0.4.7 (Genomic DNA from strain GP biomass was extracted using the cetyltrimethylammonium bromide method . For Nanon 0.4.7 . Unicyclon 0.4.7 .rdh) subunit A genes, including cerA (locus tag number HX448_10020), which encodes a VC rdh of D. formicexedens strain NSZ-14T (D. formicexedens strain NSZ-14T (GenBank accession number CP018258.1), D. alkenigignens strain IP3-3T (shotgun sequencing project accession number LFDV00000000.1), Dehalogenimonas sp. strain WBC-2 (GenBank accession number CP011392.1), and D. lykanthroporepellens strain BL-DC-9T (GenBank accession number CP002084.1), respectively. The new data expand the Dehalogenimonas pangenome and rdh sequence diversity.The genome comprises one circular 2,068,322-bp chromosome with a G+C content of 51.9%. The genome contains 2,029 coding sequences, 47 tRNA genes, and single copies of the 5S, 16S, and 23S rRNA genes. The GP genome harbors 50 nonidentical reductive dehalogenase (CP058566.1). The BioSample and BioProject accession numbers are SAMN15398252 and PRJNA258024, respectively. The raw reads were deposited in the Sequence Read Archive under accession numbers SRR12774736 (Nanopore) and SRR12774735 (Illumina).The genome has been deposited at the DNA Data Bank of Japan, the European Nucleotide Archive, and GenBank (accession number"} +{"text": "Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1\u20133 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost.Worldwide, the cultivated potato, Here, we present an updated version of the DM1\u20133 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes.Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution. Solanum tuberosum L., NCBI:txid4113) was published in 2011 by the Potato Genome Sequencing Consortium (PGSC) using a whole-genome shotgun sequencing approach [The genome of the vegetable crop potato . Howeveg; a total of 6.2 g of shoot tissue was split across 6 separate nuclei isolations. Modifications to the protocol include squeezing the homogenate through 5 layers of Miracloth instead of gravity filtering alone and 2 washes with nuclear isolation buffer. DNA was isolated from nuclei using the Nanobind Plant Nuclei Big DNA\u2014Alpha Version kit following the Nanobind Plant Nuclei Big DNA Kit Handbook v0.17 (May 2018). DNA libraries were prepared using the ONT SQK-LSK109 Ligation Sequencing kit . Six libraries were prepared and sequenced on 6 separate R9 ONT flow cells . DNA repair and end preparation were performed with an input of 1 \u03bcg of DNA. The repair and end preparation reaction were incubated for 5\u201345 minutes at 20\u00b0C and 5\u201345 minutes at 60\u00b0C. The reaction was cleaned using Agencourt AMPure XP beads with an incubation time of 5\u201310 minutes on a rotator mixer and eluted for 2\u20135 minutes. Ligation of adapters to the prepared DNA was performed at room temperature for 10\u201360 minutes. The ligation reaction was cleaned using Agencourt AMPure XP beads on a rotator mixer with an incubation time of 5\u201310 minutes with an elution time of 10 minutes. Sequencing was performed on an ONT MinION with the current release of MinKNOW (version 1.15.0). Sequencing was run for 48\u201392 hours (RRID:SCR_016383) in paired-end mode, generating 150\u00a0nt reads (DM plants were grown in Murashige and Skoog (MS) medium , shoots harvested, and flash frozen in liquid nitrogen. Nuclei were isolated following the Workman et al. protocol92 hours . DNA wasnt reads . Hi-C lint reads .RRID:SCR_018927) [RRID:SCR_017016) [RRID:SCR_017642) [RRID:SCR_018550) [RRID:SCR_016157) [RRID:SCR_002105) [RRID:SCR_014731) [RRID:SCR_011841) [RRID:SCR_010910) [RRID:SCR_006525) [RRID:SCR_006525), all using default parameters. Pilon was run using the \u201c\u2013fix bases\u201d option. The polished contigs are composed of 1,382 contigs with a total size of 745.6 Mb with an N50 contig size of 17.3 Mb and a maximum contig length of 42.1 Mb on an A_018927) to remov_017016) with the_017642) . For eac_018550) with the_016157) . Reads w_016157) with the_002105) . An upda_014731) . The Ill_011841) to remov_006525) , and theRRID:SCR_017226) [RRID:SCR_017227) [RRID:SCR_016665) [S. tuberosum mitochondrion genome using blastn v2.9.0 [To construct chromosome-scale pseudomolecules, the Hi-C library was first processed using the juicer.sh pipeline from the Juicer package (git commit 6403a27) . The pse_017227) and the _017227) (Supplem_017227) database_016665) with the_001598) . FifteenRRID:SCR_011841) [RRID:SCR_010910) [RRID:SCR_015008) [k-mers (k = 21) from the cleaned Illumina whole-genome shotgun library (PEP_AA_01) using Jellyfish2 v2.2.10 [k-mer count histogram was analyzed by the online version of GenomeScope [To assess completeness and accuracy of the v6.1 assembly, \u223c458 million paired-end reads from a whole-genome Illumina sequencing library was used_010910) . Alignme_015008) software_015008) . Of 1,61_005491) . The k-m_017014) and the RRID:SCR_018970) [RRID:SCR_018969) [RRID:SCR_017623) [Arabidopsis thaliana TAIR10 (LAI = 14.9), Fragaria vesca v4.1 (LAI = 16.9), and Solanum pennellii (LAI = 14.8) [The Long Terminal Repeat (LTR) Assembly Index (LAI) metric w_018970) , LTR_FIN_018969) , and LTR_017623) . LTR seq = 14.8) . The LAIin situ hybridization (oligo-FISH) probes, which mark 26 regions on the 12 chromosomes, have been used to characterize potato karyotypic variation [Solanum species. We aligned the oligo-FISH probes to v6.1 using BWA-MEM v0.7.12-r1039 [Two \u201cbarcode\u201d oligonucleotide fluorescent ariation , as well_010910) to confiRRID:SCR_018968) [RRID:SCR_010910) [RRID:SCR_006646) [Cen12 is properly positioned on the short arm of v6.1 chromosome 12 with 200_018968) . ChIP-se_010910) using de 12 Fig.\u00a0. The imp6.1 Fig.\u00a0. In v4.0nce Fig.\u00a0. The siznce Fig.\u00a0. These cRRID:SCR_018967) [To better depict the improved contiguity and accuracy of v6.1 relative to v4.04, D-GENIES was usedRRID:SCR_015027) [RRID:SCR_001653) [RRID:SCR_012954) [A custom repeat library (CRL) was generated using RepeatModeler2 v2.0.1 with the_015027) using bl_001653) with an Cen4, Cen6, Cen10, Cen11, and Cen12) lack typical centromere-specific satellite repeats and, instead, are composed of single- or low-copy sequences resembling neocentromeres [Cen1, Cen2, Cen3, Cen5, Cen7, and Cen8) that contain megabase arrays of satellite repeats. Interestingly, the satellite repeats for these 6 centromeres are unique to individual chromosomes, some of which are derived from retrotransposons. Centromeric repeat sequences from Gong et al. [RRID:SCR_004870) [Cen2, Cen5, and Cen7 in v.6.1 but not in v4.04 with aliRRID:SCR_018966) [RRID:SCR_018927) [RRID:SCR_018550) with the parameters -a -x splice -uf -G 5000; 5,783,924 (99.98%) of the 5,784,833 filtered reads aligned to the DM assembly. The cDNA alignments were assembled using Stringtie2 v2.1.2 [RRID:SCR_018965) [RRID:SCR_011841) [RRID:SCR_015530) [RRID:SCR_016323) [RRID:SCR_018965) [To facilitate annotation of gene models, ONT complementary DNA (cDNA) sequences were generated from DM. DM was grown under a 16-hour day length in tissue culture and RNA was isolated from whole tissue-culture plants using a modified hot borate method . DNA con_018966) to ident_018927) to remov_016323) (-L -m 5_018965) . Illumin_011841) with the_015530) with the_016323) with the_018965) . Both thRRID:SCR_018964) [RRID:SCR_008417) [RRID:SCR_011930) [ab initio gene predictions. The BRAKER2 pipeline was run using the command line: braker.pl \u2013species = DM_v6_1 \u2013gff3 \u2013softmasking \u2013UTR = off \u2013bam {RNA-seq.alns.bam}. Ab initio gene predictions were refined using PASA2 v2.4.1 [RRID:SCR_004726) [RRID:SCR_005305) [RRID:SCR_016582) [The BRAKER2 (git commit 6219573) gene pre_011930) and the _005305) with a c_016582) .Arabidopsis proteome [RRID:SCR_004726) [RRID:SCR_002380). Search results were processed in the same order, and the function of the first hit encountered was assigned to the gene model. The quality of the annotation was evaluated using BUSCO [High-confidence gene models were defined as having a TPM value >\u00a00 in \u22651 RNA-Seq library and/or having a PFAM domain match. Gene models that were partial or had matches to transposable element\u2013related PFAM domains were excluded from the high-confidence model set. A total of 32,917 loci encoding 44,851 gene models are contained within the high-confidence set . To assi_004618) , the PFA_004726) , and theng BUSCO , and botUsing improved sequencing technologies, the genome sequence of the reference potato genotype DM was vastly improved in contiguity relative to the previous release, DM v4.04. Version 6.1 of the DM genome assembly represents 87.8% of the estimated genome, with 595-fold increase in N50 contig size, 99% reduction in number of contigs, and a 44-fold increase in N50 scaffold size. Importantly, 731.2 Mb of the 741.6-Mb assembly is non-gapped and anchored to the 12 chromosomes, indicating a high degree of contiguity that was reflected in a \u201creference quality\u201d LAI score, demonstrating the ability of advanced sequencing methods to assemble large contiguous regions of a medium-sized plant genome. With access to full-length cDNA sequences, 32,917 high-confidence protein-coding genes encoding 44,851 gene models were annotated, which provided a substantial improvement in representation of conserved orthologs compared with the previous annotation that will facilitate future studies in potato biology, genetics, and genomics.GigaScience GigaDB [The clone, DM1\u20133516 R44, is available through the United States Department of Agriculture Potato Genebank via PI GS 233 . The rawe GigaDB , Dryad De GigaDB , and on e GigaDB , 73 via Supplementary Figure S1. Hi-C contact map showing the inter- and intra-chromosomal chromatin interactions in DM v6.1. Inter-chromosomal chromatin interactions are off the diagonal axis and intra-chromosomal chromatin interactions are within the blue boxes. Each pixel represents the degree of interaction between each 1-Mb locus, with a dark red color indicating a greater number of reads involved in the interaction. The blue boxes represent the boundaries of each pseudomolecule, and individual scaffold boundaries are represented by the green boxes.k-mer of 21.Supplementary Figure S2. Estimation of heterozygosity of the DM genome as determined by GenomeScope. The DM genome has an estimated heterozygosity rate of 0.0383% using a RRID:SCR_018968) [Supplementary Figure S3. Mapping of the DM \u00d7 RH F1 population markers to the (a) DM v4.04 and the (b) DM v6.1 assembly. Flanking sequence (200\u00a0nt) of the markers was used for sequence alignments to the assembly using Vmatch . The y-aSupplementary Table S1. Sequence datasets used in this study. Total reads for Oxford Nanopore Technologies sequencing are passed reads after base-calling.Supplementary Table S2. Oxford Nanopore Technologies whole-genome shotgun sequence reads used in the DM v6.1 assembly.Supplementary Table S3. Illumina whole-genome shotgun sequence read mapping statistics.Supplementary Table S4. BUSCO results Supplementary Table S5. Centromere positions in the DM v6.1 assembly.Supplementary Table S6. Repetitive sequence content in v4.04 and v6.1 DM 1\u20133516 R44 genome assemblies.Supplementary Table S7. DM v6.1 gene annotation summary.giaa100_GIGA-D-20-00167_Original_SubmissionClick here for additional data file.giaa100_GIGA-D-20-00167_Revision_1Click here for additional data file.giaa100_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giaa100_Reviewer_1_Report_Original_SubmissionJian-Feng Mao, Ph.D. -- 7/7/2020 ReviewedClick here for additional data file.giaa100_Reviewer_2_Report_Original_SubmissionAlexis Sullivan -- 8/10/2020 ReviewedClick here for additional data file.giaa100_Supplemental_FilesClick here for additional data file.in situ hybridization; ONT: Oxford Nanopore Technologies; PASA: Program to Assemble Spliced Alignments; PGSC: Potato Genome Sequencing Consortium; RNA-Seq: RNA-sequencing; SRA: Sequence Read Archive; TPM: transcripts per million.BLAST: Basic Local Alignment Search Tool; bp: base pairs; BUSCO: Benchmarking Universal Single-Copy Orthologs; cDNA: complementary DNA; ChIP-Seq: chromatin immunoprecipation sequencing; CRL: custom repeat library; Gb: gigabase pairs; kb: kilobase pairs; LAI: LTR Assembly Index; LTR: long terminal repeat; Mb: megabase pairs; mRNA: messenger RNA; NCBI: National Center for Biotechnology Information; nt: nucleotide; oligo-FISH: oligonucleotide fluorescent The authors declare that they have no competing interests.C.R.B. conceived the study. G.M.P., J.P.H., B.V., and J.C.W. performed the experiments. J.T.B., J.P.H., J.J., G.M.P., S.O., B.V., J.C.W., and H.Z. analyzed data. C.R.B., J.P.H., J.J., G.M.P., B.V., J.C.W., and H.Z. wrote the manuscript. All authors approved the final manuscript."} +{"text": "Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018, Serratella sp. Liaoning-2019, Torleya grandipennis and T. tumiforceps. These mitogenomes were employed to reveal controversial phylogenetic relationships among the Ephemeroptera, with emphasis on the phylogenetic relationships among Ephemerellidae. The lengths of the six mayfly mitogenomes ranged from 15,134 bp to 15,703 bp. Four mitogenomes of Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018 and Serratella sp. Liaoning-2019 had 22 tRNAs including an inversion and translocation of trnI. By contrast, the mitogenomes of T. tumiforceps and T. grandipennis had 24 tRNAs due to an extra two copies of inversion and translocation of trnI. Within the family Ephemerellidae, disparate gene rearrangement occurred in the mitogenomes of different genera: one copy of inversion and translocation trnI in the genera Ephemerella and Serratella, and three repeat copies of inversion and translocation of trnI in the genus Torleya. A large non-coding region (\u2265200 bp) between trnS1 (AGN) and trnE was detected in T. grandipennis and T. tumiforceps. Among the phylogenetic relationship of the Ephemeroptera, the monophyly of almost all families except Siphlonuridae was supported by BI and ML analyses. The phylogenetic results indicated that Ephemerellidae was the sister clade to Vietnamellidae whereas Teloganellidae was not a sister clade of Ephemerellidae and Vietnamellidae.As a small order of Pterygota (Insecta), Ephemeroptera has almost 3,500 species around the world. Ephemerellidae is a widely distributed common group of Ephemeroptera. However, the relationship among Ephemerellidae, Vietnamellidae and Teloganellidae is still in dispute. In this study, we sequenced six complete mitogenomes of three genera from Ephemerellidae (Insecta: Ephemeroptera): BecauseSiphluriscus chinensis (Siphluriscidae) had one extra trnK-like gene (trnK 2 (AAA) had an inversion of trnI (Alainites yixiani (GU479735) (Baetidae) showed a gene arrangement of trnI-trnW-trnQ-trnY-trnM. Therefore, these different sets of data suggested that specific gene rearrangements may occur in the mitogenomes of different families. The present study is important and original in that it explores the relationships between mitogenome rearrangements and taxonomic categories of Ephemeroptera.Gene rearrangements can be frequently observed in insect mitogenomes , whereas 2 (AAA) . Within of trnI . AdditiotrnI inversion in the Family Ephemerellidae and explore the phylogenetic relationships of Ephemerellidae, we sequenced six complete mitogenomes belonging to three genera of Ephemerellidae. The compositional and structural features of these six mitogenomes are described and gene rearrangements were analyzed to explain the mechanism of mitochondrial gene rearrangements.In order to discuss the characteristics of Ephemerella sp. Yunnan-2018, S.\u00a0zapekinae, Serratella sp. Yunnan-2018, Serratella sp. Liaoning-2019, T.\u00a0grandipennis and T.\u00a0tumiforceps were separately captured from Ning\u2019er Yunnan province, Xiuyan Liaoning province, Ning\u2019er Yunnan province, Kuandian Liaoning province, Longquan Zhejiang province and Tonglu Zhejiang province, China, respectively. After morphological identification, the specimens were deposited at \u221240\u00a0\u00b0C in the Animal Specimen Museum, College of Life Sciences and Chemistry, Zhejiang Normal University, China. Total genomic DNA was extracted from tissues of each complete specimen by Ezup Column Animal Genomic DNA Purification Kit . The Animal Research Ethics Committees of Zhejiang Normal University approved the experimental design.The voucher specimens of Takara Taq and Takara LA Taq DNA polymerase in a reaction volume of 50 \u03bcL. The amplifications for both normal PCR and Long-PCR were performed under the conditions as described in Several partial fragments were amplified using common primers , as deschttp://mitos.bioinf.uni-leipzig.de/index.py) (http://rna.tbi.univie.ac.at/forna) (12S and 16S rRNA). The trnI sequences of T.\u00a0grandipennis and T.\u00a0tumiforceps were aligned using the Clustal W program implemented in Mega 7.0 (MT274127\u2013MT274132. The mitogenome maps of the six mayfly species were drawn using GenomeVx (http://wolfe.ucd.ie/GenomeVx) (http://tandem.bu.edu/trf/trf.submit.options.html) using tht/forna) . After ut/forna) to compaMega 7.0 . Then, wMega 7.0 . The sixenomeVx) . Codon uenomeVx) . Using tenomeVx) , we calcns.html) . Additions.html) .Siphluriscus chinensis acted as the outgroup to \u22120.017 (Serratella sp. Yunnan-2018) whereas the GC-skew for the majority strand ranged from \u22120.234 (Ephemerella sp. Yunnan-2018) to \u22120.159 (S. zapekinae). In addition, we analyzed the sizes and nucleotide compositions of the previously published mayfly mitogenomes. Differences in mitochondrial sequences of Ephemeroptera were mainly determined by different sizes of the CR. Among all sequenced Ephemeroptera mitogenomes was the longest because of the longest CR (Baetis sp. PC-2010 (GU936204) was the shortest CR (340 bp). The AT-skews of mitogenomes on the majority strand were negative ranging from Baetis sp. PC-2010 (GU936204) (\u22120.093) to Caenis sp. YJ-2009 (GQ502451) (\u22120.001) except for positive skews in Ephemera orientalis (EU591678) (0.03), S. chinensis (0.019) (Ameletus sp. MT-2014 (0.01) (Habrophlebiodes zijinensis (GU936203) (\u22120.296) to S. chinensis (\u22120.139) (Baetis sp. PC-2010 (GU936204) (0.006), A. yixiani (GU479735) (0.14) and Ameletus sp. MT-2014 (0.202) , whereas (0.019) and Amel4 (0.01) . The GC-(\u22120.139) except f (0.202) .ND3 (Ephemerella sp. Yunnan-2018) and ND6 along with GTG assigned to ND1 (Serratella sp. Yunnan-2018), ND3 (Serratella sp. Yunnan-2018), ND4 (Serratella sp. Liaoning-2019), and ND5 . Typical stop codons (TAA/TAG) were found in most PCGs, except for incomplete terminal codons, such as T used for COX2 , COX3 , Cyt b , ND4 (Serratella sp. Liaoning-2019), ND5 and ND6 (Serratella sp. Liaoning-2019), as well as TA used for ND4 . Incomplete terminal codons perform a significant function in polycistronic transcription cleavage and polyadenylation processes of the six mayfly mitogenomes . The anaEphemerella sp. Yunnan-2018, S. zapekinae, Serratella sp. Yunnan-2018 and Serratella sp. Liaoning-2019 had 22 tRNA genes in S. zapekinae (trnQ and U-G in the T \u03c8C (T) arm of trnN and trnS1 (AGN). In general, these mismatches are fundamental units of tRNA secondary structure and are nearly isomorphic to normal base pairs, as commonly observed in mayflies or other insects and Epeorus sp. MT-2014 (A. yixiani ( GU479735)]. It has also been observed in other insect orders such as Mantodea , such as Anthonomus rectirostris, A. rubi, A. eugenii and A.\u00a0pomorum and trnV. Unexpectedly, the 12S rRNA was located between trnV and trnI due to the translocation of trnI. The sizes of the 16S rRNA genes in these six mayfly species varied from 1,212 bp (T. grandipennis) to 1,230 bp (Serratella sp. Yunnan-2018), and the sizes of 12S rRNA ranged from 769 bp (T. grandipennis and T. tumiforceps) to 778 bp (Serratella sp. Yunnan-2018). Their length fit within the lengths detected in other Ephemeroptera mitogenomes (Serratella sp. Yunnan-2018 had the highest A+T content of the rRNA genes (68.8%) whereas the mitogenome of T. grandipennis had the lowest (63.1%). In the six mayfly mitogenomes, the AT bias of both 16S rRNA and 12S rRNA was slightly positive (\u22640.075), whereas the GC bias was strongly positive (\u22650.22), which revealed that the contents of A and G outnumbered T and C nucleotides, respectively to 68.5% (Serratella sp. Liaoning-2019) . The CRsng-2019) . We obseapekinae . It has apekinae . The secapekinae , are shoslippage . These sslippage .Ephemerella sp. Yunnan-2018, S. zapekinae and Serratella sp. Yunnan-2018 were obviously lower than the A+T content of corresponding whole mitogenomes, which was also observed in other mayflies (Mecopoda niponensis) and Hemiptera , Caenis sp. JYZ-2018 and Epeorus sp. MT-2014 (Siphlonurus immanis (FJ606783)] and Isonychiidae [Isonychia ignota (HM143892)].Interestingly, the A+T content of CRs in us youi) . This phrostris) . The abnrostris) . In the of 43.6% . Also, tsequence . Moreove insects . HoweverJYZ-2018 and CaenJYZ-2020 ], Heptag MT-2014 ], SiphloS. zapekinae, Serratella sp. Yunnan-2018 and Serratella sp. Liaoning-2019 contained 4, 6, and 6 non-coding intergenic spacer sequences, respectively, with total lengths of 22 bp, 32 bp and 29 bp, whereas Ephemerella sp. Yunnan-2018 had 7 non-coding intergenic spacer sequences of 92 bp in total length due to an intergenic spacer of 68 bp between ND4L and trnT. An intergenic spacer between trnS2 (UCN) and ND1 ranging from 17 bp to 19 bp was also detected in these four mitogenomes and is commonly found in Ephemeroptera. In terms of the intergenic spacer between ND4L and trnT in Ephemerella sp. Yunnan-2018, we also detected a similar sequence of 62 bp with a similarity of 72.58% in Ephemerella sp. MT-2014 , we observed a large intergenic spacer between trnS1 (AGN) and trnE within the mitogenomes of T. tumiforceps and T. grandipennis, with lengths of 531 bp and 200 bp, respectively. The large intergenic region in T. tumiforceps and T. grandipennis had 52.17% and 52% A+T content, respectively, with a strongly positive GC-skew (0.31 and 0.13). The large intergenic region in T. tumiforceps and T. grandipennis had a similar starting sequence of 20 bp (GGGSCKAAAGGSCCTACCTA) and a conserved sequence of 19 bp (TTTTTAGCGAACTTAGGGG), respectively, with 4 tandem repeats of 87 bp and 3 tandem repeats of 42 bp along with 4 partial sequences, respectively. The repeat unit of T. tumiforceps could be folded into three stem-loop secondary structures, whereas T. grandipennis folded into two stem-loop secondary structures and trnE could be synapomorphic for the genus Torleya owing to the fact that sequences located between trnS1 (AGN) and trnE within mitogenomes of other Ephemeroptera were short (<13 bp) and the large intergenic spacer has only been found in Torleya. This is the first finding of a large intergenic region in the mitogenomes of mayflies. As a consequence of the non-coding particularity of the intergenic spacer sequence, these species may well have gone through further sequence divergence swiftly ], whereas an intergenic spacer between trnQ and trnM ranging from 26 bp to 53 bp was found in Caenidae and Ephemeridae [E. orientalis (EU591678)]. In terms of the mitogenomes of Heptageniidae, we detected an intergenic spacer between trnA and trnR, ranging from 33 bp to 47 bp ))), as reported by P. youi + (P. cupulatus + (Epeorus sp. JZ-2014 + (Epeorus sp. MT-2014 + E. herklotsi)))), as reported by P. youi, P. cupulatus and (Epeorus sp. JZ-2014 + (Epeorus sp. MT-2014 + E. herklotsi)), with low support. On the whole, the monophyly of all Ephemeroptera families was supported except the family Siphluriscidae.Derived from both BI and ML analyses, the phylogenetic trees showed an identical topology, excluding the internal relationship among Heptageniidae and 5. T12S, 16S, 18S, 28S and H3 genes, Ephemerellidae was supported as a monophyletic group, and their relationship with Teloganellidae and Vietnamellidae remains problematic + Serratella sp. Yunnan-2018) + (T. tumiforceps + T. grandipennis)) + (Ephemerella sp. Yunnan-2018 + Ephemerella sp. MT-2014)). The inversion and translocation of one copy of trnI was found in Ephemerella and Serratella, whereas the inversion and translocation of three copies of trnI was found in Torleya (Serratella + Torleya) + Ephemerella), we can deduce that the inversion and translocation of one copy of trnI is characteristic of the ancestral Ephemerellidae. Unfortunately, the presence of only one mitogenome of Teloganellidae restricted a discussion of its monophyly, which requires more species to be added.Our findings indicated that Ephemerellidae was the sister clade to Vietnamellidae, but Teloganellidae was the sister clade to Baetidae , which mblematic . In addi Torleya . AccordiEphemerella sp. Yunnan-2018, S. zapekinae, Serratella sp. Yunnan-2018, Serratella sp. Liaoning-2019, T. grandipennis and T. tumiforceps. The mitogenomes of the genera Ephemerella and Serratella showed similar gene features to Ephemerella sp. MT-2014 (KM244691) and had the same inversion and translocation of trnI, whereas two extra copies of trnI were found in the genus Torleya. The translocation and extra copies of trnI could be explained by the tandem duplication/random loss model, whereas the inversion of trnI could be interpreted by the mitogenome recombination model. The evidence from this study suggests that these specific mitogenome rearrangements may be molecular markers of the family Ephemerellidae, especially the three copies of trnI as a synapomorphy for the genus Torleya. The occurrences and mechanisms of the large intergenic region between trnS1 (AGN) and trnE, detected in T. tumiforceps and T. grandipennis, require more mitogenomes of Torleya species to be investigated. Phylogenetic analyses based on BI and ML trees both supported the monophyly of Ephemerellidae and Vietnamellidae. Moreover, Ephemerellidae acted as the sister clade to Vietnamellidae whereas Teloganellidae existed in the other clade. Considerable work may be needed to increase the number of mitogenomes to resolve the phylogenetic relationships of Ephemeroptera.We successfully determined the complete mitogenomes of 10.7717/peerj.9740/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj.9740/supp-2Supplemental Information 2Click here for additional data file.10.7717/peerj.9740/supp-3Supplemental Information 3Click here for additional data file.10.7717/peerj.9740/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.9740/supp-5Supplemental Information 5Click here for additional data file.10.7717/peerj.9740/supp-6Supplemental Information 6Click here for additional data file.10.7717/peerj.9740/supp-7Supplemental Information 7 Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018. and Serratella sp. Liaoning-2019; (B) Torleya grandipennis and Torleya tumiforceps. The figure is written permission from Yu-Rou Cao to publish. She helped drawing under our CC BY 4.0 license.External genes on the circle are encoded by the positive strand (5\u2019 \u21923\u2019) and internal genes are encoded by the negative strand (3\u2019 \u21925\u2019). (A)Click here for additional data file.10.7717/peerj.9740/supp-8Supplemental Information 8trnI; (B) trnQ; (C) trnM; (D) trnW; (E) trnC; (F) trnY; (G) trnL (CUN); (H) trnK; (I) trnD; (J) trnG; (K) trnA; (L) trnR; (M) trnN; (N) trnS (AGN); (O) trnE; (P) trnF; (Q) trnH; (R) trnT; (S) trnP; (T) trnS (UCN); (U) trnL (UUR); (V) trnV.A) Click here for additional data file.10.7717/peerj.9740/supp-9Supplemental Information 9trnI; (B) trnQ; (C) trnM; (D) trnW; (E) trnC; (F) trnY; (G) trnL (CUN); (H) trnK; (I) trnD; (J) trnG; (K) trnA; (L) trnR; (M) trnN; (N) trnS (AGN); (O) trnE; (P) trnF; (Q) trnH; (R) trnT; (S) trnP; (T) trnS (UCN); (U) trnL (UUR); (V) trnV.(A) Click here for additional data file.10.7717/peerj.9740/supp-10Supplemental Information 10trnI; (B) trnQ; (C) trnM; (D) trnW; (E) trnC; (F) trnY; (G) trnL (CUN); (H) trnK; (I) trnD; (J) trnG; (K) trnA; (L) trnR; (M) trnN; (N) trnS (AGN); (O) trnE; (P) trnF; (Q) trnH; (R) trnT; (S) trnP; (T) trnS (UCN); (U) trnL (UUR); (V) trnV.(A) Click here for additional data file.10.7717/peerj.9740/supp-11Supplemental Information 11trnI; (B) trnQ; (C) trnM; (D) trnW; (E) trnC; (F) trnY; (G) trnL (CUN); (H) trnK; (I) trnD; (J) trnG; (K) trnA; (L) trnR; (M) trnN; (N) trnS (AGN); (O) trnE; (P) trnF; (Q) trnH; (R) trnT; (S) trnP; (T) trnS (UCN); (U) trnL (UUR); (V) trnV.(A) Click here for additional data file.10.7717/peerj.9740/supp-12Supplemental Information 12trnI; (B) trnI; (C) trnI; (D)trnQ; (E) trnM; (F) trnW; (G) trnC; (H) trnY; (I) trnL (CUN); (K) trnK; (K) trnD; (L) trnG; (M) trnA; (N)trnR; (O) trnN; (P) trnS (AGN); (Q) trnE; (R) trnF; (S) trnH; (T) trnT; (U) trnP; (V) trnS (UCN); (W) trnL (UUR); (X) trnV.(A) Click here for additional data file.10.7717/peerj.9740/supp-13Supplemental Information 13trnI; (B) trnI; (C) trnI; (D)trnQ; (E) trnM; (F) trnW; (G) trnC; (H) trnY; (I) trnL (CUN); (K) trnK; (K) trnD; (L) trnG; (M) trnA; (N)trnR; (O) trnN; (P) trnS (AGN); (Q) trnE; (R) trnF; (S) trnH; (T) trnT; (U) trnP; (V) trnS (UCN); (W) trnL (UUR); (X) trnV.(A) Click here for additional data file.10.7717/peerj.9740/supp-14Supplemental Information 14Click here for additional data file.10.7717/peerj.9740/supp-15Supplemental Information 15Serratella zapekinae;(B) the repeat unit (100 bp) in Serratella zapekinae;(C) the repeat unit (109 bp) in Serratella sp. Liaoning-2019; (D) the repeat unit (72 bp) in Serratella sp. Liaoning-2019.(A) the repeat unit (90 bp) in Click here for additional data file.10.7717/peerj.9740/supp-16Supplemental Information 16T. tumiforceps; (B) the repeat unit (42 bp) in T. grandipennis.(A) the repeat unit (87 bp) in Click here for additional data file.10.7717/peerj.9740/supp-17Supplemental Information 17trnS1 (AGN) and trnE. The CS indicates the 19 bp conserved sequence TTTTTAGCGAACTTAGGGG. Gene sizes are not drawn to scale. Genes located on the majority strand are shown along the top of the boxes whereas genes located on the minority strand are shown on the bottom. White boxes represent genes with the same relative position as in the ancestral insect arrangement pattern. Grey boxes represent non-coding regions. The remaining genes and gene orders that were identical to the ancestral insect are left out.The duplication/random loss model can explain the NCR between Click here for additional data file.10.7717/peerj.9740/supp-18Supplemental Information 18Click here for additional data file.10.7717/peerj.9740/supp-19Supplemental Information 19Click here for additional data file.10.7717/peerj.9740/supp-20Supplemental Information 20Ephemerella sp. Yunnan-2018. Blue shading represents Serratella zapekinae. Yellow shading represents Serratella sp. Yunnan-2018. Green shading represents Serratella sp. Liaoning-2019.Orange shading represents Click here for additional data file.10.7717/peerj.9740/supp-21Supplemental Information 21Click here for additional data file.10.7717/peerj.9740/supp-22Supplemental Information 22Click here for additional data file.10.7717/peerj.9740/supp-23Supplemental Information 23Click here for additional data file."} +{"text": "Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 90% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or an average of one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics. As a member of the Gondwanan family Proteaceae (Macadamia (F.Muell.) is a basal eudicot and is phylogenetically divergent from other tree crops , Macadamtivation , is a mitivation . MacadamMacadamia were then anchored and oriented to 14 pseudo-chromosomes using methods to maximize colinearity across seven genetic linkage maps . An herbarium specimen was submitted to the Southern Cross Plant Science Herbarium [accession PHARM-13-0813]. On collection, samples were snap frozen in liquid nitrogen or placed on dry ice and stored at -80\u00b0 prior to extraction. Previously described methods for and DNA/RNA extraction for Illumina , new libraries with 200, 350 and 550 bp insert sizes were prepared with TruSeq DNA PCR-free kits and sequenced with Illumina HiSeq 2500 producing 57.0, 29.8 and 29.6 Gb paired-end sequence data. A PacBio library (20-Kb) was prepared and sequenced across 10 SMRT cells on a PacBio RSII system (P6-C4 chemistry) generating 6.44 Gb data. Transcriptome sequencing of leaf, shoot and flower tissue followed previously described methods .de novo assembly, scaffolding and gap closing was performed using MaSuRCA , Eucalpytus grandis and Coffea canephora (coffee) genomes. Pairwise sequence similarities were determined applying a BLASTP E-value cut-off of 1E-05 and an inflation value of 1.5 for OrthoMCL Markov clustering. Macadamia specific gene clusters were tested for GO enrichment using OrthoVenn2.Orthologous gene clusters were identified and compared using OrthoVenn2 with 180 \u00d7 coverage of the genome and a scaffold N50 of 413 kb and 93.5% of corrected PacBio reads tagged as primary alignments by Minimap2 aligned reliably to the assembly. No Pacbio reads aligned to two different scaffolds at a cutoff of 1/2 read length. At 1/3 read length, 130 reads (mean length 7833 bp representing < 0.14% of the assembly) aligned to two scaffolds and no reads aligned to more than two scaffolds.M. integrifolia of 652 Mb (600-700 Mb) that was based on 51.6 Gb Illumina short read data of the assembly. As reported for many other plant genomes, long terminal repeat (LTR) retrotransposons were the most abundant repeat type (30.5%). Small RNAs including pseudogenes and active small RNA genes including tRNA and snRNA accounted for 0.54% of the assembly .N. nucifera, A. thaliana, P. persica, E. grandis and C. canephora identified 8,961 orthologous clusters of which 2,051 contained a single gene from each of the six eudicot species. M. integrifolia and N. nucifera both belong to the basal eudicot order Proteales. These species and contained similar numbers of clusters with 13,491 and 13,321 respectively and shared the largest number of clusters (503) of any species pair (P = 4.8E-05) and fruit ripening .Annotation of the final assembly, identified 34,274 high-confidence gene models. Of these, 25,779 (75.2%) were anchored to pseudo-chromosomes and 8,495 were located on unanchored scaffolds . Comparaies pair . Tests fHere we present the first chromosome-scale genome assembly for the nut crop macadamia and the large Gondwanan plant family Proteaceae. This provides a platform for unraveling the genetics of macadamia and is expected to underpin future breeding, and comparative and horticultural genomics research.Versions and parameters of the tools implemented in data analysis are provided below:BBMap version 36.62: ktrim = r k = 23 mink = 11 hdist = 1 tpe tbo maxns = 1 minlen = 50 maq = 8 qtrim = rl trimq = 20LoRDEC version 0.4: lordec-correct -2 input_for_read_correction.fastq -k 19 -S out.stat.txt -s 3 -T 12 -i PacBio_filtered_reads.fasta -o out.pacbio.corrected.fastaNUM_THREADS = 16, JF_SIZE = 20000000000 (jellyfish hash size)MaSuRCA version 3.2.1. Default parameters except: vs.macaAssembly.psl -noHead -out = pslL_RNA_scaffolder: blat -t = dna -q = dna scaffolds_gapClosed_min1000.fa Trinity.fasta transcript.ALLMAPS version 0.7.7: Default parametersJellyfish version 2.0: jellyfish count -t 14 -C -m 27 -s 8G -o 27mer_maca_illumOnly_out jellyfish histo -t14 27mer_maca_illumOnly_out> 27mer_maca_illumOnly_out.histofindGSE: Default parametersGenomeScope version 2.2.6:kmer length 27, read length 125bp, Max kmer coverage 1000Trinity, version 2.0.3: Trinity\u2013seqType fq\u2013max_memory 100G \u2013left reads_S_R1_clean.fq,reads_F2_R1_clean.fq,reads_YL_R1_clean.fq\u2013right reads_S_R2_clean.fq,reads_F2_R2_clean.fq,reads_YL_R2_clean.fq\u2013CPU 8RepeatModeler version 2.0.1. Default parametersRepeatMasker version 4.0.9. Default parametersMAKER, version 2.31.10. Default parameters except: Gene prediction methods Augustus and SNAP (trained with previously generated macadamia gene models); AED score = 0.40; Minimum protein length: = 50 amino acidsBUSCO version 3.0.2: busco -i proteins.fasta -l viridiplantae_odb10 -m proteins -o output_nameMinimap2 version 2.17. Default parameters (paftool.js bundled with Minimap2): minimap2 -ax sr ref_assemblyfasta fastq1stReadPair fastq2ndReadPair > ref_readPairs_aln.paf; k8 paftools.js stat ref_readPairs_aln.paf > alignment_mapstatscf.gz -ERC GVCF -heterozygosity 0.01GATK HaplotypeCaller version 4.1.4.1: gatk\u2013java-options \u201c-Xmx8g\u201d HaplotypeCaller -R refGenome.fasta -I input.bam -O output.g.vcf.gz -O output.vcf.gz\u2013heterozygosity 0.01GATK GenotypeGVCFs version 4.1.4.1: gatk\u2013java-options \u201c-Xmx4g\u201d GenotypeGVCFs -R refGenome.fasta -V input.g.vcf.gz -F CHROM -F POS -F TYPE -F REF -F ALT -F HET -GF GT -GF AD -O output_genoGVCF.table.txt.GATK VariantsToTable version 4.1.4.1: gatk-4.1.4.1/gatk\u2013java-options \u201c-Xmx8g\u201d VariantsToTable -V output.v"} +{"text": "RAS wild-type metastatic colorectal cancer (mCRC) treated with anti-EGFR based first-line treatment is still debated. Methods: This multicenter, real-world, retrospective study is aimed at evaluating the effectiveness of second-line Bevacizumab- and Aflibercept-based treatments after an anti-EGFR based first-line regimen. Clinical outcomes measured were: objective response rate (ORR), progression free survival (PFS), overall survival (OS) and adverse events (AEs) profiles. Results: From February 2011 to October 2019, 277 consecutive mCRC patients received Bevacizumab-based or Aflibercept-based regimen. No significant difference was found regarding ORR. The median follow-up was 27.7 months (95%CI: 24.7\u201334.4). Aflibercept-treated group had a significantly shorter PFS compared to Bevacizumab-treated group (HR = 1.34 (95%CI: 0.95\u20131.89); p = 0.0932). The median OS of the Bevacizumab-treated group and Aflibercept-treated group was 16.2 (95%CI: 15.3\u201318.1) and 12.7 (95%CI: 8.8\u201317.5) months, respectively (HR= 1.31 (95%CI: 0.89\u20131.93) p = 0.16). After adjusting for the key covariates Bevacizumab-based regimens revealed to be significantly related with a prolonged PFS (HR = 1.44 (95%CI: 1.02\u20132.03); p = 0.0399) compared to Aflibercept-based regimens, but not with a prolonged OS (HR = 1.47 (95%CI: 0.99\u20132.17); p = 0.0503). The incidence of G3/G4 VEGF inhibitors class-specific AEs was 7.5% and 26.5% in the Bevacizumab-treated group and the Aflibercept-treated group, respectively (p = 0.0001). Conclusion: Our analysis seems to reveal that Bevacizumab-based regimens have a slightly better PFS and class-specific AEs profile compared to Aflibercept-based regimen as second-line treatment of RAS wild-type mCRC patients previously treated with anti-EGFR based treatments. These results have to be taken with caution and no conclusive considerations are allowed.Background: The optimal anti-angiogenic strategy as second-line treatment in RAS genotype 1\u20132 and 3\u20134). Toxicities were summarized and compared among subgroups according to three key subgroups: VEGF inhibitors class-specific AEs , hematologic AEs , and non-hematologic AEs . Only AEs which occurred in more than 5% of patients were included in the safety analysis.KRAS, NRAS and BRAF mutational status was assessed with Sanger sequencing, real-time PCR techniques and next-generation sequencing (NGS) ; Pyromark Q96 ID System, Qiagen ; EasyPGX and Myriapod Colon Status, Diatech Pharmacogenetics ). MSI (microsatellite instability) status and/or MMR (mismatch repair) proteins expression were assessed with molecular sequencing and Immunohistochemistry (IHC) ; Ultraview Universal Detection Kit and Ventana platform, Roche Tissue Diagnostics and Ventana Medical Systems ).All the molecular analyses were performed according to the local clinical practice of the participating centers. p < 0.05. Hazard Ratios (HRs) with 95% confidence intervals (CIs) were calculated using the logistic regression model. All statistical analyses were performed using MedCalc Statistical Software version 18.11.3 .Baseline patients\u2019 characteristics were reported with descriptive statistics and compared among subgroups with the Chi-square test. Chi-square test was also used to compare ORR and the incidence of AEs across subgroups. Logistic regression was used for the multivariate analysis of ORR. Median PFS and median OS were evaluated using the Kaplan\u2013Meier method. Median period of follow-up was calculated according to the reverse Kaplan-Meier method. Cox proportional hazards regression was used for the univariate and multivariate analysis of PFS and OS. The alpha level for all analyses was set to RAS wild-type mCRC patients were treated with Bevacizumab-based or Aflibercept-based second-line regimens. The median age was 64.5 years (range: 29\u201384). Patients features are summarized in p < 0.0001). According to the clinical indication of Aflibercept, also the previously received first-line regimens (p < 0.0001) and second-line chemotherapy backbone (p = 0.0148) were significantly different. A total of 277 consecutive The activity profile for the overall population and according to subgroups is summarized in p = 0.0932) (p = 0.1600) (p = 0.0399) compared to Aflibercept-based regimens, but not with a prolonged OS (HR = 1.47 (95%CI: 0.99\u20132.17); p = 0.0503).The second-line median follow-up for the study population was 27.7 months (95%CI: 24.7\u201334.4); median PFS and median OS were 7.1 months and 15.7 months . Median PFS of the Bevacizumab-treated group was 7.1 months , while median PFS of the Aflibercept-treated group was 5.6 months , without statistically significant difference at the univariate analysis (HR = 1.34 (95%CI: 0.95\u20131.89); 0.0932) A. Median 0.1600) B. Table p = 0.1908). The incidence of G3/G4 VEGF inhibitors class-specific AEs was 7.5% and 26.5% in the Bevacizumab-treated group and in the Aflibercept-treated group, respectively (p = 0.0001) (p = 0.0033), while the incidence of G3/G4 non hematologic AEs was 4.4% and 10.2%, respectively (p = 0.1032). The incidence of G1/G2 hematologic AEs was 24.6% and 22.4% in the Bevacizumab-treated group and in the Aflibercept-treated group, respectively (p = 0.7545), while the incidence of G3/G4 hematologic AEs was 3.1% and 18.4%, respectively (p < 0.0001).The toxicity profile for the overall study population and according to subgroups is summarized in 0.0001) . The incp = 0.2236). A total of 136 patients (69.4%) and 24 patients (60%) were treated with a third-line systemic therapy, among those who discontinued second-line treatment in the Bevacizumab-treated group and Aflibercept-treated group, respectively (p = 0.5930). A total of 67 patients (29.4%) and nine patients (18.4%) underwent a maintenance therapy after an induction phase, in the Bevacizumab-treated group and in the Aflibercept-treated group, respectively , and this might have affected the clinical outcomes [BRAF mutant patients [BRAF mutational status , identifying a study population with good prognosis overall [Despite the unbalanced grouping of the study population according to the received regimens (82.3% Bevacizumab-based vs. 17.7% Aflibercept-based), most of the patients characteristics were balanced between the subgroups, such as elderly patients, number of metastatic sites and primary tumor location see . On the outcomes . The clipatients , are ali overall .RAS wild-type patients were eligible) might also partially explain these discrepancies. Interestingly, genotype based post-hoc analyses reported an OS of 15.4 months for KRAS wild-type patients of the experimental arm of the ML18147 [RAS wild-type patients of the experimental arm of the VELOUR trial [Even though studies results comparisons are not methodologically correct, some speculations are allowed. The median PFS of the Bevacizumab-treated group (7.1 months) was comparable to the PFS reported in the E3200 and ML18147 trials ,13, wher ML18147 , and an UR trial . Moreovep = 0.0399), whereas a not significant trend towards a shorter OS was reported (HR = 1.47 (95%CI: 0.99\u20132.17); p = 0.0503). Concerning safety data, we found a significant higher incidence of G3/G4 VEGF inhibitors class-specific AEs among Aflibercept-treated patients, compared to the Bevacizumab-treated patients . This aspect might be also related to the different pharmacodynamic mechanisms of action of Bevacizumab and Aflibercept ) [p = 0.0033) and G3/G4 hematologic AEs (3.1% vs. 18.4%) to the detriment of the Aflibercept-treated patients, was found. The latter aspect could be related to the different chemotherapy backbone .Intriguingly, the multivariate analysis revealed that the Aflibercept-treated group had a statistically significant shorter PFS compared to the Bevacizumab-treated group (HR = 1.44 (95%CI: 1.02\u20132.03); (PIGF)) . FurtherOur results suggest a slightly better clinical performance for second-line Bevacizumab-based regimens compared to Aflibercept-based regimens. In our opinion, the different safety profile might had affected the effectiveness of Aflibercept-based regimens compared to Bevacizumab-based regimens, leading to a higher discontinuation rate and a worse PFS.According to the RAISE trial results , it woulRAS wild-type patients, are awaited. The STRATEGIC-S1 trial (NCT01910610) [RAS wild-type mCRC patients: an oxaliplatin-based second-line regimen with Bevacizumab after fist line FOLFIRI-Cetuximab vs. an irinotecan-based second-line regimen with Bevacizumab after a first-line OPTIMOX Bevacizumab, followed by an anti-EGFR based third-line treatment. The DISTINCTIVE trial (NCT04252456) [RAS wild-type mCRC patients after an oxaliplatin/fluoropyrimidines-based first-line regimen combined with either Panitumumab or Cetuximab. Results from important prospective phase II-III studies, comparing different sequencing strategies of available biological agents for 1910610) is an in4252456) is a proRAS wild-type mCRC patients.There are some obvious limitations in this study, including its retrospective design, which expose to selection bias, therefore the results must be taken with caution. Further analysis with a larger sample size and a prospective translational design are certainly needed to better define and personalize the anti-angiogenic strategy as a second-line treatment in RAS wild-type mCRC patients who received first-line anti-EGFR based treatments. These results have to be taken with caution and no conclusive consideration are allowed.Our analysis seems to reveal that Bevacizumab-based regimens have a slightly better efficacy and safety profile compared to Aflibercept-based regimens as second-line treatment of"} +{"text": "Kernel weight and morphology are important traits affecting cereal yields and quality. Dissecting the genetic basis of thousand kernel weight (TKW) and its related traits is an effective method to improve wheat yield.QTkw.cas-1A.2 and QTkw.cas-4A explained the largest portion of the phenotypic variance for TKW and kernel length (KL), and the other two stable QTLs QTkw.cas-6A.1 and QTkw.cas-7D.2 contributed more effects on kernel width (KW). Conditional QTL analysis revealed that the stable QTLs for TKW were mainly affected by KW. The QTLs QTkw.cas-7D.2 and QKw.cas-7D.1 associated with TKW and KW were delimited to the physical interval of approximately 3.82\u2009Mb harboring 47 candidate genes. Among them, the candidate gene TaFT-D1 had a 1\u2009bp insertions/deletion (InDel) within the third exon, which might be the reason for diversity in TKW and KW between the two parents. A Kompetitive Allele-Specific PCR (KASP) marker of TaFT-D1 allele was developed and verified by PG-RIL and a natural population consisted of 141 cultivar/lines. It was found that the favorable TaFT-D1 (G)-allele has been positively selected during Chinese wheat breeding. Thus, these results can be used for further positional cloning and marker-assisted selection in wheat breeding programs.In this study, we performed quantitative trait loci (QTL) analysis using recombinant inbred lines derived from the cross \u2018PuBing3228\u2009\u00d7\u2009Gao8901\u2019 (PG-RIL) to dissect the genetic basis of kernel traits. A total of 17 stable QTLs related to kernel traits were identified, notably, two stable QTLs TaFT-D1 could be the candidate gene for QTLs QTkw.cas-7D.2 and QKw.cas-7D.1.Seventeen stable QTLs related to kernel traits were identified. The stable QTLs for thousand kernel weight were mainly affected by kernel width. Triticum aestivum L.) is one of the most important cereal crops for feeds 40% of population in the world (http://www.fao.org/). Wheat yield is determined by thousand kernel weight (TKW), kernel number per spike, and effective tiller number [Common wheat in tetraploid wheat [Recently, high-density single nucleotide polymorphism (SNP) arrays technology provides a superior approach to identify QTLs for wheat kernel-related traits \u201331. To did wheat , 42. HowUsing a RIL population derived from \u2018PuBing 3228 (P3228)\u2009\u00d7\u2009Gao8901 (G8901)\u2019, the objectives of this study were to (i) identify stable and major QTLs for TKW, KL, KW and KL/W under different field conditions; (ii) reveal the contribution of the other kernel traits to TKW using conditional QTL analysis; (iii) predict candidate gene(s) for targeted QTLs interval based on reference genome annotation information; (iv) develop KASP markers of the candidate gene(s) and verified by PG-RIL and a natural population consisted of 141 cultivar/lines for marker-assisted selection in high-TKW wheat breeding.H) of four traits were higher than 0.60 are listed in Table\u00a0A total of 47 putative QTLs were detected for TKW, KL, KW and KW/L Figs.\u00a0.Fig. 3GQTkw.cas-1A.2, QTkw.cas-4A, QTkw.cas-5D, QTkw.cs-6A.1 and QTkw.cas-7D.2 ranged from 8.31 to 11.84% were significant in at least two environments . The favorable alleles of the five QTLs were derived from the parent G8901 , 1B, 4B, 6A, 7A (two) and 7D, respectively were found in at least two environments .A total of 10 QTLs for KL/W were identified on chromosomes 1A, 1B, 2A, 5A (two), 5D, 7A (two) and 7D (two), with PVE of individual QTL ranging from 1.79 to 22.41% \u2009=\u200921.93%), indicating that the major QTLs QTkw.cas-4A and QKl.cas-4A for TKW and KL, respectively, were significantly affected by the environment interactions were detected at 43 loci for TKW, KL, KW and KW/L were identified to be associated with KW, but independent of KL and KL/W , a homolog of Arabidopsis FLOWERING LOCUS T, was considered as the candidate gene for QTkw.cas-7D.2 and QKw.cas-7D.1 closely linked to the two stable QTLs (QTkw.cas-7D.2 and QKw.cas-7D.1) and 1\u2009bp InDel of TaFT-D1 were further converted to KASP markers -allele) and P3228-allele (TaFT-D1(\u2212)-allele) plants -allele was significantly higher than those of the TaFT-D1(\u2212)-allele .Two SNPs markers -allele in modern cultivars was higher in the seven agro-ecological wheat production regions , suggesting that TaFT-D1(G)-allele have undergone positive selection during wheat breeding process -allele can be used in different wheat production regions.To determine whether the two g season , 52. ComQTkw.cas-1A.2, QTkw.cas-5D, QTkw.cas-6A.1, QTkw.cas-7D.2) account for TKW, while two (QTkw.cas-4A and QTkw.cas-5D) on KL -allele associated with TKW and KW has been positively selected during Chinese wheat breeding. In addition, the current study provided new options for dissecting the genetic basis of yield and molecular-assisted breeding.In this study, we performed QTL analysis using the PG-RIL population in four environments for kernel-related traits , which were mainly distributed on chromosomes 1A, 1B, 4A, 5D, 6A, 7A and 7D Fig. . Notably6\u20139 RILs derived from \u2018PuBing3228\u2009\u00d7\u2009Gao 8901 \u2018was developed by single seed descent method. The wheat germplasm P3228 was developed by Dr. Lihui Li . G8901 is a commercial cultivar released by Gaocheng institute of agricultural science, Hebei, China. The P3228 has higher kernel number per spike and the G8901 has higher thousand kernel weight . The H was calculated using the QGAStation 2.0 (http://ibi.zju.edu.cn/software/qga/v2.0/index c.htm) and the following formula H\u2009=\u2009VG/VP; where VG and VP are the genetic variance and phenotypic variance, respectively.For the four environments, 10 representative plants were sampled from each plot to investigate kernel-related traits. At seed maturity, the TKW and kernel morphometric traits of at least 500 kernels were measured three times using the rapid SC-G grain appearance quality image analysis system . Analysis of variance (ANOVA), mean values of traits, standard deviations and variation coefficients (CV) were performed with SPSS Statistics v20.0 software . Effects among genotypes, environments, and GE interaction were estimated by ANOVA. BLUP for all four traits across four environments was calculated using R software ) of TKW in wheat were obtained by the mixed-model approach. The conditional phenotypic value can be partitioned as.Conditional QTL analysis was performed to analyze the genetic contributions of kernel-related traits to TKW, by the procedure of inclusive composite interval mapping . The cony(TKW|KL)=\u03bc(TKW|KL)\u2009+\u2009G(TKW|KL)\u2009+\u2009E(TKW|KL)\u2009+\u2009e(TKW|KL).y(TKW|KL) is the conditional phenotypic value of TKW on KL; \u03bc(TKW|KL) is the conditional population mean, G(TKW|KL) is the conditional general genotypic effect; E(TKW|KL) is the conditional effect for the environment and e(TKW|KL) is the conditional residual error.where (TKW|KL) denote TKW conditional on KL; y(TKW|KL), y(TKW|KW) and y(TKW|KL/W)) are the conditional phenotypic value of TKW on KL, KW or KL/KW in the corresponding environment, which were estimated using QGAStation2.0 (http://ibi.zju.edu.cn/software/qga/). MapChart\u00a02.2 (http://www.biometris.nl/uk/Software/MapChart/) was used to draw the genetic map.The conditional phenotypic values and physical (right) positions for SNPs mapped on the chromosome 7DS in PG-RIL genetic map. Fig. S2 A 1\u2009bp InDel in TaFT-D1 caused a frameshift mutation of the protein. (a) Sequence alignment of TaFT-D1 showing 1\u2009bp InDel between P3228 and G8901. (b) Protein alignment of TaFT-D1 showing frameshift mutation in P3228. Fig. S3 Heatmap showing the expression profile of DEGs at 15 development stages. Fig. S4 Allelic segregation of KASP markers AX-111061288 (a) and AX-111184541 (b) for QTkw.cas-7D.2 and QKw.cas-7D.1."} +{"text": "Chronic isoleucine supplementation prevents diet-induced weight gain in rodents. Acute-isoleucine administration improves glucose tolerance in rodents and reduces postprandial glucose levels in humans. However, the effect of chronic-isoleucine supplementation on body weight and glucose tolerance in obesity is unknown. This study aimed to investigate the impact of chronic isoleucine on body weight gain and glucose tolerance in lean and high-fat-diet (HFD) induced-obese mice. Male C57BL/6-mice, fed a standard-laboratory-diet (SLD) or HFD for 12 weeks, were randomly allocated to: (1) Control: Drinking water; (2) Acute: Drinking water with a gavage of isoleucine (300 mg/kg) prior to the oral-glucose-tolerance-test (OGTT) or gastric-emptying-breath-test (GEBT); (3) Chronic: Drinking water with 1.5% isoleucine, for a further six weeks. At 16 weeks, an OGTT and GEBT was performed and at 17 weeks metabolic monitoring. In SLD- and HFD-mice, there was no difference in body weight, fat mass, and plasma lipid profiles between isoleucine treatment groups. Acute-isoleucine did not improve glucose tolerance in SLD- or HFD-mice. Chronic-isoleucine impaired glucose tolerance in SLD-mice. There was no difference in gastric emptying between any groups. Chronic-isoleucine did not alter energy intake, energy expenditure, or respiratory quotient in SLD- or HFD-mice. In conclusion, chronic isoleucine supplementation may not be an effective treatment for obesity or glucose intolerance. The branched-chain amino acids (BCAAs), isoleucine, leucine and valine, are essential amino acids accounting for ~35% of the essential amino acids comprising muscle proteins in humans and ~40% of the pre-formed amino acids required by all mammals . In popudb/db) mice, a model of morbid obesity and hyperglycaemia [Acute administration of isoleucine and leucine in rats improved glucose tolerance, with isoleucine showing greater effectiveness than leucine . This walycaemia . This evIt is known that postprandial blood glucose levels are influenced by the rate of gastric emptying . In partThe current study aimed to determine whether chronic dietary supplementation with the BCAA isoleucine, alters body weight gain, adiposity, glucose tolerance, and energy metabolism in mice with HFD-induced obesity.This study was approved by the South Australian Health and Medical Research Institute Animal Ethics Committee. All experimental protocols were performed in alignment with the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes.n = 54) were group-housed in a 12:12 h light-dark cycle within a temperature (24 \u00b1 1 \u00b0C) controlled facility. Mice were provided ad libitum access to either a standard laboratory diet or HFD . Consistent with the previous literature, the HFD-induced obese mouse model was chosen as both a model of obesity [n = 10; SLD-Chronic (Ch)) and HFD-mice received ad libitum isoleucine supplemented in the drinking water. The remaining SLD (n = 20) and HFD-mice (n = 16) continued with ad libitum access to normal drinking water. At 16 weeks, all mice were singly housed and underwent an OGTT (at 1400 h) and gastric emptying breath test (at 0900 h) in random order with a three-day recovery between tests. In each diet group, the mice provided normal drinking water were subdivided into two groups, receiving either an oral gavage of water ; n = 8, HFD-C) or isoleucine ; n = 8, HFD-A) 30 min before the OGTT or GEBT. The SLD and HFD-Ch mice received an oral gavage of drinking water similar to the control groups. The doses for acute and chronic isoleucine treatments were chosen based on previous studies [Eight-week-old male C57BL/6 mice to consume voluntarily within 1 min. Breath samples were collected before isoleucine administration and again at regular intervals after egg consumption. Breath samples were analysed for the 13CO2 content using an isotope ratio mass spectrometer . The 13CO2 excretion data were analysed by non-linear regression analysis for curve fitting and for calculation of gastric half emptying time (t \u00bd) [Gastric emptying of a solid meal was determined using a non-invasive breath test as previously described ,22. Miceme (t \u00bd) . Gastric2/VO2), and total activity were measured and analysed using the ExpeData data analysis software .Mice were individually housed in Promethium metabolic cages for 72 h of continuous metabolic monitoring. Energy intake (kJ), energy expenditure (kJ/lean mass), respiratory quotient then anaesthetised with isoflurane . The nose-to-tail length and abdominal circumference of mice were measured. Blood was collected from the abdominal aorta and transferred to ethylenediaminetetraacetic acid (EDTA) tubes . Plasma was extracted by centrifugation at 1000 g and 4 \u00b0C for 15 min, and snap-frozen in liquid nitrogen prior to storage at \u221280 \u00b0C until further analysis. Liver, gonadal fat pads, and inter-scapula brown fat pads were collected and weighed. Lean mass was determined by the final body weight minus the weight of collected fat pads. A section of the liver was fixed in 4% paraformaldehyde for 4 h, cryoprotected overnight in 30% sucrose in a phosphate buffer, frozen in Tissue-Tek O.C.T. compound and stored at \u221280 \u00b0C before processing for histology. Plasma total triglycerides, total cholesterol, and high-density lipoprotein (HDL)-cholesterol concentrations were measured using commercial enzymatic kits ) on a Beckman AU480 clinical analyser . Plasma low-density lipoprotein (LDL)-cholesterol concentrations were estimated using the Friedewald equation : LDL-cho2 area using the ImageJ-win64 software.The histological lysochrome lipid stain Oil Red O was performed on liver sections using a standard protocol . Slides 0\u2013120 min blood glucose area under the curve (AUC) was generated using the IBM SPSS Statistics 26 software . A correlation between gastric half emptying time (t \u00bd) and OGTT0\u2013120 min blood glucose AUC for SLD groups was performed in the GraphPad Prism v8 software. The coefficient of determination value (r2) was considered significant at p < 0.05.Results are expressed as the mean \u00b1 SEM. A two-way ANOVA was performed to assess diet and isoleucine treatment effects with a Tukey\u2019s post hoc test for multiple comparisons, using the GraphPad Prism v8 software . The OGTTp < 0.001, unpaired t-test; p < 0.0001, F = 28.17, diet effect; p = 0.1262, F = 2.418, isoleucine effect; SLD-C/A; 34.8 \u00b1 0.7 g (n = 20), SLD-Ch; 37.2 \u00b1 1.3 g (n = 10), HFD-C/A; 42.3 \u00b1 1.6 g (n = 16), and HFD-Ch; 44.1 \u00b1 1.7 g (n = 8)).At the beginning of week 12, prior to isoleucine supplementation, HFD-mice gained significantly more weight than SLD-mice = 19.21, diet effect; In weeks 12\u201315, HFD-mice continued to gain more weight compared to SLD-mice = 24.78, diet effect; SLD-C, 9.3 \u00b1 0.2 cm, SLD-Ch, 9.9 \u00b1 0.5 cm, HFD-C, 11.4 \u00b1 0.3 cm, and HFD-Ch, 11.2 \u00b1 0.3 cm). In addition, HFD-mice had heavier gonadal fat pads and brown fat pads than SLD-mice = 11.13 and F = 11.44, respectively, diet effect; At week 18, abdominal circumference was greater in HFD-mice than SLD-mice, but was not affected by chronic isoleucine treatment = 18.34, diet effect; p < 0.0001, F = 37.31, diet effect; HFD-mice had heavier livers than SLD-mice = 4.157, diet effect; p < 0.05, F = 5.715, diet effect; HFD-mice consumed more energy across 24 h = 9.151, p < 0.05, F = 6.499, p < 0.01, F = 11.25, respectively, diet effect; p < 0.05, F = 5.416, interaction; p < 0.05, F = 6.468, interaction; p < 0.05, Sidak\u2019s post hoc test), but not in HFD-mice.HFD-mice had a significantly lower energy expenditure compared to SLD-mice across 24 h, during the light phase or dark phase = 19.66, diet effect; p < 0.05, F = 4.082, diet effect; p < 0.001, F = 38.4, diet effect; HFD-mice had lower RQ values compared to SLD-mice across 24 h = 31.28, diet effect; p < 0.001, F = 40.02, diet effect; p < 0.001, F = 40.16, diet effect; p < 0.0001, F = 25.36, diet effect; HFD-mice had elevated plasma total triglycerides = 19.34, diet effect; HFD-mice had higher fasting blood glucose levels than SLD-mice = 34.44, diet effect; p < 0.05, one-way ANOVA; HFD-mice had a greater glucose AUC than SLD-mice (n = 8); SLD-A, 144.4 \u00b1 15.3 min (n = 8) and SLD-Ch, 126.7 \u00b1 5.1 min (n = 7)).There was no significant difference in the gastric half emptying time (t \u00bd) between different isoleucine groups in SLD-mice ; SLD-C, r2 = 0.0197, SLD-A, r2 = 0.2602, and SLD-Ch, r2 = 0.004292).There was no correlation between gastric half emptying time and blood glucose AUC in SLD-mice mice, significantly reduced blood glucose levels in response to an OGTT, albeit at a higher dose of 0.5 g/kg [In the current study, acute isoleucine orally administered at a dose of 0.3 g/kg, had no effect on postprandial blood glucose levels in SLD- or HFD-mice. Previously, acute administration of 0.3 g/kg isoleucine in lean and diet0.5 g/kg . ConsideConsistent with a previous report , the chr13CO2 content in the breath following a gastric emptying breath test, but did not significantly affect the 13CO2 AUC, Cmax, or Tmax values (peak concentration and the time at which it occurred) compared to controls [Slowing gastric emptying allows for efficient digestion and absorption of nutrients, including glucose ,36,37. Icontrols .The acute and chronic isoleucine supplementation had no beneficial effect to limit HFD-induced body weight gain, adiposity, fasting blood glucose levels, and glucose tolerance. In contrast, the chronic isoleucine treatment impaired glucose tolerance in SLD-mice. Therefore, the chronic isoleucine supplementation is unlikely to be an effective dietary intervention for the treatment of obesity and type 2 diabetes."} +{"text": "Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, resistant to at least one of three clinically relevant antimicrobial classes, were screened for resistance determinants. All ciprofloxacin-resistant isolates (n = 99) harboured the C257T nucleotide mutation (conferring the Thr-86-Ile substitution) in conjunction with other synonymous and nonsynonymous mutations, which may have epidemiological value. The A2075G nucleotide mutation and amino acid substitutions in L4 and L22 were detected in all erythromycin-resistant isolates (n = 5). The tetO gene was detected in 100% (n = 119) of tetracycline-resistant isolates and three of which were found to harbour the mosaic tetracycline resistance gene tetO/32/O. Two streptomycin-resistant C. jejuni isolates (isolated from the same flock) harboured ant(6)-Ib, located in a multidrug resistance genomic island, containing aminoglycoside, streptothricin (satA) and tetracycline resistance genes (truncated tetO and mosaic tetO/32/O). The ant(6)-Ie gene was identified in two streptomycin-resistant C. coli isolates. This study highlights the widespread acquisition of antimicrobial resistance determinants among chicken-associated Campylobacter isolates, through horizontal gene transfer or clonal expansion of resistant lineages. The stability of such resistance determinants is compounded by the fluidity of mobile genetic element.Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter is the most commonly reported foodborne bacterial pathogen causing human gastroenteritis in the European Union (EU) and Ireland, most often associated with the broiler reservoir [Campylobacter spp. of food animal origin continues to limit the spectrum of clinically useful antimicrobials and is internationally recognised as a major societal challenge. Veterinary antimicrobials used therapeutically and prophylactically are often the same as, or belong to the same class as those used clinically [eservoir . Irelandeservoir . Frequeninically .Campylobacter spp. isolates, while resistance to erythromycin is typically low to moderate across Europe [Macrolides, fluoroquinolones and aminoglycosides are classified as critically important antimicrobials, while tetracycline is considered a highly important antimicrobial . Resistas Europe ,5,6. Macs Europe ,8,9. Syss Europe and resigyrA and gyrB, respectively), catalysing ATP-dependent negative supercoiling of DNA to regulate replication, repair and gene expression [Campylobacter spp. is largely mediated by chromosomal mutations in the quinolone resistance-determining region (QRDR) of gyrA, typically conferred by the C257T nucleotide mutation (Thr-86-Ile) [In Gram negative bacteria, DNA gyrase is the primary target of fluoroquinolones . DNA gyrpression ,13,14. R-86-Ile) . The QRD-86-Ile) . rplD and rplV, respectively) or the presence of the emerging ermB gene contribute to macrolide resistance [ermB was reported recently for the first time in thermophilic Campylobacter spp., located on a chromosomal multidrug resistance genomic island (MDRGI) (likely originating from a Gram positive species) in a high-level erythromycin-resistant Campylobacter coli (C. coli) isolate (ZTC113) of swine origin in China [Macrolides act by binding to the 50S bacterial ribosomal subunit and inhibit translational elongation, and interfere with protein synthesis and subsequent ribosomal subunit assembly ,17. Polysistance ,18. \u0392etasistance ,20. Mutasistance . The ribin China . ErmB diin China . Campylobacter spp. contributes to baseline resistance against structurally diverse antimicrobials [cmeABC operon encodes a tripartite multidrug efflux pump that consists of an outer membrane channel protein (cmeC), an inner membrane efflux transporter (cmeB) and a periplasmic fusion protein (cmeA) [cmeR) binding to an inverted repeat (IR) (TGTAATAAATATTACA) in the intergenic region between cmeR and cmeA transcriptionally represses the cmeABC operon [The intrinsic, chromosomally encoded resistance-nodulation-division (RND) CmeABC (Campylobacter multidrug efflux) efflux pump in crobials ,24,25,26n (cmeA) . RepressC operon ,29. ConsC operon ,30.Campylobacter spp. is largely conferred by a ribosomal protection protein (RPP), TetO, capable of displacing tetracycline from its primary binding site on the 30S ribosomal subunit [Campylobacter tetO can be located chromosomally but is often plasmid-mediated [tetO gene exists in at least eleven bacterial genera, including four Gram negative and seven Gram positive genera [tetO between members of different bacterial genera indicates that conjugative plasmids, transposons, or recombination events contribute to the dissemination and maintenance of the tetO gene [Tetracycline resistance in subunit ,31. Bact subunit ,33,34. Cmediated ,37,38,39tetO acquisition is the most prevalent genetic event conferring tetracycline resistance among Campylobacter spp., mosaic tet genes have also been reported within the genus [tetO, W, 32 [tetM, S [tet genes are widespread among Gram positive and Gram negative genera in human and animal isolates [Although he genus . Mosaic O, W, 32 ,40,41,42[tetM, S ) to form[tetM, S . Mosaic Campylobacter spp. resistance to aminoglycosides is mediated by reduced antimicrobial binding affinity for target sites due to enzymatic modification, via acetylation, phosphorylation or adenylation of amino or hydroxyl groups of the aminocyclitol nucleus or sugar moieties [ant(6)-I-sat4-aphA3), first isolated from Staphylococci [Campylobacter spp. isolates [Aminoglycosides are broad spectrum antimicrobials and inhibit protein synthesis by binding to 16S rRNA of the 30S ribosome ,45. Campmoieties ,45,46. Amoieties ,48,49, wmoieties ,51. The ylococci ,53. ANT and C. coli isolates recovered from Irish broiler neck skin and caecal samples over a one-year period (2017\u20132018).Despite the high prevalence of broiler ,57,58,59 broiler ,59,60,61 broiler or rumin broiler ,63 isolagyrA gene and 100% of isolates (n = 99) harboured a C257T point mutation, which is the dominant mutation conferring resistance among campylobacters. Resistant isolates were grouped into C. jejuni gyrA and C. coli gyrA sequence types based on the presence of synonymous and nonsynonymous mutations present in the portion of the gyrA gene sequenced (C. jejuni isolates (n = 85) were grouped into three GTJs . A large proportion (47.1%) carried the Thr-86-Ile substitution exclusively (GTJ1). Synonymous mutations T72C, C243T, T357C, C360T, C471T, T483C, and C622T were exclusively associated with C. jejuni and were present in both GTJ-II and GTJ-III. Nonsynonymous Ser-22-Gly (A64G) and Ala-206-Thr (G616A) mutations were present in 35.3% and 17.7% of isolates of ciprofloxacin-resistant C. jejuni isolates, respectively and were the basis of defining GTJ-II and GTJ-III, respectively. Both GTJ-II and GTJ-III were associated with the Asn-203-Ser (A608G) substitution. All CIP-resistant C. coli isolates tested (n = 14) harboured one nonsynonymous mutation only (Thr-86-Ile), but were grouped into seven GTCs based on the presence of various synonymous mutations quinolone-resistant isolates tested and minimum inhibitory concentrations (MICs) ranged from 0.5\u20138 mg/L.rplD gene was detected in the five isolates, and the partial sequences shared 100% homology with the rplD gene of erythromycin-sensitive C. coli isolates (GenBank accession numbers: MH084640.1 and MH084639.1) [rplV sequence in all erythromycin-resistant isolates: double point mutation at positions 308 and 309 , A325G (Thr-109-Ala), a double point mutation at positions 332 and 333 (Ala-111-Glu), G340A (Ala-114-Thr) and C358A (Pro-120-Thr). Nonsynonymous mutations in rplV were also identified in all erythromycin-resistant isolates. Partial rplV sequences in this study were homologous to a high-level erythromycin-resistant clinical C. coli isolate rplV gene (GenBank accession number: GU384982.1) [cmeR-cmeA intergenic region, upstream of the IR (positions 66-80), homologous to sequences derived from erythromycin-resistant (GenBank accession number: FJ797673.1) and erythromycin-sensitive (GenBank accession number: FJ797671.1) strains [ermB gene was not detected among the erythromycin-resistant isolates tested.Five erythromycin-resistant isolates were screened for mutations contributing to erythromycin resistance. All five erythromycin-resistant isolates harboured the A2075G mutation in the 23S rRNA gene. A T82C mutation (Ser-28-Pro substitution) in the strains . The ermtetO gene was detected in 100% of tetracycline-resistant isolates (n = 119). Three isolates , accounting for 2.5% of the tetracycline-resistant isolates, harboured the mosaic tetO/32/O type II gene, confirmed by PCR/partial sequencing and genomic sequencing (Streptococcus suis (S. suis) (GenBank accession number: KY994102.1) tetO/32/O gene (Campylobacter spp. (GenBank accession numbers: WP_052855148.1) and Clostridiales (WP_117823345.1) TetO/32/O sequences. A portion of the quencing B. Isolat2/O gene . EquallyC. jejuni isolates CITCj625-18 and CITCj727-18 were found to harbour multiple resistance genes, including a truncated tetO , mosaic tetO/32/O type II (1920 bp), aminoglycoside-6-nucleotidyltransferase (ant(6)-Ib)), and streptothricin acetyltransferase (satA). These antimicrobial resistance genes were located circumjacent to proteins involved in replication and recombination (C. jejuni isolates CITCj625-18 (first thin) and CITCj727-18 were nearly identical with an average nucleotide identity (ANI) of 99.99% and 30.5% GC content, indicating that the isolates had been circulating within and had been maintained by the flock. The pair belonged to sequence type ST-45 clonal complex (ST-137) and harboured LOS locus class C.bination A. The MDant(6)-Ie gene (900 bp), with almost identical sequences (99.89% identity). ANT(6)-Ie in this study shared 99.66% amino acid identity with each other, where CITCc3448-18 harboured a nonsynonymous G820A mutation and was identical to a C. coli ANT(6)-Ie protein (GenBank: WP_052786298.1). CITCc1631-18 and CITCc3448-18 ANT(6)-Ie shared between 29.7-36.1% identity to ANT(6)-Ia, ANT(6)-Ib, ANT(6)-Ic, and ANT(6)-Id amino acid sequences [CITCc1631-18 and CITCc3448-18 belonged to ST-828 clonal complex and harboured the ctively) ,51,65. N-acetyltransferase (AAC(3)) (261 amino acids) was also detected in both CITCj625-18 and CITCj727-18, 44.3% identical to a aminoglycoside 3-N-acetyltransferase (AAC(3)) variant (239 amino acids) in both CITCc1631-18 and CITCc3448-18. However, these isolates were gentamicin-susceptible, although this protein may confer resistance to other aminoglycoside antibiotics [C. coli variant was identical to AAC(3) genes reported in Campylobacter spp., 37.5% identical to AAC(3)-Ia described in Serratia marcescens (GenBank accession number: Q7B9H0), and 19\u201332.25% similar to AAC(3) orthologous, including types AAC(3)-Ib/Ic/Id/Ie/IIa/IIb/IIc/IId/IIe/IIf/IIIa/IIIb/IIIc/IVa/VIa/VIIIa/Ixa/Xa/XIa. The AAC(3) variant in CITCj625-18 and CITCj727-18 was identical to Campylobacter AAC(3) variants and was 19.3\u201325.84% similar to orthologues reported in other bacterial genera.Aminoglycoside 3-ibiotics . The C. Campylobacter spp. isolates have been detailed previously [The antimicrobial resistance rates of this pool of broiler-associated thermophilic eviously , and areCampylobacter isolates, collected throughout the Republic of Ireland, from the three largest poultry processors, over a one-year period (2017\u20132018). This study reports the antimicrobial resistance determinants circulating among Irish broiler-associated Campylobacter spp. [n = 99) tested in the current study, similar to reports published worldwide [Campylobacter spp. isolates [The Thr-86-Ile mutation is the predominant genetic alteration conferring (fluoro)quinolone resistance among ter spp. , and wasorldwide ,70,71. Sisolates ,62,72, iCampylobacter spp. are ecologically competitive and persistent even in the absence of antimicrobial selective pressure [Campylobacter isolates (3.1% to 28.9%) in Ireland between 1998 and 2000 [Fluoroquinolone-resistant pressure ,74,75. Dand 2000 ,76, in 2and 2000 . Clonal and 2000 ,78,79.C. jejuni isolates harbouring multiple amino acid substitutions in the gyrA QRDR (GTJ-II and GTJ-III) were necessary to produce high level moxifloxacin resistance [gyrA [gyrA QRDR have a negligible effect on (fluoro)quinolone resistance.GTJ-III) had ciprsistance ,85. MoxigyrA alleles within a population of Campylobacter isolates have been identified as epidemiological markers and may serve as a supplementary approach to classical epidemiological typing methods [C. coli gyrA type in 0.23% (n = 1) of 430 C. jejuni isolates tested, and 1.4% (n = 4) C. coli isolates harboured a typical C. jejuni gyrA type. The amino acid substitutions present in each of the three GTJ , while MICs ranged from 128 mg/L to \u2265 128 mg/L. Three of these isolates were collected from the same flock in north-central Ireland while one isolate was collected from a farm approximately 10 km away, the following week. The fifth erythromycin-resistant isolate was recovered from a farm in the mid-south-west of Ireland, two months previously, but all birds from these farms were processed in the same processing plant. Identical mutations in the 23S rRNA, rplV gene, encoding the 50S ribosomal protein L22 were detected in the C-terminal region (amino acids 109\u2013142) [cmeR regulatory IR. The effects of mutations detected in this study in rplD, rplV, and the intergenic region of cmeR-cmeA are unknown, but may contribute to erythromycin resistance.The A2075G point mutation in the 23S rRNA gene remains the most prevalent genetic event conferring macrolide resistance ,92 and w109\u2013142) , includi109\u2013142) . Mutatio109\u2013142) ,93) are ermB gene was not detected among the erythromycin-resistant isolates tested. Resistance mediated by ermB in Campylobacter spp. is largely confined to China, which may reflect the extensive use of antimicrobials in food producing animals in China [ermB-positive C. coli isolates recovered from poultry exist in Europe [ermB-positive isolate was detected for the first time in the United States in a C. jejuni isolate of clinical origin [ermB gene was recently detected in 18.3% of 240 thermophilic Campylobacter spp. retail meat associated-isolates in South Africa [C. jejuni 23S rRNA has been associated with a fitness cost and reduced doubling times [The in China . Three rn Europe ,95,96 anl origin , while th Africa . Mutationg times ,100,101,tetO gene, while three isolates harboured the mosaic tetO/32/O type II gene were detected. Mosaic tetracycline resistance genes in Campylobacter spp. are typically derived from tetO and tet32 sequences in the type II conformation, with a shorter central tet32 segment [Campylobacter spp. The first mosaic tetracycline RPP gene was detected in Megasphera elsdenii, composed of a central tetW region flanked by two tetO regions [tetO primers [tetO gene and enable the detection of mosaic tet genes with a central portion flanked by an initial tetO region until position 228. The tetO/32/O type II gene reported here was associated exclusively with an MIC of 64 \u00b5g/L. However, 27 of 119 (22.7%) tetracycline-resistant Campylobacter spp. isolates tested had MICs of 64 \u00b5g/L or \u2265 64 \u00b5g/L, indicating that other factors contribute to enhanced tetracycline resistance. It should be noted that in this study, all three isolates harbouring mosaic tetracycline genes were also co-resistant to streptomycin, enabling co-selection and persistence of these antimicrobials. The burden of mosaic tetracycline resistance genes within the genus should be considered as part of the approach to elucidate developing and newly acquired antimicrobial resistance determinants within the genus. All tetracycline-resistant isolates harboured a portion of the segment , althoug regions . However regions ,43. The primers used in n = 4) isolates had MICs of \u2265 16 mg/L. Streptomycin-resistant C. jejuni isolates CITCj625-18 and CITCj727-18 (ST-137) harboured sialylated LOS locus class C, which has been identified as a risk factor for post-infectious Guillain-Barr\u00e9 syndrome and increased severity of enteric disease [C. jejuni ST-45 clonal complex [All streptomycin resistant revealed identical genes in a multidrug resistance genomic island and Campylobacter spp. (GenBank accession number: WP_002823161.1). The presence of multiple tet genes (coding for similar or different mechanisms) in Gram negative isolates has also been documented [tetO genes have also been reported in C. coli MDGRI containing aadE (ant(6)-Ib) and ermB [ant(6)-Ib (867 bp)) and streptothricin resistance (satA) genes were also located within the multidrug resistance island (satA) is frequently reported in Gram positive bacilli [sat4) reported in Campylobacter [Genomic sequencing of tetracycline-/streptomycin-resistant c island A. Both icumented . Howeverand ermB . Aminogle island A. Strept bacilli and sharlobacter ,111,113.C. coli of swine origin in Spain, America, and Grenada [C. coli ST-6543 on the PubMLST Campylobacter database at the time of writing [CITCc3448-18 belonged to ST-828 clonal complex (ST-1096). ST-1096 has been isolated from a case of gastroenteritis in the United Kingdom (UK) in 2016 and has Grenada ,115,116. Grenada . There a writing , includiC. coli isolates (CITCc1631-18 and CITCc3448-18) harboured the emerging ant(6)-Ie gene (900 bp), found widely disseminated among clinical and animal C. coli isolates [Campylobacter ant(6) genes, ant(6)-Ie appears to be inherent to C. coli and does not have a Gram positive ancestor [ant(6)-Ie gene was originally detected in a hypervariable genomic region, unaccompanied by other resistance genes [ant(6)-Ie genes were located chromosomally, and were not located near other resistance determinants. Both streptomycin-resistant C. coli isolates were co-resistant to ciprofloxacin/nalidixic acid (GTC-V) and tetracycline. C. coli isolate 1631-18 harboured tetO (1920 bp), while C. coli isolate CITCc3448-18 also harboured the mosaic tetracycline resistance gene, tetO/32/O (1290 bp), highly homologous with that detected in CITCj625-18 and CITCj727-18. Both streptomycin-resistant isolates ,65. UnliCampylobacter isolates (296 C. jejuni and 54 C. coli) were recovered from free range and intensively-reared broiler carcasses using ISO 10272-2:2017 [C. jejuni and 18 C. coli) isolates tested were resistant to at least one antimicrobial and were subsequently tested for resistance determinants.A total of 350 thermophilic 2-2:2017 for thei2-2:2017 ,119. Ove2, 10% CO2, 85% N2) and subcultured. DNA was extracted using the PureLink Genomic DNA Mini Kit , according to manufacturer\u2019s instructions and DNA was standardised to 50\u2013100 ng/\u03bcL.Briefly, isolates were recovered from \u221280 \u00b0C on Columbia blood agar and incubated for 24 h at 42 \u00b0C, under microaerobic conditions (5% OtetO/32/O and tetO/W/O) were designed on SnapGene2.3.2 software and regions of primer complementarity were assessed on Primer-BLAST [Primer sets, target genes and annealing temperatures are listed in er-BLAST .PCRs were performed with 2.5 U of Amplitaq polymerase , 1 \u00d7 PCR buffer I and 2.5 mM magnesium chloride (Applied Biosystems), 0.2 mM of each deoxyribonucleotide , 0.2 pmol/\u03bcL of each primer, and 1 \u00b5L (1\u20132 ng/\u03bcL) of DNA. Reaction conditions were denaturation at 94 \u00b0C for 2 min, 35 cycles of denaturation at 94 \u00b0C for 30 s, annealing for 30 sn = 99) were screened for mutations in the QRDR of the gyrA gene [gyrA of the reference C. jejuni (GenBank accession number: L04566.1 and AL111168.1) and C. coli sequences (GenBank accession number: AF092101.1 and NZ_UIGM01000003.1) on SnapGene 2.3.2. Ciprofloxacin-resistant isolates and the regulatory site of the cmeABC operon in five erythromycin-resistant C. coli isolates are listed in C. coli type strain NCTC 11366 (ATCC 33559) 23S rRNA (GenBank accession number: GQ167698.1), rplD (GenBank accession number: DQ639752.1 and UIGM01000003.1), rplV (GenBank accession number: UIGM01000003.1) and cmeABC operon (GenBank accession number: FJ797670.1) sequences was performed on SnapGene 2.3.2. Isolates were also screened for the presence of ermB, according to Wang et al. (2014). The primers used for the amplification and sequencing of domain V of 23S rRNA, n = 119) were screened for the presence of tetO, according to Aminov et al. (2001) and products were visualised on 2% agarose gel electrophoresis. The tetO amplicon of a tetracycline-resistant C. jejuni isolate (CITCj382-18) from this study was purified and sequenced (as described above) as a positive control. Consensus sequences were aligned to the C. jejuni tetO gene (GenBank accession number: M18896.2).Tetracycline-resistant isolates (tetO/W/O (tetO (GenBank accession number: M18896.2) and mosaic tetO/WO genes (GenBank accession numbers: EF065524.1 and AY196921.1). Two tetO/32/O-targeting primers (tetO (GenBank accession number: M18896.2) and tetO/32/O type I genes with a longer central tet32 region (GenBank accession numbers: AJ295238.3 and JQ740052.1) and tetO/32/O type II genes with a shorter central tet32 segment [Primers were designed to target tetO/W/O based on primers were des00033.1) .n = 4) were screened for sialylated LOS locus class A/B and C (C. jejuni 81-176 (ATCC BAA2151) and C. jejuni NCTC 11168 (DSM 27585), respectively, as positive controls. Streptomycin-resistant isolates were tested for moxifloxacin susceptibility. Briefly, isolates were recovered from \u221280 \u00b0C on CBA (Fannin Ltd) for 24 h at 42 \u00b0C under microaerobic conditions, and subcultured to CBA for 20 \u00b1 2 h at 42 \u00b0C under microaerobic conditions. In microtiter plates, 100 \u00b5L serial dilutions of moxifloxacin (Sigma Aldrich) were prepared in of Mueller Hinton broth with lysed horse blood ranging from 0.125\u201316 mg/L. A 0.5 McFarland inoculum was prepared in 5 mL demineralised water (Thermo Fisher Scientific) and 100 \u00b5L was transferred to 11 mL of Mueller Hinton broth with lysed horse blood (Thermo Fisher Scientific). Moxifloxacin serial dilutions were inoculated with 100 \u00b5L of cell suspension and incubated for 20 \u00b1 2 hat 42 \u00b0C under microaerobic conditions.All (fluoro)quinolone-resistant isolates (C. jejuni isolates CITCj625-18 and CITCj727-18 and C. coli isolates CITCc1631-18 and CITCc3448-18) were sequenced. DNA was quantified in triplicate with the Quant-iT dsDNA Assay Kit (Thermo Fisher Scientific). Genomic DNA libraries were prepared using the Nextera-XT protocol , with changes including 2 ng of input DNA and a minute PCR elongation time. DNA quantification and library preparation were performed on a Hamilton Microlab STAR system. Pooled libraries were quantified using the Kapa Biosystems library quantification kit on a Roche light cycler 96 qPCR machine. Libraries were sequenced on the Illumina HiSeq using a 250 bp paired-end protocol. Reads were adapter trimmed using Trimmomatic 0.30 with a sliding window quality cut-off of Q15 [The genomes of four streptomycin-resistant isolates (f of Q15 . De novof of Q15 and assef of Q15 .Genomes were annotated using Prokka 1.14.3 . SimilargyrA GT was submitted for each type. This whole-genome project has been deposited at DDBJ/ENA/GenBank under the accession number PRJNA612628. CITCj625-18, CITCj727-18, CITCc1631-18, and CITCc3448-18 genomes can be accessed using SAMN14379027, SAMN14379028, SAMN14379029, and SAMN14379030. The partial and complete gene sequences deposited in GenBank are listed in Campylobacter spp. hosts. The broiler industry serves as a reservoir for the dissemination of resistant campylobacters. The enrichment and stability of Campylobacter spp. resistance determinants is noteworthy but the natural competence and potential of recombination or acquisition of mobile genetic elements contributes to the Campylobacter. Taken together, the data collected in this study point to the diversity of resistance determinants circulating among Irish broilers, contributing to the development of resistance to clinically relevant antimicrobials. Although non-poultry sources contribute to campylobacteriosis incidence, poultry are natural thermophilic"} +{"text": "Splenocyte proliferation was tested using thymidine incorporation. Th1 and Th17 cells were analyzed by flow cytometry. Results: Oral KLHTT treatment (50 and 100 mg/kg) ameliorated mouse CIA by decreasing the levels of interleukin (IL)-1\u03b2, IL-6, IL-17A, and tumour necrosis factor-\u03b1 in the paw homogenates and serum. KLHTT also suppressed anti-CII antibody formation, splenocyte proliferation, and splenic Th1 and Th17 cell numbers. Additionally, KLHTT showed antioxidant activity by reducing the concentrations of MDA and H2O2 in paw tissues. Conclusions: The therapeutic effects of KLHTT in CIA mice were through regulating oxidative stress and inflammatory responses. Our results suggest that KLHTT has potential to treat RA.Background: Kan-Lu-Hsiao-Tu-Tan (KLHTT) exhibits anti-psoriatic effects through anti-inflammatory activity in mice. However, the therapeutic effects of KLHTT on rheumatoid arthritis (RA), another significant autoimmune inflammatory disorder, have not been elucidated. Herein, we explored the anti-arthritic effects of KLHTT on collagen-induced arthritis (CIA) in mice. Methods: KLHTT was extracted by boiling water and subjected to spectroscopic analysis. Chicken collagen type II (CII) with complete Freund\u2019s adjuvant was intradermally injected to induce CIA in DBA/1J mice. Anti-CII antibody, cytokines, malondialdehyde (MDA), and hydrogen peroxide (H Rheumatoid arthritis (RA) is an autoimmune disease affecting approximately 1% of the global population, which is characterised by synovitis, cartilage damage, and bone resorption in the joint , cervicaRA is characterised by synovitis accompanied by the infiltration of immune cells , includiKan-Lu-Hsiao-Tu-Tan (KLHTT), a Chinese medicine (CM), has been used to treat inflammatory conditions such as RA, systemic lupus erythematosus, dermatomyositis , sinusit3H labelled thymidine was purchased from Amersham Pharmacia Biotech, Arlington Heights, IL, USA. Brefeldin A and Freund\u2019s adjuvant were bought from Sigma-Aldrich, St. Louis, MO, USA. Phycoerythrin (PE)-conjugated anti-mouse CD4 (clone GK1.5), FITC-conjugated anti-mouse IL-17A (clone TC11-18H10.1), and FITC-conjugated anti-mouse interferon (IFN)-\u03b3 (clone XMG1.2) antibodies were ordered from Biolegend, San Diego, CA, USA. Formalin was bought from AVANTOR, Center Valley, PA. Bovine serum albumin (BSA) was purchased from EMD Millipore, Billerica, MA, USA. Tween 20 was obtained from EMD Millipore, Alsace, France.KLHTT (batch number: 0503-2-403-01) was supplied by Sun Ten Pharmaceutical Corporation, New Taipei City, Taiwan. Chicken collagen type II (CII) was purchased from Chondrex, Inc., Woodinville, WA, USA. Mycobacterium tuberculosis H37RA was bought from Difco Laboratories Inc., Detroit, MI, USA. Methotrexate (MTX) and EDTA were ordered from Bio Basic Inc., Toronto, ON, Canada. Enzyme-linked immunosorbent assay (ELISA) kits were obtained from eBioscience, San Diego, CA, USA. An IL-17A ELISA kit was purchased from R&D Systems Inc., Minneapolis, MN, USA. A hydrogen peroxide assay kit was purchased from Cell Biolabs, Inc., San Diego, CA, USA. Goat anti-mouse IgG1 and goat anti-mouse IgG2a secondary antibodies were purchased from Jackson ImmunoResearch Laboratories, West Grove, PA, USA. 2,2\u2019-Azinobis [3-ethylbenzothiazoline-6-sulfonic acid]-diammonium salt (ABTS) substrate solution was ordered form Roche Diagnostic Systems, South San Francisco, CA, USA. A Artemisia capillaris Thunb. (seedling), 4.17 g Scutellaria baicalensis Georgi (root), 2.50 g Acorus gramineus Soland. (rhizome), 2.08 g Clematis armandii Franch. (rattan and stem), 2.08 g Fritillaria cirrhosa D. Don (bulb), 1.67 g Pogostemon cablin (Blanco) Benth. (plant shoot), 1.67 g Forsythia suspensa (Thunb.) Vahl (fruits), 1.67 g Amomum kravanh Pierre ex Gagnep. (fruits), 1.67 g Mentha haplocalyx Briq. (stem and leaf plot), and 1.67 g Belamcanda chinensis (L.) DC (rhizome)) was extracted by boiling water (12 times the weight of the herbs) for 1 h, and then concentrated to a voucher specimen (CGU_KLHTT-01) by the freeze dryer [The herbs of KLHTT were purchased and identified by Sun Ten Pharmaceutical Corporation, New Taipei City, Taiwan. A total of 27.93 g of herbs comprising an LC-30AD pump, SIL-30AC auto-sampler, CTO-20AC column, and SPD-M20A photodiode array detector . Prior to being loaded onto the UPLC column, 1 mg of KLHTT extract was first dissolved in 1 mL of methanol and filtered through a 0.45 \u03bcm membrane. Sample injections of 1 \u03bcL were then performed automatically. Liquid chromatography was performed using a CORTECS UPLC C18 column . The mobile phase was a mixture of MeCN (A) and water . A gradient sequence was executed as follows: 0\u201310 min, 10\u201320% A; 10\u201314 min, 20\u201325% A; 14\u201324 min, 25\u201330% A; 24\u201328 min, 30\u201340% A; 28\u201333 min, 40\u201350% A; 33\u201338 min, 50\u201375% A; 38\u201340 min, 75\u2013100% A; and 40\u201343 min, 100% A. The column temperature was set at 35 \u00b0C. The flow rate was at 0.4 mL/min. The range of detection wavelengths was fixed in the 190\u2013500 nm.Multiple reaction monitoring (MRM) experiments (in negative) were carried out using Shimazu LCMS-8045 triple quadrupole mass spectrometry to identify the constituents of KLHTT extract. The precursor ion settings of the corresponding profiling peaks were determined using the full scan experiment (50\u20131000 amu). The product ions were settled according to previously reported data. The dwell time was fixed at 100 ms and the collision energy was set at 25\u201345 eV. All MS data were acquired and processed using LCMS LabSolutions software Version 5.93 .DBA/1J mice were purchased from Jackson Laboratories and maintained at 20\u201325 \u00b0C with half day light/dark cycle under a specific pathogen-free condition. All mice were treated according to the guidelines of the Institutional Animal Care and Use Committee of National Chung Hsing University (NCHU). The study protocol was approved by NCHU ethics committee .2O, KLHTT, or MTX was administered orally once a day from day 21 to 42. Mice were divided into four groups (n = 6/group) randomly as follows: Group I, Normal; Group II, Vehicle (ddH2O) + CII; Group III, KLHTT (50 mg/kg) + CII; Group IV, KLHTT (100 mg/kg) + CII. MTX (0.5 mg/kg) was used as a positive control. Mice were euthanized with CO2 exposure (100% CO2 for 5 min) by experienced experimenters humanely on day 42. The arthritis severity score was recorded every 3 days after the treatment of drugs. The biochemical and histological assays were performed on day 42.CIA was induced by active immunisation with chicken CII . BrieflyThe body weight and arthritis severity score were obtained . The artAfter the mice were humanely sacrificed, the hind limbs were fixed in 10% buffered formalin, decalcified in 15% EDTA, and embedded in paraffin. Serial paraffin sections (5 \u03bcm) were stained with haematoxylin and eosin. The severity of histopathological lesions was scored as folloHind paw was dissected and homogenised in ice-cold saline using a tissue homogeniser. After being centrifuged at 3000 rpm , the hind paw homogenates were harvested. Blood was collected from the heart. The levels of cytokines in hind paw homogenates and serum were measured by ELISA .2O2) concentration was measured using a colorimetric OxiSelect\u2122 hydrogen peroxide assay kit at 560 nm [Malondialdehyde (MDA) concentration was determined by thiobarbituric acid reactive substances assay at 532 nm. The standard curve was obtained using 1,1,3,3-tetramethoxypropane. Hydrogen peroxide at 4 \u00b0C overnight. The plates were washed and incubated with goat anti-mouse secondary antibodies IgG1 (1:500 dilution) or IgG2a (1:500 dilution) at 25\u201327 \u00b0C for 1 h. After being washed, ABTS substrate was added and the reactions were stopped by adding H2SO4. The level of IgG1 and IgG2a was measured at 450 nm by an ELISA reader [Serum samples were diluted 1:250 for IgG1 or 1:125 for IgG2a in Tris-buffered saline , and then transferred to CII (10\u2009\u03bcg/mL) pre-coated 96-well plates (Microtiterzerland) .5 cells/well) were cultured with chicken CII (50 \u03bcg/mL) at 37 \u00b0C for 40 h, and then incubated with 3H for 8 h. Cell proliferation was evaluated by radioactive thymidine incorporation [Splenocytes (4 \u00d7 10poration .6 cells/well) were cultured with chicken CII (50 \u03bcg/mL) at 37 \u00b0C for 48 h, and then brefeldin A (5 \u03bcg/mL) was added for 6 h. Cells were harvested and extracellularly stained with PE-conjugated anti-mouse CD4 antibodies. After being fixed and permeabilised with Cytofix/Cytoperm solution (BD Pharmingen), cells were then intracellularly labelled with FITC-conjugated anti-mouse IL-17A and anti-mouse IFN-\u03b3 antibodies. Splenocytes were detected by an Accuri C5 flow cytometer and analysed by BD Accuri\u2122 C6 Plus software [Splenocytes , chrysin 6-C-glucoside-8-C-arabinoside (2), baicalin (3), norwogonin-7-O-\u03b2-d-glucuronide (4), chrysin 7-O-\u03b2-d-glucuronide (5), oroxylin A 7-O-\u03b2-d-glucuronide (6), wogonoside (7), and baicalein (8) B (Table lein (8) .The CIA mouse model is a well-established and commonly used model mimicking the clinical symptoms and immunopathogenesis of human RA . ImmunisHistopathological analysis of the CIA mice revealed inflammatory cell infiltration into articular tissues, exudates within the synovial space, synovial hyperplasia, and cartilage erosion. KLHTT-treated mice demonstrated well-preserved joint spaces with minimal inflammatory exudates, normal cartilage structure, and clear synovial spaces, along with improved histological arthritis severity scores . MTX 0..The pathogenesis of RA involves activated T cells promoting macrophages to release pro-inflammatory cytokines . Therefo2O2 were noted in the hind paw homogenates of CIA mice. KLHTT (50 and 100 mg/kg) significantly reduced the levels of MDA and MDA (a lipid peroxidation marker) in joint homogenates from CIA mice. MDA-related reactions are highly immunogenic. MDA levels correlate with RA severity and can be used to predict RA severity [Oxidative stress is involved in the pathogenesis of RA ,43. In tseverity . The newseverity . RA patiseverity ,47. Inflseverity . Adalimuseverity . In thisC-arabinoside-8-C-glucoside, chrysin 6-C-glucoside-8-C-arabinoside, baicalin, norwogonin-7-O-\u03b2-d-glucuronide, chrysin 7-O-\u03b2-d-glucuronide, oroxylin A 7-O-\u03b2-d-glucuronide, wogonoside, and baicalein. Previous studies have reported that baicalin ameliorated CIA in mice by down-regulating Janus kinase 1/signal transducer and activator of transcription 3 signalling and inhibiting IL-17-mediated joint inflammation [We identified eight flavonoids from KLHTT, including chrysin 6-ammation ,51. Baicammation . Intrapeammation . Chrysinammation ,55. The ammation . ObservaIn summary, our results indicate that KLHTT, a CM formulation, shows significant anti-inflammatory effects, antioxidant activities, and immunomodulatory functions in CIA mice. The present study also demonstrates that KLHTT has potential to treat RA."} +{"text": "Helicobacter pylori (H. pylori) is one of the most common human pathogens, affecting half of the world\u2019s population. Approximately 20% of the infected patients develop gastric ulcers or neoplastic changes in the gastric stroma. An infection also leads to the progression of epithelial\u2013mesenchymal transition within gastric tissue, increasing the probability of gastric cancer development. This paper aims to review the role of H. pylori and its virulence factors in epithelial\u2013mesenchymal transition associated with malignant transformation within the gastric stroma. The reviewed factors included: CagA (cytotoxin-associated gene A) along with induction of cancer stem-cell properties and interaction with YAP (Yes-associated protein pathway), tumor necrosis factor \u03b1-inducing protein, Lpp20 lipoprotein, Afadin protein, penicillin-binding protein 1A, microRNA-29a-3p, programmed cell death protein 4, lysosomal-associated protein transmembrane 4\u03b2, cancer-associated fibroblasts, heparin-binding epidermal growth factor (HB-EGF), matrix metalloproteinase-7 (MMP-7), and cancer stem cells (CSCs). The review summarizes the most recent findings, providing insight into potential molecular targets and new treatment strategies for gastric cancer. Helicobacter pylori (H. pylori) is a helix-shaped, Gram-negative, microaerophilic, flagellated bacterium that is capable of biofilm formation and converting from spiral to coccoid form ..51].As a physiological process, EMT is observed during organogenesis, tissue development, remodeling, and wound healing ,53,54; cc-MYC [During this process, epithelial cells undergo a series of biochemical changes, which lead to the loss of polarity and migratory capacity of cells, resulting in cell shape changes (cell elongation). EMT promotes the transformation of immobile epithelial cells into motile mesenchymal cells, enhancing the metastatic properties ,70. Furtc-MYC ,77,78,79c-MYC . Moreovec-MYC ,82,83.H. pylori infection significantly affects the gastric microenvironment by induction of several inflammatory responses via infiltrating macrophages, neutrophils, regulatory T-cells, and natural killer cells [H. pylori virulence factors are considered being associated with the promotion of EMT in gastric cells, which consequently causes neoplasia and malignant transformation. This review summarizes several mechanisms associated with epithelial\u2013mesenchymal transition, gastric tumor microenvironment, and the influence of H. pylori infection, although some described mechanisms are not only H. pylori-specific. Even though H. pylori-induced carcinogenesis is not fully understood, several mechanisms have already been deciphered.er cells ,85. Infler cells ,87,88. Ter cells ,90,91. AH. pylori, cag pathogenicity island (cagPAI) probably plays a key role in carcinogenesis [CagA oncoprotein [CagA into a cell, transforming its shape into the so-called \u201chummingbird phenotype\u201d characterized by an elongated cell shape commonly observed in EMT [CagA into the cell via the T4SS induces signal transduction, with one of the most relevant mecahnisms being the nuclear factor \u03baB (NF-\u03baB) signaling pathway involving extracellular regulated kinases 1/2 (ERK-1/2) [H. pylori [CagA in host cells is tyrosine phosphorylated and interacts with protein tyrosine phosphatase 2 (SHP-2), also inducing the progression of the \u201chummingbird phenotype\u201d [CagA enhances EMT via the stabilization of Snail protein, which is essential in carcinogenesis, mainly by the reduction of glycogen synthase kinase-3 (GSK-3) activity [CagA-positive H. pylori strains with CagA containing phosphorylation-functional EPIYA motifs present significantly higher expression of mesenchymal markers such as vimentin, Snail, and ZEB-1 and the stem cell marker CD44 [CagA-positive H. pylori strains induce a higher probability of gastric carcinogenesis and induction of EMT process [CagA-positive H. pylori infection present poor clinical outcome, and higher invasion and metastatic characteristics [Among many virulence factors of ogenesis ,93,94. Ioprotein ,96. The d in EMT ,98. InjeERK-1/2) ,100,101.ERK-1/2) . The inh. pylori . CagA inenotype\u201d ,105. Cagactivity . CagA-poker CD44 ,109,110. process ,112,113.eristics . Besideseristics ,116.CagA-positive H. pylori strain infection [Recent research suggests that cells that undergo EMT obtain the ability to acquire cancer stem cell (CSC) properties ,122,123.nfection ,129. Hignfection ,135,136.H. pylori in the generation of cells with CSC properties, including several gastric epithelial cell lines [CagA in the induction of CSC properties was studied on H. pylori 7.13 wild-type (WT) CagA-positive strain and its knock-out mutants\u20147.13CagA-negative and 7.13DCagE-negative H. pylori strains. Only the wild-type (WT) (7.13CagA-positive) strain-induced mesenchymal changes and EMT in cells; cells infected by CagA-positive strains, presented higher expression of mesenchymal markers\u2014CD44, Snail1, vimentin, or zinc finger E-box binding homeobox 1 (ZEB1), while an expression of epithelial markers\u2014cytokeratin 7 (CK7) or osteopontin (SSP-1) was lowered [CagA-positive H. pylori strains. The relevance of the infection by CagA-positive H. pylori strain on EMT in gastric cancer was confirmed by significantly higher expression of CD44 and mesenchymal markers in tumor samples.Bess\u00e8de et al. (2014) studied the role of MKN-74) . The rol lowered . The migCagA-positive H. pylori EMT and the induction of CSC properties [CagA-positive H. pylori infection with N-nitrosoguanidine (MNNG) stimulation causes CSC features with dysplastic lesions and mesenchymal phenotype. Amieva and Peek (2016) observed that CD44+ cells with CSC features displayed increased CagA half-life [CagA was confirmed in CD44+ gastric CSCs [H. pylori-infected (CagA-positive) gastric cancer cells exhibit CSC properties via increased expression of surface markers\u2014CD44 and Lgr5 with Nanog, Oct4, and c-myc upregulation [CagA impairs transcription factor CDX1 expression, promoting EMT, and CSC features in gastric epithelial cells [The Wnt/\u03b2-catenin signaling pathway is involved in operties . Likewisalf-life . Accumulric CSCs . H. pylogulation ,140. Cagal cells .MYC oncogene [Yes-Associated-Protein (YAP) is an element of the Hippo tumor suppressor signaling pathway, which plays a crucial role in the maintenance of the proper size of organs, tissue homeostasis, cell proliferation, and stem cell maintenance ,143,144.oncogene ,149. Besoncogene .CagA-positive H. pylori strain induces higher YAP expression and decreases E-cadherin, N-cadherin, and Slug levels, promoting EMT.Li et al. (2018) showed a significantly higher expression of YAP and TAZ in cancerous gastric tissues with a positive correlation between YAP, TAZ levels, and tumor size . During CagA, in the enhancement of the YAP pathway [CagA-positive H. pylori upregulates YAP1 and large tumor suppressor 2 (LATS2) expression in gastric epithelial cells [YAP1 is associated with aggressiveness and poor prognosis [YAP1/SLC35B4 axis; another mechanism involves altered IL-1\u03b2 levels [Other studies have shown a potential role of GSK3/\u03b2-catenin or AMP-activated protein kinase (AMPK) pathways, which are regulated by pathway ,153. Molal cells . Overexprognosis . Gastric\u03b2 levels ,157. TheH. pylori strains produce a high quantity of tumor necrosis factor-\u03b1 (TNF-\u03b1)-inducing protein (Tip\u03b1 protein), which binds to the cell surface nucleolin and induces carcinogenic alterations [H. pylori virulence [\u03b1 induces mesenchymal changes of cells via EMT progression [\u03b1, as a carcinogenic factor, activates NF-\u03baB, promoting gastric carcinogenesis by inhibiting miR-3178 expression [\u03b1 release, Tip\u03b1 also induces the expression of several chemokines, including chemokine (C-C motif) ligand 2 (Ccl2), chemokine (C-C motif) ligand 7(Ccl7), chemokine (C-C motif) ligand 20 (Ccl20), C-X-C motif chemokine 11 (Cxc11), chemokine (C-X-C motif) ligand 2 (Cxcl2), C-X-C motif chemokine 5 (Cxcl5), and C-X-C motif chemokine 10 (Cxcl10) [\u03b1 (TNF-\u03b1), or hypoxia-inducible factor 1\u03b1 (HIF1\u03b1) [\u03b1, along with CagA and VacA, plays an underlying role primarily in mucosal damage [erations ,162,163.irulence ,165. By gression ,167,168.pression ,170. Bes(Cxcl10) ,173,174. (HIF1\u03b1) ,176. In l damage ,178.H. pylori infection increases the quantity of Tip\u03b1 protein in gastric cancer tissue, inducing tumor progression in H. pylori carcinogenesis [\u03b1 reduces cell stiffness and phosphorylates various oncoproteins; it also enhances filopodia formation, morphological, and conformational changes within cells, and expression of vimentin via MEK-ERK phosphorylation, confirming its role in EMT progression [Suganuma et al. showed that ogenesis . Tip\u03b1 regression ,180.\u03b1 and nucleolin receptor (88 kDa) on the migration properties of gastric cancer cells [\u03b1 could be inhibited via small interfering RNAs targeted for the nucleolin receptor, showing its role in EMT progression [H. pylori infection by inhibiting Tip\u03b1 and nucleolin interaction [Researchers have suggested the role of Tiper cells ,181. Fujgression . Thus, peraction ,184.\u03b1 induces the formation of filopodia and a reduction of cell stiffness, predisposing cells to higher motility [\u03b1 induces higher levels of IL-1\u03b2, TNF-\u03b1, and IL-8 in SGC7901 cells [H. pylori infection promotes the Il-6/STAT3 signaling pathway in AGS cells, which is one factor promoting EMT [\u03b1 did successfully eradicate H. pylori infection [Tipmotility . It has 01 cells . Furtherting EMT . Inoue enfection .H. pylori virulence factor, promoting its colonization and survival properties [H. pylori, which enhances the stimulation of cell proliferation. Lpp20 expression is increased in the acidic pH of stomach juice and during iron depletion [The Lpp20 protein plays an important role as an operties . Lpp20 iepletion ,190.\u03b1), is one of the carcinogenic factors released by H. pylori via NF-\u03baB pathway activation [\u03b1 and Lpp20 induce EMT mainly by stimulating cell proliferation, migratory properties of cells, and filopodia formation [Lpp20 , these proteins show similar effects on gastric cancer cells by stimulating EMT and gastric cancer progression.Even though Lpp20 and TipH. pylori lowered the expression of Afadin protein independently of CagA and VacA in MKN74 and NCI-N87 cell lines [H. pylori.Afadin is a cytoplasmic actin-filament-binding protein responsible for the formation and stabilization of tight and adherens junctions ,194,195.ll lines . DownregH. pylori with an affinity for penicillin binding; any modifications within PBP might induce resistance to \u03b2-lactam antibiotics [PBP2X, PBP2B, and PBP1A [H. pylori PBPs might present unique characteristics because of several putative genes encoding PBPs.Penicillin-binding protein (PBP) is a specialized acyl serine transferase released by icillin) . These mnd PBP1A . It was PBP1A mutation-positive H. pylori (H. pylori CagA+/P+) strain and CagA+/P\u2212 in terms of clinicopathological characteristics of gastric cancer and EMT induction [H. pylori CagA+/P+ infection resulted in progressive and clinically significant EMT and gastric cancer severity. Researchers have observed decreased levels of E-cadherin and increased \u03b1-smooth muscle actin (\u03b1-SMA) levels; likewise, it was observed that PBP1A mutation is associated with decreased miR-134 levels. MiR-134 suppresses gastric carcinogenesis by targeting the KRAS gene and Golgi phosphoprotein 3 (GOLPH3) downregulation; another essential target gene of miR-134 is FoxM1 [H. pylori activity decline [Huang et al. 2019) showed significant differences between nduction . H. pylois FoxM1 ,201. The9 showed decline . Marcus decline .Micro-RNAs constitute a family of small noncoding RNAs, which are regulators of posttranscriptional gene expression by binding to the 3\u2032-untranslated region of mRNA, promoting an inappropriate translation of targeted mRNA. There is an increasing interest in micro-RNA involvement in many diseases and malignancies ,206,207.H. pylori [H. pylori infection induced the overexpression of microRNA-29a-3p in gastric cancer tissue samples, which resulted in an enhanced ability of the migration of gastric epithelial cells. Furthermore, the silencing of A20 increased the EMT markers Snail, vimentin, and N-cadherin, and decreased E-cadherin levels. The authors have suggested that the overexpression of micro-RNA-29a-3p might be associated with a higher probability of EMT induction in gastric cells.Sun et al. presented the relevance of upregulation of microRNA-29a-3p and its role in the decreased expression of A20 in patients infected by . pylori . A20 is . pylori . H. pyloTWIST1 gene [Programmed cell death protein 4 (PDCD4) is a tumor suppressor responsible for the inhibition of cell growth, tumor invasion, metastasis, or induction of apoptosis . It is lST1 gene .TWIST1, and vimentin levels in gastric cancerous tissues [CagA-positive H. pylori strain infection. PDCD4 overexpression reduced EMT. MicroRNA-21 overexpression in gastric cancer modulates the expression of the tumor suppressors phosphatase and tensin homolog (PTEN) and PDCD4, altering molecular pathways associated with cell growth, invasion, migration, and apoptosis [PDCD4 is one factor responsible for the induction of carcinogenesis . Yu et a tissues . PDCD4 dpoptosis .LAPTM4B) is a proto-oncogene relevant in the progression of tumorigenesis, regulating molecular mechanisms, and cellular functioning, including proliferation, migration, and invasion [LAPTM4B upregulation has been observed in various cancers, including hepatocellular carcinoma, breast cancer, and lung adenocarcinoma [Lysosomal-associated protein transmembrane 4\u03b2 while lowering E-cadherin levels and dysregulating cell\u2013cell junctions. Additionally, there was a noticeable increase of ZEB1, \u03b2-catenin, Snail, and Slug markers, whereas tight junction protein-1 level was decreased. LAPTM4B seems to be a factor strictly associated with EMT induction since it is responsible for regulating cells\u2019 filopodia, increasing motility of gastric cancer cells, and a higher invasion potential [LAPTM4B results in poorer prognosis in various cancers [It has been reported that ormation . Researcotential . Overexp cancers .\u03b1 in fibroblasts, which is common during CagA+VacA+ H. pylori infection [Physiologically, natural gastric stroma contains only a few fibroblasts, and those are mainly myofibroblasts. The number of fibroblasts is significantly increased in tissues affected by inflammation or neoplasm ,230,231.nfection .H. pylori infection results in the transformation of fibroblasts and myofibroblasts into CAFs [CagA+VacA+ H. pylori infection results in the overexpression of fibroblast activation protein (FAP), fibroblast surface protein (FSP) mRNA, and increased levels of the proinflammatory factors IL-6, IL-8, COX-2, and SDF-1 [\u03b1-SMA, N-cadherin, vimentin, Snail, Twist) and lowered levels of E-cadherin, antiapoptotic B-cell lymphoma 2 (Bcl-2), and proliferative marker Ki-67 protein within fibroblasts [CagA+VacA+ H. pylori infection resulted in the aberrant apoptosis process, an increased level of collagen production, and impaired fibroblast and myofibroblast differentiation into CAFs. This induced desmoplastic reactions and EMT within gastric cells, promoting carcinogenesis. The increased levels of \u03b21-integrin and COX-2, which are crucial in invasion, metastasis, and angiogenesis, enhanced the migration properties of the infected cells. CagA+Vac+ H. pylori infection results in the upregulation of HIF-1\u03b1 and tenascin-C (TNC), enhancing EMT and tumor progression, the release of proangiogenic factors, and further CAFs activation [CagA+Vac+ H. pylori infection activates gastric fibroblasts and induces the release of TGF-\u03b2 [nto CAFs . CagA+Vand SDF-1 . Overexpnd SDF-1 ,248,249.roblasts . CagA+Vativation ,251,252.of TGF-\u03b2 .The tumor-promoting ability of CAFs is enhanced by microRNA dysregulation . CAFs stH. pylori infection results in the upregulation of HB-EGF gene expression, which is a potential serological biomarker for gastric cancer [H. pylori g-glutamyltranspeptidase, activating PI3K, and p38 kinase-dependent signal transduction pathways [Heparin-binding epidermal growth factor (HB-EGF) is an epidermal growth factor receptor (EGFR) cognate ligand with mitogenic and chemotactic properties for fibroblasts and smooth muscle cells . H. pyloc cancer ,266,267.c cancer . HB-EGF pathways .H. pylori infection and is associated with EMT [H. pylori infection [Matrix metalloproteinase-7 (MMP-7) is an enzyme responsible for the degradation of adherence between cells in the extracellular matrix, and overexpression of MMP-7 induces a more aggressive course of gastric cancer ,272,273.with EMT ,275. Liknfection ,278,279.nfection ,280.H. pylori infection results in the increased release of MMP-7 and soluble HB-EGF, promoting EMT [H. pylori-induced inflammation and damage via M1 macrophage polarization suppression [Yin et al. showed that excessive gastrin secretion due to ting EMT . HB-EGF ting EMT . Besidesting EMT ,284,285.ting EMT . Gastricting EMT ,288. Howpression .H. pylori infection, neoplasia, or cancer, being involved in the migration properties of gastric cancer cells [Mesenchymal stem cells (MSCs) present a multipotent potential to differentiate into various cell types, while keeping a capacity for self-renewal ,291. MSCer cells ,293,294.er cells ,296. Naner cells .H. pylori gained a fibroblastic phenotype, enhancing EMT progression in gastric cancer cells [H. pylori showed a significant decrease in the levels of E-cadherin and overexpression of mesenchymal markers and inflammatory cytokines , VEGF, epidermal growth protein (EGF), granulocyte-macrophage colony-stimulating factor (GM-CSF), and monocyte chemoattractant protein 1 (MCP-1). High concentrations of IL-15 secreted by gastric cancer MSCs contribute to tumor cell metastasis; increased IL-17 levels promote gastric cancer invasiveness [Zhang et al. showed that human umbilical cord MSCs (hucMSCs) infected by er cells . Furthersiveness ,300.SOX4 induces EMT via a release of TGF-\u03b2 and contributes to the development of stem cell characteristics of gastric cancer cells [CagA-positive H. pylori infection induces EMT, and CSCs feature in gastric mucosal cells via overexpression of the Wnt/\u03b2-catenin signaling pathway [KRAS, STAT3, Rac1, Wnt, Notch, PTEN, ERK, NF-\u03baB signaling pathways, or hypoxic microenvironment [Increased expression of er cells . Furtherer cells . CagA-po pathway . The pro pathway ,306,307. pathway . Besidesironment ,317,318.ironment .H. pylori infection and gastric carcinogenesis remains controversial. In fact, some mechanisms are yet not fully understood. H. pylori infection seems to play an important role in terms of EMT induction within gastric mucosa (The association between c mucosa .H. pylori virulence factors. Likewise, cellular components that are associated with EMT progression can be influenced by H. pylori infection (H. pylori along with its properties and virulence factors (H. pylori during the early stages of infection, which could significantly decrease the number of gastric cancer incidents.The severity and progression of gastric cancer depends on the presence of specific nfection . EMT and factors . Specifi"} +{"text": "Escherichia coli isolates, four (13.79%) Klebsiella pneumoniae isolates, and one (3.45%) Enterobacter cloacae isolate. The analysis based on the nucleotide sequences of the ESBL resistance genes showed that all cefotaximase-Munichs (CTX-Ms) were CTX-M-15 and that all sulfhydryl variables (SHVs) were SHV-11: 41.67% CTX-M-15-producing E. coli, 16.67% CTX-M-15+SHV-11-producing E. coli, 8.33% CTX-M-15-producing K. pneumoniae, 25% CTX-M-15+SHV-11-producing K. pneumoniae, and 8.33% CTX-M-15-produced E. cloacae. This study shows for the first time the presence of multiresistant ESBL-producing enterobacteria in fruit bats in Makokou.In Gabon, terrestrial mammals of protected areas have been identified as a possible source of antibiotic-resistant bacteria. Some studies on antibiotic resistance in bats have already been carried out. The main goal of our study was to detect extended-spectrum beta-lactamases (ESBLs) that are produced by enterobacteria from bats in the Makokou region in Gabon. Sixty-eight fecal samples were obtained from 68 bats caught in the forests located 1 km from the little town of Makokou. After culture and isolation, 66 Gram-negative bacterial colonies were obtained. The double-disk diffusion test confirmed the presence of ESBLs in six (20.69%) Bats are an important, widespread, and abundant taxon of mammals with over 1300 described species . Bats haThe existence of antibiotic multi-resistant (AMR) enterobacteria that have been recurrently documented in wildlife in recent years provide important insights into the potential role of wildlife as reservoirs of resistant bacteria. AMR enterobacteria are also pertinent markers to understand the dynamics of zoonosis and the complex transmission routes among wildlife and humans . Many waPteropus poliocephalus), McDougall et al. detected the presence of resistance to several antibiotic families in 5.3% of wild flying foxes from different Australian colonies , CH17 (2) CTX-M-15 [MK559065], CH18 (3) CTX-M-15 [MK559057], CH38 (2) CTX-M-15 [MK559063], CH41 (1) CTX-M-15 [MK559058], CH41 (2) CTX-M-15 [MK559064], CH42 (1) CTX-M-15 [MK559059], CH42 (2) CTX-M-15 [MK559060], CH43 (1) CTX-M-15 [MK559066], CH71 (1) CTX-M-15 [MK559061], CH82 (1) CTX-M-15 [MK559062], CH38 (2) SHV-11 [MK590053], CH42 (2) SHV-11 [MK590054] and CH43 (1) SHV-11 [MK590055].Epomops franqueti and 22 Megaloglossus woermanni were caught; a total of 68 bats of the Pteropodidae family were collected. Of the 68 bacterial strains identified, 66 were Gram-negative bacteria (GNB). Among the GNB, 29 (42.65%) were enterobacteria, which consisted of 11 (37.93%) Escherichia coli, five (17.24%) Klepsiella pneumoniae, three (10.34%) Enterobacter aerogenes, two (5.88%) Enterobacter cloacae, two (6.89%) Serratia plymuthica, one Citrobacter freundii (3.45%), one (3.45%) Enterobacter hormaechei, one (3.45%) Ewingella americana, one (3.45%) Morganella morganii, one (3.45%) Pantoea sp., and one (3.45%) Proteus vulgaris K. pneumoniae isolates, and one (3.45%) E. cloacae isolate ESBL-producing enterobacteria. Among beta-lactams, resistance was observed by using amoxicillin (100%), ticarcillin (100%), cefotaxime (100%), ceftazidime (100%), cefpodoxime (100%), aztreonam (100%), ticarcillin/clavulanic acid (90.90%), piperacillin (90.90%), cephalexin (100%), cefepime (81.81%), amoxicillin/clavulanic acid (54.54%), cefoxitin (54.54%), ertapenem (36.36%), piperacillin/tazobactam (54.54%), and imipenem (0.00%) .As for other antibiotics tested on these positive ESBL strains, resistance was observed as follows: Erythromycin (100%), streptomycin (100%), ciprofloxacin (90.90%), kanamycin (81.81%), tetracycline (81.81%), trimethoprim/sulfamethoxazole (72.72%), gentamycin (63.63%), nalidixic acid (63.63%), tobramycin (63.63%), colistin (54.54%), ofloxacin (54.54%), levofloxacin (45.45%), netilmicin (36.36%), amikacin (27.27%), nitrofurantoin (18.18%), and chloramphenicol (0%) .E. franqueti bats species and four ESBL-producing Enterobacteriae from M. woermanni bats species were identified. These bats belong to the family of Pteropodidae -producing E. coli, 9.09% ESBL (CTX-M-15)-producing K. pneumoniae, 27.27% ESBL -producing K. pneumoniae and 9.09% ESBL (CTX-M-15)-producing E. cloacae _SHV-11, CH43 (2)_SHV-11, CH42 (2)_SHV-11 and CH38 (2)_SHV-11) clustered with human bacterial strains from Tunisia and E. cloacae and K. pneumoniae (9.09%) or was associated with SHV-11 in K. pneumoniae (27.27%). The prevalence of ESBL-producing enterobacteria (37.93%) was higher than that obtained in E. coli sampled in bats and other wild animals in Nigeria [K. pneumoniae was found in a gorilla in its natural habitat in the Dzanga Ndoki National Park [Tadarida teniotis (bats) in Portugal [E. coli, followed by K. pneumoniae [blaCTX-M beta-lactam resistance genes are the most common in the human and veterinary strains [blaCTX-M-15 is the most prevalent ESBL gene in human samples worldwide [blaCTX-M-15 and blaSHV-11 genes are recognized as plasmid-mediated resistance genes [The beta-lactam resistance phenotypes obtained in our study are also comparable to those obtained in a study on bats in Algeria , which s Nigeria ,15 and t Nigeria , in whiceumoniae .27%. Thenal Park ,46 and iPortugal . Enterobeumoniae . However strains ,49,50. borldwide and is porldwide . In addice genes . All of ce genes ,52,53. blaCTX-M-15 genes had already been identified in ESBL-producing Enterobacteriaceae from patients in the Albert Schweitzer Hospital in Lambar\u00e9n\u00e9 and in poultry [blaCTX-M-15 and blaSHV-11 genes is probably linked to antibiotics used by humans, since our phylogenetic analyses show that all the sequences obtained in bats that carry CTX-M-15 or SHV-11 clustered with one human bacterial strain from Turkey and Tunisia, respectively. This suggests that the prevalence of antibiotic resistance in wild animals depends on the antibiotics consumed by human populations at each site and the density of the human population in contact with fauna [In Gabon, the poultry ,32. The th fauna .E. coli isolated from wildlife may be acquired from the food [E. coli has already been described as an important source of infection in mammals [E. coli infections can result from food contamination [Tetrapleura tetraptera, the fruit of which is widely consumed in Gabon) and lemon. Hence, it is possible that some fruits partly eaten by humans and contaminated have been ingested by bats. Fruit bats are potential vectors and reservoirs of pathogenic bacteria such as E. coli, which carry acquired resistance [In our samples, the highest prevalence of resistance was obtained in resistance to aminoglycosides , fluoroquinolones and tetracycline, which are the most common antibiotics consumed by the Gabonese people ,54. The the food ,57,58,59the food and watethe food ; resistathe food ,52. Furt mammals . Foodbormination ,63. Secomination ,64. Mostmination ,66,67,68mination ,70. Thesmination . Severalmination ,72,73. Tsistance ,59. The sistance ,75. Batssistance . In thisThe phylogeny of CTX-M-15 was constructed using v. 1.8.1 in BioEdit v. 7.0.9.0 software. These analyses were performed with a multiple alignment matrix of obtained partial CTX-M-15 sequences and the GenBank reference sequences of human, poultry and swine from Africa (Nigeria), Asia , Europe , the Middle East (Iran), and South America (Brazil). Enterobacteriaceae carrying CTX-M-15 isolated from fruit bats of Makokou in Gabon (in pink color).K. pneumoniae from bats. Enterobacteriaceae carrying SHV-11 isolated from fruit bats of Makokou in Gabon (in pink color).The phylogeny of SHV-11 was constructed using v. 1.8.1 in BioEdit v. 7.0.9.0 software. These analyses were performed with a multiple alignment matrix of obtained partial SHV-11 sequences and the GenBank reference sequences of human, water and cattle from Europe , Asia , the Middle East (Iran), and Africa (Tunisia and Egypt). All sequences of SHV-11 were from This study showed for the first time the presence of multiresistant ESBL-producing enterobacteria in Makokou fruit bats in Gabon . The source of the contamination has not been clearly determined, but the presence of this type of resistance in bats suggests that these wild mammals could spread ESBL-producing Enterobacteriacea over long distances or across the urban landscape.Our results reinforce the need to monitor antimicrobial resistance in wild animals, in protected or unprotected areas, in order to assess environmental responses to anthropogenic pressures."} +{"text": "Scientific Reports 10.1038/s41598-019-41524-3, published online 01 April 2019Correction to: The Acknowledgements sectionin this Article is incomplete.\u201cWe are grateful to Dr. D.W. Stamer and his collaborators from Duke University Eye Center for their gift of human primary TM cells. The present work was supported by Ministerio de Economia y Competitividad and Instituto de Salud Carlos III of Spain FIS PI14/00141 (X.G.), FIS P17/00296 (X.G.), RETICs Oftared RD12/0034/0003 (X.G.), RD16/0008/0014 (X.G.), RD12/0034/0015 (M.C.), RD16/0008/0023 (M.C.), Generalitat de Catalunya 2014SGR1165 (X.G.), and National Eye Institute - NIH, EY-11906 (T.B.).\u201dshould read:\u201cWe are grateful to Dr. D.W. Stamer and his collaborators from Duke University Eye Center for their gift of human primary TM cells. The present work was supported by European Union, Fondo Europeo de Desarrollo Regional (FEDER), Ministerio de Economia y Competitividad and Instituto de Salud Carlos III of Spain FIS PI14/00141 (X.G.), FIS P17/00296 (X.G.), RETICs Oftared RD12/0034/0003 (X.G.), RD16/0008/0014 (X.G.), RD12/0034/0015 (M.C.), RD16/0008/0023 (M.C.), Generalitat de Catalunya 2014SGR1165 (X.G.), and National Eye Institute - NIH, EY-11906 (T.B.).\u201d"} +{"text": "In: Imsanguan W., Bupachat S., Wanchaithanawong V., Luangjina S., Thawtheong S., Nedsuwan S., et al. Contact tracing for tuberculosis, Thailand. Bull World Health Organ. 2020 Mar 1;98(3):212\u201318 On page 215, Table 2, should read as follows:"} +{"text": "M-SAL yielded 29.7% ND and average concentrations of 2.26 \u00b1 1.15 (SD) log10 PFU/L (somatic) and 0.59 \u00b1 0.82 (SD) log10 PFU/L (F+ ). DMF performance was inferior to D-HFUF-SAL and M-SAL methods , indicating this procedure is unsuitable for 1 L surface water sample volumes. This study represents an important step toward the use of a coliphage method for recreational water quality criteria purposes.Coliphages are alternative fecal indicators that may be suitable surrogates for viral pathogens, but majority of standard detection methods utilize insufficient volumes for routine detection in environmental waters. We compared three somatic and F+ coliphage methods based on a paired measurement from 1 L samples collected from the Great Lakes (n = 74). Methods include: 1) dead-end hollow fiber ultrafilter with single agar layer (D-HFUF-SAL); 2) modified SAL (M-SAL); and 3) direct membrane filtration (DMF) technique. Overall, D-HFUF-SAL outperformed other methods as it yielded the lowest frequency of non-detects and the highest average concentrations of recovered coliphage for positive samples (2.51 \u00b1 1.02 log Enteric viruses are the leading cause of recreational waterborne disease outbreaks , but detE. coli or enterococci) are present at 1\u20132 orders of magnitude higher concentrations (Current coliphage standard culture-based methods include single-agar layer (SAL) plaque assay , double-trations . A simplIn this study, we evaluate the performance of three somatic and F+ coliphage methods with 1 L sample volumes, including dead-end hollow fiber ultrafiltration with SALSurface waters originated from Lake Michigan (n = 37) and nearby Trail Creek (n = 37). Samples were collected during the 2015 Great Lakes beach season at a frequency of five samples per week. The sample collection procedures are detailed elsewhere . The D-HAll data were log10 transformed and expressed as plaque forming unit (PFU) per liter (L) for positive samples only as ND samples were not included in the concentration data. Statistical analyses were performed using SigmaPlot version 13.0 . One-way analysis of variance (ANOVA) followed by Holm-Sidak multiple comparisons or Kruskal-Wallis ANOVA on ranks (followed by Tukey tests) were applied to somatic and F+ coliphage datasets (from both sites), while Wilcoxon signed rank tests were used for overall comparisons between the coliphage types or sites.10 PFU/L) were comparable to M-SAL , but concentrations obtained by DMF (0.30 \u00b1 0.44 [SD] log10 PFU/L) (p < 0.001) lower than either D-HFUF-SAL or M-SAL methods. The DMF method did not yield any F+ coliphage results from Lake Michigan samples, but they were detected using the other two methods (10 PFU/L) (p < 0.001) for positive samples than either M-SAL or DMF methods, but there was no statistically significant difference in F+ coliphage concentrations obtained by the M-SAL and DMF methods (p = 0.899).Method performance metrics are summarized in 0 PFU/L) were sig methods with D-H0 PFU/L) . D-HFUF-10 PFU/L and 3.25 \u00b1 0.44 (SD) log10 PFU/L, respectively (p = 0.252) (p < 0.001) of somatic coliphage for positive samples were observed with the DMF method (2.75 \u00b1 0.49 [SD] log10 PFU/L) (p = 0.659) average concentrations of F+ coliphage in positive samples were found in Trail Creek waters using the D-HFUF-SAL method (1.25 \u00b1 0.68 [SD] log10 PFU/L) and M-SAL (1.22 \u00b1 0.85 [SD] log10 PFU/L), but concentrations obtained by the DMF method were significantly lower (p < 0.001) (p < 0.001), and concentrations of both coliphage types were typically higher in the Trail Creek samples compared to the Lake Michigan samples (p < 0.001).Somatic coliphage were consistently detected in Trail Creek water samples irrespective of the method . D-HFUF-= 0.252) . Signifi0 PFU/L) . Compara< 0.001) . OverallRegarding frequency of NDs, D-HFUF-SAL exhibited the lowest ND range overall, with 0%\u20132.7% (somatic) and 5.4%\u201335% (F+) . M-SAL r2, CaCl2, MgSO4, tryptone, glucose, Tween 80, Antifoam Y-30, sodium hexametaphosphate) but we\u2019ve excluded common laboratory disposables such as serological pipettes, pipette tips, gloves and similar. Regarding the processing time, we have assumed that sample is being processed by a single analyst familiar with the routine water quality assessment (e.g. membrane filtration and /or defined substrate technology for enumeration of E. coli and enterococci) and possessing basic knowledge of microbiological culture techniques. The cost per sample for D-HFUF-SAL and DMF was comparable, while M-SAL was approximately ten times higher, reflecting the increase in supplies and reagents needed to process 1 L sample volumes to 25% (F+) . M-SAL mSupp Data"} +{"text": "Correction to: BMC Public Health (2020) 20:1616https://doi.org/10.1186/s12889-020-09721-2It was highlighted that in the original article the lettCorrect Table 1footnotesa Mann-Whitney testb \u03c72 testc Mortality rate per 1000 person-yearCOPD Chronic Obstructive Pulmonary Disease, CKD Chronic Kidney Disease, ICU Intensive Care Unit, IMSS Mexican Institute of Social Services, ISSSTE Institute of Social Security and Services for State Workers, SS Mexican Ministry of HealthCorrect equation in Results section2 = 31.83, df = 12, p < 0.001)(\u03c7The original article has been updated."} +{"text": "O.decamerasp. nov. and O.joshiisp. nov., of the ant genus Ooceraea are described from India. These species differ from other known congeners on the basis of number of antennal segments. An illustrated key to the known species based on the worker caste is also provided.Two new species, Ooceraea Roger, 1862 has been challenging, since its inception based on the type species O.fragosa. The taxonomic ambiguity has led to its uncertain placements in different subfamilies: in Myrmicinae and no constrictions between abdominal segments IV, V and VI. Ooceraea can be distinguished from the closely allied Syscia Roger, 1861 on the basis of abdominal segment III relatively narrow in dorsal view and similar in size to the preceding abdominal segment II (petiole); in lateral view, abdominal tergite IV not folding over sternite and the anterior portion of the sternite visible; hind basitarsi not dilating distally, circular in cross-section and metabasitarsal glands absent is probably native to the Asian continent, and has been introduced to Southeast Asia, the Pacific islands, Madagascar and the Caribbean islands and Ooceraeabesucheti with nine- and eleven-segmented antennae respectively ;SL Scape length: maximum length of antennal scape excluding basal condylar bulb;MW Mesosomal width: maximum width of promesonotum in dorsal view;ML Mesosomal length: maximum diagonal length of mesosoma in lateral view, measured from posterodorsal border of pronotal flange to posterior basal angle of metapleuron;PL Petiolar length: maximum length of petiole in lateral view;PH Petiolar height: maximum height of petiole in lateral view (including subpetiolar process);PW Petiolar width: maximum width of petiole in dorsal view;PPL Postpetiolar length: maximum length of postpetiole in lateral view;PPH Postpetiolar height: maximum height of postpetiole in lateral view;PPW Postpetiolar width: maximum width of postpetiole in dorsal view;CI Cephalic index: HW/HL \u00d7 100;SI Scape index: SL/HW \u00d7 100;PI1 Petiolar index 1: PL/PH \u00d7 100;PI2 Petiolar index 2: PW/PL \u00d7 100;PPI1 Postpetiolar index 1: PPL/PPH \u00d7 100;PPI2 Postpetiolar index 2: PPW/PPL \u00d7 100;WI Waist index: PPW/PW \u00d7 100.DepositoriesPUACPunjabi University Patiala Ant Collection at Department of Zoology and Environmental Sciences, Punjabi University, Patiala, Punjab, India;MCZCMuseum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States.Taxon classificationAnimaliaHymenopteraFormicidae9DCFFE46-DF69-52AC-8558-AA33512A3640http://zoobank.org/182F8A89-653B-4604-8337-F7A5F258080B9.5627\u00b0N, 77.2348\u00b0E, 780 m.India, Kerala, Periyar Tiger Reserve Holotype worker and one paratype worker, both India, Kerala, Periyar Tiger Reserve 9.5627\u00b0N, 77.2348\u00b0E, 780 m, leaf litter, Winkler, 21 January 2017, Tarun Dhadwal leg. [PUAC].HL 0.57; HW 0.56; SL 0.34; MW 0.39; ML 0.68; PL 0.29; PH 0.34; PW 0.27; PPL 0.32; PPH 0.34; PPW 0.30; CI 98; SI, 61; PI1 85; PI2 93; PPI1 94; PPI2 88; WI 111. Paratype: HL 0.57; HW 0.56; SL 0.33; MW 0.39; ML 0.68; PL 0.29; PH 0.33; PW 0.26; PPL 0.32; PPH 0.34; PPW 0.30; CI 98; SI, 59; PI1 88; PI2 89; PPI1 94; PPI2 88; WI 111.Holotype: Head in full-face view, almost as long as broad, with lateral margin weakly convex and converging anteriorly, with posterior margin concave medially and posterior lateral corners rounded. Anterior clypeal margin reduced and slightly concave in the middle. Eyes present, small in size, with two ommatidia, parafrontal ridge prominently produced. Mandibles edentate, sub-triangular. Antenna 10-segmented; scape short and clavate, reaching almost mid-length of the head; apical funicular segment fusiform. Frontal lobes reduced. Antennal sockets fully exposed from above.Mesosoma in lateral view weakly convex; promesonotal suture and metanotal groove absent. Pronotum in dorsal view anteriorly marginate. Propodeum in dorsal view with posterior margin concave; propodeal declivity in lateral view slightly concave, with lateral margin slightly marginate; propodeal lobe reduced. Petiolar node in dorsal view as long as broad, rounded anteriorly, in lateral view hemiglobular; subpetiolar process well-developed, with sickle-shaped anteroventral apex. Postpetiole in dorsal view subtrapezoidal, with anterior margin transverse and posterior margin convex, in lateral view with anteroventral corner angulate. Gastral segment I large, occupying the most part of gaster, in lateral view with dorsal margin weakly and roundly convex.Sculpture. Head foveolate-reticulate; mesosoma, petiole and postpetiole foveolate-reticulate; gaster foveolate, with foveae smaller than those of head and mesosoma.Pilosity and Pubescence. Body covered with erect or sub-erect hairs; sides of head and legs covered with shorter hairs; scape and funicular segments covered with short decumbent or subdecumbent hairs.Body coloration. Head and gaster light brown; mesosoma, petiole and postpetiole darker than the head; legs yellowish brown.Queen. Unknown.Male. Unknown.Ooceraeajoshii sp. nov. and O.decamera sp. nov. (described below) are distinctly separated from the other valid congeners by having 10-segmented antennae. Furthermore, the two new species are well distinguished from each other by a combination of the following characters: head shape ; presence of ommatidia (present in O.joshii sp. nov. and absent in O.decamera sp. nov.); propodeal lobes (reduced versus roundly produced); petiolar node in lateral view (hemiglobular versus rectangular); subpetiolar process ; pilosity (head and body comparatively more pilose in O.joshii sp. nov.); and sculpturation .The type series was found in leaf litter samples collected from the Medaganam region of the Periyar Tiger Reserve situated at an elevation of 780 meters. The region is composed of an undisturbed tropical moist evergreen forest with low light penetration, with a mean average daytime temperature of 30 \u00b0C.Known only from the type locality.The species has been named in honor of Professor Amitabh Joshi, a distinguished evolutionary biologist based at Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India.Taxon classificationAnimaliaHymenopteraFormicidaeEFC710C7-7193-5101-BA40-0E0AD282BD0Chttp://zoobank.org/D8C9E609-7416-4081-A54A-83CAA01CEAD610.02308\u00b0N, 77.833333\u00b0E, 250\u2013350 m alt.India: Madras, Alagarkovil, 21 km. N Madurai, Holotype worker, India, Madras, Alagarkovil, 21 km N Madurai, 10.02308\u00b0N, 77.833333\u00b0E, 250\u2013350 m alt.; 2 November 1972; Besuchet Lobt Mussard leg. (Specimen number/barcode: MCZ-ENT00649398) [MCZC].HL 0.62; HW 0.46; SL 0.26; MW 0.38; ML 0.78; PL 0.26; PH 0.42; PW 0.30; PPL 0.34; PPH 0.41; PPW 0.40; CI 74; SI 57; PI1 62; PI2 93; PPI1 81; PPI2 118; WI 133.CI 74), with lateral sides weakly convex, with posterior margin concave medially, with occipital lobes/corners angulate. Anterior clypeal margin slightly projecting forward. Eyes absent. Parafrontal ridge prominent and elevated. Mandibles edentate but weakly serrate. Antennae with 10 segments; scape short, clavate, slightly surpassing the mid-length of head. Frontal lobes reduced. Antennal sockets fully exposed from above.Head in full-face view rectangular, distinctly longer than broad large occupying the most part of gaster, in lateral view with dorsal margin almost straight, base of cinctus of first gastral tergite cross-ribbed.Sculpture. Head, mesosoma, petiole and postpetiole shallowly foveolate-reticulate; mandibles and dorsal surface of gaster sparsely foveolate, foveae somewhat smaller as compared to those present on head, mesosoma, petiole, and postpetiole.Pilosity and pubescence. Whole body covered with pale yellow erect and sub-erect hairs; appressed pubescence abundant on antennae and legs.Body coloration. Mandibles, antennae, legs, subpetiolar process and gaster light brown; head, mesosoma and gaster dark brown.Queen. Unknown.Male. Unknown.The two species significantly differ from each other on the basis of dimensions of head capsule and shape of subpetiolar process.Unknown.Known only from the type locality. The place has been transformed into agricultural land and is prone to anthropogenic activities. Thus, this reinforces the concept that important biodiversity components, which are already rare, are imperiled due to local extinctions.decamera refers to the ten-segmented antennal count.The species epithet"} +{"text": "Plakobranchus cf. ocellatus (Heterobranchia: Sacoglossa), a so-called \u2018solar-powered\u2019 sea slug with long-term retention of chloroplasts. The mitochondrial genome was 14,177\u2009bp in length containing the standard set of 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The base composition of 27.3% A, 15.6% C, 18.6% G, and 38.5% T showed a strong A\u2009+\u2009T bias. The genome organization of P. cf. ocellatus is identical to the other sacoglossan mitogenomes sequenced so far, except for Ascobulla fragilis.We present the complete mitochondrial genome sequence of Plakobranchus cf. ocellatus van Hasselt, 1824 belongs to a small group of marine, heterobranch slugs, called Sacoglossa, of which certain species have the ability to sequester chloroplasts from its food algae in December 2012. The heads of about 60 slugs were dissected to remove the post-pharyngeal nerve ring, which were directly deep frozen in liquid nitrogen and then stored (\u221280\u2009\u00b0C). From these, genomic DNA was extracted using the QIAGEN DNeasy\u00ae Blood & Tissue Kit . Voucher material is stored in absolute ethanol at the Zoological Research Museum Alexander Koenig (voucher no. ZFMK-TIS-29490).Specimens of \u00ae DNA PCR-Free Library Preparation Kit according to the manufacturer\u2019s protocol and 125\u2009bp paired-end reads were sequenced on an Illumina HiSeq 2500 platform . All read pairs were used for mitochondrial genome assembly with MITObim 1.8 as seed. After verification of correct circularity, genome annotation was done with MITOS revision 656 were prepared using the TruSeqElysia chlorotica, E. ornata, Thuridilla gracilis, and Placida sp. 1 NY-2013, except for Ascobulla fragilis.The complete mitochondrial genome (GenBank accession number: KX853083) had a length of 14,177\u2009bp encoding for 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The base composition is 27.3% A, 15.6% C, 18.6% G, and 38.5% T. A total of 183\u2009bp nucleotides were observed in multiple small intergenic regions, ranging from 1 to 54\u2009bp (found between the genes coding for COX3 and trnI(gat)). The gene order was as follows: trnK(ttt), cox1, trnV(tac), rrnL, trnL1(tag), trnA(tgc), trnP(tgg), nad6, nad5, nad1, trnW(tca), trnY(gta), nad4l, cob, trnD(gtc), trnF(gaa), cox2, trnG(tcc), trnH(gtg), -trnQ(ttg), -trnL2(taa), -atp8, -trnN(gtt), trnC(gca), -atp6, -trnR(tcg), -trnE(ttc), -rrnS, -trnM(cat), -nad3, -trnS2(tga), trnS1(gct), nad4, -trnT(tgt), -cox3, trnI(gat), nad2 and is therefore identical to the other sacoglossan mitogenomes sequenced so far, i.e. P. cf. ocellatus and all other sacoglossan species with fully sequenced mitogenome were extracted, aligned with MAFFT v7.271 (G-INS-i mode) (Katoh & Standley The amino acid sequence of the 13 protein-coding genes of"} +{"text": "Chromatographic separation of androgen derivatives was optimized, carefully separating isobaric interferents and acceptable outputs for precision and trueness achieved following injection of 0.4 pg on column (approximately 34 pmol/L). HMP derivatives of all androgens tested could be detected in low plasma volumes: male (100 \u00b5L) and post-menopausal female (200 \u00b5L), and derivatives were stable over 30 days at -20\u00b0C. In conclusion, HMP derivatization, in conjunction with LC-MS/MS, is suitable for quantitative analysis of DHT, testosterone and androstenedione in low plasma volumes, offering advantages in sensitivity over current methodologies.Liquid Chromatography tandem mass spectrometry (LC-MS/MS) is the gold-standard approach for androgen analysis in biological fluids, superseding immunoassays in selectivity, particularly at low concentrations. While LC-MS/MS is established for analysis of testosterone and androstenedione, 5\u03b1-dihydrotestosterone (DHT) presents greater analytical challenges. DHT circulates at low nanomolar concentrations in men and lower in women, ionizing inefficiently and suffering from isobaric interference from other androgens. Even using current LC-MS/MS technology, large plasma volumes (>0.5 mL) are required for detection, undesirable clinically and unsuitable for animals. This study investigated derivatization approaches using hydrazine-based reagents to enhance ionization efficiency and sensitivity of analysis of DHT by LC-MS/MS. Derivatization of DHT using 2-hydrazino-1-methylpyridine (HMP) and 2-hydrazino-4-(trifluoromethyl)-pyrimidine (HTP) were compared. A method was validated using an UHPLC interfaced by electrospray with a triple quadruple mass spectrometer , analyzing human plasma following solid-phase extraction. HMP derivatives were selected for validation affording greater sensitivity than those formed with HTP. HMP derivatives were detected by selected reaction monitoring (DHT-HMP Twydrazone , specifiution MS .3.1.1.2m/z 449 , m/z 447 (androstenedione) and m/z 451 (DHT) (m/z 257 (C11H12N4F3) and m/z 269 (C12H12N4F3) for testosterone, androstenedione and EpiT resulting from the cleavage of the steroid A and B ring (m/z 288 (C19H30ON) and m/z 164 (C5H5N3F3) whereas, m/z 286 (C19H28ON) and m/z 164 (C5H5N3F3) were selected for DHA and DHEA respectively. Heterolytic cleavage of hydrazine N-N bond of derivative may form ions at m/z 288 and m/z 286, and m/z 164 characterizes the protonated trifluoromethyl-pyrimidine moiety. Ions obtained following collision induced dissociation of derivatives of stable-isotopically labeled testosterone, androstenedione and DHT corroborated potential fragmentation 14] andd B ring 14,46]. andd B r. andd B entation .3.1.23.1.2.1E and Z isomers which elute as double peaks for each androgen HMP derivatization forms two 18 columns with modified stationary phases, particle sizes and dimensions. SunFire\u00ae C18 , ACE\u00ae Excel PFP-C18 , ACE\u00ae UltraCore 2.5 SuperC18 , ACE\u00ae Excel super C18 , Acquity UPLC\u00ae BEH C18 and Acquity UPLC\u00ae BEH C18 were evaluated aiming to achieve baseline resolution of isomers and isotopologues within reasonable analytical times. Ultimately rapid chromatographic separation was achieved between isomeric HMP derivatives of each androgen and their endogenous isomers using a UPLC\u00ae BEH C18 column operated at 50\u00b0C, with run times of 10 min and gradient method and the estimated LOQs were 0.4, 0.8 and 0.4 pg on column for DHT, testosterone and androstenedione respectively. Thus, estimated LOQs were improved ~21-fold and ~ 12.5-fold for HMP-DHT and HMP-androstenedione respectively in comparison to our LC-MS/MS method for underivatized androgens 3.23.2.113C3-T 97\u00b19%, 13C3-A4 99\u00b11% and 13C3-DHT 98\u00b15%). Extraction from plasma was assessed using stable-isotope labeled standards as surrogates, showing similar results . Ion suppression of internal standards was also within acceptable limits . Establishing conditions which limited ion suppression reduced the potential for variability in quantitation brought about by impact of subtle variations in matrix composition, particularly for low abundance analytes such as DHT. Minimal differences (<0.05 mins) in retention time between 13C3 IS and endogenous steroid due to the presence of heavy isotope were recorded. The assessment of the whole process also demonstrated that the presence of matrix did not adversely affected derivatization efficiency.Recovery of analytes by extraction was maximized and matrix effect minimized to ensure the cleanest possible sample to be prepared for analysis, and thus maximising column life-span and limiting source contamination. Analytes were well retained on lipophilic polymeric adsorbent Oasis\u00ae HLB ,50. and 3.2.213C3-T 1.7, 13C3-A4 1.8, and 13C3-DHT 2.7), were comparable to those in plasma, showing differences less than 20% .Interferents close to the retention times of the peaks of interest were not observed visually. The ratios of peak areas of quantifier to qualifier mass transitions ratios in standards , but acceptable within the reference range , intra and inter assay deemed acceptable (<20% RSD for precision and trueness at the LOQ and <15%3.2.5The HMP derivatives demonstrated acceptable stability upon storage in an auto-sampler (10\u00b0C) over 24 h, with limited degradation measured for derivatized testosterone , androstenedione and DHT in extracts of plasma from male and post-menopausal female subjects, respectively. Derivatives were stable upon short-term storage in the freezer for 7 days; reduction from original response testosterone , androstenedione and DHT in extracts of samples from males and testosterone , androstenedione and DHT from post-menopausal female. Moreover, derivatives were stable upon long-term storage in the freezer for 30 days; reduction from original response testosterone , androstenedione and DHT in extracts of samples from males and testosterone , androstenedione and DHT from post-menopausal females.3.3The method was applied to samples from post-menopausal females and males and compared to typical reference ranges 1,33]. ,33. 1,334. While multi-dimensional detection in conjunction with chromatography brings anticipated benefits in selectivity In summary derivatization to form HMP derivatives of androgens, in conjunction with LC-MS/MS, is suitable for quantitative analysis of androgens in low abundance in biological fluids, offering advantages in sensitivity over analysis of underivatized DHT. The approach allows concomitant analysis of testosterone, androstenedione and DHT and this method may be extended to include further steroids with ketone functions e.g. 11-oxygenated androgens. Robust measurement was achieved across typical physiological ranges found in post-menopausal women and men offering an attractive alternative to immunoassays, which lack selectivity in the lower physiological range of concentrations and typically report only one androgenAbdullah MM Faqehi: Methodology, Formal analysis, Project administration, Resources, Validation, Writing - original draft. Scott G Denham: Methodology, Formal analysis. Gregorio Naredo: Methodology, Formal analysis, Writing - review & editing. Diego F Cobice: Methodology, Formal analysis, Writing - review & editing. Shazia Khan: Methodology, Formal analysis, Writing - review & editing. Joanna P Simpson: Methodology, Formal analysis, Writing - review & editing. Ghazali Sabil: Methodology, Formal analysis, Writing - review & editing. Rita Upreti: Investigation, Writing - review & editing. Fraser Gibb: Investigation, Writing - review & editing. Natalie ZM Homer: Methodology, Validation, Project administration, Supervision, Writing - review & editing. Ruth Andrew: Conceptualization, Methodology, Validation, Funding acquisition, Project administration, Supervision, Writing - review & editing.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "Lactococcus lactis (L. lactis)/pNZ8150-phosphatidylglycerophosphate synthetase A (pgsA)-HAsd, in which pgsA was used as an anchor protein, and investigated the immunogenicity of HAsd in a mouse model by oral administration without the use of a mucosal adjuvant. Compared with L. lactis/pNZ8150-pgsA, mice were orally vaccinated with L. lactis/pNZ8150-pgsA-HAsd and then produced strong humoral and mucosal immune responses. Importantly, L. lactis/pNZ8150-pgsA-HAsd provided cross-protection against H5N1, H3N2 and H1N1 virus infections. Our data support the hypothesis that HAsd presented on the surface of L. lactis can provide cross-protective immunity against divergent influenza A viruses. Taken together, these findings suggest that L. lactis/pNZ8150-pgsA-HAsd can be considered an alternative approach to developing a novel universal vaccine during an influenza A pandemic.Most of the current approaches to influenza vaccine design focus on antibodies against influenza (HA). However, these influenza vaccines typically provide strain-specific protection against mostly homologous subtypes. There is an urgent need to develop a universal vaccine that confers cross-protection against influenza viruses. Of note, the HA stalk domain (HAsd) is a promising target for such an influenza vaccine. In this study, we generated recombinant Abbreviations: HA, HAsd, HA stalk domain; L. lactis, Lactococcus lactis; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; IFA, immunofluorescence assay; PBS, phosphate-buffered saline; pgsA, phosphatidylglycerophosphate synthetase A; SPF, specific pathogen-free; CFU, colony-forming unit; BSL-3, biosafety level-3 laboratory; TCID50, 50% tissue culture infective dose; ELISA, enzyme-linked immunosorbent assay; OD, optical density; LTB, liable enterotoxin B subunit; CTB, cholera toxin B subunit. Influenza A viruses cause a highly infectious respiratory disease that remains a public health problem worldwide . Humans Lactococcus lactis (L. lactis) has been engineered to express heterologous proteins [L. lactis expressing HA, HA1, neuraminidase or nucleoprotein of avian influenza H5N1 virus is a safe and effective vaccine candidate against H5N1 virus infection in mouse and chicken models with the use of a mucosal adjuvant or enteric capsule [L. lactis in the absence of a mucosal adjuvant can provide cross-protective immunity against divergent influenza A viruses.proteins . Our pre capsule . HoweverL. lactis, recombinant L. lactis/pNZ8150-pgsA-HAsd was constructed, in which pgsA derived from the chromosomal DNA of Bacillus subtilis [L. lactis/pNZ8150-pgsA-HAsd, which elicited robust humoral and mucosal immune responses against influenza A viruses. Most importantly, unadjuvanted L. lactis/pNZ8150-pgsA-HAsd could provide cross-protective immunity against lethal challenge with homologous and heterologous influenza A viruses. These data suggest that recombinant L. lactis/pNZ8150-pgsA-HAsd is expected to serve as an alternative approach for a truly protective universal influenza vaccine against divergent influenza A viruses.Thus, to investigate the immunogenicity of the HAsd presented on the surface of subtilis , and wasL. lactis was determined by western blot analysis. A highly specific band (approximately 100 kDa) was detected for the pgsA-HAsd fusion protein in the L. lactis/pNZ8150-pgsA-HAsd cells . In contrast, no band was detected in the L. lactis/pNZ8150-pgsA cells .The HAsd gene of codon-optimized A/Vietnam/1203/2004(H5N1) was clonsd cells , lane 3.L. lactis, L. lactis/pNZ8150-pgsA and L. lactis/pNZ8150-pgsA-HAsd cells were examined by immunofluorescence assay (IFA) and flow cytometric analysis. There were no positive signals in the L. lactis/pNZ8150-pgsA cells . By contrast, L. lactis/pNZ8150-pgsA-HAsd consistently exhibited specific fluorescent signals, indicating that HAsd was stably expressed on the surface of L. lactis (right side).To confirm that HAsd protein was expressed on the surface of L. lactis/pNZ8150-pgsA or L. lactis/pNZ8150-pgsA-HAsd group at the prime immunization. A highly significant increase (IgG titer \u2265 25) was observed in the L. lactis/pNZ8150-pgsA-HAsd group at the boost immunization, IgG titer induced by L. lactis/pNZ8150-pgsA-HAsd reach 28.4\u00b10.894, whereas there were still no significant (IgG titer <25) changes in the PBS or L. lactis/pNZ8150-pgsA group.HA-specific antibody responses were measured by ELISA. As shown in L. lactis/pNZ8150-pgsA or L. lactis/pNZ8150-pgsA-HAsd group at the prime immunization. Only L. lactis/pNZ8150-pgsA- HAsd could induce an elevated level of IgA antibodies after the boost immunization, IgA titers in the intestine and upper respiratory washes were 27.8\u00b11.30 and 27.4\u00b11.14, respectively.Mucosal IgA antibodies were also detected in the intestine and upper respiratory washes and c. TL. lactis/pNZ8150-pgsA-HAsd orally after the prime-boost immunization could produce an elevated level of HA-specific IgG and IgA antibody responses.Collectively, these results demonstrated that mice administered L. lactis/pNZ8150-pgsA-HAsd, all vaccinated mice were challenged with 20\u00a0\u00b5L of 104 EID50 of A/Vietnam/1203/2004(H5N1), A/Beijing/47/1992(H3N2) or A/California/04/2009(H1N1) and monitored for 14\u00a0days. As shown in L. lactis/pNZ8150-pgsA showed significant body weight loss and increased virus shedding in the lung and died within 8\u00a0days after challenge with the lethal dose of virus . In contrast, mice vaccinated orally with L. lactis/pNZ8150-pgsA-HAsd experienced only mild weight loss and recovered by 14\u00a0days . Importantly, L. lactis/pNZ8150-pgsA-HAsd could confer 100% (5/5), 80% (4/5) and 80% (4/5) protection against A/Vietnam/1203/2004(H5N1), A/Beijing/47/1992(H3N2) and A/California/04/2009(H1N1), respectively .Last, to assess the cross-protective efficacy of of virus ,b and c. 14\u00a0days , b and c 14\u00a0days , E and Fectively ,\u00a0h and iNde I or EcoR I sites underlined . The resulting Nde I/EcoR I fragment was cloned into pNZ8150-pgsA at the C-terminal end, in which pgsA was used as an anchor protein [L. lactis NZ9000. The positive clone of L. lactis/pNZ8150-pgsA-HAsd was screened, and the plasmid was expressed as described previously [L. lactis/pNZ8150-pgsA was used as a negative control for subsequent analysis.The HAsd (876 bp) gene of A/Vietnam/1203/2004(H5N1) that included part of HA1 (from 831 bp to 1041 bp) and complete HA2 gene (from 1041 bp to 1707 bp) was PCR protein , and theeviously . L. lactL. lactis surface was determined by western blot analysis as described previously [6-cell L. lactis/pNZ8150-pgsA-HAsd pellets were mixed with 60\u00a0\u00b5L of 6 \u00d7\u00a0loading buffer, boiled for 10\u00a0minutes, subjected to sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to a nitrocellulose membrane . The membrane was incubated with a 1:500-diluted monoclonal mouse anti-HA of A/Vietnam/1203/2004(H5N1) antibody after blocking with 5% skim milk at room temperature for 2\u00a0h. After incubation overnight at 4\u00b0C, the membrane was incubated with affinity-purified horseradish peroxidase (HRP)-conjugated anti-mouse IgG . The membrane was reacted with West Pico Chemiluminescent Substrate and imaged using a Molecular Imager ChemiDoc XRS System . Precision Plus Protein\u2122 WesternC\u2122 was used as a standard protein marker.The expression level of HAsd displayed on the recombinant eviously . BrieflyL. lactis surface was by an IFA . Briefly, 106L. lactis/pNZ8150-pgsA-HAsd cells were washed three times with sterile PBS, incubated with monoclonal mouse anti-HA antibody at 4\u00b0C for 1\u00a0h, followed by FITC-conjugated goat anti-mouse IgG at 4\u00b0C for 30\u00a0minutes, and resuspended in 100\u00a0\u00b5L of sterile PBS. Finally, L. lactis/pNZ8150-pgsA-HAsd cells were used for the IFA. L. lactis/pNZ8150-pgsA cells were used as negative controls.The HAsd protein displayed on the L. lactis/pNZ8150-pgsA-HAsd was analyzed by flow cytometric analysis .Flow cytometry was performed very similarly to IFA, as described above. Five hundred microliters of Specific-pathogen-free (SPF) six-week-old female BALB/c mice were used in this study and housed in cages ventilated under negative pressure with high efficiency particulate air filter.L. lactis/pNZ8150-pgsA-HAsd cells was adjusted to 1012 colony forming unit (CFU)/ml with sterile PBS. The mice (n\u00a0=\u00a039 per group) were vaccinated orally with 1012 CFU of L. lactis/pNZ8150-pgsA-HAsd at days 0, 1, 2, and 3 for prime immunization and boosted at day 17, 18, 19, and 20. PBS and L. lactis/pNZ8150-pgsA cells were used as controls.The concentration of recombinant At days 15 and 34 after the initial immunization, blood samples and intestine and upper respiratory washes were collected.4 EID50 of lethal dose of A/Vietnam/1203/2004(H5N1) (n\u00a0=\u00a08 per group), A/Beijing/47/1992(H3N2) (n\u00a0=\u00a08 per group)or A/California/04/2009(H1N1) virus (n\u00a0=\u00a08 per group). The mice were monitored for 14\u00a0days, and body weight loss and survival rate post challenge were calculated.Two weeks after the last immunization, all vaccinated mice (n\u00a0=\u00a024 per group) were transferred into an enhanced biosafety level-3 laboratory (BSL-3) containment facility and challenged intranasally with 20\u00a0\u00b5L containing 1050).Additionally, lungs from vaccinated mice were harvested for the detection of virus shedding at day 3 post infection (n\u00a0=\u00a03 per group). Tissue samples were homogenized and processed as described previously . The virAntibody responses of serum IgG and IgA in the intestinal washes and upper respiratory washes were determined by ELISA using recombinant HA protein (2\u00a0\u00b5g/mL) of A/Vietnam/1203/2004(H5N1) as a coating antigen, as described previously . A 1:5,0p-value of less than 0.05 was considered statistically significant.A two-tailed Student\u2019s t-test and one-way ANOVA were used for all statistical analyses. A Due to continuous antigen gene occurring mutation, the influenza A virus is considered to have the potential to cause the next pandemic . Most ofL. lactis may provide cross-protective immunity against divergent influenza A viruses. Generally, the HAsd, including HA2 and part of HA1, was displayed on the surface of L. lactis, and L. lactis/pNZ8150-pgsA-HAsd showed a specific binding profile that could be directly with anti-HA antibody and FITC-conjugated goat anti-mouse IgG. It was then tested by IFA and flow cytometric analysis. The binding profiles observed positively correlated with the display efficacy of HAsd, demonstrating that HAsd presented on the surface of L. lactis has reactive activity in vitro, which may contribute to immunogenicity in vivo.It has been hypothesized that the HAsd present on the surface of E. coli heat-liable enterotoxin B subunit (LTB) and cholera toxin B subunit (CTB) are potent mucosal adjuvants and promote the induction of protective immunity. However, the adverse effects of these adjuvants in clinical trials, including diarrhea, low-grade fever, and vomiting, limit their further application [L. lactis has an adjuvant function because of its inherent safety profile [L. lactis/pNZ8150-pgsA-HAsd could induce an adequate humoral response and mucosal response in the absence of a mucosal adjuvant. Moreover, the contributions of HA-specific antibodies for broad-spectrum protection against divergent influenza A viruses were emphasized.It is generally recognized that lication ,24. Furt profile , and sti profile ,27. ThusL. lactis/pNZ8150-pgsA-HAsd were protected completely (100%) (5/5) from homologous A/Vietnam/1203/2004(H5N1) virus challenge, as well as 80% (4/5) against heterologous H3N2 or H1N1 virus infection, and showed a reduced degree of virus shedding in the lung. These findings provide reliable evidence that L. lactis/pNZ8150-pgsA-HAsd is an effective vaccine candidate to induce cross-protective immunity against divergent influenza A viruses.Antigen epitope is crucial in designing vaccine. The HAsd designed in this study was codon-optimized for completely matching the antigen epitope with homologous H5N1 and 60% HAsd protein sequence similarity with heterologous H3N2 or H1N1, which provides the basis of cross-protective immunity. Furthermore, virus challenge is regarded as the gold standard for assessing the efficacy of an influenza vaccine. Therefore, mice administered orally with L. lactis/pNZ8110-pgsA-HA1, in which pgsA has been used as an anchor protein, provided immune protection against homologous H5N1 virus in the mouse model [L. lactis surface. The HAsd represents a promising research target for a novel universal influenza vaccine. Notably, the HAsd presented on the surface of L. lactis has the potential to induce cross-protective immunity against divergent influenza A viruses. Thus, this study strongly demonstrates that the discovery of L. lactis/pNZ8150-pgsA-HAsd may allow for an alternative design of influenza vaccines that would afford broad coverage.It has been demonstrated previously that adjuvanted se model . In this"} +{"text": "Marine sponges are well known as rich sources of biologically natural products. Growing evidence indicates that sponges harbor a wealth of microorganisms in their bodies, which are likely to be the true producers of bioactive secondary metabolites. In order to promote the study of natural product chemistry and explore the relationship between microorganisms and their sponge hosts, in this review, we give a comprehensive overview of the structures, sources, and activities of the 774 new marine natural products from sponge-derived microorganisms described over the last two decades from 1998 to 2017. The term \u201csymbiosis\u201d was first defined by the German mycologist Heinrich Anton de Bary in 1879 as \u201cthe living together of unlike organisms\u201d . Fr [14]. F124 16) were iso JBIR-59 and new were is [18\u201319) [18] werTrichoderma sp. derived from the Caribbean sponge Agelas dispar, four novel sorbicillinoid polyketide derivatives (20\u201323) (20\u201323 showed no bioactivities . A . A 60\u201361 (86\u201388) . Compoun4 \u00b5g/mL) .Arthrinium arundinis ZSDS1-F3 cultured from a Phakellia fusca marine sponge , four new cytochalasins, arthriniumnins A\u2013D (89\u201392), a new natural product, ketocytochalasin (93), three new 4-hydroxy-2-pyridone alkaloids, arthpyrones A\u2013C (94\u201396), and a new natural product, phenethyl 5-hydroxy-4-oxohexanoate (97) inhibitory activity with an IC50 value of 0.81 \u03bcM ..107\u2013109)126\u2013127) showed superior cytotoxicity at nanomolar concentrations toward 36 human tumor cell lines . Fr. Fr166) ue (177) was puri was yieAspergillus insuetus (OY-207) originated from the Mediterranean sponge Psammocinia sp. , and it afforded three novel meroterpenoids insuetolides A\u2013C (178\u2013180) and one new drimane sesquiterpene (181) (Arthrinium sp. associated with the marine sponge Sarcotragus muscarum (Turkey) . Th. ThAsperne (192) 72]. A . A Asper2) (193) , was proA-MB-231 . Examina194\u2013201) . Their a202\u2013207), and a new polyketide, scedogiine G (208) , were pr209\u2013210) were isoe sponge ,76.211) and a monocyclic butoxyl derivative (212) , and the new phthalide herbaric acid (215) . However, their bioassays were disappointing . Th. ThDichone (262) . Compoun\u00b1 0.3 \u00b5M .263) and ent-gloeosteretriol (266) led to the isolation of two new natural products, evariquinone and isoemericellin (267\u2013268) (267 showed antiproliferative activity toward KB and NCI-H460 cells at a concentration of 3.16 \u03bcg/mL . F. FPetros364\u2013365) , were isth Korea . New \u03b1-p368\u2013369) were iso Island) . Two new370\u2013371) , were deectively . A study F (373) . Both co 33.1 \u03bcM ,120. Two374\u2013375) were isoectively . Futher ve (376) , which e\u201396.4 \u00b5M . A new d\u00b5M . A. AS)-2,43) (434) was fromioassays . A new dys anthracene derivative called mayamycin (497), and three new streptophenazines I\u2013K (498\u2013500) afforded two unusual compounds, Chlorohydroaspyrones A\u2013B (501\u2013502) was found to produce two new indole derivatives (503\u2013504) (505\u2013508) . No bioactivities were detected . F. FStrept520\u2013521) . Lobophof 7.5 \u03bcM . A marinin 524) . Compounectively . From th9 172]. . Compou 526\u2013527 were ideectively . Chemicaid (531) , which wne (533) were detn, China . Chemicane (534) . Compouncavenger .l-seryl-l-prolyl-l-glutamyl) and cyclo-(glycyl-l-prolyl-l-glutamyl) (535\u2013536) was found to produce seven new drimane sesquiterpenoids (537\u2013543), five new ophiobolin-type sesterterpenoids (544\u2013548), and the two new pyrrolidine alkaloids (549\u2013550) and exhibited cytotoxicity against the L929 (mouse fibroblast) cell line with an IC50 value approximated to 30 \u03bcM, while compound 553 was the most effective inhibitor of NF-\u03baB nuclear translocation with an IC50 value of 71 \u03bcM (654) (Aspergillus ostianus strain TUF 01F313 isolated from a marine sponge collected at Pohnpei. Three new chlorinated compounds (647\u2013649) showed antibacterial activity against the Ruegeria atlantica strain. Compounds 650\u2013652 showed cytotoxic activity against mouse lymphocytic leukemia cells (L1210) with LD50 values of 2.1, 71.0, and 2.0 \u03bcg/mL, respectively (654) were isoectively ,219,220.655\u2013656) . Both co657\u2013658) . Both coectively .659) (Aspergillus sp. (strain CNK-371) that was isolated from an unidentified sponge collected at Manele Bay, Hawaii. Compounds 660\u2013661 showed moderate cytotoxicity against human colon carcinoma (HCT-116) with IC50 values of 13.2, 10.9, and 13.9 \u03bcM, respectively . C. CAspergin (690) . Compoun25 \u03bcg/mL . One newmL [691) was isol0.07) mm .Penicillium sp. MWZ14-4, which was isolated from an unidentified sponge (collected from the South China Sea), yielded 10 new fungal metabolites, including three hydroisocoumarins, penicimarins A\u2013C (692\u2013694), three isocoumarins, penicimarins D\u2013F (695\u2013697), and four benzofurans, penicifurans A\u2013D (698\u2013701) (698) showed moderate inhibitory activity against Staphylococcus albus with an MIC value of 3.13 \u03bcM and weak activity against B. cereus [702\u2013703) . Compounds 702\u2013703 may show antiphotoaging activity in UVB-irradiated models [Chemical examination of the sponge-derived fungus 698\u2013701) . Penicif. cereus . Two new702\u2013703) , were isd models .704) , amycocyclopiazonic acid (706), and amycolactam (707) (Amycolatopsis sp. isolated from a sponge sample gathered from Micronesia. Amycolactam (707) displayed significant to moderate cytotoxicity against the gastric cancer cell line SNU638, the colon cancer cell line HCT116, A546, K562, and SK-HEP1 with IC50 values of 0.8, 2.0, 13.7, 9.6, and 8.3 \u03bcM, respectively [Penicillium adametzioides AS-53 from an unidentified marine sponge afforded a new spiroquinazoline derivative, N-Formyllapatin A (708), two new bisthiodiketopiperazine derivatives, adametizines A\u2013B (709\u2013710), two new acorane sesquiterpenes, adametacorenols A\u2013B (711\u2013712), a new dithiodiketopiperazine derivative, peniciadametizine A (713), and a highly oxygenated new analogue, peniciadametizine B (714) with an LD50 value of 4.8 \u03bcM and moderate antimicrobial potency against several microbes with MIC values ranging from 8 to 32 \u03bcg/ mL, respectively, whereas compound 710 only showed weak activity against S. aureus . Compound 712 showed significant selective activity against the NCI-H446 cell line (IC50 = 5.0 \u03bcM). Compounds 713 and 714 showed inhibitory activity against the pathogenic fungus Alternaria brassicae with MIC values of 4.0 and 32.0 \u03bcg/mL, respectively [Aspergillus terreus MXH-23, isolated from an unidentified sponge , yielded a new butyrolactone derivative, namely butyrolactone VIII (715) , was isoendently . Three nam (707) were isoectively . Chemica B (714) . Compounectively ,245,246.II (715) . Derivatactivity .716) sesquiterpenoid and two new (717\u2013718) . Compounds 717\u2013718 exhibited significant inhibitory activity against cyclooxygenase (COX-2) with IC50 values of 10.6 and 8.9 \u03bcM, respectively. Besides, compound 718 displayed activities against intestinal virus EV71 with IC50 values of 30.1 \u03bcM [Micromonospora sp. NPS2077 isolated from an unidentified marine sponge led to the isolation of a novel \u03b2-hydroxyl-\u03b4-lactone compound, neomacquarimicin (719) (Bacillus subtilis and Escherichia coli [720) . No bioactivities were detected [721) [Verrucosispora sp. FIM06054 from a marine sponge sample (the East China Sea) afforded a new compound, FW054-1 (722) xanthone 30.1 \u03bcM . The exain (719) , which ehia coli . One newli [720) , was isodetected . One newed [721) was from, China) . Chemica-1 (722) . Compoun 6.88 \u03bcM .Aspergillus sp. OUCMDZ-1583 from an unidentified sponge XD10410 yielded 18 new compounds named aspergones A\u2013Q (723\u2013739) and 6-O-demethylmonocerin (740) [Penicillium chrysogenum SYP-F-2720 from an unidentified sponge afforded a novel benzoic acid (741) afforded four new sesquiterpene lactones (742\u2013745) , a new cyclohexapeptide, similanamide (747), and a new pyripyropene derivative, named pyripyropene T (748) (747 exhibited weak activity against the MCF-7 (breast adenocarcinoma), NCI-H460 , and A373 (melanoma) cell lines, and neither of them showed antibacterial activity [Fractionation of the marine fungus in (740) . Compoun37.3 \u03bcM) . Chemicaid (741) . When adc effect . Study o742\u2013745) . Compoun193.3 \u03bcM . The inv T (748) . Only coactivity .Corynespora cassiicola XS-200900I7, isolated from an unidentified sponge XS-2009001 , yielded 12 new chromone derivatives, corynechromones A\u2013L (749\u2013760), two new naphthalenones, corynenones A\u2013B (761\u2013762), and one new depsidone, corynesidone E (763) (764\u2013765) [766\u2013767) led to the isolation of three new meroterpenoids, named austalides S\u2013U (768\u2013770) . The bio764\u2013765) , were me20.0 \u03bcM) . Two new766\u2013767) , were meectively . Chemica768\u2013770) . Compounof 90 \u00b5M .Streptomyces albus PVA94-07 strain derived from an unidentified sponge afforded two new deferoxamine analogues, compounds 771\u2013772 afforded two new polyketides, aspergchromones A\u2013B (773\u2013774) . Compounrculosis .As what we described above, temperate and tropical sea areas have become the main regions with sponge-derived microorganisms related to natural product chemistry. The statistical data shows that all the sponge hosts associated with microbes were distributed in the classes of Calcarea, Demospongiae, and unidentified sponges. The class Demospongiae sponges accounts for absolute majority at 77%, the class Calcarea and others sponges account for 1% and 22%, respectively. In the class Demospongiae, the order Haplosclerida provides the most sponge species accounting for 26.75% of the totality, followed by the orders Suberitida, Axinellida, Dictyoceratida, Tetractinellida, and Poecilosclerida etc. see .Aspergillus and Penicillium, followed by Trichoderma, Acremonium, Arthrinium, and Talaromyces. The genera Aspergillus and Penicillium obtained from many different sponge species take a percentage of 25% of the total microbes reported, the majority of which displayed wonderful chemistry diversity. Actinomycetes and bacteria account for 16% and 11% of sponge-derived microbes, respectively, which offered many novel and unique compounds. The actinomycetes studied were mainly derived from the genera Streptomyces, and the bacteria were mainly derived from the genera Pseudomonas, Pseudoalteromonas, and Bacillus [50 value of 8.8 \u03bcM against H1N1 virus [687) showed potent cell growth inhibitory activity against the murine P388 cell line with an ED50 value of 57 ng/mL [Natural products isolated from sponge-derived microorganisms have interesting pharmaceutical activities such as cytotoxicity, antioxidant, antifungal, antiviral, and antibacterial activities. Some novel compounds showed significant cytotoxic activities in the nM levels, such as two new indolocarbazole alkaloids and line14.8 \u03bcM) . Truncat46.5 \u03bcM) . Dankast8 ng/mL) . As we r8 ng/mL) . Another8 ng/mL) , antipla8 ng/mL) ,134, neu8 ng/mL) ,178, andA total of 774 new compounds from sponge-derived microorganisms, covering the last two decades from 1998 to 2017, were reviewed. These new compounds presented abundant chemical diversity except for the well-known types such as terpenes, alkaloids, peptides, aromatics, meroterpenoids, macrolides, polyketides, steroids, and so on.The total amount of new compounds from sponge-derived microorganisms has increased rapidly and has not yet reached a climax, especially in the last five years see . Among tWe should make more efforts to study the pharmacodynamic relationships and pharmacological effects of promising compounds, and conduct clinical trials to complete the drug-like evaluation of the compound. The study on the chemical constituents of sponges and their co-existing microorganisms will promote the study of the relationship between sponges and their co-existing microorganisms, develop and utilize medicinal resources, and systematically study the diversity of biodiversity and ecosystems. Given the structural differences and biodiversity of compounds derived from sponge symbiotic microorganisms, we believe that there are more resources waiting to be mined."} +{"text": "Dear Editor,Several results have been reported on the efficacy of tranexamic acid (TXA) in patients with acute traumatic brain injury (TBI). As such, Lawati et al. (2020) conductRowell et al. (2020) conductIn contrast, an RCT report presented that the adjusted RRs (95% CIs) of TXA for mild-to-moderate and severe TBI death were 0.78 (0.64-0.95) and 0.99 (0.91-1.07), respectively , and a The author declares no conflict of interest."} +{"text": "AbstractFanjingagen. nov., with type species F.digitata Yu & Yang, sp. nov., is described from the Guizhou Province of Southwest China. Habitus photos and illustrations of male genitalia of the new species are provided.A new leafhopper genus, Alebroides group of Empoascini leafhoppers includes 25 genera and 156 species, widely distributed in the Palaearctic Region and Old World tropics . For morphological terminology we mostly follow Taxon classificationAnimaliaHemipteraCicadellidaeYu & Yanggen. nov.04EA95A4-B242-55E4-AD37-69DA953F1F0Fhttp://zoobank.org/F1EB5835-F39D-4C1A-862C-3F55C8618661Fanjingadigitata Yu & Yang, sp. nov., here designated.Alebroides group of Empoascini, the new genus runs to Nulliata Lu, Xu & Qin in the key to genera by Nulliata in having the abdominal apodemes long and from Nulliata and other genera in having a finger-like process bearing micro-setae on the lower posterior margin of the male pygofer.Within the Relatively robust Figs . Head slMale basal abdominal sternal apodemes well developed Fig. . Male pyThe genus name is an arbitrary combination of letters.China (Guizhou).Taxon classificationAnimaliaHemipteraCicadellidaeYu & Yangsp. nov.FE13424B-E8A8-5677-B624-2DA047EAD319http://zoobank.org/F427C9A4-AEFC-472A-AFAB-B158C408A80ESize. Male 3.94\u20134.00mm.Whole body yellowish, anterior margin of vertex marked with two brownish patches Figs . PronotuBasal sternal abdominal apodemes extending to end of segment VI Fig. . Male py\u2642, China, Guizhou, Fanjing Mountain, 21-August-2017, coll. Yarong Gao (GUGC). Paratypes: 3\u2642, same collecting data as holotype .The new species is named from the Latin \u201cdigitalis\u201d, meaning finger, for the finger-like process of the male pygofer.Euonymus (Celastraceae).China (Guizhou)."} +{"text": "Correction to: Genome Biol (2019) 20:134https://doi.org/10.1186/s13059-019-1732-1Following publication of the original paper , the autIn the Additional file Additional file 1: Additional text 1. Supplementary methods. Additional text 2. Mapping SMURF-seq reads. Additional text 3. Short molecule sequencing with long-read sequencers. Additional table 3. Summary of sequencing runs. Figure S1. Distribution of length between restriction sites computed by measuring the distance between the recognition sites on the human reference genome. Figure S2. Schematic of SMURF-seq protocol. Figure S3. Sequencing of restriction enzyme digested normal diploid genome without SMURF-seq. Figure S4. Sequencing normal diploid genome using SMURF-seq. Figure S5. Sequencing normal diploid genome using SMURF-seq with 1D Rapid kit. Figure S6. Sequencing SK-BR-3 cancer genome using SMURF-seq. Figure S7. Replicate sequencing run of normal diploid genome using SMURF-seq. Figure S8. Replicate sequencing run of SK-BR-3 cancer genome using SMURF-seq. Figure S9. High-resolution CNV profile generated using SMURF-seq is highly concordant with the profile generated with Illumina WGS. Figure S10. SMURF-seq generates fragments at a faster rate than sequencing short molecules directly. Figure S11. CNV profile with reads obtained in first few minutes of sequencing. Figure S12. Multiplexed sequencing of normal diploid (barcode01) and SK-BR-3 cancer genome (barcode02) in a single sequencing run. Figure S13. Speed of nanopore sequencing as a function of read length. Figure S14. Biases correlated with GC content are reduced with LOWESS smoothing."} +{"text": "This letter summarizes recommendations from the interdisciplinary working group of renal tumors (IAGN) of the German Cancer Society for the systemic treatment of advanced/metastatic renal cell carcinoma in the context of the current SARS-CoV-2 pandemic During the SARS-CoV-2 pandemic, oncologists faced several new challenges of the German cancer society towards treatment of mRCC.During the process of treatment evaluation, the assessment of treatment indication must be made on an individual basis. However, once selecting treatment, patient, and tumor-specific parameters, patient\u00b4s comorbidity and the availability of local caregiving facilities should be taken into account. In our opinion, two major scenarios according to systemic treatment have to be considered: initiation or change medication of a systemic treatment upon progressing diseases and measures taken during ongoing systemic treatment.For systemic treatment, the appropriate treatment should be selected based on patient-specific factors that take the overall picture into account when searching for treatment , as well as a surprising high rate of SARS-CoV-2 diseases among cancer patients receiving surgery benefit was gained by any of the immune combinations for patients with a favorable risk profile (HR for OS: ipilimumab/nivolumab vs. sunitinib: 1.19 (95% CI 0.77\u20131.85), axitinib/pembrolizumab vs. sunitinib: 0.94 (95% CI 0.43\u20132.07), axitinib/avelumab vs. sunitinib: 0.812 (95% CI 0.336\u20131.960) ; axitinib/pembrolizumab intermediate prognosis: 0.53 (95% CI 0.35\u20130.82), poor prognosis: 0.43 (95% CI 0.23\u20130.81); axitinib/avelumab: intermediate prognosis: 0.86 (95% CI 0.615\u20131.202), poor prognosis: 0.57 (95% CI 0.363\u20130.895); Cabozantinib vs. sunitinib: 0.80 (0.53\u20131.21)] (Motzer et al. Although precise guidelines according to mRCC treatment reflects best efficacy and QoL data, within the SARS-CoV-2 pandemic a patient-centered treatment choice, which is adapted to the local pandemic situation is warranted (s. Table"} +{"text": "Dear Editor,9/L in the platelet count for mortality was 0.60 (0.43-0.84). They monitored changes in the platelet count during treatments and whether maintaining a normal platelet count was related to good prognosis. A meta-analysis conducted by Lippi et al. have presented with thrombocytopenia. Figliozzi et al. (20209 have pr) reporte 0.60 0.4-0.84. ThHowever, some reports present an inverse association. Iba\u00f1ez et al. (2020) describAlthough two meta-analyses presented that thrombocytopenia reflected poor prognosis in patients with COVID-19 , the poThe author declares no conflict of interest."} +{"text": "Microcerotermes eugnathus Silvestri showed structural damage in Bir al-Shaghala cemeteries located in the oasis of Dakhla, Egypt. The mud tubes of this termite spread inside and over the mural painted floors of the tombs. Extracts from Lavandula latifolia, Origanum vulgare, and Syzygium aromaticum were tested for their anti-termitic activity and compared with the bio-insecticide, Bacillus thuringiensis var. kurstaki (Protecto 9.4% WP) and Dursban (Chlorpyrifos 48%). The bioassay experimental showed that the extracts have low activity against M. eugnathus compared to Protecto and Dursban, but the extract from O. vulgare showed promising natural termiticides.The termite Lavandula latifolia (Spike lavender), Origanum vulgare (Marjorum), and Syzygium aromaticum (Clove) against the termite Microcerotermes eugnathus. Plant extract results were compared to two commercially used termite pesticides, the bio-insecticide, Bacillus thuringiensis var. kurstaki (Protecto 9.4% WP) and Dursban (Chlorpyrifos 48%). Gas chromatography\u2013mass spectrometry (GC-MS) analysis was used to identify the main compounds in the three plant extracts. The main compounds in Lavandula Latifolia were linalool (21.49%), lavandulol (12.77%), \u03b2-terpinyl acetate (10.49%), and camphor (9.30%). Origanum vulgare extract contained thymol (14.64%), m-cymene (10.63%), linalool (6.75%), and terpinen-4-ol (6.92%) as main compounds. Syzygium aromaticum contained eugenol (99.16%) as the most abundant identified compound. The extract of O. vulgare caused the highest termite death rate, with an LC50 of 770.67 mg/L. Exposure to lavender extract showed a high death rate with an LC50 of 1086.39 mg/L. Clove extract did not show significant insecticidal activity with an LC50 > 2000 mg/L. Significant termiticide effects were found, with LC50 values of 84.09 and 269.98 mg/L for soldiers and workers under the application of Dursban and Protecto, respectively. The LC50 values reported for nymphs were <120, <164.5, and 627.87 mg/L after exposure to Dursban, Protecto, and O. vulgare extract, respectively. The results of the study show that some of the extracts have low toxicity compared to the bioagent and Dursban, and may show promise as natural termiticides, particularly as extracts from O. vulgare.A trend towards environmentally friendly chemicals for use in termite management has been occurring globally. This study examined three naturally occurring plant extracts from Dakhla Oasis, Egypt, are the site of heavy infestation by the termite Microcerotermes eugnathus Silvestri [Termites, although important in ecosystems, are economically important structural pests to wood and cellulosic material in service ,3,4,5,6.mitidae) ,8,9,10. M. eugnathus [In Egypt, this termite was reported along the northwestern coast and in tugnathus .Treatments used to control this termite include bioagents, chemical pesticides, and natural products. Natural products investigated for termite management include plant extracts. In many parts of the world, chemical pesticides are considered poor for the environment and new research is examining the use of naturally occurring, less environmentally toxic, compounds ,12,13.Bacillus thuringiensis var. kurstaki and Stenotrophomonas maltophilia Palleroni & Bradbury have potential application as biological control agents of termites [B. thuringiensis is an example of this [S. maltophilia has shown potential application as a biocontrol agent and could degrade chitin in the termites, Coptotermes heimi (Wasmann) (Blattodea: Rhinotermitidae) and Heterotermes indicola (Wasmann) (Blattodea: Rhinotermitidae) [Bioagents such as termites ,15,16. T of this ,18. ChitDursban (Chlorpyrifos 48%) is an organophosphate pesticide that acts on the insect nervous system by inhibiting acetylcholinesterase (AChE) ,20,21. DC. intermedius Silvestri (Blattodea: Rhinotermitidae) died within 30, 40, and 110 min when exposed to 70% ethanol, aqueous, and acetone extracts from seeds of Parkia biglobosa (Jacq) Benth, respectively, at the concentration of 4 gm/L [Khaya senegalensis (Desr.) A. Juss., K. ivorensis A. Chev. and Swietenia mahagoni (L.) Jacq. showed potential insecticidal efficacy towards the dry wood termite Kalotermes flavicollis [Larix leptolepis (Lamb.) Carr. Wood, with its large quantities of flavonoids, showed strong feeding deterrent activity against the subterranean termite Coptotermes formosanus Shiraki (Insecta: Blattodea: Rhinotermitidae) [Jatropha curcas L. oil showed maximum wood protection against Microcerotermes beesoni Snyder (Termitidae: Amitermitinae) at a concentration of 20% [Natural products are being studied as potential termiticides. The termite f 4 gm/L . Seed oimitidae) . Water emitidae) . Jatrophn of 20% .Tectona grandis L.f., Dalbergia sissoo Roxb., Cedrus deodara (Roxb.) G.Don and Pinus roxburghii Sarg. rapidly lowered numbers of protozoans in the hindgut of Reticulitermes flavipes (Kollar) (Insecta: Blattodea: Rhinotermitidae) and H. indicola workers, which were closely correlated with the mortality of worker [Morus alba L. heartwood resulted in 100% mortality in R. flavipes after feeding [Microcerotermes beesoni Snyder (Termitidae: Amitermitinae) [D. sissoo showed termite mortality at 10 mg/mL against H. indicola and R. flavipes with LC50s at 5.54 and 3.89 mg/mL, respectively [H. indicola mortality reached more than 75% after feeding on Populus deltoides W.Bartram ex Marshall wood treated with extract from M. alba [Some heartwoods show resistance to termite attack, which is attributed to the presence of toxic compounds within the heartwood ,30. For feeding . Methanomitinae) . Heartwoectively . H. indi M. alba . Cymbopogon citratus (DC.) Stapf, Eucalyptus globulus Labill., Syzygium aromaticum (L.) Merr. and L. M. Perry, Origanum vulgare L., Rosmarinus officinalis L., Cinnamomum verum J.Presl, and Thymus vulgaris L. showed strong termiticidal activity against Odontotermes assamensis Holmgren (Blattodea: Termitidae) [Cananga odorata (Lam.) Hook.f. and Thomson flower extract of 2 mg/filter paper showed cumulative mortalities of 18% and 94%, after 2 and 7 days of exposure, respectively, against the termite Reticulitermes speratus (Kolbe) (Rhinotermitidae: Blattodea) [K. flavicollis pseudergates fed Casuarina sp. wood wafers, previously treated separately with Taxodium distichum (L.) Rich., E. citriodora Hook. and Cupressus sempervirens L. extracts, showed reduced numbers and vigour in spirochaete and flagellate populations [Tagetes erecta L. leaf extract, caused 100% mortality in Odontotermes obesus (Rambur) (Blattodea: Termitidae) after 24 h of exposure [Microcerotermes eugnathus.Many plants contain bioactive compounds such as phenols, terpenoids , aldehydes, ketones, and other compounds that have a strong effect against microorganisms and termites ,39,40,41mitidae) . Insectiattodea) . K. flavulations . At a doexposure . TherefoLavandula latifolia Medik.) belongs to the family Lamiaceae and is native to the Mediterranean. It is also cultivated in different regions of the world. The bioactivity of L. angustifolia Mill. and L. latifolia extracts from Spain were found to be associated with the presence of linalool, camphor, p-cymene, and limonene [\u03b1-pinene, thujene, \u03b2-pinene, sabinene, myrcene, p-cymene, limonene, camphene, camphor, 1,8-cineole, (Z)- and (E) ocimene, terpinene, terpinene-4-ol, lavandulol, lavandulylacetate, \u03b2-caryophyllene, and (Z)- and (E) farnesene [Lavender species are characterized by the presence of two main chemotypes, thymol and carvacrol, while others have \u03b3-terpinene, p-cymene, cis-sabinene hydrate, terpinen-4-ol, \u03b1-terpineol, \u03b1-terpinene, \u03b3-terpinene, sabinene, and linalool as their main compounds [O. vulgare L. ssp. vulgare extract showed the presence of caryophyllene, spathulenol, germacrene-D, and \u03b1-terpineol and had antimicrobial properties [\u03b3-terpinene, \u03b1-terpineol, thymol, carvacrol, cis-sabinene-hydrate, linalool, p-cimene, 1,8-cineole were identified as the main compounds in the extract of O. vulgare L. [O. vulgare extract and its major compounds carvacrol, p-cymene, and \u03b3-terpinene showed potent larvicidal activity against the cotton bollworm, Helicoverpa armigera (H\u00fcbner) (Lepidoptera: Noctuidae: Heliothinae) [Several ompounds ,50,51,52operties . Terpinelgare L. . O. vulgothinae) . Syzygium aromaticum (L.) Merr. and L.M.Perry, Myrtaceae family) bud extract has shown the presence of eugenol, eugenol acetate and \u03b2-caryophyllene as main compounds with percentages of 88.61, 8.89 and 1.89%, respectively. It exhibited strong contact toxicity against Cacopsylla chinensis (Yang and Li) (Hemiptera: Psyllidae) with LD50 values of 0.730 \u00b5g/adult and 1.795 \u00b5g/nymph, respectively [S. aromaticum extract gave LC50 values of 13.871 and 15.551 \u03bcL against larvae and adult Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) 48 h after fumigation [50 values of 9.45 and 10.15 \u03bcL/g, against Acanthoscelides obtectus (Say) (Coleoptera: Chrysomelidae: Bruchinae) and Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae), respectively [Clove and the chemical compound Dursban (chlorpyrifos 48%). In addition, the chemical composition of the three extracts were analyzed with using GC-MS apparatus.This research aimed to (1) determine the chemical composition of three plant extracts with potential anti-termitic activities; (2) evaluate the anti-termitic activity of the three plant extracts against Microcerotermes eugnathus foraging tubes. Termite tunnels could be observed on the floors and tomb substructure, causing cracks and separation of mortar. This termite species produces winged alates during the months of April and January, the remnants of which (wings) could often be observed around the tombs [Termite infestation in the cemeteries of Bir al-Shaghala located at the oases of Dakhla, Egypt was noted by the presence of he tombs . Figure Lavandula latifolia Medik., Lamiaceae) dry flower, Marjoram dry leaves and Clove (Syzygium aromaticum (L.) Merrill and Perry, Mytaceae) dry buds were selected for their potential effect on termites. The extraction process was carried out at the National Research Center in Cairo, Egypt. Plant material was shade air-dried in the laboratory at room temperature for one week, then ground into a fine powder in an electrical blender. About 100 g of the fine powdered material was put into a 2-L flask containing 1000 mL of distilled water (DW) and extracted by the hydrodistillation method using a Clevenger-type apparatus for 3 h [Three plant extracts from Spike Lavender with a TG\u20135MS direct capillary column (30 m \u00d7 0.25 mm \u00d7 0.25 \u00b5m film thickness). Extracts were diluted in n-hexane solvent in the ratio of 3:1 (3 n-heaxane: 1 extract sample) before being injected to the GC-MS. The column oven temperature was initially held at 50 \u00b0C and then increased by 5 \u00b0C/min to 250 \u00b0C and held for 2 min, then increased to a final temperature of 310 \u00b0C by 25 \u00b0C/min and held for 2 min. The injector and MS transfer line temperatures were kept at 270 and 260 \u00b0C, respectively; helium was used as a carrier gas at a constant flow rate of 1 mL/min. The solvent delay was 3 min, and diluted samples of 2 \u00b5L were injected automatically using an Autosampler AS1310 coupled with GC in the splitless mode. EI mass spectra were collected at 70 eV ionization voltages over the m/z range of 50\u2013650 in full scan mode. The ion source temperature was set at 250 \u00b0C. The components were identified by comparison of their retention times and mass spectra with those in the WILEY 09 and NIST 11 mass spectral databases [The chemical composition of extracts from atabases . The matatabases ,40,62,63Bacillus thuringiensis var. kurstaki\u201d (Protecto 9.4% WP) was diluted in distilled water to obtain the following concentrations: 164.5, 258.5, 376, 756, and 1410 mg/L. Dursban (Chlorpyrifos 48%) was diluted in distilled water and prepared in concentrations of 120, 240, 360, 480, and 960 mg/L.Extract concentrations for laboratory testing were prepared by mixing with 0.01% of Tween 80 and diluting with distilled water to obtain the following concentrations: 125, 250, 500, 1000, and 2000 mg/L. The bioagent \u201cMicrocerotermes eugnathus castes were collected from soil around cemeteries and kept in a container with a portion of termite nesting material. Briefly, from the experimental location, termites were placed inside a special box (4-L in capacity) for preservation and the box was covered with wool textile to maintain the temperature, because the temperatures in the interior oases are as high as 50 \u00b0C. During the transfer to the laboratory in Cairo, the death of the termites occurs due to the different environmental conditions, so it was necessary to warm the termites. Termites\u2019 death was also observed during transportation to the laboratory or even in the laboratory during the preparation for the laboratory experiment. Therefore, 10% glucose sugar solution [solution ,65 was pA no-choice bioassay method ,67 was e50) expressed as mg/L was calculated from log-concentration mortality regression lines [Untreated control replicates (five replicates) contained 10 workers, five soldiers and five nymphs, who were supplied with pieces of untreated cardboard paper only. Each concentration tested was replicated five times. All the treatments were kept in darkness at 48 \u00b1 3 \u00b0C. After seven days, the test was halted, the number of surviving termites was counted, and percent mortality was calculated. The lethal concentration , lavandulol (12.77%), \u03b2-terpinyl acetate (10.49%), camphor (9.30%), linalyl acetate (7.87%), (\u2212)-\u03b2-fenchol (5.12%), isobornyl acetate (5.00%), \u03b1-pinene (3.81%), terpineol (3.64%), and L-\u03b1-terpineol (2.62%).O. vulgare dry leaves. The main components were thymol (14.64%), m-cymene (10.63%), terpinen-4-ol (6.92%), linalool (6.75%), estragole (5.42%), \u03b3-terpinene (5.39%), anethole (5.00%), eucalyptol (3.61%), borneol (3.29%), \u03b2-caryophyllene (3.29%), \u03b1-terpinene (2.89%), carvacrol (2.58%), camphor (2.36%) and carvacryl methyl ether (2.34%). S. aromaticum extract. The main component was eugenol (99.16%).Microcerotermes eugnathus. After a seven-day exposure to this extract, the LC50 was 770.67 mg/L against soldiers and workers and 627.87 mg/L against nymphs. Lavender extract had less of toxic effect against M. eugnathus than marjoram, with an LC50 of 1086.39 mg/L for the group of soldiers and workers and 1140.74 mg/L for nymphs. Clove extract showed the lowest insecticidal activity against M. eugnathus for both nymphs and soldier/workers, with an LC50 > 2000 mg/L extract from Macedonia [p-cymen-8-ol and bornyl acetate with values of 32.3%, 12.4%, 11.7%, 8.7%, 7.7%, and 4.2%, respectively, were the main compounds in L. latifolia extract from the Northern Tunisia [L. latifolia extracts from Spain, characterized by 1,8-cineole with high amounts (36.3\u201333.65%) [L. latifolia from Iran showed the presence of linalool (31.9\u201330.6%) as the main compound [Lavandula, 1,8-cineole, 2-\u03b2-pinene, \u03b1-thujone, camphor and cis-\u03b1-bisabolene were the main compounds isolated from L. angustifolia extract [Linalool, borneol and terpinene-4-ol, 1,8-cineole, camphor, and linalyl acetate were reported in lavandin ,82, whilcompound . In othe extract .\u03b1-terpinene, \u03b3-terpinene, cis-sabinene-hydrate, linalool, terpinen-4-ol, terpineol, thymol, and carvacrol as the main compounds in O. vulgare extract with percentages of 5.58, 12.32, 3.35, 3.47, 21.43, 3.17, 9.45, and 11.67%, respectively [O. vulgare extract contained p-cymene, linalool, thymol, caryophyllene, and carvacrol. These authors showed insecticidal activity against Schistocerca gregaria (Forsk\u00e5l) (Orthoptera: Acrididae) [O. vulgare extract. Other studies reported this same compound at 9.45% [Coleus amboinicus Lour. extract caused 100% mortality to the termite Odontotermes obesus at a dose of 2.5 \u00d7 10\u22122 mg/cm3. This study found that thymol was the main compound, with 94.3% [Pittosporum undulatum Vent., Lippia sidoides Cham. and Lippia gracilis Schauer showed 100% mortality to the termite Heterotermes sulcatus Mathews (Blattodea: Rhinotermitidae) after 14 days of exposure, where the activity was related to the major compounds, limonene (80.8%), carvacrol (45.6%) and thymol (78.55%), that were identified in each extract, respectively [Previous work identified ectively . Other wrididae) . In the at 9.45% , 44.55% at 9.45% , 26.75% at 9.45% , and 58.at 9.45% . After 5th 94.3% . Extractectively .O. vulgare extract [O. vulgare extract with its main compounds of thymol (40.35%), p-cymene (17.32%), \u03b3-terpinene (15.66%), and carvacrol (12.15%), observed 72% and 88% mortality at 48 and 72 h, respectively, against Sitophilus oryzae (L.) (Coleoptera: Curculionidae) [O. vulgare extract showed toxicity in higher doses against Plutella xylustella L. [O. vulgare extract at 40% exhibited 100% repellency against Cimex lectularius Linnaeus (Hemiptera: Cimicidae) [Terpineol (22.85%), \u03b1\u2013terpinene (20.60%), caryophyllene (6.75%) and thymol (4.53%) were the main compounds isolated from extract . O. vulgionidae) . O. vulgralidae) . After amicidae) .Origanum were shown to have insecticidal activity against larvae of Culex pipiens L. (Diptera: Culicidae) [Lippia sidoides contained 44.55% thymol and showed high insecticidal activity against the termite Nasutitermes corniger (Blattodea: Termitidae) with 48 h exposure at a dose of 0.27 \u03bcg/mg [Oxygenated monoterpenes such as thymol, eucalyptol, linalool and carvacrol found in the extracts from the present study are reported to be more toxic against termite workers . For exalicidae) . The ext27 \u03bcg/mg .Microcerotermes eugnathus with an LC50 value of >2000 mg/L. Eugenol has been shown to be an effective fumigant and feeding deterrent against the termite C. formosanus [\u03b3-aminobutyric acid, causing inhibitory symptoms in the nervous system [Odontotermes assamensis Holmgren (Blattodea: Termitidae) at 2.5 mg/g after 8 days [Reticulitermes messperatus Kolbe (Blattodea: Rhinotermitidae) nymphs [S. aromaticum extract at 0.5 mL/L after 10 min of exposure showed 100% mortality against Coptotermes formosanus Shiraki (Insecta: Blattodea: Rhinotermitidae) [R. speratus [In this study, clove extract showed the lowest activity against rmosanus . Carvacrrmosanus . It causs system . Carvacrr 8 days . At 1.5 ) nymphs ,97. S. amitidae) . Clove bsperatus .M. eugnathus against termiticides than those of other termites. In addition, our results suggest that O. vulgare extract caused moderate activity against the termite M. eugnathus compared to commercial termiticides tested. Further research may show that O. vulgare extract or its derivatives could potentially be used to control and manage some termite infestations and lessen or limit the amount of more toxic pesticides currently in use. Our present results show a higher resistance of M. eugnathus. However, due to the highly toxic nature of Dursban and the fact that it has been withdrawn for use in some countries, the search for less toxic and natural termiticides from plants is of interest. Extract from the plant Origanum vulgare showed some promise as a plant-based toxicant for this termite. Chemical pesticides had the greatest impact on the mortality of the termite"} +{"text": "Bacillus sp. strains EKM417B and EKM420B (from Citrullus lanata [watermelon]) and EKM501B (from Cucurbita moschata [butternut squash]) and Paenibacillus sp. strain EKM301P (from Cucurbita pepo L. var. pepo L. [pumpkin]). These strains previously demonstrated biostimulant and biocontrol activities.Here, we announce the draft genome sequences of four endophytic bacilli isolated from surface-sterilized seeds of three cucurbit species, Bacillus sp. strains EKM417B and EKM420B (from Citrullus lanata [watermelon]) and EKM501B (from Cucurbita moschata [butternut squash]) and Paenibacillus sp. strain EKM301P (from Cucurbita pepo L. var. pepo L. [pumpkin]). These strains previously demonstrated biostimulant and biocontrol activities.Here, we announce the draft genome sequences of four endophytic bacilli isolated from surface-sterilized seeds of three cucurbit species, Bacillus/Paenibacillus genera) (Bacillus sp. strains EKM417B and EKM420B (from Citrullus lanata [watermelon]), Bacillus sp. strain EKM501B (from Cucurbita moschata [butternut squash]), and Paenibacillus sp. strain EKM301P (Cucurbita pepo L. var. pepo L. [pumpkin]) using 16S rRNA gene primer pair 799F and 1492R and then submitted to GenBank in planta; EKM501B grew on N2-free medium, produced indole-3-acetic acid (IAA/auxin) and ribonucleases, and suppressed Rhizoctonia solani; and EKM301P secreted cellulase and antagonized Fusarium graminearum and Rhizoctonia solani (Plant microbiomes have evolved to perform defensive/growth-promoting functions \u20133. 16S I\u2013 genera) , consist genera) . We isolde novo assembled using the EvoCAT pipeline (Evogene Clustering and Assembly Toolbox) and identified using KmerFinder 3.2 (Bacillus velezensis strain KD1 (GenBank accession number NZ_CP014990.2) (EKM417B and EKM420B), Bacillus cereus strain FORC087 (NZ_CP029454.1) (EKM501B), and Paenibacillus polymyxa strain SQR-21 (NZ_CP006872.1) . Genomic DNA was extracted using DNeasy UltraClean microbial kits and adjusted to 50\u2009ng/\u03bcl. Libraries were constructed using TruSeq DNA Nano library prep kits and then sequenced using the Illumina NovaSeq 6000 system to produce 1,461,384 (EKM417B), 1,659,509 (EKM420B), 1,823,824 (EKM501B), and 2,124,086 (EKM301P) raw reads in 150-bp paired-end format. Quality-trimmed reads were 06872.1) . The pro06872.1) . Peptide06872.1) . DefaultGenome mining identified candidate genes involved in biofertilizer/biocontrol metabolic pathways, including those discussed above. These genes encode proteins involved in nitrogen fixation, phytase, alkaline phosphatase, carbon-nitrogen hydrolase, trehalose-6-phophate hydrolase, and tryptophan synthase (IAA/auxin production) \u201314. Bioc\u201314\u2013This whole-genome shotgun project and the Illumina raw reads have been deposited in DDBJ/EMBL/GenBank and the SRA, respectively, under the accession numbers provided in"} +{"text": "Y.Tsiang 7712) when he described Tsugalongibracteata W.C.Cheng. Later, researchers suggested that the type is either in NAS or in PE. However, we found more than one duplicate of the type collection in both NAS and PE. Following the Shenzhen Code, we lectotypify the name T.longibracteata with Y.Tsiang 7712 (PE00003223) that bears a handwritten identification of W.C.Cheng.W.C.Cheng did not clearly indicate the herbarium repository of the type specimen ( Tsuga (Endl.) Carri\u00e8re: Tsugalongibracteata W.C.Cheng. This species differs from all known species of Tsuga in both vegetative and reproductive characters , two in NAS (NAS00070064 and NAS00070063), two in HUH (A00052508 and A00052510), one each in E (E00215871), IBSC (IBSC0012857), K (K000288277), NY (NY00001279), and S (S-C-4796) respectively. Shenzhen Code .1A55C046-BD56-5079-A68C-4A134EA9F396Nothotsugalongibracteata (W.C.Cheng) Hu ex C.N.Page, Notes Roy. Bot. Gard. Edinburgh 45(2): 390 . \u2261Y.Tsiang (\u848b\u82f1) 7712 .China. Guizhou (\u8d35\u5dde): Yinjiang Tujiazu Miaozu Zizhixian , Fanjing Shan , in densely shaded ravine, alt. 400\u2013500 m, 19 December 1930,"} +{"text": "Correction to: Arthritis Res Ther 22, 98 (2020)https://doi.org/10.1186/s13075-020-02185-0Following publication of the original article , the aut1. In Fig.\u00a02. Supplementary Figure\u00a0The original article has been corrected.Additional file 1:Figure S1. Distribution of FOI PVM enhancement in joints with increasing degree of osteoarthritis."} +{"text": "Food and Drug Administration in 2019 for the treatment of community-acquired bacterial pneumonia (CABP). In this study we evaluated the The test strains were isolated from patients across China during the period from 2017 to 2019, including 634 strains of respiratory pathogens. The minimum inhibitory concentrations (MICs) of lefamulin and comparators were determined by broth microdilution method.Streptococcus pneumoniae and Staphylococcus evidenced by 100% inhibition at 0.25 mg/L, and favorable MIC50/90 (0.125/0.125 mg/L) against S. pneumoniae (penicillin MIC \u2265 2 mg/L), MIC50/90 (\u22640.015/0.125 mg/L) against methicillin-resistant S. aureus, and MIC50/90 (\u22640.015/0.06 mg/L) against methicillin-resistant S. epidermidis. Lefamulin also had good activity against Streptococcus pyogenes and Streptococcus agalactia (MIC50/90: \u22640.015/\u22640.015 mg/L), \u03b2-lactamase-producing Haemophilus influenzae (MIC50/90: 0.5/1 mg/L), \u03b2-lactamase-negative H. influenzae (MIC50/90: 1/1 mg/L), Moraxella catarrhalis (MIC50/90: 0.25/0.25 mg/L), and Mycoplasma pneumoniae (MIC50/90: 0.03/0.03 mg/L) regardless of resistance to azithromycin. Lefamulin was generally more active than the comparators against the test strains.Lefamulin showed potent activity against Staphylococcus, S. pneumoniae, \u03b2-hemolytic Streptococcus, H. influenzae, M. catarrhalis and M. pneumoniae). In vitro activity supports the use of lefamulin in the treatment of CABP in China.In summary, lefamulin has good and broad-spectrum coverage of respiratory pathogens (methicillin-sensitive and -resistant Clitopilus scyphoides, Clitopilus passeckerianus, or other Clitopilus species in basidiomycota. Lefamulin is the first-in-class semi-synthetic pleuromutilin antibiotic for systemic use. Its molecular formula is C28H45NO5S (molecular weight 567.79 g). Lefamulin inhibits bacterial protein synthesis by binding to \u201cA\u201d and \u201cP\u201d sites of the peptidyl transferase center (PTC) of the 23s rRNA of the 50S ribosomal subunit of bacterial cell. The binding is through the mutilin core and C-14 side chain in the forms of hydrogen bonds, hydrophobic interactions, and conformational change to prevent correct orientation of tRNA\u2019s 3\u2019-CCA ends for peptide transfer coded by the transposon Tn5406 and vga(A) carried by plasmids (encoding ABC transporter) . So far,Streptococcus pneumoniae (PRSP), macrolide-resistant Mycoplasma pneumoniae, and methicillin-resistant S. aureus (MRSA) . In Auguin vitro activity of lefamulin against a broad range of respiratory pathogens.The antibacterial spectrum and activity of lefamulin have been studied in the United States and Europe , 2019, bMycoplasma pneumoniae. These strains were isolated from 29 hospitals across China, representing 23 provinces and municipalities, during the period from October 2017 to July 2019. Specifically, the test strains included S. aureus (n = 121), S. epidermidis (n = 30), \u03b2-lactamase-producing Haemophilus influenzae (n = 48), \u03b2-lactamase-negative H. influenzae (n = 48), Haemophilus parainfluenzae (n = 10), Moraxella catarrhalis (n = 54), S. pneumoniae (n = 172), Streptococcus pyogenes (n = 30), and Streptococcus agalactiae (n = 13). All the strains were re-identified before susceptibility testing. Species identification was confirmed by MALDI-TOF/MS system , and antimicrobial susceptibility testing were controlled with reference strains S. aureus ATCC29213, S. pneumoniae ATCC49619, H. influenzae ATCC49247, and M. pneumoniae ATCC 29342.A total of 634 non-duplicate strains of respiratory pathogens were tested, including 580 strains of bacteria and 54 strains of M. pneumoniae were measured according to the methods for antimicrobial susceptibility testing for human mycoplasmas described in CLSI document M43-A (2011) (The minimum inhibitory concentrations (MICs) of lefamulin and the comparators were determined by broth microdilution method according to the Clinical and Laboratory Standards Institute 2018) M M2018) MA (2011) . The antth Edition .Staphylococcus strains , 0.06 mg/L against methicillin-sensitive S. aureus (MSSA), and 0.03 mg/L against methicillin-sensitive S. epidermidis (MSSE). Lefamulin displayed MIC values ranging from \u22640.015 mg/L to 0.25 mg/L (MIC90: \u22640.25 mg/L) against 172 strains of S. pneumoniae, including penicillin-susceptible (PSSP) strains (penicillin MIC \u22640.06 mg/L), penicillin-intermediate (PISP) strains (penicillin MIC: 0.125 mg/L\u20131 mg/L), and penicillin-resistant (PRSP) strains (penicillin MIC \u2265 2 mg/L). Lefamulin inhibited the growth of all PSSP strains at \u22640.015 mg/L and all PISP and PRSP strains at 0.25 mg/L. The MIC50/90 values of lefamulin were \u22640.015/\u22640.015 mg/L against S. pyogenes and \u22640.015/0.06 mg/L against S. agalactiae. Lefamulin inhibited the growth of all the S. pyogenes and S. agalactiae strains at 0.06 mg/L . Its activity was comparable to moxifloxacin and significantly superior to erythromycin and azithromycin in this respect.In the present study, lefamulin displayed excellent antimicrobial activity against all the respiratory pathogens, including MRSA, MSSA, MRSE, MSSE, 015\u20132016 , 2019. THaemophilus and M. catarrhalis. Lefamulin was comparable to ceftriaxone in activity against S. pneumoniae strains and \u03b2-hemolytic Streptococcus, but better than ceftriaxone against PRSP, better than penicillin against PISP and PRSP, and similar to penicillin against \u03b2-hemolytic Streptococcus. Lefamulin had similar activity as moxifloxacin, vancomycin, and linezolid against Streptococcus. It inhibited the growth of all Streptococcus species at 0.125 mg/L, which was lower than the above mentioned three agents. Lefamulin was significantly better than erythromycin and azithromycin in the activity against S. pneumoniae and \u03b2-hemolytic Streptococcus.Lefamulin also displayed high antimicrobial activity against H. influenzae and M. catarrhalis. As for the \u03b2-lactamase-negative strains, lefamulin provided significantly better activity than azithromycin. Lefamulin was comparable to tigecycline, ceftriaxone, and levofloxacin, and significantly superior to azithromycin and trimethoprim-sulfamethoxazole in the activity against M. catarrhalis. These results are consistent with those reports from other countries (It has been reported that the 02 mg/L) .90 value of lefamulin was 0.5 \u03bcg/mL against the 50 strains of S. pneumoniae isolated from the patients in phase III clinical trial LEAP 1 was 0.12\u20130.25 \u03bcg/mL. The post-treatment bacterial clearance rate was up to 100%. Research results at home and abroad have shown that lefamulin had similar antimicrobial activity against S. epidermidis and S. aureus over the MIC (24 h AUC/MIC). Lefamulin achieves rapid and predictable penetration into human tissues, with a mean 5.7-fold higher concentration in the pulmonary epithelial lining fluid compared with plasma. Percent probabilities of attaining the median AUCELF/MIC ratio targets associated with a 1-log10 CFU reduction from baseline by MIC were 97.0% at a MIC of 0.5 \u03bcg/mL for S. pneumoniae and 99.4% at a MIC of 0.25 \u03bcg/mL for S. aureus .DZ and FH designed the study. SW, YZ, YG, and DY performed the experimental work. SW and YZ collected the data. FH analyzed the data. All authors read and approved the final manuscript, contributed to the article, and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "T(temperature), Moisture content (MC), sediment total phosphorus (STP), ion-exchangeable form of ammonia (IEF-NH4+-N), weak-acid extractable form of ammonia (WAEF-NH4+-N), weak-acid extractable form of nitrate (WAEF-NO3\u2212-N), and strong-alkali extractable form of ammonia (SAEF-NH4+-N) were the dominant environmental factors and explained 11.1%, 8.2%, 10.7%, 6.9%, 9.3%, 8.1%, 10.5%, 7.5%, and 7% variation, respectively, of the total variation in the microbial community. Furthermore, the network analysis showed that symbiotic relationships accounted for a major percentage of the microbial networks. The keystone aerobic denitrifying bacteria belonged to Comamonas, Rhodobacter, Achromobacter, Aeromonas, Azoarcus, Leptothrix_Burkholderiales, Pseudomonas, Thauera, unclassified_Burkholderiales, and unclassified_bacteria. The composition of the keystone aerobic denitrifying microbial community also exhibited significant differences on the basis of the adonis analysis. T, STP, IEF-NH4+-N, ion-exchangeable form of nitrate (IEF-NO3\u2212-N), WAEF-NO3\u2212-N, SAEF-NH4+-N, and TN were the dominant environmental factors that explained 8.4%, 6.2%, 4.6%, 5.9%, 5.9%, 4.5%, and 9.4% variation, respectively, of the total variation in the keystone aerobic denitrifying microbial community. The systematic investigation could provide a theoretical foundation for the evolution mechanism of the aerobic denitrifying microbial community in Baiyangdian Lake.Here, the ion-exchangeable form of nitrogen (IEF-N), weak-acid extractable form of nitrogen (WAEF-N), strong-alkali extractable form of nitrogen (SAEF-N), strong-oxidant extractable form of nitrogen (SOEF-N), residue nitrogen (Res-N), and total nitrogen (TN) showed spatial differences, and most of the sediment nitrogen fractions exhibited positive correlations in Baiyangdian Lake. High-throughput sequencing analysis revealed that the aerobic denitrification microbial community was composed of proteobacteria (42.04%\u201399.08%) and unclassified_bacteria (0.92%\u201357.92%). Moreover, the microbial community exhibited significant differences (R Thiosphaera pantotropha) [Excessive nitrogen concentrations present problems for water quality and cause eutrophication . An incrotropha) has beenotropha) , Wadden otropha) , wetlandotropha) , coastalotropha) and reseotropha) ,10. Therotropha) ,12.napA is the biomarker of aerobic denitrifying bacteria [napA) in Baiyangdian Lake.Currently, some full-scale experiments on bioaugmentation with aerobic denitrification bacteria have been conducted successfully for the remediation of wastewater, urban river, and river sediment. Such as, Duan et al. 2015) explored the nitrogen removal performance of halophilic heterotrophic nitrification-aerobic denitrification SF-16 in saline wastewater ; Du et a5 explorebacteria ,21. TherIn this study, our objectives were to (1) investigate the characteristics of environmental factors; (2) examine the composition of the aerobic denitrifying microbial community and keystone operational taxonomic unit (OTU); (3) evaluate the differences in abundance, diversity, and community structure; (4) analyze the relationship between the microbial community structure and environmental driving factors; and (5) estimate the relative contributions of the environmental driving factors.Baiyangdian Lake, located in Xiong\u2019an New Area, is the largest freshwater lake in the North China Plain a. Baiyan3\u2212-N, NO2\u2212-N, and NH4+-N were measured using DR6000 [T, DO, pH, ORP, and EC of the water samples were determined using Hydrolab DS5 . According to the standard methods, TN, NOny, USA) . The difny, USA) ,24.napA [https://submit.ncbi.nlm.nih.gov/subs/sra/) database with the accession number PRJNA623955.The whole DNA of the sediment was extracted using the Soil DNA Kit . After DNA purification, the extracted DNA was stored at \u221280 \u00b0C for PCR amplification. The extracted DNA was amplified using primer V66F, 5\u2032-TAYTTYYTNHSNAARATHATGTAYGG-3\u2032, and V67R, 5\u2032- DATNGGRTGCATYTCNGCCATRTT-3\u2032, for aerobic denitrifying bacterial napA ,25. PCR napA . High-thOn the basis of the OTU data, the richness index, Shannon index, Simpson index, Pielou index, Chao1 index, ACE index, and Good\u2019s Coverage were calculated to evaluate the alpha diversity. The differences in the microbial communities were evaluated using principal co-ordinate analysis (PCoA) and permutational MANOVA (adonis) in the vegan package (R.3.5.3). Redundancy analysis (RDA) was used to determine the correlation between the microbial community and predominant environmental factors with variance inflation factor (VIF) < 10 in the vegan package (R.3.5.3). Indicator species analysis was conducted using labdsv package (R.3.5.3). Hierarchical partitioning (HP) analysis was performed to quantitatively evaluate the relative influences of the environmental factors on the aerobic denitrifying bacterial community by using the rdacca.hp package (R.3.5.3) .Network analysis was performed to investigate the biotic interactions between the microbial populations, and the results were visualized with Gephi software (0.9.2). In this study, a positive correlation implied a mutualistic interaction, whereas a negative correlation may indicate competition . The \u201ckeNatural area. The IEF-N, WAEF-N, SAEF-N, SOEF-N, and Res-N values were 100.61, 2831.38, 1487.38, 995.42, and 1093.82 mg/kg, respectively , whereas it was negatively correlated with IEF-NO3\u2212-N , SAEF-NH4+-N , IEF- N , and IEF-NH4+-N , IEF-N , SAEF-N , IEF-NH4+-N , SAEF-NO3\u2212-N , and TAN and IEF-NO3\u2212-N . IEF-NO3\u2212-N was positively correlated with IEF-N , SAEF-NO3\u2212-N , and TAN (p < 0.05), IEF-NH4+-N , SAEF-NO3\u2212-N , TAN , SOEF-NO3\u2212-N , SOEF-N , and SOEF-NH4+-N , SAEF-NO3\u2212-N , and TAN , TAN , SOEF-NO3\u2212-N , SOEF-N , and SOEF-NH4+-N , SOEF-NO3\u2212-N , SOEF-N , and SOEF-NH4+-N , SOEF-N , and SOEF-NH4+-N and SOEF-NH4+-N .WAEF-NO < 0.05) . Res-N w< 0.001) . WAEF-NH < 0.01) . SAEF-NH < 0.01) . IEF-N w < 0.05) b. SAEF-N< 0.001) . IEF-NH4 < 0.05) . SAEF-NO < 0.05) . TAN was < 0.01) b. SOEF-N< 0.001) . SOEF-N After quality trimming, a total of 223754 sequences with an average length of 373 bp were obtained for the 14 sediment samples. MiSeq revealed a total of 1886 OTUs with 97% similarity . The Sha\u03b1-diversity was influenced by PCoA1 , MC (R = 0.70), STP (R = 1.00), IEF-NH4+-N (R = 0.97), and WAEF-NH4+-N (R = 0.80) were the dominant environmental parameters , unclassified_bacteria (0.92%\u201357.92%), 0\u20130.25%) . ProteobAt the class level , BetaproComamonas (0\u201383.37%), unclassified_bacteria (1.44\u201358.39%), Rhodobacter (0.01\u201350.84%), unclassified_Burkholderiales (0.46\u201328.84%), Aeromonas (0.08\u201323.42%), Azoarcus (1.19\u201322.78%), Thauera (0.31\u201318.17%), Achromobacter (0.02\u201311.86%), Pseudomonas (0.11\u201310.78%), Sulfuritalea (0.09\u20139.75%), unclassified_betaproteobacteria (0.28\u20139.28%), Cedecea (0\u20138.16%), Dinoroseobacter (0\u20137.61%), Sulfurospirillum (0\u20137.54%), Leptothrix_Burkholderiales (0.29\u20135.61%), Magnetospirillum (0.19\u20134.59%), Azospirillum (0.03\u20133.52%), Azospira (0\u20133.30%), Rhodopseudomonas (0.16\u20133.09%), and Rhizobium (0\u20132.10%) (Comamonas (BH), unclassified_Betaproteobacteria (BGYH), Achromobacter (BGYH), Sulfurospirillum (PH), Azospira (BGYH), and Azospirillum (PH); for the breeding area, unclassified_bacteria (FYD) and Thauera (SHD); for the tourist area, Sulfuritalea (YYD) and Dinoroseobacter (YYD); for the living area, unclassified_Burkholderiales (BTZXD), Aeromonas (ZLZ), Magnetospirillum (ZLZ), Cedecea (PYD), Leptothrix_Burkholderiales (BTZXD), and Rhizobium (BTZXD); and for the natural area, Azoarcus (ZZD), Rhodobacter (ZZD), Pseudomonas (ZZD), and Rhodopseudomonas (ZZD). Previous studies have shown that these dominant genera are aerobic denitrifying bacteria. For example, Comamonas is capable of heterotrophic nitrification-aerobic denitrification nitrogen removal, and it has been successfully used for bioaugmentation of municipal wastewater [Rhodobacter is a typical denitrifying bacterium in alkaline copper mine drainage [Aeromonas sp. HN-02 [Aeromonas, Pseudomonas, and Acinetobacter) could be successfully enriched and conducted denitrification to remove 90% of TN in a wetland test system [Azoarcus was an important genus in a denitrifying quinoline-removal bioreactor [Thauera was identified as the key potential heterotrophic nitrification and aerobic denitrification genus for principal nitrogen removal in granular reactors [Achromobacter xylosoxidans CF-S36, a typical heterotrophic nitrification-aerobic denitrification bacterium, were investigated through molecular analysis [Pseudomonas indoloxydans YY-1, through physiological and transcriptomic analyses [Pseudomonas putida strain NP5 [Azospira was the main dentrifier in a tidal flow constructed wetland [Halomonas was the dominant heterotrophic nitrifying/aerobic denitrifying genus under hypersaline conditions [Rhodopseudomonas is a potential autotrophic denitrifying genus that can use electrons and reducing power from cathodes [At the genus level, the top 20 abundant genera are as follows: 0\u20132.10%) . Moreovestewater and enristewater . Liu et nas 0\u201383.%, unclasdrainage . Chen et 1.44\u201358.%, Rhodobt system . Azoarcuoreactor , and it 0.08\u201323.%, Azoarcreactors . The dynanalyses and Yangriales 0.\u201328.84%, wetland , reservo1.44\u201358.3%, Rhodob wetland . Halomonnditions . Rhodopster 0.01\u2013.84%, uncDifferences in the composition of the aerobic denitrifying microbial community in the five areas were investigated with PCoA and NMDS analysis. RDA was used to demonstrate the links between the environmental parameters and microbial community. HP analysis was performed to investigate the relative influence of the environmental driving factors on microbial community composition.For the whole aerobic denitrifying microbial community. The PCoA results showed that PCoA1 and PCoA2 accounted for 42.91% and 17.42%, respectively, of the variability in the microbial community composition on the basis of the adonis analysis. The stress result (stress = 0.06 < 0.1) of NMDS showed that the NMDS analysis exhibited good representation on the basis of the adonis analysis. The stress result (stress = 0.04 < 0.05) of NMDS showed that NMDS analysis exhibited excellent representation , module 4 , module 6 , module 7 , and module 8 ; STP and WAEF-NO3\u2212-N exhibited a significantly negative correlation with modules 1\u20138, and the correlation reached \u22120.56 to \u22120.58 (p < 0.05) and \u22120.64 (p < 0.05); WAEF-NH4+-N, Res-N, and TN were positively correlated with modules 1\u20138, and the correlation reached 0.54\u20130.64 (p < 0.05), 0.65\u20130.70 (p < 0.05), and 0.67\u20130.71 (p < 0.01). WAEF-N was positively correlated with module 1 , module 2 , module 5 , and other modules . Especially, the keystone aerobic denitrifying microbial community exhibited a significantly positive correlation with T , WAEF-NH4+-N , Res-N , and TN and a significantly negative correlation with STP . On the basis of all the results, T, STP, WAEF-NH4+-N, WAEF-NO3\u2212-N, and TN were important environment factors, which is consistent with the RDA and HP analysis results.The correlations between the modules and environmental factors were investigated in Baiyangdian Lake c. The ennapA). In this study, the environmental parameters exhibited significantly spatial differences among the different functional areas, and most of the sediment nitrogen fractions exhibited positive correlations in Baiyangdian Lake. MiSeq revealed a total of 1886 OTUs identified as proteobacteria (42.04\u201399.08%), unclassified_bacteria (0.92\u201357.92%), and Deinococcus-Thermus (0.00\u20130.25%). The unclassified genus accounted for an important part in Baiyangdian Lake. The RDA and VIF results showed that T, MC, STP, IEF-NH4+-N, and WAEF- NH4+- N were the dominant environment parameters and explained 11%, 13.6%, 27.6%, 16.3%, and 2.8% variation in \u03b1-diversity. Moreover, the microbial community exhibited significantly spatial differences . T, MC, STP, IEF-NO3\u2212-N, WAEF-NH4+-N, WAEF-NO3\u2212-N, and SAEF-NH4+-N were the dominant environmental factors and explained the 11.1%, 8.2%, 10.7%, 9.3%, 8.1%, 10.5%, and 7.5% variation of the total variation in the whole aerobic denitrifying microbial community, respectively. The network analysis showed that symbiotic relationships accounted for a major percentage of the microbial networks, and 40.18% nodes belonged to betaproteobacteria. The keystone OTUs belonged to Comamonas, Rhodobacter, Achromobacter, Aeromonas, Azoarcus, Leptothrix_Burkholderiales, Magnetospirillum, Pseudomonas, Sulfuritalea, and Thauera. Furthermore, the composition of the keystone aerobic denitrifying microbial community also exhibited significantly spatial differences , and T, STP, IEF-NH4+-N, IEF-NO3\u2212-N, WAEF-NO3\u2212-N, SAEF-NH4+-N, and TN were the dominant environmental factors. From all the results, this study supplied a new view on investigating the distribution characteristics and driving factors of the aerobic denitrifying microbial community in Baiyangdian Lake.This is the first report of the characteristics and driving factors of the aerobic denitrifying microbial community, especially, the \u201ckeystone species\u201d and the dominant environment factor in natural water ecosystem through the aerobic denitrification functional gene ("} +{"text": "Correction to: Isr J Health Policy Res 10, 12 (2021)https://doi.org/10.1186/s13584-021-00449-xFollowing publication of the original article , the autBelow the incorrect and correct table description:Incorrect: Table\u00a01 Cumulative COVID-19 vaccination doses administered per 100 people by Feb. 1, 2021, or latest date availableCorrect: Table\u00a01: Cumulative COVID-19 vaccination doses administered per 100 people by Feb. 11, 2021, or latest date availableThe original article has been updated."} +{"text": "Stem rust in recent years has acquired an epiphytotic character, causing significant economic damagefor wheat production in some parts of Western Siberia. On the basis of a race composition study of the stem rustpopulations collected in 2016\u20132017 in Omsk region and Altai Krai, 13 pathotypes in Omsk population and 10 inAltai population were identified. The race differentiation of stem rust using a tester set of 20 North AmericanSr genes differentiator lines was carried out. The genes of stem rust pathotypes of the Omsk population are avirulentonly to the resistance gene Sr31, Altai isolates are avirulent not only to Sr31, but also to Sr24, and Sr30. A lowfrequency of virulence (10\u201325 %) of the Omsk population pathotypes was found for Sr11, Sr24, Sr30, and for Altaipopulation \u2013 Sr7b, Sr9b, Sr11, SrTmp, which are ineffective in Omsk region. Field evaluations of resistance to stemrust were made in 2016\u20132018 in Omsk region in the varieties and spring wheat lines from three different sources.The first set included 58 lines and spring bread wheat varieties with identified Sr genes \u2013 the so-called trap nursery. The second set included spring wheat lines from the Arsenal collection,that were previously selected according to a complex of economically valuable traits, with genes for resistanceto stem rust, including genes introgressed into the common wheat genome from wild cereal species. The thirdset included spring bread wheat varieties created in the Omsk State Agrarian University within the framework ofa shuttle breeding program, with a synthetic wheat with the Ae. tauschii genome in their pedigrees. It was establishedthat the resistance genes Sr31, Sr40, Sr2 complex are effective against stem rust in the conditions of WesternSiberia. The following sources with effective Sr genes were selected: (Benno)/6*LMPG-6 DK42, Seri 82, Cham 10,Bacanora (Sr31), RL 6087 Dyck (Sr40), Amigo , Siouxland , Roughrider , Sisson, and Fleming , Pavon 76 (Sr2 complex) from the ISRTN nursery; No. 1 BC1F2(96 \u00d7 113) \u00d7 145 \u00d7 113 , No. 14\u0430 F3 (96 \u00d7 113) \u00d7 145 , No. 19 BC2F3 (96 \u00d7 113) \u00d7 113 , and No. 20 F3 (96 \u00d7 113) \u00d7 145 from the Arsenal collection; and the Omsk State AgrarianUniversity varieties Element 22 , Lutescens 27-12, Lutescens 87-12 , Lutescens 70-13, andLutescens87-13 . These sources are recommended for inclusion in the breeding process for developingstem rust resistant varieties in the region. Stem rust of wheat caused by Puccinia graminis f. sp. triticiErikss. for a long time had a weak manifestation in the territoryof Western Siberia and only in the recent years acquiredan epiphytotic nature, causing significant economic damagefor wheat production in the region. First of all, this is due tothe deterioration of the phytosanitary situation in the region,the general trend of climate warming and cultivation of susceptiblewheat varieties on large area . The threat of stem rust race Ug99 appearance and theemergence of new pathotypes of this race, affecting varietieswith genes Sr24 and Sr36 present a serious threat for wheatproduction in West Siberian region. Genetic diversity of cultivatedwheat varieties for resistance to Ug99 and stem rustin general is very limited .Enhancement of genetic resistance to pathogens can besolved germplasm exchange, and also cultivation of varietieswith different level of resistance to diseases and to differentraces. Crop protection is necessary to restrain the evolutionof pathogens and the emergence of new virulent races.Such programs are widely used in Europe and America. Theduration of the variety cultivation in advanced countries is3\u20134 years, while in Russia \u2013 7\u201310 years . Inthis regard, the breeding of spring wheat varieties, whichhave a diverse genetic basis of resistance to stem rust, is veryrelevant.Amigo .Since the 1950s, many resistance genes introduced intobread wheat have lost their effectiveness .The most significant genes for breeding practice are Sr2,Sr23, Sr24, Sr25, Sr31, Sr33, Sr36, Sr38, Sr45, Sr50, SrTmp,Sr1RSIntrogression of resistance genes of wild and cultivatedwheat relatives allows to expand the genetic diversity ofvarieties and contributes to their long-term protection . To date, about 86 Sr genes have beenidentified,of which 26 stem rust resistance genes havebeen transferred into bread wheat from other cereal species. For example, T. turgidum was thesource of the stem rust resistance genes Sr2, Sr9d, Sr9e, Sr9g,Sr11, Sr12, Sr13, Sr14, and Sr17, of which the Sr2, Sr13, andSr14 genes are effective against Ug99 race; T. monococcumwas the source of Sr21, Sr22, and Sr35 genes .Genes that caused the resistance to stem rust have beenintroduced into wheat gene pool from the genome of variousAegilops L. species: Ae. speltoides \u2013 Sr32, Sr39, Sr47;Ae. comosa \u2013 Sr34; Ae. ventricosa \u2013 Sr38 . Ae. tauschii contributed genes Sr33, Sr45, Sr46 . Direct hybridization of T. aestivum withAe. tauschii and following backcrosses allowed introductionof new resistance genes SrTA1662, SrTA1017, and SrTA10187effective against Ug99 race . The searchof new resistance genes in wild wheat relatives continues, forexample, G. Yu et al. (2017) identified two new Sr genes inAe. sharonesis.One of the objectives of Kazakh-Siberian Spring WheatImprovement Network (KASIB) is expanding of the geneticpolymorphism of new varieties, including resistance to harmfuldiseases . This is based onshuttle breeding with CIMMYT (Mexico). Varieties andbreeding lines developed through shuttle breeding with participationof Ae. tauschii and T. dicoccum, as well as linesof the \u201cArsenal\u201d collection, which have wild species in theirpedigree are of interest for breeding for resistance to stemrust in the region.The aim of the research was analysis of the racial compositionof the Western-Siberian stem rust population, resistanceassessment of spring bread wheat lines and varieties with identified resistance genes and identification of the sourceswith effective Sr genes for breeding under Western Siberianconditions.http://agro.au.dk/forskning/internationaleplatforme/wheatrust).The racial composition of Puccinia graminis f. sp. tritici populationscollected in 2016\u20132017 in Omsk region ) and Altai region were analyzed in the Global Rust Reference Center was carriedout. Monopustule isolates were reproducted to identifyrace Ug99 with usage of the test PCR-Stage 1. A total of19 single pustule isolates were selected from Omsk populationand 20 \u2013 from Altai population (Table 1).Selection of single pustule isolates according to requirementsof GRRC protocols (Differentiation of stem rust races was performed with useof the set of 20 North American differentiator lines containingSr genes: Sr5 (ISr5-Ra), Sr21 (CnS_Triticum monoc.Deriv.), Sr9e (Vernstein), Sr7b (ISr7b-Ra), Sr11 (ISr11-Ra), Sr6 (ISr6a-Ra), Sr8a (ISr8a-Ra), Sr9g (CnSr9g), Sr36(W2691SrTt-1), Sr9b (W2691Sr9b), Sr30 (BtSr30Wst),Sr17+13 (Combination VII), Sr9a (ISr9a-Ra), Sr9d (ISr9d-Ra), Sr10 (W2691Sr10), SrTmp (CnsSrTmp), Sr24 (LcSr24Ag),Sr31 (Benno Sr31/6*LMPG), Sr38 (VPM-1), SrMcN(McNair 701). Infected plants were evaluated in 14\u201316 daysafter inoculation according to modified E.C. Stakman scale. Virulence phenotypes were classifiedaccording to North American system .The varieties and lines of bread wheat from three germplasmsets were evaluated in Omsk at least 4\u20135 times for reaction tostem rust on scales recommended by Koyshibaev et al. (2014).The type of reaction on E.B. Mains and H.S. Jacksonscale(1926) and severity \u2013 on modified Peterson scale were considered: 0 \u2013 immunity, uredopustulesnot formed; R (Resistance \u2013 high resistance), 1 score, severity 5\u201310 %; MR (Moderately resistant \u2013 average resistance),2 score, severity 10\u201325 %; M (heterogeneous type), pustulesof different sizes, surrounded by chlorotic and necrotic spotsor without them; MS (Moderately susceptible \u2013 averagesusceptibility), 3 score, severity 40\u201350 %; S (Susceptible \u2013susceptibility), 4 score, severity more than 60 %.In 2016\u20132018, International Stem Rust Trap Nursery with58 genotypes with identified Sr genes was evaluated to Omskstem rust population (Table 2). Varieties and lines of nurserytrapwere sown manually in 100 cm-long rows with stem rustresistant (Element 22) and susceptible checks (Chernyava 13)alternating every entries.1F2 (96 \u00d7 113) \u00d7 145 \u00d7 113]; No. 13, 14\u0430 [F3 (96 \u00d7 113) \u00d7 145];No. 16, 17, 17\u0430 [BC1F4 (96 \u00d7 113) \u00d7 113]; No. 19 [BC2F3(96 \u00d7 113) \u00d7 113]; No. 20, 22\u0430 [F3 (96 \u00d7 113) \u00d7 145]. The lineswere studied in 2016\u20132018 in un-replicated trial with the plotsize of 2 m2.In 2015, 9 spring wheat lines originating from wide crosses\u201cArsenal\u201d collection were kindly provided by I.F. Lapochkinafor evaluation in Omsk. These lines carry a pyramid ofstem rust resistance genes \u2013 No. 1[BCNine spring wheat varieties and breeding lines from advancedyield trial at Omsk SAU developed through utilizationof synthetic wheat with the Ae. tauschii genome (Lutescens24-12 (Kasibovskaya), Lutescens 27-12, Lutescens87-12, Lutescens 70-13, Lutescens 87-13, Lutescens 88-13(Silantiy), Lutescens 124-13, Lutescens 53-15, Lutescens 128-15) were evaluated for stem rust resistance and other traits in2016\u20132018. The plot size was 25 m2 with four replications.The checks were Pamyati Azieva (early maturing), Duet (mediummaturing), and Element 22 (late maturing).http://maswheat.ucdavis.edu/protocols/StemRust/index.htm). The resistance genes of spring bread wheat lines and varietiesfrom nursery-trap and from collection \u201cArsenal\u201d were identifiedearlier .Sr genes of Omsk SAU varieties were identified usingmolecular markers: Xsts638 \u2013 Sr15, Xcfa2123 \u2013 Sr22,Xgwm210 \u2013 Sr23, Xscs73 \u2013 Sr24, Xwmc221 \u2013 Sr25,BE518379 \u2013 Sr26, Xscm09 \u2013 Sr31, SCS421 \u2013 Sr34,Xcfa2170 \u2013 Sr35, Xstm773-2 \u2013 Sr36, Ventriup-LN2 \u2013 Sr38,Lr34plus \u2013 Sr57, according to established protocol . In all studiedWestern-Siberian populations of P. graminis Ug99 and Sicilianraces were not identified. Genes of stem rust pathotypesof Omsk population were avirulent only to Sr31 gene, whileAltai pathotypes were avirulent to Sr31, Sr24, and Sr30.The race composition analysis of stem rust populationsidentified a significant number of pathotypes: in the Omskpopulation \u2013 13 and in Altai population \u2013 10 (see Table 1).Unlike many regions of the world where stem rust is a harmfuldisease for decades, for example in Krasnodar region of Russia, for Western Siberia this is surprisingresult considering a short period of time since its appearance.Most of the identified pathotypes of stem rust population inOmsk and Altai regions were not identical in virulence to thepathotypes, which were found in recent years in Asia andAfrica (Low frequency of virulence (10\u201325 %) of Omsk populationpathotypes was established for Sr11, Sr24, Sr30 genes, forAltai population \u2013 for Sr7b, Sr9b, Sr11, SrTmp genes, whichwere ineffective in Omsk region. The results of laboratoryevaluation of virulence of P. graminis pathotypes collectedin Omsk region were confirmed by field of trap nursery withidentified Sr genes (see Table 2).Genotypes with Sr31: Sr31(Benno)/6*LMPG-6 DK42,Seri 82, PBW343=Attila with Sr31, Cham 10=Kauz//Kauz/star, Bacanora=Kauz\u2019s\u2019 showed high level of resistance toOmsk stem rust population in all years of study (2016\u20132018).Line 28 LcSr24Ag + BTSr24Ag with Sr24 gene was characterizedby moderate resistance. For some Sr genes, resistanttype of reaction under epiphytotic conditions was observedon the stage of adult plants, and susceptible type \u2013 on theseedling stage in the laboratory conditions.For example, variety Trident (entries 46 and 47) withSr38 gene had high resistance (R\u20135MR) in the field; varietyEinkorn (entry 25) with Sr21 gene, and line W2691SrTt-1CI 17385 (entry 44) with Sr36 gene had moderate resistance(10M) in the field conditions. In the laboratory conditionsthe seedlings plants with above mentioned genes were classifiedas susceptible. Genotypes of ISRTN nursery with agene pyramid had high resistance to stem rust in all years ofresearch: entry 50 Amigo (Sr24 + 1RS-Am), entry 51 Siouxland(Sr24 + Sr31), entry 52 Roughrider (Sr6 + Sr36), entry 53Sisson (Sr6 + Sr31 + Sr36), entry 55 Fleming (Sr6 + Sr24 +Sr36 + 1RS-Am). The results of stem rust resistance evaluationof \u201cArsenal\u201d collection and Omsk SAU germplasm arepresented in Table 3.Lines from \u201cArsenal\u201d collection are of great interest assources of resistance to pathogen since they possess thegene pyramid: Sr2 (T. turgidum), Sr36, Sr40 (T. timopheevii),Sr44 (Th. intermediate). The pedigree of selected linescontains spring wheat line 13/00/i-4 with 7 resistance genes: Sr2, Sr36, Sr39, Sr40, Sr44, Sr47, Sr15, and winter lineGT 96/90 with genes Sr15, Sr24, Sr31, Sr36, Sr40, Sr47.In Omsk SAU varieties 3 resistance genes were identified:Sr23, Sr31, Sr36. Variety Element 22, which has winter wheatAurora in its pedigree also possesses wheat-rye translocation1BL.1RS with Sr31 gene . Thecombination of effective resistance genes Sr31 and Sr35 inthis variety results a high level of resistance to stem rust. Element22 is one of the few varieties with combined resistanceto stem and leaf rust. It was included into State register ofbreeding achievements in Western Siberian region. This varietyis the check of the late maturity group at the State VarietyTrials in Omsk region.Stem rust resistant breeding lines Lutescens 27-12, Lutescens70-13, Lutescens 87-13, Lutescens 88-13 were selectedfrom a cross Lutescens 30-94*2/3/T. dicoccon PI 94625/Ae. squarrosa (372)//3*Pastor involving Kazakhstan springwheat line Lutescens 30-94 and CIMMYT line developedby hybridization of synthetic wheat with variety Pastor. Theline Lutescens 87-12 originated from a cross Kazakhstanskaya25/2*Attila/3/T. dicoccon PI 94625/Ae. squarrosa alsoinvolving synthetic wheat. Omsk SAU germplasm possesseddifferent combinations of genes Sr23, Sr31, and Sr36.In modern conditions, stem rust is the most dangerous diseasefor grain production in Western Siberia. In the epiphytoticyears the grain losses of wheat in the region were about 2 milliontons. Unfortunately, stem rust resistant varieties includedinto the State register occupy about 10\u201315 % of the totalwheat sowing area in the region. In 2015\u20132016, evaluationof spring wheat varieties at Moskalenskiy State Variety Trialof Omsk region (southern forest-steppe zone) demonstratedthat out of 57 varieties tested only Element 22 (Sr31 + Sr35),Omskaya 37, Sigma, Uralosibirskaya (Sr31), and Sigma 2(Sr31 + Sr25) were resistant to stem rust (5\u201315MR). The othervarieties were affected by pathogen in medium and high degreerequiring the use of chemical protection . Previously, Shamanin et al. (2016b) identified thestem rust resistance genes in the germplasm developed bybreeding institutions of Western Siberia. High frequency ofgenes Sr25, Sr31, and their combination was observed. Highvariability of the race composition of the pathogen population,as shown in our studies, and the uniformity of resistance genesto stem rust in cultivated varieties, threaten grain productionstability in Western Siberia.The breeding strategy should focus on limiting diseasedevelopment in the region. The study of the populations ofP. graminis, formed on wheat in the different regions, is veryessential to guide the breeding efforts. There were no clonesavirulent to Sr24 gene in Omsk population of P. graminiswhile in Altai region there were no clones virulent to Sr24,which remains its effectiveness in Novosibirsk region . The results of the population compositioncomparison suggest that Omsk and Altai subpopulations haverelatively independent sources of genetic diversity and the contact zone. Western Siberian population of P. graminis hasquite complex structure. Two subpopulations are assumed toexist: Omsk and Altai \u2013 with independent sources of geneticdiversity, and zone of genotypic exchange on wheat crop inNovosibirsk region .Omsk stem rust population analysis showed that the spectrumof effective resistance genes has narrowed due to lossesof some genes to the local population of P. graminis.Highly resistant varieties and lines of ISRTN nurserywere identified: Sr31 (Benno)/6*LMPG-6 DK42, Seri 82,Cham 10, Bacanora (Sr31), RL 6087 Dyck (Sr40), Amigo, Siouxland , Roughrider , Sisson , Fleming , Pavon 76 (Sr2 complex). Selected varieties andlines are recommended for using as sources of resistance inbreeding programs to create resistant wheat varieties to stemrust. Effective resistance genes Sr31, Sr40, Sr2 complex,and their combinations with ineffective genes are recommendedfor use in breeding, taking into account the constantrotation, combination of genes of nonspecific resistance, aswell as the possibility of infection threat from neighboringterritory.The resistance gene Sr2, widely used in breeding for resistanceto virulent stem rust races, is common in commercial varietiesin a number of countries around the world, particularlyin the United States, Australia, India, and Mexico. This geneis practically absent in the commercial varieties of RussianFederation, however, for effective protection against stem rust,its pyramiding with other resistance genes is recommended.For the development of varieties with long-term resistance,the strategy of combining genes responsible for differenttypes of resistance in one genotype is used. Pyramiding ofspecific resistance genes withAPR gene Sr2, which causes the slow development of thedisease (slow rusting), will provide longer protection ofwheat crops from stem rust in Western Siberia in the presentphytosanitary situation.1F2 (96 \u00d7 113) \u00d7 145 \u00d7 113 ; No. 14\u0430 F3(96 \u00d7 113) \u00d7 145 ; No. 19 BC2F3 (96 \u00d7 113) \u00d7 113; No. 20 F3 (96 \u00d7 113) \u00d7 145 represent a promising starting material for breedingand creation of varieties with long-term resistance.In this regard, the lines from \u201cArsenal\u201d collection \u2013 No. 1BCIt is justified to include resistance sources to stem rust withminimum number of negative traits that reduce their breedingvalue. In this regard, stem rust resistant germplasm fromOmsk SAU with identified effective genes Element 22 , Lutescence 27-12, Lutescence 87-12 ,Lutescence 70-13, Lutescence 87-13 ,Lutescence 88-13 (Sr23) are valuable starting material forbreeding in the region.1F2 (96 \u00d7 113) \u00d7 145 \u00d7 113 , No. 14\u0430 F3(96 \u00d7 113) \u00d7 145 , No. 19 BC2F3 (96 \u00d7 113) \u00d7 113, No. 20 F3 (96 \u00d7 113) \u00d7 145 , varieties of Omsk Agrarian University \u2013 Element 22, Lutescens 27-12, Lutescens 87-12 ,Lutescens 70-13, Lutescens 87-13 arerecommendedfor inclusion into breeding process of thecreation of resistant to stem rust varieties in the region. Furthermonitoring of the virulence of stem rust pathogen andcoordination strategy of breeding programs in Western Siberia,and neighboring regions of the Kazakhstan Republic isrecommended. Incorporation of effective resistance genes, inparticular Sr2 and Sr40, will improve the phytosanitary situationand expand the segment of resistant varieties in the region.Thus, the genetic similarity of spring wheat varieties on stemrust resistance genes cultivated over large areas in WesternSiberia, and the predominance of varieties with race specific resistance genes contribute to spreading and high variabilityof the pathogen. The lines from collection \u201cArsenal\u201d \u2013 No. 1BCThe authors declare no conflict of interest.Ablova I.B., Bespalova L.A., Kolesnikov F.A., Nabokov G.D.,Kovtunenko V.Ya., Filobok V.A., Davoyan R.O., KhudokormovaZh.N., Mokhova L.M., Levchenko Yu.G., Tarkhov A.S. Principlesand methods of wheat breeding on tolerance to diseasesin KRIA named after P.P. Lukiyanenko. Zernovoe KhozjaistvoRossii = Grain Economy of Russia. 2016;5:32-36. (in Russian)Baranova O.A., Lapochkina I.F., Anisimova A.V., Gajnullin N.R.,Iordanskaya I.V., Makarova I.Yu. Identification of Sr genes innew common wheat sources of resistance to stem rust race Ug99using molecular markers. Russ. J. Genet.: Appl. Res. 2016;6(3):344-350.Gomez-Becerra H., Morgounov A., Abugalieva A. Evaluation ofyield grain stability, reliability and cultivar recommendation inspring wheat (Triticum aestivum) from Kazakhstan and Siberia.Central Eur. J. Agriculture. 2006;6:649-660.Jin Y., Szabo L.J., Pretorius Z.A., Singh R.P., Ward R., Fetch T.,Jr. Detection of virulence to resistance gene Sr24 within raceTTKS of Puccinia graminis f. sp. tritici. Plant Dis. 2008;92:923-926.Kerber E.R., Dyck P.L. Resistance to stem and leaf rust in Aegilopssquarrosa and transfer of a gene for stem rust resistanceto hexaploid wheat. In: Ramanujam S. (Ed.). Proceeding of the5th International Wheat Genetics Symposium. New Delhi: Ind.Soc. of Genetics and Plant Breeding, Ind. Agric. Res. Institute,1979;358-364.Koyshybaev M., Shamanin V.P., Morgunov A.I. Screening of Wheatfor Resistance to Major Diseases. Ankara: FAO-SEK, 2014. (inRussian)Lapochkina I.F., Baranova O.A., Shamanin V.P., Volkova G.V.,Gainullin N.R., Anisimova A.V., Galinger D.N., Lazareva E.N.,Gladkova E.V., Vaganova O.F. The development of the initialmaterial of spring common wheat for breeding for resistance tostem rust (Puccinia graminis Pers. f. sp. tritici), including theUg99 race, in Russia. Russ. J. Genet.: Appl. Res. 2017;7(3):308-317. DOI 10.1134/S207905971703008X.Leonova I.N., Orlovskaya O.A., R\u00f6der M.S., Nesterov M.A., BudashkinaE.B. Molecular diversity of common wheat introgressionlines (T. aestivum/T. timopheevii). Russ. J. Genet.: Appl.Res. 2015; 5(3):191-197. DOI 10.1134/S2079059715030090.Mains E.B., Jackson H.S. Physiologic specialization in the leaf rustof wheat, Puccinia triticina Erikss. Phytopathology. 1926;16(2):89-120.McIntosh R.A., Dubcovsky J., Rogers W.J., Morris C., Xia X.C.Catalogue of gene symbols for wheat: 2017 Supplement. Availableat: http://shigen.nig.ac.jp/wheat/komugi/genes/macgene/supplement 2017.pdfMcIntosh R.A., Yamayaki Y., Dubcovsky J., Rogers W.J., MorrisC., Appels R., Xia X. Catalogue of Gene Symbols for Wheat:2013\u20132014 Supplement. Available at: http://www.shigen.nig.ac.jp/wheat/komugi/genes/macgene/supplement2013.pdfOlson E.L., Rous M.N., Pumphrey M.O., Bowden R.L., Gill B.S.,Poland J.A. Introgression of stem rust resistance genesSrTA10187 and SrTA10171 from Aegilops tauschii to wheat.Theor. Appl. Genet. 2013;126:2477-2484. DOI 10.1007/s00122-013-2148-z.Peterson R.F., Campbell A.B., Hannah A.E. A diagrammatic scalefor estimating rust intensity on leaves and stems of cereals. Can.J. Res. (Sect. C). 1948;26:496-500.Roelfs A.P., Martens J.W. An international system of nomenclaturefor Puccinia graminis f. sp. tritici. Phytopathology. 1988;78:526-533.Sanin S.S. Problems of phytosanitary of grain production. In: Protectionof Cereal Crops Against Diseases, Pests, and Weeds:Progress and Problems: Proc. of the Int. sci. and pract. conf.Bolshye Vyazemy, 5\u20139 Dec. 2016. Moscow, 2016;4-15. (in Russian)Schneider A., Moln\u00e1r I., Moln\u00e1r-L\u00e1ng M. Utilisation of Aegilops(goatgrass) species to widen the genetic diversity of cultivatedwheat. Euphytica. 2008;163:1-19. DOI 10.1007/s10681-007-9624-y.Shamanin V.P., Morgunov A.I., Petukhovskiy S.L., Likhenko I.E.,Levshunov M.A., Salina E.A., Pototskaya I.V., Trushchenko A.Ju. Breeding of spring bread wheat for resistance to stem rustin West Siberia. Omsk: FGOU VPO OmGAU Publ., 2015. (inRussian)Shamanin V.P., Pototskaya I.V., Klevakina M.V. Assessment of theSiberian collection of spring wheat on resistance to stem rustin the southern forest-steppe of Western Siberia. Vestnik KazanskogoGAU = The Herald of Kazan State Agrarian University.2016a;2(40):55-59. (in Russian)Shamanin V., Salina \u0415., Wanyera R., Zelenskiy Yu., Morgounov A.Genetic diversity of spring wheat from Kazakhstan and Russiafor resistance to stem rust Ug99. Euphytica. 2016b;12:287-296.DOI 10.1007/s10681-016-1769-0.Singh R.P., Hodson D.P., Huerta-Espino J., Jin Y., Njau P., WanyeraR., Herrera-Foessel S.A., Ward R.W. Will stem rust destroythe world\u2019s wheat crop? Adv. Agron. 2008;98:271-309. DOI10.1016/S0065-2113(08)00205-8.Singh R.P., Hodson D.P., Jin Y., Lagudah E.S., Ayliffe M.A., BhavaniS., Rouse M.N., Pretorius Z.A., Szabo L.J., Huerta-EspinoJ., Basnet B.R., Lan C., Hovm\u00f8ller M.S. Emergence andspread of new races of wheat stem rust fungus: Continued threatto food security and prospects of genetic control. Phytopathology.2015;105:872-884.Singh R.P., Huerta-Espino J., Bhavani S., Herrera-Foessel S.A.,Singh D., Singh P.K., Velu G., Mason R.E., Jin Y., Njau P., CrossaJ. Race non-specific resistance to rust diseases in CIMMYTspring wheats: breeding and advances. Euphytica. 2011;179:175-186. DOI 10.1007/s10681-010-0322-9.Skolotneva E.S., Bukatich E.Ju., Bojko N.I., Piskarev V.V., SalinaE.A. Screening of an international stem rust nursery trapfor Ug99 in the Priobie forest-steppe in 2017. In: Gene Pooland Plant Breeding: Proc. IV Int. sci. and pract. conf., 4\u20136 April2018. Novosibirsk, 2018;313-318. (in Russian)Skolotneva E.S., Kel\u2019bin V.N., Morgunov A.I., Bojko N.I., ShamaninV.P., Salina E.A. Races composition of the Novosibirskpopulation of Puccinia graminis f. sp. tritici. Mikologiya iFitopatologiya= Mycology and Phytopathology. 2020;54(1):49-58. (in Russian)Yu G., Champouret N., Steuernagel B., Olivera P.D., Simmons J.,Williams C., Johnson R., Moscou M.J., Hern\u00e1ndez-Pinz\u00f3n I.,Green P., Sela H., Millet E., Jones J.D.G., Ward E.R., SteffensonB.J., Wulff B.B.H. Discovery and characterization of twonew stem rust resistance genes in Aegilops sharonensis. Theor.Appl. Genet. 2017;130:1207-1222."} +{"text": "The F2 populations derived from these crosses were genotyped using InDel marker specific to crtRB1. Severe marker segregation distortion was observed. Seventeen crtRB1 inbreds developed through marker-assisted pedigree breeding and seven inbreds generated using marker-assisted backcross breeding were characterized using 77 SSRs. Wide variation in gene diversity (0.08 to 0.79) and dissimilarity coefficient (0.28 to 0.84) was observed. The inbreds were grouped into three major clusters depicting the existing genetic diversity. The crtRB1-based inbreds possessed high \u03b2-carotene (BC: 8.72\u03bcg/g), \u03b2-cryptoxanthin (BCX: 4.58\u03bcg/g) and proA (11.01\u03bcg/g), while it was 2.35\u03bcg/g, 1.24\u03bcg/g and 2.97\u03bcg/g in checks, respectively. Based on their genetic relationships, 15 newly developed crtRB1-based inbreds were crossed with five testers (having crtRB1 gene) using line \u00d7 tester mating design. 75 experimental hybrids with crtRB1 gene were evaluated over three locations. These experimental hybrids possessed higher BC (8.02\u03bcg/g), BCX (4.69\u03bcg/g), proA (10.37\u03bcg/g) compared to traditional hybrids used as check . Environment and genotypes \u00d7 environment interaction had minor effects on proA content. Both additive and dominance gene action were significant for proA. The mean proportion of proA to total carotenoids (TC) was 44% among crtRB1-based hybrids, while 11% in traditional hybrids. BC was found to be positively correlated with BCX (r = 0.68) and proA (r = 0.98). However, no correlation was observed between proA and grain yield. Several hybrids with >10.0 t/ha grain yield with proA content >10.0 \u03bcg/g were identified. This is the first comprehensive study on development of diverse proA rich maize hybrids through marker-assisted pedigree breeding approach. The findings provides sustainable and cost-effective solution to alleviate vitamin-A deficiency.Malnutrition has emerged as one of the major health problems worldwide. Traditional yellow maize has low provitamin-A (proA) content and its genetic base in proA biofortification breeding program of subtropics is extremely narrow. To diversify the proA rich germplasm, 10 elite low proA inbreds were crossed with a proA rich donor (HP702-22) having mutant DeficieVarious avenues namely, food-fortification, medical-supplementation and food-diversification are implemented to alleviate VAD ,7. HowevZea mays L.) is an important cereal crop grown in almost all parts of the world and cultivated across diverse climatic spectrum [CrtRB1 gene that codes for \u03b2-carotene hydroxylase is associated with higher accumulation of proA especially BC and BCX in maize. Rare natural variation in crtRB1 gene limits the hydroxylation of BC and BCX [crtRB1, while the TE is absent in mutant version [Maize characterize the newly developed crtRB1-based inbreds using microsatellite markers, (iii) study combining ability of the crtRB1-based inbreds for different carotenoid fractions, and (iv) identify promising hybrids with high proA and grain yield.Diverse proA rich inbreds have been developed in the tropics \u201319. Howeermplasm ,20. Therviz., UMI-1200, UMI-1230, BML-6Q, BML-7Q, LM-11Q, LM-12Q, LM-13Q, LM-14Q, PDM-4341 and PDM-4251, possessing good general combining ability for greater yield but low in proA were selected as recipient parents. To incorporate favourable allele of crtRB1 into these inbreds, a CIMMYT-HarvestPlus bred inbred i.e., HP704-22 was used as donor. All these recipient inbreds represent a great extent of adaptation range as parental lines of released/promising hybrids while the donor HP704-22 has poor adaptation in Indian conditions (1s were raised and selfed during winter season (December-April) of 2015\u201316 at the Winter Nursery Centre (WNC), ICAR-Indian Institute of Maize Research (ICAR-IIMR), Hyderabad (17\u00b021\u00b450.39\u02baN and 78\u00b029\u00b442.31\u02baE). Ten F2 populations consisting of 99\u2013111 plants of each cross were then grown at ICAR-IARI, New Delhi during rainy season (2016) .1s were tested for hybridity using crtRB1-based InDel marker present in 3\u2019UTR. The true F1s were selfed to derive F2 populations. Genomic DNA was extracted from three weeks old seedlings of F2 progenies using standard procedure of CTAB with minor modification [3\u2019TE-InDel-based marker for crtRB1 [viz., Forward (F): 5\u2019ACACCACATGGACAAGTTCG3\u2019, Reverse1 (R1):5\u2019ACACTCTGGCCCATGAACAC3\u2019 and Reverse2 (R2): 5\u2019ACAGCAATACAGGGGACCAG3\u2019. The primers were custom synthesized from Macrogen Inc., Seoul, South Korea. Polymerase chain reaction (PCR) protocol for crtRB1 [In-vitro amplification using ready-to-use master mix OnePCRTM including Taq buffer, MgCl2, dNTPs and Taq Polymerase was used to perform PCR reaction in 96 well microtiter plate (M/s Genaxy) using GenePro thermal cycler (M/s Hangzhou Bioer Technology Co. Ltd.). The amplified product was resolved on 1.5% Seakem LE agarose gel .The Ffication . The quar crtRB1 , viz., Fr crtRB1 standard2 segregants with homozygous crtRB1 were selfed and derived F3 progenies were raised at ICAR-IARI, New Delhi during rainy season (2017). The F4s were raised during winter season (2017\u201318) at WNC, ICAR-IIMR, Hyderabad, and F5 progenies during rainy season (2018) at ICAR-IARI, New Delhi. To avoid chances of out-crossing, the presence of favourable allele of crtRB1 in each generation was validated using crtRB1-based InDel marker. Desirable segregants were advanced to further generation based on plant-, ear- and grain- characteristics.The FcrtRB1-based inbreds (MGU-PVMAS-1 to MGU-PVMAS-15) from 10 F2 populations were selected for molecular characterization earlier developed by marker-assisted backcross breeding (MABB) at ICAR-IARI were also included. PMI-PV-1 and PMI-PV-2 are parental inbreds of India\u2019s first proA rich maize hybrid (Pusa Vivek QPM9 Improved). PMI-PV-5, PMI-PV-6, PMI-PV-7, PMI-PV-8 and PMI-PV-9 are the parents of MABB-derived proA rich hybrids . Further, HP465-41, a CIMMYT-derived proA rich inbred derived through marker-assisted pedigree breeding was also included for characterization. Two low proA elite inbreds were also included as control for quality analysis. These 26 inbreds were planted in randomized complete block design (RCBD) at ICAR-IARI, New Delhi in rainy season of 2018. Each inbred was planted with two replications, in rows of 3 m with a plant-to-plant distance of 20 cm. The rows were spaced 75 cm apart. Recommended cultural practices were followed to raise a good experimental crop. To avoid contamination by foreign pollens, 2\u20133 plants in each row were selfed for estimation of carotenoids.Fifteen rization . The doncrtRB1 were used for molecular analysis using simple sequence repeats (SSRs) markers. DNA was isolated from seeds using standard sodium dodecyl sulphate (SDS) extraction protocol [http://www.maizegdb.org). PCR was carried out as per Choudhary et al. (2016) [Selfed seeds of 24 inbreds with favourable allele of protocol . A totalviz., gene diversity, major allele frequency, total number of alleles detected, heterozygosity and polymorphism information content (PIC) were estimated using PowerMarker v3.0 [For each allele, presence of a band in a genotype was indicated by 1 and absence of the band as 0. Five parameters, ker v3.0 . An alleker v3.0 . Principker v3.0 .crtRB1 and two inbreds with unfavourable allele of crtRB1) were extracted from maize endosperm through protocol of Kurilich and Juvik (1999) [30 column and detected with a diode array detector-3000 (RS). The mobile phase comprised of methanol: tert-butyl methyl ether with flow rate at 1 ml/min and peaks were detected at 450 nm. For each carotenoid component, viz., BC, BCX, LUT and ZEA, six dilutions of standards were used to construct the regression curve. To estimate proA concentration, amount of BC was added to one-half of BCX amount, while sum of LUT and ZEA gave the non-proA fractions [Carotenoids from the selfed seeds of 26 inbreds with modractions . Total cractions .crtRB1-based inbreds developed under the current study were crossed with five crtRB1-based tester inbreds as per line \u00d7 tester mating design [crtRB1-based promising inbred. These five testers belonged to two different groups viz., -A (PMI-PV-5 and HP465-41), -B . The 75 hybrid combinations and five commercial check hybrids were evaluated using RCBD at three locations, viz. ICAR-IARI, New Delhi; CCS-HAU Regional Station, Uchani ; and ICAR-IARI Regional Research Centre, Dharwad in rainy season of 2018. Each entry was evaluated in two replications, and was grown in a single row of 3 m length, with a row-to-row distance of 75 cm and plant-to-plant distance of 20 cm. Combining ability of the inbreds for carotenoids was calculated as per Singh and Choudhary (1985) [A set of 15 g design at WNC, y (1985) .In each of the 75 experimental hybrid combinations generated from crosses, 2\u20133 plants were selfed to avoid contamination by the foreign pollen. The selfed seeds were used for estimation of carotenoids using UHPLC as per the procedure depicted for the inbreds.Grain yield (YLD) per plot was converted to t/ha as per the standard procedure. Magnitude of heterosis in hybrids over five commercial checks was estimated following Singh and Choudhary (1985) .The statistical analyses on ANOVA, correlation coefficients and combining ability were computed using Windostat 8.0.1s had both 296 and 543 bp amplicons. The 10 F2 populations were genotyped using crtRB1-specific 3\u2019TE-InDel-based marker were 407 and 435, respectively. Thus, crtRB1 showed severe marker segregation distortion both cumulatively as well as in individual populations. Out of 201 favourable homozygotes, 75 segregants were selected based on ear- and grain- characteristics, and advanced to generate F3 progenies. Finally, 15 locally adapted F4 progenies to 270 bp (bnlg1537). The average major allele frequency was 0.62 with a range from 0.29 (phi126) to 0.96 (umc2167 and umc1068). A set of 24 SSRs showed major allele frequency of \u22640.5. The average gene diversity was 0.49, ranging from 0.08 (umc2167 and umc1068) to 0.79 (bnlg1740) (umc2167 and umc1068) to 0.75 (bnlg1740) with an average of 0.43. Of the 77 SSRs, 29 loci had PIC \u22650.5. The current study also detected 14 unique alleles and 23 rare alleles. The heterozygosity existing among the inbreds varied from 0.00 to 0.25 with a mean of 0.04.Some loci such as umc1446 (0.25) and bnlg1346 (0.25) showed high heterozygosity to 0.84 (MGU-PVMAS-13 and MGU-PVMAS-8) with mean of 0.67 . The PICzygosity . Genetic of 0.67 . Cluster of 0.67 . PCoA di of 0.67 .crtRB1-based inbreds and two check inbreds . Among 15 inbreds developed under the study, MGU-PVMAS-11 (14.63 \u03bcg/g), MGU-PVMAS-5 (13.09 \u03bcg/g), MGU-PVMAS-4 (12.53 \u03bcg/g), MGU-PVMAS-12 (12.52 \u03bcg/g) and MGU-PVMAS-2 (12.28 \u03bcg/g) were the most promising ones (crtRB1-based inbreds had significantly low mean LUT (12.16 \u03bcg/g), ZEA (5.86 \u03bcg/g) and non-proA (18.02 \u03bcg/g) compared to check inbreds . However,TC was nearly comparable among the crtRB1-based (31.31 \u03bcg/g) and check inbreds (36.34 \u03bcg/g).ANOVA revealed significant variation for BC, BCX, proA, LUT, ZEA, non-proA and total carotenoid (TC) among 24 inbreds . The meaectively , Fig 4. ing ones . Six inbcrtRB1-based inbreds, BC and BCX contributed 28% and 15% of TC, while LUT and ZEA contributed 39% and 18%, respectively. The contribution of BC and BCX to TC was only 6% and 3% in check inbreds, while the same for LUT and ZEA was 58% and 33%, respectively.Among crtRB1-based hybrids had significant variation for BC, BCX, proA, LUT, ZEA, non-proA and TC (\u00d7 environment (G \u00d7 E) interaction was also low with 8% (non-proA) to 22% (BCX).Pooled ANOVA revealed that A and TC . The proThe mean BC and BCX among experimental hybrids were 8.02 \u03bcg/g and 4.69 \u03bcg/g, as compared to 2.36 \u03bcg/g (BC) and 1.53 \u03bcg/g (BCX) among low-proA checks . High-prThe experimental crosses possessed low LUT and ZEA relative to low-proA checks . High-proA checks also possessed low LUT (5.22 \u03bcg/g) and ZEA (10.56 \u03bcg/g). The non-proA fraction among experimental hybrids varied from 10.78 to 23.50 \u03bcg/g, with an average of 16.47 \u03bcg/g. The non-proA fraction in low-proA checks was higher (31.88 \u03bcg/g) than that of high-proA checks (15.78 \u03bcg/g). TC in experimental hybrids varied from 21.92 to 37.86 \u03bcg/g, with a mean of 29.18 \u03bcg/g. Low-proA checks showed a mean of 35.77 \u03bcg/g, while high-proA commercial checks showed a mean of 29.80 \u03bcg/g .In case of experimental hybrids, the contribution of BC and BCX towards TC was 27% and 17%, while LUT and ZEA contributed 38% and 18%, respectively . In caseCorrelation analysis revealed that BC was positively correlated with BCX (r = 0.68**). Whereas, BC and BCX were negatively correlated with LUT and ZEA , respectively. LUT and ZEA, however, were positively correlated (r = 0.70**). ProA and non-proA carotenoids were also negatively correlated (r = -0.57**). BC, BCX and proA were not correlated with TC, while LUT (r = 0.72**), ZEA (r = 0.72**) and non-proA (r = 0.78**) showed strong positive association with TC. The present study revealed that kernel carotenoid components and grain yield exhibited non-significant relationships (r = -0.18 to 0.15) except for ZEA (r = 0.29**).Pooled ANOVA revealed that environment was highly significant for all the carotenoids except for ZEA . Line efThe proportion of additive and dominance variance, and the contribution of lines, testers and line \u00d7 testers for pooled dataset are presented in GCA effect for proA varied from -1.52 to 1.27. Nine lines and one tester showed significant positive GCA effects for proA . Among tat par with CoMH-08-292. Among high proA checks, \u2018Pusa HQPM-5 Improved\u2019 emerged as the best check with 8.6 t/ha. A total of 26 experimental hybrids were significantly better than \u2018Pusa HQPM-5 Improved\u2019 for grain yield. These hybrids showed heterosis of 8.04% to 31.63% over the best high proA check.Heterosis of the 75 experimental hybrids was estimated over commercial low-proA and high proA checks. CMH08-292 and DHM-121 were medium maturing hybrids with low-proA. \u2018Pusa Vivek QPM-9 Improved\u2019 is an early maturing proA rich hybrid and was released as country\u2019s first proA rich maize hybrid during 2017. \u2018Pusa HQPM-5 Improved\u2019 and \u2018Pusa HQPM-7 Improved\u2019 are the medium maturing proA rich hybrids released in 2020. All the experimental hybrids matured in 92\u2013100 days, thus had medium maturity. The mean grain yield among experimental hybrids was 8.9 t/ha, with the highest yield of 11.4 t/ha Tables. crtRB1 significantly enhances proA in maize kernel [crtRB1 in the Indian maize germplasm is quite low (3.38%) [crtRB1 inbreds have been developed in India. Thus, targeted breeding approach for selection of crtRB1 is essential for broadening the genetic base of proA rich maize germplasm [Plant based-food is the major source of nutrition especially in developing world. Traditional yellow maize lacks the required level of proA . The mute kernel . Diversee kernel ,19. Howe (3.38%) . So far,ermplasm .2 populations indicated that crtRB1 did not segregate as per the expected 1:2:1. This observation drives strength from earlier results of Lu et al. (2002) [crtRB1 gene could be precisely selected due to the reliable gene-based marker. In case of linked marker, there is always chance of selection of false positive individuals due to crossing over between the gene and marker [crtRB1-based inbreds using marker-assisted pedigree breeding. Earlier, Muthusamy et al (2014) [crtRB1 into the elite inbreds using MABB approach. In case of MABB, the improved lines are genetically similar to the recurrent parents except for gene under introgression [crtRB1-based inbreds were developed from F2 populations, the genetic makeup remains novel leading to development of new and diverse crtRB1-based inbreds. The MAS-based selection of crtRB1 is quite cost-effective, as selection of genotypes for high proA using UHPLC involves US$30\u201335 per sample. On the contrary, PCR marker-based selection of crtRB1 employed here costs only US$0.5\u20131.0 per sample. Molecular breeding is now a preferred choice among the maize breeders to develop proA rich germplasm [Genotyping of F. 2002) and Babu. (2002) . The seg. (2002) . Since, d marker . The prel (2014) , Liu et l (2014) , Zunjarel (2014) and Goswl (2014) have intgression . In the 002 and Knowledge of the genetic relationship among inbreds is essential for efficient exploitation in breeding programme. Molecular markers have been successfully employed to derive the genetic distance in maize . High dicrtRB1-based inbreds and hybrids recorded nearly 3\u20134 folds more proA (8\u201314 \u03bcg/g) over the traditional checks (2\u20133 \u03bcg/g). Muthusamy et al., (2014) [crtRB1-based maize genotypes, respectively. However, traditional yellow maize possesses low concentration of proA (<2.5 ppm) [crtRB1, while low proA genotypes harbour the wild-type allele [The , 2014) and Zunj, (2014) also rep14 and Z2.5 ppm) . The acce allele ,17.phytoene synthase 1 (psy1) or Yellow 1 (Y1) gene condenses two geranyl-geranyl pyrophosphate molecules into one molecule of phytoene [y1 allele is unable to catalyze the reactions and white grains are formed due to no synthesis of carotenoids. However, when the Y1 is functional, crtRB1 causes hydroxylation of BC and BCX into ZEA. CrtRB1 located on chromosome 10 codes for \u03b2-carotene hydroxylase. The mutant version of crtRB1 drastically slows down the conversion, leading to more accumulation of proA carotenoids [crtRB1 allele, a large variation in proA was observed. This could be due to variation in the activity of other key genes such as psy1, lycopene \u03b2-cyclase (lcyB), lycopene \u03b5-cyclase (lcyE), phytoene desaturase (pds) and \u03b6-carotene desaturase (zds) catalyzing the carotenoid biosynthesis [lcyE present on chromosome 8 has been observed [lcyE along with crtRB1 is beneficial in enhancing proA in maize. Besides, several modifier loci/QTLs alone or in combination with other pathway genes could also influence the accumulation of proA in maize [In the carotenoid biosynthesis pathway, phytoene . The mutotenoids . Though ynthesis . Allelicobserved . Zunjareobserved reportedin maize ,48.crtRB1-based and check- genotypes, thereby, suggesting greater flux of lycopene towards \u03b1-branch than the \u03b2-branch of pathway [crtRB1-based genotypes, the conversion of BC to ZEA is partially blocked, leading to higher proportion of BC next to LUT. ProA content among the crtRB1-based genotypes constituted 43\u201344% of TC as against 9\u201311% in the check genotypes. The non-proA component was less (56\u201357%) among crtRB1-based genotypes compared to 89\u201391% in checks [Among carotenoids, proportion of LUT was higher in both pathway . LUT ser pathway . Howevern checks ,49. In sn checks .BC, BCX and proA showed strong positive correlations, as BCX is produced from BC, while both contribute to proA . Since, crtRB1 possesses much higher proA compared to heterozygote [crtRB1 in all hybrids. Since, all the hybrids were homozygous for favourable allele of crtRB1, other modifier loci could be the reason for dominance effects for further influencing the proA. Several lines including testers were identified as the best general combiners for proA. MGUH-57 (14.90 \u03bcg/g), MGUH-52 (14.60 \u03bcg/g), MGUH-27 (14.36 \u03bcg/g) and MGUH-32 (14.26 \u03bcg/g) possessed high proA, and had both the parents being high in GCA effects as well. Besides, MGUH-1, MGUH-14, MGUH-15, MGUH-18, MGUH-19, MGUH-28, MGUH-31, MGUH-48, MGUH-50 and MGUH-75 had one of the parents (used as line) having high GCA effects for proA. The inbreds with high GCA for proA thus serve as a promising inbreds in the future breeding programme [The current study revealed that environments had minor effect on BC, BCX and proA. Muthusamy et al. (2015b) also reprozygote ,17,22. Crogramme .at par with CoMH08-292 and significantly better than DHM-121 for grain yield potential.Several promising experimental hybrids with >10.0 t/ha grain yield and >10.0 \u03bcg/g proA were identified. MGUH-15 , MGUH-50 , MGUH-72 , MGUH-54 and MGUH-55 were the most promising combinations. Most of these promising hybrids belongs to different clusters. These hybrids are much higher yielding than the \u2018Pusa Vivek QPM-9 Improved\u2019 , the first proA rich hybrid released in India. This is primarily due to extra-early maturity of \u2018Pusa Vivek QPM-9 Improved\u2019. Besides, two of the proA hybrids, \u2018Pusa HQPM5 Improved\u2019 and \u2018Pusa HQPM7 Improved\u2019 in the medium maturity groups have been recently released. Thus, these identified hybrids are higher yielding than the proA check hybrids as well. These selected hybrids also possessed higher proA than the normal best check (CoMH08-292 and DHM-121), but were crtRB1-donor was only 1.4t/ha, thereby suggesting its poor adaptability in subtropical conditions. The high grain yield of new crtRB1-based inbreds depicts better adaptability. The high yielding proA rich hybrids identified here would thus provide more productivity and profit to the farmers, and offer higher vitamin-A to the consumers [Further, parents of these proA rich hybrids also produce high yield from seed production perspective. The average grain yield among parental inbreds (used as lines) developed under this programme was 3.1t/ha with a range of 2.6\u20133.5t/ha. The same in onsumers . The procrtRB1-based inbreds have been developed in the study through marker-assisted pedigree breeding. These new inbreds possessed significantly higher proA than the checks. Molecular characterization of the inbreds depicted their diverse genetic nature. Genetic analysis revealed that both additive and non-additive variances were important. The crtRB1-based inbreds were successfully used in development of proA rich hybrids. Promising high yielding hybrids with very high concentration of proA have been identified. These proA rich hybrids are higher yielding than the exiting proA checks and at par with the normal checks in grain yield but with higher proA. The present study demonstrated the successful application of markers-assisted pedigree breeding in broadening the genetic base, and developing promising hybrids with higher grain yield as well as improved nutritional quality.Diverse S1 Tableopaque2 versions, TNAU: Tamil Nadu Agricultural University; ANGRAU: Acharya N. G. Ranga Agricultural University; PAU: Punjab Agricultural University.Q: Represents the (DOC)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table1. MGU-PVMAS-13, 2. PMI-PV-8, 3. PMI-PV-7, 4. MGU-PVMAS-6, 5. MGU-PVMAS-5, 6. MGU-PVMAS-11, 7. MGU-PVMAS-9, 8. MGU-PVMAS-4, 9. MGU-PVMAS-8, 10. MGU-PVMAS-15, 11. MGU-PVMAS-14, 12. MGU-PVMAS-7, 13. HP465-41, 14. PMI-PV-1, 15. MGU-PVMAS-3, 16. MGU-PVMAS-2, 17. MGU-PVMAS-12, 18. MGU-PVMAS-10, 19. HP704-22, 20. PMI-PV-6, 21. PMI-PV-9, 22. PMI-PV-5, 23. PMI-PV-2, 24. MGU-PVMAS-1, Inb. = Inbred.(DOCX)Click here for additional data file.S4 TableBC: \u03b2- Carotene, BCX: \u03b2-Cryptoxanthin, ProA: Provitamin A, LUT: Lutein, ZEA: Zeaxanthin, Non-ProA: Non-Provitamin A, TC: Total carotenoids, YLD: Yield.(DOCX)Click here for additional data file.S5 Table*Significant at p = 0.05; **Significant at p = 0.01, BC: \u03b2- Carotene, BCX: \u03b2-Cryptoxanthin, ProA: Provitamin-A, LUT: Lutein, ZEA: Zeaxanthin, Non-ProA: Non-Provitamin-A, TC: Total carotenoids, SE: Standard Error.(DOCX)Click here for additional data file.S6 Table*Significant at p = 0.05; **Significant at p = 0.01.(DOCX)Click here for additional data file.S1 File(DOCX)Click here for additional data file."} +{"text": "Coronavirus disease-2019 (COVID-19) is now an unprecedented worldwide pandemic. However, there are no specific antiviral drugs available for its treatment. A handful of studies have summarized convalescent plasma (CP) transfusion in severe or critical cases ,4,5,6, w9/L with 78% neutrophils, 9.2% lymphocytes, 2.3% basophils, 0.4% eosinophils, and 10.1% monocytes; hemoglobin of 51 g/L; platelet count of 79x109/L; high-sensitivity C-reactive protein of 57.43 mg/L; and interleukin-6 level of 59.25 pg/mL. The real-time polymerase chain reaction (RT-PCR) assay of the throat swab was positive for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. A chest CT obtained on February 21 revealed bilateral ground-glass opacities primarily distributed along the pleura starting in November 2017, but a drug-related hematologic adverse event occurred quickly. As a result, dasatinib (150 mg/day) was given instead. She had not achieved complete hematological remission at the diagnosis of COVID-19 due to poor responses to these therapies. At admission , the most relevant clinical findings included white blood cell count of 4.93x10e pleura and 1d. e pleura that expe pleura . RT-PCR e pleura accordin2) oscillating between 90% and 93%, after receiving conventional antiviral therapy including arbidol (200 mg three times daily), oseltamivir (75 mg twice daily), ribavirin (500 mg every 12 hours), and interferon-alpha-2b inhalation (5 million units twice daily). A follow-up chest CT scan showed increased consolidation and extended opacities . Three repetitive RT-PCR tests were negative from the 6th to 8th day after CP transfusion. Chest images showed absorption of opacities within 10 days (th\u00a0day of admission.The patient developed worsening hypoxemia, with oxyhemoglobin saturation (SaOpacities and 1e. 10 days and 1f. A recent study showed a 10% case rate of COVID-19 among 128 patients with hematological cancers in Wuhan . The tre"} +{"text": "Tepidicella baoligensis strain B18-50T, isolated from a high-temperature oil well in Baolige Oilfield, China. The estimated genome is 2.87\u2009Mb, with 2,653 protein-coding sequences.We report the draft genome sequence of Tepidicella baoligensis strain B18-50T, isolated from a high-temperature oil well in Baolige Oilfield, China. The estimated genome is 2.87\u2009Mb, with 2,653 protein-coding sequences.We report the draft genome sequence of Tepidicella species are slightly thermophilic Gram-negative rods that are distributed in geothermal areas. These organisms do not assimilate carbohydrates or polyols but use organic acids as carbon and energy sources and oxidize thiosulfate to sulfate in the presence of an assimilable carbon source in China. The liquid sample was diluted with sterilized enrichment medium (EN), plated onto EN agar, and incubated at 50\u00b0C , and 1.0 g liter\u22121 tryptone (Oxoid). Genomic DNA was prepared from an overnight culture by using the phenol-chloroform extraction method (Strain B18-50 at 50\u00b0C . A pure 2 medium supplemehttps://github.com/aquaskyline/SOAPdenovo2) libraries were prepared from the sheared fragments using the NEXTflex rapid DNA-Seq kit and sequenced in 150-bp paired-end mode using the Illumina HiSeq X Ten platform at Majorbio Bio-Pharm Technology, Inc. . The sequencing generated 3,449,944 pairs of raw reads totaling 1,041,883,088\u2009bp, giving approximately 362\u00d7 coverage. The reads were quality trimmed with Trimmomatic v0.36 (http://ccb.jhu.edu/software/glimmer/index.shtml) (http://trna.ucsc.edu/software/) (https://github.com/tseemann/barrnap) was used for rRNA prediction. The predicted CDSs were annotated from the nonredundant (NR), Swiss-Prot, Pfam, GO, COG, and KEGG databases using the sequence alignment tools BLAST+ v2.3.0 was usedftware/) was used+ v2.3.0 , Diamond+ v2.3.0 , and HMM+ v2.3.0 . A totalJACCDB000000000; the raw reads are available under SRA accession number SRR12179937. This announcement represents the first version of the genome.This whole-genome shotgun sequencing project has been deposited in DDBJ/ENA/GenBank under the accession number"} +{"text": "Orthobunyavirus, family Peribunyaviridae) is an arthropod-borne virus that causes congenital abnormalities in ruminants. Here, we report the complete genome sequences of two AKAV strains causing nonsuppurative encephalomyelitis in cattle by postnatal infection in Japan.Akabane virus (AKAV) is an arthropod-borne virus that causes congenital abnormalities in ruminants. Here, we report the complete genome sequences of two AKAV strains causing nonsuppurative encephalomyelitis in cattle by postnatal infection in Japan.Akabane virus (AKAV) (genus Akabane orthobunyavirus . Since it was first isolated from mosquitos in Gunma, Japan, in 1959, it has been widely detected in Australia, Asia, and Africa (Culicoides spp.) and causes spontaneous abortions, stillbirths, and congenital malformations in pregnant ruminants (Akabane virus (AKAV) is an enveloped, tripartite, negative-sense RNA virus of the species AKAV strains are clustered into four genogroups based on phylogenetic analysis of their medium (M) segments , 2. Genohttps://jorgensen.biology.utah.edu/wayned/ape), with the OBE-1 strain (the genogroup II strain that is the progenitor of the vaccine strain used in Japan) as the reference .Both virus strains were propagated in HmLu-1 cells. Their genomic RNA was extracted using the QIAamp virus RNA minikit . Reverse transcription-PCR was performed using SuperScript IV reverse transcriptase and PrimeSTAR GXL DNA polymerase . Primer sequences are available on request. The 5\u02b9- and 3\u02b9-terminal sequences of all of the genomic RNA segments were determined using 5\u2032 and 3\u2032 rapid amplification of cDNA ends (RACE) . The seqThe full-length S, M, and L segments of KM-2/Br/06 are 856, 4,309, and 6,869 nucleotides (nt), respectively, whereas those of FI-1/Br/06 are 867, 4,308, and 6,867\u2009nt, respectively. The GC contents of the segments were also determined . The nucThe sequences determined in this study will be useful in identifying the virulence factors implicated in bovine postnatal encephalomyelitis.LC552047.1 (KM-2/Br/06 S segment), LC552048.1 (KM-2/Br/06 M segment), LC552049.1 (KM-2/Br/06 L segment), LC552050.1 (FI-1/Br/08 S segment), LC552051.1 (FI-1/Br/08 M segment), and LC552052.1 (FI-1/Br/08 L segment).The sequences are available in GenBank under the accession numbers"} +{"text": "Correction to: BMC Rheumatol 4, 4 (2020)https://doi.org/10.1186/s41927-019-0105-4Following publication of the original article , the autThe original article has been updated.AbstractResults: In those without DM GC use had a 4.4-fold increased all-cause mortality RR : 3.77 to 5.07) compared to non-use, whilst those with DM had a lower RR for GC use ). However, those with DM had a higher RD associated with GC use because of their higher baseline risk. In those with DM, GC use was associated with an additional 44.9 deaths/1000 person-years (pyrs) (95% CI: 32.9 to 56.8) compared to non-use, while in those without DM GC use was associated with an additional 34.4 deaths/1000 pyrs (95% CI: 30.1 to 38.7). A similar pattern was seen for CV mortality. The adjusted Cox proportional hazards model showed no evidence of multiplicative interaction, but additive interaction indicated a non-significant increased risk. For CV mortality there was no interaction on either scale.In the \u201cAll-cause mortality\u201d sub-section it now correctly reads \u201cDuring follow-up there were 1005 deaths\u201d rather than 1002 deaths."} +{"text": "Background: Cancer treatments induce symptoms/signs superimposing on individual patient's clinical status, determining heterogenous toxicity syndromes (TS). We reviewed intensive first line triplet chemotherapy-based regimens in metastatic gastro-intestinal cancers (mGI), based on FIr/FOx schedule, fluorouracil and weekly alternating irinotecan/oxaliplatin, to point out limiting TS (LTS) relevance.Methods: Metastatic colo-rectal (mCRC), pancreatic ductal adenocarcinoma (mPDAC), gastric carcinoma (mGC) patients were enrolled by careful decision-making including age, performance status (PS), and comorbidity status in real life phase II studies: FIr-B/FOx adding bevacizumab (B) overall, FIr-C/FOx-C adding cetuximab (C) in KRAS/NRAS wild-type mCRC; FIr/FOx in mPDAC; FD/FOx adding docetaxel (D) in mGC. Toxicity, individual LTS, LT alone or associated to other limiting/G2 toxicities were evaluated, compared by chi-square test. In FIr-C/FOx-C, 5-fluorouracil/irinotecan pharmacogenomic biomarkers, 5-fluorouracil degradation rate (5-FUDR), SNPs ABCB1, CYP3A4, DYPD, UGT1A1 were evaluated, related with LTS.Results: FIr-B/FOx, FIr-C/FOx-C in mCRC, FIr/FOx in mPDAC, FD/FOx in mGC, showed activity, efficacy, toxicities similar to reported triplet regimens. LTS: mCRC FIr-B/FOx 44%, LTS-ms 24%, LTS-ss 20%, in young-elderly 46%, LTS-ms significantly increased vs. LTS-ss; FIr-C/FOx-C 65.5%, significantly increased LTS-ms vs. LTS-ss, in young-elderly 83%; mPDAC FIr/FOx 27.5%, mostly LTS-ms, in young-elderly 38.4% all LTS-ms; mGC FD/FOx 30%, all LTS-ms, in young-elderly 25%. Reduced FUDR, SNPs CYP3A4, UGT1A1, >1 positive pharmacogenomic biomarkers were prevalent in patients with gastrointestinal LTS.Conclusions: LTS is an innovative clinical parameter of toxicity burden, differential treatment-related TS in individual patient. LTS can evaluate pharmacogenomic biomarkers predictive relevance to select mGI patients fit for intensive treatments, at risk of limiting gastrointestinal toxicity.Trial Registrations: The trials were registered at Osservatorio Nazionale sulla Sperimentazione Clinica dei Medicinali (OsSC) Agenzia Italiana del Farmaco (AIFA) Numero EudraCT 2007-004946-34, and Osservatorio Nazionale sulla Sperimentazione Clinica dei Medicinali (OsSC) Agenzia Italiana del Farmaco (AIFA) Numero EudraCT 2009- 016793-32. Addition of more drugs in a chemotherapy combination requires the design of proper schedule and doses, to provide the balance between projected/received (>80%) dose intensity (DI) and treatment-related toxicity . This clThe conventional evaluation of toxicity of cancer treatments depends upon grading of the clinical relevance of each toxicity symptom and sign, by evaluation of the type, prevalence and intensity of toxicity, more specifically of limiting G3-4) toxicity, related to the administered treatment regimen, and determined by National Cancer Institute Common Toxicity Criteria . Thus, safety profile and toxicities induced by cancer treatments are conventionally defined, according to the number of administered cycles and treated patients, as severe (G3-4), moderate G2), mild (G1), or absent. This evaluation does not individually describe the toxicity burden experienced in a single patient, defining a spectrum of toxicity syndromes (TS). To better evaluate individual toxicity of intensive treatments, we introduced the concept of Limiting Toxicity Syndromes (LTS), consisting of at least a limiting toxicity alone or associated to other limiting or G2-3 non-limiting toxicities 66.7%, progression-free survival (PFS) 12 months, and overall survival (OS) 20 months as first line mCRC treatment. Thus, we developed intensive first line regimens, based on FIr/FOx triplet chemotherapy schedule: FIr-B/FOx (We previously developed doublet chemotherapy schedule of 12 h (10 p.m. to 10 a.m.) timed-flat infusion (TFI) 5-FU , associaIr-B/FOx , respectIr-B/FOx ; FD/FOx Ir-B/FOx .Patients treated with triplet chemotherapy-based regimens were enrolled by decision-making process including age, performance status (PS), and comorbidity status evaluated by Cumulative Illness Rating Scale (CIRS) . CIRS stin label for treatment in Italian public hospitals, and published in Gazzetta Ufficiale Repubblica Italiana . MCRC clinical trials were approved by Local Ethical Committee , and conducted in accordance with Declaration of Helsinki. PDAC study was approved by the Regional Review Board . All patients provided written, informed consent concerning the proposed treatment, and biological evaluations.Proposed regimens were approved by Agenzia Italiana del Farmaco for administration 2, days 1\u20132, 8\u20139, 15\u201316, 22\u201323; CPT-11 160 mg/m2 days 1,15; OXP 80 mg/m2, days 8, 22; every 4 weeks; B 5 mg/kg, days 1,15. In KRAS/NRAS wild-type mCRC, FIr-C/FOx-C . In mGC, FD/FOx week week2, dschedule 11): TF: TF2, da, FD/FOx 14): TF: TF2, da6 cells/min, and Single Nucleotide Polimorphisms (SNPs) ABCB1 , CYP3A4 , DYPD1 , UGT1A1 (28) were preliminarily related with the occurrence of LTS . To better evaluate toxicity of intensive treatments in the individual patient, LTS, consisting of at least a limiting toxicity alone (LTS-ss) or associated to other limiting or G2-3 non-limiting toxicities (LTS-ms) were evaluated , 14, 20.e of LTS , 25.2, respectively per cycle for all the drugs at the recommended doses were \u226580% (2/w); CPT-11 76% (45.5 mg/m2/w); OXP 66% (26.5 mg/m2/w); C 71% (178.5 mg/m2/w); yE patients showed significantly worse OS compared to non-elderly (P 0.045) . . 2, respP = 0.022). In mPDAC patients treated with FIr/FOx, median rDI per cycle were: 5-FU 70.4% (1268.5 mg/m2/w); CPT-11 70% (56 mg/m2/w); OXP 72.5% (29 mg/m2/w). In yE, 5-FU 83.3%, CPT-11 80%, OXP 85%. Overall, 17% discontinued FIr/FOx treatment due to LT. Limiting cumulative G3-5 toxicities were: diarrhea 17%, asthenia 14%, neutropenia 17%, mucositis 6%, hypokaliemia 7%, hypertransaminasemia 7%, nausea/vomiting, hypoalbuminemia, anemia, thrombocytopenia 3%, respectively. One case of toxic death (3%) was observed.In mPDAC patients, FIr/FOx showed ORR 53%, PFS 4 months, OS 11 months; among yE/old-elderly patients, median PFS 4 months, and median OS 5 months ; D 91% (22.75 mg/m2/week); OXP 83.8% (33.5 mg/m2/week). Cumulative G3-4 toxicities were represented by: asthenia 20%, neutropenia 50%, leucopenia 20%, mucositis and hypoalbuminemia 10%.In mGC patients, FD/FOx at recommended 5-FU 1000 mg/m7 months . Median KRAS/NRAS wild-type mCRC patients treated with FIr-B/FOx, overall LTS were observed in 22 patients (44%) (P 0.05). LTS were prevalently characterized by G2-3 diarrhea, 9 patients (69.2%), 8 LTS-ms and 1 LTS-ss. The 2 LTS-ms with double LT were observed in yE patients. The 10 LTS-ms, defined by LT added to other, at least G2, non-limiting toxicities, were prevalently determined by G2-3 diarrhea (90%), plus G2-3 nausea/vomiting (70%). The 10 LTS-ss were prevalently characterized by G3 diarrhea (50%), G3 asthenia, hypertension, hypertransaminasemy, neutropenia, thrombocytopenia 10%, respectively.In ts (44%) : LTS-ms ts (44%) . LTS-ms KRAS/NRAS wild-type mCRC patients treated with FIr-C/FOx-C, LTS were observed in 19 patients (65.5%), 5 out of 6 yE (83%): LTS-ms 17 (59%), LTS-ss 2 (7%) (P 0.006). LTS-ms characterized by \u22652 LT 7 (24%); LT associated to other toxicities 10 (34%). LTS were prevalently characterized by G3-4 diarrhea and G3 asthenia associated to other toxicities.In s 2 (7%) . LTS werIn mPDAC patients treated with FIr/FOx, overall LTS were 8 (27.5%); 5 out of 13 yE/old-elderly (38.4%); LTS-ms 7 (24.1%), LTS-ss 1 (3.4%) . LTS-ms CYP3A4, UGT1A1, and >1 positive pharmacogenomic biomarkers. Specifically, the exploratory analysis of 5-FUDR reduction and ABCB1, CYP3A4, DYPD, UGT1A1 SNPs evaluated in 14 KRAS/NRAS wild-type mCRC patients (48.3%) treated with FIr-C/FOx-C .Furthermore, the analysis of SNPs represented an exploratory analysis in colorectal cancer patients treated with intensive triplet chemotherapy plus cetuximab, according to FIr-C/FOx-C schedule, to better evaluate the safety profile, particularly gastrointestinal. Patients who reported gastrointestinal LTS, prevalently showed reduced fluorouracil degradation rate (FUDR), Single Nucleotide Polimorphisms (SNP) -C/FOx-C , 25, andOver the past 10 years, we developed intensive triplet chemotherapy-based regimens in fit mGI cancer patients , 11, 14,KRAS/NRAS wild-type mCRC , to obtain the description of cumulative and prevalent limiting (G3-G4), moderate (G2), mild (G1), or absent toxicities directly determined by the cancer treatment, according to the number of administered cycles and treated patients. This way does not really represent the clinical burden of toxicity in the individual patient, nor define prevalent individual TS affecting a patient population equivalently treated and their variability. Thus, in reported intensive first line triplet chemotherapy-based regimens developed in mGI cancer patients, we added the description of individual TS, and specifically of LTS, to describe cumulative and individual toxicity, that include differential spectrum and intensities of TS, depending from medical treatment and patients' individual clinical conditions.The integration of the evaluation of LTS to the conventional treatment-related toxicity, contributed a patient-related clinical indicator of toxicity burden, providing a global evaluation of patient-related limiting toxicity , 14, 20:In yE patients, LTS evaluation showed the differential tolerability of intensive triplet chemotherapy based regimens: in mCRC, FIr-B/FOx LTS 46%, but significantly prevalent LTS-ms , 27; FIrKRAS/NRAS wild-type MCRC patients treated with FIr-C/FOx-C showed that reduced 5-FUDR, and CYP3A4 and UGT1A1 SNPs may predict individual LTS occurrence, particularly at recommended doses, specifically gastrointestinal LTS and in 9 who showed LTS (47.4%), exploratory data of pharmacogenomic biomarkers compared with LTS occurrence in Thus, LTS meets the need of an innovative clinical parameter of patient-related toxicity burden, to measure personalized safety of intensive first line triplet chemotherapy-based regimens proposed in mGI, also associated to targeted agents (B or C). Its clinical relevance should be prospectively evaluated as a model in clinical practice. The integration of LTS and conventional toxicity evaluations may help proper selection of patients fit for intensive first line medical treatments in mGI cancers, to more properly weigh toxicity analysis with activity and clinical outcome and its contribution to address selection of patients suitable for intensive triplet chemotherapy-based regimens. The equivalent, integrated evaluation and monitoring of individual safety by LTS, can help properly select first line intensive medical treatment, and safely administer and manage an intensive first line regimen, that could guarantee increased clinical outcomes and good safety profile in real life.In the era of precision oncology, integrating molecular characterization of cancer affecting the individual patient to specifically address targeted treatments, such as in mCRC \u201332, the Analysis of TS could be integrated in the therapeutic pathway of cancer patients in clinical practice and in clinical studies to globally evaluate tolerability of cancer treatments. It could be, also, particularly useful for a more proper evaluation of tolerability in the therapeutic pathway of individual cancer patients unfit for standard treatments, due to elderly status and/or their clinical status, or unfit for intensive regimens , 34, to More, in intensive regimens such as FIr-C/FOx-C, characterized by high discontinuation rate of treatment, highly prevalent (>50%) LTS and heterogeneity of LT, LTS may help directly relate individual patient- and drugs-related toxicity with pharmacogenomics biomarkers referred to the individual genetic identity of the cancer patient.TS, specifically LTS, represents an innovative clinical parameter of cumulative and individual patient-related toxicity burden, defining differential spectrum and intensities of treatment-related TS, depending from the clinical status of the individual cancer patient, particularly according to elderly, and PS.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation, to any qualified researcher.Proposed regimens were approved by Agenzia Italiana del Farmaco for administration in label for treatment in Italian public hospitals, and published in Gazzetta Ufficiale Repubblica Italiana . MCRC clinical trials were approved by Local Ethical Committee , and conducted in accordance with Declaration of Helsinki. PDAC study was approved by the Regional Review Board . All patients provided written, informed consent concerning the proposed treatment, and biological evaluations.GB contributed in conceptualization, data curation, formal analysis, investigation, methodology, project administration, validation, and writing original draft. ER contributed in conceptualization, data curation, formal analysis, investigation, methodology, project administration, supervision, validation, and writing\u2014review original draft.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Populus trichocarpa) upon infection with the generalist root pathogen Phytophthora cactorum (Oomycetes). P. cactorum infection led to an induced accumulation of terpenes, aromatic compounds, and fatty acids in poplar roots. Transcriptome analysis of uninfected and P. cactorum-infected roots revealed a terpene synthase gene PtTPS5 that was significantly induced upon pathogen infection. PtTPS5 had been previously reported as a sesquiterpene synthase producing two unidentified sesquiterpene alcohols as major products and hedycaryol as a minor product. Using heterologous expression in Escherichia coli, enzyme assays with deuterium-labeled substrates, and NMR analysis of reaction products, we could identify the major PtTPS5 products as -guaia-4(15)-en-11-ol and -guaia-4-en-11-ol, with the former being a novel compound. The transcript accumulation of PtTPS5 in uninfected and P. cactorum-infected poplar roots matched the accumulation of -guaia-4(15)-en-11-ol, -guaia-4-en-11-ol, and hedycaryol in this tissue, suggesting that PtTPS5 likely contributes to the pathogen-induced formation of these compounds in planta.Pathogen infection often leads to the enhanced formation of specialized plant metabolites that act as defensive barriers against microbial attackers. In this study, we investigated the formation of potential defense compounds in roots of the Western balsam poplar ( Plants are constantly under attack from a multitude of pests, including pathogens and herbivores. Such biotic stresses often induce the formation of specialized plant metabolites that play major roles in plant defense. Terpenoids represent the largest class of natural compounds, and to date, more than 200,000 terpenoids are known, of which ~40,000 can be produced by plants . Beside 10), -farnesyl diphosphate , and -geranylgeranyl diphosphate . The prenyl diphosphates are substrates for terpene synthases (TPS), which catalyze the formation of the basic mono-(C10), sesqui-(C15), and diterpene (C20) skeletons D20 = +47.8 . HRMS (EI): m/z = 222.1978 . GC (HP5-MS): I = 1660. MS : m/z (%) = 222 (0.3), 204 (29), 189 (24), 175 (2), 161 (24), 149 (22), 133 (11), 121 (19), 107 (31), 91 (41), 81 (54), 67 (25), 59 (100), 53(13), 41 (35). IR (diamond ATR): /cm\u20131 = 2953 (m), 2923 (s), 2854 (m), 1714 (w), 1650 (w), 1456 (m), 1376 (m), 1260 (m), 1094 (s), 1020 (s), 873 (m), 800 (s).-Guaia-4-en-11-ol (2). Yield: 0.6 mg . TLC (pentane/ether = 4:1): Rf = 0.21. Optical rotation: [\u03b1]D20 = +21.7 . HRMS (EI): m/z = 222.1975 . GC (HP5-MS): I = 1661. MS : m/z (%) = 222 (4), 204 (81), 189 (69), 175 (7), 161 (75), 147 (27), 133 (29), 119 (37), 105 (61), 91 (81), 79 (68), 67 (30), 59 (100), 51(5), 41 (55). IR (diamond ATR): /cm\u20131 = 2954 (s), 2923 (s), 2854 (s), 1723 (w), 1670 (w), 1459 (m), 1376 (m), 1260 (w), 1096 (w), 1025 (w), 800 (w).S,5S,7R,10R)-guaia-4(15)-en-11-ol and -guaia-4-en-11-ol. For the reactions with DMAPP (1 mg in 1 mL water) and (Z)-IPP or (E)-IPP (1 mg in 1 mL water), protein preparations of PtTPS5 (1 mL) and FPPS and incubation buffer (6 mL) were added. For the reactions with (R)-IPP or (S)-IPP (1 mg in 1 mL water), protein preparations of PtTPS5 (1 mL), FPPS and incubation buffer (6 mL) were added. After incubation with shaking at 28 \u00b0C overnight, the reaction mixtures were extracted with C6D6, the extracts were dried with MgSO4 and analyzed by NMR and GC-MS.Isotopic labelling experiments were performed to determine the absolute configurations of , MgCl2 S , IDI , MgCl2 Throughout the manuscript, data are presented as means \u00b1 SE. Statistical analysis was performed with SigmaPlot 11.0 for Windows and is described in the figure and table legends for the respective experiments. Whenever necessary, the data were log transformed to meet statistical assumptions such as normality and homogeneity of variances.Raw reads of the RNAseq experiment were deposited in the NCBI Sequence Read Archive (SRA) under the BioProject accession PRJNA660564 \u2018Oomycete-induced changes in the root transcriptome of poplar\u2019."} +{"text": "T (Collection de Souches de l\u2019Unit\u00e9 des Rickettsie CSUR P6417\u2009=\u2009Colecci\u00f3n Espa\u00f1ola de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp\u2013long with a G\u2009+\u2009C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter schmidteae sp. nov.Pedobacter schmidteae sp. nov. strain EG Schmidtea mediterranea is an invertebrate living in environmental water. This flatworm is used as a model of development, because of its extraordinary abilty to regenerate after amputation, because of his high contents in stem cells known as neoblasts1. It has been shown that S. mediterranea is an excellent model to investigate host-pathogen relationships3, notably in the context of human pathogens. To date, the gut microbiota of S. mediterranea remains poorly studied5. Using the microbial culturomics approach6, we investigated the S. mediterranea microbiota. Culturomics is a concept in which diversified culture conditions are used to enable isolation of a maximum of bacterial species from the human microbiota10. During this analysis, we isolated a bacterial strain from S. mediterranea that could not be identified using Matrix Assisted Laser Desorption-Ionisation Time of Flight-Mass Spectrometry (MALDI-TOF-MS). We used the taxono-genomics strategy that combines phenotypic assays and genome sequencing to further characterize this bacterium14. This enabled us to describe a new bacterial strain that exhibited enough genetic and phenotypic differences with closely related bacteria. We propose it as a new species named Pedobacter schmidteae sp. nov.Schmidtea mediterranea asexual clonal line ClW42 is a laboratory planarian strain that has been preserved in our laboratory for the past 10 years, by cutting animals in tree fragments each month. S. mediterranea were kept in the dark, in filtered tap water, at 19\u2009\u00b0C without antibiotics. The animals were fed once per week with homogenized calf liver and were starved for at least two weeks prior to studying them. Filtered water was obtained using a device consisting of two 0.2\u2009\u00b5m filters, one containing charcoal and ceramics , and the other being a 0.20\u2009\u00b5m membrane . Filtered water was checked for sterility prior to be used for planarian culture.S. mediterranea were washed in filter-sterilized water and then one ground worm was inoculated in Buffered Charcoal Yeast Extract (BCYE) , Luria Bertani (LB) and 5% sheep blood-enriched Columbia agar . All inoculated media were incubated at 19, 28 and 37\u2009\u00b0C. Each individual bacterial colony was harvested and identified by MALDI-TOF-MS 15. The obtained spectra were imported into the MALDI Biotyper 3.0 software and analysed against the reference spectra of bacteria included in the database (Bruker database constantly updated with the Mediterranee-Infection database (http://www.mediterranee-infection.com/article.php?larub=280&titre=urms-database). The MALDI Biotyper RTC software was used to interpret the results according to the obtained score values: a colony was likely identified at the species level for a score > 2.0, probably identified for a score between 1.99 and 1.7, but not identified for a score <1.7.Following two weeks of starvation, https://www.codoncode.com/). For taxonomic assignation, a BLASTn search was performed against the nr database16. A sequence similarity threshold of 98.65% by comparison with the phylogenetically closest species with standing in nomenclature was used to delineate a putative new species17. Phylogenetic relationships were inferred from the comparison of 16S rRNA sequences using the MEGA7 software18.Bacterial colonies that were not identified at the species level using MALDI-TOF MS were further tested using 16S rRNA sequencing. Genomic DNA was extracted using an EZ1 automate and the DNA tissue kit . The complete 16S rRNA gene amplification and sequencing was performed using eight primers on an ABI Prism 3130xl Genetic Analyzer capillary sequencer . The primers used were Fd1 (5\u2032-AGAGTTTGATCCTGGCTCAG-3\u2032), Rp2 (5\u2032-ACGGCTACCTTGTTACGACTT-3\u2032), F536 (5\u2032-CAGCAGCCGCGGTAATAC-3\u2032), R536 (5\u2032-GTATTACCGCGGCTGCTG-3\u2032), F800 (5\u2032-ATTAGATACCCTGGTAG-3\u2032), R800 (5\u2032-CTACCAGGGTATCTAAT-3\u2032), F1050 (5\u2032-TGTCGTCAGCTCGTG-3\u2032) and R1050 (5\u2032-CACGAGCTGACGACA-3\u2032) . The CodonCode Aligner software was used for sequence alignment, assembly and correction (strain EG and P. nyackensis strain NWG-II14T (DSM19625) was attempted at various growth temperatures in 5% sheep blood-enriched Columbia agar (bioM\u00e9rieux) under anaerobic, aerobic and microaerophilic atmospheres using GasPak\u2122 EZ generators . Sporulation was tested by thermal shock, which consists in exposing bacteria to a temperature of 80\u2009\u00b0C for 30\u2009minutes and then monitoring their growth for 4 days. Various salinity and pH conditions were tested. Gram staining and motility from fresh colonies were observed using a DM1000 photonic microscope with a 40 \u00d7 objective lens. Catalase and oxidase activities were tested by using a BBL DrySlide according to the manufacturer\u2019s instructions . The size of bacterial cells was measured using transmission electron microscopy. API strips were used to study the biochemical characteristics of the strains. Bacterial susceptibility to benzylpenicillin, amoxicillin, ampicillin, ceftriaxone, imipenem, ciprofloxacin, amikacin, gentamicin, streptomycin, daptomycin, doxycycline, metronidazole, rifampicin, and vancomycin was assessed using E-tests and a 0.5 McFarland concentration of strains EG and NWG-II14T. Cellular fatty acid methyl ester (FAME) analysis was performed by GC/MS. Two samples were prepared with approximately 120\u2009mg of bacterial biomass per tube harvested from several culture plates. Fatty acid methyl esters were prepared as described by Sasser30 and GC/MS analysis was carried out as previously described31. Briefly, FAMES were separated using an Elite 5-MS column and monitored by mass spectrometry . Spectral database search was performed using MS Search 2.0 operated with the following Standard Reference Database 1\u2009A and FAMEs mass spectral database .Culture of strain 32. Briefly, sequencing was performed using the Mate-Pair strategy and a Miseq sequencer . A concentration of 1.5\u2009\u03bcg of gDNA prepared following the Nextera Mate-Pair Illumina guide was used to prepare the Mate-Pair library. The gDNA was simultaneously fragmented and tagged using a Mate-Pair junction adapter. Then the fragmentation pattern was validated using a DNA 7500 labchip on a BioAnalyzer . The size of the DNA fragments ranged from 1.5\u2009kb to 11\u2009kb. No size selection was performed and 662\u2009ng of labelled fragments were circularized. Next, circularized DNA was mechanically sheared using a Covaris device S2 into small fragments with an optimal size at 1200\u2009bp. The library profile was analysed on a High Sensitivity Bioanalyzer LabChip (Agilent Technologies) and the concentration library was measured at 61.4 nmol/l. Then, the library was loaded on the sequencer after a denaturation step and a dilution at 15 pM. Automated cluster generation and sequencing were performed in a single 39-h run in a 2\u2009\u00d7\u2009251-bp and sequencing reads were assembled using the A5 pipeline. Genomic annotation was obtained using the Prokka software. A search for virulence factors was performed by comparaison with the VFDB database (http://www.mgc.ac.cn/VFs/) using BLASTn34.The bacterial genomic DNA (gDNA) of strain EG was extracted using an EZ1 automate and the DNA tissue kit and then was quantified using a Qubit assay at 82.6\u2009ng/\u03bcL. The bacterial gDNA was prepared and sequenced as previously describedPedobacter africanus strain DSM 12126\u2009T (NZ_FWXT00000000.1), P. antarcticus strain 4BYT (NZ_JNFF00000000.1), P. ginsengisoli strain T01R-27 (NZ_CP024091.1), P. heparinus strain DSM 2366\u2009T (NC_013061.1), P. nutrimenti strain DSM 27372 (NZ_QKLU00000000.1), P. nyackensis strain DSM 19625 (NZ_FWYB00000000.1), P. panaciterrae strain 048 (NZ_LGEL00000000.1) and P. steynii strain DX4 (NZ_CP017141.1). Degrees of genomic similarity between strain EG and compared genome were evaluated using the GGDC (http://ggdc.dsmz.de/ggdc.php#)16 and Orthologous Average Nucleotide Identity (Ortho-ANI) (https://www.ezbiocloud.net/tools/orthoani)35 softwares.The genome from strain EG was compared to those of Pedobacter nyackensis strain NWG-II14T with which it exhibited a sequence similarity of 98.29%. When compared to other Pedobacter species, strain EG exhibited 16S rRNA similarity values of 97.84%, 97.69%, 97.63%, 97.93%, 97.43%, 97.28%, 97.33%, 97.62%, 97.93%, 97.32%, 97.32% and 97.0% with P. heparinus strain DSM 2366\u2009T, P. steynii strain WB2.3\u201345\u2009T, P. metabolipauper strain WB2.3\u201371\u2009T, P. nutrimenti strain J22T, P. duraquae strain WB2.1\u201325\u2009T, P. africanus strain NBRC 100065\u2009T, P. panaciterrae strain Gsoil 042\u2009T, P. ginsengisoli strain Gsoil 104\u2009T, P. seoulensis strain THG-G12T, P. trunci strain THG-DN3.19\u2009T, P. humi strain THG S15\u20132T and P. antarcticus strain 4BYT\u200940, respectively .Strain EG was isolated on 5% sheep blood-enriched Columbia agar (bioM\u00e9rieux) after 2 days at 28\u2009\u00b0C in aerobic atmosphere at pH 7. The 16S rRNA-based phylogenetic tree demonstrated that strain EG was most closely related to S. mediterranea revealed the presence of strain EG in 11 S. mediterranea sp. nov. Strain EG is a member of the family Sphingobacteriaceae within the phylum Bacteroidetes(Table\u00a01).The analysis of 13 , rod-shaped, motile, and non-spore-forming bacilli. Using the Image J software, their mean length and width were 1.98\u2009\u00b5m and 0.69\u2009\u00b5m, respectively , without any flagellum. For the two strains EG and P. nyackensis NWG-II14T, no growth was obtained in anaerobic or microaerophilic conditions. Both strains grew at temperatures ranging from 6 to 30\u2009\u00b0C in aerobic atmosphere at pH values ranging from 5.5 to 9; the strains also grew at salinity concentrations lower than 25\u2009g/L. Catalase and oxidase activities were positive for both strains.After 4 days of culture on blood-enriched Columbia agar, colonies from strain EG were small (0.4\u2009mm of diameter), transparent, round with a convex shape and smooth. Bacterial cells were Gram-negative Fig.\u00a0, rod-shaely Fig.\u00a0, withoutP. nyackensis strain NWG-II14T were susceptible to benzylpenicillin, ampicillin, ceftriaxone, imipenem, gentamicin, doxycycline and rifampicin (Table\u00a0). Both strains were resistant to amoxicillin, amikacin, daptomycin, metronidazole and vancomycin. Pedobacter nyackensis, but not P. schmidteae, was susceptible to ciprofloxacin and streptomycin.Strain EG and in Table\u00a0. Both stP. nyackensis NWG-II14T, strain EG differed by exhibing of Esterase (C4), Esterase lipase (C8), Valine arylamidase, \u03b2-galactosidase and \u03b2-glucosidase activities (Table\u00a0). By comparaison with all other tested species, strain EG differed in production of esterase (C4) and \u03b2-glucosidase.Positive and negative reactions obtained using API 50CH, API 20NE, API Zym, and API 20E strips are presented in Table\u00a0es Table\u00a0. By comp(Table\u00a0). 15-methyl-Hexadecenoic acid, 14-Methylpentadec-9-enoic acid is detected only in strain EGT. In contrast to P. nyackensis NWG-II14T, the strain EG have in its membrane composition the 3-hydroxy-Hexadecanoic acid, 13-methyl-Tetradecanoic acid, 3-hydroxy-13-methyl-Tetradecanoic acid, 3-hydroxy-15-methyl-Hexadecanoic acid, 15-methyl-Hexadecenoic acid and 14-Methylpentadec-9-enoic acid; and for the absence of Dodecanoic acid, 3-hydroxy-8-methyl-nonanoic acid, 9-Heptadecenoic acid, 9-Octadecenoic acid.The analysis of the composition in fatty acid of the strain EG revealed that the major fatty acids were 13-methyl-tetradecanoic acid 49.8%), 9-Hexadecenoic acid (27.7%) and 3-hydroxy-15-methyl-Hexadecanoic acid (7.5%). Other fatty acids included 15-methyl-Hexadecenoic acid (3.6%), 14-Methylpentadec-9-enoic acid (3.4%), Hexadecanoic acid (3.3%), 3-hydroxy-13-methyl-Tetradecanoic acid (1.9%), Tetradecanoic acid (1.4%) and 3-hydroxy-Hexadecanoic acid (1.0%). Minor amounts (<1%) of the fatty acids were also detected as Pentadecanoic acid and 9,12-Octadecadienoic acid 9.8%, 9-H\u22123) and a score of 52 with the GacS [GacS/GacA two-component system]42 sensor histidine kinase/response regulator in Pseudomonas putida strain KT2440 according to the VFDB database. It has been reported that the two-component system signaling pathways are the major signaling mechanisms in bacteria and as well in Archaea43 to monitor external and internal stimuli 44. This pathway is also found in simple eukaryota and higher plants45. In opportunistic bacterial pathogens, the use of two-components systems is required to regulate the expression of genes necessary for the transition from the environmental reservoir to the host46. Digital DNA-DNA hybridization values (dDDH) obtained using the GGDC software are reported in Table\u00a0P. nutrimenti to 21.50% with P. nyackensis. Such values were lower than the 70% threshold recognized to delineate distinct species. Similarly, Ortho-ANI values ranged from 70.98% with P. nutrimenti to 74.65% with P. nyackensis, which is lower than the 95% threshold used to discriminate bacterial species. Thus, we could confirm that strain EG belonged to a separate Pedobacter species for which we propose the name Pedobacter schmidteae sp. nov.The genome sequence from strain EG was assembled into one contig of 6,198,518\u2009bp with a G\u2009+\u2009C content of 41.13%. We identified a total of 5,012 predicted protein-coding genes, in addition to 3 complete rRNA operons, 52 tRNAs and 1 tmRNA. Comparison of these genomic data with those from of closely related species is presented in Table\u00a0P. schmidteae sp. nov. Interestingly, P. schmidteae sp. nov. is present in 84.6% of S. mediterranea worms tested. To best of our knowledge, P. schmidteae sp. nov has never been identified anywhere else than in S. mediterranea. Indeed, no nucleotide sequence linked to this new strain has been found in the nr database (BLASTn https://blast.ncbi.nlm.nih.gov). To date, we assume that P. schmidteae sp. nov is unique to S. mediterranea, but we cannot exclude formally that it might be present in other living organisms of the environment.Using the taxono-genomic approach, we concluded that strain EG is the representative strain of the new species 47. Pedobacter schmidteae . The bacterium belongs to the family Sphingobacteriaceae within the phylum Bacteroidetes. The type strain EGT (CSUR P6417\u2009=\u2009CECT9771) was isolated on 5% sheep blood-enriched Columbia agar after 2 days at 28\u2009\u00b0C in aerobic atmosphere at pH 7 from the microbiota of the planarian S. mediterranea. Colonies are small, round, smooth, transparent and convex. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The main cellular fatty acids detected are 13-methyl-tetradecanoic acid (49.8%), 9-Hexadecenoic acid (27.7%), 3-hydroxy-15-methyl-Hexadecanoic acid (7.5%), 15-methyl-Hexadecenoic acid (3.6%), 14-Methylpentadec-9-enoic acid (3.4%), Hexadecanoic acid (3.3%), 3-hydroxy-13-methyl-Tetradecanoic acid (1.9%), Tetradecanoic acid (1.4%) and 3-hydroxy-Hexadecanoic acid (1.0%). We found traces (<1%) of Pentadecanoic acid and 9,12-Octadecadienoic acid.The protologue is to standardize the format of descriptions of new taxa, supported by the Judicial Commission of the International Committee on Systematic BacteriologyT exhibits positive reactions for catalase, oxidase, alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, acid phosphatase, Naphtol-AS-BI-phosphohydrolase, \u03b2-galactosidase, \u03b1-glucosidase, \u03b2-glucosidase, N-acetyl-\u03b2-glucosaminidase, esculin ferric citrate, glucose, D-mannose, N-Acetyl-glucosamine and D-maltose, but negative reaction for lipase (C14), cystine arylamidase, trypsin, \u03b1-chymotrypsin, \u03b1-galactosidase, \u03b2-glucuronidase, \u03b1-mannosidase, \u03b1-fucosidase.Using an APIZYM strip, strain EGT is unable to metabolize glycerol, starch, amygdalin, arbutin, D-adonitol, D-arabinose, D-arabitol, D-cellobiose, D-fructose, D-fucose, D-galactose, D-glucose, D-lactose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-saccharose, D-sorbitol, D-tagalose, D-trehalose, D-turanose, dulcitol, D-xylose, erythritol, gentiobiose, glycogen, inositol, inulin, L-arabinose, L-arabitol, L-fucose, L-rhamnose, L-sorbose, L-xylose, methyl-\u03b1D-Glucopyranoside, methyl-\u03b1D-Mannopyranoside, methyl-\u03b2D-xylopyranoside, potassium 2-CetoGluconate, potassium 5-Cetogluconate, potassium gluconate, salicin, xylitol.Using a API 50CH strip, strain EGT use potassium nitrate, L-tryptophane, L-arginine, urea, gelatin, D-mannitol, malic acid, phenylacetic acid, L-lysin, trinatriumcitrate, L-ormithin, Esculin ferric citrate, Glucose, D-mannose, N-Acetyl-glucosamine and D-maltose.In addition, strain EGT is 6,198,518 bp\u2013long with a G\u2009+\u2009C content of 41.13%.The genome of strain EGThe 16S rRNA gene and genome sequence are deposited in GenBank under accession numbers LS453293 and LS999839, respectively.Pedobacter schmidteae strain EGT is available at http://www.mediterranee-infection.com/article.php?laref=936The MALDI-TOF MS spectrum of T is TA00631 in the http://imedea.uib-csic.es/dprotologue/ website.The 16S rRNA gene sequence and genome sequence were deposited in GenBank under accession numbers LS453293 and LS999839, respectively. The Digital Protologue database Taxonumber for strain EGT was deposited in the CSUR (Collection de Souches de l\u2019Unit\u00e9 des Rickettsies WDCM 875) and CSCT (Colecci\u00f3n Espa\u00f1ola de Cultivos Tipo) strain collections under numbers CSUR P6417 and CECT9771, respectively.Strain EG"} +{"text": "Escherichia coli strain Tj, isolated from the Varzob River in Tajikistan, is presented. This strain possesses four prophage elements related to Shigella phage SfV, E. coli O157:H7-specific phage \u03d5V10, lambdoid phage HK225, and coliphage Ayreon. It contains a gene encoding a hemolysin E toxin.The 4.6-Mbp draft genome sequence of Escherichia coli strain Tj, isolated from the Varzob River in Tajikistan, is presented. This strain possesses four prophage elements related to Shigella phage SfV, E. coli O157:H7-specific phage \u03d5V10, lambdoid phage HK225, and coliphage Ayreon. It contains a gene encoding a hemolysin E toxin.The 4.6-Mbp draft genome sequence of Escherichia coli (Migula 1895) Castellani and Chalmers 1919 is a Gram-negative, facultatively anaerobic, enteric bacterium that inhabits the intestines of warm-blooded animals and humans and frequently contaminates environmental waters and food. E. coli strain Tj was isolated from the Varzob River in Tajikistan, during a laboratory course at the Center of Biotechnology of the Tajik National University, on Endo LES agar plates at 44\u00b0C as a dark-red colony and confirmed as E. coli by its API 20E profile (5-0-4-4-5-5-2). The 16S rRNA gene sequence, obtained by PCR amplification and Sanger sequencing as described elsewhere . The genome was sequenced at Eurofins Genomics using a NEBNext Ultra II DNA library preparation kit and Illumina HiSeq 2500 paired-end sequencing technology with a read length of 2 \u00d7 150\u2009bp, yielding 6,416,190 reads and 1,924,857,000 sequenced bases. Reads with a maximum of 7 bases with a Phred score below 28 were initially discarded, and additional quality control procedures were performed using the Trim Reads tool in the CLC Genomics Workbench v. 8.5.1. Unless otherwise stated, all software was used with default values. Assembly was performed using the CLC de novo assembly tool, resulting in 4,627,784\u2009bp of unique sequence data distributed into 96 contigs with an N50 value of 111,402\u2009bp, coverage of 417\u00d7, and GC content of 50.8%. The draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www.ncbi.nlm.nih.gov/genome/annotation_prok). Genome completeness was estimated as 99.96% by CheckM v. 1.0.18 values of\u2009\u226597.0% (http://www.mgc.ac.cn/VFs) (E. coli phage Ayreon (P-1) (Shigella flexneri (P-2) (NC_019717), and phage \u03d5V10, which specifically infects E. coli O157:H7 (P-4) using IsE. coli strain Tj have been deposited in DDBJ/ENA/GenBank under accession numbers MT920313 and GCA_007049865.1, respectively. The associated BioProject, SRA, and BioSample accession numbers are PRJNA506592, SRR12336902, and SAMN10464432, respectively.The partial 16S rRNA gene and whole-genome shotgun sequences of"} +{"text": "In Russia, cancer is the second leading cause of death following cardiovascular diseases. Adoptive transfer of NK cells is a promising approach to fight cancer; however, for their successful use in cancer treatment, it is necessary to ensure their robust accumulation at tumor foci, provide resistance to the immunosuppressive tumor microenvironment, and to engineer them with higher cytotoxic activity. NK lymphocytes are known to kill cancer cells expressing a number of stress ligands; and the balance of signals from inhibitory and activating receptors on the surface of the NK cell determines whether a cytotoxic reaction is triggered. We hypothesized that stronger cytotoxicity of NK cells could be achieved via gene editing aimed at enhancing the activating signaling cascades and/or weakening the inhibitory ones, thereby shifting the balance of signals towards NK cell activation and target cell lysis. Here, we took advantage of the CRISPR/Cas9 system to introduce mutations in the coding sequence of the shp-2 (PTPN11) gene encoding the signaling molecule of inhibitory pathways in NK cells. These shp-2 knock-outNK cells were additionally transduced to express a chimeric antigen receptor (CAR) that selectively recognized the antigen of interest on the target cell surface and generated an activating signal. We demonstrate that the combination of shp-2 gene knockout and CAR expression increases the cytotoxicity of effector NK-like YT cells against human prostate cancer cell line Du-145 with ectopic expression of PSMA protein, which is specifically targeted by the CAR. Natural killer cells are cells whose primary function is toeliminate infected and transformed cells in the body. Cytotoxicactivity of NK cells is regulated by the balance of signalstriggered by the interaction of activating and inhibitory receptorswith appropriate ligands on the surface of target cells.Inhibitory receptors play an central role in NK cell biologysince most of their ligands are represented by Major HistocompatibilityComplex I (MHC-I) molecules, that are presenton the surface of nearly all healthy cells and frequently absenton cancer or infected cells . This ensures that normal cells are spared by NK cells,whereas the cells that have lost MHC-I expression becomeeliminated . Nevertheless,absence of MHC-I expression does not universallyguarantee that an NK cell would kill a target cell, as this activityis also heavily dependent on the presence of ligands toactivating receptors of NK cells . Inhibitory receptor signal is known to be mainlytransduced via SH2-containing inositol 5\u2032 polyphosphatase 1(SHIP-1) and/or tyrosine phosphatases Shp-1 and Shp-2. Thelatter two proteins dephosphorylate tyrosine residues withinthe ITAM motifs of activating receptors thereby aborting thesignaling cascade .NK cells are successfully used in therapy of oncologicaldiseases . Nevertheless, because tumorcells actively withstand elimination by establishing an immunosuppressivetumor microenvironment, the cytotoxicityof NK cells can be strongly affected . There are several waysof enhancing the cytotoxicity of NK cells. These includemodification of signaling pathways, altering the levels andrepertoire of NK cell receptors, or boosting the activity ofNK cells with appropriate cytokines . In this study, we explored whethermodification of the inhibitory signaling pathway through theshp-2 gene knockout in NK cells would result in the increaseof the cytotoxic activity of model NK cells.Cell lines and cell culture. YT, Du-145-PSMA, and HEK293Tcell lines were maintained in Iscove\u2019s Modified Dulbecco\u2019sMedium (IMDM) supplemented with 10 % fetal bovine serum(FBS), 100 U/ml penicillin, and 100 \u03bcg/ml streptomycin(Sigma) in a humidified atmosphere of 5 % CO2 at 37 \u00b0C.Plasmid construction. Two shp-2-specific sgRNAs wereidentified using publicly available bioinformatics tools . The following target sequences were selected: gtgcagatcctacctctgaaagg andacagtactacaactcaagcagg (PAM site underlined).The lentiCRISPRv2 vector provided by Prof. Feng Zhang was usedfor co-delivery of sgRNAs and Cas9. Oligonucleotides correspondingto the selected targets were denatured in a boilingwater bath followed by slow renaturation and cloned into thelentiCRISPRv2 vector between BsmBI restriction sites.The plasmid DNA of clones lentiCRISPRv2-Shp2g1 andlentiCRISPRv2-Shp2g2 encoding shp2-specific sgRNA1 andsgRNA2, was mixed with the DNA of packaging plasmidspsPAX2 and pMD2.G (provided by Prof. D. Trono) in thefollowing weight ratio: 10:10:7.5:2.5, in the total amountof 3 \u03bcg. Using calcium phosphate transfection , the resulting plasmid DNA mix was delivered toHEK293T cells. Supernatants containing VSV-G pseudotypedlentiviral particles were collected 48 hours after transfection,filtered through 0.45 \u03bcm PES filters and used either fresh orstored at \u201370 \u00b0C.YT cell transduction. To improve transduction rate ofYT cells, a spinoculation protocol was used . YT cells were seeded in 24-well plates (1 \u00d7 105 cells) inthe presence of polybrene (8 \u03bcg/ml) followed by the additionof supernatants containing pseudotyped lentiviral particles.Cells were centrifuged at 500 g for 40 minutes at 32 \u00b0C andincubated in a CO2 incubator for 16 hours. The next day,the supernatant was replaced with a fresh culture medium.After 3 days, selection of transduced cells was performed byadding puromycin to a final concentrationof 5 mg/ ml (1 week), with non-transduced cells serving ascontrols.Western blot analysis. For western blot analysis, transducedYT cells and control non-transduced cell lines YT-wtand HEK293T were lysed in lysis buffer . Cell lysateswere centrifuged, boiled in a water bath for 5 minutes,separated by SDS-PAGE in a 10 % polyacrylamide gel andtransferred onto a nitrocellulose membrane . After blocking in 3 % milk in PBST, the membrane wasincubated with rabbit monoclonal antibodies against Shp-2, followedby an HRP-labeled secondary goat-anti-rabbit antibody. Equal loading was controlled byusing hybridization with control antibodies against \u03b2-actin. Signal was detected usingan ECL-prime substrate in accordance with the manufacturer\u2019srecommendations and AmershamImager 600 with an exposure time of 1 min.Flow cytometry. For phenotyping CAR-YTshp-2\u2013/\u2013 celllines, 105 cells were washed in PBS and incubated for 30 minuteswith the biotinylated protein L (3.3 \u03bcg/ml) at a temperature of 4 \u00b0C. Then the cells werewashed and incubated with streptavidin-APC in accordance with the manufacturer\u2019s recommendations.Vital dye 7AAD was used to excludedead cells from the analysis. The samples were analyzed usingBD FACSCanto\u00ae II (Becton Dickinson and Company) andBD FACSDiva software.Real Time Cytotoxicity Assay (RTCA). Adherent targetcells (5 \u00d7 104 cells per well) were seeded in 8-well E-plates and left to grow for 16\u201318 hours.The next day, the medium was removed and replaced witha fresh one containing 105 effector cells. Cell growth wasmonitored for 24 hours using the RTCA iCELLigence system.Cytotoxicity was calculated using the formula: [CI (targetcells without effector cells) \u2013 CI (target cells with effectorcells) \u00d7 100/CI (target cells without effector cells)], where CIis the normalized impedance value in the wells .Flow cytometry-based cytotoxicity assay. Cells were labeledwith Cell Proliferation Dye eFluor 670 . 50,000 target cells per well were seeded into a 96-wellplate. Next, an equal number of effectors was added .Cells were incubated for 4 hours in a humidified atmosphereof 5 % CO2 at 37 \u00b0C. Then the vital dye 7AAD was added toeach well and the percentage of living target cells was measuredon a BD FACSCantoII flow cytometer.Statistical analysis was performed using Prism software(GraphPad version 8.0). One-way analysis of variance (onewayANOVA) was used to detect the differences between theactivity of control cell lines that did not carry the shp-2 geneknockout and that of knockout cells. All data are presentedas mean \u00b1 standard error of the mean.In this study, we have chosen human immortalized cell lineYT that has an NK-like phenotype. These cells are known todisplay perforin-mediated target cell lysis, lack Fc receptor expressionand do not require conditioning of growth media withIL2 . To knock-out shp-2, CRISPR/Cas9 system was used.Two sgRNAs specific to the 3rd and 5th exons of the genewere cloned into a lentiviral vector lentiCRISPRv2 . The two resulting constructs lentiCRISPRv2-Shp2g1 and lentiCRISPRv2-Shp2g2 were used for producingVSV-G-pseudotyped lentiviral particles, which then wereused for transduction of YT-cells. Given that lentiCRISPRv2vector carries a puromycin resistance gene, transduced cellswere subjected to antibiotic selection and single-cell cloning. A panel of monoclonal derivatives of YT cells was analyzedby Sanger-sequencing the genomic fragments centered atsgRNA-binding sites in the shp-2 gene, in order to identifythe clones carrying biallelic mutations in this gene .Four clones were obtained that displayedtruncated shp-2 sequence . Knock-outswere verified by western-blot analysis, which confirmed thatthese clones did not express a full-length Shp-2 protein .One way to re-target NK cell cytotoxicity is via expressionof chimeric antigen receptors (CARs). Even if the target celllacks typical stress markers recognized by endogenous NK cellreceptors, binding of a CAR to its cognate target may inducepro-activation signaling in a CAR-NK cell. To test whetherCAR-mediated cytotoxicity is enhanced upon shp2-knock out,we used our previously published second-generation CAR(scFv(J591)-CD8hinge-CD28TM-CD28-CD3z) that is specific for PSMA, a common surfacemarker of prostate cancer cells . Wild-type and shp2-mutant YT cell lines weretransduced to express this CAR, which was verified by flowcytometry .shp-2\u2013/\u2013 cells exerted significantlyhigher cytotoxicity than CAR-YT cells with a functionalshp- 2 gene; no difference between the knock-out subcloneswas observed .Next, we compared the cytotoxic activity of the B1-CAR,C1-CAR, and C4-CAR cells vs CAR-YT cells against Du-145 prostate cancer cells engineered to ectopically expressPSMA. Du-145 cells have been reported to be resistant toNK cell killing , which establishes theman appropriate model for assaying possible enhancement ofNK cell-mediated cytotoxicity. We used iCELLigence platform for the cytotoxicity analysis.It was found that CAR-YTshp-2\u2013/\u2013 cells may displayunwanted cytotoxicity against healthy cells, cytotoxicity assaywas conducted with PBMCs isolated from a healthy donor. Weobserved that the percentage of dead normal cells did not differsignificantly between the wells where CAR-YTshp-2\u2013/\u2013 cells orno effector cells (control) were added . This was alsotrue for cultures, where normal cells were co-incubated witheither CAR-YT or CAR-YTshp-2\u2013/\u2013 cells.To understand whether CAR-YTCytotoxic activity of NK cells is known to be regulated bythe balance of activating and inhibitory receptor signals . Cytotoxic reaction occurswhen two conditions are met. Namely, if an activating signalis present, (i. e. when the target cell expresses the ligand(s) tothe activating receptors) and if the negative signaling is sufficientlyreduced or absent . Whenever positive signalingis absent or negative signaling outweighing the positive signaling,cytotoxic reaction will not be launched. In the contextof NK cell therapy, this translates to the failure to eliminatethe tumor cells .Absence of activating signal can be effectively solved byengineering CAR expression in NK cells, an approach alreadyactively used in practice . Nonetheless,tumor cells overexpressing the ligands of inhibitoryNK cell receptors may still remain protected from CAR-NKcell mediated lysis .One way to address this problem is to create NK cells withknock-outs of inhibitory receptors. Although technicallyfeasible, this may not be as straightforward, considering thelarge number of these receptors. In our opinion, knockingout Shp-2, a single \u201chub\u201d of NK cell signaling appears as aviable alternative . Our experiments show that YT cell line derivativeslacking SHP2 expression display stronger CAR-mediatedcytotoxicity towards NK-resistant cell line Du-145-PSMA, unlike CAR-YT cells . Thisis likely attributableto the fact that Du-145-PSMA cellshave a high density of inhibitory ligands, which results in thesuppression of activating signaling in NK cells, even uponCAR engagement. Indeed, it was reported that Du-154 cellsexpress low levels of ligands to the activating NK receptorsNKp30 and NKp46, while MHC-I expression is very high.shp-2\u2013/\u2013 cells are safe, testing ona wide panel of different healthy cell types obtained frommultiple donors may be required, which is a challenging taskfrom a technical and ethical points of view. In the currentstudy, we have measured cytotoxicity of CAR-YTshp-2\u2013/\u2013 cellstowards the lymphocytes of a healthy donor, and no significantdifference with negative control was observed. This suggeststhat reducing the inhibitory signaling in NK cells likely posesno threat provided that no strong activating signals are available.However, to address this important safety concern a morecomprehensive study is indeed required. We envisage that arepresentative and diverse panel iPS-derived normal humancell types can be obtained to test for the possible off-targetactivity of shp2-mutant YT cells.Safety of such combination is yet to be found, as it is possiblethat this may lead to increased cytotoxicity towardshealthy tissues, as a result of weakening of inhibitory signaling.To ensure that the YTThus, the best option for enhancing cytotoxicity of NK cellsand the YT cell line in particular is to induce activating signalsusing CARs in combination with the suppression of inhibitorysignaling via knocking out its key mediator, the SHP-2protein. In the future it is necessary to comprehensivelystudy the safety of modified lymphocytes, in particular, tostudy their cytotoxic activity against a wider range of healthytissues.The authors declare no conflict of interest.Becker P.S.A., Suck G., Nowakowska P., Ullrich E., Seifried E.,Bader P., Tonn T., Seidl C. Selection and expansion of naturalkiller cells for NK cell-based immunotherapy. Cancer Immunol.Immunother. 2016;65(4):477-484. DOI 10.1007/s00262-016-1792-y.Cerwenka A., Baron J.L., Lanier L.L. Ectopic expression of retinoicacid early inducible-1 gene (RAE-1) permits natural killercell-mediated rejection of a MHC class I-bearing tumor in vivo.Proc. Natl. Acad. Sci. USA. 2001;98(20):11521-11526. DOI10.1073/pnas. 201238598.Chang S.S. Overview of prostate-specific membrane antigen. Rev.Urol. 2004;6(Suppl.10):S13-S18.Chester C., Fritsch K., Kohrt H.E. Natural killer cell immunomodulation:targeting activating, inhibitory, and co-stimulatoryreceptor signaling for cancer immunotherapy. Front. Immunol.2015;6:601. DOI 10.3389/fimmu.2015.00601.Childs R.W., Carlsten M. Therapeutic approaches to enhance naturalkiller cell cytotoxicity against cancer: the force awakens. Nat.Rev. Drug Discov. 2015;14:487. DOI 10.1038/nrd4506.De Charette M., Marabelle A., Houot R. Turning tumour cells intoantigen presenting cells: the next step to improve cancer immunotherapy?Eur. J. Cancer. 2016;68:134-147. DOI 10.1016/j.ejca.2016.09.010.Deaglio S., Zubiaur M., Gregorini A., Bottarel F., Ausiello C.M.,Dianzani U., Sancho J., Malavasi F. Human CD38 and CD16are functionally dependent and physically associated in naturalkiller cells. Blood. 2002;99(7):2490-2498.Del Zotto G., Marcenaro E., Vacca P., Sivori S., Pende D., DellaChiesa M., Moretta F., Ingegnere T., Mingari M.C., Moretta A.,Moretta L. Markers and function of human NK cells in normaland pathological conditions. Cytometry B. Clin. Cytom. 2017;92(2):100-114. DOI 10.1002/cyto.b.21508.Doench J.G., Fusi N., Sullender M., Hegde M., Vaimberg E.W.,Donovan K.F., Smith I., Tothova Z., Wilen C., Orchard R., VirginH.W., Listgarten J., Root D.E. Optimized sgRNA design tomaximize activity and minimize off-target effects of CRISPRCas9.Nat. Biotechnol. 2016;34(2):184-191. DOI 10.1038/nbt.3437.Edsparr K., Speetjens F.M., Mulder-Stapel A., Goldfarb R.H.,Basse P.H., Lennern\u00e4s B., Kuppen P.J.K., Albertsson P. Effects ofIL-2 on MMP expression in freshly isolated human NK cells andthe IL-2-independent NK cell line YT. J. Immunother. 2010;33(5):475-481. DOI 10.1097/CJI.0b013e3181d372a0.Freund-Brown J., Chirino L., Kambayashi T. Strategies to enhanceNK cell function for the treatment of tumors and infections.Crit. Rev. Immunol. 2018;38(2):105-130. DOI 10.1615/CritRevImmunol.2018025248.Golubovskaya V., Berahovich R., Zhou H., Xu S., Harto H., Li L.,Chao C.C., Mao M.M., Wu L. CD47-CAR-T cells effectivelykill target cancer cells and block pancreatic tumor growth. Cancers(Basel). 2017;9(10):139. DOI 10.3390/cancers9100139.Gorchakov A.A., Kulemzin S.V., Kochneva G.V., Taranin A.V.Challenges and prospects of chimeric antigen receptor T-cell therapy for metastatic prostate cancer. Eur. Urol. 2019. DOI10.1016/j.eururo. 2019.08.014.Hanke T., Takizawa H., Mcmahon C.W., Busch D.H., Pamer E.G.,Miller J.D., Altman J.D., Liu Y., Cado D., Lemonnier F.A.,Bjorkman P.J., Raulet D.H. Direct assessment of MHC class Ibinding by seven Ly49 inhibitory NK cell receptors. Immunity.1999;11(1):67-77. DOI 10.1016/S1074-7613(00)80082-5.Hewitt E.W. The MHC class I antigen presentation pathway: strategiesfor viral immune evasion. Immunology. 2003;110(2):163-169. DOI 10.1046/j.1365-2567.2003.01738.x.Hood S.P., Foulds G.A., Imrie H., Reeder S., Mcardle S.E.B.,Khan M., Pockley A.G. Phenotype and function of activatednatural killer cells from patients with prostate cancer: patientdependentresponses to priming and IL-2 activation. Front. Immunol.2019;9:3169. DOI 10.3389/fimmu.2018.03169.Igarashi T., Wynberg J., Srinivasan R., Becknell B., McCoy J.P.,Takahashi Y., Suffredini D.A., Linehan W.M., Caligiuri M.A.,Childs R.W. Enhanced cytotoxicity of allogeneic NK cells withkiller immunoglobulin-like receptor ligand incompatibilityagainst melanoma and renal cell carcinoma cells. Blood. 2004;104(1):170. DOI 10.1182/blood-2003-12-4438.Imai C., Iwamoto S., Campana D. Genetic modification of primarynatural killer cells overcomes inhibitory signals and induces specifickilling of leukemic cells. Blood. 2005;106(1):376-383. DOI10.1182/blood-2004-12-4797.Ingegnere T., Mariotti F.R., Pelosi A., Quintarelli C., De Angelis B.,Tumino N., Besi F., Cantoni C., Locatelli F., Vacca P., Moretta L.Human CAR NK cells: a new non-viral method allowing highefficient transfection and strong tumor cell killing. Front. Immunol.2019;10:957. DOI 10.3389/fimmu.2019.00957.K\u00e4rre K., Ljunggren H.G., Piontek G., Kiessling R. Selective rejectionof H\u20132-deficient lymphoma variants suggests alternativeimmune defence strategy. Nature. 1986;319(6055):675-678.DOI 10.1038/ 319675a0.Kulemzin S.V., Matvienko D.A., Sabirov A.H., Sokratyan A.M.,Chernikova D.S., Belovezhets T.N., Chikaev A.N., Taranin A.V.,Gorchakov A.A. Design and analysis of stably integrated reportersfor inducible transgene expression in human T cells and CARNK-cell lines. BMC Med. Genomics. 2019;12(Suppl.2):44. DOI10.1186/s12920-019-0489-4.Kutner R.H., Zhang X.-Y., Reiser J. Production, concentration andtitration of pseudotyped HIV-1-based lentiviral vectors. Nat.Protoc. 2009;4(4):495-505. DOI 10.1038/nprot.2009.22.Lee S.K., Gasser S. The role of natural killer cells in cancer therapy.Front. Biosci. (Elite Ed). 2010;2:380-391.Malarkannan S. The balancing act: inhibitory Ly49 regulateNKG2D-mediated NK cell functions. Semin. Immunol. 2006;18(3):186-192. DOI 10.1016/j.smim.2006.04.002.Mamessier E., Sylvain A., Thibult M.-L., Houvenaeghel G., JacquemierJ., Castellano R., Gon\u00e7alves A., Andr\u00e9 P., Romagn\u00e9 F.,Thibault G., Viens P., Birnbaum D., Bertucci F., Moretta A.,Olive D. Human breast cancer cells enhance self tolerance bypromoting evasion from NK cell antitumor immunity. J. Clin.Invest. 2011;121(9):3609-3622. DOI 10.1172/JCI45816.Moreno-Mateos M.A., Vejnar C.E., Beaudoin J.D., Fernandez J.P.,Mis E.K., Khokha M.K., Giraldez A.J. CRISPRscan: designinghighly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.Nat. Methods. 2015;12(10):982-988. DOI 10.1038/nmeth.3543.Nayyar G., Chu Y., Cairo M.S. Overcoming resistance to naturalkiller cell based immunotherapies for solid tumors. Front. Oncol.2019;9:51. DOI 10.3389/fonc.2019.00051.O\u2019Doherty U., Swiggard W.J., Malim M.H. Human immunodeficiencyvirus type 1 spinoculation enhances infection throughvirus binding. J. Virol. 2000;74(21):10074-10080. DOI 10.1128/jvi.74.21.10074-10080.2000.Pasero C., Gravis G., Granjeaud S., Guerin M., Thomassin-PianaJ., Rocchi P., Salem N., Walz J., Moretta A., Olive D. Highlyeffective NK cells are associated with good prognosis in patientswith metastatic prostate cancer. Oncotarget. 2015;6(16):14360-14373. DOI 10.18632/oncotarget.3965.Pasero C., Gravis G., Guerin M., Granjeaud S., Thomassin-PianaJ., Rocchi P., Paciencia-Gros M., Poizat F., Bentobji M.,Azario-Cheillan F., Walz J., Salem N., Brunelle S., Moretta A.,Olive D. Inherent and tumor-driven immune tolerance in theprostate microenvironment impairs natural killer cell antitumoractivity. Cancer Res. 2016;76(8):2153. DOI 10.1158/0008-5472.CAN-15-1965.Paul S., Lal G. The molecular mechanism of natural killer cellsfunction and its importance in cancer immunotherapy. Front.Immunol. 2017;8:1124. DOI 10.3389/fimmu.2017.01124.Purdy A.K., Campbell K.S. SHP-2 expression negatively regulatesNK cell function. J. Immunol. 2009;183(11):7234-7243. DOI10.4049/jimmunol.0900088.Quintarelli C., Sivori S., Caruso S., Carlomagno S., Boffa I., OrlandoD., Guercio M., Cembrola B., Pitisci A., Di Cecca S., LiPira G., Vinti L., De Angelis B., Moretta L., Locatelli F. CD19redirected CAR NK cells are equally effective but less toxic thanCAR T cells. Blood. 2018;132(Suppl.1):3491. DOI 10.1182/blood-2018-99-118005.Rehman A.U., Rahman M.U., Khan M.T., Saud S., Liu H., Song D.,Sultana P., Wadood A., Chen H.F. The landscape of proteintyrosine phosphatase (Shp2) and cancer. Curr. Pharm. Des.2018;24(32):3767-3777. DOI 10.2174/1381612824666181106100837.Rezvani K., Rouce R., Liu E., Shpall E. Engineering natural killercells for cancer immunotherapy. Mol. Ther. 2017;25(8):1769-1781. DOI 10.1016/j.ymthe.2017.06.012.Rusakiewicz S., Semeraro M., Sarabi M., Desbois M., Locher C.,Mendez R., Vimond N., Concha A., Garrido F., Isambert N.,Chaigneau L., Le Brun-Ly V., Dubreuil P., Cremer I., CaignardA., Poirier-Colame V., Chaba K., Flament C., Halama N.,J\u00e4ger D., Eggermont A., Bonvalot S., Commo F., Terrier P.,Opolon P., Emile J.-F., Coindre J.- M., Kroemer G., Chaput N.,Le Cesne A., Blay J.-Y., Zitvogel L. Immune infiltrates areprognostic factors in localized gastrointestinalstromal tumors. CancerRes. 2013;73(12):3499. DOI 10.1158/0008-5472.CAN-13-0371.Sanjana N.E., Shalem O., Zhang F. Improved vectors and genomewidelibraries for CRISPR screening. Nat. Methods. 2014;11(8):783-784. DOI 10.1038/nmeth.3047.Sivori S., Vacca P., Del Zotto G., Munari E., Mingari M.C., MorettaL. Human NK cells: surface receptors, inhibitory checkpoints,and translational applications. Cell. Mol. Immunol. 2019;16(5):430-441. DOI 10.1038/s41423-019-0206-4.Suen W.C.W., Lee W.Y.W., Leung K.T., Pan X.H., Li G. Naturalkiller cell-based cancer immunotherapy: a review on 10 yearscompleted clinical trials. Cancer Invest. 2018;36(8):431-457.DOI 10.1080/07357907.2018.1515315.Yang L., Shen M., Xu L.J., Yang X., Tsai Y., Keng P.C., Chen Y.,Lee S.O. Enhancing NK cell-mediated cytotoxicity to cisplatin-resistant lung cancer cells via MEK/Erk signaling inhibition.Sci. Rep. 2017;7(1):7958. DOI 10.1038/s41598-017-08483-z.Yodoi J., Teshigawara K., Nikaido T., Fukui K., Noma T., Honjo T.,Takigawa M., Sasaki M., Minato N., Tsudo M., Uchiyama T.,Maeda M. TCGF (IL 2)-receptor inducing factor(s). I. Regulationof IL-2 receptor on a natural-killer-like cell-line (YT-cells).J. Immunol. 1985;134(3):1623-1630.Yusa S.-I., Campbell K.S. Src homology region 2-containingprotein tyrosine phosphatase-2 (SHP-2) can play a direct rolein the inhibitory function of killer cell Ig-like receptors in humanNK cells. J. Immunol. 2003;170(9):4539. DOI 10.4049/jimmunol.170.9.4539."} +{"text": "Egglestonichthysfulmensp. nov. (Teleostei: Gobiidae) is described on the basis of a single specimen (21.7 mm in standard length) collected from 250 m depth off Okinawa Island, Ryukyu Islands, Japan. The new species is characterized by the following combination of characters: anal-fin rays I, 9; pectoral-fin rays 17, lower rays not free from membrane; longitudinal scale series 25; transverse scales 8; pre-dorsal-fin scale rows 8; cheek and opercle naked; pelvic frenum absent; caudal fin lanceolate, its length 32.2% of SL; interorbital width very narrow, 1.2% of HL (much narrower than pupil diameter); no spicules or odontoid processes on outer surface of gill arches; and body whitish, upper half with broken zigzag pattern of bright yellow patches and associated scattered black melanophores in fresh specimens (melanophores retained in preserved specimens). Several characters, including pectoral-fin ray count, interorbital width, and coloration uniquely distinguish the new species from congeners. Egglestonichthys Miller & Wongrat, 1979. Although a generic reassessment of the genus Egglestonichthys is needed , Egglestonichthyspatriciae Miller & Wongrat, 1979, Egglestonichthysrubidus Allen, Erdmann & Brooks, 2020, and Egglestonichthysulbubunitj Larson, 2013] Fig. ; no spicer) Fig. .SL (% of HL in parentheses): head length 30.3; head depth 16.7 (55.1); head width 18.3 (60.6); body depth 14.9; body width 12.9; caudal-peduncle length 19.1, depth 9.4; snout length 5.9 (19.3); eye diameter 7.3 (24.0); interorbital width 0.4 (1.2); upper-jaw length 11.8 (39.0); pectoral-fin length 31.0; pelvic-fin length 28.1; caudal-fin length 32.2; and longest dorsal-fin spine (2nd) length 12.8.Dorsal-fin rays VI + I, 10; anal-fin rays I, 9; pectoral-fin rays 17; segmented caudal-fin rays 16; caudal-fin ray pattern 9/7; branched caudal-fin rays 7/5; unsegmented (procurrent) caudal-fin rays 6/6; longitudinal series scales 25; transverse scales 8; pre-dorsal-fin scale rows 8 ; circumpeduncular scales 12; gill rakers on outer face of first arch 3 + 11 (counted on right side); vertebrae 10 + 16. The following morphometrics are expressed as percentage of Body slender, compressed, width much less than depth Fig. . Anus siHead lacking sensory canal pores Fig. . Head seBody covered with relatively large cycloid scales. Pre-dorsal- and pelvic-fin regions covered with cycloid scales; anterior margin of pre-dorsal-fin scales reaching to vertical through preopercle margin; pre-pelvic-fin scales reaching to just behind anteroventral point of gill opening. Pectoral-fin base with 2 relatively large cycloid scales. Side of head naked , last rays well separated from caudal-fin base. Pectoral fin long, pointed, middle rays longest, tips reaching to below origin of 2nd dorsal-fin soft ray; all rays connected by membrane, uppermost and lower 3 rays unbranched. Pelvic fins completely connected by membrane, without frenum; posterior tip reaching below 2nd dorsal-fin origin when appressed; pelvic-fin origin located just below ventral end of pectoral-fin base. Caudal fin lanceolate, its length much greater than head length.First dorsal fin triangular, 2Fresh coloration . Scattered black melanophores throughout bright yellow patches on head and body. Dorsal-fin rays whitish with yellow interspaces (possibly barred in undamaged specimens). Other fins whitish; upper end of pectoral-fin base with yellow spot; caudal-fin base with faint yellow vertical bar and broad rectangular patch of melanophores.ion Fig. . Body whColoration when preserved , neither could be confirmed in the present specimen. A detailed investigation of species currently assigned to Egglestonichthys must precede any redefinition of the genus .The holotype and only known example of the new species lacks head sensory pores, but has a transverse sensory papillae pattern on the cheek and a wide gill opening , thereby matching the diagnostic characters of aracters . Althougenus see : 153. NeEgglestonichthysfulmen is unlikely to be misidentified as one of its congeners, having the following characters: 17 pectoral-fin rays ; interorbit very narrow (width 1.2% of HL), much less than pupil diameter [vs. variously broad: 38.5\u201347.6% HL in E.bombylios (described as 4.9\u20135.9 in HL in Larson and Hoese 1996); 17.0\u201320.4% HL in E.melanoptera (4.9\u20135.9 in HL in Larson and Hoese 1996); equal to pupil diameter in E.patriciae .E.fulmen and E.melanoptera both lack a pelvic frenum, the former has much lower scale counts than the latter . E.ulbubunitj; all are connected by membrane in E.fulmen. In addition, E.fulmen has fewer anal-fin rays . Egglestonichthysfulmen also has fewer longitudinal series scales than E.bombylios and E.patriciae , a lanceolate caudal fin (length 32.2% of SL), and scales absent on the cheek and opercle .Although"} +{"text": "Mycobacterium smegmatis mc2155. While the Awesomesauce genome is 57,054 bp with 94 protein-coding genes, the LastJedi genome is 55,149 bp with 94 protein-coding genes. Nucleotide sequence comparison in Phamerator detected synteny between Awesomesauce gp49 to gp61 and singleton LilSpotty. Whole-genome BLASTn alignments revealed that LastJedi strongly resembles Clifton (99.41% identity).Bacteriophages Awesomesauce and LastJedi infect Mycobacterium smegmatis mc2155. While the Awesomesauce genome is 57,054 bp with 94 protein-coding genes, the LastJedi genome is 55,149 bp with 94 protein-coding genes. Nucleotide sequence comparison in Phamerator detected synteny between Awesomesauce gp49 to gp61 and singleton LilSpotty. Whole-genome BLASTn alignments revealed that LastJedi strongly resembles Clifton (99.41% identity).Bacteriophages Awesomesauce and LastJedi infect Mycobacterium smegmatis mc2155, a prominent acid-fast Gram-positive soil bacterium. Awesomesauce inhabited damp, shaded soil at Brown University , while LastJedi was from mud near shrubs at the State University of New York College at Old Westbury . Both were isolated (with enrichment at 23 to 24\u00b0C), purified, and amplified in M. smegmatis mc2155, as described in the SEA-PHAGES Discovery Guide (https://seaphagesphagediscoveryguide.helpdocsonline.com/home). The bacteriophages form clear plaques (\u223c1 mm), exhibit Siphoviridae morphology (images are available at https://phagesdb.org/phages/Awesomesauce and https://phagesdb.org/phages/LastJedi), and are F cluster/F1 subcluster members (Bacteriophage Awesomesauce and LastJedi genomes were examined in collaboration with the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program in efforts to characterize viral diversity. Both bacteriophages infect https://phagesdb.org/DNAMaster). PECAAN resources applied to identify genes included Glimmer v3.0 (https://seaphages.org/software), ARAGORN v1.2.38 (http://www.cbs.dtu.dk/services/TMHMM), TOPCONS v2 (Following DNA extraction (Promega Wizard DNA clean-up system), sequencing libraries were produced (NEBNext Ultra II DNA library prep kit) and sequencing on an Illumina MiSeq system (MiSeq reagent kit v3) was perfmer v3.0 , GeneMarmer v3.0 , Phameramer v3.0 , Starter v1.2.38 , and tRN v1.2.38 . Functio v1.2.38 , HHpred v1.2.38 , TMHMM2 PCONS v2 , and thePCONS v2 . All proIn both genomes, key structural and assembly genes are on the left arm and nonstructural coding sequences are on the right arm. On the left arm, both genomes encode small and large terminase subunits, portal protein, capsid maturation protease, scaffolding protein, major capsid protein, head-to-tail adaptor, head-to-tail stopper, tail terminator, major tail protein, tail assembly chaperones, tape measure protein, minor tail proteins, lysin A/lysin B, and DNA polymerase III subunit. On the right arm, both code for genes regulating lysogeny , as well as WhiB family transcription factor, mobile element MPME1, and two glycosyltransferases.MH020243) , Misha28 (MH020242) , and Piper2020 (MK494120) . The Awesomesauce genome also includes Cas4-like exonuclease (gp66), two HNH endonucleases (gp1 and gp74), and two DNA methylases (gp73 and gp76). A rare synteny block (gp49 to gp61) that is highly conserved in 4 of the other 169 F1 mycobacteriophages was identified. BLASTn comparison revealed remarkable colinearity and sequence similarity (98% identity) between the Awesomesauce synteny block and gp49 to gp61 in the singleton LilSpotty (MK977707), suggesting a common origin for the two. Excise (gp48) and MPME1 (gp62) border the synteny block and may facilitate its transposition. It was also noted that homologues to Awesomesauce gp82 (function unknown) occurred in 13 subcluster A1 bacteriophages but only 2 F1 mycobacteriophages (TootsiePop and Misha28) in addition to LilSpotty, suggesting shared origins for A1 and F1 bacteriophages.Whole-genome BLASTn alignments revealedMH371115; 99.41% identity, with 95% coverage) and Brocalys . Notable features include a toxin/antitoxin system (gp35 and gp36), two helix-turn-helix DNA binding domains (gp53 and gp54), Ku-like double-stranded DNA break-binding protein (gp57), AAA-ATPase (gp58), HNH endonuclease (gp59), DNA helicase (gp60), and two GIY-YIG endonucleases (gp65 and gp82).LastJedi is highly homologous to F1 bacteriophages Clifton (The Awesomesauce and LastJedi genomes are available in DDBJ/ENA/GenBank under accession numbers sdb.org) , MargotM"} +{"text": "The 2010 Patient Protection and Affordable Care Act includes the Annual Wellness Visit (AWV) for older adult (OA) patients. Medicare pays for an initial AWV per beneficiary and subsequent visits annually. Many Medicare beneficiaries have not taken advantage of the AWV preventive health benefit. The Saint Louis University Geriatrics Workforce Enhancement Program (GWEP) developed an AWV for OA, NH residents. This project describes the NH AWV and reports results. Data include age, gender, comorbidities, medications, hospitalizations, depression, frailty, pain, sarcopenia, sensory impairment, cognition, nutrition, smoking, falls, and advance directives. Two suburban academic for-profit NHs are included in this study (2016-17). OA NH residents (N=247) completed an AWV and 36.8% (n=91) had a 1-year follow-up AWV. OA NH residents were female and a majority ages 75+ . Most (96.3%) had a documented advance directive. Comorbidities (7.8\u00b12), polypharmacy (92.3%), vision impairment (52.8%), hearing impairment (52.8%), depression (65.2%), frailty (75.7%), sarcopenia (84.4%), risk of weight loss (53.9%), MCI (11.7%), and dementia (75.8%) were prevalent. Among OA NH residents (n=91) with an AWV follow-up, there was modest worsening in total comorbidities and medications as well as frailty, sarcopenia, and cognition scores (ps\u22640.05). Pain, depression, and nutrition did not change. To our knowledge, no one has specifically analyzed the Medicare AWV in NHs. Data from the traditional AWV is an extension of the routine clinical care of OAs and therefore could also be useful for healthcare professionals focused on providing care to OA patients in the NH setting."} +{"text": "Culex (Melanoconion) (Diptera: Culicidae) as vectors of several arboviruses that cause diseases in humans and other animals, there are few taxonomic studies focusing on species of the subgenus, especially providing morphological keys for species identification.Despite the importance of some species of Culex (Melanoconion) were reviewed, five new species are described, and two taxonomic changes are proposed: Cx. (Mel.) exedrus Root, 1927 and Cx. (Mel.) loturus Dyar, 1925 are resurrected from synonymy with Cx. (Mel.) dunni Dyar, 1918 and Cx. (Mel.) zeteki Dyar, 1918, respectively. The Atratus Group now includes fourteen species: Cx. (Mel.) atratus Theobald, 1901; Cx. (Mel.) caribeanus Galindo & Blanton, 1954; Cx. (Mel.) columnaris S\u00e1 & Hutchings n. sp.; Cx. (Mel.) commevynensis Bonne-Wepster & Bonne, 1919; Cx. (Mel.) comptus S\u00e1 & Sallum n. sp.; Cx. (Mel.) dunni; Cx. (Mel.) ensiformis Bonne-Wepster & Bonne, 1919; Cx. (Mel.) exedrus; Cx. (Mel.) longisetosus S\u00e1 & Sallum n. sp.; Cx. (Mel.) longistylus S\u00e1 & Sallum n. sp.; Cx. (Mel.) loturus; Cx. (Mel.) spinifer S\u00e1 & Sallum n. sp.; Cx. (Mel.) trigeminatus Clastrier, 1970; and Cx. (Mel.) zeteki. Keys, descriptions and illustrations for the identification of the male, female, pupal and fourth-instar larval stages of each species are provided. The treatment of each species includes a complete synonymy, descriptions of available life stages, a taxonomic discussion, updated bionomics and geographical distribution, and a list of material examined.Thirteen species of the Atratus Group of Culex (Melanoconion) is updated, including descriptions of five new species. The number of valid species is greater than the number recognized in the previous taxonomic study of the group, increasing from seven to 14 species. Distributional and bionomical data are updated. Morphology-based identification keys for females, males, fourth-instar larvae and pupae provided in this study will facilitate species identification.The taxonomy of the Atratus Group of Melanoconion Theobald, 1903 of Culex Linnaeus, 1758 are considered to be of public health importance because they are vectors of several arboviruses, such as the West Nile virus, viruses of the Venezuelan equine encephalitis complex, and eastern equine encephalomyelitis virus [Species of the subgenus is virus \u20139. Althois virus .Melanoconion includes 160 valid species and 79 synonyms for several species from both the Spissipes and the Melanoconion Sections [Melanoconion was proposed by Sirivanakarn [The subgenus Sections , 10\u201312. vanakarn , with soc oxidase subunit 1 (cox1) and two nuclear genes: hunchback (hb) and carbamoyl-phosphate synthetase 2, aspartate transcarbamylase and dihydroorotase (CAD) of 43 species. The authors demonstrated the monophyly of the Spissipes and Melanoconion Sections, and that most of the morphology-based groups of the Spissipes Section are also monophyletic, corroborating the morphological classification previously proposed by Sirivanakarn [The Spissipes Section comprises 23 species separated into eight groups and three subgroups . The Melvanakarn . In contCx. atratus Theobald, 1901 ; Cx. caribeanus Galindo & Blanton, 1954; Cx. commevynensis Bonne-Wepster & Bonne, 1919; Cx. dunni Dyar ; Cx. ensiformis Bonne-Wepster & Bonne, 1919; Cx. trigeminatus Clastrier, 1970; and Cx. zeteki Dyar, 1918 . The geographical distribution of the Atratus Group ranges from southern South America to northern Central America with Cx. atratus dispersed on some Caribbean islands, and Cx. dunni as the only member of the group recorded in Mexico [The Atratus Group includes seven valid species and fiven Mexico \u201316.Culex dunni has epidemiological importance as a potential vector of arboviruses that can infect and cause encephalitis in humans, as it has been found naturally infected with Pacora (PCA) virus [Cx. dunni has been reported to be vector of Venezuelan equine encephalitis (VEE) virus in Panama [A) virus . In addin Panama .Culex atratus, Cx. zeteki, Cx. dunni, Cx. commevynensis, Cx. ruffinis and Cx. loturus in the Melanoconion Section. Edwards [Cx. commevynensis in Group B, and Cx. atratus, Cx. zeteki, Cx. dunni (syn. Cx. ensiformis), Cx. ruffinis (syn. Cx. exedrus) and Cx. loturus in Group C. Komp [Cx. ruffinis as a synonym of Cx. dunni and Cx. loturus as a synonym of Cx. zeteci. Rozeboom & Komp [Cx. zeteci to Cx. zeteki, in accordance with provisions of the International Code of Zoological Nomenclature. Galindo & Blanton [Cx. caribeanus and Clastrier [Cx. trigeminatus, both based on unique features of the male genitalia. Sirivanakarn [Several taxonomic changes have been made related to the species of the Atratus Group before the classification proposed by Sirivanakarn . Dyar 1 placed C Edwards , based o C. Komp considerm & Komp correcte Blanton describelastrier describevanakarn classifiAccurate species identification is necessary for studies focusing on biology, ecology, vectorial capacity and vector competence. This study aimed to review the taxonomy of the Atratus Group and update the data on species bionomics and distributions. Additionally, five new species are formally named and described, two species are elevated from synonymy and illustrated identification keys to the species level are provided for females, males, fourth-instar larvae and pupae.Cx. commevynensis Bonne-Wepter & Bonne, 1919 and Cx. trigeminatus Clastrier, 1970. Female and male genitalia along with immature specimens from the same locality and habitat were examined when available. When available, male genitalia, larval and pupal exuviae associated to the pinned adult were mounted on the same slide. Character measurements, of 2\u20135 specimens when available, were obtained in the same manner as Sallum & Hutchings [Culex classification adopted is that proposed by Harbach [The specimens examined during this study are from the Cole\u00e7\u00e3o Entomol\u00f3gica de Refer\u00eancia, Faculdade de Sa\u00fade P\u00fablica, Universidade de S\u00e3o Paulo (FSP-USP), S\u00e3o Paulo, Brazil and from the Cole\u00e7\u00e3o de Invertebrados, Instituto Nacional de Pesquisas da Amaz\u00f4nia (INPA), Manaus, Brazil. All specimens come from field collections made in several localities in the Brazilian states of Acre, Amazonas, Mato Grosso do Sul, Minas Gerais, Par\u00e1, Rond\u00f4nia and S\u00e3o Paulo. Type specimens of the nominal species, deposited in the Diptera Collection in the National Museum of Natural History (USNM), Washington, D.C., USA and in the Natural History Museum (NHM), London, UK, were also examined, except for the types of utchings . Illustrutchings , 26, witutchings . Only th Harbach . The Ano Harbach .Geographical distributions are based on both literatute records and material examined, including field collections and museum specimens examined. Distribution records of the material examined are listed in the following format: country, state, municipality and/or locality name, latitude and longitude.Culex commevynensis is not included in this revision because the type specimen could not be examined.International Code of Zoological Nomenclature (ICZN) [To comply with the regulations set out in Article 8.5 of the amended 2012 version of the e (ICZN) , detailsThe abbreviations used are: L, larva; Le, larval exuviae; P, pupa; Pe, pupal exuviae; \u2642, male; \u2640, female; \u2642G, male genitalia; Syn., synonym; distr., distribution; tax., taxonomy; info., information; desig., designation; emend., emendation; FSP-USP, Faculdade de Sa\u00fade P\u00fablica of Universidade de S\u00e3o Paulo, S\u00e3o Paulo, Brazil; INPA, Instituto Nacional de Pesquisas da Amaz\u00f4nia, Manaus, Amazonas, Brazil; NHM, Natural History Museum, London, UK; USNM, National Museum of Natural History, Washington DC, USA; MNHN, Museum National d\u02bcHistoire Naturelle, Paris, France.Atratus GroupAccording to Sirivanakarn , the folTaxonomic treatmentCulex (Melanoconion) atratusTheobald, 19011901Culex atratus Theobald, 1901: 55 [1901: 55 l1909Culex falsificator Dyar & Knab, 1909: 258 [909: 258 (\u2642) lect1938Culex advieri Senevet, 1938: 185 [938: 185 Melanoconion atratus of Theobald (1903: 238) [Melanoconion).03: 238) [15: 388) atratus of Dyar (1923: 187) [23: 187) (\u2642G); Bo23: 187) (\u2642G); Fo23: 187) (type in23: 187) (type in23: 187) (tax.); 23: 187) [909: 50) (distr.)909: 50) (tax.); 909: 50) falsificator of Edwards (1932: 214) [Cx. atratus); Stone & Knight (1957: 49) [32: 214) (synonym957: 49) (desig. 957: 49) .Culex advieri of Rozeboom & Komp (1950: 87) [Cx. atratus)950: 87) (synonymCulex (Melanoconion) advieri of Floch & Abonnenc (1945: 29) [945: 29) (type in945: 29) .Type material: Lectotype, pinned adult male (NHM 010630134) in poor condition associated with male genitalia, and paralectotype pinned adult female (NHM 0106300135) in good condition in the Diptera Collection, Natural History Museum (NHM), London, UK; topotypic male and female in the Diptera Collection, National Museum of Natural History (USNM), Washington, DC, USA. Lectotype male and paralectotype female of Cx. atratus examined as photographs provided by the Natural History Museum, London, UK, for comparisons.Material examined: 36 specimens: 25 \u2642G, 5 Le, 3 Pe, 7\u2642. USNM, Jamaica: JA798-90 (\u2642); JA 798-30 ; JA798-32 (\u2640); JA6- 101 (\u2642G); JA25-102 (\u2642G); JA2/3-84 (\u2642G); JA871-102 (\u2642G); JA744-90 ; JA798-96 ; JA414-103 (\u2642G); JA701-67/208-2 (\u2642G); JA727-102 ; JA719-6/208-3 (\u2642G); JA871-103 (\u2642G); JA899-10 (\u2642G); JA701-67/213-15 (\u2642G); JA719-67/213-16 (\u2642G); JA759-91 (\u2642G); JA798-40 (\u2642G); JA744-95 (\u2642G); JA862-67/213-17 (\u2642G); JA862-67/208-4 (\u2642G); JA744-1 (Le); JA798-3 (Le); JA899 (Le); JA862-2 (Le). Dominican Republic: RD1 ; RD2 (Pe); RD3 (Pe). French West Indies: FWI201-14 (\u2642G); FWI198-101 (\u2642G). Haiti: HAT11-103 (\u2642G); HAT8-680923-8 (\u2642G). Synonym Culex falsificator: Lectotype, pinned adult male (USNM no. 12108), with associated dissected genitalia (USNM no. 408) in good condition in the Diptera Collection, National Museum of Natural History (USNM), Washington, DC, USA.Distribution:Culex atratus has been found in Cuba [ in Cuba ; Jamaica in Cuba ; Dominic in Cuba ; Dominic in Cuba ; Brazil in Cuba \u201350; Caym in Cuba ; Florida in Cuba ; Venezue in Cuba and Pana in Cuba . The occDescriptionMale. [Figs.\u00a0Head: antenna dark, verticillate; length 1.17\u20121.25 (1.20) (n\u2009=\u20093); proboscis entirely dark-scaled, length 1.56\u20131.74 (1.67) (n\u2009=\u20093); maxillary palpus dark-scaled, length 2.08\u20132.21 (2.13) (n\u2009=\u20093); palpomere III with few long, strong setae at apex and inconspicuous basal white ring; palpomeres IV-V entirely covered with long, strong setae; clypeus and antennal pedicel dark. Vertex with narrow, white decumbent falcate scales on central area and erect, dark forked scales; large lateral patch of broad, decumbent white scales extending dorsally; ocular line with narrow, white falcate scales extending dorsally; occiput with dark erect forked scales. Thorax: integument brown; scutum covered with narrow, dark brown falcate scales with lightly golden-coppery reflections. Scutal setae large, dark brown with golden-coppery reflections. Scutellar scales similar to prescutellar scales on median and lateral lobes; median lobe with 4\u20136 large, dark setae; lateral lobes each with 3 or 4 setae. Pleural integument with pattern of pale and dark brown areas as follows: dark brown on postspiracular area, upper mesokatepisternum, upper and lower mesepimeron; pale on lower mesokatepisternum, mesomeron. Pleural setae with 2 types of colouring: setae dark brown with bronzy reflections: 7 or 8 antepronotal, 4\u20136 prealar; and pleural setae pale golden, hyaline: 4 or 5 upper mesokatepisternal, 3\u20135 lower mesokatepisternal, 3 or 4 upper mesepimeral and 1 large lower mesepimeral. Pleura with patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few scales not forming patch. Wing: dark-scaled, length 2.26\u20132.31 (2.29) (n\u2009=\u20093). Dorsal scales broad, dark distally on veins R1, R2, R3, R4+5, M1+2 and M3+4; appressed, dark spatulate scales on veins C, Sc, R, proximally on M, Cu1, Cu2 and A1; linear scales on Rs, R2+3; remigium with appressed spatulate scales and 2 setae. Halter: scabellum yellowish; pedicel yellowish, narrow, with brown dorsal strip; capitellum brown, with few scales with golden reflections. Legs: coxae pale; ventral surface of fore- and midfemur with longitudinal stripe of white scales; tibiae dark-scaled; joints of fermur-tibia and tibia-tarsomere I with ring of pale scales; tarsi entirely dark-scaled. Abdomen: tergum I with dark scales, terga III-VIII dark-scaled with basolateral patches of white scales; sterna II-VII with broad basal white bands. Genitalia: ninth tergal lobes pear-shaped, each with 12\u201314 slender, aciculate setae inserted at 0.67 from base, apex glabrous; distance between lobes 0.6 of width of one lobe at base. Gonocoxite small, narrow, oblong; subapical lobe divided into 2 columnar divisions; proximal division with 2 parallel, apically pointed setae (a and b); seta a shorter, slender, inserted basal to seta b; seta b spatulate and stronger than seta a. Distal division with short columnar process, with 5 setae: 3 filiform, narrow, pointed, apically inserted, subequal in size (setae f), 1 long seta, with hook-like apex (seta h), 1 large, broad, asymmetrical, ribbed seta arising subapically (seta l); 1 saber-like, ribbed seta (seta s) arising apically. Gonocoxite with 4 or 5 broad, hyaline, flattened, apically curved setae borne ventromesally between proximal and distal divisions. Gonostylus slender, slightly curved, tapering towards apex; apex moderately blunt, ventral surface with 2 apical hyaline setae; one short leaf-like gonostylar claw arising apically. Aedeagal sclerite and lateral plate equal in length; lateral process of lateral plate sclerotized, slightly pointed, directed dorsolaterally; ventral process almost straight. Aedeagal sclerite curved in lateral view. Proctiger with tergum X somewhat triangular, slender in outline, inner process pointed. Basal plate with concave inner margin. Paraproct elongate, crown with 9 or 10 simple blades. Cercal sclerite with 1 or 2 setae.e. Figs.\u00a0, 2a SmalFemale. Not examined.Pupa. [Figs.\u00a0Cephalothorax: setae 1,2-CT 4-branched (n\u2009=\u20092); setae 3,4-CT 2-branched; seta 5-CT 4-branched; seta 6-CT 2-branched; seta 7-CT 3-branched; seta 8-CT 5- or 6-branched; seta 9-CT 2- or 3-branched; seta 10-CT 5- or 6-branched; seta 11-CT single; seta 12-CT 2- or 3-branched. Trumpet moderately tanned. Pinna small, V-shaped in lateral view; tracheoid area, darker, extending almost 0.45 from base; trumpet index c.7. Abdomen: lightly tanned; seta 9-VIII with 4 aciculate branches. Paddle weakly tanned; setae 1,2-Pa single, 1-Pa longer than 2-Pa.a. Figs.\u00a0a, 4a IntLarva. [Figs.\u00a0Head: wider than long; capsule moderately tanned; lateralia and collar darker; length and width not measured; dorsomentum with 1 large median tooth and 4 small teeth on either side. Antenna lightly tanned with dark rings at base and level of seta 1-A; setae 2,3-C absent (n\u2009=\u20092); seta 4-C single; seta 5-C with 6 long branches reaching 6-C insertion; seta 6-C single, long, reaching anterior margin of head, with sparse minute spicules on basal 0.5; seta 7-C with 12 aciculate branches; seta 8-C 5- or 6 branched; seta 9-C 4-branched; seta 10-C 3-branched; seta 11-C double; seta 12-C 4- or 5-branched; seta 13-C single; seta 14-C 3-branched; seta 15-C with multiple hyaline branches. Thorax: integument hyaline; pleura without darker patches under integument. Abdomen: integument hyaline; comb of segment VIII with 19\u201328 sub-equal scales arranged in 3 rows. Segment X with complete saddle, apico-lateral margin dark with spicules; seta 1-X with 4 hyaline branches; seta 2-X with 1 long branch, 3 shorter; seta 3-X single; ventral brush (seta 4-X) with 5 pairs of 5-branched setae. Anal papillae slender, gradually tapering to apex. Siphon: long, at least 3 times longer than saddle, darker in mid-length; pecten with 18 spines on basal 0.3. Seta 1-S usually in 4 ventral pairs and 4 dorsal pairs; seta 2-S hook-shaped with small, curved secondary branch.a. Figs.\u00a0a, 6a HeaBionomics. Immature stages of Cx. atratus were collected in permanent and semi-permanent partially shaded habitats, such as ponds, stream margins, swamps and ditches, in association with herbaceous vegetation such as reeds, grass and algae, in fresh, clear or dark water. Larvae and pupae were found in association with Nyssorhynchus albimanus Wiedemann, 1820 and Anopheles grabhamii Theobald, 1901 and less frequently with Cx. nigripalpus Theobald, 1901 Uranotaenia socialis Theobald, 1901 and Ur. cooki Root, 1937 [Cx. atratus were found in artificial containers with Aedes albopictus in Florida Key, Florida, USA [ot, 1937 . Larvae ida, USA . In the ida, USA found laida, USA .RemarksCulex atratus was described as a species of the genus Culex by Theobald [Cx. atratus to the newly created genus Melanoconion, based on the arrangement of wing scales. Dyar [Cx. atratus as the type of genus Melanoconion, and Howard et al. [Cx. falsificator from adults collected in Cuba, and Bonne & Bonne-Wepster [Cx. falsificator with Cx. atratus, which was accepted by Edwards [Culex advieri was described by Senevet [Cx. advieri from Guadeloupe. Rozeboom & Komp [Cx. advieri with Cx. atratus; the synonymy was also recognized later by Belkin et al. [Cx. atratus can be identified by the following combination of characters: wings dark-scaled; small patch of pale scales on upper mesokatepisternum; scutum with very narrow, bronzy scales; mesepimeron entirely dark, without median pale area; terga II-VIII with basolateral patches of white scales. Males can be readily distinguished from the other species of the Atratus Group by the presence of 4 or 5 broad, hyaline, flattened, apically curved setae arising ventromesally between the proximal and distal divisions of the gonocoxite. In addition, other characteristics of the male genitalia can be employed to identify Cx. atratus: lateral plate without apical process and lateral process directed dorsolaterally, and ninth tergal lobe pear-shaped with aciculate setae arising at basal 0.6. Fourth-instar larvae can be distinguished by having the scales of the comb of segment VIII of equal size and arranged in four irregular rows; seta 5-C reaching the insertion of seta 6-C; siphonal pecten spines with large coarse marginal denticles. Culex atratus pupae can be distinguished by having a V-shaped pinna and seta 9-VIII with 4 or 5 aciculate branches.Theobald based onTheobald transferes. Dyar selectedd et al. described et al. describe-Wepster synonymi Edwards and Belk Edwards . Culex a Senevet from mal Senevet associatm & Komp synonymin et al. and Belkn et al. . In spitCulex(Melanoconion)caribeanusGalindo & Blanton, 19541954Culex (Melanoconion) caribeanus Galindo & Blanton, 1954: 244 [954: 244 (\u2642) holoCulex (Melanoconion) caribeanus of Pecor et al. [16, 124) (distr.)Type material: Holotype, adult male mounted on slide with dissected male genitalia (USNM 01347) and paratype male mounted on slide with dissected male genitalia (USNM 01160) deposited in the Diptera Collection, National Museum of Natural History (USNM), Washington, DC, USA.Material examined: 4 specimens: 4 \u2642G, 2 \u2642: INPA, Brazil: Amazonas State, Ipixuna Municipality, Lago Grande, Seringal Recreio, Greg\u00f3rio River , coll. Hutchings et al. 2011, 20\u201321.v.2011, det. Hutchings & Sallum, 3.vii.2012 ; coll. Hutchings et al. 2011, 18\u201319.v.2011, det. Hutchings & Sallum, 3.vii.2012 . Amazonas State, Barcelos Municipality, Ararinha, Padauari River , coll. Hutchings et al. 2010, 6\u20137.vi.2010, det. Hutchings & S\u00e1, 01.iii.2017 . Amazonas State, Mau\u00e9s Municipality, Picada Pirarara, Abacaxis River , coll. Hutchings et al. 2008, 28\u201329.v.2008, det. S\u00e1, 01.iii.2017 .Distribution:Culex caribeanus has been found in Mojinga Swamp, Canal Zone, Panama [Cx. trigeminatus) [, Panama and in tminatus) , Barcelominatus) and IpixDescriptionMale. [Figs.\u00a0Head: antenna dark, verticillate, length 1.04\u20131.38 (1.21) (n\u2009=\u20092); proboscis dark-scaled, with conspicuous, median, dorsal patch of whitish scales, length 1.30\u20131.51 (1.40) (n\u2009=\u20092); maxillary palpus length 1.69\u20131.90 (1.79) (n\u2009=\u20092); palpomere I entirely whitish-scaled; palpomere II with basal patch of whitish scales; palpomere III with conspicuous patch of whitish scales on median portion. Thorax: scutum covered with bronzed scales, except whitish scales on anterior promontory, scutal fossa, dorsocentral and supraalar areas forming a pattern. Scutellar scales whitish; median lobe with 4 or 5 setae; lateral lobes with 3 or 4 setae each. Pleural setae with 2 types of colouring: dark brown with bronzy reflections: 7 or 8 antepronotal, 5 or 6 prealar; and pleural setae golden, hyaline: 4 or 5 upper mesokatepisternal, 3 or 4 lower mesokatepisternal, 5 or 6 upper mesepimeral, and 1 large lower mesepimeral. Pleura with patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few scales not forming patch. Wing: dark-scaled as in Cx. atratus; length 2.31\u20132.47 (2.39) mm (n\u2009=\u20092). Halter: scabellum and pedicel whitish; capitellum brown with few scales with golden reflections. Legs: fore- and midfemora with preapical ring of white scales. Abdomen: tergum I dark-scaled; terga III-VIII dark-scaled with basal bands of white scales. Genitalia: tergum IX lobes with concave inner margin, pointed and apex glabrous, median portion each with 14\u201316 slender, simple and aciculate setae; distance between lobes smaller than half basal width of 1 lobe. Gonocoxite narrow, oblong; proximal division of subapical lobe with 4 parallel, apically pointed setae : seta a more basal, spoon-shaped; seta b longer than others, spatulate, sinuous subapically; seta c thin, slender, filiform, inserted between setae b and d; seta d implanted on tubercle apical to seta b, filiform, long. Distal division with elongated columnar process, with 5 setae: 3 filiform, narrow, pointed, apically inserted, subequal in size (setae f), 1 filiform, with hook-like apex (seta h) and 1 large, broad, asymmetrical, ribbed seta arising subapically (l seta); 1 saber-like, ribbed seta (seta s) arising apically. Gonocoxite with 4 or 5 slender, hyaline, short, inconspicuous setae borne ventromesally between proximal and distal divisions. Gonostylus as in Cx. atratus, except on dorsal surface of apex with 2 or 3 inconspicuous folds. Ventral process of lateral plate with large convexity on upper border and conspicuous pointed projection directed ventrobasally. Proctiger with tergum X somewhat triangular in outline, inner process pointed and long.e. Figs.\u00a0b, 7 HeadFemale, pupa and larva. Unknown.Bionomics. Adult males were collected using CDC light traps with UV lamps in upland (terra firme) Amazon Forest [n Forest .RemarksCulex caribeanus was described by Galindo & Blanton [Cx. caribeanus can be misidentified as Cx. trigeminatus if the male genitalia are not properly dissected and mounted in lateral view. Based on characteristics of the female, Cx. caribeanus is similar to Cx. trigeminatus in possessing preapical rings of white scales on the fore- and midfemora and proboscis with patch of whitish scales on the median portion of ventral surface. Culex caribeanus differs from Cx. trigeminatus in having palpomere I entirely white-scaled, palpomere II with basal patch of white scales, palpomere III with conspicuous patch of white scales on median portion close to pale patch of proboscis, and wings entirely dark-scaled on ventral and dorsal surfaces. In Cx. trigeminatus, the palpomeres I and II are dark-scaled, palpomere III has a small basal patch of pale scales, and palpomere IV has an inconspicuous proximal patch of whitish scales, and the wings have veins C and R with basal patches of white scales. The male genitalia of Cx. caribeanus have simple and aciculate setae on the median portion of the ninth tergal lobes, whereas in Cx. trigeminatus the setae are simple. In addition, Cx. caribeanus differs from Cx. trigeminatus in possessing a pronounced convexity on the apical margin of the lateral plate, and a conspicuous pointed projection directed ventrobasally in the ventral process. In Cx. trigeminatus, the apical margin of the ventral process of the lateral plate is straight and bears a short projection. Blanton from mal Blanton found thCulex(Melanoconion)columnarisS\u00e1 & Hutchings n. sp.Type locality: Senador Guiomard Municipality in Fazenda Experimental Catuaba, UFAC, BR-364 Km 23 , Acre State, Brazil. Adults were collected using a CDC trap with UV light in terra firme forests at an elevation of 205 m.Type material: Holotype, pinned adult male with associated dissected genitalia on slide , with following collection data: Brazil: Acre State, Senador Guiomard Municipality, Fazenda Experimental Catuaba, UFAC, BR-364 Km 23 , coll. Hutchings & Carmo, 23-24.viii.2016, det. S\u00e1, 2017, deposited in the Cole\u00e7\u00e3o de Invertebrados, Instituto Nacional de Pesquisas da Amaz\u00f4nia (INPA), Manaus, Amazonas State, Brazil. Paratypes: 2 pinned adult males with dissected genitalia on separate slides from same collection as holotype and deposited in INPA; and 2 pinned adult males with dissected genitalia on separate slides , from same collection as holotype and deposited in the Cole\u00e7\u00e3o Entomol\u00f3gica de Refer\u00eancia, Faculdade de Sa\u00fade P\u00fablica, Universidade de S\u00e3o Paulo (FSP-USP), S\u00e3o Paulo State, S\u00e3o Paulo municipality, Brazil.ZooBank registration: The Life Science Identifier (LSID) for Culex (Melanoconion) columnaris n. sp. is urn:lsid:zoobank.org:act: 139D4046-50EC-4D2A-AE1B-51502EC47A44.Etymology: From the Latin adjective columnaris, meaning rising in the form of column, in reference to the long columnar process of the proximal division of the subapical lobe.DescriptionMale. [Figs.\u00a0Head: antennal length 1.06\u20131.60 (1.40) (n\u2009=\u20095); proboscis entirely dark-scaled, length 1.44\u20131.70 (1.55) (n\u2009=\u20095); maxillary palpus dark-scaled, length 1.82\u20132.21 (1.96) (n\u2009=\u20095); occiput with dark brown erect forked scales. Thorax: scutum with narrow, brown, falcate scales with golden reflection, prescutellar area with whitish scales. Scutellar scales whitish, median lobe with 6 setae; lateral lobes each with 3 or 4 large setae. Pleural setae with 2 types of colouring: dark brown: 3\u20135 antepronotal, 4\u20136 prealar; and pleural pale golden, slender setae: 4 or 5 upper mesokatepisternal, 3 or 4 lower mesokatepisternal, 4 or 5 upper mesepimeral; lower mesepimeron with one strong, long, pale golden seta. Mesepimeral integument dark, with indistinct pale spot on median area, not dividing upper and lower areas. Pleura with less evident patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few white scales. Wing: dark-scaled; length 2.19\u20132.54 (2.35) (n\u2009=\u20095). Halter: scabellum, pedicel and capitellum whitish. Legs: coxae pale; ventral surface of fore- and midfemur with a longitudinal stripe of white scales; tibiae dark-scaled; joints of femur-tibia and tibia-tarsomere I with ring of pale scales; tarsi entirely dark-scaled. Abdomen: tergum I with dark scales; terga III-VII dark-scaled with proximal white bands; tergum VIII with dark scales. Genitalia: tergum IX lobes elongate, each with 14 slender, apically bifid, simple setae in median portion; apex glabrous. Distance between lobes about 1/3 of basal width of 1 lobe. Gonocoxite oblong, narrow; proximal division with long, apically divided, columnar process bearing 2 parallel setae (a and b): seta a basal, slender with pointed apex; seta b slightly sinuous with apex curved. Distal division with long columnar process with 5 setae: 3 narrow, filiform, apically pointed setae of different sizes (seta f), 1 long seta hook-like at apex (seta h), and 1 large, long, asymmetrical seta arising subapically (seta l); 1 saber-like seta with broad apex and without peduncle on base (seta s) arising apically; gonocoxite with 2 short, hyaline setae on ventromesal surface. Gonostylus slender, slightly curved, with moderately pointed apex, ventral surface with 2 apical hyaline setae; 1 short gonostylar claw arising apically. Aedeagus with apical process slightly curved dorsally and ventral process with rounded prominence. Proctiger with tergum X asymmetrical, with outer process rounded.e. Figs.\u00a0c, 8 InteRemarksCx. columnaris n. sp. bear more morphological similarities to Cx. zeteki than to other species of the Atratus Group. However, adult specimens of the new species differ from Cx. zeteki in having the mesepimeron with a slightly light stain on the median area, not divided into upper and lower areas. The male genitalia differ from those of Cx. zeteki in having the seta s without peduncle on base and with a broad apex, IX tergal lobes with bifid setae in the ventromedial region, and a lateral plate without undulations on the apical process. Furthermore, Cx. columnaris n. sp. has the proximal division of subapical lobe with an apically divided long columnar process which bears only two setae (a and b).The male genitalia and adults of Culex(Melanoconion)comptusS\u00e1 & Sallum n. sp.Type locality: Presidente Epit\u00e1cio Municipality near Horto Florestal , S\u00e3o Paulo State, Brazil. Larvae were collected in partially shaded, permanent habitats, with turbid water, associated with Pistia sp., in remnants of the Atlantic Forest and in transition areas between the Cerrado and the Atlantic Forest biomes, cohabiting with Cx. dunni.Other localities: Bolivia, Brazil, Panama and Suriname. In Brazil, the species occurs in the municipalities of Presidente Epit\u00e1cio and Dourado, S\u00e3o Paulo State, in Santo Ant\u00f4nio do I\u00e7\u00e1, Manacapuru and Juta\u00ed, Amazonas State, and in the municipality of Juruti, Par\u00e1 State (present study).Type material: Holotype, pinned adult male with dissected genitalia, larval and pupal exuviae on the same slide , with following collection data: Brazil, S\u00e3o Paulo State, Presidente Epit\u00e1cio Municipality, near Horto Florestal , coll. S\u00e1 & Chaves, 15.iii.2016, det. S\u00e1, 2016, deposited in the Cole\u00e7\u00e3o Entomol\u00f3gica de Refer\u00eancia, Faculdade de Sa\u00fade P\u00fablica, Universidade de S\u00e3o Paulo (FSP-USP), S\u00e3o Paulo Municipality, S\u00e3o Paulo State, Brazil. Paratypes: 2 pinned adult males with dissected genitalia, larval and pupal exuviae on separate slides ; 2 pinned adult females associated with larval and pupal exuviae on separate slides ; 2 pinned adult males with dissected genitalia and pupal exuviae on separate slides ; 1 pinned adult female with associated pupal exuviae on slide , from same collection as holotype and deposited in FSP-USP; 2 pinned adult males with dissected genitalia on separate slides , with following collection data: Brazil, Amazonas State, Santo Ant\u00f4nio de I\u00e7\u00e1 Municipality, Parana do Canini, Solim\u00f5es River , coll. Hutchings et al. 2003; 1 pinned adult male with dissected genitalia on slide , with following collection data: Brazil, Amazonas State, Jutai Municipality, S\u00e3o Raimundo, Parana do Cervalho, Solim\u00f5es River , coll. Hutchings et al. 2003; 1 pinned adult male with dissected genitalia on slide , with following collection data: Brazil, Amazonas State, Manacapuru Municipality, Parana do Cururu, Solim\u00f5es River , coll. Hutchings et al. 2003; and 1 pinned adult male associated with dissected male genitalia , with following collection data: Brazil, Par\u00e1 State, Juruti Municipality, Recreio, Parana de Dona Rosa, Amazon River , coll. Hutchings et al. 2003, deposited in the Cole\u00e7\u00e3o de Invertebrados, Instituto Nacional de Pesquisas da Amaz\u00f4nia (INPA), Manaus, Amazonas State, Brazil.Material examined: 21 specimens: 10 \u2642G, 16 Pe, 14 Le, 4 \u2642, 10 \u2640. FSP-USP, Brazil, S\u00e3o Paulo State, Presidente Epit\u00e1cio Municipality , coll. S\u00e1 & Chaves, 15.iii.2016, det. S\u00e1, 2016: SP172-06 ; SP172-17 ; SP172-28 ; SP172-32 ; SP172-34 ; SP172-36 ; SP172-37 ; SP172-39 ; SP172-43 ; SP 172-45 ; SP172-46 ; SP172-47 ; SP172-49 ; SP172-110 . S\u00e3o Paulo State, Dourado Municipality, SP255Km, Obelisco coll. Sallum et al., 7.v.2009, det Sallum 2012: E-15439 (Pe). Dourado, SP255 km, Santa Leonor Farm , coll. Sallum et al. 7.v.2009, det. Sallum 2012: E-15440 . USNM, Panama: PA37-115 (\u2642G); PA2-101 (\u2642G). Suriname: (USNM) S.S det., 1978: MEP-AC634-20 (\u2642G); MEP-AC634-21 (\u2642G). Bolivia: Catalog no. 82164 (\u2642G).ZooBank registration: The Life Science Identifier (LSID) for Culex (Melanoconion) comptus n. sp. is urn:lsid:zoobank.org:act: 260B62E3-BD5B-4384-980A-AD7000EC8E17.Etymology: From the Latin adjective comptus, meaning ornate, adorned, in reference to the dark brown to black and pale golden scales that form a pattern on the scutum.DescriptionFemale. Integument dark brown, with pale areas on thoracic pleura. Head: antenna dark, flagellum normal, whorls with 5 setae, length 1.00\u20131.38 (1.21) (n\u2009=\u20095); proboscis dark-scaled, length 1.35\u20131.44 (1.42) (n\u2009=\u20095); maxillary palpus dark-scaled, length 0.21\u20130.26 (0.24) (n\u2009=\u20095). Occiput with dark brown erect forked scales. Thorax: integument dark brown; scutum covered with narrow, dark brown to black falcate scales; may have pale golden scales forming a pattern on anterior promontory, scutal fossa, dorsocentral, prescutelar and supraalar areas. Scutellar scales whitish; median lobe with 5 or 6 setae; lateral lobes each with 3 or 4 setae. Pleural setae with 2 types of colouring: brown, large: 3\u20137 antepronotal, 3\u20135 prealar; and pleural setae golden, hyaline: 4 or 5 upper mesokatepisternal, 3 or 4 lower mesokatepisternal, 4 or 5 upper mesepimeral and 1 large lower mesepimeral. Pleura with patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few white scales. Wing: dark-scaled; vein C with small proximal patch of white scales, vein Sc occasionally with inconspicuous proximal patch of white scales, vein R with proximal patch of white scales separated by median patch of dark scales; wing length 2.44\u20133.05 (2.79) (n\u2009=\u20095). Halter: scabellum and pedicel whitish; pedicel with narrow, brown, dorsal strip; capitellum brownish. Legs: coxae pale; ventral surface of fore- and midfemur with longitudinal stripe of white scales; tibiae dark-scaled; joints of femur-tibia and tibia-tarsomere I with ring of pale scales; tarsi entirely dark-scaled. Abdomen: tergum I dark-scaled; terga II-VIII dark-scaled with basal bands of white scales.Male. [Figs.\u00a0Head: antenna verticillate, length 0.92\u20131.37 (1.10) (n\u2009=\u20095); proboscis length 1.48\u20131.59 (1.55) (n\u2009=\u20095); maxillary palpus length 1.54\u20132.16 (1.89) (n\u2009=\u20095). Wing: length 2.37\u20132.63 (2.51) (n\u2009=\u20095). Genitalia: tergum IX lobes somewhat conical, elongate, narrow with glabrous apex, median portion each with 11\u201315 slender, simple setae; distance between lobes larger than basal width of 1 lobe. Gonocoxite oblong; proximal division of subapical lobe with 2 parallel, pointed setae (a and b): seta a basal, short, narrower than seta b, with pointed apex; seta b long, spatulate, with pointed apex and implanted on salient tubercle. Distal division with long columnar process, with 5 setae: 3 filiform, narrow, pointed, apically inserted, subequal in size (seta f); 1 filiform, with hooked apex (seta h); 1 large, long, broad, asymmetrical, ribbed seta arising subapically (seta l); and 1 saber-like, ribbed seta (seta s) arising apically. Gonocoxite with 3 or 4 hyaline, filiform, median, inconspicuous setae on ventromesal surface. Gonostylus slender, slightly curved, with moderately blunt apex, ventral surface with 2 apical hyaline setae, gonostylar claw extremely short. Aedeagal sclerite with few, inconspicuous spicules on ventral surface; lateral process pointed and directed dorsolaterally. Proctiger with tergum X somewhat triangular in outline, inner process pointed.e. Figs.\u00a0d, 9 EssePupa. [Figs.\u00a0Cephalothorax: trumpet cylindrical, pinna small, irregular in shape, pinna length 0.07\u20130.12 (0.10) (n\u2009=\u200910), distal margin opposite meatal cleft, with small emargination; tracheoid area darker, extending 0.20\u20130.25 (0.23) (n\u2009=\u200910) from base; trumpet index 13.8\u201316.2 (15.4) (n\u2009=\u200910). Abdomen: seta 9-VIII with 3 simple branches; paddle index 1.32\u20131.57 (1.47) (n\u2009=\u200910).a. Figs.\u00a0b, 4b CepLarva. [Figs.\u00a0Head: length 0.62\u20130.71 (0.67) (n\u2009=\u200910), width 1.04\u20131.10 (1.06) (n\u2009=\u20095). Antennal length 0.49\u20130.60 (0.55) (n\u2009=\u200910). Seta 1-A inserted 0.38\u20130.40 (0.38) (n\u2009=\u200910) from antennal base; seta 4-C double; seta 5-C with 3 or 4 long branches reaching 6-C insertion; seta 13-C double. Abdomen: comb of segment VIII with 25\u201328 sub-equal scales arranged in 3 rows. Segment X length 0.34\u20130.38 (0.36) (n\u2009=\u200910), saddle complete, apicolateral margin dark with spicules; siphon/saddle index 4.17\u20135.18 (4.67) (n\u2009=\u200910). Siphon: long, slender, index 8.7\u201311.0 (9.7) (n\u2009=\u200910); pecten with 12 marginal spines on basal 0.30 of siphon. Seta 1-S usually with 4 ventral pairs and 4 dorsal pairs.a. Figs.\u00a0b, 6b HeaRemarksCx. comptus n. sp. are more morphologically similar to Cx. commevynensis than to any other species of the Atratus Group. These species have in common characteristics such as the shape and size of seta l of the distal division, the length of the columnar process of the distal division and the number and form of setae in the proximal division. However, the male genitalia of Cx. comptus n. sp.\u00a0differ from those of Cx. commevynensis in possessing slightly conical, narrow and elongate tergum IX lobes. On the other hand, in the original description of the Cx. commevynensis adult, Bonne-Wepster & Bonne [Cx. comptus n. sp., the vertex and occiput possess whitish, curved, narrow scales and the scutum is covered with narrow and dark brown to black falcate scales and some pale golden scales forming conspicuous pattern on the anterior promontory, scutal fossa, dorsocentral, prescutelar and supraalar areas. The fourth-instar larva of Cx. comptus n. sp. differs from the larva of Cx. zeteki in having three rows of comb scales and slender pecten spines with serrate edges. The pupa of Cx. comptus n. sp. differs from the pupa of Cx. zeteki in having the pinna of the trumpet slightly smaller and differs from the pupa of Cx. trigeminatus in having the trumpet clearer and with the distal margin bearing a more conspicuous notch opposite the meatal cleft.Based on the original description of Bonne-Wepster & Bonne , and ill & Bonne mention Culex(Melanoconion)dunniDyar, 19181918Culex (Melanoconion) dunni Dyar, 1918: 123 [918: 123 l1924Culex (Melanoconion) ruffinis Dyar & Shannon, 1924: 144 [924: 144 Culex (Melanoconion) dunni of Dyar (1923: 188) [Cx. ensiformis); Dyar (1928: 340) [23: 188) (synonym of Dyar 23: 188 [28: 340) (\u2642G); Fo28: 340) ; 28: 340) (desig. 28: 340) (distr.)28: 340) (Guatema28: 340) (Venezue28: 340) (distr.)Culex (Melanoconion) ruffinis of Dyar (1928: 341) [Cx. dunni). of Dyar 28: 341 [28: 341) , with dissected genitalia on slide (USNM no. 901).Material examined: 56 specimens: 45 \u2642G, 15 Le, 18 Pe, 18 \u2642, 16 \u2640. FSP-USP, Brazil: S\u00e3o Paulo State, Canan\u00e9ia Municipality, Vilarinho , coll. S\u00e1 et al. 14.vii.2015, det. S\u00e1 2015: SP166-03 ; SP166-04 (Pe); SP166-21 . S\u00e3o Paulo State, Presidente Epit\u00e1cio Municipality , coll. S\u00e1 & Chaves 2016, det. S\u00e1 2016: SP172-35 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, Itapitangui , coll. Forattini et al. 1985, det. Sallum 1985: EP014-1 ; EP058-1 ; EP058-3 ; EP070-1 . S\u00e3o Paulo State, Dourado , coll. Forattini et al. 1980, det. Sallum 1980: 02 (\u2642G); 28 (\u2642G); 148 . S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality, Pariquera-Mirim , coll. Forattini et al. 24.vii.1984, det. Sallum 1984: HEP414-7 ; HEP414-8 ; HEP414-9 ; HEP414-18 ; HEP414-20 ; HEP429-3 ; HEP429-7 ; HEP440-7 . Minas Gerais State, Goian\u00e1 Municipality , coll. Bergo et al. 30.xi.2008, det. Sallum 2008: MG24-102 , Minas Gerais State, Carmo da Mata Municipality, Rural das Pedras Farm , coll. Bergo et al. 13.iv.2010, det. Sallum 2014: MG46-02 . INPA, Brazil: Par\u00e1 State, Almeirim Municipality, Arumanduba, Amazon River , coll. Hutchings et al. 19\u201320.viii.2003, det. Hutchings: ProV-047641 (\u2642G); ProV-047649 (\u2642G); ProV-047741 (\u2642G). Par\u00e1 State, Almeirim Municipality, Paraiso, Paranacuara, Amazon River , coll. Hutchings et al. 21\u201322.viii.2003, det. Hutchings: ProV-055512 (\u2642G). Par\u00e1 State, Prainha Municipality, Fazenda JK, Amazon River , coll. Hutchings et al. 22\u201323.x.2003, det. Hutchings & S\u00e1: ProV-049099 (\u2642G). Par\u00e1 State, Prainha Municipality, Curuauna River , coll. Hutchings et al. 24\u201325.x.2003, det. Hutchings & S\u00e1: ProV-049615 (\u2642G). Par\u00e1 State, Juruti Municipality, Recreio, Parana de Dona Rosa, Amazon River , coll. Hutchings et al. 30\u201331.x.2003, det. Sallum, Hutchings & S\u00e1: ProV-053664 (\u2642G); ProV-053667 (G); ProV-053670 (G); ProV-053674 (G); ProV-053678 (\u2642G); ProV-053679 (\u2642G); ProV-053688 (\u2642G). Amazonas State, Iranduba Municipality, Ramal do Lago Grande , coll. Hutchings et al. 8\u201310.ix.2008, det. Hutchings: IRam-000751 (\u2642G); IRam-000752 (\u2642G); IRam-000759 (\u2642G); IRam-000760 (\u2642G); IRam-000945 (\u2642G); IRam-002062 (\u2642G); IRam-002061 (\u2642G); IRam-002060 (\u2642G); IRam-001933 (\u2642G); IRam-001932 (\u2642G); IRam-001931 (\u2642G); IRam-001212 (\u2642G). Amazonas State, Juru\u00e1 Municipality, Igarap\u00e9 de Tamaniqua, Solim\u00f5es River , coll. Hutchings et al. 19.ix.2003, det. Sallum, Hutchings & S\u00e1: ProV-015891 (\u2642G); ProV-015900 (\u2642G). Amazonas State, Juta\u00ed Municipality, S\u00e3o Raimundo , coll. Hutchings et al. 16\u201317.ix.2003, det. S\u00e1 1.iii.2017: ProV-006542 (\u2642G). Amazonas State, Urucara Municipality, L\u00edrio do Vale , coll. Hutchings et al. 3.xi.2003, det. Sallum, Hutchings & S\u00e1: ProV-056752 (\u2642G). Synonym species Culex ruffinis: lectotype, pinned adult male in good conditions and male genitalia (USNM no. 1928), deposited in the Diptera Collection, National Museum of Natural History (USNM), Washington, DC, USA.Distribution:Culex dunni has been found in Central and South America, including Belize [Cx. dunni was collected in the municipalities of Iranduba, Juru\u00e1, Juta\u00ed, Manaus and Urucar\u00e1, Amazonas State; in Bataguassu Municipality, Mato Grosso do Sul State; Carmo da Mata and Goian\u00e1 Municipalities, Minas Gerais State; Almeirim, Juruti and Prainha Municipalities, Par\u00e1 State; Canan\u00e9ia, Dourado, Pariquera-A\u00e7u, and Presidente Epit\u00e1cio Municipalities in S\u00e3o Paulo State (present study).g Belize , Brazil g Belize , Colombig Belize , 65, Cosg Belize , French g Belize , 67, Guag Belize , Mexico g Belize , 16, Nicg Belize , Panama g Belize , Surinamg Belize and Veneg Belize , 62, 68.DescriptionFemale.Head: antenna dark, flagellum normal, whorls with 4 or 5 setae, length 1.21\u20131.35 (1.26) (n\u2009=\u20095); proboscis dark-scaled, length 0.58\u20131.44 (1.19) (n\u2009=\u20095); maxillary palpus dark-scaled, length 0.18\u20130.19 (0.19) (n\u2009=\u20095). Occiput with dark brown erect forked scales. Thorax: integument brown; scutum covered with narrow, bronze falcate scales; possibly with whitish scales on anterior promontory, scutal fossa, dorsocentral and supraalar areas, but not forming a pattern. Scutellar scales withish; median lobe with 5 or 6 setae; lateral lobes each with 3 or 4 setae. Pleural setae with 2 types of colouring: brown with bronzy reflections: 5\u20137 antepronotal, 3\u20135 prealar; and pleural setae golden, hyaline: 5 or 6 upper mesokatepisternal, 4 or 5 lower mesokatepisternal, 4 or 5 upper mesepimeral, and 1 large lower mesepimeral. Pleura with patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few white scales. Wing: dark-scaled, vein R with 2 proximal patches of white scales separated by large patch of dark scales; occasionally vein C with small proximal patch of white scales; length 2.67\u20133.00 (2.86) (n\u2009=\u20095). Halter: scabellum, pedicel and capitellum brownish. Legs: as in Cx. atratus. Abdomen: tergum I dark-scaled; terga III-VIII dark-scaled with basal bands of white scales.Male. [Figs.\u00a0Head: antenna verticillate, length 1.03\u20131.19 (1.13) (n\u2009=\u20095); proboscis length 1.13\u20131.68 (1.45) (n\u2009=\u20095); maxillary palpus length 1.25\u20131.77 (1.51) (n\u2009=\u20095); palpomere III with inconspicuous whitish basal ring. Wing: length 2.49\u20132.76 (2.61) (n\u2009=\u20095). Genitalia: tergum IX lobes slightly globose, apex glabrous, median portion each with 15\u201320 slender, simple setae; distance between lobes smaller than half basal width of 1 lobe. Gonocoxite oblong; proximal division of subapical lobe with 4 parallel setae : seta a more basal, narrow, with pointed apex; seta b long, spatulate, rounded apex, implanted on salient tubercle; seta c thin, slender, filiform, slightly curved, inserted between setae b and d; seta d filiform, long, spatulate, implanted on tubercle, with blunt apex. Distal division with short columnar process, with 5 setae: 3 filiform, narrow, pointed, apically inserted, subequal in size setae (seta f), 1 filiform seta with hooked apex (seta h), and 1 large, long, broad, asymmetrical, ribbed seta arising subapically (seta l); 1 saber-like, ribbed seta (seta s) arising apically. Gonocoxite with 5 slender, hyaline, short, inconspicuous setae on ventromesal surface; sternomesal surface with long, strong evenly dispersed setae. Gonostylus as in Cx. atratus, with large gonostylar claw, with slightly rounded apex. Aedeagus with ventral process of lateral plate with numerous spicules; lateral process pointed and directed dorsolaterally. Proctiger with tergum X long, sinuous, somewhat elongated in outline, inner process pointed, narrow and long.e. Figs.\u00a0e, 10 EssPupa. [Figs.\u00a0Cx. atratus except for followings characters. Cephalothorax: setae 1,2-CT 4- or 5-branched; seta 4-CT 3-branched; seta 8-CT 4-branched; seta 11-CT single or double; seta 12-CT double. Trumpet with pinna of median size, irregular in shape, length 0.16\u20130.23 (0.20) (n\u2009=\u200910), distal margin opposite to meatal cleft, which has a large and conspicuous emargination; tracheoid area, darker, extending 0.15\u20130.23 (0.20) (n\u2009=\u200910) from base; trumpet index 12.4\u201320.0 (14.5) (n\u2009=\u200910). Abdomen: seta 9-VIII with 2 simple branches; paddle index 1.56\u20131.95 (1.71) (n\u2009=\u200910).a. Figs.\u00a0c, 4c SimLarva. [Figs.\u00a0Cx. atratus except for followings characters. Head: length 0.64\u20130.79 (0.74) (n\u2009=\u200910), width 1.02\u20131.16 (1.11) (n\u2009=\u20095). Antennal length 0.48\u20130.57 (0.54) (n\u2009=\u200910). Seta 1-A inserted 0.34\u20130.38 (0.37) (n\u2009=\u200910) from antennal base; seta 14-C double, strong. Abdomen: comb of segment VIII with 25\u201335 scales of similar size arranged in 3 or 4 rows. Segment X length 0.31\u20130.35 (0.34) (n\u2009=\u200910), siphon/saddle index 3.36\u20134.22 (3.87) (n\u2009=\u200910). Siphon: long, slender, index 6.2\u20138.9 (7.4) (n\u2009=\u200910); pecten with 12 marginal spines as from on basal 0.30. Seta 1-S with 4 ventral pairs and 6 dorsal pairs.a. Figs.\u00a0c, 6c In Bionomics. Immature specimens of Cx. dunni were collected in permanent and semi-permanent partially shaded ground habitats, with slightly turbid water, associated with herbaceous vegetation such as Pistia sp. The larvae were collected in remnants of the Atlantic Forest in southeastern Brazil and in transition areas between the Cerrado and the Atlantic Forest biomes, in association with Cx. ensiformis and Cx. comptus\u00a0n. sp.RemarksCulex dunni was described by Dyar [Cx. dunni to be identical to Cx. ensiformis of Bonne-Wepster & Bonne based on characteristics of the male genitalia. Bonne & Bonne-Wepster [Cx. dunni with Cx. ensiformis, and that Cx. ensiformis can be distinguished from Cx. dunni by the crescent-shaped plate at base of gonocoxite and the pattern of scales on the scutum. Dyar & Shannon [Cx. ruffinis from an adult male from Barro Colorado Island, Canal Zone, Panama. Komp [Cx. ruffinis with Cx. dunni, considering a possible misinterpretation of some features of the male genitalia in the original description. In addition, the author hypothesized that the male genitalia of Cx. commevynensis were similar to those of Cx. dunni, and that the differences noted by Bonne-Wepster & Bonne [Cx. dunni to a probable confusion with Cx. ensiformis, considered by them as a morphologically close species. Rozeboom & Komp [Cx. commevynensis possesses \u201ca hair-like\u201d seta on the proximal division of the subapical lobe, while Cx. dunni has several \u201cspines\u201d in that position, distinguishing the species. Later, Foote [Cx. commevynensis and suspected that this species was not valid; this author considered Cx. dunni, Cx. commevynensis and Cx. zeteki to be closely related species. Although there has been intense discussion about the taxonomy of Cx. dunni, this species bears characteristics that clearly differ from the other species of the Atratus Group, especially with regard to features of the male genitalia and of the immature forms. The male genitalia of Cx. dunni differ from those of Cx. ensiformis and Cx. commevynensis in having four parallel setae on the proximal division of the subapical lobe while the other species have only two setae. Culex dunni has a long seta l in the distal division of the subapical lobe and Cx. ensiformis has a short seta. Culex dunni also differs in possessing several spicules on the ventral process of the lateral plate and in having tergum X appearing long, sinuous and elongated in outline while Cx. ensiformis and Cx. commevynensis have a lateral plate without spicules and a shorter tergum X. Based on larval characteristics, Cx. dunni differs from Cx. ensiformis in having subequal comb scales; double and strong seta 14-C, and short pecten spines with a conspicuously serrate border. Additionally, Cx. dunni differs from Cx. ensiformis and the other species in having a pinna of median size and a conspicuous emargination on the distal margin opposite the meatal cleft. With respect to adult specimens, both Cx. dunni and Cx. ensiformis bear a patch of pale scales separated by dark scales on the base of vein R and occasionally a small pale patch on the base of vein C. However, Cx. dunni has bronze scales on the scutum, not forming a pattern and in the male, an inconspicuous whitish basal ring on palpomere III, different to what is observed in Cx. ensiformis, which possesses scutal scales with different colour that form a pattern and palpomere III of the male dark-scaled. by Dyar from spe by Dyar , conside-Wepster mentione Shannon describema. Komp synonymi & Bonne were the & Bonne attributm & Komp verifiedr, Foote describeCulex(Melanoconion)ensiformisBonne-Wepster & Bonne, 19191919Culex (Melanoconion) ensiformis Bonne-Wepster & Bonne, 1919: 176 [919: 176 ensiformis of Dyar (1923: 188) [Cx. dunni); Bonne & Wepster-Bonne (1925: 272) [Cx. zeteki); Foote (1954: 97) [Cx. zeteki, lectotype desig.); Pecor et al. (1992: 25) [23: 188) (synonym25: 272) (resurre25: 272) (\u2642G); Ro25: 272) (synonym954: 97) (resurre992: 25) (distr.)992: 25) (Brazil)992: 25) (distr.)Type material: Paratypes, pinned adult male with associated larval and pupal exuviae on slide, in poor condition (USNM no. 22709-BB638) and pinned adult female with associated larval and pupal exuviae on slide (USNM no. 22709-BB625) deposited in the Diptera Collection, National Museum of Natural History (USNM), Washington, DC, USA.Material examined: 155 specimens: 77\u2642G, 98Le, 143Pe, 7\u2642, 5\u2640. FSP-USP, Brazil: S\u00e3o Paulo State, Canan\u00e9ia Municipality, Vilarinho , coll. S\u00e1 et al. 14.vii.2015, det. S\u00e1 2015: SP166-02 ; SP166-07 ; SP166-08 ; SP166-09 ; SP166-11 ; SP166-12 ; SP166-14 ; SP166-15 ; SP166-16 ; SP166-17 ; SP166-18 ; SP166-19 ; SP166-20 ; SP166-22 ; SP166-24 ; SP166-25 ; SP166-26 ; SP166-27 ; SP166-28 ; SP166-33 ; SP166-34 ; SP166-35 ; SP166-37 ; SP166-38 ; SP166-39 ; SP166-40 ; SP166-41 ; SP166-42 ; SP166-44 ; SP166-46 ; SP166-47 ; SP166-48 ; SP166-49 ; SP166-52 ; SP166-53 ; SP166-55 ; SP166-56 ; SP166-57 ; SP166-58 ; SP166-59 ; SP166-60 ; SP166-62 ; SP166-65 ; SP166-66 ; SP166-68 ; SP166-69 ; SP166-70 ; SP166-73 ; SP166-75 ; SP166-76 ; SP166-77 ; SP166-78 ; SP166-79 ; SP166-80 ; SP166-81 ; SP166-82 ; SP166-88 ; SP166-89 ; SP166-91 ; SP166-93 ; SP166-94 ; SP166-96 ; SP166-97 ; SP166-99 ; SP166-100 (Pe); SP166-101 (Pe); SP166-102 ; SP166-103 (Pe); SP166-105 ; SP166-111 (Pe); SP166-112 (Pe); SP166-113 ; SP166-115A (Pe); SP166-115B (Pe); SP166-117 ; SP166-118 (Pe); SP166-119 ; SP166-120 (Pe); SP166-121 ; SP166-301 ; SP166-304 ; SP166-305 ; SP166-311 ; SP166-313 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, Folha Larga Farm , coll. S\u00e1 et al. 14.vii.2015, det. S\u00e1 2015: SP167-07 ; SP167-09 ; SP167-10 ; SP167-13 ; SP167-16 ; SP167-17 ; SP167-18 ; SP167-20 ; SP167-21 ; SP167-24 ; SP167-25 ; SP167-32 ; SP167-33 ; SP167-39 ; SP167-124 ; SP167-127 ; SP167-129 ; SP167-133 ; SP167-134 (Pe). S\u00e3o Paulo State, Canan\u00e9ia Municipality, Vilarinho , coll. S\u00e1 et al. 12.ii.2016, det. S\u00e1 2016: SP171-07 ; SP171-08 ; SP171-09 ; SP171-10 ; SP171-11 ; SP171-12B ; SP171-111 ; SP171-118 (Pe); SP171-119 ; SP171-143 ; SP171-144 (Pe); SP171-146 (Pe); SP171-147 (Pe). B.M.M-9 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, Itapitangui , coll. Forattini et al. 1983, det. Sallum 1983: HEP81-04 ; HEP81-05 (Pe); HEP 81-06 ; HEP81-07 (Pe); HEP81-08 ; HEP81-11 ; HEP81-12 (Pe); HEP81-13 ; HEP81-14 ; HEP81-15 ; HEP81-16 ; HEP81-18 ; HEP81-19 ; HEP81-20 ; HEP81-21 ; HEP81-23 ; HEP81-24 ; HEP81-25 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, Itapitangui , coll. Forattini et al. 1983, det. Sallum 1983: HEP81-10 ; HEP81-31 ; HEP81-33 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, estrada de Canan\u00e9ia , coll. Forattini et al. 12.ix.1984, det. Sallum 1984: HEP434-04 . Amazonas State, Humait\u00e1 Municipality, Realidade, , coll. Chaves et al. 22.vii.2016, det. S\u00e1 2016: Coleta07-Humait\u00e1-01 ; Coleta07-Humait\u00e1-02 . INPA, Brazil: Amazonas State, Manaus Municipality, Acampamento Colosso, Fazenda Esteio , coll. Hutchings et al. 2002, det. Sallum & Hutchings: Fam-000631 ; Fam-000632 (\u2642G); Fam-002314 (\u2642G); Fam-002925 (\u2642G); Fam-002927 (\u2642G); Fam-002932 (\u2642G). Amazonas State, Manaus Municipality, Fazenda Esteio ; coll. Hutchings et al. 2003, det. Sallum & Hutchings: Fam-004667 (\u2642G). Amazonas, Manaus, Fazenda Esteio , coll. Hutchings et al. 2002, det. Sallum & Hutchings: Fam-003224 (\u2642G). Amazonas State, Manaus Municipality, Fazenda Porto Alegre, BR-174 , coll. Hutchings et al. 2002, det. Sallum & Hutchings: Fam-003557 (\u2642G). Amazonas State, Manaus Municipality, Fazenda Porto Alegre, BR-174 , coll. Hutchings et al. 2002, det. Sallum & Hutchings: Fam-002343 (\u2642G). USNM, Brazil: Par\u00e1 State, Altamira Municipality, km 158, coll. Reinert et al. 9.xi.1974: 446Coll- 111-109 (Pe \u2642); 111-133 (Pe \u2640); 111-107 (Pe \u2640); 111-129 (Pe \u2642).Distribution:Culex ensiformis has been collected in Belize [n Belize , Bolivian Belize , Brazil n Belize , French n Belize and SuriDescriptionFemale.Head: antenna dark, flagellum normal, whorls with 5 setae, length 1.25\u20131.74 (1.49) (n\u2009=\u20095); proboscis dark-scaled, length 1.16\u20131.52 (1.40) (n\u2009=\u20095); maxillary palpus with dark scales, length 0.24\u20130.31 (0.27) (n\u2009=\u20095). Occiput with dark brown erect forked scales. Thorax: scutum covered with narrow, bronze, and golden falcate scales on acrostichal and dorsocentral areas; occasionally whitish scales on anterior promontory, supraalar, and prescutellar areas forming a pattern. Scutellar scales whitish; median lobe with 5 or 6 dark setae; lateral lobes each with 3 or 4 setae. Pleural setae with 2 types of colouring: brown with bronzy reflections: 8 or 9 antepronotal, 4 or 5 prealar; and pleural setae golden, hyaline: 3\u20135 upper mesokatepisternal, 3 or 4 lower mesokatepisternal, 4 or 5 upper mesepimeral and 1 large lower mesepimeral. Pleura with large patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few white scales. Wing: dark-scaled, vein R with 2 proximal patches of white scales separated by small patch of dark scales; vein C with proximal patch of white scales; wing length 2.58\u20133.38 (3.06) (n\u2009=\u20095). Halter: scabellum, pedicel and capitellum brownish. Legs: as in Cx. atratus. Abdomen: tergum I with dark scales; terga III-VII dark-scaled with basal bands of white scales; tergum VIII dark-scaled.Male. [Figs.\u00a0Head: antenna verticillate, length 1.05\u20131.63 (1.36) (n\u2009=\u20095); proboscis length 1.39\u20131.93 (1.65) (n\u2009=\u20095); maxillary palpus length 1.71\u20132.15 (1.99) (n\u2009=\u20095). Wing: length 2.69\u20133.16 (2.88) (n\u2009=\u20095). Genitalia: tergum IX lobes conical, elongate, slender, with apex glabrous, median portion each with 14\u201320 slender, simple setae; distance between lobes equivalent to basal width of 1 lobe. Gonocoxite oblong; proximal division of subapical lobe with 2 parallel setae (a and b): seta a more basal, narrow, slender, with pointed apex; seta b long, spatulate, with pointed apex, implanted on salient tubercle. Distal division with elongate columnar process, with 5 setae: 3 filiform, narrow, pointed, inserted apically, subequal in size (seta f), 1 filiform seta with hooked apex (seta h), and 1 short, broad, asymmetrical, ribbed seta arising subapically (seta l); 1 saber-like, ribbed seta (seta s) arising apically. Additionally, 1 small, hyaline, inconspicuous seta basally on columnar process. Gonocoxite with 3 or 4 slender, hyaline, short, inconspicuous setae on ventromesal surface. Gonostylus as Cx. atratus, with large gonostylar claw, with slightly pointed apex. Aedeagus with ventral process of lateral plate with small convexity; aedeagal sclerite with spicules on ventral surface. Proctiger with tergum X narrow, somewhat triangular in outline, with slightly pointed inner process.e. Figs.\u00a0f, 11 SimPupa. [Figs.\u00a0Cephalothorax: setae 1,2-CT 4- or 5-branched; seta 3-CT double; seta 4-CT 5-branched; seta 5-CT 3-branched; seta 6,7-CT 3-branched; seta 8-CT 7-branched; seta 9-CT 3-branched; seta 10-CT 6-branched; seta 11-CT double; seta 12-CT 4-branched. Trumpet long, slender, with dilated apex; pinna small, opening circular, pinna length 0.07\u20130.13 (0.11) (n\u2009=\u200910), distal margin opposite meatal cleft with shallow depression; tracheoid area extending 0.20\u20130.34 (0.29) (n\u2009=\u200910) from base; trumpet index 16.2\u201329.7 (24.2) (n\u2009=\u200910). Abdomen: seta 9-VIII with 2 simple branches; paddle index 1.49\u20131.95 (1.68) (n\u2009=\u200910).a. Figs.\u00a0d, 4d CepLarva. [Figs.\u00a0Head: length 0.70\u20130.81 (0.79) (n\u2009=\u200910), width 1.08\u20131.20 (1.13) (n\u2009=\u200910). Antennal length 0.62\u20130.70 (0.67) (n\u2009=\u200910); seta 1-A inserted 0.42\u20130.46 (0.45) (n\u2009=\u200910) from antennal base. Seta 5-C with 8 long branches; seta 11-C 3-branched; seta 13-C double. Abdomen: comb of segment VIII with 16\u201322 scales of different sizes arranged in 2 or 3 rows: upper rows with small, pointed scales; lower row with 5\u20139 large, pointed scales. Segment X length 0.32\u20130.39 (0.36) (n\u2009=\u200910), siphon/saddle index 4.26\u20134.95 (4.51) (n\u2009=\u200910). Siphon: long, slender, index 7.6\u201310.4 (9.2) (n\u2009=\u200910); pecten with 10 spines on basal 0.30 of siphon. Seta 1-S usually with 4 ventral pairs and 4 dorsal pairs.a. Figs.\u00a0d, 6d HeaBionomics. Immature specimens of Cx. ensiformis were collected in semipermanent partially shaded groundwater habitats with herbaceous vegetation such as Pistia sp. in remnants of the Atlantic Forest in association with Cx. dunni. Adults were collected in the Amazon Forest.RemarksCulex ensiformis was described by Bonne-Wepster & Bonne [Cx. dunni. Bonne & Wepster-Bonne [Cx. dunni. According to Bonne & Wepster-Bonne [Cx. dunni and Cx. ensiformis in the same material, because Cx. ensiformis possesses morphological differences, such as the crescent-shaped lateral plate and the scale pattern of the scutum, that can distinguish it from Cx. dunni. Senevet & Abonnec [Cx. ensiformis to be close to but distinct from Cx. dunni, and resurrected it from synonymy again. Rozeboom & Komp [Cx. ensiformis with Cx. zeteki and considered the former to be a synonym of Cx. zeteki based on features of the male genitalia and the color pattern of the scales on the scutum. Likewise, Foote [Cx. ensiformis in synonymy with Cx. zeteki based on the presence of two types of comb scales in the larva. Belkin [Cx. ensiformis as a distinct species close to Cx. commevynensis but not conspecific with Cx. zeteki, and designated a lectotype male associated with larval and pupal exuviae while resurrecting Cx. ensiformis . Pecor et al. [Cx. ensiformis and Cx. commevynensis based on the morphology of the pupal stage. According to these authors, Cx. ensiformis is most readily distinguished from Cx. commevynensis and the other species belonging to Atratus Group in the pupal stage, because it bears morphological characteristics markedly unique to this species, as follows: trumpet distinctly flared at the apex and a trumpet index greater than 10. Culex zeteki has a trumpet with a smaller pinna than in Cx. ensiformis. Culex dunni has a trumpet with a larger pinna than in Cx. ensiformis and with a conspicuous emargination. Culex commevynensis has a straight pinna which is not flared apically as in Cx. ensiformis. Regarding the larval stage, Cx. ensiformis can be distinguished from the other species belonging to the group in having seta 5-C with 5 or more long branches , and comb scales of two different sizes in 2 or 3 rows . Comb scales of uneven sizes can also be found in Cx. trigeminatus; however, Cx. ensiformis differs from Cx. trigeminatus in having a few large scales and in having seta 5-C with long branches reaching the base of seta 6-C. Adults of Cx. ensiformis can be distinguished from the other species in possessing vein R with two proximal patches of white scales separated by small patch of dark scales, vein C with a proximal patch of white scales and the scutum with a pattern of whitish, bronze and golden scales, whereas Cx. zeteki has entirely dark-scaled wings, Cx. trigeminatus has a single large patch of whitish scales on vein R, Cx. dunni has two short patches of whitish scales on vein R and Cx. comptus n. sp.\u00a0has dark and whitish scales on the scutum. Regarding male genitalia, Cx. ensiformis can be readily distinguished from Cx. dunni, Cx. zeteki and Cx. trigeminatus in having two parallel spatulate setae on the proximal division of the subapical lobe and conspicuous spicules on the ventral surface of the aedeagal sclerite. Culex ensiformis differs from Cx. comptus n. sp.\u00a0in having a short columnar process and a short seta l on the distal division of the subapical lobe. & Bonne from adu & Bonne synonymier-Bonne resurrecer-Bonne , Dyar ma Abonnec considerm & Komp comparede, Foote maintain. Belkin considerr et al. providedCulex(Melanoconion)exedrusRoot, 19271927Culex (Melanoconion) exedrus Root, 1927: 580 [927: 580 exedrus of Dyar (1928: 341) [Cx. ruffinis); Rozeboom & Komp (1950: 89) [Cx. dunni), Stone & Knight (1957: 49) [ of Dyar 28: 341 [950: 89) (synonym957: 49) , in poor condition, with dissected genitalia on slide (USNM no. 30-1) deposited in the Diptera Collection, National Museum of Natural History (USNM), Washington, DC, USA.Distribution:Culex exedrus has been collected in the Porto das Caixas and Paracambi municipalities, Rio de Janeiro State, Brazil [, Brazil .Description Male. [Fig.\u00a0Cx. dunni, except as follows: Genitalia: gonocoxite with long, strong setae, aligned from base to apex on sternomesal surface. Proximal division of subapical lobe with 3 parallel setae : seta a inserted basally, narrow; seta b long, spatulate, borne on salient tubercle; seta c filiform, long, spatulate, borne on small tubercle, apex blunt; and 1 saber-like, ribbed seta (seta s) with broad apex, arising apically. Proctiger with tergum X long, sinuous, somewhat elongate in outline, inner process pointed, long and wide.le. Fig.\u00a0 EssentiaFemale. Not examined.Pupa and larva. Unknown.Bionomics. Immatures of Cx. exedrus were collected in ground water sites such as river margins, lagoons and ponds, associated with thick aquatic vegetation [getation .RemarksCulex exedrus was described by Root [Cx. exedrus with Cx. ruffinis Dyar & Shannon [Cx. exedrus as a junior synonym of Cx. dunni and maintained this taxonomic status until Cx. exedrus was resurrected from synonymy. Culex exedrus can be distinguished from Cx. dunni by features of the male genitalia, mainly a large number of long setae visibly lined up on the sternomesal surface of the gonocoxite; additionally, Cx. exedrus has seta s of the gonocoxite with a wider apex and a proctiger with the inner process of tergum X wider than in Cx. dunni. by Root based on by Root synonymi Shannon . Rozeboo Shannon considerCulex(Melanoconion)longisetosusS\u00e1 & Sallum n. sp.Type locality: Pariquera-A\u00e7u Municipality , S\u00e3o Paulo State, Brazil. Adults were collected in the Atlantic Forest and in seasonally flooded v\u00e1rzea forests along the Amazonas and Solim\u00f5es Rivers.Other localities: Pariquera-A\u00e7u Municipality, S\u00e3o Paulo State; Santo Ant\u00f4nio do I\u00e7\u00e1, Juta\u00ed, Coari and Itacoatiara municipalities, Amazonas State; and, in Juruti and Almeirim municipalities, Par\u00e1 State, Brazil.Type material: Holotype, pinned adult male with associated dissected genitalia on slide , with following collection data: Brazil, S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality , coll. Forattini et al., 11.i.1979, with Shannon trap, deposited in the Cole\u00e7\u00e3o Entomol\u00f3gica de Refer\u00eancia, Faculdade de Sa\u00fade P\u00fablica, Universidade de S\u00e3o Paulo (FSP-USP), S\u00e3o Paulo, S\u00e3o Paulo State, Brazil. Paratypes: 7 pinned adult males with associated dissected genitalia on slide from same collection as holotype and deposited in FSP-USP: specimen field no. 2661, accession no. FSP-USP E-15900 (coll. 10.vi.1980), specimen field no. 2695, accession no. FSP-USP E-15892 (coll. 17.vi.1980), specimen field no. 2756, accession no. FSP-USP E-15893 (coll. 11.xii.1980), specimen field no. 02, accession no. FSP-USP E-15894 (coll. 9.ii.1981), specimen field no. 2173, accession no. FSP-USP E-15895 (coll. 10.ii.1981), specimen field no. 01, accession no. FSP-USP E-15896 (coll. 29.i.1981), and specimen field no. 2967, accession no. FSP-USP E-15897 (coll. 12.iii.1981); 1 pinned adult male with associated dissected genitalia on slide , with following collection data: Brazil, S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality, Experimental Farm, 7.v.1984; 1 pinned adult male with associated dissected genitalia on slide , with following collection data: Brazil, S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality, Pariquera-Mirim district on 2-II-1985, both deposited in the FSP-USP; and 5 pinned adult males with associated dissected genitalia on separate slides, from different locations: specimen field no. ProV-053607, accession no. INPA-DIP 004574, with following collection data: Brazil, Par\u00e1 State, Juruti, Recreio, Parana de Dona Rosa, Amazon River , coll. Hutchings et al. 30-31.x.2003, det. Sallum & Hutchings 2016; specimen field no. ProV-047936, accession no. INPA-DIP 004575, with following collection data: Brazil, Par\u00e1 State, Almeirim Municipality, Arumanduba, Amazon River , coll. Hutchings et al. 19-20.x.2003, det Sallum, Hutchings & S\u00e1 2017; specimen field no. ProV-005165, accession no. INPA-DIP 004576, with following collection data: Brazil, Amazonas State, Santo Ant\u00f4nio do I\u00e7\u00e1 Municipality, Parana do Canini, Solim\u00f5es River , coll. Hutchings et al. 15-16.ix.2003, det. Hutchings & S\u00e1 2017; specimen field no. ProV-044118, accession no. INPA-DIP 004577, with following collection data: Brazil, Amazonas State, Coari Municipality, Ilha do Botija, Trocaris, Solim\u00f5es River , coll. Hutchings et al. 25-26.ix.2003, det. Hutchings & S\u00e1 2017; specimen field no. ProV-057487, accession no. INPA-DIP 004573) with following collection data: Brazil, Amazonas State, Itacoatiara Municipality, S\u00e3o Jorge, Parana da Eva, Amazon River , coll. Hutchings et al. 7-8.ix.2003, det. Hutchings & S\u00e1 2017, all deposited in the Cole\u00e7\u00e3o de Invertebrados, Instituto Nacional de Pesquisas da Amaz\u00f4nia (INPA), Manaus, Amazonas State, Brazil.Material examined: 3 G\u2642, 3 \u2642. INPA, Brazil: Par\u00e1 State, Juruti Municipality, Recreio, Parana de Dona Rosa, Amazon River , coll. Hutchings et al. 30\u201331.x.2003, det. Sallum & Hutchings 2016: ProV-053597 (\u2642G). Par\u00e1 State, Almeirim Municipality, Arumanduba, Amazon River , coll. Hutchings et al. 19\u201320.x.2003, det. Sallum, Hutchings & S\u00e1 2017: ProV-047940 (\u2642G). Amazonas State, Juta\u00ed Municipality, S\u00e3o Raimundo, Parana do Cervalho, Solim\u00f5es River , coll. Hutchings et al. 16-17.ix.2003, det. Hutchings & S\u00e1 2017: ProV-007278 (\u2642G).ZooBank registration: The Life Science Identifier (LSID) for Culex (Melanoconion) longisetosus n. sp. is urn:lsid:zoobank.org:act: 2F0C0B21-08FE-458E-94D3-EB8D2550B5C8.Etymology: The name longisetosus is derived from a combination of the Latin noun saeta, meaning \u201cseta, bristle\u201d and with the Latin adjective l\u0101tus, meaning \u201cextensive, broad\u201d. Culex longisetosus is named in reference to the four long and spatulate setae borne ventromesally between the proximal and distal divisions of the subapical lobe of the male genitalia.Description Male. [Figs.\u00a0Head: antennal length 1.02\u20131.71 (1.25) (n\u2009=\u20095); proboscis entirely dark-scaled, length 1.04\u20131.65 (1.43) (n\u2009=\u20095); maxillary palpus dark-scaled, length 1.32\u20131.98 (1.71) (n\u2009=\u20094); palpomere II with small, basal patch of whitish scales; palpomere III with inconspicuous proximal patch of whitish scales; palpomeres IV and V dark-scaled, with long, strong setae. Occiput with dark brown, erect forked scales. Thorax: scutum covered with narrow, dark brown falcate scales, except anterior promontory and prescutellar area with whitish scales. Median scutellar lobe with 6 dark large setae; lateral lobes each with 4 setae. Pleural setae with 2 types of colouring: dark brown: 3\u20135 antepronotal, 4 or 5 prealar; and pleural pale golden, slender setae: 4 upper mesokatepisternal, 5 lower mesokatepisternal, 4 or 5 upper mesepimeral; lower mesepimeron with 1 long, strong seta. Pleura with distinct patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few white scales. Wing: dark-scaled; length 2.37\u20132.49 (2.45) (n\u2009=\u20095). Halter: scabellum and pedicel whitish, capitellum whitish with few brown scales. Legs: coxae pale; ventral surface of fore- and midfemur with longitudinal stripe of white scales; tibiae dark-scaled; joints of femur-tibia and tibia-tarsomere I with ring of pale scales; tarsi entirely dark-scaled. Abdomen: tergum I with dark scales; terga III-VII dark-scaled, with white basal bands. Genitalia: tergum IX lobes elongate, each with 12\u201314 slender, apically bifid, and simple setae in median portion; apex glabrous; distance between lobes less than basal width of 1 lobe. Gonocoxite oblong, narrow, small; subapical lobe divided into 2 columnar divisions; proximal division with 2 pointed setae (a and b); seta a shorter, slender, inserted basal to seta b; seta b spatulate, robust; gonocoxite with 4 long, spatulate setae on ventromesal surface; distal division with long columnar process, with 5 setae: 3 filiform, narrow, pointed, different in size (seta f), 1 long seta with hooked apex (seta h), and 1 large, broad, asymmetrical seta arising subapically (seta l); 1 saberlike seta (seta s) arising apically. Gonostylus with apex moderately rounded, short leaf-like gonostylar claw borne apically. Aedeagus with ventral process with small convexity.e. Figs.\u00a0g, 13 HeaRemarksCx. longisetosus n. sp. differ from Cx. atratus in possessing an inconspicuous basal patch of whitish scales on palpomere III and a small basal patch of whitish scales on palpomere II. The male genitalia of Cx. longisetosus n. sp.\u00a0can be distinguished from those of other species of the Atratus Group in having a long columnar process in the distal division, elongate and slightly widened from the base to the apex of the ninth tergal lobe, and 4 long, spatulate setae on the ventromesal surface of the gonocoxite.Adults of Culex(Melanoconion)longistylusS\u00e1 & Sallum n. sp.Type locality: Dourado Municipality , S\u00e3o Paulo State, Brazil. Adults were collected in transitional vegetation areas between the Atlantic Forest and Cerrado biomes, and in seasonally flooded v\u00e1rzea forest areas along the Amazon River.Other localities: Dourado and Presidente Epit\u00e1cio municipalities, S\u00e3o Paulo State; Bataguassu Municipality, Mato Grosso do Sul State; Senador Guiomard Municipality, Acre State; Itacoatiara Municipality, Amazonas State; Almeirim, Prainha, Obidos, Santar\u00e9m and Juruti municipalities, Par\u00e1 State.Type material: Holotype male pinned with associated dissected genitalia on slide , with following collection data: Brazil, S\u00e3o Paulo State, Dourado Municipality , coll. Forattini et al. 2.ix.1980, with CDC light trap at the edge of the forest, deposited in the Cole\u00e7\u00e3o Entomol\u00f3gica de Refer\u00eancia, Faculdade de Sa\u00fade P\u00fablica, Universidade de S\u00e3o Paulo (FSP-USP), S\u00e3o Paulo, S\u00e3o Paulo State, Brazil. Paratypes: 1 pinned adult male with dissected genitalia on slide , from the same collection as the holotype and deposited in the same institution (FSP-USP); 1 pinned adult male with dissected genitalia on slide , with following collection data: Brazil, Par\u00e1 State, Santar\u00e9m Municipality, Parana de Ituqui, Amazon River , coll. Hutchings et al. 25\u201326.x.2003, det. Hutchings 2015; 2 pinned adult males with dissected genitalia on separate slides , with following collection data: Brazil, Acre State, Senador Guiomard Municipality, Fazenda Experimental Catuaba, UFAC, BR-364 km 23 , coll. Hutchings & Carmo 23\u201324.viii.2016, S\u00e1 3.iii.2017; 2 pinned adult males with dissected genitalia on separate slides , with following collection data: Brazil, Par\u00e1 State, Almeirim Municipality, Para\u00edso, Paranaquara, Amazon River , coll. Hutchings et al. 21\u201322.x.2003, det. Hutchings 2015, deposited in the Cole\u00e7\u00e3o de Invertebrados, Instituto Nacional de Pesquisas da Amaz\u00f4nia (INPA), Manaus, Amazonas State, Brazil.Material examined: 50 G\u2642, 2 \u2642. FSP-USP, Brazil: S\u00e3o Paulo State, Presidente Epit\u00e1cio Municipality, Peixe River , coll. Gomes et al. 10.xii.1997, det. S\u00e1 2015: LAM. no. 01 (\u2642G); LAM. no. 02 (\u2642G). S\u00e3o Paulo State, Presidente Epit\u00e1cio Municipality, Jo\u00e3o Baiano Farm , coll. Gomes et al. 2.v.1998, det. S\u00e1 2015: LAM. no.05 (\u2642G); LAM. no. 06 (\u2642G); LAM. no. 07 (\u2642G). S\u00e3o Paulo State, Presidente Epit\u00e1cio Municipality, Campinal , coll. Gomes et al. 4.i.1999, det. S\u00e1 2015: LAM. no. 03 (\u2642G). Mato Grosso do Sul State, Bataguassu Municipality, Romualdo Farm , coll. Gomes et al. 2.viii.1997, det. S\u00e1 2015: LAM. no. 08 (\u2642G). INPA, Brazil: Par\u00e1 State, Almeirim Municipality, Arumanduba, Amazon River , coll. Hutchings et al. 19\u201320.x.2003, Hutchings and Sallum det.: ProV-047634 (\u2642G); ProV-047673 (\u2642G); ProV-047692 (\u2642G); ProV-047764 (\u2642G); ProV-047962 (\u2642G). Par\u00e1 State, Prainha Municipality, Fazenda JK, Parana do Mouratuba, Amazon River , coll. Hutchings et al. 22\u201323.x.2003, det. Hutchings 2015: ProV-048997 ; ProV-049054 (\u2642G); ProV-048945 (\u2642G). Par\u00e1 State, Prainha Municipality, Boca do Rio Curuauna, Amazon River , coll. Hutchings et al. 24-25.x.2003, det. Hutchings 2015: ProV-049608 . Par\u00e1 State, Almeirim Municipality, Para\u00edso, Paranaquara, Amazon River , coll. Hutchings et al. 2003, det. Hutchings 2015: ProV-055464 ; ProV-055376 . Par\u00e1 State, Obidos Municipality, Ilha do Amador \u201cIlha Grande\u201d, Parana do Capivara, Amazon River , coll. Hutchings et al. 29\u201330.x.2003, det. Hutchings 2015: ProV-050860 (\u2642G); ProV-050878 (\u2642G); ProV-050909 (\u2642G); ProV-050910 (\u2642G); ProV-050943 (\u2642G); ProV-050964 (\u2642G); ProV-050974 (\u2642G); ProV-050978 (\u2642G); ProV-050982 (\u2642G); ProV-051027 (\u2642G); ProV-051033 (\u2642G); ProV-051049 (\u2642G); ProV-051053 (\u2642G); ProV-051055 (\u2642G); ProV-051079 (\u2642G); ProV-051092 (\u2642G); ProV-051104 (\u2642G); ProV-051106 (\u2642G); ProV-051181 (\u2642G). Par\u00e1 State, Juruti Municipality, Recreio, Parana de Dona Rosa, Amazon River , coll. Hutchings et al. 30\u201331.x.2003, det. Hutchings 2015: ProV-053577 (\u2642G); ProV-053593 (\u2642G); ProV-053599 (\u2642G); ProV-053600 (\u2642G); ProV-053618 (\u2642G); ProV-053657 (\u2642G); ProV-053668 (\u2642G); ProV-053683 (\u2642G). Amazonas State, Itacoatiara Municipality, S\u00e3o Jorge, Parana da Eva, Amazon River , coll. Hutchings et al. 7\u20138.xi.2003, det. Hutchings 2015: ProV-057494 (\u2642G); ProV-057497 (\u2642G). USNM, Ecuador: (as Cx. ensiformis), coll. 3.xii.1981: EC8-1263(n 866) (\u2642G). Brazil: S\u00e3o Paulo State, Iguape Municipality (as Cx. ensiformis), coll. unknown, det. S.S. 1987: no. 050977-14 (\u2642G); S\u00e3o Paulo State, Canan\u00e9ia Municipality (as Cx. ensiformis) coll. unknown, det. S.S. 1987: no. 050977-15 (\u2642G).ZooBank registration: The Life Science Identifier (LSID) for Culex (Melanoconion) longistylus n. sp. is urn:lsid:zoobank.org:act:C0FD06D0-B7E2-4775-A8BB-DC776858132F.Etymology: The specific epithet longistylus is a combination of the Latin adjective longus (long) and the Latin noun stylus , in reference to the long columnar process in the distal division of the subapical lobe of the male genitalia.DescriptionMale. [Figs.\u00a0Head: antennal length 0.92\u20131.47 (1.23) (n\u2009=\u20096); proboscis entirely dark-scaled, length 1.23\u20131.64 (1.48) (n\u2009=\u20096); maxillary palpus dark-scaled, length 1.40\u20132.23 (1.73) (n\u2009=\u20096). Occiput with dark brown erect forked scales. Thorax: scutum covered with narrow, dark brown falcate scales, except prescutellar area with whitish scales. Median scutellar lobe with 6 large, dark setae; lateral lobes each with 4 setae. Pleural setae with 2 types of colouring: dark brown with bronzy reflections: 3\u20136 antepronotal; 3\u20135 prealar; and pleural setae golden, hyaline: 4 or 5 upper mesokatepisternal, 4 or 5 lower mesokatepisternal; 5 upper mesepimeral; lower mesepimeron with 1 long, strong seta. Pleura with patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few scales, extending dorsally on posterior margin. Wing: mostly dark-scaled, sometimes with minute patch of white scales at proximal end of vein C; length 2.08\u20132.45 (2.27) (n\u2009=\u20096). Halter: scabellum and pedicel whitish; capitellum pale brown with few golden scales. Legs: coxae pale; ventral surface of fore- and midfemur with longitudinal stripe of white scales; tibiae dark-scaled; joints of fermur-tibia and tibia-tarsomere I with ring of pale scales; tarsi entirely dark-scaled. Abdomen: tergum I with dark scales, terga III\u2013VII dark-scaled with white basal bands. Genitalia: tergum IX as illustrated ; seta a short, slender, inserted basal to seta b; seta b spatulate; gonocoxite with 3 short filiform setae with pointed apices on ventromesal surface; distal division with long columnar process, with 5 setae: 3 narrow, filiform, apically pointed setae, subequal in size (seta f), 1 long seta with hook-like apex (seta h), and 1 large, broad, ribbed asymmetrical seta arising subapically (seta l); 1 saber-like seta (seta s) arising apically. Gonostylus slender, slightly curved, tapering towards apex, apex moderately blunt, ventral surface with 2 apical hyaline setae; 1 short leaf-like gonostylar claw. Aedeagus with sclerotized, slightly pointed, dorsolaterally directed lateral process; ventral process straight; apical process convex. Proctiger with tergum X somewhat triangular in outline, inner process pointed. Paraproct elongate, crown with 9 or 10 simple blades. Cercal sclerite with 1 seta.e. Figs.\u00a0h, 14 HeaRemarksCulex longistylus n. sp. differ from the adults of Cx. atratus in having dark-scaled wings, occasionally with an inconspicuous patch of white scales on the base of vein C, and dark-scaled terga III-VII with white basal bands. Based on male genitalia, Cx. longistylus n. sp.\u00a0can be distinguished from the other species of the Atratus Group in possessing fine, subapically bifid setae interspersed with simple setae on tergum IX lobes, a long columnar process of the distal division with a large, broad and ribbed seta, lateral plate of the phallosome with a straight ventral process, and 3 short filiform setae on the ventromesal surface of the gonocoxite.Adults of Culex(Melanoconion)loturusDyar, 19251925Culex (Melanoconion) loturus Dyar, 1925: 241 [925: 241 (\u2642) holoCulex (Melanoconion) loturus of Dyar (1928: 342) [Cx. zeteki). of Dyar 28: 342 [28: 342) , in poor condition, with associated genitalia on slide (USNM no. 30-1) deposited in the Diptera Collection, National Museum of Natural History (USNM), Washington, DC, USA.Distribution:Culex loturus was collected in Venezuela at the margin of the Catatumbo River [bo River .DescriptionMale. [Fig.\u00a0Cx. zeteki, except as follows: Genitalia: distal division of subapical lobe with median columnar process; seta l large, long, asymmetrical, ribbed; aedeagus with apical process of lateral plate pointed, without ripples.le. Fig.\u00a0 EssentiaFemale, pupa and larva. Unknown.RemarksCulex loturus was described by Dyar [Cx. loturus and in Cx. zeteki he mentioned the presence of two appendages. Komp [Cx. loturus with Cx. zeteki Dyar [Cx. loturus which are identical to those of Cx. zeteki. Although Cx. loturus bears three setae on the proximal division, this species can be distinguished from Cx. zeteki in possessing a large subapical seta l on the distal division, and a slender apical process of the lateral plate that lacks ripples. by Dyar based on by Dyar mentionees. Komp synonymieki Dyar based onCulex(Melanoconion)spiniferS\u00e1 & Sallum n. sp.Type locality: Pariquera-A\u00e7u Municipality , S\u00e3o Paulo State, Brazil. Adults were collected in the southeastern Atlantic Forest.Type material: Holotype, pinned adult male with dissected genitalia on slide (accession no. FSP-USP E-15901), with following collection data: Brazil, S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality , coll. Forattini et al. 6.iii.1980, det. Sallum 1980, deposited in the Cole\u00e7\u00e3o Entomol\u00f3gica de Refer\u00eancia, Faculdade de Sa\u00fade P\u00fablica, Universidade de S\u00e3o Paulo (FSP-USP), S\u00e3o Paulo, S\u00e3o Paulo State, Brazil. Paratypes: 1 pinned adult male with dissected genitalia on slide (accession no. FSP-USP E-15902) from the same collection as the holotype; 1 pinned adult male with dissected genitalia on slide (accession no. FSP-USP E-15903), coll. Forattini et al. 19.iv.1979, det. Sallum 1980; 1 pinned adult male with dissected genitalia on slide (accession no. FSP-USP E-15904), coll. Forattini et al. 6.ix.1980, det. Sallum 1980, all deposited in FSP-USP.ZooBank registration: The Life Science Identifier (LSID) for Culex (Melanoconion) spinifer n. sp. is urn:lsid:zoobank.org:act:4C1F6F37-F488-4EBF-9F69-3523902A29F1.Etymology: From the Latin adjective spinifer meaning spiny. Culex spinifer is named in reference to the spicules present on the ventral process of the lateral plate of the aedeagus.DescriptionMale. [Figs.\u00a0Head: antennal length 1.41\u20131.71 (1.59) (n\u2009=\u20094); proboscis dark-scaled, with inconspicuous median, dorsal patch of whitish scales; proboscis length 1.41\u20131.66 (1.52) (n\u2009=\u20094); maxillary palpus dark-scaled, length 2.28\u20132.05 (2.15) (n\u2009=\u20094); palpomere II with inconspicuous basal patch of whitish scales; palpomere III with small basal patch of whitish scales; palpomere IV with inconspicuous basal patch of whitish scales; palpomere V dark-scaled, with long, strong setae. Occiput with dark brown forked erect scales. Thorax: integument dark brown; scutum with narrow, dark brown forked scales, mainly on median prescutellar area and median scutal fossa; with whitish scales on anterior promontory and other prescutellar areas. Median scutellar lobe with 6 large, dark setae; lateral lobes each with 3 or 4 setae. Pleural setae with 2 types of colouring: dark brown: 3\u20136 antepronotal, 3 or 4 prealar; and pleural pale golden, slender setae: 4 or 5 upper mesokatepisternal, 4 or 5 lower mesokatepisternal, 4 or 5 upper mesepimeral; lower mesepimeron with 1 strong, long seta. Pleura with distinct patch of broad, white scales on upper mesokatepisternum; lower mesokatepisternum with few white scales. Wing: dark-scaled, with inconspicuous basal patch of whitish scales on vein C; large basal patch of whitish scales on vein R; wing length 2.93\u20132.65 (2.79) (n\u2009=\u20094). Halter: scabellum, pedicel and capitellum whitish. Legs: coxae pale; ventral surface of fore- and midfemur with a longitudinal stripe of white scales; tibiae dark-scaled; joints of femur-tibia and tibia-tarsomere I with ring of pale scales; tarsi entirely dark-scaled. Abdomen: tergum I with dark scales; terga III-VII dark-scaled, with basal bands of white scales. Genitalia: tergum IX lobes elongate, each with 7\u201310 slender simple setae and few apically bifid setae in median portion, apex glabrous. Distance between lobes equivalent to basal width of 1 lobe. Gonocoxite oblong, small; subapical lobe divided into 2 columnar divisions; proximal division with 2 pointed setae (a and b); seta a shorter, slender, inserted basal to seta b; seta b spatulate, robust and stronger than seta a; gonocoxite with 2 or 3 short, pointed, hyaline setae on ventromesal surface; distal division with short columnar process, with 5 setae: 3 narrow filiform, apically pointed setae of different in sizes (seta f), 1 longer hook-like seta (seta h), and 1 short, broad, asymmetrical seta arising subapically (seta l); 1 saber-like seta (seta s) arising apically. Gonostylus with broad leaf-like gonostylar claw with pointed apex, arising apically. Aedeagus with ventral process slightly convex and with spicules. Proctiger with tergum X with slightly pointed inner process.e. Figs.\u00a0i, 16 HeaRemarksCulex spinifer n. sp. has spicules on the ventral process of the lateral plate similar to Cx. dunni. However, Cx. spinifer n. sp.\u00a0differs from Cx. dunni in having elongate and slender ninth tergal lobes. Moreover, it has only two filiform setae on the proximal division of the subapical lobe and a somewhat triangular-shaped tergum X. Culex spinifer n. sp.\u00a0differs from Cx. comptus\u00a0n. sp., Cx. longisetosus n. sp.\u00a0and Cx. longistylus n. sp.\u00a0by having a short columnar process on the proximal division of the subapical lobe, a broad seta l, however shorter than filaments of seta f, and a large and broad gonostylar claw. Additionally, adults of Cx. spinifer n. sp.\u00a0differ from those of Cx. caribeanus and Cx. trigeminatus in having the femora without pre-apical whitish rings and palpomere II with an inconspicuous proximal patch of whitish scales.Culex(Melanoconion)trigeminatusClastrier, 19701970Culex (Melanoconion) trigeminatus, Clastrier 1970: 473 [970: 473 (\u2642) holoCulex (Melanoconion) trigeminatus of Pecor et al. (1992: 27) [992: 27) (distr.)992: 27) (distr.)Type material: Holotype, pinned adult male from For\u00eat du Gallion, French Guiana, collected on 19\u201320.iv.1968 , deposited in the Museum National d\u02bcHistoire Naturelle (MNHN), Paris, France.Material examined: 56 specimens: 40 G\u2642, 24 Le, 37 Pe. FSP-USP, Brazil: S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality, Bra\u00e7o Magro, coll. S\u00e1 et al. 2014, 20.viii.2014, det. S\u00e1 2014: SP152-01 ; SP152-02 ; SP152-03 ; SP152-04 ; SP152-05 ; SP152-09 ; SP152-12 ; SP152-14 ; SP152-15 ; SP152-19 ; SP152-100 ; SP152-101 ; SP152-102 ; SP152-104 ; SP152-105 ; SP152-106 ; SP152-107 ; SP152-108 . S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality, road to Bra\u00e7o Magro farm, Lagoon in forest environment, coll. S\u00e1 et al. 2014, 16.ix.2014, det. S\u00e1 2014: SP157-03 ; SP157-08 ; SP157-10 ; SP157-12 ; SP157-16 ; SP157-18 ; SP157-19 ; SP157-101 ; SP157-104 ; SP157-107 . S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality, road to Bra\u00e7o Magro farm, stream on forest A, coll. S\u00e1 et al. 16.ix.2014, det. S\u00e1 2014: SP158A-01 ; SP158A-08 ; SP158A-09 ; SP158A-16 . S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality, Bra\u00e7o Magro, Lagoon, coll. S\u00e1 et al. 2016, det. S\u00e1 2016: SP184-22 (\u2642G). S\u00e3o Paulo State, Canan\u00e9ia Municipality, Taquari , coll. Forattini et al. 25.iii.1980, det. Sallum 1980: no. 241 ; no. 225 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, Itapu\u00e3 Farm , coll. Forattini et al. 6.iv.1981, det. Sallum 1981: no. 136 . S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality , coll. Forattini et al. 8.i.1981, det. Sallum 1981: no. 2242 ; no. 2491 . S\u00e3o Paulo State, Iguape Municipality , coll. Forattini et al. 6.x.1982, det. Sallum 1982: no. 3251 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, Folha Larga Farm \u2212\u200924.89273, \u2212\u200947.919048), coll. Forattini et al. 19.iv.1983, det. Sallum 1983: no. 3470 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, Vilarinho farm , coll. Forattini et al. 7.ii.1984, det. Sallum 1984: no. 3515 . S\u00e3o Paulo State, Canan\u00e9ia Municipality, Itapitangui , coll. Forattini et al. 11.iv.1985, det. Sallum 1985: EP035-01 , EP035-08 .Distribution:Culex trigeminatus has been collected in Brazil and French Guiana [h Guiana . In Brazh Guiana , Canan\u00e9ih Guiana , Par\u00e1 StDescriptionFemale.Head: antennal length 1.28\u20131.70 (1.46) (n\u2009=\u20095); proboscis dark-scaled, with median, dorsal patch of whitish scales, length 1.23\u20131.33 (1.28) (n\u2009=\u20095); maxillary palpus dark-scaled, length 0.21\u20130.25 (0.23) (n\u2009=\u20095). Occiput with erect, forked, pale brown scales. Thorax: scutum with narrow, dark brown to black falcate scales and narrow, whitish falcate scales on scutal fossa, dorsocentral, anterior promontory and supraalar areas forming a pattern. Scutellar scales whitish, median lobe with 5 or 6 setae, lateral lobes each with 3 setae. Pleural setae with 2 types of colouring: dark brown: 4\u20136 antepronotal, 4 or 5 prealar; and pleural setae golden: 4 upper mesokatepisternal, 3 or 4 lower mesokatepisternal, 4 upper mesepimeral, 1 large lower mesepimeral. Pleura with distinct patch of broad, whitish scales. Wing: dark-scaled, vein C with small proximal patch of whitish scales, vein R with large proximal patch of whitish scales; wing length 2.63\u20132.84 (2.67) (n\u2009=\u20095). Halter: scabellum, pedicel and capitellum pale brown. Legs: fore- and midfemur with conspicuous preapical ring of white scales. Abdomen: terga II-VII with basal bands of white scales, tergum VIII dark-scaled.Male. [Figs.\u00a0Head: antenna verticillate, length 0.96\u20131.12 (1.11) (n\u2009=\u20095); proboscis dark-scaled, with median patch of whitish scales, proboscis length 1.47\u20131.63 (1.53) (n\u2009=\u20095); maxillary palpus length 1.71\u20132.28 (1.96) (n\u2009=\u20095), palpomere III with basal patch of whitish scales; palpomeres IV and V with small basal patch of whitish scales. Wing: length 2.32\u20132.81 (2.51) (n\u2009=\u20095). Genitalia: tergum IX lobes with convex outer edge, apex glabrous, median portion each with 20\u201322 slender, simple setae; distance between lobes shorter than half basal width of 1 lobe. Gonocoxite narrow, oblong; proximal division with 4 parallel setae : seta a more basal, spoon-shaped; seta b robust, spatulate, inserted on tubercle; seta c thin, slender, filiform, inserted between setae b and d; seta d borne on tubercle apical to seta b, filiform, long, with slightly narrowed apex. Distal division with medium-sized, elongate columnar process, with 5 setae: 3 filiform, narrow, pointed, apically inserted, subequal sized (seta f), 1 filiform, hook-like apex (seta h), and 1 large, broad, asymmetrical ribbed seta with apex slightly pointed on median portion, arising subapically (seta l); and 1 saber-like, ribbed seta (seta s) arising apically. Gonocoxite with slender, hyaline, short, inconspicuous setae on ventromesal surface. Gonostylus as in Cx. atratus, except for dorsal surface of the apex which may bear 2 or 3 superficial, inconspicuous emarginations. Lateral plate of aedeagus with rounded apical process, ventral process with short pointed projection directed ventrobasally. Proctiger with tergum X somewhat triangular in outline, inner process pointed and short.e. Figs.\u00a0j, 17 EssPupa. [Figs.\u00a0Cephalothorax: seta 4-CT 3-branched; seta 5-CT 4-branched; seta 8-CT 6-branched; seta 12-CT 3- or 4- branched. Trumpet long, slender; pinna small, opening circular, pinna length 0.05\u20130.08 (0.06) (n\u2009=\u20099), distal margin opposite meatal cleft with small notch; tracheoid area extending 0.15\u20130.25 (0.22) (n\u2009=\u20099) from base; trumpet index 14.8\u201330.5 (20.9) (n\u2009=\u20099). Abdomen: seta 9-VIII with 2 simple branches; paddle index 1.40\u20131.71 (1.50) (n\u2009=\u20099).a. Figs.\u00a0e, 4e CepLarva. [Figs.\u00a0Head: length 0.65\u20130.73 (0.69) (n\u2009=\u20099), width 1.05\u20131.12 (1.09) (n\u2009=\u20099). Antennal length 0.52\u20130.63 (0.56) (n\u2009=\u20099); seta 1-A inserted 0.39\u20130.46 (0.41) (n\u2009=\u20099) from antennal base. Seta 5-C with 5 short branches not reaching 6-C insertion; seta 10-C 4-branched; seta 13-C 3-branched. Abdomen: comb of segment VIII with 18\u201322 scales of different sizes arranged in 2 or 3 irregular rows: upper rows with small, pointed scales; lower row with 7\u20139 large, pointed scales. Segment X length 0.30\u20130.36 (0.33) (n\u2009=\u20099), siphon/saddle index 4.62\u20135.28 (4.88) (n\u2009=\u20099). Siphon: long, slender, index 7.7\u201313.0 (10.8) (n\u2009=\u20099); pecten with 13 spines on basal 0.30 of siphon. Seta 1-S usually with 4 ventral pairs and 2 dorsal pairs.a. Figs.\u00a0e, 6e HeaBionomics. Immatures of Cx. trigeminatus were collected in large, shaded lagoons with aquatic vegetation and, in small, flooded, shaded depressions and floodplain terraces of streams in Atlantic Forest, associated with Cx. albinensis and Cx. zeteki.RemarksCulex trigeminatus was described by Clastrier [Culex trigeminatus is more closely related to Cx. caribeanus within the Atratus Group, especially regarding adult specimens. However, Cx. trigeminatus differs from Cx. caribeanus in having palpomeres I and II dark-scaled, palpomere III with small basal whitish patch, palpomeres IV and V with inconspicuous whitish basal patches, and wings with proximal patches of white scales on veins C and R. The male genitalia of Cx. trigeminatus differ from those of Cx. caribeanus by having the median portion of the apex of seta l slightly pointed, robust and with blunt apex and proximal division with seta b strong, the lateral plate of the aedeagus having a rounded apical process and a ventral process with short, pointed projection directed ventrobasally. Fourth-instar larvae of Cx. trigeminatus differ from those of the other species of the Atratus Group by having seta 5-C with short branches that do not reach the insertion of seta 6-C and a siphon with only two pairs of dorsal setae. Furthermore, Cx. trigeminatus differs from Cx. ensiformis in possessing strongly serrated comb scales and short pecten spines. With respect to pupae, Cx. trigeminatus can be distinguished from the other species by having a slender trumpet and with the pinna small and appearing heart-shaped in dorsal view.lastrier based onCulex(Melanoconion)zetekiDyar, 19181918Culex (Melanoconion) zeteki Dyar, 1918: 122 [Cx. zeteci) deposited in the USNM. Type locality: Gat\u00fan, Canal Zone, Panama.918: 122 holotypeCulex (Melanoconion) zeteki of Dyar (1928: 339) [Cx. zeteci); Komp (1935: 9) [Cx. zeteci); Rozeboom & Komp (1950: 98) [Cx. zeteki); Pecor et al. (1992: 56) [ of Dyar 28: 339 [1935: 9) (\u2642 as Cx950: 98) (distr.)992: 56) with dissected genitalia (USNM no. 953) on slide, in poor condition, deposited in the Diptera Collection, National Museum of Natural History (USNM), Washington, DC, USA.Material examined: 37 specimens: 15 Le, 20 Pe, 10 \u2640, 10 \u2642. (FSP-USP): Brazil: S\u00e3o Paulo State, Pariquera-A\u00e7u Municipality, Pariquera-Mirim , coll. S\u00e1 et al. 2014, 21.viii.2014, det. S\u00e1 2014: SP155-29 . S\u00e3o Paulo, Pariquera-A\u00e7u, coll. S\u00e1 et al. 2014, 16.ix.2014, det. S\u00e1 2014: SP157-105 ; SP158A-04 ; SP158A-05 ; SP158A-06 ; SP158A-07 . Minas Gerais State, Cl\u00e1udio Municipality, Marcelo Farm, V\u00e1rzea da Rocinha , coll. Bergo et al. 2010, 13.iv.2010, det. Sallum 2014: MG50-10 . S\u00e3o Paulo State, Dourado Municipality , coll. Forattini et al. 7.i.1981, det. Sallum 1981: no.147 (\u2642G); no.150 ; no.151 (\u2642G); no.152 ; no.156 ; no.157 (\u2642G). S\u00e3o Paulo, Canan\u00e9ia Municipality, Iririaia-A\u00e7u , coll. Forattini et al. 18.i.1984, det. Sallum 1984: HEP352-07 . S\u00e3o Paulo, Canan\u00e9ia, Itapitangui , coll. Forattini et al. 11.iv.1984, det. Sallum 1984: HEP387-01 ; HEP387-03 ; HEP387-04 ; HEP394-05 . S\u00e3o Paulo, Canan\u00e9ia, Folha larga , coll. Forattini et al. 26.vii.1985, det. Sallum 1985: EP0005-01 ; EP0005-02 ; EP0005-04 (Pe); EP0005-05 ; EP0005-06 ; EP0005-07 ; EP0005-09 . S\u00e3o Paulo, Canan\u00e9ia, Itapitangui , coll. Forattini et al. 25.x.1988, det. Sallum 1988: EP0003-06 . Amazonas State, Humait\u00e1 Municipality, Realidade , coll. Chaves et al. 22.vii.2016, det. S\u00e1 2017: Coleta07-Humait\u00e1-03 (\u2640); Coleta07-Humait\u00e1-04 (\u2640); Coleta07-Humait\u00e1-05 (\u2640); Coleta07-Humait\u00e1-06 (\u2640); Coleta07-Humait\u00e1-74 (\u2640). Amazonas State, L\u00e1brea Municipality, Umari coll. Sallum et al. viii.2015, det. S\u00e1 2017: AM47-06 (\u2642). (INPA): Amazonas State, Manaus Municipality, Acampamento Colosso, Fazenda Esteio , coll. Hutchings & Aquino 2002, det. Sallum & Hutchings: Fam-000630 (\u2642G); Fam-000939 (\u2642G); Fam-002679 (\u2642G). Amazonas State, Jutai Municipality, S\u00e3o Raimundo, Parana do Cervalho, Solim\u00f5es River , coll. Hutchings et al. 16\u201317.ix.2003, det. S\u00e1 2017: ProV-007250 (\u2642G); ProV-007254 (\u2642G).Distribution:Culex zeteki has been found in Belize [n Belize , Brazil n Belize , Colombin Belize , French n Belize , Honduran Belize , Nicaragn Belize , Paraguan Belize , Panama n Belize , Surinamn Belize , 15, 69 n Belize , 70, 76,n Belize , Minas Gn Belize and S\u00e3o n Belize , 81.DescriptionFemale.Head: antennal length 0.81\u20131.31 (1.08) (n\u2009=\u20095); proboscis dark-scaled, length 1.07\u20131.33 (1.20) (n\u2009=\u20095); maxillary palpus dark-scaled, length 0.16\u20130.26 (0.22) (n\u2009=\u20095). Occiput with brown, erect, forked scales. Thorax: scutum with narrow, bronzy falcate scales. Median lobe of scutellum with 6 setae, lateral lobes each with 4 setae. Pleural setae with 2 types of colouring: dark brown: 4\u20136 antepronotal, 4 or 5 prealar; and pleural setae golden: 3 or 4 upper mesokatepisternal, 3 or 4 lower mesokatepisternal, 4 upper mesepimeral, 1 large lower mesepimeral. Pleura with indistinct broad patch of whitish scales. Mesepimeral integument dark, with distinct median whitish area completely separating darker upper and lower areas. Wing: dark-scaled, length 2.23\u20132.88 (2.55) (n\u2009=\u20095). Halter: scabellum, pedicel and capitellum whitish. Legs: as in Cx. atratus. Abdomen: tergum II-VII with basal bands of white scales, tergum VIII dark-scaled.Male. [Figs.\u00a0Head: antennal length 0.96\u20131.32 (1.15) (n\u2009=\u20095); proboscis entirely dark-scaled, length 1.24\u20131.81 (1.63) (n\u2009=\u20095); maxillary palpus dark-scaled, length 1.68\u20132.19 (1.85) (n\u2009=\u20095). Wing: length 2.28\u20132.74 (2.64) (n\u2009=\u20095). Genitalia: tergum IX lobes elongate, each with 20\u201322 slender, simple setae on median portion, apex glabrous, slightly pointed. Distance between lobes shorter than basal width of 1 lobe. Gonocoxite oblong, narrow; proximal division with 3 long, parallel setae : seta a long, slender with \u201copened\u201d apex; seta b, long with rounded apex; seta c slender, filiform, with curved apex. Distal division with median columnar process with 5 setae: 3 filiform, narrow, apically pointed and differently sized setae (setae f), 1 long seta hook-like at apex (seta h), and 1 large, long, asymmetrical seta arising subapically (seta l); 1 saber-like seta (seta s) arising apically; gonocoxite with short, inconspicuous, hyaline setae on ventromesal surface. Gonostylus as in Cx. atratus, except for dorsal surface of apex with 3 or 4 conspicuous folds and large gonostylar claw. Aedeagus with apical process with rounded ripples; ventral process slightly straight. Proctiger with tergum X asymmetrical, with rounded outer and inner processes.e. Figs.\u00a0k, 18 EssPupa. [Figs.\u00a0Cephalothorax: seta 5-CT 4-branched; seta 7-CT double. Trumpet slender; pinna small, asymmetrical, length 0.09\u20130.15 (0.12) (n\u2009=\u200910), distal margin opposite the meatal cleft with small, inconspicuous emargination; tracheoid area extending 0.15\u20130.21 (0.18) (n\u2009=\u200910) from base; trumpet index 12.0\u201320.0 (15.9) (n\u2009=\u200910). Abdomen: seta 9-VIII with 3 simple branches; paddle index 1.57\u20132.03 (1.69) (n\u2009=\u200910).a. Figs.\u00a0f, 4f CepLarva. [Figs.\u00a0Head: length 0.66\u20130.77 (0.71) (n\u2009=\u200910), width 1.04\u20131.13 (1.09) (n\u2009=\u200910). Antennal length 0.49\u20130.57 (0.53) (n\u2009=\u200910); seta 1-A inserted 0.35\u20130.39 (0.37) (n\u2009=\u200910) from antennal base. Seta 5-C with 4 long branches; seta 13-C double; seta 14-C with 2 strong branches. Abdomen: comb of segment VIII with 28\u201334 scales equal in size arranged in 3 or 4 irregular rows. Segment X length 0.30\u20130.37 (0.33) (n\u2009=\u200910), siphon/saddle index 3.90\u20134.88 (4.43) (n\u2009=\u200910). Siphon: long, slender, index 6.5\u20138.9 (8.1) (n\u2009=\u200910); pecten with 12 spines on basal 0.30 of siphon. Seta 1-S usually with 4 ventral pairs and 4 dorsal pairs.a. Figs.\u00a0f, 6f HeaBionomics. Immature specimens of Cx. zeteki were collected in shaded, stagnant lagoons with abundant aquatic vegetation.RemarksCulex zeteki was described by Dyar [Cx. zeteci. Rozeboom & Komp [Cx. zeteki. Culex zeteki differs from Cx. columnaris n. sp.\u00a0in having the gonostylus with folds on the dorsal surface. Fourth-instar larvae of Cx. zeteki can be distinguished by having comb scales with lateral fringes on the middle of the lateral margins and seta 5-C with 4 or 5 long branches which may reach seta 7-C insertion. Pupae of Cx. zeteki can be distinguished from the other species of the group by possessing a slender trumpet with a small pinna and having the distal margin opposite the meatal cleft with an inconspicuous rounded emargination. by Dyar as Cx. zm & Komp correcteThe primary diagnostic characters of the larval and pupal forms are summarized in Tables\u00a0Keys for identification of the Atratus Group and the species of the group(i)Keys based on adult morphology1Vertex with narrow, curved or linear decumbent scales; broad decumbent scales restricted to small lateral patches\u20262\u2013Vertex with broad decumbent scales\u2026Melanoconion Section (in part)2(1)Vertex with few narrow decumbent scales restricted to median area; lateral patch of broad decumbent scales large, evident in dorsal view\u20263\u2013Vertex with numerous narrow decumbent scales; lateral patch of broad decumbent scales small, almost indistinct in dorsal view\u2026Spissipes Section (in part)3(2)Thoracic pleural integument yellowish or lighter, contrasting with brown scutal integument\u2026Spissipes Section\u2013Thoracic pleural integument similar in color or lighter, not contrast sharply with scutal integument\u202644(3)Thoracic pleural integument lighter than scutal integument, with pattern of dark and pale areas on mesepimeron and mesokatepisternum; upper mesokatepisternum with a patch of white scales; legs with conspicuous or inconspicuous ring of white scales at all femur-tibia joints\u2026Atratus Group (Melanoconion Section)\u2013Thoracic pleural integument without pattern of dark and pale areas; upper mesokatepisternum without or with a small patch or a few white scales; legs with or without ring or patch of white scales at femur-tibia joints\u2026Other Groups (Melanoconion Section)Atratus GroupProboscis with distinct dorsal and median patches of whitish scales; fore- and midfemur with preapical ring of whitish scales Fig.\u00a0a\u20262Proboscis dark-scaled or with indistinct patch of pale scales; fore- and midfemur without preapical ring of whitish scales Fig.\u00a0b\u20263Fig.\u00a01Cx. caribeanusCosta (C) dark-scaled; vein R entirely dark-scaled. Male: palpomere I pale-scaled; palpomere III with long, distinct median patch of whitish scales on dorsal surface Fig.\u00a0a\u2026Cx. carCx. trigeminatusCosta (C) with proximal patch of whitish scales; vein R with a long line of whitish scales proximally. Male: palpomere I entirely dark-scaled; palpomere III with small, basal patch of whitish scales Fig.\u00a0b\u2026Cx. triCx. spinifer n. sp.Proboscis with indistinct dorsomedian patches of whitish scales; costa (C) with inconspicuous proximal patch of whitish scales; vein R with 1 long basal patch of whitish scales. Male: palpomere III with inconspicuous proximal patch of whitish scales Fig.\u00a0a\u2026Cx. spiProboscis without dorsal patch of whitish scales; vein R dark-scaled or with 2 basal patches of whitish scales separated by a dark scale-patch Fig.\u00a0b\u20264Fig.\u00a02Vein R with 2 basal whitish patches separated by dark-scaled patch Fig.\u00a0a\u20265Vein R entirely dark-scaled Fig.\u00a0b\u20267Fig.\u00a02Scutal integument dark brown/black with whitish and golden scales with patch of broad whitish scales as long as the mesothoracic spiracle (MS) Fig.\u00a0a\u20268Upper corner of mesokatepisternum (Mkm) with patch of broad whitish scales shorter than the mesothoracic spiracle (MS) Fig.\u00a0b\u20269Fig.\u00a02Cx. longisetosus n. sp.Costa entirely dark-scaled Fig.\u00a0a. Male: Cx. longistylus n. sp.Costa with proximal whitish scale-patch Fig.\u00a0c. Male: Cx. zeteki / Cx. loturusMesepimeral integument (Mm) dark with distinct median whitish area completely separating darker upper and lower areas Fig.\u00a0a\u2026Cx. zetMesepimeral integument (Mm) entirely dark or with indistinct median whitish area not completely separating the dark areas Fig.\u00a0b\u202610Fig.\u00a0Cx. atratusMesepimeral integument (Mm) dark, without median pale area; terga II-VIII (II-VIII-Te) with basolateral patches of whitish scales, without basal pale bands Fig.\u00a0a\u2026Cx. atrCx. columnaris n. sp.Mesepimeral integument (Mm) dark, with indistinct median pale area that does not completely separate the dark area; terga II-VIII (II-VIII-Te) with pale basal bands Fig.\u00a0b\u2026Cx. col Keys based on the morphology of male genitaliaAedeagal sclerite (AeS) broad and curved in lateral view, largely connected to dorsal process of lateral plate (LP)\u2026Spissipes SectionAedeagal sclerite (AeS) narrow and curved in lateral view, lightly connected to dorsal process of lateral plate (LP)\u20262Gonocoxite (Gc) small, narrow, oblong; gonostylus (Gs) narrow, dorsal area without setae; lateral plate (LP) with concave ventral process and pointed apical process\u2026Atratus Group (Melanoconion Section)Gonocoxite (Gc) conical, ovoid or globose; gonostylus variously modified; lateral plate (LP) with ventral and lateral processes otherwise modified\u2026Other Groups (Melanoconion Section)Atratus GroupProximal division of subapical lobe (pSL) without columnar process, setae only inserted on tubercles or directly inserted on surface of the gonocoxite Fig.\u00a0a\u20262Cx. columnaris n. sp.Proximal division of subapical lobe (pSL) with long columnar process divided apically Fig.\u00a0b\u2026Cx. colProximal division of subapical lobe (pSL) with 2 setae Fig.\u00a0a\u20263Proximal division of subapical lobe (pSL) with 3 or more setae Fig.\u00a0b\u20268Fig.\u00a03b of proximal division) columnar process with a short columnar process with a long with seta th) Fig.\u00a0a; tergumth) Fig.\u00a0b; gonocoth) Fig.\u00a0c\u20265l long with seta th) Fig.\u00a0d; tergumth) Fig.\u00a0e; gonocoth) Fig.\u00a0f\u2026Cx. atrCx. ensiformisTergum IX lobe (IX-TL) with simple setae Fig.\u00a0a; aedeagCx. spinifer n. sp.Tergum IX lobe (IX-TL) with simple and apically bifid setae Fig.\u00a0d; aedeagTergum IX lobe (IX-TL) elongate, longer than wide, with only simple setae or simple and few apically bifid setae Fig.\u00a0a\u20267Cx. longistylus n. sp.Tergum IX lobe (IX-TL) somewhat rounded, wider than long, with few simple and several apically bifid setae Fig.\u00a0b\u2026Cx. lonCx. comptus n. sp.Tergum IX lobe (IX-TL) slender, with simple setae Fig.\u00a0a; aedeagCx. longisetosus n. sp.Tergum IX lobe (IX-TL) slightly broad, with simple, apically bifid setae Fig.\u00a0d; aedeagLateral plate (LP) of aedeagus with spicules on ventral process Fig.\u00a0a; tergumLateral plate (LP) of aedeagus without spicules on ventral process Fig.\u00a0c; tergumCx. dunniGonocoxite (Gc) with long and dispersed setae on sternomesal surface Fig.\u00a0a; tergumCx. exedrusGonocoxite (Gc) with long and aligned setae on sternomesal surface Fig.\u00a0c; tergumProximal division of subapical lobe (pSL) with 3 setae Fig.\u00a0a; apicalProximal division of subapical lobe (pSL) with 4 setae Fig.\u00a0c; lateral of distal division of subapical lobe (dSL) with rounded and laterally directed apex of aedeagus with distinct ripples on apical process Fig.\u00a0a; seta lpex Fig.\u00a0b; gonostpex Fig.\u00a0c\u2026Cx. zetl of distal division of subapical lobe (dSL) with pointed and laterally directed apex of aedeagus with indistinct ripples on apical process Fig.\u00a0d; seta lpex Fig.\u00a0e; gonostpex Fig.\u00a0f\u2026Cx. lotl of distal division of subapical lobe (dSL) with rounded apex; seta b of proximal division of subapical lobe (pSL) long, slender, apically sinuous with pointed apex; seta b of proximal division of subapical lobe (pSL) long and stout Keys based on pupal morphology1Seta 9-VIII inserted at or near to caudolateral margin; caudolateral angle of segment VIII blunt\u2026Spissipes Section\u2013Seta 9-VIII inserted above of caudolateral margin; caudolateral angle of segment VIII slightly pointed\u202622(1)Trumpet narrow, long, length/width ratio 7\u00a0to\u00a030\u2026Atratus Group (Melanoconion Section)\u2013Trumpet thick, of shorter length, length/width ratio 5\u00a0to\u00a08\u2026Other Groups (Melanoconion Section)Atratus GroupTrumpet (T) with distal margin of pinna (Pi) without emargination; if present, emargination indistinct Fig.\u00a0a\u20262Trumpet (T) with distal margin of pinna with conspicuous emargination Fig.\u00a0b\u20264Fig.\u00a04Cx. atratusTrumpet (T) with a V-shaped pinna (Pi); trumpet large, wider at apex than at base Fig.\u00a0a; trumpePinna (Pi) small, not V-shaped; trumpet narrow from base to apex Fig.\u00a0c; trumpeCx. trigeminatusTrumpet index 20; pinna (Pi) short, somewhat rounded, meatal cleft (MC) short; distal margin opposite meatal cleft with small notch Fig.\u00a0a\u2026Cx. triCx. zetekiTrumpet index 17; pinna (Pi) heart-shaped in lateral view, becoming slender at base, meatal cleft (MC) long; distal margin opposite meatal cleft with small, rounded emargination Fig.\u00a0b\u2026Cx. zetCx. ensiformisTrumpet (T) long; pinna (Pi) cup-shaped in lateral view; trumpet index > 20; distal margin opposite meatal cleft (MC) with indistinct, shallow transverse depression Fig.\u00a0a\u2026Cx. ensTrumpet (T) moderately long; pinna (Pi) narrow; trumpet index < 16; distal margin opposite meatal cleft with indistinct longitudinal notch Fig.\u00a0b\u20265Fig.\u00a04c.14\u2026Cx. dunniTrumpet (T) widened distally; distal margin opposite meatal cleft with large emargination Fig.\u00a0a; trumpec.15\u2026Cx. comptus n. sp.Trumpet (T) narrow; distal margin opposite meatal cleft with indistinct longitudinal fissure Fig.\u00a0b; trumpe(iv)Keys based on fourth-instar larvae morphology1Seta 2-C present; seta 14-C inserted anteriorly to 15-C\u2026Spissipes Section \u201cpartim\u201d\u2013Seta 2-C absent; seta 14-C and 15-C inserted at same level or 14-C slightly anterior to 15-C\u202622(1)Siphon slender and long, index 7\u201310; seta 1-S with 2\u20134 short pairs of dorsolateral setae; thoracic and abdominal integument without spicules; segment X with few spicules on posterior margin\u2026Atratus Group (Melanoconion Section)\u2013Siphon thick and short, index lower than 7; seta 1-S with 2 short or long pairs of dorsolateral setae; thoracic and abdominal integument with distinct or indistinct spicules; segment X with several spicules on posterior margin\u2026Other Groups (Melanoconion Section)Atratus GroupComb scales (CS) of segment VIII different in size and shape: long, pointed and laterally fringed, and shorter apicolaterally fringed scales Fig.\u00a0a\u20262Comb scales (CS) of segment VIII similar in size and shape Fig.\u00a0b\u20263Fig.\u00a04Cx. trigeminatusSeta 5-C with 5 short branches not reaching 6-C insertion; seta 13-C triple Fig.\u00a0a; siphonCx. ensiformisSeta 5-C with 8 long branches extending beyond 6-C insertion; seta 13-C double Fig.\u00a0d; siphonSegment VIII with comb scales in 3 rows Fig.\u00a0a; seta 1Segment VIII with comb scales in 4 rows Fig.\u00a0c; seta 1Cx. atratusSeta 13-C simple Fig.\u00a0a; pectenCx. comptus n. sp.Seta 13-C double Fig.\u00a0c; pectenCx. zetekiSeta 2-VIII with 2 or 3 branches; seta 5-VIII with 3 branches Fig.\u00a0a; comb sCx. dunniSeta 2-VIII with 1 or 2 branches; seta 5-VIII with 3 or 4 branches Fig.\u00a0c; comb sCx. atratus, Cx. caribeanus, Cx. commevynensis, Cx. dunni, Cx. ensiformis, Cx. trigeminatus, and Cx. zeteki. Adults of the group can be readily identified by having the vertex with narrow, decumbent scales restricted to the central area, a pleural integument with a striking pattern of dark and pale areas, and a patch of white scales on upper mesokatepisternum. In the male genitalia, the aedeagal sclerite is slender and curved in lateral view, the gonocoxite is oblong and narrow, and the gonostylus is narrow, simple and tapering to the apex. The trumpet of pupae is thin, long with a length/width ratio of 10 or higher. The fourth-instar larvae have a long, slender and tapering to apex siphon, with 3 or 4 pairs of small dorsolateral setae 1-S.The Atratus Group proposed by Sirivanakarn includedCx. atratus is 7.0 and Cx. trigeminatus larvae possess only 2 pairs of dorsolateral setae on the siphon. These characteristics disagree with the diagnosis for the group provided by Sirivanakarn [Cx. atratus and Cx. trigeminatus from the other species of the Group, being diagnostic of these two species.Thus, according to Sirivanakarn , immaturvanakarn but theyCx. theobaldi (Lutz).In addition, there are several characters that are useful for identification of species of the Atratus Group. Our comparative observations of adults of all examined species clearly indicate that the presence of a ring of white scales on all of the femoro-tibial joints, represents a character that helps recognize species of the group. However, other species of the Melanoconion Section also possess white scales on the knees, such as Culex exedrus can be distinguished from Cx. dunni by having several long setae visibly lined up on the sternomesal surface of the gonocoxite, seta s of gonocoxite with a large apex, and a proctiger with a large inner process of tergum X. Therefore, these features justify the resurrection of Cx. exedrus from synonymy with Cx. dunni. Similarly, Cx. loturus was resurrected from synonymy with Cx. zeteki based on the possession of a large seta l borne subapically on the distal division of the subapical lobe and a slender apical process without ripples of the lateral plate of the aedeagus.Furthermore, examination of the available material resulted in the discovery of five new species of the Atratus Group, based on morphological characters of adults, male genitalia and, where possible, of immature stages.Culex (Melanoconion) currently comprises 14 species and it has been markedly updated with respect to the number of known species, their bionomics and distribution, providing tools to facilitate the identification of the adult and immature stages of the species in the group. As a result, the current knowledge leads us to suggest the following composition of the Atratus Group: Cx. atratus , Cx. caribeanus, Cx. commevynensis, Cx. columnaris n. sp., Cx. comptus n. sp., Cx. dunni (syn. Cx. ruffinis), Cx. ensiformis, Cx. exedrus, Cx. longisetosus n. sp., Cx. longistylus n. sp., Culex loturus, Culex spinifer n. sp., Culex trigeminatus and Culex zeteki. Additional studies utilizing molecular methods, particularly to investigate phylogenetic relationships within the Atratus Group, and to determine the placement of the group within the genus Melanoconion, are necessary.The Atratus Group of"} +{"text": "Gryllus bimaculatus, is registered as an edible insect by the Korean food and drug administration. The aim of this study was to investigate the effect of Gui-A-Gra on testicular damage induced by experimental left varicocele in male Sprague Dawley rats. A total of 72 rats were randomly divided into the following six groups (12 rats in each group): a normal control group (CTR), a group administrated with Gui-A-Gra 1.63 gm/kg (G1.63), a group administrated with Gui-A-Gra 6.5 gm/kg (G6.5), a varicocele (VC)-induced control group (VC), a VC-induced group administrated with Gui-A-Gra 1.63 gm/kg (VC + G1.63), and a VC-induced group administrated with Gui-A-Gra 6.5 gm/kg (VC + G6.5). Rats were administrated 1.63 or 6.5 gm/kg Gui-A-Gra once daily for 42 days. Indicators of sperm parameters, histopathology, reproductive hormones, oxidative stress, endoplasmic reticulum (ER) stress, inflammation, and mitochondrial apoptosis were analyzed to evaluate effects of Gui-A-Gra on VC-induced testicular dysfunction. Gui-A-Gra administration to VC-induced rats significantly (p < 0.05) increased sperm count and sperm motility, Johnsen score, spermatogenic cell density, serum testosterone, testicular superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase, GPx4, and steroidogenic acute regulatory protein (StAR) level. Moreover, pretreatment with Gui-A-Gra significantly (p < 0.05) decreased terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) positive cells/tubules, serum luteinizing hormone (LH), serum follicle-stimulating hormone (FSH), testicular tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin-6 (IL-6), malondialdehyde (MDA), reactive oxygen species (ROS)/reactive nitrogen species (RNS) level, glucose-regulated protein-78 (Grp-78), phosphorylated c-Jun-N-terminal kinase (p-JNK), phosphorylated inositol-requiring transmembrane kinase/endoribonuclease 1\u03b1 (p-IRE1\u03b1), cleaved caspase-3, and BCL2 associated X protein: B-cell lymphoma 2 (Bax: Bcl2) ratio in VC rats. These results suggest that protective effects of Gui-A-Gra on VC-induced testicular injury might be due to its antioxidant, anti-inflammatory, and androgenic activities that might be mediated via crosstalk of oxidative stress, ER stress, and mitochondrial apoptosis pathway.Gui-A-Gra, a commercial insect powder from Varicocele (VC) is characterized by dilation and tortuosity of internal spermatic vein (pampiniform plexus), a network of veins that drains testicular tissues . VC is cOxidative stress and testicular apoptosis are well documented causes of testicular dysfunction ,3. PlasmGryllus bimarculatus powder that has recently been registered as an edible insect in Korea [Gryllus bimarculatus has pharmacological activity such as antioxidant and anti-inflammatory effects [Gryllus bimarculatus have beneficial antioxidant, hypocholesterolemic, and antimicrobial properties [G. bimaculatus include glycosaminoglycan which exhibits anti-inflammatory effects [Gryllus bimarculatus extract can prevent diabetes, liver disease, and arthritis [Gryllus bimarculatus on male reproductive functions has not been reported yet. Therefore, the objective of this study was to determine the protective effect of Gryllus bimaculatus powder for the recovery from testicular dysfunction and its associated male fertility condition in a VC-induced rat model. The roles of inflammation, oxidative stress, endoplasmic reticulum (ER) stress, and mitochondrial (intrinsic) pathway in VC testicular tissues were also examined to determine molecular mechanisms involved in the protective effect of Gryllus bimaculatus.It has been reported that antioxidant supplements can alleviate male infertility by scavenging ROS and modulating inflammatory responses and the antioxidant system . Gui-A-Gin Korea . Gryllus effects ,18. A reoperties . The con effects . Recent rthritis ,22,23. Hp < 0.05). Pretreatment with G 6.5 significantly increased sperm count in both vas deference and epididymis of VC rats (p < 0.05). Sperm motility in vas deference and epididymis in VC rats showed remarkable increases after pretreatment with G1.63 or G6.5 (p < 0.05) . The fer < 0.05) .p < 0.05). Johnsen\u2019s score and spermatogenic cell density in the VC group were significantly (p < 0.05) decreased compared to those in the CTR group as compared to the CTR group. However, serum LH and FSH levels were significantly decreased in VC + G1.63 and VC + G6.5 groups. Levels of IL-6 and TNF-\u03b1 were remarkably (p < 0.05) upregulated in the VC group as compared to the CTR group. Pretreatment with Gui-A-Gra significantly (p < 0.05) downregulated these parameters in the VC + G1.63 and VC + G6.5 groups (Serum testosterone level was significantly decreased in the VC group as compared to the CTR group . It was 5 groups .p < 0.05) enhanced MDA level and ROS/RNS level compared to rats in the CTR group. Treatment with G1.63 and G6.5 significantly (p < 0.05) restored these parameters in the VC group. VC-induced rats showed significant decreases of testicular levels of SOD, GPx, and catalase levels as compared to rats in the CTR group. These levels were remarkably (p < 0.05) increased after pre-treatment with G1.63 or G6.5. No significant difference in these parameters was observed between VC + G1.63 and VC + G6.5 groups.Results of lipid peroxidation parameters , ROS/RNS) and antioxidant enzymes in testicular tissues are presented in p < 0.05) increases of GRP-78, p-IRE1\u03b1/ IRE1\u03b1, and p-JNK/JNK as compared to rats in the CTR group. In contrast, levels of GRP-78, p-IRE1\u03b1/IRE1\u03b1, and p-JNK/JNK levels in VC + G6.5 group were remarkably (p < 0.05) decreased as compared to those in the VC group. Levels of GRP 78 and p-JNK/JNK in VC + G1.63 group were lower than in the VC group, although differences between the two groups were not statistically significant. However, the p-IRE1\u03b1/IRE1\u03b1 level in VC + G1.63 group was significant decreased as compared to the VC group. Levels of pro-caspase-3 were similar among all groups. VC-induced rats showed prominently increased expression of cleaved caspase-3 and Bax:Bcl2 ratio compared to rats in the CTR group, although the increase was not statistically significant compared with the CTR group. In contrast, the cleaved caspase 3 and Bax:Bcl2 ratio in the VC + G6.5 group was significantly (p < 0.05) decreased as compared to the VC group : B-cell lymphoma 2 (Bcl2) ratio, StAR, and Gpx4 were analyzed in testis tissues by western blotting. Results are shown in VC group E. The clVC-induced rats showed significantly decreased expression levels of StAR as compared to rats in the CTR group. However, treatment with Gui-A-Gra restored levels of StAR in varicocelized rats. Cell-specific expression of StAR, Grp 78, and cleaved caspase 3 proteins in testis tissues was further analyzed by immunohistochemistry staining A\u2013C. A daThe present work used an experimental VC model to determine treatment effect of Gui-A-Gra on VC. This work extended studies on pathophysiological mechanisms associated with VC and suggested an ameliorative effect of Gui-A-Gra on VC. This study is first to report a protective effect of Gui-A-Gra on testicular dysfunction and male infertility using a VC-induced rat model. Pretreatment with Gui-A-Gra significantly improved sperm parameters, regulated levels of reproductive hormones, and promoted spermatogenesis in VC rats. Results of testicular morphological analysis, TUNEL assay, immunohistochemistry, and western blot analyses indicated that Gui-A-Gra could also decrease germ cell apoptosis.Previous studies have shown testicular hypotrophy in patients with clinical VC, but not in patients with subclinical VC . In the In our study, VC-induced rats showed degenerative changes in mammalian testis such as testicular atrophy, apoptosis of germ cell, aberration of STs, and impaired spermatogenesis. Similar findings have been reported in previous experimental VC studies ,2,3. TesLeydig cells are located in the interstitial tissue of the testis where testosterone is synthesized. They are essential for spermatogenesis . The StAIn the present study, higher concentrations of testicular MDA were detected in VC rats. The results of our study were similar to the MDA results of human testicular biopsy samples from infertile patients with VC . FurtherApoptosis is another detrimental factor involved in the impairment of sperm quality in patients with VC . IncreasGryllus bimarculatus powder material under the name of Gui-A-Gra used for the experiments was supplied from 239bio Inc. , a facility accredited for hazard analysis and critical control point (HACCP) and good manufacturing practice (GMP). Cultivated adult G. bimarculatus were subjected to 1-day of defecation before sacrifice. The G. bimarculatus were then cleansed with tap water three times, sterilized at 100 \u00b0C for 3\u20135 min, and dried for 6 h to have moisture less than 5%. Finally, dried G. bimaculatus were ground and homogenized. The powder was then stored at \u221220 \u00b0C for further use.A commercial Seventy-two 7\u20138 weeks old male Sprague Dawley rats were purchased from Koatech and randomly divided into six groups (12 rats/group): (1) normal control (CTR) group; (2) Gui-A-Gra 1.63 gm/kg p.o. group (G1.63); (3) Gui-A-Gra 6.5 gm/kg p.o. group (G6.5); (4) varicocele (VC) group; (5) VC + Gui-A-Gra 1.63 gm/kg p.o. group (VC + G1.63); and (6) VC + Gui-A-Gra 6.5 gm/kg p.o. group (VC + G6.5). Rats were maintained in plastic cases (47 \u00d7 18 \u00d7 40 cm) (four rats per case) in controlled environment conditions . Rats had free access to water ad libitum and standard rat chow diet. All experiments were performed according to the Institutional Animal Care and Use Committee (IACUC) of Jeonbuk National University Hospital Laboratory Animal Center (cuh-IACUC-2017-13). After one week of acclimatization, left VC was induced for VC group, VC + G1.63 group, and VC + VC + G6.5 group of rats according to standard protocols . CTR and6 sperms/mL. Motile spermatozoa were analyzed with the formula of \u00d7 100). Results for sperm motility are expressed as percentages.Epididymal and vas deference sperm count and sperm motility were evaluated as described previously . In brieTestis tissues were fixed in Bouin\u2019s solution, dehydrated, embedded in paraffin wax, and sectioned into 5 \u03bcm slices. Testis sections were subjected to hematoxylin and eosin (H&E) staining and TUNEL staining as described previously . At leasSerum levels of testosterone , luteinizing hormone (LH) , and follicle-stimulating hormone (FSH) were measured using enzyme-linked immunosorbent assay (ELISA) per each manufacturer\u2019s protocols.Whole tissue supernatants were prepared as described previously . TesticuMalondialdehyde (MDA) levels in testis tissues were assessed using reagents provided by Northwest Life Science Specialties LLC . Briefly, MDA reaction of a colored complex was measured at an absorbance of 532 nm using a kinetic spectrophotometer . MDA levels are expressed as \u03bcmole of MDA/mg of wet testis tissue. Testicular ROS/RNS levels were quantified using an OxiSelect in Vitro ROS/RNS Assay Kit according to the manufacturer\u2019s protocol. Fluorescence of dichlorofluorescein (DFC) was measured with a SpectraMax Gemini XS fluorimeter at excitation/emission wavelengths of 480/530 nm as described previously [Paraffin-embedded consecutive testis tissue sections (5 \u03bcm in thickness) were deparaffinized with xylene, dehydrated with alcohol, and subjected to heat-mediated 1\u00d7 target retrieval solution at pH 6.0 . Endogenous peroxide activity was blocked with peroxidase-blocking solution (DAKO) for 15 min and washed with 1\u00d7 PBS buffer twice (5 min each). Non-specific bindings of testis section were further blocked with serum block solution for 10 min (DAKO) and incubated with primary antibodies cleaved caspase 3 , StAR , and Grp 78 at 4 \u00b0C overnight. Sections were then washed with 1\u00d7 PBS twice (5 min each) and incubated with a horseradish peroxidase (HRP)-labeled micropolymer conjugated secondary antibody at room temperature for 1 h. Prior to incubation, sections were rinsed with AEC substrate chromogens . Slides were then rinsed with deionized water for 5 min, counter-stained with hematoxylin, rinsed with distilled water, and mounted with mounting medium .Extraction of protein from testis tissue was conducted as described previously . Proteinp < 0.05. GraphPad PRISM 6.0 was used for graphical analysis .All quantitative data are expressed as mean \u00b1 standard error of the mean (SEM). Statistical analyses were performed using SPSS version 22 . One-way analysis of variance (ANOVA) was used to compare groups followed by Tukey\u2019s test for post-hoc analysis. Statistical significance was considered at In summary , our res"} +{"text": "Enterobacterales and its association with plasmid mediated quinolone resistance (PMQR), aminoglycoside modifying enzymes (AME) and Trimethoprim/Sulfamethoxazole (TMP-SMX) resistance is little known from North India. Therefore, the current study was aimed to investigate the frequency of Non-\u03b2-Lactam antibiotic resistance associated genes in extended spectrum \u03b2-Lactamase producing Enterobacterales. For this study, Non-Duplicate phenotypically confirmed ESBL producing Enterobacterales isolates (N = 186) were analyzed for ESBLs, PMQRs, AMEs and TMP-SMX resistance genes using polymerase chain reaction (PCR). PCR detected presence of PMQR genes in 81.29% (N = 139) of ESBL isolates (N = 171), AME genes in 60.82% and TMP-SMX resistance genes in 63.74% of the isolates. Molecular characterization of ESBL producing Enterobacterales showed 84.79% TEMbla followed by 73.68% CTX-Mbla, 43.86% SHVbla, 19.88% PER andbla 9.94% VEBbla, respectively. Analysis of PMQR genes revealed 77.7% aac(6\u2032)-lb-cr the most commonly detected gene followed by 67.63% oqxB, 62.59% oqxA, 43.17% qnrB, 19.42% qnrD, 18.7% qnrS, 9.35% qnrA, 3.6% qepA and 2.88% qnrC, respectively. Analysis of AMEs gene profile demonstrated 81.73% aac(6\u2032)-Ib, the most frequently encountered gene followed by 46.15% aph(3\u2032)-Ia, 44.23% ant(3\u201d)-Ia, respectively. A 100% prevalence of sul1, followed by dfrA (54.63%) and sul2 (15.74%) was observed. In summary, prevalence of ESBL-Producing genes (particularly TEMbla and CTX-Mbla) along with PMQR, AMEs, and TMP-SMX resistant genes may potentially aid in the transfer of antimicrobial resistance among these strains.Genetic context of extended spectrum \u03b2-Lactamase (ESBL) producing Enterobacterales [Enterobacterales and other clinically significant Gram-negative bacteria [Enterobacterales [Enterobacterales [qnr) gene mediated (ii) quinolones modifying aminoglycoside acetyltransferase encoding genes (aac(6\u2032)-Ib-c), (iii) plasmid-mediated quinolone efflux pumps qepA, oqxA, and oqxB [\u03b2-Lactam antibiotics are used for treating most of the human infections that are caused by Gram-negative bacteria belonging to the family cterales . Howevercterales . ESBLs abacteria ,2. Genesbacteria . Furthercterales . Chromoscterales ,5. Genercterales ,6,7,8. PEnterobacterales demonstrate resistance to TMP-SMX as well. However, little has been reported on the genetic context of various species of ESBL producing Enterobacterales and its association with, PMQR, AMEs TMP-SMX resistance exclusively from North India. Therefore, the current study was designed to analyze the distribution of non-\u03b2-lactam antibiotic resistance associated genes prevailing in ESBL producing Enterobacterales. To our knowledge, this is the first study that investigated the distribution of AME, PMQR and TMP-SMX resistance genes among ESBL producing Enterobacterales that are isolated from North India. Furthermore, this study included clinical isolates of different members of Enterobacterales , while the earlier studies limited their molecular characterization in two species (E. coli and K. pneumoniae) [Enterobacterales, an observation that has been made only a few times earlier.Literature indicates that synthesis of aminoglycoside modifying enzymes (AMEs) is an important AMR mechanism that produce high level of aminoglycoside resistance among Gram- negative bacteria ,10. Thesumoniae) ,10,13. IK. pneumoniae 16.13% (30/186), E. coli 9.67% (18/186), K. oxytoca 2.15% (4/186), P. mirabilis 1.61% (3/186) and P. vulgaris 0.53% (1/186) were resistant to all the antibiotics tested. Enterobacterales. The highest antibiotic resistance rate was noted for ampicillin 95.89% (70/73) followed by TMP-SMX 90.86% (169/186). The resistance rate of \u03b2-lactams were: cefazolin 94.08% (175/186), amoxicillin-clavulanic acid 77% (124/161), cefotaxime 82.8% (154/186), cefepime 66.67% (124/186), ceftazidime 89.78% (164/186), ceftriaxone 88.17% (164/186), cefoxitin 76.83% (126/164), cefpodoxime 86.11% (155/180), cefuroxime 86.02% (160/186), and ceftizoxime 83.3% (155/186), respectively. The resistance rate of fluoroquinolones were 75.27% (140/186), 69.89% (130/186), 76.88% (143/186), 75.27% (140/186), and 71.51% (133/186) for ciprofloxacin, levofloxacin, nalidixic acid, gatifloxacin, and moxifloxacin, respectively. Similarly, the resistance rate of aminoglycosides were 64% (119/186), 61% (114/186), 49% (91/186), and 59% (109/186) for gentamycin, tobramycin, amikacin, and kanamycin, respectively. The lowest resistance rates were associated with imipenem 43.01% (80/186) and meropenem 46.77% (87/186), respectively obtained, ectively .Enterobacterales. Among the total phenotypically confirmed ESBL isolates (N = 186), PCR confirmed presence of ESBL genes in 91.94% (171/186) of Enterobacterales isolates. However, genes coding for ESBL production were not detected from K. pneumoniae 2.69% (5/186), E. coli 2.69% (5/186), K. oxytoca 1.07% (2/186), P. mirabilis 1.07% (2/186), C. freundii 0.54% (1/186) and therefore, these isolates were not included for further analysis. ESBL genes were detected from pus (N = 97), respiratory tract specimens (N = 44), blood and body fluids (N = 30), respectively , E. coli 30.99% (53/171), P. mirabilis 7.6% (13/171), C. freundii 7.02% (12/171), K. oxytoca 5.2% (9/171), E. cloacae 5.2% (9/171), P. vulgaris 1.75% (3/171), and M. morganii 1.75% (3/171), respectively. Of the 91.94% (N = 171) genotypically confirmed isolates, TEMbla 84.79% (145/171) was the most common ESBL gene followed by CTX-Mbla 73.68% (126/171), SHVbla 43.86% (75/171), PERbla 19.88% (34/171) and VEBbla 9.94% (17/171), respectively.ectively . The detEnterobacterales (N = 139) as follows; K. pneumoniae 44.6% (62/139), E. coli 31.65% (44/139), P. mirabilis 8.63% (12/139), C. freundii 5.03% (7/139), K. oxytoca 5.03% (7/139), E. cloacae 2.16% (3/139), P. vulgaris 2.16% (3/139), and M. morganii 0.72% (1/139), respectively (aac(6\u2032)-lb-cr 77.7% (108/139) followed by oqxB 67.63% (94/139), oqxA 62.59% (87/139), qnrB 43.17% (60/139), qnrD 19.42% (27/139), qnrS 18.71% (26/139), qnrA 9.35% (13/139), qepA 3.6% (5/139), and qnrC 2.88% (4/139), respectively , majority of the isolates to had co-existence with TEMbla (13/13) and CTX-Mbla (8/13) gene (qnrB gene (N = 60) demonstrated coexistence with TEMbla (46/60), CTX-Mbla (43/60), and SHVbla (27/60). In contrast, strains carrying Aac-ib-cr gene (N = 108), most of the isolates showed coexistence with TEMbla (98/108), CTX-Mbla (84/108), SHVbla (47/108), PERbla (28/108), and VEBbla (13/108) (oqxA and oqxB as well. Among the isolates that carrying oqxA (N = 87) gene, majority of the isolates were possessing TEMbla (72/87), CTX-Mbla (66/87) and SHVbla (39/87), PERbla (17/87) and VEBbla (12/87), respectively (oqxB genes was carrying TEMbla (80/94), CTX-Mbla (71/94) and SHVbla (46/94), PEblaR (15/94) and VEBbla (11/94), respectively. It was also noted that Enterobacterales isolates that having higher minimum inhibitory concentration (MIC) values for ciprofloxacin (\u226516 \u03bcg/mL), nalidixic acid (\u226564 \u03bcg/mL), levofloxacin (\u226532 \u03bcg/mL),gatifoxacin (\u226532 \u03bcg/mL) and moxifloxacin (\u226532 \u03bcg/mL) mainly harboured Aac-ib-cr, qnrB, oqxA and oqxB genes. Further, the frequency of PMQR genes were high in isolates with higher quinolone MIC than their low MIC counterparts , 81.72% (152/186), 70.43% (131/186), and 90.32% (168/186), were resistant to fluoroquinolones, aminoglycosides and TMP-SMX, respectively. Out of the 91.94% (171/186) of the genotypically confirmed ESBL strains, PCR could detect 81.29% (PMQR), 60.82% (AME), 63.74% (TMP-SMX) of genes in these strains. Of the total PMQR genes (81.29%) detected, the distribution of genes in different members of ectively . PMQR geectively . Of the ectively . Among t13) gene . Similar(13/108) . This coectively . Similarterparts .Enterobacterales (N = 104) is as follows; K. pneumoniae 44.23% (46/104), E. coli 38.46% (40/104), P. mirabilis 2.89% (3/104), C. freundii 5.77% (6/104), K. oxytoca 3.84% (4/104), E. cloacae 2.89% (3/104), P. vulgaris 0.96% (1/104), and M. morganii 0.96% (1/104), respectively (aac(6\u2032)-Ib 81.73% (85/104), followed by aph(3\u2032)-Ia 46.15% (48/104), ant(3\u201d)-Ia 44.23% (46/104), aac(3)-IIa 45.19% (47/104), aph(3\u201d)-Ib 35.58%, (37/104), armA 14.42% (15/104), ant(4\u201d)-IIa 12.5% (13/104), aac(3)-Ib 10.58%(11/104), ant(2\u201d)-Ia 8.65% (9/104), aac(3)-Ia 6.73% (7/104), respectively (aac(2\u2032)-Ia, aac(6\u2032)-Ia, aac(6\u2032)-Ic and aph(3\u201d)-Ia were not detected in any of the strains analyzed (Out of the 60.82% (104/171) of AME genes detected, the distribution of these genes in the ectively . The disectively . Howeveranalyzed .TEMbla (43/47) and CTX-Mbla (38/47) genes. Similarly, strains carrying aac(6\u2032)-Ib gene (N = 85) demonstrated coexistence with TEMbla (75/85), CTX-Mbla (72/85), and SHVbla (43/85). However, strains carrying ant (3\u201d)-Ia gene (N = 46), majority of isolates showed co-existence with TEMbla (41/46), CTX-Mbla (35/46) and SHVbla (23/46). This coexistence of genes were also observed among the isolates that carrying aph(3\u201d)-Ia and aph(3\u201d)-Ib wherein majority of the strains were equally harbouring both TEMbla and CTX-Mbla genes (aac(6\u2032)-Ib, aph(3\u201d)-Ia, aac(3)-IIa, ant(3\u201d)-Ia genes, respectively that carried aac(3)-IIa genes (N = 47), majority of the isolate had co-existence with -M genes . Furtherectively . The ratectively .Enterobacterales isolates, the distribution of TMP-SMX resistance genes are as follows; K. pneumoniae 42.59% (46/108), E. coli 34.26% (37/108), P. mirabilis 5.56% (6/108), C. freundii 6.5% (7/108), K. oxytoca 5.56% (6/108), E. cloacae 4.63% (5/108), P. vulgaris 1.86% (2/108), and M. morganii 0.92% (1/108), respectively (sul1 100% (108/108), followed by dfrA 54.63% (59/108) and sul2 15.74% (17/108), respectively (Of the 63.74% (108/171) of TMP-SMX resistant ESBL producing ectively . These Tectively .TEMbla (95/108), CTX-Mbla (81/108) and SHVbla (51/108) genes, respectively. Similarly, strains carrying dfrA1 gene (N = 59) demonstrated coexistence with TEMbla (53/59) and CTX-Mbla (48/59) for TMP-SMX mainly harbored sul1 and dfrA1 genes. It was also observed that the frequency of TMP-SMX genes was higher in strains with high TMP-SMX MIC values , majority of the isolates were having co-existence with (48/59) . FurtherC values .p < 0.05) different from that found in the respiratory tract specimens were comparable with earlier studies [TEMbla (84.79%) followed by CTX-Mbla (73.68%), SHVbla (43.86%), PEblaR (18.71%) and SHVbla (9.94%), respectively. These findings were in accordance with an earlier study wherein most prevalent ESBL gene found was TEMbla (73%) followed by CTX-Mbla (25\u2013100%) and SHVbla (23%) [PERbla and VEBbla in the present study were comparable with the data reported by Khurana et al. [The current study investigated the frequency of non-\u03b2-lactam antibiotic resistance associated genes among ESBL producing studies ,22. The K. pneumoniae (44.6%) was having higher number of PMQR genes detected followed by E. coli (31.65%). This observation is in accordance with an earlier study wherein, PMQR genes were more frequently encountered among E. coli, Klebsiella species, and Enterobacter species [Enterobacter cloacae in this study. This is probably due to the difference in the geographical location as the earlier study was conducted in the southern part of India (where the usage of antibiotics is different). Further, the widespread antibiotic resistance prevalent in India may be attributed to readily availability of antibiotics across the pharmacy counters. This could play a major role in increased distribution of antibiotic-resistance genes throughout the population. This study included isolates that obtained from wound, respiratory tract, body fluid and blood specimens while other studies were performed mostly using isolates that are collected from urine [aac(6\u2032)-lb-cr (77.7%) which is in agreement with an earlier report wherein the prevalence rate was found to be 64.5% [qnrB (43.17%) was observed, which was in accordance with Yang et.al observation [qnrD, qnrS, qnrA, and qnrC [Enterobacterales isolates were found to be oqxB (67.63%), oqxA (62.59%) and qepA (3.6%), respectively. However, this efflux pump mediated drug resistance mechanism of bacteria can be subdued using various efflux inhibitory molecules [Enterobacterales in North India. However, the oqxA and oqxB prevalence rates were comparable with earlier reports wherein the prevalence rates were found to be 88% and 30% for oqxA and oqxB genes, respectively [oqxA and oqxB genes may be attributed to the geographical distribution and type of isolates studied, as most of the studies were conducted on E. coli and K. pneumonia isolates [qepA observed (3.6%) was similar with previous data (2%) in the literature [qepA in the current study may also indicate low incidence of qepA gene among different strains of Enterobacterales across the world [TEMbla and CTX-Mbla) were more likely to carry aac(6\u2032)-Ib-cr and qnrB genes. The genes that code for both ESBL and PMQR proteins are usually located on same plasmids and consequently that may have higher chances of transfer among the members of Enterobacterales. Therefore, it is very pertinent to comprehend the drug resistance mechanisms prevalent among the members of medically important bacteria as it may be a major concern for patient safety and in determination of therapeutic strategies.In the present study, PCRs detected presence of PMQR genes in 81.29% N = 139) of genotypically confirmed ESBL isolates (N = 171), indicating the presence of high frequency of PMQR genes among ESBL strains. Interestingly, 9 of genoeumoniae 4.6% was om urine . Of the coli 31.6%. This oand qnrC ,23. It wolecules , for insolecules . Furtherolecules . Furtherectively . Furthercoli 31.6%. This oisolates . The lowterature . This locoli 31.6%. This oEnterobacterales. This relatively higher prevalence rate of AMEs in ESBL producing strains may be due to co-existence of genes encoding ESBLs and AMEs in Gram-negative bacteria [K. pneumoniae (44.23%) and E. coli (38.46%). This was in accordance with an earlier study conducted by Haidar et al., wherein a higher prevalence of AME genes were reported among K. pneumoniae [aac(6\u2032)-Ib (81.73%) which is in agreement with the earlier studies [aac(6\u2032)-Ib with other AME genes observed may be attributed to the fact that the gene coding for aac(6\u2032)-Ib enzyme is frequently located within class I integrons. Further, it is known that the gene cassettes that carry other genes coding for AMEs can be easily incorporated into class I integrons resulting in the development of resistance to currently used aminoglycosides [aph(3\u2032)-Ia (46.15%), followed by ant(3\u201d)-Ia (44.23%), aac(3)-IIa (45.19%), and aph(3\u201d)-Ib (35.58%). The higher prevalence of aph(3\u2032)-Ia and aph(3\u201d)-Ib is alarming as this type of resistance may usually produce high level of aminoglycoside resistance. The prevalence of other AME genes were found to be relatively low, which is comparable with earlier studies [Genes encoding AMEs are prevalent in various groups of bacteria ,30,31,32bacteria . In thiseumoniae . In the was 73%) . The preycosides . The oth-IIa 45.1%, and aponiae 44.% and E. sul1, sul2, or dfrA genes are likely to be present either on chromosome or on plasmids [Enterobacterales. Further, among the genotypically confirmed TMP-SMX resistant strains (N = 108), 42.59% of K. pneumonia isolates were carrying TMP-SMX resistance genes, followed by E. coli (34.26%). However, due to the paucity of literatures, the comparison with earlier studies could not performed. To our knowledge, this new study report, the prevalence of TMP-SMX resistance genes among various clinical strains of ESBL producing Enterobacterales. A higher prevalence of sul1 (100%) followed by dfrA (54.63%) and sul2 (15.74%), genes were noted in this study. This higher prevalence of sul1 gene may be attributed to the fact that the sul1 genes are usually located within class I integrons and this particular characteristic might have further helped in its wide distribution [dfrA1 (33.91%) gene in the present study was in agreement with an earlier study wherein in the prevalence rate was also found to be high [Enterobacterales isolates that showed elevated MICs for TMP-SMX mainly harbored sul1 and dfrA1 genes indicating the likelihood of these genes in imparting resistance to TMP-SMX. However, no genes were detected from number of isolates that were having higher MIC values, suggesting the existence of alternative pathways of resistance in TMP-SMX resistant isolates.The TMP-SMX resistance genes such as plasmids ,34. In tplasmids . Howeverribution . The com be high . EnterobEnterobacterales. This hospital laboratory receives samples from two civil hospitals and three primary health care centers that are attached to it. Among the total samples analyzed (N = 2134), a total of 186 non-repetitive phenotypically confirmed ESBL producing Enterobacterales isolates (one organism per patient was included to avoid duplication) were obtained. All the isolates were identified by manual API\u00ae system and the results interpreted as recommended by the manufacturer. The strains included were K. pneumoniae (N = 74), E. coli (N = 58), P. mirabilis (N = 15), C. freundii (N = 13), K. oxytoca (N = 11), E. cloacae (N = 9), P. vulgaris (N = 3) and M. morganii (N = 3). All the clinical isolates were identified by standard laboratory procedure [Between July 2018 and June 2019, a total of 2134 clinical samples received in the Microbiology laboratory, Government Medical College and Hospital, Badaun, India were analyzed for ESBL producing strains of toca N = , E. cloaK. pneumoniae, C. freundii, K. oxytoca, E. cloacae, P. vulgaris, and M. morganii against Ampicillin (b) C. freundii, E. cloacae, and M. morganii against amoxicillin- clavulanic acid (c) C. freundii, and E. cloacae against cefoxitin (d) P. vulgaris, and M. morganii against cefpodoxime, respectively [E. coli (ATCC 25922) and Pseudomonas aeruginosa (ATCC 27853).The antibiotic susceptibility testing was conducted by modified Kirby Bauer disc diffusion method as recommended by the Clinical Laboratory Standards Institute (CLSI) . The antectively . QualityThe MIC of fluoroquinolones , aminoglycosides and TMP-SMX were determined by broth micro dilution method and the results were interpreted in accordance with the CLSI guidelines . The MICE. coli, K. pneumoniae, and K oxytoca). However, zone size with \u226422 mm cefpodoxime (10 \u03bcg), \u226422 mm with ceftazidime (30 \u03bcg), \u226427 mm with cefotaxime, indicated ESBL production for P. mirabilis [ESBL activity was initially screened using disk diffusion method as recommended by CLSI . Isolateirabilis .The double-disk synergy diffusion test (phenotypic confirmatory test for ESBL) was carried out as per CLSI recommendations. Briefly, ceftazidime (30 \u03bcg) and cefotaxime (30 \u03bcg) alone and in combination with clavulanic acid were used. The ESBL production is confirmed when there is an increase of zone diameter (\u22655 mm) around disk with antibiotic-clavulanic acid combination .E. cloacae, C. freundii, P. vulgaris, and M. morganii strains. This test was performed as disc diffusion assay on Mueller-Hinton agar (MHA). Briefly, antibiotic discs containing aztreonam (30 \u03bcg), ceftazidime (30 \u03bcg), ceftriaxone (30 \u03bcg), and cefotaxime (30 \u03bcg) were kept 30 mm apart (center to center) around amoxicillin-clavulanic acid (20 \u03bcg + 10 \u03bcg) disc on MHA plate inoculated with the organism to be tested. The MHA plates were incubated at 37 \u00b0C for 24 h. An increased zone of inhibition of any of the test antibiotic towards amoxicillin-clavulanic acid was considered as ESBL production [E. coli ATCC 25922 (non-beta-lactamases producer) and K. pneumoniae ATCC 700603 (ESBL producer), respectively.The disc approximation test was used to confirm the ESBL production in Enterobacterales using QIAamp DNA Mini Kit . The DNA samples obtained by this procedure were segregated into two aliquots; first aliquot was used as template for the subsequent PCR reactions and the second aliquot was stored at \u221280 \u00b0C , Ghaziabad, India) for future use.Bacterial DNA was obtained from the phenotypically confirmed ESBL strains of Enterobacterales isolates were subjected to molecular characterization of the relevant encoding genes such as SHV, blaCTX-M, blaTEM, blaPERbla, and VEBbla by PCR using primers and PCR conditions shown in All the phenotypically confirmed ESBL producing Enterobacterales isolates that resistant to fluoroquinolones were subjected to PCRs for detection of (i) qnr proteins coding genes such as qnrA, qnrB, qnrC, qnrD, and qnrS (ii) quinolones modifying aminoglycoside acetyltransferase coding genes (acc(6\u2032)-Ib-cr) and (iii) plasmid-mediated quinolone efflux pump protein encoding genes using primers and PCR conditions depicted in ESBL producing Enterobacterales were screened for AMEs coding genes aac(2\u2032)-Ia, aac(3)-Ia, aac(3)-Ib, aac(3)-IIa, aac(6\u2032)-Ia, aac(6\u2032)-Ib,aac(6\u2032)-Ic,ant(2\u201d)-Ia, ant(3\u201d)-Ia, ant(4\u201d)-IIa, aph(3\u2032)-Ia, aph(3\u201d)-Ia, aph(3\u201d)-Ib, armA using primers described in ESBL producing aminoglycosides resistant strains of sul1, sul2 and dfrA genes using primers and PCR conditions shown in 4)2SO4, 3 mM MgCl2, 0.2% Tween 20), 200 mM of each dNTPs, 0.5 \u00b5M of each primer, and 2.0 units of AURA Taq DNA polymerase. Amplification was carried out as follows: initial denaturation at 95 \u00b0C for 5 min; 30 cycles of denaturation at 95 \u00b0C for 30 s, annealing at 50\u201362 \u00b0C for 30 s, extension/elongation at 72 \u00b0C for 45 s; and a final elongation step at 72 \u00b0C for 5 min. PCR-generated products were detected by electrophoresis of 7 \u03bcL of each amplification mixture in 2% agarose gels in 1% Tris Borate-EDTA buffer and 0.5 \u00b5g/mL ethidium bromide.All isolates phenotypically resistant to TMP-SMX were subjected to PCR for detection of To identify the ESBL, PMQR, AME, and TMP-SMX resistance genes detected in the PCR assays, automated DNA sequencing of the amplicons were conducted. More specifically, multiplex PCR-generated products were separated in 2% low melting agarose gel with 1% Tris-acetate-EDTA buffer. The PCR products were excised from the agarose gel and purified using the QIAquick PCR purification kit as recommended by the manufacturer. The nucleotide sequencing of amplicons was conducted using an ABI 3730xl DNA Analyzer . Basic Local Alignment Search Tool (BLAST) program was used to compare each ESBL, PMQR, AME, and TMP-SMX resistance gene sequences against those available in gene bank at the National Center of Biotechnology Information database.p < 0.05 were considered as significant.Chi-squared test was used to compare the association between the origin of strain and type of resistance genes detected. The null hypothesis will be accepted if the presence of genes in all the groups were similar. Dunn\u2019s multiple comparisons test was performed to compare the differences in the number of resistance genes obtained between two categories of samples. All statistical analyses were performed using Graph pad Prism . The statistical difference values showing Enterobacterales and the association of these genetic determinants with PMQR, AME, and TMP-SMX resistance genes in the north India. The current study demonstrated widespread occurrence of PMQR, AME, and TMP-SMX drug resistant genetic determinants in the ESBL producing Enterobacterales strains. Screening of PMQR genetic elements in ESBL producing Enterobacterales strains revealed high prevalence of both aac(6\u2032)-Ib-cr and qnrB. However, molecular analysis of AMEs producing Enterobacterales strains showed high prevalence of aac(6\u2032)-Ib followed by aph (3\u2032)-Ia. On examination of TMP-SMX resistant strains, sul1 was found to be the most frequently encountered gene followed by dfrA. The association of ESBL-producing genes with the PMQR, AMEs, and TMP-SMX resistance genes may potentially aid in transfer of drug resistance determinants among these strains. Therefore, a complete understanding of PMQRs, AMEs, and other drug resistance mechanisms will help in determining rationale of treatment and infection control measures in hospital settings.In summary, this is the first study that investigated the occurrence of genetic determinants prevailing in ESBL producing"} +{"text": "Introduction: Intensive oncological treatment integrated with resection of metastases raised the clinical outcome of metastatic colorectal cancer (MCRC). In clinical practice, complex evaluation of clinical , and biological parameters addresses tailored, personalized multidisciplinary treatment strategies. Patients with MCRC unsuitable for first-line intensive medical treatments are prevalent and showed worse clinical outcome. After progression to oxaliplatin-based chemotherapy, aflibercept/FOLFIRI significantly improved clinical outcome, even if no survival benefit was reported in adjuvant fast relapsers by aflibercept addition. The case reported a young-elderly (yE) patient with KRAS mutant colorectal cancer rapidly progressing to adjuvant chemotherapy, unfit owing to comorbidities, with multiple pharmacogenomic alterations, who gained long-term survival in clinical practice by multidisciplinary treatment strategy consisting of first-line and re-introduction of aflibercept-containing chemotherapy and two-stage lung metastasectomies.Case presentation: A 71-years-old yE patient, unfit for intensive oncological treatments owing to Cumulative Illness Rating Scale (CIRS) stage secondary, affected by KRAS c.35 G>T mutant colorectal cancer, rapidly progressing with lung metastases after adjuvant XelOx chemotherapy, reached long-term survival 66 months with no evidence of disease after first-line and re-introduction of tailored, modulated aflibercept (4 mg/kg) d1,15-irinotecan (120 mg/m2) d1,15-5-fluorouracil (750 mg/m2/day) dd1\u20134, 15\u201318; and secondary radical bilateral two-stage lung metastasectomies. Safety profile was characterized by limiting toxicity syndrome at multiple sites (LTS-ms), requiring 5-fluorouracil discontinuation and aflibercept reduction (2 mg/kg), because of G2 hand-foot syndrome (HFS) for >2 weeks, and G3 hypertension. Pharmacogenomic analyses revealed multiple alterations of fluoropyrimidine and irinotecan metabolism: severe deficiency of fluorouracil degradation rate (FUDR), single nucleotide polymorphisms of UGT1A1*28 variable number of tandem repeats (VNTR) 7R/7R homozygote, ABCB1 c.C3435T, c.C1236T, MTHFR c.C667T homozygote, DPYD c.A166G, TSER 28bp VNTR 2R/3R heterozygote.Conclusions: In clinical practice, a complex management evaluating clinical parameters and RAS/BRAF genotype characterizing an individual patient with MCRC, particularly elderly and/or unfit owing to comorbidities, is required to properly address tailored, multidisciplinary medical and surgical treatment strategies, integrated with careful monitoring of superimposing toxicity syndromes, also related to pharmacogenomic alterations, to gain optimal activity, and long-term efficacy. KRAS/NRAS/BRAF genotype . We previously demonstrated that first-line intensive FIr-B/FOx triplet chemotherapy plus bevacizumab reached an objective response rate (ORR) of 82%, median progression-free survival (PFS) of 12 months, and overall survival (OS) of 28 months . Integragenotype . In non-tastases . In patitastases . Patienttastases , 8.KRAS/NRAS/BRAF genotype) parameters addresses tailored, multidisciplinary treatment strategies and biological d1, capecitabine (825 mg/m2 bid) d1\u201314, cycles repeated every 21 days, for six cycles. Safety profile was characterized by LTS-ms, specifically G2 HFS associated with G2 anemia d1,15-irinotecan (120 mg/m2) d1,15-5-fluorouracil (750 mg/m2/day) dd1\u20134, 15\u201318, cycles repeated every 28 days of secondary lung metastases with intra-lesion necrosis mutant MCRC rapidly progressing to adjuvant chemotherapy with bilateral lung metastases, unfit for intensive medical treatment owing to comorbidities, who was treated by first-line and re-introduction of aflibercept-containing chemotherapy followed by two-stage lung metastasectomies and gained in clinical practice by multidisciplinary treatment strategy long-term OS 66 months of metastatic disease with no evidence of disease at PFI 40 months.The case reported a yE patient with KRAS c.35 G>T (G12V) mutation mutation and shownd death , with sind death ; the poond death , 19. KRA cancers .KRAS c.35 G>A mutant status was significantly associated with worse clinical outcomes of patients with MCRC treated with FIr-B/FOx compared with KRAS/BRAF wild-type and other KRAS mutant patients , consistidedness . Adjuvanidedness , 8; in Sidedness , 30 and with PFS , 32. Aflwith PFS . Afliberwith PFS . Afliberwith PFS . At progS mutant . TripletS mutant .Then, because of long-term control of bilateral lung metastastes during first-line aflibercept/irinotecan and re-challenge, bilateral resections of lung metastases were performed. The diagnosis of mucinous lung metastases may justify such a long OS 66 months of metastatic disease without evidence of disease at PFS 50 months and PFI 40 months from second stage lung metastasectomies, thus realizing the effectiveness of the integrated lung metastasectomies. In a retrospective Spanish real-life analysis of 32 patients who underwent surgical resection after aflibercept/FOLFIRI , PR was Reported yE, unfit patient underwent first-line MCRC treatment with reduced doses of aflibercept, irinotecan, and fluorouracil. Nevertheless, safety profile was characterized by LTS-ms, particularly G2 HFS lasting >2 weeks with different other G2\u2013G1 toxicities. Because of limiting HFS and multiple pharmacogenomic alterations, 5-fluorouracil was discontinued; then, LTS-ms was observed, characterized by G3 hypertension, and re-introduction was planned with further aflibercept dose reduction. Reported prevalent toxicities with FOLFIRI/aflibercept were diarrhea (19.3%), mucositis 13.7%), asthenia (16.9%), HFS 2.8%), hypertension (2.9%), arterial (1.8%) and venous (7.9%) thromboembolic events, neutropenia (36.7%), and thrombocytopenia (3.3%) %, hypert. In Span.7%, asthUGT1A1*28 homozygote 7 repeats, ABCB1 c.C3435T and C1236T heterozygote, MTHFR\u2014c.C667T homozygote, DPYD c.A166G heterozygote, and TSER 28bp heterozygote VNTR 2R/3R. Dihydropyrimidine dehydrogenase gene (DPYD) and UGT1A1 SNPs variably influence fluoropyrimidines and irinotecan tolerability (DPYD c.496A > G (P = 0.022) and c.1896 T > C (P = 0.027), trendly with UGT1A1*28 SNPs (P = 0.054) , ABCB1 (71%), CYP3A4 (14%), and DYPD (15%), in the reported range , thus predicting occurrence of LTS-ms in patients at risk of gastrointestinal LT . UGT1A1*tropenia \u201349. 5-FUtropenia , 51. To ed range , 49. MosRAS/BRAF genotype of patients with MCRC, particularly the elderly and/or those who are unfit because of comorbidities, is required to properly tailor multidisciplinary medical and surgical treatment strategies to gain optimal activity and long-term efficacy, integrated with careful monitoring of toxicity syndromes, potentially related to pharmacogenomic alterations.In clinical practice, a complex management evaluating patient-related clinical parameters and Written informed consent was obtained from the patient for the publication of any potentially identifiable images or data included in this article.GB and ER were the medical oncologists responsible for clinical and bioclinical management of patient. AD'A, SG, and EAR were abdominal and thoracic surgeons responsible for surgical management of patient. MS performed pharmacogenomic analyses. All authors read and approved the final manuscript. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer AB declared a past co-authorship with one of the authors MS to the handling editor."} +{"text": "Chrysomallon squamiferum) is highly adapted to deep-sea hydrothermal vents and has drawn much interest since its discovery. However, the limited information on its genome has impeded further related research and understanding of its adaptation to deep-sea hydrothermal vents.The scaly-foot snail (Gigantopelta aegis), which inhabits similar environments. Using Oxford Nanopore Technology, 10X Genomics, and Hi-C technologies, we obtained a chromosome-level genome of C. squamiferum with an N50 size of 20.71 Mb. By constructing a phylogenetic tree, we found that these 2 deep-sea snails evolved independently of other snails. Their divergence from each other occurred \u223c66.3 million years ago. Comparative genomic analysis showed that different snails have diverse genome sizes and repeat contents. Deep-sea snails have more DNA transposons and long terminal repeats but fewer long interspersed nuclear elements than other snails. Gene family analysis revealed that deep-sea snails experienced stronger selective pressures than freshwater snails, and gene families related to the nervous system, immune system, metabolism, DNA stability, antioxidation, and biomineralization were significantly expanded in scaly-foot snails. We also found 251 H-2 Class II histocompatibility antigen, A-U \u03b1 chain-like genes, which exist uniquely in the Gigantopelta aegis genome. This finding is important for investigating the evolution of major histocompatibility complex (MHC) genes.Here, we report the whole-genome sequencing and assembly of the scaly-foot snail and another snail (Our study provides new insights into deep-sea snail genomes and valuable resources for further studies. Bathymodiolus platifrons) showed that, while most of the genes present in a related shallow-water mussel (Modiolus philippinarum) have been retained, many gene families have expanded in the\u00a0B. platifrons genome. These families include those that are associated with stabilizing protein structures, removing toxic substances from cells, and the immune response to symbionts , Octopus bimaculoides [GCF_0\u00a0011\u00a094135.1], Biomphalaria glabrata [GCF_000457365.1], Crassostrea gigas [GCF_000297895.1], Lottia gigantea [GCF_000\u00a0327385.1], Pomacea canaliculata [GCF_003073045.1], Pinctada fucata [GCA_0\u00a0022\u00a016045.1], and Helobdella robusta [GCF_000\u00a0326865.1] from the NCBI database and C. squamiferum and G. aegis from this research) were compared using blastp with the E-value threshold set as 1e\u22127. Then, alignment segments of each protein pair were concatenated using the in-house software Solar v0.9.6 [The TreeFam tool was usedr v0.9.6 . H-scorer v0.9.6 .RRID:SCR_011812) [A. californica\u2014C. gigas (\u223c516.3\u2013558.3 MYA), A. californica\u2014P. canaliculata (\u223c310\u2013496 MYA), A. californica\u2014O. bimaculoides (\u223c551\u2013628 MYA), C. gigas\u2014H. robusta (\u223c585\u2013790 MYA), and C. gigas\u2014P. fucata (394\u2009 MYA) [We obtained 406 one-to-one single-copy orthology gene families based on gene family classification. Then, these gene families were extracted and aligned using guidance from amino acid alignments created using the default parameters of the MUSCLE programm_011812) , 74 was 94\u2009 MYA) were useC. squamiferum and G. aegis using BWA-MEM (v0.7.12-r1039) [RRID:SCR_002105) [RRID:SCR_001876) [Approximately 50\u00d7 clean WGS reads were mapped to genomes of _010910) with def_002105) and \u201cSor_001876) with def_001876) .We used CAFE v2.1 to analyCNP0000854. The raw sequencing reads were also uploaded to the SRA database under accession No. CNP0000854. All supporting data are available in the GigaScience GigaDB database [The genome assemblies of these 2 genomes have been deposited in GenBank under accession No. database .Supplementary Figure S1.17-mer frequency distribution for C. squamiferum and G. aegis genomes.Supplementary Figure S2.Construction of Phylogenetic trees for ten representative molluscs using coding sequences of 407 single-copy orthologs.Supplementary Figure S3.Box plot of Ka and Ks values of 1,324 single copy orthologous genes from two deep-sea snails, one shallow-water snail, and two fresh-water snails.Supplementary Figure S4.Expansion pattern of HTR4 genes in two deep-sea snails.Supplementary Figure S5.KEGG enrichment analysis of unique gene families of G. aegis.Supplementary Table S1.Statistics of raw sequencing data of Chrysomallon squamiferum.Supplementary Table S2.Statistics of raw sequencing data of Gigantopelta aegis.Supplementary Table S3.Summary from the genome assembly of Chrysomallon squamiferum without using Hi-C data.Supplementary Table S4.Lengths of the 16 chromosomes assembled for Chrysomallon squamiferum.Supplementary Table S5.BUSCO assessment of the assembled genome of Chrysomallon squamiferum using metazoa_odb9 database.Supplementary Table S6.Summary of the genome assembly for Gigantopelta aegis.Supplementary Table S7.BUSCO assessment of the assembled genome for Gigantopelta aegis using the metazoa_odb9 database.Supplementary Table S8.General statistics of predicted protein-coding genes of Chrysomallon squamiferum.Supplementary Table S9.General Statistics of Predicted Protein-coding Genes of Gigantopelta aegis.Supplementary Table S10.Summary of predicted gene functions of the Chrysomallon squamiferum gene set.Supplementary Table S11.Summary of predicted gene functions of the Gigantopelta aegis gene set.Supplementary Table S12.Summary of repeat contents in four selected species.Supplementary Table S13.Gene family clusters in selected species.Supplementary Table S14.Estimation of mutation rates of two deep-sea snails.Supplementary Table S15.Ka and Ks values of 1,324 single copy orthologous genes from five snails.Supplementary Table S16.KEGG enrichment of expanded gene families of C. squamiferum.Supplementary Table S17.KEGG enrichment of unique gene families in G. aegis genome.bp: base pairs; BTBD6: BTB/POZ domain-containing protein 6; BUSCO: Benchmarking Universal Single-Copy Orthologs; BWA: Burrows-Wheeler Aligner; CAFE: Computational Analysis of gene Family Evolution; CAT: catalase; CR1: chicken repeat 1; DLD: dihydrolipoyl dehydrogenase; DLST: dihydrolipoyl succinyltransferase; DMBT1: deleted in malignant brain tumours 1; DNB: DNA nanoball; GAFT: glutamine-fructose-6-phosphate transaminase; GATK: Genome Analysis Toolkit; Gb: gigabase pairs; GP340: glycoprotein-340; Hi-C: high-throughput chromosome conformation capture; HIF-1\u03b1: hypoxia-inducible factor-1\u03b1; HIV: human immunodeficiency virus; Hsp90: heat shock protein 90; HTR4: 5-hydroxytryptamine receptor 4; IDH: isocitrate dehydrogenase; IUCN: International Union for Conservation of Nature; kb: kilobase pairs; KEGG: Kyoto Encyclopedia of Genes and Genomes; LINE: long interspersed nuclear element; LTR: long terminal repeat; Mb: megabase pairs; MHC: major histocompatibility complex; ML: maximum likelihood; MYA: million years ago; NCBI: National Center for Biotechnology Information; OGDC: \u03b1-ketoglutarate dehydrogenase complex; OGDH: oxoglutarate dehydrogenase; ONT: Oxford Nanopore Technologies; ORF: open reading frame; PAML: Phylogenetic Analysis by Maximum Likelihood; PSMC: pairwise sequential Markovian coalescent; SAG: salivary agglutinin; SNP: single-nucleotide polymorphism; SRA: Sequence Read Archive; SRCR: scavenger receptor cysteine-rich; TCA: tricarboxylic acid; TE: transposable element; TLR13: Toll-like receptor 13; TNF: tumour necrosis factor; Txn1: Thioredoxin 1; WGS: whole-genome sequencing.The authors declare that they have no competing interests.This work was supported by the National Key R&D Programme of China (No. 2018YFC0310702).Zongze Shao, S.L., G.F., and X.L. conceived and managed this project and amended the manuscript. X.Z., Y.Z., L.M., and I.S. performed the evolutionary analysis and wrote the manuscript. L.M., J.C., and Y.S. performed genome assembly and annotation. J.B., S.L., X.F., C.W., Zenghua Shao, H.L., N.L., and L.W. were responsible for sample collection, DNA extraction, and library construction.giaa139_GIGA-D-20-00187_Original_SubmissionClick here for additional data file.giaa139_GIGA-D-20-00187_Revision_1Click here for additional data file.giaa139_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giaa139_Reviewer_1_Report_Original_SubmissionTakeshi Takeuchi, Ph.D -- 7/31/2020 ReviewedClick here for additional data file.giaa139_Reviewer_1_Report_Revision_1Takeshi Takeuchi, Ph.D -- 10/9/2020 ReviewedClick here for additional data file.giaa139_Reviewer_2_Report_Original_SubmissionMathew J. Jenny -- 8/5/2020 ReviewedClick here for additional data file.giaa139_Reviewer_3_Report_Original_SubmissionReuben William Nowell, Ph.D. -- 8/10/2020 ReviewedClick here for additional data file.giaa139_Supplemental_Tables_and_FiguresClick here for additional data file."} +{"text": "MAPK mutations favor HNSCC survival, revealing the broad clinical utility of MAPK pathway mutations in prognosis and potentially in precision immunotherapy. TP53 mutations (median \u223c14 yr). We explored underlying outcome-favoring mechanisms with omics followed by preclinical models. Strikingly, multiple hotspot and non-hotspot MAPK mutations all abrogated ErbB3 activation, a well-established HNSCC progression signal. Inhibitor studies functionally defined ERK activity negatively regulating phospho-ErbB3 in MAPK-mutants. Furthermore, pan-pathway immunoprofiling investigations identified MAPK-mutant tumors as the only \u201cCD8+ T-cell\u2013inflamed\u201d tumors inherently bearing high-immunoreactive, constitutive cytolytic tumor microenvironments. Immunocompetent MAPK-mutant HNSCC models displayed active cell death and massive CD8+ T-cell recruitment in situ. Consistent with CD8+ T-inflamed phenotypes, MAPK-mutant HNSCC patients, independent of tumor-mutational burden, survived 3.3\u20134 times longer than WT patients with anti-PD1/PD-L1 immunotherapies. Similar prognosticity was noted in pan-cancers. We uncovered clinical, signaling, and immunological uniqueness of MAPK-mutant HNSCC with potential biomarker utilities predicting favorable patient survival.MAPK pathway mutations affect one-fifth of head and neck squamous cell carcinoma (HNSCC). Unexpectedly, MAPK pathway aberrations are associated with remarkably long patient survival, even among patients with The incidence of head and neck squamous cell carcinoma (HNSCC) is approaching 0.7 million/year globally . DespiteTP53 wild-type (WT) status which allows proper execution of drug-induced apoptosis by functional p53 responses in HNSCC, with proven biology demonstrated in PI3K-mutant, PI3K-activated preclinical models of HNSCC and retrospective patient cohorts positivity in patients\u2019 tumors can be potentially used as a favorable prognostic biomarker (mainly for cancer from the oropharynx subsite), which can clinically stratify patients for treatment de-intensification purposes . The bioonal p53 . Similar cohorts . These sTP53 mutations (median \u223c14 yr), much longer than that of HPV-positive HNSCC (median \u223c5.5 yr). The favorable prognosticity of MAPK pathway mutations in HNSCC was found to be independent of HPV. Subsequent molecular dissections revealed two plausible underlying mechanisms operative by MAPK mutations in patient tumors, followed by preclinical HNSCC models. First, multiple hotspot and non-hotspot MAPK mutations all abrogated ErbB3 activation, an established signal for HNSCC progression. Inhibitor studies functionally defined ERK activity negatively regulating p-ErbB3 in MAPK-mutants. Second, comprehensive pan-pathway immune landscape investigations identified MAPK-mutant tumors as the only \u201cCD8+ T-cell\u2013inflamed\u201d tumors with inherently immunoreactive tumor microenvironments with constitutive cytolysis, subsequently validated in immunocompetent HNSCC models. As low tumoral phospho-ErbB3 levels and elevated CD8+ T-cell infiltrations are recently established events driving good patient survivals in HNSCC , were able to identify subsets of HNSCC patients benefiting significantly from anti-PD1/PD-L1 immunotherapy clinically. Similar prognosticity of MAPK pathway mutations were noted in pan-cancer immunotherapy settings. Our study uncovers novel clinical, biological, and immunological uniqueness of MAPK-mutant HNSCC and may indicate important clinical utilities of MAPK pathway mutations in this cancer.Here, we first reported that MAPK pathway mutations in HNSCC predict remarkably long patient survival, even among patients bearing in HNSCC , our stuAs of today, the clinical significance of somatic genomic aberrations in HNSCC remains underexplored. Here, using a comprehensive pan-pathway approach, we examined the prognostic impact of mutational events of seven major cancer-related signaling pathways on HNSCC patient survivals with The Cancer Genome Atlas (TCGA) dataset . These include three major mitogenic pathways, the PI3K, MAPK(ERK), and JAK/STAT pathways; two differentiation-related pathways, the Notch and TGF-\u03b2/Smad pathways; the inflammation-related NF-\u03baB pathway; and the stem cell\u2013related WNT pathway, representing a total of 81% of cases . PathwayNOTCH1 mutations predict recurrences with poor outcomes .Among all seven pathways examined, only mutations in the MAPK pathway and the Notch pathway are associated with patient outcomes . Mutatiooutcomes . Unexpec p.E322K ; Fig S2)TP53-mutated patients (TP53 double mutant\u201d patients (N = 363) have an extreme long median OS of 169.25 mo (\u223c14 yr), which is 4.77 times longer than that of the \u201cMAPK-WT/TP53-mutated\u201d counterparts . The double mutant patients also have a 55.26% reduction in chances of death (OR = 0.4474) versus MAPK-WT counterparts .Most strikingly, MAPK pathway mutations are also prognostic for markedly improved survival even among iveness) . In factP = 0.01003, 0.03372, respectively, Table S1). Importantly, unlike HPV-positive HNSCC with favorable outcomes, MAPK pathway mutations span multiple head and neck anatomic subsites, including the oral cavity sites, larynx, oropharynx, and others (Table S2). More than 87% (83/95 cases) of MAPK pathway-mutated tumors are HPV-negative. Upon HPV stratification, MAPK pathway mutations are still found to be prognostic for HPV-negative HNSCC , but potentially associated with lower alcohol intake per TCGA alcohol history, and a higher occurrence in females .Table S1 Subsite distribution of MAPK pathway mutations in HNSCC tumors (upper panel) and subsite distributions of HPV positivity in TCGA HNSCC cohort (lower panel).Table S2 Pan-cancer analyses results for associations between MAPK proteome components in patient tumors and overall survival in 33 cancer types (TCPA database).Table S3 H/N/K-RAS, A/B-RAF, RAF-1, MAP2K1/2, and MAPK1) were also prognostic of favorable HNSCC patient outcome expression versus control expressions in HNSCC cell models and the hotspot ARAF p.S214F mutations inhibited p-ErbB3(Y1289) expressions. In addition to these mutants, overexpression of either MAP2K1-WT or BRAF-WT was also sufficient to inhibit p-ErbB3(Y1289) expressions by \u223c60% and 50%, respectively.ErbB3 activation contributes to HNSCC proliferation and is ag/tcpa/, , 2017a) in HNSCC , we thusl models and S4A.Top 19 proteins significantly associated with patient OS in the HNSCC TCPA dataset.Table S4 MAPK1 p.R135K and HRAS p.G12S mutations and the HSC-6 cell line harboring MAPK1 p.E322K, >100\u2013200% increases of p-ErbB3 expression were observed, whereas such an increase was not observed in MAPK-WT cells (HSC-4). The data suggested MAPK (ERK) activity negatively regulates p-ErbB3 in a mutant-specific manner in HNSCC. Such a mutant-specific phenomenon was further supported by proteomic findings in MAPK-mutant HNSCC cell lines and 0.4333 levels. Therefore, we further tested this non-canonical MAPK/ErbB3 relationship using the pharmacological GDC-0994 MAPK1/2-RSK inhibitor in HNSCC cells harboring endogenous MAPK pathway mutations. As shown in a [CCLE] ) and in Response to therapy is an important factor determining cancer patient survival. Yet, there was no clear association between MAPK mutations and responses to cisplatin, docetaxel, 5-flurouracil, methotrexate, and cetuximab in CCLE HNSCC drug-sensitivity database . SimilarSupplemental Data 1, there were 1,793 significant differentially expressed genes (DEGs) in MAPK-mutated versus WT HNSCC tumors with P-values < 0.05 and false discovery rate (FDR) < 0.05, among which 130 protein-coding DEGs showed a >1.41-fold difference (log2 fold-change > 0.5) in gene expression with FDR < 0.05 (Perforin (PRF1), and four granzymes, GZMA (Cytotoxic T-Lymphocyte-Associated Serine Esterase-3), GZMB (Cytotoxic T-Lymphocyte-Associated Serine Esterase-1), GZMH (Cytotoxic Serine Protease C), and GZMK (Tryptase II) were all significantly up-regulated in MAPK-mutated tumors differentially expressed protein-coding genes (DEGs) in MAPK-mutated tumors (versus WT) with all immune-related genes highlighted in red.A list of 130 significantly up-regulated .A complete list of 1,793 significant differentially expressed genes (DEGs) in MAPK-mutated tumors versus WT tumors in TCGA HNSCC provisional cohort . Most importantly, MAPK-mutant tumors have the most remarkable \u201cCD8+ T-cell\u2013inflamed status\u201d along with most significant and concurrent increases in all three major immunoreactive signature scores, including high cytolytic process (CYT) and neutrophil infiltration levels in MAPK-mutant tumors and neutrophils, which were discrete from signatures for B cell, CD4+ T-cell, and macrophage infiltrations analysis , 2017 ress (CYT) , T-effecss (CYT) , and antss (CYT) , all eviss (CYT) . Whereas in situ . We alsotrations . Overall as well and S8B.+ T-cells (accompanied by dendritic cells and neutrophil infiltrations) by immunohistochemistry, consistent with the TIMER-predicted CD8+ T-cell\u2013inflamed, immunoactive microenvironments borne by MAPK-mutated HNSCC tumors in TCGA , whereas such infiltrates were not detected in WT tumors .Increases of CD8+ T-cell infiltration in HNSCC tumor microenvironment alone are known to independently predict favorable patient survival Hartman. Our in- in TCGA and S10.+ T-cell infiltration in HNSCC dictate patient outcomes , and their abilities to induce intratumoral CD8+ T-cell infiltration in vivo were compared. As shown in HRAS p.G12V (mHRAS p.G12V), mMAPK1 p.D319N , and mMAPK1 p.E320K mutations , were all potent recruiters for CD8+ T-cell infiltration in situ. Furthermore, consistent with our findings that MAPK-mutated human HNSCC tumors have inherently high active cytolytic signatures were all survival-favoring features among HNSCC patients . Importantly, MAPK pathway-mutated HNSCC patients bearing high IFN-\u03b3 scores, high CYT scores, and high T-eff scores have long-term survivals . At the most relaxed median cutoff, both the IFN-\u03b3 and T-eff scores could still separate patient survival (P < 0.05), but not CYT score (P = 0.2) (In addition to high CD8P = 0.2) \u2013S13.Notably, among MAPK-mutated HNSCC patients, we found that those with high IFN-\u03b3, CYT, or T-eff scores (both at 20% and 50% cutoffs) do not significantly overlap with patients of low p-ErbB3 and oropharyngeal cancer (N = 32) were two major cancers with sufficient case numbers for survival analysis. Strikingly, among advanced oral cancer patients treated with PD1/PD-L1 inhibitors, MAPK pathway mutations appeared to predict a 3.3 times longer median OS versus WT . This wact test) .Notably, as high as 49% of HNSCC tumors (53/110) sequenced by + T-cell\u2013inflamed/cytolytically active HNSCC patients who may potentially benefit from ICIs. Our study uncovers novel clinical, biological, and immunological uniqueness of MAPK-mutant HNSCC and may indicate wide clinical utilities of MAPK pathway mutations in this cancer.Overall, MAPK pathway mutations may represent novel and important HNSCC biomarkers for prognosis in HNSCC. Based on our transcriptome findings, validated in immunocompetent models, MAPK mutations likely identify highly CD8TP53-mutated HNSCC patients (median OS >14 yr). Thus, MAPK mutations may represent novel prognostic or even de-intensification biomarkers for HNSCC with broad applicability in terms of HNSCC subsites.We reported for the first time that MAPK pathway mutations have significant survival-favoring clinical, signaling, and immunological impacts in HNSCC. Among seven major cancer-signaling pathways examined, MAPK (ERK) pathway mutations, predominated by many activating mutations, were prognostic for remarkably long patient survivals. This is contradictory to the known role of MAPK-mitogenic signaling in HNSCC tumorigenesis and progression . This fiHRAS and MAPK1 hotspot mutations and potentially others, have remarkable tumoral ErbB3-suppression . Mechanistically, our findings identified a previously undescribed mechanism of p-ErbB3 regulation by MAPK pathway-mutants. Such a negative regulation of p-ErbB3 by ERK activity is uniquely found in MAPK-mutant, but not in MAPK-WT HNSCC. Most importantly, MAPK-mutant HNSCC tumors are the only tumors having significant \u201cCD8+ T-cell\u2013inflamed\u201d and inherently immunoactive tumor microenvironment (versus six other pathway-mutant tumors), with constitutive cytolysis. The ability of MAPK mutations to drive a CD8+ T-cell\u2013inflamed status in vivo with marked apoptosis is proven in immunocompetent HNSCC models. As low tumoral phospho-ErbB3 levels and elevated CD8+ T-cell infiltrations are recently established events indicative of good patient survivals in HNSCC , MAPK1/3(ERK2/1), RPS6KA1, SHC1/2/3/4, GRB2, and Erk1/2-specific DUSP3/5/6/7/9. The PI3K pathway was defined as AKT1/2/3, PIK3CA/B/D/G/2A/2B/2G, PIK3AP1, PIK3IP1, PDK1, MTOR, TSC1, TSC2, PTEN, RICTOR, RPTOR, RHEB, and PIK3R1/2/3/4/5/6. The NF-\u03baB pathway was defined as TAB1/2/3, MAP3K7/14, CHUK, IKBKB, IKBKG, NFKBIA, NFKBIE, REL, RELA/B, NFKB1/2, LTBR, TNF, TNFAIP3, TNFSF11/13B, TNFRSF1A/8/11A/13C, BTRC, CYLD, NLRC5, TRADD, CD40, CD40LG, LTA, TRAF2/3/5/6, IL1B, and IL1R1. The JAK/STAT pathway was defined as JAK1/2/3, STAT1/2/3/4/5A/5B/6, PTPN11, IL6, IL6R, IL6ST, and SOCS3. The Notch pathway was defined as DLL1/3/4, JAG1/2, NOTCH1/2/3/4, NUMB, DTX1/3L, NEDD4, MAML1, RBPJ, POFUT1, HES1/5, and HEY1/2/L. The WNT pathway was defined as WNT1/3A/5A/5B/7A, CTNNB1, HNF1A, FZD1/2/3/7/8/9/10, AXIN1, LEF1, LOXL2, DVL2/3, NKD1/2, TAB1/2, GSK3B, CSNK1A1, NLK, and LRP5/6. The TGF-\u03b2/Smad pathway was defined as SMAD1/2/3/4/5/6/7/9, TGFB1/2/3, TGFBR1/2, INHBA/B/C/E, NODAL, ACVR1/1B/1C/2A/2B, BMP2/4/7, BMPR1A/B/2, AMHR2, LTBP1, BAMBI, ZFYVE9, SMURF1/2, and LIMK1. All TCGA whole-exome sequencing data and clinical data of TCGA are downloaded from the www.cbioportal.org generated from Kaplan\u2013Meier curves as in P-value < 0.05 (significant) would we consider them having favorable/unfavorable OS. CCLE-proteomic database was downloaded from DepMap portal (http://www.depmap.org) as published by the CCLE study . The Platinum-A (PLAT-A) retrovirus packaging cell line was purchased from Cell Biolabs. The HSC-6 cell line was a generous gift from Dr J Inazawa , and SCC VII mouse HNSCC cell line was kindly provided by Dr Sven Branduau . Pt-25 primary cultures were prepared from a female recurrent HNSCC patient. For GDC-0994 treatment, the cells were plated at \u223c30% confluency for overnight and then subjected to either vehicle or 0.5 \u03bcM of GDC-0994 for 30 min. The cells were then washed with 1\u00d7 PBS, and protein lysates were prepared for Western blot analyses.2. Retroviruses were removed from the infection medium at postinfection, and cells were then cultured in their respective culture media. Gene expression were then validated by Western blotting. For mouse HNSCC tumor cell inoculation was used for ectopic expression of genes and mutants into HNSCC cells. In brief, the desired genes/mutants cloned into the pMXs-puro retroviral expression vector backbone were transfected into PLAT-A cells using Lipofectamine 3000 (Thermo Fisher Scientific) for the generation of retroviruses. Retroviruses were filtered through a 0.45-\u03bcm mixed cellulose ester membrane filter to remove cell debris and subsequently used for infection of FaDu cells or SCC VII cells for 48\u201372 h at 37\u00b0C, 5% COckground ), 2\u20133 miCells were washed with cold 1\u00d7 PBS and lysed with the NP40 lysis buffer . Cell lysates were centrifuged, and the supernatant was quantified with Protein Assay Dye Reagent (Bio-Rad). 50 \u00b5g of protein lysates were mixed with a 4\u00d7 protein loading dye and then separated by SDS\u2013PAGE. Separated proteins were transferred to nitrocellulose membrane, which was then blocked with 5% nonfat dry milk and probed with primary antibody at 4\u00b0C overnight. Primary antibodies include AKT (#9272), pi-AKT (#9271), ARAF(#4432), pi-ARAF(S299) (#4431), BRAF (#2696), pi-BRAF(S445) (#2696), pi-ErbB3 (#2842), ErbB3 (#12708), MAPK (#9102), pi-MAPK (#9101), pi-MEK1/2 (#9154), and RSK1 (#8408), all from Cell Signaling Technology, USA. Anti-\u03b2-actin (sc-69879) antibody was from Santa Cruz. Anti-MEK1/2 (YT2714) and anti-N/H/K-RAS (YT2960) antibodies were from ImmunoWay. The probed membrane was then washed three times with 1\u00d7 TBST, followed by a 1\u20132-h incubation with the respective secondary antibody , followed by 3\u00d7 washings with 1\u00d7 TBST. ECL detection solution was then applied onto the membrane for the development of chemiluminescence, which was captured by autoradiography.+ T-cell, CD4+ T-cell, macrophage, neutrophil, and dendritic cell) in 512 TCGA-HNSCC head and neck squamous carcinoma tumor samples are extracted from the TIMER Web site (https://cistrome.shinyapps.io/timer/_w_20aca96c/immuneEstimation.txt) and grouped according to the mutational information downloaded from cBioPortal . The Wilcoxon rank sum test was performed to calculate the statistical significance between two groups in the TIMER plots.We adopted the methodology of TIMER analysis for immune infiltration level estimation , 2017b. https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-HNSC%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_category%22%2C%22value%22%3A%5B%22Transcriptome%20Profiling%22%5D%7D%7D%5D%7D&searchTableTab=files) using GDGZMA and PRF1 as previous described by GZMA, GZMB, PRF1, IFN-\u03b3, EOMES, and CD8A (offset 0.01) was calculated by the geometric mean of the TPM of et 0.01) . AntitumMAP2K1 and MAPK1. It also captured selection regions of ARAF, BRAF, HRAS, KRAS, and MAP2K2 to cover all well-known hotspot sites. The sequenced locations for these partially sequenced genes are listed in the following table, and variants were called by the Ion Reporter Software (Thermo Fisher Scientific).Tumor tissues and blood samples were collected from patients under written informed consents according to clinical research approvals by the Institutional Review Board of the University of Hong Kong/Hospital Authority Hong Kong East Cluster Research Ethics Committee , the Joint Chinese University of Hong Kong\u2013New Territories East Cluster Clinical Research Ethics Committee , Hong Kong SAR, and the Research Ethics Committee, Kowloon West Cluster , Hong Kong SAR. Genomic DNA from samples were extracted with the DNeasy Blood & Tissue Kit (QIAGEN), followed by quantification and targeted sequencing by next-generation sequencing using the IonS5 platform (Thermo Fisher Scientific). All samples were sequenced with a mean depth of >500\u00d7 using a custom-designed gene panel on major MAPK pathway genes. The custom gene panel consisted of amplicons that covered all exons of Patient tumors were freshly fixed with 10% formalin and dehydrated in a serial manner in ethanol. The formalin fixed and paraffin embedded tumor samples were then sectioned and dewaxed and rehydrated in xylene, 100% ethanol, 70% ethanol, and running tap water. Antigen retrieval was performed at 95\u00b0C for 20 min in citrate buffer . The VECTASTAIN Elite ABC Universal PLUS Kit Peroxidase (Horse Anti-Mouse/Rabbit IgG) (Cat. no. PK-8200) was used for immunohistochemical staining. Endogenous peroxidase activity was quenched by BLOXALL Blocking Solution, followed by blocking in 2.5% Normal Horse Serum for 20 min at room temperature. CD8 mouse antihuman antibody , CD11c rabbit antihuman antibody , and neutrophil elastase rabbit antihuman antibody and phospho-HER3/ErbB3(Tyr1289) (21D3) rabbit antihuman antibody were used as primary antibodies to stain patient tumors for overnight incubation at 4\u00b0C. CD8 rabbit antimouse antibody and cytokeratin mouse antibody were used. The secondary antibody (prediluted biotinylated horse antimouse/rabbit IgG secondary antibody) was added for 1-h incubation at room temperature. For signal amplification and detection, the slides were incubated with VECTASTAIN Elite ABC reagent for 30 min and ImmPACT DAB EqV solutions for 30 s. After counterstaining with hematoxylin for 1 min, clearing, and mounting, pictures were taken under a light microscope. The Roche In Situ Cell Death Detection Kit, Fluorescein (Cat. no. 11684795910) was applied for TUNEL assay. Proteinase K solution was used to pretreat the rehydrated sections. Then the TUNEL reaction mixture was incubated on the section in dark at 37\u00b0C for 1 h in dark. The section was mounted with VECTASHIELD vibrance antifade mounting medium (Cat. no. H-1800)."} +{"text": "The structures were determined based on spectroscopic evidence including 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and high resolution mass spectrometry (HRESIMS) data, along with comparisons to reported data. The leaves were used to extract compounds with different solvents. The extracts were tested for antioxidant activity with a variety of in vitro tests including 2,2-diphenyl-1-picrylhydrazyl (DPPH\u2022), 2,2\u2032-azino-bis (3-ethylbenzothiazoline-6-sulfonate (ABTS\u2022+), ferric reducing antioxidant power assay (FRAP), superoxide, and nitric oxide radical scavenging assays. The dichloromethane fraction was most active, displaying significant free radical scavenging activity. The n-butanol fraction also showed notable activity in all assays. Therefore, these findings support the potential use of A. vacillans leaves as an antioxidant medication due to the presence of polyphenolic compounds.A new dihydroisocoumarin glucoside, vacillanoside ( Aloe spp. are members of the bitter or Asphodelaceae family (previously known as Liliaceae). This family is represented by more than 600 species endemic to tropical and southern Africa, Madagascar, Jordan, the Arabian Peninsula, East Asian countries, and various islands in the Indian Ocean + , m/z 529.1320 [M+Na]+ , and m/z 545.1069 [M+K]+ with 162 amu more than that of 2, suggesting the presence of a monosaccharide moiety. A significant fragment using the high-resolution electron impact mode (HR-EIMS) appeared at 327.0868 corresponding to C18H15O6 (M+-glucose). A positive Molisch\u2019s test reflected the glycosidic nature \u2212 at m/z 579.1509 with 17 degrees of unsaturation. Thirty carbon resonances were clear in the 13C-NMR and were sorted in a DEPT experiment into two oxymethylenes , 16 methines, and 12 quaternary carbons. The HR-EI-MS for both compounds showed strong peaks at 256.0735 with a relative abundance of 100% calculated for C15H12O4 and assigned to the aloe-emodin anthrone aglycone in 10 and in 11. These data matched data reported for caffeic acid + , m/z 507.1500 [M+H]+ , m/z 529.1320 [M+Na]+ , m/z 545.1069 [M+K]+ .White amorphous powder (1 mg); [\u03b1]23D + 16.8\u00b0 ; UV \u03bbmax MeOH (log \u03b5) nm: 209 (4.63), 244 (4.42), 300 (3.92), 330 (3.61); IR (KBr) vmax 3400, 1720, 1640, 1606, 1511, 1240 cm\u22121; 1H and 13C NMR .Red amorphous powder (6 mg); [\u03b1] NMR see ; HR-ESI-23D \u2212 4.7\u00b0 ; UV \u03bbmax MeOH (log \u03b5) nm: 209 (4.63), 244 (4.42), 300 (3.92), 330 (3.61); IR (KBr) vmax 3400, 1720, 1640, 1606, 1511, 1240 cm\u22121; 1H and 13C NMR , m/z 581.1651 [M+H]+ , m/z 603.1469 [M+Na]+ .Red amorphous powder (8 mg); [\u03b1] NMR see ; HR-ESI-t-test. Data were expressed as mean \u00b1 SD, and the difference was considered significant at p < 0.05 compared to the control. All statistical calculations used OriginLab software and Microsoft Excel.Analysis of variance (ANOVA) was used to evaluate significance differences, followed by the Student\u2019s 3), 3,4 dihydro-6 glucopyranozyl-8-hydroxy-3--methyl-1H-[6), and two new anthraquinone derivatives, vacillantins A and B (10 and 11) were isolated from the leaves of A. vacillans (Asphodelaceae) together with nine known compounds . The structures of these compounds were elucidated through extensive spectroscopic analyses. The total alcohol extract and different fractions were tested for their antioxidant activities in five spectrophotometric assays. The dichloromethane fraction exhibited promising free radical scavenging activity in most of the assays. Our findings add new information to the literature on the structural diversity and pharmacological activities of Aloe species. Our results suggest A. vacillans as a potential source of secondary metabolites with pharmacological and industrial importance. Moreover, these results advocate further investigation of the remaining fractions with the aim of isolating bioactive compounds exhibiting interesting biological capacities.In summary, a new dihydroisocoumarin derivative, vacillanoside ("} +{"text": "P < 0.001 for both comparisons). Positive resistin expression was significantly associated with tumor size, grade, stage, estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) status, and molecular classification; strongly positive resistin expression was associated with tumor grade, ER, PR, HER2 status, and molecular classification. Significantly positive correlations were observed between positive and strongly positive resistin expression and corresponding levels of EGFR expression. Relapse-free and overall survival was worse for patients with high levels of both proteins than for those with high levels of only one protein or normal levels of both proteins. Our evidence suggests that combined high levels of resistin and EGFR expression correlate with survival in patients with breast cancer.Elevated levels of resistin and epidermal growth factor receptor (EGFR) facilitate the development of breast cancer, although there are no reports of any correlation between these proteins. This study analyzed 392 human breast cancer tissue specimens and 42 samples of adjacent normal tissue. Rates of positive and strongly positive resistin expression were significantly higher in breast cancer tissue than in the adjacent nontumor tissue (83.2% vs. 23.8% and 20.9% vs. 0.0%, respectively; Elevated levels of circulating resistin have been linked to a higher risk of breast cancer , 2, and Epidermal growth factor receptor (EGFR), a member of the HER family of receptor tyrosine kinases, is abnormally expressed and activated in many epithelial tumors and plays a critical role in the initiation and development of cancer via modulating downstream signaling pathways , 10. OurThis paper describes our insights derived from immunohistochemistry (IHC) analyses of resistin and EGFR expression in breast cancer and healthy normal breast tissue specimens obtained from 392 Chinese Han women. We detail the clinical prognostic significance of a positive association between resistin and EGFR expression in breast cancer.+/PR+[\u226520%]/HER2\u2013, Ki\u201067 < 14%); luminal B, containing hormone receptor-positive cases that did not meet the conditions of luminal A; HER2-enriched ; or triple-negative breast cancer (TNBC) . Follow-up information was available for 239 breast cancer patients with a median follow-up time of 60 months . The Ethics Committee of the Affiliated Dongyang Hospital of Wenzhou Medical University approved this study. All study methods satisfied the relevant guidelines and regulations issued by the Affiliated Dongyang Hospital of Wenzhou Medical University.Breast cancer tissue samples were obtained from 392 untreated Chinese Han women aged 24\u201390 years (median 50 years) who underwent surgery in the Affiliated Dongyang Hospital of Wenzhou Medical University between 2007and 2019. Forty-two samples of adjacent normal breast tissue were also obtained following surgical resection. Pathohistological diagnoses followed the World Health Organization breast tumor classification criteria . HistoloWe followed the methods described by Wang et al. .We followed the methods of Wang et al. . The priThe entire section was scanned and scored independently by 2 pathologists. Resistin and EGFR expression staining intensity was scored on a 4-point scale from 0 (negative) to 1 (weak), 2 (moderate), or 3 (strong) . A case We followed the methods of Wang et al. .We followed the methods of Wang et al. . MultivaP < 0.001 and P = 0.001, respectively) (P = 0.012), grade (P < 0.001), stage (P = 0.042), ER (P < 0.001) and PR (P < 0.001) status, HER2 status (P = 0.021), and molecular classification (P < 0.001). Strongly positive resistin expression was associated with higher tumor grade (P < 0.001), ER (P < 0.001) and PR (P < 0.001) status, HER2 status (P = 0.001), and molecular classification (P < 0.001).The rate of positive resistin expression in breast cancer tissue specimens was 83.2% (326/392), which included 82 (20.9%) strongly positive cases; corresponding rates in normal breast tissue specimens were 23.8% (10/42) and 0.0% (0/42), respectively. Rates of positive and strongly positive resistin expression were significantly higher in breast cancer tissue than in normal breast tissue (ctively) . As showP < 0.001) and 15.2% [10/66] (P = 0.001), respectively, r = 0.250 and P < 0.001 and r = 0.166 and P = 0.001, respectively). Similarly, as shown in P < 0.001) and 27.4% [85/310] (P < 0.001), respectively). Spearman correlation analysis revealed significantly positive correlations between strongly positive levels of resistin expression and EGFR-positive or strongly positive expression in breast cancer tissue specimens . Similarly, a positive correlation was observed between staining intensity scores of resistin and EGFR in breast cancer tissues (Rates of positive and strongly positive EGFR expression in breast cancer tissues were 52.0% (204/392) and 32.4% (127/392), respectively. When we analyzed the relationship between resistin and EGFR expression in breast cancer tissue specimens, we found significantly higher levels of positive or strongly positive EGFR expression among resistin-positive cases compared with resistin-negative cases (24.2% [16/66] (< 0.001) .P = 0.237, P = 0.128, P = 0.171, and P = 0.105, respectively) had a mean RFS of 51.5 months (an estimated 5-year RFS rate of 68.9%); patients whose tumors were either resistin-positive or strongly EGFR-positive (n = 129) had a mean RFS of 54.3 months (an estimated 5-year RFS rate of 83.7%), while patients whose tumors were resistin-negative and not strongly EGFR-positive (n = 36) had a mean RFS of 54.1 months . Patients whose tumors were both resistin-positive and strongly EGFR-positive experienced worse OS compared with patients whose tumors were either resistin-positive or strongly EGFR-positive and patients whose tumors were resistin-negative and not strongly EGFR-positive (P = 0.099).As shown in Figures n = 29) had a mean RFS of 49.1 months (an estimated 5-year RFS rate of 62.1%); patients whose tumors were either strongly resistin-positive or strongly EGFR-positive (n = 73) had a mean RFS of 54.2 months (an estimated 5-year RFS rate of 79.5%), and patients whose tumors were not strongly resistin-positive and not strongly EGFR-positive (n = 137) had a mean RFS of 53.9 months . Patients whose tumors were both strongly resistin-positive and strongly EGFR-positive experienced worse OS compared with patients whose tumors were either strongly resistin-positive or strongly EGFR-positive and patients whose tumors were not strongly positive for either protein (P = 0.453). Cox proportional hazards regression analysis did not reveal any significant associations between resistin-positive and strongly EGFR-positive tumor tissue (hazard ratio (HR) = 0.736, 95%CI = 0.198\u20132.734, P = 0.648; 0.765, 0.110\u20135.323, P = 0.786), strongly resistin-positive and strongly EGFR-positive tumor tissue , and RFS or OS.As shown in Figures n = 61) had a mean RFS of 51.3 months (an estimated 5-year RFS rate of 67.2%); patients whose tumors were either resistin-positive or strongly EGFR-positive (n = 111) had a mean RFS of 55.2 months (an estimated 5-year RFS rate of 86.5%), while patients whose tumors were resistin-negative and not strongly EGFR-positive (n = 36) had a mean RFS of 54.1 months . Non-TNBC patients whose tumors were both resistin-positive and strongly EGFR-positive experienced worse OS compared with patients whose tumors were either resistin-positive or strongly EGFR-positive and also patients whose tumors were resistin-negative and not strongly EGFR-positive (P = 0.065). As shown in Figures n = 23) had a mean RFS of 48.3 months (an estimated 5-year RFS rate of 60.9%); patients whose tumors were either strongly resistin-positive or strongly EGFR-positive (n = 59) had a mean RFS of 54.5 months (an estimated 5-year RFS rate of 78.0%), and patients whose tumors were not strongly resistin-positive and not strongly EGFR-positive (n = 126) had a mean RFS of 54.6 months . Non-TNBC patients whose tumors were both strongly resistin-positive and strongly EGFR-positive experienced worse OS compared with patients whose tumors were either strongly resistin-positive or strongly EGFR-positive and patients whose tumors were not strongly positive for either protein (P = 0.135).We analyzed the effect of combined high expression of resistin and EGFR on the prognosis of non-TNBC or TNBC, ER-negative or ER-positive, HER-negative or HER2-positive tumors. As shown in Figures As shown in Figures The cytokine resistin participates in several physiological and pathological processes, including metabolism, inflammation, autoimmunity, and various cancers, including breast cancer \u20136, 21\u201324\u03baB)/signal transducer and activator of transcription 3 (STAT3) signaling pathway-mediated induction of mesenchymal phenotypes and stemness properties [Our previous study have shown that EGFR promotes breast cancer invasion through downstream p44/p42 MAPK (ERK1/2) signaling , and resoperties . These rIn this study, both resistin and EGFR impacted adversely upon survival in breast cancer, but neither protein alone had a significant impact. Breast cancer patients whose tumors were both resistin-positive and strongly EGFR-positive, or were both strongly resistin-positive and strongly EGFR-positive, had worse RFS than all other breast cancer patients. In the non-TNBC and TNBC subgroup analyses, similar results were observed with non-TNBC, but not with TNBC. This may be due to the fact that there were too few cases for analysis. Further study should examine the effects of combined high resistin and EGFR expression on the prognosis of patients with TNBC. These results suggest that resistin and EGFR are potential clinical biomarkers of disease progression and prognosis in breast cancer and that simultaneously targeting these proteins is a potentially useful therapeutic strategy in this disease."} +{"text": "Candida infections C. glabrata, in cases of azole-resistant isolates , the general and long-term therapeutic use of FLZ (or other triazoles) can result in acquisition of molecular mechanisms that enable Candida isolates to exhibit antifungal resistance , fluconafections , 3. Howeisolates . Except sistance . It is ksistance . Fenticoisolates . Thus, aisolates but alsosistance .C. albicans (20 isolates) and C. glabrata (30 isolates) species, respectively. In each isolate\u2019s pair, the FLZ-resistant (derivative) isolate originated from the FLZ-susceptible or susceptible-dose-dependent isolate following resistance development during patient infection isolates exhibit known molecular resistance mechanisms, which consisted of upregulation of drug efflux pump-encoding genes and/or point mutations of 14-\u03b1-lanosterol demethylase-encoding ERG11 gene . MIC values to FEZ and FLZ\u2014both obtained as standard powders from Sigma-Aldrich \u2014were determined using the protocol specified in the Clinical and Laboratory Standards Institute (CLSI) M27-A3 document without modifications -specific clinical breakpoints reported in the CLSI M27-S4 document (P\u2009<\u20090.05) differences between GM MIC values obtained for isolate groups from each species (see below), using repeated-measures analysis of variance (ANOVA) on log2 MICs followed by Bonferroni-Dunn\u2019s multiple-comparison test from nfection . All excications . Only foson test .in vitro, 15 C. glabrata and 1 C. albicans isolate overexpressed drug efflux pumps alone, whereas 9 C. albicans isolates combined overexpression of drug efflux pumps and ERG11 amino acid substitution(s) (Table S1). For C. albicans isolates, FEZ MIC ranges were 0.25 to 2\u2009mg/liter among FLZ-nonresistant isolates and 1 to 8\u2009mg/liter among FLZ-resistant isolates . For C. glabrata isolates, FEZ MIC ranges were 0.5 to 2\u2009mg/liter among FLZ-nonresistant isolates and 0.5 to 4\u2009mg/liter among FLZ-resistant isolates . C. albicans and C. glabrata, respectively. Interestingly, the GM MICs \u00b1 CIs of C. albicans FEZ MICs in FLZ-nonresistant isolates differed significantly from that in FLZ-resistant isolates . Conversely, no significant difference was seen between the GM \u00b1 CIs of C. glabrata FEZ MICs in FLZ-nonresistant isolates and that in FLZ-resistant isolates .Of 25 isolates with molecular mechanisms contributing to the FLZ resistance phenotype observed Candida species, including C. albicans and C. glabrata. Remarkably, differences were more prominent in FLZ-resistant isolates than their nonresistant counterparts but were statistically significant only for C. albicans. Our data demonstrate that FEZ exhibits higher activity than FLZ. FEZ activity was less dependent on drug efflux pump-mediated FLZ resistance in Candida species such as C. glabrata. Based on these findings, FEZ should be evaluated as a candidiasis treatment, particularly in patients with recurrent or antifungal-recalcitrant Candida infections.In conclusion, we showed that FEZ MIC values were lower than FLZ MIC values in 50 well-characterized isolates from two clinically relevant"} +{"text": "In contrast, after the subchronic administration of therapeutic-relevant concentration of valproate (VPA), acute administration of therapeutic-relevant concentration of CLZ drastically increased Cx43-associated astroglial releases. VPA increased Cx43 expression in cytosol fraction without affecting plasma membrane fraction, whereas CLZ increased Cx43 expression in both fractions. Acute administration of therapeutic-relevant concentration of CLZ drastically increased Cx43 expression in the plasma membrane fraction of astrocytes subchronically treated with VPA. The present findings suggest that CLZ-induced the activation of Cx43-associated channel activity and transported Cx43 to plasma membrane, probably contribute to the double-edged sword clinical action of CLZ, such as improvement of cognitive dysfunction and CLZ-induced myocarditis.Clozapine (CLZ) is a gold-standard antipsychotic against treatment-refractory schizophrenia, but is one of the most toxic antipsychotic agents. Pharmacological mechanisms of the double-edged sword clinical action of CLZ remain to be clarified. To explore the mechanisms of CLZ, the present study determined the astroglial transmission associated with connexin43 (Cx43), which is the most principal expression in astrocytes and myocardial cells, and expression of Cx43 in primary cultured astrocytes. Both acute and subchronic administrations of CLZ concentration-dependently increased Cx43-associated astroglial release of N-methyl-d-aspartate (NMDA)/glutamate receptor (NMDAR) contributes to the pathophysiology of schizophrenia [It has been established that dysfunctions of both dopaminergic and glutamatergic transmission play important roles in the pathophysiology of schizophrenia, with various antipsychotics improving dysfunctions of mesolimbic and mesocortical dopaminergic transmissions with thalamocortical glutamatergic transmission ,4,5,6,7;ophrenia ,10,11,12ophrenia ,14 and eophrenia . Moreoveophrenia . Based ol-glutamate and d-serine induced by CLZ are one of the major mechanisms of agonistic action of CLZ against impaired NMDAR [Clozapine (CLZ) is considered the double-edged sword antipsychotic drug, since CLZ is one of the most effective but toxic antipsychotics against antipsychotics-resistant schizophrenia . In facted NMDAR .In terms of management of CLZ-induced seizure, possible strategies include reduction of CLZ dose and addition of antiepileptic drugs, including valproate (VPA), which is the most commonly used for management of CLZ-induced seizures ,21 due tBoth clinical and preclinical studies have emphasized that thalamocortical disturbance is particularly relevant for cognitive dysfunction in several neuropsychiatric disorders, including schizophrenia, Attention-deficit hyperactivity disorder (ADHD), intellectual disability, autism, and epileptic psychosis ,9,26,27.Accumulating evidences indicate connexin (Cx) composed transmembrane channels (Cxs) are crucial to the coordination and maintenance of physiologic activity including neuronal excitability, synaptic plasticity, tripartite synaptic transmission, and homeostasis maintenance in the central nervous system ,29. Cx il-glutamate and d-serine associated with Cxs and the astroglial expression of Cx43 using primary cultured astrocytes.Our recent preclinical study demonstrated that CLZ acutely activated astroglial Cxs activity, in a concentration-dependent manner. Clinically, survival analysis has suggested that the lower limit of the therapeutic range of CLZ serum concentration is 0.6 \u03bcM , whereasClozapine (CLZ) was purchased from Sigma . Sodium valproate (VPA) was obtained from Wako Chemicals . The hemichannel/gap junction (Cxs) blocker, carbenoxolone (CBX) , and selAll animal care and experimental procedures described in this report complied with the Ethical Guidelines established by the Institutional Animal Care and Use Committee at Mie University, Japan (No. 2019-3-R1) and are reported in accordance with the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines . AstrocyN = 48) sacrificed by decapitation at 0\u201324 h of age. The cerebral hemispheres were removed under dissecting microscope. Tissue was chopped into fine pieces using scissors and then triturated briefly with micropipette. Suspension was filtered using 70 \u00b5m nylon mesh and centrifuged. Pellets were then resuspended in 10 mL Dulbecco\u2019s modified Eagle\u2019s medium containing 10% fetal calf serum (fDMEM), which was repeated three times. After culture for 14 days (DIV14), contaminating cells were removed by shaking in standard incubator for 16 h at 200 rpm. On DIV21, astrocytes were removed from flasks by trypsinization and seeded directly onto translucent poly ethylene terephthalate (PET) membrane (1.0 \u03bcm) with 24-well plates (BD) at a density of 1 \u00d7 105 cells/cm2 for experiments From DIV21 to DIV28, the culture medium (fDMEM) was changed twice a week, and CLZ or VPA was added for subchronic administrations (7 days). On DIV28, cultured astrocytes were washed out using ACSF, and this was repeated three times. The ACSF comprised NaCl 150.0 mM, KCl 3.0 mM, CaCl2 1.4 mM, MgCl2 0.8 mM, and glucose 5.5 mM, buffered to pH 7.3 with 20 mM HEPES buffer. The remaining adherent cells contained 95% GFAP-positive and A2B5-negative cells, detected using immunohistochemical staining [2 incubator (pretreatment incubation). After the pretreatment, astrocytes were then incubated in ACSF, 50 mM K+ or 100 mM K+ containing the same agents of pretreatment (20 min) and collection of the ACSF, MK-ACSF, or HK-ACSF for analysis. Each 100 \u03bcL of collected ACSF, MK-ACSF, or HK-ACSF was filtered by Vivaspin 500-3K and freeze-dried for storage at \u221280 \u00b0C until needed for analyses.Pregnant Sprague-Dawley rats , which were housed individually in cages, were kept in air-conditioned rooms set at 12 h light/dark cycle, with free access to food and water. Cultured astrocytes were prepared from cortical astrocyte cultures of neonatal Sprague-Dawley rats . Both plasma membrane and cytosol fractions were solubilized by radio immunoprecipitation assay buffer containing protease inhibitor cocktail .+ containing ACSF), or HK-ACSF (100 mM K+ containing ACSF) containing the same agent of pretreatment incubation for 20 min. Especially, to determine the astroglial releases associated with Cxs, after pretreatment incubation, astrocytes were incubated in ACSF, MK-ACSF, or HK-ACSF containing the same agent of pretreatment incubation with Cx43 selective inhibitor, CAP19 (20 \u03bcM), or nonselective Cxs inhibitor, CBX (100 \u03bcM), for 20 min.During DIV21 to DIV28, astrocytes were incubated in fDMEM, not containing any target agents. On DIV28 during pretreatment incubation, astrocytes were incubated in ACSF containing CLZ for 60 min. After pretreatment incubation, astrocytes were incubated in ACSF, MK-ACSF . On DIV28 during pretreatment incubation, astrocytes were incubated in ACSF containing the same agent for 60 min. After pretreatment incubation, astrocytes were incubated in ACSF, MK-ACSF, or HK-ACSF containing the same agent for 20 min. Especially, to determine the astroglial releases associated with Cxs, after pretreatment incubation, astrocytes were incubated in ACSF, MK-ACSF, or HK-ACSF containing the same agent with CAP19 (20 \u03bcM) or CBX (100 \u03bcM) for 20 min.l-glutamate and d-serine, during DIV21 to DIV28, astrocytes were incubated in fDMEM, not containing any target agents. On DIV28 during pretreatment incubation, astrocytes were incubated in ACSF containing VPA for 60 min. After pretreatment incubation, astrocytes were incubated in ACSF, MK-ACSF, or HK-ACSF containing the same agent of pretreatment incubation for 20 min.To determine the effects of acute administration of VPA on astroglial releases of l-glutamate and d-serine, during DIV21 to DIV28, astrocytes were incubated in fDMEM containing VPA . On DIV28 during pretreatment incubation, astrocytes were incubated in ACSF containing the same agent for 60 min. After pretreatment incubation, astrocytes were incubated in ACSF, MK-ACSF, or HK-ACSF containing the same agent of pretreatment incubation for 20 min.To determine the effects of subchronic administration of VPA on astroglial releases of During DIV21 to DIV28, astrocytes were incubated in fDMEM containing CLZ . On DIV28 during pretreatment incubation, astrocytes were incubated in ACSF containing the same agent (CLZ) with therapeutic-relevant concentration of VPA (1000 \u03bcM) for 60 min. After pretreatment incubation, astrocytes were incubated in ACSF, MK-ACSF, or HK-ACSF containing the same agent of pretreatment incubation for 20 min.During DIV21 to DIV28, astrocytes were incubated in fDMEM containing the therapeutic-relevant concentration of VPA (1000 \u03bcM). On DIV28 during pretreatment incubation, astrocytes were incubated in ACSF containing the same agent (1000 \u03bcM VPA) with CLZ for 60 min. After pretreatment incubation, astrocytes were incubated in ACSF, MK-ACSF, or HK-ACSF containing the same agent for 20 min.l-cysteine and o-phthalaldehyde [l-cysteine (2 mg) and o-phthalaldehyde (1 mg) in 0.1 mL ethanol, followed by the addition of 0.9 mL sodium borate buffer . Automated pre-column derivatives were obtained by drawing up a 5 \u03bcL aliquot of the standard or blank solution and 5 \u03bcL of the derivative reagent, and holding them in vials for 5 min before injection. The derivatized samples (5 \u03bcL) were injected by autosampler . Analytical column was maintained at 45 \u00b0C and a flow rate of 500 \u03bcL/min. Linear gradient elution was performed over 10 min in mobile phases A and B . The excitation/emission wavelengths of the fluorescence detector were set at 280 and 455 nm, respectively [Levels of L-glutamate and GABA were determined by the fluorescence resonance energy transfer method ,47,48 usaldehyde ,26,27. Dectively ,47,48.Simple Western analyses were performed using Wes according to the ProteinSimple user manual . Lysate N = 6) that were predetermined based on our previous studies [p value less than 0.05 was considered statistically significant. Statistical analyses were performed in BellCurve for Excel Version 3.2. . Astroglial transmitter concentrations were analyzed by Mauchly\u2019s sphericity test, followed by multivariate analysis of variance (MANOVA) using BellCurve for Excel. When the data did not violate the assumption of sphericity (p > 0.05), the F-value of MANOVA was analyzed using sphericity-assumed degrees of freedom. However, if the assumption of sphericity was violated (p < 0.05), the F-value was analyzed using Chi-Muller\u2019s-corrected degrees of freedom. When the F-value for the agent/concentration factors of MANOVA was significant, the data was analyzed by Tukey\u2019s post hoc test. Protein expression of Cx43 in cytosol and plasma membrane fractions was analyzed by two-way analysis of variance (ANOVA) with Tukey\u2019s post hoc test using BellCurve for Excel.All experiments were designed with equal-sized groups = 39.4 (p < 0.01), FCLZ = 210.0 (p < 0.01), Fstimulation*CLZ = 114.4 (P < 0.01)) and D-serine = 55.4 (p < 0.01), FCLZ = 179.5 (p < 0.01), Fstimulation*CLZ = 86.7 (p < 0.01)) (+-evoked stimulation (50 and 100 mM) concentration-dependently increased astroglial releases of L-glutamate and D-seine concentration-dependently increased basal and K< 0.01)) A,B. The D-seine A,B. The +-evoked astroglial releases of L-glutamate = 8.5 (p < 0.01), FCLZ = 259.1 (p < 0.01), FGAP19*CLZ = 22.6 (p < 0.01)) and D-serine = 11.8 (p < 0.01), FCLZ = 220.8 (p < 0.01), FGAP19*CLZ = 13.8 (p < 0.01)) = 20.6 (p < 0.01), FCLZ = 226.1 (p < 0.01), FCBX*CLZ = 66.3 (p < 0.01)) and D-serine = 26.5 (p < 0.01), FCLZ = 178.1 (p < 0.01), FCBX*CLZ = 48.1 (p < 0.01)) , decreased the CLZ-induced 100 mM K< 0.01)) A,B. The < 0.01)) A,B. Ther+-evoked astroglial releases of L-glutamate = 67.1 (p < 0.01), FCLZ = 268.1 (p < 0.01), Fstimulation*CLZ = 128.9 (p < 0.01)) and D-serine = 80.6 (p < 0.01), FCLZ = 287.8 (p < 0.01), Fstimulation*CLZ = 125.2 (p < 0.01)) (+-evoked stimulation (50 and 100 mM) concentration-dependently increased astroglial releases of L-glutamate and D-seine concentration-dependently increased basal and K< 0.01)) A,B. The D-seine A,B. The +-evoked astroglial releases of L-glutamate = 19.7 (p < 0.01), FCLZ = 276.5 (p < 0.01), FGAP19*CLZ = 27.0 (p < 0.01)) and D-serine = 22.7 (p < 0.01), FCLZ = 336.1 (p < 0.01), FGAP19*CLZ = 18.6 (p < 0.01)) = 35.6 (p < 0.01), FCLZ = 279.7 (p < 0.01), FCBX*CLZ = 72.0 (p < 0.01)) and D-serine = 38.3 (p < 0.01), FCLZ = 296.3 (p < 0.01), FCCBX*CLZ = 52.0 (p < 0.01)) , decreased the CLZ-induced 100 mM K< 0.01)) A,B. The < 0.01)) A,B. Ther+-evoked astroglial releases of L-glutamate or D-serine = 13.6 (p < 0.01), FVPA = 97.9 (p < 0.01), Fstimulation*VPA = 16.4 (p < 0.01)) and D-serine = 16.5 (p < 0.01), FVPA = 66.0 (p < 0.01), Fstimulation*VPA = 13.1 (p < 0.01)) (+-evoked releases of L-glutamate and D-serine were increased by supratherapeutic concentration of VPA (3000 \u03bcM), but not affected by therapeutic-relevant concentration of VPA (300\u20131000 \u03bcM) did not affect basal or KD-serine A,B. Cont< 0.01)) C,D. Basa1000 \u03bcM) C,D.+-evoked astroglial releases of L-glutamate and D-serine A,B. Acut\u2013100 \u03bcM) A,B.+-evoked astroglial releases of L-glutamate and D-serine = 37.9 (p < 0.01), FCLZ = 439.4 (p < 0.01), FVPA*CLZ = 265.6 (p < 0.01)) and D-serine = 48.3 (p < 0.01), FCLZ = 270.2 (p < 0.01), FVPA*CLZ = 184.9 (p < 0.01)) (+-evoked releases of L-glutamate (from 100 \u03bcM to 10 \u03bcM) and D-serine (from 30 \u03bcM to 10 \u03bcM).Acute administration of CLZ concentration-dependently increased KD-serine A,B. Subc< 0.01)) A,B. Subc+-evoked releases of L-glutamate = 30.1 (p < 0.01), FCLZ = 291.8 (p < 0.01), FVPA*CLZ = 40.3 (p < 0.01)) and D-serine = 16.3 (p < 0.01), FCLZ = 94.7 (p < 0.01), FVPA*CLZ = 11.5 (p < 0.01)) (+-evoked releases of L-glutamate (from 30 \u03bcM to 3 \u03bcM) and D-serine (from 10 \u03bcM to 3 \u03bcM).Subchronic administration of therapeutic-relevant concentration of VPA (1000 \u03bcM) increased astroglial CLZ-induced 100 mM K< 0.01)) A,B. SubcFragment = 7.4 (p < 0.01), FLevel = 15.0 (p < 0.01), FFragment*Level = 3.8 (p < 0.05)) = 5.0 (p < 0.05), FLevel = 22.1 (p < 0.01), FFragment*Level = 6.2 (p < 0.01)) (p < 0.05) (Subchronic administrations of VPA (1000 and 3000 \u03bcM) concentration-dependently increased Cx43 expression in cytosol fraction without affecting that in plasma membrane fraction (F< 0.05)) A. Contra< 0.01)) B. The th < 0.05) B.Fragment = 33.4 (p < 0.01), FLevel = 15.6 (p < 0.01), FFragment*Level = 17.0 (p < 0.01)) (p < 0.01) concentration-dependently increased Cx43 expression in plasma membrane but not cytosol fraction of astrocytes subchronically treated with therapeutic-relevant concentration of VPA (1000 \u03bcM) (F< 0.01)) C. The th < 0.01) C.+-evoked astroglial releases of L-glutamate and D-serine were 100 \u03bcM, 30\u2013100 \u03bcM and 10\u201330 \u03bcM, respectively. The K+-evoked astroglial release was composed of astroglial exocytosis [2+, K+, and plasma membrane voltage [+-evoked astroglial releases of L-glutamate and D-serine. These results suggest that the K+-evoked astroglial releases of L-glutamate and D-serine, at least partially, comprise the output through Cxs. Therefore, acute administration of CLZ concentration-dependently enhances astroglial releases of L-glutamate and D-serine associated with Cxs, but the stimulatory effects of CLZ on astroglial releases were observed in the supratherapeutic range. The therapeutic concentration of VPA was considered, ranged 350\u2013700 \u03bcM [+-evoked astroglial releases of L-glutamate and D-serine. Therefore, acute administration of VPA did not affect Cxs activities.The present study demonstrated that CLZ enhanced astroglial releases of L-glutamate and D-serine, in a concentration-dependent manner. Survival analysis has suggested that effective relapse prevention requires the maintenance of patients at CLZ serum concentrations above 0.6 \u03bcM ; howeverocytosis ,24,44, oocytosis ,41,42, a voltage . During voltage . In the 0\u2013700 \u03bcM . Neither+-evoked astroglial releases of L-glutamate and D-serine. The stimulatory effects of subchronic administration of CLZ on basal and K+-evoked astroglial releases were predominant compared with those of acute CLZ administration, since the threshold concentrations of subchronic administration of CLZ on basal, 50 mM and 100 mM K+-evoked astroglial releases of L-glutamate and D-serine were reduced to 30 \u03bcM (acute: 100 \u03bcM), 30 \u03bcM (acute: 30\u2013100 \u03bcM), and 10 \u03bcM (acute: 10\u201330 \u03bcM), respectively. Similar to CLZ, subchronic administration of supratherapeutic concentration of VPA (3000 \u03bcM) increased K+-evoked astroglial releases of L-glutamate and D-serine without affecting basal release. These discrepancies between acute and subchronic administrations of CLZ and VPA on basal and K+-evoked astroglial releases of L-glutamate and D-serine suggest that subchronic administration of CLZ and VPA possibly increases expression of Cxs in plasma membrane.Contrary to acute administrations, chronic administration of CLZ also increased basal and KIndeed, simple western analysis detected the subchronic administration of CLZ and VPA increased astroglial expression of Cx43, which is the principal Cx isoform in astrocytes ; howeverThe Cx gene regulation system, transcriptional factors , and epigenetic processes have been identified ,52. HistContrary to VPA, CLZ activates the inhibitory and stimulatory expression regulating system on Cx43 synthesis, such as HDAC2, Wnt pathway, transcription factor specificity protein 1, and activator protein 1 complex ,60,61,62Cx43 is the principal Cxs in astrocytes, but Cx26 and Cx30 are also expressed in astrocytes [The incidence of seizures with CLZ is ranged from 2% to 7.5%, and the risk of CLZ-induced seizures increased with higher doses . The risIn the present study, neither acute nor subchronic administrations of therapeutic-relevant concentration of CLZ (1\u20133 \u03bcM) affected astroglial transmission; however, acute administration of therapeutic-relevant concentration of CLZ drastically increased astroglial releases of L-glutamate and D-serine from astrocytes which were chronically administrated with therapeutic-relevant concentration of VPA (1000 \u03bcM). Therapeutic-relevant concentration of CLZ (3 \u03bcM) also drastically increased Cx43 expression in the plasma membrane fraction without affecting that in cytosol fraction of therapeutic-relevant concentration of VPA-administrated astrocytes. These results suggest that increased Cx43 in the cytosol fraction induced by subchronic administration of therapeutic-relevant concentration of VPA (1000 \u03bcM) is transported to plasma membrane by CLZ. The rapid titration of CLZ dose and VPA administration at the commencing CLZ are significantly associated with increasing risks of CLZ-induced myocarditis/cardiomyopathies . It has The present study determined the concentration- and time-dependent effects of CLZ and VPA on astroglial transmission of L-glutamate and D-serine associated with Cx43, to explore the mechanisms of the multimodal action of CLZ. Both acute and subchronic administrations of CLZ and VPA increased astroglial releases of L-glutamate and D-serine concentration-dependently, but the therapeutic-relevant concentration of neither CLZ nor VPA affected these releases. The stimulatory effects of subchronic administrations of CLZ and VPA on astroglial releases were more predominant compared with those of acute administrations. Subchronic administrations of both VPA and CLZ concentration-dependently increased Cx43 expression in astrocytes, but the therapeutic-relevant concentration of neither CLZ nor VPA affected Cx43 expression. Especially, VPA increased Cx43 expression in cytosol fraction of astrocytes, whereas CLZ increased Cx43 expression in both cytosol and plasma membrane fractions. After subchronic administration of CLZ, acute administration of therapeutic-relevant concentration of VPA did not affect CLZ-induced astroglial transmitter releases; however, after subchronic administration of therapeutic-relevant concentration of VPA, acute administration of CLZ drastically increased astroglial transmitter releases. Therapeutic-relevant concentration of CLZ alone could not affect astroglial release, whereas after the subchronic administration of therapeutic-relevant concentration of VPA, acute administration of therapeutic-relevant concentration of CLZ could increase astroglial transmitter releases. During subchronic administration of therapeutic-relevant concentration of VPA, acute administration of therapeutic-relevant concentration of CLZ enhanced the transport of cytosol Cx43 to plasma membrane. Therefore, CLZ enhances astroglial functional Cxs via activation of transport of cytosol Cx43 to plasma membrane. These results suggest that the hyperactivation of astroglial Cxs activities induced by supratherapeutic concentration or rapid titration of CLZ, at least partially, contributes to CLZ-induced seizure, but inhibitory effects of VPA on CLZ-induced seizure are not modulated with astroglial transmission associated with Cxs. Interestingly, VPA intake at the commencing CLZ increases risk of CLZ-induced myocarditis/cardiomyopathies, probably via reciprocal activation of Cxs between VPA and CLZ."} +{"text": "Kocuria varians 80 was sequenced and assembled into a single 2.82-Mb chromosome. Genome sequence comparison of K. varians strain 80 and previously sequenced strains revealed predicted proteomic differences that can impact its technological properties.The genome of the meat starter culture strain Kocuria varians 80 was sequenced and assembled into a single 2.82-Mb chromosome. Genome sequence comparison of K. varians strain 80 and previously sequenced strains revealed predicted proteomic differences that can impact its technological properties.The genome of the meat starter culture strain Kocuria varians is used as a starter culture for processed meat and dairy products. In combination with other starter cultures or by itself, it can participate in proteolysis, denitrification, and biogenic amine degradation (\u2013Staphylococcus carnosus TM300 (Staphylococcus xylosus (Lactobacillus sakei (Kocuria varians strain 80 (SSCA-2165).radation \u20133, whichus TM300 , Staphyl xylosus , Lactobaus sakei , and othKocuria varians strain 80 was received from State Scientific Center for Antibiotics Culture and was originally isolated from dried fermented sausages in 1978 . We used the NEBNext Ultra DNA library prep kit for Illumina HiSeq 2500 sequencing. For PacBio RS II single-molecule real-time (SMRT) sequencing, we used the SMRTbell template prep kit v1.0 following the 20-kb template preparation protocol using the BluePippin size selection system. In total, there were 2.1 billion (2\u2009\u00d7\u2009250-bp) Illumina reads and 158,304 PacBio reads .K. varians was assembled with SPAdes v3.11 , and K. varians G6 (GCA_900014985.1). After circularization using Simple Circularise v1.0 (https://github.com/Kzra/Simple-Circularise), the genome assembly consisted of a single contig with a 2,823,038-bp circular chromosome . The genome has a 70.55% GC content. We found 2,465 protein-coding sequences, 48 tRNA genes, and 9 rRNA genes.After read and adapter trimming with Trimmomatic v0.36 with thees v3.11 , with eres v3.11 ; every pes v3.11 search. es v3.11 for K. vK. varians C6, both K. varians 80 and K. salsicia G1 contain the xylB gene, according to KEGG pathway analysis. Also unlike K. varians G6 and K. salsicia G1, strain 80 has a complete metabolic pathway from d-glucose-1P to l-rhamnose, which is potentially important to its properties as a meat-fermenting starter culture.Unlike SRR13177364 and SRR13177365, respectively. The genome sequence of K. varians strain 80 (SSCA-2165) has been deposited at GenBank under accession number GCF_002250745.2.The PacBio and Illumina reads were submitted to the SRA under accession numbers"} +{"text": "J Clin Endocrinol Metab. 2020;105(8):2515\u20132531; doi: 10.1210/clinem/dgaa238), the following transcriptional error occurred in the published paper: \u201cThe y-axis title for Figure 3 (page 9) incorrectly describes the plasma testosterone (T) concentration in units of ng/mL instead of ng/dL.\u201dIn the above-named article by Swerdloff RS, Wang C, White WB, Kaminetsky J, Gittelman MC, Longstreth JA, Dudley RE, and Danoff TM (The authors have provided an updated version of Figure 3.10.1210/clinem/dgaa238doi:"} +{"text": "Common clinical features of patients with Coronavirus disease-2019 (COVID-19) vary from fever, to acute severe respiratory distress syndrome. Several laboratory parameters are reported as indicators of COVID-19 severity. We hereby describe the possible novel severity biomarkers for COVID-19, CD11b+CD33+HLA-DR-CD14+ cells and CD11b+CD33+HLA-DR-CD66b+ cells. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of COVID-19. COVID-19 has already led to massive infection and deaths worldwide and was declared a pandemic by the World Health Organization.Common clinical features of patients with COVID-19 vary from fever, cough, dyspnea (among others) to acute severe respiratory distress syndrome (ARDS), and shock. Reports of fatal outcomes in hospitalized patients vary from 6.2 to 21.5% in patients recently infected with SARS-CoV-2.n = 16, 7 males, 9 females, median age 49.7 years).We investigated the presence of CD33+CD11b+HLA-DR-CD14+ and CD33+CD11b+HLA-DR-CD66b+ cells in the peripheral blood of 104 patients infected with COVID-19, 62 males and 42 females. The diagnosis of COVID-19 was confirmed by the detection of SARS-CoV-2 RNA by reverse-transcriptase polymerase chain reaction (RT-PCR), and patients tested negative for respiratory syncytial virus (RSV) and influenza. The study was approved by the Ethics Committee of Hospital das Cl\u00ednicas da Faculdade de Medicina da Universidade de S\u00e3o Paulo\u2014HCFMUSP (no. 30800520.7.0000.0068-2020) and was carried out in conformity with the 2013 revision of the Declaration of Helsinki. Healthy controls (HC), without SARS-CoV-2, RSV or influenza infection, were recruited for flow cytometry assays .During hospitalization, COVID-19 patients received systemic treatment. All patients received antibiotics and anticoagulants, 45/104 systemic corticosteroids, 39/104 antivirals. EDTA plasma samples were obtained from a single venipuncture. Laboratory analysis was performed at the Central Laboratory of Hospital das Clinicas, Faculdade de Medicina da Universidade de S\u00e3o Paulo , and included: complete blood counts (CBC), coagulogram, liver enzymes , alkaline phosphatase (AP), bilirubin, urea, creatinine, glucose, sodium, potassium, lactate dehydrogenase, magnesium, phosphorus, total proteins and fractions immunoglobulins, CRP, ferritin, pH, pO2, pCO2, D-dimer, and erythrocyte sedimentation rate in arterial blood collected in K2EDTA tubes.P < 0.05).Flow cytometry analysis was performed using 0.1 mL of whole blood in K2EDTA collection tubes . Samplesp = 0.0382), pCO2 (p = 0.0167), mean corpuscular volume (p = 0.0226), enhanced leukocytes (p = 0.0001), neutrophils (p = 0.0001), neutrophil-to-leukocyte ratio (p = 0.0001), and augmented levels of alkaline phosphatase (p = 0.0150), total bilirubin (p = 0.0363), direct bilirubin (p = 0.0113), glutamyl transferase gamma (p = 0.0388), creatinine (p = 0.0121), lactate dehydrogenase (p = 0.0121), CRP (p = 0.0408), urea (p = 0.0016) and D-dimer (p = 0.0012) .Such laboratory parameters reinforce the need for biomarkers such as neutrophil-to-lymphocyte ratio, urea and d-dimer as a predictive factor of disease outcome , 4. MorePrevious reports verified an immune dysregulation in circulating immune cells in the blood of COVID-19 patients, with a significant increase in neutrophil-to-lymphocyte ratio in COVID-19, and a further increase in severe COVID-19 . Here, wp = 0.0471). We also verified an increase in CD33+CD11b+HLA-DR-CD14+ cells in the blood of ICU patients in comparison with HC individuals (p < 0.0001) and GW patients (p = 0.0388) .p = 0.0178). Again, we also verified an increase in CD33+CD11b+HLA-DR-CD66b+ cells in the blood of ICU patients in comparison with HC individuals (p < 0.0001) and GW patients (p = 0.0175) patients in comparison with HC individuals ( 0.0175) .Overall, these findings suggest a correlation between the quantification of CD33+CD11b+HLA-DR-CD14+ cells and CD33+CD11b+HLA-DR-CD66b+ cells and the severity of COVID-19. These cells have been previously characterized as myeloid derived suppressor (MDSC) cells by this cytometry panel , but furEnhanced CD33+CD11b+HLA-DR\u2013CD14\u2013CD66b+ and CD33+CD11b+HLA-DR\u2013CD14+CD66b\u2013 cells in the blood of ICU patients, classified as severe COVID patients, could represent not only a predictor of prognosis for COVID-19, but also specific therapy targets for treating this virus infection in the near future.All datasets generated for this study are included in the article/supplementary material.This studies involving human participants were reviewed and approved by Ethics Committee of Hospital das Cl\u00ednicas da Faculdade de Medicina da Universidade de S\u00e3o Paulo\u2014HCFMUSP (no. 30800520.7.0000.0068-2020). The patients/participants provided their written informed consent to participate in this study.RA and MS: conception, performed experiments, analysis, write, and review. MAn, AB, AP, NP, IF, LO, FT, DB, EO, SG-S, YR, and CdB: performed experiments and review. MAr, RO, VA, and AD: patient care and review. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Technology in Cancer Research & Treatment. 2020;19: 1-8. doi: 10.1177/1533033819892251Xuefang Z, Ruinian Z, Liji J, et al. miR-331-3p Inhibits Proliferation and Promotes Apoptosis of Nasopharyngeal Carcinoma Cells by Targeting elf4B-PI3K-AKT Pathway. The published version of Figure\u00a02 is incorrect. The correct version of the figure is as given below:"} +{"text": "Sir,Escherichia coli have identified a globally disseminated high-risk clone named ST131, with strains belonging to three clades and three different subclades . While C2 is associated with CTX-M-15, clade C1-M27 has been associated with CTX-M-27.blaCTX-M-27 nor E. coli ST131 C1-M27 have been reported so far.Surveillance studies of ESBL-producing Perna perna) and oysters (Crassostrea spp.) were collected from 14 near-shore sites located at different distances from the port of Santos (the largest port of Latin America). Mussel (n\u2009=\u200910) and oyster (n\u2009=\u200910) samples, collected from each site, were placed into sterile plastic bags. The samples were kept refrigerated and processed within 3\u2009h after collection. Following standard methods for the examination, 25\u2009g of bivalves were distributed in sterile plastic bags containing 225\u2009mL of Brain Heart Infusion broth and incubated at 37\u00b0C for 24\u2009h. Subsequently, the samples were streaked onto MacConkey agar plates supplemented with ceftriaxone (2\u2009mg/L), meropenem (2\u2009mg/L) or colistin (2\u2009mg/L), following incubation at 37\u00b0C for 24\u2009h.During a local surveillance study conducted to monitor the presence of WHO critical priority pathogens in impacted marine ecosystems, brown mussels (E. coli isolates were recovered from mussel (E. coli 6M) and oyster (E. coli MO) samples collected from two different sites close to the port. Antimicrobial susceptibility testing, performed by disc diffusion and/or Etest methods,,E. coli MO was resistant to nalidixic acid (>32\u2009mg/L) and ciprofloxacin (>4\u2009mg/L). PCR screening and Sanger sequencing revealed that these isolates were positive for the blaCTX-M-27 ESBL gene.Two ceftriaxone-resistant E. coli strains were subjected to WGS using the Illumina NextSeq (2\u205f\u00d7\u205f150\u2009bp) platform . De novo assemblies were performed using Spades v. 3.11. WGS data were analysed using bioinformatics tools available from the Center for Genomic Epidemiology (www.cge.dtu.dk).E. coli 6M (accession number: NCWA00000000.1) belonged to serotype O86:H18 and sequence type ST38/CC38, whereas E. coli MO (accession number: NCVZ00000000.1) belonged to serotype O25b:H4 and ST131/CC131. These STs have been globally disseminated among humans, animals and aquatic environments, being commonly associated with CTX-M variants.,,E. coli 6M revealed the presence of iss , astA (EAST-1 toxin), eatA (enterotoxigenic autotransporter A), capU (hexosyltransferase homologue), nfaE (diffuse adherence fibrillar adhesin) and eilA genes, whereas iha (adherence protein), sat (secreted autotransporter toxin), gad (glutamate decarboxylase), senB (enterotoxin) and iss genes were found in E. coli MO. Moreover, E. coli MO carried fimH30 (associated with ST131) and the C1 subclade-specific prophage-like region (M27PP1).iha, sat, gad, iss and senB genes) of E. coli MO was identical to that of other E. coli strains of ST131 and C1-M27 clade.,strA, strB and aadA5), \u03b2-lactams (blaCTX-M-27), sulphonamides (sul1 and sul2), trimethoprim (dfrA17) and tetracycline [tet(A)], as previously observed in E. coli of ST131 and C1-M27;2,3 whereas mutations in the quinolone resistance-determining regions of gyrA , parC and parE (Ile529Leu) genes were only identified in the E. coli MO strain. FIB and FII, and Col156, FIA, FIB and FII replicon types were identified in E. coli 6M and MO strains, respectively.blaCTX-M-27 genes, was achieved by bacterial transformation using E. coli TOP10. FIB and FII replicons were identified in p6M (FAB formula F2:A\u2212:B10), whereas FIA, FIB and FII replicon types were confirmed in pMO (FAB formula F1:A2:B20). The complete sequence of the pMO plasmid (GenBank accession no. MG886288) was obtained using de novo assembly, followed by gap closure by PCR and Sanger sequencing.Mobilization of plasmids \u223c130\u2009kb in size (named pMO and p6M), bearing blaCTX-M-27, the pMO plasmid harboured aadA5, sul1, dfrA17, tet(A) and mphA resistance genes, similarly to F1:A2:B20 plasmids harboured by the C1-M27 clade , of which 129 CDS encoded proteins with known functions . Besides blaCTX-M-27 genes, carried by both E. coli strains, revealed the presence of IS26 and IS903 mobile elements, E. coli MO presented a truncated IS903 upstream of the blaCTX-M-27 gene, whereas E. coli 6M presented a truncated ISEcp1 downstream of the blaCTX-M-27 gene, and tonB and ORF genes (Figure\u2009Although analysis of the genetic environment of E. coli strains, of ST131 and clade C1-M27, in Brazil. In this regard, since CTX-M-27-positive E. coli strains were recovered from areas impacted by intensive maritime traffic and transoceanic shipping activities, a possible introduction of international clones via commercial shipping routes could be speculated.E. coli in South American countries remains necessary to elucidate the local epidemiology and dynamics of the transmission of high-risk clades with pandemic potential.In summary, to our knowledge, we report the first identification of CTX-M-27-producing"} +{"text": "T isolated from the roots of Acacia mangium Willd. showed potential plant growth promoting (PGP) activity. Phylogenetic analysis, based on 16S rRNA gene, indicated that strain GKU 173T was the most closely related to Fodinicola feengrottensis HKI 0501T\u2014the only species in the genus Fodinicola. Morphology and chemotaxonomy of strain GKU 173T indicated that it belongs to the genus Fodinicola by having meso-diaminopimelic acid in the cell wall and xylose as the characteristic cell-wall sugars. The cellular fatty acid profile mainly comprised iso-C16:0, anteiso-C17:0, iso-C18:0, and iso-C17:0. The major menaquinones were MK-9(H4), MK-9(H6), and MK-9(H8). The main polar phospholipids contained diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylinositol (PI). Genome analysis signified DNA G+C content of 67.81 mol%. The level of digital DNA-DNA relatedness between strain GKU 173T and the type strain was 21.30%. On the basis of polyphasic characteristics, strain GKU 173T clearly represents a novel species of the genus Fodinicola, for which the name Fodinicolaacaciae sp. nov. (= TBRC 10620T = NBRC 114213T) is proposed. Furthermore, genome analysis of both strains suggested that members of the genus Fodinicola are promising sources of beneficial PGP-actinomycetes and novel secondary metabolites.A novel endophytic actinomycete strain GKU 173 Endophytic actinomycetes colonize the internal plant tissues and usually have a beneficial effect to the host plant by promoting growth and protecting the plant from biotic and abiotic stresses without any damage or morphological changes to the plant ,2. IsolaFodinicola was first proposed by Carlsohn et al. was determined on ISP 3 agar for three weeks. Catalase and oxidase activities were observed with 3% (v/v) hydrogen peroxide solution and 1% (v/v) tetramethyl-p-phenylenediamine solution [Growth of strain GKU 173solution , respectsolution . The utisolution . Degradasolution after insolution ,38. Hydrsolution . Milk coT in Bennett\u2019s broth on a rotary sharker at 28 \u00b0C for 14 days. Cells were harvested by centrifugation, washed with distilled water, and freeze-dried. Cell wall peptidoglycan was prepared using the modified method described by Kawamoto et al. [N\u03b1--D-leucinamide (FDLA) derivatization according to the method of Fujii et al. [N-acyl group of muramic acid in the peptidoglycan was examined using the previously described method [For chemotaxonomic analysis, biomass was prepared by growing strain GKU 173o et al. to analyo et al. after N\u03b1i et al. . The LC/i et al. and by Li et al. . The isoi et al. . N-acyl d method . Mycolicd method . Phosphod method . Cellulad method by the Sd method , and anaT and F. feengrottensis HKI 0501T were extracted from the culture grown in Bennett\u2019s broth at 28 \u00b0C for seven days according to standard procedure [T and F. feengrottensis HKI 0501T were sequenced using Illumina Hiseq PE 150 serviced by Novogene and PacBio Sequel systems at Chulabhorn Royal Academy, Thailand. Prior to assembly, the reads were trimmed for adapter sequences and filtered for sequence quality and checked by Fast QC tool [Genomic DNA of strain GKU 173rocedure . Whole g QC tool . Sequenc QC tool and dete QC tool . G+C conAverage Nucleotide Identity (ANI) and Ortho ANI were comT was isolated from surface-sterilized roots of the black wattle tree (Acacia mangium Willd.) on starch-casein agar. It is an aerobic Gram-stain-positive non-sporulating actinobacterium. Morphological observation on ON agar indicated that strain GKU 173T formed a branched substrate mycelium and abundant white aerial hyphae that fragmented into irregular rod-like elements tricalcium phosphate . The strain also showed a remote relationship (<95% similarity) with other species including Cryptosporangium eucalypti EURKPP3H10T (94.64%), Cryptosporangium phraense A-T 5661T (94.57%), Cryptosporangium aurantiacium DSM 46144T (94.50%), Jiangella anatolica GTF31T (94.36%), Cryptosporangium minutisporangium IFO 15962T (94.36%), and Frankia coriariae BMG5.1T (94.34%). Neighbor-joining phylogenetic analysis indicated that strain GKU 173T grouped tightly with the only member of the genus Fodinicola indicated that strain GKU 173dinicola . The posp values . Genus Fn et al. is monopngiaceae within t0501T 97.%. The st in 2008 . Based oT and its closely related species, F. feengrottensis HKI 0501T, were phenotypically characterized. Strain GKU 173T showed better growth than F. feengrottensis HKI 0501T in most tested media with good growth at concentration up to 3% (w/v). Strain GKU 173T showed oxidase-negative and catalase-positive. The difference of acidic production, and carbon/nitrogen utilization of strain GKU 173T and F. feengrottensis HKI 0501T are summarized in T can be distinguished from F. feengrottensis HKI 0501T.Strain GKU 173ed media . Its sub pigment . Strain T contained meso-diaminopimelic acid, D-alanin, D-glutamic acid, and glycine. Cell wall sugars were xylose and mannose. The N-acyl type of muramic acid in the peptidoglycan was N-acetyl. Mycolic acids were absent. The polar phospholipids comprised of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylinositol (PI), several unknown phospholipids, and unknown ninhydrin-positive compounds (16:0 (58.22%), anteiso-C17:0 (9.94%), iso-C18:0 (9.35%), and iso-C17:0 (6.58%); and a small proportion of 10-methyl C17:0 (3.87%), 10-methyl C18:0 (1.9%), iso-C16:1 (1.63%), sum in feature 8 , and summed feature 8 . The menaquinones were MK-9(H4) (25%), MK-9(H6) (36%) and MK-9(H8) (39%). All chemotaxonomic results revealed that strain GKU 173T shared apparent characteristics with the only member of the genus Fodinicola particularly, the presence of xylose as the diagnostic cell-wall sugar [T as a novel species within the genus Fodinicola.The analysis of the cell wall peptidoglycan by TLC and LC/Mompounds . The fatll sugar . AltogetT and strain HKI 0501T were sequenced and compared. The assembled draft genomes of strain GKU 173T and strain HKI 0501T contained 4 and 107 contigs with a total length of 8.86 Mbp (GenBank accession number WOTN00000000) and 8.71 Mbp (GenBank accession number WOTO00000000), respectively. The N50 value of genomes of strains GKU 173T and HKI 0501T was 2.35 Mbps (L50 = 2) and 1.15 Mbps (L50 = 26), respectively. The ANI value between strain GKU 173T and strain HKI 0501T was 77.92% which was much lower than the ANI threshold range (95%\u201396%) for species delineation [T and F. feengrottensis HKI 0501T were 67.81% and 66.61%, respectively. The difference in G+C value was higher than 1% indicating distinct species according to Meier-Kolthoff et al. [T was distinguished from the closely related type strain and represents a novel species of the genus Fodinicola, for which the name Fodinicola acaciae sp. nov. (= TBRC 10620T = NBRC 114213T) is proposed.Genomes of strain GKU 173ineation . The dDDineation . The calf et al. . On the Fodinicola acaciae myo-inositol, lactose, mannitol, D-raffinose, D-sorbitol, sucrose, D-tretalose, and D-xylose, but not from rhamnose. L-tyrosine, Tween 20, and Tween 80 are degraded, but adenine, hypoxanthine, starch, urea, xanthine, and xylan are not. Adonitol, L-arabinose, D-fructose, D-glucose, glycerol, myo-inositol, lactose (weakly), mannitol, D-raffinose, rhamnose, D-sorbitol, sucrose, D-trehalose, and D-xylose are used as carbon sources. L-arginine, L-cysteine, L-histidine, L-isoleucine, L-phenylalanine, potassium nitrate, L-tryptophan, and L-valine are used as nitrogen sources. By API ZYM system, production of acid phosphatase, alkaline phosphatase, \u03b1-chymotrypsin (weakly), cysteine arylamidase (weakly), esterase (C4), \u03b1-galactosidase, \u03b2-galactosidase, N-acetyl-\u03b2-glucosaminidase, \u03b1-glucosidase, \u03b2-glucosidase, leucine arylamidase, lipase (C8), lipase (C14), \u03b1-mannosidase, naphthol-AS-BI-phosphohydrolase, and trypsine are positive, but not \u03b1-fucosidase and \u03b2-glucuronidase. The cell wall peptidoglycan contains meso-A2pm, D-alanine, D-glutamic acid, and glycine. The muramic acid in peptidoglycan is N-acetylated. The cell-wall sugars are xylose and mannose. The predominant menaquinones are MK-9(H4), MK-9(H6), and MK-9(H8). The polar phospholipids comprise diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylinositol (PI), several unknown phospholipids, and unknown ninhydrine-positive compounds. Mycolic acids are absent. The predominant cellular fatty acid profiles contain iso-C16:0, anteiso-C17:0, iso-C18:0, and iso-C17:0. The G+C content is 67.81% (determined from the genome sequence).Gram-stain-positive, aerobic, non-motile, catalase-positive, oxidase-negative actinomycete that produces branched substrate mycelium and abundant aerial mycelium. Aerial hyphae break up into irregular rod-like elements. Colonies are wrinkled, beige to orange in color. Red-series diffusible pigment is produced on Bennett, ISP 2, ISP 3, organic medium 79, and MS media. Growth occurs between 14 and 42 \u00b0C, good growth at 28 \u00b0C, and no growth below 14 \u00b0C or above 42 \u00b0C. Good growth occurs at pH 7.0 and pH 8.0, but no growth occurs at pH 3 nor pH 12. NaCl tolerance is up to 6% (w/v). Nitrate is not reduced. Gelatin liquefaction, milk coagulation and peptonization are positive. Acid production from adonitol, L-arabinose, D-fructose, glycerol, D-glucose, T (= TBRC 10620T = NBRC 114213T) was isolated from the roots of black wattle tree (Acacia mangium Willd.) collected at Kasetsart University, Bangkok, Thailand. Type strain GKU 173T showed 8705 coding sequences and 55 RNAs, while F. feengrottensis HKI 0501T showed 11,978 coding sequences and 57 RNAs. The genome annotation revealed genes related to the PGP traits according to those in vitro activities of strain GKU 173T and HKI 0501T of lucA/lucC family protein [RAST annotation of genome sequences of strain GKU 173KI 0501T . Indole-lubility . The gen protein .T and F. feengrottensis HKI 0501T were investigated by antiSMASH. The results showed that strain GKU 173T carried 16 BGCs including 5 known BGCs and 11 uncharacterized BGCs constitutes a novel species within the genus Fodinicola of which Fodinicola acaciae sp. nov. was proposed under the type strain GKU 173T (= TBRC 10620T = NBRC 114213T). Genome analysis of the novel strain and the closely related strain, F. feengrottensis HKI 0501T, revealed potential PGP-traits including genes involved in phosphate solubilization, IAA and siderophore production; and a variety of uncharacterized BGCs comprising NRPs, RiPPs, Type I PKs, Type II PKs, Type I PK-NRP hybrid, and terpenes. The results suggested that members in the genus Fodinicola have potential activity as beneficial PGP-bacteria and specialized secondary metabolite producers. Based on the polyphasic taxonomic study demonstrated that strain GKU 173"} +{"text": "Their absorption and emission behaviours in dilute solutions were investigated in order to explain structure\u2013property associations and demonstrate the impact of different aryl substituents on the terpyridine scaffold as well as the role of the metal on the complexes. Photo-luminescence analysis of the complexes in acetonitrile solution revealed a transition from hypsochromic to bathochromic shift. All the compounds displayed remarkable photo-luminescent properties and various maximum emission peaks owing to the different nature of the functional groups. Furthermore, the anti-microbial potential of ligands and complexes was evaluated with docking analyses carried out to investigate the binding affinity of terpyridine-based ligands along with corresponding proteins (shikimate dehydrogenase and penicillin-binding protein) binding sites. To obtain further insight into molecular orbital distributions and spectroscopic properties, density functional theory calculations were performed for representative complexes. The photophysical activity and interactions between chromophore structure and properties were both investigated experimentally as well as theoretically.A series of different substituted terpyridine (tpy)-based ligands have been synthesized by Kr\u00f6hnke method. Their binding behaviour was evaluated by complexing them with Co(II), Fe(II) and Zn(II) ions, which resulted in interesting coordination compounds with formulae, [Zn(tpy) Thorough photophysical and computational studies of the new complexes provide an insight into their electronic structure, which provides a significant extension of newly published terpyridine-transition metal complexes. In addition, we have established a detailed structure\u2013activity relationship (SAR) between these architectures and their biological and spectrophotometric properties.2.3) and acetonitrile (CH3CN) solutions, respectively, on a Jasco UV-Vis V-660 instrument using a QUARTZ cell. The luminescence spectra were obtained using a Shimadzu 8101AFT-IR instrument. Thin-layer chromatography (TLC) was conducted on silica gel TLC plates purchased from Merck and chromatograms were viewed with a UV-lamp at 254 and 365 nm.All chemicals were bought from Merck and Sigma-Aldrich and used as received. Melting points have been recorded with an electrothermal device and are uncorrected. The FTIR spectra have been obtained on a Bio-Rad spectrophotometer and the infrared values are listed in \u1fe1 units. The UV-Vis spectra were recorded in chloroform in methanol (20 ml), a substituted aryl aldehyde (10.0 mmol) was added, followed by potassium hydroxide (KOH) pellets and 35% aqueous ammonia solution (40.0 ml). The reaction mixture was refluxed for 4\u20136 h. After the reaction was completed (determined by TLC monitoring), the solvent was removed under vacuum and the precipitates were filtered, washed with plenty of distilled H2.1.2.2Cl2 solution (20.0 ml) of the substituted terpyridine ligand under continuous stirring. The colour of the reaction mixture instantly changed and the reaction mixture was stirred for approximately 2 h at room temperature. Upon addition of an excess of NH4PF6 precipitation occurred. The precipitates were filtered, washed with ice-cold MeOH (5.0 ml) and (C2H5)2O (15.0 ml) to obtain a pure complex. Recrystallization from acetonitrile or methanol or a mixture of both yielded the analytically purified complex.A hot methanolic solution (20.0 ml) of metal salt (0.5 mmol) was introduced dropwise to a CH2.2.1\u2013L9L) and 520 nm for complexes (1\u2013C27C).RF-6000 Spectrofluorophotometer was used to produce an emission spectrum for ligands and their complexes. The emission spectra of the synthesized ligand in chloroform and of complexes in acetonitrile were obtained by using a fluorescence spectrophotometer. The emission spectra were checked by keeping the excitation value of the synthesized compounds at 325 nm ,67\u201372. T2.3.2.3.1.http://www.rcsb.org/pdb/home/home.do] [Chemical structures of the terpyridines were developed with ChemBio Draw which also produced their MOL format files. The shikimate dehydrogenase (PDB ID: 3DON) and penicillin-binding protein (PDB ID: 1VQQ) three-dimensional crystal structures have been accessed and downloaded from the protein data bank database (PDB) [home.do] .2.3.2.The active sites of the target protein were examined using the molecular operating environment (MOE) software. An active site was distinct from the ligand coordinates in the original protein sites ,72\u201375.2.3.3.A theoretical ligand-target docking method has been used to classify structural complexes of the shikimate dehydrogenase crystal structure and penicillin-target protein with ligand molecules to recognize the molecular basis of the specificity of these protein targets. Eventually, the MOE program performs docking. The energy of these derivatives to interact with the protein targets is given \u2018grid level\u2019.2.4.13C were optimized using the B3LYP* hybrid functional and double zeta (DZ) basis sets.Computational calculations were performed by using DFT-B3LYP*(DZ) in the Amsterdam Density Functional (ADF) modelling suite . The gro2.5.2.5.1.in vitro anti-bacterial activity against Gram-negative Escherichia coli (ATCC 25922) and Pseudomonas aeruginosa (ATCC 9721) and Gram-positive Staphylococcus aureus (ATCC 6538) bacterial strains. Cefixime was used as a positive standard and dimethyl sulfoxide (DMSO) as a negative control. Various sample solutions were prepared by dissolving 4.0 mg of each sample in 1.0 ml of DMSO. The lawn was developed on nutrient agar plates using bacterial strains of equal turbidity that is accomplished using 0.5% of McFarland's solution. The well depth was 8 mm and they were all made at the correct distances from each other. The sample and standard are poured into their respective tubes. The sample quantity used was 80 \u00b5l in a well together with the two controls. The prepared dishes were incubated for 24 h at 37\u00b0C, and the findings were reported as the average diameter of zone of inhibition (ZOI) of bacterial development around the discs in millimetres for each compound +\u00b7 : 387.0713.Light-purple amorphous solid; Yield: 85%; m.p. above 300\u00b0C; UV 3.12.\u03bbmax (CH3CN) = 314 nm; \u03bbem (CH3CN): 379, 776 nm; FTIR (cm\u22121): 1616 (C=N), 1471 (C=C), 1245 (C-N), 1110 (C-H), 623 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 705.2176.Brick-red amorphous solid; Yield: 85%; m.p. above 300\u00b0C; UV 3.13.\u03bbmax (CH3CN) = 327 nm; \u03bbem (CH3CN): 394, 742 nm; FTIR (cm\u22121): 1611 (C=N), 1483 (C=C), 1286 (C-N), 1058 (C-H), 627 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 702.2194.Dark-purple amorphous solid; Yield: 79%; m.p. above 300\u00b0C; UV 3.14.\u03bbmax (CH3CN) = 243 nm; \u03bbem (CH3CN): 370, 521, 732 nm; FTIR (cm\u22121): 1595 (C=N), 1476 (C=C), 1250 (C-N), 1107 (C-H), 584 (Zn-N); MS (MALDI-ToF) of [M]+\u00b7 : 416.0979.Brown amorphous solid; Yield: 72%; m.p. above 300\u00b0C; UV 3.15.\u03bbmax (CH3CN) = 290 nm; \u03bbem (CH3CN): 547, 683 nm; FTIR (cm\u22121): 1595 (C=N), 1473 (C=C), 1248 (C-N), 1125 (C-H), 625 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 763.2707.Candy-orange amorphous solid; Yield: 76%; m.p. above 300\u00b0C; UV 3.16.\u03bbmax (CH3CN) = 324 nm; \u03bbem (CH3CN): 365, 638, 751 nm; FTIR (cm\u22121): 1587 (C=N), 1468 (C=C), 1247 (C-N), 1090 (C-H), 629 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 760.2725.Dark-purple amorphous solid; Yield: 77%; m.p. above 300\u00b0C; UV 3.17.\u03bbmax (CH3CN) = 428 nm; \u03bbem (CH3CN): 294, 359, 451, 717 nm; FTIR (cm\u22121): 1660 (C=N), 1487 (C=C), 1286 (C-N), 1105 (C-H), 589 (Zn-N); MS (MALDI-ToF) of [M]+\u00b7 : 540.1292.Brown amorphous solid; Yield: 80%; m.p. above 300\u00b0C; UV 3.18.\u03bbmax (CH3CN) = 308 nm; \u03bbem (CH3CN): 273, 453, 722 nm; FTIR (cm\u22121): 1584 (C=N), 1506 (C=C), 1284 (C-N), 1050 (C-H), 621 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 1011.3310.Marmalade (dark-yellow) amorphous solid; Yield: 70%; m.p. above 300\u00b0C; UV 3.19.\u03bbmax (CH3CN) = 437 nm; \u03bbem (CH3CN): 341, 747 nm; FTIR (cm\u22121): 1582 (C=N), 1505 (C=C), 1285 (C-N), 1150 (C-H), 627 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 1008.3351.Maroon amorphous solid; Yield: 66%; m.p. above 300\u00b0C; UV 3.20.\u03bbmax (CH3CN) = 286 nm; \u03bbem (CH3CN): 454, 856 nm; FTIR (cm\u22121): 1600 (C=N), 1477 (C=C), 1295 (C-N), 1110 (C-H), 581 (Zn-N); MS (MALDI-ToF) of [M]+\u00b7 : 403.0663.Greyish-purple amorphous solid; Yield: 78%; m.p. above 300\u00b0C; UV 3.21.\u03bbmax (CH3CN) = 286 nm; \u03bbem (CH3CN): 426, 704, 856 nm; FTIR (cm\u22121): 1610 (C=N), 1473 (C=C), 1301 (C-N), 1098 (C-H), 625 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 737.2075.Clay-brown amorphous solid; Yield: 66%; m.p. above 300\u00b0C; UV 3.22.\u22121; Yield: 58%; m.p. above 300\u00b0C; UV \u03bbmax (CH3CN) = 336 nm; \u03bbem (CH3CN): 409, 503, 759, 854 nm; FTIR (cm\u22121): 3345 (C=N), 1607 (C=C), 1432 (C-N), 1057 (C-H), 628 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 734.2092.Dark-purple amorphous solid; Mol. Wt.: 1024.55 g mol3.23.\u03bbmax (CH3CN) = 287 nm; \u03bbem (CH3CN): 853 nm; FTIR (cm\u22121): 1616 (C=N), 1443 (C=C), 1326 (C-N), 1298 (C-H), 583 (Zn-N); MS (MALDI-ToF) of [M]+\u00b7 : 441.0431.Red-violet amorphous solid; Yield: 73%; m.p. above 300\u00b0C; UV 3.24.\u03bbmax (CH3CN) = 285 nm; \u03bbem (CH3CN): 405, 737, 850 nm; FTIR (cm\u22121): 1617 (C=N), 1473 (C=C), 1327 (C-N), 1250 (C-H) 627 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 813.1611.Brick-red amorphous solid; Yield: 55%; m.p. above 300\u00b0C; UV 3.25.\u03bbmax (CH3CN) = 286 nm; \u03bbem (CH3CN): 403, 685, 850 nm; FTIR (cm\u22121): 1612 (C=N), 1448 (C=C), 1327 (C-N), 1128 (C-H), 630 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 810.1629.Dark-purple amorphous solid; Yield: 70%; m.p. above 300\u00b0C; UV 3.26.\u03bbmax (CH3CN) = 283 nm; \u03bbem (CH3CN): 401, 685, 851 nm; FTIR (cm\u22121): 1617 (C=N), 1447 (C=C), 1327 (C-N), 1284 (C-H), 590 (Zn-N); MS (MALDI-ToF) of [M]+\u00b7 : 441.0431.Lilac (light purple) amorphous solid; Yield: 65%; m.p. above 300\u00b0C; UV 3.27.\u03bbmax (CH3CN) = 285 nm; \u03bbem (CH3CN): 361, 735, 859 nm; FTIR (cm\u22121): 1615 (C=N), 1476 (C=C), 1328 (C-N), 1197 (C-H), 627 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 813.1611.Brick-red amorphous solid; Yield: 78%; m.p. above 300\u00b0C; UV 3.28.\u03bbmax (CH3CN) = 286 nm; \u03bbem (CH3CN): 361, 580, 737, 865 nm; FTIR (cm\u22121): 1612 (C=N), 1450 (C=C), 1328 (C-N), 1265 (C-H), 629 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 810.1629.Dark-purple amorphous solid; Yield: 71%; m.p. above 300\u00b0C; UV 3.29.\u03bbmax (CH3CN) = 286 nm; \u03bbem (CH3CN): 409, 856 nm; FTIR (cm\u22121): 1619 (C=N), 1448 (C=C), 1329 (C-N), 1198 (C-H), 592 (Zn-N); MS (MALDI-ToF) of [M]+\u00b7 : 441.0431.Light-purple amorphous solid; Yield: 70%; m.p. above 300\u00b0C; UV 3.30.\u03bbmax (CH3CN) = 289 nm; \u03bbem (CH3CN): 360, 730, 867 nm; FTIR (cm\u22121): 1617 (C=N), 1480 (C=C), 1332 (C-N), 1267 (C-H), 623 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 813.1611.Chocolate-brown amorphous solid; Yield: 65%; m.p. above 300\u00b0C; UV 3.31.\u03bbmax (CH3CN) = 286 nm; \u03bbem (CH3CN): 358, 578, 732, 869 nm; FTIR (cm\u22121): 1615 (C=N), 1457 (C=C), 1334 (C-N), 1210 (C-H), 626 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 810.1629.Dark-purple amorphous solid; Yield: 66%; m.p. above 300\u00b0C; UV 3.32.\u03bbmax (CH3CN) = 347 nm; \u03bbem (CH3CN): 365, 680, 743, 855; FTIR (cm\u22121): 1603 (C=N), 1467 (C=C), 1348 (C-N), 1073 (C-H), 585 (Zn-N); MS (MALDI-ToF) of [M]+\u00b7 : 310.040.Light-purple amorphous solid; Yield: 74%; m.p. above 300\u00b0C; UV 3.33.\u03bbmax (CH3CN) = 334 nm; \u03bbem (CH3CN): 391, 699 nm; FTIR (cm\u22121): 1614 (C = N), 1530 (C=C), 1246 (C-N), 1151 (C-H), 627 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 767.1565.Chocolate-brown amorphous solid; Yield: 65%; m.p. above 300\u00b0C; UV 3.34.\u03bbmax (CH3CN) = 328 nm; \u03bbem (CH3CN): 402, 684, 856 nm; FTIR (cm\u22121): 1614 (C=N), 1474 (C=C), 1351 (C-N), 1025 (C-H), 629 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 764.1584.Dark-purple amorphous solid; Yield: 70%; m.p. above 300\u00b0C; UV 3.35.\u03bbmax (CH3CN) = 287 nm; \u03bbem (CH3CN): 474, 850 nm; FTIR (cm\u22121): 1619 (C=N), 1476 (C=C), 1359 (C-N), 1167 (C-H), 587 (Zn-N); MS (MALDI-ToF) of [M]+\u00b7 : 310.040.Caramel (brown) amorphous solid; Yield: 77%; m.p. above 300\u00b0C; UV 3.36.\u03bbmax (CH3CN) = 289 nm; \u03bbem (CH3CN): 428, 563, 850 nm; FTIR (cm\u22121): 1616 (C=N), 1471 (C=C), 1245 (C-N), 1245 (C-H), 628 (Co-N); MS (MALDI-ToF) of [M]+\u00b7 : 767.1565.Chocolate-brown amorphous solid; Yield: 76%; m.p. above 300\u00b0C; UV 3.37.\u03bbmax (CH3CN) = 287 nm; \u03bbem (CH3CN): 565, 848 nm; FTIR (cm\u22121): 1618 (C=N), 1472 (C=C), 1350 (C-N), 1287 (C-H), 630 (Fe-N); MS (MALDI-ToF) of [M]+\u00b7 : 764.1598.Dark-purple amorphous solid; Yield: 83%; m.p. above 300\u00b0C; UV 3.38.1\u2013L9L), strong, broad absorption bands appear in the range 234\u2013325 nm, while for the complexes (1\u2013C27C), the absorption bands were seen in the range 240\u2013429 nm. All these absorptions are attributed to \u03c0\u2013\u03c0* electronic transitions in the aromatic system of the terpyridines. The absorption maxima for 1\u2013C27C are somewhat shifted from those of the free ligands by affixing either electron-releasing or -withdrawing groups at the central pyridine. The longest absorption wavelength in the 1L UV-Vis spectrum (\u03bbmax = 325 nm) is broad and comparable to that of the un-substituted parent terpyridine at \u03bbmax = 587 nm and the bands at 284 nm and 426 nm are due to ligand-centred (LC) transitions. A slight redshift when related to the reference iron (II) terpyridine complex has been detected. The spin allowed the MLCT band in the visible region to undergo a rise in intensity and a redshift, regardless of electron-donor or -acceptor nature of the substituents. The intense absorption bands of the Zn(II) complexes were seen in the range 215\u2013586 nm. These absorption peaks are mainly due to the metal\u2013ligand charge transfer of \u03c0\u2013\u03c0* and n\u2013\u03c0* transitions having \u03bbmax = 586 nm. This redshift could be credited to a decrease in the LUMO energy values of the complexes. The absorption bands of the Co(II) complexes were seen in the range 209\u2013571 nm and their MLCT transitions have a maximum value at 530 nm.With a broad class of terpyridine compounds in hand, we examined their initial photophysical properties. The UV-Vis spectra of terpyridines and their metal complexes are recorded in chloroform and acetonitrile solutions, respectively, and the related data are given in pyridine . The UV-p-methoxyphenyl at the 4\u2032-position of the terpyridine ring in Zn(II) and Co(II) complexes shifts \u03bbmax towards longer wavelengths, resulting in a 30 nm bathochromic shift. This result supports the concept that the MLCT state can be higher in energy by nitration of the terpyridine ligand-based metal complexes, the 4-methoxyphenyl group at the 4\u2032-position of the terpyridine ring in the complexes have a shorter wavelength, and a significant maximum enhancement in MLCT band energy was observed. The absorption bands are influenced significantly by the aryl substituents on the terminal phenyl moiety. Generally, the absorption spectra of all complexes are typically well correlated with those found for the respective uncomplexed ligands.Surprisingly, the electron-donating group 3.39.p-position may not only open several paths towards the development of advanced supramolecular structures but may also influence the fluorescence properties of the compounds. Due to their potential applications in chemical sensors, electroluminescent displays and fluorescent materials, inorganic-organic hybrid complexes, particularly those with d10 transition metal centres, are now of great interest. From the structural analysis, the ligand can be seen to have a large p-conjugated aromatic system that can possess strong fluorescence and efficient transfer of energy. The photo-luminescence spectra of the Zn, Co and Fe (1\u2013C27C) complexes were recorded in acetonitrile solutions at ambient temperature with an excitation \u03bb of 320 nm for the Zn(II) complexes, 286 nm for the Co complexes and 295 nm for the Fe complexes. All 1\u2013C27C complexes display emission bands in the visible region of the electromagnetic spectrum. The maximum emission peaks for the Zn, Co and Fe complexes were observed at 857, 859 and 865 nm, respectively, as described in 1\u2013L9L was observed at about 340 nm irrespective of the location of the substitution and the number of phenyl groups. The excitation spectrum observed between 330 and 400 nm at any stage was similar to the corresponding absorption spectra, indicating that the excitation of the lowest energy absorption of 1\u2013L9L led to the emitting state. In the p-position of the 4-phenyl complex, several substituents with different electron-donating or -withdrawing properties were added to further analyse and modify the fluorescence properties of 4-phenyl terpyridine. The p-substituted terpyridine complexes 1\u2013C27C absorption and fluorescence maxima are listed in Attaching various functional groups to terpyridine at the 1\u2013C4C in solution and at ambient temperature are characterized by the fluorescence spectra presented in figures\u00a01C has two bands in its emission spectrum, a lower intensity one at ca 405 nm and another with higher intensity at ca 704 nm. Similarly, compound 2C has two bands in its emission spectra, a low-intensity one at ca 379 nm and another with higher intensity at ca 776 nm. Compared with the previously reported 2+ complexes have revealed that introduction of either electron-donating 2, -N(Ph)2, -OCH3) or electron-withdrawing groups onto the aryl-terpyridine scaffold alters absorbance as well as fluorescence properties and thus resulted in bathochromic shifted and structurally varied absorption and emission spectra. In addition, we have observed that the introduction of d-block transition metals into the terpyridine derivatives modified their absorption and emission properties as compared with terpyridine ligands (1\u2013L9L), and most complexes (1\u2013C27C) showed red-shifted absorption and emission spectra of varied appearance in contrast with the 2,2\u2032:6\u2032\u2032,2\u2032-terpyridines. Many of the new compounds have interesting photo-luminescent properties with high emissions. Importantly, almost all the functionalized terpyridine complexes display longer emission \u03bb and they are stronger emissive in contrast with the unsubstituted 2,2\u2032:6\u2032,2\u2033-terpyridine.We have presented the spectroscopic, photophysical, and anti-microbial studies of Zn(II), Co(II) and Fe(II) complexes of the variously substituted 2,2\u2032:6\u2032,2\u2032\u2032-terpyridine motif. New substrates of symmetrically substituted in vitro). The analysis revealed that the complexes (1\u2013C27C) exhibited more potent activity than free ligands (1\u2013L9L). Overall, the entire compounds exhibited moderate to excellent anti-microbial activities. These results provide new possibilities for therapeutic purposes. The experimental results complemented with in silico studies provided insights into structure\u2013property relationships. We are quite confident that the reported structures may find applications in organic electronics as well as medicines as potential materials and this will be the target of our future investigations. The investigation permitted the selection of materials with the most promising properties with special emphasis on the nature of the substituents.The ligands and complexes were also evaluated for their anti-microbial potential ("} +{"text": "Bothrops brazili, is a poorlystudied pit viper distributed in lowlands of the equatorial rainforests ofsouthern Colombia, northeastern Peru, eastern Ecuador, southern andsoutheastern Venezuela, Guyana, Suriname, French Guiana, Brazil, andnorthern Bolivia. Few studies have been reported on toxins isolated fromvenom of Ecuadorian and Brazilian B. brazili. The aim ofthe present study was to elucidate the qualitative and quantitative proteincomposition of B. brazili venom from Par\u00e1 (Brazil), and tocarry out a comparative antivenomics assessment of the immunoreactivity ofthe Brazilian antibothropic pentavalent antivenom [soroantibotr\u00f3pico (SAB) in Portuguese] against the venoms ofB. brazili and reference species, B.jararaca.The Brazil\u2019s lancehead, B.brazili venom from Par\u00e1 (Brazil). Using third-generationantivenomics, the specific and paraspecific immunoreactivity of theBrazilian SAB against homologous (B. jararaca) andheterologous (B. brazili) venoms was investigated. We have applied a quantitative snake venomics approach, includingreverse-phase and two-dimensional electrophoretic decomplexation of thevenom toxin arsenal, LC-ESI-MS mass profiling and peptide-centric MS/MSproteomic analysis, to unveil the overall protein composition of 2 molecules; 7-11 snake venommetalloproteinases of classes PI (21%) and PIII (6%); 10-12 serineproteinases (14%), and 1-2 L-amino acid oxidases (6%). Other toxins,including two cysteine-rich secretory proteins, one C-type lectin-likemolecule, one nerve growth factor, one 5'-nucleotidase, onephosphodiesterase, one phospholipase B, and one glutaminyl cyclase molecule,represent together less than 2.7% of the venom proteome. Third generationantivenomics profile of the Brazilian pentabothropic antivenom showedparaspecific immunoreactivity against all the toxin classes of B.brazili venom, with maximal binding capacity of132.2 mg venom/g antivenom. This figure indicates that 19% of antivenom'sF(ab')2 antibodies bind B. brazili venomtoxins. The venom proteome of the Brazil\u2019s lancehead (Par\u00e1) is predominantly composedof two major and three minor acidic (19%) and two major and five minor basic(14%) phospholipase AB.brazili and B. jararaca (the reference venomfor assessing the bothropic antivenom's potency in Brazil), provides cluesabout the proper use of the Brazilian antibothropic polyvalent antivenom inthe treatment of bites by the Brazil\u2019s lancehead. The proteomics outcome contribute to a deeper insight into the spectrum oftoxins present in the venom of the Brazil\u2019s lancehead, and rationalize thepathophysiology underlying this snake bite envenomings. The comparativequalitative and quantitative immunorecognition profile of the Brazilianpentabothropic antivenom toward the venom toxins of Bothrops includes at least 50 species of pit vipers that are widely distributed throughout the Americas, fromMexico to southern Argentina, in different ecoregions, from tropical and subtropicalforests to arid and semiarid regions, and from sea level to altitudes of more than3000 m neutralizes 50 mg of B.jararaca venom (the reference venom for assessing the bothropicantivenom potency in Brazil).Pooled venom from olecules , 33. A vg for 10 min at room temperature, and the proteinscontained in 40\u00b5L (600 \u00b5g) were separated by RP-HPLC using a Agilent LC 1100High Pressure Gradient System equipped with a Teknokroma Europa C18 column and a DAD detector. The columnwas developed at a flow rate of 1.0 mL/min with a linear gradient of 0.1% TFA inMilliQ\u00ae water (solution A) and 0.1% TFA in acetonitrile (solutionB), isocratic (5% B) for 5 min, followed by 5-25% B for 10 min, 25-45% B for 60min, and 45-70% B for 10 min. Protein detection was carried out at 215 nm with areference wavelength of 400 nm. Fractions were collected manually across theentire elution range, dried in a vacuum centrifuge , and redissolved in MilliQ\u00ae water. Molecular masses ofthe purified proteins were estimated by non-reduced and reduced Tris-TricineSDS-PAGE (on 15% polyacrylamide gels) , with orwithout 40 mM DTT. IPG strips were then placed on top of SDS-15% polyacrylamidegels and run in a Protean II (Bio-Rad) electrophoresis unit at room temperature.Protein spots were visualized by Coomassie Brilliant Blue G250 staining. \u00ae,ThermoSavant), redissolved in 14\u00b5L of 5% ACN containing 0.1% formic acid, and7\u00b5L submitted to LC-MS/MS. Tryptic peptides were separated by nano-AcquityUltraPerformance LC\u00ae (UPLC\u00ae) as above. Protein bands of interest were excised from Coomassie Brilliant Blue-stainedSDS-PAGE and 2-DE gels and subject to in-gel disulfide bond reduction and cysteine alkylation , followed by overnight digestion withsequencing-grade trypsin , using a Genomics Solution ProGest\u2122 Protein Digestion Workstation.Tryptic digests were dried in a vacuum centrifuge (SPD SpeedVacde novo sequencing), ii) usingthe on-line form of the MASCOT Server (version 2.6) at http://www.matrixscience.com against the last update of NCBI non-redundant database, and iii) processed inWaters Corporation\u2019s ProteinLynx Global SERVER 2013 version 2.5.2. (withExpression version 2.0). The following search parameters were used: Taxonomy:bony vertebrates; Enzyme: trypsin ; MS/MS masstolerance was set to \u00b1 0.6 Da; carbamidomethyl cysteine and oxidation ofmethionine were selected as fixed and variable modifications, respectively. Allmatched MS/MS data were manually checked. Peptide sequences assigned byde novo MS/MS were matched to homologous proteins availablein the NCBI non-redundant protein sequences database using the online BLASTPprogram was determined spectrophotometrically using an extinction coefficient for a 1mg/mL concentration (\u03b50.1%) at 280 nm of 1.36 (mg/mL)-1cm-1 by the [total amount of antibody(F(ab')2) (in mg) per antivenom vial] [The percentage of antivenom anti-toxin F(ab')om vial] , 45, 46.B. brazili (Par\u00e1)was decomplexed and quantified by reverse-phase HPLC and downstream SDS-PAGEanalysis of the chromatographic peaks (B. brazili (Par\u00e1) venom investigated inthis work, RP-HPLC fractions 2-46 were submitted to molecular mass determinationby LC-ESI-MS mass profiling. The venom proteome of 600 \u00b5g of crude venom of ic peaks . Twenty ic peaks , inset. 50 in the range of 0.15-0.95 mM) of the fibrinogenolyticactivity of multiple snake venom Zn2+-metalloproteinases (SVMP) of 27,623.1, 27,455.2 and 13,930.5; 27,636.5 and 13,803.2; and30,360.4, 29,663.4 and 13,781.9, respectively. These molecular masses maycorrespond to the minor (<0 .1% TVC) PLA13.1 Da) ; MTx-II 13.1 Da) ; Brazili, Brazil or SerpeB.atrox , 48, andave: 29,899.2 Da, 30,130.2 Da and 30,421.9 Da), 19, 20 , 38 and 42/43 were ten2s, which together account for approximately 30% (w/w) of itsproteome, one minor (1.6%) CRISP molecule, one major and at leastten minor (< 2.3%) SVSPs, and 2-3 abundant and amajor PI-SVMPs. In addition, SDS-PAGE analysis displayed inAs a whole, the above data suggested that the Brazil\u2019s lancehead venom comprisednine minor and five major (> 4.4%)PLAdenovo gathered peptide ion sequences was fractionated by RP-HPLC/SDS-PAGE and 2-DEB. brazili (Par\u00e1), comprisedby at least 40-47 components and PIII , 10-12 SVSPs (14%) and 1-2 LAOs (6%). Other toxinclasses are: two CRISPs, one C-type lectin-like (CTL), one nerve growth factor(NGF), one 5'-nucleotidase (5'NT), one phosphodiesterase (PDE), onephospholipase B (PLB), and one glutaminyl cyclase (GC) represent together lessthan 2.7% of the venom proteome (50) and hemorrhagic, dermonecrotic and defibrinogenatingeffects reported for Peruvian B. brazili venom in the murinemodel andMTx-II , 54, andliase-II .ClearlyTwo-dimensional electrophoretic (2-DE) analysis provides a rapid way to visualizethe overall venom protein complexity of a snake's venom in a single image. 2-DEand RP-HPLC/SDS-PAGE are complementary approaches that combined provide a morecomprehensive view of a venom proteome than each approach separately. Inaddition, each of these approaches serves, by itself, a specific purpose. Thus,the presence and subunit composition of covalent complexes in a venom proteomecan be conveniently addressed by comparing the 2-DE protein maps resolved undernon-reducing (NRed) conditions in both directions (IEF and SDS-PAGE) versusnon-reducing/reducing (Red) conditions . 2 subproteome, which is made of two major acidic , two strongly basic (pI 9.5-9.8) (spots 13 and 14), and onemildly basic (pI 7.8) (spot 12), and five low abundant PLA2 molecules(spots 3-7) within the pI range 5.3-7.3. The latter spots also yielded CTLpeptide ions, and molecules belonging to this toxin family were identified inspots 6, 9-11 andsemi-quantitative (ELISA) evidence that these antivenoms exhibited variableparaspecific immunoreactivity towards nineteen venoms of bothropic snakes,including B. brazili in addition to B.alternatus, B. atrox, B.bilineatus, B. castelnaudi, B.cotiara, B. erythromelas, B.fonsecai, B. hyoprorus, B.insularis, B. itapetiningae, B.jararaca, B. jararacussu, B.leucurus, B. marajoensis, B.moojeni, B. neuwiedi, B. pirajai,and B. pradoi. In Brazil, envenomings by bothropic species are clinically treated with equinepolyspecific pentabothropic (SAB) or antibothropic-lachetic F(ab')z et al. haverepB. brazili (Par\u00e1) and B. jararaca(reference venom). Analysis of the concentration-dependent immunocapturingprofile of the SAB antivenom affinity columns showed paraspecificimmunoreactivity against all the toxin classes of B. brazilivenom 2 antigen-recognition sites were occupied, the antivenomicsresults suggest that 19% of the SAB antibodies recognized toxins from B.brazili venom. This figure fall within the range of percentages(6-28%) of antitoxin antibodies determined for a number of commercial antivenoms[Here, we have applied third-generation antivenomics , 41 to clivenom , Table 1B. jararaca(SE) venom proteinsper vial. Assuming full occupancy of the two F(ab')2antigen-recognition sites, the antivenomics results indicate that 23.7% of SABF(ab')2 are toxin-binding antibodies. Moreover, theneutralization potency of the SAB antivenom specified by Butantan Institute, 50mg of Bothrops jararaca reference venom/vial (10 mL), mirrorsits maximal binding capacity, indicating that virtually all (50/50.6 = 98.8%)toxin-binding F(ab')2 antibodies may contribute to the capability ofthe SAB antivenom to neutralize the lethality of the homologous venom. On theother hand, the paraspecificity of SAB toward toxins of the heterologousB. brazili venom is due to the remarkable conservation ofantigenic determinants already present in the venom of the last common ancestorof the \u201cjararaca\u201d and \u201cjararacussu\u201d clades, an event that has been dated closeto the base of the radiation of genus Bothrops in the middleMiocene 14.07 Mya (CI95% 16.37-11.75 Mya) [For comparison, analysis of the concentration-dependent antivenomics profile ofthe SAB antivenom against the reference venom of aca(SE) , Table 2.75 Mya) , 57.in vitro preclinical data to an invivo scenario is not straightforward. Thus, although the similartotal binding capacity of SAB antivenom towards B. jararaca andB. brazili venoms could be interpreted as indicative forits equivalent therapeutic potential against human envenomings by eitherspecies, the devil is in the details. In this regard, it is worth noting thatalthough the major toxin classes PLA2, PIII-SVMP, PI-SVMP, and SVSPrepresent, respectively, 30.6%, 24.6%, 15.5%, and 13.5% of the total venomarsenal of B. brazili, the SAB antivenom\u2019s antibodiescontributing to its paraspecific recognition of B. brazilitoxins are biasedly distributed against PI-SVMP (41%), PIII-SVMP (32%), SVSP(9.3%), and PLA2 (8.8%). This suggests that the ability of SAB toneutralize the toxic activities of Brazil\u2019s lancehead venom associated withPIII- and PI-SVMPs, and SVSPs is equivalent to, or greater than, the B.jararaca reference venom. On the other hand, counteracting thetoxic activities of the major B. brazili venom PLA2molecules may require several times the amount of antivenom. Translating B. brazili is about 270 mg dry weight. For comparison, theaverage yield reported for B. jararaca .These figures suggest that the same therapeutic potency of SAB against bothvenoms. However, the treatment of a Brazil's lancehead bite injecting an averageamount of venom would require a 5-13 higher SAB dose than for a similarenvenoming by B. jararaca. The average venom yield of y weight ;40-70 mB. brazili geographically restricted to regions north(Guiana Shield clade) and south of the AmazonRiver [B. brazili clades has been dated back to the Miocene-Plioceneborder, 4.65 Mya, and the best\u2010fit scenario includes colonization of the AtlanticForest from an ancestor from the Guiana Shield region through a northern bridgeduring the Pleistocene about 0.36 Mya, pointing to former rain forest expansions innorth\u2010eastern South America [The Brazil\u2019s lancehead is a wide-ranging species endemic to lowlands of equatorialrainforests of northern South America. Phylogenetic analyses recovered two majorlineages of onRiver . The div America . B. brazili are consistent withthe idea that the establishment of the Amazon River has favored divergence bypromoting vicariant separation between lineages [Historical demographic analyses of lineages . The orilineages , 61. Thelineages , 63. TheB. brazili venom provide a reference map for future comparativestudies of the intraspecific intra- and inter-population variations of the venomproteome of this wide geographic distributed, yet poorly studied, rainforest snakespecies. This work represents the first comprehensive characterization of the venom proteomeof the Brazil\u2019s lancehead. The venom was sourced from Par\u00e1, a Brazilian state southof the Amazon River. The complementary RP-HPLC/SDS-PAGE and 2-DE protein profiles ofB.jararaca and B. brazili withpotencies of 5.5 and 1.6 mg venom/mL, respectively. The antivenom showed potenciesof 6.2 and 1.4 mg/mL, respectively, in the neutralization of the PLA2activity of B. jararaca and B. brazili venoms. Thevolume of SAB antivenom that neutralized one minimal hemorrhagic dose (MHD) [B. jararaca andB. brazili venoms was 5 mL and 7.8 mL, respectively.Understanding the basis of the different effectivity of SAB antivenom againsthomologous (B. jararaca) and heterologous (B.brazili) venoms demands the quantitative assessment of itstoxin-resolved immunorecognition profile. The ability of SAB antivenom to recognize a broad spectrum of medically importantbothropic venoms has been documented in previous works spanning the last threedecades , 64-67. se (MHD) of B. jaB. brazili is mostly due to large conservation ofimmunoreactive epitope on hemorrhagic PI- and PIII-SVMPs across much of the naturalhistory of Bothrops. On the contrary, SAB paraspecificity againstPLA2s, which comprise the major toxin class of the Brazil\u2019s lanceheadvenom arsenal, is disproportionately diminished. Our antivenomics data allow therationalization, in molecular terms, of the conclusions of the invivo neutralization assays of Muniz et al. [Herein, we have applied third-generation antivenomics to compare the specific andparaspecific immunoreactivity of the SAB antivenom against these venoms. Theremarkable paraspecificity exhibited by the Brazilian SAB antivenom against thevenom of z et al. , and pro50: median lethal dose; MCD-F:minimum coagulant dose against fibrinogen; MCD-P: minimum coagulant dose againstplasma; MDD: minimum defibrinogenating dose; MHD: minimum hemorrhagic dose; MND:minimum dermonecrotic dose; NGF: nerve growth factor; NR: non-retained; P-BAV:Peruvian bothropic antivenom; PDE: phosphodiesterase; PLA2:phospholipase A2; PLB: phospholipases B; R: retained; SAB:soro antibotr\u00f3pico (Portuguese); SDS-PAGE:SDS-polyacrylamide gel electrophoresis; SVMP: snake venom metalloproteinase;SVSP: snake venom serine proteinase; TFA: trifluoroacetic acid; TVC: total venomcomponents. 2-DE: two-dimensional gel electrophoresis; 5'-NT: 5\u2032-nucleotidase; ACN:acetonitrile; CTL: C-type lectin-like; GC: glutaminyl cyclase; IEF: isoelectricfocusing; LAO: L-amino acid oxidase; LD"} +{"text": "Objective: Associate the impact of oral health with quality of life and subjective well-being in the community-dwelling older adults in Mexico. Methods: Non-random sample; 326 subjects: age collected (60-69 / \u2265 70); gender ; marital status (couple / no partner); schooling (0-6 years / \u22657); income for basic needs (yes / no); no depression (GDS-15), no cognitive impairment (MMSE) and comorbidity (no disease / \u2265 1 disease) to control biases. Oral conditions; Caries index (ICPOD) WHO criteria: Very low-Low; Moderate and High. Need for dental prostheses : No prostheses needed ; moderate to severe xerostomia > 17 points. Dependent variables: Quality of Life Related to Oral Health (GOHAI); 57-60 points: High perception. Subjective well-being: Moral Scale of the Geriatric Center of Philadelphia (PGCMS): Low score (0-11). Results: Age: 71.84 \u00b1 7,278; female / male (70.9 / 29.1%). Controlling confounding factors, multiple logistic regression showed that the need for multi-unit or total prostheses; high CPOD index; severe xerostomia; and low perception of well-being subjective, were associated with low GOHAI scores: P = 0.000; P = 0.004; P = 0.003; P = 0.02 respectively. Subjective well-being only was associated with severe xerostomia and low CVRSO perception: P = 0.0 1; P = 0.02 respectively. Conclusion: Taking into account various confounding factors, the Quality of Life related to Oral Health was the most affected by the deterioration of oral health."} +{"text": "Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Gl\u00e4sser\u2019s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen.The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1\u2014a plasmid observed in ST328\u2014to confer antibiotic resistance.6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6\u2019)-Ie-aph(2\u201d)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13\u201391.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors and drug resistance genes in G. parasuis were identified. Resistance determinants -Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location.The ST328 genome contained a novel TnG. parasuis isolates provides valuable insight into the emergence and transmission of G. parasuis in the swine industry. The result suggests the importance of transposon-related and/or plasmid-related gene variations in the evolution of G. parasuis.Our comparative genomic analysis of worldwide Glaesserella parasuis, a gram-negative bacterium in the family Pasteurellaceae and multiple target gene mutations. To date, two \u03b2-lactam resistance genes (blaROB\u22121 and blaTEM), an aminoglycoside-resistance gene (aac (6\u2032)-Ib-cr) and a mutation in the six copies of the 23S rRNA gene, associated with macrolide resistance, have been reported in G.\u00a0parasuis -Ib, aph(6)-Id, floR, sul1, and sul2 (hhdBA), iron acquisition genes , the restriction modification system hsdS, and genes involved in sialic acid utilization . RecentlG.\u00a0parasuis strains, the structural organization of genetic information, ARGs, potential pathogenicity determinants, and evolutionary relationships among global G.\u00a0parasuis strains remain unclear. In this study, we sequenced a multidrug-resistant isolate from diseased swine in Dongguan, China, then compared this genome sequence with those of 54 isolates from China sequenced by us and 39 strains from China and eight other countries sequenced by other researchers in order to improve our understanding of genomic diversity in G.\u00a0parasuis and provide information for gaining better control to treat these infections.Though significant effort has been focused on exploring ARGs, virulence factors and other genetic characteristics of various G.\u00a0parasuis isolate HPS-1 examined in this study belongs to serotype 4 and was originally isolated from the lungs of a pig suffering from Gl\u00e4sser\u2019s disease in a commercial pig farm in Dongguan city, Guangdong province, China, in 2017. Susceptibility to 19 antimicrobial agents was determined by the disc agar diffusion method and the broth microdilution method .Isolates were cultured on tryptic soy agar or in tryptic soy broth supplemented with 10 mg/mL nicotinamide adenine dinucleotide and 5% bovine serum at 37\u00a0\u00b0C in 5% COCP040243. The plasmid pYL1 and transposon Tn6678 of HPS-1 were submitted to GenBank under accession number MK182379 and and MK994978, respectively. Genomic libraries of the other 53 genomes were generated and sequenced using the Illumina HiSeq 4000 system as previously described against 6 databases: Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), NCBI non-redundant protein database (NR), Swiss-Prot, Gene Ontology (GO), and TrEMBL.Among the 55 isolates, one multidrug-resistant isolate (HPS-1) and one sensitive isolate (HPS-2) from diseased swine in Guangdong were randomly selected for WGS using the PacBio RSII and Illumina MiSeq platforms as previously described . The genescribed . WGS datescribed . Gene prescribed , and a wescribed searchesG.\u00a0parasuis strains and 39 previously published genome sequences using single-copy core orthologs and single nucleotide polymorphisms (SNPs) software to generate non-paralogous gene clusters .Two phylogenetic trees were constructed to assess the relatedness of the 55 s (SNPs) . Phyloges (SNPs) . The WAGE-value \u2264 1e\u22125, minimal alignment length percentage \u2265 80%) was performed against four databases for pathogenicity and drug resistance analysis: Pathogen Host Interactions (PHI), Virulence Factors of Pathogenic Bacteria (VFDB), Carbohydrate-Active enZYmes Database (CAZy), and Integrated Antibiotic Resistance Genes Database (IARDB).A whole-genome BLAST search -Ie-aph(2\u2033)-Ia, which confer to \u03b2-lactams and aminoglycosides resistance. To determine the contributions of pYL1 to penicillin and aminoglycoside antibiotic resistance, electrotransformation experiments were performed using Staphylococcus aureus RN4220 as the recipient as previously described (aac(6\u2032)-Ie-aph(2\u2033)-Ia and blaROB\u22121 genes in transformants was confirmed by PCR amplification followed by DNA sequence analysis. The primers for blaROB\u22121 (494 bp) were 5\u2032-CGCTTTGCTTATGCGTCCAC-3\u2032 (forward) and 5\u2032-ACTTTCCACGATGTTGGCGT-3\u2032. The primers for aac(6\u2032)-Ie-aph(2\u2033)-Ia (412 bp) were 5\u2032-AGAGCCTTGGGAAGATGAAGTT-3\u2032 (forward) and 5\u2032-TGCCTTAACATTTGTGGCATT-3\u2032 (reverse). The primers were designed using NCBI Primer-BLAST. The PCR conditions were as follows: initial denaturation at 95\u00a0\u00b0C for 5 min, 30 cycles of amplification , followed by extension at 72\u00a0\u00b0C for 10 min. The PCR products were purified and sequenced by Majorbio Company . The MICs of S.\u00a0aureus RN4220 and five transformants were determined by Etest (Liofilchems.r.l.) according to the manufacturer\u2019s instructions.Plasmid pYL1 harboring two antimicrobial resistance genes, escribed . Transfoaac(6\u2032)-Ie-aph(2\u2033)-Ia and blaROB\u22121 was determined by serial passages for 15 consecutive days at 1:1000 dilutions into fresh BHI, with or without antibiotic (kanamycin) pressure. Serially diluted cultures were spread on BHI agar plates with or without kanamycin (8 \u00b5g/mL), and the resistance retention rate was determined by randomly picking at least 50 colonies from the BHI plates, spotting them onto new BHI plates with kanamycin (8 \u00b5g/mL), and calculating the ratio of resistant to total colonies. Both the resistant and susceptible colonies from the plates were randomly picked and subjected to PCR for detection of blaROB\u22121 and aac(6\u2032)-Ie-aph(2\u2033)-Ia.The stability of plasmids carrying G. parasuis gene content compared with the core genomes and the number of unique genes ranged from 0 to 103 indicating that 0\u20134.6% of the genome consists of strain-specific accessory genes core biosynthesis, and galU and galE, resulting in impaired biofilm formation, were universally present in the G. parasuis isolates.Variation in virulence and stress resistance genes was observed among ubgroups . All 94 G. parasuis, including the \u03b2-lactam-resistant gene blaROB\u22121, tetracycline resistance genes tetB, aminoglycoside resistance genes aph(3\u2032)-Ib and aac(6\u2032)-Ie-aph(2\u2033)-Ia, fluoroquinolone resistance gene norA, chloramphenicol resistance genes catIII and floR, sulfonamide resistance gene sul2 were discovered (sul2 and aph(3\u2032)-Ib, and \u03b2-lactam-resistant genes pbp1a and pbp3a were universally present in the G. parasuis isolates , aminoglycosides (aph(3\u2032)-Ib, aac(6\u2032)-Ie-aph(2\u2033)-Ia), and \u03b2-lactam (blaROB\u22121) (bcr) and multidrug resistance (acrB).Following sequencing and assembly, a 2,326,414-bp chromosome with an average G+C content of 40.03%, and a 7,777-bp small plasmid sequence (pYL1) with an average G+C content of 33.32% were identified in strain HPS-1 . HPS-1 elaROB\u22121) . Furtherhttps://transposon.lstmed.ac.uk/). This transposon harbours two 966-bp IS110 family transposases at both ends, two toxin genes pilT and phd, two genes associated with the two-component signal transduction system cpxA and cpxR, one efflux pump-associated gene bcr, and four genes encoding hypothetical proteins with unknown function (34)-methyltransferase MnmD/FAD-dependent 5-carboxymethylaminomethyl-2-thiouridine (34) oxidoreductase MnmC flanked the transposon to the right and left, respectively.We also identified a novel transposon in the ST328 isolate, designated Tn6678 in the Tn Number Registry , SH0165 , ZJ0906 , and str. Nagasaki ]. The only differences in these five chromosomes were in the transposases, but transposon Tn6678 had two complete inverted repeats of IS110 transposases flanked by 32-bp inverted repeats of ISNme5 at both ends were identified in four oth ends , suggestbcr gene returned a large set of divergently related sequences using default parameters. These sequences were annotated as bicyclomycin/multidrug efflux system, Bcr/CflA family drug resistance efflux transporter, Bcr/CflA family multidrug efflux major facilitator superfamily (MFS) transporter or drug resistance transporter, and Bcr/CflA subfamily. Phylograms revealed that the bcr gene in HPS-1 was most closely related to homologs identified in other members of the Pasteurellaceae, particularly G. parasuis, Actinobacillus indolicus, Bibersteinia trehalosi, Actinobacillus , and Mannheimia (M. haemolytica and M. varigena), all of which are known causative agents of upper respiratory tract infections -Ie-aph(2\u2033)-Ia. Four ORFs were identified to encode a 3\u2032-truncated transposase protein ISApl1 (30 amino acids), a Rep-like protein (444 amino acids) involved in plasmid replication, and two Mob proteins, MobC (144 amino acids) and MobA (541 amino acids), associated with plasmid mobilization . This finding indicated that plasmid pYL1 carrying blaROB\u22121 and aac(6\u2032)-Ie-aph(2\u2033)-Ia contributed to the penicillin resistance and aminoglycoside antibiotic resistance in S. aureus RN4220 transformants. Furthermore, the plasmid showed low stability in S. aureus without antibiotic pressure, as only 52.5%, 30.48%, and 2.68% of transformants maintained the kanamycin resistance after five, six, and seven subcultures, respectively. However, the plasmid can be conserved in S. aureus cultured with kanamycin, as 100% of the colonies remained resistant to kanamycin after 10 subcultures, as confirmed by PCR mapping.Transformation of pYL1 into G. parasuis pan-genome is vast, and unique genes can be continuously be identified upon sequencing more G. parasuis genomes. However, the isolates in this study with \u223c3.34% core genes, primarily isolated from China, displayed further diversity and higher variability than isolates with only \u223c14% core genes, primarily obtained from the UK , in line with potentially virulent strains isolated from the nasal cavities of healthy pigs -Ib, tetB, tetD, aac(6\u2032)-Ie-aph(2\u2033)-Ia, catIII, and floR genes have previously been identified in G. parasuis family, has been analysed to date. Efflux pump AcrB may play a role in multidrug resistance, and the acrAB gene cluster could affect the efflux of macrolides in G. parasuis have been reported in G. parasuis -Ie-aph(2\u2033)-Ia. The ROB-1 of plasmid pYL1 had a typical size of 305 bp, in line with functionally active members of the ROB-1 family from different plasmids in Pasteurellaceae species. AAC(6\u2032)-Ie-APH(2\u2032)-Ia, the most important aminoglycoside-resistance enzyme in gram-positive bacteria conferring resistance to almost all known aminoglycoside antibiotics in clinical use, also had a typical size of 479 amino acids in this family (aac(6\u2032)-Ib-cr is considered the most prominent aminoglycoside-resistance gene in G. parasuis and drug resistance genes in G. parasuis. Resistance determinants -Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Future research focused on a larger sample of G. parasuis isolates worldwide will further increase understanding of the rapid development of antibiotic resistance associated with mobile genetic elements in this important animal pathogen.In summary, our results shed new light on the importance of genomic variations, especially transposon-related and/or plasmid-related gene variations, in the evolution of 10.7717/peerj.9293/supp-1Table S1P. aeruginosa .MIC: minimum inhibitory concentration; R: resistant; S: susceptible. a Interpreted according to Clinical and Laboratory Standards Institution (CLSI) guidelines for Click here for additional data file.10.7717/peerj.9293/supp-2Table S2N.A. represents unknown information; ST: sequence type; UT: untypeable.Click here for additional data file.10.7717/peerj.9293/supp-3Table S3Click here for additional data file.10.7717/peerj.9293/supp-4Table S4Click here for additional data file.10.7717/peerj.9293/supp-5Table S5Click here for additional data file.10.7717/peerj.9293/supp-6Figure S1The tree was constructed with MEGA 7 using a maximum-likelihood optimality criterion as implemented in PhyML v3.0 with 1, 000 bootstrap replicates. The annotation rings surrounding the tree, from inside to outside, depict (1) serotype, (2) host, (3) geographic region and (4) year of sample collection. The branch colors denote two major lineages, lineage I (pink) and lineage II (green).Click here for additional data file.10.7717/peerj.9293/supp-7Figure S2Glaesserella sp. 15\u2013184 was chosen as an outgroup. The branch colors denote two major lineages, lineage I (pink) and lineage II (green).Click here for additional data file.10.7717/peerj.9293/supp-8Figure S3From inside to outside, the first circle represents the genome size of HPS-1; the second circle represents the GC skew; the third circle represents the GC content; the fourth circle and the seventh circle represent the COG (cluster of orthologous groups) designation of each coding sequence (CDS); the fifth and sixth circles represent the position of CDS, tRNA, and rRNA on the genome.Click here for additional data file.10.7717/peerj.9293/supp-9Supplemental Information 1Click here for additional data file.10.7717/peerj.9293/supp-10Supplemental Information 2Click here for additional data file.10.7717/peerj.9293/supp-11Supplemental Information 3Click here for additional data file.10.7717/peerj.9293/supp-12Supplemental Information 4Click here for additional data file.10.7717/peerj.9293/supp-13Supplemental Information 5Click here for 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Aquatic hyphomycetes were sampled from 40 sites, distributed by 27 permanent streams in 2015, to provide the distribution of aquatic hyphomycetes in Madeira Island streams.Aquatic hyphomycetes were recorded belonging to three classes of Ascomycota. All taxa are new records for Madeira Archipelago, except Articulosporatetracladia and four are reported for the first time in Macaronesian biogeographic region.In this study, a total of 21 species of aquatic Aquatice scarce . In factal zones . Despiteems e.g. .fungi started almost two centuries ago with the work of th century, many mycological studies increased the number of records for Madeira Archipelago (North Atlantic), including numerous descriptions of species new to science . Lying in the subtropical region, Madeira\u2019s climate is influenced by winds from NE and the Canary Islands current. The Island has a mild oceanic climate, both in winter and summer with mild temperatures ranging from 15.9\u00b0C in February up to 22.3\u00b0C in August , relative humidity between 55 and 75% and annual rainfall between 500 and 1,000 mm distributed by 27 permanent streams : 384 (1942)3690A495-A84F-50C3-A2E6-2BEDD6529505Cosmopolitan .Madeira distribution: Streams in agricultural and natural areas at low to moderate altitude: Ribeira de S\u00e3o Vicente (MAD04); Ribeira do Juncal (MAD15); Ribeira do Faial (MAD16); Ribeira Primeira (MAD18); Ribeira de S\u00e3o Jorge (MAD37).Habitat: Submerged leaf litter .(H.J. Huds.) L. Lombard & Crous, in Lombard, van der Merwe, Groenewald & Crous, Stud. Mycol. 80: 207 (2015)672BA860-8D1E-5A9B-9963-0C35130DCB8ECosmopolitan .Madeira distribution: Stream in agricultural and natural areas at low to moderate altitude: Ribeira de S\u00e3o Vicente (MAD04); Ribeira Brava (MAD07); Ribeira do Juncal ; Ribeira do Faial (MAD16); Ribeira da Janela (MAD21); Ribeira de S\u00e3o Roque do Faial (MAD33); Ribeira dos Arcos (MAD36); Ribeira de S\u00e3o Jorge (MAD17); Ribeira da Fonte do Bugio (MAD39).Habitat: Submerged leaf litter .(R.H. Petersen) Dyko, Trans. Br. mycol. Soc. 70 (3): 412 (1978)8A859C84-48D6-5382-BE6E-FC0C03AD9EDDCosmopolitan .Madeira distribution: Streams in natural areas at low to high altitude: Ribeira Brava (MAD07); Corgo da Ribeira de An\u00e9is (MAD11); Ribeira do C\u00f3rrego do Arrochete (MAD30); Ribeira de S\u00e3o Jorge (MAD37).Habitat: Submerged leaf litter [e.g. Ilexperado (xperado ].(Ingold) Sv. Nilsson ex Marvanov\u00e1 & Sv. Nilsson, Trans. Br. mycol. Soc. 57 (3): 532 (1971)15B4E8EC-42DF-52E6-B357-42CBE90D2558Cosmopolitan .Madeira distribution: Streams in natural areas at high altitude: Ribeira da Janela ; Ribeira do C\u00f3rrego do Arrochete (MAD30).Habitat: Submerged leaf litter .(Sacc. & Therry) L. Lombard & Crous, in Lombard, van der Merwe, Groenewald & Crous, Phytopath. Mediterr. 53(3): 528 (2014)9B3C3176-C801-5961-B75C-48C31DFB8EEDCosmopolitan .Madeira distribution: Streams in urban, agricultural and natural areas at low to high altitude: Ribeira Brava (MAD02); Ribeira da Vargem (MAD03); Ribeira Brava ; Ribeira dos Socorridos (MAD09); Ribeira do Juncal ; Ribeira do Machico (MAD17); Ribeira Primeira (MAD18); Ribeira da Janela ; Ribeira do Alecrim (MAD28); Ribeira do C\u00f3rrego do Arrochete (MAD30).Habitat: Submerged leaf litter .(Grove) Ingold, Trans. Br. mycol. Soc. 25(4): 371(1942)29EA0E24-82EE-5239-85A5-1555AED4BAD6Cosmopolitan .Madeira distribution: Streams in agricultural areas at low to moderate altitude: Ribeira dos Socorridos (MAD01); Ribeira Brava (MAD02); Ribeira do Juncal (MAD15).Habitat: Submerged leaf litter [e.g. Clethraarborea, Ilexperado : 624 (1974)68D79614-DC15-5AF0-991B-F21A84FD1786Cosmopolitan .Madeira distribution: Streams in urban, agricultural and natural areas at low to high altitude: Ribeira dos Socorridos (MAD01); Ribeira de S\u00e3o Vicente (MAD04); Ribeira Grande (MAD05); Ribeira Brava ; Ribeira do Cidr\u00e3o (MAD12); Ribeira do Juncal ; Ribeira do Faial (MAD16); Ribeira do Machico (MAD17); Ribeira Primeira ; Ribeira da Janela ; Ribeiro Frio (MAD29); Ribeira do C\u00f3rrego do Arrochete (MAD30); Ribeira da Metade (MAD31); Ribeira das Lajes (MAD32); Ribeira de S\u00e3o Jorge (MAD35); Ribeira dos Arcos (MAD36).Habitat: Submerged leaf litter [e.g. Acaciamelanoxylon, Acerrubrum, Alnusglutinosa, Clethraarborea, Cryptomeriajaponica, Ilexperado, Pittosporumundulatum, Quercusrobur, Rhododendronmaximum : 346 (1975)F45FE042-099D-5651-8E96-FC87B0CB74C9Cosmopolitan .Madeira distribution: Streams in agricultural and natural areas at low to moderate altitude: Ribeira dos Socorridos (MAD01); Ribeira Brava (MAD08); Ribeira do Juncal (MAD15); Ribeira do Faial (MAD16); Ribeira do Machico (MAD17); Ribeira Primeira (MAD18); Ribeira da Janela (MAD21); Ribeiro Frio (MAD29); Ribeira do C\u00f3rrego do Arrochete (MAD30); Ribeira das Lajes (MAD32); Ribeira Seca (MAD34); Ribeira de S\u00e3o Jorge (MAD35); Ribeira dos Arcos (MAD36); Ribeira de Santa Luzia (MAD38).Habitat: Submerged leaf litter [e.g. Acaciamelanoxylon, Alnusglutinosa, Clethraarborea, Ilexperado, Pittosporumundulatum, Quercusrobur : 152 (1943)E9A99FEC-221E-5C74-98E4-1A77CEA78B80Cosmopolitan .Madeira distribution: Streams in urban, agricultural and natural areas at low to high altitude: Ribeira dos Socorridos (MAD01); Ribeira Brava ; Ribeira de S\u00e3o Vicente (MAD04); Ribeira Grande ; Ribeira da Gomeira (MAD10); Ribeira do Cidr\u00e3o (MAD12); Ribeira do Juncal ; Ribeira do Faial (MAD16); Ribeira do Machico (MAD17); Ribeira Primeira (MAD18); Ribeira da Janela (MAD21); Ribeira dos Cedros (MAD25); Ribeiro Frio (MAD29); Ribeira de S\u00e3o Roque do Faial (MAD33); Ribeira Seca (MAD34); Ribeira de S\u00e3o Jorge ; Ribeira dos Arcos (MAD36); Ribeira de Santa Luzia (MAD38).Habitat: Submerged leaf litter [e.g. Acaciamelanoxylon, Acerrubrum L., Alnusglutinosa, Clethraarborea, Eucalyptusglobulus, Ilexperado, Pittosporumundulatum, Quercusrobur, Rhododendronmaximum , Leotiomycetes encompassed 43% of the taxa recorded. At the order level, the 21 ascomycetes were distributed by Helotiales (12 spp.), Hypocreales (2 spp.), Leotiales (1 sp.), Microascales (1 sp.), Sordariales (1 sp.) and Incertae sedis (4 spp.), according to In the present study, we found a total of 21 aquatic Articulosporatetracladia, Clavariopsisaquatica, Lemonnieraaquatica, Lunulosporacurvula, Tetrachaetumelegans, Tetracladiummarchalianum, Tricladiumchaetocladium and Triscelophorusmonosporus, which were the most ubiquitous aquatic hyphomycetes in Madeira streams. Two taxa, Lemonniera sp. and Tetracladiumfurcatum, had a sporadic occurrence, being found at only one or two sampling sites. A maximum of 14 species was recorded in MAD15 and a minimum of one species in MAD13 and MAD20, with a mean richness of eight species per stream site. Higher altitude stream sites (> 800 m a.s.l.) in natural areas, such as MAD07, MAD08, MAD24 and MAD26, displayed higher taxa richness , compared with coastal (< 25 m a.s.l.) and urban stream sites, such as MAD13, MAD20, MAD32, MAD33, MAD37, MAD38, MAD39 and MAD40 (5.8 \u00b1 1.2). All species, with the exception of Articulosporatetracladia reported by From the 21 species identified, none occurred in all 40 studied stream sites and only 8 taxa occurred in more than 50% of the stream sites: hyphomycetes in insular streams from Madeira Island. Twenty-one taxa are recorded for Madeira Island, which is lower than what is reported for the Azores archipelago of the Archipelago. In this context, it is essential to increase the sampling effort for both archipelagos, as well as to survey multiple matrices in order to find a greater diversity of aquatic hyphomycetes. To the best of our knowledge, no data of recorded species exist for the other Macaronesia archipelagos, such as Canary Islands and Cabo Verde Archipelago.Here we present the first study that explored the distribution of aquatic hyphomycetes species have a cosmopolitan distribution Aquatic Data typeData recordsBrief descriptionMetafileFile: oo_404009.xmlhttps://binary.pensoft.net/file/404009Raposeiro, P.M.; Faustino, H.; Ferreira, V.; Gon\u00e7alves, V.23207FAB-3574-536A-BFDF-036E130E693C10.3897/BDJ.8.e53690.suppl4Supplementary material 4Occurrence of the aquatic hyphomycete species found in this study in 15 geographic regions defined based on the geographic location and climatic influence in the western and eastern hemispheres Data typeTableBrief descriptionTableFile: oo_420217.csvhttps://binary.pensoft.net/file/420217Raposeiro, P.M.; Faustino, H.; Ferreira, V.; Gon\u00e7alves, V."} +{"text": "This is the first report of plasmid-mediated colistin resistance mcr-8 gene from a clinical Klebsiella pneumoniae K9 isolate recovered from Lebanon. The isolate was characterized phenotypically and genotypically through both short and long read whole-genome sequencing, plasmid typing and conjugation assays. k9 belonged to sequence type 15 and harbored 31 antimicrobial resistance genes. The mcr-8.1 variant was carried on a novel ~\u2009300\u2009kb multireplicon plasmid having IncFIA, IncR and IncHI1B. The plasmid was conjugative and carried a plethora of antimicrobial resistance determinants. The introduction of novel mcr variants in Lebanon poses an alarming health concern. Surveillance and screening for colistin resistant Enterobacteriaceae and mcr in livestock, animal farms, imported meat and poultry is highly recommended along with monitoring antibiotic use.Colistin is considered as a last resort treatment for infections caused by multidrug-resistant Enterobacteriaceae. Plasmid-mediated mobile colistin resistance ( Klebsiella pneumoniae (CRKP) [mcr-1, was identified in 2015 in Enterobacteriaceae, mainly Escherichia coli and K. pneumoniae, collected from animals and humans in China [mcr variants have been described, designated as mcr-1 -9, isolated from humans, animals and the environment [Colistin is the last-line treatment option for infections caused by carbapenem resistant Enterobacteriaceae such as carbapenem-resistant e (CRKP) . The firironment .mcr-8 located on an IncFII-type conjugative plasmid was first described in 2018 in China in K. pneumoniae collected from both animals and humans [d humans . Shortlyd humans and Alged humans .K. pneumoniae in Lebanon was in 2017 [mcr-1-positive E. coli from a human clinical isolate in Lebanon has been recently reported [mcr-1 was widely detected in Gram-negative bacilli isolated from poultry [mcr-8.1 gene variant in an ST-15\u2009K. pneumoniae isolate recovered from Lebanon.The first report of a colistin resistant reported . On the poultry , swine f poultry and wate poultry . This isKlebsiella pneumoniae and designated as k9.The isolate was recovered from the urine sample of a 50-years old female patient on the 28th of August 2018 at the Clinical Microbiology Laboratory of the American University of Beirut Medical Centre (AUBMC), Lebanon. The identification of the isolate was performed using Matrix-Assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) system . The isolate was identified as E. coli transconjugant was further determined by using the broth microdilution method according to the recommendations from the European Committee on Antimicrobial Susceptibility Testing (EUCAST) [Antimicrobial susceptibility testing was performed using the disk diffusion assay on Mueller-Hinton agar and included a panel of 24 antibiotics belonging to 16 different classes (Table S(EUCAST) .DNA extraction was performed from fresh bacterial colonies using the Nucleospin\u00ae Tissue kit according to the manufacturer\u2019s instructions.mcr-8 was confirmed through PCR using MCR-8F 5\u2032-AACCGCCAGAGCACAGAATT-3\u2032 and MCR-8R 5\u2032-TTCCCCCAGCGATTCTCCAT-3\u2019primer pair as previously described [The presence of escribed .Plasmid characterization was performed using the DIATHEVA plasmid based replicon typing (PBRT) kit through a polymerase chain reaction (PCR) based replicon typing method consisting of eight multiplex PCR assays for the amplification of 25 replicons: A/C, B/O, FIA, FIB, FIB-M, FIC, FII, FIIK, FIIS, HI1, HI2, HIB-M, I1, I2, K, L/M, N, P, R, T, U, W, X1, X2, and Y found in the family Enterobacteriaceae. Positive controls were included for all reactions. All PCR reactions were performed according to the manufacturer\u2019s instructions.E. coli J53 strain. Selection of transconjuguants was done on Uriselect agar supplemented with 100\u2009mg/L sodium azide and 4\u2009\u03bcg/ml colistin. E. coli transconjugants were typed by PBRT to detect plasmid replicons.Conjugation was performed with an azide-resistant Genomic libraries were constructed using the Nextera XT DNA library preparation kit with dual indexing (Illumina). The libraries were sequenced on an Illumina MiSeq with 250\u2009bp\u2009\u00d7\u20092 read length. Genome assembly was performed de novo using Spades Genome Assembler Version 3.6.0 . Qualitymcr8-carrying plasmid was sequenced using PacBio long-read sequencing technology on the Sequel platform . Library preparation was performed according to the manufacturer\u2019s instructions for microbial multiplexing. G-tubes were used for DNA shearing, and no size selection was performed.The http://rast.nmpdr.org) [www.genomicepidemiology.org) were used to determine the ST, presence of resistance genes and plasmid content, respectively. The sequences encoding for plasmids were then extracted and aligned to references obtained from NCBI as previously described [https://www-is.biotoul.fr) [wzi gene was performed using Kaptive (www.kaptive.holtlab.net) [http://bigsdb.pasteur.fr. PlasmidsSpades was used to assemble the plasmid sequences [The assembled genomes were annotated using the RAST online server (pdr.org) . MLST 2.pdr.org) , ResFindpdr.org) , PointFipdr.org) and Plaspdr.org) availablescribed . The ISftoul.fr) was usedlab.net) . The preequences . Plasmidequences .pmrA, pmrB, pmrC, pmrD, phoP, phoQ, mgrB, crrA and crrB genes were investigated in silico using both nucleic and amino acid alignments compared to the wild-type sequence of K. pneumoniae MGH 78578 (GenBank accession no. CP000647). SNAP [http://www.hiv.lanl.gov) was used to calculate synonymous and non-synonymous substitution rates based on the codon-aligned nucleotide sequences of pmrA and pmrB against the K. pneumoniae MGH 78578 references.The presence of known mutations conferring colistin resistance on the 7). SNAP and fimbriae .K9 genome size was 5,656,813\u2009bp with a GC content of 56.9%. The best match for the capsular locus was KL107 (Blastn identity: 89.60%) with idFinder includinmcr-8.1 positive isolates recovered so far (Table\u00a0R. ornithinolytica QDRO2 (Accession no. MK097469.1) [n\u2009=\u200931) than other mcr-8.1 positive isolates with 16, 18 and 23 antimicrobial resistance genes (AMRs) detected in isolates KP95, KP91 and QDRO2, respectively. The latter isolates represented different STs and were recovered from both humans and animal sources [k9 was compared to all other 97469.1) KP91, KP97469.1) , respect sources .Table 1k9 had a colistin MIC of 10\u2009\u03bcg/mL , aminoglycosides (aac(6\u2032)-Ib-cr, aadA1, aadA16, aadA2b and aph(3\u2032)-Ia), quinolones (aac(6\u2032)-Ib-cr, oqxA, oqxB, qnrB2, qnrB4, and qnrB52), sulphonamides (sul1 and sul3), fosfomycin (fosA), macrolides (mph(A),mph(E),msr(E)), tetracycline (tetD), trimethoprim (dfrA27), phenicol , rifampicin (arr-3) and colistin (mcr-8).Studying antibiotic resistance mechanisms revealed the presence of 31 different resistance genes on the plasmid including resistance to: \u03b2-lactams revealed a dN/dS ratio of 1.131 for pmrA and 1.181 for pmrB indicating a positive selection for non-synonymous mutations , ompK36 sequence (Accession no. Z33506.1) and ompK37 (Accession no. AJ011502.1). We detected a premature stop codon in ompK35 (Y76*), and 22 different amino acids in ompK36 and two in ompK37. A premature stop codon was also detected in ramR (K194*); a positive regulator of the AcrAB efflux system, compared to an intact ramR reference genes (Accession no. KY465996.1).Mutations in mcr variant was mcr-8.1 showing 100% identity to mcr-8.1 carried by K. pneumoniae plasmid pKP91 (Accession no. MG736312), a\u2009~\u200990-kb IncFII-type plasmid obtained from swine fecal material in China [Raoutella ornithinolytica QDRO2 (Accession no. MK097469.1) [Blast analysis revealed that the in China and in R97469.1) mcr-8.1 recovered from k9 was further compared with other mcr-8 variants. The amino acid sequences and the genetic environment of mcr-8.1 was most similar to mcr-8.3 and mcr-8.4 then to mcr-8.2, the latter being recovered from K. quasipneumoniae in China [mcr-8.2 also harboured more mutations compared to mcr-8.1 than the other variants and pKPN-065 isolated from China and USA [rep genes also found in pKP91 and IncHI1B rep gene also found in pKPN-065. IncFIA was bracketed by two IS1 insertion sequences while IS6 was present downstream of IncR. Parts of pk9 plasmid carrying various AMR determinants also aligned to pR50\u201374 (Accession no. CP040362.1) collected from a rabbit fecal sample in China in 2017, pYDC676 collected from patients in the USA in 2014 (Accession no. KT225462.1) [ and USA , respectsul1, aadA16, dfrA27, arr-3 and aac(6\u2032)-Ib-cr5. It closest identity to Enterobacter hormaechei plasmid pM206-NDM1 collected in Japan (Accession no. AP018830.1) [sul1, qnr, sul1, aadA16 and aac(6\u2032)-Ib-cr5 showing 100% identity and 98% coverage to K. pneumoniae Kp_29407 (Accession no. LR736030.1). Other resistance determinants present on the pk9 included tetA, qnrB4, blaDHA-1, apha1b, sul3, aadA1\u20133, cmlA, floR and ampC. Various sulfonamide resistance genes were identified including four copies of sul1 in addition to sul3 and bcr (bicyclomycin resistance protein).A plethora of resistance genes were detected on pk9. An AMR cassette was located between 14,200\u2009bp and 18,300\u2009bp encoding 18830.1) . Anothermcr gene variants represents a major health concern worldwide. In this study, we identified a multireplicon plasmid carrying the mcr-8.1 gene variant in a K. pneumoniae clinical isolate recovered from a urine sample in Lebanon. This represents the first report of mcr-8 from Lebanon. mcr-8.1 showed 100% gene sequence similarity to mcr-8.1 encoded by pKP91 plasmid originating from a K. pneumoniae KP91 collected in 2018 from swine fecal material in China [mcr variants have been described (mcr-1 to mcr-9) from human, animal and environmental sources [mcr gene in the wildlife and particularly in surface water samples [The plasmid-mediated spread of in China . The detin China , 32. Sin sources , showing samples .mcr-8.1 was located on a 324,283\u2009bp multireplicon plasmid showing highest nucleotide similarity (99\u2013100%) to plasmids pF10AN_1 (Accession no. CP026154.1) and pKPN-065 (Accession no. CP015026.1) isolated from China and USA [rep genes also found in pKP91 [rep gene also found in pKPN-065. Recently, mcr-8.2 was detected on a large, hybrid plasmid containing IncQ, IncR, and IncFII replicons [mcr gene spread [ and USA , respecteplicons confirmie spread .mcr gene family could be transmitted via the food chain, and so its prudent use in both human and veterinary medicine is of paramount importance [mcr-8 in livestock and animal farms in Lebanon as well as in imported meat and poultry is recommended to track the environmental influences contributing to the development and dissemination of resistance determinants propagating on large mobile genetic vehicles.Colistin resistant bacteria and the portance . Polymyxportance . FurtherAdditional file 1: Table S1. Antimicrobial susceptibility and MIC results of K. pneumoniae k9. Antimicrobial susceptibility was performed using the disk diffusion technique; MICs of ertapenem, imipenem and meropenem were determined using the E-test methodology; MIC of colistin was determined using the broth microdilution method. Antibiotics were divided by their drug categories. GM: gentamycin 10\u03bcg; IP: imipenem; MEM: meropenem 10\u03bcg; IPM: imipenem 10\u03bcg; PM: cefepime; CTX: cefotaxime 30\u03bcg; CXM: cefuroxime 30\u03bcg; FEP: cefepime 30\u03bcg; CZD: ceftazidime 10\u03bcg; CZN: cefazolin 30\u03bcg; SCF: cefoperazone/sulbactam 75/30\u03bcg; FOX: cefoxitin 30\u03bcg; NOR: norfloxacin 5\u03bcg; CIP: ciprofloxacin 5\u03bcg; FAD: fusidic acid 10\u03bcg; TGC: tigecycline 15\u03bcg; CMN: clindamycin 2\u03bcg; ERY: erythromycin 15\u03bcg; ATM: aztreonam 30\u03bcg; LZD: linezolid 30\u03bcg; AMX: amoxicilin 25\u03bcg; PIR: pipercacillin 100\u03bcg; AMP: amipicillin 10\u03bcg; TZP: pipercacillin/tazobactam 100/10\u03bcg; FOS: fosfomycin 200\u03bcg; TE: tetracycline 30\u03bcg; TS: trimethoprim/sulfamethoxazole; CO: colistin; Dark blue: resistant, light blue: intermediate resistance, white: susceptible; MICs are in \u03bcg/mL; NA: not available.Additional file 2: Figure S1. SNAP plots with potential synonymous and non-synonymous substitutions in pmrA (A) and pmrB (B). Alignment was performed against the query sequence of K. pneumoniae MGH 78578 wild-type chromosomal genes."} +{"text": "Since electronic cigarettes (e-cigarettes) entered the U.S. marketplace in 2007, the landscape has evolved to include different product types and flavored e-liquids , which have contributed to increases in youth use , from 7.7 million to 17.1 million units per 4-week interval. ; however, within the context of this general increase, sales fluctuated . During Among total e-cigarette unit sales during September 2014\u2013August 2019, the proportion that were prefilled cartridges increased from 47.5% to 89.4% (AIPC\u00a0=\u00a01.0) (p<0.05) . The proAmong total e-cigarette unit sales during September 2014\u2013August 2019, the proportion accounted for by mint products increased from 0.01% to 43.4% (AIPC\u00a0=\u00a010.5) (p<0.05) . During Among prefilled cartridge sales during September 2014\u2013August 2019, the percentage that were mint increased from <0.1% to 47.6% (AIPC\u00a0=\u00a014.1) (p<0.05) . During Among disposable e-cigarette sales during September 2014\u2013May 2020, the percentage of sales of tobacco-flavored and menthol-flavored products decreased; sales of tobacco-flavored e-cigarettes accounted for 17.2% and menthol-flavored accounted for 10.2% of all disposable e-cigarette sales in May 2020, (p<0.05). . During 1,2).During November 2016\u2013August 2019, total e-cigarette unit sales in the U.S. increased nearly 300%. Although prefilled cartridges remained the leading product type sold, disposable sales increased beginning in August 2019, reaching 19.8% of total sales by May 2020. Among prefilled cartridge sales, the proportion of mint-flavored products declined beginning in August 2019; by May 2020, menthol (61.8%) and tobacco (37.1%) flavors dominated the market. Among disposable e-cigarette sales, tobacco-flavored and menthol-flavored sales decreased during September 2014\u2013May 2020; during the same period, the proportion of sales that were mint and all other flavors increased, with mint reaching 10.5% and all other flavors reaching 62.1% of total sales by May 2020. Continued monitoring of e-cigarette sales could inform strategies to reduce use among U.S. youths, including strategies that address youth-appealing product innovations and flavors products. Flavored e-cigarette sales patterns by product type are likely influenced by multiple factors. For example, JUUL voluntarily removed mango, creme, fruit, and cucumber flavored cartridges from retail stores (November 2018) and online (October 2019)The findings in this report are subject to at least three limitations. First, sales data did not include purchases from the Internet or \u201cvape shops,\u201d which accounted for approximately one half of U.S. e-cigarette sales in 2019;1,2). In the U.S., e-cigarette use is markedly higher among youths than adults; in 2018, current use of e-cigarettes was 20.8% (past 30-day use) among high school students, 7.6% (everyday/someday use) among adults aged 18\u201324 years, and 3.2% (everyday/someday use) among adults aged \u226518 years entered the U.S. marketplace in 2007, the landscape has evolved to include disposable e-cigarettes and rechargeable e-cigarettes with prefilled cartridges and flavored e-liquids .During September 2014\u2013May 2020, e-cigarette sales increased by 122.2%. Sales of prefilled cartridges increased during September 2014\u2013August 2019; since then, sales of disposable products have increased. Prefilled mint cartridge e-cigarette sales increased from September 2014 to August 2019, then decreased, as menthol sales increased during August 2019\u2013May 2020.Continued monitoring of e-cigarette sales and use is critical to inform strategies to minimize risks. As part of a comprehensive approach, such strategies could include those that address youth-appealing product innovations and flavors."} +{"text": "This study was aimed at exploring the effect of long noncoding RNA LINC00324 (LINC00324) on gastric cancer (GC) and the potential molecular mechanisms. The expression of LINC00324 and miR-3200-5p in GC tissues and cells was detected by qRT-PCR. LINC00324 was silenced in GC cells by transfection of si-LINC00324. Then, the proliferation, migration, and invasion of GC cells were analyzed by MTT, wound healing, and transwell assays, respectively. The interactions between LINC00324 and miR-3200-5p and between miR-3200-5p and BCAT1 were determined by a dual-luciferase reporter and/or RNA pull-down assay. The expression of LINC00324 was upregulated in GC cells and tissues, but miR-3200-5p was downregulated. Silencing of LINC00324 inhibited the proliferation, migration, and invasion of GC cells. LINC00324 directly targeted miR-3200-5p, and miR-3200-5p directly targeted BCAT1. si-LINC00324 negatively regulated BCAT1 expression via binding to miR-3200-5p. Furthermore, silencing of LINC00324 reversed the promoting effects of BCAT1 on the proliferation, migration, and invasion of GC cells. Silencing of LINC00324 inhibited the proliferation, migration, and invasion of GC cells through regulating the miR-3200-5p/BCAT1 axis. Gastric cancer (GC), also known as stomach cancer, is the third most frequent malignancy worldwide . Less thLong noncoding RNAs (lncRNAs) are noncoding RNA transcripts, taking part in the occurrence and progression of diverse digestive organ cancers including esophageal cancer , pancreaMicroRNAs (miRNAs) are small noncoding RNAs which mediate target genes by interacting with the 3\u2032 untranslated regions (3\u2032 UTRs) . Some miBranched-chain amino acid transaminase 1 (BCAT1) is a cytosolic BCAT isozyme expressed in specific tissues . BCAT1 tHere, the effects of LINC00324 on the proliferation, migration, and invasion of GC cells were evaluated. Then, we investigated whether miR-3200-5p is a downstream target of LINC00324 and the association between miR-3200-5p and BCAT1. This study may reveal a hopeful therapeutic target for GC and the underlying mechanisms for the treatment of GC.In total, 60 GC patients were collected from our hospital between April 2016 and May 2018. Fresh GC tissues and adjacent normal tissues were obtained from GC patients who underwent surgery at our hospital. The tissues were frozen in liquid nitrogen immediately after resection and stored at -80\u00b0C for future use. This study was permitted by the ethics committee of Taian City Central Hospital, and written informed consent was obtained from all the patients.2.Three human GC cell lines, AGS, MGC803, and MKN-45, and the human normal gastric epithelial cell line GES-1 were obtained from the American Type Culture Collection. Cells were cultured in Dulbecco's Modified Eagle's Medium containing 10% fetal bovine serum at 37\u00b0C with 5% COThe siRNA-negative control (si-NC), si-LINC00324-1, si-LINC00324-2, mimics NC, miR-3200-5p mimics, miR-3200-5p inhibitor, inhibitor NC, pcDNA3.1-NC (pcDNA-NC), and pcDNA3.1 BCAT1 (pcDNA-BCAT1) were purchased from Shanghai GenePharma . MGC803 and MKN-45 cells grown to 80% confluence were transfected with these above agents using the Lipofectamine 3000 reagent . MGC803 and MKN-45 cells were divided into si-NC, si-LINC00324-1, si-LINC00324-2, mimics NC, miR-3200-5p mimics, inhibitor NC, miR-3200-5p inhibitor, si-NC+pcDNA-NC, si-NC+pcDNA-BCAT1, and si-LINC00324+pcDNA-BCAT1 groups. Cells without transfection were considered the control or blank groups.\u03b2-actin were used for the normalization of LINC00324, miR-3200-5p, and BCAT1, respectively. The primer sequences are shown in \u0394\u0394Ct- method.Total RNA was extracted from tissues and cells using the TRIzol reagent . RNA was quantified with a NanoDrop ND-1000 spectrophotometer . A total of 300\u2009ng RNA was reverse-transcribed into cDNA using a PrimeScript RT reagent kit . PCR reaction was performed on the ABI 7500HT Fast Real-Time PCR System with the following conditions: 95\u00b0C for 3\u2009min and 40 cycles of 95\u00b0C for 15\u2009s and 60\u00b0C for 30\u2009s. GAPDH, U6, and 3 cells/well). After 24, 48, 72, and 96\u2009h of culturing, 20\u2009\u03bcL MTT was added into each well, and the cells were incubated for 4\u2009h at 37\u00b0C with 5% CO2. After the supernatant was discarded, 150\u2009\u03bcL dimethyl sulfoxide was added to dissolve the formazan. The absorbance at 450\u2009nm was measured using a microplate reader .MGC803 and MKN-45 cells were seeded into 96-well plates . The wound healing rate was calculated by the fraction of cell coverage across the line.When MGC803 and MKN-45 cells were cultured at 80% confluence, an artificial scratch was created using a 10\u2009\u03bcm pore size) . MGC803 and MKN-45 cells (2 \u00d7 105) in serum-free medium were added to the upper chamber precoated with Matrigel . Roswell Park Memorial Institute- (RPMI-) 1640 medium with 10% FBS (Invitrogen) was added to the lower chamber. After 48\u2009h of incubation at 37\u00b0C, cells were removed from the upper chamber with a cotton swab, and cells in the lower chamber were fixed in methanol and stained with 0.5% crystal violet for 2\u2009min. Five random fields were photographed.The transwell assay was used to determine the cell invasion using a transwell chamber . The vectors were then cotransfected with mimics NC, miR-3200-5p mimics, and miR-3200-5p mimics+LINC00324 into MGC803 and MKN-45 cells using Lipofectamine 3000 (Invitrogen) for 48\u2009h. The luciferase activity was detected by a dual-luciferase reporter gene assay system (Promega).Bio-LINC00324-Wt, Bio-LINC00324-Mut, and Bio-NC (GenePharma) were transfected into GC cells (MGC803 and MKN-45) using Lipofectamine 3000 (Invitrogen). After culturing for 48\u2009h, cells were incubated with Dynabeads M-280 streptavidin beads for 1\u2009h. The qRT-PCR assay was employed to assess the enrichment of BCAT1.t-test. The correlation was determined by the Pearson correlation analysis. A P value < 0.05 was considered statistically significant.Statistical analysis was performed using SPSS 23.0 . Data were presented as mean \u00b1 standard\u2009deviation (SD). The differences among multiple groups were analyzed by one-way ANOVA followed by Tukey's multiple comparison test. The differences between two groups were assessed using Student's P < 0.001) (P < 0.01) (P < 0.05), lymphoma metastasis (P < 0.01), and TNM stage in GC patients (P < 0.01). However, LINC00324 expression had no connection with age, gender, and histological grade in GC patients (P > 0.05) (P < 0.01) . Additio < 0.01) . The cor > 0.05) . qRT-PCR < 0.01) . MGC803 P < 0.01) (P < 0.01) (P < 0.01) . si-LINC < 0.05) . The wou < 0.01) . The tra < 0.01) .P < 0.01) (P < 0.01) (P < 0.01) (P < 0.001) (P < 0.01) . The dua < 0.01) . In addi < 0.01) . The exp< 0.001) . There w < 0.01) . qRT-PCR < 0.01) .P < 0.01), and overexpression of LINC00324 reversed the reducing effect of miR-3200-5p mimics on the relative luciferase activity (P < 0.05) (P < 0.01) (P < 0.01) (P < 0.001) (The downstream target of miR-3200-5p was predicted by TargetScan. A binding site of miR-3200-5p on the 3\u2032 UTR of BCAT1 was predicted . Subsequ < 0.05) . The RNA < 0.01) . In addi < 0.01) . These r< 0.001) . There w < 0.01) and a po < 0.05) .P < 0.01). The expression of BCAT1 in the si-LINC00324+pcDNA-BCAT1 group was markedly decreased compared with that in the si-NC+pcDNA-BCAT1 group (P < 0.01) and 72\u2009h (P < 0.01) postculturing was markedly increased compared with that in the si-NC+pcDNA-NC group. Silencing of LINC00324 markedly reversed the promoting effect of BCAT1 on the proliferation of MGC803 cells at 72\u2009h postculturing (P < 0.01) (P < 0.01). Silencing of LINC00324 markedly reversed the promoting effects of BCAT1 on the migration and invasion of MGC803 cells (P < 0.01) . Rescue < 0.01) . Wound h Figures .Abnormal expression of lncRNAs is related to the tumorigenesis of GC , 21. SomPrevious researches have confirmed that LINC00324 takes part in cell proliferation, invasion, and migration in cancer. Wu et al. have proven that LINC00324 increases the proliferation and migration of osteosarcoma cells via targeting WDR66 . Pan et lncRNAs can serve as molecular sponges to competitively regulate miRNAs in GC. For instance, lncRNA-RMRP promotes cell proliferation by acting as a sponge of miR-206 in GC . lncRNA The expression of BCAT1 is usually upregulated in diverse cancers, such as ovarian cancer , breast In conclusion, the expression of LINC00324 was upregulated in GC tissues and cells. Silencing of LINC00324 inhibited the proliferation, migration, and invasion of GC cells through regulating the miR-3200-5p/BCAT1 axis. Our research indicated that LINC00324 might act as a potential therapeutic target for GC. However, the detailed action mechanisms of LINC00324 on GC remain limited, and further researches are still needed."} +{"text": "Orthodontic management of a non-syndromic patient with concomitant bimaxillary hypohyperdontia: a case report. Dental Press J. Orthod. [Internet]. 2020 Jan [cited 2020 Apr 15] ; 25( 1 ): 36-46.How to cite this article\u201d: Now the article should have the following \u201cEi Hsu Hlaing Ei, Ishihara Yoshihito, Fujisawa Atsuro, Yamashiro Takashi, Kamioka Hiroshi. Orthodontic management of a non-syndromic patient with concomitant bimaxillary hypohyperdontia: a case report. Dental Press J. Orthod. [Internet]. 2020 Jan [cited 2020 Apr 15] ; 25( 1 ): 36-46."} +{"text": "Azadirachta indica, Azadirachta excelsa, Azadirachta siamens, Melia azedarach, Melia toosendan, and Melia volkensii, have been subject to botanical pesticide evaluation. This review focuses on Melia volkensii, which has not been intensively studied. M. volkensii, a dryland tree species native to East Africa, has shown activity towards a broad range of insect orders, including dipterans, lepidopterans and coleopterans. Its extracts have been reported to have growth inhibiting and antifeedant properties against Schistocerca gregaria, Trichoplusia ni, Pseudaletia unipuncta, Epilachna varivestis, Nezara viridula, several Spodoptera species and other insect pests. Mortality in mosquitoes has also been reported. Several limonoids with a wide range of biological activities have been isolated from the plant, including volkensin, salannin, toosendanin, trichilin-class limonoids, volkendousin, kulactone among others. This paper presents a concise review of published information on the phytochemical composition and potential of M. volkensii for application in insect pest management.Due to potential health and environmental risks of synthetic pesticides, coupled with their non-selectivity and pest resistance, there has been increasing demand for safer and biodegradable alternatives for insect pest management. Botanical pesticides have emerged as a promising alternative due to their non-persistence, high selectivity, and low mammalian toxicity. Six Meliaceae plant species, The continuous and indiscriminate use of synthetic pesticides in crop protection has led to an increase in pest resistance, health and environmental concerns . This haMeliaceae plant family has been reported to produce a wide range of compounds, including flavonoids, chromones, coumarins, benzofurans, mono-, sesqui-, di-, and triterpenoids, but tetranortriterpenoids with a \u03b2-substituted furanyl ring at C17\u03b1 are the best known for the production of limonoids [Azadirachta indica A. Juss (Indian neem tree) is reported as a potential plant for the control of vector mosquitoes [Melia azedarach Linnaeus (chinaberry) has been reported outlining its use in folk medicine having antifertility, antiviral, cytotoxic, antibacterial, immunomodulatory, repellent, antifeedant, antilithic and anthelmintic activity from various parts of the plant [A. indica has reported its use in agriculture for application as manure, fertilizer, soil conditioner, fumigant, and as botanical pesticide [Melia volkensii (Gurke) has also been identified as one of the pesticidal plants in Africa [The imonoids . Limonoiimonoids . Alkaloiimonoids . Reviewssquitoes . Reviewssquitoes ,7. A phyhe plant ,9. A revesticide . Melia vn Africa . Anothern Africa . Detailen Africa .A. indica (Indian neem tree), Azadirachta excelsa Jack (Philippine neem tree), Azadirachta siamens Valeton (Siamese neem tree), M. azedarach (chinaberry), Melia toosendan Siebold and Zucc., and M. volkensii [A. indica (neem tree) and M. azedarach (chinaberry) [A. indica, have been effective growth regulators and feeding deterrents for a wide range of insect species [M. azedarach have also shown antifeedant activity against the juvenile and adult Xanthogaleruca luteola Muller (elm leaf beetles) and mortality against its larvae [M. azedarach are also effective against Napomyza lateralis Fallen (agromyzid leafminers) and Trialeurodes vaporariorum Westwood (whiteflies) [M. azedarach which has been commercialized in China, is an effective growth inhibitor against Ostrinia nubilalis H\u00fcbner (European corn borer), effective repellent against Pieris brassicae Linnaeus (cabbage moth) and an oviposition deterrent against Trichoplusia ni H\u00fcbner (cabbage looper) [Several plant species of the Meliaceae have shown promising bioactivity against a variety of insects . Their iolkensii . Howevernaberry) . Azadira species . Azadira species . Extracts larvae . Fruit eteflies) . Toosend looper) . Toosend looper) .M. volkensii, a dryland tree species native to East Africa has, however, not been intensively studied [M. volkensii. These include: 1-O-cinnamoyltrichilin, meliavolkinin, 1,3-diacetylvilasinin, meliavolkin, volkensin, volkensinin, 12\u03b2- and 6\u03b2-hydroxykulactone, meliavolkenin, meliavolin, meliavolen, melianinone, meliavolkensin A and B, melianin C, (E)- and (Z)-volkendousin, meliavosin, 2-9-epoxymeliavosin [M. volkensii seed kernel extracts have more insect growth inhibitory and acute lethal toxicity than azadirachtin-containing fractions from neem seed kernel extracts [M. volkensii dried fruit powder and residual fruit cake obtained after extraction with ethanol are used as goat feed, their growth and performance are not negatively affected, indicating that both fruit powder and its cake could be used as safe ruminant feed supplement [M. volkensii have also traditionally been used to control ticks and fleas in goats [M. volkensii offers a key indigenous tree species that can be used to mitigate against desertification in arid and semi-arid lands [M. volkensii in insect pest management. studied . It is a studied . The tre studied . It rema studied . Severalextracts . It has pplement . Its usepplement , and trapplement . Aqueousin goats . M. volkid lands , while aid lands . This paM. volkensii have been reported to pose activity towards a broad range of insect orders including Diptera, Lepidoptera, Coleoptera among others [Schistocerca gregaria Forsk. (desert locusts) [S. gregaria when seed extract was applied to their preferred host plants mainly Schouwia thebaica Webb, Fagonia olivieri DC (fagonbush plant) and Hyoscyamus muticus Linnaeus (Egyptian henbane) in a field trial experiment [M. volkensii extracts could affect hormone levels in S. gregaria larvae [S. gregaria, 80% mortality was recorded 48 hours after injection with crude ethanolic and methanolic extracts at a concentration of 30 \u03bcg/g of the insect [S. gregaria, M. volkensii and neem oil have been reported to cause mortality of up to 91% and 92%, respectively, after 14 days in a comparative study [Crude fruit extracts from g others as shownlocusts) . Repelleperiment . Althouga larvae . In fifte insect . When spve study . In contve study . Trichoplusia ni H\u00fcbner (cabbage looper) and Pseudaletia unipuncta Haworth (true armyworm) [T. ni (dietary EC50 = 7.6 ppm) and feeding deterrent (DC50 = 0.9 \u03bcg/cm2) [M. volkensii extracts has been observed to lead to a decrease in antifeedant response when tested against T. ni implying that the insect could develop tolerance to the extracts [Plutella xylostella Linnaeus (diamondback moth) and P. unipuncta, there was no significant decrease in feeding deterrent response to the extracts following continuous exposure [M. volkensii are responsible for the insecticidal activity in T. ni [M. volkensii extracts, other Meliaceae plant extracts and commercial botanical insecticides when tested against T. ni and P. unipuncta [Antifeedant and larval growth inhibitory effects of fruit extracts have been observed in rmyworm) ,28. Crud \u03bcg/cm2) . Prolongextracts . Howeverexposure . It has in T. ni . Comparanipuncta . M. volkensii fruit extracts when tested at concentrations ranging from 1 to 50 \u03bcg/\u03bcL showed feeding deterrence, growth disruption and mortality against Nezara viridula Linnaeus (stink bug), a polyphagous pest which attacks a variety of crops, including nuts, corn, cotton, grains and tomatoes [N. viridula [N. viridula when exposed to fruit extracts, with 10 \u03bcg/\u03bcL causing malformation in up to 85.70% of surviving adults [Coranus arenaceus Walker even though there were no deformities in resultant adults after topical application of the M. volkensii extracts at 1, 5, and 10 \u03bcg/\u03bcL [tomatoes . The disviridula . Furtherg adults . A delay10 \u03bcg/\u03bcL . M. volkensii fruit extract showed potent antifeedant properties against Epilachna varivestis Mulsant (Mexican bean beetle) [P. unipuncta (dietary EC50 = 12.5 ppm) with refined seed extracts to the leaf discs in a choice bioassay [P. unipuncta and P. xylostella, and adults of E. varivestis [M. volkensii seed extracts have been recorded to have stronger antifeedant activity compared to pure allelochemicals: digitoxin, cymarin, xanthotoxin, toosendanin, thymol and trans-anethole against P. unipuncta, P. xylostella and E. varivestis [Spodoptera litura Fabricius, neem, rotenone, M. volkensii extract, toosendanin, Annona squamosal L. extract and pyrethrum at 1% concentration recorded larval growth (% relative to control) of 4.1, 97.5, 26.2, 48.3, 61.4, and 56.6%, respectively after 96 h in a comparative study [When applied to cabbage leaf disks in a choice bioassay, beetle) . Growth bioassay . The seectively) . In factrivestis . When apM. volkensii fruit extracts have shown growth-inhibiting activity against Aedes aegypti Linnaeus (yellow fever mosquito) larvae at 2 \u03bcg/mL in water, whilst recording high mortality during the molting and melanization process with LC50 of 50 \u03bcg/mL in 48 h [A. aegypti could be a result of synergistic effects of a plethora of limonoid compounds or a single active compound exerting these effects [Dried in 48 h . At a hi in 48 h . Growth effects . M. volkensii fruit kernel extract showed growth-inhibiting activity against Anopheles arabiensis Giles with an LC50 of 5.4 \u03bcg/mL in 48 h [50 of 34.72 \u03bcg/mL in 48 h) and oviposition deterrence was observed in second-instar larvae of Culex quinquefasciatus Say (Southern house mosquito) when treated with refined methanolic fruit extracts [M. volkensii fruit acetone extract showed S- and U-shaped postures and frequent stretching in C. quinquefasciatus; such postures and stretching are a characteristic of mosquito larvae reared in M. volkensii fruit extract [C. quinquefasciatus within 36 h [M. volkensii seeds have recorded growth inhibitory effects and equal toxicity (LD50 of 30 \u03bcg/mL) for larvae and pupae of C. pipiens f. molestus Forsk\u00e5l (London underground mosquito) [M. azedarach seed extracts recorded lower toxicity (LD50 of 40 \u03bcg/mL) while pure azadirachtin A recorded higher toxicity (LD50 of 1\u20135 \u03bcg/mL) against C. pipiens when compared with M. volkensii extracts [M. volkensii may indicate the presence of saponins as toxic principles thus making it an interesting candidate for application against aquatic insects such as mosquitoes and other vectors of diseases [A column chromatography-purified fraction of in 48 h . Mortaliextracts . The graosquito) . M. azedextracts . The watdiseases .M. volkensii, as shown in M. volkensii. This indicates that insect control bioactivity is, therefore, based on other compounds than azadirachtin [M. volkensii fruit is more lipophilic than azadirachtin [Insect antifeedants have been found in major classes of secondary metabolites\u2014alkaloids, phenolics, and terpenoids . Howeverirachtin . It is pirachtin . Botanicirachtin .1) and salannin (2) have been isolated from seed extracts of M. volkensii [1) and salannin (2) were isolated from the whole fruits of M. volkensii [1) has shown antifeedant activity against Spodoptera frugiperda Smith larvae with an ED50 of 3.5 \u03bcg/cm2 [2) has also shown antifeedant activity against insect pests such as Acalymma vittata Fabricius (striped cucumber beetle), Musca domestica Linnaeus (housefly), Epilachna varivestis Mulsant (Mexican bean beetle), Heliothis virescens Fabricius (tobacco budworm), S. frugiperda and Spodoptera littoralis Boisduval (cotton leafworm) [2) has also been reported to cause feeding suppression against larvae of Earias insulana Boisduval (Egyptian stemborer), weight reduction (59%\u201389%) in Cnaphalocrocis medinalis Guenee (rice leafroller) and reduction in activities of acid phosphatases (ACP), alkaline phosphatases (ALP) and adenosine triphosphatases (ATPase), implying that gut enzyme activities were affected. 2\u2019,3\u2019-Dihydrosalannin (3), 1-detigloyl-1-isobutylsalannin (4) and 1\u03b1,3\u03b1-diacetylvilasinin (5) have also been isolated from the plant [The insect antifeedants volkensin . Salannihe plant .M. volkensii seed extracts, extracted in cold water, have been reported to contain unsaturated fatty acids (oleic acid (6), linoleic acid (7) and gadoleic acid (8)) and saturated fatty acids , stearic acid (10) and arachidic acid (11)) as shown in 6), linoleic acid (7), linolenic acid, and ricinoleic acid have enhanced insecticidal activity of organophosphates and carbamates when applied against sucking insects and defoliating insects [ insects . M. volkensii are shown in 12), which has been isolated from the root bark of M. volkensii [O. nubilalis, an effective repellent against P. brassicae and an oviposition deterrent against T. ni [13) has shown antifeedant activity towards S. littoralis having minimum antifeedant concentration (MAC) value of 1000 mg/L and a significant antibacterial activity against Porphyromonas gingivalis ATCC 33277 with minimum inhibitory concentration (MIC) value of 15.6 \u03bcg/mL [14) has been reported to have antifeedant activity against several Spodoptera species [13, 1-acetyltrichilinin 15, 1-tigloyltrichilinin 16) were tested against Spodoptera eridania Stoll (Southern armyworm) where the 12\u03b1-OH function was the most potent, followed by 12\u03b2-OH, 12-desoxy, and 12\u03b1-acetoxy groups in order of decreasing potency [13, 15, 16) [17, which has weak activity with marginally significant selectivity for breast cancer cell line (MCF-7), has also been isolated from the root bark of M. volkensii [18), isolated from methanolic extract of M. volkensii fruits [19), both insect antifeedants have also been reported [Other chemical compounds that have been isolated from various parts of olkensii , has beest T. ni . 1-Cinnaolkensii . Ohchinii fruits , and melreported . M. volkensii with different biological activities. These include volkensinin, as isolated from ethanolic extracts of M. volkensii root bark [50 = 57 \u03bcg/mL) and weak cytotoxicity against six human tumor cell lines with ED50 values of 27.90, 28.35, 33.56, 29.55, 8.43, and 28.51 \u03bcg/mL in A-498 (human kidney carcinoma), PC-3 (prostate adenocarcinoma), PACA-2 (pancreatic carcinoma), A-549 (human lung carcinoma), MCF-7 (human breast carcinoma), and HT-29 (human colon adenocarcinoma), respectively [Escherichia coli Migula and Aspergillus niger Tiegh. with respective minimum inhibitory concentration (MIC) values of 12.5 and 6.25 \u03bcg/mL [M. volkensii, showed cytotoxicity against six human solid tumor cell lines: A-549, MCF-7, HT-29, A-498, PACA-2, and PC-3 [M. volkensii root bark led to the isolation of meliavolkenin which showed moderate cytotoxicity against three human tumor cell lines with a respective ED50 value of 10.33 \u03bcg/mL, 4.30 \u03bcg/mL, and 0.67 \u03bcg/mL in A-549, MCF-7, and HT-29 cells [M. volkensii [50 values of 0.49 \u03bcg/mL and 0.25 \u03bcg/mL, respectively [E)-volkendousin, isolated from M. volkensii root bark, also showed activity against six human tumor cell lines [50 of 11.25 \u03bcg/mL, 0.57 \u03bcg/mL and 6.65 \u03bcg/mL in A-549, MCF-7 and HT-29 cells, respectively [M. volkensii root bark following activity-directed fractionation with brine shrimp test [M. volkensii and exhibited significant activity against E. coli and A. niger with a respective minimum inhibitory concentration (MIC) value of 12.5 and 6.25 \u03bcg/mL [Mycobacterium tuberculosis Zopf resulted in the isolation of 12\u03b2-hydroxykulactone, 6\u03b2-hydroxykulactone and kulonate from M. volkensii seeds with MIC values of 16 \u03bcg/mL, 4 \u03bcg/mL, and 16 \u03bcg/mL, respectively [50 = 0.57 \u03bcg/mL), MCF-7 (ED50 = 0.26 \u03bcg/mL), and HT-29 (ED50 = 0.12 \u03bcg/mL) [M. volkensii include 3-episapelin, meliavolen, melianinone [M. volkensii include scopoletin [Other compounds have also been isolated from oot bark , which sectively . Toosend25 \u03bcg/mL . Melianiand PC-3 . Bioacti29 cells . The bioolkensii , have shectively . (E)-volnd PC-3) . Meliavo25 \u03bcg/mL . Bioactiopoletin , melianiM. volkensii have proved to be effective insect antifeedants and growth inhibitors. Extensive research has been done on mosquito control using M. volkensii; however, more research needs to be done on insect pests of agricultural importance. M. volkensii has no reported adverse effect on the environment or mammals, making it a potential botanical pesticide for the biosafe application in integrated pest management. The availability of renewable resources from the tree, such as fruits, stem bark, and leaves makes this plant a potential candidate for insect control with minimal interference on the plant. In this regard, M. volkensii could be further exploited as a source of natural insecticide. Extracts and pure compounds isolated from"} +{"text": "Escherichia coli isolate INF13/18/A, which was isolated from Universiti Sains Malaysia (USM) Hospital. This isolate was identified as an extended-spectrum \u03b2-lactamase-producing Escherichia coli strain harboring the antimicrobial resistance genes TEM, CTX-M-1, and CTX-M-9.We describe here the draft genome sequence and basic characteristics of Escherichia coli isolate INF13/18/A, which was isolated from Universiti Sains Malaysia (USM) Hospital. This isolate was identified as an extended-spectrum \u03b2-lactamase-producing Escherichia coli strain harboring the antimicrobial resistance genes TEM, CTX-M-1, and CTX-M-9.We describe here the draft genome sequence and basic characteristics of Escherichia coli is one of the most versatile and widely studied species in the world Hospital.Gram-negative he world . The emehe world . The precrobials . In thisThe clinical sample was collected aseptically and incubated into the Bactec 9240 blood culture system . Gram staining and biochemical testing . The isoE. coli , with read-trimming and filtered read length threshold values of 30 and 50\u2009bp, respectively. The filtered and trimmed reads were assembled de novo using SPAdes v3.9.0 (E. coli isolates. The complete genome sequences of E. coli O157 strain AR-0427 (GenBank accession no. CP044148.1) and E. coli strain AR216.2b (GenBank accession no. CP043942), which were the top two hits, were selected to scaffold the draft genome using a graph-based approach with Medusa v1.6 v4.10 (usa v1.6 . The assP) v4.10 , which pEscherichia coli INF/13/18/A has been deposited in GenBank under the accession no. WRPL01000000 (BioProject accession no. PRJNA593306 and BioSample accession no. SAMN13474918). The raw reads are available under the SRA accession no. SRR10587526.The whole-genome project for the ESBL-producing strain"} +{"text": "Human immunodeficiency virus (HIV) is associated with co-morbid affective and stress-sensitive neuropsychiatric disorders that may be related to dysfunction of the hypothalamic-pituitary-adrenal (HPA) stress axis. The HPA axis is perturbed in up to 46% of HIV patients, but the mechanisms are not known. The neurotoxic HIV-1 regulatory protein, trans-activator of transcription (Tat), may contribute. We hypothesized that HPA dysregulation may contribute to Tat-mediated interactions with oxycodone, a clinically-used opioid often prescribed to HIV patients. In transgenic male mice, Tat expression produced significantly higher basal corticosterone levels with adrenal insufficiency in response to a natural stressor or pharmacological blockade of HPA feedback, recapitulating the clinical phenotype. On acute exposure, HIV-1 Tat interacted with oxycodone to potentiate psychomotor and anxiety like-behavior in an open field and light-dark transition tasks, whereas repeated exposure sensitized stress-related psychomotor behavior and the HPA stress response. Pharmacological blockade of glucocorticoid receptors (GR) partially-restored the stress response and decreased oxycodone-mediated psychomotor behavior in Tat-expressing mice, implicating GR in these effects. Blocking corticotrophin-releasing factor (CRF) receptors reduced anxiety-like behavior in mice that were exposed to oxycodone. Together, these effects support the notion that Tat exposure can dysregulate the HPA axis, potentially raising vulnerability to stress-related substance use and affective disorders. Human immunodeficiency virus type 1 (HIV-1) continues to be a serious health concern with over 1 million infected individuals in the U.S. . HoweverA common, but under-investigated neurological complication of HIV involves disruption of the hypothalamic-pituitary-adrenal (HPA) stress axis. Despite treatment with cART, 14\u201346% of HIV+ patients demonstrate a dysregulated HPA axis characterized by elevated basal glucocorticoids with seemingly paradoxical adrenal insufficiency in response to a stressor ,8,9. ComThe mechanisms of HIV-mediated HPA dysregulation are not known but may involve neurotoxic HIV-1 proteins. One important therapeutic target that may contribute to these effects is the regulatory protein, trans-activator of transcription (Tat). HIV-1 Tat exerts direct effects on neurons to promote excitotoxic injury and activates monocyte-derived cells (and astrocytes to a lesser extent) to promote neuroinflammation via cytokine production . We haveIn the present study, we hypothesized that HIV-1 Tat and/or oxycodone would interact to promote HPA axis dysregulation, potentiating oxycodone-mediated effects including psychomotor stimulation and affective dysfunction in a conditionally-inducible Tat transgenic mouse model. We further expected pharmacological blockade of GR and/or CRF receptors to restore HPA function and to ameliorate behavioral deficits.In Experiment 1, Tat-tg male mice had HIV-1 Tat expression induced (or not) via doxycycline administration for five days. After two days of doxycycline washout (to limit non-specific anti-inflammatory effects), mice were (or were not) exposed to a 15-min swim stress. Following stress, mice were acutely administered an injection of saline or oxycodone and psychomotor and anxiety-like behavior were assessed 15 min later A.F = 5.00, p < 0.05] = 5.00, p < 0.05] = 5.04, p < 0.05] = 27.16, p < 0.05] = 27.34, p < 0.05] of travel and decreased the frequency and time spent rearing , compared to saline administration = 8.69, p < 0.05] and made fewer transitions between compartments compared to Tat(\u2212) controls = 5.15, p < 0.05] controls, Tat(+) mice traveled a significantly greater distance [ < 0.05] B; see * < 0.05] in an op < 0.05] . Irrespe < 0.05] A; see \u2020 stration . In a licontrols . No signcontrols . When ci < 0.05] C. Tat(+)F = 13.83, p < 0.05] and speed of travel; however, no differences were observed between Tat(\u2212) and Tat(+) mice = 13.88, p < 0.05] mice D, nor we(+) mice . Similar(+) mice . As expe < 0.05] E; see *.While the initial opioid response is indicative of later abuse liability, many HIV+ patients are prescribed oxycodone and are exposed repeatedly. How repeated oxycodone exposure modifies the HPA stress response in Tat-exposed mice was of interest. In Experiment 2, Tat-tg male mice had HIV-1 Tat expression induced (or not) via doxycycline administration for five days (with two days of washout). During this time, mice received daily injections of saline or oxycodone . Mice were (or were not) exposed to a 15-min swim stress prior to testing A.F = 46.98, p < 0.05] = 46.68, p < 0.05] = 6.08, p < 0.05] = 11.18, p < 0.05] = 4.05, p = 0.05]; no such effect was observed on Tat(\u2212) controls = 3.99, p = 0.05] = 4.93, p = 0.05] = 14.79, p < 0.05] mice spent significantly less time in the brightly-lit compartment, compared to Tat(\u2212) mice [ = 0.05] . Irrespe = 0.05] . Tat(+) < 0.05] C; see *.F = 7.01, p < 0.05] = 7.10, p < 0.05] = 3.86, p = 0.05] = 9.60, p < 0.05] mice. As seen in Experiment 1, overall motor behavior was reduced following swim stress compared to that observed in non-stressed mice. Repeated oxycodone and genotype interacted such that oxycodone\u2013administered Tat(+) mice traveled a significantly greater distance [ < 0.05] D; see \u2021 < 0.05] than did = 0.05] . No diff = 0.05] . As obse < 0.05] E; see \u00a7.In order to begin identifying the important aspects of the HPA axis that are involved in the psychomotor, anxiety-like, and glucocorticoid response to oxycodone and Tat, mice were administered glucocorticoid receptor (GR) and/or corticotrophin-releasing factor-receptor (CRF-R) inhibitors concurrent with doxycycline administration A. To bloF = 2.86, p < 0.05] and speed traveled. As before, oxycodone significantly increased the distance . All Tat(+) mice administered a GR and/or CRF-R inhibitor demonstrated a modest, but significant, reduction in the distance mice = 11.54, p < 0.05]. Pretreatment with RU-486 produced a significant and large increase in circulating corticosterone among Tat(\u2212) mice = 6.11, p < 0.05]. Irrespective of genotype, at t5 oxycodone-administered mice exhibited significantly lower circulating corticosterone compared to saline-administered mice and promoting adrenal insufficiency in response to HPA activation to a natural or pharmacological challenge. HPA dysregulation occurred concurrent with anxiety-like behavior and combined Tat and oxycodone-mediated psychostimulation. Repeated oxycodone exposure was able to sensitize the Tat-suppressed HPA response, suggesting potential for pharmacological therapeutic intervention. Blocking GR attenuated combined Tat- and oxycodone-mediated psychostimulation and produced a proportional increase in corticosterone, indicating its importance in these effects. Thus, therapeutics with the capacity to restore the HPA axis may be important mediators of HIV-1 Tat/opioid interactions.Procedures were preapproved by the Institutional Animal Care and Use Committee (IACUC) at the University of Mississippi . All experiments were carried in accordance with ethical guidelines defined by the National Institutes of Health (NIH Publication No. 85-23).n = 324) were bred in the vivarium at the University of Mississippi . Mice were housed 2\u20135 per cage and be kept in a temperature-and humidity-controlled environment on a 12:12 h light:dark cycle (lights off at 09:00 h) with ad libitum access to food and water. HIV-1 Tat1\u201386 is conditionally expressed by administration of doxycycline as described previously via the administration of doxycycline QD for 5 days i.p. Given that doxycycline can attenuate neuroinflammation and could therefore mask potential effects of Tat, 2 days of doxycycline washout was carried out . All behn = 8\u20139), Tat(+)/saline (n = 7\u20138), Tat(\u2212)/oxycodone (n = 12), Tat(+)/oxycodone (n = 8\u20139), and the following swim-stressed groups were yielded: Tat(\u2212)/saline (n = 8), Tat(+)/saline (n = 9), Tat(\u2212)/oxycodone (n = 8), Tat(+) oxycodone (n = 9).To begin to determine the HPA-axis interactions involved in exposure to HIV-1 Tat and acute oxycodone, mice were randomly-assigned to undergo a 15-min swim stress (or not) followed by administration of vehicle or oxycodone only once prior to behavioral testing. Fifteen minutes after drug administration, mice were assessed in an open field to determine their psychomotor response followed immediately by assessment in a light-dark transition test to determine anxiety-like behavior A. Acrossn = 7\u20138), Tat(+)/saline (n = 10), Tat(\u2212)/oxycodone (n = 8), Tat(+)/oxycodone (n = 10), and the following swim-stressed groups were yielded: Tat(\u2212)/saline (n = 8), Tat(+)/saline (n = 8), Tat(\u2212)/oxycodone (n = 8), Tat(+) oxycodone (n = 9).Given that most patients are exposed to opioids on a repeated dosing schedule, some mice were administered sterile saline (0.9%) or oxycodone (3 mg/kg) daily throughout the 7-day doxycycline-induction/washout schedule A. As befn = 8), Tat(+)/saline/vehicle (n = 7\u20138), Tat(\u2212)/oxycodone/vehicle (n = 8\u20139), Tat(+)/oxycodone/vehicle (n = 9), Tat(\u2212)/saline/antalarmin (n = 8), Tat(+)/saline/antalarmin (n = 8\u20139), Tat(\u2212)/oxycodone/antalarmin (n = 8\u20139), Tat(+)/oxycodone/antalarmin (n = 10), Tat(\u2212)/saline/RU-486 (n = 8\u20139), Tat(+)/saline/RU-486 (n = 7\u20138), Tat(\u2212)/oxycodone/RU-486 (n = 8\u20139), Tat(+)/oxycodone/RU-486 (n = 7\u20138), Tat(\u2212)/saline/antalarmin+RU-486 (n = 9), Tat(+)/saline/antalarmin+RU-486 (n = 8), Tat(\u2212)/oxycodone/antalarmin+RU-486 (n = 9\u201310), Tat(+)/oxycodone/antalarmin+RU-486 (n = 9\u201310).To begin to identify the important receptor sites involved in HIV-1 Tat- or oxycodone-mediated disruption of the HPA axis, some mice were pretreated with the GR antagonist, RU-486, and/or the CRF-R antagonist, antalarmin, prior to testing. RU-486 was administered daily throughout the 7-day doxycycline-induction/washout schedule and 30 min prior to behavioral testing A. Antalan = 5/group) in order to assess the time-course for HPA activation. Prior work revealed peak HPA circulating corticosterone levels in HIV-1 Tat females within 30 min of testing as the between-subjects factors. For Experiment 3, behavioral and steroid analyses were assessed via separate three-way ANOVAs with pretreatment , drug condition , and genotype as the between-subjects. For Experiment 4, corticosterone steroid analyses were assessed via repeated measures ANOVA with drug condition and genotype as the between-subjects factors and time as the within-subjects factor. Main effects were followed by Fisher\u2019s Protected Least Significant Difference"} +{"text": "Neritimorpha, six Caenogastropoda, and 28 Heterobranchia). Illustrations and brief taxonomic notes/remarks are provided for every species. We also described Georrisacarinata Sutcharit & Jirapatrasilp, sp. nov. based on some distinct shell morphological characters. Since the first descriptions during the colonial period in the nineteenth century, some land snail species have not been reported subsequently. This probably reflects a lack of knowledge concerning land snail biodiversity in this country. To our knowledge, this is the first comprehensive survey of land snails in southern Cambodia. A need for more field research and systematic revision of the land snails in this interesting region is also highlighted and demonstrated.Prior to this study, few collections and records were made of the land snails in Cambodia and the historical taxa had never been reviewed. Herein a report on the land snail diversity based on specimens collected recently from karstic and non-karstic areas in southern Cambodia is provided. This checklist presents 36 species of land snails (two Cambodia forms a part of the Indo-Chinese sub-region of the Indo-Burma biodiversity hotspot . Its terHemiptera and The Natural History Museum . The placement of each genus within higher order classification followsIFReDI) of the Fisheries Administration, Phnom Penh; Chulalongkorn University Museum of Zoology (CUMZ), Bangkok; Zoological Reference Collection of the Lee Kong Chian Natural History Museum, National University of Singapore (ZRC); The Natural History Museum, London (NHMUK).All the specimens were identified to genus or species level based on shell characteristics by referring to the historical literature including original descriptions, recent catalogues of land snails from Laos by Field surveys were conducted in karstic areas in southwestern Cambodia, Kampot Province. In addition, caves and cave-like chambers which provide appropriate microhabitats for karst-dwelling snails were also surveyed. This area has a monsoonal climate with wet season (May to November) and dry season (December to April). The karst landscape in Kampot is a small, isolated hill rising precipitously from the flat lowlands Fig. . The forLowland habitats of the eastern areas of Kirirom National Park are a conglomerate of hills and a plateau reaching 900 m in elevation, straddling the Kampong Speu and Koh Kong Provinces. The bulk of the plateau is covered with a mosaic of grassland and a reticulated network of pine forest plantations Fig. . The sloThe Preah Monivong Bokor National Park, Kampot Province is in the southeastern portion of the Cardamom Mountain Ranges within a range known as the Elephant Mountains. The plateau reaches an elevation of 1,100 m, and the floral composition of this range is greatly affected by continuous, monsoonal winds arising from the Gulf of Thailand. The climate promotes a mixture of grassland and tropical moist forest that shrouds the upper elevations of the Bokor Plateau in thick fog for much of the year , the conNeritimorpha . The distribution data given under each species was retrieved from the past records.A total of 180 voucher specimen lots was collected over the survey. The total of 36 species . The aperture is round to slightly ovate, with a closed umbilicus. Although the specimens from Perak have denser spiral striation , withoutG.decora M\u00f6llendorff, 1900 and G.chrysacme M\u00f6llendorff, 1900 both of which were described from \u201cTouranne\u201d , by having a conic shell with ca. ten strong spiral ribs on the last whorl. However, G.decora has an ovate conic shape with fine radial ribs on the last whorl, and G.chrysacme has an elongate conic shape with a deep and narrow suture. In addition, the shell shape of G.monterosatiana approaches the shape of G.insulaeThis species differs from Taxon classificationAnimaliaCycloneritidaHydrocenidaeSutcharit & Jirapatrasilpsp. nov.5B5771A6-B6EC-59E9-BA7E-E23BB4736AE5http://zoobank.org/CA891381-B719-4A88-B4A9-B0E36BAB121ECUMZ-CM094/1 from locality no. 11; CUMZ-CM042 (21 shells), IFReDI (10 shells), ZRC (10 shells) and NHMUK (10 shells) from locality no. 9.Holotype 4/1 Fig. from loc10\u00b034'1.77\"N, 104\u00b028'6.13\"E).Phnom Kampong Trach Cave Temple, Kampong Trach District, Kampot Province, Cambodia, Locality no. 11 (CUMZ-CM086 (23 shells). Locality no. 17: CUMZ-CM102 (18 shells).Locality no. 12: Shell minute , conic, solid, translucent, yellowish to pale orange with darker colour on apex. Whorls 4\u00bc, last whorl large ca. two-thirds of shell height. Protoconch ca. one whorl; sculpture nearly smooth and discontinuous spiral appearing immediately after protoconch. Following whorls slightly keeled, sculptured with thin and uneven growth lines; upper periphery with irregular and strong sculpture; below periphery with discontinuous spiral ribs. Sutures angular and impressed. Aperture round to slightly ovate. Umbilicus closed. Operculum unknown.carinata represents its keeled whorls of this new species.The Latin specific name Hypselostoma spp.This new species is found from Kampot and Kep Provinces. The snails were found to live on limestone wall syntopically with other G.bocourti described from \u201cEaux douces de Preck-Scholl. Haut M\u00e9kong\u201d , by having a conic shell with 4\u00bc whorls, which are slightly keeled and sculptured with thin and uneven growth lines without conspicuous spiral ribs. However, G.bocourti has a turriform shell with 6\u20137 whorls and sculptured with conspicuous spiral ribs (Rochebrune 1881a). Georissacarinata sp. nov. differs from G.poirieri Mabille, 1887 and G.conspicua Mabille, 1887 described from \u201cTonkin\u201d [Vietnam] in that the latter two species are larger and has a turriform shell. In addition, G.poirieri has very thin, tight, wavy spiral ribs, while G.conspicua has uneven spiral ribs with additional protuberances unequally arranged along the longitudinal rows 262B8A2B-3FD7-5E65-B8DF-40373B15A5F2Cyclostoma (Cyclophorus) amoenum Pfeiffer, 1854[1852]: 62. Type locality: unknown.Cyclophorusamoenus : CUMZ-CM053 (21 shells), CUMZ-CM054 . Locality no. 11: CUMZ-CM071 (2 shells). The empty shells were collected from the ground among leaf litter.Locality no. 10: Cambodia and Thailand . The disCyclophorus is the genus encompassing highly variable shell morphology of both inter- and intraspecific entities. The demarcation among different species is poorly understood. Thus, both intensive and thorough revision and redescription require more effective taxonomic characters, e.g., morphometric analysis of large series of specimens and perhaps molecular phylogeny to clarify the exact species boundaries [The mountains of Dey-Crahom (red earth)], sur la rive droite du grand fleuve [on the right bank of the great river (Mekong River)]. Cyclophorus (Eucyclophorus) paviei : CUMZ-CM119 (1 shell). Locality no. 6: CUMZ-CM176 (1 shell). Locality no. 9: CUMZ-CM036 (2 shells), CUMZ-C037 . Locality no. 12: CUMZ-CM096 (1 shell). Locality no. 16: CUMZ-CM168 (2 shells), CUMZ-CM169 (1 specimen in ethanol), CUMZ-CM170 (1 specimen in ethanol). The snails were found to live on the ground among leaf litter.Locality no. 13: Cambodia . The disCyclophoruspaviei was described from \u201cLes montagnes de Dey-Crahom\u201d, from Cambodia. It differs from C.cambodgensis Morlet, 1885, which was described from the same area in having a smaller (shell width 32 mm) conical shell, with a white-yellowish apertural lip, while C.cambodgensis has a larger (shell width 42 mm) and turbinate conic shell, with an orange to reddish apertural lip.Taxon classificationAnimaliaArchitaenioglossaCyclophoridaeB24D7F7F-272C-5CAE-BE1A-4ADB522E60F7Rhiostomabernardii Pfeiffer, 1862: 45, 46, pl. 6, fig. 5. Type locality: Siam [Thailand]. Cyclotusbernardii : Opisthoporusbernardii : CUMZ-CM043 (8 shells). Locality no. 13: CUMZ-CM127 (2 shells), CUMZ-CM118 (2 shells). Locality no. 10: CUMZ-CM062 . The snails were found to live on the ground among leaf litter.Locality no. 9: Cambodia, Laos and Thailand .Opisthoporusbernardii was originally described from \u201cSiam\u201d [Thailand], and it has been reported from Cambodia A8BA2B42-822F-538E-889B-28DC9E7AA101Cyclophorusklobukowskii Morlet, 1885[1884]: 391, 392, pl. 12, fig. 1. Type locality: Near the Kamchay rapids, around the K\u00e9bal-R\u00e9m\u00e9as cave (Kampot-Hatien road); commonly found on mountains, in forests, up to Compong-Som, and on the banks of Tap-Ch\u00e9ang. Lagocheilusklobukowskii : CUMZ-CM044 (7 shells), CUMZ-CM045 (12 specimens in ethanol). Locality no. 10: CUMZ-CM068 (3 specimens in ethanol). Locality no. 11: CUMZ-CM079 (2 shells). Locality no. 13: CUMZ-CM128 (3 shells), CM129 \u2026\u201d. We collected topotypic specimens that tend to have a variable shell colour from yellowish Fig. . This liLagocheilusklobukowskii was originally placed in the genus Cyclophorus and later was transferred to the genus Lagocheilus , and a thick calcareous, multispiral and plate-like operculum, whereas Cyclophorus has a turbinate shell, a thick and expanded lip, and a corneous multispiral operculum.ilus see . The disTaxon classificationAnimaliaArchitaenioglossaCyclophoridae614B5E69-1CA9-527D-9220-C0A030BE666ECyclophoruslandesi Morlet, 1885[1884]: 392, 393, pl. 11, fig. 5, 5a. Type locality: extr\u00e9mit\u00e9 de la cha\u00eene de \u013e\u00c9l\u00e9phant, non loin de la mer .Cyclophoruslaudesi [sic]: Lagocheiluslandesi : CUMZ-CM080 . Locality no. 12: CUMZ-CM104 (4 shells). Locality no. 14: CUMZ-CM152 , and the thick calcareous, multi-spiral and plate-like operculum characteristic of Pupina Vignard, 1829Taxon classificationAnimaliaArchitaenioglossaPupinidaeMorlet, 1883283DD709-264C-5D8D-A991-BD4F39799F14Pupinacrosseana Morlet, 1883: 108, 109, pl. 4, fig. 5. Type locality: Cambodge [Cambodia]. CUMZ-CM029 (1 shell). Locality no. 9: CUMZ-CM039 (10 shells). Locality no. 10: CUMZ-CM066 (1 shell), CUMZ-CM067 . Locality no. 13: CUMZ-CM133 (1 specimen in ethanol). Locality no. 17: CUMZ-CM142 (1 specimen in ethanol). The snails were found to live on the ground among leaf litter.Locality no. 7: Cambodia .This species was originally described from \u201cCambodge\u201d [Cambodia]. The diagnostic characters of this porcelain shell are a pupoid shell with varying shell colour from brownish to whitish, having a large, ovate last whorl ca. two-thirds of shell height. The shell has a thickened parietal callus, with a small posterior plica that is located some distance from an angular corner of aperture, which possesses a wide posterior canal. The anterior canal is a narrowly transverse slit overhung by a square and thickened columella plica. The aperture is circular with a white, thickened and slightly expanded lip.Valiguna Grimpe & Hoffmann, 1925Taxon classificationAnimaliaSystellommatophoraVeronicellidae59FA60F6-E456-561B-8B22-19E795F8A8D9Vaginulussiamensis Martens, 1867: 68, pl. 5, fig. 3. Type locality: Petshaburi .Valigunasiamensis : CUMZ-CM116 is thickened, with dark colour and scattered with brownish spots, and without median stripe. The ventral side (hyponotum) is with much lighter, pale creamy colouration, with tiny greyish spots distributed across hyponotum, and a narrow foot sole located in the middle. The foot sole is as long as and slightly narrower than the hyponotum, with pale yellowish brown colour. This slug is different from Succinea Draparnaud, 1801Taxon classificationAnimaliaStylommatophoraSuccineidaeMorelet, 1865EA06A16E-E337-58B7-B934-EF322D27ECB2Succineatenuis Morelet, 1865: 225, 226. Type locality: Cochinchina [South Vietnam]. Succineatenella Morelet, 1875: 244, pl. 12, fig. 5 [unjustified emendation].CUMZ-CM106 (2 shells), CUMZ-CM107 . Locality no. 9: CUMZ-CM087 .Hypselostomacambodjense tends to be abundant and widely distributed in several karstic hills in southern Cambodia and Vietnam B2EDA1FE-87E6-5097-B863-9DCB9ACC6E2FBulimusgracilis (?) Hutton, 1834: 84, 85, 93. Type locality: Mirzapoor; Futtehpoor Sikra; between Agra and Neemuch . (?) Allopeasgracilis [sic]: CUMZ-CM105 . The snails were found to live on the ground among leaf litter.Locality no. 12: Pantropical and subtropical .A.gracile in Cambodia. This species could be found in both natural and transformed anthropogenic habitats. This widespread and pantropical species has been introduced into many countries, including in greenhouses in temperate regions, and occurs throughout Laos, Thailand and Vietnam 3E6BACC4-C635-59E3-824E-AE4521A0DFD0Achatinafulica Bowdich, 1822: pl. 13, fig. 3. Type locality: unknown.Lissachatinafulica : CUMZ-CM065 . The snails were found to live on tree trunks and on the ground among leaf litter.Locality no. 10: Pantropical and subtropical .Angiostrongyluscantonensis . Locality no. 11: CUMZ-CM074 , CUMZ-CM076 , CUMZ-CM099 (1 shell), CUMZ-CM100 (9 specimens in ethanol). Locality no. 13: CUMZ-CM121 (21 shells), CUMZ-CM122 (1 specimen in ethanol). The snails were found to live on the ground among leaf litter in the limestone area.Locality no. 6: H.michaui , but the latter is more ovate and less oblique in shell shape. In addition, this species can be distinguished from H.pellucens , H.porrectus and H.perlissus Vermeulen et al., 2019 by having strong and prominent radial ridges. For comparison, the latter three species have a smooth to nearly smooth shell surface, H.pellucens has an oblique-ovate shell shape, H.porrectus and H.perlissus have an oblique heliciform shell shape , CUMZ-CM156 (4 shells), CUMZ-CM157 . The snails were found to live on tree trunks and leaves.Locality no. 15: Bertiacambojiensis by having a brownish shell, with spirally undulated surfaces, while B.cambojiensis has a smooth surface and D.retrorsa by having a dark brown shell, with wide angle of peripheral keels. In contrast, D.retrorsa tends to have sharp peripheral keel, D.salangana has round periphery and usually with brownish peripheral band, and both species are pale brownish in shell colour located on the plateau of Preah Monivong Bokor National Park may be young individuals, as their shell size is relatively small compared to those of other congeners recorded from peninsular Thailand. It differs from l colour .Taxon classificationAnimaliaStylommatophoraDyakiidae9963D788-2D1B-5D3C-883F-9E6D421B1761Helixweinkauffiana Crosse & Fischer, 1863: 350, 351. Type locality: Cochinchine [Southern Vietnam].Quantulaweinkauffiana : CUMZ-CM002 (8 shells). Locality no. 2: CUMZ-CM006 (10 shells). Locality no. 5: CUMZ-CM011 (2 shells). Locality no. 7: CUMZ-CM013 (82 shells), CUMZ-CM014 (1 shell), CUMZ-CM015 , CUMZ-CM035 (3 shells). Locality no. 10 CUMZ-CM052 (1 shell). Locality no. 12: CUMZ-CM093 (5 shells). Locality no. 13: CUMZ-CM120 (5 shells). Locality no. 17: CUMZ-CM135 (3 shells). Locality no. 18: CUMZ-CM143 (3 shells), CUMZ-CM144 (1 shell). Locality no. 16: CUMZ-CM166 (4 shells), CUMZ-CM177 (1 shell). Locality no. 6: CUMZ-CM174 (9 shells), CUMZ-CM175 EDC62306-0411-5BDB-93D2-C99EEEB8A0C5Helixpaviei Morlet, 1885[1884]: 386, 387, pl. 11, fig. 1, 1a. Type locality: dans les for\u00eats, entre Kampot et Phnom-Penh, particuli\u00e8rement pr\u00e8s des rapides de Kamchay (rivi\u00e8re de Kampot), sur les bois pourris et les petite plantes .Trochomorphapaviei : CUMZ-CM153 (3 specimens in ethanol). Locality no. 15: CMZ-CM162 (2 shells), CUMZ-CM163 . The snails were found to live on tree trunks and on the ground among leaf litter.Locality no. 14: Cambodia, Laos and Vietnam .T.paviei closely resembles T.saigonensis that was described from \u201cPoulo-Condor and Saigon, Cochinchine\u201d. The latter species is slightly smaller (shell width 11 mm), having the last whorl with a wide angled peripheral keel and being slightly convex below the periphery. The type specimens of both species were recently figured in This species was originally described from \u201cDans les for\u00eats, entre Kampot et Phnom-Penh\u201d. The unique characters are a depressed conic shell (shell width 12 mm) with a very strong and sharp peripheral keel, and a widely opened and deep umbilicus. The shell surface has thin and regular radial ridges, and very thin spiral ridges. Based on shell morphology, Taxon classificationAnimaliaStylommatophoraTrochomorphidaesp.4907C676-3C20-5516-A416-2FE97F57D66CCUMZ-CM057 , CUMZ-CM059 (1 specimen in ethanol). Locality no. 13: CUMZ-CM134 (3 shells). The snail was found to live on a tree trunk.Locality no. 10: T.paviei and T.saigonensis in having a larger shell (shell width 14 mm), an elevated domed spire, more whorls, and being nearly flat below the periphery. However, the identification is provisional, and further evidence from examination of genitalia or DNA will be necessary to elucidate their status.The specimens from Prasat Phnom Totong have a conic shell with a very strong and sharp peripheral keel, widely opened and deep umbilicus, and slightly convex below the periphery. The shell surface has irregular growth lines and very thin spiral ridges. These specimens tend to differ from Cryptozona M\u00f6rch, 1872Taxon classificationAnimaliaStylommatophoraAriophantidaeC459181B-410C-5886-80E0-0BA6909196F3Helixsiamensis Pfeiffer, 1856: 32. Type locality: Siam [Thailand].Hemiplectadichromatica Morlet, 1889: 124, 175, 176, pl. 6, fig. 2. Type locality: de Srak\u00e9o \u00e0 Ang-Son (Siam) .Cryptozonasiamensis : CUMZ-CM147 . The snails were found to live on the ground among leaf litter.Locality no. 4: Cambodia, Laos, Malaysia, Singapore and Thailand .C.siamensis is found throughout the country and the allozyme analysis by C.siamensis probably occupies almost all habitat types through accidental introduction or horticultural trade activities, and this species is especially abundant in human-modified landscapes.This widespread species has recently been recorded from Singapore and Peninsular Malaysia , Laos I and YunnHemiplectadichromatica Morlet, 1889\u201d which was subsequently considered to be conspecific with this species , in which its habitats are associated with human activities. In contrast, Q.weinkauffiana could be found commonly in both natural forest and anthropogenic habitats.The historical record of this species from Cambodia was probably under the name \u201c species . In thisTaxon classificationAnimaliaStylommatophoraAriophantidae4A498BFE-3341-5F92-8207-B3B3E08EF2DAHelixdistincta Pfeiffer, 1850: 69, 70. Type locality: insulis Moluccis [Molucca Islands].Hemiplectadistincta : CUMZ-CM021 (6 shells), CUMZ-CM022 (1 specimen in ethanol), CUMZ-CM023 (1 specimen in ethanol). Locality no. 11: CUMZ-CM069 (2 shells), CUMZ-CM070 . Locality no. 3: CUMZ-CM123 (1 specimen in ethanol). Locality no. 17: CUMZ-CM136 (4 shells). Locality no. 18: CUMZ-CM145 (1 shell). Locality no. 14: CUMZ-CM149 (1 shell). Locality no. 16: CUMZ-CM171 . Locality no. 6: CUMZ-CM180 (3 specimens in ethanol). The small juveniles were found on tree trunks and leaves, while the adults were found to live on the ground among leaf litter.Locality no. 7: Cambodia, Laos, Thailand and Vietnam .Hemiplectadistincta has a wide distribution from Southern Vietnam, throughout Cambodia, northeastern Thailand, and throughout Laos , CUMZ-CM033 (3 shells). Locality no. 10: CUMZ-CM050 (24 shells), CUMZ-CM051 by having a reddish-brown shell with a wide whitish or creamy area surrounding the umbilicus. Sarikabocourti, which is described from \u201cBattambang, Cambodje\u201d, has a uniform brownish shell . Locality no. 13: CUMZ-CM117 . These specimens differ from M.psyche in having a nearly flattened to slightly elevated spire, with a slightly shouldered last whorl and milky shell colour, while M.psyche has a slightly sunken spire, with a well-rounded last whorl and whitish shell colour , CUMZ-CM092 have a small shell (diameter ca. 10 mm), which is depressed, slightly thick, translucent, shiny, and pale reddish-brown. The shell surface is smooth with obvious irregular growth lines. The shell has 5 to 6 whorls, with wide and shallow suture. The spire is convex, with an elevated apex. The last whorl has a well-rounded periphery, with an ovate-lunate aperture and a simple lip. An umbilicus is widely open and deep.Macrochlamyspsyche, Sarika sp. 1 and sp. 2 by having a small size and slightly elevated spire. In contrast, M.psyche and Sarika sp. 1 have a large, whitish shell and a flatten to slightly shrunken spire, while Sarika sp. 2 has a larger, reddish-brown shell with whitish area surrounding the umbilicus. Live specimens are required so that the anatomical characters can be used to discriminate among the species.These specimens can be distinguished from Cambodiparmarion Kuznetsov & Kuzminykh, 1999Taxon classificationAnimaliaStylommatophoraAriophantidaeKuznetsov & Kuzminykh, 19997F1D24E2-D479-5F7E-96A0-A98EDACC1FA6Cambodiparmariondoroshenkoi Kuznetsov & Kuzminykh, 1999: 113\u2013116, figs 1, 2. Type locality: In tropical forest between Motel Lomherkay and Hotel Koh Pos, SW end of Kompong Som [= Sihanoukville], Kompong Som district, Kampot province, Cambodia.CUMZ-CM108 (4 shells). Locality no. 13: CUMZ-CM130 (2 shells), CUMZ-CM131 . The semi-slug was found to live on tree trunks and leaves in the limestone area.Locality no. 12: Known only from the type locality .Microparmarion Simroth,C.doroshenkoi was described, the authors did not mention the characters used to discriminate this species from Parmarionmartensi Simroth,C.doroshenkoi has a solid, ear-shape shell with ca. 2 whorls, a blackish body and mantle, and a long flagellum, while P.martensi has a thin nail-shape shell with a trace of shell coiling, a greyish to blackish body and a short flagellum , CUMZ-CM151 . The semi-slugs were found to live on tree trunks and leaves.Locality no. 14: Cambodia, Laos, Malaysia and Singapore .Parmarionmartensi has also been reported as an introduced species to Samoa and Hawaii , in which the shell is usually entirely covered with movable mantle lobes. d Hawaii .Taxon classificationAnimaliaStylommatophoraHelicarionidaeD96F0748-53E1-5B2B-845F-79B4D0954B75Vitrinarusseola Morelet, 1865: 225. Type locality: Cochinchina. Megausteniarusseola : CUMZ-CM030 was figured in Durgella. Further additional anatomical examination is necessary since the shell morphology is insufficient for species identification.A syntype of Taxon classificationAnimaliaStylommatophoraAriophantidaesp.456EF9A1-F892-5A09-BB2F-C813B4D198A7CUMZ-CM031 . It is distinguished from lamella .Amphidromus Albers, 1850Taxon classificationAnimaliaStylommatophoraCamaenidae4392F96C-9762-5E88-9AAE-9603DB4DEBB0Bulimusleucoxanthus Martens, 1864: 526. Type locality: unknown.Amphidromus (Amphidromus) atricallosusleucoxanthus : CUMZ-CM018 41CDD142-CBE9-5E02-A065-AB263656D157Bulimus (Amphidromus) semitessellatus Morlet, 1885[1884]: 387, 388, pl. 11, fig. 2, 2a. Type locality: les montagnes qui bordent le grand fleuve au del\u00e0 de Stung-Treng. Les for\u00eats et les montagnes de Kampot \u00e0 Compong-Som .Amphidromus (Syndromus) semitessellatus : Amphidromussemitessellatus : CUMZ-CM040 (2 shells). Locality no. 10: CUMZ-CM055 (1 shell). Locality no. 12: CUMZ-CM101 . The empty shells were collected from the ground, and the living snails probably live on tree trunks and leaves.Locality no. 9: Cambodia, Laos, Thailand and probably in Vietnam , 2019.A.semitessellatus due to the similarity of both brown supra-peripheral and sub-peripheral bands on the penultimate whorls and the geographical proximity. The subgenus Syndromus typically has a small shell which exhibits high variation on shell size, colour, and pattern F49A8378-19A8-5EED-A5E4-A1D43D30DF08Helixnorodomiana Morlet, 1883: 106, 107, pl. 4, fig. 3, 3a, b. Type locality: Khamchay [Cambodia].Chloritisnorodomiana : CUMZ-CM024 (2 shells). Locality no. 9: CUMZ-CM041 (35 shells). Locality no. 10: CUMZ-CM056 (1 shell). Locality no. 11: CUMZ-CM077 . Locality no. 12: CUMZ-CM103 (1 shell). Locality no. 13: CUMZ-CM125 (4 shells), CUMZ-CM126 (1 specimen in ethanol). Locality no. 16: CUMZ-CM173 CC0F820D-5140-5F03-8B7B-20ADBBD3E1F4Helix (Geotrochus) perakensis Crosse, 1879: 199, 200, pl. 8, fig. 4. Type locality: Perak .Ganesellaperakensis : CUMZ-CM159 , CUMZ-CM161 species complex which is composed of 11 nominal species and widely distributed from Western Ghats of India to Indochina and the Greater Sunda Islands from \u201cTonquin\u201d and G.vatheleti from \u201cVan Bu, Tonkin\u201d by having a strong peripheral keel. For comparison, G.subperakensis is convex below periphery, with less strong peripheral keel and without brownish spiral band , which was described from Ha-Giang (Northern Vietnam) and Siam [Thailand]. The description itself was based mainly on the Ha-Giang specimen in having a smaller shell (shell height up to 13 mm), shallow suture with 6 to 7 convex whorls, while G.lantenoisi performs an elongate trochoid, larger shell (shell height up to 18 mm), suture flattened and smooth 9 to 10 whorls. However, further investigations with both genitalia and DNA analysis will be necessary to elucidate the exact relationship between them.This species is very similar to Taxon classificationAnimaliaStylommatophoraCamaenidaeS. Tumpeesuwan & C. Tumpeesuwan, 20209E87B72C-4CCB-5F6D-86FE-0B4A4924EFC2Ganesella (Giardia)Mollusca: Eupulmonata: Camaenidae). Preoccupied by K\u00fcnstler, 1882: (Metamonada: Diplomonadida: Hexamitidae). Ancey, 1907: 195, 203 (Pseudobuliminus (Giardia) : Pseudobuliminus (Girardius) Richardson, 1983: 94. [incorrect subsequent spelling]Giardia : Anceyoconcha Tumpeesuwan & Tumpeesuwan in The distinguished shell character of this genus is sinistral, elongate cylindrical to more or less conical, with 6\u201310 convex whorls. The last whorl is rounded (not keeled), with the aperture ovate to slightly trapezoid and the apertural lip expanded. The columella is vertical, with the umbilicus narrowly opened.Giardia as the subgenus of Ganesella Blanford, 1863 to include two Indochinese sinistral species: Bulimussiamensis Redfield, 1853 and Bulimusrhombostomus Pfeiffer, 1861. Subsequently, this nominal name was used as a subgeneric level of Buliminopsis Heude, 1890 (family Fruticicolidae) by Bradybaenidae as the subgenus of Pseudobuliminus Gredler, 1886, and also designated Bulimussiamensis Redfield, 1853 as the type species. Zilch\u2019s classification was subsequently accepted and used by later authors . authors . Recentlmaenidae . HoweverBradybaenidae, Girardius\u201d, accompanied by diagnostic characters and attributed Bulimussiamensis Redfield, 1853 as the type species. However, this name is considered incorrect subsequent spelling comb. nov., A.maestratii comb. nov., A.mantongensis comb. nov., A.obesa comb. nov., A.ovoideus comb. nov., A.pharangensis comb. nov., A.rhombostomapupoidea comb. nov., A.rhombostomarhombostoma, A.siamensismaxima comb. nov., A.siamensisnobilis comb. nov., A.siamensisobesula comb. nov., A.siamensispervariabilis comb. nov., A.siamensissiamensis, A.siamensiszonifera comb. nov. and A.vignei comb. nov.Anceyoconcha is probably within the Indochinese region of Cambodia, Laos, Thailand, and Vietnam 773E6D49-5BCA-5F83-8110-6C8F386BBA31Bulimusrhombostomus Pfeiffer, 1861: 194, 195. Type locality: Camboja [Cambodia].Ganesellarhombostoma : Anceyoconcharhombostoma : CUMZ-CM047 (66 shells), CUMZ-CM048 . Locality no. 11: CUMZ-CM085 . Locality no. 13: CUMZ-CM132 (3 shells). Locality no. 17: CUMZ-CM139 (5 shells), CUMZ-CM140 ADF2BB29-F75B-52E1-8FCE-0F006E8D1E31Buliminussiamensis var. obesulaAncey, 1888: 352. Type locality: Saigon, dans le jardin du gouverneur. CUMZ-CM027 (14 shells), CUMZ-CM028 , ovate shell and lower number of whorls. For comparison, A.siamensissiamensis 345FACC2-57F6-5EBD-A592-13F4FB14F3B7Petraeuschaudoensis Rochebrune, 1881a: 70. Type locality: Montagnes de Chaudoe Cambodge .Enachaudocensis [sic]: CUMZ-CM003 . Locality no. 3: CUMZ-CM010 (1 specimen in ethanol). The snails were found to live on tree trunks and leaves.Locality no. 1: Cambodia .This species was originally described from \u201cMontagnes de Chaudoe Cambodge\u201d probably in the area bordering Cambodia and Vietnam. The original description of this species was brief and without illustration. This species has a sinistral elongate conic to slightly ovate conic shell, with 7 to 9 whorls, which increase regularly; cylindrical, having convex whorl and wide and impressed suture. The shell surface possesses fine growth lines, and the periostracum is thin and brownish. The last whorl is well rounded and without keel near aperture and has a similar diameter to the penultimate whorl. The shell colour is light brownish and translucent (becoming whitish when worn). The aperture is semi-ovate, with expanded and whitish lip and thin or thickened with whitish parietal callus. The columella is straight and dilated, with a rimate umbilicus.A.chaudoensis can be distinguished from A.siamensisobesula in having an elongate cylindrical shell and higher number of whorls, while the latter species has an ovate conic shell and a smaller number of whorls.Based on the original description, Alycaeidae, Clausiliidae, and Plectopylidae. It is possible that the geography of the area without high mountains and other structured habitat types result in comparatively fewer species. In comparison, most of the species Sesarapolita that does not exceed 12 mm in width. However, most land snails collected in our study are large (more than 10 mm) and cover most taxonomic groups, with the exception of the families Assimineidae and Diplommatinidae, both of which have been reported by Cambodia has received the least attention from malacologists for inventorying the land snail fauna, compared to other adjacent countries within the Indo-Chinese region, e.g. Thailand , Laos I and Viet"} +{"text": "Methanobrevibacter smithii and Methanobrevibacter oralis DNA sequences, were detected in 21/527 (3.9%) sputum samples, 2/188 (1.06%) bronchoalveolar lavages, and none of 193 tracheo-bronchial aspirations. Further, fluorescence in situ hybridization detected methanogens in three sputum investigated specimens with stick morphology suggesting M. oralis and in another one bronchoalveolar lavage sample investigated, diplococal morphology suggesting M. smithii. These observations extend the known territory of methanogens to the respiratory tract and lay the foundations for further interpretation of their detection as pathogens in any future cases of isolation from bronchoalveolar lavages and the lungs.Methanogens, the sole microbes producing methane, are archaea commonly found in human anaerobic microbiota. Methanogens are emerging as opportunistic pathogens associated with dysbiosis and are also detected and cultured in anaerobic abscesses. Their presence in the respiratory tract is yet unknown. As a preliminary answer, prospective investigation of 908 respiratory tract samples using polyphasic approach combining PCR-sequencing, real-time PCR, fluorescent in situ hybridization (FISH), and methanogens culture was carried out. Methanobrevibacter oralis, Methanosarcina mazei, Methanobacterium congolense, Methanobrevibacter smithii, and Methanobrevibacter massiliense) [M. smithii [M. smithii, M. oralis, Methanosphaera stadtmanae, Methanomassilicoccus luminyensis, and Methanobrevibacter arboriphilicus) [M. smithii and M. oralis have been associated with dysbiosis affecting the oral cavity, the gut [Methanogenic archaea (referred to in this study as methanogens), the sole organisms known to produce methane, have been characterized in the oral cavity microbiota (iliense) ,2,3, in smithii , in digehilicus) ,6 and rehilicus) and blast programme of NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) were used for sequence analyses. A total of 5\u03bcL of distilled water were used as a negative control for sputum samples and bronchial aspirates, and 5\u03bcL of 0.9% NaCl saline for bronchoalveolar lavage.All samples were examined by standard polymerase chain reaction (PCR) assays targeting the 16S rRNA gene in an automated 5A PTC-200 thermal cycler . The 16S gene was amplified using broad-range rRNA primers SDArch0333aS15 (5\u2032-TCCAGGCCCTACGGG-3\u2032) and SDArch0958aA19 (5\u2032-YCCGGCGTTGTTGAMTCCAATT-3\u2032) . The PCRM. oralis cnp602F primer 5-GCTGGTGTAATCGAACCTAAACG-3 (Eurogentec); cnp602R primer 5-CACCCATACCCGGATCCATA-3 (Eurogentec) and the probe cnp602-FAM 5-AGCAGTGCACCTGCTGATATGGAAGG-3 (Eurogentec) [M. smithii ; Smit.16S-862R, 5-CTCCCAGGGTAGAGGTGAAA-3 (Eurogentec) and the probe Smit.16S FAM, 5-CCGTCAGAATCGTTCCAGTCAG-3 (Eurogentec) [The PCR products were sequenced using the same primers as used for PCRs following this program: a 1-min denaturation step at 96 \u00b0C, followed by 25 cycles of denaturation of 10 s at 96 \u00b0C, a 20-s annealing at 50 \u00b0C and a 4-min extension at 60 \u00b0C. The MultiScreen 96-well plates Millipore containing 5% of Sephadex G-50 were used to purify the sequencing products. The sequences were analyzed and edited following the protocol described previously . Furtherogentec) ) speciesBacteroides thetaiotaomicron (104 cells/mL) for hydrogen production [B. thetaiotaomicron in SAB broth were incubated at 37 \u00b0C for 7 days. Subculture was seeded on a Petri dish containing SAB medium supplemented with 15 g/L agar (Sigma-Aldrich) and deposited in the upper chamber of a double-chamber box. Methanogen colonies appeared after 9\u201312 days of incubation [A volume of 250 \u03bcL of each sample diluted in PBS was seeded under anaerobic chamber in a sterile Hungate tube ,21. Eachoduction and the cubation .Only PCR positive samples were analyzed by FISH using the method previously described ,4. In brWe used a negative methanogen PCR sputum sample and a negative methanogen bronchoalveolar lavage sample as negative controls.M. oralis-positive samples exhibiting 99% sequence similarity with M. oralis strain ZR (GenBank: NR_104878.1) and two M. smithii-positive samples exhibiting 99% sequence similarity with M. smithii ATCC 35,061 (GenBank NR: 074235.1); in 2/188 (1.06%) of bronchoalveolar lavage samples and one M. smithii-positive sample exhibiting 99.97% similarity with M. smithii strain C2 CSUR P5816 (GenBank: LR590664.1). None of the bronchial aspirate samples were PCR-positive.In the presence of negative control which remained negative, PCR-sequencing disclosed methanogens in 21/527 (3.98%) of the sputum samples including 19 M. smithii 16S rRNA gene yielded a median Ct of 35.7 \u00b1 0.47, indicating a M. smithii load of 1.32 \u00d7 104 \u00b1 0.56 \u00d7 104/mL in the case of two sputum positive samples and Ct of 36.2 indicative of an M. smithii load of 0.8 \u00d7 104/mL in case of one bronchoalveolar lavage positive sample.In the presence of negative control which remained negative, all the positive samples by PCR-sequencing were positive by real-time PCR. Real-time PCR analyses targeting the M. oralis cnp-60 gene yielded a median Ct of 33.2 \u00b1 1.07 indicative of an M. oralis load of 2.61 \u00d7 105 \u00b1 1.23 \u00d7 105/mL in the case of 19 sputum positive samples and Ct of 35.3 indicative of an M. oralis load of 1.41 \u00d7 104 in case of one bronchoalveolar lavage positive sample in the saliva ,32. Inte"} +{"text": "Beilschmiedia erythrophloia, B. robusta, B. yunnanensis, Cryptocarya concinna, C. impressa, C. infectoria, Litsea viridis, Machilus balansa, M. grandifolia, Neolitsea ellipsoidea, and Phoebe angustifolia) have been obtained by hydrodistillation and the chemical compositions analyzed by gas chromatography \u2013 mass spectrometry (GC-MS) and gas chromatography with flame ionization detection (GC-FID). The essential oils were screened for larvicidal activity against Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus, and for antimicrobial activity against Enterococcus faecalis, Staphylococcus aureus, Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, and Candida albicans. The leaf essential oil of N. ellipsoidea, rich in (E)-\u03b2-ocimene (87.6%), showed excellent larvicidal activity against Ae. aegypti with a 24 h LC50 of 6.59 \u03bcg/mL. The leaf essential oil of C. infectoria, dominated by germacrene D (55.5%) and bicyclogermacrene (11.4%), exhibited remarkable larvicidal activity against Cx. quinquefasciatus (48 h LC50 = 0.40 \u03bcg/mL). N. ellipsoidea leaf essential oil also demonstrated notable antibacterial activity against E. faecalis and B. cereus with minimum inhibitory concentration (MIC) values of 16 \u03bcg/mL, while the leaf essential oil of C. impressa showed excellent anticandidal with an MIC of 16 \u03bcg/mL. Leaf essential oils from the Lauraceae should be considered for utilization as alternative agents for controlling mosquito populations and as antimicrobial agents.The Lauraceae is a family rich in aromatic and medicinal plants. Likewise, essential oils derived from members of this family have demonstrated a myriad of biological activities. It is hypothesized that members of the Lauraceae from Vietnam will yield essential oils that may be useful in controlling mosquito populations and treating microbial infections. In this work, the leaf essential oils of eleven species of Lauraceae ( Persea americana Mill.) for its fruit, bay leaf (Laurus nobilis L.) used in cooking, and the spice cinnamon (Cinnamomum verum J. Presl) [Sassafras albidum (Nutt.) Nees) [Lindera benzoin (L.) Blume) [Aniba rosaeodora Ducke) [Cinnamomum camphora (L.) J. Presl.) [Litsea cubeba (Lour.) Pers.) [The Lauraceae is made up of around 55 genera and 3000 species of tropical and warm temperate trees and shrubs, with Southeast Asia and Brazil serving as species-rich hot spots . Several. Presl) . Several) Blume) . Many spa Ducke) , camphor Presl.) , and aro) Pers.) .Based on the utility and properties of Lauraceae essential oils, it is hypothesized that members of the Lauraceae found in Vietnam have biologically active essential oils that may be useful in controlling mosquito populations or as antimicrobial agents. Eleven species of Lauraceae from north-central Vietnam have been collected, the essential oils obtained by hydrodistillation, chemical compositions analyzed, and the oils screened for mosquito larvicidal activity and for antimicrobial activity.Beilschmiedia Nees is comprised of around 250 species of trees and shrubs [Beilschmiedia has been reviewed [The genus d shrubs and are d shrubs . The phyreviewed .Beilschmiedia erythrophloia Hayata is a tree found in Taiwan, southern China, Hainan Island, and Ryukyu Islands (Japan) [B. erythrophloia have revealed endiandric acid derivatives from the roots [E)-caryophyllene and \u03b1-humulene [ (Japan) ,13. In V (Japan) . Previouhe roots ,16, the humulene .Beilschmiedia robusta C.K. Allen is a tree, 10\u201315 m tall that is recorded from Guangzi, southwestern Guizhou, Xizang, and Yunnan provinces in China [B. robusta.in China ,18. In Vin China . A perusBeilschmiedia yunnanensis H.H. Hu is a tree, up to 18 m tall and is found in Guangdong, southern Guangxi, and southern Yunnan provinces in China [B. yunnanensis.in China . In Vietin China . A literCryptocarya R. Br. is a pantropical genus of around 300 species [Cryptocarya concinna Hance is a tree up to 18 m tall, and ranges from southern China to northern Vietnam [C. concinna have shown the roots to contain cytotoxic cryptocaryone [C. concinna. species . Cryptoc Vietnam ,12. In V Vietnam . Previouocaryone , the leaocaryone , and theocaryone . There hCryptocarya impressa Miq. is native to Vietnam, Laos, the Malay Peninsula, Borneo and Sumatra [C. impressa. Sumatra . In Viet Sumatra . To our Cryptocarya infectoria (Blume) Miq. (syn. Cylicodaphne infectoria Blume) is a tree up to 33 m tall that is native to Indo-China and Malesia [C. infectoria [N-methylisococlaurine, and N-methyllaurotetanine have also been isolated from the bark of C. infectoria [ Malesia ,25,26. I Malesia . The cytfectoria ,28. The fectoria . There hLitsea Lam. consists of around 300 species distributed in tropical and warm subtropical regions of Asia, Australia, and the Americas [Litsea viridis H. Liu is a small tree, 3-6 m tall, found in south-eastern Yunnan province (China) and Cao B\u1eb1ng, Ngh\u1ec7 An, \u0110\u00e0 N\u1eb5ng, and \u0110\u1eafk L\u1eafk provinces (Vietnam) [The genus Americas . Litsea Vietnam) ,14. TherMachilus Rumph. ex Nees is comprised of around 100 species distributed in southern and south-eastern Asia [Machilus balansae (Airy Shaw) F.N. Wei & S.C. Tang is endemic to Vietnam and is generally found at low elevations in north Vietnam [Machilus grandifolia S.K. Lee & F.N. Wei is now regarded as a new synonym of M. balansae [M. balansae or M. grandifolia.The genus ern Asia ,14. Mach Vietnam . Machilubalansae . To our Neolitsea (Benth.) Merr. Contains around 85 species distributed from Indo-Malaysia to East Asia [Neolitsea ellipsoidea K.C. Allen is a tree up to 30 m in height [The genus ast Asia ,14. Neoln height . The spePhoebe Nees [There are around 100 species in the genus ebe Nees , which rebe Nees .Phoebe angustifolia Meisn. is a small shrub found in southeastern Yunnan (China), Myanmar, India, and Vietnam [P. angustifolia from Vietnam has been reported, which showed the major components to be spathulenol (17.0%), palmitic acid (13.0%), sabinene (6.4%), bicyclogermacrene (5.9%), and artemisia triene (5.1%) [ Vietnam . In Viet Vietnam . The leae (5.1%) .The essential oil collection details and yields are summarized in B. erythrophloia, B. robusta, and B. yunnanensis are compiled in Beilschmiedia leaf essential oils were dominated by sesquiterpene hydrocarbons. A preponderance of sesquiterpene hydrocarbons has been previously seen in Beilschmiedia leaf essential oils from Malaysia [The essential oil compositions of Malaysia and fromMalaysia .B. erythrophloia essential oil were bicyclogermacrene (30.5%), (Z)-\u03b2-ocimene (26.1%), and (E)-caryophyllene (18.3%). While qualitatively similar, there are notable differences between the essential oil from Vietnam in this work and that reported by Su and Ho from Taiwan [The major components in m Taiwan ; the samB. robusta and B. yunnanensis leaf oils were rich in (E)-caryophyllene , \u03b1-humulene (13.4% and 9.9%), and bicyclogermacrene (8.6% and 8.4%). The leaf oil of B. robusta had a high concentration of germacrene D (20.3%), while B. yunnanensis oil was rich in 9-epi-(E)-caryophyllene (21.2%).Both C. concinna (from two locations), C. impressa, and C. infectoria are listed in C. impressa and C. infectoria leaf essential oils, while oxygenated sesquiterpenoids were abundant in C. concinna essential oil from Nam Dong and monoterpene hydrocarbons dominated the leaf oil of C. concinna from Pu Hoat.The leaf essential compositions of C. concinna from two different collection sites were qualitatively similar, but quantitatively different. That is, the abundant components in the Nam Dong sample were also observed in the Pu Hoat sample, and vice versa. Thus, for example, \u03b1-pinene, \u03b2-pinene, and myrcene were abundant in the Pu Hoat sample but were found in lower concentrations in the sample from Nam Dong . Conversely, the sesquiterpenoids, (E)-caryophyllene, spathulenol, and caryophyllene oxide were abundant in the sample from Nam Dong , but less concentrated in the Pu Hoat sample .The leaf essential oils of C. impressa were bicyclogermacrene (18.7%), (E)-caryophyllene (10.8%), dodecanal (10.8%), -\u03b1-farnesene (7.9%), and \u03b1-humulene (6.3%). Germacrene D (55.5%) dominated the essential oil composition of C. infectoria, which was also composed of bicyclogermacrene (11.4%) and \u03b4-elemene (5.1%) as major components. The major components of the leaf essential oil of L. viridis, M. balansae, M. grandifolia, N. ellisoidea, and P. angustifolia are compiled in The chemical compositions of the leaf essential oils of L. viridis leaf essential oil were bicyclogermacrene (25.5%), decanal (14.4%), \u03b1-pinene (11.1%), and \u03b2-pinene (8.3%). This is the first report on the essential oil from this plant.The major components in M. balansae and M. grandifolia are considered conspecific, the essential oil compositions showed pronounced differences. The leaf oil of M. balansae was dominated by bicyclogermacrene (41.5%), which was not detected in the essential oil of M. grandifolia. Likewise, the sesquiterpene alcohols (E)-nerolidol and globulol were abundant constituents in M. grandifolia , but (E)-nerolidol was much lower in M. balansae (8.7%) and globulol was not detected. The taxonomy of these two plants deserves closer scrutiny.Although N. ellipsoidea was dominated by (E)-\u03b2-ocimene (87.6%). (E)-\u03b2-Ocimene was also found to be the dominant compound (85.6%) in the leaf essential oil of N. polycarpa from Vietnam [N. sericea from Korea (13.3%) [N. variabillima from Taiwan (13.4%) [N. aciculata from Korea (9.7%) [E)-\u03b2-ocimene was only a minor component in the leaf oils of N. australiensis, N. brassii, or N. dealbata from Australia [N. pallens from India [N. foliosa leaf essential oil from India [The leaf essential oil of Vietnam , and one (13.3%) , N. vari (13.4%) , and N. a (9.7%) . In contustralia , and N. om India , and wasom India .P. angustifolia from P\u00f9 Ho\u1ea1t Nature Reserve (northern Vietnam) in this study was rich in \u03b1-pinene (26.9%), \u03b2-pinene (20.8%), spathulenol (5.4%), (E)-caryophyllene (5.3%), and p-cymene (5.0%), which differs markedly from a previous study on the leaf essential oil from Sao La Nature Reserve . The previous work reported spathulenol (17.0%), palmitic acid (13.0%), sabinene (6.4%), bicyclogermacrene (5.9%), and artemisia triene (5.1%) to be the major components [The leaf essential oil of mponents . There iThe 24-h and 48-h larvicidal activities of Lauraceae leaf essential oils from Vietnam are summarized in N. ellipsoidea showed the greatest activity against Ae. aegypti with 24-h and 48-h LC50 values of 6.59 and 4.04 \u03bcg/mL, respectively. Similar larvicidal activities were observed against Cx. quinquefasciatus (24-h and 48-h LC50 = 7.47 and 4.65 \u03bcg/mL) for this essential oil. Interestingly, although the larvicidal activities of C. infectoria leaf essential oil were not as impressive against Ae. aegypti or Ae. albopictus, the essential oil did show much better activity against Cx. quinquefasciatus (24-h LC50 = 10.8 \u03bcg/mL), particularly after 48 h of exposure (48-h LC50 = 0.402 \u03bcg/mL). Unfortunately, the limited quantities available for several of the essential oils precluded larvicidal screening. However, the larvicidal activity of the untested essential oils will be investigated in future studies.Of the Lauraceae essential oils screened for larvicidal activity, N. ellipsoidea leaf essential oil, (E)-\u03b2-ocimene (87.6%), is not likely responsible for the observed larvicidal activity. The (E)-\u03b2-ocimene-rich (94.8%) essential oil of Porophyllum ruderale showed an LC50 of 173.7 \u03bcg/mL against Ae. aegypti [Syzygium jambolana, with (Z)-\u03b2-ocimene (27.2%) and (E)-\u03b2-ocimene (12.2%), was inactive against Ae. aegypti (LC50 = 433 \u03bcg/mL) [N. ellipsoidea essential oil can likely be attributed to synergistic effects involving minor components.The major component of aegypti . Likewis3 \u03bcg/mL) . The excC. infectoria was rich in the germacrene sesquiterpenes germacrene D (55.5%) and bicyclogermacrene (11.4%), and these compounds may be responsible for the larvicidal activity. Germacrene D has demonstrated notable larvicidal activity against Ae. aegypti and Cx. quinquefasciatus [Ae. albopictus and Cx. tritaeniorhynchus [The leaf essential oil of ctively) , and bicctively) .C. concinna from Nam Dong is consistent with the marginal activities observed for the major components. (E)-Caryophyllene, caryophyllene oxide, and \u03b1-pinene have shown modest mosquito larvicidal activities [50 = 65 \u03bcg/mL against Cx. quinquefasciatus) [50 = 15.4 \u03bcg/mL against Ae. aegypti) [50 = 22.4 \u03bcg/mL against Ae. aegypti) [Tephrosia toxicaria (42.3% spathulenol) had an LC50 of 63.1 \u03bcg/mL against Ae. aegypti [Guarea sylvatica essential oil from branches (14.3% spathulenol) showed LC50 against Ae. aegypti of 274 \u03bcg/mL [The marginal larvicidal activity of tivities . \u03b2-Pinensciatus) , (LC50 =aegypti) . Spathul aegypti , while G74 \u03bcg/mL .L. viridis and N. ellipsoidea leaf essential oils demonstrated particularly notable activities against E. faecalis and B. cereus with minimum inhibitory concentration (MIC) values of 16 \u03bcg/mL. The leaf essential oil of C. impressa also showed excellent anticandidal activity against C. albicans with an MIC of 16 \u03bcg/mL.Several of the leaf essential oils of the Lauraceae were screened for antimicrobial activity . All of L. viridis leaf oil, bicyclogermacrene, has shown antibacterial activity against B. cereus [E. faecalis [L. viridis leaf essential oil, bicyclogermacrene, decanal, \u03b1-pinene, and \u03b2-pinene, can account for the observed antibacterial activity.The major component of . cereus . Likewisfaecalis as well faecalis . Similarfaecalis ,56. Decafaecalis ,58. ThusE)-\u03b2-Ocimene dominated the leaf essential oil of N. ellipsoidea, but this compound has demonstrated relatively marginal antibacterial activity [E)-\u03b2-ocimene with minor essential oil components may play a role in the antibacterial activity of N. ellipsoidea leaf oil.-caryophyllene nor \u03b1-humulene have shown strong anti-Candida albicans activity [E)-caryophyllene do not exhibit notable activity against Candida spp. [C. albicans with an MIC of 125 \u03bcg/mL [The components responsible for the anticandidal activity of activity ,56. The ida spp. ,60. Dode25 \u03bcg/mL .Leaves were collected from wild-growing trees in north-central Vietnam. Plants were identified by Do Ngoc Dai and voucher specimens have bee2 (1 mL/min), injector temperature (PTV: programmable temperature vaporization) 250 \u00b0C, detector temperature 260 \u00b0C, column temperature programmed from 60 \u00b0C (2 min hold) to 220 \u00b0C (10 min hold) at 4 \u00b0C/min. Samples were injected using a split mode with a split ratio of 10:1. The volume injected was 1.0 \u03bcL. Inlet pressure was 6.1 kPa.Gas chromatographic (GC) analysis was performed on an Agilent Technologies HP 7890A Plus Gas chromatograph equipped with a FID and fitted with HP-5ms column . The analytical conditions were: carrier gas HAn Agilent Technologies HP 7890A Plus Chromatograph fitted with a fused silica capillary HP-5ms column and interfaced with a mass spectrometer HP 5973 MSD was used for the GC/MS analysis, under the same conditions as those used for GC analysis. The conditions were the same as described above with He (1 mL/min) as carrier gas. The MS conditions were as follows: ionization voltage 70 eV; emission current 40 mA; acquisitions scan mass range of 35\u2013350 amu at a sampling rate of 1.0 scan/s. Compound identification was carried out by comparison of the MS fragmentation patterns and calculated retention indices with those available in the databases ,37 and, Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus were carried out as previously described [50 values, LC90 values, and 95% confidence limits were determined by log-probit analysis using Minitab\u00ae 19 .Larvicidal activities against escribed ; LC50 vaEnterococcus faecalis (ATCC299212), Staphylococcus aureus (ATCC25923), Bacillus cereus (ATCC14579), three strains of Gram-negative test bacteria, Escherichia coli (ATCC 25922), Pseudomonas aeruginosa (ATCC27853), Salmonella enterica (ATCC13076) and one strain of yeast, Candida albicans (ATCC 10231). Minimum inhibitory concentration (MIC) and median inhibitory concentration (IC50) values were measured by the microdilution broth susceptibility assay as previously described [The bacterial growth inhibition of the essential oils was evaluated using three strains of Gram-positive test bacteria, escribed . Neolitsea ellipsoidea, dominated by (E)-\u03b2-ocimene, showed excellent larvicidal activity against Aedes aegypti and antibacterial activity against Enterococcus faecalis and Bacillus cereus; Cryptocarya infectoria leaf essential oil, rich in germacrene D and bicyclogermacrene, showed excellent larvicidal activity on Culex quinquefasciatus and anticandidal activity against Candida albicans. The leaf essential oil of Litsea viridis, which was rich in bicyclogermacrene, also showed good antibacterial properties. The biological properties of these Lauraceae essential oils suggest that they may serve as potential \u201cgreen\u201d alternatives, as also described for Lamiaceae family plants [Of the eleven species of Lauraceae examined in this work, the leaf essential oil of y plants , for use"} +{"text": "Ribosomal protein S6 (RPS6) is the only phosphorylatable protein of the eukaryotic 40S ribosomal subunit.Ribosomes with phosphorylated RPS6 can selectively translate 5\u2019TOP--containing mRNAsthat encode most proteins of the translation apparatus. The study of translational control of 5\u2019TOP-mRNAs, which arepreferentially translated when RPS6 is phosphorylated and cease to be translated when RPS6 is de-phosphorylated,is particularly important. In Arabidopsis thaliana, AtRPS6 is phosphorylated by kinase AtRPS6K2, which should in turnbe phosphorylated by upper level kinases (AtPDK1 \u2013 at serine (S) 296, AtTOR \u2013 at threonine (T) 455 and S437) for fullactivation. We have cloned AtRPS6K2 cDNA gene and carried out in vitro mutagenesis replacing codons encodingS296, S437 and T455 by triplets of phosphomimetic glutamic acid (E). After the expression of both natural and mutatedcDNAs in Escherichia coli cells, two recombinant proteins were isolated: native AtRPS6K2 and presumably constitutivelyactive AtRPS6K2. The activity of these variants was tested in vitro. Both kinases couldphosphorylate wheat (Triticum aestivum L.) TaRPS6 as part of 40S ribosomal subunits isolated from wheat embryos,though the non-mutated variant had less activity than phosphomimetic one. The ability of recombinant non-mutatedkinase to phosphorylate TaRPS6 can be explained by its phosphorylation by bacterial kinases during the expressionand isolation steps. The phosphomimetically mutated AtRPS6K2 can serve as a tool to investigatepreferential translation of 5\u2019TOP-mRNAs in wheat germ cell-free system, in which most of 40S ribosomal subunits havephosphorylated TaRPS6. Besides, such an approach has a biotechnological application in producing genetically modifiedplants with increased biomass and productivity through stimulation of cell growth and division. Growth and division of cells depending on the availability ofnutrients, energy resources, as well as responding to internaland external stimuli are coordinated by signaling system basedon a multilevel cascade of serine-threonine protein kinases.These kinases transmit signals from internal and externalevents to the protein synthesis apparatus, causing inhibitionor enhancement of protein synthesis . The target of rapamycin (TOR) kinase \u2013is the master signaling integrator, central hub synchronizingcell growth according to the nutrient and energy status as wellas environmental influences . In mammals,TOR forms two functionally distinct protein complexes:mTORC1 containing RAPTOR (regulatory-associated proteinof mTOR), and mTORC2 containing RICTOR (rapamycininsensitivecompanion of mTOR) .In favorable conditions mTORC1 phosphorylates RPS6K. Complete activation of mammalian RPS6K byphosphorylationis dependent on another upper level PDK1kinase . The fully activated RPS6K inturn phosphorylates the S6 ribosomal protein (RPS6) .At transcriptional level, phosphorylation of pRPS6 in nucleolusleads to activation of rRNA gene promoter and ribosomogenesis. In cytosol,RPS6 phosphorylation promotes the selective translationof special group of cellular mRNAs, containing 5\u2032-terminaloligo-pyrimidine tract (5\u2032TOP) in their 5\u2032-untranslated regions(5\u2032UTRs) . The number of these5\u2032TOP-containing mRNAs, according to various estimates,ranges from one hundred to two hundred and forty . They encode almost all theproteins of the translation apparatus -binding proteins, etc.) , as well asother protein families associated with lysosome functions, metabolismand proliferation .As in yeast and animals, TOR kinase is involved in controllingplant growth and cell division . But inplants, only orthologs of genes encoding mTORC1 were found. No clear orthologs of theRICTOR have yet been found in plants . TOR proteins are highly conserved ineukaryotes. For example, in A. thaliana and Homo sapiensthey share 73 % amino acid sequence identity in the kinasedomains .Although functioning of this main regulator of cell processeshas been well studied in other eukaryotes, knowledgeof the regulation of translation and gene expression in plantsis very limited. Most studies of the regulation of cellular processby plant RPS6-kinase were performed on a model objectA. thaliana containing two very similar forms \u2013 At RPS6K1and At RPS6K2. It was shown that only At RPS6K2 is able tophosphorylate RPS6 and stimulate an increase in cell size . Forthe complete activation of At RPS6K2, it is necessary that it bephosphorylated by pPDK1 kinase (at Ser296), pTOR kinase (atThr455), as well as by one more, unknown, kinase (at Ser437).Although pTOR\u2192S6K signaling plays multiple roles intranslational control , mechanisms used byTOR kinase to impact global protein synthesis in plants are notwell understood . New data are currently appearing on the involvementof pRPS6K1 in the promotion of translation reinitiationof upstream open reading frame (uORF)-containing viral andcellular mRNAs via phosphorylation of eIF3h and in regulation of translation initiation underenergy-deficient conditions via formation of the functionaleIF4F complex . Nevertheless, the role ofplant pRPS6K2 and pRPS6 phosphorylation in translationregulation in the cytosol remains unclear .It is practically impossible to control the multiple and simultaneousphosphorylation of At RPS6K2 kinase by the kinases of theupper regulatory level for experimental purposes. Therefore, wedecided to use a different approach to achieve the phosphorylationof plant RPS6 using the mutated form of At RPS6K2,which should be stably active. We have cloned the AtRPS6K2cDNA gene and performed in vitro mutagenesis of this cDNAby replacing codons encoding serines at positions 296 and 437,as well as threonine at position 455 with triplets encoding thephosphomimetic amino acid \u2013 glutamic acid. After expressionof non-mutated and mutated cDNA gene in E. coli cells the nativeAt RPS6K2 and the phosphomimetic At RPS6K2 recombinant protein was obtained. The secondone is expected to have stable kinase activity, regardless of theupper-level kinases, that could be used as a unique tool for theartificial phosphorylation of TaRPS6 in a wheat germ cell-freetranslation system. Mutated version of cDNA gene encodingthe constantly active form of AtRPS6K2 may also be used toobtain genetically modified plants with increased productivity,earlier ripening and a higher rate of biomass accumulation.Cloning of AtRPS6K2 cDNA gene. The total RNA was isolatedfrom A. thaliana (Col-0 ecotype) leaves using Tri-reagent(Sigma). The reverse transcription reaction was performedusing Maxima Reverse Transcriptase (Thermo) and \u2018AtS6K2-rev-3UTR\u2019 primer (5\u2032-GAATTCGAGAAATAGGTTTCTTCAAACAACCGTTGATTTTG), which allowed to differentiateAt RPS6K2 from At RPS6K1 mRNAs. RT-PCR was performed in 25 \u03bcl reaction using Phusion High-fidelity DNApolymerase(Thermo), 0.2 pM primers \u2018Nde-AtS6K2-for\u2019(5\u2032- GGGCGAATTGGGTCATATGGTTTCTTCTCAGTG)and \u2018AtS6K2-Xho-rev\u2019 (5\u2032-AAACTCGAGCTACAAGTTGGATGTGGTCCGATGA) and 2.5 \u03bcl of RT-reaction mixture.Temperature regime: stage 1\u20135 min at 94 \u00b0C, 1 cycle; stage2\u201310 s at 98 \u00b0C, 20 s at 49 \u00b0C, 45 s at 72 \u00b0\u0421, 4 cycles; stage3\u201310 s at 98 \u00b0C, 20 s at 52 \u00b0C, 45 s at 72 \u00b0\u0421, 30 cycles; stage4\u20135 min at 72 \u00b0C, 1 cycle. The PCR product (~1425 bp)was digested with NdeI/XhoI and cloned into pET19b vectordigested with the same enzymes resulting \u2018Pet19b-His-At RPS6K2\u2019 plasmid.Mutagenesis. In vitro mutagenesis was performed in threesteps using QuikChange II Site-Directed Mutagenesis Kit(Agilent technologies) according to the manufacturer\u2019s protocol.At the first step \u2018Pet19b-His-AtRPS6K2\u2019 plasmid wasamplified entirely using Pfu Ultra High-Fidelity DNA polymerase(Thermo) and complementary primers: \u2018S296-Glu-dir\u2019(5\u2032-AAACACAAGATCAAACGAAATGTGTGGGACTACGGA) and \u2018S296-Glu-rev\u2019 (5\u2032-TCCGTAGTCCCACACATTTCGTTTGATCTTGTGTTT) containing correspondingnucleotide substitutions. Temperature regime: stage 1\u201330 s at95 \u00b0C, 1 cycle; stage 2\u201330 s at 95 \u00b0C, 1 min at 55 \u00b0C, 7 min30 s at 68 \u00b0C, 18 cycles. The reaction mixture was furthertreated with restriction enzyme DpnI, which cleaves methylatedDNA into fragments at 5\u2032-Gm6ATC-3\u2032 sequences. Sincethe original plasmid was methylated (dam+ E. coli strain DH5was used for plasmid enrichment), the restriction enzymeDpnI had cleaved the original non-mutated plasmid, whereas\u2018Pet19b-His-AtRPS6K2(S296E)\u2019 plasmid synthesized duringPCR-step remained intact. Subsequently, the competent E. colicells (XL1-Blue strain) were transformed with the reactionmixture. Another two mutagenesis steps for the production of\u2018Pet19b-His-At RPS6K2\u2019 and \u2018Pet19b-His-At RPS6K2\u2019 plasmids were done inthe same manner using \u2018S437-Glu-dir\u2019 (5\u2032-ACATGTCTGTTTTGGATGAACCAGCAAGTAGTCCCA)/\u2018S437-Glu-rev\u2019(5\u2032-TGGGACTACTTGCTGGTTCATCCAAAACAGACATGT) or \u2018T455-Glu-dir\u2019 (5\u2032-ACCCTTTTACAAACTTCGAATACGTCAGGCCTCCTCA)/\u2018T455-Glu-rev\u2019 (5\u2032-TGAGGAGGCCTGACGTATTCGAAGTTTGTAAAAGGGT)primers respectively. Resulting DNA-constructs were usedas templates for the next in vitro mutagenesis step. The insertscloned into the recombinant plasmids were sequencedfrom both ends by the dideoxy chain termination methodusing Big Dye Terminator v.3.1 sequencing kit (Thermo) onthe 310 genetic analyzer (Applied Biosystems) according tomanufacturer\u2019s recommendations.Expression and purification of recombinant proteins.E. coli strain BL21(DE3) cells transformed with recombinant\u2018Pet19b-His-AtRPS6K2\u2019 or \u2018Pet19b-His-At RPS6K2\u2019 plasmid were grown in 100 ml of LB mediumcontaining ampicillin (100 \u03bcg/ml) at 30 \u00b0C to A600of 0.5 unit. The expression of recombinant proteins wasinduced by 0.8 mM isopropyl \u03b2-D-1-thiogalactopyranoside(IPTG) at 30 \u00b0C for 4 h. Cells were collected by centrifugation,resuspended in His-buffer containing 10 mM imidazole, and then lysedby addition of lysozyme (1 mg/ml) and sonication. The celldebris was removed by centrifugation at 10000 g for 20 min at 4 \u00b0C. Supernatant was combined with PerfectPro Ni\u2013NTAresin suspension (5-Prime), shaken at 4 \u00b0C for 1 h followedby flow throw in column. The resin was washed twice byHis-buffer containing 20 mM imidazole at 4 \u00b0C. His-taggedproteins bound to the resin were eluted with His-buffer containing250 mM imidazole and dialyzed against dialysis buffer2, pH 7.6) at4 \u00b0C for 12 h. Dialyzed proteins were concentrated by centrifugationin 10,000 MWCO HY columns (Sartorius) accordingto the manufacturer\u2019s instructions. Protein concentration wasestimated by the Bradford protein assay .Gel-electrophoresis. Proteins were separated by standardSDS-PAGE in Tris-Glycine gel system according toU.K. Laemmli (1970). After electrophoresis, the gels werefixed and stained in PageBlue Protein Staining Solution(Thermo) or subjected to semi-dry blotting in transfer buffer ethanol) for1 h at 0.8 mA/cm2 and 20 V using 0.22 \u03bcm pore NitroBindnitrocellulose membranes (GVS).Western blotting. For immunodetection of His-At RPS6K2and His-At RPS6K2 proteins, the blotswere first \u2018blocked\u2019 by submerging them in blocking solution Tween 20, pH 7.5) containing 5 % skim milk) for 1 h at25 \u00b0C with gentle shaking. The blots were then incubated withPenta-His mouse antibodies (5 Prime) diluted in theblocking solution for 1 h at 25 \u00b0C, thoroughly washed threetimes with TBST buffer, and incubated for 1 h at 25 \u00b0C withhorseradish peroxidase-conjugated goat anti-mouse antibodies(Santa Cruz) diluted in blocking solution. Afterdouble washes in TBST and double washes in TBS, the blotswere chemiluminescence developed using ChemiluminescentPeroxidase Substrate-3 detection reagents (Sigma). Animage of the membrane was then produced on X-ray film.Monoclonal Anti-Phosphoserine Mouse Antibodies (Sigma)and Monoclonal Anti-Phosphothreonine Mouse Antibodies(Sigma) were used as 1st antibodies (at 1:300 dilution in TBSTcontaining 5 % BSA) for the detection of phosphorylationstatus of proteins.260 unit corresponds to 50 pmolof 40S subunits.40S ribosomal subunits isolation. 40S ribosomal subunitswere isolated from wheat embryos, purified from endosperm, as described previouslyfor ribosomal subunits isolation from human placenta with the ratio of buffer to embryos of6:1. It was considered that 1 AKinase assay. The reaction mixture in 20 \u03bcl contained20 mM TrisAc (pH 7.6), 90 mM KAc, 2.5 mM Mg(OAc)2,1 mM DTT, 10 pmol of 40S ribosomal subunits, 0.1 mM ATP.Purified His-At RPS6K2 or His-At RPS6K2 were added in amount of 2.5 ng/\u03bcl. The mixtures wereincubated for 20 min at 26 \u00b0C.Cloning and mutagenesis of AtRPS6K2 cDNA gene. A totalRNA preparation was isolated from A. thaliana, and reversetranscription was performed using \u2018AtS6K2-rev-3UTR\u2019primer, complementary to 3\u00b4UTR of AtRPS6K2 mRNA, butnot AtRPS6K1 mRNA, allowing to discriminate between them. Then, AtRPS6K2 cDNA was amplified by RT-PCR andcloned into pET19b vector. According to sequencing analysis,AtRPS6K2 cDNA corresponded to #AT3G08720 (GeneBank)sequence.Thus obtained \u2018Pet19b-His-AtRPS6K2\u2019 plasmid was mutatedin vitro in three steps to introduce three phosphomimeticmutations into AtRPS6K2 cDNA. At the first step, theTCC triplet encoding serine at position 296 was replaced bythe GAA triplet, which encodes glutamic acid that imitatesphosphorylated serine. In a second step, the TCT tripletof obtained mutated AtRPS6K2(S296E) cDNA encodingserine at position 437 was mutated to GAA triplet to formAtRPS6K2 cDNA. In the third step, the ACAtriplet of AtRPS6K2 cDNA encoding threonineat position 455 was replaced by the GAA triplet to form themutated AtRPS6K2 cDNA.Expression and purification of recombinant kinases.AtRPS6K2 and AtRPS6K2 cDNAgenes were expressed in E. coli cells, then recombinant Histaggedproteins respectively) were isolated using immobilizedmetal ion affinity chromatography (IMAC) followed by immunoblottinganalysis .Isolated proteins were purified by dialysis and concentrated.Preparations isolated under native conditions contained acertain amount of impurity polypeptides. Content of recombinantproteins in preparations was corrected according todensitometric analysis data (by ImageJ 1.42). The yield ofpurified and concentrated full-length recombinant proteins His-AtRPS6K2 and His-At RPS6K2was 5.22 mg and 4.52 mg per L of media respectively.Testing the activity of recombinant kinases. Both forms ofkinase (the intact one and that carrying three phosphomimeticsubstitutions) were tested for their ability to phosphorylateTaRPS6 in the composition of 40S ribosomal subunits isolatedfrom wheat embryos. The phosphorylation state of proteinswas tested using monoclonal antibodies against phosphoserine.As can be seen from the data presented in Fig. 2, bothkinases are able to phosphorylate the plant ribosomal proteinS6 (TaRPS6) in composition of 40S ribosomal subunits,although activity of His-At RPS6K2is obviously higher than that of non-mutated His-At RPS6K2. In wheat germ, there are at least two forms of the S6ribosomal protein (A and B); therefore, two bands are observed.Initially, we expected that non-mutated kinase should haveno activity since for its activation in plant cells phosphorylationat three sites is required by upper-level kinases. Thephosphorylation state of purified recombinant kinases waschecked using monoclonal antibodies against phosphoserineand phosphothreonine .As can be seen from the data presented in Fig. 3, thenon-mutated recombinant His-At RPS6K2 kinase producedin E. coli cells was phosphorylated both at serine residues and threonine residues . Thus, some bacterial kinases were able to phosphorylate His-At RPS6K2 protein resulting in its activation.It should be noted that certain non-mutated serine residuesof mutated His-At RPS6K2 recombinantkinase were also phosphorylated ,althoughthis kinase was not phosphorylated at threonineresidues .The interest in studying the mechanisms of TOR-mediatedregulation of mRNA translation in plants is high because othermechanisms of regulation of protein biosynthesis, which arewell described for mammals and yeast, either do not work orfunction within very narrow limits in plants. Indeed, in plantcells eIF4E binding proteins (eIF4E-BPs) were not found, andthere are no genes for these proteins in plant genome . The mechanism of translation suppressionby phosphorylation of peEF2 is not realized in plants. Then,out of four protein-kinases thatphosphorylate \u03b1-subunit of meIF2 in mammalian cells, onlypGCN2-kinase was detected in plants, that can be activatedunder several but not all stresses. Moreover, it was shown,that factor eIF2B is not necessary for cyclic functioning ofplant peIF2 , and neither its biochemicalactivity nor peIF2B-like factor orthologs were detected inplants till now . These circumstancesmake the TOR system one of the few currently known effectiveregulators of protein biosynthesis in plants.Having obtained the constitutively active protein kinaseAt RPS6K2 with phosphomimeticsubstitutions of key amino acids, we acquire a convenienttool that allows to considerably increase phosphorylationof TaRPS6 in the composition of 40S ribosomal subunits in wheat germ cell-free system. This allows studying importantmechanisms of preferential translation of a specific groupof cellular 5\u2032TOP-containing mRNAs, which is preferablytranslated when pRPS6 is phosphorylated and ceases to betranslated when RPS6 is de-phosphorylated . In addition to fundamental interest the use of cDNA encodingconstitutively active RPS6-protein kinase would opennovel routes for increasing crop yield through stimulation ofribosomogenesis and subsequent growth and division of plantcells. It is known that augmented expression of the At TORgene results in a dose-dependent decrease or increase, in organand cell size, seed production . In addition to regulating theprotein synthesis process, TOR acts as a master regulator ofthe cell cycle, coordinator of rRNA transcription, activation ofribosomal protein genes, ribosome assembly and may also regulate long non-coding RNAs (lncRNAs)expression . Therefore, artificial increasingof TOR gene expression in plant cells can lead to seriousundesirable consequences while using of AtRPS6K2 cDNA may help to avoid these complications.We have cloned the AtRPS6K2 cDNA gene encoding kinase 2of ribosomal protein S6 from A. thaliana and performed itsmutagenesis to obtain the AtRPS6K2kinase containing phosphomimetic substitutions. Such mutatedenzyme with constant RPS6-kinase activity may be usedto study specific molecular mechanisms mediating efficienttranslation of 5\u2032TOP-mRNAs depending on phosphorylationof RPS6 in plant cells. At the same time, the cDNA geneAtRPS6K2 may be used to obtaingenetically modified plants with increased productivity andearlier ripening.The authors declare no conflict of interest.Bakshi A., Moin M., Madhav M.S., Kirti P.B. Target of rapamycin, amaster regulator of multiple signalling pathways and a potential candidategene for crop improvement. Plant Biol. (Stuttg.). 2019;21(2):190-205. DOI 10.1111/plb.12935.Bradford M.M. A rapid and sensitive method for the quantitation ofmicrogram quantities of protein utilizing the principle of proteindyebinding. Anal. Biochem. 1976;7(72):248-254. DOI 10.1006/abio.1976.9999.Caldana C., Martins M.C.M., Mubeen U., Urrea-Castellanos R. Themagic \u2018hammer\u2019 of TOR: the multiple faces of a single pathway inthe metabolic regulation of plant growth and development. J. Exp.Bot. 2019;70:2217-2225. DOI 10.1093/jxb/ery459.Deprost D., Yao L., Sormani R., Moreau M., Leterreux G., Nicolai M.,Bedu M., Robaglia Ch., Meyer Ch. The Arabidopsis TOR kinaselinks plant growth, yield, stress resistance and mRNA translation.EMBO Rep. 2007;8(9):864-870. DOI 10.1038/sj.embor.7401043.Enganti R., Cho S.K., Toperzer J.D., Urquidi-Camacho R.A., CakirO.S., Ray A.P., Abraham P.E., Hettich R.L., von Arnim A.G.Phosphorylation of ribosomal protein RPS6 integrates light signalsand circadian clock signals. Front. Plant Sci. 2017;8(2210). DOI10.3389/fpls.2017.02210.Henriques R., B\u00f6gre L., Horv\u00e1th B., Magyar Z. Balancing act: matchinggrowth with environment by the TOR signalling pathway. J. Exp.Bot. 2014;65(10):2691-2701. DOI 10.1093/jxb/eru04.Immanuel T.M., Greenwood D.R., MacDiarmid R.M. A critical reviewof translation initiation factor eIF2\u03b1 kinases in plants \u2013 regulating protein synthesis during stress. Funct. Plant Biol. 2012;39:717-735.DOI 10.1071/FP12116.Kim Y.K., Kim S., Shin Y.J., Hur Y.S., Kim W.Y., Lee M.S., Cheon C.I.,Verma D.P. Ribosomal protein S6, a target of rapamycin, is involvedin the regulation of rRNA genes by possible epigenetic changes inArabidopsis. J. Biol. Chem. 2014;289:3901-3912. DOI 10.1074/jbc.M113.515015.Laemmli U.K. Cleavage of structural proteins during the assemblyof the head of bacteriophage T4. Nature. 1970;227:680-685. DOI10.1038/227680a0.Lee D.H., Park S.J., Ahn C.S., Pai H.S. MRF family genes are involvedin translation control, especially under energy-deficient conditions,and their expression and functions are modulated by the TOR signalingpathway. Plant Cell. 2017;29:2895-2920. DOI 10.1105/tpc.17.00563.Matasova N.B., Myltseva S.V., Zenkova M.A., Graifer D.M., VladimirovS.N., Karpova G.G. Isolation of ribosomal subunits containingintact rRNA from human placenta. Estimation of functionalactivity of 80S ribosomes. Anal. Biochem. 1991;198:219-223. DOI10.1016/0003-2697(91)90416-q.Meyuhas O., Kahan T. The race to decipher the top secrets of TOPmRNAs. Biochim. Biophys. Acta. 2015;1849:801-811. DOI10.1016/j.bbagrm.2014.08.015.Otterhag L., Gustavsson N., Alsterfjord M., Pical C., Lehrach H., GobomJ., Sommarin M. Arabidopsis PDK1: identification of sites importantfor activity and downstream phosphorylation of S6 kinase.Biochimie. 2006;88:11-21. DOI 10.1016/j.biochi.2005.07.005.Ren M., Qiu S., Venglat P., Xiang D., Feng L., Selvaraj G., Datla R.Target of rapamycin regulates development and ribosomal RNA expressionthrough kinase domain in Arabidopsis. Plant Physiol. 2011;155:1367-1382. DOI 10.1104/pp.110.169045.Rexin D., Meyer C., Robaglia C., Veit B. TOR signalling in plants.Biochem. J. 2015;470:1-14. DOI 10.1042/BJ20150505.Roustan V., Jain A., Teige M., Ebersberger I., Weckwerth W. An evolutionaryperspective of AMPK-TOR signaling in the three domains oflife. J. Exp. Bot. 2016;67(13):3897-3907. DOI 10.1093/jxb/erw211.JXB. 2016.Ryabova L.A., Robaglia Ch., Meyer Ch. Target of rapamycin kinase:central regulatory hub for plant growth and metabolism. J. Exp. Bot.2019;70(8):2211-2216. DOI 10.1093/jxb/erz108.Schepetilnikov M., Dimitrova M., Mancera-Mart\u00ednez E., Geldreich A.,Keller M., Ryabova L.A. TOR and S6K1 promote translation reinitiationof uORF-containing mRNAs via phosphorylation of eIF3h.EMBO J. 2013;32:1087-1102. DOI 10.1038/emboj.2013.61.Shaikhin S.M., Smailov S.K., Lee A.V., Kozhanov E.V., Iskakov B.K.Interaction of wheat germ translation initiation factor 2 with GDPand GTP. Biochimie. 1992;74:447-454. DOI 10.1016/0300-9084(92)90085-s.Shi L., Wu Y., Sheen J. TOR signaling in plants: conservation and innovation.Development. 2018;145(13). DOI 10.1242/dev.160887.Song Y., Li L., Yang Zh., Zhao G., Zhang X., Wang L., Zheng L.,Zhuo F., Yin H., Ge X., Zhang Ch., Yang Z., Ren M., Li F. Targetof rapamycin (TOR) regulates the expression of IncRNAs in responseto abiotic stresses in cotton. Front. Genet. 2019;9(690). DOI10.3389/fgene.2018.00690.Turck F., Kozma S.C., Thomas G., Nagy F. A heat-sensitive Arabidopsisthaliana kinase substitutes for human p70s6k function in vivo.Mol. Cel. Biol. 1998;18:2038-2044. DOI 10.1128/mcb.18.4.2038.Turck F., Zilbermann F., Kozma S.C., Thomas G., Nagy F. Phytohormonesparticipate in an S6 kinase signal transduction pathway inArabidopsis. Plant Physiol. 2004;134:1527-1535. DOI 10.1104/pp.103.035873.Werth E.G., McConnell E.W., Couso Lianez I., Perrine Z., Crespo J.L.,Umen J.G., Hicks L.M. Investigating the effect of target of rapamycinkinase inhibition on the Chlamydomonas reinhardtii phosphoproteome:from known homologs to new targets. New Phytol. 2019;221:247-260. DOI 10.1111/nph.15339.Williams A.J., Werner-Fraczek J., Chang I.-F., Bailey-Serres J. Regulatedphosphorylation of 40S ribosomal protein S6 in root tips ofmaize. Plant Physiol. 2003;132:2086-2097. DOI 10.1104/pp.103.022749.Wolters H., J\u00fcrgens G. Survival of the flexible: hormonal growth controland adaptation in plant development. Nat. Rev. Genet. 2009;10:305-317. DOI 10.1038/nrg2558.Wu Y., Shi L., Li L., Fu L., Liu Y., Xiong Y., Sheen J. Integration ofnutrient, energy, light, and hormone signalling via TOR in plants.J. Exp. Bot. 2019;70(8):2227-2238. DOI 10.1093/jxb/erz028.Xiong Y., Sheen J. Novel links in the plant TOR kinase signaling network.Curr. Opin. Plant Biol. 2015;28:83-91. DOI 10.1016/j.pbi.2015.09.006."} +{"text": "New cultivars adapted to major durum wheat growing environments are essential for the cultivationof this crop. The development of new cultivars has required the availability of diverse genetic material and theirextensive field trials. In this work, a collection of tetraploid wheat consisting of 85 accessions was tested in thefield conditions of Almaty region during 2018 and 2019. The accessions were ranged according to nine agronomictraits studied, and accessions with the highest yield performance for Almaty region of Kazakhstan were revealed.The ANOVA suggested that the performance of agronomic traits were influenced both by Environment and Genotype.Also, the collection was analyzed using seven SSR (simple sequence repeats) markers. From 3 to 6 alleles perlocus were revealed, with an average of 4.6, while the effective number of alleles was 2.8. Nei\u2019s genetic diversitywas in the range of 0.45\u20130.69. The results showed high values of polymorphism index content (PIC) in the rangeof 0.46\u20130.70, with an average of 0.62, suggesting that 6 out of 7 SSRs were highly informative (PIC > 0.5). Phylogeneticanalysis of the collection has allowed the separation of accessions into six clusters. The local accessions werepresented in all six clusters with the majority of them grouped in the first three clusters designated as A, B, and C,respectively. The relations between SSR markers and agronomic traits in the collection were studied. The resultscan be efficiently used for the enhancement of local breeding projects for the improvement of yield productivityin durum wheat. Othertetraploid wheat species Triticum turgidum L. ssp. turanicum(Jakubz.) \u00c1. L\u00f6ve & D. L\u00f6ve, Triticum turgidum L. ssp. polonicum(L.) Thell., Triticum turgidum L. ssp. carthlicum(Nevski) \u00c1. L\u00f6ve & D. L\u00f6ve, Triticum turgidum ssp. dicoc-cum(Shrank ex Sch\u00fcbler) Thell. are used as food and feedcrops in different world regions. Wild species Triticum turgidumssp. dicoccoides (Korn. ex Asch. & Graebn.) Thell. isalso often included in crossing schemes as a source for resistanceto abiotic and biotic stresses .Durum wheat (Triticum turgidum L. ssp. turgidum convar. durum(Desf.) MacKey) is a tetraploid species of wheat and is themain crop to producers of pasta and cereals. The growing areaunder durum wheat is about 17 million hectares in the worldand production is 37 million tons . In 2019, durum wheat production in Kazakhstanamounted to 560 thousand tons . Hence, the comprehensive study ofthe diverse germplasm is a very important prerequisite forthe successful conservation and rational use of plant geneticresources, including both wild and cultivated tetraploid wheatspecies . Theappropriate assessment of the genetic diversity in these collectionsdepends on the application of informative and efficienttypes of DNA markers. In many centers of the world,research is underway to find and use different types of DNAmarkers with the aim of using them to study genetic diversity,inventory, genotyping, mapping, and identifying genesassociated with useful traits of cultivated plant varieties andlines . Various types of DNA markershave been developed and are successfully used to study thegenetic diversity of accessions of the genus Triticum L. . PCR-basedmarkers,such as RAPD, AFLP, and SSR, are widely used toolsfor studying genetic diversity and discrimination both durumand common wheat .The wheat genome contains a class of specific nucleotide sequencescalled microsatellites, also known as SSRs or simplesequences repeats . SSR markers havemany advantages, being highly polymorphic, codominant,informative, reliable, and the availability of information onchromosomal localization . Microsatellites are hypervariable, they often havedozensof alleles at one locus, differing from each other inthe number of repeats. They are widely used to study geneticdiversity, as well as for the analysis of paternity and mappingof quantitative trait loci (QTLs), kinship, belonging to aspecific population, for studying hybridization, evolutionaryprocesses, and for searching for paralogs .Durum wheat polymorphism studies are currently underwayworldwide. The survey of reports demonstrated the successfuluse of SSR markers for assessment of the genetic diversityin different collections of Europe , Africa , China , Russia, Turkey ,Syria , etc. Microsatellites are also highlyeffective in tagging specific genes that play an important rolein variation for yield components and biotic stress resistance.A number of studies reported relations between SSR lociand wheat traits, such as yield, etc. For instance, Zhang etal. (2013) showed that the Xgwm11-1B locus is significant( p < 0.001) for plant height. In the study reported by Li etal. (2015) it was shown that the marker Xgwm148-2B is associatedwith the manifestations of the traits \u201cthousand grainweight\u201d, \u201cspike yield index\u201d and \u201cweight of kernels perspike\u201d. Xgwm251 was associated with lipoxygenase (LOX)activity, which is an important factor determining the colorof flour and end-use products of wheat .Vinod et al. (2014) have identified the significant associationbetween Xgwm234 and the resistance of T. turgidum to leafrust. Golabadi et al. (2011) showed that the Xcfa2114-6Amarker was responsible for 20 % of the phenotypic variationin the yield index and thousand grain weights (TGW) underdifferent environmental conditions. SSR marker Xgwm219was also shown to be associated with TGW . These examples suggest that the assessment of thegenetic diversity of the varietal gene pool of durum wheatmay provide not only proper genetic documentation of theaccessions but also hinting the identification of a valuablesource of genes associated with agronomic traits.The purpose of this work was the study the genetic diversityusing seven SSR markers and phenotypic variation in yieldcomponents in the collection of tetraploid species harvestedin the conditions of South-East Kazakhstan.1. Seeds were provided bythe Research Center for Grain and Industrial Crops , University of Bologna , Aktobe andKarabalyk Agricultural Experimental Stations (Kazakhstan).The collection included 21 cultivars and 15 promising linesof durum wheat from Kazakhstan (see Suppl. Table 1).Plant material and experimental site conditions. The plantmaterial consisted of 85 accessions of tetraploid wheat (2 Triticumturgidum ssp. dicoccoides (Korn. ex Asch. & Graebn.)Thell., 2 Triticum turgidum ssp. dicoccum (Shrank ex Sch\u00fcbler)Thell., 65 Triticum turgidum L. ssp. turgidum convar. durum(Desf.) MacKey, 10 Triticum turgidum L. ssp. turanicum(Jakubz.) \u00c1. L\u00f6ve & D. L\u00f6ve, 4 Triticum turgidum L. ssp. polonicum(L.) Thell., and 2 Triticum turgidum L. ssp. carthlicum(Nevski) \u00c1. L\u00f6ve & D. L\u00f6ve from different geographicalorigins (Supplementary Table 1)1 Supplementary Tables 1 & 2 are available in the online version of the paper:http://www.bionet.nsc.ru/vogis/download/pict-2020-24/appx9.pdfThe studied collection of tetraploid wheat was evaluated intwo randomized replicates in the field conditions of Almatyregion (Table 1).Each accession was planted in two rows with a row spacingof 15 cm, 25 seeds per row. In total, nine agronomic traits connected with the vegetation period, plant morphology, and yieldcomponents were studied. The list of traits included the headingtime , flowering time , seed maturationtime , plant height , spike length , number of fertile spikes , number of kernelsper spike , thousand kernel weight , andyield per plant .DNA extraction and SSR genotyping. Genomic DNAwas isolated from individual 4-day-old wheat seedlings, accordingto Dellaporta et al. (1983). The quality and quantityof isolated DNA were evaluated using a NanoDrop 2000 and agarose electrophoresisin 1 % gel. The list of markers used for SSR analysis wasthe following: Xgwm11, Xgwm148, Xgwm251, Xgwm234,Xcfa2114, Xgwm169, and Xgwm219 (Supplementary Table 2).Polymerase chain reaction (PCR) was conducted in a Veriti\u2122Thermal Cycler . The PCRreaction mixture (10 \u03bcl) contained from 2.5 mM of 10\u00d7 Taqbuffer; 0.2 mM of each dNTP; 1.5 mM MgCl2; 250 \u03bcM ofeach primer; 1 unit Taq polymerase and50 ng of genomic DNA.The amplification program included the following cycles:94 \u00b0C \u2013 3 min; 40 cycles: 94 \u00b0C \u2013 1 min; annealing temperature(55 or 60 \u00b0C depending on the primer) \u2013 1 min; 72 \u00b0C \u20132 min; and 72 \u00b0C \u2013 10 min. PCR products were separated on6 % polyacrylamide gels run in 0.5\u00d7TBE buffer pH 8.0 at 250 V for 1.5 h. Gels were stained withethidium bromide, and the images were recorded with a Bio-Rad Image System . Allele sizes wereestimated in comparison with 100 bp DNA ladder .http://software.dell.com/products/statistica).Statistical analyses of field data were estimated usingSPSS 22.0 and STATISTIKA 13.2 software . Thevalues of the PIC index (polymorphism information content)suggested the effectiveness of the markers used, giventhat markers with a value of PIC > 0.5 considered as highlyinformative; 0.5 > PIC > 0.25 as informative; and PIC \u2264 0.25as marginally informative . Variationamong populations was studied using Principal CoordinateAnalysis (PCoA) in the software GenAlex, ver.6.5 . The resulting similarity matrix was furtheranalyzed using the neighbor-joining clustering algorithm forthe construction of the dendrogram. The phylogenetic treewas constructed using PAST v.3.25 software . Analyses of marker-trait associations were conductedusing a simple t-test .Phenotypic variation in the studied collectionField trials for two years revealed a sharp difference inthe vegetationperiod between species of tetraploid wheat(Table 2).All accessions reached the ripening stage, with an exceptfor the wild accession PI346783 .The shortest HT was observed in genotypes of T. dicoccoides(56.5 \u00b1 3.5 days), the longest \u2013 in T. polonicum(60.7 \u00b1 3.9 days) (see Table 2).Plant height is one of the important morphological traitsof the crops. According to the species, the highest ones werethe samples from T. carthlicum (117.9 \u00b1 5.4 cm), while theaccessions from T. dicoccum were the lowest (97.4 \u00b1 7.4 cm).On the other hand for T. durum genotypes the PH rangedfrom 58.0 \u00b1 3.7 cm to 137.6 \u00b1 3.0 cm for cultivarKargala 66 (see Suppl. Table 1). As for the SL, the lowestvalue (5.0 \u00b1 0.2 cm) had the cultivar PI 184526 , while the highest value (17.5 \u00b1 1.7 cm) wasin accession PI 210845 (T. polonicum from Iran).The value of a cultivar is determined by its productivity,which consists of several components, including TKW whichis significantly affected by weather conditions, violation ofmoisture supply, and mineral nutrition of plants during theformation and maturation of grain. The highest averagedTKW values were revealed for three T. turanicum accessions and T. polonicumfrom Iraq (PI 208911 \u2013 61.8 \u00b1 4.5 g). The lowestTKW value was in accessions of T. carthlicum (29.9 \u00b1 1.1 g).The NFS ranged from 3.9 \u00b1 0.6 pcs/plant in the accessionPI 343446 (T. dicoccoides) to 2.0 \u00b1 0.5 pcs/plant in genotypesPI 210845 and PI 266846 of T. polonicum.As for NKS and YPP the highest value were on accessionsof T. durum and the lowest to T. dicoccoides (see Table 2). Themin value of NKS (24.8 \u00b1 3.8 pcs) under both conditions wasobtained in PI 343446 , the max \u2013 inKazakh cultivar Gordeiforme 254 (67.7 \u00b1 7.1 pcs) and Canadiancultivar Strongfield (62.2 \u00b1 1.2). Overall 31 T. durumaccessions prevailed the local check cultivar Gordeiforme 254(4.4 \u00b1 1.6 g/plant) by YPP. Top twenty accessions by yieldcontained cultivars from Canada (Strongfield \u2013 7.6 \u00b1 1.9 g/plant), Spain (Granizo \u2013 7.0 \u00b1 1.9 g/plant), Italy (Capeiti-8and Ancomarzio), Syria (Sharm5), Russia , Ukraine (Har\u2019kovskaya 90 andHar\u2019kovskaya 9), USA (LO92), as well as 5 cultivars and4 breeding lines (e. g. G 2607 \u2013 7.2 \u00b1 1.4 g/plant), from Kazakhstan(see Suppl. Table 1).The Pearson index analysis revealed a significant positivecorrelation ( p < 0.01) between yield components and phenotypictraits. The ANOVA test based on two-years field trialssuggested that Genotype significantly influenced the SMT,NFS, SL, and all yield components with p < 0.001 (Table 3).Microsatellite analysis of the tetraploid wheat collectionThe lines and cultivars of the studied tetraploid wheat collectionwere analyzed using 7 polymorphic microsatellite markers(see Suppl. Table 2) localized on 6 wheat chromosomes \u2013 1B,2B, 4B, 5B, 6A, 6B. The results based on using 7 SSR markershave allowed identifying a total of 32 alleles, with average4.57 alleles per marker (Table 4).The effective number of alleles ranged from 1.82 to 3.27,with a mean value of 2.77. Nei\u2019s genetic diversity index averaged0.62 (see Table 4). The average value of polymorphisminformation content (PIC) was 0.62, ranging from 0.46 forXgwm219 to 0.7 for Xgwm148, Xgwm251, and Xgwm11,respectively.The PCoA was conducted based on SSR genotyping of85 tetraploid wheat accessions using 7 SSR markers. Accessionsof the studied collection were divided into groupsdepending on their attribution to species and place of origin,respectively .The first principal component in the PCoA (46.31 %) clearlyseparated T. polonicum and T. turanicum from other species. The most genetically distant from other specieswas T. carthlicum. PCoA using origin data revealed that localgenotypes were genetically closer to the North American accessions. The accessions from Russia and NorthAfrica were genetically distant from other groups of origin.Based on the genetic diversity results using 7 polymorphicSSR markers, a phylogenetic tree of 85 accessions of tetraploidwheat was constructed .The analysis revealed a division into two large clusters. Thefirst cluster consisted mostly of cultivars of tetraploid wheatfrom Kazakhstan and North America. The second cluster wasdivided into three sub-clusters. Although the European accessionswere dominated in all three subclusters of cluster 2, allthree sub-clusters included cultivars and lines of Kazakhstan.The t-test was performed to confirm the significance of theSSR markers for the studied traits. The results identified themost informative SSR markers related to major agronomictraits (Table 5). Xgwm251 showed a significant relationshipto HT and FT. Four markers were related to variance in PH.DiscussionInitially, the studied collection was separated according totheir species classification and origin (see Suppl. Table 1).The average yield analysis in the collection of tetraploid accessionsover two years (2018 and 2019) suggested that it ishighly correlated with all studied phenotypic traits ( p < 0.01), confirming the importance of selected characters in the trials.The two-way ANOVA showed that Environment greatly influencedHT and SMT. In addition, it was found that SMT isalso influenced by Genotype, showing the prospects of possibilityto adjust maturation time in the breeding process, asearly seed maturation is vital to avoid abiotic stresses duringthe important stages of plant growth. Particularly, it was shownthat in T. polonicum the seeds are ripening nearly five daysearlier than in T. durum (see Table 2). The field trials haveallowed the identification of accessions with outstanding fieldperformances. For instance, the cultivar Strongfield (Canada)showed 7.6 \u00b1 1.9 g/plant, which was the highest yield valueamong 31 T. durum accessions that prevailed local standardGordeiforme 254 (4.4 \u00b1 1.6 g/plant). In general, two-wayANOVA indicated the great influence of the environmentalfactors, as they were affected both adaptation-related traits,such as HT and SMT, and yield components, such as SL andNKS (see Table 3).The entire collection was studied using seven SSR markersthat were located on six different chromosomes (see Suppl.Table 2). According to the previous works, a list of markers inthis study was most useful to evaluation of genetic diversityand associations with agronomic traits of durum wheat . The average PIC value was higher than 0.6,suggesting that the level of polymorphism was very high.The high level of variation in the collection has effectivelyallowed the separation of accessions according to their speciesclassification . Notably, the PC1 (46.3 %)separated T. polonicum and T. turanicum from the remainingspecies, and the PC1 (34.1 %) distinguished T. carthlicum andT. durum from T. dicoccum and T. dicoccoides. Interestingly,the accessions originated in Kazakhstan were geneticallyclose to North American samples , and it is tosome extent confirm the phylogeny of hexaploid bread wheatstudies using SNP (single nucleotide polymorphism) markers. The PC plot is suggesting that sixaccessions of durum wheat from the Russian Federation aredistinctly different from accessions with other origins . The Neighbor-joining phylogenetic tree suggestedthat all accessions can be divided into two clusters, wherecluster 1 was mostly populated by accessions from Kazakhstan.The significance of each SSR marker for studied traits wasassessed using a two-tailed t-test . The results of the test suggested that five out ofseven SSRs were significant at least for one studied trait (seeTable 5). The PH was the trait where four SSR markers, twowith negative and two with positive values, were significantlycorrelated. In addition, the test showed that Xgwm234 is significantlycorrelated with TKW and Xgwm219 and Xgwm169with YPP (see Table 5). Thus, the application of SSR markersin the analysis of tetraploid wheat collection consistingof 85 accessions was used for (1) genetic documentation ofsamples, (2) for phylogenetic clusterization based on the speciesclassification and geographic origin, and (3) associationsbetween DNA markers and studied phylogenetic traits. Hence,the results can be efficiently used for the enhancement of localbreeding projects for the improvement of yield productivityin durum wheat.The phenotypic analysis of the tetraploid wheat collectionconsistingof 85 accessions showed a high correlation ofYPP with all 8 phenotypic traits in conditions of South-EastKazakhstan. The ANOVA suggested that the environmentalconditionssignificantly affected the variation in HT and SMT,while Genotype has contributed significantly to main yieldcomponents, including TKW. Overall, 31 accessions of T. durumshowed higher average yield values in comparison withlocal check cultivar Gordeiforme 254 (4.4 \u00b1 1.6 g/plant), andCanadian cultivar Strongfield was with the highest yield value(7.6 \u00b1 1.9 g/plant). The application of seven SSR markerssuggested that local accessions were distinctly different fromdurum accession from other parts of the world. Particularly,the Principal Coordinate plot showed that local durum sampleswere most close to North American samples. The Neighborjoiningphylogenetic tree separated 85 samples to two mainclusters, where the cluster 1 was mainly represented by Kazakhaccessions and cluster 2 mostly by European accessions. Theapplication of the t-test indicated that five out of seven SSRswere significant at least with one agronomic trait. Obtainedresults can be efficiently used for the enhancement of localbreeding projects for the improvement of yield productivityin durum wheat.The authors declare no conflict of interest.Abouzied H.M., Eldemery S.M.M., Abdellatif K.F. SSR-based geneticdiversity assessment in tetraploid and hexaploid wheat populations.Br. Biotechnol. J. 2013;3(3):390-404.Abugalieva S., Volkova L., Yermekbayev K., Turuspekov Y. Genotypingof commercial spring wheat cultivars from Kazakhstan basedon use of DNA microsatellite markers. Biotekhnologiya. Teoriya iPraktika = Biotech. Theory Practice. 2012;2:35-45. DOI 10.11134/btp.2.2012.4. (in Russian)Achtar S., Moualla M.Y., Kalhout A., R\u00f6der M.S., MirAli N. Assessmentof genetic diversity among Syrian durum (Triticum turgidumssp. durum) and bread wheat (Triticum aestivum L.) usingSSR markers. Russ. J. Genet. (Genetika). 2010;46(11):1500-1506.DOI 10.1134/S1022795410110074.Adonina I.G., Leonova I.N., Badaeva E.D., Salina E.A. Genotyping ofhexaploid wheat varieties from different Russian regions. Russ. J.Genet.: Appl. Res. 2017;7:6-13. DOI 10.1134/S2079059717010014.Anuarbek S., Abugalieva S., Pecchioni N., Laid\u00f2 G., Maccaferri M.,Tuberosa R., Turuspekov Y. Quantitative trait loci for agronomictraits in tetraploid wheat for enhancing grain yield in Kazakhstanenvironments. PLoS One. 2020;15(6):e0234863. DOI 10.1371/journal.pone.0234863.Botstein D., White R.L., Skolnick M., Davis R.W. Construction of a geneticmap in man using restriction fragment length polymorphisms.Am. J. Hum. Genet. 1980;32(3):314-331.Chen X., Min D., Yasir T.A., Hu Y.G. Genetic diversity, populationstructure and linkage disequilibrium in elite Chinese winter wheatinvestigated with SSR markers. PLoS One. 2012;7(9):e44510. DOI10.1371/journal.pone.0044510.De Vita P., Taranto F. Durum wheat (Triticum turgidum ssp. durum)breeding to meet the challenge of climate change. In: Al-Khayri J.,Jain S., Johnson D. (Eds.). Advances in Plant Breeding Strategies:Cereals. Springer, Cham, 2019;5:471-524. DOI 10.1007/978-3-030-23108-8_13.Dellaporta S.L., Wood J., Hicks J.B. A plant DNA minipreparation:Version II. Plant Mol. Biol. Rep. 1983;1(4):19-21. DOI 10.1007/BF02712670.Ganal M.W., R\u00f6der M.S. Microsatellite and SNP markers in wheatbreeding. In: Varshney R.K., Tuberosa R. (Eds.). Genomic-AssistedCrop Improvement. Springer, Dordrecht, 2007;2:1-24. DOI10.1007/978-1-4020-6297-1_1.Ganeva G., Korzun V., Landjeva S., Popova Z., Christov N.K. Geneticdiversity assessment of Bulgarian durum wheat (Triticum durumDesf.) landraces and modern cultivars using microsatellite markers.Genet. Resour. Crop Evol. Publ. online 2009. Publ. 2010;57(2):273-285. DOI 10.1007/s10722-009-9468-5.Geng H., Zhang Y., He Z., Zhang L., Appels R., Qu Y., Xia X. Molecularmarkers for tracking variation in lipoxygenase activity in wheatbreeding. Mol. Breed. 2010;28(1):117-126. DOI 10.1007/s11032-010-9466-5.Golabadi M., Arzani A., Mirmohammadi Maibody S.A.M., SayedTabatabaei B.E., Mohammadi S.A. Identification of microsatellitemarkers linked with yield components under drought stress at terminalgrowth stages in durum wheat. Euphytica. 2011;177(2):207-221.DOI 10.1007/s10681-010-0242-8.Hammer \u00d8., Harper D.A.T., Ryan P.D. Past: Paleontological StatisticsSoftware Package for Education and Data Analysis. Palaeontol.Electron. 2001;4(1):9.Henkrar F., El-Haddoury J., Ouabbou H., Nsarellah N., Iraqi D., BendaouN., Mahabala U.S. Genetic diversity reduction in improveddurum wheat cultivars of Morocco as revealed by microsatellitemarkers. Sci. Agric. 2016;73(2):134-141. DOI 10.1590/0103-9016-2015-0054.Idrees M., Irshad M. Molecular markers in plants for analysis of geneticdiversity: a review. Eur. Acad. Res. 2014;2(1):1513-1540.Jaiswal S., Sheoran S., Arora V., Angadi U.B., Iquebal M.A., Raghav N.,Aneja B., Kumar D., Singh R., Sharma P., Singh G.P., Rai A., TiwariR., Kumar D. Putative microsatellite DNA marker-based wheatgenomic resource for varietal improvement and management. Front.Plant Sci. 2017;8:2009. DOI 10.3389/fpls.2017.02009.Kabbaj H., Sall A.T., Al-Abdallat A., Geleta M., Amri A., Filali-Maltouf A., Belkadi B., Ortiz R., Bassi F.M. Genetic diversity withina global panel of durum wheat (Triticum durum) landraces and moderngermplasm reveals the history of alleles exchange. Front. PlantSci. 2017;8:1277. DOI 10.3389/fpls.2017.01277.Khlestkina E.K., Pestsova E.G., Salina E., R\u00f6der M.S., Arbuzova V.S.,Koval S.F., B\u00f6rner A. Genetic mapping and tagging of wheat genesusing RAPD, STS and SSR markers. Cell. Mol. Biol. Lett. 2002;7(2B):795-802.Kim T.K. T-test as a parametric statistic. Korean J. Anesthesiol. 2015;68(6):540. DOI 10.4097/kjae.2015.68.6.540.Kudryavtsev A.M., Martynov S.P., Broggio M., Buiatti M. Evaluationof polymorphism at microsatellite loci of spring durum wheat (Triticumdurum Desf.) varieties and the use of SSR-based analysis inphylogenetic studies. Russ. J. Genet. 2004;40(10):1102-1110.Leonova I.N., Badaeva E.D., Orlovskaya O., Roder M.S., KhotylevaL.V., Salina E.A., Shumny V.K. Comparative characteristic ofTriticum aestivum/Triticum durum and Triticum aestivum/Triticumdicoccum hybrid lines by genomic composition and resistance tofungal diseases under different environmental conditions. Russ. J.Genet. (Genetika). 2013;49(11):1276-1283. DOI 10.1134/S1022795413110136.Li W., Zhang B., Li R., Chang Xi, Jing R. Favorable alleles for stemwater-soluble carbohydrates identified by association analysis contributeto grain weight under drought stress conditions in wheat.PLoS One. 2015;10(3):1-15. DOI 10.1371/journal.pone.0119438.L\u00fcders T., Ahlemeyer J., F\u00f6rster J., Weyen J., Rossa E., Korzun V.,Lex J., Friedt W., Ordon F. Verification of marker-trait associationsin biparental winter barley (Hordeum vulgare L.) DH populations.Mol. Breed. 2016;36(2):14. DOI 10.1007/s11032-016-0438-2.Maccaferri M., Sanguineti M.C., Donini P., Tuberosa R. Microsatelliteanalysis reveals a progressive widening of the genetic basis in theelite durum wheat germplasm. Theor. Appl. Genet. 2003;107:783-797. DOI 10.1007/s00122-003-1319-8.Marzario S., Logozzo G., David J., Zeuli P., Gioia T. Molecular genotyping(SSR) and agronomic phenotyping for utilization of durumwheat (Triticum durum Desf.) ex situ collection from Southern Italy:a combined approach including pedigreed varieties. Genes. 2018;9(10):465. DOI 10.3390/genes9100465.Melloul M., Iraqi D., El Alaoui M., Erba G., Alaoui S., Ibriz M., ElfahimeE. Identification of differentially expressed genes by cDNAAFLPtechnique in response to drought stress in Triticum durum.Food Technol. Biotechnol. 2014;52(4):479-788. DOI 10.17113/ftb.52.04.14.3701.Mujeeb-Kazi A., Munns R., Rasheed A., Ogbonnaya F.C., Ali N., HollingtonP., Dundas I., Saeed N., Wang R., Rengasamy P., Saddiq M.S.,De Le\u00f3n J.L.D., Ashraf M., Rajaram S. Breeding strategies for structuringsalinity tolerance in wheat. Adv. Agron. 2019;155:121-187.DOI 10.1016/bs.agron.2019.01.005.Peakall R., Smouse P.E. GenAlEx 6.5: genetic analysis in Excel.Population genetic software for teaching and research \u2013 an update.Bioinformatics. 2012;28:2537-2539. DOI 10.1093/bioinformatics/bts460.Public website of the news in Kazakhstan. https://agbz.kz/zernovojrynok-2019/ .Rahimi Y., Bihamta M.R., Taleei A., Alipour H., Ingvarsson P.K. Genome-wide association study of agronomic traits in bread wheatreveals novel putative alleles for future breeding programs. BMCPlant Biol. 2019;19:541. DOI 10.1186/s12870-019-2165-4.R\u00f6der M.S., Korzun V., Wendehake K., Plaschke J., Tixier M.-H., LeroyP., Ganal M.W. A microsatellite map of wheat. Genetics. 1998;149:2007-2023.Roncallo P.F., Akkiraju P.C., Cervigni G.L., Echenique V.C. QTL mappingand analysis of epistatic interactions for grain yield and yieldrelatedtraits in Triticum turgidum L. var. durum. Euphytica. 2017;213(12):277. DOI 10.1007/s10681-017-2058-2.Royo C., Nachit M.M., Di Fonzo N., Araus J.L., Pfeiffer W.H., StaferG.A. (Eds.). Durum Wheat Breeding: Current Approaches andFuture Strategies. Binghamton, NY: Food Products Press, 2005.Singh A.K., Chaurasia S., Kumar S., Singh R., Kumari J., Yadav M.C.,Singh N., Gaba S., Jacob S.R. Identification, analysis and developmentof salt responsive candidate gene based SSR markers in wheat.BMC Plant Biol. 2018;18(1):249. DOI 10.1186/s12870-018-1476-1.Slim A., Piarulli L., Chennaoui Kourda H., Rouaissi M., Robbana C.,Chaabane R., Pignone D., Montemurro C., Mangini G. Genetic structureanalysis of a collection of Tunisian durum wheat germplasm.Int. J. Mol. Sci. 2019;20(13):3362. DOI 10.3390/ijms20133362.Song Q.J., Shi J.R., Singh S., Fickus E.W., Costa J.M., Lewis J.,Gill B.S., Ward R., Cregan P.B. Development and mapping of microsatellite(SSR) markers in wheat. Theor. Appl. Genet. 2005;110(3):550-560. DOI 10.1007/s00122-004-1871-x.Turuspekov Y., Plieske J., Ganal M., Akhunov E., Abugalieva S. Phylogeneticanalysis of wheat cultivars in Kazakhstan based on the wheat90 K single nucleotide polymorphism array. Plant Genet. Resour.2015;15(01):29-35. DOI 10.1017/s1479262115000325.Vieira M.L.C., Santini L., Diniz A.L., Munhoz C. Microsatellite markers:what they mean and why they are so useful. Genet. Mol. Biol.2016;39(3):312-328. DOI 10.1590/1678-4685-GMB-2016-0027.Vinod C.G., Sharma J.B., Prabhu K.V. Inheritance and molecular mappingof leaf rust resistance in Triticum turgidum var. durum cv. Trinakria.Indian J. Genet. 2014;74(1):10-15. DOI 10.5958/j.0975-6906.74.1.002.Wang H., Wang X., Chen P., Liu D. Assessment of genetic diversityof Yunnan, Tibetan, and Xinjiang wheat using SSR markers.J. Genet. Genom. 2007;34(7):623-633. DOI 10.1016/S1673-8527(07)60071-X.Yildirim A., S\u00f6nmezo\u011flu \u00d6z., G\u00f6kmen S., Kandemir N., Aydin N. Determinationof genetic diversity among Turkish durum wheat landracesby microsatellites. Afr. J. Biotechnol. 2011;10(19):3915-3920.DOI 10.5897/AJB10.2240.Za\u00efm M., El Hassouni Kh., Gamba F., Filali-Maltouf A., Belkadi B.,Sourour A., Amri A., Nachit M., Taghouti M., Bassi F.M. Widecrosses of durum wheat (Triticum durum Desf.) reveal good diseaseresistance, yield stability, and industrial quality across Mediterraneansites. Field Crops Res. 2017;214:219-227. DOI 10.1016/j.fcr.2017.09.007.Zhang B., Shi W., Li W., Chang Xi, Jing R. Efficacy of pyramidingelite alleles for dynamic development of plant height in commonwheat. Mol. Breed. 2013;32:327-338. DOI 10.1007/s11032-013-9873-5."} +{"text": "Caseinolytic protease P (ClpP), which is located on the inner mitochondrial membrane, degrades mitochondrial proteins damaged by oxidative stress. The role of ClpP varies among tumor types. However, the expression pattern and biological functions of ClpP in breast cancer (BC) have not yet been investigated.The Cancer Genome Atlas (TCGA) and Kaplan Meier-plotter database were used to analyze the expression level of ClpP in BC tissues, relationships with clinicopathological characteristics, and the influence on the prognosis of BC. Protein and mRNA expression levels of ClpP in BC cell lines and tissues were detected by quantitative real-time PCR, western blot and immunohistochemical (IHC) analyses. The colony formation assay, transwell assay and flow cytometric analysis were performed to assess various functions of ClpP. Western blot analysis was also conducted to determine the mechanism of ClpP.ClpP expression was markedly increased in BC cells and tissues. High expression of ClpP was significantly correlated with the T stage, estrogen receptor (ER) expression, and poor recurrence-free survival (RFS) in TCGA and Kaplan Meier-plotter database. ClpP silencing significantly inhibited proliferation, migration, invasion, and promoted apoptosis of BC cells, which resulted in suppression of the Src/PI3K/Akt signaling pathway. The gain-of-function assay confirmed partial these results. Breast cancer (BC) is the most common malignant tumor among women worldwide . At presThe mitochondria have been a focus of cancer research since the 1950s, when it was discovered that cancer cells produce adenosine triphosphate (ATP) and employ different mechanisms to support cell growth than the normal surrounding tissues. Therefore, it was suggested that a defect in the mitochondrial mechanism will not only lead to increased glycolysis, but also to the transformation of normal cells into cancer cells . The maiin vivo, and correlated with shortened survival. However, the ClpP and ClpX subunits may not have completely overlapping function(s) in the tumor mitochondria (The ClpXP protease complex is composed of two proteins: hexamers of a AAA+ ATPase (ClpX) and the tetradecameric peptidase caseinolytic protease P (ClpP) , which cchondria .ClpP is encoded by nuclear genes in mammalian cells and plays a central role in the quality control of mitochondrial proteins via the degradation of misfolded proteins. ClpP was first identified in bacteria and has since aroused interest as a potential anti-microbial therapeutic target . StudiesThe expression level of ClpP is greater in acute myeloid leukemia (AML) cells than in normal hematopoietic cells . FurtherHuman BC tissues and corresponding adjacent normal tissues were collected from patients who underwent surgery at the First Affiliated Hospital of Chongqing Medical University from 2014 to 2018, snap-frozen in liquid nitrogen, and then stored at \u221280\u00a0\u00b0C. This study was approved by the Institutional Ethics Committees of the First Affiliated Hospital of Chongqing Medical University and conducted in accordance with the tenets of the Declaration of Helsinki. Each participant signed an informed consent form prior to study inclusion.2/95% air.Seven human BC cell lines and two normal mammary epithelial cell lines (MCF-10A and HBL-100) were obtained from the American Type Culture Collection . MCF-10A cells were cultured as described previously and all ClpP-specific and the negative control siRNAs were synthesized by OriGene . The following siRNAs sequences were generated: SR305388A-rGrCrUrCrArArGrArArGrCrArGrCrUrCrUrArUrArArCrATC; SR305388B-rGrUrUrUrGrGrCrArUrCrUrUrArGrArCrArArGrGrUrUrCTG; and SR305388C-rGrGrCrCrArUrCrUrArCrGrArCrArCrGrArUrGrCrArGrUAC. The expression vector pCMV6-Myc-DDK-ClpP was produced by OriGene ; the empty pCMV6-Myc-DDK vector was used as a control. Lipofectamine 2000 was used for siRNAs and plasmids transfection, in accordance with the manufacturer\u2019s protocols.Total RNA was extracted from cells and tissues with TRIzol reagent (Invitrogen) in accordance with the manufacturer\u2019s instructions. RT-qPCR was performed using an ABI 7500 Real-Time PCR System with the SYBR Green kit (Invitrogen). \u03b2-actin was used as an internal control. Each sample was tested in triplicate. The followig primers were used for RT-qPCR analysis: ClpP, forward primer: 5\u2032-GCC AAG CAC ACC AAA CAG A-3\u2032, reverse primer: 5\u2032-GGA CCA GAA CCT TGT CTA AG-3\u2032; \u03b2-actin, forward primer: 5\u2032-CCT GTG GCA TCC ACG AAA CT-3\u2032, reverse primer: 5\u2032-GAA GCA TTT GCG GTG GAC GAT- 3\u2032.Total proteins were extracted with radioimmunoprecipitation assay lysis buffer . Protein concentrations were determined using the bicinchoninic acid protein assay kit . Western blot analysis was conducted as previously described with theAll specimens were formalin-fixed, paraffin-embedded and cut into 4 \u00b5m-thick sections, which were mounted onto glass slides. IHC analysis was conducted as described previously . BrieflyCell apoptosis was detected with the Annexin V-FITC Apoptosis Detection Kit in accordance with the manufacturer\u2019s protocol and a FACSCalibur flow cytometer (BD Biosciences).MDA-MB-231 and ZR-75-1 cells were seeded into triplicate wells of 6-well plates at 1,000 cells/well, and cultured for 7 days. The cells were then fixed with 4% paraformaldehyde and stained with 0.1% crystal violet solution .4 cells/well) were added into the upper transwell chamber, and 800 \u00b5L of medium containing 10% FBS were added to the lower chamber. After incubation at 37\u00a0\u00b0C under an atmosphere of 5% CO2/95% air for 24 h (MDA-MB-231 and ZR-75-1 cells), or 72\u00a0h (MCF-7 and T47D cells), cells that migrated through the membrane pores were fixed in 4% paraformaldehyde for 30 min and stained with 0.1% crystal violet for 15 min at room temperature. Matrigel\u2122-coated transwell filters were used to evaluate the invasion capability of the cells. The subsequent procedures were the same as those for the cell migration assay. Cells from six random fields were counted under a microscope. All experiments were repeated three times.Transwell chambers were used to detect the migratory and invasive capabilities of BC cells. For the transwell migration assays, 200-\u00b5lL aliquots of transfected MDA-MB-231, ZR-75-1, MCF-7 and T47D cells (4 * 10https://tcga-data.nci.nih.gov/tcga/). The study cohort consisted of a total of 1010 BC patients. ClpP expression data of 112 normal breast samples were included to compare differences in ClpP expression levels in BC tissues. Overall survival (OS) and complete clinicopathological data of 990 BC patients, and RFS data of 792 BC patients were screened. ClpP expression levels were ranked from low to high based on median values. The first 50% of patients were considered as the low-expression group and the second 50% as the high-expression group.Gene expression data of BC tissues were downloaded from the TCGA database .Prognosis based on ClpP levels in BC patients was analyzed using the Kaplan Meier-plotter database and GraphPad Prism 7.0 software . The two-tailed Student\u2019s p\u00a0<\u00a00.001) (p\u00a0<\u00a00.0001) (p\u00a0<\u00a00.01) (p = 0.029) (p\u00a0<\u00a00.001) (p = 0.0154) and ER expression (p = 0.0164). Kaplan\u2013Meier survival curves from TCGA indicated that ClpP was not associated with RFS (p = 0.506) or OS (p = 0.619) (p = 0.00071) . Receive\u00a00.0001) . To veri\u00a0<\u00a00.01) . The AUC= 0.029) . ClpP pr<\u00a00.001) \u20131G. Thes<\u00a00.001) . High Cl= 0.619) and 2B. 0.00071) and 2D. ClpP mRNA and protein expression levels in a panel of BC and normal breast epithelial cell lines were determined. The results showed that ClpP was increased in most malignant cell lines, as compared with normal cells and 3B. p\u00a0<\u00a00.01 and <0.001, respectively) (The suppressive effect of ClpP silencing on cancer cell growth was confirmed by the colony formation assay. The colony formation capabilities of the BC cell lines MDA-MB-231 and ZR-75-1 were markedly inhibited by si-ClpP-B (ctively) \u20134E.The transwell migration and invasion assay was performed to quantitatively assess cell metastasis and invasiveness. The results showed that cell migration and invasion were significantly reduced in cells transfected with si-ClpP-B, as compared with control cells, due to the down-regulation of MMP7 and vimentin, and the up-regulation of E-cadherin \u20135T. Convp\u00a0<\u00a00.01 and <0.001, respectively), accompanied by increased levels of cleaved caspase-9, cleaved caspase-8 and cleaved poly (ADP-ribose) polymerase (PARP) (Flow cytometry was carried out to detect cell apoptosis. The percentages of apoptotic MDA-MB-231 and ZR-75-1 cells were increased by si-ClpP-B (e (PARP) \u20135N.To confirm the specificity of ClpP siRNAs, the same functional experiments were performed with a second siRNA (si-ClpP-A). The results of the loss-of-function studies were consistent .These data revealed the anti-proliferative, anti-migration, anti-invasion and pro-apoptotic roles of silencing ClpP in BC cells.in vivo by increasing phosphorylation of the key cellular kinases Akt and Src of 14 analyzed datasets. Importantly, high ClpP expression was correlated with shorter metastasis-free survival in BC patients and reduced RFS in those with lung adenocarcinoma . ConsistClpP is a subunit of the ClpXP complex. The Akt signaling pathway is important in the regulation of various cellular functions, including metabolism, growth, proliferation, survival, transcription, protein synthesis and tumorigenesis . MutatioIn summary, the present study provides the first evidence that ClpP is frequently up-regulated in BC and that ClpP has high diagnostic value.ClpP expression is markedly increased in BC and significantly correlated with the T stage, ER expression, and poor RFS. Silencing of ClpP significantly inhibited proliferation, migration and invasion, and promoted apoptosis of BC cells, resulting in suppression of the Src/PI3K/Akt signaling pathway. These data indicate that ClpP is an oncogene, and may be a promising diagnostic biomarker and therapeutic target in BC.10.7717/peerj.8754/supp-1Figure S1p < 0.01, ***p < 0.001.(A) The overexpressing efficiency in ClpP (MCF-7 and T47D cells) was evaluated by RT-qPCR. The effects of overexpressed-ClpP on BC cell migration were evaluated using transwell assays. The effects of overexpressed-ClpP on BC cell invasion were evaluated using transwell assays. The data are presented as mean \u00b1 SD, **Click here for additional data file.10.7717/peerj.8754/supp-2Figure S2p < 0.01, ***p < 0.001. The effects of si-ClpP-A on BC cell proliferation were analyzed using the colony formation assay. The effects of si-ClpP-A on BC cell migration were evaluated using the transwell assay. The effects of si-ClpP-A on BC cell invasion were evaluated using the transwell assay. The effect of si-ClpP-A on MDA-MB-231 cells apoptosis was analyzed using flow cytometry. The data are presented as the mean \u00b1 SD, **Click here for additional data file.10.7717/peerj.8754/supp-3Supplemental Information 3Click here for additional data file.10.7717/peerj.8754/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.8754/supp-5Supplemental Information 5Click here for additional data file.10.7717/peerj.8754/supp-6Supplemental Information 6Click here for additional data file.10.7717/peerj.8754/supp-7Supplemental Information 7Click here for additional data file.10.7717/peerj.8754/supp-8Supplemental Information 8Click here for additional data file.10.7717/peerj.8754/supp-9Supplemental Information 9Click here for additional data file.10.7717/peerj.8754/supp-10Supplemental Information 10Click here for additional data file.10.7717/peerj.8754/supp-11Supplemental Information 11Click here for additional data file.10.7717/peerj.8754/supp-12Supplemental Information 12Click here for additional data file.10.7717/peerj.8754/supp-13Supplemental Information 13Click here for additional data file.10.7717/peerj.8754/supp-14Supplemental Information 14Click here for additional data file.10.7717/peerj.8754/supp-15Supplemental Information 15Click here for additional data file.10.7717/peerj.8754/supp-16Supplemental Information 16Click here for additional data file.10.7717/peerj.8754/supp-17Supplemental Information 17Click here for additional data file.10.7717/peerj.8754/supp-18Supplemental Information 18Click here for additional data file.10.7717/peerj.8754/supp-19Supplemental Information 19Click here for additional data file.10.7717/peerj.8754/supp-20Supplemental Information 20Click here for additional data file.10.7717/peerj.8754/supp-21Supplemental Information 21Click here for additional data file.10.7717/peerj.8754/supp-22Supplemental Information 22Click here for additional data file.10.7717/peerj.8754/supp-23Supplemental Information 23Click here for additional data file.10.7717/peerj.8754/supp-24Supplemental Information 24Click here for additional data file.10.7717/peerj.8754/supp-25Supplemental Information 25Click here for additional data file.10.7717/peerj.8754/supp-26Supplemental Information 26Click here for additional data file.10.7717/peerj.8754/supp-27Supplemental Information 27Click here for additional data file.10.7717/peerj.8754/supp-28Supplemental Information 28Click here for additional data file.10.7717/peerj.8754/supp-29Supplemental Information 29Click here for additional data file.10.7717/peerj.8754/supp-30Supplemental Information 30Click here for additional data file.10.7717/peerj.8754/supp-31Supplemental Information 31Click here for additional data file.10.7717/peerj.8754/supp-32Supplemental Information 32Click here for additional data file.10.7717/peerj.8754/supp-33Supplemental Information 33Click here for additional data file.10.7717/peerj.8754/supp-34Supplemental Information 34Click here for additional data file.10.7717/peerj.8754/supp-35Supplemental Information 35Click here for additional data file.10.7717/peerj.8754/supp-36Supplemental Information 36Click here for additional data file.10.7717/peerj.8754/supp-37Supplemental Information 37Click here for additional data file.10.7717/peerj.8754/supp-38Supplemental Information 38Click here for additional data file.10.7717/peerj.8754/supp-39Supplemental Information 39Click here for additional data file.10.7717/peerj.8754/supp-40Supplemental Information 40Click here for additional data file.10.7717/peerj.8754/supp-41Supplemental Information 41Click here for additional data file.10.7717/peerj.8754/supp-42Supplemental Information 42Click here for additional data file.10.7717/peerj.8754/supp-43Supplemental Information 43Click here for additional data file.10.7717/peerj.8754/supp-44Supplemental Information 44Click here for additional data file.10.7717/peerj.8754/supp-45Supplemental Information 45Click here for additional data file.10.7717/peerj.8754/supp-46Supplemental Information 46Click here for additional data file.10.7717/peerj.8754/supp-47Supplemental Information 47Click here for additional data file.10.7717/peerj.8754/supp-48Supplemental Information 48Click here for additional data file."} +{"text": "Acanthosaura have been recorded so far, including Acanthosauraarmata from the southern region, A.cardamomensis from the eastern region, A.crucigera from the western region, A.lepidogaster from the northern region and A.phuketensis from the Phuket Island and south-western region. However, comprehensive studies of diversity patterns and distribution of Acanthosaura are still lacking in some areas and need further information for designating areas of special conservation importance and nature protection planning in Thailand.In Thailand, five species of Acanthosauraaurantiacrista is a new species of long-horned lizard of the genus Acanthosaura from northern Thailand. It is distinguished from all other species of Acanthosaura by a dagger-like nuchal spine with yellowish-orange colouration in females, bright yellow colouration in males and a combination of other morphological characters: a greater tail length to snout-vent length ratio; a larger postorbital spine, nuchal spine, dorsal spine and occipital spine compared to its head length; a smaller diastema to snout-vent length ratio; a greater number of subdigital lamellae on the fourth finger and fourth toe; and a larger gular pouch than other Acanthosaura species. Analysis of mitochondrial ND2 gene sequences revealed a sister clade between the A.aurantiacrista lineage and the A.crucigera lineage with a 100% probability of divergence, according to Bayesian analysis and strong support value for Maximum Likelihood analysis. The pairwise distance ranged from 13.8-15.0% between A.aurantiacrista and A.cardamomensis, 10.9-14.5% between A.aurantiacrista and A.crucigera and 0-1.2% amongst A.aurantiacrista populations. The discovery of this lizard increases the known endemic herpetological diversity and underscores the importance of conservation in the mountain rainforest region of northern Thailand. Acanthosaura Gray, 1831 are recognised, ranging from Myanmar, east through Thailand, Cambodia, Laos, Vietnam and southern China and southwards through the Malaysian Peninsula and archipelagoes , A.capra , A.cardamomensis Wood, Grismer, Grismer, Neang, Chav & Holden, 2010, A.murphyi Nguyen, Do, Hoang, Nguyen, McCormack, Nguyen, Orlov, Nguyen & Nguyen, 2018, A.nataliae Orlov, Truong, & Sang, 2006 and A.phuketensis Pauwels, Sumontha, Kunya, Nitikul, Samphanthamit, Wood & Grismer, 2015 are classified as a long-horned group exhibiting the largest nuchal and dorsal spines with lengths greater than 10 mm; A.bintangensis Wood, Grismer, Grismer, Northayati, Chan & Bauer, 2009, A.brachypoda Ananjeva, Orlov, Nguyen & Ryabov, 2011, A.crucigera Boulenger, 1885, A.lepidogaster , A.phongdienensis Nguyen, Jin, Vo, Nguyen, Zhou, Che, Murphy, & Zhang, 2019, A.titiwangsaensis Wood, Grismer, Grismer, Northayati, Chan & Bauer, 2009 and A.tongbiguanensis Liu & Rao, 2019 belong to a short-horned group exhibiting nuchal and dorsal spines that are shorter than 10 mm; and the nuchal crest is absent in A.coronata G\u00fcnther, 1861 or bright yellow nuchal crest on the dorsum. To clarify the taxonomic status of this Acanthosaura population, we describe the new species on the basis of its distinctive morphological and colouration characteristics and a genetic analysis. Its name is provided to be included in conservation planning for agamid species in wildlife sanctuaries and national parks in the Thanon Thong Chai Mountain Range.A recent field sampling of Specimens were collected by hand from two locations in Thanon Thong Chai Mountain Range, Thailand: one specimen from Mae Sariang District, Mae Hong Son Province on 27 April 2018; seven specimens from Sop Khong Subdistrict, Omkoi District, Chiang Mai Province on 14 November 2018; and one specimen from Nang Lae Subdistrict, Mueang District, Chiang Rai Province on 24 January 2019. For all specimens, photographs were taken to document their colour patterns prior to euthanisation. Liver samples were taken and stored in absolute ethanol. Specimens were fixed in 10% formalin before being transferred to 70% ethanol for permanent storage.Acanthosaura in Thailand were examined from the Natural History Museum, National Science Museum, Technopolis, Pathum Thani Province (THNHM) and the Queen Saovabha Memorial Institute, Thai Red Cross Society, Bangkok Province, Thailand (QSMI): Acanthosauraarmata from Hala-Bala, Narathiwat Province (THNHM15209), Sungai Kolok District, Narathiwat Province (THNHM18884); Acanthosauracardamomensis from Koh Kut, Trat Province , Khao Yai National Park, Nakhon Ratchasrima Province ; Acanthosauracrucigera from Na Yong District, Trang Province , Taksin Maharat National Park, Muang District, Tak Province , Thong Pha Phum District, Kanchanaburi Province (THNHM22658), Huai Kha Khaeng, Lan Sak District, Uthai Thani Province (THNHM18594); Acanthosauralepidogaster from Phu Luang District, Loei Province , Phu Kieo District, Chaiyaphum Province (THNHM19619), Ban Sun Phae Kae, Chiang Dao District, Chiang Mai Province (THNHM20537), Roi Praputabath, Umphang District, Tak Province (THNHM20647), Huai Na Tee, Pua District, Nan Province (THNHM10080), Doi Khun Tan National Park, Lam Phun Province ; Acanthosauraphuketensis from Ton Sai Waterfall, Thalang District, Phuket Province (THNHM08865), Khao Sok, Ban Ta Khun, Surat Thani Province (THNHM22663); and Acanthosauranataliae from Xe Sap, Samoy, Lao .Comparative materials of all currently recognised species of Acanthosaura were also taken from original descriptions and subsequent studies obtained from GenBank was prepared using an EP0402 TAQ DNA POLYMERASE. Two primers, METF6 and ACANTHND2.833. R1 (5\u2019-AGGGAGGTTATTGTTGCTAG-3\u2019), were used to amplify a 698 bp fragment of the NADH dehydrogenase subunit 2 (ND2) gene . PCR proThe ND2 sequences were aligned using ClustalW v.1.83 integratBayesian Interference was performed in Mr.Bayes v.3.1.2 , based o212B9A56-ACDD-536A-958C-C3115F384365urn:lsid:zoobank.org:act:E0D80F05-8884-4426-B2D6-6C939310D2A4Type status:Holotype. Location: country: Thailand (northern region); stateProvince: Mae Hong Son Province; county: Mae Sariang District; verbatimElevation: 728 m; verbatimLatitude: 18\u00b009'02.8\"N; verbatimLongitude: 97\u00b058'50.2\"E; verbatimCoordinateSystem: degrees minutes seconds; verbatimSRS: WGS84; Event: year: 2018; month: April; day: 27; habitat: evergreen forests on hills up to at least 600 m elevation; fieldNotes: collector = Poramad Trivalaira; Record Level: institutionCode: THNHM; collectionCode: 28064; basisOfRecord: PreservedSpecimen; dynamicProperties: sex = adult femaleType status:Paratype. Location: country: Thailand (northern region); stateProvince: Chiang Mai Province; county: Omkoi District; locality: Sop Khong Subdistrict; verbatimElevation: 935; verbatimLatitude: 17\u00b039'45.4\"N; verbatimLongitude: 98\u00b011'53.6\"E; verbatimCoordinateSystem: degrees minutes seconds; verbatimSRS: WGS84; Event: year: 2018; month: November; day: 14; habitat: evergreen forests on hills up to at least 600 m elevation; fieldNotes: collector = Kirati Kunya; Record Level: institutionCode: THNHM; collectionCode: 28521; basisOfRecord: PreservedSpecimen; dynamicProperties: sex = adult femaleType status:Paratype. Record Level: institutionCode: THNHM; collectionCode: 28522; basisOfRecord: PreservedSpecimen; dynamicProperties: sex = adult female, same collection date, collector and location as paratype THNHM28521Type status:Paratype. Record Level: institutionCode: THNHM; collectionCode: 28523; basisOfRecord: PreservedSpecimen; dynamicProperties: sex = subadult male, same collection date, collector and location as the THNHM28521Type status:Paratype. Record Level: institutionCode: THNHM; collectionCode: 28524; basisOfRecord: PreservedSpecimen; dynamicProperties: sex = subadult male, same collection date, collector and location as the THNHM28521Type status:Paratype. Record Level: institutionCode: QSMI; collectionCode: 1446; basisOfRecord: PreservedSpecimen; dynamicProperties: sex = adult female, same collection date, collector and location as the THNHM28521Type status:Paratype. Record Level: institutionCode: QSMI; collectionCode: 1447; basisOfRecord: PreservedSpecimen; dynamicProperties: sex = adult female, same collection date, collector and location as the THNHM28521Type status:Paratype. Record Level: institutionCode: QSMI; collectionCode: 1448; basisOfRecord: PreservedSpecimen; dynamicProperties: sex = adult male, same collection date, collector and location as the THNHM28521Acanthosauraaurantiacrista sp. n. ; differences of 13.8-15.0% compared to two specimens of A.cardamomensis (GenBank GU817397 and GU817400); differences of 16.2-16.3% compared to two specimens of A.armata (GenBank AB266452 and NC014175); differences of 18.0-19.6% compared to two specimens of A.lepidogaster (GenBank AF128499 and KR092427); and differences of 19.1-19.8% compared to a specimen of A.capra (GenBank AF128498) (Table 4). The phylogenetic relationships within the genus Acanthosaura revealed through Maximum-Likelihood trees and Bayesian Inference tree of the ND2 gene showed high posterior probabilities and high bootstrap support values , more FI (17-23 vs. 13-17), more TO (25-29 vs. 19-26), fewer NS (5-6 vs. 6-10), fewer NCS (11-13 vs. 10-17) and the presence of a BEP and more GP (1-4 vs. 1) , greater PS/HL ratio (0.24-0.84 vs. 0.07-0.19), greater DS/HL ratio (0.15-0.38 vs. 0.08-0.09), fewer DIASN (8-9 vs. 11-15), more VENT (63-66 vs. 51-55), fewer NSSOS (5 vs. 6-7), fewer NS (5-6 vs. 8) and the presence of a LKP.Acanthosauraaurantiacrista sp. n. differs from A.brachypoda in presenting greater PS/HL ratio (0.24-0.84 vs. 0.11), greater DS/HL ratio (0.15-0.38 vs. 0.06), fewer RS (4-6 vs. 5-9), fewer NS (5-6 vs. 9) and more GP (1-4 vs. 0).Acanthosauraaurantiacrista sp. n. differs from A.capra in presenting fewer INFRAL (9-11 vs. 12-13), more FI (17-23 vs. 16-17), more TO (25-29 vs. 22-24), fewer NS (5-6 vs. 9) and the presence of an occipital spine and scales surrounding the occipital spine.Acanthosauraaurantiacrista sp. n. differs from A.cardamomensis in presenting fewer RS (4-6 vs. 7-9), fewer NS (5-6 vs. 7-10) and fewer NSSLC (9-13 vs. 10-19).Acanthosauraaurantiacrista sp. n. differs from A.coronata in presenting greater TaL/SVL ratio (1.40-1.70 vs. 0.60-1.00), more FI (17-23 vs. 13-14), more TO (25-29 vs. 17-19), fewer RS (4-6 vs. 9), fewer NS (5-6 vs. 7-9), fewer NR (1-2 vs. 3-4) and the presence of a postorbital spine, nuchal spine, dorsal spine, diastema, occipital spine, YAS, ND, BEP and more GP (1-4 vs. 0).Acanthosauraaurantiacrista sp. n. differs from A.crucigera in presenting fewer DIASN (8-9 vs. 9-25), more VENT (63-66 vs. 55-63), more FI (17-23 vs. 16-18), more TO (25-29 vs. 21-26), fewer RS (4-6 vs. 7-8), fewer NS (5-6 vs. 7-9) and more GP (1-4 vs. 1-2).Acanthosauraaurantiacrista sp. n. differs from A.lepidogaster in presenting greater TaL/SVL ratio (1.40-1.70 vs. 1.00-1.50), greater PS/HL ratio (0.24-0.84 vs. 0.06-0.17), greater NSL/HL ratio (0.35-0.95 vs. 0.12-0.15), greater DS/HL ratio (0.15-0.38 vs. 0.06-0.15), fewer DIASN (8-9 vs. 10-14), more VENT (63-66 vs. 52-61), more TO (25-29 vs. 22-23), greater OS/HL ratio (0.19-0.44 vs. 0.14-0.15), fewer NS (5-6 vs. 7-8), fewer PM (4 vs. 5), absence of scale on tympanum and more GP (1-4 vs. 0-1).Acanthosauraaurantiacrista sp. n. differs from A.murphyi in presenting greater PS/HL ratio (0.24-0.84 vs. 0.16-0.34), greater NSL/HL ratio (0.35-0.95 vs. 0.24-0.43), fewer INFRAL (9-11 vs. 12-14), more FI (17-23 vs. 15-18), more TO (25-29 vs. 21-23), fewer RS (4-6 vs. 8-9), fewer NS (5-6 vs. 7-8), fewer NR (1-2 vs. 3-4) and the absence of a tympanum scale.Acanthosauraaurantiacrista sp. n. differs from A.nataliae in presenting fewer VENT (63-66 vs. 64-71), fewer RS (4-6 vs. 7), fewer NSSLC (9-13 vs. 13-16) and the presence of an occipital spine, scales surrounding the occipital spine, ND and LKP.Acanthosauraaurantiacrista sp. n. differs from A.phongdienensis in presenting greater PS/HL ratio (0.24-0.84 vs. 0.06-0.09), greater NSL/HL ratio (0.35-0.95 vs. 0.07-0.18), larger DS/HL ratio (0.15-0.38 vs. 0.03-0.07), more FI (17-23 vs. 14-17), more TO (25-29 vs. 19-23) and the presence of a diastema.Acanthosauraaurantiacrista sp. n. differs from A.phuketensis in presenting greater NSL/HL ratio (0.35-0.95 vs. 0.21-0.39), fewer DIASN (8-9 vs. 12-17), more FI (17-23 vs. 15-17), more TO (25-29 vs. 21-24), fewer RS (4-6 vs. 5-9), fewer NS (5-6 vs. 7-8) and more GP (1-4 vs. 1-2).Acanthosauraaurantiacrista sp. n. differs from A.titiwangsaensis in presenting greater PS/HL ratio (0.24-0.84 vs. 0.14-0.18), greater NSL/HL ratio (0.35-0.95 vs. 0.11-0.18), greater DS/HL ratio (0.15-0.38 vs. 0.07-0.09), fewer DIASN (8-9 vs. 10-13), more VENT (63-66 vs. 47-57), fewer NS (5-6 vs. 8) and the presence of a LKP.Acanthosauraaurantiacrista sp. n. differs from A.tongbiguanensis in presenting greater PS/HL ratio (0.24-0.84 vs. 0.13-0.19), greater NSL/HL ratio (0.35-0.95 vs. 0.15-0.21), greater OS/HL ratio (0.19-0.44 vs. 0.16-0.23), fewer RS (4-6 vs. 6-9), fewer NS (5-6 vs. 8-9) and more GP (1-4 vs. 1-2).Acanthosauraaurantiacristasp. n. is differentiated from all other congeners by this combination of characters: A large size and a single long conical spine above the posterior margin of the eye; a large spine on the occiput between the tympanum and nuchal crest; tympanum naked, large, roundish; large developed gular pouch; scales on flanks randomly intermixed with small keeled and small tubercle scales; large nuchal crest with 8 large dagger-like and pointed spines; narrow diastema with 8-9 scales between the nuchal and vertebral crests; vertebral crest composed of large dagger-like, pointed spines beginning at the shoulder region and decreasing in size until the base of the tail; nuchal and dorsal crests are orange in females and yellow in males; tail 1.40-1.70 times the SVL; and black collar and black eye patch present, extending posteriorly until reaching the nuchal crest.Description of the holotype: Adult female. SVL 105.7 mm; TaL 151.8 mm (1.44 times SVL), tail complete; HL (23.3 mm) slightly longer than HW (18.9 mm); HL one-fifth SVL (0.22 times SVL), HW narrow (0.179 times SVL) and HD tall (0.64 times HL); head triangular in dorsal and lateral views; SL moderately long (0.46 times HL); RW wide (2.31 times RH); steeply sloping anteriorly; CS prominent, forming a large projecting shelf extending above eye, composed of 14/13 large scales; shelf terminates with a notch anterior to postorbital spine; rostrum moderate in size, rectangular, bordered laterally by first SUPRALs and posteriorly by five smaller scales; nostrils roundish, surrounded by one prenasal anteriorly, four postnasals posteriorly and two subnasals; six NS; oval supranasals; large scales above orbit weakly keeled; three rows of moderately-keeled scales below orbit extending from the anterior margin of the eye to posterior; large EYE (0.28 times HL) and ORBIT (0.44 times HL); interorbital, prefrontal and frontal scales slightly keeled and smaller than scales below orbit; seven large, keeled, azygous prefrontal scales arranged in a Y-shaped pattern; parietal eyespot surrounded by a larger row of scales; large conical PS above posterior margin of the eye surrounded by five small lanceolate scales; single row of seven large keeled scales extending from suborbital below posterior margin of eye to above tympanic margin, increasing in size posteriorly; elongated conical OS on lateral margin of nape surrounded by a rosette of five small lanceolate NSSOS; tympanum exposed, roundish, with a size two-thirds that of EYE (0.69 times EYE), surrounded by tiny conical scales; thirteen rectangular SUPRALs similar in size; mental pentagonal, larger than adjacent INFRALs; two postmentals similar in size, four scales contacting PM; chin shields large, extending posteriorly to angle of jaw, separated from infralabials by one scale row anteriorly and three at angle of jaw; eleven rectangular INFRALs of similar size; gular scales sharply keeled and spinose with a larger midventral row; extensible dewlap present; nuchal crest composed of eight elongated, dagger-like scales, bordered on each side by two rows of large, flat, keeled, triangular scales; nuchal crest followed by a diastema of nine DIASN at base of nape; dorsal body crest extending from posterior margin of diastema to base of tail; dorsal crest composed of small laterally compressed, triangular epidermal scales, bordered by a row of smaller paravertebral triangular scales; DS slightly decreasing to sacrum, then fading progressively; and nuchal and dorsal crests present as orange in live specimen and OS (5.3-7.5 vs. 4.5) and greater NSL (9.6-12.7 vs. 8.3), wider WNC (0.9-1.6 vs. 0.6), more SUPRAL (10-11/10 vs. 13/13) and fewer number of FI (18-20/17-20 vs. 23/21), higher number of NSSLC (10 vs. 13) in QSMI1446, QSMI1447, THNHM28521 and THNHM28522, and larger GP (3 vs. 1) in QSMI1446 and THNHM28522. The adult male paratype (QSMI1448) differs from the adult female holotype in presenting a longer SVL (130.1 vs. 105.7), greater TaL (202.2 vs. 151.8) and SL (22.3 vs. 10.7), wider TBW (19.2 vs. 10.3), greater HD (21.7 vs. 14.9), larger ORBIT (8.5 vs. 6.4), longer PS (19.1 vs. 5.7), OS (10 vs. 4.5), greater NSL (21.6 vs. 8.3), FOREL (54.2 vs. 49.8), HINDL (71.4 vs. 59.7) and GP (4 vs. 1) size, wider WNC (2.9 vs. 0.6), narrower DIAS (3.5 vs. 5.4) and fewer number of SUPRAL (10 vs. 13) and FI (19/18 vs. 23/21). Two subadult male paratypes are smaller and present fewer differences in morphological characters compared with the holotype, except for a longer PS (5.5-7.5 vs. 5.7) and OS (5.9 vs. 4.5) in THNHM28523, a greater WNC (0.7-0.8 vs. 0.6) in THNHM28523 and THNHM28524 and higher number of TO (29/29 vs. 27/26) and crista (crest). The name refers to a distinctive characteristic of the first discovered female specimen, which exhibited nuchal and dorsal crests with an orange colour. We suggest the following common names: kingkakhaownaam seesom (Thai), orange crested horned lizard (English), orange-verzierter geh\u00f6rnter Nackenstachler (German) and Acanthosaurus \u00e0 cr\u00eate orange (French).The specific epithet Acanthosauraaurantiacrista sp. n. occurs in the Thanon Thong Chai Mountain Range in northern Thailand: Mae Sariang District, Mae Hong Son Province at 728 m a.s.l.; Sop Khong Subdistrict, Omkoi District, Chiang Mai Province at 935 m a.s.l.; and Nang Lae Subdistrict, Mueang District, Chiang Rai Province at 636 m a.s.l. This species usually lives in rainforests on mountains at elevations over 600 m a.s.l. . This herpetological discovery yields the sixth member of the genus Acanthosaura from Thailand and the taxa in this genus that have not yet been identified, will be described in the near future.The comparisons revealed morphological characters of a new long-horned lizard species, Thailand . In addiAcanthosauraaurantiacrista sp. n. is expected to distribute throughout the Thanon Thong Chai Mountain Range, which includes several important protected areas where the biological fauna is preserved in northern regions of Thailand, such as Doi Inthanon National Park; Doi Suthep-Pui National Park; Khun Khan National Park; Mae Ngao National Park; Mae Ping National Park; Mae Tho National Park; Mae Wang National Park; Namtok Mae Surin National Park; Op Luang National Park; Op Khan National Park; Chiang Dao Wildlife Sanctuary; Lum Nam Pai Wildlife Sanctuary; Mae Lao-Mae Sae Wildlife Sanctuary; Mae Tuen Wildlife Sanctuary; and Om Koi Wildlife Sanctuary. Moreover, our research team recommends this new long-horned species, whose nuchal and dorsal crests have an appearance similar to fire, as a representative animal for drawing the attention of the local people, scientific community and government towards addressing the current problem of forest burning in northern regions of Thailand.Many forest areas in northern regions of Thailand are currently faced with deforestation due to timber logging and forest fire for human use, which negatively influences the conservation of the herpetological fauna . However6CF57014-D7C4-5583-91CF-B24FDE50E47610.3897/BDJ.8.e48587.suppl1Supplementary material 1Acanthosaura and Acanthosauraaurantiacrista sp. n., \u201c?\u201d = data not available.Comparison of morphometric (in mm) and meristic data for all currently recognised species of Data typemorphologicalBrief descriptionAcanthosaura lizardThe comparison table of morphometric for File: oo_395107.docxhttps://binary.pensoft.net/file/395107Poramad Trivalairat"} +{"text": "Callitris and Widdringtonia, the diterpene acids from Widdringtonia have never been described and no comparison to the Australian clade sister genus Callitris has been made. The critically endangered South African Clanwilliam cedar, Widdringtonia wallichii (syn. W. cedarbergensis), of the Cederberg Mountains was once prized for its enduring fragrant timbers and an essential oil that gives an aroma comparable to better known Mediterranean cedars, predominantly comprised by widdrol, cedrol, and thujopsene. In South Africa, two other \u2018cedars\u2019 are known, which are called W. nodiflora and W. schwarzii, but, until now, their chemical similarity to W. wallichii has not been investigated. Much like Widdringtonia, Callitris was once prized for its termite resistant timbers and an \u2018earthy\u2019 essential oil, but predominantly guaiol. The current study demonstrates that the essential oils were similar across all three species of Widdringtonia and two known non-volatile diterpene acids were identified in leaves: the pimaradiene sandaracopimaric acid (1) and the labdane Z-communic acid (2) with a lower yield of the E-isomer (3). Additionally, in the leaves of the three species, the structures of five new antimicrobial labdanes were assigned: 12-hydroxy-8R,17-epoxy-isocommunic acid (4), 8S-formyl-isocommunic acid (5), 8R,17-epoxy-isocommunic acid (6), 8R-17R-epoxy-E-communic acid (7), and 8R-17-epoxy-E-communic acid (8). Australian Callitris columellaris (syn. C. glaucophylla) also produced 1 and its isomer isopimaric acid, pisiferal (9), and pisiferic acid (10) from its leaves. Callitris endlicheri (Parl.) F.M.Bailey yielded isoozic acid (11) as the only major diterpene. Diterpenes 4\u20136, pisiferic acid (10), spathulenol, and guaiol (12) demonstrated antimicrobial and acaricidal activity.In spite of the evidence for antimicrobial and acaricidal effects in ethnobotanical reports of Widdringtonia were once prized for their timbers and have been heavily exploited over the course of more than a century. The most pronounced impact has been on the now critically endangered W. wallichii Endl. ex Carri\u00e8re (=W. cedarbergensis J.A.Marsh) + ; 8S-formyl-isocommunic acid (5), HRESIMS m/z 341.2094 [M + Na]+ , 8R,17-epoxy-isocommunic acid (6), HRESIMS m/z 319.2258 [M + H]+ , 8R-17-epoxy-E-communic acid (7), HRESIMS m/z 341.2081 [M + Na]+ , 8R-17-epoxy-Z-communic acid (8), HRESIMS m/z 341.2081 [M + Na]+ .Five of the compounds are undescribed. These are structures 4\u20138, which were all isolated as amorphous translucent white solids: 12-hydroxy-8Staphylococcus epidermidis (ATCC 12228), Staphylococcus aureus (ATCC 29213 & a methicillin resistant strain), Pseudomonas aeruginosa (ATCC 27703), Bacillus subtilis (University of New England strain), and Escherichia coli (ATCC 25922). The positive control used was tetracycline.The minimum inhibitory concentration (MIC) method described by Eloff , which im/z 30\u2013400.Relative abundances of essential oil components and esterified diterpene acids were studied using gas chromatography with mass spectrometric detection (GC-MS). GC-MS analyses were performed using an Agilent Technologies 7890A GC-System coupled with an Agilent 5975C mass selective detector . An autosampler unit (Agilent Technologies 7693-100 positions) held samples. Separation of 1-\u03bcL injections used an HP-5MS Agilent column (30 m \u00d7 250 \u03bcm \u00d7 0.25 \u03bcm). Operating conditions were as follows: injector split ratio 25:1, temperature 250 \u00b0C, carrier gas helium, 1.0 mL/min, and constant flow. Column temperature was 50 \u00b0C (no hold) and 5 \u00b0C per minute. Then, at 280 \u00b0C, it was held at 5 min. Mass fragmentation patterns were acquired at \u221270 eV using a mass scan range of n-alkanes, when compared with values published in Adams [Primary identifications were performed by comparison of mass spectra with an electronic library database and confin Adams by visuain Adams . Semi-quHRESIMS spectra were recorded using an AB Sciex 5600 TripleTOF mass spectrometer in positive mode."} +{"text": "Acinetobacter baumannii (XDRAB), isolated in Thailand. These results revealed multiple antimicrobial-resistant genes, each involving two sequence type 16 (ST16) isolates, ST2, and a novel sequence type isolate, ST1479.Here, we report the complete genome sequences of four clinical isolates of extensively drug-resistant Acinetobacter baumannii (XDRAB), isolated in Thailand. These results revealed multiple antimicrobial-resistant genes, each involving two sequence type 16 (ST16) isolates, ST2, and a novel sequence type isolate, ST1479.Here, we report the complete genome sequences of four clinical isolates of extensively drug-resistant Acinetobacter baumannii is one of the multidrug-resistant bacteria listed as a priority by the World Health Organization, as it exhibits resistance to most commercially available antibiotics and causes hospital-acquired infections (\u2013Acinetobacter baumannii (CRAB) infections present limited therapeutic options and are associated with high morbidity and mortality as well as longer hospitalization (A. baumannii (XDRAB) infections have been reported worldwide, including in Thailand (n = 3) and bile (n = 1) samples by a tertiary hospital in northeastern Thailand between 2017 and 2018 (gyrB multiplex PCR (n = 2) and no clonal group (n = 2) based on a multiplex PCR assay . Quality control of ONT reads was undertaken using NanoPlot v1.28.1 (https://github.com/wdecoster/NanoPlot). For the Illumina platform, the sequencing library was generated using the NEBNext Ultra II DNA library prep kit for Illumina following the manufacturer\u2019s recommendations. We applied Fastp v0.19.5 (https://github.com/relipmoc/skewer). Quality checking of the Illumina reads was performed using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Hybrid assemblies with the ONT and Illumina data were performed using Unicycler v0.4.8 (https://github.com/rrwick/Unicycler/releases), and the genome sequences were checked for quality using QUAST v5.0.2 (http://quast.sourceforge.net/). Complete circular DNA structures of the bacterial chromosomes and plasmids were automatically produced using Unicycler software. The genome sequences were submitted to the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.12 for annotation. Default parameters were used for all software unless otherwise specified.Bacterial genomic DNA samples extracted using ZymoBIOMICS DNA kits were sequenced using the Oxford Nanopore Technologies (ONT) and Illumina platforms. Library preparation for ONT sequencing followed the rapid barcoding DNA sequencing protocol with the SQK-RBK004 kit without DNA size selection, to preserve the plasmid DNA, and the libraries were sequenced using a single R9.4.1/FLO-MIN106 flow cell on a MinION Mk1B sequencer. We base called and demultiplexed the raw data using Guppy v3.4.5 (ONT), specifying the high-accuracy model (-c dna_r9.4.1_450bps_hac.cfg). The ONT adapters were trimmed using Porechop v0.2.4 ( v0.19.5 (https:/r v0.4.8 (https:/T v5.0.2 (http://https://cge.cbs.dtu.dk/services/ResFinder/) and CARD (https://card.mcmaster.ca/): blaNDM-1, blaOXA-23, blaOXA-66, blaTEM1D, blaVEB-1, blaIMP-14, blaADC-25, sul1, sul2, cmlA1, mphE, msrE, ARR2, tetB, tet(39), aac(3)-IId, aadA1, ant(2\u2033)-Ia, aph(3\u2032)-Ia, aph(3\u2033)-Ib, aph(3\u2032)-VI, aph(6)-Id, and armA. The multilocus sequence type (MLST) findings using the PubMLST database indicated that two isolates were ST16 (or ST355), and the other isolates were ST2 (or ST195) and ST1479 (new sequence type), according to the Pasteur MLST scheme (with the Oxford MLST scheme in parentheses) (https://pubmlst.org/abaumannii/).All isolates contained plasmids, and we detected seven plasmids in one isolate . From thand CARD (https:/ntheses) (https:/PRJNA647677. The accession numbers and assembly statistics are provided in These sequences have been submitted to GenBank under BioProject accession number"} +{"text": "Doppler echocardiographic (Echo) measurements of the mitral and pulmonary venous flow have been used to assess diastolic dysfunction (DD). Velocity-encoded cardiac magnetic resonance (Ve-CMR) can measure similar parameters and may potentially be used for the assessment of DD.To assess the correlation of Ve-CMR with Echo in assessing mitral inflow E/A ratio, left atrial (LA) size, and pulmonary vein (PV) flow.We prospectively enrolled 22 outpatients with a mitral inflow pattern by Echo that was normal (8), impaired relaxation (7), pseudo-normal (2), or restrictive (5). The mean left ventricular ejection fraction (LVEF) was 60.8 and two patients had left ventricular hypertrophy on echo. Ve-CMR was performed within 2 hours of the Echo. The following indices were measured: LA size, mitral inflow E-velocity (E), A-velocity (A), E/A ratio, PV waves .The mean age of the patients was 51 years. The average Echo mitral inflow absolute velocities were close to double the Ve-CMR {Echo E-velocity = 85.8 cm/sec vs. Ve-CMR E velocity = 41.4 cm/sec, Echo A-velocity 70 cm/sec vs. Ve-CMR A-velocity 32.5 cm/sec}. The average E/A ratio was 1.41 by echocardiogram and 1.48 by Ve-CMR. There was a significant correlation in LA size and Mitral inflow E/A ratio between Ve-CMR and Echo . There were no significant correlations in PV waves . Figure 1Ve-CMR has a very high correlation with Echo in the assessment of mitral inflow E/A ratio and LA size. Ve-CMR maybe useful for the assessment of diastolic dysfunction."} +{"text": "EGFR mutation-positive NSCLC at a major cancer center. This study showed the efficacy of 1G or 2G EGFR-TKIs as the 1L treatment, and subsequent therapy including 3G EGFR-TKIs in the real-world setting.The present study showed the comprehensive analysis of disease characteristics and treatment patterns in uncommon EGFR) mutations in non-small-cell lung cancer (NSCLC) are uncommon EGFR mutations. Although the efficacy of second (2G) or third generation (3G) EGFR tyrosine kinase inhibitors (EGFR-TKIs) in the patients with uncommon EGFR mutation has been proven, further studies are warranted to define the optimal treatment approach for uncommon EGFR mutation-positive NSCLC. This study retrospectively investigated the treatment patterns and outcomes of patients with uncommon EGFR mutation-positive NSCLC from January 2011 to December 2019 at the Samsung Medical Center, Seoul, Korea. During the study, 2121 patients with EGFR mutation-positive NSCLC received first-generation or 2G EGFR-TKI (afatinib) as the first-line (1L) systemic therapy. Of this, 135 (6.4%) patients harbored uncommon EGFR mutations. Of 135, 54 patients had overlapping mutations with major EGFR mutations. The objective response rate (ORR) for the 1L EGFR-TKI was 63.3%. The median progression-free survivals (PFSs) were 8.6 months (95% CI: 3.8\u201313.5), 11.7 months (95% CI: 6.6\u201316.7), 7.7 months (95% CI: 4.9\u201317.4), and 5.0 months (95% CI: 3.7\u20136.1) for major uncommon EGFR mutation , compound mutation with major EGFR mutation (Del 19 or EGFR exon 21 p.L858R), other compound mutation, and other uncommon mutations, respectively. The median overall survivals (OSs) were 25.6 months (16.9\u201334.2), 28.8 (95% CI: 24.4\u201333.4), 13.5 months (95% CI: 7.4\u201327.8), and 9.4 months (95% CI: 3.4\u201310.5) for major uncommon EGFR mutation (G719X), compound mutation with major EGFR mutation (Del 19 or EGFR exon 21 p.L858R), other compound mutation, and other uncommon mutations, respectively. The response rate, median PFS, and OS were 63.3%, 16.3 months (95% CI: 15.6\u201316.9), and 37.5 months (95% CI: 35.4\u201339.6) for common EGFR mutation-positive NSCLC. After failing 1L EGFR-TKI, repeated tissue or liquid biopsy were carried out on 44.9% (35/78) of patients with T790M detected in 10/35 (28.6%) patients. With subsequent 3G EGFR-TKI after failing the first-line EGFR-TKI, the ORR and PFS for 3G EGFR-TKI were 80% and 8.9 months (95% CI: 8.0\u20139.8). These patients showed a median OS of 34.6 months (95% CI: 29.8\u201339.4). The ORR, PFS and OS were poorer in patients with uncommon than those with common EGFR mutations. T790M was detected in 28.6% of the uncommon EGFR mutation-positive patients for whom prior 1G/2G EGFR-TKIs failed and underwent repeat biopsy at the time of progression.Approximately 10% of the epidermal growth factor receptor ( Uncommon EGFR mutations account for 7\u201323% of EGFR mutation-positive NSCLCs. Uncommon EGFR mutations can be categorized as follows: (i) de novo T790M; (ii) exon 20 insertions; (iii) \u201cmajor\u201d uncommon mutations Gly719Xaa (G719X), Leu861Gln (L861Q), and Ser768Ile (S768I); (iv) compound mutations; (v) other uncommon mutations [Exon 19 deletions (Del19) and epidermal growth factor receptor EGFR mutation-positive NSCLC has been revolutionized with the development of next-generation EGFR tyrosine kinase inhibitors (EGFR-TKIs). Currently, five EGFR-TKIs are available as the first-line (1L) therapy for advanced EGFR mutation-positive NSCLC\u2014first-generation (1G) reversible EGFR-TKIs, gefitinib, and erlotinib; second-generation (2G) irreversible ErbB family blockers, afatinib, and dacomitinib; third-generation (3G) irreversible EGFR-TKIs, osimertinib. Of the EGFR-TKI prospective randomized trials undertaken to date, only Iressa Pan-Asia Study (IPASS) [EGFR mutations. However, these studies included a small number of cases with uncommon EGFR mutations. Thus, it is unclear whether it is the best practice to use 2G or 3G EGFR-TKIs as the treatment of choice.The treatment of neration G irreverneration G irrever (IPASS) ,5 includEGFR-mutation positive NSCLC, recently, the highly anticipated findings of the phase III FLAURA trial showed 38.6 months of overall survival (OS) with frontline osimertinib, a 3G EGFR-TKI, versus 31.8 months with erlotinib or gefitinib [EGFR mutation-positive NSCLC who received sequential afatinib/osimertinib. The median OS was 41.3 months : 36.8\u201346.3) in the total population and 45.7 months (90% CI: 45.3\u201351.5) in patients with Del 19 [As to which treatment strategy is the best for the patients with major EGFR-TKIs and best sequential treatment, the bulk of these trials were limited to patients whose tumors harbored common EGFR mutations.While robust data from clinical trials have demonstrated the efficacy, tolerability, and benefits of EGFR-TKIs, followed by sequential treatment including 3G EGFR-TKI and cytotoxic chemotherapy in patients with uncommon EGFR mutation-positive NSCLC. In this study, we describe the real-world data of practice pattern and treatment outcomes in patients with uncommon EGFR mutation-positive NSCLC, including objective response rate (ORR), progression-free survival (PFS), and OS.To the best of our knowledge, there have been no prospective studies on the use of 1G or 2G EGFR mutation-positive NSCLC received gefitinib, erlotinib, or afatinib as 1L chemotherapy at the Samsung Medical Center. A total of 135 (6.4%) patients harbored uncommon EGFR mutations such as G719A/G719C/G719X, L861Q, S781I, H351I, E709K, and de novo T790M. The types of uncommon EGFR mutations are described in EGFR insertion 20 who received EGFR-TKIs as a 1L treatment. We classified patients with uncommon EGFR mutation into the major uncommon EGFR mutation , L861Q alone (n = 18), compound mutation with major EGFR mutation , other compound mutations (n = 13), other uncommon mutations (n = 2) and T790M (n = 15). There were 47.4% (64/135) male, and ex- or current smokers were 44.4% (60/135). About 25.9% of patients had symptomatic or asymptomatic brain metastasis at initial diagnosis.From January 2011 to December 2019, 2121 patients with EGFR-TKIs was 63.3% (76/120). The median PFS was 11.1 months (95% CI: 7.2\u201315.0) for uncommon EGFR mutation-positive NSCLC , compound mutation with major EGFR mutation (Del 19 or EGFR exon 21 p.L858R), compound mutation , and other uncommon mutations , respectively. The median OS were 25.6 months (16.9\u201334.2), 28.8 (95% CI: 24.4\u201333.4), 13.5 months (95% CI: 7.4\u201327.8), and 9.4 months (95% CI: 3.4\u201310.5) for major uncommon EGFR mutation (G719X), compound mutation with major EGFR mutation (Del 19 or EGFR exon 21 p.L858R), compound mutation, and other uncommon mutations, respectively. From October 2014 to December 2019, in the uncommon EGFR mutation-positive NSCLC group, the median PFS was 15.1 months (95% CI: 12.5\u201317.7) for afatinib and 7.7 months (95% CI: 1.3\u201314.1) for gefitinib or erlotinib (p = 0.165). The median OS was 25.6 months (95% CI: 18.2\u201333.0) for uncommon EGFR mutation-positive NSCLC for afatinib and 15.5 months (95% CI: 9.0\u201322.0) for gefitinib or erlotinib (p = 0.03). There was no significant difference in sequential treatment after failing 1L treatment among the three EGFR-TKIs.The ORR for the 1L 1G or 2G ve NSCLC . The medrlotinib A patients (EGFR-TKIs (8/10 patients had overlapping EGFR mutations with Del 19 or EGFR exon 21 p.L858R), seven patients who did not have T790M received other EGFR-TKIs , 41 patients received cytotoxic chemotherapy, and 20 patients did not receive any sequential treatment.Among 120 patients (except de novo T790M), 78 experienced disease progression until January 2020. Among them, patients . T790M wEGFR-TKIs and cytotoxic chemotherapy, respectively (p = 0.05). In 58 patients who experienced disease progression and received sequential treatment, the median OS2 was 15.1 months (95% CI: 9.0\u201321.2) and 11.0 months (95% CI: 5.1\u201316.9) for 3G EGFR-TKIs and cytotoxic chemotherapy, respectively (p = 0.214). The median OS was 34.6 months (95% CI: 29.8\u201339.4), 24.4 months (95% CI: 17.4\u201331.4), and 5.3 months (95% CI: 2.9\u20137.7) for 3G EGFR-TKIs, cytotoxic chemotherapy, and no sequential treatment, respectively (p < 0.001).In 58 patients who experienced disease progression and received sequential treatment, the median PFS2 was 8.9 months (95% CI: 8.0\u20139.8) and 4.2 months (95% CI: 2.3\u20136.2) for third-generation ectively A (p = 0.ectively B (p = 0.EGFR-TKIs after failing the 1L EGFR-TKI treatment. The median PFS was 4.9 months (95% CI: 3.8\u20136.0), and the median OS was 24.0 months (95% CI: 0.7\u20134.8). Patients who received 3G EGFR-TKIs showed a median OS of 38.0 months (95% CI: 10.5\u201365.4).Among the 15 patients with de novo T790M mutation, 11 patients had an EGFR exon 21 p.L858R mutation and four patients had a Deletion 19 as a coexisting mutation. As a 1L treatment, seven patients received gefitinib, one patient received erlotinib, and seven patients received afatinib. Among them, eight patients received 3G EGFR mutation group, there were relatively more male patients and current/ex-smokers than in the common EGFR mutation group (EGFR mutation group was 66.6% (75% between October 2014 and December 2019), and in the uncommon EGFR mutation group it was relatively low at 44.9%. Although there was a difference between the two groups in the re-biopsy rate, the T790M detection rate in the patients who underwent re-biopsy was 63.5% in the common EGFR mutation group but was 28.6% in the uncommon EGFR mutation group. The response rate was 63.3% and 86.6% for the uncommon and common EGFR mutation groups, respectively. The median PFS was 16.3 months (95% CI: 15.6\u201316.9) and 11.1 months (95% CI: 7.2\u201315.0) for common EGFR mutation-positive NSCLC and uncommon EGFR mutation-positive NSCLC, respectively (p < 0.001).In the uncommon on group . During ectively . In the patients who received 3G EGFR-TKIs after failing 1L EGFR-TKIs, the median OS was 44.4 months (95% CI: 38.9\u201349.9) and 34.6 months (95% CI: 29.8\u201339.4) for common EGFR mutation-positive NSCLC and uncommon EGFR mutation-positive NSCLC, respectively.In the overall population, the median OS was 37.5 months (95% CI: 35.4\u201339.6) and 25.6 months (95% CI: 18.2\u201333.0) for common ectively , compound mutation with major EGFR mutation (Del 19 or EGFR exon 21 p.L858R), afatinib showed superior OS results. In our study, less than one-third of the patients with uncommon EGFR mutation-positive NSCLC had a T790M mutation in the re-biopsy after failing 1L EGFR-TKIs. Most T790M mutation positive cases had overlapping mutations with major (Del 19 or EGFR exon 21 p.L858R) and uncommon EGFR mutations. The rate of T790M mutations after failing 1L EGFR TKI treatment in our study was only 28.6%, relatively lower than that of common EGFR mutation [EGFR mutation-positive NSCLCs than in common EGFR mutation-positive NSCLCs (27.1 % vs. 45.2%) [EGFR mutations after failing EGFR-TKI is lower than in patients with common EGFR mutations.The median ORR, PFS and OS of patients with uncommon ve NSCLC . The PFS G719X, L61Q, compmutation ,11. In a. 45.2%) . It needEGFR mutations are heterogeneous and have various sensitivities to EGFR-TKIs. In addition, the mechanism of acquired resistance to 1L EGFR-TKIs has not yet been well defined. Several retrospective studies and case reports of 1G EGFR-TKIs showed inconsistent responses in patients with uncommon EGFR mutation-positive NSCLC. A post-hoc analysis of prospectively collected data from the participants of the LUX-Lung 2, LUX-Lung 3, and LUX-Lung 6 trials showed the clinical activity of afatinib in patients with advanced uncommon EGFR mutation-positive NSCLC, especially G719X, L861Q, and S768I. However, it reported a low activity against T790M and exon 20 insertion mutations. Afatinib showed an ORR of 71% and a median PFS of 10.7 months (95% CI: 5.6\u201314.7), except for those with T790M or exon 20 insertion mutations, for whom ORR was 9\u201314%, and PFS was less than 3 months. The median OS was 19.4 months (95% CI: 16.4\u201326.9) [n = 315), it showed activity against major uncommon mutations , compound mutations , other uncommon mutations , and some exon 20 insertions in EGFR-TKI na\u00efve patients [Uncommon .4\u201326.9) . In a reEGFR-TKI na\u00efve patients with uncommon EGFR mutation-positive NSCLC (KCSG-LU15-09), 22 of the 36 patients received osimertinib as the 1L treatment [EGFR-TKIs. Osimertinib conferred an ORR of 50%. The median PFS was 8.2 months (95% CI: 5.9\u201310.5), and the median OS was not reached. Furthermore, the response rate and median duration of response (11.2 months) were lower than those observed with osimertinib in patients with common mutations . In our study, the median PFS of 1G or 2G generation EGFR-TKI was 11.1 months (95% CI: 7.2\u201315.0), and the median OS was 25.6 months (95% CI: 18.2\u201333.0) in patients with uncommon EGFR mutant-positive NSCLC.In the phase II study of osimertinib for reatment . A totalEGFR mutations because of low sensitivity compared to the NGS [EGFR mutation detection accuracy [P53) in common EGFR mutation-positive NSCLC. However, in our study, few patients had an NGS result; therefore, further studies are needed to determine the prognostic effect of co-mutations in uncommon EGFR mutation-positive NSCLC.This study has several limitations due to its retrospective nature and single center experience. We had a small number of patients with brain metastasis at initial diagnosis. This study could not evaluate for CNS-specific outcomes or subgroup analysis. Among other things, only 44.9% of the patients were evaluated by repeated tissue or liquid biopsy at the time of progression because there was no accessible site for biopsy . Furthermore, the polymerase chain reaction-based or direct sequencing methods might have had limitations in detecting compound the NGS ,16. Succaccuracy . It is aEGFR mutation-positive NSCLC, who started 1L gefitinib, erlotinib, or afatinib treatment for recurrent or metastatic NSCLC at the Samsung Medical Center between January 2011 and December 2019. This non-interventional observational study through big data analysis retrospectively collected de-identified patient data from a clinical data warehouse (CDW) using a unique algorithm with Standard Query Language (SQL) called the ROOT project. Patient demographic characteristics, such as age, sex, smoking history, performance status, and EGFR mutation type, were reviewed. We classified the uncommon EGFR mutation-positive NSCLC into the group with major uncommon EGFR mutations , compound mutations with major EGFR mutation (Del 19 or EGFR exon 21 p.L858R), other compound mutations, other uncommon mutations and T790M. Demographic information was obtained when the 1L EGFR-TKI treatment was initiated. EGFR mutations were identified using a peptide nucleic acid (PNA)-clamp kit and real-time polymerase chain reaction, COBAS (cobas\u00aeEGFR Mutation Test v2 [TM).This study included patients with Test v2 , or nextThis study was reviewed and approved by the Institutional Review Board (IRB) at the Samsung Medical Center (IRB No. 2018-05-130). The trial was conducted following the Declaration of Helsinki (as revised in 2013).EGFR-TKIs until progression or death resulting from any cause. PFS2 was defined as the first date of sequential treatment after failing 1L EGFR-TKIs until progression or death resulting from any cause. OS was defined as the first date of EGFR-TKIs until death resulting from any cause. OS2 was defined as the first date of sequential treatment after failing 1L EGFR-TKIs until death resulting from any cause. All p-values were two-sided, and p-value < 0.05 was considered statistically significant. The Korea Food and Drug Administration approved afatinib in October 2014. Among the three 1G or 2G EGFR-TKIs, PFS and OS were analyzed in patients who received EGFR-TKIs between October 2014 and December 2019.The all-data cut-off date for the analyses was February 2020. PFS and OS were calculated using a Kaplan\u2013Meier estimator and compared using the log-rank test. PFS and OS were presented as median values, with two-sided 95% CIs. PFS was defined as the first date of EGFR-mutant NSCLC showed lower ORR, PFS, and OS than the patients with common EGFR-mutant NSCLC. In particular, among the uncommon EGFR mutation, compared to the group with compounding mutation with major EGFR mutation and the group with major uncommon EGFR mutation, the group with other compounding mutation or other uncommon EGFR mutation showed inferior outcomes. Compared to common EGFR mutation-positive NSCLC, a lower percentage of patients underwent repeated biopsy and showed a lower detection rate of T790M. Less than one-third of the patients received 3G EGFR-TKI after failing the 1L EGFR-TKIs. However, like the common EGFR group, patients with T790M mutation after failing the 1L EGFR-TKI who received 3G TKI showed a favorable OS compared to other sequential treatments in the uncommon EGFR group. With the availability of more EGFR TKIs and a better understanding of tumor biology, further prospective studies are warranted to define the optimal treatment approach for uncommon EGFR mutant-positive NSCLC.The patients with uncommon"} +{"text": "Older adults self-administer prescribed medication regimens to treat chronic diseases which can lead to mismanagement, medication related harm and hospitalizations. We examined the extent to which source of purchased medications influenced the occurrence of self-reported medication mistakes and hospitalizations in community-dwelling participants who managed medications independently (N= 3899). The majority (65%) picked-up medications, 18% had medications delivered, and 17% used both (picked-up and delivery). Compared to those picking up their medications, those using delivery only were less likely to have a hospital stay (OR=0.691 [95% CI 0.507-0.943]) and no difference in odds of medication mistakes (OR=1.051 [95% CI 0.764-1.445]), while those using both methods were more likely to report hospital stays (OR=1.429 [95% CI 1.106-1.846]) and medication mistakes (OR = 1.576[95% CI 1.078-2.304]). Older adults who picked-up medications from a local pharmacy and had medications delivered were more likely to report medication mistakes and hospitalizations."} +{"text": "Scientific Reports 10.1038/s41598-019-39851-6, published online 27 February 2019Correction to: This Article contains errors in the legend of Figure 7.http://imaging.org.au/AMBMC/Model.\u201d\u201ca) Association matrix for calculating modules. The modules in (b) non-fasted and (c) fasted groups. Background image from should read:http://imaging.org.au/AMBMC/Model.\u201d\u201cAssociation matrix for calculating modules in (a) non-fasted and (b) fasted groups. The modules in (c) non-fasted and (d) fasted groups. Background image from"} +{"text": "Mycobacterium abscessus strain Taiwan-45 that lytically infects M. abscessus strain BWH-C; phiT45-1 also infects M. abscessus ATCC 1997 but not Mycobacterium smegmatis. Phage phiT45-1 has a 43,407-bp genome and carries a polymorphic toxin-immunity cassette associated with type VII secretion systems.Mycobacteriophage phiT45-1 is a newly isolated bacteriophage spontaneously released from Mycobacterium abscessus strain Taiwan-45 that lytically infects M. abscessus strain BWH-C; phiT45-1 also infects M. abscessus ATCC 19977 but not Mycobacterium smegmatis. Phage phiT45-1 has a 43,407-bp genome and carries a polymorphic toxin-immunity cassette associated with type VII secretion systems.Mycobacteriophage phiT45-1 is a newly isolated bacteriophage spontaneously released from Mycobacterium abscessus is often antibiotic resistant and refractory to treatment. M. abscessus infections are frequent among cystic fibrosis patients and those with bronchiectasis and can disseminate in immunosuppressed patients strains are mycobacterial species that do not cause tuberculosis or leprosy . Among tpatients , 3. The strains . The risernative .M. abscessus to contain prophages (M. abscessus Taiwan-45 onto a lawn of M. abscessus strain BWH-C (both provided by Chidiebere Akusobi and Eric Rubin) on solid medium at 37\u00b0C using standard methods (http://cobamide2.bio.pitt.edu) . Putativitt.edu) and HHpritt.edu) , 15. No itt.edu) . All tooM. smegmatis (48 and 49) and several predicted HNH endonucleases and immunity repressor (35) is consistent with phiT45-1 being temperate. Interestingly, phiT45-1 codes for a polymorphic toxin (PT) cassette, including an immunity protein (30), a polymorphic toxin (31) with RipA-like and WXG-100 domains (32) to phages isolated on megmatis , althougviridae) . Early l domains , 21, andins (32) , situateMW570842 and BioProject accession no. PRJNA488469. The sequencing reads are available in the SRA under accession no. SRX10050651.Phage phiT45-1 is available at GenBank under accession no."} +{"text": "T is an aerobic, non-motile and non-spore-forming Gram-positive coccus isolated from the stools of a Burkinabe woman. In this report, we present its phenotypic description including MALDI-TOF mass spectrometry analysis and genome sequencing. Strain Marseille-Q0835T; 2.9768-Mb genome exhibited a 41.9 mol% G+C content and 2699 predicted genes. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-Q0835T as the type strain of Enterococcus burkinafasonensis sp. nov., a new species within the family Enterococcaceae.Strain Marseille-Q0835 Enterococcus species purposely named Enterococcus burkinafasonensis.Culturomics strategy is a high-throughput culturing method . This stBiotyper 3.0 software and analysed against the main spectra of the bacteria included in the database.In September 2018, a fresh stool sample was collected from an apparently healthy 28-year-old Burkinabe woman who was admitted for diagnosis check-up in the Regional Tuberculosis Control Centre, Bobo-Dioulasso, Burkina Faso. A stool sample was sent to the collaborative laboratory at IHU in Marseille, France for culturomics analysis, which isolated an unidentified bacterial strain from the stool. The study was validated by the Science and Health Research Ethics Committee of Bobo-Dioulasso, under number (N/Ref.002-2018-CEIRS). The bacterium here referred to as strain Marseille-Q0835 was isolated on Columbia sheep blood agar after a 24-hour incubation under aerobic atmosphere at 37\u00b0C and pH 7.5. Purified colonies could not be identified by MALDI-TOF MS. The screening was performed on a Microflex LT spectrometer , as previously described [CodonCode Aligner software (http://www.codoncode.com). BLASTn research was conducted using nucleotide databases for cross-species comparison (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome). The search was limited to records that include sequences from type material, and exclude uncultured/environmental sample sequences. The result showed that strain Marseille-Q0835 exhibited a 97.80% sequence identity with Enterococcus gallinarum strain LMG 13129 (GenBank accession number NR_104559.2), the phylogenetically closest species with standing in nomenclature and sequencing using the Big Dye\u00ae Terminator v1.1 Cycle Sequencing Kit and ABI Prism 3130xl Genetic Analyzer capillary sequencer , as previously described . The 16Snclature . We consEnterococcus sp. Marseille- Q0835T showed negative catalase and oxidase activities. API 50CH and API ZYM tests were performed at 37\u00b0C under aerobic conditions and the results are summarized in Enterococcus sp. nov. strain Marseille-Q0835T with other bacterial species with the EZ1 DNA tissue kit and then sequenced on MiSeq technology with the Nextera XT Paired end (Illumina), as previously described . The assVelvet , Spades [Spades and Soapp Denovo ) on trimmmomatic ) or raw removed . The besEnterococcus sp. Marseille-Q0835T with closely related species was estimated using the OrthoANI software version 0.93.1 (https://www.ezbiocloud.net/tools/orthoani) [Enterococcus malodoratus strain DSM 20681 and Enterococcus gallinarum strain LMG 13129 to 91.81% for Enterococcus devriesei strain DSM 22802 and Enterococcus viikkiensis strain LMG 26075. When the isolate was compared with these closely related species, values ranged from 70.07% with E.\u00a0gallinarum strain LMG 13129 to 73.41% with Enterococcus pseudoavium strain CBA7133. These values are lower than the 95% threshold used to discriminate bacterial species [.The degree of genomic similarity of rthoani) . Values species .In silico DNA\u2013DNA hybridization values obtained using the GGDC version 2.0 online tool (http://ggdc.dsmz.de/ggdc.php) are reported in T, these values ranged from 20% with E.\u00a0devriesei strain DSM 22802 to 26.8% with Enterococcus faecium strain ISMMS VRE 1. Such values were lower than the 70% threshold recognized as delineating distinct species [. species ,17.TableT exhibited a 16S rRNA gene sequence divergence <98.65%, DNA\u2013DNA hybridization values\u00a0<\u00a070% and an OrthoANI value\u00a0<\u00a095% with its phylogenetically closest species with standing in nomenclature, together with unique phenotypic features. We formally propose strain Marseille-Q0835T as the type strain of the new species named Enterococcus burkinafasonensis.Strain Marseille-Q0835Enterococcaceae within the phylum Firmicutes. The type strain Marseille-Q0835T (CSUR P0835) was isolated after a 24-hour incubation at 37\u00b0C and pH 7.5 in an anaerobic atmosphere of a fresh stool sample collected from a 28-year-old Burkinabe woman. Colonies were smooth, white with entire edges with an average diameter of 1 mm. Bacterial cells were Gram-positive, coccus-shaped, non-motile and non-spore-forming with negative catalase and oxidase activities . The bacterium belongs to the family ties see .Fig.\u00a04HeT exhibits positive reaction for esterase lipase (C8), lipase (C14), naphthol-AS-BI-phosphohydrolase, \u03b1-galactosidase, \u03b2-galactosidase and N-acetyl-\u03b2-glucosaminidase, but negative reaction for alkaline phosphatase, esterase (C4), leucine arylamidase, valine arylamidase, cystine arylamidase, trypsin, \u03b1-chymotrypsin, acid phosphatase, \u03b2-glucuronidase, \u03b1-glucosidase, \u03b2-glucosidase, \u03b1-mannosidase and \u03b1-fucosidase. Using an API 50CH strip, positive reactions were obtained for d-galactose, d-glucose, d-fructose, l-arabinose, d-ribose, d-mannose, l-rhammose, d-mannitol, N-acetylglucosamine, arbutin, esculin, salicin, d-cellobiose, d-maltose, d-trehalose and gentibiose.Using an APIZYM strip, strain Marseille-Q0835T genome is 2.9768 Mb long, with a G-C content of 41.9%.The strain Marseille-Q0835The 16S rRNA gene and genome sequences were deposited in GenBank under accession number LR742708 and NZ_CACSLH000000000, respectively.T has been deposited in the French culture collection centre, Collection de Souches de l\u2019Unit\u00e9 des Rickettsies (CSUR), under the number Q0835.The strain Marseille-Q0835None to declare.10.13039/100007356IHU M\u00e9diterran\u00e9e Infection and by the French Government under the Investissements d'avenir (Investments for the Future) programme managed by the 10.13039/501100001665Agence Nationale de la Recherche , (reference: M\u00e9diterran\u00e9e Infection 10-IAHU-03).This work was funded by the"} +{"text": "E. coli. Terpene synthase activity was detected for 15 of these enzymes, and included mono-, sesqui- and diterpene synthase activities. A number of confirmed sesquiterpene synthases also exhibited promiscuous monoterpene synthase activity, suggesting that bacteria are potentially a richer source of monoterpene synthase activity then previously assumed. Several terpenoid products not previously detected in bacteria were identified, including aromandendrene, acora-3,7(14)-diene and longiborneol. Overall, we have identified promiscuous terpene synthases in bacteria and demonstrated that terpene synthases with substrate promiscuity are widely distributed in nature, forming a rich resource for engineering terpene biosynthetic pathways for biotechnology.Terpenes are the largest class of natural products with extensive structural diversity and are widely used as pharmaceuticals, herbicides, flavourings, fragrances, and biofuels. While they have mostly been isolated from plants and fungi, the availability and analysis of bacterial genome sequence data indicates that bacteria also possess many putative terpene synthase genes. In this study, we further explore this potential for terpene synthase activity in bacteria. Twenty two potential class I terpene synthase genes (TSs) were selected to represent the full sequence diversity of bacterial synthase candidates and recombinantly expressed in The vast majority of terpenoids have been isolated from plants and fungi; however, bacteria are also known producers of volatile odoriferous metabolites. All terpenoids are synthesised from the universal C5 isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are joined by isoprenyl transferases to form isoprenyl diphosphate substrates of varying lengths, such as geranyl diphosphate , farnesyl diphosphate and geranylgeranyl diphosphate . Terpene synthases (TSs) convert the linear isoprenyl diphosphate substrates into structurally diverse mono- (C10), sesqui- (C15) and diterpene (C20) scaffolds. Due to their structural diversity, terpenoids have a wide range of industrial applications as pharmaceuticals, flavourings, fragrances, antimicrobials, pesticides and alternative fuels . Al. AlSoranous work . When Scous work . These rubstrate .Streptomyces clavuligerus are well studied [S. clavuligerus accepts GPP and FPP [Kitasatospora setae with GPP yielded linalool as a major product and small amounts of several acyclic and cyclic monoterpenes [Until now, only two bacterial monoterpene synthases linalool synthase (bLinS) and 1,8-cineole synthases (bCinS) from studied and stru studied . Broad s studied , a bLinS and FPP , and incterpenes .CFM47198.1, ELQ82238.1, ACY98649.1, EXG82599.1, ABU58787.1, EJL71407.1, KFE96946.1 were tested for compound production with FPP and GPP but no terpenoids were detected. in vivo product formation, all identified TSs were cloned into the pBbB2a-GPPS backbone plasmid and co-expressed with pMVA plasmid in E. coli [in vivo conditions ,4,11-germacratriene as seen in the in vitro assays 11-diene and (+)-\u03b3-gurjunene when expressed in E. coli from E. coli . WhereasSM 43183 and EXG8SM 44712 producednditions .Streptomyces coelicolor A3(2) when expressed in E. coli produced various monoterpenes: \u03b2-myrcene, \u03b2-ocimene, linalool and geraniol from E. coli with two mutations D2G, C155G (ispAM22), which can function as geranylgeranyl diphosphate synthase [in vivo. GGPP synthase activity using the variant prenyltransferase was confirmed by overexpression of spata-13, 17-diene synthase from Streptomyces xinghaiensis [ispAM22). This yielded the diterpene spata-13,17-diene, where the produced compound was extracted using a nonane layer from Roseiflexus castenholzii DSM 13941 and Arctic Express (DE3) cells for recombinant protein expression.(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S4 TableKnown TSs annotated in the tree in (DOCX)Click here for additional data file.S1 FigNeighbour-joining tree constructed from the amino acid sequences of characterized terpene synthases in this study (underlined) and in previous studies. Geosmin synthases (dark red), 2-methylisoborneol synthases (orange), monoterpene (light blue), diterpene (dark blue) and sesquiterpene synthases (purple) are shown and uncharacterized bacterial terpene synthases in this study (in red).(DOCX)Click here for additional data file.S2 Fig-1) on a HP5 column and its retention time at 7.5 minutes. B. Mass spectra of geosmin.GC-MS traces showing the separation of geosmin (0.1 mg mL(DOCX)Click here for additional data file.S3 FigGC-MS chromatogram of geosmin synthase with 75 \u03bcM of FPP. Peak 1: geosmin (rt: 7.5), peak 2: Germacrene D (rt: 7.86), peak 3: germacradienol (rt: 8.84). B. Mass spectra of compounds observed in the extracts.(DOCX)Click here for additional data file.S4 Fig-1) produced in this study on a HP5 column. The internal standard, sec-butyl benzene , has a retention time of 9.5 minutes. Peak 1: R- Limonene (rt: 9.41). B: Mass spectra of limonene.A. GC-MS traces showing the separation of limonene (0.1 mg mL(DOCX)Click here for additional data file.S5 FigA. GC chromatogram of 10 \u03bcg of limonene synthase (pJBEI-6410) crude extracts with 75 \u03bcM of GPP. Peak 1: limonene (rt: 9.41). B. Mass spectra of limonene.(DOCX)Click here for additional data file.S6 FigA. GC-MS traces showing the separation of standard nerolidol mix (0.1 mg mL-1) on a HP5 column. B. MS spectra of -cis and -trans Nerolidol. C. GC-MS chromatogram of trans-nerolidol produced by AHY47823 with FPP. D. Mass spectra for trans-nerolidol produced by AHY47823.(DOCX)Click here for additional data file.S7 Fig-1) on a CP-Chirasil-DEX-CB column. B. GC-MS chromatogram of linalool isomers produced by AHY47823 with FPP. Samples were analyzed by GC on an Agilent Technologies 7890A GC system equipped with an FID detector, a 7693 auto sampler, and a CP-Chirasil-DEX-CB column . For linalool, the program initiated at a temperature of 70\u00b0C which was then increased to 90\u00b0C at 8\u00b0C/min. This was followed by an increase in temperature to 150\u00b0C at a rate of 2\u00b0C/min and then to 190\u00b0C at 40\u00b0C/min (1 min hold). The FID detector was maintained at a temperature of 200\u00b0C with a flow of hydrogen at 30 mL/min.A. GC-MS traces showing the separation of standard linalool mix (0.1 mg mL(DOCX)Click here for additional data file.S8 Fig-1) on a CP-Chirasil-DEX-CB column. B. GC-MS chromatogram of linalool isomers produced by AHY45426 with FPP. Samples were analyzed by gas chromatography on an Agilent Technologies 7890A GC system equipped with an FID detector, a 7693 auto sampler, and a CP-Chirasil-DEX-CB column . For linalool, the program initiated at a temperature of 70\u00b0C which was then increased to 90\u00b0C at 8\u00b0C/min. This was followed by an increase in temperature to 150\u00b0C at a rate of 2\u00b0C/min and then to 190\u00b0C at 40\u00b0C/min (1 min hold). The FID detector was maintained at a temperature of 200\u00b0C with a flow of hydrogen at 30 mL/min.A. GC-MS traces showing the separation of standard linalool mix (0.1 mg mL(DOCX)Click here for additional data file.S9 FigTotal ion chromatograms of products obtained from an incubation RrNerS (left) and RrBerS (right) with FPP for 3 hours at variable temperatures. Samples were analyzed by GC-QToF on HP5 column.(DOCX)Click here for additional data file.S10 FigA. \u03b1\u2013bergamotene produced by RrBerS, B. Aromandendrene produced by ScAroS, C and D. cadinene and longiborneol produced by BpLonS, E. germacrene D produced byKaGerS, F and G. copaene and acora-3,7(14)\u2013diene produced byAbAcoS, and H and I. \u03b2-elemene and 1(10),4,7(11)-germacra-triene produced by MiGerS.The reference spectra from the NIST library shown in blue and the compound spectra shown in red.(DOCX)Click here for additional data file.S11 FigA. GC-MS traces showing the separation of monoterpenoids (0.1 mg mL-1) standards used in this study on a HP5 column. The internal standard used, sec-butyl benzene , has a retention time of 9 minutes. Peak 1: cis-ocimene (rt: 9.56), peak 2: trans-ocimene (rt: 9.72), 3: linalool (rt: 10.43). B. Comparison of obtained mass spectra with NIST Library spectra and standard as shown in A. of products yielded by CAN96536 with GPP in in vitro assay.(DOCX)Click here for additional data file.S12 FigA. BpTPS; B. ScTPS1; C. CvTPS; D. SsTPS; E. ScTPS2; F. SniTPS; G.SnaTPS. The peaks in the chromatogram do not correspond to any terpenoids.GC-MS chromatograms of extracts profile with FPP are shown for (DOCX)Click here for additional data file.S13 FigA. GC-MS chromatogram for geosmin synthase products, B. mass spectra for Germacradienol, C\u2014G. Comparison of obtained mass spectra with NIST Library spectra of products yielded by GeoS.(DOCX)Click here for additional data file.S14 FigA\u2013B. SrGuaS C. TcCubS D. CaCubS.(DOCX)Click here for additional data file.S15 FigA. spata-13,17-diene produced by overexpression of ispAM22 and WP_095757924 in E. coli. B. Mass spectra of produced spata-13,17-diene.(DOCX)Click here for additional data file.S16 Fig(DOCX)Click here for additional data file.S17 Fig(DOCX)Click here for additional data file.S18 Fig(DOCX)Click here for additional data file."} +{"text": "Vitamin D (VitD) deficiency during pregnancy has been associated with adverse neonatal outcomes and increased risk of late pregnancy complications. We planned to correlate serum VitD biomarkers; 25-hydroxyvitamin D (25-OH-VitD) and 1,25-dihydroxyvitamin D levels; and their ratio with the frequency of feto-maternal pregnancy complications. A prospective cross-sectional case-control study was conducted at Aljouf Maternity and Children Hospital, Sakaka, Saudi Arabia, during the period of September 1, 2017 to September 30, 2019. 322 pregnant women were stratified into 2 groups: controls (110 cases) and complicated group (212 cases). The later comprised severe preeclamptic toxemia associated with intrauterine growth restriction (58 cases), gestational diabetes mellitus , abortion (26 cases), undisturbed ectopic pregnancy (16 cases), premature rupture of membranes , and, inevitable preterm labour (16 cases). After clinical assessment, peripheral blood samples were collected. Serum biomarkers were measured using specific immunoassays. The direct 1,25-diOH-VitD/25-OH-VitD ratio was calculated. Serum 25-OH-VitD indicated widely spreading VitD deficiency among participants with significantly higher levels in controls vs. GDM subgroup only. 1,25-diOH-VitD levels and the ratio were markedly reduced in the six complicated subgroups vs. controls, with non-significant differences amongst the complicated subgroups. ROC analysis showed very high sensitivity and specificity, to differentiate patients from controls, only for 1,25-diOH-VitD followed by the ratio but not 25-OH-VitD. In conclusions, 25-OH-VitD did not show significant changes except for GDM. 1,25-diOH-VitD levels and the ratio showed strong associations with pregnancy complications. Serum 1,25-di-OH-VitD and its ratio to 25-OH-VitD are more reliable and physiologically relevant biomarkers for VitD status in pregnancy. Vitamin D (VitD) deficiency became a global epidemic, particularly for women of reproductive age. Nuclear receptor-mediated, the dihydoxy active form of VitD, 1,25-diOH-VitD, controls cellular proliferation, differentiation and apoptosis through targeting \u22651000 genes. Nevertheless, pathogenetic role of hypovitaminosis D in a number of comorbidities is still hotly debated Linked to hypovitaminosis D, adverse fetal outcomes included abortion, intrauterine growth restriction, fetal death and congenital malformations. Maternal adverse effects involved preeclampsia, gestational diabetes mellitus (GDM) and increased risk of preterm labor We planned to assess the relationship between hypovitaminosis D and feto-maternal pregnancy complications and morbidities, using the more patho-physiologically relevant biomarkers. We measured serum 25-OH-VitD, as the established VitD biomarker, and, 1,25-diOH-VitD as a functional VitD biomarker, and their ratio, and, correlated them with the existing pregnancy feto-maternal status.This prospective cross-sectional case control study was carried out at Aljouf Maternity and Children Hospital, Sakaka, Saudi Arabia, during the period between September 1, 2017 and September 30, 2019. It was approved by the local bioethical committees of Jouf University and Ministry of Health (#6-16-4/40). Written informed consents were obtained. The exclusion criteria were uncertain diagnosis, obesity, anemia, endocrinal disorders , immobilization for any reason, on anti-convulsion drug, acute infections, malabsorption syndromes, comorbid chronic medical disorder , multiple pregnancy, antepartum hemorrhage and superimposed preeclampsia.Among 450 pregnant women attending the hospital, 322 voluntary participants fulfilling the inclusion criteria were recruited. The 322 participants were classified into 2 groups; control group of 110 women who had normal feto-maternal pregnancy, and, complicated pregnancy group comprising 212 participants. The latter group was further subdivided into: severe preeclamptic toxemia (PET) associated with intrauterine growth restriction , GDM (82 cases), abortion (26 cases), undisturbed ectopic pregnancy (16 cases), premature rupture of membranes , and, inevitable preterm labor (16 cases).After history taking and general examination , the head, face, neck, chest, heart, back, lower limbs and abdomen were systematically examined. The pregnancy was assessed ultra-sonographically for viability and fetal biometry to determine pregnancy duration and the expected fetal weight, condition of amniotic fluid and for diagnosing fetal anomalies, if present. Women with routine laboratory findings that contradict the inclusion criteria were excluded.oC. Specific quantitative ELISA immunoassay kits were used to measure total 25-OH-VitD and 1,25-DiOH-VitD . The direct 1,25-DiOH-VitD/25-OH-VitD ratio was calculated for each patient. Participants were stratified using the clinically relevant 25-OH-VitD cutoff levels of high/toxic as \u226550/>80 ng/mL, normal as \u226530-50 ng/mL, insufficient as \u226520 - <30 ng/mL, deficient as \u226510 - <20 ng/mL and severely deficient as <10 ng/mL Serum was recovered from peripheral blood samples by centrifugation and was aliquotted and stored till used at -80 Data was analyzed using SPSS . We expressed descriptive qualitative data as frequency and percentage, and, quantitative data as range and mean \u00b1 standard deviation (SD). Normal distribution was checked by Kolmogorov-Sminov test. One-way ANOVA with Tukey's post-test was employed for multiple comparisons. Correlation among variables was assessed by Spearman correlation coefficient test. Receiver Operating Characteristic (ROC) curve analysis was used to determine the area under curve (AUC) for 25-OH-VitD, 1,25-DiOH-VitD and their ratio to check their sensitivity and specificity to differentiate the cases from controls. P value of <0.05 at a confidence level of 95% was considered significant.Age was nonsignificantly different among all groups except for preeclamptics vs. each of controls (p = 0.011) and PROMs (p = 0.014), and, PROMs vs. GDM (p = 0.035). BMI showed nonsignificant difference among the investigated groups except comparing GDM vs. each of controls (p = 0.002), abortion (p = 0.02), ectopic pregnancy (p <0.001) and PROMs (p <0.001); and preeclamptics vs. each of ectopic pregnancy (p <0.028) and PROM (p = 0.045). Gravidity showed nonsignificant difference among the investigated groups except comparing GDM vs. each of controls (p <0.001), preeclamptics (p <0.001), abortion (p <0.036), ectopic pregnancy (p = 0.002) and PROMs (p = 0.002). Parity showed nonsignificant difference among the investigated groups except comparing GDM vs. each of preeclamptics (p <0.001), abortion (p = 0.035), ectopic pregnancy (p = 0.002) and PROMs (p <0.035). Duration of pregnancy showed very strong significant difference among the investigated groups with a few non-significant exceptions; it was significantly different comparing controls vs. all complication subgroups (p <0.01 - 0.001) except GDM, comparing preeclamptics vs. all other subgroups (p <0.05 - <0.001) except preterm labour, comparing GDM vs. the others (p <0.001), comparing abortion vs. the others (p <0.001) except ectopic pregnancy, and, comparing ectopic pregnancy vs. the others (p <0.001) except PROMs.Serum 25-OH-VitD levels showed nonsignificant difference among the investigated groups except comparing GDM vs. each of controls (p <0.001) and ectopic pregnancy (p = 0.01). Serum 1,25-diOH-VitD levels showed nonsignificant difference among the investigated groups of patients. However, controls had markedly higher levels vs. each of the six complicated groups (p <0.001). Similarly, the direct 1,25-diOH-VitD/25-OH-VitD ratio showed very marked significant reduction comparing controls vs. each of the six patients' groups (p <0.001), albeit, with nonsignificant difference among the complicated groups.Using serum 25-OH-VitD as the biomarker for VitD status, 43.636% of controls were deficient (\u226510 ng/mL), 38.181% were insufficient (\u226520 ng/mL), and, equal proportions (9.09%) were either normal (\u226530 ng/mL) or having toxic levels (>80 ng/mL). 82.759% of preeclamptic cases were insufficient, 13.793% were deficient and 3.448% had normal levels. 82.927% of GDM cases were deficient, 12.195% were insufficient and 4.878 had normal levels. 84.615% of abortion cases deficient, and equal proportions (7.692%) had either insufficient or toxic levels. 50.0% of ectopic pregnancy cases were deficient, 37.5% were insufficient and the rest (12.5%/2) had toxic levels. 71.429%/ of PROMs cases were deficient and 28.571% were insufficient. 75% of preterm labor cases were insufficient and 25.0% were deficient. Fortunately, severe deficiency (<10 ng/mL) was not observed in our cases. Therefore, VitD insufficiency/deficiency is widely spreading among the study participants . Controls presented a better picture only considering insufficiency/deficiency proportion, and, % of normal/super-normal levels.ROC curve analysis showed that 1,25-DiOH-VitD level is the most sensitive and most specific biomarker for differentiating between cases and controls; with an AUC of 0.965 . It is followed by 1,25-DiOH-VitD25-OH-VitD ratio; with AUC of 0.843 . 25-OH-VitD levels fell near the diagonal line with no effect, i.e., showing least sensitivity and least specificity , parity (0.468/<0.001) and BMI (0.837/<0.001), and negative relationship with the ratio (-0.155/<0.05). Gravidity showed positive relationship vs. parity (0.958/<0.001) and BMI (0.480/<0.001). Parity correlated positively with BMI (0.448/<0.001). BMI correlated negatively vs. the ratio (-0.184/= 0.027). Pregnancy duration correlated negatively with 1,25-DiOH-VitD (-0.241/<0.006) and ratio (-0.192/= 0.022). 25-OH-VitD correlated positively vs. 1,25-DiOH-VitD (0.157/<0.05) and negatively vs. the ratio (-0.647/<0.001). 1,25-DiOH-VitD correlated positively with the ratio (0.562/<0.001).For preeclamptic cases, age had positive correlation vs. gravidity (0.682/<0.001), parity (0.608/<0.001) and BMI (0.690/<0.001), and, negative correlation vs. 1,25-DiOH-VitD (-0.267/= 0.021). Gravidity related had positively with parity (0.962/<0.001) and BMI (0.497/<0.001), but, negatively vs. 1,25-DiOG-VitD (-0.282/= 0.016). Parity correlated positively vs. BMI (0.424/<0.001), and, negatively with 1,25-DiOH-VitD (-0.218/<0.05). BMI correlated positively vs. duration of pregnancy (0.333/= 0.005) and negatively vs. 1,25-DiOH-VitD (-0.275/= 0.017). 25-OH-VitD correlated negatively with the ratio (-0.490/<0.001). 1,25-DiOH-VitD correlated positively vs. the ratio (0.853/<0.001).For GDM cases, age correlated positively vs. each of gravidity (0.680/<0.001), parity (0.732/<0.001), BMI (0.657/<0.001) and 25-OH-VitD (0.239/= 0.015), but, negatively vs. each of 1,25-DiOH-VitD (-0.179/<0.05) and the ratio (-0.320/<0.002). Gravidity correlated positively with parity (0.865/<0.001), BMI (0.671/<0.001) and 25-OH-VitD (0.216/<0.026), and, negatively vs. duration of pregnancy (-0.294/<0.004) and the ratio (-0.183/<0.05). Parity correlated positively vs. BMI (0.725/<0.001) and 25-OH-VitD (0.187/0.047), and, negatively vs. duration of pregnancy (-0.179/<0.05). BMI correlated positively vs. 25-OH-VitD (0.412/<0.001) and negatively vs. the ratio (-0.225/<0.021). 25-OH-VitD correlated negatively with the ratio (-0.757/<0.001). 1,25-DiOH-VitD had positive correlation vs. the ratio (0.592/<0.001).For abortion cases, age correlated positively with gravidity (0.406/<0.02), parity (0.535/= 0.0024), BMI (0.757/<0.001), and pregnancy duration (0.337/= 0.046), and, negatively vs. 1,25-DiOH-VitD (-0.669/<0.001) and the ratio (-0.380/<0.028). Gravidity correlated positively with parity (0.815/<0.001) and duration of pregnancy (0.565/= 0.0013), and, negatively vs. each of 1,25-DiOH-VitD (-0.333/= 0.048) and the ratio (-0.381/ = 0.027). Parity related positively with duration of pregnancy (0.358/= 0.036). BMI associated negatively with 1,25-DiOH-VitD (-0.385/= 0.026). Pregnancy duration correlated negatively vs. 1.25-DiOH-VitD (-0.371/<0.031) and the ratio (-0.490/<0.006). 25-OH-VitD correlated negatively vs. the ratio (-0.773/<0.001). 1,25-DiOH-VitD correlated positively vs. the ratio (0.665/<0.001).For the ectopic pregnancy cases, age correlated positively vs. gravidity (0.884/<0.001), parity (0.927/<0.001), and BMI (0.922/<0.001), but, negatively vs. 1,25-DiOH-VitD (-0.639/<0.005) and the ratio (-0.527/<0.02). Gravidity correlated positively vs. parity (0.906/<0.001) and BMI (0.854/<0.001), and, negatively vs. 1,25-DiOH-VitD (-0.565/<0.013). Parity correlated positively with BMI (0.933/<0.001), and, negatively vs. 1,25-DiOH-VitD (-0.624/<0.006) and the ratio (-0.437/<0.05). BMI correlated positively vs. duration of pregnancy (0.433/<0.05), and, negatively vs. 1,25-DiOH-VitD (-0.443/= 0.044). Pregnancy duration related negatively vs. 1,25-DiOH-VitD (-0.504/<0.027). 25-OH-VitD correlated negatively vs. the ratio (-0.690/= 0.002). 1,25-DiOH-VitD correlated positively with the ratio (0.647/= 0.004).Among PROMs cases, age correlated positively vs. gravidity (0.578/<0.018), parity (0.578/<0.018), BMI (0.727/= 0.002), 1,25-DiOH-VitD (0.500/<0.038) and the ratio (0.474/<0.05). Gravidity correlated positively vs. parity (1.0/<0.001), BMI (0.517/= 0.03) and duration of pregnancy (0.459/<0.05), but, negatively vs. 25-OH-VitD (-0.543/<0.026). Parity associated positively vs. BMI (0.517/= 0.03) and pregnancy duration (0.467/<0.05), but, negatively vs. 25-OH-VitD (-0.543/<0.026). BMI positively correlated with 1,25-DiOH-VitD (0.800/<0.001) and the ratio (0.655/= 0.007). 25-OH-VitD correlated positively with 1,25-DiOH-VitD (0.468/<0.048). 1,25-DiOH-VitD correlated positively vs. the ratio (0.786/<0.001).Within the preterm labor cases, age correlated positively vs. gravidity (0.898/<0.001), parity (0.908/<0.001), BMI (0.952/<0.001), and the ratio (0.452/<0.042), but, negatively vs. 25-OH-VitD (-0.439/<0.05). Gravidity correlated positively vs. parity (0.933/<0.001), BMI (0.802/<0.001) and the ratio (0.503/= 0.025). Parity correlated positively vs. BMI (0.835/<0.001) and the ratio (0.454/= 0.04), but, negatively with 25-OH-VitD (-0.454/= 0.04). BMI associated negatively with 25-OH-VitD (-0.500/<0.027), but, positively vs. the ratio (0.548/= 0.016). 1,25-DiOH-VitD correlated positively vs. the ratio (0.786/<0.001).st trimester of pregnancy, PROMs occurs after 37th weeks and before onset of labor and GDM is common at beginning of the last trimester), it showed significant differences comparing all groups Age was insignificantly different among our complicated groups. It had significant difference only when controls are compared to preeclamptics. Preeclampsia usually attacks extremely aged mothers; mainly primigravida. Gravidity showed a significant difference between the controls and GDM groups. Repeated pregnancy is a definite risk factor for GDM development. BMI was significantly different only comparing GDM and controls. GDM usually associates with higher BMI. As the gestational age is unique for the occurring complication the traditionally low VitD foods, 2) a scalding local summer sun and ice-cold winter that give very narrow room for sun exposure, 3) low supplement intake, and, 4) absence of a national mandatory VitD food fortification program.The difficulties faced us carrying out this study included: 1) Absence of a reasonable number of other pregnancy complications such as congenital anomalies, stillbirth, isolated IUGR, 2) we could not correlate findings with comorbid rate of infection and inflammation, length of hospital stays, and long-term outcomes, & 3) Longitudinal analysis was not accessible.VitD deficiency/insufficiency is widely spreading in the studied population of pregnant women. Levels of 25-OH-VitD were not different among controls and complicated pregnancies except for a significantly lower level in GDM. 25-OH-VitD levels did not correlate with most of the characteristics of participants and pregnancy complications. 1,25-diOH-VitD and its ratio to 25-OH-VitD revealed very highly significant reduction in complicated pregnancy and were highly sensitive and specific in differentiating controls from complicated pregnancies. They also correlate with most of the characteristics of the participating women. 1,25-diOH-VitD and its ratio to 25-OH-VitD are potentially more functionally relevant biomarkers for VitD status particularly during pregnancy."} +{"text": "Noroviruses are a common cause of acute gastroenteritis in all age groups. These small non-envelope viruses with a single-stranded (+)RNA genome are characterized by high genetic variability. Continuous changes in the genetic diversity of co-circulating noroviruses and the emergence of new recombinant variants are observed worldwide. Recently, new recombinant noroviruses with a novel GII.P16 polymerase associated with different capsid proteins VP1 were reported. As a part of the surveillance study of sporadic cases of acute gastroenteritis in Novosibirsk, a total of 46 clinical samples from children with diarrhea were screened in 2016. Norovirus was detected in six samples from hospitalized children by RT-PCR. The identified noroviruses were classified as recombinant variants GII.P21/GII.3, GII. Pe/GII.4_Sydney_2012, and GII.P16/GII.4_Sydney_2012 by sequencing of the ORF1/ORF2 junction. In Novosibirsk, the first appearance of the new recombinant genotypeGII.P16/ GII.4_Sydney_2012 was recorded in spring 2016. Before this study, only four complete genome sequences of the Russian GII.P16/GII.3 norovirus strains were available in the GenBank database. In this work, the complete genome sequence of the Russian strain Hu/GII.P16-GII.4/RUS/Novosibirsk/NS16-C38/2016 (GenBank KY210980) was determined. A comparison of the nucleotide and the deduced amino acid sequences showed a high homology of the Russian strain with GII.P16/GII.4_Sydney_2012 strains from other parts of the world. A comparative analysis showed that several unique substitutions occurred in the GII.P16 polymerase, N-terminal p48 protein, and minor capsid protein VP2 genes, while no unique changes in the capsid VP1 gene were observed. A functional significance of these changes suggests that a wide distribution of the strains with the novel GII.P16 polymerase may be associated both with several amino acid substitutions in the polymerase active center and with the insertion of glutamic acid or glycine in an N-terminal p48 protein that blocks the secretory immunity of intestinal epithelial cells. Further monitoring of genotypes will allow determining the distribution of norovirus recombinants with the polymerase GII.P16 in Russia. Noroviruses areconsidered to be one of the common causes of outbreaks andsporadic cases of acute gastroenteritis (AGE) in humans ofall ages . Norovirus infection can causesevere outcomes of the disease in very young and elderlyindividuals, as well as chronic diarrhea, lasting from severalmonths to several years, in immunocompromised and cancerpatients, and humans after organ transplantation . Dueto the low infectious dose and highresistance in the environment, noroviruses are rapidly transmittedperson-to-person, by food and water . A meta-analysis of epidemiological datafrom many countries showed that the incidence of norovirusinfection among patients with AGE regardless of their age was17\u201320 % in 2008\u20132014 . The prevalenceof asymptomatic norovirus infection is estimated from 4 to18 % in different regions .The polyadenylated single-stranded (+)RNA genome ofnorovirus (~7.5 kb) contains three overlapping open readingframes (ORF1\u2013ORF3) . ORF1 encodes alarge polyprotein that is post-translationally cleaved by viralprotease into six nonstructural proteins, including RNAdependentRNA polymerase (RdRp); ORF2 and ORF3 encodemajor (VP1) and minor (VP2) capsid proteins, respectively.Two mechanisms of norovirus genetic variability have beenidentified: point mutations and recombination . Due to recombination events occurring in the norovirusgenome near the overlapping region of the 3\u02b9-end of ORF1(RdRp) and 5\u02b9-end of ORF2 (VP1), a dual nomenclature ofnoroviruses defining the RdRp/VP1 genotypes was recentlydeveloped .https://www.rivm.nl/mpf/typingtool/norovirus/). The average duration ofgenotype-specific immunity after norovirus infection can befrom 4 to 8 years , however, due to theexistence of a wide range of genetic variants, subsequent norovirusinfection with other antigenic variants or \u201cimmunotypes\u201dcan occur in a shorter time .Noroviruses exhibit significant genetic and antigenic diversity.Based on the VP1 amino acid sequence, noroviruses arecurrently classified into at least seven genogroups (GI\u2013GVII),which are further sub-divided into more than forty genotypes. It has been established that GI, GIIand GIV noroviruses can cause disease in humans . In the most common genogroup GII,at least 31 RdRp genotypes and 23 VP1 genotypes are distinguished,and their combination is designated as GII.Px/GII.x. In 2012, a newrecombinant GII.4 norovirus classified as GII.Pe/GII.4_Sydney_2012 appeared and later became the dominant strainworldwide . However, changes in themolecular epidemiology of norovirus have been observed inrecent years. In the winter season 2014/2015, a new GII.P17/GII.17 strain, which was first registered in China, quicklyreplaced the GII.Pe/GII.4_Sydney_2012 variant and initiallyspread to Asia, and later, to other regions . Recently, the prevalence of new recombinant norovirusstrains with the GII.P16 polymerase associated with multipleVP1 genotypes, including GII.4_Sydney_2012, has beenreported in different regions .In Novosibirsk, long-term monitoring of the genetic diversityof enteric viruses showed that noroviruses GII.P4/GII.4were a common cause of sporadic AGE cases in 2003\u20132012,while noroviruses with the GII.P16 polymerase were rarelydetected . In the spring of2016, we recorded the emergence of a new recombinant variantGII.P16/GII.4_Sydney_2012 in Novosibirsk. Before thisstudy, only four complete genome sequences of recombinantGII.P16/GII.3 noroviruses from Russia were available in theGenBank database . Theaim of this study was complete genome sequencing of the new Russian GII.P16/GII.4_Sydney_2012 strain and comparativeanalysis with similar strains from other regions and with Russian2005\u20132012 strains in which the GII.P16 polymerase wasin association with various other VP1 genotypes.Origin of virus strains. As a part of the surveillance studygenetic diversity of enteric viruses, clinical samples werecollected from children with diarrhea who were hospitalizedat Children\u2019s City Clinical Hospital No. 3 and were onoutpatient treatment in 2016. Written informed consent wasobtained from each parent/guardian of the child to participatein the study, in compliance with voluntariness in accordancewith the Federal Law \u201cOn the Principles of the Protection ofCitizens\u2019 Health in the Russian Federation\u201d. Detection anddifferentiation of viral RNA were performed by RT-PCR usinga verified laboratory primer panel, as previously described.Sequencing. The detected noroviruses were characterizedby sequencing of the genome region (~1400 nt), includingthe ORF1/ORF2 junction (20 nt). The nucleotide sequenceswere determined by the Sanger method using the BigDye\u2122Terminator v.3.1 Cycle Sequencing Kit and 3500 GeneticAnalyzer . The completegenome sequencing of the strain Hu/GII.P16-GII.4/RUS/Novosibirsk/NS16-C38/2016 was performed by the \u201cprimerwalking\u201dmethod using a panel of newly designed primers.The obtained data were analyzed by FinchTV . Partial fragments were assembled into a full-length genomesequence using SeqMan from the Lasergene EvolutionSuite software package .Norovirus genotype was determined using the Norovirus TypingTool v. 2.0 .Phylogenetic analysis. Reference norovirus sequenceswere obtained by search on BLAST 2.9.0+ (https://www.ncbi.nlm.nih.gov/). ClustalW alignment and phylogenetic analysisof nucleotide sequences were performed using MEGA 7(https://www.megasoftware.net/). Phylogenetic trees wereconstructed using the Neighbor-Joining method with theKimura 2-parameter model. The analysis was performed with abootstrap of 1000 replicas; only values >80 % were indicated.The identity of the nucleotide and amino acid sequences was calculated using BioEdit v7.2.6 software (http://www.mbio.ncsu.edu/bioedit/bioedit.html). The variability of the deducedamino acid sequences of the polyprotein comprising GII.P16RdRp, as well as the capsid proteins VP1 and VP2 of variantGII.4_Sydney_2012 was determined using the Sequence DataExplorer from MEGA 7.The nucleotide sequences obtained in this study were annotatedand deposited in the GenBank database with accessnumbers KY210919, KY210976\u2013KY210980, KY210983,MG892912 \u0438 MG892914.https://www.ncbi.nlm.nih.gov/) and RIVM (https://www.rivm.nl/mpf/typingtool/norovirus/) showed that the identified noroviruses belongedto three recombinant variants (Table 1).A total of 46 fecal samples from children aged 1 monthto 8 years were tested by RT-PCR. Enteric viruses weredetected in 15 (32.6 %) samples. Norovirus infection wasidentified in six hospitalized children aged 1 to 9 months.Analysis of nucleotide sequences (~1400 nt), including theORF1/ORF2 junction, by BLAST (The nucleotide sequences of the norovirus strains that weremost homologous to the sequences obtained in this studywere determined by search on BLAST. Isolate NS16-C32related to GII.P21/GII.3 genotype had high homology withstrains circulating in Novosibirsk (97.6\u201398.9 %) in 2010\u20132012 and in Europe (96.5\u201397.2 %) in2014\u20132016 . Two isolates NS16-C12and NS16-C13 genotyped as GII.Pe/GII.4_Sydney_2012had a high similarity (99.3\u201399.5 %) with GII.Pe/GII.4 strains(2014\u20132016) from Southeast Asia and Great Britain and 96.9\u201397.1 % identity with strains that previouslycirculated in Novosibirsk .Nucleotide sequences of three remaining isolates NS16-C36,NS16-C37, and NS16-C38 related to the new genotype GII.P16/GII.4_Sydney_2012 had 100 % identity to each otherand 96.2 % homology with isolates NS16-C12 and NS16-C13. Genetic similarity of isolates NS16-C36, NS16-C37 andNS16-C38 with strains GII.P16/GII.4_Sydney_2012 fromother regions was 97.4\u201398.9 %.Based on complete norovirus sequences available in theGenBank database, several sets of original primers were designedfor complete sequencing of ORF1, RdRp, ORF2, and ORF3 of different genotypes. For two isolates, NS16-C13and NS16-C32, nucleotide sequences (~4300 nt), includingRdRp, ORF2 and ORF3, were identified and depositedin the GenBank database as strains Hu/GII.Pe-GII.4/RUS/Novosibirsk/NS16-C13/2016 (GenBank KY210977) andHu/GII.P21-GII.3/RUS/Novosibirsk/NS16-C23/2016 (Gen-Bank KY210919).For isolate NS16-C38, complete genome sequence(7560 nt) including the 3\u02b9-untranslated region (47 nt) wasdetermined and deposited in the GenBank database as thestrain Hu/GII.P16-GII.4/RUS/Novosibirsk/NS16-C38/2016(GenBank KY210980). Analysis of the deduced amino acidsequences showed that ORF1 (5100 nt) encoded a polyproteinof 1700 amino acid (aa) residues of length; ORF2 (1623 nt) andORF3 (807 nt) encoded the capsid proteins VP1 (541 aa) andVP2 (269 aa), respectively. The complete nucleotide sequenceof the Russian strain Hu/GII.P16-GII.4/RUS/Novosibirsk/NS16-C38/2016 had 98\u201399 % homology with recombinantGII.P16/GII.4_Sydney_2012 strains that appeared in theUSA and the UK in the winter season 2015/2016. Since thestrain studied was recombinant, a comparative analysis wasperformed separately for each ORF.Comparative analysis of the ORF1Phylogenetic analysis of complete ORF1 nucleotide sequenceswith GII.P16 RdRp available in GenBank showed that theanalyzed strains were divided into three clusters ; separate clades (supported on >85 %) within them wereformed by strains with the same VP1 genotype .Cluster III contained contemporary recombinant strains withGII.P16 RdRp associated with VP1 of four genotypes, GII.1,GII.2, GII.3, and GII.4_Sydney_2012. The ORF1 homology ofthe Russian strain Hu/GII.P16-GII.4/RUS/Novosibirsk/NS16-C38/2016 with other strains of cluster III was 97.9\u201399 %.Comparative analysis showed that the complete ORF1sequences of the GII.P16 RdRp strains varied from 5094 nt(reference strain AY772730_Hu/GII.P16-GII.16/DEU/Neustrelitz/2000) to 5100 nt (cluster III). When aligned, theGAA insert in the region encoding the N-terminal protein p48was found in recombinant GII.P16/GII.17 strains (cluster I)and in all strains from cluster II. Additional insertion of GAAor GGA was detected in contemporary recombinant strainsfrom cluster III in the same region of the p48 gene. For ORF1,1317 (25.8 %) variable sites were determined, of which906 (17.7 %) were informative, i. e. were in two or more strains.For polyprotein, 182 (10.7 %) variable sites were found,104 (6.1 %) of which were informative (Table 2). Comparativeanalysis showed that 14 variable sites were unique to thenovel GII.P16 RdRp lineage (cluster III), and the substitutionsin seven positions 52, 53, 644, 845, 853, 1546, and 1549resulted in a change in amino acid chemistry. An assessmentof the functional significance of the changes revealed thatthree non-synonymous substitutions and77E/G insert were found in p48, which plays a role in virusentry through the host cell membrane . Four of the five non-synonymous substitutions within GII.P16 RdRp occurredin the active center (see Table 2), and this may have affectedthe norovirus transmission.Comparative analysis of the ORF2In addition to the sequences determined in this study, phylogeneticanalysis of ORF2 included strains of different capsidgenotypes, which were identified in combination with theGII. P16 RdRp. On phylogenetic tree of the partial ORF2sequences,the analyzed strains formed separate clusters inaccordance with the capsid genotype and were further subdividedinto separate clades depending on the RdRp genotype.The GII.4 nucleotide sequences divided into two majorclades. The most polymorphic clade includes strains withthe GII.P4 RdRp, which previously circulated in Novosibirskand belonged to six GII.4 epidemic variants: Farmington_Hills_2002, Hunter_2004, Yerseke_2006a, Den_Haag_2006b,Apeldoorn_2007 and New-Orleans_2009 . The second clade was formed by GII.4_Sydney_2012 strains, which were further divided into two separateclusters, depending on the RdRp genotype \u2013 GII.Pe or GII. P16(supported on 99\u2013100 %).The ORF2 similarity of the Russian strain Hu/GII.P16-GII.4/RUS/Novosibirsk/NS16-C38/2016 to the GII.P16/GII.4_Sydney_2012 strains from other regions was 98.8\u201399 %.Comparison of complete ORF2 sequences of the GII. P16/GII.4_Sydney_2012 strains with the GII.Pe/GII.4_Sydney_2012 and GII.P4/GII.4_New_Orleans_2009 strains revealed236 (14.5 %) variable sites, of which 132 (8.1 %) were informative.In deduced amino acid sequences of VP1, eightvariable sites were unique to the GII.4_Sydney_2012 variant, which distinguishedthem from the GII.4_New_Orleans_2009 variant,and only two of these changes (at 368 and 373) were locatedin the hypervariable epitope A (Table 3). Notably, only onevariable site at position 540 was unique to the new lineage ofGII.P16/GII.4_Sydney_2012, however, it was not located inantigenic regions of the major capsid protein VP1.Comparative analysis of the ORF3Phylogenetic analysis of complete ORF3 sequences ofstrains with the GII.P16 RdRp showed that the analyzedsequences were divided into separate clusters depending onthe VP1 genotype . Within each VP1 genotype, strainswith different RdRp genotypes were grouped into separateclades. Comparative analysis of complete ORF3 sequencesof GII.P16/GII.4_Sydney_2012 strains with those of GII.Pe/GII.4_Sydney_2012 and GII.P4/GII.4_New_Orleans_2009strains revealed 109 (13.5 %) variable sites, and 55 (6.8 %)of them were informative.In the deduced amino acid sequences of the minor capsidprotein VP2 of GII.4_Sydney_2012 strains, eight uniquevariable sites at positions 81, 108, 148, 149, 158, 164, 205,and 241 were identified (Table 4), which differed them fromGII.4_New_Orleans_2009 strains. In addition, two other variablesites (at 155 and 157) were unique to the new lineage ofGII.P16/GII.4_Sydney_2012.This work is a part of long-term monitoring of the geneticdiversity of noroviruses associated with sporadic AGE cases inNovosibirsk, Russia. In March 2016, a new variant of GII. P16/GII.4_Sydney_2012 norovirus was first isolated in feces fromhospitalized children. In samples from hospitalized adults,this variant was first identified in autumn 2016 . GenBank searchshowed that in the European part of Russia, similar GII.4_Sydney_2012 noroviruses (GenBank MK033810\u2013MK033811)were found in samples of children from Nizhny Novgorod alsoat the end of 2016, unfortunately, the RdRp genotype was notdetermined for those isolates.Until recently, noroviruses with the GII.P16 RdRp wereconsidered uncommon, although local outbreaks associatedwith GII.P16/GII.2 (2009/2010 and 2012/2014) were reportedin Japan , and thosecaused by GII.P16/GII.13 (2009/2010) in Nepal . During the 10-year (2003\u20132012) monitoring ofnorovirus genotypes in Novosibirsk, Russia , GII.P16 RdRp was identified in five samples:GII.P16/GII.16 , GII.P16/GII.3 and GII.P16/GII.5(GenBank HM596590). Until 2016 in the Russian Federation,except Novosibirsk, GII.P16/GII.3 noroviruses were rarelydetected in Omsk andSmolensk (GenBank KF895841), and GII.P16/GII.16 in Moscowand St. Petersburg . InNovosibirsk, recombinant noroviruses with the novel GII.P16RdRp, which differed from RdRp of variant 2010\u20132012 andwas in combination with multiple capsid genotypes , were often found in samplesfrom adult AGE patients since 2016 (data not published).Our results confirmed the hypothesis of the spread of newlyemerged recombinant norovirus strains with the novel GII. P16RdRp in different regions of the world .Before this study, only four complete genome sequencesof recombinant GII.P16/GII.3 norovirus strains from Russianwere available in the GenBank database . In this work, complete genome sequenceof the Russian strain Hu/GII.P16-GII.4/RUS/Novosibirsk/NS16-C38/2016 related to the newly emerged recombinantgenotype GII.P16/GII.4_Sydney_2012 was determined. Thecomparative analysis showed that unique changes occurred inthe amino acid sequences of two non-structural proteins \u2013 theN-terminal protein p48 and GII.P16 RdRp, as well as in the minor capsid protein VP2; at the same time, no significantchanges were detected in the major capsid protein VP1 ofGII.4_Sydney_2012.RNA-dependent RNA polymerase plays a crucial role inthe replication of the norovirus genome. Recent studies haveshown that the RdRp coding region is changing quickly;however, variable mutation rates were observed in differentRdRp genotypes . Our findings are consistentwith the hypothesis of Ruiz et al. (2017) that unusualworldwide distribution of the novel GII.P16 lineage is mainlydue to changes in the polymerase active center, which couldincrease the norovirus transmission. However, we assumethat changes in the N-terminal protein p48 have also playedsome role in the wide distribution of these new recombinantstrains. It was previously shown that p48 can bind the hostrestriction factors in an infected cell, allowing norovirus toavoid the host immune response, and its coding region hasa higher evolution rate than the complete norovirus genome. In addition, it is known that p48 is ableto block the local secretory immunity of intestinal epithelialcells, induce the disintegration of the Golgi apparatus anddisrupt the intracellular traffic of proteins . We assume that the insertion ofglutamic acid residue into the region, which already containsfour consecutive glutamic acid residues, increases the negativecharge at the N-terminus of p48, and this may affect boththe norovirus entry into the intestinal epithelial cells and theGolgi disintegration rate.The minor capsid protein VP2, playing an important role invirus replication and viral particlestability , is also involved in modulation ofthe host immune response . The mutationrate of VP2 is higher than that for the major capsid protein VP1. Identified amino acid substitutionscould affect the ability of VP2 to suppress the presentationof antigens on cell membranes and the induction of humanprotective immunity.As the result of long-term monitoring of noroviruses RdRp/VP1 genotypes, the emergence of the novel GII.P16/GII.4_Sydney_2012 recombinant was recorded in Russia. Theanalysis showed that the distribution of the newly emergedrecombinant GII.P16/GII.4_Sydney_2012 is not associatedwith changes in the antigenic profile of the major capsid proteinVP1, which usually led to the emergence of new epidemicGII.4 variants. In GII.P16/GII.4_Sydney_2012 strains, a certainrole was probably played by changes in the minor proteinVP2 that might affect the antigenic composition of the viralparticle and help to avoid the cellular immune response. Inaddition, the multiple mutations in two non-structural proteins,the N-terminal protein of p48 and RdRp, probably increasedthe transmission of noroviruses with the novel GII.P16 RdRp.Further monitoring of genotypes will allow estimation of thespread of emerged recombinant noroviruses with the novelGII.P16 RdRp lineage in the Russian Federation and predictionof their epidemic potential.The authors declare no conflict of interest.Ahmed S.M., Hall A.J., Robinson A.E., Verhoef L., Premkumar P.,Parashar U.D., Koopmans M., Lopman B.A. Global prevalenceof norovirus in cases of gastroenteritis: a systematic review andmeta-analysis. Lancet Infect. Dis. 2014;14(8):725-730. DOI10.1016/S1473-3099(14)70767-4.Barreira D.M.P.G., Fumian T.M., Tonini M.A.L., Volpini L.P.B.,Santos R.P., Ribeiro A.L.C., Leite J.P.G., Souza M.T.B.M.,Brasil P., da Cunha D.C., Miagostovich M.P., Spano L.C. Detectionand molecular characterization of the novel recombinantnorovirus GII.P16-GII.4 Sydney in southeastern Brazil in2016. PLoS One. 2017;12(12):e0189504. DOI 10.1371/journal.pone.0189504.Bartsch S.M., Lopman B.A., Ozawa S., Hall A.J., Lee B.Y. Globaleconomic burden of norovirus gastroenteritis. PLoS One. 2016;11(4):e0151219. DOI 10.1371/journal.pone.0151219.Bidalot M., Th\u00e9ry L., Kaplon J., de Rougemont A., Ambert- BalayK. Emergence of new recombinant noroviruses GII. p16-GII.4 and GII.p16-GII.2, France, winter 2016 to 2017. EuroSurveill. 2017;22(15):pii=30508. DOI 10.2807/1560-7917.ES.2017.22.15.30508.Brown J.R., Roy S., Shah D., Williams C.A., Williams R., Dunn H.,Hartley J., Harris K., Breuer J. Norovirus transmission dynamicsin a pediatric hospital using full genome sequences. Clin. Infect.Dis. 2019;68(2):222-228. DOI 10.1093/cid/ciy438.Brown J.R., Roy S., Tutill H., Williams R., Breuer J. Super-infectionsand relapses occur in chronic norovirus infections. J. Clin.Virol. 2017;96:44-48. DOI 10.1016/j.jcv.2017.09.009.Bull R.A., White P.A. Mechanisms of GII.4 norovirus evolution.Trends Microbiol. 2011;19:233-240. DOI 10.1016/j.tim.2011.01.002.Cannon J.L., Barclay L., Collins N.R., Wikswo M.E., Castro C.J.,Magana L.C., Gregoricus N., Marine R.L., Chhabra P., VinjeJ. Genetic and epidemiologic trends of norovirus outbreaksin the United States from 2013 to 2016 demonstrated emergenceof novel GII.4 recombinant viruses. J. Clin. Microbiol.2017;55(7):2208-2221. DOI 10.1128/JCM.00455-17.Choi Y.S., Koo E.S., Kim M.S., Choi J.D., Shin Y., Jeong Y.S. Reemergenceof a GII.4 norovirus Sydney 2012 variant equippedwith GII.P16 RdRp and its predominance over novel variants ofGII.17 in South Korea in 2016. Food Environ. Virol. 2017;9(2):168-178. DOI 10.1007/s12560-017-9278-4.Cotten M., Petrova V., Phan M.V., Rabaa M.A., Watson S.J.,Ong S.H., Kellam P., Baker S. Deep sequencing of norovirus genomesdefines evolutionary patterns in an urban tropical setting.J. Virol. 2014;88(19):11056-11069. DOI 10.1128/JVI.01333-14.de Graaf M., van Beek J., Vennema H., Podkolzin A.T.,Hewitt J., Bucardo F., Templeton K., Mans J., Nordgren J., ReuterG., Lynch M., Rasmussen L.D., Iritani N., Chan M.C., MartellaV., Ambert-Balay K., Vinje J., White P.A., Koopmans M.P.Emergence of a novel GII.17 norovirus \u2013 end of the GII.4 era?Euro Surveill. 2015;20(26):pii=21178. DOI 10.2807/1560-7917.ES2015.20.26.21178.Eden J.S., Tanaka M.M., Boni M.F., Rawlinson W.D., White P.A.Recombination within the pandemic norovirus GII.4 lineage.J. Virol. 2013;87(11):6270-6282. DOI 10.1128/JVI.03464-12.Fernandez-Vega V., Sosnovtsev S.V., Belliot G., King A.D., MitraT., Gorbalenya A., Green K.Y. Norwalk virus N-terminalnonstructural protein is associated with disassembly of the Golgicomplex in transfected cells. J. Virol. 2004;78(9):4827-4837.DOI 10.1128/JVI.78.9.4827-4837.2004.Green K.Y. Caliciviridae: The Noroviruses. In: Knipe D.M., HowleyP.M., Griffin D.E., Lamb R.A., Martin M.A., RacanielloV.R., Roizman B. (Eds.). Fields Virology. 6th edn. LippincottWilliams & Wilkins, Philadelphia, 2013;582-608.Han J., Wu X., Chen L., Fu Y., Xu D., Zhang P., Ji L. Emergenceof norovirus GII.P16-GII.2 strains in patients with acute gastroenteritisin Huzhou, China, 2016\u20132017. BMC Infect. Dis.2018;18(1):342. DOI 10.1186/s12879-018-3259-6.Hata M., Nakamura N., Kobayashi S., Onouchi A., Saito T., Hirose E.,Adachi H., Saito N., Ito M., Yasui Y., Matsumoto M., Minagawa H.Emergence of new recombinant noroviruses GII.P16-GII.2 andGII.P16-GII.4 in Aichi, Japan, during the 2016/17 season.Jpn. J. Infect. Dis. 2018;71(4):319-322. DOI 10.7883/yoken.JJID.2017.520.Hoa-Tran T.N., Nakagomi T., Sano D., Sherchand J.B., PandeyB.D., Cunliffe N.A., Nakagomi O. Molecular epidemiologyof noroviruses detected in Nepalese children with acute diarrheabetween 2005 and 2011: increase and predominance of minorgenotype GII.13. Infect. Genet. Evol. 2015;30:27-36. DOI10.1016/j.meegid.2014.12.003.Hoa-Tran T.N., Trainor E., Nakagomi T., Cunliffe N.A., NakagomiO. Molecular epidemiology of noroviruses associated withacute sporadic gastroenteritis in children: global distributionof genogroups, genotypes and GII.4 variants. J. Clin. Virol.2013;56(3):269-277. DOI 10.1016/j.jcv.2012.11.011.Iritani N., Kaida A., Abe N., Sekiguchi J., Kubo H., Takakura K.,Goto K., Ogura H., Seto Y. Increase of GII.2 norovirus infectionsduring the 2009\u20132010 season in Osaka City, Japan. J. Med.Virol. 2012;84(3):517-525. DOI 10.1002/jmv.23211.Kirby A.E., Teunis P.F., Moe C.L. Two human challenge studiesconfirm high infectivity of Norwalk virus. J. Infect. Dis.2015;211(1):166-167. DOI 10.1093/infdis/jiu385.Kroneman A., Vega E., Vennema H., Vinje J., White P.A., HansmanG., Green K., Martella V., Katayama K., Koopmans M. Proposalfor a unified norovirus nomenclature and genotyping. Arch.Virol. 2013;158:2059-2068. DOI 10.1007/s00705-013-1708-5.Lin Y., Fengling L., Lianzhu W., Yuxiu Z., Yanhua J. Functionof VP2 protein in the stability of the secondary structure ofvirus-like particles of genogroup II norovirus at different pHlevels: function of VP2 protein in the stability of NoV VLPs.J. Microbiol. 2014;52(11):970-975. DOI 10.1007/s12275-014-4323-6.Lun J.H., Hewitt J., Yan G.J.H., Enosi T.D., Rawlinson W.D.,White P.A. Recombinant GII.P16/GII.4 Sydney 2012 was thedominant norovirus identified in Australia and New Zealand in2017. Viruses. 2018;10(10):548. DOI 10.3390/v10100548.Mallory M.L., Lindesmith L.C., Graham R.L., Baric R.S. GII.4 humannorovirus: surveying the antigenic landscape. Viruses.2019;11(2):177. DOI 10.3390/v11020177.Motomura K., Boonchan M., Noda M., Tanaka T., Takeda N.Norovirus epidemics caused by new GII.2 chimera viruses in2012\u20132014 in Japan. Infect. Genet. Evol. 2016;42:49-52. DOI10.1016/j.meegid. 2016.04.026.Ozaki K., Matsushima Y., Nagasawa K., Motoya T., Ryo A., KurodaM., Katayama K., Kimura H. Molecular evolutionary analysesof the RNA-dependent RNA polymerase region in norovirusgenogroup II. Front. Microbiol. 2018;9:3070. DOI 10.3389/fmicb.2018.03070.Parra G.I., Squires R.B., Karangwa C.K., Johnson J.A., Lepore C.,Sosnovtsev S.V., Green K.Y. Static and evolving norovirus genotypes:implications for epidemiology and immunity. PLoS Pathog.2017;13(1):e1006136. DOI 10.1371/journal.ppat.1006136.Petrignani M., Verhoef L., de Graaf M., Richardus J.H., KoopmansM. Chronic sequelae and severe complications of norovirusinfection: a systematic review of literature. J. Clin. Virol.2018;105:1-10. DOI 10.1016/j.jcv.2018.05.004.Qi R., Huang Y., Liu J., Sun Y., Sun X., Han H., Qin X., Zhao M.,Wang L., Li W., Li J., Chen C., Yu X. Global prevalence of asymptomaticnorovirus infection: a meta-analysis. EClinicalMedicine. 2018;2(2-3):50-58. DOI 10.1016/j.eclinm.2018.09.001.Roth A.N., Karst S.M. Norovirus mechanisms of immune antagonism.Curr. Opin. Virol. 2016;16:24-30. DOI 10.1016/j.coviro.2015.11.005.Ruis C., Roy S., Brown J.R., Allen D.J., Goldstein R.A., Breuer J.The emerging GII.P16-GII.4 Sydney 2012 norovirus lineage iscirculating worldwide, arose by late-2014 and contains polymerasechanges that may increase virus transmission. PLoS One.2017;12(6):e0179572. DOI 10.1371/journal.pone.0179572.Simmons K., Gambhir M., Leon J., Lopman B. Duration of immunityto norovirus gastroenteritis. Emerg. Infect. Dis. 2013;19(8):1260-1267. DOI 10.3201/eid1908.130472.Towers S., Chen J., Cruz C., Melendez J., Rodriguez J., Salinas A.,Yu F., Kang Y. Quantifying the relative effects of environmental and direct transmission of norovirus. R. Soc. Open Sci. 2018;5(3):170602. DOI 10.1098/rsos.170602.van Beek J., Ambert-Balay K., Botteldoorn N., Eden J.S., FonagerJ., Hewitt J., Iritani N., Kroneman A., Vennema H., Vinje J.,White P.A., Koopmans M., on behalf of NoroNet. Indicationsfor worldwide increased norovirus activity associated with emergenceof a new variant of genotype II.4, late 2012. Eurosurveillance.2013;18(1):pii=20345. Available online: https://www.eurosurveillance.org/content/10.2807/ese.18.01.20345-en.Vinje J. Advances in laboratory methods for detection and typingof norovirus. J. Clin. Microbiol. 2015;53(2):373-381. DOI10.1128/JCM.01535-14.Vongpunsawad S., Venkataram Prasad B.V., Estes M.K. Norwalkvirus minor capsid protein VP2 associates within the VP1shell domain. J. Virol. 2013;87(9):4818-4825. DOI 10.1128/JVI.03508-12.Woodward J., Gkrania-Klotsas E., Kumararatne D. Chronic norovirusinfection and common variable immunodeficiency. Clin.Exp. Immunol. 2017;188(3):363-370. DOI 10.1111/cei.12884.Zhirakovskaia E.V., Tikunov A.Y., Bodnev S.A., Klemesheva V.V.,Netesov S.V., Tikunova N.V. Molecular epidemiology of norovirusesassociated with sporadic gastroenteritis in children inNovosibirsk, Russia, 2003\u20132012. J. Med. Virol. 2015;87(5):740-753. DOI 10.1002/jmv.24068.Zhirakovskaia E., Tikunov A., Tymentsev A., Sokolov S., SedelnikovaD., Tikunova N. Changing pattern of prevalence andgenetic diversity of rotavirus, norovirus, astrovirus, and bocavirusassociated with childhood diarrhea in Asian Russia, 2009\u20132012. Infect. Genet. Evol. 2019;67:167-182. DOI 10.1016/j.meegid.2018.11.006."} +{"text": "Cnidium monnieri (L.) Cuss (C. monnieri) is one of the most widely used traditional herbal medicines, exhibiting a wide range of pharmacological functions for treating asynodia, trichomonas vaginitis, and osphyalgia. Its important medicinal value comes from its abundance of coumarins. To identify genes involved in coumarin biosynthesis and accumulation, we analyzed transcriptome data from flower, leaf, root and stem tissues of C. monnieri. A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of these, 119,177 unigenes were annotated in public databases. We identified differentially expressed genes (DEGs) based on expression profile analysis. These DEGs exhibited higher expression levels in flower tissue than in leaf, stem or root tissues. We identified and analyzed numerous genes encoding enzymes involved in coumarin biosynthesis, and verified genes encoding key enzymes using quantitative real-time PCR. Our transcriptome data will make great contributions to research on C. monnieri and provide clues for identifying candidate genes involved in coumarin metabolic pathways. Cnidium monnieri (L.) Cuss, an annual plant of the Umbelliferae family native to China and Vietnam, exhibits a diverse set of pharmacological activities including anti-osteoporotic has been widely applied as a powerful method for discovering and predicting functional genes, and revealing gene expression patterns, especially in non-model species for which reference genome sequences are insufficient . To dateus albus , Artemisia argyi , Arisaemophyllum , Clinopochinense and Polyyrtonema . HoweverC.\u00a0monnieri using BGI-500 sequencing technology. Numerous potential genes and differentially expressed genes (DEGs) involved in coumarin biosynthesis were screened using de novo transcriptome sequencing. Our findings will increase our understanding of the molecular mechanisms of coumarin biosynthesis in C.\u00a0monnieri and provide clues for exploring functional genes in other plants having close relationships with C.\u00a0monnieri.The purpose of this study was to uncover functional genes associated with or playing regulatory roles in coumarin biosynthesis. We conducted transcriptome sequencing and gene expression profiling in C.\u00a0monnieri plants were collected from Tongcheng city in Anhui Province, China in May 2018, with verbal permission of the Manager Zhongquan Fang , and authenticated by Professor Dequn Wang (Anhui University of Chinese Medicine). Prior to the experiment, the plants were grown at a temperature of 22\u221226\u00a0\u00b0C/14\u221218\u00a0\u00b0C (day/night) and relative humidity of 65\u201380%. All samples were rinsed in ultrapure water, and leaves, roots, flowers and stems, which were harvested from three individual C.\u00a0monnieri plants, were placed in centrifuge tubes, frozen in liquid nitrogen immediately and stored at \u221280\u00a0\u00b0C.Whole Total RNA was extracted from each tissue using RNA plant Plus Reagent according to the manufacturer\u2019s instructions. The extracted RNA was checked using a NanoDrop 2000 , and the concentration of the isolated RNA, 28S/18S and integrity (RIN) were estimated using an RNA Nano 6000 Assay Kit and the Agilent Bioanalyzer 2100 system .C.\u00a0monnieri samples from flowers, roots, leaves and stems were used for isolation of osthole as previously reported to remove DNA residues and then mixed with magnetic beads containing oligo (dT) to purify mRNA. After purification, the mRNA was fragmented into small pieces under elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers. Second-strand cDNA was synthesized using DNA Polymerase I and RNase H. These cDNA fragments had the addition of a single adenine at the 3\u2032\u00a0end for subsequent ligation of adapters. The products were then purified and enriched using PCR amplification. The quality of each sample library was evaluated using an Agilent 2100 Bioanalyzer system . Each cDNA library was sequenced using the BGISEQ-500 system at Beijing Genomics Institute (BGI) with paired-end (PE) sequencing length of 100 bp.i\u00a0\u2212\u00a0A 0.25). In the absence of a reference genome, clean reads were subjected to transcriptome assembly using Trinity software (version 2.5.1) applying the following parameters: \u2013min_contig_length 150 \u2013CPU 8 \u2013min_kmer_cov 3 \u2013min_glue 3 \u2013bfly_opts \u2019-V 5 \u2013edge-thr =0.1 \u2013stderr\u2019 , NCBI non-redundant protein sequences (NR) (update date: 23 June 2019) , clusters of euKaryotic Orthologous Groups (KOG) (http://www.ncbi.nlm.nih.gov/KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG) (update date: 1 July 2018) (http://www.genome.jp/kegg/) (http://www.uniprot.org/). Assembled unigenes were annotated against NR database using the software BLAST . And the results of NR annotation were used for Gene Ontology (GO) (update date: 1 January 2019) annotation using Blast2GO (version v2.5.0) program (Assembled unigenes were annotated against the NCBI nucleotide sequences (NT) (p/kegg/) , and a m program . Pfam using Power SYBR\u00ae Green PCR Master Mix . The actin gene (CL3748.Contig7) of C.\u00a0monnieri was used as a reference. Primers for all selected genes were designed using Premier 6.0 and are listed in \u00ae Green Master Mix. Reactions were conducted under the following conditions: denaturation at 95\u00a0\u00b0C for 1 min, followed by 40 cycles of 95\u00a0\u00b0C for 15 s and 63\u00a0\u00b0C for 25 s. Each qRT-PCR was performed using three biological replicates. The 2Ct\u2212\u0394\u0394 method was used to calculate the relative expression level of genes . qRT-PCR analysis of each gene was performed on a QuantStudioof genes .After assembly, clean reads were mapped to unigenes using Bowtie2 (version 2.2.5) , and theThe open reading frames (ORFs) of unigenes were initially detected using getorf (version EMBOSS:6.5.7.0) and furtP value <0.05 was considered to be statistically significant.The contents of osthole and all data from qRT-PCR were presented as mean\u00a0\u00b1\u00a0standard deviation. Statistics were done by GraphPad Prism 6.0. Heatmap and boxplot were performed using R software (version 3.4.4). The one-way analysis of variance (ANOVA) was used to compare the data between groups with Duncan t test. C.\u00a0monnieri. Osthole content was highest in flowers (1.372%) and lowest in stems (0.283%) . OstholeC.\u00a0monnieri using BGISEQ-500 sequencing technology. After eliminating low-quality reads, we obtained a total of 10.6 Gb, 10.47 Gb, 10.81 Gb and 10.38 Gb of clean reads from 83.42 Mb, 81.65 Mb, 84.27 Mb and 82.14 Mb sets of raw data from leaf, stem, flower and root tissue, respectively, with all Q30 values greater than 85% against seven public databases , and a total of 110,992 (63.81%), 95,603 (54.96%), 80,216 (46.12%), 86,568 (49.77%), 87,523 (50.32%), 79,335 (45.61%) and 56,429 (32.44%) unigenes were aligned, respectively (Daucus carota subsp. sativus (82.2%) and others (17.8%) (e <10ectively . We annoectively . We focuectively . Additio (17.8%) .We determined expression values of transcripts with fragments per kilobase of transcript per million mapped reads (FPKM) >1 for each tissue and found 55,421, 52,787, 48,287 and 44,717 expressed unigenes in flower, leaf, stem and root tissues, respectively . The oveC. monnieri, 86,568 (49.77%) unigenes were annotated and assigned to 135 KEGG pathways (19 subcategories) , cinnamate 4-hydroxylase , 4-coumarate\u2013CoA ligase , shikimate hydroxycinnamoyl transferase , 5-O-(4-coumaroyl)-D-quinate 3\u2032-monooxygenase , caffeoyl-CoA O-methyltransferase and feruloyl-CoA ortho-hydroxylase . Fourteeegories) . Phenylpnigenes) . These dnigenes) .C. monnieri (C4H), CL16061.Contig1 (4CL) and CL8379.Contig6 (F6H1) genes was highest in root tissue, whereas relative expression of the CL11351.Contig3 (PAL) and CL2358.Contig9 (BGA) genes was highest in flower tissue. Unigene 20867 (BGA) had a high expression level in leaf tissue. The expression levels determined by qRT-PCR were consistent with the FPKM values.We selected six unigenes encoding five key enzymes and used quantitative real-time PCR (qRT-PCR) to determine their relative expression levels in the leaf, stem, flower and root tissues of monnieri . RelativWe identified 12,635 unigenes uniquely expressed in flowers and 77,762 shared unigenes exhibiting expression in all four tissues . Total DAll DEGs were annotated in the KEGG database to further describe and evaluate their biological functions. This analysis revealed 32,060 DEGs in flower versus leaf associated with 137 pathways; these DEGs were mainly enriched in the \u201cplant hormone signal transduction,\u201d \u201cplant-pathogen interaction,\u201d \u201ccircadian rhythm - plant\u201d and \u201cphotosynthesis - antenna proteins\u201d pathways . In flowA total of 18,881 up-regulated DEGs showed flower-specific expression with |log2 (fold changes) | >2. We inferred the nature of these DEGs via GOSlim functional analysis. Sequence homology revealed that each of the 18,881 flower-specific DEGs mapped to at least one ontology term, including 2,814 for biological processes, 3,232 for cellular components and 4,508 for molecular function; many genes were enriched in \u201ccellular process\u201d and \u201ccatalytic activity\u201d subcategories within the biological processes and molecular function categories, respectively .To evaluate the biological functions of these DEGs, the 18,881 flower-specific DEGs were annotated in the KEGG database. KEGG enrichment analysis showed that these DEGs were significantly enriched in the \u201cribosome,\u201d \u201cstarch and sucrose metabolism,\u201d \u201cpentose and glucuronate interconversions\u201d and \u201cphenylpropanoid biosynthesis\u201d categories . AdditioC. monnieri transcriptome database, including 1,169, 1,032 and 920 unigenes up-regulated in flowers compared with leaves, stems and roots, respectively (Transcription factors (TFs) play an important role in regulating secondary metabolites by modulating the expression of genes related to biosynthetic pathways. We identified 3,799 unigenes encoding putative TFs in the ectively . The majectively . Of thesC. monnieri. Their structures and physicochemical properties have been well studied genes were mapped in at least one public database, while 54,761 (31.48%) genes remained unannotated because of the lack of available genomic information.Coumarins are the most important bioactive components of studied . HoweverPAL), CL2358.Contig9 (BGA), Unigene 20867 (BGA), CL3766.Contig1 (C4H), CL16061.Contig1 (4CL) and CL8379.Contig6 (F6H1) examined using qRT-PCR were consistent with the FPKM values determined by RNA-Seq. Coumarins are a major group of natural plant products derived from the phenylpropanoid pathway in Angelica gigas , 4CL (2 DEGs), HCT (13 DEGs), COMT (7 DEGs) and F6\u2032H1 (8 DEGs) were related to coumarin biosynthesis . These kArabidopsis results in increased biosynthesis and accumulation of scopoletin, which belongs to the coumarins Standard curve of osthole at 322 nm. (B) Osthole content from flowers, leaves, roots and stems of Click here for additional data file.10.7717/peerj.10157/supp-2Figure S2Click here for additional data file.10.7717/peerj.10157/supp-3Figure S3Click here for additional data file.10.7717/peerj.10157/supp-4Figure S4Click here for additional data file.10.7717/peerj.10157/supp-5Figure S5Click here for additional data file.10.7717/peerj.10157/supp-6Figure S6Click here for additional data file.10.7717/peerj.10157/supp-7Figure S7Red boxes represent enzymes annotated in the KEGG database. Photo credit: Kanehisa Laboratories.Click here for additional data file.10.7717/peerj.10157/supp-8Figure S8actin gene (CL3748.Contig7) as a reference gene for normalization. FPKM values of these genes are shown as red lines, qRT-PCR results of these genes are shown as blue bars.Relative expression of (A) CL11351.Contig3 (PAL), (B) CL2358.Contig9 (BGA), (C) Unigene 20867 (BGA), (D) CL3766.Contig1 (C4H), (E) CL16061.Contig1 (4CL) and (F) CL8379.Contig6 (F6H1) was analyzed by qRT-PCR using the Click here for additional data file.10.7717/peerj.10157/supp-9Figure S9Click here for additional data file.10.7717/peerj.10157/supp-10Supplemental Information 10Click here for additional data file.10.7717/peerj.10157/supp-11Supplemental Information 11Click here for additional data file.10.7717/peerj.10157/supp-12Supplemental Information 12Click here for additional data file.10.7717/peerj.10157/supp-13Supplemental Information 13Click here for additional data file.10.7717/peerj.10157/supp-14Supplemental Information 14Click here for additional data file.10.7717/peerj.10157/supp-15Supplemental Information 15Click here for additional data file.10.7717/peerj.10157/supp-16Supplemental Information 16Click here for additional data file.10.7717/peerj.10157/supp-17Supplemental Information 17Click here for additional data file.10.7717/peerj.10157/supp-18Supplemental Information S1Click here for additional data file."} +{"text": "This study examined the diagnostic accuracy of 18F-DCFPyL (PSMA) PET/CT for lymph-node staging in primary PCa.The detection of lymph-node metastases (N1) with conventional imaging such as magnetic resonance imaging (MRI) and computed tomography (CT) is inadequate for primarily diagnosed prostate cancer (PCa). Prostate-specific membrane antigen (PSMA) PET/CT is successfully introduced for the staging of recurrent PCa. Besides the frequently used 18F-DCFPyL PET/CT prior to robot-assisted radical prostatectomy (RARP) with extended pelvic lymph-node dissection (ePLND). Patients were included between October 2017 and January 2020. A Memorial Sloan Kettering Cancer Centre (MSKCC) nomogram risk probability of \u2265\u20098% of lymph-node metastases was set to perform ePLND. All images were reviewed by two experienced nuclear physicians, and were compared with post-operative histopathologic results.This was a prospective, multicentre cohort study. Patients with primary PCa underwent 18F-DCFPyL PET/CT detection of pelvic lymph-node metastases on a patient level were 41.2% : 19.4\u201366.5%), 94.0% (CI 86.9\u201397.5%), 53.8% (CI 26.1\u201379.6%) and 90.4% (CI 82.6\u201395.0%), respectively.A total of 117 patients was analysed. Lymph-node metastases (N1) were histologically diagnosed in 17/117 patients (14.5%). The sensitivity, specificity, positive predictive value and negative predictive value for the 18F-DCFPyL PET/CT showed a high specificity (94.4%), yet a limited sensitivity (41.2%) for the detection of pelvic lymph-node metastases in primary PCa. This implies that current PSMA PET/CT imaging cannot replace diagnostic ePLND. Further research is necessary to define the exact place of PSMA PET/CT imaging in the primary staging of PCa. Prostate cancer (PCa) is the most frequently diagnosed cancer in men in the Western world , 2. Init68gallium-labelled PSMA tracers. High detection rates for metastases were demonstrated even at low prostate-specific antigen (PSA) values (i.e. 45% for PSA <\u20090.5\u00a0ng/mL and over 95% for PSA \u2265\u20092.0\u00a0ng/mL) fluoro-pyridine-3-carbonyl)-amino]-pentyl)-ureido)-pentanedioic acid) 112\u2013123\u00a0min) of a median dose of 311\u00a0MBq 18F-DCFPyL (IQR 297\u2013324\u00a0MBq) within a median of 4.1\u00a0weeks (IQR 2.1\u20136.6) after prostate biopsy and within a median of 5.9\u00a0weeks (IQR 3.6\u201312.0) prior to surgery. Image acquisitions were performed using a Philips Ingenuity TF and a Siemens Biograph-16 TruePoint PET/CT system. The scan trajectory included mid-thigh to skull base, with 4\u00a0min (Philips) and 5\u00a0min (Siemens) per bed position. All PET scans were combined with a low-dose CT (33/117 patients) or contrast-enhanced CT scan (84/117 patients) . Images were corrected for decay, scatter, random coincidences and photon attenuation.Patients were staged with Images were reconstructed with a BLOB-based Ordered-Subsets Expectations Maximization algorithm and the All scans were clinically and prospectively interpreted in the participating centres by one of two nuclear medicine physicians with ample experience in PSMA PET interpretation (>\u2009300 scans). Upon completion of the study, all scans were reviewed by a second independent reader who was blinded to initial scan interpretation, surgery and histopathology results . A joint re-evaluation was performed in case of incongruent scan interpretation (consensus read), and used for final analysis. Lymph-node metastases were defined as increased PSMA expression, higher than the background, incompatible with physiological uptake, and in a typical site of PCa. A significant CT substrate was not an absolute prerequisite. The following parameters were recorded: detection of the primary tumour, tumour stage and presence of pelvic lymph-node metastases (N1). Pelvic lymph-node metastases were further classified in accordance with the four sections of the ePLND .To assess inter-observer variability, the proportional agreement was calculated, based on the two individual scan interpretations . Proportpeak), with correction for background uptake [peak is defined as the highest local intensity of uptake with a 6-mm-radius sphere [peak of the prostate tumour for patients with and without lymph-node metastases, the Mann-Whitney U test was used (significance set at p\u2009<\u20090.05). To compare the median SUVpeak of the prostate tumour with the corresponding Gleason score of the lesion, the Kruskall-Wallis test was used (significance set at p\u2009<\u20090.05). A linear regression was run to predict PSA from SUVpeak of the prostate index lesion (significance set at p\u2009<\u20090.05).PET/CT scans with PSMA-avid lesions in the prostate were delineated according to the reports of the nuclear medicine physicians. Semi-automatic delineation on the PET scans from both participating centres was performed with the in-house developed ACCURATE tool\u00a9 . The ACCd uptake . SUVpeaks sphere . To compThe ePLND surgical template includes removal of fatty lymphoid tissue overlying the common and external iliac vessels and within the obturator fossa . The medProstate specimens and resected lymph-node templates were fixated in formaldehyde (10%) directly after surgery and processed according to routine clinical standards . Individ18F-DCFPyL PET/CT to detect pelvic lymph-node metastases. The diagnostic accuracy of 18F-DCFPyL PET/CT was calculated with histopathologic evaluation of ePLND as a reference. The sensitivity, specificity and positive and negative predictive values of 18F-DCFPyL PET/CT for the detection of pelvic lymph-node metastases (pN1) were calculated both on a patient level and on a surgical template level. The surgical template analysis was based on the abovementioned 4 surgical templates of the ePLND, and was applied to approximate lesion based-detection using 18F-DCFPyL PET/CT. To compare the median diameter of PET/CT-detected lymph-node metastases vs. PET/CT-undetected lymph-node metastases, the Mann-Whitney U test was used (significance set at p\u2009<\u20090.05).The primary outcome of this study was the patient-based sensitivity of 18F-DCFPyL PET/CT to differentiate local advancement from prostate-confined disease (T2). This study did not investigate the exact location of local PCa advancement, only the presence of extracapsular or seminal vesicle invasion was noted. Local advancement was defined as PSMA expression outside the borders of the prostate gland, not suspect for overprojection or bladder/urethral physiological activity. Numerical variables were summarized with median values and interquartile ranges (IQR), categorical variables with proportions (%). Statistical analysis was done with IBM\u00ae SPSS\u00ae Statistics for Windows\u00ae, version 26.For the assessment for the local tumour stage (pT), we measured the accuracy of 18F-DCFPyL PET/CT, as presented in Fig.\u00a0A total of 120 patients were included in this study, and scheduled for ePLND with RALP after 18F-DCFPyL PET/CT suspicious for lymph-node metastases. Hence, the patient-based sensitivity to detect lymph-node metastases using 18F-DCFPyL PET/CT was 41.2% 19.4\u201366.5), with a specificity of 94.0% (95%CI 86.9\u201397.5), a PPV of 53.8% (95%CI 26.1\u201379.6) and a NPV of 90.4% (95%CI 82.6\u201395.0), as shown in Table Pathological features after RARP and ePLND are listed in Table 18F-DCFPyL PET/CT preoperatively identified 38 PSMA-avid regions suspect for lymph-node metastases in 18 surgical ePLND templates. Therefore, the template-based sensitivity for the detection of lymph-node metastases using 18F-DCFPyL PET/CT was 34.7% (95%CI 17.1\u201357.1), with a specificity of 97.7% (95%CI 95.7\u201398.9), a PPV of 44.4 (95%CI 22.4\u201368.6) and a NPV of 96.6% (95%CI 94.4\u201398.0) as seen in Table 18F-DCFPyL PET/CT, please see Fig.\u00a0In the 17 patients with lymph-node metastases, 31 lymph-node metastases were histologically identified in 23 surgical ePLND templates. n\u2009=\u200912) had a median tumour size of 5.5\u00a0mm (IQR 2.4\u20136.6), whereas the PET/CT-undetected lymph-node metastases (n\u2009=\u200919) had a significantly smaller median tumour size of 1.5\u00a0mm (IQR 1.0\u20134.5) (p\u2009=\u20090.03). A clinical example of a patient with both missed and detected lymph-node metastases is shown in Fig.\u00a0The median diameter of resected lymph-node metastases was 2.5\u00a0mm (IQR 1.0\u20136.0). The PET/CT-detected lymph-node metastases p\u2009=\u20090.0. A clinimm IQR 2.\u20136.6, whe18F-DCFPyL PET/CT to detect locally advanced tumour growth (pT3-4) were 45.2% (95%CI 32.7\u201358.2%), 94.4% (95%CI 83.7\u201398.6%), 90.3% (95%CI 73.1\u201397.5%) and 60.0% (95%CI 48.8\u201370.7%), respectively, as seen in Table 18F-DCFPyL PET/CT were 18.1% (95%CI 8.7\u201333.2), 97.2% (95%CI 89.4\u201399.5), 80.0% (95%CI 44.2\u201396.5) and 66.0% (95%CI 56.1\u201374.8), respectively. For the detection of pT3b sub-stage, the sensitivity, specificity, PPV and NPV of 18F-DCFPyL PET/CT were 52.9% (95%CI 28.5\u201376.1), 89.9% (95%CI 81.8\u201394.8), 47.4% (95%CI 25.2\u201370.5) and 91.8% (95%CI 83.9\u201396.1), respectively. A clinical example of seminal vesicle (pT3b) PCa involvement on PET/CT is presented in Fig.\u00a0A total of 116/117 patients (99.1%) showed PSMA expression in the prostate at PET/CT. The sensitivity, specificity, PPV and NPV of owth pT3- were 45.peak of the PSMA-avid prostate lesions was found between patients with and without lymph-node metastases (p\u2009=\u20090.46). A Gleason score of 4\u2009+\u20095\u2009=\u20099 or higher was associated with a higher median SUVpeak when compared with the lower Gleason scores . A Gleason score of 4\u2009+\u20094\u2009=\u20099 or higher was not associated with a higher median SUVpeak when compared with the lower scores . No correlation was found between SUVpeak of the PSMA-avid prostate lesions and PSA (R2\u2009=\u20090.12).No significant difference in the median SUVProportional agreement for the detection of lymph-node metastases using PET/CT was present in 94.7% (95%CI 89.8\u201397.7) overall, with a positive agreement of 78.6% (95%CI 53.4\u201393.9) and a negative agreement of 97.0% (95%CI 92.4\u201399.2). Proportional agreement for locally advanced tumours was observed in 79.1% (95%CI 71.7\u201385.3), with a positive agreement of 55.6% (95%CI 38.2\u201372.0), and a negative agreement of 86.2% (95%CI 77.9\u201391.5).18F-DCFPyL PET/CT for primary staging of PCa, assessing the diagnostic accuracy for the detection of pelvic lymph-node metastases. The results of a total of 117 patients with intermediate and high-risk PCa that underwent 18F-DCFPyL PET/CT and ePLND were analysed.PSMA PET/CT imaging is currently the imaging technique of choice for patients with biochemically recurrent disease after initial curative local treatment (EAU guidelines) . Its val18F-DCFPyL PET/CT imaging demonstrated a limited sensitivity for pelvic lymph-node metastases of 41.2%, at 94.0% specificity. The limited sensitivity indicates that 18F-DCFPyL PET/CT does not detect all lymph-node metastases. Therefore, albeit invasive, ePLND remains the gold standard for nodal staging. The 90% NPV might suggest that a negative test is reliable in the majority of times, though we should mind the low prevalence of lymph-node metastases in this cohort (14.5%). This prevalence was congruent with the median MSKCC risk for lymph-node metastases of 14.4% (IQR 10.1\u201330.2). Although specificity for lymph-node metastases was favourable in this study, the PPV was moderate at 53.8% . In this clinical setting, not all positive 18F-DFCPyL PET/CT results for pelvic lymph-node metastases represent actual metastatic disease. Good intra-observer agreement for the detection of pelvic lymph-node metastases using 18F-DFCPyL PET/CT was observed (95%).In this study, 68Ga-PSMA study from van Kalmthout et al. [n\u2009=\u2009103 patients), applying the same standardized ePLND techniques, histopathology analyses and PET positivity criteria. It revealed a patient-based sensitivity for lymph-node metastases of 41.5% (95%CI 26.7\u201357.8) and a specificity of 90.9% (95%CI 79.3\u201396.6) [18F-DCFPyL PET/CT is at least comparable with 68Ga-PSMA imaging.Our results appear to be in line with a recent prospective t et al. . This st.3\u201396.6) . Althoug68Ga PSMA ligands, which reported a specificity of 90% and higher [18F-DCFPyL PET/CT as an imaging tool for initial staging of PCa [The high specificity presented in the current study confirms results from previous retrospective studies with d higher , 29, 30.g of PCa . In 25 pg of PCa . PotentiU test: p\u2009=\u20090.03). This may explain the imperfect imaging sensitivity reported in this study. The 5-mm spatial resolution offered by PET is still an improvement compared with the detection limits of CT and MRI (i.e. >\u200910\u00a0mm [68Ga-PSMA PET/CT vs. MRI (65% vs. 41%) [PET/CT-detected lymph-node metastases were larger than lymph-node metastases that were not detected by PET/CT . This d >\u200910\u00a0mm . This st18F-DCFPyL PET/CT should still be followed by curative treatment in the form of a RALP with an ePLND. However, the threshold to perform ePLND with certain amounts of detected number of lymph-node metastases remains unclear.The therapeutic consequence of PSMA-detected pelvic lymph-node metastases remains a matter of debate. Previous research showed that patients with lymph-node metastases detected intra-operatively (with frozen sections) or preoperatively (with CT) still benefit from radical prostatectomy and complete lymph-node dissection \u201334. This18F-DCFPyL PET/CT, yet the sensitivity was limited at 45.2% (95%CI 32.7\u201358.2). Moreover, the promising specificity of the detection of pT3a-b using 18F-DCFPyL PET/CT of 94.4% (95%CI 83.7\u201398.6) is in line with previous reports on 68Ga-PSMA (specificity >\u200990% for T3b) [18F-DCFPyL PET/CT is comparable with that of mpMRI, for which a meta-analysis revealed a specificity of 88% (95%CI 85\u201397%) compared with our 94.4% (95%CI 83.7\u201398.6) [A total of 116/117 patients (99.1%) showed PSMA expression in the prostate at PET/CT. A promising PPV for the detection of pT3a-b of 90.3% (95%CI 73.1\u201397.5) was observed using for T3b) , 35, 36..7\u201398.6) . The sen.7\u201398.6) . Altoget18F-DCFPyL PET/CT for detecting distant metastases. Only patients undergoing RARP and ePLND were considered for analysis, which naturally excludes patients with distant metastases in which radical surgery is forgone. As such, our results should be interpreted as the accuracy of 18F-DCFPyL PET/CT for N-staging in patients (expected to be) free from distant metastases . Therefore, we decided to focus our study on determining the accuracy of 18F-DCFPyL PET/CT for N-staging, as hereto a solid reference standard is available (ePLND). Determining the accuracy of M-staging is certainly of interest, yet any such analysis is limited to providing a PPV, as the true prevalence of distant metastases cannot be known.Our study has inherent limitations. Firstly, this study did not assess the accuracy of 18F-DCFPyL PET images were obtained, again detecting positive lymph nodes in the surgical template. Metastasis-directed radiotherapy to these lesions was followed by a PSA-response. The ePLND may possibly have missed these lesions initially that were rightfully detected on the first PET/CT scan.Since the PET/CT resolution is confined at 5\u00a0mm, limited diagnostic accuracy for micro metastases is to be expected. Secondly, this study might not have been adequately powered, since the expected prevalence was higher than the actual prevalence (30% vs. 14.5%). Moreover, the sensitivity used for the power analysis was higher than actually realized (90% vs. 41.2%) due to the high expectations for the sensitivity of PSMA PET/CT. Lastly, we should consider that the golden standard (ePLND) is not always flawless: in two patients with PET-positive lymph nodes, the ePLND was reported to be technically challenging. Histopathological analysis did not reveal any lymph-node metastases, yet these patients soon developed a biochemical recurrence. Repeated 18F-DCFPyL PET/CT scan could be used to withhold PCa patients from an ePLND. Future studies are therefore needed to assess whether the diagnostic accuracy of 18F-DCFPyL PET/CT, its high specificity in particular, could assist in proper treatment planning of patients with intermediate and high-risk stages of disease.The follow-up data of this cohort is necessary to investigate whether a specific risk profile in combination with a negative 18F-DCFPyL PET/CT imaging for the detection of lymph-node metastatic disease in men with intermediate and high-risk prostate cancer, undergoing radical surgery. We found a limited sensitivity of 41.2% (95%CI 19.4\u201366.5) at excellent specificity (94.0%). Based on current results, 18F-DCFPyL PET/CT imaging should not replace ePLND.In this prospective cohort study, we evaluated the accuracy of"} +{"text": "Ulmus parvifolia cvs. Allee and Drake in Lake County, Florida. Nematode species were identified using both molecular analysis and morphology of perineal patterns. Meloidogyne enterolobii and M. javanica were identified from U. parvifolia cv. Allee. Meloidogyne arenaria and M. javanica were identified from U. parvifolia cv. Drake. This is a first report of these nematode species infecting Chinese Elm in Florida.Samples of galled roots, resembling those induced by root-knot nematodes, and rhizosphere soil were collected from potted plants of Ulmus parvifolia Jacq.: Ulmaceae: Rosales) are valued for their tough lumber, resistance to some elm pests and pathogens were collected directly from the rhizosphere of U. parvifolia. These samples were designated with internal FDACS-DPI sample identifiers N20-110, N20-113 (both from U. parvifolia cv. Allee), and N20-115 (from U. parvifolia cv. Drake). Round galls, resembling those commonly induced by M.\u00a0enterolobii, were observed on secondary and tertiary roots of U. parvifolia cv. Allee in one of the samples and used for qPCR, conventional PCR, and sequencing. The cytochrome c oxidase subunit I (COI) and intergenic spacer 2 (IGS2) qPCR assays were repeated with DNA from J2 extracted directly from the roots of each cultivar. Standard PCRs targeted NADH-ubiquinone oxidoreductase chain 5 (NADH5) and cytochrome c oxidase subunit II (COXII) using the primers NAD5F2/NADH5R1 and COX2F/COX2R, respectively, and thermocycle conditions described by R assays , isozymeR assays . DNA wasMeloidogyne isolates with both NADH5 and COXII sequences were further analyzed. The alignments of NADH5 (448\u2009bp) and COXII (323\u2009bp) were trimmed until data were 100% complete for each terminal taxon. Alignments were then concatenated and analyzed simultaneously. K2P . Newly generated sequences were aligned in MEGA7 using thsly. K2P distancesly. K2P .Meloidogyne spp. found infecting U. parvifolia is provided (n = 6) and were positively identified as M. enterolobii from both qPCR assays. All other samples had undetermined Ct values for the qPCR assays. COXII sequences from N20-110 samples were 100% BLASTn matches to previously published M. enterolobii data. With the concatenated matrix, isolates N20-115-1A, N20-115-6A, N20-115-10A, N20-115-16B, N20-113-1B, N20-113-14B, N20-113-18B were 100% matches to M. javanica Chitwood, 1949 Chitwood, 1949 (M.\u00a0sp. n. 1 (n = 26 for each sample) and morphology of perineal patterns were consistent with those reported for M. enterolobii isolated singly from U.\u00a0parvifolia cv. Allee (N20-110) and M. javanica also found singly on this same cultivar (N20-113), and both M.\u00a0arenaria and M. javanica identified as mixed species infecting U. parvifolia cv. Drake (N20-115). To our knowledge this is the first report of Ulmus parvifolia as a host of M. arenaria, M.\u00a0enterolobii, and M. javanica in Florida.A summary of identified provided . Samples"} +{"text": "Escherichia coli (STEC) O26:H11 strain, MBT-5 , and two draft genome sequences of Listeria monocytogenes strains MBT-6 and MBT-7 belonging to the virulent sequence types 1 and 59 , respectively, were determined. The strains were isolated in 2015 from ready-to-eat mixed greens in Germany.The complete genome sequence of a Shiga toxin-producing Escherichia coli (STEC) O26:H11 strain, MBT-5 , and two draft genome sequences of Listeria monocytogenes strains MBT-6 and MBT-7 belonging to the virulent sequence types 1 and 59 , respectively, were determined. The strains were isolated in 2015 from ready-to-eat mixed greens in Germany.The complete genome sequence of a Shiga toxin-producing Escherichia coli (STEC) serotype O26 can lead to life-threatening infections and is the second most common serotype (after O157) found in clinical and food samples in Europe for E. coli. The AX Bacteria+ kit is suitable for getting high-molecular-weight DNA. DNA quantification and paired-end and long-read sequencing were performed as previously described (https://github.com/s-andrews/FastQC). Hybrid assembly of short and long sequence reads of STEC strain MBT-5, obtained from Illumina and MinION sequencing, respectively, was performed with Unicycler v0.4.8 (L. monocytogenes strains MBT-6 and MBT-7 was done with SPAdes v3.10.0 (Cultures were grown overnight at 37\u00b0C in brain heart infusion (BHI) broth, and genomic DNA was extracted using the ZR fungal/bacterial DNA miniprep kit for escribed . For sho v3.10.0 .dnaA as the origin with Geneious v9.2. Plasmids were not rotated. Strain MBT-5 was identified as serotype O26:H11, sequence type 21 (ST21), and adhesin fimH type 440 using SerotypeFinder v2.0, MLST v2.0, and FimTyper v1.0, respectively (\u2013ehxA (enterohemolysin), espA (extracellular serine protease), toxB (toxin B), and katP , while all other virulence genes were located on the chromosome.The hybrid assembly of STEC strain MBT-5 generated a single circular chromosome of 5,705,580\u2009bp, with 6 circular plasmids . The circular chromosome of MBT-5 was rotated to ectively \u201312. Viructively \u2013 13). In. IndnaA L. monocytogenes strains MBT-6 and MBT-7 generated 21 and 24 contigs, respectively. No plasmid sequences could be determined. Genome characteristics are shown in L. monocytogenes strains showed genetic characteristics similar to those of previously reported clinical, food, and outbreak-associated populations , indicatPRJNA643697. The sequences of STEC strain MBT-5 and L. monocytogenes strains MBT-6 and MBT-7 were deposited at DDBJ/ENA/GenBank under the accession numbers CP058682 (chromosome), CP058683 (plasmid 5.1), CP058684 (plasmid 5.2), CP058685 (plasmid 5.3), CP058686 (plasmid 5.4), CP058687 (plasmid 5.5), CP058688 (plasmid 5.6), JACBGM000000000, and JACBGL000000000. The raw sequencing data were also deposited at the SRA with the accession numbers shown in The genome sequences have been deposited in GenBank under the BioProject number"} +{"text": "Correction to: Pilot and Feasibility Studies 6, 69 (2020)https://doi.org/10.1186/s40814-020-00613-1Following publication of the original article , the autStudies into TFT for non-refugee traumatized populations show higher effects (d\u2009=\u20091.08\u20141.40) [7], than for refugee populations (g\u2009=\u2009.25\u20141.01) [8].Which will be replaced by:There is evidence that non-refugee traumatized populations benefit more from TFT than traumatized groups with a refugee background .This also involves changes in reference [8].Epidemiology and psychiatric sciences, 28(4), 376\u2013388.doi.org/10.1017/S2045796019000027\u201d.\u201cTurrini, G., Purgato, M., Acarturk, C., Anttila, M., Au, T., Ballette, F., ... & Hall, J. (2019). Efficacy and acceptability of psychosocial interventions in asylum seekers and refugees: systematic review and meta-analysis. should replace:\u201cLambert JE, Alhassoon OM. Trauma-focused therapy for refugees: Meta-analytic findings. Journal of counseling psychology. 2015;62(1):28. DOI: 10.1037/cou0000048\u201d.The publishers apologise for this error."} +{"text": "E. coli pathogenic lineage ST131 suggesting the important role of flies in disseminating highly virulent pathogens in clinical settings and beyond.Multidrug-resistant gram-negative (MRGN) bacteria are a serious threat to global health. We used genomics to study MRGN obtained from houseflies in a tertiary Rwandan hospital. Our analysis revealed a high abundance of different MRGN including Escherichia (E.) coli, Klebsiella spp., Enterobacter (E.) cloacae, Acinetobacter spp., and Pseudomonas (P.) aeruginosa, and others, and cause a variety of severe infections like diarrhea, pneumonia, sepsis, endocarditis and urinary tract infection (UTI). Studies estimate 700.000 fatalities caused by antibiotic-resistant pathogens each year with increasing numbers [E. coli from flies captured in a livestock facility was thus unsurprising [Multidrug-resistant gram-negative (MRGN) bacteria include numbers . In addi numbers . The detrprising . Anotherrprising . We inverprising , flies mE. coli, Klebsiella spp., Enterobacter spp., Acinetobacter spp., P. aeruginosa, Citrobacter spp., and Raoultella spp., we confirmed the bacterial species using MALDI-TOF . Additional phenotypic resistance screening was performed on the VITEK 2 system and for colistin resistance on 96-well microtiter plates investigating minimal inhibitory concentrations in triplicates. Randomly selected strains . After de-novo assembly using shovill/SPAdes and Velvet, draft genomes were polished by mapping all trimmed reads back to the contigs with bwa (https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2) and calling variants with Pilon (https://github.com/broadinstitute/pilon/releases/download/v1.23/pilon-1.23.jar). E. coli plasmid sequences of PBIO711 and PBIO1939 were manually extracted using similarity searches (BLASTn Megablast) against the NCBI nucleotide collection for visualization in BRIG (Blast Ring Image Generator) (https://sourceforge.net/projects/brig/files/dev/BRIG-0.95-dev.0004.zip/download). Sequence type (ST), antibiotic resistance/virulence gene and single-nucleotide polymorphism (SNP) detection was carried out using mlst, abricate, and snippy . We inferred a core SNP phylogeny for ST5474. Alignments were filtered for recombinations using Gubbins (https://github.com/sanger-pathogens/gubbins/archive/v2.3.4.tar.gz) and core SNPs extracted using snp-sites . A maximum likelihood tree was inferred with RAxML-NG (https://github.com/amkozlov/raxml-ng/releases/download/0.9.0/raxml-ng_v0.9.0_linux_x86_64.zip) using GTR\u2009+\u2009G. The best-scoring maximum likelihood tree was midpoint-rooted and visualized in FigTree .We examined 42 flies randomly captured in fly traps within 4 weeks in a tertiary hospital in Rwanda in 2014 . SamplinE. coli, 19% (8/42) E. cloacae, 9% (4/42) K. oxytoca, 7% (3/42) C. freundii, 4% (2/42) R. ornithinolytica, 4% (2/42) P. aeruginosa, and 2% (1/42) A. baumannii. Twelve flies (29%) carried more than one antibiotic-resistant bacterial genus of which three carried three different pathogens of flies carried antibiotic-resistant bacteria. Thirty-six percent 15/42) carried ESBL-producing 5/42 carrblaCTX-M-15,aac [-IIa, and tet(A)/(B) Table\u00a0. Eight dd to UTI causing diarrhea [In addition, we observed five diarrhea . This miE. coli strains , which did not only originate from individual flies captured in different wards but belonged to two different clonal lineages (ST410 and ST617), carried similar resistance genes (Table The two C) Table . OverallC) Table b.E. coli lineage ST131. High pre-admission and even higher discharge rates at this facility [Our results demonstrate that half of the flies in this tertiary hospital in Rwanda carried virulent MRGN pathogens including the pathogenic clonal facility may suggfacility at that facility .Additional file 1: Table S1. Results based on whole genome sequence analysis. Abbreviations: BLA: beta-lactams ; GEN: gentamicin; CIP: ciprofloxacin/moxifloxacin; SXT: sulfamethoxazole-trimethoprim; TET: tetracycline; ST: sequence type; resistance, virulence and plasmid genes are based on the abricate (https://github.com/tseemann/abricate) abbreviations using the databases Resfinder, ARG-ANNOT, CARD, NCBI Bacterial Antimicrobial Resistance Reference Gene Database, PlasmidFinder, VFDB, and Ecoli_VF.Additional file 2: Figure S2. Phylogenomic tree of five E. coli sequence type (ST) 5474 fly isolates (strain names colored according to Fig."} +{"text": "Drosophila; CRB1-3 in mammals) is a transmembrane determinant of epithelial cell polarity and a regulator of Hippo signalling. Crb is normally localized to apical cell-cell contacts, just above adherens junctions, but how apical trafficking of Crb is regulated in epithelial cells remains unclear. We use the Drosophila follicular epithelium to demonstrate that polarized trafficking of Crb is mediated by transport along microtubules by the motor protein Dynein and along actin filaments by the motor protein Myosin-V (MyoV). Blocking transport of Crb-containing vesicles by Dynein or MyoV leads to accumulation of Crb within Rab11 endosomes, rather than apical delivery. The final steps of Crb delivery and stabilisation at the plasma membrane requires the exocyst complex and three apical FERM domain proteins \u2013 Merlin, Moesin and Expanded \u2013 whose simultaneous loss disrupts apical localization of Crb. Accordingly, a knock-in deletion of the Crb FERM-binding motif (FBM) also impairs apical localization. Finally, overexpression of Crb challenges this system, creating a sensitized background to identify components involved in cytoskeletal polarization, apical membrane trafficking and stabilisation of Crb at the apical domain.Crumbs (Crb in \u2022Crumbs is transported apically along microtubules and actin filaments.\u2022Dynein is the key microtubule motor protein transporting Crumbs.\u2022Myosin V is the key F-actin motor protein transporting Crumbs.\u2022Crumbs polarises the cytoskeleton, which then directs further Crumbs delivery. How epithelial cells polarize is a fascinating unsolved problem in biology. A key determinant of epithelial polarity is the transmembrane protein Crumbs, which localises specifically to the apical domain of epithelial cells and then helps direct the apical-basal polarization of the entire epithelial cell. How Crumbs itself becomes localized apically is still poorly understood. Here we define a key role for two motor proteins which can transport Crumbs apically along microtubules and actin filaments, respectively. Thus, a polarised cytoskeleton directs Crumbs delivery, which then helps define the apical-basal axis, which feeds back to polarize the cytoskeleton - a positive feedback loop. In fertS.\u00a0pombe . The actS.\u00a0pombe . HoweverS.\u00a0pombe . In Drossymmetry . In epitDrosophila epithelial cells exhibit a more complex polarization than oocytes, with the plasma membrane divided into distinct apical and basolateral domains, separated by a ring of adherens junctions and Patronin for acentrosomal nucleation apically . The actcrb and sdt mRNA (Here we show that the actin motor protein Myosin-V (MyoV), previously implicated in Rab11-mediated apical secretion and found to co-localise with Crb , as wellsdt mRNA , both fusdt mRNA to the asdt mRNA . Crb mus2Drosophila ovarian follicle cell epithelium. Previously, loss of Dynein was reported to cause decreased levels of Crb protein in follicle cells due to failure of crb or sdt mRNA transport driver driver . We findle cells C. Co-standosomes D. These dynein-RNAi expressing follicle cells is disrupted by simultaneous expression of kinesin-RNAi, leading to an abnormal depolarised localization of Crb , which has been previously shown to form a complex with Crb and to promote apical secretion from Rab11 endosomes in the receptor . Class Vilaments , 2004, ailaments , suggestilaments , fails tilaments A,B. Use l domain C\u2013E. The extruded F\u2013H, or bextruded . Co-staiextruded F,G. ThesGiven our findings with MyoV, we sought to confirm that the F-actin cytoskeleton is also necessary for apical localization of Crb. As expected, disruption of F-actin by acute treatment with Latrunculin A (Lat A) caused a strong loss of MyoV-GFP and Crb-GFP from the apical domain, with Crb-GFP accumulating in endosomes A\u2013F. TreaDrosophila , Expanded (Ex) and Moesin (Moe). FERM domains link the actin cytoskeleton to the plasma membrane and bindosophila . Mer andr domain . Moe hasr domain . We find mutants A,B. Doubt on Crb C. Howevelization D. Accordlization also redlization E,F. ThesS.\u00a0cerevisiae . Importacomplex) . Thus, tDrosophila neuroblasts, which are polarized along the apical-basal axis by Baz, there is no role for either Crb or membrane trafficking . Notably, CRB3 lacks the homophillic extracellular domain of CRB1 and CRB2, but is still able to localise to tight junctions, suggesting that other tight junction proteins such as JAMs, Occludins or Claudins may mediate extracellular domain clustering, with the entire complex clustered by intracellular multi-PDZ domain proteins such as ZO-1 and MUPP1/PATJ driver, the actin \u2018flip-out\u2019 and MARCM systems. The tj.Gal4 line is weakly expressed from the beginning of follicular development and strongly from stage 7 onward. For \u2018flip-out\u2019 clones, third instar larvae were heat-shocked at 37\u00a0\u200b\u00b0C for 20\u00a0\u200bmin, and dissected 3 days after eclosion. Fly crosses were kept at a temperature of 25\u00b0.Drosophila stocks were obtained from the Bloomington Drosophila Stock Centre and are described in FlyBase. Mitotic clones were generated using the FLP/FRT system and were either marked positively or negatively (absence of GFP). Third instar larvae were heat-shocked once at 37\u00a0\u200b\u00b0C for 1\u00a0\u200bh and dissected 3 days after eclosion. Expression of UAS-driven transgenic lines was achieved with 4.1Ovaries were dissected in PBS, fixed for 20\u00a0\u200bmin in 4% paraformaldehyde in PBS, washed for 30\u00a0\u200bmin in PBS/0.1% Triton X-100 (PBT) and blocked for 15\u00a0\u200bmin in 5% normal goat serum/PBT (PBT/NGS). Primary antibodies were diluted in PBT/NGS and samples were incubated overnight at 4\u00a0\u200b\u00b0C. Secondary antibodies were used for 2\u00a0\u200bh at room temperature and then mounted on slides in Vectashield (Vector Labs). Images were taken with a Leica SP5 confocal using 40x oil immersion objective and processed with Adobe Photoshop and ImageJ.Primary antibodies used were: rat anti-Crumbs , mouse anti-Crumbs (Cq4) , rat anti-Crb intra (1:500\u00a0\u200bM.Bhat), rabbit anti-Lgl , mouse anti-Dlg and FITC-conjugated anti-GFP .Secondary antibodies used were goat Alexa fluor 488, 546 or 647 , Phalloidin to stain F-actin and DAPI to visualize nuclei.4.2Crb:GFP was performed by isolating egg chambers and culturing them as described Fig 1A: w; tj.Gal4/+; crb-GFP/UAS.dynein-IR(28054 VDRC)Fig 1B: w hs.flp; actin.FRT.STOP.FRT.Gal4 UAS.GFP/UAS.dynein-IR(28054 VDRC)Fig 1C: w hs.flp; actin.FRT.STOP.FRT.Gal4 UAS.GFP/UAS.dynein-IR(28054 VDRC)Fig 1D: w;crb-GFP/+Fig 2A: w; tj.Gal4/+; crb-GFP/UAS.dynein-IR(28054 VDRC)Fig 2B: w; tj.Gal4/UAS.kinesin-IR; crb-GFP/Fig 2C: w; tj.Gal4/UAS.kinesin-IR; crb-GFP/UAS.dynein-IR(28054 VDRC)Fig 2D: w; tj.Gal4/+; UAS.MyoV-GFP/+Fig 3A: w; tj.Gal4/+; UAS.GFP-MyoV-GT/+Fig 3B: wFig 3C: w; tj.Gal4/+; UAS.GFP-MyoV-GT/+Fig.\u00a03D\u2013E&G: w; tj.Gal4/+; UAS.GFP-MyoV-GT/UAS.dynein-IR(28054 VDRC)Fig.\u00a03F&H: wFig.\u00a04A\u2013B: w; tj.Gal4/+; UAS.MyoV-GFP/+Fig.\u00a04C\u2013D: w;crb-GFP/+Fig.\u00a04E\u2013G: w hs.flp FRT19A moePL106/FRT19A ubi.RFPFig 5A: w hs.flp FRT19A mer4/FRT19A ubi.RFP; FRT40Aexe1/FRT40A GFPFig 5B: w hs.flp FRT19A mer4moePL106/FRT19A ubi.RFPFig 5C: w hs.flp FRT19A mer4moePL106/FRT19A ubi.RFP; FRT40Aexe1/FRT40A GFPFig 5D: w hs.flp; FRT82B crb\u0394FBM/FRT82B ubi.nlsGFP Fig 5E: w hs.flp; FRT82B crb\u0394FBM/FRT82B ubi.nlsGFP Fig 5F: w hs.flp; FRT82Bsec151/FRT82B ubi.nlsGFPFig 5G: yw hs.flp tub.Gal4 UAS.GFPnls/+; FRT40Asec5e10/FRT40A tub.Gal80Fig 5H: wFig 6A: (27654 VDRC)w; tj.Gal4/UAS.patronin-IR(41858 BLOOMINGTON)/+w; tj.Gal4/+; UAS.shot-IRw; tj.Gal4/+; UAS.myoV-IR/+w; tj.Gal4/+; UAS.GFP-MyoV-GT/+w; tj.Gal4/+; UAS.\u03b1-Cat-IR/+1/FRT82B tub.Gal80w hs.flp UAS.GFPnls tub.Gal4/+;FRT82B sec15w; tj.Gal4/UAS.Crb-FLFig 6B: (27654 VDRC)w; tj.Gal4/UAS.Crb-FL UAS.patronin-IR(41858 BLOOMINGTON)/+w; tj.Gal4/UAS.Crb-FL; UAS.shot-IRw; tj.Gal4/UAS.Crb-FL; UAS.myoV-IR/+w; tj.Gal4/UAS.Crb-FL; UAS.GFP-MyoV-GT/+w; tj.Gal4/UAS.Crb-FL; UAS.\u03b1-Cat-IR/+1/FRT82B tub.Gal80w hs.flp UAS.GFPnls tub.Gal4/+; UAS.Crb-FL/+; FRT82B sec1532/FRT82B tub.Gal80yw hs.flp UAS.GFPnls tub.Gal4/+; UAS.Crb-FL/+; FRT82B kibyw hs.flp tub.Gal4 UAS.GFPnls/+; fosCrbICD/+; FRT82B crb11A22/FRT82B tub.Gal80Fig.\u00a06C\u2013E:"} +{"text": "Enterobacteriaceae (CPE) carriage, we studied 21 CPE carriers for \u00bb1 year. Mean carriage duration was 86 days; probability of decolonization in 1 year was 98.5%, suggesting that CPE-carriers\u2019 status can be reviewed yearly. Prolonged carriage was associated with use of antimicrobial drugs.To determine the duration of carbapenemase-producing Enterobacteriaceae (CPE) poses a public health threat , and species identification was performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry . Antimicrobial susceptibility testing was performed by using VITEK-2 (bioM\u00e9rieux). All Enterobacteriaceae isolates with a MIC of >2 mg/L for meropenem or >1.0 mg/L for ertapenem underwent PCR to detect blaNDM-1, blaKPC, blaOXA-48, blaIMI-1, and blaIMP genes (https://www.illumina.com). We used the Shannon diversity index to measure \u03b1-diversity for fecal microbial communities (https://cran.r-project.org/web/packages/vegan/vegan.pdf).The fecal samples were inoculated onto selective chromogenic agar colonized, CP\u2013Klebsiella pneumoniae (CP-KP) colonized, and CP-EC/KP co-colonized (https://www.R-project.org) and RStan (http://mc-stan.org).We analyzed data by using Bayesian multistate Markov models to account for interval censoring . First, olonized Figure 22 of difference in proportions = 14.8, simulated p = 0.0005) (K. pneumoniae (18 [85.7%]) and E. coli (16 [76.2%]). The most frequently observed carbapenemase genes were blaOXA-48 (11 [52.4%]) and blaKPC (8 [38.1%]). We obtained 76 CP-KP isolates from the samples; the most common sequence type (25 [32.9%]) was 307. Among the 83 CP-EC isolates, the most common sequence type (22 [26.5%]) was 131. Sample positivity was continuous until clearance for most (17 [81.0%]) of the 21 participants. For 4 participants, negative samples were followed by positive samples; the longest period was 3 negative samples over 3 consecutive weeks (We enrolled 21 patients . Mean (\u00b1 0.0005) Table 1.ve weeks Figure 5The estimated mean duration of CPE carriage was 86 days. The probability of decolonization in 1 year was 98.5% (95% CrI 95.0%\u201399.8%), assuming a constant decolonization rate within the time interval. The longest observed carriage duration was 387 days. We performed a sensitivity analysis that included 16 participants who became decolonized during follow-up . This analysis gave a mean carriage time of 77 (95% CrI 53\u2013108) days and a 98.8% (95% CrI 96.5%\u201399.9%) probability of decolonization within 1 year.As time-fixed covariates, we analyzed age, co-colonization with other multidrug-resistant organisms, presence of a urinary catheter, antimicrobial drug use during follow-up, Charlson Comorbidity Index score, and readmission; as a time-varying covariate, we used the Shannon Diversity Index score to explore the covariates\u2019 association with decolonization Figure 3CPE infections are typically preceded by asymptomatic carriage, especially in vulnerable patients such as those who are immunocompromised and critically ill patients had intervening negative samples, 1\u20133 weeks apart. This finding suggests that a patient should have Enterobacteriaceae carriage in hospital patients.Supplementary methods and results for study of duration of carbapenemase-producing"} +{"text": "Enterobacter hormaechei 2B-MC1, isolated from a shrimp sample collected from a farmer\u2019s market in Atlanta, Georgia. The assembled genome sequence observed was 4,661,561 bp long with a G+C content of 55.3%. The isolate harbored sul1, sul2, qnrA1, oqxB, dfrA23, blaACT, floR, fosA, tet(A), aph(6)-Id, and aph(3\u2033)-Ib antibiotic resistance genes.Here, we announce the draft genome sequence of Enterobacter hormaechei 2B-MC1, isolated from a shrimp sample collected from a farmer\u2019s market in Atlanta, Georgia. The assembled genome sequence observed was 4,661,561 bp long with a G+C content of 55.3%. The isolate harbored sul1, sul2, qnrA1, oqxB, dfrA23, blaACT, floR, fosA, tet(A), aph(6)-Id, and aph(3\u2033)-Ib antibiotic resistance genes.Here, we announce the draft genome sequence of Enterobacter hormaechei 2B-MC1 strain from raw farm-raised shrimp from Ecuador which was collected from a farmer\u2019s market in Atlanta, Georgia, on 30 March 2019. Thirty-one shrimp samples were screened for the presence of extended-spectrum \u03b2-lactam strains as previously described . The quality and quantity of the DNA were measured using a NanoDrop One spectrophotometer (Thermo Fisher). Libraries from the DNA sample were prepared and sequenced at a Florida State University molecular cloning facility. Libraries were sequenced using a MiSeq 2 microkit (Illumina) at 9 pM with 5% PhiX. Default parameters for all software were used during analyses unless otherwise specified. The raw Illumina sequences were quality filtered using Trimmomatic (v0.36) (de novo assembled with Velvet (1.2.10) v0.36) . The hig . The hiine tool with theine tool annotatilvet 1.2. . A total of 1,567 genes were associated with KEGG pathways. The closest relatives of E. hormaechei 2B-MC1 found by MiGA in the database were Enterobacter sp. strain CRENT-193 (GenBank accession number NZ_CP024812.1) and E. hormaechei (NZ_CP030076) with an average nucleotide identity of 99.19%. AMRFinder identified genes and mutations that confer resistance to sulfonamides (sul1 and sul2), quinolones (qnrA1), phenicol/quinolones (oqxB), trimethoprim (dfrA23), beta-lactamases (blaACT), phenicols (floR), fosfomycin (fosA), tetracycline [tet(A)], and aminoglycosides [aph(6)-Id and aph(3\u2033)-Ib]. The following six putative plasmids were present in the draft genome: pESBL176 (MT230180.1), pESBL31 , pESBL87 (MT230381.1), pESBL96 (MT230424.1 and MT230426.1), unnamed4 plasmid (NZ_CP020513.1), and pKP2442_7c331 (NZ_KX434882.1).A total of 4,397,799 paired-end reads were sequenced. These raw sequences were trimmed and then quality filtered (about 8% of the reads were eliminated), resulting in approximately 363,705 reads. These high-quality reads were assembled into contigs. CheckM estimated the completeness of this genome as 99.8%. This assembly produced 160 contigs and an JACVEK000000000. The version described in this paper is the first version, JACVEK010000000. Raw Illumina data have been deposited in the NCBI Sequence Read Archive with the accession number SRR12586817 under the BioProject accession number PRJNA661375.This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number"} +{"text": "In this paper, we present the first optimized implementation of ARIA block cipher on low-end 8-bit Alf and Vegard\u2019s RISC processor (AVR) microcontrollers. To achieve high-speed implementation, primitive operations, including rotation operation, a substitute layer, and a diffusion layer, are carefully optimized for the target low-end embedded processor. The proposed ARIA implementation supports the electronic codebook (ECB) and the counter (CTR) modes of operation. In particular, the CTR mode of operation is further optimized with the pre-computed table of two add-round-key, one substitute layer, and one diffusion layer operations. Finally, the proposed ARIA-CTR implementations on 8-bit AVR microcontrollers achieved 187.1, 216.8, and 246.6 clock cycles per byte for 128-bit, 192-bit, and 256-bit security levels, respectively. Compared with previous reference implementations, the execution timing is improved by 69.8%, 69.6%, and 69.5% for 128-bit, 192-bit, and 256-bit security levels, respectively. Data encryption is a fundamental technology for secure network communication in the Internet of Things (IoT). However, the data encryption operation imposes high overheads for low-end microcontrollers. For this reason, the efficient implementation of data encryption is important to achieve the high availability of IoT services. Many block cipher algorithms have been suggested by cryptography researchers to achieve this goal.The international block cipher standard suggested by the National Institute of Standards and Technology (NIST) is the Advanced Encryption Standard (AES) was first introduced in 1998\u00a0. AES hasThe ARIA block cipher was first introduced in 2004\u00a0. This blIn this work, we first optimized the ARIA block cipher on low-end embedded processors. Two modes of operation, including the electronic codebook (ECB) and the counter (CTR) operation, are efficiently implemented with optimized rotation operation, a substitute layer, a diffusion layer, and a pre-computed table for repeated data of the initialization vector (IV) in the CTR.Primitive operations for the ARIA block cipher, including a substitute layer, a diffusion layer, and rotation operation, are efficiently implemented on target 8-bit AVR microcontrollers. The proposed method reduces the number of memory accesses and the number of instructions required for primitive operations. Compared with previous implementations, the proposed implementations for key scheduling and encryption optimized the execution timing by 89.1% and 68.0%, respectively.The ARIA-CTR mode of operation is further optimized with repeated data of IV. Two add-round-key, one substitute layer, and one diffusion layer are pre-computed in the form of a look-up table (LUT). By accessing the pre-computed table, these expensive operations are efficiently optimized away. ARIA-CTR implementations on 8-bit AVR microcontrollers require 187.1, 216.8, and 246.6 clock cycles per byte for 128-bit, 192-bit, and 256-bit key lengths, respectively.The remainder of this paper is organized as follows. A round of the ARIA block cipher consists of three steps, including add-round-key, a substitution layer, and a diffusion layer. The add-round-key performs XOR operation with a 128-bit round key and plaintext. The substitution layer is defined as four types of substitution operations; S-BOX, which are an affine transformation of the inversion function over A overview of the ARIA encryption and decryption processes is presented in The electronic codebook (ECB) mode is the simplest of the encryption modes. The long message is divided into blocks. Each block is encrypted separately.An alternative mode of operation is the counter (CTR) mode. The counter mode turns a block cipher into a stream cipher. The CTR mode generates the next keystream block by encrypting successive values of a counter value.FLASH memory, 8 MHz working frequency, two-stage pipeline design, and 4 KB RAM. The number of available registers is 32. Among them, six registers (i.e R26 \u223c R31) are reserved for address pointers, and the remaining registers are used for general purpose registers. The basic arithmetic instruction takes one clock cycle, while the memory access takes two clock cycles per byte. A detailed instruction set summary for implementation is presented in AVR is a modified Havard architecture 8-bit RISC single-chip microcontroller\u00a0. AVR micA number of implementation studies have been conducted to improve the performance of block ciphers on 8-bit AVR microcontrollers. Block cipher structures are largely divided into two categories. First, Addition, Rotation, and eXclusive- or (ARX)-based block ciphers have been efficiently implemented on low-end microcontrollers\u00a0,14,15,16In WISA\u201913, the LEA block cipher was introduced by an institute attached to Electronics and Telecommunications Research Institute (ETRI)\u00a0. The worIn CHES\u201906, the HIGHT block cipher was introduced\u00a0. 64-bit The US National Security Agency (NSA) presented two lightweight block ciphers, namely, SIMON and SPECK . The SIMZ address pointer for fast memory access. The mix-column computation was efficiently handled with the conditional branch skip. However, previous implementations have mainly focused on ECB mode of operation. However, the CTR mode of operation is most widely used in practice [Second, Substitution Permutation Network (SPN)-based block ciphers have also been actively investigated. Among them, AES implementations have received considerable attention because the block cipher is an international standard. In , the S-bTLS/SSL) . In CHESTLS/SSL) . The FACTLS/SSL) . With a In this work, we first implemented the ARIA block cipher on low-end 8-bit AVR microcontrollers. Then, the CTR mode of operation for the ARIA block cipher were optimized. By utilizing the repeated IV data and the inner architecture of ARIA, two add-round-key, one substitute layer, and one diffusion layer are replaced with one LUT access.The ARIA block cipher consists of key scheduling, encryption, and decryption functions. As encryption and decryption operations can be performed in one architecture, only the implementation of encryption operation is required. First, the ARIA-ECB mode of operation is optimized. This is the most basic mode of operation for block ciphers, in which 128-bit plaintext is encrypted with the ARIA encryption in specific security keys . The encryption operation outputs 128-bit ciphertext.Key scheduling generates round keys based on the master key. First, the master key is transformed to 128-bit variables :Instead of registers, these variables are stored in a Z address pointer, the target address of the STACK memory is accessible.After the address setting by adjustment of the 0x00 value. Only higher 8-bit of address includes the S-BOX starting address. As the offset of the table is 8-bit long, only the lower address must be updated for memory access.The substitute layer of ARIA consists of sixteen 8-bit-wise S-BOX layers, including four S-BOX1 (i.e. SBOX1_tbl) is set to the higher address of the Z pointer. In Steps 2\u20139, four S-BOX1 accesses are performed with input intermediate results by assigning them to the lower address of the Z pointer (R30). Afterward, results are loaded from the FLASH memory to input registers .Algorithm 1 Optimized four S-BOX1 accesses in a source code level.Input: Higher address of S-BOX1 SBOX1_tbl, intermediate results .4: MOV R30, reg2Output: Output results 5: LPM reg2, Z1: LDI R31, hi8(SBOX1_tbl)6: MOV R30, reg2: MOV R30, reg18: MOV R30, reg43: LPM reg1, 9: LPM reg4, ZThe memory access is performed in a grouped way. In each group, four S-BOX layers are grouped as shown in The diffusion layer requires several XOR operations with input variables. Some of these XOR operation duplicate each other. The diffusion layer is optimized in by re-orAlgorithm 2 8-bit optimized diffusion layer [on layer .Input: Intermediate results , and the remaining XOR operations for these registers are also performed. Similarly, the STACK memory rather than the registers. In Steps 49, 54, 59, and 64, intermediate results are pushed to the STACK memory. Similarly, in the STACK memory in Steps 73, 78, 83, and 88. In Steps 89 to 96, the pushed results are restored from the STACK memory to the registers. In Steps 97 to 104, intermediate results are moved to the output registers for result alignment.Algorithm 3 Proposed implementation of 8-bit optimized diffusion layer in a source code level.Input: Intermediate results (Y0\u223cY15), temporal register .Output: diffusion layer intermediate results (Y0\u223cY15).// 2:EOR TMP1, Y43:EOR TMP1, Y94:EOR TMP1, Y145:MOV Z0, TMP16:EOR Z0, Y67:EOR Z0, Y88:EOR Z0, Y139:MOV Z5, TMP110:EOR Z5, Y111:EOR Z5, Y1012:EOR Z5, Y1513:MOV Z11, TMP114:EOR Z11, Y215:EOR Z11, Y716:EOR Z11, Y1217:MOV Z14, TMP118:EOR Z14, Y019:EOR Z14, Y520:EOR Z14, Y11// 21:MOV TMP1, Y222:EOR TMP1, Y523:EOR TMP1, Y824:EOR TMP1, Y1525:MOV Z1, TMP126:EOR Z1, Y727:EOR Z1, Y928: EOR Z1, Y1229: MOV Z4, TMP130:EOR Z4, Y031:EOR Z4, Y1132:EOR Z4, Y1433:MOV Z10, TMP134:EOR Z10, Y335:EOR Z10, Y636:EOR Z10, Y1337:MOV Z15, TMP138:EOR Z15, Y139: EOR Z15, Y440:EOR Z15, Y10// 41:MOV TMP1, Y142:EOR TMP1, Y643:EOR TMP1, Y1144:EOR TMP1, Y1245:EOR TMP1, Y1246:EOR TMP2, Y447:EOR TMP2, Y1048:EOR TMP2, Y1549:PUSH TMP250:MOV TMP2, TMP151:EOR TMP2, Y352:EOR TMP2, Y853:EOR TMP2, Y1354:PUSH TMP255:MOV TMP2, TMP156:EOR TMP2, Y057:EOR TMP2, Y558:EOR TMP2, Y1459:PUSH TMP260:MOV TMP2, TMP161:EOR TMP2, Y262:EOR TMP2, Y763:EOR TMP2, Y964:PUSH TMP2// 65:MOV TMP1, Y066: EOR TMP1, Y767:EOR TMP1, Y1068:EOR TMP1, Y1369:MOV TMP2, TMP170: EOR TMP2, Y571:EOR TMP2, Y1172:EOR TMP2, Y1473:PUSH TMP274:MOV TMP2, TMP175:EOR TMP2, Y276:EOR TMP2, Y977:EOR TMP2, Y1278:PUSH TMP279:MOV TMP2, TMP180:EOR TMP2, Y181:EOR TMP2, Y482:EOR TMP2, Y1583:PUSH TMP284:MOV TMP2, TMP185:OR TMP2, Y386:EOR TMP2, Y687:EOR TMP2, Y888: PUSH TMP2//Finalization89:POP Y1390:POP Y891:POP Y692:POP Y393:POP Y1294:POP Y995:POP Y796:POP Y297:POP Y298:MOV Y5, Z599:MOV Y11, Z11100:MOV Y14, Z14101:MOV Y1, Z1102:MOV Y4, Z4103:MOV Y10, Z10104:MOV Y15, Z15The 8-bit optimized diffusion layer approach is efficiently implemented on 8-bit AVR microcontrollers. Detailed descriptions are given in Algorithm 3. The process of x) is efficiently implemented on 8-bit AVR microcontrollers. First, the offset for multiple of 8-bit is performed byte-wise rather than bit-wise. Then, the remaining offset is performed bit-wise. The ARIA block cipher requires five different rotation operations. The 8-bit optimized rotation operation is as follows.The ARIA block cipher requires 128-bit wise rotation operation. Multi-precision rotation on 128-bit wise data (reg16.Algorithm 4ROR_1: 1-bit right rotation for 128-bit data.Input: Intermediate results (reg1\u223creg16)Output: 1-bit right rotated intermediate results (reg1\u223creg16)1:BST reg16, 02:LSR reg13:ROR reg24:ROR reg35:ROR reg46:ROR reg57:ROR reg68:ROR reg79:ROR reg810:ROR reg911:ROR reg1012:ROR reg1113:ROR reg1214:ROR reg1315:ROR reg1416:ROR reg1517:ROR reg1618:BLD reg1, 7Taking an example of 19-bit right rotation, 2-byte is right rotated first and then 3-bit is right rotated. Efficient 1-bit right rotation for 128-bit data is given in Algorithm 4. In Step 1, the most significant bit is cached. Afterward, 1-bit is shifted from the least significant byte to the most significant byte. In Step 18, the least significant bit is replaced with the cached bit from MOVW instruction, which ensures 2-byte-wise register copying. In Steps 10 to 12, the remaining 3-bit right rotation is performed with Algorithm 4 by calling 3 times.Algorithm 5ROR_19: 19-bit right rotation for 128-bit data.Input: Intermediate results (reg1\u223creg16), temporal registers (tmp_reg1)Output: 19-bit right rotated intermediate results (reg1\u223creg16).1:MOVW tmp_reg1, reg152:MOVW reg15, reg133:MOVW reg13, reg114:MOVW reg11, reg95:MOVW reg9, reg76:MOVW reg7, reg57:MOVW reg5, reg38:MOVW reg3, reg19:MOVW reg1, tmp_reg110:ROR_1 reg1, \u2026, reg1611:ROR_1 reg1, \u2026, reg1612:ROR_1 reg1, \u2026, reg16The process of 19-bit right rotation for 128-bit data is given in Algorithm 5. First, 16-bit wise right rotation is performed with the Algorithm 6ROL_1: 1-bit left rotation for 128-bit data.Input: Intermediate results (reg1\u223creg16), temporal register (tmp_reg).Output: 1-bit left rotated intermediate results (reg1\u223creg16).1:CLR tmp_reg2:LSL reg163:ROL reg154:ROL reg145:ROL reg136:ROL reg127:ROL reg118:ROL reg109:ROL reg910:ROL reg811:ROL reg712:ROL reg613:ROL reg514:ROL reg415:ROL reg316:ROL reg217:ROL reg118:ADC reg16, tmp_regEfficient 1-bit left rotation for 128-bit data is given in Algorithm 6. In Step 1, one register is initialized. Then, 1-bit is shifted to the left from the most significant byte to the least significant byte. In Step 18, the most significant bit is replaced by the carry bit generated from Step 17.MOVW instruction. In Step 11, the remaining 1-bit right rotation is performed with Algorithm 6.Algorithm 7ROR_31: 31-bit right rotation for 128-bit data.Input: Intermediate results (reg1\u223creg16), temporal registers (tmp_reg1).Output: 31-bit right rotated intermediate results (reg1\u223creg16).1:MOVW tmp_reg3, reg152:MOVW tmp_reg1, reg133:MOVW reg15, reg114:MOVW reg13, reg95:MOVW reg11, reg76:MOVW reg9, reg57:MOVW reg7, reg38:MOVW reg5, reg19:MOVW reg3, tmp_reg310:MOVW reg1, tmp_reg111:ROL_1 reg1, \u2026, reg16, tmp_reg1The process of 31-bit right rotation for 128-bit data is given in Algorithm 7. First, 32-bit wise right rotation is performed with the As shown in In this section, efficient implementations of ARIA-CTR encryption for low-end processors are proposed. The main idea is caching the primitive operations of the ARIA block cipher; this approach skips the operations by the add-round-key of round 2.The first operation of the ARIA block cipher is add-round-key. This is a byte-wise XOR operation with plaintext and round keys. In particular, the CTR mode of operation assigns a (non-constant) 32-bit counter and a (constant) 96-bit IV. Between the first and second blocks, only counter 1 is different in the 32-bit counter section. After the add round key operation, this difference is maintained because it only performs XOR operations. By exploiting this condition, the output of the add-round-key operation can be cached except the counter parts. Detailed descriptions are given in The cache table is further extended to the add-round-key operation of round 2. The substitution layer only updates the data byte-wise. The other (constant) bytes are maintained and can be cached. This is presented in detail in However, for the diffusion layer, one byte updates other bytes. Taking an example of After the 256-th block, 2 bytes , RAM (byte), and execution time (clock cycles per byte). The software was implemented over Atmel Studio 7, and the code was compiled in -O2 option. All ARIA implementations are written in assembly language. The function call and variable assignment are written in C language.The proposed ARIA implementations were evaluated on a low-end 8-bit ATmega128 microcontoller. The microcontroller supports a 128KB In Previous works saved four S-BOX tables in RAM. Each S-BOX table requires 256-byte\u00a0[FLASH memory, which reduces the expensive RAM consumption\u00a0[The execution timings of the proposed ARIA-128-ECB for key scheduling, encryption, and decryption are 214.9, 198.3, and 198.3 clock cycles per byte, respectively. Compared with previous reference implementations, the proposed implementations for key scheduling and encryption optimized the execution timing by 89.1% and 68.0%, respectively [The execution timing of the proposed ARIA-CTR-128 requires 187.1 clock cycles per byte. This result is 5.6% faster than the speed-optimized ECB implementation. Similarly, the implementations of ARIA-CTR-192 and ARIA-CTR-256 require 216.8 and 246.6 clock cycles per byte, respectively. These are faster than ECB implementations by 4.9% and 4.3%, respectively. The code sizes of the speed-optimized ARIA-CTR implementation for key scheduling and encryption are 5938 bytes and 3602 bytes, respectively. Compared with the ECB implementation, the CTR implementation requires 1 KB more for the pre-computed substitute layer and diffusion layer.In this paper, we presented the optimized implementation of the ARIA block cipher on AVR microcontrollers. Optimization techniques are generally divided into AVR specific optimization and generic optimization. In this section, we describe these optimizations in detail.First, memory access is efficiently performed in a grouped way. The memory address is aligned 8-bit wise, which ensures multiple memory accesses with simple offset modifications. This is described in detail in Algorithm 1.Second, the 8-bit optimized diffusion layer is presented. The target microcontroller has a limited number of registers. The proposed approach reduces the number of memory accesses by utilizing available registers. This is described in detail in Algorithm 3.Finally, 5 different rotation operations are optimized for the 8-bit microcontroller. This reduces the offset only below 8-bit wise. This is described in detail in Algorithms 4 and 5.Although the ARIA-CTR encryption (ACE) method is optimized for low-end microcontrollers, the proposed method is a generic algorithm. For this reason, the ACE method can optimize the implementation of ARIA-CTR encryption on other platforms, such as 32-bit ARM and Intel processors, without difficulties. The main idea of the proposed method is pre-computation of the ARIA round function. Because the 96-bit nonce value is constant, a large portion of the round function can be re-used. The pre-computed table skips two add-round-key, one substitute layer, and one diffusion layer operations.In this paper, we proposed optimized implementations of ARIA\u2013ECB and ARIA-CTR on low-end 8-bit AVR microcontrollers. The implementation of ARIA\u2013ECB is improved with optimized rotation, substitute layer, and diffusion layer operations. Then, ARIA\u2013CTR implementation is further optimized with two cache tables. This novel approach skips ARIA\u2013CTR computations by the add-round-key operation of Round 2. With these efficient implementation methods, ARIA-CTR implementations on 8-bit AVR microcontrollers require 187.1, 216.8, and 246.6 clock cycles per byte for 128-bit, 192-bit, and 256-bit, respectively.In future work, the proposed method will be applied to other lightweight block ciphers, such as SIMON and SPECK. Furthermore, we will investigate other microcontrollers to achieve high-speed implementation of the ARIA block cipher."} +{"text": "Few longitudinal studies link objectively assessed sleep and cognitive performance in ecologically-valid environments. Participants enrolled in the community-based Einstein Aging Study cohort . Wake after sleep onset (WASO) was associated with worse cognitive performance with and without MCI . Models include age, gender, ethnicity, education, learning effects, sleep duration, WASO*MCI interaction . Associations were stronger among those with MCI, thirty minutes more nightly WASO predicted a 500ms longer Symbol Match response time (p<0.0001), 5.05% higher Color Dot error proportion (p=0.002), 0.184 points lower Color Shape accuracy (p<0.0001). In those without MCI, WASO was associated with worse cognition: thirty minutes more nightly WASO predicted +166.7ms Symbol Match response time (p=0.03) and -0.06 points Color Shape accuracy (p=0.013). Actigraphic sleep quality associated with ambulatory cognitive performance (and worse with MCI status) suggests targets for prevention/mitigation of cognitive decline. Part of a symposium sponsored by the Sleep, Circadian Rhythms and Aging Interest Group."} +{"text": "Correction to: BMC Cell Biol 17, 21 (2016)https://doi.org/10.1186/s12860-016-0101-0Following publication of the original article , an erroc Morphological changes in HKGECs induced by TGF-\u03b21 (20\u2009ng/ml) were examined using phase contrast microscopy. Cells were counterstained with DAPI to visualize nuclei (blue).Fig. 1"} +{"text": "Correction to: World Journal of Emergency Surgery 15, 88 (2020)https://doi.org/10.1186/s13019-020-01143-wThe age in Biological AVR group should instead be 65.6 +/\u2212\u20094.3The age in Mechanical AVR group should instead be 64.8 +/\u2212\u20095.1The original article contains"} +{"text": "Correction to: BMC Biol 18, 163 (2020)https://doi.org/10.1186/s12915-020-00893-2The original publication of this article containeIn this correction article the correct and incorrect version of figure 4 are published along with the updated Additional file The original article has been updated.Incorrect figure 4.Correct Figure Additional file 1: Fig. S1. Excision of the primary tumor elicits gradual regression of early-stage metastases. Table S1. Cytokines pointed out by the cytokine array. Fig. S2. ELISA validation of in-vitro tumor secretion of the chosen cytokines. Fig. S3. Elevated levels of Serpin E1, IL-8, MIF and PDGF-AA are correlated to poor survival in lung cancer patients. Fig. S4. Associations between levels of DKK1, IL-6, M-CSF and LIF and survival in breast cancer patients."} +{"text": "Scientific Reports 10.1038/s41598-019-48799-6, published online, 23 August 2019Correction to: This Article containedan error in the Author Information section where:\u201cE. Rasmark Roepke, V. Bruno, M. Rub\u00e9r and J. Ernerudh contributed equally.\u201dnow reads:\u201cE. Rasmark Roepke and V. Bruno contributed equally. M. Rub\u00e9r and J. Ernerudh jointly supervised this work.\u201dThis error has now been corrected in the PDF and HTML versions of the Article."} +{"text": "Correction to: BMC Evolutionary Biology (2020) 20:44https://doi.org/10.1186/s12862-020-01605-8Following publication of the original article , the autFig. 1 STRUCTURE bar plot showing the individual membership coefficients assigned to each K number of groups (K\u2009=\u20092) defined as populations. The individuals are classified according to their sampling site: 1) Carrizal de Bravo, Guerrero. (2) San Mateo R\u00edo Hondo, Oaxaca. (3) Motozintla, Chiapas. (4) Tacan\u00e1 volcano, Chiapas. (5) San Crist\u00f3bal de las Casas, Chiapas. (6) Acatenango volcano, Chimaltenango. (7) Chimaltenango Quetzaltenango. (8) Totonicap\u00e1n. (9) Sierra de los Cuchumatanes, Huehuetenango."} +{"text": "The article presents a variant of maturity onset diabetes of the young type 2, caused by a rare mutationin the GCK gene. Maturity onset diabetes of the young (MODY) is a hereditary form of diabetes with an autosomaldominant type of inheritance, an onset at a young age, and a primary defect in pancreatic \u03b2-cell function. Thistype of diabetes is different from classical types of diabetes mellitus (DM1 and DM2) in its clinical course, treatmentstrategies, and prognosis. Clinical manifestations of MODY are heterogeneous and may vary even amongmembers of the same family, i. e., carriers of identical mutations. This phenotypic variation is due to the interactionof mutations with different genetic backgrounds and the influence of environmental factors . Usingnext-generation sequencing technology, the c.580\u20131G>A substitution located in anacceptor splice site of intron 5 of the GCK gene was found in a proband. The identified variant cosegregated witha pathological phenotype in the examined family members. The GCK gene encodes glucokinase (hexokinase 4),which catalyzes the first step in a large number of glucose metabolic pathways such as glycolysis. Mutations in thisgene are the cause of MODY2. The illness is characterized by an insignificant increase in the fasting glucose level, isa well-controlled disease without medication, and has a low prevalence of micro- and macrovascular complicationsof diabetes. The presented case of MODY2 reveals the clinical significance of a mutation in the splice site of theGCK gene. When nonclassical diabetes mellitus is being diagnosed in young people and pregnant women, genetictesting is needed to verify the diagnosis and to select the optimal treatment method.Key words: human; maturity onset diabetes of the young; MODY2; glucokinase gene; next-generation sequencing;genetic analysis; bioinformatics. Maturity onset diabetes of the young (MODY) is a hereditaryform of diabetes with autosomal dominant inheritance and ischaracterized by onset at a young age and by the presenceof an initial defect in pancreatic \u03b2-cell function. This type ofdiabetes differs from classic types of diabetes mellitus-type 1(DM1) and type 2 (DM2) in disease progression, in treatmentstrategies, and prognosis . Up to 80 % ofMODY cases are not detected or are misdiagnosed as DM1 orDM2; therefore, patients with an incorrectly diagnosed typeof diabetes are often prescribed inadequate therapy . On average, MODY is detected in 2\u20135 % of casesof diabetes (the rest being mostly DM1 and DM2) . To reliably diagnose MODY in a patient, moleculargenetic analysis should be carried out. To date, 14 types ofMODY (MODY1 through MODY14) have been identified,each associated with mutations in a specific gene: HNF4A,GCK, HNF1A, PDX1, HNF1B, NEUROD1, KLF11, CEL,PAX4, INS, BLK, KCNJ11, ABCC8 and APPL1 . FourteenMODY-associated genes explain 70\u201385 % of the disease casesand are involved in various stages of glucose metabolismregulation . According to various researchers, 11to 30 % of MODY cases are caused by mutation in other genes. These formsof MODY are commonly referred to as MODY-X. Becausethe vast majority of pathogenic mutations are found in exonsand adjacent splicing sites of genes , it isreasonable to perform whole-exome sequencing on genomicDNA from individuals with MODY, with subsequent genetictesting of their relatives for the identified mutation. MODYverification allows for successful patient management andensures healthy pregnancy and provision of genetic counselingto families . Examination of relatives ofMODY probands makes it possible to diagnose hyperglycemiain the preclinical phase.In this report, we describe a clinical case of a family withMODY2 associated with a rare splice site mutation in theglucokinase (GCK ) gene identified by the next-generationsequencing technology.The study protocol was approved by the local Ethics Committeeof the Institute of Internal and Preventive Medicine. Written informedconsent to be examined and to participate in the study wasobtained from each patient. For individuals younger than18 years, the informed consent form was signed by a parentor legal guardian.Blood samples were collected from the ulnar vein forbiochemical analysis in the morning on an empty stomach.Lipid levels andglucose concentration were determined on a KoneLab 300ibiochemical analyzer with Thermo Fisher Scientific reagents.https://broadinstitute.github.io/picard/).Genomic DNA was isolated from leukocytes of venousblood by phenol-chloroform extraction . Quality of the extracted DNA was assessed on acapillary electrophoresis system, Agilent 2100 Bioanalyzer. Sequencing of patients\u2019DNA was carried out on an Illumina HiSeq1500 instrument. The enrichment andlibrary preparation were performed with the SureSelectXTHuman All Exon V5 + UTRs Kit . Reads were mapped to the reference human genome(GRCh37) by means of the Burrow\u2013Wheeler Alignment tool(BWA v.0.7.12) . Polymerase chain reaction(PCR)-generated duplicates were removed in the PICARDsoftware (A search for single-nucleotide variants (SNVs) was conductedusing the Genome Analysis Toolkit v.3.3 package bythe procedure for local remapping of short insertions/deletionsand recalibration of read quality . Thedepth of coverage was 34\u00d7 to 53\u00d7. SNVs with genotype qualityscores < 20 and coverage depth < 10\u00d7 were filtered out andexcluded from further analysis. Annotation of the SNVs wasperformed in the ANNOVAR software using the 1000 Genomes Project and The Genome Aggregation Database(gnomAD) databases. We selectedthe spectrum of rare and novel sequence variants in MODYgenes .Rare variants were selected if their minor allele frequency(MAF) was \u2264 0.5 in the 1000 Genomes Project and gnomAD.Heterozygous substitution c.580\u20131G>A (IVS5 \u20131G>A) at anacceptor splice site of intron 5 of the GCK gene was found in the proband and her sister. To predict the possible effectof the SNV on splicing regulation, we employed the SPANRsoftware .The substitution was corroborated by Sanger sequencingof the DNA fragment containing exons 5 and 6, intron 5,and parts of introns 4 and 6 using the following forward andreverse primers: 5\u2032-CAGGGAGCCTCAGCAGTCTGGA-3\u2032and 5\u2032-GCCACGAGGCCTATCTCTCCCC-3\u2032. The oligonucleotideswere designed in the Primer-Blast software (https://www.ncbi.nlm.nih.gov/tools/primer-blast/) and were synthesizedby the Biosset company . Thesequencing reactions were carried out on an automated ABI3500 DNA sequencer withthe BigDye Terminator v3.1 Cycle Sequencing Kit . PCR was set up using BioMasterLR HS-PCR (2\u00d7) , 1 \u03bcL of each primer,and 1 \u03bcL of DNA, with a total final volume of 25 \u03bcL. Thethermocycling program consisted of initial denaturation at94 \u00b0C for 3 min and then 35 cycles at 94 \u00b0C for 30 s, 66 \u00b0Cfor 30 s, and 72 \u00b0C for 50 s. The PCR products were evaluatedby electrophoresis in a 5 % polyacrylamide gel after visualizationwith an ethidium bromide solution. A 100 bp DNALadder (BioLabMix) was simultaneously run on the gel asmolecular size markers. The amplicons were purified usingAgencourt AMPure Xp beads . Thesequencing reactions were conducted on an automated ABI3500 DNA sequencer viathe BigDye Terminator v3.1 Cycle Sequencing Kit (ThermoFisher Scientific). The sequences were analyzed in the VectorNTI\u00ae Advance software (Thermo Fisher Scientific). The hg19version of the human genome served as a reference sequencefor the alignment.The white European 44-year-old female proband was undermedical observation. When she underwent routine screening in2012 (at age 40), hyperglycemia at 7.2 mmol/L was revealed.No complaints were registered. During subsequent glycemiacontrol, maximal fasting glucose was 7.2 mmol/L, and thepostprandial one was 8.9 mmol/L. C-peptide was 1.83 ng/mL(reference range 0.5\u20133.2 ng/mL), immunoreactive insulin was7.9 \u03bcU/mL (reference range 2.0\u201325.0 \u03bcU/ mL), and glycatedhemoglobin (HbA1c) was 7.1 %. Antibodies to insulin, topancreatic islet cells, and to glutamic acid decarboxylasewere absent. Blood biochemical analysis and determinationof thyroid status did not reveal any abnormalities. Ultrasonographyof internal organs, echocardiography, and a studyof brachiocephalic vessels did not uncover any pathology.The body mass index (BMI) was 20.2 kg/m2. DM2 was diagnosedin the patient, and sitagliptin was prescribed. At theage of 26, the patient spontaneously delivered a healthy girlat 39 weeks of gestation; hyperglycemia was not detectedduring the pregnancy.The sister of the proband is a white European 35-yearoldwoman. At age 23, during tests before mastectomy formastopathy, she got a diagnosis of fasting hyperglycemia(6.3 mmol/L). The patient did not have any complains, anda proper diet was recommended. At the age of 29, duringadditional examination before cholecystectomy for cholelithiasis,she received a diagnosis of DM2, and vildagliptin was prescribed at the dose of 50 mg twice a day. At age 31, the proband\u2019ssister visited an endocrinologist at the outpatient clinicof the Institute of Internal and Preventive Medicine withcomplaints of a failure to get pregnant within a year. On examination,BMI was 20.6 kg/m2, and the objective status was unremarkable.Blood biochemical analysis revealed hypercalcemia(3.25 mmol/L), increased levels of high-density lipoproteincholesterol (85 mg/dL), hypercholesterolemia (220 mg/ dL),and hyperglycemia (6.8 mmol/L), but other analyzed parameterswere within reference ranges. The HbA1c level was7.1 %. Antibodies to insulin, to pancreaticislet cells, and toglutamic acid decarboxylase were absent. Thyroid-stimulatinghormone concentration was 0.759 mU/ mL (referencerange0.4\u20134.0), whereas the prolactin level was 216 ng/ mL (referencerange 1.2\u201319.5). Echocardiography, Doppler sonography ofextracranial parts of cerebral vessels, and abdominal and renalultrasonographic examination revealed no pathology. Cystswere found in both thyroid lobes during the ultrasonography.Given the existence of the proband\u2019s relatives with impairedglucose metabolism, persistence of normal C-peptide levels,the absenceof diabetes-associated autoantibodies, normalBMIs of the proband and her sister, and stable mild hyperglycemia,MODY was assumed.Exons and adjacent splice sites of MODY-associated geneswere analyzed by whole-exome sequencing in the proband andher sister. As a result, heterozygous substitution c.580\u20131G>A(IVS5 \u20131G>A) at an acceptor splice site of intron 5 of theGCK gene was found in the proband and her sister. The IVS5(\u20131G>A) polymorphism of GCK was submitted in ClinVarwith an accession number of rs1554335421 , but was absent in the 1000 Genomes Project , in gnomAD projectdatabases at the moment of publication. Subsequent geneticanalysis by Sanger sequencing of the family members uncovered segregationof the substitution with DM as an autosomal dominanttrait .Our results, literature data, and databasessuggest that this splice site mutation is likely pathogenic.After confirmation of GCK-MODY in the proband and hersister, their relatives were screened for carbohydrate metabolism disorders. The proband\u2019s mother and daughter did nothave any abnormalities. The proband\u2019s father showed impairedfasting glucose. No complaints were registered, venous plasmafasting glucose was 6.3 mmol/L, and 2 h after the oral glucosetolerance test, it was 7.5 mmol/L. At present, the man doesnot take any medication. The same heterozygous substitutionrs1554335421 (IVS5 \u20131G>A) in the proband\u2019s father\u2019s GCKgene was detected by genetic testing.The proband\u2019s sister had her first pregnancy in 2014 (atage 31). In 2015, a boy weighing 3640 g was born by a caesareansection at 39 weeks of gestation. The pregnancy wascomplicated: premature rupture of membranes, weakness oflabor, and fetal hypoxia. After delivery, due to stable glycemicindexes, it was decided that insulin therapy should bediscontinued. In January 2018, during treatment with diet,the patient\u2019s HbA1c was 6.4 %.The neonatal period of the proband\u2019s nephew was unremarkable.In 2017, his blood biochemical analysis resultedin a diagnosis of hyperglycemia (6.9 mmol/L). HbA1c was6.3 %, and the C-peptide level was 0.54 ng/mL. Antibodiesto insulin, pancreatic \u03b2-cells, and glutamic acid decarboxylasewere undetectable. The same heterozygous substitutionrs1554335421 in the GCK gene was identifiedby genetic testing. At present, the child is under medical observationat Almazov Federal Medical Research Centre ; because of GCK-MODY, a balanceddietwas recommended.DiscussionIt is known that in young patients with impaired carbohydratemetabolism, DM1, DM2, or rarer monogenic forms of diabetesmay be diagnosed. At the onset of the disease, the probandand her sister had no symptoms characteristic for the commontypes of diabetes, fasting hyperglycemia was not progressing,and carbohydrate metabolism disorders were detected duringroutine screening. The presence of DM in the proband\u2019s sister,persistence of normal C-peptide levels, a lack of autoantibodies,and a normal BMI in the proband and her sister pointedto MODY .Heterozygous splice site mutation c.580\u20131G>A(rs1554335421) in intron 5 of their GCK gene was identifiedby genetic testing. Mutations in this gene are associated withDM2, MODY, and neonatal DM . More than 600 variants of the GCK gene associated with MODY have been described, and the list ofthe mutations is constantly growing. The vast majority of themutations are missense substitutions, but splice site mutations,deletions, and insertions are reported too .The GCK gene is located in chromosomal region 7p15.3-p15.1 and consists of 12 exons that encode a 465-amino-acidprotein, glucokinase , which is one of fourmembers of the hexokinase family of enzymes. In 1992, GCKwas the first gene to be linked to MODY. It plays an importantregulatory role in glucose metabolism. Glucokinase catalyzesphosphorylation of glucose to produce glucose-6-phosphate asthe first step of glycolysis in pancreatic \u03b2-cells . Most individuals with heterozygousGCK mutations show fasting plasma glucose levelsbetween 5.5 and 8.0 mmol/L and a small increase in plasmaglucose (< 3 mmol/L in 70 % of the patients) 2 h after the oralglucose test . This feature also explainsasymptomatic fasting hyperglycemia (HbA1c range 5.8\u20137.6 %(40\u201360 mmol/mol)) and rare microvascular and macrovascularcomplications in patients with GCK-MODY . Most patients have an aberrantfasting glucose level or impaired glucose tolerance, and lessthan 50 % of the affected individuals have diabetes, whichis diagnosed during childhood, adolescence, or pregnancy. In a study on Italian patients under 18years of age with incidental hyperglycemia, it was estimatedthat 15 % of these cases are caused by GCK mutations .It was found here that the proband and her sister carrya heterozygous substitution, c.580\u20131G>A , at an acceptor splice site of GCK intron 5.This allelic variant is of interest because consensus donor(GT dinucleotide) and acceptor (AG dinucleotide) splicesites are highly conserved. Point mutations at these loci canlead to cryptic splice site activation and synthesis of aberrantprotein isoforms.In silico analysis of the functional significance of this substitutionsuggested that the inclusion of exons 5, 6, and 7 ingene transcripts will be reduced in case of the detected variant(see the Table).DM and a family history of gestational diabetes. Experimentson lymphoblastoid cells indicate that rs1554335421(IVS5 \u20131G>A) of GCK can activate a cryptic splice site inintron 5 and cause retention of 27 bp of the intron . Information about rs1554335421 (IVS5 \u20131G>A)of GCK is absent in the 1000 Genomes Project, The ExomeAggregation Consortium, and GNOMAD (https://gnomad.broadinstitute.org/) databases; however, taking into accountthe previous study and the data we obtained here, carriage ofthe A allele at position \u20131 of intron 5 is most likely a causative dominant variant of the GCK gene in MODY-affected people.Cryptic splice site activation and formation of several alternativetranscripts with intron 7 fragments\u2019 retention weredemonstrated in a system of model GCK minigenes withacceptor site mutation IVS7 (\u20131G>C) .Model mice with the homozygous mutation in the splicesite of \u03b2-cell-speci\ufb01c exon 1 IVS1A (\u20131G>T) show hyperglycemia,glucosuria, and growth retardation and die within the\ufb01rst week after birth. This phenotype can be explained by exonskipping or intron retention . Splicing sitesaffected by mutations have been described for many pathologicalphenotypes: neurofibromatosis type 1 ,familial hypercholesterolemia ,Wiskott\u2013Aldrich syndrome and chronic colitis , hypophosphatemic rickets , andothers. Mutations affecting splicing have been found not onlyin canonical splicing sites but also in introns and exons andmay have a tissue-specific effect, as in familial dysautonomia. Thatanalysis indicated that the donor splice site mutations weremore prevalent than the acceptor splice site variants (ratio1.5:1.0) . Because the mutationsin the GCK gene can cause a mild clinical phenotype, whichcan vary under the influence of many genetic and lifestylefactors, research on the carriers of these mutations is essentialfor identifying additional risk factors.GCK-MODY is inherited as an autosomal dominant traitmanifested throughout the lifespan as stable, mild fastinghyperglycemia usually reaching 6.7 mmol/L and higher onlyin middle age . A similar patternwas observed here in the proband and her sister. Nonetheless,the metabolic disturbances in the carriers of GCK mutationsare present from birth and can be identified already in the firstyears of life, almost all of them after puberty . The proband\u2019s nephew, who is a heterozygous mutationcarrier, developed carbohydrate metabolism disorders attwo years of age.It has been reported that carriers of GCK gene mutationswith a long history of hyperglycemia (48.6 years on average)usually have micro- and macrovascular complications of diabetesand are at a risk of cardiovascular diseases that is identicalto that in the general population .Patients with GCK-MODY in childhood and adolescencecan be treated only with diet in most cases, and glucoseloweringtherapy should be considered during pregnancy. The present subtype of MODY2 (in theproband and her sister) currently is treated with diet resultingin sufficient glycemic control.The presence or absence of a GCK mutation in the fetusaffects its sensitivity to maternal hyperglycemia . If the fetus does not have the mutation, then itwill secrete insulin excessively and as a result have a risk ofmacrosomia . In that case, low doses ofinsulin should be prescribed during pregnancy . During her pregnancy, the proband\u2019s sister wasgiven insulin injections in small doses. After delivery, insulintherapy was discontinued. Subsequently, the child was foundto carry the same substitution.The presented subtype of MODY2 reveals the clinical significanceof the mutation in a splice site of the GCK gene. Whennonclassical diabetes mellitus is being diagnosed in youngpeople and pregnant women, genetic testing is needed to verifythe diagnosis and to select the optimal treatment method.The authors declare no conflict of interest.Abramowicz A., Gos M. Splicing mutations in human genetic disorders:examples, detection, and confirmation. J. Appl. Genet. 2018;59:253-268. DOI 10.1007/s13353-018-0444-7.An\u0131k A., \u00c7atl\u0131 G., Abac\u0131 A., B\u00f6ber E. Maturity-onset diabetes of theyoung (MODY): an update. J. Pediatr. Endocrinol. Metab. 2015;28:251-263. DOI 10.1515/jpem-2014-0384.Bonnefond A., Philippe J., Durand E., Dechaume A., Huyvaert M.,Montagne L., Marre M., Balkau B., Fajardy I., Vambergue A., VatinV., Delplanque J., Le Guilcher D., De Graeve F., Lecoeur C.,Sand O., Vaxillaire M., Froguel P. Whole-exome sequencing andhigh throughput genotyping identified KCNJ11 as the thirteenthMODY gene. PLoS One. 2012;7(6):e37423. DOI 10.1371/journal.pone.0037423.Caetano L.A., Jorge A.A., Malaquias A.C., Trarbach E.B., Queiroz M.S.,Nery M., Teles M.G. Incidental mild hyperglycemia in children: twoMODY 2 families identified in Brazilian subjects. Arq. Bras. Endocrinol.Metabol. 2012;56(8):519-24. http://dx.doi.org/10.1590/S0004-27302012000800010.Chakera A.J., Carleton V.L., Ellard S., Wong J., Yue D.K., Pinner J.,Hattersley A.T., Ross G.P. Antenatal diagnosis of fetal genotypedetermines if maternal hyperglycemia due to a glucokinase mutationrequires treatment. Diabetes Care. 2012;35(9):1832-1834. DOI10.2337/dc12-0151.Chakera A.J., Spyer G., Vincent N., Ellard S., Hattersley A.T.,Dunne F.P. The 0.1 % of the population with glucokinase monogenicdiabetes can be recognized by clinical characteristics in pregnancy:the Atlantic Diabetes in Pregnancy cohort. Diabetes Care. 2014;37(5):1230-1236. DOI 10.2337/dc13-2248.Chakera A.J., Steele A.M., Gloyn A.L., Shepherd M.H., Shields B.,EllardS., Hattersley A.T. Recognition and management of individualswith hyperglycemia because of heterozygous glucokinase mutations.Diabetes Care. 2015;38(7):1383-1392. DOI 10.2337/dc14-2769.Edghill E.L., Minton J.A., Groves C.J., Flanagan S.E., Patch A.M.,Rubio-Cabezas O., Shepherd M., Lenzen S., McCarthy M.I.,EllardS., Hattersley A.T. Sequencing of candidate genes selectedby beta cell experts in monogenic diabetes of unknown aetiology. J.Pancreas \u2013 JOP. 2010;11(1):14-17. http://dx.doi.org/10.6092/1590-8577/3864.Esmaeilzadeh H., Bordbar M.R., Dastsooz H., Silawi M., Fard M.A.F.,Adib A., Kafashan A., Tabatabaei Z., Sadeghipour F., Faghihi M.A.A novel splice site mutation in WAS gene in patient with Wiskott-Aldrichsyndrome and chronic colitis: a case report. BMC Med. Genet.2018;19(1):123. DOI 10.1186/s12881-018-0647-0.Fajans S.S., Bell G.I., Polonsky K.S. Molecular mechanisms and clinicalpathophysiology of maturity-onset diabetes of the young. N. Engl. J.Med. 2001;345(13):971-980. DOI 10.1056/NEJMra002168.Igudin E.L., Spirin P.V., Prassolov V.S., Rubtsov P.M., Zubkova N.A.,Tyul\u2019pakov A.N., Petryaikina E.E. Functional characterization of two novel splicing mutations of glucokinase gene associated withmaturity-onset diabetes of the young type 2 (MODY2). Mol. Biol.2014;48(2):248-253. DOI 10.1134/S0026893314020071.Inoue M., Sakuraba Y., Motegi H., Kubota N., Toki H., Matsui J., ToyodaY., Miwa I., Terauchi Y., Kadowaki T., Shigeyama Y., Kasuga M.,Adachi T., Fujimoto N., Matsumoto R., Tsuchihashi K., Kagami T.,Inoue A., Kaneda H., Ishijima J., Masuya H., Suzuki T., Wakana S.,Gondo Y., Minowa O., Shiroishi T., Noda T. A series of maturityonset diabetes of the young, type 2 (MODY2) mouse models generatedby a large-scale ENU mutagenesis program. Hum. Mol. Genet.2004;13(11):1147-1157. DOI 10.1093/hmg/ddh133.Iynedjian P.B. Molecular physiology of mammalian glucokinase. Cell.Mol. Life Sci. 2009;66(1):27-42. DOI 10.1007/s00018-008-8322-9.Jang M.A., Kim Y.E., Kim S.K., Lee M.K., Kim J.W., Ki C.S. Identificationand characterization of NF1 splicing mutations in Koreanpatients with neurofibromatosis type 1. J. Hum. Genet. 2016;61:705-709. DOI 10.1038/jhg.2016.33.Karczewski K.J., Francioli L.C., Tiao G., Cummings B.B., Alf\u00f6ldi J.,Wang Q., Collins R.L., Laricchia K.M., Ganna A., Birnbaum D.P.,Gauthier L.D., Brand H., Solomonson M., Watts N.A., Rhodes D.,Singer-Berk M., England E.M., Seaby E.G., Kosmicki J.A., WaltersR.K., Tashman K., Farjoun Y., Banks E., Poterba T., Wang A.,Seed C., Whiffin N., Chong J.X., Samocha K.E., Pierce-Hoffman E.,Zappala Z., O\u2019Donnell-Luria A.H., Minikel E.V., Weisburd B.,Lek M., Ware J.S., Vittal C., Armean I.M., Bergelson L., CibulskisK., Connolly K.M., Covarrubias M., Donnelly S., Ferriera S.,Gabriel S., Gentry J., Gupta N., Jeandet T., Kaplan D., LlanwarneC., Munshi R., Novod S., Petrillo N., Roazen D., Ruano-RubioV., Saltzman A., Schleicher M., Soto J., Tibbetts K., Tolonen C.,Wade G., Talkowski M.E.; The Genome Aggregation DatabaseConsortium, Neale B.M., Daly M.J., MacArthur D.G. Variationacross 141,456 human exomes and genomes reveals the spectrumof loss-of-function intolerance across human protein-coding genes.bioRxiv.2019;531210. https://doi.org/10.1101/531210.Lachance C.H. Practical aspects of monogenic diabetes: A clinicalpoint of view. Can. J. Diabetes. 2016;40(5):368-375. DOI 10.1016/j.jcjd.2015.11.004.Landrum M.J., Lee J.M., Benson M., Brown G.R., Chao C., ChitipirallaS., Gu B., Hart J., Hoffman D., Jang W., Karapetyan K., Katz K.,Liu C., Maddipatla Z., Malheiro A., McDaniel K., Ovetsky M., RileyG., Zhou G., Holmes J.B., Kattman B.L., Maglott D.R. ClinVar:improving access to variant interpretations and supporting evidence.Nucleic Acids Res. 2018;46(D1):D1062-D1067. DOI 10.1093/nar/gkx1153.Li H., Durbin R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics. 2009;25(14):1754-1760. DOI10.1093/bioinformatics/btp324.Lorini R., Klersy C., d\u2019Annunzio G., Massa O., Minuto N., Iafusco D.,Bellann\u00e8-Chantelot C., Frongia A.P., Toni S., Meschi F., Cerutti F.,Barbetti F.; Italian Society of Pediatric Endocrinology and Diabetology(ISPED) Study Group. Maturity-onset diabetes of the youngin children with incidental hyperglycemia : amulticenter Italianstudy of 172 families. Diabetes Care. 2009;32(10):1864-1866. DOI10.2337/dc08-2018.Ma S.L., Vega-Warner V., Gillies C., Sampson M.G., Kher V., Sethi S.K.,Otto E.A. Whole exome sequencing reveals novel PHEX splice sitemutations in patients with Hypophosphatemic rickets. PLoS One.2015;10(6):e0130729. DOI 10.1371/journal.pone.0130729.Matschinsky F., Liang Y., Kesavan P., Wang L., Froguel P., Velho G.,Cohen D., Permutt M.A., Tanizawa Y., Jetton T.L. Glucokinase aspancreatic cell glucose sensor and diabetes gene. J. Clin. Invest.1993;92(5):2092-2098. DOI 10.1172/JCI116809.McDonald T.J., Ellard S. Maturity onset diabetes of the young: Identificationand diagnosis. Ann. Clin. Biochem. 2013;50:403-415. DOI10.1177/0004563213483458.McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., KernytskyA., Garimella K., Altshuler D., Gabriel S., Daly M., DePristoM.A. The Genome Analysis Toolkit: A MapReduce frameworkfor analyzing next-generation DNA sequencing data. Genome Res.2010;20(9):1297-1303. DOI 10.1101/gr.107524.110.Osbak K.K., Colclough K., Saint-Martin C., Beer N.L., Bellann\u00e9-ChantelotC., Ellard S., Gloyn A.L. Update on mutations in glucokinase(GCK), which cause maturity-onset diabetes of the young, permanentneonatal diabetes, and hyperinsulinemic hypoglycemia. Hum.Mutat. 2009;30:1512-1526. DOI 10.1002/humu.21110.Ovsyannikova A.K., Rymar O.D., Shakhtshneider E.V., KlimontovV.V., Koroleva E.A., Myakina N.E., Voevoda M.I. ABCC8-relatedmaturity-onset diabetes of the young (MODY12): clinical featuresand treatment perspective. Diabetes Ther. 2016;7(3):591-600.DOI 10.1007/s13300-016-0192-9.Plengvidhya N., Boonyasrisawat W., Chongjaroen N., Jungtrakoon P.,Sriussadaporn S., Vannaseang S., Banchuin N., Yenchitsomanus P.T.Mutations of maturity-onset diabetes of the young (MODY) genesin Thais with early-onset type 2 diabetes mellitus. Clin. Endocrinol.(Oxf.). 2009;70(6):847-853. DOI 10.1111/j.1365-2265.2008.03397.x.Pruhova S., Dusatkova P., Kraml P.J., Kulich M., Prochazkova Z.,Broz J., Zikmund J., Cinek O., Andel M., Pedersen O., Hansen T.,Leb J. Chronic mild hyperglycemia in GCK-MODY patients doesnot increase carotid intima-media thickness. Int. J. Endocrinol.2013;2013:718254. DOI 10.1155/2013/718254.Sambrook J., Russell D.W. Purification of nucleic acids by extractionwith phenol:chloroform. Cold Spring Harbor Protoc. 2006;2006(1):4455. DOI 10.1101/pdb.prot4455.Shakhtshneider E.V., Ivanoshchuk D.\u0415., Makarenkova \u041a.V., Orlov P.S.,Timoshchenko \u041e.V., Bazhan S.S., Nikitin Yu.P., Voevoda \u041c.I. Cascadegenetic screening in diagnostics of heterozygous familial hypercholesterolemia:clinical case. Russ. J. Cardiol. 2017;6(1460):178-179. http://dx.doi.org/10.15829/1560-4071-2017-6-178-179.(in Russian)Shields B.M., Hicks S., Shepherd M.H., Colclough K., Hattersley A.T.,Ellard S. Maturity-onset diabetes of the young (MODY): how manycases are we missing? Diabetologia. 2010;53(12):2504-2508. DOI10.1007/s00125-010-1799-4.Slaugenhaupt S.A., Blumenfeld A., Gill S.P., Leyne M., Mull J., CuajungcoM.P., Liebert C.B., Chadwick B., Idelson M., Reznik L.,Robbins C., Makalowska I., Brownstein M., Krappmann D.,Scheidereit C., Maayan C., Axelrod F.B., Gusella J.F. Tissue-specificexpression of a splicing mutation in the IKBKAP gene causes familialdysautonomia. Am. J. Hum. Genet. 2001;68(3):598-605. DOI10.1086/318810.Spyer G., Macleod K.M., Shepherd M., Ellard S., Hattersley A.T. Pregnancyoutcome in patients with raised blood glucose due to a heterozygousglucokinase gene mutation. Diabet. Med. 2009;26(1):14-18.DOI 10.1111/j.1464-5491.2008.02622.x.Steele A.M., Shields B.M., Wensley K.J., Colclough K., Ellard S., HattersleyA.T. Prevalence of vascular complications among patientswith glucokinase mutations and prolonged, mild hyperglycemia.JAMA. 2014;311(3):279-286. DOI 10.1001/jama.2013.283980.Stenson P.D., Mort M., Ball E.V., Evans K., Hayden M., Heywood S.,Hussain M., Phillips A.D., Cooper D.N. The Human Gene MutationDatabase: towards a comprehensive repository of inherited mutationdata for medical research, genetic diagnosis and next-generation sequencingstudies. Hum. Genet. 2017;136(6):665-677. DOI 10.1007/s00439-017-1779-6.Stride A., Vaxillaire M., Tuomi T., Barbetti F., Nj\u00f8lstad P.R., Hansen T.,Costa A., Conget I., Pedersen O., S\u00f8vik O., Lorini R., Groop L.,Froguel P., Hattersley A.T. The genetic abnormality in the beta celldetermines the response to an oral glucose load. Diabetologia. 2002;45(3):427-435. DOI 10.1007/s00125-001-0770-9.Thanabalasingham G., Owen K.R. Diagnosis and management of maturityonset diabetes of the young (MODY). BMJ. 2011;343:d6044.DOI 10.1136/bmj.d6044.The 1000 Genomes Project Consortium, Auton A., Brooks L.D.,Durbin R.M., Garrison E.P., Kang H.M., Korbel J.O., Marchini J.L.,McCarthy S., McVean G.A., Abecasis G.R.A global reference for human genetic variation. Nature. 2015;526(7571):68-74. DOI10.1038/nature15393.Toaima D., N\u00e4ke A., Wendenburg J., Praedicow K., Rohayem J., EngelK., Galler A., Gahr M., Lee-Kirsch M.A. Identification of novelGCK and HNF1A/TCF1 mutations and polymorphisms in Germanfamilies with maturity-onset diabetes of the young (MODY). Hum.Mutat. 2005;25(5):503-504. DOI 10.1002/humu.9334.Wang K., Li M., Hakonarson H. ANNOVAR: functional annotationof genetic variants from high-throughput sequencing data. NucleicAcidsRes. 2010;38(16):e164. DOI 10.1093/nar/gkq603.W\u0119drychowicz A., Tob\u00f3r E., Wilk M., Zi\u00f3\u0142kowska-Ledwith E.,Rams A., Wzorek K., Sabal B., Stelmach M., Starzyk J.B. PhenotypeHeterogeneity in glucokinase-maturity-onset diabetes of the young(GCK-MODY) patients. J. Clin. Res. Pediatr. Endocrinol. 2017;9(3):246-252. DOI 10.4274/jcrpe.4461.Xiong H.Y., Alipanahi B., Lee L.J., Bretschneider H., Merico D.,Yuen R.K., Hua Y., Gueroussov S., Najafabadi H.S., Hughes T.R.,Morris Q., Barash Y., Krainer A.R., Jojic N., Scherer S.W., BlencoweB.J., Frey B.J. The human splicing code reveals new insightsinto the genetic determinants of disease. Science. 2015;347(6218):1254806. DOI 10.1126/science.1254806."} +{"text": "Micronutrients are minerals and vitamins and they are essential for normal physiological activities. The objectives of the study were to describe the progress and determinants of micronutrient levels and to assess the effects of micronutrients in the treatment outcome of kalazar.A prospective cohort study design was used. The data were collected using patient interviews, measuring anthropometric indicators, and collecting laboratory samples. The blood samples were collected at five different periods during the leishmaniasis treatments: before starting anti-leishmaniasis treatments, in the first week, in the second week, in the third week, and in the 4th week of anti-leishmaniasis treatments. Descriptive statistics were used to describe the profile of patients and to compare the treatment success rate. The generalized estimating equation was used to identify the determinants of serum micronutrients.Hookworm (\u2212\u20094.48 [\u2212\u20096.82 - -2.14]), chronic diseases (B -7.44 [95% CI: \u2212\u20099.75 - -5.13]), and HIV (B -5.51 [95% CI: \u2212\u20098.23 - -2.78]). The serum selenium level of visceral leishmaniasis patient was affected by HIV (B -18.1 [95% CI: \u2212\u200920.63 - -15.58]) and family size (B -11.36 [95% CI: \u2212\u200913.02 - -9.7]). The iodine level of visceral leishmaniasis patient was affected by HIV (B -38.02 [95% CI: \u2212\u200941.98 - -34.06]), DDS (B 25 .84 [95% CI: 22.57\u201329.1]), smoking (B -12.34 [95% CI: \u2212\u200915.98 - -8.7]), chronic illness (B -5.14 [95% CI: \u2212\u20097.82 - -2.46]), and regular physical exercise (B 5.82 [95% CI: 0.39\u201311.26]). The serum vitamin D level of visceral leishmaniasis patient was affected by HIV (B -9.43 [95% CI: \u2212\u200910.92 - -7.94]), DDS (B 16.24 [95% CI: 14.89\u201317.58]), malaria (B -0.61 [95% CI: \u2212\u20093.37 - -3.37]), and family size (B -1.15 [95% CI: \u2212\u20092.03 - -0.28]). The serum vitamin A level of visceral leishmaniasis patient was affected by residence (B 0.81 [95% CI: 0.08\u20131.54]), BMI (B 1.52 [95% CI: 0.42\u20132.6]), DDS (B 1.62 [95% CI: 0.36\u20132.88]), family size (B -5.03 [95% CI: \u2212\u20095.83 - -4.22]), HIV (B -2.89 [95% CI: \u2212\u20094.44 - -1.34]),MUAC (B 0.86 [95% CI: 0.52\u20131.21]), and age (B 0.09 [95% CI: 0.07\u20130.12]).The mean age of the patients were 32.88\u2009years [SD (standard deviation) \u00b115.95]. Male constitute 62.3% of the patients and problematic alcohol use was present in 11.5% of the patients. The serum zinc level of visceral leishmaniasis patients was affected by alcohol (B\u2009\u2212\u20092.7 [95% CI: \u2212\u20094.01 - -1.5]), DDS (B 9.75 [95% CI: 7.71\u201311.79]), family size (B -1.63 [95% CI: \u2212\u20092.68 - -0.58]), HIV (B -2.95 [95% CI: \u2212\u20094.97 - -0.92]), and sex (B\u2009\u2212\u20091.28 [95% CI: \u2212\u20092.5 - -0.07]). The serum iron level of visceral leishmaniasis patients was affected by alcohol (B 7.6 [95% CI: 5.86\u20139.35]), family size (B -5.14 [95% CI: \u2212\u20097.01 - -3.28]), malaria (B -12.69 [95% CI: \u2212\u200914.53 - -10.87]), The micronutrient levels of visceral leishmaniasis patients were significantly lower. The anti-leishmaniasis treatment did not increase the serum micronutrient level of the patients. The three forms of leishmaniasis are cutaneous leishmaniasis, mucocutaneous leishmaniasis, and visceral leishmaniasis . Male constitute 62.3% of study participants and problematic alcohol use was observed in 11.5% of the patients (Table\u00a0mcg/dl). Female kalazar patients had 1.28 mcg/dl less zinc level than males. High dietary diversification increases the serum zinc level by 9.75 mcg/dl. High family size decreases the serum zinc level by 1.63 mcg/dl. The serum zinc level of HIV positive visceral leishmaniasis patients was 2.95 mcg/dl less than HIV negative visceral leishmaniasis patients. The anti-leishmaniasis treatment did not increase the serum zinc level of the patients.Problematic alcohol use decreases the serum zinc level by 2.7 micrograms per deciliter (mcg/dl. Chronic illness decreases the serum iron level of the patients by 7.44 mcg/dl. Malaria co-infection decreases the serum iron level of the patients by 12.69 mcg/dl. Hookworm infection decreases the serum iron level of visceral leishmaniasis patients by 4.48 mcg/dl. High family size decreases the serum iron level of the patients by 5.14 mcg/dl. HIV infection decreases the serum iron level of the patients by 5.54 mcg/dl. The serum iron level of patient increase by 0.11mcq/dl per a year increase in the patient age. The serum iron level of the patient increase by 0.75 mcq/dl per a centimeter increase in the MUAC of the patient. The anti-leishmaniasis treatment increases the serum iron level of the patient by 0.67 mcg/dl.Problematic alcohol use increases the serum iron level of the patients by 7.6 ng/ml less serum selenium level than HIV negative visceral leishmaniasis patients. High family size decreases the serum selenium level of the patients by 11.36\u2009ng/ml. The anti-leishmaniasis treatment increases the serum selenium level by 3.04\u2009ng/ml.HIV positive visceral leishmaniasis patient had 18.1\u2009mcg/l. High DDS increases the iodine level of the patients by 25.84 mcg/l. Smoking decreases the iodine level of the patients by 12.34 mcg/l. HIV decreases the iodine level of visceral leishmaniasis patients by 38.02 mcg/l. Chronic illness decreases the iodine level of visceral leishmaniasis patients by 5.14 mcg/l. The anti-leishmaniasis treatment increases the iodine level of patients by 13.67 mcg/l.Malaria decreases the iodine level of visceral leishmaniasis patients by 3.78 mcg/dl. Chronic illness decreases the serum vitamin A level of the patients by 2.56 mcg/dl. Urban residence increases the serum vitamin A level of the patient by 0.81 mcq/dl. High DDS increases the serum vitamin A level of the patient by 1.62 mcg/dl. Malaria co-infection decreases the serum vitamin A level of the patient by 4.8 mcg/dl. High family size decreases the serum vitamin A level of visceral leishmaniasis patients by 5.03 mcg/dl. HIV infection decreases the serum vitamin A level of the patients by 2.89 mcg/dl. A centimeter increase in the MUAC of visceral leishmaniasis patients increases the serum vitamin A level by 0.86 mcg/dl. The anti-leishmaniasis treatment did not increase the serum vitamin A level of the patient.Problematic alcohol use decreases the serum vitamin A level of visceral leishmaniasis patients by 1.09 ng/ml. High DDS increases the serum vitamin D level of the patients by 16.24\u2009ng/ml. Malaria decreases the serum vitamin D level of the patients by 0.61\u2009ng/ml. In the presence of hookworm infection, the serum vitamin D level of visceral leishmaniasis patients decreased by 3.94\u2009ng/ml. High family size decreases the serum vitamin D level of the patients by 1.15\u2009ng/ml. HIV co-infection decreases the serum vitamin D level of the patient by 9.43\u2009ng/ml. The anti-leishmaniasis treatment did not increase the serum vitamin D level of visceral leishmaniasis patients (Table A unit increase in the BMI of visceral leishmaniasis patients increases the serum vitamin D level by 1.52\u2009The micronutrient level directly affects treatment outcome of visceral leishmaniasis; especially the treatment outcome was not successful if the serum zinc, iron, vitamin A and vitamin D levels were lower than the first quartile. The overall treatment success rate of visceral leishmaniasis treatment was 84.7% [95% CI: 82.77 - 86.67%] Tables\u00a0, 4.Tablmcg/dl, and the serum vitamin A level by 1.09 mcg/dl. This finding was in line with previous research outputs . A systematic review and meta-analysis estimate also supports this finding .Low serum zinc level decreases the treatment outcome of visceral leishmaniasis. This finding was in line with finding from India . This isHigher patient iron level increases the treatment success rate of visceral leishmaniasis. This finding supports the results of previously published work . This isHigher serum vitamin A and Vitamin D level favors good treatment outcome in visceral leishmaniasis. This finding agrees with previous researchers outputs \u201379. ThisPossible limitation of this study was a failure to address all the vitamins and minerals status of visceral leishmaniasis patients, but since practically it is very difficult to address all of them this study gives the baseline evidence on main vitamins and mineral levels.The serum micronutrient levels of visceral leishmaniasis patients were low. Problematic alcohol use affects the serum zinc, iron, vitamin A levels. DDS affects the serum zinc, iodine, vitamin A, and vitamin D level. Family size affects the serum zinc, iron, selenium, vitamin A, and vitamin D levels. HIV infection affects the serum zinc, iron, selenium, iodine, vitamin A, and vitamin D levels. Anti-leishmaniasis drug slightly increases the serum iodine and selenium levels, but it doesn\u2019t increase the serum iron, zinc, vitamin A, and vitamin D levels. The serum levels of zinc, iron, vitamin A, and vitamin D significantly affect the treatment outcomes of visceral leishmaniasis.The visceral leishmaniasis treatment guideline should incorporate supplementing the micronutrients as part of anti-leishmaniasis intervention."} +{"text": "Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) were the most common (52.7% and 44.2%). K. pneumoniae was most susceptible to colistin, amikacin, ertapenem, and imipenem . E. coli was most susceptible to colistin (100%), amikacin (94.1%), imipenem (90.4%), and ertapenem (83.6%). ESBL was detected in 96.2% and ESBL genotypes included blaCTX-M-15 (70.1%), blaTEM-OSBL (48.5%), blaSHV-OSBL (27.9%), and blaCTX-M-14 (10.7%). AmpC resistance genes were identified in 9.7% of the isolates, dominated by blaCMY-2 (5.7%). Carbapenem resistance genes were detected in 45.3% of the isolates. In K. pneumoniae, blaOXA-48 dominated (40.6%), followed by blaNDM-1 (23.7%) and blaOXA-232 (4.5%). In E. coli, the most frequent genes were blaNDM-5 (9.6%), blaOXA-181 (5.5%), blaOXA-244 (3.7%), and blaNDM-1 (3.7%). blaKPC-2 was identified in 0.4% of isolates. Notably, 32.3% of isolates carried more than one resistance gene. Our findings emphasize the continued need for molecular surveillance of MDR pathogens, implementation of strict infection control measures, and antimicrobial stewardship policies in our hospitals.High rates of antimicrobial resistance (AMR) among Gram-negative pathogens (GNP) have been reported in Egypt. Antimicrobial surveillance and identifying the genetic basis of AMR provide important information to optimize patient care. In this study, we aimed to identify the beta-lactam resistance phenotypes and genotypes of multidrug-resistant (MDR) non-repetitive GNP from 3 tertiary hospitals in Egypt. WZe studied 495 non-repetitive MDR Gram-negative isolates from patients with complicated intra-abdominal infections (cIAI), complicated urinary tract infection (cUTI), and lower respiratory tract infection (LRTI), collected as part of the \u201cStudy for Monitoring Antimicrobial Resistance Trends\u201d (SMART) conducted in 3 tertiary hospitals in Cairo, Egypt, from 2015 to 2016. Identification and susceptibility testing of GNP to antimicrobials were tested in each hospital laboratory and confirmed in a reference laboratory , Inc., Schaumburg, IL, USA). Molecular identification of extended-spectrum beta-lactamases (ES\u0392Ls), AmpC, and carbapenem resistance genes was conducted in IHMA. Among the 495 MDR isolates, A high rate of AMR has been reported in Egypt since more than 20\u00a0years, among GNP causing nosocomial infections and outbreaks \u20133. AMR rin Egypt \u20138. As thEnterobacteriaceae, because no CLSI breakpoints exist [This study was conducted in 3 major tertiary care Egyptian hospitals participating in the \u201cStudy for Monitoring Antimicrobial Resistance Trends\u201d (SMART) from 2015 to 2016. The hospitals were Ain Shams University Hospital, Ain Shams Specialized University Hospital, and Dar Al-Fouad Hospital. Isolates were collected according to SMART protocol as previously reported \u201311. Briets exist .The suscblaTEM, blaSHV, blaCTX-M, blaVEB, blaPER, and blaGES; blaAmpC \u03b2-lactamase genes (class C)\u2014blaACC, blaACT, blaCMY, blaDHA, blaFOX, blaMIR, and blaMOX; and carbapenemases (class A)\u2014blaKPC and blaGES; (class B)\u2014blaNDM, blaIMP, blaVIM, blaGIM, and blaSPM; and (class D)\u2014blaOXA-48-like. Then the genes encoding ES\u0392L, carbapenemases, and AmpC were sequenced in their entirety in IHMA [The molecular characterization of ESBL and carbapenemases was done using the Check-Points MDR CT103 microarray kit, which detects most carbapenemase, ESBL, and AmpC genes: ES\u0392Ls (class A)\u2014 in IHMA .Klebsiella pneumoniae and Escherichia coli were the most common (52.7% and 44.2%) and were also the predominant organisms in cIAI , cUTI , and LRTI . E. coli remained most susceptible to colistin (100%), amikacin (94.1%), imipenem (90.4%), and ertapenem (83.6%).The 495 MDR isolates were derived from cIAI 181, 36%), LRTI , and cUTI . Overall 81, 36%, blaCTX-M-15 (70.1%), blaTEM-OSBL (48.5%), blaSHV-OSBL (27.9%), and blaCTX-M-14 (10.7%). The predominant ESBL gene in both E. coli and K. pneumoniae was blaCTX-M-15 , followed by blaNDM-1 (23.7%) and blaOXA-232 (4.5%). In E. coli, the most frequent genes were blaNDM-5 (9.6%), blaOXA-181 (5.5%), blaOXA-244 (3.7%), and blaNDM-1 (3.7%). blaKPC-2 and blaVIM-2 were less frequently identified (Table Carbapenem resistance genes were detected in 45.3% of the MDR isolates. In blaCMY-2 was the most predominant one (Table blaCTX-M-15 with blaNDM-5 (2.6%); the commonest combination of 3 genes was blaSHV-OSBL, blaCTX-M-15, and blaNDM-1 (9.2%); the commonest combination of 4 genes was blaSHV-OSBL, blaTEM-OSBL, blaCTX-M-15, and blaNDM-1 (12.4%); and the commonest combination of more than 4 genes was blaSHV-OSBL, blaTEM-OSBL, blaCTX-M-15, blaCTX-M-14, blaNDM-1, and blaOXA-48 (5.9%) . We identified 43 resistance phenotypes distributed among isolates from the 3 hospitals. Typing of nosocomial GNP in each hospital based on the phenotypic resistance patterns showed no clonal spread except for few isolates in each hospital (data not shown).K. pneumoniae was a common pathogen in all 3 types of infection, and most isolates were MDR. Due to its large accessory genome including plasmids and chromosomal loci, K. pneumoniae isolates may act as opportunistic pathogens. Such strains infect critically ill and immunocompromised patients mostly, whereas other strains of K. pneumoniae (hyper-virulent) may even infect healthy people in community settings. Many of the virulent strains encode carbapenemases [E. coli was a frequently identified pathogen from cIAI and cUTI, which is consistent with previous reports, and was also a frequent pathogen in LRTI. E. coli pneumonia is uncommon and may result from micro-aspiration of colonized upper airway secretions in severely ill patients; hence, it is a well-known cause of nosocomial pneumonia [E. coli pneumonia may also be community-acquired in patients who have underlying diseases such as diabetes mellitus, alcoholism, chronic obstructive pulmonary disease, and E. coli UTI [E. coli isolates compared with 42.5% and 48.1% in K. pneumoniae isolates, respectively.enemases . E. colineumonia . Howevercoli UTI . Our rescoli UTI that shocoli UTI , ESBL anblaCTX-M-15 and blaCTX-M-14 are the most commonly identified worldwide as the genes encoding CTX-M enzymes (blaCTX-M) can be horizontally mobilized by various genetic elements [blaCMY-42, blaDHA, and blaACT-like. This is in keeping with recent reports on acquisition of plasmid-mediated cephalosporinase producing Enterobacteriaceae after a travel to the tropics and North Africa including Egypt [E. coli isolates in Egypt [Among the many types of ES\u0392Ls reported, elements . This reng Egypt , 21. Theng Egypt . Moreovein Egypt . This isin Egypt , 25.blaOXA followed by blaNDM genes dominated, while only 2 isolates of K. pneumoniae harbored blaKPC-2 genes. These results confirm previous small-scale reports that the blaNDM and blaOXA genes are the predominant in Egypt and Middle East [The most important mechanism of carbapenem resistance is the production of carbapenemases; therefore, all isolates were investigated to identify the carbapenemase genes. We identified them in 45.4% of tested isolates; dle East .The present study detected massive coexistence of different resistance genes among tested isolates. This coexistence could have contributed to the observed elevated variability in resistance phenotypes and genotypes among GNP in Egypt .In conclusion, our study detected alarming rates of resistance and identified many resistance mechanisms in clinical GNP from Egyptian tertiary care hospitals. These high resistance rates highlight the importance of continuous monitoring of the resistance trends, adherence to infection control policies, and underscore urgently implementing a national antimicrobial stewardship plan in Egypt."} +{"text": "Cryptophyceae sp. CCMP2293. The circular genome is 139,208\u2009bp in length and contains 142 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, 6 ribosome RNA (rRNA) genes, and 1 transfer-messenger RNA (tmRNA) gene. The overall nucleotide composition is: 33.6% A, 32.5% T, 16.8% C, and 17.1% G with a total A\u2009+\u2009T content of 66.1%. The phylogenetic tree was constructed to explore the taxonomic status of Cryptophyceae sp. CCMP2293, which is closely related to G. theta and R. salina.In this study, we present the complete plastid genome of Cryptophyte algae are an evolutionarily significant group which inhabits marine, brackish, and freshwater environments . The single specimen was provided by the Culture Collection of Marine at the Ocean University of China in Qingdao (OUC-2013060210). Illumina paired-end DNA library was prepared and sequenced using HiSeq 2500 Sequencing System (Gene Denovo Laboratory). The pre-processed sequences were assembled using NOVOPlasty and aligned via BLASTX and BLASTN searches at NCBI (http://blast.ncbi.nlm.nih.gov/). The tRNAs were identified using the tRNAscan-SE 1.21 web server (http://lowelab.ucsc.edu/tRNAscan-SE/), and the rRNAs were identified using the RNAmmer 1.2 server (http://www.cbs.dtu.dk/services/RNAmmer/). The complete plastid genome of Cryptophyceae sp. CCMP2293 is 139,208\u2009bp in length and contains 142 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, 6 ribosome RNA (rRNA) genes and 1 transfer-messenger RNA (tmRNA). There are 4 function-unknown open reading frames. The overall nucleotide composition is: 33.6% A, 32.5% T, 16.8% C, and 17.1% G, with a total A\u2009+\u2009T content of 66.1%.Here, we reported and characterized the complete Cryptophyceae sp. CCMP2293, the phylogenetic tree was constructed with 6 published complete plastid genomes obtained from the Genbank, where Costaria costata served as outgroup. 56 concatenated protein-coding amino acid sequences were aligned using the program MAFFT (Katoh et\u00a0al. Cryptophyceae sp. CCMP2293 clustered with G. theta and R. salina (To elucidate the phylogenetic position of . salina . The det"} +{"text": "Desulfuromonas sp. strain AOP6, with iron(III)-reducing activity, was isolated from subseafloor sediment in Nankai Trough. We report the complete genome of this strain determined by Illumina MiSeq sequencing and PCR/Sanger sequencing-based gap closing. The genome includes the genes encoding c-type cytochromes, type IV pili, and fatty acid degradation enzymes. Desulfuromonas sp. strain AOP6, with iron(III)-reducing activity, was isolated from subseafloor sediment in Nankai Trough. We report the complete genome of this strain determined by Illumina MiSeq sequencing and PCR/Sanger sequencing-based gap closing. The genome includes the genes encoding c-type cytochromes, type IV pili, and fatty acid degradation enzymes. Geobacter spp., can reduce not only soluble ferric iron but also poorly crystalline Fe(III) oxides (Desulfuromonas sp. strain AOP6 (formerly described as Pelobacter sp. AOP6) was isolated from subseafloor sediment in Nankai Trough using acetate and goethite (\u03b1-FeOOH) as the electron donor and acceptor, respectively reduction is an important anaerobic respiration process \u20134. Some \u2013) oxides , 5. Howelmitatis , followeylenicus and Geoaerraneus . Here, whttps://github.com/najoshi/sickle/releases/tag/v1.33) with default settings, a two-step combination of the genome assembly was performed. Briefly, the obtained sequence was preassembled using Unicycler v0.4.8 -NTA] as the electron donor and acceptor, respectively . These tr v0.4.8 with defr v0.4.8 with ther v0.4.8 . This rerrn operons, 2 CRISPR features, 50 tRNA loci, and 3,000 protein-coding sequences (CDSs) were predicted using the DDBJ Fast Annotation and Submission Tool (DFAST) v1.2.2 oxides . Two ) v1.2.2 with def) v1.2.2 . Functio) oxides , 16. Mor) oxides . AdditioDesulfuromonas sp. strain AOP6 has been deposited in DDBJ/ENA/GenBank under accession number AP022810. The raw sequence reads for the paired-end and mate pair libraries are available at accession numbers DRR194005 and DRR194004, respectively.The complete genome sequence of"} +{"text": "AbstractFothergilla is a small genus of deciduous shrubs native to the southeastern United States that depending on circumscription comprises two to four species. Recent treatments recognized only two species in the genus: F.gardenii (tetraploid) and F.major (hexaploid). Until recently, no diploid taxon of Fothergilla was known. However, recent investigations identified a number of diploid populations in Alabama, Florida, Georgia, and South Carolina. A subsequent phylogenomic analysis showed that the diploids segregated into two, well-supported lineages, corresponding to largely allopatric populations. A re-examination of the morphology of diploid plants, in combination with the genetic evidence, has led us to the recognition of two species of diploids in the genus \u2013 a resurrected F.parvifolia and a new species \u2013 bringing the total number of recognized species in Fothergilla to four. A revised taxonomic treatment of the genus is provided. Fothergilla L. is a small genus of deciduous shrubs native to the southeastern United States that depending on circumscription comprises two to four species . F.major based on \u201chaving a spike of flowers, three inches or more in length; [...] later flowering, and [...] leaves [...] very broad, and much more toothed\u201d , leaf base (cordate in F.parvifolia vs. cuneate to rounded in F.gardenii), and leaf margin (toothed from below the middle to the apex in F.parvifolia vs. toothed only near the apex in F.gardenii). This circumscription was followed by F.parvifolia as a synonym of F.gardenii (F.gardenii (incl. F.parvifolia) and F.major (incl. F.monticola) (Kearney in segregatgardenii . In factnticola) .Fothergillagardenii is found in wet savannas and pocosins in the coastal plains of North Carolina, South Carolina, Georgia, Florida, and Alabama, whereas F.major occurs primarily in woodlands, bluffs, and riverbanks of the upper Piedmont and mountains of North Carolina, South Carolina, Georgia, Alabama, Tennessee, and Arkansas , smaller leaves (<5.2 cm wide vs. > 5.2 cm wide in F.major), leaf dentations , base symmetry (symmetric vs. asymmetric in F.major), hypanthium length (3\u20134.5 mm vs. 4\u20139.2 mm in F.major), number of stamens per flower (12\u201324 vs. 22\u201332 in F.major), and seed size (4.8\u20136.3 mm long vs. 6.2\u20137.8 mm long in F.major) . Weaver F.major and F.gardenii sensu n = 5x = 60) and named the nothospecies F.\u00d7intermedia Ranney & Fantz, a finding that cleared up previous controversy as to whether common cultivars (such as \u2018Mount Airy\u2019) represented F.major or F.gardenii. No pentaploids have been identified in nature.Although Fothergilla was known. However, recent sampling and cytometric analysis identified a number of diploid populations in Alabama, Florida, Georgia, and South Carolina (F.gardenii and F.major and their relationship to the diploid populations (F.gardenii and F.major). Furthermore, the diploid OTUs segregated into two, well-supported lineages, corresponding to largely allopatric populations. A re-examination of the morphology of diploid plants, in combination with the genetic evidence, has led us here to the recognition of two species of diploids in the genus: a resurrected F.parvifolia and a new species (F.milleri) as described below. A revised taxonomic treatment of the genus is provided.Until recently, no diploid taxon of Carolina . This woulations . These aFothergilla from throughout the southeastern United States, planted and grown in a common garden at the Mountain Horticultural Crops Research and Extension Center in Mills River, North Carolina (Table PSC) sensu IW), and (2) the length of the midvein interval between the junction of the midvein and lowermost secondary vein and the junction of the midvein and the next-most distal secondary vein on the same side of the leaf . We also searched the SERNEC portal to identify any additional specimens of the diploid taxa we recognized. This search resulted in six additional specimens, which we added to the list of exsiccatae in the taxonomic treatment below . The combined sets of specimens of known ploidy (Table Specimens studied in the course of preparing this revision included: 1) 34 accessions of 34 accesPopulation Aggregation Analysis revealed four distinct aggregate profiles, each corresponding to one of the major lineages identified by F.parvifolia Kearney , the shape is actually a combination of a short cuneate section adjoining the petiole that broadens out laterally into the more general cordate or rounded shape. We here use the terms V-cordate and V-rounded to describe this type of base (the \u201cV\u201d representing the cuneate section) and consider it structurally distinct from the neatly cordate leaf bases of F.parvifolia , F.major (6x), F.milleri (2x), and F.parvifolia (2x). An updated taxonomic treatment follows.Based on these results, Taxon classificationPlantaeSaxifragalesHamamelidaceaeL., Syst. Veg. ed. 13. 418. 1774F9AB60B8-9179-5DF2-813D-AEFB92A8716DFothergillagardenii L., Syst. Veg. ed. 13. 418. 1774 [as F.Gardeni] \u00d7 0.9\u20132.7(\u20134.3) mm; petioles 3.9\u201310.5 mm long, usually \u00be the length of the IL or longer, brown-yellow pubescent; blades mostly spreading, green, narrowly ovate to ovate, (1.8\u2013)2.8\u20138.7 \u00d7 (1.0\u2013)2.5\u20135.3 cm, pinnately 8\u201311-veined, bases asymmetrical or symmetrical, usually rounded to cuneate, sometimes shallowly cordate, margins crenate to serrate above middle, teeth 3\u201310, apices acute to obtuse, both surfaces stellate-pubescent, rarely glabrous, abaxial surface sometimes glaucous, IW:IL < or = 0.49 (x\u0304 = 0.33). Inflorescences appearing before leaves, spikes terminal, appearing lateral on short lower branches, sessile or on short peduncles. Flowers: stamens 10\u201324, filaments 3.6\u201313.8 mm long. Capsules 6.6\u20139.0 \u00d7 5.5\u20136.6 mm. Seeds white to mottled brown or red-brown, ellipsoid to slightly ovoid, 5.1\u20135.8 \u00d7 2.5\u20133.5 mm, apices mostly obtuse. Genome size and ploidy 3.33\u20133.76 pg, tetraploid (2n = 4x = 48).Flowering beginning late Mar; fruiting by late Apr through Jul.Acerrubrum L., Amelanchierobovalis (Michx.) Ashe, Aroniaarbutifolia (L.) Pers., Clethraalnifolia L., Cyrillaracemiflora L., Gaylussaciadumosa (Andrews) Torr. & A. Gray, G.tomentosa (A. Gray) Pursh ex Small, Ilexcoriacea (Pursh) Chapm., I.glabra (L.) A. Gray, I.vomitoria Aiton, Kalmiacuneata Michx., K.latifolia L., Liquidambarstyraciflua L., Lyonia Nutt. spp., Magnoliavirginiana L., Perseapalustris (Raf.) Sarg., Pinusserotina Michx., Pteridiumaquilinum (L.) Kuhn, Quercuslaevis Walter, Q.virginiana Mill., Rhododendronviscosum (L.) Torr., Vacciniumcrassifolium Andrews, V.myrsinites Lam., and Zenobiapulverulenta (W. Bartram ex Willd.) Pollard (fide colectoris).This species can be found along the Atlantic coastal plains of North Carolina, South Carolina, and Georgia Fig. . It occuFothergillagardenii was apparently cultivated in England as early as 1765, grown at Kew Gardens by 1789, and English and French plant nurseries were offering seeds for sale by the early 1800s (mblebees . The autrphidae) .Fothergillagardenii s.l. is considered Vulnerable, currently ranked by NatureServe as follows: G3G4; Alabama (S1), Florida (S1), Georgia (S2), Mississippi (SNR), North Carolina (S3S4), South Carolina (SNR) . In light of the removal of the diploid taxa F.milleri and F.parvifolia from the broader historical concept of F.gardenii, the conservation status of this species, as well as that of the diploid taxa, warrants re-evaluation; such re-evaluation is likely to result in a more imperiled ranking than the G3G4 current assessment, following removal of a significant number of populations and a narrower distribution following its narrower taxonomic circumscription. Due to its sensitive status, we provide only skeletal collections data below..Lynch 43 (NCSC); 2012-078, 13 Jun 2014 (V), Phillips 49 (NCSCm); 12 Jul 1997 (V), Sorrie 9349 (NCUm). McDuffie: Jun 1911 (V), Bartlett 2636 .Georgia. Effingham: 2012-078, 15 Apr 2014 (FL), Coker s.n. (NCU); 14 May 1966 (FL), Blair 415 (NCSC); 21 Jun 1965 (FR), Sawyer 2475 (NCUm); 5 Nov 1956 (V), Ahles & Leisner 21471 (NCUm); 20 Apr 1957 (FL), Ahles & Ramseur 23593 (NCUm); 31 May 2003 (FR), Horn 4437 (BRITm); 25 Jan 1937 (FL), Melvin 3613 (BRITm); 7 Jul 1994 (V), Nifong 400 (NCUm). Brunswick: 8 Jun 1951 (FR), Boyce & Wells 1656 (NCSC); 13 May 1950 (FL), Godfrey & Wiebe 50341 ; 18 Apr 1999 (FL), Hill 31327 (BRIT); 6 Mar 1974 (V), Kologiski 54 (NCSCm); 7 May 1974 (FL), Kologiski 125 (NCSC); 23 Jul 1974 (V), Kologiski 311 (NCSC); 6 Jun 1975 (FR), Kologiski 423 (NCSC); 27 Apr 1976 (FL), Kologiski 551 (NCSC); 18 Apr 1965 (FL), Mullen s.n. (NCSC). Carteret: 2011-096, 26 Mar 2012 (FL), Lynch 9 (NCSC); 2011-096, 2 Jul 2012 (V), Lynch 76 (NCSCm); 2011-096, 13 Jun 2014 (FR), Phillips 50 (NCSC); 2011-103, 21 Mar 2012 (FL), Lynch 3 (NCSC); 2011-103, 2 Jul 2012 (V), Lynch 75 (NCSCm); 22 May 1976 (V), Wilson 1792 (NCUm); 9 Apr 1977 (FL), Wilson 3067 (NCU). Columbus: 25 Apr 1958 (FL), Bell 11417 (NCU). Craven: 19 Apr 1958 (Fl), Radford 31924 (NCU). Cumberland: 11 Oct 1957 (V), Ahles 36621 (NCUm); 28 Apr 1933 (FL), Tallin & Harbison s.n. (NCU). Duplin: 27 Apr 1957 (V), Ahles & Ramseur 23990 (VDBm); 27 Apr 1957 (FR), Radford & Ramseur 23990 (NCUm). Harnett: 10 Apr 1957 (FL), Laing 843 (NCU); 30 Jun 2005 (FR), Sorrie 11634 (NCUm). Hoke: 2011-097, 21 Mar 2012 (FL), Lynch 4 (NCSC); 2011-097, 2 Jul 2012, (V), Lynch 72 (NCSCm); 2011-097, 13 Jun 2014 (FR), Phillips 71 (NCSC); 16 May 1976 (V), Kral 58099 (VDB m); 26 Jun 1975 (FR), Ahles & Haesloop 29627 (NCUm). Lee: 19 Apr 1958 (FL), Stewart 149 (NCU); 7 Jun 1958 (FR), Stewart 451 (NCUm). Montgomery: 9 Oct 1956 (V), Radford 19633 (NCUm). Moore: 17 Jul 1942 (FR), Wicker s.n. (NCUm); 8 Apr 1973 (FL), Carter 449 (NCU); 24 Apr 1949 (FL), Woods 2256 (NCSC). New Hanover: 6 Jun 1929 (FR), Wells s.n. (NCSCm); 29 Jun 1963 (V), McCrary 607 (NCU m); 30 Mar 1991 (FL), Pyne & Seneca 91-013 (NCSC). Onslow: 11 May 1948 (FR), Boyce & Moreland 647 (NCSC); 28 Apr 1951 (FL), Beaman s.n. (NCSC); 2 June 1948 (FR), Boyce & Moreland 700 (NCSCm); 24 Jun 1965 (FR), Wilbur 8398 (BRITm). Pamlico: 12 Oct 1957 (V), Radford 42285 (NCUm). Pender: 17 May 1925 (FR), A.C.W. s.n. (NCSC); 1 Jun 1945 (V), Wells s.n. (NCSC); 19 Apr 1957 (FL), Ahles & Ramseur 23440 (NCU); 25 Apr 1947 (FL), Fox & Wells 162 (NCSC); 12 May 1951 (FR), Fox 4621 (NCSC); 26 Aug 1983 (V), Leonard 8199 (UWFPm); 14 Apr 1925 (FL), Wells s.n. (NCSC). Richmond: 2011-123, 11 Apr 2012 (FL), Lynch 13 (NCSC); 2011-123, 21 Aug 2012 (V), Lynch 74 (NCSCm); 2011-085, 21 Mar 2012 (FL), Lynch 5 (NCSC); 2011-085, 2 Jul 2012 (V), Lynch 73 (NCSC); 2011-085, 13 Jun 2014 (V), Phillips 55 (NCSCm); 19 May 2007 (FL), Boyle 1 (NCU). Robeson: 18 Apr 1956 (FL), Terrell 3019 (NCU). Sampson: 10 Apr 1938 (FL), Godfrey 3394 (NCSC). Scotland: 20 Apr 1999 (FL), Hill 31345 (BRITm); 20 Jun 1957 (FR), Ahles & Haesloop 28637 (NCU); 20 Jun 1957 (FR), Ahles & Haesloop 28601 (NCUm); 4 Jun 2004 (FR), Sorrie 11264 (NCUm).North Carolina. Beaufort: 27 Mar 1949 (FL), Duncan 5923 (NCSC). Charleston: 2012-075, 15 Apr 2014 (FL), Lynch 42 (NCSC); 2012-075, 13 Jun 2014 , Phillips 48 (NCSC m); 2012-77, 15 Apr 2014 (FL), Lynch 37 (NCSC); 2012-077, 21 Aug 2012 (V), Lynch 30 (NCSCm); 2012-77, 13 Jun 2014 (FR), Phillips 53 (NCSC); 2 Apr 1944 (FL), Duncan 5885 (NCSC). Chesterfield: 25 Apr 1968 (FR), Ewel 666 (NCSC); 5 Jun 1956 (V), Radford 12431 (NCUm); 5 Apr 1968 (FL), Leonard & Radford 1219 (NCU). Clarendon: 20 Apr 1957 (FL), Radford 21097 (NCU). Colleton: 5 Apr 1956 (FL), Bell 1862 (NCU); 17 Apr 1974 (FL), Hardin 13420 . Darlington: 25 Mar 1935 (Fl), Matthews s.n. (NCU); 26 Mar 1935 (FL), Matthews & Smith s.n. (NCU); 10 Apr 1940 (FL), Smith 1378 (NCU). Dillon: 7 Apr 1940 (FL), Radford & Stewart 56 (NCU). Dorchester: 20 Jul 1957 (V), Ahles & Leisner 31966 (NCUm). Georgetown: 18 Apr 1987 (FL), Taggart 78 (NCU); Near Georgetown, 28 Jul 1928 (FR), Ashe s.n. (NCUm). Horry: 2012-076, 15 Apr 2014 (FL), Lynch 41 (NCSC); 2012-076, 13 Jun 2014 , Phillips 51 (NCSC m). Lee: 26 Jul 1957 (V), Radford 27396 (NCUm). Marlboro: 4 May 1968 (FL), Leonard & Radford 1218 (NCU).South Carolina. Berkeley: 9 Apr 1944 (FR), Taxon classificationPlantaeSaxifragalesHamamelidaceae2.Lodd., Bot. Cab. 16: Pl. 1520. 18298DC644F4-B01B-567E-B9EB-DF10E90AE717F.monticolaW.W. Ashe 1509 Ashe, Bot. Gaz. 24: 374. 1897. Type. North Carolina, mountains, C. Loddiges Illustration Pl. 1520. Figs Shrub, erect, robust, frequently >1 m tall (to 8 m); stems in clumps of 3 or more, branching. Leaves: stipules ovate to lanceolate, 3.5\u201311.8 \u00d7 1.9\u20134.0 mm; petioles 8.3\u201317.1(\u201318.9) mm, \u00bd as long or longer than the IL, brown-yellow pubescent; blades mostly spreading, green, broadly ovate or elliptic to suborbiculate, rarely obovate, 3.6\u201313.7 \u00d7 3.2\u201313.0 cm, most within the upper end of those ranges, pinnately 7\u201312-veined, bases oblique, occasionally symmetrical, usually V-cordate, rarely nearly rounded, margins crenate or serrate to nearly entire, toothed from at or below middle to the apex, teeth 11\u201324, apices acute to obtuse, often pubescent, both surfaces glabrous to sparsely stellate-pubescent, abaxial surface sometimes glaucous, IW:IL > or = 0.51 (x\u0304 = 0.96). Inflorescences usually appearing with leaves, spikes sessile or on short peduncles. Flowers: stamens 14\u201332, filaments 7.3\u201316.2 mm long. Capsules 6.8\u201312.7 \u00d7 6.5\u20138.6 mm. Seeds nearly white to completely brown or red-brown, usually ellipsoid, 5.3\u20137.4 \u00d7 2.7\u20133.6 mm, apices rounded to obtuse. Genome size and ploidy 5.21\u20135.25 pg, hexaploid (2n = 6x = 72).Flowering beginning late Mar; fruiting late May through mid-Jul.F.major can be found growing in seepage community with Coastal Plain-affinity species. In this habitat, where burning is frequent, this species may be <1 m in height. However, height variance is apparently not simply a factor of fire frequency. Fothergillamajor varies considerably in habit, ranging from colonial shrubs less than 2 m tall, typically found growing on sandy dampish sites in the southwestern part of the range and lower elevations to larger tree forms growing to 6 m, with offsets but no rhizomes, typically found in more upland mountain dry forest sites with igneous geology found to the North and East . Commonly associated upland species include Acerrubrum, Aesculussylvatica W. Bartram, Alnusserrulata, Aroniaarbutifolia (Aiton) Willd., Calycanthusfloridus L., Carpinuscaroliniana Walter, Cornusflorida L., Gaylussaciafrondosa (L.) Torr. & A. Gray, Hamamalisvirginiana L., Hepaticaamericana (DC.) Ker Gawl, Hypericumnudiflorum Michx. ex Willd., Ilexopaca Aiton, Kalmialatifolia, Liquidambarstyraciflua, Liriodendrontulipifera L., Magnoliaacuminata (L.) L., Polystichumacrostichoides (Michx.) Schott, Quercusalba L., Q.rubra L., Rhododendroncatawbiense Michx., and Stewartiaovata (Cav.) Weath. (fide colectoris).This species can be found in the mountains and Piedmont of Alabama, Arkansas, Georgia, North Carolina, South Carolina, and Tennessee Fig. . HabitatFothergillamajor is considered Vulnerable rangewide, ranked by NatureServe as follows: G3; Alabama (S2), Arkansas (S1), Georgia (S1), North Carolina (S3), South Carolina (S2), Tennessee (S2); http://explorer.natureserve.org/, accessed 11 Dec 2019). Due to its sensitive status, we provide only skeletal collections data below..Lynch 91 (NCSCm). Cherokee: 12 Apr 1969 (FL), Kral 34269 ; 10 May 1970 (FL), Kral 39052 (BRITm); 14 Jul 1966 (FR), Clark & Landers 5122 . Cullman: 17 Apr 1931 (FL), Ashe s.n. (NCU); 16 Apr 1924 (FR), Wolf s.n. (AUAm); 4 Jul 1911 (FR), Wolf 813 (AUAm); 28 May 1931 (V), Wolf s.n. (VDB). DeKalb: 2008-009, 21 Mar 2012 (FL), Lynch 7 (NCSC); 2008-009, 2 Jul 2012 (V), Lynch 81 (NCSCm); 14 Jul 1966 (FR), Clark & Landers 5023 ; 22 May 1972 (FL), Whetstone 1935 (NCUm). Marshall: 2011-092, s.d. (FL), Lynch 79 (NCSC); 2011-092, 2 Jul 2012 (V), Lynch 17 (NCSCm); 2011-147, 21 Aug 2012 (V), Lynch 24 (NCSCm); 15 Apr 1973 (FL), Kral 49636 . St. Clair: 31 May 1947 , McVaugh 8594 (BRIT m): Unspecified: n.d. (FL), Buckley s.n. (FLAS).Alabama. Blount: 2011-093, 2 Jul 2012 (V), Lynch 10 (NCSC); 2011-082, 2 Jul 2012 (FR), Lynch 80 (NCSCm).Arkansas. Searcy: 2011-082, 26 Mar 2012 (FL), Duncan & McDowell 12200 (NCU); 30 Mar 1951 (FL), Duncan & McDowell 12200 ; 6 May 1951 (FL), Duncan & Venard 12339 (BRIT m). Fulton: 2011-169, 21 Aug 2012 (V), Lynch 28 (NCSC). Lumpkin: 2011-164, 21 Aug 2012 (V), Lynch 27 (NCSCm). Walker: 2011-146, 21 Aug 2012 (V), Lynch 25 (NCSC); 15 Apr 1986 (FL), Coile 4547 (NCSC).Georgia. Bartow: 30 Mar 1951 (FL), Gavalak 3306V90 (BRIT m).Illinois. DuPage: Cultivated at Morton Arboretum, 9 May 1990 (FL), Dewolf & Bruns 2235 (BRIT).Massachusetts. Suffolk: Cultivated at Arnold Arboretum, Harvard University, 13 May 1968 (FL), Gillis 15041 (BRIT m).Michigan. Ingham: Cultivated at Michigan State University, 9 May 1979 (FL), Lynch 81 (NCSCm); 7 Oct 1966 (V), Downs 408 (NCSC); 2 Aug 1977 (FR), Kral 60712 (VDBm); 25 Aug 1989 (FR), Lance & Wood s.n. (NCUm); 1 Sep 1952 (FR), Radford 6676 (NCUm); 9 Sep 1976 (V), Smith 182 (NCSC); 5 Jul 1940 (FR), Stewart 1554 (NCU); 27 May 1964 (FR), Wilbur 7012 (VDBm). Chatham: 25 Apr 1988 (FL), Swab 75 (NCSC); 4 May 1988 (FL), Swab 97 (NCSC); 28 May 1988 (FR), Swab 236 (NCSC). Gaston: 19 May 1919 (FR), Coker s.n. (NCUm). Harnett: 18 Apr 2006 (V), Sorrie & Hart 11770 (NCUm). Montgomery: 2011-122, 21 Aug 2012 (V), Lynch 23 (NCSCm); 11 Oct 2002 (FR), Diamond 1606 (NCUm); 14 Jul 2004 (V), Schwartzman 30 (NCUm); 20 Jul 2004 (V), Weakley s.n. (NCUm); 15 Oct 2004 (V), Weakley s.n. (NCU). Orange: 2011-124, 19 Apr 2012 (FL), Lynch 14 (NCSC); 2011-124, 2 Jul 2012, Lynch 78 (NCSCm); 2011-124, 24 Jun 2014 (FR), Phillips 62 (NCSC); Apr 1899 (FL), Ashe s.n. (NCU); Jun 1899 (FR), Ashe s.n. (NCU); 31 Apr 200 (FL), Wally & Wichmann 125 (NCUm); 4 May 1910 (FR), Clerces s.n. (NCU). Person: 7 Jul 2005 (FR), LeGrand s.n. (NCUm). Polk: 30 May 1930 (FL), Ashe s.n. (NCSC); 20 Apr 1897 (FL), Biltmore 6565 (BRITm); 20 Apr 1897 (FL), Biltmore 708 (NCU). Randolph: 22 Apr 1958 (FL), Melvin s.n. (NCU). Rutherford: 2011-163, 21 Aug 2012 (V), Lynch 26 (NCSCm); 2011-163, 15 Apr 2013 (FL), Lynch 39 (NCSC); 2011-163, 24 Jun 2014 (FR), Phillips 64 (NCSC); 21 Apr 1956 (FL), Bell 2118 (NCU). Stokes: 23 Apr 1950 (FL), Fox et al. 3565 (NCSC); s.d. (FR), Harbison s.n. (NCU); 5 May 1936 (FL), Hunt 13474 ; 7 Jul 1969 (FR), Leonard & Russ 2553 (NCUm); 21 Apr 1974 (FL), Massey 3900 (VDB); 26 Apr 1958 (FL), Matthews 54 (BRIT); 15 Jun 1967 (FR), Radford 45392 ; 4 Jun 1958 (FR), Radford 34675 (VDB m); 9 Apr 1933 (FL), Schallert 3613 (BRIT). Surry: 19 May 1935 (V), Harbison s.n. (NCU). Transylvania: 2011-112, 2 Jul 2012 (V), Lynch 16 (NCSC); 2011-112, 24 Apr 2014 (FL), Lynch 47 (NCSC); 2011-112, 24 Jun 2014 (FR), Phillips 63 (NCSC); 2011-131, 21 Aug 2012 (FR), Lynch 22 (NCSCm); 19 Jun 1965 (FR), Eggers 1262 (VDB m); 26 Jul 1962 (FR), Rodgers 62064a (NCUm); 24 May 2006 (FR), Schwartzman 29 (NCUm). Wake: 28 Oct 2005 (V), Bruhn s.n. (NCU).North Carolina. Burke: 2011-105, 2 Jul 2012 (V), Fogg 1 (UWFP).Pennsylvania. Marion: Cultivated at the Arboretum of the Barnes Foundation, 27 Apr 1968 (FL), Kral 58130 (VDB m); 15 Oct 1988 (V), Hill 20066 (BRIT m); 23 May 1996 (V), Townsend 874 (VDB m). Oconee: 2011-091, 28 Mar 2012 (FL), Lynch 12 (NCSC); 2011-091, 2 Jul 2012 (V), Lynch 77 (NCSCm); 26 Apr 1965 (FL), Radford 44707 (NCU); 20 Apr 1973 (FL), Rogers & Green 73078 (FLAS-2). Pickens: 15 June 1992 (FT), Hill 23387 (BRIT m);South Carolina. Greenville: 17 May 1976 (FR), Sharp 556 ; 30 Apr 1931 (FL), Jennison & Sharp s.n. (NCU); May 3 1936 (Fl), Sharp & Underwood 4205 . Greene: 17 May 1970 (FL), Sharp et al. 45204 . Scott: 2012-065, 21 Aug 2012 (V), Lynch 29 (NCSC m); 2012-065, 15 Apr 2014 (FL), Lynch 44 (NCSC); 23 Apr 1972 (FL), Clebsch s.n. (VDB); 19 Apr 1979 (FL), Whitten & Noss s.n. (FLAS-2); 23 Jun 1978 (FR), Wofford et al. 78-112 (VDB m). Sevier: 1 May 1960 (Fl), Sharp 26818 ; 25 Apr 1970 (FL), Williams 82 (AUA m); 25 Apr 1970 (FL), Pippin 83 (VDB); 2 Apr 1938 (FL), Jennison 53 (VDB m); 26 Apr 1957 (FL), Sharp 21575 (BRIT m).Tennessee. Grainger: 20 Apr 1931 (FL), Meyer 37144 (FLAS).Washington D.C. U.S. National Arboretum, 16 Oct 1990 (V), Taxon classificationPlantaeSaxifragalesHamamelidaceae3.W.D.Phillips & J.E.Haynessp. nov.DC5E3CB6-8D0A-57AA-96CC-7D6838D9DC9Furn:lsid:ipni.org:names:77208304-1Nathan Lynch 70 . Figs Florida. Walton Co.: Voucher specimen from containerized plant at Mountain Horticultural Crops Research and Extension Center, Mills River, NC (leaves and stem collected 19/7/2012), , 2011-088, 19 Jul 2012 (V), Fothergillamilleri is morphologically most similar to F.gardenii, but differs from the latter by leaves held erect (vs. spreading in F.gardenii), blades blue-green or gray-green (vs. green in F.gardenii), petioles 1/3\u20131/2 the length of the IL (vs. \u00be the length of the IL or longer in F.gardenii), and seed apices acute to acuminate (vs. rounded or obtuse in F.gardenii).Shrub, rhizomatous, erect, to 1.5 m tall, clump-forming, multi-stemmed, branching. Leaves: stipules ovate to lanceolate, 2.5\u20137.8 \u00d7 1.0\u20133.0 mm; petioles 2.6\u20138.0 mm long, usually 1/3\u20131/2 the length of the IL, brown-yellow pubescent; blades erect, blue-green to gray-green, obovate, 3.2\u20138.0 \u00d7 3.0\u20134.8 cm, pinnately 8\u201310-veined, bases rounded to truncate, margins crenate to serrate above middle and mostly near the apex, sometimes appearing crenate to entire, apices mostly obtuse to acute, both surfaces conspicuously stellate-pubescent, sometimes sparsely so, abaxial surface not glaucous, IW:IL < or = 0.48 (x\u0304 = 0.29). Inflorescences appearing before leaves, spikes on short peduncles or sessile. Flowers: stamens 15\u201322, filaments 4.3\u201310 mm long. Capsules 7.0\u20139.0 \u00d7 5.0 \u20137.0 cm. Seeds usually completely brown to red-brown, ovoid, 4.5\u20136.2 \u00d7 2.4\u20133.2 mm, apices acuminate, often recurved. Genome size and ploidy: 1.70\u20131.78 pg, diploid (2n = 2x = 24).Flowering beginning late Mar; fruiting late May through the end of Jul.Cyrillaracemiflora or Taxodiumascendens swamp forests. Plant associates include Acerrubrum, Arundinariatecta Muhl., Clethraalnifolia, Hibiscusaculeatus Walter, Hypericumcistifolium Lam., Juncustrigonocarpus Steud., Dichantheliumscoparium (Lam.) Gould., Osmundastrumcinnamomeum (L.) C. Presl, Rhexiavirginica L., Rhynchosporachalarocephala Fernald & Gale, and Xyrisfimbriata Elliott (fide colectoris).This species can be found in the panhandle of Florida, in Alabama in the Gulf coastal plain, and is also known from one county in Georgia Fig. . This spThe species is named in honor of Dr Ron Miller, Pensacola, Florida, who championed this project, originally suggested that diploid cytotypes might still exist, and ultimately found them. Dr Miller\u2019s extensive effort and field work (with colleagues) provided the foundation for this research and establishment of ex situ living collections, including accessions in the U.S. National Plant Germplasm System.F.major. Consequently, only skeletal collections data are provided below.The conservation status of this species must be reassessed. It is presently known from only seven counties, and would appear to have an imperilment status at least as severe as that of .Lynch 1 (NCSC); 2011-087, 2 Jul 2012 (V), Lynch 68 (NCSCm); 2011-087, 13 Jun 2014 (FR), Phillips 58 (NCSC); 16 Jun 1984 (FR), Hedges 156 (UWFPm); 19 Apr 2001 (FR), Schotz 1830 (UNA [online!]). Covington: 25 Jun 1906 (FR), Harper 108 (NY [online!]). Escambia: 11 Apr 1964 (FL), Kral 19698 (AUAm). Geneva: 25 Jul 1968 (V), Kral 32029 (VDBm); 26 Apr 1969 (FL), Kral 34524 (VDBm); 7 Sep 1994 (V), Simmers s.n. (HTTU [online!]). Monroe: 15 Jun 1959 (V), Grelen s.n. (FLASm).Alabama. Baldwin: 2011-087, 21 Mar 2012 (FL), Lynch 2 (NCSC); 2011-083, 2 Jul 2012 (FL), Lynch 67 (NCSC); 2011-083, 13 Jun 2014 (FR), Phillips 57 (NCSCm); 20 Apr 1991 (FL), Burkhalter 12638 ; 5 Aug 1990 (V), Burkhalter 12211 (UWFPm); 13 Jul 1996 (V), Burkhalter 15064 (UWFP); 18 May 1993 (FR), Naczi 3028 (KNK [online!]). Walton: 8 Apr 1899 (FL), Biltmore Herbarium 7609b (FLASm); 2011-088, 28 Mar 2012 (FL), Lynch 11 (NCSU); 2012-060, 19 Mar 2013 (FL), Lynch 34 (NCSC); 2012-060, 2 Jul 2012 (V), Lynch 15 (NCSC); 2012-060, 13 Jun 2014 (FR) Phillips 59 (NCSC); 18 Aug 1990 (V), Orzell and Bridges 14757 .Florida. Okaloosa: 2011-083, 21 Mar 2012 (FL), Lynch 8 (NCSC); 2011-178, 2 Jul 2012 (V), Lynch 69 (NCSCm).Georgia. Taylor: 2011-178, 26 Mar 2012 (FL), Taxon classificationPlantaeSaxifragalesHamamelidaceae4.Kearney in Small, Fl. S.E. U.S. 509, 1331. 1903988E10E7-FD07-532B-8B40-80EC41C51904Kearney s.n. . Figs Georgia. Wayne Co., Jesup, dry soil, 4 June 1893 (FR), Shrub, rhizomatous, erect, to 1 m tall, clump-forming, multi-stemmed, branching. Leaves: stipules ovate to lanceolate, 3.5\u20136.0 \u00d7 8.0\u201313.0 mm, curved downward; petioles 4.4\u201317.8 mm long, usually nearly as long to longer than the IL, brown-yellow pubescent; blades drooping, green, mostly ovate, 3.2\u201312.1 \u00d7 3.0\u20136.2 cm, pinnately 8\u201310-veined, bases cordate, margins crenate to serrate from middle, apices acute, adaxial and abaxial surfaces not glaucous, stellate-pubescent, sometimes sparsely so, IW:IL > or = 0.62 (x\u0304 = 0.96). Inflorescences appearing before leaves, spikes on short peduncles or sessile. Flowers: stamens 15\u201320 per flower, filaments 6.6\u20139.3 mm long. Capsules 7.5\u201310.0 \u00d7 5.0 \u20137.6 mm. Seeds usually completely brown to red-brown, ovoid, apex obtuse, 4.5\u20136.2 \u00d7 2.4\u20133.2 mm, apices obtuse to acute. Genome size and ploidy 1.73\u20131.82 pg, diploid (2n = 2x = 24).Flowering Mar\u2013May; fruiting May\u2013Sep.This species range is restricted to Georgia, South Carolina, and Alabama Fig. . BecauseF.major. Consequently, only skeletal collections data are provided below.The conservation status of this species needs to be assessed. It is presently known from only eight counties, and would appear to have an imperilment status at least as severe as that of .Harbison 1033 (NCUm).Alabama. Montgomery: 12 Sep 1899 (FR), Cuthbert s.n. (FLAS). Brantley: 23 Aug 1947 (V), Thorne & Norris 6284 (GEO [online!]). Emanuel: 2011-170, 2 Jul 2012 (V), Lynch 19 (NCSCm); 2011-170, 15 Mar 2013 (FL), Lynch 33 (NCSC); 2011-170, 14 Jun 2014 (FR), Phillips 60 (NCSC). Long: 2011-171, 2 Jul 2012 (V), Lynch 20 (NCSCm); 2011-171, 14 Mar 2013 (FL), Lynch 32 (NCSC); 2011-171, 13 Jun 2014 (FR), Phillips 61 (NCSC); Tattnall: 2011-168, 19 Mar 2013 (FL), Lynch 35 (NCSC); 2011-168, 2 Jul 2012 (V), Lynch 18 (NCSCm). Wayne: 31 Aug 1904 (V), Biltmore Herbarium 14940 (NY [online!]).Georgia. Augusta-Richmond: 2 Apr 1898 (FL), Lynch 40 (NCSC); 2012-084, 13 Jun 2014 (V), Phillips 56 (NCSCm). Lexington: 13 Sept 1988 (V), Pittman 9139817 (BRITm); 27 May 1957 (FR), Radford 23378 (NCUm).South Carolina. Aiken: 2012-084, 15 Apr 2014 (FL),"} +{"text": "Numerous individual studies have investigated the diagnostic value of EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG detection for nasopharyngeal carcinoma (NPC), but the conclusions remain controversial. This meta-analysis aimed to determine the value of EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG detection in the diagnosis of NPC.PROSPERO registration number: CRD42019145532. PubMed, EMBASE, Cochrane Library, and Chinese data libraries were searched up to January 2019. The pooled sensitivity, specificity, and positive likelihood, negative likelihood, and diagnostic odds ratios were conducted in this meta-analysis. Summary receiver operating characteristic curves evaluated the test-performance global summary. Publication bias was examined by Deek\u2019s funnel plot asymmetry test.EBV-DNA in diagnosis of NPC were: 0.76 (95% CI 0.73\u20130.77), 0.96 (95% CI 0.95\u20130.97), 14.66 (95% CI 9.97\u201321.55), 0.19 (95% CI 0.13\u20130.28), 84 (95% CI 50.45\u2013139.88), 0.96 (SE: 0.001), and 0.55 (95% CI 0.54\u20130.57), 0.96 (95% CI 0.96\u20130.97), 12.91 (95% CI 9.55\u201317.45), 0.35 (95% CI 0.29\u20130.43), 39.57 (95% CI 26.44\u201359.23), 0.94 (SE: 0.002) for the EA-IgA, and 0.85 (95% CI 0.84\u20130.85), 0.89 (95% CI 0.88\u20130.89), 6.73 (95% CI5.38\u20138.43), 0.17 (95% CI 0.12\u20130.23), 43.03 (95% CI 31.51\u201358.76), 0.93 (SE: 0.007) for the VCA-IgA, and 0.86 (95% CI 0.85\u20130.88), 0.87 (95% CI 0.88\u20130.90), 7.55 (95% CI 5.79\u20139.87), 0.16 (95% CI 0.13\u20130.19), 50.95 (95% CI 34.35\u201375.57), 0.94 (SE: 0.008) for the EBNA1-IgA, and 0.70 (95% CI 0.69\u20130.71), 0.94 (95% CI 0.94\u20130.95), 9.84 (95% CI 8.40\u201311.54), 0.25 (95% CI 0.21\u20130.31), 40.59 (95% CI 32.09\u201351.35), 0.95 (SE: 0.005) for the Rta-IgG. The EBV-DNA had larger AUC compared with other EBV-based antibodies (P\u2009<\u20090.05), while the difference between EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG was not statistically significant (P\u2009>\u20090.05).Forty-seven studies with 8382 NPC patients (NPC group) and 15,089 individuals without NPC (Control group) were included in this meta-analysis. The sensitivity, specificity, positive likelihood (+\u2009LR), negative likelihood (-LR), DOR and AUC of EBV-DNA, VCA-IgA, EBNA1-IgA and Rta-IgG detection have high accuracy in early diagnosis NPC. In addition, EBV-DNA detection has the higher diagnosis accuracy in NPC. On the other hand, EA-IgA is suitable for the diagnosis but not NPC screening.The online version contains supplementary material available at 10.1186/s12935-021-01862-7. Nasopharyngeal carcinoma (NPC) is the most common malignant tumor in head and neck surgery and it is highly prevalent in southern China and Southeast Asia . UnfortuPROSPERO registration number: CRD42019145532.Literature review was separately conducted by two investigators that queried online databases, including PubMed, EMBASE, Cochrane Library, and Chinese data libraries , and the search concluded in January 2019, using the following keywords: nasopharyngeal carcinoma, Epstein-Barr virus, capsid antigen-IgA, early antigen antibody, nuclear antigen antibody, BRLF1 transcription activator IgG, EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG.Studies that assessed the performance of EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG detection for untreated NPC identification;All patients included in the study were diagnosed using a reference test ;Studies that used a pre-specified threshold;Studies that clearly stated the number of true positive, false positive, false negative, and true negative results in the diagnosis of NPC or these values could be calculated from the data;Studies that provided a clear definition of the control sources ;In cases of multiple reports describing the same population, the most recent or most complete report was selected.Reported results were insufficient for construction of the 2\u2009\u00d7\u20092 table;Studies that failed to clearly define the control types;The NPC group contained other tumors;Basic research, review articles, comments, letters, case reports, abstracts in conference, responding letters and experimental animal studies.Study quality assessment was conducted using the diagnostic accuracy (QUADAS) II checklist . StudiesQ test and inconsistency index (I2) were used to estimate the heterogeneity within studies [P\u2009<\u20090.05 or I2\u2009>\u200950%. If statistically significant heterogeneity existed, meta-analysis was performed using the random effects model, otherwise, a fixed effect model was used.Standard methods recommended for meta-analyses of diagnostic test evaluations were used to perform this meta-analysis . Review studies . HeterogThe accuracy indexes of EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG was pooled by meta-analysis, such as sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR) and AUC. The likelihood ratios (PLR and NLR) are clinically meaningful for the measurement of diagnostic accuracy; PLR\u2009>\u200910 and NLR\u2009<\u20090.1 are considered high . The DORP values were two sides and P\u2009<\u20090.05 was regarded as statistically significant.Sensitivity analyses were performed to explore the sources of heterogeneity of the included studies by removing each included study consecutively. The heterogeneity was investigated by meta-regression according to different covariates, including publication year (Year\u2009\u2265\u20092011 or\u2009<\u20092011), NPC size (NPC\u2009\u2265\u2009100 or NPC\u2009<\u2009100), control sources , detection method, and article language (English or Chinese). Publication bias was examined by Deek\u2019s funnel plot asymmetry test. All In this meta-analysis, 47 publications on the role of EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG concentrations in the diagnosis of NPC that met the criteria for inclusion were included in the analysis \u201358. FiguI2\u2009=\u200977.5%, P\u2009<\u20090.001; EA-IgA:77.3%, P\u2009<\u20090.001; VCA-IgA: 87.0%, P\u2009<\u20090.001; EBNA1-IgA:78.9%, P\u2009<\u20090.001; Rta-IgG: 60.5%, P\u2009<\u20090.001) indicated significant heterogeneity among the studies. The result showed that there was no threshold effect in the pooled analysis of EBV-DNA (P\u2009<\u20090.001), EA-IgA (P\u2009<\u20090.001), VCA-IgA (P\u2009<\u20090.001), EBNA1-IgA (P\u2009<\u20090.001) and Rta-IgG (P\u2009<\u20090.001).The inconsistency index (EBV-DNA: P\u2009<\u20090.05), while EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG were no statistically different from each other (P\u2009>\u20090.05) in Table The pooled sensitivity, specificity, PLR, NLR, DOR and AUC for the value of EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG in the diagnosis of NPC are displayed in Table P\u2009<\u20090.0095).The sensitivity analysis showed that the results were not affected by the exclusion of any individual trial. As meta-regression result indicated that publication year, NPC or control size, control sources, detection method, cutoff value, and article language are not the DOR heterogeneity of EBV-DNA, VCA-IgA, EBNA1-IgA and Rta-IgG, whereas detection method was possible DOR heterogeneity sources for the EA-IgA (P\u2009=\u20090.14), EA-IgA (P\u2009=\u20090.26), EBNA1-IgA (P\u2009=\u20090.56) and Rta-IgG (P\u2009=\u20090.16), other than VCA-IgA (P\u2009=\u20090.03) and 0.89 (95% CI 0.88\u20130.90) [CI 0.90\u20130.92) and specificity 0.92 (95% CI 0.92\u20130.93), with SROC 0.98. But the Li\u2019s study existed language bias and publication bias. For the Rta-IgG, Cui et al.pooled 17 studies involving 2658 NPC patients, and the\u00a0results pointed out that the sensitivity of Rta-IgG for detecting NPC was 90.83 (95% CI 0.78\u20130.87), the specificity was 0.92 (95% CI 0.90\u20130.93) [Previous meta-analyses have been published on the value of some EBV-based markers in the detection of NPC. For the EBV-DNA, Han et al.conducted a meta-analysis based on 18 studies involving 1492 NPC cases and 2461 health controls in Asians, in which the pooled sensitivity and specificity of EBV-DNA detection for NPC were 0.73 (95% 88\u20130.90) . Further88\u20130.90) . The Han88\u20130.90) , which wP\u2009<\u20090.05). Additionally, the pooled DOR of EBV-DNA (84.00) that differed 33.05\u201344.43 was higher than other EBV-based antibodies. These results indicated that EBV-DNA detection had higher accuracy in diagnosis of NPC. In addition, a meta-analysis included 8128 NPC cases showed that pre-EBV-DNA levels can also be a prognostic indictor for patients with NPC [To our knowledge, this is the first meta-analysis to determine the usefulness of EA-IgA and EBNA1-IgA and compare the accuracy EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgA in diagnosis of NPC. In this study,\u00a0the highest sensitivity was EBNA1-IgA (0.86), and the specificity of EBV-DNA (0.96) and EA-IgA (0.96) were highest. Besides, the sensitivity of EA-IgA (0.55) was lowest, and screening for NPC using only EA-IgA may lead to misdiagnosis, but the specificity was high, which indicated that EA-IgA was suitable for the diagnosis but not screening of NPC. EA-IgA or EBV-DNA detection combined with other indicators may also improve the sensitivity and specificity for the serological diagnosis of NPC , 51. Thewith NPC . A recenwith NPC , seventywith NPC . In addiwith NPC , 71. In with NPC , 72, it Several strengths of present meta-analysis should be highlighted. This study compered five EBV-related diagnostic markers for NPC with comprehensive calculations of their diagnostic performance, shedding light on the value of these tests in clinical settings. In the context of current availability of studies on EBV-DNA and immunoglobin antibody tests in the literature, this meta-analysis covers a large sample size pooled from rigorously included studies, and the results were stable. However, this meta-analysis should be interpreted with caution due to certain limitations. First, there was large heterogeneity among the included studies with differences in characteristics of the study and participants. The inability to obtain raw data on patient age and gender may have led to the heterogeneity and hindered a more detailed analysis. Second, most of the included populations were Chinese, which could lead to population selection bias and should not allow for generalization to other ethnicity groups, rendering further research needed. Third, technical methods for testing of EBV-related markers vary across different studies, including the inconsistent cut-off values and different antigen sets used despite of a same generic name. Use of enzyme-linked immunosorbent assay or immunofluorescence assay may have contributed to the different results . FinallyNotwithstanding heterogeneity of currently available data, the studies included in our analysis are of a large sample size and high-quality, thus providing a considerable power. EBV-DNA, VCA-IgA, EBNA1-IgA and Rta-IgG detection have high accuracy in early diagnosis NPC and can improve the effectiveness of screening. In addition, EBV-DNA detection has the higher diagnosis accuracy in NPC. On the other hand, EA-IgA is suitable for the diagnosis but not NPC screening. Further well-designed clinical trials need to be carried out in order to improve early diagnosis rate.Additional file 1: Forest plots of sensitivity, specificity, PLR, NLR, DOR for acoustic analysis of EBV-DNA, EA-IgA, VCA-IgA, EBNA1-IgA and Rta-IgG, and Funnel plots for publication bias test."} +{"text": "AbstractPhyllodiaptomus (Phyllodiaptomus) roietensissp. nov. was collected from temporary water bodies in Roi Et and Nakhon Ratchasima provinces in northeastern Thailand and Kampong Thom Province in central Cambodia. The new species is closely related to Phyllodiaptomus (P.) surinensis Sanoamuang & Yindee, 2001 in that it shares common morphological characters in the males: urosomites 2\u20133, P5 intercoxal sclerite, right P5 Exp-2, and left P5 Exp. Minor differences on the right antennule, right caudal ramus, P5 basis and Enp exist. The females differ in their Pdg 5, genital double-somite, and P5. An updated key to the species of the genus Phyllodiaptomus Kiefer, 1936 is provided. Phyllodiaptomus Kiefer, 1936, is among the most common freshwater copepods in Southeast Asia (Phyllodiaptomus (Phyllodiaptomus) blanci from Uzbekistan; P. (Ctenodiaptomus) annae from Sri Lanka; P. (P.) tunguidus Shen & Tai, 1964 from China; P. (P.) longipes Kiefer, 1965 from Indonesia; P. (C.) sasikumari Ranga Reddy & Venkateswarlu, 1989 and P. (C.) wellekensae Dumont & Ranga Reddy, 1993 from India; P. (C.) praedictus Dumont & Ranga Reddy, 1994, P. (P.) christineae Dumont, Ranga Reddy & Sanoamuang, 1996, P. (P.) surinensis Sanoamuang & Yindee, 2001, and P. (P.) thailandicus Sanoamuang & Teeramaethee, 2006 from Thailand; and P. (P.) irakiensis Khalaf, 2008 from Iraq. In addition, P. (C.) praedictussulawesensis as a subspecies of P. (C) praedictus from Indonesia; this subspecies was later found in the Philippines roietensis sp. nov. from two localities in Roi Et and Nakhon Ratchasima provinces, northeast Thailand, and two localities in Kampong Thom Province in central Cambodia . After 10 min the animals were transferred to pure glycerol. The animals were dissected and prepared in a glycerin-mounted slide under a stereomicroscope at 40\u2013100-x magnifications. The dissected specimens were mounted in pure glycerin on a glass slide and sealed under a cover glass with transparent nail varnish. All un-dissected specimens were stored in 70% ethanol in 1.5 mL microtubes.All appendages and body ornamentation were examined at 1000-x magnification under an Olympus CX31 compound microscope. The drawings were made using an Olympus U-DA drawing tube mounted on a compound microscope. The final versions of the drawings were made using the CORELDRAW 12.0 graphic program.SEM) were dehydrated in an ethanol series for 15 min at each concentration. Specimens were dried in a critical-point dryer and were mounted on stubs using adhesive tape under a stereomicroscope. Dried specimens were coated with gold in a sputter-coater. The SEM photographs were taken using a scanning electron microscope (FEI Helios NanoLab G3 CX).Specimens for scanning electron microscopy and at the Applied Taxonomic Research Center, Khon Kaen University (Thailand) (KKU).Specimens were deposited at the Abbreviations used in this paper are as follows:ae aesthetasc;Enp endopod;Exp exopod;Exp/Enp-n exopodal segment n/endopodal segment n;Pdg pediger;Pdg 1\u20135 pedigers 1\u20135;P1\u2013P5 legs 1\u20135;sp spine.The descriptive terminology follows Diaptominae Kiefer, 1932Sub-family Phyllodiaptomus Kiefer, 1936Genus Phyllodiaptomus Dumont, Ranga Reddy & Sanoamuang, 1996Subgenus Taxon classificationAnimaliaCalanoidaDiaptomidae0B9F97DA-0E9E-5345-88D4-29E2AF212FBEhttp://zoobank.org/59131C6D-A0DE-4BE0-9383-20C0DA8A709D-1.A pool in the rice field at Ban Nakae, Khilek Subdistrict, Pathum Rat District, Roi Et Province, northeastern Thailand; pH of water 8.6, water conductivity 126 \u00b5S cmHolotype: one adult male completely dissected , Ban Nakae , Khilek Subdistrict, Pathum Rat District, Roi Et Province, northeastern Thailand; collected on 12 June 1999 by L. Sanoamuang. Allotype: one adult female completely dissected ; same data as for holotype. Paratypes: two adult females and three adult males undissected preserved in 70% ethanol (NHMUK 2019.9\u201313), one adult female completely dissected (KKU-COP-2019-S-01); one adult female with eggs and three adult males undissected preserved in 70% ethanol (KKU-COP-2019-T-01); same data as for holotype.15\u00b010'55\"N, 102\u00b023'46\"E), Than Lalot Subdistrict, Phimai District, Nakhon Ratchasima Province, northeastern Thailand; collected on 17 October 2017 by N. Plangklang; (2) a roadside canal, Tropeang Chouk village , Baray District, Kampong Thom Province, central Cambodia; collected on 14 June 2007 by R. Chaicharoen; (3) a temporary pond, Kropeu village , Steung Sen District, Kampong Thom Province, central Cambodia; collected on 14 June 2007 by R. Chaicharoen.(1) a temporary pond, Ban Non Lakki , 3+ae (II), 1+ae (III), 1(IV), 1+ae (V), 1 (VI), 1+ae (VII), 1+sp (VIII), 2+ae (IX), 1 (X), 1 (XI), 1+ae+sp (XII), 1 (XIII), 1+ae (XIV), 1 (XV), 1+ae (XVI), 1 (XVII), 1 (XVIII), 1+ae (XIX), 1 (XX), 1 (XXI), 2 (XXII), 2 (XXIII), 2 (XXIV), 4+ae (XXV).Antennule Fig. symmetriExp-1\u20137 with 1, 3, 1, 1, 1, 1, and 1 inner seta, respectively; Exp-7 with three additional apical setae. Enp-1 with two inner median setae. Enp-2 with eight inner and seven apical setae.Antenna Fig. biramousEnp-1 with four inner distal setae; Enp-2 with nine apical setae plus tiny spinules along posterior surface. Exp-1\u20134 with 1, 1, 1, 3 setae, respectively.Mandible Fig. with sixEnp with seven apical setae. Exp with six setae.Maxillule Fig. with 13 Enp-1 and 2 with three setae each.Maxilla Fig. with twoEnp-1\u20136 with 2, 3, 2, 2, 2, 4 setae, respectively.Maxilliped Fig. with fouExp longer than Enp, Exp and Enp three-segmented except P1 Enp bi-segmented. Armature formula of P1\u2013P4 as follows :P1\u2013P4 Fig. with rouExp-1. Exp-1 sub-rectangular, more than twice as long as wide, longer than Enp. Exp-2 triangular, right side stout and shorter than left one; with row of strong spinules along margins and proximolateral spine at basal Exp-3; with two longitudinal grooves on anterior view , 3+ae (II), 1+ae (III), 1 (IV), 1+ae (V), 1 (VI), 1+ae (VII), 1+sp (VIII), 2+ae (IX), 1+sp (X), 1+sp (XI), 1+ae+sp (XII), 1+ae+sp (XIII), 2+ae+sp (XIV), 2+ae+sp (XV), 2+ae+sp (XVI), 1+sp (XVII), 1+sp (XVIII), 2+ae+sp (XIX), 3+sp (XX), 2 (XXI), 4+ae (XXII); geniculated between segments 18 and 19; segment 20 (antepenultimate) with serrated process distally (3\u20134 teeth), and with longitudinal hyaline membrane along outer margin.Antennule Figs , 7G, H aLeft antennule, antenna, mouthparts, and P1\u2013P4 as in female.Exp-1. Enp roietensis sp. nov. with the male P5 Exp-2 displays an affinity to the subgenus Phyllodiaptomus sensu Exp-2, medially concave in posterior view, principal lateral spine inserted on distal to mid-outer margin and three accessary spines arranged from proximal, middle, and distal, respectively; the left Exp-2 with patch of strong spinules along medial margin.Exp-1 (4) Exp-2 oval and concave, with strong, flat, curved principal spine and three accessary spines, and (5) bi-lobed Enp. The left P5 with long and narrow hyaline lamella along inner margin, Exp-2 with patch of strong spinules along medial margin, and bi-segmented Enp.The male of the new species has serrated outgrowth on the antepenultimate segment of the right antennule. The right caudal ramus with small chitinous spine near distal margin on ventral side and triangular prominence along proximal one-third length of outer margin. The P5 intercoxal sclerite produced, with convex distal margin. The right P5 with (1) short, strong spine on posterior lobe of coxa, (2) triangular hyaline lamella on proximal inner margin and large chitinous outgrowth on posterior surface of basis, (3) acute distal outer corner of Pdg 5 wings, left wing more elongated in posterio-lateral direction; posterior and dorsal spines short and strong. Genital double-somite with posterolateral directed process on right side. One pair of genital spines on lateral side slightly symmetrical and strong. P5 Exp-2 with conveyor canal on anterior surface. P5 with bi-segmented Enp.Female with asymmetrical roietensis is taken after the type locality, Roi Et Province. The name with the Latin suffix \u201c-ensis\u201d is the adjective for a location.The specific name Dentodiaptomusjavanus , Eodiaptomussanoamuangae Ranga Reddy & Dumont, 1998, Mongolodiaptomuscalcarus , M.malaindosinensis , Neodiaptomuslaii Kiefer, 1974, and Phyllodiaptomus (Phyllodiaptomus) christineae Dumont, Ranga Reddy & Sanoamuang, 1996.Known only from four temporary water bodies from Roi Et and Nakhon Ratchasima provinces, Thailand and Kampong Thom Province, Cambodia Fig. . PresencPhyllodiaptomus has been recorded in Asia, including south China, Turkey, Israel, Uzbekistan, Iran, Iraq, India, Sri Lanka, Nepal, Indonesia, Thailand, Laos, Philippines and Cambodia (P. (C.) annae, P. (C.) wellekensae, and P. (C.) sasikumari) are endemic to India; two species (P. (P.) thailandicus and P. (P.) surinensis) are endemic to Thailand; P. (P.) tunguidus, P. (P.) irakiensis, and P. (P.) longipes are endemic to China, Iraq, and Indonesia, respectively. Only P. (P.) blanci is widely distributed, extending across many countries. Five species have been recorded in Thailand, namely P. (C.) praedictus, P. (P.) christineae, P. (P.) thailandicus, P. (P.) surinensis, and P. (P.) roietensis sp. nov. (P. (P.) surinensis and P. (P.) roietensis sp. nov. are rare. In 3,000 samples collected within Thailand, each has been recorded in only two localities in the northeast. This is in contrast to another endemic Thai species, P. (P.) thailandicus, which is widely distributed in both temporary and permanent water bodies in the east and south of Thailand roietensis sp. nov., Mongolodiaptomusloeiensis Watiroyram & Sanoamuang, 2017, and Mongolodiaptomusmekongensis Sanoamuang & Watiroyram, 2018 differ from P. (P.) surinensis and other diaptomids by having additional spines on segments 17\u201319 thailandicus. However, the characteristic that differentiates the new diaptomid from P. (P.) thailandicus is the presence of a single process on each side of the genital double-somite; P. (P.) thailandicus has two processes only on the right side surinensis have unique females which can be easily differentiated. The female P5 Exp-2 of the new species is obviously asymmetrical compared with that of P. (P.) surinensis which has a slightly asymmetrical P5 Exp-2. Exp-2 in females is species-specific and unique to the genus Phyllodiaptomus: the new species has two longitudinal ridges on the anterior surface versus multi-longitudinal ridges in P. (P.) surinensis surinensis. The new species has substantial left genital double-somite proximal bulging versus only slight asymmetry in P. (P.) surinensis. The genital double-somite of P. (P.) surinensis has a bi-lobed hyaline outgrowth ventrally, which is absent in the new species. The genital spines in the female of the new species are oriented to a posterolateral direction in dorsal view, whereas they are pointed to the lateral direction in P. (P.) surinensis. The new species has tiny spinules on Pdg 4\u20135 laterally; these are present dorsally in P. (P.) surinensis roietensis sp. nov. has a number of morphological differences from other members of the blanci-species group as follows:The male of P. (P.) longipes.a) Antepenultimate segment with a serrated process versus smooth in P. (P.) thailandicus, P. (P.) christineae, and P. (P.) blanci.b) Urosomite(s) with a long hair or hair-like setae versus bare in P. (P.) surinensis and P. (P.) tunguidus. However, a ventral prominence is also present on the left ramus of P. (P.) tunguidus (but is absent in the left ramus of the new species) and there are only two prominences in the new species but five in P. (P.) surinensis.c) Right caudal ramus with ventral prominences as in P. (P.) irakiensis and P. (P.) thailandicus. The new species has a round or semi-circular distal margin versus triangular in P. (P.) blanci, P. (P.) christineae, P. (P.) longipes, and P. (P.) tunguidus.d) Intercoxal sclerite is modified distally into single lobe versus two lobes in P. (P.) thailandicus and slender in P. (P.) christineae.e) Right P5 coxal spine is strong and acute versus rectangular in P. (P.) irakiensis and P. (P.) blanci. In addition, three species, P. (P.) longipes, P. (P.) christineae, and P. (P.) tunguidus, have a longitudinal ridge on the posterior surface, which is absent in the new species (the first one has two minute prominences on the ridge). The right P5 basis has a triangular hyaline lamella at inner margin versus elongated in P. (P.) christineae, P. (P.) longipes, and P. (P.) tunguidus, and round in P. (P.) blanci. The left P5 basis has inner lamella versus bare in P. (P.) irakiensis and P. (P.) longipes, digitiform in P. (P.) tunguidus, and small in P. (P.) blanci. The new species lacks any ornamentation on the anterior surface but P. (P.) surinensis has two minute lateral spines (see f) Right P5 basis with a three-lobed chitinous prominence on posterior surface versus bare in ines see : fig. 54Exp-2 with three accessary lateral spines versus bare in P. (P.) tunguidus and P. (P.) blanci, and one in P. (P.) irakiensis, P. (P.) christineae, and P. (P.) longipes.g) Right P5 Enp with a bi-lobed shape versus conical in the rest of the species except P. (P.) surinensis.h) Right P5 Enp versus one-segmented in P. (P.) thailandicus, P. (P.) surinensis, P. (P.) blanci, P. (P.) christineae, and P. (P.) longipes.i) Left P5 with bi-segmented P. (P.) surinensis. However, there are three major differences among the males, i.e. the right caudal ramus, left P5 basis, and left P5 Enp as described above. The fine detail on its inner hyaline lamella on the right P5 basis is also different: triangular in the new species versus oval bi-lobed in P. (P.) surinensis.With regard to the comparative morphology above, the male of the new species is most similar to those of Phyllodiaptomus (P. (P.) tunguidus, P. (P.) blanci, P. (P.) longipes, P. (C.) annae, P. (C.) wellekensae, and P. (C.) sasikumari); he also gave morphological descriptions of these six species. In this study, the key is updated as follows:Males:Females:"} +{"text": "Adiantum philippense revealed bioactive Nigrospora sphaerica from the leaf segment. Chemical and biological profiling through TLC\u2013bioautography and hyphenated spectroscopic techniques confirmed the presence of phomalactone as an antimicrobial metabolite.Endophyte bestows beneficial aspects to its inhabiting host, along with a contribution to diverse structural attributes with biological potential. In this regard, antimicrobial profiling of fungal endophytes from medicinal plant Escherichia coli by disc diffusion assay. The MIC was found to be significant against both Escherichia coli and Xanthomonas campestris in the case of bacteria and dermatophyte Candida albicans at 150\u2009\u03bcg/ml, respectively.The chemical investigation of the broth extract by bioassay-guided fractionation confirmed phomalactone as a bioactive antimicrobial secondary metabolite. The antimicrobial activity of phomalactone was found to be highest against Nigrospora sphaerica exhibiting a broad spectrum of antimicrobial activity against human and phytopathogenic bacteria and fungi. This work is the first report regarding the antibacterial activity of phomalactone.Overall, the results highlighted the antimicrobial potential of phomalactone from the endophyte Taxomyces andreanae inhabiting Taxus brevifolia -5, 6-dihydroxy-2\u2009h-pyran-2-one].HPLC: The purified compound eluted at RT-4.89 with 86% purity : 2.05 , 2.80 , 4.53 , 4.76 5.67\u20135.69 , 6.03\u20136.04 : 17.6 (C-9), 63.8 (C-5), 122.3 (C-3), 132.7 (C-8), 144.8 (C-4), 162.1 , 83.3 (C-6), 123.5 (C-7). MS : 154.06, (100%), 155.07 (M + 1) , 1750\u20131720 (ether), 1680\u20131600 , 1448 (CH3-bond), 1050\u20131150 (> C=O (1160) stretch), 1380 (\u2013CH-bond) . The results obtained indicated that Gram-negative bacteria were found to be more susceptible when compared to Gram-positive.The MIC was found to be lowest against Nigrospora sphaerica has also been reported from a vast range of host viz., Ginkgo biloba [Moringa oleifera [Phoenix dactylifera [Saccharum arundinaceum [N. sphaerica, extracted with ethyl acetate showed a significant antimicrobial activity against bacteria and fungus viz., S. aureus, B. subtilis, S. epidermidis, E. coli, K. pneumonia, P. aeruginosa, S. typhi, S. flexneri, X. campestris, V. parahaemolyticus, and C. albicans, respectively. Several bioactive compounds have been reported from N. sphaerica which suggests the potential for discovery of pharmaceutically relevant substances. Previously, it was reported N. sphaerica to produce new antimicrobial bioactive secondary metabolites, such as nigrosporolides [o biloba , Moringaoleifera , Phoenixtylifera and Saccdinaceum . In thisorolides , nigrosporolides , lactoneorolides , epoxydoorolides , and nigorolides .Nigrospora [Xylaria [Aspergillus [Verticillium [Drechslera [Hirsutella (entomopathogenic) [Paecilomyces (entomopathogenic) [Phoma [Aspergillus fumigatus [Phomalactone is quite insecticidal\u00a0 and has grospora , 33, Xyl[Xylaria , Aspergiergillus , Verticiicillium , Drechslechslera , Hirsutehogenic) , Paecilohogenic) , and Pho) [Phoma . Phomalaumigatus , nematocumigatus , immunomumigatus , insectiumigatus , and phyumigatus .Xylaria sp. exhibited to possess weak activity at 13\u2009\u03bcg/ml against protozoan Plasmodium falciparum was reported by Carlos et al. 2008. A study conducted by Kumudini et al. 2015 reported phomalactone from N. sphaerica had larvicidal, adulticide activity against Aedes aegypti and Anopheles quadrimaculatus mosquitoes with LD50 value 0.64\u2009\u03bcg/org and 0.20\u2009\u03bcg/org, respectively. The investigation of biopotential endophytes inhabiting Zoysia japonica Steud by Kim et al. 2001 revealed phomalactone isolated from N. sphaerica exhibited potent fungitoxic activity against Phytophthora infestans and Phytophthora capsici. Its ecological role(s) in each of these species has not been rigorously studied, but its phytotoxic, fungitoxic, and insecticidal activities may be important to the various fungi that produce phomalactone.Phomalactone from endophyte N. sphaerica from medicinal plant A. philippense. Chemical investigation through bioautography N. sphaerica displayed a broad spectrum of antimicrobial activity, which indicated that endophytic N. sphaerica as a potent producer of bioactive phomalactone derivative with great potential as a natural product drug molecule.In conclusion, this is the first report on the isolation of Additional file 1: Supplementary Figure 1. HPLC analysis of purified bioactive compound phomalactone.Additional file 2: Supplementary Figure 2. LCMS spectra of purified bioactive compound phomalactone.Additional file 3: Supplementary Figure 3. Proton (1H) NMR Spectra of purified bioactive compound phomalactone.Additional file 4: Supplementary Figure 4.13C NMR Spectra of purified bioactive compound phomalactone.Additional file 5: Supplementary Figure 5. FT-IR Spectra of purified bioactive compound phomalactone."} +{"text": "Escherichia coli is the causative agent of diarrhea in infants and animals worldwide. Many isolated strains recovered from pigs with postweaning diarrhea are multidrug resistance (MDR), and hybrids of E. coli are potentially more virulent, as enterotoxigenic E. coli (ETEC)/Shiga-toxigenic E. coli (STEC) hybrids. Here, we used whole-genome sequencing to analyze clinical isolates of the five colistin-resistant E. coli. The E. coli CAU15104, CAU15134, and CAU16060 belonged to ETEC/STEC hybrids, displaying the same serotype O3:H45 and sequence type ST4214. The E. coli CAU16175 and CAU16177 belonged to atypical enteropathogenic E. coli (aEPEC), display O4:H11 and O103:H2, ST29, and ST20, respectively. The E. coli CAU16175 carries six plasmids. An IncHI2-type plasmid, pCAU16175_1, harbors an IS26-enriched MDR region, which includes 16 antimicrobial-resistant genes. An IncFII-type plasmid, pCAU16175_3, harbors mcr-1.1, tet(M), and blaTEM\u22121B, whereas mcr-1.1 is located within a Tn2 derivative. Our findings indicate that the ETEC/STEC strains of the O3:H45 serotype as well as the aEPEC strains of the O4:H11 and O103:H2 serotypes are associated with postweaning diarrhea in swine and that some of diarrheagenic E. coli contains IS26-enriched MDR region and the mcr-1 gene located within a Tn2 derivative on IncFII plasmid.Diarrheagenic Escherichia coli (DEC) is a leading cause of infectious diarrhea in humans and animals around the world (E. coli has six well-described pathotypes: enteropathogenic E. coli (EPEC), which is subdivided into typical EPEC (tEPEC) and atypical EPEC (aEPEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli, enteroaggregative E. coli, diffusely adherent E. coli, and enterohemorrhagic E. coli, which is subgroup of Shiga-toxigenic E. coli (STEC) encoded by ltc, and heat-stable enterotoxin (ST) encoded by st (stx2e (E. coli strains are defined as forming the attaching and effacing (A/E) lesions mediated by genes located on the locus of enterocyte effacement (LEE) pathogenicity island (including eae) in the intestinal epithelium but not produce Shiga-like toxin (Stx) are present during PWD , 4. All i (STEC) . Enteroted by st . In pigst (stx2e . Enteropin (Stx) . Moreoveand stx\u2212 . Three pring PWD , 10. Thering PWD . Atypicaring PWD .E. coli isolates, 94.15% of the strains were MDR, with antimicrobial resistance rates ranging from 2.34% for meropenem to 90.05% for nalidixic acid Gram-negative Enterobacteriaceae has been increasing worldwide between humans and animals . In the xic acid . Among tmcr-1), which has received widespread attention in different species of Enterobacteriaceae found in animals and humans around the world since it was first reported (mcr-1 (mcr-2 to mcr-10) have been detected (mcr-1 (mcr-1.1 to mcr-1.22), mcr-2 (mcr-2.1 to mcr-2.3), mcr-3 (mcr-3.1 to mcr-3.30), mcr-4 (mcr-4.1 to mcr-4.6), mcr-5 (mcr-5.1 to mcr-5.4), and mcr-8 (mcr-8.1 and mcr-8.2) (E. coli isolates (mcr-1 were higher than the rates of mcr-1\u2013positive E. coli (64.6 vs. 49.2%) .26 and Tn2, which is a member of the IS6 family and Tn3 family, respectively, play a key role in the dissemination of antimicrobial-resistant genes in Gram-negative bacteria and transposons (Tns), arguably most numerous autonomous transposable elements, are crucial to shape their host genomes, particularly important in the bacterial antimicrobial resistance . IS26 anbacteria , 26. IS2 of IS26 . Tn2 is E. coli. . ISSwi1-with Tn2 . ISApl1,of mcr-1 , 30.E. coli isolates recovered from pigs with PWD and to characterize the complete sequence of a Tn2 derivative carrying mcr-1.1 on IncFII plasmid, pCAU16175_3, from a swine aEPEC isolate.In the present study, we used whole-genome sequencing (WGS) to analyze virulence and resistant genes of the five clinical colistin-resistant E. coli strains were obtained from feces samples or small intestinal content from pigs with diarrhea in China between 2014 and 2016 and identified with polymerase chain reaction (PCR) amplification of the uspA gene based on the multilocus sequence typing and caused severe damage to IPEC-J2 cells , and two MDR aEPEC isolates (E. coli CAU16175 and CAU16177) were randomly chosen for WGS.A total of 455 Escherichia coli ATCC 25922 was used as the quality control. According to the MIC determined for each antimicrobial, the isolates were defined as \u201csusceptible,\u201d \u201cintermediate,\u201d or \u201cresistant.\u201dThe susceptibility of the five isolates to 18 antimicrobials were tested by determining the minimum inhibitory concentration (MIC) using the US Clinical and Laboratory Standards Institute (CLSI) broth micro method . The resE. coli isolates and further used WGS by the Oxford Nanopore Technologies MinION platform to get complete genome of the E. coli CAU16175.Bacterial isolates were recultured from stock; DNA was extracted using a TIANamp Bacteria DNA kit . We used WGS by the Illumina Hiseq platform to get draft genome of the five https://cge.cbs.dtu.dk). Insertion sequence typing was carried out using the ISFinder database (https://www-is.biotoul.fr/). The complete genome sequences were initially annotated with Rapid Annotation using the Subsystem Technology server (http://rast.nmpdr.org) and curated manually using the BLAST server (https://blast.ncbi.nlm.nih.gov/Blast). The obtained plasmid sequences were aligned with homologous plasmid sequences from NCBI using the BRIG tool . The serotype, multilocus sequence type, plasmid type, antimicrobial-resistant gene, and virulence gene detection were performed using the Center for Genomic Epidemiology server (RIG tool .E. coli CAU16175 as the donor and the E. coli J53 (resistant to sodium azide) as the recipient. The transconjugant was screened on BHI agar plates containing sodium azide (150 mg/L) and colistin (4 mg/L). The presence of mcr-1 in the transconjugant was confirmed by PCR, and the MICs of antimicrobial agents for the transconjugant were determined using the agar dilution method. The conjugation experiment was repeated three times, and the conjugation frequencies were calculated as the number of transconjugants per recipient. The transconjugant strains were distinguished from donor occurring natural mutants of sodium azide\u2013resistant E. coli by verifying eae, which is marker gene for E. coli CAU16175 donor.The conjugation experiment was carried out using the E. coliCAU15104, CAU15134, CAU16060, and CAU16177 isolates have been deposited at GenBank under SRA accession no. SRR10828049, SRR10828048, SRR10828047, and SRR10828046, respectively. The complete genome sequences of the E. coli CAU16175 have been deposited at GenBank under SRA accession no. SRR10813965.The draft genome sequences of the Antimicrobial susceptibility testing of the five isolates showed that they were MDR exhibiting resistant to at least three different classes of antimicrobials . All theE. coli CAU15104, CAU15134, and CAU16060 belonged to ETEC/STEC hybrid strains, display the same serotype O3:H45 and sequence type ST4214, which are identical sequence type with the strains swine19 (LVMV00000000), swine22 (LVMY00000000), swine54 (LVMV00000000), and swine67 (LVOR00000000) from the NCBI database, all carrying fedA, fedF, iha, stb, ltcA, sepA, stx2A, and stx2B virulence genes and antimicrobial-resistant genes conferring resistant to KAN (aph(3\u2032)-Ia), STR , TE [tet(A) and tet(M)], SXT and PB (mcr-1.1) and aac(6\u2032)Ib-cr (associated to quinolone and aminoglycoside antibiotic). The E. coli CAU15134 and CAU16060 carry dfrA1 (associated to SXT), mcr-3.1 (associated to PB), oqxA, and oqxB, which are efflux pump conferring antibiotic resistance, and exhibit resistant to AMP associated to blaTEM\u22121B.The clinical isolates of the mcr-1.1) , 2. Besitibiotic . The E. E. coli CAU16175 and CAU16177, belonged to aEPEC , display different serotype and sequence type, O4:H11 and O103:H2, ST29 and ST20, respectively. They both carry cif, eae, espA, espB, espJ, gad, iss, nleB, and tir virulence genes and antimicrobial-resistant genes conferring resistance to beta-lactam antibiotic (blaOXA\u22121), KAN (aph(3\u2032)-Ia), GEN (aac(3)-IVa), STR (aadA1 or aadA2 or strA or strB), TE [tet(A) and/or tet(M)], SXT , and PB (mcr-1.1 and/or mcr-3.1) (E. coli CAU16175 and CAU16177 both carry aac(6\u2032)Ib-cr (associated to quinolone and aminoglycoside antibiotic), aph(4)-Ia (associated to aminoglycoside antibiotic), ARR-3 (associated to rifamycin antibiotic), catB3, cmlA1, and floR (associated to phenicol antibiotic) .The clinical isolates of the mcr-3.1) , 2. In aibiotic) . InteresE. coli CAU16175 has a total GC content of 50.47% with a single chromosome and six plasmids. The 5.62 Mb chromosome has a GC content of 50.66%. The six plasmids sequences of E. coli CAU16175 range in length from 6.99 to 190.22 kb with a GC content from 47.10 to 51.35% (mdf (A) antimicrobial-resistant gene. The pCAU16175_1 (IncHI2 type) harbors an IS26-enriched MDR region, which includes blaOXA\u22121 and 15 additional antimicrobial-resistant genes. The pCAU16175_2 (IncFIB type) harbors katP, sepA, and perA virulence genes. The pCAU16175_3 (IncFII type) harbors mcr-1.1, tet(M), and blaTEM\u22121B antimicrobial-resistant genes. The pCAU16175_5 harbors celb virulence gene (The 6.07-Mb complete genome of o 51.35% . The chrnce gene .mcr-1) increased to 8 and 16 mg/L, respectively database. An overall nucleotide sequence identity (99.66\u201399.86%) with query coverages of 90\u201399% to pSH16G4498 (MH522423), pSH16G2457 (MH522421), pHNYJC8 (KY019259), pHNLDF400 (KY019258), pHXY0908 (KM877269), and other 25 IncHI2-type plasmids were observed (6 family insert sequences (IS26/IS15DI/IS15DIV/IS1006/ISEc59) . The structure of the MDR region comprises twelve IS6 family insert sequence that flank containing different antimicrobial-resistant genes. The MDR region contains floR, sul2, aph(4)-Ia, aac(3)-IVa, aac(6')-Ib-cr, blaOXA\u22121, catB3, ARR-3, sul1 (two copies), dfrA12, aph(3')-Ia, sul3, aadA1, cmlA1, aadA2b, and tet(A). The MDR region is also interspersed with a number of different mobile elements including \u0394TnAs3, \u0394ISVsa3, ISVsa3, ISAba1, \u0394Tn5393, \u0394Tn2, \u0394IS15, and \u0394TnAs1.The 190.22-kb plasmid observed . We chos/ISEc59) . The pCAin China . In the pCAU16175_3 was blasted against the GenBank Nucleotide collection (nr/nt) database. An overall nucleotide sequence identity (94.46\u201397.88%) with query coverages of 80\u201389% to pEC1515-3 (CP021847), pEC974-3 (CP021843), pH1038-142 (KJ484634), pFORC_081_1 (CP029058), plasmid R1 (KY749247), and other 27 IncFII-type plasmids were observed (mcr-1pKP81-BE (KU994859) for comparison analysis , which are close to the mcr-1.1 gene.The 76.63-kb plasmid observed . We chosanalysis . Althoug2 derivative (mcmM (encoded microcin M). A five-nucleotide direct duplication (TATTT) was identified flanking the structure. Unlike the Tn2, this structure harbors mcr-1\u2013pap2-\u0394ISApl1 and IS1X2-hp-tet(M)-IS15DI, deletes the resolvase (tnpR), and truncates the transposase (tnpA). Besides, the striking features of the insertion sites of ISApl1 were found, which includes high AT content and 2-bp direct repeats (DRs) (AA) (AA) . From thRs) (AA) . The mcrE. coli isolates recovered from feces samples or small intestinal content from pigs with diarrhea in China between 2014 and 2016 to know the E. coli pathotype and the antimicrobial susceptibility of the isolates -Ia), phenicol-resistant genes (cmlA1 and floR), tetracycline-resistant genes [tet(A) and tet(M)], trimethoprim-resistant gene (dfrA12), sulfonamide-resistant genes , streptomycin-resistant genes (strA and strB), and colistin-resistant genes (mcr-1.1). The ST4214 ETEC/STEC also harbored fimbrial adhesin genes (fedA and fedF), adherence gene (iha), heat-labile enterotoxin (LT) gene (ltcA), heat-stabile enterotoxin (ST) gene (stb), Shigella extracellular protein gene (sepA), and Shiga toxin 2 variant e genes (stx2A and stx2B). We observed the ST4214 strains were recovered from different provinces and years in China, which indicated this clone strains have spread in swine and should be brought to our attention.The clinical isolates of the ype ST10 . In the E. coli CAU16175 and CAU16177 belonged to aEPEC, displaying different serotype and sequence type, O4:H11 and O103:H2, ST29 and ST20, respectively. For aEPEC, serotypes O45 and O123 are frequently occurring in diarrheagenic pigs , aminoglycoside-resistant genes (aac(3)-IVa, aac(6\u2032)Ib-cr, aph(3\u2032)-Ia and aph(4)-Ia), phenicol-resistant genes , tetracycline-resistant genes [tet(A)], trimethoprim-resistant gene (dfrA12), sulfonamide-resistant genes , rifampicin-resistant gene (ARR-3), and colistin-resistant genes (mcr-1.1). Interestingly, E. coli CAU16177 also harbored mcr-3.1. Four mcr-1\u2013 and mcr-3-positive E. coli have been reported, and three E. coli isolates were recovered from pigs , non\u2013LEE-encoded effector gene (nleB), glutamate decarboxylase gene (gad), increased serum survival gene (iss), a marker gene for EPEC, intimin gene (eae), and translocated intimin receptor gene (tir).In addition, the clinical isolates of the nic pigs , 42. TheE. coli CAU16175 carries IS26-enriched MDR region in pCAU16175_1 (IncHI2 type). The IncHI2-type plasmids have been discovered as genetic elements mediating the transmission of MDR genes . The emergence of the mcr-1 gene can be traced back to the E. coli isolated in the 1980s, and the outbreak of chicken-derived mcr-1\u2013containing E. coli started in 2009 , we noticed the mcr-5 gene and the mcr-3.6 gene could be mobilized by Tn6452 and Tn6518 (belonged to Tn2 family). For the Tn6452, the mcr-5 gene was embedded within a Tn3-family Tn with 38-bp inverted repeats and flanked by 5-bp DRs, which were usually generated during the insertion can be found below: The animal study was reviewed and approved by the Animal Ethics Committee of the China Agricultural University under the protocol CAU20140616-1.LG and YZ conceived and designed the experiments. LG, JW, SW, JS, and XW performed the experiments. LG analyzed the sequencing data and wrote the manuscript. YZ revised the manuscript. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Hibiscus schizopetalus (Dyer) Hook.f. is an ornamental plant. The aim was to investigate its antimicrobial and antioxidant activities. In vitro antiviral, antibacterial, and antioxidant activities of the 70% ethanolic extract (Et-E) of the aerial parts of the plant were determined. The Dichloromethane Fraction (DCM-F) and the n-Butanol Fraction (Bu-F) were assessed using Liquid chromatography\u2013mass spectrometry (LC-MS). The DCM-F showed higher antiviral activities against Coxsackie B4 (CoxB4) viruses (IC50 = 64.13 \u00b5g/mL) and adenoviruses (IC50 = 54.88 \u00b5g/mL) than acyclovir . The DCM-F showed higher anti-helicobacter pylori activity (MIC = 3.9 \u00b5g/mL) than clarithromycin (MIC = 1.95 \u00b5g/mL). The DCM-F inhibited Herpes Simplex Virus (HSV) Type I (IC50 = 29.85 \u00b5g/mL) and HSV Type II (IC50 = 74.17 \u00b5g/mL). The Bu-F showed higher anti-mycobacterial activity (MIC = 7.81 \u00b5g/mL) than isoniazid (MIC = 0.24 \u00b5g/mL) and higher antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA)(MIC = 7.81 \u00b5g/mL) than vancomycin (MIC = 3.9 \u00b5g/mL). Antioxidant assays included total antioxidant capacity (TAC), 2,2\u2032-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS), 2,2-diphenyl-1-picryl-hydrazyl (DPPH), and iron reducing power. The Bu-F showed the highest antioxidant activity. Chemical profiles were analyzed using HPLC-HR\u2013ESI\u2013MS to identify the metabolites responsible for these biological activities. We identified more than 60 metabolites that belong to anthocyanins, flavonoids, phenolics, terpenes, sterols, and fatty acids. In conclusion, Hibiscusschizopetalus is endowed with metabolites that could be used against viruses and antibiotic-resistant bacteria. They can also be potent antioxidants. Antimicrobial resistance to classical antibiotics is a major problem that negatively impacts treatments of common infectious diseases caused by fungi, bacteria, viruses, and parasites. In order to overcome this major problem, natural products offer a viable alternative .Hibiscus is a member of Malvaceae family and is cultivated globally as an ornamental and medicinal plant -2,5-diphenyl tetrazolium bromide (MTT) was performed spectrophotometrically using a Perkin-Elmer ELISA reader (HTS 7000 plus) at 540 nm . The minimum concentration required for the inhibition of bacterial growth (MIC) and the concentration required for inhibition of 90% of the bacterial growth (MIC90) were determined from the corresponding dose-response curve. The MTT assay was done using an automatic BioTek plate reader at 620 nm. Activity against n method . H. pyloM. tuberculosis (M. Tub ATCC 27294) was detected using the Microplate Alamar Blue Assay (MABA) [M. tuberculosis inoculum (105 CFU/mL) was added. Plates were incubated at 37 \u00b0C for 4 days, then 20 \u03bcL of Alamar Blue solution and 12.5 \u03bcL of 20% Tween 80 were added. The plates were re-incubated at 37 \u00b0C for 24 h. The color intensity was measured using an ELISA microplate reader at 590 nm. The experiment was done in triplicates.The anti-mycobacterial activity against y (MABA) . Isoniaz(MRSA ATCC 27294) was assessed using the microdilution method in the presence of tetrazolium salts [6 CFU/mL), and 50 \u03bcL of the sample dilutions (0.24\u2013125 \u03bcg/mL) were added. The plates were incubated at 37 \u00b0C for 24 h. To each well, 40 \u03bcL of XTT were added and incubated for 1 h in the dark at 37 \u00b0C. For each well, the color intensity was measured at 492 nm.The anti-MRSA activity um salts . VancomyA.Total antioxidant capacity assay (TAC).The antioxidant activity of the samples was assessed using the phosphomolybdenum method ,49. AbsoB.2,2\u2032-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) radical scavenging assay.Hibiscus extract and its fractions [The ABTS radical scavenging assay was used to assess the free radical scavenging activity of the ractions ,49. MeasC.2,2-diphenyl-1-picryl-hydrazyl (DPPH) radical scavenging assay.The anti-oxidant activity was measured as previously described AbsorbanD.Reducing power assay.The reducing power was assessed by the evaluating the ability of the samples to change potassium ferricyanide to potassium ferrocyanide. Absorbance was measured at 700 nm ,49. The Experiments for antioxidants were done in triplicates and means were calculated.m/z 150\u20131500. The crude methanolic extract and fractions for mass spectrometry were prepared at 1 mg/mL. Metabolomic analysis of the samples was done using LC-HR-ESI-MS ,51. We uThe data were imported and analyzed using MZmine 2.20 . The masp < 0.05.Data analysis was done using analysis of variance (ANOVA). The significance of differences between means was done using Duncan\u2019s multiple range tests at H. schizopetalus is endowed with a lot of chemical compounds (more than 60 metabolites) that could be clinically used in fighting viruses, such as adenoviruses, HSVI, and CoxB4. They can also be used as effective therapies against antibiotic resistant pathogens such as M. tuberculosis, MRSA, and H. pylori. Finally, they can be potent antioxidants that can protect cells from free radical damage in cancer, heart diseases, and other serious health conditions."} +{"text": "Tumor metastasis accounts for the majority of cancer-related deaths; it is therefore important to develop preclinical models that faithfully recapitulate disease progression. Here, we generated paired organoids derived from primary tumors and matched liver metastases in the same colorectal cancer (CRC) patients. Despite the fact that paired organoids exhibit comparable gene expression and cell morphology, organoids from metastatic lesions demonstrate more aggressive phenotypes, tumorigenesis, and metastatic capacity than those from primary lesions. Transcriptional analyses of the paired organoids reveal signature genes and pathways altered during the progression of CRC, including SOX2. Further study shows that inducible knockdown of SOX2\u00a0attenuated invasion, proliferation, and liver metastasis outgrowth. Taken together, we use patient-derived paired primary and metastatic cancer organoids to model CRC metastasis and illustrate that SOX2 is associated with CRC progression and may serve as a potential prognostic biomarker and therapeutic target of CRC. To the Editor,Tumor heterogeneity plays a key role in cancer progression and therapy resistance . HoweverInvasion is a fundamental step in tumor progression toward metastasis. To study collective invasion, we cultured paired organoids in a 3D invasion matrix Fig. a. AlthouP < 0.05; fold change > 2.5) that were significantly upregulated in metastatic organoids inducible expression of shRNA targeting SOX2 was established in metastatic organoids Fig. SC and D. nes Fig. E-G. Furtnts Fig. H. We thents Fig. . Taken tIn summary, the present study highlights the potential of patient-derived paired primary and metastatic cancer organoids as an experimental model for investigating CRC progression. We identified a significantly dysregulated gene between paired organoids, SOX2, which could be a prognostic biomarker, and perhaps a potent therapeutic target in the treatment of CRC.Additional file 1: Supplementary\u00a0Table S1. Summary of patient-derived CRC organoid lines and corresponding clinical data.Additional file 2: Supplementary Figures. Figure S1. Paired organoids derived from primary and metastatic CRC recapitulate the histopathological structure of parental tumor. A and B, Organoids architecture resembles parental tumor epithelium. Representative bright-field images of organoids together with H&E staining of parental tumors and patient-derived organoids. The scale bar represents 100 \u03bcm. C and D, Representative IHC sections for the intestinal epithelial marker CDX2. The scale bar represents 100 \u03bcm. Figure S2. Organoids derived from liver metastatic lesions exhibited the most aggressive phenotypes with significant high tumorigenic and metastatic potential. A, Representative micrographs of organoids in 3D invasion assay. Tumor organoids showed the smooth and protrusive leading fronts, respectively. B, Micrographs of the paired organoids stained with phalloidin\u2013F-actin (right). The scale bar represents 100 \u03bcm. C, qRT-PCR analysis of MMP-2 in paired organoid lines. Error bars indicate SEMs. *P=0.0207, **P =0.0083, ***P=0.0008 , ***P=0.0006 . D, Western blot analysis of the MMP-2 protein expression in paired organoid lines. \u03b1-tubulin was used as a loading control. E, Representative IHC sections for Ki67 in human colorectal tumor tissues and paired organoid lines. The scale bar represents 100 \u03bcm. F, Representative IHC sections for Ki67 in organoid xenografts and organoids derived from xenografts. The scale bar represents 100 \u03bcm. G, Representative gross image, histopathology and Ki67 staining of whole liver from primary organoid xenografts. The scale bar of the whole liver represents 1cm. The black scale bar represents 100 \u03bcm. Figure S3. A, Representation of the up-regulated genes in 13L organoids. Error bars indicate SEMs. *P = 0.0283, ***P = 0.0004, ****P < 0.0001 (one-way ANOVA). B, qRT-PCR analysis of the up-regulated genes in 13L organoids. Values were normalized to mean levels in 13a organoids. Error bars indicate SEMs. *P=0.02, ***P=0.0008 ****P < 0.0001 (one-way ANOVA). C, RNA sequencing analysis of SOX2 in human colorectal cancer tissues and normal colon tissues. D, qRT-PCR analysis of SOX2 in tumor tissues and paired normal colon tissues. Values were normalized to mean levels in normal colon tissues. Error bars indicate SEMs. **P = 0.0018, ****P < 0.0001 (one-way ANOVA). E, Western blot analysis of the SOX2 protein expression in tumor tissues and paired normal colon tissues. \u03b1-tubulin was used as a loading control. F, Representative IHC sections for SOX2 in human colorectal tumor tissues and paired normal colon tissues. The scale bar represents 100 \u03bcm. Figure S4. Silencing SOX2 in metastatic organoids attenuated cell invasion and proliferation and suppressed liver metastasis in vivo. A, qRT-PCR analysis of SOX2 in paired organoid lines (left). Values were normalized to mean levels in 21a organoids. Error bars indicate SEMs. ****P < 0.0001(Unpaired t test). Western blot analysis of the SOX2 protein expression in paired organoid lines. \u03b1-tubulin was used as a loading control (right). B, Representative IHC sections for SOX2 in human colorectal tumor tissues and organoids. The scale bar represents 100 \u03bcm. C, qRT-PCR analysis of SOX2 in the 13L-shRNA-1/2 (left) and 21L-shRNA-1/2 (right) organoids after 3 days of Dox-induction. The level of SOX2 was compared to that in the untreated sample. Error bars indicate SEMs. ***P=0.0001, ****P < 0.0001 (two-way ANOVA). D, Western blot analysis of the expression of SOX2 in the 13L-shRNA-1/2 and 21L-shRNA-1/2 organoids after 3 days of Dox-induction. \u03b1-tubulin was used as a loading control. E, Representative micrographs of Dox-transduced the 21L-shRNA-1/2 organoids after 5 days and stained with phalloidin\u2013F-actin. The scale bar represents 100 \u03bcm. F, Proliferation of the 21L-shRNA-1/2 organoids were examined by CTG cell viability assays following 3- or 5-days growth in the presence or absence of Dox. Error bars indicate SEMs. **p=0.0019, ****P < 0.0001 (two-way ANOVA). G, Representative micrographs of colonies arising from the 21L-shRNA-1/2 organoids (top), with magnified insets showing colonies (bottom). The scale bar represents 200 \u03bcm. Colony forming efficiency in G was calculated and compared (right). Error bars indicate SEMs. **P=0.0015 (two-way ANOVA). H, Representative Ki67 immunostaining of liver metastases of the 13L-shRNA-1/2 organoids (left) and ratio of Ki67-positive tumor cells in liver metastases (right). Scale bars, 200 \u03bcm (top) and 100 \u03bcm (bottom). Each dot indicates individual mice. Error bars indicate SEMs. *p=0.0197, **P=0.0044 (two-way ANOVA). Figure S5. SOX2 is overexpressed in primary organoids. A, qRT-PCR analysis of SOX2 in primary organoid lines. Values were normalized to mean levels in control organoids. Error bars indicate SEMs. ****P < 0.0001 (one-way ANOVA). B, Western blot analysis of the SOX2 protein expression in primary organoid lines. \u03b1-tubulin was used as a loading control. C, Representative micrographs of colonies arising from the control, LV-Vector and LV-SOX2 primary organoid lines. The scale bar represents 200 \u03bcm. D-F, Colony forming efficiency in C was calculated and compared. Error bars indicate SEMs. ***P=0.0008, ****P < 0.0001 (one-way ANOVA). G, Proliferation of the control, LV-Vector and LV-SOX2 primary organoid lines were examined by CTG cell viability assays. Error bars indicate SEMs. ***P=0.0008, ****P < 0.0001 (one-way ANOVA). H, Representative micrographs of organoids in 3D invasion assay. Arrowheads, protrusive leading fronts. Micrographs of the paired organoids stained with phalloidin\u2013F-actin. The scale bar represents 100 \u03bcm.Additional file 3. Supplementary Materials and Methods."} +{"text": "Correction to: Mol Neurodegeneration 15, 34 (2020)https://doi.org/10.1186/s13024-020-00383-7The original article [incorrectly displays 6th author, Bj\u00f6rn Oskarsson\u2019s name with middle initial. The correct presentation can be viewed in this Correction article. article incorrec"} +{"text": "In this study, we investigated the presence of carbapenemase genes, mcr-1, and tet(X) in 298 Escherichia coli strains obtained from a teaching hospital in China. In total, eight (2.68%), six (2.01%), and one (0.34%) E. coli isolates carried blaNDM, mcr-1, and tet(X4), respectively. The blaNDM gene was located on IncX3 (n = 4), F2:A-:B- (n = 3), and F2:A1:B1 (n = 1) plasmids, with high similarity to multiple plasmids belonging to the same incompatibility type from Enterobacteriaceae. Six MCR-producing strains contained mcr-1-carrying IncI2 plasmids, organized similarly to other mcr-1-bearing IncI2 plasmids from animals in China. The blaCTX\u2212M\u221255/64/132/199 gene located within a typical transposition unit (ISEcp1-blaCTX\u2212M-orf477\u0394) was inserted near dnaJ to generate 5-bp direct repeats in four mcr-1-positive plasmids. The tet(X) and another four resistance genes were co-located on an IncX1 plasmid, highly similar to other tet(X4)-carrying IncX1 plasmids from Escherichia and Klebsiella of animal or food origin, except that the conjugative transfer region of IncX1 plasmids was absent in our plasmid. Although a low prevalence of blaNDM, mcr-1, and tet(X) was observed in E. coli from patients in this study, their dissemination associated with some successful pandemic plasmids is of great concern. The continued surveillance of these crucial resistance genes in patients should be strengthened.The emergence and spread of carbapenemase genes, colistin resistance genes Escherichia coli as the leading pathogen bacteria are rapidly increasing, which poses a serious threat to clinical therapy and public health WHO, . In 2019Escherichia coli is one of the predominant carriers of blaNDM; some lineages, such as ST167, ST410, and ST617, and popular plasmids are associated with blaNDM global dissemination in E. coli in E. coli from pigs in China can reduce the clinical efficacy of these agents gene has recently been increasingly reported in E. coli from different sources , mainly in China in E. coli , and carbapenemases in human or animal gut microbiomes , and carbapenemases is worrisome, as options for therapy are limited. Therefore, there is an urgent need for evaluating and monitoring the prevalence of pathogenic bacteria carrying mcr, tet(X), and carbapenemases. In this study, we investigated the prevalence and characterization of mobilized resistance genes tet(X4), mcr-1, and blaNDM in E. coli strains isolated from a teaching hospital in Jiangsu Province, China.A previous study reported the discovery of E. coli strains were isolated from patients in a teaching hospital in Jiangsu Province, China. The presence of tet(X), mcr-1, and carbapenemase genes was detected by PCR and sequencing according to previously described protocols -carrying E. coli is described in From November 2019 to November 2021, 298 non-duplicate blaNDM/mcr-1/tet(X)-carrying E. coli isolates were tested for susceptibility to 14 antimicrobial agents, namely, ampicillin, cefotaxime, meropenem, gentamycin, amikacin, streptomycin, tetracycline, tigecycline, chloramphenicol, nalidixic acid, ciprofloxacin, colistin, fosfomycin, and sulfamethoxazole/trimethoprim, by using the agar dilution method or broth microdilution method (limited to colistin and tigecycline). E. coli ATCC 25922 was used as the quality control strain. The results were interpreted according to Clinical and Laboratory Standards Institute (CLSI) M100, 30th edition .The on CLSI, . StreptoblaNDM/mcr-1/tet(X)-carrying E. coli isolates as donor bacteria and E. coli C600 (high-level streptomycin resistance) as the recipient strain following a previously described protocol , colistin (for mcr-1), or tigecycline [for tet(X)]. They were further confirmed by detecting the presence of blaNDM, mcr-1, and tet(X) using PCR. Transfer frequencies were calculated as the number of transconjugants per recipient. Conjugation experiments were performed at least in triplicate.Conjugation experiments were performed using blaNDM/mcr-1/tet(X)-carrying E. coli isolates using a TIAN amp Bacteria DNA kit and sequenced by the Illumina Hiseq platform. The 150 bp pair-end raw reads were trimmed with the NGSQC toolkit v.2.3.3 and assembled into contigs using SPAdes v.3.8.2 , XYEH3783 (blaNDM \u2212 5), and XYEH3934 [tet(X4)], were sequenced using Nanopore MinION and assembled with Unicycler version 0.4.9. The remaining blaNDM/mcr-1-carrying plasmid contigs were assembled into a complete plasmid sequence using PCR and Sanger sequencing (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The genome sequences were analyzed for multi-locus sequence typing (MLST) and resistance genes using MLST and ResFinder, respectively (https://cge.food.dtu.dk//services). Analysis and annotation of all blaNDM/mcr-1/tet(X4)-carrying plasmids were performed using the RAST server , ResFinder, PlasmidFinder (https://cge.food.dtu.dk/services/PlasmidFinder/), BLAST, and the Gene Construction Kit 4.5 . Blast Ring Image Generator (BRIG) version 0.95 was used to visualize the blaNDM-carrying plasmid comparisons -positive E. coli strains and blaNDM-positive E. coli ST167 in this study and the NCBI database was constructed based on core genome single nucleotide polymorphisms (SNPs) using ParSNP v. 1.2 (https://github.com/marbl/parsnp), respectively. ChiPlot (http://chiplot.online/#) was used to visualize the phylogenetic tree.The phylogenetic tree of all blaNDM/mcr-1/tet(X4)-carrying plasmids have been deposited in GenBank under accession number PRJNA901528.The genome sequences and blaNDM gene has been globally distributed as the third most common carbapenemase-encoding gene or blaNDM \u2212 6 (n = 1) (E. coli were resistant to meropenem (MIC \u2265 8 mg/L), ampicillin, cefotaxime, gentamicin, tetracycline, chloramphenicol, nalidixic acid, ciprofloxacin, and sulfamethoxazole/trimethoprim , ST167 (n = 2), ST361 (n = 1), and ST1193 (n = 1), respectively . None ofethoprim . Resistaectively . E. coliecipient .blaNDM gene was located on IncX3 (n = 4), F2:A-:B- (n = 3), and F2:A1:B1 (n = 1) plasmids were obtained from four ST156 NDM-5-producing E. coli strains. These IncX3 plasmids were identical, except that two copies of IS1294 were inserted into the accessory replication gene bis and DNA relaxase gene taxC, respectively, in pYUXEEH1271-NDM and pYUXEEH1278-NDM of animal or human origin and F2:A1:B1 plasmid pYUXYEH3783-NDM . These IncFII plasmids showed high similarity to multiple plasmids belonging to the same incompatibility type from Enterobacteriaceae from food-producing animals or humans have been identified in Enterobacteriaceae from animals, humans, and the environment , ampicillin, cefotaxime, nalidixic acid, ciprofloxacin, and some other agents , tet(A) (n = 3), fosA3 (n = 3), and rmtB (n = 1) (All r agents . In addi (n = 1) . The pre (n = 1) .mcr-1-positive E. coli strains could transfer mcr-1 to E. coli C600 by conjugation with frequencies of 10\u22126 to 10\u22124 transconjugants/recipient from E. coli and pSCS23 from Salmonella , was inserted near dnaJ to generate 5-bp direct repeats (5\u2032-GAAAA-3\u2032) . The blaAAAA-3\u2032) . The co-tet(X4) in E. coli from pigs in China in 2019 has been rarely reported in E. coli from patients. It was detected in 4.5% fecal samples of hospital patients in Guangdong province, and only 0.07% E. coli isolates from patients in China were identified to carry tet(X4) -positive E. coli isolate, XYEH3934. This strain exhibited high-level tigecycline resistance (MIC = 32 mg/L) and was also resistant to ampicillin, cefotaxime, streptomycin, tetracycline, chloramphenicol, nalidixic acid, fosfomycin, and sulfamethoxazole/trimethoprim (tet(X4) to E. coli C600 by conjugation.Since the discovery of the plasmid-mediated tigecycline resistance gene ethoprim . Howevertet(X) and another four resistance genes were co-located on an IncX1 plasmid pYUXYEH3934-2 with a size of 31,816 bp. It was highly similar to other tet(X4)-carrying IncX1 plasmids from porcine E. coli in China, such as plasmids pYUYZMP62 (MW439254) and pDW28-tet(X4) (ON390803), as well as tet(X4)-positive plasmids from Escherichia and Klebsiella (tet(X4) was also associated with ISCR2 in pYUXYEH3934-2 (tet(X4) is mainly mediated by the horizontal transfer of insertion sequences and plasmids such as IncX1 in the present study -positive E. coli strains has been previously described, such as E. coli ST877, ST10, and ST48 between animals and humans and four plasmids . Among tebsiella . Howeverebsiella , which mebsiella , tet(X4)EH3934-2 . The rap Aminov, . HoweverblaNDM/mcr-1/tet(X4)-positive E. coli isolates in the present study. The results showed that the 15 E. coli strains were divided into four clades and Italy (n = 1) were clustered in one clade with a close relationship was observed in E. coli isolates from patients in one hospital in this study, their dissemination in E. coli associated with some successful pandemic plasmids is of great concern. Conversely, E. coli strains from food or food-producing animals in China show a higher prevalence of blaNDM, mcr-1, and tet(X) can be found below: LS and JW conceived the study. LS, G-ZS, YJ, C-YM, H-YW, and G-MK carried out the experiments. LS, YJ, Z-YW, and JW analyzed the data. JW wrote the manuscript. XJ revised the manuscript. All authors have read and approved the final version of the manuscript."} +{"text": "Aspergillus is a filamentous fungus renowned for its extraordinary ability to produce active natural products of high therapeutic value and economic importance. This review is the first to focus on Aspergillus-derived alkaloids. Through an extensive literature review and data analysis, 263 alkaloids are categorized according to their structural features into those containing cytochalasans, diketopiperazine alkaloids, quinazoline alkaloids, quinoline alkaloids, indole alkaloids, pyrrolidine alkaloids, and others. These metabolites exhibited diverse biological activities, such as antibacterial activity, cytotoxicity, anti-inflammatory activity, and \u03b1-glucosidase, ACE, and DPPH inhibitory activities. The bioactivity, structural diversity, and occurrence of these alkaloids are reviewed in detail.Alkaloids represent a large family of natural products with diverse structures and bioactivities. These compounds and their derivatives have been widely used in clinics to treat various diseases. The endophytic Aspergillus is one of the most widely studied filamentous fungi and renowned for its extraordinary productivity when it comes to active natural products with therapeutic values, making it of economic importance quinazoline-3,6-dione (163) and protuboxepin K (164). Compounds 153, 160\u2013164 exhibited mosaic virus TMV inhibitory activity, with IC50 values of 34.8, 37.9, 32.2, 42.4, 39.5, and 35.2 \u03bcM, respectively -L-tryptophan methyl ester (236), N-[(2S)-2hydroxy-1-oxo-3-phenylpropyl]-L-tryptophan (237), acudioxomorpholine (238), and emindole SB (239) benzodiazepine-5,11-dione (241) [The fungus ne 241) , Table 6 , Table de (242) .A. fumigatus was studied and yielded the known metabolites 14-norpseurotin (243) and pseurotin A (244). Compound 243 promoted the neurite outgrowth of PC12 cells at 10.0 \u00b5M [244 was also produced from Aspergillus sp. EJC08 associated with Bauhinia guianensis [A. fumigatus associated with Erythrophloeum fordii Oliv [A. fumigatus associated with Heteroscyphus tener (Steph.) Schiffn [A. fumigatus D associated with Edgeworthia chrysantha Lindl [Aspergillus sp. 87 [244 exhibited inhibition of S. aureus, B. subtilis, Pseudomonas aeruginosa, and E. coli, with MICs of 15.62, 31.25, 31.25, and 15.62 \u03bcg/mL, respectively [50 value of 5.20 \u00b5M [The endophyte 10.0 \u00b5M . Compounianensis , A. fumidii Oliv , A. fumi Schiffn , A. fumiha Lindl , and Asps sp. 87 . Compounectively , and inh 5.20 \u00b5M .A. fumigatus LN-4 obtained from Melia azedarach led to the discovery of 244 and pseurotin A1 (245), which demonstrated nontoxicity toward brine shrimps [A chemical study of shrimps .246), and the known compound 11-O-methylpseurotin A (247) were collected from A. fumigatus Y0107 of Crocus sativus Linn (saffron). These compounds were inactive against Pantoea agglomerans, Agrobacterium tumefaciens, Erwinia sp, and Ralstonia solanacearum [A new alkaloid, 11-acetyl-pseurotin A2 and adenine (250). Compound 248 was also isolated from A. fumigatus LN-4 obtained from Melia azedarach. Compounds 248 and 250 suppressed melanin production in B16 melanoma cells with IC50 values of 144.7 \u00b1 2.35 and 100.4 \u00b1 3.05 \u00b5M, respectively [A chemical study on unds 248 , Table 7ectively ,38.251), obtained from A. fumigatus collected from Erythrophloeum fordii Oliv. (Leguminosae), did not inhibit NO production [The known alkaloid lumichrome (oduction .Aspergillus sp. TJ23 collected from leaves of Hypericum perforatum (St John\u2019 Wort) yielded a new pyridone alkaloid, asperpyridone A (252), which improved glucose uptake in HepG2 cells at 50 \u03bcM [The endophyte at 50 \u03bcM .253) and 4-amino-2-hydroxymethylpyridin-5-ol (254) and the known compound 5-hydroxy-2-hydroxymethylpyridine-4(1H)-one (255) were obtained from A. flavus GZWMJZ-288 on Garcinia multiflora. None of them demonstrated any inhibitory activity against gram-positive S. aureus ATCC6538, S. aureus ATCC25923, MRSA, gram-negative Pseudomonas aeruginosa ATCC10145, or E. coli ATCC11775, nor against the pathogenic fungi C. albicans ATCC10231 or C. glabrata ATCC2001 at 100 \u03bcg/mL [New alkaloids 2-Hydroxymethyl-5-(3-oxobutan-2-yl)aminopyran-4(4H)-one , cyclopeptine (257), and trans-3-(3\u2032-hydroxybenzylidene)-3,4-dihydro-4-methyl-1H-1,4-benzodiazepin2,5-dione (258). None of them showed any AChE inhibitory activity [A study on activity .259), together with known compounds penipanoid A (260), and fuscoatramide (261) were obtained from A. flavipes DZ-3 of Eucommia ulmoides Oliver. These compounds were inactive against antioxidant and \u03b1-glucosidase capacities [A new alkaloid, asperflaloid B (pacities .262), obtained from the fungus Aspergillus sp. 87, was devoid of antibacterial activity [A new alkaloid, aspergilamide A -1-(4-hydroxy-phenyl)-4-(4-methoxyphenyl)buta-1,3-diene-2,3-diyl)diformamide (263) was isolated from the A. fumigatus HQD24, but it did not display inhibition of splenic lymphocyte growth [N,N\u2019-, followed by A. versicolor , A. flavipes , A. terreus , A. nidulans , other species including A. aculeatus (1), A. amstelodami (1), A. cristatus (1), A. creber (1), A. micronesiensis (1), and A. ochraceus (1), and Aspergillus unknown species . Detailed analysis revealed that the discovery probability of known alkaloids is high (61.98%) . The micrsicolor , 10.87%,82) displayed potent inhibitory activity against the human FLT3-ITD mutant AML cell line MV4-11, with an IC50 value of 0.22 \u03bcM [252) improved glucose uptake and is a potential hypoglycemic agent [The alkaloids summarized in this literature exhibited antibacterial activity; cytotoxicity; anti-inflammatory activity; and \u03b1-glucosidase, ACE, and DPPH inhibitory activities. Many of these metabolites demonstrated potent biological activity. For example, gartryprostatin C ( 0.22 \u03bcM . Asperpyic agent . HoweverAspergillus is a dominant community in natural products exploration. In this literature, the bioactivity, structural diversity, and biosources of alkaloids derived from plant endophytic Aspergillus species during January 2004 to May 2023 were described. Approximately 263 alkaloids isolated from 46 strains of Aspergillus species were reviewed according to their structural features, including cytochalasans, diketopiperazine alkaloids, quinazoline alkaloids, quinoline alkaloids, indole alkaloids, pyrrolidine alkaloids, and others. Among them, 149 alkaloids have significant physiological activities, such as antibacterial activity, cytotoxicity, anti-inflammatory activity, and \u03b1-glucosidase, ACE, and DPPH inhibitory activities. Therefore, these active alkaloids have tremendous potential as lead compounds for the exploitation of new drugs. The interdisciplinary research of chemistry, biology, and pharmacology for alkaloids derived from plant endophytic Aspergillus sp. has attributed to driving the application of alkaloids in the drug discovery and development.Plant endophytic fungi have provided abundant resources of natural products with unique structural features and diverse biological activities, which play a critical role for drug development. The plant endophytic"} +{"text": "Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) frequentThe amygdala is also preferentially affected by argyrophilic grains (AGs) and age-related tau astrogliopathy (ARTAG). AGs are age-related lesions in which four-repeat tau is selectively accumulated . AGs areAt present, the pathogenic relationship between LATE-NC, AGs, and GFAs in the amygdala remains to be elucidated. For example, although a few previous studies supported the potential relationship between LATE-NC and AGs , 4, a reTo address these issues, first, we examined whether amygdala GFAs and AGs are independent risk factors of LATE-NC in a Japanese series with a low to moderate Braak neurofibrillary tangle (NFT) stage. Then, independent pathological risk factors of the formation of AGs in this series were also explored. Finally, whether LATE-NC, AGs, and amygdala GFAs have independent effects on severe loss of neurons in the amygdala was examined.From 1,180 autopsy cases who were registered in the database at the Department of Neuropsychiatry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences as of the end of June 2023, we first selected 501 cases in which all of the following pathological data were available: Braak NFT stage, Thal phase, CERAD neuritic plaque score, LBD subtypes, Braak Parkinson\u2019s disease stage, Saito AG stage , LATE-NCFrom 501 cases, we excluded any cases having following pathologies: NFTs with Braak stages V-VI, Lewy bodies in any regions including the olfactory bulb, NFTs which quantity fit the NINDS-PSP criteria, tufted astrocytes and astrocytic plaques in any region, amyotrophic lateral sclerosis or frontotemporal lobar degeneration with TDP-43-positive or FUS-positive inclusions, Pick\u2019s disease, globular glial tauopathy, multiple system atrophy, trinucleotide repeat diseases, inflammatory diseases, leukodystrophies, and lysosomal storage diseases. Finally, 72 cases that were Braak NFT stages I-IV and Thal phases 0\u20134 but lacked any other neurodegenerative changes except for AGs, GFAs, LATE-NC, or HS which is closely associated with LATE-NC, were extracted .The mean age at death in 72 cases was 71.6\u2009\u00b1\u200911.6\u00a0years. Of 72 cases, 52 cases had GFAs in the amygdala (72.2%), and 26 had AGs (36.1%) Table : Fig. S2Four of 72 cases (5.6%) had HS Figs.\u00a0E. All HSp < 0.001, Fig. Among 72 cases, five (6.9%) had severe neuronal loss in the amygdala (Table p\u2009=\u20090.0264) and amygdala GFA stage 4 were significant predictors of LATE-NC demonstrated that the age at death and amygdala GFA stage 4 were independent risk factors of AGs revealed that the age at death was an independent risk factor of severe neuronal loss with stage 3.In the multivariate binomial logistic regression regarding tissue degeneration in the amygdala , only Saito AG stages II-III independently contribute to amygdala degeneration. Although LATE-NC was not a statistically significant factor in the present study, it might be explained by the small number of LATE-NC-positive cases in our series. Indeed, it was reported that LATE-NC was associated with the amygdala volume assessed using postmortem MRI . RegardiAdditional file 1: Fig. S1. Representative figures of neuronal loss stage in the amygdala. A\u2013C Stage 0. Neuronal loss and glial proliferation is absent. D\u2013F Stage 1. Mild neuronal loss with minimal gliosis is noted. G\u2013I Stage 2. Moderate neuronal loss with gliosis is present, but tissue rarefaction is not evident. J\u2013L Stage 3. Severe neuronal loss with remarkable glial proliferation is noted. Tissue rarefaction is also seen. Scale bars: A, D, G, J 200 \u03bcm, B, E, H, K 100 \u03bcm, C, F, I, L 50 \u03bcm.Additional file 2: Table S1. Demographic data in cases with Braak stages I-IV by LATE-NC status.Additional file 3: File S1. Supplementary file 1: Supplementary materials and methodsAdditional file 4: Fig. S2. TDP-43 pathology, granular fuzzy astrocytes (GFAs), argyrophilic grains, hippocampal sclerosis, and tissue degeneration in the amygdala in representative cases. A\u2013F Pathological findings in a case with Braak NFT stage II, Thal phase 0, amygdala GFA stage 2, Saito AG stage III, and LATE-NC stage 2. A, B Phosphorylated TDP-43 accumulation in the amygdala A and dentate gyrus in the hippocampus B. pS409/410 immunohistochemistry. Scale bar: 25 \u03bcm. C A GFA in the amygdala. AT8 immunohistochemistry. Scale bar: 25 \u03bcm. D AGs in the amygdala. Gallyas method. Scale bar: 25 \u03bcm. E Hippocampal sclerosis. Hematoxylin-eosin stain. Scale bar: 100 \u03bcm. F Severe loss of neurons with gliosis in the amygdala. Hematoxylin-eosin stain. Scale bar: 25 \u03bcm. G\u2013L Pathological findings in a case with Braak stage II, Thal phase 0, amygdala GFA stage 4, Saito AG stage III, and LATE-NC stage 0. G This case lacked phosphorylated TDP-43-positive lesion in any region. The amygdala. pS409/410 immunohistochemistry. Scale bar: 25 \u03bcm. H, I GFAs in the amygdala. AT8 immunohistochemistry. Scale bar: 25 \u03bcm. J AGs in the amygdala. Gallyas method. Scale bar: 25 \u03bcm. K Neither loss of pyramidal neurons nor gliosis is noted in the hippocampal CA1. Hematoxylin-eosin stain. Scale bar: 100 \u03bcm. L Severe neuronal loss with gliosis in the amygdala. Hematoxylin-eosin stain. Scale bar: 25 \u03bcm."} +{"text": "S-adenosylmethionine (SAM) and total cysteine (tCys) concentrations. Serum 5-MTHF concentrations demonstrated a stronger negative correlation with tHcy/tCys than with tHcy alone. The negative correlation between betaine and tHcy concentrations was stronger in the low 5-MTHF group than in the high 5-MTHF group. The 5-MTHF status could be linked to Hcy flux into the transsulfuration pathway via SAM. Therefore, the tHcy/tCys ratio may be a more sensitive indicator of the 5-MTHF status than tHcy alone. Furthermore, a low 5-MTHF status can enhance Hcy metabolism via betaine.Maintaining optimal one-carbon metabolism (OCM) is essential for health and pregnancy. In this cross-sectional study, folate status was assessed based on 5-methyltetrahydrofolate (5-MTHF) levels, and the association between 5-MTHF and OCM-related metabolites was investigated in 227 female Japanese university students aged 18\u201325 years. The participants were divided into high and low 5-MTHF groups based on their folate status. Serum samples of the participants were collected while they were fasting, and 18 OCM-related metabolites were measured using stable-isotope dilution liquid chromatography\u2013electrospray tandem mass spectrometry. The association between serum 5-MTHF and OCM-related metabolite concentrations was assessed using Spearman\u2019s rank correlation coefficient. Serum 5-MTHF concentrations were negatively correlated with total homocysteine (tHcy) concentrations and positively correlated with S-adenosylmethionine (SAM)-dependent methyl transfer reactions [One-carbon metabolism (OCM) comprises a folate cycle and choline metabolic pathway linked to a methionine cycle; homocysteine (Hcy) in the methionine cycle is connected to the transsulfuration pathway . OCM is eactions , nucleiceactions ,2, and aeactions .2-dependent MTHF reductase [S-methyltransferase , which is expressed primarily in the liver and kidneys and remethylates Hcy to produce methionine and dimethylglycine (DMG) [S-adenosylhomocysteine (SAH) [6-dependent enzyme cystathionine-\u03b2-synthase , which condenses serine to Hcy thiol [6-dependent enzyme cystathionine \u03b3-lyase to Cys [Folate mediates the transfer of one-carbon units in OCM . Folic a.5.1.20) . The maj.5.1.20) ,8. Methi.5.1.20) ,7,8. Cho.5.1.20) . Betainene (DMG) ,11. Methne (DMG) . SAM is ne (SAH) . Methylane (SAH) ,15. SAH ne (SAH) . Both thne (SAH) . Hcy is ne (SAH) ,19. Hcy cy thiol ,20. Then) to Cys ,21. Cys ) to Cys ,19.OCM metabolic markers have been linked to various diseases. Intracellular Hcy concentrations increase when OCM fails to function adequately ,22. The Previous studies have assessed folate concentrations in circulation using a microbiological assay ; howeverThe characteristics of the study population are summarized in 6, folate, and vitamin C intakes, but significantly lower sodium intake than the low 5-MTHF group.p = 0.059). However, tHcy and cystathionine concentrations and tCys/tHcy ratios were significantly lower in the high 5-MTHF group than in the low 5-MTHF group. Serum homocysteic acid, pyridoxamine, and pyridoxine concentrations were below the limit of quantification in all samples.The serum OCM-related metabolite concentrations in the high and low 5-MTHF groups and in the overall study sample are summarized in p < 0.001) than in the high 5-MTHF group . The positive correlation between DMG and tHcy concentrations was weaker in the low 5-MTHF group than in the high 5-MTHF group . The correlation matrix between serum OCM-related metabolite concentrations and enzyme activity indices is summarized in p < 0.001) than in the high 5-MTHF group . The 5-MTHF concentrations and betaine/DMG ratios showed a significant positive correlation. The significant negative correlation between 5-MTHF concentrations and tHcy/tCys ratios was stronger than the correlation between 5-MTHF and tHcy concentrations alone than the low 5-MTHF group. On the other hand, the high 5-MTHF group exhibited higher energy and micronutrient intake than the low 5-MTHF group, suggesting a potential dietary influence on OCM. Because food nutrients are complex, it is likely that the intake of folate-rich foods, such as vegetables, altered the intake of other micronutrients. The intake of methionine, cystine, glycine, serine, zinc, riboflavin, and vitamin BHerein, the median serum 5-MTHF concentration in young Japanese women was 19.2 nmol/L, which was comparable to or slightly higher than that reported in previous studies involving healthy adults in countries where FA fortification of grains is not mandated, such as Japan ,64. HoweConcentrations of 5-MTHF exhibited a significant positive correlation with SAM and tCys concentrations and a significant negative correlation with tHcy concentrations. Similarly, a previous study involving older adults found a positive correlation between 5-MTHF and SAM concentrations, and FA intervention significantly increased plasma SAM concentrations in the intervention group compared with the control group . In addiThe negative correlation between serum 5-MTHF concentrations and tHcy/tCys ratios was stronger than that between 5-MTHF and tHcy concentrations alone . The tHcHerein, 5-MTHF concentrations exhibited significant positive correlations with betaine concentrations or betaine/DMG ratios . SimilarHerein, a negative association between serum 5-MTHF and cystathionine concentrations was observed . A negatSerum FA concentrations were not correlated with OCM-related metabolite concentrations associated with 5-MTHF concentrations. This suggests that the concentration of 5-MTHF, a bioactive folate molecule species, as a biomarker may be more useful than that of total folate, which was considered in previous studies .This study has several strengths. Early morning fasting blood samples were collected, and standardized blood collection protocols were used to minimize the following effects on OCM-related metabolites: changes in the blood concentration of the measured substance due to eating immediately before the blood sample is collected; errors related to human activities at the time of blood collection; and variation in the deterioration of the substance being measured. Furthermore, the serum concentrations of OCM-related metabolites were measured using the stable-isotope dilution mass spectrometry method with internal standards for all measured components, yielding high-quality quantitative results .12-dependent reaction, and vitamin B12 is an important determinant of Hcy [6 intake may have promoted transsulfuration pathway flux. Finally, single-nucleotide polymorphisms may have an impact on OCM [However, this study has several limitations. First, given the cross-sectional survey design, it is impossible to establish a causal association between OCM metabolic dynamics. Further intervention studies on FA or 5-MTHF are required. Second, serum OCM-related metabolites do not always directly reflect OCM dynamics in organ cells. Third, 5-MTHF-dependent Hcy remethylation is a vitamin Bt of Hcy ,107; howt of Hcy ; howevert of Hcy ,109. In t on OCM ; howeverThis study was conducted at Kagawa Nutrition University, Saitama, Japan, between October and December 2018. This was a cross-sectional study designed to investigate the association between diet and blood components such as biochemical test values, OCM-related metabolites, fatty acids, and antioxidants; we reported associations between serum OCM-related metabolites.Healthy female university students aged 18\u201325 years majoring in nutrition were included. The following students were excluded: (1) those with health conditions that may affect the biomarker concentration; (2) those with a history of, or who have serious hepatic, renal, cardiac, pulmonary, gastrointestinal (including gastrectomy), or organ disorders; diabetes; food allergies; or other serious diseases; (3) those receiving medicines that can affect lipid metabolism or FA metabolism or anti-inflammatory and antioxidant drugs that may affect the measured values in this study; (4) those pregnant and lactating or planning for pregnancy and lactation; (5) those with systolic blood pressure <90 mmHg; (6) those who had previously donated large amounts of blood; (7) those participating in other clinical trials or studies or within 4 weeks of the end of those studies; (8) those with BMI >25 because BMI may affect blood SAM and SAH levels ,111; andn = 9), lost contact (n = 6), health problems (n = 1), busyness (n = 4), and withdrawals (n = 11), leaving 227 participants. The participants completed a lifestyle questionnaire and underwent physical measurements, and their fasting blood samples were collected after at least 10 h of fasting.A total of 258 eligible participants consented to the study, including proxy consent for minors. After the study began, 31 participants dropped out owing to consent withdrawals (The study protocol was approved by the Ethics Committee of Kagawa Nutrition University (protocol code no. 204) and was conducted in accordance with the Helsinki Declaration. All participants provided written informed consent before participating in the study.g, and the serum was then separated within an hour and frozen at \u221280 \u00b0C. Under these storage conditions, the concentrations of OCM-related metabolites measured in this study have been reported to be generally stable [To minimize dietary effects ,67,112, y stable ,113,114.m/z 460.2\u2192313.2 (5-MTHF), m/z 465.2\u2192313.2 (5-MTHF\u221213C5), m/z 442.2\u2192295.2 (FA), m/z 447.2\u2192295.2 (FA\u221213C5), m/z 104.0\u219260.1 (choline), m/z 113.0\u219269.1 (choline-d9), m/z 118.1\u219258.0 (betaine), m/z 129.0\u219266.1 (betaine-d11), m/z 104.1\u219258.1 (DMG), m/z 110.1\u219264.0 (DMG-d6), m/z 150.1\u2192104.0 (methionine), m/z 153.0\u2192107.0 (methionine-d3), m/z 399.1\u2192250.3 (SAM), m/z 402.2\u2192250.2 (SAM-d3), m/z 385.2\u2192134 (SAH), m/z 389.2\u2192136.2 (SAH-d4), m/z 136.0\u219290.0 (Hcy), m/z 140.0\u219293.9 (Hcy-d4), m/z 184.1\u2192138.3 (homocysteic acid), m/z 188.1\u2192142.0 (homocysteic acid-d4), m/z 223.2\u2192134.1 (cystathionine), m/z 227.1\u2192138.1 (cystathionine-d4), m/z 122.1\u219259.1 (Cys), m/z 124.2\u219261.0 (Cys-d2), m/z 126.1\u2192107.8 (taurine), m/z 128.1\u2192110.2 (taurine\u221213C2), m/z 106.1\u219260.1 (serine), m/z 109.1\u219263.1 (serine-d3), m/z 76.0\u219230.0 (glycine), m/z 78.0\u219231.9 (glycine-d2), m/z 377.1\u2192243.1 (riboflavin), m/z 383.2\u2192249.1 (riboflavin\u221213C415N2), m/z 169.2\u2192152.2 (pyridoxamine), m/z 172.1\u2192155.1 (pyridoxamine-d3), m/z 170.1\u2192134.1 (pyridoxine), and m/z 172.1\u2192136.0 (pyridoxine-d2)) [We previously described the method for measuring OCM-related metabolites . After cine-d2)) . Hcy andine-d2)) . AnalystData regarding the participants\u2019 ages were collected using a self-administered questionnaire.Dietary data were collected for 7 days before blood collection using a continuous, non-weighted dietary record in conjunction with digital images captured using a digital camera or smartphone according to a validated dietary survey method ,118,119.Blood pressure was measured using a P2000 Electronic Blood Pressure Monitor . The mean systolic and diastolic blood pressure was measured twice in the resting state according to the Japanese guidelines for managing hypertension .The participants\u2019 anthropometric measurements were collected using standardized methods during laboratory visits for blood sampling. Body weight and body fat percentage were measured using TBF-110 .U test was used to compare these groups. The enzyme activity indices included the betaine/DMG ratio [p-value of <0.05. IBM Statistical Package for the Social Sciences Statistics, Version 28 was used for statistical analysis.The distribution of subject characteristics data, nutrient intake, and serum concentrations of OCM-related metabolites used in the analysis were mostly non-normal and continuous variables were expressed as medians . Since there are no thresholds established for serum 5-MTHF concentrations such as deficiency, insufficiency, sufficiency, or excess, based on a previous study , a mediaMG ratio for BHMTMG ratio for methMG ratio for enzyPrevious studies assessed folate status without considering folate molecular species. Thus, we extended the findings of previous studies by comprehensively measuring OCM-related metabolites, including 5-MTHF, a major reduced folate. FA showed no association with important OCM-related metabolites, indicating that blood 5-MTHF levels could be useful for evaluating folate status. The 5-MTHF state could be linked to the Hcy flux into the transsulfuration pathway via SAM. Therefore, the tHcy/tCys ratio may be a more sensitive indicator of the 5-MTHF status than tHcy concentrations alone. A low 5-MTHF status may affect the choline metabolic pathway, particularly BHMT or CBS activity via betaine, implying that the folate cycle and choline metabolic pathway should be evaluated simultaneously in Hcy studies. Further intervention studies on FA or 5-MTHF are warranted to determine the causal association between the abovementioned findings."} +{"text": "Correction: Journal of Translational Medicine (2013) 11:29 10.1186/1479-5876-11-29Since the publication of our article , it has https://jeccr.biomedcentral.com/articles/10.1186/1756-9966-27-15. Copyright \u00a9 2008, Liao et al.; licensee BioMed Central Ltd.(A) The levels of CSE1L expression in B16-EV, B16-CSE1L, COLO-EV, and COLO-CSE1L cells were assayed by immunoblotting with anti-CSE1L antibody. The \u03b2-actin levels were assayed as a control. The invasive ability of the cells was analyzed by in vitro invasion assays using chemotaxis chambers, as described in \u201cMaterials and Methods\u201d. The left panel is adapted with permission from Fig.\u00a05C in Liao CF, Luo SF, Li LT, Lin CY, Chen YC, Jiang MC. CSE1L/CAS, the cellular apoptosis susceptibility protein, enhances invasion and metastasis but not proliferation of cancer cells. J Exp Clin Cancer Res. 2008; 27:15."} +{"text": "Infections after LT are common, but standard of care testing (SOCT) often fails to identify a cause. We prospectively compared longitudinal mcfDNA sequencing vs SOCT to determine the utility of mcfDNA sequencing for infection surveillance after LT.Single center prospective observational study of new LT patients (pts). We collected plasma on days 0, 1, 2, 3, 7, 14, and 30 post LT for mcfDNA sequencing; results were not available clinically. We reviewed outcomes and SOCT through 6 months (mo).Candida, oral or gastrointestinal commensals, Enterococci, or obligate pathogens ; most had polymicrobial mcfDNA sequencing results. In 36.67% (11/30), mcfDNA sequencing detected pathogens of unclear significance . In 8 pts with positive SOCT, mcfDNA sequencing did not detect at least 1 pathogen found on SOCT. In 13% (4/30), mcfDNA sequencing detected a pathogen before it was detected by SOCT (n=1 each): VRE surgical site infection (SSI), invasive candidiasis, Enterobacter pneumonia, and M. hominis SSI (a known donor-derived syndrome) with HHV-8/Kaposi Sarcoma .We enrolled 30 LT pts . 93.3% (28/30) received broad-spectrum antibiotics, although only 40.0% (12/30) had SOCT yielding pathogenic bacteria. 43.33% (13/30) had unexplained leukocytosis. Table 2 shows serial mcfDNA sequencing results, clinical course, and adjudication of mcfDNA sequencing. 96% (29/30) had at least 1 positive mcfDNA sequencing test, including 68.75% (11/16) with presumed infection or unexplained leukocytosis and negative SOCT, but diversity of organisms on mcfDNA sequencing, e.g., Table 1.Table 2 legend.Table 2.Plasma mcfDNA sequencing revealed potential occult explanations for unexplained leukocytosis and infectious syndromes with negative SOCT early post LT. mcfDNA sequencing also detected infection earlier than SOCT in 4 pts but did not detect known pathogens from 8 pts; > 1/3 had presumed FP mcfDNA sequencing results. Larger studies with longer follow-up are needed to determine the utility of mcfDNA sequencing in diagnosing infection, optimizing antibiotic use, and monitoring donor-derived infection post LT.Ghady Haidar, MD, Allovir: Grant/Research Support|AstraZeneca: Advisor/Consultant|AstraZeneca: Grant/Research Support|Karius: Advisor/Consultant|Karius: Grant/Research Support|NIH: Grant/Research Support Timothy A. Blauwkamp, PhD, Karius: Board Member|Karius: Ownership Interest Georgios Kitsios, MD, PhD, Karius, Inc: Grant/Research Support"} +{"text": "This study reports on the E. coli and 92 S. saprophyticus isolates were collected during 2022 from 45 medical centers located within the United States. Most isolates (77%) tested were cultured from urine specimens collected from patients seen in ambulatory, emergency, family practice, and outpatient medical services. Bacterial identifications were confirmed by MALDI-TOF MS. Isolates were tested for susceptibility by CLSI methods at a central laboratory (JMI Laboratories). MIC results for oral antibiotics licensed for the treatment of uUTI and drug-resistant subsets were interpreted per CLSI guidelines.A total of 1,001 50/90, 2/4 \u00b5g/mL) displayed good activity against 1,001 E. coli isolates as 98.8% of all observed gepotidacin MICs were \u22644 \u00b5g/mL (Table). Other oral agents tested against these isolates demonstrated the following rates of susceptibility (S): amoxicillin-clavulanate (85.2% S), ampicillin (55.6% S), ciprofloxacin (78.8%S), fosfomycin (99.3% S), mecillinam (93.5%S), nitrofurantoin (97.5% S), and trimethoprim-sulfamethoxazole (73.3% S). Gepotidacin maintained similar MIC50 values (ranging from 1 \u2013 2 \u00b5g/mL) and MIC90 values (ranging from 2 \u2013 4 \u00b5g/mL) against these drug-resistant subsets. Against S. saprophyticus isolates, gepotidacin inhibited all isolates at \u22640.12 \u00b5g/mL. Most oral agents showed >90% S against S. saprophyticus isolates, except for penicillin (7.6% S).Gepotidacin (MICin vitro activity against contemporary E. coli and S. saprophyticus from US urine isolates. This activity remained unaffected by resistance to other oral standard-of-care antibiotics.Gepotidacin demonstrated S J Ryan Arends, PhD, Cipla: Grant/Research Support|GSK: Grant/Research Support Renuka Kapoor, PhD, GSK: Grant/Research Support Didem Torumkuney, PhD, GSK: Grant/Research Support Nicole E. Scangarella-Oman, MS, GSK: Employee and shareholder Rodrigo E. Mendes, PhD, AbbVie: Grant/Research Support|Basilea: Grant/Research Support|Cipla: Grant/Research Support|Entasis: Grant/Research Support|GSK: Grant/Research Support|Paratek: Grant/Research Support|Pfizer: Grant/Research Support|Shionogi: Grant/Research Support"} +{"text": "Acinetobacter spp., including carbapenem-resistant Acinetobacter baumannii-calcoaceticus complex (ABC) organisms. In this study, the susceptibility testing of zosurabalpin was carried out against a panel of 150 randomly selected Acinetobacter spp. isolates (100 A. baumannii & 50 non-A. baumannii) representing 11 sites in China and a broad susceptibility profile (65% of which were multi-drug resistant [MDR]) collected in 2021.Zosurabalpin (RG6006) is the first representative of a novel class of tethered macrocyclic peptide antibiotics active against MICs were performed using the Clinical Laboratory Standards Institute (CLSI) broth dilution method cation-adjusted Mueller Hinton broth (CA-MHB) supplemented with either 20% of human serum (HS) or 20% of horse serum (HoS). For a fraction of isolates (10-25%), MIC determination for zosurabalpin is affected by aberrant readings in CA-MHB. This effect complicates routine susceptibility testing. Supplementation of CAMHB with serum allows accurate MIC determinations without any major effects on the MIC distribution.Summary data from the study are shown in Table 1.Acinetobacter spp., with an MIC50/90 of 0.12/0.5 \u03bcg/mL and 0.25/1 \u03bcg/mL in CA-MHB supplemented with HoS and HS, respectively (MIC range of 0.015/0.03 to 8 \u03bcg/mL). Against ABC isolates (n=133), the MIC50/90 for zosurabalpin was 0.12/0.25 \u03bcg/mL and 0.25/0.5 \u03bcg/mL, in HoS and HS, respectively (MIC range of 0.015/0.03 to 1 \u03bcg/mL). A similar activity was observed against carbapenem-resistant ABC isolates.Zosurabalpin was active against all in vitro antibacterial activity against Acinetobacter clinical isolates circulating in China. These data support the continued clinical development of zosurabalpin for infections caused by ABC isolates, including difficult to treat carbapenem-resistant isolates.In addition to the potent activity observed against isolates from USA and Europe, zosurabalpin exhibited potent Stephen Hawser, PhD, Allecra: study funding|Innoviva Specialty Therapeutics, Inc.: Honoraria|Roche: Honoraria|Roche: This project has been funded by BARDA (HHSO100201600038C). Nimmi Kothari, PhD, Allecra: Allecra (study funding)|Innoviva Specialty Therapeutics, Inc.: Honoraria|Roche: Honoraria|Roche: This project has been funded by BARDA (HHSO100201600038C). Thomas Valmont, BS, Roche: Honoraria|Roche: This project has been funded by BARDA (HHSO100201600038C). S\u00e9verine Louvel, PhD, F. Hoffmann-La Roche Ltd: employee of the company Claudia Zampaloni, n/a, F. Hoffmann-La Roche Ltd.: Full time employee of Roche"} +{"text": "Detection of SARS-CoV-2 in hospitalized patients is an important measure to prevent transmission to vulnerable individuals. Admission screening using nucleic acid amplification test such as PCR testing or rapid antigen testing (RAT) is proven to be beneficial in certain situations. However, the usefulness of SARS-CoV-2 antibody testing for COVID-19 screening in real-world setting is unclear.In this study, we aimed to investigate the effect of antibody testing on the results of SARS-CoV-2 screening tests. Anti-SARS-CoV-2 spike protein antibody (S-Ab) and anti-SARS-CoV-2 nucleocapsid protein antibody (N-Ab) were measured using an electrochemiluminescence immunoassay in all patients who presented to the emergency department and subsequently administered to Nagasaki University Hospital. PCR testing and RAT were also performed for the detection of SARS-CoV-2. The diagnostic performance of each antibody testing to PCR and RAT was retrospectively evaluated by Fisher's exact test and odds ratio (OR).A total of 2,692 patients were tested for S-Ab, N-Ab, RT-PCR, and RAT from Jan 2022 to Feb 2023. Among them, S-Ab were positive ( >0.7 U/mL) for 2,195 patients (81.5%), N-Ab ( >1.0 U/mL) 307 patients (11.4%), PCR 215 patients (7.9%), RAT 174 patients (6.5%).P=0.35, OR 0.8397) and RAT 1.8% . For those with N-Ab positive (n=307), PCR positivity was 6.8% and RAT 2.6% . Comparing the group of both S-Ab > 10,000 U/mL and N-Ab positive (n=128) with that of both negative (n=2564), PCR positivity was 4.7% vs. 8.1% , and RAT positivity was 1.6% vs. 6.7% .For those with S-Ab > 10,000 U/mL (n=625), PCR positivity was 7.0% (Antibody testing of S-Ab, N-Ab, or a combination of both showed performance in reducing the probability of positive PCR or RAT tests, indicating vaccine and infection-induced protective effect. However, the need for PCR and RAT tests for virus detection was suggested.Kosuke Kosai, M.D., Ph.D., FUJIFILM Toyama Chemical Co., Ltd.: Commissioned research|KYORIN Pharmaceutical Co.,Ltd.: Commissioned research Koichi Izumikawa, M.D., Ph.D., Asahi Kasei Pharma Corporation: Grant/Research Support|Asahi Kasei Pharma Corporation: Honoraria|Astellas Pharma Inc.: Honoraria|DAIICHI SANKYO COMPANY, LIMITED: Grant/Research Support|DAIICHI SANKYO COMPANY, LIMITED: Honoraria|KYORIN Pharmaceutical Co.,Ltd.: Honoraria|Merck & Co., Inc.: Honoraria|Pfizer Japan Inc.: Honoraria|Shionogi & Co., Ltd.: Grant/Research Support|Shionogi & Co., Ltd.: Honoraria|Sumitomo Pharma Co., Ltd.: Grant/Research Support|Sumitomo Pharma Co., Ltd.: Honoraria|TAIHO PHARMACEUTICAL CO., LTD.: Grant/Research Support Katsunori Yanagihara, MD, PhD, FUJIFILM Toyama Chemical Co., Ltd.: Commissioned research|KYORIN Pharmaceutical Co.,Ltd.: Commissioned research"} +{"text": "Artemisia heptapotamica Poljak led to the isolation of ten known compounds, including four alkyl p-coumarates: octadecyl trans-p-coumarate (1), icosy trans-p-coumarate (2), docosyl trans-p-coumarate (3), and tetracosyl trans-p-coumarate (4), one sesquiterpene lactone: santonin (5), four flavonoids; axillarin (6), quercetin 3-O-methyl ether (7), luteolin (8), and quercetin (9), and one phenolic acid derivative: p-coumaric acid (10). The structures of the isolated compounds were identified by various spectroscopic analyses. Additionally, the antimicrobial activity of the total extract and different fractions was screened, and they exhibited no inhibition of the growth of Candida albicans, C. neoformans, Aspergillus fumigatus, methicillin-resistant Staphylococcus aureus (MRS), E. coli, Pseudomonas aeruginosa, Klebsiella pneumonia, and Vancomycin-resistant Enterococci (VRE) at the tested concentrations ranging from 8 to 200 \u03bcg/mL. The identification and tentative characterization of the secondary metabolites were conducted using LC-QToF analysis. This method helps in the putative characterization of sesquiterpene lactones, flavonoids, coumarate derivatives, and aliphatic compounds. The developed method identified 43 compounds, of which the majority were sesquiterpene lactones, such as eudesmanolides, germacranolides, and guaianolide derivatives, followed by flavonoids. The proposed LC-QToF method helps develop dereplication strategies and understand the major class of chemicals before proceeding with the isolation of compounds.Phytochemical investigation of the aerial parts of Artemisia L. is the largest genus belonging to the family Asteraceae + and [M + Na]+ adduct precursor ions. The tentative characterization of compounds was processed based on the molecular features, such as accurate mass, fragment ions , and precursor ion molecular formula. The representative base peak chromatograms (BPC) in negative and positive modes, along with LC-DAD profiles at 210 nm, are shown in The secondary metabolites from aerial parts of Artemisia species. To perform characterization using LC-QToF, a few sesquiterpene lactones, e.g., santonin (compound 19), were isolated from aerial parts of A. heptapotamica in this study. Santonin mass fragmentation initiated with loss of water molecules, resulting in m/z 228.1219 [M + H-H2O]+. The following loss of -CO and sequential loss of -C2H4 and -CH4 resulted in m/z 201.1271, 173.0954, and 157.0648, respectively. Further loss of -CO ion resulted in the opening of the lactone moiety. Further loss of ketene moiety (-C2H2O) from the opened six-membered ring resulted in the formation of m/z 115.0542. Fragments with the least molecular weight (m/z 105.0698 and 91.0544) were useful in determining the backbone skeleton of the molecule. These characteristic fragments matched with the reported santonin fragmentation pathway \u2212 and fragment ions are shown in 25 showed m/z 509.1284 [M + H]+ with a C23H24O13 molecular formula. The corresponding fragment ions resulted in m/z 347.0762 [M + H-Glc]+, 331.0434, and 289.0329, respectively. The compound was characterized as 3,4,5,7-tetrahydroxy-3-methoxyflavone 7-O-\u03b2-D-glucopyranoside. Similarly, the flavone derivatives were characterized based on their fragmentation pathways. Along with hydroxy/methoxy flavone derivatives, simple aglycone flavonoids such as quercetin (compound 27) and luteolin (compound 26) were identified. Quercetin showed m/z 303.0491 [M + H]+ and m/z 301.0354[M-H]\u2212 with fragment ions at m/z 153 and 151, respectively. Furthermore, luteolin showed m/z 287.0548 [M + H]+ and 285.0406 [M-H]\u2212 in both positive and negative ionization modes. In addition, one quercetin derivative (compound 33) was identified with m/z 317.0658 [M + H]+ with fragment ions at m/z 301.0343 (such as quercetin aglycone), 274.0465, and 137.0233. The compound was characterized as quercetin 3-O-methyl ether.Using the isolated reference compounds and exact mass measurements, fourteen flavonoid compounds were identified. Most of the compounds are flavone derivatives. There are two quercetin derivatives, along with quercetin and luteolin. Flavonoids have established mass fragmentation patterns based on the literature previously reported ,23,24,25m/z 165.0546 [M + H]+ and 163.0398 [M-H]\u2212 with fragment ions at m/z 119.0502 [M-H-CO2]\u2212 in the negative mode of ionization. The compound was characterized as p-coumaric acid (compound 37). In addition, an aliphatic compound was identified with chemical formula C10H18O3. Compound 38 was tentatively characterized based on the exact mass at m/z 185.1186 [M-H]\u2212 and corresponding fragment ion at m/z 167.1077 [M-H-H2O]\u2212. Compound 39 was identified as 3,4,5-tri-caffeoylquinic acid with a precursor ion at m/z 677.1524 [M-H]\u2212. The corresponding fragment ions were at m/z 515.1198 [M-H-Glc]\u2212, 353.0822 [M-H-Glc-Glc]\u2212, and 191.0572 [quinic acid] , respectArtemisia species.The isolated compounds, as well as chromatographic peaks with distinctive fragment ions, were confirmed based on the reported literature studies whose corresponding references are listed in 1H and 13C NMR spectra were recorded on a Bruker Avance 400 MHz instrument. HR-ESI-MS was taken on BrukerBioApex-FTMS with electron spray ionization. Solvents used in this work, e.g., n-hexane, dichloromethane (DCM), ethyl acetate (EtOAc), methanol (MeOH), and ethanol (EtOH), were purchased from Fisher Scientific, USA. Deuterated solvents purchased from Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA, including methanol-d4 (CD3OD), chloroform-d3 (CDCl3), and pyridine-d5 (C5H5N-d5), were used for nuclear magnetic resonance (NMR) spectroscopic analyses. Acetonitrile, methanol, and formic acid of HPLC-certified grade were used for LC-MS analysis, and water was purified using a Milli-Q system . Column chromatography (CC) was performed using silica gel 60 . Thin-layer chromatography (TLC) analyses were carried out using pre-coated silica G plates w/UV254 . An ultraviolet lamp was used for visualization of spots on thin-layer chromatograms at 254 and/or 365 nm. Spots were visualized by spraying with 2% vanillin in sulfuric acid\u2013ethanol followed by heating at 110 \u00b0C.A. heptapotamica was collected in October 2021 from Kokpek village, Almaty, Kazakhstan. Identification and authentication were performed by Dr. Danilov Mikhail Petrovich. The sample was stored with the voucher number 0000723 in the Main Botanical Garden of the Institute of Botany and Phyto-introduction, Almaty, Kazakhstan. The same sample was assigned with the NCNPR number 25173 and stored in the National Center for Natural Product Research Botanical Repository, University of Mississippi, USA.The whole plant of A. heptapotamica were first dried in the shade and then crushed into small pieces. The dried plant material (1.65 kg) was extracted by maceration with 95% methanol three times at room temperature and was concentrated under reduced pressure to yield 253.35 g of the total extract. The total extract was mixed with a small amount of distilled water and successively fractionated with n-hexane and ethyl acetate. The fractions were concentrated under reduced pressure to produce n-hexane (29.1 g) and ethyl acetate fractions (58.74 g).The collected aerial parts of n-hexane and EtOAc and finally washed with MeOH, affording 6 fractions. Fraction F-4 (395.9 mg) was subjected to silica gel CC , using DCM\u2013MeOH gradient mixtures to increase the polarity gradually in 2% MeOH till 80 % MeOH and finally 100% MeOH were produced, yielding 37 subfractions. The seventeenth subfraction (21.1 mg) afforded a mixture of compounds 3 and 4. The eighteenth subfraction (12.9 mg) produced a mixture of compounds 2\u20134. The nineteenth subfraction (16.5 mg) produced a mixture of compounds 2\u20134. The twentieth subfraction (6.2 mg) furnished a mixture of compounds 1\u20134.The EtOAc (58.74 g) fraction was subjected to fractionation using VLC silica gel CC using 5 (45 mg). The eighteenth subfraction was precipitated to give compound 6 (27 mg). Subfraction F-5-21 (1.26 g) was purified on silica gel CC using DCM\u2013MeOH gradient mixtures to gradually increase the polarity in 2% MeOH till 80% MeOH was produced, affording compound 7 (8.4 mg). Subfraction F-5-24 (342.8 mg) was rechromatographed over silica gel CC using DCM\u2013MeOH gradient mixtures to gradually increase the polarity in 2% MeOH till 80% MeOH was reached, producing a mixture of compounds 7 and 8 (14.5 mg) and 9 (24.4 mg). Subfraction F-5-26 (450.1) was purified on silica gel CC using DCM\u2013MeOH gradient mixtures to gradually increase the polarity in 2% MeOH till 80% MeOH was reached, producing compound 10 (8.2 mg).Fraction F-5 (14.3 g) was subjected to silica gel CC , using DCM\u2013MeOH gradient mixtures to gradually increase the polarity in 2% MeOH till 80% and finally 100% MeOH were produced, affording 29 subfractions. The eleventh subfraction was crystalized to produce compound The antimicrobial activity of the total extract and different fractions was evaluated using the method reported by Samy et al. .About 25 mg of extract was sonicated in 1.0 mL of methanol for 5 min, followed by centrifugation for 15 min at 7000 rpm. The clear filtered supernatant solution was used for analysis.TM HSS C18 column . The mobile phase consisted of water with 0.1% formic acid (A) and acetonitrile with 0.1% formic acid (B) at a flow rate of 0.23 mL/min. Analysis was performed using the following gradient elution: 15% B to 40% B in 30 min, then to 100% B in the next 15 min. Each run was followed by a 5 min wash with 100% B and an equilibration period of 15 min with 85% A/15% B. Two microliters of the sample were injected. The column temperature was 40 \u00b0C.The liquid chromatographic system was an Agilent Series 1290, and separation was achieved on an Acquity UPLC2) flow rate, 13 L/min; drying gas temperature, 325 \u00b0C; nebulizer pressure, 30 psi; sheath gas temperature, 300 \u00b0C; sheath gas flow, 11 L/min; capillary voltage, 3500 V; nozzle voltage, 0 V; skimmer, 65 V; Oct RF V, 750 V; and fragmentor voltage, 125 V. All the operations, acquisition of data, and analysis of data were controlled using Agilent MassHunter Acquisition Software ver. A.10.1 and processed with MassHunter Qualitative Analysis software ver. B.07.00. Each sample was analyzed in positive and negative modes over the range of m/z 50\u20131700 and an extended dynamic range. Accurate mass measurements were obtained by employing ion correction techniques using reference masses at m/z 121.0509 (protonated purine) and 922.0098 in positive ion mode, while m/z 112.9856 (deprotonated trifluoroacetic acid-TFA) and 1033.9881 (TFA adducted HP-921) were used in negative ion mode. Samples were analyzed in all-ion MS\u2013MS mode, where experiment 1 was carried out with a collision energy of zero and experiment 2 with a fixed collision energy of 45 eV.The mass spectrometric analysis was performed with a QToF-MS-MS equipped with an ESI source with Jet Stream technology, using the following parameters: drying gas , which matched with the authentic samples of A. heptapotamica.Ten compounds were isolated from the ethyl acetate fraction of"} +{"text": "Immune responses after COVID-19 vaccination should be evaluated in different populations around the world. This study compared antibody responses induced by ChAdOx1 nCoV-19, CoronaVac, and BNT162b2 vaccines. Blood samples from vaccinees were collected pre- and post-vaccinations with the second and third doses. The study enrolled 78 vaccinees, of whom 62.8% were women, with the following median ages: 26 years\u2014ChAdOx1 nCoV-19; 40 years\u2014CoronaVac; 30 years\u2014BNT162b2. Serum samples were quantified for anti-RBD IgG and anti-RBD IgA and anti-spike IgG by ELISA. After two vaccine doses, BNT162b2 vaccinees produced higher levels of anti-RBD IgA and IgG, and anti-spike IgG compared to ChAdOx1 nCoV-19 and CoronaVac vaccinees. The third dose booster with BNT162b2 induced higher levels of anti-RBD IgA and IgG, and anti-spike IgG in CoronaVac vaccinees. Individuals who reported a SARS-CoV-2 infection before or during the study had higher anti-RBD IgA and IgG production. In conclusion, two doses of the studied vaccines induced detectable levels of anti-RBD IgA and IgG and anti-spike IgG in vaccinees. The heterologous booster with BNT162b2 increased anti-RBD IgA and IgG and anti-spike IgG levels in CoronaVac vaccinees and anti-RBD IgA levels in ChAdOx1 nCoV-19 vaccinees. Furthermore, SARS-CoV-2 infection induced higher anti-RBD IgA and IgG levels in CoronaVac vaccinees. Several preventive strategies have been developed and continue to be generated to control SARS-CoV-2 transmission, the most important being vaccines . CurrentMost vaccines developed against SARS-CoV-2 induce an immune response toward the receptor-binding domain (RBD), a portion of the spike protein present at the S1 region, which is essential for binding the virus to angiotensin-converting enzyme-2 (ACE2) on the cell surface and to establish cellular infection . Thus, aAfter COVID-19 vaccination, IgG and IgA are mostly involved in virus neutralization, especially IgA since this Ig can neutralize SARS-CoV-2 at the mucosal surface entrance . Some stThe anti-SARS-CoV-2 vaccines comprise platforms of inactivated viruses , proteinThe present study was evaluated and approved by the Research Ethics Committee of the Hospital das Cl\u00ednicas, Universidade Federal de Goi\u00e1s, under the number CAAE: 30804220.2.0000.5078 and is in accordance with Resolution 466/2012 of the National Health Council, which regulates research involving human beings. The collection of data and blood samples was conducted after the individuals selected for the sample had agreed to participate and had signed the informed consent form.Blood samples were collected from 78 volunteers before immunization (ChAdOx1 nCoV-19 and BNT162b2) and after the administration of the second doses of ChAdOx1 nCoV-19, CoronaVac, and BNT162b2 vaccines, and after the third dose (booster) with BNT162b2 vaccine. In addition, nasopharyngeal swab samples were collected from individuals belonging to the ChAdOx1 nCoV-19 and BNT162b2 vaccine groups at the pre-vaccine collection and 1 month after the second dose to assess whether these individuals could be infected with SARS-CoV-2 during the period.Participants were recruited by phone or in person while in the queue for vaccination, and during the vaccination of health professionals at the Instituto de Patologia Tropical e Sa\u00fade P\u00fablica (IPTSP), Universidade Federal de Goi\u00e1s (UFG), Goi\u00e2nia-GO, Brazil. The inclusion criteria were individuals at least 18 years old, vaccinated with two doses of CoronaVac, ChAdOx1 nCoV-19, or BNT162b2, and those who may have received the third dose, but not necessarily.Primary pre-vaccine samples were collected at the queues for vaccination, in a physical space adjacent to the line, right before the first dose was administered. Post-vaccination samples were collected in three different periods: 1 month and 4\u20136 months after the second dose, and 1 month after the third dose. Samples were collected 1 month after the second and third doses because the peak of the antibodies occurs around four weeks after vaccination ,30,31,32\u00ae Viral RNA Mini Kit was used, following the manufacturer\u2019s protocol. Samples were submitted to real-time polymerase chain reaction post reverse transcription (RT-qPCR) after the RNA extraction, using the Promega GoTaq\u00ae Probe 1-Step RT-qPCR System, according to the manufacturer\u2019s protocol [For Ribonucleic acid (RNA) extraction, the commercial QIAampprotocol . The priprotocol was usedg for 10 min at room temperature. All samples were processed on the day of collection. Serum was separated and stored in 2 mL polypropylene cryotubes in a \u221280 \u00b0C freezer for subsequent enzyme immunoassay ELISAs.After blood collection from vaccinated individuals, whole blood was centrifuged at 600\u00d7 For the ELISAs, 96-well high-binding polystyrene half-area plates were coated with 50 \u00b5L per well with the RBD protein, expressed according to Amanat et al. (2020) , at a co2 > 0.5. For all tests, p < 0.05 was considered significant.All analyses of individual samples were conducted using GraphPad Prism version 9 . The variables distribution patterns were evaluated via the Kolmogorov\u2013Smirnov and Shapiro\u2013Wilk tests. For paired comparisons between groups, the non-parametric Wilcoxon Matched-Pairs Signed Rank test was used. Paired analyses were assigned to samples from the same individuals at different collection times. Unpaired groups were analyzed with the non-parametric Mann\u2013Whitney U test. The non-paired analyses were attributed to a total group. For frequency calculations, we used the Fisher exact test. Multiple group comparisons were analyzed by running non-parametric Kruskal\u2013Wallis statistical tests and were corrected using Dunn\u2019s and Dunnett\u2019s methods. Spearman correlation test was used for association analyses. The existence of correlation was adopted for rn = 78) were divided into three groups according to the vaccines they had received: ChAdOx1 nCoV-19 (n = 33), BNT162b2 (n = 27), and CoronaVac (n = 18). The ChAdOx1 nCoV-19 group was composed of 33 individuals, 23 (69.7%) women and 10 (30.3%) men. The BNT162b2 group was composed of 27 individuals, 11 (40.7%) women and 16 (59.3%) men. Finally, the CoronaVac group was made up of 18 participants, 15 (83.3%) women and 3 (16.7%) men (Study participants (.7%) men . Therefo.7%) men . ParticiWhole blood collection periods comprise T1 (pre-vaccine), T2 (1 month post-second dose), T3 (4\u20136 months post-second dose or pre-third dose), and T4 (1 month post-third dose or booster dose). All participants who had their samples collected at T4 received the booster dose, mostly BNT162b2. Of 78 participants, 56 received the third dose. This information can be better observed in Only the pre-vaccine nasopharyngeal samples from the ChAdOx1 nCoV-19 group were tested via reverse transcription followed by the real-time polymerase chain reaction (RT-qPCR), and all samples were negative for SARS-CoV-2 RNA. In addition, a rapid test assay to detect IgM/IgG was performed on all serum samples collected , and only a few samples were positive. Some of them belonged to individuals who reported SARS-CoV-2 infection during the application of the questionnaire. Therefore, we believe that the rapid test positivity was due to a previous SARS-CoV-2 infection.p = 0.0027, median\u2014pre-vaccine: 0.6250, post-vaccine: 0.8310; anti-RBD IgG, p < 0.0001, median\u2014pre-vaccine: 0.8990, post-vaccine: 10.16; anti-spike IgG, p < 0.0001, median\u2014pre-vaccine: 1.549, post-vaccine: 10.75; BNT162b2: anti-RBD IgA, p < 0.0001, median\u2014pre-vaccine: 0.6460, post-vaccine: 4.023; anti-RBD IgG, p < 0.0001, median\u2014pre-vaccine: 0.9560, post-vaccine: 11.80; anti-spike IgG, p < 0.0001, median\u2014pre-vaccine: 1.254, post-vaccine: 11.22 A,D,G.p < 0.0001, median\u2014ChAdOx1 nCoV-19: 0.7890; BNT162b2: 3.731; IgG, p = 0.0268, median\u2014ChAdOx1 nCoV-19: 9.991; BNT162b2: 10.87) and CoronaVac . Individuals immunized with CoronaVac exhibited lower anti-RBD IgG levels compared to those with ChAdOx1 nCoV-19 and CoronaVac E. This w: 11.28) H.p < 0.0001, median\u2014ChAdOx1 nCoV-19: 1.634; BNT162b2: 6.217) and IgG , and in comparison, to CoronaVac, for anti-RBD IgA . In addition, comparisons made in relation to the previous collection period (4\u20136 months after the second dose or before the third dose) showed differences between anti-RBD IgA and IgG levels, after the booster dose, for the ChAdOx1 nCoV-19 C and Corr: 1.925 C; anti-Rr: 11.07 F), with : 10.80) I.p < 0.0001). Individuals administered with BNT162b2 showed a higher frequency of anti-RBD IgA production compared to those administered with ChAdOx1 nCoV-19 (p < 0.0001) and CoronaVac (p < 0.0001) at 4\u20136 months after the second dose (p = 0.0030) (All study vaccinees (100%) produced detectable levels of anti-RBD and anti-spike IgG after each vaccine dose. The frequency of individuals who produced anti-RBD IgA at post-vaccination collection times is shown in ond dose B. At 1 m 0.0030) C.p < 0.0001; T1 vs. T3, p = 0.0028, median\u2014T1:0.6250, T2: 0.8310, T3: 0.7890, and T4: 1.634) (p < 0.0001) for anti-RBD IgA, and anti-spike IgG . The longitudinal analysis performed for BNT162b2 (p = 0.0313). For the CoronaVac group , T2 (1 month post second dose vaccine), T3 (4\u20136 months post second dose vaccine), and T4 (1 month post third dose vaccine). The results of this evaluation for the ChAdOx1 nCoV-19 group A,D,G rev: 1.634) A and IgG: 10.59) D, and an: 10.76) G. The da: 10.76) A C and IgG: 11.07) F and for: 10.80) I.p = 0.0165, median\u2014men: 11.03; women: 10.63) .p = 0.0089; IgG, p = 0.0146) and women also vaccinated with ChAdOx1 nCoV-19 (p = 0.0145) ) (p = 0.0080) (median (BNT162b2 men: 11.49)) (ChAdOx1 nCoV-19 women: 10.46)). At 4\u20136 months after the second dose, the group of men vaccinated with BNT162b2 exhibited higher anti-RBD IgA levels compared to men (p = 0.0030) and women (p = 0.0003) immunized with ChAdOx1 nCoV-19 (p = 0.0273) and men (p < 0.0001) in the BNT162b2 group ) (p = 0.0014) and men (p = 0.0024) in the BNT162b2 group and compared to men in the ChAdOx1 nCoV-19 group (p = 0.0448) (median (ChAdOx1 nCoV-19: men: 10.05) (CoronaVac: women: 5.224)) (p = 0.0003) and women (p = 0.0182) vaccinated with BNT162b2 (CoronaVac: women: 9.895)) (p = 0.0021) and men (p = 0.0297) vaccinated with ChAdOx1 nCoV-19 (BNT162b2: men: 9.279)) (The comparison of sexes between vaccine groups at post-vaccination collection periods indicate 0.0001) A,D. In a 11.90)) A. The ev 11.90)) G, reveal nCoV-19 B. At the0.6920)) B. Women 5.224)) E. Women 9.895)) H. At 1 m 9.279)) C. The an 9.279)) F,I.Furthermore, we stratified the data of vaccinees in three age groups\u201418\u201330 years, 31\u201350 years, and >50 years old\u2014to evaluate the influence of age on antibody production.p = 0.0062) (median (ChAdOx1 nCoV-19: 0.9070) (BNT162b2: 4.135)). Individuals vaccinated with BNT162b2 also presented higher anti-RBD IgA levels (p = 0.0188) (median (BNT162b2: 18\u201330 years: 4.135) (ChAdOx1 nCoV-19: >50 years: 0.7880)) and anti-spike IgG (p = 0.0075) (median (BNT162b2: 18\u201330 years: 12.20) (ChAdOx1 nCoV-19: >50 years: 10.09)) than those older than 50 years vaccinated with ChAdOx1 nCoV-19 (p = 0.0038) and those older than 50 years (p = 0.0460) vaccinated with ChAdOx1 nCoV-19 (p = 0.0084) (p = 0.0379) in the CoronaVac group and compared to individuals aged 18\u201330 years in the ChAdOx1 nCoV-19 group (p = 0.0369) (CoronaVac: 31\u201350 years: 0.7570)) (p = 0.0002) and ChAdOx1 nCoV-19 (p = 0.0405) compared to those aged 31\u201350 years in the CoronaVac group (p = 0.0218) (median (ChAdOx1 nCoV-19: 18\u201330 years: 9.872) (CoronaVac: 31\u201350 years: 4.402)). Analysis of anti-spike IgG levels showed that individuals aged 18\u201330 years vaccinated with BNT162b2 presented higher levels of this antibody compared to those aged 31\u201350 years vaccinated with CoronaVac (p = 0.0030) (median (BNT162b2: 18\u201330 years: 12.12) (CoronaVac: 31\u201350 years: 9.761)) B. Those 0.7570)) B. Assessac group E. Furthe 9.761)) H.p = 0.0296), and those aged 18\u201330 years (p = 0.0142), both in the ChAdOx1 nCoV-19 group (BNT162b2: 18\u201330 years: 7.252)) (p = 0.0259) (median (ChAdOx1 nCoV-19: 10.21) (BNT162b2: 12.08)) (p = 0.0347) (median (BNT162b2: 12.24) (ChAdOx1 nCoV-19: 10.30)) ) C. The as 12.08)) F. The an 10.30)) I.p = 0.0096, median\u2014comorbidities: 10.67; no comorbidities: 12.06) , none of: 12.06) . This wa: 12.06) .p = 0.0180, median\u2014COVID-19+: 1.673; COVID-19\u2212: 0.7415) and CoronaVac groups compared to na\u00efve individuals (uninfected) (n = 3).We next determined serum antibody levels of vaccinees with a history of COVID-19, infected with SARS-CoV-2 at any moment, before or during the study. Of the 22 infected individuals, 13 were infected with SARS-CoV-2 before any vaccine dose was administered and nine were infected after one, two, or three vaccine doses. Due to the reduced number of individuals who had the infection, we were unable to analyze them according to the period in which they presented COVID-19. For anti-RBD IgA, individuals who were infected with SARS-CoV-2 at any moment showed higher antibody levels at 4\u20136 months after the second dose of ChAdOx1 nCoV-19 (nfected) A. The sa: 3.446) B. The ev: 3.446) C. We did: 3.446) for anti: 10.86) . At 1 mo: 10.88) . However2 = 0.5979, p = 0.0013) D, after 0.0013) E,F.In this study, we investigated the specific humoral immune response against RBD and spike proteins after COVID-19 vaccination with three vaccine formulations: ChAdOx1 nCoV-19, BNT162b2, and CoronaVac. The data showed that, after the primary vaccination regimen (two-dose regimen), all vaccinees showed an increase in anti-RBD IgG and IgA and anti-spike IgG levels and were able to maintain these antibody levels for 4\u20136 months after two doses. BNT162b2 induced greater production of anti-RBD IgG and IgA and anti-spike IgG compared to ChAdOx1 nCoV-19. These findings are similar to those of Zhang et al. (2022), who detected higher anti-spike and anti-RBD IgG levels induced by mRNA vaccines compared to adenovirus and recombinant protein vaccines . The booThe longevity of the immune response induced by vaccines may vary according to the vaccine platform used, among other factors. We found positive levels of anti-RBD IgG and IgA and anti-spike IgG antibodies up to 4\u20136 months after the second dose for the three vaccine formulations evaluated. Similarly, in other studies using sera from individuals immunized with mRNA vaccines such as mRNA-1273 (Moderna), neutralizing and binding antibody activity against SARS-CoV-2 variants was detected six months after the primary vaccination regimen ,42. GreaThe use of booster doses has already proven to be essential in improving the immune response, especially against SARS-CoV-2 variants . Many stTo assess whether host factors, such as sex, age, and comorbidities, could influence the response to the vaccines, these factors were evaluated to observe changes in anti-RBD IgG and IgA and anti-spike IgG production since some host characteristics can interfere with the development of immune responses against SARS-CoV-2 . No diffThe next evaluation conducted according to biological characteristics was the effect of age on antibody production. Aging has already been shown to be responsible for a decrease in cellular immune function due to the process known as immunosenescence ,53. It cAlthough the presence of comorbidities may hinder the induction of immune responses by different vaccines ,57,58, iOur research demonstrated higher production of anti-RBD IgG and IgA in individuals with a history of SARS-CoV-2 infection compared to na\u00efve individuals, during the collection period 4\u20136 months after the second dose, suggesting that the infection could have potentiated antibody production, especially for individuals in the CoronaVac group. This hypothesis can be corroborated by a study conducted by Padoan et al. (2021), which showed increased anti-S-RBD IgG levels in individuals previously exposed to SARS-CoV-2 and immunized with two doses of BNT162b2 vaccine compared to na\u00efve individuals . Chua etSome limitations of our study include the small size of the cohort and the differences between age and sex in each vaccine group. These limitations could have influenced the analysis of antibody production, but most of the results obtained in this work, such as the longevity of the antibody response and higher antibody levels induced by the heterologous regimen, are similar to those of other studies ,44,45,61In conclusion, two doses of the BNT162b2, ChAdOx1 nCoV-19, and CoronaVac vaccines were sufficient to induce detectable levels of anti-RBD IgG and IgA and anti-spike IgG antibodies. The heterologous booster dose with BNT162b2 increased the levels of anti-RBD IgA and IgG and anti-spike IgG for CoronaVac and anti-RBD IgA for ChAdOx1 nCoV-19 vaccinees. In addition, individuals who presented the SARS-CoV-2 infection at any time during the study had higher anti-RBD IgA and IgG levels at 4\u20136 months after the second dose, compared to uninfected individuals. Further studies involving larger cohorts should be conducted to investigate and find answers to unresolved questions."} +{"text": "Correction to: Lossy Image Compression in a Preclinical Multimodal Imaging Study\u00a0https://doi.org/10.1007/s10278-023-00800-5The corresponding author for this paper should be Andreas Walter; details are below.Andreas WalterCentre of\u00a0Optical Technologies, Aalen University, Aalen, Germanyandreas.walter@hs-aalen.deThe original article has been corrected."} +{"text": "Discovery of molecular mechanisms of primary osteoporosis development is fundamental to understand the pathogenesis of musculoskeletal diseases in general and for identifying key links in the genetic and epigenetic regulation of bone remodelling genes. The number of identified molecular genetic markers for osteoporosis is increasing but there is a need to describe their functional interactions. These interactions have been determined to be associated with the control of expression of a number of transcription factors and the differentiation of mesenchymal stem cells through the pathway of osteoblastogenesis or adipogenesis, and monocytic precursors through the pathway of osteoclastogenesis. The results of epigenetic studies have significantly increased the understanding of the role of post-translational modifications of histones, DNA methylation and RNA interference in the osteoporosis pathogenesis and in bone remodelling. However, the knowledge should be systematised and generalised according to the results of research on the role of epigenetic modifiers in the development of osteoporosis, and the influence of each epigenetic mechanism on the individual links of bone remodelling during ontogenesis of humans in general, including the elderly, should be described. Understanding which mechanisms and systems are involved in the development of this nosology is of interest for the development of targeted therapies, as the possibility of using microRNAs to regulate genes is now being considered. Systematisation of these data is important to investigate the differences in epigenetic marker arrays by race and ethnicity. The review article analyses references to relevant reviews and original articles, classifies information on current advances in the study of epigenetic mechanisms in osteoporosis and reviews the results of studies of epigenetic mechanisms on individual links of bone remodelling. Primary osteoporosis (OP) is an age-associated disease ofmultifactorial aetiology, which is based on a violation ofthe balance of bone remodelling, leading to a decrease inthe level of bone mineral density (BMD) and a violationof the structure of bone microarchitectonics, which resultin the appearance of an incorrect spatial structure of thespongy and cortical bone . Bone massis reduced to 26 % in individuals predisposed to OP. Inroughly 80 % of women, the mineral content in the spinefalls below the threshold value at the age of 60\u201370 years,and at 85 years \u2013 in more than 90 % .According to statistics, the frequency of fractures in womenis 33 %, in men, 20 % .Until recently, OP was diagnosed only by secondarysigns, such as low height and bone pain . In 1940, the American endocrinologist F. Albright,describing postmenopausal osteoporosis, suggestedthat it developed due to estrogen deficiency . On this basis, clinicians developed the now obsoleteconcept of two forms of OP, one associated withestrogen deficiency during menopause and the other withcalcium deficiency and skeletal ageing, both of which arecharacteristic of both sexes .Current evidence defines OP as a musculoskeletal diseaseassociated with profound metabolic changes not only inbone, but also in whole-body homeostasis: micro-nutrientand endocrine dysregulation, as well as a complex interactionof genetic, endogenous and environmental factors thatcontribute to a complex disease phenotype . Risk factors with regards to OP are assumedto be the female sex, being of the Caucasoid or Mongoloidrace , early menopause, old age, familyhistory, insufficient insolation, comorbidities with impairedbone matrix micronutrient absorption, smoking, alcoholabuse, sedentary lifestyle, taking hormonal drugs andrheumatoid arthritis. DNA testing has not been introducedinto diagnostic practice because significant populationdifferences in the frequency distribution of risk markersprevent the development of universal test systems, despitethe existence of significant and validated genetic markersfor OP .The first multicentre molecular genetic studies basedon the genome-wide association search (GWAS) methodconfirmed that OP is associated with genes for local andsystemic regulation of bone cell function. The lion\u2019s shareof risk markers, specifically, single-nucleotide polymorphisms,have been identified not in exons but in intronsand promoters of regulatory genes, transcription factor,receptor (ESR2) and growth factor (FGF2) genes .Certain markers have been identified in non-coding RNA(ncRNA) sequences, including microRNA . Significant levels of associationswith fractures have been identified among the genesof systemic and local regulators ,transmembrane receptors, as well as WNT signalling genes,nuclear transcription factors and enzymesthat produce or inactivate local bone regulators .Bioinformatics studies have concluded that the main enrichmentpathways by means of the functional affiliation ofgenes associated with histone modifications and microRNApatterns are significantly associated with the regulation ofRUNX2, FGF2 and SOX9 transcription factors. Moreover,they are also associated with the regulation of mesenchymalstem cell (MSC) differentiation .Thus, particular epigenetic factors in the pathogenesis ofosteoporosis have been identified. However, at present, it ismore interesting to consider the molecular pathogenesis ofOP in terms of individual functional links in the regulationof bone remodelling, in particular how RANK/RANKL/OPG, WNT, RUNX2 transcription factor and others areepigenetically regulated.Controlled differentiation of osteoblast and osteoclast precursors(mononuclear phagocytes) is necessary to maintainthe balance of bone remodelling .Osteoclast activity is primarily regulated by the RANK/RANKL/OPG (receptor-activator nuclear factor k\u03b2/RANKligand/osteoprotegerin) system. RANKL is produced byosteoblasts and its binding to RANK on the osteoclast surface activates the expression of osteoclastogenic genes.The role of gene polymorphisms of this system in increasedrisk of fracture and the formation of low BMDhas previously been shown . Inthe RANKL gene sequence, two CpG sites were detected:one in the upstream sequence with 18 CpG sites, localizedat a distance of 14,415 pairs of nucleotides (bp) from thetranscription start site of the TSS I major isoform and onein the downstream sequence with 59 CpG sites, whichstarts at 260 and ends at 615 pairs of nucleotides of theTSS I isoform. In the OPG gene sequence, one island of56 sites spanning from \u2013402 to +850 nucleotide pairs fromthe transcription site of the TSS isoform was observed. In , a groupof patients from Guangzhou Medical University Hospitalwith osteoporotic fractures had significantly higher RANKLgene mRNA levels from femoral bone cells compared tocontrols, with downregulated methylation status .Dysregulation of the expression of these genes is knownto be a key link in the development of steroid-inducedosteonecrosis of the femoral head and was noted to be associatedwith increased DNA methylation levels of OPGand RANK genes and with decreased levels in the RANKLgene . Previously, J. Delgado-Calle et al.(2012) performed a comparative analysis of the expressionlevels and methylation profile of the RANKL and OPGgenes in bone tissue samples from patients with osteoporoticfemoral neck fractures and osteoarthritis (OA) ofthe hip joint, which obtained remarkable results. RANKLexpression levels were significantly higher in patientswith fractures ( p = 0.012), while no significant changes inOPG gene expression levels were observed. The ratio ofRANKL ligand to OPG was higher in bone samples withOP . Differentialmethylation analysis revealed that the upstream promoterregion of the RANKL gene was strongly methylated inall samples, while individual CpG junctions of the genewere equally hypomethylated in the comparison groups.There is evidence of the contribution of miRNA tothe regulation of the RANK/RANKL/OPG system. In2014, C. Chen et al. published results measuring miR-503microRNA levels in peripheral blood cells, the overexpressionof which in CD14+ mononuclear cells inhibitedRANKL-induced osteoclastogenesis. In CD14+ cells frompostmenopausal women with osteoporosis, the baselinelevel of miR-503 was lower than in normal controls andhad no change after induction by RANKL factor, suggestingthe direct role of miR-503 in the regulation ofRANK expression . miR-142-3p andmiR-21- 5p are potential biomarkers of OP as they have ahigh affinity with the OPG gene mRNA and are involvedin the regulation of several signalling pathways involved inbone formation . Thus, theepigenetic regulation of the RANK/RANKL/OPG systemis dynamic and dependent on the DNA methylation statusand a number of microRNAs.Transcription factor 2 (RUNX2) plays a crucial role inosteoblast differentiation. Gene expression is predominantlyhigh in the early stages of bone cell developmentwhen MSCs are differentiating into osteoblast precursors,but naturally decreases at the osteocyte maturation stage.The gene contains several functional regions: activationdomain, runt domain, PST domain, etc. . In terms of epigenetic regulators of RUNX2,microRNAs are well studied. In particular, miRNA-194modulates MSC differentiation andaccelerates osteoblast differentiation by regulating RUNX2nuclear translocation by way of STAT1 signal transducer. miR-133a-5p inhibits RUNX2 geneexpression at the transcription and translation level by bindingto the 3\u2032-untranslated mRNA site .During the early stages of osteoblast maturation, miR-125b affects RUNX2 expression by affinity binding to the3\u2032-untranslated region of the gene, indirectly participatingin the formation of a complex with Cbf\u03b2 that inhibits differentiationof these cells. Using microarray technology,P. Garmilla-Ezquerra et al. (2015) discovered a significantreduction in miR-187-3p gene expression levels andinduction of miR-518f in bone with low BMD. In theirresearch, Y. Zhang et al. (2017) observed the involvementof miR-221 in the formation of low mineral density throughregulation of RUNX2 activity based on bioinformaticsanalysis . Several microRNAs affecting the activity of thisfactor are presented in Table 1.Phosphorylation of RUNX2 mobilises chromatin regulatoryfactors and accelerates MSC maturation. RUNX2 isphosphorylated at specific serine residues 301 and 319, inducingosteocyte maturation through MAPK-dependentsignalling and BMP2-sensitive transcription . Phosphorylationof S104 leads to prevention of RUNX protein degradation. The ERK-MAPKsignalling pathway plays a crucial role in the regulationof RUNX2 gene expression and bone formation . MKK6 is a protein kinase with dual specificity thatparticipates in the MAP kinase signal transduction pathwayand promotes RUNX2 phosphorylation . Inaddition, parathormone, which is one of the main regulatorsof blood calcium levels, activates the phosphorylation ofthe RUNX2 factor by means of the PKA signalling pathway.This process is associated with the activation of the promoter of the MMP13 gene, which plays an essentialrole in bone resorption .Post-translational modification of histones, in particularhistone methylation, plays an important role in bone formation.The so-called JUMONJI protein is considered to bea transcription factor and is encoded by the JARID2 gene.The domain containing 3 JMJD3 is a histone demethylasespecifically catalysing the removal of trimethylation ofhistone H3K27me3. JMJD3 was found to inhibit the differentiationof RUNX2 osteoblasts. Conversely, inhibitionof JMJD3 activity decreases RUNX2 promoter activitywhile increasing H3K27me3 activity in promoter regions.Histone acetylation affects the state of chromatin compactionby neutralising the positive charge of histone tailsand reducing the electrostatic interactions of histone tailswith deoxyribonucleic acid. Studies have revealed thatosteoporosis induced by glucocorticoid therapy leads todecreased acetylation of H3K9/K14 and H4K12 in theregulatory regions of the RUNX2 and OSX genes andincreases the hyperacetylation of H3K9/K14 and H4K12in the PPAR\u03b32 regulatory region in bone marrow-derivedMSCs from osteoporosis. The transcriptional activity of theRUNX2 factor gene is enhanced by P300 acetyltransferaseand nicotinamide phosphoribosyltransferase (NAMPT),which, in turn, promote osteogenic differentiation of MSCsby H3K14 acylation and MC3T3-E1 cells through H3K9acylation, respectively .Thus, an extremely significant number of regulatorsof RUNX2 gene expression have been identified, whichis a promising therapeutic gene model in culture studies,as blocking or enhancing the activity of this gene andmonitoring its expression level during the induction ofosteogenic lines allows the identification of key switchesof mesenchymal stem cell differentiation.The WNT signalling pathway is one of the most importantsystems regulating embryonic development and cell differentiation.This pathway represents one of the centrallinks in the control of bone development and remodelling.Among the various genes involved in this system, methylationof the SOST (encoding sclerostin) gene promoterhas been comprehensively studied in osteoblast cultures.Sclerostin produced by osteocytes inhibits WNT signallingand reduces the rate of bone formation. DNA methylationof the gene is necessary for the transition of osteoblasts toosteocytes . In women withprimary OP, SOST methylation is elevated in iliac bonecells whilst sclerostin levels are decreased and the WNTpathway is enhanced .Several studies have shown that histone deacetylationunder the regulation of the WNT6, WNT10B, WNT10A andWNT1 genes inhibits WNT signalling and increases the riskof primary osteoporosis . Thus, elevatedlevels of HDAC5 deacetylase reduce SOST gene expressionin osteocytes, contributing to bone mass loss. Deficiency ofthis deacetylase is associated with the acetylation of histoneH3 lysine 27 as well as the interaction of MEF2C with theSOST gene enhancer, therefore suggesting the significantrole of sclerostin in the regulation of osteocyte maturation. High levels of the zeste 2 homologueenhancer methyltransferase (EZH2) have been demonstratedto suppress osteogenic differentiation of MSCs,while low ones decrease the levels of the H3K27me3 tagnear the transcription start site of osteogenesis genes, includingWNT10B . EZH2 increasesH3K27me3 levels at the WNT1, WNT6 and WNT10Apromoters and inhibits WNT signalling .Many regulatory microRNAs are associated with WNTsignalling. miR-433-3p inhibits DKK1 (Dickkopf-1)gene expression, enhancing osteoblast differentiation.Dickkopf-1 acts as an antagonist of the WNT signallingpathway and enhances bone resorption .miR-139-5p induces WNT signalling via the inhibition ofNOTCH1 . R.E. Makitie et al. (2018)screened a specially designed panel of 192 microRNAsin patients with a genetically determined WNT signallingdisorder with a heterozygous missense mutation c. 652 T>G(p. C218G) in exon 4 of the WNT1 gene. It was determinedthat miR-22-3p, miR-34a-5p and miR-31-5p levels werelower in mutation carriers compared to controls .Another common inhibitor of osteogenic differentiationis miR-31, the level of which drops in MSCs differentiatinginto osteoblasts. This was confirmed by S. Weilner et al.(2016), who observed increased levels of this microRNA in plasma in elderly patients with OP . miR-31 isreleased from extracellular vesicles of endothelial cellsand inhibits osteogenesis in stromal stem cells by bindingto the Freisled 3 protein. Furthermore, decreased levels ofmiR-199a-5p result in glucocorticoid-mediated inhibitionof osteogenesis . More recently, L. Duanet al. (2018) identified that high levels of miR-16-2* maycontribute to the development of primary OP: knockdownof this microRNA may promote RUNX2 activation. ThismicroRNA has an affinity for the WNT5A gene mRNA. miR-148a-3p has been revealed toenhance both osteoclastogenesis andadipogenesis in osteogenic progenitor cells . Plasma levels of this microRNA are significantlyhigher in patients with OP compared to controls withoutOP . miR-30e is another importantmicroRNA in the pathogenesis of OP, playing a role inregulating adipocyte and osteoblast differentiation throughthe inhibition of LRP6 . Thus, the WNTsignalling pathway is regulated by a complex epigeneticsystem, notably microRNAs.The role of non-coding RNAs in bone remodellingMicroRNAs are considered to be the most studied epigeneticfactors in osteoporosis .They are conventionally divided into two classes: those thatpromote bone formation or bone resorption. In particular,several microRNAs that slow down the progression of OPhave been identified. For example, miR-33-5p is a mechanosensitivemicroRNA that positively regulates osteoblastogenesisby way of inhibition of HMGA2 high mobilitygroup proteins . miR-96 enhances osteogenicdifferentiation by inhibiting phosphorylation ofepidermal growth factor receptor EGFR and the expressionof major osteoblast factors RUNX2 and OSTERIX. miR-216a enhances bone formation byregulating the c-Cbl-mediated PI3K/AKT pathway . Table 2 shows the microRNAs separated bydirection of action in bone remodelling .miR-124 is a positive regulator of adipogenic and neurogenicdifferentiation, while being a negative regulator ofmyogenic and osteogenic differentiation. It directly targetsthe DLX3, DLX5 and DLX2 homeobox genes . In one pharmacogenetic study, patients with OP,after three months of treatment with the parathormoneanalogue Teriparatide, had reduced expression levels ofmiR-33 and one year later, miR-133a. Simultaneously,there was a general tendency: the increase in the level ofBMD increased with a decrease in the level of expressionof these microRNAs. Post-transcriptional regulation ofDKK-1 changes due to a decrease in miR-33 microRNAlevels and the action of parathyroid hormone, which leads toa decrease in the negative impact of DKK-1 on an alternativeregulatory mechanism that improves optimal controlof WNT signaling..Of interest are the results of studies on the effects oflong non-coding RNAs on the regulation of Sirtuins,nicotinamide adenine dinucleotide-dependent deacetylases.These molecules have a broad spectrum of action and areassociated with longevity and resistance to age-relateddiseases. It was established that SIRT1 gene expression isinversely related to HIF1A-AS1 ncRNA expression, whileHOXA-AS3 ncRNA interacts with EZH2 and is requiredfor RUNX2 trimethylation of lysine-27 H3 (H3K27me3)factor. Hence, HOXA-AS3 is important for bone formationin general .The long ncRNA HOTAIR reduces protein expressionand inhibits WNT signalling. DKK1 reduces the proteinlevels of C-myc, \u03b2-catenin, HOTAIR and RUNX2, whichtheoretically counteracts the regulatory effect of HOTAIR. If the expression level of p21 ncRNA islow, WNT signalling becomes more active due to increasedE2 secretion, which ultimately increases the rate of boneformation . Also, reduced levels of H19ncRNA reduce the level of DKK4 gene expression . AK045490 ncRNA levels are significantlyelevated and inhibit bone formation by inhibiting nucleartranslocation of \u03b2-catenin and suppressing TCF1, LEF1 andRUNX2 expression . Similarly, AK016739ncRNA inhibits osteogenic differentiation as it can reducethe expression and activity of osteoblastogenesis transcriptionfactors .Inhibition of UCA1 ncRNA promotes bone formationvia activation of the BMP-2/(Smad1/5/8) pathway in osteoblasts. As a result, microRNAs andlong ncRNAs remain among the most studied epigeneticfactors involved in the pathogenesis of primary OP butrequire further systematisation.The mechanisms of the relationship between bone andadipose cell formation are complex and remain an area ofactive research. Works performed on the cell cultures ofosteoblasts and MSCs convincingly show an inverse relationshipbetween differentiation of bone marrow MSCs intoadipocytes or osteoblasts. An imbalance between adipogenesisand osteogenesis has been proposed as a mechanismfor the development of OP, but obesity itself is not alwaysa predictor of an increased risk of osteoporosis.Post-translational modifications of histones play a keyrole in this system. Among them, histone methylation iscrucial, in particular in chromatin reorganisation. In particular,lysine methylation in H4K20, H3K27 and H3K9 isassociated with decreased levels of transcription, whereasmethylation of H3K79, H3K36 and H3K4, with active genetranscription .However, concerning osteogenic inducers, the homeoboxgene HOXA10, which contributes to osteogenic clone determinationby enriching the trimethylation of the 4th lysineresidue in histone, activating RUNX2, alkaline phosphataseand osteocalcin, thus stimulating bone cell maturation, isimportant . It is known that the combinationof methylation and demethylation can function as anepigenetic switch of osteogenesis to adipogenesis based onEZH2 activity, catalysing the trimethylation of histoneH3on lysine 27 key regulatory genes (such as RUNX2). Simultaneously,removal of this tag by lysindemethylase 6Ainhibits adipogenesis and induces osteoblastogenesis. Proteinsthat can be targeted by EZH2 and are involved in MSCswitching are HDAC9c and HDAC .A direct correlation was realised between increased levelsof EZH2 and decreased levels of HDAC9c gene expression. The methyltransferase activity ofEZH2 is reduced by phosphorylation and is associated withosteogenic induction It is acknowledged that during osteocyte aging there isan accumulation of adipose tissue in the bone marrow and,at the same time, the number of mesenchymal stem cellsincreases in the intercellular phase. From this perspective,it is interesting that overexpression of miR-1292 acceleratesthe senescence of human adipose-derived stem cellsand inhibits bone formation via the Wnt/\u03b2-catenin signallingpathway, while miR-10b inhibits adipose stem celldifferentiation via the TGF-\u03b2 pathway .Several bone-associated cells, including multipotentbone mesenchymal stem cells, osteoblasts that form bonetissue and osteoclasts that break it down, are in a symbioticrelationship throughout life. A growing body of evidencesuggests that epigenetic cell modifications induced byaging contribute to impaired bone remodelling and leadto osteoporosis. A variety of epigenetic mechanisms areinvolved, including DNA/RNA modifications, histonemodifications, microRNAs (miRNAs) and long non-codingRNAs (dnRNAs), and chromatin remodelling . Thus, epigenetic mechanisms can switch the directionof mesenchymal stem cell differentiation betweenosteoblastogenesis and adipogenesis.Molecular genetic determinants of endophenotypes ofosteoporosis, such as fracture risk and BMD levels, can beconverged through the whole epigenome. In the researchthey conducted, J.A. Morris et al. (2017), leveraging thetechnological capabilities of Infinium HumanMethylation450,performed a whole-genome methylome analysis,measuring site-specific DNA methylation in 5515 individualsof European descent. Following a meta-analysisof their results, they were able to identify the CpG sitecg23196985, which was significantly associated with lowMPCT adjusted for multiple comparisons without regard togender( pBH = 1.30 \u00d7 10\u20132) and in females (pBH = 3.41 \u00d7 10\u20135).The CpG cg23196985 site is localized to the 5\u2032-translatedregion of the hepatic carboxylase 1 gene CES1, which isexpressed in the liver and peripheral blood . J.G. Zhang et al. (2015), performing transcriptomeanalysis based on Affymetrix GeneChip Human Exon 1.0ST Array and microRNA analysis on Capitalbio Cor. microarrays,as well as methylome sequencing in patientswith low MPCT hip and controls, identified the mostenriched functional molecular pathways associated withOP or MPCT variability: a network of 12 interacting genesand 11 microRNAs. Among the genes are AKT1, STAT5A,PIK3R5, etc., while among the microRNAs, miR-141 andmiR-675 \u2013 their levels correlate with the expression ofthese genes and global DNA methylation status .D. Cheishvili et al. (2018) performed a full-epigenomicanalysis in women without OP and in women with earlypostmenopausal OP. Genes in which CpG sites with significantlevels of differential methylation were identifiedwere ZNF267, ABLIM2, RHOJ, CDKL5, PDCD1, ABRAand HOJ . At the human femurlevel, DNA methylation profile studies using pyrosequencingand qRT-PCR-based gene expression studies provedthat DNA methylation status was inversely correlated withthe expression of the iNOS and COL9A1 genes, but notcatabolic genes including MMP13 and IL1B. Significantdemethylation of the osteocalcin gene promoter was alsoshown between the embryonic and adult stages of development,demonstrating the importance of DNA methylation atthe tissue level . It is anticipated that theresults of these studies will confirm the whole-epigenomeapproach as being sufficiently robust to allow large-scalestudies of women at risk of developing OP.Despite the great advances and the wide range of workperformed in the study of the epigenetics of primary osteoporosis, understanding remains fragmentary. The researchdescribes key epigenetic regulators of bone remodelling,but it is difficult to build a coherent picture of the pathogenesisof osteoporosis from these data, common to all keypathogenetic processes in bone tissue.It is recognised that the key epigenetic changes in osteoporosisare converging on the regulation of MSCs differentiationand that the multi-step system of activity regulationof the transcription factor RUNX2, sclerostin,DKK1 protein, RANKL-RANK-OPG system and factorsinvolved in the regulation of WNT signalling is of greatimportance. A separate issue is the systematisation andcreation of a unified genetic network of a vast number ofregulatory microRNAs that affect key signalling pathwaysand the transcription factors associated with osteoporosis.However, these microRNAs influence the ultimate risk ofosteoporosis indirectly and it remains to be understoodhow they can be systematised for relevance and functionalinvolvement in pathogenesis due to their dynamism anddifferent levels depending on tissue specificity.Approaches necessary to implement early diagnosis ortargeted therapies for osteoporosis still need to be developed.The task is complicated by experimental data frommethylome studies, in which genes other than critical regulatoryfactors, such as RUNX2, sclerostin or DKK1, wereobserved to be key and most important. The data presentedin this review show that epigenetic modifications can havea strong influence on the determination, differentiation andactivity of mesenchymal stem cells and, therefore, maycontribute to the pathophysiology of age-related bone massloss. The results update further basic research on osteoporosisand, with the available data, broaden the horizons fora more insightful and detailed approach to new epigeneticstudies of this disease and the prospects for new and effectivepersonalised therapiesThe authors declare no conflict of interest.Afzal F., Pratap J., Ito K., Ito Y., Stein J.L., Wijnen A.J., Stein G.S.,Lian J.B., Javed A. Smad function and intranuclear targeting sharea Runx2 motif required for osteogenic lineage induction and BMP2responsive transcription. J. Cell. Physiol. 2005;204(1):63-72. DOI10.1002/jcp.20258.Albright F., Bloomberg E., Smith P.H. Postmenopausal osteoporosis.Trans. Assoc. Am. Phys. 1940;55:298-305.Amjadi-Moheb F., Akhavan-Niaki H. Wnt signaling pathway in osteoporosis:Epigenetic regulation, interaction with other signalingpathways, and therapeutic promises. J. Cell. Physiol. 2019;234(9):14641-14650. DOI 10.1002/jcp.28207Anastasilakis A.D., Makras P., Pikilidou M., Tournis S., Makris K.,Bisbinas I., Tsave O., Yovos J.G., Yavropoulou M.P. Changes ofcirculating MicroRNAs in response to treatment with teriparatideor denosumab in postmenopausal osteoporosis. J. Clin. Endocrinol.Metab. 2018;103(3):1206-1213. DOI 10.1210/jc.2017-02406.Bedene A., Bedrac S.M., Jese L., Marc J., Vrtacnik P., Prezelj J., KocjanT., Kranjc T., Ostanek B. MiR-148a the epigenetic regulator ofbone homeostasis is increased in plasma of osteoporotic postmenopausalwomen. Wien. Klin. Wochenschr. 2016;128(7):519-526. DOI10.1007/s00508-016-1141-3.Bolland M.J., Siu A.T., Mason B.H., Horne A.M., Ames R.W.,Grey A.B., Gamble G.D., Reid I.R. Evaluation of the FRAX andGarvan fracture risk calculators in older women. J. Bone Miner. Res.2011;26(2):420-427. DOI 10.1002/JBMR.215.Cheishvili D., Parashar S., Mahmood N., Arakelian A., Kremer R.,Goltzman D., Szyf M., Rabbani S.A. Identification of an epigeneticsignature of osteoporosis in blood DNA of postmenopausalwomen. J. Bone Miner. Res. 2018;33(11):1980-1989. DOI 10.1002/jbmr.3527.Chen C., Cheng P., Xie H., Zhou H.D., Wu X.P., Liao E.Y., Luo X.H.MiR-503 regulates osteoclastogenesis via targeting RANK. J. BoneMiner. Res. 2014;29(2):338-347. DOI 10.1002/JBMR.2032.Chen Y.H., Chung C.C., Liu Y.C., Yeh S.P., Hsu J.L., Hung M.Ch.,Su H.L., Li L.Y. Enhancer of zeste homolog 2 and histone deacetylase9c regulate age-dependent mesenchymal stem cell differentiationinto osteoblasts and adipocytes. Stem Cells. 2016;34(8):2183-2193. DOI 10.1002/stem.2400.Chen Y.H., Yeh F.L., Yeh S.P., Ma H.T., Hung S.C., Hung M.C., Li L.Y.Myocyte enhancer factor-2 interacting transcriptional repressor(MITR) is a switch that promotes osteogenesis and inhibits adipogenesisof mesenchymal stem cells by inactivating peroxisome proliferator-activated receptor \u03b3-2. J. Biol. Chem. 2011;286(12):10671-10680. DOI 10.1074/jbc.M110.199612.Cheng P., Chen C., He H.B., Hu R., Zhou H.D., Xie H., Zhu W.,Dai R.C., Wu X.P., Liao E.Y., Luo X.H. miR-148a regulates osteoclastogenesisby targeting V-maf musculoaponeurotic fibrosarcomaoncogene homolog B. J. Bone Miner. Res. 2013;28(5):1180-1190.DOI 10.1002/jbmr.1845.Curtis E.M., Fuggle N.R., Cooper P., Harvey N.C. Epigenetic regulationof bone mass. Best Pract. Res. Clin. Endocrinol. Metab. 2022;36(2):101612. DOI 10.1016/j.beem.2021.101612.Delgado-Calle J., Sanudo C., Fernandez A.F., Garcia-Renedo R., FragaM.F., Riancho J.A. Role of DNA methylation in the regulationof the RANKL-OPG system in human bone. Epigenetics. 2012;7(1):83-91. DOI 10.4161/epi.7.1.18753Duan L., Zhao H., Xiong Y., Tang X., Yang Y., Hu Z., Li C., Chen S.,Yu X. miR-16-2\u2217 interferes with WNT5A to regulate osteogenesis ofmesenchymal stem cells. Cell. Physiol. Biochem. 2018;51(3):1087-1102. DOI 10.1159/000495489.Dudakovic A., Camilleri E.T., Riester S.M., Paradise C.R., GluscevicM., O\u2019Toole T.M., Thaler R., Evans J.M., Yan H., SubramaniamM., Hawse J.R., Stein G.S., Montecino M., McGee-LawrenceM.E., Westendorf J.J., Wijnen A.J. Enhancer of zeste homolog 2inhibition stimulates bone formation and mitigates bone loss causedby ovariectomy in skeletally mature mice. J. Biol. Chem. 2016;291(47):24594-24606. DOI 10.1074/jbc.M116.740571Dudakovic A., Camilleri E.T., Xu F., Riester S.M., McGee-LawrenceM.E., Bradley E.W., Paradise C.R., Lewallen E.A., Thaler R., DeyleD.R., Larson A.N., Lewallen D.G., Dietz A.B., Stein G.S., Mon-tecinoM.A., Westendorf J.J., Wijnen A.J. Epigenetic control of skeletaldevelopment by the histone methyltransferase Ezh2. J. Biol.Chem. 2015;290(46):27604-27617. DOI 10.1074/jbc.M115.672345.Estrada K., Styrkarsdottir U., Evangelou E., \u2026 Ioannidis J.P.A.,Kiel D.P., Rivadeneira F. Genome-wide meta-analysis identifies56 bone mineral density loci and reveals 14 loci associated with riskof fracture. Nat. Genet. 2012;44(5):491-501. DOI 10.1038/ng.2249.Feng Y., Wan P., Yin L., Lou X. The inhibition of microRNA-139-5ppromoted osteoporosis of bone marrow-derived mesenchymal stemcells by targeting Wnt/beta-catenin signaling pathway by Notch1.J. Microbiol. Biotechnol. 2020;30(3):448-458. DOI 10.4014/jmb.1908.08036.Foger-Samwald U., Dovjak P., Azizi-Semrad U., Kerschan-Schindl K.,Pietschmann P. Osteoporosis: pathophysiology and therapeutic options.EXCLI J. 2020;19:1017-1037. DOI 10.17179/excli2020-2591.Gao J., Yang T., Han J., Yan K., Qiu X., Zhou Y., Fan Q., Ma B.MicroRNAexpression during osteogenic differentiation of humanmultipotent mesenchymal stromal cells from bone marrow. J. Cell.Biochem. 2011;112(7):1844-1856. DOI 10.1002/jcb.23106.Garmilla-Ezquerra P., Sanudo C., Delgado-Calle J., Perez-Nunez M.I.,Sumillera M., Riancho J.A. Analysis of the bone MicroRNome inosteoporotic fractures. Calcif. Tissue Int. 2015;96(1):30-37. DOI10.1007/s00223-014-9935-7.Ge C., Xiao G., Jiang D., Franceschi R.T. Critical role of the extracellularsignal-regulated kinase-MAPK pathway in osteoblast differentiationand skeletal development. J. Cell Biol. 2007;176(5):709-718.DOI 10.1083/JCB.200610046Ge C., Xiao G., Jiang D., Yang Q., Hatch N.E., Roca H., FranceschiR.T. Identification and functional characterization of ERK/MAPK phosphorylation sites in the Runx2 transcription factor.J. Biol. Chem. 2009;284(47):32533-32543. DOI 10.1074/jbc.M109.040980.Ge C., Yang Q., Zhao G., Yu H., Kirkwood K.L., Franceschi R.T. Interactionsbetween extracellular signal-regulated kinase 1/2 and P38Map kinase pathways in the control of RUNX2 phosphorylation andtranscriptional activity. J. Bone Miner. Res. 2012;27(3):538-551.DOI 10.1002/JBMR.561.Gomathi K., Akshaya N., Srinaath N., Moorthi A., Selvamurugan N.Regulation of Runx2 by post-translational modifications in osteoblastdifferentiation. Life Sci. 2020;245:117389. DOI 10.1016/J.LFS.2020.117389.Hassan M.Q., Tare R., Lee S.H., Mandeville M., Weiner B., MontecinoM., Wijnen A.J., Stein J.L., Stein G.S., Lian J.B. HOXA10controls osteoblastogenesis by directly activating bone regulatoryand phenotypic genes. Mol. Cell. Biol. 2007;27(9):3337-3352. DOI10.1128/mcb.01544-06.Hu H., He X., Zhang Y., Wu R., Chen J., Lin Y., Shen B. MicroRNAalterations for diagnosis, prognosis, and treatment of osteoporosis: acomprehensive review and computational functional survey. Front.Genet. 2020;11:181. DOI 10.3389/FGENE.2020.00181/BIBTEXHuang B., Li G., Jiang X.H. Fate determination in mesenchymal stemcells: A perspective from histone-modifying enzymes. Stem CellRes. Ther. 2015;6(1):35. DOI 10.1186/s13287-015-0018-0.Huang G., Shigesada K., Ito K., Wee H.J., Yokomizo T., Ito Y. Dimerizationwith PEBP2\u03b2 protects RUNX1/AML1 from ubiquitin-proteasome-mediated degradation. EMBO J. 2001;20(4):723-733. DOI10.1093/emboj/20.4.723Jing H., Liao L., An Y., Su X., Liu S., Shuai Y., Zhang X., Jin Y. Suppressionof EZH2 prevents the shift of osteoporotic MSC fate to adipocyteand enhances bone formation during osteoporosis. Mol. Ther.2016;24(2):217-229. DOI 10.1038/mt.2015.152.Jing H., Su X., Gao B., Shuai Y., Chen J., Deng Z., Liao L., Jin Y. Epigeneticinhibition of Wnt pathway suppresses osteogenic differentiationof BMSCs during osteoporosis. Cell Death Dis. 2018;9(2):176. DOI 10.1038/s41419-017-0231-0.Lei S.F., Papasian C.J., Deng H.W. Polymorphisms in predicted miRNAbinding sites and osteoporosis. J. Bone Miner. Res. 2011;26(1):72-78. DOI 10.1002/jbmr.186.Letarouilly J.G., Broux O., Clabaut A. New insights into the epigeneticsof osteoporosis. Genomics. 2019;111(4):793-798. DOI 10.1016/J.YGENO.2018.05.001Li B., Liu J., Zhao J., Ma J.X., Jia H.B., Zhang Y., Xing G.S., Ma X.L.LncRNA-H19 modulates Wnt/\u03b2-catenin signaling by targeting Dkk4in hindlimb unloaded rat. Orthop. Surg. 2017;9(3):319-327. DOI10.1111/os.12321.Li D., Tian Y., Yin C., Huai Y., Zhao Y., Su P., Wang X., Pei J.,Zhang K., Yang C., Dang K., Jiang S., Zhiping M., Li M., Hao Q.,Zhang G., Qian A. Silencing of lncRNA AK045490 promotes osteoblastdifferentiation and bone formation via \u03b2-catenin/TCF1/Runx2signaling axis. Int. J. Mol. Sci. 2019;20(24):6229. DOI 10.3390/ijms20246229Li H., Li T., Fan J., Li T., Fan L., Wang S., Weng X., Han Q., Zhao R.C.mIR-216a rescues dexamethasone suppression of osteogenesis, promotesosteoblast differentiation and enhances bone formation, byregulating c-Cbl-mediated PI3K/AKT pathway. Cell Death Differ.2015;22(12):1935-1945. DOI 10.1038/cdd.2015.99.Li H., Xiao Z., Quarles L.D., Li W. Osteoporosis: mechanism, moleculartarget and current status on drug development. Curr. Med.Chem. 2020;28(8):1489-1507. DOI 10.2174/0929867327666200330142432.Li J., He X., Wei W., Zhou X. MicroRNA-194 promotes osteoblastdifferentiation via downregulating STAT1. Biochem. Biophys. Res.Commun. 2015;460(2):482-488. DOI 10.1016/J.BBRC.2015.03.059Li Y., Ge C., Franceschi R.T. MAP kinase-dependent RUNX2 phosphorylationis necessary for epigenetic modification of chromatinduring osteoblast differentiation. J. Cell. Physiol. 2017;232(9):2427-2435. DOI 10.1002/jcp.25517.Lorentzon M., Cummings S.R. Osteoporosis: the evolution of a diagnosis.J. Intern. Med. 2015;277(6):650-661. DOI 10.1111/joim.12369.Makitie R.E., Hackl M., Niinimaki R., Kakko S., Grillari J., MakitieO. Altered microRNA profile in osteoporosis caused by impairedWNT signaling. J. Clin. Endocrinol. Metab. 2018;103(5):1985-1996. DOI 10.1210/jc.2017-02585.Marshall D., Johnell O., Wedel H. Meta-analysis of how well measuresof bone mineral density predict occurrence of osteoporoticfractures. Br. Med. J. 1996;312(7041):1254-1259. DOI 10.1136/bmj.312.7041.1254.Morris J.A., Tsai P.C., Joehanes R., Zheng J., Trajanoska K., SoerensenM., Forgetta V., Castillo-Fernandez J.E., Frost M., SpectorT.D., Christensen K., Christiansen L., Rivadeneira F., TobiasJ.H., EvansD.M., Kiel D.P., Hsu Y.H., Richards J.B., Bell J.T.Epigenome-wide association of DNA methylation in whole bloodwith bone mineral density. J. Bone Miner. Res. 2017;32(8):1644.DOI 10.1002/JBMR.3148.Qadir A.S., Um S., Lee H., Baek K., Seo B.M., Lee G., Kim G.S.,Woo K.M., Ryoo H.M., Baek J.H. miR-124 negatively regulatesosteogenic differentiation and in vivo bone formation of mesenchymalstem cells. J. Cell. Biochem. 2015;116(5):730-742. DOI10.1002/JCB.25026.Raisz L.G. Pathogenesis of osteoporosis: concepts, conflicts, and prospects.J. Clin. Invest. 2005;115(12):3318-3325. DOI 10.1172/JCI27071.Reppe S., Noer A., Grimholt R.M., Halldorsson B.V., Carolina M.G.,Gautvik V.T., Olstad O.K., Berg J.P., Datta H., Estrada K., HofmanA., Uitterlinden A.G., Rivadeneira F., Lyle R., Collas P., GautvikK.M. Methylation of bone SOST, its mRNA, and serum sclerostinlevels correlate strongly with fracture risk in postmenopausalwomen. J. Bone Miner. Res. 2015;30(2):249-256. DOI 10.1002/JBMR.2342.Riggs B.L., Wahner H.W., Seeman E., Offord K.P., Dunn W.L., MazessR.B., Johnson K.A., Melton L.J. Changes in bone mineraldensity of the proximal femur and spine with aging. Differencesbetween the postmenopausal and senile osteoporosis syndromes.J. Clin. Invest. 1982;704(4):716-723. DOI 10.1172/JCI110667.Rivadeneira F., Styrkarsdottir U., Estrada K., \u2026 Stefansson K., IoannidisJ.P.A., Uitterlinden A.G. Twenty bone-mineral-density lociidentified by large-scale meta-analysis of genome-wide associationstudies. Nat. Genet. 2009;41(11):1199-1206. DOI 10.1038/ng.446.Selvamurugan N., He Z., Rifkin D., Dabovic B., Partridge N. Pulsedelectromagnetic field regulates microRNA 21 expression to activateTGF-\u03b2 signaling in human bone marrow stromal cells to enhanceosteoblast differentiation. Stem Cells Int. 2017;2017:2450327. DOI10.1155/2017/2450327Selvamurugan N., Pulumati M.R., Tyson D.R., Partridge N.C. Parathyroidhormone regulation of the rat collagenase-3 promoter by proteinkinase A-dependent transactivation of core binding factor \u03b11.J. Biol. Chem. 2000;275(7):5037-5042. DOI 10.1074/JBC.275.7.5037.Selvamurugan N., Shimizu E., Lee M., Liu T., Li H., Partridge N.C.Identification and characterization of Runx2 phosphorylation sitesinvolved in matrix metalloproteinase-13 promoter activation. FEBSLett. 2009;583(7):1141-1146. DOI 10.1016/J.FEBSLET.2009.02.040.Shi C., Huang P., Kang H., Hu B., Qi J., Jiang M., Zhou H., Guo L.,Deng L. Glucocorticoid inhibits cell proliferation in differentiatingosteoblasts by microRNA-199a targeting of WNT signaling. J. Mol.Endocrinol. 2015;54(3):325-337. DOI 10.1530/JME-14-0314.Soltanoff C.S., Yang S., Chen W., Li Y.P. Signaling networks that controlthe lineage commitment and differentiation of bone cells. Crit.Rev. Eukaryot. Gene Expr. 2009;19(1):1-46. DOI 10.1615/CritRevEukarGeneExpr.v19.i1.10.Souza M.P.G. Osteoporosis diagnosis and treatment. Rev. Bras. Ortop.2010;45(3):220-229. DOI 10.1016/S2255-4971(15)30361-X.Stein G.S., Lian J.B., Wijnen A.J., Stein J.L., Montecino M., Javed A.,Zaidi S.K., Young D.W., Choi J.Y., Pockwinse S.M. Runx2 controlof organization, assembly and activity of the regulatory machineryfor skeletal gene expression. Oncogene. 2004;23(24):4315-4329.DOI 10.1038/sj.onc.1207676.Sun M., Cao Y., Yang X., An F., Wu H., Wang J. DNA methylation inthe OPG/RANK/RANKL pathway is associated with steroid-inducedosteonecrosis of the femoral head. BMC Musculoskelet. Disord.2021;22(1):599. DOI 10.1186/s12891-021-04472-6.Sveshnikov A.A. Mineral Density of Skeletal Bones, Muscle Mass, andIssues of Fracture Prevention. Moscow: Akademiya YestestvoznaniyaPubl., 2013. (in Russian)Tang X., Lin J., Wang G., Lu J. MicroRNA-433-3p promotes osteoblastdifferentiation through targeting DKK1 expression. PLoS One.2017;12(6):0179860. DOI 10.1371/JOURNAL.PONE.0179860.Thomas P.A. Racial and ethnic differences in osteoporosis. J. Am. Acad.Orthop. Surg. 2007;15(1):26-30. DOI 10.5435/00124635-200700001-00008.Tobeiha M., Moghadasian M.H., Amin N., Jafarnejad S. RANKL/RANK/OPG pathway: a mechanism involved in exercise-inducedbone remodeling. Biomed. Res. Int. 2020;2020:6910312. DOI10.1155/2020/6910312.Wang H., Sun Z., Wang Y., Hu Z., Zhou H., Zhang L., Hong B.,Zhang S., Cao X. miR-33-5p, a novel mechano-sensitive microRNApromotes osteoblast differentiation by targeting Hmga2. Sci. Rep.2016;6:23170. DOI 10.1038/SREP23170Wang J., Guan X., Guo F., Zhou J., Chang A., Sun B., Cai Y., Ma Z.,Dai C., Li X., Wang B. miR-30e reciprocally regulates the differentiationof adipocytes and osteoblasts by directly targeting low-densitylipoprotein receptor-related protein 6. Cell Death Dis. 2013;4(10):845. DOI 10.1038/cddis.2013.356.Wang P., Cao Y., Zhan D., Wang D., Wang B., Liu Y., Li G., He W.,Wang H., Xu L. Influence of DNA methylation on the expressionof OPG/RANKL in primary osteoporosis. Int. J. Med. Sci. 2018;15(13):1480-1485. DOI 10.7150/ijms.27333Wee H.J., Huang G., Shigesada K., Ito Y. Serine phosphorylation ofRUNX2 with novel potential functions as negative regulatorymechanisms. EMBO Rep. 2002;3(10):967-974. DOI 10.1093/emboreports/kvf193.Wei Y., Chen Y.H., Li L.Y., Lang J., Yeh S.P., Shi B., Yang C.C.,Yang J.Y., Lin C.Y., Lai C.C., Hung M.C. CDK1-dependent phosphorylationof EZH2 suppresses methylation of H3K27 and promotesosteogenic differentiation of human mesenchymal stem cells.Nat. Cell Biol. 2011;13(1):87-94. DOI 10.1038/ncb2139.Weilner S., Schraml E., Wieser M., Messner P., Schneider K., WassermannK., Micutkova L., Fortschegger K., Maier A., Westendorp R.,Resch H., Wolbank S., Redl H., Jansen-Durr P., Pietschmann P.,Grillari-Voglauer R., Grillari J. Secreted microvesicular miR-31 inhibitsosteogenic differentiation of mesenchymal stem cells. AgingCell. 2016;15(4):744-754. DOI 10.1111/acel.12484Wein M.N., Liang Y., Goransson O., Sundberg T.B., Wang J., WilliamsE.A., O\u2019Meara M.J., Govea N., Beqo B., Nishimori S., NaganoK., Brooks D.J., Martins J.S., Corbin B., Anselmo A., SadreyevR., Wu J.Y., Sakamoto K., Foretz M., Xavier R.J., Baron R.,Bouxsein M., Gardella T.J., Divieti-Pajevic P., Gray N.S., KronenbergH.M. SIKs control osteocyte responses to parathyroid hormone.Nat. Commun. 2016;7:13176. DOI 10.1038/ncomms13176Wein M., Spatz J., Nishimori S., Doench J., Root D., Babij P., NaganoK., Baron R., Brooks D., Bouxsein M., Pajevic P.D., KronenbergH.M. HDAC5 controls MEF2C-driven sclerostin expression inosteocytes. J. Bone Miner. Res. 2015;30(3):400-411. DOI 10.1002/jbmr.2381.Wiedl A., Forch S., Fenwick A., Mayr E. Fractures\u2019 associated mortalityrisk in orthogeriatric inpatients: a prospective 2-year survey.Eur. Geriatr. Med. 2020;12(1):61-68. DOI 10.1007/s41999-020-00392-1.Wood C.L., Stenson C., Embleton N. The developmental origins ofosteoporosis. Curr. Genomics. 2015;16(6):411. DOI 10.2174/1389202916666150817202217.Xu F., Li W., Yang X., Na L., Chen L., Liu G. The roles of epigeneticsregulation in bone metabolism and osteoporosis. Front Cell Dev.Biol. 2020;8:619301. DOI 10.3389/fcell.2020.619301.Xu Y., Ma J., Xu G., Ma D. Recent advances in the epigenetics ofbone metabolism. J. Bone Miner. Metab. 2021;39(6):914-924. DOI10.1007/s00774-021-01249-8.Yalaev B.I., Khusainova R.I. Epigenetics of osteoporosis. MeditsinskayaGenetika = Medical Genetics. 2018;17(6):3-10. DOI 10.25557/2073-7998.2018.06.3-10. (in Russian)Yalaev B.I., Khusainova R.I. Study of the rs2910164 polymorphicvariant of miR-146a microRNA gene in patients with primary osteoporosis.Geny i Kletki = Genes and Cells. 2020;15(4):40-45. DOI10.23868/202012007. (in Russian)Yalaev B.I., Tyurin A.V., Mirgalieva R.I., Khusnutdinova E.K., KhusainovaR.I. Investigating the role of osteoprotegerin gene polymorphicvariants in osteoporosis. Russ. Open Med. J. 2021;10(1):e0101.DOI 10.15275/RUSOMJ.2021.0101.Yang D., Okamura H., Nakashima Y., Haneji T. Histone demethylaseJmjd3 regulates osteoblast differentiation via transcription factorsRunx2 and osterix. J. Biol. Chem. 2013;288(47):33530-33541. DOI10.1074/jbc.M113.497040Yang K., Tian N., Liu H., Tao X.Z., Wang M.X., Huang W. LncRNAp21promotes osteogenic differentiation of mesenchymal stem cells inthe rat model of osteoporosis by the Wnt/\u03b2-catenin signaling pathway.Eur. Rev. Med. Pharmacol. Sci. 2019;23(10):4303-4309. DOI10.26355/EURREV_201905_17935.Yang M., Pan Y., Zhou Y. miR-96 promotes osteogenic differentiationby suppressing HBEGF-EGFR signaling in osteoblastic cells.FEBS Lett. 2014;588(24):4761-4768. DOI 10.1016/J.FEBSLET.2014.11.008.Yang Y., Yujiao W., Fang W., Linhui Y., Ziqi G., Zhichen W., Zirui W.,Shengwang W. The roles of miRNA, lncRNA and circRNA in the developmentof osteoporosis. Biol. Res. 2020;53(1):40. DOI 10.1186/s40659-020-00309-z.Yin C., Tian Y., Yu Y., Wang H., Wu Z., Huang Z., Zhang Y., Li D.,Yang C., Wang X., Li Y., Qian A. A novel long noncoding RNAAK016739 inhibits osteoblast differentiation and bone formation.J. Cell. Physiol. 2019;2347(7):11524-11536. DOI 10.1002/jcp.27815.Yu W., Wang H.L., Zhang J., Yin C. The effects of epigenetic modificationson bone remodeling in age-related osteoporosis. Connect.Tissue Res. 2022;1-12. DOI 10.1080/03008207.2022.2120392.Zhang J.G., Tan L.J., Xu C., He H., Tian Q., Zhou Y., Qiu C., Chen X.D.,Deng H.W. Integrative analysis of transcriptomic and epigenomicdata to reveal regulation patterns for BMD variation. PLoS One.2015;10(9):0138524. DOI 10.1371/journal.pone.0138524Zhang R.F., Liu J.W., Yu S.P., Sun D., Wang X.H., Fu J.S., Xie Z.LncRNA UCA1 affects osteoblast proliferation and differentiationby regulating BMP-2 expression. Eur. Rev. Med. Pharmacol. Sci.2019;23(16):6774-6782. DOI 10.26355/eurrev_201908_18715.Zhang W., Wu Y., Shiozaki Y., Sugimoto Y., Takigawa T., Tanaka M.,Matsukawa A., Ozaki T. miRNA-133a-5p inhibits the expressionof osteoblast differentiation-associated markers by targetingthe 3\u2032 UTR of RUNX2. DNA Cell Biol. 2018;37(3):199-209. DOI10.1089/dna.2017.3936Zhang Y., Gao Y., Cai L., Li F., Lou Y., Xu N., Kang Y., Yang H.MicroRNA-221 is involved in the regulation of osteoporosis throughregulates RUNX2 protein expression and osteoblast differentiation.Am. J. Transl. Res. 2017;9(1):126-135."} +{"text": "Enterobacterales (MDR-Ent) has reached worrisome levels worldwide. In this context, Escherichia ruysiae is a recently described species mostly found in animals. However, its spread and impact on humans is poorly understood. A stool sample from a healthy individual living in India was screened for the presence of MDR-Ent using culture-based methods. Colonies were routinely identified using matrix-assisted laser desorption ionization\u2013time of flight mass spectrometry (MALDI-TOF MS) and phenotypically characterized by broth microdilution. Illumina and Nanopore whole-genome sequencing (WGS) platforms were implemented to generate a complete assembly. E. ruysiae genomes deposited in international databases were used for a core genome phylogenetic analysis. An extended-spectrum \u03b2-lactamase (ESBL)-producing E. coli strain (S1-IND-07-A) was isolated from the stool. WGS confirmed that S1-IND-07-A was indeed E. ruysiae, belonged to sequence type 5792 (ST5792), core genome (cg) ST89059, serotype O13/O129\u2212:H56-like, clade IV phylogroup, and possessed five virulence factors. A copy of blaCTX-M-15 and five other antimicrobial resistance genes (ARGs) were detected in a conjugative IncB/O/K/Z plasmid. A database search identified 70 further E. ruysiae strains from 16 countries . The core genome phylogeny revealed five major STs: ST6467, ST8084, ST2371, ST9287, and ST5792. Three out of the seventy strains possessed important ARGs: OTP1704 , SN1013-18 , and CE1758 . These strains were of human, environmental, and wild animal origin, respectively. E. ruysiae may acquire clinically important ARGs and transmit them to other species. Due to its zoonotic potential, further efforts are needed to improve routine detection and surveillance across One Health settings.Gut colonization with multidrug-resistant IMPORTANCEEscherichia ruysiae is a recently described species of the cryptic clades III and IV of the genus Escherichia and is commonly found in animals and the environment. This work highlights the zoonotic potential of E. ruysiae, as it has been shown to colonize the human intestinal tract. Importantly, E. ruysiae may be associated with conjugative plasmids carrying clinically relevant antibiotic resistance genes. Therefore, it is important to closely monitor this species. Overall, this study highlights the need for improved identification of Escherichia species and continued surveillance of zoonotic pathogens in One Health settings. Escherichia is comprised of 3 monophyletic species , including cryptic clades I, II, III and IV (E. ruysiae), and V (E. marmotae) corresponding to specific host/source niches where this pathogen can be found, such as commensal E. coli of the gastrointestinal tract in humans (groups A or B1) and animals (group B1) and the environment , such as those encoding extended-spectrum \u03b2-lactamases , which compromise the treatment (The genus armotae) \u20133. FurthB2 or D) . On thisreatment .E. ruysiae has been recently reported from animal and environmental sources, but it is still very rarely isolated in humans , unless a PCR-based approach or whole-genome sequencing (WGS) are used blaCTX-M-14-possessing Escherichia cryptic clade IV strain (OPT1704) was recently isolated from the stool of a traveler to Asia isolated from a fecal sample of a healthy individual living in India. To investigate the spread of E. ruysiae in humans, we searched for other E. ruysiae genomes in international databases and compared the results using core genome phylogenetic analysis. Furthermore, we investigated the distribution of the associated ARGs, plasmids, virulence factors, and serotypes characteristic of strains isolated from various human and nonhuman samples.In this work, we characterized a E. ruysiae strain isolated from a person living abroad. To contextualize our findings, the second aim was to search global databases for other reported E. ruysiae strains isolated from different sources to perform a core genome phylogeny analysis. Finally, we examined the associated ARGs, plasmid replicons, virulence, and serotype distribution of all E. ruysiae strains included in this study to evaluate the potential of E. ruysiae as a human pathogen.The first aim of this study was to characterize a rare ESBL-producing E. coli . As shown in Screening of the individual\u2019s stool yielded a third-generation cephalosporin-resistant strain (S1-IND-07-A) that was identified by MALDI-TOF MS as E. ruysiae . This was also supported by in silico phylotyping, which determined that the species belonged to Escherichia cryptic clade IV.Using WGS, the species was confirmed as blaCTX-M-15, aadA1, dfrA1-like (99.79% identity), qnrS1, sul2, and tet(A). In the chromosome, mutations encoding for the quinolone resistance-determining region substitution (S83A) in GyrA were identified, together with the mdf(A)-like ARG (91.32% identity) . Overall, the genotypic screening results were consistent with the observed phenotype (S1-IND-07-A was of sequence type 5792 (ST5792) and core genome (cg) ST89059. Its genome consisted of a 4.4-Mb chromosome and 2 circular plasmids of 105.8\u2009kb (IncB/O/K/Z) and 1.5\u2009kb [Col(MG828)]. Most ARGs were carried by the IncB/O/K/Z plasmid (p1-S1-IND-07-A): henotype .in silico serotyping revealed that S1-IND-07-A carried O13/O129-like and H56-like antigens. Several virulence factor genes were also identified, including those encoding colonization factors (fimH), fitness (iutA and kpsMII), and toxins (pic and sat) (Table S1). Of note, p1-S1-IND-07-A carried the colicin Ib virulence factor gene cib, which is known to enhance virulence in, for example, E. coli and Salmonella enterica (Table S1) \u201313.E. ruysiae strains of the same sequence type and core genome sequence type (ST5792 and cgST89059). We also included strains isolated from different sources to identify potential ARG hot spots and evaluate the pathogenic potential of E. ruysiae in humans. Overall, we included a total of 70 E. ruysiae genomes with complete metadata from the NCBI and Enterobase databases.To investigate the origin of S1-IND-07-A, we performed a database search for other E. ruysiae strains belonging to the cryptic clades III (n\u2009=\u200936) and IV (n\u2009=\u200935), detected between 1989 and 2022 , environmental , and human sources . The strains originated from 16 countries, mainly from the United States (n\u2009=\u200931) and the United Kingdom (n\u2009=\u200916).As a result, along with our strain, we identified a total of 71 n\u2009=\u20099), ST8084 (n\u2009=\u20098), ST2371 (n\u2009=\u20096), ST9287 (n\u2009=\u20094), and ST5792 (n\u2009=\u20094) were observed. Overall, they consisted of strains isolated from poultry in the UK (C17-1 and C10-7), companion animals in Australia (MVC117 and MVC118), and the environment in the United States \u201317.\u2013E. ruysiae strains from clade IV carried \u03b2-lactamase (bla) genes: CE1758 (blaCMY-2), OPT1704 (blaCTX-M-14 and blaLAP-2), and SN1013-18 (blaCTX-M-15 and blaTEM-1). The blaCTX-M-14 and blaLAP-2 genes in OPT1704 were associated with an IncI plasmid, while the blaCMY-2, blaCTX-M-15, and blaTEM-1 genes in CE1758 and SN1013-18 were unspecified (As depicted in mdf(A) and sitABCD. Furthermore, many replicon sequence types were detected in both clades III and IV, most frequently Col and IncFI type or O36-like (n\u2009=\u200910) and H42-like (n\u2009=\u200915), H52-like (n\u2009=\u200911) and H56-like (n\u2009=\u200910), while clade IV strains were O36-like (n\u2009=\u200911) or O13/O129-like (n\u2009=\u20098) and H56-like (n\u2009=\u200920). Furthermore, many virulence factors were also detected, but only a few were clinically relevant, as they were related to host colonization (fimH), fitness (iutA and kpsMII), toxins , and effectors (aaiC) and pic and sat . Both estB and astA genes have been reported in enterotoxigenic E. coli strains in both diseased pigs and pigs with diarrhea, while pic and sat have been found in enteroinvasive E. coli strains . Compared to p1-S1-IND-07-A, the other plasmids were missing an IS26 flanking region containing tet(A) and sul2 and including a disrupted class I integron (missing sul1) region associated with the dfrA1-aadA1-qacE\u03941-IS26-\u0394blaTEM-1 cassette. Similar integron regions have been reported in hyperepidemic carbapenemase-producing E. coli strains also carrying blaTEM-30-associated IncI1 plasmids from colonized employees of a Swiss veterinary clinic (In our is study . Howevery clinic .blaCTX-M) and multiple hosts \u201327. In f J53d-R1 , thus coEnt in the gut, which may include zoonotic diseases that can be transmitted between humans, animals, and the environment and transfer them to other clinically important bacteria. Therefore, the application of WGS surveillance methods is essential for the discovery and characterization of novel Escherichia species with zoonotic potential and the ability to serve as reservoirs for resistance plasmids. In this context, it is crucial to develop and improve routine laboratory identification techniques such as MALDI-TOF MS to distinguish between Escherichia species.In the present work, we showed that Enterobacterales (MDR-Ent) on his return to Switzerland in 2022 as part of an ongoing prospective screening study (https://data.snf.ch/grants/grant/192514). The stool sample was collected by the volunteer in a sterile container and sent within 1\u2009day to the Institute for Infectious Diseases in Bern for processing (see below). No hospitalization or diarrhea was reported, but previous antibiotic use (not specified) was noted in two independent episodes 2 and 4\u2009months before arrival in Switzerland. The study participant provided written consent, and the study was approved by the ethical committee of the Canton Bern, Switzerland (2020-01683).A healthy 62-year-old Swiss man living in India for 1.3\u2009years was screened for intestinal carriage of multidrug-resistant A stool sample (~50\u2009\u03bcg) was preenriched for 6\u2009h in 10\u2009mL Luria-Bertani (LB) broth supplemented with cefuroxime . The preenrichment was then diluted to a 0.5 McFarland standard, and a 100-\u03bcL aliquot was plated overnight at 36\u2009\u00b1\u20091\u00b0C on a CHROMID ESBL agar plate (bioM\u00e9rieux). The resulting colonies were subcultured on MacConkey II agar overnight at 36\u2009\u00b1\u20091\u00b0C for further processing.Enterobacterales .Species identification of overnight-grown colonies was conducted using MALDI-TOF MS . Antimicrobial susceptibility testing (AST) was performed by broth microdilution implementing the Sensititre GNX2F panel (Thermo Fisher Scientific). Results were interpreted according to the 2023 European Committee on Antimicrobial Susceptibility Testing (EUCAST) v13.0 breakpoints for https://github.com/usadellab/Trimmomatic) and Porechop v0.2.4 (https://github.com/rrwick/Porechop), respectively. Long reads were filtered by read quality using Filtlong v0.2.1 (https://github.com/rrwick/Filtlong) . A complete genome assembly was generated using the hybrid pipeline from Unicycler v0.4.8 (https://github.com/rrwick/Unicycler), and its completeness was confirmed with an independent long-read-only assembly using Flye v2.9-b1768 (https://github.com/fenderglass/Flye) (parameters: \u201c\u2013nano-raw\u201d and \u201c\u2013iterations 5\u201d). Genome assembly coverage was calculated using QualiMap v2.2.2-dev .Genomic DNA for WGS was extracted from strain S1-IND-07-A using the Invitrogen PureLink microbiome DNA purification kit (Thermo Fisher Scientific), and the quality was assessed using NanoDrop and Qubit 3 (Thermo Fisher Scientific). Short-read WGS was performed on a NovaSeq 6000 platform , while long-read WGS was conducted on a MinION sequencer (Oxford Nanopore) using a rapid barcoding library prep (SQK-RBK004) and a FLO-MIN 106D R9 flow cell, as described previously \u201331. In b\u2013E. coli number 1 configuration), cgMLSTFinder v1.2 (parameter: E. coli [Enterobase]), SerotypeFinder v2.0, and VirulenceFinder v2.0 (parameters: 60% minimum coverage and 95% minimum identity), respectively, from the Center for Genomic Epidemiology (https://www.genomicepidemiology.org/). In addition, the phylogroup was determined using the ClermonTyping tool (Clermont Type) available at Enterobase (https://enterobase.warwick.ac.uk/) (Escherichia/Shigella database). Finally, the species ID was confirmed using the Type (Strain) Genome Server (TYGS) (https://tygs.dsmz.de/) and by ANIb (based on BLAST) using JSpeciesWS (https://jspecies.ribohost.com/jspeciesws/) with the genome assembly.The genome assembly of S1-IND-07-A was screened for ARGs, plasmid replicon sequences, sequence type (ST), core genome ST (cgST), serotype, and virulence using ResFinder v4.1, PlasmidFinder v2.1 (parameters: 60% minimum coverage and 50% minimum identity), MLST v2.0 (parameter: https://isfinder.biotoul.fr/) with the BLASTn algorithm. Circular BLASTn plasmid comparisons were performed using BLAST Ring Image Generator v0.95 (https://brig.sourceforge.net/) with the most similar plasmids retrieved from NCBI BLASTn (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and PLSDB v2021_06_23_v2 (https://ccb-microbe.cs.uni-saarland.de/plsdb/) on 27 January 2023.The genome assemblies were automatically annotated using the NCBI Prokaryotic Genome Annotation Pipeline. Insertion sequences (ISs) were manually confirmed using ISfinder and Enterobase (https://enterobase.warwick.ac.uk/species/index/ecoli) databases on 30 January and 2 March 2023, respectively. The species IDs of all the retrieved genomes were confirmed using the TYGS tool as described above.GCA_902498915.1) as the mapping reference. Genome regions with recombination were detected and removed using Gubbins v2.3.4 (https://github.com/nickjcroucher/gubbins). Furthermore, IS regions were identified with ISEScan v1.7.2.3 (https://github.com/xiezhq/ISEScan) and subsequently used to mask single nucleotide variants (SNVs) localized within these regions . A maximum likelihood core genome phylogeny (unrooted) was inferred using IQ-TREE v2.1.2 (http://www.iqtree.org/) with the general time reversible (GTR) model with ascertainment bias correction (parameters: GTR\u2009+\u2009ASC), 1,000 ultrafast bootstraps , and the SH-aLRT test . The tree was visualized and annotated using iTOL v6.7.2 (https://itol.embl.de/). Unless otherwise noted, all software analyses described above were performed with default parameters.A core genome alignment was performed using Snippy v4.4.5 with strain OPT1704 (GenBank assembly accession number E. coli recipient strain J53d-R1 was conjugated with the donor S1-IND-07-A as previously described (blaCTX-M group I primers (The rifampicin-resistant escribed . In shor primers . ExperimCP112983 to CP112985) and under BioProject accession number PRJNA903117.The complete genome sequence of S1-IND-07-A has been deposited at GenBank (accession numbers"} +{"text": "Healthcare personnel (HCP) are at risk for acquiring and transmitting coronavirus disease 2019 (COVID-19) at work. Vaccination against COVID-19 is a primary strategy to prevent transmission in healthcare settings. Our objectives were to describe HCP reporting employer COVID-19 vaccine requirements, identify differences across occupations and settings, and describe policies.In a national opt-in internet panel survey of HCP in April 2022 to assess influenza and COVID-19 vaccination coverage, respondents were also asked about employer vaccination requirements. We weighted responses to the U.S. HCP population by age, sex, race, ethnicity, work setting, and U.S. census region. We assessed differences using two-tailed t tests with significance set at p< 0.05. We used multivariable logistic regression to identify factors associated with reporting employer requirements.Of 3,618 responding HCP, 60.0% reported employer requirements for the COVID-19 primary series. Of those, 95.5% reported completing the primary series vs. 81.9% without requirements (p< 0.001). In addition, 24.0% of HCP reported employer requirements for a booster dose. Of those eligible, 90.8% reported receiving a booster vs. 60.2% without a requirement (p< 0.001). Employer requirements for the primary series varied by occupation [46.1% (assistants/aides) to 77.5% (nurses)] and work setting [40.4% to 75.4% ]. Of 2,157 HCP reporting a primary series requirement, employer accepted reasons for not being vaccinated included medical (56.8%), religious (50.9%), philosophical (10.0%), all three reasons (16.7%), and no reason (14.9%). Factors independently associated with no reported primary series requirements included working as an assistant/aide, in a non-clinical or other clinical occupation, in ambulatory care, long-term care/home health, or other clinical setting, and in the Midwest and South.Most HCP in this sample reported employer requirements for the COVID-19 vaccination primary series although requirements were less common for boosters. Differences by healthcare setting exist. Implementing workplace strategies, including vaccine requirements, may lead to higher COVID-19 vaccination coverage.All Authors: No reported disclosures"} +{"text": "Wikstroemia indica, a plant belonging to the Thymelaeaceae family, was investigated by LC-MS/MS analysis. As a result, 21 daphnane diterpenoids (1\u201321) in the stems of W. indica were detected. Among these, six major compounds were isolated and their structures were unequivocally identified through a comprehensive analysis of the MS and NMR data. For the minor compounds , their structures were elucidated by in-depth MS/MS fragmentation analysis. This study represents the first disclosure of structurally diverse daphnane diterpenoids in W. indica, significantly contributing to our understanding of bioactive diterpenoids in plants within the Thymelaeaceae family.Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has emerged as a powerful tool for the rapid identification of compounds within natural resources. Daphnane diterpenoids, a class of natural compounds predominantly found in plants belonging to the Thymelaeaceae and Euphorbiaceae families, have attracted much attention due to their remarkable anticancer and anti-HIV activities. In the present study, the presence of daphnane diterpenoids in Liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-HR-MS/MS), usually equipped with an electrospray ionization source, has high adaptability across a broad spectrum of compounds, offering high mass accuracy and sensitivity. Moreover, it provides information-rich fragmentation through product ion spectra, thereby potentially revealing details about the molecular formula and structure of diverse secondary metabolites found in plants . The contrans-fused 5/7/6-tricyclic skeleton, have garnered attention for their diverse biological activities, including anticancer +) were observed in positive ion mode, while deprotonated molecular ions ([M\u2013H]\u2212) and/or formate adduct ions ([M + HCOO]\u2212) were observed in negative ion mode. (2) In the product ion spectrum obtained from the protonated molecular ion as a precursor ion, a diagnostic ion at m/z 253 (C17H17O2) or 269 (C17H17O3) was observed in the positive ion mode . Th. Th12, 1e G (12) , wikstro + appeared with greater intensity in the mass spectrum of peak 3 + (1), m/z 1028.4264 [M + NH4]+ (2), m/z 585 [M + H\u2013H2O]+ (3), m/z 547.2888 [M + H]+ (4), m/z 655.3469 [M + H]+ (5), m/z 719.3062 [M + H]+ (6), m/z 533.3104 [M + H]+ (7), m/z 775.3690 [M + H]+ (8), m/z 691.3133 [M + H]+ (9), m/z 721.3203 [M + H]+ (10), m/z 775.3687 [M + H]+ (11), m/z 912.4147 [M + NH4]+ (12), m/z 667.3107 [M + H]+ (13), m/z 673.2999 [M + H]+ (14), m/z 533.3107 [M + H]+ (15), m/z 557.3109 [M + H]+ (16), m/z 675.3151 [M + H]+ (17), m/z 639.3527 [M + H]+ (18), m/z 643.3458 [M + H]+ (19), m/z 639.3525 [M + H]+ (20), and m/z 585.3409 [M + H]+ (21). All data collected in the profile mode were acquired and processed using Thermo Xcalibur 4.1 software.The LC-MS/MS analysis was performed using the same instruments and column as in previous experiments . For LC W. indica through a combination of LC-MS guided isolation and MS/MS fragmentation elucidation. The investigation revealed that W. indica contained structurally diverse daphnane diterpenoids, including orthoester daphnane type, polyhydroxy daphnane type, and macrocyclic daphnane orthoester type compounds. The application of MS/MS fragmentation elucidation for structural analysis enabled the rapid and precise identification of these diterpenoids within crude plant extracts. This methodology holds great promise for future research endeavors aimed at discovering bioactive diterpenoids from plants of the Thymelaeaceae family.This study represents the first comprehensive identification of 21 daphnane diterpenoids from the stems of"} +{"text": "Correction: Respiratory Research (2022) 23:291 10.1186/s12931-022-02195-3Following the publication of the original article , it was The original article has been corrected.Additional file 8: Table S1. The RECORD statement\u2014checklist of items, extended from the STROBE statement, that should be reported in observational studies using routinely collected health data.Additional file 9: Table S2. Disease names adopted as inclusion criteria.Additional file 10: Table S3. Disease names adopted as exclusion criteria."} +{"text": "Mycobacterium marinum strain, which was isolated from skin tissue of a wound infection. This strain was subjected to short- and long-read sequencing. Its complete genome contains a single 6,393,703-bp circular chromosome. Phylogenomic analysis of all M. marinum genomes assigned this strain to cluster I.We report the complete genome sequence of a Mycobacterium marinum is an opportunistic human pathogen were filtered using NanoFilt v2.8.0 (de novo using Canu v2.2 (https://github.com/nanoporetech/medaka).Genomic DNA was extracted using a QIAamp minikit. Large DNA fragments were recovered using a Blue Pippin recovery system. Barcodes were added using PCR-free EXP-NBD104, adapters were ligated using a SQK-LSK109 connection kit (Oxford Nanopore), and long-read sequencing was performed using the Nanopore PromethION platform. Raw Nanopore signals were subjected to base calling, demultiplexing, and adapter trimming using Guppy v6.3.9 with a sanu v2.2 , Flye v2https://github.com/usadellab/Trimmomatic) and were used to polish the Nanopore assembly with two alternating rounds of Polypolish v0.5.0 . Paired reads were trimmed using Trimmomatic v0.39 , M. pseudoshottsii JCM15466T (AP018410.1), M. shottsii JCM12657T (AP022572.1), and M. ulcerans Agy99T (CP000325.1) was 98.56%, 98.36%, 97.70%, and 98.09%, respectively, as determined using FastANI v1.33 rotated to start with NI v1.33 . Neverthm 050012 , 18, conM. marinum genome assemblies (n = 51) and SRA reads (n = 88) from NCBI. SRA reads were trimmed using Trimmomatic and assembled de novo using SPAdes v3.15.3 (n = 26) were removed. All genomes (n = 113) were identified as M. marinum as described above. Single nucleotide polymorphisms (SNPs) were called using M. marinum CCUG20998T as a reference using Snippy v4.6.0 (https://github.com/tseemann/snippy) with --ctgs option and Gubbins v3.2.1 with a general time-reversible (GTR) model plus gamma distribution and a 100-bootstrap test (M. marinum strains belong to two major clusters (I and II), consistent with previous findings and SRR23294010 (Illumina reads), and GenBank nucleotide accession number CP118910.Complete genome sequences of"} +{"text": "Scientific Reports 10.1038/s41598-023-33920-7, published online 27 April 2023Correction to: The original version of this Article contained errors in the Materials and methods section, under the subheading \u2018Software and hardware specification\u2019, where links to used resources were omitted and the present link was incorrect.https://docs.nvidia.com/deeplearning/frameworks/tensorflow-release-notes/rel_21-03.html).\u201d\u201cThe sMRI preprocessing was done through the SPM12 v7771 software. All further steps used Python 3.8.5 and Tensorflow 2.4.0. The machine learning experiments were performed on an NVIDIA DGX-2 server, within a Docker virtual machine containing 4 CPUs @2.7Ghz and 1 GPU TESLA V100-SXM3-32 GB. All source codes are available at Github (now reads:https://www.fil.ion.ucl.ac.uk/spm/software/spm12/). All further steps used Python 3.8.5 and Tensorflow 2.4.0 (https://docs.nvidia.com/deeplearning/frameworks/tensorflow-release-notes/rel_21-03.html). The machine learning experiments were performed on an NVIDIA DGX-2 server, within a Docker virtual machine containing 4 CPUs @2.7Ghz and 1 GPU TESLA V100-SXM3-32 GB. All source codes are available at Github .\u201d\u201cThe sMRI preprocessing was done through the SPM12 v7771 software (The original Article has been corrected."} +{"text": "Adherence to antiretroviral therapy (ART) is critical for persons with HIV (PWH) for achieving durable virologic suppression and minimizing drug resistance. This study aimed to characterize ART adherence and its effect on quality of life (QoL) among PWH using real-world data.Data were drawn from the Adelphi HIV Disease Specific Programme\u2122, a cross-sectional survey of physicians and PWH in the U.S., collected between July-2021 and March-2022. At consultation, each of 60 physicians reported demographics, clinical characteristics, ART adherence and satisfaction on 10 consenting PWH. These PWH were then invited to complete questionnaires reporting QoL . Physicians categorized adherence as completely adherent (C-Adh), mostly adherent (M-Adh), or less adherent (L-Adh). Comparisons were made using Chi squared test.Of 578 PWH with physician-reported adherence status; mean [SD] age 44.9 [12.8] years, 70.4% cisgender male, 50.5% White. A total of 389 (67%) were C-Adh, 155 (27%) M-Adh, and 34 (6%) L-Adh. L-Adh (55.9%) and M-Adh (46.5%) PWH had the higher proportion of ART side effects compared to C-Adh (29.3%); p< 0.001. Also, L-Adh (75.8%) and M-Adh (50.8%) were more likely to report current HIV-associated symptoms than C-Adh PWH (29.3%); p< 0.001. C-Adh PWH were perceived as very satisfied with their ART (68.4%), compared to M-Adh 39.4% and L-Adh 23.5%; p< 0.001. Reasons for PWH skipping ART included forgetting, difficulties integrating into routine, and ART side effects . QOL survey was completed by 229 PWH. QoL was higher for C-Adh PWH, measured by PozQol score mean, and EQ-5D score mean .About one-third of PWH who were not fully adherent to ART, and this was correlated with having poorer QoL. These findings highlight the need to better understand factors leading to sub-optimal ART adherence, to provide targeted interventions to improve quality of life.Girish Prajapati, M.B.B.S., MPH , Merck & Co., Inc.: Employee|Merck & Co., Inc.: Stocks/Bonds Bekana K. Tadese, PhD, MPH, Merck and Co Inc: Employee"} +{"text": "We report the genome sequences of two genetic variants of grapevine rupestris stem pitting-associated virus (GRSPaV) from Idaho, USA. The coding-complete, positive-strand RNA genome of 8,700 nucleotides contains six open reading frames characteristic of foveaviruses. The two Idaho genetic variants belong to GRSPaV phylogroup 1. Foveavirus (family Betaflexiviridae) (Vitis vinifera L. and its hybrids (\u2013\u2013Grapevine rupestris stem pitting-associated virus (GRSPaV) has flexuous filamentous particles and belongs to the genus viridae) . GRSPaV viridae) . The vir hybrids \u20134. The vhybrids \u2013, 5, 6; ihybrids \u2013\u20139.V. vinifera reference genome using bowtie2 v2.4.4 in local mode from British Columbia, Canada. The same Riesling sample also yielded three additional contigs of 2,514, 2,893, and 506 nt, which exhibited 98.3%, 98.6%, and 98.8% identity, respectively, to the GRSPaV isolate AMCF clone 3 (GenBank accession number MG938311) from France contig (GRSPaV-ID1) that spanned six ORFs and, based on the BLASTn program , exhibited 98.5% identity to the GRSPaV isolate 12G412 under BioProject accession number PRJNA931750.The coding-complete genome sequences of GSPaV-ID1 and GSPaV-ID2 are available in GenBank under accession numbers"} +{"text": "Invasive fungal infections present a significant risk to human health. The current arsenal of antifungal drugs is hindered by drug resistance, limited antifungal range, inadequate safety profiles, and low oral bioavailability. Consequently, there is an urgent imperative to develop novel antifungal medications for clinical application. This comprehensive review provides a summary of the antifungal properties and mechanisms exhibited by natural polyketides, encompassing macrolide polyethers, polyether polyketides, xanthone polyketides, linear polyketides, hybrid polyketide non-ribosomal peptides, and pyridine derivatives. Investigating natural polyketide compounds and their derivatives has demonstrated their remarkable efficacy and promising clinical application as antifungal agents. Candida, Cryptococcus, and Aspergillus species . Th. ThFusar B1 (87) . The C. toxicity . Parnafud D (93) , analogstructure . Parnafu 5 \u03bcg/mL (Table 194) shows antifungal activity against C. albicans, C. neoformans, and S. cerevisiae, with MIC values of 2, 2, and 15.6 \u03bcg/mL, respectively [94) has been shown to possess fungicidal activity against C. albicans, C. neoformans, and S. cerevisiae with minimum fungicidal concentrations of 4, 4, and 15.6 \u03bcg/mL, respectively [95) (S. cerevisiae (MIC > 200 \u00b5M), indicating the importance of the aldonic acid group for the antifungal activity of khafrefungin (94) [96) (94), indicating that the aldonic acid group not only enhances the water solubility of khafrefungin (94) but also plays a role in its antifungal activity [97) (94), highlighting the essentiality of the configuration of the 4-methyl group for the antifungal activity of khafrefungin (94) [94) under acidic conditions forms a six-membered lactone derivative (98) (S. cerevisiae (MIC = ~10 \u00b5M) to that of native khafrefungin (94) [The polyketide chain skeleton was catalyzed by type I PKSs and then subjected to complex post-modifications, including glycosylation, to form linear polyketide . There a94) , isolateaffected . Khafrefectively . Additioectively . Notablyely [95) greatly gin (94) . The pre94) [96) has beenactivity . Furtherity [97) has beengin (94) . Additioive (98) that exhgin (94) Table 194 (S. ceBacillus laterosporus PNG 276 [99) (62) were administered to human diploid fibroblasts, with basiliskamide A (99) exhibiting minimal cytotoxicity at a concentration of 100 \u03bcg/mL, while cytopathic effect was observed with amphotericin B (62) only 12.5 \u03bcg/mL [99) demonstrated antifungal activity against C. albicans and A. fumigatus, with MIC values of 1 and 2.5 \u03bcg/mL, respectively, whereas basiliskamide B (100) (101) (99), inhibits the growth of C. albicans at a concentration of 25 \u03bcg/mL and has no effect on the growth of A. fumigatus at a concentration of 50 \u03bcg/mL [101) exhibits an additional methylene group compared to the linear polyketide chain of basiliskamide A (99), potentially accounting for the diminished antifungal activity of YM-45722 (101) [Basiliskamide A and B are isolated from PNG 276 . Basilis276 [99) and amph.5 \u03bcg/mL . Further B (100) exhibite0) (101) , an anal50 \u03bcg/mL (Table 122 (101) .FKS1 and FKS2 genes results in the inhibition of biosynthesis of \u03b2--D-glucan, an important component of the fungal cell wall, which destroys the integrity of fungal cell wall and disrupts the osmotic balance, ultimately leading to fungal death [Candida and Aspergillus species, but they are ineffective against C. neoformans [0 (102) (103) (0 (102) are discussed in this section. Pneumocandin B0 (102) is isolated from the filamentous fungus Glarea lozoyensis [0 (102) is a lipopeptide composed of myristic acid and a hexapeptide ring. PKSs catalyze the assembly of 10, 12-dimethylmyristic acid, and then, catalyzed by a series of enzymes, the polyketide intermediate localizes to NRPSs to acylate the 4, 5-dihydroxyornithine of pneumocandin B0 (102), initiating cyclic hexapeptide elongation.Echinocandins are novel lipopeptide antifungal products synthesized by a heterozygous pathway of non-ribosomal peptides synthases (NRPSs)-PKSs. Compared with azole and polyene antibiotics, echinocandins have a completely different mechanism of action and exert their antifungal effect by destroying the cell wall. Non-competitive binding of echinocandins to the catalytic subunits of \u03b2--D-glucan synthetase encoded by the al death ,83. Echioformans , the lea2) (103) , is assezoyensis ,88. Pneu104) and 1097 (105) (Burkholderia ambifaria 2.2N [S. cerevisiae (MIC = 0.4 \u03bcg/mL), C. albicans (MIC = 12.5 \u03bcg/mL), and A. niger (MIC = 12.5 \u03bcg/mL) [S. cerevisiae (MIC = 1.6 \u03bcg/mL), A. niger (MIC = 1.6 \u03bcg/mL), and C. albicans (MIC = 12.5 \u03bcg/mL). Burkholdine 1215 (106), 1119 (107), and 1213 (108) (Burkholderia ambifaria [106) exhibits potent antifungal activity against S. cerevisiae (MIC = 0.15 \u03bcg/mL), C. albicans (MIC = 0.15 \u03bcg/mL), and A. niger (MIC = 0.15 \u03bcg/mL) [107) exhibits potent antifungal activity against S. cerevisiae (MIC = 0.1 \u03bcg/mL), C. albicans (MIC = 0.4 \u03bcg/mL), and A. niger (MIC = 0.1 \u03bcg/mL) [108) exhibits potent antifungal activity against S. cerevisiae (MIC = 2.0 \u03bcg/mL), C. albicans (MIC = 31.0 \u03bcg/mL), and A. niger (MIC = 2.0 \u03bcg/mL) [106) and 1119 (107) containing 2,4-diaminobutyric acid adjacent to the 3-OH-Tyr structure is higher than that of burkholdines 1229 (104), 1097 (105), and 1213 (108) containing Asn adjacent to the 3-OH-Tyr structure [106) and 1119 (107) is significantly higher than hemolytic activity, but the antifungal activity of burkholdines 1229 (104), 1097 (105), and 1213 (108) is equivalent to hemolytic activity [107), assigning an Asn replaced a 3-OH-Asn and attaching a \u03b2-xyloside glycosyl portion replaced a \u03b1-xyloside glycosyl portion compared to burkholdine 1215 (106), shows weaker activity against C. albicans (MIC = 0.4 \u03bcg/mL) and stronger activity against A. niger (MIC = 0.1 \u03bcg/mL). Burkholdine 1213 (108), attaching an Asn replaced a 2,4-aminobutyric acid of burkholdine 1119 (107), shows weaker activity against both C. albicans (MIC = 31.0 \u03bcg/mL) and A. niger (MIC = 2.0 \u03bcg/mL). Burkholdine 1229 (104), assigning a 3-OH-Asn replaced an Asn of burkholdine 1213(108), shows stronger activity against C. albicans (MIC = 12.5 \u03bcg/mL) and weaker activity against A. niger (MIC = 12.5 \u03bcg/mL). Burkholdine 1097 (105), removing the \u03b2-xyloside glycosyl portion of burkholdine 1229 (104), shows the same activity against C. albicans (MIC = 12.5 \u03bcg/mL) and stronger activity against A. niger (MIC = 1.6 \u03bcg/mL) (Burkholdines 1229 (97 (105) are isolria 2.2N . Burkhol5 \u03bcg/mL) . Burkhol13 (108) are isolmbifaria . Burkhol5 \u03bcg/mL) . Burkhol1 \u03bcg/mL) . Burkhol0 \u03bcg/mL) . The anttructure . The antactivity . Burkhol6 \u03bcg/mL) .109) , C. utilis (MIC = 5 \u00b5g/mL), C. neoformans (MIC = 2 \u00b5g/mL), S. cerevisiae (MIC = 20 \u00b5g/mL), T. mentagrophytes (MIC = 15 \u00b5g/mL), T. rubrun (MIC = 3.9 \u00b5g/mL), M. gypseum (MIC < 0.12 \u00b5g/mL), Blastomyces derniatitidis (MIC < 0.12 \u00b5g/mL), and Hormodendrum pedrosoi (MIC = 15 \u00b5g/mL) [109) has demonstrated significant potent efficacy in vivo, as evidenced by its ability to effectively treat T. mentagrophytes hyphae infection in guinea pigs. Specifically, a hydrophilic ointment containing 0.5% funiculosin had a cure rate of 97% within 10 days [109) to guinea pigs and rabbits was negligible, as evidenced by the survival of guinea pigs injected intraperitoneally with 500 mg/kg of the compound. However, it should be noted that funiculosin is toxic to mice and rats, with an LD50 of 5\u20137 mg/kg for both oral and intraperitoneal administration [Funiculosin (109) , a neutrsum THOM , has beesum THOM ,93 and w5 \u00b5g/mL) ,94 (Tabl110) and skyrin (111) inhibits the growth of C. albicans ATCC 10231 (MIC = 6.25 \u03bcg/mL), A. niger ATCC 13496 (MIC = 12.5 \u03bcg/mL), and skyrin (111) inhibits the growth of C. albicans ATCC 10231 (MIC = 12.5 \u03bcg/mL) [112) (Fusarium oxysporum (N17B) and exhibits potent antifungal activity against C. albicans with a MIC of 0.78 \u03bcg/mL [113) inhibits mammalian phosphatidylinositol 3-kinase in vitro and in vivo and membrane-associated phosphatidylinositol 4-kinase of the fungus Schizosacchromyces pombe [114) and B (115) (Microsphaeropsis species RA10-14 collected from the South China Sea [114) and B (115) have great broad-spectrum antifungal activity against C. albicans, Colletotrichum truncatum, Gloeosporium musarum, and Pestalotia calabae (MICs = 1.56\u20133.13 \u03bcg/mL) [116) and C (117) (Amycolatopsis species M39 [116) shows antifungal activity against C. albicans ATCC 10231 (MIC = 10 \u03bcg/mL) and S. cerevisiae ATCC9763 (MIC = 5 \u03bcg/mL) [117) shows weaker antifungal activity against C. albicans ATCC 10231 (MIC = 25 \u03bcg/mL) and S. cerevisiae ATCC9763 (MIC = 20 \u03bcg/mL) [118), hakuhybotrol (119), cladobotric acid A (120), cladobotric acid F (121), cladobotric acid E (122), cladobotric acid H (123), and pyrenulic acid A (124) , B (126), C (127), and D (128) , B (126), C (127), and D (128) show antifungal activity against C. neoformans H99 with MIC values of 8 \u03bcg/mL, 4 \u03bcg/mL, 4 \u03bcg/mL, and 8 \u03bcg/mL, respectively (Emodin (in (111) are anths ZH-154 . Emodin 5 \u03bcg/mL) . HippolaL) [112) is a fur\u03bcM [113) is a fur78 \u03bcg/mL . Wortmanes pombe . Microke B (115) are isolhina Sea . Microke3 \u03bcg/mL) . Macrote C (117) are macrcies M39 . Macrote5 \u03bcg/mL) . Macrote0 \u03bcg/mL) . F2928-1 A (124) are isola FKA-73 . These clentulus . Campafu D (128) are isolectively .In conclusion, this review provides a comprehensive overview of natural antifungal polyketides encompassing various subclasses such as polyethers, macrolides, xanthones, linear polyketides, anthraquinone, polyphenols, pyridine derivatives, furan derivatives, pyranan derivatives, monophenyl derivatives, macrolactam polyketides, hybrid polyketide non-ribosomal peptides, and other polyketides. Additionally, this review discusses the origin, in vitro and in vivo antifungal activities, structure\u2013activity relationship (SAR), safety profile, mechanism of action, and the impact of structural modifications on the SAR of these polyketides. Previous studies on polyketides have demonstrated the substantial antifungal properties exhibited by certain natural polyketides, such as amphotericin B and caspofungin. This observation suggests that polyketide lead compounds hold considerable potential for the future treatment of fungal infections. Given the remarkable antifungal activities displayed by natural polyketides, this class of compounds has garnered significant interest as a potential therapeutic avenue for fungal infections in the future. Currently, the predominant research emphasis lies in synthesizing novel polyketides, while the clinical utilization of pre-existing polyketide compounds as antifungal medications remains limited. Consequently, further comprehensive and meticulous clinical investigations are imperative to substantiate their efficacy in the future. Moreover, the antifungal properties of unnatural polyketide compounds can potentially be harnessed through combinatorial biosynthesis. Numerous PKSs facilitate the production of primary polyketide compounds, which lack biological activity until they undergo modification by PKS post-modifying enzymes, thereby presenting a promising avenue for exploring new antifungal drugs. Polyketides\u2019 chemical composition and fungicidal properties can be altered by utilizing various post-modification enzymes, including cyclase, aromatase, glycosylase, and halogenase. Unconventional antifungal polyketides have been synthesized by modifying the modules, domains, and subunits of PKSs and employing site-directed mutagenesis techniques. Furthermore, the enhancement of antifungal polyketide production or the acquisition of novel antifungal polyketides can be achieved by combining initiation substrates and elongation units from different hosts and implementing targeted modifications. Only a small number of antifungal natural polyketide compounds have been identified. Many habitats of microorganisms, plants, animals and marine organisms have not been explored, and many antifungal polyketide products urgently need to be discovered. Natural polyketides from microorganisms such as fungi are scarce and difficult to obtain. The solubility, safety, and in vivo bioavailability of natural polyketides should also be considered. Semisynthetic components of natural products will play an important role in developing antifungal candidates in the future."} +{"text": "Passive immunization via maternal antibodies (Ab) is a key mechanism for infant protection in early life. This study analyzed the landscape of passive immunization induced by SARS-CoV-2 infection and/or vaccination by comparing the magnitude and durability of the transferred Ab.Prospective multicenter observational cohort study of SARS-CoV2-infected and/or vaccinated pregnant women and their infants. We collected maternal and cord blood samples at delivery and neonatal/infant samples at delivery, and at 1, 2, 6 and 12 months (mo) of age. RBD and Spike IgG Ab titers were measured by ELISA.10 ng/ml and from infected and vaccinated mothers [4.61 (4.27-4.93)] log10 ng/ml were higher than those from infected mothers [2.20 (0.10-3.30)] log10 ng/ml, p< 0.001. These differences were observed until 6 mo of age, when only 1/13 (7.7%) infant from infected mothers had detectable maternal Ab compared to 14/15 (93.3%) and 8/8 (100%) from the vaccinated, and infected and vaccinated groups, respectively. At 12 mo none of the infants born to infected mothers had detectable maternal Ab, while in the vaccinated group (n=11), 3 (27.3%) had persistent Ab, and 4 (36.4%) suspected infection. At 12 mo in the infected and vaccinated group (n=6) 3 had no Ab, and 3 had suspected infection. The median [IQR] placental Ab transfer ratio was higher in the vaccinated only group (2.94 [1.34-3.74]) than the infected only group (1.19 [0.33-2.52]) p< 0.01. Linear regression analyses demonstrated that the mean RBD Ab transfer ratio for infants from vaccinated vs infected women was 1.76 higher after adjusting for trimester of infection or vaccination. Similar results were observed with Spike Ab.215 mothers and 174 infants were enrolled. At birth RBD Ab titers median [IQR] of infants from vaccinated mothers [4.28 (3.48-4.80)] logDemographic and clinical characteristics of the study populationm; median. IQR; interquartile range. N/A; not applicable.Infants from vaccinated mothers demonstrated maternal Ab up to 6 mo with higher titers than infants born from infected mothers. Antibodies generated by vaccination were transferred more efficiently than those generated by infection regardless of the trimester in which occurred.Asuncion Mejias, MD, PhD, MsCS, Astra-Zeneca: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Sanofi-Pasteur: Advisor/Consultant Octavio Ramilo, MD, AstraZeneca: Honoraria|Bill & Melinda Gates Foundation: Grant/Research Support|Janssen: Grant/Research Support|Merck: Advisor/Consultant|Merck: Grant/Research Support|Merck: Honoraria|NIH: Grant/Research Support|Pfizer: Advisor/Consultant|Pfizer: Honoraria|Sanofi: Advisor/Consultant|Sanofi: Honoraria"} +{"text": "Candida, Aspergillus, and Pneumocystis spp. in BMT.Rezafungin (RZF) once weekly (QWk) is a next-generation echinocandin in development for treatment of candidaemia and invasive candidiasis (IC) and for prevention of invasive fungal disease caused by The Phase 3 ReSTORE treatment trial (NCT03667690) demonstrated RZF QWk noninferiority to caspofungin (CAS) QD. This sub-analysis evaluated efficacy and safety outcomes in patients identified as immunocompromised (immuno-c) during the trial.As previously described, adults with confirmed candidaemia and/or IC were randomized to RZF QWk (400 mg Wk1 then 200 mg QWk) or CAS QD for \u226514 days (\u22644 weeks) with optional oral fluconazole stepdown for CAS. In this sub-analysis, immuno-c patients were those with prior and/or concomitant use of immunosuppressants and/or medical history ongoing at screening of neutropenia, BMT, SOT, lymphoma or leukaemia.Of 187 patients (mITT population), 90 were immuno-c as defined. Results are for those with data available for analyses: Day 14 global cure\u2014Immuno-c: RZF, 51.1% (23/45); CAS, 55.6% (25/45); \u2013No immuno-c: RZF, 66.7% (32/48); CAS 65.3% (32/49). Day 5 mycological eradication\u2014Immuno-c: RZF, 64.4% (29/45); CAS, 51.1% (23/45); no immuno-c: RZF, 72.9% (35/48); CAS, 71.4% (35/49). Among immuno-c, more had \u22651 AE (96.9%) and \u22651 SAE (64.6%) versus no immuno-c (79.0% and 45.0% respectively).In this sub-analysis of ReSTORE, immune-c status reduced efficacy rates overall but did not change efficacy rate differences between RZF and CAS."} +{"text": "Wheat (Triticum aestivum L.) is a staple food and major source of dietary calories in Pakistan. Improving wheat varieties with higher grain yield and disease resistance is a prime objective. The knowledge of genetic behaviour of germplasm is key. To achieve this objective, elite wheat varieties were crossed in 4 by 3, line \u00d7 tester design, and tested in 2019 in a triplicate yield trial to estimate genetic variance, general and specific combining ability, mid-parent heterosis and stripe rust (Puccinia striiformis L.). High grain 3358 kg\u00b7ha\u20131 was recorded in F1 hybrid (ZRG-79 \u00d7 PAK-13). Analysis of variance (ANOVA) revealed significant genotypic variance in grain yield. Broad sense heritability (H2) was recorded in the range of 28 to 100 %. General combining ability (GCA) significant for grain yield in parents except FSD-08 and PS-05 was recorded, while specific combining ability (SCA) was recorded to be highly significant for grain yield only in two crosses (ZRG-79 \u00d7 NR-09 and ZRG-79 \u00d7 PAK-13). Mid-parent heterosis was estimated in the range of \u201328 to 62.6 %. Cross combinations ZRG-79 \u00d7 PAK-13 depicted highly significant mid-parent heterosis (62.6 %). Highly significant correlation was observed among spike length, spikelets per spike, plant height and 1000-grain weight. Rust resistance index was recorded in the range of 0 to 8.5. These findings suggest exploitation of GCA for higher grain yield is important due to the presence of additive gene action and selection in the filial generations will be effective with improved rust resistance, while cross combinations ZRG-79 \u00d7 PAK-13 high GCA are best suited for hybrid development. Wheat (Triticum aestivum L.) is an important cereal cropworldwide playing a crucial role in the daily dietary and nutritionalrequirement not only for human beings but also foranimals. It is the major food for one third of world populationand its chief use is the flour for making bread. It is grownaround all continents. Increasing human population, climatechange and global pandemics have an overwhelming impacton food security, especially wheat on crop with current inadequategenetic improvement of wheat to meet future demand.In Pakistan, wheat is grown in an area of 9.2 million ha withthe production of around 25.5 m tonnes and hardly meets the total requirement of the country. But thisfigure is continuously under fluctuation because of stagnantyield of cultivars, disease impact, drought, and floods. Apartfrom these factors, injudicious selection of parental selectionfor a breeding program without prior knowledge of geneticbehaviour in germplasm and lack of indigenous breedingprograms for genetic improvement of wheat is another constraintin the yield.Genetic recombination in germplasm by hybridization isa robust conventional breeding tool for obtaining transgressivesegregants and genetic variation, which provides meansof selection of ideotypes. Gene action and combining abilityanalysis are a most reliable biometric procedure for the studyof genetic behaviour of yield and yield-related components. General combining ability is the averageperformance of genotypes in a series of cross combinations,while specific combining ability is the performance of a particulargenotype in a specific cross combination. Mode ofselection depends based on genetic action in traits of interest.In self-pollinated crops, especially in wheat, plant breedersare usually interested in selection of segregants having additivegene action with high specific combining ability. Additivegene action boosts yield and yield components by cumulativeaddition of genes. Dominance genetic variance exploits heterosisin cross combinations and specific combining abilityprovides the presence of dominant or non-additive gene actionin a particular trait and provides optimalparental identification . Equalmagnitude of both general and specific combining ability ina breeding population means preponderance of both additiveand dominant genes for the traits of interest; selection in thiscase is most effective for variety development . The term combining ability was first introduced andfurther refined as general combining ability (GCA) and specificcombining ability (SCA) by Sprague and Tatum (1942).GCA distinguishes between the mean performances of parentsin cross combinations whiles SCA is the deviation ofindividual crosses from the average performance of the parentsinvolved. GCA and SCA represent the additive and nonadditiveportions of genotypic variance respectively . The estimates from GCA and SCA provide anassessment of relative merits of the individual genotypes incross combinations to guide selection and testing schemes.Thus, line \u00d7 tester analysis is among the genetic-statisticalapproaches developed to assist in selection of parents based ontheir combining ability and the potential to produce promisingsegregating populations . According toGCA and SCA impacts, positive values are desirable for mostcrop plants characteristics, such as growth and yield-relatedattributes. Negative GCA and SCA impacts, on the otherhand, are desirable for characters where minimum values areessential and appealing, such as early flowering.Heterosis is a phenomenon where F1 hybrids are superiorin traits as compared to their parental genotypes. There areseveral theories that explain the genetic basis of heterosis,including over-dominance, dominance, and genetic balance.The over-dominance theory of heterosis, first proposed byShull and East (1908), suggests that heterozygous individuals,since they carry two different alleles, have an advantage overhomozygous individuals as they carry two identical alleles fora particular gene. This advantage is thought to mean that thetwo different alleles can supplement with each other, leadingto a vigorous phenotype in F1 hybrids. The dominance theory,presented by Jones (1917), suggests that hybrid vigour iscaused by dominant alleles that are more valuable than therecessive alleles. According to this theory, F1 hybrids accedetwo copies of the dominant allele, resulting in a vigorousphenotype. The third heterosis theory is the \u201cLerner\u2019s geneticbalance theory\u201d, suggested by Lerner (1954), that describesthat heterosis is the result of a balance between the expressionof genes that promote growth and those that hamper growth.In F1 hybrids, the expression of growth-promoting genes isincreased, whereas the expression of growth-retarding genesis decreased, leading to better growth and development.Heterotic studies for increasing wheat grain yield have beenan interest of early wheat researchers. Mid-parent heterosisis the percent of the increase or decrease in the F1 value ascompared to the average value of both parents for any metrictrait. In the early green revolution era Pal and Alam (1938)reported mid-parent heterosis (MPH) in wheat. After thegreen revolution and introduction of semi-dwarf wheat varieties,various wheat researchers reported MPH heterosisin wheat . Barbosa-Neto et al. (1996) reported MPH in soft redwinter wheat in the range of \u201320 to 57 %. Liu et al. (1999),Dreisigacker et al. (2005), Basnet et al. (2019) reported MPHin CIMMYT wheat varieties in the range of 9.5 to 14 %.Wheat crop faces numerous challenges that cause yieldlosses, including stripe rust (Puccinia striiformis f. sp. tritici), which is a major disease in areas where cool to mild warmtemperature prevails during the months of February and Marchin the wheat-growing season. Under conducive environmentalconditions, disease causes yield losses ranging from 10 to70 % depending upon susceptibility of genotypes . Development of cultivars containing genetic resistanceis the most cost-effective and environmentally friendlystrategy to mitigate yield losses by stripe rust . Stripe rust spores continue to mutate and evolve newvirulent races causing damage to previously resistant cultivars. Wheat crop in Pakistan has faced severedamage caused by stripe rust pathogen in recent years . Due to climate change and rapid mutation instripe rust pathogen, new races overwintering on alternativehost barberry in hilly areas at high altitudes evolve . Under these circumstances, the already resistantgenotypes become susceptible .There are two types of resistance mechanism against rustpathogens in wheat, vertical resistance, and horizontal resistance.Vertical resistance is conferred by a single gene toa specific pathogenic race of rust, while horizontal resistanceinvolves the use of multiple genes that provide broad spectrumdisease resistance against multiple pathogenic races of rust.There are several resistance genes present in the Pakistanibread wheat varieties that confer resistance against yellow rust,which include Yr5, Yr10, Yr15, Yr17, and Yr18. Qamar et al.(2014) reported Lr34/Yr18 gene complex that confers broadspectrum resistance against yellow rust and leaf rust in mostof Pakistani wheat varieties. Intikhab et al. (2021) reportedthe presence of Lr46/Yr29 gene complex in Punjab-2011 andPirsabak-2005 cultivars that confer resistance against striperust. Khan S.N. et al. (2022) reported the presence of Yr17 andYr5 gene complex in Pakistani wheat varieties Punjab-2011and Pirsabak-2005. Utilization of these resistance sources inthe breeding program for development of varieties resistantagainst stripe rust is an ultimate objective to ensure high yieldon sustainable basis.Various biometrical techniques and breeding designs areused for genetic evaluation and genetic behaviour of germplasmto be utilized in crop breeding programs, but line \u00d7 testeranalysis is an efficient mating design providing reliable informationabout GCA and SCA that ultimately depicts the modeof gene action in a particular trait . GCAand SCA are important to apprehend the genetic architectureof quantitative traits and create the road map for initiation ofan efficient breeding program .Several studies investigating the GCA and SCA effectshave been conducted in wheat. Zhao et al. (2013) reportedsignificant effects for both GCA and SCA for yield and itscomponents and inferred that selecting parental genotypeswith high GCA and SCA effects could lead to the developmentof high-yielding wheat hybrids. Similarly, researchers assessedthe GCA and SCA effects in spring wheat and durum wheatF1 hybrids by using line \u00d7 tester model for combining abilityestimate and concluded that GCA effects were more importantthan SCA effects for grain yield and yield-related traits, andselection of parental genotypes with high GCA effects couldincrease the prospective yield of wheat hybrids . They found thatboth GCA and SCA effects were significant for grain yieldand its components and suggested that selecting parents withhigh GCA and SCA effects could lead to the development ofhigh-yielding wheat hybrids. Selecting parents with high GCAand SCA effects can improve the yield potential and diseaseresistance of wheat hybrids, and the use of line \u00d7 tester designscan provide valuable information about the genetic effects ofparents and their hybridsThe objectives of this study is to elucidate the general andspecific combing ability, heterotic potential, and stripe rust(Puccinia striiformis f. sp. tritici) resistance behaviour ofindigenous elite wheat varieties and their breeding population.Experimental site and plant material. The research was carriedout at the experimental site of a wheat research program,National Agricultural Research Center, Islamabad Pakistanduring 2017\u20132018 wheat growing season. The soil type of thesite is clay loam from 0 to 20 cm, and at the 20\u201340 cm depthit is moderate clay loam. Five widely adopted approved wheatvarieties were used as lines and three widelyadopted, registered and approved varieties for rainfed areasof Pakistan were used as a tester, namely, NARC-2009,Pakistan-2013 and Borlaug-2016 (Table 1). These testers arewidely adopted and due to their ability to withstand rainfed anddrought-prone areas of Pakistan their leaves have the abilityto stay green during high terminal heat and drought stress.Field experiment and crossing scheme. Eight parents werehybridized to produced 15 F1 cross combinations accordingto line \u00d7 tester crossing fashion as described by Kempthorne(1957) during 2017\u20132018 wheat growing season and crossingwas conducted during March 2018. 15 cross combinationsand seven parents were planted in Randomized CompleteBlock Design (RCBD) with three replications during 2018\u20132019 wheat growing season. In every replication, parents andF1 hybrids were sown in 1 m length with row-to-row spacing25 cm and plant-to-plant spacing 15 cm. The experimentwas conducted in an irrigated field and a total of 6 irrigationswere applied after sowing to harvesting time. Recommendeddoses of fertilizers, i. e. 120 kg N \u00b7 ha\u20131 and 80 kg P \u00b7 ha\u20131, wereapplied. Half of the fertilizers were used at the time of soilpreparation, the second half was applied at the time of tillering,and weedicides were used for eradication of broad leaves and narrow leavesweeds respectively according to the doses mentioned by themanufacturer. Herbicide was applied before the jointing stageof the crop. Leaf area was measured when leaves were fullyturgid and green.Data collection. Grain yield and some yield-related parameterswere measured in parents and hybrid combinations.Grain yield per plant was measured in grams and 1000-grainweight was measured after counting 500 grains of each wheatgrain sample on a counting tray once and the second samplewas repeated for the other 500 grains.Canopy temperature was measured by using a portablethermal gun . Readingsfor canopy temperature were taken at three Feeks stages like booting, kernel water ripening and grainmilking stages . All readings were taken at the angle of 30\u00b0 and above 50 cm of the crop canopy,avoiding land temperature by pointing thermal gum only atthe canopy. The observations were taken between 11:00 amand 14:00 pm under stagnant air conditions and clear sky asdescribed by . Observations for Normalizeddifference vegetative index (NDVI) were recorded 50 cmabove the canopy by using a hand-held Green Seeker with anoptical sensor unit at three stages ofbooting and grain filling between 11:00 hours to 14:00 hourswith clear sky . Values of NDVI rangefrom \u20131 to +1 (the strongestgreen vegetative stage) .Statistical analysis. Data for other traits were recorded from6 randomly selected plants. Data recorded were arranged inmean data and subjected to Analysis of Variance (ANOVA)accordingto Steel and Torrie (1980) and Line \u00d7 Tester analysis,according to Kempthorne (1957), combining ability andgene action were studied byusing R Package agricolae . Genotypic variance and phenotypicvariance were estimated as mentioned by Almutairi (2022) inMS Excel 2016, by using the following formula:Environmental variance was estimated according to Comstockand Robinson (1952). Broad sense heritability was calculatedby using the following formula as described by Burtonand Devane (1953):Heterosis was estimated in percentage increase or decreaseof the F1 hybrids value over mid-parental value by followingthe formula as described by Fonseca and Patterson (1968):Disease observations and scoring. Observations for striperust were recorded at the time of appearance of disease anddata were recorded when rust pathogen was fully developedon leaves of a susceptible check cultivar and leaves\u2019 surfacewas fully covered with rust\u2019s spores. Disease observation wasrecorded in three replicates of each parental line and F1 hybridsaccording to the Cobb Scale method as described byPeterson et al. (1948). The severity of disease was expressedas the percentage of leaf area covered, and 0 % score wasgiven when there was no infection on the leaf and 100 %score was considered when the leaf area was fully coveredwith rust spores and infection. Readings of percent severitywere recorded with the following descriptions for scoringand response values: , response values, coefficient of infection(CI), average coefficient of infection (ACI), country averagerelative percentage attack (CARPA) and rust resistanceindex (RRI) according to Akhtar et al. (2002). The followingformula was used for the calculation of RRI:RRI was calculated by considering the scale of 0 to 9 fromCARPA, where 0 represents a most susceptible genotypeand 9 represents a highly resistant response of the genotypeto rust pathogen.Analysis of variance (ANOVA)Analysis of variance (ANOVA) results presented in Table 1show that the lines had statistically significant differencesfor all the trails. The testers showed statisticaldifferences for days to heading, plant height, peduncle length,spike length, days to maturity, grains per spike, 1000-grainweight and grain yield, while non-significant results forflag leaf area, tillers per plant and spikelets per spike wereshown. Interaction of line \u00d7 tester was significant in case ofplant height, flag leaf area, peduncle length, days to maturity,grains per spike and 1000-grain weight. Parents used in this study provided a broad range of expressionfor various characters as shown in Table 2. There weresignificant differences ( p \u2264 0.05) among the means of genotypes(Table 3) for days to heading (DH), highly significant( p \u2264 0.01) for plant height (PH), flag leaf area (FLA), tillers perplant (TPP), peduncle length (PL), spikelets per spike (SPS),days to maturity (DM), grains per spike (GPS), thousand grainweight (TGW), grain yield (GY) and NDVI value.The values for days to heading (DH) were maximum in thetester PAK-13 (119 days) and minimum in the lines PB-11, PS-05 and MRJ-08 (117 days). DH are thekey indicator of earliness in crop production. Plant breedersare keen to create new varieties of wheat genotypes with earlymaturity. So, early heading is a desirable trait. Delayed headingleads to a reduction in yield and earlyheading increases the grain filling duration, which ultimatelyresults in high yield . Plant height (PH)was the highest in the female parent FSD-08 (103 cm) andthe lowest in the male parent NR-09 (83 cm). Minimum PHis preferred due to expected lodging losses. Similarly, thetester NR-09 (83 cm) can be assessed for developing droughttolerant variety with reduced plant height for future breedingprograms. Likewise, minimum flag leaf area (FLA) is alsodesirable for drought tolerance due to reduced transpirationlosses from a reduced area exposed to sunlight. The testers PAK-13 and BOR-16 showed the minimum values offlag leaf area: 29.57 and 29.83 cm2, respectively. Pedunclelength was longest in the female parent PS-05 (16.67 cm) andshortest in the male parent NR-09 (7.20 cm). PS-05 producedthe maximum grain yield (2531.8 kg \u00b7 ha\u20131) while minimumgrain yield (1696.1 kg \u00b7 ha\u20131) was recorded in ZRG-79.Mean performance of parents and their cross combinationsMean performance for line, testers and cross combinationsfor days to maturity (DH) ranged from 117 to 119 days. Theparental lines FSD-08, PB-11, PS-05, MRJ-08, ZRG-79 andBOR-16 were revealed to have 117 DH, while NR-09 andPAK-13 had 118 and 119 days to heading, respectively (seeTable 2). Among F1 hybrids Zargoon-79 \u00d7 Pakistan-2013 had119 days for heading while the rest of the cross combinationsshowed 117 DH. The grand means for parents, crosses, linesand testers were 117.67, 117.56, 117.27 and 118.33, respectively.The coefficient of variance 0.67 % obtained for DHwas also in the acceptable range.Average minimum plant height was recorded in NARC-2009 (83 cm) followed by cross combination of Punjab-2011 \u00d7Pakistan-2013 (86 cm), and maximum plant height of 104 cmwas recorded in the cross-combination Faisalabad-2008 \u00d7Borlaug-2016 followed by one of parent viz. Faisalabad-2008(103 cm). Grand mean, coefficient of variance (CV) and leastsignificant variance (LSD) for plant height of lines, testers andtheir parental combinations was revealed to be 95.92 cm, 3.64and 5.73, respectively.The cross-combination Punjab-2011 \u00d7 Pakistan-2013showed minimum value (26.8 cm2) for flag leaf area followedby the lines Pakistan-2013 (29.5 cm2) and Borlaug-2016(29.8 cm2). Maximum leaf area was recorded in the linePunjab-2011 (39.2 cm2) followed by the F1 combination,Faisalabad-2008 \u00d7 Pakistan-2013 (36.9 cm2). Grand mean,CV, LSD and standard error for leaf area of lines, testers andcross combinations was recorded as 10.46, 5.7 and 2.0 cm2respectively.Maximum 13 tillers per plant (TPP) was recorded in thetester Pakistan-2013 followed by 12.3 tillers in Borlaug-2016while minimum 7.6 tillers were observed in the female parentPunjab-2011 followed by Pirsabak-2005 (8.33). In thecross combinations a maximum of 10 tillers was recorded inPunjab-2011 \u00d7 NARC-2009 and Miraj-2008 \u00d7 NARC-2009and grand mean for TTP was recorded as 9.49 with CV, LSDand SE 11.66, 3.61 and 1.27 respectively.Maximum peduncle length was observed in the line Pirsabak-2005 while minimum peduncle length was recordedin the tester parent NARC-2009. Grand mean for pedunclelength was observed to be 11.96 cm with CV 9.7 % and LSD(\u03b1 0.05) value 1.9.Mean performance for spike length (SL) was observed12.36 cm in parents and their cross combinations. MaximumSL was observed in cross combinations Miraj-2008 \u00d7Pakistan-2013 followed by Miraj-2008 \u00d7 Borlaug-2016, butminimum SL was observed in the parental line Faisalabad-2008.Grand mean for spikelets per spike (SPS) for parents andcross combination was recorded as 20.33 with a maximumof 21.9 spikelets observed in Pakistan-2013 in addition to theF1 hybrid combination of Miraj-2008 \u00d7 Pakistan-2013 and inthe Pirsabak-2005 \u00d7 Pakistan-2013. Grains per spike (GPS)was recorded maximum in parental line Punjab-2011. Averagethousand grain weight was calculated to be 34.52 withhigher TGW in Faisalabad-2008 (43.73 g) and the crosscombination of Faisalabad-2008 \u00d7 Pakistan-2013 (43.53 g),and lower value for TGW was depicted by the parental lineNARC-2009 (22.47 g). Average grain yield was obtainedin all the parents and cross combinations (2344.5 kg \u00b7 ha\u20131),while average GY was higher in crosses as compared to theparents\u2019 grain yield, the maximum was recorded in the crosscombination ZRG- 79 \u00d7 PAK-13 (3358 kg \u00b7 ha\u20131), followed byPB-11 \u00d7 NR-09 (2820 kg \u00b7 ha\u20131), while minimum grain yieldwas recorded in the cross combination of ZRG-79 \u00d7 NR-09(1372 kg \u00b7 ha\u20131).Maximum normalized differences in vegetative index(NDVI) value was observed in the parental line PS-05 (0.73)followed by PB-11 \u00d7 PAK-13 and PS-05 \u00d7 NR-09 with thesame value. Average NDVI value for parents and crosses wasrevealed to be 0.67; lines, testers and crosses also containedsimilar values for NDVI.There were significant differences among the means ofcrosses combinations for almost all the traits studies exceptDH, TPP an SL. The lines also depictedhighly significant differences in all the parameters under considerationexcept SL. The testers also revealedhighly significant differences for all the traits except for FLA,SL, SPS, and NDVI. Interaction of lines \u00d7 testers depictedhighly significant differences in their mean performance forthe traits of PH, FLA, PL, DM, GPS, TGW and NDVI value.Estimates of genetic variance componentsEstimation of genotypic variance, phenotypic variance, environmentalvariance, variance due to general combining ability,variance due to specific combining ability and variance dueto GCA over SCA is mentioned in Table 4.Phenotypic variance was depicted more as compared togenotypic variance in some traits, i. e. PH, FLA, SL, DM,and GY, while only GY showed high environmental variance.Broad sense heritability (H2) was estimated in the rangeof 28.11 % (GY) to 100 % (CT). PH, PL, GPS, TGW, NDVIvalue and CT showed broad sense heritability of more than91 %, while DH and GY depicted less heritability. The traitswith high genetic variance, low environmental variance andhigh broad sense heritability have preponderance of additivegenes and these are stable characters and selection in the filialgenerations can be made by keeping eye on these traits. Grainyield (GY) and DH attained low broad sense heritability andshowed that environmental influence is more important forthe expression of these traits. Selection in the filial generationshould be made for these traits by considering diseaseincidence and drought proxy parameters, i. e. NDVI and CTvaluesProportional contribution of lines, testers,and their interactions to total varianceProportional contribution of total variance for yield andyield-related metric traits for lines, testers and their crosscombinations was estimated . For DH, PH, TPP andCT it was recorded to be higher as compared to the testersand combinations of both lines and testers. Contribution ofL\u00d7T to total variance was recorded as high in FLA, PL, SL,SPS, DM, GPS and NDVI value, while variance contributionof testers to TGW and GY was estimated higher as comparedto the lines and L\u00d7T combinations.General combining abilityGeneral combining ability (GCA) estimates for all the traitsare given in Table 5. Both positive and negative GCA effectswere observed for lines and testers. For DH, the value of GCAeffects ranged between 0.00 and 0.56. As a good general combiner,significant positive (0.56) and negative (\u20130.56) GCAeffectswere observed for lines Zargoon-79 and Pirsabak-2005,respectively. Similarly, in the testers, positive and significant(0.51) GCA effect was observed for Pakistan-2013 only (seeTable 5). Patel et al. (2020) demonstrated ( p \u2264 0.01) significantnegative and desirable GCA effects in lines and non-additivegene action was primarily involved in days to heading.For plant height, negative general combining ability effectsare more important since more emphasis is placed upon selectionfor short stature in segregating the population because itultimately turns out that a short stature line is more responsiveto fertilizer and tolerant to lodging. In this study, GCA effectsranged between \u20135.82 and 3.24 for PH. Significant positive(3.07) and negative (\u20135.82) GCA effects were observedfor the lines Pirsabak-2005 and Punjab-2011, respectively.Similarly, highly significant positive (3.24) was estimated forthe tester BOR-16 and highly significant but negative (\u20132.56)GCA effects were observed for the testers PAK-13, respectively.These results are in accordance with the results of.For flag leaf area (FLA), negative general combining abilityeffects are more important because FLA is much influencedby transpiration losses due to disclosure to sunlight, whicheventually affects the grain yield. Hence, more emphasis isretained on the selection of genotypes with smaller FLA.From that, among the female parents, Pirsabak-2005 andPunjab-2011 showed a highly significant negative GCA effect:\u20132.16 and \u20132.10, respectively. On the other side, no significantGCA effects were observed among the testers for FLA. Theseresults confirm the findings of .In case of tillers per plant (TPP), GCA effects ranged between\u20130.58 and 0.98. As a good general combiner, highlysignificant positive (0.98) GCA effects were observed only forthe line MRJ-08 while there were no significant GCA effectsamong the testers for TPP. To begin with, TPP is a significantyield-boosting characteristic that contributes to increased grainyield. A higher number of tillers per plant confirms optimalplant populations and as a result higher grain yield . For this point of view, the female line MRJ-08showed better performance. These findings are in accordancewith the results of .GCA effects ranging between \u20131.16 and 1.39 were observedfor peduncle length (PL). Highly significant positive (1.39)and negative (\u20130.76) GCA effects were observed for the lines FSD-08 and ZRG-09, respectively. In the same way,highly significant positive (0.65) and negative (\u20131.16) GCAeffects were observed for the testers BOR-16 and PAK-13, respectively. Likewise, in PH, shorter PL is preferred becausean increase in PL ultimately increases the PH and we prefera plant with short stature. In current study, two female parents,ZRG-79 (\u20130.76) and MRJ-08 (\u20130.70), showed negative generalcombining ability. Also, one male parent, PAK-13, showedsuperior general combining ability for this trait. So, it can beconcluded that the above-mentioned parents are desirable foruse in the breeding program. The findings of supported the results.Greater spike length (SL) and larger number of spikeletsper spike (SPS) are essential for enhanced yield. Among parents,one line , MRJ-08, showed significant positivevalues(0.77) for SPS. One tester, Pakistan-2013, exhibitedhigh GCA for SPS. These results were quite close to thefindings of . Number of grains per spike (GPS) is also animportantfactor for enhanced grain yield. Therefore, positiveGCA effects are more important due to positive contributionof grain yield. Among male parents, only NR-09 showedpositive and higher values (3.26) of GCA effects for GPS.Among female parents, MRJ-08 and PS-05 showed positiveand higher values, i. e. 2.90 and 2.02 respectively. It shouldbe noted that values of male parents were higher than thoseof female parents. These findings match with the results of. These results are different fromthe findings of Nazir et al. (2005).For grain yield per plant (GY), only one female parentMRJ-08, and among the male parents, BOR-16 and NR-09,exhibited positive general combining ability effects. Similarresults were also found by .Specific combining abilitySpecific combining ability (SCA) estimates for all the traitsare given in Table 6. Both positive and negative SCA effectswere observed among the crosses.As for SCA effects for DH, all the fifteen crosses were ofnon-significant nature with positive and negative magnitude(see Table 6). The result indicates the involvement of bothadditive and non-additive genetic effects in the inheritance ofDH, with greater proportion of additive genetic effect. Lineswith maximum SCA effects can be used in development ofhybrid cultivars. Only six among fifteen crosses depicted negativeSCA effects for plant height. If parents with tallness arethe ideal ones, then the crosses FSD-08 \u00d7 NR-09, FSD-08 \u00d7PAK- 13, PB-11 \u00d7 NR-09, PB-11 \u00d7 PAK-13, PS-05 \u00d7 BOR-16and MRJ-08 \u00d7 BOR-16 would be considered good. However,the remaining crosses exhibited higher SCA effects. Thesefindings confirmed the results of . Furthermore,non-additive type of gene action is detected for PH and supportedby . Also, our results concur withAli F.K.H. and Abdulkhaleq (2019) for plant height.GCA effects for flag leaf area range from negative \u20133.80 topositive 3.33. Roughly 50 % of the crosses showed smallervalues of SCA effects for flag leaf area, which is desirable.As less flag leaf area is required for drought tolerance, thecrosses with significant SCA effects, i. e. FSD-08 \u00d7 BOR-16and PB-11 \u00d7 PAK-13 may be used in a future breeding programbecause they have high negative SCA values contributingtowards minimum FLA. However, the remaining crossesexhibited higher positive SCA effects for FLA. Comparableresults have also been stated by .Negative SCA effects are needed to reduce the pedunclelength (PL). In this study, two crosses showed significantlynegative SCA effects. FSD-08 \u00d7 NR-09 and MRJ-08 \u00d7 BOR- 16are the best hybrids for reduced PL. Similar results were reportedby .In case of spike length (SL), all the fifteen crosses were ofnon-significant nature with positive and negative magnitude(see Table 6). For a number of SPS, positive specific combiningability effects were shown in 6 out of 15 crosses but onlytwo crosses, FSD-08 \u00d7 NR-09 and PB-11 \u00d7 BOR-16, havesignificant GCA effects. These hybrids performed best andcan be suggested for future breeding programs. These resultsare in the conformity with those of .For grain yield per plant, SCA effects found varied muchamong crosses. The poorest cross with respect to SCA forgrain yield per plant was ZRG-79 \u00d7 PAK-13 whereas the crossthat appeared to be the best and the most promising specificcombination was ZRG-79 \u00d7 NR-09. Positive specific combiningability effects were displayed in 8 out of 15 crosses.But only ZRG-79 \u00d7 NR-09 showed such significant positiveeffects among crosses. Similar results were also reported by.Mid-parent heterosis estimation for grain yieldMid-parental heterosis (MPH) for GY was estimated for15 F1 hybrids . F1 hybrids ZRG-79 \u00d7 PAK-13 showedhigher mid-parental value (62 %) followed by FSD-08 \u00d7PAK- 13, ZRG-79 \u00d7 BOR-16, and PB-11 \u00d7 NR-09, whichrevealed mid-parent heterosis value above 30 % . Cross combinations PS- 05 \u00d7 PAK- 13,MRJ- 08 \u00d7 NR-09, MRJ-08 \u00d7 PAK-13, FSD- 08 \u00d7 NR- 09 depictedmid-parental heterosis value more than 15 %. Threecross combinations, ZRG-79 \u00d7 NR-09, MRJ-08 \u00d7 BOR- 16and PB-11 \u00d7 BOR-16, depicted negative heterosis.Cross combinations with more than 30 % mid-parentalheterosis can be used in hybrid breeding in wheat. Heteroticstudies for increasing wheat grain yield has been an interestof early wheat researchers. Pal and Alam (1938) reportedmid-parent heterosis in the pre-green revolution era. After theintroduction of semi-dwarf wheat in the post-green revolutionera, various wheat researchers reported mid-parent heterosisin wheat, i. e. . Barbosa-Neto et al. (1996) reported MPH in red softwinter wheat in the range of \u201320 to 57 %. Liu et al. (1999),Dreisigacker et al. (2005), Basnet et al. (2019) studied MPHin CIMMYT wheat varieties and reported MPH in the rangeof 9.5 to 14 %. Parental lines and tester used in present studieshave CIMMYT background and the majority of the genotypesexhibited similar results for MPH. However, crosses combinationZRG-79 \u00d7 PAK-13 has one indigenous parent ZRG-79and exhibited a high percentage of MPH. These finding candemonstrate that crosses among parents with CIMMYT backgroundhave low heterotic potential and additive gene actiongoverned the GY potential in these cross combinations andselection in the filial generation will be key for transgressive segregants, but in case of crosses among indigenous parentsand genotypes with a CIMMYT parent it will be good sourceof hybrid breeding.Correlation study of agronomic traitsCorrelation study among yield and related traits under rainfedconditions of eight parents and 15 wheat crosses is mentionedin Figure 3. High significance was observed between PH andTGW with the value of 0.9 ( p < 0.001), SL and SPS had acorrelation coefficient value of 0.72 ( p <0.001) followed byDH and DM with 0.57 ( p <0.01). PL also showed highlysignificant and positive correlation with TGW and PH . PL and TGW also revealedsignificant but negative correlation with DH \u20130.6 and \u20130.5,respectively ( p < 0.01).Positive and significant correlation among PH and PL withTGW showed that the higher the plant height the higher thethousand grain weight and peduncle length. Careful considerationshould be made while selecting the genotypes with stiffand strong stem girth to avoid lodging. Correlation betweenSL and SPS revealed that an increase in spike length leadsto an increase in spikelets per spike, genotypes with longspikes will be a good selection criterion for increasing yielddue to the increase in number of spikelets per spike. Positiveand significant correlation among DH and DM depicted thatgenotypes with early DH would mature earlier, so selectionof genotypes with early flowering is good for early maturityand short duration variety development. Significant but negativecorrelation between TGW and DH indicated that a delayin days to flowering leads to a reduced TGW and vice versa.TGW showed negative correlation with TPP and these findingsare in line with the results of Almutairi (2022). Low correlationof GY with other parameters in wheat was also reportedby Gowda et al. (2010).Stripe rust responses of parental linesand their cross combinationsThe response to stripe rust (Puccinia striiformis f. sp. tritici)on parental lines used in the study and their offspring(crosses) is recorded for disease scoring, coefficient of infection(CI), average coefficient of infection (ACI), country averagerelative percentage attack (CARPA) and rust resistanceindex (RRI) (Table 7). All the parental lines showed moderateresistant (MR) to highly resistant (R) reaction against striperust (Pst). The female parents (lines) FSD-08, PB-11, PS-05,MRJ-08 and ZRG-79 showed 20M, 20M, 5M, 30M and 40Mscores respectively, while the pollen parents (testers) viz.PAK-13, BOR-16 and NR-09 depicted 10MR, 5R and 40Mresponse against stripe rust. All these parents showed a slowrusting response against rust pathogen that is under the controlof multiple genesCross combinations of these parental lines showed a variedresponse, moderately resistant to moderately susceptible reaction against stripe rust. The F1 hybrids combinations PS- 05 \u00d7PAK-13, PS-05 \u00d7 BOR-16 and PS-05 \u00d7 NR-09 showed 10MR,10MR and 5MR reaction, the crosses FSD-08 \u00d7 PAK- 13,FSD-08 \u00d7 BOR-16, PB-11 \u00d7 PAK-13, PB-11 \u00d7 BOR-16, andMRJ-08 \u00d7 BOR-16 showed 20M reaction, the cross combinationMRJ-08 \u00d7 PAK-13 showed 30M reaction, while the restof the crosses showed moderately susceptible to susceptiblereaction against stripe rust.Average coefficient of infection (ACI) for the parentsPS- 05, PAK-13, BOR-16 and FSD-08 was recorded as 2.0,6.7, 4.3 and 14.0 respectively and these varieties revealeda very good level of resistance against stripe rust. Rust resistanceindex (RRI) of these parents was also high (ranged 5.8to 8.5), which indicated a good resistance response of thesevarieties. Among the cross combinations, PS-05 \u00d7 BOR-16,MRJ-08 \u00d7 PAK-13, PB-11 \u00d7 BOR-16, PB-11 \u00d7 PAK-13 andPS-05 \u00d7 NR-09 depicted ACI values of 4.0, 8.3, 12.0, 13.1, and14.7, respectively. These F1 hybrids had a resistant responseto stripe rust. RRI value of the F1 hybrids was higher (ranging from 5.6 to 8.1).The higher the RRI value and the lower the ACI valuemeans of genotypes with a resistant response to the diseasepathogen and under the influence of slow rusting genes, theslower the disease progress and the lesser the yield losses.Genotypes with higher RRI values (>5.0) represent moderatelyresistant to highly resistant response against rust pathogen.The parental genotypes viz. PS-05, PAK-13 and BOR-16had higher values for RRI showing a highly resistant response against stripe rust pathogen.Cross combinations revealed an intermediate responseagainst stripe rust as compared to parents, especially testes,and resistant genes are under the control of additive geneaction. These results indicate that repeated backcross can bea better strategy for accumulation of resistant genes in thesecross combinations. Selection in these cross combinations byfollowing backcrosses with recurrent parents is efficient fordisease resistance in the filial generations. These results arevery much in line with the findings of Afzal et al. (2009) andMahmoud et al. (2015).According to these findings, it can be concluded that highergeneral combining ability and low broad sense heritabilityfor grain yield suggest the presence of additive genes, andexploitation of general combining ability for high grain yieldis important due to presence of additive gene action, and selectionin the filial generations and family rows will be effective. For development of heterotic population, it is important toexploit specific combining ability for dominant gene actionby crossing indigenous genotypes with exotic germplasmwith improved rust resistance, which will be a useful futurebreeding strategyThe authors declare no conflict of interest.Afzal S.N., Haque M.I., Ahmedani M.S., Munir M., Firdous S.S.,Rauf A., Ahmad I., Rattu A.R., Fayyaz M. Resistance potential ofwheat germplasm (Triticum aestivum L.) against stripe rust diseaseunder rainfed climate of Pakistan. Pak. J. Bot. 2009;41(3):1463-1475.Ahmad M.W., Ahmed M.S., Tahir H.N. Combining ability analysis forachene yield and related traits in sunflower (Helianthus annuus L.).Chil. J. Agric. Res. 2012;72(1):21-26. DOI 10.4067/S0718-58392012000100004Ahmadi J.A., Zali A., Yazdi-Samadi B., Talaie A., Ghannadha M.R.,Saeidi A. A study of combining ability and gene effect in breadwheat under drought stress condition by diallel method. Iranian J.Agric. Sci. 2003;34(1):1-8.Akhtar M.A., Ahmad I., Mirza J.I., Rattu A.R., Hakro A.A., Jaffery A.H.Evaluation of candidate lines against stripe and leaf rusts under nationaluniform wheat and barley yield trial 2000\u20132001. Asian J.Plant Sci. 2002;1:450-453. DOI 10.3923/ajps.2002.450.453.Ali F.K.H., Abdulkhaleq D.A. Inheritance of some growth and yieldtraits in bread wheat using line \u00d7 tester analysis. J. Zankoy Sulaimani.2019;21(2):131-149. DOI 10.17656/jzs.10763.Ali Y., Khan M.A., Hussain M., Sabir W., Atiq M., Aatif H.M., AhmadS., Ijaz M., Ahmad J.N. Virulence analysis of leaf and striperust populations in Pakistan through avirulence to virulence formula.Arch. Phytopathol. Plant Prot. 2020;53(17-18):844-855. DOI10.1080/03235408.2020.1802565Almutairi M.M. Genetic parameters estimation for some wild wheatspecies and their F1 hybrids grown in different regions of SaudiArabia. Saudi J. Biol. Sci. 2022;29(1):521-525. DOI 10.1016/j.sjbs.2021.09.015.Arshad M., Chowdhry M.A. Impact of environment on the combiningability of bread wheat genotypes. Pak. J. Biol. Sci. 2002;5(12):1316-1320. DOI 10.3923/pjbs.2002.1316.1320Arzu K. Gene action and combining ability in line \u00d7 tester populationof safflower (Carthamus tinctorius L.). Turk. J. Field Crops. 2017;22(2):197-203. DOI 10.17557/tjfc.356216.Awan S.I., Malik F.A., Siddique M. Combining ability analysis in intervarietalcrosses for component traits in hexaploid wheat. J. Agric.Soc. Sci. 2005;1(4):316-317.Babar M., Ullah H., Afridi K., Raza H., Ali S., Ali M., Subhan G.,Khan J., Khan H. Line \u00d7 tester analysis for combining ability andidentification of gene action in F2 populations of bread wheat. Int. J.Agric. Biol. 2022;27(6):381-392. DOI 10.17957/IJAB/15.1938.Barbosa-Neto J., Sorrells M., Cisar G. Prediction of heterosis in wheatusing coefficient of parentage and RFLP-based estimates of geneticrelationship. Genome. 1996;39(6):1142-1149. DOI 10.1139/g96-144.Basnet B.R., Crossa J., Dreisigacker S., P\u00e9rez-Rodr\u00edguez P., Manes Y.,Singh R.P., Rosyara U.R., Camarillo-Castillo F., Murua M. Hybridwheat prediction using genomic, pedigree, and environmental covariablesinteraction models. Plant Genome. 2019;12(1):180051.DOI 10.3835/plantgenome2018.07.0051.Burton G., Devane H. Estimating heritability in tall fescue (Festucaarundinacea), from replicated clonal material. Agron. J. 1953;45(10):478-481. DOI 10.2134/agronj1953.00021962004500100005x.Chen X., Penman L., Wan A., Cheng P. Virulence races of Pucciniastriiformis f. sp. tritici in 2006 and 2007 and development of wheatstripe rust and distributions, dynamics, and evolutionary relationshipsof races from 2000 to 2007 in the United States. Can. J.Plant. Pathol. 2010;32(3):315-333. DOI 10.1080/07060661.2010.499271.Chowdhary M.A., Sajad M., Ashraf M.I. Analysis on combining abilityof metric traits in bread wheat, Triticum aestivum. J. Agric. Res.2007:45(1):11-17.Comstock R., Robinson H. Genetic parameters, their estimation andsignificance. In: Proceedings of the Sixth International GrasslandCongress . Pennsylvania: StateCollege, 1952;248-291.De Mendiburu F., Simon R. Agricole \u2013 ten years of an open sourcestatistical tool for experiments in breeding, agriculture and biology.PeerJ PrePrints. 2015:3:e1404v1. DOI 10.7287/peerj.preprints.1404v1.Dragov R.G. Combining ability for quantitative traits related to productivityin durum wheat. Vavilov J. Genet. Breed. 2022;26(6):515-523. DOI 10.18699/VJGB-22-63.Dreisigacker S., Melchinger A., Zhang P., Ammar K., Flachenecker C.,Hoisington D., Warburton M.L. Hybrid performance and heterosisin spring bread wheat, and their relations to SSR-based genetic distancesand coefficients of parentage. Euphytica. 2005;144:51-59.DOI 10.1007/s10681-005-4053-2.Fakthongphan J., Graybosch R.A., Baenziger P.S. Combining abilityfor tolerance to pre-harvest sprouting in common wheat (Triticumaestivum L.). Crop Sci. 2016;56(3):1025-1035. DOI 10.2135/cropsci2015.08.0490.FAOSTAT. Food and Agriculture Organization of the United Nations.Rome : FAOSTAT, 2016.Fasahat P., Rajabi A., Rad J.M., Derera J. Principles and utilizationof combining ability in plant breeding. Biom. Biostat. Int. J. 2016;4(1):1-22. DOI 10.15406/bbij.2016.04.00085.Fellahi Z.E.A., Hannachi A., Bouzerzour H., Boutekrabt A. Line \u00d7 testermating design analysis for grain yield and yield related traits in breadwheat (Triticum aestivum L.). Int. J. Agron. 2013;2013:201851. DOI10.1155/2013/201851.Figueroa M., Dodds P.N., Henningsen E.C. Evolution of virulence inrust fungi \u2013 multiple solutions to one problem. Curr. Opin. PlantBiol. 2020;56:20-27. DOI 10.1016/j.pbi.2020.02.007.Fonseca S., Patterson F.L. Hybrid vigour in seven parent diallel crossesin common wheat (Triticum aestivum L.). Crop Sci. 1968;8(1):85-89. DOI 10.2135/cropsci1968.0011183X000800010025xGorjanovi\u0107 B.M., Kraljevi\u0107-Balali\u0107 M.M. Inheritance of plant height,spike length and number of spikelets per spike in durum wheat. Proc.Nat. Sci. Matica Srpska Novi Sad. 2007;112:27-33. DOI 10.2298/ZMSPN0712027G.Gowda M., Kling C., W\u00fcrschum T., Liu W., Maurer H.P., Hahn V.,Reif J.C. Hybrid breeding in durum wheat: heterosis and combiningability. Crop Sci. 2010;50(6):2224-2230. DOI 10.2135/cropsci2009.10.0637.Hallauer A.R., Carena M.J., Miranda Filho J.D. Quantitative Geneticsin Maize Breeding: Handbook of plant breeding. Springer, 1988.Hasnain Z., Abbas G., Saeed A., Shakeel A., Muhammad A., RahimM.A. Combining ability for plant height and yield relatedtraits in wheat (Triticum aestivum L.). J. Agric. Res. 2006;44(3):167-173.Hassan G., Muhammad F., Afridi S.S., Khalil I.H. Combining abilityin F1 generations of diallel cross for yield components in wheat.SarhadJ. Agric. 2007;23(4):937-942.Intikhab A., Awan S.I., Mur L.A.J., Saeed M.S., Ahmed M.S. Molecularand phenotypic analysis of bread wheat varieties in relation todurable rust resistance. Int. J. Agric. Biol. 2021;26(2):329-336. DOI10.17957/IJAB/15.1841.Iqbal A., Khalil I.H., Shah S.M., Kakar A.M.S. Estimation of heritability,genetic advance and correlation for morphological traits inspring wheat. Sarhad J. Agric. 2017;33(4):674-679. DOI 10.17582/journal.sja/2017/33.4.674.679Iqbal M.M. Combining ability analysis in wheat. Pak. J. Agric. Sci.2007;44(1):1-5.Ishaq M., Ahmad G., Afridi K., Ali M., Khan T.U., Shah I.A., AhmadB., Ahmad N., Ahmad I., Saleem A., Miraj M. Combining ability and inheritance studies for morphological and yield contributingattributes through line \u00d7 tester mating design in wheat (TriticumaestivumL.). Pure Appl. Biol. 2018;7(1):160-168.Javaid M.M., Zulkiffal M., Ali Y., Mehmood A., Ahmed J., Hussain M.,Muhammad F., Sabir W., Tanveer M.H., Yasin O. Impact of environmentaland pathogenic variability on breaking of host rust resistancein wheat cultivars under changing climatic conditions. Adv. Zool.Bot. 2018;6(1):31-40. DOI 10.13189/azb.2018.060104.Jones D.F. Dominance of linked factors as a means of accounting forheterosis. Proc. Natl. Acad. Sci. USA. 1917;3(4):310-312. DOI10.1073/pnas.3.4.310.Kaushik P. Line \u00d7 tester analysis for morphological and fruit biochemicaltraits in eggplant (Solanum melongena L.) using wild relativesas testers. Agronomy. 2019;9(4):185. DOI 10.3390/agronomy9040185.Kempthorne O. An Introduction to Genetic Statistics. New York: JohnWiley and Sons, 1957.Khan A., Ahmad M., Shah M.K.N., Ahmed M. Genetic manifestationof physio-morphic and yield related traits conferring thermotolerancein wheat. Pak. J. Bot. 2020;52(5):1545-1552. DOI 10.30848/PJB2020-5(27).Khan S.N., Hassan G., Khan M.R., Facho Z.H., Singh D., Sandhu K.S.,Sanaullah M., Imtiaz M., Ali S. Field assessment and molecularmarkers-based characterization of yellow rust resistance in wheathybrid progenies. J. Anim. Plant Sci. 2022;32(1):127-137. DOI10.36899/JAPS.2022.1.0409.Knott D.R. Heterosis in seven wheat hybrids. Can. J. Plant Sci. 1965;45:499-501.Kumar R., Silva L. Light ray tracing through a leaf cross section. Appl.Opt. 1973;12(12):2950-2954. DOI 10.1364/AO.12.002950.Large E.C. Growth stages in cereals illustration of the Feekes scale.Plant Pathol. 1954;3(4):128-129. DOI 10.1111/j.1365-3059.1954.tb00716.x.Lerner I.M. Genetic Homeostasis. New York: John Wiley and Sons,1954Liu Z., Pei Y., Pu Z. Relationship between hybrid performance andgenetic diversity based on RAPD markers in wheat (Triticum aestivumL.). Plant Breed. 1999;118(2):119-123. DOI 10.1046/j.1439-0523.1999.118002119.x.Mahantashivayogayya K., Hanchinal R., Salimath P. Combining abilityin dicoccum wheat. Karnataka J. Agric. Sci. 2004;17(3):451-454.Mahmoud A.F., Hassan M.I., Amein K.A. Resistance potential of breadwheat genotypes against stripe rust disease under Egyptian climate.Plant Pathol. J. 2015;31(4):402-413. DOI 10.5423/PPJ.OA.12.2014.0127.Malik M.F.A., Awan S.I., Ali S. Genetic behaviour and analysis ofquantitative traits in five wheat genotypes. J. Agric. Soc. Sci. 2005;1(4):313-315.Nazir S., Khan A.S., Ali Z. Combining ability analysis for yield contributingtraits in bread wheat. J. Agric. Soc. Sci. 2005;1:129-132.Okello D.K., Manna R., Imanyowoha J., Pixley K., Edema R. Agronomicperformance and breeding potential of selected inbred linesfor improvement of protein quality of adapted Ugandan maize germplasm.African Crop Sci. J. 2006;14(1):37-47.Pal B., Alam N. The effect of certain external factors upon the manifestationof hybrid vigour in wheat. Proc. Indian Acad. Sci. 1938;7:109-124. DOI 10.1007/BF03051095Patel P.U., Patel B.C., Sidapara M.P., Sharma D.D. Combining abilityand gene action studies for yield and its component traits in breadwheat (Triticum aestivum L.). Int. J. Curr. Microbiol. Appl. Sci.2020;9:2463-2469.Peterson R.F., Campbell A.B., Hannah A.E. A diagrammatic scale forestimating rust intensity on leaves and stems of cereals. Can. J. Res.1948;26(5):496-500. DOI 10.1139/cjr48c-033.Qamar M., Ahmad S.D., Rabbani M.A., Shinwari Z.K., Iqbal M. Determinationof rust resistance genes in Pakistani bread wheats. Pak. J.Bot. 2014;46(2):613-617.Rashid M., Cheema A.A., Ashraf M. Line \u00d7 tester analysis in Basmatirice. Pak. J. Bot. 2007;39(6):2035-2042.Rashmi K., Prasad L.C., Prasad R., Thakur P., Chandra K. Inheritancestudy of yield traits and spot blotch disease resistance in wheat underepiphytotic environment. Plant Arch. 2020;20(2):6590-6594.Raza W., Ghazanfar M.U., Rehman A.U., Fayyaz M. Screening ofwheat germplasm against stripe rust disease under field conditionsin Pakistan. Plant Prot. 2018;2(3):87-92.Reynolds M.P., Singh R.P., Ibrahim A., Ageeb O.A.A., Larque-SaavedraA., Quick J.S. Evaluating the physiological traits to complementempirical selection for wheat in warm environments. Euphytica.1998;100:85-94. DOI 10.1023/A:1018355906553.Saeed A., Chowdhry M.A., Saeed N., Khaliq I., Johar M.Z. Line \u00d7 testeranalysis for some morpho-physiological traits in bread wheat. Int. J.Agric. Biol. 2001;3(4):444-447.Saeed M.S., Chowdhry M.A., Ahsan M. Genetic analysis for some metrictraits in Aestivum species. Asian J. Plant Sci. 2005;4(4):413-416.DOI 10.3923/ajps.2005.413.416.Shamsuddin A K. Genetic diversity in relation to heterosis and combiningability in spring wheat. Theor. Appl. Genet. 1985;70:306-308.Sharma A., Garg D. Combining ability over environments in breadwheat (Triticum aestivum L.). J. Maharasahtra Agric. Univ. 2005;30(2):153-156.Shull G.H., East E.M. The composition of a field of maize. J. Hered.1908;4(1):296-301. DOI 10.1093/jhered/os-4.1.296.Singh R.K., Chaudhary B.D. Biometrical Methods in Quantitative GeneticAnalysis. New Delhi: Kalyani Publ., 1977.Singh S., Singh L., Singh D., Kumar R. Combining ability in commonwheat (Triticum aestivum L.) grown in sodic soil. Progress. Agric.2003;3:78-80.Sprague G.F., Tatum L.A. General vs. specific combining ability insingle crosses of corn. Agron. J. 1942;34(10):923-932.Steel R.G.D., Torrie J.H. Principles and Procedures of Statistics. NewYork: McGraw Hill Book Company Inc., 1980.Sultana S.R., Ali A., Ahmad A., Mubeen M., Zia-Ul-Haq M., Ahmad S.,Ercisli S., Jaafar H.Z. Normalized Difference Vegetation Index as atool for wheat yield estimation: a case study from Faisalabad, Pakistan.Sci. World J. 2014;2014:725326. DOI 10.1155/2014/725326.The R Project for Statistical Computing. A language and environmentfor statistical computing R foundation for Statistical Computing Departmentof Agronomy, Faculty of Agriculture of the University ofthe Free State. Vienna, Austria, 2017. www.r-project.org.Tilley M.S., Heiniger R.W., Crozier C.R. Tiller initiation and its effectson yield and yield components in winter wheat. Agron. J.2019;111(3):1323-1332. DOI 10.2134/agronj2018.07.0469.Uddin M.N., Ellison F.W., O\u2019Brien L., Latter B.D.H. Heterosis inF1 hybrids derived from crosses of adapted Australian wheats. Aust.J. Agric. Res. 1992;43(5):907-919. DOI 10.1071/AR9920907.Ullah N., Ullah H., Afridi K., Alam M., Jadoon S.A., Khan W.U., AhmadM., Uddin H. Genetic variability, heritability and correlationanalysis among morphological and yield traits in wheat advancedlines. Biol. Divers. Conserv. 2018;11(1):166-180.Zhao Y., Zeng J., Fernando R., Reif J.C. Genomic prediction of hybridwheat performance. Crop Sci. 2013;53(3):802-810. DOI 10.2135/cropsci2012.08.0463"} +{"text": "Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacterales with resistance to carbapenems or third-generation cephalosporins. The aim of the present study was to investigate the in vitro activity of the novel siderophore cephaloporin cefiderocol (CID) and four comparator \u03b2-lactam-\u03b2-lactamase-inhibitor combinations and to give insights into the genetic background of CID-resistant isolates. In total, 301 clinical Enterobacterales and non-fermenting bacterial isolates were selected for this study, including randomly chosen isolates and challenge isolates . Isolates displayed CID MIC50/90 values of 0.12/0.5 mg/L (set I) and 0.5/1 mg/L (set II). Overall, the CID activity was superior to the comparators against A. baumannii, Stenotrophomonas maltophilia and set II isolates of P. aeruginosa. There were eight CID-resistant isolates detected (MIC > 2 mg/L): A. baumannii (n = 1), E. cloacae complex (n = 5) and P. aeruginosa (n = 2). Sequencing analyses of these isolates detected the acquired \u03b2-lactamase (bla) genes blaNDM-1,\u00a0blaSHV-12 and naturally occurring blaOXA-396, blaACT-type and blaCMH-3. In conclusion, CID revealed potent activity against clinically relevant organisms of multidrug-resistant Enterobacterales and non-fermenters. Antimicrobial resistance poses a global threat to public health. Of great concern are Acinetobacter baumannii (carbapenem-resistant), Pseudomonas aeruginosa (carbapenem-resistant) and the order of Enterobacterales (carbapenem-resistant and ESBL-producing) [Stenotrophomonas maltophilia [The emergence of antibiotic-resistant bacteria has been described as one of the biggest threats to global health and food safety ,2. It isoducing) . Variousoducing) ,7. New aoducing) ,9. Howevtophilia ,9. P. aeruginosa [A. baumannii (CRAB), P. aeruginosa and S. maltophilia, as well as carbapenem-resistant Enterobacterales [Klebsiella pneumoniae or OXA-23 in A. baumannii), show the weak hydrolysis of CID [P. aeruginosa and Enterobacter cloacae complex, which could otherwise cause resistance development under therapy [Cefiderocol (CID) is a novel parenteral cephalosporin carrying a catechol moiety at the 3-position side chain . It has ruginosa . It is tcterales , with his of CID . Further therapy ,15,16. C therapy ,18. In vitro data of CID from Germany are scarce. In our previous study published in 2020, CID was found to inhibit 97.2% of a randomly chosen collection of 213 Gram-negative clinical isolates of different species at the investigational susceptibility breakpoint of \u22642 mg/L . The isoThe present study aimed (I) to investigate the in vitro activity of CID against Gram-negative pathogens recovered from patients during a more recent multicentre surveillance study conducted by the PEG in 2016/17 and (II) to compare it with the susceptibility against novel \u03b2-lactam\u2013\u03b2-lactamase-inhibitor (BL-BLI) combinations. 50 and MIC90) and the number and percent of susceptible and resistant isolates were calculated with the available breakpoints of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) (P. aeruginosa) of \u22642 mg/L or the non-species-related pharmacokinetic\u2013pharmacodynamic (PK/PD) breakpoint of \u2264 2 mg/L was applied .MIC distribution data of CID are presented in (EUCAST) . OverallEnterobacterales isolates, CID inhibited 98.2% (109/111) was determined for a respiratory E. cloacae complex isolate (PEG-16-51-23) that originated from a nosocomial infection. Sequencing revealed that this isolate encoded the extended-spectrum \u03b2-lactamase SHV-12. There were two more isolates detected with CID MICs > 2 mg/L: an NDM-1-encoding P. aeruginosa (PEG-16-96-12) and another E. cloacae complex (PEG-16-75-70) harbouring blaSHV-12 (both MICs 4 mg/L). Among the 111 109/111) . In compP. aeruginosa isolates, with 89.7% of the isolates being inhibited at the respective breakpoint (R > 8 mg/L). The susceptibility rates of P. aeruginosa against the other agents were comparable to that seen with the Enterobacterales: 98.3% (CID), 96.6% (IMR), 94.8% (CTV) and 91.4% (CTT) was more active than CTT (1/4 mg/L), CTV (2/8 mg/L), IMR (0.5/2 mg/L) or MEV (1/\u2265 16 mg/L). Of the nine A. baumannii isolates, all were inhibited by CID at \u22640.5 mg/L. Based on the MIC50/90 values, all comparator compounds were less active with MIC50 values of 0.5\u2013\u2265 16 mg/L and MIC90 values of \u226516 mg/L. Two OXA-23-encoding A. baumannii isolates (PEG-16-19-60 and PEG-16-22-42) were resistant to IMR (R > 2 mg/L) and exhibited MEV MICs of 16 mg/L. Among the S. maltophilia (n = 17) isolates, CID MICs ranged from \u22640.03 to 2 mg/L, with MIC50/90 values of 0.06 mg/L and 0.5 mg/L. In comparison, all four comparators were less active in S. maltophilia with MIC50/90 values of \u226516 mg/L. Compared to Enterobacterales, MEV was less effective against the 58 4% (CTT) . Based o50/90 and susceptibility/resistance rates, where applicable).The results of set II isolates are displayed together with set I in P. aeruginosa) of \u22642 mg/L or the non-species-related PK/PD breakpoint (A. baumannii) of \u22642 mg/L was applied. There were five isolates detected with MICs > 2 mg/L A. baumannii , E. cloacae complex and P. aeruginosa . Whole-genome sequencing analysis detected the presence of carbapenemase gene blaNDM-1 in the A. baumannii isolate together with disrupted oprD and piuA genes. The resistant P. aeruginosa isolate harboured blaOXA-396, a variant of the chromosomal class D OXA-50-group in this species, together with the class A \u03b2-lactamase PDC-8, and carried a disrupted oprD. The three E. cloacae complex isolates were only positive for class C ACT-type \u03b2-lactamases or CMH-3, which naturally occur in E. cloacae.The CID MICs ranged from \u22640.03 to 32 mg/L, with an overall susceptibility rate of 95.3% (101/106) if the specifies-specific EUCAST susceptibility breakpoint , 51.3% (CTV), 46.2% (IMR) and 35.9% (MEV), while CID inhibited 97.4% (38/39) of P. aeruginosa isolates. Among the CRAB isolates, CID revealed the most potent activity compared to the other compounds with MIC50/90 values of 0.12/2 mg/L as opposed to \u226516/\u226516 mg/L.Among the 53 Enterobacterales isolates, 100% were susceptible to MEV, 98.1% were susceptible to both CTV and IMR and 77.4% were susceptible to CTT. With a susceptibility rate of 94.3% (50/53), CID exhibited slightly lower activity compared to CTV and IMR in Enterobacterales. Overall, the comparator agents were similar or less effective in the 39 The CID MIC distributions of ESBL-producing isolates, carbapenemase-producing isolates and colistin-resistant isolates from set I and II are summarized in 50/90 values of 0.5/1 mg/L. There was no difference in CID MIC distribution with regard to different resistance genes, with the exception of two blaNDM-1-encoding isolates (A. baumannii and P. aeruginosa) and two SHV-12-encoding E. cloacae complex isolates with CID MICs > 2 mg/L. With the exception of CTT, the comparator compounds revealed similar activity against ESBL-producing isolates compared to CID. The MIC50/90 values were 0.25/0.5 mg/L for CTV, 0.12/0.25 mg/L for IMR and \u22640.06/0.12 mg/L for MEV. The CID susceptibility in 47 ESBL-encoding isolates ranged from \u22640.03 mg/L to \u226564 mg/L, with MICThe overall CID susceptibility of the 47 ESBL-encoding Enterobacterales isolates was 95.7% (45/47). CTV, IMR and MEV were able to inhibit 100% of the isolates at their respective breakpoints, with only the CTT susceptibility being lower at 85.1%. 50/90 values were 0.5/2 mg/L. Fourteen of fifteen carbapenemase-producing A. baumannii isolates (93.3%) were inhibited at a CID concentration \u2264 2 mg/L. Regarding carbapenemase-producing P. aeruginosa isolates, 91.7% (11/12) exhibited CID susceptibility. CID-resistant isolates of both species (A. baumannii PEG-16-19-65 and P. aeruginosa PEG-16-96-12) encoded blaNDM-1 and revealed MIC values of the comparator substances of 16 mg/L each. With the exception of one A. baumannii isolate, all carbapenemase-encoding isolates were susceptible to colistin. The colistin-resistant isolate (MIC 8 mg/L) was susceptible to CID but resistant to all of the other tested compounds. Overall, the comparators revealed reduced activity in carbapenemase-encoding isolates compared to CID with MIC50/90 values greater or equal to their highest concentration tested. Among the 30 carbapenemase-producing isolates, CID MICs ranged from \u22640.03 to 32 mg/L, with 93.3% (28/30) of the isolates being inhibited at a concentration of \u22642 mg/L. The MIC50/90 values of 0.25/1 mg/L. Based on MIC50/90 values, CID activity was comparable to CTT (0.5/2 mg/L), CTV (0.5/4 mg/L) and IMR (0.25/1 mg/L). The distribution of MEV MICs revealed a lower MIC50 value compared to the other compounds (MIC50/90s: \u22640.06/2 mg/L). All colistin-resistant P. aeruginosa isolates (n = 14) were inhibited by CID and the comparator substances. The two colistin-resistant A. baumannii isolates (PEG-16-36-64 and PEG-16-50-50) were inhibited by a CID concentration < 2 mg/L but revealed different MIC results with regard to the comparator substances. PEG-16-36-64 was susceptible against all the other substances (MIC range 0.25\u20130.5 mg/L), while the blaOXA-23-like-positive PEG-16-50-50 exhibited MIC values of 16 mg/L against CTT, CZA, IMR and MEV.In colistin-resistant isolates (n = 37), CID MICs ranged from \u2264 0.03 to 4 mg/L, with MICA. baumannii and P. aeruginosa, as well as Enterobacterales species with acquired resistance against carbapenems or third-generation cephalosporins, all possessing a high risk of severely limited treatment options. In contrast to resistance against third-generation cephalosporins, carbapenem resistance is still rarely encountered in Enterobacterales species such as E. coli and K. pneumoniae in Germany. For example, the surveillance study originated by the Paul-Ehrlich-Society for Infection Therapy in 2016/17 revealed resistance rates of 0% against imipenem and meropenem in 571 E. coli isolates and 1.6% (5/318) against both substances in K. pneumoniae isolates. According to the annual surveillance data for Germany reported to the European Centre for Disease Prevention and Control (ECDC), the rates of carbapenem-resistant E. coli and K. pneumoniae isolates were 0.0% and 0.8% in 2021 compared to resistance rates against third-generation cephalosporins of 9.1% and 10.4% (678/6538) (Surveillance Atlas of Infectious Diseases (europa.eu); data source: invasive isolates). In Acinetobacter spp. and P. aeruginosa, carbapenem-resistance was more frequently detected with 4.3% (26/605) and 14.8% (425/2864), respectively.The WHO has designated antimicrobial resistance as one of the top ten global public health threats. Of great concern are carbapenem-resistant non-fermenting Gram-negative bacteria such as A. baumannii, MBL-producing organisms and S. maltophilia, which is intrinsically resistant against multiple antimicrobial agents, including carbapenems [The antimicrobial agents compared in this study are considered promising compounds in the treatment of infections with the above-mentioned organisms when no other options are available. In contrast to the comparators, CID possesses activity against a variety of Gram-negative species and \u03b2-lactamases of all Ambler classes, including OXA-encoding bapenems . Unlike 50/90s 0.12/0.5 mg/L) and 95.3% at \u22642 mg/L were inhibited by CID at a concentration of \u22642 mg/L, while there was only one isolate detected among fourteen CRAB isolates (set II) with an MIC of >2 mg/L. However, due to the small sample size of S. maltophilia and A. baumannii, these data should be considered with caution. Naas et al. investigated a total number of 103 S. maltophilia and 161 A. baumanni isolates and reported comparable CID activity against both species and almost identical MIC50/90 values of 0.06 mg/L and 0.25 mg/L [S. maltophilia [50/90 values of 0.06/0.25 mg/L. However, studies on CRAB yielded conflicting results. A recent study by Mushtaq et al. investigated 99 A. baumannii isolates encoding various OXA-\u03b2-lactamases, with the majority being OXA-23 (n = 41), as well as NDM enzymes (n = 20) [A. baumannii (n = 25), while isolates harbouring OXA-58 or OXA-23 were all susceptible (n = 75) [Our study observed more potent CID activity against parators . Similar.25 mg/L . Karlowstophilia . They deA. baumannii and P. aeruginosa) and SHV-12 (E. cloacae complex), or the naturally occurring \u03b2-lactamases such as class C ACT-type, CMH-3 (both E. cloacae), as well as PDC-8 together with class D OXA-396 (P. aeruginosa) . The cor0.5 mg/L ,27. In oruginosa ,29. FurtblaNDM-1 might be an exception to this and requires further investigation. CID activity was superior to the comparators against A. baumannii, S. maltophilia and challenge isolates of P. aeruginosa. In addition to ESBL-producing isolates, the majority of CP-producing and colistin-resistant isolates were inhibited at a CID concentration \u22642 mg/L, indicating good activity of CID in clinically relevant organisms. In conclusion, CID revealed potent activity against Enterobacterales and non-fermenting Gram-negative bacterial isolates from Germany. The association of CID non-susceptibility with a particular resistance determinant seemed to be unlikely, while the presence of In total, 301 Gram-negative bacterial isolates were investigated in this study. All isolates were obtained from patient samples collected at 22 German microbiological laboratories during a multicentre surveillance study conducted by the PEG in 2016/17. The majority of laboratories were affiliated with tertiary-care medical centres. Two sets of isolates were selected: random samples (set I) and challenge organisms (set II).E. coli (n = 52), K. pneumoniae (n = 34) and E. cloacae complex (n = 25) isolates. The non-fermenting bacteria included A. baumannii (n = 9), P. aeruginosa (n = 58) and S. maltophilia (n = 17) isolates. Set I included 195 isolates which encompassed 111 Enterobacterales and 84 non-fermenting bacteria which were obtained from the respiratory tract (n = 117) and from blood culture (n = 78). Isolates were randomly selected; routine clinical isolates, also including ESBL- and carbapenemase-producing isolates; as well as colistin-resistant isolates. The Enterobacterales included E. coli and five K. pneumoniae isolates were ESBL producers, which were investigated via PCR/Sanger sequencing or whole-genome sequencing in different reference laboratories as part of the PEG study. All of the ESBL K. pneumoniae isolates as well as five ESBL E. coli isolates carried the blaCTX-M-15 gene. Additionally, three of these K. pneumoniae isolates also encoded SHV-40 (n = 1) or SHV-28 (n = 2). The remaining ESBL E. coli isolates carried blaCTX-M-1 (n = 4) or blaCTX-M-27 (n = 1). Few isolates of set I encoded carbapenemases: K. pneumoniae (n = 1) encoded VIM-1, A. baumannii (n = 2) encoded OXA-23 and P. aeruginosa (n = 1) encoded NDM-1. Seven Isolates were colistin-resistant (E. cloacae (n = 3), E. coli (n = 1) and K. pneumoniae (n = 3)).Among the Enterobacterales, ten A. baumannii and P. aeruginosa isolates with a meropenem MIC above 8 mg/L and Enterobacterales that were either ertapenem-resistant (R > 0.5 mg/L) and/or possessed a meropenem MIC of >0.12 mg/L . In contrast to set I, isolates of set II were especially enriched for ESBL- and carbapenemase-producing isolates as well as colistin-resistant isolates. The investigation of resistance genes was part of the multicentre study conducted by the PEG and was performed via PCR/Sanger sequencing or whole-genome sequencing in different reference laboratories [A. baumannii isolates of this set encoded the following \u03b2-lactamases: NDM-1 (n = 1), OXA-58 (n = 1), or OXA-23 (n = 11). The E. coli isolates of this set produced CTX-M-1 (n = 3), CTX-M-14 (n = 2), CTX-M-15 (n = 9), CTX-M-15 plus CTX-M-27 (n = 1), CTX-M-27 (n = 3), or CTX-M-55 (n = 1). P. aeruginosa isolates of this set encoded the following \u03b2-lactamases: GIM-1 (n = 2), IMP-7 (n = 2), IMP-13 (n = 1), VIM-1 (n = 2), VIM-2 (n = 3) and VIM-5 (n = 1). K. pneumoniae isolates of this set encoded the following \u03b2-lactamases: CTX-M-3 (n = 1), CTX-M-15 (n = 10) and VIM-1 (n = 1). One E. cloacae complex isolate encoded OXA-48.Set II comprised 53 Enterobacterales and 53 non-fermenting bacteria with either confirmed carbapenemases or ESBL genes or with phenotypic colistin resistance or \u201emeropenem non-susceptibility\u201d. \u201eMeropenem-non-susceptible\u201d isolates included ratories ,31. A. bThe verification of species identification was performed via matrix-assisted laser desorption ionization\u2013time of flight (MALDI-TOF) mass spectrometry .5 CFU/mL (range 2\u20138 \u00d7 105). Panels were incubated at 35 \u00b1 1\u00b0C for 18 \u00b1 2 h. The MICs were read visually and, as far as possible, interpreted according to the species-specific clinical breakpoints approved by the EUCAST , I and R (resistant) [P. aeruginosa of \u22642 mg/L (S) and >2 mg/L (R) were applied. For other species, the EUCAST-approved pharmacokinetic\u2013pharmacodynamic breakpoints were applied (\u22642 mg/L (S) and >2 mg/L (R)). Reference strains E. coli ATCC 25922 and P. aeruginosa ATCC 27853 were used for quality control. The following antimicrobial agents were tested with the noted ranges: ceftazidime\u2013avibactam (CTV) (0.12/4\u20138/4 mg/L), ceftolozane\u2013tazobactam (CTT) (0.25/4\u20138/4 mg/L), imipenem\u2013relebactam (IMR) (0.03/4\u20138/4 mg/L), meropenem\u2013vaborbactam (MEV) (0.25/8\u20138/8 mg/L) and cefiderocol 0.06\u201332 mg/L). MICs were determined using the broth microdilution procedure with geometric twofold serial dilutions according to the international standard ISO 20776-1 [ mg/L. MIsistant) . For CIDIsolates with CID MICs > 2 mg/L were sent to the International Health Management Associates (IHMA) for whole-genome sequencing.p < 0.05 was assumed. The statistical significance of differences in susceptibility rates was judged by comparing 95% confidence intervals (CIs). Intervals were constructed using the Newcombe\u2013Wilson method without continuity correction. If no rate was contained in the CI of the other one, significance of"} +{"text": "Tenacibaculum haliotis strain RA3-2T , isolated from Korean wild abalone . As the only strain for this Tenacibaculum species worldwide, the information is of use for comparative genomic analyses delineating Tenacibaculum species.Here, we present the draft genome sequence of Tenacibaculum isolates are associated with fish (Tenacibaculum crassostreae from the Pacific oyster (Crassostrea gigas) (Most ith fish . Two mola gigas) and Tenahannai) .T. haliotis strain, RA3-2T. A sample of RA3-2T was obtained from the Japanese Biological Resource Centre in glass ampoules (L-dried). The strain was grown on marine agar 2216 (BD Difco). The plates were incubated at 20\u00b0C for 3\u2009days .DNA was extracted from three colonies using the InstaGene matrix (Bio-Rad) per the manufacturer\u2019s instructions. The 16S rRNA gene was PCR amplified using the universal primer pair 27F and 1492R (The NucleoSpin soil kit (Macherey-Nagel GmbH & Co. KG), purified genomic DNA, and the NanoDrop Lite spectrophotometer were used to measure the DNA concentration (Thermo Fisher Inc.). The genome was sequenced by Macrogen. A DNA library was prepared using the TruSeq Nano DNA kit and sequenced using the Illumina NovaSeq 6000 platform to generate 31,942,898 paired-end reads with an average length of 151\u2009bp.https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The next-generation sequencing reads were preprocessed using Geneious Prime v.2020.2.2 software , with a total of 2,977,857\u2009bp and 30.7% G+C content. The quantitated assembly quality indicated a minimum contig length of 1,346\u2009bp, a maximum length of 486,103\u2009bp, and an average length of 102,684\u2009bp. The draft genome sequence contained 2,728 coding DNA sequences (CDSs) with protein, 2,794 genes, 8 pseudogenes, and 61 RNAs , as determined by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.6.2 (https://github.com/ncbi/pgap) using the best-placed reference protein set, with GeneMarkS-2+ as the annotation method. The predicted tRNAs were verified using tRNAscan-SE v.2.0 rea v.5.2.0 . The assin silico genome analysis, genes were discovered with predicted associations to secretion systems (type I [T1SS] and T9SS), as detected using TXSScan . Iron-related protein families were identified using FeGenie v.1.0 (Using ie v.1.0 . Using tie v.1.0 .JAOBTH000000000. The version described here is JAOBTH010000000. The sequences are publicly available under the BioProject accession number PRJNA877611, BioSample accession number SAMN30712836, and SRA accession number SRR22752080. The GenBank accession number for the 16S rRNA gene sequence is OP381101.This whole-genome shotgun project was deposited at DDBJ/ENA/GenBank under the accession number"} +{"text": "Introduction: Varicella-zoster virus (VZV) reactivation was not listed as a side effect of any vaccine until introduction of COVID-19 vaccines. Since COVID-19 vaccines were introduced, several case reports described the link between COVID-19 vaccination and VZV reactivation. In our study we aimed to investigate how often patients developed VZV reactivation after mRNA COVID-19 vaccine compared to influenza vaccine.We used the TriNetX platform and its global health research network containing aggregated de-identified information of electronic health records on over 100 million patients from scores of healthcare organizations. Three patient groups were identified:st mRNA COVID-19 vaccine 12/20/2020-12/20/2022Patients receiving their 1nd mRNA COVID-19 vaccine 12/20/2020-12/20/2022Patients receiving their 2Patients receiving influenza vaccine 12/20/2018-12/20/2022Propensity Score Matching was used for age, gender, and Zoster vaccine status.We examined the prevalence of VZV reactivation in each group during the first 21 days following vaccination.st mRNA COVID-19 vaccine or the Influenza vaccine, 0.04% in the COVID-19 vaccine group and 0.15% in the influenza group, odds ratio (OR) 0.24 (95% CI 0.20-0.29), were diagnosed with VZV reactivation within 21 days. Among 445,382 patients in each matched group receiving either their 2nd mRNA COVID-19 vaccine or their influenza vaccine, 0.04% in the COVID-19 vaccine group and 0.13% in the Influenza group, OR 0.27 (95% CI 0.22-0.32), were diagnosed with VZV reactivation within 21 days. There was a lower risk of VZV reactivation after 1st or 2nd dose of mRNA COVID-19 vaccine than influenza vaccine.Out of 444,016 patients in each matched group receiving either their 1st or 2nd dose of mRNA COVID-19 vaccination is smaller than VZX reactivation after influenza vaccine. The risk of VZV reactivation after mRNA COVID-19 vaccine is very low and hesitance to receive COVID-19 vaccine due to concern of VZV reactivation is not substantiated.The risk of VZV reactivation after the 1David C. Kaelber, MD, PhD, MPH, FAAP, FACP, FACMI, FAMIA, Becton, Dickinson and Company: Advisor/Consultant|Dynavax Technologies Corporation: Advisor/Consultant|Merck Sharp & Dohme Corporation: Advisor/Consultant"} +{"text": "Under many kinds of stress, eukaryotic cells rapidly decrease the overall translation level of the majority of mRNAs. However, some molecular mechanisms of protein synthesis inhibition like phosphorylation of eukaryotic elongation factor 2 (eEF2), which are known to be functional in animals and yeast, are not implemented in plants. We suggest that there is an alternative mechanism for the inhibition of protein synthesis in plant cells and possibly, in other eukaryotes, which is based on the discrete fragmentation of 18S rRNA molecules within small ribosomal subunits. We identified four stress-induced small RNAs, which are 5\u2019- and 3\u2019-terminal fragments of 18S rRNA. In the present work, we studied the induction of 18S rRNA discrete fragmentation and phosphorylation of the \u03b1-subunit of eukaryotic initiation factor 2 (eIF2\u03b1) in germinated wheat embryos in the presence of glyphosate, which imitates the condition of amino acid starvation. Using northern and western blotting, we have shown that stress-induced 18S rRNA fragments started to accumulate in wheat embryos at glyphosate concentrations that did not evoke eIF2\u03b1 phosphorylation. It was also found that cleavage of 18S rRNA near the 5\u2019-terminus began much earlier than eIF2\u03b1 phosphorylation, which became noticeable only at higher concentration (500 \u03bcM) of glyphosate. This result suggests that discrete fragmentation of 18S rRNA may constitute a regulatory mechanism of mRNA translation in response to stress and may occur in plant cells in parallel with and independently of eIF2\u03b1 phosphorylation. The identified small 5\u2019- and 3\u2019-terminal fragments of 18S rRNA that accumulate during various stresses may serve as stress resistance markers in the breeding of economically important plant crops. Protein biosynthesis is a very energy-intensive process,so under stress conditions, the translation of most cellularmRNAs is inhibited in order to save energy and resources andto ensure preferential synthesis of stress proteins. Several molecularmechanisms of protein synthesis inhibition have beendescribed in mammalian and yeast cells. One of these mechanismsis the eukaryotic translation elongation factor 2 (eEF2)phosphorylation, which is carried out by a highly specific proteinkinase in response to a sharp decrease in cytosolic ATPconcentration levels. Phosphorylation inactivates mammalianeEF2 by preventing it from binding to the ribosome . However, plants do not exhibit endogenous kinaseactivity for eEF2 either under normal conditions , or under stress .The second mechanism known in animals to reduce the levelof mRNA translation is triggered under conditions of aminoacid starvation and is mediated by eIF4E-binding proteins(4E-BPs), which prevent eIF4E from binding to the m7Gcapstructure of mRNA . However,no clear homologs of these eIF4E-BPs have yet been foundin plants , nor were anyorthologues of the 4E-BPs genes found in plant genomes.Another important mechanism of eukaryotic protein synthesisinhibition is the phosphorylation of the \u03b1-subunit ofeukaryotic initiation factor 2 (eIF2\u03b1) by specific protein kinases.This process in mammalian and yeast cells leads tothe blocking of GDP \u2192 GTP exchange protein eIF2B and toa sharp inhibition of the mRNA translation initiation . However, recycling of the ternary complex inplant cells can occur without the participation of eIF2B , and eIF2\u03b1 phosphorylation in plant systemsin vitro does not lead to strong inhibition of protein synthesis. In addition, of the four protein kinases that phosphorylate theeIF2\u03b1 in mammalian cells, only pGCN2-kinase was foundin plants, and the phosphorylation of eIF2\u03b1 in plants is not auniversal response to all stress types .Thus, the mechanisms of protein biosynthesis suppressiondue to the phosphorylation of translational factors, which arewell described for mammals and yeast, are either used to alimited extent or are not realized at all in plant cells. We suggestthat another mechanism of protein synthesis inhibitioncan function in plants, which is triggered by certain abiotic andbiotic stresses. In our understanding, this mechanism is associatedwith the cleavage at certain sites of the 18S rRNA as partof 40S ribosomal subunits (40S RS). Previously, we describedthe process of 18S rRNA cleavage, leading to 5\u2032-terminal fragmentsformation of 132\u2013134 nt. and of 54\u201357 nt. , as well as a 3\u2032-terminalfragment of 100 nt. . Our data arequite consistent with the data of full-transcriptome analysis,which showed that breaks in 28S-, 18S-, and 5.8S-rRNA donot occur randomly, but discretely, which leads to the fact thatsome fragments of ribosomal RNA are detected in the cell significantlymore often than other fragments .The process of RNA cleavage is widely used by cells duringthe processing of ribosomal RNA from their precursor duringribosome biogenesis . In addition, in proandeukaryotic organisms, the mechanism of protein biosynthesissuppression is realized due to the cleavage of the 28SrRNA molecule from the large (60S) ribosomal subunit alongthe sarcin-ricin loop with the cleavage of the 3\u2032-terminal EndorRNA-fragment . Toxins of plants , fungi (\u03b1-sarcin) and bacteria (Shiga toxin) actthis way . Possibly similar endonucleasesand/or glycosylases are activatedin plant cells during stress, but targeting 18S rRNA in 40S RSinstead of 28S rRNA in 60S RS, and thus leading to temporaryor permanent suppression of mRNA translation.In this work, we have shown that in the case of glyphosatemediatedamino acid starvation, when the only specific eIF2\u03b1kinase of plants (pGCN2-kinase) is activated, in addition toplant eIF2\u03b1 phosphorylation, another protective mechanismis triggered in plant cells, namely, discrete fragmentation of18S rRNA. It was shown that the accumulation in plants of18S rRNA 5\u2032-terminal fragments of 75 nucleotides (75nt-5\u203218S) and 134 nucleotides (134nt-5\u203218S) begins earlier thanthe activation of pGCN2 kinase and becomes noticeable atrelatively low concentrations of glyphosate when plant eIF2\u03b1phosphorylation does not occur at all.Plant material and treatment. Wheat (Triticum aestivum L.cv. Kazakhstanskaya 10) seeds were sterilized in 70 % (v/v)ethanol for 2 min, then in 2 % (w/v) NaOCl for 20 min, andwashed thoroughly with sterile water. Seeds were germinatedat 26 \u00ba\u0421 on sterile filter paper soaked in water. After 18 hours,viable embryos were isolated by spatula from swollen seedsand placed in 1 % glucose solution containing 50 U/ml penicillin,50 \u03bcg/ml chloramphenicol, and 50 \u03bcg/ml nystatin. Afterthis, embryos were divided into equal portions (1 g), whichwere subjected to treatment with glyphosate (simulation ofamino acid starvation) or without any additives (control).Synthesis of probes. DIG-labeling of de novo synthetizedoligodeoxyribonucleotides 5\u203218S (5\u2032-ACAAGCATATGACTACTGGCAGGATCAACCAGGTA) and 3\u203218S (5\u2032-CAATGATCCTTCCGCAGGTTCACCTACGGAAACCT)was carried out using DIG Oligonucleotide 3\u2032-End LabelingKit (Roche) according to the manufacturer\u2019s manual. Probes(5\u203218S-DIG and 3\u203218S-DIG) were used for northern blottingNorthern blotting. Total RNA was extracted from planttissues with Tri-reagent (Sigma Aldridge) and analyzed on10 % PAGE with 8 M urea in Tris-borate buffer . RNAs were blottedto a nylon membrane (Roche) equilibrated in 0.1x TBEusing a semi-dry blotter (Sci-Plas) at 250 mA for 30 min.The membrane was dried and irradiated with UV light for2 min at 10 mJ/cm2 in a crosslinker (UVP). Hybridization ofDIG-labeled probes and subsequent chemiluminescent banddetection was performed with DIG Luminescent DetectionKit for Nucleic Acids (Roche) according to the manufacturer\u2019sprocedure. The hybridization temperature was 55 \u00b0C.Anti-Digoxigenin-AP Fab fragment conjugates (Roche) wereused to detect bound DIG-labeled probes. The blots weredeveloped using a commercial alkaline phosphatase substrateCSPD (Roche).SDS-polyacrylamide gel electrophoresis (SDS-PAGE)and immunoblotting. Frozen embryos were ground toa powder in a mortar and then homogenized in Laemmlisample buffer . Proteins were separated by12.5 % SDS-PAGE with 0.1 % SDS. The separated proteinswere transferred to a nitrocellulose membrane (GVS) thatwas afterwards stained with Ponceau S (Sigma-Aldrich). Theantibodies against human phospho-eIF2\u03b1 (S51) produced inrabbit were used for theimmune-detection of phosphorylated T. aestivum (Ta) eIF2\u03b1(TaeIF2(\u03b1P)). Then horseradish peroxidase-conjugated antirabbitsecondary antibodies produced in donkey were used.The effect of glyphosate concentration on 18S rRNA fragmentationin wheat embryos. Since the mechanisms ofmRNA translation inhibition mediated by 4E-BPs and eEF2Kare not implemented in plants, it is believed that the mainresponse in plants to amino acid starvation is eIF2\u03b1 phosphorylationwith pGCN2 kinase . To testwhether the process of discrete fragmentation of 18S rRNAis also induced under these conditions, the herbicide glyphosatewas used. Glyphosate targets 5-enolpyruvoylshikimate3-phosphate synthase, which catalyzes the key penultimatereaction in the shikimate pathway .Therefore, it inhibits the synthesis of many aromatic plantmetabolites including the amino acids tryptophan, tyrosine,and phenylalanine and leads to pGCN2 kinase activationand phosphorylation of the plant eIF2\u03b1 .Germinated wheat embryos were treated with glyphosate atvarious concentrations, after which the content of 18S rRNAsmall fragments and the phosphorylation status of TaeIF2\u03b1were assessed in their cells. The results are present in Figure 1.Phosphorylation of TaeIF2\u03b1 becomes noticeable only atrelatively high concentrations (0.5 and 5 \u03bcM) of glyphosate, at which wheatembryos stopped to grow . Theappearance of 3\u2032-terminal fragments 100nt-3\u203218S and 70nt-3\u203218S was observed at the same concentrations of glyphosate. At the same time,5\u2032-terminal fragments of 18S rRNA, 134nt-5\u203218S and 75nt-5\u203218S, began to accumulate in noticeable amounts even atvery low concentrations (5 \u03bcM) of glyphosate .The results of semi-quantitative optical densitometry analysisfor this experiment are presented in Table 1. Since the 134nt-5\u203218S fragment can be a precursor of 75nt-5\u203218S, and the100nt-3\u203218S fragment can act as a precursor for 70nt- 3\u203218S,it is reasonable to estimate the sum of these small 18S rRNAfragments.The dynamics of glyphosate influence on 18S rRNA fragmentationin wheat embryos. Then, we assessed how quicklywheat embryos respond to glyphosate treatment by measuringthe time dependence of TaeIF2\u03b1 phosphorylation and of discretefragmentation of 18S rRNA. For this, a glyphosateconcentrationof 500 \u03bcM was chosen, which induced quite effectivephosphorylation of TaeIF2\u03b1, as well as a significantincrease in the content of 18S rRNA small fragments: 134nt-5\u203218S, 75nt-5\u203218S, 100nt-3\u203218S and 70nt-3\u203218S . The results of the experiment are shown in Figure 2.The results of semi-quantitative optical densitometry analysisof the data presented in Figure 2 are shown in Table 2.Data presented in Figure 2 and Table 2 show that TaeIF2\u03b1phosphorylation begins 45 min after the start of glyphosatetreatment , and TaeIF2\u03b1P becomes quite noticeable after 60 minof such treatment .The 3\u2032-terminal fragmentation of 18S rRNA is observedafter 3 hours after the start of glyphosate treatment: fragments100nt-3\u203218S and 70nt-3\u203218S become detectable as faintlyvisiblebands on track 7 of Figure 2, b (right panel). Theamount of these 3\u2032-coterminal fragments is significantly lowerthan after 10 hours of the same treatment with glyphosate.As for fragmentation from the 5\u2032-terminus of 18S rRNA,the amount of both 5\u2032-coterminal fragments, 134nt-5\u203218Sand 75nt-5\u203218S, is significantly increased as early as by the15th min after the start of treatment of wheat embryos withglyphosate . Notably, the amountof the fragment 134nt-5\u203218S is higher than that of 75nt-5\u203218Sfragment during 30\u201345 min of incubation with glyphosate.By 60 min of incubation their amounts become almost equaland after that, the amount of 75nt-5\u203218S fragment becomeshigher (by 90 min) and even obviously prevalent by 180 min. Similar interrelation can be seenin Figure 1, b (right panel) regarding the applied concentrationsof glyphosate.These observations suggest that cleavage at 134th nucleotidemay happen more quickly and this site is more susceptibleat the beginning of stress. The cleavage site at 75th nucleotidebecomes more prevalent with an increase of stress durationand severity. The cleavage sites at the 3\u2032-terminal segmentof 18S rRNA occur only at very high severity and durationof stress. Therefore, there seemingly exist several differentmechanisms for the cleavage at 5\u2032- and 3\u2032-termini of 18SrRNA, which may result in several different consequencesfor the functioning of 40S RS.No phosphorylation of eIF2\u03b1 was observed in plants underosmotic and oxidative stresses , heatshock and during unfolded protein response in plants . At the same time, during these stresses a significantdecrease in the translation level of most mRNAs is observedwith exception only for those templates that are responsiblefor the synthesis of stress proteins . Most likely, in plants, other mechanismsof protein biosynthesis suppression are realized,than eIF2\u03b1 phosphorylation . In addition,eIF2\u03b1 phosphorylation is not the only possible mechanism ofresponse to some types of stress in different eukaryotic cells.For example, when yeast cells are exposed to harsh ultravioletlight, phosphorylation of eIF2\u03b1 is observed, as well as a suppressionof the overall level of protein synthesis. However,inhibition of mRNA translation upon exposure to UV lightoccurs even in cells containing a mutant form of eIF2\u03b1 that isnot capable of phosphorylation .We postulate that the process of discrete fragmentationof 18S rRNA observed under glyphosate mediated amino acid starvation may lead to a decrease in the level of mRNAtranslation. This molecular mechanism can be realized inparallel with the known mechanism of translational regulationmediated by eIF2\u03b1 phosphorylation and independentlyof it.Understanding the molecular mechanisms of plant adaptationto stresses can make it possible to increase the efficiencyof breeding work to obtain genetic lines and varieties ofeconomically important plant species that are characterizedby increased resistance to certain stresses.This paper presents data indicating that in plant cells the imitationof amino acid starvation induces, in addition to eIF2\u03b1phosphorylation, another cellular response that involves thecleavage of the 18S rRNA molecule with the formation ofdiscrete 5\u2032- and 3\u2032-terminal fragments. At the same time,3\u2032-terminal fragments of 18S rRNA appear only at lethalconcentrations of glyphosate and after a prolonged period ofstress (3 hours or more). In contrast, 5\u2032-terminal fragments of18S rRNA began to accumulate in wheat embryos at relativelylow glyphosate concentrations, at which wheat embryos couldcontinue development, and already 15 min after the start ofglyphosate treatment. Thus, the process of 18S rRNA fragmentationin wheat embryo 40S RS is triggered even underconditions where eIF2\u03b1 phosphorylation does not occur. Wesuggest that such cleavage of the 18S rRNA molecule, whichis activated during amino acid starvation, may result in eitherglobal or selective suppression of mRNA translation.The authors declare no conflict of interest.Altschuler M., Mascarenhas J.P. Heat shock proteins and effects of heatshock in plants. Plant Mol. Biol. 1982;1(2):103-115. DOI 10.1007/BF00024974.Baird Th.D., Wek R.C. Eukaryotic initiation factor 2 phosphorylationand translational control in metabolism. Adv. Nutr. 2012;3:307-321.DOI 10.3945/an.112.002113Ballard D.J., Peng H.-Y., Das J.K., Kumar A., Wang L., Ren Y.,Xiong X., Ren X., Yang J.-M., Song J. Insights into the pathologicroles and regulation of eukaryotic elongation factor-2 kinase. Front.Mol. Biosci. 2021;8:839. DOI 10.3389/fmolb.2021.727863.Browning K.S., Bailey-Serres J. Mechanism of cytoplasmic mRNAtranslation. Arabidopsis Book. 2015;13:e0176Chen Z., Sun Y., Yang X., Wu Z., Guo K., Niu X., Wang Q., Ruan J.,Bu W., Gao S. Two featured series of rRNA-derived RNA fragments(rRFs) constitute a novel class of small RNAs. PLoS One. 2017;12:e0176458. DOI 10.1371/journal.pone.0176458Echevarria-Zomeno S., Yanguez E., Fernandez-Bautista N., Castro-Sanz A.B., Ferrando A., Castellano M.M. Regulation of translationinitiation under biotic and abiotic stresses. Int. J. Molec. Sci. 2013;14:4670-4683. DOI 10.3390/ijms14034670.Endo Y. Mechanism of action of ricin and related toxins on the inactivationof eukaryotic ribosomes. Cancer Res. Treat. 1988;37:75-89.DOI 10.1007/978-1-4613-1083-9_5.Gallie D.R., Le H., Caldwell C., Tanguay R., Hoang N.X., BrowningK.S. The phosphorylation state of translation initiation factorsis regulated developmentally and following heat shock in wheat.J. Biol. Chem. 1997;272:1046-1053. DOI 10.1074/jbc.272.2.1046.Gallie D.R., Le H., Caldwell C., Browning K.S. Analysis of translationelongation factors from wheat during development and followingheat shock. Biochem. Biophys. Res. Comm. 1998;245:295-300. DOI10.1006/bbrc.1998.8427.Henras A.K., Plisson-Chastang C., O\u2019Donohue M.F., Chakraborty A.,Gleizes P.E. An overview of pre-ribosomal RNA processing ineukaryotes.Wiley Interdiscip. Rev. RNA. 2015;6(2):225-242. DOI10.1002/wrna.1269.Hernandez G., Altmann M., Lasko P. Origins and evolution of themechanisms regulating translation initiation in eukaryotes. TrendsBiochem. Sci. 2010;35(2):63-73. DOI 10.1016/j.tibs.2009.10.009.Immanuel T.M., Greenwood D.R., MacDiarmid R.M. A critical reviewof translation initiation factor eIF2\u03b1 kinases in plants \u2013 regulatingprotein synthesis during stress. Funct. Plant Biol. 2012;39(9):717-735. DOI 10.1071/FP12116.Kamauchi S., Nakatani H., Nakano C., Urade R. Gene expression inresponse to endoplasmic reticulum stress in Arabidopsis thaliana.FEBS J. 2005;272(13):3461-3476. DOI 10.1111/j.1742-4658.2005.04770.x.Kast A., Klassen R., Meinhardt F. rRNA fragmentation induced bya yeast killer toxin. Mol. Microbiol. 2014;91(3):606-617. DOI10.1111/mmi.12481.Knutsen J.H., R\u00f8dland G.E., B\u00f8e C.A., H\u00e5land T.W., Sunnerhagen P.,Grallert B., Boye E. Stress-induced inhibition of translation independentlyof eIF2\u03b1 phosphorylation. J. Cell Sci. 2015;128(23):4420-4427. DOI 10.1242/jcs.176545.Laemmli U.K. Cleavage of structural proteins during the assembly ofthe head of bacteriophage T4. Nature. 1970;227(5259):680-685.DOI 10.1038/227680a0.Lageix S., Lanet E., Pouch-Pelissier M.N., Espagnol M.C., Robaglia C.,Deragon J.M., Pelissier T. Arabidopsis eIF2\u03b1 kinase GCN2 is essentialfor growth in stress conditions and is activated by wounding.BMC Plant Biol. 2008;8:134. DOI 10.1186/1471-2229-8-134.Padgette S.R., Kolacz K.H., Delannay X., Re D.B., LaVallee B.J., TiniusC.N., Rhodes W.K., Otero Y.I., Barry G.F., Eichholtz D.A., PeschkeV.M., Nida D.L., Taylor N.B., Kishore G.M. Development, identificationand characterization of a Glyphosate-tolerant soybean line.Crop Sci. 1995;35(5):1451-1461. DOI 10.3389/fpls.2016.01009Ruberti C., Kim S.J., Stefano G., Brandizzi F. Unfolded protein responsein plants: one master, many questions. Curr. Opin. Plant Biol.2015;27:59-66. DOI 10.1016/j.pbi.2015.05.016.Shaikhin S.M., Smailov S.K., Lee A.V., Kozhanov E.V., Iskakov B.K.Interaction of wheat germ translation initiation factor 2 with GDPand GTP. Biochimie. 1992;74(5):447-454. DOI 10.1016/0300-9084(92)90085-s.Smailov S.K., Lee A.V., Iskakov B.K. Study of phosphorylation oftranslation elongation factor 2 (EF-2) from wheat germ. FEBS Lett.1993;321(2-3):219-223. DOI 10.1016/0014-5793(93)80112-8.Zhang Y., Wang Y., Kanyuka K., Parry M.A., Powers S.J., Halford N.G.GCN2-dependent phosphorylation of eukaryotic translation initiationfactor-2alpha in Arabidopsis. J. Exp. Bot. 2008;59(11):3131-3141. DOI 10.1093/jxb/ern169Zhanybekova S.S., Polimbetova N.S., Nakisbekov N.O., Iskakov B.K.Detection of a new small RNA, induced by heat shock, in wheat seedribosomes. Biochemistry (Moscow). 1996;61:862-870.Zhigailov A.V., Alexandrova A.M., Nizkorodova A.S., Stanbekova G.E.,Kryldakov R.V., Karpova O.V., Polimbetova N.S., Halford N.G.,Iskakov B.K. Evidence that Phosphorylation of the \u03b1-subunit ofeIF2 does not essentially inhibit mRNA translation in wheat germcell-free system. Front. Plant Sci. 2020;11:936. DOI 10.3389/fpls.2020.00936.Zhigailov A.V., Polimbetova N.S., Borankul R.I., Iskakov B.K. Investigationof discrete fragmentation of 18S rRNA within 40S ribosomalsubparticles of plant cells. Vestnik KazNU. Biological Series.2013;2:81-87. (in Russian)Zhigailov A.V., Polimbetova N.S., Doshchanov Kh.I., Iskakov B.K.Detection in plant cells of a new 75-nucleotide cytoplasmic RNAcorresponding to the 5\u2032-terminal fragment of 18S RNA. VestnikKazNU.Biological and Medical Series. 2014;1:191-194. (in Russian)Yu Ch.-Y., Cho Y., Sharma O., Kanehara K. What\u2019s unique? The unfoldedprotein response in plants. J. Exp. Botany. 2021:erab513.DOI 10.1093/jxb/erab513."} +{"text": "Gordonia phage Nebulosus was isolated from soil on Gordonia terrae and is a siphovirus. The genome is 52,175 bp in length, has 62% GC content, and encodes 96 protein-coding genes. Nebulosus encodes a partitioning system, ParABS, which is likely involved in lysogeny maintenance.The temperate Gordonia terrae 3,612 on PYCa agar plates, and incubated at 30\u00b0C for 2 days. Plaques were purified after seven rounds of plaque purification using standard methods (A DNA phenol-chloroform extraction method was performed on a high-titer lysate . DNA wasGTGGTTA) . The genGTGGTTA) , 7.http://cobamide2.bio.pitt.edu) and PECAAN (https://blog.kbrinsgd.org/) (http://phages.wustl.edu/starterator) (\u2013The Nebulosus genome was auto-annotated using GLIMMER v3.02 and GeneMark v2.5 within DNA Master v.5.23.6 (gd.org/) , 12. Traterator) . Putativterator) \u201315. Threerator) \u2013, 17. A merator) \u2013 (7). Neberator) \u2013.Streptomyces kanamyceticus kanamycin biosynthetic gene cluster downstream from the DNA polymerase I (gp46) with strong HHpred hits to a domain of unknown function DUF6197) found in a 7 found i"} +{"text": "In the published article, there was an error in the legend for in vivo. Scale bar, 500\u03bcm.\u201d\u201cHucMSC-Exosomes accelerate wound healing. (A) Schematic overview of the study design. (B) Microscope image of huc-MSCs. The scale bar is 500 \u00b5m. (C) Flow cytometry analysis of HLA, CD29, CD34, CD45, CD73, CD90 and CD105 expression on the huc-MSC surface. (D) Transmission electron microscopy image of hucMSC-Exosomes. Scale bar, 100 nm. (E) Density plot of hucMSC-Exosomes. (F) Western blot of hucMSC-Exosome markers (G) Representative images of wound closure process of hucMSC-Exosomes treatment and PBS control. The scale bar is 4\u00a0mm. (H) Wound closure rate of hucMSC-Exosomes treatment and PBS control group. Two-tailed unpaired t-test (n=6). Error bar: mean standard deviation. ns, not significant, *p < 0.05, ***p < 0.001, ****p < 0.0001. (I) H & E and Masson staining of wounds seven days after injury. Scale bar = 1mm. (J) Uptake of hucMSC-Exosome by skin wound The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Opportunities for PrEP continue to be missed in key populations. We established a PrEP navigation program (\u201cSNAPS\u201d) with the goals to (1) increase PrEP uptake among groups disproportionately impacted by HIV and (2) preserve and improve PrEP adherence in an NYC safety-net hospital setting.SNAPS consisted of 5 components: (1) Surveillance of clinical sites where STI testing is high but PrEP use is rare e.g., ED and Women\u2019s Health Clinic (WHC), (2) Navigation for PrEP-eligible individuals (3) Accelerated follow-up with PrEP experts, (4) Point-of-care counseling and lab testing, and (5) Seamless longitudinal care. SNAPS launched 6/2019 with 2 full-time navigators. One year pre- vs post-SNAPS implementation we compared the sociodemographic profiles of PrEP initiators, their site of enrollment, and their medication possession ratios (MPRs), a proxy for PrEP adherence. Those on PrEP were a mixture of urgent and continuity care adults initiating PrEP at a safety-net hospital system. Bivariable analyses, employing Chi-square and t-test statistics, were conducted to compare sociodemographic profiles and MPR pre- vs post-SNAPS.We analyzed data on 274 (n=147 pre-SNAPS and n=127 post-SNAPS) individuals on PrEP. Compared to the pre-SNAPS period, post-SNAPS individuals were more likely to be cisgender women (33.9% vs 13.6%), Black or Latinx (84.3% vs 49.6%), uninsured (35.4% vs 29.3%), and Spanish speaking (58.3% vs 17.0%) (Table 1). Post-SNAPS individuals were more likely to be started on PrEP from the ED (51.2% vs 0%) or WHC clinic (10.2% vs 0%). Mean MPR for post-SNAPS was significantly lower than pre-SNAPS, 0.64 vs 0.89 (p < 0.001). Among post-SNAPS individuals, MSM were more likely to have higher MPRs compared to MSW and WSM individuals (Table 2). Furthermore, no difference in MPR was noted by race, preferred language, or insurance type.SNAPS successfully identified and linked key populations historically missed for PrEP opportunities. Efforts to improve SNAPS should target medication adherence.All Authors: No reported disclosures"} +{"text": "Aeromonas caviae is an increasingly recognized etiological agent of acute gastroenteritis. Here, we report five draft genomes of A. caviae isolated from suspected cholera cases during the 2022\u20132023 cholera outbreak in Malawi. Aeromonas species cause a range of clinical infections, including gastroenteritis, bacteremia, septicemia, peritonitis, pneumonia, and wound infections were identified as A. caviae by sequencing.The eviously . Genomiceviously . Of 68 iAeromonas species. The non-human reads were assembled using SPAdes v3.14.0 (A. caviae were identified by scanning the assemblies against PubMLST typing schemes (https://github.com/tseemann/mlst). The reads of A. caviae isolates from Malawi and those obtained from GenBank were mapped to the A. caviae reference genome strain 8LM (GenBank accession: CP024198) (https://github.com/tseemann/snippy) to generate pseudo-whole-genome alignments. Single nucleotide polymorphisms (SNPs) were identified in the alignment using snp-sites v2.5.1 Aeromonass v2.5.1 . Coding s v2.5.1 . Genome"} +{"text": "Background: Breast cancer (BRCA) represents the most frequent diagnosed malignancy in women worldwide. Despite treatment advances, BRCAs eventually develop resistance to targeted therapies, resulting in poor prognosis. The identification of new biomarkers, like immune-related long non-coding RNAs (lncRNAs), could contribute to the clinical management of BRCA patients. In this report, we evaluated the LINC00426 expression in PAM50 BRCA subtypes from two clinical independent cohorts (BRCA-TCGA and GEO-GSE96058 datasets).Methods and results: Using Cox regression models and Kaplan-Meier survival analyses, we identified that LINC00426 expression was a consistent overall survival (OS) predictor in luminal B (LB) BRCA patients. Subsequently, differential gene expression and gene set enrichment analyses identified that LINC00426 expression was associated with different immune-related and cancer-related pathways and processes in LB BRCA. Additionally, the LINC00426 expression was correlated with the infiltration level of diverse immune cell populations, alongside immune checkpoint and cytolytic activity-related gene expression.Conclusion: This evidence suggests that LINC00426 is a potential biomarker of immune phenotype and an OS predictor in PAM50 LB BRCA. In 2020, breast cancer (BRCA) was the most frequent diagnosed malignancy and the leading cause of cancer-related death in women worldwide . BRCA isLncRNAs are a class of non-protein-coding transcripts greater than 200 nucleotides in length. Within a cell, lncRNAs are key players in a wide range of biological functions like regulation of gene expression, chromatin modification, genomic imprinting, transcriptional and translational processing . PreviouLINC00426 is a human lncRNA gene which contains 38,105 bases in length and is in the 13q12.3 region of the DNA antisense strand of public databases. Using Cox regression models and Kaplan-Meier survival analyses, we found that LINC00426 expression is associated with OS in LB BRCA patients from both cohorts. Differential gene expression (DGE) and gene set enrichment analyses (GSEA) revealed that LINC00426 is associated with different immune-related and cancer-related pathways and processes in LB BRCA. Additionally, the LINC00426 expression correlates with immune-cell infiltration, expression of immune checkpoint genes (ICG) and cytolytic activity-related genes (CARG). These data suggest that LINC00426 is a potential biomarker of immune phenotype and an OS predictor in PAM50 LB BRCA.https://www.cbioportal.org/) and GDC Data Portal . Female patients who received neoadjuvant treatment and/or were lacking OS data were excluded, leaving a total of 927 patients analyzed in this study . The raw expression data were normalized to transcripts per million (TPM) and log2(TPM+1). A validation cohort (GSE96058) of 3,052 patients was obtained from GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96058). Again, female patients were lacking OS data and/or samples with label \u201crepl\u201d were excluded. For both datasets, patients were stratified in groups of low and high expression of LINC00426 by PAM50 BRCA subtypes, based on the lower (25%) and upper quartile (75%), respectively.Clinical information and raw RNA-seq expression data from BRCA patients in different PAM50 subtypes were obtained from TCGA database through cBioPortal and survminer (version 0.4.9). The absolute number of patients at risk by time (in months) was determined through the survfit command and n.risk option from survival (version 3.4.0). Univariate analyses were performed through Cox proportional hazards regression models to identify clinicopathological variables associated with OS of patients stratified by PAM50 BRCA subtypes. Multivariate analyses were performed using Cox proportional hazards regression models and OS predictor variables, statistically significant, obtained via univariate analyses. Hazard ratios (HR) and 95% confidence intervals were obtained for each clinicopathological variable. These analyses were performed via survival (version 3.4.0) and survminer (version 0.4.9). p values < 0.05 were considered statistically significant.Considering the OS data (in months), Kaplan-Meier survival analyses were performed through the log-rank test in patients stratified by PAM50 BRCA subtypes, according to the low and high expression of LINC00426. These analyses were performed using the R packages DESeq2 (version 1.38.1) (2FoldChange (LFC) > 1.5 and <\u22121.5 with adjusted p values < 0.05. Volcano plots were generated using the R package EnhancedVolcano (version 1.16.0). The list of differentially expressed genes was used to perform Gene Ontology (GO) over-representation analyses for biological processes and molecular functions, using the R package clusterProfiler (version 4.6.0) . Raw coun 4.6.0) . Kyoto EGSEA (version 4.1.0) with default parameters and 1,000 permutations. Gene sets with nominal p values < 0.05 and FDR <25% were considered statistically significant, according to the GSEA User Guide instructions for sample size and phenotype permutations (https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideFrame.html?Interpreting_GSEA).Using the normalized RNA-seq expression data from groups of patients with low and high expression of LINC00426, a GSEA was perfhttps://cibersortx.stanford.edu/). This analysis was performed using the normalized gene expression data with 1,000 permutations. p values < 0.05 were considered statistically significant.Using CIBERSORTx, an analytical software based on transcriptome deconvolution method to infer the cell-type-specific gene expression and cell type abundance from RNA-seq data, the relative abundance of 22 tumor-infiltrating immune cell populations was determined: naive B cells, memory B cells, plasma cells, CD8 T cells, naive CD4 T cells, memory CD4 T cells (resting), memory CD4 T cells (activated), T follicular helper cells, regulatory T cells, gamma-delta T cells, NK cells (resting), NK cells (activated), monocytes, M0 macrophages, M1 macrophages, M2 macrophages, dendritic cells (resting), dendritic cells (activated), mast cells (resting), mast cells (activated), eosinophils and neutrophils . Similarnd PRF1) .http://gepia2.cancer-pku.cn/#general) . The OS GraphPad Prism (version 8.3.0) and R package ggpubr (version 0.5.0). The non-parametric Kruskal-Wallis test was performed to identify differences in the LINC00426 expression between PAM50 BRCA subtypes. The non-parametric Mann-Whitney U test was performed to determine differences in the infiltration level of immune cell populations, ICG and CARG expression between groups of BRCA patients with low and high expression of LINC00426. Spearman correlation analyses were performed to determine statistical relationships between the LINC00426 expression and the infiltration level of immune cell populations, ICG and CARG expression . p values < 0.05 were considered statistically significant.Statistical analyses were performed through n = 927) found high expression of LINC00426 in non-luminal compared to luminal BRCA subtypes. Significant differences were identified between LA and BL (p = 0.0063), LB and HER2-enriched (p = 0.0089), LB and BL (p = 0.0004) subtypes. No significant difference was observed in the LINC00426 expression between LA and HER2-enriched subtypes (p = 0.0878) (p = 0.28), HER2-enriched (p = 0.21) and BL BRCA patients (p = 0.12) (p = 0.01) (p = 0.024), with no significance observed in LA (p = 0.288), HER2-enriched (p = 0.246) and BL (p = 0.133) subtypes . The cli = 0.12) . However = 0.01) , respectsubtypes . The OS subtypes . These rsubtypes .CLEC6A, IFNG, PLA2G2D, DCD and GNAT3) and 224 genes were upregulated . Subsequd NELL1) , alongsi < 0.05) . The KEG < 0.05) .p-value < 0.05 and FDR <25%) with eight immune-related gene sets and seven cancer-related gene sets . In contDR <25%) . Altogetp = 0.0242), plasma cells (p = 0.0324), CD8 T cells (p < 0.0001), memory CD4 T cells (resting) (p = 0.0220), memory CD4 T cells (activated) (p < 0.0001), gamma-delta T cells (p < 0.0001), M1 macrophages (p < 0.0001) and increased infiltration of memory B cells (p < 0.0001), NK cells (resting) (p < 0.0001), M0 macrophages (p < 0.0001), M2 macrophages (p < 0.0001), mast cells (resting) (p = 0.0018), mast cells (activated) (p = 0.0005) and eosinophils (p < 0.0001). These immune cell infiltration patterns are reverted in patients with high expression of LINC00426 (p > 0.05) . These rPDCD1, PDCD1LG2, CD274, CTLA4, LAG3, TIGIT and IDO1) and CARGs expression in the PAM50 LB subtype from the BRCA-TCGA cohort. Spearman correlation analyses indicated that LINC00426 expression, positively and significatively, correlates with PDCD1 (R = 0.797), PDCD1LG2 (R = 0.736), CD274 (R = 0.618), CTLA4 (R = 0.821), LAG3 (R = 0.639), TIGIT (R = 0.901), IDO1 (R = 0.738), GZMA (R = 0.878), GZMB (R = 0.749), PRF1 (R = 0.830), ICG (R = 0.843) and CARG signatures (R = 0.845) (p < 0.001) (p < 0.0001) (p < 0.001) . Concord 0.0001) . Further< 0.001) . These rn = 3,052). The clinicopathological characteristics of PAM50 BRCA patients from this cohort are described in p < 0.0001), LA and BL (p < 0.0001), LB and HER2-enriched (p < 0.0001), and LB and BL BRCA subtypes (p < 0.0001) (p = 0.98) (p = 0.042) (p = 0.005) and BL (p = 0.005) BRCA patients in the GEO-GSE96058 cohort . Kaplan- = 0.98) , while t= 0.042) . In cont8 cohort . These f8 cohort . Multiva8 cohort . In addi8 cohort .p = 0.0003), plasma cells (p = 0.0225), CD8 T cells (p < 0.0001), memory CD4 T cells (resting) (p < 0.0001), memory CD4 T cells (activated) (p < 0.0001), gamma-delta T cells (p = 0.0004), M1 macrophages (p < 0.0001) and increased infiltration levels of memory B cells (p = 0.0049), NK cells (resting) (p < 0.0001), M0 macrophages (p = 0.0059), M2 macrophages (p < 0.0001), mast cells (resting) (p < 0.0001), mast cells (activated) (p < 0.0001) and eosinophils (p < 0.0001) (p = 0.0020), regulatory T cells (p < 0.0001), NK cells (activated) (p < 0.0001) and increased infiltration of naive CD4 T cells (p = 0.0137), dendritic cells (activated) (p = 0.0038) and neutrophils (p < 0.0001) (p > 0.05) . In addi 0.0001) , when co 0.0001) . The inf > 0.05) .PDCD1 (R = 0.763), PDCD1LG2 (R = 0.687), CD274 (R = 0.648), CTLA4 (R = 0.770), LAG3 (R = 0.664), TIGIT (R = 0.807), IDO1 (R = 0.737), GZMA (R = 0.783), GZMB (R = 0.705), PRF1 (R = 0.763), ICG (R = 0.792) and CARG signatures (R = 0.773) (p < 0.001) (p < 0.0001) (p < 0.001) (We corroborated that LINC00426 expression positively correlates with the expression of < 0.001) . The exp 0.0001) . Also, t< 0.001) . These rThe expression of lncRNAs vary between different cancer types and can promote or antagonize tumor progression ; therefoIn this study, we found that LINC00426 expression is a consistent OS predictor in PAM50 LB BRCA in the BRCA-TCGA and GEO-GSE96058 cohorts, in contrast to other subtypes. Particularly, the low and high expression of LINC00426 was associated with reduced and increased OS in LB BRCA patients, respectively. Interestingly, a previous study showed a similar prognostic behavior for LINC00426 in LUAD and NSCLC . In contPrevious reports demonstrated that LINC00426 promotes LUAD progression and doxorubicin resistance in OSA, suggesting a potential oncogenic role of LINC00426 in these cancers . ConversSeveral studies demonstrated that tumor-intrinsic factors, like dysregulations on diverse oncogenic pathways, modulate the host\u2019s anti-tumor immune response depending on the cancer type and cellular context . We idenCCL2 through epigenetic pathways and hnRNPL binding to the promotor region of CCL2, which results in the recruitment of tumor-associated macrophages to the TIME of bladder cancer, promoting lymphatic metastasis via VEGF-C excretion . In addition, previous studies showed relationships between lncRNAs, including FENDRR and BCAR4, with the expression of cytokines and chemokines in cancer, which could modulate the infiltration of immune cells to the TIME . Chen etxcretion . FurtherGZMA and PFR1) are important to determine the functional status of local anti-tumor immune response and CARGs . We suggest that LINC00426 could be involved, directly or indirectly, in the regulation of ICGs and CARGs expression in PAM50 LB BRCA. Studies demonstrated that the lncRNAs XIST, TSIX and MALAT1 regulate the PD-L1 expression in BRCA through ceRNA networks and cytolytic activity markers (i.e., response . Reportsresponse with Xiain ccRCC . We idennetworks . AdditioAlthough the importance of the immune response was reported in LB BRCA , there aThe main limitations of our study are related to its retrospective nature and bioinformatics approach based on transcriptomic data, limiting the mechanistic conclusions of LINC00426. Validation of these findings is needed through methodologies like multiplex immunofluorescence or flow cytometry. Future studies focused on LINC00426 in PAM50 LB BRCA are needed that include experimental approaches to gain a wide understanding about the exact functional role of LINC00426. Despite these limitations, we conclude that LINC00426 is a potential biomarker of cancer immune phenotype whose expression has a consistent and an OS prognostic value in PAM50 LB BRCA patients in two independent cohorts, which suggest a potential use for immunotherapies selection in patients, but further analyses are mandatory to confirm this hypothesis."} +{"text": "Prostate Cancer and Prostatic Diseases 10.1038/s41391-022-00555-0, published online 03 June 2022.Correction to: In Table The original article has been corrected.Page 4: Last sentence before the section of Survival analysis.p < 0.0001; Table In patients with pre-existing CVD and receiving ADT for \u22656 months, a 70% lower risk of composite CV events was determined in GnRH antagonisttreated patients than GnRHa-treated patients (aHR 0.30; 95% CI, 0.16\u20130.54;"} +{"text": "The correct name is: Yuelong Yan. The correct citation is: Yan Y, Zhang C, Hao J, Wang X-L, Ming J, Mi L, et al. (2019) DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program. PLoS Biol 17(6): e3000324."} +{"text": "Anaerostipes hadrus strains BA1 and GIF7 were isolated from a healthy man. The complete genomes\u2019 sizes are 2,946,270 bp (BA1) and 2,907,308 bp (GIF7), with high average nucleotide identity (ANIb = 100%) and alignments \u226596.86% between strains. Conversely, both strains share 97.47% (ANIb) identity and \u226477.36% alignments to A. hadrus ATCC 29173T. Anaerostipes of Bacillota phylum and Lachnospiraceae family are known most prominently for producing butyrate was first isolated in 1976 agar (Oxoid) were sub-cultured in BHI broth (4 mL) for DNA extraction. Cells were lysed using MP Biomedicals bead-beating tubes on a Fast-Prep 24/5G at 6.0 m/sec for 40 s followed by DNA purification using a Promega Maxwell-16-FFS kit without modifications to the manufacturer\u2019s protocol. Paired-end 150-bp reads were sequenced on an Illumina NovaSeq without modifications to TruSeq Nano DNA library prep kit. Default software parameters were applied unless stated otherwise. Trimmomatic v.0.39 was used to trim and remove adapters from Illumina reads . Bo. BoA. haentities . A high entities ."} +{"text": "J Clin Endo Metab Case Reports. 2023; 1(1): 10.1210/jcemcr/luac017), a production error occurred in the PDF version of Figure 1 regarding patient information.In the above-named article by Raven LM, Greenfield JR, and Muir CA (The article has been corrected online.The publisher regrets the error.10.1210/jcemcr/luac017doi:"} +{"text": "Applying data-reduction techniques to extract meaningful information from electronic performance and tracking systems (EPTS) has become a hot topic in football training load (TL) monitoring. The aim of this study was to reduce the dimensionality of the internal and external load measures, by a principal component approach, to describe and explain the resultant equations for TL monitoring during a standard in-season microcycle in sub-elite youth football. Additionally, it is intended to identify the most representative measure for each principal component. A principal component analysis (PCA) was conducted with a Monte Carlo parallel analysis and VariMax rotation to extract baseline characteristics, external TL, heart rate (HR)-based measures and perceived exertion. Training data were collected from sixty sub-elite young football players during a 6-week training period using 18 Hz global positioning system (GPS) with inertial sensors, 1 Hz short-range telemetry system, total quality recovery (TQR) and rating of perceived exertion (RPE). Five principal components accounted for 68.7% of the total variance explained in the training data. Resultant equations from PCA was subdivided into: (1) explosiveness, accelerations and impacts (27.4%); (2) high-speed running (16.2%); (3) HR-based measures (10.0%); (4) baseline characteristics (8.3%); and (5) average running velocity (6.7%). Considering the highest factor in each principal component, decelerations (PCA 1), sprint distance (PCA 2), average HR (PCA 3), chronological age (PCA 4) and maximal speed (PCA 5) are the conditional dimension to be considered in TL monitoring during a standard microcycle in sub-elite youth football players. Current research provides the first composite equations to extract the most representative components during a standard in-season microcycle in sub-elite youth football players. Futures research should expand the resultant equations within training days, by considering other well-being measures, technical-tactical skills and match-related contextual factors. This isimpacts) . Otherwiimpacts) . The resimpacts) . Combiniimpacts) .Additionally, the emergent tracking tools appears to have created confusion in dose-response considerations given the data analysis requirement to extract relevant information from large amounts of data . This kiPrincipal component analysis (PCA) is one of the most used data-reduction techniques to extract redundant information from TL data in football . Using an = 20), U17 (n = 20) and U19 (n = 20) sub-elite youth football academy 15 was assured to perform PCA analysis within a little pocket on the upper back between both scapulae of a custom-made vest (The training data eligibility considered the following inclusion criteria: (a) youth football players aged between 13 and 20 years old (and U19) ; (b) youand U19) ; (c) traand U19) ; (d) traand U19) , 2022a. and U19) . For ETLade vest . All metade vest .n = 41), MD-2 (n = 38), and MD-1 (n = 44) (Using a \u201cmatch day minus format\u201d (MD), the weekly microcycle included the training sessions MD-3 (Tuesday), MD-2 (Wednesday), and MD-1 (Friday). The number of observation for each training day was: MD-3 ((n = 44) , 2021b. (n = 44) . All tra 52\u201366%) .i.e., MD-3, MD-2 and MD-1) was categorized in accordance with nd MD-1) . Small, \u00ae, Northern Ireland) (\u00ae devices was good (bias 5%) (\u22121)), maximal running speed (MRS (m\u00b7s\u22121)), relative high-speed running (rHSR (m): 19.8\u201325.1 km\u00b7h\u22121) distance (m), high metabolic load distance (HMLD (m) > 25.5 W\u00b7kg\u22121), number sprints (n) and average sprint distance (SPR (m) (>25.1 km\u00b7h\u22121)) (m), dynamic stress load (DSL (a.u.)), number of ACC (>3 m\u00b7s\u22122) and number of decelerations (DEC < 3 m\u00b7s\u22122) coupled with accelerometer (100 Hz), magnetometer (10 Hz) and gyroscope (100 Hz) (STATSports ApexIreland) . With a Ireland) . The accbias 5%) . The ETL3 m\u00b7s\u22122) , 2022a (3 m\u00b7s\u22122) .\u00ae TM HR band was used to capture HR-based measurements utilizing a 1 Hz short-range telemetry system (max), average heart rate (HRmean), percentage of HRmax (%HRmax) and individual players\u2019 training impulse (TRIMP) were monitored , 2022a .\u00ae with minimum clothing. Height (cm) was collected using an electronic stadiometer . Players\u2019 height (m), weight (kg) and sitting height (cm) were recorded by the average of three measurements to the nearest 0.1 using international units (IU). Body mass index (BMI) was calculated by dividing weight by the square of height (kg/m2). BMI\u2019s cut-offs used were: underweight < 18.5 kg/m2, normal 18.50\u201324.99 kg/m2, overweight \u2265 25 kg/m2, obese \u2265 30 kg/m2 (n = 52), mid-PHV (n = 65) and post-PHV (n = 207).Players\u2019 individual characteristics were collected by height (m), weight (kg), chronological age (years), sitting height (cm) and experience level (years). Anthropometric measures were measured using standard the International Society for the Advancement of Kinanthropometry (ISAK) guidelines . Body ma30 kg/m2 . Relativ30 kg/m2 . Based o30 kg/m2 . Sub-elii.e., anthropometric and maturational status) and the ITL measures of the first principal component. The loadings must have a sum of squares of exactly one. This is due to the possibility of a considerable variation when loadings are of a great magnitude.n), along which data varies the most have mean values equal to zero and standard deviations equal to one and its weighted load vector (d vector .r < 0.4 (p < 0.05. Data are presented as the mean \u00b1 SD using JASP software (jasp-stats.org).A data reduction technique was conducted using a principal component analysis (PCA) with 95% confidence intervals (95% CI) . Monte Cr < 0.4 . Weightir < 0.4 . Kolmogovia HRmax, AvHR, %HR and TRIMP. The fourth PCA explained 8.3% of the baseline outset . The fifth PCA explained 6.7% of the accumulated TL . Constantly, PHV, relative age, experience level and BMI were excluded from the PCA (r < 0.4).i.e., PHV, relative age, experience level and BMI). Also, KMO\u2019s criteria reported a sampling adequacy of sampled data, reporting a considerable proportion of the variance as result of the underlying factors (KMO = 0.73). Furthermore, significant Barlett Sphericity test was significant (p < 0.001).The weightings (eigenvectors) of the PCA analysis are represented by a path graph in The resultant equations from extracted principal component are presented in The aim of this study was to reduce the dimensionality of the internal and external load measures, by a PCA approach, in order to describe and explain the resultant equations for TL monitoring during a standard microcycle in a sub-elite youth football players. Additionally, it is intended to identify the most representative measure for each principal component. After data reduction, five principal components were extracted from TL dataset explaining 68.7% of the total variance. The TL measures with the highest weight in each PCA were DEC, SPR distance, average HR, chronological age and MRS.i.e., HRmax, AvHR, %HRmax and TRIMP), confirming the correlation between HR-based measures and ETL outcomes explosiveness, ACC and impacts (27.4%); (2) HSR (16.2%); (3) heart bate-based measures (10.0%); (4) baseline characteristics (8.3%); (5) average running velocity (6.7%). Considering the highest representative factor in each principal component, the variables considered were DEC (PCA 1), SPR distance (PCA 2), average HR (PCA 3), chronological age (PCA 4) and MRS (PCA 5). In football, outcomes . The fououtcomes . In lineoutcomes . Also, toutcomes . Indeed,outcomes . Effectioutcomes , 2018. Loutcomes , 2022c. outcomes , 2020.i.e., eigenvalues between 1.0% and 68.0%) . Albeit,d 68.0%) .Current applied PCA determine the resultant equations from individual-based principal components, expressing by major component weightings . Indeed,i.e., small-sided and conditioned games), training day , age group and maturational bands . Additioost-PHV) . Also, tost-PHV) . Howeverost-PHV) . Furtherost-PHV) . In geneost-PHV) . Furtherost-PHV) . Finallyost-PHV) , 2021b. ost-PHV) .Current resultant composite equations can be applied to relative contribution of the ITL and ETL measures for monitoring and management load in sub-elite youth football.Data reduction techniques decrease the redundant information and dimensionality of the training data, expressing in the following principal components: explosiveness and impacts, high-speed running, heart bate-based measures, baseline characteristics and average running velocity.Considering the highest factor in each principal component, DEC (PCA 1), sprint distance (PCA 2), average HR (PCA 3), chronological age (PCA 4) and maximal speed (PCA 5) are the conditional dimension to be considered in TL monitoring during a standard microcycle in sub-elite youth football players.Maturational status should be carefully considered in the TL monitoring together with relative age effect, chronological and baseline characteristics.Self-perception and practice experience may affect the variance explained by perceived exertion and pacing behavior.Training intensity and volume can be more accurately measured by current resultant composite equations and/or most representative factor for a standard microcycle in sub-elite youth football players.Futures research should expand the resultant equations for TL monitoring in sub-elite youth football with well-being, technical-tactical and match-related contextual factors.Using a PCA approach, five principal components could be applied to extract to describe and explain resultant equations for TL monitoring during an in-season standard microcycle in sub-elite youth football. Current research provides the first composite equations to extract the TL in this specific population expressed as explosiveness and impacts, high-speed running, HR-based measures, baseline characteristics and average running velocity. Considering the highest factor in each principal component, DEC (PCA 1), SPR distance (PCA 2), average HR (PCA 3), chronological age (PCA 4) and maximal SPR (PCA 5) are the conditional dimension to be considered in TL monitoring during a standard microcycle in sub-elite youth football players.Future research should expand the resultant equations within the microcycle, by considering other well-being measures, technical-tactical factors and match-related contextual factors.10.7717/peerj.15806/supp-1Supplemental Information 1The individual data of the variables selected for this study.Click here for additional data file."} +{"text": "Arthrobacter globiformis B-2979 culture. MrAaronian has > 99% nucleotide identity with cluster AW arthrobacteriophages Michelle, Stayer, Sloopyjoe, and StarLord.Arthrobacteriophage MrAaronian contains a 54,509 bp DNA genome with 87 predicted protein-coding genes. MrAaronian has siphovirus morphology and was collected from a flowerbed soil sample in Poughkeepsie, NY, and isolated on an Arthrobacter group of bacteria is unusual since they appear as Gram-negative rods in young cultures and as Gram-positive cocci in older cultures coordinates: 41.72201 N, 73.930158 W]. The sample was washed with peptone-yeast calcium (PYCa) liquid media, and the supernatant was passed through a 0.22 \u00b5m syringe filter. The filtrate was incubated with host biformis . High-tiry Guide .Bacteriophage genomic DNA was extracted using a Promega Wizard DNA Clean-Up System , and sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit . Libraries were sequenced by Illumina MiSeq at the Pittsburgh Bacteriophage Institute to generate 607,351 total single-end reads of 150-base read length. A single bacteriophage contig with 6,670\u00d7 coverage was assembled using Newbler v2.9 and checked for completeness and genomic termini using Consed v29 (https://discover.kbrinsgd.org), and DNA Master v5.23.6 (http://phagesdb.org/DNAMaster/). Consistent with other cluster AW bacteriophages, no tRNA genes were identified using Aragorn v1.1 (12) and tRNAscan-SE v2.0 (BLASTn query of-SE v2.0 . TmHmm a-SE v2.0 assessed-SE v2.0 and HHPr-SE v2.0 , which i-SE v2.0 showing -SE v2.0 . All too"} +{"text": "Nacubactam is a new non-\u03b2-lactam diazabicyclooctane \u03b2-lactamase inhibitor that inhibits penicillin binding protein 2 (PBP2) of Enterobacterales and acts synergistically as a \u03b2-lactam enhancer when combined with \u03b2-lactams. Nacubactam is under development for the treatment of serious Gram-negative infections. We evaluated the in vitro activity of cefepime-nacubactam against carbapenem-resistant Enterobacterales (CRE) clinical strains isolated at six medical facilities in Japan.Activity of cefepime-nacubactam (1:1 ratio) was tested against 376 CRE (MIC of meropenem or imipenem: \u22652 mg/L). The MICs were evaluated by the broth microdilution method according to the CLSI using frozen-panels containing various antimicrobial agents. The percentage susceptible (%S) for cefepime-nacubactam was calculated using the CLSI susceptible breakpoint of cefepime.Escherichia coli, 27; Klebsiella spp., 89; Enterobacter spp.; 56; others, 12), the MIC50/MIC90 and %S were 8/32 mg/L and 4.9%S for meropenem, 4/32 mg/L and 29.3%S for imipenem, 32/ >128 mg/L and 31.1%S as 8 mg/L for cefepime and 2/4 mg/L and 95.7%S for cefepime-nacubactam, respectively. Against non-CPE , the MIC50/MIC90 and %S were 0.5/8 mg/L and 53.6%S for meropenem, 2/8 mg/L and 12.0%S for imipenem, 2/ >128 mg/L and 66.7%S as 8 mg/L for cefepime and 0.25/4 mg/L and 99.0%S for cefepime-nacubactam, respectively. The MIC50/MIC90 and %S of cefepime-nacubactam was 2/4 mg/L and 94.9%S against 156 MBL-producing CRE, and 0.5/2 mg/L and 100%S against non-MBL-producing CRE including 14 KPC and 8 OXA-producing strains and 6 strains producing other carbapenemases. Nacubactam alone showed limited activity against CPE and non-CPE .The collection included 184 carbapenemase-producing Enterobacterales (CPE) strains and 192 carbapenemase-non-producing Enterobacterales (non-CPE) strains. Against CPE (In vitro activity of cefepime-nacubactam against CRE isolated in JapanCefepime-nacubactam demonstrated potent activity against both CPE and non-CPE/CRE clinical strains. This is the first study to report the activity of cefepime-nacubactam against carbapenemase-non-producing CRE, which accounts for 80% of CRE in Japan.Katsunori Yanagihara, MD, PhD, FUJIFILM Toyama Chemical Co., Ltd.: Commissioned research|KYORIN Pharmaceutical Co.,Ltd.: Commissioned research Hiroshige Mikamo, M.D, Ph.D, Asahi Kasei Pharma Corporation: Grant/Research Support|Merck Sharp & Dohme: Honoraria|Pfizer Inc.: Grant/Research Support|Pfizer R&D Japan: Honoraria|Sumitomo Pharma Co., Ltd.: Grant/Research Support|Sumitomo Pharma Co., Ltd.: Honoraria Yohei Doi, MD, PhD, bioMerieux: Advisor/Consultant|FujiFilm: Advisor/Consultant|Gilead: Advisor/Consultant|Gilead: Honoraria|GSK: Advisor/Consultant|Meiji Seika Pharma: Advisor/Consultant|Moderna: Advisor/Consultant|Moderna: Honoraria|MSD: Advisor/Consultant|MSD: Honoraria|Shionogi: Advisor/Consultant|Shionogi: Grant/Research Support|Shionogi: Honoraria"} +{"text": "T and NL03-T5-1, were isolated from a soil sample collected from the Nanling National Forests, Guangdong Province, PR China. The two strains were Gram-stain-positive, aerobic, rod-shaped and had lophotrichous flagellation. Strain NL03-T5T could secrete extracellular mucus whereas NL03-T5-1 could not. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains belong to the genus Cohnella, were most closely related to Cohnella lupini LMG 27416T (95.9% and 96.1% similarities), and both showed 94.0% similarity with Cohnella arctica NRRL B-59459T, respectively. The two strains showed 99.8% 16S rRNA gene sequence similarity between them. The draft genome size of strain NL03-T5T was 7.44 Mbp with a DNA G+C content of 49.2 mol%. The average nucleotide identities (ANI) and the digital DNA\u2013DNA hybridization (dDDH) values between NL03-T5T and NL03-T5-1 were 99.98% and 100%, indicating the two strains were of the same species. Additionally, the ANI and dDDH values between NL03-T5T and C. lupini LMG 27416T were 76.1% and 20.4%, respectively. The major cellular fatty acids of strain NL03-T5T included anteiso-C15:0 and iso-C16:0. The major polar lipids and predominant respiratory quinone were diphosphatidylglycerol (DPG) and menaquinone-7 (MK-7). Based on phylogenetic analysis, phenotypic and chemotaxonomic characterization, genomic DNA G+C content, and ANI and dDDH values, strains NL03-T5T and NL03-T5-1 represent novel species in the genus Cohnella, for which the name Cohnella silvisoli is proposed. The type strain is NL03-T5T (=GDMCC 1.2294T = JCM 34999T). Furthermore, comparative genomics revealed that the genus Cohnella had an open pan-genome. The pan-genome of 29 Cohnella strains contained 41,356 gene families, and the number of strain-specific genes ranged from 6 to 1649. The results may explain the good adaptability of the Cohnella strains to different habitats at the genetic level.Two strains, designated NL03-T5 Cohnella, which lies within the family Paenibacillaceae of the order Bacillales, was first proposed by K\u00e4mpfer et al. with the description of Cohnella thermotolerans as the type species , and catalase activity was determined by bubble production after mixing cells with 3% H2O2. Gliding motility was checked by observing the edges of colonies formed on 1:6-diluted R2A and using the hanging drop technique as described by Bernardet et al. (2002) [w/v), CM-cellulose , Tween 20 and 40 were examined as described by Son et al. [The morphological features of strains NL03-T5. (2002) . Hydrolyn et al. . Other pT and its related species were harvested from R2A agar after being incubated for 4 d at 30 \u2103. Fatty acid methyl esters were extracted using the Sherlock Microbial Identification System (MIDI) protocol version 6.1 and analyzed by gas chromatography as previously described [For cellular fatty acids, polar lipids, and respiratory quinones analysis, strain NL03-T5escribed . The polescribed . Respiraescribed and analT and NL03-T5-1 were sequenced on the Illumina HiSeq platform at Shanghai Majorbio Bio-Pharm Technology Co., Ltd. . Sequencing reads were assembled into contigs and scaffolds by applying SPAdes version 3.11.1 with default parameters [http://rast.nmpdr.org/, accessed on 1 August 2023) with default parameters. The genes encoding carbohydrate active enzymes (CAZymes) were identified using the dbCAN2 meta server with HMMER annotation , and biosynthetic gene clusters (BGCs) were annotated using antiSMASH bacterial version 6.1.1 with default parameters, respectively. All 27 reference genomes of the genus Cohnella were downloaded from the NCBI database. A pan-genome analysis was performed using the bacterial pan-genome analyses tool (BPGA) pipeline [https://www.bic.ac.cn/ImageGP/, accessed on 1 August 2023). The genomic DNAs of strains NL03-T5rameters , and thepipeline . The dathttps://ggdc.dsmz.de/, accessed on 1 August 2023) [www.ezbiocloud.net/tools/ani, accessed on 1 August 2023) [Cohnella was reconstructed based on 92 up-to-date core genes using the software UBCG version 3.0 [Overall genome relatedness indices (OGRI) including the digital DNA\u2013DNA hybridization (dDDH) and average nucleotide identity (ANI) values were calculated using the Genome-to-Genome Distance Calculator (GGDC) (st 2023) and Orthst 2023) , respectsion 3.0 with a mT and NL03-T5-1 showed 99.8% 16S rRNA gene sequence similarity. In the EzBiocloud and NCBI databases, the two strains were closely related to the species of the genus Cohnella and showed the highest similarities with C. lupini LMG 27416T (95.9% and 96.1%), and they both exhibited 95.3% and 94.0% similarities with C. abietis HS21T and C. arctica NRRL B-59459T, respectively. The 16S rRNA gene phylogenetic trees based on the ML, NJ, and ME methods NaCl NaCl . StrainsT and its reference species C. abietis HS21T, C. lupini LMG 27416T, and C. arctica NRRL B-59459T are given in T contained a large amount of anteiso-C15:0 (50.7%) and iso-C16:0 (21.2%), and small amounts of C16:0 (7.2%), iso-C15:0 (5.5%), anteiso-C17:0 (4.0%), iso-C14:0 (3.7%), iso-C14:0 (1.9%), anteiso-C13:0 (1.6%) and C14:0 (1.3%). The prominent fatty acids were similar to other species of the genus Cohnella, indicating that strain NL03-T5T is a member of the genus Cohnella. However, strain NL03-T5T contained a higher amount of iso-C16:0 than its closely related species C. abietis HS21T, and it contained a lower amount of C16:0 and a higher amount of iso-C15:0 and iso-C16:0 than C. lupini LMG 27416T and C. arctica NRRL B-59459T. Moreover, strain NL03-T5T did not contain alcohol-C16:1\u00a0\u03c97c (6.5%) or C16:1\u00a0\u03c911c (7.0%) whereas C. lupini LMG 27416T did. These significant differences in the fatty acids clearly distinguished strain NL03-T5T from other related species. The major polar lipids of strain NL03-T5T were DPG and PE, which were in common with its closely related species. Otherwise, four unidentified amino phospholipids (APLs) were also detected in strain NL03-T5T , and higher than C. abietis HS21T (44.8%) , amino acids and derivatives (17.3%), protein metabolism (9.3%) and cofactors, vitamins, prosthetic groups, and pigments (8.9%) and carbohydrate-binding modules (CBMs) constituting the most abundant families . The diss (8.9%) . In addi strains . The antfamilies . Additiomination , indicatCohnella strains comprised 41,356 gene families. The core genes were present in all 29 genomes, accessory genes were present in 2\u201328 genomes, and unique genes were present only in one genome. The numbers of core genes, accessory genes, and unique genes were 492 (1.2%), 19,166 (46.3%), and 21,698 (52.5%), respectively in the power-law regression function. New gene distribution and gene family distribution of the 29 Cohnella strains are shown in Cohnella strains to different habitats through gene gains or losses during frequent evolutionary changes at the genetic level. The pan-genome of the 29 ectively a. The nuectively b, sugges genomes c. The cuT and NL03-T5-1, from a soil sample collected from the Nanling National Forests, PR China. The two strains showed 99.8% 16S rRNA gene sequence similarity. The ANI and dDDH values between them are 99.98% and 100%. These results indicate the two strains are of the same species. However, strain NL03-T5T could secrete extracellular mucus whereas NL03-T5-1 could not [Cohnella strains contained 41,356 gene families, and the numbers of core genes, accessory genes, and unique genes were 492, 19,166, and 21,698, respectively (Cohnella strains might be associated with their colonized environments.The genus er (HGT) . The panectively a,c. TettCohnella silvisoli .w/v) NaCl. Oxidase and catalase are -negative. It can hydrolyze Tween 20, but not Tween 40, casein, or CM-cellulose. Additionally, it can hydrolyze gelatin or not. The major fatty acids (>10%) include anteiso-C15:0 (50.7%) and iso-C16:0 (21.2%). The predominant polar lipid is DPG. The main respiratory quinone is MK-7. The API ZYM test result was positive for alkaline phosphatase, esterase, lipase, leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase, \u03b1-galactosidase, \u03b2-galactosidase, \u03b1-glucosidase, \u03b2-glucosidase, N-acetyl-\u03b2-glucosaminidase and \u03b1-mannosidase; but negative for valine arylamidase, cystine arylamidase, trypsin, \u03b1-chymotrypsin and \u03b1-fucosidase. The API 20NE test results were positive for gelatin hydrolysis, 4-nitrophenyl-\u03b2-d-galactopyranosidase and \u03b2-glucosidase or not; but negative for nitrate reduction, indole production, glucose fermentation, arginine dihydrolase and urease. It can assimilate glucose, L-arabinose, mannose, mannitol, N-acetyl-D-glucosamine, maltose, gluconate, adipate, malic acid, citric acid, phenylacetic acid and capric acid or not.Cells are aerobic, Gram-stain-positive, lophotrichous flagellation, rod-shaped, 1.2\u20132.0 \u03bcm long and 0.4\u20130.6 \u03bcm in diameter after incubation on R2A agar for 4 d. Colonies on R2A agar are white-cream, circular, convex with extracellular secretions or not. Growth occurs at 15\u201337 \u2103 and at a pH range from 5.0 to 8.5 . Cells can tolerate 0.5% (T (=GDMCC 1.2294T = JCM 34999T), which was isolated from a soil sample collected from the Nanling National Forests, Guangdong Province, PR China. The genomic DNA G+C content of the type strain is 49.2 mol%.The type strain is NL03-T5"} +{"text": "Correction: BMC Genomics 24, 212 (2023)https://doi.org/10.1186/s12864-023-09310-8Following publication of the original article , it was Additional file 1: Supplementary table 1. List of candidate genes for WES analysis. Supplementary table 2. Annotation of candidate variants identified in the 22 eoRCC patients.Additional file 2: Supplementary Table 8."} +{"text": "TERT (rs2736100), CCDC26 (rs4295627), CDKN2A/B (rs4977756) and RTEL1 (rs6010620) gene polymorphisms as the risk factors specific to glioma. However, the data samples of previous genetic-epidemiological studies are modest to determine whether they have definite association with glioma.Previous genetic-epidemiological studies considered The study paid attention to systematically searching databases of PubMed, Embase, Web of Science (WoS), Scopus, Cochrane Library and Google Scholars. Meta-analysis under 5 genetic models, namely recessive model (RM), over-dominant model (O-DM), allele model (AM), co-dominant model (C-DM) and dominant model (DM) was conducted for generating odds ratios (ORs) and 95% confidence intervals (CIs). That was accompanied by subgroup analyses according to various racial groups. The software STATA 17.0 MP was implemented in the study.TERT gene rs2736100 polymorphism, CCDC26 gene rs4295627 polymorphism, CDKN2A/B gene rs4977756 polymorphism and RTEL1 gene rs6010620 polymorphisms increased the risk of glioma in Caucasians to different degrees. In Asian populations, the CCDC26 gene rs4295627 polymorphism and CDKN2A/B gene rs4977756 polymorphism did not exhibit a relevance to the risk of glioma. It is suggested to cautiously explain these results as the sample size is small.21 articles were collected. According to data analysis results, in four genetic models TERT (rs2736100), CCDC26 (rs4295627), CDKN2A/B (rs4977756) and RTEL1 (rs6010620) genes in glioma might increase risk of glioma, but there are ethnic differences. Further studies evaluating these polymorphisms and glioma risk are warranted.The current meta-analysis suggested that the SNP of Based oTERT), 8q24.21 , 9p21.3 , and 20q13.33 (TERT) is crucial for telomerase activity in preserving telomeres and cellular immortality (CCDC26) downregulates telomerase activity and increases apoptosis. Cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) can partially control the cell cycle. Regulator of telomere elongation helicase 1 (RTEL1), as a DNA helicase, can inhibit homologous recombination for directly maintaining the genomic stability . Telomerortality . In conttability . These gTERT (RS2736100), CCDC26 (RS4295627), CDKN2A/B (RS497756), and RTEL1 (rs6010620).In this meta-analysis, we expanded sample size by enrolling up 21 articles and used five genetic models to examine the relationship between glioma and SNPs of 2The meta-analysis in the study was performed as per the Preferred Reporting Items for Systematic reviews and Meta-Analysis version.2.1Literature search was carried out comprehensively in eight databases, namely PubMed, Embase, WoS, Scopus, Cochrane Library, and Google Scholars. The MeSH term were as follows: \u201c OR (SNP) OR OR (SNP) OR (SNP) OR (SNPs) OR (variation) OR (mutation)) AND ((Gliomas) OR (Glioma) OR OR OR OR OR (Mixed Glioma) OR OR OR OR (Astrocytoma) OR (Glioblastoma) OR (Diffuse Intrinsic Pontine Glioma) OR (Ependymoma) OR OR (Ganglioglioma) OR (Medulloblastoma) OR (Oligodendroglioma) OR (Optic Nerve Glioma)) AND (rs xxxxxxx)\u201d. In addition, we screened relevant reviews and references from previous meta-analyses to increase the number of other eligible studies. The retrieval process was performed by two researchers independently. Any discrepancy was adjudicated by a senior investigator.2.2TERT gene, rs4295627 polymorphism of CCDC26 gene, rs4977756 polymorphism of CDKN2A/B gene and rs6010620 polymorphism of RTEL gene with glioma susceptibility;(1) case-control or cohort study and genome-related study regarding the association of rs2736100 polymorphism of (2) studies containing allelic and genotypic data or ORs and 95% CIs for susceptibility;(3) appropriate statistical methods and reliable data with clear and unambiguous expression of results, allowing calculation of the ORs and 95% CIs;(4) no overlapped data, and studies involving the same data or overlapped by the same authors, only the one that had the largest sample size or the most recently published.2.3(1) review, commentary, abstract, and case report types;TERT (rs2736100), CCDC26 (rs4295627), CDKN2A/B (rs4977756) and RTEL1 (rs6010620);(2) articles with original literature content did not involve (3) articles were unrelated to glioma research;(4) articles with insufficient data, such as those lacking gene frequency information or ORs with 95% CIs;(5) articles with non-human study subjects.2.4Each study covered the data of: the first author\u2019s name, publication year, ethnicity , number of cases and controls with relevant genotypes, ORs and 95% CIs. In addition, the genetic model used in the article was checked. We applied the Newcastle-Ottawa Scale for evaluating the literature quality. Two researchers performed independent data extraction and evaluated the literature quality. A senior investigator took charge of discrepancy arbitration.2.5p<0.05 reported statistical significance). Second, we measured the association degree of TERT (rs2736100), CCDC26 (rs4295627), TERT (rs2736100) and RTEL1 (rs6010620) with glioma risk under five genetic models using the ORs and 95% CIs, which were the RM, O-DM, AM, C-DM and DM.STATA 17.0 MP was implemented for all statistical analyses in this study. First, we performed the Hardy-Weinberg Equilibrium (HWE) test .We merged the ORs and 95% CIs that satisfied the criteria under the same models. In addition, in all genetic models, subgroup analyses were carried out according to ethnic differences and the 33.1We initially searched 640 literature and eventually enrolled 21 eligible articles covering Caucasian, Asian, and others , 17\u201336. 3.23.2.1TERT gene rs2736100 polymorphism, allele G is the risk gene (TERT gene rs2736100 polymorphism led to increased glioma risk in 5 genetic models (AM (G vs T): OR=1.29, 95% CI: 1.25 to 1.34; RM (GG vs TT+TG): OR=1.31, 95% CI: 1.18 to 1.44; DM (TG+GG vs TT): OR=1.52, 95% CI: 1.34 to 1.73; C-DM (GG vs TT): OR=1.69, 95% CI: 1.56 to 1.82; C-DM (GT vs TT): OR=1.40, 95% CI: 1.31 to 1.49; O-DM (TT+GG vs TG): OR=0.93, 95% CI: 0.88 to 0.98). When stratifying the analysis according to ethnicity, we obtained similar results in Caucasians, although in the O-DM results only showed a trend of association with glioma (AM (G vs T): OR=1.28, 95% CI: 1.23 to 1.33; RM (GG vs TT+TG): OR=1.29, 95%CI: 1.13 to 1.47; DM (TG+GG vs TT): OR=1.51, 95% CI: 1.29 to 1.76; C-DM (GG vs TT): OR=1.64, 95% CI: 1.50 to 1.80; C-DM (GT vs TT): OR=1.37, 95% CI: 1.27 to 1.49; O-DM (TT+GG vs TG): OR=0.93, 95% CI: 0.87 to 1.00). Among Asians, we included only one study, and the results were similar to those of Caucasians. In the study of a multi-ethnic population, we included the study of Wrensch and Safaeian which revealed the relevance of the TERT gene rs2736100 polymorphism to increased glioma risk.In the isk gene Figure\u00a023.2.2CCDC26 gene rs4295627 polymorphism, allele T was the risk gene : OR=0.92, 95% CI: 0.81 to 1.03. In one study, the RM (GG vs TT+TG): 0.52; 0.25~1.05; DM (TG+GG vs TT): 0.86; 0.60 to 1.23; C-DM (GG vs TT): 0.50; 0.24 to 1.05; C-DM (GT vs TT): 0.95; 0.65 to 1.38; O-DM (TT + GG vs TG): 0.97; 0.67 to 1.40.3.2.3CDKN2A/B gene rs4977756 polymorphism, allele T was the risk gene : OR=1.03, 95% CI: 0.91 to 1.17. In one study, the RM (GG vs AA+AG): 1.12; 0.53 to 2.34; DM (AG+GG vs AA): 0.96; 0.66 to 1.39; C-DM (GG vs AA): 1.09; 0.52 to 2.32; C-DM (GA vs AA): 0.94; 0.63 to 1.38; O-DM (AA+GG vs AG): 1.08; 0.73 to 1.58. In other study, RM (GG vs AA+AG): 0.68; 0.25 to 1.81; DM (AG+GG vs AA): 0.98; 0.60 to 1.58; C-DM (GG vs AA): 0.69; 0.25 to 1.87; C-DM (GA vs AA): 1.04; 0.63 to 1.73; O-DM (AA+GG vs AG): 0.93; 0.56 to 1.52.3.2.4RTEL1 gene rs6010620 polymorphism, allele T was the risk gene : OR=1.35, 95% CI: 1.22 to 1.48; RM (GG vs AA+AG): 2.04; 1.61 to 2.57; DM (AG+GG vs AA): 1.35; 1.20 to 1.52; C-DM (GG vs AA): 2.41; 1.09 to 3.04; C-DM (GA vs AA): 1.22; 1.07 to 1.38; O-DM (AA+GG vs AG): 0.93; 0.83 to 1.05.3.3Our study adopted Egger\u2019s Test for evaluating the literature publication bias and the results are shown in In rs2376100, there was publication bias in AM (p=0.469). In rs4295627, publication bias existed in dominant, co-dominant and O-DM (DM (TG+GG vs TT): p=0.426; C-DM (GT vs TT): p=0.436; O-DM (TT+GG vs TG): p=0.427). In rs4977756, publication bias existed in O-DM (p=0.111). In rs6010620, publication bias existed in the recessive, dominant and O-DM (RM (GG vs AA+AG): p=0.010; DM (AG+GG vs AA): p=0.014; O-DM (AA+GG vs AG): p= 0.461).4Our study is one of the first ones with conducting the first meta-analysis with the largest sample size as far as we concern and we performed detailed analyses of multiple associated SNPs under five genetic models. Besides, stratified analyses were carried out considering ethnicity. This indicates reliable meta-analysis results.From the meta-analysis, allele G in the SNP at the rs2736100 locus differentially elevated glioma risk, which conforms to studies by Di Stefano . In partTERT is the most important component in regulating telomerase activity. A few scholars found the relevance of TERT expression to glioma grade and patients\u2019 prognosis presented shorter telomeres relative to people who possessed TG genotype and p15 (CDKN2B) oncoproteins which play multiple roles in cellular stress recognition, senescence regulation, differentiation as well as apoptosis in the developmental and proliferative phases of cells regions of genes. Intron SNPs possibly facilitate aberrant exon inclusion or deletion by altering mRNA splicing and the formation and addition regarding nonsense transcripts (RTEL1 gene rs6010620 on 20q13.33 is a vital candidate genetic variant that has been widely reported (RTEL1 was a direct target of miR-4530. The abnormal expression of RTEL1 could lead to obvious reversion of the miR-4530 overexpression in glioma cell lines. The miR-4530/RTEL1 axis acts as a latent treating target specific to gliomas (RTEL1 has been linked to the development of astrocytoma and Hoyeraal-Hreidarsson syndrome (RTEL1 can maintain genomic stability by studying its ability to maintain telomere homeostasis and promote DNA replication, there are still a lot of questions that shall be highlighted. Nowadays, researches have not confirmed the regulation of RTEL1 and its recruitment to impact the replication forks and telomeres (nscripts , 57. Thereported . As repo gliomas . Not onlStudying the association between the risk of glioma and SNPs is definitive, because it could help clinicians use such polymorphisms as pragmatic molecular biomarkers of glioma risk, assist drug developers innovate relevant targeted therapeutic agents for the benefit of patients, and allow for basic researchers to explore the molecular mechanisms of glioma pathogenesis and accurately regulate glioma progression. According to meta-analysis results, racial differences exist in the risk of glioma, but there is a paucity of studies on Asian ethnicity, which requires researchers to conduct relevant studies. Exploration of SNPs at other loci and risk of glioma is also necessary.5Some limitations should be noted when interpreting the current results. The study also presents some limitations, which shall be noted during the interpretation of current studies.First, there were scarce studies on Asian populations. Studies on results in Asian populations should be interpreted with caution.In addition, the absence of more specific individual information about interaction within genes and that between gene and environment prohibited us from conducting a more precise analysis.Finally, some unavoidable publication bias in the results of meta-analysis should also be taken into account.6TERT gene rs2736100 polymorphism, CCDC26 gene rs4295627 polymorphism, CDKN2A/B gene rs4977756 polymorphism and RTEL1 gene rs6010620 polymorphism might all increase the risk of glioma development, but there are ethnic differences. It is necessary to well develop case-control studies with large sample sizes and a focus on more races or glioma types to overcome the limitations described earlier to make the conclusions more accurate.In summary, our study suggested that the All authors contributed to the article and approved the submitted version. YQW: Writing articles, searching literature and extracting literature. JZho and ZT: Analyzing the quality of articles. JZha: Analyzing Data. XC: Providing methodology. SL: Editing of articles."} +{"text": "Computer-aided detection (CAD) using artificial intelligence (AI) to analyze chest radiographs is an important tool for community tuberculosis (TB) screening in high burden countries. Most current algorithms use a universal cut-off score to select individuals for confirmatory TB testing; however, using a tailored cut-off based on client demographics (age and sex) may improve performance.Community-based TB screening was conducted using portable X-ray with CAD as part of a cluster-randomized trial in Uganda. Individuals scoring above a specified threshold were offered sputum Xpert Ultra testing. This threshold was initially set at 0.5 (range: 0-1) but was later lowered to 0.2 and then 0.1 for research purposes. For clients with scores \u2265 0.1 who did not undergo Xpert testing, we used multiple imputation to infer Xpert-positive status. We assumed that those with X-ray scores < 0.1 would be Xpert-negative if tested, but considered 0.1% or 0.5% prevalence of Xpert-positive TB in sensitivity analysis. We compared the sensitivity and specificity of using a universal screening threshold of 0.5 versus tailored thresholds based on client age and sex.A total of 15,375 individuals were screened using AI-interpreted digital X-ray, of whom 1,748 (11.4%) had valid sputum Ultra results; 157 (9.0%) tested positive. Assuming that people with qXR scores < 0.1 would test negative on sputum Ultra, the manufacturer-recommended universal threshold of \u2265 0.5 had an estimated sensitivity of 75.8% (95%CI: 70.3-81.6) and specificity of 95.3% (95% CI 95.2-95.4). A sex-differentiated threshold had similar specificity but significantly higher sensitivity: 81.3% (95% CI 76.3-86.3). Sex-stratified thresholds also outperformed a universal threshold when assuming higher positivity among people with qXR scores < 0.1. Stratification by age did not significantly improve accuracy.Using differentiated CAD score thresholds based on client sex could improve the accuracy of digital X-ray for TB screening. Future research should validate these findings in other populations and explore the value of incorporating additional client characteristics into TB screening algorithms.All Authors: No reported disclosures"} +{"text": "Correction to: Translational Neurodegeneration (2023) 12:5 10.1186/s40035-023-00337-1Following publication of this article , three eCorrection 1:136. Crocker TF, Brown L, Lam N, Wray F, Knapp P, Forster A. Information provision for stroke survivors and their carers. Cochrane Database Syst Rev. 2021;11:CD001919.Should be corrected as follows:136. Menni C, Valdes AM, Polidori L, Antonelli M, Penamakuri S, Nogal A, et al. Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: a prospective observational study from the ZOE COVID study. Lancet. 2022;399:1618\u201324.Correction 2:Lina and colleagues reported that 51% of patients with VITT present with cerebral venous sinus thrombosis (CVST) (95% CI 36\u201366%) [188].\u201d should be corrected to \u201cPalaiodimou and colleagues reported that 51% of patients with VITT present with cerebral venous sinus thrombosis (CVST) (95% CI 36\u201366%) [188].\u201d\u201c188. Palaiodimou L, Stefanou MI, Katsanos AH, Aguiar De Sousa D, Coutinho JM, Lagiou P, et al. Cerebral venous sinus thrombosis and thrombotic events after vector-based COVID-19 vaccines: a systematic review and meta-analysis. Neurology. 2021;97:e2136\u201347.Correction 3:Shi and colleagues found that APOE \u03b54/\u03b54 genotype induces an increased rate of SARS-CoV-2 infection than the APOE \u03b53/\u03b53 genotype. Moreover, APOE4 astrocytes exhibited a more severe response following SARS-CoV-2 infection. This study provides the first insight into a possible APOE-mediated mechanism of COVID-19 vulnerability and severity [211].\u201d should be corrected to \u201cIn human induced pluripotent stem cell (iPSC)-derived neurons and astrocytes, Wang and colleagues found that APOE \u03b54/\u03b54 genotype induces an increased rate of SARS-CoV-2 infection than the APOE \u03b53/\u03b53 genotype. Moreover, APOE4 astrocytes exhibited a more severe response following SARS-CoV-2 infection. This study provides the first insight into a possible APOE-mediated mechanism of COVID-19 vulnerability and severity [211].\u201d\u201cIn human induced pluripotent stem cell (iPSC)-derived neurons and astrocytes, 211. Wang C, Zhang M, Garcia G Jr, Tian E, Cui Q, Chen X, et al. ApoE-isoformdependent SARS-CoV-2 neurotropism and cellular response. Cell Stem Cell. 2021;28:331\u201342.e5.The original article has been"} +{"text": "This cohort study evaluates the incidence of COVID-19 and hospitalizations across variant eras in 2021 and 2022 among vaccinated solid organ transplant (SOT) recipients. Understanding longitudinal COVID-19 outcomes on a population scale has implications for future counseling and risk prediction; thus, we quantified changes in COVID-19 burden among transplant recipients, hypothesizing reduced disease severity in recent variant eras among SARS-CoV-2 vaccine uptake.Solid organ transplant recipients experienced severe COVID-19 outcomes before vaccination and high breakthrough rates despite primary vaccine series.STROBE reporting guideline and was approved by Johns Hopkins University, with waiver of documentation of informed consent because of no more than minimal risk intervention.Transplant recipients reporting 1 or more SARS-CoV-2 vaccination within a national prospective cohort were surveyed following immunoprophylaxis events to ascertain incident COVID-19 (self-reported positive molecular or antigen test result) and hospitalizations between January 2021 and December 2022, with additional cohortwide surveys in January and June 2022 and unsolicited reporting were compared between post-BA.1 and pre-Delta, Delta, and BA.1 waves using Poisson regression. Two-sided P\u2009<\u2009.05 was significant. Stata/SE, version 17 was used for analysis.Cohort characteristics, COVID-19 incidence rate, and hospitalization ratio were reported by variant era: pre-Delta (January to May 2021), Delta (June to December 2021), and Omicron BA.1 (January to March 2022), BA.2 (April to June 2022), and BA.4-BA.5-BQ.1 (July to December 2022). Monthly transplant recipient COVID-19 incidence rate was plotted against US population case counts.P\u2009<\u2009.001) and similar if less than 2 years vs 2 years or more from transplant and in lung vs nonlung recipients . Transplant recipient COVID-19 incidence paralleled US population case counts responded to 1 or more survey. Vaccinations increased over time . COVID-1e counts , A, peakP\u2009=\u2009.02) and lung transplant . Hospitalization ratios (per 100 incident infections) were 14.1 for pre-Delta; 11.8, Delta; 9.2; BA.1; 2.3, BA.2; and 3.5, BA.4-BA.5-BQ.1 (P\u2009=\u2009.75) and less than 2 years vs 2 years or more from transplant yet higher in lung vs nonlung recipients .There were 37 COVID-19-related hospitalizations among 35 of 464 participants (7.5%). Hospitalized participants more often reported stronger immunosuppression , with a similar ratio of serious COVID-19 disease . Of 16 reported deaths, 5 were COVID-19 related (1 post-BA.1); 6, non-COVID-19 related (3 post-BA.1); and 5, unknown cause (4 post-BA.1).Hospitalization ratio comparing post-BA.1 vs pre-Delta, Delta, and BA.1 was 0.27 (95% CI, 0.11-0.69; In this study, 19.7% of participants reported incident COVID-19, 7.5% of whom required hospitalization. Transplant recipient COVID-19 incidence followed US case count trends, with higher incidence in later Omicron waves potentially due to home test capture and/or increased susceptibility to SARS-CoV-2 variants.4 improved therapeutics,5 home testing access, and/or differing viral pathogenicity.6 Limitations include sampling and recall bias due to observational study design, lack of SARS-CoV-2 sequencing or longitudinal testing frequency, and incomplete death ascertainment.COVID-19-related hospitalization among transplant recipients markedly decreased after the BA.1 wave, likely owing to changing population immunity,"} +{"text": "Time to appropriate antimicrobial therapy is the most important predictor of survival among patients with sepsis due to Gram-negative bacteria (GNB). Infections due to multidrug-resistant (MDR) pathogens often result in inappropriate empiric treatment (tx). The GenMark ePlex identifies organisms and resistance markers within 1.5 hours from blood culture positivity compared to 48-72 hours by conventional methods.We are conducting a single-center study to assess outcomes before and after ePlex implementation. The pre-intervention period included patients with GN bacteremia from January to June 2021. Patients were excluded if they received comfort-only care within 48 hours, had polymicrobial GN bacteremia, or were infected by an organism not on the ePlex panel. Primary outcome is time to in-vitro active therapy from blood culture collection.Table 1). 16% of patients were infected by MDR GNB and 21% received inactive empiric tx. Overall median (IQR) time to in-vitro active tx was 3.9 (1\u201319) hours, but was 39.5 (13.6-71.9) hours among those who received inactive empiric tx. Median (IQR) time to first antibiotic modification was 2.7 (1.0-3.4) days. 38% of patients were transitioned to oral antibiotics at a median (IQR) of 4.2 (3.1-6.1) days. The median (IQR) duration of tx was 15 (10-17) days; 4.5% of patients were treated with \u2264 7 days. Median (IQR) length of hospitalization was 15.5 (7-36) days. 7.8% were re-admitted within 30 days (Table 2). In-hospital and 30-day mortality rates were numerically higher among patients who received inactive empiric therapy when compared to patients who received active empiric therapy .208 patients were identified during the pre-intervention period; 154 met inclusion criteria. Median age was 64 years, 49% were male, and 28% were immunocompromised. Median (IQR) Charlson Comorbidity index and Pitt Bacteremia scores were 6 (4-8) and 2 (1-8), respectively (Results Table 1: Patient demographics, underlying conditions and infection and treatment characteristics in the pre-intervention groupResults Table 2Results Figure 1Our pre-intervention data highlight opportunities to improve the management of GN bacteremia. Implementation of ePlex is likely to decrease the proportion of patients treated with inactive therapy, shorten time to optimal tx and reduce lengths of stay.Ryan K. Shields, PharmD, MS, Allergan: Advisor/Consultant|Cidara: Advisor/Consultant|Entasis: Advisor/Consultant|GSK: Advisor/Consultant|Melinta: Advisor/Consultant|Melinta: Grant/Research Support|Menarini: Advisor/Consultant|Merck: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Roche: Grant/Research Support|Shionogi: Advisor/Consultant|Shionogi: Grant/Research Support|Utility: Advisor/Consultant|Venatorx: Advisor/Consultant|Venatorx: Grant/Research Support"} +{"text": "Arthritis is a leading cause of activity limitations, disability, and chronic pain, and is associated with dispensed opioid prescriptions, substantially contributing to health care costs.During 2019\u20132021, 21.2% of U.S. adults (53.2 million) reported diagnosed arthritis. Approximately one half (52.2%\u201362.4%) of adults aged \u226565 years with self-reported diagnosed dementia, chronic obstructive pulmonary disease, stroke, heart disease, diabetes, or cancer also had a reported diagnosis of arthritis.These prevalence estimates can be used to guide public health policies and activities to increase equitable access to physical activity opportunities within the built environment and other community-based, arthritis-appropriate, evidence-based interventions.Arthritis includes approximately 100 conditions that affect the joints and surrounding tissues. It is a leading cause of activity limitations, disability, and chronic pain, and is associated with dispensed opioid prescriptions, substantially contributing to health care costs. Combined 2019\u20132021 National Health Interview Survey data were analyzed to update national prevalence estimates of self-reported diagnosed arthritis. An estimated 21.2% (18.7% age-standardized) of U.S. adults aged \u226518 years (53.2 million) had diagnosed arthritis during this time frame. Age-standardized arthritis prevalences were higher among women (20.9%) than men (16.3%), among veterans (24.2%) than nonveterans (18.5%), and among non-Hispanic White (20.1%) than among Hispanic or Latino (14.7%) or non-Hispanic Asian adults (10.3%). Adults aged \u226545 years represent 88.3% of all U.S. adults with arthritis. Unadjusted arthritis prevalence was high among adults with chronic obstructive pulmonary disease (COPD) (57.6%), dementia (55.9%), a disability (54.8%), stroke (52.6%), heart disease (51.5%), diabetes (43.1%), or cancer (43.1%). Approximately one half of adults aged \u226565 years with COPD, dementia, stroke, heart disease, diabetes, or cancer also had a diagnosis of arthritis. These prevalence estimates can be used to guide public health policies and activities to increase equitable access to physical activity opportunities within the built environment and other arthritis-appropriate, evidence-based interventions.Arthritis includes approximately 100 conditions that affect the joints and surrounding tissues. If not managed properly, arthritis can result in severe pain, activity limitations, and disability is an annual, nationally representative household survey of the noninstitutionalized U.S. civilian population.NHIS sample sizes and response rates for 2019, 2020, and 2021 were 31,997 (59.1%), 21,153 (48.9%), and 29,482 (50.9%), respectively.Approximately 53.2 million (95% CI = 52.1\u201354.4) or 21.2% (18.7% age-standardized) of U.S. adults aged \u226518 years had diagnosed arthritis . Age-sta2; 56.8%), dementia (56.1%), diabetes (54.0%), or cancer (52.2%) also had diagnosed arthritis were aged \u226565 years, and 40.0% (21.3 million) were aged 45\u201364 years. Age-standardized prevalence of arthritis was higher among adults with dementia (47.8%),rthritis Figure)2; 56.8%)During 2019\u20132021, 53.2 million (21.2%) U.S. adults aged \u226518 years had diagnosed arthritis. Approximately one half of adults aged \u226565 years with a chronic disease also reported diagnosed arthritis. Consistent with previous NHIS"} +{"text": "Andixius Emeljanov & Hayashi, 2007 are described and illustrated from China. These are A.flagellihamus Wang & Chen, sp. nov., A.gracilispinus Wang & Chen, sp. nov., A.productus Wang & Chen, sp. nov. and A.truncatus Wang & Chen, sp. nov. Photographs of the new species and an identification key to all Andixius species are provided.Four new species of the genus Andini consists of 129 species in three genera worldwide and A.venustus . A.longispinus and A.trifurcus, to the genus. Later, A.cultratus and A.lingulatus.The planthopper tribe orldwide . Within A.flagellihamus Wang & Chen, sp. nov., A.gracilispinus Wang & Chen, sp. nov., A.productus Wang & Chen, sp. nov. and A.truncatus Wang & Chen, sp. nov., which are described here. Hence, the number of Andixius species is now 10, with nine species occurring in China.Recent study of some Chinese specimens has found four new species, The morphological terminology follows IEGU).The type specimens are deposited in the Institute of Entomology, Guizhou University, Guiyang, Guizhou Province, China , Japan (Ryukyu Islands).A.cultratus Wang, Zhi & Chen, 2020; China (Guangdong).A.flagellihamus Wang & Chen, sp. nov.; China (Xizang).A.gracilispinus Wang & Chen, sp. nov.; China (Xizang).A.lingulatus Wang, Zhi & Chen, 2020; China (Guangxi).A.longispinus Zhi & Chen, 2018; China (Yunnan).A.nupta Emeljanov & Hayashi, 2007; Japan (Ryukyus).A.productus Wang & Chen, sp. nov.; China (Xizang).A.trifurcus Zhi & Chen, 2018; China (Yunnan).A.truncatus Wang & Chen, sp. nov.; (Guangxi).A.venustus ; China (Taiwan).Taxon classificationAnimaliaHemipteraCixiidae\ufeffWang & Chensp. nov.4A130AF2-7552-5EC5-BFB7-D1E5DCAE7E08https://zoobank.org/5BB7E534-9C4C-4507-8FA5-CA5C1D3D5646Holotype: \u2642, China: Xizang Province, Medog County, Beibeng Town , 15 August 2020, Yongjin Sui leg.; Paratypes: \u2642, same data as holotype.n = 2).Body length: male 6.65\u20137.00 mm Fig. .flagellihamus, referring to the 1-hooked spinose process arising from the apex of the endosoma.The specific name is derived from the Latin adjective This species can be distinguished from the other species of the genus by the following characters: basal right side of periandrium with a U-shaped spinose process; basal ventral margin of periandrium with a long spinose process, apex curved upwards, forming a hooked process; apex of endosoma with a hooked spinose process.Taxon classificationAnimaliaHemipteraCixiidae\ufeffWang & Chensp. nov.BECD8207-9CC0-51A5-91D1-51B9D3F7165Chttps://zoobank.org/4CF579B2-3F5B-4926-99D8-59E7F8E16E85Holotype: \u2642, China: Xizang Province, Bom\u00ea County, Yigong Town, Tongmai Village , 18\u201320 August 2020, Yongjin Sui leg.; Paratypes: \u2642, same data as holotype.n = 2).Body length: male 5.63\u20135.82 mm Fig. .gracilispinus, referring to the one long spinose process arising from the apical right side of the ventral margin of the periandrium.The specific name is derived from the Latin adjective A.gracilispinus sp. nov. are similar to A.venustus Tsaur & Hsu, 1991 in appearance, but differs in: (1) basal left side of ventral margin of periandrium with a triangular laminal process, of which middle right side concaved heavily, forming two large processes (A.venustus with a spinose process in the same position); (2) near apical right side of ventral margin of periandrium with a long spinose process, slightly curved ; (3) basal dorsal margin of periandrium with a grooved laminal process (without process in A.venustus).Male genitalia of Taxon classificationAnimaliaHemipteraCixiidae\ufeffWang & Chensp. nov.F58ABCA6-C31E-5A1D-A365-33C0937A010Chttps://zoobank.org/AE3FAE97-597C-41D8-92B8-7C8A2CCB5464Holotype: \u2642, China: Xizang Province, Medog County, Damu Town, 80K , 18 August 2020, Yongjin Sui leg.; Paratypes: 6\u2642\u2642 2\u2640\u2640, same data as holotype.n = 7), female 7.78\u20137.90 mm (n = 2).Body length: male 5.71\u20136.90 mm Fig. .productus, referring to the one long spinose process arising from the apical ventral margin of the periandrium.The specific name is derived from the Latin adjective A.productus sp. nov. are similar to A.trifurcus Zhi & Chen, 2018, but differs in: (1) periandrium with an expanded laminal process around the left side and dorsal margin of periandrium ; (2) basal ventral margin of periandrium with laminal process, of which ventral margin with two processes (A.trifurcus with three long spinose processes in the same position); (3) right side of ventral margin of periandrium with three spinose processes (right side of middle part of periandrium with a spinose process in A.trifurcus); (4) middle part of periandrium with a thick and long spinose process (without process in A.trifurcus).Male genitalia of Taxon classificationAnimaliaHemipteraCixiidae\ufeffWang & Chensp. nov.6AAFC595-BABB-5FB0-862A-EE78D8C83C99https://zoobank.org/1EE35403-E65B-43C5-B171-54C7CC313B23Holotype: \u2642, China: Guangxi Province, Longsheng County, Huaping National Natural Reserve , 18 July 2020, Xiaoya Wang, Yongjin Sui, Zhicheng Zhou and Jing Wang leg.; Paratypes: 9\u2642\u2642 5\u2640\u2640, same data as holotype.n = 10), female 7.25\u20138.86 mm (n = 5).Body length: male 6.56\u20137.20 mm Fig. .truncatus, referring to the ventral margin of periandrium with a long, broad laminal process having a truncated apex.The specific name is derived from the Latin adjective Andixius species by the following characters: forewing general black-brown, with an irregular yellowish-white spot slightly below stigma and near claval fork; ventral margin of periandrium with a long and broad laminal process, apex truncated, margin with small teeth; endosoma curving ventrally in right angle, base of dorsal margin with a long spinose process.This species can be distinguished from the other Andixius once again emphasizes the need for further study on the group based on male genitalia whenever possible , of which only the latter two genera and 18 species occur in China forming a short common stalk, while ScP, RP and MP emerge independently or very close to the basal cell in the other Andini genera. The outer edge of the apical half of the fore coxae is extended and smoothly protruding in Parandes, but the outer edge of the apical half of the fore coxae is straight and does not extend in Andes.Currently the tribe in China . A compa"} +{"text": "Figure 2 as published. In the legend for Figure 2, \u201c(N) Brown adipose tissue (BAT).\u201d is a duplicate and needs to be deleted because the BAT is explained in the legend for Figure 2I. The corrected legend appears below.In the published article, there was an error in the legend for (A) Body weight (BW). (B) BW gain. (C\u2013E) Organ wet weight. (F) Inguinal white adipose tissue (iWAT). (G) Perirenal white adipose tissue (pWAT). (H) Epididymis white adipose tissue (eWAT). (I) Brown adipose tissue (BAT). (J) iWAT/BW ratio. (K) pWAT/BW ratio; (L) eWAT/BW rati. (M) BAT/BW ratio. (N) Representative rat liver images of hematoxylin and eosin (H and E) and Oil Red O staining per group (X200). (O) Representative iWAT, pWAT, eWAT, BAT. One-way analysis of variance (ANOVA) was conducted for the group comparison. n = 8, data are presented as mean \u00b1 SEM.*p < 0.05, **p < 0.01, ***p < 0.001 vs. MOD group. EPC, P. cocos ethanol extract; CON, normal diet control group; MOD, high-fat diet group; FC, Fenofibrate capsules; EPC-L, low-dose P. cocos ethanol extract; EPC-H, high-dose P. cocos ethanol extract.].\u201cFIGURE 2 | EPC ameliorated MAFLD in rats. Furthermore, there was an error in"} +{"text": "Translational Psychiatry 10.1038/s41398-023-02499-y, published online 09 June 2023Correction to: The reference numbers in the Figs. 2 and 3 were given not correct. The figures have been corrected.Corrected Fig. 2Corrected Fig. 3"} +{"text": "Bacterial nitrogen (N) fixation in alder nodules is a key process providing nitrogen to nutrient-limited arctic biomes. Here, 45 prokaryotic metagenome-assembled genome (MAG) sequences from root nodules of arctic alder are reported. Alnus viridis subsp. fruticosa, an N-fixing deciduous alder shrub that is an important contributor to N cycling in high-latitude ecosystems , which is located 103\u2009km from Nome, Alaska. At this location, alder is found in two distinct communities, short and dispersed alder growing in lowland areas (savanna) and tall alder growing as dense shrublands along the hillslope (shrubland) . Sequence processing and metagenome-assembled genome (MAG) generation were performed via metaWRAP v1.1 of \u22651\u2009kb. Contigs were binned with MaxBin2 v2.2.5 (https://tinyurl.com/4dtt38mt) by minimum information about a metagenome-assembled genome (MIMAG) standards . DNA froRAP v1.1 . DefaultRAP v1.1 , resulti2 v2.2.5 to detertandards . GTDB-Tktandards with thetandards , was use1.1 N50, ,779\u2009bp oPRJNA830531, and nodule metagenomes were deposited under SRA accession no. SRR18933204 for alder savanna and SRR18933205 for alder shrubland. GenBank accession numbers for the MAGs are listed in https://figshare.com/articles/dataset/Quality_metrics_for_metagenome-assembled_genomes_of_Alnus_viridis_spp_Fruticose_nodules/22096520/1.MAGs were deposited in the National Center for Biotechnology Information (NCBI) BioProject database under accession no."} +{"text": "Citrus sinensis leaves and roots were investigated. Our findings indicated that increased pH mitigated Cu toxicity-induced alterations of HRMs, and Cu toxicity increased low-pH-induced alterations of HRMs. Increased pH-mediated decreases in ABA, jasmonates, gibberellins, and cytokinins, increases in (\u00b1)strigol and 1-aminocyclopropanecarboxylic acid, and efficient maintenance of salicylates and auxins homeostasis in 300 \u03bcM Cu-treated roots (RCu300); as well as efficient maintenance of hormone homeostasis in 300 \u03bcM Cu-treated leaves (LCu300) might contribute to improved leaf and root growth. The upregulation of auxins (IAA), cytokinins, gibberellins, ABA, and salicylates in pH 3.0 + 300 \u03bcM Cu-treated leaves (P3CL) vs. pH 3.0 + 0.5 \u03bcM Cu-treated leaves (P3L) and pH 3.0 + 300 \u03bcM Cu-treated roots (P3CR) vs. pH 3.0 + 0.5 \u03bcM Cu-treated roots (P3R) might be an adaptive response to Cu toxicity, so as to cope with the increased need for reactive oxygen species and Cu detoxification in LCu300 and RCu300. Increased accumulation of stress-related hormones (jasmonates and ABA) in P3CL vs. P3L and P3CR vs. P3R might reduce photosynthesis and accumulation of dry matter, and trigger leaf and root senescence, thereby inhibiting their growth.The effects of copper (Cu)\u2013pH interactions on the levels of hormones and related metabolites (HRMs) in Citrus orchards due to long-term and heavy application of Cu-containing fungicides against fruit and foliar diseases and pests [Like other heavy metals, micronutrient copper (Cu) has high phytotoxicity at high concentrations . Currentnd pests ,3. Sincend pests . Root grnd pests ,6,7.3 (GA3), 1-naphthylacetic acid , indole-3-acetic acid (IAA), jasmonic acid (JA), salicylic acid (SA), 6-benzyladenine (BAP), and kinetin can mitigate Cu toxic inhibition on plant growth by reducing Cu uptake, inhibiting Cu translocation from roots to shoots, improving nutrient status, maintaining cellular redox homeostasis and/or preventing oxidative damage [Phytohormones, namely cytokinins (CKs), gibberellins (GAs), auxins (AUXs), abscisic acid (ABA), ethylene (ETH), jasmonates (JAs), salicylates (SAs), and strigolactones (SLs) play a role in plant Cu tolerance . Evidence damage ,15,16,173, and GA4 in maize (Zea mays) root apex, concluding that Cu toxicity-induced alterations of hormonal homeostasis at the root apex contributed to the strong root growth inhibition. Reckova et al. [Citrus grandis leaves, Cu excess led to increased levels of indole-3-lactic acid (ILA), IAA, ABA, L-tryptophan (TRP), cis-zeatin-9-glucoside (cZ9G), and total AUXs; and decreased levels of 5-deoxystrigol (5DS) and N6-benzyladenine-7-glucoside (BAP7G) [Raphanus sativus) hypocotyls [3 in Arabidopsis thaliana roots, and dihydrozeatin riboside (DHZR) and t-ZR in A. thaliana shoots [Populus deltoides), sunflower (Helianthus annuus), and maize leaves and roots [P. deltoids) [Cu toxicity had great impacts on hormone biosynthesis and concentrations in various plant tissues (organs). Matayoshi et al. observeda et al. reported (BAP7G) . Other rpocotyls ; trans-za shoots ; ABA in nd roots ,23,24; aCitrus sinensis roots, concluding that increased pH-induced decrease in total CKs, and increases in IAA, SA, total JAs, JA and methyl jasmonate (MEJA) in Al toxic roots might confer Al-tolerance by reducing Al uptake, increasing the Al-triggered release of malate and citrate and Al sequestration in vacuole, and maintaining the homeostasis of nutrients and the balance between ROS and MG biosynthesis and removal. Thus, hormones might play a role in elevated pH-mediated mitigation of Cu toxicity in plants. Currently, such data are very rare.Evidence shows that high pH can counteract the adverse impacts of Cu toxicity on plants ,25. MostCitrus are mainly planted in acid soils with high Cu bioavailability [C. sinensis leaves and roots. The objectives were (a) to elucidate how Cu\u2013pH interactions affect the abundances of HRMs in leaves and roots, and (b) to test the hypothesis that hormones play a role in elevated pH-mediated amelioration of Cu toxicity.lability . Here, wWe tested 88 HRMs in leaves , 55 of wWe detected higher concentrations of iP7G, tZOG, 2MeScZR, DHZ7G, cZ9G, BAP7G, and total CKs, and lower concentrations of DHZR and IPR in P3CL vs. P3L; higher concentration of IPR in P5CL vs. P5L and P3L vs. P5L; and higher concentrations of iP7G, tZOG, DHZ7G, cZ9G, and total CKs, and lower concentrations of DHZR and IPR in P3CL vs. P5CL. BAP9G was detected only in P3CL and P5CL, and its level was similar between the two. K9G, IP, and cZ were not detected in P5L, P5L, and P3CL, respectively, and their levels were similar among the other three detected treatments .We observed higher concentrations of IAA-Glu, TRP, IAA, IAA-Trp, IAA-Val, MEIAA, ICAld, ILA, IAN, and total AUXs in P3CL vs. P3L; higher concentration of IAA-Trp in P5CL vs. P5L; lower concentration of IAA-Val in P3L vs. P5L; and higher concentrations of IAA-Glu, TRP, IAA-Trp, IAA, IAA-Val, MEIAA, ICAld, ILA, and total AUXs in P3CL vs. P5CL. IAA-Leu and IAGlc were not detected in P3CL and P5CL, respectively, and their concentrations did not significantly differ among the other three detected treatments. TRA and IAM were detected only in P3CL .24, ABA, ABA-GE, total ABAs, SAG, SA, total SAs, ST, and total SLs, and lower concentrations of H2JA, OPDA, and 5DS in P3CL vs. P3L; higher concentration of JA-ILE in P5CL vs. P5L; higher concentrations of H2JA and OPDA in P3L vs. P5L; and higher concentrations of ABA, SAG, total SAs, ST, and total SLs, and lower concentrations of H2JA, JA-Val and 5DS in P3CL vs. P5CL and roots (56) to Cu\u2013pH interactions. PC1 and PC2 accounted for 43.25% and 14.05% for leaves, and 39.35% and 21.62% for roots .We detected 25 upregulated HRMs, upregulated total CKs, total AUXs, total ABAs, total SAs, and total SLs, and seven downregulated HRMs in P3CL vs. P3L; 18 upregulated HRMs, upregulated total CKs, total AUXs, total SAs, and total SLs, and seven downregulated HRMs in P3CL vs. P5CL; six upregulated and one downregulated HRMs in P5CL vs. P5L; five upregulated and one downregulated HRMs in P3L vs. P5L; 28 upregulated HRMs, upregulated total CKs, total AUXs, and total SAs, and six downregulated HRMs in P3CR vs. P3R; 25 upregulated HRMs, upregulated total AUXs, total CKs, total GAs, and total SAs, and three downregulated HRMs in P3CR vs. P5CR; 11 upregulated HRMs, 17 downregulated HRMs, and downregulated total CKs, total JAs and total GAs in P5CR vs. P5R; and seven upregulated HRMs, 17 downregulated HRMs, and downregulated total CKs, total JAs and total GAs in P3R vs. P5R . These rA. thaliana root tips. Exogenous application of 1-NAA mitigated Cu excess-induced reduction in primary root growth, while application of 1-N-naphthylphthalamic acid promoted Cu excess-induced reduction in primary root growth. Choudhary et al. [A. thaliana cotyledons and root apices, and decreased hypocotyl and primary root lengths and cotyledon area, concluding that endogenous hormonal balance and signal transduction played a role in Cu excess-triggered severe morphological responses. Sofo et al. [A. thaliana root and shoot growth, increased IAA concentration in roots, and did not affect IAA concentration in shoots. Wang et al. [A. thaliana seedlings. Wu et al. [C. grandis leaves, concluding that Cu toxicity-induced upregulation of auxin biosynthesis, transport, and levels might contribute to leaf Cu-tolerance by enhancing photosynthesis and water use efficiency (WUE). Ouzounidou and Ilias [Pisum sativum) seedlings Cu toxicity by decreasing Cu concentrations in shoots and roots and providing a thiol redox state to protect the proteins against oxidation. In Brassica juncea, foliar spray of IAA-mediated alleviation of Cu toxicity involved the increase in antioxidant capacity and the decreases in ROS, malondialdehyde (MDA), and electrolyte leakage levels in Cu toxic plants. Additionally, IAA application can improve plant nutrient status; maintain leaf function and photosynthesis; reduce root cell death; and ultimately increase Cu toxic plant biomass [A. thaliana roots, which might contribute to Cu toxicity-induced inhibition of primary root elongation. TRP can act as a precursor for the biosynthesis of IAA and melatonin, which play a role in plant Cu-tolerance [We obtained upregulated total AUXs, TRA, IAM, TRP, IAA-Trp, IAA-Glu, MEIAA, IAA, ICAld, ILA, IAN, and IAA-Val, and downregulated IAA-Leu in P3CL vs. P3L; upregulated total AUXs, MEIAA, ICAld, IPA, TRA, IAA-Glu, IAA-Phe-Me, IAA, OxIAA, ICA, TRP, and IAA-Asp, and downregulated IAA-Val and IAA-Leu in P3CR vs. P3R; upregulated IAA-Trp and downregulated IAGlc in P5CL vs. P5L; and upregulated IAA-Glu, OxIAA, IAA-Asp, and IAA, and downregulated ICA, ICAld, and IAM in P5CR vs. P5R . Auxin hy et al. observedy et al. observedo et al. observedg et al. found thu et al. identifind Ilias found thnd Ilias observed biomass . Yuan et biomass showed tolerance . Collectolerance . The incWe detected upregulated total AUXs, IAGlc, TRA, IAM, TRP, IAA-Glu, MEIAA, ILA, IAA, IAA-Trp, ICAld, and IAA-Val, and downregulated IAA-Leu in P3CL vs. P5CL; upregulated total AUXs, IAA, ICA, TRA, MEIAA, ICAld, IPA, IAA-Phe-Me, and TRP in P3CR vs. P5CR; downregulated IAA-Val in P3L vs. P5L; and upregulated IAA-Leu and IAA-Val, and downregulated IAN, ICA, and IAM in P3R vs. P5R , suggestNicotiana tabacum) plants had decreased shoot (leaf) growth, but enhanced root growth, concluding that CKs played an opposite role in regulating shoot and root growth. Foliar application of two CKs (kinetin and BAP) conferred castor (Ricinus communis) Cu-tolerance by reducing Cu level in shoots and improving antioxidant ability [A. thaliana roots might contribute to Cu toxicity-induced inhibition of root growth [A. thaliana seedlings. Massot et al. [Phaseolus vulgaris) prior to Al-induced inhibition of root growth. Al-induced rapid increment of CKs might contribute to root growth inhibition either directly or indirectly by influencing hormone homeostasis. Plant metallothioneins (MTs) have been shown to play a role in Cu-tolerance by lowering Cu toxicity-induced oxidative damage and binding Cu [C. sinensis seedlings, Al toxicity led to increased and decreased total CKs concentrations in pH 3.0- and pH 4.0-treated roots, respectively. Increased pH lowered the accumulation of CKs in roots, thereby ameliorating Al toxicity-induced inhibition of root growth [As shown in ability . Observat growth . Sofo ett growth reportedt et al. observednding Cu . Thomas nding Cu suggestending Cu . The elending Cu ,26. In Ct growth . Taken tC. sinensis roots [Atractylodes lancea roots was greater at pH 5.3 than at pH 6.0 [We detected upregulated total CKs, DHZ7G, iP7G, cZ9G, and tZOG, and downregulated DHZR, IPR, and cZ in P3CL vs. P5CL; upregulated total CKs, pT, K9G, 2MeSiP, BAP9G, cZ, IP, 2MeSiPR, tZOG, tZ, and cZROG, and downregulated tZR in P3CR vs. P5CR; upregulated K9G, IP, and IPR in P3L vs. P5L; and upregulated 2MeSiP, tZ and pT, and downregulated total CKs, tZR, BAPR, tZOG, IPR, BAP, and BAP7G in P3R vs. P5R . This agis roots , and that pH 6.0 . These fPhaseolus coccineus and Allium cepa root growth, and maize leaf growth, and that JA synthesis inhibitors-namely ibuprofen (IB) and salicylhydroxamic acid (SHAM), mitigated Cu toxicity-induced growth inhibition in P. coccineus roots and maize leaves, but not in A. cepa roots. Using metabolome and transcriptome analyses, Hu et al. [Cucumis melo) via repressing JA biosynthesis. Taken together, increased pH prevented Cu toxicity-induced changes in JAs in leaves, thus alleviating leaf Cu toxicity; while Cu toxicity lowered the levels of JAs in pH 4.8-treated roots, thus improving root growth.As shown in u et al. demonstrWe detected downregulated H2JA and JA-Val in P3CL vs. P5CL; upregulated JA-ILE in P3CR vs. P5CR; upregulated H2JA and OPDA in P3L vs. P5L; and downregulated total JAs, JA-ILE, OPC-4, JA-Val, JA, and OPDA in P3R vs. P5R , suggestC. grandis leaves [Populus x euramericana), B229 and PE19/66. Cu toxicity increased ABA concentrations in PE19/66 leaves and roots, and in B229 leaves, but had no significant impacts on ABA concentrations in M1 leaves and roots, and in B229 roots. Obviously, Cu toxicity impacts on ABA concentrations depended on Cu concentration, pH, tissue (organ), and genotype.As shown in s leaves , and mais leaves . Cu exces leaves . Kebert s leaves investigo/ABS) in P3CL vs. P3L, but not in P5CL vs. P5L [Penicillium funiculosum LHL06 mitigated the synergistic toxicity of heavy metals on soybean (Glycine max) by reducing uptake of heavy metals, accumulation of ABA and JA, and oxidative damage due to decreased H2O2 accumulation and enhanced antioxidant system in roots. Zehra et al. [2O2 production rates in pH 3.0-treated leaves and roots, but not in pH 4.8-treated leaves and roots [ABA can increase non-photochemical quenching (NPQ), the first line of defense to protect photosystem II (PSII) reaction centers against photo-oxidative damage . The upr vs. P5L . The inc vs. P5L . Bilal e vs. P5L indicatea et al. reporteda et al. . A studynd roots . Taken tVicia faba). The critical pH, below which net H+ exudation and root growth ceased, were 3.5 for maize and 4.00 for broad bean at 1 mM Ca2+. With the decrease in pH of the medium, both H+ exudation and root growth decreased gradually. Additional ABA in root medium led to increased H+ exudation and root growth for maize at pH 4.0, but decreased H+ exudation and root growth for broad bean at pH 4.1. Yang et al. [C. sinensis roots decreased with the decrease in pH. Taken together, low pH increased ABA concentration and decreased H+ exudation in RCu300, thus reducing root growth, but not in RCK. This agreed with the report that low pH affected root growth more at 300 \u03bcM Cu than at 0.5 \u03bcM Cu [We detected upregulated ABA in P3CL vs. P5CL; upregulated ABA in P3CR vs. P5CR; and downregulated ABA in P3R vs. P5R . The uprg et al. observedSalvia officinalis [Oryza sativa) [Gossypium spp.) [As shown in icinalis , bean [4icinalis , rice (O sativa) , sunflow sativa) , and cotum spp.) by reducum spp.) ,50.We detected upregulated SAG and total SAs in P3CL vs. P5CL and P3CR vs. P5CR, and downregulated SA in P3R vs. P5R , suggest24 in P3CL vs. P3L, upregulated GA9 and GA24 in P3CR vs. P3R, and downregulated GA1 and total GAs in P5CR vs. P5R. Saleem et al. [3 mitigated Corchorus capsularis Cu toxicity by enhancing growth and photosynthesis, and reducing oxidative damage. Additionally, GA3 increased Cu accumulation in roots, stems, and leaves. Similar results have been obtained for pea [4 is biosynthesized from GA24 via GA9 [24 in P3CL vs. P3L and GA24 and GA9 in P3CR vs. P3R might be an adaptive strategy to Cu toxicity, while the downregulation of GA1 and total GAs in P5CR vs. P5R and unaltered GAs in P5CL vs. P5L agreed with the finding that raised pH lessened Cu accumulation in Cu toxic roots, stems, and leaves [As shown in m et al. observed for pea and sunf for pea . Bioacti via GA9 . Thus, t7, GA1, GA24, GA9, and total GAs in P3CR vs. P5CR, and upregulated GA7 and downregulated GA1 and total GAs in P3R vs. P5R. The upregulation of GA7, GA1, GA24, GA9, and total GAs in P3CR vs. P5CR might be an adaptive response to low pH, while the downregulation of GA1 and total GAs in P3R vs. P5R agreed with the report that low pH increased Cu concentrations in roots, stems and leaves less under 0.5 \u03bcM Cu than under 300 \u03bcM Cu [As shown in Brassica juncea) was reduced by ethephon (ethylene source) and sulfur, which resulted in reduced oxidative damage, upregulated antioxidant system, and elevated photosynthesis. Both ethephon- and sulfur-treated plants displayed more tolerance to Cd. S-mediated alleviation can be reversed by aminoethoxyvinylglycine (ethylene biosynthesis inhibitor). Thao et al. [We obtained upregulated ACC in P5CR vs. P5R . Flora eo et al. suggesteWe identified downregulated ACC in P3CR vs. P5CR, and upregulated ACC in P3R vs. P5R , suggestHordeum vulgare) Cd-tolerance by reducing Cd uptake and oxidative damage due to reduced H2O2 accumulation and elevated concentrations of ascorbate and reduced glutathione and activities of antioxidant enzymes in leaves and roots. Mostofa et al. [d10 and d17 displayed less tolerance to arsenic stress accompanied by increased arsenic concentration, decreased sequestration of arsenic in vacuole, and enhanced oxidative damage in roots. The upregulation of ST in P5CR vs. P5R and the downregulation of ST in P3CR vs. P5CR agreed with the findings that increased pH-mediated amelioration of Cu toxicity involved reduced Cu uptake and oxidative damage in roots, and that low pH caused oxidative damage and a greater increase in Cu uptake in RCu300, but not in RCK [We detected upregulated ST in P5CR vs. P5R and downregulated ST in P3CR vs. P5CR . Qiu et a et al. indicatet in RCK . HoweverCitrus sinensis (L.) Osbeck cv. Xuegan) seedlings were transplanted to 6 L pots (two seedlings per pot) containing sand, and then cultivated in a greenhouse under the natural conditions at Fujian Agriculture and Forestry University, Fuzhou with an annual average relative humidity, temperature, and sunlight of ~ 76%, 20 \u00b0C and 1600 h, respectively [2 \u00d7 pH 3.0 or 4.8 (adjusted by 1M HCl) until dripping (~500 mL per pot). Cu concentrations and pH levels of solutions were chosen based on our previous reports [2, and then stored in a \u221280 \u00b0C freezer until extraction of HRMs.Plant material culture and treatments referred to Zhang et al. . Six weeectively . After s reports . Each trhttps://www.metware.cn/, accessed on 1 June 2022) for assay of hormones. After frozen samples were ground into powder in liquid N2, 50 mg of the powder was transferred to 2 mL tube containing 1 mL of methanol:water:formic acid and ten \u03bcL of internal standard mixed solution (100 ng mL\u22121). After 10 min of vortex, the mixture was centrifuged at 16,000\u00d7 g for 5 min at 4 \u00b0C. The yielding supernatant was evaporated to dryness in N2 flow, dissolved in 100 \u03bcL of 80% methanol (v/v), and then filtered through a 0.22 \u03bcm filter. The filtrate was used for HRMs assay.Equal amounts of frozen leaves (roots) from five seedlings from different pots were mixed as one biological replicate. There were three biological replicates per treatment. Samples were sent to Wuhan MetWare Biotechnology Co., Ltd. [The concentrations of HRMs in the filtrate were determined using an ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) system .p < 0.05 using DPS 7.05 . PCA was made with SPSS statistical software .Data were analyzed by two-way ANOVA (two (Cu levels) \u00d7 two (pH levels)), followed by the least significant difference (LSD) at Citrus Cu toxicity, the mechanisms by which different hormones alleviate Cu toxicity are unclear and require further research.Our results showed that elevated pH prevented the alterations of HRMs levels caused by Cu toxicity, while Cu toxicity aggravated the changes in HRMs levels caused by low pH. A model for the role of hormones in elevated pH-mediated mitigation of Cu toxicity in leaves and roots was proposed . Elevate"} +{"text": "Infection caused by Streptococcus pneumoniae, mainly invasive pneumococcal disease (IPD) and pneumococcal pneumonia (PP), are a major public health problem worldwide. This study investigated population-based incidence and risk of PP among Catalonian persons\u2009\u2265\u200950 years-old with and without specific underlying conditions/comorbidities, examining the influence of single and multi-comorbidities in the risk of suffering PP.Population-based cohort study involving 2,059,645 persons\u2009\u2265\u200950 years-old in Catalonia, Spain, who were retrospectively followed between 01/01/2017-31/12/2018. The Catalonian information system for development of research in primary care (SIDIAP) was used to establish baseline characteristics of the cohort (comorbidities/underlying conditions), and PP cases were collected from discharge codes (ICD-10: J13) of the 68 referral Catalonian hospitals.Global incidence rate (IR) was 90.7 PP cases per 100,000 person-years, with a 7.6% (272/3592) case-fatality rate (CFR). Maximum IRs emerged among persons with history of previous IPD or all-cause pneumonia, followed by haematological neoplasia (475.0), HIV-infection (423.7), renal disease (384.9), chronic respiratory disease (314.7), liver disease (232.5), heart disease (221.4), alcoholism (204.8), solid cancer (186.2) and diabetes (159.6). IRs were 42.1, 89.9, 201.1, 350.9, 594.3 and 761.2 in persons with 0, 1, 2, 3, 4 and \u2265\u20095 comorbidities, respectively. In multivariable analyses, HIV-infection , prior all-cause pneumonia , haematological neoplasia , chronic respiratory disease and prior IPD were major predictors for PP.Apart of increasing age and immunocompromising conditions , history of prior IPD/pneumonia, presence of chronic pulmonary/respiratory disease and/or co-existing multi-comorbidity are major risk factors for PP in adults, with an excess risk near to immunocompromised subjects. Redefining risk categories for PP, including all the above-mentioned conditions into the high-risk category, could be necessary to improve prevention strategies in middle-aged and older adults. Young children, individuals with at-risk or immunocompromising conditions and elderly people support the greatest burden of pneumococcal disease, with higher incidence and mortality in these persons registered in the electronic primary care medical records of each cohort member at baseline:Chronic pulmonary/respiratory disease: it included chronic bronchitis/emphysema (J41-J44), asthma (J45-J46) and/or other chronic pulmonary diseases .Chronic heart disease: it included congestive heart failure (I50), coronary artery disease and/or other chronic heart diseases .Diabetes mellitus (E10-E14).Chronic liver disease: it included chronic viral hepatitis (B18), cirrhosis (K74) and/or alcoholic hepatitis (K70)).Alcoholism .Smoking (F17).Anatomic or functional asplenia .Primary immunodeficiency (D80-D84).HIV infection (B20-B24).Chronic renal disease: it included nephrotic syndrome and severe chronic renal failure (N18-N19 with glomerular filtration rate\u2009\u2264\u200930 ml/min).Cancer: it included solid organ or haematological neoplasia (C00 to C97) diagnosed within previous 5 years.Immunosuppressive therapy: it included long-term immunosuppressive medication and/or radiotherapy in the previous 12 months (coded according to specific SIDIAP codes)."} +{"text": "Outpatient parenteral antimicrobial therapy (OPAT) is administering intravenous antibiotics in the outpatient setting. Herein we wish to understand the Atlanta VAMC (AVAMC) home OPAT population, infection details, and risk factors for hospital readmission, adverse drug events (ADEs), and clinical failure.Medical records of AVAMC veterans receiving home OPAT January 1, 2019 and June 30, 2022 were reviewed. Data collected included: demographic and co-morbidity data, OPAT indication/infection type, microbiological information, presence of surgical debridement, and antimicrobial selection and duration of therapy.Clostridioides difficile infection. Other information include modification of OPAT plan (drug or duration), patient follow-up visit occurrence, re-hospitalization, and clinical resolution of infection. Univariate regression analyses were conducted on a subset of patients with musculoskeletal (MSK) infections .Outcomes included ADEs such as venous access events, laboratory abnormalities, and S. aureas was the predominant bacteria isolated (20%). See included table for full details.A total of 149 veterans were reviewed, with median age 66 years, 92% male, and 44% white race. Median CCI score was 5, and 80/149 (54%) patients had diabetes. The majority of infections were bone infections (30%), followed by diabetic foot osteomyelitis (24%). Methicillin-sensitive In the full cohort, 100/149(68%) had clinical resolution at 6 months and 20/149 (13%) had ADE during therapy. Rehospitalization occurred in 29 (20%) pts. Diabetes was associated with increased risk of failure -- Risk Ratio (RR) 1.68 (95% CI 1.01-2.77). Patients with clinic follow-up had a RR of 0.39 (95% CI: 0.21-0.73) for rehospitalization versus pts without follow-up.For pts with diabetes in the MSK group (N=97), risk of failure was 1.50x higher than those without diabetes (95% CI: 0.67-3.34).The RR for rehospitalization was 0.23 (95% CI: 0.06-0.82) for patients who received follow-up compared to patients who did not receive follow-up.AVAMC OPAT population demographic data, N = 149The AVAMC OPAT cohort is an older group with largely MSK-related infections and MSSA. Few ADEs occurred, and clinical failure remained high.All Authors: No reported disclosures"} +{"text": "GRT-R910 , a self-amplifying mRNA (samRNA) vaccine expressing the spike protein plus T-cell epitopes of SARS-CoV-2 (D614G variant), was tested in a phase 1 study as a booster in healthy adults.This phase 1 open-label, dose escalation study enrolled healthy adults who previously received an approved mRNA COVID-19 vaccine series. Groups of 10 adults aged 18-60 years were boosted with GRT-R910 at 3 or 6 mcg. Adults > 60 years were boosted with GRT-R910 at 3, 6, or 10 mcg. All participants > 60 years in the 6 and 10 mcg dose groups received prior mRNA COVID-19 boosters; none in other groups had prior boosts. Study boosts occurred at least 112 days after completion of primary series/boost of authorized mRNA COVID-19 vaccine or prior SARS-CoV-2 infection. Solicited local and systemic reactogenicity events were collected for 7 days, unsolicited adverse events for 28 days, and serious adverse events (SAEs) for 366 days post-vaccination. Humoral are being assessed at multiple time points over 1 year after study vaccination. Participants who self-reported SARS-CohV-2 infection or receipt of non-study COVID-19 booster during the study were censored in the immunogenicity analyses.No severe local reactogenicity events were observed. Overall, out of 48 enrolled across all groups, 8 reported at least 1 severe systemic reactogenicity event (figure 1). Most severe systemic reactogenicity events were transient, with most graded severe for 1 day or less. No SAEs have been reported. Neutralizing antibody responses remain durable up to 1 year after 3 and 6 mcg boosts in adults 18-60 years (figure 2) and up to 6 months after 3, 6, and 10 mcg boosts in adults > 60 years .GMT= geometric mean titer; Boxes and horizontal bars denote interquartile range (IQR) and median AUC, respectively. Whisker endpoints are equal to the maximum and minimum values below or above the median +/- 1.5 x IQR. All participants in the 3 \u03bcg GRT-R910, 18-60 yo and 6 \u03bcg GRT-R910, 18-60 yo groups received a mRNA two dose primary COVID-19 vaccination series prior to enrollment. None were previously SARS-CoV-2 infected.GMT= geometric mean titer; Boxes and horizontal bars denote interquartile range (IQR) and median AUC, respectively. Whisker endpoints are equal to the maximum and minimum values below or above the median +/- 1.5 x IQR. All participants in the 3 \u03bcg GRT-R910, > 60 yo group received a mRNA two dose primary COVID-19 vaccination series prior to enrollment. All participants in the 6 \u03bcg GRT-R910, > 60 yo and 10 \u03bcg GRT-R910, > 60 yo groups received a mRNA two dose primary COVID-19 vaccination series plus a mRNA booster vaccine prior to enrollment. Two participants each in the 6 \u03bcg GRT-R910, > 60 yo and 10 \u03bcg GRT-R910, > 60 yo groups had a previous COVID-19 infection at enrollment (green dots). D1, D15, D29 testing for Groups 9 and 10 are planned against BA.4/5.While transient systemic reactogenicity with GRT-R910 as a booster was observed, no safety signals were identified. Preliminary immunogenicity data demonstrate durable neutralizing antibody responses for 6-12 months in both younger and older age groups. Forthcoming T cell response data will aid in assessing the immunogenicity of this novel vaccine.Nadine Rouphael, MD, Icon, EMMES, Sanofi, Seqirus, Moderna: Advisor/Consultant Anna Wald, MD, MPH, Aicuris: Advisor/Consultant|Bayer: Advisor/Consultant|Curevo: Participation on Data Safety Monitoring Board|GSK: Grant/Research Support|Sanofi: Grant/Research Support|UpToDate: Royalties or licenses Pedro Garbes, MD, Gritstone bio, Inc.: Employee|Gritstone bio, Inc.: Employee|Gritstone bio, Inc.: Stocks/Bonds|Gritstone bio, Inc.: Stocks/Bonds Karin Jooss, PhD, Gritstone bio: employee|Gritstone bio: Stocks/Bonds Andrew Allen, MD, PhD, Gritstone bio: Board Member|Gritstone bio: Ownership Interest|Gritstone bio: Stocks/Bonds Amanda Eaton, MBA, Moderna: Grant/Research Support David M. Koelle, MD, Curevo Vaccines: Board Member|MaxHealth LLC: Board Member|Sanofi Pasteur: Grant/Research Support Daniel F. Hoft, MD, PhD, Moderna: Advisor/Consultant|Poolbeg: Advisor/Consultant"} +{"text": "Coccidioidomycosis is an endemic mycosis in the southwestern United States. While most infections are mild or asymptomatic, severe cases are associated with high morbidity and mortality. We aimed to evaluate the clinical outcomes of patients admitted to the intensive care unit (ICU) with proven culture-positive coccidioidomycosis.Coccidioides spp. culture within a multi-healthcare system between 10/01/2017 \u2013 07/01/2022. Clinical information was collected by chart review.After institutional review board approval, we retrospectively included ICU patients with positive Coccidioides spp. culture, 145 patients required ICU stay. The median age was 51 (32-62), with 100 (68.9%) male, 56 (38.6%) White non-Hispanics, and 25 (17.2%) Blacks. Fifty-seven (39.3%) received azole antifungals before hospitalization. Seventy-two (49.7%) had another fungal, bacterial, or viral infection during their hospitalization, and 41 (28.3%) had extrapulmonary coccidioidomycosis. The majority, 131 (90.3%), received antifungal therapy during their hospital stay. The median hospital length of stay was 18 days (10-37). Almost half (48.3%) died during the study period, with liver cirrhosis and age ( >60 years) resulting in statistically significant mortality, 12/13 (92.3%), p-value < 0.001, and 31/43 (72.1%) p-value =0.001, respectively. Mechanical ventilation and/or intravenous vasopressor support was associated with a high risk of mortality 66/113 . Failure to receive antifungal therapy before ICU admission was associated with increased mortality, 46/70 .Of the 392 hospital encounters with positive Patients with coccidioidomycosis admitted to the ICU face an increased risk of mortality. Risk factors associated with ICU mortality include advanced age, cirrhosis, and delay in the administration of antifungal therapy. Future studies are needed to evaluate these risks further.Tirdad Zangeneh, DO, AiCuris: Grant/Research Support Mohanad Al-Obaidi, MD, MPH, La Jolla Pharmaceuticals: Honoraria"} +{"text": "Immunotherapeutic targets in multiple myeloma (MM) have variable expression height and are partly expressed in subfractions of patients only. With increasing numbers of available compounds, strategies for appropriate choice of targets (combinations) are warranted. Simultaneously, risk assessment is advisable as patient\u2019s life expectancy varies between months and decades.We first assess feasibility of RNA-sequencing in a multicenter trial . Next, we use a clinical routine cohort of untreated symptomatic myeloma patients undergoing autologous stem cell transplantation 64 months) to perform RNA-sequencing, gene expression profiling (GEP), and iFISH by ten-probe panel on CD138-purified malignant plasma cells. We subsequently compare target expression to plasma cell precursors, MGUS (n=59), asymptomatic (n=142) and relapsed (n=69) myeloma patients, myeloma cell lines (n=26), and between longitudinal samples (MM vs. relapsed MM). Data are validated using the independent MMRF CoMMpass-cohort .de novo (LfM-HRS) defined risk scores. LfM-HRS delineates three groups of 40%, 38%, and 22% of patients with 5-year and 12-year survival rates of 84% (49%), 67% (18%), and 32% (0%). R-ISS and RNA-sequencing identify partially overlapping patient populations, with R-ISS missing, e.g., 30% (22/72) of highly proliferative myeloma.RNA-sequencing is feasible in 90.8% of patients (GMMG-MM5). Actionable immune-oncological targets (n=19) can be divided in those expressed in all normal and >99% of MM-patients , those with expression loss in subfractions of MM-patients , aberrantly expressed in MM , and resistance-conveying target-mutations e.g., against part but not all BCMA-directed treatments. Risk is assessable regarding proliferation, translated GEP- and RNA-sequencing based assessment of risk and targets for first choice treatment is possible in clinical routine. Clinical signs and symptoms relate to displacement of normal hematopoiesis, generation of osteolytic bone disease, and renal impairment . TreatmeMM is treated by combination treatment whenever possible , 13: effThe situation is different for immune-oncological therapies in development or recently approved. Bispecific antibodies or CAR-T cells against e.g., BCMA, GPRC5D, or FCR5H show single agent remission rates of 60-80% , 30\u201338. Presence or absence and height of target expression is an evident selection criterion for treatment choice, as shown, e.g., for CD38 and GPRCin situ hybridization [iFISH]) incorporating clinical factors and molecular alterations in malignant plasma cells , t assessed by interphase fluorescence [iFISH]) . Innovat[iFISH]) or \u201cscor[iFISH]) \u201352.de novo risk score by RNA-sequencing (termed LfM-HRS). Findings are validated in the independent MMRF CoMMpass-cohort (n=767 patients).In this manuscript, we first assess applicability of RNA-sequencing in the GMMG-MM5 multicenter phase III clinical trial setting (604 patients) based on our low-input RNA-sequencing protocol . Secondl22.16 cells (Patients (n=604) were included in the prospective GMMG MM5-trial , 54 betw6 cells .iFISH using cytospins from CD138-purified plasma cells was performed centrally . Data could be obtained for 556/573 patients with available bone marrow aspirates (97%) and 556/559 patients with available CD138-purified plasma cells, respectively (99.5%). The median proportion of malignant plasma cells determined per iFISH, i.e., the highest percentage of a chromosomal aberration, was 95% .Samples for RNA-extraction followed by quality control were collected over two weeks and subjected to GEP by DNA-microarrays. In total, n=458 transcriptome datasets are available, i.e., 81.9% of patients with available CD138-purified plasma cells. Of these, two patients were excluded from further analysis for not fulfilling the trial\u2019s inclusion criteria. Gene expression profiling could not be performed in 53 cases due to low RNA quality (9.5%) and further 48 cases (8.6%) in which not enough RNA was available .Using our standardized RNA-sequencing protocol , asymptomatic , symptomatic, therapy-requiring myeloma , relapsed myeloma , as well as healthy donors (n=10) as comparators were included in the study approved by the ethics committee after written informed consent. For patient characteristics, see + memory B-cells (n=4) were FACS-sorted and polyclonal plasmablasts (n=4) were in vitro differentiated as described and myeloma cells were purified using anti-CD138 microbeads . Peripheral blood CD27escribed . A totalRNA-sequencing data of 52/142/535/69 patients with MGUS/AMM/MM/MMR and 26 HMCLs were used. GEP-data of 534 patients with MM were used for score definition and validation .2.3Independent validation of risk assessment and target identification was performed using the Multiple Myeloma Research Foundation (MMRF) CoMMpass trial (NCT01454297), i.e., n=767 previously untreated myeloma patients with RNA-sequencing data available (release 13).2.42.4.1RNA was extracted using the Qiagen AllPrep DNA/RNA kit according to the manufacturer\u2019s instructions. Quality control and quantification was performed using an Agilent 2100 bioanalyzer .2.4.2RNA-sequencing was performed as published . In brie2.4.3Gene expression profiling (GEP) using U133 2.0 plus arrays was performed as published , 56\u201359. 2.5iFISH analysis was conducted on CD138-purified plasma cells using probes for chromosomes 1q21, 5p15, 5q31 or 5q35, 8p21, 9q34, 11q22.3 or 11q23, 13q14.3, 15q22, 17p13, 19q13, IgH-breakapart, as well as translocations t, t, and t according to the manufacturer\u2019s instructions and data were analyzed as published .2.6https://www.r-project.org/) and Bioconductor (https://www.bioconductor.org/) versions 3.3.2 and 3.4 (score implementation) and versions 3.4.4 and 3.6 .GEP and RNA-seq analysis were performed as previously described , 51, 58 Overall (OS) and event-free (EFS) survival were investigated for symptomatic multiple myeloma undergoing high-dose therapy using Cox\u2019s proportional hazard model as published .Survival curves were computed with nonparametric survival estimates for censored data using the Kaplan-Meier method . DiffereEffects were considered statistically significant if the P-value of corresponding statistical tests was below 5%. For comparisons of parameters , or ADC, antibody-radio-conjugates, bispecific antibodies, or CART-products in trials .Based on the expression pattern, we divided targets in those expressed in normal and almost all (>99%) malignant plasma cell samples , those constitutively expressed in all normal plasma cells with expression loss in a subfraction of malignant plasma cells , and targets aberrantly expressed in malignant plasma cells, i.e., not expressed in normal bone marrow plasma cells . CD70 is expressed in half of BMPC decreasing to 24.5% in MM. Of assessed targets, CD1B is not expressed, CD25 at very low frequency and expression height only (2.9%). Results for expressed targets are summarized in RNA-sequencing allows detection of somatic variants and mutated transcripts; e.g., for BCMA, we found in 25% of patients coding non-synonymous single nucleotide variants present with a median allele frequency of 1 in patients harboring the aberration. If present, a resistance conveying mutation would thus have been detected but expectedly could not, as none of the patients has been treated with BCMA-targeting agents prior to analysis.Targets expressed in all myeloma patients show high inter-patient variation, e.g., 6.8 (CD38), 6.9 (BCMA), 9.9 (GPRC5D), and 10.9 (FCRH5) log-fold variation . Of targets aberrantly expressed in malignant plasma cells, i.e., not expressed in BMPC , NY-ESO1 shows significantly higher expression from MGUS to MMR. Regarding a potential use of immune-oncological agents in early-stage myeloma, we assessed differences between AMM to MM to MMR, (instead of MGUS-AMM-MM-MMR) yielding similar results , BCMA, GPRC5D, FCRH5, TACI, CD74, CD44, CD37 and CD79B, seven show significant lower expression from MGUS to MMR , i.e., SLAMF7 (CS1), BCMA, GPRC5D, FCRH5, TACI, CD74, and CD37. If adjusted for multiple testing by Benjamini-Hochberg correction, significance is maintained for BCMA, FCRH5, TACI, CD74, and CD37. Targets with expression loss in a subfraction of malignant plasma cells of previously untreated patients are all significantly lower expressed from MGUS to MMR , a change in expression of any of the investigated antigens could be found in 56 patients (88.9%) with both losses and gains occurring ; median OS was 35 vs. 86 vs. 130 months , we \u201ctranslated\u201d these. The RS-, UAMS70- and SKY92-score delineated a population of 10%, 19%, and 13% of high risk and 67% of medium risk (Rs-score) patients. High- (medium) risk patients showed significantly inferior EFS and OS, i.e. the RS-score - RSGEP and RNA-sequencing based scores showed a concordance of 71.7% - 92.5% regarding patients identified as high risk (3.4de novo generated a RNA-sequencing based proliferation index (RPI). In comparison to normal bone marrow plasma cells or non-proliferating memory B-cells, malignant plasma cells showed a significant and stage-dependent increase from early disease MGUS vs. asymptomatic vs. symptomatic, therapy-requiring multiple myeloma , to 2nd (61%), 3rd 38%, 4th(15%) and 5th line (1%). Furthermore, use of \u03b3-secretase inhibitors . This first relates evidently to targets not expressed in all myeloma patients, as being either lost in a subfraction of malignant plasma cells, i.e., BAFF-R, CD19, CD20, and CD22, or gained, i.e., NY-ESO1/2, MUC1, and CD30. Secondly, it relates to high inter-patient variation of target expression. Considering targets expressed in all myeloma patients, 10.9 log-fold (FCRH5) differences were found. With reported relation of expression height and response for CD38 and GPRCacestat) in case acestat) . It exemdifferent BCMA-targeting agents. As downregulations and mutations discussed here occur primarily under selection pressure of the respective treatment and, in part, different aberrations occur in a subclonal manner . Genes with stage-dependent loss of expression, like CD19, CD22, and BAFF-R, showed high dynamics with both gains and losses of expression occurring. The cancer testis antigens MUC1 and NY-ESO1/2 were predominantly gained in MMR. These findings are in line with a subclonal architecture in myeloma leading to clonal tides and spat4.3Introduced in myeloma research in 2002 and 2011\u00ae, Signal Genetics\u2122 , suggestart.org) or the Mart.org) . But thea priori evident.Immediate usefulness would be perceived if either response could be predicted, or targets selected in for personalized treatment. Despite factors associated with response have been identified , 25, it GEP/NGS-based approaches would be significantly fostered by the use of appropriated clinical trial designs, especially for regulatory and approval purposes , 95 espe5RNA-sequencing is applicable in 90% of patients (comparable to iFISH), is of overall equal predictive power as the current gold standard R-ISS, but identifies a further fraction of myeloma patients, e.g., with highly proliferative myeloma cells. It allows personalized target identification for immune-oncological drugs based on presence and height of expression. RNA-sequencing used for \u201ceducated first guess\u201d could be considered as \u201cIOnc drug and risk advisor\u201d in analogy to other decision tools.https://www.ebi.ac.uk/arrayexpress/, E-MTAB-4715; https://www.ebi.ac.uk/arrayexpress/, E-MTAB-4717; https://www.ebi.ac.uk/arrayexpress/, E-MTAB-5212; https://www.ebi.ac.uk/arrayexpress/, E-TABM-937; https://www.ebi.ac.uk/arrayexpress/, E-TABM-1088; https://www.ebi.ac.uk/ena, PRJEB37100; https://www.ebi.ac.uk/ena, PRJEB36223.The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: Patients were included in the study approved by the ethics committee of the medical faculty of the Ruprecht Karls University Heidelberg, Germany, after written informed consent. The studies were conducted in accordance with the local legislation and institutional requirements. The participants provided their written informed consent to participate in this study.ME-R: Conceptualization, Formal Analysis, Investigation, Methodology, Validation, Writing \u2013 review & editing. SB: Formal Analysis, Writing \u2013 review & editing. VB: Writing \u2013 review & editing, Investigation, Methodology. HS: Investigation, Writing \u2013 review & editing. UB: Investigation, Writing \u2013 review & editing. CS: Investigation, Writing \u2013 review & editing. MH: Investigation, Writing \u2013 review & editing. KW: Investigation, Writing \u2013 review & editing. TH: Investigation, Writing \u2013 review & editing, Methodology. MR: Investigation, Writing \u2013 review & editing. HG: Investigation, Writing \u2013 review & editing, Funding acquisition. AJ: Investigation, Writing \u2013 review & editing. KM: Investigation, Writing \u2013 review & editing. EB: Investigation, Writing \u2013 review & editing. EM: Investigation, Writing \u2013 review & editing. KD: Investigation, Writing \u2013 review & editing. JM: Investigation, Writing \u2013 review & editing. KV: Investigation, Writing \u2013 review & editing. AS: Conceptualization, Formal Analysis, Funding acquisition, Investigation, Supervision, Writing \u2013 original draft. DH: Conceptualization, Formal Analysis, Funding acquisition, Investigation, Methodology, Supervision, Validation, Writing \u2013 original draft."} +{"text": "Bloodstream infections (BSIs) are major causes of morbidity and mortality for which prior analyses and validated scoring tools have attempted to stratify risk. This study investigated institutional and epidemiologic predictors of mortality with Gram-negative BSIs to better identify targeted antimicrobial stewardship efforts to improve outcomes.All patients with aerobic, monomicrobial, Gram-negative BSIs admitted and discharged from our academic medical institution between July 2022 and March 2023 were included. Data collected included patient demographics, microbiological data, clinical management, length of stay, ID consultation, and clinical outcomes . Univariate and multivariable logistic regression models were performed to identify variables that were primary drivers for inpatient mortality.E. coli (37.8%), K. pneumoniae (11.2%), P. aeruginosa (10.0%), S. marcescens (8.5%), and E. cloacae (6.2%). The majority (65.3%) were community acquired infections with 41.7% in the ICU, and 46.7% received an infectious diseases consult. The overall mortality was 14.7% with the highest mortality due to P. aeruginosa (34.6%) followed by S. marcescens (27.3%), K. pneumoniae (13.8%), E. cloacae (12.5%), and E. coli (8.2%). Overall mortality was significantly associated with several parameters in a univariate analysis (Table 1). In multivariable regression analysis hospital-acquired infection (0=0.002), cancer (p=0.012), qPitt > 2 (p< 0.001), SBP< 100 or vasopressor use at 72-96 hrs after positive blood culture (p=0.017) was associated with increased risk of mortality. The only parameter to reduce mortality within the multivariable regression analysis, by more than two-fold, was ID consultation (p=0.022).Overall, 259 patients were identified. The most common organisms were Parameters Associated with Mortality in Univariate AnalysisThe only factor found to significantly reduce mortality was formal ID consultation. ID consultation should be considered part of routine care for all patients with Gram-negative bacteremia.Katie B. Olney, PharmD, BCIDP, The Society of Infectious Diseases Pharmacists (SIDP): Grant/Research Support"} +{"text": "Prior literature establishes bidirectional associations between suicide and substance use disorders (SUDs), particularly opioid use disorder (OUD). However, the context of mental health services utilization remains under-investigated. This analysis examined patterns of mental health services utilization in patients with SUDs and suicidality, identified associated risk factors, and evaluated the impact of patient engagement on subsequent mental health outcomesSee above.Electronic health records (EHRs) derived from 7 health systems across New York City between 2010-2019 were analyzed. Suicidality was identified as any ICD-9/10 diagnosis of suicide attempt, suicidal ideation, or self-harm injury. SUDs were identified as any opioid, cannabis, cocaine, hallucinogen, inhalant, sedative/hypnotic/anxiolytic, amphetamine, or other substance abuse or dependence. Quasi-Poisson regression adjusted for age, gender, and chronic diseases was used to model associations between OUD exposure and the frequency of encounters and estimate the relative risk (RR) of significant covariates.A total of 6977 adults with suicidality and any comorbid SUD were selected, including 2203 (31.6%) with a diagnosis of OUD and 4774 (68.4%) without a diagnosis of OUD. Most patients were male (54.8%) and aged between 25-64 years (79.3%). Many (61.3%) had over 3 chronic diseases, including depression (80.8%), hypertension (60.6%), anemia (43.0%), and hyperlipidemia (41.9%). Compared to patients with other SUDs, those with OUD had higher odds of self-harm injury [OR: 1.26 (95% CI: 1.13-1.41)], depressive disorders [1.47 (1.29-1.67)], anxiety disorders [1.65 (1.48-1.84)], psychotic disorders [1.23 (1.11-1.37)], personality disorders [1.30 (1.16-1.48)], and post-traumatic stress disorder [1.37 (1.20-1.57)]. Patients with OUD were more likely to utilize all-cause outpatient (RR: 1.16), emergency department (ED) (RR: 1.43), and inpatient (RR: 1.60) services (p<0.001). Among OUD patients, males were less likely to have outpatient visits (RR: 0.79) and inpatient hospitalizations (RR: 0.88), and older age was protective against ED admissions (RR range: 0.62-0.71). Additionally, individuals with OUD were more likely than those with other SUDs to have SUD-related encounters, as well as suicide-related ED admissions and inpatient hospitalizations (p<0.0001). Those who had more mental health outpatient visits were less likely to have suicide-related ED admissions (RR: 0.85), however this association was weaker among younger or male patients with comorbid OUD.Among suicidal adults with comorbid SUDs, those with a diagnosis of OUD were more likely to utilize mental health services and have psychiatric comorbidity. Males and older adults were less likely to utilize services.None Declared"} +{"text": "Serum anti-spike IgG and neutralizing antibody against SARS-CoV-2 are recognized as immune correlates of protection (ICP) for COVID-19. However, there are limited data available on the ICP after the introduction of BA.4/5 bivalent vaccine. Thus, our study aimed to investigate the antibody response as correlates of protection against COVID-19, and the effects of BA.4/5 bivalent booster vaccine.A prospective cohort of healthcare workers was enrolled at Asan Medical Center, a 2,700-bed tertiary care hospital in South Korea between December 2022 and January 2023. Study participants had received a booster vaccination and either planned to receive a bivalent BA.4/5 vaccine or not. Blood samples were collected from study participants. Immunological assessments were performed using ELISA to measure variant-specific SARS-CoV-2 S1-IgG antibodies, and virus reduction neutralization test (VRNT) to measure neutralizing antibody levels.A total of 483 participants were enrolled, of whom 45 (9.3%) underwent subsequent infection after study enroll, while 438 (90.7%) did not. Of these 483 participants, 166 (34.4%) received the BA.4/5 bivalent booster vaccination. There was a significant difference in Wuhan-Hu-1 S1-IgG, BA.5 S1-IgG and neutralizing antibody against BA.5 levels between individuals with and without subsequent infection . While Wuhan S1-IgG and BA.5 S1-IgG (both P < 0.001) were found to be independent protective factors against subsequent SARS-CoV-2 infection, neutralizing antibody against BA.5 did not show significant protective effects. Hybrid immunity was robust predictive factor for subsequent infection in all analysis based on each immune marker . The predictive sensitivity of neutralizing antibody for subsequent infection was improved from 80.0% to 90.0% when combined with hybrid immunity and 100% with bivalent vaccine.Taken together, humoral immune responses seem to be reliable markers for immune correlates of protection against SARS-CoV-2 infection, and hybrid immunity showed independent protective effect from subsequent infection.All Authors: No reported disclosures"} +{"text": "Globally 20-50% population suffer from periodontal diseases. Bidirectional link exists between periodontal diseases and comorbidities. Limited evidence is available on antibiotic effectiveness in patients of dental infections with comorbidities.This retrospective, multi-centric, observational electronic medical record study gathered real world Indian evidence to assess effectiveness of cephalexin-clavulanic acid fixed-dose combination (FDC) compared to amoxicillin-clavulanic acid (amoxicillin CV) FDC and cefuroxime in adults with dental infections. Following data represents effectiveness in subset of patients with and without comorbidity.Overall, 89% (316/355) patients were without comorbidity ; while 11% (39/355) patients had comorbidities .Time to overall clinical improvement was less in patients without comorbidities compared to those with comorbidities .In patients without comorbidity, 98.13% (157/160), 100% (70/70), and 97.67% (84/86) showed overall clinical improvement within 10 days, in cephalexin CV, cefuroxime, amoxicillin CV groups, respectively.In patients with any comorbidity, 100% (14/14) patients showed improvement in cephalexin CV against 94% (16/17) in cefuroxime and 87% (7/8) in amoxicillin CV group within 10 days (p >0.05).Overall clinical improvement in patients with and without comorbidities on Day 5 and 7 is presented in Table. In metabolic and cardiovascular disorders subsets, 100% patients showed improvement within 10 days in cephalexin CV group, while 92% (12/13) and 100% (5/5), respectively in cefuroxime group; and 88% (7/8) and 67% (2/3), respectively in amoxicillin CV (p >0.05).In patients with dental infections, presence of comorbidities delays overall clinical improvement. All patients with comorbidity treated with cephalexin CV showed overall clinical improvement within 10 days of treatment. No significant difference was observed between treatments for overall clinical improvement.Archana Karadkhele, MBA, Sun Pharma Laboratories Limited: Full time employee Shruti Dharmadhikari, MSc, Sun Pharma Laboratories Limited: Full time employee Chintan Khandhedia, MD, Sun Pharma Laboratories Limited: Full time employee Neeraj Markandeywar, MD, Sun Pharma Laboratories Limited: Full time employee Amey Mane, MD, Sun Pharma Laboratories Limited: Full time employee Suyog Mehta, MD, Sun Pharma Laboratories Limited: Full time employee"} +{"text": "Pseudomonas aeruginosa high-risk clones pose severe threats to public health. Here, we characterize the imipenem/relebactam (IR) resistance mechanisms in P. aeruginosa high-risk clones sequence type 235 (ST235) and ST463 in China. Minimum inhibitory concentrations (MICs) were determined, and Illumina short-read sequencing was performed for 1,168 clinical carbapenem-resistant P. aeruginosa (CRPA) isolates. The gene copy number and expression level were analyzed by Illumina sequencing depth and reverse transcription-quantitative PCR, respectively. Resistance conferred by blaGES-5 was evaluated by cloning experiments. ST463 and ST235 accounted for 9.8% and 4.5% of total isolates, respectively, and showed high frequencies of extensively drug-resistant and difficult-to-treat resistant phenotypes. The overall IR-resistant rate in CRPA was 21.0% . However, the IR resistance rate was 81.7% (94/115) in ST463-PA and 52.8% (28/53) in ST235-PA. Of the ST463 isolates, 92.2% (106/115) were Klebsiella pneumoniae carbapenemase-producing P. aeruginosa (KPC-PA), and all 94 IR-resistant ST463-PA produced KPC-2. Compared to IR-susceptible ST463 KPC-2-PA, IR-resistant ST463 KPC-2-PA exhibited significantly higher blaKPC-2 copy numbers and expression levels. In ST463 KPC-2-PA, 16 mg/L relebactam resulted in additional fourfold reductions in imipenem MIC50/90 values compared to 4 mg/L relebactam. In ST235, 1.9% (1/53) carried blaIMP carbapenemase and 54.7% (29/53) carried blaGES carbapenemase. Other than the IMP producer, all 27 IR-resistant ST235-PA produced GES-5. Cloning experiments revealed that imipenem resistance in blaGES-5-carrying PAO1 transformants was generally unaffected by relebactam. In conclusion, IR-resistant CRPA isolates in China were mainly distributed in P. aeruginosa high-risk clones ST463 and ST235. The major underlying IR resistance mechanisms were blaKPC-2 overexpression and blaGES-5 carriage. Pseudomonas aeruginosa (CRPA) has emerged as an urgent public health issue. Although P. aeruginosa isolates usually exhibit great clonal diversity, the dissemination of certain high-risk clones is an essential step for CRPA to maintain an antibiotic-resistant phenotype. Among the high-risk clones detected globally, sequence type 235 (ST235) has been identified across five continents and is considered the most widespread 5. The hP. aeruginosa. In a multicenter study involving 4,927 MDR-PA isolates from adult patients, although 13.5% of samples produced metallo-\u03b2-lactamases (MBLs), nearly 70% of isolates were still susceptible to IR (Imipenem/relebactam (IR), a novel \u03b2-lactam-\u03b2-lactamase inhibitor (BLBLI) combination, has been developed and applied clinically to treat CRPA infections. Relebactam exerts strong inhibitory effects on many class A and class C \u03b2-lactamases and is almost unaffected by OprD inactivation or efflux pump extrusion , 10. Conle to IR .in vitro activity of IR against P. aeruginosa, the IR resistance mechanisms in CRPA high-risk clones remain largely unexplored. In this study, we evaluated the IR resistance profiles in clinical CRPA isolates from China, with a particular focus on the IR activity against ST235 and ST463 CRPA strains. Notably, we identified a surprisingly high IR resistance rate in ST235 and ST463 CRPA isolates. The underlying IR resistance mechanisms were further explored in detail.Currently, although many studies emphasize the A total of 1,168 clinical CRPA isolates, defined as resistant to either meropenem or imipenem according to the Clinical and Laboratory Standards Institute (CLSI) breakpoints , were inEscherichia coli ATCC 25922, P. aeruginosa ATCC 27853, and Klebsiella pneumoniae ATCC 700603 and ATCC BAA-1705 were used as quality controls. For all antimicrobials except fosfomycin, CLSI breakpoints phenotype were defined according to the criteria established by Magiorakos et al. and Tamma et al. respectively of amikacin, imipenem, meropenem, IR (relebactam fixed at 4 mg/L), ceftazidime, cefepime, ciprofloxacin, levofloxacin, piperacillin/tazobactam, aztreonam, fosfomycin, and polymyxin B were determined using the broth microdilution method with Thermo Scientific Sensititre System. To facilitate comparison between different antimicrobials in ST463 KPC-2-producing and ST235 GES-5-producing strains, the MICs of imipenem and IR (relebactam fixed at 4 mg/L or 16 mg/L) were simultaneously obtained by the agar dilution method described in CLSI standard M07 . Escheriakpoints for P. aakpoints for Enteectively , 15.De novo assembly was accomplished using shovill version 0.9.0 (https://github.com/tseemann/shovill). Multilocus sequence typing (MLST) was performed, and antimicrobial resistance genes were detected using mlst version 2.19.0 (https://github.com/tseemann/mlst) and ABRicate version 1.0.0 (https://github.com/tseemann/abricate). The oprD gene of clinical strains was compared with that of P. aeruginosa PAO1. OprD inactivation was confirmed if any of the following criteria were met: (1) truncation or absence of the oprD gene; (2) mutations leading to an OprD frameshift; and (3) mutations leading to the creation of a premature stop codon in OprD.The genomic DNA of all CRPA isolates was extracted using QIAamp DNA Mini Kit and underwent short-read sequencing . blaKPC-2 copy number was further calculated based on WGS. For each sample, a SAM alignment file was obtained by mapping Illumina raw reads to references using bowtie2 version 2.2.5 (https://github.com/BenLangmead/bowtie2) with the option \u201c-I 0 -X 800 --fast -q.\u201d After transforming the alignment results into BAM files, the sequencing depths of the blaKPC-2 gene and seven MLST alleles were analyzed by BEDTools version 2.30.0 (https://github.com/arq5x/bedtools2) with the option \u201cbedtools coverage -mean.\u201d Finally, the blaKPC-2 copy number of each strain was calculated as the depth of blaKPC-2 divided by the average depth of the seven MLST alleles.For KPC-2-producing strains, the P. aeruginosa isolates, genome assemblies were first annotated using Prokka version 1.14.6 (https://github.com/tseemann/prokka). Core gene alignment was then obtained by pangenome analysis using Panaroo version 1.2.9 . Reverse transcription was conducted using PrimeScript RT Reagent Kit . Quantitative PCR was performed in biological triplicates using TB Green Premix ExTaq . Each biological triplicate was assayed in technological triplicates. The housekeeping gene rpoD was chosen as the endogenous reference for normalization. The primers used for quantitative PCR are listed in Table S1.To compare the expression levels of blaGES-5 and blaGES-15 genes with the same upstream promoter sequences were amplified from clinical strains R16-15 and R20-99, respectively. The cloned sequences were homologously recombined into the pGK1900 plasmid. The constructed plasmids were then transformed into both E. coli DH5\u03b1 and P. aeruginosa PAO1. Transformants verified by Sanger sequencing were eventually selected for antimicrobial susceptibility testing. The primers used for cloning experiments are listed in Table S1.The P < 0.05.Statistical analysis was performed using the Fisher\u2019s exact test, the Mann\u2012Whitney U test, and the Kruskal\u2012Wallis test in SPSS version 25. The results were considered statistically significant when P. aeruginosa from other STs. The frequency of XDR/PDR phenotype was 88.7% (102/115) for ST463-PA and 73.6% (39/53) for ST235-PA ; the frequency of DTR phenotype was 90.4% (104/115) for ST463-PA and 52.8% (28/53) for ST235-PA . In contrast, the proportions of XDR/PDR-PA and DTR-PA in CRPA isolates from other STs were only 24.4% and 24.5% , respectively. Therefore, the resistance status of ST463-PA and ST235-PA was significantly more severe.Among the 1,168 CRPA isolates included in this study, MLST analysis revealed 285 different STs (excluding 69 isolates belonging to unknown STs). In 21 out of these 285 STs, the CRPA strain numbers were more than nine . ST463 and ST235 were found to be the most prevalent STs. The resistance phenotypes of ST463-PA and ST235-PA to traditional antipseudomonal agents were compared with those of 50/90 of 16/>128 mg/L; however, only 245/1,168 (21.0%) isolates were resistant to IR with an MIC50/90 of 2/32 mg/L isolates were resistant to imipenem with an MIC/32 mg/L . The add90 value ; Fig. 1.The phylogenetic tree was then constructed for IR-resistant isolates, and the clonal characteristics were analyzed. Among 245 IR-resistant isolates, 62 different STs were identified (excluding five strains with unknown STs). In 16 of these 62 STs, the IR-resistant strain numbers were more than one . As shown in P. aeruginosa (non-CPPA), while 106/115 (92.2%) isolates were KPC-producing P. aeruginosa (KPC-PA). The identified KPC alleles included blaKPC-2 and blaKPC-33 . In ST235-PA, in addition to 23/53 (43.4%) non-CPPA isolates, 54.7% (29/53) were carbapenemase-type GES-producing P. aeruginosa (GES-PA) and 1.9% (1/53) were IMP-15-producing P. aeruginosa. The carbapenemase-type GES alleles consisted of blaGES-5 and blaGES-15 .To further describe the molecular epidemiology and interpret the IR resistance data of ST463 and ST235 isolates, genomic analysis was subsequently conducted. As listed in Table S2, the strong association between class A carbapenemase types and STs could be clearly distinguished. In ST463-PA, 9/115 (7.8%) isolates were non-carbapenemase-producing blaKPC-33-carrying P. aeruginosa were IR intermediate, while 94/104 (90.4%) blaKPC-2-carrying P. aeruginosa were IR resistant blaGES-5-carrying P. aeruginosa were IR resistant esistant ; in ST23esistant . Overall50 and MIC90 values. However, with 4 mg/L relebactam, restoration of imipenem susceptibility was only achieved in 9/104 (8.7%) ST463 KPC-2-PA isolates, while the majority still exhibited high-level imipenem resistance (64 mg/L to 256 mg/L). Therefore, we proposed that 4 mg/L relebactam might be insufficient for inhibiting blaKPC-2 expression in ST463.IR resistance mechanisms were further explored in ST463 KPC-2 producers. As shown in 50 and MIC90 values were achieved by 16 mg/L relebactam ST463 KPC-2-PA isolates became susceptible or intermediate to imipenem. Notably, with 16 mg/L relebactam, only three ST463 KPC-2 producers still exhibited high-level imipenem resistance (MIC: 64 mg/L). In comparison to 4 mg/L relebactam, additional fourfold reductions in imipenem MIClebactam .blaKPC-2 copy numbers were compared between ST463 KPC-2 producers showing different IR resistance phenotypes. Compared with ST463 KPC-2-PA isolates susceptible or intermediate to IR, IR-resistant ST463 KPC-2-PA isolates exhibited significantly higher blaKPC-2 copy numbers . In stra 0.0001) . Besides < 0.01) . AltogetblaKPC-2 expression level was quantitively analyzed. In total, 18 blaKPC-2-carrying ST463 isolates were selected from three phenotypic groups . These strains shared similar genetic elements surrounding blaKPC-2 and the same blaKPC-2 promoter sequences. As shown in blaKPC-2 expression level differed significantly among these three groups , showing that blaKPC-2 overexpression was related to the attenuated inhibitory effects of 4 mg/L relebactam.Finally, to further verify our hypothesis, the relative mexE and mexY genes in ST463 KPC-2-PA, only the expression levels of mexA and mexD genes were analyzed. Interestingly, under 16 mg/L relebactam, compared with isolates susceptible to imipenem (MIC: 1 mg/L), ST463 KPC-2-PA isolates resistant to imipenem (MIC: 32 mg/L to 64 mg/L) displayed much lower mexA and mexD expression levels . This suggested that the IR resistance phenotype differences among ST463 KPC-2-PA could not be attributed to efflux pump overexpression. With regard to OprD inactivation, among imipenem-susceptible and imipenem-nonsusceptible ST463 KPC-2-PA (under 16 mg/L relebactam), the proportions of OprD-inactivating strains were 36.4% (4/11) and 96.8% (90/93), respectively (P < 0.0001). This significant difference indicated the potential contribution of OprD inactivation to imipenem resistance, which further led to IR resistance in ST463 KPC-2-PA.Although additional decreases in imipenem MICs were achieved when relebactam was increased from 4 mg/L to 16 mg/L, the majority of ST463 KPC-2-PA were still not susceptible to imipenem. Previous studies have identified IR resistance associated with mutations in OprD and regulators of MexAB-OprM , 20. Thu50/MIC90 values or the cumulative inhibition curves of imipenem, suggesting that IR resistance in ST235 GES-5-PA could not be attributed to blaGES-5 overexpression.Mechanisms of IR resistance were also investigated in detail for ST235 GES-5-PA. As illustrated in blaGES allelic variants on imipenem and IR resistance were analyzed. The imipenem MICs were generally higher in ST235 GES-5 producers (32 mg/L to 128 mg/L) than in ST235 GES-15 producers (16 mg/L). The IR resistance rate was 100% (27/27) for blaGES-5-carrying ST235-PA isolates, with MIC50/MIC90 values of 32/32 mg/L. In contrast, all blaGES-15-harboring ST235-PA isolates were susceptible or intermediate to IR, exhibiting MIC50/MIC90 values of 4/4 mg/L. The above data demonstrated the potential involvement of blaGES-5 carriage in IR resistance.Subsequently, the impacts of blaGES-5 carriage was acquired. In another in vitro study were published. In one in vitro multistep selection study . Under these circumstances, clinical treatment choices would be greatly constrained.Generally, IR resistance related to KPC enzymes has seldom been reported. Until 2022, four studies investigating IR resistance development in KPC-producing on study , IR-resisistance \u201332, GaP. aeruginosa in previous studies . According to Hujer et al.\u2019s study (Although GES producers were found among IR-resistant studies , 33, the\u2019s study , GES-20 exoU+ genotype and various resistance-related mutations. In a study on P. aeruginosa bacteremic pneumonia, a 29.8% increase in 5-day mortality and a 34.4% increase in 30-day mortality were noted in patients infected with ST235-PA (exoU and exoS genes, the ST463 clone also exhibits a hypervirulent phenotype. In a recent study by Zhang et al. (Galleria mellonella larvae infection model. The included ST463-PA isolates showed hypervirulence comparable to that of ST235-PA. Moreover, in a clinical retrospective cohort study conducted in East China (The poor outcome associated with ST235 and ST463 CRPA, mainly caused by their hypervirulence and MDR/XDR/PDR profiles, is concerning. Generally, hypervirulence is defined as the ability to cause higher mortality and more severe acute infections . ST235 CblaKPC-2 overexpression as the major driver of high-level IR resistance in ST463-PA. In addition, we also confirmed that blaGES-5 carriage mediated IR resistance in ST235-PA. Overall, this epidemiological survey systematically deciphered the IR resistance mechanisms in P. aeruginosa global high-risk clone ST235 and regional high-risk clone ST463.In conclusion, our data highlighted the distinct IR resistance characteristics between CRPA isolates from high-risk clones and other STs. Of particular concern is the association of high-risk clones with IR resistance phenotype and XDR/DTR phenotype, which may worsen clinical outcomes and restrict therapeutic options. Using whole-genome analysis methods and quantitative PCR, we identified"} +{"text": "Author Correction: Genome Biol 24, 187 (2023)https://doi.org/10.1186/s13059-023-03023-7Following publication of the original article , the autThese errors do not affect the main results and conclusions of the paper. The original article has beenAdditional file 2: Supplementary Methods [165-182]. Fig. S1. Imputation accuracy of individual samples for sites with MAF > 1%. Fig. S2. Median copy-number across the genome for wolves. Fig. S3. Repeatmasker classification of SINE variation. Fig. S4. Distribution of variation across the genome for breed and other dogs . Fig. S5. Nucleotide diversity along chr26. Fig. S6. Signature of a retrogene detected at the TEX2 locus."} +{"text": "Correction : Environmental Microbiome (2020) 15:3 10.1186/s40793-019-0348-0Microviridae viruses found in the metagenomes in the Abstract (Results), Results , Discussion , and Conclusions. Since the article\u2019s publication it has come to light that the sequences associated with the Microviridae viruses belong to PhiX 174 (Genbank Accession Number NC_001422), a member of Microviridae family. These sequences were a contamination originating from the use of PhiX DNA as a control in Illumina sequencing platforms [Microviridae virus(es). After removing PhiX 174-associated sequences from the metagenomic data, the most abundant viral sequences were affiliated with Myoviridae, a viral family which includes phages that are suspected to affect Chlorobi [The original article briefly discusses Additional file 1. Supplementary Materials, Methods and Results. Figure S1.Natural blooms in Trunk River. Figure S2.Color and appearance ofsamples from all holes, depths, and timepoints. Figure S3.Filters thatwere used for biomass measurements and spectral analysis. Figure S4.Total cell count of three samples . Figure S5. Depthprofile representation of chemical data presented in Fig.2. Figure S6. Physicochemistry. Iron, nitrate, ammonium, acetate, Ca2+, and K+measurements. Figure S7. Individual diversity indices of all samples. Figure S8. Trajectories of community structure in hole A, E and K. Figure S9. Relative sequence abundance of the 20 most abundant clades onphylum, class, order, family and genus level, as well as the 20 mostsequence abundant ASVs (amplicon sequence variants). Figure S10.Relative sequence abundance of Chlorobiales ASVs. Figure S11.Relativechange of ASV abundance between surface (V1) and deeper layers (V2-4). Figure S12.Chlorobiales phylogeny. Figure S13. Circular map ofmetagenome-assembled genomes (MAGs). Figure S14. Chlorobiales phy-logenomics. Figure S15. Protein comparison of Bin 6. Figure S16.Pro-tein comparison of Bin 10. Figure S17. Genes involved in sulfurcycling. Figure S18. CRISPR arrays and cas genes predictions Bin 6.Figure S19. CRISPR arrays and cas genes predictions Bin 10. Figure S20. Relative sequence abundance of viral family-level clades. Table S1. Over-view of sequencing output and diversity indices. Table S2. Genome sta-tistics. Table S3. Average nucleotide identity (ANI) comparisons. Table S4. Oxidative phosphorylation and chlorophyll biosynthesis genes of Bin6 and Bin 10. Table S5. CRISPR-Cas system information for eachmetagenome-assembled genome."} +{"text": "Moreover, Patients with AoAC showed a lower incidence of first-pass successful recanalization and a higher incidence of postprocedural hemorrhage than those without AoAC. On multivariate analysis, AoAC was independently associated with first-pass successful recanalization . Conclusions: AoAC on chest radiography can be used as a preoperative predictor of successful first-pass recanalization in patients undergoing EVT for AIS.Background: Vascular conditions can affect the recanalization rates after endovascular thrombectomy (EVT) for acute ischemic stroke (AIS). Chest radiography can assess the conditions of the aortic arch based on the presence or absence of aortic arch calcification (AoAC). The aim of this study was to investigate the relationship between AoAC on chest radiography and first-pass successful recanalization . Methods: We compared the rate of first-pass successful recanalization between patients with and without AoAC. A total of 193 patients with anterior circulation occlusion who underwent EVT between January 2017 and December 2021 were included. Results: AoAC was observed in 80 (41.5%) patients. Patients with AoAC were older (74.5 \u00b1 7.78 vs. 63.9 \u00b1 12.4 years, Several randomized clinical trials have established the clinical efficacy of endovascular thrombectomy (EVT) for acute ischemic stroke (AIS) ,2,3,4,5.Recent retrospective studies have reported a relationship between the number of device passes and clinical outcomes and documented that recanalization with fewer device passes is associated with better clinical outcomes ,13,14,15Intracranial atherosclerotic stenosis (ICAS) and tortuous vascular anatomy are common causes of EVT failure ,18,19. IAtherosclerosis is a diffuse progressive disease characterized by vascular calcification, which is associated with disease progression ,21,22. CThe aim of this study was to investigate the relationship between AoAC on chest radiography and first-pass recanalization after EVT for AIS.n = 31) and (2) posterior circulation occlusions (n = 29). Eventually, 193 consecutive patients were included symptomatic AIS, (2) large vessel occlusions confirmed using magnetic resonance (MR) angiography or computed tomography (CT) angiography, (3) less than 24 h from symptom onset to treatment, and (4) at least one-half mismatch between cerebral blood flow and cerebral blood volume map with MR perfusion imaging. A total of 253 patients who met the inclusion criteria were included. From the 253 patients, 60 were excluded because of (1) tandem occlusions , the imaging data and medical records of patients were reviewed. Data regarding the baseline characteristics of the patients, treatment characteristics, and radiological and clinical outcomes were obtained from the medical records. Baseline characteristics included age, sex, past medical history, occlusion side and site, etiology of stroke, AoAC on chest X-ray, type of aortic arch, National Institutes of Health Stroke Scale (NIHSS) at admission, onset-to-door time, and onset-to-puncture time. Treatment characteristics included intravenous thrombolysis, balloon guide catheter, EVT technique, and procedural time. Radiological and clinical outcomes included TICI grades, postprocedural hemorrhage, and the 3-month modified Rankin Scale (mRS) score.The occlusion sites were divided into three categories: (1) internal carotid artery (ICA), (2) M1 segment of the middle cerebral artery (MCA), and (3) M2 segment of MCA. The M1 and M2 segments were defined as the horizontal and vertical segments of MCA, respectively. The etiology of stroke was classified based on the Trial of ORG 10172 in Acute Stroke Treatment (TOAST) criteria. Two experienced radiologists (7 (KHR) and 6 (JB) years of experience) independently evaluated all chest X-rays in a binary manner. During the analysis, all radiologists were blinded to the radiological and clinical outcomes after EVT. AoAC assessments on chest radiographs are shown in There were three neurosurgeons who specialized in neurointerventions at our hospital. When EVT was planned for large vessel occlusion, it was performed by one of these three neurosurgeons. The procedures were performed under local anesthesia via femoral access. The primary EVT modality was at the surgeon\u2019s discretion. The use of a balloon guide catheter was based on the surgeon\u2019s discretion.p-value of <0.05 was considered statistically significant. Multivariable logistic regression analysis was used to evaluate factors affecting first-pass successful recanalization and good clinical outcomes after EVT for AIS. Variables with a p-value of <0.20 in the univariate analysis were included in the multivariate logistic regression analysis. The interobserver agreement for each chest X-ray feature and the presence of AoAC between the two radiologists was assessed using the Cohen kappa statistic. The degree of agreement was classified using kappa values according to the Landis and Koch recommendation as follows [Baseline characteristics, treatment characteristics, and radiological and clinical outcomes were compared between patients with AoAC and those without, between patients first-pass successful recanalization and those without, and between patients with good clinical outcomes and those without. Categorical variables were analyzed using the chi-squared test or Fisher\u2019s exact test. Continuous variables were analyzed using Student\u2019s t-test or the Mann\u2013Whitney U test. A follows : kappa vn = 37, 19.2%), cardioembolic occlusion , and unknown . AoAC was observed in 80 (41.5%) patients, while aortic arch types 1, 2, and 3 were observed in 46 (23.8%), 99 (51.3%), and 48 (24.9%) patients, respectively. ICAS was observed in 49 (25.4%) patients. Intravenous tissue plasminogen activator was administered to 78 (40.4%) patients. A balloon guide catheter was used in 34 (17.6%) patients. As first-line EVT strategies, stent retrievers, catheter aspiration, and a combination technique were used in 44 (22.8%), two (1.04%), and 147 (76.2%) patients, respectively. The total number of EVT attempts was one (n = 76), two (n = 43), three (n = 28), four (n = 26), five (n = 12), six (n = 3), seven (n = 2), eight (n = 2), and 12 (n = 1). Successful recanalization was achieved in 162 (83.9%) patients, and first-pass successful recanalization was achieved in 69 (35.8%) patients. Good clinical outcomes were achieved in 110 (57.0%) patients.A total of 193 patients were analyzed. Of the 193 patients, 41 (21.2%), 119 (61.7%), and 33 (17.1%) had occlusion in the ICA, M1 and M2 segments, respectively. Stroke etiologies included atherosclerotic occlusion (p < 0.001) and were more likely to have hypertension (52/80 (65.0%) vs. 43/113 (38.1%), p < 0.001) and atrial fibrillation (45/80 (56.3%) vs. 39/113 (34.5%), p = 0.003). Aortic arch type 3 was more frequently observed in patients with AoAC (34/80 (42.5%) vs. 14/113 (12.4%), p < 0.001). Patients with AoAC had more EVT attempts . Procedural time was significantly longer in patients with AoAC . Successful recanalization (60/80 (75.0%) vs. 102/113 (90.3%), p = 0.005) and first-pass successful recanalization (15/80 (18.8%) vs. 54/113 (47.8%), p < 0.001) were achieved less frequently in patients with AoAC. Postprocedural hemorrhage was observed more frequently in patients with AoAC (36/80 (45.0%) vs. 31/113 (27.7%), p = 0.015). Although ICH was observed more frequently in patients with AoAC (22/80 (27.5%) vs. 17/113 (15.0%), p = 0.045), the frequency of SAH did not differ significantly between the two groups (14/80 (17.5%) vs. 13/113 (11.5%), p = 0.293). Patients with AoAC had a higher incidence of good clinical outcomes (37/80 (46.3%) vs. 73/113 (64.6%); p = 0.013). On multivariate logistic regression analysis for factors affecting AoAC on chest radiography, including age, sex, hypertension, atrial fibrillation, occlusion site, and NIHSS at admission, age (adjusted odds ratios (OR): 1.106, adjusted 95% confidence interval (CI): 1.063\u20131.151; p < 0.001), and hypertension were independently associated with AoAC on chest radiography (iography .p = 0.030). Patients with first-pass successful recanalization showed a lower incidence of AoAC on chest X-ray (15/69 (21.7%) vs. 65/124 (52.4%), p < 0.001). Intravenous thrombolysis was administered more frequently in patients with first-pass successful recanalization (35/69 (50.7%) vs. 43/124 (34.7%), p = 0.033). Patients with first-pass successful recanalization had a shorter procedural time . Postprocedural hemorrhage was more frequently observed in patients with first-pass successful recanalization (11/69 (15.9%) vs. 56/124 (45.5%), p < 0.001). Patients with first-pass successful recanalization had a higher incidence of both SAH and ICH (4/69 (5.8%) vs. 23/124 (18.5%), p = 0.016) (7/69 (10.1%) vs. 32/124 (25.8%), p = 0.009). Good clinical outcomes were achieved more frequently in patients with first-pass successful recanalization (53/69 (76.8%) vs. 57/124 (46.0%), p < 0.001). Multivariate logistic regression analysis for factors affecting first-pass successful recanalization after EVT for AIS, including sex, hypertension, occlusion site, AoAC on chest X-ray, and intravenous thrombolysis revealed that AoAC on chest X-ray and intravenous thrombolysis were independent factors ( factors .p = 0.003). Hypertension was observed less frequently for patients with good clinical outcomes (47/110 (42.7%) vs. 48/83 (57.8%), p = 0.043). Left-side occlusion was observed less frequently for patients with good clinical outcomes (42/110 (38.2%) vs. 46/83 (55.4%), p = 0.020). Good clinical outcomes were less frequently achieved for patients with ICA occlusion than for those with M1 or M2 occlusions (16/110 (14.5%) vs. 25/83 (30.1%), p = 0.012). Patients with AoAC achieved good clinical outcomes less frequently than those who did not (37/110 (33.6%) vs. 43/83 (51.3%), p = 0.013). Patients with good clinical outcomes had fewer EVT attempts , shorter procedural time , higher rates of successful recanalization (103/110 (93.6%) vs. 59/83 (71.1%), p < 0.001), and first-pass successful recanalization (53/110 (48.2%) vs. 16/83 (19.3%), p < 0.001). Postprocedural hemorrhage (26/110 (23.9%) vs. 41/83 (49.4%), p < 0.001) and ICH (13/110 (11.8%) vs. 26/83 (31.3%), p = 0.001) were observed less frequently in patients with good clinical outcomes; however, the frequency of SAH did not differ significantly between the two groups (13/110 (11.8%) vs. 14/83 (16.9%), p = 0.402). Multivariate logistic regression analysis of factors affecting good clinical outcomes after EVT for AIS, including age, sex, hypertension, diabetes mellitus, atrial fibrillation, occlusion side, occlusion site, AoAC on chest X-ray, aortic arch type 3, intravenous thrombolysis, total number of EVT attempts, procedural time, successful recanalization, first-pass successful recanalization, postprocedural hemorrhage, and ICH revealed that left-side occlusion , first-pass successful recanalization , successful recanalization , and ICH were independent factors ( factors .p < 0.001).The interobserver agreement showed moderate agreement between the two radiologists but not atherosclerotic occlusion (TOAST 1) . These results suggest that AoAC on chest X-ray may reflect atherosclerotic changes in a type 3 aortic arch but not intracranial atherosclerotic changes. Previous studies have reported that the pathophysiology of ICAS is different from that of extracranial atherosclerosis [Our results showed that AoAC on chest radiography was significantly associated with a type 3 aortic arch . Recent studies have reported that first-pass recanalization is strongly associated with favorable clinical outcomes ,16,33,34We believe that the ability to predict first-pass successful recanalization, which indicates the procedure\u2019s difficulty before EVT for AIS, could be helpful in deciding the strategy for EVT. Observation of AoAC on preprocedural chest radiography allows neurointerventionalists to prepare for the possibility of longer procedural times and multiple EVT attempts. If the neurointerventionalists can predict the difficulty of the procedure in advance, they can select the techniques or devices that they are familiar with rather than unfamiliar new techniques or new devices; this can help achieve better radiological and clinical outcomes.During the initial examination of patients with AIS, brain CT angiography or MR angiography is performed, and brain CT angiography provides more information about AoAC than chest X-rays. Therefore, chest X-rays may be less useful when brain CT angiography is taken. However, neurointerventionalists try to check brain CTA focusing on intracranial lesions or carotid lesions, and they do not try to check brain CTA focusing on AoAC. Although our study was based on chest X-ray, we can suggest that we have to check AoAC on brain CT angiography as well as intracranial lesions or carotid lesions.First, this was a retrospective, single-center study, and selection bias cannot be ruled out. Second, the sample size was small. Therefore, the statistical power may be low. Third, we demonstrated a significant relationship between AoAC on chest radiography and first-pass successful recanalization after EVT for AIS; however, this was not a causal relationship. Fourth, AoAC was assessed based on the presence of calcification in a qualitative rather than quantitative manner. The impact of AoAC on first-pass successful recanalization should be evaluated quantitatively or semi-quantitatively using more detailed AoAC grades. More evidence with larger sample sizes is required to confirm these preliminary results.Our results suggest that AoAC on chest radiography is a useful predictor of first-pass successful recanalization after EVT for AIS; however, further evidence is required."} +{"text": "Telomeres are the terminal regions of chromosomes that ensure their stability while cell division. Telomere shortening initiates cellular senescence, which can lead to degeneration and atrophy of tissues, so the process is associated with a reduction in life expectancy and predisposition to a number of diseases. An accelerated rate of telomere attrition can serve as a predictor of life expectancy and health status of an individual. Telomere length is a complex phenotypic trait that is determined by many factors, including the genetic ones. Numerous studies indicate the polygenic nature of telomere length control. The objective of the present study was to characterize the genetic basis of the telomere length regulation using the GWAS data obtained during the studies of various human and other animal populations. To do so, a compilation of the genes associated with telomere length in GWAS experiments was collected, which included information on 270 human genes, as well as 23, 22, and 9 genes identified in the cattle, sparrow, and nematode, respectively. Among them were two orthologous genes encoding a shelterin protein (POT1 in humans and pot-2 in C. elegans). Functional analysis has shown that telomere length can be influenced by genetic variants in the genes encoding: (1) structural components of telomerase; (2) the protein components of telomeric regions (shelterin and CST complexes); (3) the proteins involved in telomerase biogenesis and regulating its activity; (4) the proteins that regulate the functional activity of the shelterin components; (5) the proteins involved in telomere replication and/or capping; (6) the proteins involved in the alternative telomere lengthening; (7) the proteins that respond to DNA damage and are responsible for DNA repair; (8) RNA-exosome components. The human genes identified by several research groups in populations of different ethnic origins are the genes encoding telomerase components such as TERC and TERT as well as STN1 encoding the CST complex component. Apparently, the polymorphic loci affecting the functions of these genes may be the most reliable susceptibility markers for telomere-related diseases. The systematized data about the genes and their functions can serve as a basis for the development of prognostic criteria for telomere length-associated diseases in humans. Information about the genes and processes that control telomere length can be used for marker-assisted and genomic selection in the farm animals, aimed at increasing the duration of their productive lifetime Telomeres are the terminal regions of chromosomes that ensuretheir stability and represented by evolutionary conservedtandemly repeated DNA sequences of several kb in length . For example, theirlengths in humans at birth are 10\u201315 kb .3\u02b9 terminal end of a telomere is a single-stranded guanine-richDNA region (150\u2013200 nucleotides), whose end interacts withthe double-stranded region to form the so-called T-loop at thetelomere end. T-loop formation and stabilization are ensuredby a shelterin complex . This structure prevents recognitionof a chromosome terminal region by repair proteins.DNA polymerase is unable to fully replicate the 3\u02b9-end ofa linear DNA during cell division, which leads to a loss of50\u2013200 nucleotides of the telomeric sequence at each celldivision . Telomere shortening can also befacilitated by other factors and processes 1,such as oxidative stress, inflammation, UV irradiation, effectsof toxic agents, DNA replication errors, etc. . These factors are likely to producedifferent effects depending on cell types and the organism\u2019sdevelopment stage and species .http://vavilov.elpub.ru/jour/manager/files/Suppl_Ignatieva_Engl_27_3.pdf.Supplementary Materials are available in the online version of the paper:Telomere shortening initiates cellular senescence. Activationof DNA damage response signaling pathways results ina cell cycle arrest, which may in turn lead to apoptosis andeventually \u2013 to progressive tissue degeneration . The datacollected at the cellular level in vitro and in model organismslay the foundation for using the telomere length as a predictorof life expectancy and health status of an individual. Indeed,studies in humans , mice , sheep , cattle , wild birds , and other animals haveshown that shorter telomere length may be associatedwithreduced life expectancy. The studies in humans discovered anassociation between the telomere length and cardiovasculardiseases, cancer, diabetes, inflammation, and other pathologicalstates .Telomere shortening is prevented by telomerase, a specializedribonucleoprotein complex acting as a reverse transcriptase.In humans, telomerase is active in almost all thecancer cells studied , in blastocyst, in mostsomatic tissues at 16\u201320 weeks of development (except forbrain cells), and ovary and sperm cells at all ontogeneticstages (except for mature spermatozoids and oocytes) .Telomerase activity is controlled by the proteins regulatingexpression of telomerase components, their movementto various cell compartments, processing, and assembly aswell as by the proteins maintaining stability of the telomerasecomplex or, on the contrary, activating its degradation .The main stages of telomerase biogenesis are presented inFigure 2. The examples of proteins affecting the telomeraseactivity are presented in Suppl. Material 2. In addition, thetelomerase activity is also affected by the shelterin and CST complex .Telomere length is a complex phenotypic trait determinedby multiple factors including genetic ones. The meta-analysisof heritability data for this trait performed in eighteen vertebratespecies showed the averaged heritability index of 45 %.The studies showed the value of 52 % in humans, 42 % \u2013 inHolstein cattle breed, 35 % \u2013 in hamadryas baboons, and5 % \u2013 in sheep .The problem of genetic basis of telomere length regulationis of interest for many researchers. The information on telomerase components and proteins involved in telomere lengthregulation canbe found in The Telomerase Database (http://telomerase.asu.edu/) . Joyce and co-workers (2018)presented a set of 80 human genes with telomere-related functions.The GWAS data also indicate a polygenic nature of telomerelength heritability. For instance, the GWAS Catalog (https://www.ebi.ac.uk/gwas/) cites 99 human genes that either includeor neighbor the telomere length-associated allelic variants.One of the largest GWA studies presents the data on 138 humangenomic loci, whose allelic variants are associated withtelomere length .In addition to the telomere length association data gatheredusing GWA studies in various human population samples,the data obtained in other animal species also appear to be of interest. However, these studies are rather scarce and areavailable only for Holstein\u2013Friesian cattle , house sparrow nestlings , andC. elegans .The objective of this review was to characterize the geneticbasis of telomere length regulation using the GWAS datacollected in various human populations and to compare themwith the results of similar experiments in other animal species.For this purpose, (1) the data on genes identified in GWAStelomere length experiments were systematized; (2) functionalannotation of genes was performed, and the set of biologicalprocesses affecting telomere length was identified.The data on telomere length-associated genes were obtainedfrom the papers available in the PubMed database (https://pubmed.ncbi.nlm.nih.gov/) using such keywords as \u2018telomerelength\u2019 and \u2018GWAS\u2019. Functional annotation of genes wasperformed using information obtained from the papers presentingGWAS data, PubMed, The Telomerase Database (http://telomerase.asu.edu/) queries, and the DAVID knowledgebase(https://david.ncifcrf.gov/) .Human genes identified through GWA studiesPubMed queries produced 18 scientific papers presenting theresults of identifying telomere length-associated polymorphicloci in human genome based on GWAS data. These paperswere analyzed, and the data on 270 telomere length-associatedgenes were collected . Most genes (262)were identified in European-ancestry population samples, thedata on 15 genes were obtained from the studies in SoutheastAsian population samples , five genes were identified as a result of trans-ethnicmeta-analysis of Singaporean Chinese and European ancestrydata , and one gene was found in AfricanAmericans .The data on functional significance in the context oftelomere length regulation were presented by the authors ofGWA studies for 52 genes out of 270 .The fact that the data on gene significance in the context oftelomere length regulation were unavailable for a number ofloci reflects the capabilities and limitations of GWAS methodology.Most loci identified by GWAS and associatedwith the trait of interest are located in intergenic regions. Asa rule, in these cases, the set of candidate genes includes thenearest genes, whose functional significance is often difficultto interpret. To identify the mechanisms and genes, throughwhich intergenic variants affect the studied traits, additionalexperiments are required. For example, it was shown thatT-to-C substitution of rs1421085 in the intron of FTO geneaffects the expression of IRX3 and IRX5, whose transcriptionstart sites are far away (~520 and ~1160 kb) from rs1421085.Main functional groupsof human telomere length-associated genesA functional classification was performed for a set of 52 humangenes for which there was information about their functionalsignificance in the context of telomere length regulation. As a result, several functional groups ofgenes have been identified Genes encoding telomerase components: TERC is thetelomerase RNA component acting as a matrix for DNA strandextension at the telomere end and TERT is a reverse transcriptaseenzyme subunit .Genes encoding shelterin proteins: components of thiscomplex can bindto both double-stranded and single-stranded telomeric DNAregions , stabilize them, protect them from exonucleases, reduce telomerase access, and inhibit the proteinsactivated by damaged DNA and involved in double-strandedbreak repair . TheGWAS data on telomere length association were obtained forthe genes coding for five out of six shelterin proteins .Genes encoding CST proteins: CTC1, STN1, TEN1. CSTcomplex acts as a telomerase negative regulator at the late Sto G2 phase of the cell cycle .Genes encoding proteins involved in telomerase biogenesisand regulating its activity. One of these genes, ZCCHC10,encodes a protein regulating telomerase synthesis at transcriptionallevel: ZCCHC10 suppresses TERT transcription. Processing and assembly of a telomeraseRNA subunit involves DKC1, NAF1, and SHQ1 , ribonuclease PARN, exoribonuclease DIS3, thecomponent of a nuclear exosome targeting (NEXT) complex,ZCCHC8 , SMUG1 , and CELF4/BRUNOL4 . Noncanonicalpolymerase TENT4B/PAPD5 ,trimethylguanosine synthetase TGS1 , andEXOSC10 RNA exosome component cause a decrease in the level of active TERC. The assemblyof telomerase nucleoprotein complex involves ATPaseRUVBL1/pontin and telomerase-associatedprotein TEP1 . Two proteins (WRAP53/WDR79/TCAB1 and NOLC1/NOPP140) provide telomeraseaccumulation in Cajal bodies, the small nuclear organelleswhere processing of small nuclear and nucleolar RNAs andassembly or ribonucleoprotein complexes occur . Telomerase activityis modulated by activator protein SMG6/EST1A, which alsobinds to a single-stranded DNA , and PMLprotein, whose isoform PML-IV suppresses telomerase activity.Genes encoding proteins regulating functional activityof shelterin proteins. CSNK2A2 and CSNK2B are the subunitsof casein kinase which phosphorylates TERF1, increasingits binding to telomeres .ATM serine/threonine kinase, on the contrary, decreasesTERF1 binding to the telomeric DNA . PeptidaseUSP7 and ubiquitin ligase SIAH1 activate proteasomaldegradation of POT1 and TERF2, respectively . ADP ribosylases PARP1 and PARP2 reduce the DNAbinding activity of TERF2 .Genes encoding proteins involved in telomere replicationand/or capping: (1) enzymes RRM1 and TYMS involved insynthesis of deoxynucleoside triphosphates (dNTP) and thymidylatesrequired for DNA synthesis ; (2) helicases RTEL1 and MCM4; (3) RPA1 and RPA2, the subunitsof the RPA complex capable to unfold G-quadruplex structuresthat may block DNA replication ;(4) HNRNPA1 promoting telomere capping after DNA replication.Genes encoding proteins affecting the alternative telomerelengthening pathway. This telomerase-independentmechanism includes the recombinationbetween telomeric regions of two DNA molecules. Three genes identified inGWA studies were attributed to this group . These genes encode SMC6 which activates ALT and its two inhibiting proteins: ATRX withchromatin remodeling activity and SLX4 endonuclease .Genes encoding DNA damage response proteins: (1) peptidaseSENP7 ; (2) chaperone protein BAG6; (3) DCAF4 interacting with CUL4-DDB1ligase ; (4) RFWD3 interacting withRPA protein (replication protein A) .Genes encoding subunits of RNA exosomes: EXOSC6,EXOSC9 and MPHOSPH6 . These proteins are functionally significant, becauseit is known that TERC may be subjected to 3\u02b9-processing,and the RNA-exosomes are involved in this process .Human candidate genes identified in more than one studyAs mentioned above, we have analyzed 18 papers on identifyingtelomere length-associated human genome loci based onGWA studies and collected the data on 270 such genes . Notably, only 16 genes were identified inat least two studies .The most frequently identified genes were the ones encodingboth telomerase components (TERC and TERT ) and STN1encoding a component of the CST complex . Three genes POT1, TERF1,and TERF2 encoding components of the shelterin complexwere mentioned in 4, 3, and 2 publications, respectively.Three more genes DCAF4, RTEL1, and NAF1 controlling theDNA damageresponse, telomere replication, and telomerasebiogenesis were identified in four studies. ATM, PARP1,MPHOSPH6, RFWD3, SENP7, and TYMS were identifiedin 3 or 2 papers.Most of 16 genes listed above were identified in populationsamples of different ethnic origin: (1) TERC in three ethnicgroups, namely Europeans, Bangladeshis, and SingaporeanChinese; (2) DCAF4, MPHOSPH6, and TYMS in Europeansand as a result of the trans-ethnic meta-analyses (SingaporeanChinese+Europeans); (3) TERT, STN1, POT1, RTEL1, NAF1,TERF1, ATM, PARP1 in two ethnic groups, namely Europeansand Singaporean Chinese.Identification of the genes related to telomerelength regulation according to DAVIDUsing DAVID, we found the terms from the GOTERM_BP_DIRECT dictionary that were significantly (FDR < 0.05) associatedwith the list of 270 human genes presented in Suppl.Material 3. Sixteen terms indicating biological processes thatdirectly control telomere length are presented in Suppl. Material6, and the remaining fifteen terms are listed in Suppl.Material 7. There were 30 genes associated with the termsfrom the first group , with two of them (SIRT6 and TP53) previously not recognized as biologicallyinterpretable without comment on their functional significance inthe context of telomere length regulation). The analysis ofscientific papers showed that proteins encoded by both genescan function in the subtelomeric regions of chromosomes, which means theycould be indirectly involved in telomere length regulationThen, the genes associated with the second group ofGOTERM_BP_DIRECT terms identified at FDR< 0.05 were analyzed. Among them, 29 geneswere found that had no biological interpretation .This group of 29 genes included the above mentioned SIRT6and TP53, as well as BRCA1, SAMHD1, and BRCC3 associatedwith the maximum number of GO terms . Apparently, the genes from the list thusobtained may also be of interest in the context of telomerelength regulation.Telomere length-associated genesfound in other animal speciesGenome-wide search for telomere length-associated loci andgenes was carried out in three animal species: cattle (Bostaurus), sparrows (Passer domesticus), and nematodes (Caenorhabditiselegans).A GWA study to investigate the species Bos taurus wascarried out on 702 animals of the Holstein\u2013Friesian breed. The study of the DNA isolatedfrom the whole blood of cows sampled at birth showed sixtelomere length-associated polymorphic loci, and three additionalloci were identified when analyzing the DNA from bloodsamples at the first lactation. An analysis of the quantitativetrait loci (QTL) corresponding to the identified genetic variantsrevealed 14 candidate genes at birth and 9 at the first lactation. The authors wereunableto find any data on direct involvement of the identifiedgenes in processes associated with telomere length regulation.NUP93 nucleoporin gene encoding a nuclear pore componentwas considered a potential regulator, because it was shownearlier in yeast that nucleoporins facilitated silencing of genesin proximity of telomeric regions .The recently published results of GWA study in house sparrow (Passer domesticus) nestlings madeit possible to identify 22 candidate genes . According to the authors, the genes ofinterest in the context of telomere length regulation seem tobe as follows: (1) WNT9B encoding a protein component ofWnt/ \u03b2-catenin signaling pathway due to \u03b2-catenin involvementin Tert activation in embryonic stem cells of mice; (2) CDCA4,GH, and GHRHR regulating cell proliferation, apoptosis, andbody growth; (3) RHOF involved in cytoskeletal organization;(4) RNF34 (E3 ubiquitin-protein ligase RNF34) regulatingubiquitination; (5) AQP1 due to involvement of aquaporinprotein in transport of nitrogen oxide and active forms ofoxygen,which increases oxidative stress which can in turnaffect telomerase activity; (6) SCN4A, because its expressionin human stem cells correlates with telomere length.Our analysis showed that none of the candidate genes identifiedin cattle (23 genes) and house sparrows (22 genes) (see theTable) had orthologs among the 270 genes identified based onGWA studies in humans and presented in Suppl. Material3.The study in C. elegans produced9 candidate genes .One out of nine genes, pot-2, is orthologous to POT1 encodinga shelterin complex component in humans. The authorsassume that another gene ZK1127.4 may also be involved intelomere length regulation, because BCCIP encoded by anorthologous human gene interacts with BRCA2 involved inDNA replicationIn general, when comparing sets of candidate genes identifiedin humans and three other animal species, almost noorthologous genes are detected, which may be due to speciesspecificfeatures of telomere length regulation, some peculiaritiesof regulation at various ontogenetic stages, and differencesin sampled tissues or gender of the studied individuals.In the present paper, a compilation of telomere length-associatedgenes identified based on GWA studies and includingthe data on 270 human genes , as wellas 23, 22, and nine genes identified in cattle, house sparrow,and nematode (see the Table) is presented. The analysis offunctions of 52 human genes with functional interpretationavailable showed that telomerelength may be affected by variants of genes encoding: (1) thestructural components of telomerase; (2) the protein componentsof telomeric chromosome regions (shelterin complexand CST complex); (3) the proteins involved in telomerasebiogenesis and regulating its activity; (4) the proteins regulatingfunctional activity of shelterin subunits; (5) the proteinsinvolved in telomere replication and/or capping; (6) the proteinscontrolling the alternative telomere lengthening pathway;(7) DNA damage response and repair proteins; (8) RNA exosomecomponentsCandidate human genes identified by several researchgroups in population samples of different ethnic origin aredetermined: genes encoding telomerase components (TERCand TERT ) and STN1 encoding a subunit of CST complex. It seems that polymorphic loci that affect thefunctions of these genes can potentially be the most reliablepredisposition markers for telomere length-associateddiseases.Comparison of the data obtained from GWA studies inhumans with the results of similarexperiments obtained for other animal species confirmed and expanded the understandingof the complex polygenic nature of telomere lengthregulation. In addition, a pair of orthologous genes encodinga shelterin protein (POT1 in humans and pot-2 in C. elegans)was identified; this finding demonstrates the high biologicalsignificance of this gene in various species.Systematized data on genes and their functions may lay thefoundation for development of prognostic criteria for humanpathologies explicitly associated with telomere length. Inaddition, the data on biological processes affecting telomerelength and genes regulating these processes may be used formarker-assisted and genomic selection of the farm animalsaimed at increasing the duration of their productive lifetimeThe authors declare no conflict of interest.Aviv A., Shay J.W. Reflections on telomere dynamics and ageing-relateddiseases in humans. Philos. Trans. R. Soc. Lond. B Biol. Sci.2018;373(1741):20160436. DOI 10.1098/rstb.2016.0436.Bichet C., Bouwhuis S., Bauch C., Verhulst S., Becker P.H., Vedder O.Telomere length is repeatable, shortens with age and reproductivesuccess, and predicts remaining lifespan in a long-lived seabird.Mol. Ecol. 2020;29(2):429-441. DOI 10.1111/mec.15331.Bizarro J., Bhardwaj A., Smith S., Meier U.T. Nopp140-mediated concentrationof telomerase in Cajal bodies regulates telomere length.Mol. Biol. Cell. 2019;30(26):3136-3150. DOI 10.1091/mbc.E19-08-0429.Chen L., Roake C.M., Galati A., Bavasso F., Micheli E., Saggio I.,Schoeftner S., Cacchione S., Gatti M., Artandi S.E., Raffa G.D. Lossof human TGS1 hypermethylase promotes increased telomeraseRNA and telomere elongation. Cell Rep. 2020;30(5):1358-1372.e5.DOI 10.1016/j.celrep.2020.01.004.Chen L.Y., Redon S., Lingner J. The human CST complex is a terminatorof telomerase activity. Nature. 2012;488(7412):540-544. DOI10.1038/nature11269Chik H.Y.J., Sparks A.M., Schroeder J., Dugdale H.L. A meta-analysison the heritability of vertebrate telomere length. J. Evol. Biol.2022;35(10):1283-1295. DOI 10.1111/jeb.14071.Claussnitzer M., Dankel S.N., Kim K.-H., Quon G., Meuleman W.,Haugen C., Glunk V., Sousa I.S., Beaudry J.L., Puviindran V., AbdennurN.A., Liu J., Svensson P.-A., Hsu Y.-H., Drucker D.J., MellgrenG., Hui C.-Ch., Hauner H., Kellis M. FTO obesity variant circuitryand adipocyte browning in humans. N. Engl. J. Med. 2015;373:895-907. DOI 10.1056/NEJMoa1502214Codd V., Nelson C.P., Albrecht E., Mangino M., Deelen J., Buxton J.L.,Hottenga J.J., Fischer K., Esko T., Surakka I., \u2026 Boomsma D.I.,Jarvelin M.R., Slagboom P.E., Thompson J.R., Spector T.D., vander Harst P., Samani N.J. Identification of seven loci affecting meantelomere length and their association with disease. Nat. Genet. 2013;45(4):422-427. DOI 10.1038/ng.2528.Codd V., Wang Q., Allara E., Musicha C., Kaptoge S., Stoma S.,JiangT., Hamby S.E., Braund P.S., Bountziouka V., Budgeon C.A.,Denniff M., Swinfield C., Papakonstantinou M., Sheth S., NanusD.E., Warner S.C., Wang M., Khera A.V., Eales J., OuwehandW.H., Thompson J.R., Di Angelantonio E., Wood A.M., ButterworthA.S., Danesh J.N., Nelson C.P., Samani N.J. Polygenicbasis and biomedical consequences of telomere length variation.Nat. Genet. 2021;53(10):1425-1433. DOI 10.1038/s41588-021-00944-6.Cook D.E., Zdraljevic S., Tanny R.E., Seo B., Riccardi D.D., Noble L.M.,Rockman M.V., Alkema M.J., Braendle C., Kammenga J.E., Wang J.,Kruglyak L., F\u00e9lix M.A., Lee J., Andersen E.C. The genetic basis ofnatural variation in Caenorhabditis elegans telomere length. Genetics.2016;204(1):371-383. DOI 10.1534/genetics.116.191148Crocco P., De Rango F., Dato S., Rose G., Passarino G. Telomere lengthas a function of age at population level parallels human survivalcurves. Aging (Albany NY ). 2021;13(1):204-218. DOI 10.18632/aging.202498de Lange T. Shelterin-mediated telomere protection. Annu. Rev. Genet.2018;52:223-247. DOI 10.1146/annurev-genet-032918-021921.Diotti R., Loayza D. Shelterin complex and associated factors at humantelomeres. Nucleus. 2011;2(2):119-135. DOI 10.4161/nucl.2.2.15135.Dorajoo R., Chang X., Gurung R.L., Li Z., Wang L., Wang R., BeckmanK.B., Adams-Haduch J., M Y., Liu S., Meah W.Y., Sim K.S.,Lim S.C., Friedlander Y., Liu J., van Dam R.M., Yuan J.M.,Koh W.P., Khor C.C., Heng C.K. Loci for human leukocyte telomerelength in the Singaporean Chinese population and trans-ethnicgenetic studies. Nat. Commun. 2019;10(1):2491. DOI 10.1038/s41467-019-10443-2.Egan E.D., Collins K. Biogenesis of telomerase ribonucleoproteins.RNA. 2012;18(10):1747-1759. DOI 10.1261/rna.034629.112.Fan H.C., Chang F.W., Tsai J.D., Lin K.M., Chen C.M., Lin S.Z.,Liu C.A., Harn H.J. Telomeres and cancer. Life (Basel ). 2021;11(12):1405. DOI 10.3390/life11121405.Ilska-Warner J.J., Psifidi A., Seeker L.A., Wilbourn R.V., UnderwoodS.L., Fairlie J., Whitelaw B., Nussey D.H., Coffey M.P., BanosG. The genetic architecture of bovine telomere length in earlylife and association with animal fitness. Front. Genet. 2019;10:1048. DOI 10.3389/fgene.2019.01048.Jafri M.A., Ansari S.A., Alqahtani M.H., Shay J.W. Roles of telomeresand telomerase in cancer, and advances in telomerase-targetedtherapies. Genome Med. 2016;8(1):69. DOI 10.1186/s13073-016-0324-x.Joyce B.T., Zheng Y., Nannini D., Zhang Z., Liu L., Gao T., KocherginskyM., Murphy R., Yang H., Achenbach C.J., Roberts L.R., HoxhaM., Shen J., Vokonas P., Schwartz J., Baccarelli A., Hou L. DNAmethylation of telomere-related genes and cancer risk. Cancer Prev.Res. (Phila). 2018;11(8):511-522. DOI 10.1158/1940-6207.CAPR-17-0413.Kong C.M., Lee X.W., Wang X. Telomere shortening in humandiseases.FEBS J. 2013;280(14):3180-3193. DOI 10.1111/febs.12326Kroustallaki P., Lirussi L., Carracedo S., You P., Esbensen Q.Y.,G\u00f6tz A., Jobert L., Als\u00f8e L., S\u00e6trom P., Gagos S., Nilsen H. SMUG1promotes telomere maintenance through telomerase RNA processing.Cell Rep. 2019;28(7):1690-1702.e10. DOI 10.1016/j.celrep.2019.07.040.Li C., Stoma S., Lotta L.A., Warner S., Albrecht E., Allione A., Arp P.P.,Broer L., Buxton J.L., Da Silva Couto Alves A., \u2026 Butterworth A.S.,Danesh J., Samani N.J., Wareham N.J., Nelson C.P., Langenberg C.,Codd V. Genome-wide association analysis in humans links nucleotidemetabolism to leukocyte telomere length. Am. J. Hum. Genet.2020;106(3):389-404. DOI 10.1016/j.ajhg.2020.02.006.Mangino M., Christiansen L., Stone R., Hunt S.C., Horvath K., EisenbergD.T., Kimura M., Petersen I., Kark J.D., Herbig U., Reiner A.P.,Benetos A., Codd V., Nyholt D.R., Sinnreich R., Christensen K., NassarH., Hwang S.J., Levy D., Bataille V., Fitzpatrick A.L., Chen W.,Berenson G.S., Samani N.J., Martin N.G., Tishkoff S., Schork N.J.,Kyvik K.O., Dalg\u00e5rd C., Spector T.D., Aviv A. DCAF4, a novel geneassociated with leucocyte telomere length. J. Med. Genet. 2015;52(3):157-162. DOI 10.1136/jmedgenet-2014-102681Mangino M., Richards J.B., Soranzo N., Zhai G., Aviv A., Valdes A.M.,Samani N.J., Deloukas P., Spector T.D. A genome-wide associationstudy identifies a novel locus on chromosome 18q12.2 influencingwhite cell telomere length. J. Med. Genet. 2009;46(7):451-454. DOI10.1136/jmg.2008.064956Monaghan P., Ozanne S.E. Somatic growth and telomere dynamics invertebrates: relationships, mechanisms and consequences. Philos.Trans. R. Soc. Lond. B Biol. Sci. 2018;373(1741):20160446. DOI10.1098/rstb.2016.0446Nagpal N., Wang J., Zeng J., Lo E., Moon D.H., Luk K., Braun R.O.,Burroughs L.M., Keel S.B., Reilly C., Lindsley R.C., Wolfe S.A.,Tai A.K., Cahan P., Bauer D.E., Fong Y.W., Agarwal S. SmallmoleculePAPD5 inhibitors restore telomerase activity in patientstem cells. Cell Stem Cell. 2020;26(6):896-909.e8. DOI 10.1016/j.stem.2020.03.016Nersisyan L., Nikoghosyan M., Genome of the Netherlands consortium,Arakelyan A. WGS-based telomere length analysis in Dutchfamily trios implicates stronger maternal inheritance and a role forRRM1 gene. Sci. Rep. 2019;9(1):18758. DOI 10.1038/s41598-019-55109-7.Oh W., Ghim J., Lee E.W., Yang M.R., Kim E.T., Ahn J.H., Song J.PML-IV functions as a negative regulator of telomerase by interactingwith TERT. J. Cell Sci. 2009;122(Pt.15):2613-2622. DOI10.1242/jcs.048066Ohira T., Kojima H., Kuroda Y., Aoki S., Inaoka D., Osaki M., WanibuchiH., Okada F., Oshimura M., Kugoh H. PITX1 protein interactswith ZCCHC10 to regulate hTERT mRNA transcription. PLoS One.2019;14(8):e0217605. DOI 10.1371/journal.pone.0217605.Pepke M.L., Kvalnes T., Lundregan S., Boner W., Monaghan P., SaetherB.E., Jensen H., Ringsby T.H. Genetic architecture and heritabilityof early-life telomere length in a wild passerine. Mol. Ecol.2021. DOI 10.1111/mec.16288Podlevsky J.D., Bley C.J., Omana R.V., Qi X., Chen J.J. The telomerasedatabase. Nucleic Acids Res. 2008;36(Database issue):D339-D343.DOI 10.1093/nar/gkm700Potts P.R., Yu H. The SMC5/6 complex maintains telomere length inALT cancer cells through SUMOylation of telomere-binding proteins.Nat. Struct. Mol. Biol. 2007;14(7):581-590. DOI 10.1038/nsmb1259Saxena R., Bjonnes A., Prescott J., Dib P., Natt P., Lane J., Lerner M.,Cooper J.A., Ye Y., Li K.W., Maubaret C.G., Codd V., Brackett D.,Mirabello L., Kraft P., Dinney C.P., Stowell D., Peyton M., RalhanS., Wander G.S., Mehra N.K., Salpea K.D., Gu J., Wu X.,Mangino M., Hunter D.J., De Vivo I., Humphries S.E., Samani N.J.,Spector T.D., Savage S.A., Sanghera D.K. Genome-wide associationstudy identifies variants in casein kinase II (CSNK2A2) to beassociated with leukocyte telomere length in a Punjabi Sikh diabeticcohort. Circ. Cardiovasc. Genet. 2014;7(3):287-295. DOI 10.1161/CIRCGENETICS.113.000412.Schrumpfov\u00e1 P.P., Fajkus J. Composition and function of telomerase-Apolymerase associated with the origin of eukaryotes. Biomolecules.2020;10(10):1425. DOI 10.3390/biom10101425.Seeker L.A., Underwood S.L., Wilbourn R.V., Dorrens J., Froy H.,Holland R., Ilska J.J., Psifidi A., Bagnall A., Whitelaw B., CoffeyM., Banos G., Nussey D.H. Telomere attrition rates are associatedwith weather conditions and predict productive lifespan indairy cattle. Sci. Rep. 2021;11(1):5589. DOI 10.1038/s41598-021-84984-2.Sherman B.T., Hao M., Qiu J., Jiao X., Baseler M.W., Lane H.C.,Imamichi T., Chang W. DAVID: a web server for functional enrichmentanalysis and functional annotation of gene lists (2021 update).Nucleic Acids Res. 2022;50(W1):W216-221. DOI 10.1093/nar/gkac194.Snow B.E., Erdmann N., Cruickshank J., Goldman H., Gill R.M., RobinsonM.O., Harrington L. Functional conservation of the telomeraseprotein Est1p in humans. Curr. Biol. 2003;13(8):698-704.DOI 10.1016/s0960-9822(03)00210-0.Sobinoff A.P., Pickett H.A. Alternative lengthening of telomeres: DNArepair pathways converge. Trends Genet. 2017;33(12):921-932. DOI10.1016/j.tig.2017.09.003Sobinoff A.P., Pickett H.A. Mechanisms that drive telomere maintenanceand recombination in human cancers. Curr. Opin. Genet. Dev.2020;60:25-30. DOI 10.1016/j.gde.2020.02.006Stuparevi\u0107 I., Nova\u010di\u0107 A., Rahmouni A.R., Fernandez A., Lamb N.,Primig M. Regulation of the conserved 3\u2032-5\u2032 exoribonucleaseEXOSC10/Rrp6 during cell division, development and cancer.Biol. Rev. Camb. Philos. Soc. 2021;96(4):1092-1113. DOI 10.1111/brv.12693.Tennen R.I., Bua D.J., Wright W.E., Chua K.F. SIRT6 is required formaintenance of telomere position effect in human cells. Nat. Commun.2011;2:433. DOI 10.1038/ncomms1443.Tseng C.K., Wang H.F., Burns A.M., Schroeder M.R., Gaspari M.,Baumann P. Human telomerase RNA processing and quality control.Cell Rep. 2015;13(10):2232-2243. DOI 10.1016/j.celrep.2015.10.075Tutton S., Azzam G.A., Stong N., Vladimirova O., Wiedmer A., MonteithJ.A., Beishline K., Wang Z., Deng Z., Riethman H., McMahonS.B., Murphy M., Lieberman P.M. Subtelomeric p53 bindingprevents accumulation of DNA damage at human telomeres.EMBO J. 2016;35(2):193-207. DOI 10.15252/embj.201490880.Van de Vosse D.W., Wan Y., Lapetina D.L., Chen W.M., Chiang J.H.,Aitchison J.D., Wozniak R.W. A role for the nucleoporin Nup170p inchromatin structure and gene silencing. Cell. 2013;152(5):969-983.DOI 10.1016/j.cell.2013.01.049.Vera E., Bernardes de Jesus B., Foronda M., Flores J.M., Blasco M.A.The rate of increase of short telomeres predicts longevity in mammals.Cell Rep. 2012;2(4):732-737. DOI 10.1016/j.celrep.2012.08.023.Wilbourn R.V., Moatt J.P., Froy H., Walling C.A., Nussey D.H.,Boonekamp J.J. The relationship between telomere length and mortalityrisk in non-model vertebrate systems: a meta-analysis. Philos.Trans. R. Soc. Lond. B Biol. Sci. 2018;373(1741):20160447. DOI10.1098/rstb.2016.0447Wright W.E., Piatyszek M.A., Rainey W.E., Byrd W., Shay J.W. Telomeraseactivity in human germline and embryonic tissues and cells.Dev. Genet. 1996;18(2):173-179. DOI 10.1002/(SICI)1520-6408(1996)18:2<173::AID-DVG10>3.0.CO;2-3.Zeiger A.M., White M.J., Eng C., Oh S.S., Witonsky J., Goddard P.C.,Contreras M.G., Elhawary J.R., Hu D., Mak A.C.Y., Lee E.Y.,Keys K.L., Samedy L.A., Risse-Adams O., Maga\u00f1a J., HuntsmanS., Salazar S., Davis A., Meade K., Brigino-Buenaventura E.,LeNoir M.A., Farber H.J., Bibbins-Domingo K., Borrell L.N.,BurchardE.G. Genetic determinants of telomere length in AfricanAmerican youth. Sci. Rep. 2018;8(1):13265. DOI 10.1038/s41598-018-31238-3."} +{"text": "Citrobacter braakii strain GW-Imi-1b1 was isolated from a hospital wastewater sample in Greifswald, Germany. The genome comprises one chromosome (5.09\u2009Mb), one prophage (41.9\u2009kb), and 13 plasmids (2 to 140.9\u2009kb). The genome harbors 5,322 coding sequences, shows a high potential for genomic mobility, and includes genes encoding proteins for multiple drug resistances.The imipenem-resistant Citrobacter strains thrive in soil, water, and gut microbiota of humans and animals. They cause nosocomial infections and show various degrees of antibiotic resistance on Mueller-Hinton agar .sistance . CitrobaC. braakii GW-Imi-1b1 was extracted using the MasterPure complete DNA purification kit , from a strain that had been isolated by repeated streaking and regrowth in 10\u2009mL Mueller-Hinton broth (Carl Roth GmbH & Co.) at 37\u00b0C. Illumina paired-end sequencing libraries were prepared with the Nextera XT DNA sample preparation kit and sequenced using a MiSeq system and reagent kit v3 (2 \u00d7 300 cycles). Nanopore sequencing library preparation was performed with 1.5\u2009\u03bcg high-molecular-weight DNA, a ligation sequencing kit 1D (SQK-LSK109), and the native barcode expansion kit (EXP-NBD104). Sequencing was performed for 72 h using a MinION Mk1B system with a SpotON R9.4.1 flow cell and MinKNOW v22.05.5 and Guppy v6.2.1 (hac mode) software.The manufacturer\u2019s recommendations were followed unless otherwise stated. Genomic DNA of NC_001422) leftovers. Furthermore, long reads were treated with Porechop v0.2.4 (https://github.com/rrwick/Porechop) and adjusted to 100\u00d7 coverage with Filtlong v0.2.1 (https://github.com/rrwick/Filtlong), and chimeric reads were removed with unicycler_scrub of Unicycler v0.4.9 (C. braakii GW-Imi-1b1. Unicycler v0.5.0 (de novo hybrid assembly of plasmids (confirmed by BLAST) . Finallyy BLAST) and Polyy BLAST) , employihttps://figshare.com/articles/figure/Supplementary_Figure_1/22133567]), and 13 circular plasmids (0.2 to 140.9\u2009kb). The coverages of all genetic entities were calculated with Qualimap v2.2.2 (Citrobacter braakii ASM207534v1 (GenBank accession number GCF_002075345.1), with a FastANI . Genome analysis with Resfams revealed the presence of 27 genes involved in antibiotic resistance, including resistance to \u03b2-lactams, aminoglycosides, quinolones, macrolides, nitroimidazoles, streptomycin, and chloramphenicol and efflux pumps .The genome contains one circular chromosome (5.1 Mbp), one circular (pro)phage . The whole-genome project of Citrobacter braakii GW-Imi-1b1 has been deposited in GenBank under the accession numbers CP115723 (chromosome), CP115737 (phage), CP115724 (plasmid 1), CP115729 (plasmid 2), CP115730 (plasmid 3), CP115731 (plasmid 4), CP115732 (plasmid 5), CP115733 (plasmid 6), CP115734 (plasmid 7), CP115735 (plasmid 8), CP115736 (plasmid 9), CP115725 (plasmid 10), CP115726 (plasmid 11), CP115727 (plasmid 12), and CP115728 (plasmid 13), with BioProject accession number PRJNA524094 and SRA accession numbers SRR23033312 (Oxford Nanopore Technologies MinION reads) and SRR23033313 (Illumina MiSeq reads).The assembled genomic entities , nucleotide and amino acid sequences, and GenBank records are accessible via Figshare ("} +{"text": "Pseudomonas aeruginosa (PSA) is a common cause of acute pulmonary exacerbations in adult cystic fibrosis (CF) patients. In this setting, culture isolates are often multidrug resistant (MDR) or exhibit difficult-to-treat resistance (DTR) due to frequent antimicrobial exposure, resulting in the use of last-line or novel therapies using a collection of clinical PSA isolates recovered from adult CF respiratory specimens.herapies . Cefiderherapies \u20137. TheA total of 31 adult CF PSA isolates were selected from an internal repository . These rin vitro potency compared with I-R, C-T, and CZA (50/MIC90 of CFDC was 0.25/16 \u00b5g/mL, respectively. The MIC50/MIC90 of I-R, C-T, and CZA was 2/32, 1/128, and 2/128 \u00b5g/mL, respectively (50 compared with the other novel agents (CFDC MIC50/MIC90 of 1/128 \u00b5g/mL; 75% susceptible per CLSI; Overall, CFDC retained the greatest and CZA . The MICectively . Of notein vitro potency against PSA compared with C-T, CZA, and I-R. However, changes in target binding sites of PSA-derived AmpC \u03b2-lactamases may result in an increase in CFDC MICs (Antibiotic management of pulmonary exacerbations in the setting of CF is challenging as the etiologic agents often exhibit MDR. CFDC has enhanced activity against MDR PSA and is, therefore, an attractive option for intervention; albeit, CFDC resistance may occur , 13. TheFDC MICs . FurtherFDC MICs . Our stu"} +{"text": "Response to NACT was evaluated using CA125 response and chemotherapy response score (CRS). Compared with the non-responders, the responders displayed a larger proportion of tumors showing increase in the infiltration of CD20+ cells (P = 0.046) and in the M1/M2 ratio (P = 0.038) as well as fewer tumors showing increase in the infiltration of CD56bright cells (P = 0.041). No association was found between pre-NACT TIME and response to NACT. Density of pre-NACT CD8+ cells was positively associated with longer progression-free survival (PFS) (P = 0.011) and overall survival (OS) (P = 0.048). Post-NACT CD20+ and CD163+ macrophages (M2) infiltrates were associated with prolonged (P = 0.005) and shortened PFS (P = 0.021), respectively. Increase in the density of CD4+ T cells was predictive for longer PFS (P = 0.022) and OS (P = 0.023). In the multivariate analysis, high density of CD8+ cells pre-NACT (P = 0.042) were independently associated with improved OS.Little is known about the association between efficacy of neoadjuvant chemotherapy (NACT)/survival and the dynamic change of tumor immune environment (TIME) during treatment in epithelial ovarian cancer (EOC). This study investigated the TIME landscape of treatment-naive EOC tumors using multiplex immunofluorescence and associated the TIME before and after platinum-based NACT with treatment efficacy and prognosis in 33 patients with advanced EOC. NACT significantly increased the density of CD8 Ovarian cancer is the most lethal gynecologic malignancy . Epithel+ cytotoxic cells, and CD3+ T cells] or deleterious to ovarian cancer patients of treatment-na\u00efve tumor has allowed for identifying components of immune contexture that are beneficial . Serous carcinoma was the predominant histologic subtype , and most of the patients had FIGO stage III disease . Almost all the tumors were grade 3 . Approximately half of the patients had lymph node metastasis. The median CA125 level was 1632.0 U/mL at baseline. Seventy-six percent of patients received two cycles of NACT . CA125 response to 1 (57.6%) Table\u00a01.+ T cells, significantly increased . No significant difference was found in the density of other immune cell subsets, including CD3+, CD4+Foxp3+, CD4+, CD68+CD163- and PD-1+CD8+ . We also observed a significant increase in the infiltrates of PD-1+ cells (P = 0.048), PD-L1+CD68+ macrophages (P = 0.017), CD20+ B cells (P = 0.033), and CD56dim (P = 0.022) , PD-1+ cells (P = 0.011), PD-L1+CD68+ macrophages (P = 0.023) and PD-1+CD8+ cells (P = 0.035) in the stoma of CRS2 responders (+Foxp3+ Treg cells (P = 0.036) and PD-L1+CD68+ macrophages (P = 0.022) in the stroma and decreased M1/M2 ratio (P = 0.016) in the tumor of CRS1 non-responders (+ cells (P = 0.046) and in the M1/M2 ratio (P = 0.038) as well as fewer tumors showing increase in the infiltration of CD56bright cells (P = 0.041) and M2 macrophages in the tumor and PFS (P = 0.034) (Data not shown), and lower density of CD68+CD163+ M2 macrophages in the post-NACT tumor were found to predict better PFS and OS (log-rank P = 0.023) , and OS and tumoral CD8+ pre-NACT were independently associated with improved OS. The difference in PFS between pre-NACT CD8high and pre-NACT CD8low patients was marginally significant (P = 0.054) Table\u00a03.+ T cell, CD20+ B cells, and PD-L1+CD68+ macrophages. The biopsies pre-NACT from patients with good response to NACT had significantly increased infiltration of CD8+ T cells and CD20+ B cells compared with tumor specimens post-NACT. Infiltrates of CD8+ T cells pre-NACT, CD20+ B cells and CD163+ macrophages post-NACT, and marked change in CD4+ T cells during NACT are associated with prolonged survival.In the current study, we reported that the infiltration of immune cells in the tumor lesions pre-NACT and post-NACT was associated with response to NACT and long-term survival benefits. With mIF, we analyzed multiple immune cell subsets closely associated with cancer dissemination in a cohort of patients with paired pre-NACT and post-NACT specimens. We show that NACT altered the balance of immune cell subsets of T cells, B cells, and macrophages, showing significantly elevated density of CD8+ T cells, CD3+ T cells, CD20+ B cells, and PD-1+ cells were associated with prolonged and shortened PFS, respectively. There is evidence that a high M1:M2 ratio post-NACT is predictive of improved PFS and OS for the publication of any potentially identifiable images or data included in this article.GC: Acquisition of data, writing-review and editing. DH: Methodology, writing-review and editing. JL: Data curation, formal analysis, writing-review and editing. XZ: Data curation, formal analysis, writing-review and editing. ZZ: Data curation, formal analysis, writing-review and editing. BZ: Data curation, formal analysis, writing-review and editing. TB: Writing\u2013original draft, writing\u2013review and editing. LC: Conceptualization, resources, supervision, writing\u2013review and editing. SC: Conceptualization, resources, supervision, writing\u2013review and editing. SW: Resources, data curation, writing-review and editing. LZ: Conceptualization, resources, supervision, methodology, project administration, writing\u2013review and editing. All authors contributed to the article and approved the submitted version."} +{"text": "Correction: Arthritis Res Ther 25, 143 (2023)https://doi.org/10.1186/s13075-023-03129-0Following publication of the original article , the autThe sentence currently reads:17 studies were included , indicating that multiple sclerosis patients are more likely to suffer from periodontal diseases and TMD [7]. TMD and periodontal disease might be the first symptoms of several rheumatic diseases [8].The sentence should read:Unilateral mastication due to PD could induce pain and structural changes in the temporomandibular joint [7]. In addition to clinical observational studies, two symptoms often occur together in many diseases, such as rheumatic diseases and multiple sclerosis [10].Updated references:J Periodontal Implant Sci 2017, 47(4):211-218.7. Jeon HM, Ahn YW, Jeong SH, Ok SM, Choi J, Lee JY, Joo JY, Kwon EY: Pattern analysis of patients with temporomandibular disorders resulting from unilateral mastication due to chronic periodontitis. Journal of clinical medicine 2018, 8(1).8. Gualtierotti R, Marzano AV, Spadari F, Cugno M: Main Oral Manifestations in Immune-Mediated and Inflammatory Rheumatic Diseases. Reumatol Clin (Engl Ed) 2020, 16(4):262-271.9. Gonz\u00e1lez-Ch\u00e1vez SA, Pacheco-Tena C, Campos Torres RM, Qui\u00f1onez-Flores CM, Reyes-Cordero G, Caraveo Frescas TJ: Temporomandibular and Odontological Abnormalities in Patients with Rheumatoid Arthritis. Evidence-based dentistry 2021, 22(1):44-45.10. Al-Ansari A: Is there an association between multiple sclerosis and oral health? The original article has been"} +{"text": "Predictors of SOF/VEL/VOX failure were genotype 3, active HCC, baseline cirrhosis, and prior SOF/VEL. Baseline RAS mutation and ribavirin supplementation were not associated with higher SVR12. Treatment discontinuation because of drug-related adverse events was uncommon . In summary, SOF/VEL/VOX is efficacious and safe for retreatment in DAA-experienced CHC patients, even with RAS mutation. Our findings support SOF/VEL/VOX as a first-line rescue treatment for DAA-experienced CHC patients. About 5% of chronic hepatitis C (CHC) patients experienced treatment failure with direct-acting antiviral (DAA) treatment. The global data on the practice and treatment outcomes of Sofosbuvir/Velpatasvir/Voxilaprevir (SOF/VEL/VOX) in DAA-experienced CHC patients remains sparse. We performed a systematic review and meta-analysis to evaluate the efficacy and safety of SOF/VEL/VOX as a salvage treatment in DAA-experienced CHC patients. We searched five electronic databases from inception to 31 January 2023. The study outcomes were SVR12 and treatment-related adverse effects, with subgroup analysis performed based on genotype, cirrhosis, HCC, prior SOF/VEL exposure, and region. We identified and analyzed data from 24 studies (2877 DAA-experienced CHC patients); 17.2% had prior SOF/VEL exposure, 25% received ribavirin with SOF/VEL/VOX, and 42% had pre-treatment resistance-associated substitution (RAS) testing performed. Eastern Mediterranean had a higher pooled SVR12 than the America and Europe regions ( Chronic hepatitis C (CHC) infection affects 56.8 million people globally, with about 1.5 million new infections every year, resulting in 400,000 deaths each year . VirologTreatment options remain limited in DAA-experienced CHC patients who fail to achieve SVR12. Retreatment of CHC patients with DAA failure could be challenging because of the emergence of resistance-associated substitution (RAS). Current guidelines recommend Sofosbuvir/Velpatasvir/Voxilaprevir (SOF/VEL/VOX) as a salvage treatment for DAA-experienced CHC patients who failed to achieve SVR12 . SOF/VELThe global data on practice and treatment outcomes of SOF/VEL/VOX remained lacking, especially in regions such as Asia and Africa. Although some studies reported a lower SVR12 among CHC patients with liver cirrhosis or genotype 3, which is prevalent in south Asia ,10, suchWe followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline for data extraction and reporting . With thWe included all studies that met one of the following inclusion criteria, regardless of publication dates and publication status. Our inclusion criteria were as follows: (1) DAA-experienced, adult CHC patients (age > 18 years old) treated with 12 weeks of SOF/VEL/VOX, with or without Ribavirin, and (2) reported data on either SVR12 or adverse events. Our exclusion criteria were (1) paediatric CHC patients; (2) animal studies; (3) studies that did not report study outcomes; (4) case reports or case series with less than 10 patients; (5) reviews, editorials, or guidelines; and (6) clinical trials. Three authors independently performed the initial screening of the title and abstract identified in the primary search for eligibility. Any discrepancy in the article selection was resolved by discussion and consensus with the senior author (W.Y.J.). The data from each study were independently extracted using a standardized form. We contacted the corresponding author to verify any missing information. The data extracted included demographics of the study participants (age and genotype of hepatitis C virus), location, sample size, RAS testing at baseline, SVR12, concurrent use of ribavirin (RBV), and treatment-related adverse events requiring discontinuation of treatment.The outcomes studied were as follows: (1) SVR12 (both the intention-to-treat (ITT) and per-protocol (PP) analysis) and (2) frequency of adverse events leading to treatment discontinuation. The ITT analysis included all subjects treated with SOV/VEL/VOX, while the PP analysis only included SOF/VEL/VOX-treated CHC patients with available SVR12 results. Subgroup analysis was performed based on region, HCV genotype, baseline cirrhosis status, prior SOF/VEL exposure, hepatocellular carcinoma, RAS mutation, and concurrent use of ribavirin. p-value of less than 0.05 was considered to be statistically significant. Study heterogeneity was assessed by the 2I% statistics. We used Review Manager Software version 5.3 to perform our meta-analysis. The effect measures were estimated using the odds ratio (OR) for categorical outcomes and mean difference (MD) for continuous outcomes together with the respective 95% confidence interval (95%CI). The meta-analysis was performed using the random-effects model. A The quality of all included studies was independently assessed by three authors using the Risk Of Bias In Non-Randomized Studies of Interventions (ROBINS-I) tool (non-randomized studies) and the . Most studies had either a low risk [From an initial total of 522 citations identified using our search strategy, 92 full texts were reviewed. We excluded 68 citations for the following reasons: clinical trial (n = 41), treatment-na\u00efve CHC patients (n = 8), case report or study with less than 10 patients n = 17), and missing data (n = 2). Finally, a total of 24 studies were included for analysis . Most st, and mislow risk ,21,22,23low risk ,31,32,33A total of 2887 DAA-experienced CHC patients from 24 studies were included. All patients received 12 weeks of SOF/VEL/VOX, with or without ribavirin. The patient characteristics of the included studies are summarised in p = 0.0006), Western Pacific region (five studies: 94.7% (95%Cl: 91.3\u201397.1%), p = 0.019), and Europe region (nine studies: 95.8% (95%Cl: 94.5\u201396.7%), p = 0.04) (p < 0.001) and GT3 infection . The real-world studies had a lower pooled SVR12 than the clinical trials (87.7% (95%CI: 86.4\u201389.2%) vs. 98.2% (95%CI: 95.9\u201399.2%), p < 0.0001). The overall SVR12 for DAA-experienced CHC patients treated with SOF/VEL/VOX based on PP and ITT analysis was 95% (95%CI: 94.0\u201395.8%) and 88% (95%CI: 86.7\u201389.5%), respectively. The SVR12 in the Eastern Mediterranean region (two studies: 98.2% (95%Cl: 96.0\u201399.3%)) was significantly higher than the region of Americas , = 0.04) . The higI2 = 7%) and non-GT3 DAA-experienced CHC patients treated with SOF/VEL/VOX was 86.1% (95%CI: 82.3\u201389.3%) and 94.9% (95%CI: 93.4\u201396.1%), respectively. GT3 HCV infection was associated with a lower odds of SVR12 .I2 = 0%) (I2 = 3%) and 97.7% (95%CI: 95.5\u201399.0%), respectively. Liver cirrhosis was associated with a lower odds of SVR12 A. DecompI2 = 3%) B.I2 = 54%) and 91.7% (95%CI: 90.0\u201393.5%), respectively. Prior SOF/VEL exposure was associated with a lower odds of SVR12 A. I2 = 0%) and 92.8% (95%CI: 90.3\u201395.3%), respectively. Active HCC during SOF/VEL treatment was associated with a lower odds of SVR12 B.I2 = 34%) and 91.6% (95%CI: 85.1\u201398.1%), respectively. The odds of SVR12 were similar among DAA-experienced CHC patients receiving SOF/VEL/VOX, with or without baseline RAS testing .I2 = 55%) and 96.2% (95%CI: 94.0\u201398.5%), respectively. The odds of SVR12 were similar among DAA-experienced CHC patients receiving SOF/VEL/VOX, with or without ribavirin .From a total of 1283 DAA-experienced CHC patients received SOF/VEL/VOX, the pooled risk of severe adverse events that occurred during SOF/VEL/VOX treatment was 1.94% (95%CI: 1.2\u20132.8%). The types of serious adverse events are summarised in In this meta-analysis, we found that SOF/VEL/VOX is an efficacious and safe salvage therapy among DAA-experienced CHC patients. The pooled SVR12 was high and treatment discontinuation due to treatment-related SAE was uncommon. Predictors for a lower SVR12 rate by SOF/VEL/VOX were genotype 3, active HCC, baseline cirrhosis, decompensated cirrhosis, and prior SOF/VEL exposure. Meanwhile, the presence of baseline RAS mutation and addition of ribavirin to SOF/VEL/VOX was not associated with higher SVR12. The higher overall SVR12 among the Eastern Mediterranean studies is likely attributed to a lower proportion of patients with GT3 infection and liver cirrhosis. SOF/VEL/VOX, being a protease-inhibitor based DAA, was discouraged in patients with decompensated cirrhosis because of potential toxicity from delayed drug clearance. Among 34 decompensated CHC patients treated with SOF/VEL/VOX in five different studies ,31,32,33Current EASL guidelines recommend the use of RBV with SOF/VEL/VOX in patients with a higher risk of treatment failure; however, the benefits of routine addition of RBV remain unclear . We founThis meta-analysis provides a comprehensive global perspective on the effectiveness and safety of SOF/VEL/VOX among DAA-experienced CHC patients. Prior to this, information on practice and treatment outcomes of SOF/VEL/VOX use among Asian and African population was limited. We acknowledge that there are limitations when interpreting our findings. Most studies did not report the compliance and potential drug interaction among patients receiving SOF/VEL/VOX. The number of patients within subgroups of decompensated cirrhosis was small because the current guidelines discourage the use of SOF/VEL/VOX in these patients. Nevertheless, the results of this meta-analysis provide important data to support the recommendation of using SOF/VEL/VOX as a first-line option among DAA-experienced CHC patients and could be considered level 1 evidence. To conclude, SOF/VEL/VOX is a well-tolerated and highly effective rescue therapy among DAA-experienced CHC patients who failed to achieve SVR12. Predictors of treatment failure include GT3, liver cirrhosis, and active HCC. Safety data of SOF/VEL/VOX among decompensated cirrhosis patients should be investigated in further studies."} +{"text": "Cryptosporidium spp. are important zoonotic agents of bovine diarrhea. However, little is known about microbiota and short-chain fatty acids (SCFAs) changes in yaks infected with Cryptosporidium spp. Therefore, we performed 16S rRNA sequencing and detected the concentrations of SCFAs in Cryptosporidium-infected yaks. Results showed that over 80,000 raw and 70,000 filtered sequences were prevalent in yak samples. Shannon (p<0.01) and Simpson (p<0.01) were both significantly higher in Cryptosporidium-infected yaks. A total of 1072 amplicon sequence variants were shared in healthy and infected yaks. There were 11 phyla and 58 genera that differ significantly between the two yak groups. A total of 235 enzymes with a significant difference in abundance (p<0.001) were found between healthy and infected yaks. KEGG L3 analysis discovered that the abundance of 43 pathways was significantly higher, while 49 pathways were significantly lower in Cryptosporidium-infected yaks. The concentration of acetic acid (p<0.05), propionic acid (p<0.05), isobutyric acid (p<0.05), butyric acid (p<0.05), and isovaleric acid was noticeably lower in infected yaks, respectively. The findings of the study revealed that Cryptosporidium infection causes gut dysbiosis and results in a significant drop in the SCFAs concentrations in yaks with severe diarrhea, which may give new insights regarding the prevention and treatment of diarrhea in livestock.Diarrhea is a severe bovine disease, globally prevalent in farm animals with a decrease in milk production and a low fertility rate. The long-haired ruminant yak is a plateau bovine species living in the 3000-5000\u00a0m high-altitude regions and is mostly found on the Qinghai Tibet plateau . DiarrheEscherichia coli, Salmonella spp., and Cryptosporidium spp. have been commonly observed in infected cattle with equal number of negative samples (n=4) were sequenced and divided into infected (INF) and healthy (H) groups, respectively.Fecal samples (n=40) were collected from free-ranged yaks in Xining, Qinghai and examined for sted PCR and posiThe extraction of total genomic DNA was performed by utilizing a commercial TIANamp Stool DNA Kit (Tiangen Biotech (Beijing) Co., Ltd, China) according to the product\u2019s specifications. Fecal DNA concentration, purification, and quality examination were performed through NanoDrop 2000 UV-Vis spectrophotometer and 1.2% agarose gel electrophoresis, respectively. Then the hypervariable regions of bacterial 16S rRNA gene (V3-V4) were amplified using primers 338F and 806R as described in a previous study . All PCR\u00ae OnePot II DNA Library Prep Kit for Illumina\u00ae according to the product\u2019s instructions, and sequenced through the Illumina NovaSeq platform . Quality control of sequencing data was performed by employing QIIME2 (https://docs.qiime2.org/2019.1/) to generate amplicon sequence variant (ASV) (p<0.05 and log2 (FoldChange) > 2), clustering heatmap (with Z-score > 0.5 or < -0.5) and evolutionary tree (p<0.05) methods to reveal differences in bacterial abundance among yak samples and taxont (ASV) . Analysi samples . Microbi samples , and parpost-hoc test to measure the individual differences in microbial function between the yak groups with a p<0.05 as statistically significant.The potential KEGG Ortholog (KO) functional profiles of yak microbiota was predicted with PICRUSt by annotvia t-test.The concentrations of SCFAs in fecal samples were detected by employing GC-MS , and theP values < 0.05 were considered as statistically significant.The differences between different yak groups were calculated by the chi-square test piloting IBM SPSS Statistics (SPSS 22.0). p<0.01) and Simpson (p<0.01) were both significantly higher in group INF than in group H , Proteobacteria (8.97%), and Actinobacteria (8.72%) in group H, while Firmicutes (56.38%) and Bacteroidetes (29.83%) were the main phyla in group INF (Clostridia (51.13%) and Bacilli (17.28%) were the primary classes in healthy yaks, while Clostridia (51.13%) and Bacteroidia (29.83%) were the major classes in infected yaks , Lactobacillales (8.20%), and Bacillales (8.10%) were the primary orders in healthy yaks, while Clostridiales (51.04%) and Bacteroides (29.83%) were the main orders in infected yaks (Ruminococcaceae and Lachnospiraceae in groups H and INF (Pseudomonadaceae Pseudomonas (6.13%), and Lactobacillus (6.00%) were the dominating genera in healthy yaks, while unclassified (69.25%), Prevotellaceae Prevotella (5.13%) and Arthrobacter (2.45%) were the main genera in infected yaks (Veronii (6.11%), and Alactolyticus (1.66%), while unclassified (95.15%), Flavefaciens (1.50%) and Veronii (1.12%) were the main bacteria in group INF and evolutionary tree (top 50 abundance) with heat map analysis were plotted. The results revealed that at the order level, infected yaks showed an abundance of Bacteroidia and Deltaproteobacteria, while healthy animals showed abundance of Bacilli, Erysipelotrichi, Betaproteobacteria, Alphaproteobacteria, and Nitriliruptoria as expressed in the clustering heatmap. The evolutionary tree also showed an obvious abundance difference in Betaproteobacteria, Fibrobacteria, SJA_176, 4C0d_2, Nitriliruptoria, Clostridia, and Bacilli between groups H and INF , Bacteroidetes (p<0.0001), Armatimonadetes (p<0.0001), Fibrobacteres (p<0.01), and Synergistetes (p<0.01) were visibly higher in infected yaks, while Cyanobacteria (p<0.0001), Proteobacteria (p<0.0001), Armatimonadetes (p<0.0001), Euryarchaeota (p<0.0001), Actinobacteria (p<0.01), Firmicutes (p<0.01), and Elusimicrobia (p<0.05) were significantly lower (p<0.0001), Prevotellaceae_Prevotella (p<0.0001), CF231 (p<0.0001), L7A_E11 (p<0.0001), BF311 (p<0.0001), Desulfovibrio (p<0.0001), Succiniclasticum (p<0.0001), Desemzia (p<0.0001), Anaerovorax (p<0.0001), Pseudobutyrivibrio (p<0.0001), Acinetobacter (p<0.0001), Fibrobacter (p<0.0001), Ruminococcaceae_Ruminococcus (p<0.0001), Anaerorhabdus (p<0.0001), Treponema (p<0.0001), Selenomonas (p<0.001), Clostridium (p<0.001), Shuttleworthia (p<0.001), Dehalobacterium (p<0.001), TG5 (p<0.01), unclassified (p<0.01), Anaerostipes (p<0.01), Syntrophomonas (p<0.01), Brachymonas (p<0.01), Pyramidobacter (p<0.01), SHD_231 (p<0.05), Butyrivibrio (p<0.05), Desulfobulbus (p<0.05), RFN20 (p<0.05), and Anaerofustis (p<0.05) were significantly higher in infected yaks, while Turicibacter (p<0.0001), Lactobacillus (p<0.0001), Sporosarcina (p<0.0001), Ralstonia (p<0.0001), Akkermansia (p<0.001), Streptococcus (p<0.001), Methylobacterium (p<0.01), Adlercreutzia (p<0.01), Faecalibacterium (p<0.01), Roseburia (p<0.01), Paenibacillus (p<0.01), Methanosphaera (p<0.01), Pseudomonadaceae_Pseudomonas (p<0.01), Peptostreptococcaceae_Clostridium (p<0.01), Slackia (p<0.01), Cupriavidus (p<0.01), Halomonas (p<0.01), Gemmiger (p<0.01), Dietzia (p<0.01), Blautia (p<0.05), Agrobacterium (p<0.05), Nesterenkonia (p<0.05), Sanguibacter (p<0.05), Phascolarctobacterium (p<0.05), Actinomycetospora (p<0.05), Bifidobacterium (p<0.05), SMB53 (p<0.05), and Dorea (p<0.05) were significantly lower in infected animals were found between healthy and infected yaks, with 119 higher and 116 lower abundance enzymes in INF yaks , propionic acid (p<0.05), isobutyric acid (p<0.05), butyric acid (p<0.05) and isovaleric acid was significantly lower in infected yaks, respectively, while there was no significant difference of valeric acid and caproic acid between H and INF groups and Simpson (p<0.01) can be found below: The animal study was reviewed and approved by ethics committee of Nanjing Agricultural University.KL and QW, research idea and methodology. HD, XC, XZ, and CZ, reagents, materials, and analysis tools. KL, writing-original draft and preparation. KM, MF-E-A, ZB, QW, JZ, SN, and KL, writing-review and editing. KL, JZ, and QW, visualization and supervision. All authors contributed to the article and approved the submitted version."} +{"text": "L265P and MYD88other.This study aims to investigate the clinical and molecular differences between diffuse large B-cell lymphoma (DLBCL) patients with MYD88L265P and MYD88other were investigated.DLBCL patients with MYD88 variations were collected from the Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College (CHCAMS), and Suzhou Municipal Hospital from February 6th, 2007 to May 20th, 2022. Clinicopathological parameters and treatment outcomes between MYD88L265P, while 54 were MYD88other. MYD88L265P was more common in non-GCB subtype than MYD88other . Besides, MYD88L265P was significantly related to higher proportion of testicle/ central nervous system involvement , PIM1 mutation , and PIM1 hypermutation , compared with MYD88other. Compared with MYD88L265P, MYD88other were more likely to have higher percentage of advanced stage , extranodal site\u2009\u2265\u20092 , elevated LDH , positive CD10 expression , BCL-6 translocation , and NOTCH pathway gene alteration . In non-GCB DLBCL subtype, patients with MYD88other were significantly associated with worse progression free survival (PFS) than those with MYD88L265P when treated initially with R-CHOP/R-CHOP-like regimen (P\u2009=\u20090.010).A total of 132 patients with MYD88 variations from a cohort of 475 DLBCL patients were included, among which, 78 were MYD88L265P and MYD88other are likely to be two subgroups with different clinical and molecular characteristics. The survival of patients with MYD88other is not superior than those with MYD88L265P, even poorer when focusing on the non-GCB subtype.The findings of this study indicate that DLBCL patients with MYD88The online version contains supplementary material available at 10.1007/s00432-023-04714-1. A total of 132 patients with MYD88 variations were included for analysis. The inclusion criteria were as follows: (1) patients were histologically diagnosed with DLBCL based on the World Health Organization classification of Tumors of Hematopoietic and Lymphoid Tissue (2008) performance status (PS), number of extranodal involvement sites, lactate dehydrogenase (LDH) level, International Prognostic Index (IPI) score, bulky disease, B symptoms, primary site, testicle/central nervous system (CNS) involvement, relapse, bone marrow/peripheral blood involvement, cell of origin (COO) type, first-line therapy, protein expression of CD5, CD10, CD20, BCL-2, BCL-6, c-MYC, MUM-1, Ki-67, and PD-L1, genetic alteration of CD79, TP53, BCL-2, BCL-6, c-MYC, PIM1, SGK1, cell cycle-related genes , NOTCH pathway-related genes , JAK-STAT pathway-related genes , PI3K pathway-related genes , immune-related genes , epigenetics-related genes , RAS pathway-related genes . Any gene occurred alteration in the pathway will be defined as \u201cpathway gene alteration\u201d.Formalin-fixed paraffin-embedded (FFPE) tissues were obtained from included patients. The protein expression of CD5, CD10, CD20, BCL-2, BCL-6, c-MYC, MUM-1, and Ki-67 were evaluated by immunohistochemistry (IHC) using associated antibodies . The Programmed death-ligand 1 (PD-L1) expression was detected using the 22C3 anti-PD-L1 rabbit monoclonal antibody . The COO classification was confirmed according to the Hans algorithm was performed on three-micrometer-thick FFPE tumor tissues using Vysis LSI CMYC/BCL2/BCL6 Dual Color Break Apart Rearrangement Probe according to the manufacturer\u2019s instructions. Assessment of FISH signals was performed using Zeiss Axio Imager M2 epifluorescence microscope . Fifty tumor cells were counted, and the percentage of tumor cells with split-signal over 15% indicated the translocation of c-MYC, BCL-2, or BCL-6.Genomic DNA was extracted from the collected FFPE DLBCL tissues using the QIAamp DNA FFPE tissue kit . DNA concentration was quantified using Qubit dsDNA HS Assay Kit . DNA fragmentation was conducted using Covaris S2 Ultrasonicator . Fragments of 200\u2013250\u00a0bp were selected by AMPure beads . End repair, phosphorylation, adaptor ligation, hybridization with capture-probe baits, hybrid selection with magnetic beads, and polymerase chain-reaction amplification were subsequently processed. Two capture panels were adopted, one consisted of 112 commonly altered genes in lymphoma and hematologic malignancies, the other covering 413 frequently mutated genes in DLBCL. There were 101 overlapping genes between the two panels. Capture-based targeted sequencing was performed on a Next Seq500 Sequencer with pair-end reads at Geneplus-Beijing or Burning Rock Biotech . Detailed sequencing procedure was performed as our previous study described .Chi-squared test or Fisher\u2019s exact test when appropriated was adopted for the comparisons between categorical variables. Kaplan\u2013Meier survival curve and log-rank test were performed for comparing the PFS and OS. L265P, while 41% (54/132) were MYD88other. Among patients with MYD88other, the p.S219C (14/54), p.L273P (10/54), and p.S243N (6/54) were the top three frequently occurred mutations . Among the patients with MYD88 variation, 59% (78/132) occurred MYD88L265P and MYD88other variants . A total of 21 patients eventually occurred death. No statistically significance was observed in PFS and OS between MYD88L265Pand MYD88other , which is consistent with previous reports domain, which is the same domain as MYD88L265P resides. As regards the ability to activate NF-\u03baB, MYD88wild\u2212type presents modest activity, MYD88L265P has strong activity, as does MYD88M232T and MYD88S243N, while MYD88S222R and MYD88T294P exert intermediate effect. Their results suggested MYD88other can contribute to the constitutive NF-\u03baB activation in ABC DLBCL as with MYD88L265P and NFKB2/p52 Below is the link to the electronic supplementary material."} +{"text": "R. Soc. Open Sci.10: 230437 (Published online 6 September 2023). (https://doi.org/10.1098/rsos.230437)et al. [Corrigendum to the last five papers in the reference list of Bandeli et al. : referenWith Veasey 2020 re-inserted (and two other references swapped in position) the correct numbering for the last few references (now [101\u2013105]) is below:Panthera tigris altaica) as a model species. Animals10, 1536. (doi:10.3390/ani10091536)101. Veasey JS. 2020 Can zoos ever be big enough for large wild animals? A review using an Expert Panel Assessment of the psychological priorities of the Amur tiger 102. Kirchgessner ML, Sewall BJ. 2015 The impact of environmental, social, and animal factors on visitor stay times at big cat exhibits. Behavioural Brain Research33, 229\u2013240. (doi:10.1016/S0166-4328(89)80118-4)103. Cahusac PM, Miyashita Y, Rolls ET. 1989 Responses of hippocampal formation neurons in the monkey related to delayed spatial response and object-place memory tasks. et al. 2017 Suite of simple metrics reveals common movement syndromes across vertebrate taxa. Movement Ecology5, 12. (doi:10.1186/s40462-017-0104-2)104. Abrahms B Scientific Reports6, 36361. (doi:10.1038/srep36361)105. Tidi\u00e8re M, Gaillard JM, Berger V, M\u00fcller DW, Bingaman Lackey L, Gimenez O, Clauss M, Lema\u00eetre JF. 2016 Comparative analyses of longevity and senescence reveal variable survival benefits of living in zoos across mammals. In the text, this means that in the final two paragraphs of the Discussion, reference [101] should be [103], reference [103] should be [104], and reference [104] should be [105].This has been corrected on the publisher's website."} +{"text": "The signal pathway of actin remodeling, including LIM-kinase 1 (LIMK1) and its substrate cofilin, regulates multiple processes in neurons of vertebrates and invertebrates. Drosophila melanogaster is widely used as a model object for studying mechanisms of memory formation, storage, retrieval and forgetting. Previously, active forgetting in Drosophila was investigated in the standard Pavlovian olfactory conditioning paradigm. The role of specific dopaminergic neurons (DAN) and components of the actin remodeling pathway in different forms of forgetting was shown. In our research, we investigated the role of LIMK1 in Drosophila memory and forgetting in the conditioned courtship suppression paradigm (CCSP). In the Drosophila brain, LIMK1 and p-cofilin levels appeared to be low in specific neuropil structures, including the mushroom body (MB) lobes and the central complex. At the same time, LIMK1 was observed in cell bodies, such as DAN clusters regulating memory formation in CCSP. We applied GAL4 \u00d7 UAS binary system to induce limk1 RNA interference in different types of neurons. The hybrid strain with limk1 interference in MB lobes and glia showed an increase in 3-h short-term memory (STM), without significant effects on long-term memory. limk1 interference in cholinergic neurons (CHN) impaired STM, while its interference in DAN and serotoninergic neurons (SRN) also dramatically impaired the flies\u2019 learning ability. By contrast, limk1 interference in fruitless neurons (FRN) resulted in increased 15\u201360 min STM, indicating a possible LIMK1 role in active forgetting. Males with limk1 interference in CHN and FRN also showed the opposite trends of courtship song parameters changes. Thus, LIMK1 effects on the Drosophila male memory and courtship song appeared to depend on the neuronal type or brain structure. Memory formation and forgetting serve as the basis of behavioralplasticity. Whereas memory is a specific process ofinformation acquisition, storage and retrieval by the nervoussystem, active forgetting is defined as \u201ca mechanism or seriesof mechanisms to remove memories that become unused\u201d. Associative memory formation andactive forgetting occur in both mammals and invertebrates,including Drosophila melanogaster , whichis a well-known object of classical genetics. Having a shortlife cycle and relatively simple nervous system, the fruit flymakes it easy to perform genetic analysis of the molecularbasis of behavioral and cognitive processes.There are several experimental techniques to form associativememory in Drosophila, including short-term memory(STM) and protein synthesis-dependent long-term me-mory(LTM). The most widely used technique is classical Pavlovianlearning with negative electroshock reinforcement,or olfactory aversive learning (OAVL), which revealed genesresponsible for different types of memory .More natural is conditioned courtship suppression paradigm(CCSP) .GAL4 \u00d7 UAS binary expression system is usedto study the effects of specific genes on memory processes.The fine neural organization of the mushroom bodies (MB),a principle structure responsible for associative olfactorylearning in Drosophila, was evaluated in detail. The MB outputneurons (MBON) are the main effectors of MB, whereasspecific clusters of dopaminergic neurons (DAN) regulate theactivity of MB \u2013 MBON synaptic contacts . Among them are aSP13 DAN of the protocerebralanterior medial cluster (PAM), which innervate \u03b35 area ofMB, playing a crucial role in CCSP learning and memory.The molecular and neural mechanisms of active forgettingimplicate the activity of DAN and Rac1-dependent signalpathways . Small GTPases of the Rho family,including Rho and Rac, regulate neuronal actin polymerizationduring the Drosophila nervous system development. Rho viaits effector ROCK or Rac/Cdc42 via its effector Pak activateLIM-kinase 1 (LIMK1), which phosphorylates Drosophilacofilin (twinstar) protein, blocking its actin-depolymerizationactivity and inhibiting axon growth. Rac also acts through Pakindependentpathway to antagonize LIMK1 and promote axongrowth . In addition to its role in neurogenesis,Rac is crucial for both interference-induced and passiveforgetting in OAVL paradigm. PAK/LIMK1/cofilin pathwayprobably acts downstream Rac1 . Forgettingspecific types of memory depends on different signal proteins.Forgetting in OAVL paradigm is caused by several DANof the protocerebral posterior lateral 1 (PPL1) cluster, whichinnervates some MB structures, such as pedunculus, lowerand upper stalk. Memory acquisition and forgetting are regulatedby different dopamine receptors, dDA1 and DAMBrespectively . Coincidence of conditionedand unconditioned stimuli creates a memory trace in MBON-\u03b32\u03b1\u02b91, probably inhibiting the MB > MBON-\u03b32\u03b1\u02b91 synapses.The unconditioned stimulus alone activates DAN-\u03b32\u03b1\u02b91,which in turn disinhibit MB > MBON-\u03b32\u03b1\u02b91 synapses andcause forgetting . DAN that innervate theMB \u03b1\u03b1\u02b9 tip induce the interference-based forgetting throughthe scaffold protein Scribble, binding together Rac1, PAK3and cofilin .Whereas multiple data prove the importance of DAN andactin-remodeling signal pathway for forgetting in OAVL paradigm,there is virtually no data for molecular mechanisms ofmemory decay in CCSP. Effects of LIMK1-dependent signalcascade on CCSP learning and memory were firstly shown forthe temperature-sensitive mutant agn ts3, with LIMK1 increasein the adult brain compared to the wild type Canton-S (CS).Temperature rise leads to a decrease in agn ts3 LIMK1 level,simultaneously restoring its learning ability and 3 h memory,which are drastically impaired in the norm . agn ts3 has multiple polymorphisms within and nearlimk1 gene, as well as a changed profile of microRNA expression,and can serve as a model object for Williams syndrome. Thetemporal profile of STM learning index (LI) was assayedin CCSP for agn ts3, as well as for the wild-type strains withlimk1 polymorphisms, CS and Oregon R. Only CS was able tolearn and store memory up to 24 h .The behavioral effects of LIMK1 changes in agn ts3 do notgive information about specific cell types, where LIMK1 canbe involved in learning and memory. In this study, we performedthe analysis of memory decay for several DrosophilaGAL4 \u00d7 UAS strains with neuronal type-specific limk1 RNAinterference. LIMK1 distribution in the Drosophila brainstructures was studied in detail using confocal microscopy. Theeffect of limk1 interference on fly memory ability dependedon both neural type and memory form. LIMK1 also appearedto be involved in regulation of male courtship song: limk1interference in different neuronal types specifically affectedsome song parameters.Drosophila strains. Fly strains were provided by the ResearchCenter \u201cBiocollection of Pavlov Institute of Physiology RASfor the study of integrative mechanisms of the nervous andvisceral systems\u201d. The strain numbers (#) are given in accordancewith the Research Center and Bloomington DrosophilaStock Center, USA . The following strainswere used:1. \u0421anton-S (\u0421S) \u2013 the wild-type strain with limk1 polymorphisms.2. agn ts3 \u2013 temperature-sensitive mutation on CS geneticbackgroundwith limk1 polymorphisms, characterized bylearning and memory defects.3. Strains expressing GAL4 in specific neuronal types:#6794: w[*]; P{w[+mC]=nrv2-GAL4.S}8 P{w[+mC]=UAS-GFP.S65T}eg[T10]. GAL4 and green fluorescentprotein (GFP) are expressed in nervous system under Nrv2regulatory element;#6793: w[*]; P{w[+mC]=ChAT-GAL4.7.4}19BP{w[+mC]=UAS-GFP.S65T}Myo31DF[T2]. GAL4 andGFP are expressed in cholinergic neurons (CHN) underChAT and VAChT regulatory elements;#7009: w[1118]; P{w[+mC]=Ddc-GAL4.L}Lmpt[4.36].GAL4 is expressed in dopaminergic (DAN) and serotoninergic(SRN) neurons;#30027: w[1118]; P{w[+mW.hs]=GawB}fru[NP0021].GAL4 is expressed in fruitless neurons regulating matingbehavior.4. Act-GAL4: w[1118]; P{w[+mC]=} 25FO1/CyO, y[+];Canton-S background. GAL4 is expressed in the wholebody under actin promoter.5. Strains with UAS-dependent limk1 suppression:#26294: y[1] v[1]; P{y[+t7.7] v[+t1.8]=TRiP.JF02063}attP2. The strain expresses interfering RNA against limk1(RNAi) under UAS .#36303: y[1] v[1]; P{y[+t7.7]=CaryP}attP2. The controlstrain with genetic background identic to that for #26294,but lacking RNAi (limk1\u201c+\u201d).6. Strains with GFP gene regulated by UAS:#32186: w[*]; P{y[+t7.7] w[+mC]=10XUAS-IVS-mCD8::GFP}attP40.#32202: w[*]; P{y[+t7.7] w[+mC]=10XUAS-IVS-GFPWPRE}attP2.To induce limk1 RNA interference in specific neuronaltypes, a strain carrying GAL4 activator expressed under tissue-specific promoter was crossed to UAS strain #26294. The\u0441ross product of a GAL4 strain and #36303 strain served asa control.Flies were raised on the standard yeast\u2013raisin medium at25 \u00b1 0.5 \u00b0C and a 12:12 daily illumination cycle. For behavioraltests, experimental males were collected without anesthesiaand kept individually. 5\u20136-day-old males were used in experiments.Females (CS) were collected as virgins and broughttogether with CS males for fertilization in CCSP one daybefore experiment.Antibodies. Primary antibodies: Rat anti-LIMK1 multi-specificmonoclonal ; mouse anti-Drosophila cysteine string protein (CSP);rabbit anti-Drosophila tyrosine hydroxylase (TH) ; rabbit anti-GFP .Secondary antibodies: Goat anti-mouse Alexa Fluor 488, donkey-anti-rat Alexa Fluor 594, goat anti-rabbit AlexaFluor 633 .RNA extraction and RT-PCR analysis of limk1 expression.The level of limk1 expression was assayed usingsemi-quantitative PCR in complex with reverse transcription(RT-PCR). Flies were anesthetized by freezing. 10 male fliesor 70 male heads were homogenized in 300 \u03bcl TRI reagent. Total RNA was extracted from homogenatesaccording to the manufacturer\u2019s protocol. The quality ofRNA was checked by 1.5 % agarose gel electrophoresis. 1 \u03bcgRNA was reverse-transcribed by MMLV reverse transcriptase according to the manufacturers\u2019 protocol,using random hexamer primers and RNAse inhibitor . Semi-quantitative PCR was performed on a StepOnePlus using qPCRmixHSSYBR+LowROX containing direct andreverse primers (0.5 mM each). Baseline and cycle thresholdvalues were determined by automatic analysis using StepOnesoftware v2.3 . rpl32 transcriptwas used as an internal control. The predesigned limk1 primers were used to bind all five limk1 cDNA isoforms,both premature and mature forms, as primers do notspan the exon-intron borders. The relative limk1 transcriptlevel was calculated using the comparative \u0394\u0394Ct method. Thenumber of biological replicates (independent RNA extractionswith reverse transcription) was 3\u20135, the number of technicalreplicates was 3.The primer sequences were the following:rpl32:Forward: 5\u2032-TATGCTAAGCTGTCGCACAAATGGC-3\u2032Reverse: 5\u2032-GTTCTGCATGAGCAGGACCTCCA-3\u2032limk1:Forward: 5\u2032-GTGAACGGCACACCAGTTAGT-3\u2032Reverse: 5\u2032-ACTTGCACCGGATCATGCTC-3\u2032PCR parameters:1. 1 cycle: 95 \u00b0\u0421 \u2013 5 min.2. 45 cycles. 95 \u00b0\u0421 \u2013 20 s, 60 \u00b0\u0421 \u2013 20 s, 72 \u00b0\u0421 \u2013 20 s, 77 \u00b0\u0421 \u201315 s (detection).3. Melting curve: 95 \u00b0\u0421 \u2013 15 s, 60 \u00b0\u0421 \u2013 1 min, 60\u201395 \u00b0\u0421.Immunofluorescent staining of Drosophila brains.5\u20136-day-old imago males were anesthetized by freezing. Thebrains were prepared in PBS buffer (pH 7.5) using needlesharptweezers , fixed in 4 % paraformaldehydein PBS for 1 h at RT and stained according to , without a freezing stage. Antibodies were dilutedin PBT as 1:200, foranti-CSP \u2013 1:20. Previously, for better staining of brains, weincreased the time of incubation with primary antibodies upto 5 days . Here, the incubation wasperformed at 4 \u00b0\u0421 for 3 days (with primary antibodies) orovernight (with secondary antibodies). Brains were mountedwith Vectashield mounting medium containing DAPI .Protein distribution analysis in the brain by confocalmicroscopy. Brains were scanned frontally using laser scanningconfocal microscopy .Scanning was performed using X63 objective at differentdepths (z-step 2 \u03bcm). Images were analyzed using Fiji software.The brain structures were visually mapped using theDrosophila brain online atlas . To measurethe average level of LIMK1 inside the brain structures, theaverage signal intensity was measured in three small squareareas (~10 \u00d7 10 \u03bcm) within each of the structures. The averagevalues were obtained and normalized to the average structureintensity for the given brain. Colocalization Threshold analysis was performed to measure co-localization of LIMK1 withneurospecific markers. To prepare figures, auto contrast functionwas used for each optical slice.Learning and courtship suppression tests in Drosophilamales. Flies learning and STM were estimated in CCSP, asdescribed in . In the case of long termmemory (LTM), learning was performed by placing flies infood-containing glasses for5 h . Courtship index (CI) and learningindex (LI) were estimated at the following time pointsafter learning: for short-term memory (STM) analysis: 0 min(learning), 3 h; for STM decay analysis: 15, 30, 60 min,24 h; for LTM analysis: 0 min, 2 days, 8 days. In all groups,naive males (without mating experience) served as a controlto calculate LI:where CIN is the middle CI for naive males, and CIT is themiddle CI for males after training. The naive and trainedmales were the same age. The decrease in LI compared toLI (0 min) was considered a time-dependent memory decay.The decrease in LI for a mutant strain compared to that for thewild-type strain CS was considered a strain-specific impairmentof learning or memory.Courtship song analysis. The 5-day-old imago malecourtship song was recorded as in . A naive male of the studied line and a fertilizedfemale (CS) were placed together in a Perplex chamber witha latticed bottom on top of a microphone. The chamber wasplaced in a foam box in a soundproof room. The sounds wererecorded for 5 min using Audacity software . The sound signals were filtered to excludenoises, obtaining signals within 100\u2013800 Hz. The level ofnoise was decreased using a standard Audacity plugin. Thesoftware Drosophila courtship song analysis (DCSA) was used to automatically detect pulse and sinesong components.The results of analysis were manually edited. The meanvalues of the song parameters were calculated for each fly.The following parameters were estimated: pulse song index, pulse song initiation frequency, sine song index , sinesong frequency , interpulse interval ,period of song pulse train , intertrain interval ,train duration (TrainDur), pulse number in train (PulseN), sinesong duration , sine song amplitude ,IPI variance (Var(IPI), ms2). Per is the time between the startsof the neighboring trains. ITI is the time between the end ofthe previous and the start of the next train.Statistical analysis. Analysis of LIMK1 mRNA level wasperformed using two-sided t-test, Social Science Statisticonline resource ( p < 0.05). Analysis of LI and courtship songparameters was performed using two-sided randomizationtest at significance level \u03b1 of 0.05 (n = 20), using DrosophilaCourtship Lite software , with 10000 iterations. The program is freelyavailable from the author upon request. Randomization testwas reported to be better for LI comparison than t-test orsome nonparametric tests . Courtshipsong parameters were also analyzed using two-sidedMann\u2013Whitney U-test. Python 3 scripts were used to drawthe box plots charts.limk1 RNA level in Drosophila UAS \u00d7 GAL4 hybridsTo check that GAL4 really induces limk1 RNA interferencein 26294 strain, we compared limk1 RNA level in the UAS (f)> GAL4 (m) hybrids. Females with and without transgenicRNAi for limk1 suppression were crossed to Act-GAL4 males, expressingGAL4 in the whole body. The level of total limk1 RNA wasapproximately 2-fold lower in the hybrid with limk1 interference.These data confirmed the efficiency of RNAi-dependentlimk1 suppression in 26294 strain (limk1-KD) upon its activationby GAL4. At the same time, there were no differences forlimk1-KD > 6794 and limk1\u201c+\u201d > 6794, where RNA expressionwas measured in heads and was regulated by neuronaltype-specific GAL4 . Thus, limk1 RNA differencesafter neural type-specific limk1 RNA interference might belocal or too low to be detected in the whole Drosophila heads.LIMK1 distribution in the Drosophila brainWhen studying LIMK1 distribution, we focused on thecentralpart of the Drosophila brain, without the optic lobes(OL), mainly at the level of the superior medial protocerebrum(SMP) and gamma-lobes (\u03b3L) of MB. Here the PAMclusters of DAN are located , responsiblefor the Drosophila courtship learning and memory . Additionally, the area including the central complex(CC) and calyx surrounded by Kenyon cells (KC)was studied. The CSP-positive neuropil structures and tyrosinehydroxylase (TH)-positive DAN cell bodies and processesserved as landmarks in describing the LIMK1 distribution.The following description is given for the wild-type strainCS 1.https://vavilovj-icg.ru/download/pict-2023-27/appx9.pdfSupplementary Materials are available in the online version of the paper:The distribution of DAN clusters corresponded to thatdescribed in . PAM clusters were clearlyobserved near SMP, with processes extending towards thecentral part of the brain. The processes formed glomerularstructures around the MB horizontal lobes , probablybeing the synaptic endings innervating the correspondareas. The structure #3 was located above \u03b3L, the structures#5 and 8 \u2013 in the \u03b2\u2032L area, the commissure #9 was seen in thecentral part of the brain. TH signal was relatively low in \u03b2L. PPL1, PPM2 and other DAN clusterswere observed around Cal, sending their processes to the differentbrain areas .LIMK1 was concentrated in the neuropil structures of theanterior part of the brain, such as SMP and AL. The LIMK1-positive granularity was observed inside SMP, between the \u03b2\u2032Ltips (#8) and around the ellipsoid body (EB) of CC .LIMK1 level was also high in thin tissue layers adjacentto neuropil and some neural tracts, such as #12 around thegreat commissure, #13 around wedge (W) and #15 near esophagus(ES), morphologically resembling glia . LIMK1 signal was lower in cell bodies of the neuronssurrounding AL (ALCB), probably being the cell bodies of theprojection neurons, as well as in KC surrounding Cal. Here,LIMK1 was mainly concentrated in the cytoplasm, beyondthe nuclei. LIMK1 level was significantly decreased in all theMB lobes and pedunculus (Ped), as well as in the CC structures,whereas in Cal and the protocerebral bridge (PB) it wasrelatively high . LIMK1 and TH colocalizationwas observed in SMP, AL, Cal, the TH-positivecells and processes, and in glomerular densities, such as #3,5 and 6 .To check that the antibody specifically binds to LIMK1, thedistribution of LIMK1 main product p-cofilin was assayed inCS. The pattern of p-cofilin distribution was generally similarto that for LIMK1 . The level of p-cofilinwas low in MB and CC . In contrast to LIMK1, p-cofilin wasmainly concentrated in the cell nuclei in the peripheral area ofthe fly brain, such as Kenyon cells around Cal, as well as in PB,subesophageal ganglion (SEG), and cell bodies surrounding AL. p-Cofilin was also localized in diffuse layers within thebrain structures, such as EB, probably formed by glia. Thep- cofilin-enriched cells were found in SEG, forming structureswith two glomerular branches (*), and around CC structures,fan-shaped body (FB) and EB (**).Several GAL4 activators were used to initiate limk1 RNAinterference. Both 6793 and 6794 strains specifically expressthe green fluorescent protein (GFP) under GAL4 promoter.In strain 6794, GAL4 was reported to be expressed in OL,thoracic ganglion, different nerves, and cortex glia . In 6794 > limk1-KDhybrid, GAL4-driven GFP expression was detected in glialikecells, surrounding the neuropil structures, such as AL,SMP, CC and its parts, as well as in the MB lobes, Ped andsome KC . GFP level was higher in \u03b1Land \u03b2L compared to \u03b1\u2032L, \u03b2\u2032L and \u03b3L. The signal was lowerin Cal and virtually absent in most neuropil structures, suchas AL, SMP, CC and others. Thus, limk1 interference shouldoccur in Cal and some glia cells, where the levels of bothGAL4 and LIMK1 were relatively high. Similar distributionwas observed in the control 6794 > limk1\u201c+\u201d strain . In the strain 6793, GAL4 is expressedin cholinergic neurons (CHN), with GFP signal in OL, ALwith the surrounding interneurons, the parts of CC, the greatcommissure (GC), Cal and the mechanosensory area of SEG. In the strains 6793 > limk1- KDand 6793 > limk1\u201c+\u201d , we observeda strong GFP signal in cell bodies surrounding SMPand AL, as well as in some KC, several neuropil structures, and GC. In all the studied strains, LIMK1distribution character appeared to be similar to that in CS.To check that GAL4 is active in 7009 and 30027 strains,we crossed them to strains expressing GFP under GAL4 promoter.In 7009 > 32186 hybrid, we observed a prominent GFPsignal in cell clusters near SMP, morphologically similar tothe TH-positive PAM clusters. Some cells might be SRN, butthey constitute the minority of the observed neurons in thisarea . The processesof PAM neurons extended to the horizontal MB lobes, including\u03b3L, and the densely innervated \u03b2\u2032L tip (#5) connected by a commissure, and to a much lesser extent the \u03b2L tip . EB was surrounded by the GFP-positive processesextending from different parts of the brain. The GFPpositiveDAN around Cal were also observed. Hence, GAL4activator of 7009 should suppress limk1 inside DAN, includingPAM neurons, which regulate memory storage in CCSP. Thefruitless-positive neurons (FRN) are responsible for matingbehavior. In 30027 > 32202 hybrid, we observed GFP insome KC, in the cell bodies located near SMP and AL, andglomerular structure, forming a ring-like structure around Ped. Similar structures were describedin . The distribution of LIMK1 in the hybridstrains with and without limk1 knockdown in the above neuronswas similar to that in CS .The normalized intensity of LIMK1 signal was calculatedfor several brain structures . The LIMK1 relative levelsin specific structures were very similar for the CS brain andthe average brain of all the strains. The biggest differenceswere observed for the TH-positive glomerular structure #6(TH+(6)), which is possibly responsible for memory formationin CCSP. In the average brain, ALCB had the normalizedLIMK1 level about 1. Compared to them, AL, SMP andTH+(6) structures had the higher LIMK1 level, whereas theMB lobes, EB and Ped had the lower LIMK1 level. In agn ts3,AL and ALCB had the higher LIMK1 level compared to CS,whereas most of the rest studies structures had lower LIMK1level. This corresponds to more contrast LIMK1 staining inagn ts3 relative to CS . There were no prominentdifferences after limk1 knockout, except for severalstructures with minor changes. The interstrain differencesmight be local or beyond the resolution of the method.3 h STM differs in hybridswith and without limk1 interference3 h STM was estimated for limk1-KD (f ) > 6794 (m) and thecontrol limk1\u201c+\u201d (f ) > 6794 (m) hybrids. In both cases, weobserved the decrease of courtship index (CI) after learning,with its partial recovery after 3 h. The box plot height wasminimal for CS and rather big for UAS \u00d7 GAL4 hybrids,showing that the value of courtship suppression significantlyvaried for individual flies. All strains were capable to learn inCCSP, with learning index LI (0 h) immediately after trainingof about 60\u201370 % . The CS LI was still high after 3 h,indicating STM preservation, in agreement with . The strain with limk1 interference also preservedSTM: although its LI (3 h) was only about 20 %, it did notstatistically differ from that for CS, as well as from LI (0 h). Inthe control strain, LI (3 h) decreased compared to LI (0 h) anddid not differ from zero, indicating the impaired STM. Thus,while 3 h memory storage or retrieval was impaired in thecontrol strain, limk1 interference seems to improve 3 h STM.At the same time, it did not affect the impaired 8 day LTM,with only minor positive effect on 2 day LTM .Neuron type-specific limk1 interferencedifferentially affects STM dynamicsTo investigate the dynamics of STM decay in different strainswith limk1 interference, we performed LI analysis immediatelyand 24 h after learning . To exclude the possible effectof eye color on learning and memory abilities, we appliedGAL4 (f ) > UAS (m) crossing scheme, where both the strainwith limk1 knockdown and the control strain had the samewild-type eye color. For 6794 activator (MB and glia), thecontrol strain showed nearly the same LI within 24 h, whereasthe strain with limk1 interference demonstrated a steeperforgetting curve. Hence, 6794 > limk1-KD showed high LIafter learning, but seemed to increase the speed of memoryforgetting on the interval 0\u201330 min. limk1 knockdown in CHN(6793) was associated with significant decrease of LI within60 min after training.For DAN and SRN activator (7009), both the strain withlimk1 interference and the control strain showed nearly thesame dynamics of STM decay, except for 30\u201360 min period.limk1 interference was associated with a dramatic defect onlearning: LI did not differ from zero. LI (24 h) was negativein both hybrids, possibly being the effect of sensitization:males did not suppress the courtship activity but courted moreactively some time after training. For FRN activator (30027),the effect of limk1 knockdown was the opposite to that ofMB/glia and CHN activators: limk1 interference decreasedthe speed of forgetting, and LI (30 min) did not differ fromzero. Thus, the effect of limk1 interference on STM dynamicsappeared to depend on the neuronal type.LIMK1 interference in CHN and FRN neuronsdifferentially affects courtship song parametersFinally, we studied the influence of limk1 interference on themale courtship song parameters. The hybrids with CHN andFRN drivers were studied . There were no interstraindifferences in interpulse interval (IPI), the species- and population-specific parameter , and IPI variance(Var(IPI)), the marker of neurodegenerative processes. limk1 interference in CHN(6793) decreased the pulse song index and frequency , increasing the mean period (Per), intertrain interval (ITI),train duration (TrainDur), sine song duration (Sdur) and trainpulse number (PulseN). On the contrary, in the strain with FRNactivator (30027), limk1 interference resulted in PFr increase,as well as Per, ITI, SInd and SDur decrease. limk1 knockdownby two different activators had the opposite effects on PInd,PFr, Per, ITI and SDur, leveling the initial differences betweenSInd, TrainDur and PulseN. Thus, limk1 interference in CHNseemed to decrease the rate of switching from the singingmode to silence mode and back, resulting in longer trains andITI, while limk1 interference in FRN neurons generally hadthe opposite effect.In mammals, LIMK1- and cofilin-dependent actin remodelingis widely involved in regulation of synaptic processes,such as exocytosis, receptor trafficking and remodeling ofdendritic spines. These processes underlay long-term potentiation(LTP), long-term depression (LTD) and different forms ofmemory. LIMK1 also affects gene expression through CREBand LTM formation. Deregulation of LIMK1-dependentactin remodeling is involved in multiple pathologies, such asAlzheimer\u2019s and Parkinson\u2019s diseases, Williams syndrome,schizophrenia, and autism .In mature neurons, actin is enriched in both pre- and postsynapticstructures, such as dendritic spines, regulated byRho signaling pathway. The action of LIMK1 on actin polymerizationand memory processes is rather complex, beingdependent on the mode of LIMK1 regulation (transient orlong-term overexpression) and cofilin level. While the activecofilin destabilizes fibrillar actin, in high concentrations itincreases actin polymerization and nucleates actin filamentsin dendritic spines during long-term potentiation . Thus, it is hard to predict the integral effect of LIMK1 and cofilin activity on memory processes.It was crucial to check the behavioral effects of Drosophilalimk1 suppression in specific types of neurons.Using paraffin section staining, both LIMK1 and its productp-cofilin were shown to be homogeneously distributed in thebrain neuropil, with maximum level in CC . Our results of the confocal microscopy analysis gavea different picture of LIMK1 distribution, quite similar for allthe studied strains. We have shown a specific LIMK1 decreasein MB, which is responsible for associative learning, as well asin CC, involved in higher movement control . This puts under question the role of LIMK1 inthe aforementioned processes. However, LIMK1 was presentin the cell bodies and processes of DAN, which interact withMB and CC and regulate memory andforgetting. The observed p-cofilin distribution resembled thisfor LIMK1: its level was low in the MB lobes and CC. The lowlevel of p-cofilin in the MB lobes had been previously shown . In contrast to LIMK1, p-cofilin level waslow in Cal formed by PN and KC terminals and high in cellnuclei. The latter corresponds to its functioning in the cell, ascofilin phosphorylation is necessary for its translocation intothe nucleus .The effectiveness of limk1 suppression at the RNA level wasconfirmed using Act-GAL4 activator in the whole Drosophilabody. GAL4 was also active in specific brain areas of the correspondingstrains. However, we failed to quantitatively checkthe changes of limk1 expression in Drosophila UAS \u00d7 GAL4hybrids with neuronal-specific GAL4 expression. The decreasein LIMK1 level might be local or too small. limk1interference might also induce the compensatory activationof LIMK1 translation.To study limk1 knockdown effects on memory, we usedCCSP modification applied by :training was performed with the mated female. In this case,courtship learning results from the rise of sensitivity to theantiaphrodisiac cis-vaccenyl acetate (cVA) due to unsuccessfulcourtship. cVA is not required for learning, being necessaryfor memory performance. aSP13 DAN, which innervate thefru-positive tip of \u03b3L, are necessary and sufficient for courtshiplearning . 24 h memory consolidationrequires the prolonged aSP13 stimulation and Orb2 dimerizationin some \u03b3 neurons . \u03b1/\u03b2 neurons areinvolved in LTM processes . Hence, other DAN innervating \u03b1/\u03b2L of MB,including PAM and PPL1 cells , may alsobe involved in LTM.The behavioral differences were observed after limk1 interference,e. g., the restoration of 3 h STM for limk1-KD >6794 strain. GAL4 drivers themselves affected memoryabilities,which were generally decreased compared to CS.The drivers also significantly affected the forgetting curves.Thus, we studied the effects of limk1 interference relative toa control strain with the same GAL4 driver. We applied twodifferent crossing schemes \u2013 UAS (f) > 6794 (m) and reverse . In the first case, the control UAS > limk1\u201c+\u201dhybrid had bright eyes due to v[1] recessive allele, in contrastto UAS > limk1-KD hybrid with the wild type dark red eyes.The observed 3 h STM differences are unlikely to be associatedwith the differences in eyes pigmentation, as v[1] fliesshowed a normal 3 h STM and 2 day LTM in CCSP , while both forms of memory were impaired in thecontrol strain. However, memory retention depends on parentaffect, with some paternal epigenetic factors affecting STMstrength . For 6794 > limk1-KD strain,we did not see STM difference from the control strain, thoughlearning ability slightly increased after limk1 knockdown . Thus, when studying LIMK1 effects on learning andmemory, it is necessary to consider the crossing direction.Acetylcholine is the major excitatory neurotransmitter inDrosophila. Among CNH are: PN forming synapses on KCof MB , the MB intrinsic neurons thatare responsible for olfactory memory, expressing ChAT andVAChT , and the \u03b1/\u03b2 core neurons requiredfor LTM consolidation . In the hybridswith 6793 driver (GAL4 expressed in CHN), GFP level wasspecifically high in \u03b1/\u03b2L compared to the other MB lobes.Here, limk1 interference resulted in faster STM forgetting.This contradicts the cofilin role in active forgetting shown inOAVL, where cofilin was proposed to be regulated by LIMK1. The involvement of LIMK1 and cofilinin forgetting may occur locally, within specific neuronalpopulations or synaptic terminals. At the same time, LIMK1may be crucial for memory storage and retrieval in CCSP.The glutamatergic MBON M6 neurons serve for STM output:aSP13 DAN prolongs potentiation of \u03b3L \u2013 M6 synapses . Some cholinergic MBON appeared to regulatethe Drosophila visual appetitive memory .As the extrinsic MB cells responsible for CCSP memory weresimilar to those used for appetitive memory , the decrease in 60 min STM might occur due to limk1suppression in some of these neurons.The hybrids with 7009 driver (DAN and SRN) showedgenerally low CI values and negative LI values 24 h afterlearning. Males of these strains had pale pink eyes because ofdefects of eyes pigmentation, due to non-complete w[1118]rescue. w[1118] males demonstrated low courtship activityand success, presumably due to some defects of sexual developmentand maturation . However, thecontrol 7009 > limk1\u201c+\u201d strain had normal LI up to 60 minafter training. limk1 knockdown by 7009 driver was associatedwith dramatic defects of learning and memory: LI just aftertraining did not statistically differ from zero. Thus, LIMK1-dependent signaling in DAN and SRN seems to be importantfor learning and memory in CCSP.limk1 knockdown by 30027 driver (FRN) decreased theforgetting rate in the time interval 30\u201360 min. This correspondsto the role of actin-remodeling pathway in forgettingin OAVL paradigm . LI of the controlstrain did not differ from zero starting from 30 min afterlearning, while limk1 knockdown increased it. In males, FRNare responsible for courtship behavior. There are ~1500 FRNin the Drosophila brain, including sensory organs, lateralhorn, lateral protocerebrum, SMP arch and motor controlcenters. Together they provide multisensory integration toregulate the male courtship process . Some CHN and DAN are also Fru-positive, suchas ~300 \u03b3L neurons and aSP13 DAN located in SMP, whichregulates courtship learning and memory. The activity of frugene was reported to decrease upon LTM formation in CCSP. Hence, suppression of some FRN activitymay be associated with memory prolongation and consolidation.In addition to memory processes, limk1 interference affectedsome parameters of the male courtship song. As well as forcourtship memory, we observed the opposite functional effectsof limk1 knockdown in FRN and CHN. FRN of the P1 classinitiate Drosophila courtship behavior and trigger courtshipsong. pIP10 neurons possibly convey the P1 signal to thoracicdPR1 and vPR6 neurons, proposed to be the parts of a centralpattern generator (CPG), which defines the time and shape ofthe pulse song. vPR6 possibly encode IPI . Pulse and sine CPG either contain FRN or interactwith them. As sine and pulse song normally do not overlap,the mutually inhibitory mechanisms must exist, switching between quasilinear and relaxation modes of oscillation forsine and pulse song, respectively. Some descending interneuronsmay control the type of the song, while the others triggersinging or terminate the song .Indeed, we observed the opposite changes of PInd/PFr andSInd/SDur upon limk1 interference in CHN and FRN, movingthe balance toward the sine and pulse song, respectively. Theincrease in PFr after limk1 knockdown in FRN might indicatethe negative role of LIMK1-dependent signaling on activityof the pulse CPG or the upstream brain centers, which switchthem from active to silent mode. \u0421\u0421 is important for control ofstability of pacemakers, which regulate the rhythmic structureof courtship song. PB destruction leads to sound signal distortions,FB and EB destruction additionally decreases sine andpulse trains . CC includes a large numberof neuronal types, such as CHN, DAN, SRN, and others. CHNare present in FB, EB, No and PB ,similarly to what we observed in our research. Hence, theyprobably play some role in regulation of male singing. Theopposite effects of limk1 interference in CHN and FRN mayindicate a specific role of LIMK1 in courtship controllingnetwork, whereas the other parts of the brain possibly havea total antagonistic effects on its activity. Alternatively, CHNand FRN fru neurons may differ in some aspects of regulationof LIMK1-dependent signaling pathway.In summary, we have shown that effects of limk1 interferencein Drosophila male courtship memory and song depend onboth the neuronal type and specific behavioral parameter.limk1 interference in CHN and FRN had generally oppositeeffects, whereas its suppression in DAN and SRN impaired theflies\u2019 ability to learn. Using activator strains with a narrowerpattern of GAL4 expression would help to better localize thebrain structures, where LIMK1 regulates memory and forgettingin CCSP. Among such putative structures are \u03b3L andaSP13 DAN innervating \u03b35 area, as well as other DAN participatingin memory formation, consolidation and retrieval.Studying the behavioral consequences of limk1 overexpressionin different brain areas will complement the estimates of theeffects of its suppression. The above investigation should alsofocus on LIMK1 partner proteins, such as cofilin in its activeand phosphorylated form.The authors declare no conflict of interest.Abe H., Nagaoka R., Obinata T. Cytoplasmic localization and nucleartransport of cofilin in cultured myotubes. Exp. Cell Res. 1993;206(1):1-10. DOI 10.1006/excr.1993.1113.Abe T., Yamazaki D., Murakami S., Hiroi M., Nitta Y., Maeyama Y.,Tabata T. The NAV2 homolog Sickie regulates F-actin-mediatedaxonal growth in Drosophila mushroom body neurons via the noncanonicalRac-Cofilin pathway. Development. 2014;141(24):4716-4728. DOI 10.1242/dev.113308.Albin S.D., Kaun K.R., Knapp J.M., Chung P., Heberlein U., SimpsonJ.H. A subset of serotonergic neurons evokes hunger in adultDrosophila. Curr. Biol. 2015;25(18):2435-2440. DOI 10.1016/j.cub.2015.08.005.Aso Y., Gr\u00fcbel K., Busch S., Friedrich A.B., Siwanowicz I., TanimotoH. The mushroom body of adult Drosophila characterized byGAL4 drivers. J. Neurogenet. 2009;23(1-2):156-172. DOI 10.1080/01677060802471718.Aso Y., Hattori D., Yu Y., Johnston R.M., Iyer N.A., Ngo T.B., DionneH., Abbott L.F., Axel R., Tanimoto H., Rubin G.M. The neuronalarchitecture of the mushroom body provides a logic for associativelearning. eLife. 2014a;3:e04577. DOI 10.7554/eLife.04577.Aso Y., Sitaraman D., Ichinose T., Kaun K.R., Vogt K., Belliart-Gu\u00e9rinG., Pla\u00e7ais P., Robie A.A., Yamagata N., Schnaitmann C.,RowellW.J., Johnston R.M., Ngo T.B., Chen N., Korff W., NitabachM.N., Heberlein U., Preat T., Branson K.M., Tanimoto H.,Rubin G.M. Mushroom body output neurons encode valence andguide memory-based action selection in Drosophila. eLife. 2014b;3:e04580. DOI 10.7554/eLife.04580.Barnstedt O., Owald D., Felsenberg J., Brain R., Moszynski J.P., TalbotC.B., Perrat P.N., Waddell S. Memory-relevant mushroom bodyoutput synapses are cholinergic. Neuron. 2016;89(6):1237-1247.DOI 10.1016/j.neuron.2016.02.015Ben Zablah Y., Zhang H., Gugustea R., Jia Z. LIM-kinases in synapticplasticity, memory, and brain diseases. Cells. 2021;10(8):2079-2103. DOI 10.3390/cells10082079Berry J.A., Cervantes-Sandoval I., Nicholas E.P., Davis R.L. Dopamineis required for learning and forgetting in Drosophila. Neuron.2012;74(3):530-542. DOI 10.1016/j.neuron.2012.04.007.Berry J.A., Phan A., Davis R.L. Dopamine neurons mediate learningand forgetting through bidirectional modulation of a memory trace.Cell Rep. 2018;25(3):651-662. DOI 10.1016/j.celrep.2018.09.051Cervantes-Sandoval I., Chakraborty M., MacMullen C., Davis R.L.Scribble scaffolds a signalosome for active forgetting. Neuron.2016;90(6):1230-1242. DOI 10.1016/j.neuron.2016.05.010.Clyne J.D., Miesenb\u00f6ck G. Sex-specific control and tuning of the patterngenerator for courtship song in Drosophila. Cell. 2008;133(2):354-363. DOI 10.1016/j.cell.2008.01.050Cook K.R., Parks A.L., Jacobus L.M., Kaufman T.C., Matthews K.A.New research resources at the Bloomington Drosophila Stock Center.Fly (Austin). 2010;4(1):88-91. DOI 10.4161/fly.4.1.11230Cuberos H., Vall\u00e9e B., Vourc\u2019h P., Tastet J., Andres C.R., B\u00e9n\u00e9detti H.Roles of LIM kinases in central nervous system function and dysfunction.FEBS Lett. 2015;589(24 Pt.B):3795-3806. DOI 10.1016/j.febslet.2015.10.032.Davis R.L., Zhong Y. The biology of forgetting \u2013 a perspective. Neuron.2017;95(3):490-503. DOI 10.1016/j.neuron.2017.05.039Duffy J.B. GAL4 system in Drosophila: a fly geneticist\u2019s Swiss armyknife. Genesis. 2002;34(1-2):1-15. DOI 10.1002/gene.10150Gao Y., Shuai Y., Zhang X., Peng Y., Wang L., He J., Zhong Y., Li Q.Genetic dissection of active forgetting in labile and consolidatedmemories in Drosophila. Proc. Natl. Acad. Sci. USA. 2019;116(42):21191-21197. DOI 10.1073/pnas.1903763116Hartenstein V. Morphological diversity and development of glia inDrosophila.Glia. 2011;59(9):1237-1252. DOI 10.1002/glia.21162.Iliadi K.G., Kamyshev N.G., Popov A.V., Iliadi N.N., RashkovetskayaE.L., Nevo E., Korol A.B. Peculiarities of the courtship songin the Drosophila melanogaster populations adapted to gradient ofmicroecological conditions. J. Evol. Biochem. Physiol. 2009;45(5):579-588. DOI 10.1134/S0022093009050041.Jones S.G., Nixon K.C.J., Chubak M.C., Kramer J.M. Mushroombody specific transcriptome analysis reveals dynamic regulation oflearning and memory genes after acquisition of long-term courtshipmemory in Drosophila. G3: Genes Genomes Genetics (Bethesda).2018;8(11):3433-3446. DOI 10.1534/g3.118.200560Kahsai L., Winther A.M. Chemical neuroanatomy of the Drosophilacentral complex: distribution of multiple neuropeptides in relationto neurotransmitters. J. Comp. Neurol. 2011;519(2):290-315. DOI10.1002/cne.22520Kamyshev N.G., Iliadi K.G., Bragina J.V. Drosophila conditionedcourtship: two ways of testing memory. Learn. Mem. 1999;6(1):1-20.Kasture A.S., Hummel T., Sucic S., Freissmuth M. Big lessons fromtiny flies: Drosophila melanogaster as a model to explore dysfunctionof dopaminergic and serotonergic neurotransmitter systems.Int. J. Mol. Sci. 2018;19(6):1788-1805. DOI 10.3390/ijms19061788Keleman K., Vrontou E., Kr\u00fcttner S., Yu J.Y., Kurtovic-Kozaric A.,DicksonB.J. Dopamine neurons modulate pheromone responses inDrosophila courtship learning. Nature. 2012;489(7414):145-149.DOI 10.1038/nature11345Kr\u00fcttner S., Traunm\u00fcller L., Dag U., Jandrasits K., Stepien B., Iyer N.,Fradkin L.G., Noordermeer J.N., Mensh B.D., Keleman K. SynapticOrb2A bridges memory acquisition and late memory consolidationin Drosophila. Cell Rep. 2015;11(12):1953-1965. DOI 10.1016/j.celrep.2015.05.037.Liu W., Ganguly A., Huang J., Wang Y., Ni J.D., Gurav A.S., AguilarM.A., Montell C. Neuropeptide F regulates court-ship in Drosophilathrough a male-specific neuronal circuit. eLife. 2019;8:1-29.DOI 10.7554/eLife.49574.Lopatina N.G., Zachepilo T.G., Chesnokova E.G., Savateeva-PopovaE.V. Mutations in structural genes of tryptophan metabolic enzymesof the kynurenine pathway modulate some units of the L-glutamatereceptor \u2013 actin cytoskeleton signaling cascade. Russ. J.Genet. 2007;43(10):1168-1172. DOI 10.1134/S1022795407100110.Mao Z., Davis R.L. Eight different types of dopaminergic neurons innervatethe Drosophila mushroom body neuropil: anatomical andphysiological heterogeneity. Front. Neural Circuits. 2009;3:1-17.DOI 10.3389/neuro.04.005.2009Mazzoni D., Dannenberg R. Audacity\u00ae. Audacity Team, 2020. URL:https://audacityteam.org. Last access: 05.12.2021Medina J.H. Neural, cellular and molecular mechanisms of active forgetting.Front. Syst. Neurosci. 2018;12:1-10. DOI 10.3389/fnsys.2018.00003.Medvedeva A.V., Molotkov D.A., Nikitina E.A., Popov A.V., KaragodinD.A., Baricheva E.M., Savvateeva-Popova E.V. Systemic regulationof genetic and cytogenetic processes by a signal cascade of actinremodeling: locus agnostic in Drosophila. Russ. J. Genet. 2008;44(6):669-681. DOI 10.1134/S1022795408060069Medvedeva A.V., Tokmatcheva E.V., Kaminskaya A.N., Vasileva S.A.,Nikitina E.A., Zhuravlev A.V., Zakharov G.A., Zatsepina O.G.,Savvateeva-Popova E.V. Parent-of-origin effects on nuclear chromatinorganization and behavior in a Drosophila model for Williams\u2013Beuren Syndrome. Vavilovskii Zhurnal Genetiki i Selektsii =Vavilov Journal of Genetics and Breeding. 2021;25(5):472-485.DOI 10.18699/VJ21.054.Montague S.A., Baker B.S. Memory elicited by courtship conditioningrequires mushroom body neuronal subsets similar to those utilizedin appetitive memory. PLoS One. 2016;11(10):e0164516. DOI10.1371/journal.pone.0164516.Ng J., Luo L. Rho GTPases regulate axon growth through convergentand divergent signaling pathways. Neuron. 2004;44(5):779-793.DOI 10.1016/j.neuron.2004.11.014Nikitina E.A., Medvedeva A.V., Zakharov G.A., Savvateeva-PopovaE.V. The Drosophila agnostic locus: involvement in the formationof cognitive defects in Williams syndrome. Acta Naturae. 2014;6(2):53-61. DOI 10.32607/20758251-2014-6-2-53-61.Nikitina E.A., Zhuravlev A.V., Savvateeva-Popova E.V. Effect of impairedkynurenine synthesis on memory in Drosophila. IntegrativnyayaFiziologiya = Integrative Physiology. 2021;2(1):49-60.DOI 10.33910/2687-1270-2021-2-1-49-60. (in Russian)Okamoto N., Nishimura T. Signaling from glia and cholinergic neuronscontrols nutrient-dependent production of an insulin-like peptidefor Drosophila body growth. Dev. Cell. 2015;35(3):295-310. DOI10.1016/j.devcel.2015.10.003.Popov A.V., Peresleni A.I., Savvateeva-Popova E.V., Vol\u2019f R., HeisenbergM. The role of the mushroom bodies and of the central complexof Drosophila melanogaster brain in the organization of courtshipbehavior and communicative sound production. J. Evol. Biochem.Phys. 2004;40:641-652. DOI 10.1007/s10893-004-0005-z.Redt-Clouet C., Trannoy S., Boulanger A., Tokmatcheva E., Savvateeva-Popova E., Parmentier M.L., Preat T., Dura J.M. Mushroombody neuronal remodelling is necessary for short-term but not forlong-term courtship memory in Drosophila. Eur. J. Neurosci. 2012;35(11):1684-1691. DOI 10.1111/j.1460-9568.2012.08103.x.Ritchie M.G., Yate V.H., Kyriacou C.P. Genetic variability of the interpulseinterval of courtship song among some European populationsof Drosophila melanogaster. Heredity (Edinb). 1994;72(Pt.5):459-464. DOI 10.1038/hdy.1994.64.Salvaterra P.M., Kitamoto T. Drosophila cholinergic neurons and processesvisualized with Gal4/UAS-GFP. Brain Res. Gene Expr. Patterns.2001;1(1):73-82. DOI 10.1016/s1567-133x(01)00011-4.Savvateeva-Popova E.V., Popov A.V., Grossman A., Nikitina E.A.,Medvedeva A.V., Peresleni A.I., Molotkov D.A., Kamyshev N.G.,Pyatkov K.I., Zatsepina O.G., Schostak N., Zelentsova E.S., PavlovaG., Panteleev D., Riederer P., Evgen\u2019ev M.B. Non-coding RNAas a trigger of neuropathologic disorder phenotypes in transgenicDrosophila. J. Neural Transm. (Vienna). 2008;115(12):1629-1642.DOI 10.1007/s00702-008-0078-8.Savvateeva-Popova E.V., Popov A.V., Heinemann T., Riederer P. Drosophilamutants of the kynurenine pathway as a model for ageingstudies. Adv. Exp. Med. Biol. 2003;527:713-722. DOI 10.1007/978-1-4615-0135-0_84.Savvateeva-Popova E.V., Zhuravlev A.V., Br\u00e1zda V., Zakharov G.A.,Kaminskaya A.N., Medvedeva A.V., Nikitina E.A., TokmatchevaE.V., Dolgaya J.F., Kulikova D.A., Zatsepina O.G., Funikov S.Y.,Ryazansky S.S., Evgen\u2019ev M.B. Drosophila model for the analysisof genesis of LIM-kinase 1-dependent Williams\u2013Beuren syndromecognitive phenotypes: INDELs, transposable elements of the Tc1/mariner superfamily and microRNAs. Front. Genet. 2017;8:123.DOI 10.3389/fgene.2017.00123.Shuai Y., Lu B., Hu Y., Wang L., Sun K., Zhong Y. Forgetting is regulatedthrough Rac activity in Drosophila. Cell. 2010;140(4):579-589. DOI 10.1016/j.cell.2009.12.044Shuai Y., Zhong Y. Forgetting and small G protein Rac. Protein Cell.2010;1(6):503-506. DOI 10.1007/s13238-010-0077-z.Siegel R.W., Hall J.C. Conditioned responses in courtship behavior ofnormal and mutant Drosophila. Proc. Natl. Acad. Sci. USA. 1979;76(7):3430-3434. DOI 10.1073/pnas.76.7.343.Strauss R., Heisenberg M. A higher control center of locomotor behaviorin the Drosophila brain. J. Neurosci. 1993;13(5):1852-1861.DOI 10.1523/JNEUROSCI.13-05-01852.1993.Sun B., Xu P., Salvaterra P.M. Dynamic visualization of nervous systemin live Drosophila. Proc. Natl. Acad. Sci. USA. 1999;96(18):10438-10443. DOI 10.1073/pnas.96.18.10438.Thapa A., Sullivan S.M., Nguyen M.Q., Buckley D., Ngo V.T.,Dada A.O., Blankinship E., Cloud V., Mohan R.D. Brief freezingsteps lead to robust immunofluorescence in the Drosophila nervoussystem. Biotechniques. 2019;67(6):299-305. DOI 10.2144/btn-2018-0067.Tully T., Preat T., Boynton S.C., Vecchio M.D. Genetic dissection ofconsolidated memory in Drosophila. Cell. 1994;79(1):35-47. DOI10.1016/0092-8674(94)90398-0.Virtual Fly Brain. URL: https://v2.virtualflybrain.org. Last access:01.12.2021.von Philipsborn A.C., Liu T., Yu J.Y., Masser C., Bidaye S.S., DicksonB.J. Neuronal control of Drosophila courtship song. Neuron.2011;69(3):509-522. DOI 10.1016/j.neuron.2011.01.011.Winbush A., Reed D., Chang P.L., Nuzhdin S.V., Lyons L.C., ArbeitmanM.N. Identification of gene expression changes associatedwith long-term memory of courtship rejection in Drosophila males.G3: Genes Genomes Genetics (Bethesda). 2012;2(11):1437-1445.DOI 10.1534/g3.112.004119.Xiao C., Qiu S., Robertson R.M. The white gene controls copulationsuccess in Drosophila melanogaster. Sci. Rep. 2017;7(1):7712-7725. DOI 10.1038/s41598-017-08155-y.Yasuyama K., Meinertzhagen I.A., Sch\u00fcrmann F.W. Synaptic organizationof the mushroom body calyx in Drosophila melanogaster.J. Comp. Neurol. 2002;445(3):211-226. DOI 10.1002/cne.10155Yi W., Zhang Y., Tian Y., Guo J., Li Y., Guo A. A subset of cholinergicmushroom body neurons requires Go signaling to regulate sleep inDrosophila. Sleep. 2013;36:1809-1821. DOI 10.5665/sleep.3206.Yu J.Y., Kanai M.I., Demir E., Jefferis G.S., Dickson B.J. Cellularorganization of the neural circuit that drives Drosophila courtshipbehavior. Curr. Biol. 2010;20(18):1602-1614. DOI 10.1016/j.cub.2010.08.025.Zalomaeva E.S., Falina V.S., Medvedeva A.V., Nikitina E.A., Savvateeva-Popova E.V. Learning and forgetting in Drosophila melanogasterin limk1 gene polymorphism. Integrativnyaya Fiziologiya =Integrative Physiology. 2021;2(3):318-327. DOI 10.33910/2687-1270-2021-2-3-318-327. (in Russian)Zhang X., Li Q., Wang L., Liu Z.J., Zhong Y. Cdc42-dependent forgettingregulates repetition effect in prolonging memory retention.Cell Rep. 2016;16(3):817-825. DOI 10.1016/j.celrep.2016.06.041Zhao X., Lenek D., Dag U., Dickson B.J., Keleman K. Persistent activityin a recurrent circuit underlies courtship memory in Drosophila.eLife. 2018;7:1-16. DOI 10.7554/eLife.31425.Zhuravlev A.V., Shchegolev B.F., Zakharov G.A., Ivanova P.N., NikitinaE.A., Savvateeva-Popova E.V. 3-Hydroxykynurenine as apotential ligand for Hsp70 proteins and its effects on Drosophilamemory after heat shock. Mol. Neurobiol. 2022;59(3):1862-1871.DOI 10.1007/s12035-021-02704-3.Zhuravlev A.V., Vetrovoy O.V., Ivanova P.N., Savvateeva-Popova E.V.3-Hydroxykynurenine in regulation of Drosophila behavior: thenovel mechanisms for cardinal phenotype manifestations. Front.Physiol. 2020;11:971. DOI 10.3389/fphys.2020.00971."} +{"text": "To date, etravirine (ETR) is the only NNRTI indicated in people living with HIV (PLHIV) after virologic failure (VF) to first-generation NNRTIs. Data about susceptibility to ETR, doravirine (DOR) and rilpivirine (RPV) after VF in PLHIV from Latin American countries are scarce. The aim of this study is to determine the prevalence of resistance to ETR, DOR, and RPV in PLHIV who experienced VF to a first-line NNRTI-based regimen, and factors associated with high-level resistance (HLR) to ETR.Retrospective cohort study. Prevalence of resistance to ETR, DOR and RPV was assessed by analyzing genotyping tests of adult PLHIV who experienced VF to a first-line NNRTI-based regimen, in Buenos Aires, Argentina (2010 to 2020). Stanford HIVdb v9.4 was used to interpret resistance profiles. We defined resistance as both intermediate resistance (IR) and HLR interpretations. A sample size of 125 subjects was calculated to allow estimation of the primary endpoint with sufficient precision (95%CI). A cross-sectional analysis was carried out to identify risk factors associated with HLR to ETR.2=4.5, p=0.034).N=125; 81.6% were male. Median age at VF was 39.5 years (IQR: 34.0-35.0); 82,4% received efavirenz and 17.6% nevirapine. Duration of VF: 245 days (IQR 133-413). Median HIV-1 viral load (VL): 11255 c/mL (3606-45100); median CD4+ cell count: 192 cell/uL (86-333). Seventy-seven samples (61.6%) had ETR resistance-associated mutations (RAMs); 25 (20%) had mutations associated with the highest levels of reduced susceptibility . Most frequent ETR RAMS were: 100I (16%), 190A (16%) and 181C (12%); DOR RAMs: 100I (16%), 188L (8.8%) and 106M (4.8%), and RPV RAMs: 100I (16%), 181C (11.2%) and 138A (7.2%). Prevalence of resistance to ETR was 44.8% , resistance to DOR: 64% and to RPV: 52% . ETR maintained susceptibility to DOR resistant strains in 27.2% of the cases. We found a statistically significant association between HIV-1 VL >10000 c/mL and the risk of developing HLR to ETR (XIn our cohort, resistance to ETR after VF to a NNRTI-containing regimen was lower than to DOR and RPV. HLR was uncommon and associated with high HIV-1 VL. Almost one third of DOR-resistant strains remained susceptible to ETR.Ver\u00f3nica Mingrone, GSK/ViiV: Educational Courses|Janssen Pharmaceutical Companies: Educational Courses Eliana Loiza, n/a, GSK/ViiV: Educational Courses|Janssen Pharmaceutical Companies: Educational Courses Norma Porteiro, n/a, GSK/ViiV: Advisor/Consultant|GSK/ViiV: Grant/Research Support|GSK/ViiV: Educational Courses|Janssen Pharmaceutical Companies: Advisor/Consultant|Janssen Pharmaceutical Companies: Grant/Research Support|Janssen Pharmaceutical Companies: Educational Courses Ezequiel C\u00f3rdova, n/a, GSK/ViiV: Advisor/Consultant|GSK/ViiV: Grant/Research Support|GSK/ViiV: Educational Courses|Janssen Pharmaceutical Companies: Advisor/Consultant|Janssen Pharmaceutical Companies: Grant/Research Support|Janssen Pharmaceutical Companies: Educational Courses"} +{"text": "These results should be taken into consideration for the elderly patients under treatment.COVID-19 inactivated vaccine-induced humoral responses in patients with lung cancer (LCs) to SARS-CoV-2 wild-type (WT) strain and variants BA.4/5 after the primary 2-dose and booster vaccination remained unknown. We conducted a cross-sectional study in 260 LCs, 140 healthy controls (HC) and additional 40 LCs with serial samples by detecting total antibodies, IgG anti-RBD and neutralizing antibodies (NAb) toward WT and BA.4/5. SARS-CoV-2-specific antibody responses were augmented by the booster dose of inactivated vaccines in LCs, whereas they were lower than that in HCs. Enhanced humoral responses waned over time after triple injection, notably in NAb against WT and BA.4/5. The NAb against BA.4/5 was much lower than WT. Age\u2009\u2265\u200965 was risk factor for immunization of NAb to WT. Undergoing treatment resulted in a lower antibody response than those without and radiotherapy was a also risk factor for seroconversion of NAb to WT. Lower lymphocyte counts contributed to a lower titer of IgG anti-RBD and NAb against BA.4/5 in LCs than HCs. Specifically, total B cells, CD4The online version contains supplementary material available at 10.1186/s13045-023-01443-3. Since SARS-CoV-2 spread all over the world, patients with lung cancer (LCs) had an estimated case fatality rate of more than 30%, compared with 0.7% to 8.0% in general population . As the In addition, the Omicron variant harboring 30\u201340 mutations in the viral spike protein produced high immune evasion . HomologP\u2009<\u20090.05) than the second in LCs. A durability of total antibodies was found in LCs, but it decreased faster than HCs and the result showed it was 3.8-fold higher in HCs than LCs after 180\u00a0days post-booster vaccine (P\u2009=\u20090.0003) in LCs in LCs and Omicron BA.4/5 in LCs (P\u2009=\u20090.0339). The lower immunization may be explained by lower number total B cells, CD4+T cells and CD8+T counts in LCs as their correlation to the humoral response (Additional file Moreover, our results suggested undergoing various anticancer therapies influenced the antibody response of post-booster vaccine. LCs received radiotherapy generated lower level of total antibodies than other therapeutic strategies post-booster inactivated vaccines. The IgG anti-RBD antibodies titer, NAbs against WT and Omicron BA.4/5 were significantly lower in patients receiving various therapies than those without (Fig.\u00a0Overall, our study revealed strengthened humoral responses post-booster vaccine among LCs, albeit lower than HCs. However, the booster dose failed to establish a potent and durable antibody response for Omicron BA.4/5, which gives rise to the risk of breakthrough infections of Omicron variants, especially in those old and undergoing anticancer therapies. Given the lower antibodies in LCs receiving various active anticancer therapies, further studies are needed to determine whether increased dosage, mixing vaccine types or additional doses enhance immunogenicity.Additional file 1: Methods.Additional file 2: Table S1. Matched demographics between 260 patients with LC and 140 HCs. Table S2. Antibody Response to SARS-CoV-2 inactivated Vaccine between 260 patients with LC and 140 HCs. Table S3. Demographics and clinical characterization of 40 patients with LC with sequential samples. Table S4. Comparative analysis of neutralizing effect responses to SARS-CoV-2 WT and Omicron variant BA.4/5 in 260 patients with LC. Table S5. Antibody response to SARS-CoV-2 inactivated vaccination in 260 LCs and 140 HCs aged\u2009<\u200965 and\u2009\u2265\u200965\u00a0years. Table S6. Antibody response to SARS-CoV-2 inactivated vaccination in 260 LCs receiving various treatment regimens. Table S7. Risk factors associated with seropositivity of SARS-CoV-2 antibodies in 144 LCs received booster vaccine.Additional file 3: Figure S1. SARS-CoV-2 antibodies response in 40 LC patients after the second or booster dose of inactivated vaccine. Total antibodies against SARS-CoV-2. Concentrations of IgG anti-RBD antibodies. Inhibition rates of NAb against SARS-CoV-2 WT. Inhibition rates of NAb against Omicron BA.4/5.Additional file 4: Figure S2. Comparison of neutralizing effect responses to SARS-CoV-2 WT and Omicron variant BA.4/5 in LCs. The figures show the median and quartiles. *P\u2009<\u20090.05, **P\u2009<\u20090.01, ***P\u2009<\u20090.001 and ****P\u2009<\u20090.0001. LC, lung cancer; WT, wild type.Additional file 5: Figure S3. Comparison of lymphocytes counts in 260 LCs and HCs. The figures show the median and quartiles. **P\u2009<\u20090.01.Additional file 6: Figure S4. Correlation of biological variables and magnitude of SARS-CoV-2 antibodies after the booster dose."} +{"text": "The aim of this prospective multicentre, French observational study was to describe the conditions of Ceftolozane/Tazobactam (C/T) use in hospital settings, and outcomes. This sub-analysis focuses on the cystic fibrosis (CF) patients included in the overall cohort.Adult patients suffering from CF having received at least one dose of C/T and followed up as per routine clinical practice until stop of C/T were included in this analysis. Additional data related to CF were collected.Between October 2018 and December 2019, 63 patients with CF were enrolled from 28 sites. Mean age was 33.6 years and 44.4% were males. 12 patients (19.0%) received a lung transplant, 46.0% had comorbidities with diabetes (34.9%) being the most frequent. Most patients (69.8%) had normal renal function, almost one-third (28.6%) were immunosuppressed. One-half of patients presented with class 2 mutation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. None of the patients received CFTR modulators due to non-availability during the study period.About one-half of patients (52.4%) experienced intolerance/allergy to antibiotics; of these, 78.1% was associated with Ceftazidime.Pseudomonas aeruginosa was the most predominant pathogen representing 89.9% (71/79) of the isolates. C/T showed a very high susceptibility rate of 91.5% across those strains (Table 1). C/T demonstrated higher susceptibility rates than other B-lactam agents (Table 2).Microbiology results showed that Treatment duration until complete cure had a median of 15 days and occurred in 44.4% of patients. Treatment duration until partial cure or end of treatment was a median of 15 days and occurred in 46% of patients (Table 3). Only 2 patients experienced an adverse event leading to a discontinuation of treatment.Treatment with C/T had a positive impact on pulmonary function measured by FEV1 (Table 4) with a mean increase after treatment from 1.33L (range 0.5 - 4.1L) to 1.47L (range 0.6 - 4.6L).Pseudomonas aeruginosa.These results suggest that C/T is an effective and safe option for the treatment of CF patients with a potential positive impact on FEV1 when treating bacterial infections mainly caused by Xavier Bourge, PharmD, Merck: Employe Brune Akrich, MD, MSD: Employee David Boutoille, MSD France: Board Member Isabelle Brassac, Scientist, MSD France: salary Carole Mackosso, n/a, MSD France: MSD employee Jean-Fran\u00e7ois Timsit, MD, merck: Advisor/Consultant Bernard Castan, MD, ADVANZ: SPEAKER MODERATOR|BIOMERIEUX: SPEAKER MODERATOR|GILEAD: Advisor/Consultant|MSD France: Board Member|MSD France: SPEAKER MODERATOR|SANOFI: Advisor/Consultant|SHIONOGI: Advisor/Consultant Pierre-Regis Burgel, MD,PHD, ASTRA-ZENECA: Honoraria|BOEHRINGER INGELHEIM: Honoraria|CHIESI: Honoraria|GSK: Honoraria|INSMED: Honoraria|NOVARTIS: Honoraria|PFIZER: Honoraria|VERTEX: Grant/Research Support|ZAMBON: Honoraria"} +{"text": "Burkholderia cepacia complex (Bcc) and Burkholderia gladioli strains. The addition of taniborbactam to cefepime shifted cefepime minimum inhibitory concentrations toward the provisionally susceptible range in 59% of the isolates tested. Therefore, cefepime-taniborbactam possessed similar activity as first-line agents, ceftazidime and trimethoprim-sulfamethoxazole, supporting further development.The novel clinical-stage \u03b2-lactam-\u03b2-lactamase inhibitor combination, cefepime-taniborbactam, demonstrates promising activity toward many Gram-negative bacteria producing class A, B, C, and/or D \u03b2-lactamases. We tested this combination against a panel of 150 Pseudomonas aeruginosa, including strains producing VIM-2 producers (Taniborbactam (formerly VNRX-5133) is a novel bicyclic boronic-acid \u03b2-lactamase inhibitor being deng VIM-2 \u201311, 13roducers , 14\u201317Burkholderia cepacia complex (Bcc) is a group of >20 related non-fermenting pathogens (Burkholderia gladioli can cause chronic infections in the immunocompromised and those with cystic fibrosis (CF) with 8%\u201310% of CF patients acquiring Bcc or B. gladioli by end stage, leading to increased morbidity and mortality and AmpC (class C) \u03b2-lactamases as well as \u03b2-lactam-\u03b2-lactamase inhibitor combinations , while tic acid) . Severalin vitro , 28\u201330isolates , 28, 29.ambifaria, arboris, cenocepacia, cepacia, contaminans, diffusa, dolosa, multivorans, pseudomultivorans, pyrrocinia, seminalis, stabilis, ubonensis, and vietnamiensis) and 10 B. gladioli from the Burkholderia cepacia Research Laboratory and Repository (University of Michigan) . Minimum inhibitory concentration (MIC) results were interpreted using Clinical Laboratory Standards Institute (CLSI) breakpoints, where available (P. aeruginosa of susceptible (\u22648 \u00b5g/mL), intermediate (16 \u00b5g/mL), and resistant (>32 \u00b5g/mL) , 25, 31 vailable . Cefepimsistant > \u00b5g/mL (3nd lung) \u201317 andnd lung) , 34. Theli panel , 32. Of 50 value decreased by fourfold from 32 to 8 \u00b5g/mL shifted the MICs toward the provisionally susceptible range; the MICge panel . MoreoveblaPenA , 31. Poiocepacia . Alteratdomallei ; efflux species .Burkholderia species with MIC50 of 4 \u00b5g/mL compared to 32 \u00b5g/mL for cefepime. The addition of 8 \u00b5g/mL of vaborbactam further increased the potency of meropenem with meropenem-vaborbactam yielding an MIC50 of 2 \u00b5g/mL. Levofloxacin performed similarly to cefepime alone with 26% vs 23% of isolates testing susceptible, respectively. Notably, only 4/150 strains (3%) possessed high MIC values to cefepime, cefepime-taniborbactam, meropenem, meropenem-vaborbactam, and levofloxacin. The rank order of potency by percent susceptibility or percent provisional susceptibility (\u226416 \u00b5g/mL for cefepime-taniborbactam) against these Burkholderia spp. was as follows: meropenem-vaborbactam (89%S) > cefepime-taniborbactam (69%S) > meropenem (55%S) > levofloxacin (26%S) > cefepime (23%S) but much lower than relebactam and vaborbactam 3.2 and 38 \u00b5M, respectively (koff rate was for taniborbactam. These results demonstrate that the efficacy of cefepime-taniborbactam is largely the result of the taniborbactam inhibition of PenA1 \u03b2-lactamase. Taniborbactam and avibactam inhibited PenA1 in vitro with relatively similar potencies, while relebactam and vaborbactam exhibited weaker inhibitory kinetic profiles in comparison. In summary, cefepime-taniborbactam will be a welcome addition to the antibiotic arsenal due to its broad-spectrum activity against Enterobacterales and P. aeruginosa producing class A, B, C, and D \u03b2-lactamases. With broader analyses, cefepime-taniborbactam may also be valuable to treat infections caused by Burkholderia species.The parameters for inhibition of the ectively (22, 29,ectively . Moreove"} +{"text": "On September 1, 2022, the Advisory Committee on Immunization Practices recommended a bivalent mRNA COVID-19 booster dose for persons who had completed at least a primary COVID-19 vaccination series \u22652 months earlier. Early data showed high effectiveness of a bivalent booster in preventing COVID-19-associated hospitalization within 45 days of receipt; however, little is known about the durability of this protection.Data from the Investigating Respiratory Viruses in the Acutely Ill (IVY) Network were used to conduct a case-control analysis measuring bivalent vaccine effectiveness (VE) against COVID-19\u2013associated hospitalization over time. During September 8, 2022\u2013April 1, 2023, immunocompetent, hospitalized adults aged \u226565 years with COVID-19-like illness were enrolled at 25 hospitals in 20 U.S. states. COVID-19 case-patients tested positive for SARS-CoV-2 by a nucleic acid or antigen test within 10 days of illness onset, while control-patients tested negative for SARS-CoV-2 during the same interval. Multivariable logistic regression was used to measure absolute and relative bivalent VE adjusted for age, sex, race and ethnicity, admission date, and U.S. Health and Human Services region. Unvaccinated patients and patients who received 2\u20134 doses of monovalent-only mRNA vaccine were used as the reference group for absolute and relative VE, respectively. Bivalent VE was calculated for 7\u201389 days and 90\u2013179 days from booster dose receipt to illness onset.A total of 2,787 immunocompetent, hospitalized adults aged \u226565 years were enrolled in the IVY Network during the study period . Absolute VE of a bivalent booster dose against COVID-19-associated hospitalization was 58% (95% CI=42%\u201370%) after 7\u201389 days and 27% (95% CI= -7% to 50%) after 90\u2013179 days. Relative VE of a bivalent booster dose was 54% (95% CI=41%\u201364%) after 7\u201389 days and 19% (95% CI= -8% to 39%) after 90\u2013179 days .Bivalent mRNA vaccination provided moderate protection against COVID-19-associated hospitalization within 90 days of receipt among adults aged \u226565 years, with waning protection after 90 days. Additional booster doses could improve protection against COVID-19-associated hospitalization among older adults.Adit A. Ginde, MD, MPH, AbbVie: Grant/Research Support|Faron Pharmaceuticals: Grant/Research Support Ithan Peltan, MD, Asahi Kasei Pharma: Institutional support|Regeneron: Institutional support Emily T. Martin, PhD, MPH, Merck: Grant/Research Support Matthew Exline, MD, Abbott Labs: Honoraria|Regeneron: Grant/Research Support Adam S. Lauring, MD, PhD, Roche: Advisor/Consultant|Sanofi: Advisor/Consultant"} +{"text": "Our objective was to assess their Kp clinical isolates were selected. Minimum inhibitory concentrations (MICs) were determined by broth microdilution in triplicate. Time-kill analyses were used to test CZA and MVB alone (1 and 4x MIC) and in combination with colistin , fosfomycin , gentamicin , meropenem , and tigecycline against 1x108 cFu/mL. 24 hour log-kill was calculated as log cFu/mL decrease from time 0.15 KPC-ompK36 WT, IS5, or GD. 27% and 73% were KPC-3 and KPC-2, respectively. 100% were susceptible to CZA and MVB. None were resistant to COL. 3 were non-susceptible to GEN, which were all IS5 (Table 1).5 isolates each had Figure 1). Mean log-kills did not vary for CZA + COL, GEN, or TGC against ompK36 mutants vs WT; however, log-kills were significantly lower for CZA + FOS or MEM against ompK36 mutants compared to WT. Synergy rates were reduced from 100% against WT to 80%, 60%, and 40% against mutant isolates for CZA + COL, MEM, and FOS, respectively .In combination with CZA 1x MIC, each of COL, GEN, and MEM were bactericidal against all isolates; mean \u00b1 standard error (SE) log kills were -7.39 \u00b1 0.3, -6.58 \u00b1 0.93, and -5.81 \u00b1 0.21, respectively . Mean \u00b1 SE log kills were significantly greater against porin mutants compared to WT for MVB + COL , FOS , or TGC . Rates of synergy were also higher against porin mutants vs WT for MVB + FOS or COL .MVB 1x MIC in combination with COL, FOS, GEN, and TGC were bactericidal 67, 27, 80, and 47% of the time, with corresponding log kills of -3.96 \u00b1 1.1, -1.56 \u00b1 0.83, -5.05 \u00b1 0.82, and -2.53 \u00b1 0.28, respectively and MVB (meropenem-vaborbactam) at 1X MIC, stratified by ompk36 status: wild-type (WT) versus mutant (MUT). Bactericidal is defined as -3 log kill from time 0 at 24 hours and indicated by the dotted horizontal line. COL = colistin; FOS = fosfomycin; GEN = gentamicin; MEM = meropenem; MIC = minimum inhibitory concentration; TGC = tigecycline.Figure 2Proportion of bactericidal, synergistic, and antagonistic outcomes for ompK36 wild-type versus mutant KPC-Kp isolates tested against CZA (ceftazidime-avibactam) or MVB (meropenem-vaborbactam) at 1X MIC as single agents and in combination with colistin (COL), gentamicin (GEN), tigecycline (TGC), meropenem (MEM), or fosfomycin (FOS). Bactericidal activity was defined as -3 log kill from time 0 at 24 hours; synergy and antagonism were defined as -2 or +2 log kill at 24 hours compared to most active single agent, respectively.Porin mutations negatively impact CZA synergy with other antibiotics compared to WT, though 24-hour log kills for COL, FOS, GEN, and MEM remained below the bactericidal threshold. Conversely, porin mutations potentiate synergy between MVB and COL, FOS, or TGC.Ryan K. Shields, PharmD, MS, Allergan: Advisor/Consultant|Cidara: Advisor/Consultant|Entasis: Advisor/Consultant|GSK: Advisor/Consultant|Melinta: Advisor/Consultant|Melinta: Grant/Research Support|Menarini: Advisor/Consultant|Merck: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Roche: Grant/Research Support|Shionogi: Advisor/Consultant|Shionogi: Grant/Research Support|Utility: Advisor/Consultant|Venatorx: Advisor/Consultant|Venatorx: Grant/Research Support"} +{"text": "Scientific Reportshttps://doi.org/10.1038/s41598-019-41543-0, published online 21 March 2019Correction to: This Article contains errors. In Figure 6C the OS image for SCR siRNA is incorrectly duplicated as the Figure 8C OS image for CNT. The correct Figure"} +{"text": "Kosakonia pseudosacchari RX.G5M8, a putative methylotroph, was isolated from garden soil in Hong Kong. Its complete genome, a single chromosome of 4,953,935 bp (GC content 53.91%), was established through hybrid assembly. Kosakonia, designated in 2013 after reassignment of four species of Enterobacter was vortexed with 900 \u00b5L 0.9% (wt/vol) saline and a 10-\u00b5L aliquot used to inoculate 1 mL of a minimal salts medium (MSM) containihttps://github.com/FelixKrueger/TrimGalore) , giving 2,137,624 read pairs totaling ~534 Mbp. Long-read libraries, prepared from the same extracted DNA using the Rapid Barcoding Kit SQK-RBK004 (without size selection), were sequenced via Oxford Nanopore\u2019s Spot-ON Flow Cell (vR9.4.1) and MinION sequencer, with MinKNOW v20.06.2 software and basecalling by Guppy v6.1.5 high-accuracy mode. The final long-read data set, trimmed by Filtlong v0.2.1 (https://github.com/rrwick/Filtlong) , totaled 63,710 reads (984 Mbp) with mean length 15,448 bp . Default parameters were used for all software unless otherwise specified.A paired-end short-read sequencing library (NEB Next Ultra DNA Library Prep Kit) was sequenced via the NovaSeq 6000 platform using an SP PE250 flowcell and v1.5 Reagent Kit. Reads were quality filtered and trimmed using TrimGalore! v0.6.7 (Kosakonia pseudosacchari strain BDA62-3 (CP063425), with an average nucleotide identity of 98.67%.Unicycler v0.4.3 combinedRX.G5M8 possesses a glutathione-dependent formaldehyde detoxification pathway for methanol metabolism . The nit"} +{"text": "The primary objective of this study was to characterize meropenem (MERO) pharmacokinetics (PK) in critically ill infants and children with septic shock to develop dosing recommendations to achieve therapeutic drug exposure in this complex population with a spectrum of renal function from augmented renal clearance (ARC) to acute kidney injury (AKI).Children \u22654 weeks old hospitalized with septic shock requiring fluid resuscitation and pressors, receiving MERO 20 mg/kg IV every 8 hr as standard-of-care, were enrolled and studied prospectively from 2019 to 2023. Population PK modeling was used to derive Bayesian post-hoc PK parameters (NONMEM 7.3). Renal biomarkers were evaluated as covariates. Estimated glomerular filtration rate (e-GFR) was calculated by the modified Schwartz equation.A total of 304 MERO serum concentrations were included from 26 participants. Median age was 12.6 yr (range 1.2-19.6); weight 38.4 kg (10-98); SCr 0.36 mg/dL (0.09-2.57); CYS 448.9 mg/d (178.3-1824.1), and NGAL 176.05 ng/mL (29.3-1000). Median MERO serum concentration was 11 mcg/mL . A two-compartment model with allometrically scaled weight on clearance (0.75) best described the data. Significant covariates were e-GFR, CYS, NGAL, age, diagnosis of appendicitis and albumin. Using the final model, the median CL was 0.15 L/hr/kg and V1 0.20 L/kg, with GFR 139 mL/min/1.73 m2 . The distribution of MERO concentrations, CL and GFR across quartiles documents wide variations in renal function observed in septic shock, from AKI to ARC .Meropenem Serum Concentration, Meropenem Renal Clearance, and Glomerular Filtration Rate, by QuartilesWide variation in MERO plasma exposure was documented in children with septic shock across the spectrum of renal function. GFR-based dosing recommendations may optimize MERO dosing and improve outcomes in this population.This work was supported by NICHD grant 1 R01 HD095547-01Edmund Capparelli, PharmD, Melinta: Advisor/Consultant"} +{"text": "The physicochemical properties of silver nanocomposites (MTP(BTP)/Ag NCs) were fully elucidated using spectroscopic and microscopic tools. The antibacterial activity of the nanocomposites was screened against six multidrug-resistant pathogenic strains, comparable to ampicillin and ciprofloxacin commercial drugs. The antibacterial performance of BTP was more substantial than MTP, notably with the best minimum inhibitory concentration (MIC) of 0.0781 mg/mL towards Bacillus subtilis, Salmonella typhi, and Pseudomonas aeruginosa. Among all, BTP provided the clearest zone of inhibition (ZOI) of 35 \u00b1 1.00 mm against Salmonella typhi. After the dispersion of silver nanoparticles (AgNPs), MTP/Ag NCs offered dose-dependently distinct advantages over the same nanoparticle with BTP; a more noteworthy decline by 4098 \u00d7 MIC to 0.1525 \u00d7 10\u22123 mg/mL was recorded for MTP/Ag-1000 against Pseudomonas aeruginosa over BTP/Ag-1000. Towards methicillin-resistant Staphylococcus aureus (MRSA), the as-prepared MTP(BTP)/Ag-1000 displayed superior bactericidal ability in 8 h. Because of the anionic surface of MTP(BTP)/Ag-1000, they could effectively resist MRSA (ATCC-43300) attachment, achieving higher antifouling rates of 42.2 and 34.4% at most optimum dose (5 mg/mL), respectively. The tunable surface work function between MTP and AgNPs promoted the antibiofilm activity of MTP/Ag-1000 by 1.7 fold over BTP/Ag-1000. Lastly, the molecular docking studies affirmed the eminent binding affinity of BTP over MTP\u2014besides the improved binding energy of MTP/Ag NC by 37.8%\u2014towards B. subtilis-2FQT protein. Overall, this study indicates the immense potential of TP/Ag NCs as promising nanoscale antibacterial candidates.Newly synthesized mono- and bis-thioureidophosphonate (MTP and BTP) analogues in eco-friendly conditions were employed as reducing/capping cores for 100, 500, and 1000 mg L Recently, the emergence of antibiotic-resistant microbes has been seen as a global health concern affecting many people\u2019s lives . Regardi\u22121. The nuclear magnetic resonance (NMR) spectra were consecutively recorded at 400, 101, and 162 MHz in DMSO-d6 using a Bruker Avance III HD, 600 MHz-NMR spectrometer probe, and BBFO cryoprobe . The elemental analysis of samples was undertaken for the raw TP derivatives (MTP and BTP) by CHNS Vario EL III Elementar analyzer, Germany. The phosphorus content (%) was estimated via the chemical digestion in sulfuric/nitric solution and photometric measurements at \u03bbmax = 410 nm. Melting points (m.p) were recorded using without correction. The surface images of nanocomposites were obtained using transmission electron microscope (TEM) by JEOL, JEM-2100 Tokyo, Japan. The crystalline properties of nanocomposites were obtained using powder X-ray diffraction (XRD) analysis using Shimadzu 6000 X-ray diffractometer with Cu K\u03b1-radiation (\u03bb = 1.54 nm) at 25 \u00b0C in the 2\u03b8 range of 10\u201380\u00b0 operating at a scan rate of 1 deg/min. X-ray photoelectron spectroscopy (XPS) was conducted using a Perkin Elmer PHI 5600, Perkin Elmer Instruments, Waltham, MA, USA, with analytical zone\u2019s diameter of 1 mm and indium sheets for sample deposition using Al K\u03b1 X-rays radiation source (200 W). The photometric assays of antibacterial results were measured by (Infinite F50 Robotic absorbance microplate reader) in the wavelength range of 400 to 750 nm. The zeta potential charge of silver nanocomposites was determined via dynamic light scattering using Zetasizer Nano ZS, Malvern Instruments Ltd., Malvern, UK. Scanning electron microscopy (SEM) was performed using JSM 6390 LA, JEOL, Tokyo, Japan, with a 15 KV accelerating voltage.The Fourier transform infrared spectroscopy (FT-IR) analysis has been accomplished for all samples on Bruker Alpha II spectrometer, Bremen, Germany, in the wavenumber range 4000\u2013400 cm3) were purchased from Aladdin . Solvents, such as acetonitrile (CH3CN), ethanol, and methanol were obtained from a commercial supplier and used without further drying and purification. Deionized water was used to prepare all solutions and suspensions.Thiourea and triphenyl phosphite were obtained from Macklin . Terephthalaldehyde , pyridinium trifluoromethanesulfonate (as protic ionic liquid), and silver nitrate with the aid of a pyridinium trifluoromethanesulfonate (pyridinium triflate) as a Lewis acid protic ionic liquid-based catalyst. In the meantime, thiourea /, terephthalaldehyde, triphenyl phosphite /, and pyridinium triflate / in 5 and 10 mL of CH3CN were progressively incorporated, affording MTP and BTP in a molar ratio of 1:1:1 and 2:1:2, respectively. Further, both solutions were magnetically stirred overnight under ambient conditions and the reaction was monitored via qualitative thin layer chromatography (TLC) using hexane\u2013methylene chloride (3:1) as eluent mixture. Eventually, the final products were filtered off under vacuum, washed with methanol, dried, and kept in a desiccator for 2 days giving MTP and BTP in good yields.The synthesis process included preparation of two different systems of mono and bis thioureidophosphonate (TP) products, where the involved components were dissolved in acetonitrile (CHDiphenyl ((4-formylphenyl) (thioureido)methyl) phosphonate, denoted as mono-thioureidophosphonate (MTP):\u22121 (NH)str. + (NH2) str. overlapped, 3057.58 cm\u22121 , 2894.63 cm\u22121 , 1698.02 cm\u22121 , 1590.99 cm\u22121, (NH+NH2) bending, 1525.42 cm\u22121 (>C=C<) phenyl rings, 1488.78 cm\u22121 (>C=S) asym., 1194.69 cm\u22121 (-P=O), 944.95 cm\u22121 (P-O-C), 760.78 cm\u22121 (P\u2013C), and 684.61 cm\u22121 (>C=S) sym. 1H-NMR; \u03b4 ppm: 5.50 , 6.63\u20137.99 , 9.40\u20139.52 , 9.76 , and 10.04 . 13C-NMR ; \u03b4 ppm: 54.59 and 56.16 ppm (P-C\u2013H), 115.24, 120.22, 120.53, 125.39, 127.96, 128.92, 129.90, 149.80 (Ar-C), 183.84 (>C=S), and 192.73 (-CHO). 31P-NMR ; \u03b4 14.08 ppm. Elemental analysis calc. (%) for C21H19N2O4PS: C, 59.15; H, 4.49; N, 6.57; P, 7.26; S, 7.52; and O, 15.01; meas. (%): C, 57.85; H, 4.27; N, 6.34; P, 6.97; and S, 6.99.Light-beige solid, yield: , m.p: 160\u2013163 \u00b0C, FT-IR: 3457.74\u20133311.18 cmTetraphenyl ) bis(phosphonate) denoted as bis-thioureidophosphonate (BTP):\u22121 [(NH)str. + (NH2) str. overlapped], 3057.58 cm\u22121 , 2895.59 cm\u22121 , 1591.95 (>NH + -NH2) bending, 1527.35 cm\u22121 (>C=C<) phenyl rings, 1489.74 cm\u22121 (>C=S) asym., 1195.65 (-P=O), 947.84 (P-O-C), 761.74 cm\u22121 (P\u2013C), and 761.74 cm\u22121 (>C=S) sym. 1H-NMR; \u03b4 ppm: 5.93 , 6.54\u20137.61 , 9.21\u20139.33 , and 9.38 ppm . 13C-NMR ; \u03b4 ppm: 54.50 and 56.06 (P-C\u2013H), 115.26, 120.29, 120.86, 125.40, 127.50, 129.33, 129.84, and 149.94 (Ar-C), and 183.83 (>C=S). 31P-NMR ; \u03b4 ppm: 14.85 ppm. Elemental analysis calc. (%) for C34H32N4O6P2S2: C, 56.82; H, 4.49; N, 7.82; P, 8.62; S, 8.92; and O, 13.36; found: C, 54.97; H,4.36; N, 8.18; P, 8.83; and S, 7.91.Light-yellow solid, yield: , m.p: 135\u2013137 \u00b0C, FTIR: 3310.21 cm3 solution of 100, 500, and 1000 mg L\u22121 concentrations. Then, the prepared solutions were magnetically stirred (200 rpm) for 12 h, at ambient conditions. Afterward, the attained colloidal solutions were centrifuged, and the settled nanoparticles were washed with ethanol/deionized water and then oven-dried at 50 \u00b0C for further characterization ..36].Well dispersed AgNPs were produced via one-pot synthesis method using thioureidophosphonates (TPs) as dual-functioning reducing and capping agents. This affords spherical AgNPs different dispersion patterns based on the reaction conditions of AgNPs precursor concentrations and the structure of TPs .\u22121) illustrated meaningful changes in the characteristic absorption bands of capping agent (MTP) was also involved in the interaction and reduction of Ag+ ions in all concentrations of 100, 500, and 1000 mg Ag L\u22121, respectively. Further, the aliphatic (H-C-P) bond was dramatically shifted from \u03bd = 2895 cm\u22121 to \u03bd = 2914 cm\u22121 in MTP/Ag-1000. On the other side, the FT-IR spectra of BTP and its AgNP dispersions displayed similar changes, with a substantial shifting of amine functional groups from \u03bd = 3310 cm\u22121 to \u03bd = 3306, 3305, and (3320\u20133428) cm\u22121, consecutively a. Notablcutively b. Hence,cutively . Basicalg Ag L\u22121 .+ ions, while the higher density of chelating centers in BTP significantly improved the reduction rate of Ag+ ions (with deeper color); thus, some smaller AgNPs were attained with the BTP surface (The morphology and dispersion nature of developed silver nanoparticles (AgNPs) were scrutinized using microscopic techniques. Accordingly, the TEM imaging for MTP/Ag-500 displayed good dispersion of spherical AgNPs with an average mean size range of 6.8\u201320.1 nm a\u2013c. On t surface d\u2013f. The Moreover, the crystallinity of the as-synthesized TPs after AgNPs functionalization was investigated compared to that of raw capping agents using XRD analysis. First, broad XRD patterns were individually centered at 2 theta (2\u03b8) = 21.7\u00b0 with (110) diffraction phases, reflecting the amorphous structure of both raw MTP and BTP analogues. The emergence of broad patterns stemmed from the strong inter- and intra-molecular hydrogen bonding in raw TP cores . Further+ ions incorporation and formation of AgNPs, X-ray photoelectron spectroscopy analysis (XPS) was carried out for MTP/Ag-500. The XPS results of MTP/Ag-500 were studied based on evaluating the changes in binding energies (BEs), atomic percentages (%), electronic properties, and chemical composition of MTP before and after Ag+ ion interactions. Five elemental signals of C 1s (at BE: 285.84\u2013287.23 eV), N 1s (400.72\u2013401.63 eV), O 1s (533.02\u2013534.81 eV), P 2p (134.32\u2013134.57 eV), and S 2p (163.19\u2013164.19 eV) were mainly evolved, consecutively eV, besides considerable changes in the atomic percentages (%) of raw elemental functional groups that were estimated from 0.72\u201325.57%. Basically, these notably affected functional groups were ordered, respectively, in a descending mode according to changes in BEs as follows: C\u2013S (2p1/2) > C\u2013C, C\u2013H, and C=C > HC=O and -OH (H2O) > C\u2013S (2p3/2) > P\u2013C and P\u2013O (2p1/2) > >NH and -NH2 > C=S > C\u2013N > \u03c0\u2013\u03c0* sat, benzene rings, and C=S > C-OH, P\u2013O, and C\u2013O\u2013C > C\u2013O, C\u2013N, C\u2013P, and C=O on the MTP, the main signal deconvolution assessed that Ag+ ions may be sorbed in their hydrated form . In this regard, the changes that occurred in BEs after AgNPs decoration were consistent with the results discussed before.To validate the most significant changes that occurred to raw functional groups after Agcutively . Regardiectively b 62]. H. H+ ions and C=O . FurtherStaphylococcus aureus (MRSA), Streptococcus mutans, and Bacillus subtilis) and Gram-negative bacteria as well. Moreover, zone of inhibition diameters, minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), time\u2013kill kinetics, antiadhesion activity, and antibiofilm assay with morphological investigation were assessed for all developed compounds.The antibacterial potency of synthesized thioureidophosphonates (TPs) and their fabricated AgNPs-based composites was evaluated against several strains. The antibacterial activity using the agar well diffusion method was conducted against six clinical bacterial strains and their ATCC references of Gram-positive (methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus mutans (S. mutans), and Bacillus subtilis (B. subtilis), compared to Ampicillin and Ciprofloxacin as reference antibiotics resulted in higher MIC values = 1.25 mg/mL for both analogues. MTP and BTP recorded MICs at lower concentrations of 0.625 and 0.3125 mg/mL against S. mutans (ATCC-35668) and B. subtilis (ATCC-6633), progressively. The zone of inhibition (ZOI) was measured for each strain with DMSO as a negative control. Including the diameter of each well (6 mm) before treatment, MTP gave ZOIs in a range of 28 \u00b1 1.0, 30 \u00b1 1.00, and 24 \u00b1 1.00 mm, whereas the treatment with BTP increased the ZOIs width towards MRSA, S. mutans, and B. subtilis strains, respectively. Both TPs with MBC/MIC ratio of 2(+) have bactericidal properties, unlike Ampicillin and Ciprofloxacin. TPs loaded with silver nanoparticles (AgNPs) were used to investigate the antibacterial properties towards three strains accompanied with a dose-dependent improvement in susceptibility. A clear MIC decline to very minute concentrations was appreciated from 0.156 to 0.1525 \u00d7 10\u22123 mg/mL with the three strains. The MIC of MTP significantly dropped by (4 \u00d7 MIC) after treating MRSA and S. mutans with MTP/Ag-100. Afterward, MTP/Ag-500 and MTP/Ag-1000 showed increased bactericidal properties against both strains, i.e., 16 and 2049 times sequentially. The treatment of MTP/Ag- to B. subtilis increased the potential bactericidal activity by 16, 128, and 1024 times, respectively. BTP/Ag-100 showed a more significant decline in MIC values by two and eight times against MRSA and B. subtilis, compared to MTP/Ag NCs. BTP/Ag-500 had less biocidal effects by 4 and 16 times that of MTP/Ag-500 on MRSA and B. subtilis, consecutively. This reflected that BTP and AgNPs have less synergistic interactions than MTP. However, BTP/AgNPs had the same bactericidal activity as MTP/AgNPs against S. mutans in 100 and 500 dispersions. Noteworthy, MTP and BTP loaded with 1000 mg L\u22121 resulted in a decrease in MICs by 2049 times against MRSA while BTP/Ag-1000 showed higher MIC against S. mutans and B. subtilis by only 1023 and 512 times, respectively , 38 \u00b1 1.00 (MTP/Ag-500), and 42 \u00b1 1.00 mm for MTP/Ag-1000, respectively. Likewise, ZOIs exhibited a gradual increase from 37 \u00b1 1.00 in BTP to 40 \u00b1 1.00 (BTP/Ag-100), 43 \u00b1 0.60 (BTP/Ag-500), and 49 \u00b1 0.100 mm (BTP/Ag-1000). MTP and BTP gave higher ZOIs with diameters of 35 \u00b1 1.00, 38 \u00b1 1.00, and 40 \u00b1 1.00 mm and 36 \u00b1 1.00, 41 \u00b1 1.00, and 41 \u00b1 1.00 mm, respectively, for B. subtilis , Salmonella typhi (S. typhi), and Serratia marcescens (S. marcescens) than previously screened Gram-positive bacteria and reference antibiotics against P. aeruginosa than MTP, indicating higher susceptibility towards Gram-negative strains. Both MTP and BTP compounds had excellent inhibitory properties against S. typhi and S. marcescens, as their MIC ratio was reduced fourfold. Regarding the Ampicillin and Ciprofloxacin, 5\u00d7 and 20\u00d7 MIC reductions by MTP were recorded against S. typhi, while 5.0 and 1.2\u00d7 MIC were dropped with S. marcescens. On the contrary, BTP decreased the MICs of Ampicillin and Ciprofloxacin by 20 and 80 times towards S. typhi, and to 20 and 5 times against S. marcescens, respectively. Furthermore, the selectivity of these TP derivatives was determined against P. aeruginosa (ATCC-27853), S. typhi (ATCC-6539), and S. marcescens (ATCC-13880). Meanwhile, the MICs obtained by inoculating both ATCC isolates of P. aeruginosa and S. marcescens with MTP were 1.25 mg/mL for S. typhi (ATCC-6539). The selectivity of MTP was more effective, affording an MIC value of 0.625 mg/mL. BTP had two lowered MIC values against P. aeruginosa (ATCC-27853), S. typhi (ATCC-6539), and S. marcescens, with 0.3125 mg/mL for P. aeruginosa and 0.625 mg/mL for S. marcescens (ATCC-13880). On the other hand, ZOI results of MTP and BTP against P. aeruginosa, S. typhi, and S. marcescens were 28 \u00b1 1.00, 28 \u00b1 1.00, and 35 \u00b1 1.00 mm for MTP, while 33 \u00b1 0.60, 35 \u00b1 1.00, and 38 \u00b1 1.00 mm for BTP, consecutively. Therefore, MBC values ranged from 1.25 to 0.156 mg/mL, resulting in a significant bactericidal efficacy against all bacterial strains with MBC/MIC ratio = 2(+). Notably, AgNPs improved the antibacterial susceptibility of TP cores, lowering MIC values from 0.01953 mg/mL to 7.629 \u00d7 10\u22125 mg/mL. Basically, MTP/Ag-100 minimized the MIC concentration of raw MTP by around 32 times towards P. aeruginosa, and 16 times for both S. typhi and S. marcescens, successively. MTP/Ag-500 reduced MICs by 256 times for P. aeruginosa and 128 times for S. typhi and S. marcescens compared to raw MTP. For MTP/Ag-1000, MTP displayed an elevated antibacterial activity towards P. aeruginosa, S. typhi, and S. marcescens. Nevertheless, the net antibacterial activity of BTP was higher than MTP, and the combinatorial interactions of AgNPs with MTP were more tunable, unlike BTP. In the meantime, BTP/Ag-100 lessened the MIC ratio to raw BTP by fourfold towards P. aeruginosa and eightfold against both S. typhi and S. marcescens. BTP/Ag-500 had a remarkable bactericidal effect on S. typhi up to 128 times. Then, the BTP/Ag-1000 reduced the dose of MIC to 512 times with P. aeruginosa and 1023 times with both S. typhi and S. marcescens, respectively. Pertinently, BTP loaded with AgNPs manifested less powerful bactericidal potency than MTP capped AgNPs started to dramatically decline after 1 h of treatment (10) and (1.8 log10) CFU/mL after 18 h of incubation, respectively. However, once MRSA was treated with TP/Ag NCs, the picture was changed where the MTP/Ag-100 induced the killing potential with cell count reductions to (2.2 log10) and (0.9 log10) CFU/mL for MTP/Ag-500, consecutively. More significant reductions of the cultural population of MRSA were achieved to (1.1 log10) and (0.3 log10) CFU/mL for BTP/Ag-100 and BTP/Ag-500, progressively. Despite the higher killing efficacy of BTP/Ag NCs than MTP/Ag NCs, the combination between AgNPs and MTP brought more bactericidal advantages over BTP, which was observed from the gradual improvement of killing (%) between dose 100 and 500 for both AgNPs formulations. Remarkably, the entire population was reduced and killed within 8 h, for both MTP (BTP)/Ag-1000 composites. Interestingly, the bactericidal rates towards MRSA were previously confirmed by both TP/Ag-1000; where both reduced MBC values to the same degree of 2049 times of MRSA (ATCC-43300) suspensions for 18\u201324 h, using vancomycin hydrochloride (VAN) as a positive control, and the negative control was tryptic soy broth (TSB). Antiadhesion activity was quantitatively estimated against MRSA (ATCC-43300) on the microplate reader at \u03bbmax = 570 nm, validating an increase in MRSA (ATCC-43300) detachment in a dose-dependent manner within 1.25, 2.5, 5.0, and 10 mg/mL than MTP, which could be attributed to its superior hydrophobic characteristics as the non-polar parts (aromatic rings) exceeded the polar ones, based on its molecular formula (M.F), namely, C34H32N4O6P2S2, comparable to MTP with M.F of C21H19N2O4PS. Moreover, the electrostatic repulsion forces assessed between the negatively charged MTP/Ag NCs and MRSA (ATCC-43300) surface played a critical role . Ad. Ad6 CFUactivity . On thisStaphylococcus aureus (MRSA) is one of the most opportunistic and resistant pathogens, being able to produce an extracellular polymeric substance (EPS) inducing biofilm growth prior to the occurrence of cross infection [MRSA (ATCC-43300) as a Gram-positive bacterium with reference to vancomycin hydrochloride (VAN) as a positive control. The biofilm disintegration activity (%) was validated by the microtiter plate assay using a semi-quantitative analysis based on crystal violet staining. Regarding 96-well plates treated with raw MTP and BTP, the biofilm (violet color circle) was slightly eliminated, while the gradual removal was notably viewed by six TP/Ag NCs, (max \u2248 570 nm with respect to the negative control of tryptic soy broth (TSB). The results showed a significant reduction in biofilm growth when treated with raw TPs, even after 24 h of incubation. The biofilm inhibition (%) was promoted with the gradual increase in the concentrations of tested compounds in the 1.25, 2.5, 5.0, and 10.0 mg/mL (MRSA (ATCC-43300). The studied TP cores (\u03b1-aminophosphonate derivatives) are considered structural bio-isosteres of \u03b1-amino acids (peptides) with a common amine functional group, but the carboxylic groups in \u03b1-amino acids are replaced with related phosphorous-containing moieties such as phosphonic acid. However, the reported data about their antibiofilm mechanism of action towards MRSA biofilm are directed for hybrid \u03b1-APs; thus, the inhibitory actions of mentioned \u03b1-APs analogues were proposed [Methicillin-resistant nfection . The ant/Ag NCs, . Therefo.0 mg/mL . Yet, frproposed ,73. Firsproposed . Moreoveproposed . It was proposed ,76.+ ions and reactive oxygen species (ROS), which increased the toxic effects on the integrity of bacterial cell wall. Additionally, ROS can cause the total impairment of envelope-bound proteins, deoxyribonucleic acid (DNA), respiratory coenzymes, and antioxidants such as glutathione (GSH) [MRSA (ATCC-43300) in the next section [After AgNPs functionalization, biofilm inhibition capability (%) was promoted for both MTP and BTP in all studied concentrations , consecutively. The most effective and synergistic concentration needed for the disruption of MRSA (ATCC-43300) biofilm was observed at 5.0 mg/mL for both TP/Ag NCs. For 10.0 mg/mL, the biofilm eradicating ability for both MTP(BTP)/Ag-1000 reached maximum values at 79.5 and 83.6%, progressively . Nonethene (GSH) . RemarkaMRSA (ATCC-43300) was also qualitatively verified through scanning electron microscopy (SEM) after incubation by 100 \u00b5g/mL of raw compounds and their TP/Ag-1000. The two upper images (MRSA (ATCC-43300) surface on which aggregating grape-like colonies were developed to form the biofilm. On the contrary, low percentages of biofilm clusters were present on the surfaces of MRSA (ATCC-43300) after treatment with raw MTP and BTP, indicating that these compounds could prevent bacterial biofilm formation and induce cell death. Moreover, almost no biofilm matrices could be observed on MRSA treated with MTP and BTP decorated with AgNPs, validating the potent biofilm disintegration ability of TP/Ag NCs. In summary, these observations were in line with antibiofilm investigation results and other studies referring to the ability of synthesized AgNPs to severely interfere with cell wall (biofilm) components, thus hampering metabolic functions, and thereby, MRSA (ATCC-43300) cells are killed [The biofilm inhibition of r images represene killed .MRSA and B. subtilis) and Gram-negative (P. aeruginosa and S. typhi) bacterial proteins with respective codes of PDB: 4DKI, 2FQT, 5ZHN, and 3ZQE, in addition to confirming their illegibility as antibacterial agents with the experimental work. Furthermore, the docking results for the prepared raw compounds (MTP and BTP) in all downloaded proteins, along with type of chemical bonding and the amino acids involved in the interaction with the protein, were estimated. Additionally, values recorded for binding affinity and root mean square deviation (RMSD) were tabulated. There are different types of interactions, including hydrogen and hydrophobic H-pi interactions, with the binding sites of all the investigated proteins for MRSA, with values of \u22127.9776 kcal/mol and \u22127.9074 kcal/mol, respectively. Amino acids involved in the interaction between BTP and the B. subtilis protein were GLY127 , GLY127 , and GLU57 , which are the same amino acids involved in the interaction of the co-crystallized ligand and the protein and TYR446 and thereby for biofilm growth [Molecular docking studies were conducted for the prepared TP compounds to investigate their binding affinity for Gram-positive , while Tcutively . It was 1.2593 \u00c5 . Interesproteins . These bm growth ,82; thusIt is pertinent to note that in this study, the structural and functional diversity of raw TP surfaces afforded highly tunable surface interactions and synergy, with AgNPs giving remarkable antibacterial activity. Additionally, the molecular docking studies were in good coherence with most experimental results for TPs and TP/Ag NCs. Based on the above considerations, some structural modifications may be applied in the future to exploit these compounds in various applications such as antibacterial textile fabrics, antibacterial food packaging films, and antibacterial thermoplastic polymer nanocomposites ,84,85.p > \u22122.5 [50 value was 0.335 and 0.285log \u03bcg/L for MTP-AgNPs and BTP-AgNPs, respectively. The anticipated scores are summarized below.Absorption, distribution, metabolism, and excretion (ADME) analysis is very helpful in simplifying clinical trials, especially in the early stage of drug design. Intestinal absorption, skin sensitization, and oral bioavailability are absorption parameters considered in drug discovery . An intep > \u22122.5 ; howeverp > \u22122.5 ; it measp > \u22122.5 , MTP-AgNp > \u22122.5 . Regardip > \u22122.5 ,88. Comp+ ions affording TP/Ag NCs, the physicochemical properties of which were thoroughly investigated through FT-IR, -NMR, elemental analysis, and TEM, XRD, and XPS analyses, respectively. The antibacterial properties of the as-prepared raw cores were studied via tuning different concentrations of silver nitrate, i.e., 100, 500, and 1000 mg L\u22121. Both raw Mono-TP and Bis-TP analogues proved to be bactericidal towards all isolates. In a dose-increasing manner, time\u2013kill assay results manifested the record-breaking bactericidal effect of both MTP(BTP)/Ag-1000 towards all MRSA cells within 8 h. At high concentrations, the antifouling characteristics of evaluated compounds were influenced by the surface electrostatic repulsion with MRSA (ATCC-43300), while hydrophobicity played a critical role at lower concentrations. Targeting the biofilm of MRSA (ATCC-43300) was confirmed, with net activity of 79.5 and 83.6% for MTP/Ag-1000 and BTP/Ag-1000, progressively, at highest used concentration. Nonetheless, higher net antibiofilm activity was observed in BTP/Ag NCs; the simpler MTP structure tuned the surface work function with Ag+ ions, giving better colloidal AgNPs and a gradual improvement in the biofilm disruption % after the nanoloading. The docking results were in line with the experimental work, where the best results were estimated for raw BTP towards B. subtilis-2FQT protein, recording binding energy (BE) of \u22127.9776 Kcal/mol. Interestingly, the progress in BE of MTP/AgNPs to \u22127.6668 Kcal/mol could stem from the exerted Ag-acceptor bonds with both amino acids (SER80 and GLU57) of B. subtilis-2FQT protein. Further, in silico pharmacokinetics assessment was conducted as a step to predict the potential safety and toxicity of the TP/Ag NCs, which revealed AMES toxicity for one of the compounds with neither hepatic toxicity nor skin sensitization. In summary, this study has provided a good design for the synthesis and development of a new generation of nano-based aminophosphonate composites as promising antibacterial candidates, although their safety should be carefully evaluated for each specific application; further studies are needed to fully understand the toxicity mechanisms and the optimal conditions for their pharmaceutical application.Two potent antibacterial agents were facilely synthesized in a one-pot green Kabachnik\u2013Fields reaction and then exploited as reducing/capping surfaces for Ag"} +{"text": "Weight gain associated with integrase strand transfer inhibitors (INSTI) has been well documented among patients with HIV. However, recent reports suggest that the observed weight gain among patients who switch to INSTIs may be associated in part with their pre-switch regimen.We conducted retrospective analyses of a 50% sample of all treatment-experienced patients who switched to second-generation INSTI containing regimen (bictegravir/dolutegravir) at the Duke Adult Infectious Diseases Clinic between 1 January 2014 and 31 December 2021. Covariates included sex at birth, age, race, ethnicity, pre-switch regimen, body mass index (BMI), CD4 count and HIV-1 viral load. All weights documented within 24 months from regimen switch were included. Outcomes of interest were percent change in weight and absolute weight change. Ordinary least squares was used to obtain average percent weight change from baseline, adjusted for covariates.Overall, 339 persons were included in the analyses. Cohort demographics were: median age 51.2 , 73% male sex at birth, 56% Black, 4% Hispanic ethnicity. At regimen switch, median CD4 count was 671 (IQR 460-935), and 78% had a viral load < 200 copies/cc. Mean weight at regimen switch was 87.8 kg (standard deviation [SD] 22.1kg), and mean total weight change over 24 months post-switch was +1.3 kg (SD 7.1 kg). Overall, 28% of cohort members gained >5% of baseline body weight within 24 months of switch. Hispanic ethnicity and BMI < 20 were associated with post-switch weight gain. Only efavirenz-containing pre-switch regimens were significantly associated with weight gain over 24 months post-switch; EFV/FTC/TDF , all other EFV-containing regimens (6.3% [95% 0.1-12.4]).Pre-switch regimens containing efavirenz were significantly associated with weight gain after switch to second-generation INSTI-based regimens, consistent with findings from non-US based cohorts.Nwora Lance Okeke, MD MPH, Gilead Sciences: Advisor/Consultant"} +{"text": "PurposeMarijuana use has been increasing in the adolescent population. Our objective was to examine the prevalence of marijuana use among a sample of adolescents and young adults, determine an association with risk-taking behaviors, identify reported medical symptoms, and delineate common beliefs about marijuana use.MethodsA questionnaire was administered to a sample of patients aged between 12 and 23 years old presenting to the emergency department of Penn State Hershey Medical Center, Hershey, Pennsylvania. Data were stratified by marijuana users and non-users, and further stratified by traditional and non-traditional use.ResultsThe analysis was based on 200 questionnaires. Thirty-nine percent (n=78) reported marijuana use. Marijuana users were more likely to report previous sexual intercourse , as well as the use of alcohol , cigarettes , prescription pain medications , and cocaine . Users more likely reported texting while driving and experienced physical or electronic victimization due to bullying . Users were more likely to report gastroesophageal reflux disease (GERD), attention deficit disorder (ADD), anxiety, and depression. The most common symptoms associated with marijuana use were anxiety (65.4%), headache (61.6%), nausea/vomiting (53.8%), cough (51.3%), and abdominal pain (47.4%). Sixty-nine percent of respondents believed marijuana was \u201csafer than other drugs\u201d.ConclusionBased on our sample, we identified risk-taking behaviors, medical symptoms, and beliefs associated with marijuana use. Healthcare professionals may use these data to provide screening and anticipatory guidance to adolescents who use marijuana and consider marijuana use in their differential diagnosis. According to the 2021 Monitoring the Future study, marijuana use by adolescents declined from the late 1990s to the late 2000s but has since begun to rise again, peaking in 2020 with legalization both recreationally and medically in many states [Despite these negative consequences, many benefits of marijuana use have been cited. Clinical indications for medical marijuana vary by state but can include epilepsy and seizure disorders, cancer, HIV/AIDS, neurodegenerative disease, chronic pain, nausea, and post-traumatic stress disorder .In recent years, CBD has quickly grown in popularity in the form of oils, tinctures, and vapes as a treatment for a wide variety of diseases ranging from cancer to epilepsy, anxiety, pain control, and palliative care, with forms of epilepsy being the only FDA-approved indication to date . Many ofWhile there are many studies documenting different adverse effects associated with marijuana use -12, therWe conducted an observational, self-administered questionnaire-based study between August 2019 and September 2020, utilizing a sample of 200 patients presenting to the emergency department at the Penn State Hershey Medical Center, Hershey, Pennsylvania, aged 12 and 23 years. We excluded patients presenting with altered mental status, severe pain, developmental delay, acute psychiatric illness, or respiratory distress. Patients were also excluded if they were under 18 years of age, did not have a guardian present, were non-English speakers, or had previously completed the questionnaire.Once potential subjects were identified, the study team approached the patient and their guardian (for those less than 18 years old), obtained verbal consent, and provided the questionnaire and writing utensil. The questionnaire included 35 questions, focusing on demographics , risk-taking behaviors , self-esteem , medicalData were stratified by whether participants were marijuana users or non-users, and marijuana users were further stratified by traditional and non-traditional use. Marijuana users were those who reported marijuana use; non-users were those who did not report marijuana use. Traditional marijuana users were classified as those reporting using vapes, pipes, or edibles, and non-traditional marijuana users were those using oils or concentrates, topical creams, or others.Descriptive statistics were generated, including means and standard deviations for continuous variables. This was an exploratory survey to find out more information about marijuana, and therefore, no formal sample size calculation was performed. Comparisons between categorical variables were analyzed using contingency table analysis; significance levels were determined by Chi-square tests. Data were stratified by marijuana users and nonusers, and marijuana users were further stratified by traditional and nontraditional use. The internal consistency of Likert scale questions was assessed by Cronbach's alpha, which was found to be 0.89. No adjustments for multiple tests were made. Tests were two-sided and based on a significance criterion of p<0.05. A multivariable logistic regression was then run, including all variables that were significant in the univariate analyses. All analyses were performed with the use of the SAS statistical package, version 9.4 . The Pennsylvania State University Institutional Review Board approved this study .Data analysis was performed on 200 completed questionnaires. The mean age of respondents was 17.5 years; 62.5% were female, and 66% identified as White (Table Marijuana use was reported in 39% (n=78) of respondents: 59% (n=46) were traditional, and 41% (n=32) were non-traditional. Marijuana users were less likely to live in a two-parent household than non-users (30.8% (95% CI: 22-42) vs. 54.1% (95% CI: 45-63); p= 0.0055).When stratified by frequency of use, compared to non-users, users were also more likely to have had previous sexual intercourse (79.5% (95% CI: 69-87) vs. 32.8% (95% CI: 25-41.6); p=<0.0001), and have had coitarche before age 18 (53.8% (95% CI: 43-64.5) vs. 21.3% (95% CI: 15-29.5); p=<0.0001) vs. 10.7%% (95% CI: 6-17.5); p=<0.0001), cigarettes use (41% (95% CI: 30-52) vs. 8.2% (95% CI: 4-14); p=<0.0001), cigars use (30.8% (95% CI: 22-42) vs. 3.3% (95% CI: 1-8); p=<0.0001), chewing tobacco use (18% (95% CI: 11-28) vs. 0.8% (95% CI: 0-4); p<0.0001), prescription pain medications without a prescription (20.5% (95% CI: 13-31) vs. 4.1% (95% CI: 1-9); p=0.002), and cocaine use (14.1% (95% CI: 8-24) vs. 0.8% (95% CI: 0.01-5); p=0.0017) (24.4% (95% CI: 16-35) vs. 9.0% (95% CI: 5-15.6); p=0.0164), anxiety (57.7% (95% CI: 47-68) vs. 35.2% (95% CI: 27-44); p=0.007), attention deficit disorder (ADD) (29.5% (95% CI: 20-40) vs. 10.7% (95% CI: 6-17.5); p=0.003), and depression (51.3% (95% CI: 40-62) vs. 27.9% (95% CI: 21-36); p=0.002). There were no significant differences between users and non-users who reported the following symptoms during the previous six months: chest pain, racing heart, difficulty breathing or coughing, dizziness, abdominal discomfort, nausea or vomiting, headache, tremors, sleep disturbances, or dehydration. However, there was a statistically significant increase in reports of anxiety in users as compared to non-users (66% (95% CI: 55-76) vs. 47% (CI: 38-56); p=0.009) (Table The most common symptoms associated with marijuana use were anxiety (65.4%), headache (61.6%), nausea/vomiting (53.8%), cough (51.3%), and abdominal pain (47.4%); there was no significant difference in symptom reports between traditional and nontraditional users.Vapes (25.6%) and pipes (25.6%) were the most common forms of marijuana use reported, and 61.6% of respondents reported using marijuana recreationally Table .With respect to perceived beliefs, 64% of respondents believed cannabis products are \u201cless addictive than other drugs,\u201d 69% believed they are \u201csafer than other drugs,\" 48% believed they \u201chelp to treat my medical illness\u201d and 33% believed that marijuana use is \u201cjust for fun.\" When asked to report a myth regarding cannabis products, respondents reported many common phrases, including \u201cit is a gateway drug\u201d (n=11), \u201cit is addictive\u201d (n=9), and \u201cit can kill you\u201d (n=7).After a multivariable logistic regression of all variables that were significant in the univariate analyses, the variables that ended up being significant in the final model were: bullying, sex, cigars, weakness, ADD, and anxiety , and anxiety complaints. More research is necessary to ensure the safe and appropriate use of marijuana as a plant-derived medication for adolescents and adults alike. Discovering key clinical symptomatology will aid physicians in identifying adolescents using marijuana. Furthermore, physicians should consider marijuana use in adolescents and young adults with high-risk behaviors presenting with anxiety-related complaints or other common symptoms associated with marijuana use, such as headache, nausea/vomiting, cough, and abdominal pain."} +{"text": "The last few years have witnessed dramatic advances in our understanding of the structure and function of the mammalian mito-ribosome. At the same time, the first attempts to elucidate the effects of mito-ribosomal fidelity (decoding accuracy) in disease have been made. Hence, the time is right to push an important frontier in our understanding of mitochondrial genetics, that is, the elucidation of the phenotypic effects of mtDNA variants affecting the functioning of the mito-ribosome. Here, we have assessed the structural and functional role of 93 mitochondrial (mt-) rRNA variants thought to be associated with deafness, including those located at non-conserved positions. Our analysis has used the structural description of the human mito-ribosome of the highest quality currently available, together with a new understanding of the phenotypic manifestation of mito-ribosomal-associated variants. Basically, any base change capable of inducing a fidelity phenotype may be considered non-silent. Under this light, out of 92 previously reported mt-rRNA variants thought to be associated with deafness, we found that 49 were potentially non-silent. We also dismissed a large number of reportedly pathogenic mtDNA variants, 41, as polymorphisms. These results drastically update our view on the implication of the primary sequence of mt-rRNA in the etiology of deafness and mitochondrial disease in general. Our data sheds much-needed light on the question of how mt-rRNA variants located at non-conserved positions may lead to mitochondrial disease and, most notably, provide evidence of the effect of haplotype context in the manifestation of some mt-rRNA variants. Aminoglycoside antibiotics (AGs) are some of the most commonly prescribed antibacterials, despite their well-known capacity to cause toxic side effects to the kidneys and inner ear . AlthougOur understanding of the mito-ribosome has advanced much more slowly than that of other ribosomal systems. In particular, the issue of the maintenance of mito-ribosomal fidelity, defined as the accuracy of decoding during mitochondrial translation, could not be tackled until very recently. Despite this, evidence obtained mostly from studies with chimeric mito-bacterial ribosomes, as well as in yeast, has been successfully used to ascertain that decreased mito-ribosomal fidelity was behind the deleterious effect caused by the two known ototoxic variants . The recIn this analysis, we used a total of 83 and 9 variants, identified in deafness patients, that mapped to the mito-ribosomal small and large subunit (SSU and LSU) mt-rRNAs, respectively. The variants originated from 35 studies reported in the literature (80 variants), MITOMAP (2 variants), and this work (1 variant) Ruiz-Pe. Figure The low conservation of most variants made the comparison to heterologous structures largely useless, implying that the type of evidence used in our previous heterologous inferential analysis (HIA) studies with exceptionally rare mt-rRNA variants could not be raised in this case . In the More than half of the 92 variants could cause structural distortions, possibly resulting in some degree of defective mito-ribosomal function and constituting valid candidates for deafness-inducing variants under the new theoretical framework for the evaluation of the pathogenic potential of mt-rRNA variants. Forty-one variants, including the nine mapping to 16S mt-rRNA, were deemed likely silent and two unclear . TertiarThis section contains the structural description of all 49 variants regarded as potentially non-silent. Given the number of variants analyzed, most accompanying figures are provided as The existence of pathogenic mutations in several mt-SSU mito-ribosomal proteins is a good indication that variants in mt-rRNA residues interacting with these proteins may also lead to deleterious phenotypes. Early binding proteins are also of particular interest, as they constitute key nucleation sites for the assembly of the mt-SSU. Hence, mt-rRNA variants that interfere with the binding of these proteins could lead to defective mito-ribosomal assembly and other functional defects. All these variants will be discussed in this section.Escherichia coli S12 and mitochondrial MRPS12/uS12m variant has been detected in several studies targeting hearing-impaired patients (22U (m.669U) base pairs with 281A (m.928A) in h3 of the SSU and 4 (m.651) of h1 is visible (22U>C (m.669U>C) variant would replace a Watson:Crick U:A base pair with a C\u2022A mismatch at the junction between helices h1 and h3 and in an rRNA region that is surrounded by proteins MRPS12/uS12m and MRPS5/uS5m, the potential for a fidelity mutation is high.The patients . Positio the SSU . A hydro the SSU , in clos the SSU . Positio the SSU , with tw the SSU is also the SSU , one of visible . As the 283G>A (m.930G>A) has been found to be associated with deafness in three studies (283G (m.930G) lies in the single-stranded stretch linking h3 and the functionally important central pseudoknot (helices h1 and h2) to h19 (283G (m.930G) has been modeled 2.39\u00a0\u00c5 away from Arg 47 of MRPS12/uS12m (283G (m.930G) to MRPS12/uS12m makes the 283G>A (m.930G>A) variant constitute a good candidate for a pathogenic residue. However, in light of its abundance in the population to h19 (Brink e) to h19 . In the ) to h19 , the O6 12/uS12m , whose e12/uS12m . However12/uS12m . Despite139G>A (m.786G>A) rare variant was detected by The 178U>A (m.825U>A) and 180A>G (m.827A>G) are both haplotype markers that were found in association with deafness in several studies (178U (m.825U) and 180A (m.827A) are located in the single-stranded RNA stretch linking helices h5 and h15 (178U (m.825U) and 179A (m.826A) (178U (m.825U) and the N7 of 180A (m.827A) (178U (m.825U) is located \u223c3\u00a0\u00c5 away from the factor, indicating that this region might have an important role during translocation. In addition to this, 180A (m.827A) is an almost universally conserved residue (position 364 in E. coli 16S rRNA) (2 group at position N3 due to the 180A>G (m.827A>G) base change might result in a slight structural distortion of the region, perhaps by interfering with its interaction with helix h3. A similar structural argument could be made for the 178U>A (m.825U>A) variant in that the insertion of a bulkier adenosine at this position could also slightly induce the distortion of the local structure. Hence, the potential for a fidelity variant exists in both cases.The variants studies . In the and h15 , a regio and h15 . Several and h15 . Additio(m.826A) . These M(m.826A) . Notably(m.827A) . The bas(m.827A) , thus ph(m.827A) . Positio(m.827A) . Since t(m.827A) , as judg(m.827A) . Specifi6S rRNA) , althoug295A>G (m.942A>G) variant was found in two patients with hearing loss (295A (m.942A) is located at the 5\u2032 end of h20 (295A>G (m.942A>G), namely, 400A (m.1047A) and 401C (m.1048C), where an A>G and a C>U transition were, respectively, identified in patients with hearing loss (401C (m.1048C) is modeled as part of a water-mediated, hydrogen bonding interaction with one of the phosphate oxygens of NAD (401C (m.1048C) O2\u2032 to NAD O2\u2032 and a hydrogen bond between spermine N1 and the RNA backbone at position 400A (m.1047A) (not shown). 400A (m.1047A) is unpaired and its base stacks onto that of 401C (m.1048C) (295A (m.942A) and 400A (m.1047A) OP1 (295A (m.942A) also forms water-mediated hydrogen bonds with the backbone of h19\u00a0at positions 487\u201388 (m.1134\u201335). Notably, position 487G (m.1134G) is within 3\u00a0\u00c5 of MRPS12/uS12m (295A (m.942A) is the Watson:Crick base pairing formed by positions 294G (m.941G) and 486C (m.1133C) . A hydro47A) OP1 . The sam12/uS12m . Adjacen295 (m.942) is involved in the stabilization of mito-ribosomal structure via direct (and water-mediated) hydrogen bonds, namely, in the interaction between helices h19, h20 in the neighborhood of protein MRPS12/uS12m. Guaran et al. found the 295A>G (m.942A>G) variant together with the 35delG/35delG allele in the gene GJB2, encoding the protein connexin 26, which is the most common cause of genetic sensorineural deafness in Caucasian patients (295A>G (m.942A>G) variant to the observed symptoms is unclear in this patient. No GJB2 mutations were reported together with 295A>G (m.942A>G) in the other study (400A>G (m.1047A>G) and 401C>U (m. 1048C>U) variants, the situation is uncertain. The base of 401C (m.1048C) only interacts via a water-mediated hydrogen bond with NAD (401C (m.1048C) and NAD is of any relevance to mitochondrial translation is unknown. The abundance of the 401C>U (m. 1048C>U) variant, itself a haplotype marker, clearly indicates that the C>U base change is well-tolerated at this position. In the case of 400A (m.1047A), its base is not involved in any hydrogen-bonding interaction, prompting us to regard it as a silent polymorphism. Despite all this, due to the proximity of 401C (m.1048C) and 400A (m.1047A) to MRPS12, a potentially pathogenic role cannot be completely ruled out for these residues.Of the three variant bases, only patients . Hence, er study . As for with NAD . Whether304G>A (m.951G>A) variant is a haplotype marker that is associated with deafness in several studies (304G (m.951G) is base-paired to 396C (m.1043C) in the distal part of h20 (304G (m.951G). As the G>A base change at position 304 (m.951) would disrupt a base pair interaction next to sites of MRPS12/uS12 that are heterologous equivalents of known fidelity mutations, the potential of the variant to cause a fidelity phenotype is considered high.The studies . Positiot of h20 , a regiot of h20 , near tht of h20 variant was found in heteroplasmy in a patient with non-syndromic hearing loss while the haplotype marker 460U>C (m.1107U>C) was identified as a potential deafness-causing variant in three subjects from a cohort of aminoglycoside-induced and non-syndromic hearing-impaired Chinese pediatric patients (459C (m.1106C) displays a potential contact with the backbone of protein MRPS37/mS37 (459C>U (m.1106C>U) variant, the results of this loss are uncertain.The patients . In the patients . The basS37/mS37 , which hS37/mS37 . Althoug460U (m.1107U) with the N6 of 478A (m.1125A), two nucleotides away from the central domain pseudoknot that connects helices h19 and h25 of 12S mt-rRNA (shown in red in 460U (m.1107U) O2\u2032 to 290U (m.937U) OP1 is 3.217\u00a0\u00c5, possibly indicating a direct tertiary interaction with the central domain pseudoknot (E. coli and were shown to be deleterious (460U (m.1107U) is not involved in any direct interactions with other residues except for a water-mediated hydrogen bond with position 947A (m.1594G) near the 3\u2032end of the molecule suggests that the 460U>C (m.1107U>C) variant could be a simple polymorphism (but see below).A tertiary interaction is observed between the backbone at position eudoknot . Mutatioeterious . Despitemolecule . The imp459C>U (m.1106C>U) and 460U>C (m.1107U>C) cannot be ruled out.Considering all of this, as the 5\u2019 side of the central domain pseudoknot is adjacent to h19, which, in turn, wraps around MRPS12/uS12m, it is possible that even small distortions in this region could be transmitted through this protein and result in fidelity defects. As a result, the potential for the creation of slight fidelity phenotypes by the variants During the early assembly, mito-ribosomal proteins MRPS16/bS16m and MRPS18B/mS40 interact with the nascent 12S mt-rRNA transcript base change was found in two patients with non-syndromic hearing loss (76A (m.723A) is involved in a triple base interaction with the 144G:150C (m.791G:797C) base pair, thus bringing together helices h7 and h12 (145C (m.792C) of h12, where a C>U base change was identified in two patients with non-syndromic hearing loss (145C (m.792C) is canonically base-paired to 149G (m.796G), closing the terminal loop of h12 (The ing loss . Positio and h12 . A seconing loss . Positiop of h12 .76A>C (m.723A>C) variant, the base change would prevent the base triple interaction, while the C>U base change at position 145C (m.792C) would result in a structurally disfavored C:G/U\u2022G exchange at a terminal base pair and the 98A>G (m.745A>G) variants were identified in a patient with idiopathic, sensorineural hearing loss and a patient with profound hearing impairment, respectively (95U (m.742U) base-pairs to 85A (m.732A) in h7 (98A (m.745A) is involved in a base quadruple interaction involving the 82U:97A (m.729U:744A) base pair and position 83A (m.730A), both of them in h7 (95U (m.742U) and 98A (m.745A) are structurally important in the context of h7 and that this helix is part of the MRPS16/bS16 binding site, a disruptive effect beyond the local structure of h7 cannot be ruled out.The ectively . PositioA) in h7 . Positioem in h7 . Althougem in h7 , known tem in h7 . Given t209A>G (m.856A>G) variant was identified in four patients with non-syndromic hearing loss (209A (m.856A) is base-paired to 183U (m.830U) at the proximal end of helix h15 (209A>G (m.856A>G) variant is considerable.The ing loss . The varing loss and Lebeing loss . Positioelix h15 . Hydrogeelix h15 . In addielix h15 . The 209During assembly, the 5\u2032 and 3\u2032 domains are brought together by the strong interactions established by the 5\u2032-domain binders MRPS16/bS16m, MRPS18B/mS40, and MRPS22/mS22 and the 3\u2032-domain binders MRPS27/mS27 and MRPS34/mS34 . The imp62G>A (m.709G>A), which has been frequently associated with hearing impairment (63U>C (m.710U>C) and 65C>A (m.712C>A) variants (62G (m.709G) is modeled, making two hydrogen bonds to Arg 48 of MRPS34/mS34 , 53A (m.700A), and 65C (m.712C) stabilizes the structure of the RNA stretch separating helices h6 and h6a and provides a recognition surface for the late-binding protein MRPS26/mS26 (pink in 62G>A (m.709G>A) clearly implies that the variant must be easily accommodated in the SSU structure. Despite this, the G>A base change is expected to disrupt the hydrogen bonding network observed in the structure, involving tertiary and quaternary contacts and likely leading to some degree of distortion. Similarly, the pyrimidine-to-purine replacement caused by the 65C>A (m.712C>A) variant is expected to disrupt the non-canonical base pair between 65C (m.712C) and 53A (m.700A). With this in mind, both variants must be regarded as potentially pathogenic.Three deafness-associated variants have been identified in the single-stranded stretch connecting helices h6 and h6a in the secondary structure map of the mt-SSU, namely, the haplotype defining variant pairment , as wellvariants (Koningsvariants . The bas pink in (Bogenha pink in . The abu62G (m.709G) is 63U (m.710U), whose base is stacked between 62G (m.709G) and Arg 30 of MRPS26/mS26 (63U (m.710U) is involved in a water-mediated hydrogen bonding interaction with 62G (m.709G) N7 (U>C base change at position 63 (m.710) is not expected to bring about any disruptive effect, as shown by the fact that a C is found at the equivalent position in the S. scrofa mito-ribosome (not shown) (Adjacent to S26/mS26 . 63U (m.709G) N7 . Despitet shown) .878C>G (m.1525C>G) variation was found by our group in a patient with profound hearing loss (878C (m.1525C) is located at the very distal end of h44 (878C (m.1525C) has been modeled, making a hydrogen bond to the backbone of protein MRPS27/mS27 (878C (m.1525C) would, in principle, argue for a silent phenotype, the rarity of the C>G variant, together with the existence of pathogenic mutations in MRPS34/mS34 (545C>A/U (m.1192C>A/U) (546U>C (m.1193U>C) (815G>A (m.1462G>A) (545C (m.1192C) and 815G (m.1462G) form a Watson:Crick base pair at the distal end of h28 (546U (m.1193U) (545C (m.1192C) and the functionally important \u03b2-hairpin of protein MRPS7/uS7m is less than 3\u00a0\u00c5 (not shown) , 545C>A/92C>A/U) , 546U>C 1193U>C) , and 8151462G>A) . Positiod of h28 . This red of h28 , which id of h28 . Contactm.1193U) . Notablym.1193U) , adjacenm.1193U) . Additiot shown) .542U>C (m.1189U>C) variant was identified in several independent studies (542U (m.1189U) maps to the single-stranded stretch of h28 (542U (m.1189U) is nearly on the same plane as the 545C:815G (m.1192C:1462G) base pair but slightly tilted, allowing it to use its O2 to form a hydrogen bond with the neighboring 544C:816G (m.1191C:1463G) base pair (542U (m.1189U) O4 to the NH2 of 782C (m.1429C) (542U>C (m.1189 U>C) variant. 542U>C (m.1189U>C) was found together with the 141A>G (m.1811A>G) variant in 16S mt-rRNA and the R127H allele in gene GJB2 (present in heterozygosity) (The studies . In the h of h28 . In the ase pair . The tilm.1429C) , a contaygosity) , both ofygosity) .In addition to elongation, this region of the mito-ribosome is also implicated in translation initiation. 545C:815G (m.1192C:1462G) base pair and the tertiary interactions of 542U (m.1189U) are important to stabilize the structurally complex and dynamic junction between helices h28 and h29. Of the three variants affecting the 545C:815G (m.1192C:m.1462G) base pair, 545C>A (m.1192C>A) and 815G>A (m.1462G>A) would replace a Watson:Crick base pair with either an A\u2022G or C\u2022A mismatch, while 545C>U (m.1192C>U) would result in a disruptive U\u2022G wobble at the end of a helical segment (546U (m.1193U) makes no hydrogen bonds which, together with the fact that a C is found in the S. scrofa structure at this position (position 544 in structure 5AJ4), strongly argues for a silent phenotype associated with the 546U>C (m.1193U>C) variant.All this evidence strongly suggests that the segment . For all596U>C (m.1243U>C) was found in association with deafness in several studies (596U (m.1243U) maps to helix h32 of 12S mt-rRNA, where it base pairs to 699A (m.1346A) (596U:699A (m.1243U:1346A) base pair by the U>C base change at position 596U (m.1243T) could affect the interaction of h32 and MRPS14/uS14m in this region. Although the abundance of the 596U>C (m.1243U>C) variation implies that the base change is well-tolerated, whether it could lead to slight phenotypic effects remains uncertain.The haplotype marker studies . Positiom.1346A) . Arg 36 m.1346A) forms a 663C>U (m.1310C>U) variant has been identified in a Japanese patient with inherited sensorineural hearing loss (663C (m.1310C) maps to h38 of 12S mt-rRNA, where it base pairs with 668G (m.1315G) (663C (m.1310C) would create a disfavored U\u2022G wobble base pair at the end of a helical segment (The ing loss . Positiom.1315G) . Its O2\u2032m.1315G) . Late-bim.1315G) also conm.1315G) and the segment with the735A>C (m.1382A>C) variant was identified in two families with hearing loss (735A (m.1382A) is base-paired to 723U (m.1370U) at the proximal end of h41 in the head of the mt-SSU (735A (m.1370U:m.1382A) base pair, the pathogenic potential of this variant must be considered.The ing loss . Positioe mt-SSU . A contae mt-SSU to the Re mt-SSU establise mt-SSU . As the 796U>C (m.1443U>C) variant was identified in a non-syndromic hearing-impaired Chinese pediatric subject (796U (m.1443U) maps to the loop that caps h43 of 12S mt-rRNA (796U (m.1443U) establishes a hydrogen bond with the RNA backbone at position 799 (m.1446) (7 (m.1443-4) are visible in the structure. The adjacent position 797A (m.1444A) makes a tertiary interaction by forming a triple base interaction with 585A (m.1232A) of h31 and 753G (m.1401G) of h42 (796U (m.1443U) (not shown) (796U>C (m.1443U>C) must be considered significant.The highly rare subject . Positio mt-rRNA . The N3 (m.1446) , an inte(m.1446) and the ) of h42 . This ant shown) . Given a805U (m.1452U) and 806A (m.1453A), presumably associated with hearing impairment, map to h43 of 12S mt-rRNA (805U (m.1452U), while MRPS9/bS9 and MRPS14/uS14m (beige in 806A (m.1453A). Position 805U (m.1452U) forms a wobble base pair with 791G (m.1438G) (791 (m.1438), which is present in only 5% of the GenBank sequences (791/805 (m.1438/1452) base pair. As a result, both the 805U>C (m.1452U>C) and the 791G>A (m.1438G>A) variants should be considered silent, as they would result in the exchange of the wobble configuration seen in the structure for a Watson:Crick base pair. Preceding the 791/805 (m.1438/1452) base pair lies position 806A (m.1453A), which forms a Watson:Crick base pair with 790U (m.1437U) (806A (m.1453A) (The sites of variation mt-rRNA (Padma a mt-rRNA . Protein mt-rRNA contact beige in do the sm.1438G) , anotherm.1438G) . In factequences . These dm.1437U) . A deafnm.1453A) that wouThe early binding proteins MRPS2/uS2m and MRPS23/uS23, together with MRPS28/bS1m, bind as a cluster to the solvent side of the 12S mt-rRNA molecule . Pathoge469A>G (m.1116A>G), 471A>G (m.1118A>G), and 472U>C (m.1119U>C) variants were found in four hearing-impaired patients (471A (m.1118A) and 472U (m.1119U) are located in the loop capping h25 (471A (m.1118A) has been modeled within 3\u00a0\u00c5 of Arg 297 of protein MRPS5/uS5m (beige in ram residue V336 within the same protein (not shown) (472U (m.1119U), its base has been modeled, making a water-mediated hydrogen bond, through its O2, to the base and the sugar of 479A (m.1126A) and 480A (m.1127A), respectively (472U (m.1119U) would be unaffected by a U>C base change, thus making 472U>C (m.1119U>C) a good candidate for a silent variant. In this particular patient, the presence of 62G>A (m.709G>A) together with 472U (m.1119U) could offer a better explanation for the observed deafness, as explained previously (469A>G (m.1116A>G) variant is different in that its base is part of a base triple with the 467U:480A (m.1114U:1127A) that would be likely affected by the base change. Additionally, Arg 100 of MRPS2/uS2m (orange in the structure) is within hydrogen bonding distance of the RNA backbone at position 469A (m.1116A). The density around 469A (m.1116A) supports these interactions. Hence, despite the peripheral location of the 469A (m.1116A) variant, the structural evidence does not permit its scoring as a silent mutation.The patients . Positioping h25 toward tbeige in and \u223c13-t shown) . Despitet shown) suggestsectively . In addiectively . All theeviously . The sit103 (m.750) is an A in the Cambridge mtDNA reference sequence (103 (m.750) is a G that forms a Watson:Crick base pair to 77C (m.724C) in h7 (103G (m.750G) is visible (103G (m.750G), the introduction of an A\u2022C mismatch at this position in h7 is expected to cause some level of structural distortion whose overall consequences cannot be predicted. Hence, the 103G>A (m.750G>A) base change is another example of a haplotype marker with a potentially pathogenic role.Position sequence . Howeversequence . Base chsequence . In the C) in h7 . A conta visible . Althoug122G>A (m.769G>A) and the 123C>U (m.770C>U) variant were described in the context of deafness in two studies (122G (m.769G) and 123C (m.770C) map to the GNRA tetraloop capping h11 (123C>U (m.770C>U) variant would not change the GNRA consensus, 122G>A (m.769G>A) would do so, likely disrupting the structure of the tetraloop and, perhaps, the binding of MRPS17/uS17m. Given the role of MRPS17/uS17m as an early binding protein, the possibility of disruptive potential in the case of the 122G>A (m.769G>A) variant must be considered.The haplotype marker studies . Positioping h11 , 358U (m.1005U), 360G (m.1007G), and 361A (m.1008A) map to h23 of 12S mt-rRNA (358U (m.1005U) is involved in a water-mediated, non-canonical base pair with 336C (m.983C) and a quaternary contact with Asn 104 of MRPS11/uS11m (pink in 360G (m.1007G) and 361A (m.1008A) form Watson:Crick base pairs with residues 334C (m.981C) and 333U (m.980U), respectively. Lys 6 of MRPS21/bS21 contacts the RNA backbone at positions 359U (m.1006U) and 360G (m.1007G) (light green in 333U>C (m.980U>C) and 360G>A (m.1007G>A) would both result in a disruptive C\u2022A mismatch, while the 361A>G (m.1008A>G) would give rise to a less damaging U\u2022G wobble. In the case of 358U>C (m.1005U>C), the hydrogen bonding pattern observed in the structure would not be maintained, possibly causing some degree of structural disruption. All variants have been identified in MITOMAP with moderate-to-high frequency (two are haplotype markers) (Positions mt-rRNA (Li et a mt-rRNA . The bas pink in . Positiomarkers) (Ruiz-Pemarkers) , indicat341G (m.988G) and 343U (m.990U) of h23 were found in the studies of 341G>A (m.988G>A) and 343U>C (m.990U>C) would disrupt the base hydrogen bonding pattern observed in the two high-resolution structures used in this analysis variant was found in several patients with sensorineural and non-syndromic hearing loss (448U (m.1095U) base-pairs to 413A (m.1060A) in h24 of 12S mt-rRNA (448U (m.1060A:1095U) base pair by the U>C transition has the potential to affect the functioning of bridge B7b and cause translational defects. Results of biochemical analyses with cybrids carrying this variant in heteroplasmy were consistent with decreased mitochondrial function and increased AG susceptibility variant was identified by Rydzanicz et al. in a patient with non-syndromic and aminoglycoside-induced hearing loss and by Chen et al. in a Uyghur patient with non-syndromic deafness (856G (m.1503G) is near the highly conserved bridge mB5, which according to lower-resolution structures of the human mito-ribosome, involves positions 858A (m.1505A) and 892C (m.1539C) in h44 of 12S mt-rRNA and MRPL14/uL14m in the LSU and 890C>U (m.1537C>U) also map to h44 of 12S mt-rRNA and the neighborhood of mB5 (861C>U (m.1508C>U) has been identified in a patient with profound hearing loss without previous exposure to AGs (890C>U (m.1537C>U) variant, it has been identified in two patients with non-syndromic hearing impairment (890C (m.1537C) establishes two hydrogen bonds, one with the N3 of the adjacent 889A (m.1536A) and the other with the O2\u2032 of 864C (m.1511C) (Variants d of mB5 . Positioe to AGs . This ree to AGs . As for pairment . The amim.1511C) .861C>U (m.1508C>U) or 890C>U (m.1537C>U) variants could affect the proper functioning of mB5. Regarding 856G>A (m.1503G>A), its high frequency in the population clearly indicates that an A must be tolerated at this position. However, the loss of a quaternary interaction involving 856G (m.1503G) and 941U (m.2611T) of 16S mt-rRNA observed in the 2.2-\u00c5 cryo-EM human mito-ribosomal structure variant was found in homoplasmy in pediatric subjects with non-syndromic hearing loss (533U>G (m.1180U>G) and 827G (m.1474G) of h28 form a wobble base pair (533U\u2022827G (m.1180U\u2022m.1474G) wobble lies position 826C (m.1473C), where a C>U transition was found in a patient with severe hearing loss (826C (m.1473C) forms a Watson:Crick base pair with 534G (m.1181G) (533U (m.1180U) lies the universally conserved 532G (m.1179G) , and 534G (m.1181G) in the cytoplasmic ribosome confer lethal phenotypes (533U (m.1180U) and 534G (m.1181G) , compensatory mutations restoring base pairing potential also restored growth (533U>G (m.1180U>G) variant would replace a U\u2022G wobble with a G\u2022G mismatch, its disruptive potential must be considered high. Hence, the use of the new structural data corroborates our previous assignment as an expectedly disruptive mutation. In the case of 826C>U (m.1473C>U), the transition would replace a Watson:Crick G:C with a G\u2022U wobble, creating a highly non-isosteric U\u2022G/G\u2022U tandem wobble combination (826C>U (m.1473C>U) variant is well tolerated, as judged by its high frequency (The very rare ing loss . We haveing loss and descase pair . Next toing loss . Positiom.1181G) . On the nd 100%) , which ind 100%) . Strikinl growth , but witin vitro . Mutagenenotypes . In the d growth . As the bination . Althougrequency , subtle 579C>G (m.1226C>G) variant was found in a pediatric subject with non-syndromic hearing loss (579C (m.1226C) is universally conserved (579C (m.1226C) is located at the single-stranded junction connecting helices h31 and h32 (579C (m.1226C) canonically base-pairs with 570G (m.1217G), also universally conserved and adjacent residues were mutated, they resulted in moderate-to-strong growth defects and elicited fidelity phenotypes (579C (m.1226C) , we cons579C (m.1226C). The 684A>G (m.1331A>G) base change was identified in one Han Chinese pediatric subject with aminoglycoside-induced and non-syndromic hearing loss (684A (m.1331A) maps to h34, it is brought into the neighborhood of 579C (m.1226C) by a tertiary interaction in the form of a trans-Watson:Crick base pair, with the base of 568U (m.1215U) (684A>G (m.1331A>G) must be considered a potentially pathogenic variant.A second variant maps to the neighborhood of position ing loss . Althougm.1215U) (Leontism.1215U) . This in910A>C (m.1557A>C) variation was identified in a Russian individual suffering from deafness . Position 910A (m.1557A) maps to a single-stranded stretch of h44 (910A>C (m.1557A>C) variant in our previous analysis of highly rare variants mapping to 12S mt-rRNA, performed in the absence of high-resolution mito-ribosomal structures (910A (m.1557A) and 911A (m.1558A) in monitoring the geometry of A-site decoding is evident from the 2.2-\u00c5 structure of the mito-ribosome was found in two aminoglycoside-induced hearing-impaired subjects (951G (m.1598G) maps to the single-stranded stretch near the 3\u2032end of the molecule (951G (m.1598G) would impact its interaction with 921U (m.1568U), possibly resulting in a distortion of the mRNA channel and leading to phenotypic effects. These effects, however, must not be drastic, as the 951G>A (m.1598G>A) base change has been found frequently in the population and 908A>G (m.1555A>G) of 12S mt-rRNA. Positions 847C (m.1494C) and 908A (m.1555A) normally form a C\u2022A mismatch at the penultimate helix of human mt-12S rRNA , which ie trauma . However (76A>C (m.723A>C) variant. Position 76A (m.723A) is involved in a triple base interaction that brings together helices h7 and h12 near the recognition sites for MRPS16/bS16 and MRPS25/mS25, both known to harbor pathogenic mutations (76A>C (m.723A>C) is expected to disrupt this triple base pair interaction, possibly affecting the helical arrangement of part of 12S mt-rRNA and the binding of MRPS16/bS16 and MRPS25/mS25. However, the triple base interaction is not conserved, as it is absent in the S. scrofa mito-ribosome and 908A>G (m.1555A>G) affect structurally non-conserved positions, forming a mismatch in the human mito-ribosome t-rRNAs) . This tyutations (Miller utations . The potribosome . This exThe possibility that haplotype context could affect the manifestation of mt-rRNA variants was recently proposed by our group and has 401C (m.1048C) (401C (m.1048C) and the NAD molecule is of any relevance to mitochondrial translation remains unknown.As mentioned in the introduction, AGs antibiotics are an important class of external agents capable of affecting the penetrance of mt-rRNA variants. HIA studies conducted by our group with highly rare mt-rRNA variants reportedly in association with diseases showed that an important number of them mapped to the vicinity of the binding sites of known ribosomal antibiotics . As a rem.1048C) (Itoh etm.1048C) . The prem.1048C) . Despite910A>C (m.1557A>C) is a good example, as it has the strongest disruptive potential. Base changes at position 910A (m.1557A) are expected to completely abolish mito-ribosomal translation by directly interfering with genetic decoding (The growing realization in the field that mtDNA disease and, more specifically, deafness can be brought about by variants with low-profile phenotypes, such as those affecting mito-ribosomal fidelity (reviewed in accompanying study by decoding . Unfortudecoding .In summary, we have provided a much-needed assessment of the structural and functional role of suspect mt-rRNA variants identified in the context of deafness. Besides highlighting the key role of the primary sequence of mt-rRNA in the etiology of deafness, this research provides a new framework to understand how mt-rRNA variants, particularly those located at non-conserved positions, may lead to deafness. Hence, the results presented here constitute an important push toward the final elucidation of the role of mt-rRNA in mitochondrial deafness and mitochondrial disease. Such elucidation will eventually require biochemical evidence obtained with mutant mitochondria carrying mito-ribosomes with altered mt-rRNAs.Structural analysis was performed with Chimera X , essenti"} +{"text": "The Supporting Information file legends are incorrect. Please view the correct Supporting Information file legends below.S1 Fig. CFTR presence and localization in the normal human pancreas. CFTR immunostaining using CFF-217 of normal pancreas from donors of different ages: 2 months (A-B), 6 months (C-D), 2 months (E-F), 7 months (G-H), 30 years (I-J), and 39 years (K-L). CFTR immunoreactivity is shown in ductal and islet endocrine cells. Shown in B, D, F, H and J are consecutive sections immunolabeled by using the pan-endocrine marker synaptophysin (SYN) to confirm CFTR expression in the pancreatic islets. A larger magnification of the section area in the inset in K is shown in L. Scale bars represent 50\u03bcm.https://doi.org/10.1371/journal.pone.0242749.s001(TIF)S2 Fig. Immunohistochemistry for CFTR. Normal human pancreas tissues obtained from three donors aged 6 months , 11 months and 4 years are immunostained by using anti-human CFTR antibodies CFF-432 (A-C), CFF-412 (D-F) and CFF-570 (G-i). CFTR expression (brown) occurs in both duct (green squares) and islet endocrine cells (red squares). Higher magnifications of the areas noted by green and white inserts i.e., ductal and islet areas, respectively, are shown under each image. Scale bars represent 100\u03bcm.https://doi.org/10.1371/journal.pone.0242749.s002(TIF)S3 Fig. CFTR antibodies not-suitable for immunohistochemistry. Normal human pancreatic tissues stained with the indicated CFTR antibodies. A. CFF-596 antibody generates non-specific immunostaining in the CFTR-negative control human tissue with the G542X truncation mutation. B-C. CFF-660 (B) and CFF-450 (C) antibodies do not generate specific immunostaining in the positive control ductal cells. D. Antibody Ab4067 does not generate immunostaining signal in the normal human pancreas. E-J. Pancreatic tissue from CftrWT (E-G) and CftrG542X mice (H-J) co-immunolabeled by using the mouse anti CFTR-specific antibody MrPink (J and H), insulin and glucagon .https://doi.org/10.1371/journal.pone.0242749.s003(TIF)S4 Fig. Original blots used in Fig 4.https://doi.org/10.1371/journal.pone.0242749.s004(TIF)"} +{"text": "Pseudomonas aeruginosa has not been fully elucidated. This study evaluated the in vitro activity of novel \u03b2-lactam/\u03b2-lactamase inhibitor combinations against Pseudomonas aeruginosa clinical isolates, determined how avibactam restored ceftazidime activity, and compared the activity of ceftazidime-avibactam (CZA) and imipenem-relebactam (IMR) against KPC-producing P. aeruginosa. Similar high susceptibility rates for CZA, IMR, and ceftolozane-tazobactam (88.9% to 89.8%) were found for 596 P. aeruginosa clinical isolates from 11 hospitals in China, and a higher susceptibility rate to ceftazidime than imipenem was observed (73.5% versus 63.1%). For CAZ-NS and IPM-NS isolates, susceptibility rates for CZA, ceftolozane-tazobactam, and IMR were 61.5% (75/122), 54.9% (67/122), and 51.6% (63/122), respectively. For CAZ-NS, IPM-NS but CZA-susceptible isolates, 34.7% (26/75) harbored acquired \u03b2-lactamases with KPC-2 predominant (n\u2009=\u200919), and 45.3% (34/75) presented overexpression of chromosomal \u03b2-lactamase ampC. Among 22 isolates carrying KPC-2 carbapenemase alone, susceptibility rates to CZA and IMR were 86.4% (19/22) and 9.1% (2/22), respectively. Notably, 95% (19/20) of IMR-nonsusceptible isolates had an inactivating mutation of oprD gene. In conclusion, CZA, ceftolozane-tazobactam, and IMR exhibit high activity against P. aeruginosa, and CZA is more active than IMR against CAZ-NS and IPM-NS isolates as well as KPC-producing P. aeruginosa. Avibactam overcomes ceftazidime resistance engendered by KPC-2 enzyme and overexpressed AmpC.The role of novel \u03b2-lactam/\u03b2-lactamase inhibitor combinations in ceftazidime-nonsusceptible (CAZ-NS) and imipenem-nonsusceptible (IPM-NS) IMPORTANCE The emergence of antimicrobial resistance poses a particular challenge globally, and the concept of P. aeruginosa with \u201cdifficult-to-treat\u201d resistance (DTR-P. aeruginosa) was proposed. Here, P. aeruginosa clinical isolates were highly susceptible to three \u03b2-lactamase inhibitor combinations, CZA, IMR, and ceftolozane-tazobactam. The combination of KPC-2 enzyme and nonfunctional porin OprD contributed to IMR resistance in P. aeruginosa, and CZA was more active than IMR in fighting against KPC-2-producing P. aeruginosa. CZA also showed good activity against CAZ-NS and IPM-NS P. aeruginosa, primarily by inhibiting KPC-2 enzyme and overproduced AmpC, supporting the clinical use of CZA in the treatment of infections caused by DTR-P. aeruginosa. Pseudomonas aeruginosa is a major cause of serious infections in humans, which often become notoriously refractory to treatment and lead to considerable morbidity, mortality, and socioeconomic impacts worldwide. In this scenario, \u03b2-lactam antibiotics remain one of the mainstays of therapy. One interesting phenomenon is the higher in vitro susceptibility rate of this pathogen to ceftazidime than to carbapenems was proposed in 2018 and fluoroquinolones (ciprofloxacin and levofloxacin) is commonly responsible for resistance to ceftazidime via structural mutations or overexpression. The intrinsic resistance-nodulation-division family of efflux systems are also critical features associated with \u03b2-lactam resistance . Mechani diverse . Mutatio diverse . Chromossistance , and theP. aeruginosa strains with inhibitory Ambler class A, C, and some D \u03b2-lactamases. IMR exhibits an antimicrobial spectrum similar to that of CZA except for inhibition activity against OXA-48 enzyme. Ceftolozane, a novel oxyimino-aminothiazolyl cephalosporin, is characterized by its stability in PDC hydrolysis. In previous studies, CZA and CT showed excellent in vitro activity against P. aeruginosa with susceptibility rates of 86.5% and 88.5%, respectively, and IMR demonstrated a susceptibility rate of 90.8% (P. aeruginosa according to the guidance of the Infectious Diseases Society of America (IDSA) , ceftolozane-tazobactam (CT), and imipenem-cilastatin-relebactam (IMR), have recently been approved and cast a new spotlight on the treatment of multidrug-resistant (MDR) Gram-negative bacterial infections. CZA expands the therapeutic coverage of ceftazidime against of 90.8% . These cP. aeruginosa isolates are emerging in China. The resistant gene blaKPC-2 is commonly located in plasmids with mobile elements and is frequently detected in sequence type 463 (ST463) isolates to 100% (16/16) , 12. Howin vitro activities of CZA, CT, and IMR against clinical P. aeruginosa isolates collected from multiple medical centers in China and uncovered the extent to which avibactam restored the activity of ceftazidime in ceftazidime-nonsusceptible (CAZ-NS) and imipenem-nonsusceptible (IPM-NS) P. aeruginosa. This study found high in vitro activities of CZA, CT, and IMR against P. aeruginosa clinical isolates. The combination of KPC-2 carbapenemase and nonfunctional porin OprD led to IMR resistance in P. aeruginosa, and CZA was more active than IMR in fighting against KPC-2-producing P. aeruginosa. CZA also retained good activity against CAZ-NS and IPM-NS P. aeruginosa isolates, as avibactam overcame the ceftazidime resistance engendered by acquired \u03b2-lactamase KPC-2 and overproduced chromosomal \u03b2-lactamase AmpC.This study investigated the P. aeruginosa isolates. The MIC50 and MIC90 for CZA were 2\u2009mg/L and 16\u2009mg/L, respectively, and avibactam restored the susceptibility of ceftazidime in 61.4% (97/158) of CAZ-NS isolates. Moreover, higher susceptibility to CAZ than to IPM was observed . The most active agents against 596 P. aeruginosa isolates were colistin and amikacin (90.8%), and susceptibility rates to the remaining six agents ranged from 58.2% (aztreonam) to 78.2% (cefepime) (P. aeruginosa accounted for 11.9% (71/596).Overall, susceptibility rates to CZA, IMR, and CT were 89.8%, 88.9%, and 88.9%, respectively, among the 596 efepime) . DTR-P. P\u2009<\u20090.001) but relatively weaker correlations between the CZA and imipenem MICs among the 596 P. aeruginosa clinical isolates ceftazidime-susceptible (CAZ-S) and imipenem-susceptible (IPM-S) isolates, 98 (16.4%) CAZ-S but IPM-NS isolates, 36 (6.0%) IPM-S but CAZ-NS isolates, and 122 (20.5%) CAZ-NS and IPM-NS isolates of these were susceptible to CZA of e to CZA . Among te to CZA . In addiP. aeruginosa isolates displayed nonsusceptibility to imipenem, 78.6% (173/220) of IPM-NS isolates were susceptible to CZA, including 98 (44.5%) CAZ-S isolates and 75 (34.1%) CAZ-NS isolates (While 36.9% (220/596) of isolates .For 122 CAZ-NS and IPM-NS isolates, susceptibility rates for CZA, CT, and IMR were 61.5% (75/122), 54.9% (67/122), and 51.6% (63/122), respectively.To illuminate how avibactam overcomes ceftazidime resistance, mechanisms of ceftazidime nonsusceptibility were investigated using whole-genome sequencing (WGS) and quantitative real-time PCR (qRT-PCR) among 75 CAZ-NS, IPM-NS but CZA-S isolates .n\u2009=\u200919), VIM-2 (n\u2009=\u20091), and GES-5 (n\u2009=\u20091), as well as coexistence of GES-5 and PER-1 (n\u2009=\u20091). The VIM-2-carrying isolate had a CZA MIC of 8\u2009mg/L. Extended-spectrum \u03b2-lactamases (ESBL) were detected in four isolates (excluded the one coexisting with GES-5): PER-1 (n\u2009=\u20092) and OXA-101 (n\u2009=\u20091), as well as coexistence of PER-1 and OXA-101 (n\u2009=\u20091) (Table S2).Among these 75 isolates, 26 (34.7%) carried horizontally acquired \u03b2-lactamases and maniampC overexpression phenotype were witnessed in 21 isolates, including a premature stop codon (n\u2009=\u20096) and amino acid substitution G154R (n\u2009=\u20093) in ampR, a frameshift mutation (n\u2009=\u20097) in ampD, and a premature stop codon (n\u2009=\u20091), frameshift mutation (n\u2009=\u20093), and amino acid substitution T428P (n\u2009=\u20091) in dacB. A total of 17 subtypes of PDC were present in the 75 isolates (Table S3), with PDC-8 (n\u2009=\u200918) being the most common, followed by PDC-5 (n\u2009=\u200916), PDC-1 (n\u2009=\u20098), and PDC-3 (n\u2009=\u20096). Additionally, overexpression of the efflux pump gene mexAB-oprM was detected in 35 isolates isolates, including frameshift mutations (n\u2009=\u200953) and premature stop codons (n\u2009=\u200912) (Inactivating mutations in (n\u2009=\u200912) .blaPER-1. These isolates did not harbor carbapenemases, nor did they show inactivating mutations in oprD. In total, 59.1% (13/22) of isolates displayed ampC overexpression, and 50.0% (11/22) of isolates exhibited alteration of regulatory factors contributing to ampC overproduction, including a premature stop codon (n\u2009=\u20091), frameshift mutation (n\u2009=\u20091), and amino acid substitution D135N/Y (n\u2009=\u20094) in ampR, a premature stop codon (n\u2009=\u20094) and frameshift mutation (n\u2009=\u20091) in ampD, and a premature stop codon (n\u2009=\u20091) in dacB. A total of 10 subtypes of PDC were detected in these 22 isolates (Table S3), with PDC-3 (n\u2009=\u200910) being the most prevalent, followed by PDC-8 (n\u2009=\u20092), PDC-16 (n\u2009=\u20092), and PDC-63 (n\u2009=\u20092).Among the 22 CAZ-NS, IPM-S, and CZA-S strains, only one isolate carried an ESBL-encoding gene, n\u2009=\u200917), ST16 (n\u2009=\u20092), ST238 (n\u2009=\u20091), ST244 (n\u2009=\u20091), and an undefined ST (n\u2009=\u20091). Notably, their susceptibility rates to CZA, CT, and IMR were 86.4% (19/22), 0%, and 9.1% (2/22), respectively.Among the 158 CAZ-NS isolates, 22 carried KPC-2 carbapenemase and did not carry metallo-\u03b2-lactamase. They were assigned to five STs, ST463 of IMR-nonsusceptible isolates had an inactivating mutation of the imipenem . The oneimipenem .P. aeruginosa clinical isolates were highly susceptible to three \u03b2-lactam/\u03b2-lactamase inhibitor combinations, CZA, IMR, and CT. In total, 89.8% of P. aeruginosa clinical isolates from China were susceptible to CZA with MIC50/MIC90 of 2/16\u2009mg/L, and avibactam restored the susceptibility to ceftazidime in 61.4% of CAZ-NS isolates. Similar results were found in a study in Spain, in which antimicrobial activity of CZA was demonstrated against 1,445 P. aeruginosa isolates, with a susceptibility rate of 94.2% and MIC50/MIC90 of 2/8\u2009mg/L was found for 2,623 P. aeruginosa isolates from Asia, and relebactam restored imipenem susceptibility from 0% to 64.6% for 805 IPM-NS isolates (P. aeruginosa (in vitro activity (88.9%) was also observed for CT in the 596 isolates, with an MIC50/MIC90 of 0.5/8\u2009mg/L. Nevertheless, variation was noted in the susceptibility to CT in different regions, which ranged from 89.1% in Europe to 98.2% in North America of IPM-NS isolates being susceptible to ceftazidime. Susceptibility to ceftazidime was also reported for carbapenem-resistant P. aeruginosa (CRPA), as evidenced by data from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program in the Asia-Pacific region from 2015 to 2019 . A global study reported a susceptibility rate to CZA of 75.9% for 29 KPC-2-positive clinical P. aeruginosa isolates, while another group from China reported a CZA susceptibility rate of 49.7% for 151 KPC-2-positive clinical P. aeruginosa isolates . Therefore, the combination of KPC-2 enzyme and nonfunctional porin OprD leads to IMR resistance in P. aeruginosa , and CZA is more active than IMR in fighting against KPC-2-producing P. aeruginosa.Among 22 isolates carrying KPC-2 carbapenemases alone, 95% (19/20) of IMR-nonsusceptible isolates had an inactivating mutation of the imipenem and furtimipenem . AdditioP. aeruginosa, supporting the clinical use of CZA in the treatment of infections caused by DTR-P. aeruginosa. We also found that 45.3% (34/75) of isolates demonstrated overexpression of AmpC in CAZ-NS and IPM-NS but CZA-S isolates, indicating that overexpressed AmpC could be inhibited by avibactam. Consistently, the addition of avibactam increased ceftazidime susceptibility for 46 AmpC-hyperproducing clinical isolates from 10.9% to 76.1% , few of which could contribute to CZA resistance were active against the majority of P. aeruginosa isolates were collected from 11 hospitals across China from July 2018 and February 2019 (Table S4) (P. aeruginosa isolates were predominantly from respiratory tract specimens (61.7%), followed by urinary tract (12.6%) and blood specimens (4.0%).A total of 596 nonduplicate clinical able S4) . The 596P. aeruginosa (www.eucast.org). P. aeruginosa ATCC 27853 served as a quality control strain.Antimicrobial susceptibility was tested by the agar dilution method, except that antimicrobial susceptibility to colistin was tested by the broth microdilution method. Susceptibility to all antimicrobial agents was interpreted according to the Clinical and Laboratory Standards Institute (CLSI) breakpoints , except https://github.com/ablab/spades) after trimming. The presence of resistance genes was explored using the Comprehensive Antibiotic Resistance Database (CARD) webtool (https://card.mcmaster.ca/home). Multilocus sequence typing (MLST) was ascertained according to the guideline on P. aeruginosa on the MLST website (https://pubmlst.org/organisms/pseudomonas-aeruginosa). A core genome phylogenetic tree was generated using kSNP and visualized using iTOL was performed after extraction from a fasta file.The CAZ-NS isolates were sent for WGS performed with an Illumina NovaSeq system. The raw reads were assembled using SPAdes were determined by qRT-PCR for clinical isolates as described previously (rpsL as the internal reference. Isolates were considered to overexpress AmpC, MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM when the transcriptional levels of ampC, mexB, mexC, mexE, and mexY were at least 10-, 3-, 10-, 10-, and 10-fold higher, respectively, than those of the PAO1 strain (The transcription levels of the gene eviously . Briefly1 strain .Data were analyzed and visualized using R software v4.1.3. Spearman rank-order correlation was used to evaluate associations between antibiotic MICs.PRJNA891673.The genomic sequence data have been submitted to the NCBI GenBank database with BioProject number"} +{"text": "A recent review indicated that physical activity (PA), facilitated by organisations/clubs, may reduce alcohol consumption in early to mid-adolescence. Our study aims were to examine these factors, and identify how health determinants may influence association.2 tests achieved p<.10.Cross-sectional secondary data analysis using UK cohort data from ALSPAC. Ages and sample-size: Time-point (TP) 1: 13-14 (n\u2009=\u20091824), TP2: 15-16 (n\u2009=\u20091334). Variables: minutes per day spent in moderate to vigorous PA\u2009>\u2009=3 days of accelerometer wear. Ancillary PA variables: Club-type (CT); and frequency of attending club (FAC) collected age 15 only. Risk of alcohol-related harm (RARH) categorised as: no current risk, increasing risk, and at risk (AR). Ordinal regression was conducted at each TP, using PA as a covariate. Explanatory variables (EVs): Psychosocial health (PSH) - Cluster membership numbers generated through K-means cluster analysis (uniquely represented at each TP); Socioeconomic status (SES); Educational attainment; BMI; Smoking status, and Gender. EVs entered into regression model if preliminary Xp<0.002). At TP2: OR 1.24 . TP1: CT (age 15) was not statistically significant at age 13. However, \u2018sports club only\u2019 (SCO), had greatest RARH vs. no CT. All EVs retained statistical significance at p<.05, excepting IDACI (p\u2009=\u2009.854) and gender (p\u2009=\u2009.917). TP2: Although CT was not statistically significant, SCO had the greatest RARH . RARH was reduced if attending club most evenings vs. no attendance . Statistically significant EVs were PSH and smoking . Model fit \u03c72 331.010, df 11, p<0.001. Pearson .455. Deviance .218. Nagelkerke .251. -2LL test of parallel lines with significance .321.Regression showed a positive association between PA and RARH at both TPs. Odds of being AR at TP1 were 1.31 greater for each 30\u2009minute increase in PA (95%CI 1.10-1.57; The relationship between PA and alcohol consumption is complex. While facilitated PA can provide many benefits for adolescents, potential unwanted consequences may be an increase in risk-behaviours like alcohol consumption. Further research is needed for greater comprehension of this association."} +{"text": "Kalamiella piersonii clinical isolate URMC-2103A041 from human bacteremia was determined using the hybrid assembly of short- and long-read sequencing chemistry. The genome contains a 3.93 Mb chromosome, three circular plasmids, and one linear plasmid.The complete genome of Kalamiella piersonii is a Gram-negative Enterobacterales in the Erwiniaceae family. First described from the International Space Station environment, a recent phylogenomic analysis of Erwiniaceae has proposed reclassification as Pantoea piersonii comb. nov ]. Biochemical identification produced Pantoea spp. (98.2% identification). The BD Phoenix NID panel identification was Shigella flexneri. Identification was resolved by 16S rRNA V1-V3 sequencing (MicroSeq 500 16S rDNA Sequening Kit) . Susceptibility was determined using zone diameter breakpoints for Enterobacterales identified the organism as Pantoea spp., URMC-2103A041 was Voges-Proskauer- and ONPG-positive, fermented mannitol, arabinose, and rhamnose, but was arginine dihydrolase positive . DNA was extracted following the protocol for \u201cPretreatment for Gram-Negative Bacteria\u201d . DNA shearing and size selection were not performed. DNA was quantified with the QuantiFluor dsDNA system (Promega).For short reads, paired-end sequencing following library preparation was performed on a MiSeq instrument . Unless otherwise specified, sequences were analyzed with tools available on the Galaxy server , using default parameters . Reads w50: 11,125 bp) for hybrid assembly and polishing (Quast v5.2.0) , SQK-RBK004]. Long-read libraries were sequenced , and base calling was performed with Guppy v6.1.5 (MinKNOW v22.05.5). Filtering generated 93,023 reads (read N v5.2.0) , 14.CP115895.1), three circular plasmids , and one linear plasmid . Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (The hybrid assembly genome was 4,990,348 bp with 57.02% GC content; it consisted of one circular chromosome (3.93 Mb, GenBank: Pipeline 17."} +{"text": "We conducted surveillance of respiratory syncytial virus (RSV) genomic sequences for 100 RSV-A and 27 RSV-B specimens collected during November 2022\u2013April 2023 in Arizona, USA. We identified mutations within prefusion F-protein antigenic sites in both subtypes. Continued genomic surveillance will be critical to ensure RSV vaccine effectiveness. Respiratory syncytial virus (RSV), an RNA virus of the family Pneumoviridae, causes acute respiratory infections, primarily in children, adults with severe lung disease, and elderly persons , panel AThe 2 major RSV subtypes, RSV-A and RSV-B, have distinct antigenic characteristics in the P, N, F, and G proteins , panel Bhttps://www.illumina.com). We used Trim Galore version 0.6.10 to quality filter and adaptor trim sequencing reads, mapped the reads to RSV-A and RSV-B reference sequences (GISAID accession nos. EPI_ISL_412866 and EPI_ISL_165399) using Burrows-Wheeler Aligner version 0.7.17-r1188 (https://bio-bwa.sourceforge.net), and generated consensus sequences using SAMtools version 1.17 (https://github.com/samtools/samtools/releases). We assembled 92 RSV-A (GA2.3.5 genotype) and 24 RSV-B (GB5.0.5a genotype) complete genome sequences and 8 RSV-A (GA2.3.5) and 3 RSV-B (GB5.0.5a) partial genome sequences . We performed genomic surveillance to determine RSV strains circulating in Arizona during the 2022\u20132023 season. We performed 2 \u00d7 150-bp paired-end next-generation sequencing using a hybrid capture enrichment panel , panel Ahttps://clades.nextstrain.org) showed that RSV-A sequences from Arizona clustered in clade GA2.3.5, indicating >3 independent introductions of RSV-A into Arizona is monovalent and Abrysvo , bivalent (The US Food and Drug Administration has approved 2 RSV vaccines for persons bivalent . RSV-B Sbivalent Figure 2Although RSV remains a substantial clinical burden, approved RSV vaccines reduce the risk of lower respiratory tract illness. By tracking RSV evolution, we can improve design of vaccine formulations to improve effectiveness. Our study was limited because we lacked understanding of potential functional consequences from mutations in F-protein antigenic sites. Although the G protein is under greater selective pressure and has higher mutation rates (Additional information about a study of respiratory syncytial virus in Arizona, USA, 2022\u20132023"} +{"text": "Escherichia coli strains isolated from the recto-anal junction of slaughter-age Irish sheep. In silico serotyping and genome analysis determined that each of the strains harbored a Shiga-toxin subtype, a complete locus of enterocyte effacement, and a rare O-island 122.This study describes the hybrid genome assemblies of four Shiga toxin-producing Escherichia coli (STEC) are significant foodborne zoonotic pathogens with primary virulence determinants being the bacteriophage encoded Shiga toxins (Stx) and the intimin adhesion protein and trimmed using Porechop (v0.2.4) for ONT or Fastp (v0.20.1) (de novo hybrid assemblies were constructed with Unicycler (v0.4.9) with 16 mg/L of novobiocin (Oxoid) and incubated at 41.5\u00b0C for 24 h. RT-PCR was performed on DNA extracted using InstaGene matrix (Bio-Rad) as described by Macori et al. to confiv0.20.1) for Illu(v0.4.9) and rang(v0.4.9) .https://github.com/phac-nml/ecoli_vf) and a customized database containing nle gene sequences (https://github.com/macgenomegue/nle_database). Protein-coding sequences, tRNAs, and insertion sequence elements were predicted using Prokka (1.14.6) (Genome annotation was conducted using the ABRIcate tool (v1.0.1) , and vir(1.14.6) , tRNA-sc(1.14.6) , and ISE(1.14.6) , respect(1.14.6) webtool."} +{"text": "Staphylococcus aureus infections.As daptomycin (DAP) CL does not scale proportionally with weight, fixed-dose DAP has been proposed to optimize efficacy and mitigate toxicity. This study evaluated systemic exposure of a fixed dose (750 mg) of DAP in patients with S. aureus infection were eligible for enrollment. DAP 750 mg was infused over 30 minutes every 24 hours. At steady state, concentrations were obtained pre-dose (0.5 hours) and 1, 12, and 24 hours after the start of infusion. Concentrations were measured using a validated LC-MS assay. Pharmacokinetic (PK) analysis was performed using first-order equations and stratified by weight: low (< 65 kg), normal (65-85 kg), and high ( > 85 kg). Therapeutic AUC24 (\u2265 666 mg*hr/L) and elevated trough (Cmin > 24.3 mg/L) were the efficacy and safety targets, respectively.Adult non-ICU patients with CrCl \u2265 30 mL/min admitted to our academic medical center warranting DAP for a e 0.078 h-1 , CL 0.87 L/h , AUC24 861 mg*hr/L , and Cmin 10.5 mg/L . Therapeutic AUC24 was achieved in 14/22 (64%) and elevated Cmin occurred in 7/22 (32%), with no differences seen among weight groups. However, differences were noted between males (n=10) and females (n=12) with significantly higher CL (median [IQR]) noted in males vs. females (p=0.027). Hence, median [IQR] AUC24 was significantly lower in males at 594 mg*hr/L vs. 1513 mg*hr/L in females (p=0.021). Therapeutic AUC24 was achieved in 40% of males versus 83% of females, while elevated Cmin was seen in 20% of males and 32% of females.Overall, 22 patients were enrolled with no differences observed in baseline characteristics . PK parameters (median [IQR]) did not differ by weight with Vd 9.9 L , K24 and Cmin) was not impacted by weight. These results support fixed, rather than weight-based, dosing of DAP in non-ICU patients with normal renal function. Notably, gender differences were observed with males having significantly higher CL, likely warranting higher doses of DAP to ensure optimal exposure.DAP PK and exposure : Grant/Research Support"} +{"text": "Streptomyces sp. strain ICN988, an actinomycete isolated from Gorgonia. The assembled genome consists of 6,122,654 bp with a GC content of 73%. A comprehensive analysis revealed 19 biosynthetic gene clusters.This study elucidates the draft genomic sequence of Actinomycetes produce many secondary metabolites, including antibiotics, antitumor agents, and immunosuppressive compounds, and are accountable for over half of the antibiotics used clinically . Marine Streptomyces sp. strain ICN988 was isolated from a Gorgonia sea-fan by-catch collected from Colachel coastal area, Tamil Nadu, India (8\u00b010'22.0\"N 77\u00b014'55.2\"E) on 28 December 2018. Initially washed with seawater to remove surface deposits, Gorgonia\u2019s holdfast was scraped aseptically, and the sand was suspended in 2% NaCl to prepare serial dilutions, then spread on Actinomycete Isolation Media (AIM) agar plates (supplemented with filter-sterilized 10 \u00b5g/mL nystatin and 50 \u00b5g/mL cycloheximide). Streptomyces sp. strain ICN988 (S5K) was one of the actinomycetes found after 7 days of incubation at 30\u00b0C. Genomic DNA was isolated from 5-day-old axenic ICN988 aerial mycelia using the NucleoSpin Tissue Kit (Macherey-Nagel). The 16S rRNA was PCR amplified with 63F forward primer and 1387R reverse primer. The actinomycete\u2019s 16S rRNA gene (GenBank: OP585661) was closely related (98.34% similarity) to Streptomyces ardesiacus NBRC 15402 (GenBank: NR_112454) via NCBI-BLAST and (96.60% similarity) to Streptomyces coelicoflavus NBRC 15399 (GenBank: AB184650) via EzBioCloud database . Sequence libraries were created using Nextera XT DNA Library Preparation Kit (Illumina). The whole-genome sequencing was obtained using Illumina HiSeq 4000 System (paired-end 150 bp). A total of 18,237,528 bp reads were obtained with 2,753,866,728 total read bases. The GC content was 71.01%, and Q30 was 88.73%. The tools such as Trimmomatic (v 0.36) for adapter trimming (The genomic DNA was extracted from a 7-day-old AIM agar plate culture using HiPurA trimming utilized(v3.0.2) revealed(v3.0.2) identifiStreptomyces sp. strain ICN988 was antagonistic to methicillin-resistant Staphylococcus aureus ATCC 33591 in agar-plug and metabolic extract disc diffusion assays.Through antiSMASH v7.0.0beta1-67b538a9 , 13, 30"} +{"text": "Correction:J Exp Clin Cancer Res\u00a042, 169 (2023)https://doi.org/10.1186/s13046-023-02723-zFollowing publication of the original article , an erro6*, Youtao Xu1* and Rong Yin1,4,5,7*Guoren ZhouThe correction do not affect the overall Conclusion of the article. The original article has been corrected."} +{"text": "Bacillus thuringiensis SS2 consists of 426 contigs assembled at the scaffold level, totaling 5,030,306\u2009bp, and contains 5,288 putative PATRIC protein-coding genes, including genes responsible for total benzoate consumption, degradation of halogenated compounds, heavy metal tolerance/resistance, biosynthesis of secondary metabolites, and microcin C7 self-immunity protein.The draft genome sequence of strain Bacillus thuringiensis is a Gram-positive, aerobic, rod-shaped, mesophilic bacterium that has been reported to metabolize persistent organic pollutants (POPs), pesticides, and heavy metals (B. thuringiensis SS2 was identified during a screen for dioxin-degrading bacteria from dibenzofuran (DF)-polluted waste dump soil obtained with a site with a history of incineration in Cele, Isolo, Lagos, Nigeria , and 2,7-dichlorodibenzo-p-dioxin (MH714859) and biochemical characterization (7-diCDD) . It was rization .B. thuringiensis SS2 was extracted using the Quick-DNA fungal/bacterial miniprep kit , from a Luria-Bertani culture that had been grown overnight at 28\u00b0C. The DNA was quantified using a QuantiFluor double-stranded DNA (dsDNA) system with a Qubit 3.0 fluorometer. Whole-genome sequencing (WGS) was performed through Illumina NextSeq paired-end sequencing. The library preparation and 2\u2009\u00d7\u2009150-bp paired-end sequencing were performed using the Nextera XT Index kit v2 (FC-131-2001 to FC-131-2004) and a NextSeq 500 system at Quadram Institute Bioscience , forming 426 contigs . The longest contig was 120,678\u2009bp, with an N50 value of 22,410\u2009bp. RASTtk identified 5,288 PATRIC protein-coding sequences and 1,174 hypothetical proteins, 66 tRNA genes, and 4 rRNA genes; the closest relative for B. thuringiensis SS2 is B. thuringiensis 97-27 (serovar konkukian).The genome sequence of B. thuringiensis SS2 revealed putative genes linked to the degradation of dioxin and other POPs similar to those of Serratia marcescens SSA1, which was isolated from the same burnt dump site. These genes include putative genes for total consumption of benzoate via hydroxylation and halogenated aromatic compound degradation, among others and copper-translocating P-type ATPase (EC 3.6.3.4) genes, suggesting heavy metal tolerance and resistance. Other putative genes, including those for microcin C7 self-immunity protein (mccf), macrocin O-methyltransferase, and CAAX amino-terminal proteins, could indicate this strain\u2019s diverse metabolic adaptations to stress in its environment.WGS of g others . B. thurB. thuringiensis SS2 at PATRICbrc (BV-BRC) can be viewed at https://www.bv-brc.org/view/Genome/1428.1921. The draft genome sequence was deposited in GenBank under the accession number JAOWLZ000000000; project data are available under BioProject accession number PRJNA888024, with BioSample accession number SAMN31205655 and SRA accession number SRR21870348. The 16S rRNA gene sequence is available under GenBank accession number MH714859.The genome annotation of"} +{"text": "Microsphaeropsis, taxonomically classified within the kingdom fungi, phylum Ascomycota, subphylum Deuteromycotina, class Coelomycetes, order Sphaeropsidales, and family Sphaeropsidaceae, exhibit a ubiquitous distribution across various geographical regions. These fungi are known for their production of secondary metabolites, characterized by both structural novelty and potent biological activity. Consequently, they represent a significant reservoir for the advancement of novel pharmaceuticals. In this paper, a systematic review was present, marking the analysis of secondary metabolites synthesized by Microsphaeropsis reported between 1980 and 2023. A total of 112 compounds, comprising polyketones, macrolides, terpenoids, and nitrogen-containing compounds, were reported from Microsphaeropsis. Remarkably, among these compounds, 49 are novel discoveries, marking a significant contribution to the field. A concise summary of their diverse biological activities was provided, including antibacterial, antitumor, and antiviral properties and other bioactivities. This analysis stands as a valuable reference, poised to guide further investigations into the active natural products derived from Microsphaeropsis and their potential contributions to the development of medicinal resources. Microsphaeropsis, taxonomically classified within the phylum Ascomycetes, subphylum Deuteromycotina, class Coelenterata, order Sphaeropsidales, and family Sphaeropsidaceae in the fungal taxonomy [Microsphaeropsis was not accurately recognized, leading to the misplacement of many fungi within the genus Coniothyrium. In 1980, Sutton meticulously elucidated the characteristics of the Microsphaeropsis genus. He subsequently reclassified species previously assigned to the genus Coniothyrium under Microsphaeropsis and renamed the genus [Microsphaeropsis have been unearthed and taxonomically elucidated. As of now, the repository of the Species Fungorum database (https://speciesfungorum.org/Names/Names.asp (accessed on 2 November 2023)) registers a total of 54 species within the genus Microsphaeropsis. It is evident that fungi within the genus Microsphaeropsis exhibit remarkable biodiversity, with a high likelihood of containing structurally novel and biologically active secondary metabolites.taxonomy , are comtaxonomy . For a lhe genus ,4. SubseMicrosphaeropsis genus by Sutton in 1980, various structural categories of compounds, including polyketides, terpenoids, nitrogen-containing compounds, macrolides, and others, were isolated from 2 known and 17 unknown species of Microsphaeropsis, and these demonstrated excellent antibacterial, antifungal, cytotoxic, and other activities and three known compounds: (4S)-4,8-dihydroxy -3,4-dihydro-1(2H)-naphthalen-1-one (2), (4S)-4,6,8-trihydroxy-3,4-dihydro-1(2H)- naphthalen-1-one (3), and chrysogeside D (94). Notably, compounds 3 and 94 were discovered for the first time in Microsphaeropsis. The research team conducted evaluations of the antifungal activity of these compounds. Compound 1 and compound 94 exhibited moderate antifungal activity against A. tenuissima with minimum inhibitory concentrations (MICs) at 64 \u03bcg/mL [Qin et al. 2017) successfully isolated four compounds from the endophyte fungus successf77), along with the known compounds (R)-mellein (8), -hydroxymellein (9), -hydroxymellein (10), and 4,8-dihydroxy-3,4-dihydro-2H-naphthalen-1-one (11), were successfully isolated from the fungus Microsphaeropsis sp. H5-50, which inhabits the marine sponges M. incrustans. Notably, both compounds displayed significant antifungal activity against E. repens and U. violacea in agar diffusion assays [The novel compound microsphaeropsisin M. arundinis PSU-G18, found within the plant Garcinia hombroniana [110), and seven new phthalides, microsphaerophthalides A-G (29\u201335), were identified, alongside eleven known compounds . Compound 44 exhibited remarkable antifungal activity, with an IC50 value of 8 \u03bcg/mL. Additionally, microsphaerophthalides A (29) and microsphaerophthalides E (33) displayed moderate antifungal activity against M. gypseum SH-MU-4 and C. neoformans, both with MIC values of 64 \u03bcg/mL. Decaspirone (57), isolated from the endophyte fungus Microsphaeropsis sp. 7291, demonstrated significant antifungal activity against M. violaceum, evidenced by inhibition zone diameters measuring 18 mm [Sommart et al. (2012) isolated nineteen compounds from the endophyte fungus broniana . Among t112), was successfully isolated from the endophyte fungus Microsphaeropsis sp. 7820, found inhabiting the plant Salsola oppositifolia. Remarkably, compound 112 exhibited moderate antifungal activity against M. violaceum, resulting in inhibition zone diameters measuring 9 mm [A novel polychlorinated triphenyl diether, microsphaerol (ing 9 mm .74) and microketides B (75), from the fungus Microsphaeropsis sp. RA10-14, and both compounds exhibited significant antifungal activity against Candida albicans, Colletotrichum truncatum, Gloeosporium musarum, and Pestalotia calabae [74) exhibited IC50 values of 1.56 \u03bcg/mL, 1.56 \u03bcg/mL, 3.13 \u03bcg/mL, and 1.56 \u03bcg/mL, respectively. Microketides B (75) displayed equal IC50 values of 3.13 \u03bcg/mL.Liu et al. (2020) isolated two novel metabolites, microketides A , were isolated from Microsphaeropsis sp. F2076 and Microsphaeropsis sp. F2078. Notably, the four microsphaerins, A, B, C, and D, exhibited significant antibacterial activity against Methicillin-resistant Staphylococcus aureus (MRSA), with IC50 values of 3 \u03bcM, 3 \u03bcM, 5 \u03bcM, and 1 \u03bcM, respectively. To delve deeper into their antibacterial activity, microsphaerins D (48) was selected for further investigation, encompassing Gram-positive and Gram-negative bacteria. Results revealed that it demonstrated moderate antibacterial activity against various Gram-positive bacteria; however, it displayed inactivity against Gram-negative bacteria, except for K. pneumoniae [Four metabolites, namely microsphaerins A\u2013D (eumoniae .1 (56), palmarumycin M2 (58), papyracillic acid C (61), microsphaeropsins A (78), and microsphaeropsins B (62), were successfully isolated, alongside three known compounds, decaspirone (57), papyracillic acids A (59), and papyracillic acids B (60), from the endophyte fungus Microsphaeropsis sp. 7291, which resides within the plant Pilgerodendron uviferum. Of significance, compounds 56, 57, and 58 exhibited moderate antibacterial activity against B. megaterium, resulting in inhibition zone diameters of 6 mm, 6 mm, and 7 mm, respectively [Five new metabolites, namely palmarumycin Mectively .Microsphaeropsis sp. 8875 residing in the plant Lycium intricatum [64\u201366), in addition to two known compounds, citreorosein (67) and emodin (68). Moreover, from a Microsphaeropsis sp. 7177 strain sourced from the plant Zygophyllum fortanesii, they identified two new metabolites, 3,4-dihydrofusidienol A (70) and microsxanthone (73), along with three known compounds, fusidienol A (69), 8-hydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylic acid methyl ester (71), and methyl 3,8-dihydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylate (72). Remarkably, all these compounds exhibited significant antibacterial activity, particularly against the Gram-negative bacterium E. coli. Microsphaerol (112), derived from the endophyte fungus Microsphaeropsis sp. 7820, displayed moderate antibacterial activity against B. megaterium and E. coli, evidenced by inhibition zone diameters measuring 9 mm and 8 mm, respectively [Krohn et al. 2009) conducted a comprehensive study resulting in the isolation of several metabolites from the endophyte fungus 09 conducectively . 74) and microketide B (75), were successfully isolated from the fungus Microsphaeropsis sp. RA10-14, which inhabits the gorgonian Anthogorgia ochracea from the South China Sea. Both compounds exhibited significant antibacterial and antifungal activities, with a notable emphasis on their antibacterial effects. Specifically, compound 74 demonstrated significant antibacterial activity against B. subtilis, B. megaterium, E. aerogenes, K. rhizophila, and P. aeruginosa, all with equal MIC values of 0.19 \u03bcg/mL, mirroring the potency of ciprofloxacin [Two novel metabolites, microketide A , was isolated alongside seven known compounds from the fungus Microsphaeropsis sp. BCC 3050. This fungal strain was collected from the lichen Dirinaria applanata. The known compounds in this collection include preussomerins E (18), F (19), G (20), H (21), I (17), deoxypreussomerins A (22), and bipendensin (23). Remarkably, all compounds, except compound 23, exhibited activities against M. tuberculosis, and compounds 16, 17, and 18 showed moderate antibacterial activity, with IC50 values of 25 \u03bcg/mL, 12.5 \u03bcg/mL, and 25 \u03bcg/mL, respectively. Compounds 19, 20, 21, and 22 showed significant antibacterial activity, with IC50 values of 3.12 \u03bcg/mL, 3.12 \u03bcg/mL, 6.25 \u03bcg/mL, and 1.56 \u03bcg/mL, respectively [94), sourced from the endophyte fungus Microsphaeropsis arundinis PH 30472, showed moderate antibacterial activity against E. coli [The new isomer, 3\u2032-O-demethylpreussomerin I ((21), I 1, deoxypr79), B (80), and C (81), were isolated alongside three known compounds from the endophyte fungus M. arundinis E12-2112, which resides within the plant Ulmus macrocarpa. Among the known compounds, one isochroman-1-one, arundinone A (27), a polyoxygenated benzofuran-3(2H)-one dimer, arundinone B (28), and 1\u03b2-hydroxy-\u03b1-cyperone (82) were identified. Significantly, compound 82 displayed moderate antibacterial activity against S. aureus with an value of 11.4 \u03bcg/mL [Three novel ent-eudesmane sesquiterpenoids, namely arundinols A (.4 \u03bcg/mL .R)-1\u2032--1\u2032-oxobutan-3\u2032-ylacetate (4), was isolated, alongside six known compounds, (R)-1--3-hydroxybut -anone (5), 1--2-buten-1-one (6), (R)-6-hydroxy-2-methyl-4-chrom -anone (7), modiolide D (84), modiolide E (85), and modiolide A (86). These compounds were obtained from the endophyte fungus M. arundinis, residing within the plant Paepalanthus planifolius [5 exhibited moderate cytotoxic activity against murine breast adenocarcinoma (LM3), with IC50 values of 36.83 \u00b1 4.86 \u03bcg/mL, while compound 6 displayed moderate cytotoxic activity against human breast cancer (MCF-7), with IC50 values of 33.95 \u00b1 3.62 \u03bcg/mL [A new metabolite, , through alterations of the culture medium for the fungus M. olivacea F010 [98 demonstrated significant cytotoxic activity against murine leukemic cells (L1210), achieving an inhibition ratio of 90% [Keusgen et al. (1996) successfully isolated a cerebroside, namely cea F010 . Remarkao of 90% .99), C (101), and E (103), in conjunction with two known compounds, TAN-1496 B (100) and D (102), were successfully isolated from the fungus Microsphaeropsis sp. FL-16144. Extensive research has revealed that these compounds act as specific inhibitors of calf thymus Topo I [Three novel metabolites, TAN-1496 A (s Topo I . Notablys Topo I . Additios Topo I .87) and macrosphelide B (88), from the fungus Microsphaeropsis sp. FO-5050 [50 values of 3.5 \u03bcM and 36 \u03bcM, respectively. Notably, in vitro cell growth assays showed that these compounds had no discernible effect on the growth of cells, including P388 leukemia, human prostate tumor cells, and L929 fibroblast cells, even when administered at a high dose of 200 mg/kg for 5 days [89) and macrosphelide D (90) from the fungus Microsphaeropsis sp. FO-5050 [89) and macrosphelide D (90) exhibited moderate cytotoxic activity, with IC50 values of 67.5 \u03bcM and 25 \u03bcM, respectively. Fukami et al. (1998) continued their exploration of the fungus Microsphaeropsis sp. FO-5050 and made further discoveries [91), macrosphelide K (92), and 6-epi-5\u2019-hydroxymycosporulone (12). Although these compounds displayed cytotoxic activity, their IC50 values exceeded 100 \u03bcg/mL. Collectively, these findings underscore the exceptional potential of the fungus Microsphaeropsis sp. FO-5050 as a source of novel macrolides with cytotoxic properties. These substances hold high promise for future development in the treatment of leukemia.It has been widely reported that cell adhesion molecules play pivotal roles in numerous physiological and biochemical processes, ranging from cancer ,42,43 to FO-5050 . To explr 5 days . Takamat FO-5050 . Macrospcoveries . They is18, 19, and 20 possess the capability to inhibit Ras farnesyl-protein transferase [16\u201321 have demonstrated significant cytotoxicity against a spectrum of cell lines, including human epidermoid carcinoma (KB cells), human breast cancer (BC-1 cells), and African green monkey kidney fibroblast (vero cells). Compound 28, sourced from the endophyte fungus M. arundinis E12-2112, has exhibited moderate cytotoxicity against human bladder carcinoma cells (T24) and human lung carcinoma cells (A549), characterized by IC50 values of 35.4 \u03bcg/mL and 81.6 \u03bcg/mL, respectively [Singh et al. (1994) previously reported that compounds nsferase . Seephonnsferase . Furtherectively .49), graphislactone A (50), ulocladol (51), botrallin (52), 2,5-diacetylphenol (53), 7-hydroxy-2,4-dimethyl-3(2H)- benzofuranone (54), and enalin (55), were isolated from the endophyte fungus M. olivacea, which resides within the plant Pilgerodendron uviferum. Remarkably, graphislactone A (50) and botrallin (52) exhibited significant activity against acetylcholinesterase (AChE), characterized by IC50 values of 8.1 \u03bcg/mL and 6.1 \u03bcg/mL, respectively. However, all these compounds displayed no discernible antibacterial or antifungal activities [Seven known compounds, namely butyrolactone I (tivities .76), from the fungi Microsphaeropsis sp. FO-5050 [76 holds great promise as a novel class of anti-influenza virus drugs, representing a potential breakthrough in the realm of influenza treatment.Fukami et al. (2000) isolated a novel anti-influenza virus antiviral, known as 10-norparvulenone ( FO-5050 . Interes95), was isolated from the endophyte fungus Microsphaeropsis sp. MF6057, found within the plant Prosopis glandulosa. Compound 95 demonstrated an IC50 value of 71 \u03bcM in binding to a cloned human B2 receptor with 3H-bradykinin, marking a noteworthy development in the pursuit of potential treatments [Bradykinin, an endogenous peptide, exerts its effects through specific cell receptors, giving rise to a plethora of physiological reactions, including pain, allergic responses, and muscle contractions. Bradykinin antagonists hold the potential to inhibit these physiological reactions, offering prospects for treating conditions such as inflammatory edema, rhinitis, and asthma. In a significant discovery, a novel non-peptide bradykinin-binding inhibitor, L-755,807 and microsphaerones B (97), were successfully isolated from the fungus Microsphaeropsis sp. KMPB W-22. Interestingly, neither of these compounds exhibited significant cytotoxicity. Additionally, they displayed either no activity or only moderate activity against S. littoralis and A. salina [Two novel . salina .83 and 104) and three fresh 1,3,6,8-tetrahydroxyanthraquinone congeners (13\u201315) were successfully extracted from the fungus Microsphaeropsis sp. KMPB W-22. Remarkably, all these compounds, with the exception of compound 104, exhibited moderate inhibitory activity against protein kinases such as PKC, CDK4, and EGF-R, encompassing an IC50 range of 18.5\u201354.0 \u03bcM [Two novel betaenone derivatives first reported on the in vitro activity of preussomerins against lciparum . Compoun44, sourced from the endophyte fungus M. arundinis PSU-G18, has exhibited significant antiplasmodial activity, boasting an IC50 value of 9.63 \u03bcg/mL. Notably, it also demonstrates significant radical scavenging capabilities, with an IC50 value of 0.018 mg/mL [1 (56), decaspirone (57), and papyracillic acids A (59), all originating from the endophyte fungus Microsphaeropsis sp. 7291, have demonstrated anti-algal activity against C. fusca. Their inhibitory effects are reflected in inhibition zone diameters of 6 mm, 13 mm, and 7 mm, respectively [112, derived from the endophyte fungus Microsphaeropsis sp. 7820, has displayed anti-algal activity against C. fusca, characterized by an inhibition zone diameter of 8.5 mm [64\u201373, apart from 8-hydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylic acid methyl ester (71), have demonstrated anti-algal activity against C. fusca [74) and microketides B (75), isolated from Microsphaeropsis sp. RA10-14, have exhibited moderate antiphytoplankton activity against P. helgolandica, showcasing IC50 values of 12.3 \u03bcg/mL and 16.8 \u03bcg/mL, respectively [Compound 18 mg/mL . In anotf 8.5 mm . Additioectively .Microsphaeropsis genus, and their activities have yet to be determined. For instance, Liu et al. (2018) isolated six known metabolites, including butyrolactones I (24), butyrolactones IV (25), aspernolide D (26), fumiquinazolines L (105), fumiquinazolines N (106), and notoamide D (107), from the fungus Microsphaeropsis sp. CF09-11, sourced from marine sediment [24\u201326 and 105\u2013107) were obtained from Microsphaeropsis for the first time. In a unique discovery, uncommon methyl-branched unsaturated fatty acids, 10-methyl-9Z-octadecenoic acid (108) and glyceride (109), were isolated from the endophyte fungus M. olivacea, which inhabits the marine sponge Agelus sp. This marks the first report of fungal fatty acids with methyl branches on a cis-double bond [63), papyracillic acids A (59), and papyracillic acids B (60), were isolated from the endophyte fungus Microsphaeropsis sp., originating from the plant Arbutus unedo. Importantly, this research led to the establishment of the absolute configuration of massarigenin A (63) [Furthermore, several compounds were isolated from fungi within the sediment . It is nble bond . Addition A (63) .Microsphaeropsis in 1980, fifty-four different species have been included. Currently, this genus has yielded an impressive array of secondary metabolites, with 112 secondary metabolites reported, of which 49 (41.96%) were identified for the first time. These compounds are distributed across various structural classes, including 76 polyketones (67.86%), 14 nitrogenous compounds (12.5%), 10 macrolides (8.9%), 7 terpenoids (6.25%), and 5 other compounds (4.46%), indicating polyketones are the predominant structural type Employ non-directional activation strategies to activate the biosynthesis of secondary metabolites, such as the OSMAC (one strain many compounds) strategy [Microsphaeropsis has not been reported in the literature so far. Thus, whole gene sequencing and analysis will be the focus of further work. (iii) Expand the scope of activity screening of existing compounds and delve into their mechanism of action to verify their potential for pharmaceutical applications. For instance, microbetides A (74), a novel polyketone compound, demonstrates remarkable antibacterial activity against Gram-positive bacteria and Gram-negative bacteria, with an IC50 of 0.19 \u03bcg/mL, comparable to ciprofloxacin. Polyketone 10-norparvulone (76) exhibits the potential to effectively inhibit virus replications, positioning it as a promising candidate for a new anti-influenza drug. Macrolide compounds like macrosphelide A (87) and macrosphelide B (88), characterized by their unique chemical structures and cytotoxicity against leukemia, hold promise as novel anticancer drugs.Fungi occupy an exceptionally pivotal role in drug discovery . Many restrategy , co-cultstrategy , and epistrategy . (ii) Hastrategy , transcrstrategy , the hetstrategy , DNA-assstrategy , and ribstrategy . However"} +{"text": "Escherichia coli (ECOL) and Enterobacter cloacae complex (ENTCC) demonstrate a range of MEM MICs. The objective of this study was to assess the in vitro killing activity of dose-optimized MEM against CRE with or without KPC that demonstrate variable MEM MICs and to determine if vaborbactam potentiates the killing activity of MEM against non-CP CRE.KPC producing CRE are common in the US; however non-carbapenemase producing (CP) CRE are as common. KPC- and non-CP Table); isolates demonstrated MEM MICs ranging from 1 to 8 mg/L. MEM standard (1g q8h over 30 minutes) and optimized (2g q8h over 3 hours) regimens were tested in 1-compartment and hollow fiber infection models (HFIM); targeted exposures were confirmed by LC-MS/MS. In HFIM, MEV (4g q 8h over 3 hours) was also tested. Resistant subpopulations were selected by agar plates containing MEM at 4x baseline MIC.8 ECOL and 8 ENTCC were characterized by whole-genome sequencing or ENTCC . Bacterial regrowth occurred more rapidly against KPC compared to non-CP isolates. For MEM optimized regimens, 72-hour log-kills decreased as MEM MICs increased against non-CP ECOL; optimized MEM regimens were not bactericidal against KPC ECOL with MICs \u22652 mg/L. For ENTCC, optimized MEM resulted in greater log-kills against non-CP than KPC isolates at each MIC level. Across all non-CP and KPC isolates with MEM MICs \u22642 mg/L (n=4 each), mean log-kills at 72 hours with optimized MEM were -4.43 and -0.26 logs, respectively (P=0.04). Colonies selected on MEM containing agar demonstrated a median (range) MEM MIC of 64 mg/L (16 \u2013 >256 mg/L). Next, we compared optimized MEM and MEV in 10 day HFIMs against isolates with MEM MICs of 4mg/L. MEV demonstrated potent bactericidal killing against KPC isolates. Unexpectedly, MEV was also bactericidal against both non-CP isolates, and potentiated MEM killing against ECOL0174 .Standard MEM regimens were largely not bactericidal against ECOL . Optimized dosing MEM 2g q8h, 3 hour infusion (green). Limit of detection is 0.7 log colony forming units (CFU)/mL, denoted by dashed line. BMD = broth microdilution. KPC = Klebsiella pneumoniae carbapenemase.Standard dosing MEM 1g q8h, 30 minute infusion (red). Optimized dosing MEM 2g q8h, 3 hour infusion (green). Lower limit of detection is 0.7 log CFU/mL, denoted by dashed line. BMD = broth microdilution. KPC = Klebsiella pneumoniae carbapenemaseStandard dosing meropenem 1g q8h, 30 minute infusion (red). Optimized dosing meropenem 2g q8h, 3 hour infusion (green), or meropenem-vaborbactam 4g q8h, 3 hour infusion (purple). Lower limit of detection is 0.7 log CFU/mL. MIC = minimum inhibitory concentration.in vitro killing of CR ECOL and ENTCC is dependent on MEM MICs and presence of KPC. Even at low MICs, optimized MEM exposures were ineffective against KPC isolates. Against non-CP CRE, killing decreases as a function of increased MEM MIC. MEV may play an additive role in killing against non-CP isolates that are not killed by MEM alone.Our data show Ryan K. Shields, PharmD, MS, Allergan: Advisor/Consultant|Cidara: Advisor/Consultant|Entasis: Advisor/Consultant|GSK: Advisor/Consultant|Melinta: Advisor/Consultant|Melinta: Grant/Research Support|Menarini: Advisor/Consultant|Merck: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Roche: Grant/Research Support|Shionogi: Advisor/Consultant|Shionogi: Grant/Research Support|Utility: Advisor/Consultant|Venatorx: Advisor/Consultant|Venatorx: Grant/Research Support"} +{"text": "In the original publication , there wThere was an error in the original publication. We examined correlations among biomarkers, which should have been analyzed by Spearman\u2019s correlation method instead of Pearson\u2019s correlation.A correction has been made to Section 2, \u201cResults\u201d; Section 2.4, \u201cCorrelations between Major CSF Proteins in CSF of CN, MCI, and AD\u201d; and Section 2.5, \u201cCorrelations between Major CSF Proteins and AD Biomarkers\u201d.rs = 0.86) and L-PGDS (rs = 0.47) levels (Table 1), while GlcNAc-Tf also correlated with L-PGDS (rs = 0.57). In contrast, Man-Tf levels did not correlate with Sia-Tf or TTR levels. High correlations were thus found among Man-Tf, GlcNAc-Tf, and L-PGDS in the CN group. In MCI, Man-Tf levels correlated well with GlcNAc-Tf (rs = 0.73) and L-PGDS (rs = 0.66) levels, while GlcNAc-Tf correlated well with L-PGDS (rs = 0.69). Man-Tf levels were negatively, but weakly, correlated with TTR (rs = \u22120.36) levels but not with Sia-Tf. Again, high correlations were observed among brain-derived proteins in the MCI group. In AD, Man-Tf levels correlated well with GlcNAc-Tf (rs = 0.79) and L-PGDS (rs = 0.62) levels but not with Sia-Tf or TTR. On the other hand, GlcNAc-Tf levels correlated well with L-PGDS (rs = 0.61) levels. These results suggest that the brain-derived proteins showed significant correlations with each other across all clinical groups.Correlations of the CSF proteins were also analyzed for the CN, MCI, and AD clinical groups. In CN, Man-Tf levels correlated with GlcNAc-Tf (rs = 0.56), tau (rs = 0.56), A\u03b240 (rs = 0.73), and A\u03b242 (rs = 0.52); GlcNAc-Tf vs. p-tau (rs = 0.76), tau (rs = 0.79), A\u03b240 (rs = 0.76), and A\u03b242 (rs = 0.49); L-PGDS vs. p-tau (rs = 0.84), tau (rs = 0.79), A\u03b240 (rs = 0.79), and A\u03b242 (rs = 0.52). The A\u03b242/A\u03b240 ratio showed negative correlations with Man-Tf (rs = \u22120.15), GlcNAc-Tf (rs = \u22120.34), and L-PGDS (rs = \u22120.44); however, none of these were statistically significant. In contrast, neither Sia-Tf nor TTR levels correlated with any AD markers. Taken together, the brain-derived CSF proteins correlated significantly with p-tau, tau, A\u03b240, and A\u03b242 levels in the CN group but the blood-derived proteins did not. In MCI, CSF protein levels also correlated with AD markers as follows: Man-Tf vs. p-tau (rs = 0.71), tau (rs = 0.53), A\u03b240 (rs = 0.45); GlcNAc-Tf vs. p-tau (rs = 0.65), tau (rs = 0.54), and A\u03b240 (rs = 0.43); L-PGDS vs. p-tau (rs = 0.49) and tau (rs = 0.41). The A\u03b242/A\u03b240 ratio showed negative correlations with Man-Tf (rs = \u22120.24), GlcNAc-Tf (rs = \u22120.45), and L-PGDS (rs = \u22120.23) but none were statistically significant. Overall, in the MCI group, the brain-derived proteins correlated moderately with AD markers. In AD, p-tau showed a moderate, though significant, correlation with the CSF proteins (rs = 0.51~0.55) but not with other AD markers. TTR negatively correlated with p-tau (rs = \u22120.42) and tau (rs = \u22120.72), while Sia-Tf correlated with tau (rs = \u22120.41). These results suggest that AD markers tend to correlate with the brain-derived CSF proteins in the AD and MCI groups; however, with the exception of p-tau, their correlation declined concomitantly with AD progression.Our previous study demonstrated that Man-Tf and p-tau were co-expressed in hippocampal neurons in the AD brain and that CSF Man-Tf levels correlated well with p-tau levels in MCI and AD. Other CSF proteins, such as Man-Tf, GlcNAc-Tf, L-PGDS, TTR, and Sia-Tf, were therefore examined for their correlation with AD markers (Table 2). In CN subjects, the CSF proteins showed significant correlations with AD markers as follows: Man-Tf vs. p-tau (The authors state that the scientific conclusions are unaffected. This correction was approved by the Academic Editor. The original publication has also been updated."} +{"text": "Serum UA , NT-proBNP levels (1090.4 (675.2\u20132664.9) vs. 759.0 (260.3\u20131474.8), p = 0.034), and MLHFQ scores (21.0 (14.0\u201347.0) vs. 14.5 (4.5\u201325.5), p = 0.012) were significantly higher, whereas 25(OH)D concentrations (17.6 (15.1\u201328.2) vs. 22.7 (19.5\u201333.8), p = 0.010) were lower in subjects with severely reduced LVEF. Also, 25(OH)D was independently associated with LVEF in univariate and multiple regression analysis, maintaining its significance even after adjusting for confounders such as age, NT-proBNP, the presence of chronic coronary syndrome, hypertension, and anemia. According to our current findings, 25(OH)D is closely associated with LVEF, further supporting the need to establish correct vitamin D supplementation schemes and dietary interventions in HF. The changes in LVEF, 25(OH)D, serum UA, and albumin levels in HFrEF and HFmrEF indicate a similar pathophysiological background.Vitamin D emerged as an important prognostic biomarker in heart failure (HF), with currently highly debated therapeutic implications. Several trials on vitamin D supplementation in HF showed improvements in left ventricular (LV) remodeling and function and health-related quality of life (HRQoL), which did not translate into mid- to long-term beneficial effects regarding physical performance and mortality. We addressed total 25-hydroxyvitamin D (25(OH)D), serum albumin, and uric acid (UA) levels, focusing mainly on vitamin D deficiency, as potential markers of LV systolic dysfunction in HF with reduced and mildly reduced ejection fraction . Seventy patients with LVEF < 50% were comprehensively evaluated using ECG, echocardiography, lung ultrasound (LUS), blood sampling, and the six-minute walk test (6MWT). HRQoL was also assessed using the Minnesota Living with Heart Failure Questionnaire (MLHFQ). Statistically significant positive correlations were found between LVEF, 25(OH)D, serum UA, and albumin, respectively ( Vitamin D is a pleiotropic hormone showing substantial cardiovascular involvement beyond its regulatory effects on calcium and phosphate homeostasis. Vitamin D deficiency is frequently associated with cardiovascular disease and is i3 2D3), the biologically active form of vitamin D, exerts its genomic and rapid, non-genomic effects via vitamin D receptors (VDRs) . R. R2 usinEchocardiography was performed using a Philips Epiq7 ultrasound machine and a Philips X5-1 xMATRIX array transducer . Clinical recommendations for multimodality cardiovascular imaging were applied ,28,29. LThe lung ultrasound (LUS) protocol consisted of an eight-zone evaluation, four on each hemithorax. Semi-recumbent positioning of patients facilitated the assessment of B-lines. The same cardiac probe was used for lung imaging as well, and depth was adjusted individually. The following threshold for abnormality (in terms of lung congestion) was applied: \u22653 B-lines per zone .Blood samples were collected after twelve-hour fasting , and centrifuged for 10 min at 3000 rpm. Laboratory tests were performed, including total-, LDL-, and HDL-cholesterol, serum triglycerides, UA, creatinine, albumin, serum iron, ferritin, and CRP using an Architect C4000 ; plasma fibrinogen was assessed with Sysmex CA-1500 . N-terminal pro-B-type natriuretic peptide (NT-proBNP) concentrations were measured using an electrochemiluminescent method on an Elecsys 2010 . Complete blood count was assessed using tripotassium ethylenediaminetetraacetic acid precoated tubes on a Mindray BC6000 .Quantitative determination ofthe total 25(OH)D in patients with HF was conducted using a competitive electrochemiluminescence protein binding assay on a Mindray CL-900i Chemiluminescence Immunoassay Analyzer . Patients were divided into tertiles based on serum 25(OH)D levels . None of the participants were taking vitamin D supplements in the two months prior to the evaluation. Dietary vitamin D intake from food sources and sun exposure were not assessed. The reference range for this assay was 30\u2013100 ng/mL.2 test. 25(OH)D concentrations were log-transformed for analysis to improve normal distribution. p-values < 0.05 were regarded as statistically significant. Microsoft Excel 2016 and GraphPad Prism 9.5.0 were used for data curation and processing.The Kolmogorov\u2013Smirnov and/or Shapiro\u2013Wilk normality tests were used for the assessment of data distribution. Paired t-test and Pearson\u2019s correlation were performed for variables showing normal distribution. Data following non-Gaussian distribution were processed using the Mann\u2013Whitney U test and Spearman\u2019s rank correlation analysis. Categorical variables were quantified for absolute and relative frequency, and 2 \u00d7 2 contingency tables were analyzed with the \u03c7p = 0.019). Patients with HFrEF had higher body mass index (BMI) (p = 0.025), LA volume index (LAVI) (p = 0.032), LVEDV index (LVEDVI) (p < 0.0001), LV end-systolic volume index (LVESVI) (p < 0.0001), lower stroke volume index (SVI) (p = 0.0002), longer-lasting heart disease (p = 0.041), compared to patients with HFmrEF. Also, study participants with HFmrEF showed better quality of life (p = 0.012). Serum UAd and NT-proBNP concentrations were significantly increased , whereas 25(OH)D levels were significantly decreased (p = 0.010) in HFrEF. Loop diuretic therapy was more frequently prescribed to patients with HFrEF. None of the participants took serum UA-lowering medication at the time of evaluation.Seventy patients with a mean age of 66 \u00b1 11 years were included in the study. p < 0.01) (Both log 25(OH)D and serum UA showed significant differences and an inverse relationship in the two study groups ( < 0.01) .p = 0.023), LVEF , platelet count , serum albumin , and HDL-cholesterol concentrations . Statistically significant negative associations were reported between serum 25(OH)D and UA levels , LVESVI , and LVGLS . No significant relationship was found connecting 25(OH)D to CRP , 6MWT distance , or NYHA class . Patients with 25(OH)D levels in the first tertile vs. the third tertile associated type II diabetes mellitus (DM) more frequently, but it did not reach statistical significance .Also, when considering 25(OH)D levels in all patients, significant positive correlations were found with diastolic blood pressure values , BMI (p = 0.006), and E/e\u2019 ratio (p = 0.037). LVEF also showed strong negative associations with NT-proBNP (p = 0.029), serum UA levels (p = 0.009), GGT activity (p = 0.006), and thyroid-stimulating hormone (TSH) concentrations (p = 0.040). Interestingly, LVEF was not linked to 6MWT distance, age, duration of heart disease, or duration of HF. Significant positive correlations were found between LVEF and both components of blood pressure\u2014systolic (p = 0.003) and diastolic blood pressure (p = 0.006), and also serum 25(OH)D levels (p = 0.008).p = 0.036 and p = 0.030, respectively). In the second model, log 25(OH)D maintained its predictive value, even after adjusting for the presence of chronic coronary syndrome (CCS).Multivariate linear regression models (A and B) were constructed in the overall study population for the prediction of LVEF in HF . Log 25(p = 0.027) (Model C). Furthermore, log 25(OH)D predicted HFrEF, maintaining its significance when corrected for age, NT-proBNP tertiles, GGT tertiles, the presence of hypertension, CCS, anemia, and hypothyroidism (p = 0.036) (Model D).Nonlinear logistic regression models (C and D) were also set up to predict LV systolic dysfunction . In the 2D is released into the bloodstream, circulating in both protein-bound and free forms [2D deficient mice developed glomerular (podocyte) injury, albuminuria, and subsequent kidney dysfunction, which were reversible upon exposure to 1,25(OH)2D [Over the last few decades, especially during the COVID-19 pandemic, vitamin D received widespread attention, mainly because of its complex biological activity, regulating gene transcription, and modulating signaling pathways . Vitaminee forms . The remee forms . Moreove25(OH)2D . Zhang e25(OH)2D . Our pat25(OH)2D ,37, vita25(OH)2D .+ currents proved to be an important cause of electrophysiological remodeling in cardiac hypertrophy, which was reversed upon exposure to 10 nM of calcitriol [2D. Calcitriol, at concentrations above 30 nM, reduced the proliferative capacity, caused mild hypertrophy, and altered cardiomyocyte morphology [p = 0.010). Currently, there is no guideline recommendation regarding screening for vitamin D deficiency and correct supplementation in HF. Both experimental and clinical trials linked vitamin D deficiency to the excessive activation of the RAAS with increased expression of the renin gene, higher plasma renin activity, and elevated plasma aldosterone and angiotensin II levels [2D increases intracellular calcium concentrations and decreases intracardiac filling pressures, thus enhancing systolic and diastolic ventricular function [p = 0.036 and p = 0.030; p = 0.027 and p = 0.031). Contrary to the results published by Khan et al., we found no significant relationship between 25(OH)D levels and the functional status of patients with HF, reflected by the 6MWT distance and NYHA class [p = 0.061). Vitamin D deficiency was previously linked to DM by regulating inflammation and inducing insulin resistance [A multiple inhibitory role regarding vitamin D in HF has been proposed: it reduces myocardial fibrosis, pathological remodeling, and atherosclerosis, by down-regulating low-grade vascular inflammation . The suplcitriol . Vitaminlcitriol . VDRs werphology . The sizrphology . VDR knorphology . There irphology . Other arphology . Our patI levels . Vitaminsistance . Cassanosistance .3 administered weekly and 400 mg of calcium citrate given BID for 6 months, failed to demonstrate the beneficial effects of cholecalciferol supplementation on physical performance in HF patients with a mean LVEF of 39.2 \u00b1 13.2%, and already on guideline-directed medical therapy [3 daily during a 3-year follow-up. Long-term intake of moderately high doses of vitamin D had no impact on mortality but was associated with a significantly greater need for mechanical circulatory support device implants in patients with baseline circulating 25(OH)D levels \u2265 30 nmol/L, who showed increased in-study concentrations > 100 nmol/L [Several trials addressed the potential benefits and pitfalls of vitamin D supplementation in HF but showed inconsistent results. The VINDICATE study enrolled vitamin D-deficient patients with HF and LVEF \u2264 45% already on optimal medical treatment. After 12 months of well-tolerated high-dose cholecalciferol supplementation (4000 IU daily), LV structure and function showed statistically significant improvements, reflected by the EF, end-diastolic, and end-systolic diameters, and volumes. Unexpectedly, the reversal of LV remodeling was not associated with improved 6MWT distance at 1 year, and further clinical outcomes were not assessed . Another therapy . The mor0 nmol/L . In a ca0 nmol/L . High pl0 nmol/L . A recen0 nmol/L ,54. Vita0 nmol/L .As seen, the trials investigating the effects of vitamin D in HF used different supplementation schemes and study outcomes, which might explain the inconclusive results.p = 0.005). We also found that patients with 25(OH)D deficiency were prone to develop hyperuricemia. The association might be explained by the severity of LV systolic dysfunction, which is associated with lower levels of vitamin D [Serum UA also sparked controversy regarding its status as a potential cardiovascular risk factor, considering its pro-oxidant\u2013antioxidant activity. Elevated levels were linked to increased risk for cardiovascular disease, including HF . Moreoveitamin D ; both viitamin D ,24. Alsoitamin D . Treatmeitamin D ,64. The itamin D . In patiitamin D . The URRitamin D . It shouWe hypothesize that the associated changes in LVEF, 25(OH)D, serum UA, and albumin levels might indicate similar pathophysiological backgrounds in HF with systolic dysfunction. One possible explanation might rely on the pleiotropic biological impact of inflammation. Abundant evidence already linked low-grade systemic inflammation to HF . TherefoVitamin D, serum UA, and albumin are already established prognostic biomarkers in HF. We found 25(OH)D to be an independent marker of LVEF using univariate and multiple regression analysis. Significant correlations were identified between LVEF, 25(OH)D, serum UA, and albumin, suggesting potential molecular interactions. Although there is currently a plethora of information regarding vitamin D deficiency in HF, its precise mechanism, clinical impact, and management still need clarification."} +{"text": "Electroconvulsive therapy (ECT) is one of the few non-pharmacological stimulation treatment which is cost effective, effecious and lifesaving in various psychiatric disorders. Although myths and misconceptions prevailed in a society undermine the usefulness of such treatment.Attitude towards Electroconvulsive therapy (ECT) among psychiatric patients.It was a descriptive cross-sectional study conducted at the Department of Psychiatry and Behavioural sciences, Jinnah Postgraduate Medical Centre (JPMC), Karachi from 22-Oct-2019 to 21-April-2020 and a total of 250 psychiatric patients were enrolled.Methode; Attitudes toward ECT were assessed using ECT attitude questionnaire6 (Annexure III). A 15 items questionnaire, each item has three alternatives based on which responses were categorized into positive, negative, or ambivalent attitudes. Mean score was calculated for each.Patients who were given 8 positive answers out of 15 were labeled as having a positive attitude. Patients who were given 8 negative answers out of 15 were labeled as having a negative attitude. Patients who were given 8 I don\u2019t know answers out of 15 were labeled as having ambivalent attitude.Age 18-65 yearsEither genderPsychiatric patients, having awareness regarding their nature of illness and could give consent for study.Patients with duration of illness >3 months.Psychiatry patients who have no awareness regarding their illness.Patients with impaired cognitiveForty-four (45.83%) patients had positive attitude, 36 (37.50%) had negative attitude and 16 (16.67%) had ambient attitude.Further stratification was also performed on the basis of educational status, occupational status, duration of illness, psychiatric diagnosis, and previous experience of ECT. There was no significant association was found of these variables with attitude regarding ECT.Mean age was 39.58\u00b112.48 years included in this study. There were 55 (57.29%) female and 41 (41.71%) male patients. There were 72 (75.00%) patients were household workers, 04 (4.17%) students, 06 (5.25%) unskilled labour, 3 (3.13%) skilled labour, 10 (10.42%) professionals and just 01 (1.04%) were law enforcement worker. 19 (19.79%) patients were diagnosed with schizophrenia, 62 (64.58%) were diagnosed with unipolar depression and 15 (15.63%) were diagnosed with bipolar disorder. Source of ECT information was 11 (11.46%) electronic media, 09 (9.38%) print media, 19 (19.79%) social media and 57 (59.38%) was from health professionals. Forty-four (45.83%) patients had positive attitude, 36 (37.50%) had negative attitude and 16 (16.67%) had ambient attitude.Knowledge regarding electroconvulsive therapy (ECT) was low in psychiatric patients in Pakistan. Only 45.83% patients showed positive attitude towards ECT.Carney S, Geddes J. Electroconvulsive therapy. Br Med J. 2003;326:1343-4Gangadhar BN., Kapur RL., Kalyanasundaram S. Comparison of electroconvulsive therapy with imipramine in endogenous depression: a double blind study. Br J Psychiatry.1982;141:367\u201371.Kellner CH., Fink M., Knapp R., Petrides G., Husain M., Rummans T., et al. Relief of expressed suicidal intent by ECT: a consortium for research in ECT study. Am J Psychiatry. 2005;162:977\u201382.Baghai T C, Moller HJ. Electroconvulsive therapy and its different indications. Dialogues Clin Neurosci. 2008 Mar; 10(1): 105\u201317.Weiner RD., Coffey CE., Folk J., Fochtmann LJ., Greenberg RM., et al. American psychiatric association committee on electroconvulsive therapy, The practice of electroconvulsive therapy. 2nd ed. Washington, DC: American Psychiatric Association; 2001None Declared"} +{"text": "Although the survival rate of patients who undergo surgery for gastric cancer has greatly improved, still many patients have a poor prognosis. This retrospective study aimed to investigate the predictive ability of the PNI-IgM score, a combined prognostic nutritional index (PNI), and immunoglobulin M (IgM), on the prognosis of patients undergoing surgery for gastric cancer.340 patients with gastric cancer who underwent surgery from January 2016 to December 2017 were selected. The PNI-IgM score ranged from 1 to 3: score of 1, low PNI (< 48.45) and low IgM (< 0.87); score of 2, low PNI and high IgM, or high PNI and low IgM; score of 3, high PNI and high IgM. We compared the differences in disease-free survival (DFS) and overall survival (OS) among the three groups, while univariate and multivariate analyses calculated prognostic factors for DFS and OS. In addition, the nomograms were constructed based on the results of multivariate analysis to estimate the 1-, 3- and 5-year survival probability.P = 0.053) and the PNI-IgM score group 3 . In stratified analysis, PNI-IgM score 1 had a worse prognosis in the age < 60 years group and CA724 < 2.11 U/m group.There were 67 cases in the PNI-IgM score 1 group, 160 cases in the PNI-IgM score 2 group, and 113 cases in the PNI-IgM score 3 group. The median survival times of DFS in the PNI-IgM score group 1, the PNI-IgM score group 2, and the PNI-IgM score group 3 were 62.20 months, not reached, and not reached, and 67.57 months vs. not reached vs. not reached in three groups for OS. Patients in the PNI-IgM score group 1 had a lower DFS than the PNI-IgM score group 2 (HR = 0.648, 95% CI: 0.418-1.006, PNI-IgM score is a novel combination of nutritional and immunological markers that can be used as a sensitive biological marker for patients with gastric cancer who undergo surgery. The lower the PNI-IgM score, the worse the prognosis. According to the World Health Organization, gastric cancer was the fifth leading cancer in the world, with nearly 1.09 million new cases of gastric cancer worldwide in 2020. Gastric cancer is the fourth leading cause of cancer deaths, with almost 770,000 deaths worldwide in 2020 \u20135. In reThe nutritional status of patients with gastric cancer, which could predict the progression of the treated cancer, has been identified an important factor \u201311. It wA large number of previous researches have pointed out that composite indicators of nutrition and immunity, such as Glasgow Prognostic Score (GPS), platelet-to-lymphocyte (PLR), and Controlling Nutritional Status (CONUT) score could predict the prognosis of gastric cancer patients , 27. HowIn this study, we evaluated the predictive effect of the PNI-IgM score on efficacy and prognosis in 340 patients with gastric cancer who underwent surgery. To further validate the PNI-IgM score, we performed a subgroup analysis and created nomograms.This is a retrospective study, so the Ethics Committee of Harbin Medical University Cancer Hospital waived informed consent. In total, we collected 340 consecutive patients with gastric cancer who received surgery at Harbin Medical University Cancer Hospital between January 2016 and December 2017 and were tested for lymphatic subsets and specific proteins. Statistical analysis of 340 patients and their clinical information was implemented according to the Helsinki Declaration and its amendments. All patients were included according to the following criteria: (1) all patients underwent surgical treatment; (2) all patients had no chronic disease; (3) all patients were tested for lymphatic subsets and specific proteins; (4) all patients did not display inflammatory response. (5) Patients with gastric cancer combined with other primary malignant tumors were excluded. Patients without complete clinical information and regular review after surgery were exclusion criteria. The flow chart of clinical case selection is shown in Patients were followed up by telephone or outpatient visit, every 3-6 months during the first 2 years, and every 6-12 months from the 3rd to 5th year, and annually thereafter. Disease-free survival (DFS) was comprehended as the period from the first day of surgery date to the date of disease progression. The evidence of progression was obtained by chest and abdomen X-ray or computed tomography. DFS was also defined as the date of death, death from any cause, or the date of withdrawal from the follow-up. Overall survival (OS) was described as the period from the first day of surgery date to the date of death, the date of withdrawal from the follow-up, or the time of the last follow-up. Electronic medical record system was used to acquire patients\u2019 clinical and pathological information.9/L). The cut-off point was obtained by the receiver operating characteristic (ROC), which was based on OS for the prediction of patients\u2019 death. The area under the ROC Curve (AUC) was used to evaluate the predictive ability of PNI and IgM. The optimal cut-off values of PNI and IgM with the highest Youden index were obtained.The peripheral venous blood was collected in fasting state after admission in all patients. The counts of peripheral lymphocytes (L) were measured and analyzed by an automatic blood analyzer (BACKMAN COULTER LH750), the levels of peripheral albumin were measured and analyzed by an automatic blood analyzer (ADVIA-2400), and the levels of peripheral IgM were measured and analyzed by a specific protein analyzer (IMMAGE800). PNI was calculated as follows: PNI = albumin (g/L) + 5 \u00d7 total lymphocyte counts and 95% confidence interval (CI). The Cox proportional hazards regression model was constructed to analyze independent prognostic factors for DFS and OS. The nomograms were also constructed to predict the 1-, 3-, and 5-year survival probability for DFS and OS. The calibration curve analysis was used to assess the prognostic predictive ability of nomogram. All statistical analyses were completed through the R 4.1.3 , IBM SPSS Statistics 25 . Finally, we considered two-sided P values < 0.05 as statistical differences.Continuous variables are presented as means with standard deviations or as medians with interquartile ranges. Categorical variables were expressed as percentages. The comparison between continuous variables used the t-tests, one-way ANOVA, Kruskal-Wails rank sum test. We used the Chi-square test or Fisher\u2019s exact test to compare the discrepancies between categorical variables. The Kaplan-Meier survival curve was used to compute the survival rate and the Log-rank test to compare the survival time difference. Univariate and multivariate analyses were performed using the Cox proportional hazards model. Variables that achieved statistical significance at P = 0.006), weight loss (P = 0.012), fatigue (P < 0.001), pTNM stage (P < 0.001) and tumor size (P = 0.003). The one-way ANOVA Kruskal-Wails rank sum test showed that PNI-IgM score was related to age (P < 0.001), BMI (P = 0.012), bleeding volume (P = 0.012). The detailed clinical characteristics of all 340 cases grouped by PNI-IgM score are displayed in The median age of patients was 60 years, and there were 105 women (30.9%) and 235 men (69.1%) in all two groups\u2019 cases. The optimal cut-off value of PNI was 48.45. The optimal cut-off value of IgM was 0.87 g/L. According to the optimal cut-off values of PNI and IgM, all patients were divided into three groups: PNI-IgM score of 3 (n = 113): high IgM (\u2265 0.87) and high PNI (\u2265 48.45); PNI-IgM score of 2 (n = 160): high IgM (\u2265 0.87) and low PNI (< 48.45), or low IgM (< 0.87) and high PNI (\u2265 48.45); PNI-IgM score of 1(n = 67): low IgM (< 0.87) and low PNI (< 48.45). The Chi-square test or Fisher\u2019s exact test showed that PNI-IgM score was related to melaena (P = 0.017), \u03b3- GT (P < 0.001), TBIL (P < 0.001), TP (P < 0.001), ALB (P < 0.001), GLOB (P < 0.001), UA (P = 0.002), ALP (P = 0.027), WBC (P < 0.001), RBC (P < 0.001), IgA (P < 0.001), IgG (P < 0.001), KAP (P < 0.001), LAM (P < 0.001) and CD3 +/CD4 + CD8 + cells (P = 0.004).In this study, we also collected patients\u2019 nutritional and hematological parameters before surgery, including total protein (TP), PALB, alanine aminotransferase (ALT), aspartate transaminase (AST), glutamyl transpeptidase (\u03b3- GT), lactate dehydrogenase (LDH), total bilirubin (TBIL), globulin (GLOB), urea, creatinine (CREA), urate (UA), alkaline phosphatase (ALP), monocyte (Mono), eosinophils (Eosi), basophil (Baso), red blood cell (RBC), platelet (P), carcinoembryonic antigen (CEA), carbohydrate antigen 199 (CA199), carbohydrate antigen 724 (CA724), carbohydrate antigen 125II (CA125II). We also collected lymphatic subsets and specific proteins, including immunoglobulin A (IgA), immunoglobulin G (IgG), transferrin (TRF), light-chain immunoglobulin (KAP), heavy-chain immunoglobulin (LAM), KAP/LAM, CD3 + cells (T cells), CD3 +/CD4 + cells (Th cells), CD3 +/CD8 + cells (CTL cells), CD4 +/CD8+ cells, CD3 +/CD4 + CD8 + cells, CD19 + cells (B cells), CD3 -/CD16 + CD56 + cells (NK cells), CD3 +/CD16 + CD56 + cells (NKT cells). We analyzed their relationship to the PNI-IgM score by Kruskal-Wails rank sum test (P = 0.001), BMI (P = 0.043), tumor size (P < 0.001), pTNM stage (P < 0.001), radical resection (P < 0.001), TBIL (P = 0.020), Eosi (P = 0.032), RBC (P = 0.032), CA724 (P < 0.001), CA125II (P = 0.003), IgG (P = 0.028), PNI-IgM score (P < 0.05). And the prognosis factors of patients in this study for OS were age (P = 0.001), melaena (P = 0.048), tumor size (P < 0.001), pTNM stage (P < 0.001), radical resection (P < 0.001), TBIL (P = 0.016), Eosi (P = 0.030), RBC (P = 0.031), CA724 (P = 0.004), CA125II (P = 0.004), IgG (P = 0.036), PNI-IgM score (P < 0.05). The multivariate analysis indicated that age (P = 0.036 vs. P = 0.035), pTNM stage (P < 0.001 vs. P < 0.001), radical resection (P = 0.006 vs. P = 0.001), and CA724 (P = 0.027 vs. P = 0.015) were both independent prognostic factors for DFS and OS. In addition, melaena (P = 0.003) was the independent prognostic factor for OS and in CA724 < 2.11U/m group or the PNI-IgM score 3 . Patients with the PNI-IgM score 1 have a shorter OS than patients with the PNI-IgM score 2 or the PNI-IgM score 3 , 65.4% (95% CI: 54.7%-78.3%), 53.1% (95% CI: 41.9%-67.3%). The PNI-IgM score 1 group\u2019s median survival time for OS was 67.57 months, the 1-, 3-, and 5-year OS probability was 89.5% (95% CI: 82.4%-97.2%), 69.0% (95% CI: 58.6%-81.3%), 55.6% (95% CI: 44.5%-69.4%). The PNI-IgM score 2 group\u2019s median survival time for DFS and OS were both not achieved. The 1-, 3-, and 5-year DFS and OS probability were 89.3% (95% CI: 84.6%-94.2%), 74.0% (95% CI: 67.4%-81.3%), 68.2% (95% CI: 61.1%-76.1%); 89.9% (95% CI: 85.4%-94.7%), 77.8% (95% CI: 71.6%-84.6%), 69.7% (95% CI: 62.8%-77.3%), respectively. The PNI-IgM score 3 group\u2019s median survival time for DFS and OS were both not achieved. The 1-, 3-, and 5-year DFS and OS probability were 93.8% (95% CI: 89.4%-98.4%), 80.5% (95% CI: 73.4%-88.4%), 80.5% (95% CI: 73.4%-88.4%); 95.6% (95% CI: 91.9%-99.4%), 82.0% (95% CI: 75.1%-89.4%), 81.0% (95% CI: 74.0%-88.7%), respectively. To further determine whether the PNI-IgM score could predict the prognosis of gastric cancer patients. The ROC curves were based on OS for the prediction of patients\u2019 death. For the traditional clinicopathologic factors, including ALB, L, PNI, and IgM, each feature and the combined PNI-IgM score were plotted, and the point with the highest AUC was illustrated on the ROC curve. The PNI-IgM score exhibited a higher prognostic accuracy for DFS and OS than PNI and other clinicopathological risk factors (P = 0.626) or the PNI-IgM score 3 . Patients with the PNI-IgM score 1 also have a shorter OS than patients with the PNI-IgM score 2 group or the PNI-IgM score 3 group . Patients in the advanced pTNM stage had lower DFS and OS than those early pTNM stage patients group (221 patients) and advanced pTNM stage (III + IV) group (119 patients). The median survival time for DFS and OS in the early pTNM stage group were both not reached. The 1-, 3-, and 5-year DFS and OS probability were 98.2% (95% CI: 96.4%-100.0%) vs. 98.2% (95% CI: 96.4%-100.0%), 89.2% (95% CI: 85.2%-93.5%) vs. 89.9% (95% CI: 86.0%-94.0%), 86.7% (95% CI: 82.2%-91.4%) vs. 87.4% (95% CI: 83.1%-92.0%). The median survival time for DFS and OS in the advanced pTNM stage group were 30.90 months and 40.27 months. The 1-, 3-, and 5-year DFS and OS probability were 76.9% (95% CI: 69.6%-84.9%) vs. 79.6% (95% CI: 72.7%-87.2%); 45.7% (95% CI: 37.2%-56.2%) vs. 54.1% (95% CI: 45.7%-64.0%); 34.7% (95% CI: 26.6%-45.4%) vs. 39.0% (95% CI: 30.9%-49.3%). Patients with the PNI-IgM score 1 have a shorter DFS than patients with the PNI-IgM score 2 (HR = 0.814, 95% CI: 0.356-1.860, This study found that age, radical resection, CA724, and pTNM stage were the independent prognostic factors for DFS. By constructing Cox proportional hazard regression model, age, melaena, radical resection, CA724, and pTNM stage were the independent prognostic factors for OS. Based on the results of multivariate analysis, the nomograms to predict the 1-, 3-, and 5-year survival probability for DFS and OS were established (Gastric cancer is a common malignant tumor in China, with the third highest incidence and mortality rate . AlthougOur study is the first to assess the association between the PNI-IgM score, which a composite indicator of immunity and nutrition, clinicopathological factors and survival. It also demonstrated that the PNI-IgM score predicted prognosis among gastric cancer patients who underwent resection. We found that low PNI and IgM were associated with poor patient prognosis. This study found that age, pTNM stage, radical resection, and CA724 were independent prognostic factors for DFS and OS. In addition, an independent prognostic factor for OS was melaena. In the Stratified analyses, we found age <60 years and CA724 < 2.11 U/m had shorter OS in PNI-IgM score 1.Although many studies have confirmed the prognostic association of PNI and IgM with gastric cancer \u201335 and oThis study also has some limitations. First, this was a single-region, single-center retrospective study with limited sample size and potential selection bias. Second, we only selected patients with gastric cancer who underwent surgery. Third, the cut-off value of PNI and IgM is usually derived from the ROC curve, and the optimal cut-off value is uncertain. Therefore, multi-regional, multi-center, and larger sample size studies are needed to validate our findings.In conclusion, our study found that the PNI-IgM score is a valid scoring tool for patients with gastric cancer who received surgery. Patients in the PNI-IgM score 1 group had a worse prognosis than those in the PNI-IgM score 2 group, and the PNI-IgM score 3 group. Therefore, the PNI-IgM score could be used as a biomarker to develop better treatment strategies for patients undergoing surgery for gastric cancer.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.This study was approved by the ethics committee of Harbin Medical University Cancer Hospital. All patients provided written informed consent before the study.Writing-original draft and Writing-review & editing: ZD, HaS; Data curation and Investigation: RZ, GD, and HP; Methodology and Supervision: YZ, RH; Resources, Funding acquisition and Project administration: YX, and HoS. All authors contributed to the article and approved the submitted version."} +{"text": "Kidney function can alter drug clearance. This is pertinent for tenofovir-based pre-exposure prophylaxis (PrEP) regimens where drug concentrations confer protection against HIV. Among transgender (TG) individuals whose kidney function is dynamic due to use of gender affirming therapy (GAT), it is unclear if there is a relationship between tenofovir diphosphate dried blood spots (TFV-DP DBS) and direct measures of glomerular filtration rate (mGFR) The objective of this study was to quantify this relationship and compare if mGFR differs between TG persons with perfect/imperfect adherence to tenofovir alafenamide/emtricitabine (TAF/FTC).A prospective cohort study was performed among TG individuals on TAF/FTC for PrEP. Inclusion criteria were age \u226518 years old, TG identity, HIV negative, use of PrEP for \u226512 weeks, and willing to receive iohexol for direct measurement of GFR. TFV DBS concentrations were evaluated after being on \u226512 weeks of TAF/FTC. Perfect adherence to TAF/FTC was defined as a TFV-DP DBS of >1800fmol/punch . Iohexol clearance was used for mGFR by subcutaneously administering 0.5ml iohexol. Plasma iohexol concentrations were assayed 3h post-injection. Pearson\u2019s correlation coefficients were computed to quantify the relationship between TFV-DP DBS and iohexol clearance. Median iohexol clearances were compared between those with perfect/imperfect adherence.2=0.10, 95% confidence interval, CI: -0.29 \u2013 0.45, p=0.62). TFV-DP DBS >1800fmol/punch (perfect adherence) was observed in 22 participants. Median (95% CI) iohexol clearance between those with and without perfect adherence did not reach significance: 78 (68-96) vs 69 (60-83)mL/min, respectively (p=0.26).Among the 28 individuals included, median age was 33.0 (26.3 \u2013 36.8) years. Three quarters were on GAT and over two thirds (67.9%) were assigned male at birth (AMAB). Median iohexol clearance and TFV-DP DBS concentrations were 76 (65 \u2013 95)ml/min and 2611 (2114 \u2013 3240), respectively. There was no significant correlation between TFV-DP DBS and iohexol clearance (rNo significant relationship was observed between iohexol clearance and TFV-DP DBS among TG individuals taking TAF/FTC for PrEP.Sheldon Morris, MD, Gilead: Grant/Research Support"} +{"text": "Skin and soft tissue infections (SSTIs) are very common bacterial infections. Numerous clinical trials have compared antibiotics for SSTI treatment. However, trials typically have non-inferiority designs that give little insight as to which antibiotic classes have superior efficacy.We performed a systematic literature review and a network meta-analysis of published SSTI treatment trials. Using standardized key words, we searched PubMed and Embase for SSTI clinical trials published from 1/1/66 to 5/31/22. We excluded trials on diabetic foot infections, non-generalizable populations , and studies with outcomes not involving clinical resolution or cure. Abstracts with relevant clinical trial data were pulled and, if inclusion criteria met, had manuscript data abstracted. Two reviewers independently performed abstract and manuscripts reviews and data abstraction. For the network meta-analyses, the comparator antibiotic class was glycopeptides. Two analyses were performed using intention to treat (ITT) and clinically evaluable (CE) populations. Clinical trial quality was measured using the PEDro score.We reviewed 5,469 abstracts, of which 260 were pulled for data abstraction and 93 contained analyzable trial data . Clinical trial quality varied widely . We identified 26 analyzable antibiotic classes or combinations for comparison. In the ITT model, cure rate for oxazolidinones (OR 1.28 [95% CI 1.10-1.49]), flucloxacillin plus clindamycin (OR 1.61 [95% CI 1.03-2.53]), lipopeptides (OR 1.66 [95% CI 1.04-2.66]), and tetracyclines OR 1.69 [95% CI 1.24-2.30]), significantly differed from glycopeptides. In the CE model, cure rate for oxazolidinones (OR 1.29 [95% CI 1.01-1.64]) and tetracyclines (OR 2.05 [95% CI 1.37-3.06]) significantly differed.We found that most (22/26) antibiotic classes or combinations used for SSTI treatment had similar efficacy to glycopeptides. However, oxazolidinones, lipopeptides, flucloxacillin plus clindamycin, and tetracyclines may have superior efficacy compared to glycopeptides. Treatment guidelines may wish to favor these latter classes for patients at high risk of treatment failure.Amy Y. Kang, Pharm.D., BCIDP, Paratek: Grant/Research Support Elliot I. Miller, BS, Epic Systems, Verona, WI: Employee Loren G. Miller, MD MPH, ContraFect: Grant/Research Support|GSK: Grant/Research Support|Medline: Grant/Research Support|Merck: Grant/Research Support|Paratek: Grant/Research Support"} +{"text": "A safe and effective method to protect against cytomegalovirus (CMV) infection is a public health priority. mRNA-1647 is an investigational mRNA-based vaccine against CMV consisting of 6 mRNA sequences encoding 2 CMV antigens (glycoprotein B and the pentameric glycoprotein complex) in lipid nanoparticles in a lyophilized presentation.This phase 2, randomized, observer-blind, placebo-controlled, dose-finding trial of mRNA-1647 was conducted in CMV-seronegative and -seropositive healthy adults aged 18-40 years (NCT04232280). In Part 1, males and females were randomized 3:1 to receive mRNA-1647 or placebo at Months 0, 2, and 6. In Part 2, females were randomized 3:1 to receive mRNA-1647 100 \u00b5g or placebo at Months 0, 2, and 6. Primary endpoints were safety throughout the study, including solicited adverse reactions (ARs) up to 7 days after each dose, and neutralizing antibody (nAb) titers against epithelial cell infection and against fibroblast infection up to 12 months after last dose. Parts 1 and 2 results are combined.Figure). Robust nAb responses against epithelial cell infection were observed after each mRNA-1647 dose and sustained through the end of the study (12 months after last dose); nAb titers against epithelial cell infection in seronegative mRNA-1647 100-\u00b5g recipients exceeded the geometric mean titer of all seropositive recipients at baseline.Of 315 adults randomized, solicited ARs following dose 1 were reported in 54.7% (placebo), 84.4% (50 \u00b5g), 87.5% (100 \u00b5g), and 91.1% (150 \u00b5g) of seronegative adults and 59.3%, 94.4%, 94.6%, and 94.4%, respectively, of seropositive adults. The most common local and systemic solicited ARs across serostatus groups after dose 1 were pain and fatigue , respectively. Similar trends in ARs were observed after doses 2 and 3. nAb titers against epithelial cell infection and against fibroblast infection were observed in all mRNA-1647 groups (Antibody-Mediated Immunogenicity of mRNA-1647 by CMV Serostatus(A) nAb titers against epithelial cell infection and (B) nAb titers against fibroblast infection are presented from day 1 through month 18 for CMV-seronegative (colored solid lines) and CMV-seropositive (colored dashed lines) treatment groups. Data are presented by serostatus, treatment group, and visit as GMT and corresponding 95% CI. Data are from the Per-Protocol Set. The solid black lines represent nAb GMTs against epithelial cell infection (GMT = 4575.7) and against fibroblast infection (GMT = 4215.5) for all CMV-seropositive participants at baseline (n = 87). Doses 1, 2, and 3 were administered on D1, M2, and M6, respectively, as represented by an arrow and syringe.CMV, cytomegalovirus; D, day; GMT, geometric mean titer; M, month; nAb, neutralizing antibody.mRNA-1647 was generally safe and well-tolerated and induced antigen-specific immune responses at all dose levels in both CMV-seronegative and -seropositive participants. These results guided selection of the 100-\u00b5g dose for the mRNA-1647 phase 3 trial.Lori Panther, MD, MPH, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Sandeep Basnet, MD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Richard Leggett, DO, Crossroads Clinical Research: Contract employee James Peterson, MD, Moderna, Inc.: Received payment as a study investigator Jiang Lin, PhD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Kai Wu, PhD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Heather Lee, BS, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Roxane Hasselbeck, BA, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Andrew Natenshon, MA, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Jacqueline Miller, MD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds"} +{"text": "Asaia bogorensis strain SC1 isolated from a human-blood-fed Aedes aegypti mosquito crop. Metabolic pathway characteristics of aerobic respiration were present in the genome, along with multiple putative antibiotic resistance mechanisms.Understanding microbe-host interactions is key to combating disease transmission by mosquitoes. Here, we report the genome sequence of Asaia bogorensis strain SC1, isolated from a human-blood-fed Aedes aegypti mosquito crop. Importantly, Asaia sp. is dominant in the crop of Ae. aegypti Aedes aegypti mosquito crop. Briefly, the crop was dissected from a mosquito using ethanol-flamed forceps, homogenized in 1\u00d7 PBS pH = 7.4, and inoculated on Luria-Bertani (LB) agar at 30\u00b0C. To ensure a pure culture, individual colonies were sequentially streaked on fresh LB plates three times. DNA was extracted from overnight LB broth cultures using the Qiagen DNeasy PowerSoil Kit and quantified via Qubit . For long-read sequencing, the Native Barcoding Kit 24 V14 Kit was used to barcode samples and prepare libraries. DNA was not sheared or size selected prior to library prep. Sequencing was performed with an R10.4.1 flow cell (FLO-MIN114) and minION device under high-accuracy mode (280 bp/s). Basecalling was performed using Guppy 6.4.6, and reads with quality scores <7 were removed. Reads were filtered with Filtlong 0.2.1 (ng 0.2.1 to removcy mode 20 bp/s. Bl FLO-MIN4 and minng 0.2.1 . Potenting 0.2.1 . Taxonomng 0.2.1 and the ng 0.2.1 .Asaia bogorensis (96.36% average nucleotide identity). GhostKOALA identified complete pathways for central carbon metabolism, including glycolysis and pyruvate oxidation, TCA cycle, and the pentose phosphate pathway. A complete oxidative phosphorylation pathway was annotated. Interestingly, pyruvate decarboxylase (pdc) was absent, but other putative fermentation genes, aldehyde dehydrogenases and alcohol dehydrogenase (adhA), were present. GhostKOALA identified genes potentially conferring resistance to vancomycin, beta-lactams, and cationic antimicrobial peptides. The genome sequence of Asaia bogorensis strain SC1 from the mosquito crop provides a valuable resource for further investigating host-microbe interactions of public health interest.The SC1 genome is 3.4 Mbp with 59.69% GC content . GTDB id"} +{"text": "Rf) genes. Accordingly, mechanisms underlying the control of the wide phenotypic variation in pollen number for breeding germplasm should be elucidated. This study aimed to identify complete linkage DNA markers responsible for male sterility at the MS-P1 region based on fine mapping. Two P-class pentatricopeptide repeat (PPR) family genes were identified as candidates for Rf based on predicted mitochondrial localization and higher expression in a male fertile variety/selected strain than in a male sterile variety. Eleven haplotypes (HT1\u2013HT11) at the MS-P1 region were defined based on genotyping of DNA markers. Association analysis of diplotypes at the MS-P1 region and the number of pollen grains per anther (NPG) in breeding germplasms harboring Kishu-cytoplasm revealed that the diplotypes in this region influenced NPG. Among these haplotypes, HT1 is a non-functional restorer-of-fertility (rf) haplotype; HT2, a less-functional Rf; HT3\u2013HT5 are semi-functional Rfs; and HT6 and HT7 are functional Rfs. However, the rare haplotypes HT8\u2013HT11 could not be characterized. Therefore, P-class PPR family genes in the MS-P1 region may constitute the nuclear Rf genes within the CMS model, and a combination of the seven haplotypes could contribute to phenotypic variation in the NPG of breeding germplasms. These findings reveal the genomic mechanisms of CMS in citrus and will contribute to seedless citrus breeding programs by selecting candidate seedless seedlings using the DNA markers at the MS-P1 region.In citrus breeding programs, male sterility is an important trait for developing seedless varieties. Sterility associated with the male sterile cytoplasm of Kishu mandarin (Kishu-cytoplasm) has been proposed to fit the cytoplasmic male sterility (CMS) model. However, it remains undetermined whether CMS in citrus is controlled by interactions between sterile cytoplasm and nuclear restorer-of-fertility ( These s Tanaka) . TherefoRf). The male sterile phenotype is a result of interaction between the CMS-associated gene and a non-functional restorer-of-fertility nuclear gene (rf) Rf2 being the first family . To eluche first . Among t) family . These P) family , with ea) family . In partstigated . Three nstigated ; however1 populations of a cross between different varieties and selected strains harboring the Kishu-cytoplasm (MS-P1). This reduced NPG is linked to the haplotype block derived from kunenbo in the MS-P1 locus (Rf are located in the MS-P1 locus and to determine the influence of a combination of haplotype blocks (including Rf) on the phenotypic variations pertaining to male sterility and fertility in individuals with Kishu-cytoplasm.Male sterility and fertility segregate in the Fytoplasm . Specifiytoplasm . In addiytoplasm . These rytoplasm and haveP1 locus . TherefoMS-P1 region within the locus using fine mapping, (2) identify candidates for Rf (Rf-MS-P1) through bioinformatic and transcriptional analysis, (3) define the number of allelic haplotypes at the MS-P1 region among the founders; and (4) reveal the association between NPG and the combination of allelic haplotypes (diplotype) at the MS-P1 region. Hybrid varieties, selected strains, and individuals in F1 populations (breeding germplasms) harboring the Kishu-cytoplasm as well as the various diplotypes in each individual were evaluated. Two mitochondrial-targeted PPR family genes at the MS-P1 region showed significant transcriptional differences between sterile and fertile varieties during flower development, indicating that they played an important Rf role in the CMS model. Assessing the combination allelic haplotypes, including the two PPR family genes, would enhance our understanding of the wide phenotypic variations observed in citrus male sterility and fertility associated with a sterile cytoplasm.To elucidate the molecular mechanism underlying male sterility in Kishu-cytoplasm and assess if it fits into the CMS genetic model, the present study aimed to: (1) identify the 1 populations, Okitsu No. 46 \u00d7 \u2018Kara\u2019 (O46-K), \u2018Sweet spring\u2019 \u00d7 Okistu No. 56 (SS-O56) and \u2018Harehime\u2019 \u00d7 Okistu No. 63 (H-O63), and the varieties/selected strains used in this study were maintained in the Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO S2. The and 2013 . The NPG1 populations and the 85 varieties/selected strains through a modified protocol using cetyltrimethylammonium bromide and a high-salt precipitation solution . Six DNA markers in the MS-P1 locus were used in a previous report (MS-P1 locus (C. clementina genome v1.0 (JGI) (https://phytozome-next.jgi.doe.gov/info/Cclementina_v1_0) (https://mikan.dna.affrc.go.jp/) were identified using BLAST (https://mikan.dna.affrc.go.jp/blast/) (https://archive.gramene.org/db/markers/ssrtool) (https://bioinfo.ut.ee/primer3/) , was obtna_v1_0) . The cor/blast/) . The idessrtool) . The pririmer3/) . Dimericrimer3/) , as descrimer3/) .MS-P1 locus were identified based on the genotype segregation pattern. A graphical genotype of the MS-P1 locus was constructed for the physical map of C. clementina genome v1.0 between 5,153,708 and 19,761,190 bp in scaffold 8. The male sterile genotypes within the MS-P1 locus in recombinant individuals were identified through comparisons with the genotype of male sterile varieties/selected strains were obtained from Phytozome (https://phytozome-next.jgi.doe.gov/info/Cclementina_v1_0) (Zea mays) Rf2 (U43082), rice (Oryza sativa) Rf2 (AB583697), rice Rf17 (Os04g0475900), and sugar beet (Beta vulgaris) Rf1 (AB646135), all of which belong to the non-PPR family of Rf, were used as the query to perform BLAST analysis against the sequences in the Mikan Genome DB under default settings. The protein sequences of the PPR family at the MS-P1 region were analyzed using TargetP v.2.0 (https://urgi.versailles.inra.fr/predotar/) (https://ihg.helmholtz-muenchen.de/ihg/mitoprot.html) (https://ppr.plantenergy.uwa.edu.au/) (https://prosite.expasy.org/scanprosite/), and phylogenetic trees were constructed using the neighbor-joining method of MEGA v.10.0.5 (https://www.megasoftware.net) with protein sequences of rice (Oryza sativa) Rf1a (DQ311053), rice Rf1b (DQ311054), rice Rf4 (KJ680249), Sorghum (Sorghum bicolor) Rf1 (Brassica napus) Rfp1 (KX671967), Petunia (Petunia hybrida) Rf-PPR592 (AY10271), Ciclev10030242m, and Ciclev10030361m. Bootstrap values were calculated through a 1,000-permutation test.The gene locus, annotations, and protein sequences at the na_v1_0) . The DNAetP-2.0) , Predotaedotar/) , and Mitot.html) to prediedu.au/) . Proteinserver/) , while Plor) Rf1 , ChineseC. clementina genome v1.0 (JGI) (https://phytozome-next.jgi.doe.gov/info/Cclementina_v1_0) using HISAT2 v.2.1.0. Transcripts per million (TPM) values were obtained to measure gene expression using StringTie v.2.1.1. TPM values were imported to Subio Platform v.1.24.5853 for normalization. Statistical analysis of the comparisons between \u2018Shiranuhi\u2019 and KyOw14 was carried out using the \u201ccompare 2 groups\u201d tool of the Subio platform. All RNA-seq data was deposited in the DDBJ Sequence Read Archive under accession number DRA015326.Bulked stamen from a sterile selected strain (KyOw14) and fertile variety (\u2018Shiranuhi\u2019) were collected seven days before flowering (DBF) and 1 DBF in a field from the Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO , as two biological replicates. Total RNA was isolated using an RNeasy Plant Mini Kit , while the RNA-seq analysis was carried out by Hokkaido System Science Co., Ltd. . RNA-seq libraries were generated from the total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina . The 150 bp paired-end sequencing of RNA-seq libraries was performed using the NovaSeq 6000 system , and the sequenced reads were trimmed using fastp v.0.22.0 and mapped to https://phytozome-next.jgi.doe.gov/info/Cclementina_v1_0) . Quantitative PCR was performed QuantStudio3 Real Time PCR System using Power SYBR Green PCR Master Mix (Thermo Fisher Scientific) under 10 min at 95\u00b0C, followed by 40 cycles of 15 s at 95\u00b0C and 60 s at 60\u00b0C. The primers for the gene expression of Ciclev10030242m , Ciclev10030361m , and Ciclev10029947m were designed at a specific region or 3\u2019UTR referred by Phytozome (na_v1_0) . The expGGATCAT) . SpecifiThe sources of cytoplasm in the 85 varieties/selected strains were determined referring to the pedigree chart .1 populations Table S1d H-O63) , althougd H-O63) of genotee chart .https://www.jichi.ac.jp/saitama-sct/SaitamaHP.files/statmedEN.html) .MS-P1 locus between 33.5cM (TSRF161) and 69.1cM (SSR08B66) on linkage group 8 (LG8) in the corresponding linkage map of Okitsu No. 46 \u00d7 Okitsu No. 56 , 66 functional genes, including 10 PPR family genes, were predicted on the 920 kb genomic region, corresponding to the newly refined MS-P1 region (Rf2 (U43082), rice Rf2 (AB583697), rice Rf17 (Os04g0475900), or sugar beet Rf1 (AB646135), which are non-PPR families of Rf, were not found among the 66 genes here. Bioinformatic analysis using PPRfinder revealed that all PPR family genes at the MS-P1 region belonged to the P-class subfamily should be expressed more in a male fertile variety/selected strain than in a male sterile variety/selected strain. Transcriptomic analyses of KyOw14 (sterile selected strain) and \u2018Shiranuhi\u2019 (fertile variety) stamens were performed at 7 and 1 DBF through RNA-seq analysis. RNA extracted from the stamens (two replicates) were used to build libraries for RNA-seq (MS-P1 region of KyOw14 and \u2018Shiranuhi\u2019 was performed (p< 0.05) than in KyOw14 (sterile strain). In addition, the existence of Ciclev10030242m and Ciclev10030361m at the MS-P1 region provides evidence that molecular mechanisms underlying citrus male sterility fit into the general plant CMS model.The protein sequence analysis showed that Ciclev10030242m and Ciclev10030361m were highly similar proteins, with 86.66% overlap , ChineseRf or rf are located; therefore, we defined allelic haplotypes at the MS-P1 region among the founders of Japanese breeding germplasm. The nearest markers to candidates for Rf-MS-P1 were narrowed down to 00918-1 through fine mapping of the MS-P1 region were genotyped (1 populations except for \u2018Willking\u2019 (see legend in MS-P1 locus (C. tangerina hort. ex Tanaka), Iyo (C. iyo hort. ex Tanaka), Ponkan (C. reticulata Blanco), or Willowleaf mandarin (C. deliciosa Ten.) were investigated (MS-P1 region (p< 0.05) (MS-P1 region (p < 0.05) (p < 0.05) corresponding to the MS-P1 region was derived from Willowleaf mandarin, which harbors HT6 to identify Rf-MS-P1 candidates was a reasonable strategy.The results here also suggest that plotypes Table\u00a02.bors HT6 ; therefoMS-P1 (MS-P1 region were not observed (data not shown). \u2018Nishinokaori\u2019 and \u2018Kara\u2019 exhibited an increased NPG, although \u2018Nishinokaori\u2019 harbored HT1/HT3 and \u2018Kara\u2019 harbored HT1/HT4, both of which are partial male sterile diplotypes were detected in our previous study .The original contributions presented in the study are publicly available. This data can be found here: DDBJ, accession DRA015326 (SG acquired funding, designed the study, performed experiments, analyzed data, and wrote the original draft. SG, HF, TE, ToS, and TaS designed the study. HH, SO, and KN produced and managed materials. SG and TaS reviewed and edited this manuscript. All authors contributed to the article and approved the submitted version."} +{"text": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has infected >600 million people in the ongoing global pandemic. Several variants of the SARS-CoV-2 have emerged in the last >2 years, challenging the continued efficacy of current COVID vaccines. Therefore, there is a crucial need to investigate a highly cross-protective vaccine effective against variants of SARS-CoV-2. In this study, we examined seven lipopeptides derived from highly conserved, immunodominant epitopes from the S, N, and M proteins of SARS-CoV-2, that are predicted to contain epitopes for clinically protective B cells, helper T cells (TH) and cytotoxic T cells (CTL). Intranasal immunization of mice with most of the lipopeptides led to significantly higher splenocyte proliferation and cytokine production, mucosal and systemic antibody responses, and induction of effector B and T lymphocytes in both lungs and spleen, compared to immunizations with the corresponding peptides without lipid. Immunizations with Spike-derived lipopeptides led to cross-reactive IgG, IgM and IgA responses against Alpha, Beta, Delta, and Omicron Spike proteins as well as neutralizing antibodies. These studies support their potential for development as components of a cross-protective SARS-CoV-2 vaccine. Recent reports suggest that nAb responses, elicited by vaccines and/or natural infections, is an accurate predictor of protection against SARS-CoV-2 \u20135. Gener+/CD8+ T cells have shown to induce cross-reactive immunity that is resistant to mutations acquired by SARS-CoV-2 variants of concerns (VOCs) and effectively preventing VOC escape and membrane (M) proteins, in addition to the spike protein . FurtherC escape . For a bin vitro and in vivo assays. We found that lipopeptides existed as larger micelle-like particles compared to their peptide counterpart, and stimulated APCs by the upregulation CD40, CD86 and HLA-DR molecules without the activation of TLR-2 and TLR-4 receptors. Intranasal immunizations with individual lipopeptides in mice generated stronger antigen-specific cellular, and mucosal as well as systemic humoral immune responses, compared to their native peptide immunizations. In addition, we provide evidence of the induction of cross-protective immunity upon mucosal immunization with the designed lipopeptides.In this study, we identified seven highly conserved, cross-reactive, immunodominant peptides from the S, N, and M proteins of SARS-CoV-2, MERS-CoV, SARS-CoV and other common cold coronaviruses that are predicted to contain epitopes for clinically protective B cells, helper T cells (TH) and cytotoxic T cells (CTL), and which also bind to multiple MHC class I and II molecules (covering >98% of human population) Table\u00a01 1, P3, P5, P7, P9, P11, and P13, ranged from 134.2-229.8 nm, 356.2-2792 nm, 79.32-309.9 nm, 1256- 4033 nm, 125.6- 1510 nm, 246.2-1856 nm, and 361-3554 nm, respectively , P4 (41.7%), P5 (7.1%), P6 (5.7%), P7 (9.6%), and P8 (17.3%) (3 (174.0%), P5 (145.5%), P6 (9.4%), P7 (15.9%), P8 (23.5%), P9 (13.9%), P10 (26.2%), P12 (4.1%), and P13 (2.4%) (5 (110.0%), P7 (7.9%), P8 (244.7%), P9 (400.7%), P10 (386.9%), P11 (332.1%), P12 (267.6%), P13 (340.0%), and P14 (289.7%) (1 (p=0.0028), P3 (p=0.0291), P5 (0.0053), P9 (p<0.0001), P11 (p=0.0015), and P13 (p=0.0005), and native peptide stimulation with P8 (p=0.002), P10 (p<0.0001), P12 (p=0.0056), and P14 (p=0.0029). THP-1 cells stimulated with lipopeptides, or peptides did not produce detectable levels of proinflammatory cytokines or stimulate human TLR-2 and -4 receptors . We found that Pnd immunization, spleens were examined for antigen-specific proliferation responses using a colorimetric BrdU incorporation assay. Splenocytes from all immunized groups were also stimulated with ConA (T cell mitogen), which was used as a positive control and P2 twice, 14 days apart. Eight days after the 21-P14, that were restimulated ex vivo with their respective native peptides (1 \u03bcg/ml). We found that splenocytes from lipopeptide immunizations, P1, P3, P9, and P13, produce higher levels of IFN-\u03b3, TNF-\u03b1, IL-2, and IL-4, compared to their respective peptide immunization groups , TNF-\u03b1 , and IL-2 significantly correlated with antigen-specific splenocyte proliferation responses , and serum samples collected from P5 (p<0.0001), P6 (p<0.0001), P7 (p=0.0041), P9 (p<0.0001), and P10 (p=0.0004) immunizations elicited a significantly higher anti-(S-N fusion)-IgA antibody response, compared to unimmunized controls (7 (p=0.0011) and P9 (p=0.0242) induced significantly higher anti-(S-N fusion)-IgA antibody titers, compared to their respective peptide immunizations. P5 induced a significantly higher anti-(S-N fusion)-IgA titer at a 1:2 dilution, compared to the P6 (p<0.0001) (5-P10) led to a significant anti-(N)-IgA antibody titer, compared to unimmunized controls -IgA titers compared to their respective peptide, with p<0.0001 and p=0.0347, respectively. Nucleocapsid-derived lipopeptide immunizations showed a strong mucosal anti-(S-N fusion)-IgA and anti-(N)-IgA antibody response compared to their respective nucleocapsid-derived peptide immunization. In contrast, membrane-derived lipopeptide and peptide (P11-P14) immunizations did not elicit anti-(M)-IgA antibodies (BAL fluid from P1-P14 immunized mice (1-P4) and nucleocapsid-derived (P5-P10) lipopeptide and peptide immunizations produced significant amounts of anti-(S-N fusion)-IgM antibodies (5-P10 immunized mice induced significantly higher anti-(N)-IgM antibodies, compared to the unimmunized controls (7 immunization induced a significantly higher anti-(S-N fusion)-IgM and anti-(N)-IgM antibody response, compared to its native peptide immunization . Also, P9 immunization induced a significantly higher anti-(N)-IgM antibody titer, compared to P10 (p<0.0001). Membrane-derived lipopeptide and peptide immunizations with P11 and P12 produced significantly higher anti-(M)-IgM antibody titers, compared to unimmunized controls (p<0.0001) -IgG antibody titres, compared to unimmunized controls (p<0.0001) (1 was significantly higher compared to its native peptide immunization (p<0.0001). Notably, P3 and P4 immunizations produced the highest anti-(S-N fusion)-IgG antibody titer compared to all other immunization groups. All nucleocapsid-derived lipopeptide and peptide immunizations have significantly higher anti-(N)-IgG antibody titres, compared to unimmunized controls (p<0.0001) (5 and P9 immunizations had significantly higher anti-(N)-IgG antibody titres, compared to their respective native peptide immunizations, with p=0.0036 and p=0.0089, respectively. Furthermore, we found that anti-(M)-IgG antibodies were only produced by P11 immunizations (1-P4), and nucleocapsid- (P5-P10) derived lipopeptide and peptide immunizations to their respective antigens.Lastly, we measured systemic IgG antibody responses against the S-N fusion, N, and M proteins of SARS-CoV-2. Immunizations with spike-derived and nucleocapsid-derived lipopeptides and peptides induced strong IgG antibody responses to their respective antigens. P1-P4) lipopeptides and peptides against SARS-CoV-2 VOCs: Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617), and Omicron (B.1.1.529). P1 immunization showed significantly higher mucosal IgA antibody titers, compared to unimmunized controls and its respective peptide immunization, against all SARS-CoV-2 VOCs , B.1.351 (p=0.0049), B.1.617 (p=0.0188), and B.1.1.529 (p<0.0001) variants of SARS-CoV-2 and B.1.617 (p=0.0088) variants , B.1.351 (p<0.0001), and B.1.1.529 (p=0.0059). Similarly, P3 immunizations induced significantly higher IgG antibody titers compared to P4, against the B.1.1.7, B.1.351, B.1.617, and B.1.1.529 variants (p<0.0001). Evidently, the spike-derived lipopeptide immunizations induced a more robust cross-variant IgG antibody response, compared to their respective peptide immunizations.From serum samples collected from P1-P4 immunizations were tested for their ability to block/neutralize viral binding to target host ACE2 receptor, using a cPass SARS-CoV-2 Neutralization kit. Serum from a non-spike lipopeptide immunization, P5, was used as a negative control. Serum antibody responses elicited by P1 and P3 immunizations showed a percent inhibition of 23.5% and 22.0%, respectively had significantly higher neutralizing capabilities compared to their respective peptides . Next, we found that BAL antibody responses from P1 (23.7%) and P2 (20.3%) immunization showed significantly higher neutralizing capabilities compared to P5 , whereas P3 (12.1%) and P4 (12.2%) immunizations showed similar neutralization capability.Antibody responses in BAL and serum samples collected from Pectively Figure\u00a06+CD3-), helper T cells , and cytotoxic T cells to identify functional changes among the immunization groups. Using clustering analysis, we identified cell clusters (Pop#) within B cells, TH and CTLs , TH cells with B cell and CTL helper function (3.0% vs. 0.0%), CTL helper function (43.9% vs. 12.7%), and B cell helper function (34.3% vs. 0.8%), and CTLs with effector (25.1% vs. 20.5%) and pleiotropic (46.2% vs. 33.6%) properties, compared to peptide immunizations , and higher percentage of regulatory B cells (45.0% vs. 31.1%), compared to peptide immunizations activated APCs more efficiently, compared to their respective peptides, enabling the integration of the innate and adaptive systems without the need of an adjuvant. Furthermore, we found that lipopeptides did not stimulate TLR-2 and -4 receptors or produce detectable amounts of proinflammatory cytokines (The upregulation of antigen-presenting (HLA-DR) and costimulatory (CD40/CD86) molecules demonstrate enhanced capacity to present antigen on APCs and prime T cells. Interestingly, we found that lipopeptides derived from SARS-CoV-2 antigens led to higher upregulation of HLA-DR, CD40, and CD86 in comparison to the corresponding peptides and medium-alone control , 36. Thie system . Our resytokines . These p1, P3, P5, P9, and P13) induced significantly higher recall responses, upon ex vivo re-stimulation by corresponding lipopeptides and native peptides, compared to peptide immunizations may drive T cells into anergic states. Anergic conditions are not desirable for a vaccine as it demonstrates the failure of our immune system to mount a response against the targeted antigen and TH2 (IL-4) cytokines have been suggested to modulate immune responses towards cell-mediated or humoral immunity. IFN-\u03b3 functions to educate immune cells to recognize and eliminate pathogens, and associates with protective immunity against intracellular pathogens marked the presence of long-lasting, antigen-specific cellular responses and cellular (cytotoxic T cell clusters) immune responses demonstrated a cross-reactive mucosal IgA and systemic IgM/IgG responses against four different SARS-CoV-2 VOCs responses, compared to the corresponding peptide groups Figure\u00a04he blood . The indIn conclusion, our results clearly demonstrate that intranasal immunization with lipopeptides, even without any added adjuvant, lead to significant induction of mucosal antibody responses and systemic cellular and humoral immune responses. This study describes an important and innovative finding that opens new avenues for developing a broadly protective vaccine for SARS-CoV-2 virus and its variants, and potentially other heterologous coronaviruses.1, P3, P5, P7, P9, P11, and P13) and their corresponding native peptides , derived from highly conserved and functional regions of the S-, N- and M-proteins of SARS-CoV-2, were custom synthesized by Genscript Inc. with >96% purity , and a standardized Sizing and Zeta report was generated by Zetasizer XPLORER software v1.10 to provide mean particle size for each sample.6 cells/ml) were seeded with P1-P14, at 1 \u03bcg/ml. The cultures were incubated in 5% CO2, at 37\u00b0C for 24 hours. The activation of THP-1 monocytes was determined by flow cytometry analysis. A total of 2\u00d7105 THP-1 cells from each culture was stained with co-stimulatory markers using established procedures from Thermofisher , and subsequently, performed a percent of control calculation (Percent of Control =100 \u00d7 iMFIExp./iMFIControl) for graphing (THP-1 monocytes (ATCC TIB-202) were grown in medium containing RPMI-1640 (Gibco), 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (P/S), and 1% L-glutamine, and maintained at a confluency between 70-80%. THP-1 cells cell lines are stably transfected with human TLR2 and TLR4 genes. Upon TLR signalling, a secreted embryonic alkaline phosphatase (SEAP) reporter gene is induced, and SEAP is secreted, which is detected by a QUANTI-Blue\u2122 detection assay.5 cells/ml) and HEK-Blue\u2122 hTLR4 (2.5\u00d7105 cells/ml) cells were seeded with P1-P14, at 1 \u03bcg/ml and 10 \u03bcg/ml, in triplicates. The cultures were incubated in 5% CO2, at 37\u00b0C for 24 hours, and supernatants were collected to run QUANTI-Blue\u2122 detection according to the assay protocol. Using a DTX 880 Plate Reader (Beckman Coulter), optical density (OD) readings were taken of QUANTI-Blue\u2122 detection assays, at 620nm. Data was expressed as mean \u00b1 SEM of triplicate cultures.HEK-Blue\u2122 hTLR2 and HEK-Blue\u2122 hTLR4 cell lines were grown according to their respective handling procedures. HEK-Blue\u2122 hTLR2 for Health Sciences and were conducted according to the guidelines of the Canadian Council of Animal Care (CCAC). Four to six-week-old male C57BL/6 mice were purchased from Charles River Laboratory and housed in a pathogen-free animal facility (HSLAS) at the University of Alberta. Mice were immunized twice, 14 days apart with individual lipopeptides or peptides (10 \u03bcg/mouse), intranasally in a total volume of 30 \u03bcL (15 \u03bcL in each nostril). Mice were euthanized 8 days after second immunization and bronchoalveolar lavages (BAL), sera, lungs, and spleens were collected. Unimmunized mice were used as controls.5 cells splenocytes from immunized mice and 4\u00d7105 antigen presenting cells were incubated with corresponding lipopeptides and peptides at various concentrations described in the figure legends and isolated lung lymphocytes (1\u00d7105 cells) from immunized mice were stained with extracellular and intracellular markers using established protocols from Thermofisher 1X for 4h at 37\u00b0C and subsequently stained with extracellular and intracellular markers as mentioned above. Samples were run on Attune NxT flow cytometer and analyzed by FlowJo v10.8 Software. Lung and spleen samples from immunized groups P1-P14 were concatenated to provide consistencies in clustering methods and creating tSNE (t-distributed stochastic neighbor embedding) plots. Using Phenograph and FlowSOM clustering algorithms, lung lymphocytes and splenocytes were classified into different clusters based on phenotypic markers that were expressed, and overlayed on tSNE plots. Violin Box was used to acquire MFI values of phenotypic markers that each cluster expressed, which was represented by heatmaps, created on Morpheus . The U-PLEX Biomarker Group 1 (mouse) assay was used to analyze cytokines profiles of IFN\u03b3, IL-10, IL-2, IL-4, and TNF\u03b1. The MSD plates were read on MESO QuickPlex SQ120 and analyzed on DISCOVERY WORKBENCH 4.0 Analysis Software.Cytokine concentrations were measured from supernatants collected from antigen-specific splenocyte proliferation cultures of PSerum and BAL samples were pooled from three immunized mice and ran in duplicates for each dilution, on 96-well plates. The plates were coated with SARS-CoV-2 nucleocapsid, membrane, a spike-nucleocapsid fusion protein, and the spike proteins of Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617), and Omicron (B.1.1.529) variants . For detection of IgG and IgM in serum, and IgA in BAL, the antibody ELISA procedure described earlier was followed . The abs1-P4 immunized groups were tested for neutralizing antibodies. Triplicate samples were run using the cPass SARS-CoV-2 Neutralization Antibody Detection Kit according to the manufacturer\u2019s instructions. Serum and BAL samples were run at 1:9 dilutions and undiluted, respectively, and read using a DTX 880 Plate Reader (Beckman Coulter). Data are expressed as mean \u00b1 SEM of triplicates.Serum and BAL samples from PP \u2264 0.05 was used to indicated significance.Data were analyzed, and graphed using GraphPad Prism Software 9.4.1. Data was presented as mean \u00b1 SEM of 2-3 replicate values of 3 pooled mice and statistical differences were analyzed by one-way or two-way ANOVAs, adjusted for multiple comparisons. In addition, Spearman\u2019s test was performed to determine the correlations between cytokines and proliferation values. A The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The animal study was reviewed and approved by University of Alberta\u2019s Animal Care and Use Committee (ACUC) for Health Sciences (AUP00000212) and according to the guidelines of the Canadian Council of Animal Care (CCAC).RP, design, planning, execution of experiments, data analyses, writing first draft and editing. BA, conception, funding, design, planning, supervision, data analyses, writing and editing. All authors contributed to the article and approved the submitted version."} +{"text": "The minimum inhibitory concentrations (MICs) were tested using a Trek Diagnostic System (Thermo Fisher Scientific). Susceptibility was determined by CLSI broth microdilution and interpreted with CLSI M100 (2021) breakpoints.From 2017-2021, 554 Gram-negative isolates were collected from 16 pediatric departments across China. GNB isolates from pediatric departments were mainly derived from bloodstream (n = 135), intraperitoneal (n = 129), lower respiratory tract (n = 198) and urinary tract (n = 92) infections (E. coli (34.30%) and K. pneumoniae (27.62%) were the most common pathogens, followed by P. aeruginosa (15.34%). Susceptibility of species with more than 20 isolates were showed in Table 1. The susceptibility of P. aeruginosa to C/T was 89.41%, which was the highest among beta-lactams and was second only to amikacin. The susceptibilities of E. coli and K. pneumoniae isolates to C/T were 92.63% and 58.17%, respectively. When exclude carbapenem-resistant E. coli and K. pneumoniae, the susceptibility to C/T increased to 96.17% and 86.14%. C/T showed similar activities to E. coli and K. pneumoniae isolated from pediatric patients < 1 year (Table 2). Thirteen P. aeruginosa isolates were collected from patients < 1 year and 13/13 were susceptible to C/T (Table 3).P. aeruginosa and E. coli obtained from pediatric patients in China showed a high susceptibility to C/T. When excluding carbapenem resistant isolates, C/T also showed good activities against K. pneumoniae.Pengcheng Li, M.D., MSD China: Employee of MSD China"} +{"text": "Polybrominated diphenyl ethers (PBDEs) are commercially used flame retardants that bioaccumulate in human tissues, including breast milk. PBDEs produce endocrine and metabolic disruption in experimental animals and have been associated with diabetes and metabolic syndrome (MetS) in humans, however, their sex-specific diabetogenic effects are not completely understood. Our past works show glucolipid dysregulation resulting from perinatal exposure to the commercial penta-mixture of PBDEs, DE-71, in C57BL/6 female mice.As a comparison, in the current study, the effects of DE-71 on glucose homeostasis in male offspring was examined. C57BL/6N dams were exposed to DE-71 at 0.1 mg/kg/d (L-DE-71), 0.4 mg/kg/d (H-DE-71), or received corn oil vehicle (VEH/CON) for a total of 10 wks, including gestation and lactation and their male offspring were examined in adulthood.In vivo glucose challenge showed marked glucose intolerance (H-DE-71) and incomplete clearance (L- and H-DE-71). Moreover, L-DE-71-exposed mice showed altered glucose responses to exogenous insulin, including incomplete glucose clearance and/or utilization. In addition, L-DE-71 produced elevated levels of plasma glucagon and the incretin, active glucagon-like peptide-1 (7-36) amide (GLP-1) but no changes were detected in insulin. These alterations, which represent criteria used clinically to diagnose diabetes in humans, were accompanied with reduced hepatic glutamate dehydrogenase enzymatic activity, elevated adrenal epinephrine and decreased thermogenic brown adipose tissue (BAT) mass, indicating involvement of several organ system targets of PBDEs. Liver levels of several endocannabinoid species were not altered.Compared to VEH/CON, DE-71 exposure produced hypoglycemia after a 11\u00a0h fast (H-DE-71). An increased fast duration from 9 to 11\u00a0h resulted in lower blood glucose in both DE-71 exposure groups. Our findings demonstrate that chronic, low-level exposure to PBDEs in dams can dysregulate glucose homeostasis and glucoregulatory hormones in their male offspring. Previous findings using female siblings show altered glucose homeostasis that aligned with a contrasting diabetogenic phenotype, while their mothers displayed more subtle glucoregulatory alterations, suggesting that developing organisms are more susceptible to DE-71. We summarize the results of the current work, generated in males, considering previous findings in females. Collectively, these findings offer a comprehensive account of differential effects of environmentally relevant PBDEs on glucose homeostasis and glucoregulatory endocrine dysregulation of developmentally exposed male and female mice. Considerable evidence points to a potential contribution of endocrine- (EDCs) and metabolism-disrupting chemicals (MDCs) to the rapid increase in the incidence of these metabolic diseases . One claetration \u201314. Thervia exposed dams and accumulate in male and female offspring liver and brain is informative in understanding the diabetic phenotype of T2D. The incretin GLP-1 is secreted by enteroendocrine L-cells and acts on pancreatic \u03b2-cells to promote postprandial insulin secretion. In T2D, this insulinotropic effect is either impaired or absent leading to hyperglycemia . ActivatHaving observed sexually dimorphic risk and susceptibility of perinatally exposed females to MetS , 29, thead libitum in glass water bottles. Procedures on the care and treatment of animals were performed in compliance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals and approved by the University of California, Riverside, Institutional Animal Care and Use Committee (AUP#20170026 and 20200018).C57BL/6N mice were obtained from both Charles River Laboratories and Taconic Biosciences . Mice were group housed 2-4 per cage and maintained in a non-specific pathogen free vivarium on a 12\u00a0h light/dark cycle at an ambient temperature of 20.6-23.9 \u00b0C and relative humidity of 20-70%. Mice were provided rodent chow and municipal tap water Dosing solutions were prepared as described previously , 32. In via the dam was accomplished as described previously and ex vivo analysis of hepatic, adipose, adrenal, and endocrine parameters (Cohort 2). The DE-71 exposure and testing paradigm is shown in Perinatal PBDE exposure eviously . In brieeviously Figure\u00a01eviously , 20, 38,ex ratio . Male ofITT, was calculated using the formula (0.693 x 100) x t1/2-1 to determine in vivo insulin sensitivity from 0-30\u00a0min post insulin injection. Fasting blood glucose was determined from baseline values (t=0) obtained in IPGTT (11h) and ITT (9h). GTT and ITT sample sizes were different because ITT effect size was expected to be less (as estimated by our previous work (Mice were fasted overnight (ON) for 11h and then injected with glucose . Glucose was measured directly from tail blood (~1 uL) at time 0, 15, 30, 60, and 120\u00a0min post-glucose challenge. A calibrated glucometer and test strips were used to measure plasma glucose concentrations. Seven days following IPGTT, an insulin tolerance test (ITT) was performed with Humulin R (Eli Lilly) bolus on mice fasted ON for 9h. Tail blood was collected, and glucose was sampled in the same manner as IPGTT . For area calculations, the area under (AUC) or above the glycemia curve (inverse AUC) from 0-120\u00a0min post injection was used. The percent blood glucose reduction rate after insulin administration, Kous work ) and, thDuring sacrifice, under terminal isoflurane anesthesia, cardiac blood (0.3-1 mL) was collected and centrifuged at 16,000 x g for 20\u00a0min at 4 \u00b0C. After the addition of a cocktail of protease inhibitors and EDTA, the plasma samples were stored at -80\u00b0C until further use. The following organs were excised and weighed: liver, pancreas, spleen, adrenal glands and interscapular brown adipose tissue (BAT). Plasma, liver and adrenal samples were snap-frozen over dry ice and stored at -80 \u00b0C for later analysis of plasma hormones, adrenal epinephrine, liver endocannabinoids and enzymatic activity.via cardiac puncture (ad libitum fed state) was analyzed for metabolic hormones using commercially available kits according to manufacturer\u2019s instructions. Plasma insulin was measured using commercial ELISA kits as previously described , 10 pmol d4-oleoylethanolamide , and 500 pmol d5-2-arachidonoyl-sn-glycerol . Following homogenization of samples, 2 mL of chloroform and 1 mL of water were added, followed by centrifugation at 2000 x g for 15\u00a0min at 4\u00b0C. The organic phase was extracted and the pooled lower phases were dried under N2 gas followed by resuspension in 0.1 mL methanol:chloroform (9:1). Analysis of endocannabinoids (EC) was performed via ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC/MS/MS) as previously described 6. The mixture was incubated at 0\u00b0C for 20\u00a0min and the oxidation reaction was stopped by the addition of 60 \u00b5L of a 9\u00a0N NaOH solution containing 4 mg/ml ascorbic acid . Fluorescence emission was determined at 520 nm (excitation wavelength at 420 nm) using a fluorescence plate reader (Promega). Epinephrine concentration was converted from the mean fluorescence intensity units of each sample using calibration standards and polynomial curve fitting.Epinephrine content in adrenal glands was measured using a modification of the trihydroxyindole method as described previously . Brieflypost hoc testing for multiple group comparisons. For parametric ANOVAs, Tukey\u2019s post hoc test was used when both sample sizes and variance were equal, and a Dunnett\u2019s T3 test was used when sample size and variance were not equal. For non-parametric ANOVA, a Dunn\u2019s post hoc test was performed. For Two-way ANOVA, Tukey\u2019s, Sidak\u2019s and Holm-Sidak\u2019s post hoc tests were used. Differences were deemed significant at p<0.05. Data are expressed as mean \u00b1 standard error of the mean (s.e.m) unless indicated otherwise.Statistical analyses were performed using GraphPad Prism v.9.4.1. A one-way analysis of variance (ANOVA) was used to test the main effect of one factor. When normality assumption failed, as determined using a Shapiro-Wilk test, a Kruskal-Wallis H ANOVA was used. A Brown-Forsythe ANOVA was used if the group variances were significantly different. Data for fasting glycemia were analyzed by two-way ANOVA for main effects of exposure and fasting duration. ITT and GTT experiments were analyzed by repeated measures two-way or mixed model ANOVA to determine main effects of exposure and time. ANOVA was followed by Exposure effect F=9.34, p<0.001, Tukey\u2019s post-hoc VEH/CON vs L-DE-71, p=0.03 and lower in L-DE-71 vs H-DE-71, p=0.0003). Relative liver weight was 8% greater in H-DE-71 relative to L-DE-71 =2.824, p=0.0675, Tukey\u2019s post-hoc L-DE-71 vs H-DE-71 p<.05). The absolute and relative weights of pancreas and spleen were similar across groups.Exposure effect F= 6.65, p<0.01; Time effect F= 24.6, p<0.0001; Exposure x Time F= 0.76 ns; Sidak\u2019s post hoc test, 11\u00a0h: VEH/CON vs H-DE-71, p<0.01; 9\u00a0h vs 11\u00a0h, L-DE-71 p<0.01, H-DE-71, p<0.05 (We examined fasting blood glucose (FBG) after 9 and 11\u00a0h fasting using glycemia values from basal time points obtained in ITT and GTT experiments, respectively. , p<0.05 Figure\u00a02=4.767, p<0.05; Time effect F=330.2, p<0.0001; Time x Exposure F =3.112, p<0.01) and 60\u00a0min post injection (p<0.05) and in L-DE-71 vs H-DE-71 at t=30 (p<0.01) and 60\u00a0min post injection (p<0.01).To investigate the effects of DE-71 on glucose tolerance, glycemia was measured during GTT over the 120\u00a0min post-injection time course =278.6, p<0.0001; Exposure effect F=9.39 p<0.001; Time x Exposure F=5.94, p<0.0001). Mean glycemia values for H-DE-71 were significantly different from VEH/CON at t=15 , 30 (p<0.01) and 60\u00a0min post injection (p<0.01) and from L-DE-71 at t=15 (p<0.01), t=30 (p<0.01) and 60\u00a0min post injection (p<0.001).Since FBG after an 11\u00a0h fast was lower in H-DE-71 relative to VEH/CON =5.21, p<0.05, Tukey\u2019s post-hoc VEH/CON vs H-DE-71, p<0.029, L-DE-71 vs H-DE-71, p<0.013; Percent basal glycemia AUC, Brown-Forsythe ANOVA: Exposure effect F=10.1, p<0.001, Dunnett\u2019s T3 post-hoc VEH/CON vs H-DE-71, p<0.004, L-DE-71 vs H-DE-71 p<0.0003 .The differences in magnitude and duration of glycemia are integrated using the area under the glucose curve, AUCTime effect F=56.2, p<0.0001; Exposure effect F=2.40, ns; Time x Exposure F=1.90, p<0.05) . When glycemia is expressed as a percent of baseline, L-DE-71 exposed mice displayed incomplete recovery or glucose clearance/utilization at 90 and 120\u00a0min after insulin injection =33.7, p<0.0001; Exposure effect F=8.014, p<0.001; Time x Exposure F=1.23, ns) and 120\u00a0min (p<0.001). This is represented as a greater mean latency to reach the minimum insulin-induced hypoglycemia in L-DE-71 relative to VEH/CON =9.07, p<0.01; Dunn\u2019s post hoc VEH/CON vs L-DE-71, p<0.01) was plotted using absolute =2.024, ns, Sidak\u2019s post-hoc VEH/CON vs L-DE-71, p<0.05) (ITTinsulin measured over the first 30\u00a0min post-injection (The inverse area under the glucose response curve (inverse AUCad libitum fed state) =3.684, p=0.0409; Dunnet\u2019s post-hoc VEH/CON vs L-DE-71 p=0.0473; Glucagon, One-way ANOVA: Exposure effect F=5.61, p=0.02; Dunnett\u2019s T3 post-hoc VEH/CON vs L-DE-71 p=0.0449) =16.06, p<.0001; Tukey\u2019s post-hoc VEH/CON vs L-DE-71 p=0.0001, VEH/CON vs H-DE-71 p=0.002). Adrenal weights were not different across experimental groups =6.82, p=0.061; Tukey\u2019s post-hoc VEH/CON vs L-DE-71 p=0.01, L-DE-71 vs H-DE-71 p=0.01) =19.51, p<.0001; Dunnett\u2019s post-hoc VEH/CON vs L-DE-71 p=0.002, VEH/CON vs H-DE-71 p<0.0001) (p=0.03).Exposure to DE-71 decreases glucose tolerance which may be due to enhanced hepatic glucose production. To examine this possibility, we tested the hypothesis that PBDEs increase the activity of GDH a hepatic gluconeogenic enzyme. We found that exposure to L- and H-DE-71 significantly <0.0001) Figure\u00a07Male F1 mice exposed to either dose of DE-71 displayed normal liver levels of the endocannabinoid (EC), anandamide , and related fatty acid ethanolamides, docosahexaenoyl ethanolamide (DHEA) and oleoylethanolamide (OEA), when compared to VEH/CON . The combination of DE-71 effects - exaggerated fasting hypoglycemia, glucose intolerance and incomplete glucose clearance/utilization in response to insulin challenge demonstrates the complex actions of PBDEs on glucose homeostasis in males. Previously, we have observed abnormal glucose metabolism and other parameters in their DE-71-exposed female siblings activity increases energy expenditure by burning fat and increasing metabolic rate and can utilize glucose especially when stimulated by insulin . TherefoIt is important to note that developmental exposure to DE-71 ends at weaning, but that dysregulated glucoregulatory phenotypes in exposed male and female offspring are observed in adulthood . We specin vivo and ex vivo parameters measured in DE-71-exposed male offspring indicate broad, complex effects of developmental exposure to PBDEs on glucose homeostasis and glucoregulatory parameters involving various organ systems. Our results support human studies reporting the positive association between body burdens of PBDEs and T2D and MetS (AUP# 20170026 and 20200018).Conceptualization, MC-C, EK. Methodology, MC-C, EK, ND, JK, BC. Validation, MC-C, EK, BC, PP, ND. Formal Analysis, EK, MC-C, PP, ND. Investigation, EK, BC, PP, JK, AB, MC-C, MD. Writing \u2013 Original Draft, EK, MC-C, AB. Writing \u2013 Review & Editing, MC-C, EK, AB. Visualization, EK. Resources, MC-C., ND. Data Curation, EK, MC-C. Supervision, MC-C, EK, ND. Project Administration, MC-C, EK. Funding Acquisition, MC-C, EK, ND. All authors contributed to the article and approved the submitted version."} +{"text": "The COVID-19 pandemic has led to a considerable increase in Central-Line Associated Bloodstream Infections (CLABSI) and Catheter Associated Urinary Tract Infections (CAUTI). However, it remains unclear how this affected different population groups.This retrospective observational cohort study included CLABSI and CAUTI in a tertiary care facility. Information was collected on patient demographics, hospitalization, comorbidities, and COVID-19 status. Chi-square and Wilcoxon rank-sum tests were used for categorical and continuous variable comparisons. GEE models compared pre- and pandemic periods by interrupted time series analysis.From 1/1/2018 to 5/31/2022 98,791 patients had 151,550 hospital admissions. Of those, 17,796 patients had 29,483 central lines placed and 45,180 patients had 65,422 Foleys. 314 patients developed 338 CLABSI and 216 patients had 217 CAUTI. 1,552 patients tested positive for COVID-19 with 22 developing CLABSI and 14 CAUTI. The pre-pandemic downward trend in CLABSI and CAUTI was reversed during COVID-19 (p< 0.05).Black patients and those with other/unknown race had higher CLABSI per patient with central lines (p< 0.02) and higher device days (p< 0.0001) compared to white patients. Hispanic/Latino patients acquired more CLABSI per patient compared to non-Hispanic/non-Latino patients (p=0.04). During COVID-19 the already higher device days in Hispanic/Latino patients further increased compared to non-Hispanic/non-Latino patients (p< 0.0001).Black patients had higher CAUTI infection rates per patient with Foleys compared to white and other/unknown patients (p< 0.05). CAUTI per device days were also higher in black patients compared to white patients (p=0.02). No difference in CAUTI burden was detected for ethnic groups throughout the study period. Black and non-Hispanic/non-Latino patients had higher Foley usage days than other patients (p< 0.0001). Foley days decreased during COVID-19 (p=0.01).We detected health outcome disparities affecting black (CLABSI and CAUTI) and Hispanic/Latino (CLABSI) patients. Infections increased during the pandemic without altering race/ethnicity differences. Device utilization was significantly higher in affected groups.All Authors: No reported disclosures"} +{"text": "In TANGO, switching to dolutegravir/lamivudine (DTG/3TC) was noninferior compared to continuing a tenofovir alafenamide (TAF)-based regimen, however switching from bictegravir (BIC)/emtricitabine (F)/TAF was not evaluated. Here, we present efficacy and safety of switching to DTG/3TC compared with continuing B/F/TAF in virologically suppressed adults through 24 weeks.DYAD (NCT04585737) is an ongoing, open-label clinical trial that randomized adults with HIV-1 RNA< 50 copies/mL and no prior virologic failure (2:1) to switch to once-daily fixed-dose DTG/3TC or remain on B/F/TAF. The primary endpoint is the proportion with HIV-1 RNA \u2265 50 c/mL at Week (W) 48 . A planned W24 interim analysis assessed noninferiority with a 6% margin.Overall, 222 adults were randomized. At W24, 3 (2%) participants on DTG/3TC and 3 (4%) on B/F/TAF had HIV-1 RNA \u2265 50 c/mL meeting noninferiority criteria. Through W24, 4 on DTG/3TC and 3 on B/F/TAF met confirmed virologic withdrawal (CVW) criteria and underwent resistance testing. 2/7 had treatment-emergent resistance. One B/F/TAF CVW developed M184M/I and G140G/S at W12; at study discontinuation (DC), HIV-1 RNA< 50 c/mL and the participant remained on B/F/TAF. One DTG/3TC CVW had no resistance on study genotype but underwent repeat genotypic testing outside the study (ordered by clinic provider) and had M184V at W12; at study DC, HIV-1 RNA< 50 c/mL on DTG/3TC and the participant was subsequently transitioned to DTG + darunavir/cobicistat (DRV/c). One non-CVW DTG/3TC participant developed M184V and K65R at W12 (genotype inadvertently collected at first episode of unconfirmed viremia); at study DC, HIV-1 RNA< 50 c/mL on DTG/3TC and the participant was subsequently transitioned to DTG+DRV/c. Drug-related adverse events (AEs) and withdrawals due to AEs occurred in 31 (21%) and 6 (4%) participants with DTG/3TC and 1 (1%) and 0 participants with B/F/TAF, respectively.DYAD demonstrated noninferior efficacy of switching to DTG/3TC vs. continuing B/F/TAF at W24. Higher AE rates in the DTG/3TC arm are likely consistent with the open-label nature of this switch study.Charlotte-Paige M. Rolle, MD, MPH, Gilead: Advisor/Consultant|Gilead: Grant/Research Support|Gilead: Honoraria|Janssen: Advisor/Consultant|ViiV: Advisor/Consultant|ViiV: Grant/Research Support|ViiV: Honoraria Federico Hinestrosa, MD, AbbVie: Honoraria|Gilead Sciences: Advisor/Consultant|Gilead Sciences: Honoraria|MSD: Honoraria|ViiV Healthcare: Advisor/Consultant|ViiV Healthcare: Honoraria Edwin DeJesus, MD, Gilead Sciences, Inc: Advisor/Consultant|Theratechnology: Advisor/Consultant|Theratechnology: Honoraria"} +{"text": "Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are frequent etiologic agents of CABP. Ceftaroline fosamil is a parenteral cephem approved treatment of patients with CABP caused by S. pneumoniae (including cases with concurrent bacteremia), methicillin-susceptible Staphylococcus aureus (MSSA), H. influenzae, and some species of Enterobacterales. In this study we report the in vitro activity of ceftaroline and comparators against isolates from community-acquired respiratory tract infections (CARTI) collected through a global surveillance program.Community-acquired bacterial pneumonia (CABP) is a frequent cause of patient morbidity and mortality. S. pneumoniae, H. influenzae, M. catarrhalis, MSSA, and methicillin-resistant S. aureus (MRSA) were tested. The isolates originated from Asia/South Pacific ; Europe ; Latin America (671/8.5%); Middle East/Africa (659/8.4%); and North America (Canada only) (380/4.8%). Ceftaroline and comparator agent MICs were determined by CLSI M07 broth microdilution methodology. MICs were interpreted using 2023 CLSI M100 MIC breakpoints.Clinically relevant, non-duplicate, isolates cultured from respiratory specimens by clinical laboratories in 54 countries in 2018-2021 were collected by the ATLAS Surveillance Program central laboratory . Community-acquired infections were defined as those from patients < 48 hours in hospital. In total, 7,886 isolates of in vitro activity of ceftaroline and comparator agents is summarized in the table. Greater than 99% of S. pneumoniae and 100% of MSSA were susceptible to ceftaroline, including penicillin-nonsusceptible S. pneumoniae based on a dosage of 600 mg every 12h. Sixty-two (9.6%) MRSA were ceftaroline-susceptible-dose-dependent (MIC 2-4 \u00b5g/mL) based on a dosage of 600 mg every 8h administered over 2h, with the majority from (n) Thailand (9), S. Korea (7), and China (6). Four isolates, from S. Korea (2), China (1), and Ukraine (1) were resistant to CPT (MIC of \u22658 \u00b5g/mL). 99.6% of H. influenzae were susceptible to ceftaroline.The in vitro activity against current pathogens associated with CABP from a global collection.Ceftaroline demonstrated potent Meredith Hackel, PhD, Pfizer Inc.: Honoraria|Venatorx: Paid fees for conducting the study and abstract preparation Gregory Stone, PhD, Pfizer: Stocks/Bonds Daniel F. Sahm, PhD, Merck & Co., Inc.: Honoraria|Pfizer Inc.: Honoraria|Venatorx: Paid fees for conducting the study and abstract preparation"} +{"text": "Dialysis, renal transplant (RTX) and autoimmune kidney disease (AKD) patients are at higher risk of COVD-19 and suboptimal humoral responses post primary SARS-CoV-2 vaccination. As such, these groups have been prioritised for further SARS-CoV-2 vaccine doses. Limited data are available on their immunogenicity.nd, 3rd and 4th SARS-CoV-2 vaccines. Endpoints were median anti-S IgG titres and seroconversion (anti-S IgG titre >1896 MFI).Patients on dialysis or with a RTX or AKD who received primary SARS-CoV-2 vaccination were prospectively recruited from three UK sites. SARS-CoV-2 IgG spike antibody (anti-S IgG) and nucleocapsid titres were measured with a Luminex assay post 2rd dose , with 27/58 (47%) of RTX and 17/46 (37%) of AKD patient non-responders seroconverting. Seroconversion among RTX and AKD patients overall improved to 78% (114/146) and 79% (122/155) respectively (p< 0.05), but not in dialysis patients post 3rd dose. 212/400 (53%) had serology post 4th dose , with 10/22 (46%) and 3/25 (12%) of RTX and AKD patient non-responders seroconverting. Anti-S IgG titre and seroconversion were similar within each group post 4th dose .628 patients comprising 240 dialysis, 194 RTX, and 194 AKD patients were recruited, with seroconversion of 96%, 61% and 70% respectively post two vaccines, and median anti-S IgG titres (IQR) of 30604 (24393\u201331826), 5829 (455\u201328296) and 18711 (1233\u201330226). 400/627 (64%) had anti-S IgG titres post 3rd dose in a multivariable model were rituximab use within six months, mycophenolate, prednisolone, chronic kidney disease and AKD , and post 4th dose, rituximab alone (p< 0.001).Predictors of non-seroconversion post 3rd but not 4th dose improved anti-S IgG titres and seroconversion in renal patients. Immunosuppressive use, particularly rituximab, was associated with reduced serologic responses . Patients on immunosuppressives should therefore be prioritised for consideration of additional pre-exposure prophylactic agents.After primary SARS-CoV-2 vaccination, a 3Michael Chen-Xu, MBChB, MRCP, MPH, GSK: Grant/Research Support Rachel Jones, MD, GSK: Advisor/Consultant|GSK: Grant/Research Support|Roche: Grant/Research Support|Vifor Pharma: Advisor/Consultant Rona M. Smith, MD MRCP, GSK: Grant/Research Support|Union Therapeutics: Grant/Research Support"} +{"text": "Remdesivir (RDV), a nucleotide analog prodrug that targets the viral RNA-dependent RNA polymerase Nsp12, is approved to treat COVID-19 in hospitalized and nonhospitalized patients. Obeldesivir (ODV), an oral mono-5\u2019-isobutyryl ester prodrug that is metabolized into the same active triphosphate as RDV, is being evaluated in Phase 3 clinical trials. The antiviral activity of RDV and ODV against previous Omicron subvariants (BA.1 to BQ.1.1) was maintained with respect to the ancestral WA1 strain. We assessed RDV and ODV antiviral activity against recent Omicron subvariants BF.7, BQ.1, XBB.1.5, CH.1.1, and XBF using clinical isolates and/or site-directed mutants (SDMs).Global Initiative on Sharing Avian Influenza Data (GISAID) EpiCoV database sequences. Structural analysis of identified substitutions was conducted on a prior cryo-electron microscopy-based model of the replication-transcription complex. Antiviral activity of RDV and ODV against subvariant clinical isolates was assessed by nucleoprotein ELISA in A549-hACE2-TMPRSS2 cells and by SDMs in the replicon systemThe prevalence of Nsp12 substitutions in Omicron subvariants was evaluated by analysis of 50 vs WA1). Evaluation of CH.1.1 and XBF by introducing variant-defining mutations into the replicon showed no change in in vitro susceptibility (< 1.8-fold change). Phenotyping of clinical isolates of BF.7, BQ.1, XBB.1.5, and CH.1.1 indicated no loss of RDV or ODV in vitro antiviral activity (< 1.3-fold change).Genomic analysis of > 2 million Omicron subvariant sequences revealed unique substitutions in Nsp12 vs WA1. No new defining substitutions in Nsp12 were found compared with earlier Omicron variants. The defining substitutions (\u2265 75% of sequences) included P323L , Y273H (BQ.1), and G671S . Less prevalent substitutions were observed with frequencies from 1-3.5%: L247F, T248I, V257F, N507I, A529V, F694Y; none had direct interaction with the incoming RDV nucleotide triphosphate or the viral RNA, except N507I. Phenotyping of individual substitutions using SDMs showed no loss of RDV or ODV susceptibility (< 1.2-fold change in ECRDV and ODV retained potent in vitro antiviral activity against all tested Omicron subvariants with potencies comparable to WA1.Lauren Rodriguez, PhD, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds Jiani Li, PhD, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds Dong Han, MS, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds Ross Martin, PhD, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds Jasmine Moshiri, PhD, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds Nadine Peinovich, MPH, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds John P. Bilello, PhD, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds Jason K. Perry, PhD, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds Charlotte Hedskog, PhD, Gilead Sciences, Inc.: Employee|Gilead Sciences, Inc.: Stocks/Bonds"} +{"text": "Agrobacterium radiobacter strain MD22b was isolated from infected fruit from Vatan Farm, a dekhkan farm in Yangibog . The 5.7-Mbp draft genome sequence presented here shares homology with chromosomes 1 and 2, as well as with the Ti plasmid from agrobacteria. Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (formerly Agrobacterium tumefaciens) . The fruit was rinsed three times in sterile distilled water and homogenized. Aliquots were spread onto Roy-Sasser agar (Agrobacterium-like colony was picked and identified as A. radiobacter by its API 20 NE (bioM\u00e9rieux) profile (1-4-6-7-7-4-4). DNA was extracted from cells cultivated in LB for 24\u2009h at 30\u00b0C with shaking using the GenElute bacterial genomic DNA kit (Sigma-Aldrich). Sequencing of the 16S rRNA gene using the primer combination 5\u2032-AGRGTTTGATYHTGGCTCAG-3\u2032 (27f_mod) and 5\u2032-TASGGHTACCTTGTTACGACTT-3\u2032 (1492r_mod) (A. radiobacter strain ATCC 23308 (GenBank accession number MT534521.1) using BLASTn v. 2.13.0 searches against the GenBank v. 252 nonredundant nucleotide database (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome). For genome sequencing by Eurofins Genomics, a NEBNext Ultra II DNA preparation kit was used, and Illumina NovaSeq 6000 S2 paired-end genomic sequencing was performed with a read length of 2\u2009\u00d7\u2009151\u2009bp, resulting in 10,125,972 reads with a Phred score of \u226528 and a total of 1,518,897,000 sequenced bases. Additional quality control was performed to remove any remaining adapter sequences using the Trim Reads tool in the CLC Genomics Workbench v. 20.1. Assembly was performed using the CLC de novo assembly tool, resulting in a total sequence length of 5,736,602\u2009bp and a total gapped length of 5,736,406\u2009bp, distributed in 38 contigs, with an N50 value of 267,803\u2009bp, coverage of 265\u00d7, and GC content of 59.44%. Unless otherwise noted, default parameters were used for all software. Annotation of the draft genome was done using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v. 6.1 (https://www.ncbi.nlm.nih.gov/genome/annotation_prok). The genome completeness was estimated at 100% using CheckM v. 1.0.18 (Agrobacterium with pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of 97.97% and 83.8%, respectively, against the type strain A. radiobacter NCPPB 3001 using the ANI calculator (http://enve-omics.ce.gatech.edu) (https://ggdc.dsmz.de/ggdc.php#) (A. radiobacter K84 was performed, revealing significant homology with both chromosomes of strain K84 (repA and repB, and the plasmid Ti replication initiator gene, repC. The reported data will be useful for future understanding of the genetic diversity and virulence potential of A. radiobacter in Central Asia.ser agar plates afile 1-4--7-7-4-4.rain K84 . A complA. radiobacter strain MD22b have been deposited in DDBJ/ENA/GenBank under accession numbers OP364099 and JANDHV000000000, respectively. The associated BioProject, SRA, and BioSample accession numbers are PRJNA856860, SRR21562299, and SAMN29594852, respectively.The partial 16S rRNA gene and whole-genome shotgun sequences of"} +{"text": "Pantoea agglomerans has been isolated from various habitats including disease plants. Here, we present the genome of P. agglomerans strain NBBC-01 obtained from rotten potatoes that were infected by Ditylenchus desstructor. The genome information will prove advantageous in elucidating its ecological role.The Gram-negative bacterium Pantoea agglomerans has been shown to promote plant growth in Wuhan, China, which was infected with a plant-parasitic nematode Ditylenchus destructor following the manufacturer\u2019s protocols. The DNA purity, concentration, and integrity were assessed with NanoDrop One spectrophotometer , Qubit v.4.0 Fluorometer , and 0.75% agarose gel electrophoresis, respectively. Size selection (20\u201330 kb) was carried out for long-read sequencing utilizing the PippinHT system . The DNA library was generated without DNA shearing utilizing a ligation sequencing kit ), Oxford, UK] and sequenced with a Nanopore PromethION sequencer instrument (ONT) on a R9.4.1 flow cell FLO-MIN106). Guppy v.4.4.2 (. Guppy vP. agglomerans DSM3493T (GenBank accession: GCA_900185875). The values of digital DNA\u2013DNA hybridization (P. agglomerans NBRC 102470 (GenBank accession: GCA_001598475) is 88.7%. Thus, NBEC-018 was identified as a P. agglomerans isolate.The high-quality short- and long-read sequences were assembled into a whole chromosome and plasmids using Unicycler v.0.4.9 . All sofdization , 13 betw"} +{"text": "There is growing evidence that people with tuberculosis (TB) are at higher risk of mortality even after treatment completion. However, there are limited data on post-TB treatment mortality rates and causes of death in the United States (U.S.).Cohort study of all adults (age \u2265 18 years) diagnosed with TB in Georgia (U.S.) who finished treatment between January 1, 2008, and December 31, 2019. We obtained post-TB treatment mortality data from the Centers for Disease Control and Prevention National Death Index and general Georgia population death rates and causes of death for the same period from public databases. We calculated age- and sex-standardized mortality rates (SMRs) for the TB cohort and general Georgia population and the SMR ratio between these two groups .Among 3,183 patients alive at the time TB treatment was stopped, 2,391 (75.1%) were culture-confirmed, 625 (19.6%) were extrapulmonary, and 15 (< 1%) were rifampin and isoniazid resistant. The median age at TB diagnosis was 44 years (interquartile range (IQR): 32-57), 2,094 (65.8%) were male, and 1,557 (48.9%) were U.S.-born. 328 (10.3%) were co-infected with HIV. Most patients completed treatment. Reasons for treatment non-completion included adverse events (n=11), patient declined treatment (n=13), and lost to follow-up (n=186). The median post-TB treatment follow-up was 6.4 years (IQR 3.4-9.0) and 233 (7.3%) patients died. Causes of death included cardiovascular disease and malignancy and HIV . The age and sex adjusted SMR ratio of the TB cohort compared to the general Georgia population was 0.93 (95% CI: 0.78-1.09). The SMR ratio in a subgroup analysis restricted to U.S.-born persons was 1.6 (95% CI: 1.36-1.77).All data is shown as n (%) unless stated otherwise. Abbreviations: TB = tuberculosis, IQR = inter-quartile range 1. Other races = American Indian/Alaska Native , multiracial 2. Other risk factors = end-stage renal disease , post-organ transplantation , TNF-a antagonist therapy , immunosuppression (not HIV/AIDS) , incomplete LTBI , other ; missing data All rates are per 1000, . Abbreviations: TB = tuberculosis 1. Entire TB cohort: deaths n = 233, person-time = 18,440 person-years 2. Georgia population: deaths n = 900,874, person-time = 90,796,252 person-years 3. Race includes only non-Hispanic White and non-Hispanic Black categories: TB cohort (race standardization): deaths n = 212, person-time = 14,095 person-years GA population (race standardization): deaths n = 888,261, person-time = 85,630,800 person-years 4. Culture-confirmed TB cohort: deaths n = 182, person-time = 12,821 person-yearsOur data suggests the overall cohort of patients who finish TB treatment are not at higher risk of death compared to the general population. Analysis restricted to U.S.-born persons, however, did show a slightly higher risk of death post-TB treatment, which suggests the so-called \"healthy immigrant effect\" could have affected our post-TB treatment mortality estimates.All Authors: No reported disclosures"} +{"text": "A simultaneous, high-throughput and sensitive method for analysing nine neonicotinoid pesticides (NEOs) and four metabolites (NEOms) in urine using a liquid chromatography-tandem mass spectrometry (LC\u2013MSMS) was developed. The method detection limit (MDL) and lowest concentration minimum reporting limit (LCMRL) of the nine NEOs were 0.0013\u20130.048 ng/ml and 0.0050\u20130.17 ng/ml, respectively. The MDL and LCMRL of the four NEOms were 0.0052\u20130.52 ng/ml and 0.011\u20131.6 ng/ml, respectively. Intermediate precision for the nine NEOs and four NEOms was 7.5\u201312.5% and 7.4\u201310.9%, respectively. Accuracy for the nine NEOs and four NEOms was 3.83\u20135.60% and 3.01\u201329.2%, respectively. The developed method was applied to analyse urine samples collected from participants of a large-scale birth cohort study, namely, the Japan Environment and Children's Study (JECS).\u2022The NEO and NEOm concentrations in 100 \u00b5l urine samples were analysed using a highly sensitive LC\u2013MSMS.\u2022Automated solid phase extraction in a 96-well plate was utilised to achieve high-throughput analysis.\u2022Intermediate precision and accuracy were less than 12.5% and 94.8\u201399.1%, respectively. Specifications tableNeonicotinoid pesticides (NEOs) are agonists of neuronal nicotinic acetylcholine receptors 13C6) (ACE-IS), thiacloprid (pyridymethyl-13C6) (TCP-IS), sulfoxaflor (SUL-IS), flonicamid (FLN-IS), thiamethoxam (THX-IS), dinotefuran (furylmethyl-13C5) (DIN-IS), clothianidin (CLO-IS), imidacloprid (pyridymethyl-13C6) (IMI-IS), nitenpyram (NIT-IS), acetamiprid-N-desmethyl (dm-ACE-IS), TCP-amid (pyridymethyl-13C6) (TCP-amid-IS), CLO-desmethyl (dm-CLO-IS) and IMD-olefin (IMI-OF-IS), were purchased from Cambridge Isotope Laboratories, Inc. . Acetonitrile (purity 99.8%), ammonium acetate (guaranteed reagent), formic acid (purity \u226598.0%), methanol (purity 99.8%) and ultrapure water were used for this analysis.The sample preparation method was based on our previous study TM 6500 mass spectrometer was used to detect and quantify target analytes. The MSMS system was operated using electrospray ionisation positive mode, and multiple reaction monitoring was performed. An ACQUITY UPLC HSS T3 was used as an analytical column. The LC and MSMS parameters are listed in The Nexera X2 system was used for separation. A Triple Quad. Sulfoxaflor (SUL) was a diastereomer. The two isomers were quantified separately as SUL-A and SUL-B. All samples that fell outside the calibration range were reanalysed following further dilution.The calibration range is shown in Table\u00a05A pooled urine sample was prepared using maternal samples collected from volunteers to create QC samples. Levels of analytes varied in actual samples, so we tried to create the QC sample to reflect such concentrations. The QC samples had the concentration of dinotefuran around 2 ng/ml. To double the concentration, NEOs and NEOms were fortified such that the concentrations of ACE, TCP, SUL-A, SUL-B, FLN, THX, DIN, CLO, IMI, NIT, dm-ACE, TCP-amid, dm-CLO and IMI-OF were 0.5, 0.5, 0.5, 0.5, 10, 2.0, 5.0, 5.0, 5.0, 5.0, 5.0, 1.0, 20 and 100 ng/ml, respectively. The QC samples were subjected to the same procedure as the unknown samples, with five replicates analysed in each analytical sequence. The lowest concentration minimum reporting limit (LCMRL) was calculated following the U.S. Environmental Protection Agency's instructions 2) higher than 0.990. Repeatability and intermediate precision were determined based on ISO 5725:1994 and 27148:2010, with QC sample measurements (n\u00a0=\u00a0100). QC for day-to-day analysis was determined using a Shewhart control chart of 1.40 (0.27), 1.36 (0.31), 0.19 (0.06) and 1.34 (0.47) ng/ml for ACE, CLO, TCP and THX, respectively, were analysed in nine replicates. All measured concentrations fell within the certified ranges samples (NMIJ CRM 7408-a) with certified concentrations at 25\u00b0C (1.0125 g/cmd ranges .Table 7RNot applicable.Yukiko Nishihama: Conceptualization, Formal analysis, Writing \u2013 original draft, Visualization. Shoji F. Nakayama: Methodology, Software, Writing \u2013 review & editing, Supervision, Project administration. Tomohiko Isobe: Methodology, Investigation, Writing \u2013 review & editing.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "Enterobacteriaceae bloodstream infections (CRE-BI) in children from Latin America and Caribbean (LAC ) is scarce.Systematic reviews about the burden and use of resource related to Carbapenem Resistant To analyze demographic, epidemiological, clinical, use of resource and microbiological data from CRE-BI in LACA systematic review following Cochrane methods, PRISMA/MOOSE statements was performed (PROSPERO 2022 CRD42022352504). We searched all databases from 1/1/2012 to 9/30/2022. Independent selection, data extraction, and risk of bias assessment (RoB) were performed with COVIDENCE. Types of study included; observational/surveillance/experimental/quasi-experimental. Population: Inpatients < 19 years old, with CRE-BI. Outcomes: age, underlying conditions, previous . treatment and use of resources. Statistical analysis: proportion meta-analyses applying an arc-sine transformation and RoBTo, We conducted proportion meta-analyses and applied arc-sine. R studio was used25/858 screened studies included for full text assessment with 243 patients were included. The most represented countries were Brazil (30%), Colombia (26%) and Argentina (22%). Median age was 34.5 months (IRQ 14-85). Predominant resistance mechanisms: KPC (96%), NDM (58%), OXA (27%). Pool proportion were: Male 55%. Underlying conditions 100% (immunocompromised host 84%), Previous Colonization with CRE was 42% (CI95% 13-78) and broad spectrum antibiotic used was 88% (CI95% 46-98%), most commonly carbapenems 84% (CI95% 72-91%) Bacteremia secondary to intra-abdominal infection was 80%. Combination antimicrobial treatment was 96% (CI95% 22-100%). Median length of stay 22.5 (IQR 22-30 days). Overall case fatality ratio was 48% (IC95% 27-69%).CRE-BI cause morbidity and mortality mainly in pediatric population with underlying disease in LAC region. Considering its high impact in public health, it's mandatory to establish adequate policies and programs to improve antimicrobial stewardship.All Authors: No reported disclosures"} +{"text": "Fig 1). Stimulation of mucosal antibodies and T cells, immune effectors also associated with protection against influenza, are anticipated to enhance VE.Adults over age 65 years exhibit increased susceptibility to influenza viruses, accounting for 70-85% of annual influenza-related US fatalities. Licensed vaccines mainly induce serum humoral immunity and remain the primary method of influenza prevention, but vaccine effectiveness (VE) remains particularly low in older individuals (Table 1). Demographics were comparable across cohorts (Table 2).A randomized, double-blind, double-dummy, placebo-controlled Phase 1b study (NCT05163847) was conducted at 6 US study sites with the investigational intranasal M2SR (M2 deficient Single Replication) and Fluzone High Dose (HD) vaccine that contained HA & NA from A/Cambodia/e0826360/2020 (Cam2020). Adults aged 65-85 years (n = 305) received either one administration of Cam2020 M2SR alone, Cam2020 M2SR along with HD, HD alone, or placebo . Moreover, M2SR coadministered with HD induced HAI and NAI antibodies in significantly higher proportion of subjects than HD alone . M2SR alone and M2SR coadministered with HD elicited significant mucosal secretory IgA (sIgA) antibodies against vaccine antigen, Cam2020, and drifted H3N2 Darwin2021 strain . Similarly, T cells positive for IFNg and GrzB secretion were significantly induced by M2SR only or by M2SR coadministered with HD . HD alone did not induce mucosal antibodies or T cell responses .Study vaccination was well-tolerated. Intranasal M2SR generated significantly increased serum HAI and NAI antibodies compared with placebo . These broad immune responses support the potential for the safe coadministration of M2SR with HD to enhance protection against influenza infection in this highly vulnerable age group.Coadministration of intranasal M2SR with intramuscular Fluzone HD resulted in a multi-faceted immune response in older adults aged 65-85 years old with a higher proportion of responders across all immune measurements compared with either vaccine alone. Coadministration of the two vaccines resulted in significant rises in serum HAI and NAI titers compared to HD alone (Joseph Eiden, MD, PhD, FluGen, Inc.: Advisor/Consultant Bryan Murray, M.D., FluGen, Inc.: Advisor/Consultant Renee Herber, B.S., FluGen, Inc.: Salary Roger Aitchison, ScM, FluGen, Inc.: Advisor/Consultant David Marshall, B.S., FluGen, Inc.: salary Michael Moser, Ph.D., FluGen, Inc.: salary Pamuk Bilsel, Ph.D., FluGen, Inc.: salary"} +{"text": "Fusarium verticillioides is a filamentous fungus that causes plant diseases and harms human health through cancer-inducing mycotoxin and life-threatening Fusariosis. Given its threat to agriculture and public health, genome assembly of this fungus is critical to our understanding of its pathobiology and developing antifungal drugs. Here, we report a gap-free genome assembly of F. verticillioides using PacBio HiFi data and high-throughput chromosome capture (Hi-C) sequencing data. The assembled 42.0\u2009Mb sequence contains eleven gapless chromosomes capturing all centromeres and 19 of all 22 telomeres. This assembly represents a significant improvement over previous version on contiguity (contig N50: 4.3\u2009Mb), completeness (BUSCO score: 99.0%) and correctness (QV: 88.8). A total of 15,230 protein-coding genes were predicted, 6.2% of which are newly annotated genes. In addition, we identified three-dimension chromatin structures such as TADs-like structures and chromatin loops based on Hi-C data of ultra-high coverage. This gap-free genome of F. verticillioides is an excellent resource for further panoramic understanding mechanisms of fungal genome evolution, mycotoxin production and pathogenesis on plant and human host. Fusarium verticillioides, a filamentous fungus belonging to Fusarium fujikuroi species complex, causes Fusarium ear rot of maize, a major crop worldwide. Besides yield loss, various mycotoxins are produced during fungal infection of maize, reducing the quality of corn products. The best characterized F. verticillioides mycotoxins are fumonisins, a group of polyketide mycotoxins associated with esophageal cancer and neural tube birth defects in human populations consuming the contaminated maize products1. Although F. veticillioides is considered nonpathogenic to healthy human being, it can become a serious threat to individuals with compromised immune system such as those infected by undergoing organ transplants2. Human infection by F. verticillioides commonly known as Fusariosis has been a surging life threat to the immunocompromised patients due to limited options of antifungal drugs for treatment and emergence of multi-drug resistance3. Therefore, elucidation of molecular mechanisms underlying fungal pathogenesis and antifungal resistance in F. verticillioides is crucial to both agricultural safety and public health.F. verticillioides strain 7600 was released in 20104 with a contig N50 of 392.3\u2009kb. Recently, several updated versions of F. verticillioides genome assemblies are available in NCBI genome database. Although these genome assemblies have since facilitated the genetic studies of fungal biological processes, they are highly fragmented with several hundreds to thousands of contigs. The fact that F. verticillioides has 11 chromosomes suggests the presence of gaps in these assembly versions. Furthermore, no telomere and centromere sequences have been reported in any F. verticillioides genome assembly available, leaving these essential and complex genomic regions unexplored. A complete genome sequence for F. verticillioides would enable accurate characterization of the fungal genome function, regulation and evolution, shedding light on mechanisms of growth, development, pathogenicity and mycotoxin production.Despite the importance of this fungus, its complete genome sequence has not been assembled and thoroughly analyzed, impeding dissection of molecular and evolutionary mechanisms underlying its pathogenesis, secondary metabolism and drug resistance. The first genome assembly of F. verticillioides, and update the genome annotations based on the improved genome assembly. We sequenced the genome of F. verticillioides strain 7600 to produce high-fidelity (HiFi) long reads of PacBio single-molecule real-time (SMRT) sequencing, and Hi-C (high throughput chromatin conformation capture) data using Illumina pair-end sequencing. In total, we generated 4.1\u2009Gb (~96.7X coverage) PacBio HiFi raw reads with a N50 of 10.0\u2009kb. and 53.8\u2009Gb Hi-C data and Flye7 to obtain draft genome assemblies which were individually polished using Nextpolish (v.1.4.0)8 followed by assembly merge using quickmerge (https://github.com/mahulchak/quickmerge) contains 11 gap-free chromosomes compared to the previous assembly Table\u00a0. CompariF. verticillioides contained all centromeres on 11 chromosomes Hi-C data containing 95.8% valid interaction pairs after initial quality control slant and stored in \u221280\u2009\u00b0C freezer. F. verticillioides 7600 mycelia and spores harvested from two-day old PDB (potato dextrose broth) culture in 150\u2009rpm shaker at 25\u2009\u00b0C were used to isolate high molecular weight DNA using CTAB (cetyltrimethylammonium bromide) method11. A total of 15\u2009\u00b5g purified genomic DNA were used to construct a standard PacBio SMRTbell library using PacBio SMRT Express Template Prep Kit 2.0 . The sequencing was performed using a PacBio Sequel II instrument at Biomarker Technologies Corporation .F. verticillioides was prepared from cross-linked chromatins of fungal mycelia using a standard Hi-C protocol12. The constructed Hi-C sequencing library was sequenced by a test run and examined for valid interaction read pair ratios using HiCPro (v.3.1.0)13 before going through high coverage sequencing. The library was sequenced by Illumina NovaSeq. 6000 to yield 10.5\u2009Gb (249.7 coverage) paired-end reads. The valid interaction pairs of Hi-C sequencing reads were used to anchor all contigs using Juicer (v.1.5)9, followed by using a 3D-DNA correction pipeline10 and manually correction with Juicebox (v.1.11.08)14. compartment A/B were analyzed using HiTC (v.1.40.1)15 and Cworld-dekker (https://github.com/dekkerlab/cworld-dekker), TADs-like structures and chromosome loop were identified by Juicer (v.1.5)9. Three-dimensional structure visualization of the whole genome using pyGenomeTracks (v.3.7)16.Hi-C library construction of 5, HiCanu (v.1.4)6 (parameters: -assemble -pacbio-hifi oeaErrorRate\u2009=\u20090.001), Flye (v.2.9)7 and NextDenovo (v.2.5.0) , to assemble, respectively, and then sorted the number of contigs of different assemblers in ascending order. Based on four assemblies we used quickmerge (v.0.3) (https://github.com/mahulchak/quickmerge) to produce a merged genome assembly, and finally used Juicebox14 to manually adjust misassemblies.To optimize the genome assembly strategy and take into account the differences of assembly algorithm between software, we used Hifiasm (v.0.16.1)F. verticillioides using Trizol agents following manufacturer recommendation protocol. The RNA Nano 6000 Assay Kit of Agilent Bioanalyzer 2100 system was used to evaluate the total RNA integrity. The total RNA used for library preparation first enriched the mRNA with polyA tail through Oligo (dT) magnetic beads. The mRNA was then subjected to sequencing library construction using Illumina True-seq transcriptome kit with an insert size of 370bp\u2013420bp, and sequenced by an Illumina Novaseq. 6000 platform at Biomarker Technologies Corporation to generate 150\u2009bp paired-end reads. RNA-seq data was checked for quality using fastp (v.0.23.2)17, mapped to F. verticillioides genome assembly using hisat2 (v.2.1.0)18, followed by calculating mapping ratios by samtools (v.1.15)19.Total RNA was extracted from the mycelia of de novo prediction and similarity aligmment to annotate it via RepeatModeler (v. 1.0.11)20 (parameters: -database -engine ncbi -pa) and softmasked genome by RepeatMasker (v. 4.1.2.p1)21. RepeatMasker\u2019s perl script (rmOutToGFF3.pl) converts various types of repeat sequence annotation results into a common generic feature format (GFF) version 3. Gene model prediction combined with the following three aspects of evidence: (a) ab initio prediction, (b) homologous protein, (c)RNA-seq evidence. During the ab initio prediction, we firstly trained the GeneMark-ET model for five rounds using BRAKER2 (v.2.1.6)22 (parameters:\u2013species\u2009=\u2009Fv\u2013fungus\u2013softmasking\u2013genome\u2013bam\u2013prot_seq\u2013prg\u2009=\u2009gth\u2013gff3\u2013rounds\u2009=\u20095), whose process employed GeneMark-ET23, NCBI BLAST24, DIAMOND25 and GenomeThreader26. We then trained the SNAP27 semi-HMM model for two rounds using MAKER28 . AUGUSTUS29 used the built-in Fusarium genome feature model. To provide homologous protein evidences for gene prediction, we downloaded the protein data of this species (anchored chromosomes) from the public database, including 7600 (NCBI Assembly ID: GCA_ 000149555.1), BRIP53590 (NCBI Assembly ID: GCA_003316995.2), BRIP53590 (NCBI Assembly ID: GCA_003317015.2) and BRIP14953 (NCBI Assembly ID: GCA_003316975.2). For transcriptome data, RNA-seq reads from the vegetative phase were firstly aligned to our genome assembly through hisat218 for BRAKER2 (v.2.1.6)22. Then, we performed reference-based assembly and de novo assembly of transcriptomes by Scallop (v0.10.5)30 and Trinity (v.2.8.4)31 , respectively. Transcripts obtained by two methods are de-redundant with CD-HIT (v.4.6)32 (parameters:-I -c 0.99 -T 50 -M 100000 -o). The above three evidences are integrated by MAKER (v.3.01.03)28 to predict the final gene model. Rfam/Infernal (v.1.1.4)33 (parameters: cmscan\u2013cut_ga\u2013rfam\u2013nohmmonly\u2013fmt 2 \u2013clanin \u2013tblout) and tRNAscan-SE (v. 2.0.9)34 (parameters: -E -X 20 \u2013f -m -b -j\u2013detail) are used to infer genome-wide non-coding RNAs. To compare the previous (NCBI: GCA_000149555.1) and our genome assembly, we performed the genome annotation on two genome assemblies by using the same software, parameters, and protein data.For repetitive sequences, we firstly use 35 with accession number of SRR2100352136, SRR2100352037, SRR2100351938, respectively. The gap-free genome assembly is deposited under the same BioProject at NCBI (GCA_027571605.1) and also in Genome Warehouse of National Genomics Data Center (https://ngdc.cncb.ac.cn/) at China National Center for Bioinformation under the accession number of GWHBQEB0000000039. Genome annotations including protein-coding regions, repeat sequence and ncRNA annotation files have been submitted to the online open access repository Figshare40.The raw PacBio HiFi sequencing data, Hi-C data and RNA-seq data have been deposited in the National Center for Biotechnology Information (NCBI) under the BioProject (PRJNA868307)14. We then aligned the species\u2019 mitochondrial genome to our assembly by megaBLAST24, which found no errors. Finally, we also used megaBLAST24 to aligned our genome assembly against a common database (ftp://ftp.ncbi.nlm.nih.gov/pub/kitts/contam_in_euks.fa.gz) to identify potentially contaminated sequences sequencing adaptor sequence (ftp://ftp.ncbi.nlm.nih.gov/pub/kitts/adaptors_for_screening_euks.fa) and nucleotide sequence database (remote mode), which again found no contamination.To get a nearly complete and error-free nuclear genome, we first manually corrected the assembly using Hi-C read alignment within the Juicebox41 (parameters: -W repetitive_k15.txt -t 104 -ax map-pb) and the quality value (QV) was assessed using Merqury (v.1.3)42 (parameters: k\u2009=\u200918 count). Second, the BUSCO 43 analysis was conducted to reflect the completeness of genome assembly. The final F. verticillioies gap-free genome assembly has a QV of 88.8, completeness of 99.7% and BUSCO score of 99%, suggesting the high accuracy and completeness of the assembly, respectively 44. This assembly has reduced the length of gaps from 90,816 in previous version to 0, and captured eleven centromeres and nineteen telomeres (TTAGGG) except missing three telomeres via trf (v. 4.09.1)45 (parameters: 2 7 7 80 10 90 2000 -d -m -l 2) from assemblies and raw sequences, one each at the end of Chr2 and Chr4 47 (parameters: intersect -wa -wb -f 1.0), which account for 99.5% of the old version genome and 93.6% of this study genome. Compared to previous version (NCBI: GCA_000149555.1), our assembly has corrected three major inversions (Fig.\u00a048 plot.The resolved fungal telomere and centromere regions have been well covered by PacBio HiFi reads that span these complex regions Fig.\u00a0 by IGV (hr4 Fig.\u00a0. There iools v.2.0.047 (paSupplementary Table 1"} +{"text": "Correction:\u00a0BMC Public Health\u00a023, 960 (2023)https://doi.org/10.1186/s12889-023-15934-yFollowing publication of the original article , the autFig. 2 correct version of Fig. 1"} +{"text": "Little is known about the first line induction chemotherapy cycles for HIV-associated diffuse large B-cell lymphoma (DLBCL) as these are less common than HIV-negative lymphoma. Currently, the optimal treatment cycles option remains undefined. Therefore, we performed a multi-center study to analyze the clinical characteristics and outcomes of HIV-associated DLBCL patients in different treatment modes in China.Totally 273 newly diagnosed HIV-associated DLBCL patients at eleven large academic centers from October 2008 to October 2021, were analyzed.p<0.001). Cox multivariate analysis showed that age \u226560 , high IPI score (3-5) , B symptoms , elevated LDH and received less than 4 cycles chemotherapy were independent risk factor for adverse prognosis based on overall survival (OS).In the entire cohort, the median age was 47 years at lymphoma diagnosis, and 223 patients were male (81.7%). One hundred and ninety-four (71.1%) patients were germinal center B-cell-like lymphoma (GCB) subtype. Most patients had elevated lactate dehydrogenase (LDH), and advanced Ann Arbor stage (78.9% 213/273) at diagnosis. High international prognostic index (IPI) score (3-5) at diagnosis was found in 65.2% (178/273) of patients. One hundred and fifty-five patients (56.8%) had extranodal involvement. The median CD4 cell count was 168/\u03bcl , of whom 174 (63.7%) had a CD4 cell count below 200/\u03bcl. The median follow\u2010up of our cohort was 10.1 (0.1-160) months. The overall 2-year OS rates 58.0%. Median OS times in the 0, 1-3, 4-6, and >6 cycles chemotherapy cohort were 7.1 months, 20.0 months, not reached, and not reached, respectively (Hazard Ratio (HR)=0.549, 95% Confidence interval (CI) 0.451-0.667; These results demonstrated that 4-6 cycles chemotherapy were significantly associated with improved outcomes in HIV-associated DLBCL patients. However, >6 cycles chemotherapy did not further improve the survival of patients. Human immunodeficiency virus (HIV)-associated lymphoma is a rare aggressive non-Hodgkin lymphoma. The incidence rate reported in 2017 was 100/100, 000 to 300/100,000 in population infected with HIV, becoming the highest incidence rate among HIV-associated cancers in the United States , regardless of chemotherapy regimen or dose intensity for HIV-associated DLBCL patients. This is because patients are easily complicated by opportunistic infections, resulting in an increase in mortality , 5. Withp<0.001) received no anti-lymphoma chemotherapy because of fear of discrimination and poor financial situation. Median survival times in the patients who no received any anti-lymphoma chemotherapy was only 3.5 months, which was significantly lower than that of patients receiving chemotherapy classification criteria.cART included two nucleoside reverse transcriptase inhibitors and one nonnucleoside reverse transcriptase inhibitor. The chemotherapy cohort included patients who received any of the following regimens: etoposide, doxorubicin, vincristine, cyclophosphamide and prednisone (EPOCH); rituximab, etoposide, doxorubicin, vincristine, cyclophosphamide and prednisone (R-EPOCH).18F-fluorodexyglucose positron emission tomography/computed tomography (PET/CT) or computed tomography (CT) were performed for radiological evaluation. Responses were classified according to standard criteria per each institution, typically aligning with Lugano criteria, which including complete response (CR), partial response (PR), stable disease (SD) and progressive disease (PD).Progression-free survival (PFS) was defined as the time from lymphoma diagnosis to disease progression, relapse or death from any cause. Overall survival (OS) was defined as the time from lymphoma diagnosis to last follow-up or death from any cause. Survival was estimated using Kaplan\u2013Meier curves and compared by the log-rank test. The Cox proportional hazards regression model was used in multivariate analysis to determine prognostic factors. All statistical tests were two\u2010sided, and p \u2264 0.05 was considered statistically significant. All statistical data were analyzed with GraphPad Prism 9.2-microglobulin (\u03b22-MG), and advanced Ann Arbor stage (78.9% 213/273) at diagnosis. High international prognostic index (IPI) score (3-5) at diagnosis was found in 65.2% (178/273) of patients. One hundred and fifty-five patients (56.8%) had extranodal involvement. Totally 53(19.4%) patients had bone marrow involvement, 24(8.8%) patients had central nervous system (CNS) involvement, 64 (23.4%) had poor Eastern Cooperative Oncology Group performance status (ECOG PS 2-4), and 150 (54.9%) had B symptoms at diagnosis. The median CD4 cell count at diagnosis was 168/\u03bcl , of whom 174 (63.7%) had a CD4 cell count below 200/\u03bcl at diagnosis. Among the Epstein-Barr virus (EBV) status, EBV load was elevated (5\u00d7103 copies/ml) in 104 (38.1%) patients. Of all patients, 37(13.6%) had positive HBsAg and 7(2.6%) were positive for anti-Hepatitis C virus (HCV) antibody.Two hundred and seventy-three newly diagnosed HIV-associated DLBCL were included in this study. The median age was 47 years at lymphoma diagnosis, and 223 patients were male (81.7%). One hundred and ninety-four (71.1%) patients were germinal center B-cell-like lymphoma (GCB) subtype. Most patients had elevated lactate dehydrogenase (LDH), elevated serum \u03b22-MG, Ann Arbor stage, IPI score, extra-nodal involvement, bone marrow involvement, CNS involvement, CD4 cell count, and chemotherapy regimen. The 0 cycle chemotherapy cohort featured more cases of GCB . Baseline clinical characteristics are summarized in Patients were stratified based on the induction chemotherapy, where 38/273 (13.9%), 71/273 (26.0%), 73/273 (26.7%), and 91/273 (33.3%) were in the 0, 1-3, 4-6, and >6 cycles chemotherapy cohort, respectively. In the study, some patients received no anti-lymphoma therapy because of fear of discrimination and poor financial situation, some patients had less than four cycles of anti-lymphoma therapy also due to poor financial situation. This is because Central and Western China AIDS Lymphoma League (CALL) is located in southwest China, and the economic level of the patients is low. Patient characteristics were similar between the four cohorts, including gender, age, residence, educational level, HIV transmission route, cART therapy, years of HIV infection before lymphoma, ECOG-PS, the presence of B symptoms, elevated serum LDH, elevated serum \u03b2.In this cohort study, the median chemotherapy cycles were 4 , 38 (13.9%) received no anti-lymphoma therapy, 71 (26.0%) had less than four cycles of chemotherapy, 73 (26.7%) patients received four to six cycles of chemotherapy, and 91 (33.3%) patients received more than six cycles of chemotherapy. Of the 235 patients who received chemotherapy, 80 (34.0%) received EPOCH regimen and 155 (66.0%) received R-EPOCH regimen. 239 (87.5%) were administered cART. Totally 209 patients were evaluated for best treatment response at the end of treatment, including 65 patients who received EPOCH and 144 patients who received R-EPOCH. The results indicated an overall response rate (ORR) of 63.1% and 80.6%, respectively.CR rate were 23.1% and 42.4%, respectively . Median PFS times in the 0, 1-3, 4-6, and >6 cycles chemotherapy cohort were 7.1 months, 10.1 months, 36.5 months, and 26.4 months, respectively (Hazard Ratio (HR)=0.713, 95% Confidence interval (CI) 0.600-0.847; p<0.001) . Median OS times were 7.1 months, 20.0 months, not reached, and not reached, respectively . These results demonstrated that 4-6 cycles chemotherapy were significantly associated with improved outcomes in HIV-associated DLBCL patients. However, >6 cycles chemotherapy did not further improve the survival of patients.The median follow\u2010up of our cohort was 10.1 (0.1-160) months. Median PFS and OS were 17 months and 38.1 months respectively. The overall 2-year PFS and OS rates were 46.8% and 58.0%, respectively . Median . Medianp=0.049) . Median OS times were 27.7 months and not reached. The overall 2-year OS rates were 52.6% and 68.5%, respectively (p=0.048) . These data suggested that rituximab administration was significantly associated with improved outcomes.Median PFS times in the no received rituximab and received rituximab groups were 16 months and not reached. The overall 2-year PFS rates were 41.0% and 53.0%, respectively (p=0.049) . Median p=0.006), high IPI score (3-5) , B symptoms , poor ECOG-PS , elevated LDH , Extra-nodal involvement and received less than 4 cycles chemotherapy were predictive of worse PFS. Age \u226560 , high IPI score (3-5) , B symptoms , elevated LDH and received less than 4 cycles chemotherapy were predictive of worse OS.Univariate analysis showed that advanced stage , B symptoms and received less than 4 cycles chemotherapy were independent risk factors for adverse prognosis based on PFS. Age \u226560 , high IPI score (3-5) , B symptoms , elevated LDH and received less than 4 cycles chemotherapy were independent risk factor for adverse prognosis based on OS .Cox multivariate analysis showed that high IPI score (3-5) in May 2021. The CALL is a public welfare organization dedicated to the diagnosis and treatment of HIV-associated lymphoma patients. This is the first multi\u2010center retrospective study with HIV-associated DLBCL in eleven China academic centers from CALL from October 2008 to October 2021. The present study included 273 HIV-associated DLBCL cases, which is the largest cohort reported in China to date. To the best of our knowledge, this is also the first systematic study to explore the effect of chemotherapy cycles on prognosis in a large series of HIV-associated DLBCL.HIV-associated malignancies are divided into acquired immune deficiency syndrome-defining and non-acquired immune deficiency syndrome-defining cancers based on the coincidence rate. Kaposi\u2019s sarcoma, Non-Hodgkin\u2019s lymphoma and invasive cervical cancer are considered acquired immune deficiency syndrome- defining cancers. Other cancers, which including Hodgkin\u2019s lymphoma, hepatocellular carcinoma, oral and pharyngeal cancers, lung cancer, anal cancer, vulvar cancer and penile cancer, are considered non-acquired immune deficiency syndrome-defining cancers , 2. The The present cohort study showed that the median age was 47 years at lymphoma diagnosis, and 223 patients were male (81.7%), in agreement with the overall male-to-female HIV incidence rate in China . CompareCurrently, there are no standard guidelines for treatment of HIV-associated DLBCL. In the pre-cART era, median survival times only 5 to 8 months for HIV-associated DLBCL patients. This is because patients are easily complicated by opportunistic infections, resulting in an increase in mortality , 5. In tp=0.03) and PFS compared with HIV-negative patients (p=0.006) and median OS compared with no receiving rituximab (p=0.049). The overall 2-year OS rates were 52.6% and 68.5%, respectively (p=0.048). The current data also suggested that rituximab administration was significantly associated with improved outcomes in HIV-associated DLBCL. In AMC034, rituximab combined with EPOCH was assessed, and the results were compared with R-CHOP in AMC010. The results showed that a higher CR rate (69%) was obtained for R-EPOCH compared with R-CHOP (47%) . In the % . In thOP (47%) .p<0.001), and CR rate were significantly higher in patients who received chemotherapy (p<0.001) were independent risk factor for adverse prognosis.The optimal treatment cycles option of first line induction chemotherapy for HIV-associated DLBCL remains undefined. Compared with HIV-negative DLBCL patients, HIV-associated DLBCL patients are difficult to accept long-term hospitalization chemotherapy, whether there is an appropriate reduction in the number of chemotherapy cycles, the survival of patients will not be affected? Wu D retrospectively analyzed the clinical features of 100 HIV-associated lymphoma patients, which including 66 HIV-associated DLBCL. 15 patients (15%) did not received chemotherapy. Compared to those who did not received chemotherapy, the 2-year OS rate (41.0% vs. 0%, otherapy . In our otherapy . Once thotherapy , 20\u201324. In summary, our multi-center study suggested that received less than 4 cycles chemotherapy predicted poor OS and PFS in HIV-associated DLBCL patients. Therefore, we recommend that patients receive at least 4 cycles of systemic chemotherapy. More high-quality randomized controlled studies were needed to test our findings.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The studies involving human participants were reviewed and approved by Institutional Review Board. The patients/participants provided their written informed consent to participate in this study.CW, YW, JL, and HM conceived and designed the study, analyzed the data, and drafted and revised the paper. HZ, YC, and YL conceptualized and designed the study. All authors provided critical comments to the manuscript. All authors contributed to the article and approved the submitted version."} +{"text": "Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.Terpenes and their derivatives constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus O-containing derivatives (terpenoids) are the largest and structurally most diverse group of secondary metabolites derived from natural sources. Based on the number of isoprene units, terpene derivatives are classified into mono- (C10), sesqui- (C15), di- (C20), sester- (C25), tri- (C30), sesquar- (C35), and tetra- (C40) terpenes. Terpene derivatives are widely used in the food, cosmetics, and fragrance industries -1-epi-cubenol, firstly obtained by fermentation, was synthesized carbonyl and 2-[(2-chlorophenyl)amino]-2-oxo-acetyl, respectively, were identified among the metabolites of Streptomyces sp. SN194 [308 R=H309 R=CH3310 R1=R2=R3=H311 R1=R2=H, R3=CH3312 R1=H, R2=Cl, R3=H313 R1=OH, R2=R3=H314 R=H315 R=CH2OH316 R=CH(OH)2317 R=CHO318 R=COOH319320321 R=CH3322 R=H323 R1=H, R2=\u03b1OH, R3=H324 R1=H, R2=\u03b1OH, R3=CH3325 R1=H, R2=OCH3, R3=H326 R=CH3327 R=CH2OH328 R=H 329 R=CH3330 dixiamycin B331332333334335336337338339340341 R1=R2=H, R3=CH3, R4=H342 R1=R2=H, R3=CH2OH, R4=H 343 R1=R2=H, R3=R4=CH3344 R1=H, R2=OH, R3=CH3, R4=H345 R1=OH, R2=H, R3=CH3, R4=H346 KO-3988 , S. gris CB00830 , and Strp. SN194 synthesip. SN194 .308 R=H347 R= 348 R=349 R=351 R=NH2350 R=352 R=353 R=Streptomyces sp. T\u00fc6071 produced phenalinolactones A\u2013D (354\u2013357), tricyclic terpene glycosides, and their derivatives 359\u2013362, 365, and 366 [Streptomyces sp. T\u00fc6071 with inactivated oxygenase genes , dehydrogenase genes and putative acetyltransferase gene (plaV) yielded phenalinolactone derivatives PL HS2 (364), PL X1 (363) PL HS6 (367), and PL HS7 (368) [354) and D (357) were identified as PL IM1 (370) and PL IM2 (369), respectively [S. coelicolor M512 resulted in the formation of the non-glycosylated derivative phenalinolactone E (358) [ and 366 ,237. TheS7 (368) . Later, ectively . Heterol E (358) . 371\u2013381), close structural analogues of phenalinolactones, were discovered by genome mining of diterpene synthases in Streptomyces sp. CB03234 and Streptomyces sp. CB03238. Tiancilactones are characterized by a highly functionalized diterpene backbone, which comprises chloroanthranilate and \u03b3-butyrolactone moieties, and exhibit antibacterial activity [\u03b3-lactone, namely trinulactones A (382) and B (383), were isolated from Streptomyces sp. S006 [1R2R3R4R354OH3-CO-CH3CH355OH3-CO-CHH356OH3-CO-CH2-O-CH3-CH357H3-CO-CH3CH358H3-CO-CHOH3CH359H3-CO-CH3CH360HHH3CH361H3-CO-CHH3CH362HHOH3CH363HH3CH364H3-CO-CH2-O-CH3-CH367 R=\u03b1OH368 R=O365 R=\u03b1OH366 R=O369 R370371 R1=Cl, R2=CH3, R3=OCH3372 R1=H, R2=CH3, R3=OCH3373 R1=Cl, R2=CH3, R3=OH374 R1=Cl, R2=CH3, R3=oxo375 R1=Cl, R2=H, R3=OCH3376377378379 R=H380 R=CH3381 R=H382 R=OH383Tiancilactones A\u2013K (activity . Two newsp. S006 .R1R2R3384), its isomer 385, and fusicomycin B (386) were separated from the fermentation broth of S. violascens YIM 100212 [387) and B (388) were obtained from Streptomyces sp. KCB17JA11 [389) is new meroterpenoid derived from Streptomyces sp. CNQ-027 consisting of an unprecedented dihydronaphthalenone polyketide linked to a bicyclic diterpenoid [384 R=385 R=386 R=387388389Fusicomycin A (M 100212 . Two newCB17JA11 . Actinorerpenoid .384 R=S. platensis MA7327 and S. platensis MA7339 were shown to synthesize platensimycin (390) and platencin (391), representatives of a new class of broad-spectrum antibiotics against Gram-positive bacteria, in particular S. aureus [ent-kaurene and ent-atiserene synthases in biosynthesis of 390 and 391, representing a new biosynthetic pathway for diterpenoids [ent-copalyl diphosphate synthase involved in the biosynthesis of 390 and 391 in S. platensis CB00739, was described. PtmT2 catalyzed the cyclization of GGPP to ent-CPP, which subsequently channeled into (16R)-ent-kauran-16-ol (392) or ent-atiserene (393) by two distinct type diterpene synthases specific for biosynthesis of 390 or 391, respectively [S. platensis SB12002 and SB12600 produced 390 and 391 with yields of 323 \u00b1 29 mg/L and 255 \u00b1 30 mg/L, respectively, hundreds of times greater than those of wild-type strains [S. platensis SB12600, in addition to 391, accumulated eight new congeners, platencins A2\u2013A9 (394\u2013402) [390 using the mixed culture of S. hygroscopicus HOK021 (NITE P-02560) and Tsukamurella pulmonis TP-B0596 was patented (JP2019149945). Exemplified by 390 and 391, a method of searching for novel natural compounds based on the analysis of biosynthetic genes was proposed (WO2015200501). Data on the biosynthesis features and biological activity of natural and synthetic analogues of platensimycin and platencin were summarized in the reviews [. aureus ,246. Furrpenoids ,248,249.ectively . The met strains ,252 (US2394\u2013402) . A metho reviews ,255.N-containing aminobacteriohopanetriol (403), and adenosylhopane (405), as well as bacteriohopanetetrol (404) and ribosylhopane (406), were determined. Orf14 and orf18 of S. coelicolor A(3)2 responsible for the synthesis of 403 were identified [The intermediates of hopanoids biosynthesis, entified . Streptomyces sp. YIM 56130, triterpene glycoside soyasaponin I (407) [408) produced by S. argenteolus A-2 (FERM BP2065) has a unique structure consisting of a tetraterpene skeleton with 2-O-methylglucuronic acid and O-succinyl benzoate moieties [390391392393394 R1=OH, R2=H395 R1=H, R2=OH396 R1= R2=H397 R1=OH, R2=H398 R1=H, R2=OH399 R=OH400401 R=SCH3402 R=OCH3403 R=NH2404 R=OH405406407408Among the secondary metabolites of I (407) with a w I (407) was obtamoieties .3903913Nocardiopsis, Amycolatopsis, Isoptericola, Saccharopolyspora, Salinispora, Kitasatosporia, Verrucosispora, etc. The compounds produced are represented mainly by sesqui- and diterpenes and their derivatives.Although most of the found actinomycete terpene derivatives are synthesized by streptomycetes, there is an increasing number of publications on terpene biosynthesis by representatives of the genera Nocardiopsis chromogenes YIM 90109, two new monocyclic germacradiene-type sesquiterpenoids germacradiene-9\u03b2,11-diol (409) and 11-hydroxy-germacradien-2-one were identified along with the known geosmin-type sesquiterpenoid 46 [Kitasatospora setae KM-6054 [Micromonospora marina DSM 45555 [411) and (\u2212)-germacrene A (27), respectively. The ability to produce bicyclic 2-methylisoborneol (6) and geosmin (22) was described for Nocardia cummidelens and N. fluminea [S. avermitilis carrying the genes from Saccharopolyspora erythraea NRRL2338 yielded 2-methylisoborneol (6), while Micromonospora olivasterospora KY11048 synthesized 2-methyleneornane (412) [409410411412Among the secondary metabolites of enoid 46 . The TSs KM-6054 and MicrSM 45555 catalyzefluminea . The trane (412) .4094104413 and 414) were isolated from the culture medium of Amycolatopsis alba DSM 44262 [Isoptericola chiayiensis BCRC 16888, a new sesquiterpenoid isopterchiayione (415) was registered [Amycolatopsis benzoatilytica DSM 43387 catalyzing the formation of a bicyclic sesquiterpenoid (416) was described [Verrucosispora gifhornensis YM28-088 [Verrucosispora sp. FIM06031 produced bicyclic sesquiterpenoid cyperusol C (417) and FW03104 (418) (CN101898936), respectively. Two new monocyclic sesquiterpenoids (SM 44262 . Among tescribed . VerrucoYM28-088 and VerrStreptosporangium roseum DSM 43021 and Kitasatosporia setae KM-6054 afforded tricyclic sesquiterpenoids epi-cubebol (419) [420) and B (421) [Saccharothrix espanaensis DSM 44229 [E)-\u03b2-caryophyllene (93).413414415416417418419420421Terpene synthases from ol (419) and new B (421) ,266, resSM 44229 was incuMicromonospora marina DSM 45555 was functionally characterized to produce micromonocyclol (422), a new diterpene alcohol with a rare 15-membered ring [Mycobacterium tuberculosis H37Rv\u043d synthesized unique bicyclic diterpenoids, which presumably block the formation of phagolysosomes in human macrophages. The Rv3377c and Rv3378c genes proved to be responsible for synthesis of tuberculosinol (5(6),13(14)-halimadiene-15-ol, 423), 13R- (424) and 13S-isotuberculosinol (5(6),14(15)-halimadiene-13-ol, 425), and nosyberkol (426) (previously identified as edaxadiene). The analogs of Rv3377c and Rv3378c were found in the virulent strains of M. tuberculosis CDC1551 and M. bovis subsp. bovis AF2122/97, but did not occur in non-pathogenic strains [The TS from red ring . Mycobac strains ,271,272. strains .427) was firstly separated from the fermentation broth of Kitasatosporia griseola MF730-N6 (syn. Streptomyces griseolosporeus MF730-N6) in 1985 [ORF11 and ORF12 in S. lividans together with the GGDP synthase gene resulted in the formation of a new cyclic diterpene ent-clerod-3,13(16),14-triene with a structure similar to 427 [429) to 428, accepted labdane-type diterpene diphosphates (+)-CDP (430), syn-CDP (431), (\u2212)-ent-CDP (432), as well as halimane-type diterpene diphosphate and catalyzed the formation of corresponding derivatives (434\u2013437) [A bicyclic terpenoid terpentecin .terp1 operon from Salinispora arenicola CNS-205 in E. coli led to the generation of isopimara-8,15-dien-19-ol (438). It should be noted that this terpenoid was not observed in pure cultures of S. arenicola CNS-205. Apparently, the terp1 operon was expressed under certain conditions, for example, in the presence of other marine organisms [Salinispora sp. PKU-MA00418 accepted CPP and syn-CPP and produced syn-isopimaradiene/pimaradiene analogues . Compound 439 possess a unique and previously unreported 6-6-7 ring skeleton [447) and B (448), were isolated from the culture medium of Verrucosispora gifhornenensis YM28-088 [Micromonospora haikouensis G039 [Microbispora hainanensis CSR-4 [449) and 2\u03b1-hydroxy-8(14),15-pimaradien-17,18-dioic acid (450) were identified, respectively.Heterologous expression of the biosynthetic rganisms . The terskeleton . New hydYM28-088 . Among ssis G039 and Micris CSR-4 , new ditActinomadura sp. SpB081030SC-15 [Actinomadura sp. KC 191 [451) and actinomadurol (452), rare bacterial C-19 norditerpenoids. A norditerpenoid k4610422 (453), originally discovered from a mesophilic rare actinomycete of the genus Streptosporangium, was isolated from the culture extract of a thermophilic actinomycete Actinomadura sp. AMW41E2 [422423424425426427428429430 R=\u03b1H431 R=\u03b2H432433434435436437438439440441442443444445446447448449450451452453030SC-15 and Acti. KC 191 synthesi AMW41E2 .4224234Catenulispora acidiphila DSM 44928 and Saccharopolyspora spinosa NRRL 18395 produced new di- and tricyclic catenul-14-en-6-ol (454), isocatenula-2,14-diene (455), isocatenula-2(6),14-diene (456) [457), B (458), and 2,7,18-dolabellatriene (459) [Diterpene synthases from ne (456) , and spine (459) , respectNocardia testacea NBRC 100365 and N. rhamnosiphila NBRC 108938 accepted GGPP, but not GPP, FPP, or GFPP as a substrate, which was converted by both enzymes in a tetracyclic diterpene phomopsene (460) [Allokutzneria albata DSM 44149 encoded four diterpene synthases that catalyze the formation of mono-, tri-, and tetracyclic compounds: new spiroalbatene (461), bonnadiene (462) and allokutznerene (463), and known compounds: cembrene A (164), thunbergol (464), phomopsene (460), and spiroviolene (200) [Terpene synthases isolated from ne (460) . Allokutne (200) ,288.465\u2013482) were found in the genus Frankia [483) was isolated from the cell walls of nonpathogenic mycobacteria [454455456457458459460461462463464Hopanoid lipids (CN101921721). Saccharomonospora sp. CNQ-490 produced saccharoquinoline (485), meroterpenoid with drimane-type sesquiterpene unit [486) and B (487), were derived from Micromonospora sp. WMMC-218, a symbiont of marine ascidians Symplegma brakenhielmi [Mycobacterium tuberculosis H37Rv\u043d revealed that this enzyme catalyzed the formation of 1-tuberculosinyladenosine (488) and its two isomers, one of which was identified as 6N-tuberculosinyladenosine (489). Compounds 488 and 489 are specific diterpene nucleosides of pathogen of Mycobacterium tuberculosis and can serve as chemical markers of infection [Rv3377c-Rv3378c from M. tuberculosis H37Rv\u043d in M. kansasii led to the production of 1-tuberculosinyladenosine (488) [ene unit . Two newenhielmi . Furthernfection ,296,297.ne (488) .Nocardia brasiliensis IFM 0406 (now N. terpenica) to synthesize diterpene glycoside brasilicardin A (490) was first described in 1999 [490) displays a unique structure consisting of a diterpene skeleton with L-rhamnose, N-acetylglucosamine, amino acid, and 3-hydroxybenzoate components [N. terpenica IFM0406 and identified as brasilicardins B\u2013D (491\u2013493) [bra0-12), responsible for the synthesis of 490, in Amycolatopsis japonicum (A. japonicum::bcaAB01) led to the formation of four brasilicardin congeners, namely BraC (492), BraD (493), BraC-agl , and BraD-agl [S. griseus::bcaAB01 (pRHAMO) transformant containing the biosynthetic cluster of brasilicardin A and a plasmid with a biosynthetic cassette for the generation of TDP-L-rhamnose resulted in increased yields of compounds 492 (1669 mg/L), 495 (926 mg/L), and a new metabolite (496) (15 mg/L). The target 490 was obtained through a five-step chemical modification of 494 [The ability of in 1999 . Brasilimponents . Later, 491\u2013493) . The hetaF, 495) ,304,305.n of 494 .ato) gene cluster from Amycolatopsis tolypomycina NRRL B-24205 in S. albus led to the characterization of two unprecedented tricyclic sesterterpenoids atolypenes A (497) and B (498) [499), a new highly oxygenated unique tetracyclic 6-hydroxymeroterpenoid, was derived from Nocardiopsis sp. LGO5 [484485486487488489490 R=OCH3491 R=H492 R=OCH3493 R=H494 R=OCH3495 R=H496499497 R498 RCloning and activation of the atolypene ( B (498) . Terretosp. LGO5 .4844854Streptomyces, however, terpene biosynthesis by Allokutzneria, Amycolatopsis, Frankia, Kitasatosporia, Nocardia, Salinispora, Verrucosispora, etc., have been recently reported contains more than 3000 strains of actinomycetes with a wide range of metabolic capabilities, which are promising for biocatalytic production of terpene derivatives [An extensive development of genome-sequencing technologies and bioinformatics tools have allowed the discovery of BCGs (including silent ones) in the genome of actinomycetes. That terpenoids and meroterpenoids are predominantly found among entified . In addirganisms ,50,310. olyspora , Nocardirdiopsis , Rhodocodococcus ,314, Salinispora , Verrucoosispora , and Actnomadura have beeMF730-N6 and N. t IFM0406 revealed IFM0406 . Genomic IFM0406 ,310,321.ivatives ,325,326 epi-zizaene, pentalenene, cucumene, (E)-biformene synthases, and other TSs isolated from streptomycetes were characterized. In turn, genome mining of streptomycetes as producers of naphthoquinone-based meroterpenoids led to the discovery of unique prenyltransferase (PTase) and vanadium-dependent haloperoxidase enzymes (VHPO) [epi-zizaene synthase, the successful application of site-directed mutagenesis of the enzyme to control the range of the compounds produced was proved [Unlike the biosynthesis of well-studied secondary metabolites, such as polyketides and nonribosomal peptides, the prediction of terpene structures requires detailed understanding of the cyclization mechanisms and the structural characteristics of bacterial TSs ,327. In s (VHPO) ,183. Fors (VHPO) . It has s (VHPO) . By the s proved ,122 (WO2S. cinnabarinus PK209 and S. hygroscopicus HOK021 (NITE P-02560) synthesize the diterpene lobocompactol and the antibiotic platensimycin in the presence of the Gram-negative Alteromonas sp. KNS-16 [Tsukamurella pulmonis TP-B0596 (JP2019149945), respectively. The effectiveness of actinomycete terpenoids and meroterpenoids, namely pentalenolactone, albaflavenone, platensimycin, platencin, terpentecin, lavanducyanin, marinocyanins A\u2013C, furaquinocin L, 3-dechloro-3-bromonapyradiomycin A1, napyradiomycin A1, and merochlorin A, as promising antibiotics has been proven. This is true for cyslabdan, which enhances the action (1000-fold) of the antibiotic imipenem against MRSA. In addition to high antibacterial activity, many meroterpenoids, such as napyradiomycins B1, B3, B4, A80915A, B, C, furaquinocins A and B, murayaquinone, marinocyanin A\u2013C, and saccharoquinoline, exhibit a high cytotoxic activity against different cancer cell lines , which spread Streptomyces spores in the soil [S. coelicolor M145 spores, they synthesize albaflavenone, which may coordinate the development of the producer (quorum sensing) and/or play a role in the competitive repression of microflora (quorum suppression) in the natural environment [S. coelicolor A3(2) does not produce aminobacteriohopanetriol or produces this compound in negligible amounts. However, the triterpene generation increased sharply during the formation of an aerial mycelium and sporulation, which may be associated with structural changes in the membrane and protection against water loss [Micromonospora isolates revealed TS genes, which differ significantly from other groups of characterized bacterial TSs and may be useful as markers of the genus, while Mycobacterium tuberculosis H37Rv\u043d produced specific diterpene nucleosides, 1- and 6N-tuberculosinyladenosines, promising for development as specific diagnostic markers of tuberculosis.Actinomycete-derived terpenoids participate in specific interactions with macroorganisms , regulate the bacterial life cycle, perform protective functions, or serve as taxonomic markers. Bacterial terpenoids are often optical isomers of plant terpenoids and may represent two chemical communication channels that do not overlap even if the same habitat is occupied by prokaryotic and eukaryotic organisms producing terpenes . Soil-smthe soil . Accordithe soil . \u010cih\u00e1k eironment . In the ter loss . In addiDespite the significant (more than 300) number of publications on terpene biosynthesis by actinomycetes, the conducted patent analysis revealed only 26 patents in this research area . TerpenoThus, the synthesis of terpenes and terpenoids is an important pathway in the secondary metabolism of actinomycetes. The compounds produced may be promising therapeutic agents for the treatment of viral, inflammatory, cancerous, and other diseases in the future. Terpenoids and meroterpenoids synthesized by actinomycetes and possessing high antibacterial activity against drug-resistant pathogenic microorganisms may be useful for the development of new antibiotics. Further study of actinomycetes, accumulation of genetic information about this group of microorganisms, and employment of modern and development of novel tools of synthetic biology and genetic engineering will open prospects for creation of ideal \u201ccell factories\u201d using actinomycetes."} +{"text": "C5 convertase cleaves C5 in common complement pathways yielding the anaphylatoxin C5a and C5b, part of the membrane attack complex (MAC) that mitigates bacterial infections . C5 can also be cleaved \u201cextrinsically\u201d by other enzymes. C5a is elevated in severe COVID-19 patients (Pt). Yet, inhibiting C5 cleavage increases infections without improved survival in critically ill COVID-19 Pt . In addition, eculizumab, a C5 blocker does not prevent C5a from being generated in COVID-19 Pt . Vilobelimab (Vilo), an anti-C5a monoclonal antibody that preserves MAC, was tested in a Phase 3 multicenter, double-blind, randomized, placebo (Plc)-controlled study for its effect on survival in critically ill COVID-19 Pt .COVID-19 Pt recruited worldwide intubated within 48 hrs before treatment, received up to 6, 800mg infusions of Vilo or Plc on top of standard-of-care. The primary endpoint was 28-Day all-cause mortality with key secondary endpoints of 60-Day mortality and safety. Blood samples were assessed by ELISA at screening, Day 8 and at hospital discharge for Vilo and C5a levels. No meningococcal vaccination or prophylactic antibiotics were used in the study.vs 41.6% for Plc with similar 60-Day results. On Day 8 after 3 infusions, mean Vilo trough levels were 21,799.3 to 302,972.1 ng/mL . C5a was highly elevated and comparable between groups at screening: Vilo mean 130.3 ng/mL, Plc mean 123.2 ng/mL. By Day 8, C5a levels were reduced 87% for Vilo vs an increase for Plc (mean 129.8 ng/mL). Though post Day 8 sampling was sparse, C5a levels remained elevated for Plc and low for Vilo throughout the study. Serious AEs were 58.9% for Vilo and 63.5% for Plc. Treatment-emergent AEs were 90.9% for Vilo vs 91.0% for Plc. Infection incidence per 100 Pt days was comparable in both groups.Kaplan-Meier estimates showed a 28-Day mortality rate of 31.7% for Vilo Results from this Phase 3 study show that direct C5a inhibition by vilobelimab while presumably preserving MAC, as opposed to upstream C5 blockade, results in a survival benefit for critically ill COVID-19 Pt without increasing infections.Bruce P. Burnett, PhD, InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Employee Alexander Vlaar, MD, PhD, InflaRx: Advisor/Consultant Maria Habel, PhD, InflaRx GmbH: Employee Claus Thielert, PhD, InflaRx GmbH: Employee James Dickinson, MSc, InflaRx GmbH: Employee simon R\u00fcckinger, PhD, Metronomia Clinical Research GmbH: Advisor/Consultant Robert Zerbib, MSc, InflaRx GmbH: Advisor/Consultant Dorothee Neukirchen, PhD, InflaRx GmbH: Employee Renfeng Guo, MD, inflarx: Board Member|inflarx: I am an Inventor for Vilobelimab|inflarx: Ownership Interest|inflarx: Stocks/Bonds|InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Board Member|InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Founder|InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Employee|InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Ownership Interest Niels Riedemann, MD, PhD, InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Board Member|InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Founder|InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Employee|InflaRx GmbH, InflaRx Pharmaceuticals, Inc.: Ownership Interest"} +{"text": "Eminium intortum (Banks & Sol.) Kuntze and E. spiculatum (Blume) Schott (Araceae). A total of 83 metabolites, including 19 phenolic acids, 46 flavonoids, 11 amino, and 7 fatty acids were identified by UHPLC-HRMS in the studied extracts for the first time. E. intortum flower and leaf extracts had the highest total phenolic and flavonoid contents . Significant radical scavenging activity (32.20 \u00b1 1.26 and 54.34 \u00b1 0.53 mg TE/g for DPPH and ABTS) and reducing power (88.27 \u00b1 1.49 and 33.13 \u00b1 0.68 mg TE/g for CUPRAC and FRAP) were observed in leaf extracts. E. intortum flowers showed the maximum anticholinesterase activity (2.72 \u00b1 0.03 mg GALAE/g). E. spiculatum leaves and tubers exhibited the highest inhibition towards \u03b1-glucosidase (0.99 \u00b1 0.02 ACAE/g) and tirosinase (50.73 \u00b1 2.29 mg KAE/g), respectively. A multivariate analysis revealed that O-hydroxycinnamoylglycosyl-C-flavonoid glycosides mostly accounted for the discrimination of both species. Thus, E. intortum and E. spiculatum can be considered as potential candidates for designing functional ingredients in the pharmaceutical and nutraceutical industries.The study aimed at the metabolite profiling and evaluation of antioxidant and enzyme inhibitory properties of methanol extracts from flowers, leaves, and tubers of unexplored The search for bioactive natural compounds derived from medicinal plants is of great importance in modern medicine . NaturalEminium (Blume) Schott is a genus of the Araceae family, which includes over 300 species that grow mostly in tropical areas \u2212 at m/z 191.018 showed fragment ions at 173.008 [M-H-H2O]\u2212, 147.028 [M-H-CO2]\u2212, a base peak at m/z 111.07 [M-H-CO2-2H2O]\u2212, and was related to citric acid \u2212 at m/z 623.162 gave a base peak at m/z 299.056, corresponding to the concomitant loss of two hexoses, and was annotated as chrysoeriol 7-O-dihexoside. MS/MS spectrum of 54 [M-H]\u2212 at m/z 577.1568 showed fragment ions at m/z 431.098 [M-H-dHex]\u2212 and 413.088 [M-H-dHex-H2O]\u2212, and a base peak at m/z 269.045 [M-H-dHex-Hex]\u2212. The absence of the interglycosidic linkage breakdown is favored for 7-neohesperidoside. Thus, 54 was tentatively identified as apigenin 7-O-neohesperidoside -120]\u2212, [(M-H)-90]\u2212, and [(M-H)-30]\u2212. C-8 isomers were characterized by the base peak 0,2 X\u2212 [(M-H)-120]\u2212 as MS/MS of orientin (30), while C-6 isomers showed the base peaks [M-H]\u2212 as homoorientin (27), isovitexin (37), and chrysoeriol 6-C-hexoside (44), together with abundant fragment 0,2 X\u2212 [(M-H)-120]\u2212 (about 60%). In addition, the fragment ion 0,3 X\u2212 [M-H-90]\u2212 was favored by C-6 isomers (20 and 22 gave indicative ions at m/z 519.113 and 503.119 [(M-H)-90]\u2212, 489.103, and 473.109 [(M-H)-120]\u2212, 429.082 and 413.089 [(M-H)-120-60]\u2212, 399.072 and 383.077 [(M-H)-120-90]\u2212, 369.061 and 353.066 [(M-H)-2 \u00d7 120]\u2212, respectively. Based on 1,3 B\u2212 fragments at m/z 133.028 (20) and 117.033 (22), 20 and 22 were tentatively annotated as 6,8-C-diglucosides of luteolin and apigenin, respectively and 0,3 X1 (\u221290) or 0,2 X1 (\u2212120) at m/z 357.062 and 327.051, respectively was discernable by the fragment ions at m/z 341.067 ([(M-H)-132-90]\u2212 and 311.0561 ([(M-H)-132-120]\u2212, suggesting the presence of both O-pentosyl (X1) and C-hexosyl (X0) moieties. Additionally, the aforementioned structure was assigned on the basis of a series of fragment ions at 283.061 , 282.055 , 281.045 , and 237.055 (Among three isobars indicated as ectively . In the X0/2CO) .29 with ([M-H]\u2212 at m/z 771.179 was acquired. In (-) ESI mode, 29 yielded prominent fragment ions at m/z 447.093 [(M-H)-2 \u00d7 162.05]\u2212, 357.062 [(M-H)-2 \u00d7 162.05-90]\u2212, 327.051 ([(M-H)-2 \u00d7 162.05-120]\u2212, suggesting the presence of both O-dihexosyl and C-hexosyl moieties. The absence of the interglycosidic linkage breakdown is favored for O-sophoroside. Thus, 29 was annotated as luteolin O-sophoroside-6-C-hexosyl-orientin. Compound 32 ([M-H]\u2212 at m/z 593.151) yielded prominent ions at m/z 413.088 ([(M-H)-(162.05 + H2O)]\u2212, 353.067 ([(M-H)-(162.05 + H2O)-60]\u2212, 311.056 ([(M-H)-(162.05)-120]\u2212, 293.047 [(M-H)-(162.05 + H2O)-120]\u2212, and 281.045 Y1\u2212/0,2 X0/CH2O indicating an O-hexosyl unit at the 2\u201dof the primary hexose [32 was assigned to 2\u2033-O-hexosyl-6-C-hexosyl-apigenin and 45 ([M-H]\u2212 at m/z 799.210) shared the same fragmentation patterns yielding prominent ions at m/z 447.094 (34) and 431.098 (35), respectively, indicating a concomitant loss of hexose (162.05 Da) and sinapoyl residue (m/z 205.049 [(sinapic acid-H)-H2O]\u2212, 190.027 [(sinapic acid-H)-H2O-CH3]\u2212, and 175.003 [(sinapic acid-H)-H2O-2\u00b7CH3]\u2212. The presence of a C-hexosyl moiety on the flavonoid skeleton was deduced from the relative abundances of the ions at m/z 327.051 [M-H-120]\u2212 (79.7%) (34) and 311.056 (100%) (45) suggesting a 6-C- and an 8-C-linkage, respectively. Thus, 34 was ascribed as luteolin O-sinapoylhexosyl-6-C-hexoside, while 45 was annotated as apigenin O-sinapoylhexosyl-6-C-hexoside (Two compounds 11H10O4) . Moreovehexoside .36 and 41 were discernable by the transition [M-H]\u2212\u2192Y0 resulting from the indicative loss of 324.085 Da (C15H16O8). Precursor ions gave a series of fragment ions involved in the C-glycosyl flavon pattern: m/z 353.064 , 341.067 , 311.056 , and 283.061 (m/z 161.023 [(caffeic acid-H)-H2O]\u2212 and 133.028[(caffeic acid-H)-H2O-CO]\u2212. Accordingly, 36 and 41 were assigned to apigenin O-caffeoylhexosyl-8-C-hexoside and chrysoeriol O-caffeoylhexosyl-8-C-hexoside (Two caffeoyl esters 2 X1/CO) . Caffeoyhexoside .O-hexosyl-8-C-hexoside were deduced from the loss of feruloylhexosyl residue and the subsequent transition of m/z 447.094/431.099/461.109\u2192327.051/311.056/341.067, respectively, arising from the hexose cross ring cleavage (m/z 175.039 [(ferulic acid-H)-H2O]\u2212, 160.015 [(ferulic acid-H)-CH3]\u2212, and [(ferulic acid-H)-H2O-CH3-CO]\u2212 point out to the feruloyl moiety . The ionl moiety in the fragmentation patterns of the aforementioned compounds, accompanied with the ions at m/z 163.039 [p-coumaric acid-H]\u2212, 145.028 [(p-coumaric acid-H)-H2O]\u2212, and 117.033 [(p-coumaric acid-H)-H2O-CO]\u2212 confirmed the presence of a coumaroyl moiety (O-deoxyhexosyl-6-C-hexoside (60 and 62) were evidenced on the base of the loss of 292 Da (C15H16O6) .25, 27, 30, 35, 37, 42, 47, 50, 52, 55, 63, and 64 was confirmed by comparison with reference standards.The identification of flavonoids 71 and 73), a dipeptide (74), and six amino acid hexosides were tentatively annotated , a series of fragment ions resulting from neutral losses were registered at m/z 241.119 [M-H-H2O]\u2212, 223.108 [M-H-2H2O]\u2212, 215.140 [M-H-CO2]\u2212, 197.1287 [M-H-H2O-CO2]\u2212, and a base peak at m/z 128.033, corresponding to the loss of leucine [M-H-131.096]\u2212 from the glutamyl residue. Thus, 74 was related to \u03b3-glutamyl-leucine [66, 67, 68, 69, 70, and 72 demonstrated base peaks, resulting from the loss of a hexose moiety, with the appearance of the corresponding amino acid residue. Hence, they were annotated as hexosides of glutamic acid, valine, tyrosine, leucine, phenylalanine, and tryptophan, respectively , three monounsaturated , and five polyunsaturated free fatty acids were tentatively annotated in Eminium extracts (78\u201382) were dihydroxylated and three (75\u201377) contained three hydroxyl groups , l groups . Compounuwolffii .E. intortum and E. spiculatum methanolic extracts, we used six different methods including DPPH, ABTS cation, FRAP, CUPRAC, phosphomolybdenum, and metal chelate assays. As shown in E. intortum exhibited a much stronger antioxidant activity compared to the extracts of E. spiculatum, with values of 32.20 \u00b1 1.26 mg TE/g for leaves, 27.87 \u00b1 0.75 mg TE/g for flowers, and 26.90 \u00b1 1.61 mg TE/g for tubers. The methanolic extract of the tuber of E. spiculatum also showed good antioxidant activity with a value of 33.67 \u00b1 1.26 mg TE/g.To study the antioxidant activity of E. intortum and 86.27 \u00b1 2.74 for E. spiculatum. The methanolic extracts of the tubers and flowers of both plants showed lower antioxidant activity compared to the leaves.E. spiculatum and E. intortum showed very significant reducing activity, with values of 41.33 \u00b1 1.25 mg TE/g and 32.58 \u00b1 4.02 mg TE/g, respectively. The other extracts of both plants also showed significant results of antioxidant activity in this assay. In summary, our findings suggest that the extracts are rich in phenolic compounds with radical-scavenging activity and proton-donating ability. Polyphenols have been acknowledged for their antioxidant activity, which may account for their potential ability to prevent various diseases associated with oxidative stress. This assertion is supported by several studies [E. intortum and 61.55 \u00b1 3.97 mg EDTAE/g for E. spiculatum. It should be noted that this method is also highly specific.In the FRAP assay, a high absorbance indicates a high reducing power. The methanolic extracts of the tubers of both studies ,28,29,30The antioxidant activity of a substance is influenced by how it interacts with radicals in the reaction medium. These interactions are facilitated by active molecules that trap the radicals, and previous studies have highlighted their importance ,32,33. TEminium genus. Alkofahi et al. [E. spiculatum extract against oxidative DNA damage using the 8-hydroxydeoxyguanosine assay, while no beneficial effect on alleviating oxidative damage was observed. Al-Ismail et al. [E. spiculatum ethanolic extract using DPPH, FRAP, and vegetable oil emulsion systems, where the extract exhibited significant properties with lower IC50 values. Additionally, Janat and Al-Thnaibat [E. spiculatum exhibited higher antioxidant activity in the phosphomolybdenum assay when compared to the aqueous extract.Limited literature exists regarding the antioxidant properties of the i et al. conductel et al. reportedThnaibat reportedIn the intestinal tract, the breakdown of complex sugars into simple sugars is facilitated by two essential enzymes, namely \u03b1-amylase and \u03b1-glucosidase. The simple products, particularly glucose, are subsequently absorbed and can cause a rise in blood sugar levels. To manage diabetes, one potential therapeutic approach is to inhibit the enzymes responsible for carbohydrate hydrolysis, which can decrease postprandial blood sugar levels ,41. By iE. spiculatum also exhibited \u03b1-glucosidase inhibition, with values of 0.99 \u00b1 0.02 ACAE/g and 0.89 \u00b1 0.01 ACAE/g, respectively. Among E. intortum extracts, the leaf extract was only active against \u03b1-glucosidase (0.35 mmol ACAE/g). In addition, both tuber extracts showed no inhibitory effect on \u03b1-glucosidase. Our results demonstrate the potential of the studied leaf extracts to act as inhibitors of carbohydrate hydrolyzing enzymes. By delaying the absorption of dietary carbohydrates in the small intestine and reducing postprandial hyperglycemia, these inhibitors may be a valuable component in the development of antidiabetic drugs. This mechanism of action has been previously reported [reported ,46,47.Our study is the first to investigate the antidiabetic activity of the two plants, and we found that all studied extracts of the plants inhibited \u03b1-amylase activity, with values lower than 0.31 \u00b1 0.01 ACAE/g. The inhibitory effect of phenolic compounds on carbohydrate hydrolysis enzymes has been reported previously ,49,50, aAcetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are enzymes found primarily in nerve tissues and neuromuscular junctions. They are responsible for rapidly hydrolyzing acetylcholine, a neurotransmitter, into inert choline and acetate. Overexpression or excessive catalysis of AChE can cause neuronal disturbances and lead to neurological disorders. A potential strategy for neuroprotection is to inhibit AChE activity ,52,53. OE. spiculatum and E. intortum tubers exhibited strong inhibitory activity with values of 50.73 \u00b1 2.29 KAE/g and 48.13 \u00b1 0.24 KAE/g, respectively. Natural compounds capable of inhibiting tyrosinase activity are of great interest, with increasing demand in the fields of cosmetics and pharmaceuticals [In skin cells, tyrosinase plays a crucial role in the aging process, and inhibiting its activity is a key strategy for delaying skin aging. This enzyme catalyzes the initial two steps of melanogenesis, making it a rate-limiting factor in this process. Mutations in the tyrosinase gene or its absence can cause a reduction or cessation of pigmentation ,58. In oeuticals ,60. Numeeuticals ,63,64,65E. spiculatum. In contrast, the flower and leaves of E. intortum were grouped into Cluster III and IV, respectively was mainly associated with antioxidant assays and AChE. The second component (PC2) contained amylase, BChE, and tyrosinase, while the third component (PC3) included glucosidase and DPPH B. Althouectively C.E. spiculatum, which contained high levels of chrysoeriol O-coumaroylhexoside-8-C-hexoside, luteolin-6,8-C-diglucoside, and apigenin 7-O-synapoylhexosyl-8-C-hexoside. The leaves and flowers of E. intortum were classified in Cluster II, which were characterized by high levels of luteolin 7-O-coumaroylhexosyl-6-C-hexoside and apigenin O-feruloylhexosyl-8-C-hexoside. Cluster III contained both tuber samples. Furthermore, we conducted a correlation analysis between the biological activities and individual components, and the results are shown in C-hexoside-8-C-pentoside was the main contributor to DPPH scavenging ability, while sinapic acid-O-dihexoside and isorhamnetin-3-O-rutinoside were positively correlated with ABTS and CUPRAC. Consistent with our findings, the compounds have been described as important antioxidants by several researchers [The classifications of the tested extracts based on their chemical components is presented in earchers ,67,68. Aearchers .Eminium species in Turkey (Eminium intortum (Banks & Sol.) Kuntze: Between K\u0131z\u0131ltepe and Mardin, 533 m, GPS: 37\u00b014\u203220\u2033 N, 40\u00b038\u203210\u2033 E; Eminium spiculatum (Blume) Schott: Derik, Mardin, 661 m, GPS: 37\u00b018\u203244\u2033 N, 40\u00b016\u203216\u2033 E). The plant specimens were identified by one of our co-authors, Dr. Ugur Cakilcioglu, and one specimen from the plants was deposited at the Harran University herbarium. Prior to extraction, the plant materials were carefully washed with tap and distilled water to eliminate any soil and contaminants. After being air-dried for 10 days (in shade at room temperature), the flowers, leaves, and roots were powdered.In the summer of 2021, we collected For extraction, we employed the maceration method, in which 5 g of plant material was mixed with 100 mL of methanol and left to macerate at room temperature for 24 h. After maceration, the extracts were filtered through Whatman filter paper, and the solvents were evaporated using a rotary-evaporator. To preserve the extracts, we stored them at 4 \u00b0C until analysis.p-coumaric, o-coumaric, ferulic acids, saponarin, homoorientin, orientin, rutin, isovitexin, isoquercitrin, luteolin 7-O-glucoside, kaempferol 3-O-rutinoside, kaempferol 3-O-glucoside, isorhamnetin 3-O-glucoside, apigenin 7-O-glucoside, quercetin, and apigenin. Chlorogenic and caffeic acids were supplied from Phytolab .Acetonitrile (hypergrade for LC\u2013MS), formic acid (for LC\u2013MS) and methanol were purchased from Merck . The reference standards used for compound identification were obtained from Extrasynthese for We determined the total phenolic and flavonoid content of the extracts using the Folin\u2013Ciocalteu and AlCl3 assays, respectively, according to Zengin and Aktumsek\u2019s protocol (2014). The results of these tests were reported in terms of gallic acid equivalents (mg GAE/g dry extract) and rutin equivalents (mg RE/g dry extract) .m/z range from 100 to 1000. The mass spectrometer parameters were as follows: spray voltage 3.5 kV (+) and 2.5 kV (\u2212); sheath gas flow rate 38; auxiliary gas flow rate 12; spare gas flow rate 0; capillary temperature 320 \u00b0C; probe heater temperature 320 \u00b0C; S-lens RF level 50; scan mode: full MS , and MS/MS . The chromatographic separation was achieved on a reversed phase column Kromasil EternityXT C18 at 40 \u00b0C. The UHPLC analyses were run with a mobile phase consisting of 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile (B). The run time was 33 min. The flow rate was 0.3 mL/min. The gradient elution program was used as follows: 0\u20131 min, 0\u20135% B; 1\u201320 min, 5\u201330% B; 20\u201325 min, 30\u201350% B; 25\u201330 min, 50\u201370% B; 30\u201333 min, 70\u201395%; 33\u201334 min 95\u20135% B. Equilibration time was 4 min [The UHPLC-HRMS analyses were carried out on a Q Exactive Plus mass spectrometer equipped with a heated electrospray ionization (HESI-II) probe (ThermoScientific). The equipment was operated in negative and positive ion modes within the as 4 min . Data weas 4 min .We analyzed the extracts for a range of antioxidant and enzyme inhibitory activities, including, cupric reducing antioxidant capacity (CUPRAC), DPPH, and ABTS radical scavenging, metal chelating activity (MCA), ferric reducing antioxidant power (FRAP), phosphomolybdenum (PBD), and inhibition of amylase, tyrosinase, glucosidase, acetylcholinesterase (AChE), and butyrylcholinesterase (BChE). We employed the previously described methods to evaluate these activities . Each sap < 0.05). Then, Principal Component Analysis (PCA) and hierarchical clustered analysis (HCA) were performed to emphasize the distinct clusters in terms of their bioactivities. Furthermore, hierarchical clustered analysis (HCA) was performed to assess the (dis)similarity between samples in terms of their molecules. All used data were scale and molecules data and were log transformed before doing multivariate analysis. R v.4.2.3 statistical program was used for all analyses.All data were given as mean \u00b1 standard deviation (SD). Statistical analysis was performed by analysis of variance (ANOVA). A post hoc test (Tukey) was performed when the differences shown by data were significant varied according to the plant parts used. Generally, the leaf extract of both species exhibited higher antioxidant effects compared to flowers and tubers. However, we obtained different results for each enzyme inhibition assay, and the leaf extracts provided good anti-amylase and anti-glucosidase actions. The extracts were rich in flavonoids. These findings provide a valuable scientific basis for evaluating the potential of the Eminium genus and suggest that the tested species could be considered as a source of natural bioactive agents for health-promoting applications. Nevertheless, additional research is necessary to elucidate the potential toxicity of both the extracts and the individual chemical constituents.In our study, we explored the detailed chemical composition and biological effects of two"} +{"text": "Pseudomonas aeruginosa.To evaluate the efficacy of ceftazidime-avibactam (CZA) and aztreonam-avibactam (AZA) against bloodstream infections (BSIs) or lower respiratory tract infections (LRTIs) \u2013 caused by extensive drug-resistant or pan drug-resistant (XDR/PDR) P. aeruginosa. Whole-genome sequencing was used to analyze the resistance determinants of each isolate. Monte Carlo simulations (MCSs) were used to evaluate the probability of target attainment (PTA) and the cumulative fraction of response (CFR) of each CZA/AZA dosing regimen via traditional infusion (TI)/optimized two-step-administration therapy (OTAT).The two-fold dilution method was used to determine the minimum inhibitory concentrations (MICs) of CZA/AZA against XDR/PDR P. aeruginosa isolates producing IMP-45, VIM-1, or VIM-2 were inhibited by AZA at a concentration of 2 to 8 mg/L. All isolates producing IND-6 plus other serine \u03b2-lactamases were high-level resistant to CZA/AZA (MICs >64 mg/L). All simulated dosing regimens of CZA/AZA against BSIs-causing XDR/PDR P. aeruginosa achieved 100% PTA when the MIC was \u226432 mg/L.We found that XDR/PDR P. aeruginosa may carry some rare MBLs . P. aeruginosa producing IMP-45, VIM-1, or VIM-2. OTAT with sufficient pharmacodynamic exposure may be an optimal treatment option for XDR/PDR P. aeruginosa with a high-level MIC of CZA/AZA.AZA has been considered as an option for the treatment of infections caused by XDR/PDR P. aeruginosa displays resistance to various antibiotics, making treatment challenging . CZA has good safety and was regarded as a vital treatment option for P. aeruginosa infections. CZA showed good capabilities against P. aeruginosa with a sensitivity rate ranging from 76.2% to 97.8% (P. aeruginosa infections ranged from 64.3% to 90.6% (Ceftazidime/avibactam (CZA) is a novel \u03b2-lactam/\u03b2-lactamase inhibitor (BL/BLIs). And it was approved by the Chinese National Medical Products Administration (CNMPA) in 2019 for the treatment of complicated intra-abdominal infections (cIAIs), hospital-acquired pneumonia (HAP), and ventilator-associated pneumonia (VAP), and in adult patients with limited treatment options for infections caused by the following gram-negative bacteria sensitive to this product: to 97.8% . In termto 90.6% .\u03b2-lactamases against which ATM is ineffective. Avibactam (AVI) is a \u03b2-lactamase inhibitor with a wide enzyme inhibition spectrum, including Ambler class A , class C (AmpC), and class D (OXA-48 type) \u03b2-lactamase. The combination of ATM and AVI can potentially inhibit MBL-producing bacteria (Aztreonam (ATM) was the first monobactam antibiotic to be used in clinical therapy. It was approved by the U.S. Food and Drug Administration (FDA) in 1986 for treatment of various infections caused by sensitive aerobic gram-negative bacteria. ATM was stable to hydrolysis by Ambler class B Metallo-\u03b2-lactamases (MBLs) . Howeverbacteria .P. aeruginosa in this study. Whole-genome sequencing and bioinformatic analysis were used to identify resistance genes of each isolate. Besides, we combine the population pharmacokinetic parameters (PPKs) of CZA/AZA with minimum inhibitory concentration (MIC) distribution of XDR/PDR P. aeruginosa to evaluate the efficacy of various dosing regimens. Therefore, the objectives of our work are as follows. Firstly, our work aims to compare the in vitro activity of CZA and AZA against XDR/PDR P. aeruginosa. Secondly, our team wants to evaluate the relationship between resistance genes and CZA/AZA sensitivity rates of XDR/PDR P. aeruginosa. Thirdly, we assess the efficacy of CZA and AZA for the treatment of critically ill patients with BSIs/LRTIs caused by XDR/PDR P. aeruginosa.We performed antimicrobial susceptibility testing (AST) on XDR/PDR 22.1P. aeruginosa from critically ill patients admitted to the First Medical Centre of Chinese PLA General Hospital from January 2016 to November 2021. A total of 10 P. aeruginosa strains were categorized as XDR according to CLSI criteria. Moreover, 57 P. aeruginosa strains were categorized as PDR . Ceftazidime, avibactam, and aztreonam standards were purchased from MedChemExpress. The resistance rates of XDR/PDR Pseudomonas aeruginosa to cefoperazone-sulbactam, imipenem, ciprofloxacin, piperacillin-tazobactam, ceftazidime, levofloxacin, meropenem, tobramycin, amikacin and gentamicin were 89.6%, 100%, 89.6%, 100%, 97%, 89.6%, 100%, 97.1%, 100%, 100%, respectively.We collected 67 d as PDR . All P. 2.2P. aeruginosa. A fixed concentration of AVI at 4 mg/L, 8mg/L, and 16mg/L combined with 2-fold diluted CAZ and ATM were used in ASTs. The quality control strains of our tests were E. coli ATCC 25922 and P. aeruginosa ATCC 27853. The MICs are defined as the lowest concentration of antibiotics that inhibits the growth of bacteria. The definition of MIC50 is a drug concentration that inhibits the growth of bacteria by 50%. Similarly, MIC90 is a drug concentration inhibiting 90% of bacterial growth. MIC distributions of CZA/AZA against P. aeruginosa were represented by cumulative inhibition rates (CIRs). Besides, all experiments were conducted three times following Clinical and Laboratory Standards Institute (CLSI) standards.We used the broth two-fold dilution method to determine the minimum inhibitory concentrations (MICs) of CZA/AZA against XDR/PDR 2.3P. aeruginosa were subjected to whole-genome sequencing (WGS) using Illumina MiSeq short-read sequencing . Sequenced isolates were evaluated using FASTQC, version 0.11.6, and MultiQC, version 1.6. Trimmomatic, version 0.39, removed adapters and trimmed low-quality paired end reads. Comprehensive Antibiotic Resistance Database v.1.2.0 was used to identify drug resistance genes in the strains.67 2.4fT > MIC is the best indicator for assessing BSIs. Besides, %50fT > 5 \u00d7 MIC is the best indicator for assessing LRTIs. When combined with CAZ, %50fT > CT of 1 mg/L was considered the Pharmacokinetic (PK)/Pharmacodynamics (PD) target of avibactam. PK/PD targets of ATM for BSIs was %60fT > MIC. And PK/PD targets of ATM for LRTIs were %60fT > 5 \u00d7 MIC. As for avibactam, %50fT > CT of 2.5 mg/L was considered appropriate for guiding dosage selection for AZA (fT > n \u00d7 MIC equation was based on previous studies (Population pharmacokinetic (PPK) parameters of CZA and AZA were obtained from previously published articles . CAZ is for AZA . Optimiz studies .2.5d, CL, t1/2) followed a log-normal distribution. All simulated dosing regimens via traditional infusion (TI)/optimized two-step-administration therapy (OTAT) were listed in MICi means each MIC value. p(MICi) means the percentage of each MIC value. A CFR \u2265 90% is adequate PD exposure for this dosing regimen.We conducted 10000-patient Monte Carlo simulations (MCSs) using Oracle Crystal Ball version.11.1.24. PK parameters were listed in P. aeruginosa with an OXA-101 also produced OXA-850. CZA was as effective as AZA against these isolates. For isolates with an OXA gene plus IMP-45, VIM-1, or VIM-2, AZA was much more potent than CZA against these isolates, with all isolates being inhibited by a concentration of 8 mg/L. For isolates with an IND-6 plus more serine \u03b2-lactamases, all isolates produced CZA/AZA MICs of >64 mg/L. For XDR/PDR P. aeruginosa with other genotypes, the efficacy of CZA against these isolates did not differ significantly from that of AZA.The comparative MICs (mg/L) of CZA and AZA against 67 XDR/PDR 3.43.4.1The probability of target attainment (PTA) of each simulated dosing regimen for BSIs was listed in 3.4.2The PTA of each simulated dosing regimen for LRTIs was listed in 3.53.5.1via traditional infusion, the CFR was 95.63% for 4g q6h. If CZA was administered via OTAT, the CFR was 96.67% for 1.25g (0.5h) +1.25g (2h) q8h, 97.35% for 1.25g (0.5h) +1.25g (2h) q6h, 93.60% for 0.675g (0.5h) +0.675g (2h) q8h and 93.53% for 0.675g (0.5h) +0.675g (2h) q8h. If AZA was administered via traditional infusion, the CFR was 92.50% for 2.5g q6h and 96.36% for 4g q6h. If AZA was administered via OTAT, the CFR was 96.95% for 1.25g (0.5h) +1.25g (2h) q8h, 98.25% for 1.25g (0.5h) +1.25g (2h) q6h. The above dosing regimens are considered to provide adequate PD exposures for the treatment of CZA/AZA against XDR/PDR P. aeruginosa BSIs.The cumulative fraction of response (CFR) of each simulated dosing regimen for BSIs was listed in 3.5.2P. aeruginosa. CFRs were less than 90% for all simulated dosing regimens + 1.25 g (2h)] q6h, 2.5 g q8h, 4g q6h, 4g q8h).4P. aeruginosa has spread widely worldwide and the treatment of BSIs or LRTIs caused by XDR/PDR P. aeruginosa has become a tough problem . AVI is ineffective against MBL-producing isolates. However, the combination of AVI and ATM was a treatment option for MBL-producing isolates. Lee et\u00a0al. also found that the combination of ATM and CZA may be a treatment option for VIM-2-producing P. aeruginosa . IND-6 is a highly divergent IND-type MBL. It was first isolated from Chryseobacterium indologenes strain 597 in Burkina Faso . Besidesutations . Mobile fections . Our worinfusion . Besideshe blood .P. aeruginosa was confined to a small sample size and northern China. Secondly, our study only focused on partial beta-lactamases (class B \u03b2-lactamases and class D \u03b2-lactamases). Therefore, large-scale animal or clinical trials are needed in the future to confirm the efficacy of CZA/AZA against BSIs caused by XDR/PDR P. aeruginosa.Our study had several limitations that should be noted. Firstly, the collection of P. aeruginosa are intrinsic, mutational, and horizontally acquired resistomes (P. aeruginosa drug resistant. The efflux pump was also considered in the study of this article (see the whole genome sequencing results in the The main resistance mechanisms in sistomes . We founP. aeruginosa harbouring IMP-45, VIM-1, or VIM-2. Secondly, OTAT with sufficient PD exposure may be an optimal treatment option for BSI caused by XDR/PDR P. aeruginosa with a high-level MIC of CZA/AZA.In conclusion, our work has the following results. Firstly, AZA was considered as an option for the treatment of XDR/PDR The original contributions presented in the study are publicly available. This data has been deposited into the NCBI repository under accession: PRJNA967114.Ethical approval was granted by the Chinese People\u2019s Liberation Army General Hospital.YK and JC designed and managed the project. YK performed all\u00a0the experiments and wrote the manuscript. LX analyzed bioinformatics analysis. JY provided technical guidance. All\u00a0authors contributed to the article and approved the submitted version."} +{"text": "Two novel reassortant highly pathogenic avian influenza viruses (H5N1) clade 2.3.4.4b.2 were identified in dead migratory birds in China in November 2021. The viruses probably evolved among wild birds through different flyways connecting Europe and Asia. Their low antigenic reaction to vaccine antiserum indicates high risks to poultry and to public health. Since the Gs/GD/96-lineage highly pathogenic avian influenza virus (HPAIV) (H5N1) was identified in 1996, H5 HPAIVs have evolved into divergent clades and caused continuous outbreaks in birds (https://wahis.woah.org/#/event-management). Human cases of H5N1/H5N6/H5N8 infection were sporadically documented , highlighting the zoonotic risk of H5 HPAIVs. Since 2021, H5 HPAIVs have caused at least 9 outbreaks in wild birds rather than poultry in mainland China . However, large outbreaks of H5N1 HPAIVs in domestic poultry were reported during 2021\u20132022 in Europe and the United States . In this study, we explored the genetic origin, spread patterns, and antigenicity of H5N1 viruses identified from 2 dead migratory birds in China.Starting during 2020\u20132021, a new wave of HPAIV H5N1/H5N8 clade 2.3.4.4b outbreaks was reported in wild and domestic birds in Eurasia (http://www.mabsky.com).We collected oral swab specimens and lung tissues from a dead whooper swan in northern China (Inner Mongolia) on November 3, 2021, and a deceased black swan in eastern China (Zhejiang) on November 15, 2021. We performed virus isolation in 10-day-old specific pathogen-free chicken embryos and GISAID . We reconstructed phylogenetic trees for each gene of the 3 H5N1 isolates together with reference viruses from GISAID and the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi), using the maximum-likelihood method with a general time-reversible model plus gamma distribution in RAxML 8.2.12 (https://cme.h-its.org/exelixis/web/software/raxml) , A/whooper swan/Northern China/11.03 IMEEDSAK2-O/2021 (Ws/NC/AK2-O/2021), and A/black swan/Eastern China/11.15 ZJHZ74-Lg/2021 (Bs/EC/74-Lg/2021). We deposited whole genomes in NMDC (e/raxml) Table. We/raxml) .https://www.who.int/publications/i/item/manual-for-the-laboratory-diagnosis-and-virological-surveillance-of-influenza) to test the reactivities of antiserum of H5 Re-11/Re-13/Re-14 vaccines against these new H5N1 isolates and H5N8 HPAIVs identified in 2020 (http://www.moa.gov.cn/govpublic).We performed hemagglutination inhibitor (HI) assays ; however, they have only been identified in wild birds in mainland China. Compared with high HI antibody titers (256) between homologous antiserum and antigens of H5 vaccines, the recent H5N1/H5N8 viruses presented low HI titers (2\u201316) against Re-11/Re-13 antiserum and Bs/2021-like (Bs/EC/74-Lg/2021) reassortants Figure 4We reconstructed the genetic reassortment history for these H5N1 viruses clade 2.3.4.4b reassortants in migratory birds, China.Additional information for study of novel avian influenza virus (H5N1) clade 2.3.4.4b reassortants in migratory birds, China."} +{"text": "Integrase strand-transfer inhibitors (INSTIs) are associated with body weight gain among women living with HIV (WLH) in the Women\u2019s Interagency HIV Study (WIHS). The role of antiretroviral therapy (ART) pharmacokinetics in INSTI-associated weight gain is unknown. We report the relationship between INSTI plasma concentrations and weight change in WLH.Model-adjusted estimates of percent body weight change by integrase inhibitor plasma concentrationModel-adjusted estimates of percent body weight change with 95% confidence band (y-axis) by integrase inhibitor plasma concentration in ng/mL (x-axis). Models were adjusted for baseline age, race/ethnicity, baseline obesity (body mass index \u2265 30 kg/m2), history of prior non-nucleoside reverse transcriptase use, and self-reported antiretroviral therapy adherence (100% vs <100%). Abbreviations: RAL=raltegravir, DTG=dolutegravir, EVG=elvitegravirData from 2006-2017 were analyzed from virologically suppressed (< 200 copies/mL) WLH in the WIHS who switched/added raltegravir (RAL), dolutegravir (DTG), or elvitegravir (EVG) to ART. Percent body weight change was calculated using weights obtained 6-12 months pre- and post- INSTI switch/add. INSTI random plasma concentrations were measured with validated LC/MS-MS assays 6-12 months post INSTI switch/add. Area under the curve (AUC) was calculated using estimates from published models and updating individual-level parameters with plasma concentrations. Linear models assessed the relationship between plasma concentrations or AUC and weight change for each INSTI separately. Models were adjusted for age, race/ethnicity, baseline obesity, history of non-nucleoside reverse transcriptase use, and self-reported ART adherence.2 (\u00b18.8), and 57% reported 100% ART adherence. Mean percent body weight change was +2.3% (\u00b16.0) for RAL, +1.8% (\u00b19.0) for DTG, and +2.8% (\u00b110.5) for EVG. AUC was able to be calculated in 167 (95%) of women. In adjusted linear models, higher RAL plasma concentration was associated with greater percent body weight change (p=0.016), Figure 1. No association of drug AUC with body weight change for any INSTI was observed.176 WLH contributed plasma drug concentrations with a mean \u00b1SD 1.5 (\u00b10.1) years follow-up: 43 (24%) were on RAL, 87 (49%) on DTG, and 47 (27%) on EVG. Mean age was 51 years (\u00b1 9), 64% were Non-Hispanic Black, baseline BMI was 31.6 kg/mIn WLH, random RAL plasma concentrations, but not the RAL AUC, was associated with body weight gain. In contrast, the effect of DTG and EVG plasma drug exposure on short-term body weight change appears to be limited. Mechanisms contributing to body weight gain may be INSTI-specific. In addition to further pharmacologic assessments, other mechanisms to explain INSTI-associated weight gain should be examined.Cecile D. Lahiri, MD, MS, Merck: Grant/Research Support|Theratechnologies, LLC: Advisor/Consultant|Theratechnologies, LLC: Honoraria Julie B. Dumond, PharmD, Merck: Grant/Research Support Cyra Christina Mehta, PhD, MSPH, Merck: Grant/Research Support Igho Ofotokun, MD, MSc, FIDSA, Merck: Grant/Research Support Maria L L. Alcaide, MD, Discidium Biosciences: Board Member|Gilead: Honoraria|Merk & Co: Honoraria|Senhwa Biosciences: Honoraria|Virology Education: Honoraria Jordan Lake, MD, Gilead Sciences: Grant/Research Support|Theratechnologies: Advisor/Consultant Phyllis C. Tien, MD, MSc, Merck: Grant/Research Support"} +{"text": "Rheumatology key messageVEXAS syndrome is venulitis with severe thickening of the walls of large veins.Dear Editor, VEXAS syndrome is an often fatal, X-linked disease characterized by haematological dysplasia overlapping with severe autoinflammatory manifestations. Acquired somatic mutations of the ubiquitin-like modifier activating enzyme (UBA1) gene impairs ubiquitylation, causing activation of the innate immune system and release of pro-inflammatory cytokines, TNF-\u03b1, IL-8, IL-6, IFN-\u03b3 and IFN-inducible protein-10 (IP-10) that culminate in severe systemic inflammation , which is independent of age, disease duration, history of thrombosis and major organ involvement, disease activity, acute phase response and corticosteroid treatment [s.d. 0.1)] but not significant with APS [0.49\u2009mm (s.d. 0.1)] [Rheumatology online).Previous studies have shown that venous inflammation causes VWT . Varicosm s.d. 0.4 vs 0.27reatment . Additiom s.d. 0.4 vs 0.27The pathogenesis of organ inflammation in VEXAS syndrome is not entirely understood. UBA1 is essential for the initiation of ubiquitylation, a widely used post-translational protein modification mechanism that regulates many biological processes, including intracellular signalling, proteasomal/lysosomal protein degradation and antimicrobial defence . Consequkead168_Supplementary_DataClick here for additional data file."} +{"text": "Correction to: Clinical Proteomics (2022) 19:4810.1186/s12014-022-09385-7Unfortunately, in the original publication of the article, the following errors were identified after online publication of the article.The Additional file In Abstract, line 11, the text that reads as \u201cphospho-heavy-labeled-spiketide FAIMS Stepped-CV DDA (pHASED)\u201d should read as \u201chospho-heavy-labeled-spiketide FAIMS stepped-CV DDA (pHASED)\u201d.The original article has been corrected.Additional file 2: Table S1. SBDS heavy-labeled phosphorylated peptide standards. Table S2. Common and unique phosphoproteins identifed across all four CVs based on PSM acquisition. Table S3. High confdence modifcation sites identifed in LFQ (p < 0.01). Table S4. High confdence modifcation sites identifed in pHASED (p < 0.01). Table S5. Unique and common phosphoproteins identifed in LFQ and pHASED datasets. Table S6. Phosphorylated master protein kinases identifed in LFQ dataset (p < 0.01). Table S7. Phosphorylated master protein kinases identifed in pHASED dataset (p < 0.01). Table S8. FLT3-D835 mutations associated with resistance to tyrosine kinase FLT3 inhibitors. Table S9. Kinase-Substrate analysis of LFQ dataset for resistant cells in comparison to FLT3-ITD (log2 fold change\u00b10.5). Table S10. Kinase-Substrate analysis of pHASED data?set for resistant cells in comparison to FLT3-ITD (log2 fold change\u00b10.5). Table S11. Canonical pathways identifed as signifcantly associated with LFQ dataset for resistant cells in comparison to FLT3-ITD. Table S12. Canonical pathways identifed as signifcantly associated with pHASED dataset for resistant cells in comparison to FLT3-ITD. Table S13. Kinase activity inferred by KSEA analysis of phosphorylation changes in pHASED dataset for resistant cells in comparison to FLT3-ITD. Table S14. Mutation-specifc response to sorafenib. IC50 compared to FLT3-ITD. Table S15. Bliss Synergy scores for sorafenib in combination with KU-60019 at diferent doses. Table S16. Unique ATM substrates identifed with increased phosphorylation (log2\u22650.5) in pHASED dataset for resistant cells in comparison to FLT3-ITD. Table S17. Vector mutations in FLT3 gene."} +{"text": "Correction to: Sport Sciences for Health 10.1007/s11332-022-01012-0The reference no. 4 has been incorrectly published in the original publicaiton. The complete correct reference [4] is given below.Coronavirus disease (COVID-19): the need to maintain regular physical activity while taking precautions. J Sport Health Sci 9(2):103.4. Chen P et al (2020)"} +{"text": "Korean J Women Health Nurs 2023;29(1):66-75.https://doi.org/10.4069/kjwhn.2023.03.15This corrigendum is for correcting a reference that was mistakenly reported in the above article.4. Pereira-Kotze C, Feeley A, Doherty T, Faber M. Maternity protection entitlements for non-standard workers in low-and-middle-income countries and potential implications for breastfeeding practices: a scoping review of research since 2000. Int Breastfeed J. 2023;18(1):9. https://doi.org/10.1186/s13006-023-00542-8The corrected reference is as below. The authors apologize for any inconvenience that this may have caused.4. Brandhagen M, Lissner L, Brantsaeter AL, Meltzer HM, H\u00e4ggkvist AP, Haugen M, et al. Breast-feeding in relation to weight retention up to 36 months postpartum in the Norwegian Mother and Child Cohort Study: modification by socio-economic status? Public Health Nutr. 2014;17(7):1514-1523. https://doi.org/10.1017/s1368980013001869."} +{"text": "Cytomegalovirus (CMV) infection is associated with significant morbidity and mortality among kidney transplant recipients (KTR). Given toxicities and costs of antivirals, there is growing interest in assays that measure CMV-specific T-cell immunity (TCI), which may predict protection against clinical infection. The Viracor\u00ae CMV TCI Panel (TCIP) uses flow cytometry and intracellular cytokine staining to measure %CMV-specific CD4+ and CD8+ T-cells; it is the only commercially available TCI assay in the US. In this investigator-initiated study, we evaluated the performance of the TCIP in predicting clinically significant CMV events. To our knowledge, this is the first prospective blinded clinical study of the TCIP.We enrolled consecutive donor (D) or recipient (R) CMV seropositive KTR, who had TCIP testing monthly until either discontinuation of valganciclovir prophylaxis or the primary outcome. We also enrolled KTR with low-level untreated DNAemia, or after completion of valganciclovir treatment, to evaluate assay predictive values for progression or relapse of CMV infection, respectively. The primary outcome was CMV DNAemia (tested at the discretion of the treating provider for symptoms or laboratory findings), prompting treatment initiation. Secondary outcomes were any DNAemia and DNAemia >1000 IU/mL. Treating providers were unaware of TCIP results.p=0.024), and the CMV protection ROC AUC was significant . The positive predictive values of both CD4+ and CD8+ T-cell positivity >0.2% for CMV protection were 96.3% (95%CI 81-99.9%) for the primary outcome, 92.6% (95%CI 75.7-99.1%) for any DNAemia, and 100% (one-sided 95%CI 87.2%) for DNAemia >1000 IU/mL.We included 46 KTR. Median age was 50.5 (range 18-74) years. 73.6% identified as men, 10.8% Black, 8.7% Hispanic; 41.3% had CMV D+/R- status. KTR with CMV events had significantly lower %CMV-specific CD8+ T-cells (5R25AI140490) Dimitrios Farmakiotis, M.D., Astellas: Grant/Research Support|Merck: Grant/Research Support|Viracor: Advisor/Consultant|Viracor: Grant/Research Support"} +{"text": "QTRL.caas-4A.1 and QTRL.caas-4A.2), TRA (QTRA.caas-4A and QTRA.caas-4D), and NRT (QNRT.caas-5B and QNRT.caas-5D) were identified and each explaining 5.94%\u20139.47%, 6.85%\u20137.10%, and 5.91%\u201310.16% phenotypic variances, respectively. Among these, QTRL.caas-4A.1 and QTRA.caas-4A overlapped with previous reports, while QTRL.caas-4A.2, QTRA.caas-4D, QNRT.caas-5B, and QNRT.caas-5D were novel. The favorable alleles of QTRL.caas-4A.1, QTRA.caas-4A, and QTRA.caas-5B were contributed by Doumai, whereas the favorable alleles of QTRL.caas-4A.2, QTRA.caas-4D, and QTRA.caas-5D originated from Shi 4185. Additionally, two competitive allele-specific PCR (KASP) markers, Kasp_4A_RL (QTRA.caas-4A) and Kasp_5D_RT (QNRT.caas-5D), were developed and validated in 165 wheat accessions. This study provides new loci and available KASP markers, accelerating wheat breeding for higher yields.Identifying loci for root system architecture (RSA) traits and developing available markers are crucial for wheat breeding. In this study, RSA-related traits, including total root length (TRL), total root area (TRA), and number of root tips (NRT), were evaluated in the Doumai/Shi4185 recombinant inbred line (RIL) population under hydroponics. In addition, both the RILs and parents were genotyped using the wheat 90K single-nucleotide polymorphism (SNP) array. In total, two quantitative trait loci (QTLs) each for TRL ( Wheat production is influenced seriously by abiotic stresses. Breeding higher-yielding and more stable accessions under abiotic stress is a crucial objective in modern wheat breeding . Root syPrevious breeding programs predominantly focused on aboveground traits such as disease resistance, grain quality, and harvest index, while the application of RSA traits has been limited due to the complexity of phenotypic evaluation . PreviouIn this study, we conducted linkage mapping for RSA traits using the wheat 90K assays in a biparental recombinant inbred line (RIL) population derived from the Doumai/Shi 4185 cross. The primary objective of this study is to uncover the genetic basis of these traits and develop available KASP markers for improving wheat RSA.2:6 RILs derived from the Doumai/Shi 4185 were used for evaluating RSA-related traits. A hydroponic experiment was conducted with three replicates in a greenhouse. There were 20 seeds from each line that were surface sterilized with10% H2O2 for 20\u00a0min. Subsequently, the cleaned seeds were placed in Petri dishes with moist filter paper. When the coleoptiles reached about 2\u00a0cm in length, wheat seedlings were transferred to plastic trays (53 \u00d7 27\u00a0cm) containing Hoagland\u2019s nutrient solution. Plastic trays were kept in 25\u00b0C with a 16-h light and 8-h darkness cycle. After 3 weeks, roots were evaluated for RSA-related traits .Three RSA-related traits, namely, total root length (TRL), total root area (TRA), and number of root tips (NRT), were assessed using the WinRHIZO root analysis system (LA6400XL). The roots were arranged systematically in a dish and scanned using the Expression 11000XL. Subsequently, the images were imported into WinRHIZO software and analyzed using a fixed threshold parameter of 40. Each accession was scored on five plants for RSA traits, and means of three replicates were obtained. Basic statistical analyses and frequency distributions were conducted using SAS v9.3 by CapitalBio Corporation. SNPs with missing data >20% or minor allele frequency (MAF) <0.5 were filtered for further analysis. The filtered SNPs were then analyzed using the BIN function of IciMapping v4.2 and grouThe inclusive composite interval mapping (ICIM) method using IciMapping v4.1 was applQTRL.caas-4A.1, QTRA.caas-4A, and QNRT.caas-5D) were converted to KASPs (http://www.polymarker.info/) (SNPs flanking QTL with higher PVE (to KASPs and desir.info/) Table S2r.info/) .https://wheat.pw.usda.gov/GG3/). Genes, excluding hypothetical proteins, transposon proteins, and retrotransposon proteins with SNPs in the coding region, were considered as candidate genes. Quantitative real-time PCR (qRT-PCR) was conducted to test expression differences of the candidate genes between Doumai and Shi 4185. The roots were sampled for RNA extraction after phenotyping. RNA was extracted using the TRIzol method, and the cDNA was synthesized with the HiScript II 1st Strand cDNA Synthesis Kit. Primers were designed using the Primer Premier V5.0. PCR was conducted with a mixture of 20 \u03bcl, including 2 \u03bcl cDNA, 10 \u03bcl ChamQ Universal SYBR qPCR Master Mix, and 0.4 \u03bcl of each primer. qRT-PCR was conducted in the ABI StepOnePlus Real-Time PCR System with Tower, and the gene expression level was analyzed by the 2\u2013\u0394\u0394CT method. All assays were performed in two biological replicates and three technical replicates. TaActin1 was used as the internal control to normalize the expression levels of different samples.To identify candidate genes involved in the QTL for RSA-related traits detected in the Doumai/Shi 4185 RIL population, the genes located in the LD block region around the peak SNP of each QTL were extracted from the wheat IWGSC v1.1 annotation (2 (range: 6.9 cm2\u201315.2 cm2), and 328.2 root tips (range: 94.7\u2013772.0). The standard deviation and coefficient of variation for TRL, TRA, and NRT were 18.1\u00a0cm (24.2%), 1.7 cm2 (16.4%), and 126.4 (38.5%), respectively. A significant correlation was observed between TRL, TRA, and NRT, with the correlation coefficient of 0.603 (P < 0.05) between TRL and TRA, 0.371 (P < 0.05) between TRL and NRT, and 0.312 (P < 0.05) between TRA and NRT.All three RSA-related traits exhibited continuous and significantly wide variation across the 262 RILs (QTRL.caas-4A.1 (BobWhite_c20306_147-Tdurum_contig54973_1510) and QTRL.caas-4A.2 (BS00059454_51-Kukri_c19883_816), respectively. These QTLs explained 5.94% (additive effect: 5.17) and 9.45% (additive effect: \u22127.12) of the total phenotypic variances and QTRL.caas-4D (Ex_c6665_1067-wsnp_J-D_rep_c51623_35119179), respectively, explaining 7.10% (additive effect: 0.40) and 6.85% (additive effect: \u22120.39) of the total phenotypic variance. The favorable allele of QTRA.caas-4A TRA was contributed by Doumai, while the favorable allele of QTRA.caas-4D was originated from Shi4185, respectively. Two QTLs for NRT were detected on chromosomes 5B and 5D and named as QNRT.caas-5B (wsnp_Ex_rep_c67320_65870601-Tdurum_contig10191_996) and QNRT.caas-5D (IAAV6218-Kukri_c46526_103), respectively, explaining 5.91% (additive effect: 26.7) and 10.16% (additive effect: 39.1) of the total phenotypic variances. The favorable alleles of QNRT.caas-5B and QNRT.caas-5D were contributed by Doumai and Shi 4185, respectively with higher phenotypic effects were used to develop KASP markers. Although attempts were made to develop a KASP marker for QTRA.caas-4A, it was unable to effectively distinguish between the two parental genotypes in the RIL population. Therefore, the marker did not yield conclusive results. Consequently, two KASP markers, Kasp_4A_RL and Kasp_5D_RT , were successfully developed based on the tightly linked SNP markers exhibited higher TRL compared to the unfavorable allele at the P = 0.05 level showed higher NRT than unfavorable allele at the P = 0.05 level encoded an ethylene-regulated nuclear protein (ERT2)-like protein; TraesCS4A01G436700 (QTRL.caas-4A.1) encoded a calcium-binding protein kinase (CDPK)-related kinase; TraesCS4A01G456300 (QTRL.caas-4A.1) encoded a cellulose synthase-like protein; TraesCS4A01G469400 (QTRL.caas-4A.2) encoded an F-box protein; and TraesCS4D01G092000 (QTRA.caas-4D) encoded an ABC transporter, whereas both the TraesCS5D01G378400 and TraesCS5D01G380200 for QNRT.caas-5D encoded E3 ubiquitin-protein ligase. The expressions of the seven candidate genes in Doumai and Shi 4185 were detected using qRT-PCR. Of these, TraesCS4A01G469400, TraesCS4D01G092000, and TraesCS5D01G380200 showed no significant differences between the parents, whereas TraesCS4A01G296500, TraesCS4A01G436700, TraesCS4A01G456300, and TraesCS5D01G378400 showed more than 1.4\u20133.9-fold higher expression in Doumai compared to Shi4185 , TRA (QTRA.caas-4A and QTRA.caas-4D), and NRT (QTRA.caas-5B and QTRA.caas-5D) TRA. Each of these QTLs accounted for 5.94%\u20139.47%, 6.85%\u20137.10%, and 5.91%\u201310.16% of the phenotypic variance, respectively.Optimization of crop root systems has long been proposed. However, genetic improvement of crop roots has been rarely attempted . A compr9 RIL lines and have identified 19 QTLs mainly distributed on chromosomes 1A, 2B, 2D, 3A, 3B, 3D, 5A, and 5D. Of these, the 5D loci (415.8 Mb\u2013457.6 Mb) overlapped with theQNRT.caas-5D (449.4 Mb\u2013454.1 Mb) identified in this study. IWB21309, 17.01 Mb) and 5B for RSA traits were also different with the loci identified in this study . Furthermore, MQTL4A.1 (651.78 Mb\u2013705.73 Mb) and MQTL4A.6 (600.04 Mb\u2013691.14 Mb) significantly associated with root length, root surface, and root tips overlapped with QTRL.caas-4A.1 (702.3 Mb\u2013721.3 Mb) and QTRA.caas-4A (594.2 Mb\u2013602.9 Mb). Rht2/Rht10 19.18 Mb, SVP3-4D/BM1-4D 469.46 Mb, Vrn2-4D/ZCCT1-4D 509.43 Mb), 5B , and 5D are different from the reported wheat genes associated with plant height and vernalization. Therefore, they represent novel genes associated with RSA-related traits. Above all, compared with the previous results and meta-analysis, QTRL.caas-4A.2, QTRL.caas-4D, QNRT.caas-5B, and QNRT.caas-5D were novel.0.00 Mb) . Based oQTRL.caas-4A.1 (702.3 Mb\u2013721.3 Mb) co-located influencing QTL clusters related to thousand kernel weight co-located with regions affecting QTL clusters related to yield, including SN, KNS, TKW, FLW, and KL . Additio65.6 Mb) . These rTraesCS4A01G436700 of QTRL.caas-4A.1 encodes the CDPK-related kinase. In plants, CDPKs play a critical role in various signaling pathways and are pivotal in root growth and development -like protein. Ethylene, a simple small molecule, plays a vital role in signal transduction, cell differentiation, division, and elongation (TraesCS5D01G380200, linked to QNRT.caas-5D, encodes an E3 ubiquitin-protein ligase, which plays essential roles in plant development (Four genes involved in the biological metabolism of plant hormones, cellulose, and the ubiquitin pathway were identified as high confidence candidate genes. Among these, elopment . Silencil length . TRA Anotivities . TraesCSongation . Ethylenongation . Additioelopment and is celopment .Kasp_4A_RL and Kasp_5D_RT were successfully developed based on tightly linked SNP markers, proving to be valuable tools for MAS in breeding programs. Additionally, accessions with more favorable alleles, superior RSA traits and appropriate agronomic traits, such as Yumai 18, Jinhe 9123, Yumai 34, Bainong 3217, Lumai 6, Jinmai 61, Lumai 5, Lumai 23, and Yumai 57 are recommended as parental lines for improvement of RSA traits.Although conventional breeding has contributed to the enhancement of root system, the selection process is time-consuming and less efficient due to the challenges in field measurements of RSA traits . KASP ofIn this study, we identified six QTLs associated with wheat RSA traits and successfully developed two KASP markers that can be utilized in wheat breeding programs aimed at achieving higher and more stable yields. This research serves as a foundational step towards gene cloning and enhancement of wheat root systems.All datasets generated for this study are included in the article or YJ: Data curation, Funding acquisition, Writing \u2013 original draft. YW: Data curation, Software, Validation, Writing \u2013 original draft, Writing \u2013 review & editing. JL: Software, Validation, Writing \u2013 review & editing. FW: Formal Analysis, Resources, Software, Investigation, Writing \u2013 review & editing. XQ: Investigation, Project administration, Writing \u2013 review & editing. PL: Funding acquisition, Supervision, Validation, Writing \u2013 original draft."} +{"text": "PrEP with T/C can prevent COVID-19 hospitalization and death in IC patients (pts) up to 6 months after injection. However, in the USA, authorization of T/C PrEP was paused in Jan 2023 due to loss of in vitro activity of T/C against dominant circulating SARS-CoV-2 variants, although loss of clinical efficacy is unclear. We investigated in vivo mechanisms of viral breakthrough in hospitalized IC pts with vs without prior T/C exposure.We analyzed remnant clinical SARS-CoV-2 PCR-positive swabs and sera from IC pts hospitalized at UPMC. SARS-CoV-2 variants and mutants were determined by whole genome sequencing and anti-RBD IgG levels by an enzyme immunoassay.Table 1). Median age was 67 yrs; 49% were male. IC conditions included organ transplant (23%) and hematologic cancer (32%) (Table 2). In IC patients with sequenced swabs, 21% received T/C (Table 3). Variant frequency mirrored national trends (Table 3). BA.5, XBB.1, and BF.7 were less common in T/C vs non-T/C pts . BA.2 and BQ.1 were more common in T/C vs non-T/C pts . The R346T and K444T/R/N mutations were more common in T/C vs non-T/C pts: 54% vs 41% and 37% vs 22% (Table 3). Anti-RBD IgG titers from 56% pts at the time of infection were higher in T/C vs non-T/C pts . COVID-19 mortality was numerically lower in T/C vs non-T/C pts . Mortality differences were consistent across variant epochs (Table 1).From Mar 28, 2022, to Mar 3, 2023, 72% (174/243) of swabs were successfully sequenced from 170 pts : Advisor/Consultant|LabSimply: Advisor/Consultant|Merck: Advisor/Consultant|Shionogi: Advisor/Consultant|Shionogi: Honoraria John W. Mellors, MD, AstraZeneca: Grant/Research Support|Gilead Sciences: Grant/Research Support"} +{"text": "The identification and characterization of plasma proteins in drug resistant and drug sensitive in HIV-1 infected/AIDS patients were carried out using the SWATH-MS protocol. In total, 204 proteins were identified and quantified, 57 proteinswere differentially expressed, out of which 25 proteins were down regulated and 32 proteins were up regulated in drug resistant patients. Six proteins such as complement C4-A, immunoglobulin heavy variable 1-2, carboxylic ester hydrolase, fibulin-1,immunoglobulin lambda constant7, secreted phosphoprotein 24 were differentially expressed in individuals with drug resistant HIV as compared to individuals with drug sensitive HIV. Gene ontology of 57 differentially expressed proteins was analysedand documented. The analysis of HIV-1 infected human plasma is an attractive medium with which differentially expressed proteins could be identified in certain disease states. Proteomic techniques are widely used globally to identify differentiallyexpressed plasma proteins in response to HIV-1 infection. Sequential window acquisition of all theoretical mass spectra (SWATH-MS) is a novel technique conceptualized with the protein library and the individual protein was identified andquantified for biomarker discovery . TherefoAmmonium formate, formic acid, dithiothreitol (DTT) and iodoacetamide (IAA) were procured from Sigma, USA. Modified trypsin (sequencing grade) was procured from Promega, USA. Polysulfoethyl SCX cartridge withcartridge holder was procured from Sciex, USA. Acetonitrile, Liquid phase-chromatography-mass spectroscopy grade water, was procured from Biosolve . Analytical grade chemicals were used for this study.The study focused on patients administered six first-line ART such as ZLE, ZLN, TLE, TLN, SLE and SLN patients and they were enrolled in the anti-retroviral therapy centre, Sarojini Naidu Medical College, Agra, India from December 2009 to November2016 as per the treatment guidelines provided by NACO, Govt. of India and the ethical guidelines formulated by the ICMR, Government of India. The age of the six patients varied from 32 years to 43 years. A patient information leaflet was used for datacollection hsa04610: Complement and coagulation cascades - Homo sapiens (human)[2] hsa05322: Systemic lupus erythematosus - Homo sapiens (human)[3] hsa05133: Pertussis - Homo sapiens (human)[4] hsa05150: Staphylococcus aureus infection - Homo sapiens (human)[1] H00080: Systemic lupus erythematosus[2] H00102: Classic complement pathway component defects[3] H01649: SchizophreniaThe six-drug respondent and drug resistant patients were in first-line ART such as ZLE, ZLN, SLN, TLE, and TLN during their course of treatment in this period. The drug interactions with these proteins were analysed (www.dgidb.org). A totalThe serial number of the down regulated and up regulated proteins in the heat map is represented in the Gene symbol: 1.C4A 2. IGHM 3. APOA4 4.HBB, 5. SERPING1 6. PZP 7. IGHG2 8.CD5L 9.HPR 10. HBA1 11. JCHAIN 12. APOL1 13. IGHV1-2 14. IGHV3-9 15.IGHV5-51 16. C4B 17. BCHE 18. LPA 19. IGLV6-57 20. SERPINA1 21. IGKV2-24 22. IGLV3-10 23. FAT-1 24.BIN3 25. PROC 26. FN1 27. IGHA1 28. GSN 29. AFM 30. TTR 31. IGLV3-21 32. KRT1 33. IGLV3-19 34. IGKV3-15 35. C4BPB 36. FBLN1 37. IGKV1-5 38. F5 39. IGKV3-11 40.IGLV7-46 41. VNN1 42. IGLC7 43. IGHA2 44. IGHV3-13 45. IGHV1OR15-1 46. SPP2 47. CDKL3 48. IGLV10-54 49. CDC42BPA 50. SP5 51. BEX5 52. PEPD 53. IGHV6-1 54. IGHV1-45 55. CDH5 56. 3 57. SERPINA 10. The heat map of differentially expressed proteins was createdby the online tool (http://www.heatmapper.ca/expression).The gene list for a category of the molecular function of the differential expressed proteins are presented in the bar diagram. The number of genes involved in the different functional role is presented in serial number in the bar diagram1. Binding (GO:0005488), 2. Catalytic activity (GO:0003824), 3. Molecular function regulator (GO:0098772), 4. Molecular transducer activity (GO:0060089), 5. Transcription regulator activity (GO:0140110), 6. Transporter activity (GO: 0005215).The molecular function of the differential expressed proteins was created by the online tool PANTHER- gene analyst ( http://www.pantherdb.org ).The red colour dots represent the down-regulated proteins and black colour dots represent the up-regulated proteins . The volcano plot was created by Graph Pad Prism 8, USA( https://www.graphpad.com /scientific-software/prism/).The details description of the protein-protein interaction network nodes represents proteins: Splice isoforms or post translational modifications are collapsed i.e. Each node represents all the proteins produced by a single protein-coding gene locus.The edges represent protein-protein associations: Network status: number of nodes: 35, number of edges:80, average node degree: 4.57, average local clustering coefficient:0.453, expected number of edges: 7, PPI enrichment p-value:< 1.0e-16. Theprotein-protein interaction network was created by using the online tool STRING Version 11.0 (https://string-db.org).The differential expression and molecular function of the Serotransferrin and Apolipoprotein A1 was identified in HIV-1 patients treated with first line ART . Now, thWe are report that proteins identified in drug resistant and drug sensitive HIV-1 infected patients who are taking first line ART over 6 years by SWATH-MS. Plasma proteins such as complement C4-A, immunoglobulin heavy variable 1-2, carboxylicester hydrolase, fibulin-1, immunoglobulin lambda constant7, secreted phosphor protein 24 were differentially expressed in individual drug resistant HIV-1 subtype C patients. The role of these proteins is reported using gene ontology analysis. Thisstudy would be helpful for further implementation in the search for biomarker discovery in HIV-1/AIDS patients taking first line ART.The project \"Characterization of drug resistant HIV-1 mutants of Agra region, India by genomic and proteomic approaches\" funded for senior research fellowship of Sushanta Kumar Barik (File No. 80/990/2015-ECD-I). M. M. Alam, JALMA, ICMR and Rakesh KumarMishra, ART centre, S.N Medical College are acknowledged for providing technical help in the collection of blood samples."} +{"text": "Kachinia Tong & Li, 2018 and Promolotra Tong & Li, 2020 are recorded from China for the first time. Two new species, Kachinialonglingsp. nov. (\u2642\u2640) and Promolotralushuisp. nov. (\u2642\u2640) are described. Descriptions, diagnoses, photographs and keys to Kachinia and Promolotra species are provided.The genera Oonopidae Simon, 1890 includes 1893 extant species in 115 genera worldwide, mainly distributed in tropical regions were taken under high vacuum with a Hitachi S-4800 after critical-point drying and gold-palladium coating. All measurements were taken using an Olympus BX51 compound microscope and are in millimeters. The terminology used in the text and figures follows SYNU) in Shenyang, China (curator: Yanfeng Tong).The specimens were examined using a Leica M205C stereomicroscope. Details were studied under an Olympus BX51 compound microscope. Photos were made with a Canon EOS 750D zoom digital camera (18 megapixels) mounted on an Olympus BX51 compound microscope. Endogyne were cleared in lactic acid. Scanning electron microscope images , Myanmar.Taxon classificationAnimaliaAraneaeOonopidae\ufeffTong & Zhangsp. nov.83FC57DD-B207-51D0-B931-DD9CFD1538A0https://zoobank.org/651BE492-19F3-480A-9EB7-CF6675FCFF21Holotype \u2642 (SYNU-640), China, Yunnan Prov., Baoshan City, Longling Co., Longxin Town, Xiaoheishan Nature Reserve, 16.02.2011, Z. Li & L. Wang; Paratypes: 1\u2640 (SYNU-641), 1\u2640 (SYNU-642), 4 \u2640 (SYNU-643-646), same data as for the holotype.K.mahmolae and K.putao by the strongly elevated epigastric region of the male . Habitus as in Fig. Female. As in male except as noted. Habitus as in Fig. The specific name is a noun in apposition taken from the type locality.Known only from the type locality.Taxon classificationAnimaliaAraneaeOonopidae\ufeffGenusTong & Li, 2020956B765C-34F2-50EC-8981-3DD686DC17FAPromolotrashankhaung Tong & Li, 2020 from Myanmar.Oonopinae Simon, 1890. According to Molotra Ubick & Griswold, 2011 by the heavily sclerotized dorsal and ventral abdominal scuta, the long spines on legs I and II, and the embolar region.The genus belongs to the subfamily Promolotrahponkanrazi Tong & Li, 2020, P.lushui sp. nov., P.shankhaung Tong & Li, 2020.China (Yunnan), Myanmar.Taxon classificationAnimaliaAraneaeOonopidae\ufeffTong & Zhangsp. nov.0111FE05-4B7A-59C2-8DCA-D3F41A907301https://zoobank.org/E02029CB-E8DA-471D-9B13-A5D39E3E20C0Holotype \u2642 (SYNU-647), China: Yunnan Prov., Lushui City, Pianma Town, 3.03.2011, Z. Li & L. Wang leg.; Paratypes: 2 \u2640 (SYNU-648-649), 3 \u2642 (SYNU-650-652), same data as for the holotype.The new species can be distinguished from congeners by the blunt end of the cymbiobulb . Habitus as in Fig. Female. As in male except as noted. Habitus as in Fig. The specific name is a noun in apposition taken from the type locality.Known only from the type locality."} +{"text": "Nirmatrelvir/ritonavir administered twice daily for 5 days (5D) (within 5 days of symptom onset) resulted in a clinically and statistically significant (6% absolute and 86% relative) risk reduction in COVID-19 related hospitalization or all cause death through Day 28 [1]. COVID-19 rebound regardless of treatment has been reported . Here, an integrated analysis of EPIC-HR/SR virology data was conducted to evaluate clinical resistance to nirm/r and if it is associated with viral load rebound (VLR) or progression to severe COVID-19 .10 copies/mL. The amino acid (AA) sequence was compared to Wuhan-Hu-1 [7] and Mpro substitutions were called if AAFREQ \u2265 10%. Emergent substitutions (ES) were called if observed post-baseline only and called treatment emergent substitutions (TES) if the ES was \u2265 2.5-fold more frequent, and had \u22653 additional occurrences, in nirm/r than placebo (PBO). Viral RNA load rebound (VLR) was defined as VL increase at D10 or D14 by \u2265 0.5 log10 copies/mL from D5 and resulting in a VL \u2265 3.0 log10 copies/mL.Next generation sequencing analysis was performed from nasal swabs with a viral RNA level \u22653.0 logpro ES did not differ between treatment arms. Among those with sequence data available , nirm/r Mpro TES were observed in: T98I/del(n=3), E166V (n=3), and W207L/del (n=3) and within the Mpro cleavage sites: A5328S/V(n=5) and S6799A/P/Y (n=4). None of the TES were associated with progression to severe COVID-19. VLR was observed in with Mpro TES observed in few VLR patients (3.4% in nirm/r and 0% in PBO). Among the Mpro TES identified, E166V is an in vitro resistance mutation . Figure 1 shows the VL trajectories of the 3 patients with E166V, one patient experienced VLR at D10, all effectively controlled the virus by D14 and did not experience severe COVID-19.In EPIC-HR/SR, the primary SARS-CoV-2 variant was Delta (91%) followed by Omicron (7.4%). The percentage of patients with Min vitro resistance substitution emerged in few patients, but was not associated severe COVID-19. Additionally, these data show VLR is not a result of treatment resistance to nirm/r driven by TES or any Mpro substitutions.In EPIC-HR/SR, an Mary Lynn Baniecki, PhD, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Shunjie Guan, PhD in Statistics, AbbVie: Stocks/Bonds|Pfizer: Stocks/Bonds Zhenyu Wang, Ph.D., Alkermes: Stocks/Bonds|Moderna: Stocks/Bonds|Pfizer: Stocks/Bonds Yan Chen, Ph. D, Pfizer, Inc: Stocks/Bonds Weihang Bao, PhD, Pfizer, Inc.: Employee of Pfizer|Pfizer, Inc.: Stocks/Bonds Wen He, PhD, Pfizer Inc.: Stocks/Bonds Elizabeth Dushin, PhD, Pfizer Inc.: Stocks/Bonds Craig Hyde, PhD, Pfizer: Employed by Pfizer|Pfizer: Stocks/Bonds Yuao Zhu, PhD, Pfizer, Inc.: Stocks/Bonds Rhonda D. Cardin, PhD, Pfizer, Inc: Stocks/Bonds Jennifer Hammond, PhD, Pfizer: Employee|Pfizer: Stocks/Bonds Sandeep Menon, PhD, Pfizer: Stocks/Bonds Charlotte Allerton, PhD, Pfizer: Stocks/Bonds Holly Soares, PhD, Pfizer: Stocks/Bonds"} +{"text": "Enterococcus faecalis.The whole-genome sequence of strain K-4, isolated from grass silage in Thailand, which constitutes a chromosome and two plasmids, is 2,914,933\u2009bp long, has a GC content of 37.5%, and contains 2,734 predicted protein-coding genes. Average nucleotide identity based on BLAST+ (ANIb) and digital DNA-DNA hybridization (dDDH) values indicated that the strain K-4 was closely related to Enterococcus comprises Gram-positive, non-spore-forming facultative anaerobic, spherical, or ovoid cells with low genomic GC content were assembled de novo using Unicycler v0.4.8 (https://github.com/rrwick/Unicycler) (dnaA for the chromosome. The genome sequence was annotated with DFAST v1.2.6 (https://dfast.nig.ac.jp/) and the Genome-to-Genome Distance Calculator 3.0 (http://ggdc.dsmz.de/ggdc.php) and decoded on the Illumina MiSeq system. Overall, 1,192,876 reads with 299,930,918 bases were decoded with an average read length of 251.4\u2009bp and spot length of 602\u2009bp with 2\u2009\u00d7\u2009301-bp paired-ends reads. Low-quality bases were trimmed, and short reads (<25\u2009bp) were removed using Platanus trim v1.0.7 (us_trim) . Data reus_trim) . Averagegdc.php) using reE. faecalis ATCC 19433T with a sequence depth of ~88. Overall, 2,734 coding regions, 60 tRNAs, 12 rRNAs, and 1 CRISPR region were annotated. The DNA sequences of two plasmids, namely, pEK4S and pEK4L , were also assembled and compared with their partial sequences using Blast and DRX314299 (Illumina).Strain K-4 genome sequence and annotation data were deposited in DDBJ/GenBank under BioProject number"} +{"text": "Professional and regulatory agency guidelines recommend that fluoroquinolones not be used as first-line therapy to treat uncomplicated UTI. Increasingly, \u03b2-lactams are being used to treat UTI despite limited evidence supporting their effectiveness. The study aim was to compare the efficacy of \u03b2-lactams and other commonly prescribed antibiotics for UTI to fluoroquinolones.< 30d, co-diagnosis where antibiotics were indicated, hospital discharge < 7d, scheduled urological procedure < 7d, pregnancy. Outcome: UTI related admission or outpatient return visit within 3-30d. Demographic, co-morbidity, vitals, laboratory, and prescription data were extracted. Propensity scores were used to balance treatments and GEE models were used to estimate outcomes.A multi-centered retrospective cohort study of outpatient visits with a UTI diagnosis between 2019-2021 was developed. Inclusion criteria: In-person visit in the Emergency Department or Primary/Urgent Care with ICD-10 documented UTI diagnosis and oral antibiotic prescription filled within 0-2 d. Exclusion criteria: Prior UTI There were 73,334 visits in 130 VA medical centers. Mean (S.D.) cohort age was 66.0 (15.8) y, 22.9% were female. Antibiotics prescribed N (%): \u03b2-lactams 27,385 (37.3%), nitrofurantoin 15,509 (21.1%), trimethoprim / sulfamethoxazole (TMP/SMX) 15,453 (21.1%), and fluoroquinolones 14,997 (20.4%). The overall 30-day clinical failure rate was 10,525 (14.4%).Comparative Effectiveness of Oral Antibiotics for Outpatient UTIsCommonly prescribed antibiotics for outpatient UTI were associated with a modest increase in 30-day clinical failure relative to fluoroquinolones. Effectiveness differences were most pronounced in male patients. Clinicians should carefully differentiate between complicated and uncomplicated UTI in males and consider preferentially prescribing fluoroquinolones.Karl Madaras-Kelly, PharmD, MPH, BioMerioux: Grant/Research Support"} +{"text": "Vaccines against SARS-CoV-2 (COVID-19) proved beneficial for COVID-19 disease attenuation and preventing virus spreading. Cumulative reports of the rarity of antineutrophil cytoplasmic autoantibodies (ANCA)-associated vasculitis (AAV) raise concerns about its relationship with COVID-19 vaccination. Several case reports described ANCA-associated pauci-immune glomerulonephritis (ANCA-GN) following COVID-19 vaccination with some uniqueness. We systematically reviewed COVID-19 vaccine-induced ANCA-GN from PubMed, SCOPUS, and Cochrane library databases until 1 January 2023 according to PRISMA guidelines and presented our three cases. Twenty-six cases from 25 articles, including our 3 cases, were analyzed. Most cases were diagnosed following the second dose of the COVID-19 vaccine (59%) with a median (IQR) interval onset of 14 (16) days. The highest prevalence was related to the mRNA-type vaccine. Anti-myeloperoxidase (MPO) ANCA was far more common than the other ANCAs, with various positive autoantibodies. Fourteen cases had extra-kidney AAV manifestation. Although severe kidney injury was observed in 10/29 (34%), remission was achieved in 89% (25/28) with no death. The mechanisms of the vaccine-inducing ANCA-GN were postulated here. Since ANCA-GN after the COVID-19 vaccine was rare, the benefit of the COVID-19 vaccine could outweigh the risk of ANCA-GN side effects in the pandemic era. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the ongoing global pandemic of coronavirus disease 2019 (COVID-19), with a cumulative confirmed case of 765 million, including a 1% death rate . In addiThe American College of Rheumatology/European Alliance of Associations for Rheumatology (ACR/EULAR) 2022 classified AAV into granulomatous polyangiitis (GPA), eosinophilic granulomatous polyangiitis (EGPA), microscopic polyangiitis (MPA), and renal-limited vasculitis (RLV) ,13. HoweTwo independent authors conducted systematic literature by searching relevant full-text articles in the PubMed, SCOPUS, and Cochrane library databases up to 1 January 2023. Keywords were AND . The eligible articles included the full-text report in the English language of biopsy-proven ANCA-GN with pauci-immune deposit by immunofluorescence (IF) study (defined as negative or weak [\u22641+] staining of Ig and complement) or by electron microscopy (EM) (defined as no or faint electron-dense deposit [EDDs]) after COVID-19 vaccination. Patients\u2019 age, vaccine types, and the disease onset from the vaccination were not restricted. The exclusion criteria were AAV without GN, ANCA-GN with a non-available IF/EM report, and AAV presenting or having disease flare before the onset of vaccination. We also included our 3 GN-ANCA cases diagnosed and treated at King Chulalongkorn Memorial Hospital, Bangkok, Thailand, from January 2022 to December 2022. Data extraction was anonymized under the General Data Protection Regulation , and infData included patient demographics, vaccine types, vaccination numbers, the interval between the last vaccination and onset of AAV, the clinical manifestation of ANCA-GN and AAV, serum creatinine (Scr) at baseline and peak, serologies , kidney pathology finding, treatment, and outcomes after treatment.Severe acute kidney injury (AKI) was defined as dialysis requirement or peak Scr > 5.7 mg/dL. Outcomes were classified into remission with relapse, remission without relapse, and non-remission . Remission of ANCA-GN/AAV was defined according to the 2012 KDIGO Guidelines for Management of Glomerular Diseases as the at-test. The continuous data were illustrated by using mean \u00b1 standard deviation (SD) for normal distribution data and median (interquartile range [IQR]) for non-normal distribution data. The categorical data were described as a ratio. Finally, the normally distributed variables were compared by A total of 2956 relevant records were initially obtained from the database search. After removing 312 duplicated records, 2644 record titles and abstracts of articles were first screened according to the inclusion criteria. 68 articles were eligible for the second screening; 43 articles (154 cases) were excluded ; 26 cases from 25 articles, including our 3 cases were recruited for the systematic review . The detThe median (IQR) age was 70 (22) years, with female predominance (59%). Most cases presented ANCA-GN after receiving the second vaccination (59%) with a median interval gap of 14 (11\u201327) days. The mRNA COVID-19 vaccine was the most common (55%), followed by the viral vector vaccine (31%) and inactivated COVID-19 vaccine (14%). The top-three most common presentations were AKI, abnormal urine sediments, and constitutional symptoms. Extra-kidney manifestations included pulmonary involvement , neuromuscular involvement , otologic/optic involvement , and Wallerian degeneration . Severe AKI was observed in 34% (10/29). MPO-ANCA/pANCA was positive in 79% (23/29). A discrepancy of ANCA serologies was observed in one case . A dual-positive ANCA (pANCA and cANCA) was detected in 3% (1/29). Autoantibodies were positive in 52% (13/25 cases), including ANA , Coombs antibody , cryoglobulin , and RF . The 2021 KDIGO Guidelines for Management of Glomerular Diseases were adoWe described three cases of ANCA-GN following viral vectors (case #1) and mRNA (case #2 and #3) COVID-19 vaccines. Only one patient (case #2) was classified as microscopic polyangiitis (MPA) by ACR/EULAR 2022 . Case #19/L with a neutrophil predominance (83%), Scr 3.5 mg/dL, and albumin 2.5 g/dL. Urinalysis demonstrated similar profiles with dysmorphic erythrocytes. The urine protein-creatinine ratio (UPCR) was 7.5 g/g creatinine. pANCA was positive with negative MPO-ANCA and PR3-ANCA. Serologies were positive for ANA , RF 30 (0\u201320) IU/mL, and Coombs antibody (1+), while others were negative . Complement levels were within normal values. The kidney biopsy disclosed 24 glomeruli with 7 global sclerosis (GS) and 7 cellular crescents. Fibrinoid necrosis of arteries and severe tubulointerstitial inflammation were observed. Interstitial fibrosis and tubular atrophy involved 30% of cortical tissue. IF revealed IgG (1+), C3 (1+), Kappa (1+), and Lambda (1+). Focal trivial subepithelial and intramembranous EDDs with diffuse thickening of GBM were observed on EM. Hence, ANCA-GN without extra-kidney organ involvement was diagnosed. Three-day of 1 gm/day pulse methylprednisolone and 500 mg pulse cyclophosphamide was started. Unfortunately, her kidney function remained deteriorated, requiring maintenance hemodialysis.A 76-year-old female with type 2 diabetes mellitus, hypertension, and dyslipidemia presented with leg edema for 11 days prior to admission. She received the second COVID-19 vaccine (AZD1222) 3 months ago. A few weeks later, she developed chronic fever, weight loss, and productive cough. Several blood cultures were performed, yielding negative results. Non-contrast chest computed tomography (CT) revealed unusual interstitial pneumonia (UIP). Sputum cultures depicted normal flora. She denied a history of SARS-CoV-2 infection and had negative PCR for COVID-19. Her Scr was 1.5 mg/dL over the past year. Three-week before admission, her Scr increased to 1.7 mg/dL with 2+ proteinuria and erythrocyte of 10\u201320/HPF. A week later, she developed leg edema and foamy urine. Physical examination (PE) revealed temperature 38.9 \u00b0C, respiratory rate (RR) 20/min, blood pressure (BP) 165/91 mmHg, and bilateral 3+ leg pitting edema. Blood chemistries revealed hemoglobin 7.6 g/L, leukocyte count of 11.9 \u00d7 10Case #29/L with neutrophils predominance (83%), and platelet counts 386 \u00d7 109/L. Urinalysis depicted trace protein, erythrocytes 3\u20135 cells/HPF, and UPCR 0.5 g/g creatinine. pANCA and MPO-ANCA were positive, with negative PR3-ANCA and cANCA. Serologies were positive, including ANA , cryoglobulin, and 1+ direct antiglobulin test, while the others were negative . Complement levels were within normal values. Serum protein electrophoresis and immunofixation demonstrated polyclonal gammopathy. No structural kidney abnormalities were detected by ultrasonography. The kidney biopsy disclosed 13 glomeruli with 2 GS and 10 cellular crescents. Fibrinoid necrosis was found on the vasculitic medium-sized artery. Mild tubulointerstitial fibrosis was observed. IF revealed non-specific staining for all immunoreactants. Hence, AAV with ANCA-GN was diagnosed. She received plasma exchange \u00d77 times, pulse methylprednisolone, and oral cyclophosphamide. One year later, she remained well without dialysis requirements and active AAV manifestation. Her serum creatinine 2.3 mg/dL and negative erythrocyturia.A 69-year-old female presented with AKI while investigating anorexia, weight loss, and fatigue. She had hypertension for 2 decades and received 2 doses of AZD1222 and a COVID-19 vaccine booster with BNT162b2 (3 months ago). One month later, she developed anorexia, fatigue, a weight loss of 8 kg within 2 months, and established mixed conductive and sensorineural hearing loss. Chest X-ray and contrast computerized tomography (CT) revealed a subcentimeter pulmonary nodule. Two weeks after CT, her Scr increased from 0.7 to 2.4 mg/dL, and contrast-associated AKI was suspected. However, despite receiving an intravenous fluid infusion, she had a steadily increasing Scr. Her urinalysis revealed 1+ protein, leukocyte 50\u2013100/HPF, and erythrocyte 3\u20135/HPF. Ciprofloxacin was prescribed on suspicion of having a urinary tract infection. PE revealed temperature 38.0 \u00b0C, BP 120/60 mmHg, marked pale conjunctivae, and no leg edema. Blood chemistries were notable for Scr 7.1 mg/dL, albumin 2.5 g/dL, hemoglobin 6.6 g/dL, leukocyte counts 12.1 \u00d7 10Case #39/L with neutrophils predominance (80%), and platelet counts 209 \u00d7 109/L. Urinalysis depicted 2+ protein, leukocytes 30\u201350/HPF, erythrocytes 1\u20132/HPF, and UPCR 1.2 g/g creatinine. cANCA and MPO-ANCA were positive, with negative PR3-ANCA. Positive direct antiglobulin test at 1+ was detected, while others were negative . Complement levels were normal. Serum protein electrophoresis and immunofixation demonstrated polyclonal gammopathy. No structural kidney abnormalities were detected by ultrasonography. The kidney biopsy disclosed 20 glomeruli with 2 GS and 7 cellular crescents. Fibrinoid necrosis was noted in 6 glomeruli. Diffuse tubulointerstitial inflammation with abundant eosinophils and trivial tubulointerstitial fibrosis (<5%) were observed. IF revealed non-specific staining for all immunoreactants. ANCA-GN with eosinophilic interstitial nephritis was diagnosed. Due to the alteration of consciousness, magnetic resonance imaging (MRI) of the brain and orbits were performed, demonstrating Wallerian degeneration of the right corticospinal tracts and pons and bilateral optic neuritis. Intravenous pulse methylprednisolone and intravenous immunoglobulin were administered as per AAV. Temporary hemodialysis was initiated for 2 weeks. Subsequently, she remained well without AAV clinical flare with low-dose prednisolone and immunosuppressive agents; her Scr was 1.6 mg/dL with negative proteinuria and bland urine sediment.An 84-year-old female with underlying diseases of hypertension and dyslipidemia presented with a fever for one week prior to admission. She received complete primary series of AZD1222 and a booster dose of the COVID-19 vaccine with mRNA-1273 four months ago. One month later, she developed bilaterally severe sensorineural hearing loss and tinnitus. A few weeks before admission, she developed drowsiness, progressive dysphagia, decreased urine volume, and a weight loss of 8 kg. PE revealed BP 154/66 mmHg, temperature 38.5 \u00b0C, mildly pale conjunctivae, right eye episcleritis with afferent pupillary defect (RAPD), and 1+ leg edema. Blood chemistries were notable for Scr 5.1 mg/dL (baseline 0.9 mg/dL), albumin 2.7 g/dL, hemoglobin 9.6 g/dL, leukocyte counts 26.0 \u00d7 10ANCA-GN secondary to COVID-19 vaccination was more prevalent in the patients with mRNA vaccinations , older age, and female gender. The top three most common manifestations were AKI, abnormal urine sediment, and constitutional symptoms. MPO-ANCA was distinctly dominant compared to the other ANCAs. Concomitant autoantibodies were documented in 52%, particularly Coombs antibody, ANA, and cryoglobulin. Although one-third (34%) presented with severe ANCA-GN, most cases had good outcomes, with a remission rate of 89%. No death occurred. The higher immunogenicity and more common usage of the mRNA COVID-19 vaccine might explain its higher prevalence on ANCA-GN ,19. The Most AAVs have unknown etiology, known as primary AAVs; however, AAVs can be secondary to drugs ,25,26,27in-vitro experiment and found that the influenza vaccine (RNA vaccine) was able to induce PR3-ANCA production from peripheral blood mononuclear cells (PBMCs), while the decoy molecule, inactivated split virion influenza vaccine 2007, could not [AAV/ANCA-GN induced by vaccination has been well documented in post-influenza vaccination ,32. The ould not . In addiould not ,34. Unfoould not . COVID-19 vaccine induces ANCA-GN and AAV, possibly through molecular mimicry, stimulating productions of MPO-ANCA and PR3-ANCA via the adaptive immune system, likewise inducing antiviral neutralizing antibodies ,37,38. TTreatment of ANCA-GN following the COVID-19 vaccines in this systematic review mostly complied with the 2021 KDIGO Guidelines , wherebyANCA-associated glomerulonephritis following the COVID-19 vaccine is rare, according to billions of vaccine doses that have been administered worldwide. The benefits of COVID-19 vaccination outweigh the risks of possible induced autoimmune diseases and ACNA-GN. Avoid unnecessary booster doses of the COVID-19 vaccine in high-risk patients should warrant."} +{"text": "South African Journal of Physiotherapy 78(1), a1611. https://doi.org/10.4102/sajp.v78i1.1611, there was an error regarding the affiliations for the authors. Instead of:In the published article, Anwar, S., Arsalan, S.A., Zafar, H., Ahmed, A., Gillani, S.A. & Hanif, A., 2022, \u2018Effects of breathing re-education on endurance, strength of deep neck flexors and pulmonary function in patients with chronic neck pain: A randomised controlled trial\u2019, Authors:\u20181https://orcid.org/0000-0002-6603-3185Sahreen Anwar1https://orcid.org/0000-0003-3492-7050Syed A. Arsalan1,2https://orcid.org/0000-0001-9318-3691Hamayun Zafar1https://orcid.org/0000-0002-1965-6224Ashfaq Ahmed3https://orcid.org/0000-0002-2996-0764Syed A. Gillani4https://orcid.org/0000-0002-2670-6402Asif HanifAffiliations:1Department of Physical Therapy, Faculty of Rehabilitation Sciences, University of Lahore, Lahore, Pakistan2Department of Physical Therapy, Faculty of Rehabilitation Sciences, King Saud University, Riyadh, Saudi Arabia3Department of Biostatistics, Faculty of Rehabilitation Sciences, University of Lahore, Lahore, Pakistan\u2019It should be:\u2018Authors:1https://orcid.org/0000-0002-6603-3185Sahreen Anwar1https://orcid.org/0000-0003-3492-7050Syed A. Arsalan1,2https://orcid.org/0000-0001-9318-3691Hamayun Zafar1https://orcid.org/0000-0002-1965-6224Ashfaq Ahmed3https://orcid.org/0000-0002-2996-0764Syed A. Gillani4https://orcid.org/0000-0002-2670-6402Asif HanifAffiliations:1University Institute of Physical Therapy, University of Lahore, Lahore, Pakistan2Faculty of Rehabilitation Sciences, King Saud University, Riyadh, Saudi Arabia3Faculty of Allied Health Sciences, University of Lahore, Lahore, Pakistan4University Institute of Public Health, University of Lahore, Lahore, Pakistan\u2019.In addition, there was an error on page 2. The following paragraph is updated as it was incorrectly formulated:The original incorrect wording:n = 34 in each group, Z1-\u03b1/2 = standardised level of significance = 95% = 1.96, Z1-\u03b2 = Power of test = 80% = 1.28, \u00b51 = Mean in control group = 4.60, \u00b52 = Mean in physiotherapy group = 5.40, \u03b412 = standard deviation in control group = 0.84, \u03b422 = standard deviation in physiotherapy group = 0.59. The primary outcome used to estimate sample size was vital capacity (VC) (Duymaz 2019). A difference of 0.5 in the standard deviation was regarded as a meaningful change .Here, The revised and updated wording:n = 15 in each group, Z1-\u03b1/2 = standardised level of significance = 95% = 1.96, Z1-\u03b2 = power of test = 80% = 1.28, \u00b51 = mean in control group = 4.60, \u00b52 = mean in physiotherapy group = 5.40, \u03b412 = standard deviation in control group = 0.84, \u03b422 = standard deviation in physiotherapy group = 0.59. The primary outcome used to estimate sample size was vital capacity (VC) (Duymaz 2019). A difference of 0.5 in the standard deviation was regarded as a meaningful change .Here, The authors apologise for these errors. The corrections do not change the study\u2019s findings of significance or overall interpretation of the study\u2019s results or the scientific conclusions of the article in any way."} +{"text": "Nonspecific presentation and limited diagnostic solutions of acute infections and sepsis in emergency departments (EDs) result in early antimicrobial administration at a cost to antimicrobial stewardship. We validated the host response classifiers, IMX-BVN-3b and SEV-3b, to determine bacterial and viral infection status and illness severity. We also assessed antibiotic over- and underuse.We prospectively enrolled adult ED patients with suspected acute infections or sepsis with \u22651 vital sign abnormal across 7 sites. At enrollment, we surveyed treating physicians on infection probability and antibiotic prescribing. BVN/SEV-3b were calculated using NanoString nCounter\u00ae on PAXgene\u00ae blood samples. We compared BVN-3b likelihood of bacterial and viral infection to post-hoc clinical adjudication infection status and SEV-3b likelihood of severe outcomes to 7-day need for ICU care and 30-day mortality.Of 568 enrolled patients, 346 had consensus adjudications . The BVN-3b area under the receiver operating curve (AUROC) for bacterial infections was 0.82 (95%CI 0.77-0.87), compared to 0.76 (95%CI 0.71-0.81) for procalcitonin (p = 0.011). BVN-3b AUROC for viral infections was 0.89 (95%CI 0.84-0.95). SEV-3b AUROC was 0.78 (95%CI 0.69-0.86) and 0.88 (95%CI 0.73-1) for 7-day ICU care and 30-day mortality, respectively. Of the 346, 226 patients had a pre-lab result physician questionnaire; of these, 110 patients received antibiotics. Of these, BVN-3b would have corrected 71% of antibiotic prescribing errors (34/48 overprescriptions and 13/18 underprescriptions).BVN-3b and SEV-3b accurately identified bacterial and viral infections and risk status. If implemented in a rapid workflow, these tests may improve patient management and antibiotic prescribing, reducing healthcare costs in the ED.Arianna Beltran, BS, Inflammatix: Internship Uan-I Chen, MS, Inflammatix: Stocks/Bonds Edward A. Michelson, MD, Inflamatix: Research expense reimbursement for sponsored clinical trial Alexandra Weissman, MD, Inflammatix Inc: Advisor/Consultant Evangelos J. Giamarellos-Bourboulis, PhD, D(ABMM), Abbot Product Operations AG: Grant/Research Support|Abbot Product Operations AG: Honoraria|bioMerieux: Grant/Research Support|bioMerieux: Honoraria|Horizon 2020 European Program: Grant/Research Support|Horizon Health European Program: Grant/Research Support|Sobi AB: Advisor/Consultant|Sobi AB: Grant/Research Support|Sobi AB: Honoraria Oliver Liesenfeld, MD, Inflammatix Inc.: Ownership Interest Natalie N. Whitfield, PhD, D(ABMM), GenMark Dx/Roche: Employee|GenMark Dx/Roche: Stocks/Bonds|Inflammatix: Employee|Inflammatix: Stocks/Bonds"} +{"text": "The 13-valent pneumococcal conjugate vaccine (PCV13) was introduced for infant use in the United States in 2010, replacing PCV7. A U.S. case-control study (2010\u20132014) demonstrated vaccine effectiveness (VE) for \u22651 dose of PCV13 at 86%; however, this study lacked statistical power to examine VE by number of doses and against individual serotypes.We used the indirect cohort method to estimate VE of PCV13 against vaccine-type invasive pneumococcal disease among children < 5 years in the U.S. from May 1, 2010 to December 31, 2019. We included IPD cases identified through CDC\u2019s Active Bacterial Core surveillance in 10 U.S. states; during 2010 \u2013 2014, we additionally included cases enrolled in a post-licensure matched case-control study from expanded sites. Cases and controls were defined as individuals with PCV13-type-IPD (VT-IPD) and non-PCV13-type-IPD (NVT), respectively; serotype 6C was categorized as VT. We used logistic regression to estimate the adjusted odds of prior PCV13 receipt, controlling for confounders identified a priori including age category, race/ethnicity, sex, state, year, and any immunocompromising and/or chronic conditions.>3 PCV13 doses; 47 cases (21.1%) and 53 controls (5.7%) had received no PCV doses. Serotypes 19A (N=96), 3 (N=60), and 19F (N=45) caused 90.1% (201/223) of VT-IPD. VE of >1 or \u22653 PCV13 doses against VT-IPD was 81.7% and 87.8% (75.2\u201394.0%), respectively. VE of \u22653 PCV13 doses was 87.0% (75.8\u201393.0%), 54.6% (-8.8\u201381.0%), and 92.9% (74.4\u201398.0%) against serotypes 19A, 3, and 19F, respectively. VE was 87.6% (67.9-95.2%) for three primary doses before 12 months of age and 92.4% (78.2\u201397.2%) for three primary doses and a booster at 12 months of age or older.A total of 1,161 IPD cases were identified; 223 (19.2%) were VT cases and 938 (80.8%) were non-VT controls. Of those, 108 cases and 600 controls had received Vaccine effectiveness estimates against PCV13-type IPD among US children under five years of age, 2010 - 2019VE of \u22651 PCV13 dose against IPD was consistent with the previous estimate from the case-control study, and \u22653 doses appear to provide substantial protection. Among the most commonly circulating VT-IPD, PCV13 was protective against serotypes 19A and 19F IPD; protection against serotype 3 IPD did not reach statistical significance.Lee Harrison, MD, GSK: Advisor/Consultant|Merck: Advisor/Consultant|Pfizer: Advisor/Consultant|Sanofi: Advisor/Consultant Tamara Pilishvili, PhD MPH, GSK: Employed by GSK since February 2023. At the time of data collection and analysis for this work was employed by the CDC"} +{"text": "T/C authorization in the US for PrEP of COVID-19 in IC individuals was initially based on a randomized trial (PROVENT). However, < 5% of enrollees in PROVENT were IC. We sought to assess real-world effectiveness of T/C PrEP among IC pts.We conducted a retrospective, observational, propensity-score matched cohort study at UPMC from Jan 1, 2022, to Mar 31, 2023. We assessed effectiveness at \u2264 6 months of T/C 600 mg against chart confirmed COVID-19 hospitalizations and COVID-19\u2013related deaths among IC pts.Table 1). During the study period encompassing circulating variants both susceptible and resistant to T/C, there were 15 vs 18 COVID-19 hospitalizations across 377,832 person-days in T/C vs non-T/C pts (Table 2). Thus, 0.72% vs 0.87% of T/C exposed vs unexposed pts were hospitalized for COVID-19 . There was no difference in effectiveness by T/C dosing pattern (Table 2). Effectiveness was numerically higher in the BA.5 period, although there were few events in other variant eras (Table 2). There was a non-significant 50% lower risk of hospitalization in T/C patients with solid tumors or autoimmune conditions, and no significant difference by exposure status in patients with organ transplant or hematologic cancer (Table 2). There were 5 COVID-19 ICU admissions per exposure group, and 2 inpatient COVID-19\u2013related deaths (1 per group) (Table 3). Limitations included overall low event rate limiting power and an open healthcare system leading to possibility of missing hospitalizations due to pts seeking care elsewhere.Before matching, there were 2931 T/C vs 157,225 non-T/C pts. After matching, 2301 matched pairs remained . Most pts had moderate/severe IC conditions : Advisor/Consultant|LabSimply: Advisor/Consultant|Merck: Advisor/Consultant|Shionogi: Advisor/Consultant|Shionogi: Honoraria John W. Mellors, MD, AstraZeneca: Grant/Research Support|Gilead Sciences: Grant/Research Support"} +{"text": "Their structures and stereochemistry were determined from analysis of NMR spectroscopic and circular dichroism (CD) data. Compound 2 represents the first report of naturally occurring arylnaphthalide lignan triglycoside. The cytotoxic activities of all isolated compounds were evaluated against A-549 and SMMC-7721 cell lines. Compounds 7\u201310 and 14\u201316 were more toxic than cisplatin in two tumor cell lines. This investigation clarifies the potential effective substance basis of D. versipellis in tumor treatment.One new dibenzyltyrolactone lignan dysoslignan A ( Arylnaphthalide lignans have received much attention due to their potent antiviral, antineoplastic, anti-inflammatory, and immunosuppressive properties . The repDysosma versipellis (Hance) M. Cheng ex Ying, belonging to the family of Berberidaceae, is widely distributed in the central/south regions of China + ; NMR data (DMSO-d6), see Dysoslignan A (2): white, amorphous powder; + ; NMR data (DMSO-d6), see Dysoslignan B (3): white, amorphous powder; UV (MeOH) \u03bbmax (log \u03b5) 204 (4.49), 225 (4.19), 264 (4.35), 326 (3.76), 363 (3.60) nm; IR (iTR)\u03bdmax 3367, 2989, 2946, 2833, 1741, 1608, 1520, 1467, 1420, 1348, 1274, 1213, 1186, 1115, 1090, 1027 cm\u22121; HR-ESI-MS (positive): m/z 385.0920 [M + H]+ , m/z 407.0737 [M + Na]+ ; NMR data (DMSO-d6), see Dysoslignan C (4): white, amorphous powder; UV (MeOH) \u03bbmax (log \u03b5) 202 (4.48), 225 (4.29), 263 (4.38), 312 (3.82), 355 (3.60) nm; IR (iTR)\u03bdmax 3410, 2939, 2839, 1745, 1605, 1535, 1465, 1352, 1244, 1131, 1094, 1030 cm\u22121; HR-ESI-MS (positive): m/z 383.0768 [M + H]+ ; NMR data (DMSO-d6), see Dysoslignan D (1 (1.0 mg) and 2 (1.0 mg) were dissolved in 1.0 mL of 2M HCl, and then hydrolyzed at 90 \u00b0C for 3 h. The HCl in the reaction mixture was removed under reduced pressure. The remaining reaction mixture was extracted with CH2Cl2. The water layers were directly analyzed by HPLC . The peaks at 13.15 and 14.27 min were coincided with D-glucose and D-galatose.The absolute configurations of the galatose and glucose moieties were determined by the previously reported method . Compoun1\u201318 were evaluated against human lung cancer A-549, hepatocellular carcinoma SMMC-7721 cell lines. The cells were cultured in RPMI-1640 medium, supplemented with 10% fetal bovine serum (FBS) at 37 \u2103 under 5% CO2 in a humidified atmosphere. Cell viability was assessed by conducting colorimetric measurements of the amount of insoluble formazan formed in living cells based on the reduction of 3--5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS). To be brief, 100 \u00b5L of cells were seeded into each well in a 96-well cell culture plate in advance. After 24 h, various concentrations of all test compounds were added. After the incubation for 48 h, MTS (20 \u03bcL) was added to each well, and the incubation continued for 4 h at 37 \u2103. The optical density at 492 nm was determined using a 96-well microtiter plate reader. The IC50 values were calculated by the Reed\u2013Muench method. Statistical analysis were performed by SPSS 20.0 software . All experiments were performed in triplicate.By the previously reported MTS method , the cytD. versipellis resulted in the isolation of one new dibenzyltyrolactone lignan dysoslignan A (1), three new arylnaphthalide lignans dysoslignan B\u2013C (2\u20134), along with fourteen known metabolites (5\u201318). Compound 2 is the first reported example of naturally occurring arylnaphthalide lignan triglycoside. All isolated compounds were tested for their in vitro cytotoxic activity against A-549 and SMMC-7721 cell lines using MTS assay. Among them, compounds 7, 14, and 15 were cytotoxic, with IC50 values of less than 1\u03bcM. Our research further demonstrated that the arylnaphthalide lignans are mainly responsible for the potent anticancer effect of D. versipellis.Further phytochemical studies on"} +{"text": "Staphylococcus/Mammaliicoccus spp. isolates from contralateral healthy skin and DFU from 44 hospitalized patients.Diabetic foot infections (DFIs) are the most common complications of diabetic foot ulcers (DFUs), and a significant cause of lower extremity amputation. In this study we used whole genome sequencing to characterize the clonal composition, virulence and resistance genetic determinants of 58 S. aureus (n\u2009=\u200932) and S. epidermidis (n\u2009=\u200910) isolates were recovered from both DFUs and healthy skin, whereas, S. haemolyticus (n\u2009=\u20098), M. sciuri (n\u2009=\u20091), S. hominis (n\u2009=\u20091) and S. simulans (n\u2009=\u20093) were recovered exclusively from healthy skin. In contrast, S. caprae (n\u2009=\u20092) and S. saprophyticus (n\u2009=\u20091) were recovered only from DFUs. Among S. aureus isolates, MRSA were present with high prevalence , 18 of which (66.7%) were from DFUs and 9 (33.3%) from healthy skin. In contrast, the coagulase-negative Staphylococcus (CoNS)/Mammaliicoccus isolates (n\u2009=\u200926), in particular S. epidermidis and S. haemolyticus were more prevalent in healthy skin, and , respectively. MLST, spa and SCCmec typing classified the 32 S. aureus isolates into 6 STs, ST672, ST80, ST241, ST1, ST97, ST291 and 4 unknown STs (STNF); 8 spa types, t044, t037, t3841, t1247, t127, t639, t937 and t9432 and 2 SCCmec types, type IV and type III(A). Among CoNS, the S. epidermidis isolates belonged to ST54, ST35 and ST640. S. haemolyticus belonged to ST3, ST25, ST29, ST1 and ST56. The sole M. sciuri isolate was found to carry an SCCmec type III(A). A wide range of virulence genes and antimicrobial resistance genes were found among our isolates, with varying distribution between species or STs. The pan-genome analysis revealed a highly clonal population of Staphylococcus isolates, particularly among S. aureus isolates. Interestingly, the majority of S. aureus isolates including MRSA, recovered from the healthy skin and DFUs of the same patient belonged to the same clone and exhibited similar virulence/resistance genotype.Staphylococcus/Mammaliicoccus spp. in DFIs, which could serve as a basis for further studies on these as well as other groups of pathogens associated with DFIs.Our study provides clinically relevant information on the population profile, virulence and antibiotic resistance of The online version contains supplementary material available at 10.1186/s12866-023-03087-2. Diabetes is a fast-growing global problem with huge social, health, and economic consequences . The prePeople with diabetes are at increased risk of long-term complications such as coronary heart disease, cerebrovascular and peripheral vascular diseases and diabetic foot ulcers (DFUs) . It was Microbial infections of the DFUs, termed diabetic foot infections (DFIs) are key contributors to the amputation risk . Limb loStaphylococcus are common colonizers of skin and mucous membranes of humans and animals, but also opportunistic pathogens capable of causing a wide range of infections. The staphylococci can be differentiated into Coagulase-Positive (CoPS) and Coagulase-Negative (CoNS), based on their ability to produce coagulase. Recently, five species among the CoNS , and belonging to S. sciuri group, were reclassified into the novel genus Mammaliicoccus, with Mammaliicoccus (M.) sciuri as the type species , Staphylococcus/Mammaliicoccus species were identified among the 58 isolates, including S. aureus , S. epidermidis , S. haemolyticus , S. simulans , S. caprae , S. hominis, S. saprophyticus and M. sciuri . The characteristics of the 58 isolates included in this study are shown in Table\u00a0Eight S. aureus isolates, 23/32 (71.9%) were recovered from DFUs and 9/32 (28.1%) from healthy skin. The 10 S. epidermidis isolates were recovered from 8 patients, including 6/10 (60%) from healthy skin and 4/10 (40%) from DFUs. All the S. haemolyticus (n\u2009=\u20098), M. sciuri (n\u2009=\u20091), S. hominis (n\u2009=\u20091) and S. simulans (n\u2009=\u20093) isolates were recovered exclusively from healthy skin, but S. caprae (n\u2009=\u20092) and S. saprophyticus (n\u2009=\u20091) were recovered only from DFUs.Among the 32 S. aureus isolates, 27/32 (84.4%) carried the mecA gene, and were therefore MRSA; 18/27 of which (66.7%) were from DFUs and 9/27 (33.3%) from healthy skin.Among the 32 S. aureus including MRSA isolates and CoNS were significantly associated with the source of isolation .Statistically, S. aureus were characterized based on the combination of MLST, SCCmec and spa typing. In silico determination of MLST revealed that S. aureus isolates belonged to 6 known STs including ST80 , ST241 , ST672 , ST1 , ST97 and ST291 , and 4 STNF .Clones of S. aureus isolates. The dominant one was t044 , followed by t037 , t3841 , t1247 and t127 , t639, t9432 and t937 .Eight spa types were identified among mec types were identified among MRSA isolates, type IV and type III(A) . The type IV isolates were assigned to subtype IVc(2B) and IVd(2B) .Two SCCMammaliicoccus isolates, SCCmec type III(A) was detected in the sole M. sciuri isolate.Among CoNS/The dominant MRSA clone was ST80- t044- IVc(2B), followed by ST241-t037- III(3\u00a0A)) ; whereas, ST672- t3841- IVd(2B) and STNF- t037- III(3\u00a0A) were each represented by 3/27 (11.1%) isolates. In addition, 2 other spa types were detected among ST80- IVc(2B) isolates, t1247 and t639 .2/5 (40%) of MSSA isolates belonged to ST1-t127, while ST97-t9432, ST291-t937 and STNF-t037 were each represented by one isolate .S. epidermidis isolates, 6/10 (60%) belonged to ST54, 2/10 (20%) to ST35 and 1/10 (10%) to ST640. 3/8 (37.5%) S. haemolyticus belonged to ST3 and 2/8 (25%) to ST25, while ST29, ST1 and ST56 were each represented by 1/8 (12.5%) isolate.Among The presence and distribution of the virulence genes are summarized in Tables\u00a02,S. aureus isolates including 42 adhesion genes and a large number of type 8 capsular polysaccharide, immune evasion and exoenzyme genes.A total of 116 virulence genes were detected among hlgA, hlgB, hlgC, hlb, hld and hla/hly), 13 staphylococcal enterotoxins (se) and staphylococcal enterotoxin-like toxins (sel) , with different carriage proportions ranging from 3.1 to 100%. ST1 isolates carried the highest number (n\u2009=\u20097) of se/sel genes, sea, seb, seh, sek, seq, selk and selq. In contrast, none of the se/sel genes were detected among the ST80 isolates.Thirty-five toxin-encoding genes were found among MRSA/MSSA isolates including 6 hemolysins or a toxic shock syndrome toxin (tst) gene.Remarkably, none of the lukD, lukE) were detected in all S. aureus isolates , while lukF/lukS-PV were detected only in ST80 isolates . In addition, edinB gene encoding epidermal cell differentiation inhibitors was also detected only in ST80 isolates and in ST291- t937 .The leukocidins genes , which was exclusively present in S. epidermidis isolates .On the other hand, the sole virulence factor found among the 26 CoNS/S. aureus ST or CoNS/Mammaliicoccus species was statistically significant. In contrast, no statistically significant association was found between the presence/absence of virulence genes and PEDIS grades or the source of isolates .The association of virulence genes with S. aureus is shown in Tables\u00a0mecA and blaZ, were detected among S. aureus isolates at frequencies of 84.4% (27/32) and 50% (16/32), respectively.The distribution of the genetic determinants of antibiotic resistance among the AME), aph(3\u2019)- III/ aph(3\u2019)- IIIa, were the most prevalent among S. aureus isolates . All ST80 isolates were positive for ant(6)-Ia and aph(3\u2019)-III/ aph(3\u2019)-IIIa genes, and all ST241 isolates were positive for 3 AME genes, ant(9)-Ia, aac(6\u2019)- aph(2\u2019\u2019) and aph(3\u2019)- III.The genes encoding aminoglycoside-modifying enzymes (S. aureus isolates. The msr(A) and mph(C) genes were detected in all the ST672 isolates , and the erm(A) in all the ST241 isolates .Four genes encoding resistance to macrolide-lincosamide-streptogramin B (MLSB) were detected in S. aureus isolates, tet(M) , tet(K) and tet(38) . Remarkably, only isolates belonging to t037 and harboring SCCmec-III (ST241 and STNF) carried tet(M).Three genes encoding resistance to tetracycline were detected among fusB and fusC genes coding for fusidic acid resistance were detected in all the ST80-t1247 and ST1-t127 , respectively. The dfrG gene coding for trimethoprim-sulfamethoxazole resistance was detected only in ST241 isolates .The M. sciuri isolates. 18/26 (69.2%) carried both mecA and blaZ genes. Remarkably, the single M. sciuri isolate harbored both mecA and mecA1 . 9/10 (90%) S. epidermidis isolates carried both fusB and fosB genes. In addition, msr(A) and mph(C) were detected in S. epidermidis and S. haemolyticus isolates. Moreover, ermC was found in S. haemolyticus and S. epidermidis isolates. aac(6\u2019)- aph(2\u2019\u2019)/ aac(6\u2019)-Ie/aph(2\u2019\u2019)-Ia genes were detected in S .haemolyticus and M. sciuri .As presented in Table\u00a0aph(3\u2019)-III/ aph(3\u2019)-IIIa and tet(K) genes were found exclusively in S. haemolyticus and in S. epidermidis, respectively. Genes conferring resistance to streptogramin (vat(B), vat(C) and vgb(B)), macrolides (vga(B) and vga(A)LC), kanamycin/neomycin (aadD), tetracycline (tet(L)), streptomycin (str) and to quaternary ammonium compounds (qacB) were detected only in S. haemolyticus isolates, at a frequency of one gene per isolate.The S. epidermidis , S. aureus , S. haemolyticus and M. sciuri . This is consistent with earlier findings that S. aureus isolates recovered from 4 distinct anatomical sites of patients with type 2 diabetes were highly related in the same patient was performed using Roary . Tree cop-value for describing possible associations between species/ST and virulence/resistance genes with PEDIS grades and the source of isolates. p-values\u2009<\u20090.05 were considered statistically significant.Data were analyzed using the Statistical Package for Social Sciences . Contingency tables were constructed and Chi-squared tests were used to calculate Below is the link to the electronic supplementary material.Supplementary Material 1Supplementary Material 2Supplementary Material 3"} +{"text": "Correction to: Psychometrika 10.1007/s11336-022-09879-1Second line in Eq. (15): \u201cbelow Eq. (23): \u201cSecond line in Eq. (27): \u201cThe original version of the article contains the below listed errors. The following transcription errors have been corrected:"} +{"text": "The HVTN 704/HPTN 085 clinical trial (AMP study) assessed the efficacy of VRC01 broadly neutralizing antibody infusions for HIV prevention. It offered access to oral pre-exposure prophylaxis (PrEP) at no-cost to all participants as standard of HIV prevention care. Understanding PrEP initiation among trial participants and describing its impact on study endpoints can guide future HIV prevention trial design.We characterized sociodemographic and geographic features of PrEP initiation (by self-report) using descriptive statistics. We used Cox models to identify factors associated with PrEP initiation and the association between PrEP initiation (as a time-dependent exposure) and HIV incidence.Of 2221 participants off PrEP at enrollment, 31.8% initiated PrEP during the trial. Median time to PrEP initiation was 60 days (range 1-673 days). Brazil had the highest proportion of PrEP initiation among their enrolled participants (83.2%) and Peru had the lowest (5.3%). In US sites, 54.2% initiated PrEP. Southern US sites had the highest proportion of PrEP initiation (68.8%) and the Midwest had the lowest (28.4%).In multivariate analysis, prior PrEP use [HR (95% CI) = 2.2 (1.3-4.0)] was associated with PrEP initiation. Participants from Switzerland [0.5 (0.3-1.0)] and Peru [0.08 (0.06-0.1)] had lower likelihood of PrEP initiation compared to the US, while participants from Brazil had higher likelihood [2.6 (2.0-3.3)]. Age, race, gender, and sexual orientation were not associated with PrEP initiation. HIV incidence rate was 3.6/100 person-years (PY) before PrEP initiation, compared to 1.2/100 PY after PrEP initiation. PrEP initiators had 58% less risk of acquiring HIV after adjusting for behavioral risk score and treatment arm. In the US, higher local PrEP-to-need ratio was also associated with lower PrEP initiation [0.9 per 5 units (0.8-1.0)].Providing PrEP access to AMP participants reduced HIV acquisition among PrEP initiators. Study endpoints were still met due to heterogenous regional PrEP uptake and lower PrEP effectiveness than expected. These data suggest that offering oral PrEP to HIV prevention trial participants as standard of care is a feasible option to consider for future efficacy HIV prevention trial design.Valeria D. Cantos, MD, Gilead Sciences: Grant/Research Support Srilatha Edupuganti, MD MPH FIDSA, Sanofi: Grant/Research Support Colleen F. Kelley, MD, MPH, Gilead Sciences: Grant/Research Support|Humanigen: Grant/Research Support|Moderna, Inc.: Grant/Research Support|Novavax, Inc: Grant/Research Support|Viiv Healthcare: Grant/Research Support"} +{"text": "Phage-antibiotic combinations (PAC) have been proposed for high inoculum daptomycin-nonsusceptible (DNS) MRSA infections refractory to conventional therapy. We studied PAC with synergistic activity against two DNS MRSA clinical bloods isolates .9 CFU/mL) using: i) modified checkerboard (CB) minimum inhibitory concentration (MIC); and ii) 24h time-kill assays (TKA). Synergistic activity in CB assays was defined as either: a fractional inhibitory concentration (FIC) index \u2264 0.5 in modified CB assays; or a \u2265 2 log10 CFU/mL reduction by PACs vs the most active single-agent regimen. Significant differences between regimens were assessed by ANOVA with Tukey\u2019s post hoc modification (P < 0.05).PAC containing DAP and/or ceftaroline (CPT) (each at \u00bd MIC) plus a 2-phage cocktail were tested at a high MRSA inoculum plus either DAP or DAP + CPT demonstrated robust synergistic activity vs. the next most effective regimen of CPT + Intesti13+Sb1 (P < 0.05 each). Against C37, Intesti13 + Sb1 (MOI of 1 and 0.1) with CPT or DAP + CPT were equally potent and effective regimens (-\u03947.14 log10 CFU/mL each), but neither were significantly better than the synergistic regimen of DAP + Intesti13 + Sb1 (-\u03946.65 log10 CFU/mL).By CB assay, synergistic activity was demonstrated with Intesti13 + Sb1 (MOI of 10 to 0.01) plus either DAP or DAP + CPT (FIC \u2264 0.5 for each combination). In 24h TKA vs These studies demonstrated positive phage-antibiotic synergy (PAS), with phage cocktail Intesti13 + Sb1 and either DAP or DAP + CPT. Addition of these phages to DAP or DAP + CPT combinations caused bactericidal and synergistic killing vs. CPT + phages. *, P<0.05. Abbreviations: CFU: colony forming units, GC: growth control, DAP: daptomycin, CPT: ceftaroline, MOI: multiplicity of infection, PAC: phage-antibiotic combination.These studies demonstrate positive phage-antibiotic synergy (PAS) with phage cocktail Intesti13 + Sb1 added to DAP, CPT, and DAP + CPT at an MOI of 1 and 0.1. Abbreviations: CFU: colony forming units, GC: growth control, DAP: daptomycin, CPT: ceftaroline, MOI: multiplicity of infection, PAC: phage-antibiotic combination.in vivo investigations of these candidate PACs, for treatment of high inoculum DNS MRSA infections is warranted.The two-phage cocktail used (Intesti13 + Sb1) demonstrated impressive synergistic activity against two DNS MRSA isolates in combination with DAP or DAP + CPT. Further experimental Arnold S. Bayer, MD, Akagera Medicines: Grant/Research Support|ContraFect Corporation: Grant/Research Support Michael J. Rybak, PharmD, PhD, MPH, Abbvie, Merck, Paratek, Shionogi, Entasis, La Jolla, T2 Biosystems: Advisor/Consultant"} +{"text": "Triticale is of great interest as an insurance crop that can ensure the stability of the gross harvest of feed and food grains at a lower cost. In Western Siberia, only winter triticale varieties are cultivated, however, spring triticales are important for cultivation in regions not suitable for winter crops. To create spring varieties with high yields and good grain quality, it is necessary to study and enrich the gene pool, identify donors of economically valuable traits. One of the possible ways to solve this problem can be through the production of secondary hexaploid triticales with the involvement of the tetraploid wild-growing species of emmer wheat Triticum dicoccum (Schrank) Schuebl. The aim of this work was to create and study hybrids of emmer T. dicoccum (Schrank) Schuebl. with hexaploid triticale using genomic in situ hybridization for staining of meiotic chromosomes and analysis of plant productivity elements in F4\u2013F8. DT4, DT5, DT6 plants and the prebreeding F6 forms obtained from them \u2013 DT 4/168, DT 5/176 and DT 6/186 \u2013 were selected according to the characteristics of the productivity and the nature of the grain in the F4 hybrid population. The offspring of hybrids DT4 and DT5 and prebreeding forms DT 4/168 and DT 5/176 had an increased grain nature (over 750 g/l), but low productivity. The hybrid DT6 and the breeding form DT 6/186 obtained from it had high grain productivity , but, like the paternal form of triticale UK 30/33, had a reduced nature of the grain. In F8 DT 6/186 plants, 7 homologous pairs of rye chromosomes and from 27 to 30 wheat chromosomes were found in meiosis, which indicates the presence of a complete rye genome and two wheat \u0410\u0410\u0412\u0412 genomes. Rye chromosomes showed stable formation of bivalents in contrast to wheat chromosomes, which caused the presence of aneuploids in plant populations. Thus, hexaploid forms DT 4/168 and DT 5/176 with well-made smooth grain and high grain size were obtained, which can be used as a source of this trait for selection of food-grade triticale. DT 6/186 is a promising form for further breeding in order to obtain high-yielding forms of triticale. Triticale is a wheat and rye hybridof a relatively short evolutionary history as an allopolyploidspecies. The first naturally created fertile wheat\u00d7rye hybridswere discovered in the late 1920s at the South-Eastern agriculturalexperimental station in Saratov . Theplants had intermediate traits and were described as a new botanicalspecies Triticum Secalotriticum saratoviense Meisterby G.K. Meister . Meister immediately predictedthe practical value of these intergeneric crossings. Thefirst man-made wheat\u00d7rye hybrids were obtained in 1888 by the German plant breeder W. Rimpau, who described 12 plants descending froma wheat\u00d7rye hybrid generally recognized as the first triticales. The cytological analysis of thefirst triticales developed in Russia and Germany showed thesomatic chromosome number of 56 (8\u0445) , which demonstrated the combinationof four genomes as follows: AABBDDRR, AABBDD,soft wheat, and RR rye.Octoploid triticales were of great interest for plant breedersdue to high seed set per spike, increased plant pathogen resistance,and resistance to environmental stresses. However, theprimary triticale lines suffered from meiotic errors and high frequency of aneuploidy in earlier generations, which caused reduced fertility. Grain shriveling andlatenessof maturity in octoploid forms were also consideredas limitations for their introduction as cultivars. As a result,there have been global efforts to develop the technology forobtaining more promising lines with various valuable breedingtraits, which eventually produced hexaploid triticales.Primary hexaploid triticales of the AABBRR genome typewere obtained as crossings of tetraploid wheats and S. cereale rye . However, undesirabletraits were not completely eliminated. Agronomicallyvaluable traits were improved by enriching the triticalegene pool with crossing experiments involving octoploidlines and commercial soft wheat varieties, as well as hexaploidtriticales with full rye genome and two wheat genomesidentified in the progeny of octoploid triticales as a resultof D-genome chromosome elimination . The crossing of two primaryoctoploid triticales produced hexaploid offspring, and breed-ingprograms were focused on hybridization of these octoploidswith the hexaploids identified in the progeny .Hexaploid triticales were more stable in terms of productivity. As a result, various recom-binantforms of secondary triticales were derived and karyotyped,and some of them having combined wheat-rye genomesshowed commercial value .Agronomic traits of triticales were further improved byintergeneric and interspecific crossings. Aegilops crassa , Ae. juvenalis , Ae. squarrosa and Ae. triaristata , Agropyron intermedium ssp. trichophorum(2n = 42) , Hordeum parodii Covas, H. vulgare L. and T. monococcum L. plants wereused in hybridization experiments with hexaploid triticales.Intergeneric polyploid triticales were also bred through hybridizationwith intermediate forms sharing at least one setof chromosomes (genome) with the triticale genome. Thesehybridization efforts produced plants with resistance genesagainst diseases. Lines isolated in the progeny of triticale hybrids(AABBRR) and amphidiploids were resistant toyellow rust . Hybridization of a hexaploidtriticale and an amphiploid intermediate form produced addition andsubstitution lines with the 3Sv Ae. variabilis chromosome carryingthe powdery mildew resistance gene Pm13 . Addition and substitution lines for chromosome 2Dwith the leaf-rust resistance gene Lr39 and semidwarf geneRht8, as well as chromosome 3D (or 3D/3B) with the Lr32 gene were isolated in the progeny of triticale \u00d7 amphiploid hybrids .Thanks to breeding achievements, triticale has becomea new economically significant cereal species characterizedby high grain and vegetative mass productivity, that could beused as forage and green feed . In the last three decades, its products have becomeincreasingly significant, which is demonstrated by increasingcrop acreage across the world, from 1,453,269 ha in 1994 to4,157,018 ha in 2016. Triticale grains are used to producebioethanol and food wrap, as well as various food products , andbran is used as the source of prebiotics and antioxidants foryoghurts. Food-grade triticale grains are comparable to wheatin macro- and micronutrient contents . Proteincontent in triticale grains is 1\u20131.5 % higher than in wheat and3\u20134 % higher than in rye, gluten content matches that in wheator is 2\u20134 % higher . However, triticaleunderperforms in test weight. This parameter is closely relatedto the plumpness and hardness of grains, as well as to theirsize and shape. Average test weight for wheat is 700\u2013810 g/l.At test weights below 740 g/l, flour yield tends to decreaserapidly as test weight goes down. Most spring triticales haveshriveling grains and low flour yields, which limits their usein bread making .Development of domestic high-productivity triticale varietieswith high grain quality requires further study and enrichmentof the gene pool, as well as identification of donors foreconomically valuable traits. One way to solve this problemis to obtain secondary hexaploid triticales using emmer wheatT. dicoccum (Schrank) Schuebl., a tetraploid wild-growingwheat with long, large, and plump grains.The goal of the present study was to breed new forms ofhexaploid triticales (\u0410\u0410\u0412\u0412RR genome type) with improvedtest weights by crossing emmer with triticale and study their productivity and meioticstability with chromosome staining using genomic in situhybridization.Plant material. New forms of hexaploid triticale were obtainedby hybridization of emmer (T. dicoccum (Schrank)Schuebl.) and triticale . IntergenericF1 hybrid of emmer lines (L133 \u00d7 PKK) \u00d7 k-25516 (AABBgenome) was used as maternal plants. Awned semi-hullessemmer (L133 \u00d7 PKK) created by VIR researchers is characterizedby brittle spikes and low productivity, and awnlessemmer k-25516 was obtained at Siberian Research Instituteof Plant Production and Breeding (SRI PPB), ICG SBRAS from the population of awned emmer wheat from theVIR collection. The paternal plants were represented by a selectionform of hexaploid triticale UK 30/33 selected fromthe population of cytogenetically unstable octoploid triticaleUK30 (AABBDDRR genome) developed at the SRI PPB bycrossing the Ulyanovka soft wheat variety with the Korotkostebelnaya69 short stem rye with subsequent doubling ofchromosome number induced by colchicine water solution.The progeny of three F4 hybrids DT4, DT5, and DT6, andthree selection forms DT 4/168, DT 5/176, and DT 6/186 isolatedin F5 from hybrid populations DT4, DT5, and DT6 respectivelywas selected for the study. In 2020, their F6 progenywas seeded for research purposes along with F4 hybrids atthe nursery for distant wheat hybrids in the field of SRI PPB.Fluorescence in situ hybridization of meiotic chromosomes.To evaluate the meiotic stability in the selection forms,two most productive plants DT 6/186/156 and DT 6/186/165were selected in the F7 progeny of plant DT 6/186, and theirF8 seeds were seeded in the hydroponic greenhouse of theICG SB RAS in spring 2021. The chromosomal behavior ofthe progeny was studied using routine acetocarmine stainingprotocol and FISH staining (fluorescence in situ hybridization)following the technique described earlier .The meiocytes were analyzed at the diakinesis stage, metaphaseI (\u041cI), anaphase I (AI), and telophase II (TII). Theprobes used in the analysis were as follows: Aegilops tauschiipAet6-09 specific for centromere repeats in rice, wheat,rye, and barley chromosomes ; pAWRcspecific for centromere repeats in rye chromosomes , and rye genomic DNA. DNA repeat samples ofpAet6- 09 and pAWRc were the courtesy of Dr. A. Lukaszewcki.Centromere-specific probes were labeled with biotin 16-dUTPor digoxigenin 11-dUTP by means of polymerase chain reaction(PCR). The total rye DNA was labeled by Nick translationwith digoxigenin 11-dUTP. The probes were combined indifferent proportions and mixed with blocking wheat DNA.The preparations were mounted in Vectashield antifade solution(Vector Laboratories) slowing down fluorescence fadingand including 1 \u03bcg/ml DAPI for chromatin staining. Allpreparations were analyzed using an Axio Imager M1 microscope, the images were recorded usinga ProgRes MF camera at the Centerof Microscopic Analysis of Biological Objects, SB RAS andprocessed using Adobe Photoshop CS2 software.Analysis of economically valuable traits. Structuralanalysis of the plants was performed at the facility equippedfor metric measurements, threshing, and seed weighting. Asa result, the following data on productivity elements wereobtained: spike length; spike density; grain weight per spike;thousand kernel weight; grain number per spikelet; testweight measured using a microchondrometer ; and grain productivity per 1 m2. Statisticalprocessing of the results was carried out following thestandard technique . Significance of differencesbetween mean values of two samples was estimatedusing Student\u2019s t-test.The parental-line plants had different spike and grain morphology.The emmer plants (L133 \u00d7 PKK) had short, awned,brittle spikes and smooth, long grains . The k-25516emmer sample was an awnless plant with thin, long grains . Triticale UK 30/33 had a dense, awned spike and grains similar to those of soft wheat in shape but shriveling.Plants of three emmer\u00d7triticale F4 hybrids had differentspike morphology . The DT6 hybridhad a dense, awned spike. The plants of the remaining twohybrids had looser spikes. The spikes were sterile at the endsand therefore often susceptible to ergot.All hybrids had a hair neck similar to the paternal triticaleUK 30/33. This means that these genotypes have a gene responsiblefor manifestation of this trait localized in the longarm of chromosome 5R.Triticale UK 30/33 had a short spike, low test weight, andmedium grain productivity (see Table 1). Selection forms andhybrids, except for DT5, had a longer spike than the paternalform UK 30/33. Hybrid DT5 had low productivity due toflower sterility in the upper part of the spike and low thousandkernel weight. Hybrid DT4 had a high thousand kernelweight of 50 \u00b1 2 g, and the highest test weight of 806 \u00b1 14 g/l. However, its grain productivity, although higher than that ofDT5, was still not too high due to low seed set of spikes andspikelets. Flowers at the top of the spike were often sterile aswell. Hybrid DT6 was characterized by dense spikes and highgrain productivity (785 \u00b1 41 g/m2), as well as seed set of spikesand spikelets. The spikes were fertile along their full length.Selection forms DT 4/168, DT 5/176, and DT 6/186 haddifferent grain weights per spike, grain numbers per spike,test weights, and productivities. DT 4/168 had denser spikesand slightly higher seed sets of spikes and spikelets comparedto the DT4 hybrid it was obtained from. Breeding sampleDT 5/176 was more productive than the initial DT5 hybrid,but it had the lowest productivity among the three breedingsamples studied. Small spike size and sterility of 3\u20137 spikeletsin the upper part of the spike resulted in low productivityof hybrids DT5 and DT 5/176. The DT 6/186 line had thehighest seed set and productivity among the studied lines.Despite the lowest test weight values similar to triticaleUK 30/33 (706 \u00b1 25 g/l), grain productivity per plot reached822 \u00b1 74 g/ m2. DT 6/186 had a smoother overall morphologythan the initial hybrid DT6, but higher breeding value due toits higher grain productivity.Cytological analysis of the progeny of two plants (DT 6/186/156 and DT 6/186/165) from the highly productive DT 6/186line revealed instability in chromosome number and errors inchromosomal behavior in the first and second meiotic divisions.Chromosome staining using genomic in situ hybridizationin these plants showed 14 rye chromosomes formingbivalents, which implied the presence of seven homologouspairs . However, the bivalent chromosomes demonstratedpremature separation in some meiocytes (desynapsis),with rye chromosomes becoming univalent and distributinganomalously between the poles .Chromosome number in the discovered aneuploid plantsvaried from 2n = 41 to 2n = 44. Among the ten plants from theDT 6/186/156 progeny, only one plant had chromosome number2n = 42 , while there were no plants with euploidchromosome numbers in the progeny of DT 6/186/165.Univalents were discovered in the metaphase I , which were lagging at the equator during chromosomeseparation in anaphase I in 86.75 \u00b1 4.56 and61.32 \u00b1 2.81 % of cells in DT 6/186/156 and DT 6/186/165respectively . The lagging chromosomeswere divided into sister chromatids or broken at the centromere. Instability of chromosome separationduring the division resulted in micronuclei formation atthe tetrad stage . Micronuclei were observed in 60.29 \u00b1 3.14 and 72.16 \u00b1\u00b1 2.29 % tetrads in DT 6/186/156 and DT 6/186/165, respectively(see Table 2). Even the euploid plant with 2n = 42(DT 6/186/156) had micronuclei in 51.48 % tetrads, whichprevented us from considering this plant fully cytogeneticallystable.Plants with the minimum number of anomalous meiocytesin anaphase I and telophase II were selected from populationsDT 6/186/156 and DT 6/186/165 based on the results of theanalysis.Triticale as an agricultural cropcombines wheat\u2019s high yield potential with rye\u2019s resistanceto biotic and abiotic stresses, which increases its adaptability to cultivation conditions in salty or highly acidic soils and inpresence of toxic heavy metals. Thanks to these traits, triticaleis of great interest as an emergency crop ensuring stable grossharvest of forage and food grains at lower costs . Despite today\u2019s applications of triticale grainsbeing mostly restricted to forage in animal husbandry and productionof feed and bioethanol, there is a rising interest in theuse of triticale grains in human food products. Triticale grainshave proven nutritional and dietary value , since they include not only proteins, carbohydrates,and fats, but also vitamins, minerals, and dietaryfibres (14\u201318 %) . Comparedto that of wheat, the protein from its grains has a richer aminoacid profile, particularly in indispensable amino acids, suchas lysine, threonine, and leucine . Triticale starch amounting to 3/4 of thekernel weight has a significantly lower amylose content comparedto rye and wheat , which ensures its betterdigestion by humans .To increase the share of triticales in production of breadsand pastries, in recent decades breeding efforts have beenaimed at increasing the quality of grains and finished products,which has resulted in development of triticale bread-makingvarieties , so State standards for triticaleflour have been developed (State Standard 34142-2017).The characteristics of winter triticale varieties also includeapplicability for bread making. Triticale breeding efforts inRussia and other countries are primarily aimed at developingwinter varieties . However, grainquality assessment of the samples from the spring triticalecollection showed that spring triticales have good potentialfor creating bread-making varieties . The samples with such improvedparameters as protein content, test weight, falling number,vitreousness, gluten quantity and quality, etc., are used inbreeding for improved grain quality .A trait such as high test weight can be transferred by distanthybridization. This parameter is closely related to geneticallydetermined parameters such as grain plumpness, hardness, andshape. In the present paper, tetraploid emmer wheat T. dicoccum(Schrank) Schuebl. with long, large, and plump grainswas used as the maternal line for hybridization with hexaploidtriticale . As a result, new hexaploidforms of triticale with AABBRR genome types were created,which is confirmed by the analysis of meiotic chromosomalbehavior using genomic in situ hybridization. Seven pairs ofrye chromosomes and 27 to 30 wheat chromosomes were observedin the plants, which implies the presence of a completerye genome and two wheat genomes. Three plants, DT4, DT5,and DT6, were isolated in the F4 population, the progeny ofwhich demonstrated test weight values significantly exceedingthose of the initial triticale line, and test weights in the progenyof DT 4/168, DT 5/176, and DT 6/186 forms from F6 werehigher or on par with those of the initial triticale line. Theseplants had different productivity values, with the highest onesin F4 recorded in the DT6 line (785 \u00b1 41 g/m2). The respectivevalue for DT 6/186, i. e., the progeny of the latter in F6,reached 822 \u00b1 74 g/m2. The DT 4/168 and DT 5/176 lines areof moderate interest for further research into improvement ofbread-making properties of triticale grains.The study of the meiotic behavior of rye and wheat chromosomesin the progeny of F8 plants DT 6/186/156 andDT 6/186/165 showed that they had not yet achieved cytogeneticstability, which was indicated by the discovered chromosomeseparation errors and the presence of aneuploids in thepopulations. Chromosome separation errors mostly occurredin wheat chromosomes due to their monosomy. Cytologicalinstability and aneuploidy in octoploid and hexaploid wheatryeallopolyploids have been an issue from the start , but secondary triticales turned outto be more cytogenetically stable than primary ones . Cytological study of triticales showed that the interactionbetween wheat and rye genomes in the cells of the sameplant resulted in physiological defects in cells persisting fordecades at least. Meiotic and mitotic errors were found bothin the triticale obtained by Rimpau in 1888 and in the triticales obtained later. Despite thecomplete set of chromosomes, meiotic univalents were foundin triticales with different ploidy levels . The studyinto meiotic chromosomal behavior in triticales in the presentand earlier papers demonstrated that while only bivalentswere present at the diakinesis stage, univalents appeared inmetaphase I as a result of to produce lagging chromosomes atthe equator . Presumably, aneu-ploidcells in triticales may emerge as a result of asynchronousseparation of rye and wheat chromosomes and their laggingin anaphase and telophase . Thepresumed cause of meiotic instability in the obtained amphidiploids is an imbalance in the genetic system of meioticpairing and the differences in cell cycles between wheat andrye .It is known for a fact that chromosome separation dependson kinetochore function . It was found thatkinetochore protein CENH3 produced by one of the parentsmaintained the function of other parental kinetochores in stablehybrids, despite the differences between DNA sequences ofcentromere regions in parental lines . It wasalso shown that cytogenetic stability in triticales could also belinked to increased expression of rye-specific CENH3 formsin a hybrid genome .Another possible cause of cytogenetic instability of theobtained triticales could be a nuclear-cytoplasmic incompatibility,because the hybrids are bred using an intergenericF1 hybrid of emmer lines (T. dicoccum (Schrank) Schuebl.)(L133 \u00d7 PKK) \u00d7 k-25516 (genome AABB) as the maternal form.The AABB genomes in paternal triticale forms originate fromsoft wheat, while the rye genome is used as the base. Selectionof genotypes of wheat varieties during triticale backcrossingmay lead to recovery of fertility and cytogenetic stability innew forms, as exemplified by alloplasmic soft wheat lines(H. vulgare)-T. aestivum .The result of this work was to create and study hybrids ofemmer T. dicoccum (Schrank) Schuebl. with hexaploid triticale.According to the characteristics of productivity and testweight values of the grain, hexaploid prebreeding forms F6were isolated \u2013 DT 4/168, DT 5/176 and DT 6/186. Thus,hexaploid forms DT 4/168 and DT 5/176 with well-filled,smooth grains and high test weights that can be used as thesource of said traits in food-grade triticale breeding havebeen obtained. The DT 6/186 line shows promise in terms ofbreeding for high yields. As a result of the analysis of meioticdivision in DT 6/186 plants, this sample is unstable forwheat chromosomes, therefore, aneuploids will occur in theoffspring. To restore fertility and cytogenetic stability of newforms of triticale with emmer cytoplasm and chromosomes, itis necessary to select the genotypes of wheat varieties duringbackcrossingThe authors declare no conflict of interest.Abdelkawy R.N.F., Turbayev A.Zh., Solov\u2019iev A.A. Technologicalproperties of spring triticale grain grown in the Central EconomicRegion, Russia. Vestnik Kurskoy Gosudarstvennoy SelskokhozyastvennoyAkademii = Bulletin of the Kursk State Agricultural Academy.2020;5:87-97. (in Russian)Ammar K., Mergoum M., Rajaram S. The history and evolution of triticale.In: Triticale Improvement and Production (FAO Plant Productionand Protection Paper. 179). Rome, 2004;1-10.Ayalew H., Kumssa T.T., Butler T.J., Ma X.-F. Triticale improvementfor forage and cover crop uses in the Southern Great Plains of theUnited States. Front. Plant Sci. 2018;9:1130. DOI 10.3389/fpls.2018.01130.Badaev N.S., Badaeva E.D., Bolsheva N.L., Maximov N.G., ZeleninA.V. Cytogenetic analysis of forms produced by crossing hexaploidtriticale with common wheat. Theor. Appl. Genet. 1985;70(5):536-541. DOI 10.1007/BF00305987Balyan H.S., Fedak G. Meiotic study of hybrids between barley(Hordeum vulgare L.) and Triticale .J. Hered. 1989;80(6):460-463. DOI 10.1093/oxfordjournals.jhered.a110898Bocharnikova O.G., Gorbunov V.N., Shevchenko V.E. Assessment ofspring triticale varieties in performance and grain quality. VestnikVoronezhskogo Gosudarstvennogo Agrarnogo Universita = Vestnikof Voronezh State Agrarian University. 2017;2(53):23-30. DOI10.17238/issn2071-2243.2017.2.23. (in Russian)Cheng Z.J., Murata M. Loss of chromosomes 2R and 5RS in octoploidtriticale selected for agronomic traits. Genes Genet. Syst. 2002;77(1):23-29. DOI 10.1266/ggs.77.23.Dospekhov B.A. Methodology of Field Experiments. Moscow: AgropromizdatPubl., 1985. (in Russian)Dou Q., Tanaka H., Nakata N., Tsujimoto H. Molecular cytogeneticanalyses of hexaploid lines spontaneously appearing in octoploidTriticale. Theor. Appl. Genet. 2006;114(1):41-47. DOI 10.1007/s00122-006-0408-x.Evtushenko E.V., Lipikhina Y.A., Stepochkin P.I., Vershinin A.V. Cytogeneticand molecular characteristics of rye genome in octoploidtriticale . Comp. Cytogenet. 2019;13(4):423-434. DOI 10.3897/CompCytogen.v13i4.39576.Francki M.G. Identification of Bilby, a diverged centromeric T1-copiaretrotransposon family from cereal rye . Genome.2001;44(2):266-274. DOI 10.1139/g00-112.Fu S., Ren Z., Chen X., Yan B., Tan F., Fu T., Tang Z. New wheat-rye5DS-4RS\u00b74RL and 4RS-5DS\u00b75DL translocation lines with powderymildew resistance. J. Plant Res. 2014;127(6):743-753. DOI10.1007/s10265-014-0659-6.Grabovets A.I., Krokhmal A.V., Dremucheva G.F., KarchevskayaO.E.Breeding of triticale for baking purposes. Russian AgriculturalSciences.2013;39(3):197-202Gruszecka D., Tarkowski C., Stefanowska G., Marciniak K. Cytologicalanalysis of F1 Aegilops hybrids with Triticosecale. In: Guedes-Pinto H., Darvey N., Carnide V.P. (Eds.) Triticale: Today and Tomorrow.Developments in Plant Breeding. Vol. 5. Dordrecht: Springer,1996;195-201. DOI 10.1007/978-94-009-0329-6_24.Gupta P.K., Fedak G. Intergeneric hybrids between \u00d7 Triticosecalecv. Welsh (2n = 42) and three genotypes of Agropyron intermedium(2n = 42). Can. J. Genet. Cytol. 1986a;28(2):176-179. DOI 10.1139/g86-024.Gupta P.K., Fedak G. Variation in induction of homoeologous pairingamong chromosomes of 6x Hordeum parodii as a result of threetriticale cultivars. Can. J. Genet. Cytol.1986b;28(3):420-425. DOI 10.1139/g86-062Gustafson J.P., Bennett M.D. Preferential selection for wheat-rye substitutionsin 42-chromosome triticale. Crop Sci. 1976;16(5):688-693. DOI 10.2135/cropsci1976.0011183X001600050022x.Hao M., Luo J., Zhang L., Yuan Z., Yang Y., Wu M., Chen W., Zheng Y.,Zhang H., Liu D. Production of hexaploid triticale by a synthetichexaploid wheat-rye hybrid method. Euphytica. 2013;193:347-357.DOI 10.1007/s10681-013-0930-2.Ishii T., Karimi-Ashtiyani R., Houben A. Haploidization via chromosomeelimination: means and mechanisms. Annu. Rev. Plant Biol.2016;67:421-438. DOI 10.1146/annurev-arplant-043014-114714.Ivanova Yu.N., Solovey L.A., Loginova D.B., Miroshnikova E.E.,Dubovets N.I., Silkova O.G. The creation and characterization ofthe bread wheat line with a centric translocation T2DL.2RL. VavilovskiiZhurnal Genetiki i Selektsii = Vavilov Journal of Geneticsand Breeding. 2019;23(7):846-855. DOI 10.18699/VJ19.558. (inRussian)Jenkins B.C. History of the development of some presently promisinghexaploid Triticales. Wheat Inform. Serv. 1969;28:18-20.Kaltsikes P.J. Univalency in triticale. In: Macintyre R., Campbell M.(Eds.) Triticale: Proceedings of an international symposium.El Batan, Mexico: Int. Develop. Res. Centre, 1974;159-167.Kang H., Wang H., Huang J., Wang Y., Li D., Diao C., Zhu W., Tang Y.,Wang Y., Fan X., Zeng J., Xu L., Sha L., Zhang H., Zhou Y. Divergent development of hexaploid triticale by a wheat\u2013rye\u2013Psathyrostachyshuashanica trigeneric hybrid method. PloS One. 2016;11(5):e0155667. DOI 10.1371/journal.pone.0155667Krokhmal A.V., Grabovets A.I. Triticale grain quality formation. IzvestiyaOrenburgskogo Gosudarstvennogo Agrarnogo Universiteta =Proceedings of the Orenburg State Agrarian University. 2015;2(52):46-48. (in Russian)Krolow K.D. Aneuploidie und Fertilitat bei amphidiploiden Weizen-Roggen-Bastarden . I. Aneuploidie un Selection auf Fertilit\u00e4tbei oktoploiden Triticale-Formen. Z. Pflanzenzucht. 1962;48(2):177-196Kwiatek M., Belter J., Majka M., Wi\u015bniewska H. Allocation of theS- genome chromosomes of Aegilops variabilis Eig. carrying powderymildew resistance in triticale . Protoplasma.2016;253:329-343. DOI 10.1007/s00709-015-0813-6.Kwiatek M., Majka M., Wi\u015bniewska H., Apolinarska B., Belter J. Effectivetransfer of chromosomes carrying leaf rust resistance genesfrom Aegilops tauschii Coss. into hexaploid triticale using Ae. tauschii \u00d7 Secale cereale amphiploid forms. J. Appl.Genet. 2015;56:163-168. DOI 10.1007/s13353-014-0264-3.Levitsky G.A. On the history of prolific intermediate constant wheatryehybrids. In: Levitsky G.A. Plant Cytogenetics. Moscow: NaukaPubl., 1978;251-253. (in Russian)Levitsky G.A., Benetzkaja G.K. Cytology of the wheat-rye amphidiploids.In: Levitsky G.A. Plant Cytogenetics. Moscow: Nauka Publ.,1978;224-250. (in Russian)Li H., Guo X., Wang C., Ji W. Spontaneous and divergent hexaploidtriticales derived from common wheat \u00d7 rye by complete eliminationof D-genome chromosomes. PLoS One. 2015;10(3):e0120421. DOI10.1371/journal.pone.0120421Lukaszewski A.J., Gustafson J.P. Translocations and modifications ofchromosomes in triticale \u00d7 wheat hybrids. Theor. Appl. Genet. 1983;63(1):49-55. DOI 10.1007/BF00303771.Lukaszewski A.J., Gustafson J.P. Cytogenetics of triticale. In: Janick J.(Ed.) Plant Breeding Reviews. 1987;5:41-93. DOI 10.1002/9781118061022.ch3.McGoverin C.M., Snyders F., Muller N., Botes W., Fox G., Manley M.A review of triticale uses and the effect of growth environmenton grain quality. J. Sci. Food Agric. 2011;91(7):1155-1165. DOI10.1002/jsfa.4338.Meister G.K. Natural hybridization of wheat and rye in Russia.J. Hered. 1921;12(10):467-470. DOI 10.1093/oxfordjournals.jhered.a102049Meleshkina E.P., Pankratieva I.A., Politukha O.V., Chirkova L.V., ZhiltsovaN.S. Evaluation of triticale grain quality. Khleboprodukty= Grain Products. 2015;2:48-49. (in Russian)Mergoum M., Singh P.K., Pe\u00f1a R.J., Lozano-del R\u00edo A.J., Cooper K.V.,Salmon D.F., G\u00f3mez-Macpherson H. Triticale: a \u201cnew\u201d crop withold challenges. In: Carena M. (Ed.) Cereals. Handbook of PlantBreeding. Vol. 3. New York: Springer, 2009. DOI 10.1007/978-0-387-72297-9_9.Merker A. Chromosome composition of hexaploid triticale. Hereditas.1975;80(1):41-52. DOI 10.1111/j.1601-5223.1975.tb01498.x.M\u00fcntzing A. Genetic Research. Stockholm: Lts F\u00f6rlag, 1961. M\u00fcntzing A. Historical review of the development of triticale. In:Macintyre R., Campbell M. (Eds.) Triticale: Proceedings of an internationalsymposium. El Batan, Mexico, 1\u20133 October 1973. Int.Develop. Res. Centre, 1974;13-30.Neumann M., Kison H.U. Hybridization between hexaploid triticaleand Triticum monococcum L. II. The F1 generation AuAbBR.Hereditas. 1992;116(3):291-294. DOI 10.1111/j.1601-5223.1992.tb00157.x.Oettler G. The fortune of a botanical curiosity \u2013 Triticale: past, presentand future. J. Agric. Sci. 2005;143(5):329-346. DOI 10.1017/S0021859605005290.Olesczuk S., Lukaszewski A.J. The origin of unusual chromosome constitutionsamong newly formed allopolyploids. Am. J. Bot. 2014;101(2):318-326. DOI 10.3732/ajb.1300286.Orlovskaya \u041e.\u0410., Leonova I.N., Adonina I.G., Salina \u0415.\u0410., KhotylevaL.V., Shumny V.K. Molecular cytogenetic analysis of triticaleand wheat lines with introgressions of the genetic material of Triticeaetribe species. Russ. J. Genet. Appl. Res. 2016;6(5):527-536.DOI 10.1134/S2079059716050087.Pershina L.A., Belova L.I., Trubacheeva N.V., Osad\u0441haya T.S., ShumnyV.K., Belan I.A., Rosseeva L.P., Nemchenko V.V., AbakumovS.N. Alloplasmic recombinant lines (H. vulgare)-T. aestivumwith 1RS.1BL translocation: initial genotypes for production ofcommon wheat varieties. Vavilovskii Zhurnal Genetiki i Selektsii =Vavilov Journal of Genetics and Breeding. 2018;22(5):544-552.DOI 10.18699/VJ18.393Pershina L.A., Numerova O.M., Belova L.I., Devyatkina E.P., ShumnyV.K. Restoration of fertility in backcross progeny of barleywheathybrids Hordeum vulgare L. (2n = 14) \u00d7 Triticum aestivum L.(2n = 42) in relation to wheat genotypes involved in backcrosses.Russ. J. Genet. 1999;35(2):176-183.Pisarev V.E. Breeding of Grain Crops. Moscow, 1964. (in Russian)Rakha A., \u00c5man P., Andersson R. Dietary fiber in triticale grain: variationin content, composition, and molecular weight distribution ofextractable components. J. Cereal Sci. 2011;54(3):324-331. DOI10.1016/j.jcs.2011.06.010.Sanei M., Pickering R., Kumke K., Nasuda S., Houben A. Loss ofcentromeric histone H3 (CENH3) from centromeres precedes uniparentalchromosome elimination in interspecific barley hybrids.Proc. Natl. Acad. Sci. USA. 2011;108(33):E498-E505. DOI 10.1073/pnas.1103190108.Shishkina A.A., Badaeva E.D., Soloviev A.A. Features of karyotypeorganization in some forms of spring triticale. Izvestiya TimiryazevskoySelskokhozyaystvennoy Akademii = Proceedings of the TimiryazevAgriculturalAcademy. 2009;2:123-130. (in Russian)Shkutina F.M., Khvostova V.V. Cytological investigation of Triticale.Theor. Appl. Genet. 1971;41:109-119. DOI 10.1007/BF00277752.Shulyndin A.F. Genetic grounds for the synthesis of various triticalesand their improvement by breeding. In: Triticale: Study and Breeding.Leningrad: VIR Publ., 1975;53-56. (in Russian)Silkova O.G., Ivanova Y.N., Loginova D.B., Solovey L.A., SychevaE.A., Dubovets N.I. Karyotype reorganization in wheat\u2013rye hybridsobtained via unreduced gametes: is there a limit to the chromosomenumber in triticale? Plants. 2021;10(10):2052. DOI 10.3390/plants10102052.State Register for Selection Achievements Admitted for Usage . Vol. 1. Plant varieties . Moscow:Rosinformagrotech, 2022. (in Russian)State Standard 34142-2017. Tritical Flour: Specifications. 2018. Availableat: https://docs.cntd.ru/document/1200146040 (in Russian)Stepochkin P.I. The appearance of 6x triticale plants among the C2offspring of homogenomic 8x triticale. Genetika = Genetics (Moscow).1978;14(9):1658-1659. (in Russian)Stepochkin P.I., Vladimirov N.S. Chromosome number, seed set, andwinter hardiness in C1 winter lines of homogenomic 8x triticale.Genetika = Genetics (Moscow). 1978;14(9):1597-1603. (in Russian)Stepochkina N.I., Stepochkin P.I. Use of microchondrometer for determinationof grain nature of single plants of triticale and wheat.Dostizheniya Nauki i Tekhniki APK = Achievements of Science andTechnology of AIC. 2015;29(11):39-40. (in Russian)Torikov V.Ye., Shpilev N.S., Mameyev V.V., Yatsenkov I.N. Comparativecharacteristics of grain quality of winter triticale varieties grownin the south-west of Russia. Vestnik Altayskogo GosudarstvennogoAgrarnogo Universiteta = Bulletin of the Altai State AgriculturalUniversity. 2019;2(172):49-56. (in Russian)Trubacheeva N.V., Divashuk M.G., Chernook A.G., Pershina L.A.The effect of chromosome arm 1BS on the fertility of alloplasmic recombinant lines in bread wheat with the Hordeum vulgare cytoplasm.Plants (Basel). 2021;10(6):1120. DOI 10.3390/plants10061120Turbayev A.Z., Sergaliev N.K., Soloviev A.A. Comparative study ofsome genotypes of spring triticale for grain qualities. Izvestiya TimiryazevskoySelskokhozyaystvennoy Akademii = Izvestiya of TimiryazevAgricultural Academy. 2019;1:19-33. (in Russian)Weimarck A. Elimination of wheat and rye chromosomes in a strainof octoploid Triticale as revealed by Giemsa banding technique.Hereditas. 1974;77(2):281-286. DOI 10.1111/j.1601-5223.1974.tb00940.x.Yerzhebayeva R.S., Tajibaev D., Abugalieva A.I. Grain quality ofsamplesof the spring triticale collection ].Sibirskii Vestnik Sel\u2019skokhozyaistvennoi Nauki = Siberian Heraldof Agricultural Science. 2020;50(3):111-121. DOI 10.26898/0370-8799-2020-3-12. (in Russian)Zhang P., Wanlong L., Fellers J., Friebe B., Gill B.S. BAC-FISH inwheat identifies chromosome landmarks consisting of different typesof transposable elements. Chromosoma. 2004;112(6):288-299. DOI10.1007/s00412-004-0273-9.Zhou J., Zhang H., Yang Z., Li G., Hu L., Lei M. Characterization ofa new T2DS.2DL-?R translocation triticale ZH-1 with multiple resistancesto diseases. Genet. Resour. Crop Evol. 2012;59:1161-1168.DOI 10.1007/s10722-011-9751-0.Zhu F. Triticale: nutritional composition and food uses. Food Chem.2018;241:468-479. DOI 10.1016/j.foodchem.2017.09.009"} +{"text": "Conversely, plasma cell and M2 macrophage levels were lower. The follicular helper T cells in tumor cell-enriched regions were negatively correlated with resting NK cells and positively correlated with activated NK cells. In immune cell-enriched regions, this relationship was reversed. We also explored the heterogeneity of HLA gene families, immune checkpoints, and metabolism-related genes in the three regions. In tumor cell-enriched regions, we obtained 19 prognosis-related metabolism genes via univariate cox analysis. We used multiplex immunofluorescence to verify the elevated expression of SLC8A1 and MDH1 in immune cell-enriched regions and tumor cell-enriched regions, respectively, both of which were associated with prognosis of NPC. In conclusion, we explored the spatial heterogeneity of the NPC tumor environment and found specific diagnostic and prognostic markers that can be used to differentiate tumor cell-enriched regions from immune cell-enriched regions in NPC.The heterogeneity of nasopharyngeal carcinoma (NPC) leads to mixed clinical outcomes. We collected 92 regions of interest from 41 biopsies of patients with untreated NPC and obtained their transcripts using GeoMx Digital Spatial Profiling (DSP) technology. Spatial heterogeneity was determined by measuring the expression of marker genes in tumor cell-enriched (PanCK-expressing), immune cell-enriched (CD45-expressing), and normal epithelial (Endo) regions. We screened 16 prognostic markers in tumor cell-enriched regions and 4 prognostic markers in immune cell-enriched regions. The levels of CD8 Nasopharyngeal carcinoma (NPC) is mainly prevalent in North Africa, the Middle East, and Southeast Asia. Its occurrence is mainly attributed to the local environment, genetics, and infection with Epstein-Barr virus (EBV) The tumor microenvironment is composed of tumor cells, immune cells, stromal cells, metabolites, cytokines, and the extracellular matrix The current study explored the spatial heterogeneity of NPCs in both composition and function. The digital spatial profiling (DSP) technology 2 tissue cores obtained from 58 patients using a TMArrayer (Pathology Devices). Regions consisting of high tumor content with large numbers of tumor infiltrating lymphocytes (TILS) were selected following preparation of the TMA block using H&E sections from the whole tissue block to ensure the presence of NPC cells in each sample. Subsequent DSP RNA assays were performed using 41 cores including 95 regions of interest . Three regions of interest (ROIs) were excluded from paired analyses due to loss of tissue integrity during staining. Finally, 38 cores containing paired tumor cell- and immune cell-enriched ROIs were included in the differential analysis.We collected paraffin-embedded tumor tissue from 58 NPC patients who underwent initial nasopharyngeal biopsy without treatment at the Affiliated Houjie Hospital of Guangdong Medical University. This study was approved by the Ethics and Scientific Committee of the Affiliated Houjie Hospital of Guangdong Medical University. A tissue microarray (TMA) was constructed with 1.5 mmAnother commercial NPC TAM containing 126 cases of NPC tissue were used for Immunofluorescence analysis. Five cores were excluded from analyses due to loss of tissue integrity during staining. Extreme values were excluded from survival analysis.NanoString GeoMx DSP RNA assays were performed at CapitalBio Technology using the standard protocol. Slides were prepared following the Manual RNA Slide Preparation Protocol in the GeoMx DSP Slide Preparation User Manual . The Whole Transcriptome Atlas (WTA) probe reagent was added to slide. We stained the tissue with GeoMx Solid Tumor TME Morphology Kit to distinguish various morphology: epithelial cells were positively stained with PanCK while immune cells were positively stained with CD45, and nuclear stained with SYTO13. The pathologist distinguishes normal epithelial cells from cancerous epithelial cells based on histological morphology. Regions of interest (ROIs) were selected and assessed by a pathologist and illuminated using UV light. The indexing oligonucleotides released from each ROI were collected and deposited into designated wells on a microtiter plate. DSP assay sequencing data were processed with the GeoMx NGS Pipeline (DND). After sequencing, the reads were trimmed, merged, and aligned to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicates and duplicate reads, thus converting reads into digital counts. The limit of quantitation (LOQ) was estimated as the geometric mean of the negative control probes plus two geometric standard deviations of the negative control probes. Targets that consistently fell below the LOQ were removed, and the datasets were normalized via upper quartile (Q3) normalization. We used the prcomp function to perform principal component analysis from the gene expression matrix and plotted it with the scatterplot3d package.Comparisons between the two groups were performed using the Mann-Whitney U test or Wilcoxon signed-ranks test. Genes of significance were defined based on a fold change > 1.5 and p-values <0.05. Gene ontology (GO) enrichment and KEGG enrichment analyses of DEGs were performed using clusterProfiler R-packages with Benjamini-Hochberg multiple testing adjustment.2 =0.89) for the Pearson correlation coefficient matrix. A topology overlap matrix (TOM) was constructed to perform hierarchical clustering with at least 50 genes per module (minClusterSize =50). The cutreeDynamic function was used to automatically cut the clustered modules and merge similar modules (abline = 0.25). The turquoise module contained 569 genes. The green module carried 267 genes and the blue module included 1010 genes. The genes of modules were extracted for GO (q =0.05) and KEGG (p =0.05) functional enrichment analysis. The R packages involved in these analyses were: clusterProfiler, org.Hs.eg.db, enrichplot, and ggplot2. Genes from the turquoise module (n=569), green module (n=267) and blue module (n=1010) were respectively submitted to the STRING database (http://www.string-db.org/). Parameter settings were as follows: network type (full STRING network), meaning of network edges (confidence), and minimum required interaction score (high confidence (0.700). Protein interaction data obtained from the STRING database were entered into the Cytoscape software. The cytoHubba plugin was used to screen core genes in the PPI network.Weighted correlation network analysis (WGCNA) of 2940 differential genes filtered from 18675 genes from matched 38 PanCK-expressing and 38 CD45-expressing regions was performed using the WGCNA and limma packages. The gene expression matrix was converted into a Pearson correlation coefficient matrix. The adjacency matrix was constructed based on the optimal power value obtained from 38 PanCK-expressing regions was screened for 16 prognosis-related genes by univariate Cox analysis. The optimal cutoff value of each of these genes was determined according to the surv_cutpoint and surv_categorize functions. The expression of each gene was grouped according to the optimal cutoff value, followed by survival analysis with the log-rank test. The turquoise module (n=569) of 38 CD45-expressing regions was screened for four prognosis-related genes by univariate Cox analysis. The optimal cutoff value for each of these four genes was determined according to the surv_cutpoint and surv_categorize functions. The expression of each gene was categorized according to the optimal cutoff value, followed by survival analysis with the log-rank test. The R packages involved in the above process were survival and survminer.The relative content of 22 immune cells was calculated for each of the 92 ROIs using the CIBERSORT algorithm. Immune cells were visualized in 90 ROIs at P < 0.05. Differences in immune cell levels among the three regions were identified using the Kruskal-Wallis test with the reshape2 and ggpubr packages. A set of genes related to immune function was obtained based on previous studies Differential expression of HLA genes in the three regions (92 ROIs) was determined using the limma, reshape2, ggplot2, and ggpubr packages via Kruskal-Wallis test. Differential expression of immune checkpoint-related genes in the three regions was explored using limma, ggplot2 and ggpubr packages via Wilcoxon test. Correlation analysis between immune checkpoint gene expression and immune cell levels was performed in PanCK- and CD45-expressing regions using the limma, reshape2, tidyverse, and ggplot2 packages with Spearman correlation coefficients. This analysis was visualized.http://www.gsea-msigdb.org/gsea/downloads.jsp). GSVA of metabolism-related genes was performed in 92 ROIs using the packages GSEABase, GSVA, limma, and pheatmap. Parameters were set to P < 0.05 and only 20 pathways were shown. A total of 134 genes were obtained by intersecting 944 metabolic genes with 2940 differential genes (PanCK- vs CD45-expressing regions) and plotting the Venn diagram based on the Bioinformatics (http://bioinformatics.psb.ugent.be/webtools/Venn/) website. Univariate Cox analysis (P < 0.05) of 134 genes was performed in 38 (PanCK-expressing) ROIs to screen for prognosis-related metabolic genes, survival analysis, and ROC curve plotting. A total of 171 genes were obtained by intersecting 944 metabolic genes with 2514 differential genes (PanCK-expressing vs Endo regions). Univariate cox analysis, survival analysis, and ROC curve plotting of 171 genes were performed in 38 (PanCK-expressing) ROIs. The R packages involved in univariate cox analysis, survival analysis, and ROC curve plotting were survivor, survminer, and timeROC.We obtained 944 genes related to metabolism based on the literature TMA section was deparaffinized to retrieve the antigen and block endogenous peroxidase, according to manufacturer's instructions. Tissue sections were blocked with 3% BSA in TBST for 30 min, and then incubated with the antibody for CD45 for 30 min. The antibody was detected using the corresponding secondary antibody tagged with HRP, before visualization using CY3-TSA. Subsequently, antigen was retrieved again to prepare the slides for the next antibody. All samples were stained sequentially with CK visualized with FITC-TSA, MDH1 visualized with Opal 647 TSA, and SLC8A1 visualized with Opal 594 TSA. Slides were counterstained with DAPI for nuclei visualization for 10 min and coverslipped using the antifade mountant. All markers stained with multiplex immunofluorescence were reviewed by a pathologist.Single-cell transcriptome data (GSE162025) from 10 NPC tissues with 82,622 cells was analyzed using Seurat to deal with the expression matrix. By setting filtering parameters, we filtered out cells with mitochondrial gene ratio>10% to exclude cells in abnormal state, and filtered out cells with gene number<500 or >3000 to exclude data with poor sequencing quality and non-single cells, and finally obtained 75710 cells. We used the Harmony package for data integration and batch removal. We performed unsupervised clustering using the default parameters in the Seurat package and then annotated these cell populations. We used the FindAllMarkers function in the Seurat package to calculate the differential genes between cell populations (log2FC=0.25 and P<0.05). The obtained differential genes were sorted to get the top ten highly expressed genes with significant differences for each cell population, and the expression matrix of these genes was obtained using the FetchData function, and plotted using the corrplot package.All immunofluorescence slides were scanned using the Pannoramic Digital Slide Scanner (3DHistech) and images visualized in CaseViewer2.4 (3DHistech). TMA core images were analyzed in HALO (Indica Labs). Area Quantification FL V2.1 module in Halo V3.0.311.314 analysis software was used to quantify the positive area and colocalization-positive area of the target region, respectively. Extreme values were excluded to minimize data variability.The study protocol is shown in Figure CDK1, CCNB1, MCM2, TOP2A, CDC6, DTL, TPX2, UBE2C, KIF2C, RFC4, TYMS, MCM4, NUSAP1, MCM7, CENPF, FOXM1, RRM1, PCNA, MRPL13 and MRPL12 as the core genes were used to construct the PPI network. Turquoise modular genes including CD4, CD8A, CD3E, CD247, ZAP70, LCK, CD3G, CD3D, FYN, VAV1, LCP2, CD28, ITK, PTPRC, LAT, CD2, CD80, PRKCQ, IL2RB and CTLA4 as the core genes were used to construct the PPI network , while the turquoise module was significantly positively correlated with CD45 expression (r=0.73 and P= 8e-14) Fig. A. A tota network C. EnrichCD27, CEP85L, DOK3, MAST4, SEC24A and UPK3B appeared to serve as protection factors. Conversely, the genes BZW2, DLL4, GTPBP4, LSM4, MBD3, PAICS, PALM2AKAP2, PAQR4, RUVBL1 and TGS1 represent risk factors; the higher the expression of these genes, the higher the risk of death in patients with NPC , CEP85L (P < 0.001), DOK3 (P <0.001), MAST4 (P<0.001), SEC24A (P <0.001), and UPK3B (P <0.001) in PanCK-expressing regions of NPC patients correlated with better prognosis. In contrast, the expression of BZW2 (P <0.001), DLL4 (P <0.001), GTPBP4 (P <0.001), LSM4 (P <0.001), MBD3 (P <0.001), PAICS (P <0.001), PALM2AKAP2 (P =0.001), PAQR4 (P <0.001), RUVBL1 (P =0.006) and TGS1 (P =0.124), correlated positively with worse prognosis in patients with NPC , CCL21 (P =0.012), FCGR2C (P <0.001), and SLC8A1 (P =0.003) was associated with poorer prognosis in patients with NPC . In PanCK-expressing regions, the genes NPC Fig. . A total+ T cells, follicular helper T cells, activated NK cells, monocytes, M0 macrophages, M2 macrophages, resting mast cells, and activated mast cells differed among the three groups . The relative levels of plasma cells were the highest in CD45-expressing regions, while the number of CD8+ T, follicular helper T cells, and activated NK cells were the highest in PanCK-expressing regions. M0 macrophages were the highest in PanCK-expressing regions, while M2 macrophages were the highest in CD45-expressing regions , and activated dendritic cells with CD40 (P <0.001) and IDO1 (P <0.01). Conversely, negative correlations were found between CD4 memory activated T cells and BTLA (P <0.01), activated mast cells and CD244 (P <0.01), and CD40LG (P <0.01), macrophages M1 and LAIR1 (P <0.01) and TNFSF14 (P <0.001), macrophages M1 and CTLA4 (P <0.001), and B memory cells and CD40 (P <0.001). Negative correlations were found between CD8+ T cells and BTNL2 (P <0.01), plasma cells with TNFSF14 (P <0.001), resting NK cells with IDO1 (P <0.01), macrophages M0 and TNFSF4 (P <0.01), resting dendritic cells and CD27 (P <0.01), and B memory cells and CD276 (P <0.01). We performed cluster annotation of 75710 cells from 10 NPC tissues and obtained a total of 18 cell populations are shown in Figure CD200 (P =0.04), CD40 (P =0.036) and ICOSLG (P =1.4e-05) was higher in PanCK-expressing regions than in CD45. The expression of CD244 (P =0.0032), CD160 (P =0.0075), CD80 (P =8.5e-06), CD48 (P =1.3e-07), CD40LG (P =1.4e-06), CD28 (P =0.0034), CD27 (P =2.1e-09), BTLA (P =0.00033), ICOS (P =0.00075), HAVCR2 (P =0.0044), CTLA4 (P =2e-06), NRP1 (P =1.4e-09), LAIR1 (P =1e-05), LAG3 (P =0.0054), PDCD1LG2 (P =0.0016), TNFRSF8 (P =0.017), TNFRSF4 (P =0.021), TMIGD2 (P =0.019), TIGIT (P =8.2e-05), and TNFSF18 (P =0.0033) was higher in CD45-expressing regions than in PanCK-expressing regions. In Endo regions, the expression of CD200 (P =0.0013), CD70 (P =0.00057), CD44 (P =0.029), CD40 (P =0.0062), CD276 (P =0.0043), ICOSLG (P =1.1e-05), TNFRSF9 (P =0.0016), and TNFSF4 (P =0.0038) was lower than in PanCK-expressing regions, while the expression of NRP1 (P =0.046), IDO1 (P =0.0056), and VTCN1 (P =0.0025) was higher than in PanCK-expressing regions (The expression of HLA genes differed in the three regions (P <0.05) Fig. A. The ex0 P =0.03 and ICOSIn PanCK-expressing regions, metabolic genes Figure A were ma-expressing regions revealed 11 prognosis-related metabolic genes. The expression of COMT (P = 0.012), DUT (P =0.040), GMPS (P =0.043), MDH1 (P = 0.039), MDH2 (P = 0.020), NME1 (P =0.029), PAICS (P =0.011), POLR2I (P =0.039), PTGS2 (P =0.034) and UCK2 (P =0.029) increased the risk of NPC, while PLCB2 (P = 0.048) was a protective factor , GMPS (P <0.001), MDH1 (P =0.001), MDH2 (P <0.001), NME1 (P <0.001), PAICS (P <0.001), POLR2I (P <0.001), and UCK2 (P =0.004), the worse was the prognosis of NPC. In contrast, a higher expression of PLCB2 (P <0.001) was associated with a better prognosis for survival in patients with in NPC predicted 2-, 4-, and 5-year survival rates in patients with NPC with a high degree of accuracy. MDH1 expression is higher in PanCK than in CD45 (P < 0.001). Multiplexed immunofluorescence analysis revealed higher levels of MDH1 protein in PanCK than in CD45 (P < 0.001), and the higher the MDH1 protein level (P = 0.048), the worse was the prognosis of patients with NPC Fig. B. Univartor Fig. C. In PanNPC Fig. D. The RONPC Fig. F.ADCY3 (P = 0.027), ADCY9 (P =0.028), CYP2J2 (P = 0.038), DNMT1 (P = 0.024), EPHX1 (P =0.022), MBOAT7 (P =0.018), POLD1 (P = 0.016) and UAP1 (P = 0.041) correlated positively with survival risk in patients with NPC , and were also metabolism-related genes. The expression of these genes correlated with a higher risk of death in patients with NPC.Higher expression of ADCY3 (P = 0.005), ADCY9 (P =0.008), CYP2J2 (P = 0.001), DNMT1 (P <0.001), EPHX1 (P <0.001), MBOAT7 (P <0.001), POLD1 (P = 0.001) and UAP1 (P < 0.001) was associated with worse prognosis in patients with NPC B. Univarwith NPC C. Notablwith NPC D. The ROEither bulk-RNA seq or microarray sequencing was used to explore biomarkers of NPC before GeoMx DSP technology emerged CEP85L, KRT5, MAST4, MYO1G, SLA, SMARCC2, UPK3B, ATF5, BEX3, BIK, CADM4, CDK2AP1, CLDN1, DLL4, IGFBP2, NFE2L3, PTGS2, SMC1A, SUSD4 and VRK2) and 4 prognostic markers in immune cell-enriched regions . We also screened for metabolism-related genes that affect the prognosis of patients with NPC in tumor cell-enriched regions .Using DSP technology, we screened 20 prognostic gene markers located in tumor cell-enriched regions associated with PDAC cell survival + T, CD4+ T-helper, na\u00efve T-cells, cytotoxic T-cells, exhausted T-cells, and Tregs) and B cells + and CD8+ T cell clusters in NPC were highly activated and depleted and co-expressed effector markers such as IL-2, GZMB, INFG, NKG7, GNLY, and GZMK. They also expressed depletion markers such as PDCD1, HAVCR2, LAG3, TIGIT, and CTLA4 + T, follicular helper T cells, activated NK cells, and M0 macrophages were higher in tumor cell-enriched regions than in immune cell-enriched regions. In contrast, plasma cells and M2 macrophages were more abundant in immune cell-enriched regions, suggesting that cellular immunity was predominantly exerted in tumor cell-enriched regions, while humoral immunity was mainly observed in the peritumor area. Interestingly, in tumor cell-enriched regions, follicular helper T cells were negatively correlated with resting NK cells and positively correlated with activated NK cells. In immune cell-enriched regions, the opposite was true, highlighting the need to use single-cell sequencing to further explore the interactions between these two cell types. In tumor cell-enriched regions, PDCD1 expression was negatively correlated with the levels of monocytes and CD4+ memory-activated T cells. The expression of LAG3 positively correlated with the levels of CD4+ memory-activated T cells and CD8 T cells. The expression of TIGIT positively correlated with monocyte levels and negatively correlated with follicular helper T cell levels. In immune cell-enriched regions, the PDCD1 expression negatively correlated with the number of eosinophils and CD4+ na\u00efve T cells. The expression of HAVCR2 negatively correlated with the number of gamma/delta T cells and positively correlated with the levels of CD4+ memory resting T cells. The expression of LAG3 positively correlated with the levels of CD4+ memory activated T cells, CD4+ memory resting T cells, M1 macrophages, and CD8+ T cells, but negatively correlated with the number of plasma cells. The expression of TIGIT was positively related with the levels of Tregs, CD8+ T cells, and CD4+ memory resting T cells, while negatively correlated with the number of plasma cells. The expression of CTLA4 positively correlated with the levels of CD8+ T cells, CD4+ memory resting T cells, activated NK cells, and M1 macrophages, while negatively correlated with the number of naive B cells. We therefore analyzed the relationship between these immune cells and depletion markers in locations that were complementary to previous studies. However, the specific mechanisms of interactions between cells at various spatial locations need to be further explored.The predominantly infiltrating lymphocytes in the NPC microenvironment are T (CD8Limitations of this study include the small sample size, which restricts the correlation between the tumor immune characteristics, treatment, and outcomes. Even though our study is small the strength is the paired samples. Another limitation is that the biomarkers we screened have not yet been validated in functional experiments, and the roles of these biomarkers still need to be further elucidated through in vivo and in vitro experiments in the future.In conclusion, we used DSP technology to explore the heterogeneity of the NPC microenvironment and its regional and metabolic prognostic markers and characterized the immune infiltration. The screened prognostic biomarkers may provide a theoretical basis for clinical diagnosis, targeted therapy, and new drug development.Supplementary figures and tables.Click here for additional data file."} +{"text": "Metastatic rhabdomyosarcoma (RMS) is a challenging tumor entity that evades conventional treatments and endogenous antitumor immune responses, highlighting the need for novel therapeutic strategies. Applying chimeric antigen receptor (CAR) technology to natural killer (NK) cells may offer safe, effective, and affordable therapies that enhance cancer immune surveillance. in vitro and in a metastatic xenograft mouse model.Here, we assess the efficacy of clinically usable CAR-engineered NK cell line NK-92/5.28.z against ErbB2-positive RMS in vitro and significantly prolong survival and inhibit tumor progression in mice. The persistence of NK-92/5.28.z cells at tumor sites demonstrates efficient antitumor response, which could help overcome current obstacles in the treatment of solid tumors.Our results show that NK-92/5.28.z cells effectively kill RMS cells These findings encourage further development of NK-92/5.28.z cells as off-the-shelf immunotherapy for the treatment of metastatic RMS. AdoleDeveloping new therapeutic strategies to overcome tumor resistance remains a critical unmet need for these heavily pretreated patients. Chimeric antigen receptor (CAR)-engineered cells, which target and inhibit the proliferation and spread of tumor cells, are revolutionizing the treatment of r/r malignancies. However, this therapy can also lead to severe, albeit treatable, side effects, such as cytokine release syndrome (CRS), immune effector cell-associated neurotoxicity syndrome (ICANS), and secondary hemophagocytic lymphohistiocytosis/macrophage activation syndrome .The lack of suitable CAR target antigens, as well as the immunosuppressive nature of the tumor microenvironment (TME), and advanced-stage disease, renders CAR-T cells nonresponsive or exhausted against many solid tumors , 9. HoweHere, we employed a molecularly and functionally well-defined clonal derivative of the natural killer (NK) cell line NK-92 (NK-92/5.28.z) as effector cells \u201317, carrin vitro aRMS xenograft model.To further develop the NK-92/5.28.z cell therapy towards clinical application as a consolidation treatment for children and young adults with r/r, metastatic, ErbB2-positive RMS tumors after re-induction radiotherapy/chemotherapy, we performed detailed preclinical 22.1The NK-92 cell line was derived from a 50-year-old patient with non-Hodgkin\u00b4s lymphoma . NK-92/5PAX3-FOXO1) derived from a patient with alveolar RMS was purchased from DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH). Cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with GlutaMAX (Gibco) containing 10% heat-inactivated fetal bovine serum (FBS) . For in vivo cell tracking, stable GFP/luciferase-expressing RH30 cells (RH30GFP/luc+) were generated by lentiviral transduction with the pSIEW-luc2 plasmid encoding enhanced green fluorescent protein (eGFP) and firefly luciferase linked by a T2A peptide (GFP/luc+ cells were enriched by fluorescence-activated cell sorting using a FACSAria II instrument (BD Biosciences).The aRMS cell line RH30 ( peptide . GFP-posPAX3-FOXO1), RMS127 (PAX3-FOXO1), and RMS335 (PAX7-FOXO1) were generated from tumor biopsies of patients and subsequently stained with ErbB2 antibody for 20 minutes. After washing, 1x104 events were recorded by flow cytometry using FACSDiva software . Fluorescence minus one (FMO) controls were used as references. The actual ErbB2 receptor number was quantified using BD Quantibrite Beads (BD Biosciences) according to the manufacturer\u2019s instructions. ErbB2 expression was determined using FlowJo Software .Tumor organoid RMS cells were stained with phycoerythrin (PE)-conjugated antibody for ErbB2 and subsequently analyzed with a FACSCanto 10c flow cytometer (BD Biosciences). Cells were stained according to the manufacturer\u2019s instructions. In brief, aliquots of 5x102.3The short-term toxicity of NK-92/5.28.z cells against tumor organoid RMS cells was determined using a europium release assay as reported elsewhere . In brie2.45 cells were washed in phosphate-buffered saline (PBS) and subsequently stained with ErbB2 antibody or an IgG1\u03ba isotype control for 20 minutes according to the manufacturer\u2019s instructions. After washing, 1x104 events were recorded by flow cytometry using FACSDiva software . In addition, ErbB2-CAR surface expression of NK-92/5.28.z cells was assessed. For this purpose 2x106 either NK-92/5.28.z or NK-92 cells were washed once with DPBS and then incubated with Human TruStain FcX\u2122 (Biolegend) for 20 minutes at 4\u00b0C. After another washing step in DPBS, the cells were incubated with 10 \u00b5g recombinant ErbB2 with human Fc tag for 20 minutes. After two additional washing steps, cells were stained with APC antibody directed against the Fc tag (Biolegend), 410712 cells, washed again, and analyzed using a BD FACS Canto 10c instrument (BD Biosciences).The integrity of RH30 target and NK-92/5.28.z effector cells was verified. In brief, aliquots of 5x10in vitro: tumor cells were resuspended and were counted by Neubauer-improved hemocytometer. 5000 RH30GFP/luc+ cells per well were seeded in 200 \u03bcl of RPMI +10% FBS into ultralow attachment 96-well round-bottom plates without prior coating (Corning) and spun down. On day four of culture, 100 \u00b5l of supernatant was carefully removed, and 1x105 NK-92 or NK-92/5.28.z cells resuspended in 100 \u00b5l of NK-92 medium were added. Spheroids without effector cells were used as controls. Every three to four days, the medium was replaced by X-Vivo 10 medium with 5% FFP and 100 IU/ml IL-2. Spheroids were imaged on day 4, 5, 6, 8 and 10 after initial seeding using a Celigo Image Cytometer (Nexcelom Bioscience) with F-theta lens and AVT PIKE camera. The size of spheroids was quantified by the GFP signal using Fiji software (Version 2.3.0) and were conducted according to the requirements of the German Animal Welfare Act.5 RH30GFP/luc+ cells resuspended in 100 \u00b5l of PBS were injected intravenously (iv) via the tail vein. Considering them as having an immanence risk for disease progression with then limited treatment options as previously shown or NK-92/5.28.z cells . Both effector cell types were resuspended in X-Vivo 10 medium with 5% FFP and 100 IU/ml IL-2. Group size was set based on the experience from previous experiments with the same xenograft model.Twenty-seven female 10- to 12-week-old nonobese diabetic (NOD)/severe combined immunodeficient (SCID)/Il2receptorgamma\u2212/\u2212 (NSG) mice received sublethal irradiation with 2.5 Gy (Biobeam 2000) (d-1) according to the protocol for previously established metastatic RMS xenograft model closely resembling a clinical situation . One dayly shown , immunotin vivo grade VivoGlo luciferin (Promega) in 100 \u00b5l of PBS per mouse. Fifteen minutes later, images were acquired in dorsal and ventral positions and subsequently analyzed by Living Image In Vivo Imaging Software (Perkin Elmer). Uniform regions of interest were used for all mice, and total flux (photon/s) was used for measurement. The signals of dorsal and ventral images were combined into a luminoscore, and statistical analysis of the tumor burden was performed by one-way ANOVA (Tumor growth was monitored weekly by bioluminescence imaging (BLI) using an IVIS Lumina II system (Perkin Elmer). Mice were anesthetized by isoflurane inhalation and received subcutaneous injections of 150 \u00b5g ay ANOVA .Altogether, tumor-bearing mice were randomly divided into the following three groups:- Control: one course of six serial infusions with X-Vivo 10 media with 5% FFP and 100 IU/ml IL-2, n=56 cells, one course of six serial effector cell infusions, n=12- NK-92: 10x106 cells, one course of six serial effector cell infusions, n=10- NK-92/5.28.z: 10x10During the experiment, animals were monitored daily for disease symptoms, xenogenic graft versus host disease (GVHD) and other adverse effects of the NK cell therapies for a maximum of 105 days. Mice with visible signs of disease progression, discomfort or physical abnormalities were painlessly sacrificed by isoflurane anesthesia followed by cervical dislocation.2.5.1Peripheral blood (PB), BM, lung, liver, gut and spleen samples were isolated and analyzed for persistence of human tumor or effector cells: BM was flushed out of the femur and tibia of mice. PB and BM were incubated with red blood cell lysis buffer (RBC Lysis Buffer (10x), BioLegend) according to the manufacturer\u00b4s instructions and washed once with PBS. The organs were cut in representative halves, and one half was preserved in formaldehyde for fluorescence microscopy. The other half was incubated with collagenase D solution , filtered through a 70 \u00b5m cell strainer, and washed with PBS. Aliquots of the cell suspensions were analyzed by flow cytometry and quantitative polymerase chain reaction (qPCR). Sample identity was blinded for the executors of the consecutively analyses.2.5.2GFP/luc+ was assessed shortly before use in experiments with a FACS Canto 10c device (BD Biosciences). CAR expression of NK-92/5.28.z cells was analyzed using a chimeric ErbB2-Fc protein after nonspecific Fc receptor blocking and subsequent staining with an anti-IgG-Fc secondary antibody conjugated with allophycocyanin (APC) .GFP expression of RH30Cell samples from mouse organs were washed once in PBS and stained with phycoerythrin-cyanin 7 (PE/Cy7)-conjugated anti-human CD45 antibody .Analyses were performed with FlowJo Software .2.5.3Genomic deoxyribonucleic acid (DNA) from murine organs was extracted using the Extractme Genomic DNA Kit (BLIRT S.A.). The percentage of human cells in the different murine tissues was determined by a quantitative real-time approach specifically amplifying the human albumin gene. In a second step, the proportions of NK-92 or NK-92/5.28.z cells and tumor cells within the human cell fraction were determined by a human-specific short tandem repeat (STR) genotyping approach. The tumor burden of each mouse was quantified in organs previously described as RMS metastatic sites , 32. For2.5.4For histological analyses, organ sections were fixed in 4% buffered formalin, paraffin embedded, cut, and stained with hematoxylin-eosin (HE). Immunohistochemistry (IHC) antibodies targeting CD56, MYOD1, DESMIN and MYOGENIN were used to evaluate the RMS phenotype of the tumors. The stained tissue sections were rated by a pathologist for the expression of each protein .2 fragment goat-anti-mouse conjugated to Alexa 647 and goat-anti-rabbit IgG conjugated to Alexa 488 were used, and nuclei were stained with 4\u00b4,6-eiamidino-2-phenylindole (DAPI) (Sigma-Aldrich). The localization of immune cells in the tumor tissue relative to blood vessels was determined by staining with rat-anti-mouse Meca32 antibody and secondary goat-anti-rat Alexa546 antibody . The samples were examined with a BZ-X810 All-in-One Fluorescence microscope (Keyence) with basic lenses and filter cubes Ex: 360/40 DM: 400 BA: 460/50 (DAPI), Ex: 470/40 DM: 495 BA: 525/50 (GFP), Ex: 620/60 DM: 660 BA: 700/75(Cy5).Immunofluorescence staining was used to observe immune cell infiltration in organs and tumors: organ slices were deparaffinized and rehydrated. After antigen retrieval and a blocking step, primary mouse-anti targeting human CD45 antibody and rabbit-against GFP antibody were added. For detection, secondary antibodies F(ab`)In addition, the stained tissue sections with immune cell infiltration were analyzed by a pathologist for xenogenic GVHD.2.6p< 0.05 (*), p< 0.01 (**), p< 0.001 (***) and p<0.0001 (****) were considered statistically significant.For statistical analyses and graphical presentation, GraphPad Prism software was used. The results are given as the mean \u00b1 standard deviation (SD). Differences between different groups were evaluated by two-tailed Student\u00b4s t test or one-way ANOVA using the Bonferroni-Dunn (nonparametric) method. Overall survivals are given as median with 95% confidence interval, Differences between the survival of different treatment groups were analyzed by the log-rank (Mantel-Cox) test. Differences with 33.1in vitro assessment of efficacy, parental NK-92 or NK-92/5.28.z cells were tested against patient-derived tumor organoid aRMS cells in a 2D europium release assay. Maintaining actively growing rare patient-derived cells is challenging, but the tumor organoid RMS cells RMS102 (PAX3-FOXO1), RMS127 (PAX3-FOXO1) and RMS335 (PAX7-FOXO1) could be successfully passaged in vitro using previously published cultivation conditions on day 10 (p = 0.0013) and NK-92-treated spheroids (p = 0.0425) xenograft were used to assess homing, tumor invasion, persistence, and antitumor effects as well as the xenogenic cytotoxicity (GVHD) of parental NK-92 and NK-92/5.28.z cells. Sequential infusions of effector cells were given preemptively during the low tumor burden period, and mice were followed for 105 days (end of experiment) (p = 0.0101) and NK-92-treated (p = 0.0159) animals at the time of first in vivo response assessment on day +50 (p = 0.2120) . In contrast, NK-92/5.28.z cell therapy (81.0 \u00b1 8.8 days) significantly improved overall survival compared to that of the parental NK-92-treated (p = 0.0329) and untreated controls (p = 0.0366) . All detectable tumor lesions expressed CD56 , MYOD1 , DESMIN and MYOGENIN .Tumor lesions were primarily observed in the livers and lungs of mice except in those with complete response to immunotherapy with NK-92/5.28.z cells. Multiple large (macroscopic) lesions were more likely to be present in the untreated and NK-92-treated mice vs. single small (microscopic) lesions in the NK-92/5.28.z-treated mice . In vivo treatment of mice with parental NK-92 cells had no significant effect, indicating that the observed therapeutic efficacy of NK-92/5.28.z cells was mainly mediated by the second-generation ErbB2-CAR construct.In summary, our data show that NK-92/5.28.z cells exhibit high cytotoxicity in r/r ErbB2-positive 2D patient-derived tumor organoid RMS cells and 3D aRMS tumor spheroid models in vivo expansion of NK-92/5.28.z cells upon irradiation may be addressed by repeated dosing and combination with checkpoint inhibition or other anticancer therapies that could further enhance or benefit from the immunomodulatory activity of the cells.NK-92/5.28.z cell therapy is already under safety evaluation in patients with recurrent glioblastoma, which is an advantage when considering to extend clinical application of this ready-to-use CAR-engineered product to other cancer indications such as metastatic aRMS. We therefore propose to use NK-92/5.28.z cells for consolidation therapy of r/r, metastatic ErbB2-positive RMS following re-induction radiotherapy/chemotherapy to benefit from their multiple endogenous cytolytic pathways in addition to direct CAR-mediated killing. Thereby, the limited life-span and lack of The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The animal study was approved by Regierungspr\u00e4sidium Darmstadt, Darmstadt, Germany; Gen.-Nr. TVA FK/1070. The study was conducted in accordance with the local legislation and institutional requirements.CH, LM, WW, EU, HB, MM and ER conceived and designed the experiments. CH, LM, HK, HB, EG, EU, MM and ER performed the experiments. CH, LM, HK, HB, EU, MM and ER analyzed the data. HK, HB, TT, WW, EG, EU, MM, MK, FH, JD, J-HK, PB contributed to reagents, materials and analysis tools. CH, LMM and ER wrote the manuscript. HK, HB, TT, WW, EG, EU, MM, M, FH, JD, J-HK, PB and MM revised the manuscript. J-HK and PB supervised the research. All authors contributed to the article and approved the submitted version."} +{"text": "Correction: Implementation Sci 18, 31 (2023)https://doi.org/10.1186/s13012-023-01286-zThe original publication of this In the second paragraph, Lyon and Bruns was incorrectly cited as reference 1, where it should have been cited as reference 70.The correct reference 70 is supplied below:70. Lyon AR, Bruns EJ. User-Centered Redesign of Evidence-Based Psychosocial Interventions to Enhance Implementation\u2014Hospitable Soil or Better Seeds? JAMA Psychiatry. 2019;76(1):3\u20134. doi:10.1001/jamapsychiatry.2018.3060The original article has been"} +{"text": "Ornithobacterium hominis type strain MSHR-COH1 (ATCC TSD-185/NCTC 14317), a bacterial species isolated from the human nasopharynx. Long-read sequencing reveals that the genome is 2,036,909 bp in length, with a GC content of 35.72%.We report the complete genome sequence of the Ornithobacterium hominis is a species in the family Weeksellaceae, for which partial genomes were first described from nasopharyngeal samples from Thailand (ATCC TSD-185), streaked on Columbia agar with 5% sheep blood , and incubated at 37\u00b0C for 72 h under humid microaerobic conditions using the CampyGen atmosphere generation system plus approximately 20\u2009mL water. All bacterial colonies were scraped into phosphate-buffered saline and immediately processed using the MasterPure complete DNA/RNA purification kit following the manufacturer\u2019s protocol. The sequencing library was prepared with the 24-plex native barcoding kit v12 . No DNA shearing or size selection was employed.N50 value of 10,303 bp and an N90 value of 5,608 bp.The library was sequenced on an ONT MinION device with an R10.4 flow cell , with Guppy v6.4.6 base calling using the SUP model and adaptor/barcode removal. Reads were trimmed using Prowler (SRR8360295]) mapped with Minimap2 v2.24 , and 3 rRNA operons. Sites that may disrupt short-read assemblies include the rRNA operons, 450-bp noncoding sequences associated with putative Fibrobacter succinogenes domain genes, >500-bp rearrangement hotspot (RHS) domain sequences, and >1-kb sequences within putative type III fibronectin domain genes. Unusually, the dnaA gene is situated near the proposed genome terminus rather than near the origin of replication , Flye v2.9.2 (https://github.com/fenderglass/Flye), Trycycler v0.5.3 (https://github.com/rrwick/Trycycler), Ori-Finder 2022 (http://tubic.tju.edu.cn/Ori-Finder2022/public/index.php) (accessed 11 January 2023), Pilon v1.24 (https://github.com/broadinstitute/pilon), Minimap2 v2.24 (https://github.com/lh3/minimap2), and Proksee (https://proksee.ca) (accessed 27 April 2023).The following software was used: Guppy v6.4.6 (ONT), Prowler (commit ID c3041ba) under BioProject accession number"} +{"text": "Urinary tract infections (UTIs) are common healthcare-associated and community-acquired bacterial infections in children. Data on pediatric UTIs in the Gulf Cooperation Council (GCC) region have not been collated. Our aim is to review the published literature on the risk factors, etiology, antimicrobial susceptibility, and treatment of pediatric (aged <18 years) UTIs from healthcare and community settings in the GCC countries. Up toEscherichia coli accounts for 80%\u201390% of pediatric UTIs (E. coli urinary isolates from children in the Gulf Cooperation Council (GCC) region (Uropathogenic s (UAE)] . Furthers (UAE)] .The challenges of managing pediatric UTIs in the GCC region have not been documented in a single article. Therefore, this review will collate data on risk factors, pathogens, resistance phenotypes, and antimicrobial management practices for pediatric UTIs within the region. Our objective is to provide a comprehensive assessment of the current knowledge on pediatric UTIs to improve diagnostic accuracy and help clinicians make rational therapeutic choices for UTIs, to improve the health of children in the region.2.2.1.This review evaluated relevant studies published between 1st January 2011 and 31st March 2022 on the PubMed and Google Scholar databases. We excluded non-English language articles, case reports, letters, books, editorials, notes, and conference abstracts.The primary search terms were \u201curinary tract infection\u201d and \u201cpediatric\u201d, followed by secondary terms relating to the review topics shown in . A free 2.2.Following initial identification and screening of publication titles, 38 full-text articles remained . Nine articles were excluded for not differentiating data for extraction.The final GCC study number totaled 28: 24 retrospective studies \u201334 and 43.3.1.The Saudi Pediatric Infectious Diseases Society (SPIDS) guidelines on community-acquired UTI (CA-UTI) recommend transurethral catheterization for collecting urine from infants and non-toilet-trained children to minimize bacterial contamination from the skin . Cathete3.2.SPIDS defines UTI as significant bacteriuria in a symptomatic patient (febrile and/or with urinary symptoms) and recurrent UTI as \u22652 episodes of symptomatic UTI within 12 months . Their tP\u2009=\u20090.001) (P\u2009=\u20090.044) and nitrite (P\u2009=\u20090.046) were significantly sensitive to detect E. coli UTI, compared with non-E. coli UTI , 2815, 2=\u20090.001) 26). Py. PyP\u2009=\u20090coli UTI (26).3.3.SPIDS advocates renal and bladder ultrasonography as a safe, noninvasive procedure for the detection of abnormalities and renal infections in preference to micturating or voiding cystourethrogram (MCUG or VCUG) . Renal u3.4P\u2009<\u20090.001)] (The predominant symptom was fever (50.3%\u201386.6%), with a regional prevalence of 60.7% 15, 16,, 27, 32.\u20090.001)] (32). Tw\u20090.001)] , 35.P\u2009=\u20090.002), whereas rates of abdominal pain and urinary symptoms were higher in older children [2\u201314 years (P\u2009<\u20090.001)] (P\u2009<\u20090.001) (Other common symptoms (>20% of each study cohort) were urinary frequency, urgency or dysuria, nausea, vomiting, and abdominal pain 15, 16,,16, 25. <\u20090.001) 32)..P\u2009=\u20090.00Blood C-reactive protein (>5\u2005mg/L) did not significantly change with patient age or betwe4.4.1.4.1.1.The prevalence of pediatric UTI across four studies including adults was 18.6%\u201368.7% , 33. In 4.1.2.P\u2009<\u20090.001), P\u2009=\u20090.001)]. Boys presented with CA-UTI at a significantly younger age than girls of UTI patients were girls. More girls than boys had a UTI in 15 studies 11, 12,, 36, 38; of UTI pan girls (11).4.1.2.1In other studies, being uncircumcised was associated with UTI , 41. In 4.2.4.2.1.P\u2009=\u20090.018), antibiotic use (P\u2009=\u20090.015) and VUR (P\u2009=\u20090.019) were associated with UTI (P\u2009=\u20090.02) and duration of fever of >36\u2005h (P\u2009=\u20090.001), but not with the isolated uropathogen ..P\u2009=\u20090.01P\u2009=\u20090.05) (P\u2009=\u20090.025) and age >2 months (P\u2009=\u20090.006) (P\u2009<\u20090.0001) were associated with UTI (\u2009=\u20090.05) . UTI amo=\u20090.006) 14). In. InP\u2009=\u20090\u20090.0001) .Following cardiac surgery, 7.0% of patients had UTIs . Prolong4.2.2.E. coli, non-E. coli UTIs were associated with hospitalization >7 days (P\u2009=\u20090.042), male sex (P\u2009<\u20090.0001), younger age [<4 years (P\u2009=\u20090.01)], prior use of antibiotics (P\u2009=\u20090.011), or history of UTI (P\u2009=\u20090.012) (E. coli UTIs (E. coli species (E. coli (49%) and non-E. coli (51%) in patients with normal ultrasound were comparable (Compared with =\u20090.012) 28). Si. SiE. cooli UTIs .4.2.3.E. coli, and ESBL-producing E. coli were associated with VUR in children (P\u2009=\u20090.044) ; in neonates than older children and infants (P\u2009=\u20090.016) (One study of adults and children in Saudi Arabia found that significantly more UTI patients had non-ESBL-producing than ESBL-producing =\u20090.044) 12). Th. ThE. co=\u20090.016) ; and in =\u20090.016) . In cont=\u20090.016) 22). An. AnE. co=\u20090.016) and 40.64.2.4.P\u2009<\u20090.005)] 13, 15,, 32. The\u20090.005)] .5.5.1.E. coli was predominant (26.1%\u2013100% of isolates), with a regional prevalence of 64.9% and 19.8% (37 of 187 K. pneumoniae), respectively (P\u2009=\u20090.05) (thogens) , 32\u201334. thogens) 11, 12,thogens) . The reg,thogens ectively , 32\u201334. \u2009=\u20090.05) (11).Klebsiella spp. (predominantly Klebsiella pneumoniae) were the second most common uropathogens (3.8%\u201335.2% of isolates), with a regional prevalence for K. pneumoniae of 13.8% (thogens) , 27, 30.Pseudomonas aeruginosa, Proteus mirabilis, Enterococcus spp., and Enterobacter spp. and cefazolin (94.0%) in Bahrain and Saudi Arabia (P\u2009<\u20090.001) for recurrent UTIs , 34E. coi Arabia among E. to 2020 (34). Moeropenem . In Omanent UTIs .E. coli from children in Bahrain (E. coli) from Qatar were resistant to ceftriaxone (More than 96% of ESBL-producing Bahrain 34) and andE. cotriaxone 36)..E. coli K. pneumoniae, >90% of isolates were susceptible to cefotaxime, ceftriaxone, and meropenem was 26.9% among enterococci from recurrent UTIs (P\u2009<\u20090.001) . CoE. coli, 83%) from Qatar were resistant to amikacin, with higher resistance to nitrofurantoin (13.0%), gentamicin (24.4%), and trimethoprim-sulfamethoxazole (59.7%) (E. coli from Bahrain was highest to nitrofurantoin and fosfomycin (71.0%\u2013100%) (No ESBL-producing isolates ( (59.7%) 36). Su. SuE. co0%\u2013100%) 33). Al. AlE. co0%\u2013100%) .K. pneumoniae, >90% of isolates were susceptible to the tested aminoglycosides . Th. ThE. co5.3.E. coli isolates (61.1%) harbored the blaCTX\u2212M\u2212G1 gene, whereas 46.2% of ESBL-producing K. pneumoniae carried blaSHV, blaTEM and blaCTX\u2212M\u2212G1 genes (Most pediatric ESBL-producing G1 genes 36). Th. ThE. coE. coli and K. pneumoniae (52.2% of isolates were urinary) (Similar findings were demonstrated by a study in Qatar of pediatric ESBL-producing urinary) . CTX-M gurinary) .E. coli; 30% K. pneumoniae) in Qatar revealed that carbapenem resistance was largely attributed to a limited number of OXA-48-like and NDM carbapenemases, suggesting that certain international high-risk clones associated with other carbapenemase genes such as blaKPC-type, have not spread locally , mostly a cephalosporin (43.5%) or penicillin (44.2%), namely amoxicillin-clavulanic acid (29.4%) or cefprozil (23.0%) 19). In. In19). 7.The evidence presented in this review indicates limited published data from the UAE and a lack of studies on HA-UTIs. Also, most studies specified a patient age of <14 years, while four studies included patients aged 14\u201318 years , 33. GCC8.E. coli (including ESBL-producing isolates). ESBL-producing uropathogens are an established cause of UTI in the region, whereas CRE organisms are emerging should be reserved for critically ill children, particularly those having a previous UTI caused by, or other risk factors for, ESBL-producing uropathogens. Alternatively, ceftazidime-avibactam, a novel cephalosporin/\u03b2-lactamase inhibitor combination that inactivates ESBL and OXA-48-type enzymes, could be considered a treatment option for ESBL pyelonephritis (Empirical use of aminoglycosides due to the high prevalence of uropathogens resistant to 3GC has been proposed in Kuwait . Gentamiountries , 36. Theountries , 48\u201351. ephritis .E. coli in our region.The treatment of UTIs caused by carbapenemase-producing uropathogens in our region is challenging. Although aztreonam is stable against NDM and 3GC against OXA-48 enzymes, none of these agents can be empirically used to treat UTI caused by NDM and OXA-48 producers as most isolates in our region co-produce CTX-M-type ESBL . It coulIn conclusion, our review showed that UTIs are increasingly caused by antimicrobial-resistant uropathogens in the pediatric population of GCC countries. Further epidemiological and clinical studies are needed to optimize diagnostic and antimicrobial stewardship strategies in pediatric UTIs in the GCC region."} +{"text": "Correction: Microbiome 10, 226 (2022)https://doi.org/10.1186/s40168-022-01430-9Following publication of the original article , the autThe updated additional file is included here and original article has been updated.Additional file 1:Fig. S8.\u00a0L. reuteri improves metabolic control in DIO mice treated with CQA. HFD-fed mice were treated twice per week with L. reuteri + CQA by oral gavage for 5 weeks. Related to Fig. 6. (a) GTT and AUC. (b) Serum HDL-C. (c) Serum LDL-C. (d) Liver weight. (e) Hepatic mRNA expression of lipid synthesis-related genes. Representative FL-IR images and BAT temperature. (h) Relative mRNA expression of thermogenic genes in BAT. (i) Representative H&E (upper) and UCP1 (lower) staining of BAT sections, scale bar: 50 \u03bcm. n = 8/group. Data are presented as mean \u00b1 SD. *, p < 0.05; **, p < 0.01; and ***, p < 0.001. ns means not statistically significant."} +{"text": "Dicranomyia (Erostrata) jejuensissp. nov. and D. (E.) koreanasp. nov., from Korea are described on the basis of morphology and mitochondrial COI sequences. DNA barcode sequences for other four D. (Erostrata) species from Korea are also provided for the first time. The identification key for all known D. (Erostrata) species is presented.Two new crane fly species, Dicranomyia Stephens, 1829, is the largest genus of the Limoniidae and, as such, contains 1,136 species and 24 subgenera, including the subgenus D. (Erostrata) Savchenko, 1976. Twelve species of this subgenus have been reported from the Palearctic, Nearctic, and Oriental regions (D. (E.) globithorax has been reported in fungus on decaying logs tabashii (as Limonia (Limonia) tabashii) from Suigen (= Suwon) in Korea, and Dicranomyia species of the subgenus Erostrata including three new species and suggested that Limoniacongesta Alexander, 1976 and Limoniastriopleura Edwards, 1919 be classified as members of subgenus Erostrata based on non-genitalic characters.D. (Erostrata) crane fly species are described from Korea, providing identification for all Korean members of the subgenus. A DNA barcode (COI) dataset for six Dicranomyia species of the subgenus Erostrata from Korea is also presented for the first time.Here, two new Crane fly adults were collected using insect nets or Malaise traps and preserved in 80% ethanol Table . Wings aThe terminologies used to describe the morphology generally follow KUEM \u2013 Korea University Entomological Museum, Seoul, Republic of Korea;NIBR \u2013 National Institute of Biological Resources, Incheon, Republic of Korea.Specimen depositories are as follows:COI sequences were amplified and sequenced following COI. All sequences were submitted to GenBank .Total genomic DNA was extracted from the leg muscle of using the DNeasy Blood & Tissue Kit according to the manufacturer\u2019s instructions. COI sequences (Table D. (Erostrata) species (10 sequences), and the outgroup species D. (Dicranomyia) kandybinae Savchenko, 1987 (1 sequence). Phylogenetic analyses were conducted using the neighbor-joining (NJ) method and Kimura-2-parameter model (p-distances) in MEGA X, using the complete deletion option.DNA barcode analysis was performed using 11 er model , with 1,er model . SequencDicranomyia (Erostrata) canis Dicranomyia (Erostrata) cnephosa Dicranomyia (Erostrata) congesta Dicranomyia (Erostrata) cynotis Dicranomyia (Erostrata) globithorax Osten Sacken, 1869Dicranomyia (Erostrata) globulithorax Alexander, 1924Dicranomyia (Erostrata) jejuensis sp. nov.Dicranomyia (Erostrata) koreana sp. nov.Dicranomyia (Erostrata) melas Dicranomyia (Erostrata) reniformis Kato, Tachi & Gelhaus, 2018Dicranomyia (Erostrata) striopleura Dicranomyia (Erostrata) submelas Kato, Tachi & Gelhaus, 2018Dicranomyia (Erostrata) tabashii Dicranomyia (Erostrata) yazuensis Kato, Tachi & Gelhaus, 2018Limoniidae Speiser, 1909Family Limoniinae Speiser, 1909Subfamily Taxon classificationAnimaliaDipteraLimoniidae\ufeffSubgenusSavchenko, 1976C69BCB6D-4C3F-5FAE-A61B-87A541D8AD53Dicranomyia (Erostrata) Savchenko in Dicranomyiaglobithorax Osten Sacken, 1869 .Rostrum is very short or reduced. Number of palpomeres ranges from one to three. Wings have no patterns, even in stigmal region. Third and fourth tarsomere are slightly swollen. Internal sac or notch is located on the male seventh sternite. Gonocoxite has ventromesal lobe. Gonostylus is one paired, with one or two setae arising from small tubercle on outer surface.Taxon classificationAnimaliaDipteraLimoniidae\ufeff15076BEE-3A44-562E-8FC1-6CF43A4FF557https://zoobank.org/9659D5F8-C578-4FAA-B16A-6AF8A9AE39E5Holotype: Korea \u2022 \u2642; Jeju-do, Seogwipo-si, Namwon-eup, Sillye-ri, Iseungi-oreum Volcanic Cone; 33\u00b020.24'N, 126\u00b037.25'E; alt. 450 m; 4 Aug.\u20138 Sep. 2021; Y. J. Bae leg.; Malaise trap; GenBank: OM102981; CF21-0150H; NIBR.Paratypes: Korea \u2022 1 \u2640; same data as holotype, 14 Jul.\u20134 Aug. 2021; GenBank: OM102983; CF21-0151; KUEM \u2022 1 \u2642; same data as holotype; GenBank: OM102982; CF21-0150P; KUEM.Palpus is 3-segmented. Male seventh sternite has shallow V-shaped notch. Outer face of gonostylus has single seta arising from tubercle. Distal lobe of paramere has a hooked tip with a subapical process.Male (holotype). Body length 4.3 mm, wing length 4.6 mm, antenna length 0.9 mm. General body coloration pale yellow to yellowish brown . General body coloration brighter than male. Femur I 2.8 mm; II 3.2 mm; III 3.4 mm; tibia I 3.2 mm; I: 3.1 mm; III 3.4 mm; tarsus I 3.0 mm; II 2.6 mm; III 2.4 mm.Female terminalia submelas.Adults of this species are found in deciduous forests with moss-covered rocks along intermittent, rocky mountain streams Fig. and co-oAdults were collected from June through early September.Dicranomyia (E.) jejuensis sp. nov. is morphologically similar to D. (E.) yazuensis based on the male genital structures, but it can be distinguished by the following characters: pleuron entirely dull yellow ; palpus 3-segmented (vs 2-segmented); distal 1/2 of gonostylus tapered to tip ; posterior margin of male seventh sternite with shallow V-shaped notch (vs long triangular notch); distal part of paramere with hooked tip (vs straight tip).Taxon classificationAnimaliaDipteraLimoniidae\ufeff9F0ADF72-CF20-5AA1-80E4-B4473CD6363Chttps://zoobank.org/163BF75E-826C-4E64-AAE4-CFAA23F2E22DHolotype: Korea \u2022 \u2642; Jeju-do, Seogwipo-si, Hawon-dong, Mt. Hallasan; 33\u00b020.95'N, 126\u00b029.72'E; alt. 1220 m; 13 Jun.\u20134 Aug. 2021; Y. J. Bae leg.; Malaise trap; GenBank: OM102979; CF21-0148; NIBR.Paratypes: Korea \u2022 1 \u2642; Gyeonggi-do, Gapyeong-si, Buk-myeon, Jeokmok-ri, Garim-gyo (Br.); 37\u00b058.60'N, 127\u00b026.55'E; alt. 300 m; 25 Jul.\u20131 Aug. 2015; Y. J. Bae leg.; Malaise trap; published as D. (E.) tabashii by KUEM \u2022 2 \u2642\u2642, 1 \u2640; same data as for preceding; 2\u20138 Aug. 2015; published as D. (E.) tabashii by KUEM \u2022 1 \u2642; same data as for preceding; 23\u201329 Jul. 2016; published as D. (E.) tabashii by KUEM \u2022 1 \u2642; Gangwon-do, Inje-gun, Girin-myeon, Bangdong-ri, Mt. Bangtaesan; 37\u00b054.50'N, 128\u00b024.41'E; alt. 690 m; 30 Jul.\u201316 Sep. 2019; Y. J. Bae leg.; Malaise trap; KUEM \u2022 1 \u2642; Gyeonsangnam-do, Sancheong-gun, Sicheon-myeon, Jungsan-ri, Jungsan-ri Campsite, Mount Jirisan; 35\u00b018.63'N, 127\u00b045.09'E; alt. 700 m; 28 Jul. 2021; J. Kim, C. Lim, D. Lee, W. Lee leg.; sweeping; GenBank: OP081140; CF21-0152; KUEM.Palpus is 3-segmented. Center of male seventh sternite has a deep conical internal sac that has a wide, round entrance. Outer face of gonostylus has two setae arising from a small tubercle. Paramere is elongated and narrow, distally with a darkened tip.Male (holotype). Body length 3.5 mm, wing length 4.5 mm, antenna length 0.7 mm. General body coloration yellow . General body coloration lighter than male.Female terminalia globulithorax on Mount Bangtaesan and with D. (E.) tabashii on Mount Jirisan.This species is found along intermittent mountain streams in moist mixed forests with grassy vegetation Fig. and in wAdults are mainly active from July through August.D. (E.) koreana sp. nov. is similar to D. (E.) tabashii, but it can be distinguished by the following characters: palpus 3-segmented (vs 2-segmented); male seventh sternite with weakly darkened, conical internal sac with round entrance ; paramere with darkened tip (vs without). This species is also similar to another species, D. (E.) jejuensis sp. nov. based on the male genital structures, but it can be distinguished by the following characters: male seventh sternite with a deep, conical internal sac ; gonostylus with two setae from tubercle (vs a single seta); paramere without hook at tip (vs with hook).In terms of the shape of the male terminalia, D. (E.) koreana sp. nov. from Mount Bangtaesan differs from other materials of the species based on the shape of the seventh sternite internal sack and paramere distal lobe (pointed tip). However, additional specimens are needed to determine whether this difference is due to intra- or interspecific variation.The male genitalia of COI sequences contained 190 variable sites, of which 156 were parsimony-informative. The interspecific divergences (p-distances) within subgenus D. (Erostrata) ranged from 11.54% to 16.42%, with a mean distance of 13.17% across the entire dataset (Table D. (E.) jejuensis sp. nov., 0.59% in D. (E.) koreana sp. nov., and 0.15% in D. (E.) tabashii. The maximum intraspecific genetic distance (0.59%) was much smaller than the minimum interspecific one (11.54%). The NJ tree species. The present study identified two new species using both morphological and molecular data. According to the NJ tree jejuensis sp. nov., D. (E.) koreana sp. nov., D. (E.) tabashii, and D. (E.) yazuensis can be distinguished from other members of their subgenus based on the shape and mesal face of their gonostyli. Two hypotheses may be considered: i) this clade can be classified into morphological species groups, or ii) it can be elevated to a new subgenus. Additional materials are needed to more accurately reconstruct phylogenetic relationships within genus Dicranomyia.This is the first study to use DNA barcoding for the delimitation of the ree Fig. , the subD. (E.) tabashii by D. (E.) koreana sp. nov. Based on our observation, unknown cryptic species of crane flies could also be detected and identified using molecular data.Based on our morphological examinations of the materials, we also found that some specimens identified as"} +{"text": "Granulomatous polyangiitis (GPA) is a rare autoimmune disease that can involve multiple systems throughout the body, including the ear, nose, upper and lower respiratory tracts. It is classified as an antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis. Telitacicept is a novel recombinant fusion protein targeting B-lymphocyte stimulator (BLyS). Telitacicept can inhibit the development and maturation of abnormal B cells by blocking BLyS, and inhibit the production of antibodies by abnormal plasma cells by blocking APRIL (A proliferation-inducing ligand), which is expected to become a new drug for the treatment of GPA. We report a 64-year-old man diagnosed at our hospital with GPA involving multiple systems including kidneys, lungs, nose and ears. Renal involvement was severe, with a clinical characteristic of rapidly progressive glomerulonephritis and a pathologic manifestation of crescentic nephritis with plasma cell infiltration. The patient was treated with hormones, immunoglobulins and cyclophosphamide (CYC) with the addition of telitacicept and a rapid reduction in hormone dosage. The patient\u2019s renal function improved significantly within a short period of time, and his hearing and lung lesions improved significantly. At the same time, he did not develop serious infections and other related complications. Our report suggests that short-term control of the patient\u2019s conditions is necessary in GPA patients with organ-threatening disease. Telitacicept combined with CYC and glucocorticoids may be an induction therapy with safety and feasibility. However, more clinical trials are needed to validate the efficacy and safety of the therapeutic regimen. Necrotizing vasculitis primarily involves small and medium-sized vessels and can involve life-threatening organs, such as alveolar hemorrhage. Rapidly progressive glomerulonephritis which manifests pathologically as crescentic glomerulonephritis, carries a high risk of progression to end stage renal disease (ESRD) or dialysis-dependent risk . GPA is Compared with normal people, naive B cells increased during AVV activity and GPA remission period , 5, and As we reported below, we observed favorable safety and efficacy of telitacicept in combination with conventional therapies for the treatment of patients with severe, rapidly progressive renal impairment who with pathological manifestations of crescentic nephritis with plasma cell infiltration.22. He developed hearing loss and no purulent discharge in the external ear canal. No obvious abnormality was found in cardiopulmonary examination. Admission laboratory examination: Blood examination: white blood cells (WBC) 12.13 \u00d710^9/L (reference range 3.5-9.5*10^9/L), hemoglobin (Hb) 90 g/L (reference range 130-175 g/L); Urine examination: 5-10 red blood cells/HP were detected by microscopy (reference range 0-2/HP); 24-hour urinary protein quantification: 0.5-0.7 g/24h (reference range 0-150 mg/24h); Erythrocyte sedimentation rate (ESR): 29 mm/h (reference range 0-43.5 mm/h) C-reactive protein 118 mg/L (reference range<10 mg/L); Biochemical indicators: Urea 16.3 mmol/L (reference range 3.1-8.0 mmol/L), Creatinine (CRE) 382 \u03bcmol/L (reference range 57-97 umol/L), albumin 27 g/L (reference range 40-55 g/L). pANCA (+/-) (reference range -), MPO (++) (reference range -); Immunoglobulin indicators: IgG 19.9 g/L (reference range 7.0-16.0 g/L), IgA 1.35 g/L (reference range 0.7-4.0 g/L), IgM 0.436 g/L (reference range 0.4-2.3 g/L). Imaging examination: Lung CT: 1. Multiple nodules and spots in both lungs, and neoplastic lesions cannot be excluded; 2. Multiple lymph nodes enlargement in the mediastinum see Figure\u00a013Systemic vasculitis diseases are considered as diseases with multisystem involvement. GPA commonly involves the ear, nose, upper and lower respiratory tracts . In 2022It has been shown that GPA is predominantly characterized by C-ANCA antibody positivity 73.3-76%) and PR-3 ANCA 74-82.2%) antibody positivity, and also by P-ANCA antibody positivity (9.8-13%) and MPO-ANCA antibody positivity (5-8.1%) .The datasets presented in this article are not readily available because this is a case report. Requests to should be directed to Liqi Huang for the publication of any potentially identifiable images or data included in this article.LH: Investigation, Project administration, Writing \u2013 original draft. WL: Investigation, Visualization, Writing \u2013 original draft. YLiu: Investigation, Methodology, Writing \u2013 original draft. JZ: Resources, Writing \u2013 review & editing. YLi: Conceptualization, Resources, Writing \u2013 review & editing. ZZ: Conceptualization, Funding acquisition, Writing \u2013 review & editing. CT: Conceptualization, Funding acquisition, Writing \u2013 review & editing."} +{"text": "Correction: Clinical Epigenetics (2023) 15:105 10.1186/s13148-023-01521-wThe wrong Additional file 4 was originally published with this article . It has The original article has been corrected.Additional file 4. Table S6. Application for NNLS model with 6 CpGs."} +{"text": "Scientific Reports 10.1038/s41598-022-15180-z, published online 07 July 2022Correction to: The original version of this Article contained an error in the Acknowledgements section.\u201cI.I. acknowledges the partial financial support from the SONATA BIS project 2020/38/E/ST5/00176.\u201dnow reads:\u201cI.I. was partly funded by the NCN SONATA-BIS Program (UMO-2020/38/E/ST5/00176).\u201dThe original Article has been corrected."} +{"text": "Dear Editor,. Some previous studies had suggested an association between higher interleukin(IL)-6 levels and mortality risk in prevalent HD patients. The influence of serum IL-6levels on nutritional status remains, however, to be elucidated. The aim of this studywas to evaluate the association between serum IL-6 levels and nutritional status, andits impact on short-term mortality in prevalent HD patients.Inflammation has been associated with increased mortality in hemodialysis (HD) patients+), and calcium (Ca2+). PTH was measured byelectrochemiluminescence and IL-6 levels were measured by ELISA. Baselinecharacteristics and laboratory data were compared among groups using the Student\u2019st-test for normally distributed continuous variables, Mann-Whitney U-test for skeweddistributed continuous variables, and Chi-square test for categorical variables.One-year all-cause mortality was assessed using standard survival methods. Statisticalanalysis was performed using SPSS (Version 23 for Mac OSX).We conducted a retrospective single-center study of prevalent HD patients between January2020 and January 2021. Patients with acute or chronic inflammatory or infectious diseaseand active malignancy were excluded. According to the mean IL-6 level measured atbaseline, patients were categorized into two cohorts: IL-6 \u2264 17pg/mL and IL-6 >17pg/mL. Baseline clinical and demographic data were collected. Laboratory parameterswere measured before the second HD session of the week, including hemoglobin (Hgb),ferritin, serum iron, transferrin saturation index (TSI), albumin, C-reactive protein(CRP), phosphorus (Pp = 0.045), had higher c-reactive protein(CRP) , lower serum iron, and lower transferrinsaturation index (TSI) .Those patients had also higher serum ferritin levels, although not statisticallysignificant . Regarding nutritional parameters, patients with IL-6 > 17 pg/mL had loweralbumin , lean mass index(LMI) , bodymass index (BMI) , and cholesterol , but without statistical significance. During the study follow-up period, 9(14.8%) patients died. One-year survival was 91.4% in the group with IL-6 \u2264 17 pg/mL and64.3% in those with IL-6 > 17 pg/mL .Using a Cox proportional hazards analysis, we observed that patients with IL-6 > 17pg/mL had an increased risk of all-cause mortality at one year compared to those withIL-6 \u2264 17 pg/mL .The mean age of the included 61 prevalent HD patients was 74.96 \u00b1 12.89 years, 34 (55.7%)were male, and 25 (41%) were diabetic. Mean IL-6 level was 17.3 \u00b1 28.19 pg/mL. Fourteenpatients (23%) had IL-6 > 17pg/mL. There was no gender, comorbidity, HD vintage, ormodality difference among groups. Patients with IL-6 > 17pg/mL were older , and cardiovascularmorbidity to be interrelated in HD patients, each additionally contributing to highermortality in prevalent HD patients."} +{"text": "Correction: Psicol. Refl. Cr\u00edt. 36, 19 (2023) https://doi.org/10.1186/s41155-023-00262-2Following publication of the original article (Fitzpatrick et al., Maira Almeida Lopes to Ma\u00edra Lopes Almeida, Giana Frizzo to Giana Bitencourt FrizzoThe original article (Fitzpatrick et al.,"} +{"text": "Long-acting cabotegravir and rilpivirine (CAB/RPV) offers a promising alternative to daily oral antiretroviral therapy (ART); however, system-level and individual challenges in wide scale implementation are anticipated. We describe a community, infusion center-based model (ICBM) for administration of CAB/RPV and associated clinical outcomes.This was a single-center, retrospective cohort study of adults with HIV who were referred for enrollment in the ICBM from 3/1/22 to 2/28/23 . We investigated demographics, system-level implementation variables, individual factors, and clinical outcomes among CAB/RPV recipients.79 patients were referred for enrollment in the ICBM and 64 patients received at least 1 dose of CAB/RPV. Reasons for CAB/RPV not being administered include insurance barrier, N=2 (13.3%); changed mind, N=3 (20%); unable to reach, N=2 (13.3%), difficulty with collecting labs, N=1 (6.7%), and CAB/RPV started outside of study period, N=4 (26.7%). Of those who received at least one dose of CAB/RPV, 79.9% were male, 48.4% were African American, 42.4% were Medicaid beneficiaries, 67.2% reported mental illness and 39.1% reported alcohol or non-tobacco substance use. Other baseline factors are listed in Table 1. Mean time from referral to first injection was 38.8 days excluding oral lead in time. Mean treatment duration was 176 days (range 20-326 days). 211 maintenance injections were administered during the study period; 16 (7.6%) were outside of the injection window with 10 (62.5%) oral bridges administered. All patients were virally suppressed at end of study period. Overall, 1,122 interventions were completed . Table 2 describes interventions performed.Implementation of CAB/RPV requires a collaborative effort to address system-level and individual challenges. Utilizing existing infrastructure allows for resource optimization to engage vulnerable populations and enhance equitable access. Our program shows successful treatment with CAB/RPV in individuals with adherence barriers (Table 3) at community infusion centers.Carlos Malvestutto, MD MPH, Pfizer: Advisor/Consultant|ViiV Healthcare: Advisor/Consultant"} +{"text": "Outpatient parental antibiotic therapy is safe and effective. Our institution is one of two tertiary public hospital pediatric centers in Singapore. We aim to describe characteristics and outcomes of pediatric OPAT (p-OPAT).We retrospectively reviewed p-OPAT patients from May 2013-Dec 2022. Clinically stable inpatients were referred to the pediatric infectious disease team for assessment, caregiver training, and weekly review. Two main delivery models were used; daily bolus/short infusion at an outpatient unit, and home self-administration via elastomeric device. Electronic medical records were analyzed for demographics, clinical and microbiological data, treatment, and outcomes. Institutional review board approval and written informed consent were waived.219 patients completed 249 p-OPAT episodes; 46.6% female, 53.3% male. Median age was 8 years 5 months (range 11 days-29 years). Patient ethnicities were 53.9% Chinese, 12.3% Indian, 20.5% Malay, 13.3% others.53/219 (24.2%) patients were immunocompromised; three had primary immunodeficiency, 50 had acquired immunodeficiency. 89/219 (40.6%) patients had chronic illness.176/249 (70.7%) episodes had only one pathogen identified (Tab 1). Pathogens were gram positive (21.7%), gram negative (38.2%), fungal (5.2%), mycobacterial (5.6%) (Tab 2). 18.9% episodes were culture-negative, 1.6% episodes had no cultures. Infection sites varied considerably; osteoarticular infection +/- bacteremia were most common (Tab 3). Ceftriaxone was the most frequent antimicrobial . Peripherally inserted central catheter was most commonly used .Complete success, partial success, and failure were seen in 174 (69.9%), 43 (17.3%) and 32 (12.8%) episodes respectively. Main adverse events (AE) were vascular site dermatitis, infection, and line dislodgement. 235 (94.4%) episodes achieved infection cure. Mean p-OPAT duration was 16.9 days (range 1-177 days), saving 4208 admission bed days.We describe one of the largest series of children receiving p-OPAT over 10 years and report good outcomes for a broad spectrum of infections. Vascular access issues were common AEs despite preventive measures.All Authors: No reported disclosures"} +{"text": "The use of medical 3D printing has expanded dramatically for breast diseases. A writing group composed of the Radiological Society of North America (RSNA) Special Interest Group on 3D Printing (SIG) provides updated appropriateness criteria for breast 3D printing in various clinical scenarios. Evidence-based appropriateness criteria are provided for the following clinical scenarios: benign breast lesions and high-risk breast lesions, breast cancer, breast reconstruction, and breast radiation (treatment planning and radiation delivery).The online version contains supplementary material available at 10.1186/s41205-023-00171-1. Currently, medical 3D printing is performed for a variety of indications. In 2018, the RSNA 3D printing SIG published appropriateness criteria for medical 3D printing for various clinical scenarios [The RSNA Special Interest Group (SIG) on 3D Printing Guidelines Committee has initiated and revised several documents regarding the Clinical scenarios for which 3D Printing is considered an appropriate representation or extension of data contained in a medical imaging examination. This document highlights appropriateness of medical 3D printing for clinical utilization, research, scientific and informational purposes within breast diseases. This work is loosely modeled after the American College of Radiology (ACR) Appropriateness Criteria\u00ae in that 1\u20133, rarely appropriate. There is a lack of a clear benefit or experience that shows an advantage over usual practice.4\u20136, maybe appropriate. There may be times when there is an advantage, but the data is lacking, or the benefits have not been fully defined.7\u20139, usually appropriate. Data and experience show an advantage to 3D printing as a method to represent and/or extend the value of data contained in the medical imaging examination.The SIG Guidelines Chairperson oversees the ratings via a vote among Special Interest Group members at in-person meetings. The results of the ratings follow the following 1\u20139 format (with 9 being the most appropriate):Clinical scenarios included in this document are stratified by histopathologic diagnosis and treatment. These include benign breast lesions and high-risk breast lesions, malignant breast lesions, breast reconstruction, and breast radiation (treatment planning and radiation delivery).th, 2022 SIG Appropriateness Committee Meeting. Afterwards, 2-week period for comments by SIG members was posted on the SIG\u2019s members-only online forum. All included studies were graded with a strength of evidence assessment according to ACR Appropriateness Criteria Evidence Document.An exhaustive English language PubMed literature search was performed (May 2022) which enabled the querying and retrieval of pertinent clinical documents regarding the appropriateness of 3D printing in each of the scenarios. The supporting evidence was obtained through structured searches, as detailed in each category. For each category, from the pool of total results, the number of publications considered \u201crelevant results\u201d was curated by consensus between physicians with expertise in 3D printing and breast care. Relevant publications that were not retrieved by the structured PubMed search were manually entered. The following categories were excluded because they were considered outside the project scope . All final components of this section were vetted and approved by vote of Special Interest Group members virtually at the July 20Benign breast lesions and high-risk breast lesions: Benign breast diseases are common and include a wide range of entities [entities . The mosentities . Fibroadentities . Benign entities , 4.High-risk breast lesions may confer an increased risk for breast cancer, may be associated with a higher risk for future breast cancer, and may be precursors in breast carcinogenesis. Management of high-risk lesions after core needle biopsy may include close imaging and clinical follow-up or excisional biopsy to evaluate for cancer \u20138. High-Surgical management of these entities may be needed in cases where cosmesis is altered or when symptom relief is needed. Surgical management may impact developing breast tissue in young women leading to alterations in its proper development . TherefoPubMed Search: ((3D printing) AND (fibrocystic change)) OR ((3D printing) AND (benign breast masses)) OR ((3D printing) AND (mastitis)) OR ((3D printing) AND ) OR ((rapid prototyping) AND (fibrocystic change)) OR ((rapid prototyping) AND (benign breast masses)) OR ((rapid prototyping) AND (mastitis) OR ((rapid prototyping) AND ). ((3D printing) AND ) OR ((3D printing) AND ) OR ((3D printing) AND (lobular neoplasia)) OR ((3D printing) AND ) OR ((3D printing) AND (papillary lesions) OR ((3D printing) AND (mucocele-like lesions)) OR ((rapid prototyping) AND ) OR ((rapid prototyping) AND ) OR ((rapid prototyping) AND (lobular neoplasia) OR ((rapid prototyping) AND ) OR ((rapid prototyping) AND (papillary lesions)) OR ((rapid prototyping) AND (mucocele-like lesions))PubMed Results: No results found.Preliminary rating: 1Malignant breast lesions: Breast cancer is the most common solid malignancy in women in the United States [d States . Approxid States , 12. Bred States . Understd States . They ard States . 3D prind States . This ind States \u201319. AddiPubMed Search: ((3D printing) AND (breast cancer) OR ((rapid prototyping) AND (breast cancer))PubMed Results: 14 [aSchulz-Wendtland R, Harz M, Meier-Meitinger M, et al. Semi-automated delineation of breast cancer tumors and subsequent materialization using three-dimensional printing (rapid prototyping). J Surg Oncol. 2017;115(3):238\u2013242.bSantiago L, Volk RJ, Checka CM, et al. Acceptability of 3D\u2010printed breast models and their impact on the decisional conflict of breast cancer patients: A feasibility study. Journal of surgical oncology. 2021;123(5):1206\u20131214.cBarth RJ, Krishnaswamy V, Paulsen KD, et al. A Patient-Specific 3D-Printed Form Accurately Transfers Supine MRI-Derived Tumor Localization Information to Guide Breast-Conserving Surgery. Annals of Surgical Oncology. 2017;24(10):2950\u20132956.dRao N, Chen K, Yang Q, Niu J. Proof-of-Concept Study of 3-D-Printed Mold-Guided Breast-Conserving Surgery in Breast Cancer Patients. Clin Breast Cancer. 2018;18(5):e769-e772.eKo BS, Kim N, Lee JW, et al. MRI-based 3D-printed surgical guides for breast cancer patients who received neoadjuvant chemotherapy. Scientific Reports. 2019;9(1):11,991.fFernandez RAS, Lau RWH, Yu PSY, Siu ICH, Chan JWY, Ng CSH. Use of custom made 3-dimensional printed surgical guide for manubrio-sternal resection of solitary breast cancer metastasis: case report. AME Case Rep. 2020;4:12.gWu ZY, Alzuhair A, Kim H, et al. Magnetic resonance imaging based 3-dimensional printed breast surgical guide for breast-conserving surgery in ductal carcinoma in situ: a clinical trial. Sci Rep. 2020;10(1):18,534.hOck J, Lee S, Kim T, et al. Accuracy evaluation of a 3D printing surgical guide for breast-conserving surgery using a realistic breast phantom. Computers in Biology and Medicine. 2021;137:104,784.iWu ZY, Kim HJ, Lee J, et al. Breast-conserving surgery with 3D-printed surgical guide: a single-center, prospective clinical study. Sci Rep. 2021;11(1):2252.jWu ZY, Kim GB, Choi S, Lee S, Kim N, Ko B. Breast-Conserving Surgery after Neoadjuvant Chemotherapy Using a Three-Dimensional-Printed Surgical Guide Based on Supine Magnetic Resonance Imaging: A Case Report. J Breast Cancer. 2021;24(2):235\u2013240.kWu ZY, Lee YJ, Shin Y, et al. Usefulness of 3-Dimensional-Printed Breast Surgical Guides for Undetectable Ductal Carcinoma In Situ on Ultrasonography: A Report of 2 Cases. J Breast Cancer. 2021;24(3):349\u2013355.lWu ZY, Kim GB, Lee S, Choi SH, Kim N, Ko B. Case Report: A 3D-Printed Surgical Guide for Breast-Conserving Surgery After Neoadjuvant Chemotherapy. Front Oncol. 2021;11:633,302.mLee HS, Kim HJ, Chung IY, et al. Usefulness of 3D-surgical guides in breast conserving surgery after neoadjuvant treatment. Sci Rep. 2021;11(1):3376.nSantiago L, Adrada BE, Caudle AS, Clemens MW, Black DM, Arribas EM. The role of three\u2010dimensional printing in the surgical management of breast cancer. Journal of surgical oncology. 2019;120(6):897\u2013902.ults: 14 , 18\u201329aSPreliminary Rating: 7Breast reconstruction: Breast reconstruction surgeries include either implant-based or autologous flap reconstructions. In autologous flap reconstructions, 3D printed models have been shown to facilitate the intramuscular dissection of perforator vessels by depicting the course and trajectory of the subfascial vascular tree and allowing the surgeon to view the model from various vantage points [e points , 30, 31.e points . 3D modee points , 34.PubMed Search: ((3D printing) AND (breast reconstruction) OR ((rapid prototyping) AND (breast reconstruction)PubMed Results: 11 [aJablonka EM, Wu RT, Mittermiller PA, Gifford K, Momeni A. 3-DIEPrinting: 3D-printed models to assist the intramuscular dissection in abdominally based microsurgical breast reconstruction. Plastic and Reconstructive Surgery Global Open. 2019;7(4).bChae MP, Rozen WM, McMenamin PG, Findlay MW, Spychal RT, Hunter-Smith DJ. Emerging applications of bedside 3D printing in plastic surgery. Frontiers in surgery. 2015;2:25.cChae MP, Hunter-Smith DJ, Rostek M, Smith JA, Rozen WM. Enhanced preoperative deep inferior epigastric artery perforator flap planning with a 3D-printed perforasome template: technique and case report. Plastic and Reconstructive Surgery Global Open. 2018;6(1).dChae MP, Hunter-Smith DJ, Spychal RT, Rozen WM. 3D volumetric analysis for planning breast reconstructive surgery. Breast Cancer Res Treat. 2014;146(2):457\u2013460.eHummelink S, Verhulst AC, Maal TJ, Ulrich DJ. Applications and limitations of using patient-specific 3D printed molds in autologous breast reconstruction. European journal of plastic surgery. 2018;41(5):571\u2013576.fDeFazio MV, Arribas EM, Ahmad FI, et al. Application of Three-Dimensional Printed Vascular Modeling as a Perioperative Guide to Perforator Mapping and Pedicle Dissection during Abdominal Flap Harvest for Breast Reconstruction. J Reconstr Microsurg. 2020;36(5):325\u2013338.gMehta S, Byrne N, Karunanithy N, Farhadi J. 3D printing provides unrivalled bespoke teaching tools for autologous free flap breast reconstruction. Journal of Plastic, Reconstructive & Aesthetic Surgery. 2016;69(4):578\u2013580.hChae MP, Hunter-Smith DJ, Chung RD, Smith JA, Rozen WM. 3D-printed, patient-specific DIEP flap templates for preoperative planning in breast reconstruction: a prospective case series. Gland Surg. 2021;10(7):2192\u20132199.iChen K, Feng CJ, Ma H, et al. Preoperative breast volume evaluation of one-stage immediate breast reconstruction using three-dimensional surface imaging and a printed mold. J Chin Med Assoc. 2019;82(9):732\u2013739.jOgunleye AA, Deptula PL, Inchauste SM, et al. The utility of three-dimensional models in complex microsurgical reconstruction. Arch Plast Surg. 2020;47(5):428\u2013434.kTomita K, Yano K, Taminato M, Nomori M, Hosokawa K. DIEP Flap Breast Reconstruction in Patients with Breast Ptosis: 2-Stage Reconstruction Using 3-Dimensional Surface Imaging and a Printed Mold. Plast Reconstr Surg Glob Open. 2017;5(10):e1511.ults: 11 \u201340aJabloPreliminary rating: 8Breast Radiation (Treatment planning and Radiation delivery): 3D printing can be used to design customized patient specific boluses and shields that allow homogeneous distribution of radiation dose to the area of interest while sparing adjacent normal tissue [l tissue . 3D prinl tissue PubMed Search: ((3D printing) AND (breast radiation) OR ((rapid prototyping) AND (breast radiation)PubMed Results: 8 [aPoulin E, Gardi L, Fenster A, Pouliot J, Beaulieu L. Towards real-time 3D ultrasound planning and personalized 3D printing for breast HDR brachytherapy treatment. Radiother Oncol. 2015;114(3):335\u2013338.bAristei C, Lancellotta V, Piergentini M, et al. Individualized 3D-printed templates for high-dose-rate interstitial multicathether brachytherapy in patients with breast cancer. Brachytherapy. 2019;18(1):57\u201362.cYang K, Park W, Ju SG, et al. Heart-sparing radiotherapy with three-dimensional printing technology after mastectomy for patients with left breast cancer. Breast J. 2019;25(4):682\u2013686.dHe C, Zhang S, Shi L. Three-Dimensionally-Precise Breast Conformal Device for IMRT in Breast Cancer Patients Treated With Breast-Conserving Surgery-A Pilot Randomized Controlled Trial. Technol Cancer Res Treat. 2020;19:1,533,033,820,971,563.eRobar JL, Moran K, Allan J, et al. Intrapatient study comparing 3D printed bolus versus standard vinyl gel sheet bolus for postmastectomy chest wall radiation therapy. Pract Radiat Oncol. 2018;8(4):221\u2013229.fPark SY, Choi CH, Park JM, Chun M, Han JH, Kim JI. A Patient-Specific Polylactic Acid Bolus Made by a 3D Printer for Breast Cancer Radiation Therapy. PLoS One. 2016;11(12):e0168063.gPoulin E, Gardi L, Fenster A, Pouliot J, Beaulieu L. A novel approach for real-time, personalized breast HDR brachytherapy treatment using 3D printing technology. Brachytherapy. 2014;13:S18.hPark K, Park S, Jeon MJ, et al. Clinical application of 3D-printed-step-bolus in post-total-mastectomy electron conformal therapy. Oncotarget. 2017;8(15):25,660\u201325,668.sults: 8 , 42\u201348aPPreliminary rating: 6Table Limitations of this work include its lack of objective data collection and inferential statistics. Although such an analysis would be desirable, it is not practical with most published breast related applications due to the small number of publications and patients. PubMed search terms, were based on prior search terminology from previously published guidelines . The RSNThis document provides updated appropriateness criteria for 3D printing in breast conditions. Adoption of common clinical standards regarding appropriate use, information and material management, and quality control are needed to ensure the greatest possible clinical benefit from 3D printing. With accruing evidence for in 3D printing, this consensus guideline document, created by the members of the RSNA 3D printing Special Interest Group, will provide a reference for clinical standards of 3D printing. The document will be periodically refined, based on expanding clinical applications and growing medical literature.Additional file 1."} +{"text": "Chronic obstructive pulmonary disease (COPD) is a multifactorial disease of the respiratory system which develops as a result of a complex interaction of genetic and environmental factors closely related to lifestyle. We aimed to assess the combined effect of the PI3K/AKT/mTOR signaling pathway and sirtuin genes to COPD risk. SNPs of SIRT1 , SIRT3 , SIRT6 (rs107251), AKT1 (rs2494732), PIK3R1 , MTOR , PTEN genes were genotyped by real-time polymerase chain reaction (PCR) among 1245 case and control samples. Logistic regression was used to detect the association of SNPs in different models. Linear regression analyses were performed to estimate the relationship between SNPs and lung function parameters and smoking pack-years. Significant associations with COPD were identified for SIRT1 (rs3818292) , SIRT3 (rs3782116) and SIRT3 (rs536715) under the dominant model, SIRT6 (rs107251) , PIK3R1: , rs831125 , rs3730089 ), PTEN: , and rs2735343 ). A significant genotype-dependent variation of lung function parameters was observed for SIRT1 (rs3818292), SIRT3 (rs3782116), PIK3R1 (rs3730089), and MTOR (rs2536). Gene-gene combinations that remained significantly associated with COPD were obtained; the highest risk of COPD was conferred by a combination of G allele of the PIK3R1 (rs831125) gene and GG of SIRT3 (rs536715) (OR = 3.45). The obtained results of polygenic analysis indicate the interaction of genes encoding sirtuins SIRT3, SIRT2, SIRT6 and PI3KR1, PTEN, MTOR and confirm the functional relationship between sirtuins and the PI3K/AKT/mTOR signaling pathway. Chronic obstructive pulmonary disease (COPD) is a multifactorialrespiratory system disease that affects the distalparts of the respiratory tract and lungparenchyma with lung emphysema development . \u0421hronic obstructive pulmonary disease developsas a result of complex interaction between molecular geneticand environmental factors, closely related to lifestyle, andsmoking is considered the main cause of COPD . Published data suggest that the COPD pathogenesismay involve dysregulation of stress responses that inhibitcellular senescence, which includes a wide range of signalingcascades and their regulators .The PI3K/AKT/mTOR intracellular signaling pathway isa universal pathway controlling cell growth, metabolism, andproliferation . The key components of thissignaling pathway are phosphatidylinositol-3 kinase (PI3K),serine/threonine protein kinase (AKT), and serine/threoninekinase . Signal transduction through the PI3K/AKT/mTOR signaling cascade is essential for cellular senescence.This signaling pathway is inhibited by the tyrosine phosphatasesPTEN (phosphatase and tensin homolog) and SHIP-1(inositol polyphosphate-5-phosphatase D). Both enzymeshave oxidation-sensitive cysteine residue in the active region.Oxidative stress is the main mechanism that causes acceleratedsenescence through its damaging effects on DNA and thePI3K/AKT/mTOR signaling pathway activation . In COPD and other age-associated diseases, the expressionof genes encoding endogenous antioxidant molecules isreduced, which leads to an increased level of oxidative stressand cellular senescence activation .NAD-dependent protein deacetylases from the sirtuins familyare considered as potential factors that decrease senescence.We aimed to assess the combined effect of the PI3K/AKT/mTOR signaling pathway andsirtuins genes on COPD risk.DNA samples were collected from unrelated subjects whowere Tatars in ethnicity and resided in the Republic of Bashkortostan.The study was approved by the Ethics Committeeat the Institute of Biochemistry and Genetics . All participants of this study providedwritten informed consent. The COPD group included 621patients (539 (86.79 %) males and 82 (13.21 %) females) witha mean age of 64.42 \u00b1 10.71 years. There were 510 (82.13 %)smokers and former smokers and 111 (17.87 %) nonsmokersin the COPD group. The smoking index was 45.34 \u00b1 23.84pack years in the smokers and former smokers. The controlgroup included 624 subjects (555 (88.94 %) males and 69(11.06 %) females) with a mean age of 59.67 \u00b1 12.31. Therewere 526 (84.29 %) smokers and former smokers and 98(15.71 %) nonsmokers in the group; the smoking index was38.75 \u00b1 24.87 pack years in the smokersIn all patients, spirometry was performed to assess lungfunction, including vital capacity (VC), forced vital capacity(FVC), forced expiration volume in the first second (FEV1),and the FEV1/FVC ratio. The group of patients had the followingparameters : FEV1 = 40.75 \u00b1 18.33;FVC = 45.01 \u00b1 18.22; VC = 49.32 \u00b1 14.34; FEV1/FVC =59.5 \u00b1 12.34. Inclusion and exclusion criteria for the COPDand control have been previously described .Genotyping. DNA was isolated from peripheral bloodleukocytes by phenol-chloroform extraction. The set includedSNPs of the following genes: SIRT1 ,SIRT3 , SIRT6 (rs107251), AKT1(rs2494732), PIK3R1 ,MTOR , PTEN 1.http://vavilov.elpub.ru/jour/manager/files/Suppl_Korytina_Engl_27_5.pdfSupplementary Materials are available in the online version of the paper:The SNPs were selected for the study based on the followingcriteria: functional effect of SNP on gene expressionor relation to non-synonymous substitutions, and/or associationswith complex human diseases; minor allele frequency (MAF) of \u2265 5 % in the European populations according tothe National Center for Biotechnology Information database(http://www.ncbi.nlm.nih.gov/projects/SNP/). The functionalsignificance of the SNPs was verified using RegulomeDBVersion 1.1 (https://regulomedb.org), SNPinfo Web Server(https://snpinfo.niehs.nih.gov), and HaploReg v3 . Data were presented in Supplementary Material 2.SNP genotyping was performed by real-time polymerasechain reaction (PCR) using commercial kits for fluorescencedetection anda BioRad CFX96TM instrument . The methods of analysis were described in detailpreviously .Statistical analyses. Statistical analyses of the results wereperformed using the software packages IBM SPSS Statis-tics 22.0 and PLINK v. 1.07 . The methodswere described in detail previously .Association analyses of allele or genotype combinationswith COPD were carried out using the APSampler 3.6.1program (http://sourceforge.net/projects/apsampler/). TheBenjiamini\u2013Hochberg correction for multiple testing wasperformed using special software (http://www.sdmproject.com/utilinies/?show=FDR) to decrease the false discoveryrate (FDR) and to obtain \u0420cor- FDR. The linkage disequilibriumstructure LD (D\u2019) and haplotype frequencies were calculatedwith Haploview 4.2.Before analyzing the association of candidate gene alleleswith COPD, we verified whether the genotype frequencydistributions corresponded to the Hardy\u2013Weinberg equilibriumand evaluated minor allele frequencies (MAF) both in thecombined group of patients and healthy subjects and in eithergroup individually . All studiedSNPs were in Hardy\u2013Weinberg equilibrium in the controlgroup: SIRT1 (rs3758391) (PX-B = 0.24), SIRT1 (rs3818292)(PX-B = 0.47), SIRT3 (rs3782116) (PX-B = 0.5), SIRT3(rs536715) (PX-B = 0.75), SIRT6 (rs107251) (PX-B = 0.67),AKT1 (rs2494732) (PX-B = 0.2), PIK3R1 (rs10515070)(PX-B = 0.65), PIK3R1 (rs831125) (PX-B = 0.25), PIK3R1(rs3730089) (PX-B = 0.22), MTOR (rs2295080) (PX-B = 0.15),MTOR (rs2536) (PX-B = 0.24), PTEN (rs701848) (PX-B = 0.85),PTEN (rs2735343) (PX-B = 0.06).The groups of COPD patients and healthy controls differedsignificantly in the genotypes and/or alleles frequencydistributions of SIRT1 (rs3818292), SIRT3 , SIRT6 (rs107251), AKT1 (rs2494732), PIK3R1, and PTEN (Table 1). Statistically significant results ofassociation analysis of the studied gene loci and COPD areshown in Table 2.An association of SIRT1 (rs3818292) with COPD was establishedin the dominant model .The risk of COPD was increased in heterozygous individuals. An association of COPD with theheterozygous genotype and in thedominant model of SIRT3 (rs3782116) and in the dominant, log-additive models and with the heterozygous genotype of SIRT3 (rs536715). It shouldbe noted that in both cases the COPD risk was associatedwith the frequent G allele (rs3782116 \u2013 OR = 1.21 95 % CI1.03\u20131.43 \u0438 rs536715 \u2013 OR = 1.58 95 % CI 1.32\u20131.91) andthe GG genotype (rs3782116 \u2013 OR = 1.44 95 % CI 1.16\u20131.81\u0438 rs536715 \u2013 OR = 1.99 95 % CI 1.58\u20132.51).We carried out a linkage disequilibrium analysis of thers3758391 and rs3818292 loci of the SIRT1, rs3782116 andrs536715 of the SIRT3, which showed the absence of linkagedisequilibrium between the loci of the SIRT1 gene and the SIRT3 gene . Basedon the obtained data, haplotypes association analysis wasnot performed. Association of SIRT6 (rs107251) with thedevelopment of COPD was detected in the dominant model, but the association with the heterozygousCT genotype was more significant . The risk of COPD was associated with the CC ge-notype of SIRT6 (rs107251) (OR = 1.54 95 % CI 1.23\u20131.93).We have identified the association SNPs of the PIK3R1 gene with COPD. The risk ofCOPD was associated with heterozygous genotypes of thestudied SNPs of the PIK3R1 gene: rs10515070 , rs831125 and withthe GG genotype of rs3730089 .We showed the absence of linkage disequilibrium betweenrs10515070, rs831125, rs3730089 of the PIK3R1 gene:for rs10515070 and rs831125 , forrs10515070 and rs3730089 , forrs831125 and rs3730089 .Based on the obtained data, haplotypes association analysiswas not performed. Association of PTEN (rs701848)and COPD was established in the dominant , recessive andlog-additive models Padj = 0.0015, OR = 1.35). We haveidentified the association of PTEN (rs2735343) with COPD inthe log-dominant model and for theheterozygous genotype . Linkagedisequilibrium between the rs701848 and rs2735343 was notdetected , thus, haplotype associationanalysis was not performed.Association of the studied genes lociand quantitative phenotypes with lungfunction parameters and smoking indexLung function decline is a key clinical feature of airwayobstruction in COPD that indicates progression of the disease.We investigated the relationship between the studied genes lociand lung function parameters: Forced Vital Capacity (FVC),Forced Expiration Volume in 1 s (FEV1), and FEV1/FVCratio in COPD patients (Table 3). The heterozygous genotypeof PIK3R1 (rs3730089) (P = 0.013) and the TT genotypeof MTOR (rs2536) (P = 0.013) were associated with adecrease in the FVC value. Carriers of the SIRT3 (rs3782116)AA genotype exhibited a higher FVC value (P = 0.0015).Individuals that presented the AA genotype of SIRT1(rs3818292) (P = 0.017), the GG genotype of PIK3R1(rs3730089) (P = 0.025), and the AA genotype of SIRT3(rs3782116) (P = 0.0028) showed a significant increase in theirFVC. Meanwhile, carriers of the heterozygous genotypes ofSIRT1 (rs3818292) (P = 0.04), MTOR (rs2295080) (P = 0.025),and SIRT3 (rs3782116) (P = 0.016) exhibited a lower FVC value (see Table 3). The carriers of the heterozygous genotypeof PIK3R1 (rs831125) (P = 0.0082), the AA genotype ofSIRT1 (rs3818292) (P = 0.036) had a significantly highersmoking index.Analysis of gene-gene interactionsUsing the APSampler algorithm, we have identified gene-genecombinations significantly associated with \u0441hronic obstructivepulmonary disease. In order to identify significant interactionsof functionally related sirtuins genes, SIRT2 (rs10410544) wasincluded in the analysis . We obtained2324 patterns associated with \u0441hronic obstructive pulmonarydisease. Table 4 shows the results of the most significant genegenecombinations with PFDR less than 0.05 and OR morethan 2.0 for risk combinations) or less than 0.35 for protectivecombinations. A total of 19 gene-gene combinations fulfilledthe above-mentioned criteria. Nine patterns were associatedwith an increased risk of COPD; ten were protective. Allele Gand genotype GG of PIK3R1 (rs831125) contributed to themost significant combinations associated with COPD risk(four patters).The highest risk of COPD was conferred by the combinationof these variants of PIK3R1 (rs831125) with the GG genotypeof SIRT3 (rs536715) (OR = 3.45); and with the C alleleof PTEN (rs2735343) (OR = 3.06) and their combination:genotype GA of PIK3R1 (rs831125) together with the G alleleof SIRT3 (rs536715) and the C allele of PTEN (rs2735343)(OR = 2.86). The analysis on the gene-gene interaction of thestudied gene loci established an association of the T alleleof MTOR (rs2536) only in combinations with the G alleleof PIK3R1 (rs831125) (OR = 2.71). Three of the identifiedpatterns included the G allele of PIK3R1 (rs3730089) in combination with the GG genotype of SIRT3 (rs536715)(OR = 2.09), or with the CC genotype of SIRT6 (rs107251)(OR = 2.01).The most significant protective patterns included the A alleleor the AA genotype of PIK3R1 (rs831125) and the A alleleof PIK3R1 (rs3730089) in combination with the A allele orthe AG genotype of SIRT3 (rs3782116) and the A allele ofSIRT3 (rs536715) (see Table 4). Thus, the PIK3R1 (rs831125),PIK3R1 (rs3730089), and SIRT3 (rs536715) loci exhibited anallele-specific effect, when the G allele of PIK3R1 (rs831125),the G allele of PIK3R1 (rs3730089), and the G allele and theGG genotype of SIRT3 (rs536715) were part of risk patterns,and alternative alleles of the same polymorphic loci werepresent in protective patterns.As a result our study, significant associations between theSIRT1 (rs3818292), SIRT3 , SIRT6(rs107251) polymorphic variants and COPD were found.SIRT1 is the most studied member of the mammalian sirtuinfamily. It has been shown that SIRT1 plays an important rolein signaling pathways involved in cellular senescence andcell death . SIRT1 deacetylates manykey regulatory proteins and transcription factors involved inDNA repair, inflammation, expression of antioxidant genes,and cellular senescence, including the PI3K/AKT/mTORsignaling pathway genes, transcription factor FOXO3a, p21,p16, Klotho proteins .Increased expression of SIRT1 inhibits the TGF-\u03b21/SMAD3signaling pathway and impairs epithelial-mesenchymal transformation,which leads to a decrease in COPD-associatedairway remodeling . SIRT1 levels arereduced in peripheral pulmonary and peripheral blood mononuclearcells of patients with COPD .We found that the COPD risk is higher in heterozygouscarriers of SIRT1 (rs3818292). Moreover, this polymorphicvariant demonstrates an association with a decrease in FV\u04211, which reflects the progression of the disease. Functionalanalysis showed that SIRT1 (rs3818292) is in linkage witha SNP in the 5\u2032-untranslated DNA region (rs3740051) thatchanges the NFKB transcription factor binding site. We didnot associate SIRT1 (rs3758391) with COPD. The results ofour study are in agreement with the previously published datareported for the Han Chinese population .According to functional analysis, rs3758391 is located in thepromoter region of the SIRT1 gene, and the C variant disruptsbinding sites for several transcription factors and regulatoryproteins, affecting gene expression. The role of rs3758391in the development of age-associated diseases is well known.Mitochondrial dysfunction in respiratory epithelial cellsplays an important role in the pathogenesis of COPD . SIRT3 is the main mitochondrial deacetylaseregulating many enzymes involved in energy metabolism,respiratory chain components, the tricarboxylicacid cycle,ketogenesis, and fatty acid beta-oxidation .SIRT3 can directly control the production of reactive oxygenspecies (ROS) by deacetylating manganese superoxidedismutase (SOD2), the main mitochondrial antioxidant enzyme. SIRT3 is involved in regulatingthe activity of the DNA repair enzyme OGG1, which leadsto increased damage to mtDNA and apoptosis of alveolarepithelial cells . A number of studies haveshown the SIRT3 association with various complex diseases.We studied the association between two SIRT3 gene functionalpolymorphisms (rs3782116 and rs536715) and \u0441hronicobstructive pulmonary disease. Functional analysis showedthat rs3782116 is located in the region of binding sites forhsa-miR-328; polymorphic loci rs3782116 and rs536715 arelocated in DNA regions that bind regulatory proteins. Bothpolymorphic loci were associated with COPD in our cohort;the disease development risk was associated with the G allelesof rs3782116 and rs536715. It should be noted that the carriersof the homozygous rare allele A of rs3782116 of the SIRT3gene had higher values of VC and FVC1. The contributionof SIRT3 variants to COPD has not been studied previously.At the same time, effects of the SIRT3 gene SNPs have beenfairly extensively investigated in age-associated diseases inwhich oxidative stress and cellular senescence play a key role.We obtained significant associations of SIRT6 (rs107251)with COPD; the frequent C allele is associated with COPDrisk, while the heterozygous genotype has a protective effecton the disease development. rs107251 is located in the DNAregion that binds to the SOX8 regulatory protein and it is inclose linkage with rs350846, localized in the 3-non-translationalregion of the SIRT6 gene \u2013 a binding site for severalmiRNAs . SIRT6 participates in the regulationof genome stability, NF-kB signaling, glucose homeostasis,exhibits ADP-ribosyltransferase and histone deacetylase activity,plays a role in DNA repair and maintenance of telomericchromatin integrity . In the studyby N. Takasaka et al. (2014), a decrease in SIRT6 levels wasshown in respiratory epithelial cells of COPD patients due tocigarette smoke exposure, leading to cellular senescence anddisruption of autophagy processes. Association of the SIRT6gene SNPs with COPD has not been studied previously, butthere is evidence of their association with cardiovasculardiseases, which are often comorbid pathologies in COPD.The PIK3R1 gene encodes regulatory subunit 1 of phosphoinositide3-kinase, a key element of the PI3K/AKT/mTORsignaling cascade . We investigated threePIK3R1 gene polymorphic loci , which showed a significant association withCOPD in our studied group. Carriers of rare alleles of thesepolymorphic loci had a high risk of COPD. In addition, weinvestigated the relationship between rs3730089 genotypesand VC and FVC1 values; thus, heterozygotes have lowervalues, and these results are in agreement with associationanalysis. Functional analysis showed that an intronic variantrs831125 is located in a binding site for regulatory proteins;rs3730089 is a missense variant with a \u201cbenign\u201d effect accordingto the PolyPhen-2 database (http://genetics.bwh.harvard.edu/pph2/), located in a binding site for regulatory proteinsand affecting splice sites. SNPs of the PIK3R1 gene have notbeen evaluated for COPD before. Previously, an associationhas been observed between rs3730089 and type 2 diabetes.The phosphatase PTEN regulates the activity of phosphoinositide-3 kinase (PI3K) . Smokingas a major risk factor for COPD provokes oxidative stress,which, in turn, affects PTEN expression .We investigated two PTEN gene functional polymorphicloci; rs70184 is located in PTEN gene 3\u2032 region and changesbinding sites for hsa-miR-1252 and hsa-miR-1304 miRNA;rs2735343, located in the intronic region, affects binding sitesfor several regulatory proteins.Significant associations with COPD in our sample werefound with PTEN gene loci; thus, homozygous carriers ofthe rare C allele of rs701848 and heterozygous carriers ofrs2735343 had a significant risk of COPD development.Published data have demonstrated an association betweenPTEN (rs701848) and COPD; the risk was significantly reducedfor homozygous T allele carriers, which is consistentwith the data obtained for our sample .PTEN participates in the regulation of various biologicalprocesses, including cell proliferation, apoptosis, inflammatoryreactions, transcription, and genomic stability . Decreased levels of PTEN lead to activation of PI3Ksignaling and increased cell senescence in COPD . It has been shown that decreased PTEN activity inCOPD increases the activity of matrix metalloprotease MMP9in bronchial epithelial cells, which consequently contributesto the progression of inflammation and extracellular matrixdegradation .The analysis of gene-gene interactions revealed significantsynergy between polymorphic loci of genes encodingphosphoinositide-3-kinase (PIK3R1) and mitochondrialdeacetylase (SIRT3), which were present in most significantcombinations associated with an increased risk of \u0441hronicobstructive pulmonary disease. The C allele in the PTEN(rs2735343) was part of four informative combinations associatedwith a high risk of \u0441hronic obstructive pulmonarydisease.The results of polygenic analysis indicate the interactionof genes encoding sirtuins SIRT3, SIRT2, SIRT6 and PI3KR1,PTEN, MTOR and confirm the functional relationship betweensirtuins and the PI3K/AKT/mTOR signaling pathway.The obtained results of single locus and polygenic analysis indicatethe contribution of SIRT3 , SIRT6(rs107251) and PIK3R1 polymorphisms to COPD and interaction of genes enco-ding the key components of the PI3K/AKT/mTOR signallingpathway and sirtuins, and confirm the involvement of cellularsenescence mechanisms with COPD developmentThe authors declare no conflict of interest.Barnes P.J., Baker J., Donnelly L.E. Cellular senescence asa mechanism and target in chronic lung diseases. Am. J.Respir. Crit. Care Med. 2019;200(5):556-564. DOI 10.1164/rccm.201810-1975TR.Cai B., Yang L., Do Jung Y., Zhang Y., Liu X., Zhao P., Li J.PTEN: An emerging potential target for therapeutic interventionin respiratory diseases. Oxid. Med. Cell Longev.2022;2022:4512503. DOI 10.1155/2022/4512503.Cao L., Liu C., Wang F., Wang H. SIRT1 negatively regulatesamyloid-beta-induced inflammation via the NF-\u03baB pathway.Braz. J. Med. Biol. Res. 2013;46(8):659-669. DOI10.1590/1414-431X20132903.Chuchalin A.G., Avdeev S.N., Aisanov Z.R., Belevskiy A.S.,LeshchenkoI.V., Ovcharenko S.I., Shmelev E.I. Federalguidelines on diagnosis and treatment of chronic obstructivepulmonary disease. Pul\u2019monologiya = Pulmonology.2022;32(3):356-392. DOI 10.18093/0869-0189-2022-32-3-356-392. (in Russian)Dikalova A.E., Itani H.A., Nazarewicz R.R., McMaster W.G.,FlynnC.R., Uzhachenko R., Fessel J.P., Gamboa J.L., HarrisonD.G., Dikalov S.I. Sirt3 impairment and SOD2 hyperacetylationin vascular oxidative stress and hypertension.Circ. Res. 2017;121(5):564-574. DOI 10.1161/CIRCRESAHA.117.310933.Ersahin T., Tuncbag N., Cetin-Atalay R. The PI3K/AKT/mTORinteractive pathway. Mol. Biosyst. 2015;11(7):1946-1954.DOI 10.1039/c5mb00101cFinkel T., Deng C.X., Mostoslavsky R. Recent progressin the biology and physiology of sirtuins. Nature.2009;460(7255):587-591. DOI 10.1038/nature08197.Gao S.L., Wang Y.H., Li C.Y., Yang L.W., Zou B.A., Chen Z.G.,Yao W.M., Song Z.Q., Cheng J.F., Lin Z.Y., Liu G. A highlysignificant association between Cathepsin S gene polymorphismsrs12068264 and chronic obstructive pulmonary diseasesusceptibility in Han Chinese population. Biosci. Rep.2018;38(4):BSR20180410. DOI 10.1042/BSR20180410.Hosgood H.D., Menashe I., He X., Chanock S., Lan Q. PTENidentified as important risk factor of chronic obstructive pulmonarydisease. Respir. Med. 2009;103(12):1866-1870. DOI10.1016/j.rmed.2009. 06.016.Ito K., Barnes P.J. COPD as a disease of accelerated lung aging.Chest. 2009;135(1):173-180. DOI 10.1378/chest.08-1419.Karado\u011fan A.H., Arikoglu H., G\u00f6kt\u00fcrk F., \u0130\u015f\u00e7io\u011flu F., \u0130pek\u00e7i S.H.PIK3R1 gene polymorphisms are associated with type 2diabetes and related features in the Turkish population.Adv. Clin. Exp. Med. 2018;27(7):921-927. DOI 10.17219/acem/68985.Kirkham P.A., Barnes P.J. Oxidative stress in COPD. Chest.2013; 144(1):266-273. DOI 10.1378/chest.12-2664.Korytina G.F., Akhmadishina L.Z., Aznabaeva Y.G., KochetovaO.V., Zagidullin N.S., Kzhyshkowska J.G., Zagidullin S.Z.,Viktorova T.V. Associations of the NRF2/KEAP1 pathwayand antioxidant defense gene polymorphisms with chronicobstructive pulmonary disease. Gene. 2019;692:102-112.DOI 10.1016/j.gene.2018.12.061.Kugel S., Mostoslavsky R. Chromatin and beyond: the multitaskingroles for SIRT6. Trends Biochem. Sci. 2014;39(2):72-81. DOI 10.1016/j.tibs.2013.12.002.Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A.,Bender D., Maller J., Sklar P., de Bakker P.I., Daly M.J.,Sham P.C. PLINK: a tool set for whole-genome associationand population-based linkage analyses. Am. J. Hum. Genet.2007;81(3):559-575. DOI 10.1086/519795.Ragland M.F., Benway C.J., Lutz S.M., Bowler R.P., HeckerJ., Hokanson J.E., Crapo J.D., Castaldi P.J., DeMeo D.L.,Hersh C.P., Hobbs B.D., Lange C., Beaty T.H., Cho M.H.,Silverman E.K. Genetic advances in chronic obstructive pulmonarydisease. Insights from COPDGene. Am J. Respir.Crit. Care. Med. 2019;200(6):677-690. DOI 10.1164/rccm.201808-1455SO.Rajendrasozhan S., Yang S.R., Kinnula V.L., Rahman I. SIRT1,an antiinflammatory and antiaging protein, is decreased inlungs of patients with chronic obstructive pulmonary disease.Am. J. Respir. Crit. Care Med. 2008;177(8):861-870. DOI10.1164/rccm.200708-1269OC.Ryter S.W., Rosas I.O., Owen C.A., Martinez F.J., Choi M.E.,Lee C.G., Elias J.A., Choi A.M.K. Mitochondrial dysfunctionas a pathogenic mediator of chronic obstructive pulmonarydisease and idiopathic pulmonary fibrosis. Ann. Am.Thorac. Soc. 2018;15(Suppl. 4):S266-S272. DOI 10.1513/AnnalsATS.201808-585MG.Song X., Wang H., Wang C., Ji G., Jiang P., Liang D., WangX. Association of sirtuin gene polymorphisms with susceptibilityto coronary artery disease in a North Chinesepopulation. Biomed. Res. Int. 2022;2022:4294008. DOI10.1155/2022/4294008.Sun W., Liu C., Chen Q., Liu N., Yan Y., Liu B. SIRT3: A newregulator of cardiovascular diseases. Oxid. Med. Cell Longev.2018;2018: 7293861. DOI 10.1155/2018/7293861Takasaka N., Araya J., Hara H., Ito S., Kobayashi K., Kurita Y.,WakuiH., Yoshii Y., Yumino Y., Fujii S., Minagawa S., TsurushigeC., Kojima J., Numata T., Shimizu K., Kawaishi M.,Kaneko Y., Kamiya N., Hirano J., Odaka M., Morikawa T.,Nishimura S.L., Nakayama K., Kuwano K. Autophagy inductionby SIRT6 through attenuation of insulin-like growth factorsignaling is involved in the regulation of human bronchialepithelial cell senescence. J. Immunol. 2014;192(3):958-968.DOI 10.4049/jimmunol.1302341.Vannitamby A., Seow H.J., Anderson G., Vlahos R., ThompsonM., Steinfort D., Irving L.B., Bozinovski S. Tumour-associated neutrophils and loss of epithelial PTENcan promote corticosteroid-insensitive MMP-9 expressionin the chronically inflamed lung microenvironment.Thorax. 2017;72(12):1140-1143. DOI 10.1136/thoraxjnl-2016-209389.Wang C.H., Wu S.B., Wu Y.T., Wei Y.H. Oxidative stress responseelicited by mitochondrial dysfunction: implication in the pathophysiology of aging. Exp. Biol. Med.2013;238(5):450-460. DOI 10.1177/1535370213493069.Ward L.D., Kellis M. HaploReg v4: systematic mining of putativecausal variants, cell types, regulators and target genesfor human complex traits and disease. Nucleic Acids Res.2016;44(D1):D877-D881. DOI 10.1093/nar/gkv1340.Worby C.A., Dixon J.E. PTEN. Annu. Rev. Biochem. 2014;83:641-669. DOI 10.1146/annurev-biochem-082411-113907.Wu Q.J., Zhang T.N., Chen H.H., Yu X.F., Lv J.L., Liu Y.Y.,Liu Y.S., Zheng G., Zhao J.Q., Wei Y.F., Guo J.Y., Liu F.H.,Chang Q., Zhang Y.X., Liu C.G., Zhao Y.H. The sirtuin familyin health and disease.Signal Transduct. Target. Ther.2022;7(1):402. DOI 10.1038/s41392-022-01257-8.Zhang X.Y., Li W., Zhang J.R., Li C.Y., Zhang J., Lv X.J. Roles ofsirtuin family members in chronic obstructive pulmonary disease.Respir. Res. 2022; 23(1):66. DOI 10.1186/s12931-022-01986-y."} +{"text": "Even though NoShow\u2019s 52,825 bp genome is most similar to phages in cluster AB, its Mycobacterium abscessus revealed a siphovirus morphology , prepared for sequencing using the NEB Ultra II library kit, and sequenced on Illumina MiSeq (v3 reagents), yielding 59,426 single-end 150-base reads. Raw reads were assembled and checked for completeness using Newbler (v2.9) and Consed (v29) with default settings (MK279840), Muddy , and FF47 (Geneious Prime (2022.0.2)) and has the highest G + C content . NoShow possessed 11 bp 3\u2032 single-stranded genome termini (5\u2032-CGGAGAGGCTT-3\u2032) (NoShow\u2019s DNA was extracted by Phenol-Chloroform (settings . Within http://phages.wustl.edu/starterator), ARAGORN (v1.2.38) and tRNAscan-SE (v1.3) (The genome was annotated using PECAAN (v2021) , PhameraE (v1.3) , 11, HHPE (v1.3) , and BlaE (v1.3) , and theE (v1.3) . DefaultConsistent with cluster AB phages, NoShow lacks any identifiable immunity repressor or integrase functions and is, therefore, considered a lytic phage \u201318. Unli\u201321\u2013"} +{"text": "The name of the first author was incorrectly expressed in the Citation. The correct Citation is: Winck FV, Arvidsson S, Ria\u00f1o-Pach\u00f3n DM, Hempel S, Koseska A, et al. (2013) Genome-Wide Identification of Regulatory Elements and Reconstruction of Gene Regulatory Networks of the Green Alga Chlamydomonas reinhardtii under Carbon Deprivation. PLoS ONE 8(11): e79909. doi:10.1371/journal.pone.0079909."} +{"text": "AbstractDoryctopambolusgen. n. is erected to contain Doryctopambolus pilcomayensis , comb. n., which was previously placed within Pambolus (Pambolinae), as well as three new species, Doryctopambolus clebschisp. n., Doryctopambolus dominicanussp. n. and Doryctopambolus sarochensissp. n. Members PageBreakof this new genus are mainly characterised by the presence of at least one pair of conspicuous propodeal apico-lateral projections, which are similar to those present in all members of Pambolinae and in species of three Australasian doryctine genera. We generated DNA barcoding sequences for the three newly described species. We discuss the morphological similarity between species of the Australasian Echinodoryctes Belokobylskij, Iqbal & Austin and Doryctopambolus. A key for the described species of Doryctopambolus is provided.The new Neotropical doryctine genus Eucharitidae, Figitidae, Ichneumonidae and Braconidae, among others. Within the cyclostome group of subfamilies belonging to Braconidae, the presence of acute tubercles or spines on the apical lateral region of propodeum has been considered as the main diagnostic character employed to distinguish members of the cosmopolitan Pambolinae , all belonging to the cyclostome subfamily Doryctinae, also have these propodeal projections, indicating that this feature has actually evolved on separate occasions within Braconidae.The presence of propodeal or scutellar spines is a common feature found in species of a number of hymenopteran parasitoid families, including mbolinae . HoweverPambolus described to date , comb. n. and three additional Neotropical species described herein. We also molecularly characterise the three newly described species with the DNA barcoding locus , Colecci\u00f3n Nacional de Insectos, Instituto de Biolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico (CNIN-IB UNAM), Museo Argentino de Ciencias Naturales \u201cBernardino Rivadavia\u201d, Buenos Aires, Argentina (MACN), and Museo de La Plata, Argentina (MLP). Terminology for body structure, sculpture and wing venation features follows Digital colour photographs of all the species included in this work were taken with a Leica\u00ae Z16 APO-A stereoscopic microscope and a Leica\u00ae DFC295/DFC290 HD camera, and were edited using the Leica Application Suite\u00ae program. Digital scanning electron microscope (SEM) photographs of DNA sequences belonging to the barcoding locus [~650 bp of the cytochrome oxidase I (COI) mitochondrial DNA gene; Nunes & Zald\u00edvar-River\u00f3ngen. n.urn:lsid:zoobank.org:act:2C42D9FA-392C-4F6E-8A6E-CA00EAE711C0http://species-id.net/wiki/DoryctopambolusPambolus pilcomayensis van Achterberg & Braet, 2004Doryctopambolus can be distinguished from members of most doryctine genera except Concurtisella bidens, Echinodoryctes, Fijispathius and Ryukuspathius by having the propodeum with at least one pair of conspicuous apico-lateral projections. SpePageBreakPageBreakcies of Doryctopambolus and Concurtisella bidens are the only Neotropical doryctine taxa reported to have these projections, though they mainly differ by their first subdiscal cell and ovipositor length . Doryctopambolus differs from the Australasian Fijispathius and Ryukyuspathius mainly by the fore wing first subdiscal cell open at apex (closed in the later two genera) and the first metasomal segment not petiolate . Doryctopambolus is morphologically similar to the Australian Echinodoryctes , propodeum evenly curved and strongly rugose-areolate (globose and mostly smooth in Echinodoryctes), hind coxa without basoventral tubercle and all femora without dorsal protuberances (both present in Echinodoryctes).Species ofdoryctes . HoweverHead: head globose; antennal sockets distinctly separated from each other by at least 0.5 times its diameter; frons almost flat, without median carina or furrows; ocelli arranged in equilateral triangle; eye with distinct and sparse setae; gena and temple smooth; malar suture absent; first flagellomere slightly shorter than scape and pedicel combined, slightly longer than second flagellomere; antenna with 16\u201328 antennomeres; occipital carina meeting hypostomal carina before mandible. Mesosoma: Length of mesosoma about two times its maximum width; neck of pronotum fairly long; pronotal crest conspicuous; mesoscutum declivous anteriorly; mesoscutal lobes smooth and polished medially; notauli complete and strongly impressed; scutellar sulcus deep, with its height 0.8\u20130.9 times height of scutellar disc; precoxal sulcus complete and scrobiculate, as long as mesopleuron; prepectal carina coarse and complete; propodeum evenly curved and strongly rugose-areolate, with at least one pair of conspicuous apico-lateral projections; propodeal bridge absent. Legs: fore tibia with a row of 7\u20138 stout spines; middle tibia without spines; femora without dorsal protuberances; hind coxa without basal tubercle. Wings: partially reduced to well-developed wings; fore wing veins r-m and 2RS present; m-cu arising interstitial or slightly antefurcal with vein 2RS, cu-a distinctly postfurcal with vein 1M; first subdiscal cell open at apex; hind wing vein M+CU equal length of vein 1M; cu-a present, m-cu absent; stigma present on male hind wing. Metasoma: length of first metasomal tergum 1.3\u20131.6 times its apical width, apical width about 2.0\u20132.3 times basal width; basal sternal plate (acrosternite) about 0.33\u20130.5 times length of tergum; suture between second and third metasomal tergites absent; second metasomal tergite at least sculptured basally; third metasomal tergite usually smooth, sometimes sculptured basally; remaining metasomal tergites entirely smooth and polished; ovipositor about same length of metasoma.Small size, 2.2\u20133.6 mm; black to light brown species. Neotropical. Known from central Argentina to northern Venezuela, and from Dominican Republic in the Caribbean.Doryctopambolus and Doryctopambolus pilcomayensis comb. nov. are described and redescribed in this study, respectively. Four additional speciePageBreaks belonging to this genus, two from Cerro Saroche, Lara, Venezuela, and two from Argentina, were also identified. The two Argentinian species could not be described due to their bad state of preservation.Of the two species from Venezuela, one was represented by a single male and the other one by an incomplete female, and their allospecificity was corroborated with DNA barcoding sequences . The Parque Nacional Cerro Saroche is a natural reserve of about 32,294 h mainly composed of xeric vegetation with deciduous and semideciduous shrubs comb. n.Pambolus pilcomayensis van Achterberg & Braet 2004: pp. 341\u2013344.Doryctopambolus sarochensis sp. n. by having one pair of propodeal apico-lateral projections (two pairs in Doryctopambolus sarochensis sp. n.) and third metasomal tergite entirely smooth . Doryctopambolus pilcomayensis differs PageBreakfrom Doryctopambolus dominicanussp. n. and Doryctopambolus clebschi sp. n. by having the vertex striate (smooth in Doryctopambolus dominicanus sp. n. and Doryctopambolus clebschi sp. n.), first metasomal tergite not petiolate (at least 0.5 of tergum) and second metasomal tergite entirely sculptured (mostly smooth).This species distinguishes from Colour: head light to dark brown, antenna light brown, malar space light brown to yellowish, mandible and palpi light brown; propleuron and pronotum light brown, remainder of mesonotum brown to black; wings slightly infuscate, narrow banded with brown veins; metasoma brown to black, first two metasomal tergites darker; legs brown to dark brown, fore and middle coxae, trochanter, trochantellus and tarsi light brown to pale yellow; ovipositor and sheaths light brown with dark apex. Head: antero-dorsal surface of eyes bordered by groove; eyes setose; face costate-rugose laterally, central area slightly swollen and smooth; clypeus costate-rugose; malar space 0.8\u20131.0 times eye height; frons and vertex striate; temple in dorsal view 0.7 times eye width; antenna with 26 antennomeres. Mesosoma: length of mesosoma 2.0 times its maximum height; pronotum rugose; pronotal groove wide and scrobiculate laterally, dorsally smooth; propleuron costate-rugose; notauli deep and scrobiculate, meeting scutellum with parallel carinae; scutellum smooth and setose; scutellar sulcus with three parallel carinae; mesopleuron porcate dorsally, smooth near precoxal sulcus and ventrally; ventral portion of mesopleuron separated by shallow crenulate median groove with some rugosities near middle coxae; propodeum with one pair of conspicuous apico-lateral projections, longer than first flagellomere; median carina present only basally. Legs: hind coxa costate to costate-rugose dorsally. Wings: fore wing length 3.7\u20134.8 times its maximum width, r:3RSa:3RSb = 2:8-12:18-32; 2RS:3RSa:r-m = 6:8-12:2-3; m-cu arising interstitial or slightly antefurcal to vein 2RS; 1cu-a interstitial with 1M. Metasoma: length of first metasomal tergite 1.3 times its apical width, apical width about 2.0 times basal width costate-rugose, with two or three longitudinal carinae reaching apex of tergum; second metasomal tergite strongly costate; remaining metasomal tergites smooth and polished; basal sternal plate (acrosternite) about 0.33 times length of tergum; ovipositor nearly as long as metasoma.Females. Body length 3.0\u20133.6 mm, fore wing 2.0 mm, ovipositor 1.8 mm. Males. Essentially as females; body length 2.1\u20133.0 mm; body brown, with antennae, trochanter, trochantellus, tarsi, fore and middle coxae light brown to yellowish; face, frons and vertex slightly sculptured; stigma present in hind wing.Brazil: Goi\u00e1s State (GO), Itumbiara, Malaise trap, C.H. Marchiori col.: one female 24-I-1998, three males 28-I-1998, one female and one male 31-I-1998, two males 7-II-1998, three females and one male 28-II-1998, one female and one male 7-III-1998, one female 1-IV-1998, one female and one male 15-IV-1998, one female 08-XI-1998 (DCBU); Mato Grosso do Sul State (MS), Bodoquena, Parque Nacional da Serra da Bodoquena, Faz. Pitangueiras, Bandeja Am. 21 (yellow pan trap), Crepaldi RA et al. col: one female V-2009 (DCBU). Argentina: Misiones Province, Estaci\u00f3n Experimental Loreto, Dr. A. Ogloblin: one female 15-VI-1930 (MLP); Buenos Aires Province, Reserva Ecol\u00f3gica de Vicente L\u00f3pez, 34.492\u00b0S, 58.480\u00b0W: one male 16-I-2011 (MACN); one male, no data (MLP).Twenty-two specimens . PageBreakSouthern Brazil to Argentina.Doryctopambolus pilcomayensis near Buenos Aires can be explained by the courses of the Parana and Uruguay basins, which carry downstream many plant and animal species from tropical areas to higher latitudes.The presence of Zald\u00edvar-River\u00f3n & Mart\u00ednezsp. n.urn:lsid:zoobank.org:act:0992A72F-1163-48FB-A1BF-D5E59F7D117Fhttp://species-id.net/wiki/Doryctopambolus_clebschiDoryctopambolus clebschi is morphologically similar to Doryctopambolus dominicanus sp. n. However, Doryctopambolus clebschi differs from the latter species by having the face smooth medially and slightly rugose laterally (entirely rugose in Doryctopambolus dominicanus sp. n.), mesopleuron mostly smooth (mostly smooth-rugose), first metasomal tergite mostly smooth apically , and second metasomal tergite mostly smooth, slightly costate baso-laterally . These two species distinguish from the remaining two described species of Doryctopambolus, Doryctopambolus pilcomayensis comb. n. and Doryctopambolus sarochensis sp. n., by having the vertex smooth , first metasomal tergite distinctly petiolate (not petiolate), and second metasomal tergite partially smooth .. Body length 2.8 mm; fore wing 2.3 mm; ovipositor 1.7 mm. Colour: head brown, antennae brown, turning honey yellow to apex, palpi yellow; mesosoma and first metasomal tergites brown, second metasomal tergite honey yellow, remaining metasomal tergites light brown; wings hyaline; veins and stigma light brown; legs light brown to honey yellow; ovipositor and sheaths light brown to brown, apex strongly sclerotised and dark. Head: antenna with 16-17 antennomeres; eyes small, ovoid and setose; face smooth and glabrous medially, slightly rugose and pilose laterally, median area not swollen; clypeus slightly rugose; malar space 0.4 times eye height; frons and vertex smooth; temple in dorsal view 2.7 times eye width. Mesosoma: 1.8 times longer its maximum height; pronotum rugose laterally; pronotal groove wide and scrobiculate; propleuron slightly rugose; mesoscutal lobes entirely smooth and polished, sparsely pilose; notauli wide, deep and scrobiculate, meeting before scutellum in a longitudinally costate area; scutellum smooth, sparsely setose; scutellar sulcus with three parallel carinae; height of scutellar sulcus 0.8 times height of scutellar disc; subalar sulcus wide and scrobiculate, joining mesopleural sulcus, remaining area of mesopleuron mostly smooth and polished, slightly rugose near mesopleural sulcus; venter of mesopleuron smooth; propodeum with one pair of long and sharp apico-lateral projections, shorter than first flagellomere. Legs: hind coxa mostly smooth, slightly rugose ventrally. Wings: fore wing length 3.6 times its maximum width, r:3RS:3RSb = 2:3:10; 2RS:3RSa:r-m = 4:3:2; m-cu arising antefurcal with vein 2RS; 1cu-a interstitial with 1M; hind wing vein M + CU about equal length of vein 1M. Metasoma: length of first metasomal tergum 1.5 times its apical width, apical width about 2.3 times basal width, first metasomal tergite costate basally and medially, smooth apically; second metasomal tergite mostly smooth and polished, slightly costate baso-laterally; remaining metasomal tergites smooth and polished; basal sternal plate (acrosternite) about 0.5 times length of tergum; ovipositor about 1.1 times longer than metasoma.FemaleVariation. Females. Body length 2.6\u20132.8 mm.Males. Unknown.PageBreakHolotype. Female (CNIN IB-UNAM). Dominican Republic: A. Bermudez NP, La Ci\u00e9nega, Telostablones, 19.066\u00b0N, 70.863\u00b0W, 15-16-IX-2009, sweep, H. Clebsch col. . Paratype. One female (CNIN IB-UNAM), same data as holotype.Dominican Republic.This species is named in honour to our good friend and colleague Hans Clebsch, who collected the specimens assigned to this species.Zald\u00edvar-River\u00f3n & Mart\u00ednezsp. n.urn:lsid:zoobank.org:act:99C34338-DB4F-4AE2-A662-4DDA9957BA43http://species-id.net/wiki/Doryctopambolus_dominicanusD. Clebschi.See . Body length 2.7 mm; fore wing 1.8 mm; ovipositor 1.3 mm. Colour: head light brown, antennae light brown, turning honey yellow to apex, palpi yellow; mesosoma and first and basal two thirds of second metasomal tergites dark brown; wings hyaline; veins and stigma light brown; legs light brown to honey yellow; ovipositor and sheaths honey yellow, apex strongly sclerotised and dark. Head: PageBreak16 flagellomeres about 0.5 times length of tergum; ovipositor 0.9 times as long as metasoma.FemaleHolotype.Female (CNIN IB-UNAM). Dominican Republic: Punta Cana , Malaise trap, Masner col. .Dominican Republic.The name of this species refers to the country where the holotype was collected, Dominican Republic.Nunes & Zald\u00edvar-River\u00f3nsp. n.urn:lsid:zoobank.org:act:9C8C7812-2519-4849-A2CB-D3EED92F7FFBhttp://species-id.net/wiki/Doryctopambolus_sarochensisDoryctopambolus sarochensis sp. n. distinguishes from the remaining species of the genus by having the vertex striate-rugose (striate in Doryctopambolus pilcomayensis comb. n. and smooth in the remaining two species), two pairs of propodeal apico-lateral projections, the basal ones small and blunt and the second pair long and distinctly truncate, and third metasomal tergite costate baso-laterally (entirely smooth in the other species).. Body length 3.0 mm; fore wing 2.0 mm; ovipositor 1.7 mm. Colour: head brown, malar space honey yellow, antenna honey yellow, turning brown at apex, mandible honey yellow, palpi yellow; mesosoma and metasoma dark brown to black; wings slightly infuscate; veins and stigma brown; fore leg honey yellow; middle leg honey yellow, with femur light brown; hind coxa and femur brown,PageBreak trochanter, trochantellus, tibia and tarsi honey yellow; ovipositor and sheaths honey yellow, apex strongly sclerotised and dark. Head: 23 antennomeres; eyes setose; face striate medially, striate-rugose laterally, with median area slightly swollen; clypeus costate-rugose; malar space 0.6 times eye height; frons and vertex striate-rugose; temple in dorsal view 0.8 times eye width. Mesosoma: two times longer its maximum height; pronotum rugose laterally; pronotal groove wide and scrobiculate; propleuron costate-rugose; mesoscutal lobes mostly smooth and shinning, rugose along notauli and at lateral edges; notauli narrow and scrobiculate, meeting before scutellum in a longitudinally costate-rugose area; scutellum smooth, with some setae; scutellar sulcus with three parallel carinae; height of scutellar sulcus 0.8 times height of scutellar disc; subalar sulcus wide, deep and scrobiculate, joining mesopleural sulcus in an inverted \u201cV\u201d shape; mesopleuron porcate dorsally, porcate-rugose laterally, smooth ventrally; venter of mesopleuron smooth; propodeum with two pairs of apico-lateral projections, the most basal one small and blunt, the apical one long and distinctly truncate, longer than first flagellomere. Legs: hind coxa strongly costate-rugose dorsally, poorly sculptured ventrally. Wings: fore wing length 3.8 times its maximum width, r:3RS:3RSb = 3:6:22; 2RS:3RSa:r-m = 8:6:5; m-cu arising antefurcal with vein 2RS; 1cu-a interstitial with 1M. Metasoma: length of first metasomal tergite 1.5 times its apical width, apical width about 2.0 times basal width, costate rugose with two dorsal carinae converging at apex; second metasomal tergite strongly costate; third metasomal tergite mostly smooth, costate baso-laterally, remaining metasomal tergites smooth and polished; basal sternal plate (acrosternite) about 0.33 times length of tergum; ovipositor as long as metasoma.FemaleVariation.Females. Body length 2.7\u20133.0 mm; antenna with 22\u201323 antennomeres. Males. Unknown.Holotype.Female (CNIN IB-UNAM). Venezuela: Lara, Parque Nacional Cerro Saroche, Ca\u00f1aote #3, 10\u00b011'083\"N, -69\u00b026'013\"W; 1000 msnm; R. Brice\u00f1o, R. Paz, W. Rom\u00e1n, D. Torres colls.; . Paratype. Onefemale (CNIN IB-UNAM), same data as holotype .NortheastVenezuela.The name of this species refers to the place where the type material was collected..Echinodoryctes tetraspinosus Belokobylskij, lqbal & Austin. One specimen. Paratype. Female. Australia: Prevelly Park, W of Margaret\u00a0River, 1 nov. 1984 W.A., I. & N. Lawrence, in marri nuts on ground. Doryctopambolus cf. pilcomayensis: Doryctopambolus sp. 1: one female (MLP): Argentina, Misiones, Estaci\u00f3n Experimental Loreto, Dr. A. Ogloblin, 25-VI-1931; one male (MLP): Argentina, Misiones, Estaci\u00f3n Experimental Loreto, Dr. A. Ogloblin, 8-VI-1933; Doryctopambolus sp. 2: one male (MACN): Argentina, Ciudad Aut\u00f3noma de Buenos Aires, Reserva Ecol\u00f3gica Costanera Sur, trampa de ca\u00edda, Mamani, Turienzo, Zapata, 19-I-2009; Doryctopambolus sp. 3 (CNIN IB-UNAM): Venezuela, Lara, Parque Nacional Cerro Saroche, Ca\u00f1aote, 10\u00b011'083\"N, 69\u00b026'013\"W; 1000 m; R. Brice\u00f1o, R. Paz, PageBreakW. Rom\u00e1n, D. Torres colls. ; Doryctopambolus sp. 4 (CNIN IB-UNAM): Venezuela, Carabobo, Palmichal, 10.2859N, 68.2399W, 931 m, 30-31-iii-07, YPT/64 plates, shade coffee/Orange grove plantations, H. Clebsch col. .Doryctompambolus, Doryctopambolus clebschi (two specimens), Doryctopambolus dominicanus (one specimen), Doryctopambolus sarochensis (two specimens) and the two undescribed species from Venezuela (one specimen each), was congruent with the interspecific variation observed in other braconid genera, ranging from 4.2 to 14%. The lowest interspecific genetic distance occurred between specimens of the two Dominican species, Doryctopambolus clebschi and Doryctopambolus dominicanus.Interspecific variation of the barcoding locus among the examined species of"} +{"text": "Postoperative Atrial Fibrillation (POAF) is the most common arrhythmia in cardiac surgery. Its incidence ranges between 20-40%. The objective of this study was to determine the predictive factors of POAF that occurred in patients undergoing coronary artery bypass grafting (CABG), and the impact of this event on morbidity and mortality.This bi-directional and longitudinal cohort study was made with 3,010 patients undergoing CABG between June/2009 and July/2010, aged \u2265 18 years. We excluded 382 patients for chronic or paroxysmal atrial fibrillation, atrial flutter, or association of the surgery evaluated with other procedures.The incidence of POAF was 12.4% ; rate female: male ratio of 1:3; CRI (p=0.001), creatinine >/= 2.2mg/dl (p=0.002); COPD (p=0.001), ICC (p=0.004), EuroSCORE (p<0.001), blood transfusion (p<0.001), Peripheral Arterial Insufficiency (PAI) ; emergency surgery/emergency (p= 0.006), postoperative stroke (p<0.001) and RI postoperatively (p <0.001). Patients with POAF had longer postoperative hospital stay (p<0.001), higher mortality at one year (p <0.001) and a higher rate of readmission within 30 days (p = 0.004).The age, male gender, CRI, COPD, peripheral arterial disease, creatinine >/= 2,2mg/dl, CHF, EuroSCORE, blood transfusion, emergency surgery/emergency (p= 0.006), postoperative stroke (p<0.001) and RI postoperatively (p<0.001) variables were independently predictive of POAF event. Due to the strong correlation with the increased length of hospitalization, mortality and re-hospitalization in these patients, we must implement strategies for POAF prophylaxis and prevention."} +{"text": "Computerized testing of neurocognitive function yields an accurate and reliable assessment . There iThe purpose of this study was to investigate neurocognitive function and recovery patterns in college students who incur migraine headaches compared to college students who do not.Volunteers (ages 18-29) completed computerized neurocognitive baseline (B) testing. Forty-four migraineurs incurring a migraine (M) were matched to 44 non-migraine (NM) controls for sex, age and education level. Verbal and visual memory, processing speed and reaction time were measured at 24 hours, 48 hours and 7 days post migraine.Repeated measures ANOVAs revealed declines in neurocognitive function of migraineurs in verbal memory , visual memory [md (24hr-B)M=-4.70 +15.61, NM=3.05+10.94; p=.041), and reaction time [md(24hr-B)M=.02\u00b1.09, NM=-.01\u00b1.04."} +{"text": "Fragility fractures are a common and increasing cause of morbidity and mortality in the general population; risk factors for fractures are commoner in HIV . This study aims to determine the prevalence and associations of low bone mineral density (BMD) and high fracture risk (FR) in an HIV cohort, suggest screening and management guidelines.A cross-sectional study of 223 randomly selected HIV-infected outpatients was undertaken. Recruitment was stratified by gender for age groups 30-39, 40-49 yrs and \u226550 yrs. Osteopenia and osteoporosis were diagnosed according to the WHO criteria. Patients completed a detailed questionnaire including combination HIV drugs (cART) history, & a dual-energy X-ray absorptiometry (DEXA) of Lumbar spine & Left Hip. Investigations included serum Ca, phosphate, 25OH vit D, alkaline phosphatase (Alk P) PTH, albumin, sex hormone binding globulin (SHBG), testosterone, CD4, HIV RNA. BMD risk factors were recorded including previous fractures, smoking, malabsorption, alcohol consumption, BMI, chronic diseases, physical activity index and past medication. FRAX score (10yr probability major fractures), and remaining lifetime fracture probability (RLFP) were calculated. Controls were from the Twin Research Unit at Kings College London. Data were analysed using multivariate logistic regression.Demographics: 133(60%) were male, 106(48%) were Caucasian, 71(33%) had AIDS at diagnosis. 190(85%) were taking cART, of whom 50(26%) were on their first line therapy. Osteoporosis/osteopenia were present in 13%/39% of males, 11%/29% females, and was approximately 2.4/3.0 fold greater than age-matched controls. The overall mean 10 yr fracture risk was 3.16%. RLFP exceeded 1.0 in 76% HIV patients, and <20% controls.Factors associated with low BMD after multivariate analysis: adjusted OR(95 % CI)/p-value BMI 0.90, p<0.001, Alk P 1.01, p 0.05, testosterone 1.04, p 0.01, Initiated cART 3.61, p 0.01. The lack of association with age is notable, adjusted OR 1.08, p 0.35Reduced bone mineral density and subsequent fracture risk is much commoner in patients with HIV compared to controls, especially, and those taking cART, and occurred across the age ranges. Hence screening for BMD and risk factors for fragility fractures is indicated in patients with HIV at a younger age than in the general population, especially if they are on cART."} +{"text": "Staphylococcus aureus Hospitalizations,\" by Matthew J Kuehnert et al., an error occurred. In Table 3, columns 3 and 5, the rates shown for hospitalization with S. aureus and MRSA-related discharge diagnoses were per 10,000 discharges, rather than per 1,000 discharges, as indicated.In \u201cMethicillin-resistant\u2013http://www.cdc.gov/eid/11/6/04-0831-t3.htmThe corrected table appears in the updated article at We regret any confusion this error may have caused."} +{"text": "The article title is incorrect. \u201cThe correct title is: MicroRNA-130b Suppresses Migration and Invasion of Colorectal Cancer Cells through Downregulation of Integrin \u03b21.\u201dThe correct Citation is: Zhao Y, Miao G, Li Y, Isaji T, Gu J, et al. (2014) MicroRNA-130b Suppresses Migration and Invasion of Colorectal Cancer Cells through Downregulation of Integrin \u03b21. PLoS ONE 9(2): e87938. doi:10.1371/journal.pone.0087938"} +{"text": "The Sanger Mouse Genetics Project was incorrectly abbreviated in the citation. The correct citation is: Migdalska AM, van der Weyden L, Ismail O, White JK, Sanger Mouse Genetics Project, et al. (2012) Modeling Partial Monosomy for Human Chromosome 21q11.2-q21.1 Reveals Haploinsufficient Genes Influencing Behavior and Fat Deposition. PLoS ONE 7(1): e29681."} +{"text": "Granulicella mallensis MP5ACTX8T is a novel species of the genus Granulicella in subdivision 1of Acidobacteria. G. mallensis is of ecological interest being a member of the dominant soil bacterial community active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. G. mallensis is a cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates. These include gene modules encoding the carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides including plant based carbon polymers. The genome of Granulicella mallensis MP5ACTX8T consists of a single replicon of 6,237,577 base pairs (bp) with 4,907 protein-coding genes and 53 RNA genes. T (= ATCC BAA-1857T = DSM 23137T), is the type strain of the species Granulicella mallensis [Granulicella, in subdivision 1 of Acidobacteria, was first described by Pankratov et al. in 2010 [Granulicella mallensis was described along with other species of the genus Granulicella isolated from tundra soil [Granulicella species.Strain MP5ACTX8Acidobacteria is one of the most ubiquitous bacterial phyla found in diverse habitats and is abundant in most soil environments [Acidobacteria are phylogenetically and physiologically diverse [Acidobacterium [Terriglobus [Edaphobacter [Granulicella [Acidipila [Telmatobacter [Acidicapsa [Bryocella [Bryobacter [Blastocatella [Thermotomaculum [Holophaga [Geothrix [Acanthopleuribacter [Candidatus Koribacter versatilis\u2019 [Candidatus Solibacter usitatus\u2019 [Candidatus Chloracidobacterium thermophilum\u2019 [Acidobacteria are relatively difficult to cultivate with slow growth rates and typically require up to several weeks to develop visible colonies on solid media. Nevertheless, the phylogenetic diversity, ubiquity and abundance of this group suggest that they play important ecological roles in soils. The abundance of Acidobacteria has been found to correlate with soil pH [Acidobacteria being most abundant in slightly acidic soils. Our previous studies have shown that Acidobacteria dominate in the acidic tundra heaths of northern Finland [Acidobacteria [T was classified as a novel species of the genus Granulicella [Granulicella mallensis MP5ACTX8T , G. sapmiensis S6CTX5AT (96.2%) and G. arctica MP5ACTX2T (96.1%) and 94.6 \u2013 97.4% to G. rosea TPO1014T (94.6%), G. aggregans TPB6028T (96.0%), G. pectinivorans TPB6011T (96.1%), G. paludicola OB1010T (96.5%) and G. paludicola LCBR1 (97.4%). Phylogenetic analysis based on the 16S rRNA gene of taxonomically classified strains of family Acidobacteriaceae placed G. paludicola type strain OB1010 T as the closest taxonomically classified relative of G. mallensis MP5ACTX8T at pH 3.5\u20136.5 (optimum pH 5) and at +4 to +28 \u00b0C (optimum 24\u201327 \u00b0C) [T forms opaque white mucoid colonies with a diameter of approximately 1 mm. Cells are Gram-negative, non-motile, aerobic rods, approximately 0.5\u20130.7 mm wide and 0.6\u20131.3 mm long. Growth observed with up to 1.5% NaCl (w/v) (T is shown in 4\u201327 \u00b0C) . On R2 aCl (w/v) . The celG. mallensis utilizes D-glucose, maltose, cellobiose, D-fructose, D-galactose, lactose, lactulose, D-mannose, D-ribose, raffinose, sucrose, trehalose, D-xylose, N-acetyl-D-glucosamine, glucuronate, glutamate, melezitose and salicin, but does not utilize D-arabinose, acetate, formate, pyruvate, malate, mannitol, D- or L-alanine, D-glycine, L-leucine, L-ornithine, gluconic acid, aspartate, dulcitol, butyrate, caproate, valerate, lactate, oxalate, propionate, fumarate, adonitol, methanol, ethanol, succinate, D-sorbitol or myoinositol, when grown using VL55 mineral medium with 100 mg yeast extract l-1. G. mallensis hydrolyzes aesculin, starch, pectin, laminarin and lichenan, but not gelatin, cellulose, xylan, sodium alginate, pullulan, chitosan or chitin on R2 medium. Strains show positive reaction for acid and alkaline phosphatases, leucine arylamidase, a-chymotrypsin, naphthol-AS-BI-phosphohydrolase, \u03b1- and \u03b2-galactosidases, \u03b1- and \u03b2-glucosidases, N-acetyl- \u03b2-glucosaminidase, \u03b2-glucuronidase, trypsin and valine arylamidase, but negative for \u03b1-fucosidase, \u03b1-mannosidase, esterase (C4 and C8), lipase (C14) and cystine arylamidase. Strain MP5ACTX8T reduces nitrate to nitrite. Strain MP5ACTX8T is resistant to the antibiotics erythromycin, chloramphenicol, neomycin, rifampicin, streptomycin, gentamicin, polymyxin B and penicillin, but susceptible to ampicillin, kanamycin, tetracycline, lincomycin, novobiocin and bacitracin [G. mallensis are iso-C15:0 (45.3%), C16:1\u03c97c (28.7%), iso-C13:0 (8.3%) and C16:0 (8.9%). The cellular fatty acid compositions of strain MP5ACTX8T were relatively similar to that of other Granulicella strains with fatty acids iso-C15:0 and C16:1\u03c97c being most abundant in all strains. Strain MP5ACTX8T contains MK-8 as the major quinone.The major cellular fatty acids in G. mallensis strain MP5ACTX8T was selected for sequencing in 2009 by the DOE Joint Genome Institute (JGI) community sequencing program. The Quality Draft (QD) assembly and annotation were completed on December 26, 2010. The complete genome was made available on Dec. 1, 2011. The genome project is deposited in the Genomes On-Line Database (GOLD) [T is deposited in GenBank (CP003130). e (GOLD) and the G. mallensis MP5ACTX8T was cultivated on R2 medium as previously described [escribed . Genomicescribed .G. mallensis MP5ACTX8T (JGI ID 4088692) was generated at the DOE Joint genome Institute (JGI) using a combination of Illumina [The finished genome of Illumina and 454 Illumina . The 454Illumina . The 454Illumina . The sofIllumina was usedIllumina was usedIllumina or sequeGenes were identified using Prodigal as part The genome consists of one circular chromosome of 6,211,694 bp in size with a GC content of 57.8 mol% and consists of 53 RNA genes . Of the Granulicella mallensis type strain MP5ACTX8T has the largest genome size of 6.2 Mbp. among the three tundra soil strains of subdivision 1 Acidobacteria [Granulicella mallensis identified a high abundance of genes assigned to COG functional categories for transport and metabolism of carbohydrates (9.1%) and amino acids (6.7%) and involved in cell envelope biogenesis (8.3%) and transcription (8.6%). Further genome analysis revealed an abundance of gene modules encoding for functional activities within the carbohydrate-active enzymes (CAZy) family [G. mallensis hydrolyzed complex carbon polymers, including CMC, pectin, lichenin, laminarin and starch, and utilized sugars such as cellobiose, D-mannose, D-xylose, D-trehalose. This parallels genome predictions for CDSs encoding for enzymes such as cellulases, pectinases, alginate lyases, trehalase and amylases. In addition, the G. mallensis genome contained a cluster of genes in the neighborhood of the cellulose synthase gene (bcsAB) which included cellulase (bscZ) (endoglucanase Y) of family GH8, cellulose synthase operon protein (bcsC) and a cellulose synthase operon protein (yhjQ) involved in cellulose biosynthesis. Detailed comparative genome analysis of G. mallensis MP5ACTX8T with other Acidobacteria strains for which finished genomes were available is reported in Rawat et al. [G. mallensis is involved in hydrolysis, the utilization of stored carbohydrates, and in the biosynthesis of exopolysaccharides from organic matter and plant based polymers in the soil. Therefore, we infer that strain G. mallensis may be central to carbon cycling processes in arctic and boreal soil ecosystems.bacteria . Genome ) family involvedt et al. . The dat"} +{"text": "Hepatic dysfunction has been associated with outcome of ICU patients. However, most scoring systems including APACHE II only marginally reflect acute liver dysfunction on admission. Indocyanine green (ICG) is eliminated by hepatobiliary excretion. Therefore, the ICG plasma disappearance rate (ICG-PDR) is used as a dynamic liver function test. ICG-PDR has been associated with mortality in several studies.A prospective study to compare prediction of 28-day mortality by ICG-PDR, other markers of liver function and scoring systems (primary endpoint). In the subgroup of patients with transpulmonary thermodilution (TPTD) monitoring , predictive capabilities of ICG-PDR were compared with cardiac index (CI), extravascular lung water index (EVLWI), global end-diastolic volume index (GEDVI) and pulmonary vascular permeability index (PVPI). ICG-PDR and all other predictors were determined within 48 hours after admission. Statistics: IBM SPSS 20.P <0.001) and SOFA . Among markers of hepatic function on admission, ICG-PDR provided the largest AUC , which was larger than for GOT , bilirubin and INR . Among TPTD parameters, only PVPI significantly predicted 28-day mortality , whereas CI, GEDVI and EVLWI were not predictive. Prediction of 28-day mortality by SOFA could not be improved by models including any hepatic parameter. By contrast, ICG-PDR was independently (P = 0.036) associated with mortality when included in a model (R = 0.58) with APACHE II. This model based on APACHE II and ICG-PDR provided the largest of all ROC-AUCs . ICG-PDR itself was independently associated with age (P = 0.025), but not with any other biometric parameter .A total of 154 patients , age 59 \u00b1 13 years, APACHE II score 16.0 \u00b1 5.7, SOFA score 7.6 \u00b1 4.2. Etiology: sepsis 14.4%, cirrhosis 28.8%, GI bleeding 8.9%, ARDS 17.8%, cardiogenic shock 4.1%, acute renal failure 3.4%, various 22.6%. The 28-day mortality was significantly predicted by APACHE II (ROC-AUC: 0.762; ICG-PDR on admission is an independent predictor of 28-day mortality. Predictive capabilities particularly of APACHE II can be improved by combination with ICG-PDR. Among TPTD-derived parameters, only PVPI provides significant prediction of mortality."} +{"text": "The authors would like to add Matthias Gunther as the 6th author. The updated byline is: David A. Feinberg1,2,3*, Steen Moeller4, Stephen M. Smith5, Edward Auerbach4, Sudhir Ramanna1, Matthias Gunther1, Matt F. Glasser6, Karla L. Miller5, Kamil Ugurbil4, Essa Yacoub4The updated author contributions are: Conceived and designed the experiments: DAF SMS KU EY. Performed the experiments: DAF SM EA SR MG EY. Analyzed the data: DAF SM SMS EY KLM MFG. Contributed reagents/materials/analysis tools: DAF SM EA SR SMS MG MFG. Wrote the paper: DAF SM SMS KU EY KLM."} +{"text": "Plasmopara viticola, is one of the most severe diseases of grapevine and is commonly controlled by fungicide treatments. The beneficial microorganism Trichoderma harzianum T39 (T39) can induce resistance to downy mildew, although the molecular events associated with this process have not yet been elucidated in grapevine. A next generation RNA sequencing (RNA-Seq) approach was used to study global transcriptional changes associated with resistance induced by T39 in Vitis vinifera Pinot Noir leaves. The long-term aim was to develop strategies to optimize the use of this agent for downy mildew control.Downy mildew, caused by P. viticola inoculation. RNA-Seq analysis resulted in the identification of 7,024 differentially expressed genes, highlighting the complex transcriptional reprogramming of grapevine leaves during resistance induction and in response to pathogen inoculation. Our data show that T39 has a dual effect: it directly modulates genes related to the microbial recognition machinery, and it enhances the expression of defence-related processes after pathogen inoculation. Whereas several genes were commonly affected by P. viticola in control and T39-treated plants, opposing modulation of genes related to responses to stress and protein metabolism was found. T39-induced resistance partially inhibited some disease-related processes and specifically activated defence responses after P. viticola inoculation, causing a significant reduction of downy mildew symptoms.More than 14.8 million paired-end reads were obtained for each biological replicate of T39-treated and control leaf samples collected before and 24\u2009h after The global transcriptional analysis revealed that defence processes known to be implicated in the reaction of resistant genotypes to downy mildew were partially activated by T39-induced resistance in susceptible grapevines. Genes identified in this work are an important source of markers for selecting novel resistance inducers and for the analysis of environmental conditions that might affect induced resistance mechanisms. Plasmopara viticola (Berk. and Curt.) Berl. and de Toni is a biotrophic oomycete that causes downy mildew in grapevine Release 3 [78] in control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants. Expression values in each biological replicate (numbered from 1 to 3) and each sequencing replicate (named A and B) are also listed. Click here for fileCorrelations between sequencing replicates of RNA-Seq analysis. Comparison of the expression levels of all grapevine genes, expressed as fragments per kilobase of transcript per million fragments mapped (FPKM), in the two sequencing replicates (named A and B) of (A) control (C) biological replicate no. 1; (B) C biological replicate no. 2 (B); (C) C biological replicate no. 3; (D) Trichoderma harzianum T39-treated (T39) biological replicate no. 1; (E) T39-treated biological replicate no. 2; (F) T39-treated biological replicate no. 3; (G) Plasmopara viticola-inoculated control (C+P.v.) biological replicate no. 1; (H) C+P.v. biological replicate no. 2; (I) C+P.v. biological replicate no. 3; (J) P. viticola-inoculated T39-treated plants (T39+P.v) biological replicate no. 1; (K) T39+P.v biological replicate no. 2; and (L) T39+P.v biological replicate no. 3. Click here for filePrincipal component analysis of grapevine treatments. Principal component analysis (PCA) is based on the expression values (FPKM) of all grapevine genes for each sequencing replicate (named A and B) of each biological replicate (numbered from 1 to 3) for control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants. Click here for filePearson\u2019s correlation coefficients between sequencing and biological replicates of RNA-Seq analysis. Pearson\u2019s correlation coefficients are based on the gene expression values (FPKM) of all grapevine genes in two sequencing replicates (A and B) of each biological replicate (numbered from 1 to 3) for control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants. Click here for fileExpression levels, clustering, and annotation results of differentially expressed genes. Gene expression values (FPKM) and standard errors are reported for differentially expressed genes in control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants. Differentially expressed genes were identified by the DESeq package with a false discovery rate (FDR) of 5% and a fold-change greater than two in at least one pairwise comparison. Fold-changes, clustering results, and functional annotation are reported for each gene. Click here for filePrimer sequences of the grapevine genes analysed by real-time RT-PCR. Forward and reverse primer sequences of real-time RT-PCR analysis are reported for 24 selected grapevine genes. Grapevine Actin (TC81781) and VATP16 (XM_002269086.1) [94] were used as constitutive genes for normalising the real-time RT-PCR data. Click here for fileExpression levels of grapevine genes that are members of the actin gene family. Gene expression values (FPKM) and standard errors are reported for grapevine genes belonging to the Actin gene family in control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v) plants. Click here for file"} +{"text": "Corrigendum to Anthony L. Cunningham, Andrew N. Harman, Najla Nasr (2013) Initial HIV mucosal infection and dendritic cells. EMBO Mol Med 5 (658\u2013660) DOI: 10.1002/emmm.201202763The name of the second author in this article, \u201cAndrew N. Harman,\u201d missed the middle initial N. The correct author names are listed above."} +{"text": "O-Sulfated Heparan Sulfate Recognized by the Antibody HS4C3 Contributes to the Differentiation of Mouse Embryonic Stem Cells via Fas Signaling.The word \"Contributes\" is misspelled in the article title. The correct title is: 3-O-Sulfated Heparan Sulfate Recognized by the Antibody HS4C3 Contribute to the Differentiation of Mouse Embryonic Stem Cells via Fas Signaling. PLoS ONE 7(8): e43440. doi:10.1371/journal.pone.0043440 The correct citation is: Hirano K, Sasaki N, Ichimiya T, Miura T, Van Kuppevelt TH, et al. (2012) 3-"} +{"text": "Long-term potentiation (LTP) at thalamic input synapses to the lateral nucleus of the amygdala (LA) has been proposed as a cellular mechanism of the formation of auditory fear memories. We have previously shown that signaling via ERK/MAPK in both the LA and the medial division of the medial geniculate nucleus/posterior intralaminar nucleus (MGm/PIN) is critical for LTP at thalamo-LA synapses. Here, we show that LTP-inducing stimulation of thalamo-LA inputs regulates the activation of ERK and the expression of ERK-driven immediate early genes (IEGs) in both the LA and MGm/PIN. Further, we show that pharmacological blockade of NMDAR-driven synaptic plasticity, NOS activation, or PKG signaling in the LA significantly impairs high-frequency stimulation-(HFS-) induced ERK activation and IEG expression in both regions, while blockade of extracellular NO signaling in the LA impairs HFS-induced ERK activation and IEG expression exclusively in the MGm/PIN. These findings suggest that NMDAR-driven synaptic plasticity and NO-cGMP-PKG signaling within the LA coordinately regulate ERK-driven gene expression in both the LA and the MGm/PIN following LTP induction at thalamo-LA synapses, and that synaptic plasticity in the LA promotes ERK-driven transcription in MGm/PIN neurons via NO-driven \u201cretrograde signaling\u201d. Fear conditioning is a type of associative learning that is widely studied as a model of learning and memory across a variety of species. Fear conditioning has been extensively characterized at the behavioral level, particularly auditory fear conditioning, in which a tone is paired with footshock . In brief, auditory fear conditioning is thought to involve transmission and integration of sensory information from CS and US pathways within the lateral nucleus of the amygdala (LA), where alterations in synaptic transmission are believed to encode key aspects of the learning \u20133. In suLong-term potentiation (LTP), an experimental model of synaptic plasticity, is widely believed to be a potential mechanism by which fear conditioning promotes synaptic alterations in the LA , 6. In sin vitro slice recording methods have pointed to a role for a number of intracellular signaling pathways in LTP at thalamic input synapses to the LA, including CaMKII or 60\u2009min , or 60\u2009min (ERK1: t(5) = 1.847, P > .05; ERK2: t(5) = 0.434, P > .05) time points. Further, this effect was not observed in LFS controls = 0.725, P > .05; pERK2: t(5) = 0.759, P > .05), or 30\u2009min (pERK1: t(7) = 1.076, P > .05; pERK2: t(7) = 0.300, P > .05) time points following LFS. The findings for the LA are presented in Figures Figures , left. I Figures , right; t(5) = 2.897, P < .05; pERK2: t(5) = 2.596, P < .05) and 30\u2009min after stimulation (pERK1: t(3) = 5.655, P < .05; pERK2: t(4) = 3.747, P < .05). No significant differences were observed for the 60\u2009min time point (pERK1: t(4) = 0.405, P > .05; pERK2: t(4) = 0.073, P > .05) = 0.520, P > .05; ERK2: t(5) = 0.731, P > .05), 30\u2009min (ERK1: t(4) = 0.661, P > .05; ERK2: t(4) = 0.648, P > .05), or 60\u2009min (ERK1: t(4) = 1.131, P > .05; ERK2: t(4) = 0.195, P > .05) time points. Interestingly, LFS controls were also observed to have elevated levels of phospho-ERK1 and phospho-ERK2 in MGm/PIN at 5 minutes (pERK1: t(5) = 3.193, P < .05; pERK2: t(5) = 4.073, P < .05), but not at 30\u2009min (pERK1: t(5) = 0.529, P > .05; pERK2: t(5) = 0.067, P > .05) = 1.551, P > .05; ERK2: t(5) = 0.691, P > .05) or 30\u2009min (ERK1: t(4) = 0.224, P > .05; ERK2: t(4) = 1.611, P > .05) time points following LFS. The fact that both HFS and LFS induced increases in ERK activation in the MGm/PIN at 5\u2009min suggests that the elevated ERK phosphorylation in MGm/PIN at this time point was due to local electrical stimulation. Importantly, at the 30\u2009min time point only HFS promoted significant ERK activation in the MGm/PIN, suggesting that the enhanced ERK phosphorylation in MGm/PIN at this later time point is specifically associated with LTP. The findings for the MGm/PIN are presented in Figures Figures , left. I Figures , right. In our first series of experiments, we observed significant increases in ERK activation in the LA and MGm/PIN following HFS of the thalamo-LA pathway. In the present experiments, we used a combination of Western blotting and immunohistochemistry to examine whether LTP-inducing stimulation of thalamic input synapses to the LA regulate the ERK-driven IEGs Arc/Arg3.1, EGR-1 and c-Fos in the LA and the MGm/PIN. As before, anesthetized rats received either HFS or LFS of thalamic inputs to the LA and were sacrificed by decapitation 2 hours later Figures , a time t(8) = 6.502, P < .05; c-Fos: t(8) = 3.901, P < .05; EGR-1: t(8) = 5.273, P < .05; t(8) = 1.294, P > .05; c-Fos: t(8) = 0.241, P > .05; EGR-1: t(8) = 2.822, P > .05; t(8) = 3.642, P < .05; c-Fos: t(5) = 3.403, P < .05; EGR-1: t(6) = 2.59, P < .05; t(8) = 1.163. P > .05; c-Fos: t(5) = 0.094, P > .05; EGR-1: t(6) = 1.720, P > .05; The results of our Western blotting experiments are depicted in Figures t(5) = 6.894, P < .05; t(5) = 0.124, P > .05; t(5) = 3.822, P < .05; c-Fos: t(5) = 4.144, P < .05; Figures t(5) = 0.709, P > .05; c-Fos: t(5) = 0.121, P > .05; Figures Immunohistochemical localization of the three IEGs after HFS and LFS in both the LA and MGm/PIN can be seen in Figures t(6) = 22.556, P < .05], EGR-1 , and c-Fos proteins = 1.913, P > .05; EGR-1: t(5) = 0.227, P > .05; c-Fos: t(5) = 0.395, P > .05]. Rats receiving HFS exhibited Arc/Arg3.1, EGR-1, and c-Fos labeled cells throughout the MGm and PIN, while very few labeled cells were observed in the MGv = 4.075, P < .05; pERK2: t(4) = 3.904, P < .05; t(4) = 0.173, P > .05; pERK2: t(4) = 1.273, P > .05] or 7-Ni , however, significantly impaired HFS-induced ERK activation in the LA (t(4) = 5.026, P < .05; pERK2: t(4) = 3.640, P < .05; The findings are depicted in Figures n the LA . Interest(4) = 3.035, P < .05; pERK2: t(4) = 3.864, P < .05; t(5) = 1.405, P > .05; pERK2: t(5) = 1.348, P > .05], 7-Ni , or c-PTIO . In the MGm/PIN, we observed a significant increase in phospho-ERK1/2 activation 30\u2009min after HFS in vehicle-infused controls [pERK1: Thus, blockade of NMDAR-driven synaptic plasticity and NO signaling at the level of the LA impairs HFS-induced ERK activation not only in the LA, but also in the MGm/PIN. Further, extracellular release of NO in the LA is required for HFS-induced ERK activation in the MGm/PIN, but not in the LA. In this series of experiments, we examined whether blockade of NMDAR-driven synaptic plasticity and NO signaling in the LA impairs HFS-induced expression of the IEGs Arc/Arg3.1, c-Fos, and EGR-1 in both the LA and the MGm/PIN. As in the previous experiment, anesthetized rats were given intra-LA infusion of ifenprodil, 7-Ni, or c-PTIO prior to LTP-inducing stimulation of the thalamo-LA pathway . In addit(7) = 3.440. P < .05; c-Fos: t(7) = 2.405, P < .05; EGR-1: t(7) = 5.009, P < .05; t(7) = 0.377. P > .05; c-Fos: t(7) = 0.708, P > .05; EGR-1: t(7) = 0.306, P > .05; t(7) = 2.629. P < .05; c-Fos: t(7) = 3.783, P < .05; EGR-1: t(7) = 3.440, P < .05; t(7) = 0.211. P > .05; c-Fos: t(7) = 0.592, P > .05; EGR-1: t(7) = 0.139, P > .05; The findings for rats infused with ifenprodil are depicted in Figures t(7) = 2.374. P < .05; c-Fos: t(7) = 2.462, P < .05; EGR-1: t(7) = 2.402, P < .05; t(7) = 0.672. P > .05; c-Fos: t(7) = 1.101, P > .05; EGR-1: t(7) = 1.499, P > .05; t(7) = 3.066. P < .05; c-Fos: t(7) = 2.383, P < .05; EGR-1: t(7) = 2.687, P < .05; t(7) = 0.065. P > .05; c-Fos: t(7) = 0.025, P > .05; EGR-1: t(7) = 0.460, P > .05; The findings for rats infused with 7-Ni are depicted in Figures t(7) = 2.374. P < .05; c-Fos: t(7) = 2.462, P < .05; EGR-1: t(7) = 2.402, P < .05; t(7) = 2.545. P < .05; c-Fos: t(7) = 2.406, P < .05; EGR-1: t(7) = 2.509, P < .05; t(7) = 3.066. P < .05; c-Fos: t(7) = 2.383, P < .05; EGR-1: t(7) = 2.687, P < .05; t(7) = 1.241. P > .05; c-Fos: t(7) = 0.696, P > .05; EGR-1: t(7) = 1.600, P > .05; The findings for rats infused with c-PTIO are depicted in Figures t(7) = 7.972. P < .05; c-Fos: t(7) = 3.686, P < .05; EGR-1: t(7) = 4.599, P < .05; t(6) = 1.688. P > .05; c-Fos: t(7) = 0.631, P > .05; EGR-1: t(7) = 1.287, P > .05; t(7) = 7.972. P < .05; c-Fos: t(7) = 4.064, P < .05; EGR-1: t(7) = 4.901, P < .05; t(6) = 1.688. P > .05; c-Fos: t(7) = 1.101, P > .05; EGR-1: t(7) = 0.401, P > .05; The findings for rats infused with PKG inhibitor Rp-8-Br-PET-cGMPS are depicted in Thus, similar to the findings of our ERK experiments, blockade of NMDAR-driven synaptic plasticity and NO signaling at the level of the LA impairs HFS-induced IEG expression not only in the LA but also in the MGm/PIN. Further, extracellular release of NO in the LA appears to be required for HFS-induced IEG expression in the MGm/PIN, but not in the LALong-term potentiation (LTP) at thalamo-LA synapses has been proposed as a candidate cellular mechanism of the formation of auditory fear memories, yet little is known about the molecular mechanisms underlying LTP at this synapse. In the present study, we have examined the regulation of ERK and that of three different ERK-driven IEGs at both sides of the thalamo-LA synapse after LTP-inducing stimulation. We found that LTP-inducing stimulation at thalamo-LA synapses is accompanied by ERK activation and ERK-driven gene expression not only in the LA, but also in regions of the MGm/PIN that are presynaptic to the LA. Further, pharmacological disruption of either NMDAR-driven synaptic plasticity or NO-cGMP-PKG signaling at the level of the LA impairs ERK activation and IEG expression in each region. Collectively, these findings suggest that NMDAR-driven synaptic plasticity and NO signaling within the LA coordinately regulate ERK activation and ERK-driven gene expression in both the LA and the MGm/PIN following LTP induction at thalamo-LA synapses.A recent study in our lab showed that LTP-inducing stimulation of thalamo-LA inputs induces ERK activation in the LA, and that intra-LA infusion of ERK/MAPK inhibitor impairs LTP at thalamo-LA synapses . HoweverOur findings also revealed that LTP-inducing stimulation of thalamo-LA synapses regulates the expression of the ERK-driven IEGs Arc/Arg3.1, c-Fos, and EGR-1 in both the LA and MGm/PIN. Previous studies have extensively documented the role of Arc/Arg3.1 \u201332 and EIn contrast to Arc/Arg3.1, both EGR-1 and c-Fos are thought to behave as transcription factors, regulating the expression of late-response genes that are critical for long-term synaptic plasticity. Importantly, several studies have observed associative increases in the expression of c-Fos and EGR-1 in the LA after cued fear conditioning \u201340. FurtOur findings of enhanced activation of ERK-driven transcriptional regulation in both LA and MGm/PIN neurons is consistent with previous work that has shown that infusion of a MEK inhibitor into either the LA or the MGm/PIN impairs LTP in the LA , 23 and in vitro [While most widely studied in the hippocampus , 58\u201363 ain vitro , 18.\u223c2-3\u2009mm distance in such a rapid manner. However, previous reports have suggested that retrograde transport can occur very rapidly in neurons, between \u223c4\u20138\u2009mm/hr [In the present study, we used pharmacological methods to ask whether NMDAR-driven synaptic plasticity and NO-cGMP-PKG signaling may be regulating both ERK and ERK-driven transcription within the LA and the MGm/PIN. We showed that blockade of NR2B (via ifenprodil), NOS (via 7-Ni), or PKG (via Rp-8-Br-PET-cGMPS) significantly impaired HFS-induced activation of ERK and ERK-driven gene expression in both the LA and the MGm/PIN. Remarkably, however, blockade of extracellular NO signaling (via c-PTIO) significantly impaired HFS-induced activation of ERK and ERK-driven gene expression in the MGm/PIN, but not in the LA. These findings suggest that the ERK activation and downstream IEG expression in MGm/PIN following LTP is driven by NO \u201cretrograde signaling\u201d at the level of the LA. The identity of the signal that links NO release at the level of the LA with ERK activation and ERK-driven gene expression at the level of the MGm/PIN is currently unknown, as is how such a signal may propagate in a retrograde manner from synapse to nucleus across a \u20138\u2009mm/hr . Further\u20138\u2009mm/hr , or inhi\u20138\u2009mm/hr , which m\u20138\u2009mm/hr . The present findings are consistent with a revised model of the molecular events underlying synaptic plasticity at thalamo-LA synapses in which NMDAR-driven synaptic plasticity and NO signaling in LA neurons promotes pre- and postsynaptic alterations at thalamo-LA synapses via regulation of ERK-driven gene expression in MGm/PIN and LA neurons, respectively, . In thatIn support of this model, recent studies from our lab and others have shown that ERK-driven transcription in the MGm/PIN is required not only for fear memory consolidation , 67, 68 In summary, our findings suggest that NMDAR-driven synaptic plasticity and NO signaling within the LA coordinately regulate ERK activation and ERK-driven gene expression in both the LA and the MGm/PIN following LTP induction at thalamo-LA synapses, and further suggest that synaptic plasticity in the LA promotes ERK-driven transcription in MGm/PIN neurons via NO-driven \u201cretrograde signaling\u201d. These findings further extend what is known about the molecular basis of LTP within the LA, and provide additional evidence that studying LTP at thalamo-LA synapses may inform us about the molecular basis of fear memory formation in the amygdala."} +{"text": "These brain and renal injuries were associated with increased gene expression of NADPH oxidase components, NADPH oxidase activity and oxidative stress in brain and kidney tissues as well as systemic oxidative stress. Treatment with the ARB, olmesartan (10 mg/kg/day) reduced blood pressure in saline-drinking KK-Ay mice and attenuated cognitive decline, BBB disruption, glomerular injury and albuminuria, which were associated with a reduction of NADPH oxidase activity and oxidative stress in brain and kidney tissues as well as systemic oxidative stress. Furthermore, a suppressive dose of azelnidipine (3 mg/kg/day) exaggerated these beneficial effects of olmesartan. These data support the hypothesis that a CCB enhances ARB-associated cerebrovascular-renal protective effects through suppression of NADPH oxidase-dependent oxidative stress in type 2 diabetes.Recent clinical trials have demonstrated that combination therapy with renin-angiotensin system inhibitors plus calcium channel blockers (CCBs) elicits beneficial effects on cardiovascular and renal events in hypertensive patients with high cardiovascular risks. In the present study, we hypothesized that CCB enhances the protective effects of an angiotensin II type 1 receptor blocker (ARB) against diabetic cerebrovascular-renal injury. Saline-drinking type 2 diabetic KK-A The beneficial effects of renin-angiotensin system (RAS) inhibition with angiotensin converting enzyme inhibitors (ACEIs) and angiotensin II type 1 receptor blockers (ARBs) have been demonstrated in hypertensive patients with high cardiovascular-renal risks including heart failure , diabetePrevious large-scale epidemiological studies have indicated that CKD is not related to the incidence of stroke . Howevery mice treated with the ARB, olmesartan [It has been highlighted that type 2 diabetes and hypertension are risk factors for cerebrorenal injury including cognitive decline ,22, BBB mesartan .y mice [Experimental protocols and animal care were performed according to the guidelines for the care and use of animals established by Kagawa University, Japan. The experiments were approved by the Animal Experimentation Ethics Committee at Kagawa University (No. 112). At the end of the experiment, organs were dissected under sodium pentobarbital anesthesia . Six-week-old male type 2 diabetic KK-Ay mice and contn = 11) and saline-drinking C57BL6 mice . Type 2 diabetic KK-Ay mice were divided into four groups: tap water drinking KK-Ay mice ; saline-drinking KK-Ay mice ; saline-drinking KK-Ay mice treated with olmesartan ; saline-drinking KK-Ay mice treated with olmesartan plus azelnidipine . It has previously been reported that azelnidipine at 3 mg/kg body weight/day did not change blood pressure in KK-Ay mice [y mice .After a two week period of acclimatization and measuring basal parameters, 8-week-old mice were underwent combination treatments for 16 weeks. Control C57BL6 mice were divided into two groups: tap water drinking C57BL6 mice was monitored in conscious mice by tail-cuff plethysmography . Urinary albumin and creatinine concentrations were measured by using commercially available assay kits . PostpraAt the end of the experiment blood, brain and kidney samples were harvested under anesthesia with sodium pentobarbital . The brain and kidney tissues were harvested and fixed in 10% buffered paraformaldehyde or embedded in Tissue-Tek OCT compound , and remaining tissues were snap-frozen in liquid nitrogen. Small amounts of brain and renal cortical tissues were collected in RNAlater and stored overnight at 4\u00b0C RNAlater-treated samples were subsequently snap-frozen in liquid nitrogen and stored at -80\u00b0C until processing for RNA extraction and reverse transcription-polymerase chain reaction (RT-PCR) analysis.A passive avoidance test was performed to evaluate cognitive function as described previously . Detailsn = 6 per group) as previously described [BBB permeability was determined using the EB extravasation technique and Mallory-Azan reagents to evaluate glomerular sclerosis and tubulointerstitial fibrosis, respectively ,32. The Glomerular podocyte injury was evaluated by immunohistochemical analysis of desmin and was performed as previously described ,31. To investigate oxidative stress in the brain and kidney tissues, DHE immunofluorescence staining was performed as previously described . DetailsNADPH oxidase-derived superoxide anion generation was measured using lucigenin-enhanced chemiluminescence, as described previously . Details The mRNA expression in brain and renal cortical tissues were analyzed by RT-PCR using a LightCycler FastStart DNA Master SYBR Green I kit and an ABI Prism 7000 Sequence Detection System as previously described ,31. The Plasma and urine 8-hydroxy-2\u2019-deoxyguanosine (8-OHdG) , plasma level of non-esterified fatty acid (NEFA), triglyceride (TG), total cholesterol (TCho) , and insulin were measured using commercially available kits.post hoc test. Values of P < 0.05 were considered statistically significant. All values are presented as means \u00b1 S.E.M.. Statistical comparisons of differences among groups were performed using one-way repeated-measures analysis of variance (ANOVA), followed by the Newman-Keuls y mice showed elevated SBP compared with that in age-matched C57BL6 or C57BL6 + 0.9% NaCl mice . In addi tissues . These dy mice, DHE staining was significantly increased in kidney tissues compared with that in C57BL6 mice Click here for additional data file.Table S1(DOCX)Click here for additional data file.Figure S1Body weight changes during the experimental period. KK-Ay mice showed higher body weight compared to C57BL mice. However, none of the treatments affected body weight gains in KK-Ay + 0.9% NaCl mice (n=11). aP < 0.05 vs. C57BL/6, bP < 0.05 vs. C57BL/6 + 0.9% NaCl.(TIF)Click here for additional data file.Figure S2NADPH oxidase subunits gene expression in brain tissues analyzed by RT-PCR. NADPH oxidase subunits gp91phox (A) and p47phox (B) mRNA levels in whole brain tissues. Saline-dinking KK-Ay mice showed upregulation of NADPH oxidase subunit mRNA levels in brain tissues, which were attenuated by treatment with olmesartan. Furthermore, the combination of olmesartan plus azelnidipine completely prevented these changes resulting in levels similar to that in C57BL6 mice (n=8). aP < 0.05 vs. C57BL/6, bP < 0.05 vs. C57BL/6 + 0.9% NaCl, cP < 0.05 vs. KK-Ay, dP < 0.05 vs. KK-Ay + 0.9% NaCl, eP < 0.05 vs. KK-Ay + 0.9% NaCl + olmesartan.(TIF)Click here for additional data file.Figure S3NADPH oxidase subunits gene expression in kidney tissues analyzed by RT-PCR. NADPH oxidase subunits gp91phox (A) and p22phox (B) mRNA levels in renal cortical tissues. In saline-dinking KK-Ay mice, superoxide production in renal tissues was associated with upregulation of NADPH oxidsase subunit genes expression. Treatment with olmesartan markedly attenuated these changes. Furthermore, the combination of olmesartan plus azelnidipine completely prevented these changes resulting in levels similar to that in C57BL6 mice (n=8). aP<0.05 vs. C57BL/6, bP<0.05 vs. C57BL/6 + 0.9% NaCl, cP<0.05 vs. KK-Ay, dP<0.05 vs. KK-Ay + 0.9% NaCl, eP<0.05 vs. KK-Ay + 0.9% NaCl + olmesartan.(TIF)Click here for additional data file."} +{"text": "Salmonella enterica strains that are representatives of the S. enterica serovar Typhimurium complex in reference collection A (SARA) are closely related but exhibit differences in antibiotic resistance, which could have public health consequences. To better understand the mechanisms behind these resistances, we sequenced the genomes of two multidrug-resistant strains: SARA64 (Muenchen) and SARA33 (Heidelberg).The Salmonella enterica is one of the most important bacterial enteric pathogens and has been implicated in food-borne illnesses worldwide .orldwide . Emergenorldwide , 3. Explorldwide , 5, consintI1) . Two of these strains, SARA64 and SARA33, exhibited resistance to ampicillin, chloramphenicol, tetracycline, streptomycin, sulfisoxazole, and kanamycin. SARA33 also showed resistance to gentamicin. Both strains were positive for the integrase found in integrons class I (intI1) ; howeverintI1) . In ordede novo assembled using CLC Genomics Workbench version 5.5.1 . The G+C mol% values of SARA64 and SARA33 were 52.0 and 52.1%, respectively, which are similar to the reported GC content for other Salmonella strains . The genomes were sequenced using an Ion Torrent (PGM) sequencing system with the 200-bp reads chemistry at 30 to 40\u00d7 coverage, using an Ion PGM 200 sequencing kit, according to the manufacturer\u2019s instructions. Genomic sequence contigs for each strain were strains . Strain http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html) (in silico multilocus sequence typing (MLST) (http://cge.cbs.dtu.dk/services/) -laa, aph(3\u2032)-la, strA, strB, and aadA1], sulfonamides (sul1 and sul2), beta-lactams (blaOXA), tetracycline (tetB), and phenicol (catA1), which explain its MDR phenotype. Some of these resistance genes were on a genomic island similar to GI-DT12 in Salmonella enterica serovar Typhimurium T000240 (intI1-blaOXA-aadA1-qacE\u03941-sul1). The genes strA, strB, and sul2 were located on a plasmid.These draft genome sequences were annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (ne.html) . Identitrvices/) using thdatabase ; strain database . Antibiocreening . SARA64 T000240 , which caac(6\u2032)-ly, aadA5, aadB, aa(6\u2032)-33, and aadA1], sulfonamides (sul1 and sul2), beta-lactams (blaOXA-2 and blaTEM), and tetracycline (tetD). A novel integron cassette was identified that contained one hypothetical protein (hp) with unknown function, followed by aadA1 and aa(6\u2032)-33 genes [intI1-hp-aac(6\u2032)-33-aadA1].In contrast, SARA33 carried resistance genes for aminoglycosides [Salmonella enterica strains are now available in GenBank under accession numbers AUQD00000000 for strain SARA33 (2213-Heidelberg) and AUQE00000000 for strain SARA64 (2244-Muenchen).The draft genome sequences of these two"} +{"text": "Immunohistochemical studies suggest that the rheumatoid nodule (RN) is a Th1 granuloma , yet theWe measured circulating cytokines of DMARD-na\u00efve early RA patients, and compared profiles of patients with RN to those without RN.A cross-sectional cohort of 149 DMARD-na\u00efve adults with early RA (symptom duration \u2264 2 years). Assessments included a smoking history, the presence of subcutaneous RN, the Simplified Disease Activity Index (SDAI), and X-rays scored using the modified Larsen method, Rheumatoid Factor (RF) and anti cyclic citrullinated peptides (aCCP) tests. Serum cytokines were measured using the Bio-Plex\u00ae suspension array system. Differences between patients with RN and those without RN were explored using univariate and multivariate techniques, correcting for SDAI by regression analysis.Of 149 patients , the majority were Black Africans (93%) and 34 (22.8%) had RN. Patients with RN were more likely to be males, but neither smoking history nor symptom duration was significantly different between the two groups. RN patients had severe RA with higher SDAI (p=0.04) and X-ray scores (p=0.004), and higher RF (p=0.005) and aCCP (p=0.04) titers. Cytokine profiles in the RN patients showed significant elevation of predominantly Th1 cytokines, with higher interferon-gamma (IFN-G) (p=0.05), interleukin (IL)-12 (p=0.02), and IL-2 (p=0.05). In addition, cytokines of macrophage and fibroblast origin were significantly higher in these patients. Multivariate analysis showed IL-7 (p<0.001) and IFN-G (p=0.001) to be independently significant.DMARD-na\u00efve early RA patients with RN have a unique serum cytokine profile, with significant elevation of predominantly Th1 and fibroblast cytokines."} +{"text": "Diastolic dysfunction (DD) is common in patients with cardiovascular disease. Current cardiac magnetic resonance techniques for assessment of DD require the acquisition of tagged imaging sequences, and complex post-processing. A new post-processing software allows for rapid strain assessment using feature tracking analysis (FT) based on conventional steady-state free precession (SSFP)-Cine sequences. The aim of this study was to compare tagging (TAG) with FT for assessment of diastolic function in patients with DD and healthy controls.20 healthy volunteers and 10 patients with echocardiographic diagnosed DD Grade II-III were investigated by the 2 techniques. Cardiovascular magnetic resonance imaging (Philips Intera 1.5T) using CSPAMM and SSFP-Cine sequences was performed for matched mid-ventricular short-axis slices. Each modality was analyzed offline using dedicated post-processing software and early-diastolic strain rate (EDSr) was calculated from both datasets. EDSr derived from CSPAMM and SSFP-Cine data were compared and inter-observer and intra-observer variability assessed using Bland-Altman analysis and Pearson correlation coefficient.-1) was highly correlated with TAG EDSr (76.71+/- 17.45s-1), Bland-Altman analyses for method comparison yielded a mean difference of 1.4 (95% CI: 0.0 to 2.9). Limits of agreement (+/- 1.96 SD) were -14.9 and 12.0. In patients with DD FT EDSr (61.40+/- 15.60s-1) was not significantly different to TAG EDSr (57.60+/- 12.30s-1) (p=ns). The same was found in the control group FT EDSr (86.52+/- 10.55s-1) and TAG (86.27+/- 10.31s-1) (p=ns). Intra-observer variability yielded a mean difference of 1.2+/- 4.9 (FT) and 0.9+/- 3.5 (TAG). Inter-observer variability displayed a mean difference of 2.8+/- 5.84 (FT) and 0.3+/- 3.7 (TAG). Pearson correlation coefficient was (0.96 (FT); 0.97 (TAG)) for intra-observer variability and (0.94 (FT); 0.97 (TAG)) for inter-observer variability.For all measurements FT EDSr (78.15+/- 17.17 sAssessment of EDSr using a novel feature tracking technique shows good agreement with tagging derived data and may thus be used for rapid clinical determination of diastolic dysfunction. However, compared to feature tracking, tagging revealed lower intra - and inter-observer variability and may therefore remain the preferred technique for research applications.None."} +{"text": "AbstractCerapachys Smith are keyed. Twelve species are recognized of which 6 are described as new. The species are: Cerapachys aitkenii Forel, Cerapachys aliisp. n., Cerapachys anokhasp. n., Cerapachys besucheti Brown, Cerapachys biroi Forel, Cerapachys indicus Brown, Cerapachys longitarsus (Mayr), Cerapachys nayanasp. n., Cerapachys schoedlisp. n., Cerapachys seemasp. n., Cerapachys sulcinodis Emery and Cerapachys wightisp. n. Geographic distribution and group affinities of the new species are discussed. A revised key to the Indian species is provided. The rare ergatoid queens of Cerapachys nayana, Cerapachys schoedli and Cerapachys seema are reported. Formed in response to selective pressures these ergatoid queens have a significant role in dispersal strategies and contribute much to our understanding of the biology of these ants.The Indianspeciesof the ant genus Cerapachys includesmainly myrmecophagous ants which raid the nests of other ants for prey .The ant genus for prey . The genfor prey . Cerapacglobally . The triCerapachys in India is currently represented by 6 species flank to the midpoint of the frontovertextal margin to the posterior extension of the propodeal lobes = Weber\u2019s length measured from WL to the dorsal edge of the mesosomaMH IIIAL software. Later, images were cleaned as per requirement with Adobe Photoshop CS6. Description style and morphological terminology for measurements and indices follow l margin ; HW = Hesal view ; EL = Eye of eye ; SL = Sc condyle ; WL = Weal lobes ; MH = Memesosoma ; PrW = Psal view ; PL1 = Psal view ; PW1 = Psal view ; IIIAL =helcium) ; IIIAW =sal view ; IVAW = sal view ; IVAL = etergite ; CI = Ce Natural History Museum, London, U.K.BMNH Punjabi University Patiala, Ant Collection at Department of Zoology and Environmental Sciences, Punjabi University, Patiala, Punjab, India.PUACPageBreakhttp://zoobank.org/52540038-860B-4EA4-BA1E-40217FF6D555http://species-id.net/wiki/Cerapachys_alii10\u00b045'N, 76\u00b044'E, 118m a.s.l., 10.x.2011, Winkler method (coll. Shahid A. Akbar); Holotype in PUAC and paratype in BMNH.Holotype and 6 paratypes (worker): India, Kerala, Salim Ali Bird Sanctuary, Measurements (holotype in brackets): HL 0.46-0.51 (0.48); HW 0.37-0.39 (0.38); WL 0.47-0.49 (0.49); MH 0.28-0.31 (0.31); PrW 0.25-0.29 (0.25); PL1 0.16-0.20 (0.17); PW1 0.16-0.19 (0.18); IIIAL 0.20-0.22 (0.22); IIIAW 0.22-0.27 (0.23); SL 0.21-0.22 (0.22); IVAL 0.43-0.49 (0.49); IVAW 0.39-0.41 (0.41). Indices: CI 76-80 (79); SI 56-57 (57); PI 95-105 (105) (n=5).rd of its length.Head. Rectangular, longer than broad, sides converge anteriorly; vertexal margin concave, posterior lateral corners rounded. Parafrontal ridges prominent, raised. Eyes absent. Mandibles dentate; narrow, with strongly incurved apical tooth; anterior clypeal margin entire and projects forward as a low rounded transparent lobe or apron. Lateroclypeal teeth reduced. Antennae 9 segmented; scapes short, clavate, each falling short of posterior margin of head by 1/3Mesosoma. Stout, wider anteriorly; dorsal surface slightly convex, almost flat, the dorsal surface gently rounded along sides without any distinct margin. Declivous face of propodeum with cariniform margins across the top and along lateral margins.Metasoma. Petiole as long as broad, without overhanging dorsolateral margins. Anterior face transverse and posterior face shallowly convex. Subpetiolar process prominent, acute, posteriorly directed; no fenestra present. Postpetiole slightly longer than broad, lateral angles uniformly rounded. Gaster elongate; base of cinctus of first gastral tergite with cross ribs; sting exerted.Sculpture. Mandibles punctured. Head strongly foveate. Mesosoma, petiole and postpetiole with similar prominent foveate sculpture.Vestiture. Body with reduced white pilosity; moderate, decumbent or subdecumbent hairs distributed evenly throughout. Apical funicular segments and legs with small standing hairs.Colour. Dark red with mandibles, antennae and legs castaneous.PageBreakThe species is named in honor of Dr. Salim Ali, renowned Indian Ornithologist.Cerapachys alii can be easily separated from other species known from India. Only eight other known species of Cerapachys are reported to have 9 segmented antennae. These eight species are placed in the typhlus group and include; Cerapachys biroi Forel, 1907; Cerapachys cryptus Mann, 1921; Cerapachys edentatus Forel, 1900; Cerapachys fuscior Mann, 1921; Cerapachys papuanus Emery, 1897; Cerapachys pawa Mann, 1919; Cerapachys pusillus Emery, 1897 and Cerapachys typhlus Roger, 1861. The new species can be easily separated from all of them. Cerapachys cryptus and Cerapachys fuscior are larger species (HW > 0.70 mm) while Cerapachys alii is a smaller species (HW< 0.40 mm). Cerapachys typhlus has the postpetiole more than half as long as the succeeding gastric segment while in Cerapachys alii it is less than half as long as the succeeding gastric segment. Cerapachys papuanus, Cerapachys pawa and Cerapachys pusillus have the anterolateral shoulders of the first gastric segment abruptly rounded, accentuating the medium concavity that receives the postpetiole while in Cerapachys alii theanterolateral shoulders of the first gastric segments as seen from above broadly rounded and gradually widening caudad. Cerapachys biroi and Cerapachys edentatus predominantly have punctuate body sculpture while Cerapachys alii has predominantly foveate body sculpture. Cerapachys alii can also be confused with Cerapachys fragosus Roger, 1862 and Cerapachys coecus Mayr, 1897 which has similar prominent foveate body sculpture, however these two species are characterized by 11 segmented antennae while as Cerapachys alii has 9 segmented antennae.With its 9 segmented antennae Ecology. This subterranean species seems to be of rare occurrence as it was encountered only once during the extensive surveys in the region. The specimens were collected from a leaf litter sample taken from Salim Ali bird Sanctuary. A low-land evergreen forest area, located between the branches of Periyar river. The region is considered as the richest bird habitat on peninsular India.http://zoobank.org/2A8BE8D2-BED1-4DAC-A73F-E9AC2189FE23http://species-id.net/wiki/Cerapachys_anokha9\u00b0.30'N, 77\u00b0.16'E, 1003m a.s.l., 15.x.2011, hand picking method (coll. Shahid A. Akbar). Holotype in PUAC and paratype in BMNH.Holotype and 3 paratypes (worker): India: Kerala, Periyar tiger reserve, Thanikkudy, Measurements (holotype in brackets): HL 0.69-0.73 (0.72); HW 0.60-0.63 (0.63); EL 0.20-0.22 (0.22); WL 0.72-0.80 (0.80); MH 0.33-0.38 (0.38); PrW 0.42-0.47 (0.47); PL1 0.29-0.33 (0.33); PW1 0.38-0.41 (0.41); IIIAL 0.38-0.45 (0.41); IIIAW 0.44-0.55 (0.52); SL 0.29-0.32 (0.32); IVAL 0.85-0.92 (0.92); IVAW 0.57-0.64 (0.64). Indices: CI 86-87 (87); SI 48-51 (51); PI 124-131 (124) (n=4).PageBreakParafrontal ridges present. Eyes prominent, placed below midline of head. Mandible triangular with acute apices and sharp concave, edentate, masticatory margins; anterior clypeal margin with small apron shaped transparent structure. Lateroclypeal teeth small, blunt and projecting slightly inwards. Antennae 12 segmented; scape short and clavate, reaching up to 1/3rd of posterior margin of head.Head. Rectangular, longer than broad, widest at about mid-length; sides parallel; vertexal margin slightly concave, posterior lateral corners are weakly acute to rounded. Mesosoma. Stout, rectangular in dorsal view; dorsal surface convex, the dorsal surface gently rounded along sides without any distinct margin. Declivous face of propodeum lacking cariniform margins across the top and along sides.Metasoma. Petiole highly convex, broader than long, with traces of reduced dorsolateral margins, anterior and posterior faces continuous with dorsum. Subpetiolar process prominent, wedge like, with apex directed backward; no fenestra present. Postpetiole wider than long, uniformly rounded. Gaster elongate; base of cinctus of first gastral tergite with cross ribs; sting exerted.st gastral, with few cross ribs.Sculpture. Mandibles smooth and shining. Head with few small punctures. Sculpture on dorsal surface of mesosoma, petiole and postpetiole consist of very small, uniform punctures, distributed throughout the surface. Gaster mostly smooth, with few scattered punctures. Cinctus of 1Vestiture. Body covered with decumbent or subdecumbent hairs. Longer hairs are also present on postpetiole and gaster. Head also consists of few long hairs; apical funicular segments and legs with standing hairs.Colour. Black with mandibles, antennae and legs castaneous.The species epithet is Hindi for \u201cunique\u201d, in reference to its unique nature of propodeal declivity.PageBreakCerapachyinae. The new species show interesting variation in the form of the petiole. The petiolar node has the inferior as well as the superior posterolateral angles produced, but not sharply angular. The sides of the petiole could not be considered either immarginate (Cerapachys lineage) or marginate (Phyracaces lineage). This makes the placement of this species somewhat transitional between the two lineages and easily distinguishes it from other reported species of the genus. When using Cerapachys anokha comes close to singaporensis Viehmeyer, 1916. The two species however can be easily separated. Cerapachys singaporensis has the body arrayed with long pale hairs; and copiously pubescent, and the dorsal sides of the petiole strongly marginate, while Cerapachys anokha has only decumbent or subdecumbent body hairs, little pubescence and the dorsolateral sides of petiole are not marginate. Cerapachys anokha could also be confused with Cerapachys nayana which has similar habitat preferences and body colouration; however the two species can be easily separated: Cerapachys nayana has larger eyes (EL 0.24\u20130.27 mm), the declivous face of the propodeum has cariniform margins across the top, and the petiole has marginate dorsolateral sides; while Cerapachys anokha has smaller eyes (EL 0.20\u20130.22 mm), the declivous face of its propodeum lacks cariniform margins across the top, and the petiole is without marginate dorsolateral sides.This species is unique in having the declivous face of the propodeum lacking cariniform margins across the top and along the sides, features unique in described workers of the This species seems to be infrequent. It is from the Western Ghats. Four specimens were collected by handpicking from the Thanikkudy region of the Periyar tiger reserve. Which is a primary, undisturbed tropical moist evergreen forest. The area is situated at 1003 meters elevation. It is a shady place with little sunlight penetration.http://zoobank.org/46F8FF78-D753-4BEF-8FCB-7A83D4149E8Dhttp://species-id.net/wiki/Cerapachys_nayana11\u00b05'N, 76\u00b026'E, 897m a.s.l., 25.ix.2011, hand picking. Paratypes: 2 workers and 1 ergatoid queen with same data as holotype; 6 workers and 2 ergatoid queens, India, Karnataka, Gundlupet 11\u00b08'N, 76\u00b068'E, 800m a.s.l., 27.ix.2010, hand picking; 2 workers and 1 ergatoid queen, India, Kerala, Periyar tiger reserve, 9\u00b046'N, 77\u00b014'E, 1005m a.s.l., 10.x.2011, hand picking (coll. Shahid A. Akbar). Holotype in PUAC and paratype in BMNH.Holotype worker: India: Kerala, Silent valley national park, Measurements (holotype in brackets): HL 0.55-0.66 (0.66); HW 0.48-0.51 (0.51); EL 0.24-0.27 (0.25); WL 0.60-0.66 (0.66); MH 0.34-0.37 (0.34); PrW 0.33-0.38 (0.34); PL1 0.20-0.23 (0.23); PW1 0.25-0.29 (0.29); IIIAL 0.30-0.44 (0.44); IIIAW 0.37-0.47 (0.37); SL 0.21-0.27 (0.27); IVAL 0.58-0.61 (0.61); IVAW 0.47-0.52 (0.52). Indices: CI 77-87 (77); SI 44-53 (53); PI 125-126 (126) (n=10).PageBreakth of posterior margin of head.Head. Rectangular, longer than broad, widest at about its midlength; sides parallel, vertexal margin transverse to shallowly concave, posterior lateral corners weakly acute. Parafrontal ridges present but not raised, very low. Eyes large prominent. Mandibles subtriangular; masticatory margin without a row of small denticles. Lateroclypeal teeth small and reduced. Antennae 12 segmented; scapes short, reaching up to 4/5Mesosoma. Moderately stout, rectangular in dorsal view; dorsal surface flattened, bordered laterally by a distinct angle, but no margin. Declivous face of propodeum with cariniform margins across the top and along the lateral margins.Metasoma. Petiole broader than long, with strong overhanging dorsolateral margins. Anterior face concave while posterior face is transverse. Subpetiolar process small with stout acute apex, directed forward, located beneath anterior 1/3rd of the petiole; no fenestra present. Postpetiole sub trapezoidal, wider behind with the posterolateral angles uniformly rounded. Gaster elongate; base of cinctus of first gastral tergite with cross ribs; sting exerted.st gastral segment smooth and shining.Sculpture. Mandibles smooth and shining. Head with small punctures, spaced wider than their diameter, dorsum of head also with faint rugae in between the punctures. Similar sculpture on dorsal surface of mesosoma and petiole. Small continuous punctures produce a matt like appearance on the dorsum of the postpetiole. Gaster with similar matt-like appearance but less prominent. Cinctus of 1Vestiture. Body covered with moderate decumbent or subdecumbent hairs most prominent on postpetiole and gaster, head devoid of such hairs, only a few along sides; apical funicular segments with standing hairs.PageBreakColour. Black with mandibles, antennae and legs castaneous.HL 0.66-0.77; HW 0.55-0.60; EL 0.22-0.24; WL 0.79-0.82; MH 0.36-0.41; PrW 0.44-0.47; PL1 0.24-0.27; PW1 0.44-0.47; IIIAL 0.44-0.47; IIIAW 0.51-0.55; SL 0.18-0.22; IVAL 0.58-0.63; IVAW; 0.60-0.66. Indices: CI 77-83; SI 33-37; PI 174-183 (n=3).Like the workers of the same colony, but larger, with thicker body, especially mesosoma and gaster. Ocelli present on vertex, prominent. The pilosity is much more prominent compared to workers. Distinction between ergatoid queens and worker is vague, with size variation of workers very high.There is a considerable amount of size variation between individual specimens, the smaller workers are lighter in body colouration compared with larger specimens; the body sculpture and pilosity also differs between individuals.The species epithet is Sanskrit for \u201ceyes\u201d, in reference to the large eye size of the species.PageBreakCerapachys anokha from which it is separated by the combination of characters given in the diagnosis of the latter species. Cerapachys nayana is compared with Cerapachys longitarsus which also has marginate dorsolateral sides to the petiole; however, the two species can be easily separated. Cerapachys longitarsus has characteristic bicolouration, with the head brown, trunk red or brown, petiole and postpetiole light to dark reddish and the gaster brown or black, while Cerapachys nayana is uniformly black coloured with mandibles, antennae and legs castaneous. The new species also resembles the Philippines, Cerapachys luzuriagae but can be easily separated from it. Cerapachys nayana is coloured black with the petiole broader than long, and with concave anterior and transverse posterior faces, the postpetiole with dense punctures and without dentition; while Cerapachys luzuriagae is reddish brown with the petiole as long as broad, with convex anterior and truncate posterior faces; postpetiole without dense punctures, and mandibles with prominent dentition.With themarginate dorsolateral sides of its petiole, this species is easily distinguished from other Indian species of its genus. The new species sharesmost characters with This species is widely distributed in the Western Ghats. It was collected from non-forested and forest habitats from small bushes, and foraging over dry soil surfaces.http://zoobank.org/38E7EC5E-E9F2-4FCC-B467-10E9208AA155http://species-id.net/wiki/Cerapachys_schoedli11\u00b05'N, 76\u00b026'E, 897m a.s.l., 25.ix.2011, Winkler. Paratypes: 13 workers and 3 ergatoid queens, same data as holotype; 2 workers, India, Kerala, Salim Ali Bird Sanctuary, 10\u00b045'N, 76\u00b044'E, 118m a.s.l., 6.xi.2011, Winkler; 10 workers, India, Kerala, Periyar tiger reserve, Manalar, 9\u00b035'N, 77\u00b018'E, 1630m a.s.l., 27.x.2011, hand picking (coll. Shahid A. Akbar). Holotype in PUAC and paratype in BMNH.Holotype worker: India. Kerala, Silent valley national park, Measurements (holotype in brackets): HL 0.64-0.68 (0.68); HW 0.44-0.46 (0.46); EL 0.07-0.11 (0.11); WL 0.62-0.69 (0.69); MH 0.41-0.48 (0.48); PrW 0.31-0.35 (0.35); PL1 0.24-0.27 (0.27); PW1 0.28-0.31 (0.31); IIIAL 0.28-0.32 (0.32); IIIAW 0.39-0.41 (0.41); SL 0.31-0.33 (0.33); IVAL 0.70-0.74 (0.74); IVAW 0.58-0.60 (0.60). Indices: CI 67-69 (67); SI 70-72 (72); PI 114-116 (114) (n=11).rd of its length.Head, rectangular, longer than broad; sides parallel; vertexal border transverse. Posterior lateral corners acute. Parafrontal ridges present, raised. Eyes medium sized, almost circular. Mandibles subtriangular; masticatory margins without a row of small denticles. Lateroclypeal teeth small. Antennae 12 segmented; scapes short, each falling short of posterior margin of head by 1/3Mesosoma. stout, humped in profile view; dorsal surface convex, continuous with sides, no lateral margins. Declivous face of propodeum with cariniform margins across the top and along the lateral margins.Metasoma. Petiole broader than long, and gently rounded towards the sides. Anterior and posterior faces transverse. Subpetiolar process stout, fenestra present. Postpetiole almost rectangular, wider behind, with the posterolateral angles not tuberculate but uniformly rounded. Gaster elongate; base of cinctus of first gastral tergite with cross ribs; sting exerted.Sculpture. Mandibles with small punctures. Head smooth and shining with some punctures. Mesosoma mostly smooth and shining with some punctures along the sides. Petiole, postpetiole and gaster with continuous punctures.PageBreakVestiture. Body covered with moderate, decumbent or subdecumbent hairs, most prominent on gaster; apical funicular segments and legs also with standing hairs.Colour. Bright yellowish orange to dark red.PageBreakHL 0.80-0.84; HW 0.59-0.63; EL 0.14-0.16; WL 0.88-0.92; MH 0.51-0.55; PrW 0.49-0.53; SL 0.41-0.43; PL1 0.29-0.31; PW1 0.38-0.41; IIIAL 0.44-0.50; IIIAW 0.57-0.59; IVAL 0.88-0.90; IVAW 0.86-0.88. Indices: CI 73-75; SI 68-69; PI 131-132 (n=3).Like the workers of the same colony, but larger, with more stout body, especially the mesosoma and gaster. Ocelli absent on vertex. Distinction between ergatoid queens and worker is vague, with size variation of workers very high.The species is named in the honor of the late Dr. Stefan Sch\u00f6dl.Cerapachys schoedli sharesmost characters with Cerapachys seema, from which it can be easily distinguished by the combination of characters given in the diagnosis of the latter species. The new species can also be compared with Cerapachys luteoviger Brown, 1975 which also has small punctures on the cephalic dorsum, with diameter lesser than the average distance separating them. However, the peculiar petiolar node and rounded head shape of Cerapachys luteoviger easily separates it from Cerapachys schoedli, which has the petiolar node broader than long and the posterior lateral corners of the head acute.This species is aberrant in many characters, with the cephalic dorsum bearing small punctures with average diameter lesser than the average distance separating them, a highly shinning body and reduced body sculpture, which separates it from other reported Indian species. This species seems to be common in the Western Ghats; it was collected in non-forest as well as forest habitats in leaf litter and on dry soil surfaces.http://zoobank.org/AE131489-5514-422C-BE6E-5BDBCCA2F111http://species-id.net/wiki/Cerapachys_seema9\u00b035'N, 77\u00b018'E, 1630m a.s.l., 24.x.2011, hand picking. Paratypes: 4 workers, 3 ergatoid queens and 1 gyne, same data as holotype (coll. Shahid A. Akbar). Holotype in PUAC and paratype in BMNH.Holotype worker: India. Kerala, Periyar tiger reserve, Manalar, Measurements (holotype in brackets): HL 0.72-0.74 (0.74); HW 0.52-0.56 (0.56); EL 0.07-0.19 (0.19); WL 0.77-0.82 (0.77); MH 0.38-0.45 (0.45); PrW 0.37-0.40 (0.38); PL1 0.23-0.29 (0.26); PW1 0.36-0.41 (0.41); IIIAL 0.41-0.46 (0.41); IIIAW 0.51-0.54 (0.51); SL 0.33-0.41 (0.41); IVAL 0.70-0.74 (0.74); IVAW 0.62-0.69 (0.63). Indices: CI 72-75 (75); SI 63-73 (73); PI 141-157 (157) (n=9).rd the distance to the posterior margin of head.Head, longer than broad; sides converging posteriorly; vertexal margin transverse. Posterior lateral corners weakly acute. Parafrontal ridges prominent, raised. Eyes small. Mandibles subtriangular; masticatory margins deflexed and downcurved, with a row of small denticles. Lateroclypeal teeth prominent. Antennae 12 segmented; scapes clavate, reaching up to 2/3PageBreakMesosoma moderately stout, rectangular in dorsal view; dorsal surface flattened and gently rounded towards the sides. Declivous face of propodeum with cariniform margins across the top and along its lateral margins.PageBreakrd of the petiole; fenestra present. Postpetiole broader than long with posterolateral angles uniformly rounded. Gaster elongate; base of cinctus of first gastral tergite with cross ribs; sting exerted.Metasoma, Petiole broader than long, lacking dorsolateral margins. Anterior and posterior faces transverse. Subpetiolar process well developed, located below the anterior 1/3st gastral segment with prominent transverse ribs.Sculpture. Mandibles smooth with few punctures. Head with prominent punctures, spaced more widely than their diameter. Similar sculpture on dorsal surface of mesosoma. Petiole and postpetiole with larger punctures, forming a rugae-like surface on the dorsum. Gaster with similar sculpture to mesosoma. Cinctus of 1Vestiture. Whole body covered with dense decumbent or subdecumbent yellowish hairs, sides of head and mesosoma with fewer hairs; apical funicular segments and legs with standing hairs.Colour. Dark brownish black with mandibles, antennae and legs castaneous.HL 0.73-0.82; HW 0.55-0.60; EL 0.14-0.18; WL 0.81-0.86; PL1 0.27-0.29; MH 0.36-0.41; PrW 0.41-0.44; PW1 0.36-0.39; IIIAL 0.44-0.50; IIIAW 0.51-0.53; SL 0.39-0.42; IVAL 0.75-0.76; IVAW 0.72-0.77. Indices: CI 73-75; SI 70-71; PI 133-134 (n=3).Like the workers of the same colony, but larger, with a more stout body, especially the mesosoma and gaster. Ocelli present on vertex, prominent. The pilosity is much more prominent when compared with the workers. Distinction between ergatoid queens and workers is vague with size variation of workers very high.PageBreakHL 0.77; HW 0.55; EL 0.08; WL 0.93; MH 0.44; PrW 0.41; PL1 0.27; PW1 0.36; IIIAL 0.38; IIIAW 0.49; SL 0.38; IVAL 0.76; IVAW 0.73. Indices: CI 71; SI 69; PI 133 (n=1).Resembles the worker, with modifications expected for caste and the following differences; three prominent ocelli present on vertex, thicker body with heavy pilosity and prominent sculpture.The species epithet is Hindi for border, in reference to its type locality, Manalar, a place which marks border between Kerala and Tamil Nadu.Cerapachys schoedli. However the two species can be easily separated. Cerapachys seema has dull body colouration, sculpture much more prominent and course, pilosity denser, eyes not breaking the lateral margins of head and head almost oval, with anterior and posterior sections of the sides converging, while Cerapachys schoedli is brightly coloured, its sculpture and pilosity are reduced, its eyes break the lateral margins of the head and the head is rectangular with parallel sides.Thespecies is characterized by the punctures on the dorsum of the head being relatively small, separated, with their diameter smaller than the average distance separating them. The new species sharesmost characters with Manalar, part of Periyar tiger reserve, the type locality of this species is a fascinating green hill station (with plenty of leaf litter) surrounded on all sides by the tea gardens of Tamil Nadu. This species was found nesting beneath the marker stone on the border which separates Kerala and Tamil Nadu. It is presumed that the nest was in its initial stages of establishment as there were hardly any galleries and underground chambers. A single queen, 3 ergatoid queens and 7 workers were collected. This species seems uncommon in the Western Ghats range, since it was not encountered again from any other locality.http://zoobank.org/EB5CD657-F22C-4E1B-8352-995242B9531Dhttp://species-id.net/wiki/Cerapachys_wighti11\u00b05'N, 76\u00b026'E, 897m a.s.l., 25.ix.2011, Winkler (coll. Shahid A. Akbar). Holotype in PUAC and paratype in BMNH.Holotype and paratype worker: India. Kerala, Silent valley national park, Measurements (holotype in brackets): HL (0.69)-0.71; HW (0.58)-0.59; EL (0.05); SL (0.38)-0.40; WL (0.66)-0.70; MH (0.43)-0.47; PrW (0.33)-0.35; PL1 (0.28)-0.29; PW1 (0.32)-0.33; IIIAL (0.41)-0.44; IIIAW (0.47)-0.49; IVAL (0.71)-0.72; IVAW (0.66)-0.68 Indices: CI 83-(84); SI (65)-67; PI 113-(114).Head rectangular, longer than broad; sides rounding posteriorly, vertexal margin transverse, posterior lateral corners gently rounded, weakly acute. Parafrontal ridges raised, prominent. Eyes reduced. Mandibles subtriangular; masticatory margin without a row of small denticles. Lateroclypeal teeth reduced. Antennae 12 segmented; scapes short, clavate.PageBreakMesosoma stout, compact, rectangular in dorsal view; dorsal surface slightly convex, the sides gently rounded without any distinct margin. Declivous face of propodeum with the upper sides margined.Petiole broader than long, without strong overhanging dorsolateral margins. Anterior and posterior faces transverse. Subpetiolar process stout with hook like ventral margin; no fenestra present. Postpetiole sub trapezoidal, wider behind, posterolateral angles uniformly rounded. Gaster elongate; base of cinctus of first gastral tergite with cross ribs; sting exerted.st gastral with cross ribs.Sculpture. Mandibles punctured. Punctures on dorsum of head large, crowded, their diameter as large, or larger than, the average distance separating them. Mesosoma, petiole and postpetiole similarly sculptured. Gaster with smaller sized punctures compared with head, mesosoma and metasoma. Cinctus of 1Vestiture. Body with reduced pilosity; moderate decumbent or subdecumbent hairs. Mostly prominent on postpetiole and gaster. Apical funicular segments and legs with standing hairs.Colour. Dark reddish brown with mandibles, antennae and legs lighterThe species is named after botanist Robert Wight, who historically explored the area in 1847.Cerapachys wighti shares most characters with Cerapachys indicus, which also has large crowded punctures on cephalic dorsum. However the two species can be easily separated. Cerapachys wighti is smaller in size (HW 0.59 mm), has lighter body colouration and reduced eyes (EL 0.05 mm), while Cerapachys indicus is larger in size (HW 0.77 mm), with darker body colouration and large eyes (EL 0.24 mm).The new species can easily be separated from most of the Indian species on the basis of the large crowded punctureson its cephalic dorsum, with diameter as large, or larger than, the average distance separating them. PageBreakThe species seems to be of rare occurrence as it was encountered only once during the extensive surveys conducted in the area. It was collected from a litter sample taken near the Kuntipuzha river, which drains the entire length of the silent valley national park. With a pesticide free catchment area the region is rich in soil biota and ideal for cryptic ant species.Cerapachys from India. 12 species are recognized of which 6 are described as new. Partly for convenience the 12 Indian species are placed into arbitrary groups. Group I species with 12 segmented antennae viz., Cerapachys sulcinodis, Cerapachys anokha, Cerapachys schoedli, Cerapachys seema, Cerapachys indicus, Cerapachys aitkenii, Cerapachys wighti, Cerapachys longitarsus and Cerapachys nayana. Of the 9 species given above the first four i.e., Cerapachys sulcinodis, Cerapachys anokha, Cerapachys schoedli and Cerapachys seema, have the punctures on the dorsum of the head relatively small, separated, with their diameter smaller than the average distance separating them. Among these Cerapachys anokha, with the declivous face of the propodeum lacking cariniform margins, and Cerapachys sulcinodis, with the dorsal surface of the petiolar node with a smooth, median area are distinct species in the group. Cerapachys schoedli and Cerapachys seema are easily separated. Cerapachys seema has dull body colouration, sculpture much more prominent and coarse, pilosity denser and head almost oval, with the anterior and posterior sections of its sides converging, while Cerapachys schoedli is brightly coloured, with sculpture and pilosity reduced and the head rectangular with parallel sides. The next 3 species i.e., Cerapachys indicus, Cerapachys aitkenii and Cerapachys wighti, have the punctures on the dorsum of the head large, their diameter greater than the average distance separating them. Among these Cerapachys wighti has the smallest size (HW 0.59 mm) and relatively reduced eyes (EL 0.05 mm) wereas Cerapachys aitkenii and Cerapachys indicus are easily separated from each other on the basis of body sculpture and colouration. Cerapachys aitkenii has characteristic bicolouration and its body sculpture is foveate, wereas Cerapachys indicus is mostly piceous with bluish iridescent sheen and reduced sculpture. The remaining 2 species i.e., Cerapachys longitarsus and Cerapachys nayana are members of \u2018Phyracaces lineage\u2019 and easily recognized, with strong overhanging dorsolateral margins to the petiole. The two species are separated from each other on the basis of body colouration. Cerapachys longitarsus has characteristic bicolouration with head brown, trunk red or brown, petiole and postpetiole light to dark reddish and gaster brown or black, while Cerapachys nayana is uniformly black in colour, with mandibles, antennae and legs castaneous. Group II species have antennae with less than 12 segments viz., Cerapachys biroi, Cerapachys alii and Cerapachys besucheti. Among these Cerapachys besucheti has 11 segmented antennae while Cerapachys biroi and Cerapachys alii have 9 segmented antennae. Cerapachys biroi is characterized by its opaque body with closely spaced piligerous punctures, while Cerapachys alii has prominent foveate body sculpture.Herewe present a review of genus PageBreakCerapachys . Here we present ergatoid queens of three more species - Cerapachys nayana, Cerapachys schoedli and Cerapachys seema. In evaluating morphometric data of the three castes of Cerapachys seema i.e. worker, ergatoid queens and queen castes ) are excluded from this paper. The two species can be easily separates from other reported Indian species. Cerapachys browni shares mostaffinitieswith Cerapachys aitkenii but with black colour (unicolorous), rugo-reticulate sculpture and strongly constricted cintus of gaster. Cerapachys costatus with remarkable costate sculpture, which is not reported in any other Indian species.Two unpublished new species (PageBreak"} +{"text": "AbstractThrasorinae are revised and Mikeius is transferred to Mikeiinae Paretas-Mart\u00ednez & Pujade-Villar, subfam. n., and Mikeius clavatus Pujade-Villar & Restrepo-Ortiz, sp. n., is described. Two new genera of Thrasorinae are erected: Cicatrix Paretas-Mart\u00ednez, gen. n., including Cicatrix pilosiscutum(Girault), comb. n. from Amblynotus, Cicatrix schauffi (Buffington), comb. n. from Mikeius, and Cicatrix neumannoides Paretas-Mart\u00ednez & Restrepo-Ortiz, sp. n.; and Palmiriella Pujade-Villar & Paretas-Mart\u00ednez, gen. n., including Palmiriella neumanni (Buffington), comb. n. from Mikeius, Thrasorus rieki Paretas-Mart\u00ednez & Pujade-Villar, sp. n., is also described. A phylogenetic analysis of 176 morphological and biological characters, including all these new taxa and all genera previously included in Thrasorinae, was conducted. All subfamilies were recovered as monophyletic, with the following relationships: Parnipinae (Euceroptrinae (Mikeiinae (Plectocynipinae (Thrasorinae)))). A worldwide key to the subfamilies of Figitidae is provided that includes the new subfamily, as well as a key to genera Thrasorinae.The Australian Figitidae (Hymenoptera: Cynipoidea) are parasitoids of the larvae of other insects, principally cyclorraphous Diptera on various trees and bushes. They are parasitoids of the gall inducers or other hymenopteran inhabitants in the galls with which they are associated , Mikeius Buffington , Myrtopsen R\u00fcbsaamen (eleven species: two Holarctic and nine Nearctic), and Scutimica Ros-Farr\u00e9 . Thrasorinae are characterized by the circumtorular impression and the Queensland Museum (QM), as well as the type material of all species included in Mikeius Buffington, new questions arose regarding the taxonomy of Thrasorinae. First, an undescribed species of Mikeius was discovered (described herein); second, two species originally described in Mikeius were determined to render the genus polyphyletic, and new generic assignments are required; and third, phylogenetic analyses determined that the inclusion of Mikeius within Thrasorinae renders the subfamily paraphyletic with respect to Plectocynipinae. In response to these discoveries, Mikeiinae is described as a new subfamily to accommodate Mikeius, and species previously described in Mikeius are moved into other genera. In two cases, no current genus concept could accommodate these species, and the two new genera Cicatrix, gen. n., and Palmiriella, gen. n., are herein described. The goal of this study is to bring clarity to the taxonomic and phylogenetic relationships of these unusual groups of figitid wasps.Following the examination of many undetermined specimens of List of RepositoriesQueensland Museum, Brisbane, Australia (C. Burwell).QMAustralian National Insect Collection, CSIRO, Canberra, Australia .ANICPageBreakSpecimen illustration and observation. Environmental scanning electron micrographs (ESEM) were obtained at Barcelona University with the FEI Quanta 200 ESEM without any coating at 15 KV. Additional ESEM images were obtained either with a Hitachi TM3000 E-SEM, or an Amray 1810 SEM under a vacuum, using a lanthanum hexaboride electron source (LaB6) at 10 Kv, both housed at the National Museum of Natural History, Smithsonian Institution. Images were edited using Adobe CS4 Software . The terminology for morphological structures comes from Phylogenetic analysis. Twenty-two taxa were included in the phylogenetic analysis , so as to capture the morphological diversity of each genus. Parnips nigripes was chosen as an out-group based on Parnips nigripes as the reference taxon, followed by 1000 bootstrap replicates, each replicate employing 100 TBR swapping replications.analysis , represeParetas-Mart\u00ednez & Pujade-Villarsubfam. n.urn:lsid:zoobank.org:act:9A0F4DEB-C4CE-44E2-BAAC-D86A88DC25CEhttp://species-id.net/wiki/MikeiinaeMikeius Buffington, 2008.Thrasorinae by the absence of a circumtorular impression that induce galls on species of Acacia (Fabaceae)and Eucalyptus (Myrtaceae), although most of these host records await verification through isolated rearing .Associated with Australia.Mikeius Buffington, 2008.Pujade-Villar & Restrepo-Ortizsp. n.urn:lsid:zoobank.org:act:8D74319A-2A25-48A6-B857-80E6ABB2BE9Chttp://species-id.net/wiki/Mikeius_clavatusMikeius in having the antenna strongly clavate with the six terminal segments 1.5 times wider than previous segments with the following specific characters.Length. Female 2.8 - 3 mm. Male unknown.Coloration. Head and mesosoma black, antenna yellowish, except scape, brown, metasoma pale brown. Legs pale yellow, except coxae, brown.Antenna. : 4(4): 5(3): 3(3): 3(3): 3(3.5): 4(5): 5(6): 5(6): 6(5): 5(6): 5(6): 7(4). Placoid sensillae from F7 to terminal segment.Antenna. Female. PageBreakPageBreakMesosoma. Mesoscutum slightly striate. Notauli complete of uniform width. Antero-admedian lines weak. Median mesoscutal line very short. Scutellar foveae round to subquadrate, not delimited posteriorly. Mesopleural furrow absent.Forewing. Radial cell 2.4 times longer than wide.Metasoma. Base of T3 with an almost complete hairy ring.Mikeius clavatus P-V & R-O\u201d (red label). PARATYPE \u2640 (ANIC) with the following labels: \u201cW sidPageBreake Cobungra Hill 20km WbyN, Omeo Vic. 27 Feb. 1980, I.D. Naumann J. C. Cardale\u201d (white label), \u201cex alcohol collection\u201d (white label), \u201cAUST. NAT. INS. COLL.\u201d (green label), \u201cParatype Mikeius clavatus P-V & R-O\u201d (red label).HOLOTYPE \u2640 (ANIC) with the following label data: \u201cAUSTRALIA: Vict. Mt. Donna Buang, 1200m 11\u201317.i. 80, Eucalyptus-Nothofagus forest, A. Newton, M. Thayer\u201d (white label), \u201cflight intercept window/trough trap\u201d (white label), \u201cAUST. NAT. INS. COLL.\u201d (green label), \u201cHolotype Unknown.Victoria, Australia.The specific name refers to the strongly clavate antenna.Kovalev, 1994http://species-id.net/wiki/ThrasorinaeThrasorus Weld, 1944.Euceroptrinae by the absence of an areolet in the forewing and the absence of a lateral pronotal carina. Additional characters that distinguish Thrasorinae from other Figitidae can be found in the key to subfamilies below.Distinguished from other figitids by the presence of a circumtorular impression , 9A, B ; furtherThrasorus, In the redescription of Unknown.Australia, South America and North America.Cicatrix, gen. n.; Myrtopsen R\u00fcbsaamen, 1908; Palmiriella, gen. n., Scutimica Ros-Farr\u00e9, 2007; Thrasorus Weld, 1944.Paretas-Mart\u00ednezgen. n.urn:lsid:zoobank.org:act:F831C129-F846-4A87-A668-524A2EA64E19http://species-id.net/wiki/CicatrixCicatrix pilosiscutum (Girault), comb. n.Cicatrix neumannoides, sp. n., Cicatrix pilosiscutum (Girault), Cicatrix shauffi (Buffington), comb. n.Cicatrix, gen. n., is distinguished from Myrtopsen, Palmiriella, gen. n., and Scutimica by having T3 and T4 as separate sclerites as well as Cicatrix neumannoides, sp. n., and Cicatrix schauffi (Buffington), comb. n.(Girault)comb. n.http://species-id.net/wiki/Cicatrix_pilosiscutumAmblynotus pilosiscutum Girault, 1929Melanips pilosiscutum (Girault) Weld, 1952Cicatrix neumannoides and Cicatrix schauffi by having female antenna with 11 flagellomeres ), much stronger carinae crossing the entire face .Length. Female 4.4 mm. Male unknown.As in generic description (see above) with the following specific characters: PageBreakColoration. Completely light brown except mesosoma, which is dorsally dark.Head. : 5(3): 10(3): 9(2.5): 8.5(2.5): 8(3): 8(3): 8(3): 7(3): 5(3): 5(3): 4.5(3): 7.5(3). Placoid sensillae absent on basal half of F1 to F4, scarce on dorsal half; abundant from F5 to F11.Mesosoma. Median mesoscutal impression absent. Scutellar foveae subtriangular.Amblynotus pilosiscutum \u2640, Type Girault\u201d , \u201cXyalophoroides pilosiscutum (Gir), E. F. Riek det 1953\u201d , QM Reg. No. T99348\u201d (yellow label), \u201cCicatrix pilosiscutum P-M det-2009\u201d (white label).HOLOTYPE \u2640 (QM) with the following labels: \u201c25. 10. 23, National Pk., Q. H. Hacker.\u201d (white label), \u201cHOLOTYPE\u201d (pink label), \u201cUnknown.Australia. Label data suggest the single specimen was taken in Royal National Park in Sydney.(Buffington)comb. n.http://species-id.net/wiki/Cicatrix_schauffiMikeius schauffi Buffington, 2008.Cicatrix neumannoides, sp. n., in having female antenna with 10 flagellomeres , but differs from Cicatrix neumannoides sp. n. by having a long median mesoscutal impression and subtriangular scutellar foveae with the following specific characters: Coloration. Completely light brown.Head. : 4(3): 5(3): 4(3): 4(3): 4.2(3.1): 4.2(3.1): 4.3(3.3): 5.2(3.3): 4.6(3.3): 3.5(3.3): 6(4). Placoid sensillae present from F4, abundant from F6 through terminal segment.Antenna. Female. Mesosoma. with the following label data: \u201c23.36S 133.35E 32 km WNW of Alice Springs, NT 8 Oct. 1978 J:C: Cardale\u201d (white label), \u201cex alcohol collection\u201d (white label), \u201cAUST. NAT. INS. COLL.\u201d (green label). \u201cHOLOTYPE, Mikeiusschauffi, Buffington\u201d (red label), \u201cCicatrix schauffi P-M det-2009\u201d (white label).PageBreakUnknownCentral Australia.Thrasorinae, not in Mikeiinae. We transfer this species to Cicatrix gen. n., because it possesses all the diagnostic characters of that genus.The circumtorular impression present in this species indicates that it belongs in Paretas-Mart\u00ednez & Restrepo-Ortizsp. n.urn:lsid:zoobank.org:act:1A6D286B-94AF-43F8-945B-D9AF124EEC57http://species-id.net/wiki/Cicatrix_neumannoidesCicatrix schauffi, comb. n., having female antenna with 10 flagellomeres and a face with horizontal strigae only on the lateral areas , but differs from Cicatrix schauffi comb. n. by having short median mesoscutal impression and rounded scutellar foveae (Similar to r foveae .As in generic description (see above) with the following specific characters.Length. Female: 2.9 to 3.0 mm. Male unknown.Coloration. Shiny chestnut, scutum darker in center.Head. Frons and face with piliferous punctures; face with a few carinae from internal margin of eye reaching center of face.Antenna. Female. 10 flagellomeres, antennal formula: 6(2): 4(2.8): 6(2.5): 4.1(2.8): 4.1(2.8): 4(3): 4(3): 4(3): 4.8(3.1): 3.8(3.3): 3.5(3.3): 5.6(4). Placoid sensillae starting from F4, F4 to F6 are scarce, abundant from F7-F10.Mesosoma. , \u201cAUST. NAT. INS. COLL.\u201d (green label), \u201cMikeius neumanni Det. M. L. Cicatrix neumannoides P-M & R-O\u201d (red label)\u201d. PARATYPE \u2640 (ANIC) with the following labels: \u201cCrowea St. For. nr Pemberton W.A. Nov.-Dec. 1978 S.J. Curry Malaise trap open forest\u201d (white label), \u201cAUST. NAT. INS. COLL.\u201d (green label), \u201cParatype Cicatrix neumannoides P-M & R-O\u201d (red label)\u201d.HOLOTYPE \u2640 (ANIC) with the following labels: \u201cAUSTRALIA: NSW Peak Hill Range, Braidwood, Cooma Road, At top of pass. 30 December 1994. A. Sundholm & R de keyzer. On Acacia.Unknown; label data suggests an association with New South Wales and Western Australia, Australia.Mikeius neumanni in the collection at ANIC, he used only one specimen in his description of the taxon, designating it as the holotype. The species neumanni (based on PageBreakthe holotype) is transferred to Palmiriella, gen. n., below, and the second specimen, in addition to another specimen discovered in ANIC, belongs to Cicatrix.Although Pujade-Villar & Paretas-Mart\u00ednezgen. n.urn:lsid:zoobank.org:act:5F540007-4494-49BF-A619-F0A54F5CE41Ehttp://species-id.net/wiki/PalmiriellaPalmiriella neumanni (Buffington), comb. n., by present designation and monotypy.Palmiriella, gen. n., can be distinguished from other thrasorines by having the face smooth, without any sculpturing , 4F. Addcutimica , with miyrtopsen ); from Tsoscutum comb. n.http://species-id.net/wiki/Palmiriella_neumanniMikeius neumanni Buffington, 2008.Length. Female 3.2 mm. Male unknown.PageBreakColoration. Head and mesosoma black, antennae yellowish except scape, brown, metasoma medium brown. Legs light yellow except tibia and metatarsi, brown.Head : 4(4): 4(3): 4.5(3): 4.5(3): 4.5(3): 4(3): 4(3): 4(3): 3(3): 3(3): 3(3): 5(4). Placoid sensillae from F7 to terminal segment.Antenna . Female.Mesosoma , \u201cPalmiriella neumanni P-V & P-M det-2009\u201d (white label).HOLOTYPE \u2640 (ANIC) with the following labels: \u201cMt Nebo, S. E. Qld, 24. Xi. 1970, S. R. Monteith\u201d (white label), \u201cAUST. NAT. INS. COLL.\u201d (green label). \u201cHOLOTYPE, Unknown.Queensland, Australia.Weld, 1944Thrasorus pilosus Weld, 1944.Thrasorus pilosus Weld, Thrasorus rieki, sp. n., Thrasorus schmitdae Buffington.Paretas-Mart\u00ednez & Pujade-Villarsp. n.urn:lsid:zoobank.org:act:BCD3677F-EA0D-4D37-B62B-F093CEDF7B02http://species-id.net/wiki/Thrasorus_riekiThrasorus by having small scutellar foveae not clearly defined in posterior margin . PARATYPES: 4 \u2642 and 1 \u2640 (on the same pinned card as the holotype) with the same data as the holotype, \u201cParatype Thrasorus rieki P-M & P-V det-2009\u201d (red label); 1 \u2642 and 5 \u2640 (ANIC) with the following labels: \u201cOut of Acacia galls ???? 19.1.16 QLD\u201d (handwritten below the label with the insects), \u201cAUST. NAT. INS. COLL.\u201d (green label), \u201cParatype Thrasorus rieki P-M & P-V det-2009\u201d (red label); 1 \u2640 (QM) with the following labels: \u201cAmblynotus berlesei \u2640 Girault types\u201d (white label handwritten), PageBreak\u201cHOLOTYPE\u201d (pink label), \u201cThrasorus berlesei (Gir) EF Riek det 1953\u201d (white label handwritten), \u201cQM reg. No. T99347\u201d (yellow label), \u201cParatype Thrasorus rieki P-M & P-V det-2009\u201d (red label).HOLOTYPE \u2640 with the following labels: \u201cOut of large galls on mullee acacia On 18\u20131-16\u201d (handwritten below the label with the insects), \u201cThrasorus berlesei (Grlt) Riek det\u201d , \u201csp 7 (berlesei) det ML Buffington 2006\u201d (white label), \u201cHolotype Acacia galls (based on label data).PageBreakUnknown host on Australia, Queensland.Cynipoidea.Named after E.F. Riek, who worked before us on Australian Amblynotus berlesei\u2019 by Girault. In ANIC, there are six specimens on one large card with a determination label placed by Riek, stating that taxon is \u2018Thrasorus berlesei (Grlt)\u2019. But as nomen nudum after Thrasorus rieki, sp. n., mixed with Chalcidoidea specimens.In the QM, there is one specimen labelled as \u2018Thrasorinae: the circumtorular impression . The portion of the plate that is reduced is the posterior part of the pronotal plate, or the portion of the plate dorsal to the submedial pronotal depressions. The arrow in Palmiriella , and T3-T4 fused into a syntergum . The primary difference between Thrasorus and Cicatrix is the sculpturing of the mesoscutum. Though the sculpturing on the mesoscutum can be variable in other groups of Figitidae, in the \u2018pool\u2019 of genera treated in this paper, mesoscutal sculpture is useful and unique character. Thrasorus is the only genus, not only among Thrasorinae but also among all the genera previously included in this subfamily , that aside from notauli, lacks sculpturing of any kind in the mesoscutum; we believe that this character is enough to justify the separation of Thrasorus from Cicatrix and the other thrasorines.The morphology of the metasoma is a very important character and is frequently used in all Palmiriella from Scutimica and Myrtopsen are detailed in the diagnosis of the genus (see above). The combination of the smooth face , shape of syntergum T3-T4, shape of scutellum, shape of pronotum, and absence of sculpturing on pronotum, distinguish Palmiriella from Scutimica and Myrtopsen. The differences between Scutimica and Myrtopsen have already been remarked and discussed in The characters that differentiate Parnipinae (Euceroptrinae (Mikeiinae (Plectocynipinae (Thrasorinae)))). It is clear that Mikeius renders the Thrasorinae paraphyletic, supporting the description of Mikeiinae, and that Cicatrix and Palmiriella are distinct clades. Erecting a new subfamily for a single genus is not desirable, but the only alternative to this while respecting the clades recovered in the phylogenetic analysis would be grouping together Mikeius, Palmiriella, Thrasorus, Cicatrix, Scutimica, Myrtopsen, Plectocynips and Pegascynips in a single subfamily; we feel this grouping is undesirable from the standpoint of predictability, since these genera contain species possessing markedly different biological and morphological attributes, and still would lack a single common diagnostic character for all of them. As currently defined, each of the subfamilies recognized here has its own diagnostic character: long metatibial spur for Plectocynipinae, circumtorular impression for Thrasorinae and two carinae in median area of pronotum not forming a projected pronotal plate for Mikeiinae.PageBreakThe results of the phylogenetic analysis are summarized in Thrasorinae from Australia are one of the most poorly known groups of figitids. More field data and specimens would help to clarify the status of this group and some taxa described here. However, there is no single researcher in Australia dedicated to the study of Cynipoidea, and workers on Figitidae wanting to study the systematics PageBreakof this group must rely on \u2018rare\u2019 specimens coming from non-target collections while pursuing the sampling of other groups. The study we present here has been done with all the thrasorines and Mikeius that have been collected, curated, and deposited in museums worldwide.PageBreakThe"} +{"text": "Over the last decade implementation of targeted therapy has improved the functional ability in JIA-children. Also, the attitude towards participation of JIA-children in sport has become less restrictive with growing evidence of the benefits of physical activity on e.g. disease, fitness and quality of life.To explore the habits in gym classes and sport in 10-16 year-old JIA-children compared to gender- and age-matched healthy controls.68 JIA-children , age 12.74 (\u00b11.70) years, disease duration 5.72 (\u00b14.17) years, and 118 healthy controls , age 12.36 (\u00b11.74) years, answered questionnaires on sport and exercise habits and functional ability (CHAQ38). For JIA: VAS-pain, Patient- and Physician-GA were noted.Mean CHAQ38 scores for JIA: 0.1896 (\u00b10.2025), controls: 0.0359 (\u00b10.0799) indicated only minimal functional impairment in both groups. Pain assessments correlated well to CHAQ38 scores in JIA .No significant differences were found between sport-active JIA-children and controls concerning type and number of sport activities or amount of time spent in sport. Significantly more JIA-children were not sport-active (38% (26/68) vs. 25% (29/118)), mainly due to joint pain (12/26) and getting short of breath/side-stitches (9/26).Significantly fewer JIA-children participated fully in gym (p<0.01) and reported pain (91% (62/68)) and difficulties with certain activities (p<0.01). Strategies mainly used when pain; a short break (81%), changing activity (58%), continuing despite pain (37%).JIA-children still participate less in sport activities and are more challenged in gym classes than healthy peers, despite close-to-normal functional ability. However, sport-active JIA-children do not differ significantly from sport-active healthy peers."} +{"text": "Levels of brain natriuretic peptide (BNP) increase following CABG and predict post-operative outcomes. Release kinetics of BNP, Troponin-I (TnI) and CKMB after valve replacement are not well characterized.We assessed levels of these biomarkers 24 hours prior and 6,24, 48 hrs, 1 month following mitral/aortic valve replacement in 50 patients .Mean baseline BNP, TnI and CK-MB levels were 304.01 pg/ml, 0.03 ng/ml and 0.99 ng/ml. BNP initially decreased within 6 hours of surgery, and peaked at 24 hours; TnI and CKMB showed an early rise, with declining trends by 24 hrs. Peak BNP levels occurred in 90% patients by 24-48 hrs, while for TnI and CKMB this occurred in only 15-30%.Mean delta (peak-baseline) BNP, TnI, CKMB was 660.1pg/ml, 8.1ng/ml and 32.3ng/ml.At 1 month, levels of all biomarkers were not significantly different from baseline. Patients with higher baseline BNP more commonly had atrial fibrillation , higher right ventricular systolic pressure ,higher Euroscore II,longer inotrope duration , ventilator support time , longer ICU and hospital stay . Inotrope duration>42 hrs, ventilation time>29 hrs and ICU stay>4 days was seen in 42%vs19%, 30%vs9% and 33%vs14% respectively in patients with baseline BNP >/< 200 pg/ml. Only baseline BNP was a significant predictor of inotrope duration (p=0.01) and ventilation time (p=0.02). Only 24 hour post-operative BNP and delta BNP were predictors of inotrope duration>42 hrs, ventilation time>29 hrs and ICU stay>4 days.Release kinetics of cardiac biomarkers following valve surgery are significantly different from each other. Of all the biomarkers, only BNP levels had an association with post-operative inotrope duration, ventilation time and ICU stay in patients undergoing valve replacement."} +{"text": "Cell volume can be calculated as 1-DMF%*LV mass.In severe aortic stenosis (AS), hemodynamics and conventional indices do not fully explain symptoms, prognosis or treatment response. We hypothesize that diffuse myocardial fibrosis (DMF) is a key missing factor in AS. This can now be accurately measured non-invasively using equilibrium contrast CMR (EQ-CMR) involvin(m)/DMF% (continuous variable or severity tertiles), or cell volume.63 severe AS patients with planned valve replacement underwent baseline and follow up EQ-CMR. Twenty normal controls were included. Baseline and follow-up assessment included NYHA, ECG, echocardiography , BNP and six minute walk test (6MWT). Follow up was at 6-months . EQ-CMR results were expressed as Vd(m):0.27\u00b10.04 vs 0.24\u00b10.04; DMF:17% vs 11%, p = 0.003) with a wide range (Vd(m):0.20-0.39; DMF:4-42%). Breathless patients had more DMF (NYHA class III/IV vs I/II: Vd(m):0.32\u00b10.03 vs 0.26\u00b10.04; DMF:15% vs 27%, p<0.001). DMF correlated with 6MWT and aortic valve area . DMF only correlated with EF in patients with LV impairment . Severe DMF patients had worse diastolic function (p=0.029). In a multivariate analysis of all parameters classically associated with 6MWT distance, the only independent predictor was DMF (p=0.04). On univariate analysis there was a weak correlation with BNP and age.AS patients had more fibrosis than controls . However, only patients with severe fibrosis improved their exercise capacity (p=0.03). LVH regression was shown to be cellular rather than fibrosis (36g vs 34g p=0.572) resolution, figure In this first clinical EQ-CMR study of severe AS, DMF is higher when there is LV impairment, diastolic dysfunction and more severe stenosis. DMF is the single best predictor of pre-op exercise capacity and post-op improvement. EQ-CMR shows that at 6-month post valve replacement LVH regression is predominantly reduced cell rather than fibrosis volume. EQ-CMR for the non-invasive measurement of DMF appears to be a significant cardiological advance."} +{"text": "One of the causes of septic mortality is a low cardiac output secondary to preload failure. Same patients demonstrate preload failure after aggressive volume replacement .t criteria.Ultrasound impulse-wave Doppler evaluation of transmitral flow: VmaxE, VmaxA, ejection time E,A; DT E wave, IVRT of LV. Ultrasound evaluation of end-diastolic and end-systolic LV volume, stroke volume on Teichholz L. EDLVP = 1.06 + 15.15 \u00d7 VTI peakA/VTI peakE. Coronary perfusion pressure (CPP) = EDLVP - diastolic BP. We evaluate these parameters in 34 patients (age 28.1 \u00b1 8.0 months) with septic shock (SS) diagnosed according to Consensus 2002. Control (C) - 44 healthy children (age 40.7 \u00b1 8.5 months). Statistical analyses with The increase of VmaxA and decrease of VmaxE in patients of SS are demonstrated. IVRT and DT are less than in control group. We evaluated a decrease in E/A proportion. EDLVP in patients was more, and CPP lower, than in controls. See Table Pediatric SS accompanied with LV diastolic dysfunction, which decreases the effectiveness of volume restoration therapy, reduces preload and cardiac output."} +{"text": "AbstractTetramorium tortuosum species group members encountered in the Afrotropical region, which we have placed in its own subgroup: the Tetramorium capillosum species complex. We re-describe the two previously known species Tetramorium capillosum Bolton and Tetramorium tabarum Bolton, and describe the new species Tetramorium hecatesp. n. The geographic distribution of the three species appears to be restricted to the equatorial rainforests of Central Africa. We provide a diagnosis of the Tetramorium capillosum species complex, an illustrated identification key to species level, and worker-based species descriptions, which include diagnoses, discussions, high-quality montage images, and distribution maps. Furthermore, we discuss biogeography and composition of the globally distributed Tetramorium tortuosum group.In this study we revise the taxonomy of the Tetramorium Mayr represents one of the most species-rich ant genera, a group that is also widely distributed throughout most zoogeographical regions. However, in terms of species and species group numbers, the main diversity of the genus is found in the Afrotropical and Malagasy regions, from where around 220 Afrotropical and 84 Malagasy species are currently known , London, U.K.CASC California Academy of Sciences, San Francisco, California, U.S.A.MCZ Museum of Comparative Zoology, Cambridge, Massachusetts, U.S.A.MHNG Mus\u00e9um d\u2019Histoire Naturelle de la Ville de Gen\u00e8ve, Geneva, SwitzerlandNHMB Naturhistorisches Museum, Basel, SwitzerlandTetramorium capillosum and Tetramorium tabarum, together with a small amount of non-type specimens, are found in BMNH and MHNG.The material examined in this study is located in the collections of BMNH, CASC, and MCZ. More than 95% of the specimens examined belong to CASC and were sampled during ant inventories carried out in Central Africa from 1998 to 2001 . All images presented are available online and can be seen on AntWeb (http://www.antweb.org). The measurements were taken with a Leica MZ 12.5 equipped with an orthogonal pair of micrometers at a magnification of 100\u00d7, rarely 80\u00d7. Measurements and indices are presented as minimum and maximum values with arithmetic means in parentheses. In addition, all measurements are expressed in mm to two decimal places. The measurements and indices used in this study are the same as in All new type material and all imaged specimens can be uniquely identified with specimen-level codes affixed to each pin (e.g. CASENT0078328). In the presented descriptions we list all of the available specimen-level codes for the whole type series. It should be Head length (HL): maximum distance from the mid-point of the anterior clypeal margin to the mid-point of the posterior margin of head, measured in full-face view. Impressions on anterior clypeal margin and posterior head margin reduce head length.Head width (HW): width of head directly behind the eyes measured in full-face view.Scape length (SL): maximum scape length excluding basal condyle and neck.Eye length (EL): maximum diameter of compound eye measured in oblique lateral view.Pronotal width (PW): maximum width of pronotum measured in dorsal view.Weber\u2019s length (WL): diagonal length of mesosoma in lateral view from the postero-ventral margin of propodeal lobe to the anterior-most point of pronotal slope, excluding the neck.Propodeal spine length (PSL): the tip of the measured spine, its base, and the centre of the propodeal concavity between the spines must all be in focus. Using a dual-axis micrometer the spine length is measured from the tip of the spine to a virtual point at its base where the spine axis meets orthogonally with a line leading to the median point of the concavity.Petiolar node height (PTH): maximum height of petiolar node measured in lateral view from the highest (median) point of the node to the ventral outline. The measuring line is placed at an orthogonal angle to the ventral outline of the node.Petiolar node length (PTL): maximum length of the dorsal face of the petiolar node from the anterodorsal to the posterodorsal angle, measured in dorsal view excluding the peduncle.Petiolar node width (PTW): maximum width of dorsal face of petiolar node measured in dorsal view.Postpetiole height (PPH): maximum height of the postpetiole measured in lateral view from the highest (median) point of the node to the ventral outline. The measuring line is placed at an orthogonal angle to the ventral outline of the node.Postpetiole length (PPL): maximum length of postpetiole measured in dorsal view.Postpetiole width (PPW): maximum width of postpetiole measured in dorsal view.Ocular index (OI): EL / HW * 100Cephalic index (CI): HW / HL * 100Scape index (SI): SL / HW * 100Propodeal spine index (PSLI): PSL / HL * 100PageBreakPetiolar node index (PeNI): PTW / PW * 100Lateral petiole index (LPeI): PTL / PTH * 100Dorsal petiole index (DPeI): PTW / PTL * 100Postpetiolar node index (PpNI): PPW / PW * 100Lateral postpetiole index (LPpI): PPL / PPH * 100Dorsal postpetiole index (DPpI): PPW / PPL * 100Postpetiole index (PPI): PPW / PTW * 100Tetramorium ; anterior clypeal margin usually entire without median notch; frontal carinae very well developed and usually reaching posterior head margin; antennal scrobe present, weakly to very well developed; propodeal spines medium-sized to long, elongate-triangular to spinose; propodeal lobes short, triangular to elongate-triangular; petiolar node in profile nodiform, in profile as high as long to 1.3 times higher than long (LPeI 78 - 100), in dorsal view always longer than wide (DPeI 80 - 93); postpetiole sub-globular to moderately anteroposteriorly compressed; mandibular sculpture variable; cephalic sculpturation distinct, between frontal carinae longitudinally rugose to reticulate-rugose; mesosoma predominantly longitudinally rugose; petiolar node weakly to distinctly rugose, postpetiole ranging from unsculptured to longitudinally rugose; gaster unsculptured, smooth, and shiny; all dorsal surfaces of body with abundant, long, standing hairs; first gastral tergite without pubescence, and pilosity never short, dense, and appressed; sting appendage spatulate.Taxonomic notesPageBreakTetramorium tortuosum group are unlikely to be misidentified with species from the other three groups having 11-segmented antennae. The 26 species of the Tetramorium weitzeckeri group all have a squamiform or high nodiform petiolar node, which is always significantly wider than long. This node shape strongly contrasts with the shape observed in the Tetramorium tortuosum group since all three members have a nodiform node which is much longer than wide. The second species group, the Tetramorium angulinode group, is morphologically closer to the Tetramorium tortuosum group since both groups share a nodiform petiolar node. However, they can be clearly separated by the pilosity/pubescence patterns on the first gastral tergite. In the Tetramorium tortuosum group pubescence is absent and pilosity is long and mainly erect, whereas in the Tetramorium angulinode group pubescence and pilosity are usually present, dense, appressed to decumbent, and often pointed towards a longitudinal midline of the tergite. The synonymisation of Triglyphothrix under Tetramorium , and it seems appropriate to evaluate whether the Afrotropical species fit into one of these groups or deserve their own species complex. Based on the definitions of the complexes, the Afrotropical species cannot be members of the Tetramorium jedi, Tetramorium noeli, or Tetramorium smaug complexes due to a lack of sculpture on the forecoxae and the first gastral tergite. This would argue for placement in the Tetramorium andrei complex. Two reasons prevented us from doing so however. First, there is a difference in the development of the anterior clypeal margin, which is strongly medially impressed in the Malagasy Tetramorium andrei complex while the Afrotropical species treated in this study usually have an entire margin . The second reason not to place the African species into a Malagasy complex is the current uncertainty about whether the Tetramorium tortuosum group as a whole is a natural group of closely related species, an issue discussed below. Consequently, we propose to place Tetramorium capillosum, Tetramorium hecate, and Tetramorium tabarum in their own complex, the Tetramorium capillosum species complex.Biogeographic notes on the groupPageBreakTetramorium tortuosum group have a moderately restricted distribution range since they are only known from Equatorial rainforests in the Central African countries of Gabon, Cameroon, Democratic Republic of Congo, Central African Republic, and Uganda. Given all of the known African localities, the distribution of Tetramorium capillosum and Tetramorium tabarum appears fairly disjunctive. Most localities are located in the west of the distribution range in Gabon, Cameroon, and western parts of the Central African Republic, but few localities are found much further east in the northeastern Democratic Republic of Congo and northwestern Uganda. This represents a great gap between these two groups of localities. However, we think that this lack of occurrence records is very likely due to a sampling artefact since ant sampling has been relatively fragmentary in sub-Saharan Africa. The westernmost known distribution limit is the eastern coast of the Gulf of Guinea and the easternmost known locality appears to be the Budongo Forest in northwestern Uganda. It is unlikely that they occur further east, which is supported by an inventory of the myrmecofauna of the Kakamega Forest in Western Kenya , Tetramorium philippwagneri Hita Garcia, Fischer and Peters, and Tetramorium pinnipilum Bolton, are fairly successful, common, and relatively abundant species found in many equatorial rainforests. Also, the Tetramorium weitzeckeri group, with the exception of Tetramorium humbloti Forel that has invaded the Malagasy region, is restricted in distribution to the Afrotropical region. This fact indicates that it represents a relatively young and successful development within the Afrotropical Tetramorium fauna, supporting Tetramorium weitzeckeri group, there are many more Afrotropical species groups with 12-segmented antennae that perform well in rainforests, such as the Tetramorium bicarinatum, Tetramorium camerunense, and Tetramorium flabellum groups. This very strong competition in most modern-day rainforests might well explain the depauperate Tetramorium tortuosum fauna encountered in Africa. The species-rich Malagasy group fauna does not face the same competition by other genus members within their size and niche ranges, and with 22 species seems to have undergone a fairly successful radiation, mostly in the rainforests of eastern Madagascar [MCZ] [examined]. Paratypes, seven pinned workers with same data as holotype [examined].Holotype, pinned worker, GABON, Makokou, Non-type material. CAMEROON: Mbalmayo, XI.1993 (PageBreakN. Storck); Ndupe, 20.XII.1989 (A. Dejean); Sud, Bond\u00e9 Forest, N\u2019kolo village, 27.5 km 155\u00b0 SSE Elogbatindi, 3.2217N, 10.2467E, 40 m, rainforest, 12.IV.2000 (B.L. Fisher); Sud, Campo Reserve, 2\u00b036'N, 9\u00b056'E, 40 m, 25.X.1991 (D.M. Olson); Sud, P.N. Campo, 43.3 km 108\u00b0ESE Campo, 2.2825N, 10.2062E, 290 m, rainforest, 7.IV.2000 (B.L. Fisher); Sud, Res. de Faune de Campo, Massif des Mamelles, 15.1 km 84\u00b0E \u00c9bodj\u00e9, 2.59417N, 9.9595E, 180 m, rainforest, 4.IV.2000 (B.L. Fisher); CENTRAL AFRICAN REPUBLIC: Prefecture Sangha-Mba\u00e9r\u00e9, R\u00e9serve Sp\u00e9ciale de For\u00eat Dense de Dzanga-Sangha, 12.7 km 326\u00b0NW Bayanga, 3.005N, 16.1933E, 420 m, rainforest, 10.\u201317.V.2001 (B.L. Fisher); Prefecture Sangha-Mba\u00e9r\u00e9, Parc National Dzanga-Ndoki, Mab\u00e9a Bai, 21.4 km 53\u00b0NE Bayanga, 3.0333N, 16.41E, 510 m, rainforest, 1.\u20137.V.2001 (B.L. Fisher); DEMOCRATIC REPUBLIC OF CONGO: Epulu, 1.3833N, 28.5833E, 750 m, rainforest, 1.XI.1995 (S.D. Torti); GABON: La Makande, Foret de Abeilles, I.-II.1999 (S. Lewis); Makokou, rainforest, X.1972 (I. Lieberburg); Ogooue-Maritime, Aire d\u2019Exploit. Rationnelle de Faune des Monts Doudou, 24.3 km 307\u00b0NW Doussala, 2.2264N, 10.4097E, 375 m, rainforest, 6.-9.III.2000 (B.L. Fisher); Ogooue-Maritime, Aire d\u2019Exploit. Rationnelle de Faune des Monts Doudou, 25.2 km 304\u00b0NW Doussala, 2.2275S, 10.3945E, 640 m, rainforest, 14.III.2000 (B.L. Fisher); Ogooue-Maritime, Reserve des Monts Doudou, 25.2 km 304\u00b0NW Doussala, 2.2272S, 10.3945E, 630 m, coastal lowland rainforest, 13.-20.III.2000 (S. van Noort); Ogooue-Maritime, Reserve de la Moukalaba-Dougoua, 12.2 km 305\u00b0NW Doussala, 2.3167S, 10.5333E, 110 m, rainforest, 24.II.2000 (B.L. Fisher); Ogooue-Maritime, Reserve de la Moukalaba-Dougoua, 10.8 km 214\u00b0SW Doussala, 2.4227S, 10.5453E, 110 m, rainforest, 29.II.2000 (B.L. Fisher); Ogooue-Maritime, Reserve de la Moukalaba-Dougoua, 12.2 km 305\u00b0NW Doussala, 2.2833S, 10.4972E, 110 m, coastal lowland rainforest, 24.II.\u20133.III.2000 (S. van Noort); Woleu-Ntem, 31.3 km 108\u00b0ESE Minvoul, 2.08N, 12.4067E, 600 m, rainforest, 7.II.1998 (B.L. Fisher); UGANDA: Bunyoro District, Budongo Forest FS, 1.7264N, 31.5524E, 1081 m, 8.VII.2009 (W. Freund & T. Klug).Tetramorium capillosum from the remainder of the species group: eyes of moderate size (OI 23 - 25); antennal scapes moderately long (SI 80 - 83); petiolar node nodiform with anterodorsal and posterodorsal margins relatively rounded, posterodorsal margin situated higher than anterodorsal margin, dorsum convex; mandibles strongly longitudinally rugose; petiole and postpetiole usually with weak sculpture; whole body uniformly very dark brown to black.The following character combination clearly distinguishes (N=12). HL 0.79 - 0.89 (0.84); HW 0.76 - 0.84 (0.79); SL 0.62 - 0.69 (0.65); EL 0.18 - 0.21 (0.19); PH 0.41 - 0.51 (0.46); PW 0.60 - 0.68 (0.65); WL 1.02 - 1.19 (1.12); PSL 0.26 - 0.38 (0.30); PTL 0.31 - 0.37 (0.34); PTH 0.34 - 0.41 (0.37); PTW 0.28 - 0.33 (0.31); PPL 0.28 - 0.33 (0.30); PPH 0.37 - 0.43 (0.40); PPW 0.37 - 0.44 (0.41); CI 94 - 96 (95); SI 80 - 83 (82); OI 23 - 25 (24); DMI 55 - 62 (58); LMI 39 - 43 (41); PSLI 31 - 43 (35); PeNI 45 - 49 (47); LPeI 89 - 100 (94); DPeI 86 - 94 (89); PpNI 61 - 66 (63); LPpI 70 - 78 (75); DPpI 130 - 139 (135); PPI 127 - 138 (134).PageBreakPageBreak (DPeI 86 - 94). Postpetiole in profile relatively high and moderately anteroposteriorly compressed, approximately 1.2 to 1.3 times higher than long (LPpI 70 - 78); in dorsal view around 1.3 to 1.4 times wider than long (DPpI 130 - 139). Postpetiole in profile thinner and higher than petiolar node, in dorsal view approximately 1.3 to 1.4 times wider than petiolar node (PPI 127 - 138). Mandibles strongly longitudinally rugose; clypeus longitudinally rugulose, usually with three to five rugulae, median rugula better developed; cephalic dorsum between frontal carinae irregularly longitudinally rugose to reticulate rugose, posteriorly towards posterior head margin fully reticulate-rugose, anteriorly towards posterior clypeal margin more regularly longitudinally rugose; scrobal area unsculptured, smooth, and shining; lateral and ventral head longitudinally rugose to reticulate-rugose. Mesosoma laterally and dorsally strongly irregularly longitudinally rugose. Forecoxae unsculptured, smooth, and shining. Both waist segments with strong sculpture, mainly longitudinally rugose. Gaster unsculptured, smooth, and shining. Ground sculpture generally faint to absent everywhere on body. Whole body with abundant, very long, and fine standing hairs; first gastral tergite without appressed pubescence. Anterior edges of antennal scapes with suberect to erect hairs. Body of uniform very dark brown to black colour.Head longer than wide (CI 94 - 96); posterior head margin moderately concave. Anterior clypeal margin entire and convex. Frontal carinae strongly developed, approaching or ending at posterior head margin. Antennal scrobes narrow but very well-developed with clearly defined margins all around. Antennal scapes moderately long, not reaching posterior head margin (SI 80 - 83). Eyes of moderate size (OI 23 - 25). Mesosomal outline in profile weakly convex, moderately marginate from lateral to dorsal mesosoma; promesonotal suture and metanotal groove absent; mesosoma comparatively stout and high (LMI 39 - 43). Propodeal spines relatively long to very long, spinose, and acute (PSLI 31 - 43); propodeal lobes short, triangular to elongate-triangular, and usually acute. Petiolar node in profile rectangular nodiform, approximately as high as long to weakly higher than long (LPeI 89 - 100), anterior and posterior faces approximately parallel, posterodorsal margin situated higher than anterodorsal, anterodorsal and posterodorsal angles relatively rounded, petiolar dorsum convex; node in dorsal view approximately 1.1 times longer than wide Tetramorium capillosum is found throughout Gabon, southern Cameroon, eastern Central African Republic, and then much further east in the northeastern Democratic Republic of Congo and northwestern Uganda either bicoloured or of uniform brown colour, whereas Tetramorium capillosum is noticeably larger and of a very dark brown to black colour. However, both body size and colouration are often variable within the genus Tetramorium. Tetramorium capillosum also differs from Tetramorium hecate in antennal scape length, eye size, and petiolar node shape. In Tetramorium capillosum the antennal scapes are moderately long (SI 80 - 83), eyes are of moderate size (OI 24 - 25), and the petiolar node has anterodorsal and posterodorsal margins that are relatively rounded, with the posterodorsal margin situated higher than the anterodorsal. In contrast, Tetramorium hecate scapes are relatively short (SI 73 - 77), eyes are relatively large (OI 27 - 31), and the petiolar node is rectangular nodiform with anterodorsal and posterodorsal angles sharply defined and at about the same height. Furthermore, Tetramorium tabarum significantly varies from Tetramorium capillosum in eye size, propodeal spine length, and sculpture on mandibles and postpetiole. Tetramorium tabarum has much larger eyes (OI 27 - 31), much shorter spines (PSLI 22 - 25), and the mandibles and the postpetiole are unsculptured, whereas Tetramorium capillosum has smaller eyes (OI 24 - 25), much longer spines (PSLI 31 - 43), and conspicuously sculptured mandibles and postpetiole.Within the African Tetramorium capillosum remains morphologically remarkably stable without noticeable intraspecific variation.It should be noted that despite a relatively broad distribution range from the Gulf of Guinea to northwest Uganda, Hita Garcia & Fishersp. n.urn:lsid:zoobank.org:act:BEEEF558-1DDA-40AB-8D79-597684B38033http://species-id.net/wiki/Tetramorium_hecateHolotype, pinned worker, GABON, Province Estuaire, F.C. Mondah, 21 km 331\u00b0NNW Libreville, 0\u00b034.6'N, 9\u00b020.1'E, 10 m, littoral rainforest, sifted litter , collection code BLF01742, 24.II.1998 (B.L. Fisher) [unique specimen identifier CASENT0248334] [CASC]. Paratypes, 16 pinned workers with same data as holotype .2\u00b036'N, 9\u00b056'E, 40 m, 25.X.1991 (D.M. Olson); Mbalmayo, XI.1993 (N. Storck); Nkoemvon, 16.III.1980 (D. Jackson); Sud, P.N. Campo, 43.3 km 108\u00b0ESE Campo, 2.2825N, 10.2062E, 290 m, rainforest, 7.IV.2000 (B.L. Fisher); Sud, Res. de Faune de Campo, 2.16 km 106\u00b0ESE \u00c9bodj\u00e9, 2.5678N, 9.8443E, 10 m, littoral rainforest, 9.IV.2000 (B.L. Fisher); Sud, Res. de Faune de Campo, Massif des Mamelles, 15.1 km 84\u00b0E \u00c9bodj\u00e9, 2.5942N, 9.9595E, 180 m, rainforest, 4.IV.2000 (B.L. Fisher); Sud-Ouest, Bimbia Forest, 7.4 km 119\u00b0ESE Limbe, 3.9818N, 9.2625E, 40 m, rainforest, 14.IV.2000 (B.L. Fisher); GABON: Province Estuaire, Mondah Forest, near Libreville, 3.XII.1987 (J. Noyes); Province Estuaire, F.C. Mondah, 21 km 331\u00b0NNW Libreville, 0\u00b034.6'N, 9\u00b020.1'E, 10 m, littoral rainforest, 24.II.1998 (B.L. Fisher).CAMEROON: Campo Reserve, Tetramorium hecate differs from the other species of the group by the following character combination: antennal scapes relatively short (SI 73 - 77); eyes large (OI 27 - 31); petiolar node rectangular nodiform with anterodorsal and posterodorsal margins strongly angulate and situated at about the same height; mandibles unsculptured, smooth, and shining; petiole and postpetiole usually with weak sculpture; body colouration ranging from uniformly brown to head, mesosoma, waist segments yellowish to bright orange contrasting with very dark brown to black gaster.(N=12). HL 0.58 - 0.67 (0.63); HW 0.54 - 0.64 (0.60); SL 0.41 - 0.49 (0.45); EL 0.15 - 0.20 (0.17); PH 0.28 - 0.36 (0.33); PW 0.42 - 0.52 (0.47); WL 0.69 - 0.83 (0.77); PSL 0.12 - 0.26 (0.20); PTL 0.20 - 0.26 (0.24); PTH PageBreak0.22 - 0.27 (0.25); PTW 0.17 - 0.22 (0.20); PPL 0.19 - 0.22 (0.21); PPH 0.22 - 0.28 (0.25); PPW 0.24 - 0.29 (0.27); CI 93 - 96 (94); SI 73 - 77 (76); OI 27 - 31 (28); DMI 58 - 63 (61); LMI 41 - 44 (42); PSLI 21 - 38 (32); PeNI 39 - 46 (43); LPeI 89 - 100 (94); DPeI 81 - 89 (84); PpNI 55 - 62 (57); LPpI 80 - 91 (86); DPpI 120 - 130 (126); PPI 129 - 142 (135).PageBreakwaist segments laterally weakly, irregularly rugulose/rugose, dorsally mostly unsculptured, smooth, and shining. Postpetiole and gaster unsculptured, smooth, and shining. Ground sculpture generally faint to absent everywhere on body. Whole body with PageBreakabundant, long, and fine standing hairs; first gastral tergite without appressed pubescence. Anterior edges of antennal scapes with suberect to erect hairs. Body colouration relatively variable, ranging from bicoloured with head, mesosoma, legs, and waist segments yellowish to bright orange contrasting with very dark brown to black gaster to whole body uniformly brown.Head longer than wide (CI 93 - 96); posterior head margin weakly concave. Anterior clypeal margin usually entire and convex, sometimes with very small median notch only visible under higher magnifications. Frontal carinae strongly developed, approaching or ending at posterior head margin. Antennal scrobes well developed, moderately shallow, and with clearly defined margins all around. Antennal scapes relatively short, not reaching posterior head margin (SI 73 - 77). Eyes large (OI 27 - 31). Mesosomal outline in profile weakly convex, moderately marginate from lateral to dorsal mesosoma; promesonotal suture and metanotal groove absent; mesosoma comparatively stout and high (LMI 41 - 44). Propodeal spines usually long to very long (PSLI 30 - 38), elongate-triangular to spinose, and acute, rarely spines reduced, short, elongate-triangular, and acute (PSLI 20 - 21); propodeal lobes short, triangular to elongate-triangular, and acute. Petiolar node in profile rectangular nodiform, approximately as high as long to weakly higher than long (LPeI 89 - 100), anterior and posterior faces approximately parallel, anterodorsal and posterodorsal margins situated at about the same height, anterodorsal and posterodorsal angles well-developed and rectangular, petiolar dorsum flat; node in dorsal view around 1.1 to 1.2 times longer than wide (DPeI 81 - 89). Postpetiole in profile globular to subglobular, approximately 1.1 to 1.2 times higher than long (LPpI 80 - 91); in dorsal view around 1.2 to 1.3 times wider than long (DPpI 120 - 130). Postpetiole in profile appearing less voluminous than petiolar node, in dorsal view approximately 1.3 to 1.4 times wider than petiolar node (PPI 129 - 142). Mandibles unsculptured, smooth, and shining; clypeus longitudinally rugulose, usually with three distinct rugulae, median rugula better developed than remainder, rugulae often with cross-meshes; cephalic dorsum between frontal carinae irregularly longitudinally rugose to reticulate rugose, posteriorly towards posterior head margin well reticulate-rugose, anteriorly towards posterior clypeal margin more regularly longitudinally rugose ; scrobal area mostly unsculptured; lateral and ventral head longitudinally rugose to reticulate-rugose. Mesosoma laterally irregularly rugose, dorsally distinctly longitudinally rugose. Forecoxae unsculptured, smooth, and shining. Both Tetramorium hecate. The species epithet is a nominative noun in apposition, and thus invariant.The name of the new species is inspired by the ancient Latin and Greek goddess \u201cHecate\u201d or \u201cHekate\u201d, also known as the \u201ctriple Hecate\u201d or \u201cthree-faced Hecate\u201d, and refers to the morphological variation in colouration and propodeal spine length observed in Tetramorium hecate is forest leaf litter.The new species is currently only known from Cameroon and Gabon . All locTetramorium hecate is unlikely to be misidentified with the other two species of the group. The most obvious difference between Tetramorium hecate and Tetramorium capillosum and Tetramorium tabarum is the shape of the petiolar node. In the latter two the node is nodiform with relatively rounded anterodorsal and posterodorsal margins, and, in addition, the posterodorsal margin is situated noticeably higher than the anterodorsal margin. In contrast, the node of Tetramorium hecate is nodiform, with clearly rectangular anterodorsal and posterodorsal margins, situated at about the same height. The second-most important character is antennal scape length. Tetramorium hecate has the shortest scapes of the three species (SI 73 - 77), strongly contrasting with the longer scapes of the other two species (SI 80 - 86). Furthermore, Tetramorium hecate is also a much smaller species with much larger eyes and very different colouration than Tetramorium capillosum (see description of the latter for more details). The very well developed antennal scrobes with clearly defined margins all around also separate Tetramorium hecate from Tetramorium tabarum since the scrobes of the latter are shallow and without posterior and ventral margins.PageBreakTetramorium hecate to consist of three potential new species: a strongly bicoloured one with long propodeal spines [MCZ] [examined].Holotype, pinned worker, DEMOCRATIC REPUBLIC OF CONGO, Epulu, 4.I.1949 (A. Dejean); Sud-Ouest, Bimbia Forest, 7.4 km 119\u00b0ESE Limbe, 3.9818N, 9.2625E, 40 m, rainforest, 14.IV.2000 (B.L. Fisher); CENTRALAFRICANREPUBLIC: Prefecture Sangha-Mba\u00e9r\u00e9, R\u00e9serve Sp\u00e9ciale de For\u00eat Dense de Dzanga-Sangha, 12.7 km 326\u00b0NW Bayanga, 3.005N, 16.1933E, 420 m, rainforest, 10.\u201317.V.2001 (B.L. Fisher); Prefecture Sangha-Mba\u00e9r\u00e9, Parc National Dzanga-Ndoki, 37.9 km 169\u00b0S Lidjombo, 2.3707N, 16.1725E, 360 m, rainforest, 20.\u201328.V.2001 (B.L. Fisher); GABON: Woleu-Ntem, 31.3 km 108\u00b0ESE Minvoul, 2.08N, 12.4067E, 600 m, rainforest, 17.II.1998 (B.L. Fisher).CAMEROON: Mvini, 21.XII.1988 ; eyes large (OI 27 - 31); petiolar node nodiform with anterodorsal and posterodorsal margins relatively rounded, posterodorsal margin situated higher than anterodorsal margin, dorsum convex; mandibles unsculptured, smooth, and shining; petiole with very weak sculpture and postpetiole completely unsculptured; head, mesosoma, waist segments yellowish to bright orange, gaster very dark brown to black.(N=10). HL 0.61 - 0.66 (0.63); HW 0.55 - 0.60 (0.57); SL 0.47 - 0.52 (0.49); EL 0.16 - 0.18 (0.17); PH 0.30 - 0.34 (0.32); PW 0.43 - 0.46 (0.44); WL 0.75 - 0.82 (0.79); PSL 0.14 - 0.16 (0.15); PTL 0.20 - 0.22 (0.20); PTH 0.24 - 0.27 (0.25); PTW 0.16 - 0.18 (0.17); PPL 0.19 - 0.21 (0.20); PPH 0.23 - 0.27 (0.25); PPW 0.24 - 0.27 (0.26); CI 90 - 92 (91); SI 84 - 86 (85); OI 27 - 31 (29); DMI 55 - 58 (56); LMI 38 - 43 (41); PSLI 22 - 25 (23); PeNI 37 - 39 (38); LPeI 78 - 82 (81); DPeI 80 - 85 (82); PpNI 56 - 59 (58); LPpI 79 - 85 (82); DPpI 124 - 130 (127); PPI 147 - 156 (152).PageBreakabsent; mesosoma comparatively stout and high (LMI 38 - 43). Propodeal spines relatively short to medium-sized, elongate-triangular to spinose, and acute (PSLI 22 - 25); propodeal lobes short, triangular to elongate-triangular, and acute. Petiolar node in PageBreakprofile rectangular nodiform, approximately 1.2 to 1.3 times higher than long (LPeI 78 - 82), anterior and posterior faces approximately parallel, posterodorsal margin situated higher than anterodorsal, anterodorsal and posterodorsal angles relatively rounded, petiolar dorsum convex; node in dorsal view approximately 1.2 times longer than wide (DPeI 80 - 85). Postpetiole in profile subglobular and moderately anteroposteriorly compressed, approximately 1.2 to 1.3 times higher than long (LPpI 79 - 85); in dorsal view around 1.2 to 1.3 times wider than long (DPpI 124 - 130). Postpetiole in profile appearing less voluminous than petiolar node, in dorsal view approximately 1.5 to 1.6 times wider than petiolar node (PPI 147 - 156). Mandibles unsculptured, smooth, and shining; clypeus longitudinally rugulose, usually with three rugulae, median rugula better developed; cephalic dorsum between frontal carinae with five to eight longitudinal rugae, most rugae running unbroken from posterior clypeal margin to posterior head margin, few rugae interrupted, but none with cross-meshes; scrobal area mostly unsculptured; lateral and ventral head longitudinally rugose to reticulate-rugose. Mesosoma laterally irregularly rugose, dorsally distinctly longitudinally rugose. Forecoxae unsculptured, smooth, and shining. Petiolar node laterally weakly to moderately longitudinally rugose. Postpetiole and gaster unsculptured, smooth, and shining. Ground sculpture generally faint to absent everywhere on body. Whole body with abundant, long, and fine standing hairs; first gastral tergite without appressed pubescence. Anterior edges of antennal scapes with suberect to erect hairs. Head, mesosoma, legs, and waist segments yellowish to bright orange, contrasting with very dark brown to black gaster.Head significantly longer than wide (CI 90 - 92); posterior head margin moderately concave. Anterior clypeal margin entire and convex. Frontal carinae strongly developed, approaching or ending at posterior head margin. Antennal scrobes developed, but shallow and without clearly defined posterior and ventral margins. Antennal scapes moderately long, not reaching posterior head margin (SI 84 - 86). Eyes large (OI 27 - 31). Mesosomal outline in profile weakly convex, moderately marginate from lateral to dorsal mesosoma; promesonotal suture and metanotal groove Tetramorium tabarum is known to occur in northern Gabon, western Cameroon close to the Gulf of Guinea, the southwest of the Central African Republic, and from the type locality in the northeast of the Democratic Republic of Congo , propodeal spine length (PSLI 22 - 25 vs. PSLI 31 - 43), and sculpture on mandibles and postpetiole, which is present and conspicuous in Tetramorium capillosum while absent in Tetramorium tabarum. The latter is also much smaller (WL 0.75 - 0.82) and bicoloured with a dark brown to black gaster contrasting with the remaining yellowish to orange body, which contrasts with the larger size (WL 1.02 - 1.19) and the uniformly very dark brown to black colouration of Tetramorium capillosum. Despite being often also bicoloured and within the same morphometric range, Tetramorium hecate is unlikely to be confused with Tetramorium tabarum. The antennal scapes are significantly longer in Tetramorium tabarum (SI 84 - 86) than in Tetramorium hecate (SI 73 - 77). More importantly, the petiolar node of Tetramorium tabarum has relatively rounded anterodorsal and posterodorsal margins with the posterodorsal margin situated higher than the anterodorsal, and the dorsum is convex, whereas in Tetramorium hecate the anterodorsal and posterodorsal margins are sharply defined and at about the same height. The varying development of the antennal scrobes is another difference. Tetramorium hecate possesses very well-developed scrobes with margins all around while the scrobes of Tetramorium tabarum are shallow without clear posterior and ventral margins.As already pointed out in the above descriptions of the other two species, Tetramorium tabarum is relatively limited, but it seems that intraspecific variation is very low.The material currently available for"} +{"text": "Litopenaeus vannamei, and investigated their potential roles in WSSV replication using dsRNA-mediated gene silencing. Lvcaspase2-5 have the typical domain structure of caspase family proteins, with the conserved consensus motifs p20 and p10. Lvcaspase2 and Lvcaspase5 were highly expressed in muscle, while Lvcaspase3 was highly expressed in hemocytes and Lvcaspase4 was mainly expressed in intestine. Lvcaspase2-5 could also be upregulated by WSSV infection, and they showed different patterns in various tissues. When overexpressed in Drosophila S2 cells, Lvcaspase2-5 showed different cellular localizations. Using dsRNA-medicated gene silencing, the expression of Lvcaspase2, Lvcaspase3, and Lvcaspase5 were effectively knocked down. In Lvcaspase2-, Lvcaspase3- or Lvcaspase5-silenced L. vannamei, expression of WSSV VP28 gene was significantly enhanced, suggesting protective roles for Lvcaspase2, Lvcaspase3 and Lvcaspase5 in the host defense against WSSV infection. Apoptosis plays an important role in white spot syndrome virus (WSSV) pathogenesis, and caspases are central players in apoptosis. Here, we cloned four novel caspases (Lvcaspase2-5) from the Pacific white shrimp Apoptosis plays a protective role in eliminating harmful cells and in the host response to viral infections ,2. When Interference with apoptosis by inhibiting the proteolytic activity of cysteine aspartic acid proteases (caspases) prolongs the life of virus-infected cells, resulting in enhanced viral replication and viral persistence . CaspasePenaeus monodon (Pm) caspase, inhibiting Pm caspase activity in vivo and in vitro . Lv. LvMjcasd 48 hpi . We alsospase2-3 . PmcaspaFigure S1A), Lvcaspase3 (D), Lvcaspase4 (B) and Lvcaspase5 (C) from L. vannamei.Nucleotide and deduced amino acid sequences of Lvcaspase2 ( The nucleotide (upper row) and deduced amino acid (lower row) sequences of Lvcaspase2-5 are shown. The initiation codon (ATG) and stop codon are shown in bold. The caspase family p20 and p10 domains in Lvcaspase2-5 are shaded. (TIF)Click here for additional data file.Figure S2Domain architectures of shrimp caspases.The full-length protein sequences of shrimp caspases were subjected to the simple modular architecture research tool to generate domain structures. The p20 and p10 domain are indicated as elliptical boxes, and the prodomain upstream of the p20 domain is indicated as a line. The initiator caspases have a long prodomain (> 90 amino acids) containing specific protein-protein interaction motifs that are necessary for their activation, whereas the effector caspases usually have a short prodomain of only 20-30 residues [residues .(TIF)Click here for additional data file.Figure S3A phylogenetic tree of Lvcaspase2-5 with other caspase family proteins.The full-length amino acid sequences of caspase family proteins from typical organisms were aligned using the ClustalX2.0 program . The rooted tree was then constructed by the \u201cneighbor-joining\u201d method and was bootstrapped 1,000 times using MEGA 4.0 software (http://www.megasoftware.net/index.html). The numbers at the nodes indicate bootstrap values. Lvcaspase2-5 are boxed in blue lines. Lvcasp1, L. vannamei caspase1 (Accession no. ABK88280); Lvcasp2, L. vannamei caspase2 (Accession no. KC660102); Lvcasp3, L. vannamei caspase3 (Accession no. KC660103); Lvcasp4, L. vannamei caspase4 (Accession no. KC660105); Lvcasp5, L. vannamei caspase5 (Accession no. KC660104); Pmcasp1, Penaeus monodon caspase1 (Accession no. AEW91437); Mjcasp3, Marsupenaeus japonicus caspase3 (Accession no. ABK62771); Pmcasp2, Penaeus monodon caspase2 (Accession no. ABO38430); Hscasp1, Homo sapiens caspase1 (Accession no. NP_001214); Mmcasp1, Mus musculus caspase1 (Accession no. NP_033937); Hscasp2, H. sapiens caspase2 (Accession no. AAH02427); Mmcasp2, M. musculus caspase2 (Accession no. NP_031636); Hscasp3, H. sapiens caspase3 (Accession no. NP_116786); Mmcasp3, M. musculus caspase3 (Accession no. NP_033940); Hscasp4, H. sapiens caspase4 (Accession no. NP_001216); Hscasp5, H. sapiens caspase5 (Accession no. NP_001129584); Hscasp6, H. sapiens caspase6 (Accession no. NP_001217); Hscasp7, H. sapiens caspase7 (Accession no. NP_001253987); Mmcasp7, M. musculus caspase7 (Accession no. NP_031637); Hscasp8, H. sapiens caspase8 (Accession no. NP_001073594); Hscas9, H. sapiens caspase9 (Accession no. NP_127463); Hscasp10, H. sapiens caspase10 (Accession no. AAD28403); Hscasp14, H. sapiens caspase14 (Accession no. NP_036246); DmIce, Drosophila melanogaster Ice (Accession no. NP_524551); Dmcasp1, D. melanogaster caspase1 (Accession no. AAB58237); Dmdream, D. melanogaster dream (Accession no. NP_610193); Dmdeath, D. melanogaster death executioner caspase (Accession no. NP_477462); DmNedd2, D. melanogaster Nedd2 (Accession no. NP_524017); Drcasp1, D. rerio caspase1 (Accession no. NP_571580); Drcasp2, D. rerio caspase2 (Accession no. NP_001036160); Drcasp3, D. rerio caspase3 (Accession no. NP_571952); Drcasp6, Danio rerio caspase6 (Accession no. NP_001018333); Drcasp7, D. rerio caspase7 (Accession no. NP_001018443); Drcasp7-2, D. rerio caspase7 like (Accession no. XP_002667104); Drcasp8, D. rerio caspase8 (Accession no. NP_571585); Drcasp9, D. rerio caspase9 (Accession no. NP_001007405); Ggcasp1, Gallus gallus caspase1 (Accession no. XP_003642432); Ggcasp2, G. gallus caspase2 (Accession no. NP_001161173); Ggcasp3, G. gallus caspase3 (Accession no. NP_990056); Ggcasp6, G. gallus caspase6 (Accession no. NP_990057); Ggcasp7, G. gallus caspase7 (Accession no. XP_421764); Ggcasp8, G. gallus caspase8 (Accession no. NP_989923); Ggcasp9, G. gallus caspase9 (Accession no. XP_424580); Ggcasp10, G. gallus caspase10 (Accession no. XP_421936); Ggcasp18, G. gallus caspase18 (Accession no. NP_001038154); Xlcasp1, X. laevis caspase1 (Accession no. NP_001081223); Xlcasp2, X. laevis caspase2 (Accession no. NP_001081404); Xlcasp3, Xenopus laevis caspase3 (Accession no. NP_001081225); Xlcasp7, X. laevis caspase7 (Accession no. NP_001081408); Xlcasp6, X. laevis caspase6 (Accession no. NP_001081406); Xlcasp8, X. laevis caspase8 (Accession no. NP_001079034); Xlcasp9, X. laevis caspase9 (Accession no. NP_001079035); Xlcasp10, X. laevis caspase10 (Accession no. NP_001081410); CeCED3, Caenorhabditis elegans CED3 (Accession no. NP_001255708); CeCSP1, C. elegans CSP1 (Accession no. NP_001022452); CeCSP2, C. elegans CSP2 (Accession no. NP_001023575).(TIF)Click here for additional data file."} +{"text": "S/GSK1349572, a next-generation HIV-1 integrase inhibitor, has previously demonstrated potent antiviral activity in Phase 2a with once-daily, unboosted dosing. SPRING-1 is an ongoing dose-ranging study designed to select a dose to for Phase 3 evaluation.SPRING-1 is a Phase 2b, multicentre, partially-blinded study in therapy-na\u00efve adults, randomized 1:1:1:1 to 10mg, 25mg or 50mg of S/GSK1349572 or efavirenz(EFV) 600mg once-daily with either co-formulated TDF/FTC or ABC/3TC.205 subjects received study drug: 86% male, 20% non-white, 26%>100,000c/mL HIV-1 RNA, 67% TDF/FTC. Plasma HIV-1 RNA declined rapidly across all S/GSK1349572 doses with no differences in NRTI subgroups. Three protocol-defined virologic failures occurred, 1 on EFV (<1log10 decline by Week 4), and 2 on S/GSK1349572 (Week 4 and 24 rebound >400c/mL with no INI mutation detected). No dose-related clinical or laboratory toxicities were observed. More drug-related AEs of moderate-or-higher intensity were reported on EFV (20%) than S/GSK1349572 (6%) arms; none occurred in more than 1 S/GSK1349572 subject. The most frequent category of such events reported by subjects receiving EFV and S/GSK1349572 were gastrointestinal ; other frequent events on EFV were psychiatric (6%) and rash (4%) disorders. No SAE was considered related to S/GSK1349572. Six subjects (2: S/GSK1349572 and 4: EFV) withdrew due to AEs. Mean change from baseline in LDL cholesterol was +0.023mmol/L among S/GSK1349572 subjects and +0.468mmol/L among EFV subjects. S/GSK1349572 demonstrated low pharmacokinetic variability and drug exposure increased with dose. Table 1S/GSK1349572 administered once-daily without a PK booster was well tolerated with potent antiviral activity at all doses explored in SPRING-1. The greater CD4+ cell increases on S/GSK1349572 merit further observation and confirmation."} +{"text": "Dear Editor,Escherichia coli O157 and Shigella dysenteriae, in children (E. coli serotypes (i.e. O104:H4). Thrombotic thrombocytopenic purpura (TTP) a closely related syndrome occurs more frequently in adults with more prominent neurological disorders (The hemolytic-uremic syndrome (HUS) is a serious disorder of microangiopathic hemolytic anemia, thrombocytopenia, and acute renal failure that is frequently associated with Shiga toxins produced in enteric infections by isorders . Both ofisorders . Most pa i.e. O10:H4. ThroE. coli but the strain was not specified. Ultrasound examinations showed right and left kidney dimensions were 91 and 100 mm with bilateral multiple cysts. Intravenous antibiotic therapy with ciprofloxacin and imipenem was started. Patient\u2019s general condition significantly improved and fever subsided. Platelet count dropped to 88000/\u00b5L at the third day of treatment and then dropped to 7000/\u00b5L at the sixth day of antibiotic therapy. The following laboratory data were detected; serum lactic dehydrogenase (LDH): 1150 IU/L, hemoglobin: 7.5 mg/dL, WBC: 11000/\u00b5L, reticulocyte count: 4 (0.2-2/per high power field), total serum bilirubin: 2.3 mg/dL, direct billirubin; 0.5 mg/dL and serum creatinine rose to 6.2 mg/dL, D-dimer test was negative, serum ADAMTS 13 activity was 47%. Pipheral blood smear was positive for fragmented RBC (schistocyte). With the primary diagnosis of TMA, plasma exchange with fresh frozen plasma was started (1.5 L/d). After four days, platelet count rose to 105000/\u00b5L, LDH dropped to 580 U/L, and serum creatinine level returned to 4.0 mg/dL. During all those therapeutic periods, intensive antibiotic therapy was also continued in parallel with plasma exchange.A 65-year old woman was admitted to our nephrology unit with malaise, fever and left flank pain. Her oral temperature was 39\u00b0C, pulse rate was 100 per minute, and blood pressure was 120/70 mmHg. Initial laboratory tests revealed leukocytosis 31000/\u00b5L, serum creatinin: 4.7 mg/dL, hemoglobin: 9.4 mg/dL, MCV: 88 fL (80-99), MCH: 27 pg (27-31), MCHC: 31 (32-36), cholesterol: 124 mg/dL, triglyceride: 232 mg/dL, platelet count: 246000/\u00b5L, serum calcium: 8.6 mg/dL, serum phosphor: 6.3 mg/dL, i-PTH: 768 pg/mL, plasma Na: 142 meq/L, plasma k: 4.9 meq/L, AST: 11 (0-31 IU/L), ALT: 10 (0-41 IU/L), alkaline phosphatase: 326 (64-306 U/L), serum iron: 26 (40-165 \u00b5g/dL), TIBC: 247 (250-450 IU/L), and serum ferritin was 180 . Urinalysis showed numerous white and red blood cells (RBC), without any dysmorphic RBC. Serum protein electrophoresis result was negative for paraproteinemia. Blood culture was positive for E. coli bacteremia. However this should not discourage the administration of appropriate antimicrobial agents in this situation, as it may lead to death (Antibiotic therapy could increase the risk of full-blown HUS in children with STEC enteric infection . We obseto death . We foun"} +{"text": "Orientia tsutsugamushi, is an endemic disease in Taiwan and may be potentially fatal if diagnosis is delayed.Scrub typhus, a mite-transmitted zoonosis caused by We encountered a 23-year-old previously healthy Taiwanese male soldier presenting with the right ear pain after training in the jungle and an eleven-day history of intermittent high fever up to 39\u00b0C. Amoxicillin/clavulanate was prescribed for otitis media at a local clinic. Skin rash over whole body and abdominal cramping pain with watery diarrhea appeared on the sixth day of fever. He was referred due to progressive dyspnea and cough for 4 days prior to admission in our institution. On physical examination, there were cardiopulmonary distress, icteric sclera, an eschar in the right external auditory canal and bilateral basal rales. Laboratory evaluation revealed thrombocytopenia, elevation of liver function and acute renal failure. Chest x-ray revealed bilateral diffuse infiltration. Doxycycline was prescribed for scrub typhus with acute respiratory distress syndrome and multiple organ failure. Fever subsided dramatically the next day and he was discharged on day 7 with oral tetracycline for 7 days.Scrub typhus should be considered in acutely febrile patients with multiple organ involvement, particularly if there is an eschar or a history of environmental exposure in endemic areas. Rapid and accurate diagnosis, timely administration of antibiotics and intensive supportive care are necessary to decrease mortality of serious complications of scrub typhus. Orientia tsutsugamushi, is an endemic disease in Taiwan and may be potentially fatal if diagnosis is delayed. It is an acute febrile illness characterized by a typical necrotic primary lesion (eschar), generalized lymphadenopathy, maculopapular skin rash, and nonspecific symptoms and signs. The incidence of eschar reported in patients with scrub typhus is low, < 25%, and only 5% are found over head, face and neck. An eschar in the external auditory canal has not been reported previously, so the diagnosis of scrub typhus was delayed with serious complications, including acute respiratory distress syndrome (ARDS) and multiple organ failure (MOF). In patients with scrub typhus, the incidence and mortality rate of ARDS are 11.1%-15.2% and 20%-25%, respectively. Reported here is a case of an eschar in the external auditory canal in scrub typhus complicated by ARDS and MOF in a 23-year-old previously healthy Taiwanese male soldier.Scrub typhus, a mite-transmitted zoonosis caused by 3 (reference range [RR]: 4000-11000/mm3) with 87.9% segmented neutrophils, hemoglobin 14.6 g/dL (RR: 14-16 g/dL), platelet counts 24 \u00d7 103/mm3 (RR: 140-400 \u00d7 103/mm3), blood urea nitrogen 25 mg/dL, creatinine 1.5 mg/dl (RR: 0.7-1.4 mg/dL), sodium 140 mEq/L, potassium 3.9 mEq/L, chloride 108 mEq/L, calcium 8.2 mg/dL, total protein 5.8 g/dL (RR: 6.0-8.0 g/dL), albumin 3 g/dL (RR: 3.5-5.0 g/dL), total bilirubin 4.8 mg/dL (RR: 0.1-1.2 mg/dL), direct bilirubin 2.7 mg/dL (RR: 0.0-0.2 mg/dL), C-reactive protein 16.23 mg/dL (RR <0.3 mg/dL), aspartate aminotransferase (AST) 368 IU/L (RR: 8-38 IU/L), alanine aminotransferase (ALT) 271 IU/L (RR: 4-44 IU/L), alkaline phosphatase (ALK) 324 IU/L (RR: 50-190 IU/L), lactate dehydrogenase 783 IU/L (RR: 120-240 IU/L), glucose 94 mg/dL, creatine phosphokinase 229 IU/L (RR: 10-160 IU/L), and a positive for Weil-Felix reaction with a Proteus OX-K titer of 1:1280 on day 11 of fever. Arterial blood gas analysis was pH 7.501, PaCO2 38.1 mmHg, PaO2 76 mmHg, HCO3- 30.1 mmol/l, and BEB 7.2 with a FiO2 of 60%. A central venous line was setup for monitoring his central venous pressure and fluid replacement because of hypotension. Chest x-ray , is a disease distributed throughout the Asia Pacific rim and endemic in South Korea, China, Japan, Taiwan, Pakistan, India, Thailand, Malaysia and northern Australia. It is an acute febrile illness characterized by a typical necrotic primary lesion (eschar), generalized lymphadenopathy, maculopapular skin rash, and nonspecific symptoms and signs such as fever, chills, headache, alerted sensorium, seizure, sorethroat, otalgia, cough, dysponea, vomiting, abdominal pain, jaundice, diarrhea, hepatosplenomegaly, abnormal bleeding, arthralgia and myalgia[Orientia tsutsugamushi [Proteus OX-K titer of 1:1280 was obtained on day 11 after exposure in our case. While all current scrub typhus tests have limitations and the Weil-Felix and immunofluorescent antibody (IFA) tests have low sensitivity and specificity[Scrub typhus, a mite-transmitted zoonosis caused by the intracellular Gram-negative bacteria, d myalgia-12. Unfod myalgia,12. Serid myalgia. In our d myalgia. Initiald myalgia. Acute rugamushi ,12. Abnougamushi ,8-10,12.ecificity,12. The ecificity,12. ScruWe recommend that scrub typhus should be taken into consideration in acutely febrile patients with varying degree of respiratory distress, impaired liver function, acute renal failure and hematologic involvement, particularly if there is an eschar or a history of environmental exposure in an endemic area-9,11,12.The authors declare that they have no competing interests.BJL took care of this patient in the intensive care units. CYC drew up the first draft of the report. SYH made a substantial contribution to draft the manuscript and revised the draft all over the course of submission. All authors read and approved the final manuscript.Written informed consent was obtained from the patient for publication of this study. A copy of the written consent is available for review by the Editor-in-Chief of this journal.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2334/11/79/prepub"} +{"text": "Anopheles gambiae, Aedes aegypti, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus and Rhodnius prolixus. We observed that (1) disease vectors encode a lower percentage of ubiquitin-related genes when compared to Drosophila melanogaster, Mus musculus and Homo sapiens but not Saccharomyces cerevisiae; (2) overall, there are more proteins categorized as E3 ubiquitin ligases when compared to E2-conjugating or E1-activating enzymes; (3) the ubiquitin machinery within the three mosquito genomes is highly similar; (4) ubiquitin genes are more than doubled in the Chagas disease vector (R. prolixus) when compared to other arthropod vectors; (5) the deer tick I. scapularis and the body louse (P. humanus) genomes carry low numbers of E1-activating enzymes and HECT-type E3 ubiquitin ligases; (6) R. prolixus have low numbers of RING-type E3 ubiquitin ligases; and (7) C. quinquefasciatus present elevated numbers of predicted F-box E3 ubiquitin ligases, JAB and UCH deubiquitinases. Taken together, these findings provide novel opportunities to study the interaction between a pathogen and an arthropod vector. Protein regulation by ubiquitin has been extensively described in model organisms. However, characterization of the ubiquitin machinery in disease vectors remains mostly unknown. This fundamental gap in knowledge presents a concern because new therapeutics are needed to control vector-borne diseases, and targeting the ubiquitin machinery as a means for disease intervention has been already adopted in the clinic. In this study, we employed a bioinformatics approach to uncover the ubiquitin-mediated pathway in the genomes of Vector-borne diseases are some of the most prevalent infectious illnesses worldwide. According to the World Health Organization, there are approximately 216 million cases of malaria alone, with over 1.2 million estimated deaths . OverallUbiquitin consists of a 76 amino acid protein that carries seven lysine (K) residues . UbiquitDrosophila, it is established that developmental regulation by the evolutionarily conserved Notch receptor depends on ubiquitin [Drosophila because ubiquitination also regulates these pathways in disease vectors, such as: Anopheles gambiae, Aedes aegypti, Culex quinquefasciatus and Ixodes scapularis [In biquitin , and sombiquitin . Additiobiquitin . This imapularis .An. gambiae, Ae. aegypti, C. quinquefasciatus, I. scapularis, Pediculus humanus and Rhodnius prolixus. We compared our findings to datasets available for Saccharomyces cerevisiae, Drosophila melanogaster, Mus musculus and Homo sapiens [The lack of information regarding the role of ubiquitin in disease vectors is problematic since molecular interactions depend on this posttranslational modification. These biochemical signatures may lead to novel factors to control pathogen transmission and/or acquisition . For ins sapiens -13. Whil sapiens ,15, tran sapiens ,16-19 an sapiens ,20,21, iI. scapularis, An. gambiae, Ae. aegypti, C. quinquefasciatus, P. humanus and R. prolixus were downloaded from VectorBase [S. cerevisiae, D. melanogaster, H. sapiens and M. musculus were downloaded from http://www.yeastgenome.org [Complete protein datasets encoded within the genomes of ctorBase . Proteinnome.org , http://nome.org , and httnome.org , respectnome.org , and downome.org . This in<0.5. Importantly, observed discrepancies between our results and findings previously published for S. cerevisiae, D. melanogaster, H. sapiens and M. musculus [Using the selected Pfam domains, the hmmsearch program of the HMMER v3.0 package was emplmusculus -13 were I. scapularis, An.gambiae, Ae. aegypti, and C. quinquefasciatus were aligned using the Multiple Sequence Alignment tool MUSCLE [ The resulting protein sequences from l MUSCLE availabll MUSCLE . The ful For each aligned dataset, protein phylogenies were estimated with the maximum likelihood method, employing the PhyML program availabl-like modifier (SUMO), neural precursor cell expressed developmentally downregulated gene 8 (NEDD8), autophagy-related protein 8 (ATG8), ubiquitin-related modifier-1 (URM1), homologous to ubiquitin 1 (HUB1), E1s (ubiquitin-activating enzyme 1 (UBA1), UBA2, UBA3, UBA1-like, autophagy-related E1-like enzyme (ATG7)), really interesting new gene (RING) , other E3s (homology to E6AP C-terminus (HECT), Cullin, U-box), and DUBs (ovarian tumor (OTU), Josephin, jun activation domain-binding protein (JAB), domain of unknown function (DUF) 862, Wss1p\u2010like metalloproteases (WLM), ubiquitin carboxyl-terminal hydrolase (UCH), Peptidase_C12, Peptidase_C48, and Peptidase_C54). For direct classification of ubiquitin-like proteins, we manually analyzed and categorized each protein encoded in the genomes of An. gambiae, Ae. aegypti, C. quinquefasciatus, and I. scapularis. Ubiquitin-like proteins analyzed were SUMO, URM1, NEDD8, HUB1 and ATG8. Proteins containing two or more Pfam domains were observed and recorded in Protein sequences belonging to specific subcategories of the five ubiquitination-components , ubiquitin-conjugating enzymes (E2), ubiquitin ligases (E3) and deubiquitinases) were identified based on the Pfam domain matches obtained from hmmsearch. Whenever possible, proteins were cataloged according to their major branching patterns in their respective phylogenies: ubiquitin/ubiquitin-like proteins , while P. humanus had the highest ratio at 3.13. R. prolixus had a %U of 2.25. When compared to four model species, all disease vectors possessed a much lower %U, with the model species ranging from 4.38 to 5.02. The exception was S. cerevisiae (%U = 2.24). Interestingly, D. melanogaster carried a much higher %U at 4.50. The ubiquitin machinery regulates fundamental biological processes within eukaryotic cells . Thus, wI. scapularis (31), An.gambiae (40), Ae. aegypti (48), C. quinquefasciatus (40), P. humanus (35) and R. prolixus (129) (S. cerevisiae (7), D. melanogaster (30), H. sapiens (45) and M. musculus (41). Apart from S. cerevisiae (7) and R. prolixus (129), our analysis revealed a similar number of ubiquitin proteins across species. We further analyzed sequence similarities among ubiquitin family members for An. gambiae, Ae. aegypti, C. quinquefasciatus, and I. scapularis from their multiple alignments . We alsoignments . An. gambiae, Ae. aegypti, C. quinquefasciatus, and I. scapularis ( Ubiquitin-like proteins were first discovered in 1979 and named after the interferon-stimulated gene 15 (ISG15) . Since iapularis . UbiquitAn. gambiae (2), Ae. aegypti (2), C. quinquefasciatus (1), and I. scapularis (1) . NEDD8 ih vector .An. gambiae, Ae. aegypti, C. quinquefasciatus, and I. scapularis , Ae. aegypti (2), C. quinquefasciatus (3), and I. scapularis (3) (URM1 is a ubiquitin-like protein that shares very little homology with ubiquitin . Four prapularis . HUB1 dih vector . ATG8 isaris (3) . I. scapularis (16), An. gambiae (29), Ae. aegypti (37), C. quinquefasciatus (30), P. humanus (19) and R. prolixus (26) have a very similar number of E1 proteins, while I. scapularis and P. humanus have noticeably less E1s than the other disease vectors. We also analyzed the E1 number in S. cerevisiae (8), D. melanogaster (30), H. sapiens (42), and M. musculus (25) domain. The E1 associated to ubiquitin is known as UBA1. UBA2 and UBA3 serve as activators for SUMO and NEDD8 respectively . The E1 xus (26) . The thrlus (25) . We furttimation . I. scapularis (32), An. gambiae (32), Ae. aegypti (36), C. quinquefasciatus (28), P. humanus (29) and R. prolixus (31) . The numapularis . I. scapularis (151), An.gambiae (147), Ae. aegypti (161), C. quinquefasciatus (156), P. humanus (127) and R. prolixus (86) (3HisCys4. The zf-C3HC4 subcategory was the most common RING-type ligase within selected vectors: I. scapularis (100), An. gambiae (82), Ae. aegypti (84), C. quinquefasciatus (87), P. humanus (80) and R. prolixus (56) . The numxus (56) -7. I. scapularis (28), An.gambiae (42), Ae. aegypti (43), C. quinquefasciatus (47), P. humanus (31) and R. prolixus (19) (I. scapularis (17), An. gambiae (12), Ae. aegypti (22), C. quinquefasciatus (12), P. humanus (16) and R. prolixus (11) (2HC2 motif and plays a role in DNA replication [I. scapularis (6), An. gambiae (11), Ae. aegypti (12), C. quinquefasciatus (10), P. humanus (6) and R. prolixus (8) (We report the number of zf-Apc11 proteins in xus (19) -7. RINGvxus (11) -7. Rtf2 lication . We analixus (8) -7. It isixus (8) .An. gambiae, Ae. aegypti, C. quinquefasciatus, and I. scapularis by phylogeny estimation , An. gambiae (17), Ae. aegypti (17), C. quinquefasciatus (23), P. humanus (14) and R. prolixus (16) . The numtimation . I. scapularis (5), An.gambiae (6), Ae. aegypti (9), C. quinquefasciatus (4), P. humanus (7) and R. prolixus (8) (S. cerevisiae (4), D. melanogaster (14), H. sapiens (16), and M. musculus (11) . The numlus (11) . We then ligases . SimilarI. scapularis (8), An.gambiae (10), Ae. aegypti (10), C. quinquefasciatus (12), P. humanus (7) and R. prolixus (8) . Much liixus (8) . I. scapularis (43), An. gambiae (39), Ae. aegypti (49), C. quinquefasciatus (151), P. humanus (32) and R. prolixus (39) , D. melanogaster (46), H. sapiens (111), and M. musculus (104) . We then species . I. scapularis (7), An. gambiae (9), Ae. aegypti (9), C. quinquefasciatus (9), P. humanus (7), R. prolixus (6), S. cerevisiae (2), D. melanogaster (12), H. sapiens (21), and M. musculus (18) . In mostapularis , S10. I. scapularis (2), An. gambiae (1), Ae. aegypti (1), C. quinquefasciatus (2), P. humanus (2), R. prolixus (2), S. cerevisiae (0), D. melanogaster (1), H. sapiens (13), and M. musculus (10) , a neurodegenerative condition . We repolus (10) . All selapularis . I. scapularis (12), An. gambiae (10), Ae. aegypti (11), C. quinquefasciatus (18), P. humanus (10) and R. prolixus (8) DUBs . This spixus (8) . Proteinapularis . I. scapularis (3), An.gambiae (1), Ae. aegypti (2), C. quinquefasciatus (3), P. humanus (2) and R. prolixus (11) . The numlogenies . I. scapularis (2), An. gambiae (2), Ae. aegypti (0), C. quinquefasciatus (1), P. humanus (0), and R. prolixus (0) . I. scapularis (25), An. gambiae (29), Ae. aegypti (28), C. quinquefasciatus (34), P. humanus (26) and R. prolixus (29) , Ae. aegypti (6), C. quinquefasciatus (8), and I. scapularis (5). ( DUBs containing the UCH domain have been known to release ubiquitin in polyubiquitin chains by hydrolyzing its C-terminus . We perfxus (29) . UCH-assris (5). . I. scapularis , An. gambiae , Ae. aegypti , C. quinquefasciatus , P. humanus , R. prolixus , S. cerevisiae , D. melanogaster , H. sapiens , and M. musculus protease family ,52. Pept_C54: 5) . In mosth vector . Vector-borne illnesses threaten public health in the tropics. Environmental changes due to globalization and the lack of effective vaccines are also contributing to the spread of these maladies to temperate climates. Thus, novel treatments are necessary in the clinic. One effective therapeutic strategy recently used to treat cancer, neurodegenerative disorders and some infectious diseases is pharmacological intervention targeting (de)ubiquitination. However, the use of (de)ubiquitination as a therapeutic target to combat arthropod-borne diseases has not been established. A possible reason for this gap in translational research is the inherent complexity of vector-borne diseases. Another possibility is the lack of communication among scientists. Pharmacologists and chemists do not typically interact with vector biologists, and vector biologists have little incentive to interact with the drug development community. An. gambiae, Ae. aegypti, C. quinquefasciatus, I. scapularis, P. humanus and R. prolixus. Although independent work will be necessary to validate our bioinformatics analysis, empirical evidence suggests that the ubiquitin machinery is present in disease vectors. Recently, Severo et al., 2013 characterized a RING-type E3 ubiquitin ligase named x-linked inhibitor of apoptosis protein (XIAP) and showed the importance of ubiquitination for microbial pathogenesis in ticks [Here we took advantage of publicly available arthropod genomes and described the ubiquitin machinery of in ticks . Similarin ticks . Corroboin ticks . In summTable S1Source and release date of protein datasets.(PDF)Click here for additional data file.Table S2An.List of proteins in gambiae identified by the HMM search.(XLSX)Click here for additional data file.Table S3Ae. aegypti identified by the HMM search.List of proteins in (XLSX)Click here for additional data file.Table S4C. quinquefasciatus identified by the HMM search.List of proteins in (XLSX)Click here for additional data file.Table S5I. scapularis identified by the HMM search.List of proteins in (XLSX)Click here for additional data file.Table S6P. humanus identified by the HMM search.List of proteins in (XLSX)Click here for additional data file.Table S7R. prolixus identified by the HMM search.List of proteins in (XLSX)Click here for additional data file.Table S8D. melanogaster identified by the HMM search.List of proteins in (XLSX)Click here for additional data file.Table S9H. sapiens identified by the HMM search.List of proteins in (XLSX)Click here for additional data file.Table S10M. musculus identified by the HMM search.List of proteins in (XLSX)Click here for additional data file.Table S11List of protein identifications containing sequences matching two or more Pfam domains.(XLSX)Click here for additional data file.Figure S1I. scapularis, An.Ubiquitin and ubiquitin-like proteins in gambiae, Ae. aegypti, and C. quinquefasciatus. Protein sequences matched with ubiquitin and ubiquitin-like proteins were aligned using MUSCLE and a phylogeny was estimated with the PhyML software. Sequences with a bootstrap value lower than 50 were manually removed. Bootstrap values ranged from 0.64 - 0.86 for highlighted clustered categories . (TIF)Click here for additional data file.Figure S2I. scapularis, An.Ubiquitin and ubiquitin-like activating enzymes in gambiae, Ae. aegypti, and C. quinquefasciatus. Phylogeny of ubiquitin and ubiquitin-like activating enzymes. Matched sequences for ubiquitin and ubiquitin-like activating enzymes were aligned using MUSCLE and a phylogeny was estimated with the PhyML software. Bootstrap values ranged from 0.43 - 0.83 for highlighted clustered categories .(TIF)Click here for additional data file.Figure S3I. scapularis, An.Ubiquitin and ubiquitin-like conjugating enzymes in gambiae, Ae. aegypti, and C. quinquefasciatus. Protein sequences matched with ubiquitin and ubiquitin-like conjugating enzymes were aligned using MUSCLE and a phylogeny was estimated with the PhyML software. (TIF)Click here for additional data file.Figure S4An.Phylogeny of RING and RING-like ubiquitin ligases in gambiae and Ae. aegypti. Protein sequences matched with ubiquitin and ubiquitin-like ligases were aligned using MUSCLE and a phylogeny was estimated with the PhyML software. Proteins not listed under a specific subset were categorized as zf-C3HC4. Phylogeny of RING and RING-like ubiquitin ligases in (A) An. gambiae and (B) Ae. aegypti. Bootstrap values ranged from (A) 0.41 - 0.80 and (B) 0.41 - 0.83 for highlighted clustered categories .(TIF)Click here for additional data file.Figure S5C. quinquefasciatus and I. scapularis.Phylogeny of RING and RING-like ubiquitin ligases in Protein sequences matched with ubiquitin and ubiquitin-like ligases were aligned using MUSCLE and a phylogeny was estimated with the PhyML software. Proteins not listed under a specific subset were categorized into the zf-C3HC4 classification. Phylogeny of RING and RING-like ubiquitin ligases in (A) C. quinquefasciatus and (B) I. scapularis. Bootstrap values ranged from (A) 0.43 - 0.83 and (B) 0.46 - 0.83 for highlighted clustered categories .(TIF)Click here for additional data file.Figure S6I. scapularis, An.HECT, Cullin and U-box ligases in gambiae, Ae. aegypti, and C. quinquefasciatus. Protein sequences matched with ubiquitin and ubiquitin-like ligases were aligned using MUSCLE and the phylogeny was estimated with the PhyML software. Sequences with bootstrap values lower than 50 were manually removed. Bootstrap values ranged from 0.35 - 0.88 for highlighted clustered categories .(TIF)Click here for additional data file.Figure S7An.Phylogenetic trees of F-box ubiquitin ligases in gambiae and Ae. aegypti. Protein sequences matched with F-box ligases were aligned using MUSCLE and the phylogeny was estimated with the PhyML software. Sequences with a bootstrap values lower than 50 were manually removed. Phylogenetic trees of F-box ubiquitin ligases in (A) An. gambiae and (B) Ae. aegypti. (TIF)Click here for additional data file.Figure S8C. quinquefasciatus and I. scapularis.Phylogenetic trees of F-box ubiquitin ligases in Protein sequences matched with F-box ligases were aligned using MUSCLE and the phylogeny was estimated with the PhyML software. Sequences with a bootstrap values lower than 50 were manually removed. Phylogenetic trees of F-box ubiquitin ligases in (A) C. quinquefasciatus and (B) I. scapularis. (TIF)Click here for additional data file.Figure S9An.Phylogenetic trees of deubiquitinases in gambiae and Ae. aegypti. Protein sequences were aligned using MUSCLE and a phylogeny was estimated using the maximum likelihood method. Phylogeny of deubiquitinases in (A) An. gambiae and (B) Ae. aegypti. Bootstrap values ranged from (A) 0.43 - 0.87 and (B) 0.37 - 0.84 for highlighted clustered categories .(TIF)Click here for additional data file.Figure S10C. quinquefasciatus and I. scapularis.Phylogenetic trees of deubiquitinases in Protein sequences were aligned using MUSCLE and a phylogeny was estimated using the maximum likelihood method. Phylogeny of deubiquitinases in (A) C. quinquefasciatus and (B) I. scapularis. Bootstrap values ranged from (A) 0.39 - 0.83 and (B) 0.37 - 0.78 for highlighted clustered categories .(TIF)Click here for additional data file."} +{"text": "Candida species play an important complications in severely-ill hospitalized patients which may lead to therapeutic failure. During a 5-year period from 2006-2010, 7 Candida species and 14 unidentified strains were identified from 887 candidaemia of patients admitted at Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.Bloodstream infections due to Candida species were identified according to characteristics of chlamydoconidia production and carbohydrate assimilation/fermentation profile using 13/6 carbon substrates. Only a limited number of Candida were tested for antifungal susceptibility by agar gradient diffusion (Etest\u00ae)to amphotericin B and fluconazole.Candida albicans remains a major pathogen accounted for 50.3%, followed by C. tropicalis(27.4%), C. parapsilosis (12.5%), C.guilliermondii (6%), C. glabrata (1.8%), C. krusei (0.23%), C. rugosa (0.23%), and unidentified species(1.6%). From a total of 103 C. albicans, amphotericin B MIC ranged from 0.016-1ug/ml whereas fluconazole MIC ranged were between 0.023 to > 256ug/ml. Other species tested were C. tropicalis (73 strains) which yielded MIC range of 0.19-2ug/ml for amphotericin B and 0.5->256 ug/ml for fluconazole. 34 strains of C. parapsilosis gave amphotericin B ranged from 0.023-16ug/ml and 0.094->256 for fluconazole.From a total of 887 isolates, C. albicans remains the most prevalence Candida species causing candidaemia followed by C. tropicalis, C. parapsilosis and C. guilliermondii. Those non-albicans Candida seemed to express decrease susceptibility to both major antifungal agents like amphotericin B and fluconazole whereas a small number of C. albicans gave high MIC to fluconazole.None declared."} +{"text": "Stress perfusion (SP) abnormalities predict prognosis in specific subsets of patients with coronary artery disease (CAD). However, results are more controversial in populations with stable CAD. We tried to assess prognostic value of SP cardiac magnetic resonance (CMR) in unselected patients with chronic CAD, beyond conventional risk factors such as left ventricle ejection fraction (LVEF).We considered consecutive patients undergoing CMR for definite/suspected chronic CAD. CMR included first-pass myocardial perfusion assessment after dipyridamole stress (0.56 mg/kg) and late gadolinium enhancement (LGE). CMR images were semi-quantitatively evaluated by two blinded operators. SP-CMR was judged positive if a perfusion defect \u2265 75% of myocardium wall thickness was detected in areas of myocardium without LGE. We also collected clinical and pharmacological history, atherosclerotic risk factors, ECG end Echocardiography data. Events in the follow-up , were recorded with outpatient/inpatient visits or with structured telephonic interviews. Univariate and multivariate Cox hazard analyses were performed, with continuous variables categorized according to cut-offs from the literature.We recruited 374 patients , between January 2002 and December 2006. During a follow-up period of 38\u00b121 months there were 30 deaths (8%). Moreover, 79 patients (21%) underwent revascularization procedures. Univariate analysis showed an association between SP-CMR and mortality . Stronger predictors of death were LVEF (19.1 [6.5-55.7]), LVWMSI (13.2 [4.6-38.2]), LVESV (13.1 [4.9-35.3]), LVEDV (9.2 [3.5-24.6]), LGE (8.3 [3.5-19.5]), anticoagulant (6.3 [2.7-14.3]), QTc interval (5.9 [2.9-12.2]) and loop diuretics . A significant univariate association was also found with LV diastolic function (4.4 [1.9-9.9]), aldosterone antagonist (4.2 [1.9-9.0]) and QRS duration (3.8 [1.8-7.9]). At multivariate analysis SP-CMR was found to be no more significant and independent predictors of death were only LVEF , QTc interval , non-sinusal rhythm and LGE .A positive SP-CMR was the strongest predictor of non-CMR related revascularization procedures, at univariate as well as at multivariate analysis . Other independent predictors of revascularization need in the follow-up were only diabetes and smoking habit .Our study showed lack of independent association between stress induced perfusion defects at CMR and mortality in a large group of unselected patients with stable CAD. Conversely, stress CMR was the strongest predictor of subsequent revascularization procedures unrelated to CMR itself."} +{"text": "This study aimed at assessing left ventricular (LV), left atrial (LA) and right ventricular (RV) volumes in patients before and after MitraClip\u2122 implantation by cardiac magnetic resonance imaging (CMR).The MitraClip\u2122 is a novel device for percutaneous mitral valve repair. Recent studies demonstrated a reduction of LV volumes after MitraClip\u2122 implantation using echocardiography. CMR is currently the reference method to assess cardiac volumes but has not been used to assess LV remodeling after MitraClip\u2122 implantation so far.Twelve patients with functional (n=7) or degenerative (n=5) mitral valve regurgitation grade 3 to 4 underwent CMR at baseline (BL) before and at 6 month follow-up (FU) after successful MitraClip\u2122 implantation. CMR protocol consisted of short- and long-axis slices using a steady-state-free-precession cine sequence for the assessment of LV, LA and RV volumes.2; p=0.03) as well as LVESV (82 (54-91) vs. 69 (48-99) ml/m2; p=0.03) indices significantly decreased from BL to FU. No significant difference was found for RVEDV (94 (75-103) vs. 99 (77-123) ml/m2; p=0.91), RVESV (48 (42-80) vs. 51 (40-81) ml/m2; p=0.48) and LAV (87 (55-124) vs. 92 (48-137) ml/m2; p=0.20) indices between BL and FU.Minor device-related artifacts were observed, enabling reliable delineation of endocardial borders in all patients at FU. Figure CMR enables reproducible measurements of cardiac volumes in patients with implanted MitraClip\u2122 devices. Significantly decreased LV but unchanged LA and RV volumes were found at 6 month after successful MitraClip\u2122 implantation.No external funding."} +{"text": "There was an error in the second author's name. The correct spelling is Sudhakar Agnihothram. The correct citation is: Varshney B, Agnihothram S, Tan Y-J, Baric R, Lal SK (2012) SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b. PLoS ONE 7(1): e29542."} +{"text": "DAI are a serious public health problem worldwide. The PC and optimization of the HHA have proven to be excellent tools for DAI minimization or elimination.Assess the impact of PC and HHA on DAI in our AICU.A quasi-experimental study. We calculated the average rates of DAI using NHSN,CDC methodology in two periods:pre (Pa) and post intervention (Pb). Average rates wereexpressed as number of events per 1000 device days (DD). Study periods: ventilator associated pneumonia (VAP) Pa: January 2004-January 2010, Pb: February 2010-February 2013. Catheter-associated bacteremia (BACT) Pa: January 2004-June 2010, Pb: July 2010-February 2013. Catheter-associated urinary tract infection (UTI) Pa: January 2007-October 2011Pb: November 2011-February 2013. The Institute of Healthcare Improvement (IHI) proposed PC were implemented. PC adherence was assessed periodically. In October 2009, WHO campaign to improve HHA was implemented. Periodic measurements of HHA were performed. Statistical analysis: we compared average rates of HAI in both periods with Mann-Whitney test. We calculated the Incidence Rate Ratio (IRR) as Pb average incidence rate/Pa average incidence rate.NEU rate decreased from 9.88 (Pa) to 2.60 (Pb), P <0.001. IRR 0.26, 74% rate reduction. Attributable risk: 7.28/ 1000 DD. Cases avoided in Pb: 33.4 (4589 DD in three years). BACT rate decreased from 5.35 (Pa) to 2.34 (Pb), p 0.007. IRR: 0.44, 56% rate reduction. Attributable risk: 3.01/ 1000 DD. Cases avoided in Pb: 14.99 (4983 DD in 32 months). ITU rate decreased from 2.45 (Pa) to 1.30 (Pb), P 0.32. IRR: 0.53, 47% rate reduction. Attributable risk: 1.15/ 1000 DD. Cases avoided in Pb: 3.34 (2908 DD in 16 months). Adherence to PC and HHA ranged between 80 and 95%.PC implementation and HHA optimization in our AICU was associated with statistically significant decreases in VAP and BACT rates, and similar tendency of UTI rate. The significant number of cases averted, fully justifies the implementation of these tools.None declared."} +{"text": "Once daily ritonavir-boosted darunavir (DRV/RTV) is a preferred antiretroviral regimen for treatment-na\u00efve patients. The pharmacokinetics (PK) of DRV/RTV may be influenced by patient demographics and co-medications. Also with an increased aging HIV population, investigations into the impact of older age on PK are important.0-24) and baseline CD4 cell count were 39yr (21-63), 74kg (57-105), 24kg/m2 (18-31), 4.35mg.h/L (2.27-10.99) and 500cells/mm3 (227-1129), respectively; 49 patients had undetectable viral load at time of study. PK sampling was performed at steady-state and between 1-3 PK curves were available per patient. Nonlinear mixed effects modelling (NONMEM v. VI 2.0) was applied to determine DRV PK parameters, interindividual and interoccasion variability and residual error. The following covariates were evaluated: age, weight, BMI, sex, ethnicity, RTV AUC0-24 and raltegravir co-medication (400mg twice daily). The model was validated by means of simulation and visual predictive check.Data were pooled from 3 DRV/RTV PK studies. In total 51 HIV-infected patients stable on DRV/RTV were included. Median age, weight, BMI, RTV area under the curve over 24h (AUCa 0.914h-1) and lag-time (0.358h) best described the data. Inclusion of a different apparent oral clearance (CL/F) and volume of distribution (V2/F) for one of the studies improved the fit . RTV AUC0-24 and age were significantly associated with DRV CL/F. An increase in age of 1yr produced a fractional decrease in DRV CL/F of 0.014, equivalent to a 14% reduction in CL/F with every 10yr increase in age. Based on the visual predictive check 94% of observed DRV concentrations were within the 95% prediction interval, indicative of an adequate model.A 2-compartment model with first-order absorption (k0-24 and age were significantly related to DRV CL/F. The impact of age requires further investigation and clarification over a wide age range, particularly in an elderly population.A population model describing the PK of once daily RTV-boosted DRV has been developed and validated. RTV AUC"} +{"text": "Tocilizumab (TCZ), an IL-6 receptor inhibitor, improves arthritis and systemic symptoms associated with systemic JIA. It may be a valuable option in patients with JIA who show inadequate response to anti-TNF agents.To analyze the short-term effectiveness and safety of TCZ in patients with JIA refractory to anti-TNF agents.All patients who received TCZ due to refractory disease were included. All patients had exhibited anti-TNF primary or secondary failure. Data were retrieved from the Rheumatology Section data base. TCZ was administered intravenously at a dose of 8 mg/kg for patients > 30 Kg, 12 mg/Kg for patients < 30 Kg every 2 weeks. Efficacy endpoints included improvement (ACR Pedi30), disappearance of systemic symptoms, and reduction in corticosteroid dose.9 patients with JIA were included. Median age at study entry was 10 years, disease duration 6 years. They received TCZ for 3 to 9 months. Patients had been refractory to etanercept (9), adalimumab (7) or infliximab (2). At baseline (medians): active joints: 11, joints with limited motion: 4, wellbeing (0-3): 0.1, disease activity (0-3): 0.45, ESR: 35 mm/h; CHAQ > 0.5 3 patients, fever/rash 1 patient. Six patients were receiving corticosteroids. All patients met improvement criteria, 7 before the 3rd TCZ infusion. At 1 month after TCZ therapy began: active joints: 4, joints with limited motion: 3, wellbeing: 0.05, disease activity: 0.24, ESR: 3 mm/h; CHAQ > 0.5 1 patient, fever/rash 0 patient. During the treatment, 4 patients reduced dose (< 50%) of corticosteroids. No side effects were recorded.Tocilizumab seems to be effective and safe with a rapid onset of action in children with anti-TNF refractory JIA."} +{"text": "KRAS genotype in L-L and other or multiple metastatic (O/MM) MCRC patients treated with the FIr-B/FOx regimen was retrospectively evaluated.Bevacizumab (BEV) plus triplet chemotherapy can increase efficacy of first-line treatment of metastatic colorectal cancer (MCRC), particularly integrated with secondary liver surgery in liver-limited (L-L) patients. The prognostic value of the KRAS codon 12 and 13 and BRAF mutations by SNaPshot and/or direct sequencing. Fit MCRC patients <75 years were consecutively treated with FIr-B/FOx regimen: weekly 12-h timed flat-infusion/5-fluorouracil (TFI 5-FU) 900 mg/m2, days 1, 2, 8, 9, 15, 16, 22 and 23; irinotecan (CPT-11) 160 mg/m2 plus BEV 5 mg/kg, days 1, 15; oxaliplatin (OXP) 80 mg/m2, days 8, 22; every 4 weeks. MCRC patients were classified as L-L and O/MM. Activity and efficacy were evaluated and compared using log-rank test.Tumoral and metastatic samples were screened for KRAS wild-type (53%), 28 KRAS mutant (47%). At 21.5 months median follow-up, objective response rate (ORR), progression-free survival (PFS) and overall survival (OS) were, respectively: KRAS wild-type 90%, 14 months, 38 months; KRAS mutant 67%, 11 months, 20 months. PFS and OS were not significantly different. PFS and OS were significantly different in L-L compared to O/MM evaluable patients. In KRAS wild-type patients, clinical outcome of 12 L-L compared to 18 O/MM was significantly different: PFS 21 versus 12 months and OS 47 versus 28 months, respectively. In KRAS mutant patients, the clinical outcome of 13 L-L compared to 14 O/MM was not significantly different: PFS 11 months equivalently and OS 39 versus 19 months, respectively.In all, 59 patients were evaluated: 31 KRAS genotype wild-type and mutant does not significantly affect different clinical outcomes for MCRC patients treated with the first-line FIr-B/FOx intensive regimen. KRAS wild-type patients with L-L disease may achieve a significantly prolonged clinical outcome due to integration with secondary liver surgery, with respect to KRAS mutant patients.The KRAS wild-type metastatic colorectal cancer (MCRC), reported overlapping activity and efficacy in phase III trials, ranging between objective response rate (ORR) 39% to 68%, progression-free survival (PFS) 7.2 to 10.6 months, overall survival (OS) 19.9 to 26.1 months [et al. [Triplet regimens consisting of chemotherapeutic drugs, or doublets plus bevacizumab (BEV) or cetuximab monoclonal antibody) in EGFR-overexpressing and 1 months . Phase I [et al. , proposeRAS, BRAF, PIK3CA genes, or loss of tumor suppressor function of PTEN, resulting in continuous activation of the RAS-mitogen-activated protein kinase (MAPK) or phosphoinositide 3-kinase (PI3K) pathways, characterize most colorectal cancers (CRC) [KRAS mutations represent an early event in colorectal tumorigenesis [BRAF mutations, prevalently c.1799 T>A (V600E) mutation, characterize 4.7% to 8.7% of CRC [Gain-of-function mutations of rs (CRC) -9. KRAS igenesis ,11 and oigenesis ,13, c.35igenesis , and codigenesis . They imigenesis . BRAF mu% of CRC -20.KRAS wild-type and mutant MCRC patients treated with irinotecan, 5-fluorouracil and leucovorin (IFL) plus BEV were 27.7 and 19.9 months, respectively [KRAS or BRAF wild-type compared to KRAS or BRAF mutant genotype was not significantly different, even though the hazard ratio (HR) was 0.64 and 0.38, respectively. A significantly better prognosis was reported only when KRAS/BRAF wild-type patients were compared with patients harboring mutations in the KRAS or BRAF genes (HR 0.51) [KRAS wild-type genotype significantly predicts a favorable clinical outcome of anti-EGFR or anti-vascular endothelial growth factor (VEGF) drugs added to doublet chemotherapy [the KRAS mutant genotype, BEV addition to IFL significantly prolonged PFS up to 9.3 months, without increasing OS and activity, compared to IFL [Clinical outcome according to wild-type and mutant genotype assesses the prognostic relevance of a specific biomarker, potentially including the predictive role of effectiveness of treatment strategies. In randomized studies, the predictive relevance of wild-type or mutant genotype can also be specifically assessed by comparing experimental and control arms. The reported median OS values of ectively ,21. The HR 0.51) . KRAS wiotherapy ,21-23. Id to IFL ,21.KRAS genotype in MCRC patients enrolled in a previously reported phase II study [Here, we report a retrospective exploratory analysis evaluating the prognostic value of the II study and in aII study .MCRC patients were enrolled in a previously reported phase II study and in tL-oxaliplatin (OXP) [2/day, over 12 h (from 10:00 pm to 10:00 am), days 1, 2, 8, 9, 15, 16, 22 and 23; CPT-11 , 160 mg/m2, days 1, 15; BEV , 5 mg/kg, days 1, 15; l-OXP , 80 mg/m2, days 8, 22; cycles every 4 weeks.The FIr-B/FOx regimen was developed from previously reported doublet and triplet chemotherapy schedules ,25, consin (OXP) : TFI 5-FKRAS and BRAF genetic analyses were performed on paraffin-embedded tissue blocks from the primary tumor and/or metastatic sites. Genotype status was assessed for KRAS codon 12 and 13 mutations and BRAF c.1799 T>A (V600E) mutation by SNaPshot\u00ae multiplex screening for KRAS mutations and KRAS/BRAF mutations in 36 and 32 samples, respectively [KRAS mutations in 23 samples and to confirm detected mutations. After treatment with xylene thyocyanate and selection of tumoral cell clusters, DNA was isolated using the RecoverAll\u2122 Total Nucleic Acid Isolation Kit for FFPE Tissues according to manufacturer's instructions. When considering the contamination of tumoral samples by non-malignant cells, a KRAS mutation in the tumor was defined as appearance of a mutant peak with a height of at least one-third compared to the wild-type.ectively ,27; direKRAS exon 2 and BRAF exon 15 were simultaneously amplified by polymerase chain reaction (PCR) using specific primers and purified using NucleoSpin\u00ae Extract II kit . PCR-amplified DNA was analyzed using the ABI PRISM SNaPshot Multiplex kit and five primers including an additional tail at their 5' end allowing their simultaneous detection. Sense primers allowing the extension at nucleotides KRAS c.34G, c.35G, c.37G, c.38G and BRAF c.1799T were used and a multiplex SNaPshot reaction was performed as reported [KRAS exon 2 sequencing was performed from PCR-amplified tumor DNA using the Big Dye V3.1 Terminator Kit . Labeled products were separated using an ABI Prism 3130xl Genetic Analyzer . Data were analyzed using the GeneMapper Analysis Software version 4.0 .SNaPshot multiplex assay was performed as elsewhere reported ,27. Briereported . KRAS exKRAS genotype on clinical outcome of MCRC patients treated with FIr-B/FOx as first-line treatment. Moreover, patients were classified according to involved metastatic sites, L-L and O/MM [KRAS wild-type and mutant MCRC patients. Patients with L-L metastases were evaluated at baseline and every three cycles of treatment by a multidisciplinary team, consisting of a medical oncologist, liver surgeon and radiologist, to dynamically evaluate resectability defined according to resectability categories previously reported [A retrospective analysis was planned to evaluate prognostic relevance of and O/MM , to evalreported . ResectiKRAS wild-type versus mutant, L-L versus O/MM, and KRAS wild-type L-L versus O/MM, and KRAS mutant L-L versus O/MM MCRC patients [Clinical criteria of activity and efficacy were ORR, PFS and OS. ORR was evaluated according to Response Evaluation Criteria In Solid Tumors (RECIST) criteria ; patholopatients .KRAS wild-type and mutant genotypes was 31 (53%) and 28 (47%), respectively and 19 (61%); KRAS mutant, 13 (46%) and 15 (54%). Table KRAS mutations detected in 28 patients: codon 12, 24 patients (85.7%), specifically c.35 G>A 15 patients (53.5%), c.35 G>T 7 patients (25%), c.34 G>A and c.35 G>C, 1 patient each; codon 13, 4 patients (14.2%), c.38 G>A 3 patients (10.7%) and c.37_39 dupl, 1 patient. A total of 32 tumoral samples (54%) were also analyzed for BRAF and no BRAF mutation was detected; 18 out of 31 KRAS wild-type MCRC patients were KRAS and BRAF wild-type; 14 out of 28 KRAS mutant MCRC patients were BRAF wild-type. EGFR protein expression was positive in 35 patients (59%) and negative in 24 patients (41%): among KRAS wild-type patients, positive in 23 patients (74%) and negative in 8 patients (26%); among KRAS mutant patients, positive in 13 patients (40%) and negative in 15 patients (60%).A total of 59 tumoral samples of 64 enrolled MCRC patients 92%) were available: 46 primary tumors and 13 metastases . Demographic and baseline features of patients were representative of the overall phase II study population . We observed 27 objective responses: 23 partial responses (77%) and 4 complete responses (CRs) (13%); 2 stable diseases (7%); 1 progressive disease (3%). Disease control rate was 97% (95% CI 90 to 100). Liver metastasectomies were performed in 11 patients (35%), 10 out of 12 L-L patients (83%). Median PFS was 14 months (1+ to 69+ months), 25 events occurred. Median OS was 38 months (1+ to 69+ months), 17 events occurred. Among the 18 KRAS/BRAF wild-type patients, ORR was 83% (95% CI 69 to 97), median PFS was 13 months (4 to 44 months), median OS was 31 months (8 to 66+ months). Among 27 evaluable KRAS mutant patients, ORR was 67% (95% CI 49 to 85). We observed 18 objective responses: 17 partial responses (63%) and 1 CR (4%); 4 progressive diseases (16%). Disease control rate was 85% (95% CI 71 to 99). Liver metastasectomies were performed in 7 patients (25%) out of 13 L-L patients (54%). Median PFS was 11 months (1+ to 60+ months), 20 events occurred. Median OS was 20 months (1+ to 60+ months), 17 events occurred. Overall, R0 liver resections made up 13 out of 18 liver metastasectomies (72%). Pathologic CRs were obtained in 2 patients (11%), both KRAS mutant patients, harboring codon 12 mutations, c.35 G>T and c.34 G>A, with multiple liver-only metastases. In one KRAS wild-type patient with single liver associated with lung metastases, double metastatic resections were performed. KRAS wild-type compared with mutant patients did not show significantly different PFS nor OS, even if OS seems to be favorable in KRAS wild-type patients with FIr-B/FOx according to extension of metastatic disease in KRAS ts Table . Among 2ts Table .KRAS wild-type patients, ORR in 12 L-L and 18 O/MM patients were 100% and 80%, respectively. Overall activity was 100% (ten liver metastasectomies and two cCRs) in L-L and 17% (one liver plus lung metastasectomy and two cCRs) in O/MM patients, respectively. Significantly different clinical outcome was confirmed in L-L compared to O/MM, respectively while no liver metastasectomy nor cCR was obtained in O/MM patients. The comparison of PFS and OS in KRAS mutant L-L and O/MM patients was not significantly different: median PFS 11 months (3 to 60+ months) versus 11 months (1+ to 37 months), respectively; median OS 39 months (8 to 60+ months) versus 19 months (1+ to 59+ months), respectively significantly increased median PFS up to 9.3 months, while ORR was equivalent to doublet arm , and median OS increased up to 19.9 months, even if not significantly [In ectively ,21,31,32ectively ,23,31-33patients . In KRASficantly .KRAS wild-type and mutant MCRC patients, BEV addition to triplet chemotherapy, according to FIr-B/FOx schedule, reported high activity and efficacy: ORR 90% and 67%, median PFS 14 and 11 months, median OS 38 and 20 months, respectively. A similar clinical outcome was also obtained in KRAS/BRAF wild-type patients. Equivalent efficacy was reported with FOLFOXIRI/BEV regimen: ORR 82% and 71%, median PFS 13.6 and 12.6 months, respectively [In ectively .KRAS wild-type and mutant patients, even if not significantly, while they were equivalent in the FOLFOXIRI plus BEV study [KRAS wild-type and mutant patients, respectively [KRAS/BRAF wild-type patients compared with patients harboring mutations in the KRAS or BRAF genes (HR 0.51) [KRAS wild-type and mutant MCRC patients treated with BEV-containing chemotherapy failed to significantly differentiate prognosis, as in the present study. Thus, intensive regimens adding BEV to triplet chemotherapy can further increase activity and efficacy in KRAS wild-type and mutant patients. Randomized studies would be able to properly evaluate this.Median PFS and OS values of MCRC patients treated with FIr-B/FOx were different in EV study . BEV addectively ,21. SignHR 0.51) . Direct KRAS wild-type L-L patients, accounting for 20% of fit MCRC patients, could gain 100% overall activity with an integrated medical and surgical approach, due to performed liver metastasectomies and long-lasting cCRs; median PFS 21 months and OS 47 months. A significantly favorable prognosis was demonstrated in KRAS wild-type L-L compared to O/MM patients, even if this represents a retrospective, exploratory analysis in a small cohort of MCRC patients. Using neoadjuvant cetuximab with either FOLFOX6 or FOLFIRI for unresectable colorectal liver metastases, metastasectomies were performed in 38% and 30% patients, respectively [KRAS wild-type L-L MCRC patients. In KRAS mutant patients, prevalently harboring c.35 G>A transversion (53.5%), integrated medical and surgical treatment failed to significantly increase PFS and OS in L-L compared to O/MM patients: median PFS was equivalent (11 months), in spite of 54% performed liver metastasectomies in L-L patients; median OS was 39 and 19 months, respectively. These data should be further evaluated in a larger cohort of MCRC patients. A proper multidisciplinary treatment strategy for KRAS mutant patients, showing different aggressiveness [The high activity of triplet chemotherapy plus BEV regimens correlated with increased resection rate of liver metastases and pathologic CR, particularly in L-L MCRC patients ,3,4,6. Wectively . Chrono-ectively . Furthersiveness , sensitiKRAS wild-type and mutant genotypes do not significantly affect the clinical outcomes of MCRC patients treated with the first-line FIr-B/FOx intensive regimen. KRAS wild-type patients with L-L disease may achieve significantly greater benefit from integration with liver metastasectomies compared to O/MM metastatic extension, with respect to KRAS mutant patients. The present findings should be verified in prospective trials of multidisciplinary strategies comparing clinical outcome according to KRAS genotype in patients with L-L and O/MM disease.The authors declare that they have no competing interests.Conception and design: GB, ER. Provision of study materials of patients: GB, AD, GC. Collection and/or assembly of data: all authors. Data analysis and interpretation: GB, KC, ER. Manuscript writing: GB, ER. Final approval of manuscript: all authors.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1741-7015/10/135/prepub"} +{"text": "The study investigated cardiovascular changes in adult-onset growth hormone deficiency (GHD) and showed that patients with adult-onset GHD have a left ventricular mass index (LVMi) at or below the lower limit of normal, which improves with one year of growth hormone replacement.GHD causes cardiovascular problems, with loss of cardiac response to exercise and increased cardiac mortality, however the underlying processes are poorly understood.Ten patients with adult-onset GHD and age- and sex-matched controls (n=10) underwent CMR. Patients underwent scans before disease treatment and at twelve months after treatment. Cardiac parameters were calculated and indexed to body surface area (BSA). The comparison between groups was done using Mann-U-Whitney test and within the group using Wilcoxon test. The data are presented as median values.2, p=0.315; end diastolic volume index (EDVi) 69.2 vs. 76.3 ml/m2, p=0.1655; end systolic volume index (ESVi) 24.8 vs. 28.3 ml/m2, p=0.3527 and ejection fraction (EF) 64 vs. 63 %, p=0.8197. However, patients had an LVMi beneath the lower limit of normal when compared to published normal ranges (55.4 - 74.0 g/m2).Patients with GHD did not have significantly different left ventricle (LV) mass or volumetric parameters from controls: LV mass index (LVMi) 55.0 vs. 56.6 g/m2, p=0.393), ESVi and EF in the GHD group and controls.There were no differences between right ventricular (RV) EDVi achieving statistical significance compared to pre-treatment values (p=0.0156).Patients with GHD on GH treatment for 1 year showed an increase in median insulin-like growth factor I (IGF-I) SDS from -1.83 to +0.40 (p=0.0068). There was no correlation between LVMi and IGF-I SDS . At one year the median LVMi moved into the previously published normal range (55.0 to 63.0 g/mPatients with adult-onset GHD have an LVMi at or below the lower limit of normal, which improves with one year of growth hormone replacement.Supported by departmental grants by Pfizer and Novartis."} +{"text": "However, sudden cardiac death may be the first clinical manifestation. Hence early detection of myocardial abnormalities before overt left ventricular (LV) dysfunction is warranted for a better risk stratification.Seventeen paucisymptomatic LM carries , 14 paucisymptomatic DCM patients with mild LV dysfunction (ejection-fraction 40%-55%) and 12 healthy controls underwent complete clinical, echocardiographic, biohumoral and contrast-enhanced CMR assessment. Cine CMR was used to derive LV volumes, mass and function, and post-contrast CMR to detect late gadolinium enhancement (LGE) as an index of gross fibrosis. Eight LM patients, all DCM patients and all normal controls underwent pre- and post-contrast myocardial T1 mapping with gadolinium partition coefficient calculation, as an index of interstitial fibrosis.LM carriers presented a similar LV end-diastolic volume and slightly reduced ejection-fraction (61\u00b16% p<0.001) than controls , while in DCM patients LV end-diastolic volume (102\u00b117 ml/m2) and ejection-fraction (49\u00b15%) were worse than both controls and LM carriers (p<0.001). Moreover, DCM patients presented worse diastolic dysfunction , NT-proBNP plasma levels and Doppler-estimated pulmonary pressure than LM carriers. Six (43%) DCM patients presented DE, representing 9\u00b13% of LV mass; similarly, seven (42%) LM carriers had DE, but with a larger extension . In LM carries DE distribution was patchy (2 pts) or midwall (5 pt), similarly to DCM patients . GPC reached a steady state 5 minutes after gadolinium injection. In DCM patients GPC was slightly higher than controls , while in LM carriers it was much higher (0.45\u00b10.07) than controls (p<0.01). Even excluding hyperenhanced myocardium, in LM carriers GPC remained higher than controls, while in DCM patients only slightly higher than controls.Myocardial fibrosis occurs early in LM carrier before LV dilatation and dysfunction and may represent an early phenotypic expression of cardiac involvement."} +{"text": "Bloodstream infections (BSI) are important causes of morbidity and mortality. Most of all, when are caused by drug-resistant organisms (DR).To investigate the epidemiology, etiology, systemic response and treatment of DR-BSI.EPINE-EPPS project. Comparisons between groups were performed by means of the X2 test for categorical variables or analysis of variances (ANOVA) for continuous variables.A retrospective study was conducted about all BSI diagnosed in a secondary hospital during one year. The pattern resistant pathogen study was We included 60 patients with 63 DR-BSI of which 71.5% were nosocomial and healthcare-associated BSI.Unknown and intravascular catheter-related DR-BSI accounted for 49.2% of cases. Among secundary infections, the source was 37.5% urinary track, 31.2% intra-abdominal and 15.6% respiratory track infections.S. aureus. Among DR-Gram-negative bacilli, 12.2% of enterobacteracea family produced extended-spectrum B-lactamasas. We found 5 DR-BSI caused by Acitetobacter carbapenem resistant and 3 DR-BSI by P. aeruginosa carbapenem resistant.Overall DR-BSI, DR-Gram-positive cocci were 55.6%. The most common isolated pathogens were staphylococcus coagulase-negative and Median time to diagnosis for DR-Nosocomial BSI was 14 days (IQR), 7-35 days after hospital admission. For Gram-negative was 11 days (7.5-31.5) and for Gram-positive 19 days (7-29).Only 31.7% of DR-BSI received appropriate initial empirical antimicrobial therapy versus 73.5% of non DR-BSI (p<0.001). More than one third (36.5%) of the episodes occur with significant systemic response (severe sepsis or septic shock). The crude mortality rate was 25.4 % (p<0.001). If the patient developed severe sepsis or septic shock crude mortality rose to 52.2%.Information about local epidemiology is important to develop prevention and control strategies in drug\u2013resistant microorganism and to improve the management of BSI.None declared"} +{"text": "Remarkably, while glucose potently stimulated GIP release, fructose was without effect. Similar patterns were found in the mouse and rat, with both fructose and glucose stimulating GLP-1 secretion, whereas only glucose caused GIP secretion. In GLUTag cells, a murine cell line used as model for L cells, fructose was metabolized and stimulated GLP-1 secretion dose-dependently (EC50 = 0.155 mM) by ATP-sensitive potassium channel closure and cell depolarization. Because fructose elicits GLP-1 secretion without simultaneous release of glucagonotropic GIP, the pathways underlying fructose-stimulated GLP-1 release might be useful targets for type 2 diabetes mellitus and obesity drug development.Nutrients often stimulate gut hormone secretion, but the effects of fructose are incompletely understood. We studied the effects of fructose on a number of gut hormones with particular focus on glucagon-like peptide 1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP). In healthy humans, fructose intake caused a rise in blood glucose and plasma insulin and GLP-1, albeit to a lower degree than isocaloric glucose. Cholecystokinin secretion was stimulated similarly by both carbohydrates, but neither peptide YY While it has long been known that the presence of nutrients such as glucose, fat, and protein in the intestinal lumen stimulates secretion of many gut hormones, the effects of fructose are poorly understood. While some studies have shown that fructose does not stimulate insulin secretion in: 1) humans when perfused intraduodenally, 2) in rat pancreatic preparations, or 3) in isolated human and rat pancreatic islets participated in the study, which was approved by the local ethical committee and conducted according to the principles of The Helsinki Declaration. All subjects had normal fasting blood glucose levels , and none had parents or siblings diagnosed with any type of diabetes. No subjects received medication known to interfere with glucose homeostasis. Each subject was studied on two occasions within 3 wk after the first day of study. Subjects were instructed to refrain from vigorous exercise and alcohol for at least 24 h before each study. Study days began at 0830 preceded by a 10-h overnight fast. Venous blood samples were collected at time \u221210, 0, 15, 30, 45, 60, 90, 120 min in prechilled EDTA (10.8 mg) tubes through a polyethylene cannula placed in a cubital vein. At time 0 min, the seated, single-blinded, subjects drank a sugar solution containing 75 g fructose or glucose dissolved in 300 ml water (RT) within 2 min. For palatability, solutions were refreshed with lemon juice. Upon collection, blood samples were instantly chilled on ice and centrifuged within 30 min. Plasma were stored at \u221220\u00b0C until analysis.Nine healthy volunteers (data not shown). Rats were divided into weight-matched groups (n = 4/occasion) and given a bolus of either glucose or fructose diluted in milli-Q water to a final concentration of 50% (wt/vol) or a matched volume vehicle (milli-Q water). Rats from the same cage received different treatments. Blood (200 \u03bcl) was collected into prechilled EDTA-coated capillary tubes by sublingual vein puncture and instantly transferred onto ice. The zero sample was collected 10 min before bolus administration. At time 0 min rats were stimulated with either vehicle, glucose, or fructose, and blood was collected at time 15, 30, and 60 min. Blood glucose was measured instantly after collection, and samples were centrifuged to obtain plasma, which was transferred to fresh Eppendorf tubes and immediately frozen on dry ice. Samples were stored at \u221220\u00b0C until analysis. At the end of the experiment rats were anesthetized by subcutaneous injection of hypnorm/midazolam and killed by diaphragm perforation.Studies were approved by the Danish Animal Experiments Inspectorate (2013-15-2934-00833). Male Wistar rats were obtained from Taconic and allowed at least 1 wk of acclimatization before the day of experiment. Rats followed a 12:12-h light-dark cycle with ad libitum access to standard chow and drinking water. Every day for a week up to the experiment, rats were handled to minimize stress-related responses on the day of study. Handling included restraint and gavage feeding with drinking water. Experiments were carried out on two occasions on nonfasted rats (294.9 \u00b1 3.8 g) just before their nocturnal feeding period (1700). Weight did not differ between groups or study occasions (time \u221230 min and again at time 0 min with fructose or glucose (3 g/kg) diluted in drinking water to a final concentration of 20% (wt/vol). At time 0 and 6 min, blood (75 \u03bcl) for hormone measurement was collected into prechilled EDTA-coated capillary tubes supplemented with dipeptidyl peptidase 4 inhibitor . After collection, blood samples were immediately transferred to Eppendorf tubes supplemented with 7.5 \u03bcl diprotinin A (1 mM) and centrifuged within 30 min. Plasma was transferred to fresh Eppendorf tubes, snap-frozen on dry ice, and stored at \u221220\u00b0C until analysis. Blood for glucose measurements (3 \u03bcl) was obtained by tail puncture immediately after blood sampling and directly processed for blood glucose measurements as described below. After the first day of study (13 wk), the procedure was repeated. At both occasions, mice were randomly divided into glucose- and fructose-receiving groups. Weights did not differ between fructose and glucose groups at the respective days of study . At the end of the experiment, mice were killed by cervical dislocation.Studies were carried out with permission from the Danish Animal Experiments Inspectorate (2012-15-2934-00207). Female C57BL/6 mice were obtained from Charles River and allowed 1 wk of acclimatization before the day of experiment. Mice were fasted overnight but allowed free access to water. Mice were prestimulated with a gavage of 100 \u03bcl drinking water at 2 until 70\u201380% confluent, then trypsinized and plated on a 24-well plate precoated with matrigel (1:100) as described previously supplemented with 0.1% (wt/vol) fatty acid-free BSA and incubated for 2 h with 250 \u03bcl test reagents dissolved in saline buffer. All reagents were supplied by Sigma Aldrich. Supernatants were collected and centrifuged to remove floating cells and debris and then either snap-frozen on dry ice and stored at \u221280\u00b0C or directly processed for GLP-1active measurement.GLUTag cells were cultured in T75 cell culture flasks in low-glucose (1.0 g glucose/l) DMEM 5564 medium supplemented with 10% (vol/vol) FCS, 1% (vol/vol) penicillin/streptomycin, and 1% (vol/vol) glutamine. Cells were incubated at 37\u00b0C, 5% COeviously . The folIntracellular NAD(P)H concentration levels were measured using NAD(P)H's autofluorescence properties , 23. GLUtotal (GIP1\u201342 and GIP3\u201342) was measured with GIP-ELISA , whereas GLP-1 levels were measured by the same Millipore GLP-1 (active) ELISA kit as for the GLUTag cells. In both cases, data were acquired using a Biotek EL800 plate reader controlled by Gene5 software . For the mouse, GIPtotal concentrations were measured as described above, and GLP-1 levels were determined by the Meso Scale assay system . Data were obtained with a Sector Imager 2400 device controlled by MSD Discovery workbench software. Human plasma concentrations of total GLP-1, GIP, insulin (INS), glucagon (GCG), and intact neutrotensin1\u201313 (NTS1\u201313) were determined using in-house radioimmunoassays with 125I-labeled tracers and hormone-specific antiserum, recognizing COOH-terminal epitopes, as described previously . Free and bound moieties were separated by addition of (bovine) plasma-coated charcoal . Supernatants were collected , and the radioactivity was counted in a Packard Cobra II Gamma Counter (GMI). Plasma polypeptide YY3\u201336 (PYY3\u201336) levels were measured by a commercially available RIA kit . Plasma cholecystokinin (CCK) concentrations were measured by RIA measuring all the tyrosyl-sulfated forms of CCK as described read on a SpectraMax M5 plate reader controlled by SoftMax Pro 5.4.1 software . For both human, rat and mouse, blood glucose levels were measured by the glucose oxidase method immediately after sampling by a handheld Accu-chek Compact plus device . For the rat, plasma GIPescribed . For allt-test, paired Student's t-test, or one-sample t-test, testing values against a hypothetical value of zero, as indicated. P < 0.05 was considered significant. For the human study, baseline values are presented as the mean of the \u221215 and 0 min levels. EC50 value for fructose-stimulated GLP-1 secretion from GLUTag cells (P < 0.001) with significantly higher area under the curve (AUC) values after oral glucose vs. fructose . For both groups, blood glucose concentrations returned to basal levels by the end of the study period (2 h) A. Both t, n = 9) B. Maximuod (2 h) A.P > 0.05, n = 9). There was a rise in insulin after both glucose and fructose ingestion , albeit glucose elicited a higher maximal response (P < 0.05) (P < 0.001) C. Insuli < 0.05) D. Insuli< 0.001) C.P > 0.05) (P = 0.17) (Glucagon levels did not change significantly at any time point after glucose or fructose intake ( > 0.05) E. Glucag = 0.17) F.n = 9) with progressively increasing concentrations from baseline until 45 min (P < 0.001). Levels then tended to fall, reaching an elevated plateau phase from 60 to 120 min. GLP-1 also rose after oral glucose intake , reaching significantly elevated concentrations at 15 min (P < 0.01). Thereafter, levels remained elevated until 90 min (P < 0.05) A. GLP-1 l 90 min A. Over t < 0.05) B.P > 0.05, n = 9) , reaching at plateau from 15 to 120 min , fructose did not significantly elevate GIP concentrations , also compared with basal levels (P > 0.05) (P < 0.0001) C. While > 0.05) C. GIP AU 0.0001) D.P > 0.05, n = 9) , but levels were slightly elevated at 60 and 90 min after fructose intake (P > 0.05) E. PYY co, n = 9) E. Plasma > 0.05) F.P > 0.05, n = 9) with peak values occurring 15 min after ingestion for both treatments . Thereafter, CCK concentrations decreased for both treatments, albeit with a tendency toward higher values in the glucose treatment group at later time points (P > 0.05) G. Glucose points G. CCK AU > 0.05) H.P > 0.05, n = 9) (P < 0.001), with similar peak values observed at 15 min for both treatments . NTS AUCs did not differ between treatments (P > 0.05) I. Glucos > 0.05) J.P < 0.01, n = 7). At 60 min, blood glucose levels had normalized and were not different from basal levels (P > 0.05) but not in the fructose-treated group . In contrast, fructose stimulation did not elevate GIPtotal levels at any time points (P < 0.001), but not after fructose , but GLP-1 AUCs were elevated by both glucose and fructose compared with control (P < 0.05) A. Blood , n = 6) B. Blood , n = 6) A. GIPtot, n = 6) C. GIP AUfructose D. GLP-1 < 0.05) F.P < 0.05, n = 31) albeit glucose stimulation increased levels to a greater extent than fructose (P < 0.0001) (P > 0.05). GIPtotal concentrations were elevated by glucose treatment , but fructose had no effect (P > 0.05) (C).Responses to glucose and fructose were studied on two occasions separated by 13 wk. Blood glucose increased significantly for both groups compared with basal levels A. GLP-1t n = 23) B to a si n = 23) C. Basal > 0.05) , A\u2013C.P < 0.05, n = 43) (P < 0.0001) in a dose-dependent manner, reaching a maximal response at 1 mM . Addition of gliclazide (GLI) to induce ATP-sensitive potassium (KATP) channel closure did not potentiate fructose-induced GLP-1 secretion , but stimulation with GLI alone caused GLP-1 secretion to a similar degree as tolbutamide (ATP channel opener diazoxide (340 \u03bcM) completely abolished fructose-induced GLP-1 secretion , which reached similar levels as during diazoxide exposure alone (Metabolic responses to fructose were investigated by the NAD(P)H imaging technique. Representative traces from an experiment are shown in n = 43) B. Stimul n = 43) confirme n = 27) C. Fructo = 6\u201316) D. Again,= 14\u201315) F. Presen= 10\u201312) E.1\u201313 to a similar extent as glucose, and also enhanced insulin secretion, albeit to a lower degree than glucose. In contrast, neither fructose nor glucose altered glucagon or PYY3\u201336 levels. With a view to perform mechanistic studies regarding the differential responses of the incretin hormones, we also investigated GIP and GLP-1 responses to fructose in mice and rats. In both animals, fructose stimulated GLP-1 secretion to the same extent as isocaloric glucose, but, similar to humans, GIP secretion was not stimulated.The increased intake of dietary fructose in general and high-fructose corn syrup in particular has been suggested to play a role in the current obesity epidemic , 20. MorIn mice and humans, fructose intake also increased blood glucose levels, and a similar tendency was seen in the rat. It is generally accepted that fructose can be converted to glucose in the liver by mechanisms involving rapid phosphorylation of fructose to fructose 1-phosphate by fructose kinase, which by liver-type-B aldolase activity, yields the intermediate metabolites dihydroxyacetone phosphate and glyceraldehyde, with the latter being a substrate for glucose production by further metabolic activity. However, it has also been shown that the small intestine has capacity to transform fructose into glucose by the same pathway . AlthougATP channel closure, causing cell membrane depolarization and a grant to J. J Holst from the Novo Nordisk Centre for Basic Metabolic Metabolism .The study was supported by a The authors declare no financial or other conflicts of interest.Author contributions: R.E.K., F.M.G., B.H., F.R., J.A.W., and J.J.H. conception and design of research; R.E.K., B.H., J.A.W., and J.F.R. performed experiments; R.E.K., B.H., and J.F.R. analyzed data; R.E.K., F.M.G., B.H., F.R., and J.J.H. interpreted results of experiments; R.E.K. prepared figures; R.E.K. drafted manuscript; R.E.K., F.M.G., B.H., F.R., J.A.W., and J.J.H. edited and revised manuscript; R.E.K., F.M.G., B.H., J.A.W., J.F.R., and J.J.H. approved final version of manuscript."} +{"text": "Objective(s): In the current study, the effects of selected folk medicinal herbs were evaluated in D-galactose-induced aging in male mice.Materials and Methods: Male BALB/c mice were randomly divided into 12 groups composing sham, control, and treated groups. Aging was induced by administration of D-galactose (500 mg/kg/day for 6 weeks). A positive control group was assigned that received vitamin E (200 mg/kg/day). The extract of herbs was prepared, lyophilized, and used in this study. The herbs were administered by gavage for 4 weeks to D-galactose-aged animals at the selected doses (mg/kg/day) as follows: Zingiber officinale (250), Glycyrrhiza glabra (150), Rosmarinus officinalis (300), Peganum harmala (50), Aloe vera (150), Satureja hortensis (200), Teucrium scordium (200), Hypericum perforatum (135) and Silybum marianum (150). One group of animals was assigned as sham and not given D-galactose. Results: At the end of treatment, pro-inflammatory markers including tumor necrosis factor-\u03b1 (TNF-\u03b1), interlukine-1\u03b2 (IL-\u03b2), interlukine-6 (IL-6), NF-kappaB (NF-\u03bab), total antioxidant power (TAP), thiobarbituric acid reactive substances (TBARS) as lipid peroxidation (LPO) marker and male sex hormones i.e. testosterone and dehydroepiandrosterone-sulfate (DHEA-S) were measured in the blood.Conclusion: These data for the first time indicate significant anti-aging potential of examined herbs. Results showed that D-galactose induces a significant oxidative stress and promotes proinflammatory cascade of aging while all herbs more or less recovered these changes. Among 9 herbal extracts, Silybum marianum showed the best effect in restoring aging changes. Aging as a complex of natural circumstance is exhibited by an augmentation in the chance of illness and finally death. Although some theories have been proposed as the mechanisms of aging but the one relating aging and cellular oxidative stress have received more supports. Therefore, it can be said that reduced sex hormones and augmented quantity of oxidative stress parameters or inflammatory cytokines are main biochemical manifestations of aging -2. In acOne of the problems in testing anti-aging compounds is lack of suitable animal models. Although several models have been used so far but among them, typical mouse D-galactose-induced model of aging is the best one that gives closer results to clinical studies. D-galactose is a sugar that at higher levels converts to aldose and hydro-peroxide during the catalysis of galactose oxidase, culminated in the generation of free radicals . These mMany scientists and pharmaceutical companies try to develop a drug to reduce speed of human aging but no effective drug has been discovered yet. In the last decade the importance of folk medicine and herbal medicines have been revisited that resulted in developing many effective drugs for many human diseases. For instance, in the recent years, efficacy of herbal medicines in diseases like inflammatory bowel diseases -10, obesZ. officinale, G. glabra, R. officinalis, P. harmala, A. vera,S. hortensis, T. scor-dium, H. perforatum and S. marianum to test in D-galactose-induced model of mouse aging.We recently proved anti-aging potential of naturally-based drugs like IMOD and Angipars which have strong antioxidant power . On the Chemicals3-6H2O), D-galactose, and vitamin E (Trolox) were purchased from Merck (Germany). Rat specific tumor necrosis factor-\u03b1 (TNF-\u03b1), interlukine-1\u03b2 (IL-\u03b2), interlukine-6 (IL-6), NF-kappa B (NF-\u03bab) ELISA kits were purchased from BenderMed Systems (Austria). Testosterone and dehydroepiandrosterone ELISA kits were purchased from Dia Metra . Thiobarbituric acid (TBA), trichloroacetic acid (TCA), n-butanol, hexadecyltrimethyl ammonium bromide (HETAB), tri (2-pyridyl)-s-triazine (TPTZ), HCl, malondialdehyde (MDA), ferric chloride were washed in a suitable bactericide (chlorh-exidine). The filets were grounded to a liquid, and the pulp was removed by filtering. The resultant gel was then freeze dried.Herbs were provided from the Research Institute of Medicinal Plants Karaj during June 2009 and were air-dried at room temperature. Samples were authenticated by a botanist (Y. Ajani), and voucher specimens were preserved in the central herbarium of medicinal plants (RIMP). The scientific names and tested parts of the herbal materials are detailed in AnimalsMale BALB/c mice were provided from Tehran University of Medical Sciences (TUMS) animal house. The animals were housed in standard polypropylene cages with wired-net top in a controlled room and were allowed free access to standard laboratory pellet diet and water during the experiments. All ethical issues on the use of animals were carefully considered and the study protocol was approved by TUMS review board with code number of 90-03-33-15668.Experimental designth group of animals was the sham group which was not given D-galactose. After 2 weeks, the 11 groups which had been given D-galactose were randomly divided into aging control group , positive control group and herb-treated groups including 9 groups that each received 500 mg/kg D-galactose per 1 ml drinking water plus Z. officinale (250 mg/kg/day), G. glabra (150 mg/kg/day), R. officinalis (300 mg/kg/day), P. harmala (50 mg/kg/day), A. vera (150 mg/kg/day), S. hortensis (200 mg/kg/day), T. scordium (200 mg/kg/day), H. perforatum (135 mg/kg/day) and S. marianum (150 mg/kg/day), respectively by gavage for 4 weeks , lipid peroxidation (LPO) and male sex hormones including testosterone and dehydroepiandrosterone-sulfate (DHEA-S) were measured in the serum.Measurement of LPO 2SO4 (0.05 M). After addition of TBA (0.2% in sodium sulfate), the sample was heated for 30 min in a boiling water bath. Then, TBA reactive substances (TBARS) as LPO marker adducts were extracted by n-butanol and absorbance was measured at 532 nm as described in details in our previous work (LPO was measured by the reaction of thiobarbituric acid (TBA) with lipid peroxides. Samples were mixed with TCA (20%) and the precipitate was dispersed in Hous work . Data weMeasurement of TNF-\u03b1, IL-1\u03b2, IL-6 and NF-\u03babQuantitative detection of TNF-\u03b1, IL-1\u03b2, IL-6 and NF-\u03bab levels in serum were performed using an enzyme-linked immunosorbent assay rat specific ELISA kit according to each specific brochure. The absorbance of the final colored product was measured in 450 nm as the primary wave length and 620 nm as the reference wave length. TNF-\u03b1, IL-1\u03b2, IL-6 and NF-\u03bab levels were expressed as pg/mg.Measurement of TAP 3+ to Fe2+. Interaction of TPTZ with Fe2+ results in formation of a blue color with a maximum absorbance at 593. The whole procedure has been described in our previous study . Data were analyzed by one-way ANOVA followed by Tukey post-hoc test for multiple comparisons to ensure the variances of the data are distributed properly. A P< 0.05) and a significant decrease in TAP (P<0.05) were observed when sham group was compared with D-galactose-received aged group. P<0.05; 1.2\u00b10.05 vs. 2.5\u00b10.33, P<0.05; 27\u00b13.9 vs. 49.66\u00b13.4, P<0.05; 45.7\u00b12.4 vs. 97\u00b121.2, P<0.05). As shown in P<0.05; 1.2\u00b10.2 vs. 0.6\u00b10.08, P<0.05) in aged mice was lower than that in the sham.A significant increase in TBARS , and increasing TAP , , respectively. As shown in Z. officinale increased testosterone and DHEA-S in aged mice.P<0.05), , 2. FiguEffects of G. glabra in aged miceG. glabra .G. glabra recovered D-galactose-induced increase in TNF-\u03b1, IL-6, IL-1\u03b2 and NF-kB , respectively. As shown in G. glabra increased testosterone and DHEA-S levels in aged mice.D-galactose-induced elevation of TBARS and reduction of TAP , 2 were Effects of R. officinalis in aged miceR. officinalis treatment recovered D-galactose-induced rats by reducing TBARS , and increasing TAP , respectively. As shown in R. officinalis increased testosterone, and DHEA-S in aged mice. P<0.05) , 2. FiguEffects of P. harmala in aged miceP. harmala . P. harmala recovered D-galactose-induced increase in TNF-\u03b1, IL-6, IL-1\u03b2, and NF-kB , respectively. As shown in P. harmala increased testosterone and DHEA-S in aged mice.D-galactose-induced elevation of TBARS and reduction of TAP , 2 were Effects of A. vera in aged miceA. vera treatment recovered D-galactose-induced elevation of TBARS (P<0.05), and improved reduction of TAP (P< 0.05). A. vera recovered D-galactose-induced increase in TNF-\u03b1, IL-6, IL-1\u03b2, and NF-kB , respectively. As shown in A. vera increased testosterone and DHEA-S levels in aged mice.Effects of S. hortensis in aged miceS. hortensis treatment recovered D-galactose-induced elevation of TBARS (P<0.05), and increased TAP (P<0.05). S. hortensis recovered D-galactose-induced increase in TNF-\u03b1, IL-6, IL-1\u03b2, and NF-kB , respectively. As shown in S. hortensis increased testosterone and DHEA-S in aged mice.Effects of T. scordium in aged miceT. scordium . T. scordium recovered D-galactose-induced increase in TNF-\u03b1, IL-6, IL-1\u03b2, and NF-kB , respectively. As shown in T. scordium increased testosterone and DHEA-S in aged mice.D-galactose-induced elevation of TBARS and reduction of TAP , 2 were Effects of H. perforatum in aged miceH. perforatum treatment recovered D-galactose-induced rats by reducing TBARS and increasing TAP , respectively. As shown in H. perforatum increased testosterone and DHEA-S in aged mice. P<0.05) , 2. FiguEffects of S. marianum in aged miceS. marianum . S. marianum recovered D-galactose-induced increase in TNF-\u03b1, IL-6, IL-1\u03b2, and NF-kB , respectively. As shown in S. marianum recovered D-galactose-induced reduction of testosterone and DHEA-S in aged mice.D-galactose-induced elevation of TBARS and reduction of TAP , 2 were Effects of vitamin E in aged miceP<0.05; 190\u00b113.1 vs. 120\u00b17.5, P<0.05). P<0.05; 1.4\u00b10.26 vs. 2.5\u00b10.33, P<0.05; 30.1\u00b12.2 vs. 49.66\u00b13.4, P<0.05; 57\u00b13.9 vs. 97\u00b121.2, P<0.05), respectively. As shown in P<0.05; 1\u00b10.16 vs. 0.6\u00b10.08, P<0.05) in aged mice.D-galactose-induced elevation of TBARS and reduction in TAP , 2 were In this study, for the first time, we analyzed the anti-aging potentials of nine famous herbs in a well-setup animal aging model using chronic administration of D-galactose. Our results showed that production of free radicals is the principal reason of up-regulation of pro-inflammatory cytokines and the main determinant involved in the D-galactose-induced aging model. Furthermore, these herbs dramatically diminished oxidative stress and proinflammatory cytokines in the aged mice. Supporting the mechanism of action of these herbs and the theory of oxidative stress in aging, vitamin E was used as the standard and showed the similar effects in examined markers of aging.Adapted from corresponding author\u2019s previous paper published in open access source .Interestingly, present results indicated improve-ment of testosterone and DHEA-S by herbs in the aged mice. Decline of steroid hormones with aging is already known and is believed a major contributor to elevation of pro-inflammatory markers .Recent studies have shown the mechanisms of action of anti-aging herbs in reducing aging process that is divided into four categories including anti-oxidant, anti-inflammatory, effect on memory/cog-nition/mood, and the sex hormones . This inGinger [Zingiber officinale Roscoe (Zingiberaceae)] and supplements derived from ginger like zingerone, shogaols and gingerols posse the abilities for the treatment of chronic inflammation. The protective effects of Z. officinale in lessening macromolecular damage in aged mice were shown in this study. Besides, recent study has shown that ginger extracts owns antioxidant activity or licorice is the root of G. glabra from which a sweet flavor can be extracted. The results of this study showed that G. glabra has the protective effects in declining macromolecular damage in aged mice. It has been shown that G. glabra extract is the safest pigment-lightening agent with the fewest side effects (Fam. Liliaceace) are the source of aloe vera gel. A. vera gel is greatly used in cosmetics and toiletries for its moisturizing and regenerating action. Also, the leaf of A. vera could assist cellular repairing, imbibition of foods, vitamins, minerals and vital nutrients comprises 12 species, which possess antioxidant, anti-spasmodic, anti-nociceptive and anti-inflammatory properties -b-farnesene as the major components of T. scordium Gaertn. . Interestingly, the present findings confirmed that S. marianum causes the best effects in improving antioxidant, anti-inflammatory and male sex hormones in aged mice. This effect is so important and should be considered as an advantage. This can be explained with current knowledge that among many medicinal plants, S. marianum, has been greatly used for centuries as a natural popular complementary medicine for the treatment of several diseases. The main indications for the use of silymarin are related to the hepatoprotection , a flavonoids complex known as \u2018milk thistle\u2019 is extracted from the fruit of otection , 63. Alsotection , 65. It otection . Excitinal cells . S. marianum showed the best effect in improving all the D-galactose-induced aging effects. Since all of the selected and examined herbs are already found safe in human and there are good information from traditional medicine, therefore, they can be supplemented into the diet of elderly people to reduce speed of aging. Testing the mixture of these herbs together or with other anti-aging products is among the plans of future.Taking collectively, the present results confirmed our hypothesis that the herbs with highest antioxidant power may reduce speed and rate of aging as evidenced by recovery of proinflammatory cytokines and sex hormones. Among tested herbs,"} +{"text": "It has been reported in Mexico that genotypes H and G are the most common, although genotypes prevalence in HIV co-infected patients is unknown.We estimated the prevalence and identified the resistance pattern of HBV/H and G genotypes in HIV co-infected patients and compared them in mono-infected HBV patients.A cross-sectional prevalence and analytic study were realized. Risk factors, HIV or HCV co-infections, antiretroviral therapy (ART) experience, HBsAg, HBeAg, HBV viral load and mutations genetic analysis were collected; CD4+ cells count from HIV co-infected patients and HIV viral load were measured. We calculated the prevalence and exact 95% binomial confidence interval as well the Odds ratios (OR) and 95% confidence intervals to assess the relationship between risks factors and the risk of having HBV/H or G genotype.We enrolled 84 patients, 72 men and 12 women with 41 HIV co-infected patients. The distribution of HBV genotypes was: HBV/H 56 (66%), HBV/G 22 (26.1% [95% CI 17% to 36%]), HBV/F 4 (4.7%) and HBV/A 2 (2.3%). The most frequent mutations presented in 9 HIV co-infected patients and one mono-infected patient with ART experience were rtM204V and seven of them showed genotype G (7/9). Mono-infected HBV patients exposed more probability to HBV/H genotype than co-infected HIV patients OR 13.0 (CI 95% 3.40-49.79), P=0.0001 In contrast co-infected patients presented less possibility to have genotype H, 0.56 (CI 95% 0.42-0.75).Our results suggest that HBV/G genotype predominates in co-infected patients. As well, rtM204V and rtL180M mutations are common in HBV/HIV co-infected patients with genotype G and ART experience."} +{"text": "Urinary tract infections are the main indication for antimicrobials in elderly.Despite the treat for resistance dissemination and therapy failure, clinicians are seldom informed on the per patient evolution of antimicrobial resistance in pathogens.Laboratory results were obtained from 13 voluntary diagnostic laboratories in Belgium during the year 2005. Susceptibility profiles were done by Kirby Bauer disk diffusion according to CLSI. The first two urine samples from patients older than 65 year were included.E. coli (7188/1654), E. faecalis (1282/403), P. mirabilis (1230/313), K. pneumonia (673/173), P. aeruginosa (293/120), E. aerogenes (375/203), S. aureus (158/54), M. morganii (347/89), Group B streptococci (149/31), C. freundii complex (101/29). When comparing first versus second samples antibiograms for E. coli, a decrease in susceptibility was found for the following antimicrobial agents: cotrimoxazole -6.9%; nitrofurantoin -2.8%, fosfomycin 0.0%; ciprofloxacin -10.8%; cefuroxime -5.6%; amoxicillin-clavulanic acid -5.6%; ampicillin -10.5%. For E. faecalis, marked decreases were found for nitrofurantoin -2.4%; fosfomycin -2.2%; -ciprofloxacin -10.3%; and only mild decreases for amoxicillin-clavulanic acid 0.0%; and ampicillin -1.2%. For K. pneumoniae decreases were in the range of -2.9 to -4.1% for cotrimoxazole, ciprofloxacine, cefuroxime and amoxicillin-clavulanic acid, and was -12.4% for nitrofurantoin. For S. aureus and C. freundii no decrease (<-0.1%) was seen for nitrofurantoin and fosfomycin. For E. aerogenes, decreases of -18 and -12.5% were found for cotrimoxazole and fosfomycin, respectively. M. morganii showed in consecutive samples less susceptibility for cotrimoxazole (-16.2%), fosfomycine (-13.0%) and ciprofloxacin (-10.5%), while only a marginal decrease was found for nitrofurantoin (-0.5%).Following organisms were predominantly isolated (N first samples/N second samples): The resistance selection influence of consecutive samples depends on the antibiotic-bacterium combinations, and thus might be taken into account when empiric therapy guidelines for urinary tract infections in elderly are reviewed.None declared"} +{"text": "In patients undergoing atrial fibrillation (AF) procedures, imaging of the left atrium (LA) and pulmonary veins (PV) is important for pre-ablation planning and to identify post ablation complications. Conventional MRA protocols use first-pass, non-gated sequences that require long breath-holds. Quality of non-gated MRA's can be challenging in sick or sedated patients. We developed a novel ECG-gated, respiratory navigated MRA sequence less dependent on patient compliance, which yields better clarity of LA anatomy.Eighty patients with AF underwent either conventional non-gated (n=40) vs. novel ECG-gated (n=40) MRA on a 3T Verio scanner . All MRA's were performed using 0.1 mmol/kg Multihance . A novel ECG-gated, respiratory navigated MRA was developed using 3D saturation recovery prepared, GRE sequence with fast contrast injection followed by slow infusion . Saturation pulse was applied every heart beat and fat saturation was applied immediately before data acquisition during LA diastole. Additional scan parameters were: axial imaging volume, FOV =400x400x110, voxel size=1.25x1.25x2.5 mm, TR/TE=2.8/1.3ms, flip angle=15 degrees, TI=250ms, phase encoding direction: left to right. Typical scan time was 3-5 minutes.Conventional non-gated MRA were performed with contrast injection rate 2.0 mL/sec and continuous data acquisition during single breath-hold (14 sec.). Scan parameters included: axial imaging volume, FOV=400x263x120 mm, voxel size=1.25x1.25x2.5, TR/TE=2.8/1.1ms, flip angle=27 degrees.All MRA's were randomized and quality scores were determined by two experienced readers for contrast enhancement, border sharpness, and chamber detail of the PV's, LA, and LA appendage (LAA) . in the non-gated cohort. Border sharpness scored 3.08 vs. 2.35 QS respectively. Chamber detail was also assessed with specific anatomical positions, which all yielded superiority of ECG-gated MRA ; left atrial appendage 3.11 vs. 2.25 QS ; left atrium 3.08 vs. 2.35 QS .ECG-gated MRA improves image quality with better border sharpness and anatomical detail compared to conventional non-gated MRA. These advantages may translate into improved diagnostics in AF patients including detection of PV stenosis or following LA remodeling post-ablation.No disclosures."} +{"text": "AbstractStenohya Beier, 1967 are described from China: Stenohya pengaesp. n. and Stenohya huangisp. n. .The presence of Stenohya pengaesp. n. in the tree crown of Castanopsis fabri represents a new habitat for Neobisiidae. A key and a distribution map of the Chinese Stenohya species are also provided.Two new species of the genus Stenohya Beier, 1967 is a small Asian pseudoscorpion genus of the family Neobisiidae Chamberlin, 1930. At present it includes 12 species , Stenohya curvata Zhao et al., 2011 (Yunnan Province) and Stenohya xiningensis Zhao et al., 2011 (Qinghai Province). species , of whicFagaceae, Styracaceae, Daphniphyllaceae, Lauraceae and Ericaceae by sweeping vegetation with an entomological net. After examining the specimens in the laboratory, we found them to represent a new species, which is described here under the name Stenohya pengae sp. n. When we examined the pseudoscorpions collected by Prof. Fusheng Huang from Gushan Mountain, Fujian Province, China, we found another new Stenohya species, which is also described and illustrated in this paper as Stenohya huangi sp. n.Damingshan National Nature Reserve is located in the midwest of Guangxi Zhuang Autonomous Region, lying on the Tropic of Cancer, and possesses a rich subtropical primeval forest, which is home to many rare animals and plants. Daming Mountains are densely covered by jungle, including trees of the families ricaceae . In 2011b = basal; sb = sub-basal; st = sub-terminal; t = terminal; ib = interior basal; isb = interior sub-basal; ist = interior sub-terminal; it = interior terminal; eb = exterior basal; esb = exterior sub-basal; est = exterior sub-terminal; et = exterior terminal.The specimens are preserved in 75% alcohol and deposited in the Museum of Hebei University (MHBU). Permanent slide mounts were prepared by removing the chelicerae, pedipalps, leg I and leg IV from specimens with small needles and clearing overnight with lactic acid at room temperature. Drawings were made with the aid of a camera lucida mounted above the eyepiece of a compound microscope. Photographs were taken with a Leica M165 stereomicroscope. Terminology of trichobothria follows urn:lsid:zoobank.org:act:3E8D205C-B127-4BE0-AC87-B029B7F9719Fhttp://species-id.net/wiki/Stenohya_pengae23\u00b008'N, 108\u00b017'E], alt. 1250 m, 21 May 2011, Yan-qiu Peng leg. Tree-crown layer of Castanopsis fabri. Paratypes: 17 males and 25 females, same data as for holotype.Holotype male (Ps.-MHBU-GX110521), China: Guangxi Province, Nanning City, Daming Mountain , 24 February 1975, Fu-sheng Huang. Habitat unknown.PageBreakHolotype female (Ps.-MHBU-FJ750224), China: Fujian Province, Fuzhou City, Gushan Mountain [The specific name is a patronym in honour of Prof. Fu-Sheng Huang, who collected and donated the specimen.it and et at same level.Species with slender pedipalps and slender legs IV (e.g. femur+patella 7.23 times as long as deep), with low numbers of the teeth (about 30) on movable chelal finger; trichobothria . Colour Carapace smooth, Abdomen. Pleural membrane strongly granulate. Tergal chaetotaxy: 4: 12: 10: 10: 10: 10: 11: 11: 11: 10: 9, including at least 4 tactile setae on tergites VI\u2013XI; anterior genital sternite with 22 PageBreakof femur with fine granulation; patella claviform, smooth; chelal fingers long and slender. Trichobothriotaxy: est, et and it grouped together distally; ist situated midway between isb and it, nearer to it than to isb. eb and esb situated on base of the hand, grouped very closely with ib and isb; b and sb closer to each other situated on the basal half, and st andPageBreakt closer to each other situated on the distal half of the movable finger. Fixed chelal finger with 63 pointed teeth of unequal length, movable finger with about 30 teeth which with 20 pointed teeth slightly unequal length in distal half, and 10 rounded teeth in basal half.Pedipalps . Apex ofCheliceral palm with 7 sLegs . Tibia IDimensions (in mm) and ratios (in parentheses). Body length 4.2. Carapace 1.29/0.89 (1.45); diameter of anterior eye 0.10; diameter of posterior eye 0.09. Pedipalps: trochanter 0.59/0.26 (2.27), femur 1.58/0.25 (6.32), patella 1.38/0.26 (5.31), chela (with pedicel) 2.58/0.53 (4.87), chela (without pedicel) 2.42 (4.57), hand length (without pedicel) 1.04 (1.96), movable finger length 1.44 (1.38 times longer than hand without pedicel). Chelicera 0.67/0.38 (1.76), movable finger length 0.45. Leg I: femur 0.79/0.13 (6.08), patella 0.59/0.13 (4.54), tibia 0.63/0.10 (6.30), basitarsus 0.45/0.10 (4.50), telotarsus 0.43/0.10 (4.30). Leg IV: femur + patella 1.52/0.21 (7.24), tibia 1.22/0.12 (10.17), basitarsus 0.59/0.10 (5.90), telotarsus 0.79/0.10 (7.90).This species is known only from the type locality.Stenohya huangi sp. n. is only known from the female, but it can be easily separated from most other species of this genus by the proportions of pedipalpal femur and patella . Finally, the new species differs from Stenohya vietnamensis in having an epistome. patella . Two speme level in Stenot and et : fig. 28Neobisiidae the lyrifissures near the trochanteral foramen of the pedipalpal coxa number 3 or 4 has 6 foramenal lyrifissures and 1 dorsal lyrifissure (PageBreakIn most r 3 or 4 . Having dorsally . Males o foramen : fig. 3 ifissure ."} +{"text": "AbstractBambusananus cuihuashanensissp. n. , a new bamboo-feeding leafhopper species, is described and illustrated from Shaanxi Province of China. Checklist, host plants and distribution for each species of Bambusananus is given along with a key to all known species. Athysanini, was established by Van Duzee in 1892 and is the largest tribe of Deltocephalinae, including 228 genera and 1123 species was established by Bambusananus furcatus Li & Xing, 2011, from Guizhou Province of China as its type species, and three new combinations: Bambusananus binotatus , Bambusananus bipunctatus and Bambusananus maculipennis were proposed at the same time. Bambusananus bipunctatus , Bambusananus maculipennis , Bambusananus furcatus Li & Xing, 2011, Bambusananus lii and Bambusananus yangae Xing & Chen, 2013 and are currently known only from southern mainland China and Taiwan .In the present paper, terminology follows 1.Bambusananus bipunctatus (in 1999) in Indocalamus hirsutissimus Z. P. Wang & P. X. Zhang and Qiongzhuea communis Hsueh & Yi) (Host plant. Bamboo (eh & Yi) .Distribution. China .PageBreak2.Bambusananus maculipennis Chimonobambusa pachystachys Hsuch & W. P. Zhang and Qiongzhuea communis Hsueh & Yi) (Host plant. Bamboo (eh & Yi) .Distribution. China (Guizhou) .3.Bambusananus cuihuashanensis sp. n.Host plant. Bamboo.Distribution. China (Shaanxi) .4.Bambusananus furcatus Li & Xing, 2011Chimonobambusa angustifolia C. D. Chu & C. S. Chao) (Host plant. Bamboo (S. Chao) .Distribution. China (Guizhou) .5.Bambusananus lii Host plant. Bamboo .Distribution. China (Taiwan) .6.Bambusananus yangae Xing & Chen, 2013Indocalamus sp.) (Host plant. Bamboo (mus sp.) .Distribution. China (Guizhou) .http://zoobank.org/4B853422-EEC6-41EB-AD6B-B1570C4E92E2http://species-id.net/wiki/Bambusananus_cuihuashanensisChina: Shaanxi, Xi\u2019an, Cuihuashan , on bamboo, 37 Aug. 2008, J.-D. Li; paratypes: 2 \u2642\u2642, 4 \u2640\u2640, same data as holotype.Holotype: \u2642, The new species is named after its locality, Cuihuashan, Shaanxi Province, China.Body length (from apex of vertex to tip of forewings): male 4.75\u20134.85 mm (N = 2); female 5.75\u20135.90 mm (N = 4); forewing length: male 3.95\u20134.05 mm (N = 2); female 5.00\u20135.15 mm (N = 4).Crown pale yelExternal features as in generic description. Crown shorter medially than width between eyes (0.54:1). Pronotum longer medially than crown (2.10:1). Scutellum shorter medially than pronotum (0.89:1). Forewing longer medially than width at widest part (3.38:1).Male pygofer with basBamboo.PageBreakPageBreakChina (Shaanxi) .Bambusananus bipunctatus in general appearance, but can be distinguished by: pygofer in lateral view with ventral margin broadly smoothly rounded, without notch at base of ventral process (with notch in Bambusananus bipunctatus); connective with stem slightly shorter than arms (longer in Bambusananus bipunctatus); aedeagal shaft with appendages longer, in lateral view with apex reaching to middle of aedeagus . This new species is also similar to Bambusananus lii , but can be distinguished by: upper area of frontoclypeus with a large kidney-shaped black marking (lacking in Bambusananus lii); ventral margin of pygoger without any lobe (with a lobe near middle in Bambusananus lii); appendages of aedeagal shaft mostly straight basally, apex directed laterally ; ventral margin of aedeagus without any teeth (with a row of teeth at middle in Bambusananus lii).This new species is similar to"} +{"text": "We previously reported a cross-sectional association between the presence of human herpesvirus 8 (HHV-8) serum antibodies and screen-detected prostate cancer in men living in Tobago. In the same study population, we examined the association between HHV-8 seropositivity and incident prostate cancer discovered at later screenings.In 40-81 year-old men without prostate cancer discovered at initial digital rectal examination (DRE) and prostate-specific antigen (PSA) screening, a case-cohort design measured the association between baseline HHV-8 seropositivity (modified immunofluorescence assay for antibodies against HHV-8 lytic antigens) and incident prostate cancer detected at DRE and PSA screenings three or five years later.vs. 9.9% seropositive; crude odds ratio (OR) 3.96, 95% confidence interval (CI) 1.53-10.2; age-adjusted OR 2.42, 95% CI 0.91-6.47). HHV-8 seropositivity did not increase incident prostate cancer risk (age-adjusted hazard ratio (HR) 0.88, 95% CI 0.46-1.69).Analyses included 486 unique individuals, 96 incident prostate cancer cases, and 415 randomly selected subjects representing an at-risk cohort. By design, the random sub-cohort contained 25 incident prostate cancer cases. In the sub-cohort, the frequency of HHV-8 seropositivity increased across age groupings . HHV-8 seropositivity was higher in men with elevated (\u2265 4.0 ng/mL) than men with non-elevated PSA at initial screening . Co-occurrence of HHV-8 seropositivity and PSA elevation may explain cross-sectional association between HHV-8 and PSA screen-detected prostate cancer. Neisseria gonorrhoeae, Chlamydia trachomatis, human papillomavirus (HPV) type 18, and Treponema pallidum (syphilis) measures of unadjusted and age-adjusted association between HHV-8 seropositivity measured at baseline (Wave 1) and prostate cancer detected later in time, at Wave 2 or Wave 3 [We used the chi-square test to evaluate 1) the statistical significance of differences between at-risk men with incomplete r Wave 3 . These mvs. 26.0% \u2265 60 years), smoking history (48.5% vs. 39.6%), personal cancer history (1.3% vs. 0.3%), Wave 1 PSA \u2265 4 ng/mL (13.5% vs. 5.5%), and Wave 1 DRE (64.7% vs. 76.3% negative and 20.0% vs. 10.3% missing).Table vs. 5.5% PSA \u2265 4 ng/mL), and more frequently positive Wave 1 prostate cancer screening (43.8% vs. 16.9% DRE or PSA positive). Case and sub-cohort HHV-8 seropositivity rates were 17.7% and 11.1%, respectively. When compared with 40-49 year-old sub-cohort men (3.5% HHV-8 seropositive), HHV-8 seropositivity was higher in 50-59 year-old sub-cohort men (13.6% HHV-8 seropositive) and higher yet in \u2265 60 year-old sub-cohort men (22.9% HHV-8 seropositive). HHV-8 seropositivity rates were lower in sub-cohort men with a history of smoking than those without (7.1% vs. 13.9%) and higher in sub-cohort men with a history of benign prostatic hypertrophy than those without (24.0% vs. 10.5%). HHV-8 seropositivity increased with Wave 1 PSA . HHV-8 seropositivity was higher in men with elevated (\u2265 4.0 ng/mL) than men with non-elevated PSA . HHV-8 seropositivity was higher in sub-cohort men with a positive than in men with a negative Wave 1 prostate cancer screen result (20.0% vs. 9.3% seropositive).Wave 1 HHV-8 serologic status was available for 415 (93.9% of 442) men in the sub-cohort and for 96 (88.1% of 109) men in the case group . Table vs. 3.5% and 50-59 years: 10.8% vs. 13.6%), except in the oldest age group (\u2265 60 years: 27.7% vs. 22.9%). In men with a non-elevated (< 4 ng/mL) Wave 1 PSA, the HHV-8 seropositivity rate was higher in the case group (17.1% vs. 9.9%). In men with an elevated (\u2265 4 ng/mL) Wave 1 PSA, however, the HHV-8 seropositivity rate was lower in the case group (19.2% vs. 30.4%). In the two age sub-groups with appreciable HHV-8 seropositivity, age-specific HHV-8 seropositivity rates were not consistently higher or lower in case than sub-cohort men with non-elevated Wave 1 PSA (50-59 years: 11.5% vs. 13.7% and \u2265 60 years: 28.1% vs. 20.4%) and consistently lower in case than sub-cohort men with elevated Wave 1 PSA (50-59 years: 9.1% vs. 12.5% and \u2265 60 years: 26.7% vs. 41.7%).Table Table Our previous study used an immunofluorescence assay to measure HHV-8 antibodies in 138 prostate cancer cases and in 140 age-matched controls . HHV-8 se.g., PSA \u2265 4 ng/mL, age-adjusted HR 0.39, 95% CI 0.10-1.63; Table A positive association between HHV-8 seropositivity and prevalent prostate cancer in a cross-sectional study and an iFour comparative studies of HHV-8 and prostate cancer have appeared ,11,26,27Analyses restricted to the sub-cohort showed strong association 1) between HHV-8 seropositivity and increasing age, a result also seen in Tobago women and manyStudy strengths include unique population and setting (predominantly African ancestry Tobago residents ) and a cOur prospective study could not demonstrate an association between HHV-8 seropositivity and incident prostate cancer. However, analyses uncovered a strong relationship between elevated HHV-8 seropositivity and PSA. The HHV-8 association previously observed with prevalent prostate cancer may signify enhanced detection of prostate cancer possibly caused by the effects of HHV-8 on PSA. In this context, the association we observed between HHV-8 seropositivity and PSA elevation deserves further study.HHV-8: human herpesvirus 8; DRE: digital rectal examination; PSA: prostate-specific antigen; OR: odds ratio; CI: confidence interval; HR: hazards ratio; HPV: human papillomavirus; PLCO: Prostate Lung Colorectal, and Ovarian Cancer Screening Trial.The authors declare that they have no competing interests.ACM participated in study design, data analysis and interpretation, prepared a first draft of the manuscript, and helped revise the final manuscript. FJJ completed immunofluorescence assays and helped revise the final manuscript. CHB conceived the study, acquired data, provided study coordination, and helped revise the final manuscript. JWW selected analytic methods and directed statistical analysis. ALP acquired data and provided study coordination. JLW participated in study design, data analysis and interpretation and helped revise the final manuscript. All authors read and approved the final manuscript."} +{"text": "To determine the nosocomial acquisition rate of ESBL-E among patients and healthcare workers (HCWs) during an epidemic (March 2009 to Nov 2010) in an orthopaedics ward at HUG.Universal screening made by anal swab of all patients on admission and every 2 weeks if screening remained negative. 49 samples were collected from 41 HCW and 60 environmental samples were analysed. Molecular typing was performed on all ESBL-E isolates. If there was more than 97.5% similarity, strains were considered identical.Between March 2009 and November 2010, 1\u2019531 admissions occurred to the orthopaedic ward . Among 565 anal swabs, ESBL-E were detected in 204 samples from 45 patients.E. coli (n=39), Klebsiella pneumoniae (n=10), Enterobacter spp (n=8), Citrobacter spp (n=2), Morganella morganii (n=2), and Proteus vulgaris (n=1). Two different ESBL-E strains were detected in 6 patients, and 3 others carried three distinct isolates. The ESBL-E transmitted were E. coli (14 patients), K. pneumoniae (3 patients) and both in 2 patients.The ESBL-E found were Identical ESBL-E species with epidemiological links were found in 25 cases. Only 9 of these were attributable to the unit. Most positive patients (96% [43/45]) were colonized asymptomatically with ESBL-E.Among HCWs, 6 samples (12%) were positive. Transmission was only observed between patients, not HCWs.None of the environmental samples revealed presence of ESBL-E.Transmission of ESBL-E strains was only observed between patients. No transmission between HCWs and patients occurred. HCW screening and environmental sampling is not useful during ESBL-E carriage outbreaks.E. coli.The main ESBL-E transmitted was E. coli-ESBL carriers.ESBL-E transmission can occur in units with extended length of stay, questioning the new Swiss policy of abandoning contact precautions for None declared"} +{"text": "In the Phase III, randomised, open-label ODIN trial, treatment-experienced HIV-1-infected adults with no screening DRV resistance-associated mutations received DRV/r 800/100mg qd or DRV/r 600/100mg bid (both arms + \u22652 NRTIs). At Week 48, 72.1% qd vs 70.9% bid patients achieved HIV-1 RNA <50 copies/mL , confirming non-inferiority of DRV/r qd. The relationship between DRV PK and efficacy and safety following treatment with DRV/r is explored.0h) and exposure using a population pharmacokinetic model. Relationships between PK parameters and efficacy were assessed using ANCOVAs. Relationships between PK parameters and occurrence of adverse events of interest and laboratory lipid abnormalities were evaluated using descriptive statistics.Sparse blood sampling for PK evaluations was taken at Weeks 4, 8, 24 and 48 to determine DRV trough concentrations (C0h was 1896 (184-7881) ng/mL for DRV/r qd and 3197 ng/mL for DRV/r bid. Median (range) AUC24h for DRV/r qd was 87,788 ng.h/mL and 109,401 ng.h/mL for bid. No relevant relationships were observed between DRV PK and efficacy: changes from baseline in HIV-1 RNA log10 copies/mL at Week 48 for pooled data by DRV AUC24h quartile ranges were -2.06, -2.22, -2.19, and -2.08 log10 copies/mL, respectively. The % patients achieving HIV-1 RNA <50 copies/mL by these quartile ranges were 82.0%, 88.5%, 82.6% and 76.5% (observed data), respectively. In a logistic regression analysis adjusting for baseline viral load, AAG levels and number of sensitive NRTIs in the optimised background regimen, there were no relevant relationships between PK and virological response. No apparent relationships were observed between DRV PK and occurrence of rash-, cardiac-, GI-, liver-, lipid- and glucose-related AEs or laboratory lipid abnormalities.PK data were available for 280 DRV/r qd patients and 278 bid patients. Median (range) C0h and AUC24h compared to DRV/r 600/100mg bid; however, comparable efficacy between DRV/r qd and bid confirmed adequate DRV concentrations were achieved following qd dosing. No relevant relationships were observed between DRV PK and efficacy or safety at Week 48.Dosing with DRV/r 800/100mg qd resulted in lower C"} +{"text": "Tricholepidion gertschi is the sole extant representative of the family Lepidotrichidae. Its phylogenetic position is of special interest, since it may provide crucial insights into the early phenotypic evolution of the dicondylian insects. However, the phylogenetic position of T. gertschi is unclear. Originally, it was classified among silverfish (Zygentoma), but various alternative relationships within Zygentoma as well as a sistergroup relationship to all remaining Zygentoma + Pterygota are discussed, the latter implying a paraphyly of Zygentoma with respect to Pterygota. Since characters of the head anatomy play a major role in this discussion, we here present the so far most detailed description of the head of T. gertschi based on anatomical studies by synchrotron micro-computer tomography and scanning electron microscopy. A strong focus is put on the documentation of mouthparts and the anatomy of the endoskeleton as well as the muscle equipment. In contrast to former studies we could confirm the presence of a Musculus hypopharyngomandibularis (0md4). The ligamentous connection between the mandibles composed of Musculus tentoriomandibularis inferior (0md6) is also in contact with the anterior tentorium. Phylogenetic analysis of cephalic data results in monophyletic Zygentoma including T. gertschi. Zygentoma are supported by the presence of a set of labial muscles originating at the postocciput, presence of an additional intralabral muscle, and four labial palpomeres. Character systems like the genitalic system, the mating behaviour, the segmentation of the tarsi, the overall body form, and the presence of ocelli which were proposed in other studies as potentially useful for phylogenetic reconstruction are evaluated.The relic silverfish Trichlepidion gertschi occurs only in the coastal region of northern California. The species is characterized by a number of peculiarities with respect to all other extant silverfish species (= Euzygentoma) such as the presence of ocelli (in addition to compound eyes), 5-segmented tarsi [T. gertschi is the sister species to all other dicondylians (Zygentoma + Pterygota), sister species to all other Zygentoma, or a subgroup within Zygentoma . Moleed tarsi -7 and moed tarsi -13 disagT. gertschi is crucial to understand the evolution of several morphological characters in the stem lineage of Dicondylia, e.g. presence of a proventriculus [However, the phylogenetic position of triculus , sperm ctriculus ,21, the triculus ,14 and ttriculus includintriculus .T. gertschi to remaining Zygentoma [T. gertschi with a strong focus on the documentation of mouthparts, endoskeleton and muscle equipment. We show that characters of the cephalic morphology indeed provide information on a sistergroup relationship of T. gertschi and the remaining studied Zygentoma.Available cephalic data did not help thus far to resolve the phylogenetic relationships of ygentoma ,14. Thissynchrotron radiation micro-computer tomography (SR-\u03bcCT), so that they could be used to complement the character matrix , Thermobia domestica (Lepismatidae), Lepisma saccharina Linneaus, 1758 (Lepismatidae), and Atelura formicaria Heyden, 1855 (Nicoletiidae). The outer anatomy of T. gertschi was furthermore investigated with scanning electron microscopy (SEM).All specimens were fixed in Bouin's solution and inveSR-\u03bcCT was done using the recommendations of Betz et al. and the http://www.blender.org). Both software packages are distributed under the general public license (GPL). Tables and figures were edited with GIMP ver. 2.8, Inkscape ver. 0.48 and Scribus ver. 1.4.1 . A 3D model of the head of T. gertschi is available the specimen was transferred in a series of steps into 100% ethanol, critical point dried , and sputter coated (Model Anatech Hummer VII). Microscopy was performed on a Hitachi S-2460 N scanning electron microscope using a rotatable sample holder . The terMachilis germanica was selected as the outgroup. Only unambiguous changes were mapped on the optimal trees. Character numbers and states are given in brackets using the following syntax: (character number : character state). The character matrix is derived from Blanke et al. [Parsimony analyses of 139 cephalic characters (see Appendix) and Bremer support (BR) calculations were carried out with TNT using 1,e et al. and is be et al. . Please 2. Among them, numerous (>500/100 \u03bcm2) small tubercles on the exoskeleton, possibly sensorial in function, cover the entire head : insertion directly anterior of 0md1 (muscle \"spt\" of Chaudonneret [0te2): the insertion in between the muscle bundles of 0md1 supports homologisation with the muscle \"spot\" of Chaudonneret [0te3): O, anterior side of the dorsal tentorial arm; I, frons near the dorsal part of the antennal base. M. posterotentorialis (0te4): absent. M. tentoriotentorialis longis (0te5): O, ventrolaterad on the anterior corpotentorium; I, mesad on the posterior tentorium. M. tentoriotentorialis brevis (0te6): O, anterior tentorium, along the gap towards the posterior tentorium; I, posterior tentorium, along the gap towards the anterior tentorium.Musculature: M. tentoriofrontalis posterior (donneret ); O, at donneret ; O, at tThe convex labrum Figures is cover0lb1): O, mesally on the epistomal ridge; I, mesally on the inner basal wall of the labrum. M. frontoepipharyngalis (0lb2): absent. M. epistoepipharyngealis (0lb3): this muscle can easily be confused with the 0lb2. The origin of 0lb3 lies clearly only on the epistomal ridge. O, laterally on the epistomal ridge; I, basal epipharyngeal wall. M. labralis transversalis (0lb4): absent. M. labroepipharyngealis (0lb5): O, basal labral wall; I, basal wall of epipharynx. M. labrolabralis (0lb6): O, mesobasal labral wall in between the two bundles of 0lb5; I, medioapical area of labrum.Musculature: M. frontolabralis : O, mesally on the corpotentorium; I, anterior margin of the scapus. M. tentorioscapalis posterior (0an2): O, in the posterior part of the corpotentorium; I, posterior basal margin of the scape. M. tentorioscapalis lateralis (0an3): O, at the anterior base of the dorsal tentorial arms; I, dorsal basal margin of the scape. M. tentorioscapalis medialis (0an4): O, at the dorsal tentorial arms directly over 0te1; I, dorsal basal margin of the scape. M. frontopedicellaris (0an5): absent. M. scapopedicellaris lateralis (0an6): O, broadly on the dorsolateral base of the scape; I, dorsolateral base of the pedicellus. M. scapopedicellaris medialis (0an7): O, ventrolateral base of the scape; I, ventrolateral base of the pedicel. M. intraflagellaris (0an8): absent. M. interampularis (0ah1): absent. M. ampulloaortica (0ah2): absent. M. ampullopharyngealis (0ah3): absent. M. ampullofrontalis (0ah4): absent. M. frontofrontalis (0ah5): absent.Musculature: M. tentorioscapalis anterior reaches into the lumen of the mandible directly posterad the mandibular ridge Figure . The twoThe mola is almost formed like a right-angled triangle in lateral view Figure , with th0md1): O, dorsal parts of the head, anterior of the postoccipital ridge and on this ridge; one muscle bundle also posterior of the postoccipital ridge; I, tendon originating from the proximal part of the posterior mandibular edge. M. craniomandibularis externus anterior (0md2): O, gena, anterior of the compound eye; I, tendon originating from the proximal part of the anterior mandibular edge, directly lateral to the anterior articulation complex. M. craniomandibularis externus posterior (0md3): O, directly posterior of the compound eye, with several bundles also at the postoccipital ridge; I, tendon originating from the anterior mandibular edge near the posterior articulation. M. hypopharyngomandibularis (0md4): O, small sclerite close to the loral arm of the hypopharynx; I, proximal inner side of the anterior wall of the mandible. M. tentoriomandibularis lateralis superior (0md5): O, ventrally at the anterior tentorial arm; I, anterior mandibular rim between 0md2 and 0md3. M. tentoriomandibularis lateralis inferior (0md6): O, the whole inner wall of the mandible except for the region near the incisivi and mola; I, in the same region of the other mandible and with a few muscle bundles also at the ventral anterior area of the corpotentorium. M. tentoriomandibularis medialis superior (0md7): O, at the ventral base of the anterior tentorial arms; I, proximal of the posterior articulation at the posterior mandibular rim. M. tentoriomandibularis medialis inferior (0md8): O, at the transition of the corpotentorium and the anterior tentorial arm below 0md7; I, mediodorsal wall of the mandibular cavity.Musculature: M. craniomandibularis internus is three times longer than wide in overall shape Figure . The carThe stipes is composed of a narrow basistipes and a much larger mediostipes bearing the palpus, galea and lacinia Figure . The whoThe palpus is five-segmented and densely covered with trichoid sensilla. The first segment is one third as long as the second one. The third one is slightly longer than the second one, the fourth and fifth are as long as the second one. Each segment is slightly thinner than the preceding one. The fifth segment bears distally six special sensilla formed by a basal cylindrical segment densely covered with microtrichia and four to six tubular extensions on the tip of the cylindrical base Figures . These sThe galea is sickle-shaped Figure , distall0mx1): O, laterally at the postoocipital ridge; I, basal cardinal process. M. craniolacinialis (0mx2): O, distal of 0mx1 at the postoocipital ridge; I, cuticular tendon at the basal edge of lacinia together with 0mx6. M. tentoriocardinalis (0mx3): O, at the lateral part of the posterior tentorium; I, inner wall of the cardo. M. tentoriostipitalis anterior (0mx4): O, ventral on the corpotentorium; I, at the posterior stipital rim. M. tentoriostipitalis posterior (0mx5): O, lateral on the corpotentorium; I, at the basal inner wall of the stipes. M. stipitolacinialis (0mx6): O, posterior wall of the stipes, basal to the cardostipital ridge; I, basal proximal edge of lacinia, at a common cuticular tendon with 0mx2. M. stipitogalealis (0mx7): O, posterior wall of the stipes, basal to the cardostipital ridge next to 0mx6; I, basal edge of galea. M. stipitopalpalis externus (0mx8): O, posterior wall of the stipes, opposite of the palpus; I, posterior rim of the first palpomere of the maxillary palpus. M. stipitopalpalis medialis (0mx9): O, medially at the posterior wall of the stipes; I, ventral edge of palpomere 1. M. stipitopalpalis internus (0mx10): O, posterior inner wall of the stipes, opposite of the palpus; I, anterior rim of the first palpomere of the maxillary palpus. M. stipitalis transversalis (0mx11): O, outer stipital wall, near the palpus; I, inner stipital wall, near the palpus. M. palpopalpalis maxillae primus (0mx12): O, basal edge of palpomere 1; I, basal edge of palpomere 2. M. palpopalpalis maxillae secundus (0mx13): O, mesal edge of palpomere 2; I, mesal edge of palpomere 3. M. palpopalpalis maxillae tertius (0mx14): O, basal edge of palpomere 3; I, basal edge of palpomere 4; M. palpopalpalis maxillae quartus (0mx15): unclear.Musculature: M. craniocardinalis : O, posterior side of the postoccipital ridge; I, proximal area of the glossal base. M. postoccipitoglossalis lateralis (0la2): O, posterior side of the postoccipital ridge, right next to 0la1; I, dorsolateral area of the glossal base. M. postoccipitoparaglossalis (0la3): O, posterior side of the postoccipital ridge, lateral of 0la1 & 0la2; I, distal base of the paraglossa. M. postoccipitopraementalis (0la4): O, posterior side of the postoccipital ridge, right next to 0la1 & 0la2; I, inner proximal wall of the prementum. M. tentoriopraementalis (0la5): O, lateral area of the posterior tentorium; I, laterobasal edge of prementum. M. tentorioparaglossalis (0la6): O, lateral area of the posterior tentorium, right next to 0la5; I, paraglossa, close to the labial palpus. M. tentorioglandularis (0la7): O, lateral posterior area of the corpotentorium; I, labial gland. M. submentopraementalis (0la8): O, medially on the postmentum; I, mediobasal edge of prementum. M. postmentomembranus (0la9): unclear. M. submentomentalis (0la10): absent. M. praementoparaglossalis (0la11): O, distal on the basal edge of the prementum; I, basal edge of paraglossa. M. praementoglossalis (0la12): O, more mesally on the basal edge of the prementum, right next to 0la11; I, basal edge of glossa. M. praementopalpalis internus (0la13): O, mesally on the prementum; I, anterior basal edge of labial segment 1. M. praementopalpalis externus (0la14): O, mesally on the prementum, right next to 0la13; I, posterior basal edge of labial segment 1. M. praementomembranus (0la15): O, anterolateral area of the postmentum; I, anteromedial area of postmentum. M. palpopalpalis labii primus (0la16): O, mediobasal edge of labial palpomere 1; I, medial and distal edge of palpomere 2. M. palpopalpalis labii secundus (0la17): O, mediobasal edge of palpomere 2; I, basal edge of the palpomere 3.Musculature: M. postoccipitoglossalis medialis : O, frons, near the antennal base; I, oral arms of the suspensorial sclerites. M. tentoriooralis (0hy2): O, anterior tentorial arm, near the anterior tentorial pit; I, one muscle bundle on the oral arms of the suspensorial sclerites, one bundle at the lateral buccal wall: both bundles are well separated from 0hy1. M. craniohypopharyngealis (0hy3): O, posterior tentorial arms; I, suprasalivarial sclerite. M. postoccipitalohypopharyngealis (0hy4): O, posterior wall of the postoccipital ridge, together with 0la1 & 0la2; I, hypopharyngeal fulcrum. M. tentoriosuspensorialis (0hy5): O, anterior margin of the posterior tentorium; I, suspensorium of the hypopharynx. M. postmentoloralis (0hy6): O, anterior part of the postmentum; I, loral arm of the hypopharyngeal suspensorium. M. praementosalivaris anterior (0hy7): O, distolateral wall of the prementum, close to the labial palpus; I, lateral wall of salivarium. M. praementosalivaris posterior (0hy8): O, medially on the basal part of the prementum; I, posterior wall of salivarium. M. oralis transversalis (0hy9): unclear. M. loroloralis (0hy10): O, loral arm of suspensorial sclerite; I, loral arms of the suspensorial sclerites on the other side. M. lorosalivarialis (0hy11): O, hypopharyngeal suspensorium; I, loral arm of the hypopharynx. M. hypopharyngosalivaris (0hy12): O, loral arm of the hypopharynx, right next to 0hy11; I, salivarial orifice. M. anularis salivarii (0hy13): unclear.Musculature: M. frontooralis : two distinct muscle bundles. O, postclypeus; I, roof of the cibarium. M. clypeobuccalis (0bu1): O, clypeus, near the epistomal ridge; I, roof of the bucca. M. frontobuccalis anterior (0bu2): O, frons dorsal of the epistomal ridge; I, dorsal buccal wall. M. frontobuccalis posterior (0bu3): O, more posterior than 0bu2 on the frons; I, dorsal buccal wall, posterior of 0bu2. M. tentoriobuccalis lateralis (0bu4): absent. M. tentoriobuccalis anterior (0bu5): O, anteriormost part of the corpotentorium between the anterior tentorial arms; I, ventral wall of the bucca, directly behind the anatomical mouth. M. tentoriobuccalis posterior (0bu6): O, laterally on the dorsal wall of the corpotentorium; I, lateral wall of the foregut at height of the 0ph1. M. verticopharyngealis (0ph1): O, frons right next to the 0te4; I, dorsal wall of the foregut, posterior to the supraoesophagial ganglion. M. tentoriopharyngealis (0ph2): O, laterally on the dorsal wall of the corpotentorium right next to 0bu6; I, ventral wall of the foregut, beneath 0ph1. M. postoccipitopharyngealis (0ph3): absent. M. anularis stomodaei (0st1): ring muscle layer that covers the entire foregut. M. longitudinalis stomodaei (0st2): longitudinal muscle layer covering the entire foregut, right next to 0st1.Musculature: M. clypeopalatalis , presence of M. labroepipharyngealis (0lb5), M. verticopharyngealis (0ph1), M. tentoriopharyngealis (0ph2) and the five-segmented maxillary palpus.Generally, the monophyly of Dicondylia and Pterygota is well supported by molecular and morphological data ,41 even The monophyly of winged insects is strongly supported was considered absent [Tricholepidion) exhibit an origin of this muscle exclusively on the tentorium. Our phylogenetic analysis corroborates monophyletic Zygentoma despite the inclusion of the mandible ligament in the character matrix (character 69) with high support . Euzygentoma and T. gertschi possess a remarkable set of extrinsic labial muscles originating from the postoccipital region and extending dorso-ventrally through the whole head into the labium. Archaeognatha and Pterygota clearly do not possess this set of labial muscles [gertschi and Euzygentoma, possess four labial palpomeres (103:3). Also, the intralabral muscle equipment is characterized by an additional muscle, the M. epistoepipharyngalis . In the present analysis the low number of ommatidia is a homoplastic character since Grylloblattodea also show reduced eyes [Galloisiana yuasai [T. gertschi as sister to Euzygentoma.The position of ygentoma ,18, as sygentoma ,16, or aygentoma ,19 withid absent ,14 and dd absent ,44,45. Id absent ,44,45, w muscles ,44,46. Tced eyes which hoced eyes ). A M. la yuasai . Except Tricholepidion as sistergroup to Odonata with low support while Giribet [Tricholepidion as sister taxon to Euzygentoma + Pterygota with low support. All other molecular works supported monophyletic Zygentoma [With few exceptions most molecular studies advocate monophyletic Zygentoma. Based on secondary structure alignment of the 18S unit Kjer recovere Giribet , using aygentoma ,4,6,7.T. gertschi and Lepismatidae [T. gertschi Dallai et al. [T. gertschi resembles the ancestral state of insects with a 9 + 9 + 2 axonemal pattern and accessory tubules with 16 protofilaments. The sperm pairing in T. gertschi is a true fusion between two spermatozoa along the entire sperm head region, which is different from sperm aggregations in other Zygentoma [T. gertschi in smatidae . Zrzav\u00fd smatidae considersmatidae ). In a di et al. ,21 discoygentoma . Characteognatha ). The oveognatha ) and higeognatha .T. gertschi include similarities in the mating behaviour of T. gertschi and Lepismatidae [T. gertschi and some Nicoletiidae [Petrobiellus and Mesomachillis species [T. gertschi. The widening of the apical labial palpus segment is paralleled in males of several Machilidae and Meinertellidae and, heT. gertschi, since these occur as well in several pterygote taxa and the phylogenetic significance is therefore unclear. Zrzav\u00fd [T. gertschi, it is conceivable that five-segmented tarsi already existed in the stem lineage of Dicondylia. Engel [Also, we interpret the five-segmented tarsi not as a. Zrzav\u00fd considera. Engel even cona. Engel ).T. gertschi in its own family Tricholepidiidae because the extinct type species of the Lepidotrichidae, Lepidotrix pilifera Silvestri, 1912, might be more closely related to the Euzygentoma than to T. gertschi due to the apparent absence of ocelli [T. gertschi clearly possesses three ocelli, we consider this a weak argument for this classification, since loss of ocelli occurred several times within Dicondylia, e.g. in Xenonomia (= Notoptera + Mantophasmatodea), Phasmatodea [L. pilifera is mandatory. As for the head we partThe authors declare that they have no competing interests.AB, BW and BM designed the study, AB and FW conceived the experiments. AB and FW conducted the SR\u03bcCT, AB the SEM and phylogenetic analysis. AB, MK and BW carried out the analysis of the raw data. AB, MK, BW, and BM wrote the manuscript. All authors read, revised and approved the manuscript.List of characters used for phylogenetic reconstruction0. Orientation of head: (0) orthognathous; (1) prognathous or slightly inclined; (2) hypognathous1. Number of ocelli: (0) 0; (1) 2; (2) 3.2. Compound eyes: (0) composed out of more than 80 ommatidia; (1) less than 80 ommatidia;3. Distance between eyes: (0) less than their own width; (1) greater than their own width; (2) eyes fused at single point; (3) eyes broadly fused along an eye seam4. Shape of vertex: (0) flat, not developed into large protuberance; (1) conical, or developed into a large transverse ridge5. Epicranial or coronal suture: (0) present; (1) absent6. Parietal ridge: (0) absent; (1) present.7. Postoccipital ridge: (0) present; (1) absent.8. Subgenal ridge: (0) absent; (1) present9. Pleurostomal ridge and circumocular ridge: (0) not in contact; (1) partly in contact10. Interantennal ridge: (0) absent; (1) present11. Shape of frons: (0) flat when seen from lateral; (1) outwardly bulged when seen from lateral12. Distinct convexity ventrad the antennal bases: (0) absent; (1) present13. Scutellum: (0) absent; (1) present14. x-shaped median apodeme on the frontal region: (0) absent; (1) present15. Clypeus: (0) not subdivided; (1) subdivided into ante- and postclypeus16. Postclypeus: (0) not enlarged; (1) enlarged17. Anteclypeus: (0) membranous; (1) sclerotised18. Adult mouthparts: (0) with function; (1) without function19. Oval sclerotization of labral base: (0) absent; (1) present.20. Tormae: (1) absent; (0) present21. Mesal extension of tormae: (0) present; (1) absent22. M. epistoepipharyngealis (0 lb3): (0) present; (1) absent23. M. labroepipharyngealis (0 lb5): (0) present; (1) absent24. M. labrolabralis (0 lb6): (0) present; (1) absent25. Insertion of antennae: (0) close to the anterior mandibular articulation with the pleurostomal and circumantennal ridges in contact (where applicable); (1) distinctly separated from the anterior mandibular articulation, pleurostomal and circumantennal ridges not in contact.26. Antennifer: (0) present; (1) absent27. Length of pedicel and scapus: (0) pedicel longer than scapus; (1) scapus longer than pedicel; (2) scapus and pedicel equal in length28. Oval scerite in membrane connecting scapus and pedicellus: (0) absent; (1) present.29. Size of first flagellomere: (0) not enlarged; (1) first flagellomere more than twice as long as second one.30. Antennal stridulatory organ: (0) absent; (1) present31. Areas of origin of antennal muscle 0an1: (0) anterior tentorial arms only; (1) anterior tentorial arms and tentorial bridge; (2) on dorsal tentorial arms only; (3) on dorsal arms and tentorial bridge; (4) anterior and dorsal tentorial arm.32. Areas of origin of antennal muscle 0an2: (0) anterior tentorial arms only; (1) anterior tentorial arms and tentorial bridge; (2) on dorsal tentorial arms only; (3) on dorsal arms and tentorial bridge; (4) tentorial bridge only; (5) dorsal and anterior tentorial arms.33. M. tentorioscapalis lateralis (0an3): (0) present; (1) absent34. M. tentorioscapalis medialis (0an4): (0) present; (1) absent35. Circumesophageal vessel ring branching off the dorsal aorta posterior to the brain: (0) present; (1) absent36. Ostia of dorsal vessel: (0) lips always present; (1) ostia with and without lips (excurrent ostia).37. Position and number of excurrent ostia within a segment: (0) one ventrolateral pair; (1) ventromedian.38. Antennal circulatory organs in adults: (0) present; (1) absent39. Antennal vessel wall: (0) uniform; (1) bipartite40. Contractibility of antennal ampulla: (0) absent (non-pulsatile); (1) present (pulsatile).41. M. interampullaris (0ah1): (0) absent; (1) present42. M. ampulloaorticus (0ah2): (0) absent; (1) present43. M. ampullopharyngealis (0ah3): (0) absent; (1) present44. M. ampullo-frontalis (0ah4): (0) absent; (1) present45. Connection of antennal ampulla to supraoesophageal ganglion: (0) absent; (1) present46. Oval nuclei in tissue connecting the antennal ampulla and supraoesophageal ganglion: (0) absent; (1) present47. Anterior and posterior tentoria: (0) seperated; (1) merged48. Transverse mandibular tendon: (0) present; (1) absent49. Processes of the anterior tentorial apodemes extending into the lumen of the mandibular base: (0) absent; (1) present50. Corpotentorium: (1) elongated; (0) slim.51. Apophyses on the anterior surface of the corpotentorium: (0) absent; (1) present52. Secondary anterior tentorial bridge (\u201cperforation of the corpotentorium\"): (0) absent; (1) present.53. Lateral lobes on the anterior tentorial arms: (0) absent; (1) present54. Cuticular dorsal tentorial arms: (0) absent; (1) present55. Trabeculae tentorii of posterior tentorial arms (0) present; (1) absent56. M. tentoriofrontalis posterior (0te1): (0) present; (1) absent57. M. posteriotentorialis (0te4): (0) present; (1) absent58. M. tentoriotentorialis longus (0te5): (0) present; (1) absent59. M. tentoriotentorialis brevis (0te6): (0) present; (1) absent60. Numbers of incisivi on the left mandible: (0) 2; (1) 3; (2) 5; (3) 0; (4) 1; (5) 461. Numbers of incisivi on the right mandible: (0) 2; (1) 3; (2) 4; (3) 5; (4) 0; 5 (1)62. Armament on the mesal side of the left mandible: (0) without teeth or ridges; (1) one tooth; (2) three ridges63. Dorsal cutting edge of the left mandible: (0) notched; (1) smooth64. Mandibular postmola: (0) absent; (1) present65. Anterior mandibular joint: (0) absent; (1) present66. Anterior mandibular joint: (0) cuticular hardening on the mandibular depression; (1) channel-joint (2) ball-and-socket joint67. Anterolateral part of the anterior mandibular articulation : (0) present; (1) absent68. Posterior mandibular joint: (0) cylinder-shaped (1) ball-and-socket joint69. Mandibular ligament: (0) present; (1) absent.70. M. craniomandibularis externus anterior (0md2): (0) present; (1) absent71. M. hypopharyngomandibularis (0md4): (0) present; (1) absent72. M. tentorio-mandibularis lateralis superior (0md5): (0) present; (1) absent73. M. tentorio-mandibularis medialis superior (0md7): (0) present; (1) absent74. Cardo: (0) present; (1) absent75. Division of stipes into basistipes and mediastipes: (0) present; (1) absent76. Galea: (0) present; (1) absent77. Distal field of trichomes on the galea: (0) undivided; (1) divided; (2) just a U-shaped seam78. Connection of lacinia and galea: (0) separated; (1) fused79. Shape of lacinia: (0) sickle-shaped; (1) chisel-shaped; (2) truncate; (3) short claw80. Mesally directed setae on lacinia: (0) present; (1) absent81. Lacinia: (0) free; (1) in galeal cavity82. Lacinial incisivi: (0) present; (1) absent83. Number of incisivi on lacinia: (0) 3; (1) 2; (2) 1; (3) more than 384. Dentisetae on lacinia: (0) present; (1) absent85. Proximal apodeme on the lacinia: (0) absent; (1) present86. Galeolobulus: (0) absent; (1) present87. Maxillary palpus: (0) 5-segmented; (1) 4-segmented; (2) 1-segmented; (3) 3-segmented; (4) 6-segmented; (5) 7-segmented88. Orientation of maxillary palpi: (0) ventrally oriented; (1) anteriorly or dorsally directed89. 0mx7: (0) present; (1) absent90. M. palpopalpalis maxillae primus (0mx12): (0) present; (1) absent91. Postmentum: (0) not subdivided; (1) subdivided into submentum and mentum92. Angle between submentum and mentum: (0) less than 60\u00b0 or absent; (1) more than 60\u00b093. Curvature of submentum: (0) absent; (1) curved in lateral view94. Median longitudinal tunnel of labium: (0) absent; (1) present95. Median cleft of prementum: (0) absent; (1) present96. Labium: (0) paraglossa and glossa seperated; (1) paraglossa and glossae completly fused97. Glossa: (0) present; (1) reduced98. Number of glossae: (0) 2; (1) 1;99. Number of paraglossae: (0) 2; (1) 1;100. Shape of paraglossa: (0) cylindrical, as wide as thick; (1) flat, wider than thick; (2) palpus-like.101. Relative length of paraglossae and glossae: (0) about equally long; (1) paraglossae twice as long or longer102. Orientation of labial palpi: (0) anterior or lateral; (1) ventral or posterior103. Number of labial palpomeres: (0) 3; (1) 1; (2) 2; (3) 4104. Shape of labial palpi: (0) approximately round in cross section; (1) dorsoventrally flattened105. Length of labial palpi: (0) longer than glossae; (1) about as long as the glossae106. Moveable hooks of labial palpi: (0) absent; (1) present107. M. postoccipitoglossalis medianus (0la1): (0) present; (1) absent108. M. postoccipitoglossalis lateralis (0la2): (0) present; (1) absent109. M. postoccipitoparaglossalis (0la3): (0) present; (1) absent110. M. postoccipitoprementalis (0la4): (0) present; (1) absent111. 0la5: (0) present; (1) absent112. Origin of M. tentoriopraementalis inferior 0la5 (M.29): (0) ventral apodeme; (1) posterior tentorial arms; (2) posterior tentorial arms (posttentoria) and postocciput.113. M. tentorioparaglossalis (0la6): (0) present; (1) absent114. Origin of M. tentorioparaglossalis (0la6): (0): tentorium; (1) basal edge of prementum115. M. tentorioglandularis (0la7): (0) present; (1) absent116. M. submentopraementalis (0la8): (0) present; (1) absent117. M. submentopraementalis (0la8): (0) one component; (1) two components118. M. postmentomembranus (0la9): (0) present; (1) absent119. M. submentomentalis (0la10): (0) absent; (1) present120. M. praementoparaglossalis (0la11): (0) present; (1) absent121. M. praementoglossalis (0la12): (0) present; (1) absent122. M. praementopalpalis internus (0la13): (0) present; (1) absent123. M. praementopalpalis externus (0la14): (0) present; (1) absent124. Hypopharynx overlapping paraglossae and glossae 0) absent; 1) present125. Shape of hypopharynx: (0) slope like; (1) distinctly flattened126. Superlinguae: (0) present; (1) absent127. Salivary glands and ductus: (0) present; (1) absent128. Connection of salivary ducts: (0) connected before opening, Y-shaped; (1) open separately129. M. frontobuccalis lateralis (0hy2): (0) present; (1) absent130. M. craniohypopharyngealis (0hy3): (0) present; (1) absent131. M. postmentoloralis (0hy6): (0) present; (1) absent132. M. praementosalivaris posterior (0hy8): (0) absent; (1) present133. M. lorosalivarialis (0hy11): (0) present; (1) absent134. 0hy12: (0) present; (1) absent135. M. frontobuccalis posterior (0bu3): (0) present; (1) absent136. M. tentoriobuccalis lateralis (0bu4): (0) absent; (1) present137. 0bu5: (0) present; (1) absent138. M. tentoriobuccalis posterior (0bu6): (0) present; (1) absent.139. Origin of M. tentoriobuccalis posterior 0bu6 (M.50): (0) anterior and/or posterior bridge, (1) pretentoriaHomologization of the muscular terminology with other authors. Abbreviations: +, muscle present ; -, muscle absent;/, muscle not dealt with by the author; ?, unclear homology.Click here for fileCharacter state matrix in excel format together with short descriptions of the charactes used: (?) refers to a missing or unclear character state, (-) to inapplicable characters.Click here for fileCharacter state matrix in nexus format: (?) refers to a missing or unclear character state, (-) to inapplicable characters.Click here for fileT. gertschi3D model of the head of . Please use the open source software Blender (http://www.blender.org) to view the model.Click here for fileImage stack of transversal slices through the head of T. gertschi packed in the \"avi\" movie format for easy browsing through the stack.Click here for fileComplete tree (strict consensus) showing all taxa. Character numbers above, character states below the nodes.Click here for file"} +{"text": "In \u201cProbable Tiger-to-Tiger Transmission of Avian Influenza H5N1,\u201d by Roongroje Thanawongnuwech et al., an error occurred. The GenBank accession nos. for HA and NA gene initiated from influenza A virus (A/Tiger/ Thailand/CU-T3/04) are AY842935 and AY842936.http://wwwnc.cdc.gov/eid/article/11/5/05-0007_article.htm.The corrected article appears online at We regret any confusion these errors may have caused."} +{"text": "S,6S,2R)-9,13-dimeth\u00adyl-5-methyl\u00adene-3-oxatricyclo\u00adtrideca-9,12-diene-4,11-dione], C15H16O3, is a guanolide isolated from Artemisia douglasiana. The fused-ring system contains a seven-membered ring that adopts a chair conformation, a fused planar cyclo\u00adpentenone ring and a five-membered lactone ring fused in envelope conformation. The absolute structure determined by X-ray analysis agrees with that previously assigned to this compound by NMR studies and also with that of leucodine, a closely related guaianolide .Dehydro\u00adleucodin [systematic name: (1dero 1972. Tetra\u00adh al. 1988. J. Nat. DOI: 10.1107/S1600536811048938/bg2432Isup2.hkl Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811048938/bg2432Isup3.mol Supplementary material file. DOI: 10.1107/S1600536811048938/bg2432Isup4.cml Supplementary material file. DOI: crystallographic information; 3D view; checkCIF report Additional supplementary materials:"} +{"text": "Errors were introduced in the preparation of this article for publication: incorrect symbols were inserted in the legends of Tables S2, S3, S6, S7, and S8. The corrected legends are:Table S1. White-tailed Deer RRL Contig Table (3.66Mb XLS)Table S2. White-tailed Deer RRL Informative blastn Hits Table S3. White-tailed Deer RRL Putative SNPs Table S4. White-tailed Deer RRL Functional Annotation (1.07 Mb XLS)Table S5. White-tailed Deer RRL plus RSL (Pooled) Contig Table (7.99 Mb XLS)Table S6. White-tailed Deer RRL plus RSL (Pooled) Informative blastn Hits Table S7. White-tailed Deer RRL plus RSL (Pooled) Putative and Validated SNPs Table S8. White-tailed Deer RRL plus RSL (Pooled) Mitochondrial SNP Table Table S9. White-tailed Deer RRL plus RSL (Pooled) Functional Annotation (2.71 Mb XLS)"} +{"text": "HIV-infected patients have a higher risk of developing cancer than the general population. Kaposi's sarcoma (KS), non-Hodgkin's lymphoma (NHL), primary CNS lymphoma (PCL) and invasive cervical cancers are considered AIDS-defining. An increased incidence in recent years, however, has been reported also for other malignancies after the introduction of HAART.We performed a case-control study to characterize all HIV-infected patients with both AIDS and non-AIDS-defining neoplasms observed among all consecutive patients followed at the Infectious Diseases Unit of Pescara General Hospital, since 1991 through 2012. All cases were matched with equinumerous controls without neoplasia homogeneous for age, sex and AIDS diagnosis.Out of 626 patients consecutively assisted since 1991, 57 cases of malignancy (9.1%) were observed. Of these, 45 (79.0%) occurred in males; mean age was 43.6\u00b19.3 years; 49 (86.0%) patients were diagnosed with AIDS. Tumors observed were: NHL, 17 (29.8%); SK, 13 (22.8%); HCC, 5 (8.8%); CPL, 6 (10.5%); Hodgkin's lymphoma, 4 (7.0%); solid tumors, 12 (21.1%), including 1 AIDS-defining tumor . Among these, 37 (66.1%) patients died; of them 14 (37.8%) had non-AIDS cancers. Cases were well matched with the 55 controls for sex (p=0.9), age (p=0.6) and AIDS diagnosis (p=0.6). In comparison with controls, CD4 nadirs were not different (153\u00b1151 in controls vs 136\u00b1154 cells/mmc), while CD4 at tumor diagnosis were very different between controls (463\u00b1283 cells/mmc) and cases . Among patients with malignancies, those who died had a non-significant reduction in CD4 counts (p=0.14); seemingly irrelevant were smoking status (p=0.9), working ability (p=0.4), HCV coinfection (p=0.4). Surprisingly, in patients co-infected with HBV, including HBsAg negative, antibody-positive subjects, tumors were significantly more frequent .Factors potentially relevant for carcinogenesis in the prolonged survival patients of the HAART era may include HBV coinfection in spite of the lack of active biochemical activity (HbsAg negative) in the majority of coinfected patients. The potential relevance of this finding deserves prompt assessment in a larger multicentric cohort."} +{"text": "The third author's name appears incorrectly in the citation. The correct citation is: Talman V, Tuominen RK, Boije af Genn\u00e4s G, Yli-Kauhaluoma J, Ekokoski E (2011) C1 Domain-Targeted Isophthalate Derivatives Induce Cell Elongation and Cell Cycle Arrest in HeLa Cells. PLoS ONE 6(5): e20053. doi:10.1371/journal.pone.0020053"} +{"text": "She was born small for gestational age with no catch-up growth. Congenital anomalies including right dysplastic kidney and large secundum atrial septal defect were present. She had delayed development with microcephaly and dysmorphism, including triangular facies, epicanthic folds, low set ears, micronagthia, and brachydactyly. Ophthalmological assessment showed astigmatism, myopia, and left exotropia requiring surgical correction. Audiology assessment showed bilateral mild conductive hearing loss. Thyroid function, morning cortisol, serum calcium and renal function tests were normal. Metabolic disease workup including lactate, plasma for amino acid, urine metabolic screen, VLCFA, transferrin isoelectrofocusing and clotting profile were normal. CT and MRI brain were normal. Serum IGF-1 at 13 years old was 62nmol/L (+ 0.5SD). Growth hormone study with glucagon showed peak growth hormone of 32mg/L. Bone age was 12 years at chronological age of 12-year-10month. Radiograph of both hands showed brachydactyly but no proximal implantation of 1st digit. Genetic study show normal karyotype, but MLPA and FISH later confirmed heterozygous terminal deletion of 15q26.2 with the genetic defect compatible with IGF-1 receptor mutation. Growth hormone therapy was refused by the patient and mother. Breast development started at 12-year-4month and menarche started at 13-year-5month of age. The growth spurt was absent with peak growth velocity of only 5.5cm/year. On the latest follow-up at 13-year-9month of age, her height was 128.8cm (-4.7SDS).A 5-year-9month old Chinese girl presented with severe growth retardation, height SDS -4.17 and body weight SDS -2.37. The mid-parental height was 151.2cm (3Our patient displayed typical phenotypic features of IGF-1 receptor mutation of heterozygous deletion of 15q26.2 with severe growth retardation. The condition could potentially benefit from growth hormone treatment according to recent literatures ["} +{"text": "Other studies have reported high rates of depression and anxiety among human T-lymphotropic virus type 1 (HTLV-1) infected subjects, and have even suggested that HTLV-I causes psychiatric disease.We interviewed HTLV-I, HTLV-II and demographically similar HTLV seronegative blood donors with the Mini-International Neuropsychiatric Interview (MINI). Prevalences of major depression and generalized anxiety disorder in each group were calculated and compared to published U.S. population data. Adjusted odds ratios (aOR) and 95% confidence intervals (95% CI) controlling for educational achievement, alcohol intake and self-reported health status were calculated with multivariate logistic regression.Major depression was diagnosed in 5 (5.4%) of 93 HTLV-I positive subjects and 17 (6.6%) of 256 HTLV-II positive subjects , compared to 12 (2.1%) of 585 HTLV seronegative blood donors. The prevalence of major depression among infected subjects was comparable to the 6.7% prevalence in the U.S. general population. Generalized anxiety disorder was diagnosed in 5 (5.4%) HTLV-I positive subjects and 12 (4.7%) HTLV-II positive subjects (OR = 1.65 95% CI 0.68-4.01), compared to 15 (2.6%) seronegatives and 3.1% in the U.S. general population.We observed slightly higher prevalence of major depression and generalized anxiety disorder among HTLV-I and HTLV-II subjects that was not significantly elevated after controlling for health status and other confounding variables. Comparison to U.S. population data suggested that these findings are in part explained by a \u201chealthy blood donor effect\u201d among our controls."} +{"text": "Improving trunk appearance is important for scoliotic patients. Selecting an appropriate rater is vital for effectively measuring this outcome. This study investigates whether a four-week intensive scoliosis-specific exercise programme results in improved patient body image and how this varies between patients, physiotherapists and an external scoliotic rater.82 patients with IS and mean age 30.79 years (Range 10-81) were treated with a four-week intensive scoliosis-specific physiotherapy course (ScolioGold). Patients, 2 blinded physiotherapists and a blinded scoliotic rater rated patients\u2019 body-image before and after treatment. Body-image was assessed using a 0-10 scale, for 5 elements .Mean total scores before treatment were; patients 28.51 (SD8.76), physiotherapists 22.94 (SD6.01) and external rater 20.55 (SD7.27) and after treatment were; patients 15.46 (SD7.40), physiotherapists 13.73 (SD5.88) and external rater 6.61 (SD4.10). Differences in patients (P), physiotherapists (T) and external rater(E) body-image scores were found to have statistically significantly improved after treatment using Wilcoxon-signed rank . ICC scores between P&T, P&E and T&E were; fair (0.28), slight (0.19) and moderate (0.58) before treatment and fair (0.34), fair (0.28), moderate (0.59) after treatment.Statistically significant improvements between pre-post treatment scores substantiate intensive exercise methods (ScolioGold), in the treatment of IS-related negative body image. Significant variation between patients\u2019, physiotherapists\u2019 and external rater\u2019s scoring highlight the need for patients to rate body-image due to the subjectivity of this outcome measure, to ensure we adopt a client-centred care approach in our treatment goals to improve patient body-image."} +{"text": "There was an error in the title. The correct title is: HIV-1 Tropism Determination Using a Phenotypic Env Recombinant Viral Assay Highlights Overestimation of CXCR4-Usage by Genotypic Prediction Algorithms for CRF01_AE and CRF02_AG. The correct citation is: Mulinge M, Lemaire M, Servais J-Y, Rybicki A, Struck D, et al. (2013) HIV-1 Tropism Determination Using a Phenotypic Env Recombinant Viral Assay Highlights Overestimation of CXCR4-Usage by Genotypic Prediction Algorithms for CRF01_AE and CRF02_AG. PLoS ONE 8(5): e60566. doi:10.1371/journal.pone.0060566."} +{"text": "Therefore, many individuals are capable of mitigating the presence of autoantibodies and avoiding clinical disease. The objective of this study was to investigate unique features of SLE patients compared with autoantibody-positive (aAbn = 790) were screened by multiplex, bead-based assays for autoantibodies against: dsDNA, chromatin, ribosomal P, SS-A/Ro, SS-B/La, Sm, Sm/RNP, RNP, SCL-70, Jo-1, and centromere B. Sera from aAb+ individuals, matched aAb- controls and SLE patients were tested for 52 cytokines using multiplex bead-based assays and ELISAs. Hierarchical clustering was performed and Kruskal-Wallis tests with Dunn's multiple comparisons were compared including a false discovery rate. Immune cell phenotyping and phospho-flow cytometry was performed on peripheral blood mononuclear cells from aAb+ and aAb- healthy individuals. Unpaired t tests and Mann-Whitney tests were performed.Individuals and matched aAb- healthy controls and SLE patients were selected for further analysis. While aAb+ healthy individuals displayed some similar cytokine patterns to SLE patients, they also displayed a suppressed cytokine profile that included decreased T-cell cytokines (IFN\u03b3 (P < 0.05), IL-5 (P < 0.05), IL-17F (P < 0.01)), decreased B-lymphocyte stimulator levels (P < 0.05), and increased IL-1 receptor antagonist levels (P < 0.001). An increased percentage of B cells was found in aAb+ healthy individuals compared with aAb- healthy controls (P = 0.039) that consisted of an increased percentage of memory B cells (P = 0.034) and a decreased percentage of transitional B cells (P = 0.028). Compared with aAb- healthy controls, B cells from aAb+ healthy individuals showed significantly increased pSTAT1 and pSTAT3 in response to IFN\u03b1 stimulation (P = 0.037 and P = 0.040), increased pSTAT1 in response to IFN\u03b3 stimulation (P = 0.018), and increased pSTAT3 in response to IL-21 stimulation (P = 0.041). CD4+ T cells from aAb+ healthy individuals showed decreased pSTAT3 in response to IFN\u03b3 and IL-2 stimulation (P = 0.018 and P = 0.005). IFN\u03b1, IFN\u03b3 and IL-6 stimulation significantly increased pSTAT signaling in monocytes from aAb+ healthy individuals.Of the screened individuals, 57 individuals were positive for at least one autoantibody (7.2%), with 33.3% being Native American, 57.9% European American, 8.8% African American, and 89.5% female. European American aAb+ healthy individuals exhibit features of inflammation and loss of immune tolerance, they are capable of suppressing these responses by regulatory mechanisms probably no longer functional in patients with autoimmune disease.Although aAb"} +{"text": "There was an error in the third subheading of the Results section (\"African-Americans and Caucasians\"). The correct sentence is: Single locus tests of association in the African-Americans identified seven significant allelic associations at IL12B polymorphisms rs3212227 (p = 0.002), rs2421047 (p = 0.008), rs2288831 (p = 0.008), rs10631390 (p = 0.001), rs3212220 (p = 0.003), rs6894567 (p = 0.007), and rs17860508 (p = 0.002) and three significant genotypic associations at rs3212227 (p = 0.05), rs10631390 (p = 0.05) and rs6894567 (p= 0.03) (Table 2b).”"} +{"text": "Jatropha curcas leaf extracts.Drug-resistant HIV, a major global concern, warrants the development of novel anti-virals as alternative and inexpensive therapy. In the current study, we isolated potentially drug-resistant HIV and assessed previously unreported anti-viral activity of In vitro micro-co-culture was employed for virus isolation followed by drug susceptibility assays to determine resistance to Azidothymidine (AZT) and Lamivudine (3TC).Jatropha curcasleaves were extracted using Soxhlet apparatus. Methanolic (ME) and aqueous (AE) extracts were chosen for further study. Secondary metabolites were detected by High-Performance Thin Laye rChromatography and in vitro cytotoxicity established by MTT assay. Anti-viral activity was evaluated by p24 inhibitionin post- and pre-infection interaction studies.50 values ranging from 0.001418-82.73 \u00b5M AZT and 2.645-15.35 \u00b5M 3TC.Seven HIV isolates were obtained (isolation rate: 23.33%) with drug IC50 values were 32.07 mg/mL AE and 35.5 mg/mL ME.Tannins, flavonoids, saponins were detected in AE and flavonoids, saponins in ME while CC50 values were ranging from 0.0255-0.4137 mg/mL AE and 0.00073-0.1278 mg/mL ME; pre-infection studies (1 isolate) showed 100% p24 inhibition by ME and 97.19% p24 inhibition by AE at 25 mg/mL each.In post-infection studies (4 isolates), ICJatropha curcas leaf extracts showed effective anti-viral and probable entry inhibition activity against potentially drug-resistant HIV, which has not been reported earlier. We conclude that Jatropha curcasis a good candidate for anti-HIV therapy with further research.HIV isolates potentially resistant to AZT/3TC were obtained; genotypic drug resistance is being ascertained."} +{"text": "Significance of blood glucose (BG) control in ICU patients, especially in terms of mortality reduction, has been recognized in recent years. However, the relationship between BG profile and the severity, as well as BG target, is not clearly elucidated. A preliminary study was performed in order to clarify the relationship between BG profile and the severity of ICU patients.r) between the abovementioned SOFA scores and BG parameters were calculated using two-dimensional and linear regression analysis .Forty-seven patients were studied. The following parameters were calculated during first week after ICU admission. (1) Mean and maximum value of SOFA scores . (2) Mean, standard deviation, maximum, minimum, and difference of BG levels , respectively). BG levels were measured basically every 6 hours with capillary blood. (3) Correlation coefficients ((1) rt and rl (rt/rl) between SOFAmax and BG parameters: BGsd (0.48/0.36), BGmax (0.47/0.33), BGd (0.47/0.35), BGm (0.30/0.22), BGmin (0.21/0.36). (2) (rt/rl) between SOFAm and BG parameters: BGsd (0.45/0.33), BGmax (0.45/0.28), BGd (0.45/0.30), BGm (0.28/0.17), BGmin (0.17/0.29).(1) Variable and maximum BG levels during the first week , rather than mean and minimum BG levels , were related to the severity. (2) Suppression of the higher variable and maximum BG levels was considered to link to better outcome. (3) On the other hand, part of the severe patients seemed to have the lowest of those variable and maximum BG levels, judging from two-dimensional or parabolic correlations between those BG parameters and SOFA scores."} +{"text": "Reasons for screen failures are evaluated for three phase 1 HIV vaccine clinical trials recruiting healthy low-risk participants at the Perinatal HIV Research Unit: SAAVI102/HVTN073 and SAAVI103/HVTN086 and IAVIB003/HVTN091 (Ad26 and Ad35 ENV vaccines). Recruitment strategies involved a pre-screening programme, clinics and community outreach.Protocol-specific eligibility was determined using assessments of understanding, risk behaviour, medical history, physical examination, blood and urine testing, and for HVTN073 and 086, electrocardiograms. Descriptive analysis and multivariate logistic regression of age, trial group and gender were performed.Between June 2009-2012, 225 participants, median age 22 years(IQR:20-25) were screened. Overall 53% were ineligible, 60% of females vs. 51% of males (p=0.2). Site screening-to-enrolment ratios for 073, 086 and 091 were 2.1:1, 2.3:1 and 1.7:1 respectively. Medical abnormalities contributed 59% (n=70) of ineligibility reasons, chiefly urine abnormalities , abnormal ECG (n=12), raised liver enzymes (n=10), raised blood pressure (n=9), low white cells (n=8) and hepatitis B (HBsAg+ve) or C (anti HCV+) (n=7). Other criteria excluded 41%(n=49) e.g. incomplete screening before enrolment closure (n=16), high-risk sexual behaviors (n=15), inability to comply with protocol (n=11), enrolment in another study (n=3), substance abuse , and poor understanding (n=2). In multivariate analysis, increasing age predicted ineligibility but gender did not . HVTN073&086 participants were more likely to be ineligible than HVTN091 .Screen failures in phase 1 vaccine trials in Soweto provide young people opportunities for care, especially through blood pressure, urine, risk behaviour and hepatitis B/C screening. Older participants and those in protocols stipulating ECG criteria were more likely to fail screening."} +{"text": "Gillisia limnaea Van Trappen et al. 2004 is the type species of the genus Gillisia, which is a member of the well characterized family Flavobacteriaceae. The genome of G. limnea R-8282T is the first sequenced genome (permanent draft) from a type strain of the genus Gillisia. Here we describe the features of this organism, together with the permanent-draft genome sequence and annotation. The 3,966,857 bp long chromosome (two scaffolds) with its 3,569 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. T (= DSM 15749 = LMG 21470 = CIP 108418) is the type strain of the species Gillisia limnaea . The. TheG. ln 4.9 \u00b5m , which i strains -34. MotiT are iso-C15:0, anteiso-C15:0, iso-C15:1, iso-C16:0, C17:0 2-OH, iso-C17:0 3-OH, iso-C17:1 \u03c99c, anteiso-C17:1 \u03c99c and summed feature 3 (containing iso-C15:0 2-OH and/or C16:1 \u03c97c) [T.The principal cellular fatty acids of strain R-8282 Genomic Encyclopedia ofBacteria andArchaea project [This organism was selected for sequencing on the basis of its phylogenetic position , and is project . The gen project and the G. limnaea strain R-8282T, DSM 15749, was grown in DSMZ medium 514 (BACTO Marine Broth) [et al. 2009 [e Broth) at 20\u00b0C.al. 2009 for optial. 2009 .The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website . PyroseqGenes were identified using Prodigal as part The genome consists of two scaffolds with 3,558,876 bp and 407,981 bp length, respectively, with a G+C content of 37.6% . Of the G. limnaea R-8282T revealed the presence of three rhodopsin genes related to proteorhodopsin and xanthorhodopsin protein-encoding sequences, whereas a third rhodopsin protein sequence seems to be truncated. Another finding was a set of genes involved in \u03b2-carotene biosynthesis, together with a gene encoding a \u03b2-carotene 15,15'-monooxygenase , an enzyme that oxidatively cleaves \u03b2-carotene into two molecules of retinal, which is necessary for rhodopsin function. PRs and XRs are photoactive transmembrane opsins that bind retinal and which belong to the microbial rhodopsin superfamily [E. coli cells for ATP synthesis [Salinibacter ruber M31T [Bacteria [Archaea [Genome analysis of erfamily . When exerfamily . This prynthesis as well ynthesis . In contynthesis ,52, thatber M31T ,54. Its ber M31T , resultiBacteria ,57 or ba[Archaea .Flavobacteriaceae [Krokinobacter sp. 4H-3-7-5 (AEE18495) [Dokdonia [The gene encoding the putative XR (Gilli_2340) of strain R-8282HQ04368) and KrokEE18495) , which wDokdonia ,66 , indicating that Gillisia sp. strain CBA3202 does not belong to the species G. limnaea.Interestingly, no rhodopsin-encoding sequence could be detected in the genome sequence of CBA3202 , which w CBA3202 . Digital CBA3202 between Bacteroidetes phylum were frequently found attached to aggregates [T several genes were detected that are thought to be involved in gliding motility (gldA (Gilli_1140), gldB (Gilli_2923), gldC (Gilli_2942), gldD (Gilli_1840), gldE (Gilli_1841), gldF (Gilli_3447), gldG (Gilli_3446), gldH (Gilli_2158), gldI (Gilli_0258), gldJ (Gilli_1638), gldK (Gilli_2747), gldL (Gilli_2748), gldM (Gilli_2749), gldN (Gilli_2750), espA (Gilli_3049), espB (Gilli_3050), remB (Gilli_2697), sprA (Gilli_2693) and sprE (Gilli_2130)). This observation indicates the possible gliding motility of strain R-8282T, but has never been reported in literature.Compared to free-living bacteria, representatives of the gregates and durigregates ,71. Theygregates ,73. In s"} +{"text": "There was an error in the title.The correct version of the title is: Specific Inhibition of the Redox Activity of Ape1/Ref-1 by E3330 Blocks Tnf-\u03b1-Induced Activation of Il-8 Production in Liver Cancer Cell LinesThe correct citation is: Cesaratto L, Codarin E, Vascotto C, Leonardi A, Kelley MR, et al. (2013) Specific Inhibition of the Redox Activity of Ape1/Ref-1 by E3330 Blocks Tnf-\u03b1-Induced Activation of Il-8 Production in Liver Cancer Cell Lines. PLoS ONE 8(8): e70909. doi:10.1371/journal.pone.0070909"} +{"text": "Eradicating cHCV is necessary for the subsequent management of patients with HIV and every HIV/HCV co-infected patient should be considered for treatment. We describe differences between cHCV mono-infected and cHCV/HIV co-infected patients in baseline factors and outcome of cHCV-treatment with peginterferon alfa 2a + RBV in the worldwide largest cHCV cohort.Noninterventional prospective multicenter German cohort, started January 2008 and still recruiting. Interim analysis of cHCV patients, stratified for cHCV mono-infection and cHCV/HIV co-infection. The results are based on a cross-sectional analysis of all available data in April 2010.2, na\u00efve/relapse/non-responder/re-infection: 86.4/3.8/4.5/5.3(CI), 88.0/6.1/5.3/0.6 (MI) %, source of infection (>1 answer possible): iv drug use 25.2(CI), 44.9(MI) %, sexual transmission 60.7 (CI), 4.1(MI)%, other 8.0 (CI), 24.0 (MI), unknown 13.1(CI), 33.0 (MI)%. 86.4 % of the co-infected patients received antiretroviral HIV-treatment (ART), 66.2 % of them had an HIV-RNA level below 50 copies/mL, median CD4-cells/\u00b5 count was 502. From those patients who finished treatment, 52.9% of the CI-Group and 67.7% of the MI-Group completed the planned course. Reasons for discontinuation (>1 answer possible) were non-response and patient request . Other reasons were tolerability and compliance issues .Treatment response rates, stratified by genotypes, were already available regarding RVR and EVR and 4.993 cHCV mono-infected (MI). Main baseline- characteristics: 85.9% were GT1/4/5/6 patients in the CI-Group and 63.4% in the MI-Group, age was 41.0 (CI), 42.0 (MI) yrs, 89.7 (CI), 62.9 (MI)% were male, BMI was 22.8 (CI), 24.9 (MI) kg/mIn this preliminary analysis HCV/HIV co-infected patients seemed to respond similar according to RVR and EVR in GT1/4/5/6 as HCV-mono infected patients on HCV-treatment. Treatment discontinuation due to non-response and patient request was much more common in the co-infected group. Other reasons for discontinuation like tolerability and compliance are equal in both arms.A more detailed analysis, in particular the influence of the HIV-ART on HCV-therapy outcome, may help interpreting these data. An updated analysis will be presented."} +{"text": "Radical prostatectomy (RP) is frequently responsible for erectile dysfunction (ED). Post-RP patients often show insufficient response or treatment failures to PDE5 inhibitor therapy. This study was undertaken to evaluate the acute effects of the soluble guanylate cyclase (sGC) stimulator, BAY 60-4552 and vardenafil administered alone or in combination on erectile responses to electrical stimulation of the cavernous nerve (ES-CN) in rats with cavernous nerve (CN) crush injury-induced ED.Male Sprague-Dawley rats underwent laparotomy or bilateral CN crush injury (n=57). After 3 weeks of recovery, erectile function was evaluated in urethane-anesthetized rats following ES-CN at different frequencies. The acute effects of intravenous (iv) injection of vehicle, vardenafil 0.03 mg/kg, BAY 60-4552 0.03 mg/kg or 0.3 mg/kg, or a BAY 60-4552 0.03 mg/kg + vardenafil 0.03 mg/kg combination were evaluated in CN crushed rats.Bilateral CN crush injury followed by a 3-week recovery period decreased erectile responses to ES-CN by about 50%. In CN crushed rats, both iv vardenafil 0.03 mg/kg and BAY 60-4552 at the tested dosings (0.03 or 0.3 mg/kg) increased erectile responses to ES-CN to the same extent: \u0394ICP/MAP at 10Hz ES-CN was 20.9\u00b1 1.3 % after iv vehicle, 25.3\u00b1 3.3 % (P<0.001) after iv vardenafil, and 26.3\u00b1 4.9 % and 26.6\u00b1 5.2 % after BAY 60-4552 0.03 mg/kg (P<0.01) and 0.3 mg/kg (P<0.001) respectively. The combined iv administration of vardenafil and BAY 60-4552 in CN crushed rats exerted additive effects and totally restored erectile responses to ES-CN equivalent to sham rats .The present study supports the concept that the combined administration of a sGC stimulator, BAY 60-4552 and vardenafil provides additive beneficial effects. Thus this combination could become a novel treatment option in ED patients with cavernous nerve injury showing insufficient response or treatment failures to PDE5 inhibitors."} +{"text": "AbstractNazeris Fauvel collected from Nabanhe Nature Reserve, Yunnan Province, are described under the names of Nazeris nabanhensis sp. n. and Nazeris caoi sp. n. The male sexual characters are described and illustrated. A key to the Nazeris species of Yunnan is provided. A map of the collecting sites is given.Two new species of the genus Nazeris Fauvel (1873: 298) can be readily distinguished from other Paederinae by the labrum having four teeth at the front margin and the bi-lobed 4th tarsal segments. Up to the present, 51 species and subspecies of Nazeris have been recorded from China. Yunnan is a mountainous province located in Southwest China, from PageBreakwhich nine species of Nazeris have been described: Nazeris zhangi Watanabe & Xiao (1993: 130) from \u201cYu\u2019an-shan near Kunming City\u201d, Nazeris giganteus Watanabe & Xiao (1997:2) and Nazeris daliensis Watanabe & Xiao (1997: 7) from \u201cDiancang shan Mts., Dali shi\u201d, Nazeris alpinus Watanabe & Xiao (1997: 5) from \u201cMt. Yulongxue shan, Lijiang County\u201d, Nazeris jizushanensis Watanabe & Xiao (1997: 9) from \u201cMt. Jizu Shan, Binchuan County\u201d, Nazeris baihuaensis Watanabe & Xiao (2000: 312), Nazeris ishiianus Watanabe & Xiao (2000: 319) and Nazeris nomurai Watanabe & Xiao (2000: 316) from \u201cGaoligong Shan Mts., Baoshan area\u201d, Nazeris huanxipoensis Watanabe & Xiao (2000: 318) from \u201cHuanxipo, Tengchong Xian\u201d. Only two species have become known from the three countries adjacent to Yunnan : Nazeris coomani Jarrige (1948: 40) (redescribed by Nazeris odzisan Watanabe (1996: 1) from \u201cMt. Tam Dao, Vinh Phu Prov.\u201d (Vietnam).The genus Nazeris nabanhensis sp. n. and Nazeris caoi sp. n. The male sexual characters of the two new species are described and illustrated. A map .Nazeris species was not examined. The characters used in comparative remarks and keys are according to descriptions of ; postocular portion 1.96 times as long as eye length; punctation coarse, dense, and umbilicate; interstices reduced to narrow ridges. Antennae slender; relative length of each segment from 1 to 11: 42.0 : 15.0 : 29.0 : 23.0 : 22.5 : 22.0 : 19.0 : 17.0 : 15.5 : 14.0 : 20.0; relative width of each segment from 1 to 11: 12.0 : 7.5 : 6.0 : 6.0 : 6.0 : 6.0 : 6.0 : 6.0 : 6.0 :7.5 : 7.5.convex, oval, longer than wide (length/width = 1.20), narrower (pronotum/head = 0.93) and shorter (pronotum/head = 0.94) than head; prosternum with strong longitudinal median carina, which disappears behind anterior margin. Elytra shorter than wide (length/width = 0.91), distinctly shorter (elytra/pronotum = 0.74) and slightly narrower (elytra/pronotum = 0.97) than pronotum.PageBreakdian lobe in dorsal view tri-lobed, median part cone-shaped, two outer parts acute at apices, with little agnail in each outer side near apex; dorso-lateral apophyses slightly curved inward, distinctly widened near apex, extending beyond apices of median lobe.elongate, tergites without any microsculpture. Seventh sternite trapezoiSeventh and 8th sternites simple. The other characters are similar to those of male.Nazeris daliensis Watanabe (1997: 7) from Yunnan Province in appearance, but it can be distinguished from the latter by the following characters: elytra slightly narrower than pronotum ; depth of excision of male 8th sternite nearly half of middle length of sternite ; apical part of median lobe of aedeagus in dorsal view tri-lobed . The new species can be distinguished from Nazeris coomani Jarrige (1948: 40) from Vietnam by head with umbilicate punctation (in Nazeris coomaniPageBreak punctation of head simple) and distinguished from Nazeris odzisan Watanabe (1996: 1) from Vietnam by elytra shorter than wide (in Nazeris odzisan elytra longer than wide); dorso-lateral apophyses of aedeagus extending beyond apices of median lobe (in Nazeris odzisan not extending to apices of median lobe).The new species is similar to The specific name is derived from the name of the type locality: Nabanhe Nature Reserve.urn:lsid:zoobank.org:act:3B251645-1B6B-4388-ACEC-4E5B42C4A858PageBreakParatypes 1 male, same data as holotype; 1 female, Jinghong City, Nabanhe Nature Reserve, Bengganghani, 1,900m, 1. V. 2009, Hu Jia-Yao & Yin Zi-Wei leg. SHNUC.CHINA: Holotype: Yunnan Prov.: male, Jinghong City, Nabanhe Nature Reserve, Bengganghani, 1,930m, 14. XI. 2008, Hu Jia-Yao & Tang Liang leg. Body length: 6.1\u20136.4 mm; forebody length: 3.3\u20133.6 mm. elongatesuborbicular, slightly longer than wide (length/width = 1.07); postocular portion 2.14 times as long as eye length; punctation coarse, dense, and umbilicate; interstices reduced to narrow ridges. Antennae slender; relative length of each segment from 1 to 11: 42.0 : 13.5 : 30.0 : 23.0 : 21.0 : 21.0 : 19.0 : 18.0 : 18.0 : 16.0 : 22.0; relative width of each segment from 1 to 11: 10.5 : 7.0 : 6.5 : 6.0 : 5.5 : 6.0 : 5.5 : 5.5 : 6.0 :6.5 : 7.0.PageBreak strong longitudinal median carina, which disappears behind anterior margin. Elytra slightly shorter than wide (length/width = 0.97), distinctly shorter (elytra/pronotum = 0.80) and slightly narrower (elytra/pronotum = 0.97) than pronotum.convex, oval, longer than wide (length/width = 1.19), narrower (pronotum/head = 0.88) and shorter (pronotum/head = 0.98) than head; prosternum withelongate, tergites without any microsculpture; densely and coarsely punctate. Seventh sternite distinctSeventh and 8th sternites simple. The other characters are similar to those of male.Nazeris nabanhensis sp. n. from the same locality, but can be distinguished from the latter by the following PageBreakcharacters: postocular part more than twice as long as longitudinal diameter of each eye ; median lobe of aedeagus in dorsal view bi-lobed (in Nazeris nabanhensis tri-lobed); dorso-lateral apophyses of aedeagus not extending to apices of median lobe (in Nazeris nabanhensis extending beyond apices of median lobe). The new species can be distinguished from Nazeris coomani Jarrige (1948: 40) from Vietnam by head with umbilicate punctation (in Nazeris coomani punctation of head simple), and distinguished from Nazeris odzisan Watanabe (1996: 1) from Vietnam by elytra shorter than wide (in Nazeris odzisan elytra longer than wide); median lobe of aedeagus in dorsal view bi-lobed (in Nazeris odzisan not lobed).The present new species is similar in appearance to The species is named in honor of Mr. Guanghong Cao of Nabanhe Nature Reserve, who helped us a lot during field work."} +{"text": "There was an error in the citation. The correct citation is: Aka JA, Lin S-X (2012) Comparison of Functional Proteomic Analyses of Human Breast Cancer Cell Lines T47D and MCF7. PLoS ONE 7(2): e31532. doi:10.1371/journal.pone.0031532"} +{"text": "The fifth author's name was spelled incorrectly. The correct name is: Max Schelker. The corrected citation is:Raue A, Schilling M, Bachmann J, Matteson A, Schelker M, et al. (2013) Lessons Learned from Quantitative Dynamical Modeling in Systems Biology. PLoS ONE 8(9): e74335. doi:10.1371/journal.pone.0074335In equation 7, many additional factors of 2 were added incorrectly. Please see the correct equation 7 here: In equation 8, '2A_0' should only read 'A_0.' Please see the correct equation 8 here:"} +{"text": "Neonatal mice developed neurological disease and pulmonary dysfunction after an infection with a mouse-adapted human Enterovirus 71 (EV71) strain MP4. However, the hallmark of severe human EV71 infection, pulmonary edema (PE), was not evident.To test whether EV71-induced PE required a proinflammatory cytokine response, exogenous pro-inflammatory cytokines were administered to EV71-infected mice during the late stage of infection.After intracranial infection of EV71/MP4, 7-day-old mice developed hind-limb paralysis, pulmonary dysfunction, and emphysema. A transient increase was observed in serum IL-6, IL-10, IL-13, and IFN-\u03b3, but not noradrenaline. At day 3 post infection, treatment with IL-6, IL-13, and IFN-\u03b3 provoked mild PE and severe emphysema that were accompanied by pulmonary dysfunction in EV71-infected, but not herpes simplex virus-1 (HSV-1)-infected control mice. Adult mice did not develop PE after an intracerebral microinjection of EV71 into the nucleus tractus solitarii (NTS). While viral antigen accumulated in the ventral medulla and the NTS of intracerebrally injected mice, neuronal loss was observed in the ventral medulla only.Exogenous IL-6, IL-13, and IFN-\u03b3 treatment could induce mild PE and exacerbate pulmonary abnormality of EV71-infected mice. However, other factors such as over-activation of the sympathetic nervous system may also be required for the development of classic PE symptoms. Enterovirus genus of Picornaviridae family. In general, EV71 infections are mild, such as hand, foot, and mouth disease and herpangina in young children. However, central nervous system (CNS) infections with life-threatening pulmonary and cardiac complications have occurred [Enterovirus 71 (EV71), a highly neurotropic, positive-sense single-stranded RNA virus, belongs to the occurred .Pulmonary edema (PE) and subsequent rapid onset cardiopulmonary failure are hallmarks of EV71 induced mortality . EV71-inOur previous studies showed that a mouse-adapted EV71 strain, EV71/MP4, could experimentally infect laboratory mice via oral (p.o.), intramuscular, and intracranial (i.c.) inoculation routes, resulting in CNS infection and death . Clinica7 PFU/ml. MP4 strains were tested by monoclonal antibodies for EV71 (mAb3324), EV71/coxsackievirus A16 (mAb3323), coxsackievirus A24 (mAb3302), coxsackievirus B3 (mAb3306), echovirus 9 (mAb3313), PV type 1 (mAb3331), PV type 2 (mAb3332), and PV type 3 (mAb3335) using indirect immunofluorescence staining of infected RD cell cultures, and RT-PCR using specific primers for EV71. HSV-1/KOS, a clinical isolate strain of human simplex virus-1 (HSV-1) was grown in Vero cells.Rhabdomyosarcoma (RD) cells were maintained in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum, 2 mM L-glutamine, penicillin and streptomycin. Vero cells (ATCC) were maintained in DMEM containing 5% newborn calf serum, penicillin and streptomycin. Mouse-adapted EV71 strain MP4 was prop5 PUF/mouse) or HSV-1/KOS (2 \u00d7 102 PFU/mouse) through the fontanelles using a 26-gauge needle. Control mice were given culture medium. To systemically increase proinflammatory cytokine levels, mice were intraperitoneally (i.p.) injected at three days post-inoculation with recombinant mouse IL-6, IL-13, and IFN-\u03b3 2 or 3 times within 48 h. Control mice were given bovine serum albumin (BSA). Mice were observed twice daily for clinical signs and mortality. Lung function and body weight monitored daily for one week. Lung weight/body weight analysis, histopathology, and immunohistochemistry were performed after these experiments. For i.c. microinjection, EV71/MP4 was bilaterally microinjected into the nucleus tractus solitarii of 8-week-old ICR mice in a volume of 0.2 \u03bcl (3 \u00d7 107 PFU/ml) over 10 min through a 27-gauge stainless steel cannula connected to a 10-\u03bcl Hamilton syringe driven by an injection pump . Mice were observed twice daily for clinical signs and mortality for 5 days. Clinical disease was scored as follows: 0, healthy; 1, ruffled fur and hunchbacked appearance; 2, wasting; 3, limb weakness; 4, limb paralysis; 5, moribund and death. The Institutional Animal Care and Use Committee approved all animal protocols.Specific-pathogen-free, 7-day-old ICR mice were i.c. injected with 10 \u03bcl of EV71/MP4 . Readings were collected for 3 min after 3 min of resting in the chamber.After anesthetization with pentobarbital sodium , blood was collected after axilla dissection. The levels of IL-6, IL-10, IL-13, and IFN-\u03b3 in serum and noradrenaline in plasma of EV71-infected mice were determined using ELISA kits and a noradrenaline EIA kit , respectively according to the manufacturer's instructions. The detection limits for IL-6, IL-10, IL-13, IFN-\u03b3, and noradrenaline were 15.6, 31.25, 62.5, 31.25, and 0.027 pg/ml, respectively.Changes in vascular permeability in lungs were determined by measuring the increment of wet lung weight. Individual lung lobes were removed, blot-dried on gauze, and weighed using a balance with accuracy to 0.0001 gram. Data were expressed as the ratio of total wet lung weight to body weight.Animals were perfused with isotonic saline containing EDTA. The whole brains and lungs were removed and weighed. Half of the tissues were immersion fixed in 10% buffered formalin for 48 h, bisected, embedded in paraffin, and stained with hematoyxlin and eosin (H & E) or Nissl stain. The remaining tissue samples were frozen in a liquid nitrogen-cold hexane bath in 100% OCT compound . All samples were stored at -70\u00b0 C until assayed.The presence of EV71 virions in cryosections of frozen tissues was visualized by a previously described method [U tests. The results are expressed as means \u00b1 standard errors of the means (S.E.M.). A P value of < 0.05 was considered significant.The clinical scores, lung weight/body weight ratio, and numbers of EV71-positive and NeuN-positive cells were analyzed using either the nonparametric one-way analysis of variance (ANOVA) or Mann-Whitney 5 PFU/mouse), 7-day-old mice did not gain weight and developed clinical symptoms with diffuse emphysema but no evidence of PE in the lung , IL-13 (0.15 \u03bcg/mouse), and IFN-\u03b3 (0.8 \u03bcg/mouse) to mice 3 days after an i.c. inoculation of EV71 (two doses within 48 h). At this time the animals developed mild clinical symptoms with the presence of virus in the CNS. All the mock-infected BSA-treated mice gained weight normally Figure without P = 0.0054, Figure P = 0.0318, Figure 2 PFU/mouse) prior to the administration of IL-6, IL-13, and IFN-\u03b3. HSV-1 is a neurotropic virus and its infection is known to cause diffuse encephalitis in mice, mainly in tissues of the cerebrum and cerebellu [Weight loss in EV71-infected mice resulted in increased lung weight/body weight ratios, as compared with non-infected control mice . Immunostaining showed that EV71-positive cells accumulated at the ventral medulla (VM) over time Figure and 4B. In the course of the development of a mouse model of human EV71 infection, we demonstrated that EV71 could spread from the gastrointestinal tract or muscle to and accumulate in the CNS, especially in the brainstem of mice after different routes of inoculation . FollowiClinical findings showed that increases in serum IL-1\u03b2, IL-6, IL-10, IL-13, TNF-\u03b1, and IFN-\u03b3 were associated with PE development in EV71 patients . In thisBased on the distribution of viral antigens and viral genomic sequences, EV71 is likely propagated throughout the CNS via motor pathways . Our preSurprisingly, PE did not developed in adult mice after a direct inoculation of EV71 to the NTS, an area known to contribute to the development of PE in rats upon injury ,25. In oBesides an over-stimulated proinflammatory response, sympathetic excitement has been proposed as another mechanism involved in the development PE in EV71 patients , other aCollectively, we demonstrated that IL-6, IL-13, and IFN-\u03b3 over-stimulation exacerbated pulmonary dysfunction and clinical symptoms, and provoked a mild PE in EV71-infected mice. A synergistic proinflammatory cytokine response and damage to specific brain regions, or more precisely specific neuronal cells, may be necessary for the development of EV71-induced PE.BSA: bovine serum albumin; EV71: Enterovirus 71; HSV-1: herpes simplex virus-1; PIF: peak of inspiratory flow; PEF: peak of expiratory flow; LC: Locus coeruleus; MRI: magnetic resonance imaging; MV: minute volume; NTS: nucleus tractus solitarii; PV: poliovirus; PE: pulmonary edema; TV: tidal volume.The authors declare that they have no competing interests.SWH participated in the design of the study, carried out the animal studies, performed the statistical analysis, and drafted the manuscript. YPL participated in the design of the study. YTH carried out the immunostaining studies. CHL carried out the intracerebral microinjection studies. JIC participated in design and coordinate the immunostaining studies. HYL participated in the design of the study. IJS participated in the design of the study. CKY conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.Figure 1S. Intracranial inoculation of EV71 resulted in CNS infection, clinical disease, and emphysema in mice. Seven-day-old ICR mice (n = 24) were intracranially inoculated with or without EV71/MP4 strain (4 x105 PUF/mouse). Body weight (A) and clinical disease (B) were then monitored daily after infection. Lung tissues were collected for general morphological analysis (H & E stain) . Clinical disease was scored as followed: 0, healthy; 1, ruffled hair, hunchbacked or reduced mobility. 2, wasting; 3, limb weakness. 4, limb paralysis. 5, death. Bars: 1.0 mm. Note moderate emphysema but not pulmonary edema was observed in the EV71-infected mice (arrowheads).Click here for fileFigure 2S. Exogenous IL-13 treatment exacerbated pulmonary dysfunction in EV71-infected mice. Seven day-old ICR mice (n = 12) were intracranially inoculated with EV71 (4 \u00d7 105 PFU/mouse) followed by an intraperitoneal injection IL-13 at days 3 and 4 post inoculation. Change in pulmonary functions of mice were monitored daily. Ctrl: culture medium; BSA: bovine serum albumin; PIF: peak of inspiratory flow; PEF: peak of expiratory flow; MV: minute volume; TV: tidal volume. Data represent means \u00b1 S.E.M. *, P < 0.05 and **, P < 0.01.Click here for file"} +{"text": "Lipoic acid (LA) stimulates production of an immunomodulatory molecule, cAMP, that may have therapeutic benefit in multiple sclerosis (MS). The study sought to determine the bioactivity of two forms of oral LA, racemic (R/S-LA) and R-LA, to identify factors that may improve the therapeutic effectiveness of LA in MS.Participants met the following criteria: age 18-70 years and a definite multiple sclerosis diagnosis. Consenting participants were randomized to 2 groups: R/S-LA (n=20) or R-LA (n=8). Blood was collected at baseline, 5, 10, 15, 30, 60, 90, 120, 180, 240, and 300 minutes after ingestion of a single 1200 mg LA dose. Bioactivity was determined by measuring immune cell cAMP levels (pmol/mg) at baseline and 240 minutes post ingestion. Group differences were analyzed by repeated measures analysis of variance (cAMP) and t-test (pharmacokinetics).For R/S-LA, mean baseline cAMP levels were 8.6 (SE 0.83) pmol/mg protein, which increased to 14.1 (SE 1.7) 240 minutes post-ingestion. For R-LA, baseline cAMP levels were 5.7 (SE 0.54), which decreased to 4.7 (SE 0.41) 240 minutes post-ingestion. The mean change in cAMP levels were different between groups, p<0.01. The two groups showed no differences in serum LA levels at 240 minutes (p=0.29), but showed a difference in the mean AUC (min*mcg/ml): R/S-LA is 681.8 (SE 83.4) and R-LA is 389.5 (SE 43.9) (p<0.01). Tmax (minutes) between groups differed: R/S-LA was 81.0 (SE 8.9) and R-LA was 13.1 (SE 2.7); p<0.001.At 1200 mg oral dose and comparable serum LA levels at T240, R/S-LA showed higher cAMP levels compared to R-LA. Since R-LA had an earlier Tmax, it is plausible that increases in cAMP may have occurred at earlier undetected time-points. This pilot study warrants further investigation as differences between R-LA and R/S-LA in bioactivity and pharmacokinetics would impact clinical trial design and patient care."} +{"text": "Elevated signal intensity (SI) in T2w images is often designated as area-at-risk (AAR) following acute/sub-acute MI. While AAR has been qualitatively associated with reductions in wall thickening (WT), quantitative information between the two is not available -3. QuantIn an animal model, quantify the:1) Effect of SI threshold on estimating AAR,2) Reduction in WT with AAR at increasing SI thresholds, and3) Correlation between AAR and percent scar.Acquisition Protocol: Basal, mid, and apical slices in short axis orientation were obtained in a pig (n=14) AMI model (LAD occlusion) at 3.0T :a) Cine SSFP: TR/TE/\u03b1 = 3/1.5 ms/45\u00b0; acquired temporal resolution: 12 ms.b) Delayed enhancement MRI (DE-MRI): 10 min after 0.2 mmol/kg of contrast, scar was visualized using a gated IR-TFE sequence with inversion delay (TI) adjusted to null normal myocardium.c) Dual-IR T2W imaging (BB): Effective TE/TR: 80 ms/2*RR interval; TSE readout.Data Analysis: Myocardial region was manually segmented from cine, DE-MRI, and BB images Figure using MA1) Normalized wall thickness (nWT) per segment = (WTES - WTED)/( WTED), where ED = End-Diastole, ES-End-Systole.2) Segmental scar burden, defined as ratio of pixels designated as scar to total number of pixels in each segment of DE-MRI. Scar pixel is one with SI > [mean + 5*Standard Deviation (SD) of normal remote myocardium].3) Segmental AAR, defined as regions in BB images with SI > mean + n*SD of normal remote myocardium .1) As a share of total myocardium, AAR burden was significantly higher (43 to 57 %) than scar burden (30 %) (Table 2) Spatially, AAR overlapped, and extended beyond scar regions.3) Reduction in segmental nWTwas lower in AAR regions that did not overlap scar region compared to those segments that did(108 \u00b1 36 % vs 91 \u00b1 29 %, Figure In sub-acute AMI, AAR is significantly larger than scar. In non-overlapping regions of AAR and scar, nWT, while diminished compared to normal remote myocardium, is significantly better than in regions of scar.NA"} +{"text": "The word \"Hydroxypropyl\" is misspelled in the article title. The correct title is: Enhancement of Naringenin Bioavailability by Complexation with Hydroxypropyl-\u03b2-Cyclodextrin.The correct citation is: Shulman M, Cohen M, Soto-Gutierrez A, Yagi H, Wang H, et al. (2011) Enhancement of Naringenin Bioavailability by Complexation with Hydroxypropyl-\u03b2-Cyclodextrin. PLoS ONE 6(4): e18033. doi:10.1371/journal.pone.0018033Hydroxypropyl is also misspelled in the fifth sentence of the abstract. The fifth sentence should read: Hydroxypropyl-\u03b2-cyclodextrin (HP\u03b2CD), specifically, increased the solubility of naringenin by over 400-fold, and its transport across a Caco-2 model of the gut epithelium by 11-fold."} +{"text": "Topiramate is the only approved oral preventive drug for chronic migraine (CM). However, we usually use other preventive drugs of prevention of frequent episodic migraine. Zonisamide is a neuromodulator that has showed efficacy in prevention of CM.To evaluate the efficacy of zonisamide after three months of therapy in CM patients (IHS-2006 criteria) that present inefficacy/intolerance/contraindication to topiramate, sodium valproate, \u00e2-blocks and flunarizine.Doses ZNS: 50-200mg. Primary end-point: Number of migraine days-NMD: Ineffective response-Inef(reduction of days<50%), good-G(50-75%), excellent-Exc(>75%). Secondary end-points: number of migraine episodes-NME; number of headache days-NHD; drug overuse; consumption of triptans and NSAIDs; EVA and MIDAS score, effective mean dose of ZNS, adverse events.We prospectively included 27 patients (May 2011-May 2012), 85.2% women. Twelve patients (44.4%) presented 16 adverse events (100% mild). Four of them-14.8% left the therapy. NMD, in the 23 patients who finished the three months follow-up, was Exc-39.1%, G-43.5%, and Inef-17.4%; NME was Exc-30.4%, G-43.5%, and Inef-26.1%; and NHD was Exc-34.8%, G-39.1%, and Inef-26.1%. Drug overuse disappeared in 47.8% of overusers. The consumption of triptans and NSAIDs decreased 54.3%, and 65.7%. The EVA score decreased 3.7 points (56.2%), and MIDAS scale score decreased 14.6 points (48.7%). Effective mean doses of ZNS: 106.6mg/night.Zonisamide presents a good profile of efficacy (70.3% of responses) and an acceptable tolerance. It could be a useful therapeutic option in CM patients intolerants, refractory, or with contraindications for topiramate, and the other drugs preventive drugs of migraine."} +{"text": "The proposed contrast-enhanced first-pass perfusion cardiovascular MR (CMR) protocol integrates some recent technical MRI advances towards quantitative analysis of perfusion CMR images: fast multi-slice pulse sequence , robust To evaluate an integrated first-pass perfusion cardiovascular MR (CMR) protocol designed to determine absolute contrast-agent concentrations in blood and tissues.1 shortening expected in blood and wall. First-pass perfusion CMR was performed in 7 volunteers . A signal-to-concentration model was applied to calculate Gd-DTPA concentrations in blood and tissues [1 relationship based on Bloch equation in the center of k-space. Gd-DTPA concentrations were calculated assuming: fast water exchange condition [1=3.8L.mmol-1.s-1[1 measured with a multi-point SR fit. TurboFLASH imaging parameters included: FOV=350mm\u00d7315mm, slice thickness=8mm, matrix=160\u00d7144, in-plane resolution=2.2mm\u00d72.2mm, TE/TR=1.2/2.4ms, flip angle 10\u00b0, temporal resolution=114ms, tSENSEx3, centric k-space trajectory, and receiver bandwidth=1008Hz/pix. Total image acquisition time was 523ms for the acquisition of 4 slices, namely aortic root and SA base, mid, and apex levels, with respective TD values 50-164-278-393ms. Contours for the blood and left ventricle were drawn manually, and the myocardium was divided into 6 (base-mid) or 4 (apex) standard segments.A multi-slice saturation recovery (SR) pulse sequence with sequential SR time delays (TD) after a non-selective saturation pulse was impl tissues ,5. A proondition , longituRepresentative images at peak contrast in blood and myocardium are shown Fig.The proposed integrated first-pass perfusion CMR protocol at 3T produced AIF and myocardial wall Gd-DTPA concentrations consistent with previously published results. Future work includes evaluation of the integrated protocol in cardiac patients."} +{"text": "Biventricular size and function have been studied extensively in patients after tetralogy of Fallot (TOF) repair, but little is known about atrial size and function. The atria play a crucial role in ventricular filling during diastole, and abnormalities in atrial size and function may reflect ventricular diastolic dysfunction. Diastolic dysfunction may precede systolic dysfunction and may therefore play an important role in the early detection of ventricular dysfunction.We assessed bi-atrial size and function in patients after TOF repair, and evaluated relationships with biventricular systolic and diastolic function, and clinical parameters.51 patients (21\u00b18 years) and 30 healthy controls (31\u00b17 years) were included and underwent magnetic resonance imaging. Patients also underwent exercise testing, and biomarker assessment. Bi-atrial and biventricular size, systolic and diastolic function were assessed from time-volume curves (figure 2 (patients) vs. 28\u00b18 ml/m2 (controls), p=0.001); RA reservoir function, RA early emptying fraction, and the RA early-to-late-emptying ratio (E/A ratio) were decreased (RA E/A ratio: 1.1\u00b10.5 (patients) vs. 1.9\u00b10.9 (controls), p<0.001). Patients had larger right ventricular (RV) volumes, lower biventricular ejection fraction and prolonged biventricular deceleration time (Dt) (RV Dt: 0.24\u00b10.10 (patients) vs. 0.13\u00b10.04 (controls), p<0.001). Left atrial (LA) maximal volume and LA early emptying fraction were decreased. Left ventricular (LV) E/A-filling ratio was increased (LV E/A-ratio: 4.2\u00b13.7 (patients) vs. 2.7\u00b11.3 (controls), p=0.008).In patients, right atrial (RA) minimal volume (min.vol.), RA pump function, and RA late emptying fraction were increased (RA min.vol.: 34\u00b18 ml/m2 slope: 32\u00b14 (patients with EDFF) vs. 28\u00b16 (patients without EDFF), p=0.014). Patients with abnormal RA emptying (reservoir function <30% and pump function >24%) had higher NT-proBNP levels vs. 7\u00b17 pmol/l , p=0.002) and worse exercise capacity. RA min.vol. was positively associated with RV end-diastolic volume .Patients with end-diastolic forward flow (EDFF) had larger RA and RV size, higher RA pump function (RA pump function: 27\u00b18% (patients with EDFF) vs. 20\u00b17% (patients without EDFF), p=0.003), higher N-terminal prohormone brain natriuretic peptide (NT-proBNP) levels, and higher ventilatory response to carbon dioxide production (VE/VCOIn TOF patients with good clinical condition and moderate RV dilatation, abnormal bi-atrial function and abnormal biventricular diastolic function is common. Abnormal RA emptying was associated with impaired clinical outcome, as was the presence of EDFF. These parameters, together with RA enlargement, could serve as useful markers for clinically relevant RV diastolic dysfunction.This research was funded by the Netherlands Heart Foundation: grant 2006B095."} +{"text": "ICU patients (ptes) account for a large proportion of HI. Its epidemiology allow us to identify key issues and prioritize interventions. We determined the incidence of HI in ICU in Uruguay and described specific locations, dispositive-associated rates and microorganisms.A national surveillance system for HI was implemented in 2006; prospective surveillance was performed using NNISS criteria. It is mandatory, to record online and send their data to the Ministry of Health. Data are audited and results published annually.S. aureus , A. baumanii , Ps. aeruginosa and K. pneumoniae .We present 2010 results of medical-surgical ICUs. 53 hospitals reported. 13611 ptes were surveyed (99541 ptes-days). 2340 HI episodes were reported (density of incidence rate (ID) 23.5/1000 ptes-days and cumulative incidence 17.2%). Ventilator-associated pneumonia (VAP) (34%), bronchitis (B) (28%), catheter-associated urinary tract infection (CAUTI) (21%) and central-line associated bacteremia (CLAB) (8%) were the main infectious sites. VAP ID was 14.2/1000 ventilator-days (dispositive utilization (DU) 0.5, secondary bacteremia (SB) 5.3% and contributor mortality (CM) 19.7%), CLAB ID was 1.9/1000 catheter-days 17.7%) and CAUTI ID was 5.8/1000 catheter-days 3.7%, (CM) 5.1%). Microorganisms were Respiratory tract infections are the main problem. ICUs predominance of Gram Negative Bacilli in these infections may suggest the importance of exogenous sources. VAP and CAUTI rates are also high, diminish its incidence is priority for the national program.None declared."} +{"text": "Thermus oshimai JL-2 and Thermus thermophilus JL-18 each have a circular chromosome, 2.07 Mb and 1.9 Mb in size, respectively, and each has two plasmids ranging from 0.27 Mb to 57.2 kb. The megaplasmid of each strain contains a gene cluster for the reduction of nitrate to nitrous oxide, consistent with their incomplete denitrification phenotypes.The strains Thermus comprises >15 species of thermophilic bacteria, including the biotechnologically exalted Thermus aquaticus and the genetically tractable Thermus thermophilus. We reported previously the isolation of a large number of Thermus strains from the Great Boiling Spring system in the U.S. Great Basin, typified by Thermus oshimai JL-2 and Thermus thermophilus JL-18, and described their roles in incomplete denitrification in situ (The genus T. oshimai JL-2 and T. thermophilus JL-18 were sequenced using 454-GS-FLX Titanium and Illumina GA II (2 \u00d7 75 bp) methodologies, were assembled using Newbler version 2.3 (prerelease), and were annotated using Prodigal version 1.4, Gene Prediction Improvement Pipeline (GenePRIMP) at the Joint Genome Institute (JGI) in Walnut Creek, CA. The data are available at the Joint Genome Institute (JGI) Integrated Microbial Genomes (IMG) website ; and a smaller circular plasmid, pTHEOS02 . T. thermophilus JL-18 has a 1.9-Mb circular chromosome carrying 2,057 predicted genes; a circular megaplasmid, pTTJL1801 ; and a smaller circular plasmid, pTTJL1802 .The genomes of T. thermophilus JL-18 was similar to those of T. thermophilus HB8 and T. thermophilus HB27, apart from a few chromosomal rearrangements . T. oshimai JL-2 possesses two nitrate/nitrite transporters (narK1 and narK2), which is similar to T. thermophilus HB8 (T. thermophilus JL-18 possesses a single copy of narK. Genes encoding nitrite reductase (nirS and nirK in T. oshimai JL-2 and nirS in T. thermophilus JL-18) and nitric oxide reductase (norB and norC) were also identified in close proximity to the narGHIJK operon in the megaplasmids of both T. thermophilus JL-18 and T. oshimai JL-2. However, nitrous oxide reductase (nos) genes, which are needed for the conversion of nitrous oxide to dinitrogen, are absent, concurrent with the incomplete denitrification phenotype of these strains and the high flux of nitrous oxide reported at Great Boiling Spring (T. thermophilus HB8 and HB27 (sox gene cluster that includes a sulfite dehydrogenase gene (soxCD) essential for the chemotrophic growth of Paracoccus pantotrophus , CP003250.1 (T. oshimai JL-2 megaplasmid pTHEOS01), CP003251.1 (T. oshimai JL-2 plasmid pTHEOS02), CP003252.1 (T. thermophilus JL-18 chromosome), CP003253.1 (T. thermophilus JL-18 plasmid pTTJL1801), and CP003254.1 (T. thermophilus JL-18 plasmid pTTJL1802).The genome sequences from this study are available from GenBank under the following accession no:"} +{"text": "However, its efficacy and indication are still controversial issues. Recently, randomized controlled studies are ongoing in other countries. Our hypothesis is that PMX-DHP therapy may improve the hemodynamic status in septic patients.Since 1994, Polymyxin B-direct hemoperfusion (PMX-DHP) in our ICU were included in this retrospective observational study. Patients' clinical, microbiological and PAC data were collected from medical archives. PAC variables were compared between immediately before and immediately after PMX-DHP therapy. Values were expressed as mean \u00b1 SD. Data were analyzed by Wilcoxon signed-ranks test, chi-square test and Fisher's exact probability test. 2), and oxygen delivery and consumption significantly improved after PMX-DHP therapy . The systemic venous resistance index (SVRI) (dyn second m2/cm5) and mixed venous oxygen saturation were not statistically different before and after PMX-DHP therapy . The inotropic score and P/F ratio improved after the therapy .Sixty-three patients ) were studied. The mortality rate was 30.2% at 28 days after PMX-DHP. The APACHE II score and SOFA score on the day of PMX-DHP therapy were 20.2 \u00b1 14.8 and 7.3 \u00b1 3.8, respectively. Mean arterial pressure , cardiac index (CI; l/minute/m2, VO2, inotropic score and P/F ratio improved after PMX-DHP therapy, while SVRI and SVO2 did not change. PMX-DHP could contribute to oxygen delivery due to improve hemodynamic status, while decreasing inotropic agents in septic patients.MAP, CI, DO"} +{"text": "The effects of adrenomedullin in circulatory shock states are controversially discussed: while its exogenous supplementation improved organ function and survival in expern = 11) or the adrenomedullin antibody HAM1101 . Fifteen hours later animals were anesthetized, mechanically ventilated and instrumented for a consecutive 6-hour observation period. Colloid fluid resuscitation and continuous i.v. noradrenaline were titrated to maintain normotensive (mean blood pressure >60 mmHg) and hyperdynamic hemodynamics. Creatinine blood levels and clearance were assessed as surrogate for glomerular filtration [Immediately after cecal ligation and puncture to induce peritonitis, mice randomly received vehicle (ltration . All datP < 0.001), increased total diuresis vs. 0.6 ml, P = 0.028) resulting in improved fluid balance vs. 0.26 , P = 0.011) and kidney function vs. 2.0 \u03bcg/ml, P = 0.006; creatinine clearance: 400 vs. 197 \u03bcl/minute, P = 0.006).Adrenomedullin antagonism decreased the noradrenaline requirements needed to achieve target hemodynamics vs. 0.02 \u03bcg/g/hour, In resuscitated murine septic shock, early modulation of excess adrenomedullin activity via antibody HAM1101 improves cardiovascular catecholamine responsiveness, ultimately associated with attenuation of acute kidney injury."} +{"text": "To the Editor, 9/L; ANC: 4.6 x 109/L; Hct: 6.9%; RBC count: 1.19 x 1012/L; RDW: 20.5; MCV: 58 fL; Plt count: 485 x 109/L; absolute reticulocyte count: 45.5 x 109/L . Peripheral blood smear showed hypochromic microcytic red cells, polychromasia, and nucleated red cells. Serum iron was 5 \u03bcg/dL, total iron binding capacity was 450 \u03bcg/dL, and ferritin was <1 ng/mL. A 3-year-old female toddler was referred to our pediatric emergency unit with a 2-week history of fatigue, anorexia, progressive pallor, and vomiting. Medical history showed that iron deficiency anemia was diagnosed one year before and oral iron-sulfate was given. She also had a one year history of intermittent vomiting. Her diet seemed adequate in iron-rich foods. Chest X-ray and abdominal ultrasonographic examination performed in a medical center were normal. Complete blood count findings were as follows: Hb: 1.7 g/dL; WBC count: 8.0 x 10She was hospitalized and given packed red cell transfusion. The following day she suddenly developed respiratory distress after breakfast. Chest X-ray showed a radiolucent lesion in the right paracardiac area . Congeni12/L; MCV: 70.5 fL; MCH: 21.9; MCHC: 31; RDW: 24; WBC count: 9.8 x 109/L; ANC: 4.3 x 109/L, Plt count: 453 x 109/L; absolute reticulocyte count: 11 x 109/L) [normal 50-150 x 109/L]). Peripheral blood smear showed hypochromic microcytic red cells. Esophagogastroduodenoscopy and esophageal biopsy showed erosions, gastroesophageal reflux, chronic inflammation, and hyperplasia of the epithelium. A proton pump inhibitor, domperidone, and anti-acid medications were started. Iron sucrose was administered twice weekly for 3 weeks and the Hb increased . Blood smear showed normal red cells. At the 2-year follow-up the patient had no gastrointestinal symptoms or anemia. At 6 weeks post surgery the patient had no gastrointestinal symptoms, but her Hb dropped to 7.9 g/dL and fecal occult blood test findings were positive (Hct: 25.6%; RBC count: 3.63 x 10The coexistence of Morgagni and Bochdalek defects is rarely reported . About 5CDH must be included in the differential diagnosis of severe iron deficiency anemia in the absence of such obvious causes as nutritional deficiency, melena, hematochezia, and malabsorption. Physicians must be aware that a history of intermittent vomiting and/or sudden onset respiratory distress in young children are indications for imaging of the upper gastrointestinal tract and thorax."} +{"text": "Head and Neck Oncology and is not related to the content of BMC Medicine in any way.This comment relates to articles published in archived content of the journal Head and Neck Oncology and is not related to the content of BMC Medicine in any way.This comment relates to articles published in archived content of the journal Head & Neck Oncology. In order to maintain the integrity of the BioMed Central portfolio of journals, we decided to cease publication of the journal with effect from 9th August 2012.While conducting an internal audit of publications between January and June 2012, BioMed Central discovered a number of apparent major irregularities in the content and editorial handling of the journal University College London (UCL) and University College London Hospital (UCLH) subsequently conducted a joint investigation of our concerns. This focused primarily on the actions of Editor-in-Chief Mr Colin Hopper, because neither of the other active Editors-in-Chief, Waseem Jerjes and Tahwinder Upile, were employees of UCL during the time covered by our audit, so an investigation of their actions would have been beyond the scope of UCL\u2019s investigation.Following their investigation UCL were satisfied that there was no evidence of research misconduct arising from any employee, honorary researcher or student in relation to the articles they were asked to investigate. They were also satisfied that there was no evidence of editorial or author misconduct on the part of Colin Hopper.In the absence of definitive conclusions about all of the concerns raised by its audit, BioMed Central has provided details of its findings in the form of a Publishers Note on relevant articles which will be updated if further information becomes available. If you are an author of a published article in this journal and have further questions, please contact info@biomedcentral.com.The affected articles are listed below:A review of the epidemiology of oral and pharyngeal carcinoma: updateDaniel M SamanHead & Neck Oncology 2012, 4:1http://www.headandneckoncology.org/content/4/1/1Randomized clinical trial of LigaSure versus conventional suture ligation in thyroid surgeryAnandi H.W. Schiphorst, Bas A. Twigt, Sjoerd G. Elias and Thijs van DalenHead & Neck Oncology 2012, 4:2http://www.headandneckoncology.org/content/4/1/2A decision support system for quality of life in head and neck oncology patientsJoaquim J Goncalves and Alvaro RochaHead & Neck Oncology 2012, 4:3http://www.headandneckoncology.org/content/4/1/3Etiology analysis and computed tomography imaging of a tonsillar inflammatory myofibroblastic tumor: report of an immunocompetent patient and brief reviewYun-Zhen Luo, Li-Bo Dai, Shui-Hong Zhou, Xing-Mei Luo, Jun Fan and Ling-Xiang RuanHead & Neck Oncology 2012, 4:4http://www.headandneckoncology.org/content/4/1/4cTNM vs. pTNM: the effect of not applying ultrasonography in the identification of cervical nodal diseaseWaseem Jerjes, Tahwinder Upile, Hani Radhi, Aviva Petrie, Jesuloba Abiola, Aidan Adams, Jacqueline Callear, Panagiotis Kafas, Syedda Abbas, Kartic Rajaram, Colin HopperHead & Neck Oncology 2012, 4:5http://www.headandneckoncology.org/content/4/1/5The effect of tobacco and alcohol and their reduction/cessation on mortality in oral cancer patients: short communicationWaseem Jerjes, Tahwinder Upile, Hani Radhi, Aviva Petrie, Jesuloba Abiola, Aidan Adams, Panagiotis Kafas, Jacqueline Callear, Ramin Carbiner, Kartic Rajaram, Colin HopperHead & Neck Oncology 2012, 4:6http://www.headandneckoncology.org/content/4/1/6Nimesulide inhibited the growth of hypopharyngeal carcinoma cells via suppressing Survivin expressionJia-Jun Tian, Su-Mei Lu, Liang Yu, Ju-Ke Ma, Ya-Kui Mu, Hai-Bo Wang and Wei XuHead & Neck Oncology 2012, 4:7http://www.headandneckoncology.org/content/4/1/7Primary squamous cell carcinoma of thyroid: a case report and review of literatureMutahar A Tunio, Mushabbab Al Asiri, Mosa Fagih and Rashad AkashaHead & Neck Oncology 2012, 4:8http://www.headandneckoncology.org/content/4/1/8The prognostic significance of p63 and Ki-67 expression in myoepithelial carcinomaYou-Hu Jiang, Bo Cheng, Ming-Hua Ge and Gu ZhangHead & Neck Oncology 2012, 4:9http://www.headandneckoncology.org/content/4/1/9Parapharyngeal space hemangiopericytoma treated with surgery and postoperative radiation- a case reportMuhammad Mohsin Fareed, Abdullah Suleiman Mazaed Al Amro, Rashad Akasha, Mansour A Assiry, Mushabbab Al Asiri, Mutahar Tonio and Yasir BayoumiHead & Neck Oncology 2012, 4:10http://www.headandneckoncology.org/content/4/1/10Knockdown of aberrantly expressed nuclear localized decorin attenuates tumour angiogenesis related mediators in oral cancer progression model in vitroNyla Dil and Abhijit G BanerjeeHead & Neck Oncology 2012, 4:11http://www.headandneckoncology.org/content/4/1/11A retrospective, deformable registration analysis of the impact of PET-CT planning on patterns of failure in stereotactic body radiation therapy for recurrent head and neck cancerKyle Wang, Dwight E Heron, John C Flickinger, Jean-Claude M Rwigema, Robert L Ferris, Gregory J Kubicek, James P Ohr, Annette E Quinn, Cihat Ozhasoglu and Barton F BranstetterHead & Neck Oncology 2012, 4:12http://www.headandneckoncology.org/content/4/1/12Clear cell chondrosarcoma of the head and neckSepideh Mokhtari and Abbas MirafshariehHead & Neck Oncology 2012, 4:13http://www.headandneckoncology.org/content/4/1/13Delay in pathological tissue processing time vs. mortality in oral cancer: Short communicationWaseem Jerjes, Tahwinder Upile, Hani Radhi, Aviva Petrie, Aidan Adams, Jacqueline Callear, Panagiotis Kafas, Colin HopperHead & Neck Oncology 4:14http://www.headandneckoncology.org/content/4/1/14The cost burden of oral, oral pharyngeal, and salivary gland cancers in three groups: commercial insurance, medicare, and medicaidJed J Jacobson, Joel B Epstein, Frederick C Eichmiller, Teresa B Gibson, Ginger S Carls, Emily Vogtmann, Shaohung Wang and Barbara MurphyHead & Neck Oncology 2012, 4:15http://www.headandneckoncology.org/content/4/1/15Photodynamic therapy in the management of potentially malignant and malignant oral disordersWaseem Jerjes, Zaid Hamdoon, Colin HopperHead & Neck Oncology 4:16http://www.headandneckoncology.org/content/4/1/16CO2 lasers in the management of potentially malignant and malignant oral disordersWaseem Jerjes, Zaid Hamdoon, Colin HopperHead & Neck Oncology 2012, 4:17http://www.headandneckoncology.org/content/4/1/17Expression of Glut-1, HIF-1alpha, PI3K and p-Akt in a case of ceruminous adenomaWan-Qin Shen, Ke-Jia Cheng, Yang-Yang Bao, Shui-Hong Zhou and Hong-Tian YaoHead & Neck Oncology 2012, 4:18http://www.headandneckoncology.org/content/4/1/18Systemic therapy in the management of metastatic or advanced salivary gland cancersAymen Lagha, Nesrine Chraiet, Mouna Ayadi, Sarra Krimi, Bassem Allani, Hela Rifi, Henda Raies and Amel MezliniHead & Neck Oncology 2012, 4:19http://www.headandneckoncology.org/content/4/1/19Tongue cancer in young patients: Case report of a 26-year-old patient.Aleksandra Crede, Michael Locher and Marius BredellHead & Neck Oncology 2012, 4:20http://www.headandneckoncology.org/content/4/1/20Reconstruction of scalp defects with the radial forearm free flapLarissa Sweeny, Brendan T Eby, J. Scott Magnuson, William R Carroll and Eben L RosenthalHead & Neck Oncology 2012, 4:21http://www.headandneckoncology.org/content/4/1/21The use of specific anti-growth factor antibodies to abrogate the oncological consequences of transfusion in head & neck squamous cell carcinoma: an in vitro studyTahwinder Upile, Waseem Jerjes, Sandeep Singh, Mohammed Al-Khawalde, Zaid Hamdoon, Hani Radhi, Colin HopperHead & Neck Oncology 2012, 4:22http://www.headandneckoncology.org/content/4/1/22Definitive radiotherapy for early stage glottic cancer by 6 MV photonsChi-Chung TONG, Kwok-Hung AU, Roger Kai-Cheong NGAN, Sin-Ming CHOW, Foon-Yiu CHEUNG, Yiu-Tung FU, Joseph Siu-Kei AU and Stephen Chun-Key LAWHead & Neck Oncology 2012, 4:23http://www.headandneckoncology.org/content/4/1/23Branchial cysts within the parotid salivary glandTahwinder Upile, Waseem Jerjes, Mohammed Al-Khawalde, Panagiotis Kafas, Steve Frampton, Angela Gray, Bruce Addis, Ann Sandison, Nimesh Patel, Holger Sudhoff, Hani RadhiHead & Neck Oncology 2012, 4:24http://www.headandneckoncology.org/content/4/1/24A patient with ulcerated calcifying epithelioma of Malherbe in the pinna: case reportTahwinder Upile, Waseem Jerjes, Fabian Sipaul, Ann Sandison, Panagiotis Kafas, Mohammed Al-Khawalde, Hani RadhiHead & Neck Oncology 2012, 4:25http://www.headandneckoncology.org/content/4/1/25Computed tomography and pathological findings of five nasal neurilemmomasJing Hu, Yang-Yang Bao, Ke-Jia Cheng, Shui-Hong Zhou, Ling-Xiang Ruan and Zhou-Jun ZhengHead & Neck Oncology 2012, 4:26http://www.headandneckoncology.org/content/4/1/26Metastatic rhabdomyosarcoma of the thyroid gland, a case reportMohamed T Hafez, Mohamed A Hegazy, Khaled Abd Elwahab, Mohammad Arafa, Islam Abdou and Basel RefkyHead & Neck Oncology 2012, 4:27http://www.headandneckoncology.org/content/4/1/27Squamous cell carcinoma of the oral cavity and the oropharynx in patients less than 40 years of age: a 20-year analysisSamuel E Udeabor, Majeed Rana, Gerd Wegener, Nils-Claudius Gellrich and Andr\u00e9 M EckardtHead & Neck Oncology 2012, 4:28http://www.headandneckoncology.org/content/4/1/28Structural validation of oral mucosal tissue using optical coherence tomographyZaid Hamdoon, Waseem Jerjes, Raed Al-Delayme, Gordon McKenzie, Amrita Jay, Colin HopperHead & Neck Oncology 2012 4:29http://www.headandneckoncology.org/content/4/1/29Solitary giant neurofibroma of the neck subjected to photodynamic therapy: case studyZaid Hamdoon, Waseem Jerjes, Raed Al-Delayme, Colin HopperHead & Neck Oncology 2012 4:30http://www.headandneckoncology.org/content/4/1/30Oral sex, cancer and death: sexually transmitted cancersTahwinder Upile, Waseem Jerjes, Mohammed Al-Khawalde, Hani Radhi and Holger SudhoffHead & Neck Oncology 2012 4:31http://www.headandneckoncology.org/content/4/1/31Enhanced patient reported outcome measurement suitable for head and neck cancer follow-up clinicsNaseem Ghazali, Derek Lowe and Simon N RogersHead & Neck Oncology 2012, 4:32http://www.headandneckoncology.org/content/4/1/32A patient with primary Burkitt's lymphoma of the postnasal space: case reportTahwinder Upile, Waseem Jerjes, Jesuloba Abiola, Panagiotis Kafas, Ann Sandison, Zaid Hamdoon, Mohammed Al-Khawalde and Hani RadhiHead & Neck Oncology 2012, 4:33http://www.headandneckoncology.org/content/4/1/33Positron emission tomography in the detection of occult primary head and neck carcinoma: a retrospective studyGabriel G Pereira, Joaquim C Silva and Eurico F MonteiroHead & Neck Oncology 2012, 4:34http://www.headandneckoncology.org/content/4/1/34Granulocyte colony-stimulating factor-producing squamous cell carcinoma of the lower gingiva: a case reportJun-ichi Kobayashi Dr., Akihiro Miyazaki Dr., Takashi Yamamoto Dr., Kenji Nakamori Dr., Rina Suzuki Dr., Takeshi Kaneko Dr., Naohiro Suzuki Dr. and Hiroyoshi Hiratsuka Prof.Head & Neck Oncology 2012, 4:35http://www.headandneckoncology.org/content/4/1/35Spinal metastasis in head and neck cancerGregory M Trilling, Hyongyu Cho, Mohamed A Ugas, Samerah Saeed, Asia Katunda, Waseem Jerjes and Peter V GiannoudisHead & Neck Oncology 2012, 4:36http://www.headandneckoncology.org/content/4/1/36Analysis of the compatibility of dental implant systems in fibula free flap reconstructionRamin Carbiner, Waseem Jerjes, Kaveh Shakib, Peter V Giannoudis and Colin HopperHead & Neck Oncology 2012, 4:37http://www.headandneckoncology.org/content/4/1/37p16 overexpression in malignant and premalignant lesions of the oral and esophageal mucosa following allogeneic hematopoietic stem cell transplantationYasumasa Kakei, Masaya Akashi, Hideki Komatsubara, Tsutomu Minamikawa and Takahide KomoriHead & Neck Oncology 2012, 4:38http://www.headandneckoncology.org/content/4/1/38Spinal metastasis in thyroid cancerSami Ramadan, Mohamed A Ugas, Richard J Berwick, Manisha Notay, Hyongyu Cho, Waseem Jerjes, Peter V GiannoudisHead & Neck Oncology 2012, 4:39http://www.headandneckoncology.org/content/4/1/39Feasibility of recruitment to an oral dysplasia trial in the United KingdomPaul C Nankivell, Janet A Dunn, Michael J.S. Langman and Hisham MehannaHead & Neck Oncology 2012, 4:40http://www.headandneckoncology.org/content/4/1/40Effect of human beta-defensin-3 on head and neck cancer cell migration using micro-fabricated cell islandsKevin Wang, Joanne H Wang, Harihara Baskaran, Russell Wang and Rick JurevicHead & Neck Oncology 2012, 4:41http://www.headandneckoncology.org/content/4/1/41"} +{"text": "Cardiac MRI (CMR) is used to follow patients after TOF repair to assess pulmonary regurgitation (PR), pulmonary stenosis (PS) and right ventricular (RV) function. 4D flow-sensitive MRI techniques enable visualization of complex flow patterns ,2]. Wit. Wit2]. Analyze flow patterns in superior vena cava (SVC), inferior vena cava (IVC), right atrium (RA), right ventricle (RV), and main, right and left pulmonary arteries using 3D radially-undersampled, 4D flow-sensitive MRI.3 volume, 1.0-1.25mm3 acquired isotropic spatial resolution, and VENC of 50-200cm/s. Scan time was approximately 8-12min using an adaptive respiratory bellows reading and 50% efficiency. Retrospective ECG-triggered cardiac gating was used with datasets reconstructed into 20 time frames. Flow visualization and analysis on 1.5T and 3.0T clinical systems after IRB-approval and obtaining consent. 4D flow-sensitive MRI data were acquired with a radially undersampled phase contrast (PC) sequence, PC VIPR . The. The4]."} +{"text": "With newly available 32-channel cardiac coil, 3 tesla MRI system provides increased signal-to-noise radio (SNR), reduced imaging time and improved spatial resolution. This study sought to determine the diagnostic performance of 3T stress MRMPI with 32-channel cardiac coil in detecting clinical relevant coronary artery stenosis in comparison with invasive coronary angiography (ICA).Forty four patients who were scheduled for ICA underwent stress MRMPI with 3T MRI with a 32-channel cardiac receiver coil . The total amount of contrast medium was 0.15mmole/kg with injection rate at 4ml/s. The MR protocol included gadolinium-enhanced stress first-pass perfusion , rest perfusion, and delayed enhancement (DE). Ischemia was defined as (1) a territory with perfusion defect at stress study but no DE, (2) territory with DE but additional peri-infarcted perfusion defect at stress study. Diagnostic performance was determined on a per-patient basis. Quantitative CA served as the reference standard.Coronary angiography depicted significant stenosis in 22 of 44 patients (50%). No complications were observed during Stress perfusion 3.0 tesla MRI and dipyridamole infusion. For detection of significant coronary stenosis, 3T stress MRMPI provided sensitivity: 0.91(0.75-1.00), specificity: 0.86(0.72-1.00), positive predictive value: 0.87(0.74-1.00) and negative predictive value: 0.91(0.748-1.00). The overall diagnostic accuracy was: 0.88.Our study showed that 3T stress MRMPI using 32-channel cardiac coil demonstrated high diagnostic accuracy for detection of significant stenosis, having QCA as the reference standard. Further investigation is needed to assess if advances in technology and improvement in diagnostic accuracy for CAD detection will translate in better patient care and outcomes."} +{"text": "Follow-up studies used flyback EPI to reduce image artifacts. More recently a spiral k-space trajectory was utilized for improved SNR.The original implementation of 2D cine DENSE (displacement encoding with stimulated echoes) employed a conventional EPI To evaluate and compare SNR efficiencies and strain results of these three techniques for 2D cine DENSE imaging.k-space trajectories, namely conventional bottom-up interleaved EPI, flyback bottom-up interleaved EPI, and interleaved spiral. They were compared in volunteers using a two-breath-hold protocol on a 1.5T Siemens Avanto system with a four-channel chest coil. In accordance with protocols approved by the local institutional review board, 5 healthy volunteers were imaged. Identical parameters included pixel size = 3.8 \u00d7 3.8 mm2, slice thickness = 8 mm, flip angle = 20\u00b0, cardiac phases = 15, displacement encoding frequency = 0.08 cycles/mm, two-point phase cycling, and through-plane dephasing frequency = 0.08 cycles/mm to suppress artifacts. Other parameters for conventional/flyback EPI included image matrix = 72 \u00d7 96, TE = 8.57/10.57 ms, TR = 17.69/21.19 ms, ETL = 8, segments = 16, sampling time per image = 99.8 ms, heartbeats per breath-hold = 21/20, and fat suppression by water excitation. For spiral, other parameters included image matrix = 96 \u00d7 96, TE = 1.08 ms, TR = 17 ms, interleaves = 6, interleaves per heartbeat = 2, sampling time per image = 66.8 ms, heartbeats per breath-hold = 14, and fat suppression by chemically-selective saturation pulses applied prior to displacement-encoding pulses. Based on the magnitude-reconstructed images, SNR efficiencies were calculated. Strain maps were also calculated.Cine DENSE pulse sequences were developed that employed different As shown in Figure Conventional EPI, flyback EPI and spiral cine DENSE produce similar strain results. Spiral cine DENSE provides improved SNR efficiency compared to the other two techniques."} +{"text": "Liver fibrosis (LF) progression is fated to become one of the major long-term complications in HIV patients, even in those without HCV or HBV co-infections (HIV-mono-infected). The aim of this study was to assess LF progression in HIV-mono-infected patients and associated risk factors.Observational retrospective study. All HIV naive patients who started HAART from 1996 to 2006 were included. Concordance between FIB-4 and APRI scores was assessed using the weighted kappa coefficient. Rates of transition from lower classes to higher classes were estimated by Kaplan-Meier analysis. Cox regression models were applied to assess possible predictors both at baseline and during the follow-up.1,112 naive patients were selected. A moderate concordance between FIB-4 and APRI was demonstrated (K=0.573). For FIB-4, the incidence of transition to higher classes was 0.064 PYFU , while for APRI the incidence of transition was 0.099 PYFU . Viro-immunological control during HIV infection appeared to reduce the risk of both FIB-4 and APRI transitions. HIV-RNA <500 copies/ml and higher CD4 T-cell counts only for FIB-4 (HR 0.881 p=0.0004 for 100 cells higher) during the follow-up were statistically protective. Among baseline variables, for FIB-4 transition, age \u2265 40 years (HR 1.037 p<0.0001) and higher FIB-4 values (HR 1.526 p=0.0038) were associated with increased risk of LF progression, while sexual risk factor for HIV acquisition resulted to be protective (HR 0.524 p=0.0314). For APRI, male gender (HR 1.390 p=0.017), higher GGT values (HR 1.015 p=0.014) and higher APRI values (HR 1.748 p=0.007) were independently associated with APRI transition. A sensitivity analysis demonstrated that DDX drugs as time-dependent covariates were associated with a significant risk of transition with FIB-4 (HR 1.662 p=0.0007) or APRI (HR 1.661 p=0.0001)Our data suggest that a better viro-immunological control of HIV infection may slow down fibrosis progression provided that DDX are avoided. Moreover our analysis provided a comprehensive feature of the risk factors that should be controlled in clinical practice"} +{"text": "There is an error in the title. \"gp120\" was incorrectly labeled as \"gsp120.\"The correct title is: Synergistic Cooperation between Methamphetamine and HIV-1 gp120 through the P13K/Akt Pathway Induces IL-6 but not IL-8 Expression in AstrocytesThe correct citation is: Shah A, Silverstein PS, Kumar S, Singh DP, Kumar A (2012) Synergistic Cooperation between Methamphetamine and HIV-1 gp120 through the P13K/Akt Pathway Induces IL-6 but not IL-8 Expression in Astrocytes. PLoS ONE 7(12): e52060. doi:10.1371/journal.pone.0052060"} +{"text": "We have previously shown that the tryptophan-catabolizing enzyme indoleamine-2,3-dioxygenase (IDO) critically impairs host defense against secondary bacterial pneumonia . Since iin vitro data, transgenic mice that conditionally express IDO in the airway epithelium upon doxycycline (dox) treatment and control mice were challenged with LPS (1 \u03bcg) or Klebsiella pneumoniae (104 colony-forming units) intranasally and sacrificed after 24 hours to count neutrophils in bronchoalveolar lavage fluid . Statistical analysis was performed by Student's t test or Mann-Whitney U test where appropriate. P < 0.05 was considered significant.Freshly isolated neutrophils were cultured in the presence or absence of tryptophan, kynurenine and 3-hydroxy-anthranilic acid. Apoptosis was identified by annexin V/propidium iodine staining . To confirm our P < 0.05), which was reversed by adding tryptophan. Conditional transgenic mice, which showed marked expression of IDO in the pulmonary compartment, had reduced neutrophil numbers in bronchoalveolar lavage fluid after challenge with K. pneumoniae and LPS , which was associated with active caspase-3 staining in dox-treated mice, but not in control mice.Both kynurenine and 3-hydroxy-anthranilic acid enhanced apoptosis in freshly isolated neutrophils (60.3 \u00b1 8.7% and 45.5 \u00b1 1.7% respectively vs. 33.5 \u00b1 8.1% under control conditions, both in vivo and may impair host defense against secondary bacterial infections.Neutrophils undergo apoptosis in presence of kynurenine or 3-hydroxy-anthranilic acid and the absence of tryptophan. Pulmonary IDO expression, as occurs during influenza infection, enhances neutrophil apoptosis"} +{"text": "In rheumatoid arthritis (RA) synovial tissue (ST) angiogenesis can be observed already in the earliest phase of disease. The chemokine CXCL12, which is induced via the non-canonical nuclear factor-kappaB (NF-kB) pathway, plays an important role in angiogenesis, lymphocyte transendothelial migration, and the homing of endothelial progenitor cells. Therefore, the non-canonical pathway, with its key mediator NF-kB inducing kinase (NIK), may play an important role in pathological angiogenesis and the perpetuation of synovial inflammation in RA.To study the role of non-canonical NF-kB signaling in pathological angiogenesis in RA.-/- mice in the aortic ring assay. Physiological angiogenesis was evaluated by isolectin B4 staining of the retina followed by confocal microscopy. The contribution of NIK to synovial angiogenesis was studied in vivo in antigen-induced arthritis (AIA).Expression of NIK and CXCL12 in RA ST was evaluated using immunofluorescence microscopy (IF). Angiogenesis was studied in endothelial cells (EC) in vitro using the tube formation assay and ex vivo by comparing WT and NIK-/- mice showed normal TNF- and VEGF-induced microvessel outgrowth. In contrast, whereas non-canonical NF-kB stimuli induced microvessel outgrowth in WT mice (unstim 29.94 \u00b1 6.08 vs. LT 159.1 \u00b1 50.24 vs. LIGHT 110.3 \u00b1 17.68 (mm^2) p<0.05), no microvessel outgrowth was observed in aortic rings from NIK-/- mice (unstim 28.74 \u00b1 15.89 vs. LT 45.9 \u00b1 16.71 vs. LIGHT 43.41 \u00b1 15.73 (mm^2)). In line with this, NIK-/- mice exhibited normal developmental angiogenesis in the retina, but a 50% reduction in pathological angiogenesis in synovial inflammation .NIK, p52 and CXCL12 were highly expressed in EC in RA ST, mainly in small (newly formed) blood vessels. Stimuli that induce non-canonical NF-kB signaling (lymphotoxin (LT), LIGHT, and CD40L) significantly enhanced in vitro tube formation 2,5-fold (p<0.05), which could be completely blocked by siRNA targeting NIK or IKK\u03b1. Aortic rings from WT and NIK-/- mice exhibited normal developmental and VEGF-induced angiogenesis, but reduced pathological angiogenesis in AIA. These findings point towards an important role of the non-canonical NF-kB pathway in pathological angiogenesis associated with chronic inflammation. This could be exploited for the development of future new therapies for RA.NIK is preferentially expressed in EC in RA ST and non-canonical NF-kB signaling in EC results in enhanced angiogenesis in vitro. NIK"} +{"text": "There were errors in the article title.The correct version of the title is: The Long Coiled-Coil Protein NECC2 Is Associated to Caveolae and Modulates NGF/TrkA Signaling in PC12 CellsThe correct version of the citation is: D\u00edaz-Ruiz A, Rabanal-Ruiz Y, Tr\u00e1vez A, Gracia-Navarro F, Cruz-Garc\u00eda D, et al. (2013) The Long Coiled-Coil Protein NECC2 Is Associated to Caveolae and Modulates NGF/TrkA Signaling in PC12 Cells. PLoS ONE 8(9): e73668. doi:10.1371/journal.pone.0073668"} +{"text": "To assess the feasibility of cardiac magnetic resonance imaging (MRI) and angiography (MRA) at 3.0T in pediatric patients with congenital heart disease (CHD) and to compare the technical and diagnostic performance with an age-matched and clinically comparable control group imaged at 1.5T.Forty-six patients with suspected or known CHD were evaluated (9/2008-5/2011). SSFP cine imaging, time-resolved MRA (TR-MRA), and high resolution contrast-enhanced MRA (HR-MRA) were performed. Two independent observers analyzed the MRI data for image quality, thoraco-abdominal vessel definition, and artifacts.At 3.0T, 91% of SSFP cine images (k=0.55) and 97% (374 of 387) of vascular segments (k=0.49) were rated as good or excellent image quality with 72% of SSFP cine images having mild and 27% having moderate artifacts. At 1.5T, 92% of SSFP cine images (k=0.52) and 96% (344 of 356) of vascular segments (k=0.18) were rated as good or excellent image quality with 86% of SSFP cine images having mild and 14% having moderate artifacts. The SNR and CNR of SSFP images and HR-MRA were higher at 3.0T (p<0.001) with off-resonance artifacts being more prevalent at 3.0T (45% of images at 3.0T vs 27%). However, they rarely rendered the images non-diagnostic.Cardiac MRI & MRA at 3.0T are feasible in children with CHD. Both field strengths can be used successfully for cardiac and vascular imaging; deciding which to use depends on local availability and the importance of vascular (extra-cardiac) vs. intra-cardiac imaging.Siemens Research Grant"} +{"text": "The word \"Splice\" is misspelled in the article title. The correct title is: Broad Expression Analysis of Human ANTXR1/TEM8 Transcripts Reveals Differential Expression and Novel Splice Variants.The correct citation is: Vargas M, Karamsetty R, Leppla SH, Chaudry GJ (2012) Broad Expression Analysis of Human ANTXR1/TEM8 Transcripts Reveals Differential Expression and Novel Splice Variants. PLoS ONE 7(8): e43174. doi:10.1371/journal.pone.0043174"} +{"text": "AbstractPerkinsyllis augeneri and Prosphaerosyllis chauseyensis Olivier et al., 2011 are new records for the Mediterranean Sea. Detailed information is given on the morphology, ecology and distribution of the species recorded for the first time in the studied areas. In addition, an update on the distribution of the genus Prosphaerosyllis San Mart\u00edn, 1984 in the Mediterranean is given and an identification key to the Mediterranean species is provided.The syllid fauna of three locations in Crete and Israel (eastern Mediterranean Sea) was studied, yielding 82 syllid species, many of which were found for the first time in the respective areas: Seventeen species were recorded for the first time on the Israeli coasts and 20 in Greek waters. Syllidae are a highly diverse family of polychaetes with currently around 900 valid species belonging to over 80 genera (pers. obs.) and have recently received considerable taxonomic and phylogenetic research effort, including a high number of new taxon descriptions (e.g. The ons e.g. . Syllidsons e.g. .http://www.nagisa.coml.org), a field project of the Census of Marine Life ; b) soft-sediment samples from the Israeli coast have been obtained in the framework of a project focusing on the soft bottom benthos of Haifa Bay. In all samples, Syllidae were highly abundant and yielded many species recorded for the first time in the respective area, as well as a species new to science 32\u00d735cm, volume 20 l, penetration 20 cm. The sediment was preserved in buffered formalin 10% for 3\u20137 days, then sieved through a 250 \u00b5m mesh sieve and subsequently stored in 70% ethanol. In this study, only a subset of the collected material is presented.Specimens from Israel were collected on 31 May 2009 and 11 Oct 2009 in Haifa Bay, from soft sediments of mixed grain sizes in shallow waters . SedimenSpecimens from Crete were collected in September 2007 and June 2008 from two sites in northern Crete characterized by a continuous hard bottom habitat with dense algal coverage and a moderate wave exposure . At eachSyllidae .This manuscript was prepared in a Virtual Research Environment (Scratchpads) allowing for rapid and simultaneous publication of the results in print as well as electronically in a semantically enhanced form . This puhttp://ipt.pensoft.net/ipt/resource.do?r=easternmedsyllids). The data are furthermore available in Darwin Core Archive format, a simple and extensible schema for sharing biodiversity data which has been developed by the Global Biodiversity Information Facility to allow easy and rapid mobilisation of species occurrence data through the internet. Darwin Core Archives are essentially a set of text files stored together with an XML descriptor file which describes the structure of the data files. Data are described through the Darwin Core schema, allowing for their usage within the semantic web. This new type of data publishing allows data to be indexed and discoverable through global biodiversity infrastructures such as GBIF or other data repositories, allows data to be integrated and compared with other datasets and ensures proper accreditation of the data provider (http://www.datadryad.org) and can be accessed at doi: 10.5061/dryad.4b7k408g.The underlying dataset of this study has been published under a Creative Commons license according to the Pensoft Data Publishing Policies and Guidelines for Biodiversity Data and are provider . AdditioSyllinae and Exogoninae, whereas the samples from Israel did not contain any specimens of Anoplosyllinae or Autolytinae, and 73% of the examined species belong to the small-sized Exogoninae , CELA-5d-08 (2 ind.) [coll. 12.6.2008]; CELB-10c-07 (1 ind.) [coll. 27.9.2007].Gal\u00e1pagos Islands (Pacific Ocean).Gal\u00e1pagos Islands, north-east Pacific, Atlantic, Mediterranean Sea: WB, AS. New record for the Greek coast.Zostera beds, in vermetid reefs.Shallow subtidal depths, in sandy and muddy sediments, among photophilic algae and Imajima, 1966http://species-id.net/wiki/Syllides_japonicusSyllides japonicus Imajima, 1966: 112, figs 36a\u2013h; Syllidesjaponicus: cf. Elounda, Crete, Greece: CELA-15a-07 (1 ind.) [coll. 26.9.2007]; CELA-5d-08 (1 ind.), CELB-15d-08 (1 ind.) [coll. 12.6.2008].Japan (Pacific Ocean).Japan, Australia , MediterPosidonia oceanica rhizomes.Shallow subtidal depths, in sandy and muddy sediments, on rocks with algal cover, among GenusMilne Edwards, 1845Myrianida fasciata Milne Edwards, 1845http://species-id.net/wiki/Myrianida_inermisAutolytus inermis Saint-Joseph, 1887: 237, pl. 12, fig. 117; Autolytus (Autolytides) inermis : Myrianida inermis : Elounda, Crete, Greece: CELB-1e-07 (1 ind.) [coll. 29.9.2007].Dinard, France (north-east Atlantic Ocean).North-east Atlantic, north-west Atlantic , north-eUntil 100m depth, on rocks among algae and hydrozooans, in coralligenous substrates .http://species-id.net/wiki/Myrianida_quindecimdentataAutolytus quindecimdentatus Langerhans, 1884: 249, pl. 15, figs 3a\u2013b; Autolytus lugens Saint-Joseph, 1887: 234, pl. 12, fig. 116; Fauvel, 1923: 318, fig. 122g; Odontosyllis longicornis Hartmann-Schr\u00f6der, 1960: 98, figs 101\u2013104.Myrianida quindecimdentata : Alykes, Crete, Greece: CALA-10c-08 (4 ind.) [coll. 17.6.2008]; CALA-1b-08 (1 ind.), CALB-1c-08 (1 ind.), CALB-1d-08 (1 ind.) [coll. 18.6.2008]. Elounda, Crete, Greece: CELB-5e-07 (1 ind.) [coll. 27.9.2007]; CELB-1a-07 (2 ind.), CELA-1d-07 (2 ind.), CELB-1e-07 (5 ind.) [coll. 29.9.2007]; CELA-10b-08 (1 ind.) [coll. 11.6.2008]; CELB-1a-08 (1 ind.), CELB-1b-08 (1 ind.), CELA-5d-08 (1 ind.) [coll. 12.6.2008].Madeira (Atlantic Ocean).PageBreakEast and west Atlantic , north-east Pacific, Red Sea . MediterPosidonia oceanica rhizomes, endobiontic in sponges http://species-id.net/wiki/Perkinsyllis_augeneriPionosyllis augeneri Hartmann-Schr\u00f6der, 1979: 98, figs 119\u2013125; 1980a: 52; 1981: 32, fig. 52 Non : 35; SanPerkinsyllis augeneri : Haifa Bay, Israel: ALA-IL-7 (7 ind.) [coll. 11.10.2009].Boone, west Australia.Australia, New Zealand. Mediterranean Sea: LB. New record for the Mediterranean Sea.Intertidal and shallow subtidal depths, in coarse coralline sand, in muddy sand and seagrass beds .Prostomium pentagonal with 4 eyes in trapezoidal arrangement, posterior pair closer together than anterior one. Palps longer than prostomium, basally fused. Antennae cylindrical, smooth, longer than prostomium and palps. Tentacular cirri similar to antennae but slightly longer. Dorsal cirri of some anterior segments slender, longer than body width, some shorter, in midbody alternating short and long cirri, posteriorly all shorter than body width. Parapodia with 9\u201310 falcigers per fascicle anteriorly, 6\u20137 posteriorly. Shafts smooth or slightly serrated. Blades with marked dorso-ventral gradation , coarsely serrated, with small subdistal tooth. After proventriculum, dorsal blades unidentate, elongated, spiniger-like, twice as long as anteriorly, ventral blades stout, with strong serration, especially basally. Dorsal simple chaeta first appearing on midbody, blunt, subdistally serrated. Ventral simple chaetae posteriorly, bidentate, equally sized teeth forming a right angle, some long spines subdistally. Paired aciculae anteriorly, single ones posteriorly, with rounded, slightly enlarged tip. Pharynx through 4 chaetigers, pharyngeal tooth located anteriorly. Proventricle through 5 chaetigers with ca. 20\u201322 muscle cell rows.Perkinsyllis augeneri has not yet been fully resolved. In recent molecular phylogenies the species groups either within Exogoninae or as a sister group, and forms a sister clade of Eusyllinae in all analyses , recorded for the first time in 2003 in Cyprus .GenusFauvel, 1923Pionosyllis gestans Pierantoni, 1903http://species-id.net/wiki/Parapionosyllis_elegansPionosyllis elegans Pierantoni, 1903: 236, pl. X, fig. 2: pl. XI, fig. 27.Parapionosyllis elegans : Haifa Bay, Israel: ALA-IL-7 (11 ind.), ALA-IL-10 (45 ind.) [coll. 11.10.2009].Gulf of Naples (western Mediterranean Sea).North-east Atlantic (Iberian Peninsula). Mediterranean Sea: WB, CB, AD, AS, LB. New record for the Israeli coast.PageBreakUntil 30 m depth , in mediGenusSan Mart\u00edn, 1984Sphaerosyllis xarifae Hartmann-Schr\u00f6der, 1960San Mart\u00edn, 1984http://species-id.net/wiki/Prosphaerosyllis_adelaeSphaerosyllis (Prosphaerosyllis) adelae San Mart\u00edn, 1984a: 376, figs 1\u20134.Prosphaerosyllis adelae : San Mart\u00edn: 2003: 220, fig. 116.Haifa Bay, Israel: ALA-IL-7 (11 ind.) [coll. 31.5.2009]; ALA-IL-7 (6 ind.), ALA-IL-10 (2 ind.) [coll. 11.10.2009].Balearic Islands (western Mediterranean Sea).Mediterranean Sea: WB, LB. New record for the eastern Mediterranean Sea.Posidonia oceanica rhizomes.Until 13 m depth, in coarse sands, among http://species-id.net/wiki/Prosphaerosyllis_campoyiSphaerosyllis campoyi San Mart\u00edn Acero, Contonente and Gomez, 1982: 175, fig. 2; Sphaerosyllis (Prosphaerosyllis) campoyi : Prosphaerosyllis campoyi : San Mart\u00edn, 2003: 222, figs 117\u2013118.Elounda, Crete, Greece: CELA-10a-07 (1 ind.) [coll. 27.9.2009]; CELA-10b-08 (1 ind.) [coll. 11.6.2008].Andalusia, Spain (western Mediterranean Sea).North-east Atlantic , Mediterranean Sea: WB, AS, LB. New record for the Greek coast.Until 70 m depth , on rockThe specimens agree well with the description of Olivier, Grant, San Mart\u00edn, Archambault & McKindsey, 2011http://species-id.net/wiki/Prosphaerosyllis_chauseyensisProsphaerosyllis chauseyensis Olivier et al., 2011, figs 1\u20133a, b.Haifa Bay, Israel: ALA-IL-8 (12 ind.) [coll. 31.5.2009]; ALA-IL-1 (23 ind.), ALA-IL-2 (4 ind.), ALA-IL-5 (1 ind.), ALA-IL-7 (73 ind.), ALA-IL-8 (24 ind.), ALA-IL-9 (68 ind.), ALA-IL-10 (99 ind.) [coll. 11.10.2009].Sphaerosyllis brevicirra Hartmann-Schr\u00f6der, 1960 (Typ), 29.3.56, coll. Remane/Schulz]); Prosphaerosyllis chauseyensis , C1AM et C3AV]).Chausey Islands, Normandy (north-east Atlantic).North-east Atlantic (Normandy), Mediterranean Sea: LB. New record for the Mediterranean Sea.Until 13 m depth, in medium to very coarse sand.Three specimens collected at Station ALA-IL-8 on 31 May 2009 with egg capsules attached near dorsal cirri on midbody chaetigers.The specimens from Israel agree well with the specimens from Normandy, however, the Mediterranean specimens differ from the Holotype in: a) Papillation pattern: each segment with one papilla between dorsal cirri and four papillae, situated dorso-laterally and ventro-laterally on each side of parapodium, most developed in posterior chaetigers, from mid-body additional papillae arranged in two very irregular lines along middle of dorsum, increasing in length towards posterior end (ca. 20 \u00b5m posteriorly). Ventrally 2 smaller papillae in middle of ventrum at posterior end of each segment. Specimens from Normandy have an irregular papillation pattern, but papillation is more distinct laterally, as in specimens from Israel; b) Length of anal cirri: about 125 \u00b5m, ca. 2.5\u20133 times length of posterior dorsal cirri the ana.Sphaerosyllis tetralix Eliason, 1920, from the Gulf of Elat and the Mediterranean Sea might in fact belong to Prosphaerosyllis chauseyensis. The description and illustrations agree with many characteristics of Prosphaerosyllis chauseyensis, including the characteristic papilla on the dorsal cirri. However, Ben-Eliahu reports the species to have palps widely separated anteriorly (fused in Prosphaerosyllis chauseyensis), doPageBreakrsum with four longitudinal rows of papillae (irregular rows in Prosphaerosyllis chauseyensis) and the proventriculum stretching through 4 chaetigers (5 in Prosphaerosyllis chauseyensis). The material of the species described by Ben-Eliahu could not be examined during this study, therefore it can only tentatively be assigned to Prosphaerosyllis chauseyensis.Individuals identified by http://species-id.net/wiki/Prosphaerosyllis_longipapillataSphaerosyllis longipapillata Hartmann-Schr\u00f6der, 1979: 106, figs 148\u2013150; 1982: 71; 1984: 23; 1985: 71; 1986: 43; 1991: 40;Prosphaerosyllis longipapillata : Haifa Bay, Israel: ALA-IL-7 (2 ind.) [coll. 11.10.2009].ComparativeProsphaerosyllis longipapillata .Broome, north-west Australia.Australia, Mediterranean Sea: LB. New record for the Israeli coast.Sargassum vulgare description by having alternating rows of long and short papillae on the dorsum from California. To determine the identity of the Mediterranean material and whether Prosphaerosyllis bilineata and Prosphaerosyllis longipapillata are different species or not, careful examination of all type material is needed.The specimens from Israel agree well with the material and description of \u00c7inar et al., 2003). However, both the material from Cyprus and Israel, as well as the description and illustrations of e dorsum , fig. 5.\u00c7inar, Dagli & A\u00e7ik, 2011http://species-id.net/wiki/Prosphaerosyllis_marmaraeProsphaerosyllis marmaraeHaifa Bay, Israel: ALA-IL-2 (3 ind.), ALA-IL-8 (12 ind.) [coll. 31.5.2009]; ALA-IL-7 (4 ind.) [coll. 11.10.2009].Prosphaerosyllis marmarae . Prosphaerosyllis laubieri .PageBreakErdek, Marmara Sea (eastern Mediterranean).Mediterranean Sea: LB, Marmara Sea. New record for the Israeli coast.Until 17 m depth, in muddy sand , in coarProsphaerosyllis laubieriProsphaerosyllis marmarae. Both species have eyespots, strongly papillated palps, short, retractile antennae and dorsal cirri, pharynx and proventriculum each through 4 segments and short (8\u201310 \u00b5m) blades of falcigers. These two species differ however in the following characteristics: a) Prosphaerosyllis laubieri has small, scattered papillae all over the dorsum, in Prosphaerosyllis marmarae they are restricted to the lateral margins, near the dorsal cirri; b) cirrostyles of antennae and dorsal cirri of Prosphaerosyllis marmarae are much shorter than those of Prosphaerosyllis laubieri and appear as small, retracted caps; c) dorsal cirri of Prosphaerosyllis laubieri possess a small papilla at distal end of cirrophore . Prosphaerosyllis riseri Perkins, 1981 from Florida shares with Prosphaerosyllis marmarae the shape of the dorsal cirri and antennae (short and strongly retracted), however, its palps are less densely papillated. Prosphaerosyllis sp. A , but might in fact belong to Prosphaerosyllis marmarae. The morphological characteristics of her specimens agree very well wth those of Prosphaerosyllis marmarae , retractile cirri, falcigerous blades short (7.8 \u00b5m), proventriculum longer than proboscis (through 4 segments), no discernible dorsal papillation). Differences can be found in the cutting edge of the falcigerous blades which are smooth in the Red Sea specimens, whereas those of Prosphaerosyllis marmarae are serrated. However, due to the size of the blades (8 \u00b5m) this is a feature difficult to observe under an optical microscope and might have been overlooked. The material of the species described by Ben-Eliahu was not examined during this study, therefore it can only tentatively proposed to be assigned to Prosphaerosyllis marmarae.Specimens from the Red Sea described by http://species-id.net/wiki/Prosphaerosyllis_xarifaeSphaerosyllis xarifae Hartmann-Schr\u00f6der, 1960: 103, figs 121\u2013124; 1979: 103, figs 139\u2013140; 1980b: 56; 1981: 37; 1984: 25; PageBreakSphaerosyllis sp.: Sphaerosyllis cf. xarifae :Sphaerosyllis (Prosphaerosyllis) xarifae :Prosphaerosyllis xarifae : Haifa Bay, Israel: ALA-IL-10 (5 ind.) [coll. 11.10.2009]. Elounda, Crete, Greece: CELA-10b-08 (1 ind.) [coll. 11.6.2008]; CELA-5c-08 (1 ind.) [coll. 12.6.2008].Sarso, Red Sea.Circumtropical, Mediterranean Sea: WB, CB, AS, LB. New record for both the Israeli and Greek coasts.Until 40 m depth, euryoceous, among photophilic algae, in sand, mud, seagrasses, calcareous substrates .Specimens from Israel agree well with the description of GenusMcIntosh, 1885Salvatoria kerguelensis McIntosh, 1885http://species-id.net/wiki/Salvatoria_alvaradoiPseudobrania alvaradoiSalvatoria alvaradoi : Alykes, Crete, Greece: CALB-10b-08 (5 ind.), CALB-10d-08 (2 ind.) [coll. 17.6.2008]; CALB-5a-08 (2 ind.) [coll 18.6.2008]. Elounda, Crete, Greece: CELA-15a-07 (3 ind.), CELB-20e-07 (1 ind.) [coll. 26.9.2007], CELA-10a-07 (1 ind.) [coll. 27.9.2007]; CELB-1a-07 (1 ind.) [coll. 29.9.2007]; CELB-10a-08 (1 ind.), CELA-10b-08 (4 ind.), CELB-10b-08 (3 ind.), CELB-10c-08 (1 ind.), CELA-20a-08 (1 ind.), CELA-20d-08 (3 ind.) [coll. 11.6.2008]; CELA-5a-08 (8 ind.), CELA-5c-08 (18 ind.), CELA-5d-08 (1 ind.), CELB-15a-08 (1 ind.), CELB-15c-08 (9 ind.) [coll. 12.6.2008].Balearic Islands (western Mediterranean Sea).Mediterranean Sea: WB, CB, AS, Sea of Marmara . New recPosidonia oceanica rhizomes, in sediments with much organic material.PageBreakUntil 20 m depth, among algae with much sediment, among Sard\u00e1, 1984http://species-id.net/wiki/Salvatoria_euritmicaPseudobrania euritmica Sard\u00e1, 1984: 10, fig. 1.Grubeosyllis euritmica : Salvatoria euritmica : Pionosyllis yambaensis Hartmann-Schr\u00f6der, 1990: 52, figs 18\u201322.Alykes, Crete, Greece: CALB-20b-08 (1 ind.) [coll. 17.6.2008]; CALB-1d-08 (4 ind.) [coll. 18.6.2008]. Elounda, Crete, Greece: CELA-15c-07 (2 ind.) [coll. 27.9.2007]; CELB-1b-07 (4 ind.), CELA-1d-07 (1 ind.) [coll. 29.9.2007]; CELA-10b-08 (1 ind.), CELA-20c-08 (1 ind.) [coll. 11.6.2008]; CELB-15d-08 (1 ind.) [coll. 12.6.2008].Strait of Gibraltar (western Mediterranean Sea).Caribbean Sea, Australia, north-east Atlantic , Mediterranean Sea: WB, AS, LB. New record for the Greek coast.Until 20 m depth, on hard substrates between algae, in seagrass beds, on coralligenous substrates.Pionosyllis yambaensis was synonymized with Salvatoria euritmica by http://species-id.net/wiki/Salvatoria_neapolitanaPionosyllis neapolitana Goodrich, 1930: 651, figs 1\u201312.Pseudobrania neapolitanaGrubeosyllis neapolitana : Salvatoria neapolitana : Pionosyllis subterranea Hartmann-Schr\u00f6der, 1956: 89 figs 6\u20139.Brania subterranea : Grubeosyllis subterranea : Elounda, Crete, Greece: CELA-15a-07 (2 ind.), CELB-20c-07 (2 ind.) [coll. 26.9.2007]; CELB-15a-08: (5 ind.), CELB-15c-08 (1 ind.) [coll. 11.6.2008]; CELB-1d-08 (1 ind.) [coll. 12.6.2008].Bay of Naples, Italy (western Mediterranean Sea).Circumtropical, Mediterranean Sea: WB, AS . New recUntil 20 m depth, in coarse sand, among photophilic algae.Pionosyllis subterranea was synonymized with Pionosyllis neapolitana and transferred to Grubeosyllis by Grubeosyllis with Salvatoria, which has priority over the former.http://species-id.net/wiki/Salvatoria_vieiteziPseudobrania vieitezi San Mart\u00edn, 1984b: 160, figs 31\u201332.Grubeosyllis vieitezi : San Martin 1991a: 718, fig. 2e\u2013f; Salvatoria vieitezi : Alykes, Crete, Greece: CALA-10d-08 (1 ind.), CALA-15c-08 (1 ind.), CALA-20c-08 , CALB-20c-08 (1 ind.), CALB-20b-08 (1 ind.) [coll. 17.6.2008]; CALA-1b-08 (2 ind.), CALB-1b-08 (1 ind.), CALB-5a-08 (1 ind.) [coll. 18.6.2008]; CALB-20e-07 (1 ind.) [coll. 18.9.2007]; CALA-5c-07 (1 ind.) [coll. 19.9.2007]. Elounda, Crete, Greece: CELA-20d-07 (3 ind.) [coll. 26.9.2007]; CELA-10b-07 (1 ind.) [coll. 27.9.2007]; CELA-20c-08 (1 ind.), CELA-20d-08 (7 ind.) [coll. 11.6.2008]; CELA-5d-08 (1 ind.), CELB-15a-08 (1 ind.), CELB-1b-08 (5 ind.) [coll. 12.6.2008].Balearic Islands (western Mediterranean Sea).North-east Atlantic , Caribbean, Mediterranean Sea: WB, CB, AS. New record for the Greek coast.Posidonia oceanica rhizomes.Until 30m depth, on rocky substrates among photophilic algae, as endobiont of sponges, among http://species-id.net/wiki/Salvatoria_yraidaePseudobrania yraidae San Mart\u00edn, 1984b: 156, fig. 30.Grubeosyllis yraidae : Salvatoria yraidae : Alykes, Crete, Greece: CALB-10b-08 (1 ind.), CALB-15a-08 (1 ind.), CALB-20b-08 (3 ind.), CALB-20d-08 (1 ind.) [coll. 17.6.2008]. Elounda, Crete, Greece: CELA-15b-07 (1 ind.), CELA-15e-07 (2 ind.) [coll. 26.9.2007]; CELA-5c-07 (4 ind.) [coll. 27.9.2007]; CELA-10b-08 (3 ind.), CELB-10b-08 (8 ind.), CELB-10c-08 (1 ind.), CELA-20a-08 (1 ind.), CELA-20b-08 (1 ind.) [coll. 11.6.2008]; CELB-15a-08 (6 ind.), CELB-15c-08 (4 ind.), CELA-15d-08 (5 ind.), CELB-15d-08 (5 ind.) [coll. 12.6.2008].PageBreakBalearic Islands (western Mediterranean Sea).Mediterranean Sea: WB, CB, AD, AS. New record for the Greek coast.Until 20 m depth, in sandy substrates, on rocks among algae.GenusClapar\u00e8de, 1863Sphaerosyllis hystrix Clapar\u00e8de, 1863Southern, 1914http://species-id.net/wiki/Sphaerosyllis_bulbosaSphaerosyllis bulbosa Southern, 1914: 20, plates I\u2013II, figs 2a\u2013g; Fauvel, 1923: 304, figs. 116h\u2013r; Sphaerosyllis (Sphaerosyllis) bulbosa : Haifa Bay, Israel: ALA-IL-7 (4 ind.), ALA-IL-10 (51 ind.) [coll. 11.10.2009].Ireland (Atlantic Ocean).North-east Atlantic, Arctic Sea , New CalUntil 70 m depth, in sandy or muddy sediments, on calcareous substrates.The examined material differs from the description of Perkins, 1981http://species-id.net/wiki/Sphaerosyllis_glandulataSphaerosyllis glandulata Perkins, 1981: 1123, figs 18\u201319; Sphaerosyllisglandulata: cf. Haifa Bay, Israel: ALA-IL-7 (1 ind.) [coll. 31.5.2009]; ALA-IL-7 (47 ind.), ALA-IL-10 (19 ind.) [coll. 11.10.2009]. Elounda, Crete, Greece: CELA-15d-08 (1 ind.) [coll. 12.6.2008].Florida, Hutchinson Island.West Atlantic , China MediterrUntil 120 m depth, in calcareous habitats and fine to coarse sands, among photophilic algae.Sphaerosyllis glandulata.The specimens from Israel differ from San Mart\u00edn\u2019s (2003) description in having papillated palps and a longer proventriculum . Other characteristics, especially chaetal ones, agree well with former descriptions of Somaschini & San Mart\u00edn, 1994http://species-id.net/wiki/Sphaerosyllis_gravinaeSphaerosyllis gravinae Somaschini and San Mart\u00edn, 1994: 358, figs 1\u20132; Haifa Bay, Israel: ALA-IL-8 (4 ind.) [coll. 31.5.2009].Zannone Island, Italy (western Mediterranean Sea).Mediterranean Sea: WB, AD, LB. New record for the eastern Mediterranean Sea.Shallow subtidal depths, in medium to coarse sands, among algae.Perkins, 1981http://species-id.net/wiki/Sphaerosyllis_tayloriSphaerosyllis taylori Perkins, 1981: 1140, fig. 26; Haifa Bay, Israel: ALA-IL-1 (1 ind.); ALA-IL-2 (33 ind.) [coll. 31.5.2009]; ALA-IL-7 (103 ind.), ALA-IL-10 (14 ind.) [coll. 11.10.2009].Florida, Hutchinson Island.North-east and north-west Atlantic , Pacific Ocean (Li\u00f1ero-Arana and D\u00edaz-D\u00edaz 2011), Arctic Sea , MediterPosidonia oceanica rhizomes.PageBreakShallow subtidal depths, in muddy to coarse sands with organic material, on rocks among photophilic or calcareous algae, among San Mart\u00edn 1984http://species-id.net/wiki/Sphaerosyllis_thomasiSphaerosyllis thomasi San Mart\u00edn, 1984b: 250, fig. 59; 2003: 199, figs 103\u2013104; Haifa Bay, Israel: ALA-IL-7 (2 ind.) [coll. 11.10.2009].Balearic Islands (western Mediterranean Sea).Mediterranean Sea: WB, CB, AD, AS, LB. New record for the Israeli coast.Posidonia oceanica rhizomes.Shallow subtidal depths, in muddy to coarse sands, among The examined specimens agree well with the description of GenusLangerhans, 1879Opisthosyllis brunnea Langerhans, 1879Langerhans, 1879http://species-id.net/wiki/Opisthosyllis_brunneaOpisthosyllis brunnea Langerhans, 1879: 541, fig. 7; Elounda, Crete, Greece: CELA-1d-07 (1 ind.) [coll. 29.9.2007], CELA-5d-08 (1 ind.) [coll. 12.6.2008].Madeira (Atlantic Ocean).Circumtropical. Mediterranean Sea: WB, CB, AS, LB. New record for the Greek coast.Intertidal to shallow subtidal, on hard substrates , endobiont of sponges.GenusLamarck, 1818Syllis monilaris Lamarck, 1818Moore, 1908http://species-id.net/wiki/Syllis_alternataSyllis alternata Moore, 1908: 323; 1909: 321; Typosyllis alternata : Alykes, Crete, Greece: CALB-15c-07 (1 ind.) [coll. 18.9.2007]; CALB-1a-07 (1 ind.) [coll. 19.9.2007]; CALA-10d-08 (2 ind.), CALA-15d-08 (1 ind.), CALB-20b-08 (1 ind.), CALA-20b-08 (2 ind.), CALA-20c-08 (5 ind.), CALB-20d-08 (6 ind.) [coll. 17.6.2008]. Elounda, Crete, Greece: CELB-20c-07 (1 ind.) [coll. 26.9.2007]; CELB-1a-07 (4 ind.) [coll. 29.9.2007]; CELA-10b-08 (1 ind.), CELB-10b-08 (1 ind.), CELA-10c-08 (1 ind.), CELB-10c-08 (1 ind.), CELA-10d-08 (2 ind.), [coll. 11.6.2008]; CELB-1a-08 (1 ind.), CELA-5b-08 (1 ind.), CELA-5d-08 (2 ind.), CELB-15c-08 (5 ind.) [coll. 12.6.2008].Alaska (Pacific Ocean).East Pacific (Alaska to Panama), west Atlantic (North Carolina to Cuba) , Japan , IndonesPosidonia oceanica rhizomes, calcareous algae, corals and photophilic algae compacta Gravier, 1900: 165, pl. 9, fig. 11, text-figs 35\u201338.Syllis compacta : Syllis golfonovensisSyllis golfonovensis Hartmann-Schr\u00f6der, 1962. : PageBreak CELA-10a-07 (1 ind.), CELA-10d-07 (1 ind.) [coll. 27.9.2007]; CELA-5c-07 (1 ind.), CELB-5d-07 (1 ind.) [coll. 29.9.2007]; CELA-5b-08 (1 ind.), CELA-5d-08 (2 ind.), CELB-15d-08 (3 ind.) [coll. 12.6.2008].Alykes, Crete, Greece: CALB-1e-07 (1 ind.), CALA-5e-07 (1 ind.) [coll. 19.9.2007]; CALA-15c-08 (1 ind.), CALA-20b-08 (1 ind.), CALB-20b-08 (1 ind.), CALA-20c-08 (1 ind.) [coll. 17.6.2008]. Elounda, Crete, Greece: CELA-15b-07 (1 ind.), CELA-15e-07 (3 ind.), CELB-20a-07 (2 ind.) [coll. 26.9.2007];Red Sea.Red Sea. Mediterranean Sea: WB, CB, AD, AS. New record for the Greek coast.Posidonia oceanica rhizomes.Shallow subtidal depths, on biogenic calcareous substrates, among photophilic algae and Syllis variegata Grube, 1860. Recent works [coll. 17.6.2008]. Elounda, Crete, Greece: CELB-10a-08 (1 ind.) [coll. 11.6.2008].Canary Islands (Atlantic Ocean).North-east Atlantic (Canary Islands), Mediterranean Sea: WB, CB, AD, AS, LB. New record for the Aegean Sea.Until 115 m depth, on coralligenous substrates, among photophilic algae, endobiont of sponges.http://species-id.net/wiki/Syllis_gerundensisTyposyllis gerundensis Al\u00f3s and Campoy, 1981: 21, figs 1\u20133; Syllis gerundensis : Alykes, Crete, Greece: CALA-20b-08 (1 ind.), CALB-20b-08 (1 ind.) [coll. 17.6.2008]; CALA-5d-08 (2 ind.) [[coll. 18.6.2008]. Elounda, Crete, Greece: CELB-1e-07 (1 ind.) [coll. 29.9.2007]; CELB-1d-08 (1 ind.), CELA-5d-08 (3 ind.) [coll. 12.6.2008].Columbretes Islands, Spain (western Mediterranean Sea).Mediterranean Sea: WB, CB, AD, AS, LB.New record for the Aegean Sea.Posidonia oceanica rhizomes and photophilic algae, endobiont of sponges.Shallow subtidal depths, on calcareous grounds, sandy bottoms, among San Mart\u00edn & L\u00f3pez, 2000http://species-id.net/wiki/Syllis_jorgeiSyllis jorgei San Mart\u00edn and L\u00f3pez, 2000: 430, figs 4\u20136; Typosyllis lutea : Syllis luteaSyllis lutea Hartmann-Schr\u00f6der, 1960). : Haifa Bay, Israel: ALA-IL-7 (3 ind.) [coll. 11.10.2009]. Alykes, Crete, Greece: CALA-20c-07 (1 ind.) [coll. 18.9.2007], CALB-1a-08 (1 ind.) [coll. 18.6.2008]. Elounda, Crete, Greece: CELB-1a-08 (1 ind.), CELA-1c-08 (1 ind.), CELB-5d-08 (1 ind.) [coll. 12.6.2008].Columbretes Islands, Spain (western Mediterranean Sea).East Atlantic (Canary Islands), Mediterranean Sea: WB, CB, AD, AS, LB. New record for the Israeli coast.Posidonia oceanica rhizomes and photophilic algae.Until 145 m depth , on bioghttp://species-id.net/wiki/Syllis_pulvinataTyposyllis pulvinata Langerhans, 1881: 97, 104; Syllis pulvinata : Syllis (Typosyllis) truncata mediterranea Ben-Eliahu, 1977a: 10, fig. 2.Syllis mediterranea : San Mart\u00edn, 1984b; 209, fig. 8.Elounda, Crete, Greece: CELA-1b-08 (1 ind.), CELA-5c-08 (2 ind.), CELB-15d-08 (1 ind.) [coll. 12.6.2008].Canary Islands (Atlantic Ocean).North-east Atlantic (Cantabrian Sea to Canary Islands), Red Sea, Mediterranean: WB, CB, AD, AS, LB. New record for the Aegean Sea.PageBreakShallow subtidal depths, on calcareous substrates (vermetid reefs), among photophilic algae, endobiont of sponges.http://species-id.net/wiki/Syllis_tyrrhenaTyposyllis tyrrhena Licher and Kuper, 1998: 228, figs 1\u20134; Syllis tyrrhena : Elounda, Crete, Greece: CELB-10b-08 (1 ind.) [coll. 11.6.2008].Island of Elba, Italy (western Mediterranean Sea).Brazil , MediterUntil 13 m depth, in sandy substrates of mixed grain sizes , on rockSan Mart\u00edn, 1984http://species-id.net/wiki/Syllis_westheideiSyllis westheidei San Mart\u00edn, 1984b: 403, figs 108\u2013109; 2003: 436, figs 240\u2013241; Typosyllis westheidei : Typosyllis variegataSyllis variegata Grube, 1860). : Alykes, Crete, Greece: CALB-15d-08 (1 ind.) [coll. 17.6.2008].Balearic Islands (western Mediterranean Sea).Pacific Ocean , Red Sea, Mediterranean: WB, CB, AD, AS. New record for the Greek coast.Posidonia oceanica rhizomes and vermetid reefs.Shallow subtidal depths, on hard substrates, among photophilic algae, in GenusClapar\u00e8de 1864Syllis zebra Grube, 1860Clapar\u00e8de, 1868http://species-id.net/wiki/Trypanosyllis_coeliacaTrypanosyllis coeliacaPseudosyllis brevipennis Grube, 1863: 44, pl. 4, fig. 5.Haifa Bay, Israel, eastern Mediterranean Sea, Station ALA-IL-7 (1 ind.) [coll. 11.10.2009]. Alykes, Crete, Greece: CALA-10b-08 (1 ind.), CALB-10c-08 (1 ind.) [coll. 17.6.2008]; CALA-5a-08 (1 ind.), CALB-1d-08 (2 ind.), CALB-5a-08 (1 ind.) [coll. 18.6.2008]. Elounda, Crete, Greece: CELA-15b-07 (1 ind.), CELA-15c-07 (1 ind.) [coll. 26.9.2007]; CELB-5c-07 (1 ind.), CELA-10a-07 (1 ind.), CELB-10c-07 (1 ind.) [coll. 27.9.2007]; CELB-1a-07 (2 ind.), CELB-1e-07 (1 ind.) [coll. 29.9.2007]; CELB-10b-08 (1 ind.), CELA-15a-08 (1 ind.) [coll. 17.6.2008]; CELB-1b-08 (1 ind.), CELA-5b-08 (1 ind.), CELA-5c-08 (1 ind.), CELB-5c-08 (1 ind.), CELA-5d-08 (2 ind.) [coll. 18.6.2008].Gulf of Naples (western Mediterranean Sea).Circumtropical. Mediterranean Sea: WB, CB, AD, AS, LB. New record for the Israeli coast.Posidonia oceanica rhizomes, in vermetid reefs, in coarse sand.From infralitoral depths to 760 m, on hard substrates, among algae, corals, hydrozoans, sponges and Trypanosyllis coeliaca have in the past been identified as Pseudosyllis brevipennis Grube, 1863, but according to Pseudosyllis brevipennis is regarded as a synonym of Trypanosyllis coeliaca.Specimens from Greece have a faint or no visible trepan. Individuals without trepan but otherwise identical to Exogoninae in the Mediterranean belongs to these doubtful records. Records of Sphaerosyllis brevicirra from the western MediterraneanPageBreak Sea by Prosphaerosyllis species description but in fact absent likewise do probably not belong to Prosphaerosyllis brevicirra: Ben-Eliahu\u2019s (1977a) redescription of the species based on material from the Gulf of Elat (Red Sea) differs in several aspects from Hartmann-Schr\u00f6der\u2019s (1960) descripPageBreaktion and from the type material. In particular, Ben-Eliahu does not mention or illustrate the papilla on the dorsal cirrus, her specimens have four eyes and one anterior pair of eyespots and the proventriculum occupies 4 chaetigers (3 in Prosphaerosyllis brevicirra). According to the description and illustrations, the species might in fact belong to Prosphaerosyllis marmarae (see remarks for this species above). The record of Sphaerosyllis brevicirra from the Spanish Atlantic coast . The species Prosphaerosyllis brandhorsti has been recorded in Italy by Prosphaerosyllis ranunculus . The presence of Prosphaerosyllis brandhorsti in the Mediterranean Sea has thus to be considered as doubtful. An identification key to the currently valid Mediterranean species of Prosphaerosyllis can be found below.The present study yielded a number of species reported for the first time in the respective areas, and a high number of the new additions belong to the subfamily ogoninae . This coall e.g. . The Exo species . These dt absent ), the ab species , are absic coast , though"} +{"text": "Thrombosis, mainly venous, is a rare and well-recognized extraintestinal manifestation of inflammatory bowel disease (IBD). We describe a 25-year-old Caucasian man affected by ulcerative colitis and sclerosing cholangitis with an episode of right middle cerebral arterial thrombosis resolved by intraarterial thrombolysis. We perform a brief review of the International Literature. Thrombosis, mainlyh venous, is a rare and well-recognized extraintestinal manifestation of inflammatory bowel disease (IBD). Arterial Thromboembolic (TE) complications, and in particular strokes, occur less frequently . They usA 25-year-old Caucasian man was observed in the emergency room for a sudden left-sided hemiparesis characterized by sensitive impairment, confusion and bladder incontinence. NIH stroke scale score (NIHSS) impairment was 8. A diagnosis of ulcerative colitis (UC) and sclerosing cholangitis (SC) had been made 8 years before. He also referred an episode of acute pancreatitis 7 years before as a complication of mesalazine therapy. He had no familial history of cerebral vascular disease (CVD). At clinical examination the patient was normotensive and without fever. Blood tests showed iron deficiency anemia , raised white cell counts (WBC 12.470/mmc-n.v. 4000\u201311000/mmc), erythrocytes sedimentation (ERS) 56 (n.v. < 10), reactive C protein 7.6\u2009mg/L, (n.v.\u2014until 5\u2009mg/dL), gamma Glutamil trans-peptidase (297\u2009U/L-n.v. 11\u201349), gamma globulin 2.55\u2009g/dL, (n.v. until 1.8\u2009g/dL) antinuclear antibodies 1\u2009:\u2009640 (v.n. negative). An emergency brain angio-computed tomography (A-CT) evidenced thrombosis of the M2 tract of the right middle cerebral artery, without any (apparent) other brain lesions . After aThe association of inflammatory bowel disease (IBD) and thrombosis was, for the first time, described in 1936 by Bargen and Baker . Patters"} +{"text": "The objective of this study was to evaluate the efficacy, tolerability, and safety of fosamprenavir/ritonavir (FPV/r) versus efavirenz (EFV), both in combination with abacavir/lamivudine (ABC/3TC), in a population that is often underrepresented in U.S. clinical trials.In this ongoing 96-week, open-label, prospective, randomized, multicenter study, we compared once-daily ABC/3TC 600 mg/300 mg with FPV 1400 mg/r 100 mg or EFV 600 mg in ARV-na\u00efve, HIV-1-infected subjects with entry viral load (VL) >5,000 c/mL, were HLA-B*5701 negative, and did not have major resistance mutations to study drugs. The primary endpoint was time to switch of third drug or time to development of any treatment-related Grade 3 or 4 adverse events (AEs). Results from the planned 48-week analysis are reported.3 in each group. Rate of treatment-related grade 2-4 AEs was lower in the FPV/r-arm vs. the EFV-arm primarily due to EFV-related rash and dizziness (8% each). Rates of treatment-related serious AEs and grade 3-4 lab abnormalities were similar between FPV/r vs. EFV. A total of 8 virologic failures occurred through W48. At failure, HIV PRO or RT treatment-emergent mutations were present in 4 of 5 EFV patients and 1 of 3 FPV/r patients selected an RT mutation. Median change from BL in total/HDL cholesterol ratio was unchanged in both groups but the FPV/r arm had larger changes in triglycerides (32 vs. 7 mg/dL) and in LDL cholesterol (22 vs. 11 mg/dL).SUPPORT enrolled 32% (32/101) women and 79% (80/101) non-Caucasians. Baseline and demographic characteristics were generally similar between groups. A total of 84 subjects (83%) completed study through W48. Eight patients met the primary endpoint: 3 (6%) and 5 (10%) on FPV/r and EFV, respectively. At W48, by ITT-Exposed missing-equals-failure analysis, 76% (39/51) and 82% (41/50) of subjects achieved VL <50 c/mL on FPV/r vs. EFV, respectively. Median change from baseline to W48 in CD4 cell count was 178 cells/mmThrough 48 weeks, in a diverse population, virologic/immunologic responses were not demonstrably different between FPV/r and EFV when given with ABC/3TC, but the EFV regimen had slightly more patients meeting the tolerability endpoint, treatment-related grade 2-4 AEs, virologic failures, and treatment-emergent mutations at failure."} +{"text": "KRAS wild-type and mutant metastatic colorectal cancer (MCRC) patients (pts) treated with bevacizumab (BEV)-containing chemotherapy is not significantly different. Since specific KRAS mutations confer different aggressive behaviors, the prognostic role of prevalent KRAS mutations was retrospectively evaluated in MCRC pts treated with first line FIr-B/FOx, associating BEV to triplet chemotherapy.Prognosis of KRAS codon 12, 13 and BRAF V600E mutations by SNaPshot and/or direct sequencing. MCRC pts <75-years-old were consecutively treated with FIr-B/FOx: weekly 12 hour-timed-flat-infusion/5-fluorouracil , irinotecan plus BEV ; and oxaliplatin . Pts were classified as liver-limited (L-L) and other/multiple metastatic (O/MM). Progression-free survival (PFS) and overall survival (OS) were compared using the log-rank test.Tumor samples were screened for KRAS mutant pts: c.35 G > A, 15 (25.4%); c.35 G > T, 7 (11.8%); c.38 G > A, 3 (5%); other, 3 (5%). KRAS wild-type, 31 pts (52.7%). The objective response rate (ORR), PFS and OS were, respectively: c.35 G > A mutant, 71%, 9 months, 14 months; other than c.35 G > A mutants, 61%, 12 months, 39 months. OS was significantly worse in c.35 G > A pts compared to KRAS wild-type (P = 0.002), KRAS/BRAF wild-type (P = 0.03), other MCRC patients (P = 0.002), other than c.35 G > A (P = 0.05), other codon 12 (P = 0.03) mutant pts. OS was not significantly different compared to c.35 G > T KRAS mutant (P = 0.142).Fifty-nine pts were evaluated at a median follow-up of 21.5 months. KRAS c.35 G > A mutant status may be significantly associated with a worse prognosis of MCRC pts treated with first line FIr-B/FOx intensive regimen compared to KRAS/BRAF wild type and other than c.35 G > A mutant pts. KRAS genotype, wild-type or mutant, addresses the medical treatment of metastatic colorectal cancer (MCRC) patients (pts), consisting of triplet regimens combining chemotherapeutic drugs, or doublets plus targeted agents [KRAS mutant patients [KRAS wild-type and mutant pts [d agents . The addpatients ,3; anti-tant pts ,5. In litant pts -13.KRAS genotype can be assessed by evaluation of clinical outcome , overall survival (OS)) in wild-type and mutant pts, depending on differential tumor biological aggressiveness and predictive effectiveness of treatment strategies. The median OS of KRAS wild-type and mutant MCRC pts treated with irinotecan, 5-fluorouracil and leucovorin (IFL) plus bevacizumab (BEV) was 27.7 and 19.9 months, respectively [KRAS and BRAF wild-type pts were compared with pts harboring mutations in one gene. In KRAS wild-type pts and in BRAF wild-type pts compared to mutant, HR was 0.64 and 0.38, respectively, but did not reach statistical significance [et al. [KRAS wild-type and mutant genotypes [KRAS wild-type and mutant pts , but not significantly [KRAS wild-type pts with L-L disease may achieve a significantly greater benefit from integration with liver metastasectomies, with respect to KRAS mutant patients [The prognostic relevance of the ectively ,5. The henotypes . Median ficantly . L-L ptspatients ,13.KRAS wild-type genotype predicts favorable clinical outcomes when anti-EGFR or anti-VEGF molecules are added to doublet chemotherapy [KRAS mutant genotype significantly predicts prolonged PFS up to 9.3 months, while there was no increase in OS and activity [The otherapy ,5. The Kactivity ,5, in ptKRAS mutations occur in 35% to 45% of colorectal cancer (CRC), mostly in codon 12 (80%), c.35 G > A (G12D) and c.35 G > T (G12V) transversions, representing 32.5% [in vitro model proposed by Guerrero et al. [ng 32.5% ,15 and 2ng 32.5% ,16, respng 32.5% . These mng 32.5% . In the o et al. , codon 1o et al. . Codon 1o et al. .KRAS mutant tumors seems to confer worse clinical behavior. A multivariate analysis suggested that the presence of KRAS mutation significantly increased the risk of recurrence and death; the codon 12 c.35 G > T (G12V) mutation retained an independent increased risk of recurrence and death [KRAS mutations was not confirmed in other studies [The biological aggressiveness of codon 12 nd death , and signd death . The poo studies ,23.KRAS mutation in MCRC pts enrolled in a previously reported phase II study [We report a retrospective exploratory analysis evaluating the prognostic value of the prevalent codon 12 c.35 G > A (G12D) II study and in aMCRC pts were enrolled in a previously reported phase II study and in tFIr-B/FOx association consisted of 5-fluorouracil associated with alternating irinotecan/BEV or oxaliplatin, according to a previously reported weekly schedule .KRAS and BRAF analyses were performed on paraffin-embedded tissue blocks from the primary tumor and/or metastatic site. Genotype status was analyzed for KRAS codon 12 and 13 mutations and BRAF c.1799 T > A (V600E) mutation by SNaPshot\u00ae multiplex [KRAS mutations and KRAS/BRAF mutations in 36 and 32 samples, respectively; direct sequencing of the KRAS gene was performed in 23 samples. After treatment with xylene thiocyanate and selection of tumor cell clusters, DNA was isolated using the RecoverAll\u2122 Total Nucleic Acid Isolation Kit for FFPE Tissues according to the manufacturer's instructions.ultiplex , for KRA\u00ae multiplex assay was performed as previously reported [KRAS exon 2 and BRAF exon 15 were simultaneously PCR-amplified and analyzed for the presence of mutations at KRAS nucleotides c.34G, c.35G, c.37G, c.38G and BRAF mutation at nucleotide c.1799T using the ABI PRISM SNaPshot\u00ae Multiplex kit [xl Genetic Analyzer (Applied Biosystems). Data were analyzed using the GeneMapper Analysis Software version 4.0 (Applied Biosystems).SNaPshotreported ,25. KRASCA, USA) ,25. LabeKRAS exon 2 sequence reaction was performed from PCR-amplified tumor DNA, using the Big Dye V3.1 Terminator Kit (Applied Biosystems), and run on an automated sequencer .KRAS mutant genotype on the clinical outcome of MCRC pts treated with first line FIr-B/FOx. Pts were classified as L-L and O/MM [A retrospective analysis has been planned to evaluate the prognostic relevance of the prevalent codon 12 c.35 G > A (G12D) and O/MM . Clinicaand O/MM ; patholoand O/MM . PFS andand O/MM . The logand O/MM . PFS wasand O/MM . The resThe KRAS/BRAF genotype was evaluated in 59 pts, among 64 consecutive, unselected MCRC pts recruited in the phase II study and expanded clinical enrollment of the FIr-B/FOx regimen as the first line treatment of MCRC [KRAS wild-type and 28 (47%) as KRAS mutant [KRAS mutations was: codon 12, 24 pts (40.6%), specifically c.35 G > A (G12D), 15 pts (25.4%), c.35 G > T (G12V), 7 pts (11.8%), c.34 G > A (G12S) and c.35 G > C (G12A), 1 patient each; codon 13, 4 pts (6.7%), c.38 G > A (G13D), 3 pts (5%) and c.37_39 dupl, 1 patient , 8 (61.5%) and 19 pts (61%), respectively.Table KRAS mutant, other KRAS mutant, and KRAS wild-type pts was, respectively: L-L 6 pts (40%), 7 pts (54%), and 12 pts (39%); O/MM 9 pts (60%), 6 pts (46%), 19 pts (61%).Pts' distribution according to extension of metastatic disease in c.35 G > A KRAS wild-type and mutant pts at a median follow-up of 21.5 months were previously reported [KRAS mutant pts . We observed 8 partial responses (61%), 2 stable diseases (15%), and 3 progressive diseases (23%). Median PFS was 12 months (3-37 months): 12 events occurred and 1 patient (8%) was progression-free >12 months. Median OS was 39 months (8-59+ months): 8 events occurred and 5 pts (38%) were alive. Liver metastasectomies were performed in 5 pts out of 13 (38%) and out of 7 (71%) with L-L metastases; 4 R0 liver resections (57%). Two pathologic CRs were obtained (15%) in pts with multiple L-L metastases, harboring codon 12 mutations, c.35 G > T and c.34 G > A: 1 patient progressed at 17 months, 1 patient was progression-free at 35 months. Clinical outcome according to extension of metastatic disease, L-L and O/MM [Among 13 other than c.35 G > A and O/MM ,13, was:KRAS wild-type pts was previously reported [KRAS/BRAF wild-type pts [Activity and efficacy among 30 evaluable reported : ORR wastype pts , ORR wasKRAS mutant plus KRAS wild-type pts, ORR was 81% , median PFS was 13 months (1+-69+ months) and median OS was 34 months (1+-69+ months) , median PFS was 12 months (1+-60+ months) and median OS was 20 months (1+-60+ months). Among 7 c.35 G > T KRAS mutant pts, ORR was 57% , median PFS was 12 months (3-5 months) and median OS was 21 months (11-46+ months). Among 4 codon 13 KRAS mutant pts, ORR was 75% , median PFS was 12 months (7-37 months) and median OS was 44 months (8-59+ months). Among 3 c.38 G > A KRAS mutant pts, ORR was 67% , median PFS was 12 months (7-37 months) and median OS was not reached (8-59+ months).Among 44 evaluable other than c.35 G > A KRAS mutant pts compared to KRAS wild-type pts was not significantly different while OS was significantly worse (P = 0.002). In addition, c.35 G > A KRAS mutant pts compared to other than c.35 G > A KRAS mutant pts showed significantly worse OS (P = 0.05); other than c.35 G > A KRAS mutant pts compared to KRAS wild-type pts did not have different OS ; KRAS/BRAF wild-type pts (P = 0.03); and other codon 12 mutant pts (P = 0.03) [The prognostic relevance of tant pts ,5,8,13. tant pts . BEV addKRAS mutation characterizes 10.3% of CRC and represents up to 30% of KRAS mutations [KRAS mutation and exhibited a high activity of the FIr-B/FOx intensive regimen (ORR 71%). Liver metastasectomies were performed in 13% of pts (33% of L-L disease), median PFS and OS were 9 and 14 months, respectively. In pts with the KRAS c.35 G > A mutation, activity and PFS were not significantly different, while OS was significantly worse compared to KRAS wild-type, KRAS/BRAF wild-type, and other codon 12 and 13 mutant pts. Median OS was not significantly different in other KRAS mutant compared to wild-type pts. This is the first report of a worse prognosis in KRAS c.35 G > A (G12D) mutant MCRC pts, treated with intensive triplet chemotherapy plus BEV.The prevalent c.35 G > A (G12D) utations . In the KRAS mutations may increase aggressiveness by the differential regulation of KRAS downstream pathways associated with higher AKT/protein kinase B activation, bcl-2, E-catherin, \u03b2-catenin, and focal adhesion kinase overexpression, and RhoA underexpression, whereas codon 13 KRAS mutant cells show increased sensitivity associated with increased activation of the c-Jun-NH2-terminal kinase I pathway [KRAS codon 12 with codon 13 mutations in CRC. RASCAL (Kirsten Ras in CRC) studies showed that the presence of the KRAS mutation significantly increased the risk of death by 26% [KRAS codon 12 mutations were associated with inferior survival in patients with KRAS-wild-type/BRAF-wild-type cancers [Codon 12 pathway . Severalh by 26% ,21; the h by 26% , and up h by 26% . KRAS co cancers .BRAF and KRAS mutations can confer different biological aggressiveness and effectiveness of treatment strategies; the balance between aggressiveness and effectiveness can differentiate prognosis, that is, median OS. Comparison of median OS in pts with different genotypes can discriminate this net prognostic effect. Thus, specific mutations and treatment strategies could be major parameters determining different prognoses in MCRC. The prevalent BRAF c.1799 T > A (V600E) mutation, characterizing 4.7% to 8.7% of CRC, demonstrated a negative prognostic effect compared to BRAF wild-type pts in MCRC pts treated with doublet chemotherapy alone or added to cetuximab, BEV and cetuximab plus BEV, with a median PFS of 5.6 to 8 months and median OS of 10.3 to 15.9 months [BRAF mutant MCRC pts [KRAS c.35 G > T mutation and other mutations were associated with a worse outcome when receiving chemotherapy plus cetuximab, compared with chemotherapy alone [In MCRC pts, specific 9 months ,31. The MCRC pts . Patientpy alone .KRAS c.38 G > A mutation (G13D) confers a significantly worse prognosis [KRAS mutations [KRAS wild-type pts [KRAS mutation in first line cetuximab-containing chemotherapy [KRAS c.38 G > A (G13D) mutant pts demonstrated a significantly favorable predictive effect of cetuximab-containing associations compared to other KRAS mutant MCRC, and significantly lower ORR, with no significantly different PFS and OS compared to KRAS wild-type pts [KRAS mutations and patient outcome. Opposite findings were reported when panitumumab was combined with first line oxaliplatin, whereas similar data were reported when it was combined with second-line FOLFIRI [In MCRC pts pre-treated with chemotherapy alone, the rognosis . Cetuximutations , and no type pts . Recentlotherapy : signifitype pts ,36. In p FOLFIRI .KRAS/BRAF mutations, specifically KRAS c.35 G > A (G12D), c.35 G > T (G12V), c.38 G > A (G13D) mutations and BRAF c.1799 T > A (V600E).Prospective studies should be developed to confirm the differential prognosis and predictive effect of chemotherapeutics and/or targeted agents in MCRC pts harboring KRAS c.35 G > A (G12D) mutant genotype has a significantly worse effect on the OS of MCRC pts treated with the first line FIr-B/FOx intensive regimen compared to wild-type pts or to pts harboring different other KRAS mutations, due to heterogeneous biological aggressiveness and the effectiveness of treatment strategies. The present findings should be verified in prospective trials of multidisciplinary strategies comparing clinical outcome in MCRC pts harboring specific mutations that differentially activate the downstream RAS-MAPK or PI3K pathways.The prevalent Anti-EGFR: anti-epidermal growth factor receptor; anti-VEGF: anti-vascular endothelial growth factor; BEV: bevacizumab; cCR: clinical complete responses; CR: complete response; CRC: colorectal cancer; CT: computed tomography; HR: hazard ratio; IFL: irinotecan, 5-fluorouracil, and leucovorin; L-L: liver-limited; MCRC: metastatic colorectal cancer; O/MM: other/multiple metastatic; ORR: objective response rate; OS: overall survival; PET: positron emission tomography; PFS: progression-free survival; pts: patients; RECIST: Response Evaluation Criteria in Solid Tumors.The authors declare that they have no competing interests.GB contributed to the conception and design of the study, in the provision of study materials of patients, in data analysis and interpretation and in the manuscript writing. ER contributed to the conception and design of the study, in data analysis and interpretation and in the manuscript writing. KC, TF, MT, EA participated in data analysis and interpretation. GB, KC, CF and ER provided clinical management and data on patients. DDG, AL, JCS provided molecular genetic analysis. All authors participated in the collection and/or assembly of data. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1741-7015/11/59/prepub"} +{"text": "Previous studies suggest yoga is effective for mild to moderate chronic low back pain (CLBP) in mostly white higher socioeconomic status (SES) populations. However, little is known regarding yoga\u2019s optimal dose or its effectiveness for more severe CLBP in diverse lower SES populations.From September-December 2011, we conducted a 12-week RCT comparing once vs. twice-weekly standardized 75-minute hatha yoga classes for 95 adults with nonspecific CLBP. Recruitment and classes occurred in a large safety-net hospital and five affiliated community health centers in Boston, Massachusetts. Primary outcomes were mean low back pain intensity in the previous week (0-10) and back-related function . We used two-sample t-tests to compare once/week vs. twice/week mean change scores (baseline-12 weeks) for pain and MRMD. Analyses used the intention-to-treat principle.<$30,000, and 35% with high school education or less. Baseline pain intensity and MRMD were consistent with moderate-severe CLBP. Baseline characteristics of the once/week (n=49) and twice/week (n=46) groups were similar. Overall class attendance was 73% and 62% for the once/week and twice/week participants, respectively. Both groups practiced yoga at home on average 3-4 days/week. Each group experienced statistically significant (p<.0001) and clinically meaningful improvements in pain and function: Mean pain change scores for the once/week and twice/week groups were -2.1 (SD 2.7) and -2.4 (SD 2.2), respectively. Mean MRMD change scores for the once/week and twice/week groups were -5.2 (SD 6.5) and -4.9 (SD 4.4), respectively. There were no statistically significant differences between the two groups for pain or MRMD.Participants were on average 48 years old, 76% female, 82% non-white, 63% with annual household incomes Twelve weeks of either once or twice-weekly hatha yoga classes augmented by home practice were similarly effective for moderate to severe CLBP in a diverse predominantly lower SES population."} +{"text": "In recent years a large amount of literature data emphasizes the interrelationship between pathogenic mechanisms of chronic hepatitis C virus (HCV) infection and lipid and glucid metabolism. In this study we aimed to characterize lipid and glucidic metabolic patterns in chronically HCV-infected patients and to evaluate the role of HCV on cardiovascular risk (CVR).1c), liver enzymes, and viral load (VL). Liver histology was assessed by Fibromax (Biopredictive).We conducted a cross-sectional analysis on chronic HCV-infected adult patients, monitored at the National Institute of Infectious Diseases \u201cProf. Dr. Matei Bal\u015f\u201d. Patients with diabetes mellitus, chronic alcohol consumption, other chronic liver diseases, HBV or HIV co-infections were excluded. We recorded demographic data, HCV infection history, personal and family history of CVR factors. We measured height and weight for body mass index, waist to hip ratio, blood pressure and we assessed the 10 years CVR using Framingham score. Blood samples were tested for lipid profile, serum glucose, glycosylated hemoglobin (HbA1c levels (p=0.022).Seventy-six patients with a median age of 51years (IQR 44.25-58.0) were included. Sex ratio was F:M=1.53. Median VL was 118500 IU/mL (IQR 0-600951). Twenty-five percent (19/76) of the patients had no fibrosis (F0), 51.3% (39/76) had hepatitis (F1-2), 6.5% (5/76) had a fibrosis score equivalent to transition to cirrhosis (F3), and 17.1% (13/76) had cirrhosis (F4). Mean serum cholesterol, LDL and triglycerides were 187 mg/dL (IQR 166-220), 119 mg/dL (IQR 93-147) and respectively 94 mg/dL (IQR 69.25-132.0). Patients with no fibrosis were more frequently younger and females , had higher cholesterol (p=0.014) and LDL levels (p=0.009) and lower VL (p=0.017) and CVR according to Framingham score (p=0.000). Patients with cirrhosis were more frequently males (p=0.033), and had higher viral load (p=0.011) and serum glucose (p=0.027). Fibrosis score correlated to age (p=0.000), VL (p=0.001), higher CVR (p=0.001), low LDL (p=0.034), high glucose (p=0.031). The VL correlated to HDL (p=0.023) and with lower HbAIn patients with chronic HCV infection although high fibrosis correlates to better lipid profiles, it also correlates to higher cardiovascular risk."} +{"text": "The correct title is An error was introduced in the preparation of this article for publication. The word \"At2 Receptor Antibodies Are Nonspecific\". \"Commercially Available Angiotensin II ATThe correct citation is: 2 Receptor Antibodies Are Nonspecific. PLoS ONE 8(7): e69234. doi:10.1371/journal.pone.0069234Hafko R, Villapol S, Nostramo R, Symes A, Sabban EL, et al. (2013) Commercially Available Angiotensin II AT"} +{"text": "This crystalline monohydrate addition product, formed by reaction of d-glucose and sodium hydrogen sulfite in water, forms a three-dimensional network through complex cation coordination and extensive inter\u00admolecular hydrogen bonding. Each of the independent mol\u00adecules has an open-chain structure with the carbon chains adopting a sickle-like conformation, similar to that found in the potassium salt , but there are significant differences in the patterns of complexation.The title salt, Na al. 2001. Carbohy DOI: 10.1107/S1600536812007210/su2377Isup2.cdxSupplementary material file. DOI: 10.1107/S1600536812007210/su2377Isup3.hklStructure factors: contains datablock(s) I. DOI: 10.1107/S1600536812007210/su2377Isup4.cmlSupplementary material file. DOI: crystallographic information; 3D view; checkCIF reportAdditional supplementary materials:"} +{"text": "Several studies have described a high prevalence of 25[OH]D deficiency in HIV-infected patients, as well as its role in predicting disease progression.We performed a descriptive, cross-sectional study on a group of 68 HIV-infected patients monitored in the Regional HIV/AIDS Centre Mure\u015f, during December 2012-February 2013. We determined plasma levels of 25[OH]D. We estimated the proportion of patients with 25[OH]D deficiency/insufficiency and correlated 25[OH]D levels to HIV-RNA plasma viral load, CD4+ T-cells count and associated pathology. Data were compared to those obtained from a group of healthy, HIV-negative volunteers. Statistical analysis was performed using the GraphPad program.We studied 68 C-stage HIV-infected patients, 40 male: 28 female, with an average age of 26 and a median of 23. The average plasma 25[OH]D level was 30.94 ng/mL, median 30 ng/mL in HIV-positive patients compared to an average of 44.72 ng/mL and median 39.82 ng/mL in HIV-negative subjects (p=0.0109). 25[OH]D deficiency <20 ng/mL was found in 23.52% HIV-infected patients, while 26.47% HIV-positive subjects had medium levels of 25[OH]D insufficiency, between 20-30 ng/mL. Only 2 patients had severe 25[OH]D deficiency, below 10 ng/mL. We did not find any statistically significant correlations of 25[OH]D levels with CD4+ T-cells level, HIV-RNA plasma viral load or protease inhibitor therapy. Patients with HIV-tuberculosis co-infection had significantly lower levels of 25[OH]D (p=0.0454) than HIV-positive subjects without tuberculosis.25[OH]D plasma levels are lower in HIV-infected patients compared to the general population. Low 25[OH]D levels are reported in patients with HIV-tuberculosis co-infection. Low 25[OH]D levels may indicate unfavorable outcome in HIV-infected patients."} +{"text": "There are various errors contained in the references 6, 7, 8, 9, 10, 25, 28, 29, 39, 40 and 43. A summary of issues is as follows:* References 6 - 10 contain incorrect information and numbering. They should read as follows:6. (1998) Control and surveillance of African trypanosomiasis. Report of a WHO Expert Committee. World Health Organ Tech Rep Ser 881: I-VI, 1-114.7. Chappuis F, Udayraj N, Stietenroth K, Meussen A, Bovier PA (2005) Eflornithine is safer than melarsoprol for the treatment of second-stage Trypanosoma brucei gambiense human African trypanosomiasis. Clin Infect Dis 41: 748-751.8. Kennedy PG (2008) The continuing problem of human African trypanosomiasis (sleeping sickness). Ann Neurol 64: 116-126.9. Pepin J, Milord F (1994) The treatment of human African trypanosomiasis. Adv Parasitol 33: 1-47.10. Schmid C, Richer M, Bilenge CM, Josenando T, Chappuis F, et al. (2005) Effectiveness of a 10-day melarsoprol schedule for the treatment of late-stage human African trypanosomiasis: confirmation from a multinational study (IMPAMEL II). J Infect Dis 191: 1922-1931.* Reference 25, 28 and 29 should be removed.* Reference 39 is incorrect and should read as follows:Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today: Technologies 4: 337-341.* Reference 40 is incorrect and should read as follows:Wager T, Verhoest P, Villalobos A (2010) Moving beyond Rules: The Development of a Central Nervous System Multiparameter Optimization (CNS MPO) Approach To Enable Alignment of Druglike Properties. ACS Chem Neurosci 1.* Reference 43 is incorrect and should read as follows:Sykes ML, Avery VM (2009) A luciferase based viability assay for ATP detection in 384-well format for high throughput whole cell screening of Trypanosoma brucei brucei bloodstream form strain 427. Parasit Vectors 2: 54."} +{"text": "Staphylococcus aureus (MTCC 737), Pseudomonas aeruginosa (MTCC 424), Escherichia coli (MTCC 1687), and yeast-like fungi Candida tropicalis. p-Toluidine on treatment with ammonium thiocynate formed 2-benzothiazolamines (II), which on reaction with hydrazine hydrate formed a hydrazino derivative (III). Compounds GG4 to GG8 were synthesized by reacting the hydrazine derivative with different acetophenones. All the synthesized compounds were identified by IR and 1H-NMR, and antimicrobial activity was performed on the synthesized compounds. Presence of NO2, Br, OCH3, and Cl groups to the substituted benzothiazole enhanced the antibacterial and antifungal activities.In the present study, five new derivatives (GG4 to GG8) of benzothiazoles were synthesized and evaluated against Since then, significant research has been carried out taking benzothiazole as the basic moiety. From the literature survey, it has been found that extensive work has been reported on 2-substituted benzothiazole derivatives in the past and evaluated for different activities, such as, antibacterial, antiprol1 NMR spectra on Bruker AC 30 of the NMR spectrometer 400 MHz.All the chemicals and solvents used during the experimental studies were of analytical grade and were procured from CDH, New Delhi and Sigma Chemicals, Mumbai. Melting points of all synthesized compounds were determined by using an open capillary tube and were uncorrected. Infrared (IR) data were recorded in KBr disks, on a Perkin Elmer R-IX FTIR spectrophotometer, and the Hp-Toluidine (5.35 g) was dissolved in a mixture of concentrated HCl (4.3 ml) and water (11.6 ml) by heating in a water bath. The contents were cooled and solid ammonium thiocyanate (3.5 g) was added. The mixture was heated on water bath for about 22 hours. The precipitated product was cooled and filtered, washed with water three to four times, and dried. It was recrystallized with aqueous methanol to get cream colored crystals. Yield: 88% (m.p: 130\u00b0C). IR: 3435 (N-Hstr), 2999 (Aliphatic C-Hstr), 1612 (N-Hben), 1462 (Aromatic C=Cstr), 1310 (Aromatic C-Hben) 1H-NMR: 3.35 , 7.24-7.11 , 2.30 .2SO4 was added to p-tolylthiourea (8.3 g) and the temperature of the mixture was raised to 80\u00b0C on a water bath. Next, 48% HBr (0.5 g) acid was added slowly and the reaction mixture was stirred for two hours and set at 80\u00b0C. It was then cooled to room temperature and the reaction mixture was slowly introduced to cold water and then adjusted to pH 9 or 10 by adding ammonia water. The whole mixture was stirred for one hour by heating at 70\u00b0C and then cooled to room temperature. The mixture was extracted twice with dichloromethane and the combined extract was dried with anhydrous sodium sulfate and evaporated, to obtain the title compound. Yield: 80% (m.p: 145\u00b0C). IR: 3395 (N-Hstr), 3261 (N-Hstr), 1462 (Aromatic C=Cstr), 1326 (Aromatic C-Nstr), 1253 (C-Sstr). 1H-NMR: 3.45 , 7.32-7.26 , 2.34 Fifteen milliliters of concentrated Hstr), 3162 (Aromatic C-Hstr), 3000 (Aliphatic C-Hstr), 1611.9 (N-Hben). 1H-NMR: 9.59 , 7.34-7.11 , 3.37 , 2.26 .2-Amino-6-methybenzothiazole (20 g) [0.82 mmol] and hydrazine hydrate (85%) [0.11 mmol] in 50 ml of ethylene glycol were refluxed by stirring for four hours (60\u00b0C). The color of the reaction changed to green and a homogeneous solution appeared. A white solid was precipitated at the end of the reflux period. The mixture was cooled and the product was filtered and then washed with water several times. It was air dried and recrystallized by using ethanol. Yield: 43% (m.p: 192\u00b0C). IR: 3434 (NHNHthin layer chromatography (TLC). On cooling, the solid was separated. It was filtered and washed with little water and recrystallized with absolute ethanol. Yield: 48% (m.p: 181\u00b0C). IR: 3428 (N-Hstr), 3087.8 (Aromatic C-Hstr), 1613.9 (C=Nstr), 823 (Aromatic C-Nstr). 1H-NMR: 8.77 , 7.36-7.06 , 2.38 , 2.69 .2-Hydrazino-5-methylbenzothiazole (1.5 mmol), 3-nitroacetophenone (2.2 mmol), and glacial acetic acid (2\u20133 drops) were taken in absolute ethanol (20 ml) and refluxed on a water bath for eight hours, till different spots appeared, on str), 3164 (Aromatic CHstr), 1612 (C=Nstr), 1581 (NHben), 699 (C-Brstr). 1H-NMR: 9.58 , 7.26-7.12 , 2.50 , 2.27 .2-Hydrazino -5-methylbenzothiazole (1.5 mmol), 4-bromoacetophenone (2.2 mmol), and glacial acetic acid (2\u20133 drops) were taken in absolute ethanol (20 ml) and refluxed on a water bath for eight hours till different spots appeared, on TLC. On cooling, the solid was separated. It was filtered and washed with little water and recrystallized with absolute ethanol. Yield: 52% (m.p: 189\u00b0C). IR: 3434 (NHstr), 3165 (Aromatic C-Hstr), 1612 (C=Nstr), 1581 (N-Hben), 1285 (Aromatic C-Nstr). 1H-NMR: 9.59 , 7.25-7.11 , 6.72 , 2.97 , 2.33 .2-Hydrazino-6-methylbenzothiazole (1.5 mmol), 4-Methoxyacetophenone (2.2 mmol), and glacial acetic acid (2\u20133 drops) were taken in absolute ethanol (20 ml) and refluxed on a water bath for eight hours till different spots appeared, on TLC. On cooling, the solid was separated. It was filtered and washed with little water and recrystallized with absolute ethanol. Yield: 41% (m.p: 169\u00b0C). IR: 3435 (N-Hstr), 3164 (Aromatic C-Hstr), 1612 (C=Nstr), 1582 (N-Hben), 800 (Aromatic C-Clstr). 1H-NMR: 9.59 , 7.25-7.11 , 3.40 , 2.26 .2-Hydrazino-6-methylbenzothiazole (1.5 mmol), 2,4-Dichloroacetophenone (2.2 mmol), and glacial acetic acid (2\u20133 drops) were taken in absolute ethanol (20 ml) and refluxed on a water bath for eight hours till different spots appeared, on TLC. On cooling, the solid was separated, and was filtered and washed with little water and recrystallized with absolute ethanol. Yield: 54% (m.p: 177\u00b0C). IR: 3434 (N-Hstr), 3163 (Aromatic C-Hstr), 1610 (C=Nstr), 1415 (Aromatic C=Cstr). 1H-NMR: 9.58 , 7.38-7.11 , 3.38 2.26 .2-Hydrazino-6-methylbenzothiazole (1.5 mmol), 2,4-Dimethoxyacetophenone (2.2 mmol), and glacial acetic acid (2\u20133 drops) were taken in absolute ethanol (20 ml) and refluxed on a water bath for eight hours, till different spots appeared, on TLC. On cooling, the solid was separated, and was filtered and washed with little water and recrystallized with absolute ethanol. Yield: 58% (m.p: 185\u00b0C). IR: 3433 (O-H and N-Hp-Toluidine on reacting with ammonium thiocyanate formed p-Tolylthiourea (I), which on reaction with hydrobromic acid yielded 2-benzothiazolamines (II). This on reaction with hydrazine hydrate formed hydrazino derivatives (III). The compounds (GG4 to GG8) were synthesized by reacting with hydrazine derivatives, with different acetophenones .The efficient synthetic route for the synthesis of benzothiazole derivatives is shown below . p-ToluiGram positive bacteria \u2014 Staphylococcus aureus (MTCC 737), Gram negative bacteria \u2014 Pseudomonas aeruginosa (MTCC 424), Escherichia coli (MTCC 1687), and yeast-like fungi Candida tropicalis. The concentration of the test compound used was 50 mg/ml. Ampicillin and Clotrimazole were taken as the standard drugs [Tables S. aureus [P. aeruginosa, E. coli [C. tropicalis [In the present study, the efficacy of five new compounds was detected against oli MTCC 687, and sa MTCC 44, Escher. aureus , P. aeru E. coli , C. tropopicalis , and witopicalis , respectS. aureus, E. coli, and C. tropicalis when tested at 50 mg/ml concentration taking ampicillin and clotrimazole as the standard. From the SAR studies, the presence of the electron withdrawing group in compound GG4 was assumed to be responsible for the observed activity. From the above-mentioned results, it may be concluded that the derivatives of benzothiazoles possess moderate-to-potent antimicrobial activity[Compound GG4 showed significant activity against activity5 when co"} +{"text": "MRI is a common method for detecting breast cancer in women at high risk ,2 These BRCA, 65 family history) were managed at the Royal Marsden Hospital from 1994 to 2013. Following ethical approval, data were collected retrospectively for each presentation of breast cancer: method of presentation/diagnosis , age at diagnosis, cancer type, grade, size, presence of DCIS, lymphovascular invasion (LVI), nodal status and tumour subtype. Chi-squared and ANOVA analyses determined any association between the parameters, P < 0.05 was significant.A total of 125 high-risk patients with 134 breast cancers (69 P = 0.008); mean size 17, 29, and 34 mm (P = 0.076) respectively).The majority of cancers were high-grade (68%) invasive ductal carcinomas (78%) without LVI (76%). MRI-detected cancers were triple negative in 60% (P = 0.03), node negative in 100% (P = 0.005) with DCIS in 70% (P = 0.007). Mammography-detected cancers were luminal in 77% (P = 0.03), node negative in 77% (P = 0.005), with DCIS in 81% (P = 0.007). Symptomatic cancers were luminal in 54%, triple negative in 41%, node negative in 56% and DCIS positive in 51%.Ten breast cancers were MRI detected, 43 mammography detected and 81 symptomatic (mean age 41, 51, and 45 years (In this high-risk cohort, MRI detects small, triple-negative, node-negative cancers in younger women, while mammography detects larger, luminal, cancers in older women that may be node positive."} +{"text": "AbstractZyginella menghaiensissp. n. (Hemiptera: Cicadellidae: Typhlocybinae: Zyginellini), is described from Chinaand a key to species of Zyginella from China is provided.A new species, Zyginella was established by L\u00f6w in 1885. The genus belongs in the tribe Zyginellini of Typhlocybinae and consists of twenty-two species distributed in the Oriental, Palaearctic and Afrotropical Regions. Members of the genus can be distinguished by the distinct dark spot on the 3rd apical cell of the forewing .Recent taxonomic work on the genus includes L\u00f6whttp://species-id.net/wiki/ZyginellaZyginellaZyginella pulchra L\u00f6w, 1885. L\u00f6w, 1885: 346; PyramidotettixConometopius citri Matsumura, 1907. Synonymized by Matsumura, 1932: 59; RemmiaRemmia orbigera Vilbaste, 1968. Synonymized by Vilbaste, 1968: 91; Forewing with dis1 markedly distad of point of fusion of Cu1 with M3+4.Head acutely Male pygofer with sho Oriental region, Palaearctic region, Afrotropical region.Song & Lisp. n.urn:lsid:zoobank.org:act:090D3B2C-B357-4E11-9F81-AC71C63C6743http://species-id.net/wiki/Zyginella_menghaiensis Head and thorax yellowish brown; vertex with lateral margins with soft red tinge; eyes brownish grey; pronotum brownish with two longitudinal darker stripes; scutellum with basal triangles testaceous. Forewing reddish Coronal suture extendinAbdominal apodemes slender,Pygofer lobe broad, w Body length males 2.9~3.1 mm.Holotype, male, China: Yunnan Province, Menghai County, 23 July 2008, coll. YUE-HUA SONG. Paratypes: two males, same date as holotype.Zyginella tsauri Chiang, Hsu & Knight (1989), but the forewing has a large dark costal patch ( The new species is similar to al patch and the al patch . The new species is named for its type locality: Menghai."} +{"text": "Diffusion tensor magnetic resonance imaging (DT-MRI) enables 3D evaluation of whole heart microstructure. DT invariants evaluate microstructural remodeling by quantifying trace (increases with decreasing cellularity), fractional anisotropy , and tissue mode (decreases with increasing fiber disarray) . We have2, 0.5 x 0.5 x 0.75 mm resolution). Trace, FA, and mode were segmented into epicardial, midwall, and endocardial regions. Bootstrapped histograms with 95% confidence intervals (95%-CIs) of the de-correlated (via decimation by the auto-correlation length) and segmented invariant data were defined to make statistical comparisons of non-Gaussian datasets tractable. Two-group comparisons of median invariant data of each heart were used to test for significant differences (p < 0.05) between HF and CNTL in each transmural region.HF was induced in 10-12 month old New Zealand White female rabbits (N=8) with an epicardial pacing lead placed in the lateral LV wall and tachycardia pacing at 250 beats per minute (bpm) for 3 days, 300 bpm for 3 days, and 350 bpm for 3-4 weeks. Normal weight matched rabbits (N=5) served as controls (CNTL). Hearts were excised, formalin fixed, and DT-MRI was performed on a 7T scanner (24 diffusion gradient directions, 6 nulls, TE/TR=30/500 ms, b-value=1000 s/mmFigure DT invariant data indentify statistically significant microstructural remodeling in the pacing induced HF model within epicardial, midwall, and endocardial regions.Kung - AHA Grant 12PRE9160024, Chen - NIH Grants P01HL78931, R01HL78932, a Medtronic-Zipes Endowment and the Indiana University-Indiana School of Medicine Strategic Research Initiative."} +{"text": "Bifidobacteria, Lactococcus and Streptococcus, have been described. However, information for the prophage of Mycobacterium remains poorly defined.Prophages, integral components of many bacterial genomes, play significant roles in cognate host bacteria, such as virulence, toxin biosynthesis and secretion, fitness cost, genomic variations, and evolution. Many prophages and prophage-like elements present in sequenced bacterial genomes, such as In this study, based on the search of the complete genome database from GenBank, the Whole Genome Shotgun (WGS) databases, and some published literatures, thirty-three prophages were described in detail. Eleven of them were full-length prophages, and others were prophage-like elements. Eleven prophages were firstly revealed. They were phiMAV_1, phiMAV_2, phiMmcs_1, phiMmcs_2, phiMkms_1, phiMkms_2, phiBN42_1, phiBN44_1, phiMCAN_1, phiMycsm_1, and phiW7S_1. Their genomes and gene contents were firstly analyzed. Furthermore, comparative genomics analyses among mycobacterioprophages showed that full-length prophage phi172_2 belonged to mycobacteriophage Cluster A and the phiMmcs_1, phiMkms_1, phiBN44_1, and phiMCAN_1 shared high homology and could be classified into one group.Mycobacterium.To our knowledge, this is the first systematic characterization of mycobacterioprophages, their genomic organization and phylogeny. This information will afford more understanding of the biology of The online version of this article (doi:10.1186/1471-2164-15-243) contains supplementary material, which is available to authorized users. Mycobacterium prophages.Phages can be divided into virulent or temperate based on their relationship with the host. Temperate phage inserts and integrates into its host genome upon infection, and can reside as quiescent prophage. Prophage does not infect its host and maintains the dormant state . Whole-gMycobacterium tuberculosis H37Rv genome [M. ulcerans Agy99 genome [M. marinum M and two of them, phiMmar02 and phiMmar08, are full-length prophages [M. abscessus ATCC 19977 chromosome contains a full-length prophage and three prophage-like elements [M. abscessus subsp. bolletii BD genome [M. abscessus Strain 47J26 [M. abscessus M93 is described [M. massiliense Strain M172 contains putative mycobacteriophage [M. canettii STB-I [M. simiae strain DSM 44165 [Mycobacterium prophages remain to be characterized. Knowledge regarding their genomic composition, distribution can facilitate the elucidation of the biology of Mycobacterium.There is huge gap between the number of mycobacteriophages isolated and cognate prophages found within mycobacteria. To date, there are 3427 mycobacteriophages isolated and 448 of them with genome sequenced. They can be assembled into 20 clusters (A-T) and seven of them are singletons , 7. In crophages ; the M. elements ; prophagD genome ; two proin 47J26 ; a potenescribed ; M. massriophage ; a 55-kbii STB-I ; a 40-kbMycobacterium complete genomes sequences from GenBank, shotgun assembly sequences from Whole Genome Shotgun (WGS) databases, and searched for mycobacterioprophages in published literatures. Together, 33 prophages were described in detail, and 11 of them were previously undocumented prophages among Mycobacterium genomes. The genomes, gene contents, comparative genomics studies and the relationships among them were characterized.In this study, we screened all available Mycobacterium genomes. Secondly, the presence or absence of the integrase genes was tested to exclude negative results. Finally, mycobacterioprophage sequences were identified based on the homology between prophage ORFs (open reading frames) and known phage genes. Thirty mycobacterial complete genomes , 11 prophages can be considered as full-length prophage. The remaining 22 prophages were prophage-like elements. The result showed that small prophage-like elements were more prevalent than putative full-length prophages. The small prophage-like elements might be more stable due to mutational decay and loss of some genes somehow involved in genome excision. Small prophage-like elements were more stable and can be more easily detected than the full-length prophages. Through the tRNA search tool, 19 prophages were integrated into tRNA genes to MAV_0841 (excisionase DNA binding protein), contains sixty-three ORFs strain [Mycobacterium unique protein. This implies that MAV_0835 and MAV_0790 play a role in the physiology and pathogenicity of M.avium 104.In addition to ORFs similar to other phage genes, two ORFs show unexpected similarity to bacterial key proteins. MAV_0835 encodes type VI secretion protein IcmF (Intracellular Multiplication F), a core component of type VI secretion system in bacteria \u201332. Baserequency , and hasM.avium 104, extends from MAV_1484 (integrase gene) to MAV_1504 (Phage terminase) and contains 21 ORFs , response regulator receiver protein (MAV_1485), DNA primase/polymerase (MAV_1486), Y4cG protein (MAV_1493), transposase (MAV_1498) and phage terminase (MAV_1504). Other phiMAV_2 prophage ORFs similar to known bacterial functional proteins are also identified to Mmcs_2908 (transglycosylase-like protein) and contains sixteen ORFs , whose predicted protein products are HNH endonuclease and DNA repair protein RadA, respectively. The lysogeny module consists of Mmcs_2921 (putative phage excisionase) and Mmcs_2923 (phage integrase).There are two prophage-like elements in attL and attR sites. Based on Blast-p, only 8 ORFs have sequence similarity to other phage genes at the amino acid sequence level and 4 can be assigned function, namely Mmcs_3802 (HNH endonuclease), Mmcs_3805 (phage major capsid protein), Mmcs_3814 (HNH endonuclease domain-containing protein), and Mmcs_3816 (phiRv1 integrase).The phiMmcs_2 prophage remnant inserts between Mmcs_3803 and Mmcs_3817. The prophage sequence contains 15 ORFs to BN42_21185 and contains only eight ORFs , BN42_21178 (excisionase), BN42_21179 (DNA primase), BN42_21182 (phage prohead protease), and BN42_21183 (phage major capsid protein).PhiBN42_1, phiBN44_1, and phiMCAN_1 are found in M.canettii CIPT 140060008, flanked by a 22-bp repeat , MCAN_10521 (DNA-binding protein), MCAN_10541 (DNA primase), MCAN_10551 (HNH endonuclease), MCAN_10561 (phage terminase), MCAN_10571 , and MCAN_10601 (phage major capsid protein).Prophage phiMCAN_1 Figure\u00a0, which iM.smegmatis JS623, contains 13 ORFs , Mycsm_04296 (DNA-binding protein), Mycsm_04298 (DNA primase), Mycsm_04299 (HNH endonuclease), Mycsm_04302 (phage terminase), and Mycsm_04303 . Additionally, Mycsm_04293, whose protein product is similar to glycerate kinase, is also present in phiBN44_1.Prophage phiMycsm_1 Figure\u00a0, inserteM.sp. MOTT36Y, extends from W7S_04825 (integrase gene) to W7S_04880 and contains 12 ORFs , W7S_04845 (pantothenate kinase), and W7S_04855 (transposase).Prophage phiW7S_1 Figure\u00a0 integrathttp://phagesdb.org/blast/) and dot plot matrix of the genomes of full-length mycobacterioprophages and mycobacteriophage clusters (A-T and singletons) revealed that phi172_2 shared sequence similarity to cluster A were firstly used for analyzing bacterial genome to find candidate prophages [DNA sequences of bacteria for analysis were downloaded from multiple databases, such as NCBI . PHAST (rophages . An interophages \u201320. Finarophages .http://lowelab.ucsc.edu/tRNAscan-SE/) [http://mbio-serv2.mbioekol.lu.se/ARAGORN/) [http://blast.ncbi.nlm.nih.gov/Blast.cgi) and the phagesdb.org site (http://phagesdb.org/blast/). Some data about mycobacteriophage genomes was downloaded from the phagesdb.org site (http://phagesdb.org/). DNAman was used to searching the flank of prophage to find attL and attR sites. Sequences were submitted entries to the GenBank sequence database by Sequin (http://www.ncbi.nlm.nih.gov/projects/Sequin/index.html). Comparative genomic analyses of prophage could be carried out by Blast-N for the global comparison of phiMmcs_1 (or phiMkms_1), phiBN44_1, and phiMCAN_1 and Geneious software for the dotplot of all the mycobacterioprophage-like sequences [http://embnet.vital-it.ch/software/ClustalW.html) or MEGA4 [Prophage sequence was annotated using a variety of programs including Glimmer . tRNA ancan-SE/) and ARAGRAGORN/) . BLAST aequences . Multiplor MEGA4 .Additional file 1: Table S1: Mycobacterial genomes retrieved in this study. (DOC 56 KB)Additional file 2: Table S2: Database matches for phiMAV_1. (DOC 85 KB)Additional file 3: Table S3: Database matches for phiMAV_2. (DOC 44 KB)Additional file 4: Table S4: Database matches for phiMmcs_1. (DOC 40 KB)Additional file 5: Table S5: Database matches for phiMmcs_2. (DOC 38 KB)Additional file 6: Table S6: Database matches for phiMkms_1. (DOC 40 KB)Additional file 7: Table S7: Database matches for phiMkms_2. (DOC 39 KB)Additional file 8: Table S8: Database matches for phiBN42_1. (DOC 30 KB)Additional file 9: Table S9: Database matches for phiBN44_1. (DOC 34 KB)Additional file 10: Table S10: Database matches for phiMCAN_1. (DOC 33 KB)Additional file 11: Table S11: Ddatabase matches for phiMycsm_1. (DOC 34 KB)Additional file 12: Table S12: Database matches for phiW7S_1. (DOC 34 KB)Additional file 13: Figure S1-S11: Comparative genomic analyses of phi172_2 and cluster A (subcluster A1-A11) mycobacteriophage. (DOC 5 MB)Additional file 14: Figure S12: Comparative genomic analyses of phiMAB_1 and subcluster F1 mycobacteriophage. (DOC 549 KB)Additional file 15: Figure S13-S14: Comparative genomic analyses of phiMAB47J26_1, subcluster F1 and cluster N mycobacteriophage. (DOC 1 MB)Additional file 16: Figure S15-S17: Comparative genomic analyses of phiMAB47J26_2, cluster P, subcluster F1 and cluster N mycobacteriophage. (DOC 2 MB)Additional file 17: Figure S18-S19: Comparative genomic analyses of phi172_1, subcluster F1 and cluster N mycobacteriophage. (DOC 1 MB)"} +{"text": "Shock-related hyperglycemia impairs mitochondrial function and integrity , ultimatn = 9) or imeglimin . Fifteen hours later animals were anesthetized, mechanically ventilated and instrumented for a consecutive 6-hour observation period. After a second imeglimin bolus, colloid fluid resuscitation and continuous i.v. noradrenaline were titrated to maintain normotensive and hyperdynamic hemodynamics. Then 2 mg/g/hour glucose was infused to induce hyperglycemia. Glucose oxidation and gluconeogenesis were derived from blood 13C6-glucose and mixed expiratory 13CO2/12CO2 isotope enrichment during continuous isotope infusion. Liver mitochondrial activity was assessed using high-resolution respirometry [Immediately after cecal ligation and puncture, mice randomly received s.c. vehicle by increasing whole body glucose oxidation vs. 51 % of infused isotope, P = 0.085), which coincided with partial restoration of gluconeogenesis vs. 0.31 mg/g/hour, P = 0.032), liver mitochondrial activity vs. 116 pmol O2/second/mg tissue, P = 0.003); maximal oxidative capacity vs. 147 pmol O2/second/mg tissue, P = 0.064). Imeglimin increased liver HO-1, reduced liver Bax expression and attenuated NF-\u03baB activation .Imeglimin decreased blood glucose levels vs. 192 mg/dl, Imeglimin improved whole body glucose utilization and gluconeogenesis, a well-established marker of liver metabolic capacity ,5, and a"} +{"text": "Early diagnosis of sepsis and its differentiation from non-infective SIRS is very important. The links between inflammation and coagulation play an important role in the SIRS/sepsis process. We investigated hematological and biochemical parameters (including thromboelastography (TEG)) in patients after surgical resection of esophagus. The aim of our project was to find out whether there are any changes in these parameters that could help in differentiation between SIRS and sepsis.In our study we enrolled 38 patients (aged 41 to 74) undergoing esophagectomy. Blood samples were obtained in the morning before the operation and then every 24 hours for the next 6 postoperative days (POD). Blood samples were analysed for the following parameters: procalcitonin (PCT), C-reactive protein (CRP), IL-6, aspartate transaminase (AST), lactate, white blood count (WBC), D-dimers, antithrombin (AT), international normalised ratio (INR), activated partial thromboplastin time (APTT) and parameters of TEG.P < 0.002) only; POD 2: AST (P < 0.003), lactate (P < 0.006), D-dimers (P < 0.02), PCT (P = 0.03), IL-6 (P < 0.03), WBC (P < 0.03); POD 3: AST (P < 0.03), PCT (P < 0.02), IL-6 (P = 0.006), CRP (P < 0.04), WBC (P < 0.05); POD 4: AST (P = 0.006), PCT (P = 0.007), IL-6 (P < 0.02), CRP (P = 0.03), D-dimers (P < 0.05), INR (P = 0.03); POD 5: PCT (P < 0.003), IL-6 (P < 0.04), CRP (P < 0.04), AT (P = 0.03); and POD 6: PCT (P = 0.0001), CRP (P < 0.013), WBC (P = 0.03), TEG-LY30 (P < 0.04).Nine patients developed sepsis within 6 postoperative days. Five of them had pneumonia and in four patients the cause of sepsis was dehiscention of gastroesophageal anasthosmosis. Significant differences between patients with SIRS and patients with sepsis were found in the following parameters: 0-day (before operation): no significant differences; POD 1: differences in AST (Sequential measurement of biochemical and hemato-logical parameters, mainly AST, PCT, IL-6, WBC, CRP and D-dimers, can help in early diagnosis of sepsis in patients after extensive operation such as esophagectomy. On the contrary, TEG does not seem to be helpful in differentiation of SIRS/sepsis during the early postoperative period. However, it seems to be useful after the fifth postoperative day."} +{"text": "There was an error in the title. The correct title is: The RNA Polymerase PB2 Subunit of Influenza A/HongKong/156/1997 (H5N1) Restricts the Replication of Reassortant Ribonucleoprotein Complexes. The correct citation is: Nakazono Y, Hara K, Kashiwagi T, Hamada N, Watanabe H (2012) The RNA Polymerase PB2 Subunit of Influenza A/HongKong/156/1997 (H5N1) Restricts the Replication of Reassortant Ribonucleoprotein Complexes. PLoS ONE 7(2): e32634. doi:10.1371/journal.pone.0032634"} +{"text": "Pituitary adenoma in children is rarely reported. Acromegaly is one of clinical manifestation in GH releasing-pituitary adenoma. Recurrence of clinical manifestation after resection must be evaluated for possibility of pituitary adenoma relapse.Relapse of pituitary adenoma in children must be considered in the recurrence of clinical manifestations.N,male,15-yo, came to pediatric endocrinology outpatient clinic with the main complain of acromegaly and decreased of visual field which was getting worse since two weeks before. He was consulted to ophthalmology and neurosurgery outpatient clinic. MRI with contrast revealed pituitary adenoma. Laboratories results showed TSHS:0.9773(0.35-4.94)uIU/ml, prolactin:0.51(4.04-15.2)ng/ml, testosterone less than 2.50(boys:13-17:28-1110)ng/ml, growth hormone was more than 40,00(>10.0)ng/ml. He was performed transsphenoidal removal cystic tumor. Pathological result showed macroscopic: yellowish cystous mass;0.6x0.4x0.2cm whether microscopic: appropiate to pituitary adenoma, non chromophobe. After surgery, patient was given DDAVP nasal spray 10 microgram/day, L-thyroxin 100 microgram once daily. One year after surgery, patient complaint of acromegaly, decreased visual field, especially in right and left temporal side, cephalgia. On physical examination, body weight was 91.5kg, height was184.5 cm. There was hemianopsia bitemporal. Tanner stage was A2P4G4. MRI with contrast showed pituritary adenoma relapse. Bone age was normal with height percentage based on it is about 96.8%. Tanner Whitehouse showed adult height 186.4cm. Thorax X ray showed heart and lungs were normal. Laboratories results revealed IGF1:1359(237-996)microgram/L, FT4:1(0.89-1.76)ng/dl; TSHS:0.3(0.5-4.94)microIU/ml(12-18yo), testosterone:435.1(28-1110) ng/dl. Working diagnosis was pituitary adenoma relapse post tumor resection, panhypopituitarism, diabetes insipidus. Testosterone 150mg once per month was added."} +{"text": "Herb combination has been very popular in traditional medical prescriptionssuch as Traditional Chinese Medicine (TCM). Persistent efforts and attempts have beenmade to dissect the action mode of TCM in recent years, which has provided certain evidencefor inter-herbal interactions. However, the interactions among different componentsin a single herb have been largely neglected.Curcuma WenyujinY.H.Chenet C Ling onMDA-MB-231 and MCF-7 breast cancer cell proliferation alone or in combination with afixed-dose-combination was investigated.In this experimental study, the interactions among different componentsof a single herb were explored. The effect of three main sesquiterpenes isolated from \u0394\u03c8m) changes showed similar results. However, theydemonstrated complicated interactions on the expression of apoptotic-related proteinsand key signal transduction proteins.Furanodiene significantly inhibited cancer cell proliferation while germacrone andcurdione showed no effect. Germacrone enhanced furanodiene\u2019s anti-proliferative effect.Curdione showed no effect on furanodiene\u2019s anti-proliferative effect but partly reversed theanti-proliferative effect of germacrone and furanodiene combined. The morphological andmitochondrial membrane potential (Curcuma WenyujinY.H.Chenet C Ling may exist. The intra-herb interactions should be taken intoconsideration when attempts are made to interpret the art of TCM formulation or other similarrecipes.Unpredictable and complex interactions among different components in Accumulated data have demonstrated that complementaryand alternative medicine (CAM)shows beneficial effect in the treatment of severalkinds of cancers -3. Tradisalvia miltiorrhiza. Results showed that the combinationyields synergy in the treatment of APL model by investigatingthe interaction of three pure compoundsnamely tetraarsenictetrasulfide, indirubin, and tanshinoneIIA which were selected to represent threeherbs respectively: realgar, indigo naturalis, andt of APL .Furthert of APL -11. HoweCurcuma WenyujinY.H.Chenet C Ling Ling is a commonlyprescribed Chinese herb with anti-cancer potentials..Curcuma In this experimental study, germacrone, curdione,and furanodiene used in this experimentalstudy were purchased from the National Instisutesfor Food and Drug Control .The RPMI-1640 culture medium was obtainedfrom Gibco (USA). Fetal bovine serum (FBS),phosphate-buffered saline (PBS), penicillinstreptomycin(PS), and 0.25% (w/v) trypsin/1mMEDTA were purchased from Invitrogen (USA).3--2,5-diphenyl tetrazoliumbromide (MTT), 5, 5', 6, 6'- tetrachloro-1,1', 3, 3'-tetraethyl-benzimidazolylcarbocyanineiodide (JC-1), phenylmethanesulfonyl fluoride(PMSF) andprotease inhibitor cocktail were purchasedfrom Molecular Probes (USA). RIPA lysisbuffer was obtained from Santa Cruz (USA).Primary antibodies against Bcl-2, p-Bcl-2, Bclxl,Bax, Bad, Bok, Bim, caspase-9, cleaved caspase-9, PARP, NF-\u03baB, p38MAPK, p42/44MAPK,\u03b2-actin, and secondary antibodies were obtainedfrom Cell Signaling (USA). In this paper, A standsfor germacrone (14.3 \u03bcM), B stands for curdione(42.9 \u03bcM), C stands for furanodiene (42.9 \u03bcM),AB stands for A (14.3 \u03bcM) and B (42.9 \u03bcM) combined while ABC is A (14.3 \u03bcM), B (42.9 \u03bcM)and C (42.9 \u03bcM) combined together and the restfollows the same pattern.2.Human breast cancer cell lines, MCF-7 andMDA-MB-231 were obtained from ATCC (USA).Cells were cultured in medium containing RPMI-1640, antibiotics , and 10 % (v/v) heat-inactivated FBSat 37\u02daC under 5 % CO4) cells in100 \u03bcL medium were seeded in 96-well plates andtreated with A (14.3 \u03bcM), B (42.9 \u03bcM) and C (42.9\u03bcM) alone or in a combination for 24 hours. Thecellular morphology was observed with AxioCamHRC CCD camera (Carl Zeiss).Exponentially growing MCF-7 was monitored by JC-1 staining as previouslydescribed using SPSS 11.5 software.Statistical differences were considered significantat p<0.05.Firstly, the effect of A, B and C alone on MDAMB-231 and MCF-7 cell proliferation was determined.As shown in figure 2, neither A nor B showedcytotoxic effect on both cell lines at 50 \u03bcM while Cdramatically inhibited both cell line proliferation.No obvious morphologic changes were observed aftertreating with A and B alone or in combination whileC significantly changed the cell morphology and decreasedthe cell number. AC, BC, and ABC inducedobvious morphologic changes . The cel\u0394\u03c8m is shown in figure3 (below), which is quite similar to those of MTTresults. Compared with the control group, no obviouschanges in the red fluorescence were observedin A, B and AB treated group. However, C, AC, BC,and ABC treated groups exhibited increased greenfluorescence. Furthermore, more green fluorescencewas observed in AC group than that of ABCgroup. These results showed that \u0394\u03c8m decreased inC, AC, BC, and ABC groups.The effect of A, B and C alone or in a combinationon MDA-MB-231 cell Both A and B showed no effect on Bcl-xl, Bcl-2and Bim expression, increased Bax andp-Bcl-2, anddecreased Bok expression. B decreased Bad expressionwhile A had no effect. C increased Bcl-2, Baxand Bim expression and decreased Bcl-xl, Bok andBad without affecting p-Bcl-2. AB decreased Bcl-xl,Bok and Bad expression, while increasing Bcl-2, p-Bcl-2, Bax, and Bim expression. AC decreased Bclxl,Bok and Bax expression, increased Bcl-2 andBim without affecting p-Bcl-2 and Bad expression.BC decreased Bok expression, increased Bax and-Bim expression while showing no effect on Bcl-xl,Bcl-2, p-Bcl-2 and Bad expression. ABC decreasedBcl-xl, increased Bax and Bim without affectingBcl-2, p-Bcl-2, Bok, and Bad expression .AC and BC decreased caspase-9 expression while Cand AC increased cleaved caspase-9 expression. It isinteresting to note that B, C, AB, AC, BC ABC couldsignificantly increase PARP expression, especially inAC, BC and ABC groups .A, B and C alone or in a combination showedno effect on NF-\u03baB expression. It is interesting tonote that A, B, C alone increased p42/44 MAPKexpression while in a combination showed no effect.A, C, AB, AC, BC, ABC showed no effecton p38 MAPK expression while B decreasedp38MAPK expression .AIDS), malaria and tuberculosis.Mixtures of compounds produced by plants mayprovide important combination therapies and provideclinical efficacy beyond the reach of single compoundbaseddrugs -negative cell line, while the latter is an ER positivecell line. MDA-MB-231 cells also demonstrateddrug resistant characteristics. Present results suggestthat although both cell lines respond equally to thesecompounds, the underlying mechanisms maybe quitedifferent, which needs further study to elucidate.Drug combination therapy, in which two or moreagents interact with multiple targets simultaneously, isconsidered a rational and efficient form of pharmacotherapydesigned to control complex diseases such ascancer . The fixeddrugs . The appeddrugs . Furthereddrugs , 5.Howeeddrugs -27. Littwenyujin. The MTT\u0394\u03c8m, an early marker for apoptosis. A and B alone or ina combination did not affect \u0394\u03c8m while C significantlydecreased \u0394\u03c8m suggesting that C might induce apoptosis.This was consistent with previous observationsin HL-60 cells (\u0394\u03c8m (\u0394\u03c8m and proliferation.Actually, our study showed that less than 50 \u03bcM Aexhibit no significant cytotoxic effect on breast cancercells (Morphological observations demonstrated similarresults. JC-1 staining is a common method to study the60 cells . Our reclls (\u0394\u03c8m , 18. Theercells . Althougercells , 29, no To further confirm the interactions among A, Band C at the molecular level, some apoptotic-relatedproteins and several key signaling molecularwere determined. Results demonstrated that A, Band C alone showed complex effects on the expressionof Bcl-2 family proteins. For example, Cincreased the anti-apoptotic protein Bcl-2 and thepro-apoptotic protein Bax, Bim at the same time.Also, it decreased Bok but increased the Bim protein,two other pro-apoptotic Bcl-2 proteins ,31. TheCurcuma WenyujinY.H. ChenetC Ling namely germacrone, curdione, and furanodiene.Therefore, intra-herb drug interactions should betaken into consideration when attempts are made tointerpret the art of traditional medicines.Taken together, the present study provides evidencethat there are complicated interactions among thethree components of"} +{"text": "Due to an error introduced during the production process, the word \"Growth\" was misspelled in the article title. The correct title is: Exogenous Amino Acids Are Essential for Interleukin-7 Induced CD8 T Cell Growth. The correct citation is: Pearson C, Silva A, Seddon B (2012) Exogenous Amino Acids Are Essential for Interleukin-7 Induced CD8 T Cell Growth. PLoS ONE 7(4): e33998. doi:10.1371/journal.pone.0033998"} +{"text": "Acinetobacter baumannii clinical strains belonging to sequence types ST-208 and ST-218 are reported in this study. They were isolated from tracheobronchial aspirate of mechanically ventilated adult patients admitted to the intensive care unit of a Spanish tertiary hospital during 2010 to 2011.The draft genome sequences of seven multidrug-resistant Acinetobacter baumannii is among the leading etiologies of hospital-acquired infections, particularly in critically ill patients isolated from tracheobronchial aspirates. Whole-genome sequencing was performed using the Illumina MiSeq platform with 300 bp paired-end reads, resulting in mean genome coverage of 25.2 \u00b1 5.5-fold (mean \u00b1 SD of the 7 strains). Reads were preprocessed with Trimmomatic v0.32 (http://www.usadellab.org/cms/?page=trimmomatic) (de novo assembled with ABySS assembler v1.5.2 (http://www.bcgsc.ca/platform/bioinfo/software/abyss) and RAST server v1.0 (http://rast.nmpdr.org) (https://cge.cbs.dtu.dk/services/MLST/) (https://cge.cbs.dtu.dk/services/ResFinder/) (aac(6\u2032)-II, strB, and strA, were detected in pulsotype 1 strains, while pulsotype 2 strains carry aac(3)-Ia, aadA1, strB, and strA genes, and pulsotype 3 strains carry aac(6\u2032)-II, aac(3)-IIa, strB, and strA genes. Resistance genes blaOXA-58, blaOXA-66, and blaADC-25, which confer \u03b2-lactam resistance, were found in strains from pulsotypes 1 and 2; nevertheless, pulsotype 3 strains carry blaOXA-109 and blaADC-25 genes. Referring to sulfonamide resistance, all the strains have sul1 gene, and strains from pulsotypes 1 and 2 also possess sul2 gene. The gene tet(B), related with tetracycline resistance, was found in all the strains. Furthermore, point mutations in genes associated with quinolone resistance were found in all the strains using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) , resultis/MLST/) , 7. MostLIWE00000000 (AbMDR-GLH1), LIZZ00000000 (AbMDR-GLH2), LJAA00000000 (AbMDR-GLH3), LJAB00000000 (AbMDR-GLH4), LJAC00000000 (AbMDR-GLH5), LJAD00000000 (AbMDR-GLH6), and LJAF00000000 (AbMDR-GLH8). The versions described in this report are the first versions, LIWE01000000, LIZZ01000000, LJAA01000000, LJAB01000000, LJAC01000000, LJAD01000000, and LJAF01000000.These whole-genome shotgun (WGS) projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers"} +{"text": "AbstractVigna subg. Ceratotropis (Piper) Verdc. represents a homogenous and distinct group of species with highly specialized complex floral characters. It is most diverse in Asia. India, with 24 species, represents a secondary center of species diversity of the subgenus.Vignapandeyana RD Gore, SP Gaikwad & SD Randive, is described from hill slopes of the northern Western Ghats of India. It resembles Vignayadavii Gaikwad et al. and Vignadalzelliana (Kuntze) Verdc. but differs from the latter in its dimorphic shoots and densely hairy pods, from the former by its curved style, flattened style beak, foveolate seed coat and absence of standard protuberance and horn-like keel pocket in cleistogamous flowers.A new species, Vigna Savi of the tribe Phaseoleae comprises about 90 species distributed in six subgenera (Vignasubg.Ceratotropis (Piper) Verdc. has its center of species diversity in Asia and is popularly known as Asian Vigna Verdc. Verdc. . MoreoveVigna on the hill slopes near Chalkewadi in Satara district of the Maharashtra State of India which has unusual dimorphic shoots and cleistogamous flowers. It was recollected in the subsequent two years for further studies of its vegetative and floral characters. Initially, the new species was confused with Vignayadavii Gaikwad et al., as both hold cleistogamous flowers. However, a critical study of floral structures, seeds, seed coat and type of seed germination have revealed that it represents an undescribed species of Vigna subg. Ceratotropis. This has been confirmed by the perusal of relevant literature .Type status:Other material. Location: continent: Asia; country: India; countryCode: IND; stateProvince: Maharashtra; municipality: Nasik District; locality: Kasara-Ghat near Igatpuri; verbatimElevation: 365 m; verbatimLatitude: 19\u00b041'02.1\"N; verbatimLongitude: 73\u00b029'58.3\"E; Event: eventDate: 10-11-2012; fieldNumber: RD Gore 1042a; fieldNotes: Twining herbs; leaves stipulate; stipules submedifixed; chasmogamous flowers yellow & Cleistogamous flowers white; pods falcate to straight; seeds well developed; Record Level: language: English; institutionID: Botanical Survey of India, Pune (BSI).Type status:Other material. Location: continent: Asia; country: India; countryCode: IND; stateProvince: Maharashtra; municipality: Nasik District; locality: Kasara-Ghat near Igatpuri; Identification: identifiedBy: SP Gaikwad & RD Gore; Event: eventDate: 10-11-2012; fieldNumber: SD Randive 322; fieldNotes: Twining herbs; flowers yellow; pods slightly hairy; Record Level: institutionID: Herbarium of Walchand College of Arts & Science, Solapur (WCAS).Type status:Other material. Location: continent: Asia; country: India; countryCode: IND; stateProvince: Maharashtra; municipality: Nasik District; locality: Saptshrungi hills ; Identification: identifiedBy: SP Gaikwad & RD Gore; Event: eventDate: 9-11-2012; fieldNumber: RD Gore 1040; fieldNotes: Twining herbs; flowers both chasmogamous (yellow) and cleistogamous ; Record Level: institutionID: Herbarium of Walchand College of Arts & Science, Solapur (WCAS).Type status:Other material. Location: continent: Asia; country: India; countryCode: IND; stateProvince: Maharashtra; municipality: Satara District; locality: Pasarnighat; Identification: identifiedBy: MM Aitawade; Event: eventDate: 21-10-2011; fieldNumber: SP Sutar 156; fieldNotes: Vignasilvestris but differs in pod & seed number; seeds rectangularClosely resembles with ; Record Level: institutionID: Kew herbarium (K); collectionCode: K000978011; source: http://apps.kew.org/herbcat/getImage.do?imageBarcode=K000978011Type status:Other material. Location: continent: Asia; country: India; countryCode: IND; stateProvince: Maharashtra; municipality: Satara District; locality: Pasarnighat; Event: eventDate: 21-10-2011; fieldNumber: SP Sutar 156; fieldNotes: Vignasilvestris but differs in pod & seed number; seeds rectangularClosely resembles with ; Record Level: institutionID: Herbarium of Shivaji University, Kolhapur (SUK).Type status:Other material. Location: continent: Asia; country: India; countryCode: IND; stateProvince: Maharashtra; municipality: Sangli; locality: Dandoba hills; Event: eventDate: 28-09-1989; fieldNumber: AN Londhe 170037; Record Level: institutionID: Botanical Survey of India, Pune (BSI).Chasmogamous flowers: yellow, 2-4 in axillary and terminal pseudo-racemes; peduncle 5-7.5 cm long, densely hairy with whitish-brown, 1-1.5 mm long, retrosely spreading hairs; pedicels 2-2.5 mm long, densely hairy as peduncle; bracts lanceolate, 2.5-3 x 0.8-1 mm, herbaceous, acute at apex, densely hairy; bracteoles 2, linear, 4-4.5 mm long, densely hairy. Calyx campanulate, ca 2 mm long; teeth triangular, 0.2-1.2 x 0.7-1 mm, sparsely hairy along margins. Standard petal yellow, asymmetrical, broadly ovate, 6-6.5 x 7.5-8.5 mm, emarginate at apex, central protuberance present inside (up to 0.9 mm long); claw ca 1 mm long. Right wing concealing the upper portion of the keel petals; claws 0.7-1 mm long; lamina obliquely obovate, 3.5-6.5 x 2.7-3.5 mm, notched at apex. Left wing claws 1-1.2 mm long; lamina obliquely obovate, 4-6.2 x 1.2-4 mm. Keel petals spirally incurved to left, 6-6.5 x 2.5-3.5 mm; horn-like pocket present (1.5-1.7 mm long) on the left side of keel petal. Stamens 9+1, included; staminal tube 4.5-5 mm long; free filament 8-9 mm long; anthers dorsifixed, 0.2-0.3 mm long. Pistil 1.5-1.8 cm long; ovary linear, 2.2-2.4 mm long, densely covered with long whitish hairs; style filiform, 1.2-1.3 cm long, \u2018S\u2019 shaped before stigma, beaked beyond stigma; beak 0.8-1 mm long, upwardly curved at apex. Pods ascending linear, cylindrical, 2-5 x 0.3-0.5 cm, straight or slightly curved, densely covered with brownish, 2-3 mm long spreading hairs, acute at apex. Seeds 4-10 per pod, broadly rectangular, 3-3.1 x 2-2.1 mm, brown, mottled with faint black patches, rounded or rectangular at both ends; seed coat porous with mesh-like reticulation; hilum well developed, rim-aril protruded, elliptic, 1.8-2 x 0.7-0.9 mm, whitish-brown. Germination epigeal; ecophylls petioles, simple and minutely pulvinous. Cleistogamous flowers: 2-5, whitish-yellow on leafless sub-aerial branches which produce on lower nodes of stem; pedicels 1-2 mm long; bracts lanceolate, 5-6 mm long, acute at apex, densely hairy; bracteoles 2, linear, 7-9 mm long, densely covered with 1-3 mm long bulbous based hairs. Calyx as in chasmogamous flowers. Standard petal symmetrical, broadly ovate, 4.5-5 x 5.5-6 mm, emarginate at apex, inside central protuberance absent; claws 0.3-0.5 mm long. Right wing petal slightly concealing the upper portion of the keel petal; claws 0.3-0.5 mm long; lamina obliquely ovate, 4.5-5 x 2-3 mm; auricle 0.1-0.2 mm long. Left wing petal spreading; claws 0.5-0.7 mm long; lamina ovate-elliptic, 4.9-5 x 2-2.7 mm, base oblique; auricle 0.3-0.5 mm long. Keel petals slightly curved, 4.8-5 x 1.5-2.5 mm. Stamens 9+1, dimorphic, out of 9 stamens in a bundle 4 short and 5 long; short stamens sterile with ca 1 mm long filaments, whereas long stamens fertile with ca 2 mm long filaments; staminal tube ca 1.5 mm long; free stamen sterile with ca 2 mm long filament; anthers dorsifixed 0.2-0.6 mm long. Pistil filiform, up to 6.5 mm long; ovary linear, 1.7-2 mm long, glabrescent or sparsely hairy; style filiform, 3-3.5 mm long, curved (not \u2018S\u2019 shaped), densely hairy before stigma with 0.4-0.6 mm long hairs, beaked beyond stigma; beak short, 0.3-0.5 mm long, straight, pointed at apex. Pods linear, cylindrical, straight, 2.5-4 x 0.3-0.4 cm, narrowed at both ends, sparsely hairy with short hairs (0.5 mm long), white hairs. Seeds 8-9 per pod, obliquely rounded, 3.5-4 x 3-3.5 mm, dark brown; seed coat foveolatewith mesh-like reticulation; hilum well developed, protruded, broadly elliptic, 2-2.2 x 0.4-0.7 mm, whitish. Germination epigeal; ecophylls petioles, simple and minutely pulvinous. cm long, densely covered with retrorse or spreading bulbous based hairs; stipules elliptically lanceolate, medifixed, 7-9 mm long, 5-7 nerved, rounded at base, acute at apex, hairy on dorsal surface; stipels 2, linear-lanceolate, 2-3 mm long, acute or acuminate at apex, glabrous. Leaflets membranous, entire; lateral ones obliquely ovate or rhomboid to lanceolate, 2.2-5.5 x 1.5-2.3 cm, obliquely rounded at base, acute or shortly acuminate at apex, sparsely hairy; terminal leaflet ovate or rhomboid-lanceolate, 3-6.4 x 1.2-4 cm, base rounded , apex acute or shortly acuminate, sparsely hairy, margins entire or sometimes wavy; rachis 2-10 mm long, densely covered with whitish hairs. Flowers are of two kinds; the chasmogamous flowers present on leafy aerial shoots while cleistogamous flowers present on leafless subterranean shoots, which are close to soil surface. cm long,August-October.Vignayadavii similis, ramis dimorphis, floribus cleistogamis vexillo sine processo carina sine marsupio corniformi, styli rostro applanato, seminum testa foveolata, hilo bene evoluto differt.The specific epithet honors Prof AK Pandey, Department of Botany, Delhi University, New Delhi (India), in recognition of his valuable contribution to the taxonomy of flowering plants of India.India, Maharashtra, Satara district, near Chalkewadi in Patan tahsil.Carviacallosa (Nees) Bremek., Crotalarianana Burm. f., Crotalariavestita Baker, Cajanuslineatus (Wight & Arn.) Maesen, Eragrostis spp., Pseudarthria spp., Nogradalzellii (Baker) Merr. and Themeda spp.It is a twining annual herb, grows on lateritic gravelly soil on hill slopes amonggrasses and herbs at about 1200 m altitude above mean sea level in Satara district of Maharashtra, India. The species has adapted to the monsoon seasonality. It thrives in humid climate with heavy rainfall during growth season. The seed germination takes place with onset of monsoon rain in the first week of June and the plant completes its life cycle with formation of seeds when rains ceasein mid October. The common associates of the species are Vigna sect. Ceratotropis while cleistogamous floral parts correspond to the species of V. sect. Aconitifoliae of the same subgenus. Thus, it shows a combination of characters of species of both sections. The new species shows morphological similarities with Vignayadavii Gaikwad et al. and Vignadalzelliana (Kuntze) Verdc. but differs in its dimorphic branches, foveolate seed coat and absence of standard protuberance and horn-like keel pocket in cleistogamous flowers. A comparative account between above mentioned three species is given in Table Interestingly, two types of shoots are observed in the species, one a normal aerial leafy shoot and the other subterranean (close to soil surface) leafless shoot producedatthe lower nodes of the stem. The later shoots produce cleistogamous flowers, which remain closed. They show differences in the structure of their floral parts as compared to chasmogamous flowers such as standard petal without central protuberance inside, keel petals without horn-like pocket, curved style and short style beak 0.3-0.5 mm long). Figs , 5, 6\u200b. mm long."} +{"text": "The publisher apologizes for the error. The correct citation is: Mart\u00ednez de Paz A, Sanchez-Mut JV, Samitier-Mart\u00ed M, Petazzi P, S\u00e1ez M, Szczesna K, et al. (2015) Circadian Cycle-Dependent MeCP2 and Brain Chromatin Changes. PLoS ONE 10(4): e0123693. doi:Please download this article again to view the correct version. The originally published, uncorrected article and the republished, corrected article are provided here for reference.S1 File(PDF)Click here for additional data file.S2 File(PDF)Click here for additional data file."} +{"text": "Previous meta-analyses regarding the performance of interferon-gamma release assays (IGRAs) for tuberculosis diagnosis in children yielded contrasting results, probably due to different inclusion/exclusion criteria.vs. high income countries); including only microbiological confirmed TB cases; including only studies performing a simultaneous three-way comparison of the three tests, and including immunocompromised children.We systematically searched PubMed, EMBASE and Cochrane databases and calculated pooled estimates of sensitivities and specificities of QuantiFERON-TB Gold In Tube (QFT-G-IT), T-SPOT.TB, and tuberculin skin test (TST). Several sub-analysis were performed: stratification by background (low income vs. 92%) but not in low income countries (85-93% vs. 90%).Overall, 31 studies (6183 children) for QFT-G-IT, 14 studies (2518 children) for T-SPOT.TB and 34 studies (6439 children) for TST were included in the analyses. In high income countries QFT-G-IT sensitivity was 0.79 (95%IC: 0.75-0.82) considering all the studies, 0.78 (95%CI:0.70-0.84) including only studies performing a simultaneous three-way comparison and 0.86 (95%IC 0.81-0.90) considering only microbiologically confirmed studies. In the same analyses T-SPOT.TB sensitivity was 0.67 (95%IC 0.62-0.73); 0.76 (95%CI: 0.68 to 0.83); and 0.79 (95%IC 0.69-0.87), respectively. In low income countries QFT-G-IT pooled sensitivity was significantly lower: 0.57 (95%IC:0.52-0.61), considering all the studies, and 0.66 (95%IC 0.55-0.76) considering only microbiologically confirmed cases; while T-SPOT.TB sensitivity was 0.61 (95%IC 0.57-0.65) overall, but reached 0.80 (95%IC 0.73-0.86) in microbiologically confirmed cases. In microbiologically confirmed cases TST sensitivity was similar: 0.86 (95%IC 0.79-0.91) in high income countries, and 0.74 (95%IC 0.68-0.80) in low income countries. Higher IGRAs specificity with respect to TST was observed in high income countries (97-98% Both IGRAs showed no better performance than TST in low income countries. Diagnosis of paediatric tuberculosis infection remains a challenging issue. Tuberculin skin test (TST) has several limitations: sensitivity may be influenced by the child\u2019s age and immunologic status, bacille Calmette-Gu\u00e9rin (BCG) vaccination or non-tuberculosis mycobacterium-infections; in case of repeated tests a booster effect can occur and a double access to a health care facility is needed. Nevertheless, infiltrate measurement may be operator-dependent -4. InterMycobacterium tuberculosis antigens, which are absent in BCG and many non-tuberculosis mycobacteria, and displayed similar sensitivity and higher specificity than TST in adults and summarized the results in forest plots. Random-effects meta-analysis was performed using MetaDiSc\u00ae, Meta-analysis of Diagnostic and Screening tests, Version 1.4 . StudiesFor the analysis of sensitivity, 31 studies (20 conducted in high income countries and 11 in low income countries) for QFT-G-IT, including 6183 children -44, 14 sThe specificity analysis included 17 studies, overall including 3844 children (11 conducted in high income countries and 6 in low income countries) using QFT-G-IT ,34,37,43Considering the whole study population, significantly higher sensitivities of QFT-G-IT and TST in high- than in low-income countries were observed, with no difference between them, while T-SPOT.TB sensitivity was particularly low in both settings in high income countries, and 0.57 (95%IC 0.52-0.61) in low income countries, and TST pooled sensitivity was 0.78 (95%IC 0.74-0.82) in high income countries, and 0.67 (95%IC 0.64-0.70) in low income countries.Specificity of the three test was similar in low income countries while both QFT-G-IT and T-SPOT.TB displayed higher specificity than TST in high income countries. In particular, QFT-G-IT specificity was 0.97 (95%IC 0.96-0.98) in high income countries, and 0.85 (95%IC 0.82-0.88) in low income countries. T-SPOT.TB pooled specificity was 0.98 (95%IC 0.96-0.99) in high income countries, and 0.93 (95%IC 0.87-0.96) in low income countries. TST specificity was 0.92 (95%IC 0.89-0.93) in high income countries, and 0.90 (95%IC 0.87-0.92) in low income countries.Data regarding microbiologically confirmed cases were available in 16 studies (11 studies conducted in high income countries and 5 studies conducted in low income countries), overall including 3689 children for QFT-G-T ,37,40,44.In this analysis sensitivity of the three test was similar (0.81 (95%CI: 0.76-0.85) for QFT-G-IT, 0.80 (95%CI: 0.74-0.84) for T-SPOT.TB, and 0.79 (95%CI: 0.75-0.83) for TSTA sub-analysis in studies conducted in high income and low income countries was performed. In high income countries sensitivity of the three test was confirmed to be similar but IGRAs performance in low income countries was suboptimal. QFT-G-IT pooled sensitivity was 0.86 (95%IC: 0.81-0.90) in high income countries but only 0.66 (95%IC: 0.55-0.76) in low income countries. Even when excluding studies including HIV-infected children, QFT-G-IT pooled sensitivity in low income countries reached only 0.68 (95%IC: 0.55-0.76).T-SPOT.TB pooled sensitivity was 0.79 (95%IC: 0.69-0.87) in high income countries, and 0.80 (95%IC 0.73-0.86) in low income countries. TST sensitivity was 0.86 (95%IC 0.79-0.91) in high income countries, and 0.74 (95%IC 0.68-0.80) in low income countries table .Six of the available studies, including 618 children, evaluated all three tests simultaneously in the same children ,23,37,39Overall, 11 studies have assessed utility of IGRAs in paediatric populations including HIV infected children ,50,52-58Complete data for a specific subgroup-analysis were available in four studies ,34,43,50The meta-analytic estimate for sensitivity was very low and similar for QFT-G-IT and T.SPOT.TB: 0.47 (95%CI: 0.38-0.55) for QFT-G-IT and 0.54 (95%CI:0.49-0.59) for TST. The meta-analytic estimate for specificity was not performed since only data from 2 studies were available ,43. MetaSix studies, including 1733 children, included exclusively children aged \u2264 5 years ,42,59,60Debord and colleagues evaluated QFT-G-IT performance restrospectively in 19 French immunocompetent children (median age: 1.52 years) with active tuberculosis . The ratet al. \u2018s study [Although, in general, results in young children were encouraging, a specific meta-analysis for this subjects, could not be performed as complete data were not available in most studies, except for Detjen \u2018s study .vs. 70%). Other authors [vs. microbiologically confirmed TB cases [Data on IGRAs\u2019 performance in children are accumulating. In previous meta-analyses, similarly to data reported in adults, higher IGRA specificity with respect to TST has been reported. However, the reported IGRA sensitivity ranged between 62% and 89% for T-SPOT.TB and 66% and 83% for QFT-G-IT ,5,9-11. authors performefor TST) .Our study is the first paediatric meta-analysis evaluating both QFT-G-IT and T-SPOT.TB performance by setting. Moreover, we were first to present a sub-analysis of studies performing a simultaneous three way comparison using all the tests in the same child, allowing to reduce potential bias due to individual differences.vs. 75%), where T-SPOT.TB seems to have lower sensitivity than the two other tests (67%). However this result was not confirmed including only ascertained cases, with a microbiological confirmation. In this sub-analysis T-SPOT.TB sensitivity reached 80% (95%CI: 59-90) while QFT-G-IT sensitivity decreased, but not significantly, to 66% (95%CI:55-76). This finding suggests caution when interpreting results from studies including probable and ascertained TB cases in children, for possible misdiagnoses.At a first glance, our meta-analytic results showed a higher sensitivity of QFT-G-IT than TST in high income countries (79% vs. 84%).In a further sub-analysis including only studies performing simultaneously the 3 tests, all performed in high income countries, overall including 618 children, no different sensitivity of both IGRAs and TST was observed, while a higher IGRAs specifity was confirmed in children.Click here for file"} +{"text": "This is a report of the complete genome sequences of plaque-selected isolates of each of the four virus strains included in a South African commercial tetravalent African horse sickness attenuated live virus vaccine. Orbivirus, family Reoviridae). The AHSV genome consists of 10 segments of double-stranded RNA (dsRNA) collectively encoding seven structural proteins and four nonstructural proteins (African horse sickness (AHS) is an arthropod-borne equine disease caused by African horse sickness virus (AHSV) and serotype 6 (HS02/75) viruses, which are precursors of the respective AHS-ALV virus strains, are available from GenBank . The pairwise nucleotide sequence identity of AHSV-2/Labstr/ZAF/1998/OBP-252.1 and HS82/61 was 99.536%, while that of AHSV-6/Labstr/ZAF/1998/OBP-252.1 and HS02/75 was 99.350%.P = 7.56 \u00d7 10-156) composed of eight segments likely derived from AHSV7-tVP2 , and the other segments likely derived from HS39/63 (accession numbers KF860011 and KF860013).The genome sequences of the AHSV serotype 7 strain with a truncated VP2 protein (AHSV7-tVP2) from whiP = 2.71 \u00d7 10-282), and the segments encoding VP4 and NS3 likely derived from an AHSV for which whole-genome sequence data are currently not available .The genome sequences of the AHSV serotype 8 (HS10/62) from which AHSV-8/Labstr/ZAF/1998/OBP-252.1 was derived are available from GenBank (accession numbers KF860026 to KF860035). Pairwise nucleotide sequence identity between AHSV-8/Labstr/ZAF/1998/OBP-252.1 and HS10/62 over four of the 10 segments was >99.9%, while that for the remaining segments was between 76.8% and 97.4%. Analysis using RDP4.56 (KT715601 to KT715610, KT715611 to KT715620, KT715621 to KT715630, and KT715631 to KT715640, respectively.The AHSV-2/Labstr/ZAF/1998/OBP-252.1, AHSV-6/Labstr/ZAF/1998/OBP-252.1, AHSV-7/Labstr/ZAF/1998/OBP-252.1, and AHSV-8/Labstr/ZAF/1998/OBP-252.1 sequences have been deposited in GenBank under accession numbers"} +{"text": "The BSC infections increase mortality, complications, hospital stay and the costs. In our setting, BSC is one of the device-associated infections more common. The Alliance for Patient Safety, WHO, launched in 2004, the campaign for the prevention of infection associated to medical care though hand hygiene. The Working Group on Infectious Diseases of the Spanish Society of Intensive Care Medicine and Coronary Units (GTEI-SEMICYUC), developed the National Survey of Nosocomial Infection Surveillance (ENVIN) as a computerized record of the incidence of nosocomial infection for services or intensive care units (ICU). Were selected for monitoring those most serious and frequent nosocomial infections related to instrumentation, including ventilator-associated pneumonia , urinary tract infection associated with urethral catheterization and BSCWe want to show the evolution of BSC: central venous catheter (CVC) and arterial (CA) in our 18-bed unit, after the implementation of BZ program and compare it with spanish data.- Data from ENVIN 01.04.11 / 01.04.2015. 18 ICU beds.Rates: BSC/100 admitted, BSC/CVC-CA. Incidence density (ID): BSC/1000ds,BSC/1000 days CVC-CAN 4198 (patients admitted to ICU), 1659 patients with CVC-CA, 17575 days of stay(ds),11024 days of CVC, CA.- Training and educational campaign were imparted to professionals of our unit andAnesthesiology service (235 people). Some classes were presencial and another were by means of internet. Implementation of protocol for hand washing, technical skills about the insertion of CVC, cleaning and maintenance of catheters.- The main objective of BZ project was to reduce BRC DI < 4 episodes per 1000 CVCdays01.04.11-01.04.12: 3 BSC 0.29/100 admitted, 0.80/CVC-CA, 0.62/1000ds, 0.96/1000days CVC-CA. Germ A. Baumanii 33.33%, P.mirabilis 33.33%, S. Epidermidis33.33%. Sepsis 66.67%01.04.12-01.04.13: 7 BSC. 0.65/100 admitted, 1.61/CVC-CA, 1.42/1000ds, 2.1/1000days CVC-CA. Germ S. Coagulasa negativo (SCN). Severe sepsis 28.57%01.04.13-01.04.14: 5 BSC 0.44/100 admitted, 1.08/CVC-CA, 1.02/1000ds, 1.63/1000days CVC-CA. Germ S. Epidermidis. Sepsis 60%01.04.14-01.04.15: 3 BSC 0.31/100 admitted, 0.78/100 CVC-CA, 0.71/1000 ds,1.07/1000 days CVC-CA. Germ: S. epidermidis. Sepsis 100%.Spain, last year: N = 20799, 1.59/100 admitted, 2.51/100 pat CVC-CA, 2.10/1000 ds,1.69/ 1000 days CVC-CA. Germ S. Epidermidis. Sepsis 64.85%We are below the level of BSC set by the SEMICYUC with fewest BSC than the rest of the country through the implementation of the program BZ. In the last year, we have improved our numbers because the realization of program recommendations has been monitored more intensively since in the previous two years had been a relaxation and thereby increased the numbers of BSC.UCI San Cecilio"} +{"text": "The correct name is: David J. Herren. The correct citation is: Herren DJ, Norman JB, Anderson R, Tremblay ML, Huby A-C, Belin de Chantem\u00e8le EJ (2015) Deletion of Protein Tyrosine Phosphatase 1B (PTP1B) Enhances Endothelial Cyclooxygenase 2 Expression and Protects Mice from Type 1 Diabetes-Induced Endothelial Dysfunction. PLoS ONE 10(5): e0126866. doi:The publisher apologizes for this error, which was introduced during the typesetting process."} +{"text": "A 66-year-old male patient was admitted to the hospital with backache, fatigue, and paraesthesia and spasm in both legs. He had lower extremity numbness and bladder and bowel incontinence. Physical examination revealed the absence of bilateral lower extremity reflexes and lower extremity weakness. Magnetic resonance imaging showed a large mass extending from T8 to T9, fracture of T9, and compression of the spinal cord. Informed consent was obtained.Laboratory results at initial evaluation revealed the following: haemoglobin: 118 g/L, haematocrit: 33.5%, white blood cell count: 6.7x109/L, platelets: 192x109/L, blood urea nitrogen: 7.5 mmol/L, creatinine: 113.1 \u00b5mol/L, calcium: 1.9 mmol/L, total protein: 63 g/L; albumin: 31 g/L; and erythrocyte sedimentation rate: 59 mm/h. Protein studies by nephelometry revealed IgA of 4.25 g/L (reference range: 0.7-4 g/L) and lambda light chain of 3.98 g/L (reference range: 0.9-2.1 g/L). A small monoclonal spike was present upon protein electrophoresis. Urine immunoelectrophoresis documented no monoclonal light chain. Bone marrow aspirate and biopsy were performed and the patient underwent surgical decompression and stabilisation of the thoracic spine. The bone marrow aspirate and biopsy morphology showed infiltration with atypical, multilobated, cleaved, and monocytoid nuclei plasma cells . The biopsy material stained positive with lambda light chain and CD138."} +{"text": "Microcystis aeruginosa is a typical algal bloom-forming cyanobacterium. This report describes the whole-genome sequence of a non-microcystin-producing strain of Microcystis aeruginosa, NIES-44, which was isolated from a Japanese lake. Microcystis aeruginosa is a typical algal bloom-forming cyanobacteria, one of several cyanobacteria known to produce the potent hepatotoxin microcystin and combined into a hybrid assembly with the 454 reads using GS de novo assembler version 2.8 (454 Life Sciences). Gaps between the resultant 375 contigs were closed using NESONI version 0.118 (http://www.vicbioinformatics.com/software.nesoni.shtml) and Platanus version 1.2.1 (http://platanus.bio.titech.ac.jp/platanus-assembler). The draft genome was annotated using the RAST server (http://rast.nmpdr.org/rast.cgi), which predicted protein-coding sequences (CDSs). Whole-genome homology mapping of various strains, including M.\u00a0aeruginosa NIES-44, was performed using Gegenees version 2.2.1 with a paired-end library (400\u00a0bp) and a Roche/454 PE genome sequencer FLX with a mate-paired library (8\u00a0kb). HiSeq reads were assembled M.\u00a0aeruginosa NIES-44 genome comprised 80 contigs (six scaffolds) and had a total length of 4,565,330\u00a0bp and a G+C content of 43.19%. It included 4,790 protein-coding sequences and 47 RNA-coding genes . The annotation revealed that 2,614 CDSs exhibited homology to genes with known functions, and the remaining 2,176 genes were identified as encoding hypothetical proteins of unknown function.The M.\u00a0aeruginosa NIES-44 were 99.73% homologous to those of M. aeruginosa strain NIES-843 (mcy) and nonribosomal peptide synthetase gene clusters. Since M.\u00a0aeruginosa NIES-44 showed 64.69% homology to M.\u00a0aeruginosa TAIHU98, in which mcy gene cluster deficits have been previously reported (M.\u00a0aeruginosa NIES-843 (M.\u00a0aeruginosa NIES-44 has a characteristic gene structure.The 16S rRNA sequences of BBPA00000000 and refers to the first version that is described in this paper.This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number"} +{"text": "High rates of albuminuria are observed among HIV-infected individuals on stable antiretroviral therapy (ART). Though pro-inflammatory and pro-fibrotic responses are described as components of albuminuria in the general population, it is unclear how these responses are associated to albuminuria in ART-treated chronic HIV. We investigated the relationship of monocyte subsets and urine inflammatory and fibrotic biomarkers to albuminuria in ART-treated HIV-infected participants.Cross-sectional analyses were performed on Hawaii Aging with HIV-cardiovascular disease study cohort participants who were required at entry to be \u226540 years old and on ART \u22653 months. Monocyte subpopulations were determined in banked peripheral blood mononuclear cells (PBMC) using multi-parametric flow-cytometry. Entry random urine samples were assessed for albumin-to-creatinine ratios (UACR). Urine samples were measured for inflammatory and fibrotic biomarkers using Luminex technology.low/+CD16++) monocytes were significantly elevated in subjects with albuminuria (p = 0.034) and were correlated to UACR . Elevated non-classical monocyte counts were significant predictors of worsening albuminuria, independent of traditional- and ART-associated risk factors . Urine TGF-\u03b21 and collagen-IV were significantly higher in albuminuric compared to non-albuminuric participants . Urine TGF-\u03b21 was significantly correlated with non-classical monocyte counts .Among 96 HIV-infected subjects with measured UACR , 18 patients (19%) had albuminuria. Non-classical (CD14Alterations in monocyte subpopulations and urine pro-fibrotic factors may play a role in kidney dysfunction during chronic HIV infection and warrants further study. Albuminuria is a strong and independent risk factor for renal and cardiovascular disease among the general and HIV-infected populations \u20137. There++CD16-), intermediate (CD14++CD16+), and non-classical (CD14+/lowCD16++) subsets assessed to have moderately increased albuminuria (UACR 30-300mg/g) with only 2 (11%) having severe albuminuria (UACR >300mg/g). Demographics and clinical parameters are summarized in p <0.05), but not with CD4 T cells (r = 0.070), CD8 T cells (r = 0.150), activated CD8 T cells (r = -0.039), or with classical (r = 0.112), intermediate (r = 0.067), or transitional monocytes (r = 0.127).T cell and monocyte subset percentages and counts were compared between participants with and without albuminuria. Non-classical monocyte counts were significantly elevated in HIV-infected participants with albuminuria as compared to HIV-infected participants without albuminuria . No signp = 0.035, C.I. = 0.001\u20130.033; Hypertension, B = 0.463, p<0.001, C.I. = 0.235\u20130.691; HOMA-IR, B = 0.077, p = 0.010, C.I. = 0.019\u20130.136; Total cholesterol/HDL cholesterol ratio, B = 0.067, p = 0.046, C.I. = 0.001\u20130.132; Current use of Tenofovir, B = 0.215, p = 0.131, C.I. = -0.066\u20130.496; Current use of Ritonavir, B = -0.027, p = 0.827, C.I. = -0.274\u20130.220. We conclude that elevation of non-classical (CD14low/+CD16++) monocytes significantly predict worsening albuminuria in HIV-infected participants on stable ART, independent of traditional- and ART-associated risk factors.We assessed the predictive value of non-classical monocytes in a multivariable linear regression model, adjusting for traditional risk factors of age, hypertension, HOMA-IR, total cholesterol/HDL cholesterol ratio, and ART-associated risk factors of current use of Tenofovir and/or Ritonavir . Univari1 and collagen IV , while IP-10 (r = 0.008), MCP-1 (r = -0.141), IL-18 (r = -0.037), Cystatin C (r = -0.129), TGF-\u03b22 (r = 0.063), TGF-\u03b23 (r = -0.189), collagen IV (r = 0.032), and TIMP-1 (r = 0.029) did not show significant correlations. No correlations were seen between other monocyte subsets or T cell subpopulations and urine inflammatory or fibrotic biomarkers. We also assessed the correlations among the urine inflammatory and fibrotic biomarkers. TGF-\u03b21 strongly correlated with TGF-\u03b22 (r = 0.752) and TIMP-1 (r = 0.424). Furthermore, TGF-\u03b22 correlated with TGF-\u03b23 (r = 0.389), collagen IV (r = 0.617), and TIMP-1 (r = 0.730). Of the urine pro-inflammatory biomarkers, only urine MCP-1 correlated with TGF-\u03b22 (r = 0.520), TGF-\u03b23 (r = 0.362), collagen IV (r = 0.558), and TIMP-1 (r = 0.592).We assessed the correlation between the measured urine inflammatory and fibrotic biomarkers with non-classical monocytes. Urine TGF-\u03b2low/+CD16++) monocytes, independent of traditional and ART-associated risk factors. Treated HIV-infected individuals with albuminuria excrete higher levels of urine TGF-\u03b21 and collagen IV as compared to those without albuminuria, and increased non-classical monocytes are associated with increased urine TGF-\u03b21. Furthermore, urinary levels of TGF-\u03b21 are strongly associated with other urine fibrotic markers. It is important to note that although only 89% of the participants were virally suppressed, when participants with viral loads were excluded, all significant observations stated remained significant.Our study is the first report showing that albuminuria in HIV-infected individuals on stable ART is associated with increased levels of non-classical and intermediate (CD14++CD16+) subsets, are generally characterized as a pro-inflammatory cellular compartment, being potent producers of TNF-\u03b1, IL-6, IL-1\u03b2 and IL-12 [+ monocytes in human inflammatory disease states may mediate further pro-inflammatory responses. Individuals with rheumatoid arthritis have been shown to have significantly higher CD16+ monocytes as compared to healthy controls [CD16nd IL-12 \u201351. Sevecontrols , 53. Elecontrols , 54. NonElevated levels of peripheral non-classical monocytes have also been described in HIV-infected individuals as compared to HIV-uninfected controls , 55, 56.Contrasting studies in the general population have shown non-classical monocytes in humans to play a role in the resolution of inflammation and the differentiation into M2 macrophages that aide in anti-inflammatory and wound healing responses . In myocDuring the resolution of inflammation, an important component of the response is TGF-\u03b2. TGF-\u03b2 is a multi-functional cytokine that regulates many cellular functions, including cellular growth and differentiation . In the This study is limited by its relatively small sample size and the lack of HIV-uninfected controls with measured UACR and phenotyped immunologic cellular subpopulations. However, the strengths of the study are the careful clinical and cardio-metabolic characterizations performed on HIV-infected groups, as well as detailed phenotypes of T cell and monocyte subpopulations and quantification of urine biomarkers that reveal discriminating associations in the HIV-infected group.low/+CD16++) monocytes is associated with worsening albuminuria in HIV-infected individuals on ART. This association is independent of traditional- and ART-associated risk factors of albuminuria. Furthermore, HIV-infected individuals with albuminuria excrete higher levels of urine TGF-\u03b21 and collagen IV as compared to those without albuminuria, and increased non-classical monocytes are associated with increased urine TGF-\u03b21. The role of non-classical monocytes in pro-inflammatory and/or pro-fibrotic responses in the kidney of HIV-infected individuals on ART warrants further study.In conclusion, elevation of non-classical (CD14"} +{"text": "In mice, cryo plus checkpoint blockade facilitates tumor antigen release, T-cell priming, and improved survival . Here, wWomen with ESBC were treated 7-10 days preceding mastectomy with either cryo n=6), single-dose ipi at 10mg/kg (n=6), or cryo+ipi (n=6) , single- and intrCryo+ipi generated greater increases in peripheral Ki67+CD4+ (p=0.05), Ki67+CD8+ (p=0.05), ICOShiCD4+ (p=0.005), and ICOShiCD8+ (p=0.005) cells. The intratumoral T-effector/regulatory ratio was higher following cryo+ipi, but only when Ki67-gated (p=.01). Cryo+ipi generated greater increases in IL-2 (p=.01), IFN\u03b3 (p=.06), and IL-5 (p=.09). Despite negligible intratumoral changes by immunohistochemistry, cryo+ipi generated more high-magnitude (~1000 amplicon) clonal expansions by TCR sequencing (medians: 52 v. 3 clones).Cryo+ipi is associated with potentially favorable immunologic effects. Ki67-gating and TCR sequencing may identify intratumoral changes otherwise undetectable by flow or IHC."} +{"text": "Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing \u03b4-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction. Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B was isolated from groundwater of well FW-101 at The Field Research Center (FRC) at Oak Ridge National Lab (ORNL). The FRC is part of the Y-12 security complex, located in the Bear Creek drainage. ICP-MS analysis of FW-101 groundwater in late 2001 estimated uranium concentrations between 20 and 250\u00a0ppm, and chromium concentrations between 35 and 85\u00a0ppm. Previous studies have demonstrated reduction of nitrate and uranium levels in the subsurface upon bio-stimulation with ethanol at the FRC (1the FRC 13. Duringthe FRC 1.http://www.phrap.com) was used for genome finishing. Genes were identified using Prodigal (The genome was sequenced by 454\u00a0GS FLX Titanium and paired-end Illumina GAii (2\u00a0\u00d7\u00a035\u00a0bp). The pyrosequencing and Illumina reads were assembled using the Newbler (Roche) and Velvet and Desulfovibrio vulgaris (63.3% G+C). The COG predictions categorize 581 of the 3,737 protein-encoding genes as pertaining to information storage and processing, 1,183 as cellular processes, 1,576 as metabolism genes, and 596 as poorly characterized functions. Sequencing detected 2 plasmids of different sizes and G+C content, pFW10101 and pFW10102 .Sequence determination revealed a 4.1-Mb genome with 66.5% G+C content, which is comparable to D. carbinoliphilus D41T. The ANIb values calculated by JSpecies (D. vulgaris Miyazaki (69.11%), D. vulgaris Hildenborough (67.45%), and D. vulgaris DP4 (67.41%) than Syntrophobacter fumaroxidans (64.68) and Desulfovibrio desulfuricans ATCC 27774 (60.93%). The small-subunit (SSU) rRNA gene and sulfite reductase gene (dsrAB) of FW-101-2B was most similar to D.\u00a0carbinoliphilus D41T at 99% and 92% similarity, respectively.FW-101-2B was most closely related to JSpecies showed tD. carbinoliphilus D41T, physiological evidence would support classification of a new strain. Thus, we propose the classification as D. carbinoliphilus subsp. oakridgensis. This is the first genome sequence of a D. carbinoliphilus strain.Although FW-101-2B is phylogenetically very similar to ADFE00000000. The version described in this paper is the version ADFE00000000.2.The whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no."} +{"text": "Escherichia coli is an increasing problem especially in developing countries.Antimicrobial resistance among pathogenic E. coli collected from two unrelated geographical areas.To compare between resistance patterns of E. coli (n= 402) collected from hospitals in Khartoum state, Sudan and in Aseer region, Saudi Arabia were studied. Identification and antimicrobial susceptibility testing of isolates were performed following standard methods. Multi-drug resistance (MDR) was defined as non-susceptibility to \u2265 three antimicrobials.A descriptive comparative study was conducted between May 2010 and August 2011. E. coli isolates studied, MDR patterns were significantly higher among isolates from Sudan than Saudi Arabia [92.2% (214/232) vs. 70.6% (120/170)] (p = 0.000). The resistance rates of E. coli isolates were recorded as follows (Sudan and Saudi Arabia): High to moderate resistance to amoxicillin (97.7% and 94.2%), trimethoprim-sulfamethoxazole (88.3% and 82.5%), tetracycline (77.1% and 74.2%), amoxicillin- clavulanic acid (51.4% and 70%), ceftriaxone (64% and 52.4%) and ciprofloxacin (58.4% and 40%). Low resistance was to ceftazidime (35% and 20%), gentamicin (35% and 17.5%) and nitrofurantoin (22.4% and 11.7%). Resistance to amikacin was uncommon (1.9% and 5%). Significant differences (p < 0.05) in resistance rates of isolates between both countries in term to patient\u2019s gender and age. The most frequent MDR phenotypes among isolates were to 7(15.9%) in Khartoum state and to 3(20.8%) in Aseer region.Of the 402 E. coli isolates was observed in both regions. Continuous monitoring of resistance profiles, locally and international surveillance programs are required.Variation and emerging of antimicrobial resistance among pathogenic Escherichia coli is a clinically significant bacterium because they are the most common species recovered in the clinical laboratories and has been incriminated in human infectious diseases phenotypes make wide ranges of antimicrobials usefulness to treat most infections caused by this bacterium as recommended by Clinical Laboratory Standard Institute , against 15 antimicrobial agents from different categories including: amikacin (30 \u03bcg), amoxicillin (10 \u03bcg), amoxicillin-clavulanic acid (30 \u03bcg), ceftazidime (30 \u03bcg), ceftriaxone (30 \u03bcg) cefuroxime (30 \u03bcg), chloramphenicol (30 \u03bcg), ciprofloxacin (5 \u03bcg), gentamicin (10 \u03bcg), nalidixic acid (30 \u03bcg), nitrofurantoin (50 \u03bcg), ofloxacin (5 \u03bcg), tetracycline (30 \u03bcg), tobramicin (10 \u03bcg) and trimethoprim- sulfamethoxazole (25 \u03bcg) . E. coli isolate was considered non-susceptible to an antimicrobial agent when it tested resistant, intermediate or non-susceptible when using clinical breakpoints as interpretive criteria, provided by the CLSI, (2011). MDR patterns of E. coli isolates were defined as non-susceptibility to at least one agent in three or more antimicrobial categories software. Comparisons of antimicrobial resistance rate of isolates from both countries were done in term of setting, sex and age. The proportions were compared using the Chi-square test. A p-value of less than 0.05 was considered as statistically significant.E. coli isolates were examined for antimicrobial susceptibility testing using double-disk diffusion method against 15 antimicrobial agents from different categories. Out of the 402 E. coli isolates tested for their antimicrobial susceptibility, 334 isolates were characterized as MDR strains from the two geographical regions. The majority of MDR E. coli were recovered from specimens of urine (n = 220) followed by wounds (n = 59) and vaginal swabs (n = 20) with low isolation rates from other specimens were found to be MDR E. coli. These 214 MDR E. coli isolates were obtained from all age groups: 125 (58.4%) were from females and 89 (41.6%) were from males. Of these 214 MDR isolates, 168 (78.5%) were obtained from adult patients, whereas 46 (21.5%) from children.Out of 232 E. coli strains collected from hospitals in Aseer region, Saudi Arabia, MDR E. coli represented 120 (70.6%) of total isolates. These 120 isolates were obtained from females (n = 77) and males (n = 43). Eighty seven (72.5%) of the 120 isolates were from adults, whereas 33 (27.5%) were from children patients.Of the 170 E. coli sourced from Khartoum state, Sudan than that from Aseer region, Saudi Arabia isolates [92.2% (214/232) vs. 70.6% (120/170)] (p = 0.000).The occurrence of MDR patterns was found to be significantly higher among E. coli recovered from clinical specimens of patients in Kartoum state, Sudan and Aseer region, Saudi Arabia. The resistance rates among the strains from both countries were recorded as follows (Sudan and Saudi Arabia): High to moderate resistance rates of isolates were observed in amoxicillin (97.7% and 94.2%), cefuroxime (92.5% and 35.8%), trimethoprim-sulfamethoxazole (88.3% and 82.5%), tetracycline (77.1% and 74.2%), nalidixic acid (72% and 57.5%) ceftriaxone (64%). ciprofloxacin (58.4% and 40%), ofloxacin (55.1% and 38.3%), amoxicillin-clavulanate (51.4% and 70%). Low resistance rates of isolates were observed to ceftazidime (35% and 20%), gentamicin (35% and 17.5%), nitrofurantoin (22.4% and 11.7%), chloramphenicol (18.2% and 18.3%), and tobramicin (18.2% and 29.2%). Resistance to amikacin was uncommon (1.9% and 5%).E. coli isolates collected from Khartoum state, when compared to those from Aseer region. Strains from Khartoum state were more resistant to ceftazidime, ceftriaxone, cefuroxime, ciprofloxacin, gentamicin, nalidixic acid, nitrofurantoin and ofloxacin, whereas isolates fromAseer region were more resistant to amoxicillin-clavulanic acid and tobramicin. In general, Sudan sourced strains were more resistant to antimicrobial agents than those from Saudi Arabia.As shown in E. coli strains recovered from male patients in Khartoum state, Sudan and Aseer region, Saudi Arabia. Higher percentage of resistance was reported among isolates from males in Khartoum state than those from Aseer region for ceftriaxone (p < 0.001), cefuroxime (p < 0.001), gentamicin (p = 0.002), nitrofurantoin (p = 0.037), trimethoprim-sulfamethoxazole (p = 0.001). In contrast, higher resistance rates among isolates from Aseer region were observed for amoxicillin-clavulanic acid (p < 0.001) and tobramicin (p = 0.003).E. coli isolates recovered from female patients in Khartoum state to those fromAseer region of antimicrobial drugs. Among the isolates collected from Khartoum state, Sudan the most prevalent MDR phenotypes were to 7 (15.9%), followed by 8 (11.7%) of tested antimicrobial agents. While among the strains originated from Saudi Arabia, the most frequent MDR patterns were to 3 (20.8%) followed by 5 (13.3%) and 4 (15.8%) of antimicrobial agents.The most frequent resistance profiles among Sudan strains were: AML-AMC-CXM-CRO-CAZ- CIP-OFX-NA-SXT-TE (8 strains) followed by AML-CXM-CRO-CAZ-CIP-OFX-NA-SXT-TE and AML-CXM-SXT-TE (7 strains), AML-CXM-CRO-CAZ-CIP-OFX-NA-SXT-TE-GN-TOB and AML-CXM- CRO-CAZ-F-SXT-C (6 strains each). Among Saudi Arabia strains, the predominant resistance profiles were: AML-SXT-TE (12 strains), AML-AMC-CXM-CRO-CAZ-CIP-OFX-NA-SXT-TE-TOB (10 strains), AML-AMC -SXT-TE (8 strains) and AML-AMC-NA-SXT-TE (6 strains).E. coli isolates recovered from two different unrelated geographical areas of Khartoum state in Sudan and Aseer region in Saudi Arabia. Antimicrobial resistance rates vary among regions and countries, with increasing rates in the many parts of the world when comparing to a survey done in Sudan in the year 2000 in which MDR were recorded as 58% among in Sudan , Saudi Ain Sudan , other din Sudan and devein Sudan . The higin Sudan .E. coli isolates non-susceptible to fluoroquinolones have been reported in many countries as in Thailand (>50%), China (\u226570%) and India (>80%) . In the esistant . The higesistant . Also, pE. coli strains collected from Sudan than Saudi Arabia for ceftriaxone (64% vs. 31.7%) (p< 0.001) and ceftazidime (35% vs. 20%) (p = 0.004). In a study carried out at two hospitals in Makka city, Saudi Arabia, resistance rates of E. coli isolates were recorded as 36.2 % for cefuroxime, 24.6 % for ceftazidime and 18.3% for ceftriaxone , trimethoprim-sulfamethoxazole (94.4% vs. 74.4%) and gentamicin (38.2% vs. 11.6%) whereas, higher resistance to amoxicillin-clavulanic acid and tobramicin were observed in Saudi Arabia sourced strains than that from Sudan . These figures are indication of variations in resistance patterns in both countries with relatively higher rates in Sudan. The possible explanation is that this could be due to differences in prescribing patterns, types and quality of antimicrobial agents, as well as availability of drugs. Or perhaps due to better control strategies in the use of antimicrobial drugs, monitoring of resistance levels and updating prescribing policies in Saudi hospitals than in Sudan. This study indicated that there were higher significant differences in resistance levels of The common MDR phenotypes in our isolates were between amoxicillin/trimethoprim-sulfamethoxazole/cefuroxime/tetracycline/or nalidixic acid/amoxicillin-clavulanic acid. In the early study of antimicrobial resistance in bacterial isolates from patients with diarrhea and urinary tract infection in the Sudan, the most common MDR profile of isolates was reported to ampicillin, amoxicillin, tetracycline, trimethoprim-sulfamethoxazole, sulfonamide, and chloramphenicol . LikewisE. coli isolates is alarming and emerging in the both regions of Khartoum state, Sudan as well as in Aseer, Saudi Arabia, with different kinds of resistance patterns. Such high rates of resistance among isolates might be due to misuse and unnecessary prescription of antimicrobial drugs in both countries. Continuous monitoring and updating of antimicrobial resistance profile data as well as hospital policy for restriction and prudent use of antimicrobial drugs can reduce the spread of MDR strains. Antimicrobial resistance varied between settings, population and countries therefore, local and international surveillance programs in each region and setting are required.The study concluded that antimicrobial resistance of pathogenic"} +{"text": "A reader noted a number of issues with Figure 1. The figure legend was:10.1096/fj.09-136481; Figure 1D, rotated) and Sallustio et al. Kidney International (2013) . Panels D and J from the PLOS ONE paper are identical to Figure 1D of Sallustio et al. Kidney International (2013), though flipped (doi:10.1038/ki.2012.413).Figure 1 panels D, E, & F come from the same original images as panels J, K, & L (representing glomerular ARPC cells), respectively. Between E & K, there is a small overlap. Between panels D & J and F & L, respectively, the images have been rotated and there is a large overlap. Panels F and L are identical to panels in Sallustio et al. FASEB Journal (2010) , PAX2 (E), BMI-1 (F), and of glomerular ARPCs with Oct-4 (J), PAX2 (K), BMI-1 (L).10.1371/journal.pone.0087496. A correction is also being made to that article.In a subsequent PLOS ONE article, Figure 3 reproduced panels from Figure 1 of this article: Sciancalepore AG, Sallustio F, Girardo S, Gioia Passione L, Camposeo A, et al. (2014) A Bioartificial Renal Tubule Device Embedding Human Renal Stem/Progenitor Cells. PLOS ONE 9(1): e87496. doi:Fig. 1. Characterization of isolated glomerular and tubular ARPCs. Cytofluorimetric and immunofluorescence analysis of tARPCs showed the expression of: CD133 (A), CD24 (B), CD44 (C), Oct-4 (D), PAX2 (E), BMI-1 (F), Cytofluorimetric and immunofluorescence analysis of gARPCs showed the expression of: CD133 (G), CD24 (H), CD44 (I), Oct-4 (J), PAX2 (K), BMI-1 (L). CD106 expression in glomerular (M) and tubular (N) ARPCs. Original view: X63.S1 FileCharacterization of isolated glomerular and tubular ARPCs, showing immunofluorescence of tubular ARPCs with Oct-4 (D), PAX2 (E), BMI-1 (F), and of glomerular ARPCs with Oct-4 (J), PAX2 (K), BMI-1 (L).(ZIP)Click here for additional data file."} +{"text": "Streptococcus dysgalactiae subsp. equisimilis) emerged as human pathogens in the late 1970s. We report here the draft genome sequences of four genetically distinct human strains of GCS-GGS isolated between the 1960s and 1980s. Comparative analysis of these genomes may provide a deeper understanding of GCS-GGS genome and virulence evolution.\u03b2-Hemolytic group C and group G streptococci (GCS-GGS; Streptococcus dysgalactiae subsp. equisimilis can infect humans and other mammals (\u2013Large-colony-forming \u03b2-hemolytic isolates of Lancefield group C and group G Streptococci (GCS-GGS) identified as mammals , 2. GCS mammals \u20135. The tmammals \u2013, 6, 7. Tmammals \u2013, 9. The S. dysgalactiae subsp. equisimilis with 16S rRNA sequencing (GenBank accession numbers KP972460 to KP972463), and the genetic relatedness of the GCS-GGS isolates was determined via multilocus sequence typing (MLST) (GenBank accession numbers KT347549 to KT347565) 11, 12), 12S. dyhttp://www.ncbi.nlm.nih.gov/genome/annotation_prok/) and RASTtk pipelines (Assembled genomes were annotated using NCBI PGAP version 2.1 (rev. 462191) (ipelines in conjuipelines . The 16Sipelines . AutomatThe draft genome sequences have been deposited as whole-genome shotgun projects at DDBJ/EMBL/GenBank under the accession numbers listed in"} +{"text": "To evaluate the effect of surface coils for carotid MR imaging on PET quantification in a clinical simultaneous whole-body PET/MR scanner. A cylindrical phantom was filled with a homogeneous 2L water-FDG mixture at a starting dose of 301.2MBq. Clinical PET/MR and PET/CT systems were used to acquire PET-data without a coil (reference standard) and with two carotid MRI coils . PET-signal attenuation was evaluated with Osirix using 51 (PET/MR) and 37 (PET/CT) circular ROIs. Mean and maximum standardized uptake values (SUVs) were quantified for each ROI. Furthermore, SUVs of PET/MR and PET/CT were compared. For validation, a patient was scanned with an injected dose of 407.7MBq on both a PET/CT and a PET/MR system without a coil and with both coils. PET/MR underestimations were -2.2% (Siemens) and -7.8% (Machnet) for SUVmean, and -1.2% (Siemens) and -3.3% (Machnet) for SUVmax, respectively. For PET/CT, underestimations were -1.3% (Siemens) and -1.4% (Machnet) for SUVmean and -0.5% (both Siemens and Machnet) for SUVmax, respectively using no coil data as reference. Except for PET/CT SUVmax values all differences were significant. SUVs differed significantly between PET/MR and PET/CT with SUVmean values of 0.51-0.55 for PET/MR and 0.68-0.69 for PET/CT, respectively. The patient examination showed that median SUVmean values measured in the carotid arteries decreased from 0.97 without a coil to 0.96 (Siemens) and 0.88 (Machnet). Carotid surface coils do affect attenuation correction in both PET/MR and PET/CT imaging. Furthermore, SUVs differed significantly between PET/MR and PET/CT."} +{"text": "Photobacterium were isolated from bleached coral Madracis decactis (scleractinian) in the remote St Peter & St Archipelago (SPSPA), Mid-Atlantic Ridge, Brazil. Healthy M. decactis specimens were also surveyed, but no strains were related to them. The novel isolates formed a distinct lineage based on the 16S rRNA, recA, and rpoA gene sequences analysis. Their closest phylogenetic neighbours were Photobacterium rosenbergii, P. gaetbulicola, and P. lutimaris, sharing 96.6 to 95.8% 16S rRNA gene sequence similarity. The novel species can be differentiated from the closest neighbours by several phenotypic and chemotaxonomic markers. It grows at pH 11, produces tryptophane deaminase, presents the fatty acid C18:0, but lacks C16:0 iso. The whole cell protein profile, based in MALDI-TOF MS, distinguished the strains of the novel species among each other and from the closest neighbors. In addition, we are releasing the whole genome sequence of the type strain. The name Photobacterium sanctipauli sp. nov. is proposed for this taxon. The G + C content of the type strain A-394T (= LMG27910T = CAIM1892T) is 48.2 mol%.Five novel strains of Photobacterium comprises 26 formally described species were identified as P. phosphoreum, P. damselae and P. mandapamensis and coram corals . P. jeann Brazil , whereasustralia , as welln Brazil . Photobapamensis . Coral mpamensis .Madracis decactis in the Brazilian St Peter & St Paul Archipelago (SPSPA) analyzed 403 isolates , and RNA polymerase alpha subunit (rpoA) were obtained as described previously (\u00ae). Through this method, the DNA was simultaneously fragmented and tagged with sequencing adapters. The library size distribution was accessed using the 2100 Bioanalyzer and the High Sensitivity DNA Kit (Agilent\u00ae). The accurate quantification of the library was accomplished using the 7500 Real Time PCR (Applied Biosystems\u00ae) and the KAPA Library Quantification Kit (Kapabiosystems\u00ae). Paired-end (2 \u00d7250 bp) sequencing was performed on a MiSeq (Illumina\u00ae) using the MiSeq reagent kit v2 (500 cycles). R1 and R2 reads were quality filtered (Q > 20) and 3\u2019 end trimmed with Prinseq v0.20.4 . The gene sequence data obtained in this study are available through the open access website TAXVIBRIO (http://www.taxvibrio.lncc.br/). The GenBank accession numbers for the 16S rRNA, recA, and rpoA genes and genome sequences are listed in \u00ae). Spectra were generated with mMass software v5.5.0 as described previously medium at ambient temperature (\u223c27 \u00b0C) after 24\u201348 h incubation . Gene seeviously . Primerseviously . Sequenceviously . Trees weviously . The robeviously . For geneviously was used v0.20.4 . Ray v. rameters . Generalrameters . In siliGGDC 2.0 . This onGGDC 2.0 to generGGDC 2.0 . DDH preGGDC 2.0 with logGGDC 2.0 . StrainsGGDC 2.0 towards e v5.5.0 . Type steviously and by BPhotobacterium confirmed that the isolates formed a distinct lineage related to P. rosenbergii and P. gaetbulicola with their closest neighbours, respectively. These levels of similarity are below the cut-offs determined to define a species of the family Vibrionaceae ranged from 99.8% to 100% based on recA. Their rpoA sequences were identical. Trees based on partial sequences of the housekeeping genes recA (855 bp) and rpoA (969 bp) also confirmed their phylogenetic position in the genus Photobacterium and revealed they constituted a separate branch, clearly indicating that they belong to a new Photobacterium species (T genome are supplied in In silico DDH (%) values between A-394T and P. angustum S14, P. damselae subsp. damselae CIP 102761, P. halotolerans DSM18316, P. leiognathi lrivu.4.1 and P. profundum 3TCK were 21.5 (\u00b12.34), 22.7 (\u00b12.37), 20.3 (\u00b12.31), 21.6 (\u00b12.35) and 20.6 (\u00b12.31) respectively. AAI between A-394T and P. leiognathi lrivu.4.1 CIP 102761 was 75%.16S rRNA gene sequence analysis revealed that the five isolates formed a tight monophyletic branch affiliated to the genus acterium . The fivacterium . P. rosetrarenae and P. m marinum . The phybulicola . The novionaceae . The sim species \u2013S2. Gene18:0, and absence of C16:0 iso (P. rosenbergii (LMG 22223T), P. gaetbulicola (LMG 27839T) and P. lutimaris (LMG 25278T) . MLSA wa 25278T) . Based oPhotobacterium sanctipauli .\u03b2-glucosaminidase, \u03b2-galactosidase and arginine dihydrolase; but negative for lipase (C14), valine arylamidase, cystine arylamidase, trypsin, \u03b1-chemotrypsin, acid phosphatase, \u03b1-galactosidase, \u03b2-glucuronidase, \u03b1-glucosidase, \u03b2-glucosidase, \u03b1-mannosidase, \u03b1-fucosidase, lysine decarboxylase, ornithine decarboxylase, H2S production, urease activity, acetoin production (Voges\u2013Proskauer) and gelatinase. Variable reactions were obtained for esterase (C4) (\u2212), esterase lipase (C8) (\u2212), tryptophane deaminase (w) and indole production (\u2212) . Reduces nitrate to nitrite but not to N2. Positive for fermentation/oxidation of glucose and mannitol but negative for inositol, sorbitol, rhamnose, saccharose, amygdalin and arabinose. Melibiose (+) gave variable reactions. D-Salicin, \u03b1-D-glucose, D-mannose, D-galactose are used as sole energy sources. Does not utilize dextrin, D-raffinose, glycerol, N-acetyl-D-galactosamine, D-glucose-6-PO4, D-aspartic acid, D-serine, gelatin, glycyl-L-proline, L-alanine, L-arginine, L-aspartic acid, L-glutamic acid, L-pyroglutamic acid, L-serine, pectin, L-galactonic acid lactone, mucic acid, quinic acid, D-saccharic acid, p-hydroxy-phenylacetic acid, methyl pyruvate, D-lactic acid methyl ester, citric acid, D-malic acid, bromo-succinic acid, \u03b3-amino-butyric acid, \u03b1-hydroxy-butyric acid, \u03b2-hydroxy-D,L-butyric acid, propionic acid, acetic acid and formic acid. The following reactions are variable within the species: citrate (\u2212), D-maltose (\u2212), D-trehalose (\u2212), D-cellobiose (w), gentiobiose (\u2212), sucrose (\u2212), D-turanose (\u2212), stachyose (\u2212), \u03b1-D-lactose (\u2212), D-melibiose (\u2212), \u03b2-methyl-D-glucoside (\u2212), N-acetyl-D-glucosamine (\u2212), N-acetyl-\u03b2-mannosamine (\u2212), N-acetyl neuraminic acid (\u2212), D-fructose (\u2212), 3-methyl glucose (w), D-fucose (w), L-fucose (w), L-rhamnose (\u2212), inosine (\u2212), D-sorbitol (\u2212), D-mannitol (\u2212), D-arabitol (\u2212), myo-inositol (\u2212), D-glucose-6-PO4 (\u2212), L-histidine (w), D-galacturonic acid (\u2212), D-gluconic acid (\u2212), D-glucuronic acid (\u2212), glucuronamide (w), L-lactic acid (\u2212), \u03b1-keto-glutaric acid (w), L-malic acid (\u2212), tween 40 (\u2212) and acetoacetic acid (w). Does not assimilate any of the substrates included in the API 20 NE system. The most abundant cellular fatty acids are summed feature 3 , C16:0 (21.4%), C18:1\u03c97c (11.6%), C14:0 (5.2%), C12:0 and summed feature 2 , C12:03\u2013OH(2.5%), C17:0 (1.6%), Iso-C17:0 (1.5%), Iso-C15:0 and C17:1\u03c98c (1.1%), and in minor amounts C13:0, C17:1\u03c96c, C18:0 and Unknown 12.484 (0.3\u20130.5%). The G + C content of the type strain (A-394T) is 48.2 mol%. The type strain is A-394T (= LMG 27910T = CAIM 1892T). It was isolated from the tissues of bleached Madracis decactis (Scleractinia) in St Peter & St Paul Archipelago, Brazil. SPSPASt Peter & St Paul ArchipelagoMLSAmultilocus sequence analysisAAIaverage amino acid identityDDHDNA-DNA hybridizationGGDCGenome-To-Genome Distance CalculatorFAMEfatty acid methyl ester analysesMALDI-TOFmatrix-assisted laser desorption/ionization time-of-flightColonies are small, beige, irregular shaped, with smooth and translucent edge and 1\u20132 mm in diameter after 24 h at 28 \u00b0C on MA under aerobic conditions. On TCBS colonies are green, round with a smooth border and 2\u20133 mm in diameter. Cells are small bacilli measuring 2\u20133 \u00b5m in diameter, Gram-negative, motile, facultative anaerobic, oxidase and catalase-positive. Grows well between 20 and 30 \u00b0C but not at 4 and 45 \u00b0C. No growth occurs in the absence of NaCl, but grows well under NaCl concentrations of 1%\u20138% (w/v). Grows at pH 6-11. Positive for alkaline phosphatase, leucine arylamidase, naphtol-AS-BI-phosphohydrolase, N-acetyl-10.7717/peerj.427/supp-1Table S1Upper GenBank accession numbers for the 16S rRNA gene, recA and rpoA housekeeping genes and genome sequences of Photobacterium sanctipauli sp. nov.; and for recA and rpoA of P. gaetbulicola LMG 27839T (data from this study). Lower Accession numbers for the Photobacterium strains\u2019 genomes used for GGD calculation (data publicly available at GenBank).Click here for additional data file.10.7717/peerj.427/supp-2Table S2Photobacterium sanctipauli sp. nov. and source information.Strains of Click here for additional data file.10.7717/peerj.427/supp-3Table S3T (= LMG 27910T = CAIM1892T) genome determined in RAST environment.Statistics and general features of A-394Click here for additional data file.10.7717/peerj.427/supp-4Table S41, P. sanctipauli (range profile of five strains); 2, P. rosenbergii LMG 22223T . The evolutionary distances were computed using the Kimura 2-parameter method. Phylogenetic analyses were conducted in MEGA5. Bootstrap values (>50%) shown are based on 1,000 repetitions. Vibrio maritimus R-40493T was used as outgroup. Bar, 2% estimated sequence divergence.Neighbour-joining phylogenetic tree showing the position of Click here for additional data file.10.7717/peerj.427/supp-7Figure S2P. sanctipauli sp. nov based on rpoA gene sequences (969 bp). The evolutionary distances were computed using the Kimura 2-parameter method. Phylogenetic analyses were conducted in MEGA5. Bootstrap values (>50%) shown are based on 1,000 repetitions. Vibrio maritimus R-40493T was used as outgroup. Bar, 1% estimated sequence divergence.Neighbour-joining phylogenetic tree showing the position of Click here for additional data file.10.7717/peerj.427/supp-8Figure S3A\u2212T394, A-373, A-379, A-397 and A-398) showing they are not clonal. The closely related type strains of P. rosenbergii (LMG 22223T), P. gaetbulicola (LMG 27839T) and P. lutimaris (LMG 25278T) were included in the analysis. The dendrogram was constructed using Pearson correlation coefficient and UPGMA.Comparison of the MALDI-TOF MS fingerprint profiles of the 5 novel strains (Click here for additional data file."} +{"text": "To evaluate CT-morphological features of lung cancers detected in a CT lung cancer screening trial, and to determine the correlation between CT-morphological features and the histopathological diagnosis of screen-detected cancers.197 solid lung cancers (192 participants) detected in all four screening rounds of the Dutch-Belgian randomized lung cancer screening trial (NELSON) were included. CT-morphological features included nodule shape, margin, location, volume, and volume-doubling time (VDT). Based on histopathology, cancers were divided into four groups: adenocarcinoma (N=114), squamous cell carcinoma (N=37), large cell carcinoma (N=28) and neuro-endocrine cancers (N=18). Data were analyzed using ANOVA, Chi-square and Fischer\u2019s exact test.Mean participant age was 61.3 years , and 160/192 (83.3%) were male. In all four histopathologic groups, the majority of cancers had a spherical nodule shape (70.6-95.8%). Margins of malignant nodules were most often lobulated (39.3-45.9%) and spiculated (22.2-35.7%), without statistically significant difference between histopathological groups. Most cancers (63.5%) were located in the upper lobes, adenocarcinomas significantly more often than other types of cancers (p=0.004). Adenocarcinomas had a higher mean VDT than large cell carcinomas . VDTs of other histopathological subgroups did not differ significantly.Only VDT and location in the upper versus lower lobes are associated with histopathological diagnosis of screen-detected lung cancers. No discrimination can be made between different histopathologic cancer types based on CT-morphological features alone."} +{"text": "Combination antiretroviral therapy (cART) may affect vitamin D [25(OH)D], parathyroid hormone (PTH), bone mineral density (BMD) and bone turnover (BT). Reduced BMD and secondary hyperparathyroidism have been reported with tenofovir (TDF). We investigated the associations between TDF and bone markers, especially in 25(OH)D-deficient patients.2) were measured using dual-energy X-ray absorptiometry. BT was assessed by serum type 1 procollagen (P1NP) and carboxy-terminal collagen cross-links (CTX). Mann\u2013Whitney U tests compared serum markers and BT, and t-tests compared BMD according to TDF in all and 25(OH)D-deficient patients.In a single-centre longitudinal study investigating BMD in HIV-positive men, serum 25(OH)D, calcium, phosphate, PTH and alkaline phosphatase (ALP) were measured. Lumbar spine, non-dominant total hip and non-dominant femoral neck BMD years, 94% white ethnicity, 93% MSM, diagnosed HIV positive for median 9.6 years, median CD4 547 cells/\u00b5L, HIV RNA <40 copies/mL in 87% (96% of those on cART). 25(OH)D (nmol/L) was normal (>75), insufficient (50\u201375), deficient (25\u201350) and severely deficient (<25) in 14%, 29%, 50% and 7%, respectively. Of 381 men on cART, 77% were currently on TDF. TDF was not associated with median calcium (p=0.69) or phosphate (p=0.52), but patients had higher median ALP [81 vs. 73 IU/L, p=0.005) compared to non-TDF cART. There was no difference in the association between vitamin D and PTH according to whether someone currently was D deficiency, hyperparathyroidism, reduced BMD or increased BT, although patients on TDF had higher but normal ALP. We found no evidence to support additional monitoring of bone markers in patients on TDF regardless of 25(OH)D status."} +{"text": "Age is considered an independent risk factor for short and long-term mortality of elderly ICU patients, when very elderly (\u226585 years) and mid-elderly (75-84 years) populations are compared to young elderly (65-74 years) ones. However, it is not yet clear if this trend remains when very elderly are compared to mid-elderly populations.a) to compare short and long-term (6-months and 1-year) mortality of mid-elderly to very elderly patients andb) to evaluate the influence of patients' characteristics on mortality.Single center, retrospective, observational study in an 8-bed adult general ICU (January 2011-June 2014). Patients \u226575 years were divided into two age-groups, 75-84 and \u226585 years old. Characteristics on ICU admission were recorded. Patients hospitalized \u226448 hours were excluded. ICU, hospital, 6-months and 1-year after hospital discharge mortality were calculated. Univariate analysis for categorical variables was performed using Pearson\u2019s x2 or Fisher test and Student t-test for continuous data. Multivariate analysis of the time to ICU mortality was calculated using Cox regression model and for hospital, 6-months and 1-year mortality using logistic regression analysis. P value < 0.05 was considered significant.244 patients were included, 195 in the 75-84 and 49 in the \u226585 years group. Mortality rates for the two groups were: ICU, 74/195 (37.9%) vs. 24/49 (49%) (p = 0.08), hospital, 23/121 (19%) vs. 5/25 (20%) (p = 0.90), 6-months, 15/95 (17%) vs. 4/20 (20%) (p = 0.74) and 1-year, 22/80 (27.5%) vs. 7/16 (20%) (p = 0.19), respectively. in multivariable analysis, patients with malignancy as reason for ICU admission had increased ICU mortality risk . Patients with higher APACHE II score on ICU admission had more important 1-year mortality risk .More than one third of our ICU patients were mid- or very elderly. No difference was observed between the two age-groups considering short or long-term mortality. Malignancy as a reason for ICU admission and APACHE II score negatively influenced the ICU and 1-year mortality, respectively."} +{"text": "H. pylori infection. H. pylori stimulate Wnt/\u03b2-catenin pathway by activating oncogenic c-Met and epidermal growth factor receptor (EGFR), or by inhibiting tumor suppressor Runx3 and Trefoil factor 1 (TFF1). H. pylori also trigger Wnt/\u03b2-catenin pathway by recruiting macrophages. Moreover, Wnt/\u03b2-catenin pathway is found involved in H. pylori-induced gastric cancer stem cell generation. Recently, by using gastroids, researchers have further revealed that H. pylori induce gastric epithelial cell proliferation through \u03b2-catenin. These findings indicate that Wnt/\u03b2-catenin is an oncogenic pathway activated by H. pylori. Therefore, this pathway is a potential therapy target for H. pylori-related gastric cancer.A section of gastric cancers presents nuclear \u03b2-catenin accumulation correlated with Wnt/\u03b2-catenin pathway, also called canonical Wnt pathway, is crucial to embryo development and adult tissue homeostasis , 2. AberHelicobacter pylori (H. pylori) infection is a strong risk factor for gastric cancer. The underlying mechanisms include chronic inflammation in gastric mucosa, genetic and epigenetic alterations of tumor suppressor genes, activation of oncogenic signals, and generation of gastric cancer stem cells (CSC) [H. pylori can cause DNA double-strand breaks directly [H. pylori-related gastric carcinogenesis [H. pylori induce gastric epithelial cell epithelial-mesenchymal transition (EMT), and generate potential cancer stem cells [H. pylori also stimulate some oncogenic pathways. Activation of epidermal growth factor receptor (EGFR) can resist H. pylori-induced gastric epithelial cell apoptosis [H. pylori-induced gastric carcinogenesis.) Figure . Chronic (BMDCs) , 10. H. directly , and caudirectly , 13 or bdirectly . Hypermeogenesis . H. pyloem cells , 17. H. poptosis , 19. Mor\u03b2-catenin exon 3 that encodes serine-threonine phosphorylation sites for the GSK3\u03b2 [\u03b2-catenin mutation [APC mutation [APC methylation [Investigations on gastric cancer specimens showed that about 20%\u223c30% gastric cancers presented nuclear \u03b2-catenin accumulation . Some muhe GSK3\u03b2 . These mmutation . In colomutation . Unlike mutation , 24 nor hylation seemed tH. pylori to nuclear \u03b2-catenin accumulation. Nuclear \u03b2-catenin mainly localized in epithelial cells within the proliferative zone in antral glands, and appeared more frequently in H. pylori cytotoxin-associated gene A (CagA)-positive specimens, compared with either CagA-negative or uninfected patients [H. pylori could induce nuclear \u03b2-catenin accumulation in vivo and in vitro [H. pylori promoted gastric epithelial cell proliferation through \u03b2-catenin by using gastroids, three-dimensional organ-like structures [Several studies from a same group demonstrated the attribution of patients . CagA-poin vitro -28. Receructures .H. pylori induced phosphorylation of c-Met and gastric epithelial cell proliferation [H. pylori-induced gastric epithelial cell proliferation and atrophic gastritis [Aberrant activation of c-Met receptor occurred commonly in gastric cancers . Infectiferation , 32. Upoferation , 32. CD4astritis . C-Met-Pastritis . On the astritis . Interesastritis , 36, indH. pylori-related gastric cancer [H. pylori secretory protein HP0175 [H. pylori induced EGFR phosphorylation, and then activated PI3K/Akt pathway [H. pylori infection was expressed in normal gastric mucosa , but free mucosa , 56. In nfection . TFF1 innfection . On the -catenin [It has been well accepted that tumor-associated macrophages (TAMs) promote cancer development. (MCP-1) , 59 or S (MCP-1) in gastr (MCP-1) , 7 . The sup (MCP-1) . Macroph (MCP-1) . These oH. pylori. MiR-101 and miR-320 were inhibited by H. pylori through CagA [H. pylori [H. pylori infection with Wnt/\u03b2-catenin activation in gastric cancer (Table MicroRNAs (miRs) are small noncoding RNAs that can up- or downregulate the expression of oncogenes and tumor suppressors. Some miRs, such as miR-101, mir-124a, miR-203, miR-210 and miR-320, were downregulated by ugh CagA , 65. Hypugh CagA -68. The ugh CagA -73, indi. pylori -76. Thes. pylori -79. The H. pylori may activate Wnt/\u03b2-catenin pathway by affecting Wnt ligands, receptors or antagonists. H. pylori and TNF-\u03b1 could induce Wnt10a and Wnt10b expression in gastric cancer cells [H. pylori infection could also activate Wnt co-receptor LRP6, and result in nuclear \u03b2-catenin accumulation [SFRP4 and SFRP5 methylation was found to be positively correlated with H. pylori infection [H. pylori on these molecules are still unclear.Some evidence indicates that er cells , 81. H. mulation . Secretemulation . Actuallnfection . In addinfection , Wnt7a [nfection , Wnt7b [nfection and Wnt nfection , were alH. pylori colonized stomach gland epithelium, and promoted stem cell-related gene expression and Lgr5(+) stem cell proliferation [H. pylori also induced gastric epithelial cell EMT to generate gastric cancer stem cells, and this process was also via CagA [H. pylori-induced EMT and stem cell generation remain largely unknown. Wnt/\u03b2-catenin pathway was important for gastrointestinal progenitor cell proliferation and differentiation [H. pylori-induced gastric stem cell proliferation [H. pylori induce gastric stem cell generation and proliferation at least partly via Wnt/\u03b2-catenin pathway.Gastric stem cells are implicated in gastric cancer initiation and progression. Via CagA, feration . H. pylovia CagA . The molntiation , 91. Actntiation , 93. Recntiation . Moreoveferation . These fH. pylori in gastric carcinogenesis. H. pylori can upregulate Wnt/\u03b2-catenin activator c-Met and EGFR, and downregulate Wnt/\u03b2-catenin suppressor TFF1 and RUNX3. H. pylori can also activate Wnt/\u03b2-catenin pathway by recruiting tumor-associated macrophages. Importantly, via Wnt/\u03b2-catenin pathway, H. pylori induced gastric stem cell generation and expansion, promoting gastric cancer initiation and progression.Increasing evidence demonstrates Wnt/\u03b2-catenin as a crucial pathway stimulated by H. pylori infection, c-Met, EGFR, TFF1, Runx3, or else? Can dysregulations of these molecules synergize in gastric cancer development? Which virulent factor of H. pylori plays a dominant role in Wnt/\u03b2-catenin activation, CagA, VacA or else? Given the complexities of H. pylori strains and host factors, more work should be done to find the answers. In addition, the effects of H. pylori on Wnt ligands, receptors and antagonists, and the roles of miRs in Wnt/\u03b2-catenin activation in gastric cancer, need to be further investigated.However, there are still some questions need to be answered. Which signal molecule plays a dominant role in Wnt/\u03b2-catenin activation under H. pylori eradication can reduce the risk of gastric cancer, but it can not completely prevent H. pylori-related gastric carcinogenesis. One of the reasons is that the activation of oncogenic pathway, such as Wnt/\u03b2-catenin, has happened before H. pylori eradication.Recently, a series of therapies antagonizing Wnt/\u03b2-catenin pathway have entered clinical trials. As Wnt/\u03b2-catenin pathway is essential for tissue homeostasis, it remains elusive about their clinical efficacy and safety . H. pylo"} +{"text": "Childhood-onset Systemic lupus erythematosus (cLES) is an autoimmune disease with a wide spectrum of clinical manifestations, characterized by periods of activity and remission. Hematological and immunological abnormalities are commonly found. Laboratory evaluation, including the cytokine profile, assists in the diagnosis, determination of disease activity and may predict future damage caused by the disease.To determine the serum levels of Th1 (IL-12), Th2 (IL-6 and IL-10) and Th17 (IL-17) cytokines in cSLE and healthy controls. To evaluate their association whit disease activity, laboratory and treatment features and Mood and anxiety disorders.We included 63 consecutive cSLE patients [median age 18 years (range 11-25)] and 59 healthy controls [median age 20 years (8-33)]. Controls were age and sex-matched to cSLE patients. SLE patients were further assessed for clinical and laboratory SLE manifestations, disease activity [SLE Disease Activity Index (SLEDAI)], damage [Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index (SDI)] and current drug exposures. Total dose of corticosteroids and other immunosuppressant medications used since the onset of disease were calculated by data obtained by careful review of the medical charts.Mood and anxiety disorders were determined through Becks Depression (BDI) and anxiety inventory (BAI). Th1 (IL-12), Th2 (IL-6 and IL-10) and Th17 (IL-17) cytokines levels were measured by ELISA and compared by non-parametric tests.Serum IL-6 (p=0.001), IL-10 (p=0.006), IL-12 (p=0.027) and IL-17 (p=0.0001) levels were increased in cSLE patients when compared to healthy controls. IL-6 levels were significantly increased in patients whit active disease (p=0.008). IL-6 (p=0.032) and IL-12 (p=0.028) levels were significantly increased in patients with active nephritis. We observed that IL-17 was associated with migraine (p=0.045), IL-6 with thrombocytopenia (p=0.022) and IL-12 with the presence of anxiety (p=0.048). No association between cytokine levels and SDI scores or medication was observed.Cytokines play a central role in cSLE, IL-6 is associated with SLEDAI and may be a biomarker of disease activity, Th1 and Th2 responses may play a role in lupus nephritis and Th1 and Th17 may play a role in neuropsychiatric symptoms in cSLE. Longitudinal studies are necessary to confirm their ability to predict SLE related manifestations.K. Peli\u00e7ari: None declared, M. Postal: None declared, R. Barbosa: None declared, N. Sinicato: None declared, F. Peres: None declared, R. Marini: None declared, S. Appenzeller Grant / Research Support from: FAPESP CNPQ"} +{"text": "Bacillus decisifrondis E5HC-32T (DSM 11725T) is a Gram-positive, subterminal spherical spore-forming, strictly aerobic bacterium. Here, we report the 5,613,728-bp genome sequence of B.\u00a0decisifrondis E5HC-32T, which is the first genome information of this species and will provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. T was isolated from soil in Australia and was named as Bacillus decisifrondis sp. nov. .The type strain E5HC-32sp. nov. . Its phyd pH\u00a08.4 . NotablyB.\u00a0decisifrondis E5HC-32T (DSM 11725T) was performed via the Illumina Hiseq 2500 system. Two DNA libraries with insert sizes of 500\u00a0bp were constructed and sequenced. After filtering of the 0.67-Gb raw data, 0.66-Gb of clean data was obtained, providing approximately 100-fold coverage. The reads were assembled via SOAPdenovo software version 2 utilizing GeneMark, Glimmer, and tRNAscan-SE tools (The annotation of the genome was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (SE tools . A totalSE tools .LIYL00000000. The version described in this paper is version LIYL00000000.1.This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no."} +{"text": "Bacillus sp. SM1 strain MCC2138), which was isolated from marine coastal waters and has the ability to degum raw silk fabric as well as Ramie fiber. The genome comprises 1.76\u00a0Mb with a GC content of 34.5%.Reported here is the draft genome sequence of an amylase-, protease-, DNase-, oxidase-, gelatinase-, and catalase-producing, Gram-positive diplobacillus ( It could accumulate Pb, Cr, Ni, Cu, and Co with a 2.0\u00d7 coverage generated on an Illumina platform, totaling 17,69,494\u00a0bp, with a largest contig length of 5,01,909 bp and T server revealedThe important genes contained in the different contigs are as follows: ABC transporter ATP binding protein; redox-sensitive transcriptional regulator (AT-rich DNA binding protein); heat shock protein 60 family cochaperone GroES/GroEL; ATP pyrophosphatase subunit (EC 6.3.5.2); phosphate regulon transcriptional regulatory protein PhoB (SphR) (accession no. LXJX01000001.1); oligopeptide ABC transporter, periplasmic oligopeptide-binding protein OppA/B/C/D/F (TC3.A.1.5.1); hydrolase, tRNA; glycerate kinase (EC2.7.1.31); arginase (EC3.5.3.1); diadenylate cyclase spyDAC; bacterial checkpoint controller DisA with nucleotide-binding domain; phosphoglucosamine mutase ; programmed cell death toxin YdcE and YdcD; outer membrane lipoprotein receptor; Holo (acyl carrier protein) synthase (EC2.7.8.7); UV endonuclease UvdE family; DEAD box ATP-dependent RNA helicase CshA (EC3.6.4.13); t-RNA (accession no. NZ_LXJX01000007.1); ABC transporter permease protein YvcS; ABC transporter ATP-binding protein YvcR; beta-lactamase class A; secreted and spore coat\u2013associated protein 1; chitinase (EC 3.2.1.14); cell-division protein FtsW; microbial collagenase (EC 3.4.24.3); transcriptional regulator, TetR family (accession no. NZ_LXJX01000017.1); cysteine synthase (EC 2.5.1.47); chaperonin (heat shock protein 33); tRNA (Ile) lysidine synthetase (EC 6.3.4.19); AbrB family transcriptional regulator (SpoVT); transcription repair coupling factor; Fin, required for the switch from sigma F to sigma G during sporulation; peptidyl-tRNA hydrolase (EC 3.1.1.29) (accession no. NZ_LXJX01000019.1).LXJX00000000. The version described in this paper is the first version, LXJX01000000.This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number"} +{"text": "AbstractDulichiella pattaniensis is new to science, and Melitalati latiflagella Ren & Andres, 2012 has not been previously reported from Thai Waters. Dulichiella pattaniensis is characterized by male gnathopod 2 distolateral crown with 4 spines; pleonite/urosomite formula 7-7-7-5-6-2; pereopod 5-7 dactylus with 2 accessory spines. This combination of characters has not been recorded previously in the Dulichiella. The characters of the specimens are described and illustrated. All specimens are deposited in the Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Thailand.Two species of melitid amphipod were collected from the Gulf of Thailand. Rotomelita longipropoda Wongkamhaeng et al., 2013 was described. In this study, we describe a new melitid species Dulichiella pattaniensis sp. n., and our observations of Melita latiflagella Ren & Andress, 2012, which has not been previously reported in Thai Waters. Figures and descriptions of both species are provided.Melitid amphipods most commonly occur in coastal and freshwater areas. Thailand has a variety of aqueous habitats including coral reefs, seagrass beds, and mangrove forests, but only one melitid amphipod, , antennaA; , gnathopodG; , headHD; , lower lipLL; , mandibleMD; , maxillaMX; , maxillipedMP; , pereopodP; , pleopodPl; , telsonT; , uropodU; , urosomeUR; , upper lipUL; , rightr; , leftl; , male\u2642; , female\u2640. Specimens of different species were deposited into the Prince of Songkla University Zoological Collection (PSUZC).Amphipods were collected from some settlement plates in an artificial reef in Ban Pak Bang Ta Wa, Pattani Bay and from sediment of Lower Songkhla Lake . The sitStout, 1912http://species-id.net/wiki/DulichiellaPageBreakmales with bunches of long slender setae. Pereopod 7 basis in female fully expanded. Pleonites dorsally serrate. Uropod 3 inner ramus scale-like; outer ramus 4 to 5\u00d7 longer than wide, 2-articulate. Telson deeply cleft, lobes tapering distally to an acute point. Head antDulichiella spinosa Stout, 1912 (type by monotypy).Dulichiella appendiculata Say, 1818; Dulichiella australis Haswell, 1879; Dulichiella celestun Paz-Rios & Ardisson, 2014; Dulichiella cotesi Giles, 1890; Dulichiella cuvettensis Appadoo & Myers, 2005; Dulichiella fresnellii ; Dulichiella guinea Lowry & Springthorpe, 2007; Dulichiella lecroyae Lowry & Springthorpe, 2007; Dulichiella oahu Lowry & Springthorpe, 2007; Dulichiella pacifica Lowry & Springthorpe, 2005; Dulichiella pattaniensis sp. n.; Dulichiella spinosa Stout, 1912 (type species); Dulichiella takedai Tomikawa & Komatsu; Dulichiella terminos Lowry & Springthorpe, 2007; Dulichiella tomioka Lowry & Springthorpe, 2007; Dulichiella tulear Lowry & Springthorpe, 2007.PageBreakhttp://zoobank.org/212F51D8-E32A-4601-9E04-88292FBEB989http://species-id.net/wiki/Dulichiella_pattaniensis6\u00b051'55\"N, 101\u00b010'7\"E), artificial reef , 1 September 2010, Puttapreecha, R., PSUZC-CR-0192. Allotypes, \u2640 collected with holotype; PSUZC-CR-0193; Paratype, collected with holotype ).Holotype. \u2642, THAILAND, Lower Gulf of Thailand, Pattani Bay , flagellum can be 25-articulate . Antenna 2, Antenna 2 setiferous, peduncular article 2 cone gland not reaching end of article 3; article 5 subequal to 4, flagellum 9-articulate.Based on male holotype. Body length 6.3 mm (from tip of rostrum to apex of telson). Upper lip, (labrum) distally rounded. Lower lip, inner lobes well developed, pubescent. Mandible, both similar, left incisor 3 dentates, right incisor 4 dentate; left and right lacinia mobilis armed with 3 and 4 dentates respectively; palp slender with marginal setae, article 1 smooth, article 3 slightly longer than article 2. Maxilla 1, inner plate narrow with 2 apical plumose setae; outer plate with 8 apical serrate robust setae; palp 2-articulate, article 1 with 3 distal setae, article 2 with 4 apical robust setae and 4 apical setae. Maxilla 2, inner plate with mediofacial row of 29 setae and 14 apical plumose setae; outer plate broader than inner plate, distally setose. Maxilliped, inner plate borad, with 6 plumose marginal setae; outer plate margin with 11 conate robust setae, terminal with 4 plumose setae; palp 4-articulate, article 2-3 with marginal setae, article 4 tapering with fine marginal setae.Pereon.PageBreakPageBreakPageBreakPageBreakPageBreakPageBreakPageBreakPageBreakPageBreakPageBreakGnathopod 1 subchelate, smaller than gnathopod 2; coxa anterodistal corner not produced, posteroventral corner notch present, anterior margin straight; length ratio of articles from basis to dactylus 10: 3:4:7:5: 3; basis slender; merus\u2013propodus setose; palm slightly convex, defined by posterodistal corner, without posterodistal robust setae. Gnathopod 2 sexually dimorphic; left and right gnathopods unequal in size; coxa posteroventral corner notch present; (larger) length ratio of article from basis to dactylus 8:1:3:1:10:11; propodus distolateral corner crown with 4 rounded spines, palm straight, posterodistal corner produced, upturned, fit with dactylus; dactylus apically blunt; subchelate; length ratio of article from basis to dactylus 9:3:4:6:6:4; merus with sharp posteroventral spine; carpus subequal to propodus; palm straight, without posteroventral spine. Pereopod 3\u20134 alike. Pereopod 5 basis posterior margin straight, posteroventral corner rounded; carpus and propodus sparsely setose; dactylus unguis anterior margin with accessory spines. Pereopod 6\u20137 alike, basis, merus, carpus, propodus with long marginal setae. Pereopod 6 basis posterior margin straight, minutely castelloserrate; dactylus unguis anterior margin with accessory spines. Pereopod 7 basis posterior margin straight, with posterior margin minutely castelloserrate, posteroventral corner; dactylus unguis anterior margin with accessory spines.Pleon. Pleonite/urosomite dorsal spine formula (7-7-7-5-6-2). Pleonites 1\u20133 with dorsal setae. Epimera 1\u20133 posteroventral margin without spines above posteroventral corner. Epimeron 3 posterior margin smooth, posteroventral corner with strongly produced acute. Urosomite 1 with spine at midline, no medial gape. Urosomite 2 with dorsal setae. Urosomite 3 with dorsal setae, with 2 dorsal spines. Uropod 3 inner ramus scale-like, much shorter than outer ramus; outer ramus much longer (more than 2\u00d7 length) than peduncle, 2-articulate. Telson with dorsal robust setae.Female. . Length, 7.4 mm. Gnathopod 1 coxa 4 anterodistal corner not produced, posteroventral corner notch present, anterior margin excavated. Gnathopod 2 equal, coxa subrectangular, palm crenulated, oblique with setae on margins. Pereopod 7 basis expanded, posterior margin slightly convex.This species is named after the type locality.Dulichiella pattaniensis sp. n., with pleonite/urosome formular of 7-7-7-5-6-2 has only Dulichiella cotesi, Dulichiella oahu, Dulichiella pacifica and Dulichiella tulear that share this characters. This new species can be distinguished from Dulichiella cotesi, Dulichiella oahu and Dulichiella tulear by having male gnathopod 2 (large) with 4 spines on distolateral crown while those three species have 3 spines. Dulichiella pattaniensis differs from Dulichiella pacifica in the following: the male large gnathopod 2 has a fourth spine on its distolateral crown that is not well developed vs. its well-developed fourth set of spines. The male gnathopod 1 has carpus longer than its propodus vs. a carpus subequal to its propodus. Pereopods 3-4 have a dactyli with 2 accessory spines vs. 3-4 dactyli with 1 accessory spine.Dulichiella appendiculata, Dulichiella cuvettensis, Dulichiella celestun, Dulichiella fresnellii, Dulichiella guinea, Dulichiella lecroyae, Dulichiella pacifica and Dulichiella takedai share this distinct character. Dulichiella pattaniensis can be distinguished from amphipods by having pleonite/urosome formular of 7-7-7-5-6-2 while Dulichiella appendiculata, Dulichiella cuvettensis, Dulichiella fresnellii, Dulichiella lecroye and Dulichiella pacifica pleonite/urosome formula 7-7-7-5-4-2, Dulichiella guinea 9-9-7-5-4-2 and Dulichiella celestun 9-9-9-5-6-2. Moreover, Dulichiella pattaniensis differs from Dulichiella cuvettensis, Dulichiella guinea and Dulichiella lecroyae by having 2 accessory spines on pereopods 3-4 dactyli vs. 1 accessory spine. A summary of these distinguishing characters are given in The new species also has four spines on the distolateral crown of the male gnathopod 2. Only 7 species, Ren & Andress, 2012http://species-id.net/wiki/Melita_latiflagella09\u00b018'39.5\"N, 99\u00b046'46.4\"E), 1 Feb 2012, Wongkamhaeng, K. PSUZC-CR-0191. .Lower Gulf of Thailand, Songkhla Lake ."} +{"text": "Hyperoxia is frequently encountered in the intensive care unit (ICU) and during surgical procedures such as coronary artery bypass surgery (CABG). Higher oxygen concentrations intuitively provide a salutary oxygen reserve, but hyperoxia can induce adverse effects such as systemic vasoconstriction, reduction of cardiac output, increased microcirculatory heterogeneity and increased reactive oxygen species production. Previous studies in patients undergoing CABG surgery suggest reduced myocardial damage when avoiding extreme perioperative hyperoxia (>400 mmHg). Here, we compare moderate hyperoxia to near-physiological values.2s from moderate hyperoxia to near-physiological values decreases myocardial damage and organ injury.To investigate whether an oxygenation strategy towards lowering perioperative PaO2 target according to common practice (200-220 mmHg during cardiopulmonary bypass (CPB) and 130-150 mmHg in the ICU) versus a lower PaO2 target . The primary outcome was myocardial damage (CK-MB and Troponin-T), which was determined before surgery, at ICU admission and 2, 6 and 12 hours thereafter.In this single-center, open-label randomized-controlled trial, 50 patients scheduled for elective isolated CABG surgery were allocated to either a PaO2 during CPB was 220 mmHg, IQR (211-233) vs. 157 , respectively. In the ICU, weighted PaO2 was 107 (86-141) vs. 90 . Median maximum values of CK-MB were 25.8\u00b5g/L, IQR (20.3-32.6) vs. 24.9 and of Troponin-T 0.35 \u00b5g/L, IQR (0.30-0.46) vs. 0.42. Areas under the curve (AUC) of CK-MB and 0.30\u00b5g/L/h (0.25-0.44) vs. 0.39 for Troponin-T. Cardiac Index, Systemic Vascular Resistance Index, and serum lactate levels (Lactatemax median 2 mmol/L IQR(1.4-2.6) vs. 2.2) were similar between groups throughout the ICU period.Baseline and surgery characteristics were not different between groups. The mean age of patients was 66 years (SD 8) vs. 68(6), respectively. Mean duration of CPB was 105 minutes (SD 24) vs. 108(28). Weighted PaOIn the present RCT, an oxygenation strategy towards near-physiological arterial oxygen tensions did not reduce myocardial damage in comparison to moderate hyperoxia. On the other hand, conservative oxygen administration did not lead to increased lactate levels.This investigation was supported by grants from ESICM NEXT Start-Up 2014 and ZonMW"} +{"text": "To seek for possible differences in tryptase values during acute anaphylaxis induced by non-steroid anti-inflammatory drugs (NSAID) related to the suspected mechanism (selective vs non-selective reactions).Retrospective review of patients attending the Emergency Department (2009-2013) for a NSAID induced anaphylaxis and with a tryptase determination. Patients were split into 3 groups according to the allergy work-up ResultsSelective reactions (S) were defined by positive skin results and/or negative challenges with other NSAID; non-selective (NS) reactions were defined by the existence of symptoms with several NSAID or after positive challenge results. Those cases who did not comply with the previous conditions were non-conclusive (NC). We analysed: demographics, severity of the episode (Chi Square test), and rate of tryptase higher than 11.4 mcg/l (Chi Square test), median tryptase values and timing of sample obtention .86 patients were included: S group: 36 patients, NS group: 20 patients, and NC: 30 patients. Median ages were 48, 45 and 54 years, respectively. Severity of the episodes: S group: Mild: 22.2%, moderate: 30.6% and severe: 47.2%; NS group: Mild: 30%, moderate: 35% and severe: 35%; NC group: Mild: 16.7%, moderate: 26.7% and severe anaphylaxis: 56.7% (p=0.658). The most frequent eliciting drugs were metamizole , acetic derivatives and propionic acid derivatives . The median of tryptase determinations were: S group: 13.4(2.75-98.6), NS: 12.35(3.85-53.6) and NC: 13.4mcg/l (2.82-57.1) (p=0.856). Median duration of symptoms: S group: 1.5 (0.33-12), NS: 1.75 (0.5-4); NC: 1.5 hours (0.5-6h) (p=0.582).Although there have been reports of differences in tryptase releases during anaphylaxis related to different allergens, we have found no differences among the different patterns of NSAID reactions that may help us to avoid future challenges for diagnostic confirmation."} +{"text": "Rictor to impair mTORC2 activity in mouse mammary epithelia, which decreased Akt phosphorylation, ductal length, secondary branching, cell motility, and cell survival. These effects were recapitulated with a pharmacological dual inhibitor of mTORC1/mTORC2, but not upon genetic disruption of mTORC1 function via Raptor deletion. Surprisingly, Akt re-activation was not sufficient to rescue cell survival or invasion, and modestly increased branching of mTORC2-impaired mammary epithelial cells (MECs) in culture and in vivo. However, another mTORC2 substrate, protein kinase C (PKC)-alpha, fully rescued mTORC2-impaired MEC branching, invasion, and survival, as well as branching morphogenesis in vivo. PKC-alpha-mediated signaling through the small GTPase Rac1 was necessary for mTORC2-dependent mammary epithelial development during puberty, revealing a novel role for Rictor/mTORC2 in MEC survival and motility during branching morphogenesis through a PKC-alpha/Rac1-dependent mechanism.Akt phosphorylation is a major driver of cell survival, motility, and proliferation in development and disease, causing increased interest in upstream regulators of Akt like mTOR complex 2 (mTORC2). We used genetic disruption of The protein kinase mTOR is frequently activated in breast cancers, where it enhances cancer cell growth, survival, and metastastic spread to distant organs. Thus, mTOR is an attractive, clinically relevant molecular target for drugs designed to treat metastatic breast cancers. However, mTOR exists in two distinct complexes, mTORC1 and mTORC2, and the relative roles of each complex have not been elucidated. Moreover, as pathways that regulate normal tissue growth and development are often highjacked to promote cancer, understanding mTOR function in normal mammary epithelial development will likely provide insight into its role in tumor progression. In this study, we assessed the role of mTORC1 and mTORC2 complexes in normal mammary epithelial cell branching, survival, and invasion. Interestingly, while mTORC1 was not required for branching, survival and invasion of mammary epithelial cells, mTORC2 was necessary for these processes in both mouse and human models. Furthermore, we found that mTORC2 exerts its effects primarily through downstream activation of a PKC-alpha-Rac1 signaling axis rather than the more well-studied Akt signaling pathway. Our studies identify a novel role for the mTORC2 complex in mammary morphogenesis, including cell survival and motility, which are relevant to breast cancer progression. Post-natal mammary epithelial morphogenesis is a complex process during which an extensively branched ductal network develops from a rudimentary epithelial bud . Branchimammalian target of rapamycin (mTOR) regulates cellular metabolism, protein and lipid synthesis, cell survival, and cytoskeletal organization, processes that are required for proper mammary morphogenesis. mTOR regulates these processes through phosphorylation of its target substrates, including translation initiation factor 4E (eIF4E)-binding protein 1 (4E-BP1), p70S6 kinase (S6K), Akt, SGK1, and protein kinase C-alpha . For some experiments, cells were maintained for 24 hour in Starvation Media [Growth Media without serum or EGF] prior to stimulation and/or analysis. PKC-alpha inhibitor GO6976 and adenoviral particles were purchased. Cells were incubated with adenoviral particles (5 X 108 particle forming units/ml) for 3\u20135 hours at 37\u00b0C and cells were allowed to recover for 48 hours prior to experimental analysis.MCF10A and MCF10A Rictor2HPO4, 3.5 millimolar NaH2PO4, 7.7 millimolar NaN3, 0.1% bovine serum albumin, 0.2% Triton-X 100, 0.05% Tween-20] and stained with rabbit anti-pan-cytokeratin and AF621-goat anti-rabbit (1:100), counterstained with TO-PRO-3 Iodide (Invitrogen), and imaged using the Vanderbilt Cell Imaging Shared Resource Zeiss LSM 510 confocal microscope and LSM Image Browser software. For E-cadherin staining, the primary antibody used was anti-E-cadherin (BD Transduction Laboratories) and visualized with anti-mouse Alexa 594 secondary antibody . Confocal images of 3D structures were visualized using an LSM 510 META inverted confocal microscope with a 20X/0.75 plan apochromat objective.Matrigel-emdedded organoids cultured on coverslips were fixed 8 minutes in 1:1 methanol:acetone at -20\u00b0C, permeabilized in 0.5% Triton-X 100/PBS for 10 min, blocked , sonicated 10 seconds, and cleared by centrifugation at 4\u00b0C, 13,000 x g for 5 min. Protein concentration was determined using BCA (Pierce). Proteins were separated by SDS-PAGE, transferred to nitrocellulose membranes, blocked in 3% gelatin in TBS-T [Tris-buffered saline, 0.1% Tween-20), incubated in primary antibody overnight and in HRP-conjugated anti-rabbit or anti-mouse for 1 hour, and developed using ECL substrate (Pierce). Antibodies used: alpha-actin ; AKT and S473 P-Akt ; S6 and P-S6 ; Rictor ; Raptor ; Rab11 ; PKC-alpha and T638/641 P-PKC-alpha ; Rac . GST-Pak-PBD effector pulldown assays were performed using reagents from Millipore as per manufacturer\u2019s protocol.Cells and tissues were homogenized in ice-cold lysis buffer [50 millimolar Tris pH 7.4, 100 millimolar NaF, 120 millimolar NaCl, 0.5% NP-40, 100 micromolar NaIn situ TUNEL analysis was performed on paraffin-embedded sections using the ApopTag kit . IHC on paraffin-embedded sections was performed as described previously [Mammary glands were whole-mounted on slides, cleared of adipose, and stained with hematoxylin as described previously . Sectioneviously using: KMethanol-fixed PMECs were probed 1 hour with GST-PBD (Millipore) diluted 1:50 in PBS. GST (lacking PBD) was used as a negative control. Samples were washed then probed with AF488-conjugated anti-GST (1:100), stained with DAPI or AF621-phalloidin, and mounted.5) were added to upper chambers of Matrigel-coated transwells in starvation medium and incubated 5 hours to score migration in response to 10% serum-containing medium in the lower chamber. Filters were swabbed and stained with 0.1% crystal violet, [MECs has been accredited by AAALAC International since 1967 (File #000020). The AAALAC Council on Accreditation's most recent review of VU's program was done in 2011 and resulted in \"Continued Full Accreditation.\u201d Isofluorane was used for anesthesia, as well as euthanasia. For human euthanasia, cervical dislocation was used following isofluorane overdose.S1 FigA. Hematoxylin stained whole mount preparations from 6 week old RictorWT mice and RictorMGKO mice. High magnification panels show irregular ductal tracts and increased staining density in RictorMGKO samples, indicative of multiple cell layers. Data are a representation of 11 independent animals/genotype. B. Hematoxylin stained whole mount preparations from 10 week old wild-type RictorWT mice and RictorMGKO mice show sustained length defects in the ductal tracts of mammary glands lacking Rictor. C. IHC for Ki67 or TUNEL in TEBs from 6 week old wild-type RictorWT mice and RictorMGKO mice. Average percent Ki67 and TUNEL+ nuclei (\u00b1 S.D.) was determined. D. Confocal analysis of primary organoids (PMOs) stained for E-cadherin (red) revealed multiple cell layers in acinar structures and poor lumen formation in Rictor-deficient (RictorFL/FL organoids infected with Ad.Cre) PMOs relative to control PMOs (RictorFL/FL organoids infected with Ad.LacZ), consistent with the phenotype in RictorMGKO epithelium in vivo.(TIF)Click here for additional data file.S2 FigRictorFL/FL mice and infected with Ad.GFP or Ad.Cre. A. Fluorescent imaging of organoids 24 hours post-infection. B. Confocal analysis of WT organoids infected with Ad.GFP. C. Organoids were fixed 10 days post-infection and subjected to immunofluorescent staining using a pan-cytokeratin antibody (red) to confirm epithelial identity and ToPro-3 nuclear marker (blue). While Ad.LacZ-infected RictorFL/FL organoids formed hollow lumens surrounded by an organized epithelial layer, Ad.Cre-infected RictorFL/FL organoids remained rounded and disorganized. Data are a representation of 3 independent organoid isolates. D. MCF10A parental or MCF10A-RictorZFN cells were assessed for invasion through Matrigel-coated transwell filters. The cells remaining in the upper chamber after 24 hours were fixed and stained with either DAPI (blue) or Annexin V-FITC (green). The average percent viable cells (\u00b1 S.D.) left in the upper chamber was quantitated using Image J, Student\u2019s T-test.Primary organoids (PMOs) were isolated from (TIF)Click here for additional data file.S3 FigA-C. PMECs and organoids from RictorFL/FL mice were coinfected with Ad.Cre and either Ad.LacZ or Ad.AktDD. A. Western analysis of PMEC lysates. B. Organoids photographed after 10 days in Matrigel culture. Average number of branches/organoid \u00b1 S.D. (right panel) is shown. N = 7 independent organoid isolates, analyzed in triplicate. Midline values indicate average, whiskers indicate S.D., Student\u2019s T-test. C. Colony size of organoids (\u00b1 S.D.) measured in pixel area. N = 7 independent organoid isolates, analyzed in triplicate, Student\u2019s T-test.(TIF)Click here for additional data file.S4 FigA. Immunofluorescent detection of P-PKC-alpha in mammary gland sections from 6 week old virgin RictorWT and RictorMGKO mice. B.In situ detection of GTP-only control (no PBD) via IF detection of GST-PBD on mammary gland sections from 6-week old mice. C.WT PMECs cultured \u00b1 Rac inhibitor or RictorFL/FL PMECs infected with Ad.LacZ or Ad.Cre were assessed for GTP-bound Rac via IF detection of GST-PBD . D.RictorFL/FL PMECs infected with Ad.Cre or Ad.LacZ were probed with GST-PBD (green) and counterstained with phalloidin (red). Representative images are shown. E.RictorFL/FL PMECs infected with Ad.Cre or Ad.LacZ (\u00b1Ad.caRac1) were analyzed for TUNEL. F. Whole mount analysis of endogenous mammary glands harvested from WT recipient mice.(TIF)Click here for additional data file.S5 FigWT PMECs infected with Ad.LacZ or Ad.caRac1 were grown to confluence (3\u20135 days after infection) then wounded using a P200 pipette tip in the presence of DMSO or rapamycin. Monolayers were imaged after 24 hours and total wounded area (arbitrary units) remaining was measured at 24 hours after wounding. Values shown are the average \u00b1 S.D. N = 6 per time point.(TIF)Click here for additional data file.S6 FigA. Western analysis of whole mammary gland lysates from 10 week old mice. B. IF for CK8, CK14 and ZO-1 in mammary gland sections. C. IHC for Ki67 or TUNEL in TEBs from 6 week old wild-type RaptorWT mice and RaptorMGKO mice. Average percent Ki67+ and TUNEL+ nuclei (\u00b1 S.D.) was determined, Student\u2019s T-test.(TIF)Click here for additional data file."} +{"text": "Cichorium intybus L. (chicory) in acute liver injury. Pathological observation, reactive oxygen species (ROS) detection and measurements of biochemical indexes on mouse models proved hepatic protective effect of Cichorium intybus L. Identification of active compounds in Cichorium intybus L. was executed through several methods including ultra performance liquid chromatography/time of flight mass spectrometry (UPLC-TOF-MS). Similarity ensemble approach (SEA) docking, molecular modeling, molecular docking, and molecular dynamics (MD) simulation were applied in this study to explore possible mechanisms of the hepato-protective potential of Cichorium intybus L. We then analyzed the chemical composition of Cichorium intybus L., and found their key targets. Furthermore, in vitro cytological examination and western blot were used for validating the efficacy of the selected compounds. In silico analysis and western blot together demonstrated that selected compound 10 in Cichorium intybus L. targeted Akt-1 in hepatocytes. Besides, compound 13 targeted both caspase-1 and Akt-1. These small compounds may ameliorate liver injury by acting on their targets, which are related to apoptosis or autophagy. The conclusions above may shed light on the complex molecular mechanisms of Cichorium intybus L. acting on hepatocytes and ameliorating liver injury.This study aimed at investigating the possible mechanisms of hepatic protective activity of Cichorium intybus L. is a perennial herb from the Asteraceae family with both alimentary use and medicinal use. It is 40\u2013100 cm in height, usually with bright blue flowers, rarely white or pink. It has been reported that fresh chicory typically contains 68% inulin, 14% sucrose, 5% cellulose, 6% protein, 4% ash, and 3% other compounds, while dried chicory contains approximately 98% inulin and 2% other compounds + ; 1H-NMR \u03b4: 7.07 , 6.72 , 3.66 , 3.52 ; 13C-NMR \u03b4: 173.1 (C-8), 156.2 (C-4), 129.9 , 124.5 (C-1), 114.9 , 50.9 (C-1\u02b9), 39.5 (C-7).Compound 13: colorless acicular crystal (MeOH); HR-ESI-TOF-MS 153.0549 [M + H]+ ; 1H-NMR \u03b4: 7.00 , 6.67 , 3.46 , 9.27 ; 13C-NMR \u03b4: 176.1 (C-8), 157.4 (C-4), 131.3 , 126.8 (C-1), 116.2 , 41.1 (C-7).Compound http://sea.bkslab.org/) [http://www.geneontology.org) and KEGG Orthology (KO) (http://www.genome.jp/kegg/ko.html) [Target proteins of the small molecule compounds were obtained from the similarity ensemble approach (SEA) (ab.org/) . An assiko.html) ,23,24. Fhttp://www.pdb.org/pdb/home/home.do). Molecular docking was performed using the UCSF DOCK6.5 program , which utilized DOCK algorithm to address rigid body docking by superimposing the ligand on to a negative image of the binding pocket [We selected 2 effective small molecule compounds and 2 proteins as receptors. Before the docking, we downloaded initial three-dimensional geometric co-ordinates of the X-ray crystal structures of compounds and proteins from the Protein Data Bank (PDB) simulations. MD simulation of the complex was carried out with the GROMACS 4.5.4 package 3, and a protease inhibitor cocktail . Following one freeze\u2013thaw cycle, the cell lysates were centrifuged at 10,000\u00d7 g at 4 \u00b0C for 20 min and boiled in sample buffer for 5 min. The proteins were then subjected to SDS\u2013PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) and transferred to a PVDF (polyvinylidene fluoride) membrane using a semi-dry electroblotting system. After blocking with 5% skim milk in PBS, the membranes were incubated with primary antibodies (1:1000 dilution) at 4 \u00b0C overnight. The membranes were then washed with PBS containing 0.05% Tween 20 and incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies (1:5000 dilution) at room temperature for 1 h. After washing, the membranes were soaked in ECL solution for 1 min, according to the manufacturer\u2019s instructions, and exposed to film . Other materials used for protein analyses were purchased from Sigma-Aldrich [The expression levels of the selected target proteins (Akt-1 and caspase-1) in liver tissues were measured by applying western blot. Liver tissues were lysed in a buffer containing 1% Triton X-100, 50 mM Tris (pH 7.5), 10 mM EDTA, 0.02% NaNMO, USA) ,31,32.t-test. p < 0.05 was considered statistically significant.All the presented data and results were confirmed in at least three independent experiments. The data are expressed as means \u00b1 S.D. Statistical comparisons were made by One-way ANOVA and Student\u2019s Cichorium intybus L. and active compounds in Cichorium intybus L. The active compounds ameliorate liver injury by acting on Akt-1 and caspase-1, which are related to apoptosis or autophagy. In summary, our results may shed light on the complex molecular mechanisms of Cichorium intybus L. acting on hepatocytes and ameliorating liver injury.This study demonstrates the hepatic protective effect of"} +{"text": "The oral antihyperglycemic agent metformin was associated with favorable outcome and smaller myocardial infarct size in patients with diabetes undergoing percutaneous coronary interventions (PCI) for ST-segment elevation myocardial infarction (STEMI) , 2. HoweTo determine the effect of chronic metformin treatment on cardiovascular morbidity and mortality in patients with diabetes presenting with STEMI subsequently undergoing PCI.From January 2004 until June 2013, all consecutive critically ill patients undergoing primary PCI for STEMI at the University Medical Center Groningen were included in a registry and 1-year follow-up was obtained. Our primary endpoint consisted of the composite endpoint of myocardial infarction, target vessel and target lesion revascularization, and all-cause mortality (MACE). The secondary endpoint, myocardial infarction size, was estimated using peak levels of creatine kinase (CK), the myocardial band of CK (CK-MB), troponin T, and high-sensitive troponin T (hs-troponin T). The effect of metformin on myocardial infarct size from the 2004-2010 cohort has been reported previously [In total, 4776 consecutive patients underwent primary PCI for STEMI, 719 (15%) diabetic patients were included in the final analysis and 215 (30%) patients used metformin at admission. MACE and mortality rates were 21% and 12% for patients with diabetes, 23% and 19% for metformin patients, 21% and 15% for patients on sulfonylurea, and 30% and 20% for patients on insulin, respectively. Metformin was not associated with reduced risk for MACE (adjusted hazard ratio (aHR): 1.19 0.78-1.81), P = 0.42) or survival benefit (aHR: 0.23 (CI95% 0.80-2.51), P = 0.23) compared to diabetic patients not using metformin. Insulin use was an independent predictor for MACE (aHR 1.73 (CI95% 1.13-2.65), P = 0.01) and all-cause mortality (aHR 1.81 (CI95% 1.03-3.21), P = 0.04). Baseline levels of CK, CK-MB, and hs-troponin T were comparable between both groups. Median (interquartile range) peak levels of CK, CK-MB, and hs-Troponin T were all non-significant lower in the metformin group (table Chronic metformin use in patients presenting with STEMI was associated with smaller infarct-size and not with lower MACE and mortality rates, as compared to other patients with diabetes."} +{"text": "To evaluate whole-body diffusion weighted magnetic resonance imaging (WB-DWI) for staging of women with cancer during pregnancy.Twenty patients diagnosed with cancer during pregnancy underwent WB-DWI additional to conventional imaging in this prospective single centre study. Reproducibility of WB-DWI between 2 readers was evaluated using Cohen\u2019s \u03ba statistics and accuracy was compared to conventional imaging for assessing primary tumour site, nodal metastases and visceral metastases. Histopathology after surgery or biopsy was the primary reference standard.Ten patients had breast cancer, 3 lymphoma, 2 cervical uterine cancer, 1 ovarian borderline tumour, 2 colon cancer, 1 lung cancer and 1 a conjunctival tumour. The WB-DWI readers showed very good agreement for lesion detection, \u03ba = 0.94. With WB-DWI, reader 1 detected 38 of 41 malignant lesions, reader 2 thirty-nine lesions and conventional imaging 27. WB-DWI showed sensitivity of 95% (95% CI: 74-99) for both readers and specificity up to 99% (95% CI: 76-99) compared to 50% sensitivity (95% CI: 28-72) with 100% (95% CI: 97-100) specificity for conventional imaging. For staging distant metastases, WB-DWI sensitivities were 66.7% (95% CI: 13-98) and 100% (95% CI: 40-100) respectively for reader 1 and 2 with specificities of 94.1% (95% CI: 69-99) and 100% (95% CI: 40-100) compared to sensitivity of 33.3% (95% CI: 1.7-87) and specificity of 100% (95% CI: 77-100) for conventional imaging.WB-DWI is feasible for single-step non-invasive imaging based cancer staging during pregnancy showing additional value to conventional imaging procedures for detecting distant and nodal metastases."} +{"text": "Protochlamydia sp. strain HS-T3, an environmental chlamydia. This bacterium is an amoebal endosymbiont, found in Acanthamoeba isolated from a hot spring in Japan. Strain HS-T3 readily grew in mammalian cells at 37\u00b0C, a characteristic not previously reported for environmental chlamydiae.Here, we report the draft genome sequence of high-temperature-adapted Chlamydiae is a bacterial phylum and class comprising obligate intracellular bacteria. Two distinct lineages exist, pathogenic and environmental chlamydiae, and this divergence likely occurred 0.7 to 1.4 billion\u00a0years ago , sexuallindness) , and comindness) . In conteduction . Most eneduction . Howevere, Japan .Protochlamydia HS-T3 was obtained using an Illumina HiSeq 2000 sequencer , with sequencing runs for paired-end sequences. The bacterial DNA libraries were prepared using a TruSeq DNA sample kit (Illumina). The genome was assembled into 34 contigs, ranging in size from 189 to 363,061\u00a0bp, using de novo sequence assembler software (http://rast.nmpdr.org/) (http://www.genome.jp/kegg/) (The draft genome of MBL-EBI) . Gene prdr.org/) , and funp/kegg/) . The seqProtochlamydia sp. HS-T3 was 2,308,589\u00a0bp (2.3\u00a0Mb) with a G+C content of 38.74% and 950-fold genome coverage. The genome sequence contained 2,259 coding sequences, 40 tRNAs, and 2 ribosomal RNAs. Neighbor analysis using RAST revealed that the closest neighbor of Protochlamydia HS-T3 was Protochlamydia amoebophila UWE25 (NC_005861.1) and type III general secretion gene clusters but lacked the genes encoding the type IV secretion system. In addition, 1,139 hypothetical proteins and 8 unknown proteins were identified.The draft genome sequence of 5 NC_00581.1 (6), 05861.1) . SimilarProtochlamydia HS-T3 has been deposited at DDBJ/EMBL/GenBank under the accession numbers BBPT01000001 through BBPT01000034 (34 entries). The version described in this paper is the first version.The draft genome sequence of"} +{"text": "Previous studies have described improvements on lipid parameters when switching from other antiretroviral drugs to tenofovir (TDF) and impairments in lipid profile when discontinuing TDF. \u20133It is This was a randomized, crossover, double-blind, placebo-controlled clinical trial (NCT 01458977). Subjects with HIV-1 RNA <50 copies/mL during at least 6 months on stable DRV/r (800/100 mg QD) or LPV/r (400/100 mg BID) monotherapy, with confirmed fasting total cholesterol \u2265200 or LDL-cholesterol \u2265130 mg/dL and not taking lipid-lowering drugs were randomized to (A) adding TDF/FTCduring 12 weeks followed by 24 weeks without TDF/FTC, or (B) continuing without TDF/FTC for 12 weeks, adding TDF/FTC for 12 weeks and then withdrawing TDF/FTC for 12 additional weeks. Randomization was stratified by DRV/r or LPV/r use at study entry. All subjects received a specific dietary counselling. Primary endpoints were changes in median fasting total, LDL and HDL-cholesterol 12 weeks after TDF/FTC addition. Analyses were performed by ITT.46 subjects with a median age of 43 (40\u201348) years were enrolled in the study: 70% were male, 56% received DRV/r and 44% LPV/r. One subject withdrew the study voluntarily at week 4 and another one interrupted due to diarrhoea at week 24. Treatment with TDF/FTC decreased total, LDL and HDL-cholesterol from 235.9 to 204.9 (p<0.001), 154.7 to 127.6 (p<0.001) and 50.3 to 44.5 mg/dL (p<0.001), respectively. In comparison, total, LDL and HDL-cholesterol levels remained stable during placebo exposure. Week 12 total cholesterol (p<0.001), LDL-cholesterol (p<0.001) and HDL-cholesterol (p=0.011) levels were significantly lower in TDF/FTC versus placebo. Treatment with TDF/FTC reduced the fraction of subjects with abnormal fasting total-cholesterol (\u2265200 mg/dL) from 86.7% to 56.8% (p=0.001) and LDL-cholesterol (\u2265130 mg/dL) from 87.8% to 43.9% (p<0.001), which was not observed with placebo. There were no virological failures, and CD4 and triglyceride levels remained stable regardless of exposure.Coformulated TDF/FTC has an intrinsic lipid-lowering effect, likely attributable to TDF."} +{"text": "In heart failure (HF) alveolar-capillary membrane is abnormal. Surfactant-derived proteins (SPs) and plasma receptor for advanced-glycation-end-products (RAGE) have been proposed as lung damage markers.Eighty-nine chronic HF and 17 healthy subjects were evaluated by echocardiography, blood parameters, carbon monoxide lung diffusion (DLCO) and cardiopulmonary exercise test. We measured immature SP-B, mature SP-B, SP-A, SP-D and RAGE plasma levels.th\u201325th interquartile range) Vs. 11.1 (6.4), p<0.01; SP-A, 29.6 (20.1) Vs. 18.3 (13.5), p\u200a=\u200a0.01; SP-D: 125 (90) Vs. 78 (58), p<0.01]. Immature SP-B, SP-A, SP-D and RAGE values were related to DLCO, peak oxygen consumption, ventilatory efficiency, and brain natriuretic peptide (BNP), whereas plasma mature SP-B was not. The DLCO Vs. immature SP-B correlation was the strongest one. At multivariate analysis, RAGE was associated to age and creatinine, SP-A to DLCO and BNP, SP-D to BNP, mature SP-B to DLCO and creatinine, and immature SP-B only but strongly to DLCO.Immature SP-B (arbitrary units), mature SP-A (ng/ml) and SP-D (ng/ml), but not mature SP-B (ng/ml) and RAGE (pg/ml) levels, were higher in HF than in controls [immature SP-B: 15.6 (13.1, 75Immature SP-B is the most reliable biological marker of alveolar-capillary membrane function in HF. Impairment of respiratory function is part of the chronic heart failure (HF) syndrome, being both lung mechanics and gas exchange altered. In all cases, RAGE and SPs have been linked to alveolar capillary membrane damage, but a comparative evaluation among RAGE and the different SPs available as markers of alveolar capillary membrane damage in HF has not been performed yet. We therefore analyzed the correlation between lung diffusion abnormalities, in terms of carbon monoxide total lung diffusion (DLCO), and RAGE and several SPs in a population of chronic stable HF patients and healthy controls, aiming to identify the ones that better correlates with gas diffusion.We studied HF patients in stable clinical conditions and healthy subjects. Patients belong to a group of individuals regularly followed up at our HF unit and were randomly recruited between February 2012 and November 2012, whereas healthy subjects were hospital staff employees or their relatives with gender and age similar to the HF patients.Study inclusion criteria for HF patients were New York Heart Association functional classes (NYHA) I to IV, echocardiographic evidence of reduced left ventricular systolic function , optimized and individually tailored drug treatment, stable clinical conditions for at least 2 months, capability/willingness to perform a maximal or nearly maximal cardiopulmonary exercise test (CPET). Patients were excluded if they had severe obstructive and/or restrictive lung disease, anemia (hemoglobin <11 g/dL), history and/or documentation of pulmonary embolism, primary valvular heart disease, pulmonary arterial hypertension, pericardial disease, exercise-induced angina, ST changes, severe arrhythmias and significant cerebrovascular, renal, hepatic and hematological disease.At enrolment, demographical and clinical data were collected. Before CPET, in both HF and healthy subjects echocardiographic evaluation, natriuretic peptide B (BNP) and blood samples measurements, standard pulmonary function tests, including DLCO, were performed.1) and lung vital capacity (VC) , and were standardized as percentages of predicted normal values. 1/VC lower than 60% was considered indicative of a severe obstructive ventilatory defect BNP test was performed on UniCel-DxI-800 Access immunoassay with Triage-Biosite reagent . Forced expiratory volume in 1 second . 2), carbon dioxide production (VCO2) and ventilation (VE) were measured breath by breath and reported as average over 20 seconds. All tests were executed and evaluated by 2 expert readers blinded to plasma SPs and RAGE values. The anaerobic threshold (AT) was identified by a standard techniques. 2 was calculated as the slope of the linear relationship between VE and VCO2 from 1 minute after the beginning of loaded exercise to the end of the isocapnic buffering period.A CPET familiarization test was always performed. g for 10 minutes at 4\u00b0C, divided into aliquots and frozen at \u221280\u00b0C until assayed.Fresh blood (5 mL) was drawn into Vacutainer tubes containing citrate 0.129 mol/L as an anticoagulant. Plasma was immediately prepared by means of centrifugation at 1,500\u00d7versus the volume of the total proteins loaded and stained with MemCode. The values were also normalized versus the band volume of pooled plasma, loaded as control on each gel, and they are expressed as arbitrary units (AU). Inter-assay coefficient of variation was 12.1\u00b12.9%.The analysis of the immature forms of SP-B, which is detectable in the 3 predominant forms. with molecular mass ranging from 17 to 42 kDa, was performed by Western blotting on plasma samples, as previously described. The quantitative analysis of the levels of the mature form (8 kDa) of SP-B was performed by an ELISA purchased from Uscn Life Science Inc. . Inter-assay and intra-assay coefficient of variation were 11.6\u00b12.1% and 7.9\u00b11.5%, respectively.Plasma levels of SP-A, SP-D and RAGE were determined using commercially available ELISA kits . Measurements were performed in duplicate and the results were averaged. The intra-assay and inter-assay coefficients of variation for SP-A were <5% and <10%, Limit of Detection (LOD) is 0.16 ng/ml, and cut off level is 1 ng/ml. For SP-D the intra-assay and inter-assay coefficients of variation were <3% and <4%, LOD is 0.01 ng/ml, and cut off level is 1.56 ng/ml. The intra-assay and inter-assay coefficients of variation for RAGE were <6% and <8%, respectively, minimal detectable dose is 4.12 pg/ml, and the cut off level is 78 pg/ml.th percentile\u201325th percentile). Categorical variables were compared with \u03c72 test. Unpaired t-test or non-parametric Mann-Whitney test were used when appropriate for between-group comparison. One-way analysis of variance [ANOVA] followed by Kruskal Wallis test were used to compare data for the non-normally distributed variables.Unless otherwise indicated all data are expressed as means \u00b1 SD. Data with skewed distribution are given as median and interquartile range (752 (\u226515 mL/kg/min and <15 mL/kg/min), median VE vs VCO2 slope (\u226430 and >30), median LVEF (\u226436% and >36%) and median BNP (\u2264160 pg/ml and >160 pg/ml). Finally, given that it is well-reported a possible confounding role of smoke on the alveolar-capillary membrane 2 value and VE/VCO2 slope. To avoid distorted estimates of the effect, Pearson\u2019s correlations were limited to the population with HF. A Bootstrap method, Besides between healthy subjects and HF patients, statistical analysis was also performed by subdividing HF patients according to NYHA class (I\u2013II vs III\u2013IV), median DLCO (\u226580% vs <80%), median peak VO2) and 17 healthy subjects . Active smokers were 30/89 and 7/17 in the HF and control group, respectively. HF etiology was cardiomyopathy due to ischemic coronary disease in 50 cases and not-ischemic in 39 cases. Among HF subjects, 44 were in NYHA class I\u2013II and 45 in class III\u2013IV. The LVEF in HF patients was 36\u00b19%; the median BNP was 160 pg/mL . Treatment in patients with HF included angiotensin-converting enzyme inhibitors in 53 cases (60%), AT1 blockers in 21 cases (24%), \u03b2-blockers in 81 cases (91%), diuretics in 59 cases (66%), antialdosteronic drugs in 43 cases (48%), amiodarone in 37 cases (42%), digoxin in 4 cases (5%), antiplatelet in 59 cases (66%), and anticoagulant in 24 cases (27%).A total of 106 subjects were evaluated: 89 patients with HF levels. Only immature SP-B and mature SP-A were higher in patients with most severe HF considering all the above reported HF severity criteria . VO2ATKG-Oxygen uptake at anaerobic threshold (mL/min/Kg). VEVCO2slope-Ventilatory efficiency. NYHA-New York Heart Association functional class. ISCHAEMIC_ETIOLOGY-. ICD-implantable cardioverter-defibrillator . CRT-cardiac resynchronization therapy . BBLOCK-Betablocker . ACEI-Ace inhibitor . AT1 BLOCK-Angiotensin converting enzyme inhibitors . ANTIALDOSTERONIC-angiotensin type 1 receptor blockers . DIURETIC-. AMIODARONE-. DIGOXIN-. ANTICOAGULANT-. ANTIPLATELET-.PAZIENT ID-Identification number. HF-Heart failure patient . SPBIMMATURE-Immature SPB (AU). SPB-Surfactant protein B (ng/mL). SPA-Surfactant protein A (ng/mL). SPD-Surfactant protein D (ng/mL). RAGE-Plasma receptor for advanced glycation end products (pg/mL). AGE-Age (years). GENDER-. IPERTENSION-. DMII-Diabetes type II . weight-(Kg). height-(cm). BMI-Body mass index (kg/m2). FUMO-smoke . LVEF-Left ventricular ejection fraction (%). Vtd-TeleDiastolic Volume (mL). Vts-TeleSystolic Volume (mL). IM-Mitral insufficiency . severityIM-Mitral insufficiency severity (1\u20134). GradoIT-Tricuspidalic insufficiency severity. TAPSE-Tricuspid annular plane systolic excursion (mm). PAPs-Systolic Pulmonary artery Pressure (mmHg). Hb-Hemoglobin (mg/dL). Crea-Creatinine (mg/dL). Na-Sodium (mmol/L). K-Potassium (mmol/L). Uric acid-(mg/dL). BNP-brain natriuretic petide (pg/mL). VC-Vital Capacity (L). VC_P-Vital Capacity (% of predicted). FVC-forced vital capacity (L). FVC_P-forced vital capacity (%). FEV1-forced expiratory volume in 1 second (L). FEV1_A-forced expiratory volume in 1 second (L). FEV1FVC-FEV1/FVC ratio. Dladj_ass-carbon monoxide lung diffusing capacity (mL/mm Hg/min). Dladj_perc-carbon monoxide lung diffusing capacity (% of predicted). SBPBASAL-Systolic blood pressure (mmHg). DBPBASAL-Diastolic blood pressure (mmHg). HRBASAL-Heart Rate (bpm). LOAD-Load at exercise (watt). QRPICk-Respiratory exchange ratio at peak. sbpPEAK-Systolic blood pressure at peak exercise (mmHg). DBPPEAK-Diastolic blood pressure at peak exercise (mmHg). VO(XLSX)Click here for additional data file."} +{"text": "E. coli (ESBLEc) increased.We conducted an annually bloodstream infection (BSI) survey into hospitals overlapping the Centre France region (2.6 million). Since 2005, the incidence of BSIs associated with ESBL-producing To improve the understanding of the pathway and the determination of the risk factors of ESBLEc-BSIs.For each BSI, were reported patient age, sex, recent hospitalization, living in nursing home, recent antibiotherapy, urinary catheterization, BSI source, death within 7days of diagnosis.BSI isolates were studied: antimicrobial susceptibility, determination of molecular mechanism associated with ESBL-production, genetic diversity of ESBLEc (MLST).E. coli BSI were identified, including 31 ESBLEc . Incidence of community acquired(CA)- and healthcare associated(HCA)-BSI were 0.47/100,000 and 0.040/1,000 PDs, respectively.During the survey , 443 For ESBLEc-CA-BSIs, male/female ratio was 1.4, median age 80, urinary BSI source in 50% of cases, recent antibiotherapy in 33 %. Most ESBLEc were resistant to fluoroquinolones (67%), SXT/TMP (67%). High genetic diversity (8 STs including 4 ST131).For ESBLEc-HCA-BSI, male/female ratio was 0.9, median age 75, urinary BSI source in 63% of cases (recent catheterization in 1/2), recent antibiotherapy in 58%. Most ESBLEC were resistant to fluoroquinolones (79%), SXT/TMP (63%). Low genetic diversity (9 STs including 7 ST131).Among BSI, ESBLEc-BSI were associated with healthcare (p=0.004), long-stay unit (p=0.018), recent antibiotherapy (p=0.002). ESBLEc were associated with resistance to fluoroquinolones, SXT/TMP and genta./tobramycine (p<0.001).Among ESBLEc-BSI, clinical determinants and BSI characteristics similar whatever the clonal group excepted for ST131 associated with long-stay unit (p=0.042).Among ST131-BSI, clinical determinants and BSI characteristics similar for ESBLEc and non ESBLEc excepted median age higher in ESBLEc (80/67).Recent antibiotherapy (and easy spread into long-stay units for ST131): likely the major risk factor for ESBLEc BSI.None declared."} +{"text": "KRAS wild-type and mutant. Prognostic relevance of KRAS genotype was evaluated in patients unfit for FIr-B/FOx, treated with conventional medical treatments. Consecutive MCRC patients not eligible for FIr-B/FOx regimen due to age (\u226575 years) and/or comorbidities were treated with tailored conventional first-line treatments. KRAS codon 12/13 mutations were screened by direct sequencing. Activity and efficacy were evaluated and compared according to medical treatments, age (non-elderly and elderly \u226565 years), comorbidity stage , metastatic extension (liver-limited and other/multiple metastatic), and KRAS genotype, using log-rank. Selected first line treatments were medical in 37 patients (92.5%), and surgical in 3 patients (7.5%). Medical treatment regimens: triplet, 18 (45%); doublet, 15 (37.5%); mono-therapy, 4 (10%). At median follow-up of 8 months, objective response rate (ORR) was 37%, median progression-free survival (PFS) 7 months, liver metastasectomies 8% (liver-limited disease 37.5%), median overall survival (OS) 13 months. Triplet regimens failed to significantly affect clinical outcome, compared to doublet. According to KRAS genotype, ORR, PFS and OS were, respectively: wild-type 50%, 8 months, 13 months; mutant 25%, 6 months, 9 months. KRAS genotype wild-type compared to mutant significantly affected PFS, while not OS. KRAS c.35 G>A mutation (G12D) significantly affected worse PFS and OS compared to wild-type and/or other mutations. KRAS genotype, specifically the c.35 G>A KRAS mutation, may indicate poor prognosis in MCRC patients unfit for intensive medical treatments.First-line triplet chemotherapy plus bevacizumab (FIr-B/FOx) can improve efficacy of metastatic colorectal cancer (MCRC), KRAS genotype faces with different options and lines of treatment according to patients\u2019 fitness , extension of metastatic disease [liver-limited (L-L) or other/multiple metastatic (O/MM)], genotype \u20134. Firstgenotype ,5,6. Morgenotype \u20139.In clinical practice, a decision-making process including functional, nutritional, and co-morbidity status is required to tailor first line medical treatment . ElderlyKRAS mutations occur in 35\u201345% of colorectal cancer (CRC), mostly codon 12 (80%), prevalently c.35 G>A (G12D) transversion (32.5%) , impairi (32.5%) . In the ild-type \u201339; BEV activity ,37.KRAS genotype, depending on differential tumor biological aggressiveness mutant genotype may significantly affect worse OS of MCRC patients treated with FIr-B/FOx, compared to wild-type or different other mutations . Thus, it was not a clinical trial and approval by ethics committee and institutional review board was not necessary, because patients were treated with conventional treatments without any additional medical intervention out of the best common clinical practice. Patients had histological confirmed diagnosis of MCRC, age \u226518 years, PS \u22642. Criteria to define patients unfit, or not eligible for intensive regimens were: age \u226575 years; uncontrolled severe diseases; cardiovascular disease ; thromboembolic disease, coagulopathy, preexisting bleeding diatheses; proteinuria >1 g/24 h. Patients were classified according to Cumulative Illness Rating Scale (CIRS) for administration e (CIRS) . Treatme2/die, over 12 h (from 10:00 pm to 10:00 am), days 1\u20132, 8\u20139, 15\u201316, 22\u201323; CPT-11 , 120\u2013160 mg/m2, days 1 and 15; l-OXP , 70\u201380 mg/m2, days 8 and 22; cycles every 4 weeks. Other triplet, doublet and mono-regimens were administered according to previously reported schedules , associated to weekly alternating CPT-11 or L-OXP : TFI/5-Fchedules ,42. TargKRAS codon 12 and 13 mutations by direct sequencing. KRAS exon 2 sequence was performed from PCR-amplified tumor DNA using the Big Dye V3.1 Terminator kit, electrophoresis in ABI PRISM 3130xl Genetic Analyzer, and analysis using the GeneMapper Analysis software version 4.0 .Genetic analyses were performed on paraffin-embedded tissue blocks from primary tumor and/or metastatic sites, as previously reported . GenotypKRAS genotype on clinical outcomes were evaluated. Patients were classified according to: metastatic extension, L-L and O/MM , 23 (59%) were wild-type and 16 (41%) mutant. Clinical features of the 37 patients who underwent first line medical treatments were , specifically c.35 G>A (G12D), 7 (19.4%), c.35 G>T (G12V), 6 (16.6%); codon 13, 2 (5.5%), c.37 G>T (G13V), 1 (2.7%) and c.38 G>A (G13D), 1 (2.7%).Forty patients unfit for intensive regimens, among 72 consecutive MCRC (56%), were treated with : medicalnts were : male/fents were : non-eldMedical treatments were tailored according to age and CIRS stage. Triplet regimens were administered in 18 patients (49%): non-elderly 6, young-elderly 4, old-elderly 8; CIRS primary 2, intermediate 10, secondary 6. Doublet regimens were administered in 15 patients (40%): non-elderly 3, young-elderly 3, old-elderly 9; CIRS primary 1, intermediate 4, secondary 10. Mono-regimens were administered in 4 patients (11%): young-elderly 1, old-elderly 3; CIRS primary 1, intermediate 1, secondary 2.KRAS wild-type patient (33%), with primary rectal tumor and a single L-L metastasis. Twelve patients (32%) received, at least, a second line treatment.Among the 37 patients who underwent medical treatments, 10 were not evaluable for activity: 7 (19%) did not receive at least 2 cycles of treatment; 3 were on-treatment. The intent-to-treat analysis of 27 patients showed ORR 37% . We obseAmong 7 evaluable L-L patients, ORR was 71%; 3 performed liver metastasectomies (43%) and 1 cCR (14%); median PFS 11 months (3\u201313+ months); median OS 12 months (3\u201313+ months). Among 20 evaluable O/MM patients, ORR was 25%; median PFS 6 months (1\u201312 months); median OS 13 months (1+\u221223+ months). Clinical outcome (PFS and OS) in L-L compared to O/MM patients was not significantly different .Among 16 evaluable patients treated with triplet regimens , ORR wasMoreover, PFS and OS were not significantly different in non-elderly and young-elderly compared to old-elderly patients , and in primary and intermediate CIRS stage compared to secondary stage patients .KRAS wild-type patients evaluable for activity, ORR was 50% . We observed 3 partial responses (25%); 5 stable diseases (42%); 4 progressive diseases (33%). Disease control rate was 67% . No liver metastasectomies were performed. Median PFS was 6 months (1\u201311 months), 12 events occurred (80%). Median OS was 8 months (3\u201318 months), 10 events occurred. KRAS wild-type compared with mutant patients showed significantly different PFS (p=0.043), but not OS (Among 14 CI \u00b1 27) . We obset not OS . KRAS c.ctively) , and to ctively) . No diffpatients . PFS andctively) .Patients unfit for first line FIr-B/FOx intensive regimen, due to age (\u226575 years) and/or comorbidities, were prevalent (56%), mostly elderly (76%), particularly old-elderly patients (54%), prevalently PS 1\u20132 (59%), CIRS stage intermediate/secondary (89%), O/MM disease (79%). Most unfit MCRC patients were treated with triplet or doublet regimens , and some (19%) did not reach the first evaluation of activity at 2\u20133 months.Retrospective evaluations of doublets consisting of CPT-11 or OXP, associated to 5-FU or capecitabine in elderly patients eligible for clinical trials gained ORR 18\u201359.4%, PFS 4.9\u201310.0 months and OS 8.5\u201320.7 months ,31,46. BYoung-elderly patients eligible for FIr-B/FOx intensive regimen, prevalently characterised by PS 0 (89%) and intermediate CIRS stage (93%), reported ORR 79%, PFS 11 months, OS 21 months, equivalent to overall patients . A complKRAS wild-type and mutant (KRAS geno-type was reported as significantly affecting PFS and OS in patients treated with XelOx/BEV (KRAS c.35 G>A (G12D) mutant genotype may significantly affect worse OS, compared to wild-type or other mutations , PFS and OS were not significantly different in d mutant ,6,8,37 ad mutant . RecentlelOx/BEV . We receutations . PresentA mutant ,40, and KRAS genotype may indicate different PFS, and c.35 G>A KRAS mutant a significantly worse PFS and OS, compared to wild-type and other mutations. Present findings warrant prospective trials comparing clinical outcome in unfit patients, according to KRAS genotype.In conclusion, in MCRC patients unfit for first line intensive FIr-B/FOx regimen, tailored doublet and triplet medical treatments showed similar activity and efficacy, also according to age and comorbidities."} +{"text": "Klebsiella quasipneumoniae subsp. similipneumoniae, KP_Z4175. This strain, isolated as part of a hospital infection-control screening program, is resistant to multiple \u03b2-lactam antibiotics, aminoglycosides, and trimethoprim-sulfamethoxazole.We report here the draft genome sequence of a multidrug-resistant clinical isolate of Klebsiella quasipneumoniae, formerly Klebsiella pneumoniae phylogroup KpII, was recently taxonomically reclassified as a new sister species of K.\u00a0pneumoniae with two subspecies, K.\u00a0quasipneumoniae subsp. quasipneumoniae and K.\u00a0quasipneumoniae subsp. similipneumoniae using the GGDC 2.1 software generating 2 \u00d7 301-bp paired-end reads. A total of 15,256,306 reads were produced comprising 1,540,886,906 bases after adapter sequence trimming. K.\u00a0quasipneumoniae subsp. similipneumoniae strain KP_Z4175, antibiotic resistance genes were identified using ResFinder version 2.1 -IIc), two fluoroquinolone resistance genes (aac(6\u2032)Ib-cr and QnrB4), one macrolide-lincosamide-streptogramin B resistance gene (ere(A)), two phenicol resistance genes (cmlA1 and floR), one rifampin resistance gene (ARR-2), two sulfonamide resistance genes (sul1 and sul2), one tetracycline resistance gene (tet(D)), and one trimethoprim resistance gene (dfrA14). All identified resistance genes had nucleotide identities of 98.35 to 100% over 85 to 100% of the reference gene lengths. Broth microdilution testing using CLSI breakpoints for Enterobacteriaceae indicated that KP_Z4175 is resistant to gentamicin (MIC >64), tobramycin (=32), cefazolin (>64), ceftriaxone (>64), aztreonam (>64), and trimethoprim-sulfamethoxazole (>64). The isolate had intermediate resistance to ampicillin-sulbactam (=16) and pipericillin/tazobactam (=32), and was sensitive to ertapenem (\u22640.03), imipenem (=1), meropenem (\u22640.03), amikacin (=0.5), cefepime (=8), and ciprofloxacin (=1).To examine the antibiotic resistance profile of sion 2.1 . In addieumoniae , \u03b2-lactaLVCD00000000. The version described in this paper is version LVCD01000000.This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number"} +{"text": "Dysregulation of the nucleo-cytoplasmic transport of proteins plays an important role in carcinogenesis. The nuclear export of proteins depends on the activity of transport proteins, exportins. Exportins belong to the karyopherin \u03b2 superfamily. Exportin-1 (XPO1), also known as chromosomal region maintenance 1 (CRM1), mediates transport of around 220 proteins. In this review, we summarized the development of a new class of antitumor drugs, collectively known as selective inhibitors of nuclear export (SINE). KPT-330 (selinexor) as an oral agent is showing activities in early clinical trials in both solid tumors and hematological malignancies.The online version of this article (doi:10.1186/s13045-014-0078-0) contains supplementary material, which is available to authorized users. The nucleo-cytoplasmic transport of proteins plays an important role in maintaining normal cellular functions. The nuclear export of proteins depends on the activity of transport proteins, exportins. Exportin-1 (XPO1), also known as chromosomal region maintenance 1 (CRM1), mediates transport of around 220 proteins . XPO1 isXPO1 binds to the cargo proteins through a leucine rich nuclear export signal (NES) and transports the proteins through a membrane pore complex via a Ran-GTP gradient -15] . The cliin vitro with most potency. However, its use in vivo is limited by poor pharmacokinetics . KPkinetics -[25]. Th50) of 150 nmol/L and inhibited pancreatic cancer cell lines while sparing normal human pancreatic ductal epithelial cells. The in vivo effects were noted using KPT-330 (selinexor) in subcutaneous and orthoptic pancreatic cancer models in mice. Oral administration of KPT-330 led to significant tumor growth inhibition when compared with control or gemcitabine treatment . EG. EG37]. l status . The antl status . In celll status . KPT-330l status . Moreovenografts .in vitro in RCC cell lines . Tr. Tr52]. hibitors . They cohibitors ,54]. Ho. Hoet alsistance ,63],. SI. SIin vi KPT-185 . FLT3 ge KPT-185 . SINE do KPT-185 ,74]. Ko. Koin viradation . Nutlin-radation . The add,. SI. SI79]. able IC50. In vivoet al. demonstrated successful use of KPT-185 in vitro and KPT-330 in vivo in Philadelphia chromosome positive ALL (Ph + ALL) and chronic myeloid leukemia blast crisis (CML-BC). Combination with imatinib led to synergistic effects . Wa. Wa81]. effects . SINE tr effects .et al. recently. They showed that KPT-330 treatment given to heavily pretreated, refractory/relapsed AML patients had no DLT. Out of the 32 evaluable patients, 4 (12%) showed complete response (CR) with hematological recovery, 1 (3%) showed marrow CR (mCR), mCR without hematological recovery was seen in 1 (3%) patient. Partial response (PR) was seen in 2 patients (6%). Eleven patients (34%) showed progression while 12 (37%) experienced stable disease after 30 days . Pr. Pr91]. L) cells . KPT-185L) cells ,93]. KP. KPet alL) cells . In a 37L) cells .in vitro and in vivo. Su. Suin vid in vivo. C-myc ad in vivo. A studyd in vivo. BRD4, ad in vivo,99]. BR. BRin vid in vivo. JQ1, a d in vivo. This reet al. conducted an in vitro study of KPT-185 in MCL and showed that SINE increases MCL cell apoptosis primarily by increasing nuclear p53 levels -[1-[1100]-. KPT dru3 levels . They vepression . London effects . Gutierrpatients . These dMore and more targeted small molecule inhibitors are entering clinical application quickly ,84],,-113]. S. S113]. DL and KP designed the study. All authors have contributed to data preparation, drafting and revising the manuscripts. All authors have read and approved the final manuscript."} +{"text": "Blood biomarkers are increasingly used to diagnose, guide therapy in, and risk-stratify community-acquired pneumonia (CAP) patients in emergency departments (EDs). How pre-analytic factors affect these markers' initial levels in this population is unknown.In this secondary analysis of consecutive ED patients with CAP from a large multicentre antibiotic stewardship trial , we usedP = 0.02) in patients with liver insufficiency; ProADM, + 13.2% in patients with age above median; and CRP, -12.8% with steroid pretreatment.Of 925 CAP patients , 25.5% had antibiotic pretreatment, 2.4%, corticosteroid pretreatment, 22.3% chronic renal failure, and 2.4% chronic liver insufficiency. Differences associated with pre-analytic factors averaged 6.1 \u00b1 4.6%; the three largest statistically significant changes (95% Cl) were: PCT, +14.2% (+2.1 to +26.4%, The influence of pre-analytic factors on the examined biomarkers is marginal and not clinically relevant. Our observations reinforce the concept ofusing biomarkers in algorithms with widely- separated cutoff values and overruling criteria considering the entire clinical picture, without adjustment for pre-analytic factors."} +{"text": "The importance of maternal nutrition to offspring health and risk of disease is well established. Emerging evidence suggests paternal diet may affect offspring health as well.In the current study we sought to determine whether modulating pre-conception paternal B vitamin intake alters intestinal tumor formation in offspring. Additionally, we sought to identify potential mechanisms for the observed weight differential among offspring by profiling hepatic gene expression and lipid content.1638N mice were fed diets containing replete , mildly deficient (DEF), or supplemental (SUPP) quantities of vitamins B2, B6, B12, and folate for 8 weeks before mating with control-fed wild type females. Wild type offspring were euthanized at weaning and hepatic gene expression profiled. Apc1638N offspring were fed a replete diet and euthanized at 28 weeks of age to assess tumor burden.Male Apc1638N offspring of different paternal diet groups. Although in female Apc1638N offspring there were no differences in tumor incidence or multiplicity, a stepwise increase in tumor volume with increasing paternal B vitamin intake was observed. Interestingly, female offspring of SUPP and DEF fathers had a significantly lower body weight than those of CTRL fed fathers. Moreover, hepatic trigylcerides and cholesterol were elevated 3-fold in adult female offspring of SUPP fathers. Weanling offspring of the same fathers displayed altered expression of several key lipid-metabolism genes. Hundreds of differentially methylated regions were identified in the paternal sperm in response to DEF and SUPP diets. Aside from a few genes including Igf2, there was a striking lack of overlap between these genes differentially methylated in sperm and differentially expressed in offspring.No differences in intestinal tumor incidence or burden were found between male ApcIn this animal model, modulation of paternal B vitamin intake prior to mating alters offspring weight gain, lipid metabolism and tumor growth in a sex-specific fashion. These results highlight the need to better define how paternal nutrition affects the health of offspring. B, C, D) Photomicrographs of Oil Red-O stained liver sections from DEF (22.7%), CTRL (22.3%) and SUPP (37.6%) offspring respectively. Images are from mice with the highest staining area in each group. Images taken at 100x and scale bar is 200 \u03bcm. Paternal diets: DEF, B vitamin deficient; CTRL, B vitamin replete; SUPP, B vitamin supplemented.(DOCX)Click here for additional data file.S3 FigA) CpGs 1\u201314 are located at -359, -357, -347, -337, -334, -320, -314, -304, -296, -288, -280, -274, -267 and -264 bp from the start of Acaca1 exon 1 respectively. B) CpGs 1\u20139 are located at +36, +59, +50, +27, +14, +10, -3, -14, -40 and -44 bp from the start of Elovl6 exon 1 respectively. C) CpGs 1\u201319 are located -122, -113, -96, - 89, -77, -73, -64, -61, -52, -50, -48, -45, -41, -39, -33, -31, -28, -26 and -23 bp from start of Gpam exon 1 respectively.D) CpGs 1\u20138 are located -3775, -3766, -3754, -3706, -3702, -3699, -3685, -3678 and -3665 bp from start of H19 exon 1 respectively. Unless noted, for each CpG site, 2-Way ANOVA p (group) >0.05 and p (sex) >0.05. \u2018a\u2019 denotes p <0.05 for group effect and \u2018b\u2019 denotes p v0.05 for sex effect. Unless noted, repeated measures ANOVA for group effect yielded a p>0.05. Paternal diets: DEF, B vitamin deficient; CTRL, B vitamin replete; SUPP, B vitamin supplemented; M male; F female. n = 4 males and 8 females per group.DNA methylation was measured in target genes using bisulfite pyrosequencing. (DOCX)Click here for additional data file.S1 TableB denotes biotin modification of primer at 5\u2019 end of FWD or 3\u2019 end of RVS primer.(DOCX)Click here for additional data file.S2 TableValues are mean \u00b1 SEM. n = 10, 13 and 9 respectively.(DOCX)Click here for additional data file.S3 TableDMR ID is an arbitrary identifier for each differentially methylated region; CTRL, control diet; DEF, B vitamin deficient diet; m1, mean log2(636/532) for CTRL sperm; m2, mean log2(636/532) for DEF sperm; chr:position identifies the location of the DMR within the chromosome using mouse genome build mm9 coordinates; diff, mean log2(635/532) difference across the DMR; qval, q-value\u2014an adjusted p-value indicating the false discovery rate (FDR) calculated by the Wilcoxon rank sum-test. For genes with a qval < 0.1, less than 10% of genes are expected to be false positives; Gene symbol identifies the gene annotated to a DMR and its proximity in bases to the left (-) or right (+) of the DMR up to a distance of 1000 kb where all genome coordinates and gene symbols are derived from mouse genome build mm9. n = 8/gp.(XLSX)Click here for additional data file.S4 TableDMR ID is an arbitrary identifier for each differentially methylated region; CTRL, control diet; SUPP, B vitamin supplemented diet; m1, mean log2(636/532) for CTRL sperm; m2, mean log2(636/532) for SUPP sperm; chr:position identifies the location of the DMR within the chromosome using mouse genome build mm9 coordinates; diff, mean log2(635/532) difference across the DMR; qval, q-value\u2014an adjusted p-value indicating the false discovery rate (FDR) calculated by the Wilcoxon rank sum-test. For genes with a qval < 0.1, less than 10% of genes are expected to be false positives; Gene symbol identifies the gene annotated to a DMR and its proximity in bases to the left (-) or right (+) of the DMR up to a distance of 1000 kb where all genome coordinates and gene symbols are derived from mouse genome build mm9. n = 8/gp.(XLSX)Click here for additional data file.S5 Table* Values are mean \u00b1 SEM. Note that number weaned offspring is less than sired offspring due to maternal cannibalism that is common amongst first-time mothers. DEF, B vitamin deficient; CTRL, B vitamin replete; SUPP, B vitamin supplemented.(DOCX)Click here for additional data file.S6 TableValues are mean \u00b1 SEM. Paternal diets, DEF, B vitamin deficient; CTRL, B vitamin replete; SUPP, B vitamin supplemented. Sample size is in parentheses.(DOCX)Click here for additional data file.S7 TableSignificant differences according to Cuffdiff analysis combining male and female offspring (q<0.05). Expression values are Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM). CTRL, control; DEF, deficient . n = 10/gp.(XLSX)Click here for additional data file.S8 TableSignificant differences according to Cuffdiff analysis combining male and female offspring (q<0.05). Expression values are Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM). CTRL, control; SUPP, supplemented . n = 10/gp.(XLSX)Click here for additional data file.S9 TableCategories identified by Ingenuity Pathway Analysis\u00ae. DEF, B vitamin deficient; CTRL, B vitamin replete; SUPP, B vitamin supplemented . P values represent the range of p values of the sub-categories of each category.(DOCX)Click here for additional data file.S10 Tablen = 5/gp.(XLSX)Click here for additional data file.S11 Table(DOCX)Click here for additional data file."} +{"text": "Edwardsiella piscicida-like species is a Gram-negative facultative anaerobe that causes disease in some fish species. In this report, we present the complete and annotated genome of isolate LADL05-105, recovered from cultured tilapia reared in Louisiana, which contains a chromosome of 4,142,037\u00a0bp and no plasmids.An Edwardsiella, first recognized in the 1960s was designated the type strain of the recently proposed taxon, E.\u00a0anguillarum sp. nov. and Pacific Biosciences (Pac-Bio) (113\u00d7 coverage). The PBcR module of wgs-8.2beta (Celera) (Genomic DNA from (Celera) , 10 was (Celera) .The circularized and completed genome was submitted to the National Center for Biotechnology Information Prokaryotic Genomes Annotation Pipeline (PGAP) for annotation and submission to GenBank. The genome data was also subjected to RAST , 14 annoE.\u00a0piscicida-like species genome consists of one circular chromosome with 4,142,037\u00a0bp and 58.8% GC content. PGAP annotation predicted 3,686 genes encoding 3,159 proteins and 99 tRNAs. RNAmmer (http://enve-omics.ce.gatech.edu/ani). The complete genome of LADL05-105 shares an ANI of 99.84% with Edwardsiella strain 080813, which was recently proposed as the type strain for Edwardsiella anguillarum sp. nov. (GenBank accession no. CP006664) (E.\u00a0piscicida-like sp. isolate EA181011 (GenBank accession no. CP011364) (E.\u00a0piscicida isolate C07-087 (GenBank accession no. CP004141) (E.\u00a0tarda isolate FL95-01 (GenBank accession no. CP011359) , 94.39% P001600) , and 84.P011359) . These AEdwardsiella piscicida-like sp. isolate LADL05-105 has been deposited in GenBank under the accession number CP011516.The complete genome sequence for"} +{"text": "Controlling MRSA has been a challenge for Geneva University Hospitals (HUG), particularly after the introduction of ST228 SCCmecI hyperendemic clone in 1999.To describe HUG\u2019s secular trends of MRSA, infection control measures and predominant MRSA clones using Staphylococcal chromosomic cassettes (SCCmec) genotyping.nd HHC, periodic audits and feedback (2006). The intensive care unit performed MRSA screening on admission, discharge and weekly since 2004. Surveillance included: (1) incidence rates (IR) of hospital acquired (HA)-MRSA infection or colonization; (2) HA-MRSA bloodstream infections (BSI); (3) proportion of MRSA/S. aureus BSI; (4) IR of MRSA clinical cultures (CC); (5) proportion of SCCmec in MRSA strains, assessed by routine multiplex PCR assay. Representative isolates were grouped in MLVA clusters to evaluate genomic diversity and subjected to MLST.A multifaceted MRSA prevention program initiated in 1993 included patient screening, decontamination, surveillance, contact isolation, an alert system and a hospital-wide hand hygiene campaign (HHC); subsequently strengthened by: an educational campaign (2003), routine MRSA SCCmec genotyping (2005), a 2S. aureus BSI remained around 34% (2000-2009), declining to 18% (2014). SCCmecI strains declined from 83% (2005) to 32% (2014); SCCmecII and SCCmecIV were higher in non-acute settings.At HUG, from 2000-2014, 12,543 patients were MRSA-colonized or infected . From 2000-2007, annual rates of all indicators showed an increasing trend, declining since 2008. New HA-MRSA cases per 100 admissions increased from 1.36 to 2.00 (2006), and then declined to 0.29 (2014). Trends expressed by incidence density of cases per 1000 hospital-days: HA-MRSA, from 0.92 to 1.36 (2007) to 0.21 (2014); ICU-acquired HA-MRSA from 2.3 (2002) to 10.5 (2006) to 1.31 (2014); MRSA-CC rates from 0.68 to 1.44 (2008), to 0.24 (2014); HA-BSI from 0.049 to 0.07 (2009), to 0.016 (2014). The proportion of MRSA/A multifaceted prevention program and possible changes in biologic fitness of the ST228 SCCmecI clone helped to decrease endemic MRSA rates for the last 7 years.None declared."} +{"text": "In sepsis, impaired function and loss of antigen-presenting cells are observed in secondary lymphoid organs , the sitTo study seven-day lymphocyte and immunoglobulin trajectory, alterations in B cell subsets and potential mechanisms in septic ICU patients.9/L, respectively.Adults with severe sepsis from community-acquired infections without documented immunosuppression were enrolled. Hypogammaglobulinaemia and absolute lymphopenia were defined as IgG < 6.1, IgM < 0.4, IgA < 0.8 g/L and lymphocytes < 1.2 \u00d7 10Flow cytometry [FACScalibur [BD Biosciences]; FlowJo software,] was used for:Identifying na\u00efve, transitional, IgM, IgG and IgA memory and plasmablasts using anti-human CD19-PerCpCy5.5, IgG-APC H7, IgM-V450, CD24-PeCy7 [all BD Biosciences], IgA-FITC, CD38-PE, Annexin V Apoptosis detection set PE-Cy7 [all eBioscience] and live-dead stain [Invitrogen]. ADDIN EN.CITE ADDIN EN.CITE.DATA .FMO and isotype controls were used to define population gates.B cell survival ligands were measured using ELISA.\u00ae Human Apoptosis Array; false discovery rate = 5%].Differentially expressed genes in sepsis are reported and T [100%] lymphocyte counts. Trajectory of significantly higher increment immunoglobulins and lymphocyte counts occur earlier in survivors compared to non-survivors.In sepsis there wasPreferential apoptotic loss of memory B cells and plasmablasts, with apoptotic cells showing higher phosphorylated extracellular signal-regulated kinases [p-ERK fluorescence], but no differences in the phosphorylated B cell receptor linked kinases and protein kinase B.BAFF/APRIL levels were normal.Fas and bcl-2 apoptosis regulator genes were up regulated.In sepsis, activation-associated B cell apoptosis and changes in secondary lymphoid organs deplete B cell memory and contribute to long-term immunosuppression in survivors.UK NIHR, Biomedical Research Centre at Guy\u00b4s and St Thomas\u00b4 NHS Trust & King\u00b4s College London"} +{"text": "Recent nationwide shortages of low-calcium formula (LCF) suggest this problem may be widespread. CYP24A1 mutations have been identified as a potential cause of IIH.Consultations for infantile hypercalcaemia (IIH) have increased at Sydney Children\u2019s Hospital since guidelines for vitamin DTo determine if IIH is occurring more commonly, de-identified, first-measured serum calcium from all infants <6 months (n=5796) measured in our laboratory, were grouped by years 2005-2007 (n=1516), 2008-2010 (n=1945) and 2011-2013 (n=2335). In addition, we analysed 13 infants treated by our department for idiopathic infantile hypercalcaemia (IIH) from 2011-2013.2P<0.001). Rates of hypocalcaemia (<2.25mmol/L) fell steadily . Twelve mothers of our 13 infants with IIH received antenatal vitamin D3 supplementation. One infant also received 400 units/day Vitamin D3 post-natally. At diagnosis, median age was 13 days (range 4-50), 77% were breast-fed, 54% were symptomatic and 25% had nephrocalcinosis. Median initial calcium was 3.00mmol/L (range 2.84-4.03) and phosphate 2.04mmol/L (1.1-3.33). PTH was not elevated (median 1.0pmol/L [<0.3-3.1]), urinary calcium: creatinine ratio not suppressed , 25OHVitD low-normal (median 44nmol/L [17-218]) and 1,25(OH)2VitD elevated (median 232pmol/L [64-720]), in keeping with an abnormality in CYP24A1. In 7/10 infants with data available, treated with LCF for median 95 days (range 25-310), median PTH rose to 17.1pmol/L with a trend to lower 25OHVit D despite continued high-normal calcium levels (median 2.66mmol/L [2.11-2.75]).Rates of hypercalcaemia (>2.75mmol/L) increased from 2011 (1.1% vs 1.3% vs 8.7%, \u03c73 supplementation as an aetiological factor. IIH was associated with significant morbidity, including symptomatic hypercalcaemia and nephrocalcinosis. Treatment with LCF prevented further symptomatic hypercalcaemia, but resulted in elevated PTH. The biochemistry of our patients with IIH raises variations in Vitamin D metabolism or calcium set-point as potential associated factors.Concurrent changes in rates of hyper and hypo-calcaemia suggest antenatal vitamin D"} +{"text": "A range of cytokines are altered during sepsis. Multiplex analysis of inflammatory mediators makes it easier to study a larger range of mediators, and combined with newer bioinformatical tools , this has the potential to bring new knowledge of the inflammatory process during sepsis.To investigate if there are differences in expression of multiple inflammatory mediators between septic patients with and without bacteraemia during the initial phase of hospitalization, in order to identify bacteraemic patients.All together 80 adult, immunocompetent patients with sepsis and confirmed bacterial infection were included prospectively at Haukeland University Hospital during the first 24 hours of hospitalization at the HDU, ICU or medical department. Luminex analysis of plasma was used to analyse 35 mediators; 16 cytokines, 6 growth factors, 4 adhesion molecules and 9 matrix metalloproteinases/ tissue inhibitors of metalloproteinases. Mann-Whitney U-test were used analysing differences between the two groups were we examined both p-values with (< 0.0014) and without (p < 0.05) Bonferronis correction. We performed unsupervised hierarchical clustering of the five statistically most significant mediators using J-express software.In 41 patients (51%) a positive blood culture was found, while the remaining 39 (49%) had proven bacterial cause by confirmed by other tests. Among these, 37 were gramnegative, 39 were grampositive, while 4 patients had mixed infections.We found that 16 of 35 mediators showed statistical differences between bacteraemic and non-bacteraemic patients; IL1ra (p = 0.0015), IL-10 (p = 0.0009), CCL2 (p = 0.0376), CCL4 (p < 0.0001), CCL5 (p = 0.0376), CXCL8 (p = 0.0026), CXCL11 (p = 0.0468), TNF\u03b1 (p < 0.0001), HGF (p = 0.0018), E-selectin (p = 0.0004), ICAM-1 (p = 0.0009), VCAM-1 (p < 0.0001), MMP-8 (p = 0.0311), TIMP-1 (p < 0.0001), TIMP-2 (p = 0.0054) and TIMP-4 (p = 0.0036).Using unsupervised hierarchical clustering (se figure), we found that the five mediators TNF\u03b1, CCL4, E-selectin, VCAM-1 and TIMP-1 gave a reasonable good discrimination of bacteraemia patients; the patients with bacteraemia were mostly clustered in two separate groups showing higher levels of the mediators. Only 5 (12%) of the bacteraemic patients were clustered in the middle cluster, while most of the non-bacteraemia patients were clustered in this group (Chi-square p < 0.0001).We find higher levels of inflammatory markers in sepsis patients with bacteraemia, and hierarchical clustering may aid early identification of patients with bacteraemia.Upper and lower cluster contains most bacteraemia patients (red) showing higher levels of inflammatory mediators (green). Middle cluster with lower levels of mediators (blue) contains most patients without bacteraemia. Mediators are clustered horizontally and patients vertically."} +{"text": "Eosinophilic esophagitis (EoE) is an increasingly common cause of chronic and recurrent esophageal symptoms with significant impact on quality of life. Allergic responses to food and aeroallergens have been implicated in the etiology of this disease.Clinical and sensitization profile characterization of an adult population with EoE diagnosis (EoEd) followed in our Immunoallergology Department.Retrospective study using our EoE database (2009-2014) of patients (pts) \u2265 18 years.Characterization of demographic, symptomatic, laboratorial , endoscopic and histological factors and sensitization profile .We included 25 patients (pts) ; median age of symptoms onset and diagnosis: 27(13-66) and 30(16-67) years respectively; average between symptoms onset and EoEd:27(1-180) months. Follow-up for 25.3\u00b121.7(1-88) months. Reported symptoms-%pts: impaction-84,GERD-like symptoms 48, dysphagia-36, bloating-24, abdominal pain-16 and vomiting-12. Most frequent first symptom: impaction-48%pts. 60% of pts had personal history of atopy . Median peripheral Eos 388.8(40-980) and total IgE 163,8kU/L(5.6-436). The main baseline endoscopic findings (%pts): rings (43.5), furrows (26.1), hiatal hernia (21.7) and white plaques (21.7). 13% had microabcesses. After EoEd, allergic sensitization was identified in 88% pts ; food allergens ; mites (54.2); pollens (37.5). After therapeutic: all had symptomatic improved; 12.5% pts achieved Eos\u226415/HPF in esophageal biopsy, all with food allergy who underwent dietary eviction.The first and the most frequent symptom was food impaction. The prevalence of allergic sensitization was high. The potential severity of the symptoms justifies the importance of recognition and management of the disease. A multidisciplinary evaluation is essential in the clinical, diagnostic and therapeutic workup."} +{"text": "In 2012, 69.6% of adults aged \u226540 years who ever had a cardiovascular event (73.2% of men and 65.4% of women) were taking low-dose aspirin to prevent or control heart disease. Non-Hispanic white men (75.9%) were more likely to be taking low-dose aspirin compared with Hispanic (60.7%) and non-Hispanic black men (60.6%). No statistically significant differences were oberved among women by race/ethnicity.Source: National Health Interview Survey, 2012 data. Available at http://www.cdc.gov/nchs/nhis.htm.Reported by: Renee M. Gindi, PhD, iuz2@cdc.gov, 301-458-4502; Brian W. Ward, PhD."} +{"text": "Their structures were elucidated by comprehensive spectroscopic analyses including MS, IR, 1D and 2D NMR. All compounds were evaluated for their anti-AChE activities.Seven new monoterpene phenyl ethers, namely micranthumnins A-G (Supplementary material is available for this article at 10.1007/s13659-013-0007-x and is accessible for authorized users. Supplementary material, approximately 4.23 MB."} +{"text": "There are errors in the \u201cOncomine data analysis\u201d section of the Materials and Methods. It should read:Oncomine and CCLE data analysisUsmg5 copy number profiles in a large subset of cancer cell lines . In the dataset, the log2 values were analyzed. The number of DNA copies ) were calculated as advised in Oncomine instructions.We used the Oncomine Cancer Genomics Data Analysis tool [30] and Cancer Cell Line Encyclopedia, CCLE [35] to mine Usmg5 copy number in cancers\u201d section of the Results. It should read:There are errors in the \u201cUsmg5 copy number in cancer cell linesUsmg5 copy number in a large panel of cell lines of ll lines Several There are errors in Usmg5 copy number in various cancer cell lines :R215. doi: 10.1158/1541-7786.MCR-08-010766. Hu X, Stern HM, Ge L, O'Brien C, Haydu L, Honchell CD, Haverty PM et al. Genetic alterations and oncogenic pathways associated with breast cancer subtypes. Mol Cancer Res. 2009 Apr;7(4):511\u201322. doi: 10.1186/1755-8794-3-2367. Lu X, Zhang K, Van Sant C, Coon J, Semizarov D. An algorithm for classifying tumors based on genomic aberrations and selecting representative tumor models. BMC Med Genomics. 2010 Jun 22;3:23. doi: 10.1158/1541-778668.Olejniczak ET, Van Sant C, Anderson MG, Wang G, Tahir SK, Sauter G et al. Integrative genomic analysis of small-cell lung carcinoma reveals correlates of sensitivity to bcl-2 antagonists and uncovers novel chromosomal gains. Mol Cancer Res. 2007 Apr;5(4):331\u20139. Doi: 10.1172/JCI3712769. Sos ML, Michel K, Zander T, Weiss J, Frommolt P, Peifer M et al. Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. J Clin Invest. 2009; Jun;119(6):1727\u201340. doi:"} +{"text": "Beh\u00e7et's disease (BD) is an inflammatory disorder of unknown aetiology, unanimously recognized as both autoimmune and autoinflammatory disease. Indeed many of its classical manifestations overlap with those of monogenic autoinflammatory disorders. Clinically disease is characterized by multiple organ involvement, in particular by the \u201ctriple symptom complex\u201d, consisting of recurrent oral aphthosis, genital ulcers and recurrent bilateral uveitis. The abnormal activation of either innate and adaptive immunity, triggered by some microbial agents in genetically predisposed individuals, with consequent interaction of both T lymphocytes and activated neutrophils would seem to be involved in the disease onset. Therefore multiple cytokines may contribute to the pathological scenario of BD playing a pivotal role in the occurrence of the clinical manifestations.To determine serum levels of IL-8, IL-18, IFN-\u03b12a, IL-6, IFN-\u03b3, CXCL10, CXCL11, CXCL9 and serum amyloid-A (SAA) concentration in patients with BD, in comparison to healthy controls (HC), and to correlate their concentration with the status of disease activity.78 serum samples were collected from 58 BD patients . Serum cytokine levels of IL-8, IL-18, IFN-\u03b12a, IL-6, IFN-\u03b3, CXCL10, CXCL11 and CXCL9 were determined using a multiplex bead analysis as well as SAA was assessed by Enzyme linked-immunosorbent assay.In BD patients serum concentrations of IL-8 (p=0.0001), IL-18 (p=0.0058), IFN-\u03b12a (p=0.0181) and IL-6 (p=0.0233) were significantly higher than in HC. When BD patients were divided into active and inactive group, IL-8 and IL-18 resulted higher in both active- (p=0.0001 and p=0.012 respectively) and inactive-BD (p=0.0001 and p=0.0128 respectively) than in HC, while IFN-\u03b12a (p=0.0141) and IL-6 (p=0.0332) serum levels were significantly higher in active-BD than HC. Moreover, CXCL11 (p=0.0154) serum concentrations were significantly lower in inactive-BD than HC. We also compared serum cytokine profiles between BD patients with SAA serum levels \u226420 mg/L, >20 mg/L and HC. Interestingly, we observed that BD patients with SAA >20 mg/L showed higher levels of inflammatory markers than HC. Among these cytokines, IL-18, IFN-\u03b12a and IL-6 were higher in BD group with SAA >20 mg/L than HC, whereas IL-8 and CXCL9 levels were higher than in patients with SAA \u226420 mg/L and HC.BD patients exhibit elevated levels of specific inflammatory mediators, especially during active disease periods and in those patients with SAA serum levels >20 mg/L, thus suggesting a possible role of SAA in the induction of BD inflammatory manifestations."} +{"text": "To determine the agreement of manual and semi-automatic (SA) diameter and volume measurements of nodules found in low-dose computed tomography lung cancer screening.3) in 1,498 Dutch-Belgian NELSON trial participants were used. Extrapolated volume based on semi-automatic (SA) maximum diameter and mean of maximum transversal and perpendicular diameter were compared to SA volume measurements by Bland-Altman plots. Analyses were repeated by margin and shape . In 100 randomly selected nodules, diameters were measured manually by two independent radiologists, and compared to the SA diameters.Baseline data of 2,240 solid intermediate-sized nodules (volume 50-500mmMedian participant age was 59-years (interquartile range:8), 14.2% were women. Compared to SA volume, volume extrapolated from SA mean or maximum diameter led to mean overestimation of 47.2% : 44.7-49.7%) and 85.1% (95%-CI:81.2-89.0%), respectively. For irregular and non-spherical nodules, mean overestimation was higher; 161.7% (95%-CI:131.7%-191.8%) and 168.9% (95%-CI:155.2%-182.5%), respectively. Manual diameter measurement overestimated SA maximum diameter by \u226510% in 44% (44/100) and underestimated by \u226510% in 18% (18/100) of the nodules. Using a 10-mm criterion for referral, SA maximum diameter measurements of indeterminate nodules would have led to direct referral in 7.9% (177/2240). Manual measurements would have led to 31% (31/100) referrals.The agreement between manual and SA diameter, as well as between volume extrapolated from SA diameter and SA volume is poor. Applying manual and SA diameter measurement in CT lung cancer screening leads to a substantial shift in nodule stratification compared to SA volume measurements."} +{"text": "HIV-infected patients show an increased risk of cardiovascular disease (CVD). In the general population, lipoprotein-associated phospholipase A2 (Lp-PLA2) appears to be an independent predictor of CVD. We aimed to study associations between Lp-PLA2 plasma levels and other risk factors for CVD in HIV patients.A cross-sectional, comparative study of two series of cases was conducted. Eighty-seven percent HIV patients on antiretroviral therapy (ART), 72.4% with HIV-1 viral load <50 cop/mL. Inflammatory biomarkers and internal carotid intima-media thickness (IMT) were measured and CVD risk was calculated. Univariate and multivariable associations between these variables were performed.HIV patients presented higher Lp-PLA2 levels [276.81 ng/mL (209.71\u2013356.58)] than uninfected healthy controls [220.80 ng/mL (172.70\u2013256.90)], p\u22640.01. In univariate analysis of the global sample, only cigarette smoking was associated with higher Lp-PLA2 levels, p\u22640.001. In HIV group, female and smoker patients showed higher Lp-PLA2 levels, p\u22640.05. No significant association was found between Lp-PLA2 levels and another CVD risk factors, carotid IMT, Framingham and SCORE algorithms, ART, HIV-1 viral load neither and CD4+ T lymphocyte count. In multivariate analysis, cigarette smoking remained significantly associated with Lp-PLA2 levels .HIV-infected patients present higher Lp-PLA2 levels than healthy controls, and in this population, tobacco smoking is significantly associated with increased Lp-PLA2 levels. Smoking cessation should be a priority in CVD prevention in HIV-infected patients."} +{"text": "Edwardsiella tarda is a Gram-negative facultative anaerobe that has been isolated from fish, reptiles, amphibians, and mammals, including humans. This is a report of the complete and annotated genome of isolate FL95-01, recovered from channel catfish . Edwardsiella tarda is a Gram-negative intracellular facultative anaerobic bacteria infecting a wide range of avian, reptilian, fish, and mammalian hosts across the globe and Pacific Biosciences (PacBio) (88\u00d7 coverage) platforms. The longest 40\u00d7 coverage PacBio reads were error-corrected with the remaining PacBio data using the PBcR module within Celera Assembler version 8.2 beta , 16. TheThe circularized and complete genome was submitted to the NCBI Prokaryotic Genomes Annotation Pipeline (PGAP) for annotation and submission to GenBank. Furthermore, the genome was submitted for RAST , 20 annoE.\u00a0tarda genome consists of one circular chromosome with 3,620,701\u00a0bp and 57.3% GC content. PGAP annotation predicted 3,258 genes encoding 3,091 proteins and 101 tRNAs. RAST analysis predicted 505 subsystems with 3,318 coding sequences and 129 RNAs. RAST comparison of FL95-01 with Edwardsiella piscicida C07-087 showed 89 unique subsystems in FL95-01 related to carbohydrate metabolism, cell wall and capsule, and copper tolerance. Additionally, RNAmmer (http://enve-omics.ce.gatech.edu/ani). The complete genome of E.\u00a0tarda isolate FL95-01 shares an ANI of 83.4% with E.\u00a0piscicida isolate C07-087 (GenBank accession no. CP004141) (E.\u00a0piscicida isolate 080813 (GenBank accession no. CP006664) , and 83.P001600) . Edwardsiella tarda isolate FL95-01 has been deposited in GenBank under the accession number CP011359.The complete genome sequence for"} +{"text": "Right atrial thrombus (RT) provides a rationale for anticoagulation and substrate for embolic events. CMR is well validated for thrombus detection, but has yet to be used to assess prevalence and predictors of RA thrombus among at risk cohorts.The population comprised consecutive patients with central venous catheters undergoing CMR at Memorial Sloan Kettering Cancer Center . Delayed enhancement CMR (inversion recovery GRE) was used to identify RT; defined as a right atrial (RA) mass with avascular tissue characteristics (non-enhancing) on \"long TI\" (600msec) DE-CMR. Cine-CMR (SSFP) was used to quantify cardiac structure and function, including RA and RV function and chamber size. Clinical indices were categorized based on medical record review. Echo (if performed within 14 days of CMR) was retrieved from image archives and independently read for RT. Clinical records were queried for documented pulmonary embolus (PE) within 60 days of CMR.2/m2, p= 0.94), RA end-systolic area , RV end-diastolic volume , and RVEF . Cancer diagnosis , catheter depth , age and gender (both p=NS) were similar between groups. Transthoracic echo, attained 4.1\u00b13.8 days from CMR in 50% of the population, demonstrated high sensitivity (89%) but moderate specificity (75%) in relation to DE-CMR. Cine-CMR yielded similar sensitivity (82%) but improved specificity (97%) vs. the reference standard of DE-CMR (Table). 27% of patients (3/11) with RT on DE-CMR had PE; all occurred prior to DE-CMR (average of 14 days before). Conversely, no PEs occurred among patients without RT. Clinical embolic events were independent of RT size .50 cancer patients with RA catheters were studied. CMR was performed for evaluation of a suspected RA mass (36%) or unrelated clinical indications (64%). RT was present in 22% (n=11); all had RT avascularity confirmed by dedicated \"long TI\" DE-CMR. Among affected patients, 63% had a solitary RT (36% multiple). Patients with RT had similar right-sided structure and function vs. those without RT based on RA end-diastolic area (10.2\u00b13.5 vs. 10.2\u00b12.1 cmCatheter associated RT occurs independently of right-sided structure or function, and is associated with clinical embolic events. Morphologic imaging by cine-CMR and echo provide limited diagnostic utility for RT as established by DE-CMR tissue characterization.None."} +{"text": "AbstractParatenetus Spinola are reviewed and a key is presented for their identification. Five species are recognized, P. gibbipennis Motschulsky, P. fuscus LeConte, P. punctatus Spinola and two sp. n., P. exutus and P. texanus . Two syn. n. are proposed: P. cribratus Motschulsky, 1868 with P. gibbipennis Motschulsky, 1868 and P. crinitus Fall, 1907 with P. fuscus LeConte, 1850. A lectotype is selected for Paratenetus punctatus Spinola. A type species is designated for Storthephora M\u00e4klin, 1875 .The North American (north of Mexico) species of the tenebrionid genus Paratenetus was proposed by Spinola in Paratenetus lebasi from Colombia and Paratenetus punctatus from the United States of America. The last mentioned species was represented by three specimens originating from the collection of Baron Dejean who received them from John Eatton LeConte. Subsequently, the genus received very little attention. In North America, John Lawrence LeConte described a new species in Paratenetus in 1868 from the material he collected in Georgia. In The genus The purpose of this paper is to review the American species occurring north of Mexico and provide a key for their identification.The study is based on the examination of about 3110 specimens borrowed from the following collections: Atlantic Forestry Centre, Fredericton, New Brunswick. Reginald P. Webster.AFC American Museum of Natural History, New York, New York. Lee H. Herman.AMNH The Natural History Museum, London, United Kingdom. Maxwell Barclay.BMNH California Academy of Sciences, San Francisco, California. David H. Kavanaugh.CAS Canadian Museum of Nature, Gatineau, Quebec. Fran\u00e7ois G\u00e9nier.CMN Canadian National Collection of Insects, Archnides and Nematodes, Ottawa, Ontario.CNC Cornell University Insect Collection, Ithaca, New York. James K. Liebherr.CUIC Department of Entomology, University of New Hampshire. Donald S. Chandler.DENH Department of Biology, Eastern New Mexico University, Portales, New Mexico. Darren A. Pollock.ENMU Florida State Collection of Arthropods, Gainesville, Florida. Paul E. Skelley.FSCPageBreak Georgia Museum of Natural History, The University of Georgia, Athens, Georgia. E. Richard Hoebeke.GMNH Gerard J. Hilchie Collection, Edmonton, Alberta.GHC Wallis-Roughley Museum of Entomology, University of Manitoba, Winnipeg, Manitoba. Robert E. Roughley.JBWM Janet Ciegler Collection, West Columbia, South Carolina.JCC Lyman Entomological Museum and Research Laboratory, McGill University, Sainte-Anne-de-Bellevue, Quebec. St\u00e9phanie Boucher.LEMM Louisiana State Arthropod Museum, Louisiana State University, Baton Rouge, Louisiana. Matthew L. Gimmel.LSAM Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts. Philip Perkins.MCZ Museo Regionale di Scienze Naturali, Torino, Italy. Luca Picciau.MRSN Northern Forestry Centre, Edmonton, Alberta. Greg R. Pohl.NFC Royal Alberta Museum, Edmonton, Alberta. Mark Steinhilber.RAM Royal British Columbia Museum, Victoria, British Columbia. Claudia Copley.RBCM Rolf L. Aalbu Collection, Sacramento, California.RLAC Royal Saskatchewan Museum, Regina, Saskatchewan. Ronald R. Hooper.RSM Reginald P. Webster Collection, Charters Settlement, New Brunswick.RWC Snow Entomological Museum, University of Kansas, Lawrence, Kansas. Zachary Falin.SEMC Texas A&M University, College Station, Texas. Edward G. Riley.TAMU Strickland Museum, University of Alberta, Edmonton, Alberta. Danny Shpeley.UASM Spencer Entomological Museum, University of British Columbia, Vancouver, British Columbia. Karen Needham.UBC National Museum of Natural History, Smithsonian Institute, Washington, DC. Warren E. Steiner.USNM Zoological Museum, Moscow University, Moscow, Russia. Nikolay B. Nikitsky.ZMMUThe photographs were made with a Leica Digital DC500 Imaging Workstation using Zerene Stacker software and retouched with Adobe Photoshop software.For type specimens, complete verbatim label data are given with additional information enclosed within quotation marks; individual labels are separated by a slash (/).http://www.simplemappr.net/).The distribution maps were generated using the software SimpleMappr . The idea for the name came from the peculiar shape of the palpi and particularly the flattening of the first two labial palpomeres.(based on species treated only). Body short, convex, pubescent; elytra with slanting setae in addition to erect setae. Epistoma with clypeolabral membrane exposed. Eyes present, prominent. Gena not sulcate. Antenna with last three antennomeres abruptly expanded, forming a distinct, loose club. Labial palpi short, penultimate palpomere swollen, last palpomere narrow, more or less fusiform; last maxillary palpomere large, at least twice as large apically than basally. Pronotum with sides denticulate, each denticle with one or two stiff setae; surface with relatively coarse punctures. Procoxae moderately separated. Mesepimeron not closing mesocoxal cavity. Elytra without striae, with relatively coarse punctures; epipleuron distinct and relatively wide up to apex. Abdomen with distinct membrane along posterior edge of ventrites 3 and 4. Intercoxal process of first ventrite relatively wide, more or less rounded apically. Tibia not expanded apically. Metatarsomere 1 elongate, as long as next two tarsomeres combined; penultimate tarsomere deeply lobate dorsally; last tarsomere not arising at apex of penultimate tarsomere. Tarsal claw simple, not pectinate. Tarsal formula 5\u20135-4. Defensive glands absent.This genus currently includes 57 species ranging PageBreakParatenetus in his Cl\u00e9rites Coryn\u00e9to\u00efdes (currently Cleridae: Korynetinae). Cryptophagidae. Paratenetus back in the family Tenebrionidae, and placed it in the tribe Heterotarsini, a position that was followed by several authors including Paratenetus, Prataeus and Anaedus seem to be near the Lagriidae on account of the similarity in their larval stages\u201d and Heterotarsini (except Heterotarsus Latreille) from the tenebrionids to the lagriids based also on the morphology of the larvae. The study of the ovipositor structures by Paratenetus within the subfamily Lagriinae rather than the subfamily Tenebrioninae. Heterotarsini (except Heterotarsus) in the lagriine subtribe Lupropina of the tribe Adeliini. Paratenetus in the lagriid subfamily Lupropinae. Paratenetus in the lagriid subfamily Goniaderinae and Goniaderini. On the other hand, Lupropini following Paratenetus but we accept, following Goniaderini of the subfamily Lagriinae within the Tenebrionidae.We did not investigate the taxonomic position of the genus Paratenetus is poorly known. Many of the specimens seen in this study were collected in leaf litter in forested areas or in nests of the tent caterpillar genus Malacosoma (Lepidoptera: Lasiocampidae). All three winged species have been collected at black light. Paratenetus species pupate on the inner surfaces of rolled dead leaves (in which the larvae live) either hanging on fallen tree branches or on the ground.The biology of members of Paratenetus: erect and slanting. The slanting setae are characterized as subdepressed when the angle between the base of the seta and the elytra is between 10 and 40\u00b0, semierect when the angle is between 40 and 60\u00b0, and suberect when the angle is between 60 and 80\u00b0.There are two types of setae on the elytra of Motschulsky, 1868http://species-id.net/wiki/Paratenetus_gibbipennisParatenetus gibbipennis Motschulsky, 1868: 193. Type locality: \u00abAtlanta, G\u00e9orgie am\u00e9ricaine\u00bb .Paratenetus cribratus Motschulsky, 1868: 193. Type locality: \u00abG\u00e9orgie am\u00e9ricaine\u00bb . syn. n.Paratenetus gibbipennis. It bears the following labels: \u201c[green round disc] / [small brick red square label] / type [handwritten] / Paratenetus gibbipennis Motch Am. b. Mobile [handwritten on a rectangular green label].\u201d The specimen is intact although many of the setae on the pronotum and elytra are gone. The provenance of the specimen is doubtful. In the key to the Paratenetus in his collection, Motschulsky\u2019s collection at ZMMU contains a single specimen, a female, under the name Paratenetus cribratus. It bears the following labels: \u201c[green round disc] / Atlanta [handwritten] / type [handwritten] / Paratenetus cribratus Motch Am. bor. Atlanta [handwritten on a rectangular green label].\u201d The specimen is missing the left antennomeres 3\u201311 and the posterior legs.Motschulsky\u2019s collection contains a single specimen, a male, under the name Paratenetus gibbipennis and Paratenetus cribratus on the account that the first species has the lateral denticles of the pronotum very short while the second species has strong denticles. From an examination of the types, we cannot sustain Motschulsky\u2019s affirmation; the denticles are basically of the same size on both specimens.Paratenetus fuscus differ from the other three species treated by having the metaventrite very short. Paratenetus gibbipennis differs from Paratenetus fuscus by having few short erect setae on the elytra.This species and PageBreakly transverse. Pronotum with maximum width near midlength or slightly anterior to midlength; punctures moderately dense, not subcontiguous even over lateral half. Elytra very convex; slanting setae subdepressed, erect setae very few, short. Metaventrite short, length along midline clearly shorter than length of abdominal ventrite 2 along midline. Male protibia with calcar near middle along ventral surface; male mesotibia with short, in some specimens very short, more or less perpendicular preapical protuberance. Parameres with sides more or less parallel towards apex, apex not particularly acute . Rennie (CNC). Brandon (RBCM). Telford (NFC). Winnipeg (RBCM). Ontario. \u201cJonction Hwy 17 & 71\u201d (CNC). Bainsville (LEMM). Prince Edward Co. . Lancaster (LEMM). Chaffeys Locks Biol. Station (CNC). Alfred (CNC). Long Sault (CNC). 10 km W North Gower (CNC). Nepean (CNC). Belleville (CUIC). Thwartway Island, St. Lawrence Is. Nat. Park (CNC). Point Pelee (CNC). 2 km SE Spencerville (CNC). 4 km SW Kanata (CNC). Ottawa (CNC). Constance Bay (CMN). 4 km N of Westport (CNC). Campden (CNC). Rondeau Prov. Park (CNC). Arnprior (CNC). Erieau (CNC). 7 km W. Carleton Place (CNC). Blackburn (CNC). Normandale (CNC). Pelee Island (CNC). Hamilton (CNC). Flint Hill, nr Kemptville (CNC). Trenton (CNC). Toronto . Milton (CNC). Quebec. Montreal (CNC). Rigaud (CNC). Gatineau . Blind Lake, Gatineau Park (CNC). Gatineau Park (DENH). Hudson Heights (CNC). Oka (CNC). Ormstown (CNC). United States of America. Alabama.PageBreakMobile Co.: Mt. Vernon (CUIC). Monroe Co.: Haines Island Park, 3.5 mi. W Franklin (FSC). Connecticut.Fairfield Co.: Westport (AMNH). Litchfield Co.: Torrington (DENH); Canaan (TAMU); Cornwall . Georgia.Clarke Co.: 5 mi W Athens (GMNH); Whitehall Forest (GMNH). Rabun Co.: Tally Mill Crk. at Hwy 28 (CNC); Satolah (CNC). Illinois. \u201cN. Ill.\u201d (MCZ). \u201cIll.\u201d (USNM). Maine.Cumberland Co.: Portland (CNC). Kennebec Co.: Monmouth (MCZ). Oxford Co.: Paris (MCZ). Massachusetts. \u201cMass.\u201d (USNM). Bristol Co.: Swansea (MCZ); Somerset (MCZ); Dighton (MCZ); Fall River (MCZ). Hampshire Co.: Mount Tom (MCZ). Middlesex Co.: Waverly (USNM); Framingham ; Lowell (MCZ); Sherborn ; Hopkinton (CUIC); Cambridge ; Newton (MCZ). Norfolk Co.: Brookline ; Sharon (CUIC). Michigan.Marquette Co.: Marquette (USNM). Oakland Co. (CUIC). Wayne Co.: Detroit . Minnesota.Crow Wing Co.: Brainerd (CNC). Hennepin Co.: Lake Minnetonka (CUIC). Missouri.Saint Charles Co.: St. Charles (MCZ). Nebraska.Cuming Co.: West Point (USNM). New Hampshire.Grafton Co.: Franconia ; 0.5 mi S Rumney (DENH); Hanover (DENH). Rockingham Co.: Hampton ; Odiorne Point State Park (DENH). Strafford Co.: Somersworth (DENH); Durham (DENH); 3 mi. E Durham (DENH). New Jersey.Union Co.: Union ; Roselle (USNM); Elizabeth (USNM). New York. \u201cS[taten] I[sland]\u201d (MCZ). Dutchess Co.: Bulls Head (AMNH). Oswego Co.: North Pond (CUIC); Oswego (CUIC). Queens Co.: Flushing, L.I. (CUIC). North Carolina.Haywood Co.: Round Knob (USNM). Henderson Co.: 14 mi NW Hendersonville (SEMC). Macon Co.: 3 mi NW Highlands (DENH). Montgomery Co.: 2 mi S Eldorado (DENH). Yancey Co.: Black Mountains (AMNH). North Dakota.Richland Co.: Mirror Pool (USNM). Ohio. \u201cOhio\u201d (MCZ). Pennsylvania. \u201cPenn\u201d (MCZ). Allegheny Co.: Allegheny (USNM). Rhode Island. \u201cR.I.\u201d (USNM). South Carolina.Calhoun Co.: Wannamaker NP, St. Matthews (JCC). Chester Co.: Leeds (JCC). Edgefield Co.: Sumter Nat. For. (DENH). Lexington Co.: West Columbia (JCC). Newberry Co.: Billy Dreher Island State Park (JCC). Pickens Co.: Nine Times (JCC). Union Co.: Sedalia (JCC). Tennessee. \u201cChilhowee Mountain\u201d (CMN). Blount Co.: Rt. 129 just below rd. at The Narrows Overlook, GSMNP (LSAM); Ace Gap, GSMNP (LSAM). Cocke Co.: Gabes Mtn., GSMNP (LSAM). Sevier Co.: 0.5 mi W Laurel Falls Trailhead, GSMNP (LSAM); Twin Creeks, GSMNP (LSAM); Grapeyard Ridge (LSAM). Texas.Blanco Co.: Cypress Mill (USNM). Virginia.Giles Co.: Bald Knob, Mountain Lake (USNM); 9 km N Mountain Lake (USNM). Lee Co.: Pennington Gap (USNM). Wisconsin.Bayfield Co.: Bayfield (USNM). Dane Co.: Madison (TAMU). Shawano Co.: Tilleda (FSC).We have seen 660 specimens from the following localities. Canada. Females are much more abundant in collections than males. Of 183 specimens randomly selected, 8 were males (4.4%) and 175 were females (95.6%). The males came from Georgia (n=1), Alabama (n=6), and Missouri (n=1). No males were found among the 160+ randomly selected specimens from Canada and the northern states.Specimens were collected in January (n=1), February (n=1), March (n=89), April (n=64), May (n=8), June (n=61), July (n=20), August (n=95), September (n=31), October (n=38), November (n=6) and December (n=2).Labels on specimens read \u201cin leaf litter\u201d (6 specimens); \u201cin leaf litter of black birch and shrubs around and on areas of exposed rock\u201d (71); \u201cforest litter sifting\u201d (2); \u201cforest litter\u201d (3); \u201cmoist forest berlese\u201d (1).LeConte, 1850http://species-id.net/wiki/Paratenetus_fuscusParatenetus fuscus LeConte, 1850: 223. Type locality: Lake Superior (inferred from the title of the book).Paratenetus crinitus Fall, 1907: 253. Type locality: \u00abTrout Spring [New Mexico]\u00bb . syn. n.Paratenetus fuscus. It bears the following labels: \u201c[pale green round disc] / Type 4684 [partially handwritten on a red square label] / P. fuscus Lec. [handwritten].\u201d The specimen is intact.LeConte\u2019s collection at MCZ contains a single male specimen under the name PageBreakParatenetus crinitus from one specimen now at the MCZ. It bears the following labels: \u201cTrout sp. N.M. May [handwritten] / crinitus. Type [partially handwritten] / M.C.Z Type 24612 [red square label] / H.C. Fall Collection.\u201d The specimen is intact.Fall described Paratenetus crinitus and mentioned that \u201cin crinitus the metasternum is almost as short as in fuscus, which species is, however, very distinct by its subinflated elytra, more rounded sides of the prothorax and absence of erect hairs on the upper surface.\u201d Obviously Fall did not study the syntype in LeConte\u2019s collection since the specimen bears many erect hairs. LeConte never mentioned that character in his description and obviously Fall misidentified LeConte\u2019s species. We have studied the type specimens of both species and find no structural differences to separate them.Paratenetus gibbipennis by the character states listed in the description.This species differs from Paratenetus gibbipennis except for the following: slanting setae on elytra less depressed, semierect, occasionally even suberect; erect setae numerous, in seven or eight rows; metaventrite slightly longer, length along midline subequal to slightly shorter than length of abdominal ventrite 2 along midline.Same character states as This species ranges from Quebec City to the Rocky Mountains in northeastern British Columbia, north to southern Northwest Territories, south to northern New Mexico, northeastern Kansas, and Maryland .Alberta. \u201cTp. 74, Rge. 25, W. 5 Mer.\u201d (CNC). \u201cTp. 11, Rge. 1, W. 5 Mer.\u201d (CNC). Waterton Park (CNC). Calgary . Castor (UASM). Edmonton . Stettler (CNC). Cochrane (CNC). 30 km W Cochrane (CNC). Cypress Hills (CNC). Waiparous (CNC). Jumpingpound Creek (CNC). Sundre (CNC). Elkwater (CNC). British Columbia. North Pine (UBC). Pouce Coupe (UBC). Manitoba. \u201cTp. 9, Rge. 16, W. 1 Mer.\u201d (CNC). Aweme . Brandon (RBCM). Sandilands (JBWM). Birds Hill Prov. Park (ENMU). Husavik (CNC). Northwest Territories. Louise Falls, Hay River (CNC). Simpson (CAS). Ontario. Prince Edward Co. . Pelee Island (CNC). Ottawa (CNC). Constance Bay (CMN). Trenton (CNC). Arnprior (CNC). Quebec. Chelsea (CNC). Rigaud (CNC). Sainte-Croix-de-Lotbiniere (LEMM). Cap Rouge (CNC). Saskatchewan. Lac La Ronge (CNC). Morse (RSM). Rosefield (RSM). Oxbow (USNM). United States of America. Colorado.PageBreakBoulder Co.: Boulder . Custer Co. (USNM). Douglas Co.: Castle Rock (CNC). El Paso Co.: Colorado Springs (USNM). Jefferson Co.: Lookout Mountain (CUIC). Connecticut.Fairfield Co.: Westport (AMNH). District of Columbia. \u201cDC\u201d . Illinois. \u201cN. Ill.\u201d (MCZ). Champaign Co.: Urbana (USNM). Iowa. \u201cIowa\u201d . Johnson Co.: Iowa City . Story Co.: Ames (USNM). Kansas. \u201cKs\u201d (USNM). \u201cKans\u201d (USNM). Douglas Co.: Lawrence (CNC). Shawnee Co.: Topeka (USNM). Maryland. \u201cMd.\u201d (CNC). Anne Arundel Co.: 6 km ESE Laurel (USNM). Massachusetts. \u201cMass\u201d (USNM). Essex Co.: Lynn ; Salem (USNM). Middlesex Co.: Sherborn ; Tyngsboro (MCZ). Norfolk Co.: Brookline (MCZ). Michigan.Marquette Co.: Marquette (USNM). Montana. \u201cMont.\u201d (CUIC). \u201cMontana\u201d (USNM). Dawson Co.: Glendive (USNM). Powder River Co.: Fort Howes (USNM). Rosebud Co.: Colstrip (USNM). Nebraska. \u201cNeb.\u201d (USNM). Red Willow Co.: McCook (MCZ). New Mexico. \u201cN. Mex.\u201d (USNM). San Miguel Co.: Trout Spring (MCZ). New York. \u201cN.Y.\u201d . Westchester Co.: Peekskill (CUIC). New York Co.: Central Park, L.I. (USNM). North Dakota.Richland Co.: Mirror Pool (USNM). Rhode Island. \u201cR.I.\u201d (USNM). South Dakota.Jackson Co.: Cottonwood (RLAC). Tennessee. \u201cTenn.\u201d (MCZ). Vermont. \u201cVt.\u201d (MCZ). Wisconsin. \u201cWis\u201d (MCZ). Sauk Co.: Spring Green (USNM). Wyoming.Converse Co.: 11 mi N Douglas (CNC). Laramie Co.: Cheyenne (USNM).We have seen 305 specimens from the following localities. Canada. Females are a little more common in collections than males. Of 45 randomly selected specimens, 28 (62%) were females and 17 (38%) were males.Specimens were collected in February (n=1), March (n=30), April (n=58), May (n=8), June (n=40), July (n=7), August (n=19), September (n=14), October (n=5) and November (n=4).Spinola, 1844http://species-id.net/wiki/Paratenetus_punctatusLatridius pubescensnomen dubium]. Type locality: United States (inferred from title of the paper). Say, 1826: 265 \u201d; the second, a male \u201cParalectotype Paratenetus punctatus Spinola Ekis 74 [handwritten]\u201d; and the third, a female \u201cLectotype Paratenetus punctatus (Spinola) Ekis 74 [handwritten]\u201d. The first two specimens correspond neither to our concept of Paratenetus punctatus nor to any other North American species we have seen. The specimens are in poor condition, with almost all the setae gone, but they appear to be conspecific. Although Spinola indicated that all three of his specimens came from the United States and were provided by \u201cMr. [John Eatton] LeConte,\u201d these two specimens may have originated from Mexico, Central America or South America. The third specimen, a small individual (3.2 mm), fits our concept of Paratenetus punctatus and is here selected as lectotype. The label \u201cLectotype Paratenetus punctatus Spinola des. Y. Bousquet 2012\u201d has been attached to the specimen.Paratenetus punctatus can be separated from the other North American species of Paratenetus by their large size (3 mm or more). The vast majority of specimens of the other species are less than 3 mm long. Otherwise, the species can be separated from Paratenetus exutus in having the antennomere 8 subquadrate, the pronotum wider clearly anterior to the midlength, the punctation on the pronotum coarser, the slanting setae on the elytra slightly longer and more erect and the protibia of the male with a calcar along ventral surface. From Paratenetus texanus, this species is best separated in having the pronotum widest anterior to the midlength and the punctures on the pronotum coarser and denser, in part subcontiguous along the lateral half.Many specimens of Paratenetus gibbipennis and Paratenetus fuscus; slanting setae semierect in the vast majority of specimens, suberect in some specimens, erect setae few. Metaventrite long, length along midline longer than length of abdominal ventrite 2 along midline. Male protibia with calcar near middle along ventral surface; male mesotibia with very short, preapical spine, oriented perpendicularly or obliquely to long axis of tibia. Parameres with sides more or less parallel to very slightly convergent towards apex; apex more or less rounded . Victoria Beach (JBWM). New Brunswick. Jackson Falls, Carleton Co. (RWC). 10 km NW New River Beach, Charlotte Co. (AFC). 12 km SSE Upper Napan, Northumberland Co. (RWC). Cranberry Lake Protected Natural Area, Queens Co. (AFC). Acadia Research Forest, Sunbury Co. . Charters Settlement, York Co. (RWC). Canterbury, York Co. (RWC). 15 km W Tracy, York Co. (RWC). 14 km WSW Tracy, York Co. (AFC). Ontario. Ottawa (CNC). Constance Bay (CMN). Flint Hill, nr Kemptville (CNC). Ad & Lennox Co. . Pelee Island (CNC). Leamington (CNC). Hastings Co. (CNC). Walsingham (CNC). Prince Edward Co. . Point Pelee (CNC). Rondeau Prov. Pk. (CNC). Arnprior (CNC). Chaffeys Locks (CNC). Northumberland Co. (CNC). Sudbury (CNC). Hamilton (CNC). Gordon Island (St. Lawrence Is. Nat. Pk.) (CNC). 13 km W of Mattawa (CNC). Toronto (CUIC). 2\u20135 km W Mallorytown Landing (CMN). Quebec. Rouville (CNC). Fort Coulonge (CNC). Parc Provincial d\u2019Oka (CNC). Berthierville (CNC). Parc de la Gatineau (CNC). Laniel (CNC). Ile-du-Grand-Calumet (Pontiac) (CNC). Rigaud (CNC). Montreal PageBreak(CNC). Parc de la Yamaska (CNC). United States of America. Arkansas.PageBreakPageBreakGarland Co.: 3 mi W Crystal Springs (SEMC). Connecticut.Fairfield Co.: Westport (AMNH). Litchfield Co.: Litchfield (AMNH). New Haven Co.: Middlebury (USNM); Hamden (CUIC). District of Columbia. \u201cD.Col.\u201d (USNM). Takoma Park (USNM). Washington (USNM). Florida. \u201cFla\u201d (USNM). Alachua Co.: Gainesville (FSC); Newnans Lake (RLAC). Duval Co.: Jacksonville (USNM). Escambia Co.: Pensacola (FSC). Hillsborough Co.: Tampa (USNM). Indian River Co.: south of Vero Beach (FSC). Levy Co.: 4 mi SW Archer (FSC). Marion Co.: Juniper Springs (FSC); Rainbow Springs (FSC); Ocala National Forest . Palm Beach Co.: Lake Worth (CUIC). Polk Co.: Lake Marion Creek (GMNH). Putnam Co.: 2.5 mi NE Florahome (FSC); Crescent City (USNM); Welaka Exp. Sta. . Saint Johns Co.: St. Augustine (MCZ). Santa Rosa Co.: 4 mi N Munson (LSAM). Seminole Co.: Lake Mary (MCZ). Volusia Co.: South Daytona (CNC); Daytona (USNM). Georgia.Charlton Co.: 2.8 mi N Saint George (FSC). Johnson Co.: 1 mi E Kite (FSC); Suwanee Canal Rec. Area (FSC). Montgomery Co.: 5 mi W Uvalda (GMNH). Rabun Co. (MCZ); Clayton (MCZ). Tattnall Co. (FSC). Union Co.: \u201cHerbert Reece Park\u201d (GMNH). Illinois.Knox Co.: Galesburgh (MCZ). Macon Co. (FSC). Indiana.Allen Co.: \u201cSchoaf Park\u201d (USNM). Howard Co.: \u201cNW Howard Co.\u201d (LSAM). Jasper Co.: Jasper/Pulaski St. Forest (USNM). LaPorte Co.: Michigan City (USNM). Monroe Co.: Bloomington . Porter Co.: Dunes St. Pk. (RLAC). Tippecanoe Co. ; \u201cMcCormick Woods\u201d (USNM). Iowa. \u201cIowa\u201d (USNM). Johnson Co.: Iowa City (USNM). Polk Co.: \u201cBrown WDS Psv\u201d (CUIC); W. Saylorville Lake . Kansas. \u201cKans\u201d (USNM). Cherokee Co.: 2 mi S Galena (SEMC). Crawford Co.: Pittsburg (SEMC); 2 mi W Pittsburg (SEMC). Douglas Co.: 2 mi NW of Baldwin (SEMC). Jackson Co.: 6.5 km W Mayetta (SEMC). Jefferson Co.: 1 km SW Perry State Park (SEMC). Johnson Co.: Overland Park Arboretum (SEMC). Labette Co.: Big Hill Reservoir (SEMC). Neosho Co.: 2 mi SE Erie (SEMC). Sedgwick Co.: 0.5 mi S of Derby (SEMC). Shawnee Co.: S of intersection Woodring Rd & 69th St (SEMC). Kentucky. \u201cKy\u201d (USNM). Marshall Co. (FSC). Louisiana.Caddo Parish: Jacobs Nature Park (LSAM). Claiborne Parish: Corney Lake (CNC). East Feliciana Parish: Idlewild Exp. Station (LSAM). Livingston Parish: Livingston (LSAM). Natchitoches Parish: Kisatchie Nat. For. (LSAM). West Feliciana Parish: Saint Francisville (CMN); Tunica Hills, 0.5 mi W Weyanoke (LSAM). Maine.Androscoggin Co.: Wales (MCZ). Cumberland Co.: Casco (CUIC). Franklin Co.: Dead River (USNM); Farmington (USNM). Kennebec Co.: Augusta (DENH); Monmouth (MCZ). Oxford Co.: Rumford (USNM); Bethel (AMNH). Penobscot Co.: Lee (DENH); Passadumkeag (CUIC). Piscataquis Co.: Greenville (USNM). Washington Co.: Beddington (USNM). York Co.: West Lebanon (DENH). Maryland.Allegany Co.: Piclic Ridge, 5 km SE Pratt (USNM); Fifteen Mile Creek (RLAC). Anne Arundel Co.: 8 km ESE Laurel (USNM); 6 km ESE Laurel (USNM); Edgewater (USNM); 6 km S Edgewater (USNM); 3 km WSW Bristol at Jug Bay (USNM); Odenton . Baltimore Co.: 4 km SW Cockeysville (USNM); Catonsville (USNM). Calvert Co.: Plum Point (USNM). Carroll Co.: Eldersburgh (USNM). Cecil Co.: Pleasant Hill (USNM); Port Deposit (USNM). Frederick Co.: 2 mi W Thurmont (USNM). Garrett Co.: Rock Lodge, 4 km SW Bittinger (USNM); 7 mi N Oakland (USNM). Montgomery Co.: Kensington (USNM); Potomac (USNM); Rockville (USNM); Plummers Island (USNM); Great Falls (USNM); Hughes Hollow area, 5 km W Seneca (USNM). Prince Georges Co.: Cheverly (USNM); Bladensburg (USNM); Takoma Park (USNM); Laurel (USNM); Priest Bridge (USNM); Oxon Hill (USNM); Beltsville (USNM); Greenbelt (Park) (USNM); Bowie (USNM). Somerset Co.: Shelltown (USNM). Talbot Co.: 3 km SE Easton (USNM); Wittman (USNM); McDaniel (USNM). Worcester Co.: Assateague Island (USNM). Massachusetts.Barnstable Co.: Cape Cod (CNC). Bristol Co.: Dartmouth (MCZ). Essex Co.: Nahant (MCZ). Hampden Co.: Springfield (USNM). Middlesex Co.: Lincoln (MCZ); Sherborn (MCZ); Framingham (MCZ); Hopkinton (MCZ); Tyngsboro (MCZ); Natick (MCZ); Cambridge (MCZ). Norfolk Co.: Brookline (MCZ). Plymouth Co.: Marion (USNM). Suffolk Co.: Boston (MCZ); Jamaica Plain (CUIC). Michigan.Shiawassee Co.: Rose Lake Wldlf. Exp. Station (USNM). Wayne Co.: Detroit (USNM). Minnesota.Hennepin Co.: Minneapolis (CNC). Houston Co.: Winnebago Cr. Vy., 3\u20134 m NE Eitzen (USNM). Saint Louis Co.: Duluth (MCZ). Mississippi.George Co.: Lucedale (CUIC). Greene Co.: Leakesville (CUIC). Lauderdale Co.: Marion (MCZ). Missouri.Barry Co.: Mark Twain Nat. For. (FSC). Boone Co.: Ashland Wildlife Ar. (TAMU). Clay Co.: Cooley Lake (FSC). Greene Co.: near James River (TAMU). Jackson Co.: Raytown (FSC). Oregon Co.: Mark Twain Nat. For. (FSC). Randolph Co.: 1 mi E Moberly (TAMU). New Hampshire. \u201cN.H.\u201d (USNM). Coos Co.: Gorham (CNC); Mt. Washington . Grafton Co.: Mt. Moosilauke (MCZ); Bedell Bridge St. Pk. (DENH); Bath (DENH). Hillsborough Co.: Antrim (MCZ). Merrimack Co.: Concord (DENH). Strafford Co.: 1 mi SW Durham (DENH); Dover (DENH). New Jersey. \u201cN.J.\u201d (AMNH). Atlantic Co.: Buena (MCZ). Bergen Co.: Fort Lee (AMNH). Burlington Co.: Wharton State Forest (TAMU); Pemberton (USNM); 7 mi E Batsto (USNM). Cumberland Co.: Rutgers Exp. Sta. (USNM). Essex Co.: South Orange (MCZ); Eagle Rock (USNM); Montclair (USNM). Gloucester Co.: Malaga (USNM). Monmouth Co.: Highlands (USNM). Monroe Co.: Delaware Water Gap (USNM). Morris Co.: Boonton (USNM). Ocean Co.: Lakehurst . Orange Co.: Greenwood Lake . New York. \u201cS.I.\u201d (USNM). Albany Co.: Delmar (CUIC); Rensselaerville (USNM). Clinton Co.: vic. Taylor Pond Campground (GMNH). Erie Co.: Buffalo . Essex Co.: New Russia (CUIC); Whiteface Mt. (USNM). Orange Co.: Greenwood Lake (CUIC); Fort Montgomery (CUIC); West Point (USNM). Putnam Co.: Brewster (CUIC). Rockland Co.: Nyack (CUIC). Saint Lawrence Co.: Rossie (USNM). Seneca Co.: Willard (USNM). Suffolk Co.: Huntington, Long Island (DENH); Southold, L.I. (CUIC); Wyandanch, L.I. (USNM); Bellport (USNM); Yaphank (USNM). Tompkins Co.: Ithaca ; Dryden (CUIC). Yates Co.: Seneca Lake (USNM). North Carolina. \u201cN.C.\u201d (MCZ). \u201cRound Knob\u201d (USNM). Brunswick Co.: Southport (FSC). Buncombe Co.: 6 mi S Asheville (SEMC). Burke Co.: Linville Falls (CNC). Columbus Co.: Lake Waccamaw (USNM). Gates Co.: 6 km ENE Corapeake (USNM). Haywood Co.: Cove Creek (JCC); Cataloochee Divide ; 9 mi W Waynesville (SEMC). Henderson Co.: Fletcher (FSC). Jackson Co.: Balsam (USNM). Macon Co.: Nantahala Gap (CUIC); Highlands . Mitchell Co. (USNM). Moore Co.: Southern Pines (USNM). New Hanover Co.: Wilmington (USNM). Swain Co.: 2.5 mi NNE Cherokee, GSMNP (SEMC); Andrews Bald, GSMNP (LSAM); Ekaneetlee Gap, GSMNP (LSAM). Transylvania Co.: Lake Toxaway (AMNH). Watauga Co.: 3 mi NW Blowing Rock (TAMU). Yancey Co.: Black Mountains . Ohio.Ashland Co.: Mohican St. Pk. (FSC). Champaign Co.: Cedar Swamp (FSC). Ottawa Co.: Fishery Bay, S. Bass Isl. (CUIC). Union Co. (CUIC). Oklahoma.Latimer Co. ; 5 mi W Red Oak . Pennsylvania. \u201cPen\u201d . Allegheny Co.: Allegheny (CUIC). Dauphin Co.: Dauphin (CUIC). Lehigh Co.: Lehigh Gap (USNM). Luzerne Co.: Hazleton (MCZ). Montgomery Co.: Abington (MCZ). Philadelphia Co.: Frankford (USNM). Pike Co.: Twin Lakes (USNM). South Carolina. \u201cS.C.\u201d (MCZ). \u201cShiloh\u201d (JCC). Georgetown Co.: Sandy Island (JCC). Richland Co.: Pontiac (JCC). Tennessee. \u201cChimney Camp, Gt. Smoky Mts.\u201d (CUIC). Blount Co.: Cades Cove, GSMNP . Cocke Co.: Davenport Gap, GSMNP (LSAM). Sevier Co.: Goshen Prong, GSMNP (LSAM); Chimney Tops Picnic Nature Trail, GSMNP (LSAM); Roaring Fork, GSMNP (LSAM); Brushy Mnt., GSMNP (LSAM). Texas.Brazos Co.: College Station (TAMU). Vermont.Bennington Co.: Manchester (MCZ). Chittenden Co.: Burlington (USNM). Orange Co.: 12 mi E Chelsea (TAMU). Virginia. \u201cMiddletown\u201d (MCZ). \u201cFranklin Park\u201d (USNM). Arlington Co.: Glencarlyn (USNM). Fairfax Co.: Vienna (USNM); Black Pond (USNM); Great Falls (USNM); Great Falls N.P. near Clay Pond (USNM); Great Falls N.P. near quarry site (USNM). Giles Co.: Mountain Lake, Univ. Va. Biological Sta. (USNM). Lee Co.: Pennington Gap (MCZ). Loudoun Co.: Middleburg (USNM). Louisa Co.: Gum Spring (USNM). Montgomery Co.: Blacksburg (CUIC). Nelson Co. (USNM). Page Co.: Skyland . Rockbridge Co.: Natural Bridge (USNM). Shenandoah Co.: New Market (USNM). Warren Co.: 7 km NNE Linden, summit of Blue Mt. (USNM). Alexandria (USNM). West Virginia.Greenbrier Co.: W. Sulphur (USNM). Jefferson Co.: Harpers Ferry (USNM); Shepherdstown (USNM). Pocahontas Co.: Cranberry Glades (USNM). Preston Co.: Aurora (USNM). Wisconsin. \u201cWis\u201d (MCZ). Bayfield Co.: Bayfield (USNM). Douglas Co.: Bennett (USNM). Sauk Co.: Sauk City (GMNH). Shawano Co.: Tilleda (FSC). Wood Co.: Griffith State Nursery (USNM). Wyoming.Weston Co.: Newcastle (USNM).We have seen 1215 specimens from the following localities. Canada. Paratenetus fuscus but is easily separated by the coarse, irregular punctation on the pronotum and by the longer metaventrite.This species varies in regard to the punctation and setae. The punctation on the pronotum is coarse and in most specimens free on the disc and very close, in part subcontiguous over the sides; in some specimens the punctation is denser, being subcontiguous on the disc and contiguous all over the lateral sides. The slanting setae on the elytra are usually semierect but in some specimens they are less inclined and the erect setae are difficult to distinguish. The erect setae are usually short and moderately numerous but in some specimens, they can be relatively long or much more numerous; in such case the species can be confused with PageBreakFemales are more common in collections than males. Of 220 randomly selected specimens, 169 (77%) were females and 51 (23%) were males.Specimens were collected in March (n=6), April (n=89), May (n=296), June (n=384), July (n=152), August (n=67), September (n=40), October (n=9), November (n=5), and December (n=2).Malacosoma americana on Prunus serotina at mixed forest edge, shale barren area\u201d (7 specimens), \u201cshaken from and reared in moldy frass in old nest of Malacosoma americana on Prunus serotina\u201d (13), \u201cbeaten from dead leaf clusters on cut branches of Carpinus caroliniana at forest edge\u201d (6), \u201cbeaten from dead leaf clusters on branches of fallen Populus deltoides\u201d (7), \u201cbeaten from dead leaf clusters on fallen broken branch of Tilia americana in shade, mixed forest\u201d (2), \u201cbeaten from dead hanging leaf clusters on fallen Ailanthus in mixed forest\u201d (6), \u201cshaken from dead leaves on fallen branches of Quercus rubra\u201d (4), \u201cin moldy leaf clusters on fallen branch of Quercus alba in shade\u201d (6), \u201cbeaten from dead leaves of wind-blown Quercus rubra\u201d (1), \u201cbeaten from dead leaf clusters on fallen branches of Quercus rubra in mixed forest\u201d (14); \u201cat black light in longleaf pine and mixed oak, sand barrens\u201d (23), \u201cin moldy leaves on fallen branches of Acer rubrum\u201d (4), \u201cat black light in oak & longleaf pine sand barren\u201d (5); \u201cat black light; open sandy gap in mixed forest\u201d (1); \u201cat black light in mixed deciduous forest\u201d (1); \u201cat black light in mixed hardwood and loblolly pine forest\u201d (1); \u201cat black light in mixed pine and hardwood forest\u201d (3); \u201cbeaten from dead leaf clusters on branches of Castanea out ca. 2 weeks earlier\u201d (5); \u201cat black light near mixed forest, farmed fields and tidal creek\u201d (4); \u201cbeach drift\u201d (1); \u201cfrom pile of moldy thatch\u201d (1); \u201cin moldy leaf clusters on cut branches of Prunus serotina\u201d (4); \u201cin moldy leaf clusters on cut branches of Morus\u201d (2); \u201cbeaten from dead leaf clusters on cut branches of Acer rubrum at mixed forest edge\u201d (10); \u201cin old nest of Malacosoma on Prunus\u201d (2); \u201cin dead leaves on branches of fallen oak\u201d (1); \u201cshaken from dead leaves on cut Sassafras\u201d (7); \u201cbeaten from dead leaf clusters on fallen branch Acer negundo at mixed forest edge\u201d (1); \u201cat black light in tree canopy, mixed broken forest and residential area\u201d (43); \u201cat black light in mixed hardwood forest near pond and river\u201d (8); \u201cat black light in mixed forest, bluff above river\u201d (2); \u201cin old tent Malacosoma americana\u201d (5); \u201cat black light\u201d (2); \u201cin old tent nest of Malacosoma americana with moldy frass, on Prunus serotina\u201d (1); \u201cshaken from dry leaf (Vitis sp.) nest of Sciurus carolinensis in vine tangle ca. 3 m above ground\u201d (1); \u201cat black light at edge of clearing in mixed forest near drying vernal pool\u201d (2); \u201cat black light in mixed forest near vernal pools\u201d (8); \u201cat black light sheet in open mature mixed forest near river\u201d (3); \u201cbeaten from dead leaf clusters on fallen branch of Liriodendron in mixed forest\u201d (9); \u201cbeaten ex spruce\u201d (1); \u201ccollected in tents Malacosoma americana\u201d (12); \u201cin web of Malacosoma\u201d (3); \u201con Pinus strobus\u201d (2); \u201cex. canopy trap\u201d (34); \u201cintercept trap\u201d (1); \u201cbeating dead leaves\u201d (8); \u201cbtng oak blowdown\u201d (2); \u201cleaf litter\u201d (1); \u201cdead moldy leaves\u201d (1); \u201cbeating veg.\u201d (2); \u201cbeating flowers\u201d (2).Labels on specimens read \u201cin overwintered nest remains of PageBreakBousquet & Bouchardsp. n.http://zoobank.org/E79EDDDF-59F8-4A43-880F-2A86CF8EB2F2http://species-id.net/wiki/Paratenetus_exutusHolotype (\u2642) labeled \u201cTabusintac, N.S. 20-VI-1939 W.J. Brown / Holotype Paratenetus exutus Bousquet & Bouchard CNC No. 24035.\u201d The specimen is deposited in the CNC.Manitoba. Ninette, 31-V-1958, J.F. McAlpine ; same locality, 30-V-1958, R.B. Madge . New Brunswick. Tabusintac, 19-VI-1939, W.J. Brown ; same data but 20-VI. 1939 or 22-VI-1939 . York Co., 14 km WSW of Tracy, S of Rt 646, 45.6741\u00b0N, 66.8161\u00b0W, 26 April-10 May 2010, R. Webster & C. MacKay coll. . York Co., 15 km W of Tracy off Rt. 645, 45.6848\u00b0N, 66.8821\u00b0W, 19\u201325 May 2009, R. Webster & M.-A. Gigu\u00e8re coll. . York Co., New Maryland Charters Settlement, 45.8430\u00b0N, 66.7275\u00b0W, 12 July 2005, R. P. Webster coll. ; same locality but 45.8340\u00b0N, 66.7450\u00b0W, 30 April 2005 . Queens Co., Cranberry Lake P.N.A., 46.1125\u00b0N, 65.6075\u00b0W, 24 April-5 May 2009, R. Webster & M.-A. Gigu\u00e8re coll. ; same locality but 3\u201313 May 2011, M. Roy & V. Webster coll. . Carleton Co., Jackson Falls, \u201cBell Forest\u201d, 46.2200\u00b0N, 67.7231\u00b0W, 28.April-9 May 2009, R. Webster & M.-A. Gigu\u00e8re coll. . Carleton Co., Wakefield Meduxnekeag Valley Nature Preserve, 46.1890\u00b0N, 67.6766\u00b0W, 8 June 2005, M. Gigu\u00e8re & R. Webster coll. ; same locality but 46.1935\u00b0N, 67.6825\u00b0W, 19 April 2995 . Albert Co., Shepody N.W.A., Germantown Section, 45.7101\u00b0N, 64.7542\u00b0W, 30 July 2004, R.P. Webster coll. . Sunbury Co., Acadia Research Forest, 45.9866\u00b0N, 66.3841\u00b0W, 8\u201313 May 2009, 13\u201319 May 2009, 19\u201325 May 2009, 16\u201324 June 2009, R. Webster & M.-A. Gigu\u00e8re coll. . Nova Scotia. St. Peters, 25-VII-1930, M.L. Prebble . Ontario. Alfred bog, 16.VI.1981, A. Davies . Quebec. Sainte-Catherine Portneuf, 29-VIII-1971, Claude Chantal . D[ivision de] R[ecensement] Bellechasse, St-N\u00e9r\u00e9e, 10.VII.1976, J.F. Landry . Cascapedia, 11.VI.1933, W.J. Brown .Paratypes from the following localities: exutus, -a, -um (deprived of) and alludes to the fact that the protibia of the male lacks the spinelike projection found in the other American (north of Mexico) species.The specific name comes from the Latin participle Paratenetus punctatus and Paratenetus texanus in having the antennomere 8 transverse. The males are also easily recognized among the species treated here in having no calcar on the protibia and a relatively long apical spine, oriented more or less parallel to long axis of tibia, on the mesotibia.This species is best separated from PageBreaktwo abdominal ventrites in the vast majority of specimens, not or only slightly darker in a few specimens. Antennomere 8 transverse. Pronotum with maximum width at or very slightly anterior of midlength . Peace River (NFC). Manitoba. Aweme (CNC). New Brunswick. Fredericton (CNC). Nova Scotia. Kentville (CNC). Annapolis Royal (CNC). Portapique (MCZ). St. Peter\u2019s (AFC). Cape Breton . Grand River . Woodside (AFC). White Point Beach, Queens Co. (JCC). Ontario. Ridgeway (MCZ). Trenton (CNC). Prince Edward Co. (CNC). La Rose Forest, near Bourget (CNC). Quebec. Hull [= Gatineau] (CAS). Lac Duparquet (LEMM). Lac Labyrinthe [Abitibi] (LEMM). Laniel (CNC). Valcartier (CNC). Saskatchewan. Red Earth (RSM). Somme (RSM). United States of America. Alabama.PageBreakPageBreakConecuh Co.: 19 km NE Evergreen (USNM). Arkansas.Newton Co.: 12 mi. W Jasper (SEMC). Connecticut.Litchfield Co.: Cornwall . District of Columbia. Washington (USNM). Florida. \u201cFla\u201d (USNM). \u201cHaulover\u201d (USNM). Alachua Co.: Cross Creek (FSC); Gainesville (RLAC); nr. Paynes Prairie St. Pk. (FSC). Brevard Co.: Hatbill St. Pk. (FSC). Dade Co.: Everglades Nat. Pk. \u201cRoyal Palm Pk.\u201d (CMN); Everglades Nat. Pk., Royal Palm Hammock (FSC). Highlands Co.: Archbold Biological Station (TAMU). Lake Co.: Camp McQuarrie (FSC). Liberty Co.: Torreya St. Pk. (FSC). Putnam Co.: 2 mi. SW Interlachen (FSC). Volusia Co.: Enterprise (USNM). Illinois.Lake Co.: Grayslake (SEMC). Indiana.Monroe Co.: Bloomington (FSC). Iowa.Buchanan Co.: Independence (USNM). Polk Co.: Walnut Woods St. Pk. . Kansas.Bourbon Co.: 9 mi SW Ft. Scott (SEMC). Crawford Co.: 3 mi NE Pittsburg (SEMC). Jefferson Co.: 1 km SW Perry State Park (SEMC); University of Kansas Field Station, Nelson Ravine Forest (SEMC); The Falin Property, 1.5 km N jct. 94th St. & Kingman Rd. (SEMC). Marshall Co.: Alcove Springs State Park (SEMC). Neosho Co.: 2 mi SE Erie (SEMC). Osage Co.: Melvern Lake Project, Outlet Park (SEMC); Pomona Lake, Outlet Park (SEMC). Pottawatomie Co.: St. George (SEMC). Wabaunsee Co.: 10 mi SW Alma (SEMC). Kentucky. \u201cKy\u201d (USNM). Lousiana.East Baton Rouge Parish: LA 37 at Comite River (LSAM). East Feliciana Parish: Boy Scout Camp Avondale, E of Clinton (LSAM); 1.2 mi S Central (LSAM). Maine.Aroostook Co.: St. Francis (DENH); Crystal (USNM); Howe Brook (USNM); Portage (USNM); Clayton Lake (USNM); Ashland (USNM). Cumberland Co.: South Portland (CUIC). Franklin Co.: Oquossoc (DENH). Hancock Co.: Blue Hill (DENH); E. Orland (USNM). Kennebec Co.: Vassalboro (USNM); Augusta (USNM). Knox Co.: Friendship (USNM). Lincoln Co.: New Harbor (USNM); Bristol (USNM); Boothbay Harbour (USNM). Oxford Co.: Peru . Penobscot Co.: Lee (USNM); Springfield (USNM). Piscataquis Co.: Kokadjo (DENH); Dover-Foxcropt (DENH); Chesuncook (USNM). Somerset Co.: Caratunk ; Embden (USNM); Bingham (USNM); Brighton (DENH); Rockwood (USNM); Seboomook (DENH). Waldo Co.: Palermo (USNM). Washington Co.: Princeton ; Wesley ; Steuben (CNC). York Co.: West Lebanon (DENH). Maryland.Carroll Co.: Finksburg (USNM). Somerset Co.: Shelltown (USNM). Talbot Co.: Wittman (USNM); 3 km SE Easton (USNM). Michigan.Marquette Co.: Marquette (USNM). Wayne Co.: Detroit (USNM). Minnesota.Becker Co.: Itasca St. Pk. area (USNM). Crow Wing Co.: Lake Hubert (CNC). Sherburne Co.: Elk River (CNC). Mississippi.George Co.: Lucedale (CUIC). Greene Co.: Leakesville (CUIC). Missouri.Greene Co.: nr. James River (TAMU). Randolph Co.: 1 mi E Moberly (TAMU). New Jersey.Atlantic Co.: 5 mi. N Hammonton (RLAC). Cape May Co.: Anglesea (USNM). Ocean Co.: Lakehurst (CUIC). Salem Co.: Lake Hudson, near Deepwater (RLAC). Union Co.: Elizabeth (USNM). New York.Suffolk Co.: Yaphank, L.I. (USNM). Ulster Co.: West Park (CUIC); Slide Mt. (CUIC). North Carolina.Buncombe Co.: Oteen (USNM); 6 mi S Asheville (SEMC). Haywood Co.: 9 mi. W Waynesville (SEMC); Cataloochee, GSMNP (LSAM); Purchase Knob, GSMNP (LSAM). Henderson Co.: Fletcher (FSC). Swain Co.: Andrews Bald, GSMNP (LSAM); Clingmans Dome, GSMNP (LSAM). Yancey Co.: Black Mountains (AMNH). North Dakota.Richland Co.: Mirror Pool (USNM). Ohio.Fairfield Co.: Barnebey Center (RLAC). Franklin Co.: Worthington (RLAC). Hamilton Co.: Cincinnati (USNM). Highland Co. (FSC). Hocking Co.: Ward Township (RLAC). Pike Co.: Jackson Lake (RLAC). Preble Co.: Hueston Woods (RLAC). Ross Co.: Tar Hollow St. Pk. (FSC). Trumbull Co.: Phalanx (CUIC). Oklahoma.Latimer Co.: Red Oak . Pennsylvania.Fayette Co.: 5 mi. W. Ohiopyle (USNM). Tennessee.Cocke Co.: Albright Grove (LSAM). Sevier Co.: Ramsey Cascade Trail, GSMNP (LSAM); Goshen Prong, GSMNP (LSAM); Indian Gap, GSMNP (LSAM). Swain Co.: near Charlies Bunion, GSMNP (FSC). Texas.Colorado Co.: Columbus (USNM). Victoria Co.: Victoria (USNM). Virginia. \u201cFt. Monroe\u201d (USNM). Covington (FSC). Bath Co.: 9.6 km N Clifton Forge (CNC). Lee Co.: Pennington Gap (MCZ). Loudoun Co.: 3 km SE Lovettsville (USNM). Montgomery Co.: Caldwell Fields . West Virginia.Mingo Co.: Justice (CUIC). Pocahontas Co.: Cranberry Glades (USNM). Wisconsin.Bayfield Co.: Bayfield (USNM). Wood Co.: Griffith State Nursery (USNM).We have seen 416 specimens, including the type material, from the following localities. Canada. While almost all specimens from Canada and northern United States had the metaventrite distinctly darker than the first two abdominal ventrites, this is not the case with the specimens from the southern states. There is also variation in the width of the antennomere 8. Most specimens have that antennomere distinctly transverse, some specimens from the southern states (particularly Louisiana) have the antennomere 8 only slightly transverse.Females are more common in collections than males. Of 105 randomly selected specimens, 76 (72%) were females and 29 (28%) were males.Specimens were collected in March (n=9), April (n=38), May (n=84), June (n=58), July (n=79), August (n=40), September (n=22), October (n=5), November (n=3), and December (n=2).Acer rubrum\u201d (3); \u201cbeaten ex spruce\u201d (35); \u201cbeaten ex fir\u201d (10); \u201con Bumelia lanuginosa\u201d (1); \u201cex. spruce\u201d (1); \u201cex. canopy trap\u201d (15); \u201cex. FIT, near upper meadow\u201d (1); \u201cex. FIT, near lower meadow\u201d (3); \u201cex. canopy malaise, near lower meadow\u201d (9); \u201cex. canopy FIT, near lower meadow\u201d (3); \u201cmalaise trap\u201d (6).Labels on specimens read \u201cat black light near mixed forest, farmed fields and tidal creek\u201d (4 specimens); \u201cat black light at edge of mixed forest and open turf on hill\u201d (1); \u201cin moldy leaf clusters on cut branches of Paratenetus inermis Bsq. and Bouch.\u201d since it was the intended name. Unfortunately, we realized that the name was already used by Champion only after the specimens were returned to their respective collections.Most specimens of this species in collections are identified under the name \u201cPageBreakPageBreakBousquet & Bouchardsp. n.http://zoobank.org/E4FC7175-796F-4270-966D-93B4EE8E681Ahttp://species-id.net/wiki/Paratenetus_texanusHolotype (\u2642) labeled \u201cPort Isabel, Tex. 20.X.1982 Lot 2 BF&JL Carr / Holotype Paratenetus texanus Bousquet & Bouchard CNC No. 24133.\u201d The specimen is deposited in the CNC.Texas. Port Isabel, 17.X.1982, 20.X.1982, 30.III.1987, BF&JL Carr . 18 mi. E of Hebbronville, 25.III.1987, BF&JL Carr . Cameron Co., Brownsville, 19 July 1981, W.E. Steiner . Cameron Co., Palmito Hill Hist. Site, Hwy. 4 east of Brownsville, 12-X-1993, S.M. Clark . Cameron Co., 11 mi. W Boca Chica, 28 Sept. 1976, R. Turnbow . Hidalgo Co., Mission, Bentsen State Park, 17 (or 18) July 1981, W.E. Steiner . Hidalgo Co., Anzalduas Co. Pk., 19 Oct. 1985, Wappes & Downie . Bee Co., Beeville, 19 June 1974, W.E. Steiner .Paratypes from the following localities: The specific name derives from the name of the state of Texas where the species has been commonly collected.Paratenetus punctatus and Paratenetus exutus in having the punctures on the pronotum sparser, not subcontigous even on the lateral half. They can also be distinguished from most adults of Paratenetus punctatus by their smaller size and from most adults of Paratenetus exutus by the subquadrate antennomere 8 and metaventrite of same color as the first two abdominal ventrites.Members of this species can be distinguished from those of Paratenetus gibbipennis and Paratenetus fuscus; slanting setae subdepressed, erect setae short. Metaventrite long, length along midline longer than length of abdominal ventrite 2 along midline. Male protibia with calcar near middle along ventral surface; male mesotibia with short, preapical spine, wide at base and oriented perpendicularly to long axis of tibia. Parameres with sides distinctly convergent towards apex; apex markedly acute . Louisiana.Avoyelles Parish: Mansura (USNM). Cameron Parish: Holly Beach ; nr. Oak Grove (TAMU). Texas. \u201c60 mi SE Cotulla\u201d (CNC). \u201c15 mi SW Jct FR 3073 & Hwy 16\u201d (CNC). Anderson Co.: Elkhart (TAMU). Aransas Co.: Goose Island St. Park . Atascosa Co.: Pleasanton (USNM); Campbellton (TAMU). Bastrop Co.: Bastrop St. Pk. (FSC). Bee Co.: Beeville (USNM); Pettus (CNC). Bexar Co.: San Antonio (USNM). Brooks Co.: Falfurrias (CNC); 9 mi W Falfurrias (TAMU). Cameron Co.: Boca Chica ; 6 mi W Boca Chica Beach (TAMU); 6.7 mi W Boca Chica Beach (TAMU); Brownsville ; 4 mi ESE Brownsville (TAMU); 6 mi E Brownsville (TAMU); 10 mi E Brownsville ; 12.5 mi E Brownsville (TAMU); 13.5 mi E Brownsville (TAMU); W of Harlingen (TAMU); Main Reservoir near Brownsville (RLAC); Resaca de las Palomas St. Pk. (RLAC); Resaca de La Palma St. Pk. (TAMU); Sabal Palm Grove Wildlife Sanctuary ; nr. Southmost (USNM); ca. 2 mi E Los Fresnos (TAMU); Laguna Atascosa NWR (TAMU); 9.7 mi E jct Rt 1419 on hwy 4 (TAMU). Chambers Co.: Anahuac (USNM). Duval Co.: San Diego (USNM); Freer (TAMU); Sepulveda Ranch (TAMU); 3.5 mi S Realitos (TAMU). Fort Bend Co.: Brazos Bend St. Pk. (TAMU). Galveston Co.: Virginia Point (USNM); San Luis Pass (TAMU); 3.5 mi SW Jamaica Beach (TAMU); 7 mi SW Jamaica Beach (TAMU). Goliad Co.: Goliad (USNM). Hidalgo Co.: Santa Ana Nat. Wdlf. Ref. ; Bentsen Rio Grande Valley St. Pk. ; Anzalduas Park (TAMU); Delta Lake (TAMU). Jefferson Co.: 10 mi W Sabine Pass (TAMU). Jim Wells Co.: Ben Bolt (CNC); 1 mi N Ben Bolt (TAMU); Alice (USNM); 5 km W Alice (CMN); 1 mi N Premont (TAMU); 1.4 mi S Premont (TAMU). Karnes Co.: 1 mi NE Runge (TAMU). Kendall Co.: Boerne (USNM). Kenedy Co.: Sarita (CNC); 2 mi S Sarita (TAMU); 13 mi S Sarita (TAMU); 25.3 mi S Sarita (FSC); 31.8 mi S Sarita (TAMU); Armstrong (CNC); 1 mi S Armstrong (TAMU); Norias (TAMU); 5 mi N Norias (TAMU); 6 mi S Norias (TAMU); 8 mi S Norias (CNC); Loyola Beach, Baffin Bay (CNC); Baffin Bay (TAMU). Kleberg Co.: Kingsville ; Riviera ; Riviera Beach (CMN); Velederos Creek (TAMU). Live Oak Co.: 17 mi SW George West (TAMU). Nueces Co.: Corpus Christi . Refugio Co.: 8 mi E Refugio (TAMU); 7 mi S Woodsboro (TAMU). San Patricio Co.: Sinton (USNM); nr. Sinton (CNC); 3 mi N Sinton (TAMU); 7 mi N Sinton (TAMU); Welder Wildlife Refuge ; Welder Wildlife Refuge, 17 km NE Sinton (CMN); Lake Corpus Christi St. Pk. (LSAM). Starr Co.: 1.5 m E Rio Grande City (LSAM). Tyler Co.: 4 mi E Spurger (TAMU). Willacy Co.: 8 miles SW Port Mansfield (TAMU). Mexico. Chiapas. El Aguacero, 16 km W Ocozocoautla (CMN); 5 km E Ocozocoautla (CMN); 2 km S Chicoasen (CMN); Cinco Cerros (CMN). Nayarit. 15 mi N Tepic (CNC). Tamaulipas. Mpio.San Carlos, Cerro del Diente (TAMU).We have seen 515 specimens, including the type material, from the following localities. United States of America. The two specimens from Miami in Florida externally agree perfectly with those from Texas. One is a male and its genitalia are identical to those of specimens from Texas.Males are more common in collections than females. Of 106 randomly selected specimens, 42 (40%) were females and 64 (60%) were males.Specimens were collected in January (n=1), February (n=1), March (n=65), April (n=39), May (n=89), June (n=30), July (n=53), August (n=21), September (n=36), October (n=108), November (n=2), and December (n=6).Prosopis and Celtis forest, sandy soil\u201d (6 specimens); \u201con Celtis\u201d (1); \u201cex dry okra pod\u201d (1); \u201ccotton\u201d (1); \u201ccollected on Celtis\u201d (2); \u201cfallen fruit Yucca treculeana\u201d (1); \u201con flower Yucca treculeana\u201d (2); \u201con Acacia Berlandieri Benth.\u201d (1).Labels on specimens read \u201cat black light in PageBreakPageBreakParatenetus constrictus, Paratenetus corticarioides, Paratenetus nigricornis, Paratenetus punctulatus, Paratenetus tibialis, and Paratenetus villosus, and none of them are conspecific with those of Paratenetus texanus. The three species not seen are Paratenetus tropicalis Motschulsky, Paratenetus koltzei Pic, and Paratenetus mexicanus Pic.This new species occurs in Mexico and nine species have been reported from that country. We have examined the type material of the six species described by Champion and housed in BMNH, i.e.,"} +{"text": "Protective effects of boswellic acid (BA) against acetaminophen (APAP)-induced hepatotoxicity in Balb/ cA mice were examined. BA, at 0.05 or 0.1%, was supplied for 4 weeks. Acute liver injury was induced by APAP treatment. Results showed that BA intake increased hepatic BA bioavailability. APAP treatment decreased glutathione (GSH) level, increased reactive oxygen species (ROS) and oxidized glutathione (GSSG) production; and lowered activity and protein expression of glutathione reductase (GR) and heme oxygenase (HO)-1 in liver. BA intake at both doses alleviated subsequent APAP-induced oxidative stress by retaining GSH content, decreasing ROS and GSSG formations, reserving activity and expression of GR and HO-1 in liver, and lowering hepatic cytochrome P450 2E1 activity and expression. APAP treatment enhanced hepatic levels of interleukin-6, tumor necrosis factor-alpha and monocyte chemoattractant protein-1. BA pre-intake diminished APAP-induced release of those inflammatory cytokines and chemokines. APAP upregulated hepatic protein expression of toll-like receptor (TLR)-3, TLR-4, MyD88, nuclear factor kappa B (NF-\u03baB) p50, NF-\u03baB p65 and JNK. BA pre-intake at both doses suppressed the expression of NF-\u03baB p65 and p-JNK, and only at 0.1% down-regulated hepatic TLR-3, TLR-4 and MyD88 expression. APAP led to obvious foci of inflammatory cell infiltration in liver, determined by H&E stain. BA intake at both doses attenuated hepatic inflammatory infiltration. These findings support that boswellic acid is a potent hepatoprotective agent. Acetaminophen is a widely used analgesic and antipyretic drug. It is metabolized by hepatic cytochrome P450 system, especially CYP2E1, which leads to the overproduction of reactive free radicals and n-acetyl-p-benzoquinoneimine (NAPQI) , 4. In aet al. [et al. [Toll-like receptors (TLRs) are pattern recognition receptors mainly responsible for immuno modulation. The activation of TLR-3 and TLR-4 has been implicated in APAP-induced hepatic damage because both TLRs could stimulate the production of adaptor proteins including MYD88 and nuclear factor kappa B (NF-\u03baB), which in turn promote the generation of oxidants and inflammatory cytokines and chemokines , 8. Furtet al. reportedBoswellia species including Boswellia carteri, Boswellia serrata and Boswellia sacra [via its anti-oxidative and anti-inflammatory activities [et al. [Boswellic acid was synthesized and provided by Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China. APAP (98%) was purchased from Sigma Chemical Co. .Five- to six-week-old male Balb/cA mice were obtained from National Laboratory Animal Center . Mice were housed on a 12-h light-12-h dark schedule, and fed with water and mouse standard diet . Use of the mice was reviewed and approved by the China Medical University animal care committee (104-305).BA at 0.05 or 0.1 g was mixed with 99.95 or 99.9 g powder diet to prepare 0.05 and 0.1% BA diets. Mice were divided into five groups: normal group ; BA group (0.1% BA diet), APAP group ; BA-low- APAP group (0.05% BA diet plus APAP treatment); BA-high- APAP group (0.1% BA diet plus APAP treatment). After 4 weeks supplement, normal and BA groups were sacrificed, and the other three groups were treated by a single intraperitoneal injection of APAP (400 mg/kg body weight). APAP was dissolved in phosphate-buffered saline (PBS). Mice were killed with carbon dioxide after 24 h. The mortality of mice due to APAP injection was zero. After sacrificed, liver from each mouse was collected and weighted. There was no mice die before sacrificed. Blood was also collected, and serum was separated from erythrocyte immediately. Liver tissue, 0.2 g, was homogenized on ice in 2 ml phosphate buffer (pH 7.2), and the filtrate was collected. The protein concentration of serum and liver filtrate was determined by a commercial assay kit with bovine serum albumin as standard.et al. [The HPLC method of Lozano-Mena et al. was usedSerum activities of ALT and AST were determined by using commercial assay kits . CRP level (mg/l) was measured by an ELISA kit .Liver tissue was homogenized with cold PBS containing 0.05% Tween 20 and 1 mM EDTA. After centrifuging, supernatants were used for measurements. GSH and GSSG concentrations (nmol/mg protein) in liver were determined by commercial colorimetric GSH and GSSG assay kits . ROS level was quantified by using 2\u2019, 7\u2019-dichlorofluorescein diacetate. Fluorescence value was measured by using a fluorescence microplate reader at excitation and emission wavelengths of 485 and 530 nm, respectively. Relative fluorescence unit (RFU) was the difference in fluorescence values obtained at time 0 and 5 min. Results are expressed as RFU/mg protein. The activity (U/mg protein) of GPX and GR was assayed by using commercial kits purchased from EMD Biosciences Co. .Hepatic levels of IL-6, TNF-alpha and MCP-1 were measured by using cytoscreen immunoassay kits . The sensitivity of assay with the detection limit was 5 pg/ml for IL-6, and 10 pg/ml for TNF-alpha and MCP-1.The activity of CYP2E1 in freshly prepared liver microsome was estimated by colorimetrically measuring the formation of 4-nitrocatechol, a product from p-nitrophenol hydroxylation catalyzed specifically by CYP2E1. The protein concentration of CYP2E1 was measured by ELISA, and a rabbit anti-CYP2E1 antibody was used for detection. The formed 4-nitrocatechol was expressed as nmol/mg protein.Hepatic tissue, 40 mg, was homogenized in buffer containing protease-inhibitor cocktail purchased from Sigma-Aldrich Chemical Co. and 0.5% Triton X-100. Homogenate was then mixed with buffer , and followed by boiling for 5 min. Protein sample at 40 \u03bcg was electrophoresed on 10% SDS-polyacrylamide gel, and further transferred onto nitrocellulose membranes for 1 h. After blocking with a protein solution containing 5% skim milk for 1 h, membranes were treated with monoclonal antibody against heme oxygenase (HO)-1, CYP2E1 (1:1000), NF-\u03baB p50, NF-\u03baB p65, JNK (1:500), TLR-3, TLR-4, MyD88 (1:2000) at 4\u00baC overnight, and followed by incubating with horseradish peroxidase-conjugated antibody at room temperature for 3.5 h. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a loading control, and the bands were quantified by an ATTO image analyzer .Partial liver tissue from each mouse was fixed in 10% phosphatebuffered formalin, and embedded in paraffin. Paraffin section at 5 mm thickness was cut and processed with hematoxylin-eosin (H&E) stain, and followed by examining under a light microscope for histological analysis. The severity of hepatic inflammatory injury was assayed according to the Ishak scoring system . The injThe effect of each treatment was analyzed from 10 mice (n = 10) in each group. Data were reported as means \u00b1 standard deviation (SD), and subjected to analysis of variance. Differences among means were determined by the Least Significance Difference Test with significance defined at P < 0.05.P > 0.05, Table P > 0.05). The intake of BA at both doses alleviated subsequent APAP-induced elevation of ALT, AST and CRP levels in serum (P & 0.05).BA intake at 0.1% increased hepatic BA content, and did not affect body weight, feed intake, water intake and liver weight (P & 0.05); but BA pre-intake attenuated APAP-induced GSH depletion and decreased hepatic GSSG and ROS production (P & 0.05). APAP raised GPX activity and reduced GR activity in liver (P & 0.05). BA intake failed to change hepatic GPX activity (P > 0.05); but significantly maintained hepatic GR activity (P & 0.05). As shown in Figure P & 0.05). BA intake did not affect GPX protein expression (P & 0.05); but significantly retained protein expression of GR and HO-1 in liver (P & 0.05). APAP treatment enhanced CYP2E1 activity and expression ; however, BA intake significantly suppressed subsequent APAP-induced elevation of CYP2E1 activity and protein expression (P & 0.05). APAP treatment also significantly increased hepatic release of TNF-alpha, IL-6 and MCP-1 (Table P & 0.05). BA intake lowered APAP-induced hepatic production of these cytokines (P & 0.05).As shown in Table P & 0.05). BA pre-intake at both doses down-regulated the expression of NF-\u03baB p65 and p-JNK (P & 0.05), and only at high dose suppressed hepatic TLR-3, TLR-4 and MyD88 expression (P & 0.05). BA did not alter NF-\u03baB p50 expression (P > 0.05).APAP up-regulated hepatic protein expression of TLR-3, TLR-4, MyD88, NF-\u03baB p50, NF-\u03baB p65, JNK and p-JNK . BA intake at 0.05 and 0.1% decreased hepatic infiltration by inflammatory cells and lowered Ishak inflammation scores (P & 0.05), in which 0.1% BA treatment exhibited greater anti-inflammatory effects than 0.05% BA (P & 0.05).Histological data revealed that BA intake at 0.1% only (without APAP) did not cause inflammatory stress and showed similar Ishak inflammation score as normal groups Figure . APAP trBoswellia species, increased its deposit in liver and protected liver against subsequent APAP induced oxidative and inflammatory injury. Besides increasing GSH retention, we found that BA effectively decreased CYP2E1 activity and expression, lowered ROS, TNF-alpha and MCP-1 production, as well as suppressed HO-1, TLR-3, TLR-4, NF-\u03baB p65 and p-JNK expression. In addition, our histological results indicated that BA improved diffuse ballooning degeneration and lobular inflammation caused by APAP. These findings support that BA is a potent hepatic protective agent.Our present study revealed that the pre-intake of BA, an active compound of APAP at high dose led to GSH depletion and GSSG accumulation . Our datvia its anti-oxidative activities, which definitely led to less stimulation for hepatic NF-kB activation and JNK phosphorylation. Our western blot data regarding hepatic protein expression of NFkB p65 and p-JNK agreed that BA intake at both doses limited the activation of these two signal pathways. Consequently, it is reasonable to observe lower hepatic levels of IL-6, TNF-alpha and MCP-1 in BA treated mice. The decrease in serum levels of ALT, AST and CRP in BA treated mice also agreed that BA intake declined APAP caused liver inflammatory stress. In addition, our histological data further supported that BA pre-intake effectively improved hepatic inflammatory injury.APAP overdose activated NF-kB and JNK pathways through stimulating ROS generation , 23. Theet al. [et al. [in vivo anti-inflammatory data of BA, and extended BA\u2019s mediating activity to TLRs and MyD88.TLRs play crucial roles in the pathological progression of inflammatory liver diseases because TLRs recognize endogenous damage-associated molecular patterns during inflammatory reactions . TLR-3 iet al. reported [et al. reportedBA is naturally present in many edible plants including vegetables and herbs , 30. Thevia maintaining hepatic GSH content, retaining activity and expression of GR and HO-1, decreasing inflammatory cytokines and suppressing protein expression of CYP2E1, NF-\u03baB p65, JNK, TLR-3 and TLR-4. These findings support that boswellic acid was a potent hepatic protective agent.Boswellic acid pre-intake protected mice liver against subsequent acetaminophen-induced oxidative and inflammatory injury"} +{"text": "To control the double burden of communicable and non-communicable diseases (NCDs), in the developing world, understanding the patterns of morbidity and healthcare-seeking is critical. The objective of this cross-sectional study was to determine the distribution, predictors and inter-relationship of perceived morbidity and related healthcare-seeking behavior in a poor-resource setting.Between October 2013 and July 2014, 43999 consenting subjects were recruited from 10107 households in Malda district of West Bengal state in India, through multistage random sampling, using probability proportional-to-size. Information on socio-demographics, behaviors, recent ailments, perceived severity and healthcare-seeking were analyzed in SAS-9.3.2.Pri)=0.76, 95% confidence interval=0.71-0.83) and for Govt. healthcare provider(AORGovt)=0.80(0.68-0.95)], females [AORGovt=0.80(0.73-0.88)], Muslims [AORPri=0.85(0.69-0.76) and AORGovt=0.92(0.87-0.96)], backward castes [AORGovt=0.93(0.91-0.96)] and rural residents [AORPri=0.82(0.75-0.89) and AORGovt=0.72(0.64-0.81)] had lower odds of visiting qualified practitioners. Apparently less severe NCDs , gastrointestinal [AORPri=0.28(0.24-0.33) & AORGovt=0.69(0.58-0.81)], respiratory [AORPri=0.35(0.32-0.39) & AORGovt=0.46(0.41-0.52)] and skin infections [AORPri=0.65(0.55-0.77)] were also less often treated by qualified practitioners. Better education [AORPri=1.91(1.65-2.22) for \u2265graduation], sanitation [AORPri=1.58(1.42-1.75)] and access to safe water [AORPri=1.33(1.05-1.67)] were associated with healthcare-seeking from qualified private practitioners. Longstanding NCDs and serious infections [typhoid: AORPri=2.86(2.04-4.03)] were also more commonly treated by qualified private practitioners. Potential limitations included temporal ambiguity, reverse causation, generalizability issues and misclassification.Recent illnesses were reported by 55.91% (n=24600) participants. Among diagnosed ailments (n=23626), 50.92% (n=12031) were NCDs. Respiratory ), gastrointestinal and musculoskeletal problems were predominant. Non-qualified practitioners treated 53.16% (n=13074) episodes. Older children/adolescents [adjusted odds ratio for private healthcare providers(AORIn this poor-resource setting with high morbidity, ailments and their perceived severity were important predictors for healthcare-seeking. Interventions to improve awareness and healthcare-seeking among under-privileged and vulnerable population with efforts to improve the knowledge and practice of non-qualified practitioners probably required urgently. Demographic ageing, unplanned urbanization and unhealthy lifestyles are the major contributors for the changing pattern of disease in recent years, from communicable to non-communicable diseases (NCDs), globally.\u20133 This eDespite remarkable progress in socio-economic development and having an overarching aim of addressing the health needs through several comprehensive programs, health outcomes in India remained poor. During 2012, approximately 60% deaths were attributed to NCDs and 28% to communicable, maternal, perinatal and nutritional conditions in this country.,11 EvideIndividual healthcare-seeking pattern in a community is determined by complex interrelationships between socio-economic and physical environment along with individual characteristics and behaviors. Thus heaRelevant researches on morbidity and healthcare-seeking ever conducted in India were mostly limited to urban areas of southern and western part while eastern region remained largely understudied. Malda isHence, a community-based cross-sectional study was designed involving a representative population of Malda to understand the distribution of the perceived morbidity and healthcare-seeking behavior, their predictors and inter-relationship.The study protocol was reviewed and approved by the Ethics Committee of the National Institute of Cholera and Enteric Diseases, Kolkata. Written informed consent left thumb impression was obtained from residents older than 18 years and from the guardians of residents aged 1 to 17 years. Written assent was additionally obtained from residents aged 12 to 17 years.Based on the 2011 census data, the urban area of the Malda district was divided into two broad urban administrative divisions termed as Municipalities . Each Municipality was further subdivided into smaller administrative units called Wards . Using probability proportional to size (PPS) determined by the total number of households in the Wards, 4 Wards in Old Malda and 12 Wards in English Bazar were selected randomly. The rural area of the district consisted of 3701 villages and 27 rural towns from which similarly using PPS, 25 villages/census towns were selected randomly. Using an exhaustive house-list of the urban and rural areas, each selected municipal ward and village/rural town was categorized into several segments (considered as Primary Sampling Unit: PSU), each having 125 households (defined as those who shared the cooking-pot in each dwelling). Next, 4012 urban and 6095 rural households (maintaining the population ratio) were selected from the whole district, through multistage random sampling, using PPS. Thus, 16 municipal wards in urban and 24 villages/towns in rural area were selected. In each selected ward/village from the list of segments two were selected randomly and all households were surveyed there after collecting written informed consent from the residents.All the individuals residing in the selected households were interviewed at home by trained interviewers, using a structured, pre-tested, bi-lingual questionnaire. Information was collected on socio-demographic and related variables such as age, gender, religion, caste, education level and occupation of the household members, maximum education level among adults in the house, house ownership, residential area, type and location of water source, water treatment at home, material used for cooking and domestic light source. Housing type was classified as Kachha , Pacca and Semi-pacca . Sanitation level of toilet use practices were categorized as poor (if the household had no toilet and the members used open space/field/jungle for defecation), good (for households having toilets with flush to piped sewer system/flush to septic tank) and all others as average.Based on the information regarding household assets (enquired using an appropriate list of assets), number of cattle, goats/sheep, poultry, place for keeping them and the aforementioned household information, wealth index was calculated by using relative weights for each and then the cumulative wealth index scores were log-transformed and divided into quintiles of socio-economic status: SES based on the percentile distribution.For all the members of the selected households, information regarding last three episodes of ailments that forced them to seek some healthcare services within last two months was collected. Occurrence, perceived severity and healthcare-seeking behavior regarding specific NCDs like: acid peptic disorder (APD) or peptic ulcer disorder (PUD), chronic obstructive pulmonary disease (COPD), hypertension (HTN), diabetes mellitus (DM), anemia and osteoarthritis (OA) as well as communicable diseases like: gastroenteritis, respiratory tract infection (RTI), typhoid and skin infections were also collected.Thus between October 2013 and July 2014, 43999 individuals (with approximately 8% non-response) were recruited from 10107 households and collected data were analyzed using Statistical Analysis System (SAS) version 9.3.2. Distribution of the socio-demographic characteristics, morbidity pattern and healthcare-seeking were determined by conducting descriptive analyses using survey frequency procedure to determine overall and stratified frequencies, proportions and corresponding 95% confidence intervals (95%CI). Bivariate and multivariate logistic regression analyses were next conducted to determine unadjusted (OR) and adjusted odds ratios (AOR) as the measures of association (with corresponding 95%CIs) between study variables. Multinomial logistic regressions were useAmong 43999 subjects, majorities were aged 18\u201340 yrs , male , Hindu , general caste and educated up to secondary level . For 38.82% (n = 17080). Maximum adult education in the household was also up to secondary level, 95.73% (n = 42122) stayed in own house, 39.60% (n = 15888) were in sedentary work and 62.60% (n = 27543) lived in rural areas. Only 5.31% (n = 2336) were drinking safe water, 50.32% (n = 22140) had to bring drinking water from outside, 95.06% (n = 41825) were not doing any water treatment at home, 29.08% (n = 12794) were using gas/electricity for cooking, 27.20% (n = 11961) were living in pacca houses. Electricity was the source of lighting at home for 88.87% (n = 39098), regarding toilet use 30.63% (n = 13475) had good sanitary practices and overall 19.44% (n = 8553) belonged to upper SES. Overall and stratified socio-demographic distribution are presented in Regarding the distribution of self-perceived most recent (within past 2 month) morbidity, 44.09% (n = 19399) did not suffer from any such recently while for 17.28% (n = 7605), 13.48% (n = 5929) and 6.25% (n = 2749) residents the most recent morbidity was related to respiratory, gastrointestinal and musculoskeletal system respectively. Among the most recent ailments, NCDs were 50.92% (n = 12031), 53.16% (n = 13074) episodes were treated by non-qualified practitioners, 34.02% (n = 8368) by qualified practitioner from private sector and only 12.82% (n = 3153) by qualified practitioner from Govt. sector. Non-qualified practitioners were treating more communicable diseases compared to NCDs [57.52% (n = 7194) vs. 42.48% (n = 5313)]. Based on last three healthcare-seeking episodes, among specific ailments (suffered or not), 19.01% (n = 6734) suffered from RTI, 8.18% (n = 2554) had PUD/APD, 6.45% (n = 1977) experienced gastroenteritis while 3.60% (n = 1070) had some skin problems. Among subjects visiting nonqualified practitioners, only 16.85% (n = 1551) perceived their ailments as severe while this fraction for private sector qualified practitioners, was 40.85% (n = 1829). 41\u201360 = 2.01(1.82\u20132.23), AOR>60 = 2.86(2.41\u20133.39)], COPD , HTN , DM , OA , gastroenteritis and RTI .Association of socio-demographics with morbidity and healthcare-seeking are presented in Tables Compared to males, females had higher odds of suffering from APD [AOR = 1.60(1.45\u20131.77)], HTN [AOR = 1.53(1.28\u20131.83)], anemia [AOR = 16.26(10.75\u201324.59)] and OA [AOR = 2.58(2.07\u20133.22)] and lower odds for COPD [AOR = 0.59(0.48\u20130.73)] and DM [AOR = 0.73(0.57\u20130.92)]. Muslims suffered less from APD [AOR = 0.77(0.69\u20130.87)] and gastroenteritis [AOR = 0.86(0.74\u20130.99)] but more from DM [AOR = 1.40(1.06\u20131.85)], typhoid [AOR = 1.80(1.31\u20132.46)] and skin infections [AOR = 1.25(1.06\u20131.49)] than Hindus. With reference to general, backward castes suffered less from APD [AOR = 0.74(0.67\u20130.81)], HTN [AOR = 0.82(0.69\u20130.97)] and anemia [AOR = 0.77(0.60\u20130.98)] but more from typhoid [AOR = 1.93(1.40\u20132.67)].Higher Secondary = 0.57(0.47\u20130.70), AOR\u2265Graduation = 0.57(0.46\u20130.70)], COPD , anemia [AOR\u2265Graduation = 0.48(0.26\u20130.87)], OA , gastroenteritis and RTI .Compared to illiterates, higher familial education was associated with lower likelihood of APD [AORHard workers (reference = Sedentary) were more prone to APD [AOR = 1.45(1.24\u20131.71)] and anemia [AOR = 1.89(1.17\u20133.04)] but less vulnerable to COPD [AOR = 0.53(0.40\u20130.69)] and HTN [AOR = 0.60(0.46\u20130.77)]. Rural residents, compared to urban, were less likely to have HTN [AOR = 0.54(0.43\u20130.67)] but more prone to OA [AOR = 1.47(1.15\u20131.87)], gastroenteritis [AOR = 1.76(1.50\u20132.07)], typhoid [AOR = 2.85(1.86\u20134.38)], RTI [AOR = 1.27(1.16\u20131.38)] and skin infection [AOR = 1.45(1.19\u20131.77)].Upper middle = 0.64(0.44\u20130.92), AORUpper = 0.59(0.40\u20130.88)], gastroenteritis [AORUpper = 0.72(0.60\u20130.86)], typhoid [AORUpper = 0.63(0.41\u20130.99)], RTI and skin infections . Higher SES also seemed to be associated with higher odds of having HTN and DM . , AOR>60 years = 4.25(3.61\u20135.00)], familial education , sanitation level regarding toilet use practices and SES . Perception of severity was lower among hard-workers and rural residents . ]. 5\u201318 = 2.51(2.22\u20132.83)], and older residents were less likely to suffer from communicable diseases (reference = NCD). Compared to respective reference groups, females [AOR = 0.72(0.67\u20130.77)], residents having higher familial education [AOR = 0.71(0.62\u20130.83)] and higher SES [AOR = 0.84(0.75\u20130.92)] had lower likelihood of communicable diseases. Muslims [AOR = 1.18(1.09\u20131.28)], persons belonging to backward [AOR = 1.15(1.08\u20131.24)] caste, those who had higher individual education [AOR\u2265Graduation = 1.38(1.13\u20131.69)] and rural [AOR = 1.47(1.36\u20131.60)] residents suffered more from communicable diseases. , AORGovt = 0.80(0.68\u20130.95)], females [AORGovt = 0.80(0.73\u20130.88)], Muslim religion , backward caste [AORGovt = 0.93(0.91\u20130.96)], physically demanding occupation and rural residence were associated with lower likelihood of visiting qualified practitioners . Age > 40 years , higher individual [for higher secondary: AORPrivate = 1.42(1.19\u20131.69) and for \u2265 Graduation: AORPrivate = 1.30(1.06\u20131.59)] and familial education [for higher secondary: AORPrivate = 1.26(1.13\u20131.41) and for \u2265 Graduation: AORPrivate = 1.40(1.22\u20131.62)], better sanitary practices [for average practice: AORPrivate = 1.17(1.07\u20131.28) and for good practice: AORPrivate = 1.58(1.42\u20131.75)] and higher SES [for Upper middle: AORPrivate = 1.59(1.43\u20131.77) and for Upper: AORPrivate = 1.51(1.35\u20131.69)] were associated with higher odds of seeking care from qualified practitioners. , AORGovt = 0.36(0.31\u20130.43)], OA , gastroenteritis , RTI , skin infections [AORPrivate = 0.65(0.55\u20130.77)]. Those who had COPD , HTN , DM , typhoid and NCDs were more likely to visit qualified practitioners. Higher self-perceived disease severity was also positively associated with visiting qualified practitioners. of the participants suffered from some recent morbidity while respiratory, gastrointestinal and musculoskeletal diseases were most common. This observed burden of self-perceived morbidity was considerably higher than previously reported values (ranged between 27% and 48%) in similar settings.\u201329 StudiMore than half of the ailments were treated by non-qualified practitioners, which raised a few concerns. Only about 13% visited qualified physicians from Govt. sector. The scenario seemed similar to that of other parts of India, Vietnam and Bangladesh ,28,32 buAmong specific ailments, RTI was perceived to be the commonest, followed by APD, gastroenteritis and skin problem. Contrary to some other study, perceived burden of HTN and DM were found to be relatively lower. May be sWhile more than two third subjects considered their ailments as less severe, those who perceived the severity, visited qualified doctors especially in private sector. The perceived severity probably helped them to overcome the potential barriers in better healthcare-seeking.,35,38,39Corroborating with prior observation in similar settings elsewhere, children and adolescents were less likely to suffer from NCDs like APD, COPD, HTN, DM, anemia and OA but more from RTI, gastroenteritis and skin infection.,35,36,40Similar to some previous observation, females had higher likelihood of having APD, anemia and OA but less likely to suffer from COPD and DM \u201328 but gSupporting some prior evidences and contOccupation with hard work was associated with higher odds of APD and anemia but lower odds of COPD and HTN. Physical exertion, work environment and appropriate nutrition probably were the key factors. Negative association between physical activity and HTN was well-established in prior studies.Rural residents compared to urban were less prone to HTN but they had higher likelihood of having OA, gastroenteritis, typhoid, RTI and skin infection most likely due to lifestyle related factors, less awareness, poor hygiene and inappropriate sanitation. Urban preponderance of HTN was also reported previously althoughDrinking safer water was associated with higher perceived burden of HTN and DM. Subjects having better sanitary practices regarding toilet use were also suffering more from APD, HTN, DM and OA. Health awareness and knowledge as probably a confounder here that positively influenced both better practices and improved perception. Reverse causation might also be a possibility (being diagnosed with the disease resulted in better sanitation and hygiene). Drinking safer water and practicing better sanitation regarding toilet use seemed to be also associated with lower likelihood of suffering from gastroenteritis, typhoid, RTI and skin infections.Alike prior studies, we also found that, residents having comparatively higher SES were less likely to suffer from anemia, gastroenteritis, typhoid, RTI and skin infections ,29 but sPerceived severity of ailments was higher among those with higher age, better familial education, improved sanitation and upper SES and lower among hard-workers and rural residents had. Higher severity of self-perceived morbidity among elderly was also reported previously. Thus perCompared to those aged between 18\u201340 years, 5\u201318 years age group were more likely, and older residents were less likely to suffer from communicable diseases than NCDs. Female gender, better familial education and higher SES were negatively associated with risk of communicable diseases. Muslim religion, backward caste, higher individual education and rural residents had higher odds of suffering from communicable diseases.Socio-demographic predictors of Healthcare-seeking behavior in our study were quite similar to those reported from other parts of the world as well as India with some variations. While elderly subjects commonly visited qualified private and govt. sector physicians, older chSubjects suffering from NCDs were more likely to visit qualified practitioners especially the private sector. Alike soSelf-perceived severity of ailments were positively associated with odds of visiting qualified practitioners more so in private sector and this finding also supported prior evidences.,36,40 ThDespite efficient sampling design, use of detailed questionnaire and robust analyses, our study had certain limitations. Like any other cross-sectional study, causal interpretation of the observed associations is not recommended. Due to the potential vulnerability to temporal ambiguity by design, some of our observations might have suffered from reverse causation. Although self-perceived morbidity and severity are currently being considered an efficient parameter for the estimation of health needs in communities worldwide, keeping the lower literacy and potential lack of awareness in mind, the reported self-perceived morbidity pattern should only be interpreted as perceived health need of the community, not the prevalence. Residual confounding due to variables not included in our analyses could also be an issue. Information bias due to misclassification of self-reported information should always be kept in mind, especially due to the potential for differential recall. But we do not consider those to be serious issues here because we only dealt with the recent ailments, hence recall period was short and in majority of cases, medical records were consulted. Although results of our study should be extrapolated beyond the study sample with caution, still we are not worried about the generalizability of our results due to the representative nature of our study sample and very low (<8%) non-response.In this poor-resource setting, most important predictor for healthcare-seeking was the perception regarding severity and nature of ailments, while age, gender, caste, religion, familial education, SES, residential area, sanitation and hygiene influenced the morbidity pattern and relevant healthcare-seeking. Keeping the high burden of self-perceived morbidity in mind, interventions to improve physical health, awareness and care-seeking practices targeting children, elderly, females, backward castes, minority groups, illiterates, rural residents and those having lower SES, poor sanitary practices and inadequate access to safe drinking water were required urgently. Simultaneously, efforts to improve the healthcare service delivery might consider implementation of intervention targeting improvement of knowledge and practice among non-qualified practitioners in poor-resource settings where seeking healthcare services from these practitioners seemed to be a common occurrence."} +{"text": "Consequently, several molecular targets based on the sequences of housekeeping genes, non-functional RNA and structural ribosomal RNAs have been proposed for the detection and identification of mycobacteria in clinical or environmental samples. While certain of these targets were proposed as specific for this genus, most are prone to false positive results in complex environmental samples that include related, but distinct, bacterial genera. Nowadays the increased number of sequenced genomes and the availability of software for genomic comparison provide tools to develop novel, mycobacteria-specific targets, and the associated molecular probes and primers. Consequently, we conducted an M. tuberculosis H37Rv, only 11 proteins showed 80% to 100% of similarity with Mycobacterium spp. genomes, and less than 50% of similarity with genomes of closely related Corynebacterium, Nocardia and Rhodococcus genera. Based on DNA sequence alignments, we designed primer pairs and a probe that specifically detect the atpE gene of mycobacteria, as verified by quantitative real-time PCR on a collection of mycobacteria and non-mycobacterial species. The real-time PCR method we developed was successfully used to detect mycobacteria in tap water and lake samples.Among the 3989 predicted proteins from atpE gene can serve for highly specific detection and precise quantification of Mycobacterium spp. in environmental samples.The results indicate that this real-time PCR method targeting the Mycobacterium genus is constituted of several pathogenic species, including the M. tuberculosis complex (MTC) responsible for tuberculosis , M. leprae responsible for leprosy, and non-tuberculous mycobacteria (NTM), which are environmental potentially pathogenic species causing mycobacteriosis [rrs, gyrA, gyrB, hsp65, recA, rpoB, sodA genes and 16S-23S internal transcribed spacer (ITS) genes, to detect and/or identify mycobacteria species by sequence analysis [Mycobacterium genus in clinical and environmental samples, several studies have proposed targeting different loci of the 16S rRNA gene [gyrB [rpoB[hsp65[Corynebacterium, Nocardia, Rhodococcus, Mycobacterium (CNM) group [Mycobacterium genus targets with high levels of specificity and sensitivity that will be useful for studying mycobacteria in their habitat.teriosis . Detectiteriosis . Identifanalysis . In ordeRNA gene , or othene [gyrB , rpoB[19poB[hsp65. NeverthpoB[hsp65. Indeed,poB[hsp65 which alM) group and whicM. tuberculosis H37Rv), the number of mycobacterial sequences has considerably increased due to advances in sequencing capacity and the appearance of high throughput sequencing techniques [M. tuberculosis and M. bovis species), two strains of M. leprae, and eleven species and subspecies of pathogenic (P) and non-pathogenic (NP) NTM: M. abscessus (P), M. avium (P), M. avium subsp. paratuberculosis (P), M. gilvum (NP), M. marinum (P), M. smegmatis (NP), Mycobacterium sp. JLS (NP), Mycobacterium sp. KMS (NP), Mycobacterium sp. MCS (NP), M. ulcerans (P), M. vanbaalenii (NP), [M. intracellulare, M. kansasii, M. parascrofulaceum). This increasing number of completely sequenced mycobacterial genomes led to the development of the MycoHit software, which permits gene- and protein-level comparisons across mycobacteria species, [As new mycobacterial sequences are added into genetic databases, our knowledge of mycobacterial genomes is increasing and this may help to design new primers and probes that will be both specific and sensitive. Since the whole sequencing of the first mycobacterial genome in 1998 by Sangechniques . Today, ii (NP), -26. Morespecies, . This sospecies, . HoweverMycobacterium spp.. We compared in silico proteins of whole mycobacterial genomes with those of non-mycobacterial genomes using the MycoHit software, in order to find conserved sequences among mycobacteria that will not be shared with non-mycobacterial species. Based on the screening results a primer pair and a probe targeting the atpE gene were designed and tested by real-time PCR. This novel target proved to be totally specific and sensitive. It also offers the advantage of targeting a gene present as a single copy in the genome. Thus this new real-time PCR method appears promising for water quality survey, and should be useful for studying the ecology of mycobacteria in aquatic, terrestrial and urban environments.In this paper, we used this tool for screening sensitive and specific targets of rrs gene and ITS , and according to our strategy of genome comparison code for proteins which present similar conformations in non-mycobacterial studied genomes , and also for the 12 non-mycobacterial genomes studied .Excluding n Figure\u00a0 most of M. tuberculosis H37Rv genome , and less than 50% similarity levels in comparison with genomes (n\u2009=\u200912) of the other CNM group genera. As a result, among the 3989 predicted proteins of M. tuberculosis H37Rv genome , hypothetical PE or PPE family proteins (loci Rv0285 and Rv3022c), proteins coded by esxG, esxH and esxR genes in M. tuberculosis H37Rv , and proteins such as a lipoprotein coding by lppM gene (locus Rv2172c), an oxidoreductase (locus Rv0197), and a small secreted protein (locus Rv0236A).Among the 3989 predicted proteins of e Figure\u00a0, about 5e Figure\u00a0B displaycmaA1 gene, lipoprotein coding by lppM gene, as well as PE, PPE and proteins coded by esx genes esxG, esxH and esxR, were highly conserved in studies MTC species (tuberculosis and bovis) but very polymorphous in the 14 NTM species studied , the oxidoreductase (locus Rv0197), and the small secreted protein locus Rv0236A), are the less polymorphous among the 14 NTM species studied whereas quantification limits were estimated at about 100 genome equivalents. In the positive collection all 31 mycobacteria species were positively detected by the real-time PCR method. This collection includes NTM species, leprae species and MTC species as tuberculosis and bovis , and evaR Figure\u00a0A. DetectatpE gene, shows a vast diversity of mycobacteria concentration, ranging from 104 to 106 ge/L in water column and neuston samples, and 105 to 106 ge/g DW (dry weight) in sediment samples. Comparison with the previously published methods targeting 16S rRNA [Mycobacteria quantification in lake samples by real-time PCR targeting 16S rRNA shows a gyrA, gyrB, hsp65, recA, rpoB, and sodA genes are appropriate for identification purposes [gyrB [rpoB[hsp65[Helicobacter pylori show positive amplification with several Mycobacterium specific primer pairs [atpE real-time PCR method that we propose is just as specific, but more sensitive than the previously proposed rrs real-time PCR method which cannot detect some mycobacterial species [Although purposes ,4, our res [gyrB , rpoB[19poB[hsp65 genes, hpoB[hsp65. For exaer pairs . Prospec species .M. tuberculosis H37Rv, sorting proteins according to similarity requests and listing candidate proteins . Only the aptE gene could be used to design primers and a probe for mycobacteria detection. Concerning the other genes, the sequence polymorphism among NTM species did not allow designing molecular targets for Mycobacterium spp. detection. However, these genes could be of immunological or pathogenic importance. Indeed, PE and PPE family proteins represent 0.9 to 4.2% of the genome coding capacity of several mycobacteria [esx gene clusters, which encode ATP dependent specific secretion system [esx gene clusters are very small and polymorphous among genomes of the 11 NTM species compared is exclusively conserved in the genomes of the 17 mycobacterial species studied , which codes for the ATP synthase protein subunit C. These results also showed that our strategy of target design based on MycoHit software , slow mycobacteria growth, clumping of mycobacterial cells, high hydrophobicity of mycobacteria and contamination of culture media by other fast growing environmental microorganisms [rganisms .atpE with previously described method targeting 16S rRNA, [atpE gene presents two major advantages over the method targeting rrs gene. First, the new method detects all the tested mycobacterial strains, while the method targeting rrs gene cannot detect isolates of M. celatum, M. heckeshornense, and M. leprae[atpE gene is present in a single copy in the Mycobacterium genomes, while the 16S rRNA gene is present either in 1 or 2 copies in the genome [Comparison of the method targeting 6S rRNA, , showed M. leprae. Second,e genome . When coin vitro as positive controls whereas more than 150 mycobacterial species have been described so far [atpE real-time PCR method using a large representative collection of mycobacterial species , including members of MTC (n\u2009=\u20092), M. leprae species (n\u2009=\u20091), slow growing NTM (n\u2009=\u200913), and rapid growing NTM (n\u2009=\u200915). Given the broad diversity of mycobacterial species we have tested in this study, we expect the method to be applicable to all species within the Mycobacterium genus. In addition, it is the first time that a sensitive and specific molecular target has been identified based on an in silico comparison of 16 mycobacterial (13 species) and 12 non-mycobacterial genomes (4 closely related species).One of the limitations of this study is that only 31 mycobacterial species were tested Archaea. Using these databases, MycoHit, or other new software, may then be used to design new primers for real-time PCR detection or quantification, for in situ hybridization and other molecular tools. With this approach we were able to design primer pairs and a probe that target specific mycobacterial atpE gene, and could be used to detect and quantify very specifically mycobacteria in environmental samples. Although the atpE gene may not be appropriate for microdiversity studies, it appeared to be very useful for specific detection of the genus Mycobacterium in environmental samples. More generally, genome comparison used here showed its utility to identify specific genera\u2019s targets, and could be used to identify specific proteins for antimicrobial design as previously emphasized [In conclusion, although our strategy did not take into account non-coding regions, such as insertion sequences, repetitive units, non-functional RNA, and structural ribosomal RNAs, the comparison of whole bacterial genomes for design of specific primers is a promising approach not only for mycobacteria but also for other cultured bacterial or archaeal groups for which whole sequenced genomes are accumulating in databases. Metagenomic libraries from environmental samples which are increasingly performed in microbial ecology studies could alphasized .M. tuberculosis genes, presenting homologue genes in other mycobacterial genomes, and not presenting homologue genes in non-mycobacteria genomes, we used the MycoHit software version 14.17 and performed an alignment search with Stand Alone tblastn algorithm as previously described [M. tuberculosis H37Rv has been used as a reference of the Mycobacterium genus, because it is the most historically described mycobacterial genome [M. tuberculosis H37Rv, corresponding to the query sequences used in order to search for matches in the genomic DNA of other organisms , allowed identification of the conserved mycobacterial proteins presenting no homology in non-mycobacterial genomes using the accession numbers: M. abscessus ATCC 19977 (CU458896.1) (P), M. avium 104 (CP000479.1) (P), M. avium subsp. paratuberculosis K10 (AE016958.1) (P), M. bovis subsp. bovis AF2122/97 (BX248333.1) (P), M. gilvum PYR-GCK (CP000656.1) (NP), M. marinum M (CP000854.1) (P), M. smegmatis MC2 155 (CP000480.1) (NP), Mycobacterium sp. JLS (CP000580.1) (NP), Mycobacterium sp. KMS (CP000518.1) (NP), Mycobacterium sp. MCS (CP000384.1) (NP), M. tuberculosis CDC1551 (AE000516.2) (P), M. tuberculosis H37Ra (CP000611.1) (NP), M. tuberculosis H37Rv (AL123456.2) (P), M. tuberculosis KZN 1435 (CP001658.1) (P), M. ulcerans Agy99 (CP000325.1) (P), and M. vanbaalenii PYR-1 (CP000511.1) (P). In order to avoid data lost during genome comparisons performed by MycoHit software, we have chosen to ignore some mycobacterial genomes. Since the number of coding proteins is much lower compared to other mycobacterial species, M. leprae Br4923 (FM211192.1) (P), and M. leprae TN (AL450380.1) (P) were ignored in the analysis [M. bovis BCG Pasteur 1173P2 (AM408590.1) (NP) and M. bovis BCG Tokyo 172 (AP010918.1) (NP) were also not taken into account, because these vicinal genomes present mutations [M. intracellulare ATCC 13950 (ABIN00000000) (P), M. kansasii ATCC 12478 (ACBV00000000) (P) and M. parascrofulaceum BAA-614 (ADNV00000000) (P) were also not used during MycoHit proceedings, because their genomes were still not assembled at the moment we performed the first screening step of our analysis. Nevertheless, the genomes of M. leprae, M. bovis BCG, M. intracellulare, M. kansasii and M. parascrofulaceum were used during alignment of nucleic sequences of the most conserved proteins in mycobacterial genomes.In order to perform comparisons of pathogenic (P) and non-pathogenic (NP) mycobacterial genomes with 122/97 BX8333.1 (PMC2 155) ,35. GenoCorynebacterium aurimucosum ATCC 700975 (CP001601.1), C. diphtheriae NCTC 13129 (BX248353.1), C. efficiens YS-314 (BA000035.2), C. glutamicum ATCC 13032 (BX927147.1), C. jeikeium K411 (NC_007164), C. kroppenstedtii DSM 44385 (CP001620.1), C. urealyticum DSM 7109 (AM942444.1), Nocardia farcinica IFM 10152 (AP006618.1), Nocardioides sp. JS614 (CP000509.1), Rhodococcus erythropolis PR4 (AP008957.1), R. jostii RHA1 (CP000431.1), and R. opacus B4 (AP011115.1).We selected non-mycobacterial genomes of species from the CNM group using the following accession numbers: In order to check the homology of the selected mycobacterial sequences, the protein and DNA sequences of these selected proteins were aligned using the ClustalW multiple alignment of the BioEdit software 7.0.9.0 with 1000 bootstraps . Primer et al. protocol [M. avium, M. fortuitum, M. intracellulare and M. gordonae . Specificity and sensitivity were estimated against 30 non-mycobacteria (negative) strains and 31 mycobacteria (positive), respectively. The collection contained reference and environmental strains of mycobacteria, as well as, strains of the closely related CNM group, and other non-actinobacteria strains isolated from the environment [leprae species (n\u2009=\u20091), as well as species of slow growing NTM (n\u2009=\u200913), and rapid growing NTM (n\u2009=\u200915). TaqMan\u00ae real-time PCR were performed in duplicate using an ABI7500 real-time PCR system (Applied Biosystems), a Lifetech 7500 software version 2.0.6 (Applied Biosystems) and TaqMan fast virus 1-STEP Master Mix with 6-carboxy-X-rhodamine (ROX) (Applied Biosystems). The TaqMan\u00ae probes were labeled (Eurogentec) with the fluorescent dyes 6-carboxyfluorescein (5\u2032 end) and Black Hole Quencher (3\u2032 end). All reactions were performed in a 25 \u03bcl reaction mixture volume (2.5 \u03bcl of DNA) with 500 nM of forward primer, 500 nM of reverse primer, 50 nM of probe and 5 mM of MgCl2. Reverse transcriptase was inactivated immediately according to the manufacturer instruction, and real-time PCR consisted in 40 cycles of denaturation (95\u00b0C for 3 s), annealing and extension (both steps at 60\u00b0C for 30 s). Determinations of cycle threshold were performed by setting the instrument\u2019s threshold line at 0.02 \u2206Rn units .Reproducibility, sensitivity and specificity of the new real-time PCR method were estimated using DNA from a previously described microorganism collection, and according to Radomski protocol . Reproduprotocol were estironment . Mycobacet al. [et al. [In order to compare the new real-time PCR method to the culture method, 26 tap water distribution points in Paris (France) were sampled between April 2011 and July 2011, corresponding to 90 samples. Briefly, one liter of tap water was sampled in sterile plastic bottle, then centrifuged at 5000\u2009\u00d7\u2009g for 2h and finally re-suspended in 1 ml of water. Mycobacteria density was estimated by culture (Method A) in all these samples following the procedure previously described by Le Dantec et al. . In para [et al. between Mycobacterium tuberculosis H37Rv (AL123456.2) proteins and proteins of targeted mycobacterial genomes and proteins of non-targeted genomes. Targeted mycobacterial genomes include M. tuberculosis H37Ra (CP000611.1), M. tuberculosis CDC 1551 (AE000516.2), M. tuberculosis KZN 1435 (CP001658.1), M. bovis AF2122/97 (BX248333.1), M. ulcerans Agy99 (CP000325.1), M. marinum M (CP000854.1), M. avium 104 (CP000479.1), M. paratuberculosis K10 (AE016958.1), M. smegmatis MC2 155 (CP000480.1), M. abscessus ATCC 19977 (CU458896.1), M. gilvum PYG-GCK (CP000656.1), M. vanbaalenii PYR-1 (CP000511.1), Mycobacterium sp. JLS (CP000580.1), Mycobacterium sp. KMS (CP000518.1), Mycobacterium sp. MCS (CP000384.1), and non-targeted genomes include Corynebacterium aurimucosum ATCC 700975 (CP001601.1), C. diphteriae NCTC 13129 (BX248353.1), C. efficiens YS-314 (BA000035.2), C. glutamicum ATCC 13032 (BX927147.1), C. jeikeium K411 (NC_007164), C. kroppenstedtii DSM 44385 (CP001620.1), C. urealyticum DSM 7109 (AM942444.1), Nocardia farcinica IFM 10152 (AP006618.1), Nocardioides sp. JS614 (CP000509.1), Rhodococcus erythropolis PR4 (AP008957.1), R. jostii RHA1 (CP000431.1) and R. opacus B4 (AP011115.1).Click here for fileProtein sequence alignment of conserved proteins in mycobacterial genomes. Sequences are from genomes of M. abscessus ATCC 19977 (CU458896.1), M. avium 104 (CP000479.1), M. avium subsp. paratuberculosis K10 (AE016958.1), M. bovis subsp. bovis AF2122/97 (BX248333.1), M. bovis BCG Pasteur 1173P2 (AM408590.1), M. bovis BCG Tokyo 172 (AP010918.1), M. gilvum PYR-GCK (CP000656.1), M. intracellulare ATCC 13950 (ABIN00000000), M. kansasii ATCC 12478 (ACBV00000000), M. leprae Br4923 (FM211192.1), M. leprae TN (AL450380.1), M. marinum M (CP000854.1), M. parascrofulaceum BAA-614 (ADNV00000000), M. smegmatis MC2 155 (CP000480.1), Mycobacterium sp. JLS (CP000580.1), Mycobacterium sp. KMS (CP000518.1), Mycobacterium sp. MCS (CP000384.1), M. tuberculosis CDC1551 (AE000516.2), M. tuberculosis H37Ra (CP000611.1), M. tuberculosis H37Rv (AL123456.2), M. tuberculosis KZN 1435 (CP001658.1), M. ulcerans Agy99 (CP000325.1) and M. vanbaalenii PYR-1 (CP000511.1).Click here for fileDNA sequence alignment of conserved proteins in mycobacterial genomes. Sequences are from genomes of M. abscessus ATCC 19977 (CU458896.1), M. avium 104 (CP000479.1), M. avium subsp. paratuberculosis K10 (AE016958.1), M. bovis subsp. bovis AF2122/97 (BX248333.1), M. bovis BCG Pasteur 1173P2 (AM408590.1), M. bovis BCG Tokyo 172 (AP010918.1), M. gilvum PYR-GCK (CP000656.1), M. intracellulare ATCC 13950 (ABIN00000000), M. kansasii ATCC 12478 (ACBV00000000), M. leprae Br4923 (FM211192.1), M. leprae TN (AL450380.1), M. marinum M (CP000854.1), M. parascrofulaceum BAA-614 (ADNV00000000), M. smegmatis MC2 155 (CP000480.1), Mycobacterium sp. JLS (CP000580.1), Mycobacterium sp. KMS (CP000518.1), Mycobacterium sp. MCS (CP000384.1), M. tuberculosis CDC1551 (AE000516.2), M. tuberculosis H37Ra (CP000611.1), M. tuberculosis H37Rv (AL123456.2), M. tuberculosis KZN 1435 (CP001658.1), M. ulcerans Agy99 (CP000325.1) and M. vanbaalenii PYR-1 (CP000511.1).Click here for file"} +{"text": "T) was obtained in China from crickets living in cropland deserted for approximately 10 years. The isolated bacteria were Gram-negative, facultatively anaerobic, oxidase-negative rods. A preliminary analysis of the 16S rRNA gene sequence indicated that the strain belongs to either the genus Erwinia or Pantoea. Analysis of multilocus sequence typing based on concatenated partial atpD, gyrB and infB gene sequences and physiological and biochemical characteristics indicated that the strain belonged to the genus Erwinia, as member of a new species as it was distinct from other known Erwinia species. Further analysis of the 16S rRNA gene showed SCU-B244T to have 94.71% identity to the closest species of that genus, Erwinia oleae (DSM 23398T), which is below the threshold of 97% used to discriminate bacterial species. DNA-DNA hybridization results (5.78\u00b12.52%) between SCU-B244T and Erwinia oleae (DSM 23398T) confirmed that SCU-B244T and Erwinia oleae (DSM 23398T) represent different species combined with average nucleotide identity values which range from 72.42% to 74.41. The DNA G+C content of SCU-B244T was 55.32 mol%, which also differs from that of Erwinia oleae (54.7 to 54.9 mol%). The polyphasic taxonomic approach used here confirmed that the strain belongs to the Erwinia group and represents a novel species. The name Erwinia teleogrylli sp. nov. is proposed for this novel taxon, for which the type strain is SCU-B244T (= CGMCC 1.12772T = DSM 28222T = KCTC 42022T).A bacterial isolate (SCU-B244 Our aim was to explore the relationship between pesticide resistance and symbionts. Among 274 isolates cultured from Teleogryllus occipitalis, 27 strains of genera Lysinibacillus, Pseudomonas, Sphingobacterium, Exiguobacterium and Staphylococcus could evidently degrade chlorpyrifos, a common insecticide used in this field for many years. One isolate (SCU-B244T) that could degrade chlorpyrifos was cultured on TSA (tryptone soy agar) medium in August 2012 and could not be identified to the species level. A polyphasic taxonomic approach was used to investigate the strain, with the results suggesting that SCU-B244T represents a novel species of the genus Erwinia.In a recent study, we focused on the culturable strains associated with crickets was used as reference strain in this study.Three crickets were added to 100 mL sterile 0.85% (w/v) NaCl solution in a 250 mL flask and shaken at 220 rpm for 30 min. The supernatant which contained bacteria was plated onto TSA plates and subsequently incubated at 37\u00b0C for 5 days. Glycerol stock at -80\u00b0C was adopted for long term preservation of the isolates. Exponential phase cells cultured in TSB medium with shaking at 37\u00b0C were harvested for DNA G+C content and ANI analysis. Phase contrast and transmission electron microscopy were used to examine cellular morphology and motility after growth on TSA medium at 37\u00b0C for 24 h. Gram staining was performed as described by Gerhardt T, PCR amplification, primers used and DNA sequencing conditions of 16S rRNA gene were performed as previously described [www.ezbiocloud.net/eztaxon) by comparison with 16S rRNA gene sequence data. A neighbour-joining phylogenetic tree was constructed using the method of Saitou and Nei [DNA extraction from strain SCU-B244escribed , with the highest similarity scores being 96.1% to 94.1%. Neighbour-joining and maximum-likelihood phylogenetic trees were constructed using the methods described above.The results of 16S rRNA gene sequence alignment on the EzTaxon server revealed that strain SCU-B244T, other neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences were constructed, including the strain SCU-B244T and all culturable type strains of the genera Erwinia (Candidatus Erwinia dacicola) and Pantoea, based on the same methods described above.To refine the taxonomic position of SCU-B244atpD, gyrB, infB and rpoB gene sequences enables the differentiation of the phylogenetically related genera Erwinia, Pantoea and Tatumella. A good congruence has previously been observed between DNA-DNA hybridization and MLSA [atpD, gyrB, and infB, were amplified and sequenced with the primers described by Brady et al. [atpD, gyrB and infB gene sequences were constructed using the same method as described above. Strains from genera Erwinia, Pantoea and Tatumella were used in MLSA analysis, including SCU-B244T. The partial sequence of atpD, gyrB and infB gene of related strains were obtained from GenBank and the accession numbers are indicated on the figures.Multilocus sequence analysis (MLSA) of concatenated partial and MLSA \u201316. In ty et al. . NeighboT and Erwinia oleae DSM 23398T was conducted as described by De Ley et al. [260/280 = 1.8 to 1.9) was extracted using the Omega Bacterial DNA kit (E.Z.N.A.\u00ae)DNA-DNA hybridization between SCU-B244y et al. with hybT was determined by whole genome sequencing data.The DNA G+C mol% content of strain SCU-B244et al.[API 20E, API 50CHE acid production tests and API ZYM enzymatic characteristics test (BioM\u00e9rieux) were performed according to the manufacturer\u2019s instructions. BIOLOG GN2 carbon-source utilization analysis was conducted according to the instruction manual. Cellular fatty acids analysis was also performed. Biomass for fatty acid analysis was prepared by scraping growth from TSA plates after 24h incubation at 37\u00b0C. Lipids were extracted using the method of Folch et al.. Total let al., The comT, Next Generation Sequencing (Illumina Miseq) was conducted at Majorbio Inc. and the data was used to calculate the Average Nucleotide Identity (ANI). DNA extraction method and purity were described above. ANI is a similarity measure between two genome sequences and it correlates well with DNA-DNA hybridization values. [www.ezbiocloud.net/ezgenome/browse_db). We used Orthologous Average Nucleotide Identity Tool to calculate orthologous ANI values. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession LLXO00000000. The version described in this paper is version LLXO01000000.For the genome sequencing of SCU-B244 values. A value values. Genome dTeleogryllus occipitalis and a bacterial isolate (SCU-B244T) is herein described. Initial microbiological characterization of the strain revealed that the cells were Gram-negative, oxidase-negative, rod-shaped, catalase-positive and facultatively anaerobic, suggesting that the strain belongs to the family Enterobacteriaceae [In total 274 isolates belonging to 29 genera were cultured from eriaceae .T and strains of the genera Erwinia and Pantoea cluster together. The diagram shows the phylogenetic relationship between SCU-B244T and genera Erwinia and Pantoea.Neighbour-joining and maxiErwinia and Pantoea, indicated that strain SCU-B244T belongs to the genus Erwinia and is most closely related to Erwinia oleae (DSM 23398T), which is consistent with the results of the initial phenotypic analysis.Further neighbour-joining and maxiatpD, gyrB and infB gene sequences, strain SCU-B244T and Erwinia oleae (DSM 23398T) cluster together on a single branch, consistent with the previous results, suggesting strain SCU-B244T is most closely related to Erwinia oleae (DSM 23398T).In neighbour-joining and maxiT with species of genera Erwinia and Pantoea were 95.43% (Erwinia psidii LMG 7039T) and 95.42% respectively, phylogenic closest strain was Erwinia oleae (DSM 23398T) and the identity was 94.71%, which is lower than the 97% threshold that has been established to discriminate species. Strains showing less than 97% 16S rRNA gene identity are unlikely to have more than 60 to 70% DNA\u2014DNA relatedness [T is a novel species. The DNA\u2014DNA relatedness between SCU-B244T and Erwinia oleae (DSM 23398T) was 5.79 \u00b1 2.52%. The value is mean of six hybridizations \u00b1 SD, which is significantly lower than the 70% value considered to be the threshold for the delineation of bacterial species [T and related species are listed in The highest 16S rRNA gene identity of SCU-B244leae DSM 398T and T was 55.32 mol% which could be discriminated from Erwinia oleae (DSM 23398T), which has a G+C content of 54.7 to 54.9 mol%.The DNA G+C content of strain SCU-B244T strain can be discriminated from each recognized species of the genus Erwinia by at least three characteristics, and from the phylogenetically most closely related species, Erwinia oleae, by 10 API 50CHE characteristics (API 20E and API 50CHE (BioM\u00e9rieux) tests were also carried out and the results were compared to related strains . The reseristics .API ZYM enzymatic characteristics and BIOLOG GN2 carbon-source utilization results are presented as supplementary data Tables.T and related species of genera Erwinia and Pantoea is shown in T contained C16:0 (28.2%), Summed feature 4 (12.4%), C11:0 3-OH (11.6%), Summed feature 7 (10.5%), Summed feature 3 (10.0%), C14:0 (6.4%) as the major fatty acids, while strain DSM 23398T contained C16:0 (38.8%), Summed feature 4 (32.7%), Summed feature 7 (9.1%), C12:0 (7.7%), C16:0 \u03949 cyclo (4.6%) as the major fatty acids (14:0 2-OH (3.7%) and C18:0 (3.7%) were detected from strain SCU-B244T while those were not detected from strain DSM 23398T. Fatty acid composition of SCU-B244T and reference strains data from Erwinia and Pantoea showing that most of the compositions were in the range of Erwinia and Pantoea [T belongs to group Erwinia and Pantoea.Fatty acid composition analysis of SCU-B244ty acids . Summed Pantoea , which iT is a member of genus Erwinia. DNA-DNA hybridization results, ANI values and phenotypic data obtained in this study can separate this isolate from related species. In conclusion the bacterial strain isolated from a cricket (genus Teleogryllus) represents a novel species for which the name Erwinia teleogrylli sp. nov. is proposed. Strain SCU-B244T (= CGMCC 1.12772T = DSM 28222T = KCTC 42022T) is the type strain.Based on the genotypic data , it is clear that SCU-B244Erwinia teleogrylli .The colonies are milky white, circular and convex with entire margins. Cells are short Gram-negative, facultatively anaerobic rods that are oxidase-negative, catalase-positive and able to grow in 6% (w/v) NaCl. Growth pH range is 6 to 9, with optimum growth at 7. Nitrate is reduced to nitrite.2S and indole production, acid production from sorbitol and sucrose. According to API 50CHE tests (BioM\u00e9rieux), acid is formed from glycerol, L-arabinose, D-ribose, D-xylose, D-galactose, D-glucose, D-fructose, D-mannose, L-sorbose, L-rhamnose, D-mannitol, D-sorbitol, methyl-\u03b1D-glucopyranoside, N-acetylglucosamine, arbutin, esculin ferric citrate, salicin, D-cellobiose, D-maltose, D-melibiose, D-trehalose, gentiobiose, potassium gluconate, potassium 2-ketogluconate, potassium 5-ketogluconate. No acid is produced from erythritol, D-arabinose, L-xylose, D-ardonitol, methyl-\u03b2 D-xylopyranoside, dulcitol, inositol, methyl-\u03b1D-mannopyranoside, amygdalin, D-lactose, D-saccharose, inulin, D-melezitose, D-raffinose, amidon, glycogen, xylitol, D-turanose, D-lyxose, D-tagatose, D-fucose, L-fucose, D-arabitol, L-arabitol. Results obtained with API ZYM tests (BioM\u00e9rieux) gave positive enzymatic activity results for alkaline phosphatase, esterase (C4), esterase lipase (C8), acid phosphatase, naphthol-AS-B1-phosphohydrolase, \u03b2-galactosidase, \u03b2- glucosidase and N-acetyl-\u03b2- glucosaminidase, and negative results for lipase (C14), cystine arylamidase, trypsin, \u03b1-chymotrypsin, \u03b2-glucuronidase, \u03b1-glucosidase, \u03b1-mannosidase and \u03b1-fucosidase.Results obtained with API 20E tests (BioM\u00e9rieux) gave positive results for acid production from citrate, glucose, mannitol, rhamnose, melibiose, amygdalin and arabinose, and negative results for \u03b2-galactosidase, gelatinase, urease, arginine digydrolase, lysine decarboxylase and ornithine decarboxylase activity, HThe following substrates were utilized according to BIOLOG GN2 carbon-source utilization analysis: dextrin, N-acetyl-D-glucosamine, L-arabinose, D-fructose, D-galactose, \u03b1-D-glucose, maltose, D-mannitol, D-mannose, D-melibiose, \u03b2-methyl-D-glucoside, D-psicose, L-rhamnose, D-trehalose, turanose, pyruvic acid methyl ester, citric acid, formic acid, D-galactonic acid lactone, D-galacturonic acid, D-gluconic acid, p-hydroxy phenylacetic acid, \u03b1-keto glutaric acid, propionic acid, D-saccharic acid, L-alanine, L-alanyl-glycine, L-asparagine, L-aspartic acid, L-glutamic acid, glycyl-L-aspartic acid, glycyl-L-glutamic acid, L-proline, L-serine, inosine, uridine, thymidine, glycerol, D,L-\u03b1-glycerol phosphate, glucose-1-phosphate, glucose-6-phosphate.16:0 (28.2%), Summed feature 4 (12.4%), C11:0 3-OH (11.6%), Summed feature 7 (10.5%) and Summed feature 3 (10.0%), with other minor components, including C14:0 (6.4%), C17:0 \u03949 cyclo (4.9%), C12:0 (4.3%), C14:0 2-OH (3.7%), iso-C18:0 (3.6%), C18:0 14-methyl (1.9%), C14:1 \u039411 (1.1%), C8:0 2-CH2CH3 (0.6%), C15:0 (0.5%). The DNA G+C content is 55.32 mol%.Major fatty acids are CT (= CGMCC 1.12772T = DSM 28222T = KCTC 42022T), was isolated from crickets (genus Teleogryllus) sampled in Chengdu , Sichuan Province, China.The type strain, SCU-B244S1 Certification(PDF)Click here for additional data file.S2 Certification(PDF)Click here for additional data file.S1 FigErwinia teleogrylli sp. nov. and the first 66 hit strains at the EzTaxon server within the family Enterobacteriaceae. Bar, 0.5% nucleotide substitutions. Numbers at branching points are bootstrap percentage values based on 1000 replications. Only values >50% are shown.The diagram shows the phylogenetic relationship between (TIF)Click here for additional data file.S2 FigErwinia teleogrylli sp. nov. and the first 66 hit strains at the EzTaxon server within the family Enterobacteriaceae. Bar, 0.5% nucleotide substitutions. Numbers at branching points are bootstrap percentage values based on 1000 replications. Only values >50% are shown.The diagram shows the phylogenetic relationship between (TIF)Click here for additional data file.S3 FigErwinia teleogrylli sp. nov. and taxa related type species of the genera Erwinia and Pantoea except Candidatus Erwinia dacicola. Escherichia coli ATCC 11775T was used as the outgroup. Bar, 0.5% nucleotide substitutions. Numbers at branching points are bootstrap percentage values based on 1000 replications. Only values >50% are shown.The diagram shows the phylogenetic relationship between (TIF)Click here for additional data file.S4 FigErwinia teleogrylli sp. nov. and taxa related species of genera Erwinia, Pantoea and Tatumella. Bar, 0.5% nucleotide substitutions. Numbers at branching points are bootstrap percentage values based on 1000 replications. Only values >50% are shown.The diagram shows phylogenetic relationship between (TIF)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file."} +{"text": "There are a number of errors in the legends for Figs. 3, 4, and 5. The complete, correct legends for Figs. 3, 4, and 5 are:Figure 3. Wallerian degeneration in mice lacking GD3s: tissue infiltration by activated macrophages and Schwann cell proliferation. A-B; D-E: Longitudinal sections of lesioned sciatic nerves from adult WT and GD3s KO mice at 5 days after crush lesioning immunolabeled for NF-200 or F4\u201380 and imaged at the distal nerve stump. The nuclei were counterstained with DAPI. C and F: Histograms indicating the number of NF-200 fragments (C) and active macrophages (cells positive for F4\u201380) at the distal nerve stump (F). G-H; J-K: Longitudinal sections of lesioned sciatic nerves from WT and GD3s KO mice imaged at the distal stump 7 days after crush lesioning and immunolabeled for p-histone H3 (G-H) or double immunolabeled for Ki-67 and GFAP (J-K). The nuclei were counterstained with DAPI. I and L: Histograms indicating the number of cells positive for phistone H3 (I) or KI-67/GFAP (L) at the distal stump in each group of mice. M-O: Optical slices obtained by confocal microscopy from transversal sections of wildtype uninjured (M), wildtype injured (N) or GD3s Ko injured (O) sciatic nerves immunolabeled for GFAP at distal stump, 5 days after crush lesion. Bars: A-B, G-H = 100 mm; and D-E, J-K = 50 mm; M-O = 20 mm. Statistics: Mann-Whitney, ns, p>0.05. doi: 10.1371/journal.pone.0108919.g003Figure 4. Committed nerve regeneration in adult mice lacking GD3s is restored by administration of exogenous GD3 in vivo and in vitro. A: Longitudinal sections of sciatic nerves proximally or 1 mm or 3 mm distally immunolabeled for GAP-43 at 21 days after crush lesioning. B: Histogram indicating the axonal density in the regenerating nerves from WT, GD3s KO and GD3-treated GD3s KO mice. C: Images of P1 mouse DRG explants seeded on PDL/laminin coverslips. The DRG samples from WT, GD3s KO and GD3s KO exogenously treated with GD3 ganglioside were incubated for 5 days in vitro. GD3 was added on day 2 of the incubation. Low-magnification images of DRGs immunolabeled for Tuj-1. D: Histogram quantifying neurite growth. E: High-magnification images of neurites immunolabeled for R24 or CD-60b . The nuclei were counterstained with DAPI (white) Bars: A = 100 mm; C = 500 mm; and E = 20 mm. Statistics: ANOVA ***p<0.001; *p<0.01. doi: 10.1371/journal.pone.0108919.g004Figure 5. Integrin-\u03b21 expression but not calcium influx is modified in neurons lacking GD3s. A-C: Images of integrin-\u03b21 obtained by apotome microscopy of mice neonate (P1) DRGs from WT (A), GD3s KO (B) and GD3s KO with exogenous GD3 (C). Samples were cultured for 5 days. A\u2032\u2013C\u2032: High-magnification optical sections of neurites (DIC) labeled for integrin-\u03b21. A\u2033-C\u2033: High-magnification optical sections of neurites (DIC) double labeled for integrin-\u03b21 and CD60-b (9-O-ac. GD3). Yellow dots indicate colocalization of the two markers. D: DIC image of the field shown in C, illustrating DRG (lower right) and neurites extended. E, E\u2032: Histogram of quantitative analysis of the number of integrin- \u03b21 (E) or 9-O-Ac. GD3 (E\u2032) clusters along extended neurites. F and J: P1 postnatal DRGs were dissected, cleaned, dissociated and cultured for 48 h in the presence of 50 ng/ml NGF. Cell cultures from both WT (F) and GD3s KO (J) mice show typical neurons with extensive neurites and flat Schwann cells. The same fields are shown under fluorescence . Further, H and L show the same microscope field under fura-2 fluorescence, in SCCI experiments. Typical responses are shown for 4 cells in WT (I) or in GD3s KO mice (M) when stimulated with 50 mM KCl or 100 mM ATP . As shown in WT , cells #4 and #7 are neurons (with large cell bodies), whereas cells 14 and 10 are flat, typical of Schwann glia. The same is observed for GD3s KO cells , where cells #17 and #10 are neurons, and cells #28 and #39 are glia. N, O: Histograms indicating maximum calcium influx when stimulated by KCl or ATP . Bars: A-D = 500 mm; A\u2032-C\u2032, A\u2032-C\u2033 = 100 mm F-H, J-L = 20 mm. Statistics: ns, p = 0.760 Mann-Whitney; ***p<0.0001, *p<0.001 ANOVA. doi: 10.1371/journal.pone.0108919.g005"} +{"text": "P. aeruginosa an important pathogen causing lower respiratory tract infections (LRTI) both in HIV and non-HIV population. Molecular characterization of Pseudomonas spp. helps in better understanding of their clonal distribution among these patient populations. Our study aims to discriminate and generate highly specific fingerprints using 16S-rDNA PCR and amplified ribosomal DNA restriction analysis (ARDRA) techniques.Pseudomonas spp. were subjected to 16SrDNA PCR using universal primers and amplicons digested with Hae III, Alu I and Rsa I for ARDRA analysis. Nucleic acid size confirmation of the digested amplicons was done using MultiNA Bioanalyser. Phylogenetic tree was constructed by maximum parsimonious method using MEGA 4.0. Representative isolates from the major clones were sequenced and submitted to genbank for accession numbers and genetic relatedness was identified by UPGMA using NTSYS 1.80 software. Mean genetic distance (GD) and intraspecies mean GD were calculated.Seventy-two isolates of P. aeruginosa, P.putida, P.stutzeri, Alcaligenes feacalis strains by BLASTN analysis. The overall mean GD and intra-species GD of the various species was as follows: P. aeruginosa : 4.664, 16.663, 7.536, 0.733, 0.096, 2.402 and 0.221, 3.487, 2.010, 0.029, 2.728, 0.011;P.putida:11.904, 7.3 and 1.064, 1.371; P.stutzeri (JF303641) is 2.732, 0.036; Alcaligenes feacalis (JF303642) : 30.248, 5.377 respectively.Based on ARDRA banding pattern, 14 groups and 10 clones were obtained from the 72 pseudomonas isolates with the following accession numbers: JF279962-64, JF303639-45. Sequences showed 97-100% similarity with known Pseudomonas spp causing LRTI among HIV and Non HIV patients.The highly variable mean GD values amongst the isolates from different and within the same species indicates high genetic diversity among"} +{"text": "Nucleic Acids Res. 2014 Dec 16;42(22):13488\u201399. doi: 10.1093/nar/gku1097Streptococcus pneumoniae strain ST556, as shown in Table - M. Spn556I - M. Spn556II 8TTYG)- M. Spn556III 7TATC).In this article, the authors have incorrectly designated three DNA methyltransferases in In addition, the recognition sequence of the type I system encoded by MYY570-MMY572 in Figure 3A should be AAG(N)8TTYG."} +{"text": "Deep-sea fungi, the fungi that inhabit the sea and the sediment at depths of over 1000 m below the surface, have become an important source of industrial, agricultural, and nutraceutical compounds based on their diversities in both structure and function. Since the first study of deep-sea fungi in the Atlantic Ocean at a depth of 4450 m was conducted approximately 50 years ago, hundreds of isolates of deep-sea fungi have been reported based on culture-dependent methods. To date more than 180 bioactive secondary metabolites derived from deep-sea fungi have been documented in the literature. These include compounds with anticancer, antimicrobial, antifungal, antiprotozoal, and antiviral activities. In this review, we summarize the structures and bioactivities of these metabolites to provide help for novel drug development. Chromocleista sp. was described by Park et al. chromen-4-one (96), together with six known compounds (97\u2013100) -4(97\u2013100) , were isectively .101) , was isoectively .102) and dihydrooxosorbiquinol (103) against P388, A549, HL60, BEL-7402, and K562 cell lines [Two new bisorbicillinoids, named oxosorbiquinol (ol (103) , have be104\u2013106), and the known breviones (107\u2013110) (Penicillium sp. and display strong cytotoxic effects against MCF-7 cells (IC50: 7.44\u201328.4 \u03bcM). Compound 106 exhibits cytotoxic activity against A549 cells with IC50 of 32.5 \u03bcM [111\u2013113) [111\u2013113) show 25.2%\u201344.9% cytotoxicity against HeLa at 10 \u03bcg/mL. Particularly, compound 111 displays a very strong cytotoxicity to HIV-1 replication in C8166 cells with an EC50 of 14.7 \u03bcM [Three new breviane spiroditerpenoids, breviones I\u2013K (107\u2013110) have bee 32.5 \u03bcM . Similar111\u2013113) , have be. (2009) . These c 14.7 \u03bcM .d-Pro-d-Phe) (114), cyclo(d-Tyr-d-Pro) (115), phenethyl 5-oxo-l-prolinate (116), cyclo(l-Ile-l-Pro) (117), cyclo(l-Leu-l-Pro) (118), and 3\u03b2,5\u03b1,9\u03b1-trihydroxy--ergosta-7,22-dien-6-one (119) , have be120), and a known compound, cholesta-7,22-diene-3b,5a,6b-triol (121) , were idlymerase .122), ferrineoaspergillin (123), aflatoxin (124), and (11S)-hydroxyl aspergillic acid (125) (Aspergillus sp. 16-02-1. These compounds possess certain cytotoxicity against human cancer cell lines K562 (33.6%\u201343.6%), HL-60 (24.1%\u201353.3%), HeLa (18.8%\u201345.4%), and BGC-823 (36.2%\u201351.2%) at the concentration of 100 \u03bcg/mL [New aspergillic acid (id (125) have bee126) [A known antibacterial compound, xanthocillin X (126) , was iso2 \u03bcg/mL) .127) (Penicillium sp. F00120. It inhibits in vitro proliferation of mouse melanoma (B16), human melanoma (A375), and human cervical carcinoma (HeLa) cell lines with IC50 of 0.08, 0.06, and 0.12 mM, respectively [One new sesquiterpene quinone, named penicilliumin A (127) , was isoectively .128), oxisterigmatocystin B (129), and oxisterigmatocystin C (130), together with one known compound, 5-methoxysterigmatocystin (131) , have beectively .132) and 6-deoxy-5a,6-didehydrogliotoxin (133), and five known metabolites (134\u2013138) , whereas compounds 136\u2013138 containing a disulfide or tetrasulfide bond show potential inhibitory activity against histone methyltransferase (HMT) G9a (IC50: 2.1\u20136.4 \u03bcM) [Seven gliotoxin-related compounds including two new metabolites, bis(dethio)-10a-methylthio-3a-deoxy-3,3a-didehydrogliotoxin (134\u2013138) have bee\u20136.4 \u03bcM) .Antimicrobials are the most important drugs to protect human beings from infective diseases. Deep-sea fungi are one of the potential pools for screening antimicrobial metabolites, which can be developed into new drugs.139\u2013143), together with six known analogues (144\u2013148) (Emericella sp. SCSIO 05240. All of them show weak growth inhibition against bacteria. The inhibition zone of compounds 139 and 141 against Escherichia coli (ATCC 29922), Klebsiella pneumonia (ATCC 13883), Staphylococcus aureus (ATCC 29213), Enterococcus faecalis (ATCC 29212), Acinetobacter baumanii (ATCC 19606), and Aeromonas hydrophila (ATCC 7966) is 1\u20133 mm in diameter. Moreover, compound 143 displays broad antifungal activities (3\u20134 mm in diameter) against Fusarium sp., Penicillium sp., Aspergillus niger, Rhizoctonia solani, Fusarium oxysporium f. sp. niveum, and Fusarium oxysporium f. sp. cucumeris [Four new prenylxanthones, emerixanthones A\u2013D 144\u2013148) , were is , were i149\u2013163) (Spiromastix sp. These compounds exhibit significant growth inhibition (MIC: 0.1\u20138.0 \u03bcg/mL) against Gram-positive bacteria including Staphylococcus aureus, Bacillus thuringiensis, and Bacillus subtilis. In addition, compounds 154\u2013158 display potential inhibitory effects on methicillin-resistant bacterial strains of Staphylococcus aureus (MRSA) and Staphylococcus epidermidis (MRSE). Moreover, compound 158 inhibits the growth of the vancomycin-resistant bacteria of Enterococcus faecalis and Enterococcus faecium (VRE) [Fifteen new depsidone-based analogues, named spiromastixones A\u2013O (149\u2013163) , have beum (VRE) .et al. (2013) [164) against Staphylococcus aureus, Bacillus subtilis, Vibrio sp. 385, Vibrio sp. 333, and Vibrio sp. 1758 [Liu . (2013) have rep3) [164) that wassp. 1758 .165) , has bees aureus .et al. (2014) [Acremonium implicatum DFFSCS001 (AI001), Aspergillus westerdijkiae DFFSCS013 (AW013), Alternaria tenuissima DFFSCS003 (AT003), Cladosporium cladosporioides DFFSCS016 (CC016), Cladosporium sphaerospermum DFFSCS019 (CS019), Engyodontium album DFFSCS021 (EA021), Geomyces vinaceus DFFSCS022 (GV022), and Tritirachium sp. DFFSCS034 (TS034). These fungal species were isolated from sediments of the South China Sea [Loktanella hongkongensis and Micrococcus luteus, and one marine pathogenic bacterium. Based on bioassay-guided isolation technique, they have isolated five compounds (166\u2013170) have evahina Sea , and alm166\u2013170) from the.9 \u03bcg/mL .171) , has beef 276 \u03bcM .et al. (2014) [172), and five known diketopiperazine derivatives, diketopiperazine V (173), brevianamide Q (174), brevianamide R (175), brevianamide K (176), and brevianamide E (177) , 53.7% (174), 46.2% (175), 61.4% (176), and 19.3% (177) at 13.9 \u03bcM, respectively [Kong . (2014) have rep E (177) , which wectively .178 (Aspergillus westerdijkiae SCSIO 05233 and shows strong antifouling activity with an EC50 of 8.8 mg/mL [Compound 178 has been.8 mg/mL .p-hydroxyphenopyrrozin (179) , with a 79 , withnd (180) that wasalbicans .181) and penicitrinone A (182) at 100 \u03bcM [Two citrinin type compounds, phenol A acid ( A (182) , with ant 100 \u03bcM .The fungi in deep-sea environments are very diverse and abundant, making them a versatile reservoir of metabolites with both new structures and bioactivities that can be of potential use, acting as leading compounds to synthesize new modern medicine. Although the research on deep-sea fungi is not as up-to-date as the research on fungi in other environments such as terrestrial soil, fresh water, and shallow marine areas due to difficulties in both sample collection and fungal cultivation methods, more and more fungi have been cultivated from the deep sea based on culture-dependent methods. These deep-sea fungi can provide a potential source for natural bioactive product screening and new drug discovery. Up to now, more than 180 new and/or bioactive secondary metabolites from deep-sea fungi with broad bioactivities, such as anticancer, antimicrobial, antifungal, anti-larval settlement, and antiviral, have been described in the literature. Most of the investigated bioactive compounds exhibit cytotoxic activity, then antimicrobial activity. These bioactive compounds not only help deep-sea fungi to defend themselves against predators in the natural ecosystem, but also have the potential of becoming treatments for human diseases and probes for new biological targets. Work to isolate fungi from deep-sea environments and characterize their bioactive metabolites is underway and is of increased importance due to the urgent need for new drugs to overcome emerging and drug-resistant diseases."} +{"text": "Headache is a very common health problem among adolescents, causing school and social disability . This isThree hundred and seventy-six adolescents aged 11-15 years, living in the Pavia province , were recruited for this cross-sectional school-based study. They were assessed about their headache using a medical history questionnaire; headache diagnosis was made according to the new classification system of the International Headache Society (ICDH-3 Beta). Headache-related disability was assessed by means of PedMIDAS (Pediatric Migraine Disability Assessment Score).Of the 376 students enrolled 91 24.2%) had headache: 60.44% girls (n=55) and 39.56% boys (n=36). At the first diagnosis, the prevalence of any migraine was 28.6% (n=26), any tension-type headache (TTH) 60.4% (n=55), any medication-overuse headache 3.3% (n=3) and \u201cunclassifiable\u201d headache was 7.7% (n=7) .None declared."} +{"text": "BMS-663068 is a prodrug of BMS-626529, an attachment inhibitor that binds directly to HIV-1 gp120, preventing initial viral attachment and entry into the host CD4+ T-cell. AI438011 is an ongoing, Phase IIb, randomized, active-controlled trial investigating the safety, efficacy and dose\u2013response of BMS-663068 vs. atazanavir/ritonavir (ATV/r) in treatment-experienced (TE), HIV-1-positive subjects. At Week 24, response rates across the BMS-663068 arms were consistent with ATV/r.50 100 nM) were randomized equally to four BMS-663068 arms and a control arm (ATV/r 300/100 mg QD), with tenofovir disoproxil fumarate (TDF) + raltegravir (RAL). The complete safety profile through Week 24 is reported.Antiretroviral TE subjects with susceptibility to all study drugs (including BMS-626529 ICn=196)). In the ATV/r arm, Grade 2\u20134 drug-related AEs occurred in 14/51 (27.5%) subjects and were mostly secondary to gastrointestinal and/or hepatobiliary disorders. Serious adverse events (SAEs) occurred in 13/200 (6.5%) and 5/51 (9.8%) subjects receiving BMS-663068 and ATV/r, respectively; most were secondary to infections and none were related to study drugs. The most common AE reported for BMS-663068 was headache , occurring in 5/51 (10%) subjects in the ATV/r arm; in the BMS-663068 arms, this was not dose-related. There were no deaths.In total, 251 subjects were treated . No BMS-663068-related adverse events (AEs) led to discontinuation. Grade 2\u20134 drug-related AEs occurred in 17/200 (8.5%) subjects across the BMS-633068 arms; however, these events were mostly single instances and no dose-relationship was seen. Similarly, no noticeable trend for Grade 3\u20134 laboratory abnormalities was seen and Grade 3\u20134 hematologic changes and liver chemistry elevations were uncommon (neutropenia, 2.5%; AST/ALT elevations, 1% (BMS-663068 was generally well tolerated across all arms, with no related SAEs or AEs leading to discontinuation and no dose-related safety signals. There were no trends for Grade 2\u20134 AEs or clinical laboratory abnormalities. These results support continued development of BMS-663068.Previously submitted at IDWeek, Philadelphia, PA, 8 October 2014."} +{"text": "HIV-infected patients treated with Highly Active Antiretroviral Therapy (HAART) may be predisposed to hypertriglyceridemia, which gives rise to a highly atherogenic lipid profile known as atherogenic dyslipidemia (AD). We propose that genetic variability leaves some HIV-infected patients more predisposed to AD than others , 2.This was a cross-sectional, observational study conducted in 468 antiretroviral-treated HIV-infected patients attending at the outpatient clinic of a tertiary hospital over a 6-month period, who were classified as normolipidemic (n=173) or presenting with AD (triglycerides: 1.7 mmol/L and HDLc < 1.02 [men] or 1.28 mmol/L [women]) (n=148). Polymorphisms were identified in the APOA5, APOC3, LPL, CETP, HL, MTP, APOE, LRP5 and VLDLR genes.Atherogenic dyslipidemia was detected in 31% of patients, most of whom were men (77%). This group was also older and had higher levels of remnant lipoprotein cholesterol (RLPc) than normolipidemic patients. The polymorphisms rs328 in LPL, rs708272 in CETP and rs1800588 in HL were 10\u201340% significantly more frequent in normolipidemic patients. At least 1 of these polymorphisms was detected in 90% of normolipidemic patients; in AD patients, the percentage decreased to 75% (p=0.003). This effect was dependent on both the allele and the dose of HAART and independent of the regimen administered. The protective combination showed a trend towards higher HDLc (1.13 [0.40] vs 1.24 [0.23] mmol/L), lower triglycerides (2.23 [2.34] vs 1.89 [1.24] mmol/L) and lower RLPc (16.41 [11.42] vs 12.99 [11.69] mmol/L).Polymorphisms in LPL, CETP and HL protect HIV-infected patients from developing AD in a dose-dependent manner ."} +{"text": "Kabuki syndrome (KS) is a multiple congenital anomalies/intellectual disability syndrome characterized by developmental delay, specific facial features, skeletal and visceral abnormalities. This syndrome is caused by mutations in MLL2 and KDM6A gene. Autoimmune abnormalities such as idiopathic thrombocytopenic purpura, hemolytic anemia, thyroiditis, and vitiligo have been described very rarely in patients with KS ,2,3. HerCase report: A female patient aged 7 7/12 years presented with short stature. There was no consanguinity between her parents. She was born as a term neonate weighing 2100 g as the product of a twin pregnancy and had no perinatal complications. On physical examination, the patient was noted to have large and low-set ears, broad and arched eyebrows, elongated palpebral fissures with eversion of the lateral third of the lower eyelid, as well as high and narrow palate. She also had other phenotypic malformations such as numerous vitiligo lesions of different sizes in the neck, brachydactyly, prominent fetal finger pads, and hyperlaxity in her joints. Her height was 116.3 cm (-1.85 standard deviation score [SDS]) and weight was 21.7 kg (-0.78 SDS). She had sensorineural hearing loss and moderate mental retardation . She had a normal female karyotype . A clinical diagnosis of KS was considered.4) was 0.42 ng/dL (reference range: 0.91-1.92), Anti-microsomal antibody: 450.6 U/mL (reference range: 0-9), anti-thyroglobulin antibody: 2766 U/mL (reference range: 0-4)]. Thyroid ultrasonography demonstrated a rough pattern, consistent with thyroiditis. Levothyroxine (50 \u00b5g/day) replacement therapy induced a euthyroid state (TSH: 3.65 mIU/L and fT4: 1.15 ng/dL).Additionally, laboratory findings revealed autoimmune thyroiditis [thyroid-stimulating hormone (TSH): 242 mIU/L (reference range: 0.55-6.7) and free thyroxine (fTThe main causes of KS are point mutations with large intragenic deletions and duplications of the histone methyl transferase MLL2 gene ,4,5. We In several patients, KS was reported to be associated with autoimmune abnormalities such as idiopathic thrombocytopenic purpura, hemolytic anemia, thyroiditis, and vitiligo ,5. The aPeer-review: Internal peer-reviewed."} +{"text": "Current semi-quantitative cardiovascular magnetic resonance (CMR) techniques are of limited diagnostic value in patients with suspected myocarditis. T1- and T2-mapping CMR are promising novel quantitative approaches to assess myocardial injury. This study evaluated the performance of T1 and T2 mapping CMR to identify patients with myocarditis in comparison with conventional CMR techniques.This study included 104 patients with myocarditis and 26 controls, who underwent CMR at 1.5 Tesla. The CMR protocol included conventional sequences to assess myocardial edema (T2w-STIR), Early- (T1w-TSE) and Late-Gadolinium-Enhancement (PSIR). T1 quantification was performed using the modified Look-Locker inversion-recovery (MOLLI) sequence before and 15 minutes after administration of 0.075 mmol/kg Gadolinium-BOPTA. T2 quantification was performed using a free-breathing, navigator-gated multi-echo sequence. T1, T2 and extracellular volume (ECV) maps were calculated with a dedicated plug-in written for the OsiriX software. The diagnostic performance was compared between conventional parameters and global myocardial T1 (native and post-contrast), ECV and T2.The ROC areas-under-the-curve (AUC) to discriminate between patients with myocarditis and controls were 0.58 (p = 0.19) for the signal-intensity ratio myocardium/skeletal muscle on T2w-STIR, 0.67 (p = 0.01) for early myocardial enhancement on T1w-TSE and 0.80 (p < 0.0001) for presence of Late-Gadolinium-Enhancement, respectively. Furthermore, the AUC to discriminate between patients with myocarditis and controls were 0.77 (p < 0.0001) for native global myocardial T1, 0.59 (p = 0.14) for post-contrast global myocardial T1, 0.85 (p < 0.0001) for global myocardial ECV and 0.79 (p = 0.0001) for global myocardial T2, respectively.T1 and T2 mapping provide a superior performance to identify patients with myocarditis compared to conventional CMR techniques. In particular, the estimation of global myocardial ECV by T1 mapping improves the diagnostic value of CMR in patients with clinically suspected myocarditis.Marija-Orlovic-Foundation."} +{"text": "The correct name is Christiane Rollenhagen. The correct citation is: Rollenhagen C, Macura SL, Lathrop MJ, Mackenzie TA, Doncel GF, Asin SN (2015) Enhancing Interferon Regulatory Factor 7 Mediated Antiviral Responses and Decreasing Nuclear Factor Kappa B Expression Limit HIV-1 Replication in Cervical Tissues. PLoS ONE 10(6): e0131919. doi:"} +{"text": "To evaluate whole body diffusion-weighted MR imaging (WB-DWI MRI) for detection, staging and operability assessment in recurrent ovarian cancer compared with CT.Fifty-one women suspected for recurrent ovarian cancer underwent 3-Tesla WB-DWI/MRI using 2 b-values (b=0-1000 s/mm\u00b2), T2- and contrast T1-weighted sequences in addition to CT. WB-DWI/MRI and CT were compared for per-patient detection of recurrence, per-site detection of disease extent including peritoneal, serosal, retroperitoneal, periportal and distant metastases and for detecting disease extent according to institutional operability criteria. Imaging findings were correlated with surgical/pathological findings or imaging follow-up for at least 6 months.According to the reference standard, recurrence was confirmed in 48/51 patients. WB-DWI MRI showed 94% accuracy for detecting recurrence, versus 78% for CT. Per-site analysis showed significantly higher sensitivity of WB-DWI MRI over CT for assessing disease extent of the peritoneum, small bowel and colon mesentery and serosa , retroperitoneal suprarenal lymphadenopathies and periportal lesions (both p=0.031). Following institutional operability criteria, WB-DWI/MRI showed better sensitivity for detection of disease extent compromising operability; mesenteric root infiltration (p=0.008), carcinomatosis of small bowel (p=0.002) and colon (p=0.016), high volumetric peritoneal disease load (p=0.004) and irresectable distant metastases (p=0.016). WB-DWI MRI correctly predicted complete cytoreduction in 93% patients undergoing cytoreductive surgery versus 40% for CT.WB-DWI MRI showed higher accuracy compared with CT for recurrence detection while improving the sensitivity for staging and operability assessment of disease extent. WB-DWI MRI may be most valuable to select patients for surgical resection."} +{"text": "Background. Plasmid-mediated quinolone resistance (PMQR) has received considerable attention recently. Data analysis in Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER) revealed 75% of the Enterobacteriaceae isolates to be ciprofloxacin-resistant in 2012. Few reports regarding the prevalence of PMQR are available from India. Hence, the present study was carried out to ascertain the prevalence of PMQR genes among clinical isolates of ciprofloxacin-resistant Enterobacteriaceae in JIPMER.Methods. The study included 642 ciprofloxacin-resistant clinical Enterobacteriaceae isolates. JIPMER hospital\u2019s annual consumption data for fluoroquinolones were retrieved from the Department of Pharmacy. The test isolates were screened for the presence of qnr A, B, D, S and aac(6\u2032)-Ib-cr genes. PMQR-positive isolates alone were tested for the presence of class I (intI1) and class II (intI2) integrons. Randomly selected PCR amplicons were sequenced and analysed using MEGA software. A total of 30 PMQR strains chosen at random were assessed for the transferability of the PMQR genes.Results. A majority of the strains exhibited high MIC values with 106 strains exhibiting MIC values >256 \u00b5g/mL. The aac(6\u2032)-Ib-cr gene had the highest prevalence at 64% (414) while, qnrB and qnrS genes were present in 15% (97) and 10% (64) of the isolates respectively. None of the strains were positive for qnrA and qnrD. All PMQR-positive isolates were screened for class I (intI1) and class II (intI2) integrons. Class I integron was found to be predominant among the test isolates with a few of them carrying both the classes of integrons. Transferability of PMQR genes to transconjugants was identified.Conclusion. The incidence of PMQR genes in the tertiary-care setup of the JIPMER hospital was found to be high which could be probably due to the increased prescription of fluoroquinolones. Thus, there is a need for rational usage of fluoroquinolones. The ATCC strain E. coli 25922 served as the quality control in the antimicrobial susceptibility test.A total of 642 clinical isolates belonging to the family Enterobacteriaceae resistant to ciprofloxacin by Kirby-Bauer disc diffusion method subsequently confirmed by agar dilution MIC were part of the study. Only one positive culture per patient was included. Standard methods were followed for isolation and identification of the bacteria from clinical specimens like blood, pus, CSF, etc. . E. coliE. coli ATCC 25922 was included as the quality control. The lowest concentration of antibiotic at which the growth of bacteria had been completely inhibited was recorded as the MIC.The discs for amikacin (30 \u00b5g), ceftriaxone (30 \u00b5g), ceftazidime (30 \u00b5g), ciprofloxacin (5 \u00b5g) and gentamicin (10 \u00b5g), meropenem (10 \u00b5g) were prepared in-house using antibiotics in pure power form whereas cefoperazone-sulbactam disc was procured from Microxpress Tulip Diagnostics Pvt. Ltd, India. In particular cases, bacteria were also tested for imipenem and piperacillin-tazobactam . The antibiotic susceptibility of the test isolates was interpreted as per CLSI M100-S25. Similarly, Minimum Inhibitory Concentration (MIC) values were determined according to CLSI M100-S25 guidelines for ciprofloxacin alone by agar dilution method using Muller Hinton agar procured from Himedia Laboratories, India. JIPMER hospital\u2019s annual prescribing data for fluoroquinolones were retrieved from Department of Pharmacy, JIPMER.intI1) and class II (intI2) integrons. Electrophoresis and staining analysed the PCR products with ethidium bromide.DNA templates were prepared from the overnight inoculum of test strains grown on Nutrient HiVeg\u2122 Agar resuspended in MiliQ water after three rounds of washing. Crude template DNA was prepared by boiling lysis method . The reahttp://blast.ncbi.nlm.nih.gov/Blast.cgi) against the GenBank database of the National Center for Biotechnology Information. The phylogeny of the randomly sequenced aac(6\u2032)-Ib-cr amplicons were determined based on the nucleotide substitutions per site, i.e., the number of \u2019nucleotide substitutions\u2019 within the given sequence divided by the length of the sequence using MEGA software were randomly selected for assessing the transferability of the PMQR genes following a previously described method (E. coli (J53) AziR (sodium azide-resistant) as the recipient strain. Transconjugants were selected on MacConkey agar containing sodium azide (100 \u00b5g/mL) and ciprofloxacin (0.5 \u00b5g/mL) and confirmed based on the results of biochemical and antimicrobial susceptibility tests carried out for transconjugants, recipient and donor bacterial cells. Screening of the transconjugants by PCR assay determined the transferability of PMQR genes.PMQR-positive strains numbering 30 -Ib-cr. The qnrB and qnrS genes were present in 97 (15%) and 64 (10%) isolates respectively. None of the strains were positive for qnrA & qnrD, indicating the absence of these qnr alleles among the clinical isolates included in the study (aac(6\u2032)-Ib-cr, qnrB and qnrS among the clinical isolates was found to be 64.49, 15.1 and 9.96 respectively. The overall prevalence of aac(6\u2032)-Ib-cr, qnrB and qnrS genes among the clinical Enterobacteriaceae strains isolated from JIPMER hospital could probably fall in the range of 60.72\u201368.12, 12.5\u201318.04 and 7.82\u201312.47 respectively.Remarkably, out of the 642 strains, as many as 414 (64.5%) harboured he study . The proE. coli had the maximum frequency of aac(6\u2019)-Ib-cr(197) and qnrB(43) genes. E. coli constituted almost half of the total aac(6\u2032)-Ib-cr positive isolates. On the other hand, the frequency of the qnrS gene was highest among K. pneumoniae isolates (32) with Klebsiella spp. altogether accounting for more than half of the total qnrS gene identified (47). The most interesting fact was that PMQR genes were more predominant among E. coli, Klebsiella spp., and Enterobacter spp. The occurrence of qnr alleles among Citrobacter spp., Serratia spp., Proteus mirabilis and Providencia spp. were almost negligible with Proteus mirabilis alone carrying the qnrB allele -Ib-cr gene. None of the isolates harboured qnrB and qnrS simultaneously. E. coli, Klebsiella spp., Enterobacter spp. and Proteus mirabilis were the organisms carrying multiple PMQR genes but, the association of qnrS with aac(6\u2032)-Ib-cr was seen only in E. coli and K. pneumoniae. The presence of aac(6\u2032)-Ib-cr and qnrS genes were associated with high MIC values (\u226564 \u00b5g/mL) and these associations were statistically significant with p-values <0.0000001 and <0.006261 respectively.The majority of the strains were found to carry one of the PMQR genes. But 7% of the isolates were found positive for multiple PMQR genes. All these isolates carried either Out of 528 PMQR positive isolates 212 were found to carry class I integron whereas, 95 isolates were found to carry class 2 integron and 47 isolates were positive for both the classes of integrons. However, we must admit that the study neither included the integron sequence analysis nor screened the integron-positive isolates for the presence of contiguous resistance gene cassettes.aac(6\u2032)-Ib-cr, four were positive for qnrB, and two were positive for qnrS genes. It is interesting to note that one particular transconjugant was found positive for both aac(6\u2032)-Ib-cr and qnrB.Of the 30 PMQR positive strains included in the conjugation only 18 transconjugants were successfully achieved. Among the transconjugants 11 were positive for aac(6\u2032) Ib-cr, seven qnrB and four qnrS strains were sequenced but none them had novel mutations within the nucleotide sequence. We have submitted nucleotide sequences of eight aac(6\u2032) Ib-cr, two qnrB and one qnrS genes to GenBank and accession numbers assigned are: KR080535, KR080536, KR080537, KR080538, KR080539, KR080540, KR080541 and KR080543 for aac(6\u2032)-Ib-cr, KR080544 & KR080545 for qnrB and KR080546 for qnrS. All the identified PMQR genes were found to be closely related based on the pair-wise distance matrix value. The overall distance matrix for aac(6\u2032)-Ib-cr was found to be 2.642 whereas the pair-wise distance matrix for the qnrB gene sequences was found out be 1.255. The study did not attempt to identify variants of qnr genes. The pair-wise distance matrix of the aac(6\u2032)-Ib-cr gene has been summarised as percentages, i.e., the number of nucleotide substitution per 100 nucleotide in the A total of 25 qnr determinants are qnrA, qnrB and qnrS -Ib-cr genes among our isolates was found to be high. The prevalence of aac(6\u2032)-Ib-cr in previously published reports ranged between 7% and 40% . Therefore, there was a significant association between increased MIC and the presence of PMQR genes, opening up the possibility that PMQR genes could have contributed to high MICs among the test isolates. But, we must agree that the efflux pump activities of these test isolates were not elucidated and their QRDR mutation profile was also not identified. Thus, this particular finding of the study is inconclusive as to how far PMQR genes have contributed to the increase in MIC of a strain against ciprofloxacin. With future investigation of these clinical isolates for QRDR mutations and efflux mechanisms, the prominence of PMQR in fluoroquinolone resistance can be elucidated.It is known that QRDR mutations induce high-level MICs while, PMQR genes induce low-level MICs . HoweverIn the present study, we have elucidated the prevalence of the plasmid-mediated quinolone resistance genes among clinical Enterobacteriaceae isolates recovered from a tertiary care hospital in Puducherry, India. Resistance to fluoroquinolones has predominantly increased with a majority of the isolates exhibiting high MIC values. Therefore, to combat this increased fluoroquinolone resistance it would be appropriate to use fluoroquinolones rationally for treating gram-negative infections. However, the significant finding of our study is that the prevalence of PMQR genes in JIPMER hospital is very high.qnr gene are on prevalence rates from around the world and reports on mechanistic aspects at the molecular level are very few. Future research should focus more the molecular mechanism of the PMQR genes and its encoded proteins.Moreover, the majority of the literatures on 10.7717/peerj.1995/supp-1Data S1Click here for additional data file.10.7717/peerj.1995/supp-2Data S2Click here for additional data file.10.7717/peerj.1995/supp-3Supplemental Information 1Click here for additional data file.10.7717/peerj.1995/supp-4Supplemental Information 2Click here for additional data file.10.7717/peerj.1995/supp-5Supplemental Information 3Click here for additional data file.10.7717/peerj.1995/supp-6Supplemental Information 4Click here for additional data file.10.7717/peerj.1995/supp-7Supplemental Information 5Click here for additional data file.10.7717/peerj.1995/supp-8Supplemental Information 6Click here for additional data file.10.7717/peerj.1995/supp-9Supplemental Information 7Click here for additional data file.10.7717/peerj.1995/supp-10Supplemental Information 8Click here for additional data file.10.7717/peerj.1995/supp-11Supplemental Information 9Click here for additional data file.10.7717/peerj.1995/supp-12Supplemental Information 10Click here for additional data file.10.7717/peerj.1995/supp-13Supplemental Information 11Click here for additional data file.10.7717/peerj.1995/supp-14Supplemental Information 12Click here for additional data file.10.7717/peerj.1995/supp-15Supplemental Information 13Click here for additional data file.10.7717/peerj.1995/supp-16Supplemental Information 14Click here for additional data file.10.7717/peerj.1995/supp-17Supplemental Information 15Click here for additional data file.10.7717/peerj.1995/supp-18Supplemental Information 16Click here for additional data file.10.7717/peerj.1995/supp-19Supplemental Information 17Click here for additional data file.10.7717/peerj.1995/supp-20Supplemental Information 18Click here for additional data file.10.7717/peerj.1995/supp-21Supplemental Information 19Click here for additional data file.10.7717/peerj.1995/supp-22Supplemental Information 20Click here for additional data file.10.7717/peerj.1995/supp-23Supplemental Information 21Click here for additional data file.10.7717/peerj.1995/supp-24Supplemental Information 22Click here for additional data file.10.7717/peerj.1995/supp-25Supplemental Information 23Click here for additional data file.10.7717/peerj.1995/supp-26Supplemental Information 24Click here for additional data file.10.7717/peerj.1995/supp-27Supplemental Information 25Click here for additional data file.10.7717/peerj.1995/supp-28Supplemental Information 26Click here for additional data file.10.7717/peerj.1995/supp-29Supplemental Information 27Click here for additional data file.10.7717/peerj.1995/supp-30Supplemental Information 28Click here for additional data file.10.7717/peerj.1995/supp-31Supplemental Information 29Click here for additional data file.10.7717/peerj.1995/supp-32Supplemental Information 30Click here for additional data file.10.7717/peerj.1995/supp-33Supplemental Information 31Click here for additional data file.10.7717/peerj.1995/supp-34Supplemental Information 32Click here for additional data file.10.7717/peerj.1995/supp-35Supplemental Information 33Click here for additional data file.10.7717/peerj.1995/supp-36Supplemental Information 34Click here for additional data file.10.7717/peerj.1995/supp-37Supplemental Information 35Click here for additional data file.10.7717/peerj.1995/supp-38Supplemental Information 36Click here for additional data file.10.7717/peerj.1995/supp-39Supplemental Information 37Click here for additional data file.10.7717/peerj.1995/supp-40Supplemental Information 38Click here for additional data file.10.7717/peerj.1995/supp-41Supplemental Information 39Click here for additional data file.10.7717/peerj.1995/supp-42Supplemental Information 40Click here for additional data file.10.7717/peerj.1995/supp-43Supplemental Information 41Click here for additional data file.10.7717/peerj.1995/supp-44Supplemental Information 42Click here for additional data file.10.7717/peerj.1995/supp-45Supplemental Information 43Click here for additional data file.10.7717/peerj.1995/supp-46Supplemental Information 44Click here for additional data file.10.7717/peerj.1995/supp-47Supplemental Information 45Click here for additional data file.10.7717/peerj.1995/supp-48Supplemental Information 46Click here for additional data file.10.7717/peerj.1995/supp-49Supplemental Information 47Click here for additional data file.10.7717/peerj.1995/supp-50Supplemental Information 48Click here for additional data file.10.7717/peerj.1995/supp-51Supplemental Information 49Click here for additional data file.10.7717/peerj.1995/supp-52Supplemental Information 50Click here for additional data file."} +{"text": "Phytophthora infestans and Solanum nigrum, S. villosum and S. scabrum. European J of Plant Pathol 120(3): 233\u2013240. doi: 10.5580/e27. The correct reference 41 is: Rohani ER, Ismanizan I, Noor NM (2012) Somatic embryogenesis of mangosteen. Plant Cell Tiss Org Cult 110(2): 251\u2013259. doi: 10.1007/s11240-012-0147-4.References 40 and 41 are incorrectly switched. The correct reference 40 is: Lebrecka R (2008) Host-pathogen interaction between"} +{"text": "Sesquiterpene hydrocarbons (C15) not only share the structural properties thought to lend protective qualities to isoprene and monoterpene hydrocarbons, but also react rapidly with ozone, suggesting that sesquiterpenes may similarly enhance tolerance of abiotic stresses. To test whether sesquiterpenes protect plants against ozone, UVB light, or drought, we used transgenic lines of the wild tobacco Nicotiana attenuata. The transgenic plants expressed a maize terpene synthase gene (ZmTPS10) which produced a blend of (E)-\u00df-farnesene and (E)-\u03b1-bergamotene, or a point mutant of the same gene (ZmTPS10M) which produced (E)-\u00df-farnesene alone,. (E)-\u00df-farnesene exerted a local, external, and transient ozone-quenching effect in ozone-fumigated chambers, but we found no evidence that enhanced sesquiterpene production by the plant inhibited oxidative damage, or maintained photosynthetic function or plant fitness under acute or chronic stress. Although the sesquiterpenes (E)-\u00df-farnesene and (E)-\u03b1-bergamotene might confer benefits under intermittent heat stress, which was not tested, any roles in relieving abiotic stress may be secondary to their previously demonstrated functions in biotic interactions.Among the terpenes, isoprene (C Supernatants were evaporated to 250 \u03bcL in a rotary evaporator and analyzed using an Agilent 1200 HPLC/MS/MS. Sample (5 \u03bcL) was injected and eluted with a flow rate of 800 \u03bcL/min through an Agilent Zorbax Eclipse DBC18 1.8 \u03bcm column. A gradient of 0.05% formic acid and acetonitrile (ACN) began with 5% ACN from 0\u20130.5 min and progressed linearly to 100% ACN at 4.5 min followed by washing with 100% ACN from 5\u20135.5 min and 3 min re-initialization at 5% ACN. SA and ABA were quantified relative to the labeled internal standards using MS/MS monitoring for the ion pairs 140.9/97.0 ([2H4] SA), 136.8/93.1 (SA), 269/159.2 ([2H6]ABA), and 263/153.2 (ABA) as in Wang et al. [Frozen leaf tissue (100 mg) was extracted overnight at -20\u00b0C with 1.5 mL methanol containing the labeled internal standards [g et al. .For each experiment , treatment effects and genotype-treatment interactions were tested by two-way ANOVA using SPSS . Phytohormone data were log-transformed and moisture data arcsine-transformed for homoscedasticity. Complete statistical results are documented in E)-\u03b2-farnesene with ozone, which has been observed in smog chambers [E)-\u03b2-farnesene into empty chambers containing ca. 500 ppb ozone lowered within-chamber ozone concentrations by >100 ppb within a few minutes (E)-\u03b2-farnesene from chambers containing 350 ppb ozone (E)-\u03b2-farnesene.We tested whether the reaction of -\u03b2-farnesene-mediated ozone destruction in the leaf headspace would protect plants, we supplemented the ozone-susceptible N. tabacum cv. BelW3 with external (E)-\u03b2-farnesene diluted in acetonitrile and impregnated into cotton tampons. A dose of 2000 \u03bcg plant-1 h-1 visibly reduced ozone-induced foliar necrosis (-1 h-1 was not protective (E)-\u03b2-farnesene from the 2000 \u03bcg plant-1 h-1 treatment reached and was retained in the leaf, although the 10-fold greater leaf retention in the control fumigation suggested that most (E)-\u03b2-farnesene was destroyed in the headspace -\u03b2-farnesene with ozone could protect plants by destroying ozone in the headspace around leaves. Yet whether endogenous (E)-\u03b2-farnesene production would be sufficient to achieve leaf protection, either by acting in the headspace or within the leaf itself, remained unclear. To test for benefits of endogenous production, we transformed N. attenuata with two versions of a maize sesquiterpene synthase expressed behind a constitutive 35S promoter. The enzyme ZmTPS10 (TPS10 line) yielded nearly equal amounts of (E)-\u03b2-farnesene and (E)-\u03b1-bergamotene, whereas the point mutant Zmtps10M produced primarily (E)-\u03b2-farnesene (E)-\u03b2-farnesene: t(2.29) = 1.11, p = 0.36; (E)-\u03b1-bergamotene: t(2.35) = 1.21, p = 0.33). Emission of the TPS10- and TPS10M-catalyzed sesquiterpenes from the transformed N. attenuata lines was approximately twice as high as the sesquiterpene emission rate measured from herbivore-damaged maize plants, and exceeded undamaged plant emission by an order of magnitude [External supplementation indicated that the reaction of = 734.3, p<0.001) and significant decreases in moisture content = 25.95, p<0.001)) and photosynthetic rate = 7.81, p<0.016), all common effects of ozone exposure [F = 0.88, p = 0.37; moisture: F = 0.07, p = 0.80; photosynthetic rate: F = 0.04, p = 0.85). Surprisingly, ozone treatment had no significant effect on three markers of oxidative stress in leaves: malondialdehyde (MDA), a product of lipid peroxidation = 0.55, p = 0.47); oxidative radical absorbance capacity (ORAC) = 0.49, p = 0.50); and rutin = 0.16, p = 0.69), a flavonoid glycoside that dominates the leaf phenolic profile of N. attenuata and whose induction plays a role in UVB tolerance [Sesquiterpene synthase-transformed and WT reatment . Ozone-fexposure . A two-wolerance . A TPS10E)-\u03b2-farnesene\u2019s reactivity and protective potential from the ozone experiments with BelW3, and we hypothesized that protection against UVB exposure would accrue from within-leaf terpenes, we used the TPS10M line with the highest leaf (E)-\u03b2-farnesene content . To control for effects of transformation unrelated to sesquiterpenes, we included a second, independently transformed TPS10M line .To directly test for within-leaf antioxidant effects of sesquiterpenes, we exposed sesquiterpene synthase-transformed and WT plants to UVB irradiation. Since we had evidence of = 12.73, p = 0.001), while chlorophyll fluorescence = 55.20, p<0.001) and photosynthetic rate = 24.88, p<0.001) were significantly decreased, but no significant differences emerged between responses of TPS10M and WT plants = 0.62, p = 0.55; chlorophyll fluorescence: F = 0.79, p = 0.47; photosynthetic rate: F = 0.42, p = 0.66). MDA measurements did not show a significant treatment effect = 2.45, p = 0.14). The daily UVB exposure was continued for a total of 8 weeks, leading to significant decreases in height = 157.00, p<0.001) and seed capsule number = 38.15, p<0.001), but again, no differences in responses to treatment appeared between genotypes = 0.50, p = 0.61; seed capsule number: F = 0.16, p = 0.86).The morphological responses of both TPS10M and WT leaves, which assumed a curled appearance and crispy texture, testified to the severity of the UVB exposure . After 8E)-\u03b2-farnesene-mediated resistance to drought stress using the same two TPS10M lines used in the UV experiment. Within 3 d of treatment onset, all drought-treatment plants raised their leaves, a sign of water stress in N. attenuata. At the time of tissue harvest, 6 days into the treatment, abscisic acid (ABA) levels were double those in controls = 13.39, p = 0.001) and photosynthesis was decreased by 80% = 562.33, p<0.001), but responses did not differ between TPS10M and WT = 0.60, p = 0.56; photosynthesis: F = 0.12, p = 0.89). Although shoot MDA did not show a treatment effect = 1.07, p = 0.31), root MDA increased = 12.57, p = 0.001), but to a similar extent in all lines = 0.71, p = 0.50). Ion leakage also increased = 8.26, p = 0.007). Increases tended to be less dramatic in the (E)-\u03b2-farnesene emitter TPS10M1 than in WT, but TPS10M2 was no different from WT in its response, nor was the genotype x treatment term significant in an ANOVA = 1.53, p = 0.23). Total fresh mass after 6 d of treatment = 50.86, p<0.001), plant height after 2 weeks of treatment = 152.19, p<0.001), and seed capsule count after an 11 d drying period in both treatment groups = 16.94, p<0.001) all showed significant declines with drought, but no differences between the responses of TPS10M and WT = 1.72, p = 0.20; height: F = 0.53, p = 0.59; seed capsule number: F = 1.06, p = 0.35).We tested for (5) and monoterpene (C10) hydrocarbons have been demonstrated to protect plants from oxidative stress. We tested whether sesquiterpene (C15) hydrocarbons, many of which react rapidly with ozone, also confer such protection when externally supplemented or internally generated. After demonstrating the ozone-quenching properties of the sesquiterpene (E)-\u00df-farnesene in empty fumigation chambers ((E)-\u00df-farnesene protected plants of an ozone-sensitive N. tabacum cultivar, BelW3, from visible cell death symptoms of ozone exposure ((E)-\u00df-farnesene was not protective. To test for benefits of endogenous sesquiterpene production, we used N. attenuata transformed with a Z. mays sesquiterpene synthase gene (35S::TPS10) that produced an (E)-\u00df-farnesene and (E)-\u03b1-bergamotene blend, or a point mutant of the same gene (35S::TPS10M) that produced primarily (E)-\u00df-farnesene. Augmenting endogenous sesquiterpene production by engineering these genes into N. attenuata did not enhance tolerance to oxidative stress under conditions of ozone, UVB, or drought.Plant-produced isoprene -\u00df-farnesene to quench headspace ozone (-1 h-1 conferred visible benefits (Z. mays [Solanum tuberosum [(E)-\u00df-farnesene (20 \u03bcg plant-1 h-1) was not protective ((E)-\u00df-farnesene recovered from supplemented, ozone-fumigated leaves -\u00df-farnesene and (E)-\u03b1-bergamotene, in the ecological model plant Nicotiana attenuata. The transformants grew and developed normally and had no significant physical or chemical differences from WT besides emission of the target volatiles [(E)-\u00df-farnesene recovered from leaves of BelW3plants externally supplemented with 2000 \u03bcg/plant ((E)-\u00df-farnesene were mediated by within-leaf activity.External supplementation experiments do not mimic the within-leaf sesquiterpene distribution resulting from olatiles . Sesquitolatiles . Because\u03bcg/plant , our train planta benefit. Based on the mechanisms proposed for sesquiterpene function, sesquiterpenes can be hypothesized to reduce levels of reactive oxygen species (ROS), especially in lipophilic cellular compartments, and thereby reduce oxidative damage and alter ROS-mediated signaling cascades [N. attenuata [Given the demonstrated reactivity of sesquiterpenes with ozone, we expected that sesquiterpene production might reduce ozone concentrations in the leaf boundary layer, as suggested for isoprene , or provcascades . Visiblettenuata ; shorterE)-\u03b2-farnesene emitted at 20 \u03bcg plant-1 h-1 had a short lifetime in the chamber headspace and did not confer benefits to neighboring plants. Diffusion effects [It is possible that the proximity of WT and transgenic plants in the fumigation chambers could have enabled WT to benefit from transgenic neighbors\u2019 emissions. However, our experiments with BelW3 showed that -\u00df-farnesene emission increases in a number of Pinus species in response to high light levels [Z. mays grown under high light [(E)-\u00df-farnesene was protective against the effects of UVB. UVB treatment strongly affected leaf morphology -\u00df-farnesene is stimulated by herbivory and leaf excision [E)-\u03b2-farnesene conferred no protection against this stress at either the chemical or whole-plant level: the effects of drought on ABA accumulation, electrolyte leakage, photosynthetic rate, and reproductive fitness correlates were similar in N. attenuata TPS10M and WT plants.If sesquiterpenes can diffuse across membranes and quench reactive oxygen species artments . Correlaartments . Althougartments ,58, in w winters . In Citrt stress . In Z. mexcision , which iexcision . In our E)-\u03b2-farnesene.Although our results did not demonstrate that sesquiterpenes ameliorate oxidative stress, they also do not directly refute the antioxidant hypothesis for terpene-mediated abiotic stress tolerance , since tOur results also do not directly challenge the membrane stabilization-mediated thermotolerance hypothesis . SharkeyA. thaliana, but this conclusion has been questioned [Z. mays [Spinacea olearacea thylakoids [Ours is not the first study to report that terpene supplementation does not increase tolerance to abiotic stress, but our study withstands the criticisms directed at earlier studies that showed a lack of benefit from added isoprene. Loivam\u00e4ki and colleagues found noestioned because [Z. mays . Isoprenylakoids or increylakoids , but theN. attenuata. This wild tobacco has weathered extremes of temperature, drought, and light stress over its evolutionary history in the deserts of the American southwest [N. tabacum, might facilitate detection of terpene function in abiotic stress resistance. Genetic transformation of N. tabacum has previously revealed a small but significant role of isoprene production [A subtle protective influence of sesquiterpenes might be undetectable against the stress-adapted background of outhwest and has outhwest . Using moduction in toleroduction , and mig(E)-\u00df-farnesene and (E)-\u03b1-bergamotene in resistance to abiotic stress. Previous work suggests that these two sesquiterpenes may instead function against biotic stresses. ZmTPS10 transformation of A. thaliana attracted the parasitic wasp, Cotesia marginiventris, to its Lepidopteran host [(E)-\u03b1-bergamotene was emitted from N. attenuata in response to herbivore-mediated jasmonate signaling [N. attenuata\u2019s herbivores [ZmTPS10-produced sesquiterpenes may also primarily mediate biotic interactions in their native maize, where emission is more responsive to herbivory than to light, temperature, and humidity [(E)-\u00df-farnesene and (E)-\u03b1-bergamotene in biotic interactions [Our results argue against utility of ran host . Similarignaling and attrrbivores . ZmTPS10humidity . Bioassaractions .A. thaliana plants under heat stress [N. attenuata, such signaling seems unlikely, since TPS10 and TPS10M transformants were chemically indistinguishable from WT and did not influence the defense physiology of WT neighbors when the two genotypes were grown together in the same pot [Another role for sesquiterpenes might be as within- or between-plant signals. The enhanced growth of isoprene-emitting t stress , and thet stress or leaf t stress , would bt stress or primet stress . In N. asame pot . Effects(E)-\u00df-farnesene and (E)-\u03b1-bergamotene, including the highly ozone-reactive \u03b1-humulene or (E)-\u03b2-caryophyllene [Sesquiterpenes other than phyllene , might bphyllene , a diverS1 Fig(DOCX)Click here for additional data file.S2 Fig(DOCX)Click here for additional data file.S3 Fig(DOCX)Click here for additional data file.S1 Table(XLSX)Click here for additional data file."} +{"text": "In a subgroup, advanced HPs of a medium-sized teaching hospital. Adult patients with severe sepsis were included and received standard goal-directed therapy (Surviving Sepsis Guidelines). Every patient received an arterial line and a central venous line in the upper diaphragm position. A subgroup received pulse contour cardiac output (PiCCO)-guided resuscitation and PT measurements. Pearson correlation coefficients (PCCs) were calculated between HPs and SL, which were measured every 4 hours for the first 48 hours after inclusion. n = 11) and pneumosepsis (n = 7). Mean HPs (with SD and range) were respectively: MAP 73 mmHg , HR 101 beats/minute , CVP 12 mmHg , UP 55 ml/hour , SL 3.2 mmol/l , CI 4.1 ml/kg/minute , GEDI 871 ml/m2 , ELWI 11 ml/kg , PT 32.1 C , and SvO2 75% . Relevant and significant (P < 0.005) PCCs between HPs and SL were respectively: MAP -0.417, HR 0.195, UP \u22120.237, SvO2 \u22120.204 and PT \u22120.569. Figure Twenty-five patients 12 men) were included. Mean age was 68 years (30 to 93), mean APACHE II score 31 (20 to 42). The most frequent reasons for IC admission were abdominal sepsis (2 men wer2 are significantly correlated to levels of SL, but clinical value might be limited due to the relatively low correlation coefficients. In a small subgroup, PT is better correlated to the level of SL.The conventional HPs MAP, HR, UP and SvO"} +{"text": "Association of two HLA class I variants with HIV-1 pretreatment viremia, CD4+ T cell count at the care-entry and CD4+ T cell nadir.414 HIV-positive Caucasians (30% women) aged 19-73 years were genotyped for HLA-C -35 (rs9264942) and HLA-B*5701 variants. HIV-1 viral load, as well as CD4+ T cell count at care-entry and nadir, were compared across alleles, genotypes and haplotypes.HLA-C -35 C/C genotype was found in 17.6% patients, C/T genotype in 48.1%, and T/T genotype in 34.3% patients. HLA-B*5701 variant was present in 5.8% of studied population. HIV plasma viremia in the group with C allele was significantly lower (p=0.0002) compared to T/T group , while CD4+ T cell count at baseline was notably higher among C allele carriers compared to T/T homozygotes (p=0.0007). Moreover, CD4+ T cell nadir among patients with C allele [median: 205 (IQR:83.5-390) cells/\u03bcl] was significantly higher compared to T/T group [median: 133 (IQR:46-328) cells/\u03bcl] (p=0.006). Among cases with HLA-B*5701 allele, significantly lower pretreatment viremia and higher baseline CD4+ T cell count were found compared to HLA-B*5701 negative individuals. The lowest viremia (mean: 3.85 log [SD:1.3]) HIV-RNA copies/ml and the highest baseline and nadir CD4+ T cell [median: 476 (IQR:304-682) vs. median: 361 (IQR: 205-574) cells/\u03bcl, respectively) were found in individuals with HLA-B*5701(+)/HLA-C \u201335 C/C haplotype.HLA-C -35 C and HLA-B*5701 allele exert a favorable effect on the immunological (higher baseline and nadir CD4+ T cell count) and virologic variables. This protective effect is additive for the compound HLA-B*5701(+)/HLA-C -35 C/C haplotype. Human leukocyte antigens C (HLA-C) strongly influence immunological activity in chronic viral infections as well as in autoimmune diseases e.g. Crohn\u2019s disease, autoimmune liver diseases, Graves\u2019 disease and psoriasis vulgaris ,2,3,4,5.HLA-C antigens play an important role in HIV control through two mechanisms: acting as ligands for killer immunoglobulin-like receptors (KIRs) presented on natural killer (NK) cells and directly by antigen presentation to cytotoxic T cells ,6,7.inter alia, on the level of HLA-C expression (p = 0.0007) .Similarly, the CD4+ T cell nadir among patients with at least one HLA-C -35 C allele was significantly higher compared to T/T homozygotes [median: 205 (IQR: 84\u2013390) cells/\u03bcl vs. median: 133 (IQR: 46\u2013328) cells/\u03bcl] (p = 0.006) .In patients with HLA-B*5701variant, significantly lower pretreatment viral load and higher CD4+ T cell count at baseline were observed in comparison with HLA B*5701 negative group were found in the group with the compound HLA-B*5701(+)/HLA-C locus -35 C/C haplotype Figs and 2f.Associations between HLA-B*5701 and HLA-C -35 rs9264942 variants, HIV-1 viral load, baseline CD4+ T cell count and nadir were also analyzed separately for the HIV/HCV coinfected and HIV monoinfected groups. Results were in line with the findings presented for the entire group. In the HIV/HCV coinfected patients, lower pretreatment viral loads were observed for the HLA-C -35 C allele compared to T/T homozygotes [mean: 4.4 (SD: 1.0) vs. mean: 4.86 (SD: 0.85) log HIV-RNA copies/ml for the T/T] (p = 0.04), and for the HLA-B*5701 (+) [mean: 3.4 (SD: 0.49)] compared to the HLA-B*5701 (-) cases [mean: 4.6 (SD: 0.95)]. In patients without HCV coinfection, HLA-B*5701 (+) genotype was associated with higher baseline CD4+ T cell counts [median: 537 (IQR: 361\u2013682) cells/\u03bcl] vs. median 208 (IQR: 61\u2013500) cells/\u03bcl for the HLA-B*5701 (-) (p = 0.012), higher CD4+ T cell nadir [median: 437 (IQR: 313\u2013628) cells/\u03bcl] vs. median 162 (IQR: 45\u2013386) cells/\u03bcl (p = 0.08) and lower pretreatment viral loads (mean: 3.87 [SD: 1.3] vs. mean: 4.97 [SD: 0.91] log HIV-RNA copies/ml (p = 0.004). The remaining associations were not significant when analyzed separately for HIV/HCV coinfected and HIV monoinfected subgroups.2 = 0.321, p<0.0001) than among T/T homozygotes versus r2 = 0.268, p<0.0001 for HLA-B*5701(-)] Fig and 3b, (-)] Fig and 3d. 019) Fig and 3f.HCP5 locus favorable for the viremia set-point in Caucasians, was not confirmed for Afro-American population [Favorable effects of certain HLA class I alleles on the outcomes of HIV infection have been shown in many studies , 22, 23.pulation .Moreover, some studies were conducted in the populations infected with divergent HIV subtypes ,25. Our We found that the -35 SNP rs9264942 allele C is the strongest marker for the lower baseline HIV plasma viremia as well as higher CD4+ T cell count and CD4+ T cell nadirs. It is consistent with the previous studies presenting advantageous influence of this polymorphism , 22, 28.The novel finding of this report includes the observation that the HLA-B*5701(+)/HLA-C rs9264942 C/C haplotype is associated with the most favorable pattern of influence on HIV viremia and CD4+ T cell count among the analyzed variants. This haplotype is clearly linked with the lowest pretreatment plasma viral loads, the highest CD4+ T cell counts at care-entry, as well as with the highest nadir of CD4+ T cell count, and reflects delayed progression to immunodeficiency.We found that the coexistence of two protective HLA gene variants results in an additive protective effect on HIV infection. Some studies revealed that HLA-C variants independently control the HIV infection ,13, 22, The protective host genes exert immune pressure on the virus, which creates \u201cescape\u201d mutations. Such finding connected with C/C variant of rs9264942 was presented by Blais and colleagues . The freThe limitation of the study is related to the fact, that it was impossible to assess the time from infection to the care entry, therefore differences in HIV plasma viremia and CD4+ T cell counts related to the time of infection in association with investigated HLA variants were not analyzed.To conclude, we have confirmed the protective effect during the HIV infection of the analyzed HLA variants, including additive one for the compound haplotype. Analysis of genetic variants across various ethnic groups allows confirming the consistence of the genetic effect exerted by the investigated variants."} +{"text": "It has been unclear whether thrombolytic-related asymptomatic hemorrhagic transformation (AHT) affects the clinical outcome. To answer this question, we examined whether thrombolytic-related AHT affect short-term and long-term clinical outcome.All data were collected from the Thrombolysis Implementation and Monitor of Acute Ischemic Stroke in China (TIMS-China) registry. The patients were diagnosed as having AHT group and non- hemorrhagic transformation (HT) group based on clinical and imaging data. The patients with symptomatic hemorrhagic transformation were excluded from this study. Thrombolytic-related AHT was defined according to European-Australasian Acute Stroke Study (ECASS) II criteria. 90-day functional outcome, 7-day National Institutes of Health Stroke Scale (NIHSS) score, 7-day and 90-day mortalities were compared between two groups. Logistic regression analysis was used to evaluate the effects of AHT on a short-term and long-term clinical outcome.904 of all 1440 patients in TIMS-China registry were enrolled. 89 (9.6%) patients presented with AHT after thrombolysis within 24-36h. These patients with AHT were more likely to be elder age, cardioembolic subtype, and to have higher National Institutes of Health Stroke Scale score before thrombolysis than patients without AHT. No significant difference was found on the odds of 7-day (95% CI:0.692 (0.218\u20132.195), (P = 0.532) or 90-day mortalities (95% CI:0.548 (0.237\u20131.268), P = 0.160) and modified Rankin Score(0\u20131) at 90-day (95% CI:0.798 (0.460\u20131.386), P = 0.423) or modified Rankin Score(0\u20132) at 90-day (95% CI:0.732 (0.429\u20131.253), P = 0.116) or modified Rankin Score(5\u20136) at 90-day (95% CI:0.375 (0.169\u20131.830), P = 0.116) between two groups.Thrombolytic-related AHT does not deteriorate short-term and long-term clinical outcome. Intravenous thrombolysis with alteplase (recombinant tissue plasminogen activator) is the most effective therapy for acute ischemic stroke ,2. HowevAll of data were collected from the Thrombolysis Implementation and Monitor of acute ischemic Stroke in China (TIMS-China) registry , a natioEligible patients received intravenous thrombolysis within 4.5-hour. Patients with incomplete data and thrombolysis time window>4.5h or unknown were excluded. Patients with NIHSS score \u226525were excluded. Patients with symptomatic HT were excluded from this study. Eligible patients were divided into two groups: the AHT group, which had asymptomatic hemorrhagic transformation; and the non-HT group, which had no thrombolytic-related hemorrhagic transformation .The registry of TIMS-China was approved by ethics committee of Beijing Tiantan hospital in 2006. The data from the TIMS-China registry was anonymous before access and analysis by all researchers and patient treatment was assigned and determined independent of all researchers. All patients had written informed consent before being entered in the registry.Follow-up CT scans for patients were collected at 24\u201336 hours and 7-day. The diagnosis of HT on brain images was determined independently by 2 neurologists blinded to clinical data. If there was a disagreement between 2 neurologists, a third neurologist was consulted, and a consensus decision was reached. Hemorrhagic transformation must be scored according to the ECASS II classification [Results were reported as mean \u00b1 SD or the frequency of categorical variables. Pearson chi-square (\u03c72) test was used for comparisons of categorical variables. Continuous variables were analyzed using t test or Mann-Whitney U test. Percentage proportions of outcome events were calculated by dividing the number of events by the total number of patients. For each outcome variable, a separate multivariable logistic regression was performed. Odds ratios (ORs) with its 95% confidence intervals (CI) were calculated by using non-HT group after thrombolysis as the reference group. Two-sided values of P less than .05 were considered statistically significant. All statistical analyses were performed using SAS software version 9.3 .904 patients (62.8%) were enrolled from a patient population of 1440 from 67 centers across TIMS-China. Our exclusion criteria were as follows: (1) incomplete neuroimaging workups (n = 40), (2) loss to follow-up (n = 36), (3) thrombolysis time window>4.5h or unknown (n = 312), (4) symptomatic HT (n = 24), (5) Patients with severe stroke with a NIHSS score >25(n = 93). It had been reported that 89(9.6%) patients were transformed to AHT in China , 24 and mRS score (0\u20132) in patients after thrombolysis when we analyze the data without any adjustment for covariates. After adjustment for baseline relevant factors, no significant difference was found on the odds of 7-day (95% CI:0.692 (0.218\u20132.195), (P = 0.532) or 90-day mortalities (95% CI:0.548 (0.237\u20131.268), P = 0.160) and modified Rankin score(0\u20131) at 90-day (95% CI:0.798 (0.460\u20131.386), P = 0.423) or modified Rankin score(0\u20132) at 90-day (95% CI:0.732 (0.429\u20131.253), P = 0.116) or modified Rankin score(5\u20136) at 90-day (95% CI:0.375 (0.169\u20131.830), P = 0.116) between two groups . In AHT There were remarkably low rates of asymptomatic hemorrhagic transformation 4.5%) in the N.5% in tPrevious some studies have shown that thrombolytic-related AHT does not have a negative effect on the short-term or long-term functional outcome. AHT after thrombolysis has a suggestive of vascular recanalization and effective treatment . MoreoveDifferent from mechanism of symptomatic HT, we speculate that AHT may link with small artery formation rather than large artery formation. It has been showed that thrombolysis after acute ischemic infarction may lead to artery reopening and collateral circulation reperfusion6 . MoreoveOur study may have the following limitations. (1) Our sample size was relatively small, and our data exclude severe stroke(NIHSS> or = 25), which maybe have a subtle effect (either positive or negative) of AICH outcome. (2) Another limitation is that the study did not follow the randomized, double-blind principles. Despite these limitations, our results have implications that post-thrombolytic AHT in China does have not a negative effect on clinical prognosis.S1 Table(DOCX)Click here for additional data file.S2 Table(XLS)Click here for additional data file."} +{"text": "There is a lack of data on potential gender differences in the use of interventions to prevent and treat cardiovascular disease (CVD) in HIV-positive individuals. We investigated whether such differences exist in the D:A:D study.Follow-up was from 01/02/99 until the earliest of death, 6 months after last visit or 01/02/13. Rates of initiation of lipid-lowering drugs (LLDs), angiotensin-converting enzyme inhibitors (ACEIs), anti-hypertensives and receipt of invasive cardiovascular procedures were calculated in those without a myocardial infarction (MI) or stroke at baseline, overall and in groups known to be at higher CVD risk: (i) age >50, (ii) total cholesterol >6.2 mmol/l, (iii) triglyceride >2.3 mmol/l, (iv) hypertension, (v) previous MI, (vi) diabetes, or (vii) predicted 10-year CVD risk >10%. Poisson regression was used to assess whether rates of initiation were higher in men than women, after adjustment for these factors.n=13,039; median (interquartile range) 34 (29\u201340) years) were younger than men years, p=0.001), and were less likely to be current smokers , to have diabetes or to have hypertension . Of 49,071 individuals without a MI/stroke at enrolment, 0.6% women vs. 2.1% men experienced a MI while 0.8% vs. 1.3% experienced a stroke. Overall, women received ICPs at a rate of 0.07/100 person-years (PYRS) compared to 0.29/100 PYRS in men. Similarly, the rates of initiation of LLDs (1.28 vs. 2.46), anti-hypertensives (1.11 vs. 1.38) and ACEIs (0.82 vs. 1.37) were all significantly lower in women than men (At enrolment, women (than men . As expethan men . Use of most CVD interventions was lower among women than men in the D:A:D study. Our findings suggest that actions should be taken to ensure that both men and women are monitored for CVD and, if eligible, receive appropriate CVD interventions."} +{"text": "Pressure-support ventilation improves lung mechanics, blood gas exchange, hemodynamics, and work of breathing (WOB) in mild acute respiratory distress syndrome (ARDS) , 2. NeveT=6ml/kg) using two PEEP levels (2 and 5 cmH2O) in a mild ARDS model.To compare PSV and PCV target to protective tidal volume instillation. After 24 hours, animals were anesthetized, tracheotomized, and their lungs were mechanically ventilated in PSV to achieve VT = 6 ml/kg. After baseline data collection, animals were randomly divided to four groups (n=8/group):2O (PCV-P2);PCV + PEEP = 2 cmH2O (PCV-P5);PCV + PEEP = 5 cmH2O (PSV-P2);PSV + PEEP = 2 cmH2O (PSV-P5).PSV + PEEP = 5 cmHThirty-two male Wistar rats (310 \u00b1 19 g) were submitted to intratracheal RS) and peak transpulmonary pressures, and pressure-time product (PTP), as a surrogate of WOB, were evaluated.Animals were ventilated for 2 hours. Mean arterial pressure (MAP), arterial blood gases, peak airway . In accordance, PTP was lower in animals submitted to PEEP = 5 cmH2O compared to PEEP = 2 cmH2O during PSV .All animals showed better oxygenation along time, regardless of ventilator strategy. Animals submitted to PCV, regardless of PEEP, received more colloids to keep MAP>70 mmHg. Ppeak,In a mild ARDS model, pressure-support ventilation is associated to better hemodynamics, lung mechanics, and it seems to have a dependent effect of the adjusted PEEP level, as depicted by work of breathing.CNPq, FAPERJ, CAPES, PRONEX, MS-DECIT"} +{"text": "Systolic myocardial strain is load dependent, but the CMR literature largely disregards effects of myocardial afterload on strain and strain rate. This may reflect well known limitations of conventional myocardial afterload assessment using wall stress analyses, which are based on erroneous assumptions about left ventricular(LV) geometry and/or myocardial material properties. Therefore, we compared the utility of a nongeometric afterload index(NGI) derived from LV pressure(P) volume(V) and mass, which requires no assumptions about material properties, to that of conventional noninvasive end-systolic circumferential stress(CWS) as determinants of CMR LV circumferential strain(CST), ejection fraction(EF) and strain rate(SR) in normals(NL) and patients with nonischemic dilated cardiomyopathy(CM).We obtained breath-hold volumetric short-axis SSFP cines, cuff systolic P, systolic duration, LVV, M and EF, feature-tracking global CST(TomTec Imaging Systems) and mean SR in NLsyrs) and CM yrs, EF 27.2%(sd10.8%). CWS was calculated using Mirsky's formula(Biophys. J.1969) while NGI was determined as end-systolic PV/M.EF, CST and CSR were markedly reduced in CM compared to NL(EF 27.2%sd10.8)vs 58.4%(4.6), (-53%)p < 0.0001; CST -10.7%(5.3) vs -23.9%(4.3), (-55%), p < 0.0001);(CSR -32.1%/s(14.8) vs -65.7(14.9) p < 0.0001). But CWS was also markedly elevated in CM versus NL(CWS 307.6(9.2) vs 176.2(42.1)x 103 dyn/cm2,(+75%), p < 0.0001). Thus afterload excess due to adverse LV remodeling, may account for most EF, strain and strain rate reduction in CM. However, PV/M was more markedly increased than CWS, (162.6(sd48.9) vs 84.4(18.4)(+93%) p < 0.0001) and correlated more closely and significantly with EF, CST and CSR than CWS in the expected inverse relationship in both NL and CM subgroups(Table 0.8vs 58.Afterload excess due to adverse LV remodeling is an important determinant of reduced myocardial and LV chamber function in CM, making a major contribution to reductions in EF, CST and SR, but PV/M, a simple, nongeometric afterload index, is superior to conventional wall stress calculation as a quantitative afterload index.St. Francis Research Foundation."} +{"text": "P1\u2009=\u20090.007; CR vs. SD: P2\u2009<\u20090.001; PR vs. SD: P3\u2009=\u20090.004), 95.7% vs. 88.7% vs. 70.2% , 92.0% vs. 87.4% vs. 74.3% and 95.9% vs. 88.8% vs. 81.8% , respectively. Multivariate analysis identified that the tumour response to IC was an independent prognostic factor for DFS, OS and LRRFS.The prognostic value of the tumour response to induction chemotherapy (IC) for long-term survival outcomes after intensity-modulated radiation therapy in nasopharyngeal carcinoma (NPC) remains unknown. We retrospectively reviewed 1811 consecutive patients with newly diagnosed NPC treated using IMRT, and 399 eligible patients with pre- and post-induction chemotherapy magnetic resonance images were recruited. The clinicopathological features of patients with different tumour responses were compared using the Chi-square test or Fisher\u2019s exact test. Prognostic value was assessed using a multivariate Cox proportional hazards model. After IC, 101/399 (25.3%) patients had a complete tumour response overall (CR), 262 (65.7%) had a partial response (PR) and 36 (9.0%) had stable disease (SD). The 4-year disease-free survival (DFS), overall survival (OS), distant metastasis-free survival (DMFS) and locoregional relapse-free survival (LRRFS) rates for CR vs. PR vs. SD were 90.0% vs. 79.0% vs. 58.2% (CR vs. PR: Nasopharyngeal carcinoma (NPC) is a cancer with an extremely unbalanced geographical distribution, with an age standardised incidence rate of 20\u201350 per 100,000 males in south China2345et al. reported that neoadjuvant docetaxel-cisplatin followed by CCRT provided a 3-year overall survival (OS) benefit in stage III-IVB NPC891011The value of additional induction chemotherapy (IC) before CCRT in advanced NPC has received intense investigation. In 2009, Hui et al. revealed that the unsatisfactory tumour response after induction chemotherapy could predict poor prognosis for patients with advanced-stage NPCHowever, despite these negative outcomes, IC may have potential clinical value. Previous studies reported that the response to chemotherapy correlate with clinical outcome1314Of the 1811 patients with newly diagnosed non-metastatic NPC treated between November 2009 and February 2012 at Sun Yat-sen University Cancer Center, and the 399 patients for whom both pre- and post-induction chemotherapy magnetic resonance (MR) images of the nasopharynx and cervical region were available were retrospectively analysed. This study was conducted in compliance with the institutional policy regarding the protection of patients\u2019 private information and approved by the Research Ethics Committee of Sun Yat-sen University Cancer Center. All the methods were carried out in accordance with the approved guidelines of Sun Yat-sen University Cancer Center. Written informed consent was obtained from all patients prior to therapy.Routine staging workup included a complete history, clinical examinations of the head and neck, direct fibre-optic nasopharyngoscopy, magnetic resonance imaging (MRI) of skull base and whole neck, chest radiography, whole-body bone scan, abdominal sonography, and positron emission tomography-CT if clinically-indicated. Immunoglobulin A antibodies against EBV viral caspid antigen (VCA-IgA) and Epstein Barr virus early antigen (EA-IgA) were quantified. All patients underwent dental evaluations before RT.th edition of the International Union against Cancer/American Joint Committee on Cancer (UICC/AJCC) staging systemPatients were restaged according to the 7b-values\u2009=\u20090 and 1000 s/mm2; three signal averages) were obtained before contrast injection. After intravenous administration of gadopentetate dimeglumine , axial and sagittal T1-weighted spin-echo and coronal T1-weighted fat-suppressed spin-echo sequences were performed .All patients underwent MRI of the region from the suprasellar cistern to the inferior margin at the sternal end of the clavicle using a head-and-neck coil with a 3 Tesla system . T1-weighted fast spin-echo images in the axial, coronal and sagittal planes (repetition time [TR]/echo time [TE]\u2009=\u2009650 ms/9 ms), T2-weighted fast spin-echo MR images in the axial plane (TR/TE\u2009=\u20092470 ms/90 ms) and a spin-echo echo-planar DWI sequence All patients underwent IMRT while immobilized using a custom head-to-neck thermoplastic cast with the patient\u2019s neck resting on a support. A high-resolution contrast planning CT scan was taken from the vertex to 2 cm below sternoclavicular joint . Target volumes were delineated slice-by-slice on treatment planning CT scans using an individualized delineation protocol that complies with International Commission on Radiation Units and Measurements reports 50 and 62. Prescribed doses were 66\u201372 Gy at 2.12\u20132.43 Gy/fraction to planning target volume (PTV) of primary gross tumour volume (GTVnx), 64\u201370 Gy to PTV of GTV of involved lymph nodes (GTVnd), 60\u201363 Gy to PTV of high-risk clinical target volume (CTV1), and 54\u201356 Gy to PTV of low-risk clinical target volume (CTV2). All targets were treated simultaneously using the simultaneous integrated boost technique.2) with 5-fluorouracil (1000 mg/m2) (PF), cisplatin (75 mg/m2) with docetaxel (75 mg/m2) (TP), or cisplatin (60 mg/m2) with 5-fluorouracil (600 mg/m2) and docetaxel (60 mg/m2) (TPF) every three weeks for two or three or more cycles. Concurrent chemotherapy was cisplatin weekly (30\u201340 mg/m2) or on weeks 1, 4 and 7 (80\u2013100 mg/m2) of radiotherapy.According to institutional guidelines, we recommended RT alone for stage I, concurrent chemoradiotherapy (CCRT) for stage II, and CCRT +/\u2212 IC/adjuvant chemotherapy (ACT) for stage III to IVA-B. IC consisted of cisplatin . The end points (time to first defining event) were disease-free survival (DFS), overall survival (OS), distant metastasis-free survival (DMFS), locoregional relapse-free survival (LRRFS), local relapse-free survival (LRFS) and regional relapse-free survival (RRFS).P\u2009<\u20090.05 was considered significant. Stata Statistical Package 12 was used for all analyses.The Chi-square test or Fisher\u2019s exact test were used to compare categorical variables and treatment failure patterns between the CR, PR and SD groups. Life-table estimation was performed using the Kaplan-Meier method and log-rank test. The multivariate Cox proportional hazards model was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs); age, gender, smoking, drinking, pathological type, T category, N category, concurrent chemotherapy, overall response were included as variables. All tests were two-sided; n\u2009=\u2009308)-to-female (n\u2009=\u200991) ratio was 3.4:1. The median age for the whole cohort was 45 years . The baseline characteristics of patients were list in For the 399 patients, the male patients, PR for 262 (65.7%) patients, and SD for 36 (9.0%) patients. No patients had PD after IC. The local tumour response was a CR for 139/399 (34.8%) patients, PR for 195 (48.9%) patients and SD for 65 (16.3%) patients. Nineteen (4.8%) patients had N0 disease and were not included in the analysis of regional response. With regards to regional tumour response, 167/380 (43.9%), 166/380 (43.7%) and 47380 (12.4%) patients had a CR, PR and SD, respectively.P\u2009=\u20090.002; 58.3% vs. 40.1%, P\u2009=\u20090.038) and had advanced T category compared to patients who achieved a CR or PR. Obviously, patients with CR received more cycles of induction chemotherapy compared with that of patients with PR (P\u2009=\u20090.009) or SD (P\u2009<\u20090.001). No significant associations were observed between any other clinicopathological feature and the overall tumour response.Significantly more patients with SD were previous smokers . By final follow-up, 21/399 (5.3%) patients had developed local failure, 23/399 (5.8%) patients developed regional failure and 51/399 (12.8%) patients developed distant failure.P\u2009=\u20090.022) and distant failure after IMRT than patients with a CR (P\u2009=\u20090.054).With regards to overall tumour response after induction chemotherapy, patients with SD had higher rates of local failure . The local failure rates of the local PR and CR groups were almost significantly different . Patients with a regional CR after induction chemotherapy had a lower rate of distant failure after IMRT than patients with a regional PR and regional SD . Additionally, patients with a regional CR had a lower rate of regional failure after IMRT than patients with a regional PR .Patients with local SD after induction chemotherapy had higher rates of local failure after IMRT compared to patients with a local CR , 95.7% vs. 88.7% vs. 70.2% , 92.0% vs. 87.4% vs. 74.3% and 95.9% vs. 88.8% vs. 81.8% , 92.3% vs. 89.2% vs. 80.6% , 97.7% vs. 94.2% vs. 88.5% and 90.5% vs. 85.7% vs. 85.9% , 93.7% vs. 88.7% vs. 71.5% , 97.5% vs. 91.1% vs. 93.1% and 92.6% vs. 86.4% vs. 73.5% is associated with a poorer prognosis in NPC, breast cancer and gastric cancerNPC is highly chemosensitive and radiosensitive. Although most patients with advanced NPC respond well to chemotherapy, recurrence of distant metastases is the major cause of treatment failure and has a poor prognosisDespite the outcome that unsatisfactory (PR or SD) tumour response after IC indicated poor prognosis, we should pay attention to the factors which may affect the result. Firstly, using the RECIST standardThe current study showed that patients with unsatisfactory tumour responses after IC have poorer prognosis compared with that of patients with satisfactory tumour responses. Therefore, we should pay more attention to patients with SD after induction chemotherapy in clinical practice. More intensive treatment regimens like higher radiation dose and adjuvant chemotherapy should be considered. Moreover, regular follow-up should also be provided to detect early recurrence and reduce the potential risk of distant failure.This study is limited by its retrospective nature and fact the follow-up time may have been insufficient, though we selected DFS as the major endpoint to address this shortcoming. Moreover, many other prognostic factors including pre-treatment plasma Epstein-Barr virus DNA load272830Tumour response to induction chemotherapy is an independent prognostic factor for patients with NPC receiving IMRT. Assessing tumour response after induction chemotherapy may assist prognostication and refine the treatment of high-risk patients with NPC. The outcomes in this current study need to be confirmed by prospective studies with large cohorts.How to cite this article: Peng, H. et al. The Tumour Response to Induction Chemotherapy has Prognostic Value for Long-Term Survival Outcomes after Intensity-Modulated Radiation Therapy in Nasopharyngeal Carcinoma. Sci. Rep.6, 24835; doi: 10.1038/srep24835 (2016)."} +{"text": "Mucuna pruriens is the best known natural source of L-dopa, the gold standard for treatment of Parkinsonism. M. pruriens varieties are protein rich supplements, and are used as food and fodder worldwide. Here, we report L-dopa contents in seeds of fifty six accessions of four M. pruriens varieties, M. pruriens var. pruriens, M. pruriens var. hirsuta, M. pruriens var. utilis and M. pruriens var. thekkadiensis, quantified by HPTLC-densitometry. L-dopa contents varied between 0.58 to 6.42 . High and low L-dopa yielding genotypes/chemotypes of M. pruriens could be multiplied for medicinal and nutritional purposes, respectively. HPTLC profiles of M. pruriens seeds on repeated extraction (24\u2009h) in 1:1 formic acid-alcohol followed by development in butanol:acetic acid:water showed consistent degradation of L-dopa (Rf 0.34\u2009\u00b1\u20090.02) into a second peak (Rf 0.41\u2009\u00b1\u20090.02). An average of 52.11% degradation of L-dopa was found in seeds of M. pruriens varieties. Since M. pruriens seeds and/or L-dopa are used for treatment of Parkinson\u2019s disease and as an aphrodisiac both in modern and/or traditional systems of medicine, the finding of high level of L-dopa degradation (in pure form and in M. pruriens extracts) into damaging quinones and ROS is very significant. Mucuna pruriens (L.) DC. is a climbing legume distributed across the tropics. Four varieties of the species have been documented so far from south India, of which M. pruriens var. pruriens is well distributed1M. pruriens var. hirsuta and M. pruriens var. thekkadiensis are restricted to the southern parts of the Indian peninsula, and M. pruriens var. utilis occurs only in cultivationM. pruriens var. pruriens and Mucuna pruriens var. utilis find importance as food, feed, cover crop and fodder and are extensively cultivated worldwide345M. pruriens varieties propagate mostly through their seeds. M. pruriens var. pruriens is best known as the natural source of the aromatic amino acid, L-3,4-dihydroxy phenylalanine (levodopa or L-dopa) . L-dopa L-dopa and dopamine, generating semiquinones, quinones, oxygen radicals and other reactive oxygen species (ROS), play a role in neuronal cell death in PD20O-quinone products of L-dopa autoxidation are cytotoxic to cellular systems222324M. pruriens var. pruriens and L-dopa could recover spermatogenic loss which makes them the treatment of choice for infertility27PD is characterized by degeneration of dopaminergic neurons in the substantia nigra, and subsequent deficiency of the neurotransmitter dopamine in the brain areas. PD affects motor activities including writing and speaking abilities. Recent studies suggested oxidative stress, mitochondrial dysfunction and impairment of the ubiquitin-proteasome system as the major factors involved in pathogenesis of PD7891011et al., 2011 and Sundaram and Gurumoorthi, 2012 standardized protocols for HPTLC-based quantification of L-dopa in M. pruriens var. pruriens seeds29et al., 2008 , Behara et al., 2010 (4.83%), Raina and Khatri, 2011 (2.23\u20135.36%) and Raina et al., 2012 (3.29\u20135.44%) quantified L-dopa contents in M. pruriens var. pruriens seeds by HPTLC313233et al., 2007et al., 2011et al., 2008et al., 2008et al., 2010M. pruriens var. pruriens seeds (7.20%) and its formulations (4.20\u20135.60%) by spectroflourimetryStizolobium pruriens var. utilis (M. pruriens var. utilis) (3.9\u201310.6%)M. pruriens var. utilis (4.39\u20135.21%)M. pruriens var. pruriens (4.0\u20136.0%)et al., 2012 quantified L-dopa in M. pruriens var. pruriens formulations (3.0\u20136.0%) by HPLCet al., 2010 developed HPLC-based quantification of L-dopa in M. pruriens var. utiliset al., 2010 carried out HPLC-MS/MS quantification of L-dopa in rat plasmaet al., 1997 determined threshold L-dopa levels in plasma of patients with advanced PD by in vitro microdialysis-HPLCVachhani 1 2.23\u20135.% and Raiutilis 4.\u20135.21%M. M. pruriens seeds and formulations by chromatographic techniques are on limited number of samples and involved prolonged, multistep extraction procedures in acidic media. Screening of more M. pruriens varieties/accessions could lead to the discovery of high (elite) and low L-dopa yielding accessions suitable for medicinal and nutritional purposes, respectively. Secondly, in our preliminary HPTLC profiling of M. pruriens extracts and L-dopa standard, we repeatedly detected labile L-dopa-based degradation signals. Most similar HPTLC/HPLC studies never recorded this degradation signal of L-dopa562931323334353638394041M. pruriens varieties viz., M. pruriens var. pruriens (21), M. pruriens var. hirsuta (3), M. pruriens var. utilis (5) and M. pruriens var. thekkadiensis (1), collected from various locations in Kerala in south India, (ii) L-dopa contents in second generation seeds of twenty-six accessions of M. pruriens var. pruriens (21) and M. pruriens var. utilis (5) grown in an Experimental Plot (EP) under identical ecological conditions, (iii) degradation patterns of L-dopa in M. pruriens seed extracts, (iv) quantification of L-dopa degraded products in seeds of four M. pruriens varieties and (v) characterization of L-dopa degraded moieties by HPTLC, DART-MS and LC/EI-MS.Most L-dopa quantification studies in M. pruriens var. pruriens accessions varied from 0.89 to 6.42 to 3.34%. L-dopa contents in wild accessions of M. pruriens var. hirsuta ranged from 1.01 to 4.27%, and % SDP ranged from 0.01 to 1.40%. L-dopa contents in seeds of M. pruriens var. utilis wild accessions varied from 0.65 to 2.67%, and SDP contents varied from 0.12 to 3.82%. In EP grown accessions of M. pruriens var. utilis, L-dopa contents ranged from 1.33 to 3.97%, and SDP contents were zero to 0.77%. M. pruriens var. thekkadiensis wild accession showed 4.34% of L-dopa with SDP 0.01% (M. pruriens var. hirsuta and M. pruriens var. thekkadiensis in the Field Gene Bank (FGB). This is the first report of L-dopa quantification in M. pruriens var. hirsuta and M. pruriens var. thekkadiensis. This is also the first quantitative determination of degradation products of L-dopa in M. pruriens seeds.L-dopa contents in wild dr. wt.) . Percentdr. wt.) . In secoDP 0.01% . FruitinM. pruriens var. pruriens, M. pruriens var. hirsuta and M. pruriens var. utilis seeds, L-dopa contents did not show any positive correlation with altitudes of their collection locations accessions , M. pruriens var. thekkadiensis and M. pruriens var. hirsuta . Lowest L-dopa percentages were found in EP grown M. pruriens var. pruriens seeds showed lowest degradation levels . Similarly, lowest L-dopa contents were seen in seeds with high levels of degradation (In wild %/2.96%) . M. prurcessions . Highest, 0.84%) . Again, , 2.75%) .M. pruriens accessions was 52.11% of total L-dopa content (138.45%) are highly significant. Standard L-dopa also showed similar degradation into a second signal on HPTLC profile . Previous studies rarely mentionedM. pruriens seeds and formulations2931323334353638394041Total SDP 72.15%) in wild 30) and EP grown 26) 138.45%) . These d and EP g% in wild 138.45%)f 0.34\u2009\u00b1\u20090.02 (f 0.34\u2009\u00b1\u20090.02 (L-dopa) and a SDP at Rf 0.41\u2009\u00b1\u20090.02 showed two significant signals at varying ratios M. pruriens var. pruriens seed extract and decomposed L-dopa standard showed degradation patterns on HPTLC, DART-MS and LC/EI-MS showed M+H+ signals at 123.06 (medium), 154.10 , 162.07 (medium), 198.09 , 199.09 (minor) and 224.11 (minor) showed M+H+ signals at 129.08 (medium), 176.08 (major), 190.10 (major), 191.11 (minor), 192.13 (minor), 193.13 , 195.17 , 204.11 (major), 218.13 (medium), 244.12 (medium) and 245.13 (minor) on HPTLC showed only one signal at R4\u2009\u00b1\u20090.02 . But, L-1\u2009\u00b1\u20090.02 . M. prurg ratios . Fresh (LC/EI-MS . On DARTt 198.09 . Fresh M (minor) . Decompo (minor) .M. pruriens var. pruriens extract (24\u2009h extracted) showed only major signals of L-dopa and dopamine. Decomposed M. pruriens var. pruriens extract did not show L-dopa and dopamine, instead showed a group of degradation signals at the M+H+ 190.10, 191.11, 192.13, 193.13 and 195.17. These DART-MS signals correspond to dopachrome, leucodopachrome, dopaquinone, other quinones and ROS , 20\u2009mM Tris buffer and water at various time periods were tested through HPTLC profiling. Time dependent degradation was observed in M. pruriens var. pruriens extracts and in standard L-dopa at these pH values , M. pruriens var. utilis (10), M. pruriens var. hirsuta (3) and M. pruriens var. thekkadiensis (1) accessions varied between 0.58 to 6.42 . M. pruriens var. pruriens elite accessions are 4283 and 4498 and M. pruriens var. hirsuta (M. pruriens var. pruriens (4098) showed highest L-dopa content of 4.32% and M. pruriens var. utilis accessions, which showed less than 1% L-dopa, can be multiplied and utilized as protein-rich diets.Our study led to the discovery of elite genotypes/chemotypes in 56 accessions of four %, wild) . Other e, 4.27%) . Among tof 4.32% . These eM. pruriens seeds in the acidic medium of 1:1 formic acid-alcohol. On HPTLC profiling, seed extracts of all four M. pruriens varieties (collected from various wild locations and EP grown) showed L-dopa at Rf 0.34\u2009\u00b1\u20090.02 and a consistent second degradation peak at Rf 0.41\u2009\u00b1\u20090.02. This degraded peak was indentified as a labile mix of dopamine, dopachrome, leucodopachrome, dopaquinone and other ROS by HPTLC, DART-MS and LC/EI-MS. On an average, the degradation of L-dopa in a 24\u2009h extraction protocol was a high 52.11%, which is significant enough to cause adverse effects in biological systems.We consistently found degradation patterns of L-dopa in M. pruriens var. pruriens seed extract (4450) and L-dopa standard in acidic, neutral and water media showed time dependent degradation. L-dopa degradation rates in the acidic medium were equivalent or even higher compared to Tris buffer or water under identical extraction periods. In seven days, M. pruriens var. pruriens seed extract and L-dopa in these liquid media resulted in degradation with gradual appearance of a black deposit. In 30 days, both M. pruriens var. pruriens seed extract and L-dopa in these solvent media resulted in significant degradation and strong black deposits. The degradation rates of L-dopa in M. pruriens var. pruriens extracts and standard L-dopa were low at 4\u2009\u00b0C compared to room temperature.HPTLC profiles of M. pruriens seeds or L-dopa are administered for very long periods. Chronic L-dopa therapy in PD results in movement disorders or dyskinesia in most patients. M. pruriens seeds and its preparations are also used for the treatment of PD in the traditional medicinal system of Ayurveda since ancient times. Certain studies claimed that M. pruriens seeds are even more effective than L-dopa in PD treatment. Some literature reports caution insufficient evidence to recommend the clinical use of M. pruriens in the treatment of PD45M. pruriens seeds are also used in tonics for male vitality and virility in Ayurveda28Recent studies showed that L-dopa degradation products and dopamine adducts result in oxidative stress and cause selective cytotoxicity of neuronal cells inducing pathogenesis in PD1820212223242543M. pruriens seeds and/or L-dopa are used for treatment of PD and as an aphrodisiac both in modern and/or traditional systems of medicine, the finding of high level of L-dopa degradation (in its pure form and in M. pruriens extracts) into damaging quinones and ROS is very significant. Our finding of consistent degradation products suggests the need for careful review of the processing of M. pruriens seeds , L-dopa and their mode(s) of administration . Further studies are required to confirm the adverse effects of the degradation products from the \u2018cure\u2019 itself in PD patients and other users.Since M. pruriens varieties viz. M. pruriens var. pruriens (21), M. pruriens var. hirsuta (3), M. pruriens var. utilis (5) and M. pruriens var. thekkadiensis (1) were collected in January to April 2009 from various wild locations in Kerala in south India (M. pruriens accessions were recorded during field trips. Voucher specimens of these M. pruriens accessions were deposited at the Herbarium (TBGT) of Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI). Seeds of these thirty M. pruriens accessions collected were dried and powdered (separately).Seeds of thirty accessions of th India . GPS cooM. pruriens seeds collected were initially planted in a FGB of the species established at JNTBGRI. First generation seeds of 21 accessions of M. pruriens var. pruriens and 5 accessions of M. pruriens var. utilis were collected from the FGB and planted in the EP in Randomized Block Design with two replications of each accession and one plant in each replication. M. pruriens var. hirsuta and M. pruriens var. thekkadiensis accessions did not produce fruits in the FGB. Therefore, these two varieties were not planted in the EP. M. pruriens var. pruriens and M. pruriens var. utilis accessions were maintained in the EP in uniform conditions. M. pruriens accessions planted in both FGB and EP were irrigated as and when required, and not supplemented with any external fertilizers. Second generation seeds of 21 accessions of M. pruriens var. pruriens and 5 accessions of M. pruriens var. utilis were collected in January to April 2011, dried and powdered (separately) (A second set of arately) .M. pruriens seed powder (2\u2009g each) was extracted with 1:1 formic acid-alcohol at room temperature and the extract was filtered. Seed powder residue was then repeatedly extracted with 1:1 formic acid-alcohol , and extracts were filtered. This seed residue was again extracted with 1:1 formic acid-alcohol . Filtrates (of five extractions) were pooled, centrifuged and made up to 100\u2009ml using 1:1 formic acid-alcohol. This M. pruriens seed extract (5\u2009ml) was concentrated on a rotary evaporator, and the extract weight was recorded. This (concentrated) M. pruriens seed extract was dissolved in 20\u2009ml 1:1 formic acid-alcohol and used for L-dopa quantification by HPTLC-densitometry. This extraction protocol was followed for quantification of L-dopa in seeds of all (56) M. pruriens accessions made up of Linomat V sample applicator, twin-trough plate development chamber, TLC Scanner 3 and WinCATS Software 4.03. M. pruriens seed extract (5\u2009ml concentrated seed extract) was dissolved in 20\u2009ml of 1:1 formic acid-alcohol (see L-dopa extraction), 4\u2009\u03bcl of this solution was repeatedly applied to silica gel HPTLC plate as 6\u2009mm wide bands with Camag Linomat V sample applicator, fitted with a microsyringe, in N2 flow . L-dopa standard was also applied along with M. pruriens seed extracts. HPTLC plate was developed upto 80\u2009mm in the twin-trough glass chamber pre-saturated for 30\u2009min with mobile phase butanol:acetic acid:water . Developed plate was scanned densitometrically at 282\u2009nm (deuterium lamp) using TLC Scanner 3 equipped with WinCATS software. L-dopa at Rf 0.34\u2009\u00b1\u20090.02 (n\u2009=\u200956) and a second degradation peak (SDP) at Rf 0.41\u2009\u00b1\u20090.02 (n\u2009=\u200956) were found in M. pruriens seed extract in butanol:acetic acid:water it showed a clear second signal at Rf 0.41 . Similar Rf 0.41 . Other s signals . Solventf values of the standard was reproducible, and was found to be same as the values observed for the peak (L-dopa) in M. pruriens seed extracts. Calibration curve was plotted between amount of standard L-dopa (fresh) versus average response (peak area) . Linearity of the calibration curve in the range 100-1000\u2009ng was ensured. Percentage L-dopa content(s) in M. pruriens extracts were calculated from peak areas using the standard curve. Percentage of second degradation peak which is a combination of labile molecules was also quantified based on L-dopa standard curve. Repeatability of sample application was assessed by applying a sample solution on a HPTLC plate developed up to 80\u2009mm under saturation conditions with butanol:acetic acid:water as the mobile phase in the twin-trough glass chamber (previously saturated with the solvent for 30\u2009min). The spot (L-dopa) was scanned six times, % coefficient of variation was acceptable. Robustness of the method was checked by slightly altering the mobile phase composition and plate developing distance was checked. No considerable effect on the data was found. Recovery studies were carried out (in two modes) by the addition of L-dopa to pre-analyzed M. pruriens extracts and they were again analyzed (see Quantification of L-dopa). In the first mode, (i) M. pruriens var. pruriens seed powder was extracted in the five-step protocol (24\u2009h) and (ii) standard L-dopa (10\u2009mg) was added initially to M. pruriens var. pruriens seed powder and extracted in the five-step protocol (24\u2009h). (i), (ii) and (iii) fresh standard L-dopa (1\u2009\u03bcg/\u03bcl), in 1:1 formic acid-alcohol were loaded (4\u2009\u03bcl each) onto HPTLC plate, developed with butanol:acetic acid:water and peak areas were measured at 282\u2009nm . % recovery of L-dopa was calculated from peak areas as 49.78%. In the second mode, M. pruriens var. pruriens seed powder was extracted in the standard five-step protocol (24\u2009h). (i) M. pruriens var. pruriens extract in 1:1 formic acid-alcohol (4\u2009\u03bcl), (ii) M. pruriens var. pruriens extract in 1:1 formic acid-alcohol (4\u2009\u03bcl) and fresh L-dopa dissolved in 1:1 formic acid-alcohol and (iii) fresh L-dopa dissolved in 1:1 formic acid-alcohol were loaded onto HPTLC plate ((ii) co-spotted), developed and peak areas were measured. % L-dopa recovery was calculated as 99.30%. % residual standard deviations (RSD) were determined as 2.63 (L-dopa) and 3.58 (SDP). Limit of detection and limit of quantification were determined for both L-dopa and SDP 48HPTLC-based quantification of L-dopa was validated in terms of precision, accuracy, repeatability and linearity. Specificity of the assays was tested by repeated application of standard L-dopa. RM. pruriens var. pruriens seed extract (Acc. No. 4450) prepared by the five stage extraction for 24\u2009h (fresh M. pruriens var. pruriens seed extract) and standard L-dopa (fresh) were suspended in 1:1 formic acid-alcohol and kept at room temperature for seven days with occasional stirring. These resulted in decomposed M. pruriens var. pruriens seed extract and decomposed L-dopa standard, respectively. Fresh M. pruriens var. pruriens seed extract, freshly prepared L-dopa standard , decomposed M. pruriens var. pruriens seed extract and decomposed L-dopa standard were applied onto silica gel plates by HPTLC , developed in butanol:acetic acid:water and scanned at 282\u2009nm (zerland) .M. pruriens var. pruriens seed extract (100\u2009mg), decomposed M. pruriens var. pruriens seed extract (100\u2009mg) and decomposed L-dopa standard (26.1\u2009mg) were analyzed by DART-MS on an AccuTOF JMS-T100LC Mass Spectrometer having a DART . Samples were analyzed directly in front of the DART source. Dry He was used at a flow rate of 4 LPM for ionization at 350\u2009\u00b0C. Orifice 1 was set at 28\u2009V, spectra were collected, and the data from 6-8 scans were averaged (M. pruriens var. pruriens seed extract (80\u2009mg) and decomposed L-dopa standard (20\u2009mg) were subjected to LC/ESI-MS analysis on a Surveyor-LCQ Deca XP plus system with Hypersil BDS C18 column , mobile phase: methanol-water 85:15, inj. vol.: 10\u2009\u03bcl, flow rate: 0.3\u2009ml/min, run time: 30\u2009min, LC detection: PDA/UV detector, 280\u2009nm and mass detection: electro spray ionization seeds (1\u2009g each) were separately extracted with 20\u2009ml (each) of 1:1 formic acid-alcohol (strongly acidic), 20\u2009mM Tris-HCl, 20\u2009mM KCl and water at room temperature and at 4\u2009\u00b0C. Similarly, standard L-dopa (5\u2009mg) was extracted (dissolved) in 10\u2009ml each of these three solvents at room temperature and at 4\u2009\u00b0C. These M. pruriens var. pruriens seed/L-dopa extracts (3\u2009\u03bcl each) were profiled using HPTLC-densitometry (as described in Quantification of L-dopa) at various time periods viz., 1\u2009h after initiation of extraction, 1, 7 and 30 days after initiation of extraction ."} +{"text": "The purpose of this study was to determine if consumption of a powdered form of tart cherries derived from tart cherry skins . The lifters ingested the supplements one time daily (480 mg/d) for 10-d: 7-d pre-exercise, day of exercise, and 48-hr post-exercise. Subjects performed 10 sets of 10 repetitions at 70% of 1RM back squat exercises with 3-min recovery between sets, maintaining equivalent total work performed (p = 0.80) and average daily caloric consumption (p = 0.61) between groups. Isokinetic knee extension/flexion maximal voluntary contractions (MVCs) and fasting blood samples were taken pre-squat workout, 60-min following squat workout as well as after 24-h and 48-h of recovery and analyzed by MANOVA with repeated measures.23 resistance trained men were matched based on relative maximal back squat strength, age, body weight, and fat free mass. Subjects were randomly assigned to ingest in a double blind manner capsules containing a placebo or powdered tart cherries [CherryPUREPowdered tart cherry supplementation seemed to attenuate the drop from pre-lift measures in 3-repetition summation of isokinetic flexion work , extension work , and all work through 60-min and 24-h of recovery compared to placebo as reported above by Cohen's d effect size, despite not being statistically significant. The overall MANOVA analysis revealed a significant Wilks' Lambda time (p < 0.001) interaction for all inflammatory markers, but no significant group \u00d7 time pro-inflammatory (p = 0.30) and anti-inflammatory (p = 0.45) effects. Univariate measures for pro-inflammatory markers reported significant main time effects for TNF-\u03b1 (p = 0.001), IL-1\u03b2 (p = 0.30), IL-6 (p = 0.023), and IL-8 (p = 0.018). Univariate measures for anti-inflammatory markers reported significant main time effects for IL-4 (p = 0.001) and IL-7 (p = 0.033) with IL-13 trending toward significance (p = 0.055). No significant group \u00d7 time effects were observed for any of the inflammatory markers, NT, or TBARS. Serum IL-1\u03b2 levels were significantly lower in TC compared to P (p = 0.048). Delta changes were assessed at all three recovery time points from the pre-lift marker measures. The overall delta MANOVA analysis revealed a significant Wilks' Lambda pro-inflammatory interaction across time (p = 0.001) and an anti-inflammatory time interaction trending toward significance (p = 0.070), but no significant group \u00d7 time pro-inflammatory (p = 0.44) or anti-inflammatory (p = 0.30) effects. TNF-\u03b1 (p = 0.010), IFN-\u03b3 (p = 0.042), IL-1\u03b2 (p = 0.031), IL-6 (p = 0.001), IL-8 (p = 0.025), IL-10 (p = 0.019), and NT (p = 0.018) demonstrated significant main effects on time, while IL-7 approached significance across time (p = 0.095). Serum IL-2 TC (p = 0.074) and IL-10 (p = 0.10) changes from pre-lift tended to be greater across the recovery time coupled with a tendency for IL-10 (p = 0.063) TC levels to also be greater compared to P. Contrarily, serum IFN-\u03b3 (p = 0.021) TC changes from pre-lift values were significantly smaller compared to P with specific differences at 24-h and 48-h post-lift.In accordance with previous TC juice supplementation research, the isokinetic performance results of this study indicate that short-term powdered TC consumption 7 days prior to, day of, and 2 days after a single bout of intense resistance exercise may help to attenuate the strength decrement over a 48-h recovery period. The seemingly better maintenance of strength during recovery with short-term powdered TC supplementation surrounding a single bout of resistance exercise did not, however, coincide with any definitive effect on markers of oxidative damage or inflammation. This may be due to the differences in resistance exercise metabolic demands, thus indicating the need for further mechanistic research."} +{"text": "AbstractHoplolaimus Daday, 1905 belongs to the subfamily Hoplolaimine Filipiev, 1934 of family Hoplolaimidae Filipiev, 1934 with ten species, is characterized by lateral field distinct, with four incisures, excretory pore behind hemizonid; Hoplolaimus (Basirolaimus) with 18 species, is characterized by lateral field with one to three incisures, obliterated, excretory pore anterior to hemizonid, dorsal oesophageal gland quadrinucleate; and Hoplolaimus (Ethiolaimus) with four species is characterized by lateral field with one to three incisures, obliterated; excretory pore anterior to hemizonid, dorsal oesophageal gland uninucleate (Hoplolaimuspuriensis Ali, Shaheen & Pervez, 2009 has been described (Hoplolaimus reported in Vietnam, viz H.seinhorsti and H.chambus (The genus ev, 1934 . Daday e in 1905 . Hoplolaal crops \u200b. In 199ay, 1905 . Siddiqinucleate . Since tescribed . Up to nchambus .Hoplolaimusbachlongviensis sp. n. was isolated from banana soil in Bach Long Vi Island, Vietnam. The female of this species is described and illustrated below. Some diagnostic characters of this species include body slightly curved ventrally, offset lip region exhibiting three to four annules, lateral field reduced, pharyngeal glands with six nuclei, excretory pore anterior to hemizonid, epiptygma absent, intestine not overlapping rectum and male was not found. Hoplolaimusseinhorsti Luc, 1958 and H.chambus Jairajpuri & Baqri, 1973 were recorded . Soil nematodes were extracted using the decanting and modified Baermann tray method ; IEBR.Nema4050-2 .Hoplolaimusbachlongviensis sp. n. is similar to Hoplolaimusseinhorsti, H.chambus, H.columbus Sher, 1963 and H.pararobustus Sher, 1963 by having excretory pore anterior to hemizonid, lateral field reduced, represented by interruptions of annules as a single incisure, often indistinct, pharyngeal glands with six nuclei (H.bachlongviensis sp. n. differs from H.seinhorsti by epiptygma absent vs present and number of longitudinal striations on basal ring 6 vs 8-12. It differs from H.chambus by male absent vs present, epiptygma absent vs present, intestine not overlapping rectum vs overlapping rectum. Hoplolaimusbachlongviensis sp. n. differs from H.columbus in having fewer tail annuli 9-13 vs 16-22; a=22-27 vs a=30-38; b=6-8 vs b=9.1-12.4; DGO=3-6 vs DGO=9-13; epiptygma absent vs present; hemizonid located about 7 annuli behind excretory pore vs 2-5 annuli and intestine not overlapping rectum vs overlapping rectum. Hoplolaimusbachlongviensis sp. n. differs from H.pararobustus by male absent vs present, intestine not overlapping rectum vs overlapping rectum, epiptygma absent vs present and sperm absent vs present.x nuclei . HoweverHoplolaimusbachlongviensis sp. n. is distinguished from H.sherivs two incisures in lateral field; having longer stylet 44-50 vs 40-45; having fewer longitudinal striations on basal ring 6 vs 20; hemizonid is conspicuous vs obscure; a=22-27 vs a=26-30; b=6-8 vs b=9.7-11.5.Hoplolaimusbachlongviensis sp. n. differs from H.puriensis by lateral field reduced, represented by a single incisure on the body, but often indistinct vs four lateral lines, longer stylet 44-50 \u00b5m vs shorter stylet 32-35 \u00b5m."} +{"text": "Enterobacter cloacae strain S1:CND1 isolated from oil-contaminated soil in Guwahati, India. S1:CND1 contains 4,205 coding sequences and has a G+C content of 57.45%. This is the first report of the genome sequence of an E.\u00a0cloacae adapted to an oil-contaminated environment.We report here the 4.57-Mb draft genome sequence of hydrocarbon-degrading Enterobacter cloacae is a Gram-negative, rod-shaped bacterium generally associated with nosocomial infections, and is considered one of the most difficult to treat among the Enterobacter sp. , along with 16 rRNAs, 77 tRNAs, 6 noncoding RNAs (ncRNAs), and 50 pseudogenes. Rapid functional annotation for CDSs of strain S1:CND1 was carried out with the RAST annotation server (s = 650 CDSs); amino acids and derivatives (s = 467); stress response (s = 157); respiration (s = 149); fatty acids, lipids, and isoprenoids (s = 138); DNA metabolism (s = 117); regulation and cell signaling (s = 150); protein metabolism (s = 168); RNA metabolism (s = 150); membrane transport (s = 177); virulence, disease, and defense (s = 100); cell wall and capsule (s = 196); and cofactors, vitamins, prosthetic groups, and pigments (s = 253). Genome annotation revealed the presence of hydrocarbon degradation genes as alkane-1-monooxygenase, alkanesufonate monooxygenase, naphthalene 1,2-dioxygenase, and quercetin 2,3-dioxygenase, thus underlining the extensive genetic adaptation of strain S1:CND1 to oil contamination.The genomic DNA for strain S1:CND1 was extracted using an Ultra-Clean Microbial DNA Isolation Kit according to the manufacturer\u2019s protocol. Isolated genomic DNA was then sequenced with an Illumina HiSeq 2500, which generated 4,580,054 paired-end reads. After quality control measures, the reads were assembled using the v. 3.81 , SPAdes v. 3.81 , and Vel v. 3.81 , which gEscherichia coli 88.1467 (score = 501) as its closest neighbor, followed by E.\u00a0coli 88.0221 (score = 490) and E.\u00a0coli 89.0511 (score = 469). Enterobacter mori LMG 25706 (score = 344) was identified as the 18th-closest neighbor.A comparison of strain S1:CND1 with genomes in the RAST database identified E.\u00a0cloacae strain S1:CND1 has been deposited in DDBJ/EMBL/GenBank under the accession no. LUGN00000000. The version of the whole-genome sequence (WGS) described here is version LUGN01000000.This whole-genome shotgun sequencing project for"} +{"text": "Thus, AvCystatin ameliorates enhanced RSV pathology without increasing susceptibility to, or persistence of, viral infection and warrants further investigation as a possible therapy for virus-induced airway disease.Respiratory Syncytial Virus (RSV) is a major pathogen causing low respiratory tract disease (bronchiolitis), primarily in infants. Helminthic infections may alter host immune responses to both helminths and to unrelated immune triggers. For example, we have previously shown that filarial cystatin (AvCystatin/Av17) ameliorates allergic airway inflammation. However, helminthic immunomodulators have so far not been tested in virus-induced disease. We now report that AvCystatin prevents Th2-based immunopathology in vaccine-enhanced RSV lung inflammation, a murine model for bronchiolitis. AvCystatin ablated eosinophil influx, reducing both weight loss and neutrophil recruitment without impairing anti-viral immune responses. AvCystatin also protected mice from excessive inflammation following primary RSV infection, significantly reducing neutrophil influx and cytokine production in the airways. Interestingly, we found that AvCystatin induced an influx of CD4 However, due to the proposed antiviral function of neutrophils, current practice suggests to target neutrophils under the umbrella of antiviral treatment .+ T cell derived IL-10. Collectively, our findings support the testing of AvCystatin as a potential novel agent to counter virus-enhanced respiratory inflammation.This is, to our knowledge, the first time that a recombinant parasite-derived immunomodulator has been shown to down-regulate virally-enhanced inflammation without impairing responses important for anti-viral immunity. We provide evidence that AvCystatin immunomodulation may act through the production of CD4All mouse experiments were ethically approved by the Imperial College Central Biological Services (CBS) ethics committee performed in accordance with approved UK Home Office guidelines (Project License No. PPL 70/6785).Mice were treated with 20 \u03bcg AvCystatin prepared as previously described or PBS i5 PFU RSV 2 weeks thereafter. For rvv-G RSV models, mice were primed with vaccinia expressing RSV-G protein (3 x 106 PFU) by scarification of the rump and infected intranasally with 5 x 105 PFU RSV 14 days later. RSV titres were assessed by titration of lung homogenates on Hep-2 cell monolayers [RSV (strain A2) and rVV-G (vaccinia virus expressing the RSV G-protein) were propagated in Hep-2 cells (ATCC) as described previously . FI RSV nolayers . RSV L-gnolayers .BAL-accessible cells were obtained by repeated instillation of 1 ml of PBS/12 mM lidocaine via the trachea in sacrificed animals. Cytospin preparations were stained with hematoxylin and eosin and analysed by light microscopy (300 cells per slide). Lungs were homogenized and digested with collagenase D for 30 min. Mediastinal lymph nodes were dissociated and filtered through a 100 \u03bcm cell strainer.Flow cytometry was performed as previously described . Briefly6 PEC and infected with RSV i.n. 4 h later.Donor BALB/c were injected i.p. with 20 \u03bcg active or heat-inactivated AvCystatin and peritoneal exudate cells (PEC) recovered 20 h later in PBS/2 mM EDTA/0.2% BSA. Recipient mice were injected intravenously with 3x10Quantification of BAL chemokines and cytokines was performed using a 13-plex Luminex kit . Data were acquired with a Luminex 100 and Starstation software.P values of <0.05 were considered significant.GraphPad Prism software was used to analyse data, generally shown as mean \u00b1SEM of 5 animals per group. Mann-Whitney t-test and 2 way ANOVA were used to compare data. S1 FigP values reflect Mann-Whitney t-test: * p<0.05, **p<0.01.A) Schematic of the FI RSV model: i.m. intramuscular; i.p. intraperitoneal; i.n. intranasal application. B) Weight loss in the FI-RSV model. Total cell number of eosinophil (C) and macrophages in the BAL (D). Viral load in the lungs measured by RSV L-gene copies (E). Representative data of 2 experiments, 5 mice per group. Error bars indicate SEM. (TIF)Click here for additional data file.S2 Fig+ T cells in the BAL (D and E) and lungs (B and C). Representative data of 2 experiments, 5 mice per group. Error bars indicate SEM. P values reflect Mann-Whitney t-test: * p<0.05, **p<0.01.Flowcytometric analysis of IL-10 intracellular cytokine content in RSV challenged or AvCystatin/RSV challenged mice is shown (A). Graphical visualization of IFN\u03b3 and IL-10 production by CD4(TIF)Click here for additional data file.S3 Fig+ CD4+ T cells (A) and the number of IL-10+ CD4+ T cells in the mLN (B) after AvCystatin treatment and RSV challenge. Representative data of 2 experiments, 5 mice per group. Error bars indicate SEM. P values reflect Mann-Whitney t-test: * p<0.05, **p<0.01.Total number of FoxP3(TIF)Click here for additional data file.S4 FigP values reflect Mann-Whitney t-test: * p<0.05.Relative expression of MUC5a in mice lungs after the vvG RSV model (A) or primary RSV model (B). Error bars indicate SEM. (TIF)Click here for additional data file."} +{"text": "Ocimum sanctum) were explored and investigated for their diversity and antiphytopathogenic activity against widespread plant pathogens Botrytis cinerea, Sclerotinia sclerotiorum, Rhizoctonia solani and Fusarium oxysporum. 90 fungal isolates, representing 17 genera were recovered from 313 disease-free and surface sterilised plant segments (leaf and stem tissues) from three different geographic locations during distinct sampling times in consequent years 2010 and 2011 in India. Fungal endophytes were subjected to molecular identification based on rDNA ITS sequence analysis. Plant pathogens such as F. verticillioides, B. maydis, C. coarctatum, R. bataticola, Hypoxylon sp., Diaporthe phaseolorum, Alternaria tenuissima and A. alternata have occurred as endophyte only during second sampling (second sampling in 2011) in the present study. Bi-plot generated by principal component analysis suggested tissue specificity of certain fungal endophytes. Dendrogram revealed species abundance as a function of mean temperature of the location at the time of sampling. Shannon diversity in the first collection is highest in Hyderabad leaf tissues (H' = 1.907) whereas in second collection it was highest from leaf tissues of Delhi (H' = 1.846). Mukteshwar reported least isolation rate in second collection. Nearly 23% of the total fungal isolates were considered as potent biocontrol agent. Hexane extract of M. phaseolina recovered from Hyderabad in first collection demonstrated highest activity against S. sclerotiorum with IC50 value of 0.38 mg/ml. Additionally, its components 2H-pyran-2-one, 5,6-dihydro-6-pentyl and palmitic acid, methyl ester as reported by GC-MS Chromatogram upon evaluation for their antiphytopathogenic activity exhibited IC50 value of 1.002 and 0.662 against respectively S. sclerotiorum indicating their significant role in antiphytopathogenic activity of hexane extract. The production of 2H-pyran-2-one, 5,6-dihydro-6-pentyl from M. phaseolina, an endophytic fungus is being reported for the first time.Endophytic mycopopulation isolated from India\u2019s Queen of herbs Tulsi ( Endophytic fungi inhabit a unique biological niche and are categorized as highly diverse, polyphyletic group of primarily ascomycetous fungi, capable of colonizing tissues of plants asymptomatically without initiating any disease or overt negative symptoms , 2], , , 5]. 42. 425]. 4Ocimum sanctum is ubiquitous in Indian culture and tradition, called Tulsi in Hindi, . F. FO. sanThe GC-MS analysis of hexane extracts was carried on GC-MS (Agilent Technologies 7890A). For this 1mg of extract was dissolved 1 ml LR-grade dichloromethane . DB-WAX column (30 m \u00d7 250\u03bcm \u00d7 0.25 \u03bcm) was used with helium as a carrier gas at a flow rate of 1 ml/min at pressure of 11.654 psi. The GC oven temperature was kept at 120\u00b0C for 2 min and programmed to 5\u00b0C/min to 130\u00b0C for 1 min; 5\u00b0C/min to 150\u00b0C for 2 min; 2\u00b0C/min to 180\u00b0C for 3 min; 2\u00b0C/min to 200\u00b0C for 3 min; 5\u00b0C/min to 240\u00b0C for 20 min. Splitless injections were done with liquid injection method in this study. A library search was carried out using NIST library.2 placed in such a way that seven are put in periphery and one in the centre of the plate. The control experiment consisted of only methanol solvent in PDA medium , , , 39]..39].The similarity and of endophytic fungal assemblages among both tissues was compared using the following similarity indices:(QS), QS = 2a/(2a + b + c) where \u2018a\u2019 is the number of common species in both communities, while \u2018b\u2019 and \u2018c\u2019 are the number of species specified to each community under investigation, respectively .JS was calculated using the formula: JS = a/(a + b + c) where \u2018a\u2019 is the number of common species in both communities, while \u2018b\u2019 and \u2018c\u2019 are the number of species specified to each community, respectively .O. sanctum different plants parts in distinct sampling time, whilst cluster analysis deduced concurrence between species richness and temperature of geographical locations at the time of sampling. For this, software Unsrcambler X: version 10, CAMO, USA was used . M. Min vitPenicillium sp.), OSHL-5.2 (Alternaria sp.), OSHL-2.1 (M. phaseolina), OSHS-3.1(M. phaseolina), OSML-5.4 (Colletotrichum sp.), OSMS-2.2 (Aspergillus niger), OSMS-2.3 (Meyerozyma guilliermondii), OSDSL-9.8 (Fusarium proliferatum), OSDSS-2.5 (Chaetomium coarctatum), OSDSL-5.6 , OSHSS-5.2 (Sympodiomyces sp.), OSHSS-1.3 (Fusarium proliferatum) OSHSS-2.3 (Diaporthe phaseolorum) endophytic fungal isolates were multiplied on rice medium, and their crude ethylacetate extracts were subjected to intoxicated/poisoned food bioassay to investigate antiphytopathogenic activity of crude fungal extracts against all four phytopathogens. IC50 values of ethylacetate crude extracts of selected thirteen endophytic fungal isolates at five different concentrations was calculated by regression analysis are summarised as Chaetomium coarctatum recorded the highest activity against all phytopathogens with IC50 value of < 1mg/ml ranging from 0.262mg/ml\u2013 0.553 mg/ml. Second best activity was reported with Fusarium proliferatum obtained from Hyderabad with IC50 value ranging from 0.299 to 1.04 mg/ml.Based on the results of dual culture bioassay , followiFusarium proliferatum obtained from Hyderabad exhibited IC50 value of 0.51mg/ml against F.oxysporum which was stronger than another isolate of F. proliferatum recovered from Delhi in second sampling , OSHS-3.1 (M.phaseolina), OSDSS-2.5 (Chaetomium coarctatum), OSHL-5.2 (Alternaria sp.), OSML-5.4 (Colletotrichum sp.) and OSHSS-1.3 (F. proliferatum) were found positive for terpenoids in preliminary phytochemical screening. GC-MS chromatography of hexane extracts of these selected endophytic fungal isolates revealed presence of volatile compounds, fatty acids, and aliphatic constituents. GC-MS chromatogram of M. phaseolina (OSHL-2.1) showed presence of 2H-Pyran-2-one, 5, 6-dihydro-6-pentyl at RT 30.156, hexadecanoic acid at RT 53.017, linoleic acid at RT 64.986 (M. phaseolina (OSHS-3.1) showed presence 9,12-octadecadieonic acid, methyl ester at RT 61.108, trifluoroacetoxy hexadecane at RT 55.970 as major peaks reflecting strain variability (Chaetomium coarctatum (OSDSS-2.5) 2-fluorobenzoic acid at RT 38.644, 2,5-difluorobenzoic acid at RT 38.444, linoleic acid, ethyl ester at RT 64.900 were observed as major peaks (Alternaria sp. (OSHL-5.2) hexane extract, hexadecanoic acid at RT 52.990, 9,15- octadecadienoic acid, methyl ester at RT 61.036 were recorded as major peaks (Fusarium proliferatum (OSHSS-1.3)-major peaks were hexadecanoic acid at RT 52.992, linoleic acid at RT 64.902, oleic acid at RT 65.954 (Colletotrichum sp. (OSML-5.4) major peaks recorded were 7-hydroxy3- coumarin at RT 61.372, 9, 12-octadecadieonic acid at RT 61.052 . Rhizopus oryzae has been reportedly primary causal agent of tuber rot disease in sweetpotato in India and in this study has been isolated from Delhi and Hyderabad in first sampling season . I. IO. sanic fungi , 51], , , , and 7272.Additionally, cluster analysis inferred distribution and abundance of endophytic fungal species from different geographical locations as a function of temperature. It grouped together species richness of Delhi (second sampling) and Hyderabad (first sampling) when temperature ranged from 23\u201324\u00b0C into cluster 1, cluster 2 comprises of Delhi (first sampling) and Hyderabad (second sampling) when temperature ranged from 30\u201331\u00b0C and cluster 3 belongs to endophytic mycobiota of Mukteshwar where temperature range was 14\u201317\u00b0C during both sampling times. This revelation is in accordance with previous studies elucidating higher influence of temperature, precipitation and other climatic factors than geography on endophytic communities of plants , 74]..74].S. Sclerotiorum causes heavy yield losses up to the tune of 40% in Brassicas in India , , all the in India . Fusariuin India . Botryti disease . R. solahe world . Differeironment .M. phaseolina (OSHL-2.1) exhibited effective inhibitory activity against B. cinerea, F. oxysporum and R. solani with 4.504 mg/ml, 1.97mg/ml and 1.41mg/ml IC50 values respectively. Whereas hexane extract of M. phaseolina (OSHL-2.1) demonstrated highest activity against S. sclerotiorum with IC50 value of 0.38 mg/ml followed by F. oxysporum with IC50 value of 0.867mg/ml. Preliminary identification of bioactive metabolites were conducted on crude hexane extracts.GC-MS chromatogram of hexane extract of M. phaseolina illustrated presence of 2H-pyran-2-one, 5, 6-dihydro-6-pentyl at RT 30.152 and palmitic acid, methyl ester at RT 53.017, while that of C. coarctatum (OSDSL-2.5) illustrated Oleic acid at RT 61.675. Present study for the time reports antifungal activity of extracts of M. phaseolina and C. coarctatum. Antifungal activities of above mentioned pure compounds against plant pathogens resulted in remarkable revelation. Oleic acid methyl ester, palmitic acid methyl ester and 5, 6 Dihydro-2H-pyran-2-one-6 pentyl exhibited strong inhibitory activity against S. sclerotiorum with 0.547mg/ml, 0.662mg/ml and 1.002 mg/ml IC50 value while against F. oxysporum it was 0.27 mg/ml, 0.264 mg/ml and 0.27mg/ml respectively. Thereby, buttressing the fact that 2H-pyran-2-one, 5,6-dihydro-6-pentyl and palmitic acid, methyl ester are bioactive metabolites synthesised by endophytic fungus M. phaseolina which are responsible for its antiphytopathogenic activity against S. sclerotiorum. Antifungal activity of 6-Pentyl-2H-pyran-2-one and its analogs has been well documented in literature . R. RM. phalium spp . Anotheric fungi . The pro studies . Hexadecalbicans . The majNCBT 196 . Another. solani .Bipolaris maydis, Rhizoctonia bataticola and Chaetomium coarctatum in endophytic state harbored inside O. sanctum for the first time. In present study metabolites produced by M. phaseolina recovered from Hyderabad in first collection has exhibited promising antifungal activity against S. sclerotiorum and F. oxysporum broad spectrum phytopathogens. Metabolites originated from fungal endophytes hold promise to be further developed as greener and safer biocontrol agent in crop disease management. It can be concluded that fungal endophytes harbored inside leaf and stem tissues of Ocimum sanctum collected from different geographical locations in different sampling times hold great promise not only as biocontrol agents against broad spectrum and economically significant phytopathogens, but also as sustainable resource of novel antifungal secondary metabolites.The study reports noted plant pathogens such as S1 Fig(TIFF)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file."} +{"text": "Cancer patients are at risk for severe complications related to the underlying malignancy or its treatment, and therefore usually require admission to ICUs.To evaluate the clinical characteristics and outcomes in this subgroup of patients.Analysis of two prospective cohorts of cancer patients admitted to ICUs. We used multivariable logistic regression to identify variables associated with hospital mortality.P <0.001 for all analyses). ICU (47 % vs. 27 %) and hospital (63 % vs. 38 %) mortality rates were also higher in patients with complications (P <0.001). Chemo/radiation therapy-induced toxicity (6 %), venous thromboembolism (5 %), respiratory failure (4 %), gastrointestinal involvement (3 %) and vena cava syndrome (VCS) (2 %) were the most frequent complications. In multivariable analysis, the presence of cancer-related complications per se was not associated with mortality (odds ratio (OR) = 1.25 ). However, among the individual complications, VCS (OR = 3.79 (1.11-12.92)), gastrointestinal involvement (OR = 3.05 (1.57-5.91)) and respiratory failure (OR = 1.96 (1.04-3.71)) were independently associated with worse outcomes.Out of 2028 patients, 456 (23 %) had cancer-related complications. Compared with those without complications, they more frequently had worse performance status (PS) (57 % vs. 36 % with PS \u22652), active malignancy (43 % vs. 5 %), need for vasopressors (45 % vs. 34 %), mechanical ventilation (70 % vs. 51 %) and dialysis (12 % vs. 8 %) (The prognostic impact of cancer-related complications was variable. Although some complications were associated with worse outcomes, the presence of a severe acute cancer-related complication per se should not guide decisions to admit a patient to the ICU."} +{"text": "Apelin (APLN) is a powerful inotrope, is widely expressed by the cardiovascular system with its receptor APJ-R, and should be considered as an alternative noncatecholaminergic support.Dobutamine (DOB) is the actual recommended b-adrenergic inotropic drug to support sepsis-induced myocardial dysfunction when cardiac output index is still low after preload correction. In this context, DOB cardiovascular response predicts outcome in septic shock. Alternative supportive and safer therapies are however mandatory because:Perform a comparative evaluation of APLN-13 (APLN active peptide) vs DOB in terms of hemodynamic efficacy, cardioprotection and outcome in a model of \u201csepsis-induced cardiac dysfunction\u201d.E. Coli 055:B5, 10-12mg/kg intraperitoneal).A rat model of LPS-induced myocardial dysfunction .0-6-18h.in vivo: echocardiography, final hemodynamics; urine output, weight and plasma volume variation, survival study, ex vivo: Langendorff dP/dt, in vitro: APJ-R and beta1-adrenergic receptor (AR) myocardial expressions, Pi3K/Akt/GSK3/mTOR activation-expression profiles, cTnI and cleaved caspase-3 (apoptosis).Both drugs restored LPS-induced fall of left ventricular ejection fraction (LVEF) with dominant chronotropic impact and mean arterial pressure (MAP) restoration for DOB, and lower peripheral vascular resistances (PVR) for APLN. APJ-R but not beta1 AR myocardial expressions were upregulated by LPS challenge (p< 0.05). The deepness the induced LVEF drop, the higher the dP/dt response to APLN but not to DOB (p< 0.05). In 18h LPS-challenged hearts, Langendorff assays peak dP/dt responses were 3nM and 100nM for APLN and DOB, respectively (p< 0.05). Combining fluid resuscitation with APLN infusion declined urine output (UO) with plasma volume (PV) expansion, whereas DOB induced less PV expansion but more UO (p< 0.05). Survival proportions were clearly distinctive (p< 0.05).APLN further dampened down LPS-induced overphosphorylation/inhibition of Pi3K/Akt/mTOR/GSK3 and reduced injury/apoptosis (i.e. cTNI and cleaved caspase-3 expressions).APLN potentially offers distinctive mechanisms of hemodynamics, cardioprotective effects, and survival benefits, over DOB. Chemical optimization of APLN-13 with more extensive preclinical data, would pave the way for first phase clinical trials."} +{"text": "Due to increasing resistance, alternatives to mupirocin and chlorhexidine for decolonization of MRSA carriage need to be evaluated.\u00ae) vs placebo in eliminating MRSA carriage at day 28 (D28) after the end of treatment.To evaluate the efficacy of polyhexanide or placebo applied to the anterior nares and skin for 10 days. The primary outcome was MRSA decolonization at D28 assessed by both intention-to-treat and per-protocol (PP) analysis . Secondary outcomes included MRSA decolonization according to nasal MRSA carriage, safety and emergence of resistance.vs 22/75 (29.3%) in group P were MRSA-free at D28 . PP analysis confirmed the results with 19/53 (35.8%) decolonized polyhexanide-treated patients vs 17/56 (30.4%) in the placebo arm . In the subgroup of MRSA nasal carriers, PP analysis showed that 6/15 (40.0%) patients in group I vs 2/11 (18.2%) in group P were decolonized (P=0.40). Nine serious adverse events occurred in group I vs 12 in group P; none was attributable to study medication. Emergence of polyhexanide resistance was not observed.Of 2590 patients screened, 146 patients were randomized between January 2011 and July 2014. Primary outcome was missing for 11 (7.5%) patients. ITT analysis showed that 24/71 (33.8%) patients in group I This study suggests that under real-life conditions a single polyhexanide decolonization course is marginally effective in eradicating MRSA carriage.C. Landelle: None declared, E. Von Dach: None declared, T. Haustein: None declared, A. Agostinho: None declared, G. Renzi: None declared, A. Renzoni: None declared, D. Pittet: None declared, J. Schrenzel: None declared, P. Fran\u00e7ois: None declared, S. Harbarth Grant/Research support from: a peer-reviewed research grant funded by Pfizer, Consultant for: the advisory boards of Destiny Pharma, bioMerieux, Novartis, and DaVolterra"} +{"text": "COBI, a PK enhancer with no ARV activity is a more selective cytochrome P450 (CYP)3A inhibitor than ritonavir (RTV), does not induce CYP isozymes, and thus has less potential for drug-drug interactions. COBI boosts DRV PK as effectively as RTV in healthy volunteers.This 48-week, phase IIIb, open-label, single-arm, US multicentre study (NCT01440569) included HIV-infected treatment-nave and experienced adults with no DRV RAMs, viral load (VL) \u22651000 c/mL, eGFR \u226580 mL/min and genotypic sensitivity to investigator-selected N[t]RTIs. Patients received DRV/COBI 800/150 mg qd (as single agents) plus two fully active N[t]RTIs. The primary endpoint was any treatment-emergent grade 3 or 4 AEs through Week 24. We report 48-week safety, efficacy and PK/PD results in treatment-nave patients.10 c/mL and CD4+ 370 cells/mm3. Treatment-emergent grade 3 or 4 AEs regardless of causality were reported in 21 (7%) patients. AEs regardless of causality were: diarrhoea (27%), nausea (23%), URTI (15%) and headache (12%). Sixteen (5%) patients had AEs leading to study drug discontinuation, most frequently rash (three patients), hypersensitivity and nausea (two patients each). Consistent with the known inhibition of tubular creatinine secretion by COBI, there was a mean increase from BL in serum creatinine by week 2 (0.09 mg/dL), remaining stable through week 48 (mean 0.10 mg/dL increase from BL). At week 48, 83% of patients achieved VL<50 c/mL; FDA Snapshot); median increase in CD4+ was 169 cells/mm3. Eight patients met the criteria for resistance testing. M184V was detected in one pt receiving FTC. New primary RAMs were not detected in the other seven patients. The mean population PK-derived DRV AUC24h was 100,620 ng.h/mL and C0h 2,105 ng/mL (n=281). There were no clinically relevant relationships between DRV exposure and virologic response, AEs or laboratory parameters.Of 313 ITT patients, 295 were treatment-nave (94%). In the treatment-nave cohort, 90% were male, 60% white and 294 (99.7%) received a TDF-containing regimen. Median baseline (BL) VL was 4.8 logThe DRV PK of DRV/COBI was consistent with historical data for DRV/RTV. DRV/COBI 800/150 mg qd plus two N(t)RTIs had an 83% response and was well tolerated through Week 48. These results are similar to published data for DRV/RTV 800/100 mg qd, and support the use of DRV/COBI 800/150 mg qd in treatment-nave patients."} +{"text": "Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata, Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.Genome sequences of Methylobacter whittenburyi (formerly \u201cMethylobacter capsulatus\u201d = UCM-B-3033), and Methylomicrobium agile (ATCC 35068) are methanotrophic bacteria commonly found in sediment samples from wetlands have typically been obtained from meadows, dry hay, and cow mouth samples (\u2013Methylovulum miyakonense HT12T (= ATCC BAA-2070) was isolated from a forest soil (Methylosarcina fibrata AML-C10T (= ATCC 700909) was isolated from a landfill site , using the Illumina and/or P17\u2013Prodigal and GeneProdigal . AdditioProdigal and MaGeProdigal platformM. miyakonense HT12T genome (pxmABC) or urea (urtABCDE/ureABCDEFG) as the sole source of nitrogen. M. miyakonense HT12T, M. luteus 98, and M. whittenburyi UCM-B-3033 possess the key genetic elements for nitrogen fixation (nifKDHWENX).Genome statistics and predicted core metabolic pathways are shown in T genome . A funct(pxmABC) was founrogenase . Two typ protein . M. luteeductase were ideMethylobacter spp.) produce cysts (M.\u00a0luteus 98 (Many methanotrophic species (including ce cysts . We wereuteus 98 , 30. Twouteus 98 were ideThe genome sequences have been deposited in GenBank under the accession numbers listed in"} +{"text": "Simian hemorrhagic fever virus (SHFV) variant NIH LVR42-0/M6941 is the only remaining SHFV in culture, and only a single genome sequence record exists in GenBank/RefSeq. We compared the genomic sequence of NIH LVR42-0/M6941 acquired from the ATCC in 2011 to NIH LVR42-0/M6941 genomes sequenced directly from nonhuman primates experimentally infected in 1989. Arterivirus , causes viral hemorrhagic fever (VHF) in captive Asian macaques (reviewed in reference Macaca mulatta) inoculated with a whole blood suspension from a deceased SHFV-infected stump-tailed macaque (Macaca arctoides) (Simian hemorrhagic fever virus (SHFV), a member of the genus ctoides) . Resultsctoides) . Anotherctoides) .Chlorocebus aethiops; A095 and A230) and one rhesus monkey (I-618) on different days (d) postinoculation . Briefly, RNA was isolated with the omission of carrier RNA , and randomly primed double-stranded cDNA was synthesized , as previously described by Vatter et al. . FurtherKM373784, KM371111, KM371105, KM371106, KM371107, KM371108, KM371109, and KM371110, respectively.The GenBank accession numbers of SHFV variant NIH LVR42-0/M6941 isolates KS_06_17_11, RJ_03_26_10, A095-d5, A095-d7, A230_d5, A230_d7, I618_d3, and I-618_d5 are"} +{"text": "Migraine remains poorly treated with few effective preventive medications available.We evaluated the efficacy and safety of LY2951742, a fully humanized monoclonal antibody to Calcitonin Gene-Related Peptide (CGRP) for migraine prevention.Eligible subjects with 4-14 migraine headache days (MHD) per month were randomized in a double-blind manner to LY2951742 or placebo, administered subcutaneously, every other week over a 12-week period. The primary endpoint was the mean change from baseline in number of MHD in the last 28 day period (month three); secondary end points included the mean change in headache days, migraine attacks, and the 50% responder rate at month 3.Mean change in MHD (primary) was -4.2 vs. -3.0 for LY2951742 (n=107) and placebo (n=110), respectively (p = 0.003). LY2951742 was superior to placebo for all secondary endpoints including headache days -4.9 vs. -3.7 (p = 0.0117), migraine attacks -3.1 vs. -2.3 (p = 0.0051), and 50% responder rate, 70% vs. 45% . An exploratory endpoint of complete response (100% reduction in MHD in month 3) was 31.6% vs. 17.3% for LY2951742 and placebo, respectively. Adverse events reported by approximately \u22655% of LY2951742-treated patients and more frequently with LY2951742 than placebo included upper respiratory tract infections, injection site pain, neck pain, abdominal pain, dizziness, injection site erythema, rash, hypertension and pain in extremity.Treatment with LY2951742 demonstrated significant separation from placebo on the primary and secondary endpoints. LY2951742 appeared to be safe and well-tolerated."} +{"text": "Antiretroviral therapy (ART) initiation during treatment for tuberculosis (TB) improves survival in HIV/TB co-infected patients. Data on ART outcome for HIV/TB co-infected patients managed in primary health care in low-income regions is limited. We compared virological suppression rates, mortality and retention in care in HIV-positive adults receiving care in five Ethiopian health centres with regard to TB co-infection.HIV-positive ART-na\u00efve adults eligible for ART initiation were prospectively recruited from October 2011 until March 2013. At inclusion, all patients submitted sputum for microbiological TB testing . Virological suppression rates after six months of ART with regard to TB status was the primary outcome. The impact of HIV/TB co-infection on VS rates was determined by multivariate regression analysis. Mortality and retention in care were analyzed by proportional hazard models.Among 812 participants , 678 started ART during the follow-up period . Median CD4 cell counts at ART initiation were 161 cells/\u00b5L and 184 for TB and non-TB patients, respectively (p=0.05). No difference in retention in care between TB and non-TB patients was observed during follow-up; 25 (3.7%) patients died and 17 (2.5%) were lost to follow-up . Overall rates of VS at six months were 72.1% (<40 copies/mL) and 88.7% (<400 copies/mL), with similar results for subjects with and without TB co-infection (<40 copies/mL: 65/92 (70.7%) vs. 304/420 (72.4%), p=0.74; <400 copies/mL: 77/92 (83.7%) vs. 377/420 (89.8%), p=0.10, respectively). CD4 cell count increase during treatment was 87 and 103 cells/\u00b5L for TB and non-TB patients, respectively, with no significant difference between the two groups (p=0.49).High rates of VS were achieved in adults receiving ART at Ethiopian health centres managed by non-physician clinicians, with no significant difference with regard to TB co-infection. These findings demonstrate the feasibility of combined ART and anti-TB treatment at primary health care level in low-income countries. This study is registered with clinicaltrial.gov, NCT01433796."} +{"text": "Long-term prognosis after coronary artery bypass grafting (CABG) is related to the patency of coronary grafts, and pathogenesis of graft closure is linked to platelet aggregation. We analyzed the effect on late outcomes of postoperative dual antiplatelet treatment (DAT), maintained during the first year, compared to single antiplatelet treatment (SAT).A) Primary: Evaluation of adverse cardiovascular events: Hospital admission for acute coronary syndromes (ACS), unplanned target-vessel revascularization (UTVR), stroke and death of cardiovascular origin. B) Secondary: Evaluation of safety: analysis of bleeding events (BE).Retrospective study including all CABG patients during the years 2009-2010, with two years of clinical follow-up. Patients were classified in: A) SAT: daily 100 mg ASA. B) DAT: daily 100 mg ASA plus daily 75 mg clopidogrel.The study included 452 patients: 287 SAT (63.5%); 165 DAT (36.5%). 11.9% suffered a primary end-point event; 6.6% ACS; 4.4% UTVR; 1.5% stroke; 3.8% died during follow-up. Safety: 2 (0.4%) suffered a major BE, and 10 (2.2%) minor BE.DAT was associated with a reduction of the primary end-point from 14.6% to 7.3% (p = 0.020). ACS were reduced from 8.7% to 3.0% (p = 0.020). There were no differences in UTVR nor stroke. Mortality during follow-up was lower in DAT .A multivariate Cox proportional-hazards regression was performed; DAT was independently associated with the reduction of events .The greatest benefit of DAT was seen after Off-pump CABG and in diabetic patients .DAT is associated with a reduction of late adverse cardiovascular events after CABG, especially in Off-pump CABG and in diabetic patients. DAT did not increase the risk of BE."} +{"text": "Klebsiella pneumoniae strain IIEMP-3, isolated from Indonesian tempeh, is a vitamin B12-producing strain that exhibited a different genetic profile from pathogenic isolates. Here we report the draft genome sequence of strain IIEMP-3, which may provide insights on the nature of fermentation, nutrition, and immunological function of Indonesian tempeh. Klebsiella pneumoniae in Indonesian tempeh is intriguing since it produces vitamin B12 in tempeh method showed that K. pneumoniae strain IIEMP-3 was determined employing a HiSeq 2000 platform through a commercial service provider . A 350-bp paired-end library was constructed and sequenced, producing 10 million paired-end reads with read lengths of 100\u00a0bp.The nucleotide sequence of De novo assembly was processed using Velvet version 1.2.07 (n 1.2.07 with k-mn 1.2.07 resultedn 1.2.07 with 5 tn 1.2.07 with agghttp://www.ncbi.nlm.nih.gov/genome/annotation_prok). A total of 5,285 genes, 5,096 coding sequences (CDSs), 106 pseudogenes, 5 rRNAs, 77 tRNAs, and 1 noncoding RNA (ncRNAs) were identified.Genome annotation was performed employing the NCBI Prokaryotic Genome Annotation Pipeline (Klebsiella pneumoniae IIEMP-3 has been deposited in GenBank under the accession number LMAP00000000.The genome sequence of"} +{"text": "A peer-reviewed Formal Comment by Prof. Backert and colleagues discussing results relating to this work has been published as Tegtmeyer N, Lind J, Schmid B, Backert S (2014) Helicobacter pylori CagL Y58/E59 Mutation Turns-Off Type IV Secretion-Dependent Delivery of CagA into Host Cells. PLOS ONE 9(6): e97782. doi:10.1371/journal.pone.0097782Following discussion among Associate Editor Matt Hodgkinson, the authors, and the handling editor Jun Sun, and in response to the issues raised in the Formal Comment, we are posting a correction to address: 1) confirmation of the strain mutations by PCR, sequencing, and RT-PCR; 2) clarification of the availability of the strains.The authors have provided DNA sequencing and RT-PCR data in supporting information files:cagL mutant (A), revertant, and amino acid replacement mutants (B).cagL mutant, revertant, and amino acid replacement mutants using PCR.H. pylori clinical strain Hp1033 wild type, cagL insertion mutant, revertant, and amino acid replacement mutants.cagL expression for Hp1033 wild type, cagL mutant and replacement mutants co-cultured with AGS cells at pH 7.4 for 1 hour.CagL antibody, and so they are not able to show protein expression.The authors have no Anti-H. pylori reported in the manuscript may be done following a formal request. This application is necessary to comply with the regulatory processes in the authors' institution and the customs/export regulations between Taiwan and other countries.Sharing of the strains/isolates of Table S1Primers used for sequencing and RT-PCR.Click here for additional data file.Figure S1cagL mutant (A), revertant, and amino acid replacement mutants (B).The diagram of construction of Click here for additional data file.Figure S2cagL mutant, revertant, and amino acid replacement mutants by using PCR. PCR Amplicons from wild type, revertants, and amino acid replacement mutants are 1.1kb (using primer cagL-5 & cagL-6) or 1.4kb (using primer cagIL-1 & cagL-6), from cagL insertion mutants are 2kb. (A) M: marker; w: Hp1033 wild type; lane1-16: Hp1033 cagL::cat. (B) lane1-12: 26695 cagL::cat; lane 13-23: J99 cagL::cat; lane 24: Hp1033 cagL-Y58/E59 revertant. (C) lane 25-29: Hp1033 cagL-Y58D/E59 amino acid replacement mutants; lane 30: Hp1033 cagL::cat ; lane 31: Hp1035 cagL::cat. (D) lane 32-35: Hp1033 cagL-Y58/E59K amino acid replacement mutants. (E) lane 36-39: Hp1033 cagL-Y58D/E59K amino acid replacement mutants ; lane 40: Hp1035 cagL-Y58D/E59K amino acid replacement mutants. Arrows indicate the clones selected in this study.Confirming Click here for additional data file.Figure S3H. pylori clinical strain Hp1033 wild type, cagL insertion mutant, revertant, and amino acid replacement mutants. Multiple Alignments were processed by MAFFT L-INS-1 (v6.850b) from EMBL-EBI website. The blue blocks indicate the region of chloramphenicol resistance gene. The yellow block indicates the position of amino acid 58 and 59 residues.The sequencing results of Click here for additional data file.Figure S4cagL mutant and replacement mutants co-cultured with AGS cells at pH 7.4 for 1 hour, cagL expression was examined by RT-PCR. There was no difference in CagL expressions among Hp1033 wild type, revertant, and amino acid replacement mutants. The 3rd lane indicated there was no RNA contamination.After Hp1033 wild type, Click here for additional data file."} +{"text": "The publisher apologizes for the error.The word \u201cAlleviating\u201d is misspelled in the title. The correct title is: Penehyclidine Hydrochloride Pretreatment Ameliorates Rhabdomyolysis-Induced AKI by Activating the Nrf2/HO-1 Pathway and Alleviating Endoplasmic Reticulum Stress in Rats. The correct citation is: Zhao W, Huang X, Zhang L, Yang X, Wang L, Chen Y, et al. (2016) Penehyclidine Hydrochloride Pretreatment Ameliorates Rhabdomyolysis-Induced AKI by Activating the Nrf2/HO-1 Pathway and Alleviating Endoplasmic Reticulum Stress in Rats. PLoS ONE 11(3): e0151158. doi:"} +{"text": "A. baumannii, K. pneumonia and P. aeruginosa strains, isolated from critically ill patients in a Greek ICU.The emergence of multidrug-resistant (MDR) pathogens is a major cause of infection-related mortality among critically ill patients. The synergistic effect between commonly used antibiotics against difficult to treat nosocomial MDR Gram-negative strains, if present, could provide a viable option as an alternative therapy. The aim of this study was to investigate the potential of antibiotic synergy against MDR A. baumannii, 41 K. pneumoniae and 64 P. aeruginosa strains, isolated during the period 2010 to 2013. All strains were resistant to carbapenems and showed reduced susceptibility or resistance to tigecycline or colistin (MIC >2), in accordance with CLSI guidelines. We evaluated double-drug combinations of carbapenem (CRB)/colistin (COL), tigecycline (TG)/COL, rifampicin (RIF)/COL, CRB/ gentamicin (GEN), CRB/amikacin (AMK) for A. baumannii, TG/COL, CRB/COL, piperacillin-tazobactam (PIP/TAZ)/GEN, CRB/GEN for K. pneumoniae and AMK/(PIP/TAZ), AMK/aztreonam (AZT), AMK/cefepime (CEF), AMK/CRB and CRB/COL for P. aeruginosa strains. In order to perform synergy tests, the E-test methodology was used. Synergy was defined as a fraction inhibitory concentration (FIC) index \u22640.5, additive effect 0.5 to 1, indifferent or antagonistic effect >2 (Lorian definition).We tested 59 A. baumannii strains, the synergy effect of CRB/ COL was 55.9%, RIF/COL 38.9%, CRB/GEN 22%, CRB/AMK 20.3% and TG/COL 16.9%, respectively. Against 41 K. pneumoniae strains, synergy rates were: CRB/COL 43.9%, CRB/GEN 31.7%, PIP/TAZ/GEN 29.2% and TG/COL 24.4% respectively. Against 64 P. aeruginosa strains, synergy rates were: AMK/PIP/TAZ 64.6%, AMK/AZT 64.6%, AMK/CEF 58.3%, CRB/ COL 52%, AMK/CRB 25%.Against 59 MDR A. baumannii and K. pneumoniae strains tested was CRB/COL. The next most effective combination was RIF/COL and CRB/GEN respectively. No competitive effect was observed for RIF/COL combination in all cases tested. The most effective combinations for P. aeruginosa strains were AMK plus PIP/TAZ or AZT or CEF. The next most effective combination was CRB/ COL. We recommend implementation of an antibiotic synergy test for MDR pathogens as a routine antimicrobial test in the hospitals' microbiology laboratories, especially for critically ill patients, since some combinations seem to excel. Further studies are needed for the correlation of these combinations with clinical efficacy.The most effective combination for both the"} +{"text": "A 48-year-old female presented with intermittent high-grade fever, chills, and severe myalgia for 4 days. There was no lymphadenopathy or hepatosplenomegaly. Investigations revealed hemoglobin concentration of 142 g/L; leucocyte count of 3.5x109/L with 54% neutrophils, 40% lymphocytes, 1% eosinophils, and 5% monocytes; and thrombocytopenia (platelet count of 55x109/L). Peripheral smear revealed numerous plasmacytoid lymphocytes and occasional cells with eccentrically placed nucleipacked with multiple prominent cytoplasmic vacuoles, morphologically consistent with Mott cells . MeanwhiNonmalignant reactive peripheral blood plasmacytosis can occur in tumors, autoimmune conditions, and infections . Polyclo"} +{"text": "Delftia tsuruhatensis MTQ3 is a plant growth-promoting rhizobacterium (PGPR) isolated from tobacco rhizosphere. Here, we report the draft genome sequence of D.\u00a0tsuruhatensis MTQ3. Several functional genes related to antimicrobial activity and environment adaption have been found in the genome. This is the first genome sequence of D.\u00a0tsuruhatensis related to PGPR. Delftia tsuruhatensis, the type species of Delftia, is considered a plant growth-promoting rhizobacterium (PGPR) \u20133, an or (PGPR) \u2013, 5, and (PGPR) \u2013, 7. D.\u00a0tD.\u00a0tsuruhatensis MTQ3. Genomic DNA was extracted and sequenced using the Illumina HiSeq 2500 platform. The whole shotgun sequencing produced 8,206,833 paired-end reads with an average insert size of 580\u00a0bp (over 780-fold coverage). Another mate-paired (MP) library containing 3- to 5-kb inserts was constructed, and 13,462,994 paired-end reads were produced. All these raw data were then filtered by Trimmomatic v 0.30 (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/).Here, we report the draft genome sequence of c v 0.30 , and Gapc v 0.30 . Final aD.\u00a0tsuruhatensis MTQ3 is phylogenetically related to D.\u00a0tsuruhatensis 391 (98.34%) (GenBank accession no. JNWH00000000), D. acidovorans CCUG 274B (97.96%) (AGYX00000000), D.\u00a0acidovorans SPH-1 (94.94%) (NC_010002), Delftia sp. 670 (94.30%) (JNWI00000000), D.\u00a0acidovorans CCUG 15835 (92.70%) (AGYY00000000), and Delftia sp. Cs1-4 (91.37%) (NC_015563).The genome consists of 6.27\u00a0Mb, with a G+C content of 66.79%. A total of 5,005 coding sequences (CDS), 13 pseudogenes, 72 tRNA genes, 1 noncoding RNA (ncRNA), and 10 rRNA genes were identified. Average nucleotide identity (ANI) analysis revealedD.\u00a0tsuruhatensis MTQ3 were identified in the genome, such as the bacteriocin gene (AA671_02705), polyketide synthase (PKS) gene (AA671_12420), nonribosomal peptide synthetase (NRPS) gene (AA671_12430), balhimycin synthesis gene (AA671_12395), quinolinate synthesis gene (AA671_01765), and phenazine synthesis gene (AA671_00865). Some genes responsible for the processing and transport of antibiotics were identified in the genome, including antibiotic biosynthesis monooxygenase gene , macrolide transporter gene (AA671_00980), and antibiotic ABC transporter substrate-binding gene (AA671_25335).Many genes involved in the antimicrobial activity of D.\u00a0tsuruhatensis MTQ3 possesses genes with likely relevance to rhizosphere competence and adaptation in polluted environments. Specifically, quercetin dioxygenase is likely a plant microbe-signaling bacterium involved in degrading plant-produced antimicrobial root exudates (In addition, exudates , 14. Proexudates . Genes rD.\u00a0tsuruhatensis MTQ3 has been deposited in DDBJ/ENA/GenBank under the accession number LCZH00000000. The version described in this paper is the first version, LCZH01000000.The whole-genome shotgun project of"} +{"text": "Chondroitin sulfate proteoglycan 4 (CSPG4) is a membrane bound proteoglycan, composed of an N-linked 280kDa glycoprotein, and a single 450kDa chondroitin sulfate linked proteoglycan . CSPG4 e16 pediatric tumor lines were assessed for CSPG4 expression. CSPG4 was detected by flow cytometry in 69% of the cell lines assessed: osteosarcomas: 143b,HOS-MNNG,MG63; synovial sarcomas: SYO-I,HSSY-II, alveolar/embryonal rhabdomyosarcomas: Rh18c,Rh30/Rh36, medulloblastoma: DAOY, melanoma: Mel624,Mel1300. CSPG4 expression site density was estimated with BD PE Quantibrite beads by flow cytometry.Using two different single chain variable fragments (scFv) known to target CSPG4 (225.28 and TP41.2), two anti-CSPG4 second generation CAR constructs were synthesized by transient transfection of retroviral packaging lines. Both constructs have identical intracellular signaling components . Healthy donor T cells were transduced with viral supernatants, and assessed for CAR expression. Anti-tumor activity was measured by cytokine release and tumor specific lysis. Cell surface expression of the CSPG4-based CARs was detected by flow cytometry using conjugated Protein L to target the expressed scFv light chain. 225.28 and TP41.2 based CAR T cells induced 25% and 31% lysis of target pediatric tumor lines, respectively (E:T ratio of 20:1). On further investigation, TP41.2 based CAR T cells were able to specifically lyse CSPG+ cell lines 143b, Rh30, and Rh18c at 40%, 37%, and 16%, respectively (E:T ratio of 30:1). Additionally, the TP41.2 and 225.28 CAR T cells were assessed for Interferon gamma (IFNy) production by flow cytometry. Compared to mock T cells coincubated with varying tumor lines , the TP41.2 and 225.28 CAR+ T cells had significantly positive populations for IFNy production (p < 0.0001), predominantly in the CD8+ population.in vitro at significant levels (p = 0.01). Targeting CSPG4 with CAR redirected T cells represents a new strategy for eliminating these pediatric malignancies in an antigen specific, cell-mediated manner.High levels of CSPG4 are present on a variety of pediatric solid tumors. TP41.2 CSPG4-based CAR T cells target, generate significant levels of IFNy, and lyse osteosarcoma"} +{"text": "Porphyromonas gingivalis is strongly associated with periodontitis. P.\u00a0gingivalis strain trafficking and tissue homing differ widely, even among presumptive closely related strains, such as W83 and A7436. Here, we present the genome sequence of A7436 with a single contig of 2,367,029\u00a0bp and a G+C content of 48.33%. Porphyromonas gingivalis is an oral bacterium that is associated with periodontal disease and grown as previously described (escribed . Genomicescribed (Roche).https://www.ebi.ac.uk/~zerbino/velvet/) (http://www.phrap.org/consed/consed.html) (\u2013http://metagenomics.anl.gov) (http://img.jgi.doe.gov/er) (https://geneprimp.jgi-psf.org) (GS-20 reads were assembled using Velvet version 0.7.63 (velvet/) and Newbed.html) \u201324 and banl.gov) and IMG-.gov/er) , then ampsf.org) .P.\u00a0gingivalis A7436 has approximately 57-fold coverage and contains a single contig of 2,367,029\u00a0bp (G+C content of 48.33%). A total of 2,078 genes were annotated, which included 2,011 predicted coding sequences (CDSs), 53 tRNAs, 12 rRNAs, and 1 transfer-messenger (tmRNA). There are 234 subsystems in the genome. 169 protein metabolism, 164 cofactors, vitamins, prosthetic groups, and pigments, 74 RNA metabolism, 87 DNA metabolism, 96 carbohydrates, and 19 membrane transport subsystem features were observed.The genome of P.\u00a0gingivalis A7436 genome was compared to P.\u00a0gingivalis strains W83, ATCC 33277, and TDC60 using RAST (The annotated ing RAST and IMG-ing RAST . All-to-ing RAST , 17. HowP.\u00a0gingivalis strains.The availability of the A7436 genome expands our ability to compare observed behavior with genotype in a growing number of CP011995. The version described is the first version.This genome sequencing project was deposited in GenBank under accession no."} +{"text": "We also accessed the proliferative role and downstream targets of Pak1 in endometrial cancer. Pak1 was expressed in cytoplasm whereas Pak4 and p-Pak4 were expressed in both cytoplasm and nucleus of endometrial tissues. In normal endometrium, significantly higher Pak1 (P = 0.028) and cytoplasmic p-Pak2 (P = 0.048) expression was detected in proliferative endometrium than secretory endometrium. Pak1, cytoplasmic and nuclear Pak4 and nuclear p-Pak4 was significantly overexpressed in endometrial cancer when compared to atrophic endometrium . Moreover, type I endometrioid carcinomas showed significantly higher Pak1 expression than type II non-endometrioid carcinomas (P<0.001). On the other hand, Pak1, Pak4 and p-Pak4 expression negatively correlated with histological grade while p-Pak2 and cytoplasmic Pak4 expression inversely correlated with myometrial invasion . Furthermore, patients with endometrial cancers with lower cytoplasmic Pak4 expression showed poorer survival (P = 0.026). Multivariate analysis showed cytoplasmic Pak4 is an independent prognostic factor. Functionally, knockdown of Pak1, but not Pak4, in endometrial cancer cell line led to reduced cell proliferation along with reduced cyclin D1, estrogen receptor (ER\u03b1) and progestogen receptor (PR) expression. Significant correlation between Pak1 and PR expression was also detected in clinical samples. Our findings suggest that Pak1 and cytoplasmic p-Pak2 may promote cell proliferation in normal endometrium during menstral cycle. Pak1, cytoplasmic and nuclear Pak4 and nuclear p-Pak4 are involved in the pathogenesis of endometrial cancer especially in postmenopausal women. Pak1 promote endometrial cancer cell proliferation, particular in type I endometrioid carcinoma. Cytoplasmic Pak4 can be potential prognostic marker in endometrial cancer.p21-activated kinases (Paks) are serine/threonine protein kinases involved in biological events linked to malignant tumor progression. In this study, expression of Pak1, p-Pak2 Ser Endometrial cancer is the most common gynecological malignancy worldwide and its p21-activated serine/threonine kinases (Paks) are effectors for the small Rho GTPases Rac1 and Cdc42 that play important roles in a variety of cellular functions, including cell morphogenesis, motility, survival, anchorage-independent growth and angiogenesis, all of which are prerequisite steps for tumor formation and tumor invasion . Based oSer20 expression in ovarian cancer was also detected , and cleared by centrifugation at 4\u00b0C. Protein concentration was determined by DC (detergent compatible) protein assay . 20 \u03bcg protein was resolved by SDS-PAGE, transferred to polyvinylidene difluoride membrane, and hybridized with corresponding antibodies . Mann-Whitney test was applied for comparison between two groups. Kruskal-Wallis rank test was applied for comparison among multiple groups. Survival analysis was performed by Kaplan-Meier analysis and log-rank test. P = 0.001) and secretory (P = 0.004) endometrium, atypical hyperplasia (P = 0.042) and endometrial cancers (P = 0.044) (P<0.05) was observed . Signifiobserved . Althougobserved . SimilarP<0.05) except complex hyperplasia whereas nuclear p-Pak2 only showed significantly higher expression in proliferative endometrium than atrophic (P = 0.046) and secretory (P = 0.028) endometrium and endometrial cancers (P = 0.007) (P = 0.007) and pure atypical hyperplasia (P = 0.013) showed significant higher cytoplasmic p-Pak2 expression and pure atypical hyperplasia . Althougpression . Furtherctively) .P<0.05) (P = 0.047) and endometrial cancers (P = 0.036) (P = 0.026) (P<0.05) . SignifiUp-regulation of Pak1 and Pak4 mRNA and protein expression was also found in cancer cell lines compared with normal endometrial cells by qPCR and WestP<0.05), but not with other clinical parameters (P<0.05) (P<0.05) (P<0.05) and patients\u2019 age at diagnosis . There w(P<0.05) . Higher (P<0.05) . No signP = 0.026), but not Pak1, nuclear and cytoplasmic p-Pak2, nuclear Pak4, nuclear and cytoplasmic p-Pak4, resulted in a poorer survival in endometrial cancer patients .Kaplan-Meier-survival analyses revealed that lower expression of cytoplasmic Pak4 Click here for additional data file.S2 Table(DOC)Click here for additional data file.S3 Table(DOC)Click here for additional data file."} +{"text": "Postoperative morbidity after sleeve gastrectomy is decreasing, but remains significant. Bleeding and surgical fistules remain the leading causes of morbidity and mortality. In several studies in postoperative care of obese patients, non-invasive positive pressure ventilation (NPPV) reduced the risk of lower respiratory tract infection and pneumonia , thereby2 above 90%. After period: standard treatment plus NPPV - all patients were submitted to a systematic postoperative protocol: NPPV was provided using an oxygen CIPAP system with 5 cmH2O. Statistical analysis: complication rates were compared using the chi-square test. P < 0.05 was considered statistically significant.A 4-year before-after study was conducted in a 19-bed intermediate care unit of a private hospital. Before period: standard treatment - all patients received oxygen supplementation to achieve SaOP <5%.A total of 857 patients were included. Inclusion characteristics were similar in the two groups: Before group - noNPPV: 352 patients, 2010 to 2011. Age: 40.58 \u00b1 10.94, BMI: 42.79 \u00b1 5.51, sex ratio F/M: 0.81. After group - NPPV: 504 patients, 2012 to 2013. Age: 40.81 \u00b1 11.24, BMI: 42.92 \u00b1 5.09, sex ratio F/M: 0.77. There is a significant between-group difference in the complication rate: Before group - noNPPV: 10 surgical fistula (2.84%) and six postoperative bleeding (1.70%); After group - NPPV: seven surgical fistula (1.39%) and three postoperative bleeding (0.6%). The overall complication rate fell from 4.54% to 1.98%. The chi-square statistic = 4.58. The number of degrees of freedom is 1. The value returned from the chi-square statistic is Systematic use of NPPV significantly improves morbidity in the postoperative care of sleeve gastrectomy."} +{"text": "Burkholderia sp. strain MP-1 was isolated from pesticide-contaminated soil. Herein, we report the draft genome sequence of strain MP-1, which contains 168 contigs of 8,611,053 bp, with a G+C content of 62.55% and 7,631 protein-coding genes. Burkholderia spp. are widely distributed in nature and include a large variety of related environmental, clinical, and agribiotechnological species (Burkholderia now comprises 78 species (http://www.bacterio.net/burkholderia.html). A methyl parathion (MP)-degrading bacterial strain, designated as Burkholderia sp. strain MP-1 (LMG 27927 = MCCC 1K00250), was isolated from the contaminated soil of a former pesticide-manufacturing company in Jiangsu province of China. The 16S rRNA sequence of the newly isolated strain showed the highest similarity to that of Burkholderia grimmiae DSM 25160T (98.45%) of 8,611,053\u00a0bp (131-fold coverage), with an average G+C content of 62.55%. Automatic gene annotation was performed by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The genome comprises 7,791 genes, including 55 tRNA genes for all 20\u00a0amino acids, 3 rRNA genes, 1 small noncoding RNA gene, 101 pseudogenes, and 7,631 protein-coding genes (CDS) (with an average length of 950\u00a0bp), which give a coding intensity of 84.2%. In all, 4,853 proteins were assigned to Clusters of Orthologous Groups (COG) families , with a MiSeq system using paired-end sequencing technology. A total of 3,758,646 pair reads and 9,573 clean single reads were assembled using Newbler 2.6. The genome of Burkholderia strains were investigated, such as that of Burkholderia pyrrocinia CH-67, whose genome contains genes encoding enzymes for aromatic compound degradation .The draft genome sequence of strain MP-1 has been deposited at GenBank under the accession no."} +{"text": "Oncotarget. 2015; 6:15594-15609doi:10.18632/oncotarget.3709Present Figure 2: During the assembly of figure 2C, the same image was inadvertently used for both the non-transfected and empty vector control.Corrected Figure 2:"} +{"text": "As the eighth leading cause of annual mortality in the USA, influenza A viruses are a major public health concern. In 20% of patients, severe influenza progresses to acute lung injury (ALI). However, pathophysiological mechanisms underlying ALI development are poorly defined. We reported that, unlike wild-type (WT) C57BL/6 controls, influenza A virus-infected mice that are heterozygous for the F508del mutation in the cystic fibrosis transmembrane conductance regulator (HETs) did not develop ALI. This effect was associated with higher IL-6 and alveolar macrophages (AMs) at 6 days postinfection (d.p.i.) in HET bronchoalveolar lavage fluid (BALF). In the present study, we found that HET AMs were an important source of IL-6 at 6 d.p.i. Infection also induced TGF-\u03b2 production by HET but not WT mice at 2 d.p.i. TGF-\u03b2 neutralization at 2 d.p.i. (TGF-N) significantly reduced BALF IL-6 in HETs at 6 d.p.i. Neither TGF-N nor IL-6 neutralization at 4 d.p.i. (IL-6-N) altered postinfection weight loss or viral replication in either mouse strain. However, both treatments increased influenza A virus-induced hypoxemia, pulmonary edema, and lung dysfunction in HETs to WT levels at 6 d.p.i. TGF-N and IL-6-N did not affect BALF AM and neutrophil numbers but attenuated the CXCL-1/keratinocyte chemokine response in both strains and reduced IFN-\u03b3 production in WT mice. Finally, bone marrow transfer experiments showed that HET stromal and myeloid cells are both required for protection from ALI in HETs. These findings indicate that TGF-\u03b2-dependent production of IL-6 by AMs later in infection prevents ALI development in influenza A virus-infected HET mice. It has been estimated that seasonal influenza infections result in 12 influenza-related deaths per 100,000 persons per year in the United States, most of which occur in the elderly , which is associated with poor prognosis . Once AL+ absorption via epithelial Na+ channels (ENaC) and Cl\u2212 absorption or secretion through the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel were intranasally infected with 10,000 plaque-forming units (pfu)/mouse of egg-grown influenza A/WSN/33 (H1N1) in 50 \u03bcl PBS with 0.1% BSA wk old w. In our Thin sections (3 \u03bcm) were prepared from formalin-fixed, paraffin-embedded lung tissue . IL-6 wail-6 mRNA was determined by the \u0394\u0394Ct method and normalized to the endogenous control 18s rrna, which was not altered by infection at 2 d.p.i. by intraperitoneal (i.p.) injection . To neut137Cs irradiator (6/mouse) (in 0.5 ml PBS) were then transplanted by tail vein injection into recipient mice, which were placed on Baytril antibiotic water bottles for 2\u20133 wk peri-irradiation. This protocol resulted in no outward clinical signs.As in our previous studies, bone marrow-recipient mice were irradiated with 1,000 cGy given in two doses by a 2 saturation, heart rate, lung homogenate viral titers, lung wet:dry weight ratios, lung mechanics, and BALF inflammatory mediators were performed as in our previous studies . Gaussian data distribution was verified by the method of Kolmogorov and Smirnov. Differences between group means were analyzed by one-way ANOVA, with Tukey-Kramer multiple-comparison posttests. il-6 gene expression in AMs isolated from HET mice than AMs from WT mice at 6 d.p.i. (We reported previously that attenuation of cardiopulmonary dysfunction in HETs infected with the A/WSN/33 H1N1) influenza strain was associated with exaggerated AM and IL-6 responses at 6 d.p.i. N1 influeA. In con6 d.p.i. C.Given the known role of TGF-\u03b2 as an anti-inflammatory cytokine and an iTo determine whether the exaggerated IL-6 response to infection in HET mice was TGF-\u03b2 dependent, influenza A virus-infected mice were treated with a single dose of a neutralizing antibody to TGF-\u03b2 at 2 d.p.i. (TGF-N) . ControlTo determine whether altered TGF-\u03b2 and IL-6 responses to infection contribute to protection from influenza A virus-induced ALI, we examined the effects of TGF-N and IL-6-N on weight loss, viral replication, and cardiopulmonary function in influenza A/WSN/33 virus-infected mice at 6 d.p.i. We selected this time point because it would allow us to directly compare the downstream effects of treatment with anti-TGF-\u03b2 at 2 d.p.i. with those of treatment with anti-IL-6 at 4 d.p.i. Postinfection weight loss at 6 d.p.i. did not differ between untreated WT and HET mice A. IgG trIn the absence of treatment, lung water content (wet:dry weight) remained normal in HET mice at 6 d.p.i. but was significantly elevated in WT controls . Both TGIn the absence of treatment or after treatment with IgG, static and dynamic lung compliance were both significantly higher in infected HETs at 6 d.p.i. B. ProtecAs in our earlier studies, BALF from influenza A/WSN/33 virus-infected HET mice contained far greater numbers of AMs than WT controls at 6 d.p.i. A. HoweveWe previously reported that BALF IFN-\u03b3, IL-10, CC chemokine ligand 2 (CCL-2)/monocyte chemotactic protein 1 (MCP-1), CCL-5/RANTES, and CXCL-10/inducible protein 10 content did not differ between WT and HET mice at 6 d.p.i. . However, both treatments significantly reduced BALF CXCL-1/KC content in both mouse strains. In WT mice, both TGF-N and IL-6-N also significantly reduced BALF IFN-\u03b3 but increased IL-12 at 6 d.p.i. TGF-N, but not IL-6-N, also reduced BALF CCL-5/RANTES in WT mice at this time point. In contrast, neither treatment impacted BALF IFN-\u03b3 or CCL-5/RANTES in HET mice, and only IL-6-N significantly increased BALF IL-12 at 6 d.p.i. Treatment with nonspecific IgG had no effect on CXCL-1/KC, IFN-\u03b3, IL-12, or CCL-5/RANTES in either mouse strain.We previously demonstrated that HET AMs were necessary for protection from influenza A virus-induced ALI in HET mice . To deteDespite a 50% reduction in cell-surface CFTR expression and anion transport , we and Previous investigators have reported that an attenuated AM response contributes to increased influenza severity , 59, 64.We found no differences in viral replication kinetics and BALF neutrophil counts between WT mice, untreated or IgG-treated HETs, and antibody-treated HETs at 6 d.p.i. This indicates that, in our model, influenza-induced ALI is independent of these factors. Moreover, we did not find that development of ALI in HETs following TGF-N and IL-6-N was associated with development of a so-called \u201ccytokine storm\u201d , 33, 62.Some investigators have reported an association between high BALF IL-6 and increased influenza mortality , 39, 56.Greater influenza severity has also been linked to inadequate anti-inflammatory responses. TGF-\u03b2 is a potent inflammatory regulator , and inc1-subtype adenosine receptors, which induces increased CFTR-mediated Cl\u2212 secretion . A. Amer was supported by a Cystic Fibrosis Foundation Research Grant and The Ohio State University Public Health Preparedness in Infectious Diseases Program. I. Davis was supported by The Ohio State University Public Health Preparedness in Infectious Diseases Program and The National Heart Lung and Blood Institute at the National Institutes of Health (R01-HL102469).P. Woods was supported by No conflicts of interest, financial or otherwise, are declared by the authors.Author contributions: P.S.W., M.F.T., and N.M.C. performed experiments; P.S.W., M.F.T., N.M.C., and I.C.D. analyzed data; P.S.W. and I.C.D. interpreted results of experiments; P.S.W. and I.C.D. prepared figures; A.O.A. and I.C.D. edited and revised manuscript; A.O.A. and I.C.D. approved final version of manuscript; I.C.D. conception and design of research; I.C.D. drafted manuscript."} +{"text": "This study was undertaken to determine virulence factors among clinical Enterococcus species by phenotypic and molecular methods.Enterococci are opportunistic pathogens causing severe urinary tract infections, surgical wound infections, bacteremia and bacterial endocarditis. Aggregation substance was the predominant species obtained, followed by E. faecalis (73/157). 72/157(45.85%) strains were positive for hemolysin, 61/157(38.85%) gelatinase, 16/157(10.19%) strong and 66/157(42%) were moderate biofilm producers phenotypically. PCR results showed, 37/157(23.56%) cylA, 81(51.59%) gelE, 10(6.36%) hyl, 87(55.41%) asa1 and 78(49.68%) isolates were positive for esp genes. Only 25/72, 32/61, 6/16 and 7/16 isolates were phenotypically and genotypically positive for cylA +hemolysin, gelE +gelatinase, esp +biofilm and asa1 +biofilm, respectively. Interestingly, E. faecalis carried multiple virulent genes (>4 genes) when compared with E. faecium among our study isolates.asa1>gelE>esp were the predominant genes observed. Majority of E. faecalis isolates were strong and E. faecium were moderate biofilm producers.Hemolysin and gelatinase were the predominant virulence factors expressed phenotypically whereas,"} +{"text": "Feature tracking strain (FTS) is a new technique to evaluate myocardial deformation from routinely acquired cardiac magnetic resonance (CMR) cine images, however, it has not been validated in single ventricle patients. The purpose of this study is to validate FTS against myocardial tagged harmonic phase (HARP) images, considered the reference standard in non-invasive deformation analysis.We retrospectively analyzed CMRs of 15 consecutive single ventricle Fontan patients between HARP and FTS, Pearson r = 0.67, p = 0.006. Average GCS was -19 (95% CI -4.3 to -33.8) from HARP and -16.7 (95% CI -6.4 to -26.9) from FTS. FTS yielded lower values (bias -2.3) than HARP (Figure Feature tracking analysis has moderate agreement with grid-tagged HARP measurements of circumferential strain in Fontan patients, with a trend towards lower strain values via FTS. Further validation of FTS in a large sample is warranted.Dr Kevin K. Whitehead: NIH K23 Grant HL089647 from the National Heart, Lung and Blood Institute. Dr. Mark Fogel: NIH R01HL098252-01, \"Understanding mechanisms of Fontan failure and key predictors for patient outcome.\""} +{"text": "The asymmetric unit consists of one-quarter of the mol\u00adecule (S site symmetry 2) and the complete mol\u00adecule has 2/m (Ch2) point symmetry with the C=C bond in an E conformation. The geometry of the title compound is compared to those of a chloro derivative and a mercury complex.The title compound, C DOI: 10.1107/S1600536814023319/hb7285Isup2.hklStructure factors: contains datablock(s) I. DOI: Click here for additional data file.10.1107/S1600536814023319/hb7285Isup3.cmlSupporting information file. DOI: Click here for additional data file.10.1107/S1600536814023319/hb7285fig1.tif. DOI: The mol\u00adecular structure of DTCDD with displacement ellipsoids drawn at the 30% probability level. Symmetry codes: (i) 1-x, y, z; (ii) x, 1-y, 1-z; (iii) 1-x, 1-y, 1-z.Click here for additional data file.10.1107/S1600536814023319/hb7285fig2.tif. DOI: The unit-cell packing in DTCDD viewed down the b-axis.1030564CCDC reference: crystallographic information; 3D view; checkCIF reportAdditional supporting information:"} +{"text": "Hepatitis C virus (HCV) represents one of the persistent viral infections afflicting humankind, and a significant proportion of chronic HCV disease progresses over time through liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC). One potential mechanism underlying the chronic disease is believed to be viral escape from immune surveillance via upregulation of inhibitory molecules on immune cells by HCV. We investigated the diverse expression of various inhibitory molecules in PBMCs of healthy non-HCV controls and chronically HCV infected patients.The expression of inhibitory molecules on PBMCs was investigated in chronic HCV infected patients relative to healthy non-HCV controls using standard immunological and molecular methods. The serum levels of indoleamine 2, 3 deoxygenase (IDO) and cyclooxygenase-2 (COX-2) were also investigated.p\u22640.01), PD-1 (p\u22640.01), FOXP-3 (p\u22640.01), BLIMP-1 (p\u22640.01), CD160 (p\u22640.01), CTLA-4 (p\u22640.01), TRAIL (p\u22640.01), BTLA (p\u22640.01) and LAG-3 (p\u22640.01) with fold change of 1.3, 0.4, 14.6, 0.87, 6.6, 0.4, 14.7, 10.9 and 2.5 respectively in chronically HCV infected patients. The plasma IDO and COX-2 levels were significantly higher (p=0.001) in chronically HCV infected subjects relative to healthy control.The gene expression profile of chronically HCV infected patients was significantly different from control individuals. Our results showed upregulation of TIM-3 (The upregulation of inhibitory molecules on PBMCs in chronically HCV infected patients suggest the contribution of these molecules to immune cells impairment in HCV infection. Viral persistence and eventual progression following potential evasion of the host immune armory via viral impregnation of inhibitory immune biosignatures in HCV disease pathogenesis warrants further elucidation."} +{"text": "Recenortality . We repoWe assessed outcome for HO patients at CC (primary outcome) and hospital discharge, and at 6-month and 1-year follow- up. Single variable logistic regression analyses, adjusted by age, gender and haematological diagnosis, and multivariate analyses were performed to identify independent predictors of outcome using STATA.P < 0.001), number of organs supported , P/F ratio , inotropic requirement , and IMV status influenced unit survival at single variable analyses. At multivariate analysis, the P/F ratio and IMV status independently predicted outcome.A total of 225 HO patients were admitted to CC. Median age was 59 (interquartile range (IQR) 46 to 66) years. The most common haematological diagnoses on admission were acute myeloid leukaemia in 57 (25.3%) cases, non-Hodgkin lymphoma in 54 (24%) cases and multiple myeloma in 42 (18.7%) patients. Median APACHE II score was 21 (IQR 17 to 26). A total of 164 patients (72.9%) had at least one organ supported. Unit and hospital mortality rates were 34.7% (78 patients) and 49.3% (111 patients), respectively. At 6-month and 1-year follow-up, mortality increased to 63.1% (142 patients) and 70.5% (153 patients), respectively. The APACHE II score (OR = 0.93, 95% CI = 0.89 to 0.97, Organ failures and need for organ support correlated with outcome. P/F ratio and need for IMV were independent predictors of mortality, in agreement with previously published data . The CC"} +{"text": "The two symmetry-related iodide anions bridge two LiI cations, forming an inversion dimer in which the Li2I2 plane is nearly perpendicular to the imidazol-2-yl\u00adidene ring, with a dihedral angle of 85.5\u2005(3)\u00b0. No hydrogen bonding is observed in the crystal.In the title binuclear complex, [Li DOI: 10.1107/S2056989015009822/xu5851Isup2.hklStructure factors: contains datablock(s) I. DOI: Click here for additional data file.10.1107/S2056989015009822/xu5851fig1.tif. DOI: The mol\u00adecular structure of the title compound with the atom-numbering scheme and 30% probability displacement ellipsoids.Click here for additional data file.10.1107/S2056989015009822/xu5851fig2.tifa . DOI: a axis.The packing diagram viewed along the 1402139CCDC reference: crystallographic information; 3D view; checkCIF reportAdditional supporting information:"} +{"text": "The increasing prevalence of ESBL-E in the community is a cause of concern for hospitals. Early detection of ESBL-E carriers on admission could allow timely implementation of control measures or appropriate selection of antimicrobials.To describe the current prevalence of ESBL-E rates upon admission to 4 different services at HUG, in the context of a multicenter European study (R-Gnosis).Patients admitted to 4 different services were screened by rectal swabs on admission. From January 2014 through January 2015, patients admitted to 4 wards, including: Ortho1 (sport traumatology), Ortho 2 (septic); Geriatrics (2 wards) and patients undergoing elective colorectal surgery (ECS) were screened from April 2013-October 2014.E. coli ; K. pneumoniae and other Enterobacteriaceae . Among K. pneumonia carriers on admission, 24/26 (92.3%), had a previous hospitalization less than 12 months before admission screening and 21/26 (80.8%) had the previous hospitalization within 3 months only. ESBL-E carriage was 83/981 (8.4%) and 61/430 (14.2%) for Ortho 1 and 2 respectively; Geriatrics, 42/371 (11.3%); and ECS, 41/354 (11.6%).Overall, from 2394 admitted patients, 2136 were screened on admission (89.2%). Median age was 67.3 years (SD\u00b120.9); 51.6% were male. Only 92/2136 (4.3%) had a previously known status of ESBL carriage. A total of 226/2136 (10.6%) patients were found to be ESBL-E carriers: E. coli. Patients admitted to septic orthopedics, geriatrics and ECS had a higher prevalence on admission. The majority of ESBL- Klebsiella pneumonia carriers had a recent history of hospitalization.Overall 10.6% of patients screened were ESBL-E carriers upon admission at HUG, mostly due to ESBL-producing None declared."} +{"text": "Pediatric chronic nonbacterial osteomyelitis (CNO) is a sterile inflammatory bone disorder in which innate and adaptive immunity dysfunction involved. Unifocal and multifocal disease courses are known. The modern treatment modalities include non-steroid anti-inflammatory drugs (NSAIDs), steroids, sulfasalazine (SSZ), methotrexate (MTX), bisphosphonates and biologic drugs - TNF\u03b1 and IL1\u03b2-antagonists, with limited data.The aim of our study was to assess children with CNO and to evaluate efficacy of treatment modalities.Our cohort of CNO patients included 22 children, 8 boys and 14 girls. Monofocal disease course was in 9/22 children (40.9), multifocal in 13/22 (59.1) with mean 6 foci per patient. Histological confirmation was made in 13/22. Repeated MRI, CT and bone scintigraphy was performed in all patients. 3 patients have family history of autoimmunity had comorbid autoimmune diseases (different types of JIA): 5 had monoarthritis, 1 arthritis with uveitis, 1 - psoriatic arthritis, 1 - polyarthritis PF neg, 6 had enthesitis-related arthritis (3 had ankylosing spondyloarthritis) and 1 had Crohn's disease. Spine involvement was in 5/22 (22.7). Onset age was 8.5 years, the right diagnosis delay was 3.6 months.Fever at onset, high painVAS and parental VAS scores highly correlated with risk of relapse disease course. Treatment: effectiveness of NSAID only 3/10 (30%), SSZ - 1/5 (20%), corticosteroids - 0/3 (short-term effect only), MTX - 4/7 (57.1%), pamidronate (PAM) with partial response 2/12 (16.7%) and with complete response - 10/12 (83.3%). Biologics - adalimumab and etanercept were effective in 3/4 (75%) patients, who fail to NSAID, MTX, PAM and SSZ. During disease course treatment lead to decreasing sings of disease activity, such as: parental VAS (p = 0.015), pain VAS (p = 0.026), MDVAS (p = 0.026), CRP (p = 0.0008), WBC (p = 0.006), ESR (p = 0.00024), PLT (0.014). The main effectiveness belonged to PAM (p = 0.003) and biologics (p = 0.07) in decreasing of pain VAS (-100% and -80%), parental VAS (-92% and -74%) and MD VAS . We calculated the cumulative probability of survival (event of interest: CNO flare) in the entire patient sample, depending the kind of treatment obtained by the Kaplan-Meier method. Significant difference was proved comparing 3 therapeutical branches (p = 0.028). MTX treatment was effective (p = 0.04), as well as PAM (p = 0.01) than NSAID. Only flu-like syndrome during PAM treatment was in 10/12 (83.3%). No any others side effects were reported. All patients who had flu-like syndrome on first infusion had complete response to PAM, vice verse patients, who had no such complication had only partial response to this treatment.CNO is a group of chronic inflammatory conditions associated with different rheumatic diseases. The most effective treatment modalities were PAM, biologics and MTX. PAM was safety and can reach the rapid response and maintain long sustained remission.None declared."} +{"text": "Nevirapine (NVP) induces cytochrome P450 3A4 by which rilpivirine (RPV) is metabolized. Switching NVP to RPV could result in decreased RPV exposure with subsequent virological failure and dyslipidemia because NVP is regarded as the least dyslipidemic, non-nucleoside, reverse transcriptase inhibitor. This trial evaluated the efficacy, pharmacokinetics, safety and cardiovascular risks of switching NVP to RPV.Prospective open label controlled trial. HIV-1 patients with HIV-1 RNA <50 copies/mL on once daily NVP, emtricitabine/tenofovir (FTC/TDF) switched to single tablet RPV/FTC/TDF. Eligible patients on NVP, FTC/TDF were controls. Primary endpoint was week 12 HIV-1 RNA <50 copies/mL by intention to treat analysis. Secondary endpoints were week 24 HIV-1 RNA <50 copies/mL, NVP and RPV pharmacokinetics, safety and fasting lipids, Framingham risk scores (FRS) and Adult Treatment Panel III (ATP-III) lipid goals.Of 189 eligible patients, we included 50 RPV switchers and 139 NVP controls. Week 12 HIV-RNA was <50 copies/mL in 46/50 switchers (92.0%) which was not different from the hypothesized 90% week 12 suppression rate (p=.431). Forty-four of 50 switchers had week 24 HIV-1 RNA <50 copies/mL compared to 126/139 controls . NVP plasma concentrations were below detection level in all at week 3. Mean week 1 RPV trough concentration was 0.083 mg/L and comparable to phase III trial data (p=0.747). Adverse events occurred in 36 switchers, the majority (82.0%) were grade one. Two switchers discontinued RPV for side effects. Significant changes over 24 weeks (p<0.001) were observed in switchers on total cholesterol , low density lipoprotein (LDL)-C and high density lipoprotein (HDL)-C . The TC/HDL-C ratio increased 0.20 and systolic blood pressure decreased 6.0 mmHg . The median FRS did not change over 24 weeks . More patients achieved LDL-C and TC ATP-III treatment goals at week 24 on RPV.A NVP to RPV switch does not influence RPV exposure and results in adequate ongoing HIV-1 suppression. RPV could be an option for patients at risk for cardiovascular diseases."} +{"text": "Mesorhizobium ciceri strain CC1192, an efficient nitrogen-fixing microsymbiont of Cicer arietinum (chickpea). The genome consists of 6.94\u00a0Mb distributed between a single chromosome (6.29\u00a0Mb) and a plasmid (0.65\u00a0Mb).We report the complete genome sequence of Cicer arietinum (chickpea), a globally important grain legume, forms a N2-fixing symbiosis with soil bacteria (rhizobia) in the genus Mesorhizobium , 7. Thushttp://www.dpi.nsw.gov.au/content/agriculture/resources/soils/australian-inoculants-research-group) and confirmed to fix N2 effectively with C.\u00a0arietinum, using established methods (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and adaptors were removed by comparison against a comprehensive in-house adaptor sequence library. PacBio subreads were assessed using in-house software, and reads were automatically error-corrected in the assembly process.Strain CC1192 was sourced from the Australian inoculant industry mother culture ( methods . CC1192 methods . Whole-gde novo using the hybrid approach of SPAdes assembler version 3.6.2 (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The genome consists of 6,943,628 bp with an average GC content of 62.49%. There are 6,642 coding sequences distributed between a single circular chromosome of 6,295,397 bp and a single plasmid of 648,231 bp.The filtered Illumina and PacBio reads were assembled on 3.6.2 , with thon 3.6.2 . The asson 3.6.2 and annoM.\u00a0loti R7A (nif and fix) appear to be located on a 419-kb symbiosis island integrated within the chromosome of CC1192 . This region also harbors a type IV secretion system, conjugative relaxase, biotin and nicotinate biosynthetic clusters, proteins known to control excision and transfer of ICEMlSymR7A and CP015063 (plasmid pMc1192).The nucleotide sequence of the complete genome of CC1192 has been deposited in GenBank under the accession numbers"} +{"text": "E. coli that were engineered to constitutively express highly active E. coli beta-glucuronidase intracellularly to enhance the anticancer activity of CPT-11. The engineered bacteria, E. coli (lux/\u03b2G), could hydrolyze SN-38G to SN-38, increased the sensitivity of cultured tumor cells to SN-38G by about 100 fold and selectively accumulated in tumors. However, E. coli (lux/\u03b2G) did not more effectively increase CPT-11 anticancer activity in human tumor xenografts as compared to non-engineered E. coli. SN-38G conversion to SN-38 by E. coli (lux/\u03b2G) appeared to be limited by slow uptake into bacteria as well as by segregation of E. coli in necrotic regions of tumors that may be relatively inaccessible to systemically-administered drug molecules. Studies using a fluorescent glucuronide probe showed that significantly greater glucuronide hydrolysis could be achieved in mice pretreated with E. coli (lux/\u03b2G) by direct intratumoral injection of the glucuronide probe or by intratumoral lysis of bacteria to release intracellular beta-glucuronidase. Our study suggests that the distribution of beta-glucuronidase, and possibly other therapeutic proteins, in the tumor microenvironment might be an important barrier for effective bacterial-based tumor therapy. Expression of secreted therapeutic proteins or induction of therapeutic protein release from bacteria might therefore be a promising strategy to enhance anti-tumor activity.CPT-11 is a camptothecin analog used for the clinical treatment of colorectal adenocarcinoma. CPT-11 is converted into the therapeutic anti-cancer agent SN-38 by liver enzymes and can be further metabolized to a non-toxic glucuronide SN-38G, resulting in low SN-38 but high SN-38G concentrations in the circulation. We previously demonstrated that adenoviral expression of membrane-anchored beta-glucuronidase could promote conversion of SN-38G to SN-38 in tumors and increase the anticancer activity of CPT-11. Here, we identified impediments to effective tumor therapy with Clostridium (E. coli (lux) and E. coli (lux/\u03b2G) in tumors reached a plateau from days 3 to 7 or E. coli (lux/\u03b2G) displayed splenomegaly (E. coli induced an immune response. This immune response may cause the transient body weight loss (9.2%) on day 3 observed after systematic administration of E. coli (The time course of lux/\u03b2G)] . The lums 3 to 7 , demonst tissues . Determiectively . Mice innomegaly , suggest E. coli .E. coli and beta-glucuronidase in tumor sections from E. coli (lux/\u03b2G), E. coli (lux), or PBS-treated mice. DAPI (blue) stained DNA in both live tumor cells and E. coli. DAPI-stained E. coli were observed as tiny spots that formed a dense cluster under UV excitation (E. coli further confirmed the location of the bacteria. Anti-E. coli beta-glucuronidase antibody staining showed that E. coli (lux/\u03b2G) but not E. coli (lux) expressed beta-glucuronidase in the tumor microenvironment. 72.4% \u00b113.9% of E. coli (lux) and 84.9% \u00b1 9.2% of E. coli (lux/\u03b2G) were located in necrotic areas of tumors as distinguished by DAPI staining. E. coli (lux) and E. coli (lux/\u03b2G) didn\u2019t show significant differences in localization to tumor necrotic areas could enhance the anti-tumor activity of CPT-11, NOD/SCID mice bearing established HCT116 human colon tumors were i.v. injected with PBS or E. coli. Four days later, the mice were i.v. injected with 10 mg/kg CPT-11 or vehicle on two consecutive days. Treatment of mice with either CPT-11 or E. coli (lux/\u03b2G) alone significantly suppressed tumor growth as compared to treatment with vehicle alone (E. coli (lux/\u03b2G) produced significantly greater antitumor activity that either individual treatment. However, this effect did not depend on bacterial expression of beta-glucuronidase because treatment of mice with CPT-11 and E. coli (lux) suppressed tumor growth to a similar extent (E. coli (lux/\u03b2G) or E. coli (lux) produced significant but similar suppression of tumor growth (E. coli (lux/\u03b2G).To determine whether le alone . Combinar extent . Similarr growth , indicatE. coli (lux/\u03b2G) or E. coli (lux) could be caused by in vivo induction of endogenous beta-glucuronidase expression in E. coli (lux) or by in vivo loss of beta-glucuronidase expression in E. coli (lux/\u03b2G), we i.v. injected E. coli (lux/\u03b2G) or E. coli (lux) into mice bearing established HCT116 tumors and then i.v. injected a fluorescence glucuronide probe, FDGlcU, to measure in vivo beta-glucuronidase activity (E. coli (lux/\u03b2G) displayed similar luminescence emission but higher fluorescence emission than E. coli (lux) (E. coli (lux/\u03b2G) expressed significantly more beta-glucuronidase activity in tumors than did E. coli (lux). We conclude that E. coli (lux/\u03b2G) and E. coli (lux) displayed the expected high and low beta-glucuronidase activity in tumors.To investigate if the similar anticancer activity observed for treatment with CPT-11 and either activity . FDGlcU li (lux) , indicatE. coli therapy failure. To investigate differences between bacterial and adenoviral beta-glucuronidase therapy, we first compared the enzymatic activities of E. coli beta-glucuronidase (produced in E. coli (lux/\u03b2G) and murine beta-glucuronidase (produced by Ad/m\u03b2G). E. coli beta-glucuronidase hydrolyzed the glucuronidase substrate 4-Nitrophenyl \u03b2-D-glucopyranoside (pNPG) faster than did murine beta-glucuronidase at pH 7 [E. coli beta-glucuronidase displayed about 250 fold greater enzymatic activity for the hydrolysis of SN-38G compared to murine beta-glucuronidase at pH 7 (E. coli (lux/\u03b2G) or intratumoral injection of Ad/m\u03b2G. Again, the total beta-glucuronidase activity in tumors was significantly greater in mice treated with E. coli (lux/\u03b2G) than those treated with Ad/m\u03b2G (E. coli (lux/\u03b2G) can deliver more beta-glucuronidase activity to tumors as compared to direct injection of tumors with Ad/m\u03b2G.We previously showed that intratumoral injection of Ad/m\u03b2G, which allows expression of murine beta-glucuronidase as a membrane-anchored form on the surface of infected cells, can enhance the anti-tumor activity of CPT-11 . Therefo at pH 7 . Similar at pH 7 . Next, wh Ad/m\u03b2G . These rE. coli (lux/\u03b2G) or i.t. with Ad/m\u03b2G. Fluorescence signals were apparent in the tumors of mice receiving either treatment (E. coli (lux/\u03b2G) (E. coli (lux/\u03b2G) produced more beta-glucuronidase activity in tumors, the beta-glucuronidase activity generated by Ad/m\u03b2G can more effectively hydrolyze a systemically administered glucuronide probe in the tumors.To assess the functional accessibility of beta-glucuronidase to systemically administered drugs, we i.v. injected the fluorescent glucuronide probe FDGlcU and then imaging the fluorescence intensity in tumors of mice treated i.v. with reatment , but mic(lux/\u03b2G) . A relatnce from by the bnce from . Tumors (lux/\u03b2G) . We concE. coli (lux/\u03b2G) suggested that the chemical probe delivered via the tumor blood supply may not effectively contact beta-glucuronidase in the tumor. To test this idea, we compared the fluorescence in tumors after systemic (i.v.) or direct intratumoral (i.t.) injection of FDGlcU to mice previously treated with E. coli (lux/\u03b2G) or Ad/m\u03b2G. The dose of FDGlcU was decreased by 100 fold for intratumoral injection groups to prevent saturation of beta-glucuronidase in the tumors. While mice treated with Ad/m\u03b2G displayed similar fluorescence after either i.v. or i.t. injection of FDGlcU, the mice treated with E. coli (lux/\u03b2G) exhibited more tumor fluorescence after i.t. injection of FDGlcU (E. coli (lux/\u03b2G) was significantly greater when FDGlcU was directly injected into tumors as opposed to after i.v, administration to allow tumor colonization and then directly injected a mixture of lysozyme/DNase I into tumors to break the bacteria cell wall. This approach was used to release beta-glucuronidase from the bacteria because the enzyme is too large (~280 kDa) to be efficiently secreted (results not shown). Mice were first i.v. injected with FDGlcU on day 4 to measure the fluorescence generated by hydrolysis of FDGlcU by intact bacteria in the tumors. After 48 h, the lysozyme/DNase I mixture was injected into tumors and then FDGlcU was again i.v. injected and tumor fluorescence was imaged. Imaging of bacterial luminescence showed the number of bacteria in tumors on days 4 and 6 were not significantly different slow uptake of glucuronide compounds into E. coli may reduce the rate of prodrug hydrolysis and 2) the preferential accumulation of E. coli in necrotic regions of tumors may hamper efficient contact of systematically administered drugs with beta-glucuronidase. Our study suggests that both the cellular and spatial distribution of beta-glucuronidase, and possibly other therapeutic enzymes, might be an important barrier for effective bacteria-based prodrug cancer therapy.Methods to enhance the selectivity and efficacy of cancer chemotherapy are needed to improve patient outcome. Bacteria that have been modified to express enzymes for tumor-selective activation of proactive anticancer agents have been investigated as a promising approach to achieve more selective cancer therapy ,48. Heree CPT-11 ,35. Conve CPT-11 ,37. ThesE. coli was selected in our study to deliver beta-glucuronidase to tumors. There are two major advantages of using E. coli as a delivery vehicle for prodrug activation. First, E. coli can selectively colonize solid tumors, providing high tumor/normal tissue colonization ratios of around 10,000 fold [E. coli to mice. By contrast, Salmonella provides tumor/liver and tumor/spleen bacterial ratios of 100~1000 [E. coli for tumors may help reduce prodrug activation in normal tissues. Second, unlike liposomes, antibodies or replication deficient viruses, bacteria can proliferate in tumors [E. coli. These advantages have been recognized as indicated by the increasing number of papers investigating E. coli for tumor imaging and tumor therapy [E. coli used in our study (DH5\u03b1) does not express enterotoxins or lipopolysaccharides and is considered to be non-pathogenic [E. coli were also able to accumulate in murine tumors in immune-competent mice with similar toxicity as observed in immune deficient mice, suggesting that E. coli (DH5\u03b1) may be a suitable delivery vehicle for clinical applications.000 fold ,18,38. I100~1000 ,14. Like100~1000 \u201324. The n tumors \u201351. The therapy ,20,38,52thogenic . We usedE. coli [E. coli. We constitutively expressed E. coli beta-glucuronidase in E. coli (lux/\u03b2G). These bacteria expressed about 60 ng beta-glucuronidase per 107 c.f.u. of bacteria and could convert cytotoxic concentrations of SN-38 from SN-38G. Because E. coli beta-glucuronidase can hydrolyze SN-38G to SN-38 about 250-fold faster than murine beta-glucuronidase as compared to mice treated with Ad/m\u03b2G (E. coli beta-glucuronidase did not increase CPT-11 antitumor activity beyond that achievable by treating tumors with wild-type E. coli (E. coli (lux/\u03b2G) .E. coli (lux/\u03b2G) therapy differ in several important facets as indicated in E. coli preferred to colonize the margins between necrotic regions and live cells (E. coli (lux/\u03b2G) with systemically-administered drugs. Second, the enzyme location in the cells differs. Ad/m\u03b2G was designed to express beta-glucuronidase on the cell membrane of infected cells whereas E. coli (lux/\u03b2G) expresses beta-glucuronidase in the periplasmic space of the bacteria. Glucuronide drugs can directly interact with membrane-anchored beta-glucuronidase but require receptor-mediated transport into E. coli to interact with beta-glucuronidase [E. coli (lux/\u03b2G) expresses E. coli beta-glucuronidase. The enzymatic activity of E. coli beta-glucuronidase is much greater than mouse beta-glucuronidase as compared to Ad/m\u03b2G. First, beta-glucuronidase is expressed intracellularly in E. coli (lux/\u03b2G) but is present on the surface of cells as a membrane anchored form after infection with Ad/m\u03b2G. Thus, glucuronide substrates must enter bacteria, presumably via a glucuronide transporter complex present on E. coli [et al [E. coli preferentially accumulated at the border between viable cancer cells and necrotic regions significantly increased probe hydrolysis (E. coli (lux/\u03b2G) in the tumor by intratumoral injection of lysozyme and DNase I to release beta-glucuronidase also significantly increased hydrolysis of the glucuronide probe (We identified two impediments that may account for the relatively poor performance of E. coli , to cont E. coli . The seci [et al , we obse regions . Salmonef tumors , suggestf tumors \u201358 whichf tumors ,60. The drolysis , consistde probe . Taken tE. coli, other bacteria such as Salmonella and Shigella also prefer to colonize in the necrotic regions of tumors [Besides f tumors . Thus, df tumors \u201367 or inf tumors might re"} +{"text": "AbstractSymplanella Fennah, S. hainanensissp. n., S. recurvatasp. n. and S. zhongtuasp. n., are described and illustrated from South China. A checklist and a key to species of genus Symplanella are provided.Three new species of the Oriental caliscelid planthopper genus PageBreakSymplanella was erected by Symplanella breviceps Fennah, 1987) and was placed in the subtribe Augilina of the tribe Ommatidiotini of the family Issidae. Recently, the genus was transferred to the family Caliscelidae by Caliscelidae. Symplanella from China and described one new species, Symplanella unipuncta Zhang & Wang, 2009, and proposed one new combination, Symplanella brevicephala (transferred from Symplana Kirby). To date, only three species, Symplanella brevicephala (China: Yunnan), Symplanella breviceps (Burma: Dawna Hills) and Symplanella unipuncta (China: Hainan), are included in the genus Symplanella.The genus Symplanella are described and illustrated from South China . The generic characteristics are redefined. A checklist and a key to known species of Symplanella are provided.In this paper three new species of the genus Terminology follows Fennah, 1987http://species-id.net/wiki/SymplanellaSymplanella Fennah, 1987: 244; Symplanella breviceps Fennah, 1987, by original designation.PageBreaktriangular, venation as shown in Vertex , 15, 27 Oriental Region (China and Burma).Symplanella brevicephala ; China (Yunnan).Symplanella breviceps Fennah, 1987; Burma (Dawna Hills).Symplanella hainanensis sp. n.; China (Hainan).Symplanella recurvata sp. n.; China (Guangdong and Guangxi).Symplanella unipuncta Zhang & Wang, 2009; China (Hainan).Symplanella zhongtua sp. n.; China (Yunnan)http://zoobank.org/FA3249B6-4106-4928-9201-F444D3E76BEDhttp://species-id.net/wiki/Symplanella_recurvataBody length including forewing: male 5.78\u20135.98 mm (N = 6), female 6.15\u20136.25 mm (N = 12); forewing length: male 4.90\u20135.15 mm (N = 6), female 5.30\u20135.40 mm (N = 12).PageBreakPageBreaksegment. Central area of vertex and pronotum, base of mesonotum with somewhat pale yellowish red. Procoxae, mesocoxae, metapleura, abdominal sternites laterally and pregenital sternite of female fuscous.General color light yellowish brown with somewhat green. Ocelli reddish brown, eyes black brown. Antennae with one black spot at apex of second Vertex including eyes narrower than pronotum (0.86:1). Vertex shorter in middle line than broad at base (0.60:1). Frons 1.28 times longer in middle line than widest part. Pronotum slightly longer in middle line than vertex (1.21:1). Mesonotum 1.24 times as long as vertex and pronotum together in middle line. Forewing longer in middle line than broad at widest part (4.71:1). Hindwing longer in middle line than broad at widest part (2.01:1), venation as shown in Anal segment of male in posterior view nearly l23\u00b008'N, 113\u00b014'E), on bamboo , 22 Nov. 2006, X.-S. Chen; paratypes: 5 \u2642\u2642, 11 \u2640\u2640, data same as holotype; 1 \u2640, Guangxi, Daxin, Encheng, 4 May 2009, H.-R. Li.Holotype: \u2642, China: Guangdong, Guangzhou, Huanan Botanical Garden .Bamboo (South China (Guangdong and Guangxi) .Symplanella unipuncta Zhang & Wang, 2009 but differs in: i) anal segment in lateral view with one stout process at apical margin ventrally, which curves cephalad apically ; ii) posterior margin of pygofer without process (with one process in Symplanella unipuncta); iii) aedeagus without process at base .This new species is closely related to The new species is named after the strongly recurved tip of the anal tube.http://zoobank.org/C12B4D8F-BF4B-4939-977B-D13F7CEDDF9Fhttp://species-id.net/wiki/Symplanella_hainanensisBody length including forewing: male 5.45\u20135.62 mm (N = 2), female 6.00\u20136.30 mm (N = 8); forewing length: male 4.40 mm (N = 2), female 4.65\u20134.95 mm (N = 8).PageBreakPageBreakGeneral color dirty yellowish brown. Ocelli reddish brown, eyes black brown. Antennae with one black spot at apex of second segment. Frons and clypeus mostly dark brown. Central area of vertex and pronotum, base of mesonotum with somewhat pale yellowish red. Procoxae, mesocoxae, metapleura, abdominal sternites laterally and pregenital sternite of female, fuscous.Vertex including eyes as wide as pronotum. Vertex longer in middle line than broad at base (1.24:1). Frons 1.67 times longer in middle line than widest part. Pronotum shorter in middle line than vertex (0.74:1). Mesonotum 0.87 times as long as vertex and pronotum together in middle line. Forewing longer in middle line than broad at widest part (4.00:1).Anal segment of male in dorsal view with med18\u00b047'N, 109\u00b052'E), on bamboo, 9\u201312 Apr. 2009, X.-H. Hou; paratypes: 1 \u2642, 8 \u2640\u2640, data same as holotype.Holotype: \u2642, China: Hainan, Diaoluoshan National Natural Reserve (Bamboo.South China (Hainan) .Symplanella breviceps Fennah, 1987, but can be distinguished from the latter in: i) frons mostly dark brown (stramineous in Symplanella breviceps); ii) vertex with anterior margin rounded (angulated in Symplanella breviceps); iii) posterior margin of pygofer with one spinous process dorsally (absent in Symplanella breviceps); iv) genital style in posterior view broad and short (narrow and long in Symplanella breviceps).This new species is similar to the type species from Burma, The new species is named after the type locality, Hainan Province, China.http://zoobank.org/B8FADA9C-2202-4485-928A-E17811BB1A59http://species-id.net/wiki/Symplanella_zhongtuaBody length including forewing: male 6.10\u20136.35 mm (N = 4), female 6.30\u20136.50 mm (N = 2); forewing length: male 5.15\u20135.30 mm (N = 4), female 5.20\u20135.40 mm (N = 2).PageBreakPageBreakGeneral color dirty yellowish brown. Ocelli reddish brown, eyes black brown. Antennae with one black spot at apex of second segment. Frons and clypeus mostly blackish brown. Central area of vertex and pronotum, base of mesonotum with somewhat pale yellowish red. Procoxae, mesocoxae, metapleura, abdominal sternites laterally and pregenital sternite of female fuscous.Vertex including eyes narrower than pronotum (0.98:1). Vertex shorter in middle line than broad at base (0.65:1). Frons 1.41 times longer in middle line than widest part. Pronotum as long in middle line as vertex. Mesonotum 1.45 times as long as vertex and pronotum together in middle line. Forewing longer in middle line than broad at widest part (4.45:1).PageBreakapical third abruptly narrowed, stick-like, apical margin rounded, each side with one spine-like process; phallobase lobe-like, each with one small spine at apex; aedeagus in lateral view , on bamboo, 28 July 2011, W.-B. Zheng and Z.-M. Chang; paratypes: 3 \u2642\u2642, 2 \u2640\u2640, data same as holotype.Holotype: \u2642, China: Yunnan, Xishuangbanna, Menglun (Bamboo.Southwest China (Yunnan) .Symplanella brevicephala , but can be distinguished by: i) frons and clypeus mostly black ; ii) posterior margin of male pygofer having one stout spinous process at middle, directed ventro-caudad ; iii) genital style in lateral view dorso-apical angle broadly rounded ; iv) aedeagal shaft mostly straight .This new species is similar to The name is derived from transliteration of the Chinese \u201czhongtu\u201d, meaning posterior margin of male pygofer having one stout spinous process at middle.Diversity of bamboo-feeding planthoppers. The current authors paid particular attention to the species of bamboo planthopper in field research and collected large quantities of specimens in the past twelve years. A number of new taxa or new records were found and some of them have been published (Bambusoideae (Delphacidae (78 species in 15 genera), Caliscelidae (three species in two genera), Cixiidae (two species in one genus) and Tropiduchidae (one species in one genus). The genus Symplanella with three known species and three new species described in this paper, represents the second bamboo-feeding genus in the tribe Augilini after Pseudosymplanella Che, Zhang & Webb, 2009 and the International Science and Technology Cooperation Program of Guizhou (No. 20107005)."} +{"text": "A 10-year-old girl developed an enlargement of parotid and submandibular salivary glands and lymph nodes up to 2.5 cm associated with edema of her upper eyelids. In further follow-up, she developed non-palpable, vasculitic skin lesions. She received cephixime, that co-incided with partial regression of lymph nodes. Re-occurrence of vasculitic lesions with bilateral edema of upper eyelids resembling Miculitz disease was observed. At 7 years of age, she developed asthma requiring the use of bronchodilators. Clinical examination: a 10-year-old girl, pale skin, at the both calves irregularly shaped, livid, painless, vasculitic lesions, 2-3 cm in size. The upper eyelids are swollen. Parotid and submandibular salivary glands and submandibular lymph nodes are enlarged.To present clinical and laboratory investigations in IgG4-related disease in childhood.Routine laboratory tests including serum Ig concentrations, autoantibody screen, and histopathologic examination.Serum proteins were 101 g/l, albumins,38 g/l. Serum immunoglobulin IgA 1.92, IgM 0.38, IgG 42.2 g/l; IgG subclasses: IgG1 18.9 g/l (4.32-10.2), IgG2 17.05 g/l (0.72-4.3), IgG3 6.35 g/l (0.13-0.85), IgG4 9.02 g/l (0.02-0.93). Serum IgE 900 IU/ml . Coombs test negative. Autoantibody screening was negative. Serologic tests to HSV, EBV, CMV, hepatitis B and C, HIV were negative. Serum ACE was normal, 57 U/l. Neck ultrasound showed an enlargement of both parotid glands, lymph nodes and submandibular salivary glands up to 2.5 cm.Histopathathologic evaluation of lymph nodes, submandibular and parotid gland: the enclosed lymph node profiles show retained architecture with prominent reactive follicular hyperplasia. The intervening paracortex focally appears prominently hypovascular and contains a polymorphous lymphoid infiltrate comprising small lymphocytes, scattered immunoblasts, some plasma cells and focally prominent eosinophils.The salivary gland tissue shows abundant mononuclear inflammatory infiltrate with focal prominence of plasma cells and significant patchy sclerosis. The immunostainings including CD3, CD20 and CD79a show retained lymph node architecture. There is a reactive pattern of expression of Ki67, CDI0, bcl-2, bCl-G, CD21 and CD23. The immunostains also highlight fragmentation of some of the germinal centres. Most of the IgG staining plasma cells were of IgG4 positive phenotype.Bilateral, symmetrical, painless swelling of their lacrimal and salivary (parotid and submandibular) glands should raise suspicion on IgG4-related disease in childhood.None declared."} +{"text": "After an acute myocardial infarction with ST-segment elevation (STEMI) treated with percutaneous coronary intervention (PCI), the left ventricle (LV) can undergo negative remodeling (R-). We aimed to investigate whether global longitudinal strain (SGL) of the left ventricle (LV) predicts remodeling.Transthoracic echocardiography with speckle tracking imaging (TTE-STI) was performed 2 to 3 days after primary PCI and 6 months later in patients with diagnosis of STEMI. LV R- criteria were: LVEF increase \u22645% and end-diastolic volume increase \u226515%. Logistic regression and ROC curve analysis was used for the statistical analysis.n = 35, 42%) and no LV R- patients . Diabetes mellitus and TnI levels showed higher incidence in LV R- patients. SGL was -12.5 \u00b1 5.6% in no LV R- patients and -6.5 \u00b1 3.4 in LV R- patients. In the regression analysis just LV SGL and SL in left anterior descending territory remained significant, OR: 1.85 (1.24 to 2.76) (P < 0.001) and OR: 1.63 (1.15 to 2.31) (P < 0.001), respectively. The analysis of ROC curves revealed that at the cutoff level of -12.46%, SGL identifies LV R- with a sensibility of 81% and a specificity of 86% with STEMI at any LV localization and subjected to primary PCI were studied during 2012: LV R- patients (1 years wSGL assessment in the first days after primary PCI is useful in the prediction of LV R- independently of the myocardial infarction localization."} +{"text": "Erratum: Drug resistance in multiple myeloma: latest findings and new concepts on molecular mechanisms1,2, Guoan Chen3, Hong Chang1,2,4Jahangir Abdi2186-2207Oncotarget. 2013; 4:PMID: 24327604http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path%5B%5D=1497&path%5B%5D=1760The affiliation of the first author is incorrect in the published paper.1 Division of Immunopharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The NetherlandsThe corrected affiliation is provided here.1 Dept. of Laboratory Medicine & Pathobiology, University of Toronto, Ontario, Canada"} +{"text": "Enterobacteriaceae-producing extended-spectrum \u03b2-lactamases (ESBLs). A retrospective case-control study was conducted to identify independent risk factors for ESBL-producing Escherichia coli and Klebsiella pneumoniae in non-hospitalized KTPs with UTI. Forty-nine patients suffering from UTI by ESBL-producing bacteria (ESBL-P) as case group and the same number of patients with UTI by ESBL negative (ESBL-N) as control-group were compared. Clinical data, renal function parameters during UTI episodes, UTI recurrence and relapsing rate, as well as risk factors for recurrence, molecular characterization of isolates and the respective antimicrobial susceptibility profile were evaluated. Diabetes mellitus (p <0.007), previous antibiotic prophylaxis (p=0.017) or therapy (p<0.001), previous UTI (p=0.01), relapsing infection (p=0.019) and patients with delayed graft function after transplant (p=0.001) represented risk factors for infection by ESBL positive Enterobacteriaceae in KTPs. Interestingly, the period of time between data of transplantation and data of UTI was shorter in case of ESBL-P case-group (28.8 months) compared with ESBL-N control-group (50.9 months). ESBL-producing bacteria exhibited higher resistance to fluoroquinolones (p=0.002), trimethoprim-sulfamethoxazole (p<0.001) and gentamicin (p<0.001). Molecular analysis showed that blaCTX-M was the most common ESBL encoding gene (65.3%), although in 55.1% of the cases more than one ESBL gene was found. In 29.4% of K. pneumoniae isolates, three bla-genes (blaCTX-M-blaTEM-blaSHV) were simultaneously detected. Low estimated glomerular filtration rate (p=0.009) was found to be risk factor for UTI recurrence. Over 60% of recurrent UTI episodes were caused by genetically similar strains. UTI by ESBL-producing Enterobacteriaceae in KTPs represent an important clinical challenge regarding not only hospitalized patients but also concerning outpatients.Urinary tract infection (UTI) is a common complication after kidney transplantation, often associated to graft loss and increased healthcare costs. Kidney transplant patients (KTPs) are particularly susceptible to infection by Urinary tract infections (UTI) affect 5 to 36% of kidney transplant patients (KTPs), being the main infectious complication among such patient population \u20134, and oblaCTX-M [ESBLs are a large, rapidly evolving group of plasmid-enzymes that confer resistance to penicillins, first-, second-, and third generation cephalosporins, and aztreonam. They are inhibited by beta-lactamase inhibitors such as clavulanic acid \u201310. DurilaCTX-M . The prelaCTX-M \u201317. TherlaCTX-M \u201320, howeE. coli and K. pneumoniae comparatively to the respective non ESBL-producing counterparts. ESBLs encoding genes were identified. E. coli and K. pneumoniae isolates sequentially recovered from each patient were genotyped to assess about re-infection or bacterial persistence.The aim of this study was to identify risk factors, the susceptibility profile and recurrence associated to UTI caused by ESBL-producing This study was approved by Comiss\u00e3o de Etica para a Sa\u00fade (CES) do Centro Hospitalar de S\u00e3o Jo\u00e3o , signed by Prof. Manuel Pestana (Director of Nephrology Department). Patient records/information was anonymized and de-identified prior to analysis.E. coli and K. pneumoniae ESBL-producing bacteria (ESBL-P), as case-group, and 49 outpatients with UTI by the same species but ESBL negative (ESBL-N), as a control-group, was performed. All patients were kidney transplant patients (KTPs) from Centro Hospitalar S\u00e3o Jo\u00e3o, Porto with documented UTI between January 2012 and August 2012.A retrospective case-control study enrolling 49 outpatients with UTI by 2) was registered [Demographic data and clinical variables such as delayed graft function, the presence of urinary tract obstruction, bacteremia, fungemia, previous urinary tract infection, creatinine blood level (reference range 0.6\u20131.1 mg/dL), and the percentage of patients with low estimated glomerular filtration rate (eGFR) during UTI and K. pneumoniae (n = 32) were recovered from 49 KTPs (case-group): 25 patients yielded each a single isolate, 16 patients two isolates each, 7 patients three isolates each, one single patient yielding four isolates. Forty-nine ESBL negative isolates (32 E. coli and 17 K. pneumoniae) were recovered from the 49 patients of control group. All isolates were analyzed by Vitek2 System using GN card for identification and the AST-60 for antimicrobial susceptibility profile. ESBL presence was confirmed by disc diffusion method, according to the recommendations of Clinical Laboratory Standard Institute [Escherichia coli ATCC 25922 and Klebsiella pneumoniae ATCC700603 type strains, as recommended by CLSI protocol [Eighty-two isolates of ESBL-producing nstitute ; a doublprotocol and plasblaCTX-M,blaTEM, and blaSHV) were screened by PCR multiplex, as previously described [blaSHV: 5\u00b4-ATCCACTATCGCCAGCAGG-3\u00b4 and 5\u00b4-TCATTCAGTTCCGTTTCCCAG-3\u00b4; blaTEM: 5\u00b4-GAGTATTCAACATTTCCGTGTC-3\u00b4 and 5\u00b4-GGGCGAAAACTCTCAAGGATC-3\u00b4; blaCTX-M: 5\u00b4-GTTGTTAGGAAGTGTGCCGC-3\u00b4 and 5\u00b4-GCCCGAGGTGAAGTGGTATC-3\u00b4. Primers amplified the internal fragments of ESBLs genes possessing different sizes. Multiplex PCR was performed in a 25 \u03bcl reaction mixture containing 1x Dream Taq buffer (Fermentas), 2.5 mM MgCl2, 10 mM dNTPs, 2.5\u201340 pmol of specific-group primers, 50\u2013150 ng plasmid DNA and 1 U of Dream Taq Polymerase (Fermentas). Amplification reactions were carried out in Mastercycler Realplex2 (Eppendorf) under the following conditions: initial denaturation at 95\u00b0C for 2 min, followed by 30 cycles of denaturation (95\u00b0C for 30 sec), annealing (59\u00b0C for 30 sec), extension (72\u00b0 for 30 sec) and a final extension step (72\u00b0C for 10 min). PCR products were run at 80 V, during 1 hour in a 2.5% agarose gel containing 0.002% Ethidium Bromide . ESBLs bacteria exhibiting well-characterized ESBL genes kindly gift by Dr. Rafael Cant\u00f3n were used as positive controls.The most frequently ESBL genes , and involved the following steps: initial denaturation at 94\u00b0C for 1 min, followed by 45 cycles of denaturation (94\u00b0C at 1 min), annealing (34\u00b0C at 1 min), extension (72\u00b0C at 2 min), and a final extension step (72\u00b0C at 10 min). PCR products were separated by electrophoresis (60 V for 3 hours) in a 2.5% agarose gel. DNA fingerprints were compared by visual inspection with the Molecular Imager ChemiDoc XRS (BioRad). Clonality was assessed by visual inspection of the different fragments obtained, in a range of 2000\u2013200 bp for E. coli and 3000\u2013250 bp for K. pneumoniae. According to Wong et al. [Sequential isolates from case-group (ESBL-P)- 2 or more isolates (24 patients)\u2014were genotyped by RAPD. Distinct primers were used for E. coli version 20. Continuous variables were summarized as mean value and standard deviation (SD). Categorical variables, summarized as percentages, were compared using Chi-square test (or Fishers \u2018exact test whenever was necessary) and Student\u00b4s Patient clinical data, including demographic characteristics, co-morbidities, clinical laboratory data, immunosuppressive therapeutic regimen, previous UTI and antibiotic exposure are summarized in Regarding immunosuppression, all patients showed adequate therapeutic levels; mean values were: 8.1 ng/mL for tacrolimus, 190.5 ng/mL for cyclosporine and 6.28 ng/mL for everolimus. Patient death occurred solely among ESBL-P group, during the 3 months after infection . No bactK. pneumoniae susceptibility to amikacin between both study groups were detected by PCR multiplex in isolates from ESBL-P group (blaCTX-M (65.3%), either alone (18.4%) or in combination with another ESBL gene (46.9%), followed by blaTEM (61.2%) and blaSHV (40.8%). More than half of the case- group express more than one ESBL gene, being the association blaCTX-M- blaTEM the most frequent (28.5%), particularly among E. coli strains (37.5%). Among K. pneumoniae isolates, blaCTX-M-blaTEM-blaSHV (29.4%) was the most frequent association, followed by blaCTX-M-blaSHV (23.5%). Strains expressing a single ESBL gene, blaCTX-M (25%) and blaTEM (18.8%) corresponded most often to E. coli, while blaSHV was more common among K. pneumoniae isolates (17.6%) (ESBL genes (-P group . Interes (17.6%) . No corrE. coli and 63.6% in the case of K. pneumoniae) (see representative examples in Although the level of recurrence found for both groups was similar (around 40%), the relapsing percentage was significantly higher on control-group . The 48 Kidney transplant recipients display many risk factors for UTI and are considered a particular vulnerable population to such infections . Severalet al. study [blaCTX-M,blaTEM, and blaSHV) in E. coli and K. pneumoniae revealed that blaCTX-M was the most common ESBL gene. A higher predominance of blaCTX-M enzyme among ESBL positive E. coli was reported in Greece [blaCTX-M and blaTEM [E. coli and K. pneumoniae (57.3%) isolates exhibiting two or three genes was previously reported [blaSHV and blaTEM types of ESBLs have traditionally been responsible for serious health care related infections [blaCTX-M types have been mainly associated with community-onset UTI [blaCTX-M-producing bacteria and resistance to fluoroquinolones [Similar to Linares study impairmel. study . Remarkan Greece . Conversn Greece . In Port blaTEM ,36. Repo blaTEM . A high reported , similarfections while blnset UTI . The epinset UTI , being tinolones such corE. coli and K. pneumoniae. Molecular epidemiology showed that blaCTX-M was the most common ESBL encoding gene, either alone or in association with other genes. Low eGFR and high blood creatinine are risk factors for UTI recurrence. The high co-resistance to other antibiotics (non-\u03b2-lactams) found from ESBL producing bacteria in UTI from KTPs, remains a serious clinical challenge.In conclusion, we have demonstrated that delayed graft function, diabetes mellitus, previous antibiotic exposure, antibiotic prophylaxis and relapsing UTI are independent risks factors for acquiring infections by ESBL-producing"} +{"text": "Their structures and relative configurations were established by extensive spectroscopic analysis. A possible biosynthetic pathway for 1\u20134 was also proposed.Guajadials C-F (Supplementary material is available for this article at 10.1007/s13659-012-0102-4 and is accessible for authorized users. Supplementary material, approximately 2.05 MB."} +{"text": "The correct citation is: Seed Ahmed M, Pelletier J, Leumann H, Gu HF, \u00d6stenson C-G (2015) Expression of Protein Kinase C Isoforms in Pancreatic Islets and Liver of Male Goto-Kakizaki Rats, a Model of Type 2 Diabetes. PLoS ONE 10(9): e0135781. doi:"} +{"text": "MEDI4736 is an engineered human IgG1 that blocks PD-L1 binding to PD-1 and allows T-cells to recognize and kill tumor. MEDI4736 has single-agent activity and potential for further increased activity in combination. A comprehensive development programme is underway in NSCLC, as monotherapy and in combination.NSCLC data from 2 multicentre, open-label Phase I studies are reported. NCT01693562 evaluates safety and efficacy of MEDI4736 administered every 2 or 3 weeks. NCT02000947 evaluates safety and efficacy of MEDI4736 in combination with tremelimumab, a human IgG2 anti-CTLA-4 mAb, at 4-week intervals.NCT01693562: As of May 2014, NSCLC cohort included 155 patients (pts) . Median follow-up: 6 weeks (range 0-67). Treatment-related adverse events (TRAEs): 29% (Grade [Gr] \u22653: 3%); none led to treatment discontinuation. Most frequent TRAEs: fatigue (7%), nausea (5%), and vomiting (5%). No treatment-related colitis any Gr. No treatment-related Gr 3/4 pneumonitis or dyspnea. 58 pts had \u226512 weeks follow-up: 16% had partial response (as early as 6 weeks), duration of response ranged 5-54+ weeks, disease control rate 35%. PD-L1 positivity appears to enrich for response.NCT02000947: As of April, 2014, 12 pts treated at 4 dose-levels . No DLTs observed in any cohort during DLT observation period. Most frequent TRAEs: -\u2191amylase, abdominal pain, arthralgia, colitis, diarrhea, epigastric discomfort, fatigue and nausea. TRAEs \u2265Gr 3 noted in 3 pts: Gr 3 - \u2191AST/ALT & Gr 5 myasthenia (MG) (n = 1), Gr 3 diarrhea/colitis (n = 1), Gr 4 - \u2191amylase (n = 1). TRAEs led to discontinuation in two subjects: Gr 5 MG and Gr3 colitis. In 12 response-evaluable pts support continued development in NSCLC. Additional monotherapy NSCLC studies: Phase II 'ATLANTIC' (NCT02087423), Phase III 'PACIFIC' following chemo-radiotherapy (NCT02125461), Combination: Phase I + gefitinib (NCT02088112), and Phase Ib + AZD9291 (NCT02143466). Monotherapy and combination: Phase III 'ARCTIC' vs standard-of-care."} +{"text": "AbstractOphioninae is updated, based on the examination of about 800\u2013900 individuals in the South African and European museum collections. A robust interactive matrix key was built to provide quick and reliable identifications. The key is available online at http://www.waspweb.org. Two new species are described: Dicamptusmaxipolsp. n. and Enicospilusgauldetmitchellorumsp. n. Numerous new distribution and biological records are provided, and noticeable morphological intra-specific variations are detailed. Enicospilusbatus Gauld & Mitchell, syn. n. is considered as a junior synonym of Enicospilusluebberti (Enderlein).The revision of the Afrotropical Ophioninae is one of the two major subfamilies of Ichneumonidae that have been extensively revised in the Afrotropical region. The revision of the Ophioninae is mainly due to The subfamily Ophioninae in the region.It is of note that very few amendments have been brought to their work since the revision was published, except three new species descriptions and some Natural History Museum, London, UK (Gavin Broad).BMNH California Academy of Science, San Fransisco, USA (Brian Fisher).CASC Mus\u00e9um d\u2019Histoire Naturelle de La R\u00e9union, Saint Denis, France (Sonia Ribes).MHNR Mus\u00e9ul National d\u2019Histoire Naturelle, Paris, France (Claire Villemant).MNHN Mus\u00e9um Royal de l\u2019Afrique Centrale, Tervueren, Belgium (Eliane de Coninck).MRAC KwaZulu-Natal Museum, Pietermaritzburg, South Africa (Burgert Muller).NMSA Iziko South African Museum, Cape Town, South Africa (Simon van Noort).SAMChttp://www.waspweb.org.Specimens were point mounted on black, acid-free card for examination (using a Leica M205C stereomicroscope with LED light source), photography and long term preservation. Images were acquired using the Leica LAS 4.4 imaging system, which comprised a Leica\u00ae Z16 microscope with a Leica DFC450 Camera with 0.63\u00d7 video objective attached. The imaging process, using an automated Z-stepper, was managed using the Leica Application Suite V 4.4 software installed on a desktop computer. Lighting was achieved using techniques summarized in PageBreakThe terminology follows : body length, from torulus base to apex of metasoma (mm).B: fore wing length, from tegula base to wing apex (mm).F : shortest distance between eye and mandible / basal mandibular width.ML : distance between outer edges of tentorial pits / median height of clypeus.CT (post-ocellar line index): shortest distance between posterior ocelli / posterior ocellus longest diameter.POL (oculo-ocellar line index): shortest distance between eye and posterior ocellus / posterior ocellus longest diameter.OOL : length of flagellomere 1 (annellus excluded) / length of flagellomere 2.Fl1\u20132th flagellomere): length / width of flagellomere 20. .Taking into account the taxonomic updates post Gauld and Mitchell\u2019s revision, including the present one, we acknowledge here a total of 194 species of hioninae . A few ihioninae . Finallyhttp://www.waspweb.org.The matrix includes these 194 species and their known intra-specific variability. Furthermore, the dichotomous key provided in Taxon classificationAnimaliaHymenopteraIchneumonidaeRousse & van Noortsp. n.http://zoobank.org/8C1C347B-4AD0-4FB2-A126-242C3FEA947C(verbatim label data). HOLOTYPE \u2640: SOUTH AFRICA, W. Cape, West Coast Fossil Park, (5.5 km 270\u00b0 W Langebaanweg) 32\u00b057.759'S, 18\u00b005.519'E, 9\u201316 Oct 2002, S. van Noort, Malaise trap LW02-R4-M96, Rehabilitated slimes dam, SAM-HYM-P049469 (SAMC).Orange with inter-ocellar area, most of mesosoma and apex of metasoma black; mandible not twisted, with a central tuft of hairs; clypeus wide, long and flat in profile; antenna short and stout with 56 flagellomeres; mesosoma laterally coarsely punctate to rugose-punctate, dorsally densely and more finely punctate; mesoscutum with notaulus distinct and relatively long; mesopleuron with epicnemial carina not distinct above lower corner of pronotum; propodeum anteriorly densely punctate, posteriorly coarsely rugose-reticulate; disco-submarginal cell with fenestra developed but without distinct sclerite; fore tibia with dense and long spines on outer surface; fore tibial spur with a vestigial basal membrane.Dicamptus species in the world by the absence of distinct sclerites in the disco-submarginal cell; in the Afrotropical region, it seems related to Dicamptusneavei Gauld & Mitchell, 1978, which shares the dense spines on the tibia, the exceptionally reduced ocelli and a somewhat similar colour pattern; Dicamptusneavi is, however, a tropical species with shorter antennae, a stouter metasoma, and distinctly different alar indices with a distinct proximal sclerite in the disco-submarginal cell. In Gauld and Mitchell\u2019s key . B 20.8; F 11.5; ML 1.2; CT 1.2; OOL 2.0; POL 1.2; FI 20%; FColor. Orange interspersed with black; black: inter-ocellar area, entire mesosoma except for mesonotum and metanotum, base of tergite 1, tergite 5 and following, all coxae and trochanters except trochantelli; antenna orange, slightly darkening toward apex; wings hyaline, venation dark reddish to black except for pterostigma anteriorly light reddish.Head. Mandible short and stout, without longitudinal groove, with a central tuft of long hairs, upper tooth barely longer than lower tooth; malar line long; clypeus long and wide, coarsely and densely punctate, rather flat in profile, somewhat swollen medially and ventrally, ventral margin strongly impressed; face strongly transverse, densely and coarsely punctate; frons rather smooth, upper head densely punctate; gena moderately swollen behind eyes; occipital carina complete and strong; antenna short and stout with 56 flagellomeres.PageBreakMesosoma. Pronotum, mesopleuron and metapleuron coarsely and densely punctate, fading to rugose-punctate ventrally; anterior margin of pronotum simple; epicnemial carina short, indistinct above lower corner of pronotum; posterior transverse carina of mesosternum complete though ventrally weak; submetapleural carina not expanded anteriorly; mesoscutum densely and more finely punctate; notaulus long, moderate, distinct to anterior third of mesoscutum; scutellum densely punctate, carinate almost to apex; propodeum with anterior area densely punctate, anterior transverse carina complete, posterior area coarsely rugose-reticulate, abruptly declivous in profile and mid-posteriorly concave. Wings. Disco-submarginal cell with fenestra developed, without any distinct sclerite except a weak quadra centrally; Rs+2r hardly sinuate, slightly bent and thickened near pterostigma; Rs&M distal to cu-a by about its own width; hind wing with 7 hamuli. Legs. Fore tibia with dense and long spines on outer surface; fore tibial spur with a vestigial membrane basally to macrotrichial comb, membrane barely less than 0.1\u00d7 length of spur; hind coxa in profile 1.8\u00d7 as long as high; hind trochantellus mid-dorsally 0.2\u00d7 as long as wide; hind tarsal claws symmetrical with 8 pectinae.Metasoma. Slender; tergite 2 in profile 2.7\u00d7 longer than high; thyridium large, oval, separated from anterior margin of tergite 2 by 1.3\u00d7 its own length; ovipositor not reaching beyond metasomal apex.MALE. Unknown.Named after the unusually reduced ocelli, and as a result the large POL. Noun in apposition.South Africa (Western Cape).Taxon classificationAnimaliaHymenopteraIchneumonidaeRousse & van Noortsp. n.http://zoobank.org/5F861712-DBF0-41CC-9854-00DEB2913E86(verbatim label data).HOLOTYPE \u2640: Tanzania, Mkomazi Game Reserve, Ibaya Camp, 3.58S 37.48E, 18 April 1996, light trap, S. van Noort, open Combretum bushland, SAM-HYM-P015183 (SAMC).PageBreakYellow orange overall, head paler yellow; mandible with upper tooth distinctly longer than lower tooth; clypeus hardly convex in profile, its ventral margin barely concave and in-turned; occipital carinae complete; gena moderately swollen behind eye; ocelli moderately enlarged; antenna with 56 flagellomeres; pronotum unspecialized; mesopleuron and metapleuron closely and deeply punctate; epicnemial carina laterally indistinct; posterior transverse carina of mesosternum complete and noticeably strong; submetapleural carina slightly broadened anteriorly; notaulus vestigial; propodeum basally punctate, posteriorly coarsely and concentrically striate; fore wing without any sclerite in disco-submarginal cell; fore tibia with dense spines on outer surface; thyridium very shallow.Enicospilus in Afrotropical, Oriental and Australasian regions by the combination of the absence of alar sclerites and the dense spines on fore tibia. The swollen genae and the wing venation make it somewhat related to Enicospilusleucocotis, but this latter is strongly larger, with only sparse spines on tibia and slenderer antenna. In Gauld and Mitchell\u2019s key . B 18.8; F 11.5; ML 0.3; CT 1.6; OOL 0.1; POL 0.4; FI 50%; FColor. Yellowish orange overall with face and orbits paler yellow and apex of metasoma slightly infuscate.Head. Mandible basally constricted, apically parallel-sided and slightly twisted, with upper tooth distinctly longer than lower tooth (greatly worn by abrasion in holotype); outer mandibular surface sparsely setose, without longitudinal groove; labrum 0.3\u00d7 as long as wide; clypeus in profile hardly convex, its ventral margin barely concave and in-turned; clypeus and face finely and moderately densely punctate; gena moderately swollen behind eye; occipital carina complete; ocelli slightly enlarged; antenna with 56 flagellomeres.PageBreakMesosoma. Pronotum mid-dorsally long, anterior margin simple; mesoscutum densely punctate, notaulus vestigial; scuto-scutellar groove smooth; scutellum densely and shallowly punctate, barely longer than basally wide, carinate to near its apex; mesopleuron and metapleuron closely and deeply punctate, punctures arranged longitudinally but without distinct striation; epicnemial carina short, indistinct above lower corner of pronotum; submetapleural carina weakly broadened anteriorly; posterior transverse carina of mesosternum complete and strong; propodeum with anterior area finely, shallowly and densely punctate, anterior transverse carina complete, posterior area coarsely and concentrically striate Wings. Disco-submarginal cell with fenestra developed, without any distinct sclerite; Rs+2r sinuate; cu-a basal to Rs&M by 0.3\u00d7 cu-a length; hind wing with 6 hamuli and 1A basally straight. Legs. Fore tibia with numerous dense and long spines on outer surface, basally separated by far less than their own length; hind coxa elongate, in profile 2.4\u00d7 as long as high; hind trochantellus mid-dorsally 0.2\u00d7 as long as wide, its apical margin simple; hind tarsal claws symmetrical with 8 pectinae, pectinae long and acute.Metasoma. Slender; tergite 2 in profile 3.2\u00d7 longer than high; thyridium very shallow, elongate, separated from anterior margin of tergite 2 by 1.7\u00d7 its own length; ovipositor acute not reaching beyond metasomal apex.PageBreakMALE. Unknown.Enicospilusleucocotis. Let give Gauld what belongs to Gauld (updated after Mark 12:17).This species was probably mentioned in Tanzania.http://isodp.hof-university.de/fuzzyg/query/ and Google Earth http://www.google.com/earth/Provided are the verbatim label data. Only unambiguous identifications are listed. All geographical coordinates are also available on a separate file as Suppl. material Dicamptuspulchellus . The Gambia: 1\u2640 Kombo Nth district, Bilijo Forest Park, xi.1992, M. S\u00f6derlung coll., SAM-HYM-P049471 (SAMC).Euryophionlatipennis . South Africa: 1\u2640 Kwazulu-Natal, Itala Game Reserve, xii.1992, S. van Noort coll., SAM-HYM-P044187 (SAMC); 1\u2640 1\u2642 same label data except: xii.1999, SAM-HYM-P044163 and SAM-HYM-P044185 (SAMC); Zambia: 1 specimen [apex of metasoma lacking] Southern Province, Choma Nansa farm xii.1993, A.J. Gardiner coll., SAM-HYM-P044072 (SAMC).Laticoleuspalpalis Gauld & Mitchell, 1978. Kenya: 1\u2640 Eastern Province, Kenplains, x.1984, C.F. Dewhurst coll. (BMNH).Laticoleusunicolor . Botswana: 1\u2640 Xugana , xi.1979, B.H. Lamoral coll., SAM-HYM-P049474 (SAMC).Lepiscelusdistans . South Africa: 1\u2640 Kwazulu-Natal, Itala Game Reserve, xii.1999, S. van Noort coll, SAM-HYM-P044186 (SAMC); 1\u2640 Limpopo, junction Crocodile and Marico Rivers, ii.1918, R. Tucker coll., SAM-HYM-P006194 (SAMC); 2\u2642\u2642 Mpumalanga, Nelspruit, i.1939, R.F. Lawrence coll., SAM-HYM-P006193 (SAMC); Zimbabwe: 1\u2642 Essexvale, ii.1963, SAM-HYM-P006228 (SAMC).Skiapuscoalescens . The Gambia: 1\u2640 Kombo Nth district, Bilijo Forest Park, xi.1992, M. S\u00f6derlung coll., SAM-HYM-P049477 (SAMC).Enicospilusalbiger . Zambia: 1\u2642 South Luangwa near. Mfuwe, xii.2011, A. Gumovsky coll., SAM-HYM-P049484 (SAMC).Enicospilusbabaulti . Malawi: 1\u2640 Nyika National Park, Juniper forest, ix.1999, R.J. Murphy coll., SAM-HYM-P021341 (SAMC); South Africa: 1 specimen [metasoma lacking] ii.1917, C.J. Swierstra coll., SAM-HYM-P001398 (SAMC); Zimbabwe: 1\u2640 Chirinda forest, xi.1955, SAM-HYM-P006247 (SAMC).Enicospilusbebelus Gauld & Mitchell, 1978. Gabon: 1\u2640 Province Ogoov\u00e9\u2013Maritime, R\u00e9serve des Monts Doudou, iii.2000, S. van Noort coll., SAM-HYM-P041707 (SAMC).PageBreakEnicospilusbetanimenus . Ethiopia: 2\u2640\u2640 Adola, xi.1941, SAM-HYM-P047374 and SAM-HYM-P006253 (SAMC); Zimbabwe: 2\u2640\u2640 Bulawayo ii.1971, D.K.B. Wheeler coll, SAM-HYM-P006286 (SAMC).Enicospilusbicoloratus Cameron, 1912. Zimbabwe: 1\u2640 Matopos, ii.1963, SAM-HYM-P006265 (SAMC).Enicospiluscamerunensis . Mayotte: 1\u2640 Demb\u00e9ni, iii.2013, G. Cazenove coll. (MHNR).Enicospilusdivisus . Uganda: 1\u2642 Kibale National Park, Kanyawara, viii.2008, S.van Noort coll., SAM-HYM-P049506 (SAMC).Enicospilusdrakensbergi Gauld & Mitchell, 1978. Tanzania: 1\u2642 South Pare Mountains, alt. c. 1700m, xi.1995, S. van Noort coll., SAM-HYM-P014698 (SAMC).Enicospilusequatus Gauld & Mitchell, 1978. Central African Republic: 2\u2640\u2640 1\u2642 Pr\u00e9fecture Sangha-Mba\u00e9r\u00e9, R\u00e9serve Sp\u00e9ciale de For\u00eat Dense de Dzanga-Sangha, v.2001, S. van Noort coll., SAM-HYM-P049510\u2013P049512 (SAMC).Enicospilusfinalis Gauld & Mitchell, 1978. Central African Republic: 5\u2640\u2640 Pr\u00e9fecture Sangha-Mba\u00e9r\u00e9, Parc National de Dzanga-Ndoki, v.2001, S. van Noort coll., SAM-HYM-P049514 \u2013P049517 (SAMC); Mozambique: 1 specimen [apex of metasoma broken] Mt Gorongoza, ix.1957, SAM-HYM-P006229 (SAMC).Enicospilusoculator Seyrig, 1935. Zimbabwe 1\u2640 Tuli, v.1959, SAM-HYM-P006232 (SAMC).Enicospilushova Gauld & Mitchell, 1978. Uganda: 1\u2642 Kibale National Park, Kanyawara, viii.2008, S.van Noort coll., SAM-HYM-P049513 (SAMC).Enicospilusluebberti . 4\u2640\u2640 Botswana: 1\u2640 Xugana , xi.1979, B.H. Lamoral coll. (NMSA).Enicospilusmamatsus Gauld & Mitchell, 1978. South Africa: 1\u2640 Northern Cape, Sterboom farm, 1599 m, v\u2013vii 2010, S. van Noort, SAM-HYM-P054077 (SAMC).Enicospilusmnous Gauld & Mitchell, 1978. Tanzania: 3\u2640\u2640, Mkomazi Game Reserve, xi.1995, H.G. Robertson coll. and S. van Noort colls, SAM-HYM-P014159, SAM-HYM-P014161 and SAM-HYM-P014170 (SAMC); 2\u2640\u2640 same label data except: iv.1996, S. van Noort coll., SAM-HYM-P014156 and SAM-HYM-P014706 (SAMC).Enicospilusnesius Gauld & Mitchell, 1978. Central African Republic: 1\u2640 Pr\u00e9fecture Sangha-Mba\u00e9r\u00e9, Parc National de Dzanga-Ndoki, v.2001, S. van Noort coll., SAM-HYM-P054079 (SAMC).Enicospiluspallidus . Tanzania: 8\u2640\u2640, Mkomazi Game Reserve, xi\u2013xii.1995 and iv.1996, S. van Noort coll., SAM-HYM-P014157\u2013P0141578, SAM-HYM-P014171\u2013P014175 and SAM-HYM-P015200 (SAMC).Enicospiluspolemus Gauld, 1982. South Africa: 1\u2640 Kwazulu-Natal, Itala Game Reserve, xii.1999, S. van Noort coll., SAM-HYM-P044207 (SAMC); Tanzania: 1\u2640 Mkomazi Game Reserve, iv\u2013v.1996, S. van Noort coll., SAM-HYM-P015666 (SAMC).PageBreakEnicospilusquietus . Namibia: 1\u2640 Namib-Naukluft Park, x.1997, S. van Noort coll., SAM-HYM-P020721 (SAMC); 1\u2642 Otavi, xii.1918, R.M. Lightfoot coll., SAM-HYM-P006278 (SAMC); 1\u2640 Ondangua Ovamboland, 1921, K.H. Bernard coll., SAM-HYM-P006199 (SAMC); 2 specimens [metasomas lacking] Otjiperongo, i.1931, J.S. Brown coll., SAM-HYM-P047375 (SAMC).Enicospilusrubens . Madagascar: 1\u2640 Majunga Province, Maintirano District, iii.2008, M.Irwin and R.Harin\u2019Hala colls, MG-44-26 (CASC).Enicospilusrundiensis Bischoff, 1915. Namibia: 1\u2640 1\u2642 Kaross, 1925, SAM-HYM-P001381 (SAMC); 1\u2640 Warmbad, 1925, SAM-HYM-P001382 (SAMC); 1 specimen [apex of metasoma broken] Narubis, 1921, K.H. Barnard coll., SAM-HYM-P006277 (SAMC); 1 specimen [metasoma lacking] Otjiperongo, i.1931 J.S. Brown coll., SAM-HYM-P006276 (SAMC); Zimbabwe: 1\u2640 Harare, vi.1961, SAM-HYM-P006225 (SAMC).Enicospilusruscus Gauld & Mitchell, 1978. Kenya: 1\u2642 Nguruman, vii.2008, S. van Noort coll., SAM-HYM-P054106 (SAMC).Enicospilusbetanimenus . 2\u2640\u2640 from Zimbabwe SAM-HYM-P006286 (SAMC) ex Achaeacatella Guen\u00e9e, 1852 (Lepidoptera: Noctuidae).Enicospilusdubius . 2\u2640\u2640 from South Africa (SAMC SAM-HYM-P001508) ex Ctenoplusialimbirina (Guen\u00e9e) (Lepidoptera: Noctuidae).Enicospilusdolosus . 1\u2640 from Reunion ex Anomisflava (Fabricius) (Lepidoptera: Noctuidae).Enicospilusleucocotis . 2\u2640\u2640 from South Africa (SAMC SAM-HYM-P046967 and SAM-HYM-P046968) ex Mesocelismontana (H\u00fcbner) (Lepidoptera: Lasiocampidae).Enicospilusmauritii . 1\u2642 from Reunion ex Callopistriamaillardimaillardi (Guen\u00e9e) (Lepidoptera: Noctuidae) feeding on Dryopterisbernieri (Pteridophyta: Dryopteridaceae) (idaceae) .Enicospilusluebberti . 1\u2642 from South Africa (SAMC SAM-HYM-P006196) ex Graphaniaatavistis (Hampson) (Lepidoptera: Noctuidae).Enicospilusbebelus Gauld & Mitchell, 1978. 1\u2642 from Central African Republic (SAMC SAM-HYM-P049492) and 1\u2640 from Gabon (SAMC SAM-HYM-P041707) with mesosoma interspersed with dark testaceous and black markings, and tergite 1 basally black; otherwise similar to original description.Enicospilusoculator Seyrig, 1935. 1\u2640 from Zimbabwe (SAMC SAM-HYM-P006232) with central sclerite totally absent, upper tooth twice as long as lower tooth, and numeric indices slightly different: FI 80%, AI 1.0, fore wing length 14 mm. Otherwise similar to PageBreakEnicospilusgrandiflavus Townes, 1973. 1\u2640 from South Africa (SAMC SAM-HYM-P049521) with entire head strongly darkened, nearly black. Otherwise similar to Enicospilusexpeditus . 1\u2640 1\u2642 from South Africa (SAMC SAM-HYM-P054068) with hind tarsal claws less pectinate than figured in Enicospilusluebberti . Numerous specimens from South Africa , Bostwana (NMSA), and Kenya (BMNH) showed the following non-correlated variations: inter-ocellar area and metasomal apex yellowish-orange to totally black, antenna with 48\u201362 flagellomeres, longitudinal groove on mandible more or less impressed, proximal sclerite more or less elongate and central sclerite variously sclerotized. These variations encompass the definition of Enicospilusbatus Gauld & Mitchell, 1978, syn. n., described on a single specimen, which is hereby recognized as a junior synonym of Enicospilusluebberti."} +{"text": "Allergic rhinitis with/without conjunctivitis (AR/C) sufferers often rely on pharmacotherapy to relieve symptoms. Although the main goal of immunotherapy is long-term disease modification, reducing or eliminating the need for pharmacotherapy is also an important and desirable treatment goal.Ambrosia artemisiifolia; Merck/ALK-Abell\u00f3). Subjects with ragweed-pollen\u2013induced AR/C were randomized ~16 weeks before the 2010 pollen season to once-daily MK-3641 or placebo. During the trial, all subjects, whether taking MK-3641 or placebo, could use AR/C rescue medication, including oral/ocular antihistamines and intranasal/oral corticosteroids. We examined rescue medication use in all groups.Data were pooled from two trials that evaluated the efficacy and safety of short-ragweed sublingual immunotherapy tablet (SLIT-T), MK-3641 subjects receiving MK-3641 12 Amb a 1-U and 144 of 324 (44.4%) subjects receiving 6 Amb a 1-U used no rescue medication over the entire ragweed season, compared with 109 of 340 (32.1%) subjects receiving placebo. These differences represented 56% and 38% improvements over placebo. Similarly, during the peak ragweed season 173 of 311 (55.6%) subjects and 161 of 317 (50.8%) subjects in the 12 Amb a 1-U and 6 Amb 1-U groups, respectively, reported no rescue medication use, in contrast to 136 of 333 (40.8%) subjects receiving placebo. Fewer subjects taking 12 and 6 Amb a 1-U used oral antihistamine than those taking placebo; 35% and 28% fewer subjects used ocular antihistamine; and 43% and 27% fewer subjects used intranasal corticosteroid .Compared with placebo, the SLIT-T treatment MK-3641 reduced rescue-medication use among subjects with ragweed-pollen\u2013induced AR/C.ClinicalTrials.gov Identifiers: NCT00783198; NCT00770315"} +{"text": "Mevalonate kinase deficiency (MKD) is a rare autoinflammatory, autosomal-recessive defect on MVK gene. Clinical spectrum ranges from recurring febrile attacks to malformations and neurologic disorders. Gastrointestinal symptoms are cardinal. Severe gastrointestinal involvement has been described at the onset.To analyse severe gastrointestinal events (SGE) complicating MKD.Retrospective observational French cohort of MKD patients. SGE were defined as complicated inflammatory involvement, requiring an abdominal surgery and/or enteral/parenteral nutrition. Data were collected from clinical charts provided by the members of the Francophone Society for Paediatric Rheumatism and Inflammatory Diseases (SOFREMIP).25=13.7; P75=55.5); median MK activity: 2.2% . The significant co-morbidities found in SGE patients in comparison with the global cohort were: failure-to-thrive in 85.7% (6/7), pulmonary diseases in 37.5% (3/8) and feeding disorders in 28.6% (2/7) (p<0.05).From a 53-patient cohort, nine presented a SGE (17%). From these, disease onset median age was 1.0 months (0-12); one patient deceased (22 months) from a non-gastrointestinal event. Compound heterozygote mutations were found in 7/8, being Val377Ile the commonest (6/8). The main symptoms during febrile attacks were: diarrhoea , lymphadenopathy , skin lesions, joint pain , aphtous ulcers, abdominal pain , splenomegaly , hepatomegaly and vomiting . Median mevalonic aciduria: 23.05 mmol/mol of creatinine , representing 43% (3/7) of patients with severe gastrointestinal disease: abdominal adhesions and colitis/enterocolitis were mainly found. 87.5% (7/8) needed surgery and 44.4% (4/9) required enteral/parenteral nutrition. Despite digestive resection, disease progression remained; two patients needed re-intervention due to surgical complications. Aphtous/ulcerative damage was the main endoscopic feature . The most consistent microscopic finding was lymphocytic infiltrates. IL-1 antagonists were the most used/effective treatment (4/9), resulting in with complete remission in all three patients with data available.MKD severe gastrointestinal involvement presentation has a non-negligible frequency. It usually appears as an aphtous/ulcerative disease involving any part of the digestive tract or as abdominal adhesions, frequently requiring surgery. The treatment with IL-1 antagonists resulted in complete remission in a majority of treated patients. Thus, MKD should be added to the list of monogenic early-onset inflammatory bowel disease."} +{"text": "Lactobacillus brevis BSO 464 was sequenced and assembly produced a chromosome and eight plasmids. This bacterium tolerates dissolved CO2/pressure and can rapidly spoil packaged beer. This genome is useful for analyzing the genetics associated with beer spoilage by lactic acid bacteria.The genome of brewery-isolate Lactobacillus brevis BSO 464 can resist the headspace pressure and dissolved CO2 in packaged beer, making it a virulent beer-spoiler (\u2013Brewery isolate -spoiler \u20133. Lb464De Novo assembler v2.5.3. Hawkeye (xl platform).Sequencing was performed using the Roche 454 FLX platform at the National Research Council Plant Biotechnology Institute . Two separate runs yielded 330,771 unpaired and 567,735 paired reads for ~30\u00d7 coverage. Reads were assembled using Newbler GS L.\u00a0brevis KB290 with nine plasmids .The Lb464 genome was assembled into a 2,503,991-bp circular chromosome (G+C content 45.7%) that had 8,461\u00a0bp cumulative of gaps due to transposase or repetitive regions not allowing PCR-based sequencing. Additionally, eight plasmids were assembled (G+C content ranged from 39.1% to 42.4%): pLb464-1 , pLb464-2 , pLb464-3 , pLb464-4 , pLb464-5 , pLb464-6 (5018 bp), Lb464-7 (2353 bp), and pLb464-8 (Pediococcus claussenii (hitA (horA (horC (Lb464 genome annotation by the NCBI PGAP pathway producedaussenii , notablyii (hitA , horA (1tA (horA , and horrA (horC on pLb46rA (horC . Based oLactobacillus brevis BSO 464 were deposited in GenBank under accession numbers CP005977, CP005978, CP005979, CP005980, CP005981, CP005982, CP005983, CP005984, and CP005985 for the chromosome and plasmids pLb464-1 to pLb464-8, respectively.The sequences for"} +{"text": "NLRP3-gene encoding cryopyrin, leading to overproduction of IL-1\u03b2 and other NLRP3 inflammasome products. Myeloid-derived suppressor cells (MDSCs) represent a novel innate immune cell subset, are generated in tumor, infective, and proinflammatory microenvironments and are capable of suppressing T cell responses. Consequently, MDSCs are considered a key intermediary in balancing innate and adaptive immune responses, particularly under chronic disease conditions.Muckle-Wells syndrome (MWS) is caused by mutations in the We hypothesized that NLRP3 inflammasome-dependent factors induce the generation of MDSCs in MWS.highCD66bhighIL-4RainterHLA-DRlow neutrophilic cells in the PBMC fraction, according to previously established human MDSC analysis methods. The functionality of MACS-isolated MDSCs was assessed using polyclonal T cell proliferation and cytokine/chemokine secretion tests. Physician's global assessment of disease activity, CRP, ESR, and T helper cell subsets were determined at the same time points and correlated with MDSC levels. Serum samples of 22 MWS patients and 5 healthy controls were examined by multiplex technique for possible MDSC inducing factors.We studied granulocytic MDSC numbers in 25 MWS patients under anti-IL-1 therapy with canakinumab and 20 healthy controls. After Ficoll density gradient sedimentation, granulocytic MDSCs were characterized as CD33p = 0.0025), although clinical MWS-disease activity was generally low at time of examination. MDSCs were functionally competent, as they suppressed polyclonal T cell proliferation, Th1, Th2, and Th17 responses. MDSCs correlated directly with Treg/Th17 and Treg/Th1 ratios indicating an influence on T helper cell subsets. Multiplex assays revealed the established MDSC-inducing growth factors GM-CSF and VEGF elevated in MWS sera even under anti-IL-1 therapy with canakinumab.MWS patients under anti-IL-1 therapy displayed significantly elevated MDSC numbers compared to healthy controls (mean 0.45 \u00b1 0.05%; range 0.12 - 1.04%; MWS patients under anti-IL-1 therapy display significantly elevated numbers of granulocytic MDSCs. Increased MDSCs in MWS might represent a novel autologous anti-inflammatory mechanism in autoinflammatory conditions and may serve as a future therapeutic target.N. Rieber Grant/Research Support from: NR, JKD, and DH obtained research grants from Novartis GmbH, Consultant for: NR and JKD took part in advisory boards for Novartis GmbH, A. Brand: None Declared, D. Neri: None Declared, T. Hall: None Declared, I. Sch\u00e4fer: None Declared, S. Hansmann: None Declared, J. K\u00fcmmerle-Deschner: None Declared, D. Hartl: None Declared."} +{"text": "Pale-pink euhedral cobaltoan dolomite was associated with kolwezite [(Cu1.33Co0.67)(CO3)(OH)2] and cobaltoan malachite [2(CO3)(OH)2]. A crystal with a Co:Mg ratio of 1:5.6 (SEM/EDAX measurement), twinned on (11 -2 0) was used for crystal structural refinement. The refinement of the structural model of Reeder & Wenk showed that Co is totally incorporated in the Mg site, with refined occupancy Mg0.83Co0.17, which compares with Mg0.85Co0.15 from chemical data. The Co substitution reflects in the expansion of the cell volume, with a pronounced increasing of the c cell parameter. A structural study has been undertaken on a cobaltoan dolomite, with chemical formula CaMgral. 1983, 68, 769 DOI: 10.1107/S2056989015003126/br2247Isup2.hklStructure factors: contains datablock(s) I. DOI: Click here for additional data file.10.1107/S2056989015003126/br2247fig1.tif. DOI: Micro photograph of the cobaltoan dolomite specimen, where pale pink cobaltoan dolomite is associated with pale green cobaltoan malachite.Click here for additional data file.10.1107/S2056989015003126/br2247fig2.tifx . DOI: x Cartesian rotation axis. Ca-centered octa\u00adhedra are cyan, whereas Mg-centered octa\u00adhedra are yellow; carbon and oxygen atoms are represented as green and red spheres, respectively.The crystal structure of cobaltoan dolomite, in a projection along [100], slightly tilted by 5\u00b0 about along the Click here for additional data file.10.1107/S2056989015003126/br2247fig3.tif. DOI: Coordination polyhedra in cobaltoan dolomite. Displacement ellipsoids are drawn at the 50% probability.1049359CCDC reference: crystallographic information; 3D view; checkCIF reportAdditional supporting information:"} +{"text": "Aeromonas hydrophila-like arabinose-negative isolates from diverse sources sampled in Valencia (Spain) during 2004\u20132005, were characterized by 16S rRNA gene sequencing and extensive biochemical testing along with reference strains of most Aeromonas species. These isolates and all reference strains of A. hydrophila subsp. dhakensis and A. aquariorum showed a 16S rRNA sequence similarity of 99.8\u2013100%, and they all shared an identical phenotype. This matched exactly with that of A. hydrophila subsp. dhakensis since all strains displayed positive responses to the Voges-Prokauer test and to the use of dl-lactate. This is the first report of A. hydrophila subsp. dhakensis recovered from environmental samples, and further, from its original isolation in India during 1993\u20131994. This was accurately identified and segregated from other clinical aeromonads by using biochemical key tests. The API 20 E profile for all strains included in A. hydrophila subsp. dhakensis was 7047125. The prevalence of this species in Spanish sources was higher for water (9.4%) than for feces (6%) or eels (1.3%). Isolates recovered as pure cultures from diseased eels were moderately virulent (LD50 of 3.3\u00d7106 CFU fish\u22121) to challenged eels in experimental trials. They were all resistant to ticarcillin, amoxicillin-clavuranic acid, cefoxitin, and imipenem, regardless of its source. Our data point to A. hydrophila subsp. dhakensis as an emerging pathogen for humans and fish in temperate countries.Eight Aeromonas (family Aeromonadaceae) is ubiquitous in aquatic ecosystems that include chlorinated drinking water, raw sewage, and natural waters and free-living fish in such habitats during 1993\u20131994 , A. hydrophila subsp. dhakensis exhibits high divergence from A. hydrophila subsp. hydrophila and A. hydrophila subsp. ranae but 78 to 84% in the case of A. hydrophila subsp. dhakensis in November 2004 ; and stry others .A. hydrophila subsp. dhakensis CECT5743, A. hydrophila subsp. dhakensis CECT5745, A. aquariorum MDC310, and A. aquariorum MDC317 was obtained by the Colecci\u00f3n Espa\u00f1ola de Cultivos Tipo (CECT) service . Bacterial genomic DNAs were extracted according to a method described previously (Escherichia coli numbering]) (Escherichia coli numbering) (2 (100 mM), 1.0 \u03bcL dNTPs (10 mM each), 1.0 \u03bcL each forward and reverse primers (50 \u03bcM), 0.5 \u03bcL Taq polymerase and 5.0 \u03bcL template DNA (50 ng \u03bcL\u22121) in a total volume of 50 \u03bcL. PCR amplifications of the DNA templates were performed using a PTC-100 ThermoCycler (MJ Research). The conditions for 16S rRNA gene amplification were (i) 4 min at 94\u00b0C; (ii) 30 cycles of 1 min at 94\u00b0C, 1 min 30 s at 52\u00b0C and 2 min at 72\u00b0C; and (iii) a final elongation step of 10 min at 72\u00b0C. Amplified products were examined by agarose gel electrophoresis (1.2%) and ethidium bromide staining. Purified amplicons (Mo Bio Laboratories) were sequenced by the dideoxy method using the BigDye Terminator v. 3.0 Ready Reaction cycle sequencing kit and analyzed in an ABI PRISM 3730 sequencer (Applied Biosystems). Sequencing primers were the same as those used in the amplification reaction but diluted tenfold (5 pmol).The almost complete 16S rRNA gene sequence of strains ABF132, ABF144, ABF145, MA17, MA26, MA131, 133.341, 133.343, CECT4588, eviously . UniversAeromonas , A. aquariorum , A. hydrophila subsp. hydrophila (CECT839T), A. veronii bv. veronii (CECT4257T), A. veronii bv. sobria (CECT4835), A. sobria (CECT4245T), A. jandaei (CECT4228T), A. popoffii (CECT4995), A. bestiarum (CECT4227T), A. allosaccharophila (CECT4199T), A. eucrenophila (CECT4224T), A. encheleia (CECT4342T), A. trota (CECT4255T), A. enteropelogenes (CECT4487T), A. caviae (CECT838T), A. media (CECT4232T), A. schubertii (CECT4240T), and A. diversa (CECT4254T) were examined in 45 tests described by us as valuable traits for identifying Aeromonas were used in all isolates in order to know their API 20 E code.Minimal inhibitory concentrations (MICs) of kanamycin (K), tetracycline (TET), nalidixic (NA), oxolinic (OA) acid, flumequine (UB), erythromycin (ERY), rifampicin (RD) and chloramphenicol (CHL) were determined by the microbroth dilution method . In addi8, 107, 106, 105, 104, 103, 102, 101 CFU mL\u22121), or with 0.1 mL PBS (controls). Each set of six eels was kept in a 20 L aquarium under the following conditions: i) dechlorinated tap water, ii) water temperature around 20\u00b0C, iii) oxygen concentration in water was above 90% saturation, and iv) fish were not fed. Mortality was recorded daily for 10 days and was only considered if the challenged bacterium was recovered as pure culture from the internal organs.For the challenge experiment, six young eels of around 10\u201320 g were challenged by intraperitoneal injection with each of the bacterial doses , but that recovered from the ulcer was not was calculated , FJ230076 (A. sanarellii A2-67T), FJ230077 (A. taiwanensis A2-50T), AJ508765 (A. hydrophila subsp. dhakensis LMG 19562T), X60408 (A. caviae NCIMB 13016T), X60415 (A. trota ATCC 49657T), AJ508766 (A. hydrophila subsp. ranae LMG 19707T), X60410 (A. media ATCC 33907T), X60404 (A. hydrophila subsp. hydrophila ATCC 7966T), S39232 , X60412 (A. sobria NCIMB 12065T), FJ976900 (A. rivuli WB4.1-19T), X60417 (Aeromonas sp. ATCC 35941T), AJ224308 (A. popoffii LMG 317541T), X60411 (A. eucrenophila NCIMB 74T), AJ224309 (A. encheleia CECT 4342T), AY532690 (A. molluscorum 848T), X60406 (A. bestiarum CIP 7430T), AF134065 , X60405 , X60407 , AB027544 , X74680 , FM999971 (A. piscicola S1.2T), X60413 (A. jandaei ATCC 49568T), AF170914 (A. culicicola MTCC 3248T), FJ230078 , X60414 (A. veronii bv. veronii ATCC 35624T), AJ536821 (A. simiae IBS S6874T), X60416 (A. schubertii ATCC 43700T), GQ365710 (A. diversa CECT 4254T).EU085557 . These were compared with those of A. hydrophila subsp. dhakensis LMG 19562T and A. aquariorum MDC 47T and with those from other Aeromonas-type strains , in accordance with that reported solely for the type strain of these species , using both simple matching (SSM) (J) coefficients. Moreover, they were all clearly segregated from the other type strains of the Aeromonas species whose phenotypic profile was included in the numerical analysis ; \u03b2-haemolysis of sheep red blood cells; and acid production from d-fructose, d-galactose, maltose, d-mannitol, d-mannose, sucrose, and d-trehalose; however, they all were negative for: Gram staining; production of brown diffusible pigment; susceptibility to O/129 (150 \u03bcg) (Oxoid discs); growth with 6% (w/v) NaCl; hydrolysis of urea; and acid production from d-amygdalin, dulcitol, d-fucose, meso-inositol, melibiose, d-raffinose, d-sorbitol, and d-xylose.The ng (SSM) and Jaccanalysis . All str cluster showed tA. hydrophila subsp. dhakensis-A. aquariorum\u201d cluster exactly matched that described for A. hydrophila subsp. dhakensis and -positive simultaneously and positive for the utilization of dl-lactate , which was obtained from Aeromonas strains . Finally results and 2. T strains . In addi jandaei , using b jandaei .Aeromonas hydrophila subsp. dhakensis was previously isolated in India (Aeromonas-positive samples was 17 (53.1%) and 20 (26.7%), respectively, with 32 patients suffering from Aeromonas gastroenteritis. The overall prevalence of A. hydrophila subsp. dhakensis in these Aeromonas-positive specimens was of 8.7% (6/69), although it was higher for water (17.7%) than for feces (6.25%) or eels (5%). Thus, we have found a wider distribution of A. hydrophila subsp. dhakensis in Spain in comparison with its unique previous finding in association with patients but not with water or fish (Aeromonas in these waters ranged from (102 to 104 CFU mL\u22121) in winter to (104 to 107 CFU mL\u22121) in summer , or by contact with them were recovered from two siblings, a 1-year-old boy and a 6-year-old girl, who had acute gastroenteritis accompanied by bloody stools and high-grade (\u226539\u00b0C) fever and required antibiotic treatment. The fact that these clinical isolates were rather multi-resistant to antibiotics . Fortunaisolates , as alsoA. hydrophila subsp. dhakensis which have been recovered from a wild European eel suffering from hemorrhagic septicemia . The present results constitute the first report of A. hydrophila subsp. dhakensis from a temperate country, suggesting the worldwide distribution of this species.In summary, species"} +{"text": "HTLV-1 induces a persistent infection leading to an increased production of inflammatory cytokines. HIV, another retrovirus that causes systemic inflammation, is associated with atherosclerosis. However, few is known about HTLV-1-infection and atherosclerosis. To determine the prevalence and risk factors associated with atherosclerosis in patients infected with HTLV-1. a cross-sectional study involving 54 HTLV-1-infected patients (24 asymptomatic and 30 HAM/TSP), was carried out at the CHTLV between 2012 to 2013. Sociodemographic and cardiovascular risk factors were evaluated . Patients were submitted to Doppler echocardiography of both carotid and vertebral arteries to measure intimal-media layer. The association between intima-media thickness (IMT) and HAM/TSP diagnosis, HTLV-1 proviral load, low-density lipoprotrein cholesterol (LDL-c) or ultrasensitive C-reactive protein was determined. The mean age of patients was 57.1\u00b112.3 years, 72.2% were women. Clinical atherosclerosis (IMT\u22651.5mm) was found in nine patients (16.7%) and subclinical atherosclerosis (IMT>1 and <1.5) in 10 patients (18.5%). Atherosclerosis was more frequent in women (41%) compared with man (20%). Median age was significantly higher in patients with atherosclerosis . The mean of LDL-c level was 140.11\u00b143.25 mg/dl (ranging from 49 to 287mg/dl). No significant differences were observed between the mean LDL-c level in individuals with subclinical (126.10\u00b138.95mg/dl) and with atherosclerosis diagnosis (144.\u00b143.87mg/dl), compared with individuals with normal IMT (143.21\u00b144.65mg/dl), (p=0.4175). There was no correlation between HTLV-1 proviral load and IMT. No association was found between HTLV-1 infection and clinical or subclinical atherosclerosis as well as with the risk factors for cardiovascular diseases. A positive association between atherosclerosis and age was observed."} +{"text": "The LysE superfamily consists of transmembrane transport proteins that catalyze export of amino acids, lipids and heavy metal ions. Statistical means were used to show that it includes newly identified families including transporters specific for (1) tellurium, (2) iron/lead, (3) manganese, (4) calcium, (5) nickel/cobalt, (6) amino acids, and (7) peptidoglycolipids as well as (8) one family of transmembrane electron carriers. Internal repeats and conserved motifs were identified, and multiple alignments, phylogenetic trees and average hydropathy, amphipathicity and similarity plots provided evidence that all members of the superfamily derived from a single common 3-TMS precursor peptide via intragenic duplication. Their common origin implies that they share common structural, mechanistic and functional attributes. The transporters of this superfamily play important roles in ionic homeostasis, cell envelope assembly, and protection from excessive cytoplasmic heavy metal/metabolite concentrations. They thus influence the physiology and pathogenesis of numerous microbes, being potential targets of drug action. Rh. Rh20]. Using rigorous statistical criteria, we have expanded the LysE superfamily nearly four-fold. In addition to the LysE, RhtB and CadD families identified previously, this superfamily now includes the following families: NAAT, CaCA2, MntP, ILT, TerC, NicO, GAP and DsbD. Members of each of these families have been characterized and shown to play roles in transport of amino acids and resistance of heavy metal ions, along with cell surface maintenance. Most families include secondary carrier type transporters catalyzing heavy metal or amino acid efflux, but one family catalyzes amino acid uptake, another catalyzes heavy metal ion uptake, and a third catalyzes transmembrane electron transfer. GAP proteins have not been mechanistically characterized, but based on their inclusion in the LysE superfamily, we tentatively propose that GAP proteins operate as secondary carriers, where the energy source for lipid export is the proton motive force.Through sequence analyses, we were able to recognize a distinct pattern of homology. That is, LysE, RhtB, NAAT, CaCA2, MntP, ILT, TerC, NicO, GAP and DsbD proved to be homologous in 3 or more TMSs. The 3 TMSs that aligned are usually between the first 3 TMSs, the second 3 TMSs or both. This observation fits the predicted evolutionary pathway presented in According to the phylogenetic tree, amino acid exporter families RhtB and LysE branch close to each other, as suggested from previous studies . In contThis study suggests that members of the LysE Superfamily are involved in ionic homeostasis, protection from excessive cytoplasmic heavy metal/metabolite concentrations, cell envelope assembly and transmembrane electron flow. Many of the family members, however, are still poorly understood from functional and physiological standpoints. In continuing this project, genome context analyses will be conducted on members of each family. This will allow functional predictions, further promoting an understanding of the significance of these proteins. To date, no crystal structures exist for a member of this superfamily, and such studies will be crucial for understanding their mechanistic details. Thus, studies on the LysE superfamily remain in their infancy.S1 FigAlong with a step-wise description of the methods, the parameters for the programs used in major analyses are summarized.(TIF)Click here for additional data file.S2 Fig(A) LysE vs. RhtB. (B) RhtB vs. CadD. (C) LysE vs. CadD.(PDF)Click here for additional data file.S3 Fig(A) CadD vs. CaCA2. (B) LysE vs. CaCA2. (C) RhtB vs. CaCA2.(PDF)Click here for additional data file.S4 Fig(A) RhtB vs. MntP. (B) CadD vs. MntP. (C) CaCA2 vs. MntP.(PDF)Click here for additional data file.S5 Fig(A) CadD vs. ILT. (B) RhtB vs. ILT. (C) CaCA2 vs. ILT.(PDF)Click here for additional data file.S6 Fig(A) RhtB vs. TerC. (B) CadD vs. TerC. (C) LysE vs. TerC (D) MntP vs. TerC. (E) ILT vs. TerC. (F) CaCA2 vs. TerC.(PDF)Click here for additional data file.S7 Fig(A) LysE vs. NAAT. (B) RhtB vs. NAAT. (C) CadD vs. NAAT (D) MntP vs. NAAT. (E) TerC vs. NAAT.(PDF)Click here for additional data file.S8 Fig(A) RhtB vs. NicO. (B) CadD vs. NicO. (C) TerC vs. NicO (D) NAAT vs. NicO.(PDF)Click here for additional data file.S9 Fig(A) RhtB vs. GAP.(PDF)Click here for additional data file.S10 Fig(A) RhtB vs. DsbD. (B) CaCA2 vs. DsbD. (C) MntP vs. DsbD. (D) NAAT vs. DsbD. (E) GAP vs. DsbD.(PDF)Click here for additional data file.S11 Fig(A) LysE. (B) RhtB. (C) CadD. (D) CaCA2. (E) MntP. (F) NAAT. (G) NicO. (H) GAP. (I) DsbD. (J) ILT. (K) TerC.(PDF)Click here for additional data file.S12 FigGSAT comparisons between TMS#1\u20133 and TMS#4\u20136 for three CaCA2 homologues with assigned UniProt accession numbers. (A) Q2JWH3. (B) I7M883. (C) K4DX00.(PDF)Click here for additional data file.S13 FigGSAT comparisons between TMS#1\u20133 and TMS#4\u20136 for three ILT homologues with assigned UniProt accession numbers. (A) Q8YX33. (B) K9Q6B8. (C) J2KV33.(PDF)Click here for additional data file.S14 FigGSAT comparisons between TMS#1\u20133 and TMS#4\u20136 for three MntP homologues with assigned UniProt accession numbers. (A) A8SU47. (B) R9SLI6. (C) C6JCY1.(PDF)Click here for additional data file.S15 FigGSAT comparisons between TMS#1\u20133 and TMS#4\u20136 for three TerC homologues with assigned UniProt accession numbers. (A) A4IKQ1. (B) G8M4S7. (C) R9LI44.(PDF)Click here for additional data file.S16 Fig(A) LysE. (B) RhtB. (C) CadD. (D) CaCA2. (E) MntP. (F) ILT. (G) TerC. (H) NAAT. (I) NicO. (J) GAP. (K) DsbD.(PDF)Click here for additional data file.S17 Fig-20 by BLAST (Using UniProt) for each query sequence to improve the accuracy of aligning a small number of distantly related sequences. The bootstrap values are shown in blue text and located near each node.The Mafft-homologs function was set to retrieve 200 homologs at a threshold E-value of 1e(TIF)Click here for additional data file.S18 Fig(PDF)Click here for additional data file.S19 Fig(PDF)Click here for additional data file.S20 Fig(PDF)Click here for additional data file.S21 Fig(PDF)Click here for additional data file.S22 Fig(PDF)Click here for additional data file.S23 Fig(PDF)Click here for additional data file.S24 Fig(PDF)Click here for additional data file.S25 Fig(PDF)Click here for additional data file.S26 Fig(PDF)Click here for additional data file.S27 Fig(PDF)Click here for additional data file.S28 Fig(PDF)Click here for additional data file.S29 FigThe tree was generated using the SuperFamilyTree program and viewed using FigTree. It depicts the evolutionary relationship between the 11 different families in this study. Clustering indicates closer phylogenetic relationships. The tree is based on tens of thousands of BLAST bit scores generated with the SFT1 program where every protein was compared with every other protein included in the analysis. The SFT2 program was used to integrate all of the information to show the relationships of the eleven families to each other. Bootstrap values have been added in blue text and located near each node.(TIF)Click here for additional data file.S1 Supporting InformationThe corresponding zip file contains the FASTA files generated using Protocol1, for comparisons with Protocol2.(ZIP)Click here for additional data file.S2 Supporting InformationThe corresponding zip file contains the multiple sequence alignment (MSE) outputs generated using ClustalX, Mafft, and ProbCons. These MSEs have been used to generate (ZIP)Click here for additional data file.S3 Supporting InformationThe corresponding zip file contains the 100 trees generated from SFT, the consensus tree, the FASTA sequences used to generated the trees, and the newick file for the best tree generated from RAxML analyses (described in (ZIP)Click here for additional data file.S4 Supporting InformationThe corresponding zip file contains the FASTA files used to conduct MEME Suite analyses shown in Figs (ZIP)Click here for additional data file.S5 Supporting InformationThe corresponding PDF file contains the (PDF)Click here for additional data file.S6 Supporting InformationThe corresponding PDF file contains the (PDF)Click here for additional data file.S7 Supporting InformationThe corresponding PDF file contains the (PDF)Click here for additional data file."} +{"text": "Thromboembolic complications (TEC) are very common and lethal in patients suffering from traumatic injury . The trat test, univariate and multivariate logistic regression analyses were performed.A retrospective chart review (2010 to 2013) was conducted on adult trauma patients that were admitted into a level 1 Trauma Centre in Toronto. Demographics, date of PTP initiation, date of TEC diagnosis (CT-PE/US Doppler), injury type and severity were collected. A comparison between early and late PTP initiation has been made with regards to TEC development. Student's P < 0.0005), had lower ISS , shorter length of stay (LOS) , more pelvic fractures , more head injury , less blunt trauma , lower incidence of TEC (5.3% (44) vs. 8.5% (42), P = 0.023), and lower mortality rate (1.5% vs. 7.5%). Univariate analysis showed LOS (P < 0.0005), ISS (P < 0.0005), time to PTP initiation (P = 0.0018) and blunt MOI (P = 0.0099) significantly associated with TEC events. Multivariate analysis, however, showed TEC events correlated only to LOS (P = 0.0001). Stepwise multiple logistic regression confirmed LOS as independently associated with TEC events .A total of 1,312 patients received PTP, 821 (62.5%) initiated early PTP (within 48 hours) while 491 (37.5%) initiated after 48 hours. The group that initiated early prophylaxis was younger (mean: 46 vs. 55, Mortality rates in patients with delayed PTP are higher. Our study shows LOS as the only independent predictor for TEC. However, this might not necessarily reflect causation. Delayed PTP appears not to be an independent predictor to TEC events in trauma patients, which favours current clinical trends when it comes to contraindicating early PTP initiation."} +{"text": "A single-bolus non-ECG-triggered method was previously proposed to reduce the complexity of quantitative myocardial perfusion imaging . CompareData was acquired continuously with no ECG-triggering. 26 projections per slice were acquired following each SR-preparation in an interleaved manner. HYPR was used to reconstruct images with 5-fold undersampling. A sliding window was used to produce series of low resolution images in the basal slice with a temporal resolution of 44 ms. Triggering signal was derived retrospectively from the mean signal intensity in an ROI drawn around the heart. AIF was estimated using single-cardiac cycle T1 mapping [nd study, another 12 healthy volunteers underwent stress-rest studies using the proposed method. Mean myocardial perfusion reserve (MPR) was compared with previously published values.Ten healthy volunteers underwent rest perfusion MRI on a Siemens 3T Verio. A dual-bolus protocol was performed using a conventional clinical Cartesian sequence for comparison [Mean MBF values found using the ECG-triggered dual-bolus method and the non-ECG-triggered integrated T1 mapping method were 0.82 \u00b1 0.21 and 0.76 \u00b1 0.13 ml/min/g, respectively. There was no significant difference (p = 0.45) between them. The mean rest and stress MBF and MPR was 0.86\u00b10.5, 3.91\u00b11.1 ml/min/g, and 4.31\u00b11.3, respectively.A 3-slice, non-ECG-triggered, single-bolus quantitative perfusion MR method with integrated T1 mapping for AIF measurement produces similar MBF as the reference dual-bolus method with comparable ventricular coverage. Mean MPR is similar to those reported in literature. The proposed non-ECG-triggered technique improves ease-of-use, and has the potential to improve robustness to arrhythmias. This method may improve the clinical feasibility of quantitative myocardial perfusion imaging.NIH grant numbers T32 EB51705 and RO1 EB002623, NIBIB grant number EB002623, AHA Scientist Development Grant 14SDG20480123, GCRC grant MO1-RR00425, and Edythe L. Broad Women's Heart Research Fellowship UN55ES6580F."} +{"text": "Moderate-to-severe allergic rhinitis (AR) is often poorly controlled. Patients remain symptomatic on treatment, despite multiple therapies. A more effective treatment is needed. We assessed the efficacy of MP29-02* and fluticasone propionate (FP) in an advanced delivery system) during different seasons and for different symptoms and severities vs AZE, FP or placebo (PLA).Four thousand and twenty two moderate/severe SAR patients (\u226512 yrs) were randomized into 4 double-blind, PLA-controlled, 14-day, parallel-group trials to MP29-02*, AZE, FP or PLA nasal sprays (1 spray/nostril bid), during the Texas mountain cedar (MP4001), Spring (MP4002), Autumn (MP4004) and Spring/Summer (MP4006) seasons. Overall change from baseline (CFB) in reflective total nasal symptom score (rTNSS) was the primary endpoint. It was assessed by severity post-hoc in 2 ways . CFB in individual nasal and ocular symptom scores was also assessed.The response to MP29-02* was consistent across seasons; mean CFB -5.5, -5.5, -5.6 and -5.6 in each study (p<0.001 vs PLA). Nasal symptom relief was significantly greater with MP29-02* than with FP or AZE in all studies. In study MP4001 MP29-02 was approx. twice as effective as FP (relative difference (RD) 47%; p=0.0031) and 3 times as effective as AZE . For less severe AR (defined by median baseline rTNSS) the RD to MP29-02* was 42% vs FP (p=0.0188) and 64% vs AZE (p=0.0002), increasing to 49% and 70% vs FP (p=0.0436) and AZE (p=0.0035), respectively for more severe AR. When severity was categorized according to median baseline RQLQ the RD to MP29-02* was 60% vs FP (p=0.0244) and 69% vs AZE (p=0.0068) for those with less severe AR compared to 49% vs FP (p=0.0194) and 64% vs AZE (p=0.0013) for those with more severe AR. MP29-02* provided superior relief from all nasal and ocular symptoms than AZE or FP, which was particularly evident for congestion & ocular itching .MP29-02* provides consistently superior symptomatic relief to an intranasal antihistamine or topical corticosteroid in AR patients regardless of season, symptom or severity, supporting MP29-02 as the drug of choice for AR.*Dymista"} +{"text": "Erythropoietin treatment could augment the immune response and could be a tiger for systemic lupus erythematous flare-up and increasing the activity of renal and systemic lupus.Anemia is a common clinical finding in end-stage renal failure (ESRD). Systemic lupus erythematous (SLE) is an important cause of chronic kidney disease and anemia in lupus nephritis has different and complex causes, including; anemia of chronic disease (ACD), autoimmune hemolytic anemia (AHA), iron deficiency anemia (IDA), pure red cell aplasia (PRCA), pernicious anemia (PA), myelofibrosis, hemophagocytic histiocytic syndrome, thrombotic microangiopathy and drug induced myelotoxicity . Combina3/\u00b5l and reticulocyte was 1%. Also, platelets count; 156\u00d7103/\u00b5l, serum creatinine: 7.63mg/dl, BUN: 84 mg/dl, uric acid: 7.5 mg/dl, phosphorous: 5.8 mg/dl, calcium: 8.4 mg/dl. Serum complements were as follow: C3: 68 mg/dl (90-180), C4: 10 mg/dl (10-40) and CH50: 76% (90-98). Further laboratory tests revealed; anti MPO\u2013ANCA (IgG): 0.8 u/ml , Anti PR3-ANCA(IgG): 6.0 U/ml , Anti-dsDNA: 42 U/ml, LDH: 800 IU/ml (< 500 ), AST: 36 IU/ml, ALT: 38 IU/ml (<40), serum Na: 139 meq/l, serum K: 5, 0 meq/l, total bilirubin: 0.33 mg/dl (0.1-1.2), direct bilirubin: 0.09 mg/dl (0.1-0.4). Antiphospholipid antibody (IgG/IgM) was negative. Stool examination was negative for occult blood. Also upper gastrointestinal endoscopy had normal results. Peripheral blood examination revealed a large number of teardrop red blood cells. Bone marrow aspiration was unsuccessful (dry tap), bone marrow biopsy was compatible with myelofibrosis. Renal allograft biopsy revealed diffuse lupus nephritis (lupus nephritis class IV) with cellular crescents. This situation was difficult to make a decision to start an intensive immunosuppressive therapy in the presence of marrow failure. Despite receiving adequate dialysis and blood transfusion and adjusted immunosuppressive therapy her general condition worsened and died two months after the admission.We recently admitted a 23 year-old-female with advance renal failure and oliguria. Physical examination on admission revealed a blood pressure of 130/90 mmHg and pulse rate of 105 minute/min. Cardiac examination showed a loud systolic murmur. Abdominal examination disclosed a palpable spleen. Hemodialysis was started with temporary jugular vein catheter. Laboratory examination revealed; hemoglobin: 4.1 g/dl, hematocrit: 17%, MCV: 78.6 fl, MCH: 24.4 pg/cell and MCHC: 31.1 g/dl. White blood cell count: 3.6\u00d710In SLE, there is an association between the level of inflammatory cytokines and intensity of anemia. Inflammatory cytokines inhibit erythropoietin production and erythroid progenitor cells proliferation. In severe cases, inflammatory cytokines lead to myelofibrosis ,2. RenalMRA is the single author of this paper.No financial support by any institution.None to declare."} +{"text": "From 1999\u20132002 to 2009\u20132012, the prevalence of diabetes increased for non-Hispanic black and Mexican American adults, but remained stable for non-Hispanic white adults, increasing the disparity with the two minority populations. In 1999\u20132002, the prevalence of diabetes among non-Hispanic black (14.0%) and Mexican American (13.9%) adults aged \u226520 years was 1.6 times the prevalence among non-Hispanic white adults (8.5%). By 2009\u20132012, diabetes prevalence among Mexican American adults (20.5%) had increased to more than twice the prevalence among non-Hispanic white adults (9.1%); among non-Hispanic black adults (17.9%), the prevalence had increased to nearly twice that among non-Hispanic white adults.Source: Health, United States, 2014: with special feature on adults aged 55\u201364. Table 44. Available at http://www.cdc.gov/nchs/hus.htm.Reported by: Sheila J. Franco, sfranco@cdc.gov, 301-458-4331; Shilpa Bengeri."} +{"text": "Doubts on the efficacy of exercise treatment for adolescents with Idiopathic Scoliosis (IS) still exists.To verify the effectiveness of exercises in everyday clinics.Prospective observational controlled cohort study nested in a prospective database started in March 2003.Setting: outpatient tertiary referral clinics.Participants: consecutive patients from start of the database to 31/12/2010. Inclusion criteria: IS; Risser 0-2; 11\u00b0 to 20\u00b0 Cobb; age 10 years or more; first evaluation. Exclusion criteria: consultations only; immediate prescription of a brace.Groups: Physiotherapic Specific Scoliosis Exercises - SEAS school ; Controls (CON: less than 15 min/week); Usual Physiotherapy (UP: other institutes/protocols).End-Of-Treatment (EOT): medical prescription, bracing, Risser 3.Failures: bracing for scoliosis; EOT above 30\u00b0.Statistical analysis: intent-to-treat (ITT: drop-outs included as failures) and efficacy (EA: only EOT patients). Relative Risk of failure (RR), 95% Confidence Interval (CI), and clinical and radiographic changes have been calculated.Out of 327 patients, 34 (10%) were excluded due to bracing at first evaluation. We included 293 adolescents: 145 PSSE, 95 UP, 53 CON, with no differences at baseline. Physicians prescribed bracing (failure) without differences among groups.Failures and drop-outs were 84 (28.7%) and 47 (16.0%) respectively: 21.4% and 18.6% in PSSE; 33.7% and 9.5% in UP; 39.6% and 20.8% in CON.Efficacy analysis (RR): CON vs PSSE 1.90 (IC 1.48-2.33); UP vs PSSE 1.42 (1.01-1.82); CON vs UP: not significant.Intent-to-treat (RR): CON vs PSSE 1.51 (1.21-1.80); CON vs UP 1.40 (1.08-1.72); UP vs PSSE: not significant.At the end of exercises, aesthetics (TRACE) improved statistically in PSSE (1.8 points out of 12) and UP (1.5), not in CON; only PSSE improvement was statistically better than CON.Patients performing UP or nothing (CON), compared to those treated with PSSE (SEAS), increase the risk of failure (bracing and/or 30\u00b0 at EOT) 1.9 and 1.4 times respectively (EA)."} +{"text": "Evidence of the association between vitamin D, insulin resistance and oral disposition index (oDI) in obese children and adolescents is limited. We investigated serum 25(OH) D levels in obese children and adolescents in Zhejiang, China, and determined the relationship between serum 25(OH) D and glucose metabolism.A cross-sectional design was used. All together 348 obese and 445 non-obese children and adolescents (aged from 6-16 years old) were enrolled in this study. Obese children were divided into four subgroups: normal glucose tolerance (NGT), isolated impaired fasting glucose (IFG), isolated impaired glucose tolerance (IGT), combined IFG and ITG (IFG+ITG) according to the oral glucose tolerance test. We measured serum 25(OH) D levels and calculated the homeostasis model of insulin resistance (HOMA-IR), the whole body insulin sensitivity index (WBISI), the product of \u03b2-cell function and insulin sensitivity by the disposition index (DI).The levels of 25(OH)D in obese group were significantly lower than those of non-obese group; serum 25(OH)D level in obese with NGT group was higher than that of the other three subgroups, and it was significantly inversed with LogHOMA-IR , positively correlated with LogWBISI, LogHOMA0DI after control for age, sex, season, puberty stage . Obese patients with vitamin D deficiency have a significantly higher risk of disturbing the glucose metabolism, such as IFG, ITG, IFG plus ITG, either IFG or ITG, for its OR 3.198(95%CI 1.467-6.97), 5.443(95%CI 1.863-15.897), 5.560(95%CI 1.212-25.502), 4.007(95%CI 2.017-7.962).25(OH) D deficiencies or insufficiency are common in obese children and adolescents in Zhejiang, China. Obese patients with 25(OH) D deficiency (<30nmol /L) are at higher risk for abnormal glucose metabolism."} +{"text": "This study determined the effects of eight weeks of heavy resistance training combined with branched-chain amino acid (BCAA) supplementation on body composition and muscle performance.Nineteen non-resistance-trained males resistance-trained (3 sets of 8-10 repetitions) four times/week for eight weeks while also ingesting 9 g/day of BCAA or 9 g/day of placebo (PLAC) on exercise days only . Data were analyzed with separate 2 x 2 ANOVA (p < 0.05).For total body mass, neither group significantly increased with training (p = 0.593), and there also were no significant changes in total body water (p = 0.517). Also, no training- or supplement-induced (p = 0.783) changes occurred with fat mass or fat-free mass (p = 0.907). Upper-body (p = 0.047) and lower-body strength (p = 0.044) and upper- (p = 0.001) and lower-body muscle endurance (p = 0.013) were increased with training; however, these increases were not different between groups (p > 0.05).When combined with heavy resistance training for eight weeks, 9 g/day of BCAA supplementation, half given 30 min before and after exercise, had no preferential effects on body composition and muscle performance."} +{"text": "Mycobacterium abscessus complex, the third most frequent mycobacterial complex responsible for community- and health care-associated infections in developed countries, comprises of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii reviously referred as Mycobacterium bolletii and Mycobacterium massiliense. The diversity of this group of opportunistic pathogens is poorly described.M. abscessus complex genomes found a pan-genome of 6,153 proteins and core-genome of 3,947 (64.1%) proteins, indicating a non-conservative genome. Analysing the average percentage of amino-acid sequence identity (from 94.19% to 98.58%) discriminates three main clusters C1, C2 and C3: C1 comprises strains belonging to M. abscessus, C2 comprises strains belonging to M. massiliense and C3 comprises strains belonging to M. bolletii; and two sub-clusters in clusters C2 and C3. The phylogenomic network confirms these three clusters. The genome length (from 4.8 to 5.51-Mb) varies from 5.07-Mb in C1, 4.89-Mb in C2A, 5.01-Mb in C2B and 5.28-Mb in C3. The mean number of prophage regions (from 0 to 7) is 2 in C1; 1.33 in C2A; 3.5 in C2B and five in C3. A total of 36 genes are uniquely present in C1, 15 in C2 and 15 in C3. These genes could be used for the detection and identification of organisms in each cluster. Further, the mean number of host-interaction factors varies from 70 in cluster C1, 80 in cluster C2A, 74 in cluster C2B and 93 in clusters C3A and C3B. No significant differences in antibiotic resistance genes were observed between clusters, in contrast to previously reported in-vitro patterns of drug resistance. They encode both penicillin-binding proteins targeted by \u03b2-lactam antibiotics and an Ambler class A \u03b2-lactamase for which inhibitors exist.In-depth analysis of 14 published M. abscessus complex comprises three genomospecies, corresponding to M. abscessus, M. bolletii, and M. massiliense. The genomics data here reported indicate differences in virulence of medical interest; and suggest targets for the refined detection and identification of M. abscessus.Our comparative analysis indicates that The online version of this article (doi:10.1186/1471-2164-15-359) contains supplementary material, which is available to authorized users. Mycobacterium abscessus was long confused with Mycobacterium chelonae[Mycobacterium salmoniphilum[Mycobacterium immunogenum[Mycobacterium massiliense[Mycobacterium bolletii[Mycobacterium franklinii[Mycobacterium chelonae-abscessus complex. This complex is the third most frequent mycobacterial complex infecting humans in developed countries besides the Mycobacterium tuberculosis and Mycobacterium avium complexes [M. salmoniphilum[The non-tuberculous mycobacterium chelonae. Other coniphilum, Mycobacmunogenum, Mycobacssiliense, Mycobac bolletii and Mycoranklinii altogethomplexes , 8. Biblomplexes . Not onlomplexes , 11 and omplexes \u201314 are ioniphilum, 15.M. abscessus comprises two subspecies named M. abscessus subsp. abscessus and M. abscessus subsp. bolletii. Later taxon accommodates isolates previously referred as M. bolletii or M. massiliense[M. abscessus and M. bolletii, it shares 99% sequence identity with M. massiliense. RpoB gene sequencing founded the description of recent species [M. massiliense from M. bolletii. In this report, the previous nomenclature M. abscessus, M. bolletii and M. massiliense forming the M. abscessus complex, has been retained for clarity.Current nomenclature is that the species ssiliense. This no species \u201319 but y species \u201322. Mult species and mult species differenM. abscessus, 13 M. massiliense and two M. bolletii genomes in the National Center for BioInformatics (NCBI) genome database provides new opportunities to assess the diversity of this species. Here, we review 14 complete published M. abscessus complex genomes and compare them with the re-annotated M. tuberculosis H37Rv genome includes M. abscessus type strain and strains M93, 94, M152 and Go06; cluster 2 (C2) contains two subclusters: cluster 2A (C2A) includes M. massiliense type strain and strains M154 and M18; cluster 2B (C2B) includes strains 47\u00a0J26, M115, M172 and M139; cluster 3 (C3) includes two subclusters: cluster 3A (C3A) includes M. bolletii type strain and cluster 3B (C3B) includes M. bolletii strain M24 (Table\u00a0The average percentage of amino-acid sequence identity (AAI) of core proteins was determined as previously described . The AAIM. abscessus complex proteomes were further aligned using Mauve software [M. abscessus differently from the whole genome concatenated tree and BLASC1 strains have been isolated from American and Malaysian patients suffering knee infection and lower respiratory infection, respectively , M. massiliense (C2) and M. bolletii (C3). Using an AAI <97% threshold would further determine two subspecies in M. massiliense (C2A and C2B) and in M. bolletii (C3A and C3B). Recent whole genome sequencing analyses of clinical isolates in Great Britain also clearly distinguished three clusters in agreement with the three here reported [M. abscessus complex, to recognize three genomospecies M. abscessus (C1), M. bolletii (C2), and M. massiliense (C3); and four unnamed subspecies C2A, C2B; C3A, C3B.Altogether, genomics analyses revealed a more heterogeneous structure of abscessus. It has abscessus, 35. Thereported . All theM. abscessus median GC% content is 64.2%, ranging from 62.7% (M. abscessus ATCC 19977) to 64.2% (strain Go 06). The GC% is not characteristic of the clusters as the median GC% content of C1, C2A and C3 is 64.2%, close to the median 64.1% GC% content in C2B.M. abscessus M154) to 5.51-Mb (M. abscessus M24) with a median of 5.07-Mb. The median of genome size is 5.07-Mb in C1, 4.89-Mb in C2A, 5.01-Mb in C2B and 5.28-Mb in C3. Differences in the genome size correlate with the number of prophage regions which are detected in 13/14\u2009M. abscessus genomes has the smallest genome encoding no prophage whereas M. bolletii M24 (C3) has the largest genome encoding seven prophage regions and phage tape measure protein. Both ends of this region encode putative phage integrases. M. abscessus genomes encode small prophage-like regions. However, only M. bolletii has been reported to produce a mycobacteriophage that we named Araucaria after we recently resolved its electron microscopy 3D structure [M. abscessus M94 genome harbours one particular pseudo-tRNA spanning the region 51,150-57,394 in contig 33, which is not observed in the other M. abscessus genomes [M. abscessus however, no such genes were identified but phages could be targeted for the differentiation between the three M. abscessus genomospecies.However, there is a significant 14.7% variation in the genome length from 4.8-Mb genes conferring resistance to tetracyclyine and doxycycline; the number of tet(M) genes was correlated to the resistance to cyclines in Escherichia coli[M. massiliense was reported to be susceptible and M. abscessus and M. bolletii to be resistant to doxycycline [M. abscessus genomes encode resistance to fusidic acid, glycopeptides, MLS (Macrolide-Lincosamide-StreptograminB), phenicols, rifampicin, sulphonamide and trimethoprim. Also, M. abscessus genomes encode FolP homologs conferring resistance to cotrimoxazole, homolog of UDP-N- acetylglucosamine 1-carboxyvinyltransferase, a MurA protein conferring resistance to fosfomycin and homologs of 23S rRNA methylases conferring resistance to macrolides. Also, M. abscessus genome encodes an erm(41) gene which mutations were reported to confer clarithromycin resistance [In-vitro tests showed that M. massiliense clinical isolates could be distinguished from M. abscessus isolates for their susceptibility to ciprofloxacin [M. bolletii isolates were reported to be resistant to all quinolones [M. abscessus exhibiting high resistance to ciprofloxacin [M. abscessus mycobacteria encode qepA2, a plasmidic gene conferring quinolone resistance in gram-negative bacteria [M. abscessus mycobacteria were reported to be in-vitro resistant to penicillin, amoxicillin, cefoxitin, ceftriaxone, cefotaxime and imipenen [M. abscessus genomes encode an Ambler class A \u03b2-lactamase homologous to \u03b2-lactamases in gram-negative bacteria and to two \u03b2-lactamases in M. tuberculosis. \u03b2-lactamases inhibitors have not been evaluated against M. abscessus sensu lato mycobacteria.As all mycobacteria, sistance \u201344. M. aproteins ; and a msistance . M. abscsistance , 47. Indchia coli. Howeverycycline . M. abscsistance . In-vitrfloxacin whereas inolones . A mutatfloxacin . This obfloxacin . Accordibacteria . M. abscimipenen . This coimipenen , 55. M. M. abscessus are ubiquitous environmental organisms in soil and water [M. chelonae, M. abscessus, M. massiliense and M. immunogenum were reported to survive within Acanthamoeba polyphaga tropohozoites and cysts [M. abscessus genomes encode factors implicated in host interactions. The mean number of genes encoding proline-glutamate (PE), proline-proline glutamate (PPE), 10-kDa lipoprotein antigen precursor (LpqH), Mammalian Cell Entry (MCE), oxidoreductase (Yrbe) and type VII secretion system is of 70 in C1, 80 in C2A, 74 in C2B and 93 in C3. In M. abscessus, rough colonies lack mmpL4 (a gene required for glycopeptidolipid biosynthesis) and lost surface colonization, replication into human macrophages and stimulation of innate immune response; these observations suggested that glycopeptidolipid was a virulence factor [M. avium subsp. avium[M. abscessus genomes encode MCE proteins similar to M. tuberculosis H37Rv. MCE operon promotes internalization of M. tuberculosis by mammalian cells [mce operons which correlated with pathogenicity [M. abscessus genomes encode 12 (C1) to 21 copies of Yrbe proteins. As for secretion systems, recent evidences showed that mycobacteria evolved specialized type VII secretion systems to transport extracellular proteins across the cell wall [M. tuberculosis[M. abscessus, our analyses indicate that ESX-3 and ESX-4 systems are conserved lacks two proteins of the ESX-3 system and M. abscessus M93 (C1) lacks ESAT-6 like and CFP-10-like proteins secreted by the ESX-4 system. Interestingly, M. abscessus M18 (C2A) encodes ESAT-6 and CFP-10 proteins secreted by ESX-1 system. In addition, there are two or three PE and six to 12 (M. bolletii M24) PPE proteins, which are reported to be involved in the virulence of M. tuberculosis[Actinobacteria and pseudomonas (Pseudomonas aeruginosa and Burkholderia cepacia). Although distantly related, these bacteria share the same ecosystem as M. abscessus within cystic fibrosis microbiota.nd water where thnd cysts . Accordie factor \u201358. Accoe factor and biofe factor . Glycopesp. avium. M. abscan cells and initan cells . The numgenicity , varies ell wall . Type VIerculosis, 66. In erculosis. Our anaM. abscessus has a non-conservative genome, suggesting the possibility of on-going transfer of additional genetic material. Unsurprisingly, M. abscessus has already acquired antibiotic resistance. Also, phages have mediated diversity and horizontal gene transfer which drived the rapid evolution of this complex. Indeed, gene transfers have driven the evolution of M. abscessus towards three different genomospecies M. abscessus, M. massiliense and M. bolletii; and the evolution of four different yet unnamed subspecies. Each genomospecies has its own specificities in terms of genome size, prophagome and genome content. We identified 66 genes uniquely present in each genomospecies; these genes could be used in refined detection and identification of M. abscessus organisms. These genomic differences support differences in host interactions and the clinical presentation of infection with M. massiliense (C2A and C2B) being more virulent than the two other genomospecies. Host-interaction factors may contribute to the ability of M. abscessus to colonize mammalian hosts where its respiratory tract habitat put it in close proximity to other serious opportunist pathogens which can act as donors of additional host-interaction factors.Our in-depth genomic analyses indicate that M. abscessus genomespecies will help understanding their pathogenesis factors and could reveal new, more specific targets for drug design and diagnosis tools.Here reported informations regarding differences between M. abscessus strains were downloaded from Genbank (Table\u00a0The whole genomes of 14\u2009http://www.uniprot.org/), the Clusters of Orthologous Groups (COG) [Protein sequences were predicted using prodigal software to generps (COG) and a hoM. abscessus homologous genes using orthoMCL [Proteome sequences were compared using by BlastP and pairwise alignments using ClustalW and the ANI was determined by the mean percentage of nucleotide sequence identity of core proteins . We clusorthoMCL on the tM. abscessus proteomes were aligned using Mauve software [software to infersoftware . The ortsoftware . Using tsoftware .http://treebase.org/treebase-web/home.html) repository, under the accession URL http://purl.org/phylo/treebase/phylows/study/TB2:S15632.The data set of Figure\u00a0http://purl.org/phylo/treebase/phylows/study/TB2:S15632?x-access-code=6fa2ebc53b96e3ae412a8df19187ab41&format=html.Reviewer access URL: The data sets of Figure\u00a0The data sets of Figure\u00a0A-AlignedM. abscessusgenome matrix constructed using Mauve software to infer phylogeny using the Neighbor-Net algorithm in the package SplitsTree4. B- The matrix of binary discrete characters constructed using the orthologous group data found by orthoMCL to infer phylogeny using the Neighbor-Net algorithm in the package SplitsTree4. (XLS 28 KB)Additional file 1: The matrix used for Heatmap clusterisation ofMycobacterium abscessustype VII secretion system compared toMycobacterium tuberculosisH37Rv. (XLS 26 KB)Additional file 2:"} +{"text": "Coinfection in patients with SARS-CoV-2 has been associated with greater complications. We describe the clinical characteristics and outcomes of 126 pediatric patients with COVID-19 and viral, bacterial, or fungal coinfection.We retrospectively reviewed and analyzed electronic data of all pediatric patients who tested positive for SARS-CoV-2 from April 16, 2020, to April 15, 2022, in our center. Confirmation of COVID-19 was based on positive RT-PCR. Viral coinfections (VC) were identified using a multiplex RT-PCR respiratory viral panel, bacterial coinfection (BC) was determined by positive bacterial culture or clinical/radiological manifestations and antimicrobial assessment by a pediatric Infectious Diseases expert and fungal coinfection (FC) diagnosis based on Consensus definitions of invasive fungal disease.During the study period, among 400 pediatric patients with COVID-19, 126 children had coinfection. Children >10 years were the most affected age group. Underlying disease was present in 69%, hematological malignancies were the most common (17.5%). BC was detected in 76.9% (n=97), bacterial pneumonia (54.6%) was the main diagnosis, followed by oncologic patients with initial febrile neutropenia and posterior SARS-CoV-2 detection . Unusual BC as congenital syphilis w detected; acute appendicitis was the initial presentation of COVID-19 in 8 patients. VC was identified in 15.87% (n=20), prevailing rhinovirus (9.5%) and adenovirus (3.96%), One FC presented as proven pulmonary aspergillosis (0.8%). B-V and B-F coinfection were detected in 2 patients. Fever and cough were the most common symptoms, higher fever >40\u00b0C was mostly observed in the BC group (3%). Twenty-seven patients with BC (27.8%) were admitted to intensive care, with the OR 0.7 IR 95% (0.611\u20131.008), 4.1% died. One ICU admission was observed in the VC group (5%) and all VC cases resolved without complications.Pediatric patients with COVID-19 coinfection, especially BC were common in our center representing nearly one-third of the infected children, including unusual coinfections. BC was identified as a risk factor for ICU admission OR 0.7 IR 95% (0.611\u20131.008). Favorable outcomes were observed in most cases.All Authors: No reported disclosures."} +{"text": "Bloodstream infection (BSI) following arterial aneurysm repair may signify vascular graft infection (VGI). The incidence of BSI and its implications in patients with arterial grafts have received scant attention with limited contemporary study. Therefore, the aim of the current investigation is to describe the incidence and epidemiology of BSI following arterial aneurysm repair in a population-based cohort.>18 years) residing in eight counties in southern Minnesota between January 1, 2010 and December 31, 2020. All repairs were performed at Mayo Clinic Rochester. Electronic health records were screened for initial BSI episode following aneurysm repair and complicating VGI.Retrospective case-cohort study using the expanded Rochester Epidemiology Project (e-REP) to identify all arterial aneurysm repairs performed in adults overall, including 18.2 (95% CI 11.9-26.7) following open surgical repair and 10.2 (95% CI 5.8-16.6) following endovascular repair (p=0.148). Thirty-nine (92.9%) of the BSI cases were monomicrobial, with 18 (46.2%) due to Gram-positive organisms and 21 (53.8%) due to Gram-negative organisms. Of the 42 patients with BSI, 10 (23.8%) had VGI. VGI occurred in 8/18 (44.4%) monomicrobial Gram-positive BSI as compared to 2/21 (9.5%) monomicrobial Gram-negative BSI (p=0.013). The 3-year mortality rate following BSI was 52.3%.There was no statistically significant difference in incidence rates of BSI following open surgical repair and endovascular repair. Higher rates of VGI were seen with Gram-positive BSI as compared to Gram-negative BSI.Larry M. Baddour, M.D., Boston Scientific: Advisor/Consultant|Botanix Pharmaceuticals: Advisor/Consultant|Roivant Sciences: Advisor/Consultant|UpToDate, Inc.: Royalty payments - authorship duties."} +{"text": "E. coli belonging to the serotype O177 is a rare strain found in ruminants, especially cattle. When compared to shiga toxin producing E. coli (STEC) O157 and non-O157 STEC serotypes, the antimicrobial resistance, virulence factors, and genomic structure of E. coli O177 are poorly understood. Therefore, in this article, we present the whole genome sequence data of two aEPEC E. coli O177 isolates (E. coli O177_CF-154-A and E. coli O177_CF-335-B) generated using Illumina MiSeq platform. The raw data were generated, cleaned, and assembled using Trimmomatic and SPAdes. Genome data analysis yielded 5,112,402 and 5,460,435 bp, comprising contigs 101 and 191 with GC contents of 50.7% and 50.5% for E. coli O177_CF-154-A and E. coli O177_CF-335-B, respectively. Prokaryotic Genome Annotation Pipeline (PGAP) and Rapid Annotation using Subsystem Technology (RAST) showed that the complete genome of E. coli O177_CF-154-A contained 5040 coding sequences (CDS), 5146 genes, 4896 proteins, 90 RNAs, and 78 tRNA while that of E. coli O177_CF-335-B contained 5463 CDS, 5570 genes, 5230 proteins, 92 RNAs, and 80 tRNA for. A total of 426 and 425 subsystem features with 5190 and 5662 CDS were obtained for E. coli O177_CF-154-A and E. coli O177_CF-335-B, respectively. Several genes encoding virulence and antimicrobial resistance were identified in both genomes. Complete genome sequence data of both isolates have been deposited in the National Center for Biotechnology Information (NCBI), GenBank: accession numbers, VMKH00000000 (E. coli O177_CF-154-A) and VMKG00000000 (E. coli O177_CF-335-B). This data can be used as a reference for determining the virulence and antimicrobial resistance in E. coli O177 isolates from different sample sources.Atypical enteropathogenic Moreover, these data give an extensive information on the virulence and antimicrobial resistance profile of this serotype, which may contribute to understanding and improving of scientific knowledge of this pathogenic strain.These data provide genomic features of \u2022E. coli O177 serotype from different environmental samples. In addition, these data can be used in public health to establish policy framework and strategy intended to curb antimicrobial resistance, especially in humans.The data may be used by researchers to develop new methods for detection of \u2022This genome can be used as a reference, especially for comparative genomic and epidemiological studies.1E. coli O177 isolates (E.\u00a0coli O177_CF-154-A and E. coli O177_CF-335-B) were obtained from cattle faeces in the North West province, South Africa (\u221227\u00b0 00\u2032 0.00\u2033 S 26\u00b0 00\u2032 0.00\u2033 E), E. coli O177_CF-154-A and E. coli O177_CF-335-B) are summarised in E. coli O177_CF-154-A and E. coli O177_CF-335-B, respectively. There were 5040 coding sequences (CDS), 5146 genes, 4896 proteins, 90 RNAs, and 78 tRNA for E. coli O177_CF-154-A genome, while E. coli O177_CF-335-B genome contained 5463 CDS, 5570 genes, 5230 proteins, 92 RNAs, and 80 tRNA. Furthermore, both genomes contained 2 CRISPR Arrays. Based on RAST annotation, there were 426 and 425 subsystem feature counts with 5190 and 5662 CDS in E. coli O177_CF-154-A and E. coli O177_CF-335-B, respectively. As depicted in Two atypical enteropathogenic 22.1E. coli O177 isolates were obtained from Antimicrobial Resistance and Phage Biocontrol Laboratory, Department of Microbiology. The isolates were selected based on the virulence and antimicrobial resistance profiles as described in the previous studies Two atypical enteropathogenic 2.2TM-Tissue MiniPrep Kit following the manufacturer's instructions. The DNA concentration was determined using the NanoDropTM-Lite 1,000 spectrophotometer . After fragmentation, DNA libraries were constructed using the Nextera XT DNA library prep kit following the manufacturer's instruction. The fragmented DNA was amplified using 12 cycles PCR, which adds the index sequences [index 1 (i7) and index 2 (i5)]. The PCR products were purified using 0.6\u00a0\u00d7\u00a0Agencourt AMPure XP beads (Beckman Coulter), and the quality was determined using 1.5% (w/v) agarose gel. Each library was diluted to 12 pmol. Samples were normalized to 4 nM using Nextra XT Library Normalization Beads (Illumina). Normalized libraries were pooled and 150 base paired-ends sequencing was performed with MiSeq Reagent V3 600-cycle kits on the Miseq instrument (Illumina).Genomic DNA was extracted from overnight cultures using the Zymo Research Genomic DNA2.3de novo genome assembly was carried out using SPAdes (v.3.13) 4 with all parameters set at default Raw sequence data were generated and FASTQ files were obtained. The data were assessed for quality using FASTQC (v.0.11.5) and filtered for low quality reads and adapter regions using Trimmomatic (v.0.36) This study did not involve the use of human subjects or animal experiments.Peter Kotsoana Montso: Conceptualization, Methodology, Data curation, Writing \u2013 original draft, Visualization, Investigation, Software, Validation, Writing \u2013 review & editing. Victor Mlambo: Conceptualization, Methodology, Supervision, Software, Validation, Writing \u2013 review & editing. Collins Njie Ateba: Conceptualization, Methodology, Supervision, Software, Validation, Writing \u2013 review & editing.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "Inonotus hispidus (Bull.: Fr.) P. Karst (IH) is an edible and medicinal parasitic mushroom. In this study, after a systematic analysis of its nutritional ingredients, the regulatory effects of IH on lipid metabolism were investigated in mice fed a high-fat diet (HFD). In HFD-fed mice, IH reversed the pathological state of the liver and the three types of fat and significantly decreased the levels of low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), triglycerides (TG), and leptin (LEP) and increased the level of high-density liptein cholesterol (HDL-C) in serum. Meanwhile, IH ameliorated liver damage by reducing alanine aminotransferase (ALT), aspartate aminotransferase (AST), interleukin (IL)-1\u03b2, IL-6, tumor necrosis factor-alpha (TNF-\u03b1), and plasminogen activator inhibitor-1 (PAI-1) levels in the liver and serum. Compared with HFD-fed mice, IH significantly modulated the gut microbiota, changed the relative abundances of microflora at different taxonomic levels, and regulated lipid levels. The results showed that 30 differential lipids were found. Results from Western blotting confirmed that IH regulated the nuclear factor erythroid-2 related factor 2 (Nrf2)/nuclear factor-kappa B (NF-\u03baB) signaling pathway and oxidative stress. This study aimed to provide experimental evidence for the applicability of IH in obesity treatment.Obesity is frequently associated with dysregulated lipid metabolism and lipotoxicity. Obesity is a pathological condition requiring clinical intervention ; it may Obesity is frequently associated with dysregulated lipid metabolism and lipotoxicity , which mGrifola frondosa modulates ceramide levels and restores lipid metabolism by inhibiting the Toll-like receptor 4/NF-\u03baB signaling associated with inflammation and insulin resistance (IR) to treat obesity [Inonotus hispidus (Bull.: Fr.) P. Karst (IH) is an edible and medicinal parasitic mushroom belonging to the phylum Basidiomycota, class Agaricomycetes, and family Hymenochaetaceae. IH is mainly distributed in the Hebei Chengde, Shandong Linqing, Xiajin, and Xinjiang Aksu areas, and it prefers to live on mulberry, water willow, elm, poplar, and Japanese acacia. Previous investigations on IH have mainly focused on chemical composition analysis, artificial cultivation, mycelium fermentation, and pharmacological activity studies [Currently, weight loss occurs primarily through diet- and exercise-related strategies, which are often not sustainable . Bariatr obesity . Inonotu studies ,17,18,19 studies . IH petr studies . Extrace studies . HoweverIn this study, based on the detection of the main components of IH, combined with gut microbiota and lipid metabolomic analyses, the role of IH in regulating oxidative stress and inflammation, based on the Nrf2/NF-\u03baB signaling pathway, to alleviate obesity symptoms was explored in C57BL/6 mice with DIO. Our data provide experimental evidence for the applicability of IH in obesity treatment.IH fruiting bodies from Linqing, Shandong, were identified by Professor Yu Li. The general components , twenty kinds of amino acids, thirty-five kinds of fatty acids, seven kinds of minerals, six kinds of heavy metals, eight kinds of vitamins, and five kinds of nucleotides in IH were systematically detected, as we previously described ,23.n = 6/group), including an intragastrically HFD-fed group with 5 mL/kg of normal saline, an intragastrically simvastatin (SV) -treated group with 3 mg/kg of SV, and low- and high-dose intragastrically IH-treated groups with 500 and 1000 mg/kg of IH, respectively, daily for 8 weeks. The NCD mice were randomly divided into two groups (n = 6/group), including the vehicle-treated intragastrically NCD-fed group with 5 mL/kg of normal saline and the intragastrically IH-treated NCD-fed group with 500 mg/kg of IH daily for 8 weeks. Weekly measurements of body weight and plasma glucose levels were performed for all mice. After 8 weeks of drug treatment, the mice were euthanized using CO2 (the CO2 replacement rate was 30\u201370% of the container volume per minute). Peripheral blood was obtained by sampling the retro-orbital venous plexus. Organs , epididymal white adipose tissue (eWAT), inguinal white adipose tissue (iWAT), and perirenal white adipose tissue (pWAT) were dissected and weighed. The above tissue parts were stored at \u221280 \u00b0C for further biochemical analysis, and the remaining parts were fixed in a 4% tissue fixative for subsequent pathological analysis.All experiments were performed in accordance with the guidelines of the Institutional Animal Ethics Committee of Jilin University (SY202106003). Thirty-six male C57BL/6JGpt mice (5 weeks old) from GemPharmatech Co., Ltd. were maintained on either a normal chow diet or a high-fat diet under specific-pathogen-free (SPF) conditions on a 12 h light/dark cycle at a constant temperature (23 \u00b1 1 \u00b0C) and humidity (40\u201360%) for 8 weeks. To establish the DIO model for the high-fat diet study, 24 randomly selected mice were fed an HFD ad libitum during the entire experimental period. From week 9, the DIO mice were randomly divided into four groups . Serum was collected twice by centrifugation at 3500 rpm at 4 \u00b0C for 10 min. The levels of alanine aminotransferase (ALT) (MM-44625M1), aspartate aminotransferase (AST) (MM-44115M1), IL-1\u03b2 (MM-0040M1), IL-6 (MM-0163M1), TNF-\u03b1 (MM-0132M1), and plasminogen activator inhibitor-1 (PAI-1) (MM-0066M1) in the liver and serum, ROS (MM-43700M1), malondialdehyde (MDA) (MM-0897M1), and lysophosphatidylcholine (LPC) (MM-44698M1) in the liver, and high-density liptein cholesterol (HDL-C) (MM-44105M1), low-density lipoprotein cholesterol (LDL-C) (MM-43685M1), total cholesterol (TC) (MM-0632M1), triglycerides (TG) (MM-0631M1), and leptin (LEP) (MM-0622M1) in the serum were measured using enzyme-linked immunosorbent assay (ELISA) kits.Liver tissue was homogenized in normal saline, and the protein concentration was determined using a Pierce\u2122 bicinchoninic acid (BCA) Protein Assay Kit staining and Oil Red O staining were performed as described in our previous study . Fixed an = 3/group) was performed by 16S rRNA sequencing using an Illumina NovaSeq platform at Shanghai Personalbio Technology Co., Ltd. , as described in our previous study [A gut microbiota analysis of mouse cecum content in samples from NCD-, HFD-, and IH-treated groups (500 mg/kg) (us study . Sequencn = 3/group) was performed by liquid chromatography\u2013mass spectrometry (LC\u2013MS) at Shanghai Personalbio Technology Co., Ltd. , as described in our previous study [p \u2264 0.05) in metabolite levels and variable importance in projection (VIP) values \u2265 1.0 were regarded as the standard for differential lipids to filter out biomarkers.A plasma lipidome analysis of mouse serum from the NCD-, HFD-, and IH-treated groups (500 mg/kg) buffer containing protease and phosphatase inhibitors and were homogenized using a high-throughput tissue grinder . After denaturation, 40 \u03bcg of protein was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred onto a polyvinylidene fluoride (PVDF) membrane . Membranes were blocked by Rapid Closure solution and incubated with the primary antibodies overnight and then the secondary antibodies for 4 h at 4 \u00b0C. Finally, immunoreactive bands were visualized using an automated chemiluminescence image analysis system and Ultra High Sensitivity enhanced chemiluminescence (ECL) kits . Protein expression levels were measured using ImageJ software and normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Details regarding the antibodies used in this work are presented in p < 0.05.All values are presented as means \u00b1 SD. Biochemical indices were compared between different groups by one-way analysis of variance (ANOVA) followed by Tukey\u2019s test using BONC DSS Statistics 25 . Differences were considered statistically significant at The general nutritional composition of IH is 45.90% total dietary fiber, 25.50% total sugar, 15.90% protein, 9.90% ash, 9.22% total flavonoids, 6.18% moisture, 5.04% total polyphenols, 4.70% fat, 1.48% total triterpenes, 0.50% total saponins, 0.46% total alkaloids, 0.31% total sterols, etc. Among them, the total dietary fiber content was the highest. The glutamic acid content was the highest among the 20 amino acids detected. Seven minerals, including calcium (Ca), iron (Fe), zinc (Zn), selenium (Se), potassium (K), sodium (Na), and manganese (Mn), were detected, in addition to low concentrations of six heavy metals (lead (Pb), arsenic (As), mercury (Hg), cadmium (Cd), copper (Cu), and chromium (Cr)). Eight vitamins and five nucleotides were also detected . The corp < 0.05) (p < 0.05) (p < 0.001) (p < 0.01) (p < 0.01) (p < 0.05) (p < 0.05) (p < 0.001) without affecting other organs A. Compar < 0.05) B and sup< 0.001) C, TC (p < 0.01) D, and TG < 0.01) E in seru < 0.05) F. H&E st < 0.05) G. Among < 0.05) . Compare < 0.05) . IH signr organs . IH alonr organs .p < 0.001) (p < 0.001) (p < 0.001) (p < 0.001) (p < 0.001) (p < 0.05) (p < 0.05). In the serum of HFD-fed mice, IH and SV showed the same effects on AST (p < 0.05) (p < 0.05) (p < 0.001) (p < 0.01) (p < 0.05) (p < 0.01) (p < 0.05). IH failed to influence the serum levels of ALT , high degrees of lipid deposition, and large amounts of lipid droplets (H&E staining) were improved by IH and SV A. Moreov< 0.001) B, AST (p< 0.001) C, IL-1\u03b2 < 0.001) D, IL-6 (< 0.001) E, and TN< 0.001) F in the < 0.05) G in HFD- < 0.05) I, IL-6 ( < 0.05) K, TNF-\u03b1 < 0.001) L, and PA < 0.01) M. At 500 < 0.05) J and PAI < 0.01) M in HFD-s of ALT H. IH alos of ALT B\u2013M.Allobaculum, Adlercreutzia, Shigella, Dorea, Oscillospira, and Streptococcus and decreased Ruminococcus and Coprobacillus compared with the vehicle-treated HFD-fed mice (p < 0.01) D. IH and < 0.01) E.p < 0.01) (p < 0.05) (p < 0.001), IKK\u03b1 + \u03b2 (p < 0.001), and I\u03baB\u03b1 and significantly upregulated the expression levels of Nrf2 (p < 0.001), HO-1 (p < 0.01), and SOD-1 . Compared with the vehicle-treated NCD-fed mice, IH alone only increased the levels of Nrf2 (p < 0.01) and HO-1 (p < 0.05) and suppressed the activation of P-I\u03baB\u03b1 (p < 0.001) (The hepatic levels of ROS ( < 0.01) A and MDA < 0.05) B were de< 0.001) C.IH is rich in dietary fiber, which helps to improve hyperlipidemia by affecting lipid metabolism and has Allobaculum, Dorea, and Oscillospira, facilitating the production of short-chain fatty acids (SCFAs) related to metabolic processes [Ruminococcus and Coprobacillus. SCFAs such as acetate, propionic acid, and butyric acid can reduce the generation of pro-inflammatory cytokines [Allobaculum can regulate hepatic lipid metabolic processes [Allobaculum plays a role in suppressing inflammatory responses by reducing the expression of p-IKK and TNF-\u03b1 [Dorea is negatively associated with inflammatory diseases [Oscillospira and Ruminococcus are inflammatory bacteria associated with inflammatory bowel disease [Oscillospira helps to maintain lipid homeostasis [Rosa Roxburghii Tratt, possessing hypolipidemic effects, can reduce the abundance of Coprobacillus [Streptococcus may be the main force for decomposing a large amount of cellulose [In obese mice, IH increased the abundance of the genera rocesses ,34,35 whytokines , displayytokines . SCFAs cytokines ,39. Dietytokines , which hytokines , Allobacrocesses , shows arocesses , and itsrocesses . Allobacnd TNF-\u03b1 , which hnd TNF-\u03b1 , Dorea idiseases . Both Os disease ,48, and eostasis . Rosa Robacillus . Moreoveellulose , which iellulose . Meanwhiellulose ,54, and ellulose .Metabolites of intestinal flora affect the process of lipid metabolism and host lipid composition . IH coulSOD and HO-1 [HO-1, a key target gene of Nrf2, exerts antioxidant effects by resisting endogenous and exogenous stimuli [Oxidative stress leads to increased lipid peroxidation and is closely associated with hyperlipidemia-related tissue damage ,63. Nrf2and HO-1 . SOD-1 iand HO-1 . HO-1, a stimuli . Nrf2/HO stimuli .Oxidative stress and inflammation are inextricably associated . Nrf2 caThe present study had certain limitations. In this study, we first reported the hypolipidemic effects of IH and analyzed the components involved. However, the specific active components possessing hypolipidemic activity were not confirmed; thus, further investigation is needed.In conclusion, IH regulated lipid metabolism through the Nrf2/NF-\u03baB signaling pathway, which is closely related to oxidative stress and inflammatory responses, in HFD-fed mice. Our study provides insights into the application of IH as a hypolipidemic agent and will facilitate its commercial application."} +{"text": "In: Public health round-up. Bull World Health Organ. 2022 May 1; 100(5):296\u2013297, on page 297, middle column, the second sentence should read as follows: \u201cAs of 15 March, a total of 53 people were reported with suspected Yellow fever infections, six of whom died of the disease .\u201dhttps://dx.doi.org/10.2471/BLT.22.010522Public health round-up. Bull World Health Organ. 2022 May 1;100(5):296\u2013297."} +{"text": "Serrated lesions (SLs), including sessile serrated lesions (SSL) and traditional serrated adenomas (TSA) have become subject of increased interest for their role as CRC precursors.Study aim was to evaluate the risk to develop total metachronous advanced neoplasia (T-MAN) at follow-up in patients with index SL compared to a matched cohort without SL.Patients 45-74y with SLs were identified through pathology database search. SL patients were matched 2:1 by sex; age; synchronous polyps ; timing of index, to patients without SL. Primary outcome was risk of T-MAN (advanced adenoma or high-risk SL) at follow-up. Secondary outcomes included risk of T-MAN stratified by synchronous polyps and SL characteristics.1425 patients were included . The SL group had greater risk of T-MAN compared to the non-SL group [Hazard-ratio (HR)=6.12 3.91-9.58)]. Patients with SL+HRA had higher risk of T-MAN compared to HRA alone [HR=2.62 (95%CI 1.45-4.71)], as well as patients with SL+LRA compared to LRA alone [HR=7.03 (95%CI 2.78-18.44)], and SL without adenoma compared to no-adenoma [HR=14.87 (95%CI 6.51-33.95)]. Presence of proximal SSL (HR=9.30), large SSL (HR=17.87) and proximal large SSL (HR=24.99), but not distal SSL, was associated with greater risk for T-MAN.Patients with SLs are at greater risk for developing T-MAN regardless of synchronous adenomas. Patients with SL and HRA, and those with large or proximal SSLs appear to be at greatest risk for T-MAN.OtherACGR. Djinbachian Grant / Research support from: Grant from the American College of Gastroenterology for the conduction of this project, M.-L. Lafontaine: None Declared, J. Anderson: None Declared, H. Pohl: None Declared, T. Dufault: None Declared, M. Boivin: None Declared, M. Bouin: None Declared, D. von Renteln Grant / Research support from: Daniel von Renteln is supported by a \u201cFonds de Recherche du Qu\u00e9bec Sant\u00e9\u201d (FRQS) career development award and has received research funding from ERBE, Ventage, Pendopharm, Fujifilm, and Pentax., Consultant of: Boston Scientific and Pendopharm,"} +{"text": "Correction to: BMC Infectious Diseases\u00a0(2022)\u00a022, 897. https://doi.org/10.1186/s12879-022-07887-1Error 1:Following publication of the original article , the autError 2:Following publication of the original article , the aut"} +{"text": "Candida auris is a globally spreading yeast pathogen causing bloodstream infections with high mortality in critically ill patients. The inherent antifungal drug resistance of most C. auris isolates and threat of multidrug-resistant strains create a need for adjunct immunotherapeutic strategies. While C. albicans candidemia was shown to induce immune paralysis and activation of inhibitory immune checkpoints, in vivo data on host responses to C. auris bloodstream infection are lacking as is an immunocompetent murine infection model to study the immunopathology and immunotherapy of C. auris sepsis. Therefore, herein, we developed an immunocompetent C. auris sepsis model by intravenously infecting C57BL/6 mice with 1.5\u2009\u00d7\u2009108 to 8\u2009\u00d7\u2009108 yeast cells of aggregate-forming (AR-0384) and nonaggregative (AR-0381) C. auris reference isolates. Both isolates caused reproducible, inoculum-dependent increasing morbidity, mortality, and fungal burden in kidney tissue. Notably, morbidity and mortality outcomes were partially decoupled from fungal burden, suggesting a role of additional modulators of disease severity such as host immune responses. Flow cytometric analyses of splenic immune cells revealed significant upregulation of the programmed cell death protein 1 (PD-1) on T cells and its ligand PD-L1 on macrophages from mice infected with C. auris AR-0384 compared to uninfected mice. PD-L1 expression on macrophages from AR-0384-infected mice strongly correlated with fungal tissue burden (Spearman\u2019s rank correlation coefficient [\u03c1] = 0.95). Altogether, our findings suggest that C. auris sepsis promotes a suppressive immune phenotype through PD-1/PD-L1 induction, supporting further exploration of PD-1/PD-L1 blockade as an immunotherapeutic strategy to mitigate C. auris candidiasis.IMPORTANCE Health authorities consider Candida auris to be one of the most serious emerging nosocomial pathogens due to its transmissibility, resistance to disinfection procedures, and frequent antifungal drug resistance. The frequency of multidrug-resistant C. auris isolates necessitates the development of novel therapeutic platforms, including immunotherapy. However, in vivo data on host interactions with C. auris are scarce, compounded by the lack of reliable immunocompetent mammalian models of C. auris candidemia. Herein, we describe a C. auris sepsis model in immunocompetent C57BL/6 mice and demonstrate reproducible and inoculum-dependent acute infection with both aggregate-forming and nonaggregative reference isolates from different clades. Furthermore, we show that C. auris sepsis induces upregulation of the PD-1/PD-L1 immune checkpoint pathway in infected mice, raising the potential of a therapeutic benefit of immune checkpoint blockade. Our immunocompetent model of C. auris sepsis could provide a facile preclinical platform to thoroughly investigate immune checkpoint blockade and combination therapy with antifungals. Candida auris isolate bank , which rre (MSS) was quanre (MSS) \u201314, with10.1128/mSphere.00817-21.1TEXT\u00a0S1Candida auris inoculums and infection of mice, determination of fungal burden in kidney tissue, isolation of murine splenocytes, and fluorescent labelling of splenocytes. Download Text S1, DOCX file, 0.03 MB.Detailed descriptions of experimental procedures for preparation of Copyright \u00a9 2022 Wurster et al.2022Wurster et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 8 AR-0381 cells remained sublethal, and the mice developed only mild signs of distress (8 and 8\u2009\u00d7\u2009108) of AR-0381 cells caused increasing morbidity and 7-day mortality (33% and 44%) and B. Iand 44%) and B. Tand 44%) . Likewisectively .8 yeast cells of the aggregate-forming isolate AR-0384 caused robust morbidity and 17% 7-day mortality and B. Irs, 2.0) and B. Hrs, 2.0) . This trrs, 2.0) , suggestC. auris infection (in vitro and in vivo studies yielded divergent (strain- and inoculum-dependent) results regarding the comparative pathogenicity and immunopathology of aggregate-forming and nonaggregative C. auris strains and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) on T cells, natural killer (NK) cells, and natural killer T (NKT) cells was determined by flow cytometry as described in C. auris-infected mice harbored significantly higher frequencies of PD-1-positive T cells than uninfected mice (To test whether =\u20090.015) and C. I=\u20090.015) .C. auris-infected mice than in controls (P\u2009=\u20090.01) and C. I\u2009=\u20090.01) . Collect in mice and patiThe main limitations of this pilot study include testing of only one isolate per aggregation phenotype and a limited number of animals tested per condition. Furthermore, our study focused solely on the induction of coinhibitory immune checkpoint molecules and did not dynamically capture the net state of pro- and anti-inflammatory immune signals in the bloodstream and infected tissues.C. auris infection model in immunocompetent C57BL/6 mice and demonstrate the induction of coinhibitory immune checkpoint signals after C. auris bloodstream infection. These data provide a theoretical framework for PD-1/PD-L1 blockade as a potential immunotherapeutic strategy to mitigate C. auris candidiasis. We and others previously demonstrated a therapeutic benefit of the PD-1/PD-L1 pathway blockade in murine models of invasive mold infections (C. albicans sepsis (C. auris infection model in cost-efficient C57BL/6 mice could serve as a facile preclinical platform to study checkpoint inhibitors as an investigational therapy for C. auris sepsis. Furthermore, our immunocompetent model could complement the published cyclophosphamide-immunosuppressed and/or neutrophil elastase-deficient murine C. auris sepsis models (C. auris in different host backgrounds.Despite these limitations, we herein describe a simple and reproducible fections \u201322 and Cs sepsis , 23, 24.s models and allo10.1128/mSphere.00817-21.2TABLE\u00a0S1Table\u00a0S1, DOCX file, 0.02 MB.Antibodies used for flow cytometry. Antibody solutions were prepared in 100 \u03bcL of flow cytometry buffer per sample. Download Copyright \u00a9 2022 Wurster et al.2022Wurster et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the"} +{"text": "Correction to: Eur J Nucl Med Mol Imaging (2022) 49:632\u2013651https://doi.org/10.1007/s00259-021-05603-wThe authors regret a typo in the units assessing hyperglycaemia, which should be defined as > 8.9 mmol/L, and not as erroneously mentioned in the published version as > 8.9 nmol/L."} +{"text": "Gram-negative pathogens with multidrug resistance (MDR) or difficult-to-treat resistance (DTR) are increasingly common, resulting in limited treatment options. These resistant pathogens are often isolated from the respiratory tract or bloodstream and can result in significant patient morbidity and mortality. Imipenem/relebactam is a combination of imipenem with relebactam, a \u03b2-lactamase inhibitor of class A and C \u03b2-lactamases. We evaluated the activity of imipenem/relebactam and comparators against gram-negative MDR and DTR isolates that were collected from patients with lower respiratory tract (RTI) or bloodstream infections (BSI) in the United States (US).In 2018-2020, 24 clinical labs participated in the global SMART surveillance program in the US, and each collected up to 100 consecutive aerobic or facultative gram-negative pathogens per year from patients with RTI and 50 from BSI. MICs were determined using CLSI broth microdilution and interpreted with CLSI breakpoints.P. aeruginosa (n=2018), 11.9% of E. coli (n=1952), 13.1% of K. pneumoniae (n=1080), 24.1% of E. cloacae complex (n=460), 19.7% of K. aerogenes (n=304), and 6.1% of S. marcescens isolates (n=304); DTR isolates were found among 7.1%, 0.1%, 2.4%, 1.5%, 0%, and 0.8%, respectively. Imipenem/relebactam was active against 61% of MDR P. aeruginosa, 43-53 percentage points higher than the studied comparator \u03b2-lactams, and against 49% of DTR P. aeruginosa, which were nonsusceptible to all studied commonly used \u03b2-lactams and levofloxacin (Table). Imipenem/relebactam was also active against 87-100% of MDR Enterobacterales, including against 97% of MDR K. pneumoniae, 18-96 percentage points higher than the studied comparator \u03b2-lactams, and against 85% of DTR K. pneumoniae.MDR isolates were found among 13.5% of collected in vitro data, imipenem/relebactam represents a promising treatment option in the US for patients with RTI or BSI caused by highly resistant gram-negative pathogens that pose substantial treatment challenges.Based on these Fakhar Siddiqui, MD, MBA, Merck & Co., Inc.: employee|Merck & Co., Inc.: Stocks/Bonds Karri A Bauer, PharmD, Merck & Co., Inc. Merck Research Laboratories: Stocks/Bonds Charles A. DeRyke, PharmD, Merck & Co., Inc. Merck Research Laboratories: Stocks/Bonds Katherine Young, M.S., Merck & Co., Inc.: Stocks/Bonds."} +{"text": "Chronic inflammation, a hallmark of type 2 diabetes (T2D) and adiposity, increases the risk for age-related co-morbidities, including physical frailty. This study aimed to examine the effects of a mobile technology-enhanced behavioral lifestyle educational intervention on frailty and associated clinical, inflammatory, and laboratory outcomes in overweight older adults with T2D. Twenty participants with T2D were recruited to complete a single-arm 6-month lifestyle intervention modified from the Action for Health in Diabetes (Look AHEAD) study, enhanced with technology for self-monitoring of diet and physical activity. Clinical assessments were collected at baseline and end of the study and analyzed with paired t-tests. Inflammatory cytokines were quantified using a commercially available multiplex kit . Clinical lab analysis was performed by Quest Diagnostics . Eighteen participants completed the study . At baseline, 13 participants were pre-frail, 4 were frail based on Fried frailty criteria. Inflammatory cytokines and liver enzymes values were within normal limits. At follow-up, the following outcomes significantly improved: frailty score -44% (p=0.01), BMI -3% (P< 0.00), alanine transaminase -18% (p=0.03), aspartate aminotransferase -13% (p< 0.00), IL2 -33% (p=0.01), IL4 -31% (p=0.05), IFN\u03b3 -36% (p=0.03), GM-CSF -43% (p=0.03). No other significant differences were observed. The results suggest the efficacy of a technology-enhanced lifestyle intervention on frailty and associated clinical, inflammatory, and laboratory outcomes in overweight older adults with T2D."} +{"text": "Ecdyonurusaurasiussp. nov., a micro-endemic species reported from several streams within the Aur\u00e8s Mountains (north-eastern Algeria), is described and illustrated at nymphal, subimaginal and imaginal stages of both sexes. Critical morphological diagnostic characters distinguishing the new species are presented, together with molecular affinities as well as notes on the biology and distribution of the species. Ecdyonurus Eaton, 1868 belongs to the Ecdyonurinae Ulmer, 1920, a subfamily with rather challenging and controversial taxonomy as genera delineation and phylogeny are still partially unsolved or in process and Helvetoraeticus Bauernfeind & Sold\u00e1n, 2012 (15 species), according to the arrangement of setae on the superlingua, the number of bristles on the ventral side of the labrum and the number of comb-shaped bristles on the maxilla in nymphs, as well as the shape of the apical sclerite of the male genitalia.Ecdyonurusrothschildi Nav\u00e1s, 1929 and Ecdyonurusifranensis Vitte & Thomas, 1988, whereas one remains doubtful: Ecdyonurusvenosusvar.constantinicus Lestage, 1925, and the presence of Ecdyonurusvenosus mentioned by Ecdyonurus.Currently, four taxa of this genus are reported from North Africa . Two of Ecdyonurusrothschildi from an oasis in Biskra Province, north-eastern Algeria, based on a male imago. The species was redescribed by E.aurantiacus species group. Later, E.rothschildi, E.dispar and E.aurantiacus nymphs. The species is now known from all Maghreb countries and is one of the most widespread species . We collected and reared fresh material at all stages. After critical observations and comparison with other Ecdyonurus species, we have clearly distinguished a new Algerian endemic species.The present study aims to examine BNP) and the Western Aur\u00e8s Massif substitution model . Two independent analyses of four MCMC chains run for one million generations with trees sampled every 1000 generations were implemented, and 100 000 generations were discarded as a burnin after visually verifying run stationarity and convergence in Tracer ver. 1.7.2 and included 25% of parsimony informative sites. The COI gene tree grouped the five sequences of Ecdyonurusaurasius sp. nov. into a well-supported monophyletic clade, and was supported as a distinct species in the ASAP analysis to 20.1% (mean distance to E.aurantiacus), with a minimum distance of 7.1% between GBIFCH01119302 / GBIFCH00673192 and EC-CH0 sequences.The Ecdyonurinae Ulmer, 1920Taxon classificationAnimaliaEphemeropteraHeptageniidae\ufeffDambri, Benhadji & Sartorisp. nov.11A25021-4118-5EC5-B4CF-3CFE86311118https://zoobank.org/0A552D79-3329-4CCA-9724-D01492F82D7BHolotype. Algeria \u2022 male imago in ethanol, with its corresponding nymphal and subimaginal exuviae, Wilaya de Batna, Charchar, 35\u00b024'22\"N, 6\u00b023'21\"E, 1340 m. a.s.l., 09 Nov. 2021, B. Dambri coll. (GBIFCH01128855) [MZL] \u2022 Paratypes. 1 male imago, with its nymphal and subimaginal exuviae (GBIFCH01128846), 1 female imago, with its nymphal and subimaginal exuviae (GBIFCH01128858), [MZL]; 6 female imagos [IB-US], same data as holotype; 1 male imago, 1 male subimago [IB-US], 2 female imagos, 7 male subimagos [FEEL-UB2], 06 Nov. 2021; 1 male imago [IB-US], 1 male imago [FEEL-UB2], 20 Oct. 2021; 1 male imago, with its nymphal and subimaginal exuviae (GBIFCH01119304), 1 female imago, with its nymphal and subimaginal exuviae (GBIFCH01128861) [MZL], 17 Oct. 2021; 1 female imago with its subimaginal exuvia, 1 female subimago (GBIFCH01128849) [MZL], 15 Oct. 2021; 1 female subimago, 1 male subimago [IB-US], 1 male subimago (GBIFCH01128853) [MZL], 2 nymphs [FEEL-UB2], 10 Oct. 2021; 3 nymphs [IB-US], 2 nymphs (GBIFCH01128857), 1 nymph on slide (GBIFCH01119301) [MZL], 09 Oct. 2021; 7 nymphs [IB-US], 15 nymphs [FEEL-UB2], 18 Jun. 2020; 15 nymphs [IB-US], 18 nymphs [FEEL-UB2], 5 nymphs (GBIFCH01128850) [MZL], 3 Mar. 2020; same locality, B. Dambri coll; 10 nymphs (GBIFCH00832138), 2 nymphs on slide (GBIFCH00673191-GBIFCH00673192), 1 male imago (GBIFCH00673193), 1 male imago, 1 female imago, 2 female subimagos (GBIFCH00832125), 23 Jun. 2019, same locality, L. Kechemir coll. et leg. [MZL]Other paratypes. Algeria \u2022 Wilaya de Batna, Berbaga, 35\u00b024'01N, 6\u00b024'31\"E, 1445 m. a.s.l., 1 male imago, with its nymphal and subimaginal exuviae (GBIFCH01119302), 1 female subimago with its nymphal exuvia (GBIFCH01128848) [MZL], 5 Nov. 2021; 1 male imago (GBIFCH01128852), 2 nymphs (GBIFCH01128847), 1 nymph on slide (GBIFCH01119303) [MZL], 13 nymphs [IB-US], 5 nymphs [FEEL-UB2], 4 Nov. 2021; 1 male imago [IB-US], 12 nymphs [FEEL-UB2], 30 Nov. 2020; 1 nymph [IB-US], 16 nymphs [FEEL-UB2], 03 May 2020; 1 male imago [IB-US], 10 nymphs [FEEL-UB2], 02 Mar. 2020, B. Dambri coll. Algeria \u2022 Wilaya de Khenchela, Yabous, 35\u00b021'11\"N, 6\u00b038'35\"E, 1420 m. a.s.l., 2 female imagos [IB-US], 2 female subimagos, 3 nymphs [FEEL-UB2], 22 Oct. 2021; 1 female subimago [IB-US], 2 nymphs [FEEL-UB2], 1 female imago with its subimaginal exuvia, 1 female subimago (GBIFCH01128854) [MZL], 13-14 Oct. 2021; 1 male imago with its subimaginal exuvia GBIFCH01128851), 1 female imago with is subimaginal exuvia (GBIFCH01128845) [MZL], 12 Oct. 2021; 5 nymphs [IB-US], 1 female imago, 2 male subimagos, 6 nymphs [FEEL-UB2], 09 Oct. 2021; 4 nymphs [IB-US], 2 nymphs [FEEL-UB2], 1 nymph (GBIFCH01128859) [MZL], 20 Jul. 2020; 2 nymphs [IB-US], 19 nymphs [FEEL-UB2], 1 nymph (GBIFCH01128856) [MZL], 02 Jun. 2020; 1 female subimago with its nymphal exuvia [IB-US], 8 nymphs [FEEL-UB2], 09 May 2020; 1 female subimago [IB-US], 15 nymphs [FEEL-UB2], 08 Mar. 2020; 1 female subimago with its nymphal exuvia [IB-US], 3 nymphs [FEEL-UB2], 23 Feb. 2020, B. Dambri coll. Algeria \u2022 Wilaya de Batna, Inoughissen, 35\u00b016'42\"N, 6\u00b032'34\"E, 1670 m. a.s.l., 1 nymph (GBIFCH01128863) [MZL], 07 Jul. 2020; 1 nymph (GBIFCH01128865) [MZL], 18 Apr. 2020, B. Dambri coll.35\u00b033'03\"N, 6\u00b000'22\"E, 1262 m. a.s.l.,1 nymph [IB-US], 17 Jun. 2020; 3 nymphs [IB-US], 10 nymphs [FEEL-UB2], 1 nymph (GBIFCH01128860) [MZL], 20 Apr. 2020, B. Dambri coll. Algeria \u2022 Wilaya de Batna, Bouailef, 35\u00b037'01\"N, 6\u00b011'17\"E, 1060 m, 1 nymph [IB-US], 08 Mar. 2020, B. Dambri coll.Algeria \u2022 Wilaya de Batna, oued Cha\u00e2ba, Aurasiusmons; aurasius is a noun in apposition.Aur\u00e8s mountains were coined by the Berber people as Awras, meaning tawny; translated by the Romans as Male imago Size: body length: 9.0\u20139.8 mm; forewing length 9.1\u201310.9 mm; cerci broken. General body color distinctly brown to reddish-brown . The new species presents more affinities with the two other North African endemics but can be distinguished from E.rothschildi by the much longer pronotal projections, the shape of the stout setae on the dorsal surface of femora (pointed in the latter), the shape of the gills and the shape of the glossae ((inner margin rounded and convex in E.rothschildi). Ecdyonurusaurasius sp. nov. differs from E.ifranensis by the shape of the labrum (less broad in E.ifranensis), the shape of the stout setae on the dorsal surface of femora (pointed in E.ifranensis), and the shape of the glossae similar to E.rothschildi. In males, E.aurasius sp. nov. differs from E.rothschildi, E.dispar and E.aurantiacus by the compound eyes separated and not touching (character not stated in E.ifranensis description), from E.aurantiacus and E.dispar by the posterior margin of the basal sclerite smooth, and from E.ifranensis by the first transversal vein in the costal field surrounded by a dark brown maculation (the same in E.rothschildi), and by the shape of the posterior margin of the basal sclerite rounded (straight in E.ifranensis). It is also worth noting that E.aurasius sp. nov. differs from the two other North African species by the nervous ganglia tinted in purple in female imagos, whereas they are colorless in E.rothschildi and E.ifranensis.By the shape of the penis lobes and the posterolateral projections of the abdomen, E.dispar . The nymEcdyonurusaurasius sp. nov., as known so far, is restricted to the Aur\u00e8s region. The species has been recorded from only six localities in the Western Aur\u00e8s area; most habitats are located in the highest part of the streams, within altitudes ranging from 1010 to 1800 m a.s.l. These sites are represented by small mountain watercourses with gravel substrate and the lowest one was observed at the Bouailef site .ate Fig. . The aveEphemeroptera species sporadically occurring in the same sites were Caenisluctuosa , Baetischelif Soldan, Godunko & Thomas, 2005 and Baetissinespinosus Sold\u00e1n & Thomas, 1983.The mature nymphs and subimagos (together with early-instar nymphs) were observed in May/June and another generation observed in September/October, thus suggesting a bivoltine life cycle. The other"} +{"text": "Brain metabolic-sensory targets for modulatory glucose-sensitive endocrine and neurochemical signals remain unidentified. A hypothalamic astrocyte primary culture model was here used to investigate whether glucocorticoid receptor (GR) and noradrenergic signals regulate astrocyte glucose and/or energy (5\u2032-AMP-activated protein kinase [AMPK]) sensor reactivity to glucoprivation by sex. Glucose-supplied astrocytes of each sex showed increased GLUT2 expression after incubation with the GR agonist dexamethasone (DEX) or norepinephrine (NE); DEX plus NE (DEX/NE) augmented GLUT2 in the female, but not in male. Glucoprivation did not alter GLUT2 expression, but eliminated NE regulation of this protein in both sexes. Male and female astrocyte glucokinase profiles were refractory to all drug treatments, but were down-regulated by glucoprivation. Glucoprivation altered AMPK expression in male only, and caused divergent sex-specific changes in activated, i.e., phosphoAMPK (pAMPK) levels. DEX or DEX/NE inhibited or stimulated AMPK and pAMPK proteins in both glucose-supplied and -deprived astrocytes. In male, NE coincidently up-regulated AMPK and inhibited pAMPK profiles in glucose-supplied astrocytes; these effects were abolished by glucoprivation. In female, AMPK profiles were unaffected by NE irrespective of glucose status, whereas pAMPK expression was up-regulated by NE only during glucoprivation. Present outcomes document, for each sex, effects of glucose status on hypothalamic astrocyte glucokinase, AMPK, and pAMPK protein expression and on noradrenergic control of these profiles. Data also show that DEX and NE regulation of GLUT2 is sex-monomorphic, but both stimuli impose divergent sex-specific effects on AMPK and pAMPK. Further effort is warranted to characterize mechanisms responsible for sex-dimorphic GR and noradrenergic governance of hypothalamic astrocyte energy sensory function. AMPK5\u2032-AMP-activated protein kinaseCaMKK\u03b2calcium/calmodulin-dependent protein kinase kinase-betaDEXdexamethasoneGCKglucokinaseGLUT2glucose transporter-2IIHinsulin-induced hypoglycemiaNEnorepinephrinepAMPKphosphoAMPKPP1protein phosphorylase-11The glucose-regulatory neural circuitry monitors cellular metabolic status and systemic energy substrate storage to exert appropriate control of central and peripheral effector motor functions \u20135. Many l-lactate for trafficking to neurons and F = 19.86, p < 0.001; glucose status main effect: F = 16.63, p = 0.001; treatment main effect: F = 34.84, p < 0.001; glucose status/treatment interaction: F = 5.97, p = 0.006]) and GCK = 15.22, p < 0.001; glucose status main effect: F = 95.43, p < 0.001; treatment main effect: F = 2.49, p = 0.097; glucose status/treatment interaction: F = 1.20, p = 0.342] and F = 6.70, p = 0.001; glucose status main effect: F = 36.47, p < 0.001; treatment main effect: F = 3.25, p = 0.050; glucose status/treatment interaction: F = 0.220, p = 0.881]) protein expression in each sex. For each sex, treatment groups including astrocytes supplied with 5.5\u2009mM glucose (G5.5), at left, are illustrated by gray bars, while glucose-deprived (G0) treatment groups, at right, are shown in white. Data indicate that DEX or NE alone each significantly increased GLUT2 levels in glucose-supplied male and female astrocytes . DEX and NE co-incubation (cross-hatched gray bars) reduced or elevated GLUT2 content relative to vehicle controls. In each sex, GLUT2 protein profiles were unaffected by glucoprivation (G0/V [solid white bars] versus G5.5/V). In glucose-deprived male and female astrocytes, GLUT2 profiles were elevated by DEX , but were refractory to NE ; DEX plus NE treatment (cross-hatched white bars) increased GLUT2 expression to levels measured after incubation with DEX alone. In each sex, hypothalamic astrocyte GCK content was decreased in response to glucoprivation, but was altered by any drug treatment when glucose was present or absent.Research outcomes described below were obtained using a characterized hypothalamic primary astrocyte culture model to address the question of whether hypothalamic astrocyte primary cultures established from male and/or female rats express glucose-sensitive plasma membrane and glycolytic pathway glucose sensors, and these nutrient gauges are regulated by glucocorticoid or noradrenergic input alone or by interaction of these regulatory stimuli. F = 37.09, p < 0.001; glucose status main effect: F = 38.86, p < 0.001; treatment main effect: F = 54.84, p < 0.001; glucose status/treatment interaction: F = 18.78, p < 0.001] and F = 7.32, p = 0.001; glucose status main effect: F = 15.07, p = 0.001; treatment main effect: F = 11.24, p < 0.001; glucose status/treatment interaction: F = 0.82, p = 0.499]) and pAMPK = 19.16, p < 0.001; glucose status main effect: F = 13.28, p = 0.002; treatment main effect: F = 29.35, p < 0.001; glucose status/treatment interaction: F = 10.95, p < 0.001] and F = 21.65, p < 0.001; glucose status main effect: F = 3.68, p = 0.067; treatment main effect: F = 42.89, p < 0.001; glucose status/treatment interaction: F = 6.39, p = 0.002]) expression. Results show that glucose-supplied male astrocytes exhibited reductions in AMPK expression in response to DEX or NE alone; this negative response was exacerbated by DEX plus NE treatment. In the female, AMPK levels were elevated by DEX given alone or together with NE, but this protein was unaffected by NE alone. Glucose withdrawal suppressed AMPK content in male, but not female astrocytes. DEX alone or DEX plus NE decreased or stimulated AMPK expression in male versus female glucose-deprived astrocytes, respectively. Astrocyte pAMPK levels were diminished or augmented by DEX, according to sex. NE stimulated or had no effect on this protein profile in male versus female, respectively. In each sex, pAMPK content was affected similarly by DEX alone versus DEX plus NE treatment. Glucoprivation correspondingly up- or down- regulated pAMPK expression in male and female astrocytes. In glucose-deprived male glial cells, pAMPK profiles were refractory to DEX or NE, but were inhibited by DEX plus NE. Glucose-deprived female astrocytes, on the other hand, showed elevated pAMPK expression in response to all three treatments with the greatest magnitude of increase caused by DEX alone.The ultra-sensitive energy gauge AMPK monitors the cellular AMP/ATP ratio. Current work examined the premise that hypothalamic astrocyte total AMPK protein and/or activated, e.g., phosphorylated AMPK (pAMPK) protein profiles are affected by glucose withdrawal in a sex-specific manner, and the related question that AMPK activation may be differentially controlled by DEX or NE when glucose is present versus absent. Data presented in F = 7.26, p = 0.001; glucose status main effect: F = 6.05, p = 0.026; treatment main effect: F = 8.61, p = 0.001; glucose status/treatment interaction: F = 6.32, p = 0.005) or female = 11.13, p < 0.001; glucose status main effect: F = 8.34, p = 0.011; treatment main effect: F = 19.51, p < 0.001; glucose status/treatment interaction: F = 3.67, p = 0.035) astrocyte CaMMK\u03b2 protein profiles. Data reveal that CaMMK\u03b2 expression in glucose-supplied astrocytes of either sex was insensitive to DEX or NE treatment alone or together. NE inhibited this protein in glucose-deprived male cells; this decline was amplified by combinatory NE plus DE treatment. In female astrocytes incubated without glucose, CaMMK\u03b2 content was increased by exposure to either DEX or DEX plus NE. F = 9.63, p < 0.001; glucose status main effect: F = 32.24, p < 0.001; treatment main effect: F = 2.05, p = 0.147; glucose status/treatment interaction: F = 8.34, p = 0.005) or female = 6.82, p = 0.001; glucose status main effect: F = 37.94, p < 0.001; treatment main effect: F = 3.09, p = 0.057; glucose status/treatment interaction: F = 0.19, p = 0.903) astrocyte PP1 protein levels. NE alone had divergent effects on PP1 expression in male glucose-supplied (increased) versus glucose-deprived (decreased) astrocytes. NE plus DEX had no effect or suppressed PP1 profiles in male astrocytes when glucose was present or absent, respectively. Female astrocyte PP1 content was diminished during glucoprivation, but was insensitive to any drug treatment.AMPK activity is regulated in part by the upstream stimulatory kinase enzyme CaMMK\u03b2 as well as the inhibitory phosphatase PP1. It was of interest here to investigate whether action of DEX alone or in coordination with NE controls expression of these enzyme proteins in hypothalamic astrocytes. F = 17.04, p < 0.001; glucose status main effect: F = 38.47, p < 0.001; treatment main effect: F = 25.59, p < 0.001; glucose status/treatment interaction: F = 1.35, p = 0.295) or female = 5.14, p = 0.001; glucose status main effect: F = 6.70, p = 0.016; treatment main effect: F = 5.44, p = 0.005; glucose status/treatment interaction: F = 4.31, p = 0.014) astrocyte GR protein expression. Data show that GR protein was decreased in G5.5 male astrocytes after incubation with DEX, NE, or DEX plus NE, and that the magnitude of this reduction was greatest in response to the latter combinatory dosing. Meanwhile, GR expression in female G5.5 astrocytes was unaffected by any of these treatments. Glucoprivation did not modify GR expression in astrocytes of either sex. Treatment with either DEX or DEX plus NE resulted in diminished GR protein profiles in G0 male and female astrocytes.Research here addressed the issue of whether male and/or female rat hypothalamic astrocyte primary cultures are directly receptive to glucocorticoid control by means of GR expression, and if so, whether this receptor protein profile is sensitive to glucose availability and regulated by glucocorticoid and noradrenergic stimuli in the presence versus absence of glucose. F = 10.83, p < 0.001; glucose status main effect: F = 22.84, p < 0.001; treatment main effect: F = 9.43, p = 0.001; glucose status/treatment interaction: F = 8.23, p = 0.002] and F = 23.78, p < 0.001; glucose status main effect: F = 0.27, p = 0.608; treatment main effect: F = 52.99, p = <0.001; glucose status/treatment interaction: F = 2.40, p = 0.106]), \u03b12-AR = 20.78, p < 0.001; glucose status main effect: F = 77.61, p < 0.001; treatment main effect: F = 14.40, p < 0.001; glucose status/treatment interaction: F = 8.23, p = 0.002] and F = 14.31, p < 0.001; glucose status main effect: F = 5.52, p = 0.032; treatment main effect: F = 15.74, p < .001; glucose status/treatment interaction: F = 15.80, p < 0.001]), and \u03b21-AR = 3.09, p = 0.029; glucose status main effect: F = 7.39, p = 0.015; treatment main effect: F = 2.02, p = 0.152; glucose status/treatment interaction: F = 2.74, p = 0.077] and F = 7.45, p < 0.001; glucose status main effect: F = 5.86, p = 0.023; treatment main effect: F = 7.13, p = 0.001; glucose status/treatment interaction: F = 8.36, p = 0.001]) protein expression. Data show that DEX alone inhibited \u03b11-AR protein, but did not regulate \u03b12-AR or \u03b21-AR levels in glucose-supplied male astrocytes. However, DEX alone stimulated each of these AR variant proteins in the female. Glucoprivation did not alter \u03b11-AR, \u03b12-AR, or \u03b21-AR expression profiles in the male, but up-regulated \u03b12-AR and \u03b21-AR levels in female astrocytes. In glucose-deprived male astrocytes, DEX decreased \u03b12-AR content, while NE suppressed \u03b11-AR and \u03b12-AR proteins. DEX plus NE had an equivalent effect to DEX alone on \u03b11-AR expression, but had greater inhibitory effects on \u03b12-AR levels compared to DEX or NE alone. Female glucose-deprived astrocytes showed augmentation of \u03b11-AR and \u03b12-AR, but not by \u03b21-AR by DEX. DEX plus NE increased \u03b11-AR levels to an extent similar to DEX alone, but did not alter \u03b12-AR expression. Both NE alone and NE plus DEX inhibited \u03b21-AR profiles in female astrocytes deprived of glucose.A critical objective of current work was to examine whether glucose status controls AR variant protein expression in male and female hypothalamic astrocytes, and to determine if DEX and NE act alone or synergistically to regulate these proteins during glucose availability versus deprivation. 4in vivo regarding neural control of glucose homeostasis in each sex.The current project used a hypothalamic astrocyte primary culture model to address the premise that these glia express glucoprivic-responsive glucose and energy sensing molecular biomarkers, and that glucose-sensitive hormone (glucocorticoid) and/or neurotransmitter (noradrenergic) stimuli govern sensor reactivity to glucose deficiency in a sex-specific manner. Outcomes show that in astrocytes of each sex, membrane glucose sensor GLUT2 and glycolytic pathway sensor GCK protein profiles are controlled by GR and AR input or by glucose, respectively. Yet, expression and activity of the energy sensor AMPK in these cells is subject to sex-dimorphic regulation by DEX, NE, and glucose. Results provide novel evidence that glucose modulates noradrenergic control of astrocyte GLUT2 (both sexes), AMPK , pAMPK (both sexes), and \u03b11- and \u03b12-AR proteins. Evidence that co-administration of NE and DEX to male, but not female astrocytes attenuates (GLUT2) or exacerbates , effects of DEX alone infers that intersection of GR and AR signaling may be sex-specific. Ongoing work seeks to elucidate mechanisms that underlie differential male versus female astrocyte responses to GR or NE stimulation. There is also a need for understanding of functional implications of glucocorticoid and noradrenergic regulation of hypothalamic astrocyte metabolic sensory functions Present outcomes document expression of the characterized glucose sensors GLUT2 and GCK by hypothalamic astrocytes, and show that GR and AR input regulates the former, but not the latter protein in each sex. Evidence here that DEX treatment augments GLUT2 profiles in astrocytes of either sex, despite dissimilar regulatory effects of DEX on male (decreased) versus female (unchanged) astrocyte GR expression, infers that glucocorticoids may control GR input volume as well as post-receptor signaling in a sex-specific manner. GLUT2 ostensibly employs distinctive structural features to perform glucose transport versus monitoring functions . Data heThe characterized DEX dosage used here down-regulated astrocyte AMPK and pAMPK in male, but stimulated these proteins in the female, revealing bi-directional, sex-specific glucocorticoid regulation of AMPK expression and activity state in this brain cell type. This divergent hormone action may involve, in part, dissimilar GR signal volume in the two sexes as GR protein expression declined in DEX-treated male astrocytes, but was unaffected by this treatment in the female. DEX may also impose sex-contingent control of downstream post-receptor signaling, transcriptional, and/or post-translational events that govern astrocyte AMPK and pAMPK protein profiles. As the current study focused on a single DEX dose, there would be benefit from future investigation of whether varying GR ligand concentrations elicit proportionate modifications in AMPK and pAMPK levels over all or a segment of a comprehensive, physiological-like dosage range. There also remains a need to assess whether suppressive versus amplifying stimulatory effects of DEX on AMPK and pAMPK expression are associated with specific hormone concentration(s). Our findings that glucoprivation attenuates DEX-induced augmentation of male astrocyte pAMPK content infer that metabolic modulation of GR-mediated action on AMPK activation state may occur in this sex only. Noradrenergic control of this astrocyte energy sensor is evidently also sex-specific as NE incubation suppressed total AMPK protein and stimulated pAMPK levels in male astrocytes, yet had no effect either on protein profile in the female. Notably, glucoprivation was observed to elicit a directional shift in NE control on male astrocyte AMPK, and to promote a loss or gain of NE regulation of pAMPK profiles in male versus female, respectively. These data point to sex-dependent metabolic modulation of noradrenergic governance of hypothalamic astrocyte AMPK activity.Current results show that neither DEX nor NE regulates the upstream stimulatory kinase CaMKK\u03b2 in the presence of glucose, yet during glucoprivation DEX elevates this protein profile in the female, while NE suppresses CaMKK\u03b2 expression in the male. PP1 levels in glucose-supplied astrocytes of either sex are similarly refractory to DEX, whereas NE enhances this protein in the male only. Notably, the direction of noradrenergic control of PP1 expression in male astrocytes is altered, e.g., switches from stimulatory to inhibitory when glucose is withdrawn. These outcomes support the novel concept that astrocyte energy status may determine whether glucocorticoid and noradrenergic signals are able to regulate astrocyte AMPK activity via upstream enzymes that govern phosphorylation, e.g., during glucose deficiency. DEX treatment of glucose-deprived female astrocytes stimulated CaMKK\u03b2 expression without affecting PP1 profiles, coinciding with up-regulated pAMPK. Thus, in this sex, CaMKK\u03b2 is likely required for glucocorticoid augmentation of AMPK activity. Interestingly, NE did not modify either CaMKK\u03b2 or PP1 expression, but also increased pAMPK profiles, apparently by kinase/phosphatase-independent mechanisms. Glucose-deprived male astrocyte CaMKK\u03b2 and PP1 profiles were resistant or inhibited by DEX, respectively, yet pAMPK expression was unaffected by either stimulus, inferring that potential augmentation of pAMPK levels by noradrenergic diminution of PP1 may be counter-balanced by signals that blunt AMPK activation.It is intriguing to observe that glucoprivic-associated diminution of astrocyte GCK expression coincided with up- or down-regulated pAMPK protein in male versus female, respectively. These findings infer that in the latter sex, augmenting effects of diminished glucose catabolism on sensor activity are apparently offset by regulatory signals that attenuate AMPK phosphorylation and/or decreased allosteric activation of AMPK due to energy production from non-glucose substrates.Present data also show that NE did not alter any astrocyte AR variant protein profile in either sex, but \u03b11-AR (both sexes), \u03b12-AR , and \u03b21-AR proteins are responsive to DEX. The observed efficacy of DEX to up-regulate all three AR variant proteins in the female may contribute to unique effects of combinatory DEX plus NE treatment on specific astrocyte target proteins in that sex. Glucose stability evidently modulates DEX regulation of specific AR proteins in each sex, as glucoprivation abolishes DEX inhibition of \u03b11-AR profiles and allows DEX to suppress \u03b12-AR levels in the male, and in the female eliminates DEX stimulation of \u03b21-AR expression. Glucoprivic governance of noradrenergic regulation of AR protein profiles is, on the other hand, sex-specific as this metabolic stress allows inhibitory noradrenergic control of \u03b11-AR and \u03b12-AR proteins in male hypothalamic astrocytes only.in vivo models of glucose-sensitive glucocorticoid and noradrenergic signaling to the hypothalamus to understand, for each sex, hormonal and neurotransmitter regulation of astrocyte sensing and communication of cellular energetic stability or imbalance.In summary, current research presents unique proof that hypothalamic astrocytes express membrane and glycolytic pathway glucose-sensory biomarkers in addition to the energy sensor AMPK . Results"} +{"text": "Existing chemotherapy treatments for breast cancer patients are high on toxicity. There are very limited options available for triple-positive breast cancer (TPBC) patients, and there have not been any major breakthrough for targeted therapy for triple-negative breast cancer (TNBC) patients. Therefore, there is a need to identify common therapeutic targets for breast cancer patients. In this manuscript, we compared the sphingolipid profiles of cancer cell lines representing TPBC and TNBC, and correlated these profiles with the proliferation and migration properties the of cell types. We then associated the sphingolipid profiles for each subtype specific cell line with transcriptional and translational expression of corresponding metabolizing enzymes. Our results suggested that ceramide kinase (CERK) that catalyzes the synthesis of ceramide-1-phosphates from ceramides is dysregulated in both cell types. We also showed that the targeting of CERK at transcriptional level by siRNA therapeutics or inhibiting the CERK activity by hydrogel-mediated delivery of chemical inhibitors can be an effective strategy to slow down the tumor progression. Therefore, CERK emerges as a potential therapeutic target that can be explored further for cancer therapy.Sphingolipids are key signaling biomolecules that play a distinct role in cell proliferation, migration, invasion, drug resistance, metastasis, and apoptosis. Triple-negative (ER\u2212PR\u2212HER2\u2212) and triple-positive (ER+PR+HER2+) breast cancer subtypes reveal distinct phenotypic characteristics and responses to therapy. Here, we present the sphingolipid profiles of BT-474 and MDA-MB-231 breast cancer cell lines representing the TPBC and TNBC subtypes. We correlated the level of different classes of sphingolipids and the expression of their corresponding metabolizing enzymes with the cell proliferation and cell migration properties of BT-474 and MDA-MB-231 cells. Our results showed that each cell type exhibits a unique sphingolipid profile, and common enzymes such as ceramide kinase are deregulated in these cell types. We showed that siRNA/small molecule-mediated inhibition of CERK can alleviate cell proliferation in BT-474 and MDA-MB-231 cells, and cell migration in MDA-MB-231 cells. We further demonstrated that nanoparticle-mediated delivery of CERK siRNA and hydrogel-mediated sustained delivery of CERK inhibitor to the tumor site can inhibit tumor progression in BT-474 and MDA-MB-231 tumor models. In summary, distinct sphingolipid profiles of TPBC and TNBC representing cell lines provide potential therapeutic targets such as CERK, and nanoparticle/hydrogel mediated pharmacological manipulations of such targets can be explored for future cancer therapeutics. Lipid reprogramming has emerged as a key hallmark for cancer pathogenesis ,2. SphinCeramide, the central player in the sphingolipid pathway, induces apoptosis and cell senescence in response to chemotherapy and radiation therapy A 9,10].,10.9,10]+ tumors), and are categorized as triple-positive (TPBC) phenotypes . A. A21]. Aenotypes . Therefoenotypes . In contenotypes . Chemothenotypes ,28.Each breast cancer subtype has a unique molecular portrait that influences its response to therapy, prognosis, and outcome. Earlier studies have reported the sphingolipid profile in luminal (ER+PR+) and TNBC (ER\u2212PR\u2212HER2\u2212) subtypes ,30. Howe\u00ae, Saint Louis, MO, USA. Fetal bovine serum (Cat#10270) was purchased from, Waltham, MA, USA. Matrigel (Cat#354234) was purchased from Corning Inc., Bedford, MA, USA. Penicillin-Streptomycin solution (SV30079) was purchased from Cytiva HyCloneTM, South Logan, OH, USA. Trypsin (Cat#TCL007), MEM Medium (Cat#AL081) and sodium bicarbonate (GRM849) were purchased from HiMedia Laboratories, Mumbai, India.Materials. Human breast cancer cell lines BT-474 and MDA-MB-231 were purchased from American Type Culture Collection . DMEM (Cat#D5648), DPBS (Cat#D5652), Crystal Violet Dye (Cat#C0775) were purchased from Sigma\u2013AldrichTM DNase (Cat#AM2238) was from Invitrogen, Vilnius, Lithuania. iScriptTM cDNA synthesis kit (Cat#1708891) and iTaq\u2122 universal SYBR\u00aeGreen Supermix (Cat#1725124) were purchased from Bio-Rad Laboratories, Hercules, CA, USA. RNase Inhibitor (Cat#AM2694), and PierceTM BCA protein assay kit (Cat#23227) were purchased from Thermo Scientific. Complete\u2122, Rockford, IL, USA. Protease Inhibitor Cocktail (P8340-1ML) was purchased from Sigma\u2013Aldrich\u00ae, Saint Louis, MO, USA. Sigma. CerK siRNA (Cat#L-004061-00-0005) and scrambled siRNA (Cat# D-001810-10-05) were purchased from Dharmacon Inc., Cambridge, UK. Ceramide Kinase Inhibitor, NVP231 (Cat#3960) was purchased from Tocris Bioscience, Bristol, UK.Lipofectamine 2000 (Cat#11668019) and TURBO\u00ae Polar Lipids, Inc., Alabaster, OK, USA. LASS1 (CERS1) (Cat#H00010715-A01), LASS2 (CERS2) (Cat#H00029956-M01A), LASS4 (CERS4) (Cat#H00079603-M01), LASS6 (CERS6) (Cat#H00253782-M01) were purchased from Abnova, Taipei, Taiwan. LASS5 (CERS5) (Cat#ab73289), CerK (Cat#ab155061), SPHK1 (Cat#ab109522), SPHK2 (Cat#ab264042), A-SMase (SMPD1) (Cat#ab83354), N-SMase1 (SMPD2) (Cat#ab131330), N-SMase2 (SMPD3) (Cat#ab199399), N-SMase3 (SMPD4) (Cat#ab133935), UGCG (Cat#ab124296), SMS1 (Cat#ab135365), SMS2 (Cat#ab237681), GBA1 (Cat#ab88300), GLB1 (Cat#ab96239), B4GALT6 (Cat#ab200639), Goat anti-mouse IgG (L+H) (Cat#ab6789) were purchased from Abcam, Cambridge, UK. ASAH1 (Cat#HPA005468), ASAH2 (Cat#ABS457), \u03b2-actin (Cat#A5541) were purchased from Sigma\u2013Aldrich\u00ae, Saint Louis, MO, USA. Goat anti-rabbit IgG-HRP was purchased from (Cat#sc-2004) Santa Cruz Biotechnology, Inc., Dallas, TX, USA. Ceramide/Sphingoid Internal Standard Mixture II (Cat#LM6005-1EA) was purchased from AvantiN,N\u2032-methylene bisacrylamide (Cat#M7279), glycine (Cat#G8898), MTT (Cat#M5655), triethyl ammonium bicarbonate buffer (Cat#T70408), and iodoacetamide (144-48-9) were purchased from Sigma\u2013Aldrich\u00ae, Saint Louis, MO, USA. Tris (Cat#MB029), NaCl (Cat#GRM853), polyoxyethylenesorbitan monolaurate (Tween\u00ae 20) (Cat#P7949), glycerol (Cat#GRM1027), bovine serum albumin fraction-V (Cat#GRM105) were purchased from HiMedia Laboratories, Mumbai, India. Paraformaldehyde (PFA) (Cat 81847) was purchased from Thomas Baker, Mumbai, India. Ammonium hydroxide (Cat#16227) and hydrochloric acid (Cat#29505) was purchased from Thermo Fisher Scientific, Waltham, MA, USA. MOPS free acid (Cat#MB0360) and acrylamide (Cat#AB1032) were purchased from Bio Basics Inc., Markham, ON, Canada. Sodium hydroxide (Cat#13913) and potassium hydroxide (Cat#84749) was purchased from Sisco Research Laboratories Pvt. Ltd., Maharashtra, India. Developer (Cat#4908216), Fixer (Cat#4908232) and XBT X-Ray film (Cat#6568307) were purchased from Carestream, Rochester, NY USA. Transwell Migration Plate (Cat#3464) was purchased from Corning Inc., Bedford, MA, USA. Nitrocellulose (Cat#HATF00010), Immobilon Western Chemiluminescent HRP substrate (Cat#WBKLS0500), ethanol (Cat#100983), glacial acetic acid (Cat#193402), chymotrypsin (11418467001), DMSO (Cat#276855), ethidium bromide (Cat#E8751), agarose (Cat#A9539), magnesium chloride (Cat#208337), sodium dodecyl sulfate (Cat#L3771), ammonium persulfate (Cat#A3678), Methanol (Cat#34966), chloroform (Cat#25669-1L), 2-propanol (Cat#34965), acetonitrile (Cat#34967), ammonium acetate (Cat#14267-25G), formic acid (Cat#56302-50ML), water (Cat#39253-4L) and ammonium formate (Cat#14266-25G) were purchased from Honeywell International Inc., Charlotte, NC, USA. ACQUITY UPLC BEH Shield RP18 column (Cat#186002854) was purchased from Waters\u2122 Ltd., Milford, MA, USA.2 in humidified incubator. Cell culture. Human breast cancer cell lines BT-474 and MDA-MB-231 were cultured in DMEM high glucose media with 10% Fetal bovine serum, 100 units/mL penicillin, and 100 \u00b5g/mL streptomycin. Cells were grown at 37 \u00b0C with 5% CO5 per well) were seeded in six-well plate in DMEM media with 10% FBS and 10% penicillin and streptomycin, and incubated at 37 \u00b0C in CO2 incubator for 24 h. At 80\u201385% confluency, siRNA-lipofectamine complexes in 1:3 ratio were incubated for 25 min in MEM media, and cells were transfected with these complexes. After 6 h of transfection, media was removed, and cells were incubated with antibiotic-free media containing 10% FBS for 36 h. CERK silencing was confirmed by Western blotting.siRNA transfections in cell culture. BT-474 and MDA-MB-231 cells were transfected with siRNA (targeting CERK or scrambled) using Lipofectamine 2000. BT-474 and MDA-MB-231 cells (5000 cells/well) were used, and cell proliferation assay was performed following previously described method [For transwell migration assay, BT-474 and MDA-MB-231 cells or siRNA transfected cells (scrambled or CERK siRNA) transfected cells were seeded in transwell inserts (4 \u00b5m pore size). We then placed the inserts in 24-well cell culture plates containing DMEM with 10% FBS and incubated for 24 h at 37 \u00b0C. We fixed the migrated cells in 4% paraformaldehyde (PFA) (~5 min), and permeabilized with methanol (20 min). Cells were then stained with 2% crystal violet dye (15 min) followed by PBS washing to remove the extra stain on the cell surface. Cells were counted manually and imaged using a Nikon microscope. Pellet collection for RNA and protein isolation. For RNA isolation, cells were grown in 100 mm cell culture plates for 90% confluency. For pellet collection, media was aspirated from the plates and washed two times with DPBS. Trizol (1 mL) was added to the plate, and plates were incubated for 5 min. After incubation, cells were scraped and transferred into 1.5 mL centrifuge tubes, and were used immediately or stored at \u221280 \u00b0C. For protein isolation, cells were similarly washed, scraped out in DPBS, centrifuged at 5000 rpm for 5 min, and used immediately or stored at \u221280 \u00b0C.Quantitative Real-Time PCR. Total RNA extraction and qRT-PCR studies were performed using previously described method . All priWestern Blotting. Protein expression analysis was performed by Western blotting as per previously described method . ProteinIsolation and quantification of sphingolipids using LC-MS/MS. Collection of cell pellets, lipid isolation, LC-MS/MS analysis, and absolute quantitation of sphingolipids was performed as per our previously published method .Animal studies. Animal experimental protocols were reviewed and approved by the Institutional Animal Ethics Committee of Regional Centre for Biotechnology (RCB/IAEC/2021/96). The experiments were carried out as per the guidelines issued by Committee for the Purpose of Control and Supervision of Experiments on Animals (CPCSEA), Govt. of India.6 cells were injected subcutaneously in the flank. Once the tumor was palpable (20\u201330 mm3), tumor volume and weight of the mice were recorded after every two days. Tumor volume was calculated as per the formula, L \u00d7 B2/2 where L is the length of tumor and B is breadth of tumor. At the end of the experiment, tumors were excised, washed with ice-cold 1X PBS, and stored in Allprotect tissue reagent at \u221280 \u00b0C for further analysis. All tumor growth kinetic experiments were performed in female NOD SCID CB.17 mice. Prior to the cell injection, hair was shaved from flank of the mice. For comparative tumor kinetics experiments, respective cell lines (BT-474 and MDA-MB-231) were resuspended in FBS: Matrigel , and 3 \u00d7 103) were randomized into different groups with each group having 4\u20136 mice. Group 1 mice were left untreated, group 2 mice were injected intratumorally with scrambled siRNA, and group 3 mice were treated with target siRNA. The siRNA was injected in a volume of 40 \u00b5L with 300 ng of siRNA complexed with TAC6 polymer at the tumor site [For siRNA experiments, mice with palpable tumor were randomized into different groups with each group having 4\u20136 mice. Group 1 mice were left untreated, and group 2 mice were implanted subcutaneously with inhibitor (NVP-231)-loaded hydrogel [For inhibitor experiments, mice with palpable tumor .Visualization of sphingolipid metabolic pathways. Expression of genes involved in sphingolipid metabolism were quantified using RT-PCR. Protein levels were probed by Western blots and quantified using ImageJ, followed by normalization against actin. Lipidomics experiments were performed to quantify the metabolite (sphingolipid) levels. Log2 (fold changes) were calculated for MDA-MB-231 against BT-474 cells. The visualization was made using drawio, a cross-platform JavaScript based open source drawing application available on GitHub at We selected BT-474 and MDA-MB-231 breast cancer cell lines representing TPBC and TNBC subtypes. To quantify the levels of sphingolipid species in these two cell lines, we collected cell pellets, and isolated the total lipids enriched in sphingolipids. We performed qualitative and quantitative sphingolipidomics with absolute quantitation of 27 sphingolipid species including ceramides, glucosylceramides, lactosylceramides, sphingomyelins, ceramide-1-phosphates (C1P), sphingosine, and sphingosine-1-phosphate (S1P) using LC-MS/MS [p < 0.01), C18:0 , C22:0 , C24:0 , and C24:1 were elevated in MDA-MB-231 cells in comparison to BT-474 cells (p < 0.05), C18:0 , C20:0 , C22:0 , C24:0 , and C24:1 , are downregulated in MDA-MB-231 cells as compared to BT-474 cells (p < 0.05) (p < 0.05) species as compared to BT-474 cells (p < 0.05), C18:0 , C20:0 , C22:0 , and C24:0 , are less abundant in MDA-MB-231 cells as compared to BT-474 cells (p < 0.05), C18:0 , C20:0 , C22:0 , C24:0 and C24:1 , are elevated in MDA-MB-231 cells (p < 0.01) increase in levels of S1P and C24:74 cells . We also74 cells C. It is 31 cells D. We alss of S1P in MDA-Ms of S1P . TherefoSPT1) , SPT2 , delta 4-desaturase, sphingolipid 1 and 2 (DEGS1) , DEGS2 , and 3-ketodihydrosphingosine reductase (KDSR) as compared to BT-474 cells , CERS2 , CERS3 , CERS4 , CERS5 , and CERS6 in MDA-MB-231 cells as compared to BT-474 cells , ASAH2 , alkaline ceramidase 1 and 3 ACER1 , and ACER3 are significantly upregulated in MDA-MB-231 cells as compared to BT-474 cells (p < 0.0005) in the expression of sphingosine kinase 1 (SPHK1) and a ~3.3-fold (p < 0.0005) increase in SPHK2 as compared to BT-474 cells that, again, positively correlates to higher S1P levels in MDA-MB-231 cells (p < 0.01) decrease in the expression of S1P lyase (S1PL) in MDA-MB-231 cells over BT-474 cells.Among salvage pathway genes, expression of 74 cells . This inP levels B. Furthe31 cells B that coSMPD1) (p < 0.0001), SMPD2 , SMPD3 , and SMPD4 in MDA-MB-231 cells as compared to BT-474 cells (SMS1) (p < 0.0001), and downregulation of SMS2 (p < 0.0001) in MDA-MB-231 cells in glucosylceramide synthase (UGCG) and a >50-fold increase (p < 0.01) in the expression of B4GALT6 in MDA-MB-231 cells in comparison to BT-474 cells in glucosylceramidase 1 (GBA1) expression, responsible for breakdown of glucosylceramides, but we could not detect galactosidase (GLB1) expression due to low transcript levels. High expression of B4GALT6, thereby, support high lactosylceramide levels in MDA-MB-231 cells as compared to BT-474 cells in spite of high GBA1 expression (We observed a >100.0-fold increase (74 cells D. In spipression D.p < 0.05), CERS4 , CERS5 , but there was >2.0-fold (p < 0.05) decrease in the expression of CERS6 in comparison to BT-474 cells gene expression in MDA-MB-231 cells as compared to BT-474 cells but it is not translated to protein expression, that might be due to different post-transcriptional and post-translational regulatory changes (p < 0.001) in MDA-MB-231 as compared to BT-474 cells is very well correlated with gene expression data and lower levels of sphingomyelins in MDA-MB-231 cells (p < 0.05), SMS2 and lower levels of SMPD4 as compared to BT-474 cells increase in the expression of ASAH1 as expected from gene expression data, whereas there was no significant change in ASAH2 protein expression (p < 0.05), SPHK1 , and SPHK2 proteins in MDA-MB-231 cells as compared to BT-474 cells (p < 0.01) increase in UGCG expression in MDA-MB-231 cells in comparison to BT-474 cells, but there was a >7.5-fold decrease (p < 0.05) in the expression of B4GALT6 (p < 0.05) and low expression of GLB1 in MDA-MB-231 cells as compared to BT-474 cells proliferation at 72 h as compared to MDA-MB-231 cells (p < 0.001) increase in migration of MDA-MB-231 cells as compared to BT-474 cells were plated in 96-well plate, and proliferation index was determined by MTT assay. We observed that BT-474 cells exhibit >2.5-fold higher of BT-474 cells after 72 h (p < 0.05) decrease in the number of colonies in BT-474 cells (p < 0.001) in cell proliferation (p < 0.001) (p < 0.0001) on knockdown of CERK by siRNA in MDA-MB-231 cells E, and ce31 cells F.p < 0.05) decrease in cell proliferation (p < 0.01) decrease in number of colonies over untreated cells (p < 0.0001) decrease in cell proliferation of MDA-MB-231 cells on treatment with 1.0 \u00b5M of NVP-231 (p < 0.0001) decrease in number of colonies (p < 0.0001) decrease in number of migrated cells decrease in tumor volume on final day (p < 0.0001) decrease in tumor volume on final day decrease in tumor volume with NVP-231-Gel treatment on the final day as compared to untreated tumors (p < 0.05) decrease in volume of MDA-MB-231 tumors on final day , and worst prognosis, shorter survival and higher recurrence rate were positively associated to higher CERK expression among ER-negative cancers ,43. CERKPolymeric and lipid nanoparticles have emerged as effective delivery vehicles for gene therapeutics . In our CERK appears to be playing different roles in more aggressive metastatic breast cancer cell lines versus non-metastatic cell lines targeting cell migration and cell proliferation in a context-dependent manner. Hence, CERK can be a potential target for multiple breast cancer subtypes. However, more studies elucidating the molecular mechanism by which CERK controls these phenotypes and the extent of overlap in the pathways regulating them needs to be performed."} +{"text": "Infections caused by multidrug-resistant (MDR) bacteria are an increasingly common public health threat associated with worse outcomes in immunocompromised patients. Eravacycline (ERV) has potent in-vitro activity against MDR Gram-negative and Gram-positive bacteria and has demonstrated non-inferiority to meropenem in the phase III IGNITE4 trial; however, the trial excluded immunocompromised patients. We aimed to evaluate clinical and safety endpoints of immunocompromised patients receiving ERV as definitive therapy.Multicenter, retrospective, observational study conducted from October 2018 to April 2022. Adult hospitalized immunocompromised patients treated with ERV for \u226572 hours were included. Immunocompromised patients were defined as having any of the following: chemo or radiation therapy < 30 days of hospital admission, HIV/AIDS with CD4 < 200, chronic steroids age was 62 (53-70) and 61.6% were male. Hospital length of stay was 28 (13-42) days and 67% were admitted to the intensive care unit. SOFA and APACHE II scores were 3.5 (1-7) and 16 (11-20), respectively. Common infection sources were intra-abdominal (26%) and lower respiratory tract (18%); 24% were bacteremic. Most patients had cultured Enterobacterales (58.7%) and Enterococci (37%) spp. infections. Of those, 21.3% were CRE and 19% were VRE. Infectious diseases consult was obtained in 91.8% of cases. Time elapsed from index culture collection to ERV initiation was 4 (2-8) days and duration of ERV therapy was 7 (4-12) days. In total, 81.3% of immunocompromised patients achieved 30-day survival and 90.7% did not have 30-day infection recurrence. Probable drug-related adverse events occurred in 5.3% of patients .A majority of immunocompromised patients receiving ERV as definitive therapy achieved 30-day survival and did not experience infection recurrence. ERV use in immunocompromised subpopulations will benefit from studies tailored to their specific characteristics.Kimberly C. Claeys, PharmD, BioFire Diagnostics: Honoraria Bruce M. Jones, Pharm.D., FIDSA, BCPS, AbbVie: Advisor/Consultant|AbbVie: Honoraria|La Jolla: Honoraria|Melinta: Advisor/Consultant|Paratek: Honoraria|Regeneron: Honoraria."} +{"text": "Respiratory syncytial virus (RSV) is a public health burden; no vaccine is currently available. An mRNA-based RSV vaccine (mRNA-1345) encoding the RSV prefusion stabilized F (preF) glycoprotein is under clinical investigation.A phase 1, randomized, observer-blind, placebo-controlled, dose-ranging study assessed safety and immunogenicity of mRNA-1345 in younger adults and older adults (NCT04528719). YA and OA were randomized to receive 1 dose of mRNA-1345 or placebo.In all, 74 YA participants and 202 OA participants received study injections. mRNA-1345 was well-tolerated in both groups, with lower reactogenicity observed in OA vs YA at higher doses. Injection site pain was the most frequent local solicited adverse reaction . Erythema and swelling were less frequent . Overall, 57.9-100% (YA) and 53.2-78.7% (OA) of mRNA-1345 and 40.0% (YA) and 45.5% (OA) of placebo groups reported \u2265 1 systemic SAR, most commonly headache, fatigue, myalgia, and arthralgia. As expected, neutralizing antibodies (nAbs) were present at baseline ; mRNA-1345 significantly boosted antibody titers through month (M) 1 in YA and OA, with comparable immunogenicity observed across age groups. M1 geometric mean fold rise (GMFR) for RSV-A nAbs were 20.0-22.3 (YA) and 12.1-16.6 (OA) and for RSV-B, nAbs were 11.7-14.4 (YA) and 8.7-12.6 (OA). M1 PreF binding antibody (bAb) GMFRs were 16.1-21.7 (YA) and 8.4-12.1 . Peak antibody titers declined through M6, but levels remained \u2265 4.1-fold above BL with minimal dose response. M6 GMFR for RSV-A nAbs were 7.0-9.6 (YA) and 4.1-5.8 (OA) and for RSV-B, nAbs were 5.0-8.9 (YA) and 4.5-5.5 (OA). M6 PreF bAbs GMFR were 5.9-7.0 (YA) and 4.1-4.7 (OA). Antibody decline over time was comparable in YA and OA cohorts.mRNA-1345 is well-tolerated in YA and OA. Antibody levels were boosted substantially above BL through M6 in both cohorts. These data support the continued development of mRNA-1345 as an RSV vaccine.Grace L. Chen, MD, MPH, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Runa Mithani, PharmD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Archana Kapoor, PhD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Sophia Lu, PhD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Laila El Asmar, PhD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Catherine A. Panozzo, PhD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Christine A. Shaw, PhD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Sonia K. Stoszek, PhD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Allison August, MD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds."} +{"text": "Correction: Environ Health 20, 44 (2021)https://doi.org/10.1186/s12940-021-00726-xFollowing the publication of the original article , the autCV70 ultrasound imaging system using a linear array 7.5 MHz transducer .In brief, high resolution B-mode ultrasound carotid artery images were acquired using a Siemens Acuson However, the correct information should state:X 300 ultrasound imaging system using a linear arrayVF 10-5 (8.0 MHz) transducer .In brief, high resolution B-mode ultrasound carotid artery images were acquired using a Siemens Acuson"} +{"text": "Brassica species, and they play important roles in defense due to their anti-nutritive and toxic properties. Here, we conducted a genome-wide association study of six glucosinolate metabolites (mGWAS) in rapeseed, including three aliphatic glucosinolates , one aromatic glucosinolate (m157 gluconasturtiin) and two indole glucosinolates (m165 indolylmethyl glucosinolate and m172 4-hydroxyglucobrassicin), respectively. We identified 113 candidate intervals significantly associated with these six glucosinolate metabolites. In the genomic regions linked to the mGWAS peaks, 187 candidate genes involved in glucosinolate biosynthesis and novel genes were predicted based on the mGWAS, combined with analysis of differentially expressed genes. Our results provide insight into the genetic basis of glucosinolate biosynthesis in rapeseed and should facilitate marker-based breeding for improved seed quality in Brassica species.Glucosinolates (GSLs) are secondary plant metabolites that are enriched in rapeseed and related Brassica species, providing these plants with their pungent odor [Glucosinolates (GSLs) are secondary metabolites comprising sulfur and nitrogen that are specially produced in ent odor ,2,3. GSLent odor ,5. Howevent odor ,7,8,9,10\u03b2-D-thiosaccharide and (Z)-n-hydroxamic sulfate, but have variable R-side chain groups due to the precursor amino acids [\u03b3-glutamyl peptide (GGP1) and C-S lyase (Super root 1 (SUR1)), and then to the GSL core structure by glucosyltransferases (UGT74s) and sulfotransferases (SOTs) [O-methyltransferases (IGMTs) for indole GSLs [Generally, GSLs share the same basic structure, including no acids . The lenno acids ,13,14. Tno acids ,16, whicno acids ,17,18,19s (SOTs) ,22,23,24s (SOTs) . The corole GSLs ,27,28.Arabidopsis, the glucosinolate biosynthesis pathway is one of the best characterized specialized metabolite pathways [AtTSB1, AtCYP79B2, AtCYP79B3, AtCYP83B1 and AtST5a and so on), leading to the accumulation of GSLs [MYB51 and the GSL biosynthesis gene CYP83B1 to regulate the de novo biosynthesis of indole GSLs, but also regulates the expression of genes involved in side chain modification , thereby increasing the biosynthesis of indole GSLs [In pathways . Progrespathways ,32,33,34 of GSLs . The ali of GSLs ,37, whil of GSLs ,39. Seve of GSLs . Further of GSLs ,41. A reole GSLs .Brassica napus L.) is used worldwide as an oil crop and source of edible vegetable oil and feed meal. Therefore, breeding rapeseed varieties with low GSL levels in seeds is an important breeding goal. To date, many rapeseed resources with low seed GSL contents have been developed in polyploid rapeseed [B. napus seeds has been challenging. In this study, we performed a genome-wide association study for six glucosinolate metabolites in 143 rapeseed accessions using 239,945 SNP markers obtained by resequencing [B. napus with improved quality.Rapeseed , whereas the level of m172 showed a higher correlation with those of three aliphatic GSLs than with that of m165 (Based on ultrahigh-performance liquid chromatography-heated electrospray ionization-tandem mass spectrometry (UPLC-HESI-MS/MS) analysis, we obtained six glucosinolate metabolites with high content in rapeseed at 35 days after flowering (DAF), including three aliphatic GSLs , one aromatic GSL (m157 gluconasturtiin) and two indole GSLs (m165 indolylmethyl-glucosinolate and m172 4-hydroxyglucobrassicin) a,b. Corr of m165 , indicat of m165 . The coe of m165 . Further of m165 , indicat of m165 . Therefo of m165 a, but al of m165 b.p-value < 4.17 \u00d7 10\u22126. The results of mGWAS for the six glucosinolate metabolites in two years (2017cq and 2018cq) and BLUP (best linear unbiased prediction) values values are summB. napus genome in two years and BLUP values. In addition, qGSL-A01-4, qGSL-A02-2, qGSL-A03-3, qGSL-A05-2, qGSL-A06-1, qGSL-A06-3, qGSL-A09-6, qGSL-A09-7, qGSL-C04-2 and qGSL-C08-5 were repeatedly detected in at least one year or BLUP value. In these repeatedly detected interval regions, most of them were simultaneously associated with three glucosinolate metabolites or any two of these [Based on the physical positions of the significant SNPs, we mapped the intervals to the corresponding chromosomes of the reference genome h (v4.1) and searBased on the known GSL biosynthesis pathway, we identified 64 candidate genes in the GSL biosynthesis pathway (including genes encoding enzymes in this pathway and their homologs) among the intervals, which showed differential expression during seed development in BnHG vs. BnLG . \u03b3-glutamyl peptidase 1 (GGP1), S-alkyl thiohydrogen oxidase lyase (SUR1), sulfotransferases , flavin-monooxygenase glucosinolate S-oxygenase 5 (FMOGS-OX5), oxoglutarate-dependent dioxygenase (AOP3) and indole-glucoside O-methyltransferases , were identified on the following chromosomes: A01 , A02 , A03 , A04 , A05 , A06 , A07 , A08 , A09 , C02 , C04 , C06 and C07 , respectively , methylthioalkyl malate synthase (MAM1), bile acid transporter (BAT5), cytochrome P450s , UDP-glucosyl transferases , glutathione S-transferases , ectively , indicatMYB34, MYB51, MYB122 and WRKY33, which are involved in GSL biosynthesis [B. napus.Previously studies have identified MYB transcription factors that regulate GSL biosynthesis in various plants ,38,50,69ynthesis ,70, were\u03b2-glucosidases (BGLUs), one ABC transporter family protein (PEN3) and six glucosidolate glucohydrolases (TGGs), respectively , three nitrile specifier proteins (NSPs), one glutathione gamma-glutamylcysteine transferase (PCS1), fifteen ectively . Correspectively . Among tectively .IMD1, MAM1, IGMTs, MYB34, MYB51, MYB122 and so on) and novel genes were identified within the confidence intervals of GSLs. Our findings not only demonstrate the reliability of the association genetics approach, but also provide new insight into elucidating the biosynthesis of these GSLs in B. napus seeds.Altogether, numerous key homologous genes, including known genes and BnaIMD1 (BnaA02g02020D), which are located in candidate intervals qGSL-A02-1 and qGSL-C02-11, associated with three aliphogenic GSLs and one aromatic GSL and BanGS-OH (BnaA04g17900D), which participate in the side chain modification process of aliphatic GSL biosynthesis and showed higher expression profiles in BnHG vs. BnLG (CYP79 genes [CYP83 genes [GGP1 [SUR1 [UGT74 genes [SOT genes [BnaCYP79F1 (BnaA06g11010D), BnaCYP79B2 (BnaA08g16100D), BnaCYP83A1 (BnaA04g24160D and BnaC04g47910D), BnaGGP1 , BnaSUR1 (BnaA09g10030D), BnaUGT74B1 (BnaA09g29790D), BnaUGT74C1 (BnaC04g42530D), BnaSOT16 (BnaA07g31260D), BnaSOT17 (BnaA06g12720D) and BnaSOT18 , NSP genes (3), CAD1 (1), TGG genes (6) and NIT genes (3) (BnaSOT12 (BnaA02g27300D) is homologous to AtSOT12, which functions in flavonoid, brassinosteroid and salicylic acid activity, and is involved in plant responses to salt, osmotic stress and phytohormones [BnCYP81D11 (BnaA02g29380D and BnaA02g29390D), BnaCYP81D7 (BnaA03g23030D), BnaCYP81G1 , BnaCYP81F3 (BnaA08g15650D), BnaCYP81F4 (BnaA08g15660D) and BnaCYP81K1 (BnaC02g36740D), are located in the interval regions associated with glucosinolate metabolites and showed differential expression in BnHG vs. BnLG seeds . In addienes (3) , which aBnaA08g16D, BnaCYP BnaA06g10D, BnaCYLG seeds . Among tynthesis ,103, butLG seeds . SimilarCYP81F2, IGMT1 and IGMT2 [A. thaliana [B. napus biosynthesis, specifically the production of 4-methoxyindole-3-ylmethyl glucosinolate (4MI3G), by directly activating the expression of nd IGMT2 , while tnd IGMT2 ,70,105. thaliana . In thisB. napus . Our finB. napus seeds , 46 medium-glucosinolate content (45~100 \u03bcmol/g) and 27 high-glucosinolate content (>100 \u03bcmol/g), respectively and low seed glucosinolate content were selected from 143 B. napus accessions for transcriptome sequencing (RNA-Seq), respectively. The seeds of 20, 30 and 40 DAF were also collected and pooled from five or more individuals in BnHG and BnLG plants. All samples were stored at \u221280 \u00b0C until further analysis.In total, 143 ectively . All accThe total RNA was extracted from the seeds of 20, 30 and 40 DAF using an EZ-10 DNAaway RNA Mini-Preps kit following the manufacturer instructions. Then, the qualified RNA samples were used for libraries construction and sequenced on Illumina Hiseq 2000 platform with 150 bp paired-end reads . The gene expression profiles were evaluated using FPKM (fragments per kilo base of exon model per million) values. Genes were considered as differentially expressed genes (DEGs) with a minimum 2-fold difference in expression (|log2FC| \u2265\u20091). g at 4 \u00b0C for 10 min. Then, the residues were repeatedly extracted. Eventually, the mixed liquid supernatants were used for UPLC-HESI-MS/MS analysis after being filtered by a 0.22 \u03bcm nylon filter. All experiments were performed in at least three replicates for each accession.The raw metabolites were extracted from fresh seeds described in our previous research , with miThe UPLC-HESI-MS/MS was performed using Dionex UltiMateTM 3000 UHPLC system coupled to a Thermo Scientifific Q-Exactive System equipped with an S-Lens ionizer source , including the precolumn and Acquity UPLCBEH C18 column . The parameters were as follows: the mobile phases A (0.1% formic acid) and B (0.1% acetonitrile aqueous solution), 37 \u00b0C column temperature, 0.3 mL/min flow rate and 10 \u03bcL injection volume, respectively. The mobile phase gradients are 0\u20132 min, 5% B\u201310% B; 2\u201310 min, 10\u201325% B; 10\u201313 min, 25\u201395% B; 13\u201316 min, 95% B; 16\u201316.5 min, 95\u20135% B; 16.5\u201321 min, 5% B. The mass spectrometry was detected in negative ion mode with a scanning range of 100 to 1200 (m/z), 3.5 kV ion source voltage, 350 \u00b0C capillary temperature, 35 sheath gas, 10 auxiliary gas and 0 backblow air, respectively.http://prime.psc.riken.jp/compms/msdial/main.htmL#MSP, accessed on 2 April 2022), and automatically converted by ABF converter [\u22121 . Raw data of UPLC-HESI-MS/MS were firstly treated with MS-DAIL ver4.1 MSP negative database (ch 2020) . Correspch 2020) ,110. Furch 2020) , and thehttp://www.eXtension.org/pages/61006, accessed on 14 October 2020), respectively. The content of six glucosinolate metabolites in the 2017 and 2018 growing seasons and resulting values of BLUP were used as phenotypes for GWAS, respectively. The heritability was calculated by using the multi-year repeated model. In addition, the quantitative data of glucosinolate metabolites were divided into 10 grades, and Shannon\u2013Wiener Diversity Index was used to calculate metabolites [t-test) were performed [The glucosinolate metabolites were detected in two consecutive years (2017 and 2018) with replications; we further obtained the best linear unbiased prediction (BLUP) of six glucosinolate metabolites per accession using a linear model using an R script and GATK (version 3.2) to process local realignment and base quality detection for the alignment results, sequentially. Further, we then used AMtools mpileup (version 0.1.19\u201344428cd) and GATK to perform SNP calling. In total, 239,945 high-quality SNPs with a minor allele frequency (MAF) <5% were used for further analysis. The six models, including na\u00efve, Q, K, PCA, K\u2009+\u2009Q and K\u2009+\u2009PCA model, were applied to determine the statistical associations between phenotypes and genotypes. Quantile\u2013quantile (QQ) plots were used for false-positive correction for association analyses. In this study, genome-wide association analysis for six glucosinolate metabolites was carried out using the GLM with Q model and MLM with\u2009Q +\u2009K model by TASSEL 5.2.1 software. The population structure Q matrix was completed by admixture_linux-1.3.0 software [P\u2009 < \u2009P \u2009= \u20091/N , and the threshold of significance was set to p < 4.17 \u00d7 10\u22126.Detailed methods used for SNP genotyping and mapping were previously described ,47,48. I-bzh\u2019 using thsoftware . The sigbzh reference genome [The significant interval regions were mapped to the Darmor-er 2022) , which wer 2022) . Finally"} +{"text": "Correction: J Exp Clin Cancer Res 38, 435 (2019)https://doi.org/10.1186/s13046-019-1439-xFigure Figure Figure Figure Following publication of the original article , errors The corrections do not have any effect on the final conclusions of the paper.Additional file 1: Figure S1. JMJD2C promoted the metastasis of CRC LoVo cells. a-c Real time PCR and western blotting were performed to confirm the gene silencing and overexpressing efficiency for JMJD2C. LoVo was transiently transfected with shRNA/NT vector, shRNA/JMJD2C vector, empty overexpression vector, or JMJD2C overexpression vector. d Migration assays of LoVo cells transfected with shRNA/NT, shRNA/ JMJD2C, empty vector, or JMJD2C overexpression vector, respectively. e Numbers of migrated cells are shown as mean \u00b1 SD; n = 3. *, P < 0.05; **, P < 0.01 (t test)."} +{"text": "Platythyreaclypeata species group is reviewed and three species, including one new species, P.homasawinisp. nov., are recognized. This species group is distinguished from the P.parallela species group by the reddish-brown body, the elliptical shape of the propodeal spiracle, the elongate antennal scape, and the distinctly narrowed posteriad space between frontal carinae. Platythyreahomasawinisp. nov., from Thailand and China, is described based on the worker caste. The type series of the new species was collected on the forest floor from dead wood in an advanced stage of decomposition. A key to the Oriental species of the genus Platythyrea based on the worker caste is provided.The Platythyrea Roger, 1863 is a rarely collected group with recent reviews listing 39 species ; P.quadridenta Donisthorpe, 1941; P.tricuspidata Emery, 1900 and P.janyai Phengsi, Jaitrong, Ruangsittichai & Khachonpisitsak, 2018). Among them, five species are reported from Thailand, and they belong to two species groups (sensu Brown 1975): the P.clypeata group (P.clypeata and P.janyai) and P.parallela group . Our recTHNHM). The specimens were compared with high-resolution images of holotypes and paratypes of closely related species available on P.janyai were also examined. The holotype and paratypes of P.homasawini sp. nov. are deposited in THNHM.This study is mainly based on the material deposited in the Natural History Museum of the National Science Museum, Thailand process vertically to a line intersecting the dorsal most point of the node.PL Petiole length: length of petiole measured in lateral view from the anterior articulation to the posterior articulation of petiole.PW Pronotal width: maximum width of pronotum measured in dorsal view.SL Scape length: straight-line length of the antennal scape, excluding the basal constriction or neck.SI Scape index = SL/HW \u00d7100.TL Total length: total outstretched length of the individual, from the mandibular apex to the gastral apex.Abbreviations of the type depositories are as follows:BMNHThe Natural History Museum, London, U.K.MHNGMus\u00e9um d\u2019Histoire Naturelle, Geneva, Switzerland.THNHM Natural History Museum of the National Science Museum, Thailand.Platythyrea species were made at the Microscopic Center, Faculty of Science, Burapha University with a LEO 1450 VP scanning electron microscope on gold coated specimens.Scanning electron microscope images of The species group can be characterized by the following characteristics: 1) body reddish brown; 2) space between frontal carinae distinctly narrowed posteriad , deposited in MHNG . Holotype of P.thwaitesi: alate queen from Sri Lanka, deposited in BMNH .THNHM-I-24983) and 1 dealate queen (THNHM-I-24982), Laos, Vientiane, Pak Ngum District, Ban Phang Dang, ca 300 m alt., 14.VI.2010, W. Jaitrong leg., Colony no. WJT-LAO-143 (THNHM-I-24981) \u2022 1 worker (THNHM-I-24984), Laos, Vientiane, Pak Ngum District, Ban Phang Dang, 14.VI.2010, Sk. Yamane leg., Colony no. LA10-SKY-128 \u2022 1 worker (THNHM-I-24981) Laos, Vientiane, Pak Ngum District, Ban Phang Dang, ca 300 m alt., 12.VI.2010, W. Jaitrong leg. \u2013 Thailand \u2022 9 workers (THNHM-I-02423 to THNHM-I-02431), eastern Thailand, Chachoengsao Province, Tha Takiab District, Khao Ang Reu Nai Wildlife Sanctuary, 27.IX.2002, W. Jaitrong leg., Colony no. WJT270902-01 \u2022 3 workers (THNHM-I-02432 to THNHM-I-02434), same locality, date and collector, Colony no. WJT270902-1 \u2022 6 workers (THNHM-I-02435 to THNHM-I-02440), eastern Thailand, Sa Kaeo Province, Khao Ang Reu Nei Wildlife Sanctuary, 26.VI.2003, W. Jaitrong leg., Colony no. WJT03-TH-228; 22 workers (THNHM-I-02441 to THNHM-I-02452) and 1 male (THNHM-I-02453), eastern Thailand, Chanthaburi Province, Soi Dao District, 14.V.2008, W. Jaitrong leg., Colony no. WJT08-E065 \u2022 14 workers and 1 dealate queen, central Thailand, Nakhon Nayok Prov., Muang Dist., Nang Rong Temple, in rotting wood, 29.VIII.2018, W. Jaitrong leg., Colony no. WJT290819-09.Laos \u2022 10 workers (n = 10). and inhabits primary dry evergreen forest and disturbed forests. All colonies of this species were collected from dead wood on the forest floor in an advanced stage of decomposition.Sri Lanka, Vietnam, Laos (Vientiane), and Thailand Fig. .Platythyreaclypeata is similar to P.gracillima, P.janyai, and P.prizo. However, P.clypeata can be easily separated from P.gracillima by the following characteristics (characters of P.gracillima in parentheses unless otherwise stated): 1) body size smaller ; 2) eye smaller and flat ; 3) clypeus narrow and rather convex (clypeus broad and rather flat); 4) declivity of propodeum concave ; 5) seen from back propodeal declivity rounded above ; 6) petiole laterally swollen ; 7) head finely punctate (head rather smooth).Platythyreaclypeata can be distinguished from P.prizo by the following characteristics (characters of P.prizo in parentheses unless otherwise stated): 1) head shorter ; 2) eye flat and small ; 3) eye without erect pubescence (eye covered with extremely fine short erect pubescence); 4) propodeum junction obtusely angulated (propodeum junction armed with a pair of short teeth or tubercles); 5) in profile, posterodorsal corner of petiole forming an acute angle (roundly convex).P.janyai (characters of P.janyai in parentheses unless otherwise stated) by 1) head relatively longer ; 2) eye clearly smaller ; 3) eye flat (eye convex); 4) head finely punctate with dense shallow foveae ; 5) in profile petiole slightly longer than high and in dorsal view its node slightly narrower posteriorly ; 6) ventral outline of petiole feebly concave (weakly convex) , northern Thailand, Chiang Mai Prov., Doi Saket Dist., Ban Mae Pong, 24.XI.2021, K. Homasawin leg., Colony No. WJT241121-01. Paratypes: 29 workers , same data as holotype.THNHM-I-02463), northern Thailand, Chiang Mai Prov., Muang Dist., restored forest, 8.V.2002, S. Sonthichai leg. \u2022 1 worker (THNHM-I-02454), western Thailand, Kanchanaburi Prov., Thong Pha Phum N.P., Natural Forest, 8.III.2005, W. Sakchooeong leg.China \u2022 1 worker, Yunnan Prov., Menghai County, Meng\u2019a Town, Papo Village, 1280 m, No. A97-2318, collected from secondary monsoon evergreen broadleaf forest, 10.IX.1997, Zhenghui Xu leg. \u2013 Thailand \u2022 1 worker . TL 7.72\u20137.80, HL 1.56\u20131.64, HW 1.08\u20131.12, SL 1.64\u20131.68, EL 0.16\u20130.20, PW 0.96\u20130.99, ML 2.80\u20132.84, PL 1.08\u20131.12, PH 0.60\u20130.64, DPW 0.40\u20130.44, CI 68\u201369, EI 15\u201319, SI 150\u2013159.holotype and paratypes). Head and Thailand (Chiang Mai and Kanchanaburi provinces) Fig. .The specific name is dedicated to Mr Kaisihanat Homasawin, who donated the type series.P.janyai but it can be separated from P.janyai by the following characteristics (characters of P.janyai in parentheses unless otherwise stated): 1) head weakly widening anteriorly (head not widening anteriorly); 2) dorsal outline of petiole weakly convex ; 3) posterior margin of petiolar node without a concavity in the middle (posterior margin of petiolar node with a concavity in the middle): 4) body surface with thin pubescence (body surface with thick pubescence); 5) head longer ; 6) antennal scape relatively long, 1/3 of its length extending beyond posterolateral corner of head ; 7) eye smaller and flat ; 8) seen from back propodeal declivity rounded above ; 9) dorsal outline of petiole weakly convex .The new species is similar to Platythyreahomasawini can be easily separated from P.clypeata by the following characteristics (characters of P.clypeata in parentheses unless otherwise stated): 1) head in full-face view, posterior margin weakly concave ; 2) antennal scape relatively long, 1/3 of its length extending beyond posterolateral corner of head ; 3) clypeus broad (clypeus narrow); 4) eye larger ; 5) mesosoma relative longer ; 6) mesopleuron not demarcated from mesonotum ; 7) in profile view, propodeal junction roundly convex ; 8) in dorsal view, posterior margin of petiole clearly convex ; 9) lateral face of head entirely micropunctate ; 10) gaster superficially shagreened (finely reticulate).Platythyreahomasawini can be distinguished from P.gracillima by the following characteristics (characters of P.gracillima in parentheses unless otherwise stated): 1) clypeus roundly convex (rather flat in P.gracillima); 2) petiole laterally convex; 3) seen from above longer than high ; 4) seen from above a little more than twice as long as broad); 5) mandible finely micropunctate (mandible finely and densely punctate); 6) head entirely finely micropunctate (rather smooth in P.gracillima).Taxon classificationAnimaliaHymenopteraFormicidae\ufeffPhengsi, Jaitrong, Ruangsittichai & Khachonpisitsak, 201880F1B0B2-8F43-5645-B08A-D5F34E0D516DPlatythyreajanyaiHolotype (THNHM-I-02392) and three paratypes (THNHM-I-02393 to THNHM-I-02395) workers, southern Thailand, Phatthalung Province, Si Banphot District, Riang Thong Waterfall, Khao Pu Khao Ya National Park, 28.IX.2007, W. Jaitrong leg., Colony no. WJT07-TH-2060 (THNHM-I-02392), deposited in THNHM (examined).THNHM-I-02465) \u2013 Thailand \u2022 2 workers, southern Thailand, Trang Province, Na Yong District, Khao Chong Botanical Garden, 7.XI.2014, W. Jaitrong leg., Colony No WJT071114-2 (THNHM-I-02421 to THNHM-I-02422) \u2022 5 workers, same locality and collector, 26.XII.2018, Colony no. WJT261218-1 (THNHM).Malaysia \u2022 1 worker, western Malaysia, Selangor, Ulu Gombak, 22.III.2013, F. Ito leg. ((n = 4).TL 6.63\u20136.96, HL 1.42\u20131.45, HW 1.06, SL 1.39\u20131.42, EL 0.20, ML 2.21\u20132.31, PL 0.73\u20130.79, PH 0.53, DPW 0.40, CI 72\u201374, EI 18, SI 131\u2013134.holotype and paratypes). Head and Malaysia Fig. .Platythyreajanyai is similar to P.clypeata, P.homasawini and P.gracillima. However, P.janyai can be easily separated from P.gracillima by the following characteristics (characters of P.gracillima in parentheses unless otherwise stated): 1) body size smaller ; 2) eye relatively smaller ; 3) seen from back, propodeal declivity tapering above ; 4) petiole laterally convex, seen from above longer than broad . For differentiation of P.janyai and P.clypeata, see \u201cComparative notes\u201d under P.clypeata, and of P.janyai and P.homasawini, see under P.homasawini.Platythyrea are now known around the world. Among them, six species are found in Thailand, and they belong to two species groups : P.clypeata group and P.parallela group .With this study, 40 valid species of the genus The shape of the frontal lobe, mandibular shape and dentition, and shape of mesosoma and petiolar node were characters used by Brown (1975) to distinguish the two species groups mentioned here. These morphological characters were confirmed and used by several authors who described new species after Brown (1975) . The preP.clypeata group can be distinguished from other congeners mainly by the following: body reddish brown; space between frontal carinae distinctly narrowed posteriad; propodeal spiracle opening elliptical, petiole longer than high, and posterior margin concave. The worker caste of Platythyrea species is generally monomorphic with little variation in size within species. Thus, worker body size can be used for separating large and small species. In this study, worker body size has been used to separate P.homasawini sp. nov., P.janyai, and P.clypeata.The Platythyreaclypeata is distinctly allopatric with P.janyai in geographic subregion in continental Asia . However, P.clypeata and P.janyai both were found in lowland (< 300 m a.s.l.). Platythyreaclypeata inhabits various habitats including plantations, secondary forests, and primary dry evergreen forests. Platythyreajanyai is confined to primary evergreen forests. Platythyreahomasawini sp. nov. is restricted to highland hill evergreen forests.tal Asia . It has"} +{"text": "Cystobasidium ongulense has been reported from East Ongul Island near Syowa Station, East Antarctica, as a new basidiomycetous yeast species. This species has cold active lipases and cellulases that are active even at subzero temperatures. We report draft genome sequences of five Cystobasidium ongulense strains isolated from East Antarctica. Cystobasidium ongulense was isolated from East Ongul Island, East Antarctica, and reported as a new species of basidiomycete yeast isolated from East Ongul Island and three strains isolated from Inhovde, near Syowa Station.g for 5\u2009min at 4\u00b0C. The cell pellets were washed with sterile distilled water and precipitated by centrifugation again. The cell pellets were dried using a vacuum freeze dryer. The lyophilized cells were powdered in a mortar and used for genome extraction. The genomic DNA of five Cystobasidium ongulense strains was extracted and purified using a NucleoBond AXG100 column with a Nucleo buffer set III (TaKaRa Bio) according to the manufacturer\u2019s protocol. The concentration and purification of the genomic DNA were determined using a NanoDrop spectrophotometer (Thermo Scientific) and the Qubit double-stranded DNA (dsDNA) broad-range (BR) assay kit (Thermo Scientific). Then, the genomic DNA was digested using the microTUBE (Covaris), and the genomic library was constructed using the Illumina TruSeq DNA PCR-free library preparation kit (Illumina). The quality of the library was confirmed using the Quant-iT PicoGreen dsDNA assay kit, and the library size was checked using the Agilent 2200 TapeStation system . The paired-end sequence reaction was performed on a HiSeq 2500 instrument (Illumina). Adapters and low-quality bases were trimmed using fastp ver. 0.12.4 (\u2013ab initio gene predictions were carried out using AUGUSTUS ver. 3.4.0 (Each strain was cultured in yeast extract-peptone-dextrose (YPD) liquid medium (Difco) at 15\u00b0C for 5\u2009days. The cells from cultures were collected by centrifugation at 3,500\u2009\u00d7\u2009. 0.12.4 , annotat. 0.12.4 \u201311 automr. 3.4.0 . The resr. 3.4.0 and AGATr. 3.4.0 , Phobiusr. 3.4.0 , antiSMAr. 3.4.0 , and Eggr. 3.4.0 against r. 3.4.0 .C. ongulense strains is shown in A summary of the genomic analysis results of the five C. ongulense will help us understand how Antarctic fungi adapt to the extreme environment.We believe that the genomic information of PRJDB6568 with accession numbers BQUO00000000.1 (9A-2), BQUP00000000.1 (9A-5), BQUQ00000000.1 (051-20-1), BQUR00000000.1 (056-1-20Y-3), and BQUS00000000.1 (056-20-8). The raw reads are available under SRA accession numbers DRR118811, DRR118812 (9A-2), DRR118813, DRR118814 (9A-5), DRR118815, DRR118816 (051-20-1), DRR118817, DRR118818 (056-1-20Y-3), and DRR118819, DRR118820 (056-20-8).This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under BioProject accession number"} +{"text": "One of the main mechanisms of epigenetic regulation in higher eukaryotes is based on the methylation of cytosine at the C5 position with the formation of 5-methylcytosine (mC), which is further recognized by regulatory proteins. In mammals, methylation mainly occurs in CG dinucleotides, while in plants it targets CG, CHG, and CHH sequences (H is any base but G). Correct maintenance of the DNA methylation status is based on the balance of methylation, passive demethylation, and active demethylation. While in mammals active demethylation is based on targeted regulated damage to mC in DNA followed by the action of repair enzymes, demethylation in plants is performed by specialized DNA glycosylases that hydrolyze the N-glycosidic bond of mC nucleotides. The genome of the model plant Arabidopsis thaliana encodes four paralogous proteins, two of which, DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1), possess 5-methylcytosine-DNA glycosylase activity and are necessary for the regulationof development, response to infections and abiotic stress and silencing of transgenes and mobile elements. Homologuesof DME and ROS1 are present in all plant groups; however, outside A. thaliana, they are poorly studied.Here we report the properties of a recombinant fragment of the ROS1 protein from Nicotiana tabacum (NtROS1),which contains all main structural domains required for catalytic activity. Using homologous modeling, we haveconstructed a structural model of NtROS1, which revealed folding characteristic of DNA glycosylases of the helix\u2013hairpin\u2013helix structural superfamily. The recombinant NtROS1 protein was able to remove mC bases from DNA,and the enzyme activity was barely affected by the methylation status of CG dinucleotides in the opposite strand.The enzyme removed 5-hydroxymethylcytosine (hmC) from DNA with a lower eff iciency, showing minimal activityin the presence of mC in the opposite strand. Expression of the NtROS1 gene in cultured human cells resulted ina global decrease in the level of genomic DNA methylation. In general, it can be said that the NtROS1 protein andother homologues of DME and ROS1 represent a promising scaffold for engineering enzymes to analyze the statusof epigenetic methylation and to control gene activity. DNA methylation is a dedicated mechanism of gene regulation,especially developed in higher eukaryotes. The 5-methylcytosine(mC) nucleobase, formed by cytosine methylationat the C5 position, serves as a reversible epigenetic mark thatplays an important role in the control of gene expression andthe protection of the genome from mobile elements. DNAmethylation occurs in a wide range of multicellular eukaryotes;however, its significance and functions in these organismsdiffer greatly .For example, in mammals, methylation most often occurs inCpG dinucleotides, while in plants, a significant proportionof mC occurs in trinucleotides CHG and CHH (where H is\u201cnot G\u201d). The consequences of mC for gene activity are mainlymediated by proteins containing methyl-binding domains thatform complexes with histone deacetylases or themselves havethe activity of histone-specific methyltransferases, chromatinremodeling factors, etc., which leads to chromatin condensationand transcription suppression . Recent studies have shown that an oxidizedderivative of 5-methylcytosine, 5-hydroxymethylcytosine(hmC), also plays an epigenetic role in the mammaliangenome . Unlike mC, hmC is enrichedin promoters and bodies of actively expressed genes and isconsidered an activating epigenetic marker Correct methylation of various sites in the genome is extremelyimportant, since the transcriptional activity of genesdepends on it. Errors in DNA methylation can have graveconsequences. In particular, in humans, global DNA demethylationor hypermethylation of tumor suppressor genes serve ascancer markers. Maintaining the status of DNA methylation incells requires a balance of methylation and active and passivedemethylation. The mechanisms of active demethylation ofthe genomic DNA in higher eukaryotes have only been discoveredin the last decade. In mammals, active demethylationis initiated by regulated damage to mC, which can occur intwo ways: either deamination of mC to T by AID/APOBECenzymes, or oxidation of mC to hmC and further derivatives(5-formylcytosine and 5-carboxycytosine) by TET familydioxygenases . The modified bases are further perceived bycellular repair systems as damaged and are removed by theDNA base excision repair pathway.Unlike mammals, plants have unique enzymes that directlyhydrolyze N-glycosidic bonds of mC nucleotides. These DNAglycosylases \u2013 DEMETER (DME) and REPRESSOR OFSILENCING 1 \u2013 are involved in theregulation of the methylation status of the sites in the plantgenome that determine gene imprinting during paternal ormaternal inheritance and silence or activate specific promotersduring plant development and stress response .After removal of mC, the resulting apurinic-apyrimidinic site(AP site) is cleaved either by the enzyme\u2019s own AP lyase activityor by the AP endonucleases APE1L or ARP, then a normalnucleotide is incorporated by one of the DNA polymerases,and the nick is ligated by the LIG1 DNA ligase. Interestingly,DME and ROS1 can also excise hmC, which is not regardedas an epigenetic base in plants . The localizationof demethylation by DME/ROS1 is regulated bysmall RNAs that bind to the enzyme itself or to the proteincomplex that contains it .In addition to DME and ROS1, the genome of the modelplant Arabidopsis thaliana contains three more genes that arehomologous to DME and ROS1: DEMETER-LIKE 2 (DML2),DEMETER-LIKE 3 (DML3), and AT3G47830, which has notbeen characterized thus far except for participation of DML2and DML3 in maintaining correct DNA methylation . All these proteins belongto the DNA helix\u2013hairpin\u2013helix (HhH) structural superfamilyof DNA glycosylases. Other members of this superfamily areinvolved in the removal of oxidized, alkylated and deaminatednucleobases from the genome . DME/ROS1 enzymes attract attention as potentialtools for targeted regulation of gene activity: for example, thepossibility of targeted DNA demethylation in human cells byA. thaliana ROS1 (AtROS1) fused to the RNA-guided Cas9protein has been shown , and A. thaliana DME (AtDME) was used to analyze the level ofmC in genomic DNA .In plants other than A. thaliana, there were few studies onthe role of DME-like proteins in active epigenetic demethylation;some data exist for rice, wheat, barley, and tomato . In 2007, a ROS1 homolog from Nicotiana tabacum(NtROS1) was cloned, and the recombinant proteinproducedin insect cell culture was shown to cleave methylatedtobaccogenomic DNA . None of these studiesincluded a detailed biochemical characterization of the protein.We have previously shown that the NtROS1 fragment correspondingto the minimal catalytically active AtROS1 fragmenthas the activity of 5-methylcytosine-DNA glycosylase.Here, in view of the potential value of plant demethylationenzymes as tools for genetic technologies, we characterizethe substrate specificity of the recombinant NtROS1 catalyticfragment on mC and hmC in different contexts of methylatedCpG dinucleotides and show that the expression of NtROS1in human cells causes a global decrease in DNA methylation.ProtoScript II reverse transcriptase, Q5 Hot Start High-FidelityDNA polymerase, Escherichia coli uracil DNA glycosylase,ClaI and SacI restriction endonucleases were purchasedfrom New England Biolabs (USA), and bacteriophage T4polynucleotide kinase, from Biosan .Oligonucleotides listed in the Table were synthesized at theSB RAS ICBFM Laboratory of Biomedical Chemistry usingcommercially available prosphoramidites . If necessary, the oligonucleotides were 32P-labeled atthe 5\u2032-end using \u03b3[32P]ATP (SB RAS ICBFM Laboratory ofBiotechnology) and T4 polynucleotide kinase.To build a model of the NtROS1 catalytic domain in theSwiss-Model program , the AtDME(AF-Q8LK56-F1-model_v1) and AtROS1 (AF-Q9SJQ6-F1-model_v1) templates from the AlphaFold database were used.To obtain a catalytically inactive NtROS1 with theAsp1359Asnsubstitution, a pLATE31 plasmid with an insertencoding the catalytically active NtROS1 fragment (aminoacid residues 754\u20131796) was mutagenizedusing primers D1359Nfwd and D1359Nrev (seethe Table) and the Q5 Site-Directed Mutagenesis Kit (NewEngland Biolabs). The mutation was confirmed by Sangersequencing. Wild-type NtROS1 and NtROS1 D1359N wereoverproduced and purified as described previously .To study the activity of NtROS1, double-stranded substrateswere obtained by annealing oligonucleotides C1, C2,M1, M2, H1, and H2 (see the Table). The reaction mixturecontained 50 nM substrate, 50 mM Tris\u2013HCl (pH 8.0), 1 mMEDTA, 1 mM DTT, 0.1 % bovine serum albumin, and 100 nMNtROS1. The mixture was incubated at 37 \u00b0C; aliquots werewithdrawn at various times (2\u2013300 min) and mixed with anequal volume of the stop solution . Ifnecessary, the aliquots were preheated for 2 min at 95 \u00b0C inthe presence of 0.1 M NaOH and neutralized with an equimolaramount of HCl. The reaction products were resolvedby electrophoresis in a 20 % polyacrylamide gel containing7.2 M urea, visualized by prosphorimaging using the TyphoonFLA 9500 system , and quantified usingthe Quantity One v4.6.3 software . The apparent rate constants were determined using theSigmaPlot v11.0 software by nonlinearregression to the equation [P] = [P]max(1 \u2013 e\u2212kt ), where[P] is product concentration, [P]max is the maximum productconcentration, k is the reaction rate constant, and t is time.To assess the status of global DNA methylation uponNtROS1 expression in human cells, wild-type and D1359NNtROS1 coding sequences were cloned into the pIRES-eGFPpuroplasmid at the SacI and ClaI restriction sites. HEK293 Phoenix cells (1.2\u00b7106) were transfected with5 \u03bcg of the plasmid by the calcium phosphate method andgrown in a monolayer in DMEM with 10 % fetal calf serum. After 24 and 48 h, the medium was changedwith the addition of 3 \u03bcg/ml puromycin. Transfection efficiencywas determined by flow cytometry by detection of the fluorescence ofeGFP encoded by the same plasmid. NtROS1 expression inthe transfected cells was confirmed by reverse transcriptionPCR using \u03b2-actin mRNA as a control. Genomic DNA wasisolated from the cells (5\u00b7106) using a QIAamp DNA Mini Kit, and the relative content of mC wasdetermined using anti-mC antibodies . The resultswere compared using Student\u2019s t-test.Plant mC-specific DNA glycosylases are proteins of considerablesize: for example, AtDME and AtROS1, as well astheir DML2 and DML3 paralogs, are over 1000 amino acidresidues long . The extended N-terminal regions ofthese polypeptides are unstructured, although some of theirparts are necessary for enzyme activity. The C-terminal regionscontain a conserved HhH catalytic domain and an iron-sulfurcluster (FeS cluster), characteristic of many DNA glycosylasesthat recognize oxidative DNA damage, as well as an RNAbindingmotif and a CXXCtype permuted zinc finger unique to the DME/ROS1 family. Unlike in all other HhH superfamily DNAglycosylases, the catalytic domain in DME/ROS1 proteinsis disrupted by a long non-conserved insert . Based on the literature data on the AtROS1protein, we previously cloned the NtROS1 cDNA fragmentencoding amino acid residues 754\u20131796 .This region contains all elements necessary for the catalyticactivity in AtROS1 .Since the structures of the DME/ROS1 family proteins arecurrently unknown, for a more detailed understanding of theorganization of the NtROS1 catalytic fragment, we carriedout homology modeling based on the AtDME and AtROS1models from the AlphaFold template collection . The two resulting models were almost identicalexcept for the structure of the long non-homologous regions.The disrupted HhH domain folded into the \u03b1-helical structurecharacteristic of DNA glycosylases of this superfamily,in which a DNA binding groove with the catalytic residuesLys1341 and Asp1359 is evident . In addition,several more peripheral \u03b1-helices buttress the HhH domain andthe FeS cluster and are obviously important for maintainingtheir structure. The FeS cluster, zinc finger, and RRM motifform separate structural elements that leave free access to theDNA binding groove . All disordered regions ofthe structure are also located on the side of the protein globuleopposite to the DNA binding groove.To analyze the catalytic activity and substrate specificity ofNtROS1, we performed a cleavage reaction of double-strandedoligonucleotides containing a CpG dinucleotide in which thecytosine was unmethylated, methylated, or hydroxymethylatedin one or both chains . The strand to be cleaved was32P-labeled at the 5\u2032-end. NtROS1 showed virtually no activityon the substrate containing an unmethylated CpG site, whichis consistent with the literature data claiming that the C5 positionof the cytosine must carry a substitution to be cleaved byAtROS1 . Activity towards mC andhmC was observed; however, its level differed markedly forboth types of substrates. Comparing the efficiency of cleavageof M1/C2 and M1/M2 substrates with H1/C2 and H1/H2 substrates (lanes 11 and 14), one cansee that the enzyme prefers to excise mC over hmC bothfrom CpG sites modified at only one strand and from fullymodified sites. Small differences in the cleavage of M1/C2,M1/M2 and M1/H2 substrates indicatethat modifications in the complementary strand have littleeffect on the removal of mC, and hmC in the complementarystrand might even increase the cleavage. The enzymeshowed no activity against DNA substrates containing uracil or 8-oxoguanine. The NtROS1 D1359N mutant, as expected,exhibited no glycosylase activity against any substrate withvarious combinations of mC and hmC, which confirms theimportance of the Asp residue in the ROS1 catalytic centerfor the removal of modified bases from DNA.AtROS1 was reported to be an enzyme with a very lowturnover number , so it wasnot feasible to use steady-state kinetics to characterize theactivity of NtROS1. To determine the apparent reaction rateconstant, we used the conditions close to the single-turnoverkinetic regime ([E]0 > [S]0). Under these conditions, all DNAsubstrate rapidly binds to the enzyme, and the reaction rateis limited not by substrate binding or product release, butby the chemical step of the pseudo-first order reaction, thehydrolysisof the N-glycosidic bond of the modified nucleotide. Thus, following the accumulation of theproduct over time , one can estimate the reactionrate constant. The time courses for all substrates are shownin Fig. 3, b, and the rate constants calculated from these dataare summarized below:Substrate k\u00b7104, s\u22121*M1/C2 6.5 \u00b1 1.1*M1/M2 2.4 \u00b1 0.5*M1/H2 3.0 \u00b1 0.7*H1/C2 1.9 \u00b1 0.3*H1/M2 1.6 \u00b1 0.6*H1/H2 2.0 \u00b1 0.3*C1/C2 Not cleaved* 32P-labeled strand.In all cases, hmC was a worse substrate for NtROS1 comparedto mC. Based on these results, we conclude that NtROS1cleaves hemimethylated CpG sites most efficiently, while hmCin the context of HG/GM, on the contrary, is the worst substratefor this enzyme. The kinetic constants are consistent with thequalitative data on the relative cleavage efficiency for differentsubstrates .Many slow-turnover DNA glycosylases have lower APlyase activity in comparison with their DNA glycosylaseactivity. In this case, after the removal of the modified base,a part of the reaction product exists as an AP site for a longtime, and the true amount of the product can be revealed onlyupon treatment with alkali or nucleophilic amines . However, in the case of NtROS1, additional treatmentwith NaOH did not lead to a noticeable increase in theaccumulation of the reaction product . Apparently,the rate of the reaction catalyzed by NtROS1 is limitedby the hydrolysis of the N-glycosidic bond, which was alsosuggested for the enzyme from A. thaliana .To assess the ability of the NtROS1 protein to act asa demethylasewhen expressed in mammalian cells, we constructedplasmids based on the pIRES-eGFP-puro vectorencoding wild-type NtROS1 and its catalytically inactivemutant NtROS1 D1359N. Using anti-mC antibodies, we haveestimated the level of this epigenetic base in HEK293 cellsafter transfection with these plasmids. When cells were observedpost-transfection, the proliferation of cells with thepIRES-eGFP-puro-NtROS1 plasmid was reduced by about30 % compared to the control cells transfected with the plasmidwith no insert and the cells transfected with the plasmidencoding the catalytic mutant. The fraction of live cells wasthe same in all cases, which indicates that the cell cycle maybe slower in the presence of active NtROS1 due to the needto repair a large number of breaks introduced into DNA atmC residues. An analysis of the mC level revealed a ~2-folddecrease relative to control samples when wild-type NtROS1 was expressed and the absence of statistically significantchanges with the expression of NtROS1 D1359N . Ingeneral, it can be considered that the transient expression ofthe catalytic domain of 5-methylcytosine\u2013DNA glycosylaseNtROS1 in human cells indeed leads to the global erasure ofmC epigenetic marks. The amount of hmC in cells could notbe measured using anti-hmC antibodies, probably because thismodified base is about an order of magnitude less abundantthan mC .Thus, it can be concluded that NtROS1 is a DNA glycosylasespecific for 5-methylcytosine and, to a lesser extent,for 5-hydroxymethylcytosine. Its biological functions, as inthe case of AtROS1, most likely consist in the regulation ofmethylation status and gene expression during embryonicdevelopment or in the response toinfections and abiotic stress ,and the regulation of silencing of transgenes and transposableelements . The mechanism of RNA-dependent addressing of DME/ROS1 family proteins to specific demethylation sites,which has not yet been elucidated, is of great interest. TheRRM motif in these polypeptides is homologous to the motifsresponsible for nonspecific interactions with RNA in manyother proteins and, by its position in thestructure , could bind small RNAs complementaryto the DNA stretch 5\u2032 of the targeted mC. Zinc fingers ofthe CXXC type are used by many mC-recognizing proteins;however, they predominantly bind unmethylated DNA and arepresumably required for accurate positioning of the enzymein the presence of several methylation sites located at a shortdistance .The prospects for using NtROS1 and other proteins of theDME/ROS1 family as tools for genetic technologies largelydepend on the possibility of reducing the size of the catalyticfragment. A deletion of the long insert between the two partsof the HhH domain in AtROS1 fully preserves its activity, buta deletion of the C-terminal tail after the FeS cluster resultsin an inactive enzyme . Judging from thestructural models of AtROS1 and NtROS1, the HhH and RRMdomains interact with each other, and shortening the proteinhere may only be done by trimming the insert between them.In any case, DME/ROS1 proteins, including NtROS1, representa promising scaffold for enzyme engineering to analyzeepigenetic methylation status and control gene activity.The study of the demethylating DNA glycosylase ROS1 fromNicotiana tabacum reported in this work presents the onlybiochemical investigation of ROS1 beyond its homologuefrom Arabidopsis thaliana. In addition to 5-methylcytosine,NtROS1 showed the ability to remove 5-hydroxymethylcytosinefrom DNA, but the efficiency of this reaction was lowerthan for 5-methylcytosine, apparently because plants rarely ifat all use 5-hydroxymethylcytosine as an epigenetic marker.The observed decrease in global methylation upon expressionof NtROS1 in human cells suggests that this protein or itsoptimized variants can be used as a tool for epigenetic regulation,either on its own or as an active module in constructstargeted to certain genome regions.The authors declare no conflict of interest.Agius F., Kapoor A., Zhu J.-K. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc. Natl. Acad. Sci.USA. 2006;103(31):11796-11801. DOI 10.1073/pnas.0603563103Ballestar E., Wolffe A.P. Methyl-CpG-binding proteins. Targetingspecific gene repression. Eur. J. Biochem. 2001;268(1):1-6. DOI10.1046/j.1432-1327.2001.01869.x.Baubec T., Iv\u00e1nek R., Lienert F., Sch\u00fcbeler D. Methylation-dependentand -independent genomic targeting principles of the MBD proteinfamily. Cell. 2013;153(2):480-492. DOI 10.1016/j.cell.2013.03.011.Bochtler M., Kolano A., Xu G.-L. DNA demethylation pathways: additionalplayers and regulators. Bioessays. 2017;39(1):1-13. DOI10.1002/bies.201600178.Branco M.R., Ficz G., Reik W. Uncovering the role of 5-hydroxymethylcytosinein the epigenome. Nat. Rev. Genet. 2011;13(1):7-13.DOI 10.1038/nrg3080Choi C.-S., Sano H. Identification of tobacco genes encoding proteinspossessing removal activity of 5-methylcytosines from intact tobaccoDNA. Plant Biotechnol. 2007;24(3):339-344. DOI 10.5511/plantbiotechnology.24.339Choi W.L., Mok Y.G., Huh J.H. Application of 5-methylcytosine DNAglycosylase to the quantitative analysis of DNA methylation. Int. J.Mol. Sci. 2021;22(3):1072. DOI 10.3390/ijms22031072.Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., GoldbergR.B., Jacobsen S.E., Fischer R.L. DEMETER, a DNA glycosylasedomain protein, is required for endosperm gene imprintingand seed viability in Arabidopsis. Cell. 2002;110(1):33-42. DOI10.1016/s0092-8674(02)00807-3.Cl\u00e9ry A., Blatter M., Allain F.H.-T. RNA recognition motifs: boring?Not quite. Curr. Opin. Struct. Biol. 2008;18(3):290-298. DOI10.1016/j.sbi.2008.04.002.Devesa-Guerra I., Morales-Ruiz T., P\u00e9rez-Rold\u00e1n J., Parrilla-DoblasJ.T., Dorado-Le\u00f3n M., Garc\u00eda-Ortiz M.V., Ariza R.R., Rold\u00e1n-Arjona T. DNA methylation editing by CRISPR-guided excisionof 5-methylcytosine. J. Mol. Biol. 2020;432(7):2204-2216. DOI10.1016/j.jmb.2020.02.007.Fedorova O.S., Kuznetsov N.A., Koval V.V., Knorre D.G. Conformationaldynamics and pre-steady-state kinetics of DNA glycosylases.Biochemistry (Moscow). 2010;75(10):1225-1239. DOI 10.1134/S0006297910100044Gong Z., Morales-Ruiz T., Ariza R.R., Rold\u00e1n-Arjona T., David L.,Zhu J.-K. ROS1, a repressor of transcriptional gene silencing inArabidopsis,encodes a DNA glycosylase/lyase. Cell. 2002;111(6):803-814. DOI 10.1016/s0092-8674(02)01133-9.Gruber D.R., Toner J.J., Miears H.L., Shernyukov A.V., Kiryutin A.S.,Lomzov A.A., Endutkin A.V., Grin I.R., Petrova D.V., KupryushkinM.S., Yurkovskaya A.V., Johnson E., Okon M., BagryanskayaE.G., Zharkov D.O., Smirnov S.L. Oxidative damage to epigeneticallymethylated sites affects DNA stability, dynamics, andenzymatic demethylation. Nucleic Acids Res. 2018;46(20):10827-10839. DOI 10.1093/nar/gky893.Hong S., Hashimoto H., Kow Y.W., Zhang X., Cheng X. The carboxyterminaldomain of ROS1 is essential for 5-methylcytosine DNAglycosylase activity. J. Mol. Biol. 2014;426(22):3703-3712. DOI10.1016/j.jmb.2014.09.010.Iyer L.M., Abhiman S., Aravind L. Natural history of eukaryotic DNAmethylation systems. Prog. Mol. Biol. Transl. Sci. 2011;101:25-104.DOI 10.1016/B978-0-12-387685-0.00002-0.Jang H., Shin H., Eichman B.F., Huh J.H. Excision of 5-hydroxymethylcytosineby DEMETER family DNA glycosylases. Biochem.Biophys. Res. Commun. 2014;446(4):1067-1072. DOI 10.1016/j.bbrc.2014.03.060Jumper J., Evans R., Pritzel A., Green T., Figurnov M., Ronneberger O.,Tunyasuvunakool K., Bates R., \u017d\u00eddek A., Potapenko A., Bridgland A.,Meyer C., Kohl S.A.A., Ballard A.J., Cowie A., Romera-Paredes B.,Nikolov S., Jain R., Adler J., Back T., Petersen S., Reiman D., ClancyE., Zielinski M., Steinegger M., Pacholska M., Berghammer T.,Bodenstein S., Silver D., Vinyals O., Senior A.W., Kavukcuoglu K.,Kohli P., Hassabis D. Highly accurate protein structure predictionwith AlphaFold. Nature. 2021;596(7873):583-589. DOI 10.1038/s41586-021-03819-2.Kapazoglou A., Drosou V., Argiriou A., Tsaftaris A.S. The study ofa barley epigenetic regulator, HvDME, in seed development andunder drought. BMC Plant Biol. 2013;13:172. DOI 10.1186/1471-2229-13-172.Kapoor A., Agarwal M., Andreucci A., Zheng X., Gong Z., HasegawaP.M., Bressan R.A., Zhu J.-K. Mutations in a conserved replicationprotein suppress transcriptional gene silencing in a DNAmethylation-independent manner in Arabidopsis. Curr. Biol. 2005;15(21):1912-1918. DOI 10.1016/j.cub.2005.09.013.Le T.-N., Schumann U., Smith N.A., Tiwari S., Au P.C.K., Zhu Q.- H.,Taylor J.M., Kazan K., Llewellyn D.J., Zhang R., Dennis E.S.,Wang M.-B. DNA demethylases target promoter transposable elementsto positively regulate stress responsive genes in Arabidopsis.Genome Biol. 2014;15(9):458. DOI 10.1186/s13059-014-0458-3.Lee T.-F., Zhai J., Meyers B.C. Conservation and divergence in eukaryoticDNA methylation. Proc. Natl. Acad. Sci. USA. 2010;107(20):9027-9028. DOI 10.1073/pnas.1005440107.Li X., Qian W., Zhao Y., Wang C., Shen J., Zhu J.-K., Gong Z. Antisilencingrole of the RNA-directed DNA methylation pathway and ahistone acetyltransferase in Arabidopsis. Proc. Natl. Acad. Sci. USA.2012;109(28):11425-11430. DOI 10.1073/pnas.1208557109.Li Y., Kumar S., Qian W. Active DNA demethylation: mechanism androle in plant development. Plant Cell Rep. 2018;37(1):77-85. DOI10.1007/s00299-017-2215-z.Liu R., How-Kit A., Stammitti L., Teyssier E., Rolin D., Mortain-BertrandA., Halle S., Liu M., Kong J., Wu C., Degraeve-Guibault C.,Chapman N.H., Maucourt M., Hodgman T.C., Tost J., Bouzayen M.,Hong Y., Seymour G.B., Giovannoni J.J., Gallusci P. A DEMETERlikeDNA demethylase governs tomato fruit ripening. Proc. Natl.Acad. Sci. USA. 2015;112(34):10804-10809. DOI 10.1073/pnas.1503362112.Morales-Ruiz T., Ortega-Galisteo A.P., Ponferrada-Mar\u00edn M.I., Mart\u00ednez-Mac\u00edas M.I., Ariza R.R., Rold\u00e1n-Arjona T. DEMETER andREPRESSOR OF SILENCING 1 encode 5-methylcytosine DNAglycosylases. Proc. Natl. Acad. Sci. USA. 2006;103(18):6853-6858.DOI 10.1073/pnas.0601109103.Ono A., Yamaguchi K., Fukada-Tanaka S., Terada R., Mitsui T.,Iida S. A null mutation of ROS1a for DNA demethylation in riceis not transmittable to progeny. Plant J. 2012;71(4):564-574. DOI10.1111/j.1365-313X.2012.05009.xOrtega-Galisteo A.P., Morales-Ruiz T., Ariza R.R., Rold\u00e1n-Arjona T.Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are requiredfor appropriate distribution of DNA methylation marks.Plant Mol. Biol. 2008;67(6):671-681. DOI 10.1007/s11103-008-9346-0.Ortega-Galisteo A.P., Morales-Ruiz T., Ariza R.R., Rold\u00e1n-Arjona T.Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are requiredfor appropriate distribution of DNA methylation marks.Plant Mol. Biol. 2008;67(6):671-681. DOI 10.1007/s11103-008-9346-0.Pastor W.A., Aravind L., Rao A. TETonic shift: biological roles of TETproteins in DNA demethylation and transcription. Nat. Rev. Mol.Cell Biol. 2013;14(6):341-356. DOI 10.1038/nrm3589.Pastor W.A., Pape U.J., Huang Y., Henderson H.R., Lister R., Ko M.,McLoughlin E.M., Brudno Y., Mahapatra S., Kapranov P., TahilianiM., Daley G.Q., Liu X.S., Ecker J.R., Milos P.M., Agarwal S.,Rao A. Genome-wide mapping of 5-hydroxymethylcytosine in embryonicstem cells. Nature. 2011;473(7347):394-397. DOI 10.1038/nature10102.Penterman J., Uzawa R., Fischer R.L. Genetic interactions betweenDNA demethylation and methylation in Arabidopsis. Plant Physiol.2007;145(4):1549-1557. DOI 10.1104/pp.107.107730.Ponferrada-Mar\u00edn M.I., Parrilla-Doblas J.T., Rold\u00e1n-Arjona T., ArizaR.R. A discontinuous DNA glycosylase domain in a family of enzymesthat excise 5-methylcytosine. Nucleic Acids Res. 2011;39(4):1473-1484. DOI 10.1093/nar/gkq982.Ponferrada-Mar\u00edn M.I., Rold\u00e1n-Arjona T., Ariza R.R. ROS1 5-methylcytosineDNA glycosylase is a slow-turnover catalyst that initiatesDNA demethylation in a distributive fashion. Nucleic Acids Res.2009;37(13):4264-4274. DOI 10.1093/nar/gkp390.Porello S.L., Leyes A.E., David S.S. Single-turnover and pre-steadystatekinetics of the reaction of the adenine glycosylase MutY withmismatch-containing DNA substrates. Biochemistry. 1998;37(42):14756-14764. DOI 10.1021/bi981594+.Rold\u00e1n-Arjona T., Ariza R.R., C\u00f3rdoba-Ca\u00f1ero D. DNA base excisionrepair in plants: an unfolding story with familiar and novel characters.Front. Plant Sci. 2019;10:1055. DOI 10.3389/fpls.2019.01055.Waterhouse A., Bertoni M., Bienert S., Studer G., Tauriello G., GumiennyR., Heer F.T., de Beer T.A.P., Rempfer C., Bordoli L., Lepore R.,Schwede T. SWISS-MODEL: homology modelling of proteinstructures and complexes. Nucleic Acids Res. 2018;46(W1):W296-W303. DOI 10.1093/nar/gky427Wen S., Wen N., Pang J., Langen G., Brew-Appiah R.A.T., MejiasJ.H.,Osorio C., Yang M., Gemini R., Moehs C.P., Zemetra R.S., KogelK.-H., Liu B., Wang X., von Wettstein D., Rustgi S. Structuralgenes of wheat and barley 5-methylcytosine DNA glycosylasesand their potential applications for human health. Proc. Natl.Acad. Sci. USA. 2012;109(50):20543-20548. DOI 10.1073/pnas.1217927109.Wu X., Zhang Y. TET-mediated active DNA demethylation: mechanism,function and beyond. Nat. Rev. Genet. 2017;18(9):517-534.DOI 10.1038/nrg.2017.33.Yamamuro C., Miki D., Zheng Z., Ma J., Wang J., Yang Z., Dong J.,Zhu J.-K. Overproduction of stomatal lineage cells in Arabidopsismutants defective in active DNA demethylation. Nat. Commun.2014;5:4062. DOI 10.1038/ncomms5062Yu M., Hon G.C., Szulwach K.E., Song C.-X., Zhang L., Kim A.,Li X., Dai Q., Shen Y., Park B., Min J.-H., Jin P., Ren B., He C.Base-resolution analysis of 5-hydroxymethylcytosine in the mammaliangenome. Cell. 2012;149(6):1368-1380. DOI 10.1016/j.cell.2012.04.027Zahid O.K., Zhao B.S., He C., Hall A.R. Quantifying mammalian genomicDNA hydroxymethylcytosine content using solid-state nanopores.Sci. Rep. 2016;6:29565. DOI 10.1038/srep29565.Zemach A., Zilberman D. Evolution of eukaryotic DNA methylationand the pursuit of safer sex. Curr. Biol. 2010;20(17):R780-R785.DOI 10.1016/j.cub.2010.07.007.Zharkov D.O. Base excision DNA repair. Cell. Mol. Life Sci. 2008;65(10):1544-1565. DOI 10.1007/s00018-008-7543-2.Zhu J., Kapoor A., Sridhar V.V., Agius F., Zhu J.-K. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patternsin Arabidopsis. Curr. Biol. 2007;17(1):54-59. DOI 10.1016/j.cub.2006.10.059."} +{"text": "Several validated scales have been developed to measure frailty, yet it remains unknown how these measures are related. We used data from 7,070 community-dwelling older adults who participated in National Health and Aging Trend Study round 5 to construct a crosswalk among frailty measures. We operationalized the 60-item Frailty Index (FI), Study of Osteoporotic Fracture (SOF) Index, FRAIL Scale, Frailty Phenotype, Clinical Frailty Scale (CFS), Vulnerable Elder Survey-13 (VES-13), Tilburg Frailty Indicator (TFI), Groningen Frailty Indicator (GFI), and Edmonton Frailty Scale (EFS). Missing data, needed for the calculation of frailty scores, were imputed using multiple imputation by chained equations method. We then linked the scores of each frailty measure to FI using the equipercentile method, a statistical procedure that links different scales by equating percentile distributions. Participants considered frail on FI (cutpoint of 0.25) corresponded to the following scores on each frailty measure: SOF 1.3, FRAIL 1.7, Phenotype 1.7, CFS 5.3, VES-13 5.5, TFI 4.4, GFI 4.4, and EFS 5.8. Conversely, individuals considered frail on each frailty measure corresponded to the following FI scores: 0.37 (SOF), 0.40 (FRAIL), 0.42 (Phenotype), 0.21 (CFS), 0.19 (VES-13), 0.28 (TFI), 0.22 (GFI), and 0.37 (EFS). The CFS, VES-13, TFI and GFI each discriminates between non-frail and frail people in the pre- to mildly frail spectrum on the FI, whereas the SOF, FRAIL Scale, Phenotype, and EFS detect those in the higher frailty spectrum on the FI. Our results provide clinicians and researchers with a useful tool to convert and interpret frailty across scales."} +{"text": "Retraction Note: J Exp Clin Cancer Res 37, 14 (2018)https://doi.org/10.1186/s13046-018-0681-yThe Editor in Chief has retracted this article. After publication, concerns were raised about Figs. 4d, 5e, and 6h. These were addressed in a Correction . Later,"} +{"text": "Stem Cell Res Ther (2021) 12:456 https://doi.org/10.1186/s13287-021-02519-yThe authors have retracted this article. After publication, the authors noticed image duplication errors in Figs. 2A, 5K, 6B, S3E and S10B, some of which also overlapped with the authors' earlier article [All authors agree to this retraction."} +{"text": "Lactobacillus pentosus (L. pentosus) plays a neuron-protective role. This study aimed to investigate the effects of L. pentosus on neurodegenerative diseases. Neurodegenerative disease is a common neurodegenerative disorder. L. pentosus strain S-PT84. Reverse transcription-quantitative PCR (RT-qPCR) was applied to determine mRNA levels. Western blot was performed to detect protein expression. Cellular behaviors were detected using Cell Counting Kit-8 (CCK-8), flow cytometry, and TdT-mediated dUTP nick-end labeling (TUNEL) assay. The interaction between baculoviral IAP repeat containing 3 (BIRC3) and NLR family CARD domain containing 4 (NLRC4) was predicted by STING and verified by western blot. Cells were treated with lipopolysaccharide (LPS) to establish neurodegenerative diseases model in vivo and with L. pentosus suppressed LPS-induced pyroptosis and promoted the cell viability of neurons. Additionally, L. pentosus suppressed the release of proinflammatory cytokines (interleukin 1 beta (IL-1\u03b2) and IL-18) and the protein expression of pyroptosis biomarkers (cleaved caspase1 (CL-CASP1) and N-terminal fragment gasdermin D (GSDMD-N)). Moreover, L. pentosus upregulated BIRC3, which induced the inactivation of NLRC4. However, BIRC3 knockdown alleviated the effects of L. pentosus and induced neuronal degeneration. L. pentosus may play a neuron-protective role via regulating BIRC3/NLRC4 signaling pathways. Therefore, L. pentosus may be a promising strategy for neurodegenerative diseases. Dementia is a common neurodegenerative disease, characterized by progressive cognitive degeneration, which induces huge burden on public health . Elder n\u03b2 and IL-18, and cell death [Pyroptosis is a form of programmed cell death executed by Gasdermin D (GSDMD) The actill death . Previoull death \u201312. HoweLactobacillus pentosus (L. pentosus), a member of probiotics from intestinal flora, plays a neuron-protective role and mitigates aging- and scopolamine-induced memory impairment [Probiotics are considered to be a safe alternative therapy for many diseases, including cancer and neural disorders , 14. Accpairment , 17. How\u03baB) target gene activation to attenuate inflammation, which promotes the development of splenic marginal zone lymphoma [Baculoviral IAP repeat containing 3 (BIRC3) is a member of inhibitor of apoptosis proteins (IAPs) . BIRC3 slymphoma . Moreovelymphoma . However2.Human neuroblastoma cell lines SH-SY5Y were provided by American type culture collection (ATCC), USA. Cells were cultured in Dulbecco's modified Eagle's medium (DMEM) medium containing 10% FBS and 1% penicillin/streptomycin at 37\u00b0C with 5% CO5 cells) were incubated with 10\u2009\u03bcg/L of lipopolysaccharide (LPS) and/or L. pentosus strain S-PT84 .Cells . Then, PCR was performed using SYBR Premix Ex Taq . GAPDH served as loading control. Relative mRNA levels were calculated using the 2\u03b2, IL-18, procaspase1, cleaved caspase1, GSDMD-N, BIRC3, NLRP3, NLRC1, NLRP3, NLRC4, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) at 4\u00b0C overnight. Next day, the membranes were incubated with secondary antibodies. GAPDH was used as the loading control. Subsequently, the bands were captured using an efficient chemiluminescence (ECL) kit and analyzed using the ImageJ software.Total protein was extracted from SH-SY5Y cells. Protein concentration was measured using a bicinchonininc acid (BCA) kit. The protein was separated using 12% SDS-PAGE. Afterwards, the separated protein was moved onto polyvinylidene difluoride (PVDF) membranes, which was then sealed by 5% skimmed milk. The membranes were incubated with primary antibodies against IL-1Cells were collected and lysed. Then, cell lysates were centrifuged at 12,000 \u00d7 g and immunoprecipitated with specific antibodies. Afterwards, the proteins were coprecipitated and isolated using 12% SDS-PAGE. Immunoblotting was analyzed with antianalysis with the indicated primary antibodies against BIRC3, NLRC4, and GAPDH.3 cells/well). After incubated with L. pentosus for 48\u2009h, cells were cultured with Cell Counting Kit-8 (CCK-8) regents for 4\u2009h. Subsequently, optic density was determined using a microplate at 450\u2009nm.Cells were seeded into 24-well plates . Subsequently, a flow cytometry was used to calculate the pyroptosis rates: active caspase1\u2009+\u2009PI double positive cells/total cells\u2009\u00d7\u2009100%.Cells were collected and fixed with 4% paraformaldehyde. After washed with 5% PBS, cells were cultured with TUNEL solutions. Then, the cells were counterstained with DAPI. Finally, TUNEL positive cells were captured using a fluorescence microscope.t-test and one-way ANOVA. P < 0.05 dictated significant difference.All data were evaluated using GraphPad 6.0. and represented as mean\u2009\u00b1\u2009SD. The comparison was performed using Student's Lactobacillus pentosus (L. pentosus) on neuronal degeneration, cells were cultured with L. pentosus. As shown in To investigate the effects of L. pentosus, SH-SY5Y cells were exposed to LPS. As shown in Figures \u03b2 and IL-18, which was antagonized by L. pentosus. These results were consistent with that from western blot. L. pentosus treatment markedly alleviated the effects of LPS and suppressed the protein expression of IL-1\u03b2 and IL-18.Inflammation is a key factor for neuronal degeneration. To verify the effects of L. pentosus significantly decreased PI and active caspase1-positive cells induced by LPS. Additionally, LPS-mediated increase in TUNEL-positive cells was abated by L. pentosus treatment (L. pentosus on LPS-induced neuronal cell death, we determined the protein expression of pyroptosis biomarkers. LPS exposure significantly increased the protein expression of cleaved caspase1 and GSDMD-N (L. pentosus.Cellular functions were detected using flow cytometry and TUNEL assay. As shown in reatment . To furt GSDMD-N , which wL. pentosus treatment significantly increased BIRC3 mRNA levels compared with the LPS group (L. pentosus also increased the protein expression of BIRC3 (Previous studies report that BIRC3 plays a neuron-protective role. We then determined the expression of BIRC3 in neurons. As shown in PS group . Moreoveof BIRC3 .L. pentosus\u2009+\u2009sh-NC group. BIRC3 knockdown significantly suppressed the cell viability of SH-SY5Y cells (\u03b2 and IL-18 (Figures The rescue assay was performed to verify the roles of BIRC3 in neuronal degeneration. As shown in 5Y cells . Additio Figures .As shown in Figures We further investigated the underlying molecular mechanisms that BIRC3 inhibited neuronal pyroptosis. The online database STING showed that the potential genes interacts with BIRC3 . The resL. pentosus play a neuron-protective role. L. pentosus suppressed inflammatory response and pyroptosis of neuron cells. Moreover, L. pentosus upregulated BIRC3, suppressing the inactivation of NLRC4 inflammasome. Hence, L. pentosus may be a promising therapy for neurodegenerative diseases.In this study, \u03b2, and p-Tau to contribute to neuroinflammation and memory impairment [\u03b2 [L. pentosus treatment restored neuronal cellular functions, manifested by the increase in cell viability and decrease in pyroptosis rates. Previous studies evidence that L. pentosus promotes cognitive capability and alleviates aging-dependent memory impairment [L. pentosus may be a promising strategy for neurodegenerative diseases.The activation of inflammasomes increases cytotoxicity and contributes to the pyroptosis of neurons, which is a key factor for memory loss and cognitive impairment . For inspairment . High lerment [\u03b2 . NLRP1 drment [\u03b2 . These rrment [\u03b2 , which fpairment , 32. The\u03b2-induced neuronal apoptosis [L. pentosus alleviated LPS-induced downregulation of BIRC3. However, BIRC3 knockdown alleviated the effects of L. pentosus and promoted inflammation and pyroptosis of neurons. These results suggested that BIRC3 may play a neuron-protective role, which is consistent with previous studies [BIRC3 plays a vital role in neuronal function. For instance, NPD1-mediated upregulation of BIRC3 promotes neural cell survival . Additiopoptosis . Howeverpoptosis as well poptosis . Hence, studies .L. pentosus-mediated upregulation of BIRC3 contributed to inactivation of NLRC4 inflammasome, which suppressed neuronal pyroptosis.However, approximately 80% studies focused on the roles of BIRC3 cancer. The reports on its roles in neural disorders are limited. BIRC3 mainly exerts its neuron-protective functions via regulating caspases cascades, which suppresses the neuronal apoptosis . RecentlL. pentosus-induced upregulation of BIRC3 suppressed inflammatory response and pyroptosis of neurons via inactivating NLRC4 inflammasome. Therefore, L. pentosus may be an alternative strategy for neurodegenerative diseases.In conclusion,"} +{"text": "Despite tremendous success of molecular targeted therapy together with immunotherapy, only a small subset of patients can benefit from them. Chemotherapy remains the mainstay treatment for most of tumors including non-small cell lung cancer (NSCLC); however, non-selective adverse effects on healthy tissues and secondary resistance are the main obstacles. Meanwhile, the quiescent or dormant cancer stem-like cells (CSLCs) are resistant to antimitotic chemoradiotherapy. Complete remission can only be realized when both proliferative cancer cells and quiescent cancer stem cells are targeted. In the present research, we constructed a cooperatively combating conjugate (DTX-P7) composed of docetaxel (DTX) and a heptapeptide (P7), which specifically binds to cell surface Hsp90, and assessed the anti-tumor effects of DTX-P7 on non-small cell lung cancer. DTX-P7 preferentially suppressed tumor growth compared with DTX in vivo with a favorable distribution to tumor tissues and long circulation half-life. Furthermore, we revealed a distinctive mechanism whereby DTX-P7 induced unfolded protein response and eventually promoted apoptosis. More importantly, we found that DTX-P7 promoted cell cycle reentry of slow-proliferating CSLCs and subsequently killed them, exhibiting a \u201cproliferate to kill\u201d pattern. Collecitvely, by force of active targeting delivery of DTX via membrane-bound Hsp90, DTX-P7 induces unfolded protein response and subsequent apoptosis by degrading Hsp90, meanwhile awakens and kills the dormant cancer stem cells. Thus, DTX-P7 deserves further development as a promising anticancer therapeutic for treatment of various membrane-harboring Hsp90 cancer types.The online version contains supplementary material available at 10.1186/s13045-022-01274-8. To the editor,To address off-target toxicity of conventional chemotherapy, one effort is to enhance the targeted delivery by conjugating therapeutic effector through a cleavable linker to a ligand specific to a drug target, and several conjugates of targeting agents have been approved for application in oncology , 2. HoweHerein, we designed and identified a peptide-conjugated drug comprising P7 and docetaxel (DTX) (namely DTX-P7) and PI3K-Akt signaling pathway Chemical structures of DTX and DTX-P7. DTX, molecular formula: C43H53NO14, molecular weight: 807.9 g/mol, white powder. DTX-P7, molecular formula: C84H118N8O25, molecular weight: 1,639.90 g/mol, white powder. b-c) Cell viability of DTX-P7 and DTX in A549 (b) and H1975 (c) cells following 48-h treatment. IC50 values: A549 cells, DTX-P7 11.4 nM, DTX 1.11 nM; H1975 cells, DTX-P7 0.62 nM, DTX 0.50 nM.Additional file 3: Supplementary Figure S2. Biodistribution of DTX-P7 in nude mice bearing A549 xenograft tumor. DTX-P7 was quantified by free DTX released from the conjugate. a) Plasma concentration of DTX and DTX-P7 in plasma samples throughout 72-h treatment. b-e) Distribution of DTX in the heart, liver, spleen, lungs, kidneys, and brain in 1 h (b), 2 h (c), 4 h (d) and 8 h (e) after DTX or DTX-P7 was administrated to mice implanted with A549 xenograft tumor. Data are given as mean \u00b1 SD (n = 3). * p < 0.05 vs. DTX group.Additional file 4: Supplementary Figure S3. Proteome changes induced in A549 cells by DTX-P7. a-c) Gene Ontology (GO) annotation analysis of A549 cell proteins that changed more than 1.5-ratio after DTX-P7 treatment, including altered proteins for biological process (a), cellular component (b) and molecular function (c) analyses. d) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation analysis of A549 cell proteins that changed more than 1.5-ratio after DTX-P7 treatment.Additional file 5: Supplementary Figure S4. Cell growth morphology of cancer stem cell-like A549/CD133+ cells and identification of cell surface Hsp90 in A549/CD133+ cells. a) Morphology of A549 and A549/CD133+ cells. b) Hsp90 expression levels were assessed in A549/CD133+ cells by cellular fractionation and Western blotting analysis. c) Immunofluorescence analysis of cell surface Hsp90 in A549/CD133+ cells. d) Immunofluorescence assays of FITC-labeled P7 binding to A549/CD133+ cells. Competition of P7 binding to A549/CD133+ cells by excess free P7.Additional file 6: Supplementary Figure S5. Effects of DTX-P7 on survival of A549/CD133+ cells and PKH26 staining of A549/CD133+ cells. a) Cell viability of DTX-P7 and DTX in A549/CD133+ cells following 48-h treatment. b) A549/CD133+ cells were stained by PKH26 followed by fluorescence detection at Day 0, 1, 6 and 10. c) Representative fluorescence-activated cell sorting profile of A549/CD133+ cells selected for sorting 10 days after PKH26 staining as compared with those of the unstained control (negative control) and Day 0."} +{"text": "Fecal calprotectin (FC) is a sensitive marker of intestinal inflammation, and is used to both discriminate inflammatory bowel disease (IBD) from non-IBD patients and to monitor patients with IBD. It is unclear whether normal values established in adult patients are applicable in pediatrics.To evaluate FC\u2019s ability to differentiate IBD from non-IBD pediatric patients, and to understand factors influencing FC in pediatric IBD(pIBD).Stool FC samples collected on all patients<19 years of age in British Columbia(BC) from May 2020 to August 2022 were run using a Buhlmann ELISA at BC Children\u2019s Hospital(BCCH). The BCCH GI database identified patients with IBD. FC\u2019s ordered by adult IBD providers and patients awaiting endoscopy were excluded. The remaining samples were analysed as non-IBD. The sensitivity(Sn), negative predictive value(NPV) and false positive(FP) of FC were evaluated; comparisons were made using the Wilcoxon rank-sum test and chi-squared.3506 FC samples met inclusion criteria: 1853 IBD and 1653 non-IBD. 221 IBD samples were from prior to diagnosis, with median (IQR) FC 2615ug/g(1090-4183); median FC for non-IBD patients was 54ug/g(24-122). Using the Buhlmann \"normal\" cutoff of 80ug/g, the Sn was 0.991 (NPV 0.998) with a FP rate of 37%. Young patients were more likely to have FP's: <6yo's (n=305) had a FP rate of 42% vs 36% in those >6yo (n=1348)(p=0.035). With a FC cutoff of 160ug/g, Sn was 0.973 (NPV 0.996), with a FP rate of 20% . At a threshold of 250ug/g, Sn was 0.959 (NPV 0.994) with a FP rate of 13% . For patients <2yo, all 4 new IBD diagnosis had FC>1900ug/g. In the non-IBD population (n=69 samples <2yo), the FP rate was 52%, 30%, and 22% using a threshold of 80, 160, and 250ug/g, respectively.Evaluating FC as a disease-monitoring tool in IBD found that at 6, 12, 18, and 24+ months post diagnosis, FC decreased from 750(159-1883), 505(110-1566), 351(87-1379), to 308ug/g(85-1129), respectively. Similarly, the proportion of FC\u2019s <250ug/g increased from 4.1% at diagnosis to 30%, 39.7%, 41.5%, 47% during the follow up period.Patients with UC/IBD-U had higher FC\u2019s, and were less likely to achieve FC<250ug/g. By 12 months post diagnosis, median FC of CD patients was 347ug/g(96-1150) and UC/IBD-U was 745ug/g(191-2017)(p=0.036), and at 18 months, CD 273ug/g(61-902) vs UC/IBD-U 932ug/g(144-2229)(p<0.001). At 2+yrs, median FC for CD patients was 259ug/g(76-1038) vs 387ug/g(108-1577) for UC/IC (p=0.017).Patients cared for by an IBD specialist had better FC outcomes vs those managed by non-IBD GIs: median FC at 12 months was 246ug/g(n=79) vs 677ug/g(n=153)(p=0.002), with 51% vs 34% achieving FC<250(p=0.014). Similarly, at 2+yrs post diagnosis, median FC was 243ug/g(n=437) vs 356ug/g(n=407)(p=0.02).Higher FC thresholds are likely required in younger populations compared to established adult cutoffs. In this pIBD cohort, <50% achieve FC levels <250ug/g.NoneNone Declared"} +{"text": "We described emergency department (ED) visits by persons with multiple sclerosis (MS) in British Columbia, Canada (1 April2012 to 31 December 2017). We identified 15,350 MS cases using healthadministrative data; 73.4% were women, averaging 51.4\u2009years at study entry. Over4.9\u2009years of follow-up (mean), 56.0% of MS cases visited an ED . A diagnosis was documented for25,698 (69.3%) ED visits, and 18.4% were infection-related.Inpatient admissions were reported for 20.4% of all and 29.2%(1380/4725) of infection-related ED visits. Findings suggest that the ED plays asubstantial role in MS healthcare and infection management. For example,persons with MS had 41% more infection-related physician claims versus a sex-, age-, andregion-matched non-MS population. However, relatively little is known about ED utilization by persons withMS.46 Here, we described overall andinfection-related ED use in an MS population.Emergency department (ED) presentations represent an important aspect of health careutilization in the general population.), including Medical Service Plan Billing Information (providing physician claims); the Discharge Abstract Database ; PharmaNet (for prescriptions filled at outpatient/community pharmacies); Census Geodata(providing socioeconomic status estimates); Registration and Premium Billing files ; Vital Statistics (capturing death dates); and the National Ambulatory Care Reporting System dataset starting 1 April 2012).We performed a descriptive, population-based study in British Columbia (BC), Canada,using linked health administrative data code, or first disease-modifyingdrug (DMD) prescription filled, or 1 April 2012 (start of the ED date). All includedpersons were \u2a7e18\u2009years old and BC residents for \u2a7e1\u2009year pre-study entry; follow-upended at the earliest of death, emigration, or 31 December 2017. Comorbidities weremeasured using a modified Charlson Comorbidity Index during the 1-year pre-studyentry.1618 MS cases everfilling a DMD prescription during follow-up were described.All MS cases were identified with a validated algorithm.n\u2009=\u20098603) with (vs without) comorbidity at study entrywere older (mean age\u2009=\u200956.5 (SD\u2009=\u200914.3) vs 49.5 (SD\u2009=\u200913.7) years) and averaged moreED visits/person/year (1.3 (SD\u2009=\u20092.4) vs 0.9 (SD\u2009=\u20091.9)). More than a quarter of MScases had \u2a7e3 ED visits ; of these 1383 (34.0%) of 4064 had \u2a7e1comorbidity at study entry. Most ED visits by MS cases did not require an ambulance; 28.8% required a ground ambulance and>95% were of semi-urgent or higher priority .We identified 15,350 MS cases women; Supplementary Table 2). These visits were made by 74.2%(6384/8603) of MS ED users. Of these, the most frequent primary diagnoses were\u201cabdominal pain/colic\u201d , \u201curinary tract infection\u201d, and \u201cMS\u201d . When combined, 18.4% of ED visits were infection-related with 32.2% (2056/6384) of MSparticipants having at least one such visit. Nearly one-third of infection-related ED visits led to hospitalization, while 20.4% of all ED visits made by 27.9% (2404/8603) of cases did so (Supplementary Tables 2 and 3).Diagnostic codes were reported for 69.3% of ED visits (summarizedin Persons who filled \u2a7e1 DMD prescription(s) during follow-up (\u201cDMD users\u201d) wereyounger at study entry date than non-users (mean age\u2009=\u200941.9 (SD\u2009=\u200911.1) vs 53.8(SD\u2009=\u200913.3) years). However, the proportions accessing an ED at least once weregenerally similar , as was the study follow-up time (4.8\u2009years (SD\u2009=\u20091.6) for DMD usersvs 4.9 (SD\u2009=\u20091.6) for non-users).There were no clear patterns across the socioeconomic quintiles at study entryfor the MS cases: ever/never filling a DMD prescription during follow-up,ever/never being hospitalized subsequent to an ED visit, or for the five mostcommon ED diagnoses (data not shown).Over 50% of persons with MS had more than one ED consultation during our nearly6-year observation period; one-quarter visited an ED three or more times. Nearly 20%of ED visits were infection-related; one-third resulted in hospitalization, whereasone-fifth of all-cause ED visits did so. MS cases with \u2a7e1 (vs without) comorbidityat study entry averaged more ED visits/person/year. Our intentionally descriptivestudy has several limitations. While the overall burden of infection-related EDvisits was considerable in our MS population, this could be higher as diagnoses wereunavailable for one-third of all ED visits. Furthermore, our study lackedMS-specific clinical information, such as relapses, and a comparison to the generalpopulation. Our 1-year pre-study lookback period may have reduced the detection ofcomorbidities. Strengths of our study included the large cohort of MS casesidentified using a validated algorithm within a geographically defined populationwith universal healthcare coverage, including ED visits. Our results suggest thatthe ED visits by MS cases often lead to hospitalizations, perhaps more so forinfection-related visits. Further studies are necessary to better understand theimportance of ED use by persons with MS.Click here for additional data file.Supplemental material, sj-docx-1-msj-10.1177_13524585221078497 for Emergencydepartment use by persons with MS: A population-based descriptive study with afocus on infection-related visits by Jonas Graf, Huah Shin Ng, Feng Zhu, YinshanZhao, Jos\u00e9 MA Wijnands, Charity Evans, John D Fisk, Ruth Ann Marrie and HelenTremlett in Multiple Sclerosis JournalClick here for additional data file.Supplemental material, sj-docx-2-msj-10.1177_13524585221078497 for Emergencydepartment use by persons with MS: A population-based descriptive study with afocus on infection-related visits by Jonas Graf, Huah Shin Ng, Feng Zhu, YinshanZhao, Jos\u00e9 MA Wijnands, Charity Evans, John D Fisk, Ruth Ann Marrie and HelenTremlett in Multiple Sclerosis JournalClick here for additional data file.Supplemental material, sj-docx-3-msj-10.1177_13524585221078497 for Emergencydepartment use by persons with MS: A population-based descriptive study with afocus on infection-related visits by Jonas Graf, Huah Shin Ng, Feng Zhu, YinshanZhao, Jos\u00e9 MA Wijnands, Charity Evans, John D Fisk, Ruth Ann Marrie and HelenTremlett in Multiple Sclerosis Journal"} +{"text": "The immunopathogenesis of chronic spontaneous urticaria (CSU) is poorly understood, but recent research suggests that patients can be divided into autoallergic and autoimmune subtypes. Given that not all patients can be controlled with current treatment regimens, including anti-IgE monoclonal antibodies, a better understanding of the immune pathways involved in CSU may enable the repurposing of monoclonal antibodies used for other dermatologic diseases . Therefore, we investigated the implicated immune cells and pathways by reanalyzing publicly available transcriptomic data.2 fold change| \u22651. Pathway analyses were conducted using ToppGene and KEGG. Cell-type enrichment was determined by CIBERSORT and xCell and was correlated with clinical characteristics.Microarray data of CSU and healthy control (HC) skin and blood were obtained from the Gene Expression Omnibus . Differentially expressed genes were defined as a false discovery rate <0.05 and a |logTh2 and Th17-related pathways were upregulated in lesional compared to non-lesional and HC samples. In non-lesional versus lesional samples, CIBERSORT analysis revealed increased regulatory T-cells (Treg) and resting mast cells. xCell analysis established that Th1 and Th2 scores were not significantly different between lesional and HC samples. However, Th2 scores in both lesional and non-lesional samples correlated positively with disease severity. Few differentially expressed genes and pathways were identified between CSU and HC blood samples.Our results support the involvement of Th2 and Th17-related genes and pathways in CSU. Th2 scores associate with disease severity, which indicates the clinical relevance of these findings. Increased resting mast cell and Treg scores in non-lesional samples may suggest local suppression of wheal formation. Moreover, disease activity seemed to be restricted to the skin as there were limited findings from blood. Larger studies using next-generation sequencing will be helpful to confirm these results. Chronic spontaneous urticaria (CSU) is defined by the presence of wheals and/or angioedema occurring in the absence of specific external stimuli and persisting for \u2265 6 weeks . CSU is There has been a paradigm shift in the understanding of the pathogenesis of CSU and current evidence suggests that most CSU cases have an autoimmune etiology , 7. AutoSeveral studies support the involvement of dysfunction of adaptive cellular immunity in the immune pathogenesis of CSU , 11. Curin silico quantification of various cell-types from transcriptomic data of a heterogeneous cell population. CIBERSORT is one such RNA deconvolution technique that employs linear support vector regression to quantify relative proportions of cell types (GSE57178) (Transcriptomic data acquired by microarray were obtained from the Gene Expression Omnibus (GEO) . From GiSE72542) , data waSE57178) , data onDifferentially expressed genes (DEGs) were determined using the GEO2R online tgetGEO function from the GEOquery package . Select DEGs were presented by violin plots.DEG analysis was performed by The McGill Genome Centre, Montreal, Quebec. Datasets were analyzed separately. For each dataset, the normalized expression values were downloaded from the GEO database using the package , and line and 100 permutations to estimate the relative proportions of 22 cell-types . Cell abP-values and Q-values less than 0.05 were considered significant. All statistical tests were performed on RStudio version 1.4.1717 and graphs and figures were rendered using the Ggplot2 package , neutrophil degranulation (Q = 1.69E-23), innate immune system (Q = 4.50E-17), cytokine signaling in immune system (Q = 1.82E-14), staphylococcus aureus infection (Q = 2.85E-11), and signaling by interleukins (Q = 3.05E-11). Th2-related pathways including IL-4 and IL-13 mediated signaling (Q = 1.03E-13) and IL-18 signaling (Q = 2.05E-7) were upregulated. Additionally, IL-10 signaling (Q = 8.42E-14), an immunosuppressive pathway, and IL-12 mediated signaling (Q = 3.80E-3), a Th1 polarizing cytokine, were upregulated (Q = 1.04E-3), an activator directly upstream of the Th17 response, as well as IL-17 signaling (Q = 3.60E-6), and IL-6 mediated signaling events (Q = 8.28E-4) .Q = 4.42E-15), cytokine-receptor interaction (Q = 3.05E-12), and TNF signaling (Q = 4.02E-8) (Q = 3.75E-8) and Th17 cell differentiation (Q = 0.017) (Upregulated KEGG pathways comprise staphylococcus aureus infection (4.02E-8) . In line= 0.017) . Genes u= 0.017) , whereas= 0.017) . IndividIL-4R was upregulated , cytokine signaling in immune system (Q = 1.70E-10), signaling by interleukins (Q = 2.60E-10), neutrophil degranulation (Q = 1.38E-9), IL-4 and IL-13 signaling (Q = 2.15E-9), IL-18 signaling (Q = 1.72E-4), IL-17 signaling (Q = 1.04E-3), IL-23 mediated signaling events (Q = 5.59E-4), IL-6 mediated signaling events (Q = 1.28E-3), and IL-12 mediated signaling events (Q = 2.57E-2). Additionally, the IL-4 mediated signaling events pathway (Q = 2.89E-2) was also upregulated , TNF signaling (Q = 9.20E-8), and staphylococcus aureus infection (Q = 5.06E-7) (Q = 9.20E-8) and Th17 cell differentiation (Q = 0.019) were upregulated . Moreoveegulated . Upregulegulated and Th17egulated pathwaysQ = 0.033), Th17 cell differentiation (Q = 0.027), IL-5 signaling pathway and Th1/Th2 differentiation (Q = 0.027). Similarly, KEGG analysis demonstrated enriched Th1 and Th2 cell differentiation (Q = 0.045) and Th17 cell differentiation (Q = 0.045). These results must be interpreted with caution, however, because HLA-DRB3 was the only upregulated gene involved in each of these pathways.Five genes were upregulated and seven downregulated in the 20 CSU versus 10 HC blood samples. ToppGene pathway analysis of upregulated genes revealed enriched Th1 and Th2 cell differentiation (Q = 0.029) and CD8+ T-cells (Q = 0.0066) were decreased, whereas CD4+ resting memory T-cells (Q = 0.0081) were increased. Eosinophils were only detected in some lesional skin samples, but not statistically significantly greater than in HC samples. No significant differences were observed in B-cells, natural killer (NK) cells, macrophages, DCs, neutrophils, or Tregs.RNA deconvolution of 15 lesional and 12 HC skin samples was performed by CIBERSORT . In lesiQ = 0.020), CD4+ memory T-cells (Q = 0.039), common lymphoid progenitor cells (Q = 0.025), and class switched memory B-cells (Q = 0.015) had increased cell abundance scores in lesional compared to HC samples. No significant differences were observed in Th1 (Q = 0.30) or Th2 (Q = 0.55) cells; however, gamma delta T-cells (Tgd) had elevated cell abundance scores in lesional samples (Q = 0.015). Th2 scores in lesional samples correlated moderately with UAS7 (p = 0.044). Innate immune cells including M1 macrophages (Q = 0.022), mast cells (Q = 0.039), monocytes (Q = 0.015), and neutrophils (Q = 0.0055) had increased scores in lesional samples in contrast to HC samples. Similarly, total dendritic cells (DC) were elevated in lesional versus HC samples (Q = 0.0010), including activated dendritic cells (aDC) (Q = 0.0010), conventional dendritic cells (cDC) (Q = 0.047), immature dendritic cells (iDC) (Q = 0.0050), and plasmacytoid dendritic cells (pDC) (Q = 0.037). Interestingly, neurons (Q = 0.013) were decreased in lesional compared to HC samples. While basophils were detected in both lesional and HC samples, abundance scores were not significantly different.Cell abundance scores determined by xCell were compared between lesional and HC skin samples . CD4+ efQ = 0.039) in non-lesional samples. Interestingly, Tregs (Q = 0.014) and resting mast cells (Q = 0.014) were increased in non-lesional compared to lesional samples. Eosinophils were only detected in some lesional skin samples, but not statistically significantly greater than non-lesional samples. We did not detect any significant differences in B-cells, NK cells, macrophages, DCs, or neutrophils between lesional and non-lesional samples on CIBERSORT.CIBERSORT RNA deconvolution of 15 lesional versus 15 matched non-lesional samples revealedQ = 0.012). Moreover, Th2 cell abundance scores of non-lesional samples correlated strongly with UAS7 scores (p = 0.0028), whereas Th1 cell abundance scores correlated negatively with UAS7 scores (p = 0.012). Basophils were detected in both groups but were not significantly different.xCell analysis of lesional versus non-lesional skin samples revealedQ = 0.018) and decreased monocytes (Q = 0.018) in CSU blood compared to HC blood. No eosinophils were detected in either CSU or HC blood and no significant differences were detected in other cell-types. Although neutrophils were not enriched in CSU blood samples compared to HC blood, neutrophil CIBERSORT scores strongly positively correlated with UAS7 scores (p = 0.00099).RNA deconvolution using CIBERSORT of 20 CSU blood samples and 10 HC blood samples revealedp = 0.007) and Th2 (p = 0.042) cell abundance scores correlated negatively with UAS7 scores. Basophils were only detected in CSU samples but not statistically significantly greater than in HC samples. Moreover, Th2 cells were significantly decreased in ASST+ samples compared to ASST\u2013 samples (p = 0.019), but no difference was observed in Th1 cells (p = 0.82).xCell analysis did not detect differences in cell-type abundance scores between CSU and HC blood samples. Among CSU blood samples, Th1 (Q = 0.014) and resting DCs (Q = 0.014) differed on CIBERSORT analysis. However, significant differences were identified in five cell-types by CIBERSORT and 16 cell-types by xCell in HC samples and six cell-types by CIBERSORT and 13 cell-types by xCell in non-lesional samples.The Gim\u00e9nez-Arnau et al. and PateRecently, the role of Th2 dysregulation has been proposed as a potential driver of CSU pathogenesis in at least a subset of CSU patients , 31. Th2Th2 response is not only important for IgE antibody production, but also stimulates IgG1 complement binding and IgG4 antibodies underlying other autoimmune conditions . InteresIL-10 expression was shown to be increased in CSU lesions and a CSU mouse model overexpressing IL-10 exhibited increased pruritus and increased IL-2, IL-4, and IFN-\u03b3 expression, driven by JAK/STAT signaling or whether it is an insufficient immunosuppressive response.We showed that the IL-4, IL-13, and IL-18 cytokine signaling pathways were upregulated in lesional CSU biopsies versus both HC and non-lesional samples, which suggest a role in the wheal response. Other studies have shown that cytokines that initiate the Type 2 response , 34 are ignaling . It is uContrary to a previous study reporting increased Th2 cells in CSU lesions , we did IL-6) were also upregulated in lesional samples compared to non-lesional and HC samples. IL-17 and IL-23 have been shown to be elevated in the serum of CSU patients compared to controls and positively correlate with UAS7 scores . A Th1 response is usually associated with ASST positivity , but in In vivo and in vitro evidence indicate a role for Tregs in the suppression of mast cell degranulation via OX40-OX40L signaling can be found in the article/PL, EN, IL, and CP designed the study. CP, PL, SG, and ML performed the data analysis. CP and SG prepared the figures and tables. EN, PL, IL, MB-S, and AG-A supervised the study. All authors contributed to writing and editing the manuscript.EN was a consultant and speaker for Novartis and has received an investigator-initiated research grant from Novartis. MB-S was a consultant for Novartis. AG-A was a medical advisor for Uriach Pharma, Genentech, Novartis, FAES, GSK, Sanofi\u2013Regeneron, Amgen, Thermo Fisher Scientific, Almirall, she has research grants supported by Uriach Pharma, Novartis, Grants from Instituto Carlos III- FEDER and performs educational activities for Uriach Pharma, Novartis, Genentech, Menarini, LEO-PHARMA, GSK, MSD, Almirall, Sanofi\u2014Regeneron, AVENE. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Globally, a high-salt diet (HSD) has become a threat to human health as it can lead to a high risk of cardiac damage. Although some studies investigating HSD have been carried out, the majority has been conducted in males, and there are few female-specific studies, thereby ignoring any effects of sex-specific damage on the heart. In this study, we determined how HSD induces different pathways of cardiovascular diseases through sex-specific effects on cardiac damage in mice.An HSD murine model of male and female C57BL/6J mice was fed with sodium-rich chow (4% NaCl). After 8 weeks, cardiac tissues were collected, and the whole gene transcriptome of the hearts of male and female mice was characterized and analyzed using high-throughput RNA sequencing. Immunohistochemistry staining was used to further assess the harmful effects of HSD on protein expression of genes associated with immunity, fibrosis, and apoptosis in male and female mice.HSD drastically altered the cardiac transcriptome compared to that of the normal heart in both male and female mice and had a sex-specific effect on the cardiac composition in the transcriptome. HSD produced various differentially expressed genes and affected different KEGG pathways of the transcriptome in male and female mice. Furthermore, we found that HSD induced different pathways of cardiovascular disease in the male mice and female mice. The pathway of hypertrophic cardiomyopathy is significantly enriched in HSD-treated male mice, while the pathway of dilated cardiomyopathy is significantly enriched in HSD-treated female mice. Finally, metabolism, immunity, fibrosis, and apoptosis in the mouse heart showed sex-specific changes predicting cardiac damage.Our results demonstrate that HSD adversely impacts cardiac structure and function by affecting the metabolism, immunity, fibrosis, and apoptosis in the murine heart and induces the mouse to suffer from sex-specific cardiovascular disease. This study provides a new perspective and basis for the differences in the pharmacology and interventional treatment of sex-specific cardiovascular diseases induced by HSD in men and women. High salt content in diet poses various health risks and contributes to the increase in disease prevalence in high-income countries , 2. SaltExisting evidence suggests that a high-salt diet (HSD) is related to cardiovascular disease , 12, chrTo investigate the effect of sex-specific damage of HSD on the structure and function of heart tissues, we generated an HSD murine model by administering male and female C57BL/6J mice with sodium-rich chow containing 4% NaCl. The whole gene transcriptome of the mouse HSD-treated heart was characterized and analyzed by high-throughput RNA sequencing. This study determined that HSD induces cardiac dysfunction and structural damage and possibly cardiovascular disease by inducing changes to metabolism, immune response, fibrosis, and apoptosis in the hearts of male and female mice. Our research may help to reveal the molecular mechanisms of physiological damage caused by HSD to cardiac tissue and is of great significance for the development of therapeutic intervention methods for HSD-induced cardiovascular-related diseases.A schematic of the experimental design is shown in http://www.gempharmatech.com). Before starting the experiment, all mice were placed in a 12-h LD cycle to adapt to the environment for 2 weeks. Male and female mice were fed a normal diet and HSD (4% NaCl) as the normal and high-salt groups, respectively. All experimental protocols were approved by the Institutional Animal Care and Use Committee of Henan Province People's Hospital.Twelve wild-type C57BL/6J male mice and female mice (6\u20138 weeks) were purchased from GemPharmatech Co., Ltd . Echocardiography of mice anesthetized with isoflurane was performed in M-mode. Fractional shortening (FS), left ventricular (LV) internal dimension at end-diastole (LVIDd), and diastolic left ventricular thickness (LVPWd) were collected.After 8 weeks following a normal diet or HSD, the hearts of mice were rapidly harvested and weighed after death by cervical dislocation. Tissues were immediately immersed in liquid nitrogen, transported, and stored in a freezer set to maintain \u221280\u00b0C.Immunohistochemistry (IHC) analysis was performed on murine heart samples according to a previously published protocol . ParaffiMasson staining of murine hearts was performed according to a previously published study . All carAll cardiac sections from CONMH, MH8W, CONFH, and FH8W groups were placed in xylene I-III for 15\u201320 min and then rinsed with 75\u2013100% ethanol for 5 min and rinsed with distilled water. The cardiac sections were stained with hematoxylin and eosin dye solution from a hematoxylin-eosin (HE) staining Kit . After the slices were dehydrated, they were mounted with neutral gum . Microscopy, image acquisition, and analysis of cardiac sections were performed using an orthotopic light microscope . For quantification of cardiac cell size, 20 400X field images were randomly selected in a double-blind manner and cell numbers in each field were counted by ImageJ software . Average cell size is calculated as the number of cells in the field divided by the area of the field.http://bgitechsolutions.com/sequencing). Frozen mouse heart tissue was broken up using a mortar and pestle to obtain a piece, macroscopically free of fatty infiltration, fibrosis, and blood. RNA was extracted using the RNA Easy Spin Column Kit following the TRIzol RNA extraction protocol.All RNA extractions were performed by the Beijing Genomic Institute .The RNA library was prepared according to a previously published study using thpost-hoc test was set as Tykey-Kramer with 0.95, and the effect size was set as Eta-squared. The other parameters were set to default values.Principal component analysis (PCA) was performed using the Statistical Analysis of Metagenomic Profiles (STAMP) software package . PCA washttp://www.genome.jp/kegg) and NCBI RefSeq GCF_000001635.25_GRCm38.p5 as the reference gene set. Pathways with q \u2264 0.05 were defined as significantly enriched in differentially expressed genes (DEGs). The P value formula used in this study is given as follows:Kyoto encyclopedia of genes and genomes pathway annotation was performed using BLASTALL software against the KEGG database version 81.0 \u2264 0.05, as the threshold.where rrection , with q http://www.geneontology.org) and calculates the number of genes for each term. The hypergeometric test was then applied to determine the significance of the biological functions of the candidate genes in comparison to the different genetic backgrounds of this species. Referring to the software \u201cGO:: TermFinder\u201d , the calculation formula of this analysis is the same as the KEGG enrichment analysis, N is the number of genes with GO annotations, n is the number of candidate genes in N, and M is the number of genes annotated with a specific GO term in all genes. The calculated P-value was determined using the Bonferroni correction, with q \u2264 0.05 as the threshold. GO terms that met this condition were defined as significantly enriched.The molecular function and biological process of genes were analyzed by Gene Ontology (GO) , 32. Sighttps://string-db.org/, version 11.5) (Protein-protein association networks (PPANs) for fibrosis, metabolism, immunity, and apoptosis were analyzed using STRING (on 11.5) . The netP < 0.05.GraphPad Prism software was used to generate bar charts and scatter plots. The Venn diagram plotter, a network tool , was used to compare the number of transcripts between the normal and HSD-treated groups. The expression of transcripts in the normal and HSD groups was visualized using the pheatmap package in R . The data were analyzed using the two-way analysis of variance (ANOVA). The data are presented as mean values \u00b1 SEM and were considered statistically significant when P = 0.04) as well as a significant main effect of sex (P < 0.001) and HSD (P = 0.004) on body weight. These analyses revealed that the body weight of HSD-treated mice was significantly lower than that of the normal group in both male and female mice (P = 0.002) and sex (P = 0.024), but not sex \u00d7 HSD interaction (P = 0.067) on ratios of HW/BW (P < 0.001) and sex (P = 0.031), but not sex \u00d7 HSD interaction (P = 0.082) on FS; (2) a significant main effect of HSD (P = 0.003) and sex (P = 0.034), but not sex \u00d7 HSD interaction (P = 0.067) on LVIDd; (3) a significant sex \u00d7 HSD interaction (P = 0.012) as well as a significant main effect of sex (P = 0.044) and HSD (P = 0.006) on LVPWd. To study the effect of HSD on cardiomyocyte size, HE staining was performed. A two-way ANOVA demonstrated a significant sex \u00d7 HSD interaction (P = 0.037) as well as a significant main effect of HSD (P < 0.001) on cell size. In males, the cell size of cardiomyocytes demonstrated a significant sex \u00d7 HSD interaction and high-salt-treated (MH8W) groups, respectively ; for femQ value <0.05) was compared between the CONMH and MH8W groups, CONFH and FH8W groups, and CONMH and CONFH groups, respectively. As shown in Principal component analysis was used for data visualization to determine transcriptomic differences between the CONMH and MH8W groups, and CONFH and FH8W groups, respectively . The dimTo investigate the effect of excessive sodium intake on the higher expression genes, we compared the difference between the CONMH and MH8W groups, and CONFH and FH8W groups using Venn plots. As shown in P < 0.05) were identified as being unique to the CONMH group and were divided into four categories: (1) cellular processes: tight junction (P = 2.27E-03), focal adhesion (P = 8.22E-03), and lysosome (P = 4.15E-02); (2) environmental information processing: PI3K-akt signaling pathway (P = 2.89E-03), ECM-receptor interaction (P = 9.86E-03), and Rap1 signaling pathway (P = 1.37E-02); (3) human diseases: AGE-RAGE signaling pathway in diabetic complications (P = 2.39E-04), transcriptional mis-regulation in cancer (P = 3.41E-04), human T-cell leukemia virus 1 infection (P = 3.09E-02), and systemic lupus erythematosus (P = 2.85E-02); (4) organismal systems: oxytocin signaling pathway (P = 3.32E-04), complement and coagulation cascades (P = 3.15E-03), estrogen signaling pathway (P = 1.86E-03), platelet activation (P = 4.45E-03), relaxing signaling pathway (P = 5.37E-03), dopaminergic synapse (P = 6.44E-03), protein digestion and absorption (P = 1.34E-02), cholesterol metabolism (P = 1.85E-02), glucagon signaling pathway (P = 2.11E-02), circadian rhythm (P = 2.38E-02), glutamatergic synapse (P = 3.02E-02), cholinergic synapse (P = 2.90E-02), and adrenergic signaling in cardiomyocytes (P = 3.91E-02) (P < 0.05) were identified in the shared CONMH and MH8W groups and were divided into five categories: (1) cellular processes: autophagy-animal (P = 8.05E-10) and endocytosis (P = 1.02E-07); (2) environmental information processing: phosphatidylinositol signaling system (P = 1.46E-09) and TNF signaling pathway (P = 2.18E-08); (3) genetic information processing: ribosome biogenesis in eukaryotes (P = 5.72E-10), ubiquitin mediated proteolysis (P = 2.31E-09), and RNA degradation (P = 6.35E-08); (4) human diseases: herpes simplex virus 1 infection (P = 1.44E-10) and colorectal cancer (P = 1.80E-08); (5) metabolism: inositol phosphate metabolism (P = 8.35E-09) (P < 0.05) were identified as being unique to the MH8W group and were divided into four categories: (1) environmental information processing: ECM-receptor interaction (P = 1.09E-06), PI3K-Akt signaling pathway (P = 5.40E-04), and WNT signaling pathway (P = 3.63E-03); (2) human diseases: arrhythmogenic right ventricular cardiomyopathy and dilated cardiomyopathy ; (3) metabolism: tyrosine metabolism (P = 3.96E-03), phenylalanine metabolism (P = 1.07E-02), histidine metabolism (P = 1.25E-02), and glycolysis/gluconeogenesis (P = 1.31E-02); (4) organismal systems: regulation of lipolysis in adipocytes (P = 5.40E-03) . A total.35E-09) . While 1.40E-03) .P < 0.01) were identified as being unique to the CONFH group and were divided into three categories: (1) environmental information processing: AMPK signaling pathway (P = 8.81E-04), TNF signaling pathway (P = 2.13E-03), PI3K-Akt signaling pathway (P = 4.27E-03), and cytokine-cytokine receptor interaction (P = 7.40E-03); (2) human diseases: transcriptional mis-regulation in cancer (P = 2.66E-05), rheumatoid arthritis (P = 4.23E-04), hypertrophic cardiomyopathy , acute myeloid leukemia (P = 5.06E-03), measles (P = 7.51E-03), and systemic lupus erythematosus (P = 7.51E-03); (3) organismal systems: IL-17 signaling pathway (P = 3.24E-03), chemokine signaling pathway (P = 4.18E-03), intestinal immune network for IgA production (P = 4.33E-03), and adipocytokine signaling pathway (P = 5.38E-03) (P < 0.001) were identified in the shared CONFH and FH8W groups and were divided into six categories: (1) cellular processes: autophagy-animal (P = 1.33E-08), endocytosis (P = 1.63E-05), cell cycle (P = 1.69E-05), adherens junction (P = 8.86E-05), lysosome (P = 1.17E-04), apoptosis (P = 1.34E-04), signaling pathways regulating pluripotency of stem cells (P = 6.37E-04), and apoptosis-fly (P = 9.50E-04); (2) environmental information processing: phosphatidylinositol signaling system (P = 6.48E-08), TNF signaling pathway (P = 1.84E-07), notch signaling pathway (P = 2.33E-07), MAPK signaling pathway (P = 4.83E-07), ERBB signaling pathway (P = 5.01E-07), WNT signaling pathway (P = 2.14E-06), hippo signaling pathway-fly (P = 4.95E-05), RAS signaling pathway (P = 5.79E-05), rap1 signaling pathway (P = 7.87E-05), mTOR signaling pathway (P = 1.29E-04), NF-kappa B signaling pathway (P = 7.18E-04), and hippo signaling pathway-multiple species (P = 3.40E-10); (3) genetic information processing: ribosome biogenesis in eukaryotes (P = 6.93E-05), ubiquitin mediated proteolysis (P = 2.04E-04), RNA degradation (P = 2.59E-04), DNA replication (P = 3.89E-04), basal transcription factors (P = 4.25E-04), nucleotide excision repair (P = 4.46E-04), RNA transport (P = 9.61E-04), mismatch repair (P = 2.88E-06), non-homologous end-joining (P = 1.32E-05), base excision repair (P = 9.84E-05), spliceosome (P = 4.92E-04), Fanconi anemia pathway (P = 6.30E-04), and aminoacyl-tRNA biosynthesis (P = 8.04E-04); (4) human diseases: herpes simplex virus 1 infection (P = 3.40E-10), microRNAs in cancer (P = 7.55E-09), pathways in cancer (P = 1.32E-07), colorectal cancer (P = 6.54E-07), pancreatic cancer (P = 6.45E-06), hepatitis B (P = 1.19E-05), endocrine resistance (P = 1.93E-05), breast cancer (P = 6.12E-05), chronic myeloid leukemia (P = 1.23E-04), small cell lung cancer (P = 1.70E-04), prostate cancer (P = 1.95E-04), endometrial cancer (P = 1.96E-04), hepatocellular carcinoma (P = 2.80E-04), insulin resistance (P = 3.82E-04), AGE-RAGE signaling pathway in diabetic complications (P = 3.82E-04), non-small cell lung cancer (P = 4.08E-04), human papillomavirus infection (P = 5.64E-04), and choline metabolism in cancer (P = 6.17E-04); (5) metabolism: N-Glycan biosynthesis (P = 1.49E-08), inositol phosphate metabolism (P = 1.07E-07), pyrimidine metabolism (P = 2.00E-06), lysine degradation (P = 1.27E-05), terpenoid backbone biosynthesis (P = 5.54E-05), glycosylphosphatidylinositol (GPI)-anchor biosynthesis (P = 6.93E-05), one carbon pool by folate (P = 2.04E-04), purine metabolism (P = 2.59E-04), amino sugar and nucleotide sugar metabolism (P = 3.89E-04), other types of O-glycan biosynthesis (P = 4.25E-04), other glycan degradation (P = 4.46E-04), and seleno-compound metabolism (P = 9.61E-04); (6) organismal systems: axon guidance (P = 2.88E-06), FC gamma R-mediated phagocytosis (P = 1.32E-05), thyroid hormone signaling pathway (P = 9.84E-05), chemokine signaling pathway (P = 4.92E-04), B cell receptor signaling pathway (P = 6.30E-04), osteoclast differentiation (P = 8.04E-04) (P < 0.01) were identified as being unique to the FH8W group and were divided into five categories: (1) cellular processes: gap junction (P = 5.33E-06) and focal adhesion (P = 4.93E-05); (2) environmental information processing: ECM-receptor interaction (P = 6.80E-06), Rap1 signaling pathway (P = 3.88E-05), PI3K-Akt signaling pathway (P = 7.46E-05), calcium signaling pathway (P = 3.39E-03), MAPK signaling pathway (P = 4.49E-03), and WNT signaling pathway (P = 6.38E-03); (3) human diseases: melanoma (P = 4.34E-03), hypertrophic cardiomyopathy , dilated cardiomyopathy , herpes simplex virus 1 infection (P = 6.02E-03), and arrhythmogenic right ventricular cardiomyopathy ; (4) metabolism: tyrosine metabolism (P = 5.33E-03); (5) organismal systems: parathyroid hormone synthesis, secretion and action (P = 2.29E-04), platelet activation (P = 2.29E-04), relaxing signaling pathway (P = 3.79E-03), oxytocin signaling pathway (P = 4.36E-03), thyroid hormone signaling pathway (P = 6.22E-03), and circadian entrainment (P = 6.84E-03) . A total.04E-04) . While 2.84E-03) .P < 0.01) were identified as being unique to the CONMH group and were divided into four categories: (1) cellular processes: endocytosis (P = 7.91E-03); (2) environmental information processing: calcium signaling pathway (P = 9.34E-03); (3) human diseases: hepatocellular carcinoma (P = 1.23E-03), pancreatic cancer (P = 6.12E-03), and human papillomavirus infection (P = 8.82E-03); (4) organismal systems: vitamin digestion and absorption (P = 5.66E-03), cholesterol metabolism (P = 6.60E-03), and oxytocin signaling pathway (P = 9.12E-03) were identified as being unique to the CONFH group and were divided into three categories: (1) environmental information processing: PI3K-Akt signaling pathway (P = 8.93E-04), cytokine-cytokine receptor interaction (P = 5.96E-03), and WNT signaling pathway (P = 9.59E-03); (2) human diseases: transcriptional mis-regulation in cancer (P = 6.20E-04), rheumatoid arthritis (P = 2.92E-03), herpes simplex virus 1 infection (P = 7.40E-03), Kaposi sarcoma-associated herpesvirus infection (P = 8.08E-03), and microRNAs in cancer (P = 9.96E-03); (3) organismal systems: IL-17 signaling pathway (P = 8.99E-04), B cell receptor signaling pathway (P = 1.67E-03), osteoclast differentiation (P = 6.27E-03), and axon guidance (P = 6.74E-03) . Top 10 .12E-03) , which e.74E-03) . AltogetQ = 3.17E-22), dilated cardiomyopathy , arrhythmogenic right ventricular cardiomyopathy , fluid shear stress and atherosclerosis (Q = 1.37E-12), and viral myocarditis (Q = 1.65E-03) (Q = 1.43E-07), peptide antigen binding (Q = 1.91E-05), beta-2-microglobulin binding (Q = 3.35E-05), signaling receptor binding (Q = 5.43E-05), integrin binding (Q = 5.43E-05), T cell receptor binding (Q = 5.43E-05), CX3C chemokine binding (Q = 3.67E-04), metal ion binding (Q = 3.67E-04), neuregulin binding (Q = 4.95E-04), protein-containing complex binding (Q = 6.58E-04), and TAP binding (Q = 9.87E-04); (2) transporter activity, voltage-gated calcium channel activity (Q = 1.91E-05). As shown in Q = 2.31E-06), cell adhesion (Q = 2.33E-05), heterotypic cell-cell adhesion (Q = 3.57E-04), endocardial cushion fusion (Q = 4.71E-04), integrin-mediated signaling pathway (Q = 2.31E-06), positive regulation of T cell mediated cytotoxicity (Q = 7.00E-05), positive regulation of cell migration (Q = 1.10E-04), and positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation (Q = 6.21E-04); (2) cellular process: mesodermal cell differentiation (Q = 4.31E-05), cell-cell adhesion in response to extracellular stimulus (Q = 1.15E-04), endodermal cell differentiation (Q = 3.76E-04), positive regulation of vascular smooth muscle cell proliferation (Q = 6.21E-04), and cellular response to amyloid-beta (Q = 7.42E-04); (3) developmental process: heart development (Q = 2.31E-06), inner ear development (Q = 2.44E-04), ventricular cardiac muscle tissue morphogenesis (Q = 4.41E-04), and atrial septum primum morphogenesis (Q = 6.21E-04); (4) immune system process: antigen processing and presentation of peptide antigen via MHC class I (Q = 2.33E-05), antigen processing and presentation of endogenous peptide antigen via MHC class Ib (Q = 2.33E-05), antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent (Q = 2.33E-05), and antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (Q = 6.21E-04); (5) localization: calcium ion transmembrane transport (Q = 8.76E-05) and cell migration (Q = 1.15E-04); (6) response to stimulus: response to drug (Q = 4.71E-04) and response to hypoxia (Q = 4.81E-04).Evidence from clinical trials indicates that excessive sodium intake is associated with cardiovascular disease , 39. To .65E-03) . The KEGQ = 1.77E-14), ARVC (Q = 9.55E-12), HCM (Q = 3.03E-11), fluid shear stress and atherosclerosis (Q = 1.25E-06), and viral myocarditis (Q = 2.08E-05) , RNA polymerase II activating transcription factor binding (Q = 1.20E-03), transcription factor binding (Q = 1.63E-03), histone methyltransferase binding (Q = 1.63E-03), metal ion binding , R-SMAD binding (Q = 4.48E-03), integrin binding , laminin binding (Q = 5.07E-03), disordered domain-specific binding (Q = 7.41E-03), peptide antigen binding , and protein binding (Q = 8.44E-03); (2) transporter activity: calcium- and calmodulin-responsive adenylate cyclase activity (Q = 6.81E-04), adenylate cyclase activity (Q = 1.63E-03), and phosphorus-oxygen lyase activity (Q = 4.26E-03). As shown in Q value 2.03E-04 vs. 2.33E-05), cell-matrix adhesion , and integrin-mediated signaling pathway ; (2) cellular process: cellular response to cadmium ion (Q = 4.43E-04) and cellular response to reactive oxygen species (Q = 5.75E-04); (3) immune system process: antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (Q = 5.79E-06), antigen processing and presentation of exogenous peptide antigen via MHC class II (Q = 5.24E-05), antigen processing and presentation of peptide antigen (Q = 4.47E-04), and antigen processing and presentation (Q = 6.03E-04); (4) response to stimulus: response to drug . Collectively, these results demonstrate that excessive sodium intake can easily induce cardiovascular disease.To further elucidate the effect of excessive sodium intake, we next compared the expression of cardiovascular disease-related transcripts between normal and high-salt-treated hearts in female mice. As shown in .08E-05) . KEGG an.08E-05) . GO analQ < 0.05) . As show < 0.05) , S5 and < 0.05) .F = 9.958; P = 0.002) as well as a significant main effect of HSD , but not sex \u00d7 HSD interaction . As shown in P < 0.05). Further studies have found that fibrotic changes caused by HSD in the heart of female mice were approximately twice that of male mice (1.75 vs. 2.74%) . CollectQ < 0.05). Similarly, the HSD had an adverse effect on the expression of 35 metabolism-related genes with significant differences in female mice, causing a serious disorder (Q < 0.05) (P < 0.001) were identified, in six categories: (1) amino acid metabolism: valine, leucine, and isoleucine degradation (Q = 9.10E-07) and glycine, serine, and threonine metabolism (Q = 6.04E-04); (2) carbohydrate metabolism: pyruvate metabolism (Q = 4.56E-06), glycolysis/gluconeogenesis (Q = 2.74E-05), propanoate metabolism (Q = 2.25E-04), fructose and mannose metabolism (Q = 3.04E-04), and butanoate metabolism (Q = 8.03E-04); (3) energy metabolism: biosynthesis of unsaturated fatty acids (Q = 1.56E-05); (4) global and overview maps: oxidative phosphorylation (Q = 1.45E-15), fatty acid metabolism (Q = 1.70E-09), and carbon metabolism (Q = 3.65E-06); (5) lipid metabolism: biosynthesis of amino acids (Q = 5.97E-04) and glycerolipid metabolism (Q = 8.03E-04); (6) metabolism of cofactors and vitamins: porphyrin and chlorophyll metabolism (Q = 7.80E-06) and ubiquinone and other terpenoid-quinone biosynthesis (Q = 1.03E-05) (P < 0.05) were identified, in seven categories: (1) amino acid metabolism: arginine and proline metabolism (Q = 2.31E-02) and lysine degradation (Q = 2.83E-02); (2) biosynthesis of other secondary metabolites: neomycin, kanamycin and gentamicin biosynthesis (Q = 3.27E-02); (3) carbohydrate metabolism: glycolysis/gluconeogenesis ; (4) energy metabolism: sulfur metabolism (Q = 4.88E-02); (5) lipid metabolism: ether lipid metabolism (Q = 2.14E-02), glycerolipid metabolism (Q = 2.83E-02), steroid hormone biosynthesis (Q = 4.18E-02), arachidonic acid metabolism (Q = 4.18E-02), and glycerophospholipid metabolism (Q = 4.31E-02); (6) metabolism of terpenoids and polyketides: insect hormone biosynthesis (Q = 2.60E-02); (7) nucleotide metabolism: purine metabolism (Q = 1.84E-02) . To furt.03E-05) . For fem.84E-02) . The STR.84E-02) , but not.84E-02) . AltogetP = 0.198), and macrophage infiltration was increased by HSD treatment in the hearts of male and female mice . The STRING database was used to visualize the PPANs of these transcripts to further study the function and relevance of these immune-related genes. As shown in Q < 0.001) . Collectvia the cytochrome C release pathway (Q < 0.05). As shown in Q = 5.43E-16) and activation of cysteine-type endopeptidase activity involved in the apoptotic process (Q = 2.60E-03) of biological process in male and female mice were identified (P = 0.032). The HSD significantly increased the expression of cleaved caspase-3 in the hearts of both male and female mice. Collectively, these results demonstrated that excessive sodium intake can induce cardiac apoptosis.Studies have shown that a prenatal HSD can induce apoptosis of cardiomyocytes in the heart of offspring mice pathway and can pathway . In thisentified . To furtThe meaningful finding of this study is that HSD can adversely affect the mouse heart by changing metabolism, immunity, fibrosis, and apoptosis and can induce mice to suffer from sex-specific cardiovascular disease. The conclusions of this study are mainly based on the following findings: (1) HSD has a sex-specific effect on the body mass of mice, especially on the mass of heart tissue; (2) the cardiac transcriptome is different in male and female mice; (3) the HSD-treated cardiac transcriptome showed sex-specific differences; (4) compared with the normal group, HSD produced a different number of DEGs and affects different KEGG pathways in male and female mice; (5) HSD affects the expression of genes related to fibrosis, metabolism, immunity, and apoptosis in heart tissue of male and female mice; (6) KEGG pathway enrichment analysis showed that HSD induced HCM in male mice, while HSD induced DCM in female mice. These data help us understand the negative effects of HSD on the heart in different sexes.db/db mice show higher levels of pro-inflammatory cytokines and more immune cell infiltration in the kidneys than female db/db mice after HSD treatment for 4 weeks can be found in the article/The animal study was reviewed and approved by Henan Province People's Hospital Institutional Animal Care and Use Committee.SH, XC, and HW: conceptualization, funding, resources, and supervision. SH and XC: methodology, investigation, analysis, visualization, and writing\u2014review and editing. All authors contributed to the article and approved the submitted version.Research support was provided by the National Natural Science Foundation of China (Grant Number 82101089 to SH), Natural Science Foundation of Henan Province (Grant Number 222300420361 to XC), the Key R&D and Promotion Special Program of Henan Province (Grant Numbers 212102311011 and 222102310120 to SH and 212102310477 to HW), the Henan Provincial Medical Science and Technology Research Joint Co-construction Project (Grant Numbers LHGJ20200064 to SH and SB201901087 to HW), the Basic Science Project for Youth of Henan Eye Institute/Henan Eye Hospital (Grant Number 20JCQN003 to SH), and the Doctoral Research and Development Foundation of Henan Provincial People's Hospital (Grant Numbers ZC20190146 to SH and ZC20200230 to XC).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Mycobacterium smegmatis mc2155 as a host. The genome of this temperate siphovirus is 75,632 bp long , and BLASTn alignment revealed 99.86% identity with the genome of L3 mycobacteriophage Samty.Subcluster L3 bacteriophage Finnry was isolated from soil collected in Charleston, South Carolina, using Mycobacterium smegmatis mc2155 using enrichment at 37\u00b0C followed by two purification/amplification cycles in 7H9 top agar, as described in the SEA-PHAGES Discovery Guide Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program studied ry Guide . Althougile tail .TCGATCAGCC) were identified using PAUSE (https://cpt.tamu.edu/computer-resources/pause).To extract genomic DNA from high-titer lysates, the Promega Wizard DNA cleanup system was used, and a DNA library was prepared with the NEBNext Ultra II DNA library prep kit. Pittsburgh Bacteriophage Institute sequenced Finnry on an Illumina MiSeq system (MiSeq reagent kit v3) , and 771https://phagesdb.org/DNAMaster). Programs utilized to identify putative genes included GLIMMER v3.02 (https://seaphages.org/forums/topic/5398). Default parameters were used for other software.Annotation was performed with the PECAAN workflowER v3.02 , PhameraER v3.02 , GeneMarER v3.02 , StarterER v3.02 , ARAGORNER v3.02 , and tRNER v3.02 . FunctioER v3.02 , HHpred ER v3.02 , and theER v3.02 (parametFinnry\u2019s genome contains 130 predicted protein-coding genes (51 with assigned putative functions), 9 tRNAs, and no transfer-messenger RNAs. Potential gene duplications include tandem duplication of the WhiB family transcription factor sequences gp79/gp80 (BLASTp indicated 37.66% identity and 79% query coverage) and displaced duplication of gp121/gp131 (BLASTp indicated 42.59% identity and 93% query coverage).\u221250) between Finnry and related actinobacteriophages, Phamerator was used \u201320. To c\u2013was used . Finnry\u2019was used , 2 phamsGCS scores and wholThe GenBank and SRA accession numbers for Finnry are presented in"} +{"text": "This article has been corrected: Due to errors in figure preparation, the AZ-treated (72 hr) images , is an accidental duplicate of the \u2018CTRL\u2019 image in row 3, panel 1 of 1470-1489. https://doi.org/10.18632/oncotarget.28011Original article: Oncotarget. 2021; 12:1470\u20131489."} +{"text": "C-X-C Motif Chemokine Receptor 4 (CXCR4) in CD4+ T cells in LBD. CSF protein levels of the CXCR4 ligand, C-X-C Motif Chemokine Ligand 12 (CXCL12) were associated with neuroaxonal damage in LBD. Furthermore, we observed clonal expansion and upregulated Interleukin 17A expression by CD4+ T cells stimulated with a phosphorylated \u03b1-synuclein epitope. Thus, CXCR4-CXCL12 signaling may represent a mechanistic target for inhibiting pathological interleukin-17-producing T cell trafficking in LBD.Recent studies indicate that the adaptive immune system plays a role in Lewy body dementia (LBD). However, the mechanism regulating T cell brain homing in LBD is unknown. Here, we observed T cells adjacent to Lewy bodies and dopaminergic neurons in post-mortem LBD brains. Single-cell RNA sequencing of cerebrospinal fluid (CSF) identified upregulated expression of The immune system is implicated in the neurodegenerative process of Lewy body dementia. PDD is defined by changes in memory and behavior and afflicts patients in late stage Parkinson\u2019s disease (PD) . The syme models \u201313 and ie models . Moreovee models , 5, 14. P = 8.6X10\u22125; P = 0.0031; P = 6.33X10\u221213) and DLB (P = 4.02X10\u221213) presented with lower cognitive scores than PD-NCI patients and patients with clinical DLB and PD . Montrea+ T cells in close proximity to neuronal processes labeled by the dopamine enzyme tyrosine hydroxylase (TH) in the substantia nigra of PDD and DLB brains + glutamatergic neurons in the hippocampal CA2 region , a kinase essential for cytokine signaling, and the T cell activation gene Cluster Of Differentiation 69 (CD69) (C-X-C Motif Chemokine Receptor 4 (CXCR4) was also highly upregulated in PD-DLB CD4+ T cells , 16 of C subtype . Highly 9 (CD69) . The che T cells . Moreove T cells . Quantifn PD-DLB . Thus, e+ T cells in PD-DLB prompted us to determine whether clonally expanded (i.e. antigen-specific) cells were distinct in PD-DLB. To assess clonal expansion, we performed single-cell T cell receptor sequencing (scTCRseq) on the same CSF cells as above , a marker of pro-inflammatory IL-17-producing (Th17) memory CD4+ T cells and PD-NCI (P = 7.67X10\u221210) subjects = 31.697, P = 5.18X10\u221212); P = 1.00X10\u22124) and PD-NCI (P = 8.30X10\u22123) subjects = 9.161, P = 0.0002); P = 0.071); s = 0.40; P = 0.023), and these correlations were lesser in healthy and PD-NCI subjects (ANCOVA (F (P = 0.031); We next sought to determine whether levels of CSF CXCL12 were associated with cognitive impairment in PD. We measured CXCL12 in a cohort of age- and sex-matched healthy (n=84) and PD (n=79) subjects . This re+ T cells of the peripheral immune system and CSF. We performed scRNAseq on peripheral blood mononuclear cells (PBMCs) of the same subjects we analyzed by CSF scRNAseq and focused our analysis on CD4+ T cells and Actin Beta (ACTB) , which ra (ACTB) . We also T cells .Interleukin 17A (IL17A) in cells stimulated with \u03b1-synuclein from each subject (IL17A-expressing cells co-expressed CD4 and some clonotypes also expressed the Th17-associated cytokine gene Interleukin 22 (IL22; +IL-17A+ T cells in the PDD substantia nigra, which were adjacent to TH+IL-17A+ neurons (P = 0.007; IL17A RNA expression in the brain, yet the gene encoding the IL17A receptor, IL17RA, was highly expressed in the midbrain (Notably, we also detected higher expression of ynuclein . IL17A e17 cells . To detepatients . We then subject . IL17A-e22 IL22; . We conf neurons . We alsomidbrain , suggestmidbrain . Finallymidbrain .IL17A, a pro-inflammatory cytokine involved in autoimmune diseases (In conclusion, these results implicate Th17 cell involvement in the degeneration of neurons in LBD. Notably, CXCR4 regulates cell migration , and antdiseases . In animdiseases , 32. Mordiseases . Thus, odiseases .Supplementary MaterialData S3Data S2Data S1Data S4"} +{"text": "A prior study demonstrated suboptimal antibiotic prescribing in the emergency department (ED) at 77.4% for uncomplicated lower respiratory tract infections (LRTI), urinary tract infections (UTI), and acute bacterial skin and skin structure infections (ABSSSI). This study measured the effect of indication-based antibiotic order sentences (AOS) on prescribing.IRB-approved quasi-experiment of adults prescribed antibiotics in ED for uncomplicated LRTI, UTI, or ABSSSI from January - June 2019 (pre-group) or September - December 2021 (post-group). Exclusion: hospital admission, immunocompromised, active cancer, or prophylactic antibiotics. AOS are lean process, electronic discharge prescriptions retrievable by name or indication; AOS implementation occurred July 2021. Optimal prescribing was defined as the correct antibiotic selection, dose, and duration per local and national guidelines. Seven-day endpoints: antibiotic escalation, ED or hospital readmission, any outpatient contact, and reported adverse drug event (ADE). Descriptive and bivariate statistics performed. Variables considered for multivariable logistic regression had p< 0.2 or plausible association with optimal prescribing.294 patients included: 147-pre and 147-post. Patient characteristics are in Table\u00a01. Overall optimal prescribing improved from 12 (8.2%) to 34 (23.1%) (p< 0.001). Breakdown of optimal prescribing in pre- and post-groups: selection 90 (61.2%) vs 117 (79.6%) (p< 0.001), dose 99 (67.3%) vs 115 (78.2%) (p=0.036), duration 38 (25.9%) vs 50 (34%) (p=0.126). After adjustment, AOS were independently associated with optimal prescribing (Table\u00a02). Secondary endpoints: antibiotic escalation 10 (6.8%) vs 7 (4.8%) (p=0.662), hospital or ED readmission 12 (8.2%) vs 10 (6.8%) (p=0.658), outpatient contact 31 (21.1%) vs 28 (19%) (p=0.662), and ADE 2 (1.4%) vs 4 (2.7%) (p=0.684). Post-hoc analysis showed suboptimal uptake of AOS by ED prescribers.AOS is an efficient and promising antimicrobial stewardship strategy; provider re-education is needed to increase AOS uptake.All Authors: No reported disclosures."} +{"text": "Nirmatrelvir coadministered with ritonavir (nirmatrelvir/r) is a COVID-19 treatment. This study evaluated nirmatrelvir/r in nonhospitalized, symptomatic adults with COVID-19 at high risk of progressing to severe disease. We report secondary efficacy endpoints associated with COVID-19\u2500related medical visits, including hospitalization details and oxygen support, as of the primary completion data cutoff .In this phase 2/3 double-blind, interventional study, adults with confirmed SARS-CoV-2 and symptom onset \u2264 5 days (d) were randomized 1:1 to receive nirmatrelvir/r 300 mg/100 mg or placebo (PBO) orally every 12 hours for 5 d. COVID-19\u2500related medical visits were collected through Day 28. Oxygen support for COVID-19 and details of COVID-19\u2500related hospitalization, including duration, intensive care unit (ICU) status, and mechanical ventilation, were assessed.Table\u00a01). In addition to fewer hospitalizations being reported with nirmatrelvir/r (n=8 [0.8%]) vs PBO (n=65 [6.2%]), pts receiving nirmatrelvir/r had fewer hospitalized d (Table\u00a02), with mean durations of 9.6 d with nirmatrelvir/r and 11.2 d with PBO in hospitalized pts. No pts in the nirmatrelvir/r group and 9 pts (0.9%) in PBO group were admitted to the ICU. No pts in the nirmatrelvir/r group received mechanical ventilation vs 3 pts in the PBO group. Fewer other COVID-19\u2500related nonhospital medical visits were reported with nirmatrelvir/r vs PBO (Table\u00a03). In the full analysis set, fewer pts required oxygen therapy for COVID-19 with nirmatrelvir/r (n=9/1120 [0.8%]) vs PBO (n=54/1126 [4.8%]).Of the 2246 patients (pts) enrolled globally from Jul to Dec2021, 2085 started treatment and met criteria for the modified intent-to-treat population . Fewer overall COVID-19-related medical visits were reported with nirmatrelvir/r vs PBO vs pts receiving PBO. Clinical Trial: NCT04960202.Jennifer Hammond, PhD, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Heidi Leister-Tebbe, BSN, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Annie Gardner, MPH, MSPT, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Paula Abreu, PhD, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Weihang Bao, PhD, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Wayne Wisemandle, MA, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Wajeeha Ansari, MPH, Pfizer Inc.: Stocks/Bonds Rienk Pypstra, MD, MBA, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds James M Rusnak, MD, PhD, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds."} +{"text": "Correction: BMC Musculoskelet Disord 24, 49 (2023)10.1186/s12891-023-06160-zhttp://ovidsp.ovid.com/ovidweb.cgi?T=JS&PAGE=reference&D=emed8&NEWS=N&AN=2009254927)\u201d instead of Chan et al. 2013.Following publication of the original article , the autFurthermore, the word \"Specific\" in Secondary outcomes is without the \"S\" in Table 1.The original article has been"} +{"text": "Urinary tract infections (UTI) are the second most prevalent microbial infection, impacting 150 million people globally every year. Traditionally, urine culture is considered the gold standard for UTI pathogen detection. However, molecular techniques, such as real time multiplex PCR tests targeting multiple pathogens, are becoming the alternative diagnostic tools for rapid detection of pathogens with the potential to provide quick diagnosis and enable targeted treatment. Due to the serious economic and healthcare utilization burden UTIs pose, early pathogen detection with a rapid turn-around-time to results has the potential to be instrumental for improving patient care and outcomes.A total of 300 deidentified patient samples that were previously tested via urine culture were subjected to real time PCR molecular testing employing the nanofluidic Open Array \u00ae platform . Statistical analyses were performed using R version 3.6.0.Among 300 urine specimens studied, culture detected pathogens in 183 patient samples (61%), and 117 samples were deemed negative. Culture and PCR results demonstrated an overall agreement of 75.3% (n=226) with 59% positive (n=177) and 16.3% negative (n=49). Results for 24.7% samples (n=74) were discordant. A total of 2% (n=6) were culture positive and PCR negative, and 22.7% (n=68) were culture negative and PCR positive. Agreement between PCR and culture positive results was 0.97, 95%CI (177/183). Among the PCR positive samples (n=245), 32.7% were poly-microbial (n=80) and 67.3% were mono-microbial (n=165). In comparison, among culture positive samples (n=183), 33.3% (n=61) were polymicrobial and 65.6% (n=120) monomicrobial.Our study demonstrates that multiplex real time PCR-based detection of UTI bacterial pathogens has positive agreement with the traditional urine culture method. PCR based testing has the potential to deliver quick pathogen identification to enable targeted treatment options and medication adjustments. Further studies will correlate semi-quantitative cfu/mL culture values with semi-quantitative copies/mL PCR values to further refine result reporting and test performance.Pallavi Upadhyay, PhD, HealthTrackRx: Stocks/Bonds Fahida Surar, B.S., HealthTrackRx: Salaried Employee Geun Kim, M.S., HealthTrackRx: Salaried Employee Jay Reddy, PhD, HealthTrackRx: Stocks/Bonds Barbara D. Alexander, MD, Astellas: Advisor/Consultant|HealthtrackRx: Advisor/Consultant|HealthtrackRx: Grant/Research Support|Scynexis: Grant/Research Support|UpToDate: Advisor/Consultant Kimberly Hanson, MD, MHS, FIDSA, HealthTrackRx: Advisor/Consultant|HealthTrackRx: Clinical Advisory Board Member Vijay Singh, PhD, HealthTrackRx: Stocks/Bonds."} +{"text": "Enterobacterales order were detected in fecal samples among 580 patients during the period of 2017\u20132019. ESBL/carbapenemase/plasmidic AmpC producer rates were 28.8%, 2.4%, and 1.2%, respectively. A wide variety of ESBLs: CTX-M-15 (41%), CTX-M-3 (24%), CTX-M-27 (11%), and CTX-M-14 (4%) was found. The carbapenemases identified in this study were New Delhi metalo-\u03b2-lactamase (NDM)-1 (5.4%) and Klebsiella carbapenemase (KPC)-2 (1.5%). Most NDM-1 isolates also produced CTX-M-15/-3 and CMY-4 \u03b2-lactamases. They belonged to ST11 Klebsiella pneumoniae clone. The epidemiology typing revealed three main high-risk K. pneumoniae clones (26%)\u2014ST11, ST258, and ST15 and five main Escherichia coli clones\u2014ST131 (41.7%), ST38, ST95, ST405, and ST69. Sixty-one percent of ST131 isolates were from the highly virulent epidemic clone O25b:H4-ST131. Phylotyping revealed that 69% of E. coli isolates belonged to the virulent B2 and D groups. Almost all (15/16) Enterobacter isolates were identified as E. hormaechei and the most common ST type was ST90. Among all of the isolates, a high ESBL/carbapenemases/plasmid AmpC (32.4%) prevalence was observed. A significant proportion of the isolates (37%) were members of high-risk clones including two pan-drug-resistant K. pneumoniae ST11 NDM-1 producing isolates. Due to extensive antibiotic usage during COVID-19, the situation may worsen, so routine screenings and strict infection control measures should be widely implemented.The gastrointestinal tract is an important reservoir of high-risk Enterobacteria clones and a driver of antimicrobial resistance in hospitals. In this study, patients from six hospitals in four major Bulgarian towns were included in this study. Overall, 205 cefotaxime-resistant isolates (35.3%) of Klebsiella pneumoniae and hospital-acquired infections [Enterobacterales species [K. pneumoniae, Escherichia coli, and Enterobacter cloacae complex have been globally reported [\u03b2-lactams are commonly used antimicrobials due to their safe profile and broad-spectrum activity ,2,3,4,5.fections . In the species ,4,7. The species . These b species ,4,5,6. Ireported ,4,6. In reported . In addireported .The gastrointestinal tract can be an important reservoir of ESBL-/carbapenemase-producing enterobacteria in hospital settings leading Fecal carriage of ESBL/carbapenemase producers has been widely reported all over the world ,10. DiffThe aim of this study was to evaluate the prevalence of \u03b2-lactamase production and clonal relatedness of fecal ESBL- and carbapenemase-producing enterobacteria, collected from hospitalized patients .TMKPC . Bacterial isolates were identified using routine biochemical identification and were confirmed by VITEK or Phoenix . Hsp60 sequencing [Enterobacter spp. and Klebsiella oxytoca isolates.The study was conducted in six hospitals\u2014University Multiprofile Hospital for active treatment (UMHAT), Varna; UMHAT, Plovdiv; UMHAT, Pleven, and three hospitals in Sofia during the period of December 2017\u2013June 2019. The fecal samples were obtained from patients during the routine diagnostic process and were additionally inoculated on selective MacConkey agar with 1 mg/L cefotaxime and on Chromagarquencing was usedhttp://www.eucast.org/clinical_breakpoints/), last accessed on 10 August 2022. The following antibiotics were tested: amoxicillin/clavulanic acid 30 \u00b5g (AMC), ceftazidime 10 \u00b5g (CAZ), cefotaxime 5 \u00b5g (CTX), cefepime 30 \u00b5g (FEP), cefoxitin 30 \u00b5g (FOX), imipenem 10 \u00b5g (IMP), meropenem 10 \u00b5g (MEM), piperacillin/tazobactam 36 \u00b5g (PIP/TAZ), chloramphenicol 30 \u00b5g (CHL), gentamicin 10 \u00b5g (GEN), amikacin 30 \u00b5g (AMK), tobramycin 10 \u00b5g (TOB), trimethoprim/sulfamethoxazole 25 \u00b5g (SXT), ciprofloxacin 5 \u00b5g (CIP), levofloxacin 5 \u00b5g (LVX), fosfomycin 200 \u00b5g (FOS)(for E. coli isolates), and tigecycline 15 \u00b5g (TIG for E. coli isolates). Susceptibility to tigecycline in Klebsiella isolates was determined by the broth microdilution method . Susceptibility to colistin was initially tested with modified SuperPolymyxin medium [K. pneumoniae and E. coli that grew on this screening medium were tested with the broth microdilution method .Antimicrobial susceptibility testing was performed using the disk diffusion method on M\u00fcller-Hinton II agar and the microdilution broth method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines (Version 10). The susceptibility testing was carried out according to the clinical breakpoints of the EUCAST (Version 10) , a phenotypic confirmation of carbapenemase production was performed by the KPC, MBL, and OXA-48 Kit .Presumptive ESBL production was detected with the double-disk synergy method . PotentiE. coli K12:W3110 RifR lac/-/(1.2 \u00d7 107 CFU/mL). After overnight incubation at 37 \u00b0C, growth of the indicator strain on the gel localized the \u03b2-lactamase band by which the \u03b2-lactam had been inactivated.Production and number of \u03b2-lactamases were detected and analyzed by analytical isoelectric focusing (IEF) according to the method of Mathew with modblaVIM, blaIMP, blaKPC, blaNDM, blaOXA-48), AmpC , and ESBLs as previously described [blaSHV, blaCTX-M-1-group, blaCTX-M-9-group, blaCMY,blaDHA,blaKPC, and blaNDM. [All isolates were screened for the presence of carbapenemase-encoding genes , last accessed on 30 July 2022. A clone was defined as isolates showing 80% similarity.Clonal relatedness was investigated by ERIC PCR and Multilocus Sequence Typing (MLST). For Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR, ERIC-1 and -2a primers were used as described previously . GeneticK. pneumoniae MLST typing and Achtman scheme was applied for E. coli. For E. coli isolates, the assignment to allelic numbers and sequence types (STs) was performed according to the MLST database (https://bigsdb.web.pasteur.fr/ecoli/ecoli.html), last accessed on 30 July 2022. Detection of specific O25b-ST131 clone was performed with allele-specific PCR for pabB gene as previously described [Pasteur scheme was used for K. pneumoniae isolates, protocols and assignment to allelic numbers and sequence-types (STs) were carried out as described in the MLST database , last accessed on 30 July 2022. A clonal complex was defined as a group of two or more independent isolates that shared six identical alleles.For E. cloacae complex isolates, primers, protocols, and assignment to allelic numbers and sequence-types (STs) were carried out as described in the MLST database (https://pubmlst.org/organisms/enterobacter-cloacae), last accessed on 30 July 2022.For E. coli isolates as previously described [Phylotyping was applied for escribed .E. coli (n = 103); K. pneumoniae (n = 65); Klebsiella oxytoca (n = 8); E. cloacae complex (n = 16); Morganella morganii (n = 3); and Citrobacter freundii complex (n = 10).A total of 205 enterobacterial isolates resistant to cefotaxime were isolated from fecal samples, collected from 580 patients (35.3%) as follows: 61 cefotaxime-resistant isolates from 158 studied patients (38.6%) from University Hospital (UH)-Varna; 25 cefotaxime-resistant isolates from 71 patients (35.2%) from UH-Pleven; 58 cefotaxime-resistant isolates from 102 patients (56.9%) from UH-Plovdiv, and 61 cefotaxime-resistant isolates from 249 patients (24.5%) from three hospitals in Sofia. The isolates were identified as Hsp60 sequencing identified 15 E. cloacae complex isolates as Enterobacter hormaechei, subdividing them into three subspecies\u2014E. hormaechei spp. hoffmannii (n = 3); E. hormaechei spp. steigerwaltii (n = 10); and E. hormaechei spp. xiangfangensis (n = 2). One isolate was identified as Enterobacter kobei. Two isolates, initially identified as K. oxytoca, were reidentified by hsp60 sequencing as Klebsiella michiganensis.Klebsiella isolates to tigecycline was 93%. For E. coli, 17% and 3% resistance to tigecycline and fosfomycin, respectively, were found. Only five isolates of Klebsiella spp. (2.4%) were colistin nonsusceptible. The results are shown in K. pneumoniae isolates were determined as pandrug-resistant according to the criteria of Magiorakos et al. [The nonsusceptibility (resistance or intermediate susceptibility) rates in the collection of isolates were as follows: amoxicillin/clavulanic acid 93%, ceftazidime 86%, cefotaxime 100%, cefoxitin 35%, cefepime 95%, piperacillin/tazobactam 72%, imipenem 7%, meropenem 7%, tobramycin 68%, gentamicin 56%, amikacin 50%, trimethoprim/sulfamethoxazole 52%, ciprofloxacin 68%, levofloxacin 63%, and chloramphenicol 22%. The nonsusceptibility rates in the s et al. .E. cloacae complex and three C. freundii complex isolates were determined as possible inducible AmpC hyperproducers, demonstrating antagonism between amoxicillin/clavulanic acid and cefotaxime or ceftazidime.Disk diffusion synergy method (DDST) confirmed 171 isolates as ESBL producers. Four K. pneumoniae isolates, suggesting class B carbapenemase production (zone around the disk with EDTA is \u22655 mm). Three isolates (two K. pneumoniae and one E. coli) demonstrated increased zones of inhibition by the disk containing meropenem and phenylboronic acid, suggesting class A (KPC) carbapenemase activity.The phenotypic test with meropenem and meropenem/EDTA disks was positive in 11 carbapenem-resistant blaSHV-1 gene was detected (which suggests possible SHV-1 hyperproduction). Three cefotaxime-resistant isolates, susceptible to carbapenems and with positive DDST did not produce a positive PCR reaction with any of the used ESBL group-specific primers.PCR and sequencing revealed the presence of genes, encoding ESBL in 167 (28.8%) isolates, obtained from 580 patients. In one isolate, only p < 0.0001). The ESBL producers among the isolates of E. coli and K. pneumoniae were 56.2% (94/167) and 34.1% (57/167), respectively.The prevalence of ESBL producers in Sofia hospitals was significantly lower than in the other locations, 35.6% (118 ESBL producers/331 patients) (blaCTX-M-15 in 41% (84/205) of the isolates, blaCTX-M-3 in 24% (49/205), blaCTX-M-27 in 11% (22/205), and 8 isolates (3.9%) displayed blaCTX-M-14. Only one isolate was positive for blaCTX-M-9 and one for blaSHV-12 , except one isolate that showed blaCTX-M-14, were produced by E. coli strains. In contrast, blaCTX-M-3 was the prevailing ESBL among K. pneumoniae and K. michiganensis isolates. One K. pneumoniae isolate showed mixed sequences , GGT is a codon for glycine (specific for blaCTX-M-15)). All K. pneumoniae isolates were blaSHV positive. Of them, 29 representative isolates were sequenced, and blaSHV-1 (n = 21) and blaSHV-11 (n = 8) were identified. In 71 isolates, blaTEM was found and, later, 10 of them were confirmed by sequencing as blaTEM-1.Among the 205 investigated cefotaxime-resistant isolates, we observed solely laSHV-12 . blaCTX-K. pneumoniae, were carbapenemase producers. Thirteen of them coproduced ESBL or/and plasmid AmpC (K. pneumoniae isolates had blaNDM-1 together with blaCMY-4 and blaCTX-M-3/-15. Two K. pneumoniae and one E. coli isolates had blaKPC-2.Fourteen isolates (2.4%) from 580 patients, mainly mid AmpC . Ten K. E. coli isolates showed two types of plasmid AmpC, blaDHA-1, n = 5 or blaCMY-2, n = 2. Thirteen isolates (2.2%) were AmpC hyperproducers (inducible or constitutive) (Seven itutive) .Thus, 188 isolates (32.4%) were found to carry ESBL (28.8%) or carbapenemases (2.4%) or plasmid AmpC genes (1.2%).Klebsiella spp. isolates, 24 representative isolates were subjected to IEF exhibited two bands\u2014pI8.4 and pI8.8 (The isoelectric focusing was carried out in representative isolates according to the species and detected \u03b2-lactamase genes. Of 73 solates) . We confnd pI8.8 and did not show cefotaxime hydrolyzing bands corresponding to TEM and SHV ESBL \u03b2-lactamases. Three isolates with unidentified enzyme type gave bands with pI8.0 (two isolates) and pI9.2 (one isolate). They were without CTX hydrolytic activity.E. hormaechi, C. freundii complex and M. morganii isolates, 5 isolates were tested, and a single cefotaxime hydrolyzing band was detected, pIs corresponded with sequenced enzymes , ST11 , and ST37 being the dominant types. In addition, ST1198, ST280, ST34, ST15, ST258, ST17, ST253, and ST449 were also found. Six isolates demonstrated unique profiles . K. oxytoca and K. michiganensis isolates had unique ERIC profiles.Epidemiological typing revealed 18 ERIC clusters among 65profiles . The isohospital . ST11 isE. coli isolates, 40 ERIC types were identified , ST38 , ST155 , ST405 , ST1196, and ST88 .Among entified . A totalE. coli (n = 43) was detected in five centers and was associated with the production of CTX-M-27 , CTX-M-15 , CTX-M-3 , CTX-M-14 , and KPC-2 carbapenemase, found in a single isolate ; D, n = 20 ; A, n = 12; and B1, n = 20. The association between MLST types and phylotypes is shown in The following E. cloacae isolates (n = 16) demonstrated 12 ERIC clusters and 6 ST types. The most common ST was ST90, associated with CTX-M-15 production (oduction .n = 580) was similar to that in Portuguese hospitals (24%) [E. coli and K. pneumoniae isolates in Bulgaria in 2019, which was the highest in Europe and showed a stable trend during the last 5 years , last accessed on 10 August 2022. We also found increased nonsusceptibility rates in the tested ESBL fecal isolates to aminoglycosides (50%-68%) and quinolones (63\u201368%) in comparison to the rates found in 2015 (21%-57% for aminoglycosides and 15\u201327% for quinolones) [This study reveals a moderate rate of fecal colonization with ESBL producers 28.8%) among Bulgarian patients during the period 2017\u20132019. The rate of third-generation cephalosporin-resistant isolates (mostly due to production of ESBL/carbapenemase/plasmid AmpC) was high (35.3%), but lower than the rate observed in a pilot study on hospital fecal carriage in Varna city, Bulgaria in 2015 (42.5%) . A possils (24%) and highls (24%) . The obs.8% amongnolones) . A similnolones) .E. coli (56.2% versus 69%) and an increased proportion of ESBL K. pneumoniae isolates (34.1% versus 20.4%) were found [E. coli have been reported in many studies [In comparison with our previous study in 2015, a decreased rate of ESBL-producing re found . Similarre found . The pre studies ,26,27,28E. coli, as well as in all other species except Klebsiella spp. CTX-M-15-producing isolates have been reported worldwide [Klebsiella isolates. Similar to CTX-M-15, CTX-M-3 was also widely distributed among enteric strains [E. coli isolates. CTX-M-9 and CTX-M-14 intestinal producers have been reported in Portugal, Spain, China, and Bulgaria [E. coli isolates. In Bulgaria, DHA-1 enzyme was identified for the first time in 2019 in an E. cloacae complex isolate obtained from a blood sample [The main \u03b2-lactamase type in our study was CTX-M-15 41%). It was the predominant ESBL in 1%. It waorldwide ,8,9. CTX strains ,26,27,28Bulgaria ,26. CTX-d sample .K. pneumoniae isolates and in a single E. coli isolate. All carbapenem-producing isolates were obtained from hospitalized patients in Sofia. Interestingly, the frequency of ESBL producers (19.7%) was not high among these patients. The coproduction of NDM-1, CTX-M-15/-3, and CMY-4 enzymes in nine K. pneumoniae isolates is a possible explanation for the high resistance rates, identified in the NDM-1 producing isolates, two of them being pandrug-resistant.An important finding in the current study is the detection of carbapenemase-producing isolates. Although the detection rate was low (2.4%), it is an indicator that the enteric tract may act as a reservoir for these problematic bacteria. The carbapenem resistance in the present collection of fecal isolates was associated with NDM-1 and KPC-2, detected in The rates of carbapenemase producers in Europe have steadily increased during the last years in both clinical and intestinal isolates ,33,34,35n = 17, 26%) among K. pneumoniae fecal isolates. Taking the second place, ST11 was represented in 17% of K. pneumoniae isolates, all obtained from patients in Sofia hospitals. Most NDM-1 carbapenemase-producers belonged to this clone, including two panresistant and the colistin-resistant isolates. This result is in concordance with our previous study from 2019 that detected a high level of ST11 blaNDM-1/blaCTX-M-15 or-3/blaCMY-4 positive isolates in the same hospitals [blaNDM-1/blaCTX-M-15/3/blaCMY-4 positive isolates have also been detected in the Czech Republic [Another important finding in the present study is the identification of the high-risk clones ST11, ST258, and ST15 , is another high-risk clone. It is also distributed worldwide and associated with KPC-2 production [ST258 oduction ,30,33,41oduction . ST11 anoduction ,40,42,43K. pneumoniae clone which has commonly been associated with the production of ESBLs, mainly CTX-M-15 [ST15 is another high-risk CTX-M-15 ,7,44, buCTX-M-15 . In the CTX-M-15 .K. pneumoniae clones found in this study were ST37 and ST17. These clones showed a sustained persistence in Bulgaria. These ST have been already identified in clinical and fecal isolates, associated with CTX-M-15 and KPC-2 production [Other intestinal multidrug-resistant oduction ,45. ST37oduction .In the present study, ST353 was presented by a high number of isolates (19%), mainly obtained from patients hospitalized in Plovdiv University Hospital(A). ST353 isolates were associated mainly with CTX-M-3 production. This ST type has been rarely reported. In studies from China and Colombia, authors reported ST353 isolates, producing KPC and OXA-48 ,47. ST11E. coli isolates with ST131 being the predominant, found in 41.7%. The second most common ST was ST38 (10%). ST405, ST95, and ST69 were presented by single isolates only. The isolates from these high-risk clones represented 57% (n = 59) of all the studied E. coli isolates. All of them belonged to the B2 or D phylogroups. This is an important finding as these phylogroups are associated with a prolonged fecal carriage [Five high-risk clones were observed among carriage . This win = 43) were representatives of phylogroup B2 and 60% (n = 26) belonged to the O25b:H4-ST131 clone. Our study showed that the O25b:H4-ST131 clone was the major clone among fecal E. coli isolates, harboring different ESBL genes, mainly blaCTX-M-15, but also blaCTX-M-3 and blaCTX-M-14, which is in concordance with other reports [E. coli isolates were detected in all centers except the Sofia hospital 1 (D), where NDM-1-producing ST11 K. pneumoniae was observed. In addition, the frequency of ST131 isolates in the present study was higher (42%) than the rate (35%) detected in 2015 [Almost all ST131 isolates and the plasmid AmpC enzyme DHA-1. This type has also been reported as a high-risk clone, causing both nosocomial and community-acquired infections, mainly urinary tract infections [In our study, fections . The detfections .E. coli. Recently, it has been found that representatives of ST69 clone carry an intact locus of enterocytes effacement (LEE), coding second bacterial type III secretion systems involved in the pathogenesis of Gram-negative infections [E. coli were identified as ST405 (D phylogroup). This clone was previously detected in Bulgaria as a carrier of NDM-1 carbapenemases [E. coli ST405 is an emerging urosepsis pathogen, reported to carry blaCTX-M, blaNDM, and a number of virulent genes comparable with O25b:H4-ST131 [ST69 is an interesting lineage from the D phylogroup, identified in two isolates of fections . In our enemases . E. coliH4-ST131 .E. coli isolates belonging to B1 and A phylogroups, which have been reported as commensal gut bacteria [In addition to the isolates that represent highly virulent clones, we also detected bacteria ; the obsEnterobacter isolates, ST90 producing CTX-M-15 was detected as the dominant clone. Although no high-risk clones have been defined in Enterobacter spp. so far, ST90 isolates, producing different carbapenemases, were detected in many countries: VIM-1 in Greece, IMP-4 in Canada and UK, and NDM-1 in Romania [E. cloacae complex can be a candidate for an international high-risk clone.In the group of Romania . Polish Romania . So, we The fecal colonization with ESBL and/or carbapenemase producers from high-risk international clones, associated with significant virulence and invasive potential and multidrug or pandrug resistance, can be an important reservoir not only for difficult to treat nosocomial infections, but also for wide dissemination in the community. Given that this study was performed before the COVID-19 pandemic, we can assume that the increased antibiotic usage during the last three years has further worsened the situation.E. coli and 17 K. pneumoniae) were members of high risk clones (37%).Twenty six percent of the K. pneumoniae isolates were representatives of high-risk clones such as ST11, ST258 and ST15 K. pneumoniae isolates. A very worrying finding was the detection of two ST11 pandrug resistant isolates, coproducing NDM-1, CMY-4, and CTX-M-15. Among E. coli, five high risk clones (57% of E. coli isolates) were found . The investigated isolates were producers of a wide range of \u03b2-lactamases\u2014CTX-M-15, CTX-M-3, CTX-M-27 (reported for the first time in Bulgaria), CTX-M-14, NDM-1, KPC-2, and plasmid AmpC DHA-1 and CMY-2 enzymes. The detected high frequency of ESBL/carbapenemases-producing enteric bacteria before COVID-19 and the dramatically increased selective pressure during the pandemic period will negatively impact the antimicrobial resistance in clinically significant bacterial species. Further studies should closely monitor the future trends. The routine screening for colonization with MDR bacteria at hospital admission and during the hospital stay, especially in high-risk departments, as well as strict infection control measures should be widely implemented in Bulgarian hospitals to limit the further dissemination of problematic multidrug-resistant bacteria.In conclusion, a high rate of fecal colonization (32.3%) with ESBL/carbapenemase/plasmid AmpC producers among patients in Bulgarian hospitals was found. A high rate of ESBL producers (28.8%) was detected with a relatively low rate of carbapenemase producers (2.4%). Seventy six isolates (59"} +{"text": "Bacteria and archaea are central to the production, consumption, and remineralization of dissolved and particulate organic matter and contribute critically to carbon delivery, nutrient availability, and energy transformations in the deep ocean. To explore environmentally relevant genomic traits of sinking-particle-associated versus free-living microbes, we compared habitat-specific metagenome-assembled genomes recovered throughout the water column in the North Pacific Subtropical Gyre. The genomic traits of sinking-particle-associated versus free-living prokaryotes were compositionally, functionally, and phylogenetically distinct. Substrate-specific transporters and extracellular peptidases and carbohydrate-active enzymes were more enriched and diverse in particle-associated microbes at all depths than in free-living counterparts. These data indicate specific roles for particle-attached microbes in particle substrate hydrolysis, uptake, and remineralization. Shallow-water particle-associated microbes had elevated genomic GC content and proteome nitrogen content and reduced proteome carbon content in comparison to abyssal particle-associated microbes. An inverse trend was observed for their sympatric free-living counterparts. These different properties of attached microbes are postulated to arise in part due to elevated organic and inorganic nitrogen availability inside sinking particles. Particle-attached microbes also were enriched in genes for environmental sensing via two-component regulatory systems, and cell-cell interactions via extracellular secretion systems, reflecting their surface-adapted lifestyles. Finally, particle-attached bacteria had greater predicted maximal growth efficiencies than free-living bacterioplankton at all depths. All of these particle-associated specific genomic and proteomic features appear to be driven by microhabitat-specific elevated nutrient and energy availability as well as surface-associated competitive and synergistic ecological interactions. Although some of these characteristics have been previously postulated or observed individually, we report them together here in aggregate via direct comparisons of cooccurring free-living and sinking-particle-attached microbial genomes from the open ocean. Thes10\u201316\u2013in situ by divers and FL microbes found throughout the water column in the oligotrophic Pacific Ocean, we leveraged time series metagenomic samples recovered at Station ALOHA in the North Pacific Subtropical Gyre, generating a total of 407 mid- to high-quality MAGs from both sample types. FL microbes (captured on 0.2-\u03bcm-pore-size filters) were collected from surface waters to a depth of 4,000 m at Station ALOHA, and metagenomes were generated, assembled, and analyzed \u201345. In p\u2013To expand the genomic data from sympatric SPA and FL prokaryote communities throughout the water column, metagenomic data sets were prepared from time series samples collected from the surface to 4,000 m during Station ALOHA time series efforts and expeditions \u201347. Thes\u201343\u201310.1128/mbio.01569-22.6TABLE\u00a0S1Table\u00a0S1, XLSX file, 0.03 MB.Sample descriptions and metadata of metagenomes. Download Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the The FL and PA MAGs were classified into five sample types . FL MAGs10.1128/mbio.01569-22.7TABLE\u00a0S2Table\u00a0S2, XLSX file, 0.04 MB.Checkm statistics, taxonomic classification, and sample designation of the MAGs. Download Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Proteobacteria, including Alphaproteobacteria, Gammaproteobacteria, Planctomycetota, Chloroflexota, Bacteroidota, and Verrucomicrobiota. Ten other bacterial phyla were each represented by only a single MAG. This included the poorly characterized phylum UBP17, formerly known as Cloacimonetes (WWE1), of which only a few MAGs have been included in the genome taxonomy database to date FL and PA MAGs shared some taxa at higher classification levels, only nine genera were found in both the FL and PA data sets. These included MAGs closely related to Alcanivorax, Prochlorococcus_A, Thalassarchaeum, Henriciella, Idiomarina, Nitrosopumilus, Nitrosopelagicus, Roseibacillus_B, and Bythopirellula identifiers (IDs) and clustered into 49,146 orthologous protein families. Nonmetric multidimensional scaling (NMDS) profiles based on the presence of KO IDs and orth10.1128/mbio.01569-22.1FIG\u00a0S1FIG\u00a0S1, PDF file, 1.1 MB.Nonmetric multidimensional scaling (NMDS) plots of the recovered MAGs based on gene annotations. (A) NMDS plot generated based on the presence/absence of KEGG Orthology (KO) annotations. (B) NMDS plot generated based on the presence/absence of orthologous protein families. Shapes indicate the sample type designation of the MAG. Color indicates the taxonomic classification of the MAG. PA and FL designations are as described in the legend to Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the P value\u2009<\u20090.05) , and S4.\u2009<\u20090.05) . For FL 10.1128/mbio.01569-22.2FIG\u00a0S2q value of <0.05 for Fisher\u2019s exact test. Download FIG\u00a0S2, PDF file, 0.5 MB.Venn diagram of significantly enriched genes. (A and B) Venn diagrams of significantly enriched genes based on KEGG Orthology (KO) annotations and orthologous protein family. Significantly enriched KOs and orthologous gene families were determined using Scoary with a Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 10.1128/mbio.01569-22.8TABLE\u00a0S3Table\u00a0S3, XLSX file, 0.4 MB.Scoary enrichment of KO IDs (A) and orthologous protein families (B) based on sample types. Download Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 10.1128/mbio.01569-22.9TABLE\u00a0S4Table\u00a0S4, XLSX file, 0.1 MB.Count tables of transporter genes (A), peptidase genes (B), CAZyme genes (C), and extracellular secretion system genes (D) included in MAGs. Download Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the The most enriched KO IDs identified by Scoary were significantly associated with the PA_Shallow MAGs A and B. Previous studies have shown that transporters of carbohydrates and energy sources are ubiquitous in heterotrophic prokaryotic communities throughout the open water column, from the surface to abyssal depths, and are crucial for organic matter transformation . To inve10.1128/mbio.01569-22.3FIG\u00a0S3FIG\u00a0S3, PDF file, 0.1 MB.Counts of MAGs encoding substrate-specific transporters. Genes encoding putative transporters were grouped based on their substrate specificity. Download Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 10.1128/mbio.01569-22.4FIG\u00a0S4FIG\u00a0S4, PDF file, 0.1 MB.Counts of MAGs encoding substrate-specific CAZymes. Genes encoding putative CAZymes were annotated against dbCAN (3.0) with default parameters and filtCopyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the A greater proportion of MAGs encoding mannopine transporters were identified in the FL samples than in the PA samples (~6.2% versus ~1.2%) . The subGiven the higher prevalence and diversity of transporters in SPA MAGs, POC solubilization capabilities of both SPA and FL MAGs were investigated. Extracellular hydrolytic enzymes that include peptidases and carbohydrate-active enzyme (CAZymes), key components in particulate organic carbon hydrolysis, were examined in terms of their abundance, diversity, and function B and C.The SPA MAGs possessed a significantly higher count of genes encoding peptidases and CAZymes per genome than the FL MAGs and B. ASince polysaccharides constitute a large fraction of DOC and POC 59\u2013l-rhamnohydrolase (GH106), \u03b1-l-rhamnosidase (GH106), alginate lyase (PL6 and -14), endo-\u03b1-1,5-l-arabinanase (GH43), \u03b2-l-arabinofuranosidase (GH146), chitinase (GH18), and \u03b2-porphyranase (GH16). These CAZymes hydrolyze polysaccharides such as alginate, porphyran, ulvan, and xylan, which are structural components of algae, and chitin, a highly abundant polysaccharide in marine environments. These CAZymes also hydrolyze an assortment of polysaccharides, releasing sugars such as rhamnose, xylan, and arabinose, which are found enriched in spring phytoplankton blooms , was found to be enriched in FL MAGs in comparison to PA MAGs . This en63\u2013n blooms .l-fucosidase (GH29 and GH151), \u03b2-glucosidase , cellulase , cellobionic acid phosphorylase (GH94), \u03b1-N-acetylgalactosaminidase (GH109 and -114), \u03b2-galactosidase (GH2 and -42), and \u03b1-galactosidase . The enrichment of these CAZymes in SPA MAGs also correlates well with the spike in multiple sugars detected during summer phytoplankton blooms, such as mannan, fucose, glucose, galactosamine, and galactose , \u03b2-mannosidase (GH2), \u03b1-alactose .N-acetylhexosaminidase , which is involved in the hydrolysis of N-acetylated oligo/polysaccharides such as chitooligosaccharides and chitin, which are prevalent and abundant in marine crustaceans. MAGs containing genes for \u03b2-N-acetylhexosaminidase were present only within the Gammaproteobacteria and include the orders Arenicellales, Burkholderiales, Enterobacterales, Nitrosococcales, Pseudomonadales, UBA11654, and Xanthomonadales. Lastly, genes encoding laminarin endo-1,3-\u03b2-d-glucosidase (GH16 and -81) were found to be enriched in 25 SPA MAGs, which degrades laminarin, a polysaccharide abundant in microalgae such as diatoms enable rapid transcriptional responses to environmental variations, including light, temperature, and nutrient availability . TCSs arExamination of the SPA and FL MAGs for genes encoding TCSs showed significantly higher representation of histidine kinases in PA MAGs than in FL MAGs . In addiExtracellular protein secretion systems (ESSs) are widespread among bacteria and archaea and are central components in fimbria- and pilus-associated attachment and adhesion, nutrient transport, predation, cell-cell interactions, surface colonization, and pathogenicity in diverse environmental contexts and settings \u201374. The \u201310.1128/mbio.01569-22.5FIG\u00a0S5FIG\u00a0S5, PDF file, 0.1 MB.Frequency of different extracellular secretion systems in particle-associated versus free-living bacterial genomes in the water column. Genes encoding bacterial secretion systems were predicted using MacSysFinder with the TSScan reference database (v1.0rc1). Download Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Prior work has suggested that deep-sea bacteria may have larger genomes than bacteria in the epipelagic zone , 76, andPA microbial communities are often viewed as \u201chot spots\u201d for microbial activity in comparison to their FL counterparts, based on their larger cell size and cell densities, higher enzyme activities, and overall rates of heterotrophic microbial metabolism , 12, 13.77\u201380\u2013in situ inorganic nitrogen availability and depth for FL bacterioplankton at Station ALOHA had significantly larger genome sizes on average than FL microbes . In termon ALOHA 44). No. Noin sion ALOHA . As for on ALOHA . These gon ALOHA .Recently, codon usage bias CUB) metrics in genes encoding ribosomal proteins have been used to estimate the maximum growth rates (minimum doubling times) of microorganisms in both laboratory and environmental settings \u201387. We t\u2013UB metric10.1128/mbio.01569-22.10TABLE\u00a0S5Table\u00a0S5, XLSX file, 0.03 MB.Estimated growth efficiencies based on MAG codon usage biases. Download Copyright \u00a9 2022 Leu et al.2022Leu et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Prochlorococcus as well as motile heterotrophic copiotrophs like Idiomarina. These results further illustrate the distinctive microhabitat-specific phylogenetic, physiological, and ecological divergence between SPA and FL microbial communities and energy , 61, 67.Previous metagenomic and metaproteomic studies of 0.2-\u03bcm-filtered samples throughout the water column reported that total peptidases and CAZymes decreased from epipelagic (0 to 200 m) to bathypelagic microbial communities, while the percentage of extracellular enzymes and their diversity increased with depth . In our Given their particle-associated lifestyles, we postulated that SPA microbial genomes are also enriched in genes that promote environmental sensing and response, motility, attachment, colonization, and cell-cell interactions. Consistent with this hypothesis, both the shallow- and deep-water SPA microbes contained greater proportions of genes associated with two-component regulatory systems, extracellular secretion systems, and flagella than did FL microbes from the same depth horizons. The genomic distributions of TCSs support prior observations with respect to general metabolic types and suggPrior gene-centric studies have demonstrated that genome size, GC content, and genome and proteome nitrogen content tend to positively correlate with environmental inorganic nitrogen availability among FL bacterioplankton populations , 81, 82.3\u2212, NO2\u2212) to reduce the energetic costs of nitrogen acquisition. Our data further suggest that as particles sink and nitrogen depletion ensues, SPA microbial assemblages undergo dynamic compositional shifts in response to the more nutrient-depleted particle microenvironments found at greater depths.SPA microbes, however, showed an opposite trend with respect to DNA GC content and proteome N-ARSC with increasing depth. Strikingly, shallow-water SPA microbes collected at 150 m had higher DNA GC and proteome nitrogen contents than did deeper, 4,000-m SPA microbes. The higher genome and proteome nitrogen content in shallow- versus deep-water SPA microbes is consistent with recent studies of the elemental composition and energy content (in Joules per unit mass of organic carbon) of sinkiin situ maximum growth rates (minimum doubling times) of prokaryote environmental settings at 37\u00b0C for 30\u2009min. Subsequently, 50\u2009\u03bcL of a proteinase K solution (0.8\u2009mg mL\u22121) was added, followed by the addition of 50\u2009\u03bcL of 10% SDS. Samples were incubated at 55\u00b0C for 2\u2009h. Final DNA purification was robotically performed using a Chemagen MSM I instrument with the CMG-1037 DNA saliva kit .Metagenomic sequence data from FL samples see \u201346. Brie\u2013Sequencing libraries were prepared and sequencing for all the above samples was performed as described previously , 45. Brihttps://sourceforge.net/projects/bbmap/) in two passes. The first pass used parameters \u201cktrim=r k\u2009=\u200923 mink\u2009=\u200911 hdist\u2009=\u20091 tbo tpe tbo tpe\u201d for Illumina sequencing adapters, and the second pass used parameters \u201ck\u2009=\u200927 hdist\u2009=\u20091 qtrim=rl trimq\u2009=\u200917 cardinality=t mingc\u2009=\u20090.05 maxgc\u2009=\u20090.95\u201d to remove phiX, low-quality bases, and sequences with unrealistically high or low GC. Additional low-quality bases and sequences were removed with Trimmomatic 0.38 (parameters: LEADING:10 TRAILING:10 MINLEN:100) (https://github.com/lh3/seqtk). The cleaned reads from each sample were assembled using SPAdes 3.11.1 . Unpaire,99,127) .https://github.com/wwood/CoverM). For each assembled metagenome, metagenome-assembled genomes were recovered using MetaBAT1 v0.32.5 (https://github.com/wwood/finishm).Mapping of quality reads was performed using CoverM v0.4.0 with default parameters were reclassified as PA_Shallow (see Methods) , since tMethods) .Sixty-one 4,000-m PA_Deep MAGs were reannotated as PA_Shallow based on their photic zone-dependent gene representation, well documented physiologies and lifestyles , and/or depth profile read mapping densities. These included the following MAGs: DT-Alcanivorax-1, DT-Alteromonas-1, DT-Bdellovibrionales-2, DT-Bdellovibrionales-3, DT-Caenarcaniphilales-1, DT-Chromohalobacter-1, DT-Cognatishimia-1, DT-Coraliomargarita-1, DT-Dinoroseobacter-1, DT-Ekhidna-1, DT-Epibacterium_A-1, DT-Erythrobacter-1, DT-Erythrobacter-2, DT-Flavobacteriaceae-1, DT-Flavobacteriaceae-3, DT-Flavobacteriaceae-4, DT-Flavobacteriales-4, DT-Gilvibacter-1, DT-Halieaceae-1, DT-Halioglobus-1, DT-Halomonas-1, DT-Halomonas-3, DT-Henriciella-1, DT-Henriciella-2, DT-Henriciella-3, DT-Hyphomicrobiaceae-1, DT-Idiomarina-1, DT-Idiomarina-3, DT-Ilumatobacteraceae-1, DT-Legionellales-1, DT-Micavibrionaceae-1, DT-Mycoplasmatales-1, DT-Mycoplasmatales-2, DT-Oleispira-1, DT-Oligoflexales-1, DT-Parvularculaceae-1, DT-Phaeodactylibacter-1, DT-Phycisphaerales-1, DT-Pseudoalteromonas-1, DT-Pseudobacteriovorax-1, DT-Pseudomonadales-2, DT-Psychroserpens-1, DT-Psychrosphaera-1, DT-Rhizobiales-4, DT-Rhodobacteraceae-1, DT-Rhodobacteraceae-2, DT-Rhodobacteraceae-3, DT-Richelia-1, DT-Rickettsiaceae-1, DT-Rickettsiales-1, DT-Rivularia-1, DT-Salinicola-1, DT-Saprospiraceae-1, DT-Saprospiraceae-2, DT-Shewanella-1, DT-Simkaniaceae-1, DT-Verrucomicrobiales-1, DT-Vibrio-1, DT-Winogradskyella-1, DT-Winogradskyella-2, DT-Xanthomonadales-1, and DT-Crocosphaera.https://github.com/Ecogenomics/GTDBTk). Briefly, marker genes were identified in each genome, aligned, concatenated, and classified with pplacer to identify the maximum-likelihood placement of each genome\u2019s concatenated protein alignment in the GTDB-Tk reference tree. GTDB-Tk classifies each genome based on its placement in the reference tree, its relative evolutionary distance, and FastANI distance.Classification of the MAGs was determined using GTDB-Tk v.1.3.0 https://github.com/bbuchfink/diamond.git) against UniRef100 (accessed September 2019) , clusterer 2019) , and Pfaer 2019) and TIGRer 2019) . Genes wer 2019) .https://github.com/JessAwBryant/gene-characteristics.Amino acid sequences from the dereplicated genome set were used to calculate N-ARSC and C-ARSC values using custom scripts from Mende et al. and avaiGenes were annotated against dbCAN (3.0) with default parameters and filt\u221210. SignalP v5.0 domain annotations , 110. HiGenes encoding the bacterial secretion systems were predicted using MacSysFinder and the https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-5qpvoyqebg4o/v3). Prophage genes were annotated using DRAM-v.py v1.2.4 ordination analysis with the Jaccard distance matrix using the metaMDS function in the Vegan v2.6-2 package in R , 119.To calculate the relative abundance, reads from each metagenomic data set were mapped to the dereplicated MAGs using CoverM v0.3.1 with the \u201ccontig\u201d command, a cutoff of 95% minimum identity, and a minimum aligned read length of 75% of each read. Coverage of each contig was calculated with the CoverM \u201ctrimmed_mean\u201d option, and the coverage for each MAG was calculated as the average of all contig coverages, weighted by their length. The relative abundance of each MAG in each metagenomic data set was calculated as its coverage divided by total reads in the sample multiplied by 100,000,000.The presence/absence of each KO ID or orthologous family in each genome was used as input for the program Scoary to identP values that were affected by multiple testing were corrected for false discovery using the Benjamini-Hochberg procedure.The mean statistical significance of different proteins of interests and genomic characteristic metrics between sample types were determined through one-way analysis of variance (ANOVA), followed by the Tukey test using the R package multicompview v0.1-8 with the Tukey honestly significant different (HSD) function. All https://github.com/dparks1134/CompareM).Average amino acid identity (AAI) between the genomes was calculated using orthologous genes identified through reciprocal best BLAST hits by use of compareM v0.0.5 (http://bioinformatics.psb.ugent.be/webtools/Venn/). Figures were further refined using Adobe Illustrator.Figures were generated using pheatmap and ggplPRJNA482655, and assembled MAGs are available under NCBI BioSample no. SAMN14675689 to SAMN14675809. Metagenomic reads produced from DNA extracted from shallow 150-m sediment trap samples (collected in 2015) (PRJNA358725. For Station ALOHA 0.2-\u03bcm-pore-size filter-collected metagenomes/MAGs, read sequence data and FL MAGs are available at NCBI SRA under BioProject no. PRJNA352737, and assemblies can be found under BioSample no. SAMN12604809.All data were deposited in the NCBI SRA archive as follows. Deep 4,000-m-trap metagenomes and MAGs are deposited under NCBI BioProject no."} +{"text": "Invasive mucormycosis (IM) is associated with high mortality and morbidity. MAT2203 is an encochleated oral formulation of amphotericin B which has been shown to be safe and effective against murine aspergillosis and murine cryptococcal meningoencephalitis. We sought to compare the efficacy of MAT2203 to liposomal amphotericin B (LAMB) treatment in a neutropenic mouse model of IM.Rhizopus delemar 99-880 or M. circinelloides f. jenssenii DI15-131. Treatment with placebo (diluent control), oral MAT2203 or LAMB , began 16 h post infection. Survival (n=10-20/group from 1/2 experiments) through Day +21 and tissue fungal burden of lungs or brain (n=10/group) euthanized on Day +4 post infection served as a primary and secondary endpoint, respectively.ICR mice were immunosuppressed with cyclophosphamide and cortisone acetate on days -2, -3 and +8, relative to infection with intratracheally instilled Rhizopus delemar infection, doses of MAT2203 5,15 mg/kg qd or 7.5 mg/kg bid, significantly prolonged median survival time (MST) and enhanced overall survival vs. placebo-treated mice . Importantly, MAT2203 treatments were as effective as LAMB . For mice infected with M. circinelloides, MAT2203 at 15 mg/kg, qd significantly prolonged MST and enhanced overall survival vs. placebo-treated mice . In both infection models MAT2203 treatment of 15 mg/kg or LAMB resulted in significant \u223c1.0-1.5 log reduction and \u223c2.0-2.2 log reduction in lung and brain fungal burden vs. placebo, respectively (Wilcoxon Rank Sum).For in vivo efficacy in treating R. delemar or M. circinelloides pulmonary infection in immunosuppressed mice, which was equivalent to the LAMB current standard of care. Continued investigation and development of MAT2203 as a novel, and oral formulation of amphotericin antifungal agent against mucormycosis is warranted.MAT2203 demonstrated Theresa Matkovits, PhD, Matinas BioPharma: Employee Jenel Cobb, PhD, Matinas BioPharma: Employee Raphael J. Mannino, PhD, Matinas BioPharma: Employee Ashraf S. Ibrahim, PhD, Matinas BioPharma: Advisor/Consultant|Matinas BioPharma: Grant/Research Support|SFunga: Grant/Research Support."} +{"text": "Vaccination strategies that provide enhanced immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are needed. We evaluated the safety and immunogenicity of a bivalent omicron containing vaccine, mRNA-1273.214 (50 \u00b5g), administered as a second booster dose in adult participants.In this ongoing phase 2/3 trial, 50 \u00b5g of the bivalent vaccine mRNA-1273.214 or 50 \u00b5g of the authorized mRNA-1273 were administered as second boosters in adults who previously received a 2 dose (100 \u00b5g) primary series and a first booster (50 \u00b5g) dose of mRNA-1273 (\u2265 3 months prior). Primary objectives were safety and reactogenicity and immunogenicity 28 days post-booster dose.Figure). Safety and reactogenicity were similar for both vaccine groups.In participants with no prior SARS-CoV-2 infection who received booster doses of mRNA-1273.214 (n=334) or mRNA-1273 (n=260), neutralizing antibody (nAb) geometric mean titers ]) against omicron BA.1 were 2372.4 (2070.6\u22122718.2) and 1473.5 (1270.8\u22121708.4), respectively. The model-based GMT ratio (GMR [97.5% CI]) of mRNA-1273.214 compared to mRNA-1273 was 1.75 (1.49\u22122.04), meeting the pre-specified superiority criterion against omicron BA.1. The pre-specified criterion for non-inferiority against the ancestral SARS-CoV-2 strain was also met. Additionally, mRNA-1273.214 elicited higher GMTs (727.4 [632.8\u2212836.1]) than mRNA-1273 (492.1 [431.1\u2212561.9]) against omicron subvariants BA.4/BA.5 [GMR (95% CI) 1.69 [1.51\u22121.90])]. Binding antibody responses against alpha, beta, gamma, delta, and omicron were numerically higher in the mRNA-1273.214 group compared to mRNA-1273. mRNA-1273.214 GMTs were consistently higher across age (18-< 65 and \u2265 65 years) and pre-booster SARS-CoV-2 infection subgroups (The bivalent omicron containing mRNA-1273.214 elicited superior nAb responses against omicron 28 days post-immunization compared to mRNA-1273 regardless of age and prior SARS-CoV-2 infection; no new safety concerns were identified.Spyros Chalkias, MD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Stephen R. Walsh, MD, Janssen Vaccines: Grant/Research Support|Moderna, Inc.: Grant/Research Support|NIAID/NIH: Grant/Research Support|Sanofi Pasteur: Grant/Research Support Nichole McGhee, B.S., Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Joanne Tomassini, Ph.D., Moderna, Inc.: Advisor/Consultant Xing Chen, Sc.D., Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Ying Chang, M.S., Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Andrea Sutherland, M.D., MPH, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds David Montefiori, Ph.D., Moderna, Inc.: Grant/Research Support Bethany Girard, Ph.D., Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Darin Edwards, Ph.D., Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Jing Feng, M.S., Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Honghong Zhou, Ph.D., Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Lindsey R. Baden, MD, Moderna, Inc.: Grant/Research Support|NIAID: Grant/Research Support Jacqueline Miller, MD, Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds Rituparna Das, M.D., Moderna, Inc.: Salary|Moderna, Inc.: Stocks/Bonds."} +{"text": "Piper species has been studied, along with their antifungal and phytotoxic activities. These EOs contained \u03b2-bisabolene/nerolidol (Pc), \u03b2-bisabolene/\u03b4-cadinene/caryophyllene (Pt), caryophyllene oxide (Pcs), bicyclogermacrene/10-epi-Elemol (Po), bicyclogermacrene/germacrene-D/apiol (Pd), caryophyllene/germacrene-D (Pa), germacrene-D (Pr), limonene/apiol (Ps), apiol (Psf), and apiol/bicyclogermacrene (Pm) as major components, and some are described here for the first time . A composition-based dendrogram of these Piper species showed four major groups . The spore germination effects and phytotoxicity (Lolium perenne and Lactuca sativa) of these EOs were studied. Most of these Piper essential oils showed important activity against phytopathogenic fungi (except G1), especially against B. cinerea. Similarly, most of the essential oils were phytotoxic against L. perenne (except G1), with P. sancti-felicis (G4), P. casapiense (G2), and P. reticulatum (G2) being the most effective. Caryophyllene oxide, \u03b2-caryophyllene, \u03b2-pinene, limonene, \u03b1-humulene, and apiol were evaluated against B. cinerea,\u00a0with the most effective compounds being \u03b2-pinene, apiol, and limonene. This work demonstrates the species-dependent potential of essential oils from Peruvian Piper species as fungicidal and herbicidal agents.The chemical composition of essential oils (EOs) from ten Peruvian Diseases caused by plant pathogens significantly contribute to annual loss in crop yield worldwide . The appIn plants, essential oils (EOs) play a protective role against herbivores, phytopathogenic fungi, and weeds. Essential oils also represent a new class of crop protectants due to their volatility and low toxicity to the environment and have been proposed as an alternative to synthetic pesticides ,7,8,9. APiper is found in tropical and subtropical areas, and in America, there are approximately 700 species [The Piperaceae family has approximately eight genera and 3000 species . The gen species ,13, with species ,15. This species , includi species ,17,18, a species ,20, inse species ,21.Piper EOs are characterized by the presence of monoterpene hydrocarbons , oxygenated monoterpenoids , sesquiterpene hydrocarbons , oxygenated sesquiterpenoids -nerolidol, caryophyllene oxide, \u03b1-cadinol, epi-\u03b1-bisabolol), and phenylpropanoids , among others [Piper essential oils have been described as being insect antifeedant, acaricidal, nematicidal, and herbicidal agents [Piper essential oils are a promising source of new potential biopesticide ingredients.g others ,22,23,24l agents ,21. TherPiper species for their biopesticidal potential, ten species native to the Peruvian Amazonian region have been extracted by hydrodistillation to study the chemical composition of their EOs by GC-MS, along with their fungicidal activity against phytopathogens and their phytotoxic effects (against Lolium perenne and Lactuca sativa) to assess their potential applications in phytopathogen and/or weed control.As part of an ongoing project on the bioprospection of Peruvian Piper coruscans; \u03b2-bisabolene (40.2%), \u03b4-cadinene (9.8%), caryophyllene (9.7%), germacrene-D (5.0%), and nerolidol (4.5%) for P. tuberculatum; caryophyllene oxide (10.2%), and caryophyllene (4.7%) for P. casapiense; bicyclogermacrene (7.9%), 10-epi-Elemol (7.3%), caryophyllene (6.3%), \u03b1-pinene (6.0%), \u03b2-pinene (5.1%), \u03b2-selinenol (4.9%), \u03b1-eudesmol (4.5%), and camphene (4.4%) for P. oblicuum; bicyclogermacrene (16.5%), germacrene-D (10.4%), apiol (8.9%), caryophyllene (6.8%), \u03b2-pinene (6.3%), \u03b1-cubebene (5.9%), and \u03b2-elemene (4.5%) for P. dumosum; caryophyllene (11.3%), germacrene-D (9.6%), \u03b1-humulene (6.6%), \u03b4-cadinene (6.6%), and (-)-\u03b2-copaene (5.8%) for P. anonifolium; germacrene-D (12.6%), bicyclogermacrene (8.1%), \u03b4-cadinene (6.0%), copaene (4.6%), and caryophyllene (4.5%) for P. reticulatum; limonene (38.5%), apiol (15.0%), caryophyllene oxide (8.4%), eudesma-3,7-(11)-diene and copaene (5.8%) for P. soledadense; apiol (76.1%), and caryophyllene (4.1%) for P. sancti-felicis and apiol (51.6%), bicyclogermacrene (9.0%), germacrene-D (6.7%), and myristicin (4.6%) for P. mituense.The chemical compositions of the essential oils are shown in P. sancti-felicis and P. mituense, which were characterized by phenylpropanoids, and P. soledadense, which was characterized by monoterpene hydrocarbons.The overall composition of these oils is shown in Piper species (P. coruscans (Pc) and P. tuberculatum (Pt), characterized by the presence of sesquiterpene hydrocarbons; (G2) P. casapiense (Pcs), P. obliquum (Po), P. dumosum (Pd), P. anonifolium (Pa), and P. reticulatum (Pr), characterized by sesquiterpenes; (G3) P. soledadense (Ps), with monoterpenes and sesquiterpenes; and (G4) P. sancti-felicis (Psf) and P. mituense (Pm), characterized by phenylpropanoids.A dendrogram based on the composition of the species showed fPiper essential oils against Aspergillus niger, Botrytis cinerea, and Alternaria alternate is shown in B. cinerea was the fungal species most susceptible to the action of Piper essential oils. The antifungal activity showed a pattern in accordance with the grouped EOs. P. coruscans and P. tuberculatum (G1) were not active. P. casapiense (G2), P. obliquum (G2), P. dumosum (G2), P. anonifolium (G2), and P. reticulatum (G2) were only active against B. cinerea with varying potencies, with P. obliquum and P. anonifolium being the most effective. P. soledadense (G3) inhibited the spore germination of A. niger and B. cinerea. P. sancti-felicis (G4) oil was active against all three fungal species with moderate effects, and P. mituense (G4) only acted on B. cinerea, probably due to the lower concentration in apiol of this oil.The antifungal activity (spore germination inhibition) of the Piper oils components tested against B. cinerea , \u03b2-pinene showed strong antifungal activity , followed by apiol and limonene , with effective doses similar to the positive control for apiol.Among the Lactuca sativa (dicotyledonous) and Lolium perenne (monocotyledonous) plants. The phytotoxic activity did not follow the grouping pattern observed for the antifungal effects. P. sancti-felicis (G4), P. casapiense (G2), P. mituense (G4), and P. reticulatum (G2),\u00a0effectively inhibited germination, leaf and root growth of L. perenne , P. obliquum (G2), P. dumosum (G2), and P. soledadense (G3)\u00a0inhibited leaf growth (>50%), followed by P. tuberculatum (G1) with a 50% inhibition.The essential oils were tested for phytotoxic effects on ne >50%, . P. anonP. sancti-felicis, P. casapiense, P. reticulatum, and P. mituense effectively inhibited the root growth of L. sativa (data not shown). P. soledadense reduced the root growth of L. sativa (data not shown). These results show strong selective herbicidal potential of the EOs tested against monocotyledonous plants.Piper essential oils present a wide variety of chemical compounds with important biological activities that may be of interest in agriculture, medicine, and food industries, among others. These oils play an important role in the defense of the plant against pests, and many studies have reported activities as insecticidal, antifeedants, phytotoxic and antifungal [tifungal ,26,27,28Piper species described here have been previously reported to show quantitative and qualitative chemical variations that can be attributed to environmental factors [The essential oils from some of the umidity) ,29,30. AP. coruscans (Pc) and P. tuberculatum (Pt). P. coruscans EO had \u03b2-bisabolene (33.4%) and nerolidol (10.2%) as the main components, while this species collected in Ecuador contained \u03b2-caryophyllene (24.1\u201325.0%), \u03b1-humulene (11.6\u201312.0%), and caryophyllene oxide (9.3\u201310.9%) [P. tuberculatum studied here showed \u03b2-bisabolene (40.2%) as the main component followed by \u03b4-cadinene (9.8%), caryophyllene (9.7%), germacrene-D (5.0%), nerolidol (4.5%), copaene (4.2%), and \u03b2-elemene (3.3%). This Piper species (Pt) EO has been previously reported for plants collected from different locations. Pt collected in Venezuela gave an EO with \u03b1-farnesene (6.2%), humulene epoxide II (6.0%), 2-pentadecanone (4.1%), \u03b2-eudesmol (4.4%), 2-tridecanone (4.3%), ledane (3.6%), -farnesylacetone (3.6%), and \u03b1-cadinol (2.9%) [E)-caryophyllene (30.1%) [E-cariofilene (7.1%), and trans-4-muurola(14)-5-diene (9.9%) [(G1) 3\u201310.9%) . The EO l (2.9%) , while E (30.1%) or myrissabolene .4% and nP. casapiense (Pcs), P. obliquum (Po), P. dumosum (Pd), P. anonifolium (Pa), and P. reticulatum (Pr): P. casapiense (Pcs), is reported here for the first time. The EO from P. obliquum had bicyclogermacrene (7.9%), 10-epi-Elemol (7.3%), caryophyllene (6.3%), and \u03b1-pinene (6.0%). However, the Po essential oil of Ecuadorian origin contained safrole (45.9%), \u03b3-terpinene (17.1%), and terpinolene (11.5%) [P. dumosum contained bicyclogermacrene (16.5%) and germacrene-D (10.4%). Similarly, the EO from Pd plants collected in the Brazilian Amazonia had bicyclogermacrene (16.2%), \u03b2-caryophyllene (15.9%), \u03b2-pinene (16.0%), and \u03b1-pinene (12.1%) [P. anonifolium studied here contained caryophyllene (11.3%), germacrene-D (9.6%), \u03b4-cadinene (6.6%), \u03b1-humulene (6.6%), and neoalloocimene (5.5%), while a previously reported EO from the Brazilian Par\u00e1 was composed of selin-11-en-4-\u03b2-\u03b1-ol (20.0%), \u03b2-selinene (12.7%), \u03b1-selinene (11.9%), and \u03b1-pinene (8.8%) [P. reticulatum studied here contained the phenylpropanoid apiol as the main component (15.0%) while \u03b2-elemene (24.6%) and \u03b2-caryophyllene (16.7%) were abundant in a Pr oil from the northern region of Brazil [(G2) (11.5%) , while a (11.5%) . P. dumo (12.1%) as the me (8.8%) . Furthere (8.8%) . The EO f Brazil .soledadense (Ps) is reported here for the first time.(G3) P. P. sancti-felicis (Psf) and P. mituense (Pm). The EO from P. sancti-felicis and P. mituense (Pm reported here for the first time) contained the phenylpropanoid apiol as the main component . \u03b4-3-carene (35.3%) and limonene (27.1%) were the main components of the EO from P. sancti-felicis collected in Choco, Colombia [(G4) Colombia ,25.Piper have been reported to have a wide range of biological properties [P. tuberculatum -\u03b2-ocimene 14% and \u03b2-caryophyllene 32.1%) [P. anonifolium showed strong antifungal activity against Cladosporium cladosporioides and C. sphaerospermum [The essential oils studied here have shown important activities against phytopathogenic fungi (G2-4). Essential oils from the genus operties ,14,21,40operties ,38,39. Se 32.1%) , and P. ospermum .B. cinerea , \u03b2-pinene, limonene, and apiol showed strong antifungal activity. Therefore, \u03b2-pinene could contribute to the activity of Po and Pd EOs, while apiol and limonene could explain the effect of Ps, Psf, and Pm oils. \u03b2-caryophyllene (inactive) could be a synergist.The composition-based grouping of the EOs overlapped with the antifungal activity, suggesting that the presence of bicyclogermacrene, 10-epi-Elemol, germacrene-D, caryophyllene, limonene, \u03b2-pinene, and/or apiol could be responsible for significant antifungal effects. Among the oil components tested against Rhizoctonia solani, Fusarium oxysporum, Penicillium digitatum and Asperigallus niger [Botrytis cinerea [Aspergillus flavus, A. niger, A. fumigatus, and A. parasiticus [Botryodiplodia theobromae and Colletotrichum acutatum [Fusarium solani [Rhizoctonia solani and Helminthosporium oryzae [B. cinerea spore germination.(S)-Limonene has reported antifungal activity against us niger . Apiol s cinerea , Aspergiasiticus , Botryodacutatum ,46. The acutatum . Caryophm solani and carym oryzae , but in P. sancti-felicis, P. mituense, P. casapiense, P. reticulatum, P. anonifolium, P. obliquum, P. dumosum, and P. soledadense) were phytotoxic to the monocotyledonous Lolium perenne, and this activity did not overlap with the composition-based groups, suggesting a multi-component phytotoxic action. This is the first report on the phytotoxic effects of these species, except for an EO from P. sancti-felicis that was not active and did not contain apiol [Piper species, including P. hispidinervum rich in safrole [P. dilatatum rich in apiol, and P. divaricatum rich in eugenol and methyleugenol [Most of the essential oils tested here [Brassica campestris and Raphanus sativus [Echinochloa crusgalli, Lolium perenne, Amaranthus retroflexus, and Digitaria sanguinalis [Among the main compounds present in the species , apiol i plants) , and car sativus and the guinalis .2SO4. All investigated Piper species contained essential oils that range from 0.078 to 1.26% based on dry weight of the selected Piperaceae species were collected in Iquitos, Loreto Department, Peru in different seasons. The taxonomic identification was carried out at the Herbarium Amazonense of the National University of the Peruvian Amazon, Iquitos, Peru. A voucher for each species has been deposited in the herbarium. All the plants were permitted for collection . The EOs extraction was performed by hydrodistillation using the dried aerial parts of the plants. The EOs were separated by decantation and dried over anhydrous Nay weight .Essential oils were analyzed by gas chromatography (GC) on a Shimadzu 2010 and gas chromatography-mass spectrometry (GC-MS) equipped with a mass spectrometer Shimadzu GCMS-QP2010-Ultra Mass Detector . The carrier gas was helium. The capillary column was a Teknokroma TRB (95%) dimethyl (5%) dimethylpolysiloxane (30 m \u00d7 0.25 mm ID and 0.25 \u00b5m phase thickness). Working conditions were as follows: injector temperature, 300 \u00b0C; column temperature 70\u2013290 \u00b0C, for 6 min, staying at 290 \u00b0C for 15 min, temperature of the transfer line connected to the mass spectrometer, 250 \u00b0C, and ionization source temperature 250 \u00b0C. The identification of compounds was performed with standard terpenes analyzed under the same conditions and by comparison of the mass spectra with those available in the library Wiley Mass Spectral Database , while relative area% has been used for quantification of all the peaks obtained in the chromatograms. The mass spectra and Kovats retention indexes obtained were compared with the literature reported ,54.Aspergillus niger, Alternaria alternata, and Botrytis cinerea came from the fungal collection of Instituto de Ciencias Agrarias-CSIC, Madrid, Spain where they are maintained. The antifungal activity of the essential oils was determined using a modified spore germination inhibition growth assay [5 cells/mL in NaCl 0.9% for A. niger and 1 \u00d7 107 cells/mL in distilled water for B. cinerea and A. alternate. Amphotericin B (5 \u00b5g/mL) was used as a positive control.The fungal species th assay . The essA. niger and 25 \u00b0C for B. cinerea). After the incubation process, 25 uL of an MTT (5 mg/mL) plus menadione (1 mM) solution in RMPIMOPS were added, the plates were incubated again for 3 h, the medium was removed, 200 \u00b5L of acidic isopropanol (95% isopropanol and 5% 1 M HCl) was added, and the plates were incubated for another 30 min. The absorbance was read at 490 nm in an Elisa reader. The IC50 values (the effective dose to give 50% inhibition) were calculated by a regression curve of % spore germination inhibition on log dose.The samples and spore suspensions (4 replicates) were placed on 96-well plates and incubated for 24 h .Lactuca sativa, and Lolium perenne seeds (40 seeds/test) in 12-well microplates, as described previously [L. sativa) or seven days (L. perenne), and the root length was measured at the end of the experiment. A nonparametric analysis of variance (ANOVA) was performed on root/leaf length data [These experiments were conducted with eviously . The essgth data ,21.https://www.statgraphics.com, accessed on 2 July 2022).The data were analyzed using STATGRAPHICS Centurion XIX subjected to cluster analysis . The groups were chosen with a distance >2.Piper species as fungicidal and herbicidal agents based on their composition. A dendrogram based on the composition of the Piper species showed four groups: (G1) P. coruscans (Pc) and P. tuberculatum (Pt), characterized by the presence of sesquiteterpene hydrocarbons; (G2) P. casapiense (Pcs), P. obliquum (Po), P. dumosum (Pd), P. anonifolium (Pa) and P. reticulatum (Pr), characterized by sesquiterpenes; (G3) P. soledadense (Ps), with monoterpenes and sesquiterpenes; and (G4) P. sancti-felicis (Psf) and P. mituense (Pm), characterized by phenylpropanoids. The essential oils in G2-4 showed important activity against Botrytis cinereal and were phytotoxic against Lolium perenne.This work demonstrates the species-dependent potential of essential oils from Peruvian Considering the composition-based grouping of the EOs, we can conclude that the presence of bicyclogermacrene, 10-epi-Elemol, germacrene-D, caryophyllene, limonene, \u03b2-pinene, and/or apiol could be responsible for significant antifungal and herbicidal effects. \u03b2-pinene, apiol, and limonene showed antifungal activity, but not caryophyllene, suggesting that this compound could be a synergist.Piper germplasm bank and the domestication of selected species to grant a sustainable biomass source for the production of essential oils with biopesticidal activity.These findings have important implications for the development of a"} +{"text": "The aim of this study was to determine the sensitivity (SE), specificity (SP), positive predictive value (PPV), and negative predictive value (NPV) for PC-local recurrence and metastases on a per region basis.Despite increasing use for the detection of biochemically recurrent prostate cancer (rPC), the diagnostic accuracy of positron emission tomography/computed tomography (PET/CT) with [18F]PSMA-1007 PET/CT for rPC were retrospectively analysed. Six body regions were defined: prostate fossa, pelvic lymph nodes (LN), retroperitoneal LN, supradiaphragmatic LN, bones, and soft tissue. A region was counted positive if at least one PSMA-positive lesion suspicious for PC was observed. Confirmation of a true-positive PSMA-avid lesion was defined as positive by histopathology, fall in serum prostate-specific antigen (PSA) (> 50%) after targeted therapy or confirmatory further CT, MRI, PET/CT, or bone scan imaging. Regions where additional imaging was able to confirm the absence of suspicious PC lesions or regions outside exclusively targeted RT with serum PSA decline (> 50%) were counted as true-negative regions. SE, SP, PPV, and NPV were calculated for all six regions.One hundred seventy-seven consecutive patients undergoing [n = 6) was too small for an accurate statistical analysis.The overall PET-positivity rate was 91%. Conclusive follow-up for affirmation or refutation of a PSMA-positive lesion was available for 81/152 patients on a per region basis. In this subgroup, overall sensitivity, specificity, PPV, and NPV were 95% (CI: 0.90\u20130.98), 89% (CI: 0.83\u20130.93), 86% (0.80\u20130.90), and 96% (CI: 0.92\u20130.98), respectively. On a per region basis, PPV was 97% (CI: 0.83\u20130.99) for local recurrence, 93% (CI: 0.78\u20130.98) for pelvic LN, 87% (CI: 0.62\u20130.96) for retroperitoneal LN, 82% (CI: 0.52\u20130.95) for supradiaphragmatic LN, and 79% (0.65\u20130.89) for bone lesions. The number of solid organ metastases sensitivity and NPV on a per region basis. However, overall PPV was limited (86%), particularly for bone lesions (79%), which are a potential diagnostic weaknesses when using this tracer.The known high PET-positivity rate of [The online version contains supplementary material available at 10.1007/s00259-022-05693-0. Radioligands to the prostate-specific membrane antigen (PSMA) have become the gold standard for the staging of primary prostate cancer (PC) \u20134 and re68Ga]Ga-PSMA-11, a large number of alternative radioligands have become available, including but not limited to [68Ga]Ga-PSMA-I&T; [68Ga]Ga-THP-PSMA; and [18F]-labelled PSMA-radiotracers such as [18F]-rhPSMA-7, [18F]-DCFPyL, [18F]-JK-PSMA-7, or [18F]PSMA-1007 [18F]-labelled PSMA-radiotracers have numerous advantages over 68Ga-labelled ligands: [18F] is cyclotron produced with a longer half live and a lower positron energy compared to [68Ga] (0.65 MeV vs. 1.90 MeV), leading to improved spatial resolution [18F]PSMA-1007 suggest improved detection rates especially in local relapses and pelvic lymph node metastases in proximity to the urinary tract [18F]PSMA-1007 might be of benefit [68Ga]Ga-PSMA-11 can be an alternative PSMA-1007 in rPC. Hitherto, studies report only preliminary observations in small cohorts (n = 40) [18F]PSMA-1007 in a cohort of men undergoing PSMA-PET/CT for rPC in a clinical setting on a per patient and per region basis using a composite standard of truth (CSOT) for verification or refutation of imaging findings.Despite widespread adoption, few studies report the diagnostic accuracy of PSMA-1007 PET/CT in the University Clinic for Nuclear Medicine, Inselspital, Bern. The period was chosen to enable a minimum follow-up period of 12 months. Inclusion criteria were biochemical recurrence of PC (rPC) according to the ASTRO/AUA Guideline as rising PSA value after a PSA-Nadir after definitive treatment PSMA-1007 was produced as previously described [18F]PSMA-1007 solution was given by intravenous bolus injection .[escribed . The [1818F]PSMA-1007. They were investigated on either Biograph-mCT PET/CT (n = 90) or Biograph-VISION 600 PET/CT PET/CT (n = 96) scanner. The examination protocols and reconstruction algorithms used are previously published PSMA-1007 PET/CT, but where histopathology of the PSMA-avid lesion was negative, where the PSA after targeted RT did not decrease by 50% or where post therapy imaging were not confirmatory. Regions where no PSMA-positive lesion was detected with additional confirmatory imaging or regions outside exclusively targeted RT with PSA decline were counted as true-negative (TN) regions. Patients with no histopathology, no further treatment or imaging, and therefore no composite standard of truth were not included in the final analysis following exclusively targeted radiotherapy of a PSMA-positive lesion suspicious for PC were true positive (TP). The absence of PSMA-positive legions in a region where additional imaging revealed the presence of PC or where histopathology showed a positive result were counted as false negative (FN). A false-positive (FP) region was counted where a PMSA-positive lesion was observed in 8FPSMA-10 Figures .Fig. 2Co\u03b1) for \u03b1 = 0.05 PSMA-1007 in patients with rPC was 95.6% : 0.90\u20130.98).Of these 81 PSMA-PET/CTs in 73, at least one suspicious PSMA-avid lesion was detected, and therefore, the PET scan was rated as \u201cpositive\u201d. This difference in PET-positivity rate for this subgroup to the overall positivity rate was not statistically significant . On a region basis, PSMA-positive lesions were detected in the prostatic fossa in 51%, in pelvic LN in 48%, in retroperitoneal LN in 23%, in supradiaphragmatic LN in 16%, in bones in 53%, and in other metastasis (soft tissue lesions) in 7% and 0.89 (CI: 0.83\u20130.93), PPV and NPV were 0.86 (CI: 0.80\u20130.90) and 0.96 (CI: 0.92\u20130.98), and positive and negative likelihood ratio (LR+/LR-) were LR+: 8.71 (CI: 5.69\u201313.34) and LR\u2212: 0.06 (CI: 0.03\u20130.12).n = 6) showed a PPV of 0.40 (0.12\u20130.77) and a NPV of 0.97 (CI: 0.86\u20130.99). Further details are given in Figure Sensitivity and specificity on a region basis were 0.94 (CI: 0.81\u20130.98) and 0.92 (CI: 0.64\u20130.99) for local recurrence, 0.93 (CI: 0.77\u20130.99) and 0.92 (CI: 0.0.73\u20130.99) for pelvic LN, 1.00 (CI: 0.77\u20131.00) and 0.94 (0.80\u20130.98) for retroperitoneal LN, 1.00 (CI: 0.70\u20131.00) and 0.94 (CI: 0.81\u20130.98) for supradiaphragmatic LN, 0.97 CI: 0.85\u20130.99) and 0.74 (CI: 0.57\u20130.85) for bone lesions, and 0.67 (CI: 0.21\u20130.94) and 0.92 (CI: 0.79\u20130.97) for soft tissue lesions. PPV and NPV on a region basis were 0.97 (CI: 0.83\u20130.99) and 0.86 (CI: 0.60\u20130.96) for local recurrence, 0.93 (CI: 0.78\u20130.98) and 0.92 (CI: 0.74\u20130.98) for pelvic LN, 0.87 (CI: 0.62\u20130.96) and 1.00 (CI: 0.89\u20131.00) for retroperitoneal LN, 0.82 (CI: 0.52\u20130.95) and 0.96 (CI: 0.81\u20130.99) for supradiaphragmatic LN, and 0.79 (CI: 0.65\u20130.89) and 0.96 (CI: 0.81\u20130.99) for bone lesions. The small number of soft tissue lesions (\u20130.99 andROC and corresponding area under the curves (AUC) were 0.70 \u00b1 0.03 overall. For local recurrence, AUC was 0.76 \u00b1 0.05, for pelvic LN 0.71 \u00b1 0.09, for retroperitoneal LN 0.55 \u00b1 0.17, and for supradiaphragmatic LN 0.51 \u00b1 0.14. For bone lesions, the AUC was comparatively lower at 0.63 \u00b1 0.06. Corresponding ROC curves are outlined in Figure 18F]PSMA-1007 was clinically first introduced in 2015 [18F]PSMA-1007, there are currently very few evidence-based recommendations supporting its use [18F]PSMA-1007 on a patient-level and a per region basis. In this retrospective analysis of 177 patients, we present the largest cohort of men undergoing [18F]PSMA-1007 for rPC with a confirmatory standard of follow-up PSMA-1007 PSMA-1007. No significant difference in the PET-positivity rate between the subgroup with CSOT and those without was observed (p = 0.21), implying no bias in the patients with follow-up data available.One strength of our study was the high rate of follow-up available for our patients (86%). Through scrutiny of clinical imaging reports, multi-disciplinary team meeting minutes, and clinical records, we are able to demonstrate the performance of this radiopharmaceutical under clinical conditions in a large cohort of men undergoing PSMA-PET/CT in an academic nuclear medicine centre. Nevertheless, in common to all studies with rPC, follow-up data which can be used to verify imaging findings is not available for all patients. For example, a watchful waiting strategy might be chosen by the patient and his treating physicians. Using a CSOT including histopathology, PSA decline (> 50%) after targeted RT, and further imaging after the PSMA-PET showing response to system therapies, we were able to confirm or refute PSMA-PET findings. With a high number of consecutively screened patients with rPC (n = 152) is not small, the relatively smaller number of supradiaphragmatic lymph nodes (n = 13) and solid organ metastases (n = 6) precluded an accurate analysis of diagnostic performance in these regions. Further studies, ideally of prospective design, are required to confirm these data. In order to reduce selection bias, patients were consecutively followed up. This heterogeneous cohort of patients at a variety of stages of rPC and prior treatment furnishes an overview of the radiotracer\u2019s performance under routine clinical conditions. Further studies, for example, directed at early stages of recurrence should be performed, particularly since the PPV, which is dependent upon pre-test prevalence [We highlight several weaknesses with our study. Our overall cohort size was limited by the introduction of the radioligand in our centre in Oct 2019 and the requirement to collect 12 months\u2019 of follow-up. Although our cohort of patients with follow-up Below is the link to the electronic supplementary material."} +{"text": "COVID-19-related physical isolation, fear and anxiety determined de novo mental illnesses, by potentially facilitating the emergence of Hikikomori traits .The present study aims at screening a cohort of university students for the Hikikomori traits and assessing a set of psychopathological determinants associated with Hikikomori, particularly boredom and loneliness dimensions.A cross-sectional web-based survey was carried out by administering Hikikomori Questionnaire (HQ-11), Italian Loneliness Scale (ILS), Multidimensional State Boredom Scale (MSBS), Depression Anxiety Stress Scale (DASS-21) and Toronto Alexithymia Scale (TAS-20).1,148 respondents were recruited. 70.7% declared to have experienced psychological distress. HQ-11 average total score was 18.4\u00b1SD=7.5 with statistically significant higher values in the males (p=0.017) and amongst students studying Informatics, Mathematics/Physics/Chemistry, Science of Communication and Engineering. The HQ-11 positively correlated with ILS (r=0.609), MSBS (r=0.415), TAS-20 (r=0.482) and DASS-21 (r=0.434).This study represents the first screening of the Hikikomori phenomenon in Italian university students. Hikikomori traits appear to be particularly represented in the Italian youth population and should be carefully investigated in future studies.No significant relationships."} +{"text": "Salmonella have changed in recent years as multidrug-resistant (MDR) strains have become prevalent among various serovars. The recent expansion of MDR Salmonella enterica serovar Indiana sequence type 17 (ST17) poses an increasing threat to global public health, as 24.3% (61/251) of S. Indiana isolates in this study exhibited resistance to three clinically important antimicrobial agents: fluoroquinolones (ciprofloxacin), extended-spectrum \u03b2-lactams , and macrolides (azithromycin). Both the evolutionary histories and antimicrobial resistance (AMR) profiles of this serovar remain to be described. Bioinformatic analysis revealed multiple lineages have coexisted and spread throughout China. Specifically, emergence of a predominant lineage appears to be associated with accumulated various substitutions in the chromosomal quinolone resistance-determining regions (GyrA S83F D87N and ParC T57S S80R) (141 [56.2%]), as well as acquisition of an extended-spectrum \u03b2-lactamase (ESBL)-producing IncHI2 plasmid that has subsequently undergone extensive rearrangement and an IncX1 plasmid that contains mph(A), conferring resistance to azithromycin. Several other evolutionary events influencing the trajectory of this drug-resistant serovar were also identified, including sporadic acquisitions of blaCTX-M-carrying plasmids, along with chromosomal integration of blaCTX-M within subclusters. Most human isolates reside in clusters containing isolates from animals, mainly from chickens, indicating the close relationship of human isolates with those from food animals. These data demonstrate that MDR S. Indiana ST17 is already widespread and capable of acquiring resistance traits against the clinical important antimicrobial agents, suggesting it should be considered a high-risk global MDR pathogen. The complexity of its evolutionary history has implications for AMR surveillance, epidemiological analysis, and control of emerging clinical lineages.The genetic features of foodborne IMPORTANCE The emergence and worldwide spread of AMR Salmonella constitute great public health concerns. S. enterica serovar Indiana is a typical MDR serovar characterized by sporadic reports. However, comprehensive population genomics studies have not been performed on this serovar. This study provides a detailed and comprehensive insight into the rapid evolution of AMR in this important Salmonella serovar in the past 15\u2009years in eight provinces of China. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, the persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance determinants that occur at all genetic levels . There are different mechanisms of antimicrobial resistance in S. enterica serovar Indiana from those of other serovars. This study sheds light on the formation of MDR S. enterica serovar Indiana with chickens as its potential reservoirs and paves the way to curb its further expansion among food animals. Salmonella enterica (NTS) remains one of the important foodborne pathogens globally -resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antimicrobials were urgently needed , or changes in the food chain. Some clonal lineages of MDR Salmonella have shaped the epidemiology of the disease at a global level, as in the case for sequence type 34 (ST34) S. enterica serovar 4,[5],12:i:\u2212, ST313 S.enterica serovar Typhimurium, and ST198 S.enterica serovar Kentucky , extended-spectrum \u03b2-lactams , and macrolides (azithromycin [AZM]) approved by the FDA in the United States to treat infections caused by Salmonella (S. Indiana isolates can express resistance to carbapenems or colistin (CT), the last-resort antimicrobials, suggesting that these bacteria have now become a serious challenge for public health of DNA gyrase gene (gyrA) and DNA topoisomerase IV gene (parC) conferred FQs resistance, along with plasmid-mediated quinolone resistance (PMQR) genes [oqxAB and aac(6\u2032)-Ib-cr]. In addition, diverse blaCTX-M genes mapped on mobile genetic elements (MGEs) were reported earlier and found to be integrated into the chromosome (as in the case of blaCTX-M-55) (Recent studies investigated the genetic basis underpinning resistance to FQs and extended-spectrum \u03b2-lactamases (ESBLs) in TX-M-55) , 23. HowS. Indiana isolates collected from human and food-related samples in eight provinces of China during 2006 to 2017. Using phenotypic susceptibility data and whole-genome sequencing (WGS) analysis, we determined the prevalence and mechanisms of resistance and identified potential drivers of variation among the AMR profiles described within different lineages.Here, we report on the genomic epidemiology and AMR features of 251 S. Indiana isolates from eight provinces in China, 120 isolates were cultured from clinical samples taken during 2007 to 2017 and 131 isolates from food-related samples taken during 2006 to 2016 (see in silico multilocus sequence typing (MLST) as S. Indiana ST17 after whole-genome analysis.Out of the 251 confirmed 10.1128/msystems.00253-22.4TABLE\u00a0S1Salmonella Indiana isolates. Download Table\u00a0S1, PDF file, 0.01 MB.Source and basic information of Copyright \u00a9 2022 Du et al.2022Du et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the S. Indiana isolates (P < 0.05) (P < 0.05).Testing of the susceptibility of 251 isolates to 13 anisolates , with 21isolates . The res < 0.05) . Further10.1128/msystems.00253-22.5TABLE\u00a0S2S. Indiana isolates against ciprofloxacin. Download Table\u00a0S2, DOCX file, 0.02 MB.MIC value related to the PMQR gene and substitution mutations in QRDR of 251 Copyright \u00a9 2022 Du et al.2022Du et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the n\u2009=\u200911) had S83F and D87N amino acid substitutions in GyrA along with two ParC amino acid substitutions. Furthermore, five PMQR genes were detected, including aac(6\u2032)-Ib-cr (n\u2009=\u2009146), oqxAB (n\u2009=\u200968), qnrS1 (n\u2009=\u20092), qnrD (n\u2009=\u20091), and qepA (n\u2009=\u20091). PMQR genes aac(6\u2032)-Ib-cr and oqxAB coexisted in 54 isolates and were only detected with 4 amino acid substitutions in GyrA and ParC, with MICs of ciprofloxacin ranging from 8 to 256\u2009mg/L (qnrS1 and oqxAB coexisted only in two food-related isolates. Of the 97 isolates possessing amino acid substitutions in GyrA (S83F and D87G) and ParC (T57S and S80R), the detection rate (47.5% [57/120]) in human-derived isolates was higher than that identified in food-related isolates (30.5% [40/131]) (P < 0.01). However, of the 141 isolates possessing amino acid substitutions in GyrA (S83F and D87N) and ParC (T57S and S80R), the detection rate in human isolates (47.5% [57/120]) was lower than that in food-related isolates (64.1% [84/131]) (P < 0.01).The genomes of 251 isolates were screened for known genetic determinants of AMR, including mobile resistance genes and mutations within QRDRs . For mut256\u2009mg/L , while q10.1128/msystems.00253-22.6TABLE\u00a0S3S. enterica serovar Indiana isolates. Download Table\u00a0S3, DOCX file, 0.02 MB.Comparisons of the resistance genes of human and food-related Copyright \u00a9 2022 Du et al.2022Du et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the blaCTX-M subtypes were identified among the 138 ESBL-producing isolates distributed in different provinces, including blaCTX-M-65 , blaCTX-M-14 , blaCTX-M-55 , blaCTX-M-15 , blaCTX-M-27 , and blaCTX-M-123 . The three dominant subtypes blaCTX-M-65/55/14 were detected in human and food-related isolates, while blaCTX-M-15/123 was found only in human isolates. Moreover, the prevalence rate of blaCTX-M-65 among isolates from \u22641-year-old patients (42.6% [20/47]) was significantly higher than that among isolates from other patients (11.1% [8/72]) (P < 0.01), which is in line with the phenotypic characteristics of isolates from these two patient groups. In general, most of the blaCTX-M variants have been detected in humans and chickens.Six mph(A) gene, which is highly associated with azithromycin resistance, had the highest detection rate of 33.5% . The mph(E) (n\u2009=\u20097), msr(E) (n\u2009=\u20097), erm(42) (n\u2009=\u20091), and erm(B) (n\u2009=\u20091) genes were also detected.For macrolides, the 26). The pairwise co-occurrence matrix of AMR genes is shown in arr-3 (conferring resistance to rifamycin), catB3 (conferring resistance to chloramphenicols), aac(6\u2032)-Ib-cr (conferring resistance to aminoglycosides), and blaOXA-1 (conferring resistance to penicillins), which co-occurred in 58.2% of genomes (146/251); the combination of arr-3, catB3, aac(6\u2032)-Ib-cr, and blaOXA-1 occurred with sul1 (sulfonamides) in 50.6% (127/251), aac(3)-Iva (aminoglycosides)/aph(4)-Ia (aminoglycosides)/tet(A) (tetracycline) in 45.8% (115/251), floR (chloramphenicols) in 43.4% (109/251), and sul2 (sulfonamides) in 36.7% (92/251) of genomes. These co-occurring genes were formed into resistance regions comprising IS26 and tet(A), sul1, arr-3, catB3, blaOXA-1, aac(6\u2032)-Ib-cr, aac(3)-Iva, aph(4)-Ia, and sul2 located in ps15D023-IncHI2, ps12177-CTX, pIndS104-CTX, and ps11011-CTX (aph(3\u2033)-Ib, aph(6)-Id, and aadA5 co-occurred in 19.1% (48/251) of genomes; the combination of aph(3\u2033)-Ib, aph(6)-Id, and aadA5 occurred with oqxAB in 14.7% (37/251), fosA in 12.0% (30/251), blaTEM-1 in 11.5% (29/251), and blaCTX-M-65 in 9.2% (23/251) of genomes. These were caused by the resistance region IS26-aph(3\u2033)-Ib-aph(6)-Id-sul2-IS26 co-occurring with other resistance genes. Salmonella genomic island 1 (SGI1), the widely reported original chromosomal integron containing an antibiotic resistance gene cluster and identified in several S. enterica serovars . Download FIG\u00a0S2, TIF file, 0.9 MB.Sequence comparison of IncHI2 plasmids in Copyright \u00a9 2022 Du et al.2022Du et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the blaCTX-M-positive isolates, 90 (65.2%) could be classified by the locations of blaCTX-M in the genome from the fragmented short-read assemblies. blaCTX-M-14 in 14 isolates (42.4% [14/33]) and blaCTX-M-55 from 9 isolates (30.0% [9/30]) were located on the chromosome. blaCTX-M-15 from 9 isolates (100% [9/9]) and blaCTX-M-65 from 58 isolates (96.7% [58/60]) were carried by plasmids. In addition, 76 blaCTX-M-positive isolates were from humans and 62 were food related, accounting for 63% (76/120) and 47% (62/131) of the two groups, respectively. Although the positive ratio of blaCTX-M was significant higher in human isolates (P < 0.05), among the six subtypes, only the positive ratio of blaCTX-M-15 was significant higher in human isolates .Among the 138 blaCTX-M among representative nonclonal isolates from different sources, genome sequences of five isolates were successfully completed. The IndS102 and s15D023 isolates separately carried blaCTX-M-14 and blaCTX-M-55 on their chromosomes within different genetic contexts. Another three isolates carried blaCTX-M on IncHI2 plasmids ranging from 200 to 322 kbp and sharing similar core structures with the specific genetic context IS26-ISEcp1-blaCTX-M-65-IS903B located in an MDR region . BLASTn analysis demonstrated pIndS104-CTX was most similar (99.99% identity at 100% coverage) to a locus on the chromosome of Chinese blaCTX-M-65-positve S. Indiana SI43, obtained from a spiral shell in China in 2010 , indicating pIndS104-CTX may have the ability to recombine with the chromosome entirely or evolve from ancestor clones like SI43. ps11011-CTX was 263,731\u2009bp in size and possessed 783 predicted coding sequences. ps11011-CTX showed high similarity to ps12177-CTX , originating from a human sample from China in 2006, and also to Escherichiacoli plasmids pE648CTX-M-65 and pECJS-B60-267 , as well as Klebsiellapneumoniae plasmid pHNHF1_NDM-99 . ps12177-CTX was 200,106\u2009bp in size (48.61% GC content), and it encoded an MDR region different from that described in ps11011-CTX , which might have resulted from the truncation of ISEcp1 by IS26.Although genetic contexts of by IS26 . ISEcp1 mph(A) was positive in the chicken isolate IndS104 and was located on plasmid pIndS104_3_29k, a typical IncX1 plasmid of size 29,056\u2009bp. It was found to be homologous to six similar plasmids that ranged from 34,764 to 222,492\u2009bp among Salmonella spp. and E. coli, as well as a chromosomal locus in a human S. Indiana isolate SI111 (CP050764) (mph(A)-bearing IncX1 plasmids were hypothetically mobilizable and could move into the chromosome via insertion sequences such as IS26. The typical IS26-mphR(A)-mrx-mph(A)-IS26 transposition unit was embedded in the IncX1 plasmid and other MDR plasmids such as IncHI2 (S. Indiana SI111 chromosome demonstrated a variant of mph(A)-bearing IncX1 plasmid recombined into the SI85 chromosome by IS26 to generate the chromosomal IncX1 segment in SI111 (26 in the transmission of mph(A) among plasmids and chromosomes. Detailed analysis of mph(A)-bearing contigs in the 84\u2009mph(A)-positive isolates showed that the core structure mphR(A)-mrx-mph(A) (n\u2009=\u200984) and seven additional different core structures were prevalent among these isolates (mphR(A)-mrx-mph(A) were not identified because of short fragmented assembled contigs based on Illumina short-read data.Among the five isolates with complete genome sequences, P050764) , which is IncHI2 . Linear in SI111 . This hiisolates . However10.1128/msystems.00253-22.3FIG\u00a0S3mph(A)-harboring S. Indiana isolates. Seven different genetic structures are listed above. The numbers of isolates of the seven types are 1, 1, 6, 1, 11, 63, and 1, respectively. Boxes or arrows represent the ORFs. Red arrows represent the mph(A) gene. Blue arrows indicate mobile elements. mphR(A) and mrx are shown by green arrows. Light gray arrows represent the resistance gene and hypothetical protein. A triangle represents the truncated gene. Download FIG\u00a0S3, TIF file, 1.3 MB.Genetic environment comparison of 84 Copyright \u00a9 2022 Du et al.2022Du et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the S. Indiana emerged within the study period and were transmitted to those enrolled provinces. All 251 isolates harbored the mutations on gyrA and parC associated with the FQ resistance. According to core-genome-based phylogenies, we divided them into six lineages : lineage 1 included seven isolates with D87G in GyrA and T57S in ParC, lineage 2 included two isolates with S83F in GyrA and T57S in ParC, and lineage 3 included four isolates with S83F in GyrA and T57S and S80R in ParC. The other three later lineages with 4- amino acid substitutions were the dominant groups. Lineage 4 (n\u2009=\u200949) and lineage 5 (n\u2009=\u200948) had S83F and D87G in GyrA and T57S and S80R in ParC, while lineage 6 (n\u2009=\u2009141) had S83F and D87N in GyrA and T57S and S80R in ParC, which was the most common lineage (141/251 [56.2%]). Moreover, in the early stages of quinolone resistance evolution, most of the isolates with double-amino-acid substitutions in GyrA (D87G [lineage 1] or D87F [lineage 2]) and ParC (T57S) were susceptible to ciprofloxacin, except in two isolates that also carried PMQR genes (oqxAB and qnrS1), and the isolates from lineage 3 with three amino acid substitutions in GyrA (S83F) and ParC (T57S and S80R) exhibited low MIC values of ciprofloxacin , 76.7% (23/30), and 70% (42/60) of the isolates harboring each genotype, respectively (mph(A) appeared most frequently in lineage 6 (88.1% [74/84]), followed by lineage 5 (9.5% [8/84]), and only occurred once in lineage 2 and lineage 3, respectively. Furthermore, co-occurrence of mph(A) with diverse ESBL genes was observed . Both IncN and IncX1 replicons were dominantly distributed in lineage 6, with prevalence of 75.3% (55/73) and 98.5% (64/65). Based on the complete genome sequences of IndS104, mph(A) was located in an IncX1 plasmid. In addition, among the 251 isolates, mph(A) and IncX1 were both detected in 55 isolates belonging to lineage 6, and both were negative in 157 isolates. The distribution of mph(A) and IncX1 displayed a significant correlation with a calculated coefficient of 0.64 . The isolates carrying IncX1 plasmids might be more likely to carry mph(A) .Based on the 2,904 core genome single nucleotide polymorphisms (SNPs) obtained from 251 genomes, we performed phylogenic analysis and displayed the phylogenetic relationships of sequenced isolates . Multipllineages , which ifloxacin . In contfloxacin . Of noteectively . MoreoveSalmonella have changed significantly in recent years as MDR Salmonella strains have become prevalent among various serovars, such as S. 1,4,[5],12:i:\u2212, S. Kentucky, and S. enterica serovar London -Ib-cr was the dominant genotype, with the carriage rate increasing from 20% in 2006 to 65% in 2017 of the ciprofloxacin-resistant Salmonella strains of various serovars, the oqxAB and aac(6\u2032)-Ib-cr combination was the predominant one in our study, which was located in the IncHI2 plasmid. This gene combination was also located in a nonconjugative plasmid, pCFSA244-1, mainly transmitted among S. Typhimurium isolates, and qnrS2-aac(6\u2032)-lb-cr-oqxAB elements were also found on the chromosome in S. enterica serovar Derby (oqxAB-aac(6\u2032)-Ib-cr-bearing IncHI2 plasmid found in S. Indiana was mobilizable by conjugation . Furtherservoirs . Since 2servoirs . Our who E. coli . Recent E. coli . It has strains . This mijugation . The hig studies . This mi studies .S. Indiana, contributing to their cefotaxime resistance phenotypes variant of blaCTX-M-15, blaCTX-M-55, possessing enhanced cephalosporin-hydrolyzing activity, was both prevalent in both isolates from humans and those from food-related samples, particularly in lineage 6, indicating potential higher adaptability of blaCTX-M-55. IncHI2 plasmids were typical MDR plasmids positive for blaCTX-M, mcr-1, class 1 integrons, and oqxAB, similar to those found in other Enterobacteriaceae . Most blaCTX-M-55 genes in S. Indiana are located on the chromosome, which is different from its plasmid origin in other serovars, such as S.enterica serovars Enteritidis, Goldcoast, Typhimurium, and Choleraesuis . FurtherE. coli) , 41. Furplasmids . The blaosporins . The occeraesuis \u201346.S. Indiana isolates harboring the plasmid-borne mph(A), mph(E), erm(42), and erm(B) genes. Moreover, in the present study, 24% of isolates were coresistant to azithromycin, ciprofloxacin, and cefotaxime, which is considerably higher than the levels reported in a Chinese national surveillance study (0.2%) from 2005 to 2011 (mph(A) and mph(E), raising concern about the spread of resistance among bacteria (mph(A)-positive isolates were mostly grouped into lineages 5 and 6 coexisting with diverse ESBL genes. This feature is highly related to the IncX plasmid, which has played an important role in the spreading of resistance genes, such as blaNDM (IncX3) and mcr-1 (IncX4 and IncX2) (\u2013Macrolide (azithromycin) resistance was determined in 36.3% 91/251) of to 2011 and a Ch to 2011 . In the bacteria . In our d IncX2) \u201351. More of to 2 IncX2) \u2013.Salmonella. The high prevalence of IncHI2 plasmids in S. Indiana is similar to that reported for S. Typhimurium and food collected previously by the National Health Commission Key Laboratory of Food Safety Risk Assessment from four provinces in China during 2006 to 2016. In total, isolates from eight provinces were included. Clinical fecal samples were enriched in selenite brilliant green sulfa enrichment broth for 18 h at 37\u2009\u00b1\u20091\u00b0C, and anatomical site samples were enriched on blood agar plates for 18 h at 37\u2009\u00b1\u20091\u00b0C. Clinical sample isolates were purified as described previously , along with amplification of the invA gene by PCR. All isolates were identified to the serogroup level and then serotyped by slide agglutination with commercial Salmonella antisera following the Kauffmann-White scheme at the National Health Commission Key Laboratory of Food Safety Risk Assessment in Beijing, China.A total of 251 confirmed eviously . S. enteuidebook . The isoS. Indiana isolates was performed by the agar dilution method and interpreted according to 2018 Clinical and Laboratory Standards Institute (CLSI) guidelines (https://eucast.org/). The antimicrobial susceptibilities of the following antimicrobials were assessed: ampicillin (AMP), cefotaxime (CTX), cefotaxime-clavulanic acid (CTX-CLA), chloramphenicol (CHL), ciprofloxacin (CIP), nalidixic acid (NAL), gentamicin (GEN), streptomycin (STR), imipenem (IPM), meropenem (MEM), tetracycline (TET), azithromycin (AZM), sulfonamide (SUL), and colistin (CT). The MICs were calculated. Multidrug resistance was defined as resistance to three or more classes of antimicrobials. Escherichia coli ATCC 25922 and Klebsiella pneumoniae ATCC 700603 were used as the quality control strains.Antimicrobial susceptibility testing (AST) of the idelines and the in silico multilocus sequence typing (MLST) scheme was used to subtype the isolates using BLASTn and seven housekeeping genes: aroC, dnaN, hemD, hisD, purE, sucA, and thrA and then sequenced using an Illumina HiSeq 2500 platform to generate 150-bp paired-end reads from a library with an average insert size of 500 bp. Raw reads were filtered to remove low-quality reads by fastQC and then62\u2013and thrA .blaCTX-M were determined after whole-genome sequence analysis. blaCTX-M-containing contigs were examined for plasmid Inc types using PlasmidFinder was used as the reference in phylogenetic analysis. Illumina reads were mapped to the reference genome using Bowtie 2 v2.2.8, with single nucleotide polymorphisms (SNPs) identified using Samtools v1.9, and the data were combined as described previously . Multiple alignments of core genomes identified from the pairwise alignments with S. Indiana D90 were used as the input for Gubbins to detect and remove recombination sites (The complete genome sequence of eviously . The higon sites . Phylogeon sites and seleon sites . The conon sites . The phyon sites .PRJNA850394.The genome sequences in this study were deposited into the National Center for Biotechnology Information database under BioProject accession no."} +{"text": "Based on the pharmacokinetic-pharmacodynamic (PK-PD) breakpoints, cefepime-zidebactam inhibited 98.5% of Enterobacterales and 98.9% of Pseudomonas aeruginosa isolates, respectively. Against carbapenem-resistant and difficult-to-treat resistant Gram-negative bacilli, cefepime-zidebactam demonstrated better activity against Enterobacterales and P. aeruginosa . Among the 379 carbapenem-resistant Enterobacterales isolates, the most common carbapenemase genes detected were blaKPC-2 (64.1%) and blaNDM (30.9%). Cefepime-zidebactam showed an MIC90 of \u22642\u2009mg/L for 98.8% of blaKPC-positive isolates and 89.7% of blaNDM-positive isolates. Ceftazidime-avibactam also showed efficient in vitro activity against Enterobacterales (93.6%) and P. aeruginosa (87.7%). Ceftazidime-avibactam was active against 97.5% of blaKPC-positive isolates and 100% of blaOXA-232-positive isolates. Cefepime-zidebactam inhibited 97.3% of Acinetobacter baumannii isolates with an MIC50/90 of 16/32\u2009mg/L. Our study systematically evaluated the in vitro activities of these new BLBLIs against a variety of Gram-negative bacilli, provided preclinical data for the approval of these BLBLIs in China, and supported cefepime-zidebactam and ceftazidime-avibactam as potential efficient therapies for infections caused by carbapenem-resistant Enterobacterales (CRE), carbapenem-resistant P. aeruginosa (CRPA), and DTR isolates.Novel \u03b2-lactam\u2013\u03b2-lactamase inhibitor combinations (BLBLIs) are in clinical development for the treatment of infections caused by carbapenem-resistant and difficult-to-treat resistant (DTR) Gram-negative bacilli. This study evaluated the IMPORTANCEEnterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii are the most common Gram-negative bacilli to cause nosocomial infections throughout the world. Due to their large public health and societal implications, carbapenem-resistant A. baumannii (CRAB), carbapenem-resistant P. aeruginosa (CRPA), and carbapenem-resistant and third-generation-cephalosporin-resistant Enterobacteriaceae were regarded by the World Health Organization (WHO) as a global priority for investment in new drugs in 2017. The present study showed the potent in vitro activity of these novel BLBLIs and other comparators against Gram-negative bacillus isolates, including carbapenem-resistant or difficult-to-treat resistant phenotypes. Polymyxins, tigecycline, and ceftazidime-avibactam (except for blaNDM-positive isolates) were available for the treatment of infections caused by CRE isolates. Currently, cefepime-zidebactam and other BLBLIs have not yet been approved for use in China. Here, our study aimed to evaluate the in vitro activities of BLBLIs against Gram-negative bacillus isolates, especially CRE, before clinical use. Carbapenem-resistant Gram-negative bacilli have rapidly increased worldwide in the last decade, which is related to the emergence and prevalence of plasmid-mediated extended-spectrum \u03b2-lactamases (ESBLs), AmpC cephalosporinases, and carbapenemases among these isolates, conferring resistance to \u03b2-lactam antibiotics, and make difficulties in empirical treatment for clinicians were carbapenem-resistant Enterobacterales (CRE), including K. pneumoniae , E. coli , and Enterobacter cloacae .Among the tested P. aeruginosa (CRPA) and carbapenem-resistant A. baumannii (CRAB), respectively, and 11.9% of Enterobacterales isolates and 8.6% (65/756) of P. aeruginosa isolates were difficult-to-treat resistant (DTR) isolates.For glucose-nonfermenting bacteria, 228/756 (30.2%) and 471/630 (74.8%) were carbapenem-resistant in vitro activities of cefepime-zidebactam, ceftazidime-avibactam, cefepime-tazobactam, ceftolozane-tazobactam, and other comparator agents against 4,042 clinical isolates are summarized in Tables 1Enterobacterales isolates with an MIC50/90 of 0.06/1\u2009mg/L. A total of 98.5% of isolates were inhibited at the provisional cefepime-zidebactam pharmacokinetic-pharmacodynamic (PK-PD) breakpoint (\u22648\u2009mg/L), with 24 E. coli, 4 K. pneumoniae, 7 Proteus rettgeri, 3 P. mirabilis, 1 E. cloacae, and 1 Serratia marcescens isolates showing MICs of \u226516\u2009mg/L among the various genera of Enterobacterales. Besides cefepime-zidebactam, ceftazidime-avibactam was also active against all Enterobacterales clinical isolates with an MIC50/90 of 0.25/4\u2009mg/L. Among 171 ceftazidime-avibactam-resistant isolates, cefepime-zidebactam showed an MIC of 8\u2009mg/L or lower against 84.1% of the tested isolates (data not shown). Apart from cefepime-zidebactam and ceftazidime-avibactam, tigecycline (96.5% susceptible) and amikacin (90.4% susceptible) also displayed potent activity against Enterobacterales. The rate of susceptibility to cefepime-tazobactam was 85.8%, similar to those for polymyxin B (81.4% susceptible) and meropenem (85.6% susceptible), which showed good activity against the tested isolates. More than 60% of the Enterobacterales isolates were susceptible to ceftolozane-tazobactam (74.2% susceptible), imipenem (74.6% susceptible), piperacillin-tazobactam (75.5% susceptible), cefoperazone-sulbactam (69.8% susceptible), and ceftazidime (60.5% susceptible). The following other comparator agents showed limited activity: cefepime (55.3% susceptible), ceftriaxone (46.1% susceptible), aztreonam (54.7% susceptible), ciprofloxacin (42.1% susceptible), levofloxacin (48.1% susceptible), and trimethoprim-sulfamethoxazole (53.7% susceptible) (The eptible) .P. aeruginosa were highly inhibited by cefepime-zidebactam with an MIC50/90 of 2/8\u2009mg/L at a PK-PD breakpoint of \u226432\u2009mg/L (98.9% susceptible). The rate of susceptibility of P. aeruginosa to cefepime-zidebactam was similar to or slightly higher than those for ceftazidime-avibactam (87.7% susceptible), ceftolozane-tazobactam (90.2% susceptible), polymyxin B (95.6% susceptible), and amikacin (95.4% susceptible) . The rat50/90 value of cefepime-zidebactam against 630 A. baumannii isolates was 16/32\u2009mg/L , blaNDM-positive (n\u2009=\u2009117), blaIMP-positive (n\u2009=\u20098), blaOXA-232-positive (n\u2009=\u20097), blaVIM-positive (n\u2009=\u20091), as well as carbapenemase-negative (n\u2009=\u20093) isolates and polymyxin B (98.2% versus 96.9%), whereas the rates of susceptibility were 76.3% for ceftolozane-tazobactam and 68% for ceftazidime-avibactam as the most active comparators. Except for imipenem and meropenem, CRPA isolates were moderately resistant to other \u03b2-lactams, aztreonam, and fluoroquinolones, with susceptibility rates of 30% to 50%.90 values of >32\u2009mg/L.For CRAB, cefepime-zidebactam, tigecycline, and polymyxin B showed high susceptibility rates of 96.6%, 88.5%, and 96.6%, respectively, and amikacin and trimethoprim-sulfamethoxazole showed limited activity, with susceptibility rates of 18.7% and 23.1%, respectively. The MICs of other agents were higher, with MICEnterobacterales isolates with an MIC50/90 of 1/4\u2009mg/L at \u22648\u2009mg/L, and 74.7% of DTR Enterobacterales isolates were susceptible to ceftazidime-avibactam with an MIC50/90 of 2/>64\u2009mg/L. Only tigecycline (95.9% susceptible) and polymyxin B (92.4% susceptible) displayed greater in vitro activity than cefepime-zidebactam and ceftazidime-avibactam against all DTR Enterobacterales isolates demonstrated greater in vitro activity than the above-described agents against DTR P. aeruginosa isolates were blaNDM-5 positive, 12.4% (47/379) were blaNDM-1 positive, 2.1% (8/379) were blaIMP positive, 1.8% (7/379) were blaOXA-232 positive, and 0.3% (1/379) were blaVIM positive, respectively. Additionally, blaKPC-2 was mainly detected in K. pneumoniae , S. marcescens , Citrobacter freundii , and Morganella morganii . The highest prevalences of blaNDM-5 were 82.5% (33/40) in E. coli and 55.6% (5/9) in Klebsiella aerogenes isolates. blaNDM-1 was the predominant type of carbapenemase gene among E. cloacae and P. rettgeri isolates.In this study, 99.2% (376/379) of the CRE isolates had a single carbapenemase gene, and only 3 isolates were negative for all five common carbapenemase genes . Among tP. aeruginosa, and A. baumannii, which has substantially increased morbidity and mortality rates and caused nosocomial outbreaks , European Committee on Antimicrobial Susceptibility Testing (EUCAST), or U.S. Food and Drug Administration (FDA) clinical breakpoints of cefepime-zidebactam, so according to its PK-PD breakpoint (\u226432\u2009mg/L), P. aeruginosa had a rate of susceptibility to cefepime-zidebactam of 99.6%, whereas it was 98.9% in our study. The potent activity of cefepime-zidebactam against CRE, P. aeruginosa, and A. baumannii isolates harboring carbapenemase genes has been previously reported. In another study of a worldwide surveillance program, Sader et al. (n\u2009=\u2009153) had cefepime-zidebactam MICs of \u22648\u2009mg/L, similar to the results of this study (98.5%).In this study, 98.5% of \u226432\u2009mg/L , respect\u226432\u2009mg/L , the autr et al. reportedE. coli, 0.6% to 1.0% for Enterobacter spp., 0.6% to 3.0% for Klebsiella spp., and 8.4% for P. aeruginosa (data not shown). In our study, we observed slightly higher DTR rates of 1.2% for E. coli, 0.04% to 0.5% for Enterobacter spp., 9.3% for Klebsiella spp., and 8.6% for P. aeruginosa. The differences in DTR rates between the 2 studies may reflect the characteristics of the strains among different regions and different specimen sources. Kadri et al. reported that mortality was significantly higher for DTR than for carbapenem-resistant, extended-spectrum-cephalosporin-resistant, or fluoroquinolone-resistant infections (96% to 98.2%) and DTR isolates (96.9% to 97.2%).The DTR phenotype, a novel category in the study of Gram-negative bacteremia, focuses on treatment-limiting resistance to all first-line agents. The DTR phenotype was defined as an isolate that tests not susceptible (intermediate or resistant) to all \u03b2-lactam categories, including carbapenems and fluoroquinolones, and it was demonstrated that isolates that were not susceptible to first-line agents were associated with increased patient mortality and clinical failure. Karlowsky et al. studied fections . The in blaKPC- or blaOXA-48-positive isolates. blaKPC-positive isolates showed a low rate of resistance to ceftazidime-avibactam (2.5%), but the majority (87.5% to 100%) of blaNDM-positive isolates were resistant to ceftazidime-avibactam. The major resistance mechanisms that confer reduced susceptibility to ceftazidime-avibactam are as follows: the production of metallo-\u03b2-lactamases (MBLs) such as NDM, VIM, or IMP; blaKPC variants; and the transposition of KPC with porin deficiency and P. aeruginosa isolates producing important \u03b2-lactamases, including MBLs (except for ceftazidime-avibactam), KPCs, and OXA-232, for which treatment agents are limited. The results from this study support the use of cefepime-zidebactam and ceftazidime-avibactam as potential therapies for infections caused by CRE, CRPA, and DTR isolates.We studied a recent nationwide collection of Gram-negative bacilli and observed that new BLBLIs, especially cefepime-zidebactam and ceftazidime-avibactam, demonstrated potent The study protocol was approved by the Institutional Review Board of Huashan Hospital, Fudan University (no. 2019-460).Klebsiella pneumoniae (n = 979), Escherichia coli (n = 900), P. aeruginosa (n = 756), A. baumannii (n = 630), Enterobacter cloacae (n = 172), Proteus mirabilis (n = 119), Serratia marcescens (n = 118), K. aerogenes (n = 103), Morganella morganii (n = 89), Citrobacter freundii (n = 84), Proteus vulgaris (n = 51), Proteus rettgeri (n = 29), and Klebsiella oxytoca (n = 12). Among the tested clinical isolates, 23.6% of the isolates were isolated from patients in the intensive care unit, followed by outpatient and emergency departments (18.5%), urology surgery (6.7%), respiratory medicine (5.6%), neurosurgery departments (4.2%), and other departments. A total of 33.9% of the tested isolates were isolated from sputum, followed by urine (22.5%), blood , secreta (7.7%), bronchoalveolar lavage fluid (3.9%), pus (2.8%), wound (2.7%), abdominal fluid (2.0%), bile (1.7%), shunt fluid (1.3%), drain (1.2%), and other sources (8.2%). Species identification was performed at each participating site and confirmed by the central laboratory using matrix-assisted laser desorption ionization\u2013time of flight mass spectrometry . Quality control was performed according to Clinical and Laboratory Standards Institute (CLSI) guidelines using E. coli ATCC 25922 and ATCC 35218, K. pneumoniae ATCC 700603, and P. aeruginosa ATCC 27853 for antimicrobial susceptibility testing.The China Antimicrobial Surveillance Network (CHINET) is a multicenter bacterial resistance surveillance program in operation since 2005 in China. In 2019, 46 hospitals in 28 provinces or cities collected up to 4,042 nonduplicate, clinically significant Gram-negative isolates from CHINET, including Enterobacterales . Cefepime-tazobactam MICs were interpreted using provisional breakpoints of \u226416\u2009mg/L for Enterobacterales and P. aeruginosa based on PK-PD studies in the study. Quality control and test results were interpreted according to 2021 CLSI breakpoints . Difficult-to-treat resistance phenotypes were defined by testing resistance to all tested \u03b2-lactams (including carbapenems and \u03b2-lactamase inhibitor combinations) and fluoroquinolones .Enterobacterales (CRE) isolates were selected for analysis of carbapenemase. The five most common carbapenemase genes were confirmed for all of the CRE isolates by PCR with specific primers and DNA sequencing, as described previously (Carbapenem-resistant eviously ."} +{"text": "Deutereulophus Schulz, D.felixsp. nov. and D.daguisiensissp. nov., are described from China. A key to species of Deutereulophus known from China is provided.Two new species of Deutereulophus Schulz is one of several small genera of the tribe Eulophini, subfamily Eulophinae (Hymenoptera: Eulophidae). Species of the genus are distributed in all zoogeographic regions, except for the Afrotropical region. Currently Deutereulophus contains 23 valid species (D.froudei (Girault), D.interruptus Zhu & Huang, D.marginatus Zhu & Huang, and D.tennysoni (Girault) , 2002b.Deutereulophus (as Entedonomorpha Girault) was subdivided into two species groups by tennysoni-group and provides a key to all species occurring in China.The genus All specimens were collected by sweeping or yellow-pan trapping, and were dissected and mounted in Canada balsam on slides following the method of Terminology follows the F1\u20133 flagellomeres 1\u20133;MV marginal vein;OOL minimum distance between a posterior ocellus and corresponding eye margin;PMV postmarginal vein;POL minimum distance between posterior ocelli;SMV submarginal vein;STV stigmal vein.NEFU), Harbin, China.All type material is deposited in the insect collections at Northeast Forestry University : SMV = 36; MV = 36; PMV = 12; STV = 16.ing Fig. 2.1\u00d7 as Metasoma .felix, meaning lucky.Named after the Latin adjective Deutereulophusmarginatus, and can be separated using the key given above.The new species is similar to Taxon classificationAnimaliaHymenopteraEulophidae\ufeff08C5DC71-9949-5063-A04A-0D42C97F314Ahttps://zoobank.org/02F37BE0-42A2-4F4D-B908-7AF3845F0280Holotype, \u2640 , China, Hubei Province, Suizhou City, Daguisi National Forest Park, 12. VI. 2012, Guo-Hao Zu and Jiang Liu, by sweeping. Paratypes: 1\u2640 [on slide], same data as holotype.Head and mesosoma black. Vertex with scattered pits. Antennal scrobes smooth. Antenna yellowish-white with F3 dark brown, clava dark brown with apex yellowish-white. Female funicle 3-segmented, clava 4-segmented. Legs yellowish-white with procoxa and profemur dark brown. Face with raised reticulation. Metasoma dark brown. Mesoscutum strongly reticulate with large meshes. Sublateral grooves on mesoscutellum converging and meeting posteriorly. Propodeum with a raised triangular cup-shaped area anteromedially, median carina split and diverging posteriorly.Female. Length 2.4 mm, fore wing length 1.7 mm. Head and mesosoma black. Eyes gray. Ocelli pale yellow. Antenna yellowish-white with F3 dark brown, clava dark brown with apex yellowish-white. Mandibles dark brown. Petiole black. Metasoma dark brown. Legs yellowish-white with procoxa and profemur dark brown. Wings hyaline with veins brown.Head : SMV = 29; MV = 32; PMV = 12; STV = 10.ing Fig. 2.4\u00d7 as Metasoma .Named after the type locality, the Daguisi National Forest Park in Hubei Province.D.malabarensis Narendran, but can be separated from it by the following combination of characters: antenna yellowish-white with F3 dark brown, clava dark brown with apex yellowish-white ; sublateral grooves on mesoscutellum converging and meeting posteriorly ; propodeum with a raised triangular cup-shaped area anteromedially .The new species is similar to"} +{"text": "Among current e-cigarette users, 14.5% reported that the brand they usually used was Puff Bar, followed by Vuse (12.5%), Hyde (5.5%), and SMOK (4.0%). Approximately one fifth (21.8%) of current e-cigarette users reported \u201csome other brand\u201d as their usual brand.https://stacks.cdc.gov/view/cdc/121630). Among current users of flavored pods or cartridges, the reported flavor types used were fruit (58.4%); menthol (53.9%); candy, desserts, or other sweets (30.3%); and mint (27.6%). Among current users of flavored tanks or mod systems, the reported flavor types used were fruit (69.6%); candy, desserts, or other sweets (47.7%); mint (40.1%); and menthol (35.2%).Among current e-cigarette users overall, 84.9% used flavored e-cigarettes; of these, the reported flavor types, in descending order of use, were fruit (69.1%); candy, desserts, or other sweets (38.3%); mint (29.4%); and menthol (26.6%). A similar pattern was observed among current users of flavored disposable e-cigarettes: fruit (75.2%); candy, desserts, or other sweets (40.4%); mint (29.6%); and menthol (16.7%) (Supplementary Table, In 2022, 2.55 million U.S. middle and high school students currently used e-cigarettes. Most reported using flavored products, and, among those students, approximately seven of 10 used fruit flavors. Disposable products were the most commonly reported device type. Further, among middle and high school students who used e-cigarettes, approximately four in 10 reported frequent use, and approximately one in four reported daily use. The use of tobacco products in any form, including e-cigarettes, by middle and high school students is unsafe. Sustained implementation of comprehensive tobacco prevention and control strategies at the national, state, and local levels,"} +{"text": "We present a comprehensive data set that describes an anaerobic microbial consortium native to polychlorinated biphenyl (PCB)-contaminated sediments. Obtained from sediment microcosms incubated for 200\u2009days, the data set includes 4 metagenomes, 4 metatranscriptomes (in duplicate), and 62 metagenome-assembled genomes and captures microbial community interactions, structure, and function relevant to anaerobic PCB biodegradation. P < 0.0001).Polychlorinated biphenyl (PCB)-contaminated sediments threaten human and ecological health but often harbor PCB-transforming bacteria that help detoxify sediments \u20133. We es\u2013After 200\u2009days of incubation, DNA was extracted from single slurry samples (2\u2009mL) with a modified DNeasy PowerWater Sterivex kit protocol , and RNAMethanosarcina barkeri (GenBank accession number NZ_CP009530.1) and Methanobacterium subterraneum (GenBank accession number NZ_CP017768.1) were added to further deplete methanogenic archaeal rRNA sequences. RNA was sequenced on a single Illumina NovaSeq 6000 flow cell lane (2 \u00d7 150-bp paired-end reads).High-throughput DNA and RNA sequencing (4 metagenomes and 4 metatranscriptomes in duplicate) was performed at the Iowa Institute of Human Genetics (IIHG) . Indexed DNA libraries, prepared with the KAPA HyperPrep kit using sheared DNA , were pooled and sequenced on separate lanes of an S Prime NovaSeq 6000 flow cell (2 \u00d7 150-bp paired-end reads). RNA libraries were indexed and rRNA depleted with the stranded total RNA preparation with Ribo-Zero Plus kit . To improve mRNA sequencing efficiency, supplemental rRNA probes developed from Metagenome sequencing yielded 97,279,994 (E2_1), 105,614,978 (E2_2), 102,655,932 (F4_1), and 103,672, 591 (F4_2) raw reads from each bottle. Metatranscriptome sequencing (RNA-seq) yielded 50,403,972 (E2_1 metatranscriptome-A), 60,356,358 (E2_1-B), 49,353,924 (E2_2-A), 45,023,913 (E2_2-B), 54,860,340 (F4_1-A), 47,603,523 (F4_1-B), 55,440,491 (F4_2-B), and 71,530,818 (F4_2-C) raw reads. After trimming and filtering of unassembled sequence reads with Trimmomatic (v0.39) .Dehalococcoides mccartyi) (Metagenome-assembled genomes (MAGs) were obtained by removing low-abundance k-mers from quality-filtered reads with khmer (v3.0.0) , coassem12\u2013ccartyi) , which wccartyi) , is expePRJNA743546. Metagenomic data are available under SRA accession numbers SRX11347095 to SRX11347098. Metatranscriptomic data are available under accession numbers SRX14430540 to SRX14430547. PCB data are available at Iowa Research Online (https://www.doi.org/10.25820/data.006156).Raw data files (24 fastq files) and MAGs are available under BioProject accession number"} +{"text": "Actinomyces oris strain K20 was isolated from oral apical lesions. Here, we report the complete circular genome sequence of this strain, obtained by means of hybrid assembly using two next-generation sequencing datasets. The strain has a 3.1-Mb genome with 2,636 coding sequences. Actinomyces are ubiquitous in soil as well as human and animal microbiota using NanoFilt v.2.3.0 , following the manufacturer\u2019s standard protocol. Paired-end (2\u2009\u00d7\u2009156-bp) reads were obtained using a MiSeq instrument (Illumina). The raw sequencing data were processed using the FASTQ preprocessing program fastp v.0.19.5 (The strain was cultured overnight in heart infusion broth (BD Difco) at 37\u00b0C under aerobic conditions. Genomic DNA (gDNA) was extracted from the culture medium of this strain using the MagAttract high-molecular-weight (HMW) DNA kit . The obtained gDNA was subjected to long- and short-read sequencing. Long-read sequencing was performed using the GridION X5 sequencing platform ; 1.0\u2009\u03bcg unfragmented gDNA was used for library construction using a ligation sequencing kit SQK-LSK109; ONT). The prepared library was applied to an R9.4.1 flow cell . The base calling of long-read sequences using Dogfish v.0.9.6-3 generated 114,245 reads (1.1\u2009Gb), with an ; ONT. Thde novo genome assembly, the remaining long- and short-read data were processed using the Unicycler v.0.4.4 pipeline (https://dfast.ddbj.nig.ac.jp/), predicted 2,636 coding sequences, 9 rRNA genes, and 52 tRNA genes.For complete pipeline . Assemblpipeline . BlobToopipeline was usedpipeline until nopipeline , provideA. oris strain K20 has been deposited at DDBJ/EMBL/GenBank under the accession number AP025590. The associated BioProject and BioSample accession numbers are PRJDB13022 and SAMD00442649, respectively. The SRA accession numbers are DRR351395 (Illumina) and DRR351396 (Nanopore).The complete genome sequence of"} +{"text": "We found that tricalcium phosphate-solubilizing bacteria, phytate-degrading bacteria, and gcd and bpp abundances were more abundant in silt plus clay than in macroaggregate (250 to 2000\u2009\u03bcm) and microaggregate (53 to 250\u2009\u03bcm). Fertilization treatment and aggregate fractionation showed distinct effects on PSB number and P-cycling-related gene abundance. We found significantly negative correlation between gcd gene abundance and tricalcium phosphate-solubilizing bacterial number (Col-CaP) and dramatically positive correlation between bpp gene abundance and phytate-degrading bacterial number (Col-Phy). P fractions were responsible for PSB number and P-cycling-related gene abundance. The isolated Pseudomonas sp. strain PSB-2 and Arthrobacter sp. strain PSB-5 exhibited good performances for solubilizing tricalcium phosphate. The inoculation of Pseudomonas sp. PSB-2 could significantly enhance plant fresh weight, plant dry weight, and plant height. Our results emphasized distinct distribution characteristics of PSB and P-cycling-related genes in soil aggregates and deciphered a close linkage between PSB number and P-cycling-related gene abundance. Our findings might guide the isolation of PSB from agricultural soils and provide a candidate plant-growth-promoting bacterium for agro-ecosystems.Deciphering distribution patterns of phosphate-solubilizing bacteria (PSB) and phosphorus-cycling-related genes in soils is important to evaluate phosphorus (P) transformation. However, the linkage between PSB number and P-cycling-related gene abundance in soils, especially soil aggregates, remains largely unknown. Here, we estimated the numbers of PSB and abundances of P-cycling-related genes (i.e., IMPORTANCE Phosphate-solubilizing bacteria are responsible for inorganic P solubilization and organic P mineralization. Elucidating the linkage between phosphate-solubilizing bacterial number and P-cycling-related gene abundance is important to isolate plant-growth-promoting bacteria for agro-ecosystems. Our findings reveal differentiating strategies of phosphate-solubilizing bacteria in soil aggregates, and the deciphered P fractions show strong effects on distribution patterns of phosphate-solubilizing bacteria and P-cycling-related genes. Additionally, we isolated phosphate-solubilizing bacteria with good plant-growth-promoting ability. This study enriches our knowledge of P cycling in soil aggregates and might guide the production and management of farmland. Prenic acid . In contnic acid , 14. Phynic acid , 15. Phyin soils . ConsequAcinetobacter, Citrobacter, Massilia, and Pseudomonas) (21\u2013Bacillus) , 21\u201324, acillus) . For insosum L.) . Consequosum L.) , 25, 26.gcd and bpp), (ii) estimate abiotic and biotic factors on numbers of PSB, and (iii) decipher the performance of PSB for promoting plant growth. Considering that P availability affects the abundances of P-cycling-related genes circulation , 27 and 3\u201313\u2013ed genes , 30, we ed genes , 17, 31,5 to 8.77\u2009\u00d7\u2009108 CFU/g soil) was significantly higher in NPK and N fertilization treatments than that in CK (control without fertilizer), M (swine manure), and MN (combined swine manure and N fertilizer) fertilization treatments (P\u2009<\u20090.05). The phytate-degrading bacterial number (Col-Phy) (4.0\u2009\u00d7\u2009104 to 3.27\u2009\u00d7\u2009108 CFU/g soil) was remarkably higher in N and MN fertilization treatments than that in CK, M, and NPK fertilization treatments (P\u2009<\u20090.05). In five fertilization treatments, the Col-CaP and Col-Phy were basically slightly higher in silt+clay than that in macroaggregate and microaggregate rather than aggregate fractionation showed a significant effect on PSB number (Col-CaP and Col-Phy) (P\u2009<\u20090.05) but the opposite for MN fertilization treatment (P\u2009<\u20090.05). Col-CaP was slightly higher than Col-Phy in the same soil aggregate with N fertilization treatment (P\u2009>\u20090.05). These results indicated different distribution patterns of PSB in soil aggregates with different fertilization treatments.The numbers of PSB represented by CFU varied in different soil aggregates . The triCol-Phy) . Additiogcd gene (4.32\u2009\u00d7\u2009106 to 2.20\u2009\u00d7\u2009107 copies/g soil) was more abundant in M and MN fertilization treatments than in other fertilization treatments (P\u2009<\u20090.05), whereas the bpp gene (1.99\u2009\u00d7\u2009105 to 3.42\u2009\u00d7\u2009106 copies/g soil) showed no significant difference among five fertilization treatments (P\u2009>\u20090.05). Basically, gcd and bpp were more abundant in silt+clay than in macroaggregate and microaggregate with the same fertilization treatment and aggregate fractionation showed significant effects on abundances of P-cycling-related genes (gcd-harboring bacteria were significantly higher than that of bpp-harboring bacteria in the same soil aggregate with the same fertilization treatment (P\u2009<\u20090.01). These results reflected that fertilization treatment and aggregate fractionation might influence the distribution and abundance of gcd-harboring bacteria and bpp-harboring bacteria.The abundances of P-cycling-related genes varied in different soil aggregates . The gcdreatment . Consequed genes . In addigcd gene abundance was significantly negatively correlated with Col-CaP (P\u2009<\u20090.05 or P\u2009<\u20090.01 or P\u2009<\u20090.001), whereas only OP was significantly correlated with Col-Phy (P\u2009<\u20090.05). Similarly, nonphosphorus nutrients and P fractions were significantly positively correlated with both gcd and bpp gene abundances (P\u2009<\u20090.05 or P\u2009<\u20090.01 or P\u2009<\u20090.001) (Linear regressions reflected that and bpp) . Nonphos<\u20090.001) . Accordi<\u20090.001) . Additiogcd abundance, bpp abundance, Col-CaP, and Col-Phy . Additionally, soil TC and P fractions, rather than gcd abundance, showed strong indirect and direct effects on Col-CaP, respectively were identified as Bacillus, Pseudomonas, Massilia, Citrobacter, Arthrobacter, and Acinetobacter genera according to a phylogenetic tree based on 16S rRNA gene sequences and soluble P levels of PSB-2 cultured in liquid National Botanical Research Institutes phosphate growth medium (NBRIP) media were significantly higher than that for PSB-5 at the same period , and growth tended to be stable after day 5 (P\u2009>\u20090.05). The soluble P levels of PSB-5 displayed a fast increase during 5\u2009days and presented slight fluctuation after day 5. In contrast, soluble P levels of PSB-2 exhibited significantly fast increases during 8\u2009days affect abundances of P-cycling-related genes \u20138, 34. Fcd genes . The abuicient P , 39, 40.icient P and difficient P . Additioicient P . These ricient P , 43, 44,icient P , 14, 15.icient P . This phicient P .bpp gene abundance and phytate-degrading bacterial number, which is expected, and this might be because phytate is a relatively stable compound , 16, 47.rganisms , 34, whirganisms . Organicsing CO2 , which fironment , 41, 50.ironment . Consequ studies , 42; to Pseudomonas sp. PSB-2 exhibited good performance for P-solubilizing, and the best P-solubilizing level was 59.98\u2009mg/L. The solubilizing capacity for Ca3(PO4)2 by Pseudomonas sp. PSB-2 is higher than that for Pantoea dispersa Cav.cy3 (<50\u2009mg/L) (Serratia marcescens RP8 (974\u2009mg/L) but lowe93\u2009mg/L) and Serr74\u2009mg/L) . PSB in 74\u2009mg/L) , 14, 23,74\u2009mg/L) . The Pser peanut , Enterobhick pea , Acinetothaliana , and Psegeranium . The inogeranium . Previougeranium , 57. Therogenase , 57. Futgcd and bpp) in soil aggregates under different fertilization treatments. We found strong linkages between gcd gene abundance and tricalcium phosphate-solubilizing bacterial number, as well as between bpp gene abundance and phytate-degrading bacterial number. The phosphate-solubilizing bacteria Pseudomonas sp. PSB-2 and Arthrobacter sp. PSB-5 showed good performances for inorganic phosphorus solubilization. The phosphate-solubilizing bacterium Pseudomonas sp. PSB-2 could enhance growth of Chinese cabbage, showing significant increases in plant fresh and dry weight as well as plant height. Our findings extend the knowledge of mechanisms for distribution patterns of phosphate-solubilizing bacteria and P-cycling-related genes in soil aggregates and might guide the isolation of phosphate-solubilizing bacteria. Future work will use multiple techniques to investigate P-cycling-related bacterial abundance and community composition and optimize condition for P solubilization by PSB and decipher mechanisms for P solubilization at both the gene and protein levels.In conclusion, we found distinct distribution patterns of phosphate-solubilizing bacteria and P-cycling-related genes and winter wheat (Triticum aestivum L.) rotation since it was built in 1978. Five fertilization treatments were used, including CK, N, NPK, M, and MN for soil aggregates by using quantitative PCR (qPCR). Primer bppF (5\u2032-GAC GCA GCC GAY GAY CCN GCN NTN TGG-3\u2032) and primer bppR (5\u2032-CAG GSC GCA NRT CAN CRT TRT T-3\u2032) were employed to amplify the bpp gene 2 or sodium phytate solid medium and incubated at 30\u00b0C for 5 days. The NBRIP contained 10 g/L glucose, 5 g/L Ca3(PO4)2 or sodium phytate, 0.25 g/L MgSO4\u00b77H2O, 5 g/L MgCl2\u00b77H2O, 0.2 g/L KCl, 0.1 g/L (NH4)2SO4, 2\u2009mL/L trace element solution, 0.2 g/L cycloheximide, and 18 g/L agar 2 were subcultured by picking and streaking five times to isolate pure colonies. We gained six strains and identified them using simple 16S rRNA gene sequencing at Wuhan Qingke Innovation Biotechnology Co., Ltd. The universal primers 27F (5\u2032-AGA GTT TGA TCC TGG CTC AG-3\u2032) and 1492R (5\u2032-GGT TAC CTT GTT ACG ACT T-3\u2032) were used to amplify the 16S rRNA gene (Single colonies from the NBRIP containing CaRNA gene . The phy3(PO4)2 and incubated it at 30\u00b0C for 3\u2009days.The isolated PSB were incubated in both solid and liquid NBRIP to estimate their solubilization potentials for tricalcium phosphate . We inoc7 CFU/mL) (Exp group). Each treatment had five replicates. Chinese cabbage (Shanghai Qing) seeds were purchased from China National Seed Group, precultivated in sterile nutritious soils, and allowed to grow to about 10-cm length of sprouts . The original physicochemical properties and processing of experimental potted soils were described previously . Two pot sprouts . Each sporimetry .If not otherwise stated, we estimated significant differences by using the one-way analysis of variance. Permutational multivariate analysis of variance was conducted using the function adonis in the vegan package of R. Canonical analysis of principal coordinates was used to estimate effects of soil physicochemical factors on PSB number and gene abundance using the capscale function in the vegan package. A structural equation model was built to reflect potential linkage among soil physicochemical factors, gene abundance, and PSB number using IBM SPSS Amos v.21. For the structural equation model (SEM), the PC1 value of the first axis of the principal-component analysis, accounting for 99.89% of the total variation, was applied as a proxy for representing P components ."} +{"text": "Commiphora have been used in traditional medicines for centuries. More than 200 Commiphora species exhibit highly variable phytochemical compositions. A novel highly selective, sensitive, accurate HPLC-MS/MS method was developed and validated to quantify five characteristic phytosteroids and furanosesquiterpenoids, namely (E)-guggulsterone, (Z)-guggulsterone, curzerenone, furanoeudesma-1,3-diene, and myrrhone. The resulting contents and additionally GC analysis were used to classify and differentiate Commiphora oleogum resins of the species C. myrrha, C. erythraea, C. mukul, C. holtziana, C. confusa, and C. kua, as well as unspecified resins. Interestingly, a Commiphora sample from Ogaden, Ethiopia, comprised 446 ng/mg guggulsterones presumed to be unique to C. mukul from the Indian subcontinent. However, Commiphora from Ogaden differed considerably from C. mukul in respect to guggulsterones isomer\u2019s ratio. Moreover, the cytotoxicity of Commiphora extracts, essential oils, botanical drugs containing Commiphora, and pure compounds against the epidermoid carcinoma A431, malignant melanoma RPMI-7951 and SK-MEL-28 cells was investigated in vitro. Thereby, especially C. mukul extract and C. myrrha essential oil exhibited high cytotoxicity against skin cancer cells with IC50 of 2.9\u201310.9 \u00b5g/mL, but were less toxic to normal keratinocytes. In summary, Commiphora oleogum resins and its phytochemicals warrant further investigation aiming at chemotaxonomical classification as well as application in skin cancer treatment.Oleogum resins of the genus Commiphora Jacq. of the Burseraceae family are shrubs or small trees with thorny branches and aromatic oleogum resin exudates with characteristic odors Engl. (syn. C. molmol Engl.) predominantly growing in Somalia Commiphormponents . In factCommiphora oleogum resin or extract, namely Myrrhinil-Intest\u00ae and Gugulipid\u00ae were investigated. Additionally, two botanical drugs containing \u00ae is intended for use against gastrointestinal disorders, such as non-specific diarrhea, mild cramps, or flatulence. It contains chamomile flower extract (70 mg/pill), coffee charcoal (50 mg/pill), and powered C. molmol (syn. C. myrrha) oleogum resin (100 mg/pill) [C. myrrha analysis. However, Myrrhinil-Intest\u00ae contained with 0.456 \u00b5g/mg considerably less furanoeudesma-1,3-diene than the crude C. myrrha oleogum resin (87.7 \u00b5g/mg) (Myrrhinil-Intestmg/pill) . HPLC-MS7 \u00b5g/mg) a. \u00ae is considered a hypolipidemic drug containing an ethyl acetate extract of C. mukul [Z)-guggulsterone is the dominant isomer over (E)-guggulsterone with guggulsterone(ER/Z) = 0.61, which corresponds to the natural guggulsterone proportion in C. mukul [GugulipidC. mukul . ChemicaC. mukul ,22.Commiphora oleogum resin extracts and essential oils against the epidermoid carcinoma cell line A431 and the malignant melanoma cells lines RPMI-7951 and SK-MEL-28 were compared. The cell lines selected are rather resistant to treatment with the standard chemotherapeutic drugs cisplatin and 5-fluorouracil between 8.4 and 21.4 \u00b5g/mL. Furthermore, Commiphora extracts were toxic for RPMI-7951 and SK-MEL-28 with IC50 = 2.9\u201311.5 \u00b5g/mL and IC50 = 10.9\u201323.4 \u00b5g/mL, respectively, which is comparable or even higher (particularly for SK-MEL-28 cells) than the cytotoxicity of cisplatin and 5-fluorouracil. Interestingly, the extracts obtained from C. mukul exhibited the highest cytotoxicity against all cell lines investigated. Statistical analysis confirmed higher cytotoxic efficacy of a C. mukul extract compared to extracts from C. erythraea, C. holtziana, C. kua, and C. from Tarraxo to treat various conditions including cancers [C. myrrha, C. erythraea, and C. holtziana essential oils was shown to exhibit antiproliferative, proapoptotic and cytotoxic effect on human lung adenocarcinoma cells in vitro and in cancer xenografts in mice [Likewise, essential oils of ll lines . Essential cells . In Chin cancers . Particu cancers . Curzere in mice .C. mukul extract and C. myrrha essential oil were additionally tested for their cytotoxicity against non-carcinogenous human keratinocytes (MBU-IM). Here, the C. mukul extract and C. myrrha essential oil were less toxic to normal human keratinocytes than to malignant melanoma cells indicating their selectivity towards cancer cells -guggulsterone have been shown to induce caspase-dependent apoptosis in prostate cancer cells at concentrations > 10 \u00b5M [E)-guggulsterone exhibited cytotoxic effect on all three cancer cells lines with an IC50 = 12.6 \u00b5g/mL for A431, an IC50 = 3.7 \u00b5g/mL for RPMI-7951, and an IC50 = 11.1 \u00b5g/mL for SK-MEL-28. Similarly, (Z)-guggulsterone was also cytotoxic with an IC50 = 18.9 \u00b5g/mL for A431, an IC50 = 6.4 \u00b5g/mL for RPMI-7951, and an IC50 = 10.7 \u00b5g/mL for SK-MEL-28 - and (Z)-guggulsterone with regard to their toxicity against skin cancer cell lines were investigated. The combination index (CI) [E)- and (Z)-guggulsterones exhibited slight to moderate antagonistic interactions at effective doses ED50, ED75, and ED90. The only moderate synergistic interaction was observed in RPMI-7951 at ED50 . In addition to guggulsterones, C. mukul contains a further steroid substance group, termed guggulsterols [Because dex (CI) ,43, a qu at ED50 . This inlsterols . HoweverE)-guggulsterone, (Z)-guggulsterone, curzerenone, and furanoeudesma-1,3-diene were purchased from Sigma-Aldrich and myrrhone from ChemFaces . Commiphora oleogum resins were provided by field experts and subsequently deposited at the Herbarium of the Botanical Garden of Ulm University, Institute of Systemic Botany and Ecology, Germany (voucher: ULM-24224). For more precise sample information please see Commiphora botanical drugs Myrrhinil-Intest\u00ae (Batch No. 9100816) and Gugulipid\u00ae (Batch No. 1353619) were from Repha GmbH and Natural Organics Inc. , respectively.All solvents and chemicals were of analytical reagent grade. The solvents used for the extraction, sample preparation, and HPLC-MS/MS analysis were MeOH, acetic acid , and ultrapure water coupled to an Arium Pro station . The compounds and evaporated to dryness by using a rotary evaporator.For extraction, 600 mg of freshly grounded n-hexane. The solvent of the combined organic phases was evaporated at 60 \u00b0C (water bath) with nitrogen stream.Essential oils were obtained by hydrodistillation of oleogum resins as previously described . ShortlyThe HPLC-MS/MS experiments were carried out on an Agilent 1260 Infinity HPLC system coupled with an AB API 2000 triple quadrupole mass spectrometer using an electrospray ionization ion source (ESI) in positive ionization mode. Devices were controlled and data were processed by means of Analyst 1.6.1 software .The chromatographic separation was performed using an analytical reversed-phase HPLC column with a precolumn . v/v) (eluent A) and methanol (eluent B), both acidified with 0.2% acetic acid. Initial conditions were 32% eluent A and 68% eluent B followed by a linear gradient to 95% eluent B over 6.8 min, then 95% eluent B until 11.8 min. Thereafter, a linear gradient to initial conditions until 12.0 min and reequilibration continued until 17.0 min. In order to stabilize the chromatographic system, the column was kept at a temperature of 28 \u00b0C. The injection volume was set to 10 \u00b5L.By means of Design of Experiments (DoE) a novel method for chromatographic separation of guggulsterones was developed, in which the flow rate, the starting concentration of eluent B, and the gradient slope were optimized. Thus, the flow rate was 600 \u00b5L/min, the mobile phase consisted of methanol/water and m/z 97.1 (product ion) as quantifier for (E)-guggulsterone and (Z)-guggulsterone. Moreover, m/z 313.3 (precursor ion) and m/z 109.1 (product ion) were used as qualifier for both guggulsterones. The ions m/z 231.0/83.0 (quantifier) and m/z 231.0/149.1 were used for curzerenone, m/z 229.0/159.0 (quantifier) and m/z 229.0/187.2 for myrrhone, and m/z 215.0/119.1 (quantifier) and m/z 215.0/105.2 for furanoeudesma-1,3-diene. The optimized source parameters and MS tune parameter are listed in The MS/MS detection was performed in multiple reaction monitoring (MRM) mode with Commiphora oleogum resins were not mixed with Boswellia oleogum resin, all samples were additionally analyzed for ten boswellic and lupeolic acids namely, \u03b1-boswellic acid (\u03b1-BA), acetyl-\u03b1-boswellic acid (\u03b1-ABA), \u03b2-boswellic acid (\u03b2-BA), acetyl-\u03b2-boswellic acid (\u03b2-ABA), 11-keto-\u03b1-boswellic acid (\u03b1-KBA), 11-keto-\u03b2-boswellic acid (\u03b2-KBA), acetyl-11-keto-\u03b1-boswellic acid (\u03b1-AKBA), acetyl-11-keto-\u03b2-boswellic acid (\u03b2-AKBA), lupeolic acid (LA), and acetyl-lupeolic acid (ALA). The boswellic and lupeolic acid analysis by HPLC-MS/MS was carried out as previously described [To ensure that escribed ,24.Commiphora species by GC-FID and GC-MS was carried out as described previously in detail [n-alkanes and mass spectra comparison with NIST17 libraries and in-house libraries. Moreover, 2-methoxyisofuranogermacrene and dihydropyrocurzerenone were identified by comparison of retention indices and mass spectra with expert literature [Analysis of essential oils in oleogum resins of different n detail ,45. The terature ,46. ResuThe skin cancer cell lines, epidermoid carcinoma cells A431, malignant melanoma cells RPMI-7951 and SK-MEL-25, and normal human keratinocytes MBU-IM were from the German Collection of Microorganisms and Cell Cultures and cultured as recommended. 50 values were determined using SigmaPlot 14.0 software . Cells were seeded into 96-well plates and treated 24 h later using Tecan D300e digital dispenser . After 72 h incubation period, cell viability was analyzed by addition of 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide salt . Absorbance of the formed orange formazan dye was analyzed with an Infinite M1000 PRO Tecan plate reader (Tecan) at \u03bb = 450 nm with a \u03bb = 630 nm reference filter . For quaE)- and (Z)-guggulsterone in human skin cancer cell lines were carried out according to recommendations [Combination studies of cytotoxic effects of , SigmaPlot 14.0 software , and Valoo 2.10 software . All data were tested for normal distribution by the Anderson-Darling test and equality of variances by Levene\u2019s test. Sample groups were compared by one-way analysis of variance (ANOVA) and post hoc by Dunett\u2019s test. Comparison of two sample groups was carried out by Student\u2019s Commiphora by HPLC-MS/MS has been developed and validated. Additionally, essential oils of the respective oleogum resins were analyzed by GC. The phytochemical profiles were used to classify Commiphora oleogum resins of the species C. myrrha, C. erythraea, C. mukul, C. holtziana, C. confusa, and C. kua as well as unspecified Commiphora resins. Hence, patterns in the phytochemical composition were discovered assisting a chemotaxonomical differentiation among different Commiphora species. Interestingly, a Commiphora oleogum resin from the Ogaden region in Ethiopia comprised guggulsterones, which are unique for C. mukul from the India subcontinent. Considering the guggulsterones isomer\u2019s ratio and essential oil composition, Commiphora from Ogaden in Africa differs considerably from C. mukul suggesting that at least one African Commiphora species produces also phytosteroids such as guggulsterones. Moreover, the study provides evidence for cytotoxic efficacy of Commiphora extracts and essential oils against human epidermoid carcinoma and malignant melanoma cells in vitro. Here, especially C. mukul extract and C. myrrha essential oil exhibited the highest cytotoxicity against all three skin cancer cell lines investigated, but were less toxic to normal keratinocytes. Commiphora preparations and phytochemicals should be investigated more detailed regarding, for example, their systemic toxicity aiming at the development of new anticancer drugs.A highly, selective, and accurate method for the simultaneous determination of five phytosteroids and furanosesquiterpenoids in oleogum resins of the genus"} +{"text": "Cytochrome P450 1B1 (CYP1B1) gene are a major cause of PCG. Current study was conducted to screen CYP1B1 gene in highly consanguineous PCG affected families from Pakistani population consistent with the autosomal recessive pattern of PCG inheritance.Primary congenital glaucoma (PCG) is a heterogeneous rare recessively inherited disorder prevalent in regions with high consanguinity. Disease phenotype is associated with increased intra ocular pressure and is a major cause of childhood blindness. Sequence variations in CYP1B1 gene was done for all enrolled families. In-silico analysis was performed to identify and predict the potential disease-causing variations.For this study, patients and controls from 25 consanguineous families belonging to Punjab, Baluchistan and Khyber Pakhtunkhwa, Pakistan were recruited through ophthalmologists. DNA was isolated from collected blood samples. Genetic screening of Pathogenicity screening revealed sequence variants segregating with disease phenotype in homozygous or compound heterozygous form in eleven out of 25 analyzed families. We identified a total of sixteen disease causing variants among which five frameshift i.e., c.629dup (p.Gly211Argfs*13), c.287dup (p.Leu97Alafs*127), c.662dup (p.Arg222Profs*2), c.758_759insA and c.789dup (p.Leu264Alafs*63), two silent c.1314G>A, c.771T>G and six missense variations c.457C>G (p.Arg153Gly), c.516C>A (p.Ser172Arg), c.722T>A , c.740T>A (p.Leu247Gln), c.1263T>A (p.Phe421Leu), and c.724G>C (p.Asp242His) are previously un reported. However two frameshift c.868dup (p.Arg290Profs*37), c.247del (p.Asp83Thrfs*12) and one missense variant c.732G>A (p.Met244Ile), is previously reported. Furthermore, six polymorphisms c.1347T>C, c.2244_2245insT, c.355G>T, c.1294G>C, c.1358A>G and c.142C>G were also identified. In the intronic region, a novel silent polymorphism i.e., g.35710_35711insT was found in homozygous state. All the newly detected disease-causing variants were negative in 96 ethnically matched controls.CYP1B1 gene. Genetic counseling was provided to families to refrain from practicing consanguinity and perform premarital screening as a PCG control measure in upcoming generations.Among twenty-five screened families, eight families were segregating disease causing variants in recessive manner. Two families (PCG049 and PCG062) had compound heterozygosity. Our data confirms genetic heterogeneity of PCG in Pakistani population however we did not find molecular variants segregating with PCG in fifteen families in coding exons and intron-exon boundaries of GLC3A [GLC3B [GLC3C [GLC3D [CYP1B1) at GLC3A and Latent Transforming growth factor-\u03b2-binding Protein-2 (LTBP2) at GLC3D have been reported to cause PCG [MYOC) [FOXC1) [TEK) [Glaucoma is characterized by impaired vision due to increased intraocular pressure, a primary risk factor for irreversible optic nerve damage. This disorder can be categorized according to etiology (primary glaucoma/secondary glaucoma), onset and iridocorneal angle (open/close) . PrimaryGLC3A , GLC3B [A [GLC3B , GLC3C [B [GLC3C and GLC3C [GLC3D at positC [GLC3D . Among tause PCG . HoweverG [MYOC) , Forkhea [FOXC1) , and the1) [TEK) have alsCYP1B1 gene has three exons out of which the last 2 codes for a 543 amino acid (a.a) protein [CYP1B1 in development of eye is uncertain however it is believed that due to mutations in this gene, generation of some important morphogens is affected leading to structural defects in trabecular meshwork and the aqueous humour outflow pathways [CYP1B1 gene including missense, small deletions, indels, gross deletions and regulatory mutations [CYP1B1 gene in PCG cases belonging to consanguineous Pakistani families, we enrolled and screened twenty-five families for CYP1B1 variants. Each family had at least one child affected with primary congenital glaucoma. protein . Cytochr protein . This me protein . Exact fpathways , 17, 18.utations . Studiesutations , 15, 20.http://haplopainter.sourceforge.net/about.html) [Based on clinical assessment provided by ophthalmologists, 25 diagnosed families of PCG were enrolled belonging to Khyber Pakhtunkhwa (KPK), Baluchistan and South Punjab. Clinical data, family history and blood samples of patients and each available family member was collected after informed written consent following the principles of world medical association of Helsinki . The stuut.html) was usedet al., 2010 [Average 4ml of peripheral blood sample was taken from each participating individual and stored in 5ml EDTA (Ethylene Diamine Tetra Acetic acid) vacutainer. Extraction was performed using non-organic method of DNA extraction described by Kaul l., 2010 . To checet al., 2019 [et al., 2019 [https://www.mutationtaster.org/) [Amplification of coding regions and at least 50 base pairs of flanking non-coding regions was performed using primers reported previously by Afzal er.org/) . Furtherhttp://www.hgvs.org/) guidelines, Mutalyzer (2.0.35) [https://varsome.com/) [https://www.genomnis.com/access-hsf) was used to determine pathogenicity due to disruption of splicing signals because of sequence variants.For significance of each variant and to check their nomenclature according to Human Genome Variation Society HGVS (zer.nl/) was usedme.com/) was usedhttp://genetics.bwh.harvard.edu/pph2/) [https://sift.bii.a-star.edu.sg/) [http://provean.jcvi.org/seq_submit.php) [https://folding.biofold.org/i-mutant/i-mutant2.0.html) [http://mupro.proteomics.ics.uci.edu/) [fwt-\u0394Gfmut) of protein structure that corresponds to stabilizing or destabilizing effect of variations. To check the conservation between different mammalian species, Clustal omega [https://weblogo.berkeley.edu/) [https://www3.cmbi.umcn.nl/hope/) [PolyPhen-2 (Polymorphism Phenotyping v2) (u/pph2/) , SIFT (Sedu.sg/) and PROVmit.php) were use.0.html) and MUprci.edu/) softwareustalo/) was usedey.edu/) was usedl/hope/) was usedIn this study, twenty-five PCG segregating consanguineous Pakistani families were enrolled. Among these families i.e., 09 belonged to Punjab province of Pakistan, 01 to Azad Kashmir whereas 12 and 03 belonged to Khyber Pakhtunkhwa and Baluchistan respectively. At the time of enrollment, seventeen families had a single PCG affected individual, three families had two, one family (PCG058) had three, three families had four whereas family PCG050 had six affected members respectively .CYP1B1 coding regions and at least 50 base pairs of flanking noncoding region using DNA of each proband revealed thirteen novel disease-causing variations in coding regions according to mutation taster , (c.247del), (c.732G>A) and six reported polymorphisms (c.1347T>C), (c.1294G>C), (c.1358A>G), (c.2244_2245insT), (c.355G>T), (c.142C>G) were also found. Another polymorphism g.35710_35711insT was also found in intronic region in family PCG062 that has not been reported previously. Out of the novel disease-causing variants, five were frame shift variations c.629dup (p.Gly211Argfs*13), c.287dup (p.Leu97Alafs*127), c.662dup (p.Arg222Profs*2), c.758_759insA and c.789dup (p.Leu264Alafs*63). Other novel disease-causing variants include six missense variants c.457C>G (p.Arg153Gly), c.516C>A (p.Ser172Arg), c.722T>A , c.740T>A (p. Leu247Gln), c.1263T>A (p.Phe421Leu), and c.724G>C (p.Asp242His) and two silent variations c.1314G>A and c.771T>G. In addition to disease causing variants, seven polymorphisms were also detected .In family PCG049, two disease causing variations were detected. A single nucleotide substitution i.e., c.457C>G was present in heterozygous condition, it changed arginine at position 153 to glycine and was deleterious according to PROVEAN and Polyphen-2 with a score of -5.21 and 1.00 respectively Table 3Table 3. TTCGGC and Fas ESS site TGTTTC was broken. Two new ESS sites TTTTCG and GTTTTC were created for IIE and one TGTGTTTT for PESS (putative exonic splicing silencer).Insertion of thymine (T) in PCG050 in exon 2 at position 629\u2013630 changed CYP1B1 gene that replaced aspartic acid at position 83 to threonine shifting reading frame and creating stop codon after 12 residues . I-MutanCTGTGGTTTTTGTC>CTGTGGTTTTAGTC changing consensus value (CV) from 50.91 to 78.78. CV for newly created site showed that it is not a very strong site (strong site CV> 80). PCG063 had two unreported mutations, a silent heterozygous mutation c.771T>G and a frameshift homozygous mutation c.789dup , Nomascus leucogenys (XP_003262792.2), Pongo abelii (XP_009235654.1) and Pan troglodytes (XP_001167556.1) with high similarity index to Homo sapiens was founCYP1B1 coded protein is reported to cause abnormal development of ocular structures resulting in impeded outflow of aqueous humor and PCG phenotype [CYP1B1 gene varies among different populations i.e.; p.Ser476Pro is 44% prevalent in India, p.Arg469Trp, p.Arg368His, p.Arg390His, p.Gly61Glu and p.Glu173Arg are 70% prevalent in Iran, p.Gly61Glu, p. Arg390His and p.Glu229Lys are 80\u2013100% prevalent in Saudi Arabia however p.Arg330Phe and p.Arg390His are predominantly reported from China [High frequency i.e., 70\u2013100% of consanguineous marriages is the mhenotype , 36. Datom China . Founderom China . Previouom China , 38, 39;CYP1B1 analysis in 25 cases enrolled through various regions of Punjab, Baluchistan and Khyber Pakhtunkhwa, Pakistan revealed a total of seven frameshift, seven missense and two silent disease-causing variations. Among seven frameshift variations five are novel however two are previously reported in patients of different ethnicities. The variant c.868dup (p.Arg290Profs*37) (rs67543922) was initially identified in PCG affected Pakistani family by Sheikh et al., 2014 [et al., 2015 [CYP1B1 conducted on population of Sindh and Punjab province of Pakistan by Rashid et al., 2019 [In present study l., 2014 and then7) rs675422 was inl., 2019 reportedet al., 2009 [et al., 2018 [Second reported frame shift variant c.247del (p.Asp83Thrfs*12) was initially identified in a study conducted on Indian population by Tanwar l., 2009 . Accordil., 2009 . Five hol., 2018 have shol., 2018 .CYP1B1 gene. Previously compound heterozygosity has been reported in developmental glaucoma, [et al., 2021 reported that two heterozygous mutations c.1310C>T (p.P437L) and c.3G>A (p.M1I) are responsible for glaucoma in a Chinese family [et al., 2019 identified compound heterozygosity in two consanguineous families of PCG belonging to different ethnic groups of Pakistan [CYP1B1 with heterozygous TEK alleles in PCG cases [CYP1B1, recessive inheritance pattern and previously reported allelic interactions of two un linked genes for PCG phenotype [Missense disease-causing variants found in family PCG049, 052, 060, 062 and 067 and two silent disease-causing variants found in family PCG062, 063 are also previously unreported , Table 3laucoma, and primlaucoma, . Cai et e family . In anote family . Waryah Pakistan . FurtherCG cases . In preshenotype , 13, 48 CYP1B1 disease causing variations in PCG patients [LTBP2, TEK, MYOC, FOXC1 and regulatory effect of cis-acting elements, splicing elements or possible modifiers [Due to epigenetic modifications and different environmental factors incomplete penetrance and increased variability could be observed in manifestation of patients , 49. We odifiers , 40, 50.et al., 2019 [All single nucleotide polymorphisms (SNPs) identified in current study except one present in intronic region i.e., g.35710_35711insT in homozygous state are previously reported. Four reported SNPs i.e., rs1056836 (c.1294G>C), rs1800400 (c.1358A>G), rs1056827 (c.355G>T) and rs10012 (c.142C>G) showed amino acid change while two polymorphisms rs1056837 (c.1347T>C) and rs4646431 (c.2244_2245insT) were silent. Most prevalent polymorphism (45%) c.1347T>C in present study was also reported in other studies conducted on PCG cases from Pakistani population . Afzal eCYP1B1 gene to PCG pathophysiology in our population.In conclusion we identified thirteen previously unreported and three reported mutations as well as six SNPs (one novel) in PCG probands born to parents having consanguineous marriages highlighting the autosomal recessive pattern of disease. Proper genetic testing and counseling should be provided to people in high consanguinity areas to help ophthalmologists in disease management and treatment. Mass screening and additional studies are required to better understand the heterogeneous pattern and contribution of"} +{"text": "Corona virus disease-19 (Covid-19) has significantly affected organ transplantation with concerns regarding severe infection and mortality. Data on Covid-19 in renal transplant recipients (RTRs) is scarce from Pakistan. The aim of this study is find out the factors effecting mortality among Covid-19 patients in renal transplant recipients from the largest transplant center of Pakistan.All RTRs >18 years, with positive severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) polymerase chain reaction (PCR) and diagnosed as severe disease, between April to December 2020 were retrospectively reviewed. The severe disease was defined as O2 saturation < 94% at room air on admission. Survivors and non- survivors were compared. Demographics, immunosuppression, comorbid conditions, clinical features, laboratory investigations and graft function were noted.A total of 95 RTRs had severe disease. There was no difference in mortality between age, gender and co-morbid conditions among survivors and non-survivors. Both groups received similar immunosuppressive regimen. Intensive care unit (ICU) admission [16.5% vs 68.8% p< 0.001 OR 11.17 95% CI (3.3-37.6)] and high D-dimers >1.5\u00b5g/ml (p=0.052) at the time of admission were significantly associated with mortality. There was no association of graft function with mortality. Treatment with methyl-prednisolone was found to be significantly associated with survival [83% vs 43% P=0.02 OR 0.15 95% CI (0.05-0.49)]. (Table\u00a01) WHO grading of the disease is shown in figure 1, there was a 100% mortality among patients on mechanical ventilator.ICU admission and high D-dimers at the time of admission are the significant risk factors for mortality in patients with Covid-19 infection. There was no association of graft dysfunction with mortality. Steroids use has significantly improved survival in renal transplant recipients with severe Covid-19 infection.All Authors: No reported disclosures."} +{"text": "Colitis-associated cancer (CAC) is a subtype of inflammatory bowel disease (IBD)-associated colorectal cancer. Huoxiang Zhengqi (HXZQ) is a classical Chinese herbal medicine and has been used to treat intestinal disorders, however, anti-CAC effects and underlying mechanisms of HXZQ have not been reported. An azoxymethane/dextran sulfate sodium-induced CAC mice model was used to investigate the anti-CAC effect of HXZQ. HXZQ significantly reduced colonic inflammation, suppressed the size and number of tumors, and reduced the levels of pro-inflammatory cytokines and oxidative stress markers , and increased the levels of anti-inflammatory cytokines (IL-10 and IL-27) in CAC mice. Intestinal microbiota and serum metabolomics analyses indicated that HXZQ altered the gut microbial composition and the abundance of 29 serum metabolites in CAC mice. Additionally, HXZQ activated the nuclear factor-erythroid factor 2-related factor 2 (Nrf2) signaling pathway and increased the levels of antioxidants such as catalase (CAT), heme oxygenase-1 (HO-1), NAD(P)H quinone oxidoreductases-1 (NQO-1), and superoxide dismutase-1 (SOD-1). HXZQ inhibited the activation of the nuclear factor kappa-B (NF-\u03baB) signaling pathway and decreased the expression of NLR family pyrin domain containing 3 (NLRP3) by inhibiting the phosphorylation of inhibitor of nuclear factor kappa-B (I\u03baB), inhibitor of nuclear factor kappa-B kinase (IKK), and NF-\u03baB. In conclusion, HXZQ alleviated CAC in mice by modulating the intestinal microbiota and metabolism, activating Nrf2-mediated antioxidant response, and inhibiting NF-\u03baB-mediated NLRP3 inflammasome activation against inflammation. The present data provide a reference for the use of HXZQ as a therapeutic or combination agent for clinical CAC treatment. Colitis-associated cancer (CAC) is a subtype of inflammatory bowel disease (IBD)-associated colorectal cancer. IBD includes Crohn\u2019s disease (CD) and ulcerative colitis (UC) . InflammAtractylodes, regulates oxidative stress through the Nrf2 pathway and alleviates 2,4,6-trinitrobenzenesulfonic acid-induced acute colitis by influencing the composition of intestinal microbiota that does not express BF enterotoxin to prevent DSS-induced colitis and prevent the formation of polyps in the model of CAC production, which affects the homeostasis of the intestinal microbiota . ROS canel of CAC.Prescriptions of Peaceful Benevolent Dispensary for approximately 900\u00a0years and has been used to treat intestinal disorders (Huoxiang Zhengqi (HXZQ) is a classic Chinese herbal medicine that wasisorders . Recent isorders . Norfloxisorders . HoweverThe azoxymethane (AOM)/DSS-induced CAC mouse model mimics the pathology of CAC in humans and has been used for screening agents with anti-CAC properties and revealing the underlying mechanisms . In the Thirty-two 6-week-old male C57BL/6 mice (SCXK(Liao)2020\u20130,001, Liaoning Changsheng Biotechnology Co., Ltd. Benxi, China) were housed under specific pathogen-free conditions at the appropriate temperature (22 \u00b1 2\u00b0C) and humidity (50% \u00b1 10%) and kept on a 12/12\u00a0h light/dark cycle. The mice had unrestricted access to food and water. The experimental protocol complied with the ARRIVE guidelines and was approved by the Institution Animal Ethics Committee of Jilin University (SY202104007).n = 8) (serving as the model group) or 0.45 or 1.35\u00a0g/kg HXZQ (serving as the HXZQ-treated groups) daily for 6 weeks. Another eight mice were intraperitoneally injected with normal saline on the first day, received normal drinking water for the entire experimental period, and received normal saline orally daily from the fifth to 10th\u00a0week (serving as the control [Ctrl] group) on the first day, and their drinking water was changed to 2% DSS at the second, fifth, and eighth week. From the fifth week and beyond, the mice were randomly divided into three groups and orally received normal saline (] group) . Six houThe fixed colon, liver, spleen, and kidney tissues were paraffin-embedded, sectioned, and dewaxed in xylene for 40\u00a0min, anhydrous ethanol for 10\u00a0min, and 75% ethanol for 5\u00a0min, and then washed with running water. The sections were stained with hematoxylin and eosin (H&E) and treated sequentially with ethanol and xylene for dehydration. The sealed sections were observed and analyzed using an ECLIPSE E100 upright optical microscope .Paraffin slides of colorectal tumors were subjected to antigen retrieval after de-paraffinization and blocked with 3% bovine serum albumin. The slides were incubated overnight at 4\u00b0C with primary antibody for nuclear factor kappa-B factor kappa-B (NF-\u03baB) p65 in a wetn = 4) were used for 16S rRNA analysis of the gut microbiota. Nucleic acids were extracted from the contents of each cecum, and PCR amplification of the V3-V4 region of the bacterial 16S rRNA gene was performed. PCR products were quantified and 2 \u00d7 250\u00a0bp double-end sequencing was performed. Sequencing was performed at Shanghai Personal Biotechnology Co. Ltd. .The cecum contents obtained from Ctrl, Model, and HXZQ-treated mice (https://www.ncbi.nlm.nih.gov/sra/PRJNA860221). These analyses were performed as previously described (The 16S rRNA sequencing results were clustered into amplicon sequence variants (ASVs) using DADA2 with 100% similarity. Based on the ASV abundance data, a flower plot was generated, and alpha diversity indices and the weighted UniFrac distance matrix were calculated. Abundance data from each group of microbiota were used to generate a species composition heatmap and for LDA effect size (LEfse) analysis. Microbial functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. The sequences of bacteria were uploaded to the NCBI Sequence Read Archive with accession number PRJNA860221 for vortex mixing. The supernatant obtained by centrifugation of the mixture was vacuum dried to a solid state. Before the analysis, the samples were dissolved in an aqueous solution of acetonitrile . Samples were separated on an ultra-high-performance liquid chromatography system equipped with a ACQUITY UPLC BEH Amide 1.7\u00a0\u03bcm, 2.1\u00a0mm \u00d7 100\u00a0mm column and were analyzed using a quadrupole-time of flight mass spectrometer . The separation conditions were identical to those reported in previous studies .p-value <0.05 as filtering criteria were used to draw heatmaps and correlation plots. The abundance data of the microbiota and metabolites with significant changes were jointly analyzed to obtain association heatmaps. These analyses were performed as described in our previous study , and score plots were plotted. The abundance of signature metabolites screened with OPLS-DA VIP >1 and us study .The collected tumor tissues were homogenized separately in phosphate buffer solution (PBS). Protein concentrations were determined using a Pierce\u2122 BCA Protein Assay Kit . IL-1\u03b1, IL-1\u03b2, IL-6, IL-17A, IL-23, IL-27 and TNF-\u03b1 in tumor tissues were detected using the LEGENDplex\u2122 Mouse Inflammation Panel (13-plex) with a V-bottom plate . Enzyme-linked immunosorbent assay (ELISA) kits were used to measure IL-10 (#MM-0176M1), IL-21 (#MM-0688M1), granulocyte-macrophage colony-stimulating factor (GM-CSF) (#MM-0185M1), malondialdehyde (MDA) (#MM-0897M1), and ROS (#MM-43700M1) levels in tumors.Tumor tissues were lysed at low temperatures in Radioimmunoprecipitation assay (RIPA) Buffer supplemented with 1% Protease and Phosphatase Inhibitor Cocktail . Cytoplasmic and nuclear proteins in tumors were isolated by NE-PER Nuclear and Cytoplasmic Extraction Kit . Total protein in each sample was measured using the Pierce\u2122 BCA Protein Assay Kit . The protein samples were separated using 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The proteins were transferred to PVDF membranes, and the membranes were blocked with western fast blocking solution for 10\u00a0min at 25\u00b0C. The membranes were incubated with primary antibodies for 12\u00a0hp-value less than 0.05 was considered statistically significant.All values are presented as mean \u00b1 standard error of the mean (S.E.M.) Biochemical indices were compared between Ctrl and Model using Student\u2019s t-test. Comparisons among Model, 0.45\u00a0g/kg HXZQ, and 1.35\u00a0g/kg HXZQ were performed with one-way analysis of variance (ANOVA) followed by a post hoc multiple comparisons (Dunnett) test using BONC DSS Statistics 25 software . A p < 0.05) (HXZQ remarkably reduced the number and size of colonic tumors in CAC mice without influencing their body weight ( < 0.05) . Compare < 0.05) . HXZQ fa < 0.05) .Candidatus_Arthromitus, Turicibacter, Dorea, Acinetobacter, Clostridium, and Desulfovibrio, which were suppressed by HXZQ. Compared to the model group, HXZQ resulted in an increased abundance of 25 genera (p < 0.001) . The abu LDA >2) . Compara< 0.001) .p < 0.05) (The score plots of OPLS-DA showed significant differences in metabolite levels between the model and HXZQ-treated mice . The lev < 0.05) .Phascolarctobacterium, Prevotella, Helicobacter, and Butyricimonas (p < 0.05) (Candidatus_Arthromitus and p-75-a5 (p < 0.05) (Serum metabolite concentrations were significantly correlated with changes in colony abundance. Indoxyl sulfate was negatively correlated with < 0.05) . L-Gluta < 0.05) .p < 0.01) (p < 0.01) (p < 0.001) (p < 0.01) (p < 0.001) (p < 0.01) (p < 0.05) (p < 0.05) (p < 0.001) (p < 0.05) (p < 0.001) (p < 0.01) (Inflammation severity tended to correlate positively with CAC development. HXZQ do < 0.01) and ROS < 0.01) , and red< 0.001) , IL-1\u03b2 ( < 0.01) , IL-6 (>< 0.001) , IL-17A < 0.01) , IL-21 ( < 0.05) , IL-23 ( < 0.05) , TNF-\u03b1 (< 0.001) , GM-CSF < 0.05) . Corresp< 0.001) and IL-1 < 0.01) .p < 0.05), catalase (CAT) (>400%) (p < 0.001), heme oxygenase-1 (HO-1) (>400%) (p < 0.05), NAD(P)H quinone oxidoreductases-1 (NQO-1) (>470%) (p < 0.001), and superoxide dismutase-1 (SOD-1) (>220%) (p < 0.01) in colorectal tissues (p < 0.05), p-NF-\u03baB (>52%) (p < 0.05), phosphorylated inhibitor of nuclear factor kappa-B kinase (p-IKK) (>33%) (p < 0.001), IL-1\u03b2 (>51%) (p < 0.01), IL-6 (>63%) (p < 0.001), TNF-\u03b1 (>40%) (p < 0.001), and NLRP3 (>29%) (p < 0.01) in colorectal tissues (p < 0.001) ( tissues . HXZQ do tissues . HXZQ in< 0.001) . The res< 0.001) .IL10-/- mice spontaneously developed colitis, whereas upregulation of IL-10 alleviated CAC, which is consistent with our study production and a strong positive correlation with the pro-inflammatory cytokine TNF-\u03b1 (Acinetobacter activates the NLRP3 inflammasome and consequently mediates IL-1\u03b2 production (Turicibacter and Desulfovibrio is increased under inflammatory conditions (Desulfovibrio has been reported to induce secretion of IL-6 and IL-8 from endothelial cells (Notably, changes in pro-inflammatory cytokine levels may also affect host\u2019s intestinal microbiota. Accordingly, IL-33-deficient mice developed a dysregulated gut microbiota , and alt colitis . Disrupt colitis , which a colitis . The eff colitis . HXZQ inne TNF-\u03b1 . Acinetooduction . The gronditions , and Desal cells .Intestinal microbiota directly influence host metabolism . HXZQ inNLRP3 transcription (Unsurprisingly, HXZQ activated Nrf2 signaling while increasing the levels of antioxidant enzymes such as CAT, HO-1, NQO-1, and SOD-1. Moreover, HXZQ inhibited the phosphorylation of I\u03baB\u03b1, IKK\u03b1/\u03b2, and NF-\u03baB as well as the expression of NLRP3. The accumulation of ROS during chronic inflammation leads to oxidative stress that aggravates CAC development . Nrf2 cocription .The present study has some limitations. The detailed relationship between HXZQ-mediated gut microbiota regulation and the anti-inflammatory and anti-oxidant effects that underlie its anti-CAC activity requires further investigation. Second, the main components involved in the therapeutic effect of HXZQ in the treatment of CAC need to be identified. Finally, the effects of HXZQ on other IBDs require further investigation.Altogether, HXZQ alleviates CAC by modulating the intestinal microbiota and metabolism, activating Nrf2-mediated antioxidant response, and inhibiting NF-\u03baB-mediated NLRP3 in mice. Our data provide a reference for the use of HXZQ as a therapeutic agent or a combination agent for clinical CAC treatment."} +{"text": "Paenibacillus polymyxa DSM 365. The genome consists of a 5,788,318-bp chromosome, with a GC content of 45.48%. Annotation of the genome revealed a total of 5,246 genes . Gene function analysis indicated the ability to fix nitrogen (N2) and to produce value-added chemicals.We report the complete genome sequence of Paenibacillus polymyxa DSM 365 is a Gram-positive plant growth-promoting rhizobacterium . To isolate DNA, cultures were grown overnight in tryptic soy broth at 30 \u00b0C and 200\u2009rpm. Genomic DNA was extracted using the Wizard high-molecular-weight (HMW) DNA extraction kit . Library preparation and sequencing were conducted by Novogene Inc. using the Illumina NovaSeq 6000 platform. To prepare the library for sequencing, genomic DNA was randomly sheared into short fragments. The fragments were end repaired, adenine tailed, and ligated with Illumina adapters. The quantified libraries (350-bp size) were pooled and sequenced to produce 6\u2009Mb of paired-end 150-bp reads . In order to ensure accuracy and reliability, the reads were filtered using readfq software (v.10) in 47 scaffolds, with a GC content of 45.48% and an average read coverage of 291\u00d7.acterium with caphemicals \u20137. P. poe v.10) , 10, SPA , 10, SPe (v.10) , and ABye (v.10) assemblye (v.10) . Assemble (v.10) . GapClose (v.10) was usedGeneMarkS (v.4.10) was used16\u2013P. polymyxa DSM 365 was submitted to the National Center for Biotechnology Information (NCBI) database using the Prokaryotic Genome Annotation Pipeline (PGAP) (v.6.0) (e\u22125). Coding genes were predicted by Augustus (v.2.7) (nif operon), sporulation, acetoin utilization, biosynthesis of siderophores, polyketides, exopolysaccharides, and butanediol were detected.The whole-genome sequence of (v.6.0) . Homolog (v.6.0) was used (v.2.7) with homP. polymyxa DSM 365 has been deposited in GenBank under the BioProject accession number PRJNA809744, the BioSample accession number SAMN26200526, and the Sequence Read Archive (SRA) accession number SRR18173204. The whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number JAKVDC010000000.The annotated genome sequence of"} +{"text": "Data on willingness to participate in population-based long-COVID studies are sparse. We invited all citizens of Essen aged 18-74 years with a positive SARS-CoV-2 PCR test between Mar-Aug 2020 and assessed COVID-related symptoms in responders \u223c1.5 years after infection.The invited population included 1282 infected citizens (48% women). At the time of testing 64% reported symptoms. We asked responders about past and current symptoms, hospitalization, smoking, sport, pre-existing conditions , subjective health status as compared to before infection, assessed BMI, and performed descriptive statistics.2), and more pre-existing conditions (23% vs 10%). Compared to before infection, 53% rated their current health worse, with a higher rate among inpatients (81%). After \u223c1.5 years, 55% still reported symptoms: 25% fatigue, 20% concentration disorder, 18% breathing problems, 13% odor and 11% taste disorders. Persistent symptoms were more common in inpatients than in non-hospitalized (69% vs 53%).We investigated 255 participants \u223c20 month (median) after the PCR test. 95% reported symptoms at the time of testing: 67% fatigue, 58% taste disorders, 56% limb pain, 55% odor disorders, 54% headache, 50% cough, 43% fever; 10% needed hospitalization, 3% intensive care, 1.6% artificial ventilation. Compared to the non-hospitalized the formerly inpatients were more often male (62% vs 49%), older (56\u00b113 vs 49\u00b114 years), less often never smokers (42% vs 53%), had a higher BMI (31\u00b17 vs 28\u00b15 kg/mSymptomatic individuals are more likely to participate in a COVID19 follow-up study than asymptomatic ones. This may overestimate the number of individuals with long-term symptoms in population-based long-COVID study populations. However, persistent symptoms seem to be more likely in formerly inpatients compared to non-hospitalized individuals with former SARS-CoV-2 infection.\u2022\u2002Symptomatic individuals are more likely to participate in a COVID19 follow-up study than asymptomatic ones.\u2022\u2002Persistent symptoms seem to be more likely in formerly inpatients compared to non-hospitalized individuals with former SARS-CoV-2 infection."} +{"text": "Endocrine disruption is an important factor in the development of endometrial cancer. Expression of miR-149-3p is observed in some cancer types, while its role in uterine corpus endometrial carcinoma (UCEC) is unclear. The clinical and genomic data and prognostic information on UCEC were obtained for patients from the TCGA database. The Kruskal\u2013Wallis test, Wilcoxon signed-rank test, and logistic regression were used to analyze the relationship between clinical characteristics and miR-149-3p expression. Kaplan\u2013Meier survival curve analysis was used to study the influence of miR-149-3p expression and miR-149-3p target genes on the prognosis of UCEC patients. The TargetScan, PicTar, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to determine the involvement of miR-149-3p target genes in function. Immune infiltration analysis was used to analyze the functional involvement of miR-149-3p. QRT-PCR was used to validate the expression of miR-149-3p in UCEC cell lines. P < 0.001), histological type (P < 0.001), histological grade (P < 0.001), tumor invasion (P=0.014), and radiation therapy (P=0.011). High miR-149-3p expression predicted poorer overall survival (OS) , progression-free interval (PFI) , and disease-specific survival (DSS) . Low expressions of miR-149-3p target genes, including ADCYAP1R1, CGNL1, CHST3, CYGB, DNAH9, ESR1, HHIP, HIC1, HOXD11, IGF1, INMT, LSP1, MTMR10, NFIC, PLCE1, RARA, SNTN, SPRYD3, and ZBTB7A, were associated with poor OS in UCEC. MiR-149-3p may be involved in the occurrence and development of UCEC via pathways including PI3K-Akt signaling pathway, Ras signaling pathway, AGE-RAGE signaling pathway in diabetic complications, focal adhesion, and MAPK signaling pathway. miR-149-3p may inhibit the function of CD8 T cells, cytotoxic cells, eosinophils, iDC, mast cells, neutrophils, NK CD56bright cells, NK CD56dim cells, pDC, T cells, T helper cells, TFH, Th17 cells, and Treg. miR-149-3p was significantly upregulated in UCEC cell lines compared with endometriotic stromal cells. High expression of miR-149-3p in UCEC was significantly associated with age ( High expression of miR-149-3p was significantly associated with poor survival in UCEC patients. It may be a promising biomarker of prognosis and response to immunotherapy for UCEC patients. Uterine corpus endometrial carcinoma (UCEC) is one of the three main gynaecological malignancies, the incidence of which increases over time. Endometrial cancer is an epithelial tumor of the endometrium and a malignant tumor of the female reproductive system with a high incidence, posing a serious threat to the health of women worldwide , 2. It cMicroRNAs (miRNAs) are a unique class of endogenous and small noncoding RNAs that are approximately 18 to 25 nucleotides in length. They alter gene expression at the posttranscriptional level primarily through complete or incomplete base pairing with the 3\u2032 untranslated region (3\u2032UTR) of their target mRNAs. Translational repression and mRNA degradation are the 2 main pathways through which miRNAs direct gene regulation . There iIn oral squamous cell carcinoma, reduced levels of miRNA-149-3p lead to malignant progression and predict poor prognosis . IncreasThe present study examined the expression of miR-149-3p in UCECs using an online database and analyzed the relationship between expression levels and clinical characteristics. A survival curve was drawn to analyze the relationship between miR-149-3p expression level and overall survival (OS). Important contributions of miR-149-3p target genes to function were identified by TargetScan, PicTari, Gene Ontology (GO), and Kyoto Gene and Genome Encyclopedia (KEGG) analyses. The functionally significant involvement of miR-149-3p was analyzed by immune infiltration analysis. QRT-PCR was used to validate the expression of miR-149-3p in UCEC cell lines. The results of this study could provide new prognostic biomarkers for UCEC.https://portal.gdc.cancer.gov/) UCEC project. The miRNAseq data in RPM (reads per million mapped reads) format were log2-transformed.The analysis was carried out according to references , 17. R . R package was the ggplot2 package.Nomogram plot analysis was carried out according to literature , 20. R phttps://bioinfo.life.hust.edu.cn/miR_path/download.html). The UCEC prognosis-related genes were analyzed according to reference [miR-149-3p targets were obtained from Database TargetScan, miRanda, TarBase, miRTarBase, miR2Disease, miRecords, and miRWalk \u201325. UCECeference . R [P value less than 0.05) were considered significant categories.The Database for Annotation, Visualization, and Integrated Discovery (DAVID) can provide a comprehensive set of functional annotation tools to facilitate understanding of the biological significance behind a large number of genes. GO and KEGG analyses were performed on the targets of miR-149-3p using the DAVID database (rf.gov/) \u201328. GO aThe analysis was performed according to reference . R have been isolated from endometriotic tissue. Human UCEC cells Ishikawa and KLE were obtained from our laboratory. KLE cells were grown in F12. Ishikawa cells were grown in RPMI-1640. 10% fetal bovine serum was added to the medium to maintain the cell state. Add 1% antibiotics to the soil to prevent contamination. Cells were grown in a 37\u00b0C incubator containing 5% COeference . The priP values less than 0.05 were considered statistically significant.Statistical analysis was carried out according to reference . All staR0 (90.9%), 22 R1 (5.4%), and 15 R2 (3.7%). The histologic grade included 98 G1 (18.3%), 121 G2 (22.6%), and 316 G3 (59.1%). Tumor invasion (%) included 260 patients (<50) (55.3%) and 210 patients (\u226550) (44.7%). The menopause status included 34 pre (6.8%), 17 peri (3.4%), and 449 post (89.8%). The hormone therapy included 297 no (86.6%) and 46 yes (13.4%). The diabetes included 323 no (72.6%) and 122 yes (27.4%). The radiation therapy included 278 no (53.4%) and 243 yes (46.6%). The surgical approach included 207 minimally invasive (39.6%) and 316 open (60.4%). The age range was 57 to 71 years, with a median of 64 years.A total of 546 patients were analyzed in the present study . The clin\u2009=\u2009546) was significantly higher than that in normal tissues (P=0.007) . The areP=0.007) , suggestn\u2009=\u2009273) and low (n\u2009=\u2009273) expression groups. As shown in P < 0.001), histological type (P < 0.001), histological grade (P < 0.001), tumor invasion (P=0.014), and radiation therapy (P=0.011). As shown in P=0.048), age , histological type , histologic grade , tumor invasion , and radiation therapy .The characteristics of UCEC patients are shown in P < 0.001), PFI , and DSS of UCEC patients (P < 0.001), clinical stage , primary therapy outcome , age , histological type , residual tumor , histologic grade , tumor invasion , and radiation therapy . As shown in P < 0.001), primary therapy outcome , radiation therapy , and hsa-miR-149-3p were independently correlated with OS in multivariate analysis. The above data indicated that miR-149-3p is a prognostic factor, and increased miR-149-3p is associated with poor OS. A nomogram was constructed to predict the 1-, 3-, and 5-year survival probability of UCEC patients by combing the expression of miR-149-3p with clinical variables, as shown in The association between miR-149-3p expression and OS of patients with UCEC was evaluated by Kaplan\u2013Meier analysis, which indicated that the expression of miR-149-3p was correlated with poor OS , cytotoxic cells (P < 0.001), eosinophils (P < 0.001), iDC (P < 0.001), mast cells (P=0.002), neutrophils (P < 0.001), NK CD56bright cells (P < 0.001), NK CD56dim cells (P < 0.001), pDC (P < 0.001), T cells (P < 0.001), T helper cells (P=0.004), TFH (P=0.024), Th17 cells (P=0.006), and Treg (P < 0.001).As shown in Figures P < 0.001) (P < 0.001) . The exp< 0.001) . These rThe development of type I endometrial cancer is associated with continuous estrogen stimulation of the endometrium without progestin antagonism. The endometrium lacks progesterone antagonism, and continuous stimulation by estrogen will result in a prolonged state of hyperproliferation, which will further develop into endometrial cancer. MiRNAs regulate the cell cycle and cell differentiation and migration, which may also act as tumor suppressor genes or oncogenes during tumorigenesis and tumor development . MiRNAs P < 0.001), histological type (P < 0.001), histological grade (P < 0.001), tumor invasion (P=0.014), and radiation therapy (P=0.011). UCEC expressed more miR-149-3p than normal tissue, especially in patients with age (>60), histological type (mixed and serous), histologic grade (G2 and G3), tumor invasion (\u226550%), or radiation therapy (yes). These phenomena suggested that miR-149-3p may be involved in tumor development and promote proliferation. And miR-149-3p was highly expressed in UCEC, and patients with high miR-149-3p expression had poorer OS , PFI , and DSS of UCEC patients. Low expressions of miR-149-3p target genes, including ADCYAP1R1, CGNL1, CHST3, CYGB, DNAH9, ESR1, HHIP, HIC1, HOXD11, IGF1, INMT, LSP1, MTMR10, NFIC, PLCE1, RARA, SNTN, SPRYD3, and ZBTB7A, were associated with poor OS in UCEC. Lymphovascular space invasion (LVSI) has an independent influence on the poor prognosis of UCEC patients [In the present study, miR-149-3p was significantly correlated with age , histological type (P < 0.001), histological grade (P < 0.001), tumor invasion (P=0.014), and radiation therapy (P=0.011). miR-149-3p may be involved in the occurrence and development of UCEC via pathways, including PI3K-Akt signaling pathway, Ras signaling pathway, AGE-RAGE signaling pathway in diabetic complications, focal adhesion, and MAPK signaling pathway. Expression of miR-149-3p was correlated with immune infiltration in UCEC. This study partially elucidates the role of miR-149-3p in UCEC and provides a promising biomarker for prognosis and immunotherapy response in UCEC patients.miR-149-3p was highly expressed in UCECs and correlated with poorer OS compared with normal tissues. The high miR-149-3p expression in UCEC was significantly associated with age ("} +{"text": "Substantial changes in access and delivery of primary HIV care occurred during the COVID-19 pandemic. To assess how care access changed during the COVID-19 pandemic, we estimated ED use among PWH in care 2017-2021 in the southeastern US.For each calendar year, among PWH in care in the UNC CFAR HIV Clinical Cohort (defined as having a clinic visit in the current or prior year), we estimated the percent of patients with \u2265 1 ED visit in a given year, overall and by age, gender, race/ethnicity, HIV viral load (VL), and CD4 count. We estimated risk ratios (RRs) comparing patient characteristics and years 2020-2021 vs. 2017-2019, using Poisson regression with generalized estimating equations to account for repeated measures.B-F, all P< 0.05).Among 2129 PWH in care 2017-2021 (N\u22481700-1800 in each year), 57% identified as Black, 31% White, 8% Hispanic, 26% women, with median age of 47 years (IQR 35-55). During the study period, there were 3645 ED visits over 8813 person-years, a rate of 41.4 ED visits-per 100 person-years(95% CI 36.8-46.5) per 100 person-years. The 845 PWH with at least one ED visit during the study period contributed a median of 2 visits each (IQR 1-5). The unadjusted probability of having \u22651 ED visit in a given year was higher among women vs. men , Black vs. White PWH , with VL \u2265 40 copies/mL , and with CD4 < 200 or 200-349 vs. \u2265 500 cells/\u03bcL; age was not associated with ED use. Compared with 2017-2019, the annual probability of having \u2265 1 ED visit was lower in 2020-2021, with RRs of 0.83 (95% CI 0.76-0.90) in unadjusted analyses and 0.80 (95% CI 0.71-0.90) after adjusting for demographics, VL, and CD4. There was also a significant unadjusted decrease for 2020-2021 vs. 2017-2019 among women, men, PWH who were Black, White, < 40 or 50-59 years old, and with CD4 >500 (Fig.\u00a0Among PWH in HIV care, ED use was higher among women, Black PWH, and PWH with poorly controlled HIV. ED use decreased 2020-2021 in most groups, indicating that PWH during the COVID-19 pandemic may be delaying seeking care for acute conditions, or accessing care in other ways. Work is ongoing to characterize reasons for ED visits across calendar years and examine the impact of reduced ED utilization among PWH.Joseph J. Eron, MD, Adagio Therapeutics: data safety monitoring committee|Gilead Sciences: Advisor/Consultant|Gilead Sciences: Grant/Research Support|Glaxo Smith Kline: Advisor/Consultant|Merck: Advisor/Consultant|ViiV Healthcare: Advisor/Consultant|ViiV Healthcare: Grant/Research Support."} +{"text": "Gait speed is a predictor of overall health and mortality in older adults. Metabolomics may provide insights into biological mechanisms underlying gait speed. Herein, we examined the association between 193 lipid metabolites with gait speed in 1,717 adults (52.1% women) aged 82.0 \u00b1 14.5. Lipidomic analysis was performed using liquid chromatography-mass spectrometry. Gait speed was measured over 4-meters and slowness was defined as <0.8m/s. Logistic regression, adjusted for age, sex, field center, height, fasting-duration and familial-relatedness, were used to examine the association between log-transformed metabolites with slowness. A false discovery rate (FDR) of p<0.05 was employed to account for multiple comparisons. Gait speed was 0.83 \u00b1 0.32 and 53.4% had slowness. Three lipid metabolites were significantly associated with lower odds of slowness: an acylcarnitine, sphingomyelin and a ceramide non-hydroxy fatty acid-sphingosine. Our results potentially link lipids involved with mitochondrial beta-oxidation and nerve signal transduction to gait speed in older adults."} +{"text": "Klebsiella sp. CTHL.F3a was isolated from kimchi (Korean fermented cabbage/vegetables). Its complete genome sequence , comprising a chromosome and a single plasmid, was established through hybrid assembly.The cellulolytic strain Klebsiella oxytoca species complex (KoSC) may be encountered as human commensals and opportunistic pathogens in Bushnell-Haas medium (BHM) (Six samples of fresh kimchi (Korean fermented cabbage/vegetables) from Hong Kong markets were screened for cellulolytic bacteria using carboxymethylcellulose (CMC) agar, as described previously . Twelve um (BHM) containiN50, 12,200\u2009bp). Default parameters were used for all software unless otherwise specified.Paired-end short-read sequencing libraries, prepared using the NexteraXT DNA library preparation kit, were sequenced via the Illumina MiSeq platform with v3 chemistry (2 \u00d7 300 bp). Adapter sequences were removed, and 1,416,362 raw reads were quality filtered and trimmed using Trimmomatic v0.32 to give dnaA/repA on the forward strand), with genome coverage of 81\u00d7, which were submitted to NCBI PGAP v5.0 (The Illumina and Nanopore datasets were combined using Unicycler v0.4.3 to yieldGAP v5.0 and to PGAP v5.0 for annohttps://www.ezbiocloud.net/tools/ani) of 99.60% (Klebsiella sp. BDA134-6 (GenBank accession number CP064784) (bcs operons (Klebsiella pneumoniae recovered from the gut of a Chinese bamboo rat (Rhizomys sinensis) (The CTHL.F3a chromosome has an average nucleotide identity (by OrthoANIu online at f 99.60% with ricP064784) . It cont operons , punctua operons . Phyre2 operons finds thinensis) .https://bioinfo-mml.sjtu.edu.cn/KpVR/index.php) (Plasmid pCTHL.F3a was classified as IncFIB(K)_30 (clade II) by the KpVR Web-based tool (dex.php) . It contdex.php) but no aKlebsiella sp. CTHL.F3a are available through NCBI under BioProject PRJNA758781, with GenBank accession numbers CP082360 (chromosome) and CP082361 (plasmid) and SRA accessions SRX12151552 (MiSeq) and SRX12151553 (MinION). Klebsiella sp.Complete genome sequences and raw sequence data for"} +{"text": "Klebsiella pneumoniae (CR-cKp) and carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) isolates in southwestern Iran. From 2019 to 2021, 136 (88.9%) cKp and 17 (11.1%) hvKp isolates were identified using biochemical tests and polymerase chain reaction (PCR). Antibiotic resistance, beta-lactamases, and clonal relatedness of carbapenem-resistant isolates were investigated using disk diffusion, PCR, and enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), respectively. The different markers of hvKp isolates were as follows: string test , magA , rmpA , rmpA2 , iucA , and peg344 . Also, 55.1% (n = 75/136) of cKp and 47.1% (n = 8/17) of hvKp isolates were CR-cKp and CR-hvKp, respectively. All CR-hvKp isolates were MDR. Colistin, tetracycline, and tigecycline were the most effective antibiotics. The occurrence of beta-lactamase genes in 75 CR-cKp and 8 CR-hvKp isolates was as follows: blaNDM , blaIMP , blaVIM , blaGES , blaOXA\u201348\u2013like , blaCTX\u2013M , blaSHV , blaTEM , blaFOX , blaDHA , blaCMY , blaLAT , and blaACT . ERIC-PCR showed a high diversity among isolates. In this study, the occurrence of MDR CR-hvKp isolates harboring blaNDM and blaGES was detected for the first time in southwestern Iran. To prevent the spread of CR-hvKp and reduce selection pressure, long-term surveillance and more effective treatment strategies should be implemented.This study investigated the molecular epidemiology of carbapenem-resistant classic Klebsiella pneumoniae is one of the most important Gram-negative bacteria (GNB) causing a variety of community-acquired and nosocomial infections. It is estimated that about one-third of all Gram-negative infections are caused by this bacterium (K. pneumoniae (hvKp) characterized by hypermucoviscosity was first reported from a liver abscess with extrahepatic complications, including endophthalmitis, in Taiwan in 1986. HvKp has been implicated in community-associated infections in healthy people with the most common cases of pyogenic liver abscesses in Asia (acterium . Hypervi in Asia .Klebsiella pneumoniae (cKp) strains from hvKp. These include the string test, the regulator of mucoid phenotype A and A2 (rmpA and rmpA2), an aerobactin siderophore (iucA), the peg-344 gene, and the mucoviscosity-associated gene A (magA) (Some phenotypic and genotypic distinctive properties and determining factors differentiate classic A (magA) . The strA (magA) . TherefoK. pneumoniae. A recent systematic review and meta-analysis from Iran found a prevalence rate of 0.004\u201358% for carbapenem-resistant K. pneumoniae (CR-Kp) in different regions of the country GNB, including country . Accordi country . HoweverK. pneumoniae include the production of various beta-lactamases capable of hydrolyzing carbapenems as well as the reduced membrane permeability that occurs via loss or downregulation expression of outer membrane porins (OMPs) . CR-Kp is (OMPs) .Klebsiella pneumoniae carbapenemase (KPC), oxacillinases (OXA)-type enzymes such as OXA-48-like carbapenemases, Guiana extended-spectrum beta-lactamase (GES), imipenem-hydrolyzing beta-lactamase (IMI) and metallo-beta-lactamases (MBLs) including Verona integrin-encoded MBL (VIM), New Delhi MBL (NDM), and imipenemase (IMP) play a major role in the development of carbapenem resistance in Enterobacteriaceae (K. pneumoniae (Pseudomonas extended resistance), and VEB (Vietnamese extended-spectrum beta-lactamases) enzymes affiliated to the Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. Ahvaz is the capital of Khuzestan province which located at 31\u00b020\u2019 north latitude and 48\u00b040\u2019 east longitude, and ranks the second-largest city (with an area of about 215 km2) after Tehran, the capital of Iran , non-repetitive clinical isolates of of Iran . The afoK. pneumoniae isolates was performed using a series of standard biochemical tests including Gram stain, triple sugar iron (TSI) agar, sulfur-indole-motility (SIM) agar, lysine iron agar (LIA), ornithine decarboxylase, citrate utilization, and urea hydrolysis and incubated aerobically for 18\u201324 h at 37\u00b0C. Primary identification of drolysis . All medK. pneumoniae isolates were confirmed by polymerase chain reaction (PCR) using specific primers for the 16S\u201323S internal transcribed spacer (16S\u201323S ITS) gene (130 bp), as previously described to determine the size of PCR products compared to a 100 bp DNA ladder. The agarose gel was scanned using a UV light transilluminator . Confirmed isolates were stocked in tryptic soy broth (TSB) containing 20% glycerol and stored at \u201380\u00b0C for ongoing analysis.The presumptive escribed . To extrescribed . All PCRescribed for 30 smagA, rmpA, rmpA2, iucA, and peg344 were investigated by PCR using previously described primers , ampicillin/sulbactam (10/10 \u03bcg), aztreonam (30 \u03bcg), cefazolin (30 \u03bcg), ceftriaxone (30 \u03bcg), ceftazidime (30 \u03bcg), cefotaxime (30 \u03bcg), cefoxitin (30 \u03bcg), cefepime (30 \u03bcg), chloramphenicol (30 \u03bcg), ciprofloxacin (5 \u03bcg), ertapenem (10 \u03bcg), gentamycin (10 \u03bcg), fosfomycin (200 \u03bcg), imipenem (10 \u03bcg), meropenem (10 \u03bcg), piperacillin/tazobactam (100/10 \u03bcg), tetracycline (30 \u03bcg), tobramycin (10 \u03bcg), and trimethoprim/sulfamethoxazole (1.25/23.75 \u03bcg) were tested on Mueller\u2013Hinton agar (MHA) using the Kirby-Bauer disc diffusion method according to Clinical Laboratory Standard Institute (CLSI) procedures . Also, tectively . Any isoectively . Multiplectively . EscheriK. pneumoniae isolates that had breakpoints of \u226427 mm for cefotaxime (30 \u03bcg), \u226422 mm for ceftazidime (30 \u03bcg), and \u226425 mm for ceftriaxone (30 \u03bcg), were selected for primary ESBL screening were considered as primary AmpC producers. These isolates were further confirmed by a combined disk method using a cefoxitin disk (30 \u03bcg) alone and in combination with phenylboronic acid (PBA) (400 \u03bcg) . The cefoxitin disk and cefoxitin/PBA disk were dispensed onto an MHA plate that had already been inoculated with the test isolate by the standard disk diffusion method. Subsequently, the inoculated plates were incubated for 24 h at 37\u00b0C. The isolates were confirmed as AmpC producers when the zone diameter of cefoxitin/PBA increased by \u22655 mm compared to cefoxitin alone .E. coli ATCC\u00ae 25922\u2122. After 18\u201324 h incubation at 35 \u00b1 2\u00b0C, mCIM and eCIM results were interpreted as follows: carbapenemase positive (only mCIM positive): zone diameter of 6\u201315 mm, carbapenemase negative (mCIM negative): zone size \u2265 19 mm, MBL positive (both mCIM/eCIM positive): increase in eCIM zone size by \u22655 mm compared to zone size of mCIM together with EDTA-modified carbapenem inactivation method (eCIM) . For mCI of mCIM . It shoublaCTX\u2013M, blaSHV, blaTEM, blaPER, and blaVEB), AmpC , carbapenemase , and MBLs as previously described was performed with the previously described primers in a final volume of 25 \u03bcl containing 1 \u03bcl of each primer, 3 \u03bcl of template DNA, 12.5 of master mix , and 7.5 \u03bcl of nuclease-free water using the Biorad S1000 thermocycler (USA) . FollowiP-value \u2264 0.05) of variables were evaluated with Chi-square and Fisher\u2019s exact tests version 22.0 . Significant associations males and 71 females (46.4%). All isolates showed the 130 bp band of the 16S\u201323S ITS gene in PCR and were confirmed as K. pneumoniae. The mean \u00b1 SD age of patients was 43.1 \u00b1 16.3 (10\u201381 years) for males and 36.9 \u00b1 12.7 (11\u201382 years) for females. Using phenotypic and genotypic criteria, 136 (88.9%) and 17 (11.1%) isolates were identified as cKp and hvKp, respectively. Of all hvKp isolates, 6 (35.3%), 17 (100.0%), and 6 (35.3%) were positive for the string test, gene markers, and both, respectively. The occurrence of hvKp gene markers was as follows: magA , rmpA , rmpA2 , iucA , and peg344 . The co-occurrence of two or more markers was detected in 5 (29.4%) isolates as follows: magA/rmpA2 (n = 1), rmpA2/iucA/peg344 (n = 3), and magA/rmpA/rmpA2/iucA/peg344 (n = 1).Using standard bacteriology tests, a total of 153 presumptive n = 83/153), including 90.4% (n = 75/83) cKp and 9.6% (n = 8/83) hvKp isolates. In other words, 55.1% (n = 75/136) of cKp and 47.1% (n = 8/17) of hvKp isolates were CR-cKp and CR-hvKp, respectively. Imipenem was the most effective carbapenem against K. pneumoniae isolates, with a susceptibility rate of 48.4% (n = 74/153), followed by ertapenem , and meropenem . Of 75 CR-cKp isolates, 60 (80.0%), 8 (10.7%), and 7 (9.3%) isolates were resistant to ertapenem/imipenem/meropenem, ertapenem/meropenem, and imipenem/meropenem, respectively. However, all CR-hvKp isolates were simultaneously resistant to meropenem/imipenem/ertapenem. The carbapenem-resistant isolates had MICs ranging from 0.03 to 64 \u03bcg/mL, MIC50 = 8 \u03bcg/mL, MIC90 = 32 \u03bcg/mL for ertapenem; MICs ranging from 0.03 to 64 \u03bcg/mL, MIC50 = 16 \u03bcg/mL, MIC90 = 32 \u03bcg/mL for imipenem; and MICs ranging from 8 to 64 \u03bcg/mL, MIC50 = 16 \u03bcg/mL, MIC90 = 32 \u03bcg/mL for meropenem. The detailed antibiotic resistance rates of cKp, hvKp, CR-cKp, and CR-hvKp isolates were summarized in n = 150/153), tetracycline , and tigecycline and the highest resistance to ampicillin/sulbactam . Resistance rates to other antibiotics ranged from 29.4% (n = 45/153) for aztreonam to 64.7% (n = 99/153) for cefazolin. CR-cKp and CR-hvKp isolates showed resistance rates of more than 50.0% against gentamicin, tobramycin, amikacin, and piperacillin/tazobactam. Also, all hvKp isolates (n = 17) including CR-hvKp (n = 8) strains were susceptible to colistin, tigecycline, and tetracycline. There were no significant differences in the antibiotic resistance patterns of the cKp with hvKp isolates and the CR-cKp with CR-hvKp isolates except for tigecycline of all isolates were resistant against third-generation cephalosporins. Of 136 cKp, 1 (0.7%), 1 (0.7%), 1 (0.7%), 3 (2.2%), and 81 (59.6%) isolates were resistant to cefotaxime, cefotaxime/ceftazidime, ceftazidime/ceftriaxone, cefotaxime/ceftriaxone, and cefotaxime/ceftazidime/ceftriaxone, respectively. Of 17 hvKp, 11 (64.7%) isolates were simultaneously resistant to cefotaxime/ceftazidime/ceftriaxone. Of 75 CR-cKp isolates, 69 (92.0%) strains showed resistance against third-generation cephalosporin as follows: cefotaxime , ceftazidime/ceftriaxone , cefotaxime/ceftazidime , cefotaxime/ceftriaxone , and cefotaxime/ceftazidime/ceftriaxone . Also, all CR-hvKp were simultaneously resistant to third-generation cephalosporins. In total, 66.7% (n = 102/153) and 7.8% (n = 12/153) of isolates were MDR and XDR, respectively. None of the isolates were PDR. Of 75 CR-cKp, 84.0% (n = 63) and 16.0% (n = 12) were MDR and XDR, respectively. While, all CR-hvKp isolates were MDR (K. pneumoniae isolates had 57 (A1\u2013A57) different antibiotypes (antibiotic resistance patterns) (n = 10), A4 , and A5 were the most frequent patterns. Also, MARI ranged from 0.1 to 1.0 and the majority of isolates had MARI of \u22650.5.Using the carbapenem antibiotic disk diffusion test and the broth microdilution method, the overall resistance to carbapenems was 54.2% (ecycline . The carwere MDR . The 83 atterns) . A2 (12.n = 71/136), male patients , patients aged 26\u201341 years , urine samples , and men ward . Meanwhile, the highest occurrence of hvKp isolates was found in Golestan Hospital , male patients , patients aged 42\u201357 years , urine samples , and men ward . Similar results were obtained for CR-cKp and CR-hvKp isolates (n = 41/75) than in males . Also, the CR-hvKp isolates were more prevalent in intensive care unit (ICU) than other wards. However, the distribution of CR-cKp and CR-hvKp was not significantly different according to the various items . Althougisolates . Neverthus items .n = 69/75) and 100.0% (n = 8/8) of CR-cKp and CR-hvKp were presumptive ESBL producers, respectively (n = 20/75) and 12.5% (n = 1/8) of CR-cKp and CR-hvKp were ESBL producers, respectively. All CDT positive isolates were also positive for at least one ESBL gene by PCR. The distribution of ESBL genes among CR-cKp and CR-hvKp was as follows: for CR-cKp: blaCTX\u2013M , blaSHV , blaTEM ; and for CR-hvKp: blaCTX\u2013M , blaSHV , and blaTEM . None ofn = 59/75) of CR-cKp and 100.0% (n = 8/8) of CR-hvKp were presumptive AmpC producers, the confirmatory cefoxitin (30 \u03bcg)/phenylboronic acid method was positive in only 13.3% (n = 10/75) and 0.0% (n = 0/8) of CR-cKp and CR-hvKp isolates, respectively (n = 21/75) of CR-cKp and none of CR-hvKp isolates were AmpC producers. The PCR method detected a greater number of AmpC positive CR-cKp isolates compared with the phenotypic confirmatory test. The distribution of AmpC genes among CR-cKp was as follows: blaLAT , blaACT , blaFOX , blaDHA , and blaCMY . The blaACC was not detected in any isolate resistance criteria, 78.7% (ectively . However isolate . The disn = 26/75) and 25.0% (n = 2/8) of CR-cKp and CR-hvKp were carbapenemase producers, respectively , blaGES . Moreover, the occurrence of carbapenemase genes in CR-hvKp isolates was as follows: blaOXA\u201348\u2013like , blaGES , 34.7% (ectively . PCR shon = 2/8) . The blan = 18/75) and 25.0% (n = 2/8) of CR-cKp and CR-hvKp were MBL positive, respectively (n = 33/75) of CR-cKp and 25.0% (n = 2/8) of CR-hvKp isolates were MBL producers. The distribution of MBL genes among CR-cKp was as follows: blaNDM , blaVIM , and blaIMP . Moreover, 25.0% (n = 2/8) of CR-hvKp isolates carried blaNDM gene , 24.0% of CR-cKp and 25.0% (n = 2/8) of CR-hvKp isolates. Also, the blaCTX\u2013M/blaSHV was the second most prevalent pattern, detected in 6.7% (n = 5/75) of CR-cKp and 12.5% (n = 1/8) of CR-hvKp isolates. The frequency of co-occurrence of various beta-lactamases was as follows: MBL/carbapenemase/AmpC , MBL/carbapenemase/ESBL , carbapenemase/ESBL/AmpC , MBL/carbapenemase and MBL/AmpC , ESBL/carbapenemase, ESBL/MBL, and ESBL/AmpC , and carbapenemase/AmpC .The different genotypes of beta-lactam resistance genes were shown in n = 62/75) and 13 singletons with 57 different ERIC-types (E1\u2013E57), indicating high genetic diversity among the isolates (blaNDM positive). The remaining isolates had different beta-lactamase genotypes. The eight CR-hvKp isolates were also divided into two clusters (A and B) and two singletons with four ERIC -types (E1\u2013E4) consisting of 2\u20137 isolates . ElectroK. pneumoniae isolates, including 136 (88.9%) cKp and 17 (11.1%) hvKp isolates, were identified in different clinical samples. Previous reports from Iran by n = 14/52), n = 22/146), and n = 3/122) showed different prevalence rates of hvKp than the current study. However, n = 12/111) from Turkey reported almost the same prevalence of hvKp as in the current study. These discrepancies can be explained by the different nature and size of the samples studied and the detection method of the hvKp isolates. To date, there are no standard methods to differentiate hvKp from cKp strains, and several studies classified hvKp based on positivity of the string test and some virulence genes including rmpA, rmpA2, iucA, peg-344, and magA (n = 6/17) of hvKp had a positive string test, and all were also positive for at least one of the studied genes. However, 64.7% (n = 11/17) of hvKp isolates carrying gene markers had a negative string test. This phenomenon has also been reported in previous studies from Turkey and Iran , rmpA , rmpA2 , iucA , and peg344 . Simultaneous occurrence of two or more genes was also found in five (29.4%) isolates. In a previous study from Turkey, string test, iucA, and magA were positive in three (25.0%), eight of the hvKp isolates, respectively. However, the rmpA and peg344 genes were not detected of cKp and 47.1% (n = 8/17) of hvKp isolates were CR-cKp and CR-hvKp, respectively and showed various resistance rates against ertapenem, imipenem, and meropenem ranging from 47.1 to 54.4% revealed that a relatively high proportion (more than 50.0%) of cKp and hvKp isolates were resistant to aminoglycosides, beta-lactam combination agents (piperacillin-tazobactam and ampicillin/sulbactam), quinolones, folate pathway inhibitors, and different classes of cephalosporins. These findings were consistent with recent reports of increasing emergence of highly resistant XDR and PDR cKp and hvKp strains from different countries, including Iran, Turkey, Spain, India, Saudi Arabia, and Lebanon . Generalto 54.4% . Howevern = 3/75) of CR-cKp isolates were resistant to colistin. These observations coincided well with previous reports from Iran and 16.0% (n = 12/75) of CR-cKp were MDR and XDR, respectively. While all CR-hvKp isolates were MDR (n = 70/83) had a MARI of \u22650.5 and no PDR isolate was detected. In contrast to the current study, in previous reports by In this study, the majority of CR-cKp and CR-hvKp isolates had high resistance rates (more than 60.0%) against 18 of 23 tested antibiotics, so that 84.0% and CR-hvKp isolates were identified from urine samples, followed by blood samples for CR-cKp and tracheal tubes for CR-hvKp. Also, the CR-hvKp isolates were more prevalent in the ICU ward than in other wards. However, the distribution of CR-cKp and CR-hvKp did not differ significantly by sample type, hospital wards, and other demographic variables (P > 0.05) in this study. The reason for this observation was unclear.In this research, most CR-cKp . These f > 0.05) . Howevern = 20/75) and 12.5% (n = 1/8) of CR-cKp and CR-hvKp were ESBL producers, respectively. The PCR assay confirmed the results of the CDT phenotypic test and all CDT positive isolates harbored at least one ESBL gene. Also, the co-occurrence of ESBL genes was detected in both CR-cKp and CR-hvKp isolates, which was in line with previous reports from different countries , blaSHV , blaTEM ; and for CR-hvKp: blaCTX\u2013M , blaSHV , and blaTEM , blaSHV , and blaTEM . However, similar to the findings of the current study, the blaPER and blaVEB were not detected , blaTEM , and blaCTX\u2013M . These frequencies were higher than in the current study. Moreover, in contrast to this research, the prevalence of blaSHV was significantly higher (P = 0.048) in hvKp isolates than in cKp strains (n = 9) harbored blaSHV and blaCTX\u2013M, whereas blaTEM was not detected. In this study, the blaCTX\u2013M was the most frequent ESBL among carbapenem-resistant K. pneumoniae isolates that was in line with the previous report from Iraq . None ofdetected . Also, T strains . In anotrom Iraq . In the al ESBLs . Antibioal ESBLs .n = 21/75) of CR-cKp isolates as follows: blaLAT , blaACT , blaFOX , blaDHA , blaCMY , and blaACC . There is evidence for the role of AmpC beta-lactamase in resistance to carbapenems and increasing their MIC (blaCMY\u20132 (60.7%) and blaDHA\u20131 (34.4%) were found in K. pneumoniae isolates of CR-cKp and 25.0% (n = 2/8) of CR-hvKp, were carbapenemase producers using mCIM test. All mCIM positive isolates carried at least one carbapenemase gene. The distribution of carbapenemase genes among CR-cKp and CR-hvKp was as follows: blaOXA\u201348\u2013like and blaGES . Also, the blaKPC and blaIMI were not detected in any isolate. This study was the first to detect the blaGES carbapenemase in CR-hvKp isolates from Iran. In previous studies from Iran, blaGES was not detected in hvKp isolates (blaGES gene (27.8%) was the third most prevalent carbapenemase among carbapenem-resistant K. pneumoniae isolates was reported to be the most prevalent gene in carbapenem-resistant K. pneumoniae isolates.In this study, 34.7% of CR-cKp and 25.0% (n = 2/8) of CR-hvKp isolates were MBL positive using the mCIM/eCIM positivity criteria. PCR showed that all mCIM/eCIM positive isolates carried at least one MBL gene. However, PCR detected a greater number of MBL positive isolates than the phenotypic confirmatory test. This may be due to the co-occurrence of carbapenemases and MBLs, resulting in a false-negative eCIM test (n = 33/75) of CR-cKp and 25.0% (n = 2/8) of CR-hvKp isolates were MBL producers. The blaNDM gene was the most frequently detected MBL gene in CR-cKp (41.3%) and CR-hvKp isolates (25.0%), followed by blaVIM (8.0%) and blaIMP (4.0%) for CR-cKp. These results were in good parallel with available data that identified the blaNDM (30.1%) as the most predominant MBL type among K. pneumoniae isolates from Iran, followed by blaVIM (10.6%) and blaIMP (4.5%) of hvKp isolates (blaNDM and blaOXA\u201348 genes were frequently associated with hvKp isolates (n = 6/75) was the most co-occurrence pattern among CR-cKp isolates. In contrast, CR-hvKp isolates had only the ESBL co-existence pattern (blaCTX\u2013M/blaSHV). Contrary to these results, the co-occurrence of ESBLs and carbapenemases in hvKp isolates has been reported in previous studies from Iran . Howeverisolates . In mostisolates . This phisolates . Anotherrom Iran .K. pneumoniae isolates, several expensive and time-consuming molecular methods such as pulsed-field gel electrophoresis (PFGE), multiple locus sequence typing (MLST), and ribotyping are available based analysis for phylogenetic relatedness, pan-genome analysis and insights on the circulating plasmids and Inc groups especially among the colistin-resistant isolates.blaCTX\u2013M, blaSHV, blaNDM, and blaGES, in southwestern Iran. As a result of their hypervirulence coupled with multidrug resistance, these isolates pose a particular threat to healthcare systems. Hence, long-term surveillance and more effective treatment strategies should be implemented to prevent the spread of CR-hvKp and reduce selection pressure. Also, it is recommended to use a fast and cheap molecular method such as ERIC-PCR for primary evaluation of clonal relatedness of MDR isolates.This study was the first report of emergence of MDR CR-hvKp isolates harboring different beta-lactamases, including The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.This study was approved by the Ethics Committee of the Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran (ethics code: IR.AJUMS.REC.1398.489) according to the Declaration of Helsinki. All methods were performed in accordance with the relevant guidelines and regulations of the Ethics Committee of the Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. Clinical samples were not collected as part of this study. The clinical samples were collected as routine clinical care and to check the presence of any infection for referred and admitted patients. As a result, written informed consent was waived by the Ethics Committee of Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.MSak performed the experiments, analyzed majority of the data, and wrote the whole manuscript. MSav, MH, and MA prepared all the necessary materials and performed some of the experiments. MSav, MH, and SSS contributed to the discussion of experimental results. MA designed and supervised the experiments at different stages. All authors contributed to the article and approved the submitted version."} +{"text": "Similarly, Arabidopsis thaliana SAUR63 was able to increase growth of various organs, antagonize PP2C.D5 phosphatase, and increase H+-ATPase activity. Using a gain-of-function approach to bypass genetic redundancy, we dissected structural requirements for SAUR63 growth-promoting activity. The divergent N-terminal domain of SAUR63 has a predicted basic amphipathic \u03b1-helix and was able to drive partial PM association. Deletion of the N-terminal domain decreased PM association of a SAUR63 fusion protein, as well as decreasing protein level and eliminating growth-promoting activity. Conversely, forced PM association restored ability to promote H+-ATPase activity and cell expansion, indicating that SAUR63 is active when PM-associated. Lipid binding assays and perturbations of PM lipid composition indicate that the N-terminal domain can interact with PM anionic lipids. Mutations in the conserved SAUR domain also reduced PM association in root cells. Thus, both the N-terminal domain and the SAUR domain may cooperatively mediate the SAUR63 PM association required to promote growth.In plants, regulated cell expansion determines organ size and shape. Several members of the family of redundantly acting Small Auxin Up RNA (SAUR) proteins can stimulate plasma membrane (PM) H Plant organs reach their final shape and size after substantial cell expansion. Proton pumps at the plasma membrane promote cell expansion by acidifying the cell wall to loosen it, and by increasing electrochemical potential across the plasma membrane for solute uptake that maintains intracellular turgor. Plasma-membrane-associated proteins tightly regulate proton pump activity, in order for organs to grow to an appropriate extent. We have studied requirements for activity of one such regulatory protein in the model plant Arabidopsis called SAUR63. This protein is made rapidly in response to plant growth hormones, and it increases proton pump activity to promote organ growth. These activities depend on its binding to anionic lipids in the plasma membrane, and forced plasma membrane association of SAUR63 can increase growth. Many proteins in the same family are found within Arabidopsis and in all land plants, and likely differ in their affinity for the plasma membrane or in other properties. Further studies of other family members may show how such proteins regulate growth under diverse physiological contexts. Small Auxin Up RNA (SAUR) genes. SAUR genes are numerous in all land plants, and have evolved through extensive independent gene amplifications in multiple lineages ) of seedlings of indicated genotypes grown for 3d in darkness on plates with 0.5x MS medium. C,D) Root length (C) and root tortuosity index (D) of seedlings of indicated genotypes grown for 4d in long days on plates with 1x MS 1% Sucrose medium. E,F) Root length (E) and root tortuosity index (F) of seedlings of indicated genotypes grown for 4d in short days on plates with 0.5x MS medium. Graphs show means \u00b1 s.d. Letters in graphs indicate statistical classes based on Tukey\u2019s Honestly Significant Difference test. n from left to right: Panels A,B: 51, 24, 26, 28, 23, 25, 25; Panels C,D: 34, 17, 23, 14, 19, 15, 16; Panels E,F: 43, 21, 18, 17, 16, 15, 17. The same genotypes were measured in panels A-F, with genotype designations shown only in panels E and F. G,H,I) Hypocotyl epidermal cells of seedlings of indicated genotypes grown in short days for 2 days, visualized with the ML1:RFP shoot epidermis plasma membrane marker. Shown are z-stack confocal image projections of the near side of the hypocotyl. Scale bar, 0.1 mm. (TIF)Click here for additional data file.S4 FigA) Cotyledon area of seedlings of indicated genotypes grown on vertically oriented plates for 7d in long days in the absence (open bars) or presence (filled bars) of 1% sucrose. B) Root length of seedlings of indicated genotypes grown on vertically oriented plates for 4d in long days in the absence (open bars) or presence (filled bars) of 1% sucrose. C,F) Hypocotyl lengths (E) and hypocotyl tortuosity index of seedlings grown on vertically oriented plates for 3d in darkness without sucrose. D) Cotyledon areas of P35S:SAUR63 and P35S:CBL11-12:SAUR6326-142 seedlings grown for 6d on vertically oriented MS 1% Suc plates. E) Hypocotyl lengths of P35S:SAUR63 and P35S:CBL11-12:SAUR6326-142 seedlings grown for 4d on vertically oriented 0.5x MS plates. Panels D and E show data for the three homozygous single-locus P35S:SAUR63 lines that differed most from wild type among seven lines analyzed. Graphs show means \u00b1 s.d. Letters in graphs indicate statistical classes based on Tukey\u2019s Honestly Significant Difference test. n, from left to right: panel A: 26, 20, 25, 15, 22, 23, 24, 20, 22, 23, 19, 19, 21, 19, 21, 20; panel B: 19, 16, 18, 14, 20, 20, 21, 16, 21, 17, 19, 16, 18, 15, 16, 17; panel D: 77, 18, 17, 17, 19, 20; panel E: 119, 25, 24, 27, 21, 24; panels C and F: 35, 36, 45, 43, 47, 38, 41, 47.(TIF)Click here for additional data file.S5 FigA) Appearance of genotypes used for crosses presented in A and in B) Hypocotyl lengths of seedlings of indicated genotypes grown for 4d in short days in the absence of sucrose. Plants measured were F1 progeny of crosses of transgenic lines with each other or with wild-type Columbia, and were hemizygous for the indicated transgene(s). C) Appearance of PEST:SAUR63:CerFP:HA and wild-type seedlings grown with estradiol and in the absence or presence of 15 mM LiCl. Seedlings were grown for 3d under control conditions, and then transferred to plates with estradiol and with or without 15 mM LiCl, and grown for an additional 3d before imaging. Dots mark positions of root tips at the time of transfer to estradiol plates. Scale bar, 5 mm. D) Root growth of indicated genotypes in the absence (open bars) or presence (closed bars) of 15 mM LiCl. Seedlings were grown without LiCl for 5d, transferred to plates containing 0 or 15 mM LiCl, and root growth over the next three days was measured. E) HPTS fluorescence ratios around root cells of indicated genotypes. Data are pooled from measurements taken on three different days, each normalized to the average of wild-type values on those days. Graphs show means \u00b1 s.d. Letters in graphs indicate statistical classes based on Tukey\u2019s Honestly Significant Difference test. n, from left to right: panel B: 28, 24, 24, 30, 26, 27, 26, 25, 26, 25, 24, 20, 24, 26, 25; panel D: 21, 27, 16, 23, 19, 25, 20, 30, 18, 28, 21, 30, 23, 31, 18, 29; panel E: 26, 13, 14, 16.(TIF)Click here for additional data file.S6 FigA-D)P35S:SAUR63:YFP:HA. E-H)P35S:SAUR6326-142:YFP:HA. I-L)PUBQ10:WAVE 138Y expressing a PM-localized YFP fusion protein. M-P)PUBQ10:WAVE 1Y expressing a cytoplasmically-localized YFP fusion protein. Q-T)PUBQ10:WAVE 9Y expressing a YFP fusion protein localized to the tonoplast. Shown are fluorescence confocal microscopy images of YFP , FM4-64 membrane staining , and both channels together with vertical yellow lines indicating locations of quantitation of fluorescence intensity signals, scaled to the maximum signal along the line . Image color channel brightnesses were adjusted for visibility. Scale bar, 20 \u03bcm.(TIF)Click here for additional data file.S7 FigA-M) Confocal images showing YFP fluorescence of transgenic lines expressing the indicated fusion proteins behind the P35S promoter. Scale bar, 20 \u03bcm.(TIF)Click here for additional data file.S8 FigA-L) Confocal images showing YFP fluorescence of indicated SAUR63:YFP:HA variants expressed in transiently transformed N. benthamiana leaves. Scale bar, 20 \u03bcm.(TIF)Click here for additional data file.S9 FigA-E) Protein levels in multiple P35S:SAUR63:YFP:HA, P35S:SAUR6326-142:YFP:HA, and P35S:CBL11-12:SAUR6326-142:YFP:HA pooled T2 seedlings from different T1 transformants. The blot in panel E shows protein extracts from selected genotypes in panels A-D for side-by-side comparison in the same experiment. F,G) SAUR63:YFP:HA, SAUR6326-142:YFP:HA, SAUR631-25:YFP:HA, CBL11-12:SAUR6326-142:YFP:HA, and SAUR63m2:YFP:HA fusion proteins, detected by western blots in total (T), soluble (S) and microsomal (M) protein fractions. Lower panels show controls for loading or fractionation. \u03b1-HA detects SAUR63 fusion protein; \u03b1-AHA2 detects a membrane protein; \u03b1-UGPase and \u03b1-APX detect soluble proteins. Arrows indicate position of full-sized SAUR63:YFP:HA fusion proteins. FL, Full-length SAUR63:YFP:HA fusion protein. wt, wild-type Columbia lacking any transgene. In genotype designations, S63 is short for SAUR63. Letters and numbers after genotype designations indicate independent transgenic lines. H) Amount of SAUR63:YFP:HA and SAUR6326-142:YFP:HA proteins in whole seedling extracts at indicated times after start of cycloheximide treatment to block new protein synthesis. Fusion proteins were detected by western blots using anti-HA antibody. The Rubisco large subunit band from Ponceau S staining of the same gels is shown as a loading control. A repeat of this experiment gave a very similar result. In the lower gel, the larger band is the presumed intact SAUR6326-142:YFP:HA protein, and the lower band is a presumed smaller breakdown product. In genotype labels, S63 denotes SAUR63, letters and numbers after genotype names indicate distinct transgenic lines, FL denotes a strong full-length P35S:SAUR63:YFP:HA line used as a common standard line in most experiments, and wt indicates wild-type Columbia lacking any transgene.(TIF)Click here for additional data file.S10 FigA) Western blot showing presence of fusion proteins in extracts used in lipid blot experiments in 26-142:YFP:HA fusion proteins (upper arrow) and SAUR631-25:YFP:HA N-terminal domain fusion protein (lower arrow). B) Longer exposures of two lipid blots from C) Mock experiment in which extracts were incubated for 70 minutes in protein extraction buffer at the indicated temperatures, and then run on a gel for western blots. For both SAUR63:YFP:HA and SAUR6326-142:YFP:HA, similar amounts of protein are present after incubation at -20 C or after incubation at 22 C, as during the lipid blot binding experiment.(TIF)Click here for additional data file.S11 FigA)PEST:SAUR63NAAIRS:CerFP:HA lines grown on plates with estradiol or without estradiol (wild-type Columbia and PEST:SAUR63:CerFP:HA only). B) Western blots of total protein in estradiol-induced PEST:SAUR63NAAIRS:CerFP:HA lines using \u03b1-HA antibody.(TIF)Click here for additional data file.S12 FigA-D)P35S:SAUR63:YFP:HA. E-H)P35S:SAUR6326-142:YFP:HA. I-L)P35S:SAUR63m9:YFP:HA. M-P)P35S:SAUR63m13:YFP:HA. Q-T)P35S:SAUR63m15:YFP:HA. Shown are fluorescence confocal microscopy images of YFP , FM4-64 membrane staining , and both channels together with vertical yellow lines indicating locations of quantitation of fluorescence intensity signals, scaled to the maximum signal along the line . Image color channel brightnesses were adjusted for visibility. Panels A-D are the same as in (TIF)Click here for additional data file."} +{"text": "Plasmodium vivax apical membrane antigen-1 (pvama-1) is an important vaccine candidate against Malaria. The genetic composition assessment of pvama-1 from wide-range geography is vital to plan the antigen based vaccine designing against Malaria.P. vivax positive malaria patients from different districts of Khyber Pakhtunkhwa (KP) province of Pakistan. The highly polymorphic and immunogenic domain-I (DI) region of pvama-1 was PCR amplified and DNA sequenced. The QC based sequences raw data filtration was done using DNASTAR package. The downstream population genetic analyses were performed using MEGA4, DnaSP, Arlequin v3.5 and Network.5 resources.The blood samples were collected from 84 pvama-1 (DI) in KP samples with majorly prevalent H-14 and H-5 haplotypes. Pairwise comparative population genetics analyses identified limited to moderate genetic distinctions among the samples collected from different districts of KP, Pakistan. In context of worldwide available data, the KP samples depicted major genetic differentiation against the Korean samples with Fst\u2009=\u20090.40915 , while least distinction was observed against Indian and Iranian samples. The statistically significant negative values of Fu and Li\u2019s D* and F* tests indicate the evidence of population expansion and directional positive selection signature. The slow LD decay across the nucleotide distance in KP isolates indicates low nucleotide diversity. In context of reference pvama-1 sequence, the KP samples were identified to have 09 novel non-synonymous single nucleotide polymorphisms (nsSNPs), including several trimorphic and tetramorphic substitutions. Few of these nsSNPs are mapped within the B-cell predicted epitopic motifs of the pvama-1, and possibly modulate the immune response mechanism.The analyses unveiled total 57 haplotypes of pvama-1 DI among the P. vivax isolates acquired from widespread regions of KP province of Pakistan. The information may implicate in future vaccine designing strategies based on antigenic features of pvama-1.Low genetic differentiation was observed across the The online version contains supplementary material available at 10.1186/s12879-022-07798-1. Plasmodium. The P. vivax and P. falciparum are predominant species responsible for malaria [P. vivax is most widely distributed human malaria parasite, endemic in tropical and subtropical countries of Asia, South Pacific, Central and South America, Middle East, and North Africa [Malaria is an acute febrile infectious disease caused by vector-borne apicomplexan parasites of the genus malaria . The P. h Africa . Accordih Africa .P. vivax [Plasmodium species such as apical membrane antigen-1 (AMA-1), Circumsporozoite proteins (CSP), Merozoite surface proteins (MSP) and Duffy binding protein (DBP) are reported as potent malarial vaccine candidates\u2019 targets [Treatment and control of malaria have become a serious challenge due to drug resistance and lack of effective vaccines. The wide-range distribution, antigenic variation, relapsing and co-infection led to a collective interest towards the development of effective vaccine against P. vivax . The impP. vivax . Several targets .Plasmodium species as promising malaria vaccine candidate antigens [Plasmodium parasites [P. falciparum and P. vivax [The genetic composition assessment of vaccine candidates\u2019 loci is indispensable in modern-age to plan an effective vaccination strategy. There are ample of studies suggesting the AMA-1 of antigens . The AMAarasites , 9. The arasites \u201312. The arasites . The ectP. vivax \u201317. FurtP. vivax . This suPlasmodium vivax ama-1 (pvama-1) have been conducted in malaria endemic countries [pvama-1 genetic features from Pakistan. Particularly, no study till date is reported from remote malaria endemic regions of Khyber Pakhtunkhwa (KP) province of Pakistan. The current study was therefore designed to evaluate the genetic composition of pvama-1 among P. vivax isolates collected from widespread KP regions of Pakistan . Blood samples were obtained from 100 consented patients tested positive for pvama-1 was amplified by polymerase chain reaction (PCR) using the specific primers and amplification conditions as reported previously [Escherichia coli DH5\u03b1 competent cells, and positive clones were selected by colony PCR. The nucleotide sequence of cloned insert was analyzed by automatic DNA sequencing with M13 forward and reverse primers . The raw data was filtered for quality assessment using DNASTAR Lasergene package.A DNA fragment flanking the DI region of eviously , 29. Thepvama-1 sequence i.e. Sal-I (AF063138) and Genbank-deposited pvama-1 sequences from China Myanmar Boarder (KX495505\u2013KX495577), Iran (KF422636.1\u2013KF422681.1), Korea (KM230319.1\u2013KM230384.1), Myanmar (FJ157248.1\u2013FJ157285.1), Papua New Guinea (PNG) (KC702402.1\u2013KC702501.1), Sri Lanka (EF218679.1\u2013EF218701.1), Venezuela (EU346015.1\u2013EU346087.1), Thailand (FJ784891.1\u2013FJ784990.1), and India (EU282774.1\u2013EF025196.1). The comparative sequences analyses were performed using MEGA4 software suite [The DNA sequences data generated in the current study was analyzed in comparison with reference pvama-1 with a threshold score of\u00a0\u2265\u20090.5. The higher BepiPred score predicts higher binding affinity of epitopes with immune receptors. The non-synonymous SNPs (nsSNPs) mapping within the top predicted epitopes of pvama-1 was checked. The intrinsically unstructured regions (IURs) and RBC binding sites within the pvama-1 have previously been characterized [pvama-1. Additionally, the positive selection sites in B-cell epitopes were identified via the maximum likelihood method of Codeml [The BepiPred-2.0 server wcterized , 32; andf Codeml implemenf Codeml .2 index via DnaSP [D* and F* indices were calculated via a sliding window method using DnaSP. The population genetics statistical analyses, including pairwise fixation index (Fst), analysis of molecular variance (AMOVA), haplotype frequencies, and nucleotide diversity based on Nei\u2019s net distance (DA) were computed using Arlequin v3.5 [The DnaSP v6.12 software package was usedia DnaSP . The Tajuin v3.5 . The hapuin v3.5 .pvama-1, flanking the DI domain were amplified from genomic DNA of 84 P. vivax positive samples. The sequences data spanning the 322\u2013737 nucleotide positions of the reference pvama-1 sequence i.e. Sal-I (AF063138). The analyses identified a large numbers of single nucleotide polymorphisms (SNPs) in KP samples. Among these, the 68 were nsSNPs, i.e. causing amino acid substitutions, including 53 dimorphic, 10 trimorphic, 3 tetramorphic, and 2 pentamorphic nsSNPs. The two pentamorphic amino acid changes observed were R112K/T/E/S and S228D/N/R/K. The ten trimorphic amino acid substitutions include the N132D/G, A141E/G, E145A/G, K190E/Q, T191K/P, A199T/V, S209G/C, P210S/L, P223L/S, and V233L/P. While the three tetramorphic amino acid changes are K120R/S/G, E189N/K/G, and E227V/K/G. These amino acid substitutions were observed at varied frequencies in the KP samples. Among the 68 nsSNPS, 59 have previously been reported in literature for P. vivax isolates from different geographical origin. However, the rest of 9 nsSNPs were found specific to KP samples set of this study. These nsSNPs were observed at low frequencies, i.e. 1.1 to 1.19%. Few nsSNPs, including K120R, N132D, L140I, A141E, K190E, E227V, and S228D were commonly observed in KP samples, as well as in some other continental pvama-1 sequences with high frequency of 3.8\u2013100% of 0.978\u2009\u00b1\u20090.008 . The difference between dN/dS ratio for pvama-1 DI region was also found negative (\u2212\u20090.05413\u2009\u00b1\u20090.02) in case of KP samples set.The 416\u00a0bp sequences of pvama-1 DI\u00a0 were compared to the global pvama-1 sequences deposited in Genbank. The values of K and \u03c0 observed for KP sequences were more or less similar to previously reported sequences from Iran and India, however different from the rest of global sequences , followed by Swabi and Kohat samples. The lowest Fst was estimated between Swat and Bannu samples , followed by Swat and Hungo samples and mean pairwise differences (\u03c0xy) was observed between Bannu and Swabi samples, i.e. congruent to the Fst result . The Korean samples showed significant genetic distinction in pairwise comparison to rest of the global samples as well. Meanwhile, least genetic differentiation was observed among KP, Iranian, and Indian samples . Likewise, higher variance component was noticed within the population group i.e. 3.67534 as compare to among populations pattern of pvama-1 DI sequences of P. vivax isolates from KP, Pakistan. The LD index (R2) (Y-axis) plotted against nucleotide distance (X-axis) using a two tailed Fisher\u2019s exact test.Additional file 4: Fig S3. Pearson correlation plot of KP and global pvama-1 samples based on pairwise Fst values. The plot shows clustering and correlation between the groups in hierarchical order. The dark brackets and large sizes depict the minimum genetic distinction and high correlation.Additional file 5: Fig S4. The principle component analysis (PCA) of pvama-1 DI sequences. Different colors depict different populations groups. This include KP Pakistan (as a single group) and worldwide samples."} +{"text": "Subjects and Methods. The coexpression of PD-L1/PD-1 with CXCR3/CD36 on circulating lymphocytes was analyzed by flow cytometry in 78 lymphoma patients before and after therapy and in 50 healthy controls. The concentration levels of IL-19 in serum were assessed by an ELISA. Results. PD-L1 and PD-1 were expressed on circulating CXCR3+ and CD36+ lymphocytes in lymphoma and were significantly higher in patients with extranodal involvement than in lymphoma patients without extranodal involvement (P < 0.001). Elevated IL-19 levels were observed in lymphoma patients and increased significantly in extranodal involvement (P < 0.001). High percentages of PD-L1+CXCR3+ and PD-1+CXCR3+ lymphocytes were associated with high LDH levels, hepatomegaly, lymphedema, advanced tumor stage, and recurrence. Furthermore, patients with splenomegaly and generalized lymphadenopathy had high percentages of PD-L1+CXCR3+ lymphocytes. In addition, levels of PD-L1/PD-1 coexpression with CXCR3 and IL-19 were significantly associated with bone marrow, lung, and lymph vessel involvement. Further analysis revealed that high percentages of PD-L1+CD36+ and PD-1+CD36+ lymphocytes were associated with lung and bone marrow involvement. Patients with high levels of PD-L1/PD-1 coexpression with CXCR3 and IL-19 had inferior event-free survival (EFS) compared with that in lymphoma patients with low levels. EFS was decreased in patients with high percentages of PD-L1+CD36+ and PD-1+CD36+ lymphocytes. When using the receiver operating characteristic (ROC) curve, the superiority of IL-19 (area under the curve (AUC): 0.993) and PD-L1+CXCR3+% (AUC: 0.961) to PD-1+CXCR3+% (AUC: 0.805), PD-L1+CD36+% (AUC: 0.694), and PD-1+CD36+% (AUC 0.769) was evident in the diagnosis of extranodal involvement, identifying lymphoma patients with extranodal involvement from patients without extranodal involvement. Conclusions. Coexpression of PD-L1/PD-1 with CXCR3/CD36 in circulating lymphocytes and serum IL-19 levels contributes to poor prognosis and might be potential markers for extranodal involvement in lymphoma.Many studies have demonstrated that PD-L1/PD-1 signaling is an immune evasion mechanism in tumors. PD-L1/PD-1 coexpression with CXCR3/CD36 in peripheral lymphocytes in lymphoma still needs to be clarified. The current study investigated PD-L1/PD-1 coexpression with CXCR3/CD36 in circulating lymphocytes, serum IL-19 levels, and their correlation with clinical outcome and extranodal involvement in lymphoma. Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL) are the two forms of lymphoma , 2. Bothy , 8. The y .T cells express the regulatory inhibitory protein programmed death-1 (PD-1), a transmembrane element . MacrophCXCR3, a G protein-coupled cell surface receptor (GPCR), is present on CD4+ and CD8+ lymphocytes surface and other cells, like epithelial cells . Still, Cluster differentiation 36 (CD36) is a scavenger receptor on the surface of monocytes, adipocytes, dendritic cells, macrophages, and lymphocytes \u201333. CD36Interleukin-19 (IL-19) is a member of the IL-10 family . EssentiTumors have developed various strategies, disrupting \u201cimmune checkpoints\u201d to get through the host's immune system . The stuA total of 78 lymphoma patients and 50 healthy volunteers participated in the study. Healthy controls included thirty-six males and fourteen females. Healthy volunteers' range in age was from 26 to 70 years old. Seventy-eight lymphoma subjects ranged in age from 11 to 81 years, including 39 men and 39 women. Patients received treatment as soon as the primary diagnosis is confirmed. Patients with lymphoma were followed, and the patients were separated into two groups based on how well they responded to treatment: group I with no extranodal involvement and group II with extranodal involvement. Lymphoma patients' clinical outcomes were evaluated according to Cheson response criteria . AccordiA complete clinical examination was performed on all subjects to monitor lymphadenopathy and hepatosplenomegaly, and detailed history questionnaires were completed. To determine the performance, type, and stage of lymphoma, all patients underwent bone marrow aspiration and lymph node biopsy. The Ann Arbor classification has been considered for clinical staging . The modFollow-up for lymphoma patients was performed at the hematology clinic and by telephone. The posttherapy lymphoma status was evaluated in lymphoma patients by means of clinical examination and PET/CT scans. Patients will be evaluated every three months for the identification of lymphoma progression. The follow-up was only for 78 patients with lymphoma out of 92 patients. The follow-up could not be performed for these patients as some patients were referred to other centers, some have died, and some had rejected blood samples rewithdrawal. Event-free survival (EFS) measures the time between the end of therapy and the commencement of an event . Seven follicular cell lymphoma (FCL) and twenty-eight diffuse large B cell lymphoma (DLBCL) patients' subjects had CHOP therapy . In contAll subjects provided peripheral samples, which were taken under very sterile conditions. Eight milliliters of blood were collected. For a complete blood count (CBC), 2\u2009mL of blood was put into an EDTA tube. For flow cytometric analysis, 2\u2009mL of blood was inserted into an EDTA tube. A plain tube was filled with 4\u2009mL of blood, then centrifuged for 5 minutes at 3000\u2009rpm. Serum was isolated and used to analyze liver function tests , and aspartate aminotransferase (AST)), lactate dehydrogenase (LDH), kidney function tests (serum creatinine and blood urea), and random blood sugar. The leftover serum was kept at -70\u00b0C until the serum IL-19 concentrations were measured.A computerized hematology analyzer was used to determine CBC . Renal function analysis (blood urea nitrogen and serum creatinine), liver function analysis , and random blood sugar were performed using an autoanalyzer . An automated ACE chemistry analyzer assessed LDH .PD-1/PD-L1 coexpression with CXCR3/CD36 was determined in collected blood samples. To identify the various immune cells, the following human monoclonal antibodies were used, as directed by the manufacturer: PD-1 , CXCR3 monoclonal antibody , PD-L1 , and CD36 monoclonal antibody . Unstained cells were utilized as a negative control for every patient. Negative isotypic controls were performed using other tubes. As isotype controls, monoclonal PE-conjugated IgG2a and FITC IgG1 were used .The percentages of PD-L1+CXCR3+, PD-1+CXCR3, PD-L1+CD36+, and PD-1+CD36+ lymphocytes were calculated using flow cytometry BD FACSCanto II . In brief, a hundred microliters of anticoagulated-EDTA whole blood were stained with five uL of monoclonal antibodies and incubated at room temperature in the dark for twenty minutes. The cells were lysed using the lysing buffer and set aside for about ten minutes at room temperature in the dark. Cells were then washed two times with PBS and resuspended in 300\u2009uL of PBS solution. A minimum of 10,000 events were analyzed. Lymphocyte gating was carried out through the FSC/SSC plots (front scatter vs. side scatter technique) \u201360, and The concentrations of IL-19 in serum were assessed using an ELISA kit following the manufacturer's instructions. In the 96 wells of the microtiter strips, a specific monoclonal for IL-19 was coated (sensitivity for IL-19: 1.3\u2009pg/mL). A microtiter plate reader was used to determine optical densities at 450\u2009nm.The data were analyzed by applying the SPSS application version 25. Normally, quantitative data was analyzed by minimum and maximum range and mean and standard deviation (SD). The median and interquartile range (IQR) was utilized for quantitative nonparametric data, while percentage and number were employed for categorical data. Mann\u2013Whitney analysis was carried out to analyze quantitative nonparametric data between two groups. Kruskal-Wallis test was carried out to analyze nonparametric data between more than two groups, proceeded by pairwise comparisons between each two groups applying Bonferroni correction. Fisher's exact test, or the Chi-square test, was carried out to compare the qualitative data between groups. Association between continuous and qualitative ordinal variables was assessed by Spearman's correlation, while Pearson's correlation was performed for the association between 2 continuous variables.P values less than 0.05 were considered significant.The Kaplan-Meier analysis was carried out to assess EFS, comparing the survival curves using the log-rank test. The variables' cutoff point, area under the curve (AUC), specificity, and sensitivity were calculated using the receiver operator characteristic (ROC) curve. The study included 50 healthy individuals and 78 lymphoma patients. Normal controls included thirty-six males and fourteen females. Healthy volunteers ranged in age from 24 to 81 years old. Seventy-eight lymphoma subjects ranged in age from 11 to 81 years, including 39 males and 39 females. The criteria for all subjects are listed in (Supplementary Table N = 34) and patients with extranodal involvement (N = 34). Lymphoma patients with and without extranodal involvement revealed statistical significance regarding sex (P = 0.039), stage (P < 0.001), recurrence (P < 0.001), and death (P = 0.018). Among lymphoma subjects with extranodal involvement, 73.5% had a recurrence, and 20.6% died. 26.5% of patients with extranodal involvement presented with stage III diseases, while 58.8% had stage IV diseases. Only 2.9% of patients with extranodal involvement had stage I, and 11.8% had stage II .P < 0.001). Interestingly, PD-L1+CD36+% and PD-1+CD36+% in newly diagnosed lymphoma subjects were significantly higher than in healthy volunteers .n = 34) or without extranodal involvement (n = 44) (P < 0.001) (P < 0.001) . Postthe< 0.001) . When co< 0.001) .P < 0.001, respectively) . Moreover, lymphoma patients had higher posttherapy IL-19 levels than the normal controls .P < 0.001) (P < 0.001) , which was significantly higher than that of subjects without extranodal invasion with a median of 46.5\u2009pg/mL (range: 33-137.5) (< 0.001) . Interes< 0.001) .P < 0.05). Furthermore, compared to the PR, recurrence, and refractory groups, the CR group had a significant reduction in posttherapy IL-19, CXCR3+%, PD-L1+CXCR3+%, and PD-1+CXCR3+% (P < 0.05). Additionally, PD-L1+CD36+% and PD-1+CD36+% were significantly lower in subjects with CR compared to the other groups. Contrarily, comparing the CR group to the other groups, there was a substantial rise in posttherapy CD36+% .P < 0.001). However, no significant difference was observed when subjects with CR were compared to the treatment-refractory patients (P = 0.092 and P = 0.055). In addition, the CR patients' PD-L1+CD36+% and PD-1+CD36+\u2009% were significantly lower than those in the PR group (P = 0.037 and P = 0.002). However, no significant difference was detected between the CR group and the recurrence group or the refractory group (P > 0.05) (The CR group showed a significant reduction in pretherapy PD-1+CXCR3+% and posttherapy PD-L1+CXCR3+% compared to the PR group and recurrence group ( > 0.05) .P < 0.001). Additionally, the recurrence group's posttherapy IL-19 levels, PD-L1+CXCR3+, and PD-1+CXCR3+% were significantly higher than those of PR patients (P = 0.022 and P = 0.002). However, no significant differences were observed when the treatment-refractory group compared to PR or recurrence groups (P > 0.05) . Further > 0.05) .r = 0.344, P = 0.002; r = 0.375, P = 0.001; r = 0.315, P = 0.005, respectively). However, negative associations between CXCR3+%, PD-L1/PD-1+CXCR3%, and albumin levels were identified . Additionally, there was a negative association between PD-L1+CXCR3+% and hemoglobin .r = 0.464, P < 0.001; r = 0.398, P < 0.001, r = 0.335, P = 0.003). Data revealed that CXCR3+%, PD-L1+CXCR3+%, and PD-1+CXCR3+% positively correlated with lymphoma stages and general lymphadenopathy . Furthermore, CXCR3+% and PD-L1+CXCR3+% positively correlated with BCR-ABL . Additionally, CXCR3+%, PD-L1+CXCR3+%, and PD-1+CXCR3+% had a significant association with lymphoma recurrence (P > 0.05) . Moreove= 0.006) . CD36+%, > 0.05) .r = 0.349 and P = 0.002), hepatomegaly (r = 0.362 and P = 0.001), and splenomegaly (r = 0.231 and P = 0.042). Furthermore, pretherapy IL-19 levels were significantly associated with lymphedema, general lymphadenopathy, and recurrence .r = 0.771, P < 0.001; r = 0.793, P < 0.001; r = 0.528, P < 0.001). CXCR3+%, PD-L1+CXCR3+%, and PD-1+CXCR3+% had a positive association with bone marrow involvement . Moreover, CXCR3+%, PD-L1+CXCR3+%, and PD-1+CXCR3+% were positively associated with lymph vessel involvement . Additionally, a significant association between CXCR3+%, PD-L1+CXCR3+%, PD-1+CXCR3+%, and lung involvement was identified .r = 0.333, P = 0.003; r = 0.469, P < 0.001), while CD36+% had a negative association with extranodal involvement (r = \u22120.792 and P < 0.001). Of interest, PD-L1+CD36+% and PD-1+CD36+% were positively correlated with bone marrow infiltration . PD-1+CD36+% was positively correlated with lung involvement . CD36% was negatively correlated with bone marrow and lymph vessel involvement . Furthermore, percentages of CD36+ lymphocytes were correlated with spleen infiltration .r = 0.848; P < 0.001). IL-19 levels are positively associated with bone marrow and lymph vessel involvement . Similarly, a positive association between posttherapy IL-19 levels and lung involvement was identified .The effect of the markers on EFS was assessed using Kaplan-Meier statistics . SurvivaP < 0.001) (P < 0.001) (P < 0.001) . High pr< 0.001) . A prolo Figures .The effect of the immune markers on overall survival and recurrence-free survival was determined using Kaplan-Meier statistics (data not shown). Patients with low pre- and posttherapy CXCR3+%, PD-L1+CXC3+%, and PD-1+CXCR3+% do better than those with a high percentage. Furthermore, low PD-L1+CD36+% and PD-L1+CD36+% predicted a more prolonged survival and recurrence-free time.P < 0.001, respectively) . The pretherapy IL-19 cut-off was >209\u2009pg/mL, with specificity and sensitivity 75% and 91.18% at a cutoff >49, >40, and >3, respectively . Posttherapy CD36+% had the best sensitivity of 100% and the best specificity of 95.45% . Posttherapy CD36+%, PDL-1+CD36+%, and PD-1+CD36+% had cutoff levels \u226437, > 11, and>3 , with a cutoff >280\u2009pg/mL for diagnosis of extranodal involvement. IL-19 showed 100% sensitivity and 97.73% specificity . The specificity and sensitivity were 97.73% and 100% at a cut-off >280\u2009pg/mL.PD-L1/PD-1 coexpression with CXCR3/CD36 in identifying patients with extranodal involvement was assessed using ROC curves. The AUCs of the pre- and posttherapy PD-L1+CXCR3+% were 0.981 and 0.961, respectively, with high specificity and sensitivity. The cut-off values were >33 and >40. CXCR3+% and PD-L1+CXCR3+% yielded the best sensitivity and specificity. Moreover, the ROC curve was assessed for posttherapy PD-L1/PD-1+CD36+ percentages. The AUCs were 0.694 and 0.769, with reduced sensitivity and specificity. Thus, according to the findings, PD-L1/PD-1+CD36+% is insufficient for identifying extranodal involvement in lymphoma patients. Furthermore, the pretherapy IL-19 ROC curves demonstrated a pattern of extranodal involvement (This study had some limitations: (1) the small size of the subjects in this study; (2) short follow-up time, longer follow-up, and multicenter collaborations are needed to confirm PD-L1/PD-1's role; (3) PD-L1/PD-1 coexpression with CXCR3/CD36 should be investigated in tumor tissue; (4) cell function activities such as differentiation, proliferation, apoptosis, and cytokine release were not carried out; future research will investigate these issues; (5) PD-L1/PD-1 coexpression with CXCR3/CD36 was not investigated in different lymphocyte subsets; further studies are required.In conclusion, PD-L1/PD-1 coexpression with CXCR3/CD36 and serum IL-19 may be involved in lymphoma extranodal involvement and have prognostic and predictive values in lymphoma. The findings could also shed light on the role of circulating CXCR3 and CD36-positive lymphocyte cells in lymphoma. Future clinical trials and research are required to create new treatments based on PD-L1/PD-1-induced lymphoma immune evasion mechanisms and host immune response regulation. The combination of PD-L1/PD-1 blockades, anti-CXCR3/CD36, and IL-19 monoclonal antibody therapy might start a new era for immunotherapy. PD-L1+CXCR3+ lymphocytes and serum IL-19 might play a more important role in poor clinical behavior in lymphoma."} +{"text": "The second paragraph of Acknowledgments should read as follows: \u201cWe gratefully acknowledge funding from the following sources: Czech Science Foundation grants 20-23513S to H.H., 18-17529S to A.Z., and 20-04150Y to O.G.; Czech Ministry of Education grant OPVVV16_019/0000759; and Czech BioImaging grant LM2015062.\u201dVolume 6, no. 3, e00327-21, 2021,"} +{"text": "Brassica rapa, we identified 28 putative HSP70 gene family members using state-of-the-art bioinformatics-based tools and methods. Based on chromosomal mapping, HSP70 genes were the most differentially distributed on chromosome A03 and the least distributed on chromosome A05. Ka/Ks analysis revealed that B. rapa evolution was subjected to intense purifying selection of the HSP70 gene family. RNA-sequencing data and expression profiling showed that heat and cold stress induced HSP70 genes. The qRT-PCR results verified that the HSP70 genes in Chinese cabbage (Brassica rapa ssp. pekinensis) are stress-inducible under both cold and heat stress. The upregulated expression pattern of these genes indicated the potential of HSP70 to mitigate environmental stress. These findings further explain the molecular mechanism underlying the responses of HSP70 to heat and cold stress.Heat shock proteins protect plants from abiotic stress, such as salt, drought, heat, and cold stress. HSP70 is one of the major members of the heat shock protein family. To explore the mechanism of HSP70 in The heat shock transcription factor family strengthens plants under biotic and abiotic stress conditions; as a result, plants proceed with normal growth and development . TemperaArabidopsis, HSP70 deficient plants showed the stunted plant growth and abnormal leaf phenotype [Arabidopsis plant development under abiotic stress conditions [Brassica rapa family member. This vegetable-based family includes cabbage, Chinese cabbage, mustard, and turnip, which are sources of oil, amino acids, and proteins for humans and animals. These vegetables are highly susceptible to temperature stress [The HSP70 family, which encodes HSP70 proteins, has been identified and studied in many plants, such as Arabidopsis (17 genes), rice (26 genes), spinach 12 genes), and soybean (61 genes) . In Arabhenotype , double henotype . Further genes, ae stress and are e stress .Brassica rapa has gained remarkable economic and nutritional value due to its heading trait, which makes it highly susceptible to stress. Under temperature stress, the leaves become pale and weakened due to chloroplast damage, and the plant becomes unable to properly regulate photosynthesis [Brassica rapa to date. We identified and explored the members of the HSP70 gene family, constructed their evolutionary tree and synteny correlations, and predicted protein structures with available bioinformatics software. Moreover, we analyzed the expression of these proteins by qRT-PCR to determine their responses to heat shock stress in Chinese cabbage (Brassica rapa subsp. Pekinensis). These findings will open up new gates for understanding the structure, function, and expression of HSP70 genes in B. rapa.ynthesis . Under sA. thaliana HSP70 family genes (AT3G12580.1) was obtained from the TAIR Arabidopsis genome database (TAIR-Home Page arabidopsis.org (accessed on 20 April 2022). This sequence was used as a query to retrieve the HSP70 genes in the Brassica database . Secondly, the HMMER 3.1 and BLASTP with the threshold e-value set to 1e\u22125 were performed using the Hidden Markov Model (HMM V 3.0) profiles of the HSP70 gene family (PF00012) were downloaded from the Pfam protein database and used as the inquiry, The default limitation of HMMER 3.1 was set to 0.01. Finally, total of 28 HSP70 were retrieved in the Brassica rapa genome. B.rapaHSP70 proteins were further characterized by determining the molecular weight, number of amino acids, isoelectric point, and grand average of hydropathicity (GRAVY) through the ProtParam tool . The protein sequences were uploaded to the online database Wolf PSORT for the prediction of subcellular localization . Furthermore, the protein conserved domain was identified using the NCBI conserved domain online server and motif analysis was performed by using MEME Suite . The gene structure was predicted by the Gene Structure Display Server (GSDS) , using the CDS and genomic sequences of 28 selected B.rapaHSP70. Furthermore, prediction of the subcellular location pattern of each B.rapaHSP70 was carried out using the WoLF PSORT server .Arabidopsis, B. oleracea, and B. napus were retrieved to construct the phylogenetic tree using MEGA X (V 6.06) software . The sequences were multiple aligned and employed using the neighbor-joining (NJ) method with 1000 bootstrap replicates [B. rapa with B. oleracea, B. napus, and Arabidopsis were developed using MCScanX to obtain collinearity files that were used to build dual synteny plots in TBtools .The protein sequences of HSP70s from plicates . SyntenyB. rapa [B. rapa and its closely related species through TBtools [Duplicated genes were retrieved using the Blast, MCScanX, and Advance Circos features of TBtools . For theB. rapa ,20. Synt TBtools .B.rapaHSP70 genes were classified, and the 2000 bp upstream of the start codon were downloaded from the BRAD database . The PlantCARE web-based tool was used for further classification, and the results were presented using TBtools. The graphical construction of the 3-dimensional (3D) structure of B.rapaHSP70 proteins was done using the online web-based software PHYRE2 (PHYRE2 Protein Fold Recognition Server (ic.ac.uk), selecting the fold recognition method [Putative cis-elements of the 28 B.rapaHSP70 were used to determine the interaction of genes with microRNAs using the psRNATarget database , and the interactions were further prophesied by Cytoscape Software. Gene ontology (GO) annotation was performed to explore functional characteristics. The B.rapaHSP70 gene sequences were uploaded to the online eggNOG database . Then, the GO annotation data were handled by using and graphical demonstration was given by using OmicShare .CDS sequences of B.rapaHSP70 genes in different tissues, and a heat map was constructed using TbTools [http://www.ncbi.nlm.nih.gov/geo/, accessed on 20 April 2022) under accession no. GSE43245. In addition, expression profiles of B.rapaHSP70 under cold and heat stress conditions were obtained by performing qRT-PCR.RNA-seq data were used to determine the expression of TbTools . The datSeeds of Chinese cabbage were grown in pots containing soil: vermiculite mixture (3:1) in a controlled chamber until they reached the five-leaf stage. Cold and heat stress conditions were applied to five-leaf seedlings. Seedlings were transferred to 4 \u00b0C for cold stress and 45 \u00b0C for heat stress under the same day/night and humidity conditions. Three biological replications were used in both stress conditions. Leaf samples were harvested after 0, 1, 3, 6, 12, and 24 h, placed in liquid nitrogen, and stored at \u221280 \u00b0C [B.rapaHSP70 gene expression; actin was used as the internal reference gene in Chinese cabbage. All primers used in this experiment are listed in \u2212\u0394\u0394Ct method was used to check the relative expression levels, and the results were graphically represented [Leaf samples were used to extract the RNA, and qRT-PCR was performed with three replicates to check resented .B.rapaHSP70-1\u2013B.rapaHSP70-28. These proteins were further analyzed for the HSP70 domain (PF00012) , equal number and similar motif are present within each group except in group 4 , and the longest was B.rapaHSP70-28 (894 aa). The genes that translate into HSP70 proteins were distributed on 10 chromosomes, A01\u2013A10. Among these, the maximum genes were distributed on chromosome A03 and the minimum on chromosomes A02, A04 and A05 , and all selected genes were named PF00012) . Conserv group 4 A. Detail group 4 . Gene st group 4 B. The am and A05 .B.rapaHSP70, B.nHSP70, B.olHSP70, and AtHSP70 were analyzed. Based on domains and a phylogenetic tree, 77 HSP70s were clustered into six major groups and Arabidopsis.The evolutionary relationships between , and E) . The resB.rapaHSP70 genes in the B. rapa genome. We detected duplicated gene couples among the 28 B.rapaHSP70 genes identified in B. rapa , B. napus (AC), and B. oleracea (CC)\u00a0using collinearity analysis. In addition, a comparative synteny analysis of HSP70 gene pairs among B. rapa, B. napus, B. oleracea, and A. thaliana was conducted (B. rapa (such as Chinese cabbage) and B. oleracea (Cabbage) and B. napus (Mustard) was included due the presence of both sub genome (A and C). B.rapaHSP70 displayed the most collinearity with B. napus, followed by A. thaliana and B. oleracea. Results demonstrated that homologues genes from A genome of B. rapa are present in A as well as C genome of B.napus. Similar behavior was also observed in C genome of B. oleracea. These results suggest that, in addition to the whole genome duplication event, an independent duplication event also occurred during the evolution of these species.BraA10g033140.3C/BraA10g033130.3C, BraA09g038510.3C/BraA01g027130.3C, BraA01g038810.3C/BraA03g035360.3C, BraA08g029700.3C/BraA06g012060.3C, BraA03g019440.3C/BraA03g016490.3C, BraA03g051830.3C/BraA08g020460.3C, BraA02g003050.3C/BraA03g003930.3C, BraA08g021750.3C/BraA01g001130.3C, BraA03g047170.3C/BraA01g019900.3C, and BraA06g001280.3C/BraA04g004290.3C were determined A, which onducted B. We selB.rapaHSP70 genes was retrieved and uploaded to the PlantCare database to examine the cis-elements in the promoter region. The graphical representation helices and beta (\u03b2) sheets, because proteins with similar structures often have similar functions topology, thus preserving conserved signature fold of HSP70 family with central mixed \u03b2-sheet sandwiched between \u03b1-helices [B.rapaHSP70 protein family.With the advent of graphical visualization of genomic data, 3D protein structures also explain the properties, as well as facilitate the comparative studies, of proteins. All 28 unctions . Protein-helices . On the B.rapaHSP70 genes, we identified the miRNAs associated with the identified genes , cellular component (CC), and biological process (BP), were investigated to further explore the ed terms . Some ofed terms .The GO-MF (Molecular Function) enrichment results detected 19 enriched terms, namely, protein serine/threonine phosphatase activity (GO:0004722 and GO:0004674), manganese ion binding (GO:0030145), pectate lyase activity (GO:0030570), 1-phosphatidylinositol binding (GO:0005545), glycoprotein binding (GO:0005515), DNA-binding transcription factor activity (GO:0003700), calmodulin binding (GO:0005516), cobalt ion binding (GO:0050897), clathrin binding (GO:0030276), ATP binding (GO:0005524 and GO:0005524), oligopeptide transmembrane transporter activity (GO:0015198), oxidoreductase activity (GO:0016491 and GO:0016491), glutathione peroxidase activity (GO:0004602), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity (GO:0046537), protein serine/threonine kinase activity (GO:0004674), beta-amylase activity (GO:0016161), and maltose biosynthetic process (GO:0000024).The GO-BP enrichment results detected 26 enriched terms, namely, floral organ development (GO:0048437), oxidative stress responsive (GO:0006979), signal transduction (GO:0007165), signal transduction (GO:0006857), defense response (GO:0006952), pollen development (GO:0009555), male gamete generation (GO:0048235), signal transduction by cis-phosphorylation (GO:0007165), clathrin coat assembly (GO:0048268), regulation of transcription (GO:0006355), metabolic process (GO:0008152), salt stress responsive (GO:0009651), transmembrane transport (GO:0055085), plasma membrane organization (GO:0007009), glycolytic process (GO:0006096), abscisic acid responsive (GO:0009737), transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169), protein phosphorylation (GO:0006468), starch catabolic process (GO:0005983), cold stress responsive (GO:0009409), cadmium sensitivity/resistance (GO:0046686), regulation of meristem growth (GO:0010075), cadmium ion responsive (GO:0046686), temperature stimulus responsive (GO:0009409), maltose biosynthetic process (GO:0000024), and protein phosphorylation (GO:0006468).The GO-CC (cellular component) enrichment results detected 29 enriched terms, including mitochondrial protein-transporting ATPase activity (GO:0005739 and GO:0005739), plasma membrane (GO:0005886), chloroplast envelope (GO:0009941), endomembrane system (GO:0012505), nucleus (GO:0005634 and GO:0005634), chloroplast (GO:0009507), apoplast (GO:0048046), endomembrane system (GO:0012505), chloroplast stroma (GO:0009570), cytosol (GO:0005829), clathrin coat (GO:0030118), mitochondrial envelope (GO:0005740), vacuole (GO:0005773), and integral component of membrane (GO:0016021) .B.rapaHSP70 genes, we examined 8 tissues and organs of B. rapa at various growth phases based on RNA-seq data of B. rapa under accession no. GSE43245. For instance, the expression patterns of most B.rapaHSP70 genes in the silique, callus, and flower were higher than those of other tissues showed no transcript changes in any tissue/organ.To illustrate the transcript levels of the tissues . Three BB.rapaHSP70 genes varied in various tissues and organs. In silique, the expression level of B.rapaHSP70-4, B.rapaHSP70-9, and B.rapaHSP70-24 showing higher expression, and that of B.rapaHSP70-19 was lowest. In callus, B.rapaHSP70-25 was highly expressed, and B.rapaHSP70-10, B.rapaHSP70-11, B.rapaHSP70-12, B.rapaHSP70-16, B.rapaHSP70-18, B.rapaHSP70-20, B.rapaHSP70-4, and B.rapaHSP70-4 was the least expressed. In callus, B.rapaHSP70-4, B.rapaHSP70-9, B.rapaHSP70-24 and B.rapaHSP70-25 are expressing highly and B.rapaHSP70-10, B.rapaHSP70-11, B.rapaHSP70-12, B.rapaHSP70-18, B.rapaHSP70-22 and B.rapaHSP70-28 are showing no expression change. In stem, B.rapaHSP70-4, B.rapaHSP70-9, B.rapaHSP70-24 and B.rapaHSP70-25 are highly expressing, whereas B.rapaHSP70-10, B.rapaHSP70-11, B.rapaHSP70-12, B.rapaHSP70-16, B.rapaHSP70-20, and B.rapaHSP70-26 showing no expression change. In roots, B.rapaHSP70-4, B.rapaHSP70-9, B.rapaHSP70-24, and B.rapaHSP70-25 are highly expressed, whereas B.rapaHSP70-10, B.rapaHSP70-11, B.rapaHSP70-12, B.rapaHSP70-16, B.rapaHSP70-20, and B.rapaHSP70-26 showing no expression change. In flower, B.rapaHSP70-4, B.rapaHSP70-9, and B.rapaHSP70-24 are highly expressed genes, whereas B.rapaHSP70-10, B.rapaHSP70-11, B.rapaHSP70-12, B.rapaHSP70-16, and B.rapaHSP70-22 showing zero expression change. Lastly, the expression was analyzed in leaf, according to the expression pattern the B.rapaHSP70-4, B.rapaHSP70-9, B.rapaHSP70-17, B.rapaHSP70-24, and B.rapaHSP70-25 showing higher expression whereas B.rapaHSP70-10, B.rapaHSP70-11, B.rapaHSP70-12, B.rapaHSP70-16, B.rapaHSP70-20, and B.rapaHSP70-26 showing no expression change. These findings suggest that these candidate genes may play diverse roles in regulating B. rapa growth processes were upregulated under high-temperature stress at different time intervals, and most were highly expressed after 24 h of heat stress. The expression levels of 16 B.rapaHSP70s were high at different time intervals under cold stress as B. rapa. We identified 28 gene family members of HSP70 in B. rapa, which is higher than that found in Arabidopsis (11 AtHSP70) [The model plant B.rapaHSP70 were confirmed by the correlation between intron numbers and motif arrangements in combination with phylogeny. A phylogenetic tree was created to show the evolutionary relationships between B. rapa, B. napus, B. oleracea, and Arabidopsis. Recently, research has examined the evolutionary associations among these species [Notably, genes within the same phylogenetic subgroup had similar motif compositions and exon/intron structures . Genes w species ,34.B.rapaHSP70 family genes and we find all the duplicated B.rapaHSP70s are segmental duplicated.During the genome evolution process, gene duplications and chromosomal segments are major forces in the evolution of plant genome structure and content . Tandem A. thaliana were identified and subjected to promoter analysis to investigate the presence of temperature-associated (heat shock element (HSE)) and dehydration-associated cis-elements [Previously, a total of 11 HSP70 genes from nt; DRE) . Based oB. rapa stress tolerance. Furthermore, GO enrichment analysis supports the findings of the HSP70 gene association with stress tolerance [B.rapaHSP70 genes in post-transcriptional gene regulation . In the nditions ,38. For nditions . Similarinensis) . These s70 genes .StHSP20 under heat stress. In another study, the results verified the involvement of B.rapaHSP70 proteins in thermotolerance [B. rapa and other plant species. In this study, we laid a foundation for recognizing signaling controlled by HSP70 proteins under biotic and abiotic stress conditions.The expression patterns of genes are associated with their function . Severalolerance . Until nB. rapa, and 28 putative members were identified. In silico analyses were performed, including gene structure, distribution, phylogenetic relationship, and syntenic studies, which helped to explore the evolutionary properties of the HSP70 gene family in B. rapa. In addition, targeted miRNAs, promotor cis-acting regulatory elements, and gene ontology (GO) were executed. The finding of all these analysis elucidating that B.rapaHSP70s are targeted by 34 different families of microRNAs, these genes are highly responsive to light, temperature and phytohormones, and B.rapaHSP70s are involved in the Biological, cellular and molecular functioning of B. rapa, respectively. Three dimensional protein structural knowledge can help improve crop properties, such as improving stress resistance and biomass yield. Furthermore, quantitative real-time PCR results indicated that HSP70 genes are strongly involved in heat and cold stress responses in B. rapa plants. To a large extent, all analyses performed on the HSP70 gene family will lay the foundation for further studies of molecular and physiological functions in Brassica crops.In the current study, we performed a genome-wide analysis of the HSP70 gene family in"} +{"text": "Saussurea costus is a plant traditionally used for the treatment of several ailments. Our study accomplished the UPLC/T-TOF\u2013MS/MS analysis of a methanol extract of Saussurea costus roots (MESC), in addition to lipoidal matter determination and assessment of its in vivo hepatoprotective activity. In this study, we were able to identify the major metabolites in MESC rather than the previously known isolated compounds, improving our knowledge of its chemical constituents. The flavones apigenin, acacetin, baicalein, luteolin, and diosmetin, and the flavonol aglycones quercetin, kaempferol, isorhamnetin, gossypetin, and myricetin and/or their glycosides and glucuronic derivatives were the major identified compounds. The hepatoprotective activity of MESC was evaluated by measuring catalase activity using UV spectrophotometry, inflammatory cytokines and apoptotic markers using ELISA techniques, and genetic markers using PCR. Paracetamol toxicity caused a significant increase in plasma caspase 2, cytokeratin 18 (CK18), liver tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin 6 (IL-6), miRNA-34a, and miRNA-223, as well as a significant decrease in liver catalase (CAT) activity and in the levels of liver nuclear factor 1\u03b1 (HNF-1\u03b1), sirtuin-1, and C/ebp\u03b1. Oral pretreatment with MESC (200 mg/kg) showed a significant decrease in caspase 2, CK18, TNF-\u03b1, IL-6 and a significant increase in liver CAT activity. MESC decreased the levels of liver miRNA-34a and miRNA-223 and induced HNF-1\u03b1, sirtuin-1, and C/ebp\u03b1 gene expression. The histological examination showed a significant normalization in rats pretreated with MESC. Our findings showed that Saussurea costus may exert a potent hepatoprotective activity through the modulation of the expression of cellular cytokines, miRNA-34a, and miRNA-223. Saussurea costus is considered one of the most important traditional Chinese medicinal plants. It is a rich source of various bioactive phytoconstituents, and its genus comprises about 300 species +. Luteolin-O-hexoside (21) exhibited a deprotonated molecule [M-H]\u2212 at m/z 447.0966; we then observed a subsequent loss of 162 amu for hexose at m/z 285.0520 [M-H-hexose]\u2212, while luteolin-C-hexoside (31) showed a protonated molecule [M+H]+ at m/z 449.1549. Luteolin-di-O-hexoside (13) exhibited a deprotonated molecule [M-H]\u2212 at m/z 609.1462; moreover, luteolin aglycone (40) was detected with a deprotonated molecule [M-H]\u2212 at m/z 285.039, and characteristic peaks at m/z 269.1614 [M-H-OH]\u2212 and 151.0980 indicated a dihydroxy-substituted A-ring [The glycoside diosmin (24) exhibited a protonated molecule [M+H]hexoside exhibitem/z 577.1506 and a fragment at m/z 269.0386 [M-H-neohesperidose]\u2212. Apigenin-C-hexoside (22) showed a protonated molecule [M+H]+ at m/z 433.1232; however, apigenin-O-hexoside (32) showed a protonated molecule [M+H]+ at m/z 433.1851 and a fragment ion peak at m/z 271.1296 [M+H-hexose]+. Moreover, apigenin aglycone (34) was detected at m/z 269.0434 [M-H]\u2212 [O-rutinoside (10) showed a protonated molecule [M+H]+ at m/z 593.1631; on the other hand, acacetin aglycone (39) exhibited a deprotonated molecule [M-H]\u2212 at m/z 283.1895 and a production at m/z 253.1469 corresponding to [M-H-OCH3]\u2212. Baicalein-O-glycuronide (14) showed a protonated molecule [M+H]+ at m/z 477.0679.Rhoifolin glycoside (Apigenin neohesperidoside) (20) showed a deprotonated molecule [M-H] at hexoside showed a+ at m/z 319.1651 [m/z 481.1810 [M+H]+ and also showed a fragment at m/z 319.0663 [M+H-hexose]+. Quercetin hexoside (19) showed a protonated molecule [M+H]+ at m/z 465.1058; The neutral loss of 162 amu of the hexose moiety was observed in MS2 fragmentations at m/z 303.0471 [M+H-hexose]+. Quercetin glucuronide (11) was detected at m/z 477.0659 [M-H]\u2212, and the neutral loss of 176 Daltons of the glycuronic moiety was confirmed by an ion at m/z 301.0332 [M-H-glycuronic acid]\u2212. Quercetin pentoside (15) showed a deprotonated molecule [M-H]\u2212 at m/z 433.1094; however, quercetin aglycone (28) was confirmed by an ion peak at m/z 303.0966 [M+H]+ \u2212 of kaempferol neohesperidoside (16) was detected at m/z 593.1527. Isorhamnetin-O-hexoside (25) was detected by the presence of a protonated molecule [M+H]+ at m/z 479.1228, a production at m/z 317.0612 corresponding to [M+H-hexose]+, and a characteristic fragment at m/z 285.0323 319.1651 . Gossype6 [M+H]+ . Kaempfe285.0323 . The dep+ at m/z 273.0884 and a characteristic fragment at m/z 147.0214 [M+H-C6H6O3]+ [\u2212 at m/z 301.2041. Formononetin-O-hexoside (29) showed a protonated molecule [M+H]+ at m/z 431.1681 and a fragment at m/z 269.1243 [M+H-hexose]+. The deprotonated molecule [M-H]\u2212 of formononetin aglycone (37) was detected at m/z 267.0712 and yielded a fragment due to the methyl group loss at m/z 252.0420 [C-hexoside (18) showed a deprotonated molecule [M-H]\u2212 at m/z 415.1944, while daidzein aglycone (27) was detected at m/z 255.0551.Naringenin aglycone (36) showed a protonated molecule [M+H]C6H6O3]+ . Hespere+ at m/z 579.1859 and a fragment ion at m/z 561.1873 [M+H-H2O]+. Petunidin-O-hexoside (26) showed a protonated molecule [M+H]+ at m/z 479.0961 and a fragment ion at m/z 317.0662 [M+H-hexose]+. Malvidin-O-hexoside (33) was detected at m/z 491.1155 [M-H]\u2212 and confirmed by a fragment at m/z 329.0696 for [M-H-hexose]\u2212.Procyanidin B2 (12) showed a protonated molecule [M+H]m/z 191.0349 [M-H]\u2212, and daphnetin (46), which was confirmed by a peak at m/z 179.0861 [M+H]+ with a fragment at m/z 163.0503. Aldehydes were tentatively identified as hexenal (47), showing a protonated molecule [M+H]+ at m/z 99.0437 and a fragment ion at m/z 83.0493, while cinnamaldehyde (48) showed a protonated molecule [M+H]+ at m/z 133.1001 and a fragment ion at m/z 117.0684 + at m/z 415.3205, in accordance with published data [Tentatively identified coumarins were scopoletin (44), that was detected in both modes at 117.0684 . The chehed data ,29.2 as in succinic and malic acids [The common neutral loss of 44 Daltons was observed in MS2 fragmentations of phenolic and organic acids due to the loss of COctively) . The ideIn the present study, MESC was evaluated for its hepatoprotective activity in paracetamol-induced liver toxicity. Plasma caspase 2 and cytokeratin 18 (CK18) were elevated in the group Gp II in comparison with the control group. Hofer et al. reported that caspase-cleaved cytokeratin 18 (CK18-Asp396) values were increased significantly in Gp II . Caspasep < 0.01) in plasma caspase 2 and CK18 levels, corresponding to 346.39% and 139.31% increases, respectively, as compared to the levels in Gp I, considering the values in the control group as 100% (Toxicity by paracetamol (1 g/kg) led to a significant elevation ( as 100% . Pretreap < 0.01) in liver CAT level by 50.37%, compared to the levels in Gp I , resulting in inflammation ,41. MESCp < 0.05) were observed (p < 0.05) in C/ebp\u03b1, HNF-1\u03b1, and sirtuin-1 gene expression and a significant decrease (p < 0.05) of liver miRNA-34a and miRNA-223 genes expression compared to the levels in Gp II. MESC administration showed a significant increase (p < 0.05) in the expression of liver C/ebp\u03b1, HNF-1\u03b1, and sirtuin-1 genes by 404.35%, 179.55%, and 223.64%, respectively, as well as a significant decrease (p < 0.05) of liver miRNA-34a and miRNA-223 genes expression by 46.27% and 40.49%, respectively, compared with the levels in Gp II. Paracetamol overdose could suppress C/ebp\u03b1 gene expression in hepatocytes in vivo, which was accompanied by a significant accumulation of cytokines. MESC and silymarin protected rats against paracetamol-induced hepatotoxicity. Oxidative stress due to C/ebp\u03b1 gene expression depletion and uncontrolled ROS is known to be the primary pathogenic mechanism of paracetamol-induced liver toxicity, as well as the main inhibitor of hepatocytes protective factors. Our metabolomics results revealed that MESC is rich in flavonoid compounds that exerted pronounced antioxidative effects against paracetamol-induced depletion of C/ebp\u03b1 gene expression in the hepatocytes of Gp II rats [A significant decrease of the expression of HNF-1\u03b1, sirtuin-1, and C/ebp\u03b1 genes by 55.10%, 61.22%, and 77%, respectively, as well as a significant increase of the expression of liver miRNA-34a and miRNA-223 genes by 447.27% and 344.79%, respectively, in Gp II rats as compared with Gp I rats demonstrated normal hepatocytes with no fibrosis or inflammation a, while S. costus; which supports the hepatoprotective activity of this plant [S. lappa root extract in rats [S. costus root extract pretreatment.Our LC\u2013MS/MS results showed that flavonoids were the major components of is plant . Coumariis plant . Tejaswi in rats ; moreove in rats ,57. ThisMethanol (HPLC grade), paracetamol (99%), silymarin (98.5%), and Tween 80 were purchased from Merk . Other reagents were of high analytical grade.Saussurea costus Lipsch. roots were purchased from a local herbalist . Identification of the plant was performed by the Agriculture Research Center, Cairo, Egypt. In Soxhlet, powdered roots (1 kg) were extracted with methanol . The extract was left to cool, filtered, and then evaporated [zerland) . The obtn-hexane (2 \u00d7 100 mL), filtered, and evaporated. The crude oil was investigated for its composition in a GC\u2013MS system equipped with a mass spectrometer detector (5977A) at the National Research Centre, Cairo, Egypt. The GC was equipped with an HP-5MS column. Powdered roots (100 g) were macerated in m/z. The characterization of compounds was performed by the generation of the candidate formula with a mass accuracy limit of 10 ppm and also considering Rt, MS2 data, databases, and reference literature [The MESC was analyzed at the Proteomics and Metabolomics unit of the Children\u2019s Cancer Hospital Egypt 57357, Cairo, Egypt. The analysis was carried out using an Exion LC Triple TOF 5600+ system operated at 40 \u00b0C and equipped with an X select HSS T3 C-18 column and a precolumn . MESC (50 mg) was dissolved in solvent working solution (MilliQ water: methanol: acetonitrile\u201350:25:25), sonicated (10 min), then centrifugated . The stock sample (50 \u00b5L) was diluted with the working solvent (1000 \u00b5L). The phytoconstituents of MESC were analyzed using UPLC/T-TOF\u2013MS/MS in both negative and positive modes . Samplesterature . g, 10 min). The clear supernatant was tested for CAT using a Cayman Chemical Company kit . The UV spectrophotometric method for measuring catalase activity is centered on monitoring the change in 240 nm absorbance at high concentrations of hydrogen peroxide (30 mM). TNF and IL-6 levels in the liver were measured using a microplate reader at 450 nm . An anti-IL-6 or an anti-TNF-\u03b1 monoclonal antibody and a biotin-conjugated monoclonal anti-IL-6 or anti-TNF-\u03b1 antibody that binds to IL-6 or TNF-\u03b1 captured by the first antibody were used in an indirect sandwich enzyme-linked immunosorbent assay to evaluate IL-6 and TNF-\u03b1. Streptavidin\u2013HRP was added to the wells, followed by a substrate solution reacting with HRP. After stopping the reaction with acid, the absorbance was measured.Adult male albino rats were purchased from the National Cancer Institute, Cairo University, Giza, Egypt. Rats were provided water and standard diet ad libitum, observed daily, and kept in polypropylene cages under normal environmental conditions (22 \u00b1 2 \u00b0C). The prophylactic potential of MESC against paracetamol hepatotoxicity was evaluated. Ethical approval was obtained by the ethic committee of the faculty of applied medical science . Animals and the treatment schedule (4 weeks) were as follows: Gp I and Gp II (positive control); rats were orally given Tween 80 in saline daily; Gp III rats were orally treated with silymarin , daily . Gp IV r2, (1.5 mM), 0.2 mM of each dNTP, 0.4 \u03bcM of specific primers . RNA (1 \u03bcg) in reaction buffer was mixed with dithiothreitol (10 nmol/L), oligo (dT) primer (25 pg), 0.5 mmol/L of each deoxyribonucleoside triphosphate (dNTP), and 200 units superscript II Rnase H-Reverse Transcriptase. The reactions were kept at 42 \u00b0C for 2 min, 42 \u00b0C for 50 min, 70 \u00b0C for 15 min, and then chilled to 4 \u00b0C. The PCR reaction mixture consisted of PCR buffer, MgCl primers for hepaThe liver pieces were fixed in formaldehyde solution (10%) and then were examined for histopathological changes.p < 0.05 was considered statistically significant). Statistical analyses were carried out using GraphPad Prism . ANOVA with posttest Tukey\u2019s multiple comparisons were performed. Values (n = 10) are presented as mean \u00b1 standard deviation for ELISA measurements and PCR analyses of gene expression were characterized as belonging to different chemical classes, flavonoids being the major constituents besides organic acids, coumarins, and anthocyanidin. S. costus has a potent hepatoprotective activity through the modulation of cellular cytokines release and miRNA-34a and miRNA-223 expression. S. costus reduced the levels of caspase 2 and CK18, TNF-\u03b1, and IL-6 and increased catalase activity. Furthermore, it increased HNF-1\u03b1, sirtuin-1, and C/ebp\u03b1 expression and decreased miRNA-34a and miRNA-223 gene expression. S. costus minimized some negative symptoms and pathological changes. We hope that this study will attract attention towards this plant myriad chemical constituents and its great potential in health care.Herein for the first time, we were able to identify the chemical profile of"} +{"text": "Worse sleep quality and increased inflammatory markers in women with schizophrenia (Sch) have been reported . However, the physiological mechanisms underlying the interplay between sleep and the inflammatory pathways are not yet well understood .Analyze the relationship between Neutrophil/Lymphocyte (NLR), Monocyte/Lymphocyte (MLR) and Platelet/Lymphocyte (PLR) ratios, and insomnia in Sch stratified by sex.Final sample included 176 Sch patients (ICD-10 criteria) . Assessment: PANSS, Calgary Depression Scale (CDSS), and Oviedo Sleep Questionnaire (OSQ) to identify a comorbid diagnosis of insomnia based on ICD-10. Fasting counting blood cell were performed to calculate ratios. Statistics: U Mann-Whitney, logistic regression.Insomnia as comorbid diagnosis was present in 22 Sch (12.5%) with no differences between sex , neither in their age. Female patients with insomnia showed increased NLR . However, no differences in PLR and MLR were found, neither in any ratio in males. Regression models using insomnia as dependent variable and covariates were estimated. Females: presence of insomnia was associated with NLR [OR=3.564 (p=0.032)], PANSS-positive [OR=1.263 (p=0.013)] and CDSS [OR=1.198 (p=0.092)]. Males: only PANSS-positive [OR=1.123 (p=0.027)] and CDSS scores [OR=1.220 (p=0.005)] were associated with insomnia.NLR represent an inflammatory marker of insomnia in Sch but only in female patients. Improving sleep quality in these patients could help to decrease their inflammatory response.No significant relationships."} +{"text": "Non-polio Enteroviruses (EV) are important neonatal CNS pathogens. Multiple EV genotypes have been detected in pediatric CSF, e.g. Echovirus (E) 6 and E30. CSF innate immune responses to EV genotypes remain poorly defined. Most data are from EV-A71 or E30 CNS infections and do not compare responses between these or other EV types. We sought to better define innate immune responses to EV genotypes in CSF.Salvaged standard of care CSF samples from \u22646 month olds or EV PCR(-) controls) from Jan 2010 - Dec 2020 were tested in duplicate on a 21- cytokine bead panel (MilliporeSigma). EV positive samples were previously genotyped by sequencing the viral capsid gene. Cytokine levels calculated from the standard curve were compared by Kruskal-Wallis and post-hoc analysis (GraphPad Prism 8.4.3). Natural partitioning of participants was explored using principal component analysis and cluster analysis (IBM SPSS v27). The utility of cytokine signatures in predicting EV status was explored using discriminant analysis and ROC analysis (IBM SPSS v27).Data from 72 CSF with E6 (N=16), E9 (N= 9), E18 (N=9), and E30 (N=21) showed significant differences among EV genotypes vs. controls for 20 cytokines (IL-17 was excluded). Significant differences in cytokine levels in EV CSF vs controls were seen: E6 for all 20 cytokines; E9 for Fractalkine, IP10, and MCP1; E18 for Fractalkine and MCP1; E30 19 cytokines (not GM-CSF). PCA revealed only minor overlap of controls and EV positives; EV types overlapped, except E30, differing most from E9 and E18 but overlapping E6. The most important type-differentiating cytokines by PCA were MCP1, Fractalkine, IL-8, and IL-10. Patterns in DA resembled PCA; controls clearly separated from EV CSF, E30 being the most distinct. Overall, the discriminant model correctly classified EV type or controls at a 63% rate - highest for controls (94.1%) and E30 (74.1%). In the DA model, the most important cytokines were IP-10, IL-2, IL-1Ra, and Fractalkine. Discriminant scores had the largest area under the curve (AUC), 0.990. Among cytokines, IFNa2 had the largest AUC, 0.987.Preliminary data show significant EV-genotype differences in innate immune response to CNS infections. Cytokine patterns may serve as a key predictor for discerning EV genotypes.Brian R. Lee, PhD, MPH, CDC: Grant/Research Support|Merck: Grant/Research Support Christopher J Harrison, MD, Astellas: Grant/Research Support|GSK: Grant/Research Support|Merck: Grant/Research Support|Pediatric news: Honoraria|Pfizer: Grant/Research Support Rangaraj Selvarangan, BVSc, PhD, D(ABMM), FIDSA, F(AAM), BioFire: Grant/Research Support|Luminex: Grant/Research Support."} +{"text": "A vascular system in plants is a product of aromorphosis that enabled them to colonize land because it delivers water, mineral and organic compounds to plant organs and provides effective communications between organs and mechanical support. Vascular system development is a common object of fundamental research in plant development biology. In the model plant Arabidopsis thaliana, early stages of vascular tissue formation in the root are a bright example of the self-organization of a bisymmetric (having two planes of symmetry) pattern of hormone distribution, which determines vascular cell fates. In the root, vascular tissue development comprises four stages: (1) specification of progenitor cells for the provascular meristem in early embryonic stages, (2) the growth and patterning of the embryo provascular meristem, (3) postembryonic maintenance of the cell identity in the vascular tissue initials within the root apical meristem, and (4) differentiation of their descendants. Although the anatomical details of A. thaliana root vasculature development have long been known and described in detail, our knowledge of the underlying molecular and genetic mechanisms remains limited. In recent years, several important advances have been made, shedding light on the regulation of the earliest events in provascular cells specification. In this review, we summarize the latest data on the molecular and genetic mechanisms of vascular tissue patterning in A. thaliana root. The first part of the review describes the root vasculature ontogeny, and the second reconstructs the sequenceof regulatory events that underlie this histogenesis and determine the development of the progenitors of the vascularinitials in the embryo and organization of vascular initials in the seedling root. Evolutionary formation of a vascular system in plants wasa necessary prerequisite for terrestrial colonization . Vasculature provides mechanical support, effectivetransportation of water, and mineral and organic compoundsas well as signal molecules and by this has enabled plants toreach enormous sizes and populate different territories. Thevascular system consists of two domains different in theirstructure and functions. These are xylem that provides watertransportation and delivers mineral compounds from the rootto above-ground organs; and phloem that conveys organiccompounds from photosynthesizing tissues rootward .In angiosperms, the mature xylem consists of (1) watertransportationvessels; (2) fibers to provide mechanical support;(3) parenchyma cells . The vesselsare the hollow tubes formed by the cells connected in a rawand having perforations in the anticlinal walls and pores in thepericlinal walls . The vessels and fibers are a productof the programmed death of the cells that have formed a lignifiedsecondary cell wall . Meanwhile, the living cellsof parenchyma perform a storage function, participating invessel lignification and regulating the water transport speed.The phloem, on the other hand, consists of (1) sieve tubesto transport organic substances; (2) companion cells; (3) fibersand sclereids to provide mechanical support, and (4) parenchymacells . Unlikethe lignified hollow vessels of the xylem, the sieve tubes area strand of living cells (sieve elements) communicating bysieve fields, anticlinal-wall regions with high numbers ofsmall pores. The sieve elements form a thickened non-lignifiedsecondary cell wall and their main feature isthe lack most of the organelles including a nucleus, vacuole,rough endoplasmic reticulum, Golgi body, cytoskeleton,ribosomes whose presence could prevent substances transportation.The viability of the sieve elements is maintainedby companion cells \u2013 the parenchyma cells with large nucleiand mitochondria, directly contacting sieve elements. As for mechanical phloem elements \u2013 fibers and sclereids \u2013 they differfrom each other by the shape of their cells. While the formerare strongly elongated and pointed at the ends, the latter arejust slightly elongated.Organization of vascular system is different for differentorgans in different plant species at different stages of theirdevelopment . Nevertheless, the mechanisms determiningits developmentare quite conservative . Plant cells are not capable of migration, so duringmorphogenesis, the tissue and organ architecture is formedby regulating the sequence and orientation of cell divisions.In terms of its anatomy, the vascular system development hasbeen described in much detail , however, the molecular andgenetic mechanisms responsible for this process are muchless known. Our current understanding of these mechanismsis mainly based on the investigation of the model plant ArabidopsisthalianaIn the further sections of this review, we will provide a shortdescription of vascular tissue histogenesis in this plant speciesand reconstruct the corresponding sequence of regulatoryevents. We will describe the control of root vascular systemdevelopment in the embryo and seedling, i. e. the earlieststages of its formation. As for the mechanisms controllingvasculature development at later stages, their description canbe found in the recent reviews .GlossaryAmphicribral vascular bundle \u2013 a vascular bundle inwhich the phloem surrounds the xylem.Anticlinal \u2013 located in a plane perpendicular to the surfaceof a tissue or organ. Talking about anticlinal cell wallsor divisions we will mean an anticlinal plane perpendicularto the central axis of an organ.Anticlinal cell division \u2013 cell division in the anticlinalplane that leads to an increase in length.Asymmetric cell division \u2013 results in the formation oftwo daughter cells with different cell fates.Cortex \u2013 a cell layer surrounding the endodermis.Diarch vascular bundle \u2013 a vascular bundle whose phloemand xylem are located at different radii, wherein tworays of xylem are distinguished.Endodermis \u2013 the innermost cell layer surrounding thestele.Hypophysis is the upper cell of the suspensor, which acquiresits identity at the 16\u201332 cell stage; gives rise to thequiescent center and the root cap.Periclinal \u2013 located in a plane parallel to the surface ofa tissue or organ.Periclinal cell division \u2013 cell division in the periclinalplain leading to an increase in the number of cell layersin the radial direction.Pericycle \u2013 parenchyma cell layer surrounding conductivetissues and forming the stele outer layer.Primary meristem \u2013 formed during embryogenesis.Procambium \u2013 indeterminate primary vascular meristemcells located between the xylem plate and phloempoles in the root of Arabidopsis thaliana.Provascular initials \u2013 four proembryo cells occurring atthe early globular stage to form the entire provascularmeristem of the root/hypocotyl, and only it.Provascular root/hypocotyl meristem \u2013 primary meristemfrom which the primary vascular system of theseorgans differentiates after embryo germination.Root apical meristem \u2013 primary root meristem to produceall cells of the root during its post-embryonicgrowth.Secondary meristem \u2013 formed during the postembryonicperiod.Stele \u2013 primary conductive tissues locatedin the center of the axial organ, and surrounded bya pericycle.Suspensor \u2013 a structure at the base of an embryo thatconnects it to endosperm and consists of the descendantsof a two-celled pro-embryo basal cell.Vascular cambium \u2013 secondary vascular meristem toprovide root thickening.Xylem plate \u2013 a layer of primary xylem cells (or theirpredetermined precursors) located in the central planealong the root axisThere are primary (produced by the primary meristem) andsecondary (produced by the secondary meristem) vasculartissues.Development of root primary conductive tissuesAt the globule stage of A. thaliana embryogenesis the specificationof four provascular initials occurs. Provascular initialsundergo oriented divisions, finally giving rise to the provascularmeristem of the embryonic root and hypocotyl . Thecells of provascular meristem are not yet differentiated, but thecellular fate of some of them has already been determined \u2013after the embryo germination they give birth either to xylemor to phloem cells. The positions of these predetermined cellsin the provascular meristem matches that of the bisymmetric diarch organizationof the vascular system in the postembryonic root tip: in itstransverse \u2013 section, there is one layer of xylem precursor cellssurrounded on both sides by procambial cells that separate thefuture xylem from two files of phloem progenitor cells, whichlie in a perpendicular plane .This structure is surrounded by pericycle cells that are alsoderived from provascular initials, so together they form a centralcylinder or a stele . It is noteworthy that theterminology designating the cells in developing root vascularsystem is rather blurred . In particular, theterm \u2018procambium\u2019 is applied to address either indeterminate cells of the primary vascular tissue in seedlings (and theirprogenitors) or the whole embryonic provascular meristem.Soon after germination, vascular elements start to differentiatein a hypocotyl stele and cotyledon veins, the provascularmeristem of the latter comes from the shoot apical meristem. From the hypocotyl, the processspreads upwards and downwards taking the epicotyl and root,respectively . In A. thaliana, these are the protophloemsieve elements adjacent to the pericycle that differentiatefirst, and since the cells surrounding them keep elongating,protophloem cells soon die to be functionally replaced bythe metaphloem sieve elements placed closer to the center ofthe stele . Later, theprotoxylem vascular elements are formed that are located atthe poles of the xylem plate and have annular or spiral thickeningsof the secondary cell walls. The last cells to differentiateare the metaxylem cells occupying the central position in thexylem plate and having pitted or reticulate lignin deposits.While the root grows in length, its new cells are producedthrough anticlinal division of the cells in the apical meristemlocated at the root tip . In A. thaliana,the root apical meristem is closed, i. e. different stem cells can produce not any but strictly limited set of celltypes and for each differentiated cell it is easy to trace whichstem cell it has originated from . Among the steleinitials those can be distinguished that give birth to (1) protoxylem;(2) metaxylem; (3) procambium and sieve elementsof proto- and metaphloem ;(4) only procambial cells; (5) pericycle . The mutual arrangement of initials correspondsto the diarch organization of young root vasculature, so thecell identity established in the embryo provascular meristem ismaintained in the root apical meristem. Here it is worth mentioningthat apart from the proto- and metaxylem, proto- andmetaphloem and procambium there are also companion cells.Some authors designate them more srictly as companion-likecells . These cells are adjacent to the sieveelements of proto- and metaphloem and possess a number ofmorphological and physiological characteristics of companioncells but, unlike the latter, theydo not share a common initial with the proto- and metaphloemelements in the stem cell niche . Thecompanion-like cells differentiate when the protophloemsieve elements start functioning . InA. thaliana, the xylem and phloem parenchyma, fibers andtrue companion cells differentiate only during the secondarygrowth .In A. thaliana primary vascular system, periclinal divisionsof procambium cells are few, but after differentiation of theprimary vascular elements, these cells begin to actively dividepericlinally. The periclinal divisions also occur in the pericycle cells adjacent to the xylem plate. As a result, a closed cell ringforms around the xylem to give birth to the vascular cambium . It is noteworthythat only those procambium and pericycle cells in direct contactwith the xylem primary vessels give rise to the vascularcambium, i. e., have the properties of stem cells while the descendants of other proliferating procambialcells differentiate into the phloem.Thus, the diarch root vasculature transforms into amphicribralone, in which the xylem is surrounded by thephloem with the cambium placed in between .Through asymmetric division, every initial is capable of producingphloem cells outwards and xylem cells inwards, sothe root gets thicker . In some species,e. g., in the vast majority of monocots, the cambium is notformed and no secondary growth is initiated. In this case, allprocambium cells get differentiated.The development of a multicellular organism is accompaniedby a gradual increase in the limitation of cellular potencies. Atthe first stage of this process predetermination or specificationoccurs, in other words, the fate of a totipotent cell is establishedin terms of the progenitor of what type of cells it will become.Meanwhile, the cell remains undifferentiated and can changeits fate under certain conditions. The process of cell identitydetermination involves the local accumulation of signalmolecules, which either activate or suppress the activity thegene networks inherent in specific cell types. In this case, animportant role is given to the non-cell-autonomous factors ableto move between cells and form gradients .Provascular stem cells specification at the early globularstage of embryogenesis is preceded by a series of cell divisionsand embryo polarity determination . The proper accomplishment of these processes isessential for the vascular tissue to begin its development fromthe right number of cells placed in the right positions. Planthormone auxin is a key regulator of embryogenesis, whoseheterogeneous distribution provides positional information,which directs embryo development . The main auxineffector in embryogenesis is transcription factor (TF) AUXINRESPONSE FACTOR 5 (ARF5)/MONOPTEROS (MP) and it is believedthat forming the auxin signal-distribution pattern is providedmainly due to feedbacks in regulation of phytohormonebiosynthesis, its polar intercellular transport and signalingpathway . As a result, at the early stagesof embryogenesis, auxin is accumulated in the apical cells todetermine the embryo polarity . Startingfrom the early globular stage (32 cells), its maximum is shiftedto the upper cells of the suspensor including the hypophysisthat later gives rise the quiescent center of the root apicalmeristem .Although the four provascular initials are only distinguishedat the early globular stage , the cellular identity of vascular tissue progenitors is determined in the fourinner cells of the lower layer of the proembryo as early as atdermatogen stage . Via periclinaldivision at transferring to the 32-cell stage, they produceoutwards the ground tissue progenitors that lose the vascularidentity of their maternal cells . A necessary condition for provascular-initial specification is ARF5/MP-dependent activation ofthe auxin signaling pathway, but meeting this condition aloneis not enough . Whileparticular auxin assistants remain unknown, its is suggestedthat this role is performed not by a single key regulator butby a multicomponent regulatory network, and TF G-BOXBINDING FACTOR 2 (GBF2) is believed to be one of itsmembers . GBF2 is assumedto modulate ARF5/MP binding to target-gene promoters. It isworth mentioning here that the state, in which vascular systemprogenitors are uniformly specified is most likely transientwith no stable uniform cellular identity.As the oriented divisions of the provascular initials and theirdescendants continue, the hypocotyl and root vascular systemsbecome patterned through specification of particularcellular types. An important aspect at this stage is setting theboundaries for the cellular domains with different structuraland functional identities. By the end of embryogenesis, inthe embryo provascular meristem, the cell identity of all elementssuch as proto- and metaphloem, proto- and metaxylem,companion-like cells and procambium has been determinedas evidenced by the data on cell morphologyand expressionof marker genes .In A. thaliana, the bisymmetry of the future root is believedto be predetermined already at the early globular stage by theextended contact between two provascular initials locateddiagonally relative to each other . This contactis probably formed due to the inaccurate match of cell divisionplanes in proembryo (at the four-cell stage) and is importantfor xylem plate formation . Startingfrom the early heart stage, auxin begins to be activelytransported into such contacting provascular cells from thecotyledon primordia located above them, while in other cellsthe hormone levels remain low . The local increase inauxin concentration is necessary for the specification of xylemprogenitor cells .At the same time, the cells rich in auxin begin to act as anorganizing center for the provascular meristem, coordinatingits growth through periclinal divisions and establishment ofbisymmetric organization . Auxin inducesthe ARF5/MP-dependent expression of TFs TARGETOF MONOPTEROS 5 (TMO5) and TMO5-LIKE1 (T5L1), which,forming heterodimers with the auxin-independent LONESOME HIGHWAY (LHW) TF , activatethe expression of cytokinin biosynthesis genes LONELYGUY3 (LOG3) and LOG4 . Simultaneously, auxin blockscytokinin signal transduction, increasing the expression ofgene ARABIDOPSIS HISTIDINE PHOSPHOTRANSFERPROTEIN 6 (AHP6 ) encoding a cytokinin signaling pathwayinhibitor , soa local cytokinin source is formed in xylem progenitors lackingcytokinin signalingThe high cytokinin level, on the one hand, limits auxin effluxfrom xylem progenitor cells by controlling the localizationof auxin transporter PIN-FORMED 1 (PIN1) on the cell membrane. On theother hand, cytokinin diffuses into neighboring cells followingthe concentration gradient. In these cells, in the absence of theinhibitor , cytokinin activates signalingcascade to stimulate periclinal divisions .Simultaneously, cytokinin signaling suppresses cell specificationinto xylem . This mechanismprovides for the radial growth of the provascular meristem,which is accompanied by spatial separation of the domainsfor increased auxin signal (cells obtain xylem identity) andcytokinin signal . Its sufficiencyfor self-organization of the bisymmetric pattern was confirmedusing a mathematical model .In early embryogenesis, provascular-meristem progenitorsbegin to express genes encoding peptide hormone CLAVATA 3(CLV3)/EMBRYO SURROUNDING REGION 25 (CLE25)and mobile TFs of the DNA BINDING WITH ONE FINGER(DOF) family united in the PHLOEM EARLY DOF (PEAR)group marking sieve-element progenitors in the postembryonicperiod . CLE25is expressed starting from a 64-cell embryo stage . Cytokinin-independent expression of PEAR1 isdetected already at a 16-cell stage, and starting from an earlyheart stage, this gene expression is activated by cytokinin. It is assumed that the CLE25 peptidebinding to the CLE-RESISTANT RECEPTOR KINASE(CLERK)-CLV2 receptor together with the PEAR1 TF contributeto the early specification of phloem progenitor cells.However, unlike that for xylem, the mechanism to initiatephloem development in embryogenesis remains unknown.Bisymmetric pattern in steleIn the postembryonic period, the stele cells progenitors maintainthe bisymmetric pattern established in embryogenesis,so some of the mechanisms regulating the cell dynamics andvascular-system element predetermination in provascular meristemkeep functioning even after germination. However, itcannot be said with complete certainty that these mechanismsare identical.In the apical meristem, auxin-rich xylem progenitors retainthe function of an organizing center, carrying out TMO5/LHW-mediated regulation of cytokinin levels in procambialcells . The high contentof active cytokinin in xylem cells is maintained by TMO5/LHW-dependent activation of not only cytokinin biosynthesisgenes LOG3 and LOG4 but also of the BGLU44 gene encodinga \u03b2-glucosidase enzyme . Cytokinin response inxylem is blocked by auxin through AHP6 gene expression induction as well as through limitingthe activity of TMO5/LHW by activating the ACAULIS 5(ACL5)\u2013SUPPRESSOR OF ACAULIS5 LIKE3 (SACL3)regulatory module blocking the formation of the TMO5/LHWheterodimer by competing with TMO5 for binding to LHW . Meanwhile,in xylem-adjacent procambial cells, the level of thecytokinin diffusing from the xylem is limited by TMO5/ LHWdependentactivation of CYTOKININ OXIDASE 3 (CKX3).The activation is mediated by the mobile SHORT ROOT(SHR) TF, encoded by TMO5/LHW target gene. The combinedaction of multidirectional regulatory modules ensuresthe stability of the pattern to short-term fluctuations in auxinconcentrations in xylem cells, while maintaining its sensitivityto slower/stable changes . What is interestingis that the SHR gene is important not only for the rootradial symmetry but also for the functioning of the quiescentcenter .TMO5/LHW-induced cytokinin activates the transcriptionof the DOF2.1 TF in the procambial cells surrounding thexylem pole, thus controlling their division . It is worth noting that, besides xylem cells, it isdifferentiated phloem that transports the phytohormone andthus can be a source of cytokinin in the root apical meristem. However, mathematical modelinghas demonstrated that phloem cytokinin is not a fundamentalsource of the positional information for bisymmetric patternformation . At the same time, the highcytokinin content at the phloem poles arranges periclinaldivisions of procambium cells through activating the genesof mobile TFs of the DOF family united in the PEAR groupincluding PEAR1, PEAR2, TMO6, DOF6 . They create a concentration gradientand activate the periclinal divisions of the procambial cells surroundingthe phloem pole. HOMEODOMAIN LEU-ZIPPERclass-III (HD-ZIP III), TFs whose expression domain is set inthe central part of the stele (see below) limit the activity of thePEAR TFs , and PEAR1 activates the transcriptionof the genes belonging to the HD-ZIP III family, forminga negative feedback loop.Proto- and metaxylem predeterminationAs in embryogenesis, auxin is necessary for xylem cellspredeterminationin the root apical meristem. In proto- andmetaxylem predetermination, a key role is given to theSHR and miRNA165/166 mobile regulators . SHRis produced by xylem cells, from where the TF spreadstowards the periphery and, upon reaching the endodermis,activates the SCARECROW (SCR) TF, so they togetherinduce miRNA165/166 expression . MicroRNAs diffuse into neighboringcells, creating a concentration gradient towards the center ofthe root. In the stele, miRNA165/166 suppress the expressionof the genes encoding the TFs of the HD-ZIP III family, limitingit to the central domain . In such a way, themetaxylem cells are predetermined. Whether this mechanismworks in embryogenesis remains unknown, but this is a possibilitysince the PHABULOSA (PHB) TF of the HD-ZIP IIIfamily is expressed in the embryo root .Predetermination of phloem elementsThe phloem markers expressed in progenitors and induce thetissue development include a number of the DOF family TFs; strigolactonesignaling pathway suppressors SUPPRESSOR OF MAX21-LIKE 3 (SMLX3), SMLX4 and SMLX5 ; membrane proteins BREVIS RADIX (BRX), OCTOPUS(OPS), OPS-LIKE 2 (OPL2) ;phosphatase COTYLEDON VASCULAR PATTERN 2(CVP2) and its homolog CVP2-LIKE 1 (CVL1) ; the ALTERED PHLOEM DEVELOPMENT(APL) TF .The formation of protophloem elements is controlled byshifting the balance towards inducing or suppressing mechanismswith the central link connecting the opposing regulatorymodules being phloem-specific TFs of the DOF family. On the one hand, these TFs induce theexpression of phloem development activators, such as APLas well as their own genes, forming a positive feedback loop.On the other hand, DOFs induce the expression of CLE25,CLE26, and CLE45 signaling peptides migrating to neighboringcells where they trigger an inhibitory regulatory module. Interacting with the BARELY ANY MERISTEM(BAM) receptors and the CLAVATA3 INSENSITIVERECEPTOR KINASE (CIK) co-receptors, the CLE peptidesinduce the degradation of the DOF family TFs, suppressingthe formation of protophloem elements. The activity of theCLE peptide receptors can be additionally regulated, e. g., bythe MEMBRANE-ASSOCIATED KINASE REGULATOR 5(MAKR5) or CORYNE (CRN) regulators. The TFs of the DOF family activatethe expression of the genes encoding the OPS membraneprotein suppressing the BAM-CIK module .Properly positioned protophloem progenitor cells overcomethe inhibitory effect of CLE peptides due to the DOF TF accumulationdetermined by the positive feedback. Such a balancingmechanism makes it possible to repattern the phloemin case protophloem development has been disrupted . Here it should be noted that metaphloem developmentis probably regulated by other mechanisms and does notdepend on that of the protophloem .During phloem formation, the phloem/procambium stemcell divides anticlinally to produce a daughter procambiumand sieve-element progenitor to divide periclinally and forma procambium progenitor and a phloem sieve-element progenitor.The latter undergoes another periclinal division toproduce proto- and metaphloem progenitors . Companion-like cells are another product ofasymmetric division, but come from a different initial. Theseasymmetric cell divisions are controlled by a positional signal,a SHR-protein gradient whose migration into the endodermisactivates miRNA165/166 and induces asymmetric divisionsproducing companion-like cells, while SHR movement intothe phloem is necessary for the asymmetric divisions leadingto proto- and metaxylem formation .The vascular system of A. thaliana root is set at the earlieststages of embryogenesis. Wherein, the predetermination ofprovascular initials implies a labile, unstable, and reversiblespecification based on the physical arrangement of cells in theembryo and influenced by a complex regulatory network oftranscription factors. An interesting moment here is that bothxylem and phloem markers are jointly expressed by provascular initials inearly embryogenesis, but later they are separated into differentspatial domains in the provascular meristem and seedling.In A. thaliana, the vascular system is patterned by the timeof embryo maturation. Partially, the gene network that controlsthis process in embryogenesis continues to maintain thevascular system structure of the growing root of the seedlingand later during plant ontogenesis. This is associated withlocal accumulation of the molecular markers that are stablyexpressed in progenitor cells of a certain type. However,the factors working both in embryogenesis and during postembryonicdevelopment can act at these stages in differentwaysDespite the significant progress that has recently beenachieved in understanding the molecular and genetic mechanismsregulating vascular system development in plants,many questions remain open, in particular, those related tothe existence of parallel regulatory pathways and feedforwardloops. This is a good basis for building mathematicalmodels whose analysis helps shed light on the relationshipbetween various regulatory circuits and their functionalsignificance.The authors declare no conflict of interest.Agust\u00ed J., Bl\u00e1zquez M.A. Plant vascular development: mechanisms andenvironmental regulation. Cell. Mol. Life Sci. 2020;77(19):3711-3728. DOI 10.1007/s00018-020-03496-w.Bauby H., Divol F., Truernit E., Grandjean O., Palauqui J.C. Protophloemdifferentiation in early Arabidopsis thaliana development.Plant Cell Physiol. 2007;48(1):97-109. DOI 10.1093/pcp/pcl045.Baum S.F., Dubrovsky J.G., Rost T.L. Apical organization and maturationof the cortex and vascular cylinder in Arabidopsis thaliana(Brassicaceae) roots. Am. J. Bot. 2002;89(6):908-920. DOI 10.3732/ajb.89.6.908Bishopp A., Help H., El-Showk S., Weijers D., Scheres B., Friml J.,Benkov\u00e1 E., M\u00e4h\u00f6nen A.P., Helariutta Y. A mutually inhibitory interactionbetween auxin and cytokinin specifies vascular pattern inroots. Curr. Biol. 2011a;21(11):917-926. DOI 10.1016/j.cub.2011.04.017.Bishopp A., Lehesranta S., Vat\u00e9n A., Help H., El-Showk S., Scheres B.,Helariutta K., M\u00e4h\u00f6nen A.P., Sakakibara H., Helariutta Y. Phloemtransportedcytokinin regulates polar auxin transport and maintainsvascular pattern in the root meristem. Curr. Biol. 2011b;21(11):927-932. DOI 10.1016/j.cub.2011.04.049.Bonke M., Thitamadee S., M\u00e4h\u00f6nen A.P., Hauser M.T., Helariutta Y.APL regulates vascular tissue identity in Arabidopsis. Nature.2003;426(6963):181-186. DOI 10.1038/nature02100.Busse J.S., Evert R.F. Pattern of differentiation of the first vascular elementsin the embryo and seedling of Arabidopsis thaliana. Int. J.Plant Sci. 1999;160(1):1-13. DOI 10.1086/314098.Cai Q., Fukushima H., Yamamoto M., Ishii N., Sakamoto T., Kurata T.,Motose H., Takahashi T. The SAC51 family plays a central rolein thermospermine responses in Arabidopsis. Plant Cell Physiol.2016;57(8):1583-1592. DOI 10.1093/pcp/pcw113.Carlsbecker A., Lee J.Y., Roberts C.J., Dettmer J., Lehesranta S.,Zhou J., Lindgren O., Moreno-Risueno M.A., Vat\u00e9n A., ThitamadeeS., Campilho A., Sebastian J., Bowman J.L., Helariutta Y.,Benfey P.N. Cell signalling by microRNA165/6 directs gene dosedependentroot cell fate. Nature. 2010;465(7296):316-321. DOI10.1038/nature08977.Cheng C.Y., Kieber J.J. Cytokinin signaling in plants. In: Howell S.(Ed.) Molecular Biology. The Plant Sciences. Vol. 2. New York:Springer, 2014;269-289. DOI 10.1007/978-1-4614-7570-5_14.Courtois-Moreau C.L., Pesquet E., Sj\u00f6din A., Mu\u00f1iz L., Bollh\u00f6ner B.,Kaneda M., Samuels L., Jansson S., Tuominen H. A unique programfor cell death in xylem fibers of Populus stem. Plant J. 2009;58(2):260-274. DOI 10.1111/j.1365-313X.2008.03777.x.De Rybel B., Adibi M., Breda A.S., Wendrich J.R., Smit M.E.,Nov\u00e1k O., Yamaguchi N., Yoshida S., Van Isterdael G., Palovaara J.,Nijsse B., Boekschoten M.V., Hooiveld G., Beeckman T., WagnerD., Ljung K., Fleck C., Weijers D. Integration of growth andpatterning during vascular tissue formation in Arabidopsis. Science.2014a;345(6197):1255215. DOI 10.1126/science.1255215.De Rybel B., Breda A.S., Weijers D. Prenatal plumbing \u2013 vascular tissueformation in the plant embryo. Physiol. Plant. 2014b;151(2):126-133. DOI 10.1111/ppl.12091.De Rybel B., M\u00e4h\u00f6nen A.P., Helariutta Y., Weijers D. Plant vasculardevelopment: from early specification to differentiation. Nat. Rev.Mol. Cell Biol. 2016;17(1):30-40. DOU 10.1038/nrm.2015.6.De Rybel B., M\u00f6ller B., Yoshida S., Grabowicz I., Barbier de Reuille P.,Boeren S., Smith R.S., Borst J.W., Weijers D. A bHLH complexcontrols embryonic vascular tissue establishment and indeterminategrowth in Arabidopsis. Dev. Cell. 2013;24(4):426-437. DOI10.1016/j.devcel.2012.12.013.Desvoyes B., Echevarr\u00eda C., Gutierrez C. A perspective on cell proliferationkinetics in the root apical meristem. J. Exp. Bot. 2021;72(19):6708-6715. DOI 10.1093/jxb/erab303.Dolan L., Janmaat K., Willemsen V., Linstead P., Poethig S., RobertsK.,Scheres B. Cellular organisation of the Arabidopsis thaliana root.Development. 1993;119(1):71-84. DOI 10.1242/dev.119.1.71Evert R.F., Eichhorn S.E. Esau\u2019s Plant Anatomy. Meristems, Cells, andTissues of the Plant Body: Their Structure, Function, and Development.New Jersey: Wiley, 2006. DOI 10.1002/0470047380.Friml J., Vieten A., Sauer M., Weijers D., Schwarz H., Hamann T., OffringaR., J\u00fcrgens G. Efflux-dependent auxin gradients establish the apical-basal axis of Arabidopsis. Nature. 2003;426(6963):147-153.DOI 10.1038/nature02085.Furuta K.M., Hellmann E., Helariutta Y. Molecular control of cell specificationand cell differentiation during procambial development.Annu. Rev. Plant. Biol. 2014;65:607-638. DOI 10.1146/annurevarplant-050213-040306.Graeff M., Hardtke C.S. Metaphloem development in the Arabidopsisroot tip. Development. 2021;148(18):dev199766. DOI 10.1242/dev.199766.Grigg S.P., Galinha C., Kornet N., Canales C., Scheres B., Tsiantis M.Repression of apical homeobox genes is required for embryonic rootdevelopment in Arabidopsis. Curr. Biol. 2009;19(17):1485-1490.DOI 10.1016/j.cub.2009.06.070.Gujas B., Kastanaki E., Sturchler A., Cruz T.M.D., Ruiz-Sola M.A.,Dreos R., Eicke S., Truernit E., Rodriguez-Villalon A. A reservoir ofpluripotent phloem cells safeguards the linear developmental trajectoryof protophloem sieve elements. Curr. Biol. 2020;30(5):755-766.DOI 10.1016/j.cub.2019.12.043.Hazak O., Brandt B., Cattaneo P., Santiago J., Rodriguez-Villalon A.,Hothorn M., Hardtke C.S. Perception of root-active CLE peptidesrequires CORYNE function in the phloem vasculature. EMBO Rep.2017;18(8):1367-1381. DOI 10.15252/embr.201643535.Help H., M\u00e4h\u00f6nen A.P., Helariutta Y., Bishopp A. Bisymmetry in theembryonic root is dependent on cotyledon number and position.Plant Signal. Behav. 2011;6(11):1837-1840. DOI 10.4161/psb.6.11.17600.Heo J.O., Roszak P., Furuta K.M., Helariutta Y. Phloem development:current knowledge and future perspectives. Am. J. Bot. 2014;101(9):1393-1402. DOI 10.3732/ajb.1400197.Kang Y.H., Hardtke C.S. Arabidopsis MAKR5 is a positive effector ofBAM3-dependent CLE45 signaling. EMBO Rep. 2016;17(8):1145-1154. DOI 10.15252/embr.201642450.Katayama H., Iwamoto K., Kariya Y., Asakawa T., Kan T., Fukuda H.,Ohashi-Ito K. A negative feedback loop controlling bHLH complexesis involved in vascular cell division and differentiation inthe root apical meristem. Curr. Biol. 2015;25(23):3144-3150. DOI10.1016/j.cub.2015.10.051.Kim H., Zhou J., Kumar D., Jang G., Ryu K.H., Sebastian J., MiyashimaS., Helariutta Y., Lee J.Y. SHORTROOT-mediated intercellularsignals coordinate phloem development in Arabidopsis roots. PlantCell. 2020;32(5):1519-1535. DOI 10.1105/tpc.19.00455.Kuroha T., Tokunaga H., Kojima M., Ueda N., Ishida T., Nagawa S.,Fukuda H., Sugimoto K., Sakakibara H. Functional analyses ofLONELY GUY cytokinin-activating enzymes reveal the importanceof the direct activation pathway in Arabidopsis. Plant Cell. 2009;21(10):3152-3169. DOI 10.1105/tpc.109.068676.Lau S., De Smet I., Kolb M., Meinhardt H., J\u00fcrgens G. Auxin triggersa genetic switch. Nat. Cell Biol. 2011;13(5):611-615. DOI 10.1038/ncb2212Lau S., Slane D., Herud O., Kong J., J\u00fcrgens G. Early embryogenesisin flowering plants: setting up the basic body pattern. Annu. Rev.Plant Biol. 2012;63:483-506. DOI 10.1146/annurev-arplant-042811-105507.Li X., Wu H.X., Southerton S.G. Comparative genomics reveals conservativeevolution of the xylem transcriptome in vascular plants.BMC Evol. Biol. 2010;10:190. DOI 10.1186/1471-2148-10-190Lucas W.J., Groover A., Lichtenberger R., Furuta K., Yadav S.R., HelariuttaY., He X.Q., Fukuda H., Kang J., Brady S.M., Patrick J.W.,Sperry J., Yoshida A., L\u00f3pez-Mill\u00e1n A.F., Grusak M.A., Kachroo P.The plant vascular system: evolution, development and functions.J. Integr. Plant Biol. 2013;55(4):294-388. DOI 10.1111/jipb.12041.M\u00e4h\u00f6nen A.P., Bishopp A., Higuchi M., Nieminen K.M., Kinoshita K.,T\u00f6rm\u00e4kangas K., Ikeda Y., Oka A., Kakimoto T., Helariutta Y. Cytokininsignaling and its inhibitor AHP6 regulate cell fate during vasculardevelopment. Science. 2006;311(5757):94-98. DOI 10.1126/science.1118875M\u00e4h\u00f6nen A.P., Bonke M., Kauppinen L., Riikonen M., Benfey P.N.,Helariutta Y. A novel two-component hybrid molecule regulatesvascular morphogenesis of the Arabidopsis root. Genes Dev. 2000;14(23):2938-2943. DOI 10.1101/gad.189200Marhav\u00fd P., Bielach A., Abas L., Abuzeineh A., Duclercq J., Tanaka H.,Pa\u0159ezov\u00e1 M., Petr\u00e1\u0161ek J., Friml J., Kleine-Vehn J., Benkov\u00e1 E. Cytokininmodulates endocytic trafficking of PIN1 auxin efflux carrierto control plant organogenesis. Dev. Cell. 2011;21(4):796-804. DOI10.1016/j.devcel.2011.08.014.M\u00e9nard D., Pesquet E. Cellular interactions during tracheary elementsformation and function. Curr. Opin. Plant Biol. 2015;23:109-115.DOI 10.1016/j.pbi.2014.12.001.Mironova V., Teale W., Shahriari M., Dawson J., Palme K. The systemsbiology of auxin in developing embryos. Trends Plant Sci. 2017;22(3):225-235. DOI 10.1016/j.tplants.2016.11.010.Miyashima S., Roszak P., Sevilem I., Toyokura K., Blob B., Heo J.O.,Mellor N., Help-Rinta-Rahko H., Otero S., Smet W., BoekschotenM., Hooiveld G., Hashimoto K., Smetana O., Siligato R.,Wallner E.S., M\u00e4h\u00f6nen A.P., Kondo Y., Melnyk C.W., Greb T., NakajimaK., Sozzani R., Bishopp A., De Rybel B., Helariutta Y. MobilePEAR transcription factors integrate positional cues to primecambialgrowth. Nature. 2019;565(7740):490-494. DOI 10.1038/s41586-018-0839-y.Miyashima S., Sebastian J., Lee J.Y., Helariutta Y. Stem cell functionduring plant vascular development. EMBO J. 2013;32(2):178-193.DOI 10.1038/emboj.2012.301.M\u00f6ller B.K., ten Hove C.A., Xiang D., Williams N., L\u00f3pez L.G.,YoshidaS., Smit M., Datla R., Weijers D. Auxin response cell-autonomouslycontrols ground tissue initiation in the early Arabidopsisembryo. Proc. Natl. Acad. Sci. USA. 2017;114(12):2533-2539. DOI 10.1073/pnas.1616493114.M\u00f6ller B., Weijers D. Auxin control of embryo patterning. Cold SpringHarb. Perspect. Biol. 2009;1(5):a001545. DOI 10.1101/cshperspect.a001545.Muraro D., Mellor N., Pound M.P., Help H., Lucas M., Chopard J.,ByrneH.M., Godin C., Hodgman T.C., King J.R., Pridmore T.P.,Helariutta Y., Bennett M.J., Bishopp A. Integration of hormonalsignaling networks and mobile microRNAs is required for vascularpatterning in Arabidopsis roots. Proc. Natl. Acad. Sci. USA. 2014;111(2):857-862. DOI 10.1073/pnas.1221766111.Nieminen K., Blomster T., Helariutta Y., M\u00e4h\u00f6nen A.P. Vascularcambiumdevelopment. Arabidopsis Book. 2015;13:e0177. DOI10.1199/tab.0177.Ohashi-Ito K., Bergmann D.C. Regulation of the Arabidopsis root vascularinitial population by LONESOME HIGHWAY. Development.2007;134(16):2959-2968. DOI 10.1242/dev.006296.Ohashi-Ito K., Matsukawa M., Fukuda H. An atypical bHLH transcriptionfactor regulates early xylem development downstream of auxin.Plant Cell Physiol. 2013;54(3):398-405. DOI 10.1093/pcp/pct013.Ohashi-Ito K., Saegusa M., Iwamoto K., Oda Y., Katayama H., KojimaM., Sakakibara H., Fukuda H. A bHLH complex activates vascularcell division via cytokinin action in root apical meristem. Curr.Biol. 2014;24(17):2053-2058. DOI 10.1016/j.cub.2014.07.050.Palovaara J., Saiga S., Wendrich J.R., van\u2019t Wout Hofland N., vanSchayck J.P., Hater F., Mutte S., Sjollema J., Boekschoten M.,HooiveldG.J., Weijers D. Transcriptome dynamics revealed bya gene expression atlas of the early Arabidopsis embryo. Nat.Plants. 2017;3(11):894-904. DOI 10.1038/s41477-017-0035-3.Qian P., Song W., Zaizen-Iida M., Kume S., Wang G., Zhang Y., Kinoshita-Tsujimura K., Chai J., Kakimoto T. A Dof-CLE circuit controlsphloem organization. Nat. Plants. 2022;8(7):817-827. DOI 10.1038/s41477-022-01176-0.Ren S.C., Song X.F., Chen W.Q., Lu R., Lucas W.J., Liu C.M.CLE25 peptide regulates phloem initiation in Arabidopsis througha CLERK-CLV2 receptor complex. J. Integr. Plant. Biol. 2019;61(10):1043-1061. DOI 10.1111/jipb.12846.Robert H.S., Crhak Khaitova L., Mroue S., Benkov\u00e1 E. The importanceof localized auxin production for morphogenesis of reproductiveorgans and embryos in Arabidopsis. J. Exp. Bot. 2015;66(16):5029-5042. DOI 10.1093/jxb/erv256.Rodriguez-Villalon A. Wiring a plant: genetic networks for phloemformation in Arabidopsis thaliana roots. New Phytol. 2016;210(1):45-50. DOI 10.1111/nph.13527.Rodriguez-Villalon A., Gujas B., van Wijk R., Munnik T., Hardtke C.S.Primary root protophloem differentiation requires balanced phosphatidylinositol-4,5-biphosphate levels and systemically affects rootbranching. Development. 2015;142(8):1437-1446. DOI 10.1242/dev.118364.Ross-Elliott T.J., Jensen K.H., Haaning K.S., Wager B.M., KnoblauchJ., Howell A.H., Mullendore D.L., Monteith A.G., Paultre D.,Yan D., Otero S., Bourdon M., Sager R., Lee J.Y., Helariutta Y.,Knoblauch M., Oparka K.J. Phloem unloading in Arabidopsis rootsis convective and regulated by the phloem-pole pericycle. eLife.2017;6:e24125. DOI 10.7554/eLife.24125.Roszak P., Heo J.O., Blob B., Toyokura K., Sugiyama Y., de LuisBalaguer M.A., Lau W.W.Y., Hamey F., Cirrone J., Madej E., BouattaA.M., Wang X., Guichard M., Ursache R., Tavares H., Verstaen K.,Wendrich J., Melnyk C.W., Oda Y., Shasha D., Ahnert S.E., Saeys Y.,De Rybel B., Heidstra R., Scheres B., Grossmann G., M\u00e4h\u00f6nen A.P.,Denninger P., G\u00f6ttgens B., Sozzani R., Birnbaum K.D., Helariutta Y.Cell-by-cell dissection of phloem development links a maturationgradient to cell specialization. Science. 2021;374(6575):eaba5531.DOI 10.1126/science.aba5531Ruiz Sola M.A., Coiro M., Crivelli S., Zeeman S.C., Hansen S.S.K.,Truernit E. OCTOPUS-LIKE 2, a novel player in Arabidopsis rootand vascular development, reveals a key role for OCTOPUS familygenes in root metaphloem sieve tube differentiation. New Phytol.2017;216(4):1191-1204. DOI 10.1111/nph.14751.R\u016f\u017ei\u010dka K., Ursache R., Hej\u00e1tko J., Helariutta Y. Xylem development\u2013from the cradle to the grave. New Phytol. 2015;207(3):519-535.DOI 10.1111/nph.13383.Sauer M., Balla J., Luschnig C., Wisniewska J., Rein\u00f6hl V., Friml J.,Benkov\u00e1 E. Canalization of auxin flow by Aux/IAA-ARF-dependentfeedback regulation of PIN polarity. Genes Dev. 2006;20(20):2902-2911. DOI 10.1101/gad.390806.Scarpella E., Meijer A.H. Pattern formation in the vascular system ofmonocot and dicot plant species. New Phytol. 2004;164(2):209-242.DOI 10.1111/j.1469-8137.2004.01191.x.Scheres B., Wolkenfelt H., Willemsen V., Terlouw M., Lawson E.,Dean C., Weisbeek P. Embryonic origin of the Arabidopsis primaryroot and root meristem initials. Development. 1994;120(9):2475-2487. DOI 10.1242/dev.120.9.2475.Schlereth A., M\u00f6ller B., Liu W., Kientz M., Flipse J., Rademacher E.H.,Schmid M., J\u00fcrgens G., Weijers D. MONOPTEROS controls embryonicroot initiation by regulating a mobile transcription factor.Nature. 2010;464(7290):913-916. DOI 10.1038/nature08836.Seo M., Kim H., Lee J.Y. Information on the move: vascular tissuedevelopment in space and time during postembryonic root growth.Curr. Opin. Plant Biol. 2020;57:110-117. DOI 10.1016/j.pbi.2020.08.002.Sjolund R.D. The phloem sieve element: a river runs through it. PlantCell. 1997;9(7):1137-1146. DOI 10.1105/tpc.9.7.1137.Smet W., Sevilem I., de Luis Balaguer M.A., Wybouw B., Mor E.,Miyashima S., Blob B., Roszak P., Jacobs T.B., Boekschoten M.,Hooiveld G., Sozzani R., Helariutta Y., De Rybel B. DOF2.1 controlscytokinin-dependent vascular cell proliferation downstream ofTMO5/LHW. Curr. Biol. 2019;29(3):520-529.e6. DOI 10.1016/j.cub.2018.12.041.Smetana O., M\u00e4kil\u00e4 R., Lyu M., Amiryousefi A., S\u00e1nchez Rodr\u00edguez F.,Wu M.-F., Sol\u00e9-Gil A., Leal Gavarr\u00f3n M., Siligato R., MiyashimaS., Roszak P., Blomster T., Reed J.W., Broholm S., M\u00e4h\u00f6nen A.P.High levels of auxin signalling define the stem-cell organizer of thevascular cambium. Nature. 2019;565(7740):485-489. DOI 10.1038/s41586-018-0837-0.Smit M.E., Llavata-Peris C.I., Roosjen M., van Beijnum H., NovikovaD., Levitsky V., Sevilem I., Roszak P., Slane D., J\u00fcrgens G.,Mironova V., Brady S.M., Weijers D. Specification and regulationof vascular tissue identity in the Arabidopsis embryo. Development.2020;147(8):dev186130. DOI 10.1242/dev.186130.Smit M.E., Weijers D. The role of auxin signaling in early embryopattern formation. Curr. Opin. Plant Biol. 2015;28:99-105. DOI10.1016/j.pbi.2015.10.001.Smith R.A., Schuetz M., Roach M., Mansfield S.D., Ellis B., SamuelsL. Neighboring parenchyma cells contribute to Arabidopsisxylem lignification, while lignification of interfascicular fibers iscell autonomous. Plant Cell. 2013;25(10):3988-3999. DOI 10.1105/tpc.113.117176.Stadler R., Wright K.M., Lauterbach C., Amon G., Gahrtz M., FeuersteinA., Oparka K.J., Sauer N. Expression of GFP-fusions in Arabidopsiscompanion cells reveals non-specific protein traffickinginto sieve elements and identifies a novel post-phloem domain inroots. Plant J. 2005;41(2):319-331. DOI 10.1111/j.1365-313X.2004.02298.x.Tanaka H., Dhonukshe P., Brewer P.B., Friml J. Spatiotemporal asymmetricauxin distribution: a means to coordinate plant development.Cell. Mol. Life Sci. 2006;63(23):2738-2754. DOI 10.1007/s00018-006-6116-5.Truernit E. Sieve elements and their cell neighbours in the Arabidopsisroot \u2013 roles and relationships. J. Plant Physiol. 2022;268:153569.DOI 10.1016/j.jplph.2021.153569.Tvorogova V.E., Osipova M.A., Doduyeva I.E., Lutova L.A. Interactionbetween transcriptional factors and phytohormones in regulationof plant meristems activity. Ekologicheskaia Genetika = EcologicalGenetics. 2012;10(3):28-40. (in Russian)Vera-Sirera F., De Rybel B., \u00darbez C., Kouklas E., Pesquera M.,\u00c1lvarez-Mahecha J.C., Minguet E.G., Tuominen H., Carbonell J.,Borst J.W., Weijers D., Bl\u00e1zquez M.A. A bHLH-based feedbackloop restricts vascular cell proliferation in plants. Dev. Cell. 2015;35(4):432-443. DOI 10.1016/j.devcel.2015.10.022.Verma S., Attuluri V.P.S., Robert H.S. An essential function for auxinin embryo development. Cold Spring Harb. Perspect. Biol. 2021;13(4):a039966. DOI 10.1101/cshperspect.a039966.Wabnik K., Robert H.S., Smith R.S., Friml J. Modeling framework forthe establishment of the apical-basal embryonic axis in plants. Curr.Biol. 2013;23(24):2513-2518. DOI 10.1016/j.cub.2013.10.038.Wallner E.S., L\u00f3pez-Salmer\u00f3n V., Belevich I., Poschet G., Jung I.,Gr\u00fcnwald K., Sevilem I., Jokitalo E., Hell R., Helariutta Y., Agust\u00ed J.,Lebovka I., Greb T. Strigolactone- and karrikin-independent SMXLproteins are central regulators of phloem formation. Curr. Biol.2017;27(8):1241-1247. DOI 10.1016/j.cub.2017.03.014.Weijers D., J\u00fcrgens G. Auxin and embryo axis formation: the ends insight? Curr. Opin. Plant Biol. 2005;8(1):32-37. DOI 10.1016/j.pbi.2004.11.001.Yang B., Minne M., Brunoni F., Pla\u010dkov\u00e1 L., Pet\u0159\u00edk I., Sun Y., Nolf J.,Smet W., Verstaen K., Wendrich J.R., Eekhout T., Hoyerov\u00e1 K.,van Isterdael G., Haustraete J., Bishopp A., Farcot E., Nov\u00e1k O.,Saeys Y., de Rybel B. Non-cell autonomous and spatiotemporalsignalling from a tissue organizer orchestrates root vascular development.Nat. Plants. 2021;7(11):1485-1494. DOI 10.1038/s41477-021-01017-6."} +{"text": "Several antibiotics active against carbapenemase-producing organisms have recently been licensed for clinical use. These organisms usually have multiple integrative and conjugative elements with different resistance genes. The positioning of these agents for empirical use in sepsis caused by different carbapenemase-producing organisms is important in optimizing the likelihood of appropriate treatment before susceptibility testing is complete. Here we present the activities of meropenem-vaborbactam, imipenem-relebactam, eravacycline and tigecycline against NDM- and OXA-48-producing clinical isolates in a London teaching hospital.Klebsiella pneumoniae (17), Escherichia coli (10), Enterobacter aerogenes (3) and Serratia marcescens (1). NDM producers comprised K. pneumoniae (11), E. coli (10), Acinetobacter baumannii (3), Klebsiella oxytoca (1), Enterobacter asburiae (1), Enterobacter cloacae (1), Pseudomonas aeruginosa (1), Citrobacter koseri (1), Citrobacter freundii (1) and Leclercia adecarboxylata (1). MICs of meropenem/vaborbactam, imipenem/relebactam, eravacycline and tigecycline were determined using Etests. Interpretation was done using EUCAST breakpoints.Sixty-two previously characterized carbapenemase-producing Gram-negative clinical isolates were studied. These comprised 31 NDM and 31 OXA-48 producers. OXA-48 producers comprised OXA-48 producers: Eight of 17 K. pneumoniae, 8/10 E. coli and 2/3 E. aerogenes isolates were meropenem/vaborbactam susceptible. Of these, 2 K. pneumoniae, 5 E. coli and 1 E. aerogenes isolates were imipenem/relebactam susceptible. All imipenem/relebactam/susceptible isolates were also meropenem/vaborbactam susceptible. The S. marcescens isolate (1/1) was resistant to both antibiotics. The only isolates demonstrating susceptibility to the glycylcyclines were E. coli. Five of 10 were susceptible to both glycylcyclines. One of 10 was susceptible to one glycylcycline but resistant to the other. NDM producers: Five of 11 K. pneumoniae, 6/10 E. coli and 1/1 K. oxytoca, E. asburiae and C. koseri isolates were susceptible to meropenem/vaborbactam. Of these, two K. pneumoniae and the K. oxytoca (1/1) and E. asburiae (1/1) isolates were imipenem/relebactam susceptible. The L. adecarboxylata isolate (1/1) was meropenem/vaborbactam resistant but imipenem/relebactam susceptible. All P. aeruginosa, C. freundii, A. baumannii and E. cloacae isolates were resistant to both meropenem/vaborbactam and imipenem/relebactam. Seven of 10 E. coli isolates were tigecycline susceptible of which 6 were also eravacycline susceptible. One of 11 K. pneumoniae, 1/1 K. oxytoca and 1/1 L. adecarboxylata isolates were susceptible to both glycylcyclines. All other isolates were resistant to both glycylcyclines.E. coli than K. pneumoniae. Meropenem/vaborbactam provided better cover than imipenem/relebactam. Eravacycline and tigecycline showed similar activity to each other, but their activity was inferior compared with the \u03b2-lactam combinations, particularly against K. pneumoniae.In both OXA-48 and NDM producers, the activity of the four antibiotics tested was better against"} +{"text": "Hcrt), tachykinin receptor 3 (Tacr3), cocaine and amphetamine-regulated transcript (Cart) and catecholamine-related biological processes; dopa decarboxylase (Ddc), histidine decarboxylase (Hdc), tyrosine hydroxylase (Th), and vasoactive intestinal peptide (Vip). In BACHD mice, few hypothalamic genes were differentially expressed compared to age-matched WT controls. However, GSEA indicated an enrichment of inflammatory- and gonadotropin-related processes at 10 months. In conclusion, we show that both wtHTT and mHTT overexpression change hypothalamic transcriptome profile, specifically mHTT, altering neuroendocrine circuits. In contrast, the ubiquitous expression of full-length mHTT in the BACHD hypothalamus moderately affects the transcriptomic profile.Structural changes and neuropathology in the hypothalamus have been suggested to contribute to the non-motor manifestations of Huntington\u2019s disease (HD), a neurodegenerative disorder caused by an expanded cytosine-adenine-guanine (CAG) repeat in the huntingtin (HTT) gene. In this study, we investigated whether hypothalamic HTT expression causes transcriptional changes. Hypothalamic RNA was isolated from two different HD mouse models and their littermate controls; BACHD mice with ubiquitous expression of full-length mutant HTT (mHTT) and wild-type mice with targeted hypothalamic overexpression of either wild-type HTT (wtHTT) or mHTT fragments. The mHTT and wtHTT groups showed the highest number of differentially expressed genes compared to the BACHD mouse model. Gene Set Enrichment Analysis (GSEA) with leading-edge analysis showed that suppressed sterol- and cholesterol metabolism were shared between hypothalamic wtHTT and mHTT overexpression. Most distinctive for mHTT overexpression was the suppression of neuroendocrine networks, in which qRT-PCR validation confirmed significant downregulation of neuropeptides with roles in feeding behavior; hypocretin neuropeptide precursor ( HTT) gene is a fatal neurodegenerative disorder caused by a CAG repeat expansion in exon one in the huntingtin (TT) gene . The expTT) gene . The lenTT) gene . Current alleles , which sThe hypothalamus plays a primary role in the central-peripheral regulatory network that maintains body homeostasis, including regulating whole-body energy metabolism . MetabolTranscriptional dysregulation in the striatum is one of the hallmarks of HD . SpecifiAll the mice used in the study were housed in groups and maintained at a 12 h light/dark cycle with free access to a standard chow diet and water. All the experimental procedures performed on mice were carried out in accordance with the approved guidelines in the ethical permits approved by Lund University Animal Welfare and Ethics committee in the Lund-Malm\u00f6 region .Microarray profiling of the hypothalamic transcriptome was performed in Adeno-associated viral (AAV) vector-mediated groups of WT mice with targeted expression of wtHTT (AAV-HTT853-18Q) or mHTT (AAV-HTT853-79Q) fragments and BACHD mice that express full-length mHTT (97Q) . Both HDn = 5, 79Q: n = 8 and WT control: n = 5.AAV vector-mediated HD models achieve region-specific overexpression of HTT fragments in the brain through targeted injections using stereotactic surgery. AAV groups were assessed at 4 weeks post-injection since this was the earliest timepoint for a significant weight gain, as shown in previous studies . The vecn = 6 and WT: n = 6, and for 10 months of age: BACHD: n = 5 and WT: n = 3.Bacterial artificial chromosome-mediated transgenic mouse model is a transgenic mouse model of HD and ubiquitously expresses a full-length human mHTT . In the Hypothalamic tissue was dissected on ice and snap-frozen in liquid nitrogen after a terminal dose of sodium pentobarbital via intraperitoneal injection. Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit according to the manufacturer\u2019s instructions. RNA concentration and RNA quality measured in terms of RNA integrity number (RIN) were determined using the Agilent 2,100 Bioanalyzer . Samples with poor RIN (<7) were omitted from further analysis. Microarray analysis was performed on total hypothalamic RNA using the Affymetrix platform .Analyses were made using R v.4.1.1 . Raw .CEp-value followed by sorting it from the highest log2 (FC) to the lowest. The top 10 most upregulated and top 10 most downregulated significantly differentially expressed genes were identified, and their respective RMA-limma values were used to construct and color the heatmap. Heatmaps were generated using the pheatmap package in R1 (v. 1.0.12) (Limma output files for 18Q vs. WT and 79Q vs. WT were sorted based on adj. 1.0.12) . Hierarcp-value < 0.05. The 18Q vs. WT and 79Q vs. WT datasets were subsequently sorted into three gene sets: shared genes, unique genes for 18Q vs. WT, and unique genes for 79Q vs. WT. The shared and unique gene lists (ENTREZ IDs) were imported into DAVID2 . The reported p-values were further adjusted using the Benjamini-Hochberg procedure to correct for multiple testing. Outputs from GSEA can be found in ClusterProfiler (v.4.0.5) was used to perform GSEA . The funTo synthesize cDNA, 1 \u03bcg of RNA from each sample was reverse transcribed using SuperScript IV Reverse Transcriptase SuperScript IV kit according to the manufacturer\u2019s instructions. Mouse qRT-PCR primers were designed using Primer3Plus software . qRT-PCRp-value < 0.05 considered statistically significant.Statistical analysis of qRT-PCR data was performed using Graphpad Prism 9 . . Data were analyzed using non-parametric Mann-Whitney U tests with a p-value in the limma datasets comparing injected mice to uninjected (18Q vs. WT and 79Q vs. WT) showed a skewed distribution with a preference for upregulated genes in the injected mice of the microarray data showed a clear separation of the AAV-HTT groups from the WT samples . PCA of ted mice . Filteri5 cutoff .p < 0.05 cutoff, 1,422 variables remained for BACHD 2 months vs. WT variables, and we further analyzed the data using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (see text footnote 2) (p < 0.05) identified by limma between the 18Q vs. WT and 79Q vs. WT datasets (The 18Q vs. WT and 79Q vs. WT datasets had the highest number of significant (adj. tnote 2) . Previoutnote 2) . Furthertnote 2) . Therefodatasets , using tdatasets . DAVID Fn = 51 genes, (adj. p < 0.05) to 79Q vs. WT (adj. p > 0.05)] showed that the gene with the highest difference in log2(FC) was immunoglobulin heavy chain (X24 family) (Igh-VX24) followed by tripartite motif-containing 30D (Trim30d) and toll-like-receptor 7 (Tlr7) . Across all 51 genes, the mean difference with 95% CI was 0.135 > 0 and 61 with log2(FC) < 0 . Functio, 0.181) , 2.n = 12 genes, adj. p < 0.05) to 18Q vs. WT (adj. p > 0.05) showed a mean difference with 95% CI of -0.042 . In the top 5/10 cluster related to neuroactive ligands , we found a mean difference in log2(FC) of -0.067 between the 79Q vs. WT and 18Q vs. WT datasets, where the genes with the highest difference were proenkephalin (Penk) and tachykinin receptor 3 (Tacr3) > 0 and 131 with log2(FC) < 0 . Among t: -0.24] , 2.Ldlr; log2(FC) 18Q vs. WT: \u22120.49, 79Q vs. WT: \u22120.54] (The shared gene list between 18Q vs. WT and 79Q vs. WT consisted of 410 genes with log2(FC) > 0 and 39 genes with log2(FC) < 0 . An immu: \u22120.54] , 2.p and log2(FC)] in the 18Q vs. WT and 79Q vs. WT datasets , and major facilitator superfamily domain-containing 2A (Mfsd2a) (Nms), Hdc, synaptic vesicle glycoprotein 2C (Sv2c), and Tacr3 , genes tnd Tacr3 . CompariNext, we elaborated further on the functional implications of the differences in the top 10 downregulated genes between 18Q vs. WT and 79Q vs. WT. GSEA of GO-BP with leading-edge analysis was usedp-value < 0.05 for the 79Q vs. 18Q and BACHD datasets. By using GSEA, we may still identify biologically relevant pathways that exhibit noteworthy cross-correlation between genes with a subtle change in expression levels or weak statistical significance was -0.156 . The leading- edge gene with the lowest log2(FC) was prolactin (Prl) at -1.63 followed by growth hormone (Gh) -1.02, Vip -0.59, the alpha subunit of glycoprotein hormones (Cga) -0.53 and hypocretin (Hcrt) -0.35 -0.35 , 4.Acot5) and vesicular glutamate transporter 1 (Slc17a7) that were respectively part of the fatty-acid related and \u201cGlutamatergic synapse\u201d pathways . None of the three pathways identified in 2 months old BACHD vs. WT were significant in GSEA-KEGG for 10 months old BACHD vs. WT. When comparing each leading-edge gene set in 2 months old BACHD vs. WT to the same genes in 10 months BACHD vs. WT, the mean log2(FC) difference was <0.2 for all three pathways. Instead, for 10 months old BACHD vs. WT, fourteen KEGG pathways were identified (H2-Aa), and Cd74 were among the leading-edge genes with the highest log2(FC) and difference from the 2 months of age vs. WT dataset . Pathways related to gonadotropin-releasing hormone (Gnrh), all NES > 0, were also found in 10 months old BACHD vs. WT, where the alpha subunit of glycoprotein hormones (Cga) was among the leading-edge genes with the highest fold change . Only one of the 14 KEGG pathways identified by GSEA had a negative NES of -1.95, indicating suppression; \u201cOxidative phosphorylation\u201d (mmu00190). The overall change of the 59 genes in the leading-edge gene set was -0.056 [mean log2(FC) with 95% confidence interval (95% CI)].For 2 months old BACHD vs. WT, GSEA-KEGG identified three pathways; \u201cGlutamatergic synapse\u201d , \u201cBiosynthesis of unsaturated fatty acids\u201d and \u201cFatty acid elongation\u201d . Among lentified . Immune-entified . HistocoHcrt) in mice with mHTT 79Q overexpression compared to wtHTT 18Q groups and uninjected WT controls that was among the top suppressed processes in GSEA-GO BP consisted of 57 genes . We havecontrols . Here, imparison .Hdc as part of the top 10 downregulated genes and related leading-edge subsets in GSEA. Comparing GSEA-GO BP outputs between the 79Q vs. WT and 18Q vs. WT datasets showed a higher number of catecholamine-related processes that were only significant for the 79Q vs. WT dataset or Growth hormone-releasing hormone (Ghrh) . A matchransport .Cart, Tacr3, Hcrt, Vip, Th, and Ghrh, only Tacr3 was significantly downregulated compared to the age-matched WT controls.Next, we performed qRT-PCR of a subset of genes analyzed for the HTT-AAV groups in the BACHD 2 months group . Among CHdc mRNA have been reported in HD patients . Among leading-edge genes was Cga, which encodes the alpha subunit of glycoprotein hormones . Furthereriphery , notableeriphery . Expresseriphery . Furthereriphery . Similareriphery . In lineeriphery . As HD periphery . TherefoStoml3 and Sv2c associated with dopaminergic signal transmission were among the top 10 differentially downregulated in 79Q vs. WT .RS-K, \u00c5P, ED, and MB designed the experiments from RS-K and \u00c5P. ED, AD, RS-K, and SL performed the experiments. ED, NA, AD, and RS-K analyzed the data. ED, RS-K, and AD wrote the first draft of the manuscript. All authors reviewed the manuscript and approved the final version."} +{"text": "TM) can ameliorate liver fibrogenesis induced by thioacetamide (TAA) treatment. Our results showed that the TAA treatment caused lower body weight gains and enlarged livers, as well as higher serum ALT, AST, and ALP levels (p < 0.05). This liver inflammatory and fibrotic evidence was ameliorated (p < 0.05) by supplementing with GBHP01TM; this partially resulted from its antioxidant abilities, including decreased TBARS values but increased TEAC levels, reduced GSH contents and catalase/GPx activities in the livers of TAA-treated rats (p < 0.05). Additionally, fewer nodules were observed in the appearance of the livers of TAA-treated rats after supplementing with GBHP01TM. Similarly, supplementing GBHP01TM decreased fibrotic scars and the fibrotic score in the livers of TAA-treated rats (p < 0.05). Moreover, the increased hepatic IL-6, IL-1\u03b2, and TNF-\u03b1 levels after TAA treatment were also alleviated by supplementing with GBHP01TM (p < 0.05). Meanwhile, GBHP01TM could decrease the ratio of LC3B II/LC3B I, but upregulated P62 and Rab7 in the livers of TAA-treated rats (p < 0.05). Taking these results together, the CLH-based supplement (GBHP01TM) can be characterized as a natural agent against liver fibrogenesis.Chicken-liver hydrolysates (CLHs) have been characterized as performing several biofunctions by our team. This study aimed to investigate if a CLH-based supplement (GBHP01 Liver cancer ranks third among cancer categories globally, and approximately 830,000 people die with liver cancer every year . SimilarFood-derived protein hydrolysates have been suggested to provide functional properties such as antioxidant , lipid-lCandidates for functional-food ingredients should be either effective or low in cost. Regarding the poultry industry in Taiwan, approximately 10,000 metric tons of chicken livers (2.5% based on broilers\u2019 wt.) have been produced in recent years and antiTM) containing 200 mg CLH powder and 20 mg hesperidin per capsule was generously offered by Great Billion Biotech Co., Ltd., New Taipei City, Taiwan. The composition of free amino acids and imidazole-ring dipeptides in a GBHP01TM capsule were sent for analysis using an Amino Acid Analyzer in the Food Industry Research and Development Institute . The total contents of free essential and non-essential amino acids and imidazole-ring dipeptides are 13.10, 65.04, and 0.07 mg per capsule (average 650 mg), respectively, where the total free branched-chain amino acid (BCAA) and taurine content are 5.77 mg and 51.67 mg per capsule ; (2) TAA: 100 mg TAA/kg BW (i.p.) + 1.5 mL pure H2O ; (3) TAA + SIL: 100 mg TAA/kg BW (i.p.) + 150 mg silymarin/kg BW in 1.5 mL pure H2O ; (4) TAA + GBHP01(1X): 100 mg TAA/kg BW (i.p.) + 133 mg GBHP01TM content/kg BW in 1.5 mL pure H2O ; (5) TAA + GBHP01(2X): 100 mg TAA/kg BW (i.p.) + 266 mg GBHP01TM content/kg BW in 1.5 mL pure H2O . It was reported that silymarin could ameliorate livre fibrogenesis via decreasing endoplasmic reticulum stress-related gene expressions, inflammatory cytokines, collagen accumulation, and matrix metalloproteinase (MMP-2 and MMP-9) activities, as well as increasing tissue inhibitors of metalloproteinase gene expressions (TIMP-1 and TIMP-3) in livers . Additionally, serum ALB values were reduced (p < 0.05) by TAA treatment, except in the TAA + GBHP01(2X) group. Focusing on serum lipid levels, no (p > 0.05) differences on TC levels were observed among groups. The TAA group had the lowest (p < 0.05) serum TG levels among groups, but a reverse (p < 0.05) effect was observed in silymarin and GBHP01TM-supplemented groups, while TAA + SIL and TAA + GBHP01(2X) groups even showed similar (p > 0.05) serum TG levels to the CON group.After 8 weeks of experiment, TAA treatment resulted in the lower body weight of rats (approximately a 12.19% reduction), while lower weight increases and smaller food intakes were observed in TAA-treated rats than in control rats ( < 0.05) . No , while the silymarin or GBHP01TM-supplemented group had similar (p > 0.05) TBARS to the CON group and no (p > 0.05) difference in TEAC levels among GBHP01TM-supplemented groups and the CON group. Besides, the decreased pattern of reduced GSH levels was observed in TAA-treated groups, but silymarin or GBHP01TM supplementation allowed for maintenance of the reduced GSH level in TAA-treated rats, especially in the group receiving 2X doses of GBHP01TM supplementation (p < 0.05). With regard to antioxidant enzymatic activities, SOD activities were not (p > 0.05) different among groups. The TAA group showed reduced (p < 0.05) CAT and GPx activities compared to CON group, while silymarin or GBHP01TM supplementation avoided reducing CAT activities, showing a result similar (p > 0.05) even to that of the CON group; reversed (p < 0.05) effects on GPx activities were only observed in GBHP01TM supplemented groups. In hepatic proinflammatory cytokines, the TAA group had higher (p < 0.05) hepatic IL-1\u03b2 , IL-6 , and TNF-\u03b1 (28.89% increase) than the CON group. GBHP01TM supplementation reduced (p < 0.05) these increased hepatic inflammatory cytokines of TAA-treated rats to levels similar (p > 0.05) even to those of the CON group, but silymarin supplementation only reduced the hepatic IL-6 level.As the results in TM supplementation. Via H&E stained observation according to the H&E stains were increased by TAA treatments, while significant reductions (p < 0.05) in all three HAI scores were observed in the GBHP01TM supplementation group; however, silymarin only demonstrated a reduced pattern score. Silymarin treatment did not (p > 0.05) attenuate the liver Metavir score in the TAA-treated rats. Treatment with 1X or 2X GBHP01 supplement decreased (p < 0.05) the scores in TAA-treated rats, although the scores were still higher (p < 0.5) than those of the CON group , but GBHP01TM supplement significantly downregulated (p < 0.05) this ratio, reaching levels even similar (p > 0.05) to those of CON (p < 0.05) by TAA treatment (TM supplementation significantly upregulated (p < 0.05) these two proteins in livers of TAA-treated rats; meanwhile, the P62 and Rab7 protein expression in the livers of the TAA + GBHP01(1X) and TAA + GBHP01(2X) groups were reversed to similar levels to those of the CON group (p > 0.05).With regard to autophagy modulation in livers of TAA-treated rats, the ratio of LC3B II/LC3B I of TAA group was almost 1.8 relative fold to that of CON group and hesperidin, which are both characterized by antioxidant abilities , only 4.1 and 8.2 mg hesperidin/kg BW were given to rats. Hence, it was assumed that the amelioration of TAA-induced liver fibrosis by hesperidin can be considered negligible in this study. To summarize, this regulation probably mainly results from the bioactive ingredients in the CLHs of GBHP01TM supplements . Accordin (IL10) , the revsurvival . Recentlsurvival and incrsurvival . It was survival . It was survival . Besidessurvival . This phsurvival ,37. LC3Bsurvival , while Rsurvival . As the survival . Meanwhisurvival . Taurinesurvival . Similarsurvival . As explturation . Althougin/kg BW ,43,44. BTM) showed an ameliorating effect against liver fibrogenesis induced by TAA treatment against liver fibrogenesis may be attributed to the bioactive ingredients in CLHs, including anserine, taurine, glutamic acid, aspartic acid, BCAAs, etc.In this study, chicken liver hydrolysate (CLH)-based supplements (GBHP01reatment . The hep"} +{"text": "Anguilla japonica) are commercially important species, harvested extensively for food. Currently, this and related species (American and European eels) are challenging to breed on a commercial basis. As a result, the wild stock is used for aquaculture. Moreover, climate change, habitat loss, water pollution, and altered ocean currents affect eel populations negatively. Accordingly, the International Union for Conservation of Nature lists Japanese eels as endangered and on its red list. Here we presented a high-quality genome assembly for Japanese eels and demonstrated that large chromosome reorganizations occurred in the events of third-round whole-genome duplications (3R-WRDs). Several chromosomal fusions and fissions have reduced the ancestral protochromosomal number of 25 to 19 in the Anguilla lineage. A phylogenetic analysis of the expanded gene families showed that the olfactory receptors (group \u03b4 and \u03b6 genes) and voltage-gated Ca2+ channels expanded significantly. Both gene families are crucial for olfaction and neurophysiology. Additional tandem and proximal duplications occurred following 3R-WGD to acquire immune-related genes for an adaptive advantage against various pathogens. The Japanese eel assembly presented here can be used to study other Anguilla species relating to evolution and conservation.Japanese eels ( Fishes are highly diverse species living in many ecological habitats, including freshwater, estuarine, and the ocean . Over 99From the evolutionary perspective, eels are among the extant basal groups of teleost ray-finned fishes after the 3-round whole-genome duplication (3R-WGD) . The rayAnguilla japonica , was kept in a freshwater tank for a week with aeration. Blood sample was taken from the fish, snapped frozen in liquid nitrogen, and then stored at \u221280\u00b0C. Genomic DNA was extracted from the blood sample. DNA sequencing data were generated by different platforms, including Oxford Nanopore (ONT) long reads, PacBio continuous long reads (CLRs), Illumina short reads, Illumina mate-pair reads, 10\u00d7 Chromium linked reads, DNase Hi-C (Omni-C), and Bionano optical mapping .A market-purchased female Japanese eel, RRID:SCR_006255) 3.2.10. For PacBio CLR sequencing, the SMRTbell templates were prepared using Sequel Binding Kit 1.0 and sequenced on the PacBio Sequel System . For Illumina short reads and mate-pair sequencing, the libraries were prepared using the TruSeq DNA PCRFree Kit and Nextera Mate Pair Library Preparation Kit (gel plus), respectively. They were sequenced with 2\u00d7 150-bp reads on an Illumina HiSeq X Ten instrument. The library for linked reads was prepared by a 10\u00d7 Genomics Chromium system with the Chromium Genome library (v2) and sequenced with 2\u00d7 150-bp reads on an Illumina NovaSeq 6000 instrument. Dovetail Omni-C Kit was used for Hi-C library preparation, which used NEBNext Ultra enzyme and Illumina-compatible adapters. Biotin-containing fragments were isolated using streptavidin beads before PCR enrichment.\u202fThe library was sequenced with 2\u00d7 150-bp reads on an Illumina HiSeqX platform. The Bionano optical mapping was generated by 3 enzymes, 2 from Irys (Nt.BspQI and Nb.BssSI) and 1 from Saphyr (RRID:SCR_017992) (DLE1). We stretched and captured the images of fluorescently labeled DNA molecules in Irys and Saphyr G1.2 chips. The labeling distances were extracted from the images and recorded into the raw molecule files. Molecules over 150\u00a0Kbp were assembled into consensus maps using Bionano Solve for further analysis (The library for ONT long-read sequencing was prepared using the Ligation Sequencing Kit (LSK109) and sequenced using the Nanopore PromethION P48 sequencer with the flow cells (R9.4.1) and the basecaller version Guppy v2 [RRID:SCR_017225) v2.5 [RRID:SCR_017016) v2.71 [RRID:SCR_017642) v1.4.16 [RRID:SCR_014731) v1.23 [MitoZ software (v2.4) was used5880) v2 , Wtdbg2 6) v2.71 separate6) v2.71 to achie1) v1.23 for 2 roRRID:SCR_021172) v1.11.08 [We applied Tigmint v1.1.2 and ARKSv1.11.08 to extende novo approaches to annotate transposable elements (TEs) in the Japanese eel genome. For the homolog-based approach, RepeatMasker v4.0.7 [RRID:SCR_021169) v21.12 database [RRID:SCR_015247) v1.06 [de novo approach, RepeatModeler (RRID:SCR_015027) v1.0.8 was used to detect the TE families and repeat boundaries by integrating 3 complementary de novo repeat finding programs. RepeatMasker collected the union of these tools' results and annotated the genome accordingly.Tandem Repeats Finder v4.09 was applr v4.0.7 and Repedatabase to the g7) v1.06 was usedde novo, homology-based, and transcriptome-based annotations. Maker (RRID:SCR_005309) v2.31.8 [Anguilla anguilla), zebrafish (Danio rerio), Indo-Pacific tarpons , Asian arowana (Scleropages formosus), and spotted gar (Lepisosteus oculatus), based on the phylogeny of teleost fishes [Three types of methods were used to annotate the protein-coding genes in the genome, including v2.31.8 was adopt fishes .De novo annotation was performed using Augustus (RRID:SCR_008417) v3.2.1 [RRID:SCR_002127) v1 [RRID:SCR_015530) v2.1.0 [RRID:SCR_013048) v2.10.0 [) v3.2.1 and SNAP2127) v1 by train) v2.1.0 and asseGene functional annotation was performed by aligning the predicted gene sequences to protein sequences using BLAST v2.2.31 in the sRRID:SCR_015008) v5.1.2 [RRID:SCR_011980), to compare.BUSCO v5.1.2 was usedRRID:SCR_010835) 1.3.1 [RRID:SCR_001598) [RRID:SCR_007891) v12 [tRNAscan-SE (5) 1.3.1 was used_001598) . The mic891) v12 to the gRRID:SCR_006086) v2.2.3 [Anguilla rostrata , A. anguilla , A. japonica (Japanese eel), M. cyprinoides , S. formosus , Gadus morhua , Oryzias latipes , D. rerio ,L. oculatus , Erpetoichthys calabaricus , Latimeria chalumnae , and Callorhinchus milii . We estimated the divergence times for single-copy orthologos using mcmctree in PAML (RRID:SCR_014932) package v4.8a [RRID:SCR_021162) website: D. rerio with O. latipes (180.0\u2013264.0 Mya), M. cyprinoides with A. anguilla (162.2\u2013197.3 Mya), C. milii with D. rerio (442.7\u2013515.5 Mya), and E. calabaricus with D. rerio (381.0\u2013407.0 Mya). To estimate gene family expansion and contraction, we used CAF\u00c9 (RRID:SCR_005983) v4.2.1 [OrthoMCL (v2.0) was used) v2.2.3 to recon) v4.2.1 to modelRRID:SCR_011822) v2.2.26 [RRID:SCR_008493) v6.6.0 [RRID:SCR_001010) v2.2.26 to remove sequences that did not match genes already known in SwissProt and NR. InterProscan was used to determine the secondary structures of the predicted OR genes. Some genes were filtered due to lacking the 7 transmembrane domains. The maximum likelihood phylogenetic tree was reconstructed using IQ-TREE (RRID:SCR_017254) v2.2.0.3 [RRID:SCR_011811) v7.505 [We identified olfactory receptor (OR) genes using the pipeline described in GitHub , while c v2.2.26 was used) v6.6.0 . Using Ev2.2.0.3 based on) v7.505 .A. japonica, A. anguilla, A. rostrata, M. cyprinoides,and Lepisosteus oculatus. The numbers of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) were calculated using KaKs_calculator2.0 [MCscanX v1.5.1 and macrlator2.0 . In addilator2.0 , using sA. japonica (Japanese eel), M. cyprinoides (tarpon), and S. formosus . The ancestral teleosts karyotype (ATK) was constructed using zebrafish, S. formosus (arowana), and L. oculatus [Ancestral eel/tarpon karyotype (AETK) was constructed using t-group) . This wat-group) to obtait-group) .AB038556.2) of the NR database from NCBI [In this study, MitoZ software was used to assemble and annotate the mitochondrial genome 16.686 Kb) of our sample to confirm the species' identity . The data matched with the Japanese eel mitochondrial genome , we identified 29,982 coding genes loci in the 1,131 single-copy orthologs from the 12 fish species and Cypriniformes diverged from the Eloposteoglossocephala clade at 262.5 Mya. Above are fish groups that had undergone 3R-WGD. Compared to the out-groups, spotted gars, reed fish, coelacanths, and Australian ghost sharks underwent only 2 rounds of whole-genome duplication (2R-WGD).The orthology analysis of 12 species' coding genes identified 21,653 gene family clusters. The expansion and contraction of gene families reflect the evolution of organisms' adaptations to their environments. Ortholog analysis of genes from the 12 species identified 21,652 gene family clusters. By removing gene families with too many (\u2265200) or too few (\u22642) genes, we achieved 129,862 genes to evaluate the expansion and contraction of gene families Fig.\u00a0. Among t2+ and K+ channel families were identified. Calcium and potassium play significant roles in neuronal excitability, muscle contraction, fertilization, and energy metabolism. Interestingly, the other expanded gene families include (i) the assembly of thick myosin filament in skeletal muscle, (ii) lipoprotein receptor\u2013related protein (metabolic and morphogenetic pathways), and (iii) isocitrate and isopropyl malate dehydrogenases family (carbohydrate and amino acid metabolism).Comparing the Japanese eel to the other 11 species, 433 gene families increased, with a total increase of 551 genes. On the other hand, a total of 943 genes were lost from 782 gene families . It is iA. japonica, A. Anguilla, and M. cyprinoides, respectively had many paralogous pairs after splitting from the Osteoglossomorpha lineage . The obsely Fig.\u00a0. Additioely Fig.\u00a0. By idenThere are 21,249 duplicated genes identified among the 29,982 coding genes in the Japanese eel genome. Based on their duplication patterns, DupGen_finder classified the duplicated genes into 5 categories: (i) 9,890 WGDs (46.54%), (ii) 1,420 tandem duplicates , (iii) 768 proximal duplicates , (iv) 3,975 transposed duplicates , and (v) 5,196 dispersed duplicates . We then calculated the Ks and Ka/Ks values for these 5 gene categories. Ks distribution indicates that TD and PD revealed additional duplication after 3R-WGD Fig.\u00a0. In addin) is 25 for tarpons, arowana, and zebrafish; 24 for medaka; and 23 for Atlantic cod. Japanese eels have a lower haploid chromosome number (n = 19). To assess the extent of interchromosomal rearrangements in Japanese eels, we reconstructed the karyotype of the common ATK and AETK in tarpons. Comparatively, the 19 AETK chromosomes underwent 24-fusion and 18-fission to form the 13 chromosomes in Japanese eels (n = 19) in Japanese eels, of which Chr 1, and Chr 3\u20137 rearrangements are unique to Japanese eels and might play a role in speciation. Japanese eel's chromosomes were derived from AETK's with slight rearrangements. The patterns of chromosome rearrangements in Chr 8, 13, and 16\u201317 of Japanese eels were comparable with Chr 21, 6, 8, and 19 in tarpons. Without rearrangement, Japanese eel's chromosomes 10, 14, and 19 were equivalent to AETK's chromosomes 3, 6, and 22. In addition, 3 chromosomes in the Japanese eel derived directly from AETK's chromosomes , which also correspond to tarpon's chromosomes , respectively. Figure\u00a0When comparing chromosome numbers of the fishes that had all undergone 3R-WGD, the haploid chromosome number and zeta (\u03b6) group genes in the freshwater eels expanded enormously, comprising about 86% of the entire gene family. Delta (\u03b4) and \u03b6 belong to the type I genes , which a2+ channels were the significantly expanded gene families in Japanese eels. Genome studies suggest that the cellular functions of voltage-gated ion channels emerged early in Metazoan evolution [2+ during migration between waters with great variations of calcium contents. A gene expression study in marbled eel (Anguilla marmorata) showed high expression of voltage-gated Ca2+channels in brain, skin, and osmoregulatory tissues and its response to changes in water calcium levels [2+ homeostasis, Ca2+ signaling coordinates various physiological processes, including skeletal muscle contractions, nervous system activity, and cardiac and reproductive functions. The expanded gene families of thick myosin filament in skeletal muscle imply enhanced coordination of muscle contraction and performance [The voltage-gated Cavolution , 85 in dm levels . Besidesformance , especiaformance . Additioformance , 90. Isoformance . The dupformance . These eformance . Notablyformance and sturformance .n) of 26 [n = 24 or 25 in extant teleost species. In this study, we reconstructed the ancestral protochromosomes AETK (n = 25) to describe the cross-species chromosome collinearity and underpin the lineage-specific genome reorganization. The chromosome number of Anguillaspecies (n = 19) was reduced as compared with M. cyprinoides (n = 25) and S. formosus (n = 25). The Anguilliformes is made up of 15 families with remarkable karyotypic diversity [n = 19 and 21. The Anguilla lineage underwent a significant structural rearrangement upon their divergence from the common ancestor of tarpons (M. cyprinoides). The fusion and fission of their chromosome structure were the primary drivers of reducing the haploid chromosome number to 19.The acquisition of evolutionary novelty by WGD duplication and the subsequent fate change of duplicated genes is necessary for phenotype alteration, environmental adaptation, and speciation . The larn) of 26 . Evolutiiversity . The hapA. japonica whole genome sequencing and assembly are publicly available on NCBI databases under the accession number PRJNA852364. The gene models are available at Zenodo [GigaScience GigaDB database [The t Zenodo . All supdatabase .Supplementary Fig. S1. The alignment plot shows our mitochondrial genomes assembled and GenBank ID AB038556.2 of Japanese eels.Supplementary Fig. S2. Circos plot for the mitochondrial genome of Japanese eel. From outer to inner circles: protein-coding genes, rRNA, and tRNA; depth of Illumina short reads; and GC content.Supplementary Fig. S3. Multiplatform Japanese eel genome assembly.Supplementary Fig. S4. Genome comparison of Japanese (A. japonica) and European (A. anguilla) eels.Supplementary Fig. S5. Venn diagram of gene annotation based on 5 databases .Supplementary Fig. S6. KEGG-based gene function classification. The numbers represent how many genes are in the particular functions.Supplementary Fig. S7. KOG-based gene function classification. The numbers represent how many genes are in the particular functions.Supplementary Fig. S8. Length distribution of messenger RNA, CDS, exon, intron, and the number of exons in Japanese eel and the other species .Supplementary Fig. S9. Ks distributions of syntenic paralogs and orthologs. Ks value distribution is used to identify genome duplication and speciation.Supplementary Fig. S10. Comparative genomic analysis of Japanese eels (A. japonica), tarpons (M. cyprinoides), and arowanas (S. formosus).Supplementary Table S1. Genome sequencing platforms for A. japonica.Supplementary Table S2. A summary of contig statistics from the ONT long-read assembly.Supplementary Table S3. A summary of contig statistics after assembly error correction.Supplementary Table S4. Scaffolding by 10\u00d7 linked reads, Bionano optical mapping, and Hi-C.Supplementary Table S5. The completeness of A. japonica genome by BUSCO assessment.Supplementary Table S6. Statistical results for repeat sequences.Supplementary Table S7. A statistical analysis of the classification results for TE.Supplementary Table S8. Functional annotation of predicted genes from A. japonica.Supplementary Table S9. The completeness of A. japonica genes by BUSCO assessment.Supplementary Table S10. The average length of exons in Japanese eel and the 8 related fish species.Supplementary Table S11. GO enrichment analysis of the gene families expanded in the 3 freshwater eel genomes.Supplementary Table S12. GO enrichment analysis of the gene families expanded in the A. japonica genome.Supplementary Table S13. The karyotypes of M. cyprinoides (tarpons) and the common ancestor of eels and tarpons (AETK).Supplementary Table S14. The karyotypes of A. japonica (Japanese eel) and the common ancestor of eels and tarpons (AETK).giac120_GIGA-D-22-00177_Original_SubmissionClick here for additional data file.giac120_GIGA-D-22-00177_R1_Revision_1Click here for additional data file.giac120_GIGA-D-22-00177_Revision_2Click here for additional data file.giac120_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giac120_Response_to_Reviewer_Comments_Revision_1Click here for additional data file.giac120_Reviewer_1_Report_Original_SubmissionChristiaan Henkel -- 8/9/2022 ReviewedClick here for additional data file.giac120_Reviewer_1_Report_Revision_1Christiaan Henkel -- 10/6/2022 ReviewedClick here for additional data file.giac120_Reviewer_2_Report_Original_SubmissionZhong Li -- 8/22/2022 ReviewedClick here for additional data file.giac120_Supplemental_Figures_and_TablesClick here for additional data file.AETK: ancestral eel/tarpon karyotype; ATK: ancestral teleosts karyotype; BLAST: Basic Local Alignment Search Tool; bp: base pair; BUSCO: Benchmarking Universal Single-Copy Orthologs; CLR: continuous long read; DSD: dispersed duplicate; Gb: gigabase; Kbp: kilobase pair; KEGG: Kyoto Encyclopedia of Genes and Genomes; Mb: megabase; Mbp: megabase pair; Mya: million years ago; NCBI: The National Center for Biotechnology Information; ONT: Oxford Nanopore; OR: olfactory receptor; ORF: open reading frame; PD: proximal duplicate; rRNA: ribosomal RNA; TD: tandem duplicate; TE: transposable element; TRD: transposed duplicate; tRNA: transfer RNA; WGD: whole-genome duplication; 2R-WGD: 2-round whole-genome duplication; 3R-WGD: 3-round whole-genome duplication; 4R-WGD: 4-round whole-genome duplication.The experimental plan and sequencing strategy were designed by C.K.C.W., E.L.Z., A.O.L.W., K.P.L., and T.F.C. Samples were collected by A.H.M.N. and H.T.W. Bionano optical mapping and data analysis were conducted by C.Y.L.C., E.Y.C.C., and J.Z. The sequencing data for genome assembly were analyzed by E.L.Z., H.W., B.W., J.J., E.Y.C.C., and T.F.C. The manuscript was written by C.K.C.W., H.T.W., E.L.Z., H.W., and A.O.L.W."} +{"text": "Bifidobacterium bifidum DS0908 (DS0908) and Bifidobacterium longum DS0950 (DS0950). Treatment with DS0908 and DS0950 postbiotics significantly induced the expression of the brown adipocyte-specific markers UCP1, PPAR\u03b3, PGC1\u03b1, PRDM16 and beige adipocyte-specific markers CD137, FGF21, P2RX5, and COX2 in C3H10T1/2 mesenchymal stem cells (MSCs). In mice with high-fat diet (HFD)-induced obesity, both potential probiotics and postbiotics noticeably reduced body weight and epididymal fat accumulation without affecting food intake. DS0908 and DS0950 also improved insulin sensitivity and glucose use in mice with HFD-induced obesity. In addition, DS0908 and DS0950 improved the plasma lipid profile, proved by reduced triglyceride, low-density lipoprotein, and cholesterol levels. Furthermore, DS0908 and DS0950 improved mitochondrial respiratory function, confirmed by the high expression of oxidative phosphorylation proteins, during thermogenesis induction in the visceral and epididymal fat in mice with HFD-induced obesity. Notably, the physiological and metabolic changes were more significant after treatment with potential probiotic culture-supernatants than those with the bacterial pellet. Finally, gene knockdown and co-treatment with inhibitor-mediated mechanistic analyses showed that both DS0908 and DS0950 exerted anti-obesity-related effects via the PKA/p38 MAPK signaling activation in C3H10T1/2 MSCs. Our observations suggest that DS0908 and DS0950 could potentially alleviate obesity as dietary supplements.Probiotic supplements have promising therapeutic effects on chronic diseases. In this study, we demonstrated the anti-obesity effects of two potential probiotics, The mice were administered DS0908 or DS0950 pellets were fixed in 4% paraformaldehyde, embedded in paraffin, and cut into 10-\u03bcm sections. Standard H&E staining was performed using standard protocols. Five random fields of each section were evaluated, and the average adipocyte diameter was measured using the ImageJ software .Tbp was an internal control. We harvested C3H10T1/2 MSCs and extracted total RNA using an RNA Extraction Kit following the manufacturer\u2019s guidelines. We used 1 \u03bcg RNA to synthesize cDNA using the Maxime RT PreMix Kit on a Veriti 96-Well Thermal Cycler . qRT-PCR was performed using an iQ SYBR Green Supermix Kit on a CFX96 Real-Time PCR Detection System (Bio-Rad). + with ImageLab (Bio-Rad). Anti-\u03b2-actin antibody was used as a loading control for each protein expression. Protein band intensities were quantified using the ImageJ software.Differentiated and treated C3H10T1/2 MSCs were prepared in RIPA lysis buffer supplemented with protease inhibitors. The total protein concentration was measured using the BCA Protein Assay Kit (Thermo Fisher Scientific). Equal amounts of protein samples were separated on a 4\u201320% sodium dodecyl sulfate-polyacrylamide gradient gel and transferred onto polyvinylidene difluoride (PVDF) membranes. The PVDF membranes were then blocked and incubated with specific antibodies, as indicated in the figures. Immunoreactive protein bands were captured using the chemiluminescent ECL assay on ChemiDoc XRSC3H10T1/2 MSCs were seeded on 6-well plates and grown to 80\u201390% confluence. The cells were then transfected with control siRNA , PKA\u03b1 siRNA or p38 MAPK\u03b1 siRNA oligonucleotide duplexes using Lipofectamine 2000 according to the manufacturer\u2019s instructions. Transfection efficiency was determined using qRT-PCR and western blotting.t-test or two-way ANOVA were used to distinguish the statistical significance levels, where *, **, ***, and ns indicates p < 0.05, < 0.01 and < 0.001, and no significance, respectively.All values are expressed as the average \u00b1 standard error mean (SEM). The experimental determinants were confirmed by using at least triplicate biological samples. Student\u2019s B. bifidum DS0908 (DS0908) and B. longum DS0950 (DS0950) promote brown adipocyte-, beige adipocyte-, and lipolysis-related marker expressions in 3T3-L1 pre-adipocytes. Treatment with culture supernatants of DS0908 and DS0950 reduced intracellular triglyceride (TG) accumulation during thermogenesis induction, confirmed by ORO staining and TEM analysis [Ucp1 (5.60- and 3.38-fold), Pgc1\u03b1 (12.85- and 7.02-fold) and Prdm16 (4.56- and 3.59-fold) mRNA expressions and UCP1 (2.41- and 2.32-fold), PPAR\u03b3 (3.12- and 5.93-fold), PGC1\u03b1 (12.06- and 1.98-fold) and PRDM16 (0.70- and 0.31-fold) protein expressions in C3H10T1/2 MSCs (Fgf21 (8.94- and 4.94-fold) and P2rx5 (6.96- and 10.80-fold), as well as the brown adipocyte-specific marker Cox2 (9.76- and 7.10-fold) in C3H10T1/2 MSCs. However, we observed no significant change in the Cd137 and Tbx1 mRNA expression levels , Psat1 (1.51- and 1.36-fold), Resistin (1.43- and 1.00-fold) and Serpina3k (0.59- and 0.51-fold) in DS0908 and DS0950-treated C3H10T1/2 MSCs (Ucp1 (137.37- and 124.96-fold), Prdm16 (25.60- and 267.22-fold) and Ppar\u03b3 (0.07- and 16.08-fold), as well as the beige adipocyte-specific marker Cd137 (0.85- and 5.90-fold) mRNA expressions into seven groups as follows: NFD; (G1), HFD; (G2), HFD + BS (cell-free supernatant) of DS0908 (G3), HFD + BS (cell-free supernatant) of DS0950 (G4), HFD + BP of DS0908 (G5), HFD + BP of DS0950 (G6), and HFD + Rosiglitazone (G7). The HFD groups were fed a 45% HFD for four weeks to induce obesity in the animals noticeably reduced insulin levels, suggesting improved insulin sensitivity . FollowiS133 phosphorylation , and acetyl-CoA carboxylase activity , 37, 38.ogenesis , 44. Theogenesis . We alsoB. infantis and its culture supernatants can induce thermogenesis by promoting white adipocyte browning to beige and by improving brown adipocyte activity [EBF2 and FGF21 deletion blunt beige adipocyte formation, whereas their induction triggers thermogenesis in beige adipocytes [B. bifidum DS0908 and B. longum DS0950 increased mitochondrial UCP1 and OXPHOS protein expressions. In addition, mitochondrial biogenesis increases mitochondrial content, which is known to contribute to thermogenesis. PGC1\u03b1 reportedly improves mitochondrial biogenesis and oxidative phosphorylation, induced upon B. bifidum DS0908 and B. longum DS0950 supplementation [Bifidobacterium strains considered in the current study increased the PRDM16 level.Other approaches for ameliorating obesity include non-shivering thermogenesis and lipolysis activation in mature white adipocytes. Several studies demonstrated that activity , 9. Whitipocytes , 46. PPAipocytes , 21. Botipocytes , 29. Freipocytes . In our entation , 28. PRDentation . The BifaP2), Psat1, Resistin and Serpina3k; beige and brown adipocytes, by Cd137, Tbx1 and Fgf21, as well as Cox2 and P2rx5, expressions, respectively [B. bifidum DS0908 and B. longum DS0950 supplementation [e.g., AMPK, PKA, p38 MAPK and CREB) phosphorylation, further inducing downstream thermogenic (common beige and brown) protein expressions [B. infantis, can inhibit adiposity via AMPK and PKA/p38 MAPK signaling activation [B. longum positively regulated thermogenesis via PKA signaling activation [e.g., PKA, P38 MAPK and AMPK) [B. bifidum DS0908 and B. longum DS0950 activated PKA/p38 MAPK signaling in C3H10T1/2 MSCs during the promotion of thermogenesis. It is worth mentioning that multiple studies have investigated crude culture supernatants of probiotics as viable components to understand their role in alleviating obesity [B. bifidum DS0908 and B. longum DS0950 pellets and culture supernatants both in vitro and in vivo, these findings could be firmly bolstered by identifying key metabolites and investigating their anti-obesity effects via browning activation.Mature white adipocytes are characterized by adipocyte-binding protein 4 -51. In o obesity . AlthougB. bifidum DS0908 and B. longum DS0950 pellets and culture supernatants ameliorate obesity by activating the thermogenic program. In vivo study revealed that they improved the plasma lipid profile, insulin sensitivity, and glucose metabolism without altering food intake, suggesting that B. bifidum DS0908 and B. longum DS0950 and their culture supernatants might mitigate the clinical onset of obesity.In summary, our study provides in vitro and in vivo evidence that http://jmb.or.kr.Supplementary data for this paper are available on-line only at"} +{"text": "Retraction Note:J Exp Clin Cancer Res38, 223 (2019)https://doi.org/10.1186/s13046-019-1210-3The Editor-in-Chief has retracted this article. After publication concerns were raised regarding irregularities present in multiple figures in this article. There is overlap in Fig. 2A with Fig. 2A of a previously published article . Figure"} +{"text": "Klebsiella quasipneumoniae subsp. similipneumoniae strain IF3SW-P1, isolated from the International Space Station, was sequenced using Oxford Nanopore Technologies. The genome lacks a megaplasmid typical of hypervirulent and multidrug-resistant Klebsiella strains but does contain a chromosomally encoded OqxAB efflux pump associated with carbapenem resistance.The 5.2-Mb circular genome of Klebsiella pneumoniae were described as the novel species Klebsiella quasipneumoniae , carbapenem-resistant, and hypermucoviscous strains isolated from both hospital-borne and community-acquired infections on the ISS on 4 March 2015 using a \u2013nano-hq and \u2013read-error 0.03 for the Q20+ data (Escherichia coli strain Q4552 plasmid pECQ4552_IHU08 (GenBank accession number CP077071.1) (blaKPC and Inc(FII), which are known to occur in Klebsiella species (Oxford Nanopore Technologies sequencing was performed using a GridION MK1 sequencer on a R10.4 flow cell (FLO-MIN112) with a library synthesized from Q20+ EA (early access) ligation reagents (SQK-LSK112-XL). The raw reads were base called using MinKNOW v29.10.8, with a mean quality score of 16.3 and a mode of 18.03. The genome was assembled, circularized, and polished using Flye v2.9 with the parameters 20+ data . The Fly77071.1) . Notably species .K. quasipneumoniae subsp. similipneumoniae by calculating the average nucleotide identity (ANI) using the EzBioCloud calculator compared to the two subspecies\u2019 type strains, K. quasipneumoniae subsp. quasipneumoniae 01A030T and K. quasipneumoniae subsp. similipneumoniae 07A044T . Strain 0T ANI, 9.63% and iutA, which encodes a ferric aerobactin receptor, although the gene encoding the associated siderophore aerobactin (iucA) is not present and the Sequence Read Archive (SRR17974437). These data are also available at NASA GeneLab (GLDS-470).The genomic assembly and raw reads have been deposited at GenBank (accession number"} +{"text": "The COVID-19 pandemic and lockdowns may adversely affect pregnancy outcomes due to disrupted healthcare provision and increased stress, anxiety and economic hardship. We assessed changes in perinatal outcomes in 2020 using population birth data in Europe.25 Countries in the Euro-Peristat Network implemented a federated analysis using routine national data. Countries generated anonymised aggregate data files using R scripts from individual-level data formatted to a common data model with 22 variables. We compared preterm birth, stillbirth, neonatal death and caesarean delivery rates in 2020 to 2015-2019 for 2 periods: full-year (FY) and pandemic (March-September [MS]). Data from October onward were not included in the MS period because potentially declining pandemic-related fertility may affect perinatal indicators. Country-specific relative risks (RR) for the periods, adjusted for linear trends, overall and by socio-economic (SES) group, were calculated and pooled using random effects meta-analysis.Preterm birth rates decreased slightly 0.95-0.99]; 0.98MS [0.96-1.00]) in 2020. Heterogeneity was high , with 5 countries experiencing significant declines. Neonatal mortality rates were unchanged (0.97FY [0.92-1.01]) while stillbirth rates were higher . Caesarean rates were slightly raised . Increases for stillbirth were more pronounced in the lowest (1.08FY [0.99-1.16]) versus highest SES group (1.05 FY [0.93-1.17]).In 2020, there was an unexpected decline in preterm birth in some countries, while increases in stillbirths and caesarean occurred in others. High country-level heterogeneity suggests that some government policies to mitigate the pandemic might have been more protective of pregnant women and newborns than others."} +{"text": "E. coli isolates from suckling piglets with colibacillosis.Colibacillosis is a frequent enteric disease in the pig industry that causes significant economic losses. The objective of this study was to investigate the molecular characteristics of fluoroquinolone (FQ)-resistant E. coli isolates were tested in this study and all isolates showed multi-drug resistance (MDR) and mutations in quinolone resistance determining regions (gyrA or parC). Especially, FQ-resistant E. coli isolates with double mutations in both gyrA and parC were shown a high FQs minimum inhibitory concentration . Among 43 FQ-resistant E. coli isolates, 12 (27.9%) were showed plasmid-mediated quinolone resistance (PMQR) positive E. coli. Prevalence of PMQR gene, aac(6\u2019)-Ib-cr, qnrS, and qepA, were identified in 7, 3, and 2 E. coli isolates, respectively. We identified the following in PMQR-positive E. coli isolates: the tetracycline resistance genes tetD , tetE , tetA , and tetB ; \u03b2-lactamases\u2013encoding blaCMY-2 , blaTEM-1 , blaOXA-1 , blaSHV-1 , and blaAAC-2 ; and the chloramphenicol resistance genes ; the sulfonamide resistance genes sul1 and sul2 ; the aminoglycoside modifying enzyme gene aac(3)-II . The F4 , LT:STb:EAST1 , and paa were most common fimbrial antigen, combinations of toxin genes, and non-fimbrial adhesins genes, respectively. All PMQR-positive E. coli carried class I integrons but only 4 isolates carried the gene cassette. The most prevalent plasmid replicon was FIB , followed by FIC, HI1, and N , respectively.A total of 43 FQ-resistant E. coli can serve as a reservoir of FQ resistant genetic determinants that can be transferred to pathogenic bacteria in humans or pigs, this represents a public health hazard.Because FQ-resistant The online version contains supplementary material available at 10.1186/s12866-022-02632-9. Escherichia coli (E. coli) in pigs is the most frequent enteric disease and an important cause of death in suckling piglets [Colibacillosis caused by piglets . This di piglets . The useE. coli or other gram-negative bacteria. The World Health Organization (WHO) has classified FQs as \u2018\u2018critically important antimicrobials\u2019\u2019 because of their clinical importance in both human and animal medicine [E. coli have emerged in Korea after enrofloxacin was licensed to be used for veterinary purposes [FQs are broad-spectrum antimicrobials agents and have been used for the treatment of various infections caused by medicine . Becausepurposes .qnr-mediated inhibition of quinolone binding to DNA [qepA encoded efflux pump [aac(6\u2019)-Ib-cr mediated FQ acetylation [E. coli isolated from suckling piglets with diarrhea. Therefore, the purpose of this study was to investigate the molecular characteristics of FQ-resistant E. coli isolates from suckling piglets with colibacillosis.Multiple mechanisms are involved in resistance to FQ in Enterobacteriaceae. The major mechanisms of resistance to FQ involve mutations of chromosomal genes encoding DNA gyrase and/or topoisomerase IV , 6. In ag to DNA , 8, qepAlux pump , and thetylation , 11. Thetylation . Althougtylation \u201315, therE. coli isolates collected from each colibacillosis clinical case in suckling piglets from 2007\u20132018 were tested. The farms consisted of 42 different pig herds (50 to 100 sows per each herd). The aseptically collected intestinal contents and feces were inoculated on MacConkey agar containing 4\u00a0mg/mL of ciprofloxacin . Subsequently, suspected E. coli colonies were identified by VITEK II system . Thus, a total of 43 CIP-resistant E. coli were tested in this study.E. coli ATCC 25,922 was included as a quality control. Multidrug-resistance (MDR) was defined as acquired resistance to at least one agent in three or more antimicrobial classes [The disk diffusion method was performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines . The 19 classes .E. coli Reference Laboratory, Quebec, Canada).O-serogroup typing was performed using rabbit antisera purchased from SSI with the slide agglutination technique of the Animal and Plant Quarantine Agency . A standard strain was obtained from Dr. J.M. Fairbrother to identify mutations in 43 FQ-resistant E. coli isolates using primers and conditions described previously [http://www.ncbi.nlm.nih.gov/BLAST). PMQR genes -Ib-cr, and qepA) were detected by PCR amplification and sequencing analysis, as described in Table SPCR was carried out to amplify quinolone resistance determining regions (QRDRs) of the target genes -II, and ant(2\u2019\u2019)-I), \u03b2-lactam antimicrobials , chloramphenicols (cmlA and catA1), sulfonamides (sul1 and sul2), and tetracyclines . The virulence factor genes associated with the toxins , fimbriae , and non-fimbrial adhesins were also confirmed by PCR as previously described [For detection of antimicrobial resistance genes and virulence genes, PCR was performed using DNA extracted from PMQR-positive escribed .E. coli isolates. The primers used in this study targeted 18 different replicons [For plasmid replicon typing and detection of integrons and gene cassettes, PCR was performed using DNA extracted from PMQR-positive eplicons and clasE. coli J53 used as the recipient as previously described [To determine the transferability of PMQR and other genes, conjugation assays were performed using the broth mating method, with escribed . TranscoE. coli isolates from colibacillosis are shown in Table E. coli, all isolates showed MDR against 6 to 11 classes of antimicrobial agents. The rates of resistance to the various antimicrobial classes were as follows: aminoglycosides , penicillins , quinolones , tetracyclines , phenicols , \u03b2-lactam/\u03b2-lactamase inhibitor combinations , folate pathway inhibitors , cephems , monobactams , and polypeptides . The rate of resistance to 9 antimicrobial classes was the highest at 39.5%, and one (2.3%) FQ-resistant E. coli isolate was identified resistance to 11 antimicrobial classes.MDR patterns of FQ-resistant E. coli isolates are shown in Table gyrA amino acid substitutions were S83L (43 isolates), D87N (22 isolates), D87G (5 isolates), and D87E (2 isolates), and the parC mutations were S80I (23 isolates), S80R (9 isolates), E84A (5 isolates), S80K (3 isolates), S80N (1 isolates), S80W (1 isolates), E84G (1 isolates), A56C (1 isolates), and S57Q (1 isolates). The MIC ranges for CIP, ENR, and NOR were 4\u2013256\u00a0mg/mL, 8\u2013512\u00a0mg/ml, and 8\u2013512\u00a0mg/mL, respectively, and isolates with double mutations in gyrA were relatively higher than those of other isolates with single mutations in gyrA. In particular, FQ-resistant E. coli isolates with a high level of MICs range were shown to carry double mutations in gyrA in combination with double mutations in parC. PMQR genes were detected in 12 (27.9%) of the 43 FQ-resistant E. coli isolates. The aac(6\u2019)-Ib-cr, qnrS, and qepA genes were identified in seven, three, and two FQ-resistant E. coli isolates, respectively. Among 12 PMQR-positive E. coli isolates, one isolate that showed the highest MICs for CIP (256\u00a0mg/mL), ENR (512\u00a0mg/mL), and NOR (512\u00a0mg/mL), also carried the PMQR gene aac(6\u2019)-Ib-cr.The molecular characteristics of 43 FQ-resistant E. coli isolates carried the following \u03b2-lactamase encoding genes: blaCMY-2 , blaTEM-1 , blaOXA-1 , blaSHV-1 , and blaAAC-2 . Tetracycline-resistance genes were detected in all PMQR-positive E. coli isolates as follows: tetD , tetE , tetA , and tetB . Two types of aminoglycoside-modifying enzyme genes were examined, but aac(3)-II was found only in 2 (16.7%) PMQR-positive E. coli isolates. The sul1 and sul2 sulfonamide-resistance genes were detected in 9 isolates (75.0%) and 10 isolates (83.3%), respectively. The cmlA chloramphenicol-resistance gene was found in 10 isolates (83.3%). Distributions of the virotypes are shown in Table E. coli isolates, all isolates were found to have class 1 integrons. Class 1 integrons contained four types of gene cassette arrangements, aadA1-dfrA1 (2 isolates), aadA1-aadA2- aadB (1 isolate), and aadA1-aadA2- aadB-cmlA6 (1 isolate). Eight isolates did not carry any of the gene cassettes. A total of 10 plasmid replicon types were identified in all 12 PMQR-positive E. coli isolates. The most common plasmid replicon was FIB , followed by FIC, HI1, and N , respectively. Transferability was only identified in 7 isolates among 12 PMQR-positive FQ-resistant E. coli isolates.The prevalence of antimicrobial resistance genes is shown in Table E. coli worldwide [E. coli isolates showed were MDR with high levels of resistance to several antimicrobials: aminoglycosides (100.0%), penicillins (100.0%), tetracyclines (97.7%), and phenicols (90.7%). In particular, five isolates showed resistance to more than 10 classes. These results were consistent with previous studies showing co-association of resistance to other classes of antimicrobials and high MDR rates among FQ-resistant E. coli [Suckling piglets are vulnerable to colibacillosis for many reasons such as changes in environmental conditions, a decline in maternal antibody titers, and various stresses. Antimicrobials are used in intensive pig production systems to control infectious diseases. In particular, FQs are highly effective antimicrobial class with many advantages including high oral absorption, large volume of distribution, and broad-spectrum antimicrobial activity . Howeverorldwide ; thus, torldwide . In this E. coli , 27. Thi E. coli .E. coli and variety of O-serogroups has been associated with diarrhea [gyrA mutations, and 29 isolates (67.4%) were double amino acid substitutions (S83L plus substitution in aspartic acid 87). These results were consistent with previous studies showing that DNA gyrase is the primary target of FQ in gram-negative bacteria, and gyrA mutations are dominant mutations in E. coli [E. coli isolates had mutations at codon 80 in parC in the QRDRs, and the most common type of amino-acid substitution was S80I in parC. Previous studies reported that the substitution S80I was most frequently observed among substitutions in the QRDR of parC [E. coli isolates from humans [gyrA were relatively higher than those of other isolates with single mutations in gyrA. Notably, FQ-resistant E. coli isolates carrying double mutations in gyrA in combination with double mutations in parC were identified at high levels of MICs . These results are consistent with those of recent studies showing that the total number of point mutations in QRDR was positively correlated with the increased MIC.The O-serogroup is considered one of the major virulence factors of diarrhea \u201330. In tdiarrhea , 32. In E. coli . Moreove of parC , 35. Them humans , 37. AlsE. coli isolates carried three types of PMQR genes, aac(6\u2019)-Ib-cr (7 isolates), qnrS (3 isolates), and qepA (2 isolates). These PMQR variants have been previously detected in E. coli from livestock, including in healthy animals and retail meats in the Czech Republic [gyrA and harbored qnrS in its plasmid. This result showed that PMQR genes play a role in FQ resistance [In this study, 12 FQ-resistant Republic , China [Republic , and theRepublic , as wellRepublic . Also, tRepublic . Howeversistance .E. coli isolates carried a variety of antimicrobial resistance genes such as blaCMY, blaTEM, blaOXA, blaSHV, blaAAC, tetA, tetB, tetD, tetE, aac(3)-II, sul1, sul2, and cmlA and harbored mobile elements such as integrons and gene cassettes at the same time. The bla genes hydrolyze the characteristic \u03b2-lactam ring and confer resistance to most \u03b2-lactam antimicrobials, including cephalosporins [bla positive-E. coli were detected at high levels [E. coli isolates harbored class 1 integrons and four isolates also contained gene cassettes aadA or dfrA or both genes. These genes are frequently detected in class 1 integrons isolated from animals and humans in Korea [E. coli isolates from suckling piglets may have acquired the genetic determinants of drug resistance, which could become a concern.The rise of antimicrobial resistance is thought to be closely associated with the widespread transfer of resistance genes between bacterial species. In this study, all 12 PMQR-positive osporins . Previouh levels . The preh levels . Also, ain Korea . TherefoE. coli isolates. The most common plasmid replicon was IncF plasmids including FIB, and FIC. IncF plasmids were associated with the important role in the spread of virulence and resistance to important classes of antimicrobials including quinolones, \u03b2-lactams, TEs, sulfonamides, chloramphenicol, and aminoglycosides among Enterobacteriaceae [Plasmids are small DNA molecules that are distinct from chromosomes and can provide beneficial effects to bacteria such as antibiotic resistance through horizontal gene transfer . In thiseriaceae .E. coli virulence factors is important for diagnosing and establishing preventative measures for colibacillosis [E. coli isolates, respectively. These LT, STa, and STb genes damage the vessel and cause edema and a high mortality in pigs [E. coli isolates were identified as having the paa gene and coexisting with the F4 gene. Although the specific role of the paa gene in the development of pathogenic E. coli has not yet been clearly defined, various virotypes may also appear as a result of horizontal gene transferability of the paa gene [The detection of cillosis . In this in pigs . Also, t in pigs \u201352. Prev in pigs , 53. In paa gene .E. coli isolated from suckling piglets with colibacillosis. All FQ-resistant E. coli isolates showed an MDR phenotype, and the most prevalent of the mutations were double point mutations in gyrA and a single mutation in parC. Also, FQ-resistant E. coli isolates with PMQR genes carried various antimicrobial genes and harbored mobile elements and plasmid replicons. Antimicrobial resistance may become a serious problem because many drugs are probably ineffective for the treatment of colibacillosis and resistance elements can be horizontally transferred on pig farms. Also, this represents a public health hazard because FQ-resistant E. coli can serve as a reservoir of FQ resistant genetic determinants that can be transferred to pathogenic bacteria in humans or pigs. These data support the critical need for comprehensive surveillance of antimicrobial resistance on pig farms.This study investigated the molecular characteristics of FQ-resistant Additional file 1:Figure S1-1. LC716475 (SSC-1) blast alignment. Figure S1-2. LC716476 (SSC-2) blast alignment. Figure S1-3. LC716477 (SSC-3) blast alignment. Figure S1-4. LC716478 (SSC-4) blast alignment. Figure S1-5. LC716479 (SSC-7) blast alignment. Figure S1-6. LC716480 (SSC-8) blast alignment. Figure S1-7. LC716481 (SSC-10) blast alignment. Figure S1-8. LC716482 (SSC-11) blast alignment. Figure S1-9. LC716483 (SSC-12) blast alignment. Figure S1-10. LC716484 (SSC-13) blast alignment. Figure S1-11. LC716485 (SSC-14) blast alignment. Figure S1-12. LC716486 (SSC-15) blast alignment. Figure S1-13. LC716487 (SSC-16) blast alignment. Figure S1-14. LC716488 (SSC-17) blast alignment. Figure S1-15. LC716489 (SSC-19) blast alignment. Figure S1-16. LC716490 (SSC-20) blast alignment. Figure S1-17. LC716491 (SSC-21) blast alignment. Figure S1-18. LC716492 (SSC-22) blast alignment. Figure S1-19. LC716493 (SSC-23) blast alignment. Figure S1-20. LC716494 (SSC-26) blast alignment. Figure S1-21. LC716495 (SSC-27) blast alignment. Figure S1-22. LC716496 (SSC-28) blast alignment. Figure S1-23. LC716497 (SSC-29) blast alignment. Figure S1-24. LC716498 (SSC-30) blast alignment. Figure S1-25. LC716499 (SSC-31) blast alignment. Figure S1-26. LC716500 (SSC-32) blast alignment. Figure S1-27. LC716501 (SSC-33) blast alignment. Figure S1-28. LC716502 (SSC-34) blast alignment. Figure S1-29. LC716503 (SSC-35) blast alignment. Figure S1-30. LC716504 (SSC-36) blast alignment. Figure S1-31. LC716505 (SSC-37) blast alignment. Figure S1-32. LC716506 (SSC-38) blast alignment. Figure S1-33. LC716507 (SSC-39) blast alignment. Figure S1-34. LC716508 (SSC-40) blast alignment. Figure S1-35. LC716509 (SSC-41) blast alignment. Figure S1-36. LC716510 (SSC-42) blast alignment. Figure S1-37. LC716511 (SSC-43) blast alignment. Figure S1-38. LC716512 (SSC-44) blast alignment. Figure S1-39. LC716513 (SSC-45) blast alignment. Figure S1-40. LC716514 (SSC-46) blast alignment. Figure S1-41. LC716515 (SSC-47) blast alignment. Figure S1-42. LC716516 (SSC-48) blast alignment. Figure S1-43. LC716517 (SSC-49) blast alignment. Additional file 2:Table S1. Primers used for PCR and DNA sequencing.Additional file 3:Table S2. History of samples and isolates separated from each sample."} +{"text": "To date, 10 mcr variants, mcr-1 to mcr-10, have been described. mcr-8 was first identified in a carbapenem-resistant Klebsiella pneumoniae isolate pathogens infections . Liu et isolate . Unlike eumoniae , 5. In rfections . CurrentE. cloacae clinical isolate SD21 was recovered from the sputum sample of a male patient suffering from chronic obstructive pulmonary disease at a tertiary hospital in Shandong, China. The isolate was initially identified using mass spectrometry and confirmed by next-generation sequencing. MICs of 15 antimicrobial agents were determined by the broth microdilution method. The MIC of tigecycline was interpreted according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. And the interpretation of MICs of the remaining antimicrobials was based on the Clinical and Laboratory Standards Institute (CLSI) guidelines. This isolate exhibited a multidrug-resistant phenotype, with resistance to polymyxin B (>8\u2009\u03bcg/mL), cefmetazole, ceftazidime, cefotaxime, cefepime, tigecycline, ciprofloxacin, amikacin, and aztreonam (Table\u00a0S1). Conjugation assays were performed using the Escherichia coli J53 as the recipient strain and long-read nanopore MinION (CP093914) and four plasmids, namely pSD21_mcr8 (CP093916), pSD21_266kb (CP093915), pSD21_54kb (CP093917), and pSD21_4kb (CP093918). According to multilocus sequence typing, SD21 was assigned as ST1718. Notably, a mcr-8 variant exhibiting 100% identity to mcr-8.2 was identified in pSD21_mcr8 (100 852\u2009bp). The plasmid pSD21_mcr8, belonging to IncFIA(HI1)/IncFII(K), harbored mcr-8.2 within the genetic context IS903B-orf-ISRor7-orf-dgkA-baeS-copR-ISEcl1-orf-mcr-8.2-orf-ISKpn26 from K. pneumoniae , showing 99.91% identity and 100% coverage to p2019036D-mcr8-345kb. Besides, the lack of an intact tra region may be one of the aspects limiting the mobilization of pSD21_mcr8. However, the lack of tra operon did not prevent the mobilization of mcr-8-carrying plasmids between K. pneumoniae and E. cloacae. There could be other underlying mobilization mechanisms that mediate the dissemination of mcr-8-carrying plasmids in different species.To investigate the genetic structure of -ISKpn26 . The mcrblaCTX-M-55, blaTEM-1B), fosfomycin (fosA3), aminoglycosides (aac(3)-IId, aph(3\u2032)-Ia, aph(6)-Id, rmtB, aadA22), macrolides (mph[A]), quinolones (qnrS1), sulfonamides (sul3), trimethoprim (dfrA14), tetracyclines (tet[A]), rifamycin (ARR-2), amphenicols (floR), and lincosamides (lnu[F]). Therefore, this plasmid enabled SD21 to exhibit resistance to multiple antimicrobial agents. The pSD21_266kb shared 99.99% identity with p16-6773.1 (CP039861.1) from Salmonella sp. . The other two plasmids in SD21 did not harbor accessory resistance genes.In addition to pSD21_mcr8, SD21 was found to harbor another resistance plasmid, designated pSD21_266kb. The pSD21_266kb with IncHI2/IncHI2A replicon type contained genes encoding resistance to \u03b2-lactams (mcr-8 in E. cloacae, identification of an E. cloacae isolate with mcr-8.2 indicates the further dissemination of the mcr-8 variant in different species. Furthermore, the mcr-8.2-bearing plasmid coexisted with a multidrug-resistant plasmid, which increased the difficulty of clinical treatment. In conclusion, we first reported an MDR E. cloacae strain with mcr-8.2 isolated from a patient in China. We hypothesize that the mcr-8.2-located transferable genetic elements may be the genetic basis for the transmission of mcr-8.2 among different species. Further research on epidemiology and transmission mechanism should be conducted to better understand the potential dissemination of mcr-8.Given that no reports have described the existence of CP093914, CP093915, CP093916, CP093917, and CP093918 under the BioProject PRJNA816615.The complete sequences of SD21 were deposited in the NCBI database with accession numbers"} +{"text": "Retraction Note:J Exp Clin Cancer Res37, 202 (2018)https://doi.org/10.1186/s13046-018-0875-3The Editor-in-Chief has retracted this article because data presented in Figs. 2, 3 and 4 were duplicated from previously published articles. Specifically, a set of staining images in Fig. 2I had previously been published as Fig. 3E in . The act"} +{"text": "To investigate clinical characteristics, management, and prognosis of Epstein-Barr virus (EBV)-positive lymphoma-associated hemophagocytic syndrome (LAHS) patients in real-world practice.This was a retrospective, single-center cohort study. EBV-positive LAHS patients diagnosed from January 2010 to December 2021 in our center were enrolled. Clinical characteristics, treatment, overall response rate (ORR), and overall survival (OS) were investigated. Univariate and multivariate analysis of potential factors were conducted.P=0.033, P=0.000, and P=0.004, respectively). Combined treatment of anti-hemophagocytic lymphohistiocytosis (HLH) and anti-lymphoma treatment was conducted in 24 patients; anti-HLH treatment was conducted in 18 patients; anti-lymphoma treatment was conducted in three patients; glucocorticoid treatment was conducted in one patient. ORR was 47.8%, and the median OS was 61 days for overall patients. Patients who received anti-HLH treatment and turned to anti-lymphoma treatment early displayed higher ORR and OS than those of anti-HLH patients . Elevated alanine aminotransferase level was the independent risk factor of EBV-positive LAHS prognosis.Of the 51 patients, 44 were T/NK cell lymphoma; five were B cell lymphoma; two were Hodgkin lymphoma. EBV-positive T/NK cell LAHS patients were significantly younger and showed lower fibrinogen levels and C-reactive protein levels than EBV-positive B cell LAHS patients (Prognosis of EBV-positive LAHS patients was poor. Anti-lymphoma treatment should be initiated as soon as HLH was rapidly controlled. EBV maind PD-L2 , 5. The nd PD-L2 . Howeveragenesis , 8.Hemophagocytic syndrome, also named hemophagocytic lymphohistiocytosis (HLH), is a rare but lethal hyperinflammatory syndrome. Aberrant activation of lymphocytes, monocytes, and macrophages leads to substantial release of inflammatory cytokines. HLH typically manifests itself as fever, hepatosplenomegaly, and multiple organ dysfunction syndrome (MODS). HLH can be categorized into primary HLH and secondary HLH. Primary HLH is characterized by early onset and cytotoxicity-related gene mutations. Secondary HLH mainly attacks adult patients secondary to malignancy, infection, autoimmune disease, pregnancy, and other triggers, with the incidence of 0.125 per 100,000 per year . Lymphomin situ hybridization. Besides antiviral treatment, induction treatment was divided into anti-HLH treatment, anti-lymphoma treatment, and the combination of both. Anti-HLH treatment consisted of HLH-1994 regimen, HLH-2004 regimen, and GED regimen (gemcitabine-etoposide-dexamethasone). Anti-lymphoma treatment was chemotherapy depending on different subtypes of lymphoma. Treatment response was evaluated according to the following conditions. Complete response (CR) required disappearance of all HLH-related symptoms, and HLH-related lab findings returning to normal range, including ferritin, soluble CD25 (sCD25), complete blood count, triglyceride, alanine aminotransferase (ALT), etc. Consciousness should recover to normal if central nervous system was involved. Partial response (PR) required normal body temperature and improvement by over 25% in at least two symptoms or lab findings, including sCD25 decrease by at least one third, ferritin and triglyceride decrease by at least 25%, ALT decrease by at least 50% if formerly over 400U/L, and neutrophil increase by 100% without transfusion. If neutrophil counts were formerly less than 0.5\u00d7109/L, they should exceed 0.5\u00d7109/L after treatment. If neutrophil counts were formerly over 0.5\u00d7109/L but less than 2\u00d7109/L, they should exceed 2\u00d7109/L after treatment. No response (NR) was defined as being unable to reach CR or PR. Overall response rate (ORR) was calculated as (CR+PR)/total patients \u00d7 100%. OS was defined as the interval between HLH diagnosis and all-cause death. The patients were followed up until December, 2021. This study was conducted with the approval of the West China Hospital ethics committee, according to Declaration of Helsinki.Patients consecutively diagnosed as EBV-positive LAHS from January, 2010 to December, 2021 at West China Hospital, Sichuan University were enrolled , 17. EBVt test and U test, respectively. Enumeration data were evaluated with \u03c7\u00b2 test. Survival analysis was assessed with Kaplan-Meier methods, and compared with Log rank test. Univariate and multivariate analysis of prognostic predictors was conducted with Cox proportional hazard model. It was regarded as statistically significant with P<0.05.Statistical analysis was conducted with SPSS 23.0 and GraphPad Prism 7.0 software. Measurable data with normal distribution and skewed distribution were evaluated with Fifty-one EBV-positive LAHS patients were enrolled in this study, including 35 (68.6%) male patients and 16 (31.4%) female patients. Median age at HLH diagnosis was 37 (13-64) years. Three (5.9%) patients were newly diagnosed as lymphoma, while 48 (94.1%) patients were relapsed/refractory lymphoma cases. Clinical characteristics of these patients at baseline were listed in P=0.033). Fibrinogen level and C-reactive protein (CRP) level were significantly lower in T/NK cell LAHS patients than B cell LAHS patients . Plasma EBV DNA level tended to be higher in B cell LAHS patients than in T/NK cell LAHS patients, but the difference was not significant. There was no significant difference in sex, IPI score, ECOG score, clinical manifestations, complete blood count, liver and kidney function, triglyceride, ferritin, sCD25, hemophagocytosis phenomenon, and the occurrence order of lymphoma and HLH between EBV-positive T/NK cell LAHS patients and EBV-positive B cell LAHS patients . EBV-positive LAHS patients displayed significantly higher hemoglobin and triglyceride levels at baseline than EBV-negative LAHS patients . T/NK-cell lymphoma tended to account for a higher proportion of EBV-positive LAHS patients (86.3%) than EBV-negative LAHS patients (69.8%), but the difference was insignificant were significantly younger at HLH diagnosis than EBV-negative LAHS patients patients who only received anti-HLH treatment, the median weeks of induction treatment was 4 (1-8). The majority of patients received HLH-1994 regimen. HLH-2004 regimen and GED regimen were conducted in three patients each. Three (6.5%) patients only received anti-lymphoma chemotherapy. One ENKL patient and one ANKL patient received GLIDE regimen, and one DLBCL patient received chidamide-RCHOP regimen. Median number of chemotherapy cycles was 3 (2-8). One (2.2%) patient only received glucocorticoid treatment.For patients who were at higher risk or failed to achieve CR with a poor control of EBV infection, consolidation treatment was conducted, which included PD-1 monoclonal antibody treatment, chidamide treatment, and autologous or allogenic stem cell transplantation. For patients whose biopsy revealed positive PD-L1 staining of tumor cells, especially HL patients and DLBCL patients, PD-1 monoclonal antibody treatment was conducted. For patients who displayed aberrant epigenetic alterations, especially PTCL patients and double expression DLBCL patients, chidamide treatment was conducted. For young, fit, and high-risk patients with sufficient stem cells collected who were willing to receive transplantation, autologous or allogenic stem cell transplantation was conducted. Overall, seven (15.2%) patients underwent consolidation therapy. Three (6.5%) patients received PD-1 monoclonal antibody treatment, of whom the DLBCL patient also received autologous stem cell transplantation after PD-1 monoclonal antibody treatment. Two (4.3%) patients received autologous stem cell transplantation. One (2.2%) ANKL patient received allogenic stem cell transplantation. Two (4.3%) AITL patients received chidamide treatment.P=0.103). There was no significant difference in ORR among different treatment groups patients, and PR was achieved in 18 (39.1%) patients. Twenty-four (52.2%) patients remained NR. ORR was 47.8%. In the combined treatment group, CR was reached in two (8.3%) patients, and PR was reached in 12 (50%) patients. NR was present in 10 (41.7%) patients. ORR was 58.3%. For patients who first received anti-HLH treatment and turned to anti-lymphoma chemotherapy subsequently, CR was achieved in two (10.5%) patients, and PR was achieved in 10 (52.6%) patients. Seven (36.8%) patients remained NR. ORR was 63.2%. For those who first received anti-lymphoma chemotherapy and turned to anti-HLH treatment subsequently, PR was achieved in two (40%) patients, and three (60%) patients remained NR. ORR was 40%. In anti-HLH treatment group, six (33.3%) patients achieved PR and twelve (66.7%) patients remained NR. ORR was 33.3% for the total anti-HLH treatment group, the HLH-1994 regimen subgroup, the HLH-2004 regimen subgroup, and the GED regimen subgroup. In anti-lymphoma treatment group, CR was achieved in two (66.7%) patients while one (33.3%) patient remained NR. ORR was 66.7%. One patient only received glucocorticoid treatment but remained NR. Patients who first received anti-HLH treatment and turned to anti-lymphoma treatment subsequently tended to show a higher ORR than those who received anti-HLH treatment only, but the difference was not significant . In terms of treatment group, median plasma EBV-DNA of patients after treatment in combined treatment group and anti-HLH group was 272.5 copies/mL (range 0-64800 copies/mL), and 3130 copies/mL (range 0-33800 copies/mL), respectively. For the three patients in anti-lymphoma group, median plasma EBV-DNA of patients after treatment was 0 copies/mL (range 0-50 copies/mL). For the only patient in glucocorticoid group, his plasma EBV-DNA level decreased from 158000 copies/mL to 88800 copies/mL after treatment. There was no significant difference in plasma EBV-DNA level after treatment among treatment groups.At baseline, plasma EBV-DNA of all patients was positive . After induction treatment, plasma EBV-DNA decreased significantly in all patients but one, who was a ANKL patient only receiving anti-HLH treatment but remaining NR . Plasma EBV-DNA of ten patients after treatment was negative. Another three patients had a plasma EBV-DNA level lower than 50 copies/mL after treatment. There was no significant difference in plasma EBV-DNA after treatment between T/NK-cell LAHS and B-cell LAHS patients patients received combined treatment. Sixteen (40%) patients first underwent anti-HLH treatment of 3.5 (1-9) weeks, and then turned to anti-lymphoma chemotherapy. Median number of chemotherapy cycles was 1 (1-8). Another five (12.5%) patients first received anti-lymphoma chemotherapy and turned to HLH-1994 regimen subsequently. The median number of chemotherapy cycles was 1 (1-3). The median weeks of HLH-1994 treatment was 4 (2-4). In the 16 (40%) patients who only received anti-HLH treatment, the median weeks of induction treatment was 4 (1-8). Two (5%) patients only received anti-lymphoma chemotherapy. Median number of chemotherapy cycles was 2.5 (2-3). One (2.5%) patient only received glucocorticoid treatment.Of the 40 evaluable EBV-positive T/NK cell LAHS patients, CR was achieved in three (7.5%) patients, and PR was achieved in 14 (35%) patients. Twenty-three (57.5%) patients remained NR. ORR was 42.5%. In the combined treatment group, CR was reached in two (9.5%) patients, and PR was reached in nine (42.9%) patients. NR was present in 10 (47.6%) patients. ORR was 52.4%. For patients who first received anti-HLH treatment and turned to anti-lymphoma chemotherapy subsequently, CR was achieved in two (12.5%) patients, and PR was achieved in seven (43.75%) patients. Seven (43.75%) patients remained NR. ORR was 56.25%. For those who first received anti-lymphoma chemotherapy and turned to anti-HLH treatment subsequently, PR was achieved in two (40%) patients, and three (60%) patients remained NR. ORR was 40%. In anti-HLH treatment group, five (31.25%) patients achieved PR and 11 (68.75%) patients remained NR. ORR was 31.25%. In anti-lymphoma treatment group, CR was achieved in one (50%) patient while one (50%) patient remained NR. ORR was 50%. One patient only received glucocorticoid treatment but remained NR. There was no significant difference in ORR among different treatment groups.P=0.033, We also compared treatment and response of EBV-positive LAHS patients and EBV-negative LAHS patients in our department. Treatment choice for these patients was significantly different, with a higher proportion of EBV-positive LAHS patients (52.2%) receiving combined treatment than EBV-negative LAHS patients tended to display worse OS compared to patients whose plasma EBV DNA was no more than 105 copies/mL , but the difference was not significant (P=0.159) (P=0.060) (P=0.041) (P=0.003) (P=0.003) (P=0.006) days, the median OS of the total cohort was 61 (95% CI 47.9-74.1) days. The median OS of EBV-positive NK/T cell LAHS patients was 65 (95% CI 52.7-77.3) days, while that of EBV-positive B cell LAHS or EBV-positive HL LAHS was not evaluable due to limited sample size. Patients whose baseline plasma EBV DNA exceeded 10P=0.001, P=0.004, and P=0.009, respectively). ENKL or ANKL tended to associate with worse OS (P=0.069). There was no significant association between plasma EBV-DNA level after treatment and OS. There was no significant relationship between other baseline characteristics and OS. When combining baseline ALT level, combined treatment of first anti-HLH regimen and subsequent anti-lymphoma regimen, treatment response, and ENKL or ANKL subtype in multivariate analysis, elevated baseline ALT level was the independent risk factor of OS (P=0.025). Combined treatment of first anti-HLH regimen and subsequent anti-lymphoma regimen and achieving CR or PR were independent protective factors of OS Table\u00a04.P=0.001, P=0.016, P=0.044, P=0.017, and P=0.013, respectively). When combining these factors in multivariate analysis, lower ALT level, combined treatment of first anti-HLH regimen and subsequent anti-lymphoma regimen, and achieving CR or PR were independent protective factors of OS .Regarding EBV-positive T/NK cell LAHS patients, univariate analysis revealed lower ALT level, lower IL6 level, higher PT level, combined treatment of first anti-HLH regimen and subsequent anti-lymphoma regimen, achieving CR or PR were significantly related to improved OS , and achieving CR or PR were significantly related to improved OS . When combining both factors in multivariate analysis, only achieving CR or PR remained significantly related to improved OS , serving as protective factor of prognosis.We also compared prognosis of EBV-positive LAHS patients and EBV-negative LAHS patients in our department. OS of EBV-positive LAHS patients was similar to that of EBV-negative LAHS patients , Achievement Transformation Project (No. CGZH21001), 1.3.5 Project for Disciplines of Excellence, West China Hospital, Sichuan University (No. ZYJC21007), Translational Research Grant of NCRCH (No. 2021WWB03), and China Postdoctoral Science Foundation (No. 2021M692310).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Irritable bowel syndrome (IBS) includes diarrhea-predominant (IBS-D) and constipation-predominant (IBS-C) subtypes. We combined breath testing and stool microbiome sequencing to identify potential microbial drivers of IBS subtypes.2), methane (CH4), and hydrogen sulfide (H2S) levels were measured by gas chromatography, and baseline stool microbiome composition was analyzed by 16S rRNA sequencing. Microbial metabolic pathways were analyzed using Kyoto Encyclopedia of Genes and Genomes collection databases.IBS-C and IBS-D subjects from 2 randomized controlled trials (NCT03763175 and NCT04557215) were included. Baseline breath carbon dioxide, hydrogen of stool methanogens, predominantly Methanobrevibacter, as well as higher absolute abundance of Methanobrevibacter smithii in stool. IBS-D subjects had higher breath H2 that correlated with lower microbial diversity and higher breath H2S that correlated with higher RA of H2S-producing bacteria, including Fusobacterium and Desulfovibrio spp. The predominant H2 producers were different in these distinct microtypes, with higher RA of Ruminococcaceae and Christensenellaceae in IBS-C/CH4+ (which correlated with Methanobacteriaceae RA) and higher Enterobacteriaceae RA in IBS-D. Finally, microbial metabolic pathway analysis revealed enrichment of Kyoto Encyclopedia of Genes and Genomes modules associated with methanogenesis and biosynthesis of methanogenesis cofactor F420 in IBS-C/CH4+ subjects, whereas modules associated with H2S production, including sulfate reduction pathways, were enriched in IBS-D.IBS-C subjects had higher breath CHM. smithii and H2S producers such as Fusobacterium and Desulfovibrio spp, respectively.Our findings identify distinct gut microtypes linked to breath gas patterns in IBS-C and IBS-D subjects, driven by methanogens such as Irritable bowel syndrome (IBS) is estimated to affect 1 in 10 people globally, with a prevalence of 11.8%\u201314.0% in North America . Based o2) on the breath test (2S), may also be involved in diarrheal conditions. H2S is a gasotransmitter and is involved in numerous functions throughout the body, including inflammation and mucosal repair in the gastrointestinal (GI) tract (2S) have been linked to colorectal cancer and ulcerative colitis tract . However colitis ,8, which colitis . More reth IBS-D ,11, alth2 generated by syntrophic bacterial species for the generation of methane (4) is directly linked to slowing of intestinal transit in an animal model and an increased motility index in methane-producing IBS subjects . Methano methane . Interessubjects and may subjects ,16.2, CH4, and H2S) breath testing and stool microbiome sequencing to identify potential microbial drivers of clinical phenotypes in IBS.These findings demonstrate that changes in the gut microbiome are not uniform in IBS as a whole. Rather, different microbial compositions (microtypes) may account for the differing phenotypes of IBS. Identifying these microtypes may more clearly define possible microbial pathomechanisms in IBS in general. In this study, we combine 3-gas . IBS-C was diagnosed based on Rome IV criteria based on Rome IV criteria . Subject2), H2, CH4, and H2S . Interpretation of breath test results was based on the North American Consensus for breath testing lactulose breath testing using a system that allows the measurement of carbon dioxide and stored at room temperature before DNA extraction. Stool form was classified according to the Bristol Stool Form Scale stool samples were self-collected, immediately refrigerated, and then transported to the laboratory. For the IBS-C trial, only CHrm Scale .DNA extraction was performed using the MagAttract PowerSoil DNA KF Kit (Qiagen) with some modifications as described previously . ExtractMethanobrevibacter smithii and Methanosphaera stadtmanae, in stool from IBS-C and IBS-D subjects were determined by quantitative polymerase chain reaction (qPCR) using primers and probes targeting the beta subunit of RNA polymerase (rpoB) gene of each species (M. smithii stock culture and from M. stadtmanae DSM 3091 from the Leibniz Institute Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) were extracted using the same protocol, and standard curves with ten-fold serial dilutions was prepared for use as qPCR standards.Levels of 2 methanogenic archaeal species, species . Assays http://links.lww.com/AJG/C678).Details of 16S sequencing and analysis protocols are provided in the Supplementary Digital Content , SAS 9.4 , RStudio , and GraphPad Prism 9 . Graph construction was performed using GraphPad Prism 9.02 (GraphPad Software). Significance was set at P < 0.05.The descriptive analysis is presented as mean \u00b1 SD. Categorical variables were compared with \u03c7http://links.lww.com/AJG/C678). Among IBS-C subjects, 58 (47%) were CH4 negative (IBS-C/CH4\u2212) and 66 (53%) were CH4 positive (IBS-C/CH4+) and considered to have IMO (4 positive. IBS-C/CH4+ subjects were significantly older than IBS-D (P = 0.037) and IBS-C/CH4\u2212 (P = 0.029) subjects. No differences in sex distribution or body mass index were identified between groups .A total of 171 IBS subjects were included (47 with IBS-D and 124 with IBS-C). Subjects' demographics and clinical characteristics are shown in the Supplementary Digital Content (P < 0.0001).Stool form for all baseline stool samples was assessed using the Bristol Stool Form Scale. IBS-D subjects had a significantly higher average score (4.7 \u00b1 1.27), indicating looser, more watery stools, compared with IBS-C/CH2 was higher in IBS-D compared with all IBS-C subjects . Within IBS-C, 35.09% of IBS-C/CH4\u2212 subjects were positive for H2 SIBO, compared with 25.76% of IBS-C/CH4+ subjects for HFigure 2 , as weres Figure b. Signifhttp://links.lww.com/AJG/C678). Breath H2 dynamics were markedly different between IBS-D subjects and IBS-C subcategories . H2 delta values (120 minutes after lactulose ingestion vs preingestion levels) were significantly higher in IBS-D subjects vs IBS-C/CH4\u2212 (P = 0.038) and IBS-C/CH4+ . By 15 minutes after lactulose ingestion, H2 levels were already higher in IBS-D vs IBS-C/CH4+ subjects and remained significantly higher at all time points during the breath test , 15 (P < 0.0001), 30 (P = 0.011), and 75 (P = 0.037) minutes . CH4 dynamics were also different between IBS-C and IBS-D subjects , with higher CH4 levels in IBS-C/CH4+ vs IBS-D subjects at all time points during the breath test .In IBS-D and IBS-C/CH4+ subjects and 40 IBS-D subjects provided baseline stool samples. Of IBS-C/CH4+ subjects, 88.09% had detectable levels of the methanogen M. smithii compared with 17.94% of IBS-D subjects (P < 0.0001). M. stadtmanae was less abundant in stool and was only detectable in 10% of IBS-C/CH4+ and 7.69% of IBS-D subjects (P = 1). Absolute M. smithii abundance correlated positively with breath CH4 levels, regardless of time point during the breath test, but a higher correlation coefficient was obtained using the maximum CH4 level reached during the breath test . Absolute M. smithii abundance also correlated negatively with breath H2 levels at 105 minutes and 120 minutes .A total of 42 IBS-C/CH4+ and 40 IBS-D subjects) were also used for 16S rRNA sequencing. After denoising and removal of low-quality reads, a total of 3,780,543 reads were retained for taxonomic analysis . Microbial alpha diversity analysis was performed using 3 different indices, Chao1, Simpson index, and Shannon index. Chao1 is an estimator based on abundance, Simpson index gives more weight to common or dominant species , while Shannon index assumes all species (including rare species) are represented in a sample . Interestingly, higher breath CH4 AUC correlated with higher stool microbial alpha diversity . This al4+ and IBS-D subjects were evident even at higher taxonomic levels. The relative abundance (RA) of the archaeal phylum Euryarchaeota was higher in the stool microbiome of IBS-C/CH4+ subjects compared with IBS-D . Regarding bacterial taxa, the RA of phylum Firmicutes was 1.27-fold higher in IBS-C/CH4+ vs IBS-D (FDR P = 0.04), and the RA of phyla Tenericutes, Lentisphaerae, and Synergistetes were also higher in IBS-C/CH4+ vs IBS-D . By contrast, the RA of phyla Bacteroidetes , Fusobacteria , Proteobacteria , Epsilonbacteraeota , and Spirochetes were higher in IBS-D subjects vs IBS-C/CH4+ .Differences in microbial profiles between IBS-C/CH4+ subjects was characterized by higher RA of methanogenic archaea from families Methanobacteriaceae and Methanomassiliicoccaceae when compared with IBS-D subjects. The RA of genus Methanobrevibacter was higher in IBS-C/CH4+ subjects vs IBS-D , confirming the qPCR results. Bacterial families with higher RA in IBS-C/CH4+ subjects vs IBS-D included Anaeroplasmataceae , Flavobacteriaceae , Christensenellaceae , Enterococcaceae , and Ruminococcaceae , among others . Notably, the RA of family Methanobacteriaceae correlated positively with RA of these bacterial families in IBS-C/CH4+ subjects, indicating possible syntropic relationships between these microbes , Spirochaetaceae , Fusobacteriaceae , and Bacteroidaceae . Most of these bacterial families negatively affected stool microbial diversity and of Spirochaetaceae correlated with high breath H2S AUC and an unknown genus from family Desulfovibrionaceae . There was no significant difference in RA of genus Desulfovibrio in IBS-D vs IBS-C/CH4+ subjects after P value correction , but the RA of several Desulfovibrio OTUs was higher in IBS-D subjects vs IBS-C/CH4+ .At the genus level, 35 known and unknown genera had higher RA in the stool microbiome of IBS-D subjects when compared to IBS-C/CH4+ and IBS-D subjects , microorganisms encoding enzymes necessary for H2S and CH4 production correlated with breath H2S and CH4 levels in IBS subjects. RA of Fusobacterium and an unknown Desulfovibrio species correlated positively with AUC for H2S . RA of genus Methanobrevibacter correlated positively with breath CH4 levels at all time points (P < 0.0001) and with AUC for CH4 , consistent with the findings for stool M. smithii levels by PCR. Moreover, Methanobrevibacter RA correlated negatively with H2 levels at 105 minutes and 120 minutes .Although RA of numerous microbial taxa was different between IBS-C/CH4+ subjects and included enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) modules associated with methane production from CO2, methanol, and methylamine . The KEGG module predicting biosynthesis of F420, a cofactor used during methanogenesis (4+ subjects (P < 0.0001), and this module correlated with breath CH4 levels at all time points and with CH4 AUC .Microbial metabolic pathway analysis further supported these associations. A signature associated with biomethanation was characteristic of the stool microbiome in IBS-C/CHogenesis , was als2S production, including dissimilatory and assimilatory sulfate reduction pathways . Although there were no direct associations between these pathways and breath H2S levels, the assimilatory sulfate reduction pathway correlated with H2 levels .A biochemical signature associated with sulfur metabolism was characteristic of the stool microbiome in IBS-D subjects due to enrichment of KEGG modules associated with H4 breath tests, breath CH4 levels were linked to higher stool levels of the methanogenic archaeon M. smithii, confirmed by both qPCR and sequencing. IBS-C/CH4+ subjects had a distinct gut microtype when compared to IBS-D, characterized by higher RA of the archaeal family Methanobacteriaceae (which includes M. smithii) that correlated with higher RA of specific H2-producing bacterial families, Ruminococcaceae and Christensenellaceae, which include known syntrophs of M. smithii. By contrast, IBS-D subjects were characterized by elevated breath levels of H2 and H2S. Breath H2S levels correlated with RA of gut bacterial H2S producers in IBS-D subjects, including genus Fusobacterium and an unknown species from genus Desulfovibrio, and the RA of family Fusobacteriaceae correlated with the RA of the H2-producing family Enterobacteriaceae. In addition, predicted microbial metabolic pathway analysis indicated enrichment of KEGG modules associated with methane production in IBS-C/CH4+ subjects and enrichment of KEGG modules associated with H2S production in IBS-D subjects. These findings suggest that increases in M. smithii and in bacterial H2S producers including Fusobacterium and Desulfovibrio species may contribute to the predominant constipation and diarrheal subtypes in IBS subjects, respectively.In this study, we identify breath gas profiles and associated gut microtypes characteristic of different IBS phenotypes. Specifically, in IBS-C subjects with positive CH2 nor CH4 is produced by human cells correlated with the presence of SIBO and breath CH4 in IBS-C/CH4+ subjects. Interestingly, there was also an inverse relationship between CH4 and H2 levels, which may be consistent with the syntropic relationship between fermenting bacteria and hydrogenotrophic methanogens and a constipation phenotype. By contrast, IBS-D subjects are characterized by higher breath H2 and by higher breath H2S linked to increased prevalence of H2S-producing bacteria (predominantly Fusobacterium and Desulfovibrio spp) and a diarrhea phenotype. Furthermore, the predominant H2 producers were different in these distinct microtypes, with higher RA of Ruminococcaceae and Christensenellaceae in IBS-C/CH4+ and higher Enterobacteriaceae RA in IBS-D. Identification of these distinct microtypes may facilitate a better understanding of the relationship between the gut microbiome and the heterogeneous phenotypes of IBS and allow us greater precision in the development of targeted microbiome-based therapies.In conclusion, our data identify distinct gut microtypes linked to breath gas patterns in subjects with IBS-C and IBS-D. IBS-C subjects are characterized by detectable breath CHGuarantor of the article: Mark Pimentel, MD.Specific author contributions: Conceptualization: M.P., R.M. Formal analysis: G.L., M.J.V.M., J.W., A.R., M.P. Methodology: M.J.V.M., G.L., W.M., S.W., M.P. Investigation: M.J.V.M., G.L., G.P., M.L.P., G.M.B., M.S., S.A., D.C., S.W., C.C., M.R., A.H., A.F., B.C., N.P., A.R., M.P. Visualization: M.J.V.M., G.L. Funding acquisition: G.B., R.M., M.P. Project administration: R.M., M.P. Supervision: W.M., S.W., C.C., M.R., R.M., M.P. Writing\u2013original draft: M.J.V.M., G.L., G.B., W.M., J.W., M.P., Writing\u2013review & editing: M.J.V.M., G.L., G.B., W.M., J.W., A.R., R.M., M.P.Financial support: This study was supported in part by funds from The Monica Lester Charitable Trust (R.M.), The Elias, Genevieve, and Georgianna Atol Charitable Trust (R.M.), Synthetic Biologics, Inc (A.R.), Bausch Health (M.P.) and The National Philanthropic Trust (M.P.).Potential competing interests: M.P. is a consultant for Bausch Health, Ferring Pharmaceuticals Inc., and Vivante Health Inc. M.P. has received grant support from Bausch Health and Synthetic Biologics. R.M. has received grant support from Valeant Pharmaceuticals. A.R. is a consultant/speaker for and has received grant support from Bausch Health. In addition, Cedars-Sinai Medical Center has licensing agreements with Bausch Health and Gemelli Biotech. A.R., M.P., and R.M. have equity in Gemelli Biotech and M.P. has equity in Synthetic Biologics. All other authors report no conflicts of interest.Data availability: The data sets generated during the current study are available in the National Center for Biotechnology Information (NCBI) BioProject Repository https://www.ncbi.nlm.nih.gov/bioproject under BioProject PRJNA804225.\u2713 Irritable bowel syndrome (IBS) includes diarrhea-predominant (IBS-D) and constipation-predominant (IBS-C) subtypes.\u2713 The gut microbiome is associated with IBS, but the roles of specific gut microbial populations are poorly understood.2), hydrogen sulfide (H2S), and methane (CH4) are produced by gut microbes.\u2713 The gases hydrogen (H4 on the breath test is associated with IBS-C and correlates with increased predominance of methanogens, including Methanobrevibacter smithii.\u2713 Increased CH2 levels do not directly correlate with diarrhea, but H2S has recently been linked to a diarrhea phenotype.\u2713 H\u2713 Distinct gut microtypes are linked to breath gas patterns in IBS-C and IBS-D subjects.4+ IBS-C subjects, increased breath CH4 correlated with increased gut microbial diversity.\u2713 In CH2 correlated with lower microbial diversity and increased breath H2S correlated with increased predominance of H2S producers, including Fusobacterium and Desulfovibrio species.\u2713 In IBS-D subjects, increased breath H2 producers in IBS-C subjects were Ruminococcaceae and Christensenellaceae, which include known bacterial syntrophs for methanogens.\u2713 The predominant H4+ subjects and enrichment of pathways associated with H2S production in IBS-D subjects.\u2713 Predicted microbial metabolic pathway analysis indicated enrichment of pathways associated with methanogenesis in IBS-C/CH"} +{"text": "Escherichia coli strain to modify chrysazin to chrysazin-8-O-\u03b1-l-rhamnoside (CR) and chrysazin-8-O-\u03b1-l-2\u2032-O-methylrhamnoside (CRM) using rhamnosyl transferase and sugar-O-methyltransferase. Biosynthesized CR and CRM were structurally characterized using HPLC, high-resolution mass spectrometry, and various nuclear magnetic resonance analyses. Antimicrobial effects of chrysazin, CR, and CRM against 18 superbugs, including 14 Gram-positive and 4 Gram-negative pathogens, were investigated. CR and CRM exhibited antimicrobial activities against nine pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA) in a disk diffusion assay at a concentration of 40 \u00b5g per disk. There were MIC and MBC values of 7.81\u201331.25 \u00b5g/mL for CR and CRM against methicillin-sensitive S. aureus CCARM 0205 (MSSA) for which the parent chrysazin is more than >1000 \u00b5g/mL. Furthermore, the anti-proliferative properties of chrysazin, CR, and CRM were assayed using AGS, Huh7, HL60, and HaCaT cell lines. CR and CRM showed higher antibacterial and anticancer properties than chrysazin.Anthraquinone and its derivatives show remarkable biological properties such as anticancer, antibacterial, antifungal, and antiviral activities. Hence, anthraquinones derivatives have been of prime interest in drug development. This study developed a recombinant Quinones are naturally occurring organic compounds found in higher plants, fungi, bacteria, and animals. They have a lot of structural varieties. Since they are found in different colors in nature, they are considered pigments . Anthraq3/P2O3Cl4 [Synthesis of anthraquinone derivatives is of great interest recently. There are various methods for the synthesis of anthraquinones derivatives, including intramolecular condensation of aryl and o-aroylbenzoic acid using fuming sulfuric acid, benzoyl chloride, concentrated sulfuric acid, benzoyl chloride, zinc chloride, and POCl/P2O3Cl4 . The che/P2O3Cl4 .Modification of anthraquinones can be performed by glycosylation, methylation, sulfation, prenylation, and so on. Glycosylation is an important process for increasing the solubility of hydrophobic compounds, improving stability, reducing toxicity, and modifying biological activities ,16. MethO-methyltransferase (OMT) that catalyzes the transfer of the methyl group of S-adenosyl-l-methionine (SAM) to hydroxyl groups [Methyltransferases are important enzymes in the modification of different substrate. However, methylation of sugar is very rare ,21. Genel groups ,22,23.Rheum palmatum L. (Polygonaceae) [Chrysazin has been used as a medicine since ancient times. It can be found naturally. It is isolated from the root and rhizome of onaceae) . It has onaceae) ,25.E. coli sugar (thymidine diphosphate (TDP)-rhamnose) as a sugar donor, which will be used as a glycosyltransferase to conjugate to chrysazin and SAM as an O-methyltransferase to conjugate chrysazin rhamnoside. For the production of chrysazin derivatives, anthraquinone rhamnosyltransferase (7665) [Saccharothrix espanaensis and O-methyltransferase (ThnM1) [Nocardia sp. CS682 were cloned and heterologously expressed in E. coli. The recombinant strain E. coli was utilized for the production of chrysazin-8-O-\u03b1-l-rhamnoside (CR) and chrysazin-8-O-\u03b1-l-2\u2032-O-methylrhamnoside (CRM) from the substrate chrysazin (This study is based on the utilization of indigenous e (7665) from Sac (ThnM1) from Nochrysazin . Antican\u03b2-d-1-thiogalactoside (IPTG) was purchased from GeneChem Inc. . SAM was purchased from Sigma-Aldrich . Escherichia coli BL21 (DE3) was used as an expression and biotransformation host. Luria\u2013Bertani (LB) broth medium and agar plates with appropriate antibiotics were used for culture preparation, colony selection, and biotransformation. Pathogenic strains such as Staphylococcus. aureus CCARM 3640 (MRSA), S. aureus CCARM 3089 (MRSA), S. aureus CCARM 33591(MRSA), S. aureus CCARM 0205 (MSSA), S. aureus CCARM 0204 (MSSA), S. aureus CCARM 0027 (MSSA), S. aureus CCARM 3090 (MRSA), S. aureus CCARM 3634 (MRSA), S. aureus CCARM 3635 (MRSA), Bacillus subtilis ATCC 6633, Enterococcus faecalis 19433, Enterococcus faecalis 19434, Kocuria rhizophilla NBRC 12708, Micrococcus luteus, Escherichia coli ATCC 25922, Proteus hauseri NBRC 3851, Klebsiella pneumonia ATCC10031, and Salmonella enterica ATCC 14,028 were obtained from Professor Seung-Young Kim [Chrysazin/Dantron was purchased from Tokyo Chemical Industry . HPLC-grade acetonitrile and water were purchased from Mallinckrodt Baker . All other chemicals used were of high analytical grade and commercially available. Isopropyl-E. coli, anthraquinone rhamnosyltransferase (7665) [S. espanaensis and rhamnose methyltransferase (ThnM1) [Nocardia sp. CS682 were taken to prepare E. coli S2 [E. coli S2 was generated by transforming pET32a \u00b1 7665(Am) CRISPRi-S1(Cmr) and pCDFDuet-metK-thnM1(Sm) into an E. coli strain harboring the rhamnose cassette piBR181-tgs.dh.ep.kr.pgm2.glf.glk (Km) [For the production of rhamnosylated and methoxy-rhamnosylated derivatives of chrysazin using engineered e (7665) from S. (ThnM1) from Noc coli S2 . E. coliglk (Km) . RecombiE. coli S2 was cultured in a 5 mL LB medium supplemented with ampicillin, kanamycin, chloramphenicol, and streptomycin (each at 50 \u03bcg/mL) and incubated at 37 \u00b0C for 3 h. From the 5 mL seed culture, 500 \u00b5L was transferred into a flask containing 50 mL LB broth with respective antibiotics and cultured at 37 \u00b0C for around 4 h until the optical density of cells at 600 nm (OD600) reached 0.6\u20130.8. This culture had added to it 0.5 mm isopropyl \u03b2-d-1-thiogalactopyranoside (IPTG) to induce protein expression, followed by incubation at 20 \u00b0C for 20 h. To determine optimal substrate concentration, glucose concentration, and time, different concentrations of chrysazin and different concentrations of sterile glucose solution were fed into the cell culture after induction. After 20 h of adding IPTG, chrysazin dissolved in dimethyl sulfoxide (DMSO) at a final concentration of 400 \u00b5M was added along with 10% glucose. Samples (3 mL of culture broths) were withdrawn at 6, 12, 24, 36, 48, and 60 h for product analysis. After 48 h, compounds were extracted using a double volume of ethyl acetate and a Soxhlet extractor. The Soxhlet extractor was kept still to separate the mixture for 4\u20136 h at room temperature after shaking. Ethyl acetate was removed under reduced pressure and dissolved in methanol. This sample was further analyzed by HPLC and mass spectrometry. To collect a sample to characterize structurally, the biotransformation experiment was performed using a fermenter (3 L of culture). The pure fraction of the compound was collected via preparatory-high-pressure liquid chromatography (prep-HPLC).A seed culture of 18 column ). The binary mobile phase was composed of solvent A (HPLC-grade water + 0.1% trifluoroacetic acid) and solvent B . The total flow rate was maintained at 1 mL/min for the 30 min program. The ACN concentration began with 10%. A linear gradient from 10 to 50% for 10 min, 50\u201390% for 23 min, and 90\u201310% for 30 min was then used. The HR-QTOF ESI/MS was performed in positive ion mode using an Acquity mass spectrometer , which was coupled with a Synapt G2-S system (Waters). Purification of compounds was performed using a prep-HLPC instrument equipped with a YMC-Pack ODS-AQ C18 column, and a connected UV detector (420 nm). Here, a 40 min binary program with implementation of 20% (0\u20135 min), 50% (5\u201310 min), 70% (10\u201320 min), 90% (20\u201325 min), 20% (25\u201330 min), and 10% (30\u201335 min) ACN at a flow rate of 10 mL/min was used. Purified products were pooled, dried, and lyophilized to remove water or moisture. Furthermore, the fully dried pure compound was dissolved in DMSO-d6 and subjected to a 700 MHz NMR spectrometer equipped with TCI CryoProbe (5 mm). From the extracted compound, a 20 \u00b5L volume was injected and directly analyzed by reverse-phase high-performance liquid-chromatography photo-diode array (HPLC-PDA) using a Thermo Scientific Dionex Ultimate 3000 ultrahigh-performance Liquid chromatography (UHPLC) system with a reverse-phase C1H NMR and 13C NMR) and two-dimensional NMRs (heteronuclear multiple quantum coherence (HMQC), rotating frame Overhauser enhancement spectroscopy (ROESY), and heteronuclear multiple bonded connectivity (HMBC)) were used as needed to elucidate the structure of the compound.One-dimensional NMRs , incubated at 37 \u00b0C in a humidified 5% CO2 overnight, and then treated with each compound after serial dilution for 72 h. After that, 20 \u03bcL substrate solution (Promega) was added to each well. The plate was shaken for 5 min and kept in the dark for 10 min. Luminescence was measured using a multimode plate reader . IC50 values were analyzed using GraphPad Prism 5 .Three cancer cell lines , human gastric cancer cell line (AGS), and human leukemia cell line (HL60) and normal cell line (human keratinocyte cell line (HaCaT) were purchased from Korean Cell Line Bank . Huh7 cells were cultured in Dulbecco\u2019s modified Eagle\u2019s medium (DMEM) and AGS cells were cultured in Roswell Park Memorial Institute 1640 medium (RPMI1640) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin-amphotericin B . Human leukemia HL60 cells were cultured in RPMI1640 supplemented with 10% FBS, 1% penicillin-streptomycin-amphotericin B, and L-glutamine (2 mm) . HaCaT cell lines were grown in DMEM supplemented with 10% FBS, 100 \u03bcg/mL streptomycin, and 100\u2009\u03bcg/mL benzylpenicillin. All cells were maintained at 37 \u00b0C in a humidified 5% COStaphylococcus. Aureus CCARM 3640 (MRSA), S. aureus CCARM 3089 (MRSA), S. aureus CCARM 33591(MRSA), S. aureus CCARM 0205 (MSSA), S. aureus CCARM 0204 (MSSA), S. aureus CCARM 0027 (MSSA), S. aureus CCARM 3090 (MRSA), S. aureus CCARM 3634 (MRSA), S. aureus CCARM 3635 (MRSA), Bacillus subtilis ATCC 6633, Enterococcus faecalis 19433, Enterococcus faecalis 19434, Kocuria rhizophilla NBRC 12708, and Micrococcus luteus) and four Gram-negative bacteria were used to test antibacterial activities of chrysazin and its derivatives. The paper disk diffusion assay on the Mueller\u2013Hinton agar (MHA) plate was carried out according to Clinical Laboratory Standard Institute (CLSI) guidelines and the Kirby\u2013Bauer method [8 colony forming units (CFU)/mL were spread onto MHA plates. Then, 40 \u00b5g/disk compounds were placed on the surface of inoculated agar plates using sterile paper disks of 6 mm . Samples were then incubated at 37 \u00b0C for 18\u201320 h. The zone of inhibition diameter was measured in millimeters for each pathogen. Dimethyl sulfoxide (DMSO) was used as a control for the zone of inhibition as all compounds were dissolved in DMSO.Fourteen Gram-positive bacteria , S. aureus CCARM 3089 (MRSA), S. aureus CCARM 33591(MRSA), S. aureus CCARM 0205 (MSSA), S. aureus CCARM 0204 (MSSA), S. aureus CCARM 0027 (MSSA), S. aureus CCARM 3090 (MRSA), S. aureus CCARM 3634 (MRSA), and S. aureus CCARM 3635 (MRSA). They were grown in Mueller\u2013Hinton Broth (MHB) . The broth dilution method was used to determine MIC [8 CFU/mL) and then diluted to 2.5 \u00d7 106 CFU/mL in MHB. After knowing the MIC, the MBC test was performed on a fresh MHB medium by inoculating cultured samples containing MIC compounds and experimental strains.The following nine strains were used in the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) tests: E. coli strain S2 was generated by engineering E. coli BL21 (DE3), which contained a sugar transfer cassette and a sugar methylation cassette. It was cultured and prepared for biotransformation as mentioned in E. coli strain S2 was analyzed by HPLC. The HPLC chromatogram of chrysazin was obtained with its standard retention time (tR) of 21.3 min. Two new peaks of CR and CRM were obtained at tR of 14.9 min and 16.3 min, respectively, with UV absorbance at 420 nm and 2D NMR , as shown in Biotransformation was carried out through fermentation to collect CR and CRM for structure identification and further biological activity tests. The biotransformation reaction mixture was extracted with a double volume of ethyl acetate. The crude extract was subjected to preparatory-high-pressure liquid chromatography (prep-HPLC) for purification. After several rounds of prep-HPLC, purified compounds were obtained. The purified product was dried by lyophilization, dissolved in 400 \u00b5L of deuterated dimethyl sulfoxide, and analyzed by nuclear magnetic resonance (NMR) spectroscopy (700 MHz) including 1D NMR was consistent with \u03b4 5.67 , in which the anomeric proton coupling constant (J = 1.1 Hz) confirmed that the conjugation of rhamnose moiety had an \u03b1-configuration. In addition, with 13C-NMR of CR, the anomeric carbon peak appeared at \u03b4 99.08 ppm, with other peaks appearing between 70 and 80 ppm along with a CH3 peak at 18.35 ppm. In the case of CRM, there was a methylation in the 2\u2032 -OH group of rhamnose in CR, where the OCH3 spectrum was visible in both 1H and 13C NMR at 3.5 ppm and 59.44 ppm, respectively. Furthermore, to confirm the sugar and sugar-O-methylation conjugation, two-dimensional (2D)-NMR analyses such as 1H-13C HSQC, 1H-13C HMBC, 1H-1H COSY, and 1H-1H ROESY experiments were performed. Similarly, in CR, HSQC showed a cross peak illustrating a correlation between the anomeric C-1\u2032 proton (\u03b4 5.67 ppm) and the anomeric carbon (\u03b4 99.00 ppm). Moreover, the C-8 signal appearing at \u03b4 157.18 ppm showed a direct correlation with the observed anomeric proton at \u03b4 5.67 ppm in HMBC (\u03b4 3.71 ppm) and the carbon (\u03b4 80.61 ppm), and HMBC showed a cross peak depicting the correlations between C-2\u2032 (\u03b4 80.62 ppm) and the protons of the methoxy group (\u03b4 3.50 ppm) (O-\u03b1-l-rhamnoside) and methylated derivative of CR produced by E. coli S2 whole-cell biotransformation were new compounds.The in HMBC . In the .50 ppm) . Results50) values of chrysazin for AGS, Huh7, and HL60 cells were 17.08, 30.53, and 22.24 (\u03bcM), respectively. Chrysazin-8-O-\u03b1-l-rhamnoside inhibited AGS, Huh7, and HL60 cells with 50% inhibitory concentration (IC50) values of 28.58, 21.28, and 14.68 (\u03bcM), respectively. Here, CR showed better anticancer activities in Huh7 and HL60 than chrysazin. In the case of AGS cells, it showed slightly lower anticancer activity. In the case of chrysazin-8-O-\u03b1-l-2\u2032-O-methylrhamnoside, it showed higher anticancer activities than chrysazin and CR. The 50% inhibitory concentration (IC50) values of CRM for AGS, Huh7, and HL60 cells were 7.513, 4.467, and 4.540 (\u03bcM), respectively. In the case of the HaCaT normal cell line, the IC50 values were >200 \u03bcM for chrysazin, CR, and CRM -2,5- diphenyltetrazolium bromide (MTT) colorimetric assay against three different cancer cell lines and one and CRM . These cS. aureus subsp. were prepared at a concentration of 10 mg/mL. All compounds were added to each disk at a final concentration of 40 \u00b5g/disk (4 \u00b5L). Each disk was placed over Mueller\u2013Hinton agar (MHA) plates spread with bacterial strains. The diameter of the zone of inhibition was measured after 18\u201320 h. Results of disk diffusion assays revealed that chrysazin did not show any antibacterial activity against 18 different human pathogens tested. However, CR and CRM exhibited antibacterial activities against Gram-positive bacteria s subsp. . These rO-\u03b1-l-rhamnoside, and chrysazin-8-O-\u03b1-l-2\u2032-O-methylrhamnoside against nine different pathogenic bacteria were determined. MIC values of compound chrysazin, CR, CRM, and erythromycin as a positive control, against nine strains of Gram-positive bacteria S. aureus subsp were determined by the broth dilution method. The assays were performed in 96-well plates in duplicate with Mueller\u2013Hinton broth. As summarized in S. aureus CCARM 0205 (MSSA), S. aureus CCARM 0204 (MRSA), S. aureus CCARM 3640 (MRSA), S. aureus CCARM 3090 (MRSA), S. aureus CCARM 3634 (MRSA), S. aureus CCARM 0027 (MSSA), S. aureus CCARM 3089 (MRSA), S. aureus CCARM 3635 (MRSA), and S. aureus CCARM 33591(MRSA), with MIC values of 7.81\u20131000 \u00b5g/mL. After knowing the MIC value, we further analyzed MBC, the lowest concentration of a compound for killing inoculated bacteria. An MBC test was performed by inoculating cultured samples containing MIC compounds and experimental strains on a fresh MHB medium (Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) for chrysazin, chrysazin-8-B medium . MBC valE. coli strain for the sustainable production of different derivatives of chrysazin. Chrysazin-8-O-\u03b1-l-rhamnoside and chrysazin-8-O-\u03b1-l-2\u2032-O-methylrhamnoside were novel compounds. We also evaluated their activities against three different cancer cell lines . CR and CRM exhibited higher cytotoxicities than their parental compound, chrysazin. More significantly, the evaluation of antibacterial activity revealed promising bioactivities of CR and CRM. This study establishes an engineered microbial platform that can be used to produce novel bioactive compounds. This microbial platform can be further fine-tuned for the production of novel derivatives of other anthraquinones or different compounds. Furthermore, the optimization of bioprocessing parameters and rational engineering of the host using various synthetic biological tools and metabolic engineering can be employed to enhance the production titer.In this study, we successfully engineered an"} +{"text": "STING is a direct downstream target of let-7i after brain injury. Furthermore, the intranasal delivery of let-7i agomir can also effectively inhibit STING and is beneficial for inflammation resolution and neuronal survival in a mouse model of pial vessel disruption stroke. Consequently, let-7i agomir is a promising candidate for clinical application as a chemically engineered oligonucleotides-based therapeutic for brain injury.Overcoming the lack of drugs for the treatment of traumatic brain injury (TBI) has long been a major challenge for the pharmaceutical industry. MiRNAs have emerged as potential targets for progress assessment and intervention against TBI. The brain-enriched miRNA let-7i has been proposed as an ideal candidate biomarker for TBI, but its regulatory roles in brain injury remain largely unknown. Here, we find that the expression of let-7i is significantly downregulated in the early stages of a hippocampal stab wound injury. The noninvasive intranasal administration of let-7i agomir significantly improves cognitive function and suppresses neuroinflammation, glial scar formation, and neuronal apoptosis in TBI mice. Mechanically, Traumatic brain injury (TBI) is one of the leading causes of death and permanent disability worldwide and is a risk factor for developing dementia and neuropsychological diseases . AlthougMicroRNAs (miRNAs) are small single-stranded non-coding RNA molecules (about 22 nucleotides) that govern the processes of RNA silencing and the post-transcriptional regulation of gene expression. As a single miRNA regulates the expression of multiple target genes involved in many cellular processes, manipulating the expression of a single miRNA may affect the entire gene network, thus changing the phenotype of complex diseases. Mounting evidence suggests that miRNAs may serve as potential targets for progress assessment and intervention against TBI because they control a range of physiological and pathological functions, such as cell proliferation, differentiation, apoptosis, and metabolism ,9.Let-7 is a family of evolutionary conserved miRNA that are highly expressed in adult tissues and generally serve as key regulators of developmental processes . Let-7i Here, we aimed to examine whether TBI affects let-7 expression in the brain and to assess whether the restoration of let-7 levels is beneficial for suppressing neuroinflammation and reducing neuronal apoptosis after TBI. Furthermore, the mechanism of let-7 targeting for TBI was also explored.C57BL/6J mice were obtained from the SPF Biotechnology company and maintained in groups of 3~5 animals on a 12 h light/dark cycle, and they had free access to water and a standard mouse diet. Two-month-old male mice were assigned to undergo TBI or sham surgery. All animal procedures followed the ethical guidelines for the care and use of experimental animals, and all experiments were approved by the Animal Committee of the Institute of Zoology, Chinese Academy of Sciences.Hippocampal stab injury (HSI) was performed as previously described with minor modifications . Two-monPVD strokes were induced as previously described . BrieflyIntranasal administration of agomir-let-7i was conducted as described previously . Agomir-IL-6 forward TACCACTTCACAAGTCGGA, IL-6 reverse AATTGCCATTGCACAACTC; IL-1\u03b2 forward CCTCAAAGGAAAGAATCTATACCTG, IL-1\u03b2 reverse CTTGGGATCCACACTCTCC; TNF\u03b1 forward TTCTCATTCCTGCTTGTGG, TNF\u03b1 reverse TTGGGAACTTCTCATCCCT; human STING forward CACATCCACTCCAGGTACC, human STING reverse AGAAATAGATGGACAGCAGCA; mouse STING forward CTCATTGTCTACCAAGAACCC, mouse STING reverse TTCTTCCTGACGAATGTGC; let-7a forward ggcgTGAGGTAGTAGGTTGTATA, let-7b forward ggcTGAGGTAGTAGGTTGTGTG, let-7c forward ggccTGAGGTAGTAGGTTGTATG, let-7e forward ggcTGAGGTAGGAGGTTGTATA, let-7f forward ggcggTGAGGTAGTAGATTGTATA, let-7g forward ggcgTGAGGTAGTAGTTTGTACA, let-7i forward ggcTGAGGTAGTAGTTTGTGCT, common miRNA reverse GCAGGGTCCGAGGTATTC.Total RNA was isolated with TRIzol reagent according to the manufacturer\u2019s instructions. RNA quality was assessed with the Thermo NanoDrop 2000 spectrophotometer to assess 260/280 and 260/230 nm ratios. All RNA samples met a 260/280 ratio >2.0 and 260/230 ratios in the range of 2.0\u20132.2. cDNA was generated from reverse transcription of 2\u03bcg total RNA using a Transcriptor First Strand cDNA Synthesis Kit . cDNA was quantified using the SYBR Green assay, and the relative gene expression levels were calculated against GAPDH or U6 by using the \u2206\u2206Ct method. The primers we used for qRT-PCR were as follows: w/v), 0.3%Triton X-100, and 0.2% sodium azide for 2 h at room temperature. The primary antibodies we used were as follows: anti-Iba1 , anti-GFAP , anti-NeuN . After overnight incubation at 4 \u00b0C with primary antibodies and washing with PBS for 30 min, brain sections were incubated with the secondary antibodies conjugated with Alexa Fluor 488 or 594 (1:500). Finally, sections were stained with DAPI and mounted on glass slides with adhesion anti-fade medium. Confocal images were obtained on a ZEISS 710 confocal laser-scanning microscope. Image analyses and quantification were performed using ImageJ software V1.53 .Mice were anesthetized and transcardially perfused with cold phosphate-buffered saline (PBS), followed by 4% paraformaldehyde (PFA) in PBS (pH 7.4). Brains were dissected out and postfixed in 4% PFA overnight. Brains were then equilibrated in 30% sucrose and sectioned into segments 40 \u03bcm-thick. Brain sections were washed three times (10 min each) with PBS and then blocked in 3% BSA staining was performed to detect the neuronal apoptosis. Briefly, hippocampal tissue sections were washed for 10 min with PBS and incubated in 2% BSA and 0.25% triton X-100 for 30 min at RT. Sections were then incubated with 200 \u03bcL TUNEL reaction mixture at 37 \u00b0C for 1 h, followed by 3 washes with PBS. Subsequently, sections were incubated with anti-NeuN antibody overnight at 4 \u00b0C. Finally, sections were washed for 10 min with PBS 3 times and then incubated with the secondary antibodies conjugated to Alexa Fluor 488 at RT.Brain tissues were lysed with RIPA buffer . Protein samples were separated on 8\u201312% SDS-PAGE gels and transferred to polyvinylidene fluoride (PVDF) membranes . The PVDF membranes were then blocked in TBS-T containing 3% milk and incubated with primary STING antibodies at 4 \u00b0C overnight. PVDF membranes were then incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies (1:5000) at room temperature for 2 h. Finally, the immunoreactive proteins were treated with enhanced chemiluminescence reagent . The 5200CE Tanon\u2122 Chemi-Image System was used to obtain the images of the blots, and the band intensity of the blots was analyzed using the software ImageJ.STING 3\u2032UTRs were amplified from genomic DNA by PCR and cloned into the dual luciferase reporter vector pmirGLO . Primers were used for the cloning 3\u2032UTRs of STING as follows: mouse STING forward: CTGTGGTCTCCACGATGACTTGA, mouse STING reverse: CACCCAGGTCTCCAACCTTTAAA; human STING forward: CAGTGGTCTCCAAGCCTCTG, human STING reverse: ATGGAACATGACCAGGAGCCA. Mutagenesis of the putative let-7i binding sites on STING CDS or 3\u2032UTR was performed using the Quick-Change II Site-directed Mutagenesis Kit according to the manufacturer\u2019s protocol. The primers for subcloning the mutated CDS or 3\u2032UTR were as follows: mouse mutant STING forward: CATAatggagtGTTGGATGTTTGGCC, mouse mutant STING reverse: CCAACactccatTATGTCAGCAGTGTT; human mutant STING forward: TCACTGCCTatggagCCTCACG, human mutant STING reverse: TGAGGctccatAGGCAGTGATTATGA. All plasmid constructs were then verified by sequencing. Dual luciferase transfection assays were performed as previously described . A. A10]. AF = 101.2, p < 0.01; Sham vs. HSI(3 dpi), p < 0.01; Sham vs. HSI(7 dpi), p < 0.01; Sham vs. HSI(14 dpi), p = 0.986) by using qRT-PCR. The expression of let-7i at 3 and 7 dpi was significantly lower than that in the sham group, and recovered to the same level as that in the sham group at 14 dpi (= 0.986) B. Furthehttp://www.targetscan.org, accessed on 1 October 2020). Gene Ontology (GO) term analyses found that these predicted targets were related to biological functions involving transcription, regulation of transcription, transport, protein phosphorylation, pre-miRNA processing, protein ubiquitination, phosphorylation, and mRNA transport = 101.2, p < 0.001; 0 h vs. 6h, p < 0.001; 0 h vs. 1 d, p < 0.001; 0 h vs. 2 d, p < 0.001; 0 h vs. 3 d, p = 0.790) B. These TNF-\u03b1, IL-1\u03b2, and IL-6 in the hippocampi of agomir-let-7i-treated and scramble-treated mice at day 3 after HSI. Consistent with our expectation, the levels of TNF-\u03b1, IL-1\u03b2, and IL-6 were significantly elevated in the hippocampi of negative control mice after HSI = 32.44, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p < 0.05; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.05), IL-1\u03b2 = 41.83, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p < 0.05; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.01), and TNF\u03b1 = 79.65, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p < 0.01; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.001) after HSI = 42.42, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p = 0.195; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.001) and microglial branch number was greatly increased = 32.44, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p = 0.741; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.001) in the agomir-let-7i-treated HSI group = 43.44, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p < 0.01; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.05) and Iba1 (a microglia marker) revealed a considerable reduction in the size of the glial scar after agomir-let-7i treatment in comparison to the scramble control, while the sham group did not reveal any glial scar formation in the hippocampus ( < 0.05) E,F. Thes+/NeuN+ cells was significantly decreased in the agomir-let-7i-treated group compared to that in the scramble-treated group = 41.55, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p < 0.05; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.01) staining of hippocampal tissue sections from sham, scramble-treated, and agomir-let-7i-treated mice at day 7 post-injury. The number of TUNEL < 0.01) A,B, indiGiven that agomir-let-7i could reduce neuronal apoptosis as well as inflammatory response and glial scar size in the hippocampus, we speculated that agomir-let-7i-treated mice might perform better than scramble-treated mice on learning and memory tests. To test this hypothesis, we conducted the rotarod test and the Barnes maze test to evaluate hippocampal integrity in HSI mice beginning at 15 dpi.F = 173.0, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p < 0.01; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.001) B, suggesF = 26.36, p < 0.001; Sham vs. HSI + Scramble, p < 0.01; Sham vs. HSI + Agomir-let-7i, p < 0.05; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.01) D. AltogeSTING (TMEM173) is known to play a pivotal role in responding to pathogenic DNA and self-DNA in the context of neurodegenerative and autoimmune disorders [STING mRNA = 169.3, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p = 0.803; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.001) = 35.86, p < 0.001; Sham vs. HSI + Scramble, p < 0.001; Sham vs. HSI + Agomir-let-7i, p = 0.436; HSI + Scramble vs. HSI + Agomir-let-7i, p < 0.01) D. Moreov < 0.01) E. AltogeF = 159.2, p < 0.001; Sham vs. PVD stroke + Scramble, p < 0.001; Sham vs. PVD stroke + Agomir-let-7i, p < 0.001; PVD stroke + Scramble vs. PVD stroke + Agomir-let-7i, p < 0.001) and protein levels = 360.4, p < 0.001; Sham vs. PVD stroke + Scramble, p < 0.001; Sham vs. PVD stroke + Agomir-let-7i, p = 0.138; PVD stroke + Scramble vs. PVD stroke + Agomir-let-7i, p < 0.001) of STING were significantly decreased in the cortex of agomir-let-7i-treated PVD stroke mice A,B. Furtoke mice E,F. TherIn the present study, we found that TBI decreased let-7i and that the intranasal administration of agomir-let-7i reduced brain damage in TBI mice as well as in PVD stroke mice. Agomir-let-7i administration improved cognitive function in brain-injured mice. Mechanistically, agomir-let-7i administration suppressed neuroinflammation, glial scar formation, and neuronal apoptosis after brain injury, suggesting that agomir-let-7i may serve as a potential therapeutic candidate against injury-induced neuroinflammatory and neurodegenerative diseases, such as TBI and PVD stroke.Both TBI and PVD stroke have primary and secondary injury phases regardless of the severity of the insult. The primary injury encompasses mechanical damage to the brain tissues that release signals that activate microglia, astrocytes, and infiltrated peripheral immune cells to initiate the secondary injury, including inflammation, excitotoxicity, mitochondrial impairment, and neuronal cell death. The secondary injury phase evolves over minutes to days to months after the primary injury, suggesting that early interventions may ameliorate brain damage and stimulate neural regeneration and repair . The maiHuman TBI is a sophisticated disease process, and the diversity in the extent of injury as well as in pathoanatomical subtypes means that different patients are likely to experience different courses and outcomes of TBI. In addition, it is still difficult to generate animal models that can fully recapitulate all the pathophysiological aspects of human TBI. Let-7i has been considered as a promising serum biomarker for stroke and blast-induced TBI. For example, the expression of let-7i is upregulated in blood samples collected from patients with post-stroke cognitive impairment compared with patients with post-stroke cognitive normality . SimilarSTING) was a downstream target of let-7i in the brain, and the intranasal administration of agomir-let-7i could suppress the upregulation of STING, neuroinflammation, and glial scar formation in both TBI and PVD stroke mice. These findings are consistent with previous work that identified STING as a key regulator of inflammation in both rodents and human brain organoids and found that the inactivation of STING attenuates inflammation [Neuroinflammation plays an essential role in the pathophysiology of TBI and stroke. Although a low degree of neuroinflammation is initially beneficial for debris clearance and repair, a high degree of neuroinflammation elicits secondary injury that leads to chronic inflammation and neurodegeneration . Mechaniammation ,32,42,43ammation . Althougammation . Our datIn summary, we found that brain-enriched miRNA let-7i was significantly downregulated at the early stages of TBI in mouse brains. STING was a direct downstream target of let-7i, and agomir-let-7i could protect brain tissue from neuroinflammation, glial scar formation, and neural cell death after brain injury. Overall, our data suggest that the intranasal administration of agomir-let-7i is a potential therapeutic strategy for neurotrauma and PVD stroke."} +{"text": "The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with \u226550% completeness and <10% contamination, from cattle in Japan. The majority of MAGs were potentially novel strains, encoding various enzymes related to plant biomass degradation and volatile fatty acid production. The MAGs identified in the present study may be valuable resources to enhance the resolution of future taxonomical and functional studies based on metagenomes and metatranscriptomes. This study was the first to use JB (arXiv.https://arxiv.org/abs/1303.3997) to the bovine reference genome ARS-UCD1.2/bosTau9. Filtered reads were assembled in SPAdes version 3.13.0 (arXiv.https://arxiv.org/abs/1303.3997). We binned MAGs with contigs using MetaBAT2 version 2.15 to prevent arbitrary mapping between similar genomes with the following parameters: -m relative_abundance --min-read-percent-identity 0.95 -\u200d-\u200dmin-read-aligned-percent 0.75. We taxonomically classified RUG1ANI99% MAGs in GTDB-tk version 2.1.1 with GTDB release 207. We then built a phylogenetic tree in PhyloPhlAn version 3.0.60 , including Hungate1000 (strains (<99%) using the ANI outputs by dRep and GTDB-tk.Filtered reads were mapped against RUG1n 3.0.60 . To elucgate1000 using dRANI99% MAGs with Prodigal version 2.6.3 (Genomes (KEGG) database through GhostKOALA ( Carbohydrate-active enzyme (CAZyme) families, which are associated with cell wall degradation and essential for efficient lignocellulose processing in ruminants, were annotated using dbCAN2 (\u20135 to search cohesin (PF00963) and dockerin (PF00404) domains. We used PULpy in 5,414 public Bacteroidetes genomes using PULpy. bioRxiv.https://doi.org/10.1101/421024) to predict polysaccharide utilization loci (PUL), linked gene clusters that encode the cell envelope-associated enzymes required for sensing, binding, and degrading polysaccharide substrates . Following dereplication at 99% ANI, we generated 146 nonredundant RUG13.2\u200d \u200dkb . A compaectively . TherefoANI95% MAGs, we identified 32 MAGs that were present (relative abundance >0) in >90% of the tested cattle (n=20), suggesting that they are core rumen bacteria in Japan , Actinobacteriota (10 MAGs), Firmicutes (9 MAGs), Verrucomicrobiota (7 MAGs), Spirochaetota (4 MAGs), Patescibacteria (3 MAGs), Proteobacteria (2 MAGs), Methanobacteriota (2 MAGs), Planctomycetota (1 MAG), Synergistota (1 MAG), Desulfobacterota_I (1 MAG), and Elusimicrobiota (1 MAG). In Bacteroidota MAGs, 10 RUG1ANI99% MAGs were classified as Prevotella, which is the most abundant bacterial genus in the rumen with at least one gene related to acetate production . Firmicutes_C RUG1ANI99%These genes were absent from MAGs. Rumen propionate is produced via the succinate and\u200d \u200dacrylate pathways . Prevotella and GH77 (4-\u03b1-glucanotransferase), respectively, both of which are involved in starch degradation , GH3 (\u03b2-glucosidase), GH5 , GH13 (\u03b1-amylase), GH26 , GH32 (invertase), GH36 , GH43 (\u03b2-xylosidase), GH73 (lysozyme), GH94 (cellobiose phosphorylase), and GH97 (\u03b1-glucosidase).Among 146 RUG1radation . Further CAZymes , which iANI99% MAGs. The proteins containing cohesin and dockerin domains are summarized in ANI99% MAGs, including 2 Ruminococcus and 11 Ruminococcus_E MAGs. Sixteen dockerin-containing proteins carried CAZyme domains, mostly including GH families containing \u03b1-amylase . Among the 25 RUG1ANI99% MAGs, 13 had both cohesin- and dockerin-containing proteins, while 9 had only dockerin-containing proteins. Ruminococcus albus 8, which degrades cellulosic substrates, harbored no cohesion-containing protein. Therefore, we cannot rule out the possibility that RUG1ANI99% MAGs, which had no cohesion- and some dockerin-containing proteins, used an alternative mechanism for the immobilization of dockerin-containing enzymes onto carbohydrates, similar to Ruminococcus albus 8 . Ninety-eight and 80 PULs were identified in Cryptobacteroides MAG and Prevotella MAGs, respectively, and contained various CAZymes. Overall, the present results suggest that Cryptobacteroides and Prevotella are important for rumen function in cattle in Japan.In domains . The mosIn summary, we reconstructed 146 rumen-specific MAGs from cattle in Japan, with many being potentially novel. These MAGs are valuable resources for enhancing the resolution of future metagenome- and metatranscriptomic-based taxonomical and functional studies.Microbes Environ 37: ME22039.Sato, Y., Takebe, H., Oishi, K., Yasuda, J., Kumagai, H., Hirooka, H., and Yoshida, T. (2022) Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan. https://doi.org/10.1264/jsme2.ME22039Supplementary Material 1Supplementary Material 2Supplementary Material 3Supplementary Material 4Supplementary Material 5Supplementary Material 6Supplementary Material 7"} +{"text": "Correction: Immun Ageing 19, 57 (2022)https://doi.org/10.1186/s12979-022-00310-yFollowing publication of the original article , the autThe incorrect author name is: J\u00e9ssica S. de GuedesThe correct author name is: J\u00e9ssica de S. GuedesThe author group has been updated above and the original article has been"} +{"text": "ENDOGLIN (ENG) gene. Here, we generated induced pluripotent stem cells (hiPSCs) from a patient with rare mosaic HHT1 with tissues containing both mutant (ENGc.1678C>T) and normal cells, enabling derivation of isogenic diseased and healthy hiPSCs, respectively. We showed reduced ENG expression in HHT1 endothelial cells (HHT1-hiPSC-ECs), reflecting haploinsufficiency. HHT1c.1678C>T-hiPSC-ECs and the healthy isogenic control behaved similarly in two-dimensional (2D) culture, forming functionally indistinguishable vascular networks. However, when grown in 3D organ-on-chip devices under microfluidic flow, lumenized vessels formed in which defective vascular organization was evident: interaction between inner ECs and surrounding pericytes was decreased, and there was evidence for vascular leakage. Organs on chip thus revealed features of HHT in hiPSC-derived blood vessels that were not evident in conventional 2D assays.Hereditary hemorrhagic telangiectasia (HHT) is a genetic disease characterized by weak blood vessels. HHT1 is caused by mutations in the \u2022Vessels from isogenic hiPSCs from HHT1 patients compared\u2022HHT1-hiPSC-ECs show defective vascular organization in 3D microfluidic chips\u2022HHT1-hiPSC-ECs show defective EC-pericyte interaction In this article, Orlova and colleagues describe 3D vessels on chip (VoCs) composed of hiPSC-ECs from a patient with hereditary hemorrhagic telangiectasia (HHT1). HHT1-hiPSC-ECs and healthy isogenic controls behaved similarly in 2D culture, but defective vascular organization and reduced pericyte coverage were evident in HHT1-hiPSC-ECs in VoCs. The model is thus a valuable tool for mechanistic studies and future drug discovery. ENG; HHT1), Activin receptor like kinase-1 or SMAD4 (HHT3), genes that mediate signaling by transforming growth factor \u03b2 (TGF-\u03b2) and bone morphogenetic protein (BMP) in vascular endothelial cells (ECs) (in\u00a0vitro makes them unsuitable as a renewable source of ECs for reproducibly modeling the disease in humans and for drug discovery.Hereditary hemorrhagic telangiectasia (HHT) is an inherited genetic disorder caused by autosomal dominant mutations in Endoglin (ls (ECs) . Phenotyls (ECs) . These als (ECs) . More sels (ECs) . To datels (ECs) . Medicalls (ECs) , thalidols (ECs) , itraconls (ECs) , and othls (ECs) . Geneticls (ECs) . Attemptls (ECs) . Blood ols (ECs) , but thein\u00a0vitro and (2) investigating defective endothelial-pericyte interactions.In the present study, we aimed to establish an efficient and scalable system that would recapitulate the formation of defective blood vessels in patients with HHT, based on\u00a0patient-derived human induced pluripotent stem cells\u00a0(HHT1-hiPSCs). We hypothesized that HHT1-hiPSCs might be useful for (1) identifying mechanisms underlying disease predisposition and modeling clinical features of HHT1 ENG (NM_001114753.2 (ENG):c.1678C>T; p.(Gln560\u2217)), which causes ENG haploinsufficiency (c.1678C>T and HHT1WT) (c.1678C>T-hiPSC-ECs compared with HHT1WT-hiPSC-ECs (ID1 expression was significantly upregulated in HHT1c.1678C>T-hiPSC-ECs after 2\u00a0h of TGF-\u03b2 treatment (hiPSC lines were generated from somatic tissue from a patient with HHT1 with a heterozygous nonsense mutation in ficiency . The pat HHT1WT) D\u2013S1G. HH HHT1WT) ; 2014b. iPSC-ECs A and 1B.iPSC-ECs B. ENG haiPSC-ECs A. HHT1-hreatment B.Figure\u00a0c.1678C>T-hiPSC-ECs C. BarrieiPSC-ECs C and S2DiPSC-ECs C and S2DiPSC-ECs E.in\u00a0vitro was examined, as described previously .Finally, the ability to form 2D vascular networks eviously , 2014b. eviously F. Quantibranches G as wellc.1678C>T-hiPSC-ECs compared with HHT1WT-hiPSC-ECs model was then examined A. PrimariPSC-ECs B and 2C,iPSC-ECs A. QuantiiPSC-ECs C and S3Dimilarly B. Furthee nuclei E and S3Fe nuclei . Notablyc.1678C>T-hiPSC-ECs compared with HHT1WT-hiPSC-ECs.Junctional integrity was examined by immunostaining of the microvascular networks with VEC and ZO1 D and 2E.c.1678C>T-hiPSC-ECs showed reduced pericyte coverage compared with HHT1WT-hiPSC-ECs C\u2013S4E.Figc.1678C>T-hiPSC-ECs compared with HHT1WT-hiPSC-ECs was added into the medium channel of the organ-on-chip device, and real-time videos of vascular segments pre-stained using fluorescent agglutinin were made . QuantifiPSC-ECs B and 4C.in\u00a0vitro model for the genetic vascular disorder HHT using hiPSCs derived from patients with mutations in the ENG gene (HHT1). The results showed that we likely captured the direct effects of reduced ENG protein on the EC surface without compensation or adaption mechanisms that normally occur in\u00a0vivo, notably in mutant mice was used to knock down onic ECs . Completin\u00a0vivo . The generation of the lines was approved by the Leiden University ethics committee under the P13.080 \u201cParapluprotocol: hiPSC.\u201d Patient samples, fibroblasts from skin biopsies, and erythroblasts isolated from peripheral blood were used for reprogramming. Reprogramming with episomal vectors was done as described, except that a newer generation of vectors without ere used . hiPSCs ere used . KaryotyRA-FISH) , and pluOne-way ANOVA and non-parametric Student\u2019s t test for unpaired measurements were applied as appropriate to test for differences in means between the groups. Detailed statistics are indicated in each figure legend. Data are expressed and plotted as the mean \u00b1 SD. Statistical significance is indicated in each figure legend. Statistical analysis was performed with GraphPad Prism 9.0.2.V.V.O., designed the research, established functional assays, performed experiments, and wrote the manuscript; D.M.N. and A.C., performed experiments in 3D vascular chips, did imaging, and performed quantification; X.C., performed EC differentiation; C.F., performed reprogramming experiments; F.v.d.H., conducted EC differentiation and isolation and FACS; F.L., assisted with quantification of microfluidic experiments; C.J.J.W., R.J.S., and H.-J.M., provided HHT patient samples; J.K.P.v.A., conducted genetic analysis; P.t.D. and F.L. helped analyze the data; C.L.M., designed the research and wrote the manuscript.The authors declare no competing interests."} +{"text": "This study inventively combines epidermal growth factor receptor (EGFR) expression of the primary lesion and standardized uptake value (SUV) of positron emission tomography and computed tomography (PET/CT) to predict the prognosis of nasopharyngeal carcinoma (NPC). This study aimed to evaluate the predictive efficacy of maximum standard uptake value (SUVmax) and EGFR for treatment failure in patients with NPC.18F-FDG PET/CT of 313 patients with NPC. Time-dependent receiver operator characteristics was used for analyzing results and selecting the optimal cutoff values. Cox regression was used to screen out multiple risk factors. Cumulative survival rate was calculated by Kaplan\u2013Meier.This retrospective study reviewed the results of EGFR expression and pretreatment p\u2009=\u20090.0083), locoregional relapse-free survival (LRRFS) (p\u2009=\u20090.0077), distant metastasis-free survival (DMFS) (p\u2009=\u20090.013), and progression-free survival (PFS) (p\u2009=\u20090.0018) among the four groups. Patients in the EGFR-positive and SUVmax-T\u2009>\u20098.5 group had the worst survival, while patients in the EGFR-negative and SUVmax-T\u2009\u2264\u20098.5 group had the best prognosis. Subsequently, patients with only positive EGFR expression or high SUVmax-T were classified as the middle-risk group. There were also a significant difference in 3-year overall survival among the three risk groups (p\u2009=\u20090.034). SUVmax-T was associated with regional recurrence-free survival and LRRFS in multivariate analysis, whereas EGFR was an independent prognostic factor for LRRFS, DMFS, and PFS.The selected cutoff value of SUVmax-T was 8.5. The patients were categorized into four groups according to EGFR expression and SUVmax-T. There were significant differences in the 3-year local recurrence-free survival (LRFS) (The combination of SUVmax-T and EGFR expression can refine prognosis and indicate clinical therapy.The online version contains supplementary material available at 10.1186/s13014-023-02231-6. Nasopharyngeal carcinoma (NPC) is a highly aggressive malignant tumor believed to arise from nasopharyngeal epithelial cells . Accordi18F-fluorodeoxyglucose positron emission tomography and computed tomography (18F-FDG PET/CT) have been frequently used in pretreatment diagnostic evaluation and post-treatment monitoring because of their unique capability to image metabolically active lesions [The weight)]. SUVmax-Radiotherapy dose and target volume delineation were performed according to the recommendations (Radiation Therapy Oncology Group) , 23. ThePatients with stage I were treated with radiotherapy alone, while patients with stage II-IV received radiotherapy combined with chemotherapy .After RT, follow-up was conducted once every 3\u00a0months for the first 2\u00a0years, once every 6\u00a0months in years 3 to 5, and annually thereafter. The final follow-up date was March 2022. Study endpoints included local recurrence-free survival (LRFS), regional recurrence-free survival (RRFS), locoregional relapse-free survival (LRRFS), distant metastasis-free survival (DMFS), progression-free survival (PFS), and OS.P-values\u2009<\u20090.05 indicated statistical significance.Uses IBM SPSS statistical software version 22.0 and R software version 4.0.5 for the statistical analysis. The optimal cutoff values was decided by Time-dependent receiver operator characteristic (ROC) analysis . Kaplan\u2013Meier methods were used to compute the survival analyses. Between-group differences in survival outcomes were assessed using log-rank tests. Cox regression was used to screen out multiple risk factors. All tests were two-tailed, and The clinical characteristics of all eligible patients are summarized in Table P\u2009=\u20090.075), 97.9% vs. 93.2% (P\u2009=\u20090.084), 94.7% vs. 87.6% (P\u2009=\u20090.032), 97.0% vs. 87.4% (P\u2009=\u20090.018), 91.8% vs. 76.7% (P\u2009=\u20090.0017), and 96.5% vs. 90.8% (P\u2009=\u20090.058), respectively .Among 1877 patients with NPC with IHC examination for primary lesions, EGFR was detected in 73.36% (1377 patients), and the proportion of patients showing negligible intensity (negative) of EGFR staining was 26.64% (500 patients). For the enrolled 313 patients, 241 (77.00%) showed positive EGFR expression, while 72 (23.00%) showed negligible expression (negative). The 3-year LRFS, RRFS, LRRFS, DMFS, PFS, and OS rates in the EGFR-negative group vs. EGFR-positive group were 96.9% vs. 92.2% (p\u2009=\u20090.0038), 96.3% vs. 95.3% (p\u2009=\u20090.21), 93.8% vs. 84.2% (p\u2009=\u20090.0063), 93.5% vs. 86.5% (p\u2009=\u20090.022), 85.8% vs. 75.5% (p\u2009=\u20090.018), and 94.4% vs. 93.5 (p\u2009=\u20090.066), respectively .The mean SUVmax-T was 10.21\u2009\u00b1\u20095.59 , and the mean SUVmax-N was 7.53\u2009\u00b1\u20095.55 . To further evaluate the prognostic value of SUVmax, time-dependent ROC analysis was used to determine the optimal cutoff values based on the 3-year survival outcome. The optimal cutoff value of SUVmax-T was 8.5 based on the 3-year LRFS , LRRFS (p\u2009=\u20090.0077), DMFS (p\u2009=\u20090.013), and PFS (p\u2009=\u20090.0018) .To better predict the prognosis of NPC, patients were divided into the following four groups based on SUVmax-T and EGFR expression: (a) EGFR negative and low SUVmax-T, (b) EGFR negative and high SUVmax-T, (c) EGFR positive and low SUVmax-T, and (d) EGFR positive and high SUVmax-T. There were obviously statistical difference in 3-year LRFS (18) Fig.\u00a0 among thp\u2009=\u20090.0029), LRRFS (p\u2009=\u20090.0026), DMFS (p\u2009=\u20090.005), and PFS (p\u2009=\u20090.00073), the 3-year OS also showed significant difference among 3 risk groups .Figure\u00a0p\u2009=\u20090.005) and LRRFS . Moreover, multivariable survival analysis revealed that EGFR was an independent prognostic factor for LRRFS , DMFS , and PFS .Six variables were included in the univariate analysis for the six clinical endpoints, and the results are summarized in Additional file The most important prognostic factor for NPC is TNM clinical stage. However, there is considerable variability in outcomes among patients with the same TNM stage receiving the same treatment . Recent PET/CT is functional imaging, which is different from morphology and structure imaging. The parameters of PET can be used to characterize the burden of metabolically active lesions and biological aggressiveness in malignancies. SUV, TLG, and MTV are parameters that have been correlated with survival outcome \u201316. SUVmIn 2008, a retrospective study have shown SUVmax may predict DFS in NPC treated with CCRT and more aggressive treatment should be given to patients with higher SUVmax . A prospSeveral meta-analyses have shown that EGFR overexpression is significantly associated with poor OS and DFS. Thus, EGFR may serve as a potential prognostic predictor of NPC , 37, 38.p\u2009=\u20090.0083), LRRFS (p\u2009=\u20090.0077), DMFS (p\u2009=\u20090.013), and PFS (p\u2009=\u20090.0018) among the four groups. The K\u2013M curve revealed that patients in the EGFR-positive and SUVmax-T\u2009>\u20098.5 group had the worst survival, while patients in the EGFR-negative and SUVmax-T\u2009\u2264\u20098.5 group had the best prognosis. For patients in the EGFR-negative\u2009+\u2009SUVmax-T\u2009>\u20098.5 group and EGFR-positive\u2009+\u2009SUVmax-T\u2009\u2264\u20098.5 group, the cumulative survival curves were extremely close. This demonstrated that EGFR expression and high SUVmax-T may be adverse prognostic factors for NPC. Therefore, we further divided patients into three groups. Patients with positive EGFR expression or high SUVmax-T levels were defined as the middle-risk group. The 3-year OS also showed a significant difference among the three risk groups (p\u2009=\u20090.034). Moreover, SUVmax-T was associated with LRFS and LRRFS in multivariate analysis, whereas EGFR was an independent prognostic factor for LRRFS, DMFS, and PFS.To better predict the clinical outcomes of de novo NPC, we combined functional imaging data with molecular pathological data. Patients were categorized into four groups based on EGFR expression (negative or positive) and SUVmax-T (\u2264\u20098.5 or\u2009>\u20098.5). There were significant differences in 3-year LRFS ; B regional recurrence-free survival (RRFS); C locoregional relapse-free survival (LRRFS); D distant metastasis-free survival (DMFS); E progression-free survival (PFS); F overall survival (OS). Fig. S3: Kaplan-Meier curves in the low SUVmax-T (\u22648.5) group and the high SUVmax-T (>8.5) group. A local recurrence-free survival (LRFS); B regional recurrence-free survival (RRFS); C locoregional relapse-free survival (LRRFS); D distant metastasis-free survival (DMFS); E progression-free survival (PFS); F overall survival (OS)."} +{"text": "Vigna unguiculata (lobia) production remains poorly understood. Thus, we aimed to isolate and characterize the soil microbes from the rhizosphere and develop novel microbial consortia for enhancing lobia production. Fifty bacterial strains were isolated from the rhizosphere soil samples of lobia. Finally, five effective strains were identified and molecularly characterized by 16\u00a0S rDNA gene amplification. All selected strains showed positive plant growth promoting (PGP) properties in broth culture. Based on morphological, biochemical, and plant growth promoting activities, five effective isolated strains and two collected strains (Azospirillum brasilense MTCC-4037 and Paenibacillus polymyxa BHUPSB17) were selected. The pot trials were conducted with seed inoculations of lobia (Vigna unguiculata) var. Kashi Kanchan with thirty treatments and three replications. The treatment combination T3 (Pseudomonas sp. IESDJP-V2), T14 (Pseudomonas sp. IESDJP-V2\u00a0+\u00a0A. brasilense), T26 (Pseudomonas sp. IESDJP-V1+ B. cereus IESDJP-V4\u00a0+\u00a0P. polymyxa) and T27 (IESDJP-V1+ IESDJP-V5+ A. brasilense) were recorded for enhancing plant growth attributes, yield, nutritional content like protein, total sugar, flavonoid and soil properties as compared to control and others. The effective treatments T3 (Pseudomonas sp.), T14 (Pseudomonas sp. IESDJP-V2\u00a0+\u00a0A. brasilense), T26 (Pseudomonas sp. IESDJP-V1+ B. cereus IESDJP-V4\u00a0+\u00a0P. polymyxa) and T27 (IESDJP-V1+ IESDJP-V5+ A. brasilense) recorded as potential PGPR consortium for lobia production. The treatment of single (Pseudomonas sp.), duel (IESDJP-V2\u00a0+\u00a0A. brasilense) and triple combination (IESDJP-V1+ IESDJP-V4\u00a0+\u00a0P. polymyxa) and (IESDJP-V1+ IESDJP-V5+ A. brasilense) can be further used for developing effective indigenous consortium for lobia production under sustainable farming practices. These PGPR bio-inoculant will be cost-effective, environment-friendly and socially acceptable.The rhizosphere microbes play a key role in plant nutrition and health. However, the interaction of beneficial microbes and The gThe application of microbial consortium or inoculum in single, dual, triple, tetra, penta and hexa, and more combinations are widely used for increasing sustainable agricultural productivity as well as enhancing soil fertility and health ,8. PGPR Vigna unguiculata L.) is an important seed legume crop that is broadly used as green vegetables in India and other countries of World , 10.13039/501100021098Design and Innovation Centre, BHU and Indian Institute of Technology (IIT-BHU) Varanasi [DIC-BHU/Project S-23 Approval/2016-17/693].Professor Jay Prakash Verma was supported by Data associated with this study has been deposited at NCBI-GenBank and got accession number of Pseudomonas sp. IESDJP-V1 (MH362754) and Pseudomonas sp. IESDJP-V2 (MH362755), S. marcescens IESDJP-V3 (MH362756), B. cereus IESDJP-V4 (MH362757), Ochrobactrum sp. IESDJP-V5 (MH362758).The authors declare no competing interests.No additional information is available for this paper."} +{"text": "Pseudanabaena spp. are filamentous cyanobacteria widely distributed in temperate lakes. Though infrequent, they can form harmful algal blooms. Here, we present a high-quality metagenome-assembled genome of a Pseudanabaena sp. from a toxic, crimson cyanobacterial bloom in Lake Salubria, NY. Pseudanabaena spp. are filamentous, nonheterocystous cyanobacteria widely distributed in temperate lakes . In spring 2020, an algal bloom turned the lake a vivid crimson, concerning the community . Grab saN50 = 5,395\u2009bp).Filaments were filtered onto a 5-\u03bcm polycarbonate filter from which genomic DNA was extracted using standard phenol-chloroform methods (De novo assembly was conducted using Unicycler (v0.4.9b) in normal mode . Illuminmal mode . CheckM mal mode . GTDB-Tkmal mode . The genmal mode . The 16SPseudanabaena sp. Salubria-1, consisting of 107 contigs with a total length of 7,138,199\u2009bp and a GC content of 41.93%. The sequencing depth was ~191-fold. The genome was estimated at 99.1% complete with 3.3% contamination. The closest taxonomic placement (91.9% average nucleotide identity [ANI]) was to Pseudanabaena sp. strain UWO311, a red strain isolated from Dickson Lake, Ontario, Canada (Pseudanabaena/Limnothrix group (We recovered a MAG of bp N50 = 5,348\u2009bp JALQCR000000000. Reads are deposited in the NCBI Sequence Read Archive under accession numbers SRX15003418 and SRX15003417.The metagenome-assembled genome is deposited at DDBJ/ENA/GenBank under accession number"} +{"text": "In this study, we aimed to investigate the effect of p62 on angiogenesis and microRNA (miRNA) expression profiles in acute myeloid leukemia (AML) exosomes.An Exiqon v19.0 microRNA MicroArray was used to profile miRNAs in exosomes derived from parental and p62-knockdown U937 cells. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict the biological functions and potential mechanisms of differentially expressed miRNAs in AML exosomes. Endothelial cell tube formation assays using human umbilical vein endothelial cells (HUVECs) were performed to investigate the effect of AML exosomes on angiogenesis.P < 0.05). GO analysis indicated that miRNAs were most enriched in the intercellular pathways. Biological process analysis revealed that 1460 biological processes were associated with downregulated transcripts, including 19 pathways related to vesicles, and 1,515 pathways were upregulated, including 8 pathways related to vesicles. Molecular function analysis indicated that protein binding, transcription regulator activity, and DNA-binding transcription factor activity were enriched (P < 0.05). Pathway analysis indicated that 84 pathways corresponded to upregulated transcripts, and 55 pathways corresponded to downregulated transcripts (P < 0.05). We also found that exosomes derived from U937 cells promoted angiogenesis in HUVECs.We demonstrated that 2,080 miRNAs were expressed in exosomes derived from our cultured cell samples, of which 215 and 208 miRNAs were upregulated and downregulated, respectively, in p62-knockdown U937 cells (fold change \u2265 2, Our data suggest that exosomal miRNAs may play important roles in the pathogenesis of AML, which may be treated by p62 knockdown with exosomal miRNAs to inhibit angiogenesis. Acute myeloid leukemia (AML) is a fatal hematological malignancy with high recurrence rate. For patients receiving the most intensive treatment, the overall 5-year survival rate remains below 50%. For the remaining patients, the prognosis is even worse . AML is Exosomes are nanometer-scale extracellular vesicles containing many microRNAs (miRNAs) that are secreted from cells in both normal and pathological conditions . It has In this study, we constructed a miRCURYTM LNA Array (v.19.0) of miRNAs in exosomes derived from AML cells after p62 knockdown. The miRNAs in exosomes were analyzed by identifying signature miRNAs. We then investigated angiogenesis in human umbilical vein endothelial cells (HUVECs) exposed to exosomes derived from parental U937 cells, p62-knockdown U937 cells, or control cells. The data from these studies may shed light on the relationship between exosomal miRNAs and AML, further enhancing our understanding of AML progression.Our study may aid the development of potential biomarkers for the diagnosis and prognosis of AML progression.SQSTM1 gene (LV-SQSTM1-RNAi) and an empty recombinant adenovirus vector (Hu6-MCS-CMV-EGFP) were constructed. U937 cells were placed in a six-well plate. Polybrene was used for the transfection. The transfection system included 1.8 mL RPMI-1640 with 10% fetal bovine serum, 10\u00a0\u00b5L LV-SQSTM1-RNAi or Hu6-MCS-CMV-EGFP, and 0.9 \u00b5L polybrene. After transfection for 24 h, the cell suspension was collected and centrifuged at 800 rpm for 5 min, the supernatant was discarded, and two mL of RPMI-1640 with 10% fetal bovine serum was added. After transfection for 48 h, fluorescence was observed. After culturing, 5 \u00b5g/mL puromycin was added, and the cells were screened for 15 days. After selecting the surviving cells, cell lines with clonal stability were cryopreserved and characterized through RT\u2013qPCR and western blotting.The human acute monocytic leukemia cell line U937 was purchased from the Bena Culture Collection and stored in our laboratory. A recombinant lentivirus vector-mediated 4 cells/well in 96-well plates and allowed to grow for 12, 24, and 48 h. Next, 10\u00a0\u00b5L CCK-8 solution was added to the cell suspension and incubated for 2 h. Absorbance was measured using a spectrophotometer at 450\u00a0nm. The experiment was repeated at least three times.U937 cells were plated at a density of 3\u20135\u00a0\u00d7\u00a010Flow cytometry analysis using an Annexin V-FITC/PI detection kit was used to compare the apoptosis rate of p62-control and p62 knockdown U937 cells. After 48 h of incubation, the cells were washed with phosphate-buffered saline and resuspended in 400 \u00b5L of 1\u00a0\u00d7 binding buffer. Thereafter, 5 \u00b5L Annexin V-FITC and 5 \u00b5L PI were added to the mixture and stained in the dark for 15 min at room temperature. Apoptosis was detected using flow cytometry immediately after staining.P62-siRNA coated with lentivirus interfered with U937 cells to downregulate the expression of p62, with the empty virus vector used as a control. Two groups of cells were used as follows: p62-knockdown U937 cells and controls. The two groups of cells were cultured for 48 h in serum-free media. The supernatant was collected for exosome extraction via ultracentrifugation. Exosome shape and size were observed using electron microscopy, and exosomal markers were detected using western blot analysis.Total protein was extracted from U937 cells that had or had not been transfected with the p62-encoding gene using radioimmunoprecipitation assay lysis buffer . The protein concentration was determined using the BCA method. Equal amounts of protein samples were added to each well, separated using 10% SDS-PAGE, and transferred to a polyvinylidene chloride transfer membrane . The membrane was blocked with 5% skimmed milk for 2 h. It was then washed with TBST and incubated with primary antibodies against p62, TSG101, CD63, CD9, calnexin, and GAPDH overnight at 4\u00a0\u00b0C. Thereafter, the membrane was incubated with anti-rabbit or anti-mouse horseradish peroxidase-conjugated secondary antibodies at room temperature for 2 h after washing three times with TBST. An enhanced chemiluminescence substrate (Thermo Fisher Scientific) was used to detect the protein bands. Image Lab software was used to detect and analyze the density of each band .TRIzol was used to extract total RNA. A NanoDrop spectrophotometer was used to measure RNA quality and quantity. RNA integrity was assessed using gel electrophoresis. After quality control, miRNA labeling was performed according to the instructions of the miRCURY\u2122 Hy3\u2122/Hy5\u2122 Power Labeling Kit . First, 1 \u00b5L RNA in 2 \u00b5L water was mixed with 1 \u00b5L CIP buffer and CIP . The mixture was then incubated at 37\u00a0\u00b0C for 30 min. The mixture was incubated at 95\u00a0\u00b0C for 5 min to stop the reaction. Then, 3 \u00b5L labeling buffer, 1.5 \u00b5L fluorescent label (Hy3TM), 2 \u00b5L dimethyl sulfoxide, and 2 \u00b5L labeling enzyme were added. The mixture was then incubated for 1 h at 16\u00a0\u00b0C, followed by 15 min at 65\u00a0\u00b0C to terminate the reaction. Hy3-labeled samples were hybridized on the miRCURYTM LNA array according to the manufacturer\u2019s instructions. A total of 25 \u00b5L Hy3\u2122-labeled samples and 25 \u00b5L hybridization buffer were denatured at 95\u00a0\u00b0C for 2 min and then incubated on ice for 2 min. The hybridization system was used with the microarray set at 56\u00a0\u00b0C for 16 to 20 h. After hybridization, the slides were washed several times using a washing buffer kit . Finally, an Axon GenePix 4000 B microarray scanner was used to scan the slides.P value. Finally, hierarchical clustering was used to show the different miRNA expression profiles between the samples.GenePix Pro 6.0 software was used to extract data by analyzing the imported scanned images. The samples were chosen to calculate normalization factors if the replicated miRNAs were averaged and for miRNAs with intensities \u226530. Median normalization was used to normalize the data. Normalized data = (foreground background)/median; the median was the 50% quantile of miRNA intensity, which was larger than 30 in all samples after background correction. After normalization, the miRNAs with significant differences between the two groups were determined according to the fold change and http://www.targetscan.org/) and mirdbV5 (http://mirdb.org/) are online sites for miRNA target gene prediction (TargetScan7.1 (ediction . In our http://www.geneontology.org) and KEGG (http://www.genome.ad.jp/kegg/) databases to study the potential organisms and signaling pathways of differentially expressed miRNAs. Differences were considered statistically significant at P\u00a0<\u00a00.05.We used the GO , seeded at 3\u00a0\u00d7\u00a0104 cells per well. Tubules were photographed using phase microscopy after incubation for 0, 3, and 6\u00a0h at 37\u00a0\u00b0C with 5% CO2.t-test, and statistical significance was set at P\u00a0<\u00a00.05.We used GraphPad Prism 6 to corroborate the statistical significance of the data for all graphs in this study. Values are presented as the means\u00a0\u00b1\u00a0standard deviation. Differences between groups were analyzed using Student\u2019s To generate p62-knockdown U937 cells, we used a lentivirus to transfect cells and observed the transfection efficiency by fluorescence microscopy. We then conducted RT\u2013qPCR analysis to determine the expression levels of the autophagy gene encoding p62 \u20131B and wP\u00a0<\u00a00.05).We observed exosome formation using electron microscopy after ultracentrifugation. Electron microscopy revealed exosomes as vesicles with a double-layer membrane structure \u20134F, biol\u00a0<\u00a00.05) and 6A. \u00a0<\u00a00.05) . As for \u00a0<\u00a00.05) . The miR\u00a0<\u00a00.05) and 6A.http://www.targetscan.org/) and mirdbV5 (http://mirdb.org/) were employed to predict the potential target genes of miRNAs. We found that 2,018 genes co-expressed with upregulated miRNAs and 2,749 genes co-expressed with downregulated miRNAs in the two databases . Among the three groups of HUVECs+Exo(U937), HUVECs+Exo(p62-con) and HUVECs+Exo(p62-), the HUVECs+Exo(p62-) group grew slower than the other two groups (p\u00a0<\u00a00.05). In summary, the above results indicated that the fastest angiogenesis occurred in the presence of exosomes from U937 cells; the slowest angiogenesis occurred in the presence of exosomes from p62-knockdown U937 cells.HUVECs were inoculated in Matrigel and incubated with AML exosomes for a certain period of time to determine whether exosomes from AML cells could induce HUVEC tubular differentiation nificant . Microscnificant \u20137C. By cAlthough advances have been made in AML supportive care, prognostic risk stratification, and established therapies, patients with AML have poor long-term prognosis . The ideAccumulating evidence indicates that exosomes in tumors are oncogenic. Crosstalk between bone marrow tumors and endothelial cells can affect tumor progression in hematological tumors, and exosomes containing miRNAs are crucial in bone marrow angiogenesis promotion in hematological tumors. By delivering miR-365, exosomes can mediate the horizontal transfer of drug resistance in chronic myeloid leukemia cells . K562 ceP\u00a0<\u00a00.05). We used microarray technology to study the expression patterns of exosomal miRNAs derived from two U937 cell lines to further explore the relationship between exosomal miRNAs and p62. We identified 2,080 miRNAs, including 215 upregulated and 208 downregulated miRNAs in p62-knockdown U937 cells. To further validate microarray analysis results, we performed RT\u2013qPCR to validate the downregulated expression of miR-3064-3p and miR-339-5p in the same series of samples. Our future studies will involve identification of other miRNAs whose expression was the highest in our microarray results. The RT\u2013qPCR results were consistent with those obtained from microarray analysis. In addition, KEGG pathway analysis revealed that 84 pathways corresponded to upregulated transcripts, and 55 pathways corresponded to downregulated transcripts. For the downregulated transcripts, the most affected pathway was the \u201cTNF signaling pathway\u201d (Pathway ID: hsa04668), followed by the \u201cMAPK pathway\u201d (Pathway ID: hsa04010). As for upregulated transcripts, the \u201cPI3K\u2013Akt signaling pathway\u201d (Pathway ID: hsa04151) was the most enriched pathway.In our study, p62 knockdown in U937 cells inhibited cell proliferation and promoted apoptosis , VEGFC, GATA-binding protein 4 , matrix Although AML cells secrete angiogenic factors to remodel the vascular system and gain chemoresistance, anti-angiogenic drugs are generally ineffective in AML treatment. In conclusion, after a detailed examination of miRNA expression in exosomes derived from AML cells, we found that hsa-miR-3064-3p and hsa-miR-339-5p displayed downregulated expression in p62-knockdown cells, compared with control cells. In addition, we demonstrated that several differentially expressed exosomal miRNAs were closely related to multiple GO items and pathways involved in carcinogenesis, indicating that exosomal miRNAs play a key role in AML pathogenesis. This information may aid the development of potential biomarkers for diagnosis and prognosis of AML progression. In the present study, we also found that exosomes derived from AML cells promoted angiogenesis. However, the relationship between exosomal miRNAs and angiogenesis needs to be further investigated. These findings support the notion that promising new treatment strategies may be developed against AML, based on exosomal miRNA analysis.10.7717/peerj.13498/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj.13498/supp-2Supplemental Information 2Click here for additional data file.10.7717/peerj.13498/supp-3Supplemental Information 3Click here for additional data file.10.7717/peerj.13498/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.13498/supp-5Supplemental Information 5Click here for additional data file.10.7717/peerj.13498/supp-6Supplemental Information 6Click here for additional data file.10.7717/peerj.13498/supp-7Supplemental Information 7Click here for additional data file.10.7717/peerj.13498/supp-8Supplemental Information 8Click here for additional data file.10.7717/peerj.13498/supp-9Supplemental Information 9Click here for additional data file.10.7717/peerj.13498/supp-10Supplemental Information 10Click here for 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additional data file.10.7717/peerj.13498/supp-110Supplemental Information 110Click here for additional data file."} +{"text": "Microbacterium elymi KUDC0405T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405T was a rod-shaped bacterium with size dimensions of 0.3\u20130.4 \u00d7 0.7\u20130.8 \u03bcm. Based on 16S rRNA gene sequences, KUDC0405T was most closely related to Microbacterium bovistercoris NEAU-LLET (97.8%) and Microbacterium pseudoresistens CC-5209T (97.6%). The dDDH values between KUDC0405T and M. bovistercoris NEAU-LLET and M. pseudoresistens CC-5209T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405T, M. bovistercoris NEAU-LLET, and M. pseudoresistens CC-5209T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405T and its closest related type strains. The genome contained 3,596 CDCs, three rRNAs, 46 tRNAs, and three non-coding RNAs (ncRNAs). The genomic DNA GC content was 70.4%. The polar lipids included diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and unknown phospholipid, and the major fatty acids were anteiso-C17:0 and iso-C16:0. Strain KUDC0405T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405T should be considered a novel species within the genus Microbacterium, for which we propose the name M. elymi sp. nov., and the type strain as KUDC0405T . Microbacterium was classified by Orla-Jensen S [Microbacterium comprised 157 species, including Microbacterium aerolatum V-73T [M. agarici CC-SBCK-209T [M. album SYSU D8007T [M. algeriense G1T [M. amylolyticum N5T [M. aoyamense KV-492T [M. aquimaris JS54-2T [Microbacterium can be isolated from various sources, such as seawater, desert soil, maize rhizosphere, cow dung, and microfiltered milk. Members of this genus are Gram-stain-positive, rod-shaped, and have an optimum growth temperature of 20\u201330\u00b0C. Here, we report a taxonomic analysis of the novel bacterial strain, KUDC0405T, isolated from the rhizospheric soil of Elymus tsukushiensis, a plant native to the Dokdo Islands . During microbial diversity monitoring in April 2014, rhizospheric soil samples were collected from native plants of the Ulleungdo and Dokdo Islands . E. tsukushiensis var. trasiens (Hack.) Osada is native to the Dokdo Islands and is the dominant plant species on these islands, and its distribution is expanding [Brevibacterium iodinum KUDC1716 [Ochrobactrum lupini KUDC1013 and Novosphingobium pentaromativorans KUDC1065 [The genus Jensen S based onum V-73T , M. agarU D8007T , M. algeicum N5T , M. aoyaxpanding . DespiteKUDC1716 , Ochroba-4\u201210-6) were prepared. A 100 \u03bcL aliquot dilution was plated onto R2A and 1/10 diluted tryptic soy agar (TSA) and incubated at 25\u00b0C for 7 days. Morphologically different colonies were selected, and individual colonies were further purified by repeated streaking onto TSA media. The type strains used in this study were obtained from the China General Microbiological Culture Collection Centre (CGMCC) and the Korea Collection for Type Cultures (KCTC). The strains were cultivated on TSA at 25\u00b0C and maintained at -70\u00b0C in saline solution supplemented with 15% glycerol (v/v).Plant samples were collected and stored as described previously . The samhttp://macrogen.com/) using the sequencing primers (518F and 800R) and an automated sequencer . The EzBioCloud server (https://ezbiocloud.net/) [The phylogenetics of the isolated strain was determined based on a comparative analysis of the 16S rRNA gene sequence. The 16S rRNA gene sequence was amplified and the PCR products were purified as described previously . UniversRathayibacter rathayi VKM Ac-1601T, which is not affiliated with the genus Microbacterium was used as an outgroup. Trees were rooted and constructed using MEGA-X in the Newick format.All 16S rRNA gene sequences of the closest type strains were aligned using CLUSTAL_W and the et al. [et al. [T was sequenced using a MinION platform . The reads were assembled de novo using Flye (version 2.9) [T and closely related strains were calculated using the JSpeciesWS website (https://jspecies.ribohost.com/jspeciesws/) [http://enve-omics.ce.gatech.edu/) [http://ggdc.dsmz.de/distcalc2.php) [T and its two closest relatives, M. bovistercoris NEAU-LLET and M. pseudoresistence CC-5209T, using protein sequences annotated by Hyatt et al. [http://automlst.ziemertlab.com) [Chromosomal DNA was extracted in accordance with Sambrook et al. and was [et al. . The celion 2.9) . The aution 2.9) and the ion 2.9) were useion 2.9) . The aveciesws/) . The avech.edu/) . The dDDlc2.php) . The dDDt et al. and the t et al. . A multilab.com) .T was observed with a Zentech digital camera for cell morphology and size, using cells grown on TSA. The cells were treated with 1% osmium tetroxide 25\u00b0C for 1 h, and dehydrated with graded series of ethanol , followed by isoamyl acetate. After lyophilization, the samples were coated with platinum , and the cell morphology was observed using a field emission scanning electron microscope .The scanning electron micrograph of strain KUDC0405T and the reference strains (M. bovistercoris NEAU-LLET and M. pseudoresistence CC-5209T) at different temperatures and different pH values . The pH values were adjusted as described by K\u00e4mpfer et al. [Growth capability of strain KUDC0405r et al. in steriM. bovistercoris NEAU-LLET and M. pseudoresistence CC-5209T, which are related to KUDC0405T, were analyzed under the same conditions. The cell wall peptidoglycan was analyzed using an amino acid analyzer . To analyze the polar lipids, two-dimensional thin layer chromatography (TLC) analysis were used according to Minnikin et al. [T, and reference strains were incubated on TSA at 30\u00b0C for 7 days. To determine siderophore production by strain KUDC0405T, chrome azurol S (CAS) media were used as previously described [To determine hydrolysis of starch, urea, Tween 20, 40, 60, and 80, the isolate was cultured on TSA at 30\u00b0C for a week, as described by Cowan and Steel . The enzn et al. . The fatescribed , 40.T was determined as previously described [M. bovistercoris NEAU-LLET, followed by M. pseudoresistence CC-5209T (97.58%), M. resistens NBRC 103078T (97.51%), M. oleivorans NBRC 103075T (97.51%), M. testaceum NBRC 12675T (97.51%), and M. paraoxydans NBRC 103076T (97.30%). A comparison of the preliminary 16S rRNA gene sequences revealed that strain KUDC0405T is related to members of the genus Microbacterium. In the Bayesian inference tree . The complete genome of strain KUDC0405T consisted of a circular chromosome . The genomic DNA G+C content was 70.4%, which is within the range reported for the Microbacterium genus. A total of 3,654 genes were identified, of which 3,018 were protein-coding genes and 52 were RNA genes . T and closely related strains. The genome of strain KUDC0405T displayed 256 subsystems according to genome annotation using RAST. Various metabolic genes were predicted for various metabolic processes, such as the metabolism of amino acids and derivatives (311 genes), carbohydrates (247 genes), cofactors, vitamins, prosthetic groups, pigments (153 genes), proteins (151 genes), nucleosides and nucleotides (106 genes), DNA (60 genes), virulence, disease, and defense (38 genes), membrane transport (33 genes), respiration (33 genes), and other metabolic processes. KUDC0405T did not appear to be motile and the genome contained no genes encoding proteins associated with motility. The OrthoVenn diagram revealed orthologous protein clusters of strain KUDC0405T, M. bovistercoris NEAU-LLET, and M. pseudoresistens CC-5209T shared 1,510 orthologous protein clusters , T3PKS1 , T3PKS2, RRE-containing , and terpene . In the case of ANIm, <20% of the genome was aligned for M. bovistercoris NEAU-LLET, and the alignment was assigned as suspicious by the software. In silico, AAI values were analysed at 64.7% and 65.0% in strain KUDC0405T, M. bovistercoris NEAU-LLET, and strain KUDC0405T and M. pseudoresistence CC-5209T, respectively. Also, GGDC results for strains KUDC0405T, M. bovistercoris NEAU-LLET, and M. pseudoresistence CC-5209T were calculated as 17.3% and 17.5% based on formula 2 (identities/HSP length). The ANIb, ANIm, AAI, and dDDH values of strain KUDC0405T compared with those of the closely related strains are presented in T represents a novel species of the Microbacterium genus.The complete genomes determined have been deposited in the NCBI GenBank database under accession number GCF_021582895 . The terT was gram-positive, non-spore forming, non-motile, and grew anaerobically on TSA. Colonies on TSA media were smooth, circular, yellowish-white, and the cells were rod-shaped (0.3\u20130.4 \u00d7 0.7\u20130.8 \u03bcm) . Growth f plants , 42. Theand urea .T was MK-12. The polar lipids included diphospharidylglycerol, glycolipid, phosphatidylglycerol, an unidentified phospholipid, three unidentified aminolipids, and an unidentified lipid , ornithine (26.8%), alanine (25.4%), and glutamic (15.4%) as cell-wall peptidoglycans. The major fatty acids in KUDC0405T were anteiso-C17:0 (35.2%), iso-C16:0 (16.3%), and iso-C17:0 (8.0%), and the minor components included iso-C15:0 (4.0%), C16:0 (2.6%), anteiso-C15:0 (2.5%), and C18:0 (1.5%). T and the most closely related reference strains. M. bovistercoris NEAU-LLET and M. pseudoresistence CC-5209T presented anteiso-C17:0 and anteiso-C15:0 as major fatty acids. The major fatty acids in the genus Microbacterium were anteiso-C17:0.The predominant menaquinone in KUDC0405ed lipid . DiphospCC-5209T . Strain T represents a novel species of the genus Microbacterium, for which we suggest the name M. elymi sp. nov..To conclude, we suggest that strain KUDC0405T produces siderophores and contains glycine, ornithine, alanine, and glutamic acid as cell-wall peptidoglycans. The polar lipids were diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and phospholipid; the major menaquinone was MK-12; and the major fatty acids were anteiso-C17:0 and iso-C16:0. The genomic DNA GC content was 70.4%.Cells are Gram-stain-positive, catalase- and oxidase- positive, non-spore forming, non-motile, facultatively anaerobic and rod-shaped (0.3\u20130.4 \u00d7 0.7\u20130.8 \u03bcm). Colonies are smooth, circular, yellowish-white, and 3.0\u20130.4 mm in diameter on TSA with growth for 2 days. Optimal growth occurs at 25\u201330\u00b0C, at pH 7, and 0.5\u20131.2%NaCl (w/v) on TSA media. Strain KUDC0405T (=KCTC 49411T =CGMCC1.18472T), was isolated from the rhizosphere of E. tsukushiensis collected from the Dokdo Islands, Republic of Korea. The GenBank/EMBL/DDBJ accession numbers for the partial 16S rRNA gene sequence and genome sequence of KUDC0405T were MT071892 and CP091139, respectively. NCBI accession number for genomes are GCF_021582895.The type strain, KUDC0405de novo assembly are as follows: genome size, 3,610,832 bp; number of contigs, 1; coverage, 119.0 \u00d7.General features of the genome http://jmb.or.kr.Supplementary data for this paper are available on-line only at"} +{"text": "Flavobacterium sediminilitoris YSM-43T, isolated from a tidal flat in Yeosu, Republic of Korea. The whole genome consists of one circular chromosome of 3,913,692\u2009bp. A total of 3,599 genes were predicted, comprising 3,537 coding DNA sequences (CDSs), 50 tRNAs, 9 rRNAs, and 3 noncoding RNAs (ncRNAs).Here, we report the complete genome sequence of Flavobacterium, the type genus of the family Flavobacteriaceae in the phylum Bacteroidetes, is a Gram-negative, yellow-pigmented, and rod-shaped bacterium. Commonly, Flavobacterium thrives in various habitats, including both terrestrial and marine ecosystems (Flavobacterium species have been published (https://lpsn.dsmz.de/genus/flavobacterium) . Accordicterium) , two Flailitoris , 5. F. sT was cultivated on marine agar 2216 (BD). The cells were collected in a 5-mL Eppendorf tube for DNA extraction. Extraction of genomic DNA was performed using a genomic DNA extraction kit (RBC), following the manufacturer\u2019s instructions. A spin column was utilized for DNA cleanup. The NanoDrop 2000 UV-visible (UV-vis) spectrometer was used for measuring the ratio of absorbance at 260/280\u2009nm and 260/230\u2009nm. The genomic DNA (gDNA) concentration was measured using a Qubit double-stranded DNA (dsDNA) high-sensitivity (HS) assay kit (Invitrogen) with a Qubit 2.0 fluorometer. The quantity and size distribution of the purified gDNA were calculated using Agilent 2200 TapeStation software (A.01.05) were assembled de novo using Flye version 2.8.3 with the parameter \u201casm-coverage 100\u201d (https://github.com/PacificBiosciences/pbbioconda). Then, the genome was rotated using the fixstart method in Circlator version 1.5.5 (YSM-43A.01.05) . For bio N50, 7,54\u2009bp weredata set . As a resee.ca/) . To assisee.ca/) , eggNOG-see.ca/) (Table\u00a01F. sediminilitoris YSM-43T has been deposited at GenBank under the accession number CP090145. The raw data have been deposited in the SRA under the accession number SRR17867805.The complete genome sequence of"} +{"text": "The medical novelty of COVID-19 requires a comprehensive study of its impact on various areas of human health, including mental health.To study the spectrum and severity of psychopathological disorders in previously healthy patients of different age groups who have had moderate and severe COVID-19 pneumonia.Immediately after stabilization of the physical condition, patients completed the Symptom Checklist-90-R, designed to assess 11 parameters: somatization (SOM), obsessive-compulsive (OS), interpersonal sensitivity (INT), depression (DEP), anxiety (ANX), hostility (HOS), phobic anxiety (PHOB), paranoid ideas (PAR), psychoticism (PSY). Patients with cognitive impairment were excluded.The study involved 148 patients aged from 26 to 84 years. In the general sample, psychopathological symptoms were detected mainly on the SOM, DEP, ANX, HOS scales. To a lesser extent - on the INT and PAR scales; were practically not determined on the PSY and PHOB scales. Most of the symptoms are significantly more intense in patients over 46 years old (n = 129) compared with the younger population . Older patients according to SOM revealed 1.23 points (IQR 0.5) versus 0.85 (IQR 0.7) among young people, DEP - 0.88 (IQR 0.44) vs. 0.47 (IQR 0.44), ANX - 0.66 (IQR 0.44) vs. 0.43 (IQR 0.29), OS - 0.55 (IQR 0.5) vs. 0.31 (IQR 0.25) and HOS - 0.46 (IQR 0.34) vs. 0.29 (IQR 0.09).Patients recovering from severe COVID-19 pneumonia require psychiatric evaluation and subsequent differentiated psychotherapeutic rehabilitation, especially for the age group over 46.No significant relationships."} +{"text": "Imaging with positron emission tomography (PET) plays a crucial role in patient selection prior to radioligand therapy and subsequent molecular response assessment. The presented study aims to investigate the role of quantitative uptake parameters on baseline 68Gallium-PSMA-11 PET/CT imaging as to their association with lesion response to radioligand therapy at individual tumor sites. Special emphasis is placed on the utility of PSMA-uptake thresholds for pretherapeutic prediction of lesion response.The prostate-specific membrane antigen (PSMA), a transmembrane protein frequently present on prostate cancer cells, has gained considerable interest as a target for both molecular imaging and therapy. Patients with metastatic castration-resistant prostate cancer can be successfully treated by delivery of beta particle-emitting 177Lu]Lu-PSMA-617. This study aims to quantify lesion-based response to RLT in relation to pretreatment standard molecular imaging metrics derived from [68Ga]Ga-PSMA-11 PET/CT. Sixty-one patients with mCRPC underwent [68Ga]Ga-PSMA-11 PET/CT imaging before and after a median of 4 (IQR 2\u20136) RLT cycles. Maximum and mean standardized uptake values , as well as tumor-to-liver ratio (TLR), were assessed. A median of 12 (IQR 7\u201317) lesions was analyzed per patient, resulting in a total of 718 lesions. Lesions with \u226530% SUVmax decline or falling below the blood pool uptake were considered responsive; \u226530% SUVmax increase marked lesion progression. Additionally, 4-point visual scoring was performed according to E-PSMA consensus. In total, 550/718 (76.6%) lesions responded to RLT, including 389/507 (76.7%) bone metastases and 143/181 (79.0%) lymph node metastases. Baseline SUVmax, SUVmean, and TLR values were associated with lesion response by a moderate but significant correlation . For the classification of lesion progression based on baseline PSMA uptake, receiver operating characteristics (ROC) found SUVmax, SUVmean, and TLR to have comparable discriminatory value . Of 42 tumor sites with baseline uptake below the liver (V-score < 2), 19/42 (45.2%) were responsive, 9/42 (21.4%) were stable, and 14/42 (33.3%) showed progression, leaving liver uptake a threshold with low prognostic value for the identification of RLT-refractory lesions (PPV 33%). This was observed accordingly for various liver uptake-based thresholds, including TLR < 1.5, <2.0 with a PPV at 24%, 20%, respectively. Standard uptake parameters quantified by routine baseline [68Ga]Ga-PSMA-11 PET/CT are moderately associated with post-treatment lesion response to [177Lu]Lu-PSMA-617. Commonly applied liver-based uptake thresholds have limited value in predicting refractory lesions at individual tumor sites.Baseline uptake on prostate-specific membrane antigen (PSMA)-targeted imaging is a prerequisite for radioligand therapy (RLT) with [ Inclusion criteria mandated that patients receive [68Gallium was obtained from a 68Ge/68Ga radionuclide generator . [68Ga]Ga-PSMA-11 was administered by intravenous injection and target activity per patient was 1.8\u20132.5 MBq/kg body weight. Whole-body images (vertex to mid-thigh) were acquired 61 \u00b1 12 min after tracer injection and PET acquisition time was 4 min per bed position. CT data were acquired for attenuation correction and anatomical localization using an X-ray tube voltage of 130 kV with a modulated tube current . Acquisitions were carried out on a Biograph 6 PET/CT scanner , with decay, scatter, and attenuation correction performed in accordance with the procedure guidelines set out by the joint EANM and SNMMI consensus statement Lu-PSMA-617 was administered by slow intravenous injection over 30\u201360 s, preceded and followed by 1000 mL of saline infusion. RLT was performed as an inpatient procedure at the nuclear medicine therapy ward in accordance with radioprotection regulations. Six cycles with an activity of 7.4 GBq per cycle were intended; administered activities were modified in patients with potential risks for toxicity.Radiolabeling of PSMA-617 with n detail . [177Lu]s). Receiver operating characteristics (ROC) analysis was applied to determine the ability of baseline PET/CT metrics to predict treatment lesion progression at individual sites. The area under the curve (AUC) was calculated for all lesions and separately for bone metastases and lymph node metastases. Site-specific cutoff values for the detection of PL were calculated using Youden\u2019s J statistic. Various liver-based thresholds were tested as to their discriminatory value for lesion progression. Odds ratios (OR) were calculated with 95% confidence intervals (CI). Statistical analyses were performed with SPSS and GraphPad Prism . All tests were two-sided, with p-values < 0.05 denominating statistical significance.Results are presented as median with interquartile range (IQR) and mean \u00b1 standard deviation (SD) for continuous variables. Categorical variables are reported as frequencies with respective percentages. Comparison of means was performed by a paired t-test for intraindividual analysis or by using a Mann-Whitney U test if data were not normally distributed. Association of categorical parameters was analyzed using non-parametric rank correlation (Spearman\u2019s correlation coefficient denoted with r68Ga]Ga-PSMA-11 PET/CT imaging and subsequently underwent a median of 4 (IQR 3\u20136) cycles of [177Lu]Lu-PSMA-617 given with a mean treatment activity of 6.9 \u00b1 1.4 GBq per cycle. Cumulative activity per patient was 29.0 \u00b1 17.5 GBq. Of all patients, 31/61 (50.8%) showed \u226550% PSA decline 12 weeks after treatment initiation, while 15/61 (24.6%) showed PSA progression based on PCWG3 criteria (\u226525% PSA increase).Overall, 718 lesions were included in the analysis, consisting of 507 bone, 181 lymph node, 22 visceral, and 8 primary/locally recurrent sites in 61 patients with mCRPC (median age 72 [IQR 67\u201378] years). This corresponded to a median 12 (IQR 7\u201317) lesions per patient. Patient characteristics at baseline are detailed in max of 14.11 (IQR 8.25\u201323.01) and SUVmean of 8.72 (IQR 5.09\u201314.39); tumor-to-liver ratio (TLR) was 3.36 (IQR 1.98\u20135.70). Of all lesions, 550/718 (76.6%) responded to RLT, consisting of 389/507 (76.7%) bone metastases and 143/181 (79.0%) lymph node metastases. There was no significant difference in mean SUVmax decline in bone vs. lymph node metastases (p = 0.23). Responding lesions (RL) had significantly higher SUVmax, SUVmean, and TLR values at baseline than stable (SL) or progressive lesions (PL), with an SUVmax at 16.01 (RL), 10.82 (SL), 5.11 (PL) (p < 0.001), SUVmean at 9.88 (RL), 6.62 (SL), 3.18 (PL) (p < 0.001), and TLR at 3.89 (RL), 2.55 (SL), 1.36 (PL) (p < 0.001). This was observed in both lymph node and bone metastases ; the relationship is shown in Details on lesion characteristics are provided in tastases , Table 268Ga]Ga-PSMA-11 PET/CT imaging are provided in The course of all lesions per patient is depicted in max, SUVmean, and TLR values. The area under the curve (AUC) was comparable for SUVmax, SUVmean, and TLR with 0.85, 0.87, and 0.83, respectively , with the corresponding SUVmean and TLR thresholds at 4.85 and 1.76 . While liver-based thresholds allowed the stratification of lesions based on their response category in a balanced manner, their value is limited for prognostication, as shown for various liver-derived thresholds in ROC analysis was performed to classify lesion progression based on pretherapeutic SUVectively . Cutoff max decline \u2265 30%) or non-detectability; 28/42 (66.7%) lesions were non-progressive (i.e. SL/RL). Lesions declining to an uptake below the blood pool after RLT (V-score = 0) had lower uptake values at baseline than lesions showing posttherapeutic V-scores \u2265 1 with SUVmax 10.63 vs. 14.89 (p = 0.002), SUVmean 6.78 vs. 9.15 (p = 0.009), and TLR 2.71 vs. 3.48 (p < 0.001) (p = 0.09).In addition to semiquantitative PET measurements, visual scoring (V-score) was noted for all lesions. The V-score change from baseline to posttherapeutic PET assessment was registered, as depicted in < 0.001) B. A mino68Ga]Ga-PSMA-11 PET/CT at baseline are moderately associated with lesion response to [177Lu]Lu-PSMA-617 RLT. Low uptake lesions were more frequently subject to progression, whilst addressable by RLT in a significant fraction of cases. Baseline metrics and liver-based thresholds had only limited value for single-lesion response prediction.This study indicates that routine PET parameters assessed by [177Lu]Lu-PSMA-617 RLT have proven that a higher density of the transmembrane glycoprotein PSMA on prostate cancer cells is associated with increased ligand internalization and treatment efficacy Ga-PSMA-11 PET/CT are moderately associated with lesion response to [177Lu] Lu-PSMA-617. Lesions with uptake values below the liver uptake remain non-progressive in the majority of cases examined in this cohort. Non-dominant tumor sites with low PSMA expression should thus not preclude patients from undergoing RLT.Standard uptake parameters quantified by routine baseline ["} +{"text": "Dear Editor,TET2 is one of the most frequently mutated genes in myeloid malignancies . Mor. MorTET2MPN Fig. 6]. Col. ColTET2Nup98-HoxD13 (NHD13) transgenic mouse model, in which ~30% of mice develop AML. Interestingly, TET2 levels were lower in c-kit+ bone marrow (BM) cells of leukemia-transformed NHD13 mice relative to age-matched NHD13 mice, which developed MDS exclusively or corresponding control (Tet2fl/fl) mice with NHD13 mice and monitored leukemia development following poly(I:C) treatment on both genotypes counts, splenomegaly and hyper-cellularity in BM, while age-matched NHD13/Tet2-WT mice exhibited only cytopenia . At that time point, neither genotype showed signs of leukemia population relative to those of Tet2-WT NHD13 mice, whereas the Lin-c-kit+Sca-1+ (LSK) population was unchanged by Tet2 deletion from pre-leukemic NHD13/Tet2-KO or corresponding control NHD13 mice into lethally-irradiated secondary recipients to assess leukemogenicity. As expected, NHD13/Tet2-KO cell transplantation increased the percentage of CD45.2+ cells and WBCs in peripheral blood (PB) relative to NHD13/Tet2-WT cells from WT or Tet2-KO mice pool.To define mechanisms underlying MDS progression, we evaluated the mia Fig. , but Tetice Fig. . Importaon Figs. and S2E.-KO Fig. . Within ice Fig. . Moreovells Fig. or that nes Fig. . In the D13 Fig. . Tet2-KOlls Fig. . We nextls Figs. . By 16 w PB Fig. . Notablynts Fig. . Moreoveice Fig. and obseTet2 loss in HSPCs can lead to hypermutagenicity [+ cells from pre-leukemic NHD13/Tet2-KO vs. matched NHD13/Tet2-WT mice. Relative to NHD13/Tet2-WT mice, we observed 271 newly acquired alterations and 199 alterations with increased variant allele frequency in NHD13/Tet2-KO mice and ranked them based on association with AML prognosis (http://precog.stanford.edu) and mutation ratio (mutation ratio >0.5) promoted the greatest increase in colony and cell number of NHD13 c-kit+ cells Table . Accordi.5) Fig. . Pairwisons Fig. . To assesay Fig. . In the lls Fig. . Howeverity Fig. , indicatARIH2 function in leukemogenesis, we retrospectively analyzed GEO datasets and observed lower ARIH2 expression associated with shorter survival in MDS and AML patients did not, and cells harboring the mutant exhibited a growth advantage relative to ARIH2WT cells compared to those with TET2-WT or ascorbate . Relative to vehicle-treated NHD13/Tet2-KO recipients, ASC treatment in NHD13/Tet2-KO mice significantly decreased WBC counts and the frequency of c-kit+ BM cells from two TET2 mutant high-risk MDS patients (Table + cells (Fig. Given that vitamin C treatment mimics effects of toration , we treals Figs. and S6A.mia Fig. . Notably KD Fig. . Moreovency Fig. . Finallyts Table showed tlls Fig. .In summary, our results indicate that TET2 activity prevents further transformation of MDS HSPCs by decreasing the occurrence of secondary mutations, and that pharmacological enhancement of TET activity may represent an optimal strategy to block MDS malignant transformation.Supplementary data"} +{"text": "Continuous emergence of the Omicron variant, along with its subvariants, has caused an increasing number of infections, reinfections, and vaccine-breakthrough infections, seriously threatening human health. Recently, several new Omicron subvariants, such as BA.5, BA.2.75, BA.4.6, and BF.7, bearing distinct mutation profiles in their spike (S) proteins, have significantly increased their capacity to evade vaccine-induced immunity and have shown enhanced infectivity and transmissibility, quickly becoming dominant sublineages. In this study, we found the S proteins of these Omicron subvariants to have 2- to 4-fold more efficient membrane fusion kinetics than that of the original Omicron variant (BA.1), indicating that these novel Omicron subvariants might possess increased pathogenicity. We also identified that peptide-based pan-CoV fusion inhibitors, EK1 and EK1C4, showed equal efficacy against membrane fusion mediated by S proteins of the noted Omicron subvariants and infection by their pseudoviruses. Additionally, either immune sera induced by wild-type (WT) SARS-CoV-2 RBD-based vaccine or BA.2 convalescent sera showed potent synergism with EK1 against both WT SARS-CoV-2 and various Omicron subvariants, further suggesting that EK1-based fusion inhibitors are promising candidates for development as clinical antiviral agents against the currently circulating Omicron subvariants. In late 2021, the Omicron variant B.1.1.529/BA.1 was first identified in South Africa and quickly spread to many countries ,4. SubseDifferent Omicron subvariants contain distinct mutation profiles, especially in their S proteins, well known to play a crucial role in mediating viral infection. Compared with WT SARS-CoV-2 S protein, Omicron BA.1 contains more than 30 spike mutations. In particular, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, and Y505H mutations are known to occur in the Omicron BA.1 receptor binding domain (RBD) . Such mutations significantly alter the conformation of RBD in S protein and, hence, seriously threaten clinical vaccine efficacy . BA.2.12in vivo [Previous studies reported that S-mediated fusogenicity plays an important role in viral pathogenesis . For exain vivo . On the in vivo . NeverthAfter receptor engagement, heptad repeat 1 (HR1) and 2 (HR2) regions in the S2 subunit of coronavirus S protein interact to form a six-helix bundle (6-HB) structure, which, in turn, drives viral fusion with and entry into the host cell . Our preIn the current study, we found that the recently emerging Omicron subvariants showed strengthened fusion kinetics, particularly BA.2.75, BA.4.6, BA.5, and BF.7, compared to that of BA.1, indicating that they possess increased pathogenicity. Although these circulating Omicron subvariants carry distinct mutation profiles in S protein, their HR1 functional domains remain conserved. Accordingly, we found that our EK1-based fusion inhibitors maintainWe first evaluated the fusogenicity of different Omicron subvariants. To mimic authentic viral fusion with target cells, as mediated by S protein, their S proteins were expressed on the membrane surface of 293T-GFP cells, as effector cells (293T-S-GFP) of 142.02, 172.45 and 65.84 nM, respectively, while EK1C4 showed even more efficacy with IC50s ranging from 3.67 nM to 5.07 nM . On BA.21/2: 24h) and potential oral bioavailability by targeting SARS-CoV-2 HR1 in S2 subunit and RBD in S1 subunit [To further assess the efficacy of EK1-based pan-CoV fusion inhibitors against Omicron subvariants, we developed lentivirus-based nonreplicative pseudovirus systems for these Omicron subvariants. Such constructs can effectively mimic the entry process of authentic virus and are, therefore, widely used to evaluate antiviral agents . Both EK subunit . At the subunit . These f subunit and IPB2 subunit , respectCurrently, more than 12 billion vaccine doses have been administered globally , includiSince both RBD and HR1 are key in mediating viral entry , it is rMore importantly, WT-RBD-immunized mouse sera showed weak inhibitory activity against BA.2.12.1 and BA.2.75 with 31.4% and 33.1% inhibition, respectively, as did EK1 (100 nM) with 33.2% and 30.6% inhibition, respectively. However, when combined, they showed increased efficacy to 62.3% inhibition on BA.2.12.1 and 63% inhibition against BA.2.75 alone showed moderate inhibitory activity against the BA.2.12.1 sublineage with 64.6% inhibition, but little efficacy against BA.2.75, BA.4/BA.5, BA.4.6, BF.7, and WT SARS-CoV-2 . However, BA2-convalescent sera, when combined with low-dose EK1 (100 nM), showed significantly improved efficacy against BA.2.12.1, BA.2.75, BA.4/BA.5, BA.4.6, and BF.7 in the range of 57.9% to 83.0% inhibition ; HeLa and Caco2 cell lines were from the Chinese Academy of Science Cell Bank . 293T/ACE2 cells were preserved in our laboratory. All cell lines were cultured in Dulbecco\u2019s Modified Eagle\u2019s Medium (DMEM) with 10% fetal bovine serum (FBS). Plasmids, including pAAV-SARS-CoV-2-S-D614G-IRES-EGFP, pAAV-SARS-CoV-2-S-Delta-IRES-EGFP, pAAV-SARS-CoV-2-S-Omicron-IRES-EGFP, and PC-hACE2/horse_ACE2/cattle_ACE2/swine_ACE2/rabbit_ACE2/civet_ACE2/ bat_ACE2, were synthesized or preserved in our laboratory. Peripheral blood samples were collected from a convalescent BA.2 patient. Serum sample was isolated from centrifuged blood sample for inhibiting pseudovirus infection with 1:500 dilution. All collections were conducted according to the guidelines of the Declaration of Helsinki and approved by the Institutional Review Board of the Ethics Committee of Shanghai Fourth People's Hospital (2022095-001).Briefly, WT SARS-CoV-2 RBD-Fc (5 \u00b5g) formulated with an equal volume of Imject Alum adjuvant (Thermo Scientific) was used to vaccinate Balb/c mice (six-week-old) three times at two-week intervals, as previously described ,35. At tWestern blot was performed using an anti-SARS-CoV-2 S antibody and an anti-actin antibody, as previously described . BrieflyPlasmid pAAV-IRES-S-EGFP, encoding S protein and EGFP, was transfected into 293T effector cells (293T/S/GFP). Caco2 cells, naturally expressing human ACE2 receptors on the membrane surface, were used as target cells. 293T cells, transfected with plasmid pAAV-IRES-EGFP (293T/EGFP), were used as negative control. Effector cells (293T/S/GFP) were collected and resuspended. Free effector cells were added into target cells for coincubation for indicated time at 37 \u00b0C and then observation under the fluorescence microscope.HIV-1 backbone-based Pseudovirus (PsV) bearing wild or mutant SARS-CoV2 S protein was produced, as previously described . Caco2 ct-test and ANOVA test. P values less than 0.05 were significant; **P\u2009<\u20090.01; ***P\u2009<\u20090.001. The concentration for half inhibition (IC50) was calculated by CalcuSyn software [Statistical analyses were carried out using GraphPad Prism 8.0. Analyses of independent data were carried out through Student\u2019s unpaired two-tailed software .Click here for additional data file."} +{"text": "In 2019, the World Health Organization (WHO) endorsed thermal ablation (TA) for use within \u201cscreen-and-treat\u201d cervical cancer prevention programs in low- and middle-income countries (LMICs), including among women living with HIV (WLWH). We evaluated TA efficacy for treatment of biopsy-confirmed cervical intraepithelial neoplasia grades 2 and 3 (CIN2/3) among WLWH in western Kenya .Between August 2019 and November 2020, WLWH age 25-65 years underwent high-risk human papillomavirus (hrHPV) self-collection. hrHPV-positive women underwent colposcopy-directed biopsies, and thermal ablation treatment if eligible per WHO guidelines. Women with biopsy-confirmed CIN2/3 had colposcopy-directed biopsies at 12-months to determine treatment efficacy.Sixty-eight hrHPV-positive WLWH with biopsy-confirmed CIN2/3 at baseline; 14 CIN2, 54 CIN3, underwent thermal ablation. Mean age and parity were 41.2 years and 4, respectively. The mean CD4 count was 473.98 cells/mm3 and 96.9% had HIV viral suppression. Fifty-eight women (83.8%) have been seen for a 12-month follow-up visit, and pathology results are available for 54 (79.4%). Of these, 35 (66.0%) had successful treatment, defined as biopsy-confirmed CIN1 or normal findings 12-months following treatment, while 18 (34.0%) had treatment failure - persistent biopsy-confirmed CIN2/3. Treatment failure was 23.1% 95% CI (13.0 to 45.9) and 37.5%, 95% CI (22.1 to 52.0) among women with CIN2 and CIN3 at baseline, respectively.Hand-held thermal ablation devices are affordable, portable, easy to use, and hence highly scaleable within screen-and-treat programs in LMICs. However, our preliminary results, with rigorous disease status verification at both baseline and follow-up find higher than previously reported treatment failure rates for CIN3 among WLWH, a high-risk population for cervical cancer. If replicated by larger studies, this highlights a potential limitation of the current WHO cervical cancer elimination strategy, calling for better risk stratification in this population, and/or consideration of adjuvant therapy to prevent CIN2/3 recurrence following thermal ablation."} +{"text": "Dysregulation of epigenetic mechanisms have been depicted in several pathological consequence such as cancer. Different modes of epigenetic regulation (DNA methylation (hypomethylation or hypermethylation of promotor), histone modifications, abnormal expression of microRNAs (miRNAs), long non-coding RNAs, and small nucleolar RNAs), are discovered. Particularly, lncRNAs are known to exert pivot roles in different types of cancer including breast cancer. LncRNAs with oncogenic and tumour suppressive potential are reported. Differentially expressed lncRNAs contribute a remarkable role in the development of primary and acquired resistance for radiotherapy, endocrine therapy, immunotherapy, and targeted therapy. A wide range of molecular subtype specific lncRNAs have been assessed in breast cancer research. A number of studies have also shown that lncRNAs may be clinically used as non-invasive diagnostic biomarkers for early detection of breast cancer. Such molecular biomarkers have also been found in cancer stem cells of breast tumours. The objectives of the present review are to summarize the important roles of oncogenic and tumour suppressive lncRNAs for the early diagnosis of breast cancer, metastatic potential, and chemotherapy resistance across the molecular subtypes. Epigenetic dysregulations have a crucial impact on the development and progression of human cancers, including breast cancer . Epigenep = 0.003) in malignant samples could separate it breast cancer samples from normal control and correlated with advanced TNM stage (p = 0.002), poorer pathological differentiation (p = 0.004), and shorter overall survival (SOS) and disease-free survival (DFS) (p < 0.0001) in progesterone receptor (PR) positive cancer tissues (p < 0.00001). Moreover, validation using gene expression omnibus data sets and 100 breast cancer patients confirmed similar results . A meta- tissues . Moreove results . Based o results . Higher results . Additio results . Chen et results . Further results .via the regulation of SNCG (Synuclein Gamma) expression during cancer progression. LncRNA HOXD-AS1 interacts with miR-421 and inhibits its expression leading to the upregulation of SOX4, a master regulator of EMT . Similarpression . High expression . Zheng epression . In addipression . Also, hpression . Si et apression . Further-5p axis .via increasing Checkpoint kinase 2 (CHK2) phosphorylation , PARP (cleaved-Caspase-3 and cleaved-poly adenosine diphosphate-ribose polymerase) had elevated expression in low expression lncRNA BANCR group . Liu et pathway . Elevate pathway . Further pathway . The exp pathway .It was observed that lncRNAs can also regulate several cancers associated signalling pathways, including the activation of transcription factors, such as nuclear factor kappa B (NF-\u03baB). For example, overexpressed lncRNA NKILA bound to NF-\u03baB/I\u0138B masked its phosphorylation. This interaction prevented the over-activation of the NF-\u03baB pathway in inflammation stimulated breast epithelial cells . Accordivia modulation of miR-200b/axis/Wnt/\u03b2-catenin pathway signalling pathway . Dysreguviz., lncRNA YIYA regulates CDK6 (cell division protein kinase 6) dependent phosphorylation of PFKFB3 (fructose bis-phosphatase PFK2), and thus can convert glucose 6-phosphate (G6P) to fructose-2,6-phosphate gene in breast cancer (via modulating the expression of miR-4766-5p and SIRT1 (Sirtuin 1) genes (in situ hybridization) and Western blot assays in MCF-7 and MDA-MB-231 breast cancer cell. Luciferase reporter assay validated that RHPN1-AS1 inhibits miR-4261 and regulates the direct transcriptional target of c-Myc (Immunoprecipitation assays provided evidence that lncRNA H19 regulated the expression of t cancer . The res1) genes Higher eof c-Myc .p = 0.0086) . Huang a 0.0086) . Another systems . Accordi systems .Oncogenic lncRNA LINC02163 was found to be involved in breast cancer pathogenesis by mode of LINC02163/miR-511-3p/HMGA2 (high mobility group A proteins 2) axis . The finLi and et al. found that upregulation of lncRNA ZFHX4-AS1 suppresses FAT4 and increases YAP1 (yes-associated protein 1) and TAZ (Tafazzin) gene expression which is attributed to breast cancer cell proliferation . A reporp = 0.022), lymph node metastasis (p = 0.020), and higher Ki-67 positivity (p = 0.017). A multivariate analysis suggested that a low level of lncRNA EGOT acts as an independent prognostic factor for poor survival rate in breast cancer patients (There are a number of lncRNA whose downregulation contributes in breast cancer development and progression . A meta-= 0.039) . Further= 0.039) . Yang et= 0.039) . Low relvia modulating expression of cyclin A2, CDK2, p-Akt, p-p44/42 MAPK, and p-p38 MAPK cancer signalling molecules (in-vivo and in-vitro model system induced the EMT process in cancer via regulation of PI3K (phosphatidylinositide-3 kinase)/Akt pathways. Therefore, MALAT1 may act as a promising therapeutic target for breast cancer metastasis via the PI3K-Akt pathway expression. Thus, the results suggested that lncRNA MAGI2-AS3 has the potential to serve as an anticancer therapeutic candidate . Tumour olecules . Similarolecules . LncRNA olecules . Downreg pathway .A study by via the miR-190b-5p/MYLIP (Myosin regulatory light chain interacting protein) axis, thus providing evidence for potential therapeutic targets for breast cancer patients and its binding with co-activator YAP1, leading to reduced metastatic ability . Anotherpatients . On the patients .in situ (DCIS) breast cells identified lncRNA LINC00885 expression in both normal and ductal carcinoma st cells . Expressst cells . Overexpst cells . Similarst cells . Furtherst cells . In addist cells .Gene expression profiling deciphered the breast cancer into four distinct molecular subtypes such as Luminal, Her2+, Her2 enriched, TNBC, and basal like. Patients with same molecular subtype responded differently to targeted therapy and showed diverse clinical outcomes. However, the exact underlying mechanism for molecular heterogeneity remains to be elucidated. Many researchers have evaluated molecular subtype specific lncRNAs expression in breast cancers and suggested its involvement in cancer molecular heterogeneity . Computain-vivo and in-vitro systems gene expression restoration . Further systems . Another systems . Greater systems . Presenco ELAVL1 . Beltr\u00e1no ELAVL1 . Higher o ELAVL1 . By asseo ELAVL1 . Another pathway . Wang et pathway . RNA imm pathway . Further pathway .via targeting miR-205 , and ALDH1 (Aldehyde dehydrogenase 1) marker\u2019s expression . Similar miR-205 . Microar miR-205 . LncRNAs miR-205 .Chemotherapy resistance is the major cause of cancer related deaths. LncRNAs have a key role in developing resistance against radiotherapy, chemotherapy, immunotherapy, and targeted therapy. Inhibition of lncRNA LINC02582 expression increased radiosensitivity miR-200c/LINC02582/CHK1 in breast cancer samples . LncRNA via the H19/SAHH/DNMT3\u00df (DNA (cytosine-5)-methyltransferase 3 beta) axis, contributed to tamoxifen resistance in breast cancer . BermejoLong ncRNAs like H19 and XIST were discovered in the pre-genomic era, but were not fully characterized and explored until the early 2000s . Inventi"} +{"text": "Sotrovimab, a monoclonal antibody with efficacy against SARS-CoV-2 including certain Omicron variants, has been used in treatment of mild-moderate COVID-19. Limited data exists regarding its use in pregnant women.Electronic medical record review of pregnant COVID-19 patients treated with sotrovimab from 12/30/21-1/31/22 was performed. Included were pregnant individuals \u2265 12 years, weighing \u2265 40 kg, with positive SARS-CoV-2 test (within 10 days). Those receiving care outside YNHHS or receiving other SARS-CoV-2 treatment were excluded. We assessed demographics, medical history, and Monoclonal Antibody Screening Score (MASS). Clinical outcomes assessed included emergency department (ED) visit < 24 hours, hospitalization, ICU admission, and/or death within 29 days of sotrovimab. Pregnancy and neonatal outcomes were assessed until 8/15/22.2. Sixty-three percent were Caucasian, 9% Hispanic, 14% African-American, and 9% Asian. Nine percent had diabetes and sickle cell disease. Five percent had well-controlled HIV. Eighteen percent, 46%, and 36% received sotrovimab in trimester 1, 2, and 3, respectively. No infusion/allergic reactions occurred. MASS values were < 4. Only 12/22 (55%) received complete primary vaccination ; none received a booster.Among 22 subjects, median age was 32 years and body mass index was 27 kg/mThere were no ICU admissions nor deaths. One subject was hospitalized for post-partum pyelonephritis; another had an ED visit for post-partum vaginal bleeding. Median gestational age at birth was 38.9 weeks. Nine percent had premature labor and premature rupture of membranes, respectively. Median infant birth weight was 3220 g. One neonate required an ICU stay due to prenatally diagnosed omphalocele (before sotrovimab) in a mother with congenital defect history. There were no abortions, fetal loss, or other birth/neurodevelopmental defects.Pregnant COVID-19 patients receiving sotrovimab at our center tolerated it well with good clinical outcomes. Pregnancy and neonatal complications did not appear sotrovimab-related. Though a limited sample, our data helps elucidate the safety and tolerability of sotrovimab in pregnant women.All Authors: No reported disclosures."} +{"text": "Waning protection against emerging SARS-CoV-2 variants by pre-existing antibodies elicited because of current vaccination or natural infection is a global concern. Whether this is due to the waning of immunity to SARS-COV-2 remains unclear.We aimed to investigate the dynamics of antibody isotype responses amongst vaccinated na\u00efve (VN) and naturally infected (NI) individuals.n\u2009=\u2009100) in two phases: phase-I (P-I) at ~\u20091.4 and phase-II (P-II) at ~\u20095.3\u00a0months. Antibody levels were compared with those of unvaccinated and naturally infected subjects at ~\u20091.7 (P-1) and 5.2 (P-II) months post-infection. Neutralizing antibodies (NTAb), anti-S-RBD-IgG, -IgM and anti-S-IgA isotypes were measured.We followed up antibody levels in COVID-19 messenger RNA (mRNA)-vaccinated subjects without prior infection than the NI group at P-I, except for IgM. In the VN group, a significant waning in antibody response was observed in all isotypes. There was about an ~ 4-fold decline in NTAb levels (P\u2009<\u20090.001), anti-S-RBD-IgG , anti-S-RBD-IgM and anti-S1-IgA . In the NI group, a significant but less steady decline was notable in S-RBD-IgM , and a much smaller but significant difference in NTAb anti-S-RBD IgG . Unlike the VN group, the NI group mounted a lasting anti-S1-IgA response with no significant decline. Anti-S1-IgA, which were\u2009~\u20093-fold higher in VN subjects compared with NI in P-1 (P\u2009<\u20090.001), dropped to almost the same levels, with no significant difference observed between the two groups in P-II.The VN group elicited significantly greater antibody responses (Whereas double-dose mRNA vaccination boosted antibody levels, vaccinated individuals\u2019 \u2018boost\u2019 was relatively short-lived. The recent Coronavirus disease 19 (COVID-19) outbreak caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has put the globe in an emergency state.,On 21 December 2020, Qatar initiated a mass COVID-19 vaccination programme, first utilizing the BNT162b2 vaccine and then the mRNA-1273 (Moderna) vaccine.,,When vaccination was ramped up, the country had two back-to-back waves from January to June 2021, mainly dominated by the B.1.1.7 and B.1.351 (or beta) variants.According to current evidence, patients vaccinated against COVID-19 would lose around half of their neutralizing antibodies (NTAb) ~\u2009108\u00a0days post-vaccination.Although vaccine-induced immunity is being extensively studied, the body of evidence for infection-induced immunity is very limited and insufficient to establish an antibody titre threshold that shows whether a person is protected from infection.n\u2009=\u2009100) who had received two doses of the two approved mRNA vaccines in Qatar: BNT162b2 and mRNA-1273. Levels were compared with those of unvaccinated but NI subjects (n\u2009=\u200940). Venous blood samples were collected from vaccines in two phases: phase 1 (P-I) and phase (P-II). For the VN group, P-I samples were collected at 1.4\u00a0months (median\u2009=\u20096\u00a0weeks) and P-II samples were collected at 5.3\u00a0months (median\u2009=\u200923\u00a0weeks) after the second dose. For the NI group, P-I samples were collected at ~\u20091.7\u00a0months (median\u2009=\u20097\u00a0weeks) and P-II samples were collected at 5.2\u00a0months (median\u2009=\u200922\u00a0weeks) post-infection with SARS-CoV-2.The study was reviewed and approved by the Institutional Review Board at Qatar University (QU-IRB 1537-FBA/21). The study\u00a0included VN participants , i\u2009\u2265\u20091.00 Positive (IgM antibodies to SARS-CoV-2 detected). Architect automated chemiluminescent assay was used to test the samples for the previous infection by measuring the SARS-CoV-2 anti-nucleoprotein IgG antibodies (anti-N), considering that the IgG antibodies produced against the RBD on the spike protein are different from the IgG antibodies produced against the nucleoprotein of the virus. Therefore, the positive anti-N results of SARS-CoV-2 anti-nucleoprotein IgG antibodies indicate previous exposure to the whole virus.After blood collection, plasma was separated by centrifugation and heat-inactivated. Serological testings were performed using the automated analyser CL-900i\u00ae from Mindray Biomedical Electronics 20-22 to detect: (1) NTAb were measured using the automated analyser CL-900i\u00ae. This assay is a competitive binding chemiluminescent immunoassay for the quantitative determination of SARS-CoV-2 NTAb that blocks the interaction between the receptor binding domain (RBD) of viral spike protein (bound on magnetic beads) and the enzyme-conjugated ACE2 surface receptor. Phosphate-buffered saline (PBS) was used to dilute the samples with readings higher than the mentioned range. The assay has a WHO conversion factor of 1\u00a0AU\u2009=\u20093.31\u00a0IU/mL, and the reference range is 10\u00a0AU/mL to 400\u00a0AU/ml. We recently evaluated this novel assay and reported high specificity and sensitivity against two reference methods.P-values were two-sided at a significance level of 0.05.GraphPad Prism software was used to perform the statistical analysis. Continuous variables were summarized using geometric means and 95% confidence intervals (95% CIs). The collected dataset was subjected to the Shapiro\u2013Wilk normality test to evaluate the data\u2019s normality. Because of the absence of normal distribution, nonparametric tests were performed using Wilcoxon rank-sum test for pairwise group comparisons and Mann\u2013Whitney U to test for the differences between independent samples. In the different scatter plots, the central horizontal bar line shows the geometric mean titre, and the error bars show the 95% CIs. All n\u2009=\u2009100) had no previous history of infection and received two doses of either BNT16b2 or mRNA-1273. After receiving the second dose in P-I and P-II, the median weeks were 6 (1.4\u00a0months) and 23 (5.3\u00a0months) weeks, respectively (n\u2009=\u200940) were unvaccinated COVID-19-recovered individuals. In P-I 1 and P-II, the median weeks were 7 (~ 1.7\u00a0months) and 22 (5.2\u00a0months) weeks post-COVID-19 infection, respectively. The NI group comprised 20% females and 80% males and 26% (12/47), respectively. In P-II, 100% remained positive for anti-S-RBD IgG and 99% (99/100) were positive for NTAb antibodies. The anti-S1-IgA positivity rate dropped to 92% (86/93), and only 2% (1/47) remained positive for the IgM.Amongst the NI participants in P-1, the positivity rate for NTAb antibodies was 90% (35/39). For anti-S-RBD-IgG, IgM and IgA, the positivity rates were 100 (31/31), 43 (17/40) and 72% (23/32), respectively. In P-II, 90% (35/39) were positive for NTAb antibodies. However, the positivity rates dropped to 97 (30/31), 13 (5/39) and 66 (21/32) for anti-S-RBD-IgG, -IgM and -IgA, respectively.P\u2009<\u20090.001) in the levels of NTAb antibodies was observed, from the geometric mean 1328.4 (95% CI: 1086.5\u20131624.2) to 317.94\u00a0IU/mL (95% CI: 261.5\u2013386.5\u00a0IU/mL) (P\u2009<\u20090.001) was observed in the levels of anti-S-RBD-IgG antibody levels from the geometric mean 1950.93 (95% CI: 1617.5\u20132353.1) to 366.107 BAU/mL (95% CI: 294.4\u2013455.20) (P\u2009<\u20090.001) from the geometric mean 0.56 (95% CI: 0.4\u20130.8) to 0.09 (95% CI: 0.04\u20130.25) (P\u2009<\u20090.0001) from the geometric mean 6.30 (95% CI: 5.4\u20137.3) to 3.19 (95% CI: 2.6\u20133.9) . A signi\u2013455.20) . IgM dec04\u20130.25) . The lev2.6\u20133.9) .P\u2009<\u20090.001), from the geometric mean 157.3\u00a0IU/mL, 95% CI: 108.7\u2013227.7 to 107.0\u00a0IU/mL, 95% CI: 80.42\u2013142.3 (P\u2009<\u20090.001) from the geometric mean 66.54 (95% CI: 36.81\u2013120.3) to 58.65 BAU/mL (95% CI: 37.06\u201392.80) (p\u2009=\u20090.005) (P\u2009<\u20090.001) . IgM dec<\u20090.001) . No sign<\u20090.001) .,To the best of our knowledge, this is the first study to comprehensively evaluate the levels of SARS-CoV-2 neutralizing, anti-S-RBD-IgG, Anti-S-RBD-IgM and anti-S1-IgA antibodies in VN and unvaccinated NI individuals. In the current study, mRNA vaccination elicited significantly greater NTAb, anti-S-RBD- IgG and anti-S1-IgA, compared with natural immunity . These r,,However, despite the mRNA vaccination-boosted antibody levels, this \u2018boost\u2019 was relatively short-lived, with ~\u20092- to 6-fold significant waning observed in NTAb, anti-S-RBD-IgG, anti-S-RBD-IgM and anti-S1-IgA, 23\u00a0weeks post-full-vaccination . These rIn comparison with mRNA vaccine-induced immunity, natural infection elicited a significant but less steady ~\u20091\u20132-fold decline in NTAb, anti-S-RBD-IgG, and anti-S-RBD-IgM . InteresThese findings are similar to a recent report showing that natural infection exhibit a lasting IgA response.,,,This study had several limitations. It is known that recent variants, such as Omicron, need many folds of antibody titre to be neutralized compared to the original strains. That is, the mutations that emerged in different variants of the SARS-CoV-2 genome should have a significant influence on viral protein structures, shape, function and immunogenicity, which, in theory, should greatly affect the strength and the effectiveness of the immunological response and possibly duration of antibody\u2019s waning in infected patients. It would be great to study the antibody response and waning against different variants. However, it was not applicable to include variant-specific data because of the limited number of samples and lack of sequencing data. In addition, a variety of variables could influence the level of immune response elicited after infection. It should be noted that our NI group included only 45% symptomatic subjects, whereas the remaining were paucisymptomatic (20%), asymptomatic (20%) or with unspecified severity (15%), which could have affected our results. In those with more severe COVID-19, NTAb antibody titers were reported to rise faster and reach a greater peak.,Furthermore, several studies have shown a link between cycle threshold (Ct) and antibody titre, with lower Ct values linked with greater antibody titers at the population level.Despite these limitations, this study has several strengths that merit attention. First, most of the published studies have mainly focused on NTAb, IgG or IgM, whereas studies on IgA response are minimal, particularly amongst unvaccinated NI subjects. Second, in this study, we assessed anti-N antibodies, which is crucial to identify those who were exposed to a virus but were asymptomatic prior to vaccination, especially amongst those vaccinated with vaccines containing only S protein. In addition, despite the relatively small sample size across the analysed groups, we utilized strict inclusion criteria and included participants from a wide age range to achieve valid comparisons.Our findings provide important insights into the durability of vaccine- and natural infection-induced immunity. We evaluated the antibody responses of NTAb, anti-SRBD IgM, anti-S1-IgA and anti-SRBD IgG antibodies. Whereas double-dose mRNA vaccination elicited higher antibody titers compared with natural infection, this \u2018boost\u2019 was relatively short-lived in vaccinated individuals. In contrast, natural infection exhibited a less steady decline in NTAb antibodies, IgG, IgM and a lasting IgA response. Understanding the degree of waning immunity is crucial for policymaking, particularly regarding vaccination strategies, supporting the consideration of booster doses to sustain protection against COVID-19.Conceptualization, H.A.S., H.M.Y., L.J.A.-R. and G.K.N.; methodology, H.A.S., B.A.H., S.Y. and F.M.S., software, B.A.H., S.Y. and F.M.S; validation, H.A.S., B.A.H., S.Y. and F.M.S.; formal analysis, H.A.S., G.K.N., B.A.H. and S.Y.; Investigation, H.A.S., A.I., H.M.Y., L.J.A.-R. and G.K.N.; resources, H.A.S., N.L., H.Q., N.A.D., H.M.Y., L.J.A.-R and G.K.N.; data curation, H.A.S., B.A.H., S.Y. and G.K.N.; writing\u2014original draft preparation, H.A.S., S.Y. and G.K.N.; writing\u2014review and editing, H.A.S., S.Y., N.Y., D.W.A., N.A.D., H.M.Y., L.J.A.-R and G.K.N; visualization, H.A.S., B.A.H., S.Y., N.Y., D.W.A., H.M.Y., L.J.A.-R A.I. and G.K.N; supervision, H.A.-S., H.M.Y. and G.K.N.; project administration, H.A.S., H.M.Y., L.J.A.-R and G.K.N.; funding, G.K.N. All authors have read and agreed to the published version of the manuscript."} +{"text": "Streoptomyces rimosus M527 is a producer of the polyene macrolide rimocidin which shows activity against various plant pathogenic fungi. Notably, the regulatory mechanisms underlying rimocidin biosynthesis are yet to be elucidated.rimR2, which located in the rimocidin biosynthetic gene cluster, was first found and identified as a larger ATP-binding regulators of the LuxR family (LAL) subfamily regulator. The rimR2 deletion and complementation assays were conducted to explore its role. Mutant M527-\u0394rimR2 lost its ability to produce rimocidin. Complementation of M527-\u0394rimR2 restored rimocidin production. The five recombinant strains, M527-ER, M527-KR, M527-21R, M527-57R, and M527-NR, were constructed by overexpressing rimR2 gene using the promoters permE*, kasOp*, SPL21, SPL57, and its native promoter, respectively, to improve rimocidin production. M527-KR, M527-NR, and M527-ER exhibited 81.8%, 68.1%, and 54.5% more rimocidin production, respectively, than the wild-type (WT) strain, while recombinant strains M527-21R and M527-57R exhibited no obvious differences in rimocidin production compared with the WT strain. RT-PCR assays revealed that the transcriptional levels of the rim genes were consistent with the changes in rimocidin production in the recombinant strains. Using electrophoretic mobility shift assays, we confirmed that RimR2 can bind to the promoter regions of rimA and rimC.In this study, using domain structure and amino acid alignment and phylogenetic tree construction, rim genes and binding to the promoter regions of rimA and rimC.A LAL regulator RimR2 was identified as a positive specific-pathway regulator of rimocidin biosynthesis in M527. RimR2 regulates the rimocidin biosynthesis by influencing the transcriptional levels of The online version contains supplementary material available at 10.1186/s12934-023-02039-9. Streptomyces, a genus of Gram-positive bacteria with three types of PKSs , is best known for producing polyketides [Fusarium oxysporum f. sp. cucumerinum [Polyketides, a large group of secondary metabolites synthesized by polyketide synthases (PKSs), exhibit various bioactivities, including antifungal (rimocidin), antibacterial (penicillin), antitumor (daunorubicin) properties \u20133. They yketides \u20136. Polyeyketides \u20139, They yketides , nystatiyketides , amphoteyketides , and rimyketides . For exaumerinum , is a prStreptomyces causes bottlenecks, leading to low production levels and long fermentation periods [Streptomyces is a complex process involving multiple levels [However, polyketide biosynthesis in periods . Secondae levels \u201318, incle levels \u201321.Streptomyces antibiotic regulatory protein (SARP) family regulator, such as ActII-orf4, which regulates actinorhodin biosynthesis, and CcaR, which regulates clavulanic biosynthesis. These regulators are characterized by the presence of OmpR -like DNA-binding domains [Streptomyces natalensis [Streptomyces nodosus [Streptomyces noursei [Streptomyces ahygroscopicus [S. noursei ATCC 11,455 [S. natalensis [Streptmyces avermilitis [To date, the different types of regulators involved in polyene macrolide biosynthesis have been categorized as follows: (1) domains . (2) PAS domains , 24. Thetalensis . AmphRIV nodosus , and Nys noursei . (3) Lar noursei having ascopicus , and NysC 11,455 . (4) SARtalensis , and Ptermilitis . Recent rmilitis \u201335.Streptomyces rimosus M527, a rimocidin producer, was originally isolated by Lu et al. [S. rimosus M527. However, to the best of our knowledge, no pathway-specific rimocidin biosynthesis regulators are currently known.u et al. and depou et al. , fermentu et al. , were apStreptomyces diastaticus var. 108 has been predicted, and its biosynthetic gene cluster has been published (GenBank Accession No. AY442225) [S. rimosus M527 was sequenced (GenBank Accession No: NZ_SADA00000000.1), a biosynthetic gene cluster responsible for rimocidin production (GenBank Accession No. MK300953) , rimR2-deleted and rimR2-complemented strains. Subsequently, rimR2 gene was overexpressed using different promoters to improve rimocidin production. Furthermore, the regulatory mechanism of RimR2 was identified using electrophoretic mobility shift assays (EMSA).Although the rimocidin biosynthetic pathway in Y442225) , no pathS. rimosus M527 genome sequence, rimR2 gene (2757 nucleotides (nt)), located in the rimocidin biosynthesis gene cluster, encodes a protein with a predicted molecular mass of 97.3\u00a0kDa consisting of 918 aa. RimR2 protein contains a conserved nucleotide phosphate-binding domain and an HTH DNA-binding domain method analysis revealed that the mutant M527-\u0394rimR2 could not produce any rimocidin, whereas a distinct rimocidin peak was clearly observed in the WT culture filtrates located in the gene cluster. The mutant M527-\u0394rimR2 exhibited significantly lesser transcriptional levels of all the candidate rim genes than the WT strain was performed to examine the effects of ain Fig.\u00a0, and therim genes. In this experiment, His6-tagged RimR2 protein was generated in E. coli BL21 (DE3) , showing an 81.8% increase compared with the WT strain (207.2\u00a0mg/l) , M527-R3, and M527-R4 were determined via a shake-flask experiment is the consensus nucleotide sequence of the binding site of PAS-LuxR regulators has been revealed [S. rimosus M527 and found three matches similar to the sixteen conserved nucleotide sequences: (1) CTAGGGAATTCCCGAG, which was the most similar to the consensus sequence. It is located 103-bp upstream of open reading frame 18, which encodes putative GDP-mannose 4,6-dehydratase, but does not lie within its promoter region; (2) GCCAGGAATTCCCGCA, situated near the 3\u2032-end of the internal sequence of rimF, which encodes an aminotransferase, but does not lie within the putative promoter region of rimG encoding cytochrome P450 monooxygenase; (3) ACCGGAAAATCCTTAG, which is present in the intergenic region of rimE and rimD, 100-bp upstream of rimE but not within its putative promoter region. The locations of these three sequences suggest that they do not comprise the core elements for gene expression, which may explain the limited regulatory effect exerted by RimR1 on rimocidin production. The mechanism whereby RimR1 regulates structural genes in the rimocidin gene cluster will be elucidated in a future study.RimR1 shares high similarity with several well-studied transcriptional regulators of the PAS-LuxR family, for example, it shares 49.61% amino acid sequence identity with PimM from talensis . Notablytalensis . Surprisrevealed \u201347. UsinrimR1 promoter. Moreover, qRT-PCR revealed that rimR2 deletion decreased rimR1 expression and restored it to a level comparable with that in the WT strain M527 when it was complemented, suggesting that RimR2 indirectly regulates rimR1 expression. The relationship between RimR1 and RimR2 and their regulatory hierarchy are also worth investigating in a future study.The biosynthetic gene clusters encoding polyene macrolide antibiotics have been sequenced and multiple regulatory genes, usually organized in a hierarchical network, have been identified within them , 31, 42.S. rimosus M527. These two tetraenes differ in the aglycone moiety, with a propyl group in rimocidin and a methyl group in CE-108. As the elongation module is common for both rimocidin and CE-108 biosyntheses, RimR2 regulates both biosyntheses almost identically and YrimR1R (5\u2032-GATGAAGCCCTCGACGACAC-3\u2032) were designed following the rimR1 gene sequence (GenBank accession no. MK300953).RNA extraction and the analysis of the transcriptional level of o et al. . qRT-PCRrimR2 coding sequence was amplified by PCR using primers PrimR2-F2/R3 . RimR2 protein was purified using nickel-NTA column (Qiagen) and eluted using imidazole. The inducible expression and purification of were performed according to standard manipulation method described by Sambrook and Russel [A 2757-bp DNA fragment harboring the rim genes were amplified by PCR using the biotin labeled primers for the identification of clusters involved in rimocidin, and function annotation of biosynthetic gene cluster was listed in t test was used for statistical analysis.All experiments were carried out at least three times, and the results were expressed by the mean\u2009\u00b1\u2009standard deviation (SD). Students\u2019 Additional file 1: Table S1. Detailed information of RimR2 and some polyene macrolide biosynthesis regulators from other Streptomyces species in phylogenetic tree.Additional file 2: Figure S1. Construction of mutant S. rimosus M527-\u0394rimR2. Map of plasmid pWHU2653- \u0394rimR2. The sgRNA consists of the 20 nt target gene specific guide sequence of S. rimosus M527 (green) and the invariant scaffold RNA (yellow). Light blue parallelograms connect the identical UHA and DHA sequences on pWHU2653 and the S. rimosus M527 chromosome where homologous recombination can take place.Additional file 3: Figure S2. PCR verification of the mutant S. rimosus M527-\u0394rimR2. M: DL5000 DNA Marker. Lane 1, The PCR products of 2.8-kb rimR2 gene were amplified by using the primers PrimR2-F1/R1 from WT strain S. rimosus M527; Lane 2, The PCR products of 6.8-kb cassette containing 2.8-kb rimR2 gene and its 2.0-kb upstream and 2.0-kb downstream fragment were amplified by using the primers P1/P4 from S. rimosus M527; Lane 3-5, The PCR products of rimR2 gene were amplified by using the PrimR2-F1/R1 from three randomly mutant strains M527-\u0394rimR2; Lane 6-8, The PCR products of 4.0-kb cassette containing 2.0-kb upstream and 2.0-kb downstream fragment were amplified by using the P1/P4 from three randomly mutant strains M527-\u0394rimR2.Additional file 4: Figure S3. HPLC analysis of rimocidin production in the WT strain S. rimosus M527, in mutant S. rimosus M527-\u0394rimR2, and in the complemented strain S. rimosus M527-\u0394rimR2/pSET152::rimR2, and control strain S. rimosus M527/pSET152.Additional file 5: Figure S4. Purification and elution of RimR2 protein. M: Protein Marker; Lane 1, Purified His6-tagged RimR2 protein after affinity nickel-NTA column. Lanes 2-4, Eluted RimR2 protein with 250 mM, 300mM, 500mM imidazole.Additional file 6: Figure S5. Construction of recombinant plasmids for over-expression of rimR2 gene with different promoters.Additional file 7: Figure S6. Phenotypic\u00a0verification of recombinant strains recombinant strains harboring over-expression of rimR2 gene. Recombinant strains could grow on 2CMC agar medium containing 300 \u03bcg/ml apramycin, while control strain S. rimosus M527 did not. 2CMC agar medium was incubated at 28 \u00b0C for 4 days.Additional file 8: Figure S7. PCR analysis of apramycin (apr) gene from recombinant strains harboring over-expression of rimR gene. DL DNA 2000 marker was used (M). Lane 1: PCR product of apr gene from S. rimosus M527(negative control); lane 2: PCR product of apr gene from plasmid pSET152(positive control); lane 3-5: PCR product of apr gene from recombinant strains S. rimosus M527-ER; lane 6-8: PCR product of apr gene from recombinant strains S. rimosus M527-KR; lane 9-11: PCR product of apr gene from recombinant strains S. rimosus M527-NR; lane 12-14: PCR product of apr gene from recombinant strains S. rimosus M527-21R; lane 15-17: PCR product of apr gene from recombinant strains S. rimosus M527-57R.Additional file 9: Figure S8. HPLC analysis of rimocidin isolated from fermentation extracts of the recombinant strains S. rimosus M527-KR, S. rimosus M527-NR, S. rimosus M527-ER, S. rimosus M527-21R, S. rimosus M527-57R and WT strain S. rimosus M527.Additional file 10: Figure S9. Construction of recombinant plasmids of overexpression of rimR1/rimR2/rimR3 /rimR4 gene with permE* promoter.Additional file 11: Figure S10. Detection and comparison of rimocidin production (a) and cell dry weight (b) of WT strain S. rimosus M527(\u25cf), recombinant strains M527-R1(\u25a0), M527-R2(\u25b2), M527-R3(\u25bc), and M527-R4(\u25c6) in shake-flask culture experiment.Additional file 12: Figure S11. Detection and comparison of antifungal activities of WT strain M527, recombinant strains M527-R1, M527-R2, M527-R3, and M527-R4 against F. oxysporum f. sp. cucumerinum. Spore suspension (500 \u03bcl) of F. oxysporum f. sp. cucumerinum (1\u00d7106 cfu ml-1) was spread and inoculated on PDA medium at 28 \u00b0C for 1 d. A agar block (4 mm in diameter) containing actively growing WT strain M527, three random recombinant strains M527-R1(a), M527-R2(b), M527-R3(c), and M527-R4(d) was aseptically placed on aforementioned PDA medium containing pathogenic fungus at 28 \u00b0C for 3-4 d. The diameter of inhibition zone was measured as antagonistic activity. Plant-pathogenic fungus F. oxysporum f. sp. cucumerinum was used as indicator strain in antifungal activities assay.Additional file 13: Figure S12. Phylogenetic tree of RimR1 and other polyene macrolide biosynthesis regulators (PAS-LuxR).Additional file 14: Figure S13. Phylogenetic tree of RimR2, RimR3, RimR4 and other polyene macrolide biosynthesis regulators (LAL).Additional file 15: Table S2. The primers used for deletion or expression of rimR2 gene in this study.Additional file 16: Table S3. The primers used for EMSA assay in this study."} +{"text": "Results indicated that LPS decreased the villus height (p < 0.0001), increased the crypt depth (p < 0.05), and lowered the villus height to crypt depth ratio (p < 0.0001), while sodium acetate/sodium butyrate supplementation caused a significant increase in the villus height (p < 0.001), decrease in the crypt depth (p < 0.01), and increase in the villus height to crypt depth ratio (p < 0.001), especially. In mice treated with LPS, it was found that the serum level of IL-1\u03b2, TNF-\u03b1 (p < 0.001), and MDA (p < 0.01) was significantly higher; however, sodium acetate/sodium butyrate supplementation significantly reduced IL-1\u03b2 (p < 0.001), TNF-\u03b1 (p < 0.01), and MDA (p < 0.01), respectively. A total of 19 genera were detected among mouse groups; LPS challenge decreased the abundance of Lactobacillus, unidentified F16, unidentified_S24-7, Adlercreutzia, Ruminococcus, unclassified Pseudomonadales, [Ruminococcus], Acetobacter, cc 1, Rhodococcus, unclassified Comamonadaceae, Faecalibacterium, and Cupriavidus, while increased Shigella, Rhodococcus, unclassified Comamonadaceae, and unclassified Pseudomonadales in group L. Interestingly, sodium acetate/sodium butyrate supplementation increased Lactobacillus, unidentified F16, Adlercreutzia, Ruminococcus, [Ruminococcus], unidentified F16, cc 115, Acetobacter, Faecalibacterium, and Cupriavidus, while decreased Shigella, unclassified Enterobacteriaceae, unclassified Pseudomonadales, Rhodococcus, and unclassified Comamonadaceae. LPS treatment upregulated the expressions of ZO-1 (p < 0.01) and NLRP3 (p < 0.0001) genes in mice; however, sodium acetate/sodium butyrate solution supplementation downregulated the expressions of ZO-1 (p < 0.05) and NLRP3 (p < 0.05) genes in treated mice. Also, the LPS challenge clearly downregulated the expression of Occludin (p < 0.001), Claudin (p < 0.0001), and Caspase-1 (p < 0.0001) genes, while sodium acetate/sodium butyrate solution supplementation upregulated those gene expressions in treated groups. The present study revealed that sodium acetate/sodium butyrate supplementation alleviated LPS-induced diarrhea in mice via enriching beneficial bacterium and decreasing pathogens, which could regulate oxidative damages and inflammatory responses via NLRP3/Caspase-1 signaling. The current results may give insights into the prevention and treatment of diarrhea.Diarrhea is a word-widely severe disease coupled with gastrointestinal dysfunction, especially in cattle causing huge economic losses. However, the effects of currently implemented measures are still not enough to prevent diarrhea. Previously we found that dropped short-chain fatty acids in diarrhea yaks, and butyrate is commonly known to be related to the epithelial barrier function and intestinal inflammation. However, it is still unknown whether sodium acetate/sodium butyrate could alleviate diarrhea in animals. The present study is carried out to explore the potential effects of sodium acetate/sodium butyrate on lipopolysaccharide-induced diarrhea in mice. Fifty ICR mice were randomly divided into control (C), LPS-induced (L), and sodium acetate/sodium butyrate -treated groups. Serum and intestine samples were collected to examine inflammatory cytokines, antioxidant levels, relative gene expressions Diarrhea is a severe disease coupled with gastrointestinal dysfunction that has a global impact on fertility rate, milk production, and immunity in livestock . NowadayGut microflora is composed of millions of microorganisms that contribute remarkably to physiological processes, i.e., functions of nutrition absorption, metabolism, and immunity of the host by producing various metabolites . The anaLactobacillus plantarum alleviated diarrhea in a previous study by balancing gut microbiota and regulating SCFAs , and after 24 hours mice were euthanized to collect serum, small intestine, and rectum samples were purchased from Qing Long Shan Dong Wu Fan Zhi . After 30 days of rearing, mice were randomly divided into five groups, namely control (C), LPS (L), and treatment groups . Group D (400: 200), B (300:300), and A (200: 400) were treated with 600 mg/kg sodium acetate/sodium butyrate solution samples . All aniDuodenum, jejunum, and ileum samples from all the groups were preserved in 4% paraformaldehyde for at least 48 hrs and then processed for commercial H&E staining . On an Olympus CX23 microscope with an integrated digital imaging analysis system, histological slices were examined . The villus height and crypt depth were measured as depicted in the previous study .via commercial assay kits . The concentration of cytokines including interleukin 1 beta (IL-1\u03b2), interleukin 6 (IL-6), interleukin 10 (IL-10), and tumor necrosis factor-alpha (TNF-\u03b1) was measured by using commercial ELISA kits .Blood samples of mice were centrifuged at 4,000 g for 10 min and stored at \u201320\u00b0C for future analysis. Antioxidant capacity was examined by detecting the levels of superoxide dismutase (SOD), glutathione peroxidase (GSH-px), total anti-oxidation capacity (T-AOC), and malondialdehyde (MDA) by utilizing commercial assay kits . Meanwhile, the NO concentrations were determined n = 4), L (n = 4), and A (n = 4) were extracted utilizing the fast DNA Stool Mini Kit according to the manufacturer\u2019s specifications. The quantity and quality of all extracted DNA samples were examined by using NanoDrop 2000 UV-vis spectrophotometer and agarose gel electrophoresis, respectively. Gene amplification of bacterial 16S rRNA gene was performed using the V3\u2013V4 regions primers 338F (5\u2032-ACTCCTACGGGAGGCAGCAG-3\u2032) and 806R (5\u2032-GGACTACHVGGGTWTCTAAT-3\u2032). Then all amplicon products were purified by employing Vazyme VAHTSTM DNA Clean Beads and quantified using the QuantiFluor\u2122-ST . At last, all samples were sequenced by using the Illumina MiSeq platform with MiSeq Reagent Kit v3.The total microbial genomic DNA was extracted from the rectum contents of each mouse. The samples from groups C (1 (via mafft (2 (via ggtree3. Krona species composition map was generated via KronaTools (v2.7)4 (via PERMANOVA and Adonis in QIIME2 (2019.4). Venn5, heatmap, metagenomeSeq, LEFSe 4 . Signifiq, LEFSe , OPLS-DAq, LEFSe , and ranq, LEFSe was perfq, LEFSe using Mevia denaturing formaldehyde gel electrophoresis and NanoDrop 2000 analyzer to validate their integrity and concentrations, respectively. Then commercial SuperScript\u2122IV first strand cDNA synthesis kits were used for translating RNA samples into cDNA under the guidance of the manufacturer\u2019s specifications. Finally, qRT-PCR for all groups was carried out by using 25 uL of reaction mixtures consisting of 2 uL of intestinal tissues cDNA, 12.5 uL of Hieff UNICON\u00ae Universal Blue qPCR SYBR Green Master Mix , 2uL of primers, and 8.5 uL nuclease-free water, then the procedure was performed in the StepOnePlus\u2122 Real-Time PCR System . All sample reactions were repeated three times and the method of 2\u2013\u0394\u0394CT was utilized for calculating gene relative quantification. All primer pairs used in the present study were synthesized by Sangon Biotech (China) and are shown in Intestinal tissue RNA extraction from all mouse groups was performed by utilizing TRIzol reagent . All of the RNA samples were examined via ANOVA, Student\u2019s t-test, Kruskal\u2013Wallis, and Dunn\u2019s test via IBM SPSS (22.0) software. Data presented as means \u00b1 SD and statistically significant are considered when P < 0.05.All the generated data were evaluated via H&E staining and found that LPS caused a decrease in the villus height (p < 0.0001), an increase in the crypt depth (p < 0.05), and it also lowered the villus height to crypt depth ratio (p < 0.0001). Whereas, sodium acetate/sodium butyrate supplementation resulted in a significant increase in the villus height (p < 0.001), decrease in the crypt depth (p < 0.01), and increase in the villus height to crypt depth ratio (p < 0.001), especially in the mice of groups B and A (The mice were weighed on a daily basis and the weight of the mice in group A was slightly higher than mice in other groups . The dia B and A .p < 0.05), while there was no marked difference between group L and treated groups D, B, and A, respectively. In group C, the serum level of mice induced by LPS was found prominently high for IL-1\u03b2 (p < 0.001), TNF-\u03b1 (p < 0.001), and MDA (p < 0.01), respectively. However, in the serum of groups D, B, and A, sodium acetate/sodium butyrate supplementation caused a remarkable decrease in IL-1\u03b2 (p < 0.001), TNF-\u03b1 (p < 0.01), and MDA (p < 0.01), respectively and non-singleton (p < 0.05) was found between groups C and L (p < 0.05) , ANOSIM (p < 0.05), and PERMDISP (p < 0.05), respectively . Beta diectively . UPGMA aectively . Signifiectively .Proteobacteria (83.02%) and Bacteroidetes (13.00%). While Firmicutes (83.36%), Bacteroidetes (12.80%), Firmicutes (45.35%), and Proteobacteria (46.88%) were the main phyla in groups C and A. At the Class level, the main classes were Gammaproteobacteria (81.28%) and Bacteroidia (12.99%) in group L, while Bacilli (74.72%), Bacteroidia (12.80%), Clostridia (8.08%), Gammaproteobacteria (45.90%), Bacilli (44.04%), and Bacteroidia (6.80%) were the dominant classes in groups C and A, respectively. At the order level, the primary classes were Enterobacteriales (55.60%), Pseudomonadales (25.65%), and Bacteroidales (12.99%), while Lactobacillales (72.68%), Bacteroidales (12.80%), Clostridiales (8.08%), Lactobacillales (43.52%), Enterobacteriales (41.07%), and Bacteroidales (6.80%) were the staple orders in groups C and A, respectively. At the family level, the dominating families in group L were Enterobacteriaceae (55.59%), Pseudomonadaceae (25.47%), and Bacteroidaceae (9.09%), while the main families were Lactobacillales (72.47%) and S24-7 (12.50%) in group C, whereas Lactobacillales (43.35), Enterobacteriaceae (41.07%), and Bacteroidaceae (4.84%) in group A, respectively. At the genus level, the major genera in group L were Shigella (54.62%), Pseudomonas (25.42%), and Bacteroides (9.09%), while Lactobacillus (72.45%), unidentified_S24-7 (12.50), Lactobacillus (43.34%), Shigella (40.71), and Bacteroides (4.84%) were the dominating genera in groups C and A , Bacteroides (9%), and Pseudomonas (8%) in group L, while Shigella (56%), Pseudomonas (26%), and Bacteroides (9%) in group A, and unidentified S34-7 (45%), unidentified Clostridia (15%), Lachnospiraceae (7%), and Turicibacter (7%) in group C, respectively projected on the coordinate axis was clearly farther than groups A (light orange) and C (lavender), which revealed a difference between group L, and groups A and C, respectively OTUs were shared in groups C and L, while 335 (11.96%) OTUs were shared in groups C and A . Then ASm genera . ASV/OTUs genera . It is d C and A . PCA anaectively . Also, Oectively .Bacteroidales and Lactobacillales were found significantly on the upside of the broken lines with decreased ASV 102 (p < 0.05), ASV 23 (p < 0.05), ASV 14 (p < 0.05), and ASV 53 (p < 0.05), increased ASV 73 (p < 0.05), ASV 1 (p < 0.01), ASV 194 (p < 0.05), ASV 50 (p < 0.05), ASV 18 (p < 0.01), and ASV 5 (p < 0.001) between groups C and A. Different genera like Bacteroidales, Lactobacillales, Clostridiales, Burkholderiales, Desulfovibrionales, Enterobacteriales, and Pseudomonadales were found significantly in groups C and L, with 107 decreased ASV and 86 increased ASV , family S24-7, order Clostridiales, class Clostridia, genus Gemella, order Gemellales, family Gemellaceae, phylum Tenericutes, class Mollicutes, family Lachnospiraceae, order RF39, family F16, class TMT-3, order CW040, phylum TM7, and genus Ruminococcus in group C (lavender), genus Faecalibacterium, family Acetobacteraceae, and order Rhodospirillales in group A (light orange) .Clostridium, Ruminococcus, Lactococcus, Gemella, etc. Network analysis revealed that there were more edges between groups A and C than between groups L and C, which inferred a higher similarity between groups A and C , unidentified F16 (p < 0.0001), Adlercreutzia (p < 0.01), Ruminococcus (p < 0.05), [Ruminococcus] (p < 0.05), Acetobacter (p < 0.05), cc 115 (p < 0.05), and Cupriavidus (p < 0.05) in group L was obviously lower than group C, respectively. While Shigella (p < 0.05) was prominently higher in group L than in group C. Unidentified_S24-7 and unclassified RF39 were significantly higher in group C than in groups A (p < 0.05) and L (p < 0.05), respectively, while unclassified Enterobacteriaceae was significantly lower in group C than in groups A (p < 0.05) and L (p < 0.05), respectively. The abundance of unclassified Pseudomonadales (p < 0.05), Rhodococcus (p < 0.05), unclassified Comamonadaceae (p < 0.05), and Lysobacter (p < 0.05) in group L was conspicuously higher than group A, respectively. The abundance of Faecalibacterium in group L was clearly lower than groups A (p < 0.05) and L (p < 0.01), respectively. The abundance of Gluconacetobacter in group A was prominently higher than groups L (p < 0.05) and C (p < 0.01), respectively. The abundance of unclassified Bradyrhizobiaceae in group C was clearly higher than in group A (p < 0.05) .In summary, different analysis methods include relative abundance taxa, classification levels tree diagram, GraPhlAn evolutionary tree diagram, Krona species composition diagram, Venn Diagram, Genera composition heatmap, PCA, OPLS-DA, metagenomeSeq analysis, LEfSe analysis, and random forests and network analyses demonstrated that LPS challenge changed microbiota composing in mice; however, sodium acetate/sodium butyrate supplementation could partly restore the gut microbiota in animals.p < 0.05), 9 (p < 0.01), and 20 (p < 0.001) significant different pathways between groups C and L, 37 (p < 0.05), 27 (p < 0.01), and 53 (p < 0.001) significant different pathways between groups A and C, respectively (p < 0.05), 15 (p < 0.01), and 51 (p < 0.001) significant different pathways between groups C and L, while one (p < 0.001) significant different pathway between groups A and C was examined and NLRP3 (p < 0.0001) in mice of group L; however, sodium acetate/sodium butyrate solution supplementation downregulated the expression of ZO-1 (p < 0.05) and NLRP3 (p < 0.05) genes in treated mice. Furthermore, change in LPS clearly downregulated the expression of Occludin (p < 0.001), Claudin (p < 0.0001), and Caspase-1 (p < 0.0001) genes in group L, while sodium acetate/sodium butyrate solution supplementation upregulated those gene expressions in treated groups of D, B, and A (Relative gene expression of Zonula occludens 1 (ZO-1), Occludin, Claudin, Caspase-1, and NLRP3 were detected by employing qRT-PCR. LPS induction prominently upregulated the expression of ZO-1 , Phenylobacterium, and Aminobacter were positively related to inflammatory cytokines. Pseudomonas, Faecalibacterium, Gluconacetobacter, Rhodococcus, (Clostridium), and Gluconobacter were positively related to tight junction proteins, while Adlercreutzia, Candidatus Arthromitus, Lactococcus, Ruminococcus, Coprococcus, Acinetobacter, cc_115, Gemella, Anaeroplasma, Phenylobacterium, Lysobacter, and W22 were negatively related to tight junction proteins. Adlercreutzia, Ruminococcus, Coprococcus, cc_115, Roseburia, Gemella, and Anaeroplasma were negatively related to expressions of Caspase-1 and NLRP3 , intestine morphology indices, inflammatory cytokines, oxidative indices, and gene expressions was performed through Statistical Analysis System. Results showed that nd NLRP3 .Though various kinds of measures have been implemented so far to fight against diarrhea, there is still a long way to go . A recenIn the present study, mice were supplemented with sodium acetate/sodium butyrate before inducing diarrhea by utilizing LPS. Serve damage to intestines particularly jejunum, ileum, cecum, and colon was examined , which wTo explore the potential mechanisms, we detected the gene expressions of tight junction proteins in intestines. Among them Occludin and Claudins were recognized as important components of intestinal permeability . The expp < 0.01) was detected in group L; however, there was a significant decrease in MDA (p < 0.01) levels in sodium acetate/sodium butyrate supplemented groups D, B, and A, respectively (p < 0.0001) in mice in group L; however, sodium acetate/sodium butyrate solution supplementation downregulated the expression of NLRP3 (p < 0.05) genes in treated mice. Also, the LPS challenge clearly upregulated the Caspase-1 (p < 0.0001) gene in group L, while sodium acetate/sodium butyrate solution supplementation downregulated it in treated groups D, B, and A (p < 0.001) were found in group C, which was consistent with previous results found higher inflammatory factors and upregulation of NLRP3 in HUVEC cells , Acetobacter, cc 1, Rhodococcus, unclassified Comamonadaceae, Faecalibacterium, and Cupriavidus, while increased Shigella, Rhodococcus, unclassified Comamonadaceae, and unclassified Pseudomonadales in group L. Interestingly sodium acetate/sodium butyrate supplementation increased Lactobacillus, unidentified F16, Adlercreutzia, Ruminococcus, (Ruminococcus), unidentified F16, cc 115, Acetobacter, Faecalibacterium, and Cupriavidus, while decreased Shigella, unclassified Enterobacteriaceae, unclassified Pseudomonadales, Rhodococcus, and unclassified Comamonadaceae. Lactobacillus genus bacteria are probiotic microorganisms that have beneficial effects on to host .KL and QK: research idea, methodology, visualization, and supervision. XC, QK, XZ, CZ, PH, and HL: reagents, materials, and analysis tools. KL: writing\u2014original draft and preparation. MK, ZB, II, HA, QS, and KL: writing\u2014review and editing. All authors contributed to the article and approved the submitted version."} +{"text": "Limited data exist regarding longer term antibody responses following three-dose coronavirus disease 2019 (COVID-19) vaccination, and the impact of a first SARS-CoV-2 infection during this time, in people with HIV (PWH) receiving suppressive antiretroviral therapy (ART). We quantified wild-type-specific, Omicron BA.1-specific and Omicron BA.5-specific responses up to 6 months post-third dose in 64 PWH and 117 controls who remained COVID-19-naive or experienced their first SARS-CoV-2 infection during this time.Longitudinal observational cohort.We quantified wild-type-specific and Omicron-specific anti-Spike receptor-binding domain IgG concentrations, ACE2 displacement activities and live virus neutralization at 1, 3 and 6 months post-third vaccine dose.Third doses boosted all antibody measures above two-dose levels, but BA.1-specific responses remained significantly lower than wild-type-specific ones, with BA.5-specific responses lower still. Serum IgG concentrations declined at similar rates in COVID-19-naive PWH and controls post-third dose . Antibody function also declined significantly yet comparably between groups: 6 months post-third dose, BA.1-specific neutralization was undetectable in more than 80% of COVID-19 naive PWH and more than 90% of controls. Breakthrough SARS-CoV-2 infection boosted antibody concentrations and function significantly above vaccine-induced levels in both PWH and controls, though BA.5-specific neutralization remained significantly poorer than BA.1 even post-breakthrough.Following three-dose COVID-19 vaccination, antibody response durability in PWH receiving ART is comparable with controls. PWH also mounted strong responses to breakthrough infection. Due to temporal response declines, however, COVID-19-naive individuals, regardless of HIV status, would benefit from a fourth dose within 6\u200amonths of their third. In British Columbia (BC), Canada, third doses of coronavirus disease 2019 (COVID-19) monovalent mRNA vaccines were introduced in November 2021, initially to individuals at risk of severe COVID-19 outcomes, including some people with HIV (PWH). Whether offered as part of a primary vaccine series or a \u2018booster\u2019, third doses help to maintain systemic immunity and enhance protection against infection by viral variants . DespiteLongitudinal monitoring of immune responses post-third dose in PWH is critical to inform the timing of future immunizations in this group. Though some data are available on initial immunogenicity to third COVID-19 vaccine doses in PWH \u201316, no sOur cohort was described previously . The preThis study was approved by the University of British Columbia/Providence Healthcare and Simon Fraser University Research Ethics Boards. All participants provided written informed consent.50/200\u200a\u03bcl in the presence of serial two-fold plasma dilutions (1/20 to 1/2560) and added to target cells in triplicate. Viral cytopathic effects (CPE) were recorded 3 days post-infection. Neutralization was reported as the highest reciprocal dilution able to prevent CPE in all three wells. Partial or no neutralization at 1/20 dilution was considered below the limit of quantification (BLOQ) and coded as a reciprocal dilution of 10.Assays were performed as previously described ,19. IgG-U test (unpaired data) or Wilcoxon test (paired data). Relationships between continuous variables were assessed using Spearman's correlation. In participants who remained COVID-19-naive, multiple linear regression was used to investigate the relationship between HIV infection and vaccine-induced immune measures using a confounder model that adjusted for variables that could influence vaccine responses or that differed in prevalence between groups. For Omicron-specific neutralization at 6\u200amonths post-third dose, multiple logistic regression was used because of the high proportion of results BLOQ. Included variables were: HIV infection (controls as reference group), age (per year), sex at birth , ethnicity (nonwhite as reference), number of chronic conditions , dual ChAdOx1 as the initial regimen [mRNA or mixed (ChAdOx1/mRNA) regimen as the combined reference group] [P less than 0.05 considered statistically significant. Analyses were conducted using Prism v9.2.0 .Continuous variables were compared using the Mann\u2013Whitney e group] ,17, thir+ T-cell counts of 645 [interquartile range (IQR) 473\u2013958] cells/\u03bcl, and median nadir CD4+ T-cell counts of 225 (IQR 95\u2013485) cells/\u03bcl, at enrolment. PWH were a median of 57 (IQR 42\u201365) years old and 90% men; controls were a median 47 (IQR 35\u201372) years old and 73% women. PWH had a higher proportion of white ethnicity and more chronic health conditions [median 1 (IQR 1\u20133) compared with 0 (IQR 0\u20131) in controls]. More PWH (10%) than controls (<1%) received two doses of the recombinant viral vector ChAdOx1 vaccine as their initial immunization series. All third doses were monovalent mRNA vaccines, either BNT162b2 (30\u200a\u03bcg) or mRNA-1273 (50 or 100\u200a\u03bcg). Most PWH (69%) and controls (62%) received mRNA-1273, where, per local guidelines, all adults aged at least 70\u200ayears were eligible for a 100\u200a\u03bcg mRNA-1273 dose, as were PWH who met one or more of the following criteria: age at least 65\u200ayears, prior AIDS-defining illness, prior CD4+ T-cell count less than 200\u200acells/\u03bcl, prior CD4+ T-cell fraction 15% or less, any plasma HIV load greater than 50\u200acopies/ml in 2021, or perinatally acquired HIV [Characteristics of the 64 PWH and 117 controls, all of whom remained COVID-19-naive until at least 1 month post-third dose, are shown in Table P\u200a=\u200a0.4). Though SARS-CoV-2 variant information is unavailable for individual infections, most were likely Omicron BA.1 or BA.2 based on local epidemiology at the time [A total of 24 (38%) PWH and 45 (39%) controls experienced their first SARS-CoV-2 infection between 1 and 6 months post-third dose (one control experienced two infections during this period ). Based the time .10 BAU/ml in COVID-19-naive PWH and 3.67 (IQR 3.50\u20133.86) log10 BAU/ml in controls, respectively (P\u200a=\u200a0.5). Following this, wild-type-specific IgG responses declined comparably in COVID-19-naive PWH and controls. At 3 months, wild-type-specific IgG responses in PWH and controls declined to a median 3.48 (IQR 3.12\u20133.75) and 3.40 (IQR 3.21\u20133.61) log10 BAU/ml, respectively (P\u200a=\u200a0.5), while by 6 months, responses had declined to a median 2.96 (IQR 2.62\u20133.38) and 3.06 (IQR 2.82\u20133.24) log10 BAU/ml in PWH and controls, respectively (P\u200a=\u200a0.4) , whereas those in controls had declined to significantly lower than post-second dose levels (P\u200a<\u200a0.0001) . One month post-third dose, for example, BA.1-specific IgG concentrations were 2.96 (IQR 2.71\u20133.32) log10 BAU/ml in PWH, which was 0.74 log10 BAU/ml lower than wild-type-specific concentrations at this time. By 6 months, BA.1-specific IgG concentrations had declined to 2.47 (IQR 2.14\u20132.59) log10 BAU/ml in PWH, which was 0.49 log10 BAU/ml lower than wild-type-specific concentrations at this time.Similarly, Omicron BA.1-specific IgG responses were comparable in COVID-19-naive PWH and controls at all post-third dose time points , as was male sex (P\u200a=\u200a0.012 for BA.1-specific responses) (Supplementary Table 1). In fact, adjusted IgG concentrations were slightly higher in PWH compared with controls, though this was not statistically significant. Of note, receipt of an mRNA-1273 third dose (rather than BNT162b2) was associated with stronger wild-type-specific IgG responses (P\u200a=\u200a0.029), though not BA.1-specific responses (P\u200a=\u200a0.13), 6 months post-third dose. Among PWH, we also observed no significant relationship between most recent or nadir CD4+ T-cell count and either wild-type-specific or BA.1-specific IgG concentrations at this time .We next performed multivariable analyses adjusting for sociodemographic, health and vaccine-related variables to identify variables associated with wild-type-specific and BA.1-specific IgG concentrations at 6 months post-third dose in the COVID-19-naive subgroup. These analyses revealed that a higher number of chronic health conditions \u2013 but not HIV infection \u2013 was associated with poorer IgG responses at this time . Estimated BA.1-specific IgG half-lives were also comparable, at a median 71 (IQR 49\u2013104) days for PWH compared with 74 (IQR 59\u201390) days in controls (P\u200a=\u200a0.8). Multivariable analyses confirmed that HIV infection was not associated with wild-type-specific or BA.1-specific IgG half-lives post-third dose (Supplementary Table 2). Among COVID-19-naive PWH, we initially observed a weak inverse correlation between recent CD4+ T-cell count and IgG half-life, but this was not significant after excluding an outlier with a long (>200\u200aday) half-life .We estimated the half-lives of wild-type-specific IgG following three-dose vaccination to be a median 66 (IQR 47\u201389) days in COVID-19-naive PWH compared to 72 (IQR 54\u201396) days in controls, a difference that was not statistically significant , which was 0.27 log10 BAU/ml higher than at 1 month post-third dose (P\u200a<\u200a0.0001). Importantly, the magnitude of these \u2018hybrid\u2019 IgG responses was comparable between PWH and controls at all post-infection time points tested . Notably, while most participants experienced a marked boost in antibody levels following SARS-CoV-2 infection, IgG responses in a minority of PWH and controls remained constant or even declined post-infection , while by 6 months, activities had decreased to a median 87% (IQR 67.5\u201398.1) in PWH versus 93.6% (IQR 81.5\u201397.8) in controls (P\u200a=\u200a0.3), levels that were comparable or lower than after two-dose vaccination compared with 99.1% (IQR 97\u201399.6%) in controls , but these responses also declined similarly in COVID-19-naive PWH and controls , to 30.8% (IQR 23.0\u201354.1) in PWH and 25.9% (IQR 12.1\u201352.2) in controls (P\u200a=\u200a0.3), where the latter values were significantly lower than those observed after two-dose vaccination .BA.1-specific responses remained significantly lower than wild-type-specific responses at all time points . There was also no evidence that a low recent or nadir CD4+ T-cell count was associated with lower wild-type-specific or BA.1-specific ACE2 displacement activities 6\u200amonths post-third dose in COVID-19-na\u00efve PWH . This was consistent with prior observations at 1 month post-third dose, which we attributed to the observation that PWH with low nadir CD4+ T-cell counts were eligible for the higher (100\u200a\u03bcg) third mRNA-1273 dose [Multivariable analyses confirmed that, among COVID-19-naive participants, HIV infection was not associated with either wild-type-specific or BA-1-specific ACE2 displacement activities at 6\u200amonths post-third dose (Supplementary Table 3). Rather, having received a mRNA-1273 third dose was the only independent correlate of stronger wild-type-specific ACE2 displacement activity at this time (273 dose .P\u200a<\u200a0.0001), where activities at 6 months in this group were overall significantly greater than peak responses induced by three-dose vaccination (both P\u200a<\u200a0.0001) . It is again notable, however, that a minority of PWH and controls did not show appreciable increases in this activity following infection , while by 6 months, neutralization had declined to a median 80 (IQR 35\u2013160) in PWH and 40 (IQR 20\u201380) in controls (P\u200a=\u200a0.006), values that were below the levels originally elicited by two-dose vaccination (both groups P \u2264 0.01). As reported previously [One month post-third dose, wild-type-specific neutralization activity in PWH was slightly higher than in controls , though responses in PWH were not further impaired compared with controls. In fact, 1 month post-third dose, BA.1-specific neutralization was higher in PWH compared with controls: a median 60 (IQR 25\u2013160) and 40 (IQR 20\u201340), respectively (P\u200a=\u200a0.0005), though these values were five-fold to eight-fold lower than corresponding wild-type-specific responses. BA.1-specific neutralization subsequently declined rapidly; at 3 months, this was BLOQ in 67.4% of COVID-19-naive PWH and 80.5% of controls (P\u200a=\u200a0.2), whereas at 6 months, this was BLOQ in 82.4% of PWH and 92.2% of controls (P\u200a=\u200a0.2), levels that were significantly lower than peak responses after two-dose vaccination . In multivariable analyses, older age \u2013 but not HIV infection \u2013 was the only significant correlate of poorer BA.1-specific neutralization among COVID-19-naive individuals at 6-month post-third dose . We also observed no significant associations between CD4+ T-cell parameters and either wild-type-specific or BA-1-specific neutralization at 6 months among COVID-19-naive PWH .BA.1-specific neutralization was significantly lower than wild-type responses at all timepoints for all groups .By contrast, individuals who experienced breakthrough infection showed significantly stronger wild-type-specific and BA.1-specific neutralization compared with their COVID-19-naive counterparts at 3 and 6 months , and 16-fold lower than that for wild-type and wild-type .Since the emergence of Omicron BA.1, even more immune evasive variants have developed, including Omicron BA.5 that has dominated globally \u201326. We, Our results demonstrate that antibody response durability following three-dose COVID-19 vaccination in COVID-19-naive PWH receiving suppressive ART is comparable to controls without HIV. As we reported previously ,17, initBy contrast, almost all participants who experienced their first SARS-CoV-2 infection (presumably BA.1 or BA.2 ) post-th+ T-cell counts and/or who are not receiving suppressive ART. Indeed, results from several studies indicate that PWH with CD4+ T-cell counts below 500\u200acells/\u03bcl mount weaker responses to the first [Our study has several limitations. Our observations may not be generalizable to PWH with low CD4he first \u201332 and she first \u201338 doseshe first , future he first \u201344.In conclusion, our observations confirm the humoral immune benefits of third COVID-19 vaccine doses in PWH receiving suppressive ART, and further reveal that the durability of third-dose responses is comparable to that in persons without HIV. Nevertheless, regardless of HIV status, individuals who remain COVID-19-naive will benefit from a fourth dose within 3\u20136\u200amonths of their third dose, as antibody concentrations and neutralization activities declined markedly over time in this group, and the ability of vaccine-induced responses to neutralize the dominant Omicron BA.5 variant were even poorer than BA.1. By contrast, the majority of individuals who experienced their first SARS-CoV-2 infection post-third vaccine dose showed significantly higher antibody activities than those induced by vaccination alone . These observations suggest that a slightly delayed fourth dose (e.g. to 3\u20136\u200amonths following infection) would optimally benefit this group. Further studies of hybrid response durability are required, as are direct comparisons with immune responses elicited by a fourth dose in COVID-19-naive individuals, particularly in light of new bivalent formulations that include wild-type and Omicron Spike antigens.This work is dedicated to the memory of our friend and colleague Hesham Ali who sadly passed away in July 2022. We thank the phlebotomists and laboratory staff at the BC Centre for Excellence in HIV/AIDS, the Hope to Health Research and Innovation Centre, St. Paul's Hospital, and Simon Fraser University for assistance. Above all, we thank the participants, without whom this study would not have been possible.Author contributions: M.A.B. and Z.L.B. are co-principal investigators and conceived the study, with C.T.C., C.C., A.H.A., V.L., M.H., M.G.R., R.G., S.G., J.S.G.M., M.H. and M.H. additionally contributing to study design and development. M.A.B., Z.L.B., M.G.R., A.H.A., C.T.C. and C.C. obtained project funding. M.A.B., Z.L.B., H.R.L., F.M. and P.K.C. designed experiments. H.R.L., R.M., P.K.C., Y.S., F.Y., S.S., E.B., N.M.-G., S.D., M.C.D., R.K., S.E., L.Y., B.G., F.H.O., G.U., J.T., P.S., L.B. and C.J.B. contributed to specimen collection, data collection, data curation and/or data analysis. H.R.L., Y.S., D.H., M.L.D., J.S., M.N., M.G.R., M.A.B. and Z.L.B. supervised the research, laboratory assays and/or contributed to project or cohort management. Z.L.B. performed statistical analyses with support from C.J.B.. N.P., C.F.L., M.G.R., W.D., C.J.B., and M.N. provided, generated and/or validated local Omicron isolates. H.R.L. wrote the first draft of the manuscript.Funding: this work was supported by funding from Genome BC, Michael Smith Health Research BC, and the BCCDC Foundation for Public Health through a rapid SARS-CoV-2 vaccine research initiative in BC award . It was also supported by the Public Health Agency of Canada (PHAC) through two COVID-19 Immunology Task Force (CITF) COVID-19 Awards . Additional funding was received from the Canadian Institutes for Health Research , the Coronavirus Variants Rapid Response Network , the Canada Foundation for Innovation through two Exceptional Opportunities Fund COVID-19 awards , a British Columbia Ministry of Health\u2013Providence Healthcare Research Institute COVID-19 Research Priorities Grant (to C.J.B. and C.F.L.) and the CIHR Canadian HIV Trials Network (CTN) (to A.H.A.). F.M. is supported by a fellowship from the CIHR Canadian HIV Trials Network. M.L.D. and Z.L.B. hold Scholar Awards from Michael Smith Health Research BC. F.Y. and E.B. were supported by SFU Undergraduate Research Awards. M.D. is supported by a CIHR Canada Graduate Scholarships-Master's award. G.U. and F.H.O. are supported by PhD fellowships from the sub-Saharan African Network for TB/HIV Research Excellence (SANTHE), a DELTAS Africa Initiative (grant # DEL-15-006). The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS)'s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa's Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust (grant # 107752/Z/15/Z) and the UK government. The views expressed in this publication are those of the authors and not necessarily those of PHAC, CITF, AAS, NEPAD Agency, Wellcome Trust, the Canadian or UK governments or other funders.https://doi.org/10.1101/2022.11.03.22281912Posted history: this manuscript is posted to MedRxiv: There are no conflicts of interest."} +{"text": "Middle cerebral artery occlusion/reperfusion (MCAO/R) was created in mice. Oxygen-glucose deprivation/reoxygenation (OGD/R) was performed in brain microvascular vessel-derived endothelial cells (bEnd.3) to mimic ischemia/reperfusion injury in vitro. P-gp-specific siRNA and pharmacological inhibitor cyclosporine A were used to inhibit P-gp, whereas pcDNA3.1 was utilized to overexpress P-gp. Twenty-four hours after reperfusion, acute ischemic stroke outcome, BBB integrity and permeability, autophagic proteins and relative signaling pathways were evaluated. P-gp levels were markedly elevated in mouse brain and endothelial cells following MCAO/R and OGD/R, respectively. P-gp siRNA silencing or pharmacologically inhibiting (cyclosporine A) reduced infarct volume and brain edema, attenuated brain pathology, and improved neurological behavior in association with attenuated accumulation of neutrophils and macrophages, reduced expression levels of inflammatory cytokines (TNF-\u03b1 and IL-1\u03b2), matrix metalloproteinases (MMP-2 and MMP-9) and adhesion molecules (ICAM-1 and VCAM-1). P-gp silence also counteracted BBB leakage, restored the expressions of tight junction proteins , activated autophagic proteins , and diminished Akt/mTOR signal activity in mice following MCAO/R. In the endothelial cell OGD/R assay, P-gp silence downregulated the expressions of inflammatory cytokines and adhesion molecules, inhibited leukocytes adhesion and migration, increased tight junction protein levels, and activated autophagy, all were reversible by forceful P-gp expression. Additionally, treatment with an autophagy inhibitor (3-methyladenine) abolished protections against ischemic stroke and tight junction proteins reduction followed by P-gp silence. In conclusion, increased P-gp expression after ischemic injury resulted in BBB dysfunction and hyperpermeability by suppressing Akt/mTOR-induced endothelial autophagy.P-glycoprotein (P-gp) is expressed on brain microvessel endothelial cells of blood-brain barrier (BBB) and elevated after cerebral ischemia. In this study, we explored the influence and potential mechanisms of P-gp on BBB function in experimental ischemic stroke Stroke is one of leading causes of disability and mortality worldwide, with ischemic stroke accounting for 87% of all stroke-related incidents . InflammP-glycoprotein (P-gp), also known as multidrug resistance transporter-1, is a membrane transport protein belonging to adenosine triphosphate (ATP)-binding cassette (ABC) transporter superfamily . As a maAutophagy is a self-eating cellular process to maintain cellular homeostasis and normal cellular functions , and is In this study, we investigated the effect and its underlying mechanisms of P-gp on BBB integrity in the mouse model of ischemic stroke. We found that elevated microvascular endothelial P-gp degraded endothelial tight junction, increased BBB hyperpermeability, accelerated brain inflammation and thus worsened ischemic stroke outcomes in association with increased Akt/mTOR activity and reduced endothelial autophagy.Male C57BL/6 mice weighting 22-25 g were purchased from Qinglongshan Animal Breeding Centre and used in all experiments. All animals were housed and fed freely in a temperature-controlled room (22 \u00b1 2\u00b0C) with a 12 h light-dark cycle. All experimental procedures were performed under licenses that granted by China Pharmaceutical University Animal Experimental committee , in compliance with the National Institutes of Health guidelines for the care and use of animals. Mice were randomly assigned into 6 treatments, including sham treatment, middle cerebral artery occlusion/reperfusion (MCAO/R) treatment, MCAO/R with negative control siRNA (NC siRNA) treatment, MCAO/R with NC siRNA and cyclosporine A treatments (NC siRNA + CsA), MCAO/R with P-gp siRNA treatment (MCAO/R + P-gp siRNA), MCAO/R with P-gp siRNA and 3-MA treatments (MCAO/R + P-gp siRNA + 3-MA). The treatment was administered in a blinded fashion. The researcher conducting the surgeries and behavior tests was unaware of the animal groups, and the researcher analyzing the data did not know the group condition.Mice were anesthetized by 3% isoflurane and maintained using 1.5% isoflurane and placed in a stereotaxic frame as previously described . The skiAutophagy inhibitor (3-MA) and P-gp inhibitor (CsA) were purchased from MedChemExpress LLC . 3-MA was prepared in normal saline immediately before use, and intracerebroventricularly injected at a dose of 15 \u03bcg per mouse 30 min prior to MCAO surgery . CsA wasFollowing 12 h fasting, MCAO/R was performed as described previously . Mice weTwenty-four hours after MCAO/R surgery, neurological score was graded as 0-4 based on Bederson\u2019s method , with hiThe whole brain was removed after mice were sacrificed at 24 h after reperfusion, and each brain was sliced into coronal sections (2 mm thickness). Brain slices were stained in TTC at 37\u00b0C for 20 min, photographed with a digital camera, and analyzed using the ImageJ software . HemisphTo estimate brain edema, brains were weighed prior to and 12 h after drying in a 110\u00b0C oven. Brain edema was calculated as percent of water content as following : Brain wTo evaluate the integrity of BBB , mice we2) at 37\u00b0C. The cells at 70-80% confluence was transfected with mouse P-gp (GGATCCAGTCTAATAAGAA) siRNA (50 pmol per well (6-well), RiboBio, Guangzhou, Guangdong, China) or P-gp pcDNA3.1 (+) using the lipofectamine 2000 reagent to silence or overexpress P-gp, respectively. The transfection efficiency was assayed 36 h after transfection by Western blot according to the manufacturer\u2019s recommendation. The control cells were transfected with the same volume of NC siRNA (RiboBio) or NC pcDNA3.1 (+) (Sangon Biotech).bEnd.3 cells were obtained from China Pharmaceutical University and cultured in high-glucose Dulbecco\u2019s Modified Eagle\u2019s Medium supplied with 10% fetal bovine serum , D-Glucose (4.5g/L), glutamine (2 mmol/L), penicillin (80 U/mL), streptomycin (0.08 mg/mL) and pyruvate (1 mmol/L) in humidified air (5% CO2 and 5% CO2) at 37\u00b0C for 2 h [2) and maintained in serum-free high-glucose DMEM for 24 h. In control group, cells were cultured in the chamber with serum-free high-glucose DMEM and normal culture conditions for the same period. The cells were treated with an autophagy inhibitor 3-MA (1 mmol/L) 1 h prior to OGD stimulation [Confluent bEnd.3 cells were washed twice and subjected to OGD/R by replacing with serum-free low-glucose DMEM in an anoxic incubator was replenished every 2 d. Approximately 6-7 d after seeded, bEnd.3 monolayers were obtained. Leukocyte (1\u00d7106 cells in 0.2 mL of DMEM) were added to upper chamber and incubated for 4 h in bEnd.3 cells. Migrated leukocytes were counted from the lower chamber. Leukocyte transendothelial migration was quantitated as the number of leukocytes per square millimeter.Leukocyte transendothelial cell migration assay was performed as previously described with sliBrains were harvested, fixed in 4% paraformaldehyde (PFA) for 24 h, dehydrated in graded ethanol, embedded in paraffin, and sectioned (6 \u03bcm). After deparaffinization and rehydration, sections were stained with Giles\u2019 hematoxylin and eosin (H&E) and imaged on a fluorescent inverted microscope .Paraffin sections (2 \u03bcm in thickness) were used for all staining. Briefly, following blocking endogenous peroxidase with PBS containing 3% hydrogen peroxide for 5 min, sections were stained with primary antibodies for neutrophils , macrophages , intercellular adhesion molecules-1 , vascular adhesion molecule-1 , and P-gp at 4\u00b0C overnight. Then, sections were incubated with Immunohistochemical staining kit for 1 h at room temperature. All stained sections were counterstained with Giles\u2019 hematoxylin and imaged on a fluorescent inverted microscope . To quantify P-gp expression levels, neutrophil and macrophages, randomly selected fields from the ischemic cortex were analyzed by using ImageJ software.Mice were anesthetized 24 h after reperfusion and perfused intracardially with cold 4% PFA followed by perfusion with PBS. Brains were fixed with 4% PFA and embedded in optimal cutting temperature compound (OCT), and sectioned (12 \u03bcm) followed by blocking nonspecific staining with 8% goat serum for 2 h at room temperature. For culture cells, the cells were fixed in 4% PFA for 20 min and incubated with solution containing 0.3% Triton X-100 in PBS (PBST) containing 8% goat serum for 2 h at room temperature for non-specific staining blocking and permeabilization .Tissue sections and cells were incubated with the primary antibodies against CD31 ICAM-1 (1:100), VCAM-1 (1:50), Claudin-5 , Occludin , Zonula occludens-1 , light chain 3 and glucocorticoid receptor at 4\u00b0C overnight. Following 3 washes with PBST, sections or cells were incubated with Cy3-conjugated goat anti-mouse IgG and FITC-conjugated goat anti-rabbit IgG for 2 h at room temperature, washed with PBST 3 times and counterstained with 4, 6-diamidino-2-phenylindole for 30 min at room temperature. Stained images were captured by a laser confocal microscope or a fluorescent microscope , and analyzed using ImageJ software.Total RNA was extracted using the RNA isolater and was transcribed into cDNA using a HiScript II Q RT SuperMix (Vazyme Biotech). Real time PCR was performed using quantitative PCR with a fluorescent dye (SYBR Green I). mRNA levels were normalized to \u03b2-actin of the same samples and were reported as fold changes relative to sham or control treatment . The priTotal protein was extracted using RIPA lysis containing protease and phosphatase inhibitor cocktail . Protein concentrations were determined by BCA assay. Proteins were separated by SDS-PAGE and transferred onto polyvinylidene fluoride (PVDF) membranes. After blocking with 5% non-fat milk in Tris-buffered saline with 0.05% Tween 20 (TBST) for 1.5 h at room temperature, the membrane was incubated with antibodies against P-gp (1:500), Claudin-5 (1:500), Ocluddin (1:1000), ZO-1 (1:1000), LC3 (1:1000), mTOR , p-mTOR , Akt , p-Akt and \u03b2-actin at 4\u00b0C overnight. After 3 times washes with TBST, the blots were incubated with HRP goat anti-rabbit IgG (H + L) or HRP-labeled goat anti-mouse IgG (H + L) for 2 h at room temperature. The bands were visualized using the enhanced chemiluminescence (ECL) reagents (Affinity Biosciences) and were quantified with ImageJ software. The protein expression levels were expressed as the percentage of \u03b2-actin.To evaluate the function of P-gp on glucocorticoid transport, mice were injected with exogenous glucocorticoid through femoral vein at 24 h after MCAO/R. Brains were harvested and ischemic hemisphere was separated at 5 min after the injection. Brain was homogenized with pure water with a mass/volume ratio of 1:3. Dexamethasone concentration in homogenates was determined by a UPLC-MS/MS system and given as ng/g ischemic brain tissue.P<0.05. All data are presented as the means \u00b1 SD.All statistical analyses were performed using IBM SPSS Statistics 19.0 software. The distribution of all data was tested for normality via a One-Sample Kolmogorov-Smirnov test. Statistical differences among the groups were analyzed by One-Way Analysis of Variance (ANOVA) with post hoc Tukey tests if data were normally distributed and consistent with homogeneity of variance among the experimental groups. The Mann-Whitney test was used to the compare ranks if the data were not normally distributed or not consistent with homogeneity of variance. The difference was considered significant at P<0.01). Treatment with NC siRNA did not impact P-gp expression, infarct volume, and brain histopathology. Therefore, NC siRNA + MCAO/R mice were used to observe P-gp function in following experiments as model control. P-gp siRNA pretreatment reduced infarct volume, attenuated neurological impairment, and improved histopathological damage as compared to NC siRNA treatment after MCAO/R (P<0.01).Mice underwent the MCAO surgery were included for successful occlusion. P-gp expression was substantially increased at ischemic hemisphere 24 h following MCAO/R surgery. Treatment with P-gp siRNA significantly reduced P-gp expression in ischemic brain as compared to NC siRNA treatment , P<0.01.r MCAO/R , P<0.01.P<0.01).Ischemic stroke breaks down BBB, leading to the entry of serum proteins into brain fluid and edema formation . Twenty-P<0.05).MMP-2 and MMP-9 degrade collagen IV that is a major component of basal lamina, and ultimately disrupt BBB . In RT-PP<0.01). In tissue immunostaining, neutrophils (MPO) and macrophages (F4/80) were observed in the infarct site 24 h after MCAO/R. However, P-gp siRNA treatment substantially reduced the densities of both neutrophils and macrophages as compared to NC siRNA treatment (P<0.01).ICAM-1 and VCAM-1 are important for recruiting leukocytes into inflamed brain. ICAM-1 and VCAM-1 levels were significantly lower in the ischemic area of mice treated with P-gp siRNA than those in mice treated with NC siRNA , P<0.01.reatment , P<0.01.P<0.05, P<0.01). These results indicate that silencing P-gp reduced BBB permeability by increasing TJPs expression.In the CNS, tight junctions form a barrier to limit paracellular permeability. In Western-blotting analysis, the expression levels of TJPs including Occludin, Claudin-5, and ZO-1 were largely reduced in ischemic brain of NC siRNA-treated MCAO/R mice. In contrast, P-gp siRNA treatment restored the expression levels of all proteins in ischemic area . In immunofluorescence staining, P-gp knockdown also dramatically enhanced LC3 expression in endothelial cells (CD31+) (P<0.01).To determine the influence of P-gp on endothelial autophagy, we assessed the expression of microtubule-associated protein LC3 and autophagy adapter protein P62, two well established markers for autophagy activation , 39. In (CD31+) , P<0.01.P<0.01). Glucocorticoid binds to glucocorticoid receptor (GR), induces GR nuclear translocation and thus inhibits Akt/mTOR activity [P<0.01).Akt/mTOR activity suppressed autophagy . As indiactivity . In ischP<0.05, P<0.01).To determine whether autophagy contributes to the suppression of ischemic stroke by P-gp inhibition, an autophagy inhibitor 3-MA was given to mice 30 min prior to stoke induction. 3-MA treatment did not alter P-gp expression in ischemic brain of P-gp siRNA-treated mice. However, inhibiting autophagy by 3-MA counteracted the effects of P-gp siRNA treatment on ischemic stroke outcome as indicated by enlarged infraction size, increased brain edema, worsened neurological defects and brain histopathology (P<0.05). Histologically, CsA treatment reduced infarct volume, brain edema, neurological behavior defects and brain histopathology induced by MCAO/R .Additionally, similar to P-gp siRNA silence, pharmacological inhibition of P-gp with CsA significantly attenuated P-gp expression levels in ischemic brain as compared to vehicle treatment , P<0.05.P<0.01). Preincubation with P-gp siRNA inhibited mRNA expressions of TNF-\u03b1, IL-1\u03b2, MMP-2, and MMP-9 in endothelial cells induced by OGD/R (P<0.05). Consistent with in vivo findings, P-gp knockdown substantially downregulated the expression of ICAM-1 and VCAM-1 on endothelial cells following OGD/R treatment (P<0.01). P-gp silence also mitigated leukocyte adhesion and transendothelial migration (P<0.01), while increased the expression levels of TJPs in endothelial cells undergoing OGD/R .Under OGD/R condition, P-gp expression was markedly elevated in endothelial cells (bEnd.3 cells). P-gp knockdown dramatically reduced P-gp expression as compared to NC siRNA incubation , P<0.01.by OGD/R , P<0.05.reatment , P<0.01.igration , P<0.01,P<0.01) as compared to NC plasmid pcDNA3.1. P-gp overexpression increased mRNA expression levels of TNF-\u03b1, IL-1\u03b2, MMP-2, and MMP-9 following OGD/R treatment as compared to NC plasmid pcDNA3.1 (P<0.05). Additionally, P-gp overexpression also increased adhesion molecules expression, augmented leukocytes adhesion and transmigration , whereas reduced the expression levels of Claudin-5, Occludin, and ZO-1 in endothelial cells following OGD/R .To examine the effect of P-gp overexpression, endothelial cells were transfected with P-gp pcDNA3.1 plasmid to forcefully express P-gp or with pcDNA3.1 plasmid serving the NC. P-gp pcDNA3.1 transfection remarkably upregulated P-gp expression , P<0.01 pcDNA3.1 ; P<0.05.P<0.01). These data indicate that P-gp silence led to autophagy activation to protect endothelial cells against OGD/R-induced cellular injury. Further, P-gp silence largely diminished the phosphorylation of Akt and mTOR protein signaling (P<0.05), suggesting that P-gp silence may activate autophagy by inhibiting Akt/mTOR signaling activity.To assess the influence of P-gp on autophagy and potential mechanisms, endothelial cells were transfected with P-gp or NC siRNA followed by OGD/R treatment. In Western-blotting and immunofluorescence staining analyses, P-gp silence dramatically increased the the ratio of LC3-II/LC3-I as well as Beclin 1 levels, whereas reduced P62 levels ; P<0.01.ignaling , P<0.05,P<0.05, P<0.01). When endothelial cells were incubated with a small molecule inhibitor 3-MA, the upregulation of TJPs by P-gp silence was almost ablated . Expectedly, 3-MA treatment reduced the ratio of LC3-II/LC3-I and Beclin 1 expression (P<0.01), whereas increased P62 expression (P<0.01). These results indicate that autophagy activation by P-gp silence may protect OGD/R-induced endothelial dysfunction.Although OGD/R treatment dramatically reduced TJPs levels in endothelial cells, P-gp silence increased the suppression of TJPs expression following OGD/R as compared to NC siRNA treatment (pression , P<0.01,pression , P<0.01.in vivo and in vitro. P-gp silence or pharmacological inhibition alleviated ischemic stroke by improving the integrity and function of BBB. Therefore, P-gp overexpression caused BBB dysfunction and exacerbated stroke outcome by destroying TJPs and worsening inflammatory response.Despite advances in our understanding of P-gp in multiple drug resistance, the role and underlying mechanisms in BBB dysfunction induced by ischemic stroke remain largely unknown. In this study, we found increased expression of P-gp in experimental ischemic stroke both in vitro, or overexpressed P-gp by transfecting endothelial cells with P-gp pcDNA3.1. We showed that P-gp siRNA relived acute stroke injury, including reduction in infarct volume, improvement in neurological behaviors, and decrease in brain edema. Similar effects were also observed using a P-gp inhibitor CsA. Therefore, elevated P-gp expression induced by ischemic stroke is vital for aggravating acute stoke injury.P-gp is involved in the pathogenesis of certain CNS diseases by regulating inflammatory cytokine expression and immune cell infiltration , 12. ThoP-gp is mainly expressed on BMVECs of BBB that functions as a semipermeable barrier between the CNS and the peripheral circulation , 46. In TJPs including ZO-1, Claudin-5, and Occludin are important in regulating the integrity and permeability of BBB and are disrupted and redistributed after ischemic stroke , 54. We Autophagy is a crucial degradation pathway for maintaining cellular and energy homoeostasis and protecting cell death . AutophaIn conclusion, we demonstrated that elevated P-gp levels following ischemic stroke exacerbated BBB breakdown and brain inflammatory response by increasing Akt/mTOR activity and suppressing autophagy activation. Our findings help understand the role and underlying mechanisms of P-gp in brain inflammatory response and BBB integrity following ischemic stroke.www.aginganddisease.org/EN/10.14336/AD.2022.0225.The Supplementary data can be found online at:"} +{"text": "Siphoviridae phage that infects Gordonia terrae 3612. The 68,128-bp genome of StarStruck has a GC content of 65.4% and contains 92 protein-coding genes, including the gene for a HicA-like toxin. StarStruck was assigned to subcluster CR2 based on >35% shared gene content with other cluster CR genomes in the Actinobacteriophage Database.Bacteriophage StarStruck is a lytic Actinobacteria, are extremely abundant and diverse icosahedral head and a 297.5-nm flexible, noncontractile tail (n = 3 particles).Actinobacteriophages, which are viruses that infect bacteria of the phylum diverse \u20134. By chdiverse \u2013, 6. Starrae 3612 . Soil exe assays . After ilysogens . The parCGCCGCGTAC). StarStruck shares >35% gene content with members of cluster CR in the Phamerator database Actino_Draft and was assigned to subcluster CR2 . Sequencster CR2 , 10, 11.http://cobamide2.bio.pitt.edu) and PECAAN (https://blog.kbrinsgd.org/) (http://phages.wustl.edu/starterator) analyses (The genome of StarStruck was autoannotated using GLIMMER v3.02 and GeneMark v2.5 within DNA Master v5.23.6 (gd.org/) , 13. Traanalyses . Putativanalyses , 15, 16.analyses , 18. Staanalyses . The laranalyses .Like many cluster CR phages, StarStruck encodes a HicA-like toxin (gp7) within the 12,000-bp region separating the small- and large-subunit terminases. Another interesting feature of StarStruck is the location of the lysin B (gp19) within this region, rather than adjacent to the lysin A genes (protease C39 domain [gp49] and glycosyl hydrolase domain [gp50]), which are located downstream of the minor tail proteins.ON456333 and the Sequence Read jhu7 (SRA) accession number SRX14816101.StarStruck is available at GenBank with the accession number"} +{"text": "Pancreatic ductal adenocarcinoma (PDAC) is currently the most deadly cancer. Although characterized by 5\u201320% of neoplastic cells in the highly fibrotic stroma, immunotherapy is not a valid option in PDAC treatment. As CXCR4-CXCL12 regulates tumor invasion and T-cell access and PD-1/PD-L1 controls immune tolerance, 76 PDACs were evaluated for CXCR4-CXCL12-CXCR7 and PD-1/PD-L1 in the epithelial and stromal component. Neoplastic CXCR4 and CXCL12 discriminated PDACs for recurrence-free survival (RFS), while CXCL12 and CXCR7 discriminated patients for cancer-specific survival (CSS). Interestingly, among patients with radical resection (R0), high tumor CXCR4 clustered patients with worse RFS, high CXCL12 identified poor prognostic patients for both RFS and CSS, while stromal lymphocytic-monocytic PD-L1 associated with improved RFS and CSS. PD-1 was only sporadically expressed (<1%) in focal lymphocyte infiltrate and does not impact prognosis. In multivariate analysis, tumoral CXCL12, perineural invasion, and AJCC lymph node status were independent prognostic factors for RFS; tumoral CXCL12, AJCC Stage, and vascular invasion were independent prognostic factors for CSS. CXCL12\u2019s poor prognostic meaning was confirmed in an additional perspective-independent 13 fine-needle aspiration cytology advanced stage-PDACs. Thus, CXCR4-CXCL12 evaluation in PDAC identifies prognostic categories and could orient therapeutic approaches. Pancreatic ductal adenocarcinoma (PDAC) represents the fourth leading cause of cancer-related deaths in economically advanced countries . In the Patients with resectable PDAC consecutThree-micrometer sections were cut from formalin-fixed paraffin-embedded (FFPE) tissue blocks. Sections were stained with hematoxylin and eosin for adequate tumor representation.2/field) for each ROI, on Olympus BX51 microscope . The evaluation was carried out by 3 qualified observers . For CXCR7 and CXCL12, staining extension was calculated for each case by the average percentage of positively stained cancer cells for the three ROIs. For CXCR4, due to heterogeneous staining patterns, the staining value was calculated by H-score. Staining intensity was based on membrane staining and rated as absent (0), weak/low (1+), and intermediate/moderate (2+), typically with cytoplasmic localization, strong/high (3+), typically cytoplasmic with membrane localization of CXCR4 staining. The % of positive cells at each staining intensity is obtained, and an H-score is determined by the sum of each intensity rating multiplied by its corresponding percentage. CXCR4 was scored as positive at H-score > 50, corresponding to PDAC with multiple subcellular signal accumulation (membrane and cytoplasm). CXCR7 and CXCL12 cells were rated positive when stained regardless of the cellular localization. CXCR7 was scored as positive with >20% positive cells [FFPE sections were dewaxed and rehydrated, and heat-induced epitope retrieval (HIER) with appropriate Antigen Unmasking Solution was performed. After incubation with the appropriate serum for blocking non-specific background, FFPE tumor tissue slides were incubated overnight at 4 \u00b0C using primary antibodies: Mouse Monoclonal anti-human Anti-CXCR7/RDC-1 Antibody ((11G8), HIER citrate buffer pH6, 1:50 dilution, R&D Systems); Mouse Monoclonal anti-human Anti-CXCL12/SDF-1 Antibody ((79018), HIER citrate buffer pH6, 1:50 dilution, #MAB350 R&D Systems); two commercial CXCR4 antibody clones the mouse Monoclonal anti-human Anti-CXCR4/CD184 ((44716) HIER, citrate buffer pH6, 1:100 dilution, #MAB172 R&D Systems) and the rabbit monoclonal anti-human Anti-CXCR4 ((UMB-2) HIER, Tris-EDTA buffer, pH 9.0, 1:200 dilution, Abcam); two commercial PD-L1 antibodies; the rabbit monoclonal anti-human anti-PD-L1/CD274 ((E1L3N) 1:200; diluted; HIER citrate buffer pH6, #13684 Cell Signaling Technology and (22C3) ready to use with HIER Conditioning Solution (CC1) pH9 Ventana Medical Systems); Mouse monoclonal anti-human PD-1/CD279 ((NAT-105) ready to use, HIER Cell Conditioning Solution (CC1) pH9, Ventana Medical Systems). Stained pancreatic cancer cells were assessed in at least three regions of interest (ROI)/slide, recognized at low power (100\u00d7 magnification), and the cells enumerated in 5 consecutive, not-overlapping high-power fields , and p > 0.1 (remove variable). p-values less than 0.05 were considered significant. All statistical tests and graphs were conducted using SPSS version 20 and MedCalc 12.3.0 .Association between CXCR4, CXCL12, CXCR7, and PD-1/PD-L1 expression cancer cells and patients\u2019 clinic-pathological features were analyzed applying chi-square and Mann\u2013Whitney U tests for categorical and continuous variables, respectively. Recurrence-free survival (RFS) was set as the time from diagnosis to the recurrence or last follow-up. Cancer-specific survival (CSS) was set as the time from diagnosis to death for cancer. Kaplan\u2013Meier method was performed to estimate the survival curve and logrank test for statistical comparison. Cox proportional hazards regression was utilized to test the effect of multiple dichotomous covariates (risk factors) on RFS and CSS; The backward method for variable selection was applied in the final model with a conventional A population of twenty patients diagnosed with advanced PDAC, evaluated through endoscopic-US-guided pancreatic fine-needle aspiration cytology (FNAC), was considered a validation cohort. The samples were collected and analyzed at Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania \u201cLuigi Vanvitelli\u201d, Naples, Italy, from January 2020 to October 2021. Three-micrometer sections were stained for CXCL12 immunocytochemical evaluation following hematoxylin/eosin reviewing and histological confirmation. All cases were retrospectively reviewed, and the cytology on direct smears showed moderately to richly cellular samples composed of three-dimensional aggregates of epithelial cells with severe cytological atypia. The cyto-block (CB) sections were also re-examined, with a cytological morphology substantially similar to that observed on direct smears; when necessary, immunocytochemical (ICC) analysis was performed, which showed positivity in the neoplastic cells for CK19 and CA 19\u20139. In all 20 cases selected, the overall morphological analysis was consistent with the diagnosis of pancreatic adenocarcinoma (Category VI sec. Papanicolaou System). ImmunoCytoChemistry (ICC) was carried out on CB sections and stained for CXCL12 as previously described.Clinical pathological characteristics of the 76 patients are presented in CXCR4 was highly expressed in 25 out of 76 tumors (32.9%) . CXCR4 mRepresentative low\u2013moderate and high CXCR4 expressions were reported C\u2013H. CXCRCXCR7 was highly expressed in 26 out of 76 (34.2%) tumors and lowly expressed or undetectable in 50 tumors (65.8%). The CXCR7 mean expression was 13.3 \u00b1 16.7% . Unlike CXCL12 was predominantly identified in the membrane in 20 out of 76 (26.3%) tumors. The CXCL12 mean expression was 3.7 \u00b1 7.20% . RepresePD-1 and its natural ligand PD-L1 were evaluated in 76 PDAC. While PD-1 was not detectable in cancer cells, it was only sporadically expressed (<1%) in focal lymphocyte infiltrate (data not shown). PD-L1 was predominantly identified at the membrane of cancer cells in 29/76 (38.2%) PDAC. PD-L1 mean expression was 3.4 \u00b1 7.1 . FigureC\u2013H. Tumor = 0.42, p = 0.004). The relation among the evaluated markers and clinic pathologic characteristics revealed that CXCR4-positive tumor and CXCR4-positive tumor-infiltrating inflammatory cells were associated with vascular invasion (p = 0.0421 and 0.045) as expected [p = 0.002) : 20.19\u201329.85); 33.60 months for cancer-specific survival CSS : 28.907\u201338.998). A total of 71 PDAC were analyzed for RFS; 58/71 (81.7%) patients experienced recurrence, with mean RFS durations of 17.30 months, and 13 (18.3%) did not experience recurrence up to 60.52 months. Out of 76, 4 patients were excluded for cancer-unrelated death; 72 PDAC were analyzed for CSS, 56/72 (77.8%) with mean CSS durations of 25.30 months, and 16/72 (22.2%) patients were alive at a mean of 62.65 months. Univariate analyses of RFS and CSS are summarized in p = 0.0024; CSS: 21.9 months vs. 36.6 months p = 0.08, not significant) (Patients with high CXCR4 expression had a significantly worse outcome (RFS: 11.76 months vs. 26.0 months ificant) A.n = 48) (RFS: 11.05 months vs. 33.70 months p = 0.0071) (p = 0.0001) and CSS (p = 0.0001) and CSS (p = 0.017) in R0 patient\u2019s subgroup (p = 0.0441) but not CSS (p = 0.0605) ( 0.0071) A. CXCL12 0.0024) B. Moreovsubgroup B. Patien 0.0605) C. PD-L1 0.0605) D.p = 0.016) and CSS (0.047) in R0 patients, , perineural invasion (p = 0.0107), and CXCL12 (p = 0.00002) but not CXCR4, predicted shorter poor RFS (p = 0.00007), vascular invasion (p = 0.0067), and CXCL12 (p= 0.0062) but not CXCR7 nor CXCR4 expression predicted shorter poor CSS . The median age was 72 \u00b1 10 years (range 50\u201385), with 8 (40%) male and 12 (60%) female, and 17 (85%) of patients \u226560 years old. At diagnosis, the majority of patients (85%) had an advanced stage. CXCL12 was detected in 70% (14/20) PDACs predominantly at the membrane and cytoplasm of cancer cells , showing a median overall survival of 6 months. The patients with a high sharp, consistent distribution of CXCL12 expression showed short CSS with a median survival of 3 months, while low/negative CXCL12 expressing displayed short CSS with a median survival of 12 months (= 0.029) .p \u2265 0.05) as for NCCN 2022 guidelines. In our analysis, chronic pancreatitis was a \u201cpotential risk factor\u201d not retained, for irrelevance or redundancy, in the multivariate analysis. As for PD-L1, early studies showed prognostic significance for overall survival with >5 or 10% cut-off [The role of the CXCR4-CXCL12-CXCR7 axis and PD-1/PDL-1 was addressed in tumor/stromal cells in 76 consecutive single-center patients undergone surgery between January 2014/March 2015 and followed for 5 years until January 2021. We demonstrated that the entire axis CXCR4-CXCL12-CXCR7 was overexpressed in PDAC neoplastic cells as compared to TME cells. Moreover, CXCL12 significantly correlated with poor prognosis in an unrelated cohort of 20 FNAC from PDAC patients. CXCR4 was expressed by acinar cells and islets of Langerhans, surrounded by extensive dense fibrotic stroma or desmoplasia . Trefoil cut-off ,50. Alth cut-off .MMR) proteins) and sample size. In agreement with the herein reported data, Diana et al. examined the prognostic value of PD-1 and PD-L1, together with CD8+ tumor-infiltrating lymphocytes (TILs) and FOXP3+ Tregs in 145 PDAC samples, describing PD-L1 expression not prognostic [Karamitopoulou reported PD-L1 expression in about one-third of 349 samples. The authors concomitantly analyzed PD-L1, PD-1, CD3, CD4, CD8, FoxP3, and CD68, reporting that PD-L1, present with T-cell infiltration, improved overall survival . Herein,ognostic . Wang etognostic . As relaPD-L1 was recently reported in stromal cells in PDAC , and als"} +{"text": "Accurate polyp size measurement is important for guideline conforming choice of polypectomy techniques and subsequent surveillance interval assignments. Some endoscopic tools (forceps or endoscopic rulers [ER]) exist to help with visual size estimation. A virtual scale endoscope (VSE) has been developed that allows superimposing a virtual measurement scale during live endoscopies.Our aim was to evaluate the performance of VSE when compared to ER and forceps-based measurement.We conducted a randomized trial to evaluate the relative accuracy of size measurement of simulated colorectal polyps when using: VSE, ER, and forceps. Six endoscopists performed 60 measurements randomized at a 1:1:1 ratio using each method. Primary outcome was relative accuracy in polyp size measurement. Secondary outcomes included misclassification of sizes at the 5, 10, and 20mm thresholds.A total of 360 measurements were performed. The relative accuracy of biopsy forceps, ER, and VSE was 78.9% (95%CI=76.2-81.5), 78.4% (95%CI=76.0-80.8), and 82.7% (95%CI=80.8-84.8). VSE had significantly higher accuracy compared to biopsy forceps (p=0.02) and ER (p=0.006). VSE misclassified a lower percentage of polyps >5mm as \u22645mm (9.4%) compared to forceps (15.7%) and ER (20.9%). VSE misclassified a lower percentage of \u226520mm polyps as <20mm (8.3%) compared with forceps (66.7%) and ER (75.0%). 25.6%, 25.5%, and 22.5% of polyps \u226510mm were misclassified as <10mm with ER, forceps, and VSE, respectively.VSE had significantly higher relative accuracy in measuring polyps compared to ER or forceps assisted measurement. VSE improves correct classification of polyps at clinically important size thresholds.NoneR. Djinbachian: None Declared, M. Taghiakbari: None Declared, C. Haumesser: None Declared, M. Zarandi-Nowroozi: None Declared, M. Abou-Khalil: None Declared, S. Sidani: None Declared, J. Liu: None Declared, B. Panzini: None Declared, D. von Renteln Grant / Research support from: Daniel von Renteln is supported by a \u201cFonds de Recherche du Qu\u00e9bec Sant\u00e9\u201d (FRQS) career development award and has received research funding from ERBE, Ventage, Pendopharm, Fujifilm, and Pentax., Consultant of: Boston Scientific and Pendopharm,"} +{"text": "All authors agree with this retraction.1. Kang, H., Ma, D., Zhang, J. et al. Long non-coding RNA GATA6-AS1 upregulates GATA6 to regulate the biological behaviors of lung adenocarcinoma cells. BMC Pulm Med 21, 166 (2021)."} +{"text": "Cytochrome P450 family 8 subfamily B member 1 (CYP8B1) generates 12\u03b1-hydroxylated bile acids (BAs) that are associated with insulin resistance in humans.CYP8B1 in individuals without diabetes and identified carriers of complete loss-of-function (CLOF) mutations utilizing functional assays.To determine whether reduced CYP8B1 activity improves insulin sensitivity, we sequenced CYP8B1 mutation associated with lower fasting insulin in the AMP-T2D-GENES study. Exposure of primary human muscle cells to mutation-carrier CA/CDCA ratios demonstrated increased FOXO1 activity, and upregulation of both insulin signaling and glucose uptake, which were mediated by increased CDCA. Inhibition of FOXO1 attenuated the CDCA-mediated increase in muscle insulin signaling and glucose uptake. We found that reduced CYP8B1 activity associates with increased insulin sensitivity in humans.Mutation carriers had lower plasma 12\u03b1-hydroxylated/non\u201312\u03b1-hydroxylated BA and cholic acid (CA)/chenodeoxycholic acid (CDCA) ratios compared with age-, sex-, and BMI-matched controls. During insulin clamps, hepatic glucose production was suppressed to a similar magnitude by insulin, but glucose infusion rates to maintain euglycemia were higher in mutation carriers, indicating increased peripheral insulin sensitivity. Consistently, a polymorphic CLOF Our findings suggest that increased circulatory CDCA due to reduced CYP8B1 activity increases skeletal muscle insulin sensitivity, contributing to increased whole-body insulin sensitization.Biomedical Research Council/National Medical Research Council of Singapore. Cyp8b1 show almost no 12\u03b1-hydroxylated BAs and elevated non\u201312\u03b1-hydroxylated BAs (Bile acids (BAs) are products of cholesterol catabolism, accounting for approximately 50% of daily cholesterol turnover in humans, and act as surfactants to promote intestinal lipid absorption . The priNR1H4) and membrane G protein\u2013coupled BA receptor . Of these, 58 were predicted to be possibly or probably damaging by the functional prediction tool Polyphen 2.0 , and 41 were predicted to be damaging by SIFT . We generated all 100 variants in human CYP8B1 cDNA, quantified the product generated by each variant, and found a spectrum of defective CYP8B1 activities, classified as complete loss of function (CLOF) (<15% activity of wild-type), partial loss of function (PLOF) (15% to 85% activity of wild-type), or benign (>85% activity of wild-type) . We idenCYP8B1 mutation carriers, and 41 age-, sex-, BMI-, and race-matched controls to our clinical study. P = 0.04) and APOB/APOA-I (P = 0.04) ratios, suggesting reduced risk for atherosclerosis. In addition, high-sensitivity C-reactive protein (hs-CRP) levels were decreased by approximately 50% in the mutation carriers (P = 0.06), suggesting reduced systemic inflammatory status and lower atherosclerotic risk in carriers (P = 0.02), resulting in a 63% decrease in the CYP8B1 product/substrate ratio ( 0.0002) . CYP8B1\u2019 0.0001) .P = 0.003) (P = 0.01), and both glycine- (P = 0.01) and taurine-conjugated (P = 0.048) CA were decreased (P = 0.03) (P = 0.01) . Unconjuecreased . CDCA di = 0.03) . The CA/ = 0.01) . The BA CYP8B1 mutation carriers. Thus, we assessed whether CYP8B1 mutation carriers showed improved insulin sensitivity. Although fasting glucose was unchanged, fasting insulin was decreased by 28% in carriers (P = 0.03) (P = 0.03), as well as QUICKI, another measure of insulin sensitivity (P = 0.04) , insulin levels were decreased in carriers (P = 0.02) and the glucose infusion rate (GIR) was increased by 30% in carriers (P = 0.02) (P = 0.04) and GIR by 25% in carriers.12\u03b1-Hydroxylated BAs correlate with insulin resistance in humans , and 12\u03b1 = 0.03) . Accordi = 0.03) . The Mat = 0.04) , were in = 0.03) . During = 0.046) . The ins = 0.02) . The aboP = 0.38) (P = 0.48) (P = 0.58) (P = 0.19) , glucone = 0.48) , and gly = 0.58) , indicatCYP8B1 mutations have improved insulin sensitivity, we performed association analyses using the Type 2 Diabetes Knowledge Portal (http://www.type2diabetesgenetics.org), which enables association analyses between coding variation and glycemic traits in 45,231 exomes (CYP8B1 variants (R26X) was both a CLOF mutation (0.6% activity compared with wild-type CYP8B1), common in our study cohort , and present in several copies in the AMP-T2D-GENES data set. Association analyses showed that carriers of R26X had significantly lower fasting insulin levels after adjusting for BMI . These data are consistent with our findings of increased insulin sensitivity in the face of decreased CYP8B1 activity in the CYP8B1 mutation carriers.To confirm that humans with CLOF 1 exomes . Of the variants , only 1 P = 0.65) (P = 0.04) and GLP-1 during MMTT were decreased . Glucago = 0.65) . Both faecreased , in lineIRB being the predominant isoform in insulin target tissues, including muscle (256) is cytoplasmic, whereas dephosphorylated FOXO1 is retained in the nucleus where it functions as a transcription factor (256)FOXO1 was decreased in muscle cells exposed to the carrier BA mix in response to insulin, suggesting increased nuclear localization and transcriptional activity of FOXO1 in carriers (473)AKT was increased by 116% in muscle cells treated with the carrier CA/CDCA ratio in response to insulin (P = 0.004) , suggest= 0.002) . FOXO1 e = 0.04) . Phosphon factor . Phospho= 0.036) . Phospho= 0.036) . Phospho= 0.029) . Additio= 0.004) , confirm473)AKT was increased approximately 2-fold in muscle cells treated with the median carrier CA/CDCA ratio in response to insulin (P = 0.009) and lowest insulin sensitivities (CA/CDCA = 21:29). Thus, we assessed whether the median CA/CDCA ratio of the mutation carriers (CA/CDCA = 4.5:45.5) would increase muscle cell insulin signaling and glucose uptake when compared with the median CA/CDCA ratio of noncarrier controls (CA/CDCA = 8.3:41.7). Phospho(S 0.0008) . In line= 0.009) . These dCYP8B1 mutation carriers, suggesting that increased CDCA may be sufficient to increase muscle insulin sensitivity. Thus, we next assessed whether CDCA alone was sufficient to increase muscle insulin signaling. Exposure of muscle cells to CDCA, but not CA, increased phospho(S473)AKT in response to insulin (Insr and Foxo1 expression (256)FOXO1 levels (473)AKT levels , indicatP = 0.8) . Moreovepression , and decP = 0.2) . To furtCYP8B1 mutation carriers (473)AKT or glucose uptake AKT/AKT ratio , and on P = 0.6) . These dCYP8B1 improves insulin sensitivity in humans. Although BA synthesis involves several enzymes, and complex feedback and feedforward mechanisms are involved in the regulation of BA metabolism . It is possible that CDCA modulates intracellular signaling through as yet unidentified muscle-specific cell surface receptors or BA transporters. Our data suggest that CDCA modulates muscle insulin signaling through increasing muscle FOXO1 activity, and inhibition of FOXO1 reversed the increased CDCA-mediated muscle insulin signaling. How CDCA decreases muscle FOXO1 phosphorylation, thus increasing its nuclear retention and transcriptional activity, remains unclear. One possible mechanism by which CDCA may reduce phospho-FOXO1 is by increasing the activity of phosphatases acting on FOXO1. BAs do modulate other phosphatases such as Src-homology 2 domain\u2013containing tyrosine phosphatase 2 (SHP2) .The reason for the potential selectivity of CDCA for skeletal muscle in regulating insulin sensitivity is unclear. However, FOXOs show tissue-specific protein interactions to modulate their functions in metabolic regulation . DistincCYP8B1 mutation carriers showed decreased total cholesterol/HDL-C and APOB/APOA-I ratios, suggesting that CYP8B1 inhibition may reduce type 2 diabetes without proatherogenic lipid changes. In addition, hs-CRP levels were decreased by approximately 50%, and hepatic fat was decreased by 30% in the CYP8B1 mutation carriers. These observations are consistent with those in \u2013/\u2013Cyp8b1 mice, which showed increased HDL-C, decreased LDL-C, and reduced atherosclerotic lesions when fed atherogenic diets , an analog of CDCA, was assessed in type 2 diabetics . Increasic diets , 27. Addgression , suggestCYP8B1 mutation carriers.The CYP8B1 product, 7\u03b1,12\u03b1-dihydroxy-4-cholesten-3-one, was not decreased in plasma of mutation carriers. However, downstream 12\u03b1-BAs were decreased by 52%, suggesting that the 12\u03b1-hydroxylase function of CYP8B1 in the liver was indeed reduced. Significantly increased unconjugated CDCA was also not observed in mutation carriers, although the ratio of CDCA and its conjugates to total BAs was increased. The reasons for this are unclear. In the mutation carriers, plasma BAs were quantified after an overnight fast. However, it has been shown that circulatory BA levels increase postprandially, with CDCA showing the largest increase (up to 5-fold) . Further\u2013/\u2013Cyp8b1 mice are viable, with no apparent adverse phenotypes, suggesting that the absence of CYP8B1 may not be harmful. We did not identify compound heterozygous or homozygous carriers of CLOF mutations, and almost all CLOF mutations were identified in only 1 or 2 heterozygotes. Thus, homozygous or compound heterozygous CLOF mutation carriers are likely to be extremely rare. One CLOF mutation, R26X, was found at 1.6% frequency in Malays. Assuming Hardy-Weinberg equilibrium, sequencing of approximately 13,000 Malays is required to identify a single R26X homozygote. Thus, it is unsurprising that we identified no homozygous or compound heterozygous CLOF mutation carriers. Additionally, in a large publicly aggregated database (gnomAD), no individuals harboring homozygous predicted CLOF mutations were reported, confirming that these individuals are extremely rare.We establish a fundamental role for CYP8B1-mediated changes in BA composition in the regulation of peripheral insulin sensitivity. We show that reduced activity of CYP8B1 is efficacious in increasing insulin sensitivity in humans, and mechanistically link CDCA signaling to muscle insulin sensitivity. We demonstrate here a target for future therapeutic intervention for diabetes.Detailed methods are provided in the supplementary material.CYP8B1 coding region was Sanger sequenced in population cohorts of nondiabetics from the Singapore Eye Research Institute and the Saw Swee Hock School of Public Health, National University of Singapore. Sequences were assembled in Sequencher (Gene Codes) and aligned to the human CYP8B1 reference sequence (GenBank AF090320.1). All nonsynonymous variants, frameshifts, and insertions/deletions were generated in human CYP8B1 cDNA and functionally characterized.The CYP8B1 cDNA inserted into pcDNA3.1(+) (Invitrogen) was used as the template for site-directed mutagenesis. The neomycin resistance cassette in pcDNA3.1(+) was replaced with green fluorescent protein (Gfp) in order to assess transfection efficiency of the variants. Mutagenesis primers were designed for each of the CYP8B1 variants, and PCR performed with conditions adjusted for each primer pair, amplifying the entire plasmid. PCR products were isolated from the template by Dpn1 digestion, transformed into DH5\u03b1 competent cells, and amplified plasmids were extracted by E.Z.N.A. Plasmid Mini Kit II (Omega Bio-tek Inc). The mutant CYP8B1 cDNAs were sequence confirmed, subcloned into the pcDNA3.1(+)-Gfp vector, and used for the in vitro assay. For the in vitro functional assay, HEK293T (ATCC) cells in 6-well plates were transiently transfected with the plasmids harboring wild-type CYP8B1, variant CYP8B1, or empty vector using X-tremeGENE HP (Roche). After 24 hours, fresh DMEM with 10% FBS containing 10 \u03bcmol/L of the CYP8B1 substrate 7\u03b1-hydroxy-4-cholesten-3-one was added to the cells at 3 mL/well. After 4 hours, media were collected, centrifuged, and frozen until quantification of 7\u03b1,12\u03b1-dihydroxy-4-cholesten-3-one by LC/MS . Cells were washed, centrifuged, and frozen for Western immunoblotting.CYP8B1 mutations and age-, sex-, race-, and BMI-matched nonmutation carrier controls from the same cohorts were recruited at a ratio of 1 carrier to 2 controls for metabolic studies. Five participants only had 1 matched control. The studies of BAs and insulin phenotypes excluded individuals with BMI greater than 30, the World Health Organization definition of obesity, since obesity modulates insulin sensitivity. Individuals were also excluded if they had type 2 diabetes mellitus, renal impairment, elevated serum aspartate aminotransferase or alanine aminotransferase, chronic liver disease, or medications or previous gastrointestinal surgery that may alter glucose or BA metabolism were measured in plasma following overnight fasts using ultraperformance liquid chromatography\u2013multiple reaction monitoring/mass spectroscopy (UPLC-MRM/MS) (University of Victoria-Genome BC Proteomics Centre) as described previously .After 8-hour fasts, venous blood was collected for plasma glucose, insulin, and GLP-1 measurements at 0, 15, 30, 60, 90, and 120 minutes after ingestion of liquid mixed meal .2H2O for quantification of gluconeogenesis and glycogenolysis. To measure hepatic glucose production, primed-constant infusion of -glucose was performed. Insulin was infused at 40 mU/m2 body surface area/min for 180 minutes. Blood glucose was measured every 5 minutes. Blood for plasma insulin measurement was obtained every 30 minutes. Dextrose 20% (wt/vol) enriched with -glucose was infused at a variable rate to maintain blood glucose at 100 mg/dL with a coefficient of variation of less than 5%.Participants ingested 2 doses of CYP8B1 mutant R26X, selected because it was the most frequent in our study cohort, were performed using the publicly available Type 2 Diabetes Knowledge Portal (http://www.type2diabetesgenetics.org). Associations between R26X and fasting insulin, adjusted for BMI, age, and sex were calculated using the portal\u2019s Genetic Association Interactive Tool (GAIT), in which single-variant and gene-level association analysis can be conducted in 45,231 exomes from the AMP-T2D-GENES study.Association analyses for the CLOF Human adult skeletal muscle cells (Cell Applications) were differentiated following manufacturer\u2019s instructions and treated with a 50 \u03bcmol/L CA/CDCA mixture at the ratio of carrier or control, or dimethyl sulfoxide (DMSO) for 24 hours. To quantify AKT and FOXO1 phosphorylation subsequent to insulin stimulation, differentiated cells were treated with 100 nmol/L insulin . For glucose uptake assays, BA-treated cells were incubated with and without 100 nmol/L insulin, glucose uptake was quantified using fluorescence, and protein content was determined for normalization of glucose uptake.t tests. Non-normal data are reported as median (IQR) and were analyzed using the nonparametric Mann Whitney U test. Fisher\u2019s exact tests were used for categorical data, 1-way ANOVA was used for analyses of more than 2 groups, and 2-way ANOVA was used for repeated measures. All tests were 2-sided, and performed using GraphPad Prism 9.0. A P value of less than 0.05 was considered significant.All human data were first assessed for normality. Non-normal data were log transformed. Normal data are reported as mean \u00b1 SEM and were analyzed using parametric unpaired The human study received approval from the SingHealth Centralized Institutional Review Board. All participants provided written informed consent prior to the study.RRS, MRH, AKG, and HCT conceptualized the study. RRS and HCT acquired funding. RRS, HCT, FK, JLG, RMVD, RST, KAR, and CYC supervised the study. RRS wrote the original draft of the manuscript. SZ, RC, MC, DCM, BJC, KPS, THVD, JP, LJT, SVH, BR, PC, JLG, SC, JF, and XS conducted the investigation and analyses. JLG, AKG, FK, SC, JF, KAR, XS, HCT, and RRS provided resources. SZ, AKG, FK, CD, HCT, and MRH reviewed and edited the manuscript."} +{"text": "Xanthomonas is a genus of gram-negative bacterium containing more than 35 species. Among these pathogenic species, Xanthomonas albilineans is of global interest, responsible for leaf scald disease in sugarcane. Another notable Xanthomonas species is Xanthomonas sachari (Xsa), a sugarcane-associated agent of chlorotic streak disease.Xanthomonas strains was evaluated by disease index (DI) and Area Under Disease Progress Curve (AUDPC) in the susceptible inoculated plants (GT 46) and clustered into three groups of five highly potent, seven mild virulent, and twelve weak virulent strains. The highly potent strain and its weak virulent related strain were sequenced, assembled, and annotated in the circular genomes. The genomic size of JG43 was smaller than that of DD13. Both strains (JG43 and DD13) lacked a Type III secretory system (T3SS) and T6SS. However, JG43 possessed Salmonella pathogenicity island-1 (SPI-1). More pathogen-host interaction (PHI) genes and virulent factors in 17 genomic islands (GIs) were detected in JG43, among which six were related to pathogenicity. Albicidin and a two-component system associated with virulence were also detected in JG43. Furthermore, 23 Xanthomonas strains were sequenced and classified into three categories based on Single Nucleotide Polymorphism (SNP) mutation loci and pathogenicity, using JG43 as a reference genome. Transitions were dominant SNP mutations, while structural variation (SV) is frequent intrachromosomal rearrangement (ITX). Two essential genes (rpfC/rpfG) of the two-component system and another gene related to SNP were mutated to understand their virulence effect. The mutation of rpfG resulted in a decrease in pathogenicity.The virulence of 24 Xanthomonas strains and variations by 23 Xanthomonas strains. We sequenced, assembled, and annotated the circular genomes of Xal JG43 and Xsa DD13, identifying diversity detected by pathogenic factors and systems. Furthermore, complete genomic sequences and sequenced data will provide a theoretical basis for identifying pathogenic factors responsible for sugarcane leaf scald disease.These findings revealed virulence of 24 The online version contains supplementary material available at 10.1186/s12864-022-08900-2. Xanthomonas is a large genus of gram-negative, yellow-pigmented bacteria associated with plants. The genus, which locates at the base of the Gamma proteobacteria, comprises 27 species that cause severe diseases in\u2009~\u2009400 plant hosts, including a wide variety of economically important crops, such as rice, citrus, banana, cabbage, tomato, pepper, and bean \u2009\u00d7\u2009100.Furthermore, the area under the disease-progress curve (AUDPC) value was calculated , 86.\\docyi is the severity of the symptoms at the ith observation; xi\u2014day at the ith observation, and n\u2014the total number of observations.where AUDPC is the area under the disease progress curve, X. albilineans JG43 was sequenced by Oxford Nanopore Technologies (ONT) and assembled using Canu (V1.5) [X. sacchari DD13 was sequenced using SMRT II sequencing technology , and a complete circular bacterial chromosome was assembled using HGAP software [The genome of u (V1.5) . Assemblsoftware . The gensoftware .https://www.repeatmasker.org/) [http://eddylab.org/infernal/) [http://lowelab.ucsc.edu/tRNAscan-SE/) [https://www.ebi.ac.uk/Tools/psa/genewise/) [http://www.pathogenomics.sfu.ca/islandviewer/) [http://phispy.sourceforge.net/) [Assembled genome was analyzed to identify the repeat sequences that were searched against the known repeat sequence database (Repbase) in the bacterial genome using RepeatMasker (V4.0.5) (er.org/) . Non-codfernal/) , while tcan-SE/) . The Gennewise/) . Genomicviewer/) , and proge.net/) .www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/) [https://www.genome.jp/kegg/) [https://www.expasy.org/resources/uniprotkb-swiss-prot) and TrEMBL (http://www.bioinfo.pte.hu/more/TrEMBL.htm) [https://www.ebi.ac.uk/Tools/hmmer/) [https://www.blast2go.com/) [The genes were blasted against the databases of non-redundant proteins (oteins/) , Kyoto Ep/kegg/) , Swiss-PMBL.htm) . Pfam fu/hmmer/) . Functiogo.com/) , 101.http://www.cazy.org/) using HMMER software [http://www.cbs.dtu.dk/services/TMHMM/), Kohgpi (http://gpi.unibe.ch/) [http://www.cbs.dtu.dk/services/SignalP/) [https://card.mcmaster.ca/) using RGI in CARD Database [http://www.mgc.ac.cn/VFs/) [Carbohydrate EnZymes genes were annotated against Carbohydrate Active EnZymes Database (CAZyme) (software . Transmeibe.ch/) , and SigignalP/) . TransmeDatabase . The vircn/VFs/) .Xal JG43 by GATK software (https://gatk.broadinstitute.org/hc/en-us) [X. albilineans strains was sequenced using Illumina Novaseq 6000 platform, with an average coverage of 339\u2009\u00d7\u2009. The redundant reads (MarkDuplicates) were filtered by Picard software to ensure the detection accuracy of clean reads [X. albilineans, which were used to construct a phylogenetic tree. After removing ambiguous positions, a final dataset of 17,935 SNPs was generated for each sequence, which was aligned through the neighbor-joining method of MEGA7 software, utilizing the bootstrap value of 1000 replicates [Single nucleotide polymorphism (SNP) was called against the reference genome of c/en-us) . The genan reads . A totalplicates , 110.Xal genomes with Xal JG43, and the aligned reads were sorted using Samtools (V1.12) [Minimap2 (V2.17) was used to align the 23 sequenced (V1.12) . BCFtool (V1.12) . BEDTool (V1.12) . Circos (V1.12) .The single-base mutation was performed by the PNA-directed PCR clamping , and twopK18mobSacB plasmid to form a recombinant plasmid. The recombinant plasmid was digested, verified, and sequenced. The recombinant plasmid was introduced into the host bacterium by electro-transformation. The upstream and downstream of the target gene underwent single homologous exchange and double homologous exchange with the homologous fragment of the host bacterium. A 10% sucrose was used to screen double homologous exchange. Furthermore, internal and external primers were also used to screen double homologous exchange. Finally, the target gene was deleted , (c) and (d) show leaf scald symptoms after X. albilineans invade sugarcane; (b) Colony of X. albilineans isolated from diseased sugarcane plant; Right side: X. sacchari cause chlorotic streak disease. (a), (c) and (d) show chlorotic streak symptoms after X. sacchari infect sugarcane; (b) Colony of X. sacchari isolated from the diseased sugarcane plant. Fig.S2. Type III secretion system (T3SS) (a), and SPI-1 family (b) of six Xanthomonasspecies. Fig. S3. Type IV secretion system (T4SS) (a), T5SS and T6SS (b) of six Xanthomonas species. Fig. S4. Potential pathogenic factors of six Xanthomonas species, including CRISPR system, Lipopolysaccharide transport system protein, Glycogen, Type III secretion regulators, Two-component system regulators, Three-component system, and TALEs. Fig. S5. Verification of rpfC and rpfH mutations. (a) PCR amplification from the upstream and downstream 500 bp of rpfC. M: 2000 bp; Lane 1: rpfC Gene left arm; Lane 2: rpfC gene right arm. (b) Validation of enzymic fragment ligated with PK18mobsacB, a 500bp upstream and downstream fragment of rpfC gene. M: 5000 bp; Lane 1,2,3\uff1aValidation of rpfC recombinant plasmid fragment by enzyme digestion; Lane 4 not included in this experiment. (c) PCR amplified from mutants and its wild type JG43. M:1000 bp; Lane 1, 2, 3; PCR fragment amplified with mutants; Lane 4: PCR fragment amplified with JG43 as template; Lane 5: Water control; Lane 6, 7, 8: Internal primer verification of the target fragment missing in 123, none, which proves the successful deletion of rpfC gene; Lang 9: Internal primer fragment of PCR amplified with JG43 as template. (d)PCR validation of rpfHgene. M:1000 bp; Lane 1:Xcc8004; Lane 2: DD13; Lane 3: JG43; Lane 4: Water control;Lane 5: not included in this experiment. Fig. S6. rpf gene cluster of six Xanthomonas species. Fig. S7. PCR validation of single-base SNPs mutations. (a) PCR validation of single-base SNP mutations of candidate genes in FS 12. M:2000 bp; Lane 1: 1312440-G-C-L; Lane 2: 1312440-G-C-R; Lane 3: 1316566-A-G-L; Lane 4: 1316566-A-G-R; Lane 5: 1316572-A-G-L; Lane 6: 1316572-A-G-R; Lane 7: 1316840-G-A-L; Lane 8: 1316840-G-A-R; Lane 9: 1316855-T-C-L; Lane10: 1316855-T-C-R; Lane 11: 1316974-A-G-L; lane12: 1316974-A-G-R; lane13: 1317164-T-C-L; Lane 14: 1317164-T-C-R; Lane 15: 3055754-G-A-L; Lane 16: 3055754-G-A-R. (b) PCR validation of single-base SNP mutations of candidate genes in FS12 (Lanes 1 and 2), FS25 (Lanes 3 and 4), FS63 (Lanes 5 and 6) and NM10 (Lanes 7 and 8). M:2000 bp; Lane 1: 3055807-G-C-L; Lane 2: 3055807-G-C-R; Lane 3: 2749153-C-T-L; Lane 4: 2749153-C-T-R; Lane 5: 1508978-C-A-L; Lane 6: 1508978-C-A-R; Lane 7:1510223-A-C-L; Lane 8: 1510223-A-C-R. (c) SNP point mutation fusion fragment in FS12. M:2000 bp; Lane 1: 1312440-G-C; Lane 2: 1316566-A-G; Lane 3: 1316572-A-G; Lane 4:1316840-G-A; Lane 5: 1316855-T-C; Lane 6:1316974-A-G; Lane 7: 1317164-T-C. (d) SNP point mutation fusion fragment in FS12. M: 2000 bp; Lane 1:3055754-G-A; Lane 2:3055807-G-C; Lane 3: 3055836-T-G. (e) SNP point mutation fusion fragment in FS25 (Lane 1:2749153-C-T), FS63 (Lane 2: 1508978-C-A), and NM10 (Lane 3: 1510223-A-C). M:5000 bp.Additional file 2: Table S1. Basic information of Xal JG43 and Xsa DD13. Table S2. Repeat contents from genome sequence of Xal JG43 and Xsa DD13. Table S3. Genes in plasmid from the genome of Xal JG43. (.xls ) Table S4. Carbohydrate-active enzymes (CAZys) in Xal JG43 and Xsa DD13. Table S5. Comparative pathogenomics of X. albilineans JG43 and its related X. sacchari DD13. (.xls ) Table S6. Genomic island and prophages of Xal JG43 and Xsa DD13. (.xls ) Table S7. Resequencing of 23 X. albilineans strains. Table S8. Genomic variations (SNPs and SVs) obtained from 23 sequenced X. albilineans strains against JG43. Table S9. SNP mutations in 23 strains of X. albilineans. Table S10. Mutations at the DNA level in 23 strains of X. albilineans. Table S11. List of primers used in this study.Additional file 3."} +{"text": "Scientific Reports 10.1038/s41598-022-18110-1, published online 18 August 2022Correction to: The Funding section in the original version of this Article was incomplete.\u201cYayasan Universiti Teknologi PETRONAS (YUTP), Cost Center 015LC0-278 received by D. L. C. C.\u201dnow reads:\u201cYayasan Universiti Teknologi PETRONAS (YUTP), Cost Center 015LC0-278 and NCRF 015MCO-030 received by D. L. C. C.\u201dThe original Article has been corrected."} +{"text": "Correction: Inflamm Regen 42, 37 (2022)https://doi.org/10.1186/s41232-022-00217-7Following publication of the original article , authorsThe original version was:1*, Endo Yushiro1, Koga Tomohiro1,2, Yoshiura Koh-ichiro3 and Migita Kiyoshi4Atsushi KawakamiThe correct authorship has been updated in this Correction.The original article has been"} +{"text": "Concerns have been raised about ecological momentary assessment (EMA) acceptability among patients with schizophrenia spectrum disorders (SSD), which is of major relevance during the e-Mental health-focused COVID-19 pandemic.To investigate i) the levels of adherence to a passive smartphone-based EMA tool, the Evidence-Based Behavior (eB2), among SSD patients; and ii) putative predictors of this.Sample: SSD (F20-29-ICD10) outpatients, age 18-64, without financial incentives, recruited over 17/06/2019-11/03/2020 at the Hospital Universitario Fundaci\u00f3n Jim\u00e9nez D\u00edaz . Those who accepted the eB2 installation -users- and those who did not -non-users- were compared in sociodemographic, clinical, premorbid adjustment, neurocognitive, psychopathological, insight and metacognitive variables by a multivariable binary logistic regression model.Sample (N=77): n=41 males; age: 47.69\u00b19.76 years, n=24 users (31.2%). n=14 users (70%) had the eB2 installed at follow-up (median=14.50 weeks).2=25.296,df=6,p<0.001. Nagelkerke-R2=44.7%. Correctly classified: 76.9%, users:54.5%, non-users:88.4%.XAcceptability of a smartphone-based EMA application among SSD patients was low. Age (young) and good premorbid adjustment predicted acceptability. e-Mental Health methods need to be tailored for patients with SSD. Otherwise, these highly vulnerable individuals may be neglected by e-health-based services in the post-COVID-19 years ahead."} +{"text": "We assessed cross-reactivity to BA.1, BA.2, and BA.5 of neutralizing antibodies elicited by ancestral, Delta, and Omicron BA.1 SARS-CoV-2 infection in mice. Primary infection elicited homologous antibodies with poor cross-reactivity to Omicron strains. This pattern remained after BA.1 challenge, although ancestral- and Delta-infected mice were protected from BA.1 infection. The SARS-CoV-2 Omicron variant emerged nearly 2 years after the ancestral strain was identified of SARS-CoV-2/Australia/Vic/01/20 , SARS-CoV-2/Australia/Vic/18440/2021 (Delta), and SARS-CoV-2/Australia/NSW/RPAH-1933/2021 (Omicron BA.1) strains in 7- to 9-week-old female K18hACE2 transgenic mice (2 TCID50), selected so that the mice would survive primary infection . We mock-infected 15 mice with phosphate-buffered saline (PBS). We collected blood on day 27 after primary infection and then challenged mice with 104 TCID50 of Omicron BA.1 virus. We collected lungs and nasal turbinates (NTs) 2 and 4 days after challenge; we weighed and monitored 5 mice per group for clinical signs for 14 days , survived without weight loss. The control group had mean virus titers of 102.6 (day 2) and 102.7 (day 4) in NTs and 103.7 (day 2) and 103.5 (day 4) TCID50/organ in lungs after Omicron BA.1 challenge. After primary infection, all Omicron BA1\u2013infected mice survived without major weight loss, but 1 ancestral strain\u2013infected and 5 Delta-infected mice died during days 8\u201313. After challenge with 10Consistent with other reports , panel CThe homologous responses were strongest to ancestral (geometric mean titer [GMT]\u00a0709), followed by Delta (GMT\u00a0129), and were lowest to BA.1 (GMT\u00a083) . The lowPrimary Omicron BA.1 infection did not induce heterologous neutralizing activity against ancestral, Delta, BA.2, or BA.5 viruses . In contDespite the absence of detectable BA.1 virus in the respiratory tract tissues after secondary infection in mice previously infected with ancestral or Delta , panel Chttps://doi.org/10.1101/2022.01.03.21268582). A boost occurred in preexisting SARS-CoV-2 neutralizing antibodies to ancestral and Delta but not in cross-reactivity to Omicron, probably because more epitopes are shared between ancestral and Delta than between those strains and Omicron. Serologic data from humans suggest that >3 exposures to ancestral strains as infection or vaccination or a combination are needed to induce cross-reactive antibodies to BA.1 (https://doi.org/10.1101/2022.05.10.22274906), we did not detect cross-reactive neutralizing antibodies after primary infection with ancestral and Delta strains. Protection from replication of the Omicron BA.1 strain despite the lack of cross-reactive neutralizing antibodies may be attributable to mucosal immunity or T-cell responses in ancestral strain\u2013infected and Delta-infected mice (Our observations are consistent with BA.1 being antigenically distinct from the ancestral and Delta strains (K. van der Straten K et al., unpub. data, Additional information about SARS-CoV-2 Omicron BA.1 challenge after ancestral or Delta infection in mice."} +{"text": "Panax notoginseng (Burkill) F. H. Chen is not completely known. Morphological traits, N use and allocation, photosynthetic capacity and saponins accumulation were evaluated in two- and three-year-old P. notoginseng grown under different N regimes. The number and length of fibrous root, total root length and root volume were reduced with the increase of N supply. The accumulation of leaf and stem biomass (above-ground) were enhanced with increasing N supply, and LN-grown plants had the lowest root biomass. Above-ground biomass was closely correlated with N content, and the relationship between root biomass and N content was negatives in P. notoginseng (r = \u22120.92). N use efficiency-related parameters, NUE , NC (N content in carboxylation system component) and Pn (the net photosynthetic rate) were reduced in HN-grown P. notoginseng. SLN (specific leaf N), Chl (chlorophyll), NL (N content in light capture component) increased with an increase in N application. Interestingly, root biomass was positively correlated with NUE, yield and Pn. Above-ground biomass was close negatively correlated with photosynthetic N use efficiency (PNUE). Saponins content was positively correlated with NUE and Pn. Additionally, HN improved the root yield of per plant compared with LN, but reduced the accumulation of saponins, and the lowest yield of saponins per unit area (35.71 kg\u00b7hm\u22122) was recorded in HN-grown plants. HN-grown medicinal plants could inhibit the accumulation of root biomass by reducing N use and photosynthetic capacity, and HN-induced decrease in the accumulation of saponins (C-containing metabolites) might be closely related to the decline in N efficiency and photosynthetic capacity. Overall, N excess reduces the yield of root and C-containing secondary metabolites (active ingredient) in N-sensitive medicinal species such as P. notoginseng.Nitrogen (N) is an important macronutrient and is comprehensively involved in the synthesis of secondary metabolites. However, the interaction between N supply and crop yield and the accumulation of effective constituents in an N-sensitive medicinal plant Nitrogen (N) is a determinant nutrient for plant biomass or crop yield . Yellow e.g., carboxylation and bioenergetics components), results in a lowed yield of N-excess Brassica campestris L. R. Br. grown under low N condition (Datura stramonium L. is significantly increased with an increase in soluble sugar and proline content (primary metabolites) under N-excess condition balance and consequently change the content of C- and N-containing secondary metabolites in the medicinal species . Excessibacum L. . Correspondition . The N-condition . UnexpecPanax notoginseng (Burkill) F. H. Chen (Sanqi in Chineses) is a perennial medicinal plant and a member of the Araliaceae family, which is a typically shade-tolerant and N-sensitive plants enhances the accumulation of biomass and saponins though optimizing root architecture and N uptake efficiency in P. notoginseng , moderate nitrogen (MN) and high nitrogen (HN). We hypothesized that (i) root biomass of P. notoginseng might be reduced accompanying with HN-driven inhibition on photosynthetic capacity and NUE (N use efficiency); (ii) HN-driven decrease in saponin accumulation might be reflected by the C/N imbalance; (iii) N stress might reduce the yield of P. notoginseng.The present study aimed to shed light on an interaction between N availability and crop yield and saponins accumulation in the medicinal plant 2O) was 6.84, total N content was 0.17%, total phosphorus (P) was 0.23%, the available P content was 11.04 mg\u00b7kg\u22121, total potassium (K) was 0.24%, and the available K content was 127.32 mg\u00b7g\u22121.The study was conducted at the Yunnan Agricultural University teaching and experimental farm in Kunming, China , with an average annual rainfall and average annual temperature of about 1,006.7 mm and 14.5 \u00b0C, respectively. The properties of raw soil physical and chemical was determined as described by P. notoginseng, and the full sunlight irradiance is about 10% provided one-year-old P. notoginseng seedlings. Subsequently, healthy and uniform seedlings were transplanted into a plastic flowerpot (30 cm \u00d7 25 cm \u00d7 20 cm) with each containing three rootstocks (\u22122), high nitrogen ) were designed (2O5), calcium superphosphate and potassium sulfate (52% K2O), respectively. The same amounts of P (225 kg\u00b7P2O5\u00b7hm\u22122) and K (450 kg\u00b7K2O\u00b7hm\u22122) fertilizers were used in all treatments with the exception of the N fertilizer. Fertilization was applied in four times a year . In each pot, basal doses of P and K at the rates of 0.45 and 0.90 g, respectively , were applied at time while N was applied according to the treatments. N fertilizer rate 0 (LN), 0.45 (MN) and 0.90 (HN) g\u00b7pot\u22121 .A permeable black plastic net was used to create a shade-house for bout 10% . Meanwhibout 10% . Permeabotstocks . There wdesigned , and eacAt November, the two- and three-year-old plants were sampled from the experimental farm and then separated into root , stem and leaf in room. The length, width, and area of leaf were measured by LI-3000 leaf-area meter . Root tuber and stem diameter were measured by vernier caliper. Plant height, grown breadth, the length of main root and total root were determined as described by The samples were dried at 60 \u00b0C for 96 h. Dry matter was determined, and these results were used to calculate the percentage of biomass allocation into leaf , stem , roots , as well as root to shoot ratio (RSR). The root yield of per plant and economic yield (root yield of per hectare) were calculated based on root biomass data.P. notoginseng leaves were soaked. A standing period of 3 h was followed by a centrifugation of 3,000 g\u00b7min\u22121 for 10 min. A JASCO V-670 spectrophotometer was used to measure absorbance at 665 and 649 nm wavelengths. Chl a, Chl b and Chl a/Chl b were analyzed as described by In 15 mL of acetone-ethanol mixture (2:1 v/v), 0.5 g of fresh 2 concentration of 10%, 25 \u00b0C, 500 \u03bcmol\u00b7photons\u00b7m\u22122\u00b7s\u22121 and 400 \u03bcmol\u00b7CO2\u00b7mol\u22121, respectively. Photosynthetic gas exchange parameters were collected as previously described in LI-6400XT photosynthesis system was used to determine photosynthetic gas exchange parameters. Set with a blue light ratio, temperature, photosynthetic photon flux density (PPFD) and COVcmax (maximum carboxylation efficiency), Jmax (maximum electron transfer rate), SLN and Chl contents, NC (N content in carboxylation system component), NB (N content in bioenergetics component) and NL (N content in light-harvesting systems component) were analyzed according to the method described by photo) = NB + NC + NL. Photosynthetic N use efficiency (PNUE) = Pmax (maximum net photosynthetic rate)/SLN.The leaf, stem and root N contents were determined by Kjeldagl method . AdditioP. notoginseng grown under different N regimes. The following equations were used to calculate N uptake and use efficiency (\u22121) = yield (underground dry weight)/plant N accumulation; NAE (kg\u00b7kg\u22121) = (yield with N application \u2013 yield without N application)/N rate; NUPE (kg\u00b7kg\u22121) = above-ground total N content/N rate; RNF (%) = /N rate \u00d7 100; NCR (%) = (yield with N application \u2013 yield without N application)/yield with N application \u00d7 100; NPFP (kg\u00b7kg\u22121) = yield with N application/N rate.Based on the biomass and N contents, N use efficiency (NUE), N agronomic efficiency (NAE), N uptake efficiency (NUPE), recovery of N fertilizer (RNF), N contribution rate (NCR), N partial factor productivity (NPFP) were calculated in ficiency : NUE were purchased from Yuanye Bio-technology . Kit column was used for the determination, and the mobile phase was acetonitrile (ACN)-water. Chromatographic conditions: elution with 0\u20135 min, 17\u201320% ACN; 5\u201320 min, 20% ACN; 20\u201345 min, 20\u201342% ACN; 45\u201350 min, 42\u2013100% ACN; set with flow rate, injection volume, monitoring wavelength and column temperature of 1.0 mL\u00b7min\u22121, 10 \u00b5L, 203 nm and room temperature, respectively. Total saponins are the sum of Rg1, Rb1, Re, Rd and R1. The HPLC chromatograms of P. notoginseng root grown in different N environments are shown in Dry root samples of 0.3 g were extracted in 100% methanol and sonicated for 30 min. The solution volume was fixed to 25 mL. Saponin contents were determined as described by n = 5 or 7). One-way analysis of variance was used to evaluate the effect of N treatment in a year by T-test using SPSS software (IBM SPSS Statistics). LSD-test was used to compare treatment means, with significant effects having P < 0.05. Plots were made using Origin 2021 and GraphPad 8.0 software. Pearson correlation coefficients were assessed using Origin 2021. Principal component analysis loading factors were assessed using Origin 2021.All data in the tables and figures were mean \u00b1 standard deviation (SD) of 5\u20137 independent biological replicates performed (P. notogisneng between MN and LN conditions (P > 0.05). The stem and leaf N content were higher in two-year-old P. notoginseng compared with three-year-old plants . For two-year-old P. notoginseng, main root length and total root length were increased by 31.24% and 11.10% in MN-grown plants compared with HN-grown P. notoginseng, respectively . The number of fibrous roots, length of fibrous root, total root length, and root volume declined with an increase in N application . Leaf biomass was increased by 145.45% and 125.00% in MN-grown plants compared with LN- and HN-grown P. notoginseng, respectively (P > 0.05). RMF, SMF and LMF were increased by 110.00%, 88.89% and 72.73% in MN-grown plants compared with HN-grown P. notoginsneng, respectively . Leaf biomass was increased by 127.62% and 54.60% in HN-grown plants compared with LN- and MN-grown P. notoginseng, respectively (P > 0.05). SMF and LMF were improved by 27.59% and 28.57% in HN-grown P. notoginseng compared with LN-grown plants . NUE was declined by 62.96% and 34.03% in two- and three-year old P. notoginseng grown under HN condition compared with MN conditions, respectively (P < 0.05). The minimum values of NAE, NUPE, NCR, and NPFP were obtained in the HN-grown P. notoginaseng (P < 0.05). RNF was increased by 29.57% in three-year-old P. notoginseng grown under HN compared with MN condition (There were considerable differences in N efficiency of ondition .P < 0.05), and SLN was higher in two-year-old plants compared with three-year-old plants (P. notoginseng in LN and MN conditions (P < 0.05).SLN increased with an increase in N application . CE (carboxylation efficiency) and Jmax were highest in two-year-old plants under MN condition. CE and Jmax were increased by 57.14% and 57.58% in MN-grown plants comparted with HN-grown P. notoginseng, respectively (Vcmax and \u0393* (carbon dioxide compensation point) variables, were not significantly different in two-year-old plants grown under LN and HN conditions , LSP (light saturating point), Vcmax, and Rd (dark respiration rate) were significantly declined in three-year-old plants under LN condition (P < 0.05). For three-year-old plants, the maximum values of Pmax, CE, \u0393*, Jmax, Vcmax, and Jmax/Vcmax were obtained in MN plants . HN induces the increase in NL, and NC was reduced by 13.79% in two-year-old plants grown under HN compared with MN were not significantly different N regimes (P < 0.05). The minimum value of total saponins (%) were recorded in three-year-old plants grown under HN condition (P < 0.05). For three-year-old plants, the LN and HN-grown P. notoginseng showed 32.58% and 28.68% lower saponins yield of per plant than the MN ones and SLN (r = \u22120.87). Root biomass was close positively correlated with N use efficiency (as reflected by NCR (r = 0.79), NPFP (r = 0.91) and NUE (r = 1.00)). There was little correlation between root biomass and RNF, plant height and leaf area. Stem and leaf biomass were close negatively correlated with SPAD and PNUE. N application was close negatively correlated with NAE (r = \u22120.87), NCR (r = \u22120.85), NPFP (r = \u22120.91) and NUPE (r = \u22120.75). NUPE was positively correlated with the root length (r = 0.66) and root tuber diameter (r = 0.59). In addition, Pn was negatively correlated with N application (r = \u22120.88), leaf area (r = \u22120.57), Chl contents (r = \u22120.75), SLN (r = \u22120.44) and leaf N content (r = \u22120.45). The relationship between saponins and Pn (r = 0.45), root biomass (r = 0.54) as well as NPFP (r = 0.57) were positive correlation in P. notoginseng. Saponins content was negatively correlated with Chl content (r = \u22120.67) and SLN (r = \u22120.64).Pearson correlation coefficients of 27 parameters were evaluated in regimes . As showP. notoginseng biomass or saponins. In PC1, the weighting coefficients of biomass parameters , yield, NUE, SLN, SPAD and stem N content were larger . The cumulative contribution of PC1, PC2 and PC3 reached 84.80% . Thus, te larger . NUE, yie larger . In PC2,e larger . In PC3,e larger . LCP ande larger .Arabidopsis thaliana L. by increasing the length of total root and fibrous root (r = 0.66) and root tuber diameter Previouoginseng , 4. HN iativa L. . Overalle.g., Dodonaea viscosa (L.) Jacq., Lolium perenne L. and Betula spp. (P. notoginseng are exposed to HN condition (r = \u22120.93) and stem (r = \u22120.72) N content . ula spp. , and shoula spp. . These rondition . It has ondition . However content . It is aMolinia caerulea (L.) Moench , and lower NAE and NCR were obtained in HN-grown P. notoginseng (Many studies have shown that N use is not positively related to N uptake . N conte) Moench . This isce N use , 4. Howeoginseng , Table 3L and Pn were recorded in LN-grown plants and stem (r = \u22120.86) biomass and yield (r = 0.53) were positively correlated with Pn Fern.-Vill. grown under high N condition Iljinsk. is generally used as a traditional Chinese medicine is recorded in three-year-old P. notoginseng grown HN condition was recorded in HN-grown plants (Centella asiatica L. and Stevia rebaudiana (Bertoni) Hemsl. Hemsl. ). Howeve) Hemsl. , 7E, 7F. quality . In shorP. notoginseng (P. notoginseng.A model was proposed to explain the interaction between high N and the accumulation of biomass and C-containing secondary metabolites in a N-sensitive medicinal species, such as oginseng . In conc10.7717/peerj.14933/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj.14933/supp-2Supplemental Information 2Click here for additional data file.10.7717/peerj.14933/supp-3Supplemental Information 3Click here for additional data file."} +{"text": "Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease severity. The mechanistic explaining variations related to airway epithelium are relatively understudied. Here, we biobanked airway organoids (AO) by preserving stem cell function. We optimized viral infection with H1N1/PR8 and comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable AO from 20 different subjects. We discovered Tetraspanin-8 (TSPAN8) as a facilitator of SARS-CoV-2 infection. TSPAN8 facilitates SARS-CoV-2 infection rates independently of ACE2-Spike interaction. In head-to-head comparisons with Ancestral SARS-CoV-2, Delta and Omicron VOC displayed lower overall infection rates of AO but triggered changes in epithelial response. All variants shared highest tropism for ciliated and goblet cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy. \u2022Airway organoids from different donors display distinct compositions of cell types\u2022Organoid biobank models the spectrum of the epithelium response to pathogens\u2022TSPAN8 is a conserved mediator of infection for SARS-CoV-2 variants Roose and colleagues generated a biobank of 20 airway organoids for modeling variations of airway epithelium response to SARS-CoV-2. They discovered Tetraspanin-8 (TSPAN8) as a facilitator of SARS-CoV-2 infection independently of ACE2-Spike interaction. Pre-treatment of airway organoids with a blocking TSPAN8 antibody decreased SARS-CoV-2 infection levels in airway organoids, suggesting TSPAN8 as a therapeutic target for COVID-19. While most SARS-CoV-2-infected individuals develop asymptomatic to mild disease, some develop a severe disease characterized by immune cell dysfunction (trans-membrane serine proteases (TMPRSS2) results in Spike protein activation and viral entry (Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has caused a global pandemic of coronavirus disease (COVID-19) with more than half a billion cases worldwide derived from adult stem cells of different individuals. We used this biobank to first optimize viral infection of AO with H1N1/PR8 influenza, and next performed a comprehensive analysis of SARS-CoV-2 infection with repeat infections. Spectral flow analysis of infected AO was used to assess cellular and functional responses of the epithelial cell compartment. Single-cell RNA sequencing (scRNA-seq) and Spectral flow enabled the discovery of Tetraspanin-8 (TSPAN8) as a conserved mediator of SARS-CoV-2 Ancestral (WA-1)-, Delta-, and Omicron-variant infection. Reductionist HEK293T cell-pseudo-virus approaches showed that TSPAN8 facilitates viral entry independently of the Spike-ACE2 interaction. We show that TSPAN8 is not an alternative entry receptor. Blocking TSPAN8 in airway epithelial organoids prior to infection is associated with a decrease in the viral load of AOs. Based on our TSPAN8 work in the context of cancer , we proplike cells , goblet-like cells , three populations of cells expressing basal cell markers CD49f+CD271+, CD49fnegCD271+, CD49f+CD271+, and a\u00a0population of CD49fnegCD271negacTUBAnegMUC5ACnegTSPAN8neg cells. AOs derived from different donors displayed distinct cell-type compositions even though cultured in identical growth factors and environmental conditions , pre-gobnditions G. Furthenditions H and\u00a0S1Anditions B. We gennditions C. Spectrnditions D and extnditions E revealenificant I\u20131K. So,high/CD271\u2212neg ciliated cells and acTUBAneg/MUC5AC+ goblet cells A. ConfocSpectral flow analysis on five independent SARS-CoV-2 infections of 2522UL show that infections are consistent C and 3D To uncover the rules of infection with SARS-CoV-2, we selected a panel of 12 AOs A that ca+, or CD271+, or CD49fnegCD271neg cells for Mock and SARS-CoV-2-infected organoids on 21 variables A. PCA lA showed + cells\u00a0H upon SA+ cells\u00a0I\u2013S3L. Th+ cells\u00a0J, confir+ cells\u00a0. Surprison rates K and S3Gon rates , and theon rates C motivatWe infected four organoids with SARS-CoV-2 WA-1 and performed scRNA-seq. Unsupervised clustering analysis based on most variable gene expression across all cells , regardlTSPAN8 mRNA reads were present in 64% of single cells positive for SARS-CoV-2 reads (size of the circle in +TSPAN8\u2212) from pre-goblet cells (MUC5AC\u2212TSPAN8+) , allowinTSPAN8+) C but decTSPAN8+) A. As we TSPAN8+) J, most STSPAN8+) D, whereaTSPAN8+) E. FurtheTSPAN8+) F and S5BTSPAN8+) K, the prnfection G and S5Cnfection H and 5I.TSPAN8 expression decreases in airway brushes of acute illness in patients caused by non-SARS-CoV-2 respiratory viruses, while airway brushes from COVID-19 patients revealed preservation of TSPAN8 levels numbers and influences their composition . EV fromjeroen.roose@ucsf.edu.A list of materials used and detailed methods are found on the Supplementary Materials section. Materials are available upon request.GSE211562.Resources: GEO: L.H. and J.P.R.: conceived the study. L.H., S.L., and K.K.: Spectral flow. L.H., K.K., S.L., O.M.G.: organoid biobank. L.H., M.M., and L.R.: BSL3 work. C.A., A.A.R., and A.J.C.: scRNA-seq. J.C.L.: statistical analyses. C.A., L.C.L.: scRNA-seq analyses. L.R.B. and D.J.E.: advice on airway populations. N.K.S. and M.K.: H1N1 virus. L.H., S.L., O.M.G., and K.B.: microscopy. L.H., S.L., K.B.: HEK239T cell line creation. J.Z.L., V.D., S.M., M.M.: patient samples. G.K., D.M.J., M.M., A.J.C.: funding. M.O.: SARS-CoV-2 virus, and SARS-CoV-2 pseudo-viruses. S.L., M.P.: pseudo-virus infections. J.R.K.: surgery airway samples, clinical data discussion. L.H., S.L., J.P.R.: manuscript writing. J.P.R.: funding. G.K.F., D.M.J., M.M., M.O., M.M., A.J.C., D.E., A.N.S., and J.R.K.: edits on the manuscript."} +{"text": "Misgurnus anguillicaudatus), the most widely distributed species of the family Cobitidae, displays a mud-dwelling behavior and intestinal air-breathing, inhabiting the muddy bottom of extensive freshwater habitats. However, lack of high-quality reference genome seriously limits the interpretation of the genetic basis of specialized adaptations of the loach to the adverse environments including but not limited to the extreme water temperature, hypoxic and noxious mud environment.The loach (fos), a regulator of bone development, is positively selected in loach. Knockout of fos (ID: Mis0086400.1) led to severe osteopetrosis and movement difficulties, combined with the comparison results of bone mineral density, supporting the hypothesis that fos is associated with loach mud-dwelling behavior. Based on genomic and transcriptomic analysis, we identified two key elements involved in the intestinal air-breathing of loach: a novel gene (ID: mis0158000.1) and heat shock protein beta-1 (hspb1). The flavin-containing monooxygenase 5 (fmo5) genes, central to xenobiotic metabolism, undergone expansion in loach and were identified as differentially expressed genes in a drug stress trial. A fmo5\u2212/\u2212 (ID: Mis0185930.1) loach displayed liver and intestine injury, indicating the importance of this gene to the adaptation of the loach to the noxious mud.This study generated a 1.10-Gb high-quality, chromosome-anchored genome assembly, with a contig N50 of 3.83 Mb. Multiple comparative genomic analyses found that proto-oncogene c-Fos (Our work provides valuable insights into the genetic basis of biological adaptation to adverse environments.The online version contains supplementary material available at 10.1186/s12915-023-01517-1. Misgurnus anguillicaudatus), the most widely distributed species of the family Cobitidae, inhabits in the bottom of lakes, ponds, and other freshwater areas with humus-rich mud ; ugt, UDP-glucuronosyltransferase. Table S5. Primers used in this study. qPCR, quantitative PCR; # indicated T7 promoter sequences. Fos, proto-oncogene c-Fos; fmo5, dimethylaniline monooxygenase [N-oxide-forming] 5 (Mis0185930.1); hbb, hemoglobin subunit beta; hba, hemoglobin subunit alpha; atf6, cyclic AMP-dependent transcription factor; eif2ak3, eukaryotic translation initiation factor 2-alpha kinase 3; chop, DNA damage-inducible transcript 3 protein; muc2, mucin-2; Mis0185950.1, Mis0185940.1, Mis0185920.1, Mis0185970.1, Mis0186000.1, Mis0186010.1 (fmo5), dimethylaniline monooxygenase [N-oxide-forming] 5; Mis0115330.1, Mis0115330.1, Mis0135560.1 (ugt2a2), UDP-glucuronosyltransferase 2A2; Mis0072610.1 (ugt2a1), UDP-glucuronosyltransferase 2A1; npr2, atrial natriuretic peptide receptor 2; f9, coagulation factor IX; hspb1, heat shock protein beta-1; hyou1, hypoxia up-regulated protein 1; ptafr, platelet-activating factor receptor; scx, basic helix-loop-helix transcription factor scleraxis; galnt8, polypeptide N-acetylgalactosaminyltransferase 8; krt13, keratin, type I cytoskeletal 13 Cytokeratin-13; gp2, pancreatic secretory granule membrane major glycoprotein; smco3, single-pass membrane and coiled-coil domain-containing protein 3; ccl5, C-C motif chemokine 5; ifi44, interferon-induced protein 44; atf4, cyclic AMP-dependent transcription factor 4; ugt1a1, UDP-glucuronosyltransferase 1-1. Table S6. A summary of sequencing data used in genome assembly and annotation of Misgurnus anguillicaudatus.Additional file 2: Fig S1. Genome-wide Hi-C interaction map. Fig S2. Divergence distributions of four TE sequences predicted by the de novo method (a) and comparison of the distribution of several features in the final gene set for seven fish species (b). TE, transport elements; DNA, DNA transposons; LTR, long terminal repeats; LINE, long interspersed nuclear elements; SINE, short interspersed nuclear element. The seven fish species: Misgurnus anguillicaudatus, Carassius auratus, Cyprinus carpio, Danio rerio, Sinocyclocheilus graham, S. rhinocerous, and Triplophysa tibetana. Fig S3. The construction of maximum likelihood tree of fos gene and generation of the fos (ID: Mis0086400.1) knockout loach (fos\u2212/\u2212) by CRISPR/Cas9 technology. (a) Maximum likelihood tree ) of fos gene in fish species. Different branch colors represent different species. Red words indicate the knockout of fos gene in loach genome. (b) Schematic position of the CRISPR/Cas9 target site for fos gene knockout. (c) The transcription level of fos in livers of wild-type loach (WT) and fos\u2212/\u2212 loach. (d) A statistics of survival rate of fertilized eggs of WT loach and heterozygous F1 generation (F1 generation self-crossed). *** extremely significant difference (p < 0.001). hpf, hours post fertilization; fos, Proto-oncogene c-Fos. The gene in red color is a positively selected gene in the loach genome. Fig S4. Identification and expression analysis of air-breathing- and digestion/absorption- related genes in loach Misgurnus anguillicaudatus. (a) Maximum likelihood tree ) of hb gene family. Different color backgrounds represent different genes. Different branch colors and inner circle colors represent different species. hbb, hemoglobin subunit beta; hba, hemoglobin subunit alpha. (b) Expression levels of hbb and hba in posterior intestines of the loach under air exposure. (c) qPCR validation of RNA-seq data of loach posterior intestines under air exposure. (d) Maximum likelihood tree ) of air-breathing-related genes. Different branch colors represent different species. (e) Maximum likelihood tree of digestion/absorption-related genes ). Atp1a, sodium/potassium-transporting ATPase subunit; ryr, ryanodine receptor. Different color backgrounds represent different genes. Different branch colors represent different species. Npr2, atrial natriuretic peptide receptor 2; f9, coagulation factor IX; hspb1, heat shock protein beta-1; hyou1, hypoxia up-regulated protein 1; ptafr, platelet-activating factor receptor; scx, basic helix-loop-helix transcription factor scleraxis; galnt8, polypeptide N-acetylgalactosaminyltransferase 8; krt13, keratin, type I cytoskeletal 13 Cytokeratin-13; gp2, pancreatic secretory granule membrane major glycoprotein; smco3, single-pass membrane and coiled-coil domain-containing protein 3; ccl5, C-C motif chemokine 5; ifi44, interferon-induced protein 44; cldn5, claudin-5 Transmembrane protein deleted in VCFS; hspb1, heat shock protein beta-1; vegfr1 (flt1), vascular endothelial growth factor receptor 1; ctgf, connective tissue growth factor CCN family member 2. Fig S5. Identification of FMO and UGT gene families. (a) Maximum likelihood tree ) of FMO gene family. Different colors represent different FMO gene families and different branch colors represent different species. (b) Maximum likelihood tree ) of UGT gene family. Different colors represent different UGT gene families and different inner circle colors represent different species. Fig S6. qPCR validation of RNA-seq data from the drug stress trial. Fig S7. The expression levels of ugt genes in liver tissues of the loach under five drug stress. Mis115330.1 and Mis0135560.1 (ugt2a2), UDP-glucuronosyltransferase 2A2; Mis0072610.1 (ugt2a1), UDP-glucuronosyltransferase 2A1. Fig S8. Tissue expression analysis and the knockout of fmo5 (ID: Mis0185930.1) gene (fmo5\u2212/\u2212) in loach Misgurnus anguillicaudatus genome. (a) Tissue expression analysis of fmo5 (ID: Mis0185930.1) of the loach. (b) Schematic position of the CRISPR/Cas9 target site for fmo5 gene knockout. (c) The mRNA and protein expression levels of fmo5 in livers of wild-type (WT) and fmo5\u2212/\u2212 loach. Different letters above error bars indicate significant difference among different tissues (p < 0.05); *** extremely significant difference (p < 0.001). Fig S9. Survival rates of wild-type (WT) and fmo5deletion (fmo5\u2212/\u2212) loach under five drug stress."} +{"text": "There is an error in reference 5. The correct reference is: Masashi K, Norihiro S, Hidetsugu N.Regular change in spontaneous preparative behaviour on intra-abdominal pressure and breathing during dynamic lifting. Eur J Pppl Physiol. 2014; 114(11):2233\u20139"} +{"text": "Atrial fibrillation (AF) was more frequent in non-survivors (p < 0.0001), alongside a longer QTc interval (p = 0.0002), a lower Tp-e/QTc ratio (p = 0.0003), and right ventricular strain (p = 0.013). Remdesivir administration was associated with bradycardia development (p = 0.0005) but no increase in mortality rates. In a Cox regression model, AF (aHR 3.02 (95% CI 1.03\u20138.81); p = 0.042), QTc interval above 451 ms (aHR 3.24 (95% CI 1.09\u20139.62); p = 0.033), and right ventricular strain (aHR 2.94 (95% CI 1.01\u20138.55); p = 0.047) were associated with higher 28-day mortality risk. Conclusions: QTc interval > 451 ms, right ventricular strain, and AF are associated with higher mortality risk in SARS-CoV-2 hospitalized patients. ECG recording and its appropriate analysis offers a simple, quick, non-expensive, and validated approach in the emergency setting to guide COVID-19 patients\u2019 stratification.Background: Electrocardiogram (ECG) offers a valuable resource easily available in the emergency setting. Objective: Aim of the study was to describe ECG alterations on emergency department (ED) presentation or that developed during hospitalization in SARS-CoV-2-infected patients and their association with 28-day mortality. Methods: A retrospective, single-center study including hospitalized patients with SARS-CoV-2 was conducted. ECG was recorded on ED admission to determine: heart rhythm, rate, and cycle; atrio-ventricular and intra-ventricular conduction; right ventricular strain; and ventricular repolarization. A specialized cardiologist blinded for the outcomes performed all 12-lead ECG analyses and their interpretation. Results: 190 patients were included, with a total of 24 deaths (12.6%). Age ( Since the beginning of the SARS-CoV-2 global emergency in December 2019, more than 300 million cases and 5 million deaths have been recorded worldwide, and these numbers keep rising [Multimorbidity, including past cardiovascular or pulmonary disease history and older age above all, have been previously associated with severity of infection and mortality . On the 1Q3T3 sign or inferior leads T wave inversion, which reflects the associated lung involvement and is already linked to higher disease burden [Electrocardiographic abnormalities have been observed in 99% of elderly and critically ill patients infected with SARS-CoV-2 . These ie burden .Despite the bulky amount of data, a comprehensive analysis of ECG parameters on emergency presentation in COVID-19 patients is missing, as either attention is focused on specific ECG abnormalities, or solid evidence on alterations is still lacking. ECG recording represents the first step of the cardiological assessment and can prove essential for patients\u2019 risk stratification in the ongoing emergency frame, being a handy, inexpensive, and widely available tool.Therefore, this study aims to describe the prevalence and type of electrocardiographic alterations at emergency department (E.D.) arrival in subsequently hospitalized SARS-CoV-2-infected patients and to investigate the possible association between ECG parameters and 28-day mortality after adjusting for variables, including age, sex, comorbidities, and laboratory findings that could influence the endpoint.A monocentric, retrospective study was conducted at Azienda Ospedaliero Universitaria Policlinico Umberto I, a tertiary care hospital with 1235 beds, the seat of \u201cSapienza\u201d University of Rome Medical School, between March 2020 and January 2021.Patients over 18 years of age with SARS-CoV-2 infection confirmed by rapid antigen or molecular nasopharyngeal swab test subsequently admitted from E.D. to Infectious Diseases COVID-19 hospital wards in the abovementioned period were initially included in the analysis, for a total of 531 patients. Underage or discharged patients, patients with no laboratory proven infection, or those admitted to wards other than infectious diseases ward (I.D.) as well as patients receiving drugs potentially elongating the QT as well as >48 h of azithromycin or hydroxychloroquine were excluded. In addition, patients were excluded whether data were incomplete for study purpose or E.D. recorded standard twelve-lead ECGs were missing. Accordingly, the proposed criteria led to 341 excluded and 190 included patients .2/FiO2 ratio; potential ICU stay during hospitalization; in-hospital and 28-day mortality, length of hospital stay, and therapy administered against SARS-CoV-2. Patients\u2019 data were anonymously recorded from medical reports into an electronic spreadsheet for the following statistical analysis. These consisted of demographics; comorbidities included in the Charlson Comorbidity Index (CCI); plus systemic hypertension, AF, and asthma; vital signs recorded in E.D., including relative bradycardia (defined as copresence of body temperature \u2265 38.3 \u00b0C and heart rate (HR) < 90 bpm) [1Q3T3 or T3 alone pattern), and ventricular repolarization .All 12-lead ECG analyses and their interpretation were performed by a specialized cardiologist (M.C.G.) who was blinded for the outcomes. The following parameters were retrieved: heart rhythm, heart rate (expressed as bpm), and heart cycle , expressed as ms), atrio-ventricular and intra-ventricular conduction parameters , left posterior hemi-block (LPH), right or left bundle branch block (RBBB or LBBB)), morphological evaluation with particular emphasis on right ventricular strain . The need for informed consent was waived since all data were retrospectively extracted.Cardiovascular events during hospitalization were defined as the onset of new ischemic/embolic events, such as pulmonary thrombo-embolism by lung CT scan, acute cerebral ischemia, acute limb ischemia, or the development of myocardial infarction, Takotsubo syndrome, myocarditis.Heart rhythm disorders included the new onset of atrial fibrillation, supraventricular tachycardia, bradycardia, pairs of ventricular premature beats, and ventricular tachycardia.Relative bradycardia was defined as heart rate < 90 bpm and concomitant fever (tympanic temperature \u2265 38.3 \u00b0C) [Daytime bradycardia was defined as mean heart rate < 60 bpm recorded three times a day.1Q3T3 pattern or negative T wave alone in leads V1\u2013V3 or II, III, or aVF with or without ST depression [Right ventricular strain was defined as the presence of Spression .The QT interval was defined as the interval from the onset of the QRS complex to the end of the T wave and expressed as ms. Corrected QT interval (QTc) was calculated according to Bazett formula: QTc = QT\u221a . In the QT dispersion, which reflects regional differences in myocardial refractoriness and predict cardiac dysrhythmias , was expFurthermore, regional differences in myocardial refractoriness were calculated also by means of Tp-e interval . Measure\u00ae software, v. 15 (StataCorp); charts were generated using Microsoft Office\u00ae and Graphpad Prism\u00ae. Continuous data are expressed as median and interquartile range (IQR) values and categorical variables as numbers and percentage values. Categorical variables were compared using \u03c72-test or Fisher\u2019s exact test and continuous variables using Student\u2019s t-test or Mann\u2013Whitney U test as appropriate.Statistical analysis was performed using STATA2/FiO2, D-dimer, CRP, and lymphocytes count, expression of respiratory failure and inflammation during COVID-19, respectively, were performed. According to the reference values available at the laboratory of our hospital, abnormal levels of troponin corresponded to levels > 0.014 \u03bcg/L.In the subgroup of patients with troponin levels available, Spearman correlation analyses between troponin levels and PaOlogrank test. For all the statistical analyses, p < 0.05 was considered significant.Multivariate Cox regression models were used to determine the hazard ratios (HR) for mortality within 28 days from admission of the included variables accounting for covariables. Statistically and clinically relevant variables on univariate analysis were evaluated for the determination of the final multivariate model. To find the optimal cut-off of the QTc value associated with the highest sensitivity and specificity in the prediction of 28-day outcome, the Youden\u2019s Index was used. The resulting value was further inserted in the final model. Twenty-eight-day survival curves were plotted using the Kaplan\u2013Meier method and compared using the p < 0.0001), while no significant difference was observed regarding sex. No deaths were recorded within 48 h from E.D. arrival; therefore, this variable was not included in the study. Patients hospitalized during the first pandemic wave in Italy (February\u2013June 2020) were evenly distributed among the two compared subgroups (89/166 (53.6%) vs. 10/24 (41.7%); p = 0.273). This reduces possible bias in different diagnostic and therapeutic management of SARS-CoV-2 infection over time.Overall, 190 patients were included in the study, with 83/190 (44%) females . Median p < 0.0001). Besides hypertension, myocardial infarction (MI) was the most common cardiovascular comorbidity , followed by AF and chronic heart failure (CHF) , which was more prevalent in the deceased subgroup, where AF was recorded in 7/24 patients , MI in 6 , and CHF in 3 patients). Calculated CCI was significantly higher in non-survivors (median (IQR), 8 (8\u201310)) when compared to survivors (3 (1\u20136); = 0.160) .p = 0.002), whereas dyspnea was the most prevalent among deceased although not statistically significant (16/24 (66.7%) vs. 85/166 (51.2%) patients; p = 0.164). Moreover, in the latter subgroup, median time between symptoms onset and E.D. presentation was significantly shorter than in survivors (median (IQR), 1.8 (0\u20135.5) vs. 6 (2\u20139) days; p = 0.039). Relative bradycardia was registered in 22/190 patients (11.6%) and, though more frequent among survivors (21/166 patients (12.6%)), resulted as not statistically relevant (p = 0.225).Fever was the most prevalent symptom in both the overall population (149/190 patients (78.4%)) and among survivors (136/166 (82%) vs. 13/24 (54.2%) patients; 2/FiO2 ratio on triage arterial blood gas was lower in non-survivors (median (IQR), 302 (243\u2013367) vs. 357 (314\u2013424); p = 0.0007), together with high white blood cells count (7180 (5070\u20138820) vs. 5755 (4502\u20137790) cells/\u00b5L; p = 0.009) and neutrophils count (5465 (3647\u20137662) vs. 4150 (3110\u20135995) cells/\u00b5L; p = 0.0038), anemia (median Hb (IQR) 11.3 (10.2\u201314.5) vs. 13.8 (12.7\u201314.9) g/dL; p = 0.0004), high D-dimer (1995 (1012\u20133198) vs. 777 (429\u20131469) U/L; p = 0.0012) and LDH (330 (268\u2013447) vs. 275 (213\u2013349) U/L; p = 0.0001), and low serum albumin (32 (30\u201335) vs. 38 (35\u201341) g/L; p < 0.0001). Regarding serum troponin T, the test was available on admission in 125/190 patients only and was higher in non-survivors (0.031 (0.021\u20130.04) vs. 0.012 (0.007\u20130.0245) \u03bcg/L; p = 0.084). Turning to laboratory tests, PaOp < 0.0001) and paroxysmal supraventricular complexes (PSVC) in 20.8% (5/24 (20.8%) vs. 9/166 (5.4%) patients; p = 0.0193). Mean RR interval was reduced, albeit not significantly, in non-survivors (median (IQR), 637.5 (570\u2013762) vs. 767 (664\u2013875) ms; p = 0.006) as well as its standard deviation (18 (11\u201330) vs. 20 (13.4\u201335) ms; p = 0.414). Regarding ventricular conduction parameters, the only significant difference between the subgroups was observed for the higher prevalence of left anterior hemiblock (9/24 (37.5%) vs. 28 (19.8%) patients; p = 0.0258) in non-survivors, who also recorded a higher occurrence of right ventricular strain as S1Q3T3 pattern (7/24 (29.1%) vs. 18/166 (10.8%) patients; p = 0.013) or as single-components inverted T wave in DIII (T3) (15/24 (62.5%) vs. 45/166 (27.1%) patients; p < 0.0001) and prominent S wave in DI (S1) (9/24 (37.5%) vs. 30/166 (18%) patients; p = 0.034). Median QTc interval duration was longer in non-survivors (436.8 (435\u2013487) vs. 428 (402\u2013447) ms; p = 0.0002), resulting in lower Tp-e/QTc ratio (0.2 (0.158\u20130.198) vs. 0.22 (0.211\u20130.233); p = 0.0003). Prolonged QTc was observed in 55 (28.9%) subjects, higher in non-survivors than survivors (39 (23.49%) vs. 16 (66.6%), p < 0.0001). Following Youden\u2019s index, the optimal cut-off of QTc differentiating 28-day survivors from non-survivors was 451 ms ).p < 0.0001) as new onset in-hospital AF although not relevant (3/24 (12.5%) vs. 8/166 (4.8%) patients; p = 0.1477). On the other hand, daytime bradycardia was more frequent in survivors (2/24 (8.3%) vs. 28/166 (16.9%); p = 0.284).p = 0.0045) and with systemic corticosteroids (17/24 (70.8%) vs. 72/166 (43.4%), p = 0.045), while administration of macrolides, HCQ, and prophylactic dose LMWH (4.000 UI/24 h s.q.) was uniform within the two subgroups, as shown in In the non-survivor subgroup, a higher rate of patients was treated with therapeutic dose LMWH (100 U/kg/12 h s.q.) (10/24 (41.7%) vs. 33/166 (19.9%) patients; p = 0.021 and 0.036, respectively) but not with right ventricular strain (p = 0.94) and tended to be associated with abnormalities at admission ECG (p = 0.08).Troponin levels at hospital admission was available in 125/190 (65.8%) subjects. Abnormal levels of troponin (>0.014 \u03bcg/L) were associated with AF and QTc , whereas a negative correlation was observed with PaO2/FiO2 and lymphocyte count .logrank test analysis with p-values. Among electrocardiographic findings, AF on E.D. admission recording (p < 0.0001) or developed during hospitalization (p = 0.0409) or considered together as cumulative AF (p < 0.0001) were associated with lower 28-day survival rates for right heart strain (p = 0.0093) and QTc value > 451 ms (p < 0.0001). Relative bradycardia was not significantly different between survivors and deceased (p = 0.3148). In addition, age > 65 y (p = 0.0002), CRP over 4 mg/dL (p = 0.0023), D-dimer over 850 U/L (p = 0.0035), and serum albumin below 35 g/L (p < 0.0001) on E.D. admission laboratory tests were associated with lower 28-day survival rates.p < 0.05) and clinically relevant variables on univariate analysis were evaluated for the determination of hazard ratios (HRs) for 28-day mortality. Following Youden\u2019s index results, QTc value > 451 ms was considered in the final model. AF detection on E.D. arrival ECG or its in-hospital development (HR 3.02 (95% CI 1.03\u20138.81); p = 0.042), QTc > 451 ms (HR 3.24 995% CI 1.09\u20139.62); p = 0.033), and right ventricular strain (HR 2.94 (95% CI 1.01\u20138.55); p = 0.047) were associated with higher 28-day mortality risk after adjustment for age, sex, cardiac and pulmonary comorbidities , and laboratory tests that proved clinically pertinent and could potentially influence the outcome or inverted T wave on ECG recordings. This has already been described as a negative prognostic factor in patients with non-COVID19-related PTE [3 sign alone, indeed, was included in the right ventricular strain analysis as a strain mark and a recognized negative prognostic factor [2 \u2264 95% and RR > 20 bpm. Concerning laboratory tests on E.D. admission, low PaO2/Fio2 ratio, anemia, low serum albumin, leukocytosis with neutrophilia, elevated LDH, D-dimer, and CRP were prevalent in non-survivors, as previously described [Furthermore, hypoxic stress and lung damage, its related pulmonary hypertension and right ventricular heart strain, in addition to the high rates of pulmonary thromboembolism (PTE) registerated PTE and in oc factor . Our finc factor , who linescribed . Though escribed . As for escribed .A total of 15.8% of patients developed sinus bradycardia during hospitalization. This was not linked to higher mortality rates, as previously described , even thAutonomic dysfunction is shown throughout the lower heart rate variability registered in non-survivors as RR interval, which reflects the sympathovagal balance interacting with IL-6 and the ongoing pro-inflammatory boost ,33. This2/FiO2 (expression of respiratory failure), D-dimer, CRP, and lymphocytes (expression of inflammation during infection). Furthermore, abnormal troponin levels were associated with AF and QTc and, overall, tended to be associated with abnormal ECG on hospital admission. Taken together, these findings suggest that the possible myocardial damage, expressed by the troponin values, may be directly related to the infection itself rather than to a previous cardiac problem. Nevertheless, although troponin represents a marker of myocardial injury, it may be unreliable when considered alone, and therefore, it should be analyzed only when combined with additional clinical and laboratory parameters.Statistically significant correlations were found between troponin values and specific parameters of COVID-19, such as PaOThis study shows several limitations. Primarily, its retrospective design does not allow a confident generalizability. Despite controlling for demographic and clinical data, there could be other confounding variables not included in multivariate analysis, and the omission of radiologic parameters does not grant a strict clinical assessment of right heart strain and conceivable underlying pulmonary thromboembolism. Moreover, the temporal nexus between ECG findings and their development is missing, as we only analyzed the E.D. ECG, and certain abnormalities could have developed prior to SARS-CoV-2 infection; nevertheless, having these ECG abnormalities was associated with a worse prognosis. The potential association between ECG findings and serum troponin T levels could not be assessed, because of the few available TnT, as a former non-routine test on E.D. admission; nevertheless, only a statistical trend over significance was observed, and therefore, this variable was further excluded from the final model.Lastly, in consideration of the test duration and emergency situation experienced by our country during the study period, we did not have the possibility to routinely perform cardiac MRI to identify myocardial alterations in hospitalized patients and to comprehensively collect the frequency of post-COVID-19 cardiovascular sequelae. Nevertheless, the aim of the present study was to investigate the electrocardiographic features on hospital admission and in the emergency setting and not the cardiovascular sequelae, which, in our opinion, deserve per se additional investigations.To conclude, our study was conducted in an emergency, namely the first and second pandemic waves in Italy, prior to the development and approval of the anti-SARS-CoV-2 management strategies currently used. This supports the goal of investigate the untainted interaction of SARS-CoV-2 with heart rate and rhythm and, therefore, ECG, avoiding additional confounders such as new antiviral drugs and prophylactic treatments or the role of virus variants.This study demonstrates the association between older age, AF, QTc, and right ventricular strain recorded on E.D. admission ECG and higher mortality risk after adjusting for cardiopulmonary comorbidities and disease severity markers. These results endorse the role of the ongoing cardiovascular alterations in SARS-CoV-2 infection, likely related to the direct and indirect action of virus and cytokine storm on cardiomyocytes and unbiased by therapeutic strategies. ECG recording and its appropriate analysis offers a simple, quick, non-expensive, and validated approach in the emergency setting to guide COVID-19 patients\u2019 stratification in the ongoing pandemic frame, assisted by clinical and laboratory assessment."} +{"text": "The somehow prophetic 2007 publication reviews \u201cnatural disasters, climate change and mental health considerations for rural Australia\u201d (2) and pinpoints central aspects of today\u2019s debate, namely anxiety and depression, vulnerability and resilience. In addition to problems of rural areas (2), the impact of urbanicity (3) will be discussed as well as the role of air pollution on psychiatric disorders (4). (1) UN Environment Programme. https://www.unenvironment.org/explore-topics/climate-change/about-climate-change Dec 22nd, 2020. (2) Morissey SA, Reser JP. Aust J Rural Health. 2007 Apr;15(2):120-5. doi: 10.1111/j.1440-1584.2007.00865.x. (3) Krabbendam L et al. Psychol Med. 2020 Mar 11:1-12. doi: 10.1017/S0033291720000355. (4) Kim SY et al. Sci Total Environ. 2020 Dec 8;757:143960. doi: 10.1016/j.scitotenv.2020.143960.According to the UN Environment Programme \u201cclimate change is one of the most pervasive and threatening issues of our time\u201d. \u201cIn many places, temperature changes and sea-level rise are already putting ecosystems under stress and affecting human well-being\u201d (1). The presentation wants to give an overview on how climate change can affect mental health. A search was performed on PubMed for the combination of \u201cclimate change\u201d and \u201cmental health\u201d. 281 publications were identified, the first being from 2007 (the only one in that year). In 2020, until Dec 22No significant relationships."} +{"text": "During the COVID-19 pandemic, cancer patients are regarded as a highly vulnerable population. Given the unavoidable bias and unmeasured confounders in observational studies, the causal effects of cancers on COVID-19 outcomes are largely unknown. In the study, we tried to evaluate the causal effects of cancers on COVID-19 outcomes using the Mendelian randomization (MR) approach. No strong evidence was observed to support a causal role of cancer in COVID-19 development. Previous observational correlations between cancers and COVID-19 outcomes were likely confounded. Large and well-conducted epidemiological studies are required to determine whether cancers causally contribute to increased risk of COVID-19.p-values for the casual associations were all statistically insignificant: overall cancer , lung cancer , breast cancer , endometrial cancer , prostate cancer , thyroid cancer , ovarian cancer , melanoma , small bowel cancer , colorectal cancer , oropharyngeal cancer , lymphoma and cervical cancer . Sensitivity analyses and multivariable MR analyses yielded similar results. In conclusion, cancers might have no causal effect on increasing COVID-19 risk. Further large-scale population studies are needed to validate our findings.Observational studies have shown increased COVID-19 risk among cancer patients, but the causality has not been proven yet. Mendelian randomization analysis can use the genetic variants, independently of confounders, to obtain causal estimates which are considerably less confounded. We aimed to investigate the causal associations of cancers with COVID-19 outcomes using the MR analysis. The inverse-variance weighted (IVW) method was employed as the primary analysis. Sensitivity analyses and multivariable MR analyses were conducted. Notably, IVW analysis of univariable MR revealed that overall cancer and twelve site-specific cancers had no causal association with COVID-19 severity, hospitalization or susceptibility. The corresponding Coronavirus disease 2019 (COVID-19) is a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,4. ThereCancer patients are a vulnerable population during the COVID-19 pandemic ,6. CanceMendelian randomization, an epidemiological method, has been widely applied to assess the potential causal association between exposure and outcome ,15. Acco2, age \u00d7 gender, principal components and study-specific covariates by the original GWAS researchers. The COVID-19 outcomes included 1,683,768 participants for susceptibility, 1,887,658 participants for hospitalization, and 1,388,342 participants for severity, respectively. The uninfected individuals served as the controls. All cases were confirmed by laboratory, self-reported, or physician diagnosis. The severe cases were defined as patients who died or required respiratory support with COVID-19 infection [The summary statistics in the genome-wide association studies (GWASs) for COVID-19 were sourced from the COVID-19 Host Genetics Initiative V5 , which eThe summary statistics of the GWASs for cancers were obtained from the UK biobank , InternaCovariates for multivariable MR analyses were included: BMI , educatiAt the beginning of our study design, 24 site-specific cancers were considered. Overall cancer and 12 site-specific cancers were included, but another 12 types of cancer were not included due to insufficient SNPs . In p < 5 \u00d7\u200910\u22128). To ensure independence, SNPs were restricted by low linkage disequilibrium using clumping [Appropriate SNPs used as IVs must be robustly associated with cancers ; otherwise, a random-effect model was applied. In addition, we used the \u201cleave-one-out\u201d validation to determine whether a single SNP had a significant independent influence on the MR estimation.In the univariable MR analysis, the IVW analysis was chosen as the primary approach to estimate the causal effects of cancers on COVID-19 outcomes ,38. We ap-value using the Bonferroni correction was used. 0.0033 < p < 0.05 was regarded as suggestive evidence for a potential association. The \u03b2 and its SE (standard error) were calculated to reflect effect sizes. All statistical analyses were conducted in R v4.0.1 with the packages \u201cTwoSampleMR\u201d and \u201cMRPRESSO\u201d [We applied the random-effect IVW method to assess the causal effects of cancers on COVID-19 outcomes for the multivariable MR analyses, after controlling BMI, educational attainment, intelligence, smoking and alcohol consumption. Given the number of cancers and COVID-19 outcomes considered, a two-sided RPRESSO\u201d ,43.p = 0.07), ovarian cancer (p < 0.001), melanoma (p = 0.01) and cervical cancer (p = 0.08) (p = 0.34), lung cancer (p = 0.60), squamous cell lung cancer (p = 0.66), breast cancer (p = 0.43), ER+ breast cancer (p = 0.79), ER\u2212 breast cancer (p = 0.66), endometrial cancer (p = 0.79), prostate cancer (p = 0.54), thyroid cancer (p = 0.70), ovarian cancer (p = 0.62), melanoma (p = 0.79), small bowel cancer (p = 0.09), colorectal cancer (p = 0.85), oropharyngeal cancer (p = 0.31), lymphoma (p = 0.51) or cervical cancer (p = 0.25) on the COVID-19 severity were included for COVID-19 severity. Severe COVID-19 cases were defined as patients who died or required respiratory support with COVID-19 infection. The effects of each SNP in cancers on COVID-19 severity can be found in = 0.08) . Hence, severity .p = 0.03) and ovarian cancer (p = 0.01) . Although horizontal pleiotropy was observed in melanoma (p = 0.02), it showed no significant outlier. We conducted the \u201cleave-one-out\u201d analysis and found no potential SNP significantly biasing the results . After r results . Taken t results . Results results .p = 0.06), ovarian cancer (p < 0.001) and cervical cancer (p = 0.04) (p = 0.42), lung cancer (p = 0.37), squamous cell lung cancer (p = 0.66), breast cancer (p = 0.74), ER+ breast cancer (p = 0.51), ER\u2212 breast cancer (p = 0.93), endometrial cancer (p = 0.24), prostate cancer (p = 0.17), thyroid cancer (p = 0.80), ovarian cancer (p = 0.96), melanoma (p = 0.45), small bowel cancer (p = 0.08), colorectal cancer (p = 0.79) or cervical cancer (p = 0.32) on COVID-19 hospitalization . = 0.04) . The ranlization .p < 0.001; p = 0.78). The \u201cleave-one-out\u201d analysis showed no outliers (p = 0.04), estimates in the three analyses and prostate cancer (p = 0.046) when adjusting for education attainment. A significant association was also found in small bowel cancer (p = 0.047) when adjusting for smoking. However, the associations of overall cancer, prostate cancer and small bowel cancer with COVID-19 hospitalization could not be replicated when intelligence , income and alcohol consumption were adjusted , prostate cancer (p = 0.06), thyroid cancer (p = 0.06), ovarian cancer (p < 0.001), melanoma (p = 0.05) and cervical cancer (p < 0.001) (p = 0.69), lung cancer (p = 0.96), squamous cell lung cancer (p = 0.08), breast cancer (p = 0.43), ER+ breast cancer (p = 0.30), ER\u2212 breast cancer (p = 0.18), endometrial cancer (p = 0.83), prostate cancer (p = 0.58), thyroid cancer (p = 0.28), ovarian cancer (p = 0.93), melanoma (p = 0.82), small bowel cancer (p = 0.19), colorectal cancer (p = 0.30), oropharyngeal cancer (p = 0.80), lymphoma (p = 0.37) or cervical cancer (p = 0.68) on COVID-19 susceptibility were included for COVID-19 susceptibility. < 0.001) . Thus, wtibility .p = 0.02) and ovarian cancer (p < 0.001) . The \u201cleave-one-out\u201d plot showed one potential instrumental outlier (rs6983267) for colorectal cancer . After rl cancer . Howeverl cancer supporteDuring the COVID-19 pandemic, healthcare resources are extremely scarce, and there is an urgent need to allocate healthcare resources rationally . IdentifMR leverages the random allocation of genetic variants at conception, independently of confounders, to identify the causal effects that are substantially less confounded and not vulnerable to reverse causation ,15. We uAlthough many studies have generally shown positive correlations of cancers with the risk of COVID-19 ,45,46,47Risk factors may be correlated with COVID-19 outcomes, but not as a causal association. Previous MR studies have shown that many traditional risk factors have no causal association with COVID-19 outcomes, such as decreased lung function, chronic obstructive pulmonary disease, blood pressure, type 2 diabetes, chronic kidney disease, coronary artery disease, stroke and nonalcoholic fatty liver disease ,53,54,55MR design is less confounding than observational study, but limitations of this MR study need to be acknowledged. First, some types of cancer\u2014such as stomach cancer, pancreatic cancer, liver cancer and brain cancer\u2014were not included in the study because of insufficient SNPs . PotentiOverall, we used MR analysis to evaluate the causal effects of overall cancer and twelve site-specific cancers on COVID-19 severity, hospitalization and susceptibility. Results of the MR study did not suggest strong evidence to support the causal associations of any examined cancer with COVID-19 outcomes. Previous observational correlations of cancers with COVID-19 outcomes were likely confounded. More large-scale epidemiological studies are needed to validate our findings."} +{"text": "Health impact of monoclonal gammopathy of undetermined significance (MGUS) and monoclonal B-cell lymphocytosis (MBL): findings from a UK population-based cohort. BMJ Open 2021;11:e041296. doi: 10.1136/bmjopen-2020-041296Lamb MJ, Smith A, Painter D, This article was previously published with an error in table 1. MGUS control numbers and percentages by gender were transposed and should read: males 11308 (51.6) and females 10620 (48.4)."} +{"text": "Families with children may be at higher risk for influenza infection. Community transmission can suffer from underreporting as testing is often not performed. We studied the epidemiology of influenza in households with school-aged children using home-based sample collection.We conducted a remote household study surveilling respiratory viruses from November 2019-June 2021, in King County, Washington (WA), USA. Households with school-aged children were enrolled, mailed home specimen collection kits, and asked to self-assess for weekly acute respiratory illness (ARI) using remote survey platforms. Participants with ARI symptoms were prompted to complete serial illness surveys and self-collect/parent collect mid-turbinate nasal swabs. Samples were sent to a University of Washington study laboratory for RT-PCR influenza testing. Influenza rates were compared to WA Department of Health (DOH) reporting.A total of 1861 ARI events were reported among 992 adults and 869 children in 470 households; 75 influenza cases were detected (36 influenza A and 39 influenza B). The study participant median age was 32 years (0-84), 10 years (1-49) for influenza A, and 11 years (3-49) for influenza B cases. Overall 13% of households had an influenza case, of which 13 (22%) reported >1 case. A total of 81% of participants reported receipt of one dose of the 2019-2020 influenza vaccine, including 91% of influenza A and 90% of influenza B cases, and 84% received the 2020-2021 influenza vaccine. Like WA DOH, we observed a wave of influenza B cases followed by influenza A in 2019-2020. During influenza season 2020-2021, WA DOH reported 9 positive influenza tests and none observed in our study. Commonly, influenza case-patients reported were fever, cough, rhinorrhea, and fatigue. GI symptoms were more common in children than adults. Of the cases, 92% of influenza A and 78% of influenza B occurred in children.D0-Day of reported onset, D7-7 days after reported illness onset. No participants >49 years were positive for influenza. D0: 30 participants responded and of respondents, 13% <5 years, 47% 5-12 years, 3% 13-17 years, and 37% 18-49 years. D7: 31 participants responded and of respondents 13% <5 years, 48% 5-11 years, 3% 12-17 years, and 36% 18-49 years.D0-Day of reported onset, D7-7 days after reported illness onset. No participants >49 years were positive for influenza. D0: 28 participants responded and of respondents, 4% <5 years, 57% 5-12 years, 14% 13-17 years, and 25% 18-49 years. D7: 28 participants responded and of respondents, 4% <5 years, 57% 5-11 years, 18% 12-17 years, and 21% 18-49 years.Influenza illness in 2019-2020 was initially influenza B, and subsequently replaced by influenza A. Most cases were in children and adolescents, despite at least one dose of influenza vaccine. Symptoms were widely distributed and similar between influenza A and B. Influenza incidence in our cohort declined to zero with the rise of SARS-CoV-2 cases and widespread mitigation efforts.Janet A. Englund, MD, AstraZeneca: Advisor/Consultant|AstraZeneca: Grant/Research Support|GlaxoSmithKline: Grant/Research Support|Meissa Vaccines: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Grant/Research Support|Sanofi Pasteur: Advisor/Consultant Helen Y. Chu, MD, MPH, Cepheid: Reagents|Ellume: Advisor/Consultant|Gates Ventures: Grant/Research Support|Merck: Advisor/Consultant|Pfizer: Advisor/Consultant."} +{"text": "T790M mutation, the major mechanism of acquired resistance to first-generation EGFR TKI. However, resistance to AZD9291 arises eventually and EGFRC797S mutation was reported to be a major resistance mechanism. Thus, it is highly valuable to develop novel EGFR fourth-generation inhibitors targeting C797S mutation to override the acquired resistance. In this study, we identified HCD3514 as a novel EGFR fourth-generation inhibitors targeting C797S triple mutation. It strongly inhibited EGFRL858R/T790M/C797S and EGFR19del/T790M/C797S mutations with IC50 values of 1.0 and 2.0 nM, respectively. HCD3514 dose-dependently inhibited the activation of EGFR in both engineered BaF3 cells and tumor cells harboring EGFRC797S triple mutant and thus effectively suppressed the proliferation of the cells. Moreover, HCD3514 caused a dose-dependent increase of apoptosis in C797S triple mutant cells accompanied by increased levels of cleaved caspase-3 and cleaved PARP. Furthermore, HCD3514 induced tumor growth inhibition in EGFR19del/T790M/C797S xenograft model as a single oral agent by decreasing the activation of EGFR. In addition to EGFRC797S triple mutations, HCD3514 also potently and selectively inhibited EGFRT790M double mutations (L858R/T790M and 19del/T790M). Collectively, HCD3514 is a highly selective and potent EGFR inhibitor against EGFRC797S triple mutations as well as EGFRT790M double mutations and is confirmed potently anti-tumor activity in preclinical models.Osimertinib (AZD9291), a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI), has significantly improved the survival of non-small cell lung cancer (NSCLC) patients with EGFR WT), resulting in severe side effects Lung cancer is a malignant tumor with high incidence and mortality throughout the world, being responsible for almost one-quarter of all cancer-related deaths T790M/C797S resistance mutation has gained much attention.Consequently, the urgent need for highly selective third-generation EGFR TKIs that target both activating mutations and T790M resistance mutation leads to the development of osimertinib (AZD9291). AZD9291 exhibits remarkable efficacy in treating patients of T790M mutation-positive NSCLC in vitro and in vivo, but quite similar to that with EAI045 treatment, its antitumor efficacy is limited as a single agent T790M/C797S inhibitors showing potential antitumor activity of AZD9291-resistant triple mutant EGFR in vitro and in vivo, including TQB3804, LS-106 T790M. Typical examples include BI-4020 Currently, encouraging achievements have been made in the development of the fourth-generation EGFR TKIs, which could be summarized into two categories based on their discovery strategies. 1) Exploiting allosteric binding pocket that is remote from the location of C797S mutation. For example, EAI045, an allosteric inhibitor, is reported as the first fourth-generation EGFR inhibitor overcoming T790M and C797S resistance mutation T790M inhibitor AZD9291, we identified a potent fourth-generation EGFR inhibitor, HCD3514, which is effective as a single agent to overcome EGFR triple mutation (EGFRL858R/T790M/C797S and EGFR19del/T790M/C797S) and shows promising antitumor activity both in vitro and in vivo.In this study, through structural hybridization of brigatinib with EGFR2.BaF3 cells and PC-9 cells were obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) and the European Collection of Authenticated Cell Cultures (ECACC), respectively. MRC-9 cells and GSE-1 cells were purchased from the American Type Culture Collection (ATCC). All the cells were maintained in RPMI-1640 medium (Gibco) or EMEM medium (Gibco) supplemented with 10% FBS (Gibco) at 37 \u00b0C in 5% COL858R/T790M/C797S, EGFR19del/T790M/C797S, EGFRL858R/T790M or EGFR19del/T790M and cells stably expressing these mutants were subsequently selected in medium supplemented with 1 \u03bcg/mL puromycin (Sigma-Aldrich). PC-9-OR cells harboring EGFR19del/T790M/C797S mutation were constructed by CRISPR/Cas9 genome-editing technology to simultaneously knock-in the T790M and C797S mutations into PC-9 cells harboring EGFR19delBaF3 cells were transduced with retroviruses harboring genes encoding EGFR1H NMR and 13C NMR spectra was recorded on a Bruker AV-400 spectrometer at 400 MHz and Bruker AV-600 spectrometer at 151 MHz, respectively, in CDCl3. Coupling constants (J) are expressed in hertz (Hz). Chemical shifts (\u03b4) of NMR are reported in parts per million (ppm) units relative to internal control (TMS). The first-order peak patterns are indicated as s (singlet), d (doublet), t (triplet), q (quadruplet). Complex non-first order signals are indicated as m (multiplet). The high-resolution ESI-MS results were recorded on an Applied Biosystems Q-STAR Elite ESI LC-MS/MS mass spectrometer. The purity of compound was determined by reverse-phase high-performance liquid chromatography (HPLC) analysis using an Agilent 1260 system (G1310B Iso pump and G1365D MWD VL detector) with an YMC Triart C18 reversed-phase column at 254 nm. Elution was MeOH in water, and flow rate was 1.0 mL/min.1H NMR \u03b4 8.43 , 8.41 , 8.35 , 7.96 , 7.43 , 7.33 , 7.24 , 7.06 , 6.87 , 4.58 - 4.42 , 3.60 - 3.53 , 3.41 , 2.79 - 2.63 , 2.62 - 2.43 , 2.43 - 2.36 , 2.34 , 1.99 - 1.90 , 1.79 - 1.67 , 1.28 , 1.26 , 1.24 .13C NMR \u03b4 158.43, 158.22, 156.93, 150.71, 139.15, 134.79, 133.85, 130.39, 128.78, 125.49, 124.13, 123.55, 118.64, 117.55, 116.60, 113.01, 112.83, 108.99, 70.38, 61.96, 55.46 (2C), 50.81 (2C), 49.13, 48.94, 46.05, 28.80 (2C), 22.18 (2C), 8.14, 1.05. HRMS (m/z): [M+H] + calculated for C33H42ClN7O3S, 652.2831; found, 652.2814. HPLC purity: 98.1%. Brigatinib (cat. no. S8229) and AZD9291 (cat. no. S7297) were purchased from Selleck Chemicals.Compound HCD3514 was designed and synthesized by Ke Ding laboratory. L858R/T790M/C797S: cat. no. E10-12VG, EGFR19del/T790M/C797S: cat. no. E10-12UG, EGFRL858R/T790M: cat. no. E10-122DG, EGFR19del/T790M: cat. no. E10-122KG) or Eurofins Scientific (EGFRWT: cat. no. 14-531M). ELISA was used to evaluate the inhibitory activity of test compounds against EGFR, and the experiment was performed as described previously The recombinant EGFR proteins of the kinase domain were purchased from SignalChem Lifesciences (EGFRL858R/T790M/C797S was selected as the template to elucidate the binding mode of HCD3514. Protein structure was downloaded from Protein Data Bank (PDB 6LUD). The EGFR enzyme was defined as a receptor and the docking grid was centered on the ligand binding location. Docking simulations were performed in standard precision (SP) mode. Other parameters were set as default. After accomplishment of the molecular docking procedure, eight docking poses were scored and selected based on calculated energy.The molecular docking procedure was performed within Glide 7.9 software BaF3 cells, PC-9-OR cells, MRC-9 cells and GSE-1 cells were plated in 96-well plates in the corresponding medium and incubated overnight, followed by exposing to medium containing serial dilutions of compounds . After 72 h of drug treatment, cell counting kit-8 (CCK8) or sulforhodamine B (SRB) was added to each well and then measured by SoftMax Pro software at the absorbance of 450 nm or 560 nm Western blotting was performed as described previously L858R/T790M/C797S cells, BaF3-EGFR19del/T790M/C797S cells and PC-9-OR cells were seeded in 6-wells plates overnight, and exposed to indicated concentrations of compounds HCD3514 or brigatinib for 48 h. Then cells were collected and washed with PBS and measured by Annexin V-FITC Apoptosis detection kit . Signals were measured using FACS Calibur flow cytometer, and FlowJo software was used to analyze the data.BaF3-EGFR19del/T790M/C797S cells (2 \u00d7 106) were injected subcutaneously into BALB/c nude mice (Shanghai institute of medicine). After animals were randomly assigned to groups, tumor-bearing mice were orally administered vehicle, test compound HCD3514 or AZD9291 at the indicated doses once a day and tumor size were measured once per week. Tumor volume was calculated as length \u00d7 width2 \u00d7 0.5 (mm3) and the tumor growth inhibition (TGI) = [1-RTV (treated) / RTV (control)] \u00d7 100%. Mice were sacrificed and tumors were harvested for Western blot analysis. All animal study was approved by the Institutional Animal Care and Use Committee of the Shanghai Institute of Materia Medica and strictly performed according to the institutional ethical guidelines on animal care.BaF3-EGFRP < 0.05, **P < 0.01, ***P < 0.001.Data were presented as mean \u00b1 Standard Deviation (SD) and were analyzed by GraphPad Prism 8.0 software. Statistical analysis of the difference between vehicle and compound treated groups was compared by a two-tailed Student's t-test. Statistical significance was defined as *T790M/C797S, we incorporated important pharmacophore of brigatinib to the 4-indolyl-2-phenylaminopyrimidine scaffold of EGFRT790M inhibitor AZD9291 and developed a novel series of potent and mutant selective EGFRT790M/C797S inhibitor. Following extensive medicinal chemistry optimization by adding H-bond receptor of the indole ring and hydrophobic moiety on the benzene ring, we identified HCD3514 as a selective EGFRT790M/C797S inhibitor and EGFR19del/T790M/C797S (IC50 = 2.0 \u00b1 0.3 nM) with a more than 78-fold selectivity over EGFRWT (IC50 = 156.0 \u00b1 6.9 nM). By comparison, HCD3514 possessed more potent kinase inhibitory activity against EGFR triple mutations than brigatinib and more potent than AZD9291 (IC50 = 6.30 \u03bcM) and gastric mucosal (GSE-1) cell lines. As shown in Supplementary M Figure A, indicain vitro anti-tumor activity of HCD3514 in EGFRT790M/C797S triple mutant cells through suppression of EGFR phosphorylation, leading to the inhibition of cellular proliferation.Thus, these results demonstrated the L858R/T790M/C797S cells, HCD3514 triggered significant apoptosis with apoptosis rates of 72.39% and 98.27% at the concentration of 1 \u03bcM and 3 \u03bcM, respectively and cysteinyl aspartate specific proteinase-3 (caspase-3) play an important role in cellular processes, including apoptosis To gain deeper insight into the potential mechanism of apoptosis induction in EGFRin vivo in BaF3-EGFR19del/T790M/C797S xenograft mouse model. BALB/c nude mice bearing established BaF3-EGFR19del/T790M/C797S mouse xenograft tumors were daily oral treatment with HCD3514 (50 and 75 mg/kg), AZD9291 (25 mg/kg) or vehicle control. Consequently, HCD3514 resulted in an obvious growth inhibition of BaF3-EGFR19del/T790M/C797S mouse xenograft tumors in a dose-dependently manner with tumor growth inhibition (TGI) values of 22.53% and 37.73% at the dosage of 50 mg/kg and 75 mg/kg, respectively, while AZD9291 treatment did not show significant reduction of tumor growth in the xenograft model compared to the vehicle treated mice , as suggested by the molecular docking experiment showed in Figure L858R/T790M and EGFR19del/T790M mutations with IC50 values of 4.9 and 8.9 nM in biochemical, respectively. Moreover, HCD3514 showed antiproliferative activities in BaF3-EGFRL858R/T790M and BaF3-EGFR19del/T790M cells with IC50 of 0.66 \u03bcM and 0.52 \u03bcM, respectively, although the IC50 values of HCD3514 were higher than that of AZD9291. Furthermore, Western blot analysis revealed that HCD3514 dose-dependently suppressed the EGFR phosphorylation in both BaF3-EGFRL858R/T790M cells and BaF3-EGFR19del/T790M cells. Besides, we also evaluated the in vitro anti-tumor activity of HCD3514 in NCI-H1975 cells harboring EGFRL858R/T790M. HCD3514 also displayed an excellent antiproliferative potency in NCI-H1975 cells with IC50 of 0.49 \u03bcM and the expression of phospho-EGFR was down-regulated after treatment with HCD3514 in a dose-dependent manner. Thus, HCD3514 could target EGFRT790M double mutations as well as EGFRT790M/C797S triple mutations.In addition, we checked whether HCD3514 inhibits EGFR-double mutations exploiting allosteric binding pocket by allosteric inhibitors. 2) developing ATP-competitive inhibitors by structural modification of ALK/EGFR inhibitor brigatinib or the third-generation EGFR TKIs.Oncogenic mutations in EGFR are prevalent in NSCLC. Though third-generation EGFR inhibitor AZD9291 has achieved a great clinical benefit in NSCLC patients, the EGFRT790M inhibitor AZD9291, we identified a new fourth-generation EGFR triple mutant-selective inhibitor HCD3514, which possessed a promising antitumor activity both in vitro and in vivo. Compared to AZD9291, molecular docking of HCD3514 identified an additional hydrogen bond interaction towards Lys745, which was proposed to compensate for the loss of covalent bound due to the C797S point mutation and ultimately enhanced the inhibitory efficacy of HCD3514 on EGFRC797S mutations. HCD3514 displayed a single digit-nanomolar kinase inhibitory activity against triple mutant EGFR, including EGFRL858R/T790M/C797S and EGFR19del/T790M/C797S, which showed superior biochemical activity than brigatinib. Importantly, HCD3514 exhibited a sufficient EGFRWT sparing window, suggesting its low toxicity. In addition, HCD3514 simultaneously inhibited the activities of both mutant forms of EGFR at the cellular level. It showed that both engineered BaF3 cells harboring EGFRL858R/T790M/C797S or EGFR19del/T790M/C797S were sensitive to HCD3514, as well as the PC-9-OR cells (EGFR19del/T790M/C797S expressing PC-9 lung cancer cells), with enhanced inhibition the phosphorylation of EGFR. Besides, cleaved PARP and cleaved caspase-3 levels were showed to increase in three C797S mutant cells, which was consistent with apoptosis induction in a concentration-dependent manner. Furthermore, unlike EAI045 or brigatinib which showed limited antitumor effect without combined with anti-EGFR antibody C797S triple mutations but also EGFRT790M double mutations.In this study, through structural hybridization of brigatinib with EGFRin vitro and in vivo and we also provided a novel chemical scaffold and a new lead compound that worthy of further investigation.In summary, our preclinical data demonstrated that HCD3514 was effective in overcoming both triple mutant and double mutant forms of EGFR-dependent resistance mechanisms Supplementary figures.Click here for additional data file."} +{"text": "Assessing serological inflammation is difficult in tocilizumab (TCZ)-treated rheumatoid arthritis (RA) patients, as standard inflammation parameters, like erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP), are influenced by interleukin-6-receptor inhibition. Calprotectin in the serum, also named S100A8/S100A9, might be a more useful inflammation parameter in TCZ-treated patients.Sixty-nine RA patients taking TCZ were included. Serum-calprotectin levels were assessed, as well as ESR, CRP, need for a change in disease-modifying anti-rheumatic drugs due to RA activity (= active RA), and the RA clinical disease activity score (CDAI). Forty-five RA patients taking tumor-necrosis factor-inhibitors (TNFi) were investigated for the same parameters.P < 0.001). A calprotectin cut-off value of 1916.5 ng/ml resulted in a sensitivity and specificity of 80.0 %, respectively, for the detection of RA disease activity. Calprotectin values correlated with CDAI-scores . ESR and CRP were less suitable to detect RA activity in TCZ-treated patients. Also TNFi-treated patients with active RA had higher calprotectin values compared to not active RA . The calprotectin value with the best sensitivity and specificity for detecting RA activity was 3690.5 ng/ml among TNFi-treated patients.TCZ-treated patients with active RA had higher calprotectin values than not active RA patients (4155.5 [inter quartile range 1865.3\u20136068.3] vs 1040.0 [676.0\u20131638.0] ng/ml, Calprotectin in the serum can be a useful inflammation parameter despite TCZ-treatment.The online version contains supplementary material available at 10.1186/s13075-022-02887-7. Inflammation parameters in the serum are a useful tool to monitor disease activity in inflammatory rheumatic diseases. In rheumatoid arthritis (RA), mostly erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) are routinely assessed. CRP and acute phase protein synthesis in the liver is regulated by interleukin-6 (IL-6) , 2. TociCalprotectin, a heterodimer of the two calcium-binding proteins S100A8 and S100A9 , is a major cytosolic protein in monocytes and neutrophils, secreted during infections, malignancy, and inflammation , 6. CalpThe measurement of calprotectin in the serum as inflammation parameter in RA (without IL-6 receptor inhibitors) has been investigated and showed a correlation with radiographic damage scores and standard inflammation parameters . It alsoFew data is available for the use of calprotectin in RA with TCZ-treatment. Only one study of 33 patients is published , suggestOne hundred fourteen patients, fulfilling the 2010 ACR/EULAR classification criteria for rheumatoid arthritis , were inThe CDAI, comprising the sum of 28 swollen joints, 28 tender joints, patient global, and physician global assessment , was assSerum calprotectin was collected in serum-gel vials and measured with EliA\u2122 Calprotectin 2 wells with a Phadia\u2122 250 device . For each measurement cycle, a commercial negative and positive control (Thermo Fisher Scientific) was analyzed. Serum samples were centrifuged within 1h after blood collection and stored between 2 and 8\u00b0C until measurement. Stable calprotectin values can be measured with this assay within 7 days .ESR (reference range in the first hour 3\u20138 mm) and CRP (reference < 0.5 mg/dl) were measured in the central laboratory of the University Hospital of W\u00fcrzburg. CRP was detected by immunoturbidimetry .U tests were performed for continuous variables and Fisher\u2019s exact tests for categorical variables. Spearman\u2019s tests were used to calculate correlations. Receiver-operator characteristic (ROC) curves were calculated to detect cut-off values with the best sensitivity and specificity. SPSS Statistics v 28.0 was used for statistical analysis. For data collection Excel was used. Figures were grouped by using Photoshop . Two-tailed P-values less than 0.05 were considered significant.Shapiro-Wilk tests were used to test for normal distribution. As normal distribution was mostly absent, medians with interquartile ranges (IQR) were shown. To test for differences between unpaired groups, Mann-Whitney Inflammation parameters were obtained from 69 RA patients. All patients received TCZ for at least 3 months. Forty-eight of 69 (69.6 %) were female; the median age was 64.0 years (range 33\u201389). Fifty-four of 69 (78.3 %) were rheumatoid factor (RF)-positive; 51/69 (73.9 %) were anti-citrullinated protein antibody (ACPA)-positive. All ACPA-positive patients were RF-positive. Fifty of 69 (72.5 %) received TCZ subcutaneously and 19/69 (27.5 %) intravenously. No concomitant DMARD was present in 43/69 (62.3 %) patients. Thirteen of 69 (18.8 %) received prednisolone , 12/69 (17.4 %) methotrexate (MTX), and 1/69 (1.4 %) lefunomide (LEF). The median activity parameters of the TCZ-treated patients were as follows: DAS28-ESR 1.5 (IQR 1.1\u20132.2), DSA28-CRP 1.7 (1.2\u20132.2), SDAI 5.0 (2.0\u20138.0), and CDAI 5.0 (2.0\u20138.0). The median inflammation parameters of the TCZ-treated patients were as follows: ESR in 1h 4.0 (2.0\u20136.0) mm, CRP 0.0 (0.0\u20130.1) mg/dl, and calprotectin 1072.0 (686.5\u20131916.5) ng/ml. Patients\u2019 characteristics are summarized in Table n = 115) compared to the active patients (n = 10) (1040.0 (676.0\u20131638.0) ng/ml vs 4155.5 [1865.3\u20136068.3] ng/ml, P < 0.001) one group of patients, who continued their DMARD regimen (i.e. tocilizumab + concomitant medication) (not active), and (2) patients, who needed a change or escalation of their DMARDs due to inflammatory activity of RA (active). One hundred twenty-five calprotectin values were included in this study as from some patients more than one time point was measured. The calprotectin value in the serum was significantly lower in the not active RA patients ( one grouP < 0.001) had a lower median calprotectin value compared to patients with CDAI-low activity (n = 67) . Patients with CDAI-low activity had lower median calprotectin levels than patients with CDAI-moderate activity (n = 17) . Patients with CDAI-moderate disease activity had lower median calprotectin levels than patients with CDAI-high activity (n = 2) Fig. a and sigr = 0.301; P < 0.001), with DAS28-CRP , and with SDAI with IL-6-dependent composite scores was detected: with DAS28-ESR were included in this study. Patients\u2019 characteristics including sex, age, RF/ACPA-status, concomitant DMARDs, median activity scores, and median inflammation parameters are embedded in Table n = 43) had a lower serum-calprotectin (1845.0 [832.0\u20132569.0] ng/ml) than active RA patients (n = 10) receiving a change of their TNFi due to inflammatory activity of RA Fig. d.r = 0.401; P = 0.001) had a median calprotectin value of 1694.0 [773.5\u20132983.0] ng/ml, which was not significantly different from patients with CDAI-low activity (n = 26) . Patients with CDAI-low activity had lower median calprotectin levels than patients with CDAI-moderate activity (n = 5) . Patients with CDAI-moderate disease activity had numerically but not significantly lower median calprotectin levels than patients with CDAI-high activity (n = 2) , with DAS28-CRP , and with SDAI Fig. d. Patien Fig. d. P = 0.021, Fig. P < 0.001, Fig. In contrast to TCZ-treated patients, in TNFi-treated RA patients ESR and CRP showed differences between not active and active patients and also found significant correlations between calprotectin values and RA-activity composite scores , which iDisease activity scores, including DAS28-ESR and DAS28-CRP, which contain serological inflammation parameters for their calculation (to a relevant extent), were lower in our TCZ-treated group than in the TNFi-group. In prior studies, RA patients receiving TCZ-treatment had higher DAS28-ESR remission rates than CDAI or SDAI remission rates, which was supposed to be due to the high weight of the ESR in the DAS28-ESR score . TherefoIt was formerly shown that RA patients with detectable TCZ trough levels (after intravenous application) did not have lower calprotectin values than patients with undetectable TCZ trough levels, in contrast to the CRP values, which were lower when TCZ was detectable . This suThe CDAI score is usually assessed directly after each patient\u2019s visit without having the inflammatory parameters available at that time. This was also the case in our study: The CDAI scores were assessed without knowing the respective calprotectin values (neither ESR nor CRP). Thus, the decision of the investigator on the CDAI score was not biased by the knowledge of the inflammatory parameters.Concerns over the pre-analytical factors of serum-calprotectin values have been raised, but recently it was demonstrated that serum-calprotectin is stable for 1 week when kept refrigerated . This siOur study is limited due to its retrospective design and single-center approach. Additionally, future longitudinal studies are needed to evaluate calprotectin as follow-up parameter and its usefulness in detecting treatment response. Most of our patients had a low disease activity with a median CDAI value of 5, so that high inflammation parameters were only included in our study to a limited extent.Additional file 1: Supplemental Figure S1 Correlation of interleukin-6-dependend composite scores including DAS28-ESR , DAS28-CRP and SDAI with calprotectin in tocilizumab (TCZ)-treated RA patients (a-c) and in tumor necrosis factor alpha-inhibitor (TNFi)-treated RA (d-f) patients."} +{"text": "Salix species, including willow trees, are distributed in the temperate regions of Asian countries, including South Korea. Willow trees are used to treat pain and inflammatory diseases. Due to the medicinal properties of willow trees, pharmacological studies of other Salix spp. have gained attention; however, only a few studies have investigated the phytochemicals of these species. As part of our ongoing natural product research to identify bioactive phytochemicals and elucidate their chemical structures from natural resources, we investigated the marker compounds from indigenous Korean Salix species, namely, Salix triandra, S. chaenomeloides, S. gracilistyla, S. koriyanagi, S. koreensis, S. pseudolasiogyne, S. caprea, and S. rorida. The ethanolic extract of each Salix sp. was investigated using high-performance liquid chromatography combined with thin-layer chromatography and liquid chromatography\u2013mass spectrometry-based analysis, and marker compounds of each Salix sp. were isolated. The chemical structures of the marker compounds (1\u20138), 3-(4-hydroxyphenyl)propyl \u03b2-D-glucopyranoside (1), 2-O-acetylsalicin (2), 1-O-p-coumaroyl glucoside (3), picein (4), isograndidentatin B (5), 2\u2032-O-acetylsalicortin (6), dihydromyricetin (7), and salicin (8) were elucidated via nuclear magnetic resonance spectroscopy and high-resolution liquid chromatography\u2013mass spectrometry using ultrahigh-performance liquid chromatography coupled with a G6545B Q-TOF MS system with a dual electrospray ionization source. The identified marker compounds 1\u20138 were examined for their antimicrobial effects against plant pathogenic fungi and bacteria. Dihydromyricetin (7) exhibited antibacterial activity against Staphylococcus\u00a0aureus, inducing 32.4% inhibition at a final concentration of 125 \u03bcg/mL with an MIC50 value of 250 \u03bcg/mL. Overall, this study isolated the marker compounds of S. triandra, S. chaenomeloides, S. gracilistyla, S. koriyanagi, S. koreensis, S. pseudolasiogyne, S. caprea, and S. rorida and identified the anti-Staphylococcus aureus bacterial compound dihydromyricetin. Salix comprises approximately 500 species of deciduous trees and shrubs distributed in the temperate regions of Asian countries, including South Korea, and willow trees are the most representative plants of this genus anthracene-induced phorbol ester-promoted skin carcinogenesis [S. caprea. Finally, S. rorida is a deciduous tree and a willow species native to Japan, northern China, Korea, and Russia. A recent phytochemical study revealed salicin as the major constituent of S. rorida and identified other constituents, including (+)-catechin, naringenin, salipurposide, aromadendrin, isosalipurposide, aromadendrin-7-O-\u03b2-D-glucopyranoside, and taxifolin-7-O-\u03b2-D-glucopyranoside, via liquid chromatography\u2013mass spectrometry (LC/MS) analysis [S. rorida has not yet been elucidated.l (DPPH) . Despiteivatives ,11, whicinkiller . A pharmrophages . In additivities . Howeverl crafts . S. koripriority , and fewin Korea . S. koreth decay . A pharmer cells . S. kore effects ,21,22. Dnd fever Recent p effects ,25. Prevextracts ,24. S. cSalix species S. triandra, S. chaenomeloides, S. gracilistyla, S. koriyanagi, S. koreensis, S. pseudolasiogyne, S. caprea, and S. rorida. Ethanolic extracts of these Salix spp. were investigated using high-performance liquid chromatography (HPLC) combined with thin-layer chromatography (TLC) and LC/MS-based analysis, followed by the isolation of each marker compound of Salix spp. The chemical structures of marker compounds (1\u20138) were elucidated via nuclear magnetic resonance (NMR) spectroscopy and electrospray ionization (ESI) LC/MS analyses. Finally, the identified marker compounds 1\u20138 were tested for their antimicrobial effects. Herein, we report the isolation and structural characterization of marker compounds 1\u20138 as well as their bioactivity with respect to their antimicrobial effects.As part of our ongoing research projects to identify bioactive natural products and elucidate their chemical structures from natural resources ,30,31,32Salix species were collected from Chungcheongnam-do, Chungcheongbuk-do, and Gangwon-do (South Korea), thoroughly dried, and mounted. Plant specimens to obtain EtOH crude extracts.The twigs of eight pecimens were madSalix species facilitated the determination of the marker compounds for these species based on the amount of the component present in each extract. Phytochemical investigation of the crude EtOH extracts was performed via TLC and LC/MS-based analysis using column chromatography and HPLC to isolate the marker compounds (1) was isolated from S. triandra, 2-O-acetylsalicin (2) from S. chaenomeloides, 1-O-p-coumaroyl glucoside (3) from S. gracilistyla, picein (4) from S. koriyanagi, isograndidentatin B (5) from S. koreensis, 2\u2032-O-acetylsalicortin (6) from S. pseudolasiogyne, dihydromyricetin (7) from S. caprea, and salicin (8) from S. rorida propyl \u03b2-D-glucopyranoside (1) [O-acetylsalicin (2) [O-p-coumaroyl glucoside (3) [4) [5) [O-acetylsalicortin (6) [7) [8) [The marker compounds of side (1) , 2-O-aceicin (2) , 1-O-p-cside (3) , picein (3) [4) , isogran [4) [5) , 2\u2032-O-acrtin (6) , dihydro (6) [7) , and sal [7) [8) . Next, the marker compounds were tested for their antibacterial activity against the Gram-positive bacterium Staphylococcus aureus (HG003) and Gram-negative bacterium Escherichia coli (MG1655). Among the isolates, only dihydromyricetin (7) exhibited antibacterial activity against S. aureus, inducing 32.4% inhibition at a final concentration of 125 \u03bcg/mL with an MIC50 value of 250 \u03bcg/mL (1) and 1-O-p-coumaroyl glucoside (3) exhibited very weak activity against S. aureus, inducing only 1.9% and 1.3% inhibition, respectively . Twigs of S. chaenomeloides, S. koriyanagi, and S. caprea were collected from Inje-gun and those of S. rorida from Hwacheon-gun . The twigs of S. gracilistyla and S. koreensis were collected from Jecheon-si . Each material was authenticated by the author J.N.Yu. Voucher specimens of the materials were deposited at the Hongcheon Institute of Medicinal Herbs, Hongcheon-gun, South Korea.In June 2021, twigs of S. triandra twigs (1.6 kg) were dried at 35\u201345 \u00b0C in a plant-drying oven for one week, pulverized, and extracted with 80% ethanol (10 L) via sonication for 90 min three times at room temperature. The filtered ethanol extract was evaporated in vacuo to obtain the crude ethanol extract (86.6 g). The extract (10.1 g) was dissolved in MeOH (100 mL) and applied to a reverse-phase (RP) Sep-Pak column with 100% MeOH to remove the wax, lipids, and fatty acids, and the resultant residue was concentrated using an evaporator to obtain the crude extract (5.2 g). The crude extract (1.0 g) was separated via preparative RP-HPLC to obtain four fractions (P1\u2013P4). Fraction P2 (303.3 mg) was isolated via semipreparative RP-HPLC using 30% MeOH to obtain marker compound 1 .S. chaenomeloides twigs (1.8 kg) were dried at 35\u201345 \u00b0C in a plant-drying oven for one week, pulverized, and extracted with 80% ethanol (10 L) via sonication for 90 min three times at room temperature. The filtered ethanol extract was evaporated in vacuo to obtain the crude ethanol extract (144.6 g). The extract (10.3 g) was dissolved in MeOH (100 mL) and applied to an RP Sep-Pak column with 100% MeOH to remove the wax, lipids, and fatty acids, and the resultant residue was concentrated using an evaporator to obtain the crude extract (7.2 g). The crude extract (1.0 g) was separated via preparative RP-HPLC to obtain five fractions (P1\u2013P5). Fraction P4 (68.2 mg) was isolated via semipreparative RP-HPLC using 20% MeOH to obtain marker compound 2 .S. gracilistyla twigs (1.0 kg) were dried at 35\u201345 \u00b0C in a plant-drying oven for one week, pulverized, and extracted with 80% ethanol (10 L) via sonication for 90 min three times at room temperature. The filtered ethanol extract was evaporated in vacuo to obtain the crude ethanol extract (163 g). The extract (11 g) was dissolved in MeOH (100 mL) and applied to an RP Sep-Pak column with 100% MeOH to remove the wax, lipids, and fatty acids, and the resultant residue was concentrated using an evaporator to obtain the crude extract (5.6 g). The crude extract (1.0 g) was separated via preparative RP-HPLC to obtain five fractions (P1\u2013P5). Fraction P4 (468 mg) was isolated via semipreparative RP-HPLC using 23% MeOH to obtain marker compound 3 .S. koriyanagi twigs (2.0 kg) were dried at 35\u201345 \u00b0C in a plant-drying oven for one week, pulverized, and extracted with 80% ethanol (10 L) via sonication for 90 min three times at room temperature. The filtered ethanol extract was evaporated in vacuo to obtain the crude ethanol extract (167 g). The extract (10 g) was dissolved in MeOH (100 mL) and applied to an RP Sep-Pak column with 100% MeOH to remove the wax, lipids, and fatty acids, and the resultant residue was concentrated using an evaporator to obtain the crude extract (6.5 g). The crude extract (6.5 g) was subjected to HP-20 column chromatography, with eluting solvents of distilled water, MeOH, and acetone, to obtain three fractions (P1\u2013P3). Fraction P1 (2.6 g) was separated via preparative RP-HPLC to obtain five fractions (P11\u2013P15). Fraction P13 (245 mg) was isolated via semipreparative RP-HPLC using 15% MeOH to obtain marker compound 4 .S. koreensis twigs (2.3 kg) were dried at 35\u201345 \u00b0C in a plant-drying oven for one week, pulverized, and extracted with 80% ethanol (10 L) via sonication for 90 min three times at room temperature. The filtered ethanol extract was evaporated in vacuo to obtain the crude ethanol extract (101 g). The extract (9.1 g) was dissolved in MeOH (100 mL) and applied to an RP Sep-Pak column using 100% MeOH to remove the wax, lipids, and fatty acids, and the resultant residue was concentrated using an evaporator to obtain the crude extract (7.9 g). The crude extract (7.9 g) was subjected to HP-20 column chromatography, with the eluting solvents distilled water, MeOH, and acetone to obtain three fractions (P1\u2013P3). Fraction P3 (582 mg) was separated via preparative RP-HPLC to obtain four fractions (P31\u2013P34). Fraction P33 (582 mg) was isolated via semipreparative RP-HPLC using 43% MeOH to obtain marker compound 5 .S. pseudolasiogyne twigs (1.5 kg) were dried at 35\u201345 \u00b0C in a plant-drying oven for one week, pulverized, and extracted with 80% ethanol (10 L) via sonication for 90 min three times at room temperature. The filtered ethanol extract was evaporated in vacuo to obtain the crude ethanol extract (123.6 g). The extract (9.1 g) was dissolved in MeOH (100 mL) and applied to an RP Sep-Pak column using 100% MeOH to remove the wax, lipids, and fatty acids, and the resultant residue was concentrated using an evaporator to obtain the crude extract (4.0 g). The crude extract (4.0 g) was separated via preparative RP-HPLC to obtain four fractions (P1\u2013P4). Fraction P4 (306 mg) was isolated via semipreparative RP-HPLC using 39% MeOH to obtain marker compound 6 .S. caprea twigs (1.5 kg) were dried at 35\u201345\u2103 in a plant-drying oven for one week, pulverized, and extracted with 80% ethanol (10 L) via sonication for 90 min three times at room temperature. The filtered ethanol extract was evaporated in vacuo to obtain the crude ethanol extract (110.8 g). The crude extract (10.3 g) was separated using medium-pressure liquid chromatography (MPLC) to yield seven fractions (P1\u2013P7). Fraction P4 (507 mg) was isolated via semipreparative RP-HPLC using 27% MeOH to obtain marker compound 7 .S. rorida twigs (1.5 kg) were dried at 35\u201345 \u00b0C in a plant-drying oven for one week, pulverized, and extracted with 80% ethanol (10 L) via sonication for 90 min three times at room temperature. The filtered ethanol extract was evaporated in vacuo to obtain the crude ethanol extract (143.3 g). The extract (10.5 g) was dissolved in MeOH (100 mL) and applied to an RP Sep-Pak column with 100% MeOH to remove the wax, lipids, and fatty acids, and the resultant residue was concentrated using an evaporator to obtain the crude extract (7.8 g). The crude extract (7.8 g) was separated by MPLC to obtain four fractions (P1\u2013P4). Fraction P2 (218 mg) was isolated via semipreparative RP-HPLC using 15% MeOH to obtain marker compound 8 .B. cinerea (KACC40965), C. destructans (KACC 41077), F. solani (KACC 44891), F. asiaticum (KACC 46429), and R. solani (KACC 48921), were used for the in vitro antifungal activity assay. Fungi were cultivated on 25 mL of malt extract agar at 25 \u00b0C for 14 d in the dark. Marker compounds (1\u20138) were evaluated for their antifungal activities in a 96-well microplate [6 cells/mL. The absorbance at 600 nm was measured every 12 h for 96 h. The experiments were performed in triplicate. The percentage of growth inhibition (GI%) was estimated using the following formula: GI% = 100 (Acontrol \u2212 Atest sample)/(Acontrol).Five plant pathogenic fungi provided by the Korean Agricultural Culture Collection . m KACC 469, and R.S. aureus (HG033) and the Gram-negative bacterium E. coli (MG1655) were used. Staphylococcus aureus strains were maintained aerobically in tryptic soy broth or TSB 1.5% agar at 30 \u00b0C with shaking at 250 rpm. E. coli strains were maintained aerobically in lysogeny broth or LB 1.5% agar at 37 \u00b0C with shaking at 250 rpm. The qualitative antibacterial activities of the marker compounds (1\u20138) were examined using the disk diffusion assay and MIC values [1\u20138). The marker compounds were prepared in DMSO (1%) at 100 \u03bcg/mL . The assay was performed with LB and TSB plates. Sterile beads were used to inoculate the surface of each plate to ensure homogeneous bacterial growth. Sample pellet disks were placed on the surface of the agar plates at equal distances. The inhibition was measured using a ruler after 24 h incubation at 30 and 37 \u00b0C. MIC assay was performed in a 96-well plate to examine the antibacterial effects of three marker compounds . Following serial dilution of the compounds in 150 \u03bcL of Mueller\u2013Hinton broth, the culture was inoculated at an optical density (OD) of 0.002. After incubation at 30 and 37 \u00b0C for 24 h with shaking, bacterial growth was measured at OD600 using a spectrophotometer (BioTek Synergy HTX).For the antibacterial activity assay, the Gram-positive bacterium C values . The disSalix species were phytochemically investigated, followed by the isolation of their marker compounds: 3-(4-hydroxyphenyl)propyl \u03b2-D-glucopyranoside (1) from S. triandra, 2-O-acetylsalicin (2) from S. chaenomeloides, 1-O-p-coumaroyl glucoside (3) from S. gracilistyla, picein (4) from S. koriyanagi, isograndidentatin B (5) from S. koreensis, 2\u2032-O-acetylsalicortin (6) from S. pseudolasiogyne, dihydromyricetin (7) from S. caprea, and salicin (8) from S. rorida. The chemical structures of these compounds were also determined via NMR spectroscopy and HR-ESI-MS analysis. Antimicrobial tests of the marker compounds (1\u20138) using plant pathogenic fungi and bacteria revealed that dihydromyricetin (7) exhibited antibacterial activity against S. aureus, inducing 32.4% inhibition at a final concentration of 125 \u03bcg/mL, with an MIC50 value of 250 \u03bcg/mL.In the present study, indigenous Korean"} +{"text": "Ubiquitin-conjugating enzyme E2 T (UBE2T) is a potential oncogene. However, Pan-cancer analyses of the functional, prognostic and predictive implications of this gene are lacking.We first analyzed UBE2T across 33 tumor types in The Cancer Genome Atlas (TCGA) project. We investigated the expression level of UBE2T and its effect on prognosis using the TCGA database. The correlation between UBE2T and cell cycle in pan-cancer was investigated using the single-cell sequencing data in Cancer Single-cell State Atlas (CancerSEA) database. The Weighted Gene Co-expression Network analysis (WGCNA), Univariate Cox and Least absolute shrinkage and selection operator (LASSO) Cox regression models, and receiver operating characteristic (ROC) were applied to assess the prognostic impact of UBE2T-related cell cycle genes (UrCCGs). Furthermore, the consensus clustering (CC) method was adopted to divide TCGA-lung adenocarcinoma (LUAD) patients into subgroups based on UrCCGs. Prognosis, molecular characteristics, and the immune panorama of subgroups were analyzed using Single-sample Gene Set Enrichment Analysis (ssGSEA). Results derived from TCGA-LUAD patients were validated in International Cancer Genome Consortium (ICGC)-LUAD data.1 year\u2009=\u20090.720, AUC3 year\u2009=\u20090.700, AUC5 year\u2009=\u20090.630). The\u00a0CC method classified the TCGA-LUAD cohort into 4 UrCCG subtypes (G1\u2013G4). Kaplan\u2013Meier survival analysis demonstrated that G2 and G4 subtypes had worse survival than G3 . A comprehensive analysis of immune infiltrates, immune checkpoints, and immunogenic cell death modulators unveiled different immune landscapes for the four subtypes. High immunophenoscore in G3 and G4 tumors suggested that these two subtypes were immunologically \u201chot,\u201d tending to respond to immunotherapy compared to G2 subtypes (p\u2009<\u20090.001).UBE2T is highly expressed and is a prognostic risk factor in most tumors. CancerSEA database analysis revealed that UBE2T was positively associated with the cell cycle in various cancers. The risk signature of UrCCGs can reliably predict the prognosis of LUAD (AUCUBE2T is a critical oncogene in many cancers. Moreover, UrCCG classified the LUAD cohort into four subgroups with significantly different survival, molecular features, immune infiltrates, and immunotherapy responses. UBE2T may be a therapeutic target and predictor of prognosis and immunotherapy sensitivity.The online version contains supplementary material available at 10.1186/s12931-022-02226-z. To date, targeted therapy has become the first-line therapy for cancer patients harboring corresponding oncogenic driver mutations. However, drug resistance frequently occurs, resulting from de novo drug-resistant mutations, compensatory activation of collateral signaling pathways, or growth dominance of cells with preexistent drug-resistant genetic alterations . In the UBE2T gene is located in chromosome 1q32.1, encoding a protein product composed of 197 amino acids , we used a web-based analysis tool, the Gene Expression Profiling Interactive Analysis (GEPIA) (http://gepia.cancer-pku.cn/) [https://www.genome.gov/Funded-Programs-Projects/Genotype-Tissue-Expression-Project). The GEPIA included the re-computed TCGA and GTEx data that were processed from corresponding raw RNA-Seq datasets by the UCSC Xena project based on a uniform pipeline [http://ualcan.path.uab.edu/analysis-prot.html) [https://www.proteinatlas.org/) was used to explore the subcellular distribution of UBE2T in tumors [We downloaded the RNA-Seq expression data (FPKM format) of 33 different tumors from the TCGA database (pku.cn/) , to comppipeline . Batch eot.html) , 19 (Addot.html) , 19. Then tumors .Clinical data were fetched from the TCGA, including overall survival (OS), disease-specific survival (DSS), progression-free interval (PFI), and disease-free interval (DFI) survival data. Samples without survival information were excluded. (http://biocc.hrbmu.edu.cn/CancerSEA/) database to examine the association of UBE2T with 14 primary tumor-related cellular activities, such as cell cycle, proliferation, and angiogenesis [UBE2T (FDR\u2009<\u20090.05 and correlation\u2009>\u20090.3). The correlations between UBE2T and scores of functional states were visualized using the \u201cggplot2\u201d package. Our previous publication demonstrated that UBE2T promoted autophagy in LUAD; therefore, we further investigated the functional relevance of UBE2T in LUAD at the single-cell level. We chose EXP0066 (GSE69405) and EXP0067 (GSE85534) . The correlation between gene expression and immune infiltration was estimated by the Pearson correlation test with the same settings method to identify unsupervised intrinsic groups with similar biological characteristics . This mehttps://bioinformatics.mdanderson.org/estimate/disease.html) [The stromal score, immune score, and tumor purity were compared among different UrCCG subtypes by the ESTIMATE method (se.html) . Moreovehttps://tcia.at/home). The IPS is calculated based on four significant categories of tumor immunogenicity determinants, including effector cells, immunosuppressive cells, major histocompatibility complex (MHC) molecules (antigen processing), and checkpoints/immunomodulators. The IPS, ranging from 0 to 10, was calculated based on the z-score for the expression of related genes . For all analyses. A two-tailed p\u2009<\u20090.05 was regarded as statistical significance if not noted.https://portal.gdc.cancer.gov/) , comprising gene expression in normal tissues from GETX (https://www.genome.gov/Funded-Programs-Projects/Genotype-Tissue-Expression-Project). Overall, UBE2T expression was significantly upregulated in various cancers. Additionally, GEPIA-based analysis showed that UBE2T was differentially expressed in different stages in adrenocortical carcinoma (ACC), invasive breast carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), ovarian serous cystadenocarcinoma (OV), kidney renal papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), LUAD, kidney renal clear cell carcinoma (KIRC), and thyroid carcinoma (THCA) confirmed that UBE2T protein levels were significantly upregulated in LUAD, uterine corpus endometrial carcinoma (UCEC), renal cell carcinoma (RCC), OV, and BRCA revealed both cytoplasmic and nuclear distribution of UBE2T Fig.\u00a0A. For inv/) Fig.\u00a0B, we comE2T Fig.\u00a0E.Fig. 1TWe investigated the clinical relevance of UBE2T in the different tumor types using Kaplan\u2013Meier survival analysis Fig.\u00a0: Fig. S5http://biocc.hrbmu.edu.cn/CancerSEA/) [We next investigated whether UBE2T regulates some fundamental cancer-associated cellular processes by mining the CancerSEA database (cerSEA/) . UBE2T whttp://timer.comp-genomics.org/) revealed the association of the eight genes with critical immune cell infiltration . Compared with the G3 group, G2 and G4 groups had higher enrichment scores on tumor-related signaling pathways, including cell cycle, autophagy, mismatch repair, and MTORC1 signaling, but lower scores on the B cell receptor and p53 signaling pathway [Solid tumor tissue includes malignant cells, normal epithelial, stromal cells, immune cells, and vascular cells. The ssGSEA was performed on LUAD samples to analyze the differences in immune cell infiltration and tumor purity among different UrCCG subtypes by ESTIMATE (se.html) . G3 and Given the importance of immune checkpoints (ICPs) and immuhttps://tcia.at/home) to determine the sensitivity to immune checkpoint inhibitors for the four subgroups, the most comprehensive immune determinant to date [Finally, we used immunophenoscore (IPS) for LUAD patients from The Cancer Immunome Atlas genes have been reported \u201340. ProgFurthermore, based on the differential expression patterns of UrCCGs, CC analysis divided the TCGA-LUAD cohorts into G1 to G4 subtypes, with significantly different survival. G3 subtype patients had better survival than other subtypes. The four subtypes exhibited different molecular, cellular, and clinical characteristics. Consistently, the G3 subtype with better survival had lower expression levels of UBE2T than the G2 and G4 subtypes. G3 subtype patients predominated in clinical stage I and M0 subgroups, while the fraction of G2 and G2 subtypes increased with advanced stage and metastatic status. The subtypes were also associated with tumor biomarkers such as NSE, KRT19, and CA125. Overall, the survival status predicted by UrCCGs agrees with the traditional TNM stage, tumor metastasis status, and tumor biomarkers.Regarding the molecular and cellular characteristics, compared with the G3 group, G2 and G4 groups had higher enrichment scores on tumor-related signaling pathways, including cell cycle, regulation of autophagy, mismatch repair, MTORC1 signaling, MYC-targets V2, unfolded protein response, nucleotide expression repair, PI3K/AKT/mTOR, reactive oxygen species pathway, but lower scores on B cell receptor pathway and p53 pathway. EMT played an essential role in tumor metastasis . With a We analyzed the relationship between different subtypes and immunity. Intriguingly, tumors with G3 and G4 subtypes had higher levels of immune cell infiltration than tumors with G2 subtype. First, ESTIMATE analysis indicated that patients with G3 and G4 subtypes had higher stromal-score and immune-score but lower tumor purity than G2 type. The ssGSEA was adopted to calculate stromal score and immune score for each tumor sample with \u201cstromal gene signature\u201d and \u201cimmune gene signature,\u201d respectively . Second,Moreover, with a published algorithm , we compIn conclusion, UBE2T is a critical oncogene. Moreover, UBE2T-related cell cycle genes could separate the LUAD cohort into four subgroups with significant differences in survival, immune cell infiltration, and immunotherapy sensitivity. Our findings demonstrated that UBE2T could be a therapeutic target, as well as a predictor of survival and immunotherapy in cancer treatment.https://portal.gdc.cancer.gov/. Accessed 20 Nov 2021.1. The TCGA database. https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/. Accessed 11 Nov 2021.2. The Gencode (GENCODE.v32). http://gepia.cancer-pku.cn/. Accessed 15 Nov 2021.3. The Gene Expression Profiling Interactive Analysis. https://www.genome.gov/Funded-Programs-Projects/Genotype-Tissue-Expression-Project. Accessed 11 Sep 2021.4. The Genotype-Tissue Expression database. http://ualcan.path.uab.edu/analysis-prot.html. Accessed 10 Nov 2021.5. The UALCAN portal. https://www.proteinatlas.org/. Accessed 23 Oct 2021.6. The Human Protein Atlas. http://biocc.hrbmu.edu.cn/CancerSEA/. Accessed 5 Aug 2021.7. The Cancer Single-cell State Atlas. http://timer.comp-genomics.org/. Accessed 27 Nov 2021.8. The tumor immune estimation resource database. https://dcc.icgc.org/. Accessed 7 Nov 2021.9. The ICGC cohort. https://tcia.at/home. Accessed 21 May 2021.10. The Cancer Immunome Atlas. Additional file 1: Figure S1. The flowchart of the study.Additional file 2: Figure S2. Association between UBE2T gene expression and overall survival (OS) of 33 different types of tumors in TCGA database. A-K. Significant association between UBE2T and OS of ACC (A), BRCA (B), KIRC (C), KIRP (D), LGG (E), LIHC (F), LUAD (G), MESO (H), OV (I), STAD (J), and THYM (K).Additional file 3: Figure S3. Association between UBE2T gene expression and disease-specific survival (DSS) of 33 different types of tumors in TCGA database. A-J. The significant association between UBE2T and DSS of ACC (A), COAD (B), KICH (C), KIRC (D), KIRP (E), LGG (F), LUAD (G), MESO (H), OV (I), and PCPG (J).Additional file 4: Figure S4. Association between UBE2T gene expression and disease free interval (DFI) of 33 different types of tumors in TCGA database. A-J. Significant association between UBE2T and DFI of ACC (A), BRCA (B), KIRP (C), LIHC (D), LUAD (E), MESO (F), PAAD (G), PRAD (H), STAD (I), and THCA (J).Additional file 5: Figure S5. Association between UBE2T gene expression and progression-free interval (PFI) of 33 different types of tumors in TCGA database. A-K. The significant association between UBE2T and OS of ACC (A), KICH (B), KIRC (C), KIRP (D), LGG (E), LIHC (F), LUAD (G), MESO (H), PARD (I), STAD (J), and UVM (K).Additional file 6: Figure S6. Validation of discrepancies in tumor immune environment among the four UrCCG subtypes in ICGC-LUAD cohorts. A-C. Differences in the stromal score (A), immune score (B), and tumor purity (C) . D. Heatmap of 28 types of infiltrating immune cells. E. The fractions of 28 infiltrating immune cells were compared among G1-G4 subtypes.Additional file 7. Detailed methods for the construction of risk signature with UrCCGs, discovery and validation of the subtypes by the UBE2T-related cell cycle genes, and investigation of different tumor-associated cellular and molecular states and immunotherapy sensitivity among the four UrCCG subtypes."} +{"text": "Staphylococcus aureus NCTC 6571-UB, a strain that was derived from S. aureus NCTC 6571. This strain was selected for sequencing in order to provide information on the genome dynamics and the acquired resistance genes for penicillin G, trimethoprim, and sulfamethoxazole resistance.We report the draft genome sequence of the laboratory strain Staphylococcus aureus NCTC 6571 Oxford strain is a reference strain for penicillin sensitivity bioassays that was first deposited in the National Collection of Type Cultures (NCTC) by N. G. Heatley in 1943 .on assay on Oxoidon assay . Therefode novo assembled using SPAdes v3.7 (The genomic DNA (gDNA) of NCTC 6571-UB was extracted from a 37\u00b0C overnight TS broth culture. Cells were lysed in Tris buffer (10 mM Tris-HCl pH 8.0) containing lysozyme. RNase A (0.1\u2009mg/mL), proteinase K (0.1\u2009mg/mL), and SDS (0.5% [vol/vol]) were subsequently added. gDNA was purified using SPRI beads and sequenced by MicrobesNG . Multiple gDNA libraries were prepared using the Nextera XT library preparation kit , quantified using the Kapa Biosystems library quantification kit for Illumina, pooled, and sequenced with an Illumina NovaSeq sequencer (250-bp paired-end read setting). The raw data were quality filtered using Trimmomatic v0.36 , with a total of 2,661 coding DNA sequences, 58 tRNA genes, and 9 rRNA genes. The average coverage of the draft genome was 30\u00d7, and BUSCO analysis revealed 99.8% completeness. NCTC 6571-UB shared 99.86% 16S rRNA gene sequence similarity with the type strain S. aureus subsp. aureus DSM 20231 GenBank accession number AMYL01000007, but their genomes exhibited 97.5% average nucleotide identity (ANI) (in silico DNA-DNA hybridization (DDH) (accessed at https://ggdc.dsmz.de/ggdc.php#) .The sequencing resulted in 1,805,525 raw reads. The assembled draft genome of NCTC 6571-UB had a total length of 2,809,965\u2009bp, with a G+C content of 32.7%, and it consisted of 65 contigs (ty (ANI) and 76.8NCTC 6571-UB harbored a prophage-associated metallo-\u03b2-lactamase superfamily domain protein (locus tag M3M53_RS02030), which could confer penicillin resistance . ComparePRJNA835436, with BioSample and Sequence Read Archive (SRA) accession numbers SAMN28102073 and SRR19138527, respectively. The whole-genome sequence is available in GenBank under the accession number JAMFMC000000000.1.The whole-genome sequencing project was deposited in GenBank under the BioProject accession number"} +{"text": "VEGFA) and CXC chemokines have been shown to play vital roles in angiogenesis. Exploring the expression level, gene regulatory network, prognostic value, and target prediction of the CXC chemokine-VEGFA network in colon adenocarcinoma (COAD) is crucial from the perspective of tumor angiogenesis. Tumor angiogenesis plays a vital role in tumorigenesis, proliferation, and metastasis. Recently, vascular endothelial growth factor A , TRRUST (version 2), LinkedOmics, and Metascape). CXCL1/2/3/5/6/8/11/16/17 and VEGFA were markedly overexpressed, while CXCL12/13/14 were underexpressed in patients with COAD. Moreover, genetic alterations in the CXC chemokine-VEGFA network found at varying rates in patients with COAD were as follows: CXCL1/2/17 (2.1%), CXCL3/16 (2.6%), CXCL5/14 (2.4%), CXCL6 (3%), CXCL8 (0.8%), CXCL11/13 (1.9%), CXCL12 (0.6%), and VEGFA (1.3%). Promoter methylation of CXCL1/2/3/11/13/17 was considerably lower in patients with COAD, whereas methylation of CXCL5/6/12/14 and VEGFA was considerably higher. Furthermore, CXCL9/10/11 and VEGFA expression was notably correlated with the pathological stages of COAD. In addition, patients with COAD with high CXCL8/11/14 or low VEGFA expression levels survived longer than patients with dissimilar expression levels. CXC chemokines and VEGFA form a complex regulatory network through coexpression, colocalization, and genetic interactions. Moreover, many transcription factor targets of the CXC chemokine-VEGFA network in patients with COAD were identified: RELA, NFKB1, ZFP36, XBP1, HDAC2, SP1, ATF4, EP300, BRCA1, ESR1, HIF1A, EGR1, STAT3, and JUN. We further identified the top three miRNAs involved in regulating each CXC chemokine within the network: miR-518C, miR-369-3P, and miR-448 regulated CXCL1; miR-518C, miR-218, and miR-493 regulated CXCL2; miR-448, miR-369-3P, and miR-221 regulated CXCL3; miR-423 regulated CXCL13; miR-378, miR-381, and miR-210 regulated CXCL14; miR-369-3P, miR-382, and miR-208 regulated CXCL17; miR-486 and miR-199A regulated VEGFA. Furthermore, the CXC chemokine-VEGFA network in patients with COAD was notably associated with immune infiltration. Our results showed that This study revealed that the CXC chemokine-VEGFA network might act as a prognostic biomarker for patients with COAD. Moreover, our study provides new therapeutic targets for COAD, serving as a reference for further research in the future. Colon cancer is a common malignant tumor of the digestive tract. The incidence and mortality of colon adenocarcinoma (COAD) are the third highest of all cancer types . Since tVEGFA) is a vital factor that plays an essential role in tumor angiogenesis and development [VEGFA inhibitor, has been used to treat advanced renal cell carcinoma. However, the side effects of sunitinib can be quite severe and include kidney and cardiovascular damage [VEGFA are heavily regulated during tumor angiogenesis. CXCL12 can promote a malignant phenotype by promoting the clonal growth of colorectal cancer cells and regulating the expression of VEGF and ICAM-1 [Chemokines are a family of small heparin-binding proteins 8\u201310\u2009kDa in size. Four subgroups exist within the chemokine family . The CXC subgroup has been shown to play a crucial role in angiogenesis in physiological and pathological settings . Recentlr damage . CXC cheVEGFA expression and the development and prognosis of COAD, as well as to provide new insights into targeted therapies for patients with COAD.Multiple online databases were used to explore the expression level, gene regulation network, prognostic value, and regulation targets of the CXC chemokine-VEGFA network in patients with COAD from an angiogenic perspective in this study. In addition, we aimed to identify the relationship between CXC chemokine and http://ualcan.path.uab.edu/analysis.html) is a free online database that provides analysis based on The Cancer Genome Atlas (TCGA) and MET500 cohort data [VEGFA, (2) dataset: COAD, and (3) threshold setting conditions: P value cutoff = 0.05. A Student's t-test was used for the comparative analysis [UALCAN , an open-access resource, provides analyses of specific human genes and proteins [VEGFA, (2) section: tissue and pathology, (3) tissue: colon and COAD, and (4) picture of tissue types: normal colon tissue and COAD. Data were obtained on February 14, 2022.The Human Protein Atlas (proteins . Screenihttp://gepia.cancer-pku.cn/index.html) is an analysis tool that delivers RNA sequencing expression data from 9,736 cancerous and 8,587 noncancerous samples [VEGFA), dataset (COAD), and threshold conditions were set as screening criteria. The expression of CXC chemokines and VEGFA, as well as the pathological stage of COAD, was analyzed using a Student's t-test. The prognosis of patients with COAD was analyzed using the Kaplan\u2013Meier curve [GEPIA is a free online database for visualizing, studying, and analyzing cancer genomic data [z-score threshold of \u00b12.0 was used to calculate mRNA expression z-scores for all samples (log RNA Seq V2 RSEM). CXC chemokines and VEGFA were the chosen genes [cBioPortal (mic data . The anaen genes \u201316. Datahttps://string-db.org/cgi/input.pl) is a free online database that helps researchers analyze all publicly available sources of protein\u2013protein interaction (PPI) data [Homo sapiens [STRING (PI) data . We crea sapiens , 15. Dathttp://www.genemania.org) is a free online database that creates PPI networks and analyzes gene function [VEGFA [GeneMANIA (function . The intn [VEGFA \u201316. Datahttps://metascape.org) is a free online gene function analysis tool that assists users in using current common bioinformatics analysis approaches to batch gene and protein analysis to predict function [Metascape (function . We condfunction \u201316. Datahttps://www.grnpedia.org/trrust/) is a free online database for human transcriptional regulatory networks [VEGFA) were chosen in this study [TRRUST (networks . We sougis study \u201316. Datahttp://www.linkedomics.org/) is a free database that provides methods for analyzing and comparing cancer multiomics data [VEGFA), and target dataset (RNA-seq) were chosen in this study [LinkedOmics (ics data . The \u201cLiis study \u201316. Datahttps://cistrome.shinyapps.io/timer/) is a free online platform for systematically analyzing tumor-infiltrating immune cells [TIMER (ne cells . The \u201cGene cells \u201316. DataCXCL1/2/3/5/6/8/11/16/17 and VEGFA were remarkably upregulated in (1) sex , (2) pathological stage (stage 1\u20134), and (3) sample type (COAD) (P < 0.05) sex , (2) pathological stage (stage 1\u20134), and (3) sample type (COAD) (P < 0.05) sex , (2) pathological stage (stage 2), and (3) sample type (COAD) (P < 0.05) (CXCL8/11/14 expression were higher (P \u2264 0.05) . Subsequ Figures or when < 0.05) .VEGFA was altered by 1.3% in COAD patients , CXCL3/16 (2.6%), CXCL5/14 (2.4%), CXCL6 (3%), CXCL8 (0.8%), CXCL11/13 (1.9%), and CXCL12 (0.6%), were found signaling pathway . In addition, CXCL8 and VEGFA were found to be regulated by ZFP36 ring finger protein (ZFP36), X-box-binding protein 1 (XBP1), histone deacetylase 2 (HDAC2), activating transcription factor 4 (ATF4), E1A-binding protein p300 (EP300), early growth response 1 (EGR1), signal transducer and activator of transcription 3 (STAT3), and Jun proto-oncogene (JUN) (P < 0.01). Furthermore, CXCL1/5/14 and VEGFA were found to be regulated by Sp1 transcription factor (SP1) (P < 0.001). Breast cancer 1 (BRCA1) was the key transcription factor involved with CXCL1 and VEGFA in COAD patients (P < 0.01). Finally, estrogen receptor 1 (ESR1) and hypoxia-inducible factor 1 alpha subunit (HIF1A) regulated the functions of CXCL12 and VEGFA (P < 0.01).Potential transcription factors involved with the CXC chemokine-VEGFA network in COAD patients were identified . v-rel rCXCL1 were miR-518C, miR-369-3P, and miR-44. In addition, miR-518C, miR-218, and miR-493 were identified as potential miRNA targets that regulate CXCL2. Furthermore, we observed that CXCL3 was regulated by miR-448, miR-369-3P, and miR-221. miRNA target of CXCL13 is miR-423. Moreover, miR-378, miR-381, and miR-210 were identified as potential miRNA targets that regulate CXCL14. CXCL17 is regulated by miR-369-3P, miR-382, and miR-208. Furthermore, our results showed that miR-486 and miR-199A are potential miRNA targets that regulate VEGFA.The top three miRNA targets of the CXC chemokine-VEGFA network were obtained . The miRCXCL1/2/3/5/6/8/11/12/13/14/16/17 and VEGFA = 0.8921, P = 4.226e\u2013132) , CXCL2 (304e\u201390) , and ZC3882e\u201347) .CXCL2 expression, respectively , CXCL1 (304e\u201390) , and ZC3735e\u201346) . Furtherectively . Among t Figures . Express26e\u2013132) , CXCL2 (01e\u2013119) , and ZC3446e\u201351) . Our resectively . Among t884e\u201368) , IL8 (PC632e\u201363) , and MMP269e\u201362) . Our resectively . Among t Figures . CXCL6 e689e\u201359) , MMP3 (P921e\u201355) , and IL8935e\u201353) . In addiectively . Among t Figures . CXCL8 e939e\u201376) , IL1B (P.25e\u201373) , and OSM368e\u201372) . Furtherectively . Among t Figures . CXCL11 99e\u2013101) , UBD (PC935e\u201362) , and IDO137e\u201360) . Moreoveectively . Among t Figures . CXCL12 835e\u201387) , SLIT3 (915e\u201386) , and SHE928e\u201384) . Our resectively . Among t Figures . CXCL13 598e\u201389) , SH2D1A 229e\u201380) , and SIR508e\u201380) . In addiectively . Among t Figures . CXCL14 .24e\u201358) , TNFSF11643e\u201341) , and COL338e\u201341) . Furtherectively . Among t Figures . CXCL16 175e\u201383) , FLII (P248e\u201340) , and NDE486e\u201339) . We alsoectively . Among t Figures . CXCL17 148e\u201321) , GPR110 333e\u201319) , and SEM753e\u201316) . Finallyectively . Among t Figures . VEGFA e639e\u201335) , CCNL1 (411e\u201330) , and CRE606e\u201327) .CXCL1 expression in COAD patients was positively associated with CD8+ T cell infiltration, neutrophils, and dendritic cells (P < 0.05) (CXCL1 expression (P < 0.01) (CXCL2 and CXCL3 (P < 0.001) (CXCL17 expression (P < 0.001) (VEGFA expression (P < 0.01) ( < 0.05) . However < 0.01) . In addi Figures . However Figures . Further Figures . B cells Figures . The exp < 0.05) . B cells< 0.001) . CD4+ T < 0.01) .VEGFA and CXC chemokines as important participants in angiogenesis, particularly tumor angiogenesis [VEGFA have been studied in a range of tumor types; however, findings are contradictory with regard to colonic adenocarcinomas [Tumor angiogenesis plays a vital role in tumorigenesis, proliferation, and metastasis. In recent years, studies have identified ogenesis , 26\u201328. rcinomas , 30. ThiCXCL1/2/3/5/6/8/11/16/17 and VEGFA was upregulated in patients with COAD compared with that in individuals without COAD. Patients with COAD also showed downregulated CXCL12/13/14 expression. The results were similar to those reported in a previous study in patients with COAD [CXCL5/6/12/14 and VEGFA were higher in patients with COAD than those in healthy individuals. Conversely, the promoter methylation levels of CXCL1/2/3/11/13/17 were lower in patients with COAD. Thus, we hypothesized that genetic methylation and alteration within the CXC chemokine-VEGFA network might be the leading cause of abnormal gene expression levels in patients with COAD.In this study, we also examined the potential correlation between pathological stage and differential expression of COAD. The expression of ith COAD and contith COAD . This maCXCL9/10/11 and VEGFA expression and the pathological stage of COAD. Furthermore, the survival of patients with COAD was higher with low VEGFA or high CXCL8/11/14 expression levels. Therefore, the expression levels of CXCL8/11/14 and VEGFA may be potential prognostic indicators for COAD. CXCL8/11/14 and VEGFA promote tumor angiogenesis in different ways [We also observed a notable correlation between the ent ways \u201333. ThusVEGFA may promote cancer progression, and this could be through a potential interaction network. Genes in the network were mainly involved in cytokine receptor binding, chemokine and cytokine activity, leukocyte chemotaxis, and migration, all of which are closely related to angiogenesis. For instance, IL-8 (CXCL8) promotes tumor angiogenesis by binding to CXCR1 and CXCR2 receptors [The potential functions and interactions of the CXC chemokine-VEGFA network were further explored in this study. They were found to be complex and tightly connected. CXC chemokines and eceptors . In addieceptors . Collect\u03baB signaling pathway were highly involved in the CXC chemokine-VEGFA network in COAD patients, all of which are highly related to tumor angiogenesis [Furthermore, the functions of the CXC chemokine-VEGFA network in patients with COAD were mainly related to chemokine activity, cytokine activity, and growth factor activity, as demonstrated by GO enrichment analysis, all of which are closely related to tumor angiogenesis. More studies are needed to confirm the mechanism by which this happens. In this study, we further found through KEGG pathway analysis that the cytokine\u2013cytokine receptor interaction signaling pathway, IL-17 signaling pathway, and NF-ogenesis , 37. TheVEGFA. Studies have shown that RELA, NFKB1, HDAC2, SP1, ATF4, EP300, BRCA1, ESR1, HIF1A, EGR1, STAT3, and JUN regulate tumor angiogenesis, thus affecting tumor growth and prognosis [Mutated or altered transcription factors represent a unique class of drug targets that mediate aberrant gene expression, and the development of corresponding targeting drugs may impact future cancer treatments. Thus, the targets and regulators of the CXC chemokine-VEGFA network in COAD patients were further analyzed. The transcription factor targets of the CXC chemokine-VEGFA network in patients with COAD were identified. RELA, NFKB1, ZFP36, XBP1, HDAC2, SP1, ATF4, EP300, BRCA1, ESR1, HIF1A, EGR1, STAT3, and JUN were deemed crucial regulatory factors. Our results showed that these factors have potential functions in regulating tumor angiogenesis by targeting rognosis , 38\u201348. rognosis \u201352. In sVEGFA. Some of the genes with the highest correlation were positively associated with tumor angiogenesis [VEGFA-related regulatory targets may serve as a viable therapeutic oncology approach.The correlation between CXC chemokine-VEGFA network expression and differentially expressed genes in COAD patients was explored in this study. We found that in patients with COAD, approximately 20,000 genes were negatively or positively correlated with CXC chemokine-VEGFA network expression. From these, we screened for genes with the highest correlation with CXC chemokines and ogenesis , 54. RegIn this study, we determined the expression levels and gene regulatory network of the CXC chemokine-VEGFA network, which plays a vital role in angiogenesis in COAD. We also identified new prognostic biomarkers and therapeutic targets. These findings provide insight into the study and treatment of COAD."} +{"text": "Ceftazidime-avibactam (caz-avi), a novel \u03b2-lactam/\u03b2-lactamase inhibitor, is commonly utilized for carbapenem-resistant gram-negative infections (CR-GNI). However, the benefits vs risks of combining caz-avi with other agents are unclear.In this retrospective cohort study, inpatients with CR-GNI treated with caz-avi were identified at 9 U.S. hospitals. The impact of caz-avi monotherapy (MT) or combination therapy was studied using logistic regression, controlling for baseline patient and hospital factors. The primary outcome was in-hospital mortality or discharge to hospice (death), and secondary outcomes were length of stay (LOS), resolution of infectious signs and symptoms , 90-day recurrent infection and future caz-avi\u2013resistant organism. An adjusted odds ratio (aOR) with 95% confidence interval (CI) was used to assess the primary and secondary outcomes.Klebsiella spp. (44.6%) followed by Pseudomonas aeruginosa (27.7%) (table 2). Concomitant gram-negative agents are shown in table 3. Overall, 92 (28.1%) patients died and CT (vs MT) displayed similar adjusted mortality risk and LOS . CT (vs MT) was associated with greater odds of clinical response (aOR: 2.25 [95%CI:1.15-4.41]). Among survivors, similar rates of 90-day recurrent infection (50/154 (32.5%) were observed in CT vs 18/82 (22.0%) in MT group (p=0.09) and 5 (2.19%) patients had future infection with a caz-avi\u2013resistant pathogen (3 in CT and 2 in MT group).328/499 (65.7%) patients received caz-avi as targeted therapy for a CR-GNI. Overall patients treated with MT and CT were similar at baseline and had comparable baseline demographics although patients treated with CT were more likely to be in the ICU and receive a concomitant empiric in vitro-concordant antibiotic (table 1). The most common organism was Compared to patients with CR-GNI treated with caz-avi alone, those who received CT including caz-avy had similar survival and LOS but higher clinical response. The role of CT in the era of novel antibiotics warrants additional study.Helen W. Boucher, MD, American Society of Microbiology: Honoraria|Elsevier: Honoraria|Sanford Guide: Honoraria."} +{"text": "Aspergillus fumigatus (AFM) is mainly associated with mutations in cyp51A and its promoter region or its homologue cyp51B. We evaluated the in vitro activity of isavuconazole (ISC), itraconazole (ITC), posaconazole (PSC), and voriconazole (VRC) against 660 AFM collected during 2017\u20132020.Azole resistance in cyp51 genes using whole genome sequencing.Isolates from Europe (EU), North America (NA), Latin America (LA), and Asia-Pacific (APAC) were identified by MALDI-TOF and/or sequencing and tested by CLSI broth microdilution. CLSI epidemiological cut-off values (ECV) were applied. A PSC ECV of 0.5 mg/L was used. Non-wildtype (NWT) isolates to azoles were screened for alterations in the cyp51 genes. Of these AFM, 29/32 (90.1%) were NWT to ITC, 25/32 (78.1%) NWT to ISC, 17/32 (53.1%) NWT to VRC, and 11/32 (34.4%) NWT to PSC. The most frequent alteration was CYP51A TR34/L98H, carried by 14 EU isolates, all NWT to ISC and ITC. Four isolates from NA carried the alteration I242V in CYP51A . One NA isolate carried the CYP51A alteration G448S and one carried A9T (NWT to ISC). A single isolate from APAC carried a CYP51A G138C alteration and was NWT to all 4 triazoles. Multiple alterations in CYP51A were detected in 5 isolates: 4/5 NWT to ISC or ITC, 1/5 NWT to VRC, all WT to PSC. Alterations in CYP51B were noted in 7 isolates; 6/7 carried Q42L, 3 from NA , 2 from APAC , and 1 from EU . Among 34 NWT isolates without cyp51 alterations, 32.4% were WT to ISC, 47.1% WT to ITC, 85.3% WT to VRC, and 82.4% WT to PSC.Azoles had similar activities against 660 AFM isolates. Overall, AFM displayed WT MIC values to ISC (92.7%), ITC (92.9%), PSC (97.3%), and VRC (96.7%). Only 66 isolates (10.0%) were NWT to 1 or more of the azoles, and 32 harbored one or more alterations in the cyp51 alterations were detected in 32/66 NWT isolates. Only EU isolates harboured the environmental alteration TR34/L98H that was associated with a NWT phenotype to ISC and ITC. Alterations in AFM cyp51 can have variable effects on the in vitro activity of the azoles that are best delineated by testing all triazoles.The majority of AFM were WT to azoles. Ten different Michael A. Pfaller, MD, Pfizer: Grant/Research Support Cecilia G. Carvalhaes, MD, PhD, AbbVie: Grant/Research Support|Cidara: Grant/Research Support|Melinta: Grant/Research Support|Pfizer: Grant/Research Support Lalitagauri M. Deshpande, PhD, Melinta: Grant/Research Support|Pfizer: Grant/Research Support Paul Rhomberg, BS, MT(ASCP), Cidara: Grant/Research Support|Pfizer: Grant/Research Support Paul Rhomberg, BS, MT(ASCP), Cidara: Grant/Research Support|Pfizer: Grant/Research Support."} +{"text": "Lenvatinib has shown promising efficacy in targeted therapies that have been tested to treat anaplastic thyroid carcinoma (ATC) in both preclinical and clinical studies. The aim of this study was to evaluate the efficacy and safety of lenvatinib in the treatment of patients with ATC.PubMed, the Cochrane Library, Embase, and ClinicalTrials.gov were searched for potential eligible studies from inception to February 1, 2022. The outcomes included partial response (PR), stable disease (SD), disease control rate (DCR), median progression-free survival (mPFS), and median overall survival (mOS). Effect sizes for all pooled results were presented with 95% CIs with upper and lower limit.Ten studies met the inclusion criteria. The aggregated results showed that the pooled PR, SD, and DCR were 15.0%, 42.0%, and 63.0%, respectively. The pooled mPFS and mOS were 3.16 (2.18\u20135.60) months and 3.16 (2.17\u20135.64) months, respectively. Furthermore, PFS rate at 3 months (PFSR-3m), PFSR-6m, PFSR-9m, PFSR-12m, and PFSR-15m were 52.0%, 22.5%, 13.9%, 8.4%, and 2.5%, respectively. Meanwhile, the 3-month OS rate (OSR-3m), OSR-6m, OSR-9m, OSR-12m, and OSR-15m were 64.0%, 39.3%, 29.7%, 18.9%, and 14.2%, respectively. The most common adverse events (AEs) of lenvatinib were hypertension (56.6%), proteinuria (32.6%), and fatigue (32%).This meta-analysis showed that lenvatinib has meaningful antitumor activity, but limited clinical efficacy in ATC.https://www.crd.york.ac.uk/PROSPERO/], identifier [CRD42022308624].PROSPERO [ Anaplastic thyroid carcinoma (ATC), a malignancy derived from undifferentiated thyroid follicular cells , accountLenvatinib is a multi-target antiangiogenetic broad-spectrum tyrosine kinase inhibitor (TKI) that can inhibit various signal receptors \u201312. In aWe have registered our protocol on PROSPERO (registration number: CRD42022308624). This meta-analysis followed the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement . The PRIPubMed, the Cochrane Library, Embase, and ClinicalTrials.gov were searched for potential eligible studies. The search was performed from inception to February 1, 2022. The search keywords were \u201cthyroid carcinoma, anaplastic\u201d and \u201clenvatinib\u201d and the search strategy in PubMed was as follows: Thyroid Carcinoma, Anaplastic [Mesh] OR Anaplastic Thyroid Carcinoma [Title/Abstract] OR Anaplastic Thyroid Carcinomas [Title/Abstract] OR Carcinoma, Anaplastic Thyroid [Title/Abstract] OR Carcinomas, Anaplastic Thyroid [Title/Abstract] OR Thyroid Carcinomas, Anaplastic [Title/Abstract] OR Thyroid Cancer, Anaplastic [Title/Abstract] OR Anaplastic Thyroid Cancer [Title/Abstract] OR Anaplastic Thyroid Cancers [Title/Abstract] OR Cancer, Anaplastic Thyroid [Title/Abstract] OR Cancers, Anaplastic Thyroid [Title/Abstract] OR Thyroid Cancers, Anaplastic [Title/Abstract] AND Lenvatinib [Mesh] OR 4-(3-chloro-4-((cyclopropylaminocarbonyl)amino)phenoxy)-7-methoxy-6-quinolinecarboxamide [Title/Abstract] OR N-(4-((6-carbamoyl-7-methoxyquinolin-4-yl)oxy)-2-chlorophenyl)-N\u2019-cyclopropylurea [Title/Abstract] OR 4-(3-chloro-4-(N\u2019-cyclopropylureido)phenoxy)-7-methoxyquinoline-6-carboxamide [Title/Abstract] OR lenvatinib mesylate [Title/Abstract])) OR (E7080 mesylate [Title/Abstract] OR monomethanesulfonate [Title/Abstract] OR lenvatinib mesylate [Title/Abstract] OR lenvatinib methanesulfonate [Title/Abstract] OR Lenvima [Title/Abstract] OR E-7080 mesylate [Title/Abstract] OR E 7080 [Title/Abstract] OR 4-(3-chloro-4-(((cyclopropylamino)carbonyl)amino)phenoxy)-7-hydroxy-6-quinolinecarboxamide [Title/Abstract] OR E-7080 [Title/Abstract] OR ER-203492-00 [Title/Abstract] OR E7080 [Title/Abstract] OR lenvatinib metabolite M2 [Title/Abstract]. No language, region, ethnicity, age, or payment restrictions were imposed during the search process.Inclusion criteria were as follows : studiesMethodological index for non-randomized studies (MINORS) evaluates single-arm studies . JBI CriTwo investigators independently made study selection. If there were any differences between them, the third author would discuss with them together. Information on the following characteristics of included studies was recorded: authors, study type, sample size, age, criteria for tumor response , adverse events (AEs), and reported endpoints.I2 statistic. When I2 \u2264 50%, use the fixed-effects model; otherwise, use the random-effects model. For pooled results with high heterogeneity, the sensitivity analysis was performed by excluding each study individually. Begg\u2019s test, Egger\u2019s test, and the trim-and-fill method were used to assess publication bias. p < 0.05 was considered statistically significant.Analysis of pooled PR, SD, and DCR, and of the pooled K-M curves of ATC patients treated with lenvatinib was performed using R version 3.6.3. Effect sizes for all pooled results were presented with 95% CIs with upper and lower limit. Heterogeneity between studies was examined using the Cochrane Q chi-square test and We initially identified 349 studies. Finally, our study included 10 studies, namely, 2 prospective studies , 18 and Two single-arm studies , 18 scorI2 = 59.0%, p < 0.01), and the pooled PR in subgroups was different , while the other subgroups showed a pooled PR of 11% .We extracted efficacy measures from each study which included in this meta-analysis , while the subgroup of the retrospective study showed a pooled SD of 36% , and the subgroup of the prospective study resulted in a pooled SD of 59% and 59% , respectively. The total pooled DCR was 63% on the estimated pooled PR and DCR , Tianjin Municipal Science and Technology Project and Beijing-Tianjin-Hebei Basic Research Cooperation Project (20JCZXJC00120), The Science & Technology Development Fund of Tianjin Education Commission for Higher Education (2021ZD033), Tianjin Medical Key Discipline Construction Project.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Correction:J ExpClin Cancer Res41, 299 (2022)https://doi.org/10.1186/s13046-022-02501-3Following publication of the original article , author This correction does not change the result, interpretation, and conclusions of the study. The original article has been corrected.Additional file 1: Supplementary Figure S5. Blank and plasma membrane impregnated MB morphology by SEM (25.13 K magnification). Scale bar = 1 \u03bcm."} +{"text": "Nucleic acid reagents, including plasmid-encoded genes and small interfering RNA (siRNA), are promising tools for validating gene function and for the development of therapeutic agents. Native \u03b2-cyclodextrins (BCDs) have limited efficiency in gene delivery due to their instable complexes with nucleic acid. We hypothesized that cationic BCD nanoparticles could be an efficient carrier for both DNA and siRNA. Tetraethylenepentamine-coated \u03b2-cyclodextrin (TEPA-BCD) nanoparticles were synthesized, characterized, and evaluated for targeted cell delivery of plasmid DNA and siRNA. The cationic TEPA coating provided ideal zeta potential and effective nucleic acid binding ability. When transfecting plasmid encoding green fluorescent protein (GFP) by TEPA-BCD, excellent GFP expression could be achieved in multiple cell lines. In addition, siRNA transfected by TEPA-BCD suppressed target GFP gene expression. We showed that TEPA-BCD internalization was mediated by energy-dependent endocytosis via both clathrin-dependent and caveolin-dependent endocytic pathways. TEPA-BCD nanoparticles provide an effective means of nucleic acid delivery and can act as potential carriers in future pharmaceutical application. Gene expression could be modulated through the use of exogenous nucleic acids. The power of nucleic-acid-based drugs, including DNA molecules and small interfering RNAs (siRNAs), lies in their abilities to specifically enhance or silence genes of interest. The siRNA-based drugs were recently approved by US Federal Drug Administration , markingNonviral gene delivery vectors have been shown to have several advantages, such as ease of synthesis, mass production, versatile modification, and low immunogenicity . There aCationic polysaccharides can bind with siRNAs to form complexes, thereby protecting siRNA from degradation and neutralizing their negative charges . NanoparIn this study, we developed an easy and efficient strategy to generate TEPA-BCD. The 6-hydroxyl groups of BCD were activated with tosyl chloride. After nucleophilic displacement by ethylenediamine (EDA), TEPA-BCD nanoparticles were synthesized by the crosslinking reaction of EDA-BCD and TEPA via glutaraldehyde (GA). The synthesis of TEPA-BCD nanoparticles is demonstrated in \u22121 , 1036 cm\u22121 (C\u2013O vibration). Another two intense peaks around 1036 and 2900 cm\u22121 from C-O and C\u2013H stretching were also found in all BCD derivatives indicating the main BCD structure was maintained after the amine introduction .,45.44,45CPZ blocked clathrin-coated pit formation , and conDevelopment of siRNA delivery systems depends not only on their transfection efficiencies, but also on their gene-silencing effect. Although both Gen and MCD treatments showed no reduction in plasmid DNA transfection efficiency C, the geIn the intravenous delivery, the nanoparticles have to escape the various barriers such as kidney filtration, phagocytosis, and hydrolysis degradation. Sequentially, they should transport across vascular vessels, diffuse through the extracellular matrix, and reach the target cells . The enhIn summary, we developed a cationic BCD-based nanoparticle delivery system and applied it in the fibroblast 3T3 cell line and the epithelial ARPE cell line. Our results demonstrated the multifunctionality critical for internalization and activity of both gene-coded plasmid DNA and siRNA. When the TEPA-BCD/plasmid ratio was 1.71:1, the nanoparticles had a transfection efficiency of 97%, and cells maintained viability around 83%. When the TEPA-BCD/siRNA ratio was 96:1, it knocked down the fluorescent expression by 57%, yet the cell viability remained around 82%. TEPA-modified BCD demonstrated a nanometer size, positive surface charge, minimal cytotoxicity, great electrostatic interaction with nucleic acid, and efficient delivery. In both ARPE cells and 3T3 cells, TEPA-BCD entered cells through clathrin- and caveolae-mediated endocytosis. TEPA-BCD/plasmid DNA mediated high gene expression and TEPA-BCD/siRNA displayed efficient gene silencing. The TEPA-BCD provides a promising platform for delivery of therapeutic nucleic acids in vitro and warrants further development of its potential for in vivo delivery.BCD was a generous gift from Feng-Yuan Biotech . Acetone, methanol, and ethanol were purchased from Echo Chemicals . Green fluorescent protein (GFP)-expressing plasmid was obtained from Takara Bio . Fetal bovine serum (FBS) was purchased from Biological Industries . The siRNA against GFP gene was purchased from MDBio . DNA and siRNA transfection controls (PolyJet and GenMute) are purchased from SignaGen . TEPA, p-tolylsulfonyl chloride, sodium chloride, and other chemicals were purchased from Sigma-Aldrich . All reagents were used without further purification.1H NMR of BCD: \u03b4 = 5.69 , 4.84 , 4.44 , 3.62 , 3.33 ppm. 13C NMR of BCD: \u03b4 = 102.04 (C-1), 82.01 (C-4), 73.51\u201372.51 , 69.63 , 60.37 (C-6) ppm. 1H NMR of Tosyl-BCD: \u03b4 = 7.12 , 7.45 , 5.70 , 4.80 , 4.50 , 4.32 , 4.21 , 3.48 , 2.43 ppm. 13C NMR of Tosyl-BCD: \u03b4 = 128.48 , 102.44 (C-1), 82.02 (C-4), 73.55\u201372.50 , 60.41 (C-6), 31.16 (Tosyl-CH3) ppm. 1H NMR of EDA-BCD: \u03b4 = 5.70 , 4.84 , 4.44 , 3.48 , 2.1 ppm. 13C NMR of EDA-BCD: \u03b4 = 101.82 (C-1), 81.09 (C-4), 73.04\u201371.78 , 60.25 (C-6), 42.04 (BCD-C-C-N) ppm. 1H NMR of TEPA-BCD: 5.06 , 4.77 , 4.47 , 3.74 , 3.19 , 2.84 , 2.22 ppm. 13C NMR of TEPA-BCD: \u03b4 = 102.10 (C-1), 81.24 (C-4), 73.20\u201372.08 , 60.15 (C-6), 45.22 (C-NH), 30.24 (cyclic ether C-C-O) ppm.Mono-6-deoxy-6-p-tolylsulfonyl (tosyl)-BCD and EDA-BCD were synthesized as described previously ,50. BrieE. coli cells. The host E. coli was grown in LB broth with kanamycin (50 \u00b5g/mL) and the plasmid DNA was isolated using Mini Purification Kit . The concentration and quality of nucleic acids were determined using a NanoDrop spectrophotometer and the Beer\u2013Lambert law with an extinction coefficient of 50 \u03bcg/mL\u22121 cm\u22121 at 260 nm. Isolated plasmid DNA had OD 260/280 ratios of 1.80\u20131.95, indicating the quality was suitable for our application. Polyplexes were formulated by mixing 0.21\u20131.71 \u03bcg (10\u201380 \u03bcL) TEPA-BCD with plasmid DNA (1 \u03bcg) or siRNA in 100 \u03bcL DMEM medium.We transformed plasmid GFP-C3 into DH-5\u03b1 To visualize morphology of BCD derivatives, diluted samples were adsorbed onto a 100 mesh copper grid and dried overnight, followed by imaging on a transmission electron microscope . The magnification power of TEM is 50,000. The chemical groups of modified BCDs were investigated using Fourier transform infrared spectroscopy and an NMR spectrometer (Bruker AV III HD). The size and zeta potentials of the TEPA-BCD complexes were measured using ZetaSizer with 633 nm He-Ne Laser and the folded capillary cell .ARPE cells and 3T3 cells (a mouse embryonic fibroblast cell line) from the cell bank of BCRC were used for GFP plasmid delivery experiments. DNA transfection was performed as previously reported . APRE-GF4 cells/well. When reaching 90% confluence, the cells were treated with polyplex and endocytic inhibitor for 3 h. Polyplexes were formulated by mixing 1.28 \u03bcg TEPA-BCD with plasmid DNA (1 \u03bcg) or siRNA (13.3 ng) in 100 \u03bcL DMEM medium. Subsequently, the transfection medium was replaced with fresh DMEM supplemented with 10% FBS and cells were incubated for another 24 h. Imaging was conducted on an automated image analyzer for analysis of fluorescence intensity and cell viability.The cellular uptake mechanisms of polyplex were examined using different endocytic inhibitors: chlorpromazine (30 \u00b5M), genistein (200 \u00b5M), sodium azide (10 mg/mL), methyl-BCD (10 mM), and monensin (3 \u00b5M). The cells were seeded in 48-well plates at 5 \u00d7 10t-test by Analysis Toolpak in Microsoft Excel. Statistical significance is represented as * p < 0.05.All cellular data were performed by two individual experiments. The Zetasizer results were the average from three individual experiments. The mean and standard deviation were calculated using Microsoft Excel. Statistical comparisons are performed using PROC ANOVA followed by the Tukey post hoc test using SAS 9.4 software and unpaired two-tailed Student"} +{"text": "In the United Kingdom(1) and internationally(2), help-seeking for domestic violence (DV) and domestic homicides have increased(3) during COVID-19 lockdown periods. Suspension and remote delivery of face-to-face clinical services, continuing healthcare and other support services limits opportunities for DV detection and disclosure.This presentation will summarise changes in DV incidence and help-seeking during COVID-19, their impacts on health and wellbeing, and present guidance for clinicians assessing and supporting survivors.World Health Organisation recommendations to Listen, Inquire, Validate, Enhance safety and Support (\u2019LIVES\u2019) survivors of DV remain the cornerstone of first-line support (4). Urgently-issued guidelines on safeguarding(5) and responding to DV during COVID-19(6) make a range of recommendations for clinicians supporting people experiencing DV.DV is an important social determinant of physical and mental health, with a range of potential fatal and non-fatal consequences. Despite the constraints of healthcare during a pandemic, attention to patients\u2019 risk of DV and its consequences is a crucial part of bio-psycho-social assessment and management planning. References: (1) Kelly, Morgan. Coronavirus: Domestic abuse calls up 25% since lockdown, charity says. 2020. https://www.bbc.co.uk/news/uk-52157620 (2) Graham-Harrison, et al. Lockdowns around the world bring rise in domestic violence. 2020. https://www.theguardian.com/society/2020/mar/28/lockdowns-world-rise-domestic-violence (3) Roesch, et al. Violence against women during covid-19 pandemic restrictions. BMJ 2020;369. (4) WHO. Responding to intimate partner violence and sexual violence against women: WHO clinical and policy guidelines. 2013. https://apps.who.int/iris/bitstream/handle/10665/85240/9789241548595_eng.pdf;jsessionid=E19DCC3CDAB9BE390EE6F8360C6F1D7E?sequence=1 (5) RCGP. COVID-19 and Safeguarding. 2020. https://elearning.rcgp.org.uk/pluginfile.php/149180/mod_resource/content/2/COVID-19%20and%20Safeguarding%20%286%29.pdf (6) IRISi. Guidance for General Practice teams responding to domestic abuse during telephone and video consultations. 2020. https://irisi.org/wp-content/uploads/2020/04/Guidance-for-General-Practice-Covid-19-FINAL.pdfNo significant relationships."} +{"text": "Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy with high mortality and poor outcome, especially for elderly/unfit (age \u2265 60 years or unfit patients who are ineligible to receive intensive chemotherapy) with adverse genetic and molecular abnormalities in the newly diagnosed (ND) and refractory/relapsed (R/R) patients.Azacitidine (Aza), a hypomethylating agent, targets epigenetic gene silencing by inhibiting gene expression against malignant phenotypes. The complete remission (CR) rates of Aza combined regimens varied with different drugs, such as, Aza+Midostaurin (20.8%), Aza+Durvalumab 31.3%), Aza+Pracinostat (46%), Aza+Venetoclax (66.4%) in ND AML and Aza+Midostaurin (21.4%), Aza+Nivolumab (22%), Aza+Venetoclax 37.1%) in R/R AML were enrolled between Jan 2020 and Dec 2021, including 72 ND and 40\u2009R/R Fig. . The 72 2/d on days 1\u20137 subcutaneous) was given in combination with the HAG regimen . Patients who did not achieve CR/CRi (CR with incomplete blood count recovery) following the first cycle could receive a second cycle at the same doses and schedule. The patients who did not reach CR/CRi after the second cycle were withdrawn from the study. Post-remission therapy for enrolled patients, the Aza+HAG regimen was further given 4\u20136 cycles or until the disease progresses, two of whom underwent allo-SCT .Induction therapy consisted of Aza . A higher CR/CRi rate of 79.2% in ND AML compared with 40.0% in R/R AML; and sAML (75.0%) obtained a similar high CR rate as de novo AML (80.4%) achieved CR/CRi within the median time of 33.5d. Notably, 90.4% (66/73) of CR/CRi was obtained after the 1st cycle of Aza+HAG induction therapy. No statistical difference in CR/CRi rate between Aza+HAG (7-day) vs Aza+HAG (14-day) (4%) Fig. . In pati4%) Fig. . These dP\u2009=\u20090.0056; median RFS 5.21\u2009m, P\u2009=\u20090.0051) . In patients with favorable, intermediate, or poor risk, median OS was not reached, 22.8\u2009m, and 17.3\u2009m and relapse-free survival (RFS) in ND AML were 22.8\u2009m and not reached, respectively, which were longer than R/R AML Fig. . De novo48) Fig. . In pati3\u2009m Fig. ; median 3\u2009m Fig. , respectP\u2009=\u20090.016) , respectively . The baseline demographic and characteristics were generally balanced between the two cohorts Table . The CR/16) Fig. . The medely Fig. . We alsoely Fig. and S2. The most common non-hematological adverse event (AE) was infection (58.0%). Common non-hematological AEs of grade 3 or higher includes: infection (33.9%), hemorrhage (9.82%), fatigue (5.36%), hypokalemia (3.57%), cardiac arrhythmia (1.79%), and fever (1.79%). For the hematological AE, the median duration of neutropenia and thrombocytopenia were 11 d and 16d , 10 d , and 16 d , 12d and 17d for total, 7-day, and 14-day schedule, respectively. No differences were observed between the 7-day and 14-day schedule. The early deaths within 4 weeks of the induction treatment occurred in 1.79%. No patients discontinued the induction therapy due to hematological or non-hematological toxicities Table . These dDNMT3A, TET2, and NPM1 , KIT , IDH1 , NPM1 , ASXL1 , DNMT3A , RUNX1 , FLT3 and TET2 and 87.4% (90/103) of patients had more than one gene mutation. The most frequently mutated genes were PM1 Fig. . We obse14) Fig. (Table S14) Fig. . We alsoPM1 Fig. . OS and ion Fig. ; whereasype Fig. . These dIDH1 inhibitor Ivosidenib (60.9%) [IDH1-mutant ND AML or HMA\u2009+\u2009Venetoclax (71%) in IDH1/2-mutant AML [IDH1-mutant AML and the IDH1 mutant was dramatically reduced after the first cycle of Aza+HAG, suggesting that the patients with the IDH1 mutation could achieve a remarkable deep and durable remission upon Aza+HAG treatment.Recent studies reported the CR rates of patients treated with the Aza plus (60.9%) in IDH1-tant AML . This trIn summary, this trial demonstrated that the Aza+HAG regimen is a cost-effective first-line therapy with high efficacy and well tolerance for elderly/unfit AML. This trial provides a rationale for further expanding the patients for randomized clinical controlled studies and guiding suggestions for the clinical use of this novel combination therapy.Supplemental methods_tables_figures"} +{"text": "Background and Objectives: To estimate the association between admission functional outcomes and exposure to physiotherapy interventions with mortality rate in intensive care unit (ICU) inpatients with cardiovascular diseases and new coronavirus disease (COVID-19). Materials and Methods: Retrospective cohort including 100 ICU inpatients (mean (standard deviation), age 75 (16) years) split into COVID-19+ or COVID-19\u2212. The association of in-ICU death with admission functional outcomes and physiotherapy interventions was investigated using univariable and multivariable regression models. Results: In total, 42 (42%) patients tested positive for COVID-19. In-ICU mortality rate was 37%, being higher for the COVID-19+ group : 3.15 (1.37\u20137.47), p = 0.008). In-ICU death was associated with lower admission ICU Mobility Scale score (0.81 (0.71\u20130.91), p = 0.001). Restricted mobility (24.90 (6.77\u2013161.94), p < 0.001) and passive kinesiotherapy (30.67 (9.49\u2013139.52), p < 0.001) were associated with in-ICU death, whereas active kinesiotherapy (0.13 (0.05\u20130.32), p < 0.001), standing (0.12 (0.05\u20130.30), p < 0.001), or walking (0.10 (0.03\u20130.27), p < 0.001) were associated with in-ICU discharge. Conclusions: In-ICU mortality was higher for inpatients with cardiovascular diseases who had COVID-19+, were exposed to invasive mechanical ventilation, or presented with low admission mobility scores. Restricted mobility or passive kinesiotherapy were associated with in-ICU death, whereas active mobilizations were associated with in-ICU discharge in this population. Cardiovascular diseases (CVDs) are the leading cause of death globally, with estimated 31% mortality, representing about 17.9 million deaths every year . The BraThe hazards of hospitalization, particularly for older adults in the intensive care units (ICU), are a longstanding issue that ultimately favors a decline in musculoskeletal function and functional capacity . Higher Retrospective, single-center study. Data were obtained by the principal investigator through information previously contained in electronic medical records, examination reports, and notes of the health professional staff involved in the care of the patients. This study is reported following the REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statement . MinimumThis study retrospectively analyzed all data from February to November 2020 collected from patients consecutively hospitalized at the ICU of a primary-to-tertiary private hospital located in Curitiba, Paran\u00e1, Brazil.ICU admission criteria comprised at least of the following conditions: hemodynamic ; neurological ; or respiratory . Other causes for ICU admission included postoperative period of high-risk patients, postoperative period of large surgeries, postoperative cardiac surgery, postoperative neurological surgery, postoperative endovascular surgery, need for clinical monitoring, sepsis, septic shock, cardiac arrhythmia, vascular diseases of the heart, or acute renal dysfunction.Patients who had a primary diagnosis of CVD after a complete clinical exam and laboratory testing including laboratory blood tests, electrocardiogram, blood pressure, and/or echocardiography as prescribed, admission assessment by a physiotherapist, and tested for SARS-CoV-2 infection at admission were included. ICU admission was defined as an admission to the hospital\u2019s ICU for >12 h. Re-admissions of patients to the ICU within the study period were excluded from the analysis.All admission data were collected within <24 h of ICU hospitalization at the discretion of the medical staff and covered the required time for swab analysis. Data were collected retrospectively from electronic medical recordings regarding demographics, vital signs, laboratory, gasometry, presence of CVD and comorbidities, and drugs in continuous use. Date of hospital admission and discharge from the ICU or death were collected for computing the total length of ICU stay. The sample was divided into groups COVID-19+ or COVID-19\u2212 based on the ICU admission test, after a nasal and/or nasopharyngeal swab for SARS-CoV-2 by polymerase chain reaction method.Overall muscle strength was assessed by the Medical Research Council (MRC) scale, which uses a 6-point scale of 6 muscle groups bilaterally. Representative scores comprised the sum of points observed for each muscle group bilaterally, ranging from 0 (no muscle activity) to 60 .Mobility was assessed by the ICU Mobility Scale (IMS). The score varies between 0 expressing low mobility (patient who only performs passive exercises in bed) and 10 expressing high mobility .All patients were exposed to physiotherapy interventions based on the hospital standards of usual care developed according to international and national recommendations ,27,28,292O and subsequent titration of ideal PEEP, provided they were clinically stable. When they needed oxygen therapy, it was performed using a low-flow system . Spontaneous prone was also used for at least 1 h. In the supine position [Ventilatory support was characterized using non-invasive mechanical ventilation, through an orofacial or facial interface connected to the mechanical ventilator in one or two pressure levels ventilation modes, or invasive ventilatory support . Patients diagnosed with acute respiratory distress syndrome used protective strategy ventilatory parameters, which may require alveolar recruitment through the prone position or recruitment through the gradual increase of positive end-expiratory pressure (PEEP) up to 35 cmHposition , the heaMobility activities were categorized as complete bed restriction; passive kinesiotherapy ; active kinesiotherapy ; assisted or active sitting out of bed; standing; and walking.The primary outcome was in-ICU mortality as well as admission functional assessments of MRC and IMS scores. In-ICU mortality was calculated from the admission date and confirmed using electronic medical records.No missing data occurred for exposures, in-ICU mortality, or admission IMS scores. Data were missing for the admission assessment of MRC scores in 18/100 participants due to sedation.p < 0.05 (two-tailed).Statistical analysis was performed in jamovi v. 1.8.1.0 and R project version 4.0.4 with packages after importing the electronic spreadsheet. Missing data in admission measurements were reported and assumed to be missing completely at random and univariate mean imputation was performed. Evidence of statistical significance was considered at Descriptive summaries were reported as mean (standard deviation (SD)) for continuous variables or absolute and relative frequencies (%) for categorical ones. Admission demographic data were compared between COVID-19+ versus COVID-19\u2212 groups using the linear model analysis of variance or Pearson\u2019s Chi-squared test for continuous and dichotomous variables, respectively.Univariable logistic regression analysis was performed to examine the association (odds ratio (OR) with 95% confidence interval (95% CI)) of exposure to physiotherapy intervention (ventilatory support and mobility) with group (COVID-19+ vs. COVID-19\u2212) and in-ICU mortality. Multivariable logistic regression model was fitted to determine independent factors associated with in-ICU mortality; all factors related to exposure to physical therapy were force-entered as a full model. Model fit was evaluated by Akaike information criterion (AIC) and C-statistic.2). The most common underlying CVD was hypertension (91/100), followed by a history of cerebrovascular disease (22/100), coronary artery disease (21/100), heart failure (16/100), and atrial fibrillation. Overall length of ICU stay was 9.7 (15.5) days, with patients with COVID-19+ showing longer ICU stay (14.5 (21.7) vs. 6.2 (6.8), p = 0.007). Between-groups comparisons show that patients with COVID-19+ showed higher admission MRC scores (48.3 (7.9) vs. 43.8 (10.4), p = 0.021) and IMS scores (5.5 (4.0) vs. 3.9 (3.8), p = 0.039). They were also younger (68 (16) vs. 80 (13) years, p < 0.001) and presented at admission with lower leukocytes count (9565 (5473) vs. 13,456 (6444) count/mcL, p = 0.002), lower partial pressure of carbon dioxide (PCO2) (31.7 (6.5) vs. 37.7 (8.5), p < 0.001), and lower bicarbonate (21.9 (4.5) vs. 23.8 (4.9) mEq/L, p = 0.044). Sedation at admission was more frequent in the COVID-19+ group . No statistical evidence of difference was observed between groups for severity of disease based on acute physiology and chronic health evaluation (APACHE II: 30.3 (4.8) vs. 30.2 (4.9), p = 0.917).Overall, the sample was composed of older adults (75 (16) years), balanced between sexes , and with most participants (40/100) classified as overweight (body mass index = 27.1 (5.1) kg/mp = 0.011) or prone position (22.80 (4.19\u2013425.35), p = 0.003), to alveolar recruitment (19.04 (4.97\u2013125.99), p < 0.001), awake prone (5.60 (1.27\u201339.05), p = 0.038), or length of stay (1.07 (1.02\u20131.13), p = 0.008), but not to non-invasive mechanical ventilation or oxygen therapy. Multivariable logistic regression analysis showed a good linear fit (C-statistic = 0.783), with COVID-19 remaining independently associated with exposure to alveolar recruitment (22.34 (3.56\u2013224.91), p = 0.002) or awake prone (13.41 (1.62\u2013228.22), p = 0.032).As related to ventilatory support , patientp = 0.029).As related to mobility during ICU stay , no statp = 0.008). As related to ventilatory support, in-ICU mortality was more likely in patients exposed to invasive mechanical ventilation in either supine (22.71 (8.28\u201370.76), p < 0.001) or prone position (4.74 (1.42\u201318.74), p = 0.016), oxygen therapy (8.75 (2.34\u201357.11), p = 0.005) or alveolar recruitment , p < 0.001). Also, in-ICU death was associated with longer length of stay (1.04 (1.01\u20131.09), p = 0.048)), lower admission IMS score (0.81 (0.71\u20130.91), p = 0.001) but not MRC score (p = 0.055). Multivariable logistic regression analysis showed an excellent linear fit (C-statistic = 0.920), with in-ICU death still independently associated with COVID-19+ , exposure to invasive mechanical ventilation (14.81 (2.97\u201397.70), p = 0.002) and admission IMS score (0.79 (0.63\u20130.96), p = 0.023).p < 0.001), passive kinesiotherapy (30.67 (9.49\u2013139.52), p < 0.001) and longer LOS (1.04 (1.01\u20131.09), p = 0.048) were associated with in-ICU death, whereas active kinesiotherapy (0.13 (0.05\u20130.32), p < 0.001), standing (0.12 (0.05\u20130.30), p < 0.001), or walking (0.10 (0.03\u20130.27), p < 0.001) were associated with in-ICU discharge. Multivariable logistic regression analysis showed an excellent linear fit (C-statistic = 0.947), with in-ICU death still independently associated with COVID-19+ (15.44 (2.80\u2013140.82), p = 0.005), restricted mobility (10.49 (1.74\u201395.85), p = 0.017), and passive kinesiotherapy (17.66 (2.32\u2013326.56), p = 0.017).As related to mobility during ICU stay, two patterns emerged: restricted mobility (24.90 (6.77\u2013161.94), The main findings suggest that in-ICU mortality is higher for inpatients with CVD who had a COVID-19+ test result, were exposed to invasive mechanical ventilation, or presented with low admission IMS scores, whereas restricted mobility or passive kinesiotherapy were associated with in-ICU death, active mobilizations were associated with in-ICU discharge. Our findings contribute to the global discussion on the acute management of patients with COVID-19 by providing insights about the planning physiotherapy interventions aimed at reducing in-ICU fatality among patients with CVD.Demographic and clinical data from our sample in Brazil corroborate previous studies in other countries on the risk factors for hospitalization and mortality in patients with CVD and COVID-19: mainly older age, overweight, low lymphocyte count, and pre-existing comorbidities, among others ,9,31,32.Clinical algorithms and consIn-ICU mortality was higher for inpatients with CVD who had a COVID-19+ test result, were exposed to invasive mechanical ventilation, or presented with a lower admission IMS score. Altogether, these characteristics can be understood as a proxy for disease severity. Interestingly, exposure to physiotherapy intervention showed two distinct effects on in-ICU mortality rate, whereas restricted mobility or passive kinesiotherapy were associated with in-ICU death, active mobilizations were associated with in-ICU discharge. This finding corroborates previous studies showing improved mobility at hospital discharge and a higher probability of discharging home with increased frequency and longer mean duration of physical therapy visits in patients with COVID-19 admitted to acute care hospitals . ConsideThis study has some limitations. Due to the retrospective design, there were missing data for participants regarding admission assessment of functional outcomes. Clinical data at admission were collected within <24 h of ICU hospitalization and hence may differ from pre-admission status that required hospitalization. Moreover, physiotherapy interventions were delivered as per the rehabilitation team\u2019s clinical decision-making process. Whereas such lack of control in experimental factors may have influenced the delivered interventions in each group, such pragmatic approach most likely represents ICU routines in Brazil since they are based on national guidelines. Some CIs returned wide ranges, which suggests a large uncertainty about the effect and that further information is needed. Nonetheless, assessment of goodness-of-fit of the models (Akaike information criterion and C-statistics) suggest acceptable model validity. The current sample is from a single center during the first \u2018wave\u2019 (February to November 2020) of cases in Brazil when varIn-ICU mortality is higher for inpatients with CVD who had COVID-19+, were exposed to invasive mechanical ventilation, or presented with low admission mobility scores. The protective effects of routine physiotherapy interventions are highest when patients can perform active rather than passive kinesiotherapy. Patients with COVID-19 who further perform standing and walking activities appear to experience a higher survival effect."} +{"text": "Tuberculosis (TB) remains a leading infectious cause of death and morbidity globally. Rifampin-resistance or intolerance requires prolonged treatment using less effective, more toxic regimens. Recent trials demonstrated that the all-oral six-month \u201cBPaL\u201d regimen, Bedaquiline, Pretomanid and Linezolid, is 90% effective. In these trials, linezolid-induced hematologic and neurologic toxicity was high using 1200mg daily, whereas lower exposure (dose or duration) reduced toxicity. Therapeutic drug monitoring (TDM) is used by U.S. TB experts to maintain a serum linezolid trough < 2ug/ml, which correlates with reduced toxicity. Since U.S. FDA approval in 2019, BPaL has been widely implemented for the treatment of rifampin-intolerant or resistant TB disease.We evaluated a cohort of patients with TB treated from October, 2019 through April, 2022, describing patient demographics, BPaL treatment dosing, and adverse events. TDM was performed for clinical purposes using liquid chromatography\u2013mass spectrometry to measure serum levels at trough and 2 and 6h post-linezolid dose. Clinical providers adjusted linezolid dose and dosing interval targeting a trough < 2ug/ml and peak of 12\u201326ug/ml.Among 64 BPaL patients, ages were 15\u201383 years, 22 (34.3%) were female, 6 (9.3%) U.S.-born, 4 (6.3%) HIV-infected. 50 (78.1%) had only pulmonary disease, 6 extrapulmonary, and 8 had both; 61 (91.0%) were culture-confirmed. Most (n=62) started linezolid 600mg daily. Linezolid was adjusted for 39 (66.1%) of the 59 patients with TDM; 18 had a trough >2ug/ml, 30 had dosing interval increased to thrice-weekly, and 17 had a dose increase. 52 (81.3%) patients completed BPaL and 12 remain on therapy. One 81-year-old female with diabetes, hypothyroidism, and B12 deficiency discontinued linezolid at 12 weeks for worsened neuropathy (linezolid trough=1.13ug/ml). She completed 26 weeks of bedaquiline/pretomanid and her symptoms returned to baseline.Use of BPaL with clinical and TDM monitoring has transformed treatment of rifampin-resistant or intolerant TB in the U.S. Patients previously sentenced to 18\u201324 months of treatment with 5\u20137 hard-to-tolerate medications and modest efficacy can now complete treatment in 6\u20139 months with little toxicity and exceptional cure rates.All Authors: No reported disclosures."} +{"text": "Nocardia farcinica is an opportunistic pathogen that causes nocardiosis primarily in patients with compromised immune systems. In this study, we used the genetically tractable organism Caenorhabditis elegans as a model to study the innate immune responses to N. farcinica infection. We found that unlike other pathogenic bacteria such as Pseudomonas aeruginosa and Staphylococcus aureus, N. farcinica failed to kill adult worms. In another words, adult worms exposed to N. farcinica exhibited a normal lifespan, compared with those fed the standard laboratory food bacterium Escherichia coli OP50. Interestingly, deletion of three core genes in the p38 MAPK/PMK-1 pathway reduced the survival of worm exposure to N. farcinica, highlighting a crucial role of this pathway for C. elegans in resistance to N. farcinica. Furthermore, our results revealed that N. farcinica exposure up-regulated the level of PMK-1 phosphorylation. The activation of PMK-1 promoted nuclear translocation of a transcription factor SKN-1/Nrf2, which in turn mediated N. farcinica infection resistance in C. elegans. Our results provide an excellent example that the integrity of immune system is key aspect for counteract with pathogenesis of N. farcinica. Nocardia farcinica, is an opportunistic pathogen under the genus of Actinomycetes widely distributed in the soil and rotten substances, causing lung infection through inhalation of bacterial particles [N. farcinica, suppress immune responses by inhibiting Notch signal pathway in RAW264.7 macrophages [N. farcinica in mammal. The mechanism of pathogenesis in N. farcinica infection is not fully understood.articles . Since tarticles . Nocardiarticles . Nocardiarticles . A recenCaenorhabditis elegans is a free-living, bacterivorous nematode that lives in the soil, well known as invertebrate without adaptive immune system as well as specific immune cells [C. elegans often encounters a variety of pathogens, thus it exerts a strong selective pressure to evolve and develop an effective innate immune system. C. elegans therefore represents a powerful invertebrate model to study the innate immune responses to nosocomial bacterial pathogens such as Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella enterica, Salmonella typhimurium, and Serratia marcescens [Cryptococcus neoformans [Candida albicans [ne cells . In wildne cells . In the rcescens ,8,9,10, oformans and Candalbicans .C. elegans have revealed a variety of the evolutionarily conserved signaling pathways in the innate immunity, such as the DAF-2 insulin-like signaling pathway [C. elegans to regulate innate immunity [C. elegans upon P. aeruginosa infection [P. aeruginosa infection [During the last two decade, studies using pathway , the p38 pathway , and the pathway , the JNK pathway , the pro pathway , the G p pathway , the G p pathway , and the pathway . Of thesimmunity ,21. PMK-immunity . Meanwhinfection . Interesnfection . Under nnfection .N. farcinica in C. elegans. We discovered that the PMK-1/p38 MAPK signaling was required for the survival of worms upon N. farcinica exposure. Further studies indicated that PMK-1/p38 MAPK activated the transcription factor SKN-1, which in turn conferred resistance to N. farcinica infection in C. elegans.In this study, we screened the major signaling pathways that are involved in defense against N. farcinica in nematodes. However, we found that unlike worms exposed to P. aeruginosa, S. aureus, and E. faecium [N. farcinica exhibited a similar lifespan as those fed E. coli OP50, the standard laboratory food . In contrast, pmk-1(km25) mutants exhibited marked decrease in lifespan when exposed to N. farcinica, compared to worms fed on E. coli OP50 and WT (nsy-1(ag3) and sek-1(ag1) mutants exposed to N. farcinica also showed a significant reduction in lifespan, compared to E. coli OP50 diet and WT , sek-1(ag1), and pmk-1(km25) suppressed their mRNA levels , catalase (katG), and superoxide dismutase (sodF) are predicted with high expressivity in N. farcinica, which could defense against reactive oxygen species (ROS) [N. farcinica infection. Thus, ROS are unlikely to be involved in the activation of the p38 MAPK pathway in worms.We then asked if oli OP50 a,b. The osa PA14 and Cutium acnes . A previby PMK-1 . We thuspression c,d. As Fed genes , we thenA levels e. Taken es (ROS) . We thusC. elegans, SKN-1 confers resistance to Gram-negative bacteria P. aeruginosa PA14 and Gram-positive bacteria E. faecalis [N. farcinica infection, we used transgenic worms expressing SKN-1b/c::GFP+rol-6 to detect the nuclear translocation of SKN-1, which is an indicator of its activation [N. farcinica exposure. However, knockdown of nsy-1, sek-1 or pmk-1 by RNAi significantly reduced the nuclear translocation of SKN-1 in worms exposed to N. farcinica (gst-4 (encoding Glutathione S-transferase-4) is a target gene of SKN-1 [Pgst-4::gfp reporter gene to further demonstrate the activation of SKN-1 by N. farcinica infection. We found that the expression level of Pgst-4::gfp was dramatically increased in worms exposed to N. farcinica for 24 hours, The increase is abolished when worms subjected to skn-1, nsy-1, sek-1 or pmk-1 RNAi (skn-1(tm3411), nsy-1(ag3), sek-1(ag1), and pmk-1(km25) suppressed up-regulation of gst-4 expression induced by N. farcinica infection mutants was comparable to that of the pmk-1(km25) mutant subjected to skn-1 RNAi upon N. farcinica infection of N. farcinica and E. coli OP50 in the body of worms worms, skn-1 (RNAi) worms, and control group worms. As black arrows pointing out, genetic inactivation of pmk-1 and skn-1 caused necrosis in the head of worms exposed to N. farcinica, but not to E. coli OP50 , known as key immune factor, mediates resistance to Mycobacterium. spp [N. farcinica in organisms ranging from C. elegans to mammals.In ruginosa ,38 S. au. aureus , Salmonelmonella , Yersinia pestis , and Mycbacteria . The p38bacteria secreted O157:H7 . In mamm O157:H7 ,44, suggium. spp ,46. ThesP. aeruginosa, E. faecalis [Aeromonas dhakensis [N. farcinica infection. It has been reported that PMK-1 can phosphorylate SKN-1 at Ser-74 and Ser-340 [P. aeruginosa, E. faecalis and N. farcinica infection activates SKN-1 in a p38 MAPK-dependent manner. These results suggest that SKN-1 is one of downstream effectors of p38 MAPK that mediates C. elegans innate immune responses to both Gram-negative and Gram-positive pathogens. The molecular mechanism underlying SKN-1-mediated innate immunity remains unclear. Previously, we and others have demonstrated that autophagy plays an important role in C. elegans defense against a variety of pathogenic bacteria by repairing organismal insults [glp-1(e2141ts) mutants [hyl-1; lagr-1 mutants [N. farcinica infection via promoting autophagy. The opportunistic infections followed immunologic deficiency have mainly been seen in HIV infected patients, revealing that the environmental \u201charmless\u201d microorganisms could be life threaten, such as Penicillium marneffei, known as the third common opportunistic pathogen that causes penicilliosis in HIV patients. Likewise, N. farcinica is an opportunistic pathogen, with the majority of infections occurring in immunocompromised patients. In the current study, WT worms do not have a reduced lifespan when exposed to N. farcinica. These data suggested that like humans, WT worms with an intact innate immune system can resist to N. farcinica infection, but lacking key genes in the PMK-1/p38 MAPK pathway become susceptible to N. farcinica infection. In our studies, we also noticed that lack of p38 MAPK pathway and SKN-1 leads to significant increases accumulation of N. farcinica and obvious enlarged vacuoles in the head of worms. Thus, our finding emphasizes that the integrity of immune system is crucial for defense against N. farcinica infection in C. elegans.As a transcription factor, SKN-1 is involved in resistance to oxidative stress by upregulating a set of the Phase II detoxification genes . SKN-1 afaecalis , Mycobacfaecalis , and Aerhakensis . In the insults ,20,48. S mutants . Meanwhi mutants . Thus, SN. farcinica to activate the p38 MAPK/PMK-1 pathway?However, our data demonstrate that ROS are not the signal component produced by N. farcinica. Several virulence factors of N. farcinica have been reported when the pathogen infected mammals. For instance, Nfa34810 protein of N. farcinica can stimulate macrophages to produce tumor necrosis factor alpha (TNF-\u03b1) and other immune related factors through the TLR4 pathway [N. farcinica IFM 11523, which isolated from Japanese patient, secretes two pathogenesis factors nocobactin NA-a (compound 1) and nocobactin NA-b (compound 2), which act as on the notch signaling inhibitors [What are the critical signal molecules from pathway . BesidesC. elegans strains were maintained on NGM medium containing E. coli OP50 under standard condition. Strain used in this study include C. elegans Bristol N2, pmk-1(km25), mpk-1(n2521), let-60(ga89), jnk-1(gk7), hlh-30(tm1978), skn-1(tm3411), nsy-1(ag3), sek-1(ag1), skn-1b/c::gfp+rol-6(su1006), nlp-29p::gfp+col-12p::DsRed, gst-4p::gfp::NLS(pAF15) were kindly provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). Bristol N2 strain of C. elegans is used as non-genetic modified control in experiments, and labeled as wild-type (WT) in our study [The , mpk-1n21, let-60ur study .E. coli HT115 (DE3) strain carrying vector L4440 express dsRNA corresponding to targeted genes to perform double-stranded (ds)RNA-mediated RNA interference (RNAi). As experimental control, E. coli HT115 carrying empty vector (no dsRNA expression) were used, labelled as EV. All strains were grown overnight in LB medium with 100 \u03bcg/mL ampicillin at 37 \u00b0C. Cultured E. coli strains spread onto NGM plates contained 100 \u03bcg/mL ampicillin and 1 mM isopropyl 1-thio-\u03b2-D-galactopyranoside (IPTG). RNAi assay were performed according to pervious study [2 strain of C. elegans) fed on RNAi bacteria strains at 20 \u00b0C until reach to young adult. Then young adult worms were transferred on the BHI plates for further studies.Bacterial strains contain RNAi targeting genes were obtained from Ahringer library . E. colius study , in brieC. elegans strains were cultured on NGM plate with E. coli OP50 at 20 \u00b0C following the standard maintenance procedures [E. coli OP50 for further assays. To examine the effect of N. farcinica on worms\u2019 lifespan, synchronized L1 larvae were cultivated fed E. coli OP50 at 20 \u00b0C until the young adult stage. Then 50\u201360 worms were fed with either N. farcinica or laboratory standard diet E. coli OP50 on BHI medium containing 5\u2032-fluoro- 2\u2032-deoxyuridine (FUdR) (75 \u03bcg/mL) at 25 \u00b0C. The survival curves were plotted by scoring the dead worm at 24 h interval. Immobile worms unresponsive to touch were scored as dead. Three plates were analyzed per assay and all experiments were performed three times. The ocedures . Worms wocedures , eggs weskn-1b/c::gfp were fed with either N. farcinica or laboratory standard diet E. coli OP50 on BHI plates for 24 hours. Briefly, worms were mounted on slides from plates and imaged by using Nikon e800 fluorescence microscope. At least 30 worms were examined under each condition in three independent experiments.After young adult worms expressing After washed with M9 buffer, worms were homogenized in liquid nitrogen. Then the homogenate was lysed on ice for 30 min in lysis buffer RIPA . After centrifuged at 12,000 rpm for 15 min at 4 \u00b0C, the supernatant was obtained and used for Western blot analysis. The total protein extraction was loaded on 10% SDS-PAGE for electrophoresis. Proteins were then transferred to immobilon-PSQ transfer PVDF membrane . Primary antibodies were anti-phospho-p38 antibodies , and anti-\u03b1-tubulin antibodies . The secondary antibodies were peroxidase-coupled anti-rabbit IgG . Blots were developed using Super Signal chemiluminescence substrate . An imaging system (Amersham Imager 600) was used for documentation of the Western blot results. Band intensities were measured using ImageJ software (NIH).\u00ae Premix-Ex TagTM on a Roche LightCycler 480\u00ae System . act-1 gene was used for an internal control. The primers used for PCR are listed in Total RNA was isolated from worms with TRIzol Reagent . Random-primed cDNAs were generated by reverse transcription of the total RNA samples with SuperScript II (Invitrogen). A real time-PCR analysis was conducted using SYBRnlp-29p::gfp or gst-4p::gfp were exposed to N. farcinica or E. coli OP50 for 24 h. Then the worms were mounted in M9 onto microscope slides. The slides were imaged using a Nikon e800 fluorescence microscope. Fluorescence intensity was quantified by using the ImageJ software (NIH). Mean value and standard errors were calculated based on more than 30 worms under each condition in three independent experiments.For detecting fluorescence in worms, analysis, synchronized young adult worms expressing either ROS was detected by transferring worms in to M9 buffer with DHE (3 \u03bcM) and stained for 3 h before mounting in M9 buffer onto microscope slide, examined by fluorescence microscope (Zeiss Axioskop 2 Plus) .N. farcinica colonized in worms, we fed young adult worms with either E. coli OP50 or N. farcinica for 96 h on BHI plates, then worms were transferred in to M9 buffer containing 25 mM levamisole hydrochloride , 50 \u03bcg/mL kanamycin and 100 \u03bcg/mL carbenicillin , and soaking for 30 min before washing with M9 buffer for three times. Worms were collected and grinded in PBS with 0.1% Triton, and serial diluted before placing on BHI ager for incubation, then bacterial colonies were counted to measure CFU.To ask if t-test. Differences in survival rates were analyzed using the log-rank test. Difference of CFU counting was assessed by two-tailed unpaired t-test. Data were analyzed using SPSSsoftware, version 26.0 and Graphpad Prism 8.The statistical significance of differences in gene expression and fluorescence intensity was assessed by performing a one-way ANOVA followed by a Student-Newman-Keuls test and two-tailed unpaired"} +{"text": "Endoscopic Endonasal Surgery (EES) is an innovative surgical technique to remove brain tumors and lesions. Post-operative central nervous system (CNS) infections following EES are poorly described. The objective of this study was to define the epidemiology and characteristics of post-EES CNS infections.Adult patients who underwent EES between 1/2010 and 7/2021 were evaluated and included if microbiologically confirmed CNS infection occurred within 30 days of EES. Suspected contaminants, ventricular drain colonization, and pre-EES CNS infections were excluded.S. aureus, Enterobacterales, and P. aeruginosa. Among 20 patients with prior EES, pathogens included S. aureus (5/20), Enterobacterales (3/20), Enterococcus spp. (3/20) and polymicrobic infections (3/20). Overall, 35.1% (13/37) of patients developed CNS infection due to a pathogen susceptible to pre-EES prophylaxis. Among those colonized with MRSA at time of EES, 75% (3/4) developed MRSA CNS infection compared to 6.1% (2/33) of non-colonized MRSA patients (P=0.005). The overall 30-day mortality rate was 2.7% (1/37).Overall, 2005 patients underwent EES; 1.8% (37/2005) developed CNS infection. The median [IQR] age was 51 [42-60] years, 32.4% (12/37) were female, and 54% (20/37) had a prior EES. The most common indications for EES were tumor resection [67.6% (25/37)] and cerebrospinal fluid (CSF) leak repair [24.3% (9/37)]. Post-operative CSF leaks were documented in 70.3% (26/37) of patients and 24.3% (9/37) had an extra-ventricular drain or shunt in place for >48 hours at the time of infection. Ceftriaxone prophylaxis was prescribed in 64.9% (24/37) of cases and other regimens varied. The median [IQR] time from EES to diagnosis of CNS infection was 12 [6-19] days. The most common pathogens were A polymicrobic case was defined as >1 pathogen isolated from CSF (n=1) or from rhinocerebral tissue if CSF cultures were negative (n=11). Among polymicrobic cases (n=12), P. aeruginosa (n=5), Enterococcus spp. (n=4). and S. aureus (n=3) were predominant. Cases labeled as other consisted of Trichoderma spp, A. xylosoxidans, P. acnes, S. epidermidis, Peptostreptococcus spp.S. aureus, antimicrobial prophylaxis should ensure adequate coverage of this pathogen in addition to sinus flora, and programs may benefit from screening patients for MRSA colonization pre-EES. Our data also suggest that prophylaxis should target Gram-negative and other colonizing bacteria among patients with prior EES.CNS infection post-EES is rare and causative pathogens vary. Given the predominance of Ryan K. Shields, PharmD, MS, Infectious Disease Connect: Advisor/Consultant|Merck: Advisor/Consultant|Merck: Grant/Research Support|Roche: Grant/Research Support."} +{"text": "Attention-Deficit/Hyperactivity Disorder (ADHD) is associated with alterations in both reinforcement sensitivity and affective processing but the nature of the associations of these characteristics is yet to be examined. We hypothesized that individual differences in the sensitivity of the Behavioral Approach System (BAS) would exhibit differential relations with affective network connectivity \u2013 involved in emotional regulation and salience monitoring \u2013 in youth at-risk for, relative to youth not at-risk for, ADHD.n = 125; Mage=16.24 years, SD = 1.09 years; 61.6% boys) were recruited as part of The Budapest Longitudinal Study of ADHD and Externalizing Disorders. Forty-nine were classified as at-risk for ADHD , defined as exhibiting \u22654 parent-rated symptoms of either domain on the ADHD Rating Scale-5. Participants completed a 10-minute resting-state functional Magnetic Resonance Imaging session, during which they were asked to focus their attention on a fixation cross, as well as various self-report assessments, including the Reinforcement Sensitivity Theory of Personality Questionnaire (RST-PQ).Adolescents within a cluster based on functional similarity . Follow-up OLS linear regressions showed higher impulsivity scores predicted stronger functional connectivity between the (1) left amygdala-right insula = 3.298, p = .005, adjusted R2=.101), (2) left amygdala-left insula = 2.2, p = .048, adjusted R2=.055), (3) right amygdala-right insula = 3.833, p = .002, adjusted R2=.121), and (4) right amygdala-left insula = 3.064, p = .008, adjusted R2=.092) in at-risk youth, whereas an inverse relationship was apparent in not at-risk youth.Functional Network Connectivity analyses indicated an interaction effect between the RST-PQ BAS impulsivity subscale and at-risk status on functional connectivity between four affective network region-pairs (t(122)=\u22121.167, p = .246) or on functional connectivity ((1) t(122) = .383, p = .702; (2) t(122) = .195, p = .846; (3) t(122)=\u2212.107, p = .915; (4) t(122)=\u2212.206, p = .837).There was no main effect of group status on BAS impulsivity scores as the role of the amygdala-insula connection in reward sensitivity appears especially relevant for a developmental phase and a diagnostic group linked to increased risk taking."} +{"text": "Relative transformation efficiencies ranged from \u2212\u200944 to +\u200945% compared to Silwet\u00ae L-77. Surfactants S200, S240, and S279 demonstrated the greatest enhancement in transformation.Floral dip transformation of Arabidopsis has been used consistently for 20\u00a0years with little change in the protocol. Here we directly compare seven novel surfactants (BREAK-THRUThe online version contains supplementary material available at 10.1186/s13104-022-06251-5. Plant biotechnology offers tremendous promise for improving crops by increasing the sustainability and reducing the environmental impact of production. These technologies have led to crop plants with enhanced nutritional properties, abiotic stress tolerance, disease and pest resistance, and other agronomic traits, as well as crop tools for accelerated precision breeding. Although genetic engineering and genomic editing approaches have been applied successfully to various plant species, relatively few crops have an easy and efficient means of transformation, which restricts progress in research as well as agricultural deployment. Thus, additional techniques for broadly and efficiently applying transformation technologies to a wide range of crops and their constituent elite varieties are required.One of the earliest enhancements to transformation was the use of surfactants, which modify the surface properties of liquids to enhance their spreading, wetting, emulsifying, dispersing, or other characteristics. Surfactants have been used extensively in herbicide and pesticide formulations to increase their penetration. However, they must be used judicially, as surfactants may have inhibitory phytotoxic effects on plant tissue at high concentrations and stimulatory effects at low concentrations , 2.Agrobacterium-mediated transformation of Arabidopsis thaliana in water: 25 (0.1%).BREAK THRU\u00ae-S200: Trisiloxane super-spreader (more water-soluble), stable within pH range 6\u20138, Static surface tension [mN/m] in water: 22 (0.1%).BREAK THRU\u00ae-S233: Trisiloxane super-penetrant systemic products, stable within pH range 6\u20138, Static surface tension [mN/m] in water: 23 (0.1%).BREAK THRU\u00ae-S240: Trisiloxane super-spreader (liquid soluble), stable within pH range 6\u20138, Static surface tension [mN/m] in water: 22 (0.1%).BREAK THRU\u00ae-S279: Trisiloxane super-spreader (more oil-soluble), stable within pH range 6\u20138, Static surface tension [mN/m] in water: 21 (0.1%).BREAK THRUS301: Trisiloxane super-spreader, stable within pH range 6\u20138, Static surface tension [mN/m] in water: 22 (0.1%).\u00ae-SP133: Polyglycerol ester-based adjuvant , stable within pH range 4\u20139, Static surface tension [mN/m] in water: 29 (0.1%).BREAK THRU\u00ae compound see (www.evonik.com/break-thru) [For more details of the BREAK THRUak-thru) .We show an increase in transformation efficiency for Arabidopsis floral dip transformation using a published technique . HoweverAdditional file 1.\u00a0Statistics 1: Figure S1.Additional file 2.\u00a0PCR: Figure S2.Additional file 3.\u00a0Statistics 2: Table S1. Surfactant transformation efficiency. Table S2. Surfactant transformation statistics."} +{"text": "Nature Communications 10.1038/s41467-021-25159-5, published online 09 August 2021Correction to: Nat. Commun. 12, 1\u201314 (2021). The correct reference for Ref. 11 is: Zhang, Y. et al. mTORC1 couples cyst(e)ine availability with GPX4 protein synthesis and ferroptosis regulation. Nat. Commun. 12, 1589 (2021). This has been corrected in the PDF and HTML versions of the Article.The original version of this Article contained an error in Ref. 11, which incorrectly gave the reference as: Zhang, Y. et al. mTORC1 couples cyst(e)ine availability with GPX4 protein synthesis and ferroptosis regulation."} +{"text": "E.coli (STEC) infection which presents a characteristic triad of microangiopathic hemolytic anemia, thrombocytopenia, and acute renal failure. Preliminary in vitro and experimental animal studies demonstrated that Shigatoxins (STXs) induce the secretion of proinflammatory cytokines. Human neutrophil gelatinase-associated protein has been reported as a marker of acute kidney injury. Dosing serum levels of IL-8, TNF-\u03b1, IL-6, IL-1\u03b2 and N-gal in children with STEC-associated infection and HUS would allow to establish the role of these cytokines as biomarkers of renal injury and severityHemolytic Uremic Syndrome (HUS) is a complication of Shigatoxin-producing Prospective study during 2017 \u2013 2020 was performed; three groups of patients < 18 years were included: bloody diarrhea (BD), HUS requiring dialysis (HUSD) and HUS and no dialysis requirement (HUSND), all of them with presence of STX in stool. Blood samples were collected at diagnosis (t1) and at 7 days (t2). An immunoassay was used for detection of TNF-\u03b1, IL-1\u03b2, IL-6, and IL-8 . An immunoassay was used for N-gal detectionForty-nine children were admitted; 22 (49%) were male. Median age was 24 (IQR 13-36) months. Fourteen patients with BD, 24 patients with HUS: 12 HUSD and 12 HUSND. Eleven healthy children (HC) were included. At diagnosis, higher IL-8 values were found in HUSD vs. BD (p=0.0004), HUSND (0.003) and HC (p= 0.0043). Higher TNF-\u03b1 values were detected in HUSD vs. BD (P= 0.0001), HUSND (p= 0.0011) and HC (p= 0.0002). Higher TNF-\u03b1 values were found in patients with BD vs HC (p= 0.0055). HUSD exhibited higher IL-6 values as compared with BD (p= 0.0145) and HC (0.0106). N-gal concentrations were higher in HUSD vs. BD (P= 0.0120), HUSND (P= 0.0166) and HC (p= 0.0049). A decrease in IL-8 was observed in HUSD between t1 and t2 (p=0.0357). Interleukin 8, IL-6, and N-gal may be considered as potential serological markers of renal damage and dialysis requirement. TNF-\u03b1 concentrations are already increased in BD without HUS complicationsAll Authors: No reported disclosures."} +{"text": "In the published article, the reference for Immunotherapy is an emerging tool used in cancer treatment (1) was incorrectly written as Ruhlmann CH, Iversen TZ, Okera M, Muhic A, Kristensen G, Feyer P, et\u00a0al. Multinational study exploring patients\u2019 perceptions of side-effects induced by chemo-radiotherapy. Radiother Oncol (2015) 117(2):333\u20137. doi: 10.1016/j.radonc.2015.09.014. It should be Mohanty R, Chowdhury CR, Arega S, Sen P, Ganguly P, Ganguly N. CAR T cell therapy: A new era for cancer treatment (Review). Oncol Rep (2019) 42(6):2183-95. Epub 2019/10/04. doi: 10.3892/or.2019.7335.In the published article, the reference for The fourth-generation CARs added genes encoding cytokines [interleukin (IL)-12 and IL-15] to be released by the CARs to improve CAR T-cell survival in a TME (32) was incorrectly written as Haso W, Lee DW, Shah NN, Stetler-Stevenson M, Yuan CM, Pastan IH, et\u00a0al. Anti-Cd22-chimeric antigen receptors targeting B-cell precursor acute lymphoblastic leukemia. Blood (2013) 121(7):1165\u201374. doi: 10.1182/blood-2012-06-438002. It should be Chmielewski M, Kopecky C, Hombach AA, Abken H. IL-12 release by engineered T cells expressing chimeric antigen receptors can effectively muster an antigen-independent macrophage response on tumor cells that have shut down tumor antigen expression. Cancer Res (2011) 71(17):5697-706. Epub 2011/07/12. doi: 10.1158/0008-5472.Can-11-0103.In the published article, the reference for The fifth-generation CARs build on the second-generation CARs by adding cytoplasmic structural domains from the IL-2 receptor beta chain and signal transducers and activators of transcription (STAT)3/5 binding pattern, triggering three signals including T-cell receptors , costimulatory factors , and cytokines to improve the proliferation, survival, and antitumor activity of CAR T cells markedly (33) was incorrectly written as Chmielewski M, Kopecky C, Hombach AA, Abken H. IL-12 release by engineered T cells expressing chimeric antigen receptors can effectively muster an antigen-independent macrophage response on tumor cells that have shut down tumor antigen expression. Cancer Res (2011) 71(17):5697\u2013706. doi: 10.1158/0008-5472.Can-11-0103. It should be Kagoya Y, Tanaka S, Guo T, Anczurowski M, Wang CH, Saso K, et\u00a0al. A novel chimeric antigen receptor containing a JAK-STAT signaling domain mediates superior antitumor effects. Nat Med (2018) 24(3):352-9. Epub 2018/02/06. doi: 10.1038/nm.4478.In the published article, the reference for As conventional surgical treatment and antitumor drugs have limited effects, CAR T-cell therapy can provide targeted immunotherapy to patients with gastric cancer without developing drug resistance and effectively control the progression and metastasis of gastric cancer (62) was incorrectly written as Dur\u00e3es C, Almeida GM, Seruca R, Oliveira C, Carneiro F. Biomarkers for gastric cancer: Prognostic, predictive or targets of therapy? Virchows Arch (2014) 464(3):367\u201378. doi: 10.1007/s00428-013-1533-y. It should be Jiang H, Shi Z, Wang P, Wang C, Yang L, Du G, et\u00a0al. Claudin18.2-specific chimeric antigen receptor engineered T cells for the treatment of gastric cancer. J Natl Cancer Inst (2019) 111(4):409-18. Epub 2018/09/12. doi: 10.1093/jnci/djy134.In the published article, the reference for Animal models are constructed by gene editing to mimic specific biological characteristics of human diseases to introduce target genes or delete and modify endogenous genes (83) was incorrectly written as Hu W, Lazar MA. Modelling metabolic diseases and drug response using stem cells and organoids. Nat Rev Endocrinol (2022) 1\u201316. doi: 10.1038/s41574-022-00733-z. It should be Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, et\u00a0al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell (2014) 159(2):440-55. Epub 2014/09/30. doi: 10.1016/j.cell.2014.09.014.The authors apologize for these errors and state that these do not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Frequent users of Emergency Departments (EDs) are a diverse group accounting for disproportionate EDs visits. Psychiatric patients are more likely to visit EDs . EDs utilisation by psychiatric patients increased by 4.4% during COVID-19 pandemic.to determine frequent users characteristics within an Ottawa University Hospital, and assess Covid19 impact on overutilization of EDs compared to other hospitals.Retrospective study of repeat visits characteristics, data extracted from EMR database. Repeat visits defined as no less than 30 days first visit to any EDs. Period of observation: March 1st, 2018 - February 28th, 2021 Results.64% EDS visits for MH, 35% for addictions. More men (57%), age groups: 16-34 y.o. (41%), 34-64 y.o. (51%), 65 +y.o. (8%).Top presenting reasons: suicidality, self-harm, depression (40.5%). Anxiety, situational crisis (16%), bizarre behavior (12%).Most prevalent diagnoses: schizophrenia (28.7%), stress and anxiety (25.2%), personality disorders (13.5%) and depressive episode (10.6%). Only 35.1% admitted after repeat ED visits, 35.1% came by ambulance. Increase during peak pandemic exceeding 20%. Clearly pandemic created more pressures for MH services needs.Schizophrenia and personality disorders made most prevalent diagnostic groups. Even when patients are in acute needs, they do not always require hospitalization. Investigating what MH conditions that got more stressed by the Covid19 pandemic will be of interest.No significant relationships."} +{"text": "Gossypium raimondii Ulbrich (short fibers) with cultivated diploid G. arboreum L and tetraploid G. hirsutum L. (long fibers); 2) G. hirsutum short fiber mutants, Ligon-lintless 1 (Li1) and 2 (Li2) with their near isogenic line (NIL), DP-5690 (long fibers). Chemical analyses showed that the short fibers commonly consisted of greater non-cellulosic components, including lignin and suberin, than the long fibers. Transcriptomic analyses also identified up-regulation of the genes related to suberin and lignin biosynthesis in the short fibers. Our results may provide insight on how high levels of suberin and lignin in cell walls can affect cotton fiber length. The approaches combining phenomic and transcriptomic analyses of multiple sets of cotton fibers sharing a common phenotype would facilitate identifying genes and common pathways that significantly influence cotton fiber properties.Fiber length is one of the major properties determining the quality and commercial value of cotton. To understand the mechanisms regulating fiber length, genetic variations of cotton species and mutants producing short fibers have been compared with cultivated cottons generating long and normal fibers. However, their phenomic variation other than fiber length has not been well characterized. Therefore, we compared physical and chemical properties of the short fibers with the long fibers. Fiber characteristics were compared in two sets: 1) wild diploid Gossypium sp.) is the most economically important natural fiber in the world . Pe. PeArabiCW stage . Three Gi fibers .Li1 and Li2) was performed with total RNAs extracted from developing fibers at PCW stage (8\u201312 DPA) grown in greenhouse or cotton fields [Li1 and Li2 fibers were compared to their NIL, G. hirsutum DP-5690, using a 2-fold difference as a threshold. In the Li1 mutant fibers, 4,043 genes were up-regulated whereas 2,536 genes were down-regulated was performed with the spectral region (1200\u20133000 cm-1) composed of IR peak bands of suberin, lignin, and cellulose (G. hirsutum Li2 < G. hirsutum Li1 < G. raimondii D5-31 < G. hirsutum TM-1 \u2248 G. hirsutum DP-5690 \u2248 G. arboreum A2-100. The three cultivated cottons of G. arboreum A2-100 (0.369), G. hirsutum DP-5690 (0.365), and G. hirsutum TM-1 (0.326) demonstrated similar positive PC1 scores with insignificant (p = 0.587) variations. In contrast, the other three short fiber cottons of G. hirsutum Li2 (-0.738), G. hirsutum Li1 (-0.279), and G. raimondii D5-31 (-0.043) had all negative scores that were significantly (p<0.0001) variable from the cultivated cotton species. Among the three short fiber cottons, the PC1 scores also showed significant (p<0.0001) variations. These results suggested that the chemical compositions of G. raimondii D5-31, G. hirsutum Li1, and G. hirsutum Li2 were different despite a sharing of suberin and lignin fractions in addition to cellulose.For an examination of the quantitative and statistical significances of the spectral features showing different chemical components among the fiber samples used in the 1ellulose . The anaellulose . The PC1G. hirsutum Li1 and Li2 fibers (G. hirsutum Li1 (880) and Li2 (376) mutants. To identify the commonly up-regulated orthologous genes between the diploid D5 genome and polyploid AD1 genome composed of AT and DT subgenomes, we compared the diploid G. raimondii 1,385 SEGs with non-redundant UGs in polyploid G. hirsutum Li1 and Li2 (T) and a peroxidase (Gorai.013G005800_AT) involved in lignin polymerization by oxidizing lignin monomers (monolignols) [T) required for suberin biosynthesis in Arabidopsis [Arabidopsis color mutant was also up-regulated [Of the UGs in ) fibers , there w . Among t . Consistlignols) , 53, 54 bidopsis were foubidopsis was alsoegulated . The othegulated , leucineegulated , FAD-binegulated , glutathegulated , PLAT/LHm Li1 3,1 and Li2 egulated , cytokinegulated , PSBP-doegulated , cyclic egulated , and NACegulated were allG. raimondii and G. hirsutum Li1 and Li2 mutants were too short to be measured by HVI. Thus, we manually measured the maximum fiber lengths of the wet and relaxed cotton fibers from the chalezel end of cottonseeds [G. raimondii D5-6 (11.7 mm) and D5-31 (10.1 mm) as well as G. hirsutum Li1 (2.6 mm) and Li2 (8.1 mm) mutants were significantly shorter than those of cultivated diploid cotton, G. arboreum SXY1 (28.0 mm) and A2-100 (30.1 mm) as well as cultivated polyploid cotton, G. hirsutum TM-1 (41.7 mm), SG-747 (40.1 mm) and DP-5690 (38.7 mm) as shown in Figs G. hirsutum fibers. Lint fibers differentiate from ovule epidermis on the day of anthesis and they grow approximately 25~35 mm based on HVI measurements. In contrast, linter or fuzz differentiate from the ovule epidermis around 5 to 10 DPA and they do not grow longer than 15 mm [G. raimondii was often described as a lintless, non-fibered, or fiberless species [Li1 and Li2 mutants also contain \u201clintless\u201d [G. raimondii [G. hirsutum Li1 mutant [G. hirsutum Li2 mutant [G. raimondii and G. hirsutum Li1 and Li2 mutants can be classified as lint fibers according to the definition described by Lang [Physical properties of cultivated cotton fibers are generally assessed by a High Volume Instrument (HVI) which is defined by the International Cotton Advisory Committee as a standardized instrument for cotton fiber quality measurements . Cotton tonseeds . The maxan 15 mm . Wild di species , 69, 70.intless\u201d , 18. How1 mutant , and G. 2 mutant all diff by Lang .G. raimondii and two G. hirsutum mutants produced fibers containing color pigments composed of lignin and suberin and G. hirsutum Li1 and Li2 mutants (85.1~86.9%) fibers were lower than cultivated G. arboreum (95.6~100%) and G. hirsutum (95.8~98.0%) fibers and G. hirsutum Li1 and Li2 (13.1~14.9%) fibers were substantially greater than the cultivated fibers (0~4.4%). These results were consistent with the previous reports showing different cellulose contents between green and white upland cotton [G. raimondii and cultivated G. arboreum [Chemical analyses using cellulose assay, ATR FT-IR spectroscopy, and mass spectrometry consistently showed suberin and lignin components in the three short fibers. Average cellulose contents of ers Figs and 3B. d cotton and funcarboreum .G. raimondii and G. hirsutum Li1 and Li2 mutants demonstrated the signature IR spectral peaks of suberin and lignin than those of the other cultivated cotton fibers (0~ 0.6%). Recent studies suggest that lignin may play an important role in cotton fiber quality [The three short cottons of nin Figs and 5B. suberin . In natun fibers , 74, andn fibers . Suberinn fibers . In contn fibers . Generaln fibers . Our mas quality , 79.G. hirsutum Li1 (1623 cm-1), G. hirsutum Li2 (1610 cm-1), and G. raimondii D5 (1635 cm-1) Figs and 5B. -1) Figs .G. raimondii fibers, we used the RNA-seq data performed with the RNAs extracted from developing fibers of G. raimondii, G. arboreum, and G. hirsutum (Li1 and Li2) and their NIL DP-5690 were only performed with total RNAs extracted from developing fibers at PCW stage [G. raimondii fibers [G. raimondii D5 reference genome for analyzing transcriptomic profiles of the two sets because the G. raimondii genome sequence shows high homology (>96%) with the coding sequences of G. hirsutum AT and DT subgenomes. Thus, the D5 reference genome sequence has been successfully used for characterizing the Li1 and Li2 genomes by several groups [st set identified that genes involved in suberin and lignin biosynthesis were specifically expressed in G. raimondii fibers Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file."} +{"text": "Dear Editor,3. The intrinsic nature of MLKL and how it induces plasma membrane permeabilization, forming a huge pore or a channel, remain an interesting conundrum for a long time5. Our previous study demonstrated that MLKL forms cation channels and its channel activity is a primary effector of necroptosis6. In the field of MLKL, a major unsettled issue is, if MLKL does serve as channels, how it ignites the necrotic or non-necrotic pathogenic progresses5. Phosphatidylinositol 4,5-bisphosphate P2) is a necessary cofactor of various ion channels7. The physical interaction between MLKL and phosphatidylinositol phosphates (PIPs), including PIP2, facilitates MLKL-mediated liposome leakage and the necrotic membrane disruption10. These studies have been directed toward understanding whether PIP2 is a direct modulator for the MLKL channel activity. The potential effects of PIP2 on MLKL channels were thus evaluated electrophysiologically and the subsequent pathogenic influences were explored.Mixed lineage kinase domain-like protein (MLKL) emerged as executioner of necroptosisNT) is sufficient to induce oligomerization and trigger cell death9. Consistent with our previous study, MLKLNT protein exhibited channel activity, translocated onto plasma membrane, and caused cell death, similarly to full-length protein (MLKLFL) P2 was enhanced to 27.4% and phosphatidylinositol 3,5-bisphosphate P2), phosphatidylinositol 4-phosphate (PI(4)P), 1,4,5-trisphosphate inositol (IP3) and diacylglycerol (DAG), phosphatidylinositol 3,4,5-trisphosphate (PIP3)11. Among these lipids, PI(4)P is the only one that increases MLKL channel open probability P2. An increased concentration of PIP2 induced more frequent and larger currents of MLKL channel P2 levels in live cells. Stimulation of the M1 muscarinic receptor can activate PLC-\u03b2 which hydrolyzes PIP2. PLC-\u03b2-PH-GFP (PLC-PH) construct, a PIP2 reporter, is used to monitor the PIP2 distribution on plasma membrane12. Here, MLKL, M1 receptor, and PLC-PH were co-transfected into HEK293 cells. With 5\u2009\u03bcM oxotremorine M (Oxo-M) treatment, the PLC-PH probe dissociated from the plasma membrane to cytoplasm, showing PIP2 hydrolyzation in the N-terminal region of MLKL (MLKL)P2 Fig. . The ove.4% Fig. . These s.4% Fig. . Influenity Fig. . Collectnel Fig. . To furtion Fig. . Meanwhiion Fig. . These d2-induced augmentation of MLKL channel activity is correlated with cell death was examined. To elevate PIP2 concentrations in the plasma membrane, PIP5K, one of the key PIP2 biosynthetic enzymes, was transfected into L929 cells P. 1 Fig. . In addi. 1 Fig. . Similar2-sensitive ion channels, PIP2 binds with positive amino acid via \u201celectrostatic interaction\u201d13. We mutated the positive amino acids of MLKLNT to alanine and tested the channel activity P2 sensitivity or abrogate the capability of killing cells after overexpression of PIP5K, suggesting that K22 and R34 may interact with PIP2 independently P. 2 Fig. . Notably4%) Fig. . Whetherls9 Fig. . Consisttly Fig. .14. Thus, we further explored the potential function of PIP2-enhanced MLKL channel activity in an inflammation model12 through String database (https://string-db.org), and further revealed the close relationship between PIP2, MLKL and LPS-induced inflammation -like receptor protein 3 (NLRP3) in a cell-intrinsic manner before cell lysis, but its working model has not yet been clarifiedins Fig. . To inveion Fig. .+ efflux in triggering inflammation has been proposed15. We therefore hypothesized that K+ efflux during inflammation is mediated by MLKL channels. A real-time, sensitive FluxOR\u2122 assay was performed to monitor the K+ efflux during the LPS-induced inflammation. We found that the K+ efflux gradually increased in a time-dependent manner treated with LPS, Smac-mimetic compound (C) and a caspase inhibitor Q-VD-OPh (Q)14. Both the MLKL-mediated cytokine secretion and the LPS-induced K+ efflux were abrogated in MLKL-knockout (MLKL\u2013/\u2013) cells of LPS significantly stimulated the secretion of inflammatory cytokines, but did not induce cell death, while the expression level of MLKL and PIP5K increased Fig. . Accordiner Fig. . The conlls Fig. . Whetherels Fig. . Since e2 in a dose-dependent manner for the first time Pime Fig. . PIuli Fig. . WhetherSupplementary informationSupplementary Tabel S1"} +{"text": "Retraction of: Hua Liu, Jing Cheng, Heng Xu and Zhenzhen Wan. Lidocaine has antitumor effect on hepatocellular carcinoma via the circ_DYNC1H1/miR-520a-3p/USP14 axis. Open Life Sciences. Volume 16, Issue 1, doi: 10.1515/biol-2021-0072.https://doi.org/10.1515/biol-2021-0072) has been retracted due to the previously undisclosed conflict of interest between the authors. Authors apologize to the entire scientific community and Editorial team for any issues ensuant from this action.\u201cLidocaine has antitumor effect on hepatocellular carcinoma via the circ_DYNC1H1/miR-520a-3p/USP14 axis\u201d ("} +{"text": "Pandemic coronavirus causes respiratory, enteric and sometimes neurological diseases. Proteome data of individual coronavirus strains were already reported. Here we investigated of SARS-CoV-2 ssRNA and protein of spike, envelope and membrane to determine stress adaptation profile. Thermodynamic properties, Physicochemical behaviour and, amino acid composition along with their RMSD value was analysed. Thermodynamic index of SARS-CoV2 spike, envelope and membrane ssRNA is unstable in higher temperature. Presence of higher proportion of polar with positive and negative charged amino acid residues into spike (S), envelope (E) and membrane (M) protein indicate the lower stress adaptability pattern. Our study represented several unstable pockets into S, E and M proteins of SARS-CoV-2 against different abiotic stresses, specifically higher in spike protein. Contact with heat through solvent may denature the architectural network of SARS-CoV-2 spike, envelope and membrane ssRNA and structural protein. The stress instability index of SARS-CoV-2 and the interactome profile of its transmembrane proteins may help to reveal novel factors for inhibiting SARS-CoV-2 growth. Zoonotic beta coronaviruses can lead to severe acute respiratory syndrome or mild\u00a0pneumonia . Coronav. The envelope (E) protein of SARS-CoV-2 contains 76 to 109 amino acids with a small (7-12 amino acids) integral hydrophilic tail in C- terminal side; whereas the transmembrane portion having a large N-terminal domain with \u03b1 helical nature [Coronavirus structural proteins include the spike (S)protein, envelope (E)protein, membrane (M)protein, and nucleocapsid (N)protein , 7. The l nature , 22 The l nature . The M pl nature , 24, 25.SARS-CoV-2 assemble promotes by spike protein which may influence by the expression of envelope and membrane proteins. Additionally D814 to G814 mutation into spike protein of SARS-CoV-2 increases the attachment with host which results enhancing infectivity , 27. A LStudy design: Our study's objective to evaluate and build up stress stability and instability of SARS-CoV-2 based on the ssRNA along with extracellular and transmembrane protein. SARS-CoV-2 Spike ssRNA Sequence were primarily obtained from GENBANK Database. Accession number of SARS-CoV-2 Wuhan: MT079854.1, Alpha: MZ314997, Beta: MZ314998.1, Delta: OK091006.1, Gama: MZ315141.1 and Omicron: OL672836.1 were retrieve for analysis. We focused on the physicochemical and structural properties of these three (the spike (S) protein, envelope (E) protein, membrane (M) protein) protein structures available on the PDB database 6CRV, 5X29 and 3I6G accordingly.Stability index of SARS-CoV-2 ssRNA Secondary Structures: Vienna RNA Web Services (http://rna.tbi.univie.ac.at/) predicted the secondary structure of the RNAs of SARs-Cov-2 [Rs-Cov-2 , 33. In Rs-Cov-2 .Structural Simulation with diversity: Variant of concerns (VOCs) were reported by CDC i.e alpha, beta, gamma, delta, and omicron from the five most heavily affected countries also represented by \u201cNextstrain / ncov / open / global / 6m\u201d. The corresponding amino acid sequences were taken and modelled [0 with a single point charge (SPC) water model TIP3P with periodic boundary condition (PBC). Each protein was modeled using OPLS3e force where Na+ and Cl- ions were added to neutralize the charge. The system was energy minimized 2000 steps before a production run of 50 ns. RMSD and RMSF values of the backbone atoms of proteins were calculated for determining equilibrium parameters [modelled by usingmodelled . Using trameters . The RMSrameters .Amino acid frequency and structural elements: We computed the frequencies of amino acid residues in the protein sequences of the SARS-CoV-2 proteome by using MEGA [ing MEGA . Three mBased on the genomic organization, thermodynamics stability indexes of the SARS-CoV2 was analysed . Virus sThe thermodynamic parameters for the SARS-CoV2 single-stranded RNA are as follows: N-terminal domain (NTD), Receptor binding domain (RBD), Fusion protein (FP), Heptapeptide Repeat 1 (HR1), Heptapeptide Repeat 2 (HR2), Transmembrane region (TM), Cytoplasmic domain (CD), Envelope (E) and Membrane (M) the melting temperature were resulted 70.5 \u00b0C, 72.7\u00b0C, 87.8\u00b0C, 70.9\u00b0C, 72.6\u00b0C, 70.5\u00b0C, 70.9\u00b0C, 74.6\u00b0C, 73.3\u00b0C; whereas the Gibbs free energy were tabulated -196.46 kcal/mol,-113.8 kcal/mol,-11.2 kcal/mol, -42.8 kcal/mol, -29.3 kcal/mol, -19.8 kcal/mol, -28.1 kcal/mol, -54.7 kcal/mol and, -180.4 kcal/mol; similarly enthalpy were studied -2011.7 kcal/mol, -1101.5 kcal/mol, -79.5 kcal/mol, -433.7 kcal/mol, -248.5 kcal/mol, -202.9 kcal/mol, -284.5 kcal/mol, -531 kcal/mol and, -1720.8 kcal/mol; the entropy were resulted -5852.7 cal/mol, -3184.5 cal/mol, -220.2 cal/mol, -1260.3 cal/mol, -822.8 cal/mol, -590.3 cal/mol, -826.6 cal/mol, -1535.7 cal/mol and, -4966.6 cal/mol. These parameters indicate that the SARS-CoV2 ssRNA is unstable accordingly .Amino acid usage patterns are influenced by natural selection pressure at the protein structural stability level; we have compared the amino acids robustness in the chosen proteome which are the most dominant factor in determining stability. Structural comparisons reveal that S, M & E of all the VOC\u2019s are similar. RMSD value of Spike, Membrane and Envelope 0.022\u00b10.01, 0.068 and 0.055 accordingly. Furthermore, some of the propensities of non polar amino acids with polar amino acids ( i.e Thr and Ser) were higher in the case of S protein; whereas, the opposite was noticssed in E and M protein (Supplementary Table S2). The polar, non-polar, positive and negative charge amino acids distribution were plotted and displayed into the peptide of spike , envelop).The spike protein interface exhibits five thermo-unstable cavity that buries residues 155, 247, 248 250, 254 and 258 in pocket1, pocket2 and pocket3 represented turn structure whereas pocket4 and pocket5 exhibited sheet structure . Thermo-Fig. 3FE-protein represented several stress unstable and stable complexes. The heat unstable complex, pocket1 and pocket2 both have helix structure . WhereasM-protein interface cavity consistently contained cavities, few of them was stress unstable with stable pockets. The heat unstable complex; pocket1 showed sheet structure whereas pocket2 displayed helix structure . ThermosBiothermodynamics\u00a0is\u00a0the\u00a0exploration\u00a0of\u00a0the\u00a0forces\u00a0and\u00a0processes\u00a0that\u00a0cause\u00a0biological occurrence Gibbs\u00a0energy\u00a0is\u00a0the\u00a0driving\u00a0force\u00a0behind\u00a0all\u00a0natural\u00a0processes. The Gibbs free energy in growth is influenced by the chemical constitution of the organism and also depends on the environment, especially intermolecular interactions between reaction participants. By taking over the host translation machinery , virusesSTn) pockets and two stable (PST) pockets against heat, two unstable (PSALn) and four stable (PSAL) pockets against alkali, two unstable (PSAn) and stable (PSA) pockets against acidic conditions (ETn) pockets and one stable (PET) pocket against heat, one unstable and two stable pockets against alkali with an acidic condition pockets and one stable pocket against heat and acidic conditions; similarly it also represented one unstable (PMALn) and stable (PMAL) pocket against alkaline conditions in the interaction site of human ACE2 with SARS-CoV-2 spike protein (Supplementary Table S3), which may be considered for further studies for the development of a new efficient anti-corona drug [Spike protein of SARS-CoV-2 binds significantly to human ACE2, TMPRSS2 and CD26 are already reported through several amino acid residual interactions. We found a heat unstable pocket (Pona drug , 48. Theona drug , 50. OurWe thank the Oriental Institute of Science and Technology, India for supporting our work.The authors declare that they have no conflict of interest.Supplementary Material 1Supplementary Material 2"} +{"text": "There are limited data on the prevalence of doravirine (DOR)-associated drug resistance mutations in people with HIV (PWH) in Botswana. This cross-sectional, retrospective study aimed to explore the prevalence of DOR-associated resistance mutations among ART-na\u00efve and -experienced PWH in Botswana enrolled in the population-based Botswana Combination Prevention Project (BCPP).pol sequences were analysed for DOR-associated resistance mutations using the Stanford HIV drug resistance database, and their levels were predicted according to the Stanford DRM penalty scores and resistance interpretation. Virologic failure was defined as HIV-1 RNA load (VL) >400 copies/mL.A total of 6078 HIV-1C P < 0.01). Intermediate DOR-associated resistance mutations were observed in 106/1261 (7.8% [95% CI: 6.9\u201310.1]) in ART-na\u00efve individuals and 29/212 (13.7% [95% CI: 9.4\u20138.5]) among ART-experienced participants (P < 0.01). High-level DOR-associated resistance mutations were observed in 33/1261 (2.6% [95% CI: 1.8\u20133.7]) among ART-na\u00efve and 13/212 (6.1% [95% CI: 3.6\u201310.8]) among ART-failing PWH (P < 0.01). PWH failing ART with at least one EFV/NVP-associated resistance mutation had high prevalence 13/67 (19.4%) of high-level DOR-associated resistance mutations.Among 6078 PWH, 5999 (99%) had known ART status, and 4529/5999 (79%) were on ART at time of sampling. The suppression rate among ART-experienced was 4517/4729 (96%). The overall prevalence of any DOR-associated resistance mutations was 181/1473 ; by ART status: 42/212 (19.8% [95% CI: 14.7\u201325.4]) among ART-failing individuals (VL \u2265400 copies/mL) and 139/1261 (11.0% [95% CI: 9.3\u201312.9]) among ART-na\u00efve individuals (DOR-associated mutations were rare (11.0%) among ART-naive PWH but present in 62.7% of Botswana individuals who failed NNRTI-based ART with at least one EFV/NVP-associated resistance mutation. Testing for HIV drug resistance should underpin the use of DOR in PWH who have taken first-generation NNRTIs. The avaA newly approved third-generation NNRTI, doravirine (DOR), has been shown to be more potent, with distinct resistance patterns compared to the earlier-generation NNRTIs 22.1PWH aged 16\u201364 years in 30 communities in northern, central and southern parts of Botswana participated in the Botswana Combination Prevention Project (BCPP) between 2013 and 2018 2.2In this analysis, we included PWH who were either ART-na\u00efve or ART-experienced, who had HIV-1 viral load (VL) measurement at the first BCPP study visit and had available HIV-1 sequence. HIV-1 VL of participants was quantified using Abbott m2000sp/rt assay with a range of 40\u201310 000 000 copies/mL 2.3https://genome.med.harvard.edu/) and through collaboration with PANGEA HIV consortium www.sanger.ac.uk/) with high-sequencing coverage using Illumina platforms MiSeq and HiSeq Both HIV-1 proviral DNA sequences and viral RNA sequences were generated by a long-range HIV genotyping protocol described elsewhere ,23. The 2.4Generated near full-length HIV-1 sequences were subtyped by online tools REGA version 3 2.5https://hivdb.stanford.edu/hivdb/by-sequences/). The level of DOR resistance was predicted according to the Stanford HIV DRM penalty scores and resistance interpretation . Only intermediate and high-level specific DOR-associated resistance mutations were reported. The list of mutations assessed are shown in DOR-associated resistance mutations were identified according to the lists of surveillance drug resistance mutations and major drug resistance mutations (DRMs) in the Stanford University HIV Drug Resistance Database algorithm 9.1 overall; (ii) ART-na\u00efve individuals; (iii) virologic failure (VF) on ART; and (iv) viral suppression (HIV-1 RNA \u2264400 copies/mL) on ART. The DOR prevalence was compared between groups (ii) and (iii), as well as between groups (iii) and (iv). The prevalence of specific DOR-associated resistance mutations was estimated within each group and compared among groups. We also assessed the presence of DOR-associated resistance mutations in a subset of participants on NNRTI-based regimens with at least one major efavirenz (EFV)/nevirapine (NVP)-associated resistance mutation .2.6http://www.hiv.lanl.gov/) pol gene. The adjustment for hypermutations was performed before the drug resistance analysis, as a part of quality control. HIV DRMs identified as hypermutations were not included in the prevalence of DOR resistance in this study.Guanine-to-adenine transitions (G-to-A) apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC)-induced hypermutations were screened in the viral sequences using the Hypermut program available in Los Alamos National Laboratory HIV Database tools in NNRTI-failing individuals with at least one EFV/NVP-associated resistance mutation for detection of DOR-associated resistance mutations. A P value <0.05 was considered statistically significant. All the statistical analysis was done using STATA version 14 software.Patient demographics between ART-na\u00efve and individuals on ART experiencing VF were compared using Wilcoxon rank-sum test for continuous variables such as plasma log2.8The BCPP study was approved by the Institutional Review Board (IRB) at the U.S. Centers for Disease Control and Prevention and the Botswana IRB (HRDC), and it is registered at ClinicalTrials.gov (NCT01965470). All recruited participants provided written informed consent for participation.33.110 copies/mL) was similar to the median HIV-1 VL among individuals experiencing VF on ART . The study entry demographics of BCPP participants stratified by HIV-1 VL groups are in The median age at enrolment of the participants included in this analysis was 34 years , and study participants were mostly women (66%). Among 6078 participants, 5999 (99%) had known ART status (either \u2018on ART\u2019 or \u2018ART-naive\u2019). The majority of these participants, 4738 (79%), were on ART, whereas 1261 (21%) were ART-na\u00efve at the time of sampling. Among 4738 participants, a total of 4729 had HIV-1 VL data; 4517 (96%) were virally suppressed (HIV-1 VL \u2264400 copies/mL). The median HIV-1 VL among ART-na\u00efve individuals . A majority of the participants harboured intermediate DOR-associated resistance mutations with a lower prevalence of 106/1261 (7.8% [95% CI: 6.9\u201310.1]) in ART-na\u00efve individuals and 29/212 (13.7% [95% CI: 9.4-19.1]) among ART-experienced participants (P < 0.01). The prevalence of high-level DOR-associated resistance mutations was 33/1261 (2.6% [95% CI: 1.8\u20133.7]) among ART-na\u00efve individuals and 13/212 (6.1% [95% CI: 3.6\u201310.8]) among individuals experiencing VF on ART (P < 0.01). Of the two intermediate DOR-associated mutations reported in the study (V106M and Y188F), V106M was the most predominant mutation, 12/1473 (0.8%), and was common among individuals experiencing VF on ART 7/212 (3.3%) (P < 0.01). Seven high-level DOR-associated mutations predicted were V106A, Y188L, F227L and M230L, which occurred in 2/1473 (0.14%) participants, F227C and Y318F in 1/1473 (0.07%) each and the G190E 33/1473 (2.2%), which was the most predominant mutation. The prevalence of specific DOR-associated resistance mutations stratified by ART groups are summarized in A total of 1473 participants with viremia were analysed for DOR-associated resistance mutations. Of these, 1261 were ART-na\u00efve, whereas 212 were individuals experiencing VF on ART with HIV-1 VL >400 copies/mL. The overall prevalence of participants with DOR-associated resistance mutations was 181/1473 (12.3% [95% CI: 10.7\u201314.1]). Higher overall prevalence of DOR-associated resistance mutations was reported among individuals experiencing VF on ART, which was 42/212 (19.8% [95% CI: 14.7\u201325.4]) compared to 139/1261 (11.0% [95% CI: 9.3\u201312.9]) in the ART-na\u00efve population were failing ART with at least one EFV/NVP-associated resistance mutation. A total of 42/67 (62.7% [95% CI: 50.0\u201374.2]) had a combination of DOR- and EFV/NVP-associated resistance mutations. The overall prevalence of intermediate DOR-associated resistance mutations was 29/67 (43.3% [95% CI: 31.2\u201356.0]) in this group, whereas the high-level DOR resistance was reported in 13/67 (19.4% [95% CI: 10.8\u201330.9]). Mutation V106M (7/67:10.4%) was the most predominant intermediate mutation, followed by Y188F. In the high-level resistance group, G190E was the most prevalent at 3/67 (4.5%), followed by equal proportions of V106A and M230L mutations at 2/67 (3.0%), and, lastly, F227C, F227L and Y318F, all occurring at a prevalence of 1/67 (1.4%) each. Individuals without EFV/NVP-associated resistance mutations had no DOR-associated resistance. Among 67 participants with at least one major EFV/NVP-associated resistance mutation, 38 had dual resistance with at least one major NRTI-associated resistance mutation. The prevalence of DOR-associated resistance mutations was higher in this group: 29/38 (76%) overall prevalence, 21 (55%) intermediate and 8 (21.1%) high-level resistance.3.410 copies/mL were not associated with DOR-associated resistance mutations in a small population of 67 participants . The prevalence of intermediate DOR resistance was 735/4517 (16.3% [95% CI: 15.2\u201317.4]) among individuals with viral suppression on ART vs 29/212 (13.7% [95% CI:9.4\u201319.1]) among individuals with VF on ART (P\u00a0=\u00a00.32) and high-level DOR resistance was 175/4517 (3.9% [95% CI: 3.3\u20134.5]) and 13/212 (6.1% [95% CI: 3.3\u201310.3]) among individuals with viral suppression and those experiencing VF on ART, respectively (P\u00a0=\u00a00.11), were not statistically different in the ART-experienced population. Mutations reported in the two groups were G190E (161/4729:3.4%), V106M (21/4729:0.4%), F227L (7/4729: 0.15%), Y188L (6/4729: 0.13%), Y318F (5/4729: 0.11%), V106A and M230L were 4/4729 (0.08%) each and F227C (4/4729: 0.04%). The prevalence of DOR-associated mutations is stratified by individuals with viral suppression and VF on ART in Supplementary Table S1.We also compared the prevalence of HIV-DRMs associated with DOR resistance among individuals with viral suppression on ART (HIV-1 VL \u2264400 copies/mL) compared to individuals experiencing VF on ART. The overall prevalence of mutations associated with DOR resistance was similar among individuals with viral suppression on ART, 910/4517 (20.1% [95% CI: 19.0\u201321.3]), compared to 42/212 (19.8% [95% CI: 14.7\u201325.8]) among those experiencing VF on ART (P < 0.01).Of all the 1091 participants with DOR-associated resistance, 230 (21.1% [95% CI: 18.7\u201323.6]) are likely to have specific DOR-associated resistance mutations and 861 (78.9% [95% CI: 76.4\u201381.3]) with nonspecific DOR-associated resistance mutations. Among 861 with nonspecific DOR-associated resistance mutations, 850 (98.7% [95% CI: 97.7\u201399.4]) and 11 (1.3% [95% CI: 0.6\u20132.3]) had intermediate and high-level DOR-associated resistance, respectively , confirming the opportunity for the use of DOR-containing regimens among PWH who are ART-na\u00efve in Botswana. However, the prevalence of DOR-associated resistance among ART-na\u00efve individuals (11.0%: 139/1261) in this study was statistically higher than the 2.9% prevalence of other NNRTI (first-generation)-associated resistance mutations previously reported in the BCPP study P < 0.01). Some studies reported higher resistance to other NNRTI-containing regimens when compared to DOR. A study from Greece, Italy and France reported a lower prevalence of DOR-associated resistance (1.4%) compared to first-generation NNRTI-associated resistance , with no association between HIV-1 subtype and presence of DOR-associated resistance mutations A significantly lower overall prevalence of DOR-associated resistance was reported among ART-na\u00efve compared to individuals experiencing VF on ART of DOR-associated resistance mutations was among participants failing NNRTI-based therapy in our findings, this was lower when compared to 84.8% reported in a South African study The high-level DOR-associated resistance mutations G190E, F227L and Y318F all showed a similar prevalence among the three groups: ART-naive, individuals with VF, and individuals on ART with viral suppression. The similar prevalence of these mutations across the three groups highlights the importance of gaining a better understanding of their mechanisms, particularly in ART-na\u00efve and ART-suppressed individuals. It was difficult to determine if the presence of these mutations in ART-na\u00efve individuals was due to undisclosed ART use in the BCPP cohort EFV has been associated with an increased risk of developing high-level DOR-associated resistance mutations Because our study had a small number of participants on DTG-based ART, our findings cannot reveal whether DOR can be used as an alternative drug for DTG-failing participants with multi-resistance mutations. As a result, future studies should investigate DOR-associated resistance mutations in DTG-failing participants with multi-drug resistance.In conclusion, the prevalence of intermediate and high-level DOR-associated resistance mutations was low among ART-na\u00efve and ART-failing individuals, with the ART-failing group showing a statistically higher prevalence compared to the ART-na\u00efve group. Specifically, a higher prevalence was observed among PWH with EFV/NVP-associated resistance experiencing VF. Our results support the use of DOR among ART-na\u00efve patients in Botswana; however, we highly recommend HIV drug resistance testing among NNRTI-failing individuals before DOR-based regimen initiation.None declared."} +{"text": "Scientific Reportshttps://doi.org/10.1038/s41598-022-10197-w, published online 15 April 2022Correction to: The original version of this Article contained an error in the References. The authors omitted the below Reference, which is listed below as Reference 50.et al. Adsorptive purification of CO2/H2 gas mixtures of spent disposable wooden chopstick-derived activated carbon: Optimal synthesis condition. Sep. Purif. Technol.291, 120948 (2022).50. Phadungbut, P. As a result, in the caption of Figure 1 (a),\u201cRepresentative SEM images (left) and HRTEM images (right) of the (a) biochar, (b) AC7-2 and (c) AC9-2 samples.\u201dnow reads:50, (b) AC7-2 and (c) AC9-2 samples.\u201d\u201cRepresentative SEM images (left) and HRTEM images (right) of the (a) biocharAs a result of the changes, the References have been renumbered.The original Article has been corrected."} +{"text": "The SARS-CoV-2 Omicron variant has been rapidly spreading worldwide. We aimed to characterize Omicron severity by assessing in-hospital deaths and intensive care admissions in a large healthcare system in South Florida during an Omicron predominant surge.Laboratory-confirmed COVID-19 adult patients hospitalized during January 1\u201414, 2022 were retrospectively reviewed. Risks of in-hospital mortality and intensive care admission were estimated using logistic regression models. Analyses were stratified by age \u2265 65 years and vaccination status, and further adjusted for sex, comorbidities, and history of a previous COVID-19 infection.p< 0.001), with the median time from hospital admission to death being 13 days . Patients aged \u2265 65 years had 2.6 times higher rates for in-hospital mortality than those aged < 65 years, but were comparable for ICU admission . Past vaccination offered no protection against in-hospital mortality or ICU admission . In multivariable-adjusted models, patients aged \u2265 65 years had a higher in-hospital mortality than those aged < 65 years .500 consecutively hospitalized COVID-19 Omicron patients were included. The median age was 69 years, and 271 (54.2%) were women. The most common comorbidities were hypertension (65.5%), diabetes (32%), and chronic kidney disease (24%). 260 (52%) patients were fully vaccinated (defined as a patient who received 2-dose vaccines), and 32 (6.4%) were previously infected with COVID-19. 252 (50.4%) patients required supplemental oxygen, 54 (10.8%) required intensive care unit (ICU) admission, and 44 (8.8%) patients required mechanical ventilation. At study closeout of March 7, 2022, case fatality rates among patients aged 18\u201329 years, 30\u201339 years, 40-49 years, 50-59 years, 60-69 years, 70-79 years, and \u2265 80 years were 0%, 2.2%, 6.4%, 5.3%, 8.0%, 5.7%, and 15.4% respectively (This case series provides characteristics and outcomes of hospitalized adult patients with COVID-19 Omicron variant. Past COVID-19 vaccination did not impact ICU admission rate nor in-hospital mortality.All Authors: No reported disclosures."} +{"text": "To explore why these standard treatments fail for some patients, we evaluated whether the variation in HPV oncoprotein levels among HPV+ OPSCCs affects mitochondrial metabolism, a source of antioxidant capacity. In cell line and patient-derived xenograft models, levels of HPV full-length E6 (fl-E6) inversely correlated with oxidative phosphorylation, antioxidant capacity, and therapy resistance, and fl-E6 was the only HPV oncoprotein to display such correlations. Ectopically expressing fl-E6 in models with low baseline levels reduced mitochondrial mass, depleted antioxidant capacity, and sensitized to therapy. In this setting, fl-E6 repressed the peroxisome proliferator\u2013activated receptor gamma co-activator 1\u03b1/estrogen-related receptor \u03b1 (PGC-1\u03b1/ERR\u03b1) pathway for mitochondrial biogenesis by reducing p53-dependent PGC-1\u03b1 transcription. Concordant observations were made in 3 clinical cohorts, where expression of mitochondrial components was higher in tumors of patients with reduced survival. These tumors contained the lowest fl-E6 levels, the highest p53 target gene expression, and an activated PGC-1\u03b1/ERR\u03b1 pathway. Our findings demonstrate that E6 can potentiate treatment responses by depleting mitochondrial antioxidant capacity and provide evidence for low E6 negatively affecting patient survival. E6\u2019s interaction with the PGC-1\u03b1/ERR\u03b1 axis has implications for predicting and targeting treatment resistance in OPSCC.Therapy with radiation plus cisplatin kills HPV PGC-1\u03b1 (PGC-1\u03b1) . Our fin+ OPSCCs with survival outcomes annotation. In The Cancer Genome Atlas (TCGA), RNA-Seq data are available from 53 OPSCCs that express high-risk HPV transcripts and intermediate tertiles (P = 0.043) (+ OPSCC cohort (n = 47) into tertiles by the identical methodology used for TCGA cases (P = 0.048). Wide variation in therapy was apparent from characteristics of the JHU and TCGA cohorts (https://doi.org/10.1172/jci.insight.159600DS1), making the relationship between survival and response to radiation plus chemotherapy unclear. Thus, we examined a subcohort of patients within the broader VU HPV+ OPSCC cohort (n = 37). Despite small sample size, dividing these cases into tertiles revealed better 3-year OS (P = 0.041) in the lowest versus the highest tertile . This fiC cohort . DividinGA cases showed bC cohort who rece tertile . This as+ OPSCC PDX models previously established by us from treatment-naive patients mice showed a positive linear correlation with mitochondrial mass defined by MT-CO1/B2M ratio using the Cell Mito Stress Test on the Seahorse XF platform. A strong positive correlation was shown between mitochondrial mass and basal OCR in the cell lines and cell line models for prediction of increased mitochondrial mass, mitochondrial function, and cisplatin response. RNA-Seq was performed for the 7 HPVpatients . Upregulrd curve . The hig E6, E7) . This as E6, E7) . No othe E6, E7) . Althougial mass , whereasial mass . Similarll lines , whereasll lines . These f+ head and neck cancer lines with highest mitochondrial mass and lowest fl-E6 (SDHB (complex II), UQCRC2 (complex III), MTCO2P12 (complex IV), ATP5F1A (complex V), ACADM (acyl-CoA dehydrogenase medium chain-1), and MDH1 were reduced by fl-E6 overexpression (tert/1 keratinocytes expressing E7 (N-tert/E7 keratinocytes) , and theenase-1) . Similarpression . To detenocytes) . Three bnocytes) , F and Gnocytes) , H and I-CO1/B2M and basa-CO1/B2M . Increas and Broad GDAC Firebrowse repository. A total of 53 HPVpression . RNA-Seqescribed . RNA-SeqU cohort .n = 53) were aligned to HPV genomes using Bowtie2 and samples with alignment selected and identified as containing HPV 16, HPV 33, HPV 35, or HPV 56 genomes. Gene expression values were represented by the normalized reads of reads per kilobase of transcript per million mapped reads. HPV genome sequences and annotations with gene coordinates were obtained from RefSeq (https://www.ncbi.nlm.nih.gov/refseq/). Reads with mapped coordinates corresponding to regions specific for each gene were counted. Fl-E6 expression was quantitated in a region nonoverlapping with E6*. The probe region specific to E6* overlaps fl-E6 and thus represents total E6. E6* is calculated by subtracting fl-E6 from total E6. HPV 16 gene expression analysis used GenBank K02718.1, with the following gene coordinates for quantitation: E6: 227-408, total E6: 83-226, E7: 562-858, E2: 2814-3331, E4: 3332-3619, and E5: 3863-4099. HPV 33 gene expression analysis used GenBank M12732.1, with the following gene coordinates for quantitation: E6: 232-413, total E6: 109-230, E7: 573-866, E2: 2814-3325, E4: 3326-3577, and E5: 3854-4081. HPV 35 gene expression analysis used GenBank X74477.1, with the following gene coordinates for quantitation: E6: 233-414, total E6: 110-231, E7: 562-861, E1: 868-2713, E2: 2882-3293, E4: 3294-3584, and E5: 3814-4065. HPV 56 gene expression analysis used GenBank: X74483.1, with the following gene coordinates for quantitation: E6: 234-415, total E6: 102-232, E7: 572-889, E2: 2806-3221, E4: 3222-3577, and E5: 3854-4081.RNA-Seq reads within FastQ files for each TCGA OPSCC sample . Ribosomal RNA depletion was performed with Ribo-zero rRNA Removal Kit, HMR (Illumina Inc.). Library preparation was performed with the NEBNext Ultra II Non-directional Synthesis Module (New England Biolabs). Samples were sequenced on Illumina NextSeq High Output sequencer and aligned to combined genome from hg38 (human), mm10 (mouse), and the high-risk HPV genomes \u2014 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 \u2014 using STAR with default parameters. HPV sequences in all samples mapped to HPV 16 exclusively. After STAR first-pass alignment, reads mapped to mm10 were removed, and reads aligned to human genome (hg38) and HPV genomes were retained. Raw counts for each viral transcript were obtained from reads mapped to each gene based on the alignment file. Fl-E6 was computed as the ratio of the average coverage level in the first intron (approximate full-length E6 level) divided by the average coverage level in the first exon . RnaSTAR was used to identify the first introns for E6*, which are, in the format of donor-acceptor, 227-408 for HPV 16. The average coverage of read pairs within the intron was divided by the average coverage of read pairs within exon1 , where coverage was computed by dividing the number of reads by the feature width. RNA-Seq data reported here were submitted to National Center for Biotechnology Information Gene Expression Omnibus (GSE193388).The 7 treatment-naive HPVNSG mice . The PDX\u2013/\u2013 (RRID:CVCL_HD97) cells are from ATCC. UM-SCC047 (RRID:CVCL_7759) and UMSCC104 (RRID:CVCL_7712) are from Sigma-Aldrich. UDSCC2 (RRID:CVCL_E325) and 93VU147T (RRID:CVCL_L895) cell lines were gifts from Silvio Gutkind and Hans Joenje , respectively. Cell lines were authenticated using the Identify Mapping Kit (Coriell). They were cultured in DMEM-F12 (Gibco), 10% heat-inactivated FBS, 1% penicillin-streptomycin, and 1% nonessential amino acids. N/tert-1/E7 cells were cultured in keratinocyte serum-free medium (Thermo Fisher Scientific).SCC090 (RRID:CVCL_1899), SCC152 (RRID:CVCL_0113), SCC154 (RRID:CVCL_2230), HEK293(RRID:CVCL_0045), HCT116 (RRID:CVCL_0291), and HCT116 p53Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN). DNase I was used to remove genomic DNA from RNA samples. Reverse transcription was performed with oligo-dT plus random decamer primers using Superscript II (Thermo Fisher Scientific). QRT-PCR was performed with SYBR green master mix (Thermo Fisher Scientific) using Step-one Plus Real-Time PCR. Primers are in Fl-E6 was expressed transiently using the pLentiN-16E6no* plasmid (RRID:Addgene_37445) and its pLentiN vector control (RRID:Addgene_37444). Transient PGC-1\u03b1 overexpression was achieved with the pcDNA4 PGC-1\u03b1 plasmid (RRID:Addgene_10974). A total of 4 \u03bcg of each plasmid was delivered per well in 6-well plates using Lipofectamine 2000 (Thermo Fisher Scientific) and incubated for 72 hours. SiRNA silencing of PGC-1\u03b1 was performed using the mix of the 3 validated targeting siRNAs and scrambled negative control included in the PPARGC1A TriFECTa DsiRNA Kit (IDT) per supplier instructions. SiRNA was delivered at 50 nM concentration per well in 6-well plates using Lipofectamine RNAiMax (Thermo Fisher Scientific) and incubated for 72 hours.tert-E7 cells were similarly infected with the control and E6 viruses before blasticidin selection, propagation, and analysis of bulk cultures.The pLentiN-16E6no* plasmid containing full-length E6 and its pLentiN vector backbone control were used for stable fl-E6 expression. Lentiviral preparation and transduction were performed as described . BrieflyHPV 16 E6 mutant constructs 16E6, 16E6 (V42L), 16E6-8S9A10T, 16E6-I128T, and 16E6* are previously described . The pGLp-trifluoro-methoxyphenyl hydrazone, and 2 \u03bcM each of antimycin and rotenone (Sigma-Aldrich). Total protein per well was determined afterward with the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific). Results were analyzed using XFe Wave software (Seahorse Bioscience), and 1 \u00d7 105 cells were used to measure NADPH and NADP+ levels using an NADP+/NADPH colorimetric quantitation kit (Sigma-Aldrich).Mitochondrial DNA content was determined by qPCR as described . OCR wasCell viability after 72-hour treatment with cisplatin, DMNQ, MnTMPyP, and/or MitoTEMPO (Sigma-Aldrich) was determined by WST-1 and/or BrdU assays (Sigma-Aldrich). Cisplatin dissolved in saline was administered intraperitoneally in vivo at 2 mg/kg. For irradiation, cells were harvested during exponential growth and plated at 2,000 cells/mL in 60 mm dishes containing 2 mL media. After 12 hours, they received 2, 4, or 6 Gy using a Gammacell 40 irradiator (Best Theratronics). Media were changed postirradiation. Colonies were stained with crystal violet (Thermo Fisher Scientific) and counted 10 days later.t tests. Pearson correlation coefficients were based on analyzing the means. Two-way ANOVA was used when comparing xenograft growth curves. Log-rank tests were used for Kaplan-Meier analyses. P values were calculated for multiple comparisons using a 1-way ANOVA corrected with Dunnett\u2019s or Holm-\u0160id\u00e1k procedure. Tests used are indicated in figure legends. Analyses were performed using Prism (GraphPad Software). A P value less than 0.05 was considered significant.When comparing 2 groups for cell viability or gene expression, significance was calculated using 2-tailed unpaired Mouse experiments were performed under Wistar Institute IACUC protocols 201166 and 201178 . PDXs were previously established under University of Pennsylvania IRB-approved protocol 417200 \u201cHead and Neck Cancer Specimen Bank\u201d by signing a combined informed consent and HIPAA form for use of tissue for research. All clinical data shown are obtained from deidentified, publicly available data sets.MKS and DB conceived the study. DB, MKS, EAW, IMM, and BEW wrote and edited the manuscript and/or designed figures and tables. MKS, PR, LL, and VS performed experiments. PAG, PR, MKS, XW, XL, and BEW performed bioinformatic and/or statistical analyses. DB, EAW, PAG, DPK, and HN supervised the study and data analysis. DB, JBJ, RMB, XW, and XL analyzed clinical and/or pathologic data. All authors read and approved the final manuscript."} +{"text": "H)-one represents a new template for AKA inhibitors, with antiproliferative activity against cancer cells. A quinazolin-4(3H)-one derivative was further designed and synthesized in order to improve the pharmacokinetic properties and antiproliferation activity against NSCLC cell lines. The derivative, BIQO-19 (Ethyl 6-(4-oxo-3-(pyrimidin-2-ylmethyl)-3,4-dihydroquinazolin-6-yl)imidazo pyridine-2-carboxylate), exhibited improved solubility and antiproliferative activity in NSCLC cells, including epidermal growth factor receptor\u2013tyrosine kinase inhibitor (EGFR-TKI)-resistant NSCLC cells. BIQO-19 effectively inhibited the growth of the EGFR-TKI-resistant H1975 NSCLC cells, with the suppression of activated AKA (p-AKA) expression in these cells. The inhibition of AKA by BIQO-19 significantly induced G2/M phase arrest and subsequently evoked apoptosis in H1975 cells. In addition, the combination of gefitinib and BIQO-19 exhibited synergistic antiproliferative activity in NSCLC cells. These findings suggest the potential of BIQO-19 as a novel therapeutic agent for restoring the sensitivity of gefitinib in EGFR-TKI-resistant NSCLC cells.Non-small cell lung cancer (NSCLC) is the most common lung cancer subtype. Although chemotherapy and targeted therapy are used for the treatment of patients with NSCLC, the survival rate remains very low. Recent findings suggested that aurora kinase A (AKA), a cell cycle regulator, is a potential target for NSCLC therapy. Previously, we reported that a chemical entity of quinazolin-4(3 Lung cancer is the leading cause of death from cancer, and constitutes almost 25% of all cancer-related deaths . Lung caAurora kinase is a serine/threonine kinase which plays an important role in cell cycle regulation . The higH)-one is a well-known core heterocycle pharmacophore used in medicinal chemistry that exhibits a variety of biological activities, including sedative, antiviral, antibacterial, anti-inflammatory, and anticancer effects pyridine-2-carboxylate) as an FL-4 derivative (H)-one derivative FL-4 +. Compound 5, 6-(6-aminopyridin-3-yl)-3-(pyrimidin-2-ylmethyl)quinazolin-4(3H)-one, was obtained as a white solid, yield 83.4%, ESI-MS: m/z 331.1 [M + H]+. BIQO-19 was separated as white crystals, yield 87.4%, m.p. 284\u2013286 \u00b0C. 1H-NMR \u03b4 8.68 , 8.49 , 8.41 , 8.24 , 8.21 , 7.96 , 7.86 , 7.76 , 7.57 , 7.23 , 5.45 , 4.46 , 1.44 . 13C-NMR \u03b4 164.50, 163.17, 161.06, 157.58, 148.15, 147.78, 144.54, 137.61, 135.54, 132.70, 128.76, 126.98, 126.59, 125.0, 123.8, 122.9, 120.2, 119.3, 117.6, 61.4, 51.7, 14.5. HRMS (ESI-QTOF) m/z Calcd. For C23H19O3N6 [M + Na]+ m/z: 449.1333, found: 449.1324. NMR and high resolution mass spectras are shown in The synthesis of the compound BIQO-19 is summarized in Culture media, fetal bovine serum, antibiotic-antimycotic solution , and trypsin-EDTA solution (1\u00d7) were purchased from Gibco . Gefitinib (CAS No. HY-50895) was purchased from MedChemExpress . Trichloroacetic acid (TCA), sulforhodamine B (SRB), crystal violet solution, and bovine serum albumin (BSA) were purchased from Sigma-Aldrich . Anti-aurora kinase A (#14475), anti-p-aurora kinase A (T288) (#3079), anti-p21 Waf1/Cip1 (#2947), anti-cdc2 (#9116), anti-cdc25C (#4688), anti-PARP (#9532), anti-Cleaved PARP (D214) (#5625), anti-Caspase-8 (#9746), and anti-Cleaved Caspase-8 (D374) (#9496) antibodies were obtained from Cell Signaling Technology .The ADMET properties of the FL-4 and BIQO-19 compounds were calculated with the ADMET descriptors of Discovery Studio 3.0. The ADMET descriptors parameter was set as the default. Each of the ADMET profile levels were categorized by following the criteria. ADMET_Solubility_Level: 0 < \u22128.0), 1 < \u22126.0), 2 < \u22124.1), 3 < \u22122.0), 4 \u2264 0.0), 5 ), 6 (warning: molecules with one or more unknown AlogP98 types). ADMET_BBB_Level: 0 , 1 , 2 , 3 , 4 (undefined).2.The human non-small lung cancer cell lines A549, NCI-H1975, NCI-H1299, and NCI-H1993 were purchased from the American Type Culture Collection . The human non-small cell lung cancer cell lines HCC827, PC9, HCC827-gef and PC9-gef were a kind gift from Dr. Jae Cheol Lee and Dr. Jin Kyung Rho . HCC827-gef and PC9-gef cells were subcultured in the presence of 1\u2009\u00b5M gefitinib. All cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic. Cells were incubated at 37 \u00b0C in a humidified atmosphere with 5% COw/v) SRB in 1% acetic acid for 2 h at room temperature. The stained proteins were dissolved in 10 mM Tris solution (pH 10) and measured the absorbance at 515 nm with a VersaMax ELISA microplate reader .Cell viability was measured using the SRB method as described previously . BrieflyCells (500 cells/well) were seeded and cultured overnight. The compounds were treated for 48 h, the cells were washed with phosphate buffered saline (PBS), and continued incubation. Culture medium was replaced every three days for ten days. Cells were fixed with 4% paraformaldehyde solution and stained with 0.1% crystal violet.http://www.kmplot.com/lung, accessed on 6 April 2022). A total of 1925 lung cancer patient gene expression values and survival data were analyzed using multiple microarray datasets [The OS of patients with lung cancer and adenocarcinoma with different expression levels of Aurora Kinase A was analyzed through a Web-based meta-analysis Kaplan\u2013Meier plotter . Recombinant human aurora A protein (Active) (ab271368) and Recombinant human aurora B protein (Active) (ab51435) were purchased from Abcam . Myelin basic protein was selected as a substrate and staurosporine was used as a positive control. The ADP-Glo The cells were collected and lysed in sample loading buffer . Total protein concentrations were quantified using a BCA Protein Assay Kit . Quantified proteins were loaded onto SDS-polyacrylamide gels and separated by molecular weight via electrophoresis (PAGE). Then, proteins were transferred to polyvinylidene fluoride membranes ; 5% BSA in Tris-buffered saline containing 0.1% Tween-20 (TBST) was used for blocking. The membranes were blocked for 30 min at room temperature with mild shaking, then incubated with antibodies diluted in 2.5% BSA in TBST overnight at 4 \u00b0C with mild shaking. Following secondary antibody incubation and washing with TBST, the chemiluminescence signals were detected using the WEST-Queen detection system and LAS-4000 .A molecular simulation was carried out using the Molecular Operating Environment . BIQO-19 was built in MOE using the Builder program and energy-minimized for docking simulation. The 3D structure of aurora A (PDB ID: 6C2T) was obtain from the PDB databank and optimized, 3-D protonated, and energy-minimized using the default parameters of MOE. The docking site was defined by the Site Finder application, including the residues within 10 \u00c5 of the cocrystallization ligand. The docking results were analyzed using Accelrys Discovery Studio Visualizer 4.5.TM Pro version 6.0 software .Cells were seeded and starved in serum-free medium overnight. After starvation, the cells were treated with compounds for the indicated times. After incubation, cells were harvested, washed with PBS, and fixed with 70% ethanol in PBS overnight at \u221220 \u00b0C. The fixed cells were washed with PBS, resuspended in 100 \u00b5g/mL of RNase A for 30 min at room temperature, and stained with 50 \u00b5g/mL PI. Fluorescence intensity was analyzed using a FACSCalibur flow cytometer and BD CellQuestTM Pro version 6.0 software .Cells were treated with samples for 72 h and stained with an Annexin V-FITC apoptosis detection kit according to the manufacturer\u2019s instructions. Briefly, cells were collected after 72 h treatment, washed with PBS, resuspended in 1\u00d7 binding buffer, and stained with Annexin V-FITC and PI in the dark for 15 min. After incubation, the cells were diluted with 1\u00d7 binding buffer and analyzed using an FACSCalibur flow cytometer and BD CellQuestp < 0.05, ** p < 0.01, *** p < 0.001) was calculated using one-way analysis of variance coupled with Dunnett\u2019s t-test or Student\u2019s t-test.Data were obtained from three independent experiments, and are shown as the means \u00b1 standard deviation. Statistical significance -one derivative, BIQO-19, which is an aurora kinase A inhibitor that exhibits an improved ADMET profile and antiproliferative activity in NSCLC cells. The mechanisms of action for the antiproliferative activities of BIQO-19 in EGFR-TKI-resistant NSCLC H1975 cells involve aurora kinase A-mediated arrest at the G2/M phase of the cell cycle and the induction of apoptosis. Combined treatment with BIQO-19 and gefitinib exhibits synergetic activity with respect to inhibiting proliferation and inducing apoptosis in H1975 cells. Therefore, targeting aurora kinase A using a new class of inhibitors in combination with EGFR-TKIs represents a potential therapeutic strategy for treating patients with EGFR-TKI-resistant NSCLC."} +{"text": "The geometric mean end-point titer (GMT) of anti-RBD-IgG in PLWH was also reduced, especially in patients with CD4 counts <200 cells/\u00b5L, regardless of age, gender, or HIV viral load. GMTs of anti-RBD-IgG in both PLWH and healthy controls declined gradually over time. Similar results were also observed in the anti-spike-IgG response. The frequency of RBD-specific MBCs in PLWH decreased (p<0.05), and then remained stable over time. Lastly, through multivariate analysis, we found the factors that predicted a less robust response to inactivated vaccines in PLWH were a low CD4 count and long time interval after vaccination. In conclusion, inactivated vaccines are well-tolerated in PLWH but with low immunogenicity. Therefore, SARS-CoV-2 vaccines and booster doses should be given priority in PLWH, especially in patients with low CD4 counts.It is important to know the safety and efficacy of vaccination in immunocompromised people living with HIV (PLWH), but currently, there is limited data on the inactivated SARS-CoV-2 vaccines\u2019 safety and immune responses in PLWH. In this prospective observational study, 139 PLWH and 120 healthy controls were enrolled and monitored for 21\u2013105 days after a two-dose vaccination. The safety, anti-receptor binding domain IgG (anti-RBD-IgG) and anti-spike-IgG responses, and RBD-specific memory B cell (MBC) responses were evaluated. The overall adverse events within seven days were reported in 12.9% (18/139) of PLWH and 13.3% (16/120) of healthy controls. No serious adverse events occurred in both groups. Overall, the seroprevalence of anti-RBD-IgG in PLWH was significantly decreased (87.1% vs. 99.2%; Trial registration:ClinicalTrials.gov identifier: NCT05043129.. The coronavirus disease 2019 (COVID-19) epidemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in 2019 and has continued to rage worldwide, bringing a heavy burden to global public health . Even th+ T cell loss after receiving an inactivated COVID-19 vaccine in a treatment-na\u00efve HIV-positive patient was reported by a recent study vs. 278.6 [95% CI: 204.1\u2013380.4], p<0.05; 3 months: 93.3 [95% CI: 68.66\u2013126.8] vs. 150.8 [95% CI: 109.9\u2013206.8], p<0.05; 2 AU/mL, IQR [1.67\u20132.90 log2 AU/mL] vs. 2.64 log2 AU/mL, IQR [2.07\u20133.94 log2 AU/mL], p<0.01; 2 months: 1.42 log2 AU/mL, IQR [1.23\u20134.63 log2 AU/mL] vs. 2.17 log2 AU/mL, IQR [1.88\u20132.86 log2 AU/mL], p\u2009=\u20090.169; 3 months: 1.65 log2 AU/mL, IQR [1.38\u20132.01 log2 AU/mL] vs. 1.78 log2 AU/mL, IQR [1.21\u20132.29 log2 AU/mL], p\u2009=\u20090.786; To better understand the variation of humoral immune responses with passing time, we stratified three groups by time interval after full-course vaccination in the cross-sectional analysis. As expected, GMTs of anti-RBD-IgG gradually decreased over time in both PLWH and healthy controls. However, GMTs of anti-RBD-IgG in PLWH were sharply lower than that of healthy controls at every time point (1 month: 155.3 [95% CI: 128.3\u2013188.1] vs. 441.6 [95% CI: 355\u2013549.5], In summary, the weakened antibody response in PLWH kept on falling over time, whereas the impaired MBC response did not change over time.p<0.001; 2 AU/mL, IQR [1.72\u20132.98 log2 AU/mL] vs. 1.61 log2 AU/mL, IQR [1.41\u20132.03 log2 AU/mL]; p<0.001; To further explore the dynamic changes of antibody levels in PLWH, a longitudinal analysis was conducted in PLWH. Of the 96 PLWH observed after 1 month, 52 were followed up to the 6th month. As expected, GMTs of anti-RBD-IgG showed a clear downward trend in the 6th month compared with the 1st month (219.6 [95% CI: 179.3\u2013268.8] vs. 97.37 [95% CI: 83.99\u2013112.9]; Lastly, we wanted to investigate the risk factors related to inferior response to anti-RBD-IgG in PLWH. As shown in In this prospective study, we evaluated the safety, antibody responses, and RBD-specific MBC responses of inactivated SARS-CoV-2 vaccines in PLWH and healthy controls. Our results showed that inactivated vaccines were safe and well-tolerated in PLWH. The antibody and MBC responses waned in PLWH, especially in PLWH with CD4 counts <200 cells/\u00b5L. Therefore, PLWH should be vaccinated ahead of the healthy population.PLWH with SARS-CoV-2 have poor clinical outcomes, especially those who are immunosuppressed or do not receive ART ,19. HoweOur results showed that PLWH had lower anti-RBD-IgG and anti-spike-IgG titers than healthy controls 21\u2013105 days after vaccination, which is consistent with previous studies showing that PLWH had lower immune responses to the vaccine than healthy individuals . Previou+ T cells and a series of immune abnormalities [The level of immunosuppression is usually reflected by the CD4 cell counts . Usuallymalities . Howevermalities . In thismalities ,11. Thismalities . Of notemalities , hence, The MBCs produced during primary infection are quickly reactivated after a secondary infection, thus, preventing severe disease or death ,15. HencThere are some limitations in this study. First, few subjects participated in the follow-up until month 6 after full vaccination because the sporadic localized outbreaks of COVID-19 partially impeded travel. Second, the early stages of B and T cell responses were not evaluated, as we were mainly focusing on the significance of durable humoral immune responses. Therefore, further studies about the early stages of B and T cell responses in PLWH are needed. Third, the best correlation of antibody titers and vaccine efficacy in PLWH is currently unknown, and more large-scale population studies are needed. Nonetheless, we believe our results are particularly important and meaningful to clinicians.In conclusion, the inactivated SARS-CoV-2 vaccines are safe and well-tolerated in people living with HIV, with no serious adverse events reported. However, the antibody response and RBD-specific MBC response were weak, especially in PLWH with a low CD4 count. Therefore, SARS-CoV-2 vaccines and booster doses should be prioritized for this special population.Click here for additional data file."} +{"text": "Trichoderma strains isolated from forest species of the Cerrado-Caatinga ecotone as biological control agents of crop pathogenic fungi. Nineteen Trichoderma strains were used to assess the antagonistic activity by in vitro bioassays against the plant pathogens Colletotrichum truncatum, Lasiodiplodia theobromae, Macrophomina phaseolina, and Sclerotium delphinii isolated from soybean, cacao, fava bean, and black pepper crops, respectively. All Trichoderma strains demonstrated inhibitory activity on pathogen mycelial growth, with maximum percent inhibition of 70% against C. truncatum, 78% against L. theobromae, 78% against M. phaseolina, and 69% against S. delphinii. Crude methanol extracts (0.5 to 2.0 mg mL-1) of Trichoderma strains were able to inhibit the growth of C. truncatum, except Trichoderma sp. T3 (UFPIT06) and T. orientale (UFPIT09 and UFPIT17) at 0.5 mg mL-1, indicating that the endophytes employ a biocontrol mechanism related to antibiosis, together with multiple mechanisms. Discriminant metabolites of Trichoderma extracts were unveiled by liquid chromatography-tandem mass spectrometry-based metabolomics combined with principal component analysis (PCA), which included antifungal metabolites and molecules with other bioactivities. These results highlight the biocontrol potential of Trichoderma strains isolated from the Cerrado-Caatinga ecotone against crop pathogenic fungi, providing support for ongoing research on disease control in agriculture.The indiscriminate use of chemical pesticides increasingly harms the health of living beings and the environment. Thus, biological control carried out by microorganisms has gained prominence, since it consists of an environmentally friendly alternative to the use of pesticides for controlling plant diseases. Herein, we evaluated the potential role of endophytic Diseases caused by fungi are among the most harmful to plants due to their rapid spread and the ability to adapt to various environmental conditions . The mosResearch on alternative methods of controlling fungal diseases has been widely developed, often requiring the integrated implementation of several methods, known as integrated disease management (IDM) , 4. AmonA promising alternative method for plant pathogen control is based on the use of antagonistic microorganisms, such as endophytic fungi, capable of protecting their hosts from the action of pathogens , 9. ThesRecent research has revealed that although endophytic microorganisms have received global interest, there are still several gaps in knowledge, such as the different biomes explored . ConsideThe Cerrado and Caatinga biomes are recognized for their great importance. The Cerrado, also known as the Brazilian savanna, is one of the 25 biodiversity hotspots for conservation priorities in the world , 17, andTrichoderma species have been tried as BCA and used as an alternative to synthetic pesticides to control a variety of plant diseases + was identified as trigonelline (T. longibrachiatum (UFPIT02), Trichoderma sp. T2 (UFPIT05), T. koningiopsis (UFPIT07), Trichoderma sp. T5 (UFPIT11), Trichoderma sp. T6 (UFPIT13), and T. koningiopsis (UFPIT19) isolates. The MS/MS spectrum was characterized by the fragment of m/z 92.0496 [__HCOOH]+, referring to the carboxylic acid group +, identified as phomalone , T. longibrachiatum (UFPIT02), and T. orientale isolates was identified as columbianetin and Trichoderma sp. T6 (UFPIT13) isolates. The metabolite of m/z 419.1713 detected in T. orientale (UFPIT01), T. longibrachiatum (UFPIT02), Trichoderma sp. T6 (UFPIT13), and T. orientale isolates were identified as syringaresinol , was identified as brefeldin-A (BFA) . The metabolite of m/z 453.1914 was identified as physodic acid , was identified as HT-2 toxin and T. longibrachiatum (UFPIT02) isolates. The metabolite of m/z 163.0393 detected in all Trichoderma spp. was identified as 4-hydroxycoumarin , L. theobromae (B), M. phaseolina COUFPI 10 and COUFPI 11 (C), and S. delphinii COUFPI 209 and COUFPI 249 (D) paired with Trichoderma strains. Means followed by the same letter do not differ from each other by the Scott\u2013Knott test at the 5% probability level. The coefficients of variation (CVs) were 20.51% for L. theobromae, 15.99% for M. phaseolina COUFPI 10, 19.13% for M. phaseolina COUFPI 11, 10.68% for S. delphinii COUFPI 209, and 9.54% for S. delphinii COUFPI 249. Different lowercase letters indicate a significant difference between Trichoderma spp. Different capital letters indicate a significant difference between Trichoderma spp.Mycelial growth rate index (MGRI) of (TIF)Click here for additional data file.S2 Fig(TIF)Click here for additional data file.S3 Fig(TIF)Click here for additional data file.S4 Fig(TIF)Click here for additional data file.S5 Fig(TIF)Click here for additional data file.S6 Fig(TIF)Click here for additional data file.S7 Fig(TIF)Click here for additional data file.S8 Fig-1, 8.45% for 1.0 mg mL-1 and 9.36% for 2.0 mg mL-1.The coefficients of variation (CVs) were 4.65% for the concentration of 0.5 mg mL(TIF)Click here for additional data file.S9 FigTrichoderma spp. cultures generated using MetaboAnalyst. Con = Control, UFPIT01 = T1, UFPIT02 = T2, UFPIT03 = T3, UFPIT04 = T4, UFPIT05 = T5, UFPIT06 = T6, UFPIT07 = T7, UFPIT08 = T8, UFPIT09 = T9, UFPIT10 = T10, UFPIT11 = T11, UFPIT12 = T12, UFPIT13 = T13, UFPIT14 = T14, UFPIT15 = T15, UFPIT16 = T16, UFPIT17 = T17, UFPIT18 = T18, and UFPIT19 = T19.PC1 x PC2 (A) and PC1 x PC3 (B) loading plots of metabolic fingerprints of (TIF)Click here for additional data file.S10 Fig(TIF)Click here for additional data file.S11 Fig(TIF)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file."} +{"text": "Q2 and Q4 of non-HDL-C were associated with increased odds of SICH compared to Q3. Q1 and Q2 of LDL-C was associated with increased odds of mortality compared to Q3. In AIS patients who received IV tPA, low LDL-C was associated with increased odds of mortality while HDL-C may be protective against poor functional outcome.Contradicting evidence exists regarding the role of lipids in outcomes following intravenous (IV) thrombolysis with tissue plasminogen activator (tPA). Restricted cubic spline curves and adjusted logistic regression were used to evaluate associations of low-density lipoprotein cholesterol (LDL-C), non-high-density lipoprotein cholesterol (non-HDL-C), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and LDL-C/HDL-C ratio with poor functional outcome, symptomatic intracranial hemorrhage (SICH) and 90-day mortality, among 1004 acute ischemic stroke (AIS) patients who received IV tPA in a comprehensive stroke center. Quartile (Q) 1, Q2 and Q3 of HDL-C were associated with increased odds of poor functional outcome (adjusted odds ratio (adjOR) 1.66, 95% CI 1.06\u20132.60, Stroke incidence and stroke-related mortality increased substantially from 1990 to 2019, and the stroke burden will continue to increase globally, especially in underdeveloped countries ,4, with In this study, we included consecutive patients who received IV tPA from September 2006 to June 2018. All these patients had no contraindications to IV tPA use. The study obtained ethics approval from the National Healthcare Group-Domain Specific Review Board (NHG DSRB Ref: 2010/00509). Patients were assessed by a neurologist for eligibility to receive intravenous thrombolysis according to institutional protocol and American Heart Association/American Stroke Association guidelines at a standard dose of 0.9 mg/kg body weight [LDL-C was calculated by the Friedewald equation (TC-HDL-C-TG/5) , while sThe primary outcome measured was poor functional outcome of 3\u20136). Secondary outcomes measured were symptomatic intracranial hemorrhage (SICH) and 90-day all-cause mortality. SICH was based on the European Cooperative Acute Stroke Study (ECASS) II definition . The 90-p < 0.05.Analyses were performed using SPSS for Windows version 27.0 and R version 4.0.5. Restricted cubic splines with 5 knots were plotted to visually assess the univariate associations between the lipid parameters and the three outcomes. These served qualitative and descriptive purposes only. Since non-linear (U-shaped/inverse U-shaped/J-shaped/reverse tick) associations were found, lipid parameters were divided into quartiles for analysis. Descriptive statistics for continuous variables were presented as mean (SD) when normality and homogeneity assumptions were satisfied, otherwise as median (interquartile range) (IQR), and n (%) for categorical variables. Differences in continuous variables were assessed using 2 sample t-test when normality and homogeneity assumptions were satisfied; otherwise, Mann-Whitney U test was used where data was not distributed normally. Chi-square or Fisher\u2019s exact test was used for categorical variables. Covariates that were selected a priori for variable adjustment were gender, age, hypertension, atrial fibrillation, large vessel occlusion, diabetes mellitus, admitting NIHSS and admitting SBP. Logistic regression assessed the associations between lipid levels and outcomes, and with LAA. Results were presented as adjusted odds ratio (adjOR) with 95% confidence interval (CI). Statistical significance was set at two-sided This section may be divided by subheadings. It should provide a concise and precise description of the experimental results, their interpretation, as well as the experimental conclusions that can be drawn.1265 consecutive patients with ischemic stroke treated with IV tPA were analyzed and 1004 patients with valid lipid assessments were included in this study. Of 1004 patients, 589/986 (59.7%) were male, 586/883 (66.4%) were of Chinese ethnicity, 596/916 (65.1%) experienced a LVO and 190/1004 (18.9%) had AF. There were 657/1004 (65.4%) patients with history of with hypertension, 526/1004 (52.4%) with hyperlipidemia, and 306/1004 (30.5%) with diabetes mellitus. Median age was 66 (IQR 56\u201377) years while median admitting NIHSS was 15 (IQR 8\u201321). Median LDL-C, non-HDL-C, TC, HDL-C and LDL-C/HDL-C were 2.86 (IQR 2.18\u20133.50) mmol/L, 3.43 (IQR 2.70\u20134.19) mmol/L, 4.62 (IQR 3.86\u20135.36) mmol/L, 1.12 (IQR 0.95\u20131.32) mmol/L and 2.49 (IQR 1.84\u20133.30) respectively. In accordance with the TOAST classification, 322/975 (33.0%) had LAA stroke, 341/975 (35.0%) had cardioembolic (CE) stroke, 168/975 (17.2%) had small vessel occlusion (SVO), 10/975 (1.0%) had stroke of other determined etiology and 134/975 (13.7%) had cryptogenic stroke .p = 0.024) compared to Q1. Q2 and Q4 of non-HDL-C was significantly associated with increased odds of LAA compared to Q1. Q3 of HDL-C was associated with increased odds of LAA compared to Q4. Lastly, Q3 and Q4 of LDL-C/HDL-C were associated with increased odds of LAA compared to Q1 count, neutrophils, platelets, admitting NIHSS and presence of LVO were significantly higher in the LAA compared to non-LAA group . Regardied to Q1 .Of 1004 patients, 479/995 (48.1%) experienced poor functional outcomes (mRS 3\u20136), 48/1003 (4.8%) suffered SICH and 117/990 (11.8%) died. There waWhen evaluating the following relationships between lipid parameters and outcomes measured, variables adjusted for in the multivariate model include gender, age, hypertension, atrial fibrillation, large vessel occlusion, diabetes mellitus, admitting NIHSS and admitting SBP. Restricted cubic spline curves showed a \u2018reverse tick\u2019 relationship between LDL-C, non-HDL-C and TC with poor functional outcome .p = 0.028, adjOR 1.63, 95% CI 1.05\u20132.53, p = 0.027 and OR 1.56, 95% CI 1.01\u20132.44, p = 0.048 respectively) when compared to Q4. Q2 and Q4 of LDL-C/HDL-C ratio were associated increased odds of poor functional outcome when compared to Q3 when compared to Q3. Similarly, Q2 and Q4 of TC were significantly associated with increased odds SICH when compared to Q3. Q2 of HDL-C remained significantly associated with increased odds of SICH when compared to Q1 when compared to Q3. Q2 of LDL-C/HDL-C was associated with increased odds of mortality when compared to Q3. No significant associations were found to relate non-HDL-C, TC and HDL-C with mortality on multivariate analysis compared to previous thrombolysis studies. However, this study was a single institution retrospective cohort study that solely evaluated intravenous thrombolysis patients. This may limit the generalisability of results to other cohorts, warranting more prospective studies on lipid parameters and ischemic stroke outcomes. We would like to acknowledge the possibility of Type I error in the multivariate analyses in which significant associations may no longer hold true after Bonferroni correction. Excessive correction of statistical level of significance may also increase the likelihood of Type II error as a trade-off to reduce Type I error, which may increase false negatives. The multivariate relationship between HDL-C and poor functional outcome is to be interpreted with caution as no significant relationship was found on univariate analysis, in which the possible reasons can be explained statistically by Lo et al. and Wang et al. ,39. HencIn AIS patients who received IV tPA, low LDL-C was associated with increased odds of mortality while HDL-C may be protective against poor functional outcome."} +{"text": "Microbacterium foliorum NRRL B-24224. The genome has a length of 17,453\u2009bp and contains 25 total protein-coding genes, 20 of which were assigned functions. Based on gene content, Burgy was assigned to actinobacteriophage cluster EE.Burgy is a siphovirus that was isolated from compost soil near Fremont Township, Iowa, using Actinobacteria have been identified throughout aquatic, soil, and animal microbiomes , using standard methods ( plating . Transmi (n = 4) .M. foliorum (68.7%) (DNA was isolated from Burgy using the Promega Wizard DNA cleanup kit. The genome was sequenced using an Illumina MiSeq sequencer (v3 reagents) after the library was prepared using the NEBNext Ultra II FS kit, yielding 640,328 single-end 150-bp reads, which constituted ~5,500-fold coverage. Raw reads were assembled and checked for completeness using Newbler v2.9 with default parameters and Consed v29, respectively, as described previously (iorum 68.% (7). Buhttp://cobamide2.bio.pitt.edu/computer.htm), PECAAN (https://blog.kbrinsgd.org/), HHPRED (http://phages.wustl.edu/starterator), TMHMM v2.0 accession no. SRX14443487.The sequencing results for Burgy are available in GenBank with accession no."} +{"text": "Clostridium botulinum is responsible for botulism, a potentially lethal foodborne intoxication. Here, we report the draft genome sequences of C. botulinum group II strains 202F (serotype F) and Hazen (serotype E). The genomes share many similarities, including multiple mobile genetic elements. Clostridium botulinum is an anaerobic, Gram-positive, spore-forming bacterium that produces the neurotoxin that causes botulism (C. botulinum strains are divided into four groups (I to IV) , with moI to IV) , 5. HereC. botulinum strains 202F and Hazen were originally isolated from marine sediments in California, USA, in 1965 (Francisella sp. strain MA067296 plasmid (CP016929.1) was identified in 202F. Another plasmid with 99% sequence homology to C. botulinum pCBI (CP006904.1) indicative of a putative phage-like plasmid.Sequencing of strain 202F yielded 845,112 raw reads and 34 contigs with 30\u00d7 median coverage, while 629,334 raw reads and 80 contigs with 25\u00d7 median coverage were obtained for strain Hazen. The 202F and Hazen genomes comprise 3,829,425\u2009bp and 3,821,401\u2009bp, respectively, and both have 27.2% G+C content. Strain 202F contained 3,496 protein-coding sequences and 121 RNAs, while Hazen had 3,422 protein-coding sequences and 120 RNAs. A comparative analysis between the previously sequenced 202F genome (GenBank accession number C. botulinum strains 202F and Hazen have been deposited in DDBJ/ENA/GenBank under accession numbers NPMX00000000.1 and NPMY00000000.1 for the contigs and SRA accession numbers SRR17916278 and SRR17916277 for the raw reads, respectively.The genome sequences of"} +{"text": "Residents and staff of continuing care retirement communities (CCRC) experienced many challenges during the COVID-19 pandemic including loss, social isolation, and staff turnover. This study examined factors that contribute to resilience in staff during the late stage of the pandemic using the Connor-Davidson Resilience Scale. Resilience scores ranged from 0 (low) to 100 (high). A total of 96 staff were enrolled, and average age was 48.41 years (SD = 16.16). Average resilience in staff was 75.16 (SD = 11.81). Those under 35 years of age reported lower resilience scores (M = 67.38) compared to those 35-49 years of age (M = 76.65), 50-64 (M = 75.83), and 65 years and older (M = 82.71), p <.05. Staff who were married scored higher than those who were not (M = 76.63 vs 69.05), p < .05. Findings can inform professional development programs aimed at increasing coping skills in staff."} +{"text": "Correction to: BMC Psychiatry 22, 106 (2022)https://doi.org/10.1186/s12888-022-03764-yFollowing publication of the original article , the aut5. Mangolian Shahrbabaki P, Dehghan M, Maazallahi M, Asadi N. Fear and anxiety in girls aged 7 to 11 years old and related factors during the coronavirus pandemic. Clin Child Psychol Psychiatry. 2022;27(1):259-68.The original article has been"} +{"text": "We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong during November 2021\u2013February 2022. In addition to Omicron and Delta variants, we detected a BA.1/BA.2 recombinant with a breakpoint near the 5\u2032 end of the spike gene in 2 epidemiologically linked case-patients. Continued surveillance for SARS-CoV-2 recombinants is needed. We previously demonstrated the feasibility of testing incoming travelers for SARS-CoV-2 genomic surveillance (The SARS-CoV-2 Omicron variant (Pango lineage B.1.1.529) emerged in November 2021. Within a few weeks, subvariants BA.1, BA.1.1, and BA.2 were detected in varying proportions on different continents, but BA.1 initially was dominant (>100). Deduced genomes predominantly were Delta (n = 58) and Omicron variants (Using our previously described next-generation sequencing method Table 1.https://www.pfizer.com); patient 1 received the second dose on November 1, 2021, and patient 2 received the second dose on June 22, 2021.In our phylogenetic analysis, 2 additional nearly identical sequences formed a distinct branch in the Omicron clade Figure 2https://www.medrxiv.org/content/10.1101/2022.03.03.22271812v2; T. Peacock, unpub. data, https://github.com/cov-lineages/pango-designation/issues/441).The distinct topology of viral sequences from these patients suggested that they were infected by a recombinant virus. To test that hypothesis, we used previously reported BA.1- and BA.2-defining single-nucleotide polymorphisms (SNPs) to analyze the genomes . We founWe further examined our sequence data to exclude the possibility of coinfection or contamination , panel AWe found no similar BA.1/BA.2 recombinant sequences in GISIAD or GenBank , suggesting a novel recombinant. The BA.1 region of this recombinant virus is genetically close to 3 BA.1 sequences detected in Europe and the United States , panel Bhttps://doi.org/10.1101/2020.08.05.238386; P. Colson et al., unpub. data; T. Peacock, unpub. data). The high transmissibility of Omicron (Emerging Omicron subvariants could allow vaccine breakthrough and widespread reinfection. Previous studies reported detection of SARS-CoV-2 interlineage recombinants at the same time as different SARS-CoV-2 lineages were cocirculating (Additional information recombinant BA.1/BA.2 SARS-CoV-2 virus in arriving travelers, Hong Kong, China, February 2022."} +{"text": "S-gene) amplification (SGTF) in real-time reversetranscription\u2013polymerase chain reaction (RT-PCR) was used as a proxy indicator ofinfection with likely BA.5-related sublineages and S-gene targetpresence (SGTP) of infection with likely XBB/XBB.1.5-related sublineages . Specimenswith missing Ct values for N or ORF1ab were excluded.SARS-CoV-2\u2013positive specimens with either null or reduced amplification of thespike S-gene were considered tohave SGTF or SGTP (XBB/XBB.1.5-related); control-patients werethose who received a negative NAAT result. Tests among persons fulfilling any offollowing criteria were excluded from analyses: 1) presence of an immunocompromisingconditionAs of January 16, 2023, genomic sequencing data were available for a random subset ofICATT specimens with SGTP and collection dates through January 2, showing an increase inXBB.1.5 prevalence over time. During December 1, 2022\u2013January 2, 2023, XBB.1.5comprised 33% (495) of specimens exhibiting SGTP. During the interval December11\u2013January 2, XBB.1.5 accounted for 38% of sequenced ICATT specimens with SGTP(377), and during the interval December 18\u2013January 2, XBB.1.5 accounted for 43%of sequenced ICATT specimens with SGTP (252) were positive for SARS-CoV-2, including 10,596(78%) with SGTF (BA.5-related) and 3,052 (22%) with SGTP (XBB/XBB.1.5-related) . More coAcross age groups, VE was generally similar against BA.5-related infections andXBB/XBB.1.5-related infections. VE against symptomatic BA.5-related infection was 52%among persons aged 18\u201349 years, 43% among persons aged 50\u201364, and 37%among those aged \u226565 years . VEagaiThis report provides the first estimates of bivalent mRNA COVID-19 VE againstsymptomatic SARS-CoV-2 infection with XBB-related sublineages. These preliminaryestimates from national pharmacy testing conducted during December 1,2022\u2013January 13, 2023, showed relative bivalent booster dose VE to be similar for XBB/XBB.1.5sublineage\u2013related infections and BA.5 sublineage\u2013related infections.VE estimates for both sublineages included in this analysis were similar toestimates from the same ICATT network published during a period of Omicron BA.5,BQ.1, and BQ.1.1 sublineage circulation in fall 2022 -gene target presence as a proxy for BA.2sublineages, including XBB and XBB.1.5, during December 2022\u2013January2023, the results showed that a bivalent mRNA booster dose providedadditional protection against symptomatic XBB/XBB.1.5 infection for at leastthe first 3 months after vaccination in persons who had previously received2\u20134 monovalent vaccine doses.Using spike (As new SARS-CoV-2 variants emerge, continued vaccine effectiveness monitoringis important. All persons should stay up to date with recommend COVID-19vaccines, including receiving a bivalent booster dose when eligible."} +{"text": "Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aberrant DNA methylation is a mediator of epigenetic changes that are closely associated with the HCC pathogenesis and considered a biomarker for its early diagnosis. The ANDSystem software package was used to reconstruct and evaluate the statistical significance of the pathways HCV could potentially use to regulate 32 hypermethylated genes in HCC, including both oncosuppressor and protumorigenic ones identified by genome-wide analysis of DNA methylation. The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, proteinactivity, stability, and transport regulations, the expression regulation pathways being statistically significant. It hasbeen shown that 8 out of 10 HCV proteins were involved in these pathways, the HCV NS3 protein being implicatedin the largest number of regulatory pathways. NS3 was associated with the regulation of 5 tumor-suppressor genes,which may be the evidence of its central role in HCC pathogenesis. Analysis of the reconstructed pathways has demonstratedthat following the transcription factor inhibition caused by binding to viral proteins, the expression of a numberof oncosuppressors was suppressed, while the expression of others was activated. Thus, the performed gene-network reconstruction has shown that HCV proteins can influencenot only the methylation status of oncosuppressor genes, but also their transcriptional regulation. The results obtainedcan be used in the search for pharmacological targets to develop new drugs against HCV-induced HCC. Liver cancer is the third leading cause of cancer-relateddeath in the world according to year 2020 statistics with over900,000 new cases of this pathology registered the sameyear around the world . Hepatocellularcarcinoma (HCC) has been the dominant type of primaryliver cancer, comprising about 90 % of all the cases . It may be caused by several risk factors suchas aflatoxin exposure, alcohol consumption; hepatitis B orC (HCV) virus infection, liver cirrhosis, non-alcoholic fattyliver disease, non-alcoholic steatohepatitis, metabolic syndrome,obesity, type II diabetes, and genetic predisposition.Currently, a lot of data has been accumulated on HCVassociation with impaired liver function, cirrhosis and HCCdevelopment . Having gotten into a humanbody, HCV seeks to exercise control over the biologicalprocesses occurring in host cells in order to increase its survivaland replication efficiency. In more than 70 % of thoseinitially infected, the disease takes on a chronic course, so thepatients experience progressive liver-tissue fibrosis and cirrhosisaccompanied by long-term inflammation . Using various mechanisms for infected cell cooptation,the virus can inadvertently lead to HCC development. At the same time, the molecular andgenetic mechanisms of virus-induced carcinogenesis remainunderstudied.In addition, HCC pathogenesis is associated with epigeneticmodifications and aberrant DNA methylation being a mediatorof epigenetic changes thatcan serve as a biomarker for early HCC diagnosis .To establish the functional links between genes and to elucidatethe molecular mechanisms of biological processes, themethods for gene networks reconstruction have been widelyemployed. Previously, we developed the Associative NetworkDiscovery System (ANDSystem) software package designedto reconstruct gene networks based on the knowledge extractedfrom factual databases and scientific publications usingtext-mining techniques . The package has enabled one toreconstruct the molecular mechanisms of a number of pathologiessuch as preeclampsia , tuberculosis, comorbid conditions of asthma andhypertension , COVID-19 , HCV life cycle , etc.In the present study, ANDSystem was employed to reconstructthe regulatory pathways describing the potentialregulation mechanisms of the genes hypermethylated in HCCby HCV proteins. The analysis looked at the 32 genes knownto be hypermethylated HCC markers. Among the 7 types ofreconstructed regulatory pathways including protein-proteininteractions (PPI), gene expression, protein activity, stabilityand transport regulations, those responsible for gene expressionregulation turned out to be statistically significant. Ninemarker genes were identified that could potentially be subjectto regulation by HCV proteins, including three HCC suppressorgenes that could be negativelyregulated and one apoptosis suppressor gene (TERT ) that canbe positively regulated.Genes hypermethylated in HCC. Information about thehypermethylated genes was taken from publications (Table 1).Only those genes were considered whose hypermethylationwas associated with HCC and confirmed through the analysisand meta-analysis given in the publications. The schematic ofthe data-processing algorithm can be seen in Figure 1.Regulatory pathways reconstruction in ANDSystem.The regulatory pathways were reconstructed using the ANDSystemsoftware package thathad been designed to perform gene-networks reconstructionbased on automated analysis of scientific texts and factualdatabases. ANDSystem includes a knowledge base with morethan 40 million facts about molecular-genetic interactions,containing physical intermolecular interactions, gene expression,protein activity, stability and transport regulations. In thepackage, it is the the ANDVisio program that reconstructs andanalyzes gene networks using the Pathway Wizard functionperforming search calls to the knowledge base according toa given pattern. A schematic description of the used patternsis given in Table 2For instance, P4 means searching for all possible moleculargenetic pathways in the ANDSystem knowledge base thatsatisfy the following requirement: the first participant inthe pathway is the viral protein (Vp); the second is humanprotein (Hp); the third is a human gene from a list of target genes (Tg); the last member of the pathway is a Tg-encodedprotein (Tp). Further in the text, HCC marker genes will beregarded as target ones. Interactions between pathway participantsare represented by the following types: Vp and Hpare linked by PPIs; Hp and Tg are \u201cexpression regulation\u201dinteraction type (Exp reg), where Hp regulates Tg gene expression;Tg and Tp are interaction of the \u201cexpression\u201d interactiontype (Exp), i. e., the Tp protein is the expression product ofthe Tg gene. Examples of regulatory pathway reconstructionin ANDSystem using the patterns presented in the previouswork .Estimating the statistical significance of pathways. Thepattens from Table 2 were used to calculate the number ofmarker genes K participating in the regulatory pathways,as well as the number of such participants in the sample ofcontrol gene. The likelihood of observing the number K forrandom reasons was estimated using the standard hypergeometricdistribution and the hypergeom function from the SciPy 1.8.0 package (https://scipy.org). For the purposes ofstatistical processing, a group of genes proposed by Hoshidaet al. (2008) as a control to predict HCC outcomes based onthe expression level of genes was takenReconstruction of the potential regulatory pathwaysHCV proteins use to affect HCC marker genesA set of hypermethylated HCC marker genes was used toreconstruct the potential regulatory pathways through whichviral proteins could modulate the genes playing an importantrole in HCC pathogenesis (see Table 1). The set had beenbased on the published results of a genome-wide analysis ofDNA methylation and included 30 genes, the expression ofwhich, according to the studies, was reduced in hepatocellularcarcinoma, and two genes (WT1 and TERT ) with increasedexpressionTo reconstruct the regulatory pathways, the ANDSystemsoftware package was used. The search queries to the knowledgebase were formed using the pathway patterns presentedin Table 2. The patterns described different types of regulatorypathways determined by different combinations of moleculargeneticinteractions, including PPIs, gene expression, proteinactivity, stability, and transport regulationsAnalysis of the statistical significance of the pathwaysautomatically reconstructed by ANDSystem according to thegiven patterns showed that among the seven types of regulatorypathways analyzed, expression regulation ones turnedout to be statistically significant (P4 in Table 3). This patterndescribes the pathways including four participants: (1) viralproteins; (2) human transcription factors (TF) involved in PPIswith viral proteins; (3) marker genes presented in Table 1,whose expression is regulated by (2); (4) protein products ofmarker genes.The gene network describing the regulation pathways ofHCC marker genes included 8 HCV proteins, 7 intermediatehost proteins involved in PPIs with HCV proteins, and 9 genes whose aberrant expression correlated withHCC progression .Analysis of the regulatory pathwaysThe regulatory pathways involved 8 out of 10 HCV proteinsand 6 human genes, which protein products acting as the intermediateparticipants the viral proteins could form proteinheterocomplexes with. The latter included such genes oftranscription factors as STAT3 , NR4A1 (Nuclear receptor subfamily 4group A member 1), JUN (c-Jun/activator protein 1), BCL6(B-cell lymphoma 6 protein), transmembrane receptor NOTC1(Neurogenic locus notch homolog protein 1) and histonemethyltransferase SMYD3 (Lysine methyltransferase SETand MYND domain containing protein 3).Most of the viral proteins were associated with RUNX3 andWT1 regulation. Six of them interacted with NR4A1 being a general expressionregulator of these two HCC marker genes.HCV protein NS3 (p70) interacted with the largest numberof expression regulators, and through these interactions itcould potentially regulate the expression of five tumor suppressorgenes and that of TERT.Now, let us consider the possibilities of implementing ofthese regulatory pathways in more detail.p8, p21, p68, gp32, p23, NS1/NR4A1/RUNX3, WT1. Thisregulatory pathway suggests six HCV proteins can possibly affect HCC development by controllingthe activity of the RUNX3 and WT1 genes through theNR4A1 transcription factor. Indeed, NR4A1 directly interactswith the RUNX3 and WT1 promoters, suppressing RUNX3activity and activating that of WT1 . Both factors are involved in apoptosis regulation,hence, RUNX3 promotes activation of the extrinsic,TRAIL-induced apoptosis pathway , whileWT1 controls the mitochondrial apoptosis pathwaythrough the regulation of the Bcl-2 anti-apoptotic proteingene, and, depending on a cell type, affects the expressionof the Bcl-2 gene in both positive and negative ways . It has been shown that in HCC, anincreased expression of the WT1 gene is observed, which isdue to hypermethylation of its promoter and correlates witha poor prognosis . Thesedata suggest that the role WT1 plays in HCC progression isassociated with blocked apoptosis.Experiments have demonstrated that HCV core proteininhibits at least the NR4A1 and RUNX3 genes expression ininfected cells , contributing to suppressing anexternal apoptosis pathway. The Y2H test (Two Hybrid Test)has shown NR4A1 can interact with such viral proteins asCORE, E1, E2, NS2, NS4A, and NS5B , but except for CORE, the effects of the other HCVproteins on TF activity have not been investigated yet.E1, NS3, Core, p23, NS1, p68/JUN, NOTC1, STAT3/TERT. Aberrant expression of the TERT gene, associated,among other things, with hypermethylation of its promoter, isa prognostic marker of HCC . TERT affects diseaseprogression through stimulation of cell proliferation due toreactivation of its gene expression in carcinoma cells . TERT activity has beenshown to also increase in HCV-infected cells, partly throughdirect interaction of the core protein with the enzyme , however, in general, the mechanisms HCVproteins affect TERT activity are not clear. This regulatorypathway suggests the involvement of the virus NS3, Core,E1, p23, NS1, and NS5B proteins in TERT gene expressionthrough interaction with the JUN (AP-1), STAT3, and NOTC1proteinsIndeed, experiments have shown that there is a possibilityto affect TERT expression through the AP-1 and STAT3 TFs being its direct regulators , as well as through the NOTC1 signaling pathway. Moreover, it has been demonstratedthat the HCV NS3 protein affects NOTC1 activity throughthe SRCAP transcription factor and theexpression of AP1- and STAT3-regulated genes , however,the specific mechanisms of realization of these influences ininfected hepatocyte cells have not been practically examined.gp32, p70/JUN/WIF1. This regulatory pathway describesthe effect the NS3 and E1 HCV proteins have on WIF1 (Wntinhibitory factor 1) gene expression through interaction withthe c-Jun/AP-1 TF. WIF1 is a tumor suppressor that reducescell growth in HCC , and its expressionlevel is a prognostic indicator of the course of the disease.Experiments have demonstrated that there is both the possibilityof a direct effect of the NS3 and E1 proteins on theactivity of c-Jun/AP-1 , and the lattercan affect the expression of the WIF1 gene through interactionwith the DNMT1 methyltransferase (DNA methyltransferase1), suppressing WIF1 in gallbladder cancer cells . But what mechanisms of WIF1 gene suppressionare initiated in HCV-infected hepatocarcinoma cells remainsunknown.p70/STAT3/MGMT, DAPK1, SOCS1. This regulatorypathway is initiated by NS3 (p70) affecting the activity of theMGMT, SOCS, and DAPK1 genes through interaction withthe STAT3 TF. Proteins DAPK1 (Death-associated proteinkinase 1), MGMT (Methylated-DNA-protein-cysteine methyltransferase),and SOCS1 are considered tumor suppressors, and their low expressionin carcinomas correlates with disease progression .Experiments have demonstrated that NS3 can directly interactwith the STAT3 TF involvedin the regulation of the expression of the abovementionedgenes , however, the effect of STAT3on MGMT, SOCS, and DAPK1 expression is not unambiguousand may be associated with cell specialization. As forthe mechanisms regulating the expression of these genes inHCV-infected hepatocarcinoma cells, they have not beenstudied yet.p70/BCL6/TP53. TP53 is a key activator of intrinsic apoptosispathway. The NS3 (p70) protein affects TP53 throughinteraction with the BCL6 (B-cell lymphoma 6 protein) TF.TP53 is a HCC marker gene of and its low expression correlateswith poor disease prognosis . BCL6 represses the TP53 gene in lymphoid cells,and its constitutive expression protects B lymphocytes fromDNA damage-induced apoptosis . However, the data describing the effectof HCV has on TP53 and BCL6 expression in these cells areassociated with a possible mutation induction and are mutuallyexclusive . Theinteraction of NS3 and BCL6 is discussed in ,but the specific mechanisms NS3 affects the TF activity havenot been studied yet.The studied set of hypermethylated HCC marker genes (seeTable 1) included 30 downexpressed and two over-expressedgenes. Using ANDSystem, the regulatory pathways by whichHCV proteins are able to influence the expression of thesemarker genes were reconstructed. The relationship betweenthe pathways and HCC-associated key biological processes isshown in Figure 3. According to the published data, the WT1,RUNX3, TP53, and SOCS1 genes are closely associated withapoptosis ,while the MGMT, TERT, RASSF1A, and WIF1 genes \u2013 withapoptosis and cell proliferation .The analysis showed the identified pathways could potentiallybe a part of the mechanism HCV proteins affect the activityof HCC marker genes. However, the effects the proteinshave on the function of human regulatory proteins during PPIformation are currently poorly understood. This fact preventsus from unambiguous interpretation of the reconstructedpathways, because what determines if a regulatory pathwayfunctions as an activator or suppressor of target gene expressionis whether or not the ability to regulate gene expressionremains in the host regulatory protein after its interaction withthe viral protein. Investigation of these effects requires furtherexperimental studies and computer molecular modeling.The literature describes the effects viral proteins can have onthe function of host proteins, e. g., the NS5A protein is knownto bind to SMYD3 in the cytoplasm and inhibit SMYD3 translocationto the nucleus . If the regulatoryproteins of a host organism are assumed to lose their ability toregulate gene expression due to the complexes formed withviral proteins, then the following effects can be expected:when considering the pathways regulating onco-suppressorexpression, four of the seven pathways inhibiting RASF1,RUNX3, WIF1, and DAPK1 will be suppressed, which canlead to their activation by HCV proteins, and that, in turn, willprevent carcinogenesis. In the remaining three pathways, theactivation of MGMT, SOCS1 and TP53 will be suppressed,which may possibly have a protumor effect. In the presentedpathways , WT1, MGMT, SOCS1 and TP53 areactivated by the corresponding factors ,while the expression of RASF1, RUNX3, WIF1, and DAPK1genes is negatively controlled .In the case of the TERT and WT1 genes that can be attributedto those with protumor activity, suppression of theWT1 gene can be expected and will lead to a negative effecton carcinogenesis. As for the TERT gene involved in apoptosissuppression and stimulating cell proliferation , according to our results , this gene was controlled through three different regulatorypathways. Its expression was activated by two pathwaysinvolving the STAT3 and NOTC1 host genes , and one of the pathwayssuppressed the expression involving c-JUN/AP-1 . The interaction with these host proteins couldlead to a blockage of these regulatory pathways. The pathwayinvolving c-JUN/AP-1 may be of particular interest in this respect, since inhibition of this TF by viral proteins (gp32 andNS3) could promote TERT activation. These assumptions arein good agreement with the data on differential gene expressionin acute HCV infection when the infected cells showedan increased TERT expression , so thispathway can be a promising pharmacological target.Thus, the considered assumptions lead one to conclude thepresence of multidirectional regulation of the observed expressionof HCC marker genes. This may indicate that not all regulatorypathways controlled by viral proteins can be attributedto HCC risk factors. However, the regulatory pathways thatensure the protumor activity of virus proteins undoubtedlydeserve additional study to understand the mechanisms ofvirus-induced HCC carcinogenesis. In particular, the suppressionof tumor suppressor gene expression by viral proteins canenhance the effect of their methylation in HCC or mimic thiseffect when these genes are not methylated, which can eitherprovoke HCC onset or complicate its course.Using the computer methods for gene network reconstructionavailable in the ANDSystem package, the statisticallysignificant pathways for HCV proteins to regulate HCC genemarkers have been established. The obtained results describethe potential mechanisms of the proteins involvement in HCCpathogenesis and may be useful for planning experimentalstudies to search for new targets for the development of drugsand prophylactic agents to reduce the risk of HCC developingin presence of HCV infectionThe authors declare no conflict of interest.Benderska N., Schneider-Stock R. Transcription control of DAPK.Apoptosis. 2014;19(2):298-305. DOI 10.1007/s10495-013-0931-6.Bragina E.Y., Tiys E.S., Rudko A.A., Ivanisenko V.A., Freidin M.B.Novel tuberculosis susceptibility candidate genes revealed by thereconstruction and analysis of associative networks. Infect. Genet.Evol. 2016;46:118-123. DOI 10.1016/j.meegid.2016.10.030.Chen J., Li Z., Chen J., Du Y., Song W., Xuan Z., Zhao L., Song G.,Song P., Zheng S. Downregulation of MGMT promotes proliferationof intrahepatic cholangiocarcinoma by regulating p21. Clin. Transl.Oncol. 2020;22(3):392-400. DOI 10.1007/s12094-019-02140-9.Chen M., Gan X., Yoshino K., Kitakawa M., Shoji I., Deng L., Hotta H.Hepatitis C virus NS5A protein interacts with lysine methyltransferaseSET and MYND domain-containing 3 and induces activatorprotein 1 activation. Microbiol. Immunol. 2016;60:407-417. DOI10.1111/1348-0421.12383.Chen P., Meng C., Wang Q., Yang X., Huang Z., Xing X., Lin Y.,Liu X., Peng J., Lin Y. Death-associated protein kinase 1 suppresseshepatocellular carcinoma cell migration and invasion by upregulationof DEAD-box helicase 20. Cancer Sci. 2020;111(8):2803-2813.DOI 10.1111/cas.14499.Cheng J., Wei D., Ji Y., Chen L., Yang L., Li G., Wu L., Hou T., Xie L.,Ding G., Li H., Li Y. Integrative analysis of DNA methylation andgene expression reveals hepatocellular carcinoma-specific diagnosticbiomarkers. Genome Med. 2018;10(1):42. DOI 10.1186/s13073-018-0548-z.Choi J., Southworth L.K., Sarin K.Y., Venteicher A.S., Ma W., Chang W.,Cheung P., Jun S., Artandi M.K., Shah N., Kim S.K., ArtandiS.E.TERT promotes epithelial proliferation through transcriptional controlof a Myc- and Wnt-related developmental program. PLoS Genet.2008;4(1):e10. DOI 10.1371/journal.pgen.0040010.de Chassey B., Navratil V., Tafforeau L., Hiet M.S., Aublin-Gex A.,Agaugu\u00e9 S., Meiffren G., Pradezynski F., Faria B.F., Chantier T.,Le Breton M., Pellet J., Davoust N., Mangeot P.E., Chaboud A.,Penin F., Jacob Y., Vidalain P.O., Vidal M., Andr\u00e9 P., Rabourdin-Combe C., Lotteau V. Hepatitis C virus infection protein network.Mol. Syst. Biol. 2008;4:230. DOI 10.1038/msb.2008.66.Deng Y., Yu B., Cheng Q., Jin J., You H., Ke R., Tang N., Shen Q.,Shu H., Yao G., Zhang Z., Qin W. Epigenetic silencing of WIF-1in hepatocellular carcinomas. J. Cancer Res. Clin. Oncol. 2010;136(8):1161-1167. DOI 10.1007/s00432-010-0763-5.D\u2019souza S., Lau K.C., Coffin C.S., Patel T.R. Molecular mechanismsof viral hepatitis induced hepatocellular carcinoma. World J. Gastroenterol.2020;26(38):5759-5783. DOI 10.3748/wjg.v26.i38.5759.Feng L., Li J., Yan L.D., Tang J. RASSF1A suppresses proliferation ofcervical cancer cells. Asian Pac. J. Cancer Prev. 2014;15(14):5917-5920. DOI 10.7314/apjcp.2014.15.14.5917.Fern\u00e1ndez-Barrena M.G., Arechederra M., Colyn L., Berasain C., AvilaM.A. Epigenetics in hepatocellular carcinoma development andtherapy: the tip of the iceberg. JHEP Rep. 2020;2(6):100167. DOI10.1016/j.jhepr.2020.100167.Glotov A.S., Tiys E.S., Vashukova E.S., Pakin V.S., Demenkov P.S.,Saik O.V., Ivanisenko T.V., Arzhanova O.N., Mozgovaya E.V.,ZainulinaM.S., Kolchanov N.A., Baranov V.S., Ivanisenko V.A.Molecular association of pathogenetic contributors to pre-eclampsia(pre-eclampsia associome). BMC Syst. Biol. 2015:9(Suppl.2):S4.DOI 10.1186/1752-0509-9-S2-S4.Gui Y., Yeganeh M., Ramanathan S., Leblanc C., Pomerleau V., FerbeyreG., Saucier C., Ilangumaran S. SOCS1 controls liver regenerationby regulating HGF signaling in hepatocytes. J. Hepatol. 2011;55(6):1300-1308. DOI 10.1016/j.jhep.2011.03.027.Guo N., Chen R., Li Z., Liu Y., Cheng D., Zhou Q., Zhou J., Lin Q.Hepatitis C virus core upregulates the methylation status of theRASSF1A promoter through regulation of SMYD3 in hilar cholangiocarcinomacells. Acta Biochim. Biophys. Sin. (Shanghai). 2011;43(5):354-361. DOI 10.1093/abbs/gmr021.Han Y., Niu J., Wang D., Li Y. Hepatitis C virus protein interactionnetwork analysis based on hepatocellular carcinoma. PLoS One.2016;11(4):e0153882. DOI 10.1371/journal.pone.0153882.Hassan M., Ghozlan H., Abdel-Kader O. Activation of c-Jun NH2-terminal kinase (JNK) signaling pathway is essential for the stimulationof hepatitis C virus (HCV) non-structural protein 3 (NS3)-mediated cell growth. Virology. 2005;333(2):324-336. DOI 10.1016/j.virol.2005.01.008.Hassan M., Selimovic D., Ghozlan H., Abdel-Kader O. Induction ofhigh-molecular-weight (HMW) tumor necrosis factor (TNF) alphaby hepatitis C virus (HCV) non-structural protein 3 (NS3) in livercells is AP-1 and NF-\u03baB-dependent activation. Cell. Signal. 2007;19(2):301-311. DOI 10.1016/j.cellsig.2006.07.002He B., Reguart N., You L., Mazieres J., Xu Z., Lee A.Y., Mikami I.,McCormick F., Jablons D.M. Blockade of Wnt-1 signaling inducesapoptosis in human colorectal cancer cells containing downstreammutations. Oncogene. 2005;24(18):3054-3058. DOI 10.1038/sj.onc.1208511.Hernandez-Meza G., von Felden J., Gonzalez-Kozlova E.E., Garcia-Lezana T., Peix J., Portela A., Craig A.J., Sayols S., Schwartz M.,Losic B., Mazzaferro V., Esteller M., Llovet J.M., Villanueva A.DNA methylation profiling of human hepatocarcinogenesis. Hepatology.2021;74(1):183-199. DOI 10.1002/hep.31659.Hoshida Y., Villanueva A., Kobayashi M., Peix J., Chiang D.Y., CamargoA., Gupta S., Moore J., Wrobel M.J., Lerner J., Reich M.,Chan J.A., Glickman J.N., Ikeda K., Hashimoto M., Watanabe G.,Daidone M.G., Roayaie S., Schwartz M., Thung S., Salvesen H.B.,Gabriel S., Mazzaferro V., Bruix J., Friedman S.L., Kumada H., LlovetJ.M., Golub T.R. Gene expression in fixed tissues and outcomein hepatocellular carcinoma. N. Engl. J. Med. 2008;359(19):1995-2004. DOI 10.1056/NEJMoa0804525.Huang L., Li M.X., Wang L., Li B.K., Chen G.H., He L.R., Xu L.,Yuan Y.F. Prognostic value of Wnt inhibitory factor-1 expression inhepatocellular carcinoma that is independent of gene methylation.Tumour Biol. 2011;32(1):233-240. DOI 10.1007/s13277-010-0117-6.In der Stroth L., Tharehalli U., G\u00fcnes C., Lechel A. Telomeres andtelomerase in the development of liver cancer. Cancers ( Basel).2020;12(8):2048. DOI 10.3390/cancers12082048Ivanisenko N.V., Seyrek K., Kolchanov N.A., Ivanisenko V.A., LavrikI.N. The role of death domain proteins in host response uponSARS-CoV-2 infection: modulation of programmed cell death andtranslational applications. Cell Death Discov. 2020;6:101. DOI10.1038/s41420-020-00331-w.Ivanisenko T.V., Saik O.V., Demenkov P.S., Ivanisenko N.V., SavostianovA.N., Ivanisenko V.A. ANDDigest: a new web-based module ofANDSystem for the search of knowledge in the scientific literature.BMC Bioinformatics. 2020;21(Suppl.11):228. DOI 10.1186/s12859-020-03557-8.Ivanisenko V.A., Demenkov P.S., Ivanisenko T.V., Mishchenko E.L.,Saik O.V. A new version of the ANDSystem tool for automatic extractionof knowledge from scientific publications with expandedfunctionality for reconstruction of associative gene networks byconsidering tissue-specific gene expression. BMC Bioinformatics.2019;20(Suppl.1):34. DOI 10.1186/s12859-018-2567-6.Ivanisenko V.A., Gaisler E.V., Basov N.V., Rogachev A.D., CheresizS.V., Ivanisenko T.V., Demenkov P.S., Mishchenko E.L., Khripko O.P., Khripko Yu.I., Voevoda S.M., Karpenko T.N., Velichko A.J.,Voevoda M.I., Kolchanov N.A., Pokrovsky A.G. Plasma metabolomicsand gene regulatory networks analysis reveal the role of nonstructuralSARS-CoV-2 viral proteins in metabolic dysregulation inCOVID-19 patients. Sci. Rep. 2022;12:19977. DOI 10.1038/s41598-022-24170-0.Ivanisenko V.A., Saik O.V., Ivanisenko N.V., Tiys E.S., Ivanisenko T.V.,Demenkov P.S., Kolchanov N.A. ANDSystem: an Associative NetworkDiscovery System for automated literature mining in the fieldof biology. BMC Syst. Biol. 2015;9(Suppl.2):S2. DOI 10.1186/1752-0509-9-S2-S2.Iwai A., Takegami T., Shiozaki T., Miyazaki T. Hepatitis C virus NS3protein can activate the Notch-signaling pathway through bindingto a transcription factor, SRCAP. PLoS One. 2011;6(6):e20718. DOI10.1371/journal.pone.0020718.Jardin F., Ruminy P., Bastard C., Tilly H. The BCL6 proto-oncogene:a leading role during germinal center development and lymphomagenesis.Pathol. Biol. ( Paris). 2007;55(1):73-83. DOI 10.1016/j.patbio.2006.04.001.Jaroszewicz J., Flisiak-Jackiewicz M., Lebensztejn D., Flisiak R. Currentdrugs in early development for treating hepatitis C virus-relatedhepatic fibrosis. Expert Opin. Investig. Drugs. 2015;24(9):1229-1239. DOI 10.1517/13543784.2015.1057568.Jiang L.H., Hao Y.L., Zhu J.W. Expression and prognostic value ofHER-2/neu, STAT3 and SOCS3 in hepatocellular carcinoma. Clin.Res. Hepatol. Gastroenterol. 2019;43(3):282-291. DOI 10.1016/j.clinre.2018.09.011.Jing W., Peng R., Li X., Lv S., Duan Y., Jiang S. Study on the prognosticvalues of TTC36 correlated with immune infiltrates and its methylationin hepatocellular carcinoma. J. Immunol. Res. 2022;2022:7267131. DOI 10.1155/2022/7267131.Kim B.R., Park S.H., Jeong Y.A., Na Y.J., Kim J.L., Jo M.J., Jeong S.,Yun H.K., Oh S.C., Lee D.H. RUNX3 enhances TRAIL-inducedapoptosis by upregulating DR5 in colorectal cancer. Oncogene.2019;38:3903-3918. DOI 10.1038/s41388-019-0693-x.Kohsaka S., Wang L., Yachi K., Mahabir R., Narita T., Itoh T., TaninoM., Kimura T., Nishihara H., Tanaka S. STAT3 inhibition overcomestemozolomide resistance in glioblastoma by downregulatingMGMT expression. Mol. Cancer Ther. 2012;11(6):1289-1299. DOI10.1158/1535-7163.MCT-11-0801.Konnikova L., Simeone M.C., Kruger M.M., Kotecki M., Cochran B.H.Signal transducer and activator of transcription 3 (STAT3) regulateshuman telomerase reverse transcriptase (hTERT) expression in humancancer and primary cells. Cancer Res. 2005;65(15):6516-6520.DOI 10.1158/0008-5472.CAN-05-0924.Li B., Li X., Li Y., Guo H., Sun S.Y., He Q.Q., Wang Y., Luo J.,Wen J.F., Zheng H., Feng D.Y. The effects of hepatitis C virus nonstructuralprotein 3 on cell growth mediated by extracellular signalrelatedkinase cascades in human hepatocytes in vitro. Int. J. Mol.Med. 2010;26(2):273-279. DOI 10.3892/ijmm_00000462Lin B., Hong H., Jiang X., Li C., Zhu S., Tang N., Wang X., She F.,Chen Y. c-Jun suppresses the expression of WNT inhibitory factor 1through transcriptional regulation and interaction with DNA methyltransferase1 in gallbladder cancer. Mol. Med. Rep. 2018;17(6):8180-8188. DOI 10.3892/mmr.2018.8890.Liu J., Ma Q., Zhang M., Wang X., Zhang D., Li W., Wang F., Wu E.Alterations of TP53 are associated with a poor out-come for patientswith hepatocellular carcinoma: evidence from a systematic reviewand meta-analysis. Eur. J. Cancer. 2012;48(15):2328-2338. DOI10.1016/j.ejca.2012.03.001.Llovet J.M., Zucman-Rossi J., Pikarsky E., Sangro B., Schwartz M.,Sherman M., Gores G. Hepatocellular carcinoma. Nat. Rev. Dis.Primers. 2016;2:16018. DOI 10.1038/nrdp.2016.18.Loeb D.M. WT1 influences apoptosis through transcriptional regulationof Bcl-2 family members. Cell Cycle. 2006;5(12):1249-1253.DOI 10.4161/cc.5.12.2807Machida K., Cheng K.T., Lai C.K., Jeng K.S., Sung V.M., Lai M.M.Hepatitis C virus triggers mitochondrial permeability transition withproduction of reactive oxygen species, leading to DNA damage andSTAT3 activation. J. Virol. 2006;80(14):7199-7207. DOI 10.1128/JVI.00321-06.Machida K., Cheng K.T., Sung V.M., Shimodaira S., Lindsay K.L.,Levine A.M., Lai M.Y., Lai M.M. Hepatitis C virus induces a mutatorphenotype: enhanced mutations of immunoglobulin and protooncogenes.Proc. Natl. Acad. Sci. USA. 2004;101(12):4262-4267.DOI 10.1073/pnas.0303971101.Mayo M.W., Wang C.Y., Drouin S.S., Madrid L.V., Marshall A.F.,Reed J.C., Weissman B.E., Baldwin A.S. WT1 modulates apoptosisby transcriptionally upregulating the bcl-2 proto-oncogene.EMBO J. 1999;18(14):3990-4003. DOI 10.1093/emboj/18.14.3990.McGlynn K.A., Petrick J.L., El-Serag H.B. Epidemiology of hepatocellularcarcinoma. Hepatology. 2021;73(Suppl.1):4-13. DOI 10.1002/hep.31288M\u017eik M., Chmela\u0159ov\u00e1 M., John S., Laco J., Slab\u00fd O., Kiss I., Bohovicov\u00e1L., Pali\u010dka V., Nekvindov\u00e1 J. Aberrant methylation of tumoursuppressor genes WT1, GATA5 and PAX5 in hepatocellular carcinoma.Clin. Chem. Lab. Med. 2016;54(12):1971-1980. DOI 10.1515/cclm-2015-1198.Nault J.C., Ningarhari M., Rebouissou S., Zucman-Rossi J. The roleof telomeres and telomerase in cirrhosis and liver cancer. Nat. Rev.Gastroenterol. Hepatol. 2019;16(9):544-558. DOI 10.1038/s41575-019-0165-3.Neumann O., Kesselmeier M., Geffers R., Pellegrino R., RadlwimmerB., Hoffmann K., Ehemann V., Schemmer P., Schirmacher P.,Lorenzo Bermejo J., Longerich T. Methylome analysis and integrativeprofiling of human HCCs identify novel protumorigenicfactors. Hepatology. 2012;56(5):1817-1827. DOI 10.1002/hep.25870.Ni Y., Gu J., Wu J., Xu L., Rui Y. MGMT-mediated neuron apoptosis ininjured rat spinal cord. Tissue Cell. 2020;62:101311. DOI 10.1016/j.tice.2019.101311Nowyhed H.N., Huynh T.R., Blatchley A., Wu R., Thomas G.D., HedrickC.C. The nuclear receptor Nr4a1 controls CD8 T cell developmentthrough transcriptional suppression of Runx3. Sci. Rep.2015;5:9059. DOI 10.1038/srep09059.Oversoe S.K., Clement M.S., Pedersen M.H., Weber B., Aagaard N.K.,Villadsen G.E., Gr\u00f8nb\u00e6k H., Hamilton-Dutoit S.J., Sorensen B.S.,Kelsen J. TERT promoter mutated circulating tumor DNA as a biomarkerfor prognosis in hepatocellular carcinoma. Scand. J. Gastroenterol.2020;55(12):1433-1440. DOI 10.1080/00365521.2020.1837928.Papic N., Maxwell C.I., Delker D.A., Liu S., Heale B.S., Hagedorn C.H.RNA-sequencing analysis of 5\u2032 capped RNAs identifies many newdifferentially expressed genes in acute hepatitis C virus infection.Viruses. 2012;4:581-612. DOI 10.3390/v4040581.Phan R.T., Dalla-Favera R. The BCL6 proto-oncogene suppresses p53expression in germinal-centre B cells. Nature. 2004;432(7017):635-639. DOI 10.1038/nature03147.Rabaan A.A., Al-Ahmed S.H., Bazzi A.M., Alfouzan W.A., AlsulimanS.A., Aldrazi F.A., Haque S. Overview of hepatitis C infection,molecular biology, and new treatment. J. Infect. Public Health.2020;13(5):773-783. DOI 10.1016/j.jiph.2019.11.015.Revill K., Wang T., Lachenmayer A., Kojima K., Harrington A., Li J.,Hoshida Y., Llovet J.M., Powers S. Genome-wide methylationanalysis and epigenetic unmasking identify tumor suppressor genesin hepatocellular carcinoma. Gastroenterology. 2013;145(6):1424-1435.e1-25. DOI 10.1053/j.gastro.2013.08.055.Saik O.V., Demenkov P.S., Ivanisenko T.V., Bragina E.Y., Freidin M.B.,Goncharova I.A., Dosenko V.E., Zolotareva O.I., Hofestaedt R.,Lavrik I.N., Rogaev E.I., Ivanisenko V.A. Novel candidate genesimportant for asthma and hypertension comorbidity revealed fromassociative gene networks. BMC Med. Genomics. 2018;11(Suppl.1):15. DOI 10.1186/s12920-018-0331-4.Saik O.V., Ivanisenko T.V., Demenkov P.S., Ivanisenko V.A. Interactomeof the hepatitis C virus: literature mining with ANDSystem.Virus Res. 2016;218:40-48. DOI 10.1016/j.virusres.2015.12.003.Sarin K.Y., Cheung P., Gilison D., Lee E., Tennen R.I., Wang E., ArtandiM.K., Oro A.E., Artandi S.E. Conditional telomerase inductioncauses proliferation of hair follicle stem cells. Nature. 2005;436(7053):1048-1052. DOI 10.1038/nature03836Sawangarun W., Mandasari M., Aida J., Morita K.I., Kayamori K.,Ikeda T., Sakamoto K. Loss of Notch1 predisposes oro-esophagealepithelium to tumorigenesis. Exp. Cell Res. 2018;372(2):129-140.DOI 10.1016/j.yexcr.2018.09.019.Schulze K., Imbeaud S., Letouz\u00e9 E., Alexandrov L.B., Calderaro J.,Rebouissou S., Couchy G., Meiller C., Shinde J., Soysouvanh F.,CalatayudA.L., Pinyol R., Pelletier L., Balabaud C., Laurent A.,Blanc J.F., Mazzaferro V., Calvo F., Villanueva A., Nault J.C., Bioulac-Sage P., Stratton M.R., Llovet J.M., Zucman-Rossi J. Exomesequencing of hepatocellular carcinomas identifies new mutationalsignatures and potential therapeutic targets. Nat. Genet. 2015;47(5):505-511. DOI 10.1038/ng.3252.Sera T., Hiasa Y., Mashiba T., Tokumoto Y., Hirooka M., Konishi I.,Matsuura B., Michitaka K., Udaka K., Onji M. Wilms\u2019 tumour 1gene expression is increased in hepatocellular carcinoma and associatedwith poor prognosis. Eur. J. Cancer. 2008;44(4):600-608.DOI 10.1016/j.ejca.2008.01.008.Song Z., Li Z., Han W., Zhu C., Lou N., Li X., Luo G., Peng S., Li G.,Zhao Y., Guo Y. Low DAPK1 expression correlates with poor prognosisand sunitinib resistance in clear cell renal cell carcinoma.Aging ( Albany NY). 2020;13(2):1842-1858. DOI 10.18632/aging.103638.Takakura M., Kyo S., Inoue M., Wright W.E., Shay J.W. Function ofAP-1 in transcription of the telomerase reverse transcriptase gene(TERT ) in human and mouse cells. Mol. Cell Biol. 2005;25(18):8037-8043. DOI 10.1128/MCB.25.18.8037-8043.2005.Tan Y., Li Y. HCV core protein promotes hepatocyte proliferation andchemoresistance by inhibiting NR4A1. Biochem. Biophys. Res.Commun. 2015;466(3):592-598. DOI 10.1016/j.bbrc.2015.09.091.Tucci F.A., Broering R., Johansson P., Schlaak J.F., K\u00fcppers R. B cellsin chronically hepatitis C virus-infected individuals lack a virusinducedmutation signature in the TP53, CTNNB1, and BCL6 genes.J. Virol. 2013;87(5):2956-2962. DOI 10.1128/JVI.03081-12.Xu R.H., Wei W., Krawczyk M., Wang W., Luo H., Flagg K., Yi S.,Shi W., Quan Q., Li K., Zheng L., Zhang H., Caughey B.A., Zhao Q., Hou J., Zhang R., Xu Y., Cai H., Li G., Hou R., Zhong Z.,Lin D., Fu X., Zhu J., Duan Y., Yu M., Ying B., Zhang W., Wang J.,Zhang E., Zhang C., Li O., Guo R., Carter H., Zhu J.K., Hao X.,Zhang K. Circulating tumour DNA methylation markers for diagnosisand prognosis of hepatocellular carcinoma. Nat. Mater. 2017;16(11):1155-1161. DOI 10.1038/nmat4997.Yang C., Zhang Y., Wang J., Li L., Wang L., Hu M., Xu M., Long Y.,Rong R., Zhu T. A novel cyclic helix B peptide inhibits dendriticcell maturation during amelioration of acute kidney graft rejectionthrough Jak-2/STAT3/SOCS1. Cell Death Dis. 2015;6(11):e1993.DOI 10.1038/cddis.2015.338.Ye S., Zhao X.Y., Hu X.G., Li T., Xu Q.R., Yang H.M., Huang D.S.,Yang L. TP53 and RET may serve as biomarkers of prognosticevaluationand targeted therapy in hepatocellular carcinoma. Oncol.Rep. 2017;37(4):2215-2226. DOI 10.3892/or.2017.5494.Zhang C., Li J., Huang T., Duan S., Dai D., Jiang D., Sui X., Li D.,Chen Y., Ding F., Huang C., Chen G., Wang K. Meta-analysis ofDNA methylation biomarkers in hepatocellular carcinoma. Oncotarget.2016;7(49):81255-81267. DOI 10.18632/oncotarget.13221.Zhang H., Weng X., Ye J., He L., Zhou D., Liu Y. Promoter hypermethylationof TERT is associated with hepatocellular carcinomain the Han Chinese population. Clin. Res. Hepatol. Gastroenterol.2015;39(5):600-609. DOI 10.1016/j.clinre.2015.01.002.Zhu Z., Tran H., Mathahs M.M., Moninger T.O., Schmidt W.N. HCVinduces telomerase reverse transcriptase, increases its catalytic activity,and promotes caspase degradation in infected human hepatocytes.PLoS One. 2017;12(1):e0166853. DOI 10.1371/journal.pone.0166853.Zhu Z., Wilson A.T., Gopalakrishna K., Brown K.E., Luxon B.A.,Schmidt W.N. Hepatitis C virus core protein enhances Telomeraseactivity in Huh7 cells. J. Med. Virol. 2010;82(2):239-248. DOI10.1002/jmv.21644.Zong C., Qin D., Yu C., Gao P., Chen J., Lu S., Zhang Y., Liu Y., Yang Y.,Pu Z., Li X., Fu Y., Guan Q., Wang X. The stress-response moleculeNR4A1 resists ROS-induced pancreatic \u03b2-cells apoptosis via WT1.Cell Signal. 2017;35:129-139. DOI 10.1016/j.cellsig.2017.03.012.Zucman-Rossi J., Villanueva A., Nault J.C., Llovet J.M. Genetic landscapeand biomarkers of hepatocellular carcinoma. Gastroenterology.2015;149(5):1226-1239.e4. DOI 10.1053/j.gastro.2015.05.061."} +{"text": "Klebsiella pneumoniae, a leading pathogen for mortality associated with antimicrobial resistance (AMR), was responsible for > 250,000 deaths in 2019. Genomic surveillance can guide the development of vaccines and new antibiotics against this pathogen. While AMR disproportionally affects low-and middle-income countries, limited genomic data are available from these countries. To close this gap, this study provides genomic characterization of K. pneumoniae blood isolates recovered in Peru.K. pneumoniae blood culture isolates were collected during an AMR surveillance study (VIRAPERU) from Jul 2017 to Oct 2019, from 15 tertiary hospitals from 13 regions of Peru. DNA extraction , DNA library and genome sequencing were conducted. De novo assembling (SPAdes v3.13.1), quality assessment and annotation (Nullarbor v2.0), and identification of species, ST group, K/O loci, AMR (Kleborate v2.0.1) were conducted. Phylogenetic trees were built with Microreact v.192.Consecutive non-duplicate K. pneumoniae isolates, 114 were recovered and confirmed to belong to the Klebsiella taxon. Six species were identified, the most prevalent being K. pneumoniae (106), followed by K. quasipneumoniae (3). Among carbapenem-resistant isolates (n=13), 10 (77%) carried the blaNDM-1 gene, while other three carried blaKPC-2 (1), blaIMP-16 (1) or no carbapenemase (1). Phenotypic co-resistance to colistin was present in 2 isolates, both negative for mcr-1 gene. The most common mechanisms of resistance to 3rd generation cephalosporins, quinolones and to aminoglycosides were CTX-M-15 (74.4%), qnrB (63.6%), aac(6')-Ib-cr (87.5%), respectively. Many other AMR genetic determinants were identified . Sixty ST groups were identified, but only 6 ST groups carried a carbapenemase gene . A wide diversity of K and O locus was also identified (54 distinct K-loci and 14 distinct O-loci).From 119 K. pneumoniae strains, carrying multiple AMR genes. Carbapenem resistance is principally a result of blaNDM-1 carriage, found across 6 specific ST groups.Bloodstream infections in Peru are caused by a wide diversity of Omai Garner, PhD, Beckman Coulter, Inc.: Clinical trial data collection funded by Beckman Coulter, Inc. Victor Nizet, MD, Cellics Therapeutics: Advisor/Consultant|Clarametyx Biosciences: Advisor/Consultant|Vaxcyte, Inc.: Advisor/Consultant|Vaxcyte, Inc.: Grant/Research Support."} +{"text": "Liver transplanted (LT) patients for hepatocellular carcinoma (LT-HCC) or for other causes (LT-no-HCC) may develop post-transplantation malignancies. Although immune activation and senescence are frequently implicated in cancer development, no data is available on their possible role as biomarkers predictive of tumor onset in this setting. A total of 116 patients were investigated: the 45 LT-HCC patients were older than the 71 LT-non-HCC (p=0.011), but comparable for sex, HCV, HBV infection and immunosuppressive treatment. At baseline, the numbers of activated and senescent-like circulating cells were significantly higher in LT-HCC patients than in LT-no-HCC ones. After a median follow-up of 26.8 months, 6 post-transplant malignancies (PTM) occurred: 4 in LT-HCC (8.9%) and 2 in LT-no-HCC (2.8%) patients. Overall, subjects with high percentages of activated and exhausted T and B cells at baseline were at higher risk of PTM. Notably, within the LT-HCC group, a higher percentage of senescence-like T cells was also associated with cancer development. Moreover, patients with PTM had higher telomere erosion and higher levels of circulating PAMPs (16S rDNA) and DAMPs (mtDNA) when compared with matched patients without PTM. Overall, these findings suggest that immune activation and exhaustion may be useful to predict the risk of PTM occurrence, regardless of the cause of transplantation. In LT-HCC, T-cell senescence represents an additional risk factor for tumor onset. Liver transplantation is the treatment of choice for patients with end-stage liver disease, acute liver failure or hepatocellular carcinoma (HCC). In Italy, a total of 12,519 liver transplants were performed between 2010 and 2020 compared to liver transplanted patients for other causes (LT-no-HCC) followed by chronic local inflammation \u201311. Afte+ T cells. Consistently, lower thymic output and shorter telomeres were associated with a higher risk of developing cancer in the same cohort , which have been implicated in both aging and cancer development , 16. In e cohort . Further outcome .Considering the possible clinical relevance of the availability of suitable biomarkers for the prediction of tumor onset in LT patients, in the present study we have characterized immune activation, exhaustion, and senescence markers in the blood of a prospective series of LT patients with the final goal to assess their possible usefulness in the definition of the risk of PTM development.3 = 4/3 x 3.14 x (radius of the tumor nodule in mm3)\u201d. Total tumor volume (TTV) was calculated as the sum of the tumor volume of each nodule. LT-HCC patients were followed for HCC recurrence through CT-scan or MRI every 3 months during the first year, and every 6 months thereafter, according to the European Association for the Study of the Liver/European Organization for Research and Treatment of Cancer (EASL-EORTC) clinical practice guidelines for the management of hepatocellular cancer . Patients\u2019 clinical information were recorded and included personal details , transplant details score and alpha-fetoprotein levels at liver transplantation) and post-transplantation immunosuppressive schedule, considering modifications during follow-up. For LT-HCC patients, tumor characteristics were assessed through explant pathology evaluation for the following characteristics: number of HCC nodules, maximum nodular diameter, tumor differentiation and presence of macro/micro-vascular invasion. Vital tumor volume was quantified according to the following equation: \u201cTumor volume mmr cancer . As theyAfter a median follow-up of 26.8 months following liver transplantation, 6 patients developed a PTM (LT-PTM): 5 were DNMs and 1 was an HCC recurrence. DNMs were defined as neoplasms developing after transplantation in patients negative at pre-transplant screening for the HCC, or related pre-malignant lesions/conditions. DNMs were coded according to the International Classification of Diseases and Related Health Problems, 10th revision (ICD-10). Diagnosis of DNMs was established by histology on biopsies or surgical specimens of the tumor. Date of biopsy or surgical procedure was designated as the date of cancer diagnosis. All patients underwent a full pre-transplant screening aimed at excluding any type of cancer other than HCC, or related premalignant lesions/conditions, which was negative in all patients. Moreover, to avoid any accidental missing pre-LT diagnosis, lesions that appeared within 6 months after transplantation were excluded from the definition of DNM. In our cohort, the 5 DNMs were: infiltrating ductal carcinoma of the breast, ovarian cancer, larynx carcinoma, basal cell carcinoma of the external auditory canal, and prostate cancer. Among the 110 patients without PTM (LT-no-PTM), 26 subjects were selected as a matched (m)LT-no-PTM control group according to the following inclusion criteria: age, sex difference, immunosuppressive combined strategies, and a median time interval from baseline to follow-up. This study was approved by the Ethical Committee of Padova University Hospital (Prot. 4231/AO/17).Blood samples were collected in EDTA-containing tubes at baseline (at liver transplantation) and at follow-up . From samples at baseline and at closest time to the tumor onset in LT-PTM patients, or with a median time interval similar for mLT-no-PTM patients, peripheral blood mononuclear cells (PBMC) were isolated by centrifugation on a Ficoll-Paque gradient. PBMC were cryopreserved in liquid nitrogen, and plasma samples at - 80\u00b0C, until use..Immunophenotyping was performed on cryopreserved PBMC. Cells were thawed, washed, stained for 20 min in the dark with the Live/Dead Fixable Near-IR Dead Cell Stain Kit and the following labelled monoclonal antibodies (mAbs): anti-CD3 [fluorescein isothiocyanate (FITC)], anti-CD4 [peridinin chlorophyll protein (PerCP)], anti-CD38 [phycoerythrin (PE)], anti-HLA-DR [allophycocyanin (APC)], anti-CD279 [PE-Cy7], anti-CD57 [PE], anti-CD21 [BV421], anti-CD27 [PE-Cy7], anti-IgD [PE], anti-CD274 [BV421] ; anti-CD8 [VioGreen], anti-CD28 [APC], anti-CD19 [VioBright515], anti-CD10 [APC] . Cells were then washed and resuspended in phosphate-buffered saline supplemented with 1% paraformaldehyde. All samples were analyzed using LSRII Flow cytometer (Becton-Dickinson). A total of 50000 events were collected in the lymphocyte gate using morphological parameters (forward and side-scatter). Data were processed with FACSDiva Software (Becton-Dickinson) and analyzed using Kaluza Analyzing Software v.1.2 (Beckman Coulter) DNA was extracted from PBMC, using QIAmp DNA Blood Mini Kit according to the manufacturer\u2019s instructions. Relative telomere length (RTL) was determined by monochrome quantitative multiplex real-time PCR, as previously described , 21.DNA extraction from 200 \u00b5l of plasma was performed using QIAamp DNA Mini Kit , and eluted in 50 \u00b5l of AE Buffer. A quantitative method based on real-time PCR assay was performed to quantify plasma levels of 16S rDNA with primer pair (forward 5\u2019-AGTTTGATCCTGGCTCAG-3\u2019 and reverse 5\u2019-GWATTACCGCGGCKGCTG-3\u2019) and probe (5\u2019-FAM-GCTGCCTCCCGTAGGAGT-BHQ-3\u2019), as previously described , 23. ResContinuous variables were summarized using median and interquartile range (IQR), categorical variables as frequencies and percentages. The median follow-up time was based on the reverse Kaplan-Meier estimator. Clinical characteristics at baseline were compared between LT-HCC and LT-no-HCC patients using the Kruskal-Wallis test, or Fisher exact test as appropriate. A Mann-Whitney test, adjusted for age, was used to address comparisons of each immunological parameter distribution between groups of interest. The impact of the immunological parameters on the probability of experiencing HCC or PTM was estimated in univariate logistic regression models fitted by penalized maximum likelihood to address low frequency data. Each covariate was considered as a categorical variable according to high and low levels. Optimal cut-points were selected using a criterion based on maximizing the Youden index, being the summary measure of the ROC curve, over all possible cut-points. The odds ratios (ORs) were reported with their 95% confidence interval (CI). ORs were also adjusted for age as continuous variable. Subgroup analyses were performed with explorative intent. All statistical tests were two-sided and a p value <0.05 was considered statistically significant. Statistical analyses were performed using the RStudio .vs 53.0 years (45.5-61.0), p=0.011.The patients\u2019 characteristics are summarized in + T cells and memory B cells were significantly higher in LT-HCC compared to LT-no-HCC patients (%CD8+CD38+HLA-DR+: 10.89 (5.61-18.52) vs 6.59 (4.26-9.25), p=0.003; %CD19+CD10-CD21-CD27+: 10.97 (5.59-20.68) vs 7.60 (3.00-13.72), p=0.040) (+ T cells (%CD4+CD38+HLA-DR+: 7.23 (4.11-14.12) vs 6.21 (3.49-9.23), p=0.092) vs 7.54 (4.00-12.92), p=0.254; %CD4+PD-1+: 9.28 (5.66-13.50) vs 7.27 (4.54-10.34), p=0.222; %CD19+PD-L1+: 4.96 (3.12-9.75) vs 5.16 (2.18-9.00), p=0.797) vs 5.92 (3.54-10.97), p=0.006; %CD4+CD28-CD57+: 3.80 (1.36-14.03) vs 1.80 (0.48-3.41), p=0.002; %CD19+CD27-IgD-: 12.20 (6.28-17.67) vs 6.59 (4.24-12.50), p=0.019) following LT, 6 patients developed a PTM: 4 patients (8.9%) (3 DNMs and 1 an HCC recurrence) were in the LT-HCC group, and 2 were in the LT-no-HCC group Table\u00a01.To evaluate the role of immune activation, exhaustion and senescence as possible markers predictive of the risk of tumor development in this setting, we analyzed these immunological parameters at baseline in samples obtained from the 6 LT-PTM patients in comparison with those of 110 LT-no-PTM patients. At baseline, the two groups did not differ by age, sex, HCV and HBV infection vs 7.14 (4.48-11.98), p=0.002; %CD4+CD38+HLA-DR+: 14.28 (10.53-16.84) vs 6.26 (3.58-9.77), p=0.0001; %CD19+CD10-CD21-CD27+: 25.57 (10.09-28.57) vs 8.55 (4.20-15.40), p=0.024) (The percentages of activated CD8p=0.024) Table\u00a03.+PD-1+: 19.81 (16.97-28.90) vs 7.78 (4.62-14.67), p=0.000; %CD4+PD-1+: 22.71 (17.96-27.89) vs 7.75 (4.47-10.85), p=0.000; %CD19+PD-L1+: 10.15 (7.82-19.75) vs 5.01 (2.23-9.09), p=0.015) (The percentage of circulating immune cells expressing markers of exhaustion was significantly higher in LT-PTM than in LT-no-PTM patients (%CD8p=0.015) Table\u00a03.+ T cells and B cells tended to be higher in the LT-PTM than in LT-no-PTM patients vs 10.08 (5.33-12.83), p=0.002), while no difference was observed in senescent-like CD8+ and CD4+ T cells copies/\u00b5l, p=0.008); since no difference occurred in the two groups during follow-up, this level still remained higher at follow-up (64.95 (29.51-106.15) vs 26.99 (11.27-58.74) copies/\u00b5l, p= 0.074) (vs 1822 (985-3984) copies/\u00b5l, p=0.096), but they become significantly higher at follow-up (3075 (2187-6244) vs 1668 (447-2424) copies/\u00b5l, p= 0.040) vs 1.08 (0.80-1.63), p=0.391). Notably, at follow-up, the levels did not differ between the two groups (RTL: 0.79 (0.73-0.80) vs 0.77 (0.75-0.83), p=0.873), thus indicating that LT-PTM patients tended to have a higher telomere erosion during the same follow-up interval vs -0.09 , p=0.091).At baseline, relative telomere lengths (RTL) on PBMC were longer, although not statistically significant, in LT-PTM than in mLT-no-PTM patients (RTL: 1.46 (1.03-1.63) de novo malignancies (DNMs) and HCC recurrence are the most common causes of long-term morbidity and death . The patients/participants provided their written informed consent to participate in this study.MRP, SS, MT, PP, DS, PB and ADR, designed the study. MRP, ER, FC, SG, performed the investigations. SS, DS, UC, PB, provided samples and reagents. PDB performed the statistical analysis. MRP wrote the manuscript. SS, MT, SG, PDB, PP, DS, UC, RD, PB and ADR supervised the project, reviewed and editing the manuscript. All authors contributed to the article and approved the submitted version.This work was supported by Ricerca Corrente IRCCS Centro di Riferimento Oncologico, Aviano: Italian Association for Research on Cancer; Grant number: AIRC IG No. 19112; and \u201cPathogenesis of EBV-driven post-transplant malignancies\u201d granted by Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padova, Italy .The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Bifidobacterium lactis BL-99 (B.lactis BL-99) on the intestinal inflammation and functionsin the zebrafish models. After feeding for 6 hours, B.lactis BL-99 was fully retained in the larval zebrafishintestinal tract and stayed for over 24 hours. B.lactis BL-99 promoted the intestinal motility andeffectively alleviated aluminum sulfate-induced larval zebrafish constipation(p < 0.01). Irregular high glucose diet induced adultzebrafish intestinal functional and metabolic disorders. After fed withB. lactis BL-99, IL-1\u03b2gene expression was significantly down-regulated, and IL-10 andIL-12 gene levels were markedly up-regulated in this model(p < 0.05). The intestinal lipase activity was elevatedin the adult zebrafish intestinal functional disorder model afterB. lactis BL-99 treatment(p < 0.05), but tryptase content had no statisticalchanges (p > 0.05). B.lactis BL-99 improved the histopathology of the adultzebrafish intestinal inflammation, increased the goblet cell numbers, andup-and-down metabolites were markedly recovered after treatment ofB. lactis BL-99 (p <0.05). These results suggest that B. lactisBL-99 could relieve intestinal inflammation and promote intestinal functions, atleast in part, through modulating intestinal and microbial metabolism tomaintain intestinal health.This study was designed to explore the therapeutics and the mechanisms of apatented and marked gastric acid and intestine juice-resistant probiotics Probiotics consumption for health promotion and well-being has increased worldwide inrecent years and variBacillus spp [Bifidobacterium,Lactobacillus, Bacillus, and several otherbacterial species [Aeromonas hydrophila, A.salmonicida, Yersinia ruckeri, andV. anguillarum to intestinal mucus fromrainbow trout (in vitro) [L. rhamnosus also counteracts zebrafishneurotoxicity caused by PFBS [The most studied probiotic candidates in aquaculture belong to the Firmicutes phylum,namely lactic acid-producing bacteria (LAB) and llus spp , 9\u201313. Allus spp , 15. Stu species \u201318. Thes species , 20. LAB species ,and somn vitro) . Dietaryn vitro) , and die by PFBS .Bifidobacterium, which makes it difficult to reach and colonizein the intestine through gastric juice [Bifidobacterium lactisBL-99 was originally isolatedfrom the intestines of a Chinese healthy infant [Inability to acid and gastrointestinal juice is a common property ofic juice . Bifidoby infant , 26 and y infant ,28. Thiy infant .B. lactis BL-99 has no exogenous antibioticresistance genes [B.lactis BL-99 was confirmed no dose-dependent mortality andtoxicity throughout multidose oral toxicity tests in mice and rats and thusgenerally recognized as safe (GRAS) status as a probiotic [In vivo experiments inmice showed that B. lactis BL-99 significantlypromoted the growth of intestinal Bifidobacteria and Lactic acidbacteria, and inhibited Desulfovibrio and/orEnterobacter, especially Helicobacter pylori and/orEscherichia-Shiga Bacteria [ce genes and hasrobiotic . In vivoBacteria , 30. ThiBacteria .The research of probiotics on intestinal microbial balance, intestinal functions,inflammation, and intestinal metabolites, etc. mostly use traditional mammalianmodels. Conventional mammalian enteritis models are chemical-induced, for example,DSS was used to induce mice colitis , and TNBDanio rerio) intestinal composition is similar to that ofhumans, e.g., connective tissue, external-longitudinal muscle and circular muscle,et al. [B.lactis BL-99 on the digestive enzymes, motility, inflammationand metabolites in the larval and adult zebrafish models.Zebrafish and adult male zebrafishat 3.5 months post fertilization (3.5 mpf) were used in this study. Zebrafishwere maintained at 28\u00b0C in fish water . The zebrafish facility and the laboratory at Hunter Biotechnology, Inc.are accredited by the Association for Assessment and Accreditation of LaboratoryAnimal Care (AAALAC) International , 42, by B. lactis BL-99 was deposited in the ChinaCommon Microbial Culture Collection and Management Center (CGMCC 15650) on April26, 2018 [5\u2019-AGA GTT TGA TCC TGG CTC AG-3\u2019) and 1492R(5\u2019-GGT TAC CTT GTT ACG ACT T T-3\u2019) [B. lactis BL-99 culture was proliferatedwith De Man Rogosa Sharpe (MRS) medium supplemented with0.05% (w/v) L-cysteine (MRSC) for 12\u201348 hrs at 37\u00b0C aerobically [B.lactis BL-99 was 1.5*1011 CFU / g and preservedat -80\u00b0C.26, 2018 andiden T T-3\u2019) . The stawww.dingguo.com). CM-DiI cell-labeling solution and trizol reagent (cat. # 12183555) were bought from Thermo FisherScientific (China) Co., Ltd. FastKing RT Kit (With gDNase) (cat. # KR116-02) wasbought from TIANGEN BioTec (Beijing) Co., Ltd (www.tiangen.com), and iTaq Universal SYBR(R) Green Supermix waspurchased from BIO-RAD Co., Ltd. (www.bio-rad.com). Fish trypsin ELISA kit (item no. ml064285) wasbought from Shanghai Enzyme-linked Biotechnology Co., Ltd. (www.mlbio.cn). Lipase (LPS) kit (item no.A054-2-1) was bought from Nanjing Jiancheng Bioengineering Institute (www.njjcbio.com).Tricaine methanesulfonate (cat. # 886-86-2) and aluminum sulfate (cat. #D1909026) were ordered from Shanghai Aladdin Bio-Chem Technology Co., Ltd, nile red (cat. # MKBP6198V) from Sigma-Aldrich , and glucose (lot. # 20201105) was purchased from Sinopharm ChemicalReagent Co., Ltd . Tissue cell fixation solution at 4%concentration (cat. # AR-0211-250 mL) was ordered from Beijing DingguoChangsheng Biotechnology Co., Ltd containing 0.5% DMSO in PBS [B.lactis BL-99 were treated with larval zebrafish for itsretaining time determination in the intestinal tract and for its effects on theintestinal motility and digestion functions as described below. The dye istransferred from mother to daughter bacteria and fluorescent B.lactis BL-99 were clearly visible in the zebrafishintestinal tract.After collection, O in PBS at 37\u00b0C B. lactis BL-99 at a density of2.42*108 CFU/mL at 28\u00b0C. The zebrafish intestinal fluorescentimages were taken periodically at the designated time points to determine theretaining time of this probiotics. After treatment of fluorescentB. lactis BL-99 for 24 hrs, the zebrafishwere transferred into fish water for 4 and 24 hrs, respectively, 10 zebrafishwere randomly selected from each group and at each time point for visualobservation and image acquisition under a fluorescent stereomicroscope , installed with a high-speed video camera .Quantitative image analyses were performed using image-based analysis, the retaining time and lasting period ofB. lactis BL-99 in the larval zebrafishintestine tract were calculated based on the fluorescent intensity. To protectfluorescent B. lactis BL-99 from light-induceddecomposition, experiments were carried out at a constant temperature (28\u00b0C) inthe dark. All experiments were performed in duplicate and repeated for at least3 times.Wild-type larval zebrafish at 5 dpf were distributed into 6-well microplates, 30 zebrafish per well in 3 ml fish water and treated withfluorescent B. lactis BL-99at concentrations of 2.42*106, 2.42*107 and2.42*108 CFU/mL, respectively, for 24 hrs. Domperidone was usedas a positive control drug. The zebrafish treated with aluminum sulfate and nilered only served as a model control. The zebrafish without any treatment wereused as a negative control. At the end of treatments, the zebrafish were imagedunder a AZ100 fluorescent stereomicroscope, installed with a high-speed videocamera. The therapeutic effects of B. lactisBL-99 on the larval zebrafish constipation were determined based on theintestinal fluorescent quantitative analyses.The larval zebrafish of AB strain at 5 dpf were distributed into a 6-wellmicroplate, 30 zebrafish per well in 3 ml fish water. The zebrafish constipationmodel was established by treatment with 1 \u03bcg/mL aluminum sulfate at 28\u00b0C 6, 2.42*107 and 2.42*108 CFU/mL)were used for B. lactis BL-99 treatment.Untreated control zebrafish were examined in parallel. The adult zebrafish werehoused in a light and temperature-controlled aquaculture facility with astandard 14:10 h light/dark photoperiod. (1) Days 1\u20133 of the experiment: exceptfor the untreated control zebrafish, the resting groups were not fed and starvedfor 3 days. B. lactis BL-99 groups weretreated with this probiotic at 3 designated concentrations, respectively, asdescribed above in fish water every day during the daytime for 8 hrs and thenlived in fresh fish water; (2) Days 4\u201317: B.lactis BL-99 groups were treated with this probiotic duringthe daytime for 8 hrs and then transferred into 3% glucose in fish water for 16hrs. The model zebrafish were only treated with 3% glucose for 16 hrs and theuntreated control zebrafish were fed with brine shrimp twice a day. On the 18thday of the experiment, the zebrafish intestinal tissues were collected and theintestinal digestive enzymes, inflammatory and immunity factor genes andhistopathology were examined, respectively, and the interventional effects ofB. lactis BL-99 were assessed.Seventy-five male adult zebrafish of 3.5 mpf (months post fertilization)wild-type AB strain were transferred into 5 L beaker in a volume of 4 Lcontaining 15 zebrafish. In the initial tests, three concentrations, interleukin-10 (IL-10)and interleukin-12 (IL-12) were determined in the adultzebrafish intestines by real-time quantitative PCR (qPCR) [B.lactis BL-99 treatment, total RNA was extracted from 10homogenized zebrafish per group using trizol reagent. About 2 \u03bcg total RNA ofeach sample was used for cDNA synthesis using FastQuant RT Kit (With gDNase) andqPCR amplifications were carried out with a CFX Connect detection system using the iTaq Universal SYBR Green Supermix in which there werethree technical or biological replicates. The qPCR protocol was 2 minutes at95\u00b0C-40 cycles of 5 seconds at 95\u00b0C-30 seconds at 60\u00b0C. Expression data wasnormalized against the expression of \u03b2-actin and the relative quantification ofeach gene mRNA among groups was calculated as follows: The relative expressionof RNA = 2^\u0394\u0394C(t); \u0394\u0394C(t) = \u0394C(t)Model\u2014\u0394C(t)Probiotics;\u0394C(t) = \u0394C(t)Target gene\u2014\u0394C(t)\u03b2-actin. The primers used inthis study were as follows: \u03b2-ACTIN-FOR:TCGAGCAGGAGATGGGAACC, \u03b2-ACTIN-REV:CTCGTGGATACCGCAAGATTC (GenBank accession numbers57934) [IL-1\u03b2-FOR: GTCACACTGAGAGCCGGAAG,IL-1\u03b2-REV GCAGGCCAGGTACAGGTTAC [IL-10-FOR:TTCAGGAACTCAAGCGGGAT, IL-10-REV:AAGAGCAAATCAAGCTCCCCC [IL-12-FOR:AACTCCTACAAGCCCAGCAC, IL-12-REV:ACACTCGGTCGTCAAACGAA . Each primer pair was designed usingNCBI/Primer-BLAST.To explore the possible anti-inflammation and the intestinal immune mechanisms ofR (qPCR) . Brieflys57934) , 50,IL- 405770) , IL-10-F 553957) , IL-12-FB. lactisBL-99 on the intestinal functions of the adult zebrafish, ELISA kits were usedto determine the intestinal tissue lipase activity and trypsin content. Theoptical density (OD) values were measured by multifunctional microplate reader at wavelength 595 nm for the protein concentration,580 nm for the lipase activity, and 450 nm for the trypsin content,respectively. The lipase activity and trypsin content per gram of protein inzebrafish intestinal tissues were calculated based on the OD values.In order to evaluate the effects of B. lactis BL-99 intervention, weperformed the gut histopathological examinations on the adult zebrafish. At theend of the experiments, zebrafish intestinal tissues were fixed in 4%paraformaldehyde in 0.1 M phosphate buffered saline for 4 hrs at 4\u00b0C, dehydratedin graded series of ethanol solutions before paraffin embedding. Embeddedzebrafish intestines were longitudinally sectioned at 5 \u03bcm and stained withhematoxylin and eosin (H&E) [To confirm the intestinal damage caused by the irregular high-sugar diet, and theeffects of in (H&E) , 51.Thip < 0.05 and fold change \u2265 1.2 or fold change \u2264 0.8333and VIP \u2265 1; and statistically significant changes in at least two dose groups.Student\u2019s t test was used for the statistical analyses of the metabolites.Ten adult zebrafish whole guts from each group were used for the intestinalmetabolite extraction and the metabolomic analysis. Twenty-five mg intestinaltissues from each gut were homogenized with 800 \u03bcL pre-cold precipitation agent. After sonication on ice for10 minutes, let the mixture stand at -20\u00b0C for 120 minutes, followed bycentrifugation at 25000 g for 15 min at 4\u00b0C. Six hundred \u03bcL of supernatant wastaken and put in a freeze-drying machine to drain and reconstituted in 600 \u03bcL of10% methanol solution. After ultrasound and centrifugation, the supernatant waschromatographed using 2777C UPLC system , and the eluted smallmolecules were collected in positive and negative ion modes using Xevo G2-XSQTOF . Metabolite resonances were identified according to theinformation from the Human Metabolome Database (HMDB) and Kyoto Encyclopedia ofGenes and Genomes (KEGG). Significantly changed metabolites between the controland treatment groups were identified following the criteria below:p < 0.05,p < 0.01 and p < 0.001 were allconsidered statistically significant. For quantitative analysis, all data werepresented as mean \u00b1 SEM, and results were statistically compared between theprobiotics-treated and model zebrafish groups. All experiments were repeated forat least 3 times. Zebrafish natural death in untreated groups was \u2264 10%, and allintra- and inter-group coefficient of variation (CV) was \u2264 25%.One-way ANOVA followed by the Dunnett\u2019s test was used to compare differencesamong groups. All statistical analyses were performed using the GraphPadsoftware , and B.lactis BL-99 for 2, 6 and 24 hrs, the fluorescentintensities in the larval zebrafish intestinal tracts were 6.02\u00b1 0.866,10.7\u00b1 1.08 and 13.0 \u00b1 0.601 pixels, respectively. Comparing the fluorescentintensities between 24 hr and 2 hr feeding, p < 0.001,but p > 0.05 when comparing the fluorescent intensitiesbetween 24 hr and 6 hr feeding, suggesting that B.lactis BL-99 effectively retained in the larvalzebrafish intestinal tract after 6 hr feeding.As indicated in B. lactis BL-99from the treatment solutions and transferred the zebrafish into fresh fishwater for 0, 4 and 24 hrs, the larval zebrafish intestinal fluorescence was14.4\u00b1 1.31, 11.5\u00b1 1.58 and 10.5\u00b1 1.57 pixels ,indicating that the larval zebrafish constipation model was successfullyestablished. The positive control drug Domperidone significantly promotedthe intestinal motility . The dose-dependent intestinal fluorescent intensity decreases were found in theconstipation zebrafish treated with B.lactis BL-99 at 2.42*106 (476071 \u00b1 20633pixels), 2.42*107 (456847 \u00b1 15814 pixels) and 2.42*108CFU/mL (414652 \u00b1 11561 pixels), respectively .As demonstrated in IL-1\u03b2 gene expression. A concentration-dependentdownregulations of the IL-1\u03b2 gene expression was observedin the model zebrafish treated with 2.42*106, 2.42*107and 2.42*108 CFU/mL of B.lactis BL-99, and the decreases were 0.511\u00b1 0.055,0.691\u00b1 0.072 and 0.969\u00b1 0.049 folds, respectively, relative to the modelgroup .The purity of the extracted RNA (A260/A280) was in the range of 1.95\u20132.12. Asshown in IL-10 gene expression. After treatment withB. lactis BL-99 at the concentrationsof 2.42*106, 2.42*107 and 2.42*108 CFU/mL,IL-10 and IL-12 expression levels wereelevated to 3.96\u00b1 0.219, 1.27\u00b1 0.150 and 1.85\u00b1 0.176 folds and 1.01\u00b1 0.097, 1.51\u00b1 0.368 and 4.13\u00b10.745 folds , respectively, relative to the modelgroup .B. lactis BL-99 had no statisticallysignificant effect on the intestinal trypsin content, although it showed anincreased trend as indicated in As shown in B. lactis BL-99 treatmentat 2.42*107 CFU/mL led to the developed high villi, increasedgoblet cells and columnar epithelial cells, and the gut tissue morphologywas closely similar to that of normal zebrafish adult zebrafish was taken and shown in ebrafish .B. lactis BL-99 with concentration of2.42*107 CFU/mL (BL-99-10-7) and the model group showedcomplete separation , and the degrees of aggregations amongthe BL-99-10-7 treatment groups were obvious. There were 106 positive-ionmetabolites and 218 negative-ion metabolites were statisticallysignificantly changed in the intestines as compared between normal and themodel zebrafish; and 213 positive-ion metabolites and 402 negative-ionmetabolites with significant differences between the model zebrafish and themodel zebrafish treated with B. lactisBL-99.As shown in B.lactis BL-99 (6B). As shown in Tables B.lactis BL-99. Among the 23 significantly differentintestinal metabolites, 13 metabolites were identified with the knownphysiological and pathological functions: citrulline, glycerol,CDP-Ethanolamine, gluconolactone, uridine, uracil, taurine, mesaconic acid,ureidosuccinic acid, orotic acid, 4-hydroxybenzaldehyde,bis-\u03b3-glutamylcystine and R-lipoic acid. The biological significances forthe remaining 10 metabolites below were not known or unclear yet: SAICAR,isonicotinic acid, GDP-d-mannuronate, 3-dehydro-L-gulonate,-3-hydroxybutane-1,2,3-tricarboxylic acid, cob (I) yrinate a,cdiamide, 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol glucuronide,s-(2-chloroacetyl)glutathione,2,4-diacetamido-2,4,6-trideoxy-d-mannopyranose, andcarbamazepine-o-quinone.Heat maps of significantly changed metabolites between the intestinalfunctional disorder zebrafish (model) and normal (untreated) zebrafish wereindicated in B. lactis has been confirmed as a gastric acid andintestinal juice tolerable probiotics [B.lactis BL-99 effectively preserved in the larval zebrafishintestinal tract after 6 hrs of feeding and stayed in the intestinal tract for over24 hrs. B. lactis BL-99 promoted the intestinalmotility and relieved the constipation in aluminum sulfate-induced larval zebrafishmodel. This patented and marked probiotics increased digestive enzyme lipaseproduction, regulated inflammatory and immune responses, and relieved intestinalinflammation in an irregularly high-glucose diet-induced adult zebrafish intestinalfunctional disorder model. These findings imply that B.lactis BL-99 could be an effective and probably potentmodulator of the intestinal functions for both physiological and pathologicalconditions.obiotics that makL. casei SY13 and exploreits effects on gut microbial structure and diversity in mice, the authors found thatthe stable colonization of L. casei SY13 wasassociated with dosage and treatment days, and thus laid a foundation for studyinginteractions between L. casei SY13 and othermembers of the gut microbiota [B. lactis BL-99 to play itsfunctions in the intestinal health and the disease prevention and treatment.Orally administered probiotics encounter various challenges on their journey throughthe mouth, stomach and intestinal tract. The health benefits of probiotics arediminished mainly due to the substantial reduction of viable probiotic bacteriaunder the harsh conditions in the gastrointestinal cavity and the colonizationresistance caused by commensal bacteria . In a prcrobiota . The lonB. lactisBL-99 promoted the intestinal motility and relief constipation and increased thedigestive enzyme lipase production in the larval and adult zebrafish models,supporting the uses of this probiotics in preventing and treating dyspepsia andmotility disorders.In normal digestion, food is transited through the gastrointestinal tract by rhythmiccontractions called peristalsis. Slow gastrointestinal contractions could lead todigestive function disorders and constipation that areIL-1\u03b2 geneexpression, reduced intestinal immune factors IL-10 andIL-12 gene levels, lessened intestinal lipase activity, damagedintestinal histology, and disordered intestinal metabolomics. AfterB. lactis BL-99 treatment, the adult zebrafishintestinal inflammation was alleviated, the intestinal immune responses wereenhanced, and the intestinal mucus barrier and histopathology were ameliorated.Sugar consumption has dramatically increased in the past few decades and overB.lactis BL-99 treatment recovered these intestinal andmicrobiota metabolites to the levels similar or close to the normal controlzebrafish. These results suggest that B. lactisBL-99 could relieve intestinal inflammation and promote intestinal functions,probably at least in part, through modulating intestinal and microbial metabolism tomaintain intestinal health and 5 intestinal microbiota-related metabolites were found statistically different in the intestines betweenthe high-glucose fed and untreated control zebrafish. These 11 metabolites, plus 2organic compounds bis-\u03b3-glutamylcystine and R-lipoic acid, were all significantlyincreased in the gut of 3% glucose-fed zebrafish. Surprisedly, l health . These aS1 File(XLS)Click here for additional data file."} +{"text": "Venenivibrio stagnispumantis strain CP.B2T is a thermophilic, chemolithoautotrophic bacterium from the family Hydrogenothermaceae (phylum Aquificota), isolated from Champagne Pool in the Waiotapu geothermal field, Aotearoa-New Zealand. The genome consists of 1.73 Mbp in 451 contigs with a 30.8 mol% G+C content. Venenivibrio, within the phylum Aquificota (family Hydrogenothermaceae), is characterized by thermophilic microaerophilic hydrogenotrophs of M\u0101ori iwi (tribe) Ng\u0101ti Tahu-Ng\u0101ti Whaoa. The V. stagnispumantis genome has previously been sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project KMG-II (mana whenua (customary rights) over the bacterium, its genome, and the location in which it was isolated.The bacterial genus notrophs \u20133. The tt KMG-II was cultivated using a modified MSH medium within a headspace consisting of N2/H2/CO2/O2 at ratios of 50:40:7.5:2.5 (vol/vol), respectively (\u22121) of CP.B2T was performed using a NucleoSpin Soil kit according to the manufacturer\u2019s protocols. Whole-genome sequencing was undertaken using the Illumina HiSeq 2500 platform with TruSeq DNA Nano (550) library preparation for paired-end 101-bp reads . Default parameters were used for all assembly, quality control (QC), and annotation software unless otherwise specified. A total of 3.8-Gbp raw sequences (37.32 million reads) were assembled using SPAdes v3.12.0 (JAPEIW010000000) using the GeneMarkS-2+ protein reference set. A functionally equivalent annotation of 47 scaffolds using the Integrated Microbial Genomes annotation pipeline v4.16.4 .The V. stagnispumantis CP.B2T, Sulfurihydrogenibium yellowstonense SS-5T, and Persephonella marina EX-H1T genomes gave <80% similarity for each, confirming the designation of Venenivibrio as a separate genus to sister genera Sulfurihydrogenibium and Persephonella.A pairwise average nucleotide identity (ANI) comparison using FastANI v0.1.3 of the VV. stagnispumantis CP.B2T genome were deposited in the European Nucleotide Archive under the BioProject accession no. PRJEB55610. The assembled genome was deposited in the Genomes Online Database (Ga0591133), for associated annotation with the Integrated Microbial Genomes & Microbiomes platform (2799112217). This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under accession no. JAPEIW010000000. The version described in this paper is version JAPEIW010000000.1.Raw sequences for the platform (IMG gen"} +{"text": "Enterococcus spp. lower urinary tract infections (UTI). With this rationale, our clinical microbiology laboratory discontinued routine identification on Enterococcus urine isolates in 2012 and report \u201caminopenicillins are predictably reliable for uncomplicated enterococcal UTI\u201d. The study objective was to compare outcomes of patients treated with aminopenicillins (AP) versus non-aminopenicillins (NAP) for enterococcal cystitis.Aminopenicillins achieve urinary concentrations that overcome aminopenicillin resistance in E. faecalis, enterococcal UTI in past year, review of systems unavailable/altered mental status, urinary instrumentation except for stent/catheter, systemic infection, fever, genitourinary trauma, renal transplant. Primary endpoint: clinical and microbiologic success at 14 days, defined as resolution of symptoms without new symptoms and no repeat culture growth of index organism. Logistic regression evaluated characteristics associated with 14-day failure. Sample size of 178 calculated for non-inferiority using \u03b1=0.025, \u03b2=0.8, 15% non-inferiority margin.IRB approved, retrospective cohort of adults hospitalized with symptomatic enterococcal cystitis from 2013-2021. Exclusion: definitive 178 subjects included, 89 AP, 89 NAP . VRE identified: 73 (82%) AP and 76 (85%) NAP (P=0.50). Amoxicillin and ampicillin used most in AP. Linezolid and fosfomycin most common agents in NAP. 14-day clinical composite endpoint was no different between AP and NAP groups, respectively . No variables independently predicted failure (Table\u00a01). Non-inferiority analysis for AP vs. NAP for 14-day composite: mean difference 1.1% . Definite E. faecium subgroup: 14-day clinical composite success for was no different between AP and NAP groups, respectively .E. faecium. This stewardship strategy has implications to preserve VRE active therapies (e.g. linezolid) for serious infections.AP were non-inferior to NAP, supporting their use as first-line therapy for cystitis due to enterococci, including All Authors: No reported disclosures."} +{"text": "Ocimum tenuiflorum L. This study evaluated the antibacterial activity of O. tenuiflorum extract and its interaction with antibacterial drugs against common mastitis pathogens including Staphylococcus aureus, coagulase-negative Staphylococci (CNS), Streptococcus agalactiae, and Escherichia coli. Anti-inflammatory activities in LPS-stimulated RAW264.7 macrophage cells were also studied. The O. tenuiflorum extract exhibited antibacterial activities against S. aureus, CNS, and S. agalactiae with minimum inhibitory concentration (MIC) ranging from 3.9 to 31.2 \u00b5g/mL and minimum bactericidal concentration (MBC) ranging from 15.6 to 500 \u00b5g/mL. Combinations of O. tenuiflorum with penicillin or amoxicillin-clavulanic acid showed synergistic effects against all tested strains but an additive effect with cefazolin and gentamicin. Pretreatment of the extract significantly decreased the expression of inflammatory molecules generated by LPS in macrophages. Results suggested O. tenuiflorum effectiveness against various Gram-positive mastitis bacteria, with the potential to reduce antibacterial doses and combat inflammation.Mastitis is the most prevalent global illness affecting dairy cows. This bacterial infection damages and inflames the udder tissues. Several plant extracts have demonstrated synergistic antibacterial activities with standard drugs in mastitis treatment. Scant information exists on Staphylococcus aureus (S. aureus), Streptococcus agalactiae , Escherichia coli (E. coli), Enterococcus spp., and coagulase-negative Staphylococci (CNS) -bis(4-methoxy6-nitro) benzene sulfonic acid hydrate (XTT), N-methyl dibenzopyrazine methyl sulfate (PMS) were obtained from Sigma-Aldrich . The 2x qPCRBIO SyGreen 1step Lo-ROX was obtained from PCR Biosystems . Tri-RNA Reagent was purchased from Favorgen . IL-6 and PGE2 quantitative sandwich ELISA kits were obtained from Abcam . The Griess reagent was purchased from Promega . All other reagents were obtained from Sigma-Aldrich unless otherwise describedLipopolysaccharide (LPS) from O. tenuiflorum were cleaned with distilled water twice. Then, 500 g of sample was dried at 60 \u00b0C and then powdered into fine powder. Two liters of 70% ethanol were added to powdered dried plants and allowed to remain for 24 h at room temperature. The mixture was filtered and evaporated using a rotary evaporator to eliminate the ethanol. The liquid was subsequently freeze-dried and stored at \u221220 \u00b0C until used.Leaves of v/v) formic acid). Authentic standards consisted of syringic acid (>97.0% T), sinapic acid , quercetin , naringenin , myricetin (>97.0% HPLC), luteolin (>98.0% HPLC), kaempferol (>97.0% HPLC), hydroxybenzoic acid , 4\u2013hesperidin , genistein (>98.0% HPLC), ferulic acid , (\u2212)-epigallocatechin gallate (>98.0% HPLC), 3,4-dihydroxybenzoic acid (\u226597% T), p-coumaric acid , cinnamic acid (>98.0% HPLC), chlorogenic acid , caffeic acid and apigenin (>98.0% HPLC) from Tokyo Chemical Industry , vanillic acid (\u226597% HPLC), rutin (\u226594% HPLC), rosmarinic acid (\u226598% HPLC) and gallic acid (97.5\u2013102.5% T) from Sigma-Aldrich , galangin (\u226598.0% HPLC) from Wuhan ChemFaces Biochemical Co., Ltd. and isorhamnetin (\u226599.0% HPLC) from Extrasynthese . The LC\u2013ESI-MS/MS chromatograms were shown in The phytochemical profile was analyzed using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) with the conditions and validation following a well-established protocol as previously reported without S. aureus, S. agalactiae, CNS, and E. coli from clinical bovine mastitis cases were obtained from milk samples and collected from the Dairy Farming Promotion Organization of Thailand (D.P.O.), Saraburi, Thailand. Microorganism isolates were characterized based on their culture, morphological (Gram stain), and biochemical properties and sub-cultured on the selective medium following standard microbiological techniques -bis (4-methoxy-nitro) benzene sulfonic acid hydrate (XTT)-based assay to determine the concentration of 5 cells/well) or 6-well plates (1 \u00d7 106 cells/well) and then pretreated for 12 h with media containing different concentrations of O. tenuiflorum extract before stimulation with LPS (10 ng/mL) for 24 h. Culture supernatants were collected from 96-well plates for interleukin-6 (IL-6), nitric oxide (NO), and prostaglandin E2 (PGE2). Cells were harvested from the 96 or 6-well plates for qPCR analysis.RAW 264.7 cells were cultured overnight in 96-well plates (1 \u00d7 10v/v) ratio with Griess reagent -ethylenediamine). After incubation for 10 min at room temperature, absorbance was measured at 540 nm using a microplate reader . A nitrite standard curve was used to calculate nitrite concentration in the supernatant.Nitric oxide generation was assessed by measuring the quantity of nitrite in the culture medium based on the Griess reaction . FollowiO. tenuiflorum extract on LPS-induced RAW 264.7 cell inflammation, the relative mRNA levels of IL-6, tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin-1\u03b2 (IL-1\u03b2), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) were measured by RT-qPCR. Total RNA was extracted by homogenizing the cells in Tri-RNA Reagent according to the manufacturer\u2019s instructions. The RT-qPCR reaction mixture, qPCRBIO SyGreen 1-step Lo-ROX , was made according to the manufacturer\u2019s guidelines. Quantitative polymerase chain reaction (qPCR) was performed by qTOWER3 Real-Time PCR Systems . Thermal cycling conditions were used to amplify the target genes using the following parameters: reverse transcription step at 45 \u00b0C for 10 min, polymerase activation step at 95 \u00b0C for 2 min, denaturation step at 40 amplification cycles at 95 \u00b0C for 5 s, and the final step at 60 \u00b0C for 30 s. Relative levels of gene expression were normalized to glyceraldehyde 3-phosphate dehydrogenase (GAPDH) mRNA using the 2\u2212\u0394\u0394CT method [To investigate the effects of The levels of IL-6 and PGE2 in RAW 264.7 cell culture supernatants were measured using an enzyme-linked immunosorbent assay (ELISA) kit obtained from Abcam and performed according to the manufacturer\u2019s instructions.p \u2264 0.05) was considered statistically significant.Statistical analysis was performed using GraphPad Prism ver. 5 software. The values are presented as mean \u00b1 standard deviation (SD) from at least three independent replicates. Statistical significance between groups was determined using a one-way ANOVA followed by Tukey\u2019s test. Statistical significance between groups was determined using a one-way ANOVA followed by Tukey\u2019s test. A probability of 0.05 or less (O. tenuiflorum ethanolic extract as follows: (i) O. tenuiflorum had antibacterial effects against Gram-positive bacteria including S. aureus, CNS, and S. agalactiae but not Gram-negative bacteria, (ii) O. tenuiflorum extract showed synergistic effects with penicillin or amoxicillin-clavulanic acid against all tested strains, while cefazolin and amikacin had an additive effect, and (iii) O. tenuiflorum extract showed anti-inflammatory activities, with reduced expression of inflammatory molecules in LPS-treated macrophages. However, further investigations on route and dosage for therapy in animal models are required.This study explored new antibacterial candidates from plants with multi-target abilities in mastitis treatment, covering antibacterial and anti-inflammation activities. Results demonstrated promising anti-mastitis properties of"} +{"text": "JCI Insight. 2019;4(13):e125191. https://doi.org/10.1172/jci.insight.125191Original citation: JCI Insight. 2022;7(20):e165600. https://doi.org/10.1172/jci.insight.165600Citation for this corrigendum: The authors recently became aware that representative illustrations presented in n-3 DPA (n-3 DPA), including the gut-protective RvD5n-3 DPA (27) (Using liquid chromatography\u2013tandem mass spectrometry\u2013based (LC-MS/MS\u2013based) LM profiling, we identified mediators from all 4 major fatty acid bioactive metabolomes, including lipoxygenase- and cyclooxygenase-derived LMs that were identified in accordance with published criteria (33). The identity of each of the mediators was further corroborated by evaluating MS/MS spectra obtained in a subset of the samples analyzed and matching at least 6 diagnostic ions with those obtained for reference standards for each of these molecules, as shown for RvD5n-3 DPA (23). Mun-3 DPA . This sh"} +{"text": "Dear Editor,1 However, its function in subverting host translation machinery is still elusive.COVID-19 (Coronavirus Disease 2019) is causing an unprecedented public health crisis. Protein translation is crucial for virus lifecycle. Nucleocapsid (N) protein is among the most abundant SARS-CoV-2 proteins and highly conserved across coronavirus genus.2 , indicating that N mRNAs were much less efficiently translated after NPM1 depletion Fig. . SimilarIn IVT assays, ribosomes from 293T cells with exogenous N showed enhanced translation efficiency when translating N mRNAs, which was suppressed upon NPM1 knockdown Fig. , top row3 We therefore hypothesized that N protein functions via NPM1-binding snoRNAs. We first re-analyzed snoRNA expression in different tissues using public data from ENCODE,4 and found significant overlap of expression profile among lung, liver, and intestine (16/top 20, Supplementary Fig. 3 and their expression was highly correlated with ACE2, TMPRSS2, FURIN (Fig. 5 (Fig. NPM1 has been shown to function as RNA/DNA binding protein regulating 2\u2032-O-methylation of rRNA via direct binding of snoRNAs.RIN Fig. . Exploit. 5 Fig. . This wa. 5 Fig. . Besides. 5 Fig. . Knockdo. 5 Fig. , h. Besi. 5 Fig. .SNORD93 was predicted to target A576 on 18S rRNA for 2\u2032-O-Me modification Fig. , which iWe next explored strategy for SARS-CoV-2 prevention via targeting N protein-related translation machinery components. SARS-CoV-2 infection also enhanced 2\u2032-O-Me modification, as was detected by RTL-P assay (Supplementary Fig. In summary, we found that SARS-CoV-2 N protein enhances host translation efficiency by potentiating the host NPM1-snoRNA translation machinery. By interacting with NPM1 and snoRNAs, N protein significantly promotes ribosome translation efficiency, particularly for viral mRNAs, via enhancement of snoRNA-mediated 2\u2032-O-methylation on rRNAs (Supplementary Fig. Supplementary information"} +{"text": "Gordonia rubripertincta NRRL B-16540. Survivors has a 45,436-bp genome encoding 69 predicted protein-coding genes, of which 32 have assigned functions. Based on gene content similarity to sequenced actinobacteriophages, Survivors is assigned to phage cluster CT.Bacteriophage Survivors is a siphovirus isolated from Gordonia bacteria are opportunistic human pathogens with varied, important roles in bioremediation , using standard protocols from the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) Phage Discovery Guide . The soirphology . The caphttps://phagesdb.org/media/workflow/protocols/pdfs/PCI_SDS_DNA_Extraction_2.2013.pdf), prepared for sequencing using the New England BioLabs Ultra II library kit, and sequenced at the Pittsburgh Bacteriophage Institute using Illumina MiSeq (v3 reagents). There were 236,073 150-base single-end reads providing 735\u00d7 coverage. The raw reads were assembled and checked for completeness using Newbler v2.9 and Consed v29, respectively, using default settings (CGGTAGGCAT-3\u2032). Genome termini were determined through similarity to known phages, an analysis of read start buildups, and coverage levels across the genome (http://phagesDB.org), Survivors was assigned to cluster CT (:1 (httpshttp://cobamide2.bio.pitt.edu), Glimmer (v3.02b) (http://phages.wustl.edu/starterator/), Phamerator (Actino_Draft v462) (ft v462) , BLASTp ft v462) , HHPred ft v462) , ARAGORNft v462) , tRNAscaft v462) , TMHMM (ft v462) , and SOSft v462) . DefaultON970576 and has been assigned Sequence Read Archive (SRA) no. SRX14485091.Survivors GenBank accession no. is"} +{"text": "Stolephorusbengalensis or Stolephorusinsularis Hardenberg, 1933, revealed four distinct species, true S.bengalensis and three new species, viz., Stolephoruseldoradosp. nov. , Stolephorusdiabolussp. nov. and Stolephoruseclipsissp. nov. . Characters separating the four species include numbers of gill rakers on each gill arch and vertebrae and pelvic fin and dorsal-fin ray lengths. Two molecular markers demonstrated the distinction of three of the species examined morphologically and enabled a reconstruction of their phylogenetic relationships. Each species was genetically divergent from the others by 3.5%\u20137.7% mean uncorrected distance in the mitochondrial cytochrome oxidase I gene.Examination of numerous specimens characterised by predorsal scute, long maxilla, indented preopercle and pelvic scute lacking a spine and previously identified as Stolephorus Lacep\u00e8de, 1803 (Teleostei: Clupeiformes: Engraulidae), diagnosed by the presence of prepelvic scutes and an embedded urohyal and lack of postpelvic scutes, currently includes 37 valid species that preferentially inhabit marine and/or estuarine waters in the Indo-Pacific region S.insularis as Stolephorusbengalensis and regarding the nominal species S.insularis as a junior synonym of Stolephorustri . However, subsequent re-examination of specimens, identified as S.bengalensis, in fact revealed the presence of four species.The anchovy genus c region . AmongstS.bengalensis and describe three new species of Stolephorus from specimens previously regarded as S.insularis or S.bengalensis. In addition to the morphological comparisons, complete mitochondrial cytochrome b gene and partial mitochondrial cytochrome oxidase I (COI) gene sequences from 31 specimens were used to estimate the genetic distinction of three of the latter (the fourth species unavailable) plus one unidentified, but related species from Segara Anakan Lagoon, Central Java, Indonesia cytochrome b gene and partial (648 bp) COI gene. The cytochrome b gene sequences were published in COI gene was newly sequenced for 19 specimens of S.eldorado, including the holotype and several paratypes (Table COI sequences (available in GenBank) of S.diablocus , S.bengalensis (eight specimens from India), S.eldorado species of PCR) amplification and sequencing of the COI gene followed standard protocols (COI gene used the following primers: forward COI_FishF1 (5\u2019-TCA ACC AAC CAC AAA GAC ATT GGC AC-3\u2019) and reverse COI_FishR2 (5\u2019-ACT TCA GGG TGA CCG AAG AAT CAG AA-3\u2019) . PCR prob and COI sequences were determined separately by eye, requiring neither insertions nor deletions. The final alignment combining the two genes (for 31 specimens plus one outgroup) comprised 1788 nucleotide positions. Uncorrected pairwise genetic distances (i.e. p-distances) amongst species were calculated with MEGA X (ML) method of phylogenetic reconstruction using the general time-reversible model of nucleotide substitution with rate heterogeneity following a discrete gamma distribution (GTR + \u0413), using the software RAxML-NG (S.acinaces and the robustness of each node determined by bootstrap support (500 replicates).Alignments of the cytochrome h MEGA X . The relRAxML-NG as impleRAxML-NG . The treTaxon classificationAnimaliaClupeiformesEngraulidae\ufeff67E69026-8C76-5B86-84F8-C5E877CDE39CAnchoviellabaganensisbengalensis Dutt & Babu Rao, 1959: 160 and the anal-fin origin located below the origin of the second to sixth dorsal-fin ray (vs. eighth to eleventh) in having a predorsal scute and double pigment lines on the dorsum behind the dorsal fin, but differ in having deciduous body scales and lacking a spine on the pelvic scute (pelvic scute with a hard posteriorly projecting spine) . Stolephg spine) . CompariStolephorusbengalensis, S.diabolus sp. nov. and S.eldorado sp. nov. were divergent from each other by at least 3.5% COI-based mean uncorrected genetic distance (min-max = 3.5\u20137.7%) , forming clear intraspecific versus interspecific genetic gaps. The ML phylogenetic tree using COI and cytochrome b markers : IPMB-I 13.00001, 49.7 mm SL, Teluk Bahang, Penang, Malaysia.USMFC 82-0017, 43.7 mm SL, collected with the holotype; USMFC 82-0057, 4 specimens, 40.1\u201341.1 mm SL, estuary of Merbok River, Jeti Semeling, Malaysia; ZUMT 62056, 5 specimens, 28.5\u201338.4 mm SL, KAUM\u2013I. 163702, 36.3 mm SL, KAUM\u2013I. 163703, 36.4 mm SL, NSMT-P 143554, 36.4 mm SL, NSMT-P 143555, 36.6 mm SL, Singapore.14 specimens, 28.5\u201343.7 mm SL. Stolephorus with the following combination of characters: 1UGR 14\u201316 , 1LGR 20\u201323 (22), 1TGR 35\u201338 (38); 2UGR 10 or 11 (11), 2LGR 19 or 20 (20), 2TGR 30 or 31 (31); 3UGR 8 or 9 (9), 3LGR 11 or 12 (12), 3TGR 20 or 21 (21); 4UGR 6 or 7 (7), 4LGR 9 or 10 (9), 4TGR 15\u201317 (17); prepelvic scutes 5\u20137 (6); total vertebrae 39; long maxilla, posterior tip just reaching or slightly short of posterior margin of opercle; predorsal scute present; pelvic scute without spine; body scales deciduous; posterior border of pre-opercle concave, indented; paired dark patch on parietal area with little following pigmentation; distinct double pigment lines along dorsum posterior to dorsal fin; black spots below eye and on lower-jaw tip absent; anal-fin base long, 19.8\u201322.3% (mean 20.7%) of SL; maximum orbit diameter 8.1\u20138.7% (8.3%) of SL; third dorsal-fin ray short, 17.0\u201318.5% (18.0%) of SL; pelvic fin rather long, 9.6\u201311.3% (10.0%) of SL, its posterior tip not reaching to vertical through dorsal-fin origin when depressed in specimens > 40 mm SL; distance between posterior ends of supramaxilla and maxilla 5.7\u20136.4% (6.1%) of SL.A species of Data for holotype presented first, followed by data for paratypes in parentheses (if different). Counts and measurements, expressed as percentages of SL or HL, given in Tables Body uniformly pale white. A pair of distinct dark patches on parietal region, with little pigmentation on occipital area. No black spots below eye and on lower-jaw tip. Melanophores scattered on posterior margins of scale pockets on dorsum. Double pigmented lines dorsally posterior to dorsal fin. Melanophores scattered along bases of dorsal and anal fins. All fins transparent, melanophores scattered along fin rays of caudal fin and anterior parts of dorsal and anal fins.Stolephorusdiabolus sp. nov. is currently known only from the western coast of the Peninsular Malaysia (Merbok River Estuary and Penang) and Singapore ; 2TGR, 30 or 31 in S.diabolus [vs. 33 or more (rarely 30 or 31 in S.eldorado)]; 3TGR, 20 or 21 in S.diabolus [vs. 22 or more in the other three species (rarely 21 in S.eldorado)]; and 4TGR, 15\u201317 in S.diabolus (vs. 17 or more) of SL in S.diabolus vs. 8.2\u20139.9% (8.9%) in S.eldorado; Fig. S.diabolus is distinguished from S.bengalensis by having a shorter third dorsal-fin ray , shortesis Fig. and fewesis Fig. ."} +{"text": "Bartonella spp. comprises emergent and re-emergent fastidious Gram-negative bacteria with worldwide distribution. Cats are the main reservoir hosts for Bartonella henselae and dogs represent opportunistic hosts for the bacteria. Even though ticks may also play a role in transmission, their competence as vectors for Bartonella spp. has not been totally understood. Considering only a few studies had a focus on screening Bartonella in animals, humans and ectoparasites in Portugal, this study aimed to address the molecular occurrence of Bartonella sp. in 123 stray cats, 25 stray dogs, 30 humans from Lisbon and 236 questing ticks within the country. Using a qPCR targeting the nuoG gene, it was possible to detect Bartonella sp. DNA on 20.32% of cat samples (25/123). From these positive samples, 13 sequences were characterized as B. henselae, 11 as B. clarridgeiae and 1 presented co-infection with both species. The absolute quantification of nuoGBartonella DNA in sampled cats ranged from 2.78 \u00d7 10 to 1.03 \u00d7 105 copies/\u00b5L. The sampled dogs, humans and ticks were negative. These results showed that B. henselae and B. clarridgeiae are circulating in stray cats from Lisbon. Additional and more extended studies should be conducted to determine the impact of such infections on humans, particularly those in constant and direct contact with cats. Bartonella spp. encompasses small, fastidious, and facultative Gram-negative intracellular bacteria with a global distribution -3\u2032 [\u00ae (IDT-Integrated DNA Technologies) encompassing the 83 bp B. henselae-nuoG gene fragment. The number of copies was determined by the following formula: Xg/\u03bcL DNA/[fragment length in bp \u00d7 660]) \u00d7 6.022 \u00d7 1023 \u00d7 plasmid copies/\u03bcL.A quantitative PCR targeting a fragment of the NADH ubiquinone oxireductase subunit G (BHQ1]-3\u2032 was carrnuoG-based qPCR gene were afterwards used in two cPCR assays. The citrate synthase gene (gltA) was targeted for amplification of a 767 bp fragment, using the primers 443F: 5\u2032-GCTATFTCTGCATTCTATCA-3\u2032 and 1210-R: 5\u2032-GATCYTCAATCATTTCTTTCCA-3\u2032 [ribC), using the primers BARTON-1: 5\u2032-TAACCGATATTGGTTGTGTTGAAG-3\u2032 and BARTON-2: 5\u2032-TAAAGCTAGAAAGTCTGG CAACATAACG-3\u2032 [gltA cPCR assay and cycling conditions consisted of an initial denaturation at 95 \u00b0C for 5 min, 35 cycles consisting of denaturation at 94 \u00b0C for 30 s, annealing at 55 \u00b0C for 30 s and extension at 72 \u00b0C for 1 min, followed by a final extension at 72 \u00b0C for 5 min. Ultrapure water was used as a negative control. All assays were conducted in a T100\u2122 Thermal Cycler . PCR products were analyzed by horizontal electrophoresis in 1.5% agarose gel stained with Green Safe Premium (NZYTech). Positive amplicons for both cPCR targeting the genes gltA and ribC were purified using the NZYGelpure kit (NZYTech) and Sanger sequenced at StabVida .Positive samples for the TTCCA-3\u2032 . The 25 TAACG-3\u2032 . ReactioE. coli competent cells (NZYTech) according to standard cloning protocols. Briefly, the purified amplified product was ligated into the plasmid pTZ57R/T. Chemically competent E. coli cells (NZYtech) were transformed, plated in LB agar (NZYtech) and incubated at 37 \u00b0C, overnight. Positive colonies were subcultured overnight on 3 mL of LB medium at 37 \u00b0C and under 200 rpm of shaking. Finally, plasmid purification was carried out using the NZY Miniprep kit (NZYtech) following the manufacturer\u2019s recommendations, and 10 \u00b5L of purified samples together with 3 \u00b5L of M3 forward primer were sent to StabVida , for sequencing. Sequences were manually trimmed and submitted to BLAST [B. henselae gltA, B. clarridgeiae gltA, B. henselae ribC and B. clarridgeiae ribC), and a ClustalW multiple alignment was performed in Bioedit for each group of gene sequences. The number of haplotypes (h) and the haplotype diversity (Hd) was evaluated using the software DNA Sequence Polymorphism (DnaSP) v.6.12.03 [p-distance model with 1000 bootstrap replications. For the phylogenetic trees\u2019 construction, ClustalW multiple alignment was performed in Bioedit for each group of gene sequences (gltA and ribC), including representative sequences for each haplotype obtained in this study, together with other sequences selected from the GenBank (for gltA: Bartonella acomydis (AB444979.1), Bartonella alsatica (AF204273.1), Bartonella birtlesii (AF204272.1), Bartonella vinsonii subp. vinsonii (Z70015.1), Bartonella vinsonii subsp. arupensis (AF214557.1), Bartonella jaculi (AB444975.1), Bartonella rattaustraliani (EU111796.1), Bartonella japonica (AB242289.1), Bartonella coopersplainsensis (EU111803.1), Bartonella quintana (HQ014627.1), Bartonella koehlerae (AF176091.1), Bartonella henselae Human Australia (AJ439406.1), Bartonella henselae (L38987.1), Bartonella henselae Cat Flea Austria (MF374384.1), Bartonella henselae Cat Brazil (MH019304.1), Bartonella henselae Dog Chile (MG252490.1), Bartonella doshiae (AF207827.1), Bartonella rattimassiliensis (AY515124.1), Bartonella queenslandensis (EU111798.1), Bartonella elizabethae (Z70009.1), Bartonella schoenbuchii (AJ278184.1), Bartonella chomelii (AY254308.1), Bartonella capreoli (AF293392.1), Bartonella rochalimae (FN645459.1), Bartonella clarridgeiae Cat flea Chile (KY913636.1), Bartonella clarridgeiae Cat Brazil (MH019302.1), Bartonella clarridgeiae Cat Thailand (KX001761.1), Bartonella clarridgeiae (EU770616.1), Bartonella clarridgeiae strain 73 (FN645454.1), Bartonella baciliformis (DQ452947.1), Bartonella tamiae (DQ395177.1) and Brucella abortus (AE017223.1); and for ribC: Bartonella henselae Cat Brazil (HQ012583.1), Bartonella henselae fleas USA (AY953284.1), Bartonella henselae Cat Brazil (HM588661.1), Bartonella koehlerae (FJ832090.1), Bartonella quintana (AJ236917.1), Bartonella washoensis subsp. cynomysii (DQ825697.1), Bartonella heixiaziensis (KJ361664.1), Bartonella vinsonii subsp. arupensis (AY116631.1), Bartonella vinsonii subsp. vinsonii (AY116636.1), Bartonella vinsonii subsp. berkhoffii (AY116629.1), Bartonella alsatica (AY116630.1), Bartonella fuyuanensis (KJ361648.1), Bartonella doshiae (AY116627.1), Bartonella sp. Bat Kenya (HM363783.1), Bartonella bovis riboflavin synthase France (AY116637.1), Bartonella chomelii (AB290195.1), Bartonella capreoli (AB290194.1), Bartonella schoenbuchensis (AY116628.1), Bartonella bacilliformis (AJ236918.1), Bartonella clarridgeiae Cat China (EU571943.1), Bartonella clarridgeiae (AJ236916.1), Bartonella clarridgeiae Japan (AB292604.1), Bartonella clarridgeiae Cat Brazil (KR092386.1), Bartonella ancashensis (KP720649.1), Candidatus Bartonella ancashi Peru (KC886734.1), Brucella melitensis (CP008750.1)). No criteria regarding host or geographical localization were used to retrieve sequences from GenBank. Likelihood-mapping analyses were performed using the TREE-PUZZLE v5.3 program [Sequences were analyzed and manually cured using Bioedit Sequence Alignment Editor , in ordeto BLAST . Edited .6.12.03 . The hap.6.12.03 was usedlerae AF1091.1, BaBartonella spp. was not detected in ticks, dogs, and humans in the present study, but more studies need to be performed addressing this topic and putting emphasis on Bartonella spp. reservoirs and vectors. Regarding the dogs, surveys among endocarditis afflicted individuals can be carried out and similarly, studies conducted on humans should prioritize immune-compromised groups, as they are more prone to develop infections by Bartonella spp. About 20% of the cats sampled in Lisbon were positive for at least one Bartonella spp. and both B. henselae and B. clarridgeiae were identified in similar percentages. It is hoped that these results could bring attention to Bartonella sp. as an emerging pathogen in cats from Lisbon, and a potential threat for public health. As they are the main reservoir for B. henselae, preventive measurements should be implemented in order to avoid an outbreak of cat scratch disease in Lisbon.Bartonellosis is recognized as an emerging vector-borne disease that constitutes a threat to both animal and human health. Continuous and active surveillance to understand the epidemiological characteristics of bartonellosis is needed worldwide, including in Portugal."} +{"text": "Escherichia coli is a reservoir of antimicrobial resistance genes (ARGs). Here, we report the draft genome sequence of an E. coli strain (31HGR-CBG) that was isolated from a urine sample in Tamaulipas, Mexico. 31HGR-CBG harbors multiple ARGs, including blaCTX-M-15 and class 1 integron. This strain also carries multiple virulence genes. Escherichia coli represents a threat to public health (E. coli (ExPEC) are genetically diverse and complex approval nor informed consent was required. 31HGR-CBG was grown on Trypticase soy agar and CHROMagar Orientation medium and incubated overnight at 37\u00b0C. Standard biochemical tests were also performed.https://www.bioinformatics.babraham.ac.uk/projects/fastqc) and Trim Galore! v0.6.6 were used to evaluate quality and to trim the raw reads, respectively. Assembly was performed using SPAdes v3.15.2 (https://github.com/ablab/quast). Contigs smaller than 900\u2009bp were removed. Bacterial identification was confirmed by a BLASTN search (http://blast.ncbi.nlm.nih.gov) against the NCBI database and ribosomal multilocus sequence typing (rMLST) at 37\u00b0C. DNA was extracted using the Wizard genomic DNA purification kit . DNA quantification was performed with the Qubit double-stranded DNA (dsDNA) HS assay kit in the Qubit 3.0 fluorometer . Libraries were constructed with the Nextera Flex library preparation kit and were sequenced using the MiniSeq sequencing system (150-bp paired-end reads). A total of 10,918,316 raw reads were generated. FastQC v0.11.3 (http://genomicepidemiology.org). ARGs were also predicted with the CARD v3.1.4 database using RGI v5.2.0 (Automatic annotation was performed by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v5.2. Multilocus sequence typing (MLST) was executed with PubMLST v1 . SerotypI v5.2.0 . Phages I v5.2.0 . DefaultN50 value of 91,860\u2009bp, a GC content of 50.82%, and genome coverage of 220\u00d7. Annotation identified 4,939 genes, 4,850 coding sequences, and two CRISPR arrays. 31HGR-CBG belongs to sequence type 44 (ST44) and serotype 0101:H4.The genome was 4,981,584\u2009bp in size and was assembled into 141 contigs, with an aadA5, aph(6)-Id, aac(6\u2032)-Ib-cr, and aph(3\u2033)-Ib], extended-spectrum \u03b2-lactams (blaCTX-M-15 and blaOXA-1), phenicol (catB3), macrolides [mph(A)], sulfonamides (sul1 and sul2), tetracycline [tet(B)], trimethoprim (dfrA17), and quaternary ammonium compounds (qacE\u03941). In addition, plasmid replicons IncFIA, IncFIB, and IncFII were detected.Multiple ARGs were identified, including genes conferring resistance to aminoglycosides [gyrA, parC, and parE were found, indicating fluoroquinolone resistance. Virulence-associated genes and four intact prophages were identified.Chromosomal mutations in JAKJKJ000000000. The reads were deposited in the Sequence Read Archive (SRA) under the accession number SRR15258840.This draft genome has been deposited in GenBank under the accession number"} +{"text": "Spinirta Jin & Zhang, 2020 (Araneae: Corinnidae) from Jiangxi Province, China are described here: S.sanxiandiansp. nov. (\u2642\u2640) and S.sishuishansp. nov. (\u2642). Detailed descriptions and photographs of the new species are provided.Two new species of Corinnidae Karsch, 1880 has increased greatly in the past ten years . Measurements were taken with the AxioVision software (SE64 ver. 4.8.3) and are given in millimetres. Terminology of the male and female copulatory organs follows Specimens were examined using a Jiangnan SZ 6100 stereomicroscope with a Zoom Microscope System. Both male palps and female copulatory organs were detached and examined in 80% ethanol, using an Olympus CX43 compound microscope with a KUY NICE CCD camera. All specimens treated in this work are deposited in the Animal Specimen Museum, Life Science of College, Jinggangshan University . The abbreviations used in the text and figures are:ALE anterior lateral eye;AME anterior median eye;At atrium;CD copulatory duct;CO copulatory opening;CS cone-shaped spines;d dorsal;E embolus;EA embolic apophysis;FD fertilization duct;GA glandular appendage;MOA median ocular area;p prolateral;PLE posterior lateral eye;PME posterior median eye;PTA prolateral tibial apophysis;r retrolateral;RTA retrolateral tibial apophysis;Sp spermatheca;St subtegulum;v ventral;VTA ventral tibial apophysis.Taxon classificationAnimaliaAraneaeCorinnidae\ufeffGenusJin & Zhang, 2020921B6204-15E0-54B8-B299-06A67E4FBE76Spinirtajinyunshanensis Jin & Zhang, 2020. Type locality: Chongqing.Spinirta species, S.wuyishanensis Zhou, 2022 was recorded from Jiangxi Province in southeast China. It is worth mentioning that the female remains unknown.The genus includes 11 species, all of which are distributed in southern and southwest of China (WSC 2022). Currently, most of them are known only from females (three species) or males (four species) (WSC 2022). Most of China\u2019s nine species are recorded from southwestern China . Only onTaxon classificationAnimaliaAraneaeCorinnidae\ufeffLiusp. nov.E398719E-F60C-5419-B24C-A02AFD3BF57Ehttps://zoobank.org/6CEBCD02-A0B5-452B-A1AD-E0F681296427Holotype: 1 \u2642, China: Jiangxi Province, Ji\u2019an City, Qingyuan District, Donggu Town, Dawu Mountain, 26\u00b040'48.69\"N, 115\u00b025'7.79\"E, 1031 m, 25.X.2020, K. Liu et al. leg. (Cor-04). Paratype: 2 \u2640, 13.XI.2021, K. Liu et al. leg., other data same as holotype (Cor-03 and Cor-05).The specific name is derived from the type locality, Sanxiandian Temple in Dawu Mountain; noun in apposition.Spinirtasparsula Jin & Zhang, 2020 with a curved posterior part (vs. straight in S.sparsula) and the ear-shaped retrolateral tibial apophysis (RTA) without protruded base (vs. digitiform with a kidney shaped protruded base in S.sparsula). It also resembles S.sishuishan sp. nov. in having a thumb-like ventral tibial apophysis (VTA), a thick horn-like prolateral tibial apophysis (PTA) and a curved sperm duct (SD), but can be separated from it by the ear-shaped retrolateral tibial apophysis (RTA) (vs. shield-shaped in S.sishuishan sp. nov.), the anterior part of the tegulum with a broad lateral apophysis (vs. absent in S.sishuishan sp. nov.) and the sharp embolic apophysis in retrolateral view (vs. relatively blunt in S.sishuishan sp. nov.) , the shield copulatory openings (CO) (vs. round in S.qizimeiensis), and the copulatory ducts (CD) extending from the anteromedial to the posterolateral part of the epigyne .The male of this new species is similar to that of cf. Fig. . The femMale. Habitus as in Fig. AME 0.32, ALE 0.31, PME 0.2, PLE 0.27, AME-AME 0.15, AME-ALE 0.07, PME-PME 0.3, PME-PLE 0.36, AME-PME 0.25, AME-PLE 0.47, ALE-ALE 0.87, PLE-PLE 1.45, ALE-PLE 0.2. MOA 0.74 long, front width 0.77, back width 0.72. Chelicera with three promarginal and five retromarginal teeth thumb-like in ventral view. Retrolateral tibial apophysis (RTA) ear-shaped, nearly as long as tibial length, ventral surface with two lines of short cone-shaped spines (CS). Prolateral tibial apophysis (PTA) thick horn-like, strongly sclerotised, nearly as long as 1/3 of tibia. Tegulum with strongly sclerotized apex. Subtegulum (St) with many wrinkles on posterior surface. Sperm duct (SD) S-shaped in posterior part. Embolus (E) short, with thick base, forming a C-shape with short spine-like embolic apophysis (EA), nearly 3\u00d7 longer than embolic apophysis.Palp as in Fig. Female. Habitus as in Fig. AME 0.28, ALE 0.26, PME 0.19, PLE 0.24, AME-AME 0.16, AME-ALE 0.08, PME-PME 0.27, PME-PLE 0.31, AME-PME 0.26, AME-PLE 0.4, ALE-ALE 0.83, PLE-PLE 1.3, ALE-PLE 0.18. MOA 0.72 long, front width 0.66, back width 0.66. Abdomen: 5.55 long, 3.85 wide. Leg measurements: I 13.57 ; II 12.5 ; III 11.2 ; IV 14.77 ; spination large, shield, covers equal or less than half of epigynal plate, anteromedially located. Copulatory openings (CO) very large, oval, located at anterolateral atrium. Copulatory ducts (CD) very broad, anteriorly touching, posteriorly slightly separated. Glandular appendages (GA) short, located at dorsal part of copulatory ducts, extending beyond medial part of copulatory ducts, directed anteriorly. Spermathecae (Sp) relatively broad, separated by 1/2 width of copulatory ducts. Fertilisation ducts (FD) directed anteriorly, shorter than spermathecal width.Epigyne as in Figs Spinirtasanxiandian sp. nov. may be the result of the influence of their development factors.The female specimens of this new species occur exactly in the same sites explored by the authors. They are identified as the same species based on appearance and epigyne. Variability was observed in the epigyne Fig. , which mKnown only from the type locality, Jiangxi Province, China Fig. .Taxon classificationAnimaliaAraneaeCorinnidae\ufeffLiusp. nov.0FA58825-87CA-51AD-843C-D1560BD78095https://zoobank.org/F06E9311-8FE0-4858-B870-22E9F59F3262Holotype: 1 \u2642, China: Jiangxi Province, Ganzhou City, Chongyi County, Sishui Mountain, near parking lot, 25\u00b027'11.73\"N, 113\u00b055'30.04\"E, 965 m, 2.X.2020, K. Liu et al. leg. (Cor-02).The specific name, derived from the type locality, is a noun in apposition.S.sanxiandian sp. nov. by the shield retrolateral tibial apophysis (RTA) (vs. ear-shaped), the anterior part of the tegulum lacking lateral apophysis (vs. present in S.sanxiandian sp. nov.) and the relatively blunt embolic apophysis (EA) in retrolateral view (vs. sharp in S.sanxiandian sp. nov.) thumb-like in ventral view. Retrolateral tibial apophysis (RTA) shield in retrolateral view, nearly as long as tibial length, ventral surface with four lines of short cone-shaped spines (CS). Prolateral tibial apophysis (PTA) thick horn-like, strongly sclerotised, nearly as long as 1/3 of tibia. Tegulum with strongly sclerotized apex. Subtegulum (St) with many wrinkles on posterolateral tegulum. Sperm duct (SD) S-shaped in posterior part. Embolus (E) spine-like, with thick base, forming a C-shape with short blunt embolic apophysis (EA), nearly 4\u00d7 longer than embolic apophysis.Palp as in Fig. Female. Unknown.Known only from the type locality, Jiangxi Province, China Fig. ."} +{"text": "This study aims to investigate the equivalence between Cambridge Neuropsychological Test Automated Battery (CANTAB) and Montreal Cognitive Assessment, Changsha version (MoCA-CS) as cognition measures for Chinese stroke survivors. Sixteen stroke survivors were recruited from stroke center in Shanghai, China. Participants completed Paired Associates Learning (PAL) task in CANTAB, MoCA-CS and questionnaire about demo-social characteristics. Pearson correlation and hierarchical regression were used for equivalence analysis. CANTAB-PAL task performances\uff08PAL First Attempt Memory Score, PALFAMS, PAL Total Attempts 2 Patterns, PALTA2\uff09were significantly associated with score of MoCA-CS and delayed recall (\u03b2=0.528, p=0.014; \u03b2=0.198, p=0.043; \u03b2= -3.885\uff0cp=0.017; \u03b2= -1.600,p=0.026, respectively\uff09after controlling for age, gender and education. The results suggest CANTAB-PAL is a reliable tool for measuring Chinese stroke survivors\u2019 cognitive function. Future studies are needed to establish the equivalence of CANTAB in multi-tasks in larger sample of Chinese stroke survivors."} +{"text": "Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain ESEI_597 was isolated in 2013 from a stool sample from an 8-month-old child residing in Korogocho, an informal settlement northeast of Nairobi, Kenya. A pea-sized fecal sample was emulsified in 5\u2009mL buffered peptone water . Approximately 10 \u03bcL of the overnight broth inoculum was plated on MacConkey agar (Oxoid), and a biochemically identified colony was subcultured in Mueller-Hinton agar (Oxoid) before being stocked at \u221280\u00b0C in tryptone soy broth (Oxoid) with 15% glycerol. All incubations were performed at 37\u00b0C for 18 to 24 h. Labile toxin (LT) and colonization surface antigen 13 (CS13) conventional uniplex PCR screening was performed using previously described primers (https://www.well.ox.ac.uk/ogc) and preprocessed using an automated protocol developed by the Modernising Medical Microbiology (MMM) Oxford Group. Read trimming to remove remnant adaptor sequences was performed using BBDuk, part of the BBTools package (www.ncbi.nlm.nih.gov/sra), with an automated step for removal of contaminant reads. The remaining reads were mapped (using Stampy v1.0.23) to an E. coli reference genome (GenBank accession AE014075.1) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), with all per-base-sequence quality flagged as passed.Enterotoxigenic 14075.1) . The quaN50 value of 140,019\u2009bp, a G+C content of 50.71%, and a total length of 4,937,264\u2009bp. ABRicate v1.0.1 (https://github.com/tseemann/abricate) was used to detect acquired antimicrobial resistance (AMR) genes with ResFinder v2.1 (https://github.com/tseemann/mlst) and the PubMLST database (https://pubmlst.org) . Automataat operon, etpBAC operon, eatA, and tleA-like autotransporter are all absent. The cexE gene is present but truncated, with an LS-BSR value of 0.8893 (cshABCDEFGH) is 7,923\u2009bp long, and LT in ESEI_597 has been assigned to allele 29.ESEI_597 belongs to sequence type 155 (ST155) (Achtman scheme) ; plasmidf 0.8893 . The CS1The Kenya Medical Research Institute (KEMRI)/National Ethics Review Committee approved all procedures (protocol number 2507).E. coli ESEI_597 has been deposited in GenBank under the accession number JALDSW000000000. Other features of the sequence data are provided in The draft genome of"} +{"text": "M. avium complex (MAC) strains in a chronic mouse infection model either as monotherapy or in combination with standard of care .Epetraborole (EBO) is a boron-containing oral inhibitor of bacterial leucyl-tRNA synthetase, an essential enzyme in protein synthesis; EBO demonstrates potent activity against nontuberculous mycobacteria. These studies evaluated oral doses (PO) of EBO against 5 M. avium 2285R evaluated EBO at 1, 10, 30, 100, 300 and 500 mg/kg PO once daily (QD) compared to 250 mg/kg CLR PO QD. C57BL/6 mice were infected with a pulmonary aerosol of 1x1011 CFU. Treatment was administered for 56 days starting on day 28 post-infection. The bacterial burden (CFU) in lungs was evaluated on days 1, 28 and 84 post-infection by plating serial dilutions of homogenates on Middlebrook 7H11 charcoal agar plates. An additional 4 strains of MAC were evaluated with EBO doses of 100, 200, 300 or 400 mg/kg QD compared with the SOC therapy for MAC QD and SOC plus EBO 200mg/kg QD. Oral exposures of EBO were determined in a group of uninfected mice (Table\u00a01).A pilot chronic efficacy study against M. avium 2285R, a biofilm-forming strain, EBO at all doses tested was significantly better than CLR dosed at 250 mg/kg , and no CFU were detected on agar plates containing EBO (16 mg/L). In subsequent studies, SOC was compared to EBO in 4 additional MAC strains . Efficacy of EBO monotherapy was better than SOC against M. avium ATCC 700898, while it was as good as SOC with M. intracellulare 1956, M. intracellulareDNA00055, and M. intracellulare DNA00111 with CFU reductions ranging from 2 - 4.8 log10 compared to day 28 controls. In all four strains tested, 200 mg/kg EBO, which approximates the human oral equivalent dose of 500 mg, combined with SOC increased bacterial killing from 1.4 - 3.0 log10 CFU compared to SOC alone resulting in total lung CFU reductions of 4.6 - 5.6 log10.In a study with M. avium 2285R at day 84. EBO demonstrated potent in vivo efficacy against 5 MAC strains and significantly improved efficacy when combined with SOC, supporting further clinical development for EBO.In this chronic mouse lung infection model, no EBO resistance development was detected with Michelle S. DeStefano, n/a, AN2 Therapeutics: Grant/Research Support Carolyn Shoen, PhD, AN2 Therapeutics: Grant/Research Support Michael H. Cynamon, MD, AN2: Grant/Research Support|AN2: Grant/Research Support MRK Alley, PhD, ABBOTT LABS: Stocks/Bonds|ABBVIE: Stocks/Bonds|AN2 Therapeutics: Author on epetraborole patent|AN2 Therapeutics: Salary|AN2 Therapeutics: Ownership Interest|AVANOS MED INC: Stocks/Bonds|NABRIVA THERAPEUTICS PLC: Stocks/Bonds|NOVARTIS AG: Stocks/Bonds."} +{"text": "Health care workers (HCWs) possess a potential risk to acquire and spread various infections. This study was planned to assess the immune status of HCWs in pediatric departments of two tertiary care hospitals in Northern India.In this cross-sectional study, HCW\u2019s (Indians), working in pediatric departments of these hospitals, over 6-months period (July18-Dec18) were enrolled after taking written consent and their 5-ml venous blood sample was collected. Ethical clearance was obtained from Institute Ethics committee, before enrolling subjects. Serum were tested for antibodies against diphtheria-toxin (DT), pertussis-toxin (PT), measles, mumps, rubella, varicella, hepatitis-B (HbsAb) and hepatitis-A using commercial IgG (quantitative) ELISA kits.A total of 160 HCW\u2019s (M:F=77:83), having mean age 30.6\u00b17.8 years, were enrolled. Out of them 106 (66.3%) were resident doctors, 31 (19.4%) nursing-staff, 18 (11.3%) faculty members, 3 (1.9%) research-staff and 2 (1.3%) paramedical-staff. In our study, antibodies (IgG) against DT were between 0.01 to 0.1 IU/ml in 78.1% (120/160); requiring a Tdap booster; while 7 out of 125 had titers < 0.01 IU/ml, which needed 3-doses of primary vaccination. Antibodies (IgG) against PT < 30 IU/ml were seen in 60.6% (97/160), which were considered as seronegative, as per kit recommendations.A total of 3% (5/160), 13.1% (21/160), 10% (16/160), 17.5% (28/160) had titers < 12 IU/ml for IgG antibodies against measles, mumps, rubella and varicella respectively; were considered unprotected. A total of 25% (40/160) had Anti-HBs antibody titers < 20 mIU/ml; which were low, therefore were advised to take one booster dose of Hep-B vaccine. A total of 15.6% (25/160) had IgG antibodies against hepatitis-A < 10 mIU/ml; were unprotected.Alarming proportions of pediatric-HCWs had low antibody titres against DT (78.1%) and PT (60.6%), necessitating a dose of Tdap. A total of 10%, 17.5% and 15.6% lacked protective antibodies against rubella, varicella and hepatitis-A. A quarter of screened population had low anti-Hbs titres, requiring boosting of immunity. Our study emphasizes the urgent need for improving immunization status of pediatric HCW\u2019s; as they continue to remain susceptible to various vaccine preventable infectious diseases.All Authors: No reported disclosures."} +{"text": "Correction: BMC Cancer 22, 689 (2022)https://doi.org/10.1186/s12885-022-09740-9The results of colony formation assay which have been used in Fig. 4C(c) and Fig. 4D(c) were accidentally used again in Fig. The western blot result annotations \"Ctrl \"and \"MIR137HG\" were missed in Fig. Following publication of the original article , the autThe correct Fig."} +{"text": "Scientific Reports, 10.1038/s41598-023-28540-0, published online 28 January 2023Correction to: The original version of this Article contained an error in Reference 37,et al.\u00a0Inclusive Wealth Report 2022 Executive Summary. .37. Barbier, E. B.\u00a0now reads:. UNEP. Inclusive Wealth Report 2022 Executive Summary. .37The original Article has been corrected."} +{"text": "HFE p.C282Y/p.C282Y are incompletely characterized.Screening program participants with iron overload (IO) phenotypes without HFE p.C282Y and p.H63D genotyping.We studied white participants who had IO phenotypes without p.C282Y/p.C282Y in post-screening clinical examinations (CE). We defined IO phenotypes as a) elevated serum ferritin (SF) and transferrin saturation (TS) at screening and CE, and b) absence of IO treatment, anemia, transfusion >10 units, alcohol intake >30 g/d, hepatitis B or C, and pregnancy. We defined IO-related disease as elevated alanine or aspartate aminotransferase (ALT/AST) or swelling/tenderness of 2nd/3rd metacarpophalangeal (MCP) joints. All participants had HFE genotypes were 12.9 (p.C282Y/p.H63D), 3.0 (p.H63D/p.H63D), 1.9 (p.C282Y/wt), 0.9 (p.H63D/wt), and 0.5 (wt/wt) compared to 42,640 white screening participants without IO phenotypes or p.C282Y/p.C282Y. Regression on SF revealed positive associations: MCV ; swelling/tenderness of MCP joints ; and p.H63D/wt . IO-related disease occurred in 19 participants . Median MCV was higher in participants with IO-related disease . Logistic regression on IO-related disease revealed a significant association with diabetes ).There were 32 men and 26 women (mean age 54\u00b116 y). Median food/supplemental iron intakes were 14.3/0.0 mg/d. Relative risks of HFE p.C282Y/p.C282Y, relative risks of HFE genotypes p.C282Y/p.H63D, p.H63D/p.H63D, and p.C282Y/wt were significantly higher than in 42,640 white screening participants with neither IO phenotypes nor p.C282Y/p.C282Y. SF was significantly associated with MCV, swelling/tenderness of 2nd/3rd MCP joints, and p.H63D/wt. IO-related disease was significantly associated with MCV and diabetes.In the present 58 screening program participants who had IO phenotypes without HFE gene [HFE alleles p.C282Y and p.H63D were discovered in referred white patients with hemochromatosis and iron overload (IO) in 1996 [The HFE alleles [HJV, chromosome 1q21.1), transferrin receptor 2 , hepcidin antimicrobial peptide , and solute carrier family 40 member 1 (ferroportin) [Rare types of hemochromatosis, usually diagnosed in referred patients, are associated with novel alleles or deletHFE genotype and sex [Some population screening program participants who have elevated SF and elevated TS without p.C282Y/p.C282Y also have IO phenotypes due to hemochromatosis, although these participants have been incompletely characterized. A primary report of the Hemochromatosis and Iron Overload Screening (HEIRS) Study displayed separate initial screening TS and SF data of participants from a racially diverse population segregated only for and sex . Those d and sex .HFE p.C282Y/p.C282Y who participated in the HEIRS Study post-screening clinical examinations (CE) [HFE genotypes other than p.C282Y/p.C282Y and identified variables significantly associated with IO phenotypes and IO-related disease. We discuss our observations in the context of previous reports.To learn more, we studied non-Hispanic whites who had IO phenotypes without ons (CE) , 8, 9. Gons (CE) , 8, 9. Wons (CE) . We compThe National Heart, Lung, and Blood Institute/National Human Genome Research Institute HEIRS Study evaluated the prevalence, genetic, and environmental determinants, and potential clinical, personal, and societal impacts of hemochromatosis and IO in a multiethnic, primary care-based sample of 101,168 adults enrolled during the interval 2001\u20132003 at four Field Centers in the US and one in Canada . The StuHFE p.C282Y and p.H63D allele-specific genotyping [The HEIRS Study recruited participants from a health maintenance organization, diagnostic blood collection centers, and public and private primary care offices in ambulatory clinics associated with five Field Centers . Ninety-notyping .HFE p.C282Y homozygotes (regardless of screening SF and TS), to all participants whose screening SF and TS exceeded study thresholds, regardless of HFE genotype, and to selected participants who had normal screening SF and TS and HFE wt/wt, defined as absence of p.C282Y and p.H63D. Median interval between screening and CE participation was 8 months [Invitations to participate in a post-screening CE were extended to all 8 months .HFE genotype. Each participant completed a questionnaire addressing medical history and medications [At CE, eligible participants were informed of their screening SF, TS, and ications and a Unications . An HEIRications .HFE genotype based on p.C282Y and p.H63D allele-specific analyses [All testing was performed at the HEIRS Study Central Laboratory . At CE, a morning blood sample was obtained after an overnight fast to measure SF and TS , to confirm Elevated SF and TS were defined as SF >300 \u03bcg/L and TS >50% (men) and SF > 200 \u03bcg/L and TS >45% (women). Reference ranges for hemoglobin were 133\u2013177 g/L (men) and 117\u2013157 g/L (women) and for mean corpuscular volume (MCV) were 78\u2013105 fL (men) and 78\u2013106 fL (women) [Reflex testing for hepatitis B surface antigen and hepatitis C antibody was performed in all participants with elevated ALT or AST . Participants with elevated ALT or AST and positivity for hepatitis B surface antigen were defined to have viral hepatitis B . ParticiObtaining liver specimens by biopsy, estimating liver iron content using imaging techniques, and performing therapeutic phlebotomy were beyond the scope of the HEIRS Study.We defined IO phenotypes as the following: a) elevated SF and elevated TS at both screening and CE, and b) absence of IO treatment, anemia, erythrocyte transfusion >10 units, alcohol intake >30 g/d, hepatitis B or C, and pregnancy. We defined IO-related disease in participants with IO phenotypes according to modified criteria of Allen et al. : elevateHFE p.C282Y/p.C282Y who had IO phenotypes, who fasted overnight \u22658 h before CE, and whose data analyzed in this study were complete.We analyzed observations on all self-identified non-Hispanic white CE participants without Macrocytosis was defined as MCV greater than the respective sex-specific upper reference limits. Microcytosis was defined as MCV \u226477 fL.2.Estimates of dietary and supplemental iron and daily alcohol intake were taken from the Multi-Ethnic Dietary Questionnaire . We defiSelf-reported diabetes reported at screening was confirmed with medication reviews at CE . We defiPhysicians who performed physical examinations at CE recorded these manifestations as present or absent .The dataset for analyses consisted of complete observations on 58 CE participants with IO phenotypes. Age, SF, TS, hemoglobin, and MCV are expressed to the nearest integer. Descriptive data are displayed as enumerations, percentages, proportions, means (\u00b1 1 SD), or medians (range). Analyses of continuous data using d\u2019Agostino\u2019s and Shapiro-Wilk tests revealed that age and BMI values were normally distributed and thus these values are displayed as mean \u00b1 1 SD and were compared using Student\u2019s t tests (two-tailed). Continuous variables that were not normally distributed are displayed as medians (range) and were compared using Mann-Whitney U tests (unpaired data) or Wilcoxon\u2019s signed-ranks test (paired data). Percentages were compared using Fisher\u2019s exact test (two-tailed). The significance of the difference between two independent proportions was calculated using the z-ratio and two-tailed values of p. We compared screening and CE SF and TS data using Pearson\u2019s correlation coefficient.HFE genotypes other than p.C282Y/p.C282Y. We performed forward stepwise regression on SF at CE using a) all independent variables available at CE (except TS) and b) the first independent variable with p \u22650.05 as the stopping rule. TS was not used as an independent variable because its positive correlation with SF at CE was significant. We display standardized coefficients \u03b2 for each significant predictor variable in this regression.We computed relative risks of We performed logistic regression on IO-related disease using all available independent variables for which values of p in univariate comparisons were \u22640.1500. We calculated odds ratios ) for significant independent variables.\u00ae , GB-Stat\u00ae , and GraphPad Prism 8\u00ae .We defined values of p <0.05 to be significant. Analyses were performed with Excel 2000HFE genotypes [HFE p.C282Y/p.C282Y [Screening observations in 43,453 non-Hispanic white participants were evaluable for SF and TS levels and enotypes . Both sc/p.C282Y . ElevateHFE genotypes p.C282Y/p.H63D, p.H63D/p.H63D, and p.C282Y/wt in the present 58 CE participants with IO phenotypes were significantly greater than corresponding percentages in 42,640 non-Hispanic white screening participants without IO phenotypes (Percentages of enotypes . Relativenotypes . Aggregaenotypes .Detailed characteristics of 58 participants are displayed in HFE p.C282Y/p.H63D occurred in 18 participants (31.0%) and p.H63D/p.H63D in four participants (6.9%). Each of the genotypes p.C282Y/wt, p.H63D/wt, and wt/wt occurred in 12 participants. Two men and two women had SF >1000 \u03bcg/L . Macrocytosis was detected in one woman and microcytosis was detected in another woman. Median estimated daily iron intakes from food and iron supplements were 14.3 mg and 0.0 mg, respectively. Elevated ALT or AST occurred in 18 participants (31.0%). Swelling/tenderness of the 2nd/3rd MCP joints was observed in one participant (1.7%). Diabetes occurred in four participants (6.9%). 000 \u03bcg/L .HFE p.H63D/wt . This regression accounted for 32.0% of the variance of SF (regression ANOVA p = 0.0001).Forward stepwise regression on SF at CE using other CE observations (except TS) as independent variables revealed three positive associations: MCV ; swelling/tenderness of 2nd/3rd MCP joints ; and These data are displayed in There were 15 abstainers (25.9%) and 43 non-abstainers (74.1%). The difference between median MCV values of abstainers and non-abstainers was not significant (94 fL (86\u201397) vs. 96 fL (77\u2013107), respectively; p = 0.1369). All nine of 58 participants (15.5%) with MCV >100 fL were non-abstainers, although proportions of abstainers and non-abstainers with MCV >100 fL did not differ significantly .HFE p.C282Y/p.C282Y who also reported that they had not received treatment for IO. Our study design excluded non-Hispanic white CE participants who may have had elevated SF and elevated TS due to types of anemia that increase iron absorption, a history of erythrocyte transfusion >10 units, viral hepatitis B or C, or increased alcohol intake. Elevated SF without elevated TS is common in patients with obesity [SLC40A1 alleles [We evaluated observations in 58 non-Hispanic white participants in the HEIRS Study CE who had both elevated SF and elevated TS defined as IO phenotypes without obesity , metabol obesity , diabete obesity , non-alc obesity , 19, inf obesity , maligna obesity \u201322, \"cla alleles , heredit alleles , and ben alleles . Thus, oHFE genotypes p.C282Y/p.H63D, p.H63D/p.H63D, and p.C282Y/wt in the present 58 CE participants with IO phenotypes were significantly greater than corresponding percentages in 42,640 non-Hispanic white screening participants without IO phenotypes. SF was significantly associated with MCV, swelling/tenderness of the 2nd/3rd MCP joints, and p.H63D/wt. IO-related disease was significantly associated with MCV and diabetes. IO and IO-related disease were not significantly associated with estimated intake of dietary or supplemental iron. Taken together, we infer that heritable factors in addition to common HFE genotypes other than p.C282Y/p.C282Y or acquired factors we did not study contribute to or account for IO phenotypes, IO-related disease, and other potential iron-related consequences of hemochromatosis in the present participants.Percentages of HFE p.C282Y/p.H63D was increased in the present participants, although we observed no significant association of IO-related disease with p.C282Y/p.H63D. Participants in an Australian population screening program with IO phenotypes and p.C282Y/p.H63D also had a low risk of IO-related disease [Relative risk of 5 women) . In refe5 women) . In an a5 women) . In a me5 women) .GNPAT) p.D519G (rs11558492) occurred with greater prevalence in French and Australian subjects with HFE p.C282Y/p.H63D with higher SF than those with lower SF [CYBRD1) promoter polymorphism rs884409 was significantly higher in French patients with p.C282Y/p.H63D with higher SF than those with lower SF [HJV p.N196K or HAMP -72C>T [HAMP p.G71D did not modify SF and TS phenotypes [HFE iron-associated alleles probably account in part for the variable penetrance of p.C282Y/p.H63D phenotypes.Glyceronephosphate O-acyltransferase [HFE coding region allele [HAMP Met50del IVS2+1(-G) and HAMP p.G71D, respectively [Relative risk of .9, 5.8) . In a me.9, 5.8) . Compounn allele , occurren allele , 36. Refn allele , 38. In ectively .HFE p.H63D/wt was increased in the present participants. In an analysis of 14 case-control studies of hemochromatosis, the pooled odds ratio of p.H63D/wt as a contributor to hemochromatosis IO was 1.9 [HFE alleles, e.g., p.I105T (c.314T>C) [HFE allele, e.g., p.E168Q (c.502G>C), in cis with p.H63D [Relative risk of .5, 2.5) . Rarely,.314T>C) , or withh p.H63D . In a meh p.H63D . It is pHFE p.C282Y/p.C282Y [Estimated median daily intake of dietary iron in the present participants is similar to that in adults in the U.S. not selected for IO phenotypes . SF in t/p.C282Y .HFE p.C282Y/p.C282Y were significantly higher than those of control subjects [HFE genotype [MCV was significantly associated with SF and IO-related disease in this study, after adjustment for other variables. In two previous reports, mean MCV values in referred hemochromatosis patients without subjects , 45. Incgenotype . In one genotype . By desigenotype ) and thagenotype ). We obsgenotype and manygenotype , occurreHFE genotypes were p.H63D (n = 2) and p.H63D/p.H63D and wt/wt (one each). In 20,306 Canadian HEIRS Study participants linked to the Ontario Death Registry 9 years after screening, all-cause survival was significantly decreased in the 34 participants with screening SF >1000 \u03bcg/L and HFE genotypes other than p.C282Y/p.C282Y [Four of the present 58 participants had SF >1000 \u03bcg/L. Their 7 wt/wt) .HFE genotypes other than p.C282Y/p.C282Y in adults with IO phenotypes have meaningful clinical correlates. Some adults with IO phenotypes without p.C282Y/p.C282Y have hepatic steatosis [HFE hemochromatosis, or non-HFE \"modifier\" mutations. Guidelines for hemochromatosis management promulgated by expert groups in the U.S. [HFE genotyping. It is also recommended that first-degree relatives of persons diagnosed to have HFE hemochromatosis undergo TS/SF phenotyping and HFE genotyping [HFE alleles has disease-identification value other than to reveal IO risk.teatosis , 51 or cteatosis , 52, othteatosis . Adults the U.S. and Eurothe U.S. recommennotyping , 54. TheHFE p.C282Y/p.C282Y and unlikely to have other disorders that sometimes present with IO phenotype mimics. Another strength is the availability of screening and CE data sufficient to demonstrate a) significant differences in proportions and relative risks of HFE genotypes other than p.C282Y/p.C282Y and b) significant associations of IO phenotypes and IO-related disease with other potential iron-related consequences of hemochromatosis. An uncertainty of this study is that we may have excluded participants with \"classic\" SLC40A1 (ferroportin) hemochromatosis in whom SF but not TS is typically elevated [A strength of this study is that our selection criteria included only participants with IO phenotypes who were likely to have hemochromatosis in the absence of elevated .HFE genotype risk associated with IO phenotype because participants invited to the CE (other than those with HFE p.C282Y/p.C282Y or wt/wt) were selected on the basis of having both screening SF and screening TS values above HEIRS Study thresholds, not on the basis of HFE genotype [HFE p.C282Y and p.H63D. The HEIRS Study performed analyses to detect specific HFE alleles other than p.C282Y and p.H63D and specific HJV, TFR2, HAMP, SLC40A1 alleles in a small proportion of screening participants [In this study, we assessed genotype . The HEIicipants . None oficipants .HFE genotypes p.C282Y/p.H63D, p.H63D/p.H63D, and p.C282Y/wt were increased in screening program participants who had IO phenotypes without p.C282Y/p.C282Y. SF was significantly associated with MCV, swelling/tenderness of 2nd/3rd MCP joints, and p.H63D/wt. IO-related disease was significantly associated with MCV and diabetes. Novel HFE alleles, deleterious alleles of HJV, TFR2, HAMP, or SLC40A1, iron-related \"modifier\" alleles, or acquired factors could contribute to IO phenotypes and IO-related disease in some of the present participants.We conclude that proportions and relative risks of S1 Table(PDF)Click here for additional data file.S2 Table(PDF)Click here for additional data file.S3 Table(PDF)Click here for additional data file."} +{"text": "Although convenient single-tablet antiretroviral regimens have been developed to treat HIV in recent years, some patients have continued to take a multi-tablet treatment, nevirapine extended-release (NVP XR) plus two nucleoside reverse transcriptase inhibitors (NRTIs) due to its excellent safety profile. This observational study examined the demographic and clinical characteristics of HIV-positive patients who switched to dolutegravir plus lamivudine (DTG/3TC) from NVP XR plus 2 NRTIs, following discontinuation of NVP XR from the Canadian market.Virally suppressed (< 50 cps/mL) HIV-positive adults \u226518 years who switched from NVP XR plus 2 NRTIs to DTG/3TC between 20 August 2019 and 30 April 2020 were retrospectively identified from Electronic Medical Records housed at Spectrum Health in British Columbia, Canada. Baseline demographic and clinical characteristics were summarized using descriptive statistics at the date of first DTC/3TC prescription. Virologic control, CD4 cell count, weight-related changes and exploratory characteristics related to metabolic syndrome were summarized at baseline and at 12 \u00b1 6-months post-switch using descriptive statistics. Reasons for treatment discontinuation were also captured.Sixty-nine patients were identified . Mean length of use (\u00b1SD) of NVP XR was 4.6 \u00b1 2.6 years. Sixty-three (91.3%) persisted on DTG/3TC at the 12-month timepoint post-switch with 61 (96.8%) virally suppressed < 50 cps/mL and all 63 (100%) virally suppressed < 200 cps/mL. Among persistent patients with CD4 cell counts available, mean CD4 cell count (\u00b1SD) remained stable, increasing slightly from 724.4 \u00b1 238.4 to 740.3 \u00b1 240.6 cells/uL. All six (8.7%) patients who discontinued DTG/3TC, discontinued due to tolerability and not effectiveness reasons.Our findings are the first to examine real-world use of single-tablet, 2-drug DTC/3TC among patients who switched from multi-tablet, 3-drug NVP XR plus 2 NRTIs in Canada. The majority persisted on DTG/3TC and remained virally suppressed at the < 50 cps/mL level 12-months post-switch. This, coupled with excellent tolerability, demonstrates the effectiveness of DTG/3TC in maintaining viral suppression among a unique and stable group of older men.Joss de Wet, MBChB CCFP FCFP, Gilead: Advisor/Consultant|Gilead: Board Member|Gilead: Grant/Research Support|ViiV: Advisor/Consultant|ViiV: Board Member|ViiV: Grant/Research Support Joann K. Ban, PharmD, MSc, GlaxoSmithKline Canada Inc.: Employee Gustavo Verdier, BSc, BPharm, MBA, GlaxoSmithKline: Stocks/Bonds|ViiV Healthcare ULC: Salary Juejing Ling, MSc, GSK: Employee of IQVIA , a company that receives consulting fees from GSK. Andrean Bunko, MPH, GlaxoSmithKline Inc.: GSK contracted with IQVIA for this and other projects. I am acting as an author in capacity of my employment with IQVIA. Michael McKimm, BSc, ViiV Healthcare: employee."} +{"text": "Stenotrophomonas maltophilia with a 44,659-bp genome. This phage is closely related to Stenotrophomonas phage SM171, sharing 92% overall nucleotide identity as determined by BLASTn, and it shares 14 similar proteins with some Pseudomonas phages from the genus Beetrevirus.Phage Suso is a temperate siphophage of Stenotrophomonas maltophilia is emerging as a multidrug-resistant respiratory pathogen and trimmed with FASTX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). The trimmed reads were used for assembly using SPAdes v3.5.0 . Annotation of the phage genome was performed using the Center for Phage Technology (CPT) Galaxy-Apollo platform , in Wadsworth, TX, in September 2019, using reads 87,54 reads xy-pub) 79. Gene cxy-pub) 7 and Metaxy-pub) 7. tRNA gexy-pub) 7 and tRNAxy-pub) 7. Gene fuxy-pub) 7, TMHMM vxy-pub) 7, HHPred xy-pub) 7, and Sigxy-pub) 7. Genome-xy-pub) 7. All sofStenotrophomonas phage SM171 (MZ611865), sharing 92% overall nucleotide identity as determined by BLASTn. Besides this phage, Suso shares 14 similar proteins with some Pseudomonas phages from the genus Beetrevirus (taxid 2560098), such as phages B3 (GenBank accession number NC_006548), JBD67 (GenBank accession number NC_042135), and vB_Pae_BR141c (GenBank accession number MK511065).Phage Suso has a siphophage morphology possessiMZ326866. The associated BioProject, SRA, and BioSample accession numbers are PRJNA222858, SRR14095259, and SAMN18509666, respectively.The Suso sequence was deposited in GenBank with accession number"} +{"text": "Mindfulness (being present in the moment without judgement) has been linked to greater caregiver emotional health. Recent mindfulness-based interventions report improved coping skills, mood, and reduced stress in dementia caregivers. In this cross-sectional study of 141 ADRD caregivers, we assessed whether the relationship between caregiver mindfulness and caregiver experience varies by caregiver gender, relationship to patient (spouse-vs-child), etiology (AD-vs-LBD), or stage (MCI-vs-dementia). A stratified univariate analytic approach was used. Four mindfulness parameters were used: global score (GS), decentering (F1), positive (F2), and negative emotional regulation (F3). Outcomes included positive and negative appraisals of caregiving (PANAC), preparedness, care confidence, and depression. GS was linked to positive outcomes in male (rPANAC+=0.32/p=0.005), spouse caregivers (rPANAC+)=0.32/p=0.006 ) of ADRD patients regardless of etiology and stage . Inverse relationships were observed with negative outcomes in male (rPANAC-=-0.46/p=0.002 and rdepression=-0.41/p=0.005), spouse caregivers (rPANAC-=-0.25/p=0.035 and rdepression=-0.30/p=0.009) of AD patients (rPANAC-=-0.25/p=0.043 and rdepression=-0.33/p=0.009) in early stages (rdepression=-0.41/p=0.001). F2 contributed to most relationships, with F3 and F1 significant in some but not all caregiver groups. Specifically, male spouse caregivers of AD patients regardless of stage may benefit from full-scope (F1-F3) programs while those of LBD patients from programs focused on improving emotional regulation (F2-F3). Wives of AD and LBD patients may in turn benefit from programs to improve positive emotional regulation (F2). Findings suggest that tailoring mindfulness-based interventions to specific caregiver groups may be effective in improving caregiver experience and mood."} +{"text": "Rationale: Infection with the SARS-CoV2 virus is associated with elevated neutrophil counts. Evidence of neutrophil dysfunction in COVID-19 is based on transcriptomics or single functional assays. Cell functions are interwoven pathways, and understanding the effect across the spectrum of neutrophil function may identify therapeutic targets. Objectives: Examine neutrophil phenotype and function in 41 hospitalised, non-ICU COVID-19 patients versus 23 age-matched controls (AMC) and 26 community acquired pneumonia patients (CAP). Methods: Isolated neutrophils underwent ex vivo analyses for migration, bacterial phagocytosis, ROS generation, NETosis and receptor expression. Circulating DNAse 1 activity, levels of cfDNA, MPO, VEGF, IL-6 and sTNFRI were measured and correlated to clinical outcome. Serial sampling on day three to five post hospitalization were also measured. The effect of ex vivo PI3K inhibition was measured in a further cohort of 18 COVID-19 patients. Results: Compared to AMC and CAP, COVID-19 neutrophils demonstrated elevated transmigration (p = 0.0397) and NETosis (p = 0.0332), and impaired phagocytosis (p = 0.0036) associated with impaired ROS generation (p < 0.0001). The percentage of CD54+ neutrophils (p < 0.001) was significantly increased, while surface expression of CD11b (p = 0.0014) and PD-L1 (p = 0.006) were significantly decreased in COVID-19. COVID-19 and CAP patients showed increased systemic markers of NETosis including increased cfDNA (p = 0.0396) and impaired DNAse activity (p < 0.0001). The ex vivo inhibition of PI3K \u03b3 and \u03b4 reduced NET release by COVID-19 neutrophils (p = 0.0129). Conclusions: COVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration and NETosis, and impaired antimicrobial responses. These changes highlight that targeting neutrophil function may help modulate COVID-19 severity. Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) virus, was declared a global pandemic by The World Health Organization (WHO) on 11 March 2020 [Dysregulated virus induced host-immune responses are thought to be the primary cause of severe COVID-19 . NeutropAdvanced age is a recognised risk factor for severe COVID-19, including the development of ARDS ,7,8. AgeEmerging studies suggest that neutrophils are implicated in the pathogenesis of severe COVID-19 and every reporting study has described cell dysfunction (or inferred cell dysfunction through transcriptomics), which could contribute to tissue damage and secondary infection ,25,26,27These are important considerations. As neutrophil functions change with age, age matched controls are important in identifying pathological differences. Although approximately 12% of hospitalized COVID-19 patients require ICU support, the majority of hospital admissions and deaths occur on non-ICU wards ; understWe hypothesised that neutrophils from COVID-19 patients would exhibit diverse altered effector functions and changes to phenotype, with the degree of dysfunction associated with adverse patient outcomes.This study aimed to perform, for the first time, a comprehensive assessment of ex vivo neutrophil phenotypes and functions in a statistically powered cohort of hospitalized, non-ICU SARS-CoV2 infected patients compared to aged-matched controls and patients with non-COVID community acquired pneumoniae (CAP) and to investigate relationships with clinical outcomes.Recruitment is summarized in 2: FiO2 ratio (SF), converted to PaO2: FiO2 (PF) (SF = 57-0.61PF).COVID-19 patients were recruited within 48 h of hospital admission due to pneumonitis/pneumonia related to COVID-19. All patients had a positive COVID-19 PCR swab. No patients received novel treatments or were part of a COVID clinical medicinal trial on recruitment to this study. Exclusion criteria is listed in CAP patients were recruited within 48 h of hospital admission due to non-COVID-19 pneumonia. All patients had a negative COVID-19 swab. Exclusion criteria is listed in the Age matched controls (AMC) were either recruited from patients attending pre-booked face-to-face outpatient appointments or from hospital staff. AMC had no evidence of acute illness, including COVID-19, within the last two weeks, as assessed by a respiratory physician, and met the other exclusion criteria.S. pneumoniae and NETosis by the release of cell-free (cf) DNA DNA . Plasma t-test or ANOVA. A Mann-Whitney U test for unpaired data, a Wilcoxon test for paired data, or a Kruskall-Wallis test was used to analyse non-normally distributed data. Data are presented throughout as median (IQR), with each n number representing a separate study participant. Significance was defined at p < 0.05. There were no corrections for multiple comparisons, but exact p values are given. A power calculation performed on isolated neutrophil NETosis data suggested that 18 participants were required in each group . A Kolmogorov-Smirnov Test was used to determine data distribution. Normally distributed data were analysed using a student\u2019s 41 COVID-19 patients (mean age 71.5 years), two healthy AMC (mean age 70 years) and 26 CAP patients (mean age 67.5 years) were included in the study. Demographics are provided in p = 0.0332) and CAP AMC vs. 40.63 (115.2) COVID-19, S. pneumoniae was significantly decreased in COVID-19 patients compared to AMC (Median fluorescence intensity (MFI): 8.0 (4.2) AMC vs. 6.6 (2.6) COVID-19, p = 0.0366) and CAP (MFI 9.8 (4.8), p = 0.0052, p = 0.3257, p = 0.9228, p = 0.6726, Neutrophil phagocytosis of p = 0.0091), and CAP patients (MFI: 285 (211) baseline vs. 357 (260) 30 min, p = 0.038), but not in COVID-19 patients (MFI: 44.1 (35) baseline vs. 65.3 (60) 30 min, p = 0.134, p < 0.0001, Cytoplasmic (c)ROS, and nuclear/mitochondrial (n/m)ROS were measured in resting neutrophils and following phagocytosis. Compared to unstimulated cells, cROS levels were elevated after phagocytosis in both AMC (MFI: 46.8 (28) baseline vs. 64.9 (51) 30 min, p < 0.0001), but not in COVID-19 patients (MFI: 18.9 (12) baseline vs. 21.2 (12), p = 0.0329) or CAP patients (MFI: 22.2 (21) baseline vs. 26.7 (17), p = 0.989, p < 0.0001) and CAP neutrophils baseline vs. 32.0 (38), p = 0.0394, p = 0.0118, A larger increase in the level of cfDNA was detected in supernatants obtained from COVID-19 patient neutrophils post-PMA treatment compared to AMC (fold change in absorbance of neutrophils stimulated with PMA vs. vehicle control: 1.29 (0.32) AMC vs. 1.53 (1.66) COVID-19, p = 0.0396, p = 0.0186, p = 0.0322).At hospital admission, COVID-19 patients presented with higher concentrations of plasma cfDNA compared to AMC (621 ng/mL (1324) AMC vs. 1071 ng/mL (856) COVID-19, To determine whether neutrophils, via NETosis, were a source of the cfDNA, plasma samples were screened for the presence of CitH3, a protein that decorates the DNA backbone of NETs . Westernp < 0.0001, vs. 77.45% (34) CAP, p < 0.0001, Using NETs as a substrate, serum DNase activity was lower in COVID-19 patients at the time of hospital admission when compared to both AMCs and CAP patients (% degradation: 88.4% (93) AMC vs. 12.8% (49) COVID-19, To determine whether changes observed in neutrophil function were associated with phenotype, expression of key surface molecules were investigated by flow cytometry. This was compared to both AMC and CAP patients. A table of percentage receptor expression and MFI is shown in p = 0.0014, p = 0.0026, p = 0.046; MFI:1701 (1268) CAP, p < 0.0001). Compared to AMC, both the percentage of neutrophils expressing the activation marker CD11b (82% (15) AMC vs. 68% (44) COVID-19, p < 0.0001, vs. 7% (11) CAP, p < 0.0001, The percentage of neutrophils expressing CD54, a marker of reverse transmigration, was elevated in COVID-19 patients compared to both AMC and CAP patients (26% (37) AMC vs. 71% (21) COVID-19, p < 0.006, vs. 524 (264) and CAP, p < 0.0001, The percentage of neutrophils expressing CD66b, CD62L, CD10, CXCR2, CXCR4, CD11c and PD-L1 did not differ between AMC and COVID-19 patients see . The surThere was no association of neutrophil phenotypic marker expression with 4C severity score, or in survivors and non-survivors.p = 0.0322, p = 0.0273, p = 0.0420, On day three to five follow-up, relative to baseline readings, there was a decrease in CXCR2 expression: (MFI: 1960 (1601) day one vs. 1126 (1262), day three to five, p = 0.0322, p = 0.0273, p = 0.0420, On day three to five follow-up, relative to baseline readings, there was a decrease in CXCR2 expression: (MFI: 1960 (1601) day 1 vs. 1126 (1262), day three to five, p = 0.0296, CAP p = 0.0106, p < 0.0001, CAP p = 0.0032, p < 0.0001, CAP p < 0.0001, p < 0.0001, Compared to AMC, both COVID-19 and CAP patients showed elevated levels of IL-6 , p = 0.0156, Pre-incubation of COVID-19 neutrophils from cohort 2, with Pi3k delta inhibitor CAL101 and gamma inhibitor AS252434 significantly decreased PMA induced NETosis (PMA RFU 247 (228.5) vs. delta 207.5 (242.5), We present novel findings of COVID-associated neutrophil dysfunction across all main effector functions. In summary, compared to AMC and patients with CAP, systemic neutrophils from patients hospitalized with moderate severity COVID-19 demonstrated increased migration, impaired anti-microbial responses including reduced phagocytosis and nuclear/mitochondrial ROS generation after phagocytosis. Later/end phase neutrophil responses were increased, namely ex vivo NETosis with evidence of increased systemic NETosis, coupled with reduced DNase activity, which was also elevated in CAP. We also show an altered but distinct neutrophil phenotype, not compatible with a purely activated, immature, senescent or anti-inflammatory phenotype as described before (results summarised in Individually, as described in other studies, these changes to effector function could compromise aspects of the host defence. Collectively, these changes represent a clear mechanism for significant tissue damage. Poor phagocytosis would impede pathogen clearance, increasing the likelihood of secondary infection and amplifying inflammation. NETosis is implicated in tissue damage and thrombotic events in several disease settings ,38. The S. pneumoniae, the most common bacteria implicated in secondary infection in COVID-19 [Secondary infection in COVID-19 is associated with increased severity of lung disease and poorer outcomes ,41. ImpaCOVID-19 , alongsiCOVID-19 , may conElevated NETosis ,24,44 anThe collective pattern of neutrophil dysfunction in COVID-19 speaks of alterations to mechanosensing within these cells. Elevated migration and impaired phagocytosis could both be linked to reduced pseudopod extrusion, which is known to increase migratory speed . FurtherWe observed an altered neutrophil phenotype in moderate COVID-19, not compatible with previously described populations, and not in keeping with our AMC or CAP control cohorts. COVID-19 neutrophils expressed decreased levels of the activation marker CD11b and a lack of CD62L shedding, which has previously been observed in sepsis , alongsi+ CXCR2- neutrophils, confirming a report of reduced CXCR2+ neutrophils in ICU COVID-19 patients [Finally, we observed that COVID-19 neutrophils expressed elevated CD54, a marker of reverse transmigration, whereby neutrophils migrate from the tissues back into the circulation. These cells are capable of high levels of oxidative burst , which mpatients .The majority of COVID-19 hospitalisations and deaths occur in non-ICU wards , making Our data suggests a distinct cellular response in moderate COVID-19 which contributes to on-going immune mediated harm, but which may be modifiable using a targeted therapy, such as PI3K\u03b4 or PI3K \u03b3 inhibitors administered at this crucial point in disease progression.\u00ae to isolate neutrophils, and the authors combined data from multiple blood samples taken over eleven days of hospitalization. As we show changes in neutrophil phenotype and function over the three to five time course of our study, we suggest that combining time points obscures the complex changes occurring in this short-lived cell population. We also used opsonized S. pneumoniae for phagocytosis studies which may be phagocytosed by different mechanisms to S. aureus bioparticles [Our data complements studies which showed increased systemic NETosis in COVID-19 ,68, and articles , confounMore recently, Loyer et al., demonstrated the increased expression of CD11b and ROS production with decreased CD62L expression in a cohort of COVID-19 patients treated in the ICU in comparison with CAP and healthy controls . The autThis study was limited due to the safety measures required when handling biological fluids for a new infectious disease. All experiments were carried out within a BSL2 hood and methods were chosen based on tolerance to inactivation/fixation with 4% PFA. Our patients did not include an ICU group; however, mild-moderate disease affects a larger proportion of overall COVID-19 patients, and we believe it is this point in the patient pathway which holds most potential for successful intervention. Our AMC group highlights changes in COVID-19 and our CAP group highlights differences between disease types.Our study shows that moderate COVID-19 is associated with alterations in neutrophil phenotype, increased migratory capacity and NETosis, and impaired antimicrobial function, which contributes to the severity of COVID-19. Elevated NETosis in the lung is associated with disease severity, and elevated systemic NET production is likely to contribute to inflammation, which may drive ARDS associated damage and thrombosis. Targeting neutrophils and their downstream effectors may be beneficial in the treatment of COVID-19."} +{"text": "Mycobacterium smegmatis mc2155. McGee has a genome 156,008\u2009bp long, containing 237 protein-coding genes, 31 tRNA genes, and 1 transfer-messenger RNA (tmRNA) gene. McGee shares high gene content similarity to phages in actinobacteriophage cluster C1.Mycobacteriophage McGee is a myovirus isolated from a wet soil sample collected at Manassas, VA, using Mycobacterium smegmatis mc2 155 have been isolated and characterized, providing important insights into viral diversity and population structure . The soil sample was washed with 7H9 liquid medium, the wash filtered , and the filtrate plated in soft agar overlay containing Mycobacterium smegmatis mc2 155. McGee was purified with multiple rounds of plating. Negative-stain transmission electron microscopy revealed McGee to possess a Myoviridae morphology , and sequenced on an Illumina MiSeq instrument v3 reagents), resulting in 77,248 single-end 150-bp reads providing 73\u00d7 coverage. The raw reads were assembled and assessed using the programs Newbler v2.9 ( reagentshttp://cobamide2.bio.pitt.edu/) (http://phages.wustl.edu/starterator), whereas gene functional assignments were determined using BLASTp searches against the NCBI nonredundant v2.13.0 (13Genes were identified and annotated using DNA Master v5.23.6 (tt.edu/) , GLIMMER v2.13.0 and acti v2.13.0 , HHpred v2.13.0 , and Pha v2.13.0 . Aragorn v2.13.0 and tRNA v2.13.0 were use2.13.0 1315 and TM2.13.0 13, 17. AllA total of 269 putative genes were identified in McGee, including 237 protein-coding genes, 31 tRNAs, and 1 tmRNA. Among those that could be assigned a function, the virion structure and assembly genes include a major capsid protein (gp101), capsid decoration protein , tail sheath protein (gp129), tail assembly chaperones , tape measure protein (gp134), minor tail proteins , and baseplate wedge protein . The genes involved in McGee\u2019s DNA metabolism include DNA helicase (gp188), thymidylate kinase (gp197), DnaC-like helicase loader (gp201), DnaB-like double-stranded DNA (dsDNA) helicase (gp202), DNA primase (gp204), DnaJ-like chaperonin (gp206), single-stranded DNA (ssDNA) binding protein (gp207), DnaE-like DNA polymerase III \u03b1 (gp208), RF-1 peptide chain release factor (gp209), RecA-like DNA recombinase (gp210), Holliday junction resolvase (gp210), RusA-like resolvase (gp214), Ro-like RNA binding protein (gp233), and multiple proteins with a helix-turn-helix DNA binding domain . Genes involved in lysis, lysin A, holin, and lysin B are encoded by gp252, gp253, and gp254, respectively. The largest gene in McGee is a hypothetical protein gp98 and the smallest gp64 (75\u2009bp long).https://phagesdb.org/), McGee was assigned to phage cluster C1 (Based on its gene content similarity (GCS) of at least 35% to phages in the Actinobacteriophage database (uster C1 , 18, 19.ON637764, while its raw reads have been deposited under Sequence Read Archive accession number SRX14483217.The complete genome sequence for McGee can be found at GenBank under accession number"} +{"text": "However, the classification strategy and homology group of tet(X)-positive Acinetobacter spp. plasmids remain largely unknown. In this study, we classified them by genome-based replicon typing, followed by analyses of structural characteristics, transferability and in vivo effect. A total of 34 plasmids distributed in at least nine Acinetobacter species were collected, including three tet(X3)-positive plasmids and one tet(X6)-positive plasmid from our genome sequencing results. Among them, there were 28 plasmids carrying Rep_3 superfamily replicase genes and classified into six homology groups, consisting of GR31 (82.1%), GR26 (3.6%), GR41 (3.6%), GR59 (3.6%), and novel groups GR60 (3.6%) and GR61 (3.6%). Our tet(X3)-positive plasmids pYH16040-1, pYH16056-1, and pYH12068-1 belonged to the dominant GR31 group, whereas the tet(X6)-positive plasmid pYH12068-2 was unclassified. Structurally, all tet(X)-positive GR31 plasmids shared similar plasmid replication (repB), stability (parA and parB) and accessory modules [tet(X) and sul2], and 97.6% of plasmid-mediated tet(X) genes in Acinetobacter species were adjacent to ISCR2. Conjugation and susceptibility testing revealed pYH16040-1, pYH16056-1, and pYH12068-2, carrying plasmid transfer modules, were able to mediate the mobilization of multiple antibiotic resistance. Under the treatment of tigecycline, the mortality rate of Galleria mellonella infected by pYH16040-1-mediated tet(X3)-positive Acinetobacter spp. isolate significantly increased when compared with its plasmid-cured strain (p < 0.0001). The spread of such plasmids is of great clinical concern, more effects are needed and will facilitate the future analysis of tet(X)-positive Acinetobacter spp. plasmids.The rapid dissemination of plasmid-mediated Acinetobacter species is a heterogeneous group of opportunistic pathogens and easily acquires antibiotic resistance genes (ARGs) (tet(X) genes have been reported in at least 10 different Acinetobacter species, including Acinetobacter baumannii, Acinetobacter gandensis, Acinetobacter piscicola, Acinetobacter schindleri, Acinetobacter johnsonii, Acinetobacter indicus, Acinetobacter towneri, Acinetobacter lwoffii, Acinetobacter pseudolwoffii, and Acinetobacter variabilis (tet(X3) and tet(X6) genes were detected with carbapenem resistance gene blaNDM\u20131 in A. baumannii, A. indicus, A. schindleri, and A. lwoffii isolates, posing a serious public health threat Gram-negative and Gram-positive pathogens . Howevers (ARGs) . To dateriabilis . Worrisoh threat .Acinetobacter spp. genome and plays an important role in the horizontal transmission of ARGs, such as blaNDM\u20131 and blaOXA\u201323 , a series of plasmid classification schemes were developed based on replication initiator protein, mobilization protein and plasmid size (tet(X)-positive Acinetobacter spp. plasmids since the first mobile plasmid-mediated tet(X3) gene in 2019, and their homology groups remained to be analyzed (tet(X)-carrying Acinetobacter spp. plasmids by genome-based replicon typing, followed by analyses of structural characteristics, transferability, and in vivo effect.The plasmid is a self-replicating component of laOXA\u201323 . With thmid size . As the mid size . Howeveranalyzed . Herein,tet(X)-positive Acinetobacter spp. strains in China (tet(X3)-positive Acinetobacter spp. YH16040 and tet(X3)- and tet(X6)-positive Acinetobacter spp. YH12068 from pig; tet(X3)-positive Acinetobacter spp. YH16056 from soil; tet(X3)-positive A. pseudolwoffii YH18001 from human; tet(X4)-positive A. indicus Q22-2, Q85-2, and Q278-1 from migratory bird. In addition, a newly isolated tet(X6)-positive A. baumannii YC103 by CHROMagar\u2122 Acinetobacter plates containing tigecycline (2 \u03bcg/mL) from duck in 2019 was also analyzed (tet(X)-harboring Acinetobacter spp. plasmids deposited at the NCBI database were collected by tblastn -positive Acinetobacter spp. isolates were sequenced by Oxford Nanopore , respectively. Combining the clean data with our previous Illumina HiSeq data , genome assembly was performed by Unicycler version 0.4.1 and corrected by Pilon version 1.12 (Genomic DNA of eight Seq data as well ion 1.12 .tet(X)-harboring plasmids were annotated by Rapid Annotation using Subsystem Technology (RAST) version 2.0 -positive structures was conducted by Easyfig version 2.2.5 (All sion 2.0 . Plasmidsion 2.0 . Plasmidsion 2.0 . A maximsion 2.0 . Plasmidme group . Similaron 2.2.5 .tet(X)-mediated tigecycline resistance was evaluated by filter mating with rifampin-resistant Acinetobacter baylyi ADP1 and A. baumannii ATCC 19606 (tet(X) detection and PCR-based fingerprinting (Transferability of plasmid-borne CC 19606 . The putprinting . In paraprinting .tet(X3)-harboring GR31 plasmid pYH16040-1 was cured of Acinetobacter spp. YH16040 using sodium dodecyl sulfate (SDS) with adjustment (tet(X3) gene .The justment . An overX3) gene and repl1 whereas eravacycline was uninterpreted with no breakpoint. Escherichia coli ATCC 25922 served as a quality control strain.Minimum inhibitory concentrations (MICs) of all strains were determined by broth microdilution and interpreted according to the Clinical and Laboratory Standards Institute guideline M100-Ed28 . The tesG. mellonella were randomly grouped (16 per group), and then infected with GR31 plasmid-mediated tet(X3)-positive Acinetobacter spp. YH16040 or its plasmid-cured strain YH16040C via the last left proleg. After incubation at 35\u00b0C for 2 h, the infected larvae were treated with tigecycline (2 \u03bcg/g) or phosphate-buffered saline (PBS) by injection into the last right proleg. Finally, the larvae were observed for survival rates per 24 h in the next 4 days. All in vivo experiments were performed in triplicate.As previously described , the heatet(X)-positive Acinetobacter spp. isolates successfully revealed four tet(X)-carrying plasmids. These included tet(X3)-positive plasmids pYH16040-1 (GenBank accession number: CP094542) from Acinetobacter spp. YH16040, pYH16056-1 (CP094546) from Acinetobacter spp. YH16056, and pYH12068-1 (CP094556) as well as a tet(X6)-positive plasmid pYH12068-2 (CP094557) from Acinetobacter spp. YH12068 (tet(X6)-positive chromosome cYC103 (CP054560) from A. baumannii YC103 was also obtained (tet(X)-positive strains A. pseudolwoffii YH18001, A. indicus Q278-1, A. indicus Q85-2, and A. indicus Q22-2 (tet(X)-harboring plasmids or chromosomes despite repeated attempts. By querying Nanopore raw data of A. pseudolwoffii YH18001 , A. indicus Q278-1 , A. indicus Q85-2 , and A. indicus Q22-2 , a repeated structure consisting of multiple copies of tet(X) genes was detected, respectively, which may lead to the failure of complete sequence assemblies.WGS analyses of eight YH12068 . Meanwhiobtained . For theus Q22-2 , we failtet(X)-positive Acinetobacter spp. plasmids deposited at the NCBI database has been growing subtypes located on plasmids (tet(X3) , tet(X5) , and tet(X6) , of which tet(X3) usually coexisted with tet(X6) . Besides tet(X) genes, large amounts of plasmid-mediated genes conferring resistance to tetracyclines, aminoglycosides, \u03b2-lactams, phenicols, sulfonamides, macrolides, lincosamides, and rifamycins were present (tet(X)-positive plasmids ranging from 42,489 to 332,451 bp were widely distributed in A. indicus , A. baumannii , A. towneri , A. schindleri , A. variabilis , A. pseudolwoffii , A. piscicola , Acinetobacter junii , Acinetobacter pittii , and unidentified Acinetobacter spp. strains -positive MDR Acinetobacter spp. plasmids.Since the first report in 2019 , the num n = 34; , includiplasmids , namely present . Worrisotet(X)-positive Acinetobacter spp. plasmids carried replicase genes and all of them belonged to a Rep_3 superfamily (pfam01051). Therefore, plasmid classification was conducted based on nucleotide sequence alignment with already classified replicase genes (tet(X)-positive Rep_3 superfamily plasmids, a total of six homology groups were successfully identified, such as the dominant GR31 , GR26 , GR41 , and GR59 -positive plasmids pYH16040-1 (CP094542), pYH16056-1 (CP094546), and pYH12068-1 (CP094556) fell within the same group GR31, which has been sporadically detected with tet(X) genes in A. baumannii, A. indicus, A. schindleri, A. towneri, and other Acinetobacter spp. strains (tet(X6)-positive plasmid pYH12068-2 (CP094557) was unclassified due to the lack of replicase genes. In contrast, the replicase genes of tet(X3)- and tet(X6)-carrying plasmids pXMC5X702-tetX-145k (CP084302) and pYH12207-2 (CP048661) have < 75% nucleotide identities with existing homology groups GR1-GR59, and therefore were defined as novel groups GR60 and GR61 , respectively (tet(X)-positive Acinetobacter spp. plasmids.Replicon conserved domain analyses showed that 82.4% (28/34) of se genes . Among t strains . Howeverectively . We provAcinetobacter spp. isolates . In essence, the GR31 plasmids have been detected in 13 validly named Acinetobacter species, including A. baumannii , A. lwoffii , A. indicus , A. towneri , A. schindleri , and others genes especially in the genera Acinetobacter.In order to evaluate the host range of plasmids belonging to GR26, GR31, GR41, GR59, GR60, and GR61, we conducted a blastn search against the NCBI database and confirmed they were mainly distributed in d others . The plaplasmids . Particuplasmids , but thetet(X)-carrying GR31 plasmids available in the NCBI database. A total of 23 plasmids belonging to GR31 were analyzed and they exhibited GC contents ranging from 39.1 to 46.1%. According to our WGS results, pYH16040-1 was 87,435 bp and harbored 94 putative open reading frames (ORFs), whereas pYH16056-1 was 98,709 bp consisting of 107 ORFs and pYH12068-1 was 100,866 bp consisting of 115 ORFs. Although they originated from different sources, pYH16056-1 and pYH12068-1 showed an average 76.5% nucleotide coverage and 99.8% nucleotide identity to pYH16040-1, with the encoding sequence insertion, deletion and rearrangement and the accessory modules (tet(X)-positive GR31 plasmids owned a repB gene involved in plasmid replication, and parA and parB genes responsible for plasmid stability. However, only 21.7% (5/23) of them harbored plasmid transfer modules, including conjugal transfer (n = 3) and mobilization genes (n = 2). For accessory modules, they mainly consisted of ARGs and heavy-metal resistance gene clusters .Predominantly, we compared the complete plasmid sequences of pYH16040-1, pYH16056-1, and pYH12068-1 with angement . Moreoveangement . Archety modules . Our restet(X) genes in Acinetobacter species, including tet(X3) (n = 28), tet(X6) (n = 12), and tet(X5) (n = 2), were further analyzed and ISAba14 (n = 3). Similarly, the truncation by IS26 was found on GR60 (n = 2) and GR61 (n = 2) plasmids, one of which was also upstream truncated by ISAcsp12. Except the GR26 plasmid carrying a complete ISCR2-mediated transposition unit (n = 1), GR41 and GR59 plasmids were detected with truncation by IS3 (n = 1) and IS1006 (n = 1), respectively. In addition, our WGS results of A. pseudolwoffii YH18001 (JALHBG010000013), A. indicus Q278-1 (JALHBF010000002), A. indicus Q85-2 (JALHBE010000004), and A. indicus Q22-2 (JALHBD010000003) revealed the incomplete tet(X)-carrying structures were also related to ISCR2 (tet(X) variants and ISCR2 as well as truncation by other insertion sequences indicated the frequent recombination events.Genetic environments of all plasmid-mediated analyzed . The res process . For GR3to ISCR2 . The clotet(X3) genes were successfully transferred from Acinetobacter spp. YH16040 and YH16056 to the recipient A. baylyi ADP1 , but failed to A. baumannii ATCC 19606. In Acinetobacter spp. YH12068, the tet(X3)-carrying GR31 plasmid pYH12068-1 (CP094556) couldn\u2019t be transferred, which may be explained by the lack of entire conjugative transfer regions (tet(X6)-positive unclassified plasmid pYH12068-2 (CP094557) carrying plasmid transfer modules was transferred from Acinetobacter spp. YH12068 to A. baylyi ADP1 with a similar efficiency mentioned above. MICs of all transconjugants against tetracyclines increased by at least 32-fold when compared with A. baylyi ADP1, including tetracycline (\u226564 \u03bcg/mL), tigecycline (\u22654 \u03bcg/mL), the newly FDA-approved eravacycline (\u22652 \u03bcg/mL) and omadacycline gene (CP040912) was also able to be transferred from human-derived A. baumannii to A. baumannii 5AB via electro-transformation, whereas the GR31 plasmid co-harboring tet(X3) and tet(X6) genes (CP044451) was from environmental A. indicus to A. baylyi ADP1 by natural transformation. The transferability of tet(X) genes between Acinetobacter species of human, animal and environment origins reminded us to consider the \u201cOne Health\u201d approach to prevent mobile tigecycline resistance.Conjugation experiments showed the GR31 plasmid-mediated regions . Meanwhitet(X3)-mediated tigecycline resistance from Acinetobacter spp. YH16040, YH16056, and YH12068 to A. baylyi ADP1, as well as florfenicol resistance (128 \u03bcg/mL) from Acinetobacter spp. YH16040 and YH12068 and gentamicin resistance (16 \u03bcg/mL) from Acinetobacter spp. YH16056, which was consistent with the result of plasmid-mediated ARG mining (tet(X)-mediated tigecycline resistance and blaNDM\u20131-mediated carbapenem resistance between Acinetobacter species (tet(X) genes, as previously described for resistance determinants mcr-1 and blaIMP\u20131 was transferred with G mining . Recentl species . With thblaIMP\u20131 .tet(X3) gene, a plasmid-cured strain YH16040C [tet(X3)-negative] was obtained by serially passaging of tet(X3)-positive Acinetobacter spp. YH16040. For tigecycline, a significant decrease in MIC was detected (1 \u03bcg/mL) when compared with the parental isolate YH16040 , eravacycline (0.06 \u03bcg/mL), omadacycline (0.125 \u03bcg/mL), florfenicol (8 \u03bcg/mL) and sulfamethoxazole-trimethoprim (20 \u03bcg/mL) also exhibited at least 16-fold decrease. The result further confirmed the elimination of GR31 plasmid pYH16040-1 (CP094542) that co-harbored resistance genes tet(X3), floR and sul2 gene was evaluated using a G. mellonella model. 96 h later of tigecycline treatment (2 \u03bcg/g), the larval mortality rate of Acinetobacter spp. YH16040C significantly decreased to 37.5% while Acinetobacter spp. YH16040 was 87.5% gene compromised the clinical effectiveness of tigecycline. Notably, the infection by Acinetobacter spp. YH16040 and Acinetobacter spp. YH16040C under the treatment of PBS resulted in a greater larval mortality rate (100%) than PBS only (12.5%) after 48 h (p < 0.0001), whereas no significant difference was observed between Acinetobacter spp. YH16040 and Acinetobacter spp. YH16040C -positive Enterobacteriaceae bacteria have also been constructed, and therefore G. mellonella was available for in vivo functional analyses of plasmid-mediated tet(X) genes.Subsequently, the tet(X)-carrying MDR plasmids in Acinetobacter species. Our results classified the tet(X)-positive Acinetobacter spp. plasmids of Rep_3 superfamily into six homology groups, including two newly assigned GR60 and GR61. To the best of our knowledge, this study first revealed a dominant GR31 plasmid mediating the horizontal transfer of tigecycline resistance gene tet(X) across different Acinetobacter species and contributed to the failure of tigecycline treatment in vivo. Accordingly, more efforts are needed to monitor and prevent the plasmid-mediated tet(X)-positive Acinetobacter spp. strains.Taken together, the data presented in this study highlighted the diverse distribution of The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/J-LH, Y-HL, and JS designed the study. CC, P-YH, C-YC, and QH performed the experiments. CC and P-YH analyzed the data. CC wrote the draft of the manuscript. All authors reviewed, revised, and approved the final report."} +{"text": "Azadirachta indica L. and Melia azedarach L., belonging to Meliaceae family, have been shown to have medicinal benefits and are extensively employed in traditional folk medicine. Herein, HPLC analysis of the ethyl acetate fraction of the total methanolic extract emphasized the enrichment of both A. indica L., and M. azedarach L. leaves extracts with phenolic and flavonoids composites, respectively. Besides, 4 limonoids and 2 flavonoids were isolated using column chromatography. By assessing the in vitro antiviral activities of both total leaves extracts against Severe Acute Respiratory Syndrome Corona virus 2 (SARS-CoV-2), it was found that A. indica L. and M. azedarach L. have robust anti-SARS-CoV-2 activities at low half-maximal inhibitory concentrations (IC50) of 8.451 and 6.922 \u03bcg/mL, respectively. Due to the high safety of A. indica L. and M. azedarach L. extracts with half-maximal cytotoxic concentrations (CC50) of 446.2 and 351.4 \u03bcg/ml, respectively, both displayed extraordinary selectivity indices (SI>50). A. indica L. and M. azedarach L. leaves extracts could induce antibacterial activities against both Gram-negative and positive bacterial strains. The minimal inhibitory concentrations of A. indica L. and M. azedarach L. leaves extracts varied from 25 to 100 mg/mL within 30 min contact time towards the tested bacteria. Our findings confirm the broad-spectrum medicinal value of A. indica L. and M. azedarach L. leaves extracts. Finally, additional in vivo investigations are highly recommended to confirm the anti-COVID-19 and antimicrobial activities of both plant extracts.The leaves of Drug resistance to infections in humans brought on by microorganisms including bacteria, viruses and fungi is a life-endangering phenomenon with considerable number of mortalities worldwide. Medicinal herbs were applied to produce a plenty of pharmaceuticals that are currently used to alleviate various health disorders or diseases. Numerous researches are performed to find out new antimicrobial treatment alternatives that really can prevent the spread of bacteria or eradicate them without endangering humans by conducting comprehensive screenings of medicinal herbs , 2.In December 2019, the SARS-CoV-2 virus has emerged as an unknown severe respiratory illness, namely corona virus illness 2019 (COVID-19) . Few weeAzadirachta indica L. (Neem) and Melia azedarach L. (China tree) are popular medicinal herbs that belong to the Meliaceae family. A. indica L, originated in India, is extensively scattered in all countries , 1H-NMR : 7.11 , 5.45 , 2.89 ,4.29 , 4.89, 4.95, 2.67 , 1.91, 1.64 , 7.39 , 6.21 , 6.93 , 1.70 , 2.15 , 1.10 . 13C-NMR : 158.2 (C-1), 126.4 (C-2), 206.1 (C-3), 41.3 (C-4), 50.4 (C-5), 69.8 (C-6), 76.9 (C-7), 43.7 (C-8), 40.2 (C-9), 41.3 (C-10), 16.1 (C-11), 28.3 (C-12), 45.7 (C-13), 72.8 (C-14), 57.5 (C-15),33.1 (C-16), 40.2 (C-17), 122.8 (C-20), 141.8 (C-21), 111.2 (C-22), 138.7(C-23), 21.51, 171.81 (OAC), 21.9 (C-methyls). From the formentioned spectral data, this compound was identified as 14,15-\u03b2-epoxynimonol + 612 for C35H48O9, 549 (100%), 449, 389 and 371. Additionally, 1H-NMR, and13C-NMR data were in agreement with previous studies + 694 for C40H54O10, 649 for ethoxyl group loss at C-12, then 449 for two tigloyl side chain loss, followed by 389(100%) due to acetyl group loss and subsequently water loss giving 371 which are in accordance to nimbolinin limonoids fragmentation pattern. The 1H and 13C NMR data were similar to +, 552, 537 [M\u2013H2O + H]+. The data were consistent with the molecular formula C35H54O5. The 1H-NMR and13C-NMR data confirmed this compound as 3-\u03b1-tigloylmelianol which was previously identified from M. azedarach fruits by [Compound 6: yellow amorphous powder, m.p. 164\u00b0C. EI-MS (m/z): 462 (M+) for C22H22O11, in addition to 300, 285, 257, 152, 137, 116. IR data, UV absorbance in different shift reagents and 13C-NMR data characterized this compound as chrysoeriol 7-O-glucoside. This compound has been isolated for first time in the present study. The structures of the isolated compounds were illustrated in Fig 1.50), the half maximal inhibitory concentration 50 (IC50) and selectivity index (SI)(CC50/IC50) against SARS-CoV-2 were individually evaluated (Table 2). Both leaves extracts of A. indica and M. azedarach showed high safety in Vero E6 cells with CC50 values of 446.2 \u03bcg/mL for A. indica and 351.4 \u03bcg/mL for M. azedarach, respectively. Additionally, both extracts exhibited promising inhibition of SARS-CoV-2 replication in Vero E6 cells at potent IC50 concentrations of 8.541 \u03bcg/mL for A. indica and 6.922 \u03bcg/mL for M. azedarach . Interestingly, both extracts exhibited extraordinary selectivity indices (SI) (>50) (Table 2). The determined SI values are meaningfully greater than those recommended for further assessment of the bioactive compounds (> 10) [A. indica and M. azedarach indicate the bioactive potential of A. indica and M. azedarach leaves extracts. Compared to the reference drug control remedesivir , both plant extracts showed comparable safety and antiviral activities with slightly lower selectivity indices. These data demonstrate that both extracts can be considered as promising candidates for further in vitro and in vivo studies against SARS-CoV-2 virus and potentially other viruses.To appraise the antiviral efficacy of leaves extracts against SARS-CoV-2 virus, the half maximal cytotoxic concentration (CCs (> 10) , 39. TheA. indica extracts against the novel SARS-CoV-2 virus [et al. [To our knowledge, there is a few previous studies that assessed the antiviral activity of -2 virus , 41. In [et al. concludeBorkotoky and Banerjee , isolatein vitro viral inhibitory activity of M. azedarach L. leaves extract against SARS-CoV-2 which is so far not studied. Nethmini et al. found that M. azedarach L. could turn off the replication of herpes simplex virus, coxsackie virus, enterovirus, influenza A virus, and bovine rhinovirus in both epithelial and macrophage cell lines [In this study, we explored the ll lines .in vitro anti-SARS-CoV-2 effect in this study for both plant leaves extracts, the inhibitory zone assay was done to assess the in vitro antibacterial properties of the two leaves extracts against E. coli, P. aeruginosa, S. aureus, L. monocytogenes, and E. faecalis using agar well-diffusion assay. The obtained results indicated that 50 \u03bcg/ml of A. indica L. and M. azedarach L. displayed high potency for inhibiting a broad spectrum of examined Gram-negative (GN) species (.In addition to the Table 3). Results revealed that the size of ZOI of vancomycin against the selected pathogens; E. coli, S. enterica, P. aeruginosa, S. aureus, L. monocytogenes, and E. faecalis using disc diffusion assay were ranged between 7 and 11 mm as mentioned in Table 3).Simultaneously, two reference antibiotics drugs vancomycin (30 \u03bcg/disc) and ciprofloxacin (5 \u03bcg/disc) were applied in this study as a positive control . ResultsThese results show the tendency that the GN bacterial species were more susceptible to all tested plant extracts than the GP species. Conversely, the width of ZOI around discs was lower than those around wells. Our data are in agreement with previous study , in whicA. indica L. and of M. azedarach L. extracts were examined to estimate MIC values to assess their antibacterial potential during various exposure times to different bacterial strains. As shown in Figs 4, the extracts demonstrated a notable bactericidal effect against all the tested bacterial strains. The detected MIC values depend on the concentrations (mg/mL) and exposure time (min). The consequences of MICs exhibited by the extract of M. azedarach displayed that the perfect antibacterial effects against E. coli (MIC = 50 mg/mL within 30 min), S. enterica (MIC = 25 mg/mL within 30 min), P. aeruginosa (MIC = 25 mg/mL within 30 min), S. aureus (MIC = 75 mg/mL within 30 min), E. faecalis (MIC = 25 mg/mL within 30 min) and L. monocytogenes (MIC = 75 mg/mL within 30 min). The measured MIC values of A. indica plant extract were lower in GN than GP bacteria. The enhanced antibacterial activity against GN could be due to variation in active compounds in M. azedarach extract and their penetration ability through bacterial cell wall and membrane [The different concentrations (10\u2013100 mg/mL) of membrane . This fiM. azedarach extract. The results represented in Fig 4 revealed significant antibacterial effects against all test bacteria. Also here, the calculated MIC values depended on the applied extract concentrations (mg/mL) and contact time (min). The results of MIC exhibited that the extract has clear bactericidal effect against E. coli (MIC = 50 mg/mL within 30 min), S. enterica (MIC = 25 mg/mL within 30 min), P. aeruginosa (MIC = 50 mg/mL within 30 min), S. aureus (MIC = 75 mg/mL within 30 min), E. faecalis (MIC = 75 mg/mL within 30 min) and L. monocytogenes (MIC = 100 mg/mL within 30 min). Interestingly, the results showed that the M. azedarach extract possess higher antibacterial activities against the tested GN bacteria in comparison to GP bacteria, which is matching with what we detected in case of A. indica plant extract except that MIC of Listeria monocytogenes was higher than S. aureus and E. faecalis .Using the same procedure and bacterial strains, we also assessed the antibacterial activity of Table 4. The results gained revealed that there was an exceptional positive correlation with strong significance between GP and GN species and the concentrations of all plant extracts. On the other hand, results perceived that a moderate correlation had been reported for E. coli.From statistical analysis results, the potential correlation with significance between various concentrations of particular extract towards all the targeted pathogenic bacterial strains was briefly reported in S. aureus, vancomycin-resistant enterococci, and Mycobacterium tuberculosis are widely documented as challenging hospital-associated infections to treat with known antibiotics. To this point, medicinal plants are recently applied to provide a supplementary treatment line against these bacterial infections [M. azadirachta L. and A. indica L. showed powerful antibacterial activities against various GP and GN species. The Meliaceae family has a substantial percentage of polyphenolic chemicals that could possess oxidative activities. A. indica L. phytochemicals have such a broad range of biological characteristics, especially antibacterial and cancer-fighting potential [M. azedarach L. towards numerous types of bacterial pathogens [As a public biohazard with millions of deaths every year, antibiotic resistance emerged recently due to the continuous prescription of improper antibiotics at non-lethal doses. Methicillin-resistant fections . M. azadotential . This bootential . Furtherathogens . Limonoiathogens .M. azedarach L. was established to be biocidal agent against P. aeruginosa, and E. coli, the lowest activity was documented in aqueous extract of M. azedarach against E. coli (8.5 mm) and S. aureus (8.2 mm). In previous study, E. coli showed the lowest sensitivity to methanolic extract (6 mm), and no activity was observed in 10, 20, 30 \u03bcg/ml of methanolic extract of M. azedarach L. [M. azedarach L. seed extracts efficiently manage illnesses caused on by both GP and GN species and reported that the that ethyl acetate fraction exhibited greatest suppression, followed by aqueous and methanol-based extracts, each of which reduced the proliferation of all the studied pathogenic strains. The petrol and benzene extracts displayed antimicrobial activity versus 15 pathogens, however, in comparison to the polarity extracts. The findings previously illustrate that seed extracts are powerful antibiotics that can effectively prohibit both disease-caused pathogens to human infections.The ethanolic extract of arach L. . PreviouA. indica L. and M. azedarach L. leaves were chemically characterized and were found to be rich in phenolic compounds and flavonoids. In vitro assessment of both extracts revealed that they have robust antiviral activity against SARS-CoV-2 as well as antibacterial effects against broader spectra of GN and GP bacteria. These data emphasize their broad-spectrum medicinal value and demand further in vitro and in vivo investigations as anti-SARS-CoV-2 candidate and antibacterial agents."} +{"text": "Myasthenia gravis (MG) is an autoimmune disorder affecting neuromuscular junctions. Cytokines play important roles in facilitating the immune response and augmenting the pathogenic antibody production. The current study aims to sensitively characterize the serum levels of cytokines with very low concentration in generalized MG (gMG).Using ultrasensitive single-molecule arrays (SIMOA), we measured serum IL-2, IL-4, IL-5 and IL-12p70 in 228 participants including 152 immunotherapy-na\u00efve anti-acetylcholine receptor (AChR) subtype gMG from Huashan MG registry and 76 age-matched healthy controls. Subgroup analysis was then performed by stratifying patients according to the onset ages, MGFA classification, disease duration at baseline.P\u2009<\u20090.0001; 0.029\u00a0pg/mL versus 0.018\u00a0pg/mL, P\u2009=\u20090.0259; 0.215\u00a0pg/mL versus 0.143\u00a0pg/mL, P\u2009=\u20090.0007; 0.132\u00a0pg/mL versus 0.118\u00a0pg/mL, P\u2009=\u20090.0401). Subgroup analysis revealed that IL-2 levels were slightly elevated in gMG with MGFA II compared to MGFA III/IV , as well as elevated levels of IL-2 and IL-5 in late-onset gMG compared with the early-onset gMG. gMG patients with a long duration had a significant increased serum IL-12p70 than those with a short duration .Serum IL-2, IL-4, IL-5 and IL-12p70 levels were significantly elevated in gMG compared to controls (0.179\u00a0pg/mL versus 0.011\u00a0pg/mL, Serum IL-2, IL-4, IL-5 and IL-12p70 levels were increased in AChR subtype gMG using ultrasensitive measurement. Serum cytokines with very low concentrations may provide as potential biomarkers in stratifying gMG patients in future prospective cohort studies. Myasthenia gravis (MG) is characterized by fluctuating muscle weakness caused by autoantibodies against the acetylcholine receptor (AChR) and the muscle-specific tyrosine kinase (MuSK) , 2. RecePrevious studies on MG-relevant inflammatory cytokines mainly focused on Interleukin (IL)-17 (Th17 related), IL-21(Tfh related) and IL-6 \u201312. In cUltra-sensitive single-molecule arrays (SIMOA) provides an alternative and more sensitive method for detecting trace cytokines. , 17. HerA total of 228 participants were finally enrolled. Of these, 152 gMG patients were immunotherapy na\u00efve with positive anti-AChR antibodies and 76 age-matched participants were healthy controls . The median anti-AChR antibodies titer for MG is 5.86 nmol/L and thymoma concurrence is 9.9%. We further divided 152 AChR subtype gMG patients into subgroups: (1) Clinical severity according to the Myasthenia Gravis Foundation of America (MGFA): mild group with MGFA II (n\u2009=\u2009100) and moderate to severe group with MGFA III/IV (n\u2009=\u200952); (2) Onset ages: early-onset MG and late-onset MG ; (3) Disease duration: short disease duration group (n\u2009=\u200976) and long disease duration group (n\u2009=\u200976). Detailed information regarding each subgroup are listed in Table The levels for serum IL-2, IL-4 and IL-5 was higher in immunotherapy-na\u00efve gMG in comparison to HCs (measurable in 98.7% (150/152) versus 82.9% (63/76) for IL-2; 99.3% (151/152) versus 78.9% (60/76) for IL-4; 99.3% (151/152) versus 85.5% (65/76) for IL-5, respectively. For IL-12p70, the levels were equally matched in gMG and HCs (measurable in 83.6% (127/152) versus 84.2% (64/76)).P\u2009<\u20090.0001; 0.029 [0.016\u20130.045] pg/mL versus 0.018 [0.011\u20130.044] pg/mL, P\u2009=\u20090.0259; 0.215 [0.129\u20130.360] pg/mL versus 0.143 [0.077\u20130.243] pg/mL, P\u2009=\u20090.0007; 0.132 [0.092\u20130.202] pg/mL versus 0.118 [0.073\u20130.167] pg/mL, P\u2009=\u20090.0401) . In contrast, there were no differences in serum IL-4 levels , IL-5 levels , IL-12p70 levels between these two subgroups . In parallel, serum IL-5 was also elevated in patients with late-onset gMG . In contrast, there were no difference in serum IL-4 nor IL-12p70 levels between these two gMG groups with different onset age , while no significant differences in IL-2 , IL-4 and IL-5 and a negative correlation with disease course , baseline MG-ADL , QMG and MG-QoL15 . In parallel, serum IL-5 had a positive correlation with age and a negative correlation with QMG . Serum IL-4 was negatively correlated with disease course , while IL-12p70 was positively correlated with disease course . Multivariate analyses indicated that IL-4 levels had positive impact on QMG scores and MMT scores , while cytokines IL-2, IL-5 and IL-12p70 showed no statistically significant difference score, MGFA-quantitative MG test (MGFA-QMG), MG quality of life 15-item (QoL-15) questionnaire, and MG manual muscle test (MMT). Serum IL-2 had a positive correlation with age . The other cytokines showed no statistically significant difference.Moreover, the correlations between baseline cytokine levels and the short-term prognosis at 12\u00a0months after enrollment were assessed. Baseline IL-12p70 was positively correlated with MG-ADL score at 12\u00a0months-follow up , which have been demonstrated decreased and impaired in MG patients , 29. OngRecent clinical studies had emerged regarding the difference in presentations and outcomes between the EOMG and LOMG cohorts. The majority of LOMG had ocular phenotype. The presence of neither anti-titin nor anti-MuSK antibodies points to an unfavorable outcome . Still tAlthough the concordant elevation in type 1 and type 2 cytokines were demonstrated in gMG, the correlations between baseline cytokines with the short-term clinical outcome revealed some difference. IL-12p70 promotes Th1 immunity thus imposes positive effect in longitudinal autoimmune response for MG. However, the correlations are relatively weak to make any conclusions.+ T lymphocytes and B cells are required to better delineate the role of cytokines in the immunological network. Third, given the current cost and the availability, SIMOA may not be adopted for routine diagnostics in a short time. Ultrasensitive measurement of serum cytokines with very low concentrations in a large longitudinal prospective MG cohort is anticipated in future investigations to monitor the outcome and therapeutic response.Several limitations in this study are needed to be addressed. First, the normal datasets for all age groups are not available for these cytokines measured by ultrasensitive analysis. Second, the concurrent measurement of peripheral CD4We confirmed the high levels of serum IL-2, IL-4, IL-5 and IL-12p70 in a cohort of AChR subtype gMG patients. In particular, further analysis revealed significant difference in serum levels of these cytokines in gMG subgroups divided by clinical severity, onset ages and the prior disease duration. These inflammatory serum cytokines may provide as disease biomarkers in stratifying gMG patients in future prospective cohort studies.This study was conducted in accordance with the ethical standards established in the 1964 Declaration of Helsinki and was approved by the Medical Ethics Committee of Huashan Hospital affiliated to Fudan University . Written informed consent was obtained from each participant.There are 1662 MG patients registered in National center for neurological disorders, huashan hospital, Shanghai from August 8, 2012, through May 31, 2021. MG mimicking diseases including Lambert-Eaton myasthenic syndrome, peripheral neuropathy, myopathies, and motor neuron diseases were excluded before the recruiting. The patients who have already enrolled in previous study for 18 cytokine measurement have been excluded in current study and group comparisons were analyzed using Mann Whitney test as the data were previously tested for not following the normal distribution. Categorical variables were presented as No. (%) and analyzed by Chi-square test. Correlations between serum cytokines and clinical variables of MG cohort were analyzed using Spearman\u2019s method. Multiple linear-regression analyses were then further conducted. We considered a two-tailed adjusted"} +{"text": "Itraconazole is first-line treatment for mild-moderate blastomycosis and consolidation of moderate-severe disease. Itraconazole is metabolized to 3 metabolites, including an active metabolite hydroxy-itraconazole. The sum of itraconazole and hydroxy-itraconazole levels > 1.0 mcg/mL is guideline recommended for treatment of invasive fungal infections; conversely, some experts suggest targeting a parent compound level alone > 1.0 mcg/mL. This study aims to compare clinical outcomes and adverse drug reactions (ADRs) of combined itraconazole and hydroxy-itraconazole levels > 1.0 mcg/mL versus itraconazole parent compound alone > 1.0 mcg/mL in patients with blastomycosis.Blastomyces infection who received itraconazole with at least one documented serum itraconazole level. The primary outcome was rate of partial or complete treatment response in patients with a combined itraconazole and hydroxy-itraconazole level > 1.0 mcg/mL versus itraconazole parent compound > 1.0 mcg/mL for > 75% of measured levels. ADRs attributable to itraconazole were compared between the groups. Treatment response rates and ADRs were compared between groups using two proportion z-tests.This study is a single-center, retrospective chart review of patients \u2265 18 years with probable or proven Total of 80 patients were included: 36 = combined itraconazole and hydroxy-itraconazole > 1.0, 32 = itraconazole parent alone > 1.0, 12 = 75% of all levels < 1.0. No statistically significant difference was observed between groups for blastomycosis rate of partial or complete treatment response . Significantly higher mortality was observed in patients failing to achieve itraconazole or itraconazole/hydroxy-itraconazole > 1.0 . There was no significant difference in total ADRs between the three groups (p=0.56).This limited evidence supports an itraconazole therapeutic target combining itraconazole and hydroxy-itraconazole > 1.0 for blastomycosis treatment.Paschalis Vergidis, MD, AbbVie: DSMB|Cidara: Grant/Research Support|Scynexis: Grant/Research Support Christina G. Rivera, PharmD, Gilead: Grant/Research Support|Gilead: Honoraria|Insmed: Honoraria."} +{"text": "These insect-resistant inbred lines can be used as parents in maize breeding programs to develop new varieties.Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple insect-resistance against insect pests such as Asian corn borer and corn leaf aphids. Although numerous genetic loci for multiple insect-resistant traits have been identified, little is known about genetic controls regarding DIMBOA content. In this study, the best linear unbiased prediction (BLUP) values of DIMBOA content in two ecological environments across 310 maize inbred lines were calculated; and their phenotypic data and BLUP values were used for marker-trait association analysis. We identified nine SSRs that were significantly associated with DIMBOA content, which explained 4.30\u201320.04% of the phenotypic variation. Combined with 47 original genetic loci from previous studies, we detected 19 hot loci and approximately 11 hot loci supported pleiotropy for their association with two or more insect-resistant traits. Within the 19 hot loci, we identified 49 candidate genes, including 12 controlling DIMBOA biosynthesis, 6 involved in sugar metabolism/homeostasis, 2 regulating peroxidases activity, 21 associated with growth and development [(auxin-upregulated RNAs (SAUR) family member and v-myb avian myeloblastosis viral oncogene homolog (MYB)], and 7 involved in several key enzyme activities . The synergy and antagonism interactions among these genes formed the complex defense mechanisms induced by multiple insect pests. Moreover, sufficient genetic variation was reported for DIMBOA performance and SSR markers in the 310 tested maize inbred lines, and 3 highly (DIMBOA content was 402.74\u2013528.88 \u03bcg g Zea mays), is an important agro-economical crop that is utilized globally as food, animal feed, and biofuel products with production of more than 1.14 billion tons in 2018 [Ostrinia furnacalis; Lepidoptera, Pyralidae) is one of the most destructive insect pests in maize. Newly hatched ACB larvae primarily feed on leaves during the whorl stage; subsequently, the 3rd or 4th instars bore into the stalk. This may cause yield losses of 10 to 30% in the outbreaks recorded in China [Rhopalosiphum maidis; Homoptera, Aphididae), especially in tropical and warmer temperature regions [Maize provides a fine-mapping method that enables researchers to identify functional variation in a broader germplasm background . Both QT\u22121 FW (ZY19-Jiu1101) with an overall mean of 94.21\u03bcg g\u22121 FW; similarly, the average DIMBOA content of these seedlings in the E2 environment varied from 8.84 (T58) to 493.40 \u03bcg g\u22121 FW (RX20-1006) with an overall mean of 93.26 \u03bcg g\u22121 FW , umc2314 and umc2031 exhibited the maximum number of alleles . It is wIn addition, the population structure of these inbred lines was analyzed by STRUCTURE software. When various groups ranging from 1 to 12 were compared, the \u0394K reached the maximum value when K = 5, thus the 310 maize inbred lines were divided into five optimal groups A. The in\u22121 FW; accounted for 0.97%) had three genotypes, which were 19LX-1230, RX20-1006, and ZY19-Jiu1101; they were defined as high insect-resistant germplasms. Type II had 15 inbred lines including F1227, M1005, F0501, LongF1008, 1201, M1009, PH1CRW, 1512, F3202, F1220, F3208, F2260, F1233, F2303, and F3210, and they were defined as moderate insect-resistant germplasms. Type III had 27 genotypes, including ShanM3304, M1001, MeizaS2\u20133, Jizaoyu, M0803, F0306, M10202, ly6305, F2211, M1202, F0311, M1409Ying, F1501, M0124, M0822, M0105, F2502, M0505, PHHJC, 8723-2, M0306, F2222, F2213, M0824, M0125, 747, and F3226, and they were defined as insect-resistant germplasms. Type IV included 52 moderate insect-susceptible germplasms. Type V included 213 insect-susceptible germplasms . Type I (DIMBOA content in E1/E2: 467.11\u2013528.88/402.74\u2013493.40 \u03bcg grmplasms C. Furthermplasms B. The dahttps://www.maizegdb.org/data_center/map (accessed on 18 September 2022)) (p < 0.01) SSR loci associated with DIMBOA content in both environments (E1 and E2) by GLM and MLM, respectively; these SSR loci were in Bin 1.04, Bin 1.11, Bin 2.01, Bin 4.00, Bin 4.01, Bin 6.02, Bin 8.04, and Bin 10.04. The phenotypic variation explained by these SSR loci ranged from 4.30% in the E1 environment to 20.04% in the E2 environment via GLM, and ranged from 4.74% in the E2 environment to 10.57% in the E1 environment via MLM (p < 0.01) associated with BLUP values by GLM and MLM, respectively, which explained 5.41% \u201319.42% by GLM, and explained 9.29% \u201313.70% by MLM of 186 SSRs on an IBM2 2008 Neighbors map frame (r 2022)) to buildr 2022)) . Then, t via MLM ; Table 1) by MLM ; Table 1Next, we attempted to obtain hot genetic loci for multiple insect-resistant traits of ACB and CLA to lay a foundation for fine mapping and candidate gene prediction, verification, and breeding application. First, we collected 47 original genetic loci for ACB-/CLA-resistant traits including DIMBOA content, tunnel length of corn borer (TL), aphid incidence rate (AIR), average aphid incidence grade (AIG), LFR, HO, tunnel length/number of holes of corn borer (TL/HO), and aphid resistance (AR) from previous studies , and comGRMZM2G085381 (bx1), GRMZM6G617209 (bx6), GRMZM2G441753 (bx7), GRMZM2G311036 (bx10), and GRMZM2G336824 (bx11) to examine their relative expression levels in maize seedlings of RX20-1006 (high insect-resistant line) and T58 (insect-susceptible line) in the E1 environment at the V6 stage using real-time PCR (RT-qPCR). The results showed that the relative expression levels of the five genes were significantly correlated with the DIMBOA content in the two maize genotypes , DIMBOA, and 6-methoxy-3h-1,3-benzoxazol-ne (MBOA) are multifunctional defense metabolites that can protect maize against insect pests feeding and pathogens ,32,33. Df 42\u201396% . Indeed,f 42\u201396% ,34,35, sf 42\u201396% also repf 42\u201396% further f 42\u201396% . Understanding the genetic basis of the multiple insect resistance of maize is critical to the control of combinatorial attacks of ACB and CLA in the field. In this study, we observed a key trait for multiple insect resistance, i.e., the DIMBOA content in two ecological environments and their BLUP values, to detect nine significant associated SSR markers using association mapping via GLM and MLM across 310 diverse maize inbred lines from Gansu Province, China; these nine SSR markers were located in Bin 1.04, Bin 1.11, Bin 2.01, Bin 4.00, Bin 4.01, Bin 6.02, Bin 8.04, and Bin 10.04, respectively ; Table 1r); r = 0.252) and TL/HO (r = 0.229) in 162 F3 maize population to ACB resistance [Interestingly, we identified 19 hot loci (Loci 1-Loci 19) involved in maize multiple insect resistance in the present study ; Table 3According to the physical interval of the above 19 hot loci controlling 8 insect-resistant traits and the GO annotations of corresponding genes in these hot intervals, a total of 49 candidate genes were identified ; they maGRMZM2G311036 (bx10), GRMZM2G336824 (bx11), and GRMZM2G023325 (bx12) were detected in Loci 1 (Bin 1.04), and they encoded DIMBOA-glucoside O-methyltransferase; GRMZM2G046163 was mapped in Loci 3 (Bin 1.11); GRMZM2G167549 , GRMZM2G172491 ), GRMZM2G063756 ), GRMZM6G617209 , GRMZM2G085054 -one 2-D-glucosyltransferase), GRMZM2G085381 , and GRMZM2G085661 were identified in Loci 8 (Bin 4.00\u20134.03); and GRMZM2G441753 -one (TRIBOA-Glc) O methyl transferase) was located in Loci 9 (Bin 4.04) converted free indole to 2,4-dihydroxy-1,4-benoxazin-3-one (DIBOA) [bx1 was a modified form of the tryptophan synthase alpha subunit, and it was expressed constitutively in young seedlings, while igl was induced in more advanced stages of plant development and contributed to the blend of odors that attracted beneficial parasitoids [bx8 and GRMZM2G161335 (bx9) were involved in the glucosylation of DIBOA [bx6 was responsible for the hydroxylation step that converted DIBOA-Glc to TRIBOA-Glc, and this conversion likely took place in the cytosol [bx7, making DIMBOA-Glc [bx10, bx11, and bx12 were likely candidates for catalyzing the conversion of DIMBOA-Glc to HDMBOA-Glc [The 12 candidate genes were identified within three hot loci; namely, in 4.04) . The lgls larvae ,39,40. T (DIBOA) . The bx1asitoids ,39,40. T cytosol ,43. MethMBOA-Glc . In addiGRMZM2G150256 (mir2) and GRMZM2G150276 (mir1) were mapped within Loci 14 and encoded a maize insect resistance-cysteine protease (key defensive protein) against chewing insect pests in maize , Loci 5 (Bin 2.03\u20132.04), Loci 12 (Bin 5.03), Loci 17 (Bin 8.06), and Loci 18 (Bin 9.01), respectively . SimilarLOX genes, i.e., GRMZM2G017616 (LOX9) within Loci 1 (Bin 1.01\u20131.02), GRMZM2G040095 (LOX6) within Loci 4 (Bin 2.00\u20132.01), and GRMZM2G102760 (LOX5) within Loci 12 (Bin 5.03) plays critical roles in plant defense against multiple insect pests and pathogens ,45,46; ain 5.03) . LOX6 wain maize .MYB transcription factor can interact with mRNA/proteins to form a fine regulatory network to activate the expression of downstream defense genes and induce insect-resistance defense response. Interestingly, the previous findings [MYB genes were validated within Loci 2 (Bin 1.04), Loci 5 (Bin 2.03\u20132.04), Loci 10 (Bin 4.05), Loci 13 (Bin 5.05\u20135.07), Loci 14 (Bin 6.02), Loci 15 (Bin 8.01\u20138.03), Loci 16 (Bin 8.04\u20138.05), and Loci 19 (Bin 10.04) in this study, respectively , GRMZM2G018716 (incw7), and GRMZM2G018692 (incw6) within Loci 4 (Bin 2.00\u20132.01), GRMZM2G139300 (incw1) within Loci 13 (Bin 5.05\u20135.07), and GRMZM2G123633 (incw3) within Loci 19 (Bin 10.04) were identified in this study within Loci 16 (Bin 8.04\u20138.05) catalyze the irreversible hydrolysis of sucrose into glucose and fructose and play important roles in sucrose partitioning, plant development, and defense responses to biotic stresses . The hydis study . Essmann04\u20138.05) . Thereby2O2 induces POD activity, which then oxidizes and polymerizes p-coumaryl/coniferyl-/sinapyl-alcohol into lignin monomers on the cell wall [ZmPrx35 as the prevailing POD was involved in defense against pathogens and insects. Similarly, we also identified Zm00001d024752 (POD21) and Zm00001d052335 (POD23) within Loci 19 (Bin 10.04) and Loci 11 (Bin 4.08), respectively responsible for ubiquitin-conjugating enzyme 4, RMZM2G130224 responsible for restriction endonuclease type II-like superfamily protein, and GRMZM2G504910 responsible for tetratricopeptide repeat protein 27 homolog, were identified within Loci 4 (Bin 2.00\u20132.01), Loci 6 (Bin 2.04), and Loci 7 (Bin 2.05) in the present study, respectively (GRMZM2G130225 (near rs658849) and GRMZM2G102471 (near rs624256) were also identified to be involved in TL of ACB using GWAS analysis [In addition, three other candidate genes, i.e., ectively . Interesanalysis . In summary, according to the above studies, a possible molecular network underlying maize multiple insect-resistance to ACB and CLA was constructed , which cWhen assessing the genetic diversity in maize genotypes, SSR remains the preferred choice due to their co-dominant and multi-allelic nature, abundance, and loci specificity . In the In this study, the collected 310 elite maize inbred lines from different ecological environments in Gansu Province, China . A totalv/v) was added to each tube. The tubes were rotated and placed in the dark for 12 h and then centrifuged at 12,000 rpm for 20 min at 4 \u00b0C. Supernatants (600 \u03bcL) were slowly passed the corresponding Millex\u00ae needle filter and transferred into auto-sample vials for analysis by HPLC. Standard DIMBOA (CAS No.: 15893-52-4) was purchased and was used to optimize the mass spectrometric parameters and fragment spectra.The DIMBOA content was determined using high-performance liquid chromatography . Namely, freeze-dried leaves (0.2 g per sample) were homogenized and weighted into screw-capped 10 mL polypropylene centrifuge tubes, and 5 mL of HPLC grade methanol-methanoic acid solution ) were used to perform SSR analysis. Fragments were separated using polyacrylamide gel electrophoresis. The polymorphism information content (PIC) value and Shannon-Wiener\u2019s index (I) value were determined as follows [http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html (accessed on 10 August 2022)) for the assessment of groups and genetic relationships among the 310 maize inbred lines. The project was run with the set parameters of the population admixture model, and the allele frequency correlated. The optimum group number was determined by \u0394K value [https://www.maizegdb.org/data_center/map (accessed on 18 September 2022)) using BioMercator v. 4.2 software (http://www.bioinformatics.org/mqtl/wiki/ (accessed on 18 September 2022)). The linkage disequilibrium (LD) values for r2 [https://tassel.bitbucket.io/ (accessed on 10 August 2022)), following a permutation test of 10,000. The K matrix and marker-DIMBOA content association mapping was completed in Tassel 3.0 software using the genotypic data of 186 polymorphic SSRs and phenotypic data on DIMBOA content for a set of 310 inbred lines. The association analysis was conducted by a GLM with Q matrix [2) of the marker at p < 0.01 level and with the lowest false discovery rate (FDR). Using MaizeGDB (http://www.maizegdb.org/ (accessed on 20 September 2022)) and nucleotide and primer blast tools, the physical locations of associated SSR markers for DIMBOA content were determined on chromosomes.Genomic DNA was extracted from the 6th leaf of 310 inbred lines using the cetyltrimethyl ammonium bromide (CTAB) method . Then, a follows :(1)PIC=1tructure was anal\u0394K value . A linkas for r2 and D\u2032 [s for r2 between ulation) and an Mulation) . The asshttp://www.maizegdb.org/ (accessed on 23 September 2022)), NCBI (http://www.ncbi.nlm.nih.gov (accessed on 23 September 2022)), and CNKI (http://www.cnki.net (accessed on 23 September 2022)), we collected information on corresponding QTLs and associated markers for multiple insect-resistant traits from our results and previous studies via QTL analysis, GWAS, and association mapping. The hot genetic loci were the overlapping regions combining multiple genetic loci responsible for multiple insect-resistant traits or single genetic loci that explained the large R2 (10%) in 10 Mb physical intervals. Further, the physical map of all hot genetic loci and candidate genes involving multiple insect-resistant traits in these hot genetic loci regions was developed by BioMercator v. 4.2 software (http://www.bioinformatics.org/mqtl/wiki/ (accessed on 28 September 2022)) [https://agbase.arizona.edu/ (accessed on 6 October2022)) [Using public databases, i.e., MaizeGDB (r 2022)) . The funer2022)) .http://www.premierbiosoft.com/ (accessed on 9 October 2022)) , and cDNA was made using a kit , according to the manufacturer\u2019s instructions. RT-PCR was conducted using TransStart Tip Green qPCR SuperMix . The primers for five candidate genes ,64 were r 2022)) . Relativnce gene .http://www.R-project.org/ (accessed on 16 December 2021)) to calculate the BLUP of DIMBOA content values [http://www.ibm.com/products/spss-statistics (accessed on 16 December 2021)). The significance of the total and residual variances of DIMBOA content in 310 inbred lines under both ecological environments was estimated by a GLM for univariate data and by one-way analysis of variance (ANOVA). The broad-sense heritability , and r was the number of replications (r = 5). The CVg [The average DIMBOA content in 310 inbred lines from five biological replicates in each ecological environment were analyzed, respectively. A mixed linear model was fitted using the lmer function in lme4 package of R (t values . These d follows ,66,67:HB The CVg of DIMBOIn summary, the DIMBOA confers significant resistance to ACB and CLA. In this study, SSR analysis revealed a wide genetic diversity in the 310 tested maize inbred lines from four type regions of China\u2019s Gansu Province, which is the largest maize seed production and breeding area in China. Population structure indicated that 294 inbred lines were successfully assigned to one or another group at a membership probability of \u2265 0.500. DIMBOA performance evaluation screened out 3 high and 15 moderate insect-resistant inbred lines, which can be used as parents in breeding programs to develop new maize varieties with multiple insect resistance. Using linkage mapping, we detected nine significant SSRs associated with DIMBOA content in both environments. We then combined the 47 original genetic loci for 8 multiple insect-resistant traits from previous studies to detect 19 hot loci. Among them, 11 hot loci were located in Bin 1.04, Bin 2.00\u20132.01, Bin 2.03\u20132.04, Bin 4.00\u20134.03, Bin 5.03, Bin 5.05\u20135.07, Bin 8.01\u20138.03, Bin 8.04\u20138.05, Bin 8.06, Bin 9.01, and Bin 10.04 regions, and they supported pleiotropy for their association with two or more insect-resistant traits. Further, the 49 candidate genes involved in DIMBOA biosynthesis, sugar metabolism/homeostasis, and other multiple insect-resistant defense mechanisms in maize were identified in all 19 hot loci, and their highly interconnected network may form complex maize, multiple insect, pest-induced defense mechanisms."} +{"text": "Correction: BMC Nephrol 23, 348 (2022)https://doi.org/10.1186/s12882-022-02986-2Following publication of the original article , the autThe original article has been corrected.Additional file 1 Table\u00a01. Summary of literature on renal biopsy after intravitreal injection of vascular endothelial growth factor inhibitors."} +{"text": "Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858\u2009bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.Phage SN1 infects S. natans ATCC 13338 as the host using the host . An earlthe host . Host rand OT684 .S. natans ATCC 13338 in nutrient broth and agitated at 30\u00b0C (P. aeruginosa PAO1 (HER1153) in TSB/TSA medium at 30\u00b0C using both plaque assays and lysis of liquid cultures. Species identification of the above two host strains was confirmed by 16S sequencing.Here, phage SN1 was amplified with its host at 30\u00b0C . Cell deS. natans as host) using the phenol-chloroform extraction method (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and blastp (https://blast.ncbi.nlm.nih.gov/Blast.cgi) (Phage genomic DNA was purified from lysate (n method . Libraryn method . Illuminn method . Trimmedn method . Two assn method in combiast.cgi) , 9 usingast.cgi) . BioinfoPseudomonas phages with 95 to 98% nucleotide identity (73 \u2013 96% query cover). Interestingly, phage SN1 has 96.76% nucleotide identity (91% query cover) with Pseudomonas phage M6 genome, which contains hypermodified thymines . Half oON165687. Raw sequence reads are available under SRA number SRR18758685. Phage SN1 is available at www.phage.ulaval.ca.Genome sequence is available under GenBank number"} +{"text": "Globularia L. have been used as healing agents for various ailments, with utilization of Globularia alypum L. being most frequently reported. The aim of this study was to evaluate the antidiabetic, antioxidant, anti-inflammatory, antibacterial and anticancer potential of G. alypum and three related species, G. punctata Lapeyr., G. cordifolia L. and G. meridionalis (Podp.) O.Schwarz, in relation to their phytochemical compositions. Globularin and verbascoside were identified using LC-PDA-ESI-MSn as the major metabolites of G. alypum with known biological activities. G. alypum demonstrated the greatest \u03b1-glucosidase inhibitory activity and DPPH radical scavenging activity (IC50 = 17.25 \u03bcg/mL), while its anti-inflammatory activity was not significantly different from those of related species. All investigated species showed considerable antibacterial activity against methicillin-resistant Staphylococcus aureus in the broth microdilution method (MIC = 1.42\u20133.79 mg/mL). G. punctata also showed antibacterial activities against Escherichia coli (MIC = 1.42 mg/mL), Bacillus subtilis (MIC = 1.89 mg/mL), B. cereus (MIC = 2.84 mg/mL) and Enterococcus faecalis (MBC = 5.68 mg/mL). G. punctata, G. cordifolia and G. meridionalis showed greater anticancer potential than G. alypum. Obtained results indicate investigated Globularia species could serve as sources of diverse bioactive molecules, with G. punctata having the greatest antibacterial potential.Species from the genus According to the World Health Organization (WHO) statistics for 2021, the leading causes of global premature mortality from non-communicable diseases include cancer, cardiovascular diseases, diabetes, and chronic respiratory diseases. In 2019, 33.2 million people died solely from these diseases, which is 28% more deaths caused by the same four diseases than in 2000. Taken individually, there has been a 25% increase in the total global mortality from cardiovascular diseases (17.9 million deaths), a 37% increase in cancer mortality (9.3 million deaths), and a 10% increase in chronic respiratory diseases mortality (4.1 million deaths), while diabetes mortality has grown by 72% \u2212 and 153 [M\u2212H\u2212anhydroglucose]\u2212. In MS2, compound 50 was characterized by product ions at m/z 161 (\u2212330 Da) and 175 (\u2212316 Da). In MS3 of the first product ion, further loss of 28 Da (\u2212CO) was observed. The first loss in MS2 was attributed to simultaneous loss of hydroxytyrosol glucoside and a methyl group and the second to hydroxytyrosol glucoside. Loss of a methyl group was previously observed for the reference standard of ferulic acid \u2212. The compound was tentatively identified as galypumoside C (6\u2032-O-menthiafoloylverbascoside), whose presence in leaves of G. alypum was already reported \u2212. The formed radical aglycone product ion was further subjected to loss of one methyl group (\u221215 Da) in MS3 and major loss of 84 Da in MS4, attributed to the cleavage of three CO \u2212, 209 [M\u2013H\u2013anhydroglucose\u2212benzoylglucose]\u2212, 227 [M\u2013H\u2013anhydroglucose\u2212benzoylanhydroglucose]\u2212 and 371 [M\u2013H\u2013anhydroglucose\u2212benzoic acid]\u2212, indicated a similar structure to previously identified C-4 carboxylated iridoids. Second- and third-order mass spectra of compound 25 were comparable to MS3 and MS4 of compound 21, while major loss of 30 Da (\u2212CH2O) from the MS3 product ion present at m/z 165 was observed in MS4 together with minor fragment ions present at m/z 121 (\u2212C2H4O), 137 (\u2212CO) and 147 (\u2212H2O). These compounds were tentatively identified as 6\u2032-O-benzoyldeacetylasperulosidic acid glucoside and 6\u2032-O-benzoyldeacetylasperulosidic acid, keeping in mind other observed asperuloside-type iridoids and benzoylation of glucose at C-6\u2032 position, which was recorded for dumuloside in G. dumulosa \u2013, 163 [p-coumaric acid\u2013H]\u2013, 293 [M\u2013H\u2013glucose\u2013CO2]\u2013 and 355 [M\u2013H\u2013anhydroglucose]\u2013. Further MS/MS fragmentation pattern obtained in MS3 and MS4 were in accordance with those of asperuloside and besperuloside, which have acetic/benzoic acid attached at C-10 position. This compound, with UV \u03bbmax present at 191, 232 and 315 nm, comparable to those previously observed for asperuloside (191 and 239 nm) and p-coumaric acid [O-(p-coumaroyl)-deacetylasperuloside.Compound G. alypum methanolic leaf extract indicated not only the previously described high globularin content [G. alypum were glycosides of 6-hydroxyluteolin, the same as for other investigated species, while vicenin-2 was observed only in G. alypum, as well as the lignan diglucoside liriodendrin. Leaf extract of G. punctata contained high relative amounts of iridoids asperuloside, besperuloside, globularin, deacetylasperuloside, asperulosidic acid, and scandoside, while verbascoside, its isomers and glycosylated derivatives were observed as the major phenylethanoids. Solely G. punctata was characterized by acylated derivatives of 6-hydroxyluteolin, as previously reported [G. cordifolia and G. meridionalis were characterized by iridoids asperuloside and monomelittoside and their often benzoylated derivatives, with globularifolin (10-O-benzoylmonomelittoside) as the major compound, as previously reported [O-glucoside and demethoxycentaureidin 6,4\u2032-dimethyl ether were recognized as characteristic flavonoids. Other major constituents observed in investigated Globularia species included mannitol, sucrose, quinic acid and fatty acid oxidation products that have already been reported [Obtained chromatogram of content , but als content , do not reported ,40,42. Greported ,26,43. Mreported .Globularia species obtained by Soxhlet extraction was performed using LC-PDA-ESI-MSn -sophoroside, trichosanthoside B, trichosanthoside A, arenarioside, and besperuloside, with the iridoid asperuloside as the major compound. Other more prominent peaks included deacetylasperuloside and 10-O-(p-coumaroyl)-deacetylasperuloside, present also in G. cordifolia and G. meridionalis, as well as gardoside, caffeoylglucoside isomer and globusintenoside isomer present in all four species. For G. cordifolia and G. meridionalis, the major compounds were mannitol, sucrose, asperuloside and several phenylethanoids, including verbascoside, methoxyverbascoside isomer, isoverbascoside, globusintenoside isomer and benzoylrossicaside A isomer, while their distinctive peaks could be attributed to monomelittoside, 6\u2032-O-benzoylmonomelittoside and globularifolin. The major identified flavonoid characteristic for these two species was demethoxycentaureidin 6,4\u2032-dimethyl ether. Besides 6-hydroxyluteolin 7-O-glucoside, apigenin was detected in Soxhlet extracts of all investigated species.Identification of major constituents of methanolic aerial parts extracts of investigated -ESI-MSn , Table 4-ESI-MSn or thoseG. alypum using two different mobile phases . Blue zone of besperuloside, present only in G. punctata, was not clearly visible due to its overlapping with the brown zone of globularin. Shared yellow zones may be attributed to phenylethanoids present in all investigated species with verbascoside as the major shared component, while additional yellow zones observed for G. alypum and G. punctata correspond to the presence of their major unique phenylethanoids that were detected using LC-MS and glutathione peroxidase (GPx)) and two non-enzymatic biomarkers of oxidative stress (free thiol groups (-SH) and reduced glutathione (GSH)) in human hepatocellular carcinoma Hep G2 cells exposed to hyperglycemic conditions. Cell viability was evaluated using lactate dehydrogenase (LDH) and 3--2,5-diphenyltetrazolium bromide (MTT) assay. Antioxidant potential of aerial parts extracts was evaluated based on spectrophotometric measurement of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity and by performing thin layer chromatography (TLC) bioautography using the same free radical as spray reagent.p < 0.05), with G. alypum extracts being most effective (30.0\u201345.7% inhibition) and reducing diabetic complications. This can partially be achieved by inhibiting the activity of \u03b1-glucosidase, the key enzyme responsible for hydrolytic cleavage of complex carbohydrates. Inhibition of \u03b1-glucosidase may retard the absorption of glucose and decrease postprandial blood glucose levels and, therefore, it is one of the key targets for treating type 2 diabetes mellitus (T2DM) . All fouibition) . This su50 = 0.52 mg/mL) and \u03b1-amylase (IC50 = 0.57 mg/mL) was reported for diethyl ether fraction of G. alypum aerial parts extract [G. alypum in the present and in related studies [Inhibition of \u03b1-glucosidase (r = \u22120.791), was previously reported for G. trichosantha and G. orientalis [Clerodendrum bungei Stud., the phenylethanoids verbascoside (IC50 = 0.5 mM), leucosceptoside A (IC50 = 0.7 mM) and isoverbascoside (IC50 = 0.1 mM), which were found in all investigated Globularia species, exhibited stronger anti-\u03b1-glucosidase activities than the positive control (acarbose) [50 = 0.15 mM) [Globularia species. Hereby, many acylated phenylethanoids were only found in G. alypum, including galypumoside B, calceolarioside A, and calceolarioside B, of which the latter was recently identified also as a pan inhibitor of SARS-CoV-2 proteins [G. alypum, such as verminoside (caffeic acid) and specioside (p-coumaric acid). However, greater inhibition was observed for leaf extracts of G. alypum and G. meridionalis . Inhibitientalis . In a stcarbose) . The obscoside IC = 0.5 mMproteins . Phenolidionalis , which cdionalis .-O-glucoside). In Origanum majorana L. leaves, 6-hydroxyapigenin (scutellarein) (IC50 = 12 \u03bcM) and 6-hydroxyluteolin (IC50 = 10 \u03bcM) were recognized as the most potent inhibitors of \u03b1-glucosidase, while weaker inhibitions were observed for 6-hydroxyluteolin 7-O-glucoside (IC50 = 300 \u03bcM) and flavones lacking the 6-hydroxyl substituent, apigenin and luteolin (IC50 > 500 \u03bcM) [G. alypum extract compared to those of extracts of related species may also be explained by presence of additional \u03b1-glucosidase inhibitors, such as vicenin-2 (IC50 = 270.53 \u03bcM) [The observed inhibitory effect of all four species may in part be connected to the presence of 6-hydroxyflavones . The rec0.53 \u03bcM) .G. alypum [G. alypum as an antidiabetic could include prevention of diabetic complications through direct or indirect antioxidant activity, including radical scavenging activity [G. alypum methanolic leaf extract reduced glycemia and glycosylated hemoglobin levels, and improved the redox status, especially in the liver [The liver plays a vital role in blood glucose level regulation both in physiological and pathological states. In DM, liver is among the primary organs susceptible to hyperglycemia-induced oxidative stress, which may result in irreversible oxidative modifications of its macromolecules that may lead to abnormal glycogen deposition, non-alcoholic fatty liver disease, fibrosis, cirrhosis, hepatocellular carcinoma, and other liver abnormalities . Besides. alypum ,11,56, w. alypum , additioactivity ,57, enhaactivity ,59. For Globularia leaf extracts on biomarkers of oxidative stress have been evaluated in Hep G2 cells cultured under hyperglycemic conditions (p < 0.05). Increased GSH content was observed for G. alypum (+18.6%), G. punctata (+47.4%), and G. cordifolia extracts (+68.1%) at 1.0 mg/mL concentration and G. cordifolia extract at 0.5 mg/mL (+11.7%) (p < 0.05). All tested samples significantly increased free thiol groups content (+14.0\u201373.7%) and cell viability in the LDH assay (+22.2\u201376.7%) (p < 0.05), while in the MTT assay, a 21.6\u201325.4% increase was observed only for G. punctata (both concentrations) and G. cordifolia (c = 1.0 mg/mL) (p < 0.05). Overall, G. cordifolia reduced the pro-oxidant effects of hyperglycemic conditions observed in Hep G2 cells in all performed assays. Its favorable effect on oxidative status has already been recorded in human keratinocytes [In the present study, effects of two different concentrations (0.5 and 1.0 mg/mL) of nditions . Treatmeinocytes .G. cordifolia was characterized by the highest condensed tannin content , and very good positive correlation between GPx activity and condensed tannin content . Condens < 0.05) . The majpunctata , Table 3. alypum , was aspflavones , many ofr = 0.88, p < 0.01) as well as total phenolic content than its phenylethanoids (IC50 =11.8\u201315.5 \u00b5M) and iridoids (IC50 = 28.2\u201376.0 \u00b5M), as well as than quercetin (IC50 = 7.8 \u00b5M) and butylated hydroxytoluene (IC50 = 30.0 \u00b5M) [Very good positive correlation was found between cell viability assessed by the LDH assay and flavonoid content ( < 0.05) . Accordiactivity ,35,64,65punctata . The latpunctata , contain30.0 \u00b5M) . In the G. alypum [Globularia [50 values ranged from 17.25 \u03bcg/mL to 24.19 \u03bcg/mL (G. punctata). The obtained results are in accordance with our previous study, in which relatively higher antioxidant activities of both G. alypum leaf and flower extracts and relatively lower antioxidant activity of G. punctata flower extract were observed [50 value for G. alypum is comparable to previous reports for the diethyl ether fraction of its aerial parts (IC50 = 20.54 \u03bcg/mL) [50 = 15.58\u201327.54 \u03bcg/mL [50 = 25.65 \u03bcg/mL) and stems (IC50 = 22.11 \u03bcg/mL) [50 = 23.50 \u03bcg/mL) [50 value established for G. meridionalis is in accordance with that previously reported for methanolic extract of its aerial parts obtained by maceration (IC50 = 21.00 \u03bcg/mL), from whose methanolic fraction verbascoside (acteoside), isoverbascoside (isoacteoside) and apigenin 7-O-glucoside were isolated [50 values for DPPH radical scavenging activity and the estimated total phenolic content of aerial parts extracts (50 = 22.9 \u00b5M) and calceolarioside B (desrhamnosyl isoacteoside) (IC50 = 26.2 \u00b5M) [G. alypum.Direct antioxidant activity of studied species was confirmed by the DPPH assay, which is the most frequently used assay for evaluation of antioxidant activity of . alypum ,67,68,69obularia ,30, to eobserved . Obtaine4 \u03bcg/mL) , methano54 \u03bcg/mL , IC50 = isolated . Excelle < 0.05) , which i26.2 \u00b5M) , found oGlobularia species\u2019 constituents [Globularia [G. alypum [50 = 58.1 \u00b5M) than ascorbic acid [Globularia species [G. punctata showed the lowest radical scavenging activity, the second method revealed at least three zones characteristic for this species showing prominent antiradical activity . Their Rf values matched those of three orange, fluorescent zones observed at 365 nm after NP/PEG treatment, presumably of flavone origin [G. punctata (Globularia elongata Hegetschw. (syn. G. punctata) [-O-sophoroside, 6-hydroxyluteolin 7-O-(6\u2032\u2032\u2032-O-caffeoyl)-sophoroside, and 6-hydroxyluteolin 7-O-(6\u2032\u2032\u2032-O-(p-coumaroyl))-sophoroside.To identify the constituents responsible for observed activity, TLC bioautography with DPPH used as spray reagent was performed as in earlier studies of antioxidant activity of different tituents ,65,67. Bobularia , as well. alypum ,67, a mo. alypum . Two dombic acid . The for species ,39,40,64e origin . Based opunctata and lite2, PGD2, PGF2\u03b1, and PGI2) and thromboxane A2 [2 (cyclooxygenase site), which is afterwards reduced to PGH2 (peroxidase site) [G. alypum, G. punctata, G. cordifolia and G. meridionalis methanolic extract of aerial parts obtained by Soxhlet extraction was evaluated spectrophotometrically using two methods, one based on inhibition of peroxidase activity of COX-1 using N,N,N\u2032,N\u2032-tetramethyl-p-phenylenediamine dihydrochloride (TMPD assay) and the other based on inhibition of its cyclooxygenase activity assessed by the prostaglandin E2 assay (PGE2 assay). All tested species inhibited COX-1 activity to 51.3% in the TMPD assay (IC50 = 2.90 \u03bcM for indomethacin), and from 25.7% to 40.6% in the PGE2 assay (IC50 = 1.03 \u03bcM for indomethacin). The results obtained for G. alypum are comparable to those reported for methanolic leaf (5.33%) and flower extract (61.05%) of the same species tested at 33 \u03bcg/mL concentration using the TMPD assay [Cyclooxygenase isoenzymes COX-1 and COX-2 are first in the cascade of enzymes responsible for metabolism of arachidonic acid to prostaglandins (PGEoxane A2 . Due to se site) . Althougse site) . Anti-inactivity . ExtractPD assay .50 > 1 mM), one of the major metabolites found in all investigated species, was lower than that against COX-2 (IC50 = 0.69 mM) [Anisomeles indica (L.) Kuntze, of which verbascoside, isoverbascoside, calceolarioside A and apigenin were also recorded in investigated Globularia extracts, the latter compound gave the lowest docking score with COX-1 (\u22126.558) and COX-2 receptors (\u22128.441) in molecular docking analysis, which indicated its strong binding to the enzymes\u2019 active sites [G. alypum, for which the tendency of greater COX-1 inhibition was observed. Anti-inflammatory potential of investigated species could also be connected to their possible diminishing effects on other pro-inflammatory mediators , and cytokines such as interleukin-1\u03b2 (IL-1\u03b2), interleukin-6 (IL-6) and tumor necrosis factor-\u03b1 (TNF-\u03b1) [No correlation between the obtained results and assessed total phenolic or flavonoid content was found . Inhibit0.69 mM) . Among tve sites . Based ove sites , apigeni (TNF-\u03b1) ,79,80,81G. alypum and G. punctata, was recently reported to protect against glucose-induced podocyte injury by ameliorating apoptosis and inflammation through reduction of TNF-\u03b1, IL-6 and IL-1\u03b2 at 1\u201310 \u03bcM concentrations, which would suggest its preventive potential against diabetic nephropathy [G. punctata, G. cordifolia and G. meridionalis, significantly decreased the production of NO, PGE2, TNF-\u03b1, and IL-6, and inhibited the expression of inducible NO synthase (iNOS), COX-2, TNF-\u03b1, and IL-6 mRNA in LPS-induced RAW 264.7 cells [-O-benzoyl-monomelittoside), the major metabolite of G. cordifolia and G. meridionalis, was reported to significantly suppress expression of nuclear factor-\u03baB (NF-\u03baB) in LPS-stimulated cells at 200 \u03bcM concentration [G. alypum. The same compound, together with other above-mentioned compounds , as well as other major compounds identified in this study , were also reported for G. trichosantha [Catalpol, the iridoid present together with its many esters and/or derivatives (including globularin) in hropathy . The samhropathy . Similarhropathy , as wellhropathy . Asperul.7 cells . On the ntration , a lignahosantha ,64,83, whosantha , which mStaphylococcus aureus, a Gram-positive bacterium, is the main causative pathogen in diabetic foot infections, with methicillin-resistant S. aureus (MRSA) being the major multidrug resistant bacterium. Other pathogens may include Gram-positive bacteria, such as Streptococcus spp. and Enterococcus faecalis, and Gram-negative bacteria, such as Pseudomonas aeruginosa, Escherichia coli, Proteus spp., Enterobacter spp., and Klebsiella spp. [G. alypum, G. punctata, G. cordifolia and G. meridionalis was evaluated by testing the effect of methanolic extracts of aerial parts obtained by Soxhlet extraction against four Gram-positive and three Gram-negative bacterial strains using two complementary methods; well diffusion and serial broth microdilution method. In the first method, all four species showed notable inhibitory activity against S. aureus, with the greatest zone of inhibition recorded for G. alypum (25.0 mm), as well as low inhibitory activity against B. cereus and 2.84 mg/mL . Low inhibitory activity of G. alypum against P. aeruginosa (MIC = 22.73 mg/mL) and moderate to good bactericidal/inhibitory activity of G. punctata against E. faecalis (MBC = 5.68 mg/mL) and E. coli (MIC = 1.42 mg/mL) were also confirmed. Comparable antibacterial activity of G. alypum methanolic extract against S. aureus (MIC = 2\u20134 mg/mL) was reported by previous studies [P. aeruginosa (MIC = 8 mg/mL) [The results of the serial broth microdilution method followed by sub-cultivation on agar plates mainly coincided with those of the first method . Assesse MBC = 5. mg/mL an studies , while g8 mg/mL) .G. punctata showed good antibacterial activity against B. cereus (MIC = 2.84 mg/mL) and B. subtilis (MIC = 1.89 mg/mL), while much lower inhibition against B. cereus was observed for related species (MIC = 11.36 mg/mL). The latter method possibly accounted for the antibacterial activity of less hydrophilic compounds of G. punctata, which might not have been observed earlier due to their lower solubility and consequential lower diffusion into the hydrophilic (agar) medium [r = \u22120.998, p < 0.01) was found between MIC values against B. cereus and flavonoid content , were equal to 8, 8 and 64\u2013400 \u03bcg/mL, respectively, while against S. aureus no inhibitory activity was observed [Opposite to the results of the diffusion method, in the second method, ) medium . Excelle content , indicatlucoside and five clinical isolates of MRSA, were also tested (p > 0.05). Keeping in mind that these are the most common causative pathogens found in diabetic foot infections [G. alypum in the treatment of diabetes-associated foot ulcers. The anti-staphylococcal activity could partly be attributed to verbascoside, for which the assessed inhibitory activity (MIC = 227.2 \u03bcg/mL) corresponded to values previously reported against five MRSA strains (MIC = 64\u2013256 \u03bcg/mL) [S. aureus of all investigated species may also indicate contribution of other common constituents, such as isoverbascoside, rossicaside A, forsythoside A and 6-hydroxyluteolin 7-O-glucoside. Verbascoside (MIC = 60 \u03bcg/mL) was observed to have greater anti-staphylococcal activity than isoverbascoside (MIC = 130 \u03bcg/mL), while both compounds possessed lower inhibitory activities against E. faecalis (MIC = 100\u2013150 \u03bcg/mL), E. coli (MIC = 100\u2013250 \u03bcg/mL) and P. aeruginosa (MIC = 250 \u03bcg/mL) [G. alypum, also possess antibacterial potential against Gram-positive and Gram-negative bacteria [G. alypum against P. aeruginosa. The antibacterial potential of G. punctata against E. coli and E. faecalis, as well as S. aureus, may be connected to its characteristic phenylethanoids and/or flavonoids. Excellent negative correlations were found between flavonoid content and MICs against MSSA MFBF 505 and MRSA MFBF 154 .Nine additional o tested . Observefections , the obs6 \u03bcg/mL) . Compara0 \u03bcg/mL) . Other pbacteria , which mGlobularia species was evaluated using the MTT assay based on their effects against MDA-MB-231 breast cancer cell line and A1235 glioblastoma cell line. Cytotoxic effect against MDA-MB-231 cell line was observed for extracts of G. punctata (34.48%), G. cordifolia (63.41%) and G. meridionalis (82.96%) (at the highest concentration used), while cytotoxic effect against A1235 cell line was observed for all investigated species (p < 0.05) and the lowest for G. alypum (IC50 = 231.43 \u03bcg/mL) . Greates3 \u03bcg/mL) .G. meridionalis, G. cordifolia and G. punctata may be connected to asperuloside and its derivatives (Oldenlandia diffusa (Willd.) Roxb. that contained asperuloside and deacetylasperulosidic acid also reduced MDA-MB-231 and MDA-MB-453 cell viability and suppressed their colony formation capacities [50 = 0.7 \u03bcg/mL), HL60 cells (IC50 = 11.0 \u03bcg/mL) and KB cells (IC50 = 104.2 \u03bcg/mL) was recorded for asperuloside [50 = 6.1 \u03bcg/mL) [50 = 10 \u03bcM) was reported [G. cordifolia and G. meridionalis. Very good negative correlations were established between observed cell viability and concentrations of flavonoids , iridoids , and total phenolics , while excellent correlation was found between MDA-MB-231 cell viability and concentration of condensed tannins (50 = 0.159\u20130.258 \u03bcM) [The observed cytotoxic effects against MDA-MB-231 cells that were shown by ivatives [102,103s IC50 = .2 \u03bcg/mL reported , could b< 0.001) . Cytotox.258 \u03bcM) and a ra.258 \u03bcM) , the majCallicarpa nudiflora Hook. and Arn. against HeLa cells, A549 lung adenocarcinoma cells and MCF-7 cells resulted in isolation of flavonoids, phenylethanoids and iridoids, which included those found in investigated species, 6-hydroxyluteolin 7-O-glucoside, verbascoside and catalpol [50 = 1530 \u03bcg/mL) was also reported for G. alypum [Moreover, investigation of cytotoxic activity of catalpol . Weak cy. alypum .r = \u22120.95, p < 0.001), flavonoids and condensed tannins , while very good negative correlation was observed between A1235 cell viability and iridoid concentrations . Common thanoids ,111. Thi87 cells .2EDTA), 5,5\u2032-dithiobis(2-nitrobenzoic acid) , Dulbecco\u2019s modified Eagle\u2019s medium (DMEM), Type I \u03b1-glucosidase (isolated from Saccharomyces cerevisiae), glutathione (GSH), hematin, 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES), p-nitrophenyl-\u03b1-d-glucopyranoside (PNG), quercetin, N,N,N\u2032,N\u2032-tetramethyl-p-phenylenediamine dihydrochloride (TMPD), trichloroacetic acid, 2,3,5-triphenyltetrazolium chloride (TTC), trypsin-EDTA and vanillin from Sigma-Aldrich, St. Louis, MO, USA; and sodium diethyldithiocarbamate trihydrate (DDC) from VWR International, Radnor, PA, USA.Adrenalin bitartrate and indomethacin were purchased from Acros Organics, Geel, Belgium; glacial acetic acid from Alkaloid, Skopje, North Macedonia; asperuloside and catalpol from Carl Roth, Karlsruhe, Germany; hydrochloric acid from Carlo Erba, Emmendingen, Germany; arachidonic acid from Cayman Chemical Company, Ann Arbor, MI, USA; (+)-catehin, 2,2-diphenyl-1-picrylhydrazyl (DPPH), diphenylboric acid-\u03b2-ethylamino ester and LC-MS grade formic acid from Fluka, Buchs, Schwitzerland; fetal bovine serum (FBS), minimum essential medium (MEM), penicillin-streptomycin, and trypan blue from Gibco, Gaithersburg, MD, USA; absolute ethanol from Gram-Mol, Zagreb, Croatia; verbascoside from HWI Analytik, R\u00fclzheim, Germany; ethyl acetate, Folin-Ciocalteu\u2019s reagent, D-(+)-glucose, polyethylene glycol 4000 (PEG 4000), potassium chloride, potassium phosphate monobasic, sodium carbonate decahydrate, sodium hydroxide, sodium phosphate dibasic heptahydrate, sulfuric acid and Tween from Kemika, Zagreb, Croatia; gentamicin sulfate and norfloxacin from Krka, Novo mesto, Slovenia; chloroform, copper(II) sulfate pentahydrate, gallic acid, LC-MS grade acetonitrile, methanol, M\u00fcller\u2013Hinton agar, M\u00fcller\u2013Hinton broth, sodium chloride and Tryptic soy agar (TSA) from Merck, Darmstadt, Germany; Tris-HCl buffer from Santa Cruz Biotechnology, Dallas, TX, USA; formic acid from Scharlau, Scharlab, Barcelona, Spain; acarbose, aluminum chloride hexahydrate, aucubin, 1-chloro-2,4-dinitrobenzene (CDNB), cyclooxygenase-1 (COX-1) from sheep, dimethyl sulfoxide (DMSO), 3--2,5-diphenyltetrazolium bromide (MTT), disodium ethylenediamine-tetraacetic acid , Grobnik field , Ba\u0161ke O\u0161tarije, Velebit and Alan, Velebit . Plant material was identified by Prof. Kroata Hazler Pilepi\u0107. Voucher specimens are deposited in the Herbarium of the Department of Pharmaceutical Botany of the Faculty of Pharmacy and Biochemistry, University of Zagreb. Collection data are provided in Aerial parts of investigated v/v) methanol and extracted three times with chloroform. After chloroform removal, the remaining solvents were again evaporated at 30 \u00b0C and freeze-dried. All samples were stored at \u221220 \u00b0C until further use.Ultrasound-assisted extraction of powdered leaves (0.5\u20131.25 g) was performed using methanol (1:10) for 2 \u00d7 30 min. Obtained liquid extracts were filtered and evaporated to dryness using a rotavapor at 50 \u00b0C. Soxhlet extraction of powdered aerial parts (145\u2013280 g) was performed using methanol (1:5) for 8 h. Obtained extracts were evaporated to dryness using a rotavapor at 30 \u00b0C, re-suspended in 50% , was used for the analysis of methanolic leaf and aerial parts extracts composition. Zorbax SB-C18 column was used as a stationary phase. Separation of constituents and data collection were carried out under the previously described conditions [m/z 50\u20132000. Electrospray ionization (ESI) was performed in negative ionization mode. MSn spectra (MS2\u2013MS4) were obtained by collision induced dissociation (CID) of the ion of the greatest intensity in the mass spectrum of lower order with helium as the collision gas and normalized collision energy set at 35%. Data acquisition and processing were performed using Thermo Xcalibur 2.2 . Compound identification was based on the comparison of chromatographic and spectral data to those of previously identified constituents found in methanolic extracts of aerial parts of the same Globularia species obtained by heating under reflux conditions [High-performance liquid chromatography-photodiode array detection-electrospray ionization-tandem mass spectrometry, HPLC-PDA-ESI-MSnditions . UV/Vis nditions .254 aluminum plates , 10 \u00d7 20 cm, thickness 0.20 mm, using chloroform-methanol-water = 61:32:7 (v/v/v), or ethyl acetate-methanol-water = 20:2:1 (v/v/v) as the mobile phase [w/v) ethanolic vanillin-5% (v/v) ethanolic sulfuric acid reagent (5\u201310 min at 100\u2013105 \u00b0C), to those of asperuloside, aucubin and catalpol reference standards (c = 0.5 mg/mL).Constituents of methanolic aerial parts extracts obtained by Soxhlet extraction (c = 50 mg/mL) were separated on thin-layer chromatography (TLC) silica gel 60 Fle phase . Sample v/v) DMSO were mixed with 50 \u00b5L Type I \u03b1-glucosidase from Saccharomyces cerevisiae and preincubated at 37 \u00b0C. After 10 min, 50 \u00b5L PNG was added. Absorbance was measured for 5 min at 405 nm against a blank in which PNG was replaced with phosphate buffer. Results are expressed as enzyme activity % in comparison to control (2% (v/v) DMSO), which was considered to give 100% enzyme activity. Acarbose was used as positive control.Inhibition of \u03b1-glucosidase activity was assessed using PNG as previously described . Methanov/v) FBS, 20 IU/mL penicillin and 20 \u00b5g/mL streptomycin at 37 \u00b0C and 5% CO2. After removal of culture medium, cells were washed with phosphate buffered saline (PBS), trypsinized using 0.25% trypsin-EDTA solution for 5 min at 37 \u00b0C, counted under a light microscope (Leitz Diavert) after 0.04% trypan blue staining using the B\u00fcrker\u2013T\u00fcrk counting chamber and seeded into six-well plates (1.67 \u00d7 106) with FBS-free medium or 96-well plates (2 \u00d7 105) (MTT assay). After 24 h incubation at 37 \u00b0C, cells were washed with PBS and incubated with methanolic leaf extract solutions (c = 0.5 and 1.0 mg/mL) in MEM with 20 mM glucose (hyperglycemic conditions) for 24 h at 37 \u00b0C. Normal control cells were kept in MEM with 5.56 mM glucose. Prior to cell treatment, samples were filtered using sterile Nalgene filter units of pore size 0.2 \u03bcm . After incubation and washing with PBS, the cells were lysed with 1% (v/v) Tween in PBS with the help of ultrasound (4 W) (Cole-Parmer 4710) for 15 s and centrifuged for 20 min at 14,000 rpm at 4 \u00b0C. The supernatant was stored at \u221280 \u00b0C until further use.Hep G2 cells obtained from European Collection of Authenticated Cell Cultures were cultured in MEM supplemented with 10% (\u22121M\u22121). Content of free thiol groups (-SH) was evaluated spectrophotometrically using Ellman\u2019s reagent [\u22121M\u22121). For evaluation of GSH content, as previously described [v/v) trichloroacetic acid was added (100 \u00b5L), and the mixture was centrifuged . To obtained supernatant (100 \u00b5L), PBS and DTNB (50 \u00b5L) dissolved in the same buffer were added. The production of yellow colored 5-thio-2-nitrobenzoic acid (TNB) was measured at 405 nm against reagent blank. Results were calculated using the molar extinction coefficient of the product . All results are expressed per mg protein. Protein concentrations were established fluorometrically using the Qubit Protein Assay Kit (Invitrogen).Glutathione peroxidase (GPx) activity was measured spectrophotometrically using the Glutathione Peroxidase Activity Colorimetric Assay Kit . Glutathione S-transferase (GST) activity was evaluated spectrophotometrically using CDNB as the substrate . The cel reagent . Reactioescribed , to depr\u22121M\u22121). Cell viability was also evaluated based on the assessment of their metabolic/mitochondrial function using the MTT assay as previously described [Viability of Hep G2 cells was evaluated spectrophotometrically using the cell lysate supernatant by measuring lactate dehydrogenase (LDH) activity as an indicator of cell membrane damage with comescribed . After 250).Antiradical activity was assessed using the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) according to the previously described procedure . Methano254 glass plates (Merck), 20 \u00d7 20 cm, thickness 0.25 mm, using ethyl acetate-formic acid-glacial acetic acid-water as the mobile phase [w/v) methanolic solution of DPPH [w/v) methanolic diphenylboric acid-\u03b2-ethylamino ester, and 5% (w/v) ethanolic polyethylene glycol 4000 (NP/PEG reagent) [Constituents of methanolic aerial parts extracts obtained by Soxhlet extraction (c = 20 mg/mL) were separated on TLC silica gel 60 Fle phase . Sample of DPPH . Constitreagent) , to thatv/v) Tween and 300 \u03bcM DDC (c = 200 U/mL) and then in 0.1 M Tris-HCl buffer, pH 8.0 (1:100) just before the performed assay, while hematin (c = 1 mM) was dissolved in 0.01 M NaOH and afterwards diluted in 0.1 M Tris-HCl buffer, pH 8.0 (1:10). Sample was preincubated with 0.1 M Tris-HCl buffer, pH 8.0 (20 \u03bcL), 72 mM adrenalin bitartrate (50 \u03bcL), 2 U/mL COX-1 (100 \u03bcL) and 100 \u03bcM hematin (10 \u03bcL) for 5 min at room temperature. The reaction was started by the addition of 100 \u03bcM arachidonic acid (10 \u03bcL). After 20 min incubation at 37 \u00b0C, the reaction was terminated by the addition of 10% (v/v) formic acid (10 \u03bcL). Concentration of produced PGE2 was evaluated using the Prostaglandin E2 EIA Kit-Monoclonal . After 18 h sample incubation with PGE2 tracer (PGE2-acethylcholinesterase conjugate) and PGE2 monoclonal antibody at 4 \u00b0C, wells were emptied and rinsed five times with wash buffer. After 90 min incubation with Ellman\u2019s reagent, absorbance was read at 405 nm using the iEMS Reader MF type 1401 and corrected for the absorbance at 620 nm. Blank absorbance (Ellman\u2019s reagent) and non-specific binding absorbance (absence of antibody) were subtracted from the readings. From absorbances obtained for samples and control (ethanol), PGE2 tracer binding % were calculated, which were inversely proportional to the PGE2 concentrations in the wells. Results are expressed as COX-1 inhibition %, calculated from established PGE2 concentrations. Indomethacin was used as positive control.Cyclooxygenase activity of COX-1 was evaluated spectrophotometrically according to previously described protocols ,119. COXPeroxidase activity of COX-1 was evaluated spectrophotometrically using the TMPD assay , with soBacillus cereus American Type Culture Collection 11778, B. subtilis ATCC 6633, Enterococcus faecalis ATCC 29212, Staphylococcus aureus ATCC 6538 and S. aureus ATCC 29213 among Gram-positive and Escherichia coli ATCC 10536, Klebsiella pneumoniae MFBF 10402 and Pseudomonas aeruginosa ATCC 27853 among Gram-negative bacterial species. Additionally, eight clinical isolates of S. aureus, including methicillin-resistant S. aureus and methicillin susceptible S. aureus were used. Bacterial strains were sourced from the Collection of Microorganisms, Department of Microbiology, Faculty of Pharmacy and Biochemistry, University of Zagreb. Inoculums were prepared from overnight cultures that were cultured on tryptic soy agar (TSA) at 37 \u00b0C, suspended in sterile physiological saline, with the optic density adjusted to 0.5 McFarland (1.5 \u00d7 108 colony-forming units (CFUs)/mL) using a densitometer . Right before cultivation in nutrient medium, 1 mL of each prepared suspension was dissolved with 9 mL physiological saline. Prior to cell treatment, sample stock solutions in distilled water (c = 50 mg/mL) were filtered through Chromafil cellulose acetate filters of pore size 0.22 \u03bcm .Antibacterial activity was evaluated using the following strains: d = 6 mm) and filled with 50 \u03bcL of methanolic aerial parts extract solution (c = 50 mg/mL) in distilled water. Plates were incubated at 37 \u00b0C for 18 h in the dark. Diameters of the zones of inhibition of bacterial growth (mm) were read from the diameters of transparent zones around the wells. Gentamicin and norfloxacin (c = 0.2 mg/mL) were used as positive controls.Well diffusion method was carried out according to the European Pharmacopoeia . Inoculuw/v) TTC (20 \u03bcL), which in the presence of metabolically active bacteria gave red coloration/precipitate [Broth microdilution method was conducted in sterile plastic microtiter plates with 96 wells , in accordance with the Clinical and Laboratory Standards Institute (CLSI) recommendations . Two-folcipitate . This wa2, as previously described [3). Cells were incubated with methanolic leaf extract solutions in DMEM for 24 h at 37 \u00b0C. Prior to cell treatment, samples were filtered through sterile filters of pore size 0.22 \u03bcm.Human MDA MB-231 breast cancer cells obtained from Dr. Sonja Levanat and human A1235 glioblastoma cells obtained from S.A. Aaronson were culescribed . After rCell viability was assessed using the MTT assay as previously described . Prior t\u03b1-glucosidase activity, COX-1 inhibitory activity (PGE2 assay) and MDA-MB-231 and A1235 cell viability were performed in quadruplicate, and viability of Hep G2 cells in hyperglycemic conditions (MTT assay) in octuplicate, and the results are expressed as mean values and standard deviations. Concentrations that were observed to reduce the DPPH radical absorbance by 50% (IC50) were estimated using linear regression and those that reduced COX-1 activity and cell viability by 50% (IC50) using logarithmic regression.Phytochemical content, assessment of oxidative stress biomarkers and viability of Hep G2 cells in hyperglycemic conditions (LDH assay), antibacterial activity and COX-1 inhibitory activity (TMPD assay) were evaluated in triplicate and the results are expressed as mean values and standard deviations or, exceptionally, mean values . Assessment of r) was used to establish the relationship between observed biological activities and phytochemical content. In all tests, significance level \u03b1 was set at 0.05. Analyses were performed using GraphPad Prism 6.01 .Statistically significant differences were evaluated by using one-way analysis of variance (ANOVA), followed by Tukey\u2019s post hoc test (comparison between different species) or Dunnett\u2019s post hoc test (comparison between samples and control/hyperglycemia). Pearson\u2019s correlation coefficient (G. alypum and three related species, G. punctata, G. cordifolia, and G. meridionalis, considering different methods of extract preparation and different plant parts used. The bioactive compounds contained in investigated extracts of G. alypum and their observed biological activities are in accordance with the results of previous biological activity studies, as well as the reported traditional uses of this well-investigated medicinal plant, including its antidiabetic use, while those of related species suggest they too may have therapeutic potential. Observed antioxidant, anti-inflammatory, and antimicrobial activities of aerial parts extracts of investigated Globularia species support their use in cosmetics, while cytotoxicity assay results indicate further studies should preferably be carried out on G. cordifolia, G. meridionalis and G. punctata. The latter species also showed greater antimicrobial potential in comparison to G. alypum, which may be associated with its characteristic phenylethanoids and flavonoids. The paper displays how a combination of phytochemical and biological activity data obtained for extracts of several different species of the same genus may improve the understanding of their potential health benefits and facilitate the identification of compounds that are of possible interest for future biological activity studies. Future studies could focus more on the biological activities of major metabolites found in these species and elucidation of their underlying molecular mechanisms.The present study provides a greater insight into the phytochemical composition of"} +{"text": "Proteus mirabilis to imipenem allows this pathogen evade surveillance for carbapenemases. Metallo-beta-lactamases of the VIM family are widespread among Enterobacterales in Europe. We identified an outbreak of P. mirabilis carrying 2 VIM enzymes among elderly patients from a medical center in Hungary.Nonsusceptibility of P. mirabilis isolates were received from Hungary during 2020 as part of the SENTRY Antimicrobial Surveillance Program. Isolates were susceptibility tested by the CLSI reference broth microdilution method. Carbapenem-nonsusceptible isolates were submitted to whole genome sequencing, screened for resistance mechanisms, and evaluated for core genome multi-locus sequence typing (cgMLST).A total of 16 P. mirabilis isolates from Hungary, 5 carbapenem-nonsusceptible, multidrug-resistant isolates (3 from urinary tract infections and 1 each from bloodstream infection and pneumonia) were identified from patients 66-92 years old. Four of these 5 isolates were listed as community acquired. All isolates were resistant to ceftriaxone , cefepime (16- > 32), imipenem ( > 8), gentamicin ( > 16), levofloxacin (16- > 32), nitrofurantoin ( > 64), trimethoprim/sulfamethoxazole ( > 4), and plazomicin ( > 128), but susceptible to meropenem (0.25-0.5) and ertapenem (0.03-0.25). Isolates carried blaVIM-4 and blaVIM-75 on a class 1 integron within IS26 and separated by aac(6\u2019)-IIc. IS26 was located on a compound plasmid carrying other resistance-encoding genes, including armA. The integron structure is identical to the blaVIM-4 and blaVIM-1-carrying integron described from a Vibrio cholerae isolated from a seagull in France in 2015 (KR262557). blaVIM-75 is a single amino acid variant (Q60R) of blaVIM-1. All isolates carried mutations in the QRDR . Based on cgMLST analysis, these 5 P. mirabilis isolates were highly similar, with only 7-19 SNPs detected.Among the 16 P. mirabilis isolates carrying blaVIM-4 and blaVIM-75 in a Hungarian medical center is a cause of concern. Surveillance should be performed to understand the spread of and treatment options for infections caused by carbapenem-nonsusceptible P. mirabilis.The outbreak of multidrug-resistant Lalitagauri M. Deshpande, PhD, Melinta: Grant/Research Support|Pfizer: Grant/Research Support Katalin Buri\u00e1n, MD, JMI Laboratories: Grant/Research Support Ilona D\u00f3czi Cs\u00e1nyi, MD, JMI Laboratories: Grant/Research Support Mariana Castanheira, PhD, AbbVie: Grant/Research Support|Cidara: Grant/Research Support|GSK: Grant/Research Support|Melinta: Grant/Research Support|Pfizer: Grant/Research Support|Shionogi: Grant/Research Support."} +{"text": "Correction: BMC Med 20, 398 (2022)https://doi.org/10.1186/s12916-022-02595-8The labels of the two groups \u2013 response vs. non-response \u2013 were mistakenly switched.The HR in panel A was incorrectly stated as 0.38 instead of 0.308.The original article containeThe figure has been updated in the original article to reflect these amendments."} +{"text": "Stenotrophomonas maltophilia is a multidrug-resistant nosocomial pathogen that can cause life-threatening infections among immunocompromised populations. This report presents the complete 74,962-bp genome of S. maltophilia podophage Paxi, an N4-like phage sharing 85.3% nucleotide similarity to S. maltophilia podophage Pokken. Stenotrophomonas maltophilia is an environmentally ubiquitous and commensal bacterium, and it has also emerged as a nosocomial pathogen capable of causing life-threatening infections, especially among immunocompromised individuals at 30\u00b0C, and phage propagation was performed using the soft agar overlay method (www.bioinformatics.babraham.ac.uk/projects/fastqc) and FASTX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/) to yield 84,373 trimmed reads, from which a contig was assembled with 80-fold coverage using SPAdes v3.5.0 (ATGGAGCCGGAGAGATCCTT-3\u2032 (forward) and 5\u2032-ACTTCATCAAGCGTGTCGGT-3\u2032 (reverse). The CPT Galaxy-Apollo phage annotation platform was utilized for genome annotation , using otation 68. Structtation 6912. Gene tation 69\u201318. The Stenotrophomonas phage Pokken (GenBank accession number NC_049463.1) (Enterobacteria phage N4 (NC_008720.1), sharing 43 similar proteins such as virion RNA polymerase (NCBI protein accession number YP_950528.1) and an SAR endolysin N-acetylmuramidase (YP_950539.1). Paxi was predicted by PhageTerm to contain 538-bp direct terminal repeats.Phage Paxi was determined to have a podovirus-like morphology by viewi49463.1) , and BLAMZ326856. The associated BioProject, SRA, and BioSample accession numbers are PRJNA222858, SRR14095256, and SAMN18509291, respectively.The genome sequence for Paxi was deposited in GenBank under accession number"} +{"text": "At all stages of f lowering, a decisive role is played by the family of MADS-domain transcription factors,the combinatorial action of which is described by the ABCDE-model of f lower development. The current volume ofdata suggests a high conservatism of ABCDE genes in angiosperms. The E-proteins SEPALLATA are the central hub ofthe MADS-complexes, which determine the identity of the f loral organs. The only representative of the SEPALLATA3clade in tomato Solanum lycopersicum L., SlMADS5, is involved in determining the identity of petals, stamens, andcarpels; however, data on the functions of the gene are limited. The study was focused on the SlMADS5 functionalcharacterization. Structural and phylogenetic analyses of SlMADS5 conf irmed its belonging to the SEP3 clade. Anin silico expression analysis revealed the absence of gene transcripts in roots, leaves, and shoot apical meristem,and their presence in f lowers, fruits, and seeds at different stages of development. Two-hybrid analysis showedthe ability of SlMADS5 to activate transcription of the target gene and interact with TAGL1. Transgenic plants Nicotianatabacum L. with constitutive overexpression of SlMADS5 cDNA f lowered 2.2 times later than the control; plantsformed thickened leaves, 2.5\u20133.0 times thicker stems, 1.5\u20132.7 times shortened internodes, and 1.9 times fewerf lowers and capsules than non-transgenic plants. The f lower structure did not differ from the control; however, thecorolla petals changed color from light pink to magenta. Analysis of the expression of SlMADS5 and the tobaccogenes NtLFY, NtAP1, NtWUS, NtAG, NtPLE, NtSEP1, NtSEP2, and NtSEP3 in leaves and apexes of transgenic and controlplants showed that SlMADS5 mRNA is present only in tissues of transgenic lines. The other genes analyzed werehighly expressed in the reproductive meristem of control plants. Gene transcripts were absent or were imperceptiblypresent in the leaves and vegetative apex of the control, as well as in the leaves and apexes of transgenic lines.The results obtained indicate the possible involvement of SlMADS5 in the regulation of f lower meristem developmentand the pathway of anthocyanin biosynthesis in petals. Throughout the plant\u2019s life cycle, its root and shoot apicalmeristems maintain a pool of pluripotent stem cells, whichgive rise to new organs: roots and leaves respectively, duringvegetative development and flowers during reproductionstage. At the reproductive stage, the shoot apical meristemof the angiosperms turns into the inflorescence meristem,which forms determined flower meristems . In all aspects of flowering, the MADS-domain familyof transcription factors (TFs) plays a key role according to thewell-known ABCDE flower development model .The ABCDE model is based on genetic and molecularstudies, primarily of model species Arabidopsis thaliana (L.)Heynh., Antirrhinum majus L., and Petunia\u00d7hybrida hort.ex E. Vilm. . Accordingto the model, the identity of flower organs is determinedby five classes of genetic activities: A and E \u2013 sepals; A, Band E \u2013 petals; B, C and E \u2013 stamens; C and E \u2013 carpels; C, Eand D \u2013 ovules. At the molecular level, the ABCDE-model isexplained by the so-called \u201cquartet\u201d model, according to whichMADS-TFs of ABCDE classes in various combinations formtetramers: for example, C/C/E/E \u2013 to determine carpel identity,or A/B1/B2/E \u2013 to specify petal identity . These tetramers activate or suppresstranscription of target genes . The current data suggest a high structural andfunctional conservatism of A, B, C, D, and E genes in floweringplants .The genes of the E-class, A. thaliana SEPALLATA , which are involved in determiningthe identity of all floral organs, deserve special attention . The knockout of onlyone of the SEP genes does not have a significant effect on theA. thaliana flower, while the sep1 sep2 sep3 triple mutationtransforms all the flower organs into sepals; a new flowerwith the same development pattern is formed instead of thepistil . The quadruple sep1 sep2 sep3 sep4mutation leads to the replacement of all flower organs withleaf-like organs .SEP proteins are the central hub in the formation of MADSTFquartets . Among SEPs, SEP3 isthe most functionally pleiotropic and interacts with almostall MADS-TFs responsible for the identity of flower organs. SEP3 gene simultaneous ectopic expression expressionwith the A-, B-, or C-class genes transforms leavesinto flower organs .During plant evolution, SEP genes are believed to havearisen later than other flower-related MADS-box genes, butat the same time they became key players in the origin offlowering plants, as well as in the domestication and breedingof crops . Therefore,their study in cultivated plants can expand the understandingof the role of these genes in determining economicallyvaluable traits.The tomato Solanum lycopersicum L. is one of the mostimportant vegetables and, at the same time, a model forstudying the fleshy fruit development and ripening. Thetomato genome has been sequenced and annotated (https://www.solgenomics.net/), and contains several SEP genes:TAGL2 (Solyc05g015750.2.1), SlMADS6/TM29/LeSEP1(Solyc02g089200.2.1), RIPENING INHIBITOR ( MADSRIN)(Solyc05g012020.2.1), SlMADS98/SlCMB1 (Solyc04g005320.2.1), SlMADS1/ENHANCER-OF-JOINTLESS-2(Solyc03g114840.2.1), SlMBP21/JOINTLESS-2 (J2)(Solyc12g038510.1.1) and SlMADS5/TM5/TDR5/LeSEP3(Solyc05g015750.3.1) .In addition to determining the flower organ identity, SEPproteins, together with MADS-TFs of the FRUITFULL (FUL)and AGAMOUS (AG) subfamilies, are actively involvedin the regulation of fruit ripening. This is clearly demonstratedin tomato, the fruit ripening of which is controlled byFUL1/FUL2, TOMATO AGAMOUS 1 (TAG1)/TOMATOAGAMOUS-LIKE 1 (TAGL1) and MADS-RIN . At thesame time, FUL2 and TAGL1 have been shown to play anadditional role in pistil initiation and early fruit development, which is likely tobe performed in combination with the tomato SEP3 homolog,SlMADS5 .SEP1-like gene TAGL2 was shown to be expressed atstages I (anthesis) and II of the tomato fruit development. Suppression of SEP1-like TM29 causesthe development of parthenocarpic fruits and the flower reversion. Tomato SEP4-likeSlCMB1 regulates ethylene biosynthesis and the accumulationof carotenoids during fruit ripening; suppression of SlCMB1leads to a change in the inflorescence architecture and anincrease in the sepal size . SEP4-likeSlMADS1 acts as a negative regulator of fruit ripening . SEP4-like SlMBP21 specifies the sepal size mediated by ethylene and auxin signaling, as well as the abscissionzone formation .SEP4-like MADS-RIN is the main regulator of fruit ripening:gene knockout leads to the formation of an unripe fruit, includingthe absence of carotenoid accumulation .The only representative of the tomato clade SEP3, TFSlMADS5, is involved in determining the identity of theorgans of the three inner flower whorls ,interacting with MADS-TFs of the SEP and AG subfamilies. Despite the SEP3 significance, thisgene variability has been characterized in cultivated and wildtomato species, and the SlMADS5 expression was observedin some organs and tissues .The aim of the present study was to characterize the functionof S. lycopersicum SlMADS5. SlMADS5 structural, phylogeneticand expression analysis confirmed its belonging to theSEP3-clade. Analysis in the yeast two-hybrid GAL4-systemshowed the SlMADS5 TF activator properties and itsinteraction with C-class MADS-TF. Transgenic Nicotianatabacum L. plants with SlMADS5 constitutive overexpressionexhibited a pronounced phenotype of reproductive developmentsuppression.Tomato S. lycopersicum cv. Silvestre recordo and tobaccoN. tabacum cv. Samsun plants were used in the study. Tomatoaccessions were grown under controlled greenhouse conditionsuntil flowering. Roots, leaves, flowers and ripe fruits werecollected separately. Tissues were grounded in liquid nitrogenand stored at \u201370 \u00b0C. Tobacco accessions were grown in vitroon a sterile MS medium in a climatic chamber until the formationof 4\u20136 leaves.Total RNA was isolated from tomato and tobacco tissues using the RNeasy Plant Mini Kit, and used for cDNA synthesis . Genomic DNA wasisolated from leaf tissues by the standard potassium acetatemethod and used for PCR tests forthe presence of a transgene in the plant genome.Primers for gene amplification, sequencing, and expressionanalysis were generated based on the MADS-box transcriptsof S. lycopersicum cv. Heinz and tobacco N. tabacumgenes available in the NCBI (http://www.ncbi.nlm.nih.gov/); NtLEAFY; NtWUSCHEL; NtAG ;NtPLENA : NtSEP1; NtSEP3 ; NtSEP2 ) so that forwardand reverse primers are separated by at least one intron andmatch all possible transcripts for each of the analyzed genes(Table 1). The primer sequences were additionally verifiedusing Primer 3 and BLAST (https://www.ncbi.nlm.nih.gov/tools/primer-blast/). Primers for CDS in-frame cloning intoplasmid vectors (GAL4 system) contained EcoRI and SalI restriction sites at the 5\u2032 end.Full-length SlMADS5, TAG1, and FUL2 cDNAs wereamplified using the cDNA, isolated from S. lycopersicum cv.Silvestre recordo flowers; PCR conditions: initial denaturationat 95 \u00b0C for 5 min; 30 cycles of denaturation (94 \u00b0C for 30 s), annealing (55 \u00b0C \u2013 30 s) and synthesis (72 \u00b0C \u2013 1 min); finalsynthesis (72 \u00b0C \u2013 7 min). The PCR fragments of the expectedlength were purified using the MinElute Gel Extraction Kit, cloned into the pGEM\u00ae-T Easy plasmidvector at EcoRI and Sal I sitesand sequenced (Core Facility \u201cBioengineering\u201d). Further, theSlMADS5, FUL2, and TAGL1 CDSs were cloned into hybridvectors pAD-GAL4 and pBD-GAL4cam : each gene was ligated in frame with the activatordomain (pAD) and DNA-binding domain (pBD) of the yeastTF GAL4. Recombinant pJ69-4a strains carrying each pADgeneand pBD-gene construct separately, as well as in pairspAD-gene + pBD-gene, were obtained. For plant transformation,SlMADS5 cDNA was cloned in a sense orientation intoa binary vector based on pBin19, under the control of theenhanced cauliflower mosaic virus promoter 35S and nopalinesynthase (NOS) terminator. With this construct, a recombinantagrobacterial strain AGL\u00d8 was obtained.For sequence structural analysis, the NCBI-CDD (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi), MEGA 7.0 and Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/) were used. Sequence phylogeny was assessed inthe MEGA7, using Maximum Likelihood method based onthe JTT model.Gene expression analysis was performed in silico , as well as by quantitative (q) real-time (RT) PCRin two biological and three technical replicates. The kit \u201cReactionmixture for carrying out qRT-PCR in the presence ofSYBR Green I and ROX\u201d and the CFX96Real-Time PCR Detection System were applied. The qRT-PCR conditions were as follows:95 \u00b0C \u2013 5 min; 40 cycles .The reference gene actin-7 (XM_016658880.1) was used for normalizing the expressionof tobacco genes. Statistical processing of the results wascarried out usingthe GraphPad Prism v. 7.02 (https://www.graphpad.com).The analysis of SlMADS5 interactions with TAGL1 andFUL2 proteins was carried out in vivo in a two-hybrid GAL4-yeast system using the Saccharomyces cerevisiae Pj69-4astrain, according to the HybriZAP-2.1-Hybrid cDNA Two-Hybrid Synthesis Kit protocol (Stratagene).Leaf explants of tobacco (N. tabacum cv. Samsun) weretransformed using Agrobacterium tumefaciens strain AGL\u00d8.To select transgenic regenerants, an MS medium containingkanamycin for selection and carbenicillin(500 mg/L), which suppresses agrobacteria growth, was used.The rooted regenerants were adapted to the soil in greenhouseconditions and then tested for the presence of a transgene in thegenome by PCR with primers specific to the sequences of the5\u2032 end of the transgene and the NOS-terminator (see Table 1).To confirm the conservatism of the SlMADS5 function intomato (cv. Silvestre recordo), an analysis of its interactionswith MADS-TFs TAGL1 and FUL2, the interaction withwhich was and was not, respectively, shown earlier , was carried out.Structural analysis of the SlMADS5 protein was carried outin comparison with the known tomato, tobacco, and A. thalianaSEP homologs. The presence of the main domains characteristicof MIKCc type MADS-TFs was confirmed, namelythe highly conserved MEF2-like MADS-domain (1\u201376 aa),an I-region (77\u201392 aa), a conserved keratin (K)-like domain(93\u2013173 aa), and a variable C-region (174\u2013241 aa) .The performed phylogenetic analysis testified the belongingof SlMADS5 to the SEP3 clade .To characterize TF SlMADS5 functionally, we analyzedthe expression of the SlMADS5 gene in various tomato organsand the ability of SlMADS5 protein to activate gene transcriptionand interact with MADS proteins of the C and A classes.Also, transgenic N. tabacum model plants with constitutiveoverexpression of SlMADS5 cDNA were obtained.In silico analysis of the SlMADS5 expression pattern wascarried out in roots, leaves, vegetative shoot meristem, flowermeristem, flower (from bud to fully open and anthesis stage),fruits (4\u20138 days after anthesis), fruit skin and pulp (stages:Immature Green (IMG); Mature Green (MG); Breaker (BR),color change; Orange (OR); Red Ripe (RR)), and in seeds . SlMADS5 transcripts were notfound in roots, leaves, and the vegetative apical meristem. Atthe same time, SlMADS5 expression was shown in flowers(maximum \u2013 at the anthesis stage), fruits, fruit peel (maximumat MG and BR stages), fruit pulp , and seeds (maximum at IMG stage) .In vivo analysis in the yeast two-hybrid GAL4 systemshowed that TF SlMADS5 has the property of activating thetranscription of target genes, interacts with the C-class MADSprotein TAGL1, but does not interact with the A-class MADSprotein FUL2 (Table 2).The characterization of transgenic tobacco plants withSlMADS5 constitutive overexpression was performed. Independentregenerants T0 35S::SlMADS5 (18 plants) wereadapted to the greenhouse, tested by PCR for the presence ofa transgene expression cassette in the genome, and comparedwith the control (non-transgenic tobacco plants) during development.In comparison with the control, 35S::SlMADS5plants bloomed much later . Also, 35S::SlMADS5 phenotype was characterizedby a 2.5\u20133.0 times thicker stem, 2.0 times shortened internodes, thickened and darker leaves, and 2.5 times fewerflowers and capsules. The 35S::SlMADS5 flower structure didnot differ from the control.Seeds of two transgenic T0 lines (S5-16 and S5-17) witha pronounced phenotype were planted in a greenhouse.T1 plants, which gave a positive PCR signal for the presenceof a transgene in the genome, bloomed 1.3\u20131.5 times laterthan the control, had a 35S::SlMADS5 phenotype, and formedflowers with magenta-colored corolla petals, in contrast tolight pink petals in the control.Seeds of lines T1 S5-16-6, S5-16-7, S5-17-1 and S5-17-4were planted on MS medium (Km 50 mg/l); the 3:1 ratio of thenumber of Km-resistant to Km-sensitive seedlings indicated aheterozygous state of the transgene and one copy of it in thegenome of transgenic lines. In seedlings, internodes were nearabsent, and only T2 plants of the S5-16-7 line (14 accessions)formed a noticeable stem and were adapted to the greenhouse(the rest of the plants died after transfer to the soil). PlantsT2 S5-16-7 demonstrated the 35S::SlMADS5 phenotype: theybloomed 2.4 times later than the control; formed thickenedstems and leaves, shortened internodes, and 2.3 times lessseed capsules.In T1 lines S5-16-7 and S5-17-1, in comparison with thecontrol, we analyzed the SlMADS5 expression, as well as theexpression of tobacco genes associated with reproductivedevelopment: NtLFY, NtAP1 (plant transition to flowering), NtWUS , NtAG,NtPLE, NtSEP1, NtSEP2, NtSEP3 (key genes for the identityof the flower meristem and flower organs). For the analysis,we used tissues of leaves and apical meristems of transgenic and control plants.Expression of the SlMADS5 transgene was present onlyin the tissues of S5-16-7 and S5-17-1 plants. The expressionpattern of the remaining analyzed genes was similar: theirmRNA was absent or was minimal in the leaves of the controland transgenic lines, as well as in the S5-16-7 and S5-17-1apexes of undefined status. At the same time, these genes werehighly transcribed in the reproductive meristems of controlplants .In this study, a functional analysis of the SlMADS5 gene, theSEP3 homolog in tomato, was carried out. Structural analysis confirmed that SlMADS5 belongs to the SEP3clade, which may indicate the conservatism of its role in the reproductive development of tomato, namely, its participationin determining the identity of petals, stamens, carpels,and ovules.It is known that SlMADS5 is not expressed in tomato leavesand roots and is expressed in flowers and fruits . Also, SlMADS5 mRNA is present in the meristemdomains that correspond to the future three inner whorls ofthe tomato flower, as well as during organogenesis and inthe corresponding mature organs .A detailed in silico analysis of the SlMADS5 expression patterncarried out in this study revealed that SlMADS5 mRNAis absent not only in roots and leaves, but also in the shootapical meristems and flower meristems at early stages of development. Gene transcription is activated late inthe development of the flower meristem, and reaches a peakin an open flower and in the peel of an immature fruit . This corresponds not only to the well-known role ofSEP3 homologs in determining the differentiation of flowermeristem cells corresponding to the three inner whorls oforgans , but also suggests the active participation of SlMADS5 in the aspects of development andripening of tomato fruits and seeds.To characterize the SlMADS5 function, transgenic tobaccoplants with constitutive overexpression of SlMADS5 cDNAwere obtained. The phenotype of transgene overexpressiondoes not determine its function; however, it may indicate asimilarity with the already characterized homologs. Earlier,the effect of heterologous overexpression of SEP3 homologsof different plant species was studied mainly using transgenicA. thaliana plants, but there are works with the useof Nicotiana spp. plants. Tobacco, like tomato, belongs tothe Solanaceae family and has the same flower structure;therefore, in this study, a heterologous expression system intobacco was selected.Various effects of overexpression of SEP3 homologs havebeen described. Thus, SEP3 constitutive expression in A. thalianasignificantly accelerates flowering .In these plants, the APETALA3 (B-class) and AG (C-class)genes are transcribed ectopically .Overexpression of the P. \u00d7 hybrida SEP3-like gene FBP2leads to early flowering of the A. thaliana plants . Early flowering is caused by overexpression oftobacco SEP3-like gene NsMADS3 in N. sylvestris Speg. &Comes and chrysanthemum SEP3-like geneCDM44 in N. tabacum .At the same time, no influence of overexpression of SEP3-homologous genes on the flowering time was also observed.Thus, homologous overexpression of FBP2 in P.\u00d7hybrida has no effect on plant vegetation period .Heterologous overexpression of Platanus acerifolia SEP3-likegenes in A. thaliana causes early flowering only in the caseof the PlacSEP3.2 gene, while overexpression of the secondgene, PlacSEP3.1, causes early flowering only in transgenictobacco plants .In the case of SlMADS5 constitutive overexpression, asignificant delay in flowering was observed, most likely associatedwith the incorrect development of the shoot apicalmeristem . Different effects of heterologous ectopicexpression of SEP3 homologs in transgenic plants maybe associated with structural differences in encoded proteinsequences responsible for binding to promoters of target genesor to partner proteins.Normally, traces of the A. thaliana SEP3 transcripts arefound in the inflorescence meristem, and gene expression isnoticeably activated only in the flower meristem parts, fromwhich petals, stamens, and carpels are subsequently formed. Therefore, thepresence of the TF SlMADS5 in tissues, where there shouldbe no tobacco SEP3 homologs, can lead to nonspecific proteinproteinand DNA-binding interactions of SlMADS5, whichcan disrupt the pattern of meristem development.To clarify the status of transgenic meristems S5-16-7 andS5-17-1, visually ready for flowering, we analyzed the expressionof genes whose activity is associated with the identity ofthe reproductive inflorescence and flower meristems (NtLFYand NtAP1) . Considering the results obtained , only the inflorescence meristem of thecontrol plant has reproductive status. The presence of a lowlevel of LFY expression in the vegetative apex of the controland in the S5-16-7 apex suggests the initial stagesof the meristem transition to the reproductive state, since it hasbeen shown that in A. thaliana LFY begins to be expressed inthe flower meristem primordia at the periphery of the inflorescencemeristem .It is known that SEP3 is the central hub of the MADScomplexesin A. thaliana . TF SlMADS5also shows an exceptional ability to assemble tetrameric complexesof MADS TFs . The interactionof SlMADS5 with FUL2 and TAGL1 shown in this work (seeTable 2), as well as the role of FUL2 and TAGL1 in pistilinitiation and early fruit development , indicate the possible involvement ofSlMADS5 in determining the identity of the tomato pistil incomplex with FUL2 and TAGL1.One of the complexes, SEP3/SEP3/AG/AG, is requiredfor flower determination and completion of its development. This is due to a decrease in thenumber of stem cells because of the WUS gene suppressionwith the key participation of TF AG .Accordingly, in transgenic petunia plants with simultaneousoverexpression of SEP3-like FBP2 and D-class gene FBP11,where developmental arrest is observed at the cotyledonstage, transcription of AG-like FBP6 is activated and mRNAof WUS-like TERMINATOR is absent .This suggests the joint participation of SEP3, AG, and D-classgenes in the suppression of stem cells in the meristem.Taking into account the activation of AG expression inA. thaliana with SEP3 overexpression ,as well as the participation of SEP3 and AG in the suppressionof WUS transcription and the interaction of TF SlMADS5 with theAG homolog TAGL1 (see Table 2), it can be assumed thatthe ectopically synthesized TF SlMADS5 is able to activatetranscription of the tobacco AG-like genes NtAG and NtPLEin transgenic shoot meristem. Subsequent formation of complexesSlMADS5/SlMADS5/NtAG/NtAG or SlMADS5/SlMADS5/NtPLE/NtPLE can lead to inhibition of meristemdevelopment due to the tobacco WUS-like gene NtWUSsuppression, since WUS plays a key role in determining thestem cell identity, the population of which is not supportedin plants with loss of WUS function .To test this possibility, we analyzed the expression ofSlMADS5, NtWUS, AG-like genes NtAG and NtPLE, as wellas SEP-like genes NtSEP1, NtSEP2, and NtSEP3. However,the presence of SlMADS5 ectopic expression did not leadto the activation of AG-like genes, and the expression ofNtWUS was significantly higher in the tissues of transgeniclines in comparison with the control (excluding the controlinflorescence meristem) . The latter can be a probablereason for the formation of significantly thickened, incomparison with the control, stem and leaves of transgenicplants of all 11 lines with the 35S::SlMADS5 phenotype as a result of the increased number of stem cells andthe meristem overgrowth.It should also be noted that in transgenic plants, the anthocyanincolor of the flower corolla changed from pale pink(control) to magenta (35S::SlMADS5) . Previously,it was shown that the expression of the SEP-like geneMrMADS01 in Myrica rubra berries significantly increasesat the last stage of ripening, which allowed the authors tosuggest the involvement of this gene in the biosynthesis ofanthocyanins . Silencing the SEP-like genePaMADS7 in sweet cherry (Prunus avium) leads to a changein the content of anthocyanins in fruits . It canbe assumed that SlMADS5 is also involved in the regulationof anthocyanin biosynthesis in transgenic tobacco petals.Silencing of SlMADS5 gene leads to a change in the numberof flower whorls and the number of organs in whorls, as well asthe formation of green petals with signs of sepals, and sterileanthers and carpels with signs of sepals and petals, respectively, which may indicate the participation ofthe gene in determining the identity of tomato flower organs.Nevertheless, no complete homeotic transformation of certainflower organs was observed when SlMADS5 was suppressed.The data on the effect of SlMADS5 overexpression on thedevelopment of transgenic tobacco plants obtained in thisstudy also do not confirm the involvement of the gene indetermining the floral organ identity. Also, the data obtainedmay indicate that the ectopic expression of this single gene ina heterologous system (N. tabacum) is insufficient to activatetranscription of the MADS-box tobacco genes associated withflowering, but it is sufficient for a long delay in the reproductivedevelopment of the plant.The authors declare no conflict of interest.Alhindi T., Zhang Z., Ruelens P., Coenen H., Degroote H., Iraci N.,Geuten K. Protein interaction evolution from promiscuity to specificitywith reduced flexibility in an increasingly complex network.Sci. Rep. 2017;7:44948. DOI 10.1038/srep44948.Ampomah-Dwamena C., Morris B.A., Sutherland P., Veit B., Yao J.L.Down-regulation of TM29, a tomato SEPALLATA homolog, causesparthenocarpic fruit development and floral reversion. Plant Physiol.2002;130(2):605-617. DOI 10.1104/pp.005223.Angenent G.C., Franken J., Busscher M., van Dijken A., van Went J.L.,Dons H.J., van Tunen A.J. A novel class of MADS box genes isinvolved in ovule development in petunia. Plant Cell. 1995;7(10):1569-1582. DOI 10.1105/tpc.7.10.1569.Busi M.V., Bustamante C., D\u2019Angelo C., Hidalgo-Cuevas M., BoggioS.B., Valle E.M., Zabaleta E. MADS-box genes expressed duringtomato seed and fruit development. Plant Mol. Biol. 2003;52(4):801-815. DOI 10.1023/a:1025001402838.Castillejo C., Romera-Branchat M., Pelaz S. A new role of the ArabidopsisSEPALLATA3 gene revealed by its constitutive expression.Plant J. 2005;43(4):586-596. DOI 10.1111/j.1365-313X.2005.02476.x.Coen E.S., Meyerowitz E.M. The war of the whorls: genetic interactionscontrolling flower development. Nature. 1991;353(6339):31-37. DOI 10.1038/353031a0.Ditta G., Pinyopich A., Robles P., Pelaz S., Yanofsky M.F. The SEP4gene of Arabidopsis thaliana functions in floral organ and meristemidentity. Curr. Biol. 2004;14(21):1935-1940. DOI 10.1016/j.cub.2004.Dong T., Hu Z., Deng L., Wang Y., Zhu M., Zhang J., Chen G. A tomatoMADS-box transcription factor, SlMADS1, acts as a negative regulator of fruit ripening. Plant Physiol. 2013;163(2):1026-1036. DOI10.1104/pp.113.224436.Dyachenko E.A., Slugina \u041c.\u0410. Intraspecific variability of the Sus1 sucrosesynthase gene in Pisum sativum accessions. Vavilovskii ZhurnalGenetiki i Selektsii = Vavilov Journal of Genetics and Breeding.2018;22(1):108-114. DOI 10.18699/VJ18.338. (in Russian)Ferrario S., Immink R.G., Shchennikova A., Busscher-Lange J., AngenentG.C. The MADS box gene FBP2 is required for SEPALLATAfunction in petunia. Plant Cell. 2003;15(4):914-925. DOI 10.1105/tpc.010280.Ferrario S., Shchennikova A.V., Franken J., Immink R.G., AngenentG.C. Control of floral meristem determinacy in petunia byMADS-box transcription factors. Plant Physiol. 2006;140(3):890-898. DOI 10.1104/pp.105.072660.Goloveshkina E.N., Shulga O.A., Shchennikova A.V., KamionskayaA.M., Skryabin K.G. Functional characterization of chrysanthemumSEPALLATA3 homologs CDM77 and CDM44 in transgenictobacco plants. Dokl. Biol. Sci. 2012;443:87-90. DOI 10.1134/S0012496612020020.Honma T., Goto K. Complexes of MADS-box proteins are sufficient toconvert leaves into floral organs. Nature. 2001;409(6819):525-529.DOI 10.1038/35054083.Hugouvieux V., Silva C.S., Jourdain A., Stigliani A., Charras Q.,Conn V., Conn S.J., Carles C.C., Parcy F., Zubieta C. Tetramerizationof MADS family transcription factors SEPALLATA3 andAGAMOUS is required for floral meristem determinacy in Arabidopsis.Nucleic Acids Res. 2018;46(10):4966-4977. DOI 10.1093/nar/gky205.Immink R.G., Tonaco I.A., de Folter S., Shchennikova A., van Dijk A.D.,Busscher-Lange J., Borst J.W., Angenent G.C. SEPALLATA3:the \u2018glue\u2019 for MADS box transcription factor complex formation.Genome Biol. 2009;10(2):R24. DOI 10.1186/gb-2009-10-2-r24.Jang S., Hong M.Y., Chung Y.Y., An G. Ectopic expression of tobaccoMADS genes modulates flowering time and plant architecture. Mol.Cells. 1999;9(6):576-586.Jha P., Ochatt S.J., Kumar V. WUSCHEL: a master regulator in plantgrowth signaling. Plant Cell. Rep. 2020;39(4):431-444. DOI10.1007/s00299-020-02511-5.Karlova R., Chapman N., David K., Angenent G.C., Seymour G.B.,de Maagd R.A. Transcriptional control of fleshy fruit developmentand ripening. J. Exp. Bot. 2014;65(16):4527-4541. DOI 10.1093/jxb/eru316.Kumar S., Stecher G., Tamura K. MEGA7: Molecular evolutionary geneticsanalysis version 7.0. molecular biology and evolution. Mol.Biol. Evol. 2016;33:1870-1874. DOI 10.1093/molbev/msw054.Lenhard M., Bohnert A., J\u00fcrgens G., Laux T. Termination of stem cellmaintenance in Arabidopsis floral meristems by interactions betweenWUSCHEL and AGAMOUS. Cell. 2001;105(6):805-814. DOI10.1016/s0092-8674(01)00390-7.Leseberg C.H., Eissler C.L., Wang X., Johns M.A., Duvall M.R.,Mao L. Interaction study of MADS-domain proteins in tomato.J. Exp. Bot. 2008;59:2253-2265. DOI 10.1093/jxb/ern094.Li N., Huang B., Tang N., Jian W., Zou J., Chen J., Cao H., Habib S.,Dong X., Wei W., Gao Y., Li Z. The MADS-box gene SlMBP21regulates sepal size mediated by ethylene and auxin in tomato. PlantCell Physiol. 2017;58(12):2241-2256. DOI 10.1093/pcp/pcx158.Melzer R., Verelst W., Theissen G. The class E floral homeotic proteinSEPALLATA3 is sufficient to loop DNA in \u2018floral quartet\u2019-likecomplexes in vitro. Nucleic Acids Res. 2009;37(1):144-157. DOI10.1093/nar/gkn900.Pelaz S., Ditta G.S., Baumann E., Wisman E., Yanofsky M.F. B and Cfloral organ identity functions require SEPALLATA MADS-boxgenes. Nature. 2000;405(6783):200-203. DOI 10.1038/35012103.Pelaz S., Gustafson-Brown C., Kohlami S.E., Crosby W.L., YanofskyM.F. APETALA1 and SEPALLATA3 interact to promote flowerdevelopment. Plant J. 2001a;26:385-394. DOI 10.1046/j.1365-313x.2001.2641042.x.Pnueli L., Abu-Abeid M., Zamir D., Nacken W., Schwarz-Sommer Z.,Lifschitz E. The MADS box gene family in tomato: temporal expressionduring floral development, conserved secondary structures andhomology with homeotic genes from Antirrhinum and Arabidopsis.Plant J. 1991;1(2):255-266. DOI 10.1111/j.1365-313X.1991.00255.x.Pnueli L., Hareven D., Broday L., Hurwitz C., Lifschitz E. The TM5MADS box gene mediates organ differentiation in the three innerwhorls of tomato flowers. Plant Cell. 1994;6(2):175-186. DOI10.1105/tpc.6.2.175.Qi X., Liu C., Song L., Li M. PaMADS7, a MADS-box transcriptionfactor, regulates sweet cherry fruit ripening and softening. Plant Sci.2020;301:110634. DOI 10.1016/j.plantsci.2020.110634.Roldan M.V.G., P\u00e9rilleux C., Morin H., Huerga-Fernandez S., LatrasseD., Benhamed M., Bendahmane A. Natural and induced loss offunction mutations in SlMBP21 MADS-box gene led to jointless-2phenotype in tomato. Sci. Rep. 2017;7(1):4402. DOI 10.1038/s41598-017-04556-1.Schilling S., Pan S., Kennedy A., Melzer R. MADS-box genes and cropdomestication: the jack of all traits. J. Exp. Bot. 2018;69(7):1447-1469. DOI 10.1093/jxb/erx479.Schmidt G.W., Delaney S.K. Stable internal reference genes for normalizationof real-time RT-PCR in tobacco (Nicotiana tabacum)during development and abiotic stress. Mol. Genet. Genom. 2010;283(3):233-241. DOI 10.1007/s00438-010-0511-1.Shchennikova A.V., Shulga O.A., Immink R., Skryabin K.G., AngenentG.C. Identification and characterization of four chrysanthemumMADS-box genes, belonging to the APETALA1/FRUITFULL andSEPALLATA3 subfamilies. Plant Physiol. 2004;134(4):1632-1641.DOI 10.1104/pp.103.036665.Shima Y., Fujisawa M., Kitagawa M., Nakano T., Kimbara J., NakamuraN., Shiina T., Sugiyama J., Nakamura T., Kasumi T., Ito Y.Tomato FRUITFULL homologs regulate fruit ripening via ethylenebiosynthesis. Biosci. Biotechnol. Biochem. 2014;78(2):231-237.DOI 10.1080/09168451.2014.878221.Slugina M.A., Dyachenko E.A., Kochieva E.Z., Shchennikova A.V.Structural and functional diversification of SEPALLATA genes TM5and RIN in tomato species (section Lycopersicon). Dokl. Biochem.Biophys. 2020;492(1):152-158. DOI 10.1134/S1607672920030102.Smaczniak C., Immink R.G., Angenent G.C., Kaufmann K. Developmentaland evolutionary diversity of plant MADS-domain factors:insights from recent studies. Development. 2012;139(17):3081-3098. DOI 10.1242/dev.074674.Theissen G. Development of floral organ identity: stories from theMADS house. Curr. Opin. Plant Biol. 2001;4(1):75-85. DOI10.1016/s1369-5266(00)00139-4.Theissen G., Saedler H. Plant biology. Floral quartets. Nature. 2001;409(6819):469-471. DOI 10.1038/35054172.Urbanus S.L., de Folter S., Shchennikova A.V., Kaufmann K., ImminkR.G., Angenent G.C. In planta localisation patterns of MADSdomain proteins during floral development in Arabidopsis thaliana.BMC Plant Biol. 2009;9:5. DOI 10.1186/1471-2229-9-5.Vrebalov J., Pan I.L., Arroyo A.J., McQuinn R., Chung M., Poole M.,Rose J., Seymour G., Grandillo S., Giovannoni J., Irish V.F.Fleshy fruit expansion and ripening are regulated by the tomatoSHATTERPROOF gene TAGL1. Plant Cell. 2009;21(10):3041-3062. DOI 10.1105/tpc.109.066936.Vrebalov J., Ruezinsky D., Padmanabhan V., White R., Medrano D.,Drake R., Schuch W., Giovannoni J. A MADS-box gene necessaryfor fruit ripening at the tomato ripening-inhibitor (rin) locus.Science. 2002;296:343-346. DOI 10.1126/science.1068181.Wang R., Tavano E.C.D.R., Lammers M., Martinelli A.P., AngenentG.C., de Maagd R.A. Re-evaluation of transcription factorfunction in tomato fruit development and ripening with CRISPR/Cas9-mutagenesis. Sci. Rep. 2019;9(1):1696. DOI 10.1038/s41598-018-38170-6.Wang Y., Zhang J., Hu Z., Guo X., Tian S., Chen G. Genome-wideanalysis of the MADS-box transcription factor family in Solanumlycopersicum. Int. J. Mol. Sci. 2019;20(12):2961. DOI 10.3390/ijms20122961.Weigel D., Alvarez J., Smyth D.R., Yanofsky M.F., Meyerowitz E.M.LEAFY controls floral meristem identity in Arabidopsis. Cell. 1992;69(5):843-859. DOI 10.1016/0092-8674(92)90295-n.Zhang J., Hu Z., Wang Y., Yu X., Liao C., Zhu M., Chen G. Suppressionof a tomato SEPALLATA MADS-box gene, SlCMB1, generatesaltered inflorescence architecture and enlarged sepals. Plant Sci.2018a;272:75-87. DOI 10.1016/j.plantsci.2018.03.031.Zhang J., Hu Z., Yao Q., Guo X., Nguyen V., Li F., Chen G. A tomatoMADS-box protein, SlCMB1, regulates ethylene biosynthesis andcarotenoid accumulation during fruit ripening. Sci. Rep. 2018b;8(1):3413. DOI 10.1038/s41598-018-21672-8.Zhang S., Lu S., Yi S., Han H., Liu L., Zhang J., Bao M., Liu G.Functional conservation and divergence of five SEPALLATA-likegenes from a basal eudicot tree, Platanus acerifolia. Planta. 2017;245(2):439-457. DOI 10.1007/s00425-016-2617-0.Zhao H.B., Jia H.M., Wang Y., Wang G.Y., Zhou C.C., Jia H.J., Gao Z.S.Genome-wide identification and analysis of the MADS-box genefamily and its potential role in fruit development and ripening in redbayberry (Morella rubra). Gene. 2019;717:144045. DOI 10.1016/j.gene.2019.144045."} +{"text": "The diagnostic performance of 18F-DCFPyL-PET/CT in localizing primary PCa within the prostate gland was assessed, allowing for PSMA-guided targeted-prostate biopsy.In primary prostate cancer (PCa) patients, accurate staging and histologic grading are crucial to guide treatment decisions. 18F-DCFPyL-PET/CT prior to robot-assisted radical prostatectomy (RARP). Two experienced and blinded nuclear medicine physicians assessed tumour localisation within the prostate gland on PET/CT, using a 12-segment mapping model of the prostate. The same model was used by a uro-pathologist for the RARP specimens. Based on PET/CT imaging, a potential biopsy recommendation was given per patient, based on the size and PET-intensity of the suspected PCa localisations. The biopsy recommendation was correlated to final histopathology in the RARP specimen. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for clinically significant PCa were assessed.Thirty patients with intermediate-/high-risk primary PCa were prospectively enrolled between May 2018 and May 2019 and underwent 18F-DCFPyL-PET/CT were 61.4%, 88.3%, 68.1% and 84.8%, respectively.The segments recommended for potential targeted biopsy harboured csPCA in 28/30 patients (93%), and covered the highest Gleason score PCa segment in 26/30 patient (87%). Overall, 122 of 420 segments (29.0%) contained csPCa at final histopathological examination. Sensitivity, specificity, PPV and NPV for csPCa per segment using 18F-DCFPyL-PET/CT with the RARP specimens, an accurate per-patient detection (93%) and localisation of csPCa was found. Thus, 18F-DCFPyL-PET/CT potentially allows for accurate PSMA-targeted biopsy.When comparing the PCa-localisation on The online version of this article (10.1007/s00345-020-03490-8) contains supplementary material, which is available to authorized users. Prostate cancer (PCa) is the most common cancer in men in the Western world , 2. HistBesides conventional imaging modalities such as mpMRI, novel imaging techniques including prostate-specific membrane antigen-positron emission tomography/computed tomography (PSMA-PET/CT) have been introduced. PSMA is significantly overexpressed in malignant prostate cells, correlates with higher tumour grades and represents a marker of tumour aggressiveness , 10. PSM18F-DCFPyL (PSMA) PET/CT imaging for the primary detection of PCa. The primary aim was to assess the accuracy of 18F-DCFPyL-PET/CT to localise primary PCa within the prostate gland, by comparing imaging results from 18F-DCFPyL-PET/CT to final histopathology of the robot-assisted radical prostatectomy (RARP) specimen. The secondary objectives were to investigate the ability of 18F-DCFPyL-PET/CT to provide a recommendation for potential targeted biopsy and to assess the diagnostic accuracy of determining local tumour stage (pT).This is the first prospective study on the accuracy of This was a prospective, non-randomised study in patients with diagnosed primary PCa. Pre-operative imaging results were compared to histopathology following RARP. All subjects signed informed-consent for the collection of their clinical data. The study has been approved by the ethical review board of the Amsterdam University Medical Centre (AUMC) (review number 2017.543). Patients were enrolled consecutively between May 2018-May 2019 in Amsterdam UMC, location VUmc.Patients had histologically proven, intermediate or high-risk, PCa, for which they underwent RARP , 15. Of 18F-DCFPyL which was synthesised under Good Manufacturing Practices conditions, as described by Jansen et al. [18F-DCFPyL (IQR 299\u2013324\u00a0MBq), and a median of 5.4\u00a0weeks (IQR 3.0\u20137.2) prior to surgery. Image-acquisitions were performed using a Philips Ingenuity TF -PET/CT system. No diuretics were administered prior to the scan. The scan trajectory included mid-thighs to skull-base, with 4\u00a0min per bed position. All PET scans were combined with a diagnostic CT scan , without contrast-enhancement. Images were corrected for decay, scatter, random coincidences, and photon attenuation.Patients were staged with n et al. , 18. PETImages were reconstructed with a BLOB-based Ordered-Subsets Expectations Maximization algorithm ). The de18F-DCFPyL-PET/CT reading (>\u2009300 scans), in consensus. The readers used the 12-segment mapping model to demarcate the image-detected tumour extent (Appendix-1 in ESM) [max) of the suspected lesions. Finally, the readers indicated if radiological extra-capsular extension or invasion into the seminal vesicles (rT3b) was suspected.Scan interpretation was performed blinded for the pathology results and other imaging by two nuclear medicine physicians with ample experience in in ESM) . For all in ESM) guidelines . All spe18F-DCFPyL-PET/CT was matched to the histopathology results and the sensitivity, specificity, positive predicting value (PPV), and negative predicting value (NPV) were calculated on a segment basis. Correlation of 18F-DCFPyL-PET/CT with histopathology was considered if exactly the same segment was demarcated . Since there are no anatomical landmarks to delineate the segments, artificial segmentation can occur, causing a mismatch between the PET/CT- and histopathological findings while both correspond with the same lesion. Therefore, a second analysis of diagnostic accuracy was performed, in which PET correlation was also considered if there was a discrepancy of up to 1 region in the coronal or sagittal plane [18F-DCFPyL-PET/CT to differentiate locally advanced disease (>\u2009rT3a) from prostate-confined disease (rT2). Numerical variables were summarised with median values and interquartile ranges (IQR); categorical variables with proportions (%). To compare medians of non-parametric data, the Mann\u2013Whitney-Wilcoxon test and the Kruskal-Wallis test were used (significance set at p\u2009<\u20090.05). Statistical analysis was performed with IBM\u00ae SPSS\u00ae Statistics for Windows\u00ae, version 26.The localisation of the detected prostate tumour by reement) , 24. RecA total of 30 patients was included in this study, having a median initial PSA-level of 11.1\u00a0ng/ml (IQR 5.8\u201322.4). According to EAU guidelines, 10/30 (33.3%) patients had intermediate-risk PCa and 20/30 (66.6%) had high-risk PCa . Pre-ope18F-DCFPyL-PET/CT to detect csPCa per segment with total agreement was 61.4% (95%CI 52.2\u201370.0%), 88.3% (95%CI 83.9\u201391.6%), 68.1% (95%CI 58.5\u201376.6%), and 84.8% (95%CI 80.2\u201388.5%), respectively (Appendix-2 in ESM). For near-total agreement, the sensitivity, specificity, PPV and NPV of 18F-DCFPyL PET/CT to detect csPCa per segment was 84.4% (95%CI 76.5\u201390.1%), 97.0% (95%CI 94.1\u201398.5%), 92.0% (95%CI 84.9\u201396.0%), and 93.8% (95%CI 90.3\u201396.1%), respectively. The area under the curve (AUC) of 18F-DCFPyL-PET/CT was 0.78 (95%CI 0.73\u20130.84) for the total agreement scores, and 0.85 (95%CI 0.80\u20130.90) for the near-total agreement scores (Appendix-3 in ESM). True positive segments had a median SUVmax of 8.26 (IQR 5.25\u201311.40), which was significantly higher than the median SUVmax of false-positive segments of 4.06 (IQR 3.56\u20135.10) (p\u2009=\u20090.02). The median SUVmax of true positive segments did not correlate with ISUP grade groups (p\u2009=\u20090.95) (Appendix-4 in ESM).All patients showed PSMA expression in the prostate. In 30 evaluated patients, 420 segments could be used both for PET/CT and histopathological mapping evaluation. PCa was present in 129 of the 420 (30.7%) segments on histopathological examination, and csPCa was found in 122 of the 420 segments (29.0%) . The sensitivity, specificity, PPV and NPV of 18F-DCFPyL-PET/CT revealed csPCa in 28/30 (93.3%) patients. Moreover, it pinned the index PCa lesion in 26/30 (86.7%) patients. An example of potential 18F-DCFPyL-guided biopsy recommendation and concurrent histopathological examination of the RARP specimen is shown in Fig. max 8.62 (IQR 6.41\u201312.62). The recommendation for potential biopsy from the nuclear physicians that matched csPCA had a median SUVmax of 8.55 (IQR 6.34\u201313.79), and was significantly higher than the recommended potential biopsy segments that did not contain csPCa (median SUVmax of 3.10 (IQR 2.86\u20133.87) (p\u2009=\u20090.02).The primary potential biopsy recommendation by the nuclear medicine physician harboured csPCa in 24/30 (80.0%) patients and detected the index PCa lesion in 23/30 (76.6%) patients. When both the primary and secondary recommended segments would potentially be targeted, 18F-DCFPyL-PET/CT to detect locally advanced tumour growth (\u2265\u2009pT3a) was 35.7% (95%CI 14.0\u201364.3%), 93.8% (95%CI 67.7\u201399.7%), 83.3% (95%CI 36.5\u201399.1%), and 62.5% (95%CI 40.8\u201380.4%), respectively (Appendix-5 in ESM). For the detection of pT3a sub-stage, the sensitivity, specificity, PPV and NPV of 18F-DCFPyL-PET/CT were 20.0% (95%CI 3.5\u201355.8), 100% (95%CI 80.0\u2013100), 100.0% (95%CI 19.7\u2013100), and 71.4% (95%CI 51.1\u201386.0), respectively. For the detection of pT3b sub-stage, the sensitivity, specificity, PPV and NPV of 18F-DCFPyL-PET/CT were 75.0% (95%CI 21.9\u201398.7), 92.3% (95%CI 73.4\u201398.7), 60.0% (95%CI 17.0\u201392.7), and 96.0% (95%CI 77.7\u201399.8), respectively.Final histopathological analysis revealed pT3a in 10/30 (33.3%) patients, and pT3b in 4/30 (13.3%) patients. The sensitivity, specificity, PPV and NPV of 18F-DCFPyL-PET/CT imaging was used to locate primary PCa within the prostate gland, exploring the diagnostic potential of PSMA-based targeted biopsies. A total of 30 patients diagnosed with intermediate and high-risk PCa that underwent 18F-DCFPyL-PET/CT prior to RARP was analysed. When using a prostate-mapping model, the potential 18F-DCFPyL-PET/CT-based targeted biopsy recommendation detected csPCa in 28/30 (93.3%) patients. Moreover, it detected the index PCa lesion in 26/30 (86.7%) patients. Potentially, this makes PSMA-targeted biopsy a diagnostic tool that may adequately guide precision prostate biopsy. In biopsy-naive patients at increased risk of metastatic spread, and in whom staging imaging is mandatory (e.g. PSA\u2009\u2265\u200920), 18F-DCFPyL-PET/CT could potentially be used simultaneously to stage patients and to target PSMA-avid prostatic lesions suspicious for PCa.This is the first prospective study in which 18F-DCFPyL-PET/CT imaging demonstrated a moderate per segment-based sensitivity for the detection of csPCa of 61.4%, at a 88.3% specificity. The moderate sensitivity indicates that 18F-DCFPyL-PET/CT was not able to detect all localised csPCa. Segmentation of the prostate gland is problematic, as no clear anatomical landmarks are available to delineate the different segments within the prostate (Appendix-1 in ESM). A tumour located on the border of the apex and middle part of the prostate could be classified in different segments by the nuclear medicine physician and uro-pathologist, while in fact, they detected the same lesion. Therefore, the near-agreement score was introduced to approximate clinical reality. The sensitivity of the near-agreement score of 18F-DCFPyL-PET/CT imaging for the detection of csPCa was higher at 84.4% with a specificity of 97.0%.68Ga-PSMA-PET/CT and mpMRI prior to RARP [MpMRI has found a prominent place in the identification and localisation of PCa . Few stu to RARP . This st18F- PSMA-1007-PET/CT and mpMRI with subsequent RARP. Nine of the men were diagnosed with MRI-TBx and 1 with systematic biopsy.\u00a0Using a 36-segment mapping model, a similar assessment of agreement and near-total agreement was used. In 10 patients, 18F-PSMA-1007 PET/CT showed a high sensitivity , specificity , and accuracy for the detection of csPCa. Although the specificity was similar, this study did however show lower sensitivity for PSMA-PET/CT compared to mpMRI . Above mentioned studies implicate that PSMA-PET/CT imaging performs at least equal to mpMRI to locate primary PCa. The rates of mpMRI might have been overestimated as at least a part of included patients in previously mentioned studies were diagnosed by MRI-TBx. Thus, selection bias may have been introduced.In another study, Kesch et al. studied 18F-DCFPyL-PET/CT. So, similar to mpMRI, a substantial number of patients with\u2009\u2265\u2009pT3a was understaged by PSMA-based imaging [18F-DCFPyL-PET/CT of 93.8% is congruent with similar 68\u00a0Ga-PSMA studies (specificity\u2009>\u200990% for T3b disease) [There is therapeutic importance to distinguish between T2 and T3 disease [disease) , 25, 26.18F-DCFPyL-PET/CT performs in a truly biopsy na\u00efve cohort of patients. The present study was set up to evaluate the capability of PSMA-PET/CT to guide targeted prostate biopsy for the detection of csPCa, not with the goal to discriminate between those who should be or should not be biopsied. Unfortunately, not all patients received a pre-operative mpMRI, limiting direct comparison to 18F-DCFPyL-PET/CT. Moreover, some of the patients who received a mpMRI had a longer interval between the mpMRI and the PET/CT scans due to the mpMRI being performed at the referring centre. Finally, since the RARP-specimen will always change shape (due to organ slicing and shrinking artefacts) when it is removed from the body, no truly exact anatomical correlation is possible. Therefore, the partial agreement score was used to correct for this pitfall.Our study has inherent limitations. Since the PET/CT resolution is confined at 5\u00a0mm, limited diagnostic accuracy for small PCa-foci is to be expected. A selection bias has been introduced due to the selection of patients with biopsy-confirmed csPCa. It is thus unclear how 18F-DCFPyL-PET/CT with the RARP specimen using anatomical mapping, an accurate per-patient localization (93%) of csPCa was found within the prostate. 18F-DCFPyL-PET/CT proves promising for PSMA-targeted biopsy and provides a moderate local staging ability.When comparing the localisation of PCa on Supplementary file1 (JPG 61 kb)Supplementary file2 (JPG 138 kb)Supplementary file3 (JPG 79 kb)Supplementary file4 (JPG 70 kb)Supplementary file5 (JPG 177 kb)Below is the link to the electronic supplementary material."} +{"text": "Aegilops sharonensis, a wild relative of wheat, harbors diverse disease and insect resistance genes, making it a potentially excellent gene source for wheat improvement. In this study, we characterized and evaluated six wheat-A. sharonensis derivatives, which included three disomic additions, one disomic substitution + monotelosomic addition and two disomic substitution + disomic additions. A total of 51 PLUG markers were developed and used to allocate the A. sharonensis chromosomes in each of the six derivatives to Triticeae homoeologous groups. A set of cytogenetic markers specific for A. sharonensis chromosomes was established based on FISH using oligonucleotides as probes. Molecular cytogenetic marker analysis confirmed that these lines were a CS-A. sharonensis 2Ssh disomic addition, a 4Ssh disomic addition, a 4Ssh (4D) substitution + 5SshL monotelosomic addition, a 6Ssh disomic addition, a 4Ssh (4D) substitution + 6Ssh disomic addition and a 4Ssh (4D) substitution + 7Ssh disomic addition line, respectively. Disease resistance investigations showed that chromosome 7Ssh of A. sharonensis might harbor a new powdery mildew resistance gene, and therefore it has potential for use as resistance source for wheat breeding. Aegilops sharonensis Eig , a wild relative of wheat, is endemic to the coastal plains of Israel and southern Lebanon substitution line (A. sharonensis 4Ssh (4D) substitution line by using a nullisomic backcrossing procedure. A. sharonensis amphiploid (genome AABBS1S1). A. sharonensis. A. sharonensis introgression lines. Recently, both A. sharonensis amphidiploids. However, there are very few reports on the isolation of wheat plants carrying individual A. sharonensis chromosomes. A. sharonensis, and produced three 1Ssh (1A) substitution lines, two 1Ssh (1B) substitution lines, three 1Ssh (1D) substitution lines and two 1Ssh (5D) substitution lines. Therefore, the set of wheat-A. sharonensis chromosome lines is still not complete, which greatly limits the mapping and utilization of excellent genes derived from this species in wheat.ion line . Later, A. sharonensis chromosome derivatives, including three disomic addition lines, one disomic substitution + monotelosomic addition line, and two disomic substitution + disomic addition lines, were identified by (Polymerase Chain Reaction) PCR-based landmark unique gene (PLUG) markers and fluorescence in situ hybridization (FISH) analysis. In addition, the infection types (ITs) of disease resistance, spike and grain characteristics of these wheat-A. sharonensis chromosome lines were also investigated to provide useful information for the possible subsequent development of wheat-A. sharonensis translocations for wheat genetic improvement.In this study, six wheat-Triticum aestivum cv. Jinan17 (JN17) and Jimai22 (JM22) were maintained at the Crop Research Institute, Shandong Academy of Agricultural Sciences in Jinan. T. aestivum cv. Chinese Spring (CS) was provided by Prof. Z. J. Yang, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu. The diploid A. sharonensis accession (TA1995) was provided by Mr. J. Raupp, Wheat Genetic and Genomic Resources Center, Kansas State University, United States. The CS-A. sharonensis amphiploid (JIC-31) and six unidentified CS-A. sharonensis chromosome lines were kindly provided by Prof. S. M. Reader, John Innes Centre, United Kingdom.8 were synthesized by Chengdu Ruixin Biological Technology Co., Ltd. Probe sequences, the fluorochromes for probe labeling, FISH protocols and labeled DNA signal detection methods were according to 8 as a probe could be used to identify wheat chromosomes except 1A, 3D, 4D, 5D, and 6D, as described by EcoRI fragment isolated from bread wheat d JIC-31 . The karA. sharonensis chromosomes in lines JIC-32 to JIC-37 showed no signals associated with that probe. However, slightly different Oligo-pSc119.2-1 signals were found on both terminal regions of all A. sharonensis chromosomes , indicating that this pair of A. sharonensis chromosomes might be 1Ssh or 6Ssh.FISH using Oligo-pTa535-1 onto omosomes . In addie JIC-32 . MoreoveA. sharonensis chromosomes in JIC-32 to JIC-37, a total of 526 PLUG primer pairs were used to develop A. sharonensis chromosome-specific markers. As a result, fifty-one primer pairs could generate polymorphisms in A. sharonensis, the CS-A. sharonensis amphiploid, CS, JM22, and JN17. Among them, four, eight, nine, six, two, five, and seventeen belonged to chromosome homoeologous groups 1\u20137, respectively substitution + 5SshL monotelosomic addition (A. sharonensis 6Ssh disomic addition (A. sharonensis 4Ssh (4D) substitution + 6Ssh disomic addition (sh (4D) substitution + 7Ssh disomic addition line substitution + 5SshL monotelosomic addition, 6Ssh disomic addition, 4Ssh (4D) substitution + 6Ssh disomic addition and 4Ssh (4D) substitution + 7Ssh disomic addition lines were more elongated than that of CS. The CS-A. sharonensis 4Ssh disomic addition line (JIC-33) showed slightly elongated spikelets and overall longer spikes than that of CS. The CS-A. sharonensis 4Ssh (4D) substitution + 6Ssh disomic addition (JIC-36) showed shorter spikes and fewer spikelets per head than that of CS showed slender grains and darker pericarp color than that of CS (sh disomic addition (JIC-33) showed smaller grains than those of CS.Grain morphologies of the six CS-at of CS and the A. sharonensis 4Ssh (4D) substitution + 7Ssh disomic addition (JIC-37) was not obtained. The CS-A. sharonensis 4Ssh (4D) substitution + 7Ssh disomic addition (JIC-37) was nearly immune to powdery mildew, while CS and other CS-A. sharonensis chromosome lines tested were highly susceptible to powdery mildew (sh of A. sharonensis might carry powdery mildew resistant gene(s).Stripe rust, leaf rust, stem rust, and powdery mildew resistance tests showed that all the materials were moderately to highly susceptible to stripe rust, leaf rust, and stem rust except ty mildew , suggestA. sharonensis chromosomes into wheat is difficult due to the presence of gametocidal (Gc) genes that control the preferential transmission of chromosome 4Ssh (A. sharonensis additions or substitutions (T. urartu-A. sharonensis amphiploid TA3398 in North Dakota in 1972 (unpublished). A. sharonensis chromosome 4S1 (some scientists defined the genome of A. sharonensis as S1S1). A. sharonensis Gc2 gametocidal gene (Gc2mut), which opened a way for introgression of genes from A. sharonensis into wheat. 1, 3S1, 5S1, 6S1, and 7S1 in a 4S1 (4D) background. A. sharonensis introgression lines which they then separated into six groups based on different substituted chromosomes belonging to definite homoeologous groups and different numbers of translocations. A. sharonensis amphiploid (genome AABBS1S1). A. sharonensis, and produced three 1Ssh (1A) substitution lines, two 1Ssh (1B) substitution lines, three 1Ssh (1D) substitution lines and two 1Ssh (5D) substitution lines.Transferring each pair of ome 4Ssh . Therefoitutions . Maan foA. sharonensis introgression lines are very rare. Furthermore, none to date has reported the production of wheat-A. sharonensis 2Ssh introgression lines. In this research, six wheat-A. sharonensis introgression lines were identified, including a CS-A. sharonensis 2Ssh disomic addition (JIC-32), a 4Ssh disomic addition (JIC-33), a 4Ssh (4D) substitution + 5SshL monotelosomic addition (JIC-34), a 6Ssh disomic addition (JIC-35), a 4Ssh (4D) substitution + 6Ssh disomic addition (JIC-36) and a 4Ssh (4D) substitution + 7Ssh disomic addition (JIC-37). Among these six introgression lines, four possessed chromosome 4Ssh, suggesting that chromosome 4Ssh of A. sharonensis was transmitted preferentially into wheat due to the gametocidal gene, which confirms the reports of preferential transmission of gametocidal chromosomes of earlier researchers substitution + 5SshL monotelosomic addition (JIC-34) and the CS-A. sharonensis 4Ssh disomic addition line (JIC-33) were highly susceptible to powdery mildew, indicating that there were no powdery mildew resistance genes on chromosomes 4Ssh and 5SshL of A. sharonensis. However, the CS-A. sharonensis 4Ssh (4D) substitution + 7Ssh disomic addition (JIC-37) was nearly immune to powdery mildew (sh of A. sharonensis might carry new powdery mildew resistant gene(s).To date, more than 70 powdery mildew resistance genes have been permanently designated . Among ty mildew , suggestThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/CL conceived and designed the experiments. XW, ZHY, HW, JBL, and RH performed the experiments. WX, GL, and JG performed disease resistance testing. YZ, FL, DC, and AL analyzed the data. XW wrote the manuscript. HL, ZJY, JJL, and CL revised the manuscript. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "We describe a case of metastatic pulmonary calcification in a 71-year-old male, images with He was on diuretic therapy for chronic kidney disease for 4 years, followed by oral adsorptive carbon therapy for 13 months. He had been on hormonal therapy for prostate cancer (cT2cN0M0) for 9 months. He was hospitalized elsewhere for poor oral intake and general weakness. Laboratory studies at that time revealed the following : calcium 15.5 mg/dL (8.2\u201310.2 mg/dL); phosphorus 7.8 mg/dL (2.5\u20134.5 mg/dL); creatinine 3.67 mg/dL (0.7\u20131.2 mg/dL); total 25-hydroxyvitamin D level 12.06 ng/mL (approx. 30 ng/mL); and parathyroid hormone 15.71 pg/mL (15\u201365 pg/mL). 18F-fluorodeoxyglucose (FDG) PET/CT was performed to exclude the possibility of malignancy-related hypercalcemia. 18F-FDG) PET/CT images were acquired 1 h after intravenous injection of 238 MBq of 18F-FDG. The PET/CT images showed an increase in FDG uptake in the bilateral lower lungs bone scan. It also revealed significantly increased diffuse uptake in the bilateral lower lung fields (Further examination with a bone scan was therefore recommended. Since the bone scan is a sensitive test for diagnosing metastatic pulmonary calcification, we performed a bone scan to identify metastatic pulmonary calcification and determine whether bone metastasis existed . The patg fields . The sca18F-FDG PET/CT to detect metastatic pulmonary calcification [18F-FDG PET/CT findings in patients with metastatic pulmonary calcification. In conclusion, in patients with chronic kidney disease, when hypercalcemia is present and PET/CT shows ground-glass opacity with mild FDG uptake, metastatic pulmonary calcification can be considered one of the differential diagnoses, though this is rare.Metastatic pulmonary calcification is a frequently underdiagnosed disease. Because usual imaging modalities such as chest radiographs and CT scan findings are not specific ,9. Only fication ,11. Howe"} +{"text": "Biliary tract cancers (BTCs) are rare tumours with regional differences. Prognostic factors are poorly understood. Gemcitabine + platinum (GP) is the standard first-line chemotherapy in metastatic patients. We aimed to search for prognostic factors in patients with advanced disease in a cancer centre in South America.We conducted a retrospective analysis of patients with advanced BTC treated with chemotherapy. Variables were age (< or \u226570 years), Eastern Cooperative Oncology Group (ECOG) performance status (0/1 versus 2/3), gender, primary site (intrahepatic (IHC), extrahepatic (EHC), gallbladder (GB)), staging , metastatic sites, albumin (>3.5 g/dL versus <3.5 g/dL), biliary obstruction and first-line chemotherapy . Cox regression method was used to explore factors.p = 0.007), albumin < 3.5 g/dL (p = 0.001), biliary obstruction (p = 0.006), 5FU-based (p = 0.006) and single-agent (p < 0.0001) were associated with worse OS. ECOG performance status 2/3 (p = 0.058) and bone metastases (p = 0.051) were marginally related. In multivariate analysis, male (p = 0.003), bone metastases (p = 0.023), biliary obstruction (p = 0.001), 5FU-based (p = 0.016) and single-agent (p = 0.023) were independently associated with inferior OS.From 2010 to 2017, 104 patients were included. Median age was 62 years (32\u201386) and 22.1% were older than 70 years. Most patients had ECOG performance status 0/1 (63.4%), were female (51.9%) and were metastatic (82.7%). Bone metastases were found in 19.2%. Primary IHC, EHC and GB were 54.8%, 36.5% and 8.7%, respectively. GP was used by 79.8%. Median follow-up was 32.4 months. Median overall survival (mOS) was 11.4 months. In univariate analysis, male (In this retrospective study, we observed that male patients, bone metastases, biliary obstruction and regimens other than GP had worse survival. Larger studies should be conducted to confirm our findings. Biliary tract cancers (BTCs) are a rare group of malignances . Main suWe conducted a retrospective analysis of patients treated at a cancer centre in Brazil, from 2010 to 2017. Patients were included if they were 18 years of age or older, had histologic diagnosis of metastatic, recurrent or locally advanced unresectable BTC . All patients were deemed eligible to receive first-line chemotherapy by their treating physician. Exclusion criteria were absence of histologic confirmation, absence of data regarding systemic treatment and mixed histologies (hepatocellular-cholangiocarcinoma). Medical files were used as source of information. This study was approved by the local Ethics Committee (2680/19).Descriptive statistics were used for main demographic characteristics. Survival curves were estimated using Kaplan\u2013Meier method and compared with log-rank test. OS was defined as date of first chemotherapy cycle and death from any cause. Progression-free survival (PFS) was defined as date of first chemotherapy cycle and disease progression or death from any cause. Radiologic assessments of response and clinical benefit were performed according to local guidelines, typically by means of clinical examination every 2 weeks and computed tomography or magnetic resonance imaging every 8 weeks. Progressive disease was identified by the treating physician.2X tests were used to analyse categorical variables distributions between genders. To evaluate prognostic factors, univariate and multivariate analysis were performed using the Cox regression method. Age (<70 years versus >70 years), gender, staging , primary site (EHC versus IHC versus GB carcinoma), Eastern Cooperative Oncology Group (ECOG) performance status (0\u20131 versus 2\u20133), bone metastasis, baseline Carbohydrate Antigen 19-9 (CA19-9), albumin (<3.5 g/dL versus > 3.5 g/dL), biliary obstruction and first-line treatment (gemcitabine + platinum (GP) versus 5-Fluorouracil (5-FU) based versus monotherapy) were used in the univariate model. All tests were considered statistically significant with a two-sided p value of <\u20090.05. Statistical analysis was performed with IBM SPSS 20.Between July/2009 and March/2017, 104 patients were identified. Main demographics are shown in Regarding first-line chemotherapy , GP, 5-Fp = 0.32). Access to second-line was not statistically different among gender .Numerically, more female patients used GP as first-line . At time of analysis, seventy-six (73.1%) patients had died. Median OS (mOS) was 11.4 months (95% CI: 9.0\u201313.7) . Median p = 0.007), albumin < 3.5 g/dL (HR: 4.73 (95% CI: 1.96\u201311.4); p = 0.001), biliary obstruction (HR: 2.15 (95% CI: 1.24\u20133.71); p = 0.006), 5FU-based (HR: 2.64 (95% CI: 1.31\u20135.30); p = 0.006) and single-agent (HR: 6.27 (95% CI: 2.36\u201316.6); p < 0.0001) were associated with worse OS. Bone metastases (HR: 1.82 (95% CI: 0.99\u20133.34); p = 0.051) and ECOG performance status 2\u20133 (HR: 1.58 (95% CI: 0.98\u20132.53); p = 0.058) were marginally associated with prognosis.In univariate analysis, male patients (hazard ratio (HR): 1.88 (95% CI: 1.19\u20132.98); p = 0.003), bone metastases (HR: 3.53 (95% CI: 1.18\u201310.5); p = 0.023), biliary obstruction , 5FU-based (HR: 6.24 (95% CI: 1.41\u201327.6); p = 0.016) and single agent chemotherapy (HR: 7.22 (95% CI: 1.30\u201339.8); p = 0.023) were significantly and independently associated with inferior OS ; erior OS . mOS waserior OS .BTC is a rare gastrointestinal neoplasm but with increasing incidence over the past years, especially for IHC . SurgeryOur data bring relevant information about two aspects of metastatic BTC. The first is regarding the standard first-line treatment. Patients treated with GP regimens presented a more favourable outcome. GP was superior to Gemcitabine in the Phase III ABC-02 study and was established as the standard of treatment first-line therapy for metastatic biliary tract carcinomas . On the et al [p = 0.0031) and OS (13.0 versus 7.5 months (HR: 0.31 (95% CI: 0.15\u20130.63); p = 0.0013). However, in our study, 7.6% of patients were treated with FOLFOX in first-line and despite the small sample, outcomes were worse than those of patients treated with Gemcitabine combinations, reinforcing the role of GP. Clinical reasons not to employ GP were not accurately assessed in our analysis.Recently, the ABC-06 trial established FOLFOX as a new standard for second-line treatment of BTC . Based oet al publisheSecond, female gender was significatively associated with better survival. We found that survival was almost doubled among female patients. In analogous tumours like metastatic pancreatic cancer, gender is a controversial prognostic factor , 14 . Hoet al [p = 0.037). Baton et al [p = 0.0002). Another retrospective large series from Korea with 740 BTC patients [p = 0.04).Clinical data endorses our findings. Bridgewater et al describeon et al publishepatients also shop = 0.03) [Some aspects of BTC regarding access to therapeutics may help clarify this difference. Undergoing second and further lines of treatment is probably a strong prognostic factor. In a large study of second-line therapy, out of 378 patients that received first-line chemotherapy, only 96 patients (25%) received second-line. Female/male ratio was 31% and 21%, respectively ( = 0.03) . In our Currently, it is clear that there are striking differences in gastrointestinal cancer incidences among male and female patients. These differences are in part explained by exposition to risk factors such as smoking . NeverthDrug effects are also variable between genders. 5-FU based chemotherapy tends to be more toxic in women. A polled analysis of more than 28,000 patients, demonstrated that neutropenia and gastrointestinal toxicity were more likely to affect female patients . BenefitFinally, it is noteworthy that we have a growing body of evidence regarding molecular biology of BTC. Fibroblast Growth Factor Receptor (FGFR) fusions and Isocitrate Dehydrogenase (IDH) mutations are among targetable alterations in this scenario. Clinical trials have shown benefit of targeted therapies for such patients , 29. DesIn summary, our data identified prognostic factors related to outcome in metastatic BTC. Although FOLFOX has become the standard on the second-line, in our series patients receiving first-line treatment other than gemcitabine combination had worse prognosis. We also showed that bone metastasis, biliary obstruction and male gender were correlated with worse prognosis. These data could be useful for future trials in selecting patients with higher risk to more intensive and precise therapy. Further studies and multicentric collaborations are fundamental to validate our findings and also to understand the biology of this rare neoplasm.None.The authors declare that they have no conflicts of interest.Approved by local ethics committee (2680/19).Not applicable.All authors contributed to study concept and design; data acquisition; data analysis and interpretation; drafting of the manuscript; critical revision of the manuscript intellectual content and statistical analysis."} +{"text": "Bacillus cereus strain HT18, isolated from forest soil, was 5,333,415\u2009bp long. The genome included 5,825 putative coding sequences and 35.2% GC content; the strain had 5 plasmids. Average nucleotide identity based on BLAST+ (ANIb) and digital DNA-DNA hybridization (dDDH) results showed that HT18 was 98.78% and 90.70% homologous, respectively, to B. cereus ATCC 14579T.The genome sequence of Bacillus cereus group (phylum Firmicutes) comprises Gram-positive, spore-forming, facultative, anaerobic, rod-shaped bacteria with low-GC-content genomes . After colony isolation, the cells were cultured in LB broth at 37\u00b0C for 24 h. Then, genomic DNA was isolated using Marmur\u2019s method .http://platanus.bio.titech.ac.jp/pltanus_trim) (dnaA first was performed with DFAST version 1.4.0 (https://dfast.ddbj.nig.ac.jp) (http://jspecies.ribohost.com/jspeciesws/) and the Genome-to-Genome Distance Calculator version 3.0 (http://ggdc.dsmz.de/ggdc.php) and decoded on a MiSeq instrument (Illumina). A total of 1,488,012 reads with 431,000,004 bases were decoded with an average insert size of 641\u2009bp and spot length of 602\u2009bp with 2\u2009\u00d7\u2009300-bp paired ends. Low-quality bases (Q scores of <15) were trimmed, and short reads (<25\u2009bp) were removed using Platanus trim version 1.0.7 (gdc.php) using thOne contig of the assembled genome sequence was 5,333,415\u2009bp long (35.2% GC content) with a sequence depth of approximately 80. A total of 5,825 coding regions, 107 tRNAs, 42 rRNAs, and 3 CRISPR regions were annotated. Five plasmid DNA sequences were also assembled .B. cereus strains WPySW2 and AFA01, and 99.9% and 99.9% homologous to the foodborne pathogen FORC021 (https://figshare.com/articles/dataset/suppl_Table_pdf/17111096). Although strain HT18 showed high homology to B. thuringiensis serovar Berliner ATCC 10792T, it was closely related to B. cereus ATCC 14579T when it was compared to reference strains of the B. cereus group. Therefore, strain HT18 was identified as a B. cereus strain.Based on the ANIb (%) and dDDH (%) results, strain HT18 was 99.9% and 100% homologous to both PRJDB11181, BioSample number SAMD00278679, DRA number DRA011610, accession numbers AP024504 to AP024509, and SRA numbers DRX266213 (Illumina) and DRX266214 (ONT).The genome sequence and annotation data for strain HT18 were deposited in DDBJ/GenBank under BioProject number"} +{"text": "Wheatgrass Thinopyrum intermedium is a source of agronomically valuable traits for common wheat. Partial wheat\u2013wheatgrass amphidiploids and lines with wheatgrass chromosome substitutions are extensively used as intermediates in breeding programs. Line Agis 1 (6Agi2/6D) is present in the cultivar Tulaykovskaya 10 pedigree. Wheatgrass chromosome 6Agi2 carries multiple resistance to fungal diseases in various ecogeographical zones. In this work, we studied the transfer of chromosome 6Agi2 in hybrid populations Saratovskaya 29 \u00d7 skaya 10 (S29 \u00d7 T10) and Tulaykovskaya 10 \u00d7 Saratovskaya 29 (T10 \u00d7 S29). Chromosome 6Agi2 was identif ied by PCRwith chromosome-specif ic primers and by genomic in situ hybridization (GISH). According to molecular data, 6Agi2was transmitted to nearly half of the plants tested in the F2 and F3 generations. A new breeding line 49-14 (2n = 42)with chromosome pair 6Agi2 was isolated and characterized in T10 \u00d7 S29 F5 by GISH. According to the results ofour f ield experiment in 2020, the line had high productivity traits. The grain weights per plant (10.04 \u00b1 0.93 g) andthe number of grains per plant (259.36 \u00b1 22.49) did not differ signif icantly from the parent varieties. The number ofgrains per spikelet in the main spike was signif icantly higher than in S29 ( p \u2264 0.001) or T10 ( p \u2264 0.05). Plants werecharacterized by the ability to set 3.77 \u00b1 0.1 grains per spikelet, and this trait varied among individuals from 2.93 to4.62. The grain protein content was 17.91 %, and the gluten content, 40.55 %. According to the screening for fungaldisease resistance carried out in the f ield in 2018 and 2020, chromosome 6Agi2 makes plants retain immunity tothe West Siberian population of brown rust and to dominant races of stem rust. It also provides medium resistantand medium susceptible types of response to yellow rust. The possibility of using lines/varieties of bread wheatwith wheatgrass chromosomes 6Agi2 in breeding in order to increase protein content in the grain, to confer resistanceto leaf diseases on plants and to create multif lowered forms is discussed. Wild perennial common wheat relatives of the Thinopyrumgenus are broadly polymorphic. They can be sources ofcommercially valuable traits: resistance to fungal and viraldiseases ,tolerance of saline soils and drought, and high protein contentsin the grain . TheThinopyrum genus includes about 20 species of differentploidies: diploids, allotetraploids, allohexaploids, octoploids,and decaploids . The genetic poolsof two species are in the greatest use: elongate wheatgrassTh. elongatum (Agropyron elongatum) and intermediatewheatgrass Th. intermedium (Ag. glaucum). They becamedonors of genes for resistance to pests: Lr19, Lr24, Lr29,and Lr38 to brown rust; Sr24, Sr25, Sr26, Sr43, and Sr44to stem rust; Pm40 and Pm43 to powdery mildew; Bdv2to barley yellow dwarf virus; and Wsm1 to wheat streakmosaic virus .Viable wheat\u2013wheatgrass hybrids were first obtained byN.V. Tsitsin in 1930\u20131933. He crossed diploid, tetraploid,and hexaploid wheats to Ag. elongatum and Ag. glaucum and obtained octoploid forms of perennialand ratooning wheats known as intermediate wheat\u2013wheatgrasshybrids, IWWHs . Experiments on wheat hybridization to plants ofthe Thinopyrum genus were also carried out in the UnitedStates, Germany, Canada, and China. Various hybrid formswere obtained and annotated: partial amphiploids; highproteinaddition, substitution, and translocation lines andforms resistant to barley yellow dwarf virus, wheat streakmosaic virus, powdery mildew, yellow rust, brown rust,and stem rust .Partial wheat\u2013wheatgrass amphidiploids are used internationallyfor transferring valuable traits to commonwheat . In Russiatwo groups of common wheat cultivars resistant to fungalpests have been raised via IWWHs at the AgriculturalResearch Institute of the South-East and the Samara ResearchInstitute of Agriculture. In their genomes, wheatchromosome 6D is replaced by chromosome 6Agi fromwheatgrass Th. intermedium. Chromosomes 6Agi1 and6Agi2 are not identical, as they show different C bandingpatterns in Giemsa staining . In theformer case, 6Agi1 was inherited from substitution lineS29-Agro139-M2-2, obtained by crossing spring commonwheat Saratovskaya 29 to IWWH 139, and fromcv. Mnogoletka2. Then wheatgrass addition chromosomesrecombined with each other . The cultivarsraised in Samara inherited wheatgrass chromosome6Agi2 from substitution line Agis 1, obtained by crossingS29 to IWWH 644 .Since 1984, when Tulaykovskaya 5 was enlisted to theState Register of Selection Achievements, varieties withwheatgrass chromosome introgression bred in Samararetain their resistance to brown rust and powdery mildewin various ecogeographical regions of Russia . It has been shown thatthe Lr genes on chromosome 6Agi2 are not allelic to thegenes Lr9, Lr19, Lr24, Lr29, or Lr47, and the type of responseto inoculation with Puccinia triticina Eriks. isolatesconfirms their not being allelic to Lr19 or Lr38 . Testing of F2 and F3 hybrids of susceptiblevarieties with Tulaykovskaya 10 for brown rust resistanceshows that chromosome 6Agi2 houses a locus for resistanceto the West Siberian brown rust race .However, the copy number of resistance genes on 6Agi2is still unknown. The loci have not been mapped on thechromosome either.Molecular and cytogenetic markers are designed fordetectionof wheatgrass genetic material in the commonwheat genome . There are molecularmarkers specific to the Th. intermedium genome: simple sequencerepeats (SSRs) , markers designed on the base of expressed sequences (ESTs), and specificlocus amplified fragments (SLAFs) .There are several RFLP , SCAR, and ISSR markersfor Pseudoroegneria spicata (St genome), designedfor identification of particular chromosomes of the St genome.The correspondence of wheatgrass chromosomes tohomoelogical common wheat groups is tested with uniquegene markers based on PCR (PLUG markers) and SNP markers . Salina et al. (2016) designed markersspecific to the long and short arms of Th. intermediumchromosome 6Agi2Varieties bred in Samara are used in Russian breedingprograms . Thegoal of this work was to obtain breeding material with introgressedwheatgrass chromosome, test its commerciallysignificant indices, and investigate the transfer of Th. intermediumchromosome 6Agi2 present in cv. Tulaykovskaya10 by the example of a hybrid population with wheatcultivar Saratovskaya 29, which is a gold standard of grainquality. DNA markers specific to the long and short armsof 6Agi2 and genomic in situ hybridization (GISH) wereused to identify the chromosome.Plants. Experiments were conducted with spring commonwheat varieties Saratovskaya 29 (S29) and Tulaykovskaya10 (T10) and with their hybrids S29 \u00d7 T10 and T10 \u00d7 S29 (generations F2\u2013F6). The hybridgenerations were obtained by self-pollination of F1 hybrids.Varieties S29 and T10 belong to the mid-season group.Saratovskaya 29 is highly susceptible to leaf diseases. Tulaykovskaya10 is immune to brown leaf rust and mediumsensitiveto powdery mildew (https://samniish.ru/pshenicamyagkaya-yarovaya-sort-tulajkovskaya-10.html).Hybrids S29 \u00d7 T10, generations F2 and F3, and T10 \u00d7 S29,generations F2, F3 and F5, were grown in a hydroponicgreenhouse of the Laboratory of Artificial Plant Growth,Institute of Cytology and Genetics, Novosibirsk, in theautumn of 2017 and in the springs of 2019 and 2020,respectively. The temperature schedule was 22 \u00b0C in thedaytime and 16 \u00b0C at night. The light/dark schedule was16:8 h. Hybrid generations T10 \u00d7 S29 F4 and F6 were grownin the field in the Moshkovo raion of the Novosibirsk oblastin the summers of 2018 and 2020, respectively; localitycoordinates 55.14\u00b0 N and 83.63\u00b0 E.Fluorescence in situ hybridization (FISH). Mitoticchromosome slides for FISH were prepared as in Ivanova etal. (2019). Use was made of the Aegilops tauschii pAet6- 09probe specific to chromosome centromeric repeatsofrice, wheat, rye, and barley andwheatgrass genomic DNA isolated from Th. intermediumplants. A DNA sample of the pAet6-09 repeat was kindlyprovided by Dr. A. Lukaszewski . All slides were examinedunderan Axio Imager M1 microscope .Images were captured with a ProgRes MF camera in the Shared Access Center for MicroscopyAnalysis of Biologic Objects, Siberian Branch ofthe RAS, and processed with Adobe Photoshop CS2.Plant DNA isolation. DNA was isolated from youngleaves of hybrids and control plants with a Genomic DNAPurification Kit accordingto manufacturer\u2019s recommendations.PCR analysis. DNA samples were analyzed with primersMF2/MR1r2 (amplicon size 347 bp) to the long armof chromosome 6Agi2L of Th. intermedium, Te6HS476(amplicon size 200 bp) to the short arm of chromosome6Agi2S of Th. intermedium, and MF2/MR4 (ampliconsize 328 bp) to the long arm of chromosome 6DL. Theprimershad been designed at the Laboratory of Plant MolecularGenetics and Cytogenetics, Institute of Cytologyand Genetics . PCR was carried outin a Bio-Rad T-100 Thermal Cycler. The products wereresolved in 1.5 % agarose gel with ethidium bromide andvisualized with a Gel Doc XR+ gel documentation system.Assessment of commercially valuable traits. TheT10 \u00d7 S29 F4 progeny selected with molecular markers wastested for resistance to brown rust Puccinia triticina Eriks.and stem rust P. graminis Pers. in field experiments in2018. The F6 progeny selected by molecular cytologicalanalysis was tested for resistance to brown rust P. triticinaEriks., stem rust P. graminis Pers., and yellow rustP. glumarum Eriks.et Henn. in the field in 2020. The followingparameterswere recorded in generation F6 selectedby molecular and cytological methods in the field in 2000:the sprouting\u2013flowering interval, plant height, productivetillering, main spike length, number of spikelets in the mainspike, number of grains in the main spike, grain weight ofthe main spike, number of grains per spikelet in the mainspike, grain number per plant, grain weight per plant,1000 grain weight, and contents of protein and gluten inthe grain. Grains were sown on May 9, 2020, in plots of70 cm in width, 15 grains per row, and 25-cm intervalsbetween rowsThe degree of injury by fungal pests was assessed accordingto the CIMMYT scale .The contents of protein and gluten were measured with aninfrared OmegAnalyzer G . The timefrom the mass-scale appearance of sprouts till the first appearanceof yellow anthers in middle spikelets of spikeswas taken to be the sprouting\u2013flowering interval. Floweringdates were recorded in individual spikes. The significanceof differences between two mean values of two sampleswas assessed by Student\u2019s t testIdentification of wheatgrass chromosome 6Agi2in generations F2\u20133 of the S29 \u00d7 T10 and T10 \u00d7 S29 hybridswith chromosome-specific primersChromosomes 6Agi2 of wheatgrass and 6D of wheat werepresent in the F1 of S29 \u00d7 T10 and T10 \u00d7 S29 in the univalentstate. Therefore, their presence or absence in DNAsamples from generation F2 was tested by PCR with primersspecific to the wheatgrass chromosome. We tested 116and 45 DNA samples from F2 S29 \u00d7 T10 and T10 \u00d7 S29,respectively, and found samples with the absence of amplificationwith two primer pairs for the short and longarms of chromosome 6Agi2 and with amplification of themarker to chromosome 6D. Thus, there were no 6Agi2/6Dsubstitution in these samples, designated as wheat (w) type.The presence of chromosome 6D was also proven insamples with amplification of markers to either long orshort arm, being indicative of the presence of telocentrics. Altogether, 12 telocentrics forthe long arm and 29 telocentrics for the short arm were detected in samples of generations F2 and F3, and the ratioof telocentrics for the short and long arm depended significantlyon the cross direction. Telocentrics for the long armwere very rare in the T10 \u00d7 S29 cross.The presence of amplification fragments with two markersto the short and long arms pointed to the presenceof the whole chromosome 6Agi2. With regard to the presenceor absence of chromosome 6D, we suggest eitherfull 6Agi2/6D substitution (Ag type) or the heterozygousstate of the chromosome in the samples (H type).For further analysis, plants with amplification of markersto the short and long arm of the wheatgrass chromosomewere selected.Karyotyping of generation F5 of T10 \u00d7 S29 hybridsTo verify the presence of one or two wheatgrass chromosomesin chromosome sets and to confirm stable inheritanceof the substitution, we performed GISH of mitotic chromosomesat various self-pollination stages. The analysisof plants bearing substitutions according to PCR revealed42 chromosomes, of which two were whole wheatgrasschromosomes . Their long arms housed a largesubtelomeric heterochromatin block, which is consistentwith the locations of Giemsa C bands on chromosome6Agi2 in Tulaykovskaya 10 . Thecentromere-specific pAet6\u201109 repeat located on wheatgrasschromosomes showed weak signals, to demonstrate thepoor hybridization of the repeat to centromeric DNA ofwheatgrass chromosomes.In situ hybridization confirmed the stable inheritance ofthe 6Agi2/6D substitution through generations.Commercially valuable traitsin T10 \u00d7 S29 generations F5 and F6Tulaykovskaya 10 is present in the pedigrees of manymoderncommon wheat varieties. Its use in the breedingof new forms is based on its locus for brown leaf rustresistance, mapped on wheatgrass chromosome 6Agi2. Inspite of the replacement of chromosome 6D by alien chromosome6Agi2, the variety shows high grain yield, droughttolerance,and good baking quality (https://samniish.ru/pshenica-myagkaya-yarovaya-sort-tulajkovskaya-10.html).Three lines were raised from F4 plants of T10 \u00d7 S29 withidentified wheatgrass chromosomes: 33-2, 34-1, and 35-45.Analysis of the performance of T10, S29, and T10 \u00d7 S29F5 lines grown in a hydroponic greenhouse showed thatall the lines significantly outperformed T10 in all indices(Table 2). As compared to S29, the lines did not differ inproductive tillering; lines 34-1 an 35-45 did not differ ingrain number per plant or grain weight per plant; and inline 33-2, these indices were significantly lower. None ofthe lines outperformed S29 in 1000 grain weight; this indexwas significantly lower.We selected the most productive plants of generation F5of line 35-45 to analyze performance indices and the durationof the sprouting\u2013flowering interval in plants grown inthe field in 2020. Thus, daughter line 49-14 was selectedfrom the chosen segregating line 35-45.Phenological observations revealed the shortest sprouting\u2013flowering interval in line 49-14 (50.6 days), and in S29and T10 it was one day longer. The flowering durations inthe main spikes of individual plants were 11 days in 49-14,10 days in T10, and 9 days in S29.Comparison of performance indices in 49-14, S29, andT10 revealed no difference in main spike length, grainweight in the main spike, grain weight per plant, or grainnumber per plant (Table 3). Plants of line 49-14 weresignificantly taller than T10 but did not differ in height from S29. Productive tillering and main spike density in49-14 showed significant ( p \u2264 0.05) differences from thecultivars. The number of grains in the main spike in 49-14was significantly greater than in S29 ( \u0440 \u2264 0.001) or T10( \u0440 \u2264 0.05).The number of grains per spikelet in the main spike ofline 49-14 was significantly higher than in S29 ( p \u2264 0.001)or T10 ( p \u2264 0.05). Line 49-14 set 3.77 \u00b1 0.1 grains perspikelet on the average, and this trait varied among individualplants from 2.93 to 4.62 . The1000 grain weights in line 49-14 and T10 were significantly( \u0440 \u2264 0.001) lower than in S29.Grain quality analysis showed that S29, T10, and 49- 14had high contents of protein and gluten (see Table 3),characteristic of strong wheats. Grain quality in 49-14 wascomparable with S29 and T10.Screening of generations F4 and F6 of the T10 \u00d7 S29 crossfor resistance to fungal pathogensThe resistance of plants to brown rust and stem rust agentswas tested in the field in 2018 and 2020. Field resistanceto powdery mildew was not tested in those years, becauseweather conditions were unfavorable for the agent, asseen from the fact that the susceptible variety S29 wasnot injured.In tests of the resistance to the Siberian population ofthe brown rust agent P. triticina conducted in 2018, S29demonstrated the S (susceptibility) type of response, scoring4 with about 100 % damage of leaf surface .Tulaykovskaya 10 and F4 plants of T10 \u00d7 S29 showed theimmune type without P. triticina pustules .The hybrids tested and parental varieties produced aspecific response to stem rust. Plants of S29, T10, andF4 T10 \u00d7 S29 showed generally the immune response exceptfor a single case. One of the F4 plants showed a specific typeof interaction with the pathogen: occasional uredial pustuleswithout chlorosis (5S) . In practice, thedetected local but pronounced syndrome is interpreted asa sign of a rare virulent fungus race in the local population. As reported by Skolotneva et al.(2020), the stem rust population in the Novosibirsk oblastis highly heterogeneous, as it is formed by southern andwestern migrants.No signs of fungal diseases were detected in plants ofthe cultivars and line 49-14 at the stages of tillering andflowering in the field in 2020. Tests for plant resistanceto the brown rust population at the milky ripeness stageshowed type S (susceptibility) response in S29 plants, score 4 with about 100 % leaf damage, whereasT10 and 49-14 demonstrated the immune response with noP. triticina pustules .At the milky ripeness stage, on August 2\u20135, the start ofdamage of S29, T10, and 49-14 by the yellow rust agentP. striiformis was noted. The percentage of leaf area injury in S29 was 50 to 75 , corresponding to mediumsusceptibility (MS).Plants of T10 and 49-14 showed medium resistance(MR) and medium susceptibility (MS) to the yellow rustagent. The percentage of leaf area injury was 5 to 40, withchlorotic zones .No damage by stem rust was seen in plants of S29, T10,or 49-14 in the summer of 2020.Thus, the results of screening for resistance to a varietyof plant pathogens conducted in the field in different yearsindicate that chromosome 6Agi2 retains the immunity ofplants to the West Siberian brown rust population and immunityto dominant stem rust races. It also supports themedium resistant and medium susceptible types of responseto yellow rust agents.Breeding line 49-14 (2n = 42) was isolated from generationF5 of intervarietal hybrids T10 \u00d7 S29, with introgressionof a pair of wheatgrass chromosomes 6Agi2. It showshigh performance indices and immunity to West Siberianpopulationsof brown rust agents. The response of 49-14plants to the yellow rust agent varies from medium resistanceto medium susceptibility,probably because of thedifference in aggressiveness among the agent races. Stemrust injury was noted in only one plant and was interpretedas immunity to dominant stem rust races.Previously, it was demonstrated that the genetic materialof chromosome 6Agi2 in common wheat varietiesTulaykovskaya 5, Tulaykovskaya 10, Tulaykovskaya zolotistaya,Tulaykovskaya 100, and Volgouralskaya retains theresistance to brown rust populations typical of the Lowerand Middle Volga regions, Central and Ural regions, andWest Siberia . The damageof Tulaykovskaya 10 by brown rust in infection nurseriesof the Central Chernozem region reached 22 %, and thevariety was assigned to group II of epidemic resistance(moderately resistant ER II) . In Tatarstan,the damage of Tulaykovskaya 10 by stem rust was assessedas 5\u201310 % on the average, and the damage by powdery mildewscored 6; the type of response to brown rust remainedimmune . The susceptibility ofT10 to the powdery mildew population of the West Siberianregion was assessed as resistance. A genome-wideassociation search (GWAS) mapped the Pm6Agi2 gene onthe long arm of wheatgrass chromosome 6Agi2, and thisgene imparts resistance to the powdery mildew agent . In experiments in the Middle Volga region,T10 showed immunity to brown rust and medium resistance(20 % injury) to stem rust, yellow rust, and powdery mildew. Thus, T10 retains its immunity tobrown rust populations in various ecogeographical regions.It is medium susceptible to stem and yellow rusts but showsdiverse responses to the powdery mildew agent.The substitution of wheatgrass chromosome 6Agi2 for6D does not impair grain yield, grain quality, or droughttolerance ,although in some cases of using T10 as a resistance genedonor, plants with lower productive tillering and 1000 grainweight appeared among the offspring with chromosome6Agi2 . The contents of protein andgluten in line 49-14 were about the same as in S29 orT10, corresponding to the grain quality of strong wheats. Line 49-14 lagged behindthe parental varieties in productive tillering (S29), numberof spikelets in the main spike (T10), and 1000 grainweight (S29). In spite of lower productive tillering, fewerspikelets in the main spike, and lower 1000 grain weight,the indices grain weight per plant and grain number perplant in line 49-14 did not differ significantly from theparental varieties owing to the significantly higher grainnumber per spikelet in the main spike of 49-14 than inS29 ( \u0440 \u2264 0.001) or T10 ( p \u2264 0.05). Plants of 49-14 set3.77 \u00b1 0.1 grains per spikelet, the range of variation inindividual plants being 2.93\u20134.62, and up to 6 grains wereset in spikelets of the middle spike part. Spikelets werefan-shaped . This shape is a specific sign ofmultiflowered spikelets in wheat .Although common wheat has multiflowered spikelets,most of them set two or three grains. As the potential offorming more grains in wheat exceeds the actual yield byfar, many studies are dedicated to seeking tools to controlthis process. The genetic and physiological groundsof breeding for more grains in spikes and spikelets and,ultimately, more grains per unit area are extensively investigated. Analysis of thereproductive developmental stages of spikes, spikelets,florets, and grains, as well as of their genetic regulation, isthe best way to understand the formation of the trait \u2018grainnumber and spike fertility\u2019. The \u2018grain number per spikelet\u2019trait depends on the initiation of floret primordia, then onfloret survival at the next stage, and then on their efficientpollination. Normally, up to 12 floret primordia form atthe white anther stage, but later up to 60 % of the floretsmay remain underdeveloped . Thisapplies especially to apical (uppermost) florets of a spikelet.As reported by Kuperman (1969), the growth rates ofthe two lowest and upper floret apices are nonuniform atorganogenesis stage V; a spikelet may have up to five, lessoften, to seven florets. Lower florets very quickly formprimordia of generative organs, stamens, and the pistil.A delay in organ formation is observed in the third and,particularly, fourth, fifth, and subsequent florets. Pistilsmost often remain underdeveloped in the uppermost florets.Chromosomes 4A, 5A, 6A, 7A, 2B, 5B, 7B, and 7D bear QTLs responsible for the trait \u2018number of floret primordiaper spikelet\u2019 . Also, the correlation andcluster analyses performed in the same study infer thatthe number of grains per spikelet does not depend on themaximum number of floret primordia per spikelet . Hence, the number of grains in a spikelet isdetermined by the fertility of each floret .A QTL responsible for greater numbers of grains perspikelet was detected on the long arm of chromosome 2Ain GWAS of European common wheat varieties . Further studies of this locus mapped the GrainNumber Increase 1 (GNI1) gene, encoding a transcriptionfactor with the HDZip1 homeodomain. Its mutationcontributes much to greater numbers of fertile florets dueto upper florets of the spikelet . Supposedly,GNI1 was formed by gene duplication in wheatevolution, and its mutations were selected in domestication,as they increased the number of fertile florets, and,consequently, grains. Transcription factor ARGONAUTE1d(AGO1d ) also affects the grain number in the spikes ofcommon and durum wheats . AGO1dis important for the development of anthers and pollenat early developmental stages of wheat. Its malfunctionshortens the spike, reduces anther size, decreases pollenfertility, and thereby decreases the number of grains in thespike .The manifestation of traits in a plant is cumulatively affectedby the genotype, ambient conditions, and farmingtechniques. All these factors greatly influence quantitativetraits, including yield components . The day/night regime and solarspectrum are particularly important ambient factors atorganogenesis stages V and VI . Lowerintensities of the red and infrared radiation reduce thenumber of fertile florets, number of grains per plant, and1000 grain weight . The combinationsof environmental factors required for each developmentalstage stem from the conditions under which the species,varieties, and cultivars formed. With regard to their physiologicaldevelopmental features, cultivars S29 and T10belong to the Volga steppe and forest-steppe agroecologicalgroups, respectively, or morphophysiological type II (https://samniish.ru/yarovaya_myagkaya_pshenica.html). Such varieties utilize mainly winter andearly spring precipitation in regions with water shortagein the second half of summer; that is, they are tolerant ofsummer drought. Cultivars bred in West Siberia belongto morphophysiological type V. The ecotype of Siberianforest-steppe wheats is determined by the climate: cold anddry April, May, and the first half of June; relatively ampleprecipitation in the second half of summer (July), and coldtemperatures in August. The delay in organogenesis stage Vallows much better use of late summer precipitation forthe formation of large spikes and multiflowered spikelets.Owing to developmental physiological features and highdrought tolerance, varieties of morphophysiological type IIcan be grown in steppe and forest-steppe regions of WestSiberia . Thus, the genotypes of S29 andT10 are environmentally flexible. In the climate of WestSiberian forest-steppe, they synchronize the metamericgrowth of spikelets to develop four, five, or more normalflorets in a spikelet.The genetic material of crested wheatgrass Agropyroncristatum is also beneficial for yield components. Additionlines with chromosome 6P of Ag. cristatum and,particularly, substitution lines 6P/6D show high productivetillering and significantly greater grain numbers inspikes and spikelets: up to 4.5 grains per spikelet . It has been inferred thatchromosome 6P houses genes controlling the numbers offlorets and grains in a spike and spikelet .Conceivably, chromosome 6Agi2 of Th. intermedium bearsgene(s) controlling the synchronous metameric growth ofspikelets in T10, whereas the additive manifestation of thetrait \u2018grain number per spikelet\u2019 is observed in line 49-14(T10 \u00d7 S29), where up to six normal florets develop ina spikeletSakuma et al., 2019) are means for improvingwheat grain yield.The authors declare no conflict of interest.Arbuzova V.S., Dobrovolskaya O.B., Martinek P., Chumanova E.V.,Efremova T.T. Inheritance of signs of \u201cmany-flowered\u201d commonwheat and evaluation of productivity of the spike of F2 hybrids.Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journalof Geneticsand Breeding. 2016;20(3):355-363. DOI 10.18699/VJ16.125. (in Russian)Askhadullin D.F., Askhadullin D.F., Vasilova N.Z., Khusainova I.I.,Tazutdinova M.R. A variety in the spring wheat protection systemfrom leafy diseases. Vestnik Kazanskogo GAU = Vestnik ofthe Kazan State Agrarian University. 2019;3(54):10-14. DOI10.12737/article_5db8423bb4f997.64890554. (in Russian)Ayala-Navarrete L., Thompson N., Ohm H., Anderson J. Molecularmarkers show a complex mosaic pattern of wheat-Thinopyrum intermediumtranslocations carrying resistance to YDV. Theor. Appl.Genet. 2010;121:961-970. DOI 10.1007/s00122-010-1365-y.Bao Y., Wu X., Zhang C., Li X., He F., Qi X., Wang H. Chromosomalconstitutions and reactions to powdery mildew and striperust of four novel wheat-Thinopyrum intermedium partial amphiploids.J. Genet. Genomics. 2014;41(12):663-666. DOI 10.1016/j.jgg.2014.11.003.Bhusal N., Sarial A.K., Sharma P., Sareen S. Mapping QTLs for grainyield components in wheat under heat stress. PLoS One. 2017;12(12):e0189594. DOI 10.1371/journal.pone.0189594.Chang Z.-J., Zhang X.-J., Yang Z.-J., Zhan H.-X., Li X., Liu C.,Zhang C.-Z. Characterization of a partial wheat-Thinopyrumintermedium amphiploid and its reaction to fungal diseases ofwheat. Hereditas. 2010;147(6):304-312. DOI 10.1111/j.1601-5223.2010.02156.x.Cseh A., Yang C., Hubbart-Edwards S., Scholefield D., Ashling S.S.,Burridge A.J., Wilkinson P.A., King I.P., King J., Grewal S. Developmentand validation of an exome-based SNP marker setfor identification of the St, Jr and Jvs genomes of Thinopyrumintermedium in a wheat background. Theor. Appl. Genet. 2019;132:1555-1570. DOI 10.1007/s00122-019-03300-9.Cui F., Ding A., Li J., Zhao C., Wang L., Wang X., Qi X., Li X.,Li G., Gao J., Wang H. QTL detection of seven spike-relatedtraits and their genetic correlations in wheat using two related RILpopulations. Euphytica.2012;186:177-192. DOI 10.1007/s10681-011-0550-7.Danilova T.V., Zhang G., Liu W., Friebe B., Gill B.S. Homoeologousrecombination-based transfer and molecular cytogenetic mappingof a wheat streak mosaic virus and Triticum mosaic virusresistance gene Wsm3 from Thinopyrum intermedium to wheat.Theor. Appl. Genet. 2017;130(3):549-556. DOI 10.1007/s00122-016-2834-8.Davoyan R.O., Bebyakina I.V., Davoyan E.R., Zinchenco A.N., ZubanovaY.S., Mikov D.S. Introgression of common wheat lineswith genetic material of Agropyron glaucum. Vavilovskii ZhurnalGenetiki i Selektsii = Vavilov Journal of Genetics and Breeding.2015;19(1):83-90. DOI 10.18699/VJ15.010. (in Russian)Fedak G., Han F. Characterization of derivatives from wheat-Thinopyrumwide crosses. Cytogenet. Genome Res. 2005;109:360-367.DOI 10.1159/000082420.Feng N., Song G., Guan J., Chen K., Jia M., Huang D., Wu J.,Zhang L., Kong X., Geng S., Liu J., Li A., Mao L. Transcriptomeprofiling of wheat inflorescence development from spikeletinitiation to floral patterning identified stage-specific regulatorygenes. Plant Physiol. 2017;174(3):1779-1794. DOI 10.1104/pp.17.00310.Filatova E.V., Syukov V.V., Anisimkina N.V. Influence of the T-5translocation from wheat grass on the protein fractional structureof spring bread wheat. Agrarnyy Vestnik Yugo-Vostoka = AgrarianHerald of the Southeast. 2010;4:15-17. (in Russian)Friebe B., Jiang J., Raupp W.J., McIntosh R.A., Gill B.S. Characterizationof wheat-alien translocations conferring resistance todiseases and pests: current status. Euphytica. 1996;91:59-87.Fu S., Lv Z., Qi B., Guo X., Li J., Liu B., Han F. Molecular cytogeneticcharacterization of wheat-Thinopyrum elongatum addition,substitution and translocation lines with a novel source of resistanceto wheat fusarium head blight. J. Genet. Genomics. 2012;39:103-110. DOI 10.1016/j.jgg.2011.11.008Guo Z., Chen D., Alqudah A.M., R\u00f6der M.S., Ganal M.W., SchnurbuschT. Genome-wide association analyses of 54 traits identifiedmultiple loci for the determination of floret fertility in wheat. NewPhytol. 2017;214:257-270. DOI 10.1111/nph.14342.Guo Z., Slafer G.A., Schnurbusch T. Genotypic variation in spikefertilitytraits and ovary size as determinants of floret and grainsurvival rate in wheat. J. Exp. Bot. 2016;67:4221-4230. DOI10.1093/jxb/erw200.Guo Z., Zhao Y., R\u00f6der M.S., Reif J.C., Ganal M.W., Chen D.,Schnurbusch T. Manipulation and prediction of spike morphologytraits for the improvement of grain yield in wheat. Sci. Rep. 2018;8:14435. DOI 10.1038/s41598-018-31977-3.Han F., Liu B., Fedak G., Liu Z. Genomic constitution and variationin five partial amphiploids of wheat-Thinopyrum intermediumas revealed by GISH, multicolor GISH and seed storage proteinanalysis. Theor. Appl. Genet. 2004;109:1070-1076. DOI 10.1007/s00122-004-1720-y.Han H., Bai L., Su J., Zhang J., Song L., Gao A., Yang X., Li X.,Liu W., Li L. Genetic rearrangements of six wheat-Agropyroncristatum 6P addition lines revealed by molecular markers. PLoSOne. 2014;9(3):e91066. DOI 10.1371/journal.pone.0091066.Hu J., Wang X., Zhang G., Jiang P., Chen W., Hao Y., Ma X., Xu S.,Jia J., Kong L., Wang H. QTL mapping for yield-related traits inwheat based on four RIL populations. Theor. Appl. Genet. 2020;133:917-933. DOI 10.1007/s00122-019-03515-wHu L.J., Li G.R., Zeng Z.X., Chang Z.J., Liu C., Zhou J.P., Yang Z.J.Molecular cytogenetic identification of a new wheat-Thinopyrumsubstitution line with stripe rust resistance. Euphytica. 2011;177:169-177. DOI 10.1007/s10681-010-0216-x.Hu L., Li G., Zhan H., Liu C., Yang Z. New St-chromosome-specificmolecular markers for identifying wheat-Thinopyrum intermediumderivative lines. J. Genet. 2014;93:69-74. DOI 10.1007/s12041-012-0158-2.Ishikawa G., Nakamura T., Ashida T., Saito M., Nasuda S., Endo T.R.,Wu J., Matsumoto T. Localization of anchor loci representing fivehundred annotated rice genes to wheat chromosomes using PLUGmarkers. Theor. Appl. Genet. 2009;118:499-514. DOI 10.1007/s00122-008-0916-y.Ivanova Yu.N., Solovey L.A., Loginova D.B., Miroshnikova E.E.,Dubovets N.I., Silkova O.G. The creation and characterizationof the bread wheat line with a centric translocation T2DL.2RL.VavilovskiiZhurnal Genetiki i Selektsii = Vavilov Journal of Geneticsand Breeding. 2019;23(7):846-855. DOI 10.18699/VJ19.558. (in Russian)Jiang J., Friebe B., Gill B.S. Recent advances in alien gene transfer inwheat. Euphytica. 1993;73:199-212. DOI 10.1007/BF00036700.Koyshybaev M., Shamanin V.P., Morgunov A.I. Wheat Screeningfor Resistance to Major Diseases: Guidelines. Ankara: FAO-SEKPubl., 2014. (in Russian)Kroupin P., Kuznetsova V., Romanov D., Kocheshkova A., KarlovG., Dang T.X., Khuat T.M.L., Kirov I., Alexandrov O., PolkhovskiyA., Razumova O., Divashuk M. Pipeline for the rapiddevelopment of cytogenetic markers using genomic data of relatedspecies. Genes. 2019;10(2):113. DOI 10.3390/genes10020113.Krupin P.Yu., Divashuk M.G., Belov V.I., Zhemchuzhina A.I., KovalenkoE.D., Upelniek V.P., Karlov G.I. Investigation of intermediarywheat-Agropyron hybrids on resistance to leaf rust. Sel\u2019skokhozyaistvennayaBiologiya = Agricultural Biology. 2013;48(1):68-73. DOI 10.15389/agrobiology.2013.1.68eng.Krupin P.Yu., Divashuk M.G., Karlov G.I. Gene resources of perennialwild cereals involved in breeding to improve wheat crop (review).Sel\u2019skokhozyaistvennaya Biologiya = Agricultural Biology. 2019;54(3):409-425. DOI 10.15389/agrobiology.2019.3.409eng.Kuperman F.M. Physiology of the development, growth and organogenesisof wheat. In: Henkel P.A. (Ed.). Wheat Physiology.IV. Physiologyof Agricultural Plants. Moscow: Moscow UniversityPubl., 1969;7-193. (in Russian)Leonova I.N. Influence of alien genetic material on the manifestationof agronomically important traits of common wheat (T. aestivumL.). Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journalof Geneticsand Breeding. 2018;22(3):321-328. DOI 10.18699/VJ18.367. (in Russian)Leonova I.N. Influence of alien genetic material on the manifestationof agronomically important traits of common wheat (T. aestivumL.). Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journalof Geneticsand Breeding. 2018;22(3):321-328. DOI 10.18699/VJ18.367. (in Russian)Leonova I.N. Genome-wide association study of powdery mildewresistance in Russian spring wheat varieties (T. aestivum L.).Russ. J. Genet. 2019;55(11):1360-1374. DOI 10.1134/S1022795419110085.Leonova I.N., Stasyuk A.I., Skolotneva E.S., Salina E.A. Enhancementof leaf rust resistance of Siberian winter wheat varieties bymarker-assisted selection. Cereal Res. Commun. 2017;45(4):621-632. DOI 10.1556/0806.45.2017.048.Li D., Long D., Li T., Wu Y., Wang Y., Zeng J., Xu L., Fan X., Sha L.,Zhang H., Zhou Y., Kang H. Cytogenetics and stripe rust resistanceof wheat-Thinopyrum elongatum hybrid derivatives. Mol.Cytogenet.2018;11:16. DOI 10.1186/s13039-018-0366-4.Li G., Wang H., Lang T., Li J., La S., Yang E., Yang Z. New molecularmarkers and cytogenetic probes enable chromosome identificationof wheat-Thinopyrum intermedium introgression lines for improvingprotein and gluten contents. Planta. 2016;244:865-876.DOI 10.1007/s00425-016-2554-yLi H., Wang X. Thinopyrum ponticum and Th. intermedium: the promisingsource of resistance to fungal and viral diseases of wheat.J. Genet. Genomics. 2009;36(9):557-565. DOI 10.1016/S1673-8527(08)60147-2.Liu C., Yang Z.J., Li G.R., Feng J., Zhou J.P., Ren Z.L. A discussionon genetic relationship in genome between Thinopyrum andDasypyrum. Chinese High Tech. Lett. 2007;17:295-300.Ma H., Zhang J., Zhang J., Zhou S., Han H., Liu W., Yang X., Li X.,Li L. Development of P genome-specific SNPs and their applicationin tracing Agropyron cristatum introgressions in commonwheat. Crop J. 2019;7(2):151-162. DOI 10.1016/j.cj.2018.07.003.Martinek P., Watanabe N., Peng Z.S. Gene resources of wheat (Triticumaestivum L.) with different arrangement of spikelets in spike.In: 7th International Wheat Conference, Mar del Plata, 2005.Martynov S.P., Dobrotvorskaya T.V., Krupnov V.A. Genealogicalanalysisof the use of two wheatgrass (Agropyron) species incommonwheat (Triticum aestivum L.) breeding for disease resistance.Russ. J. Genet. 2016;52(2):154-163. DOI 10.1134/S1022795416020071.Philipp N., Weichert H., Bohra U., Weschke W., Schulthess A.W.,WeberH. Grain number and grain yield distribution along thespike remain stable despite breeding for high yield in winterwheat. PLoS One. 2018;13(10):e0205452. DOI 10.1371/journal.pone.0205452.Piskarev V.V., Boyko N.I., Kondratieva I.V. Sources of agronomicallyimportant traits for breeding of soft spring wheat (Triticum aestivumL.) in the forest steppe of Novosibirsk region. VavilovskiiZhurnal Genetiki i Selektsii = Vavilov Journal of Genetics andBreeding. 2016;20(3):277-285. DOI 10.18699/VJ16.166. (in Russian)Plakhotnik V.V., Zeleneva Yu.V., Sudnikova V.P. Sources and highperformance donors for spring wheat selection to increase resistanceto stress factors of environment. Voprosy Sovremennoj Naukii Praktiki.Universitet imeni V.I. Vernadskogo = Problems ofContemporary Science and Practice. Vernadsky University. 2014;1(50):109-113. (in Russian)Roelfs A.P., Singh R.P., Saari E.E. Rust Diseases of Wheat: Conceptsand Methods of Disease Management. Mexico: CIMMYT, 1992Sakuma S., Golan G., Guo Z., Ogawa T., Tagiri A., Sugimoto K.,BernhardtN., Brassac J., Mascher M., Hensel G., Ohnishi S.,Jinno H., Yamashita Y., Ayalon I., Peleg Z., Schnurbush T., KomatsudaT. Unleashing floret fertility in wheat through the mutationof a homeobox gene. Proc. Natl. Acad. Sci. USA. 2019;116(11):5182-5187. DOI 10.1073/pnas.1815465116Salina E.A., Adonina I.G., Badaeva E.D., Kroupin P.Yu., Stasyuk A.I.,Leonova I.N., Shishkina A.A., Divashuk M.G., Starikova E.V.,Khuat T.M.L., Syukov V.V., Karlov G.I. A Thinopyrum intermediumchromosome in bread wheat cultivars as a source of genesconferring resistance to fungal diseases. Euphytica. 2015;204:91-101. DOI 10.1007/s10681-014-1344-5.Salina E.A., Leonova I.N., Shcherban A.B., Stasyuk A.I. Patent RU2598275 C1. Method of creating lines of winter soft wheat withcomplex resistance to brown and stem rust and powdery mildew. Date of filing:29.07.2015. Date of publication: 20.09.2016. Bull. No. 26. (inRussian)Sibikeev S.N., Badaeva E.D., Gultyaeva E.I., Druzhin A.E.,ShishkinaA.A., Dragovich A.Yu., Kroupin P.Yu., Karlov G.I.,Thi Mai Khuat, Divashuk M.G. Comparative analysis of Agropyronintermedium (Host) Beauv 6Agi and 6Agi2 chromosomes inbread wheat cultivars and lines with wheat\u2013wheatgrass substitutions.Russ. J. Genet. 2017;53(3):314-324. DOI 10.1134/S1022795417030115.Sinigovets M.E. Transferring wheatgrass rust resistance to wheat byadding and replacing chromosomes. Genetika = Genetics (Moscow).1976;12(9):13-20. (in Russian)Sinigovets M.E. Cytogenetic fundamentals of using wheatgrass inwheat improvement. Dr. Biol. Sci. Diss. Bol\u2019shie Vyazemy, 1988.OD 71 89-3/185. Available at: https://search.rsl.ru/ru/record/01008509447. (in Russian)Skolotneva E.S., Kelbin V.N., Morgunov A.I., Boiko N.I., ShamaninV.P., Salina \u0415.\u0410. Races composition of the Novosibirsk populationof Puccinia graminis f. sp. tritici. Mikologiya i Fitopatologiya= Mycology and Phytopathology. 2020;54(1):49-58. DOI10.31857/S0026364820010092. (in Russian)Sreenivasulu N., Schnurbusch T. A genetic playground for enhancinggrain number in cereals. Trends Plant Sci. 2012;17(2):91-101.DOI 10.1016/j.tplants.2011.11.003Stasyuk \u0410.I., Leonova I.N., Salina \u0415.\u0410. Variability of agronomicallyimportant traits in spring wheat hybrids obtained by marker-assistedselection from crosses of winter wheat with spring wheatdonors of resistance genes. Sel\u2019skokhozyaistvennaya Biologiya =Agricultural Biology. 2017;52(3):526-534. DOI 10.15389/agrobiology.2017.3. 526eng.State Standard 9353-2016. Wheat: Specifications. 2018. Availableat: http://docs.cntd.ru/document/1200139414 (in Russian)State Standard 26574-2017. Wheat Bakery Flour: Specifications(amended). 2019. Available at: http://docs.cntd.ru/document/1200157423 (in Russian)Sukumaran S., Lopes M., Dreisigacker S., Reynolds M. Geneticanalysis of multi environmental spring wheat trials identifiesgenomic regions for locus-specific tradeoffs for grain weightand grain number. Theor. Appl. Genet. 2018;131:985-998. DOI10.1007/s00122-017-3037-7.Syukov V.V., Shabolkina E.N., Shevchenko S.N., Vyushkov A.A.Spring soft wheat Tulaykovskaya 110. Molodoy Uchenyy = YoungScientist. 2016;27.3:57-60. (in Russian)Tsitsin N.V. Remote Hybridization of Plants. Moscow: SelkhozgizPubl., 1954;3-64. (in Russian)Ugarte C.C., Trupkin S.A., Ghiglione H., Slafer G., Casal J.J. Lowred/far-red ratios delay spike and stem growth in wheat. J. Exp.Bot. 2010;61(11):3151-3162. DOI 10.1093/jxb/erq140.Upelniek V.P., Belov V.I., Ivanova L.P., Dolgova S.P., Demidov A.S.Heritage of academician N.V. Tsitsin: state-of-the-art and potentialof the collection of intermediate wheat \u00d7 couch-grass hybrids.Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Geneticsand Breeding. 2012;16(3):667-674. (in Russian)Volkova L.V., Bebyakin V.M., Lyskova I.V. Plasticity and stabilityof spring wheat varieties and breeding forms according to grainproductivity and quality. Russ. Agricult. Sci. 2010;36(1):1-4. DOI10.3103/S1068367410010015.Wang M.J., Zhang Y., Lin Z.S., Ye X.G., Yuan Y.P., Ma W., Xin Z.Y.Development of EST-PCR markers for Thinopyrum intermediumchromosome 2Ai#2 and their application in characterization ofnovelwheat-grass recombinants. Theor. Appl. Genet. 2010;121:1369-1380. DOI 10.1007/s00122-010-1394-6.Wang R.R.C. Agropyron and Psathyrostachys. In: Kole C. (Ed.). WildCrop Relatives: Genomic Breeding Resources. Springer, Berlin,Heidelberg, 2011;77-108. DOI 10.1007/978-3-642-14228-4_2Wolde G.M., Mascher M., Schnurbusch T. Genetic modification ofspikelet arrangement in wheat increases grain number without significantly affecting grain weight. Mol. Genet. Genomics. 2019;294:457-468. DOI 10.1007/s00438-018-1523-5.Wu J., Yang X., Wang H., Li H., Li L., Li X., Liu W. The introgressionof chromosome 6P specifying for increased numbers offlorets and kernels from Agropyron cristatum into wheat. Theor.Appl. Genet. 2006;114:13-20. DOI 10.1007/s00122-006-0405-0.Zeleneva Yu.V. Substantiation of the genetic protection of wheatfrom diseases in the Central Chernozem Belt. Dr. Biol. Sci. Diss.St. Petesburg; Pushkin, 2019. Available at: https://rusneb.ru/catalog/000200_000018_RU_NLR_BIBL_A_012131792/ (in Russian)Zeng J., Cao W., Fedak G., Sun S., Mccallum B., Fetch T., Xue A.,Zhou Y. Molecular cytological characterization of two novel durum\u2013 Thinopyrum intermedium partial amphiploids with resistanceto leaf rust, stem rust and Fusarium head blight. Hereditas.2013;150(1):10-16. DOI 10.1111/j.1601-5223.2012.02262.x.Zeng Z.-X., Yang Z.-J., Hu L.-J., Liu C., Li G.R., Ren Z.-L. Developmentof St genome specific ISSR marker. Acta Bot. Boreal. Occident.Sin. 2008;28(8):1533-1540.Zhang P., Li W., Fellers J., Friebe B., Gill B.S. BAC-FISH in wheatidentifies chromosome landmarks consisting of different types oftransposable elements. Chromosoma. 2004;112:288-299. DOI10.1007/s00412-004-0273-9.Zhang Z.Y., Xin Z.Y., Larkin P.J. Molecular characterization ofa Thinopyrum intermedium group 2 chromosome (2Ai-2) conferringresistance to barley yellow dwarf virus. Genome. 2001;44(6):1129-1135. DOI 10.1139/g01-083.Zheng Q., Lv Z., Niu Z., Li B., Li H., Xu S.S., Han F., Li Z. Molecularcytogenetic characterization and stem rust resistance offive wheat-Thinopyrum ponticum partial amphiploids. J. Genet.Genomics. 2014;41(11):591-599. DOI 10.1016/j.jgg.2014.06.003."} +{"text": "Wart (a disease caused by Synchytrium endobioticum) and golden cyst potato nematode (Globodera rostochiensis),which parasitize the roots of the host plant, cause signif icant damage to potato crop. Both of these diseasefactors are quarantined in the Russian Federation, and each registered variety is tested for resistance to their mostcommon races and pathotypes. The main method of opposing such diseases is by the development of resistant varieties.An important step in this process is the selection of resistant genotypes from the population and the estimationof the resistance of hybrids obtained by crosses during the breeding process. Conducting a permanent phenotypicevaluation is associated with diff iculties, for example, it is not always possible to work with pathogens, and phenotypicevaluation is very costly and time consuming. However, the use of DNA markers linked to resistance genes cansignif icantly speed up and reduce the cost of the breeding process. The aim of the study was to screen the GenAgropotato collection of ICG SB RAS using known diagnostic PCR markers linked to golden potato cyst nematode and wartresistance. Genotyping was carried out on 73 potato samples using three DNA markers 57R, CP113, Gro1-4 associatedwith nematode resistance and one marker, NL25, associated with wart resistance. The genotyping data were comparedwith the data on the resistance of the collection samples. Only the 57R marker had a high level of correlation between resistance and the presence of a diagnostic fragment. The diagnosticeff iciency of the 57R marker was 86.11 %. This marker can be successfully used for screening a collection, searchingfor resistant genotypes and marker-assisted selection. The other markers showed a low correlation between the presenceof the DNA marker and resistance. The diagnostic eff iciency of the CP113 marker was only 44.44 %. Spearman\u2019scorrelation coeff icient did not show signif icant correlation betweenresistance and the DNA marker. The diagnostic eff iciency of the NL25 marker was 61.11 %. No signif icant correlationwas found between the NL25 marker and resistance . The use of thesemarkers for the search for resistant samples is not advisable. Potato is one of the most important crops in the world andis the world\u2019s fifth largest staple food crop by volume . One of the possible reasons fora decrease in yield is the damage of potatoes by various factors.Especially dangerous for potatoes are golden potato cystnematode (Globodera rostochiensis) and potato wart (pathogen\u2013 Synchytrium endobioticum). They are quarantined in theRussian Federation. Data on resistance to G. rostochiensis andS. endobioticum are required when registering a potato varietyin the State Register of Selection Achievements Authorizedfor Use .Potato cyst nematode (PCN) can cause significant damageto the potato yield, which can reach 80\u201390 % . Today, 5 pathotypes of this pestare known in the world: Ro1, Ro2, Ro3, Ro4, Ro5 , while in Russia only the Ro1pathotype of PCN has been detected at the moment .Potato wart affects from 35 to 100 % of the yield. There are 43 wart pathogensin Europe today . Only a few varietiesaffected by this disease are registered in the State Registerof Selection Achievements .One of the main methods of dealing with these pests isthe development of resistant potato varieties. Accordingly,it is important to detect genes responsible for resistance toPCN, study their heritability, develop DNA markers linkedto these genes, and use genes in breeding in marker-assistedselection schemes.The potato has 7 loci of resistance to PCN on chromosomesIII ), V , H1 ,GroV1 ), VII ), X ),XI ). Four loci provide partial resistance, while three others give high resistance toone or more pathotypes . DNA markers havemade it possible to identify complex loci containing severalR-genes, including a locus containing two genes for PCN resistance, which was identified on chromosome Vin two different potato species .The H1 resistance gene is introgressed into breeding varietiesfrom Solanum tuberosum ssp. andigenum and S. vernei. This gene is dominant anddetermines resistance to pathotypes Ro1 and Ro4 of G. rostochiensis; according to other data, it determines resistanceto pathotypes Ro5 and Ro6 . This gene is located at the distal part of thelong arm of the V chromosome and encodes the CC-NBS-LRR protein (coiledcoil/nucleotide-binding/leucine-rich repeat). The H1 gene isthe only nematode resistance gene for which Flora\u2019s geneto-gene interaction concept has been validated by classicalgenetic analysis . The H1 resistance gene corresponded to theAvr gene of golden potato cyst nematode G. rostochiensis.The GroV1 gene originates from the wild potato speciesS. vernei, is linked to the H1 locus ,and is responsible for resistance to the Ro1 pathotype ofG. rostochiensis .The Gro1 locus is localized on chromosome VII andcontains a family of genes Gro1-1, Gro1-2, Gro1-3, Gro1-4,Gro1-5, Gro1-6, Gro1-8, Gro1-10, Gro1-11, Gro1-12 andGro1-14, as well as a number of pseudogenes . J. Paal andcolleagues showed that the Gro1-4 gene is a monogenicdominant gene responsible for resistance to the Ro1 pathotypeof G. rostochiensis and encodes a protein belonging to theTIR-NB-LRR class of proteins. Gro1-4 was introduced into S. tuberosum from the wild potato S. spegazzinii .A number of loci of quantitative traits associated with resistanceto cyst nematodes were mapped in the potato genome:Gro1.2, Gro1.3, and Gro1.4 determining resistance to G. rostochiensiswere localized on chromosomes X, XI, and III. Inthis case, S. spegazzinii was the source of resistance .The Grp1 locus provides a broad spectrum of resistance toboth cyst nematodes G. rostochiensis and G. pallida. It hasbeen mapped to chromosome V and determines resistance to the Ro5 pathotypeof G. rostochiensis .A significant number of diagnostic DNA markers have beendeveloped for the H1 gene. Among them are markers CD78, TG689 , N146, N195 , CP113 , TG689/TG689indel12 , 239E4left , EM15 (repulsion) and CMI (coupling) , 57R . Markers have also been designed forother genes and QTLs. For example, markers TG69 , SCAR-U14, and SCAR-X02 have been developedfor the GroV1 gene ; markers CP56 and St3.3.2 , CP56, CP51(c), GP516(c) were selectedfor the Gro1 locus . MarkersGro1-4 and Gro1-4-1 were designed forthe Gro1-4 gene. For Grp1-QTL, markers GP21 and GP179, TG432 have been developed.The TG63 marker was selected for Gro1.2-QTL . Markers Ssp75 and TG30 have been developedfor Gro1.3-QTL . The Ssp8 marker wasdesigned for Gro1.4-QTL .A number of genes for resistance to wart (S. endobioticum)have been found in potatoes. These are the followinggenes: Sen1, located on the XI chromosome ; Sen1- 4 mapped to chromosome IV ; locus Sen18-IX, located on chromosome IX; locusSen2/6/18- I, located on chromosome I ;locus Xla-TNL found on chromosome XI ; the Sen2 locus mapped to chromosome XI ; the Sen3 locus was mapped on chromosome XIin the same region as the Sen1 gene ; the authors suggested that Sen3 could be either a Sen1paralogue from the same cluster or an allelic variant of theSen1 gene.QTLs responsible for resistance to races 1, 2, 6 and 18 ofwart are found on other chromosomes: chromosome I (torace 2), chromosome II , chromosome VI , chromosome VII , chromosomeVIII , chromosome X , chromosome XI .J.E. Obidiegwu and colleagues also found additional wartresistance loci on chromosomes I, IV, X, XI, and XII thatwere less influential than the main genes . Minor QTLs located on the chromosome X furtheraffect resistance to race 18 of wart .The Sen1 and Sen1-4 genes determine the resistance torace 1 of the potato wart pathogen; in both cases, resistanceis determined by the dominant alleles of the genes. The Sen1gene is located at the distal part of the long arm of chromosomeXI . However,it should be noted that J.E. Obidiegwu et al. (2015), usinggenome-wide association studies (GWAS), identified theSen1/ RSe-XIa multi-allelic locus on potato chromosome XIas the main factor of resistance to four S. endobioticum races . The Sen1-4gene is located on the long arm of chromosome IV at a distanceof 5 cM from the centromere .The Xla-TNL locus on potato chromosome XI is linked toresistance to races 18 and 6 and can be considered as one ofthe main factors of wart resistance .The Sen2 locus is mapped to chromosome XI and isa dominant monogenic locus that provides a high level ofresistance to eight races of S. endobioticum simultaneously:1 (D1), 2 (G1), 6 (O1), 8 (F1), 18 (T1), 2 (Ch1), 3 (M1) and39 (P1). The genetic and physical distances between the Sen1and Sen2 loci were indirectly estimated at 63 cM and 32 Mbp,respectively .Sen3 is a dominant monogenic locus of resistance to races 2,6, and 18 . Locus Sen18-IX (chromosomeIX) determines resistance to race 18 S. endobioticum,and locus Sen2/6/18-I (chromosome I) to races 2, 6, and 18.A. Ballvora et al. (2011) note that resistances to races 2, 6and 18 correlate with each other, but are inherited regardlessof resistance to race 1.Several markers have been developed to detect the dominantallele of the Sen1 gene: CP58, GP125 ,NL25 , Sti046, St_At5g16710, GP125 and GP259 . Also, using a genome-wide association studies,a haplotype-specific marker PotVar0067008 associated withSen1 was identified .To identify the Sen18-IX locus, markers GP129, GP101and STM3023b can be used. The Sen2/6/18-I locus can bediagnosed using markers STM2030, SC176, GP192, GP124,and GP194 . Markers Kc8103 and RK36,located on chromosome XI and linked to the Xla-TNL locus,have shown potential diagnostic value in determining resistanceto races 18 and 6 of S. endobioticum . Three markers, 5450_3, 2502_1, and 2502_3, linked tothe Sen2 locus were developed . It is possibleto use the markers chr11_1259552 and chr11_1772869to detect Sen3 .The aim of the study was to screen the GenAgro potato collectionof the Institute of Cytology and Genetics of the SiberianBranch of the Russian Academy of Sciences (ICG SB RAS)using known diagnostic PCR markers linked to resistance togolden cyst potato nematode and potato wart.Plant material. The research material was the collection ofvarieties and hybrids of potatoes named the \u201cGenAgro\u201d plantcollection of the ICG SB RAS. The collection was representedby 73 varieties and hybrids of potatoes (Solanum tuberosum)(Supplement 1)1. The plants were grown in the field on theterritory of the Michurinsky village, Novosibirsk region, fromMay to August 2017.http://vavilov.elpub.ru/jour/manager/f iles/Suppl_Totsky_Engl.pdfSupplementary Materials are available in the online version of the paper:Field tests were carried out according to the followingscheme: the number of rows for each genotype was two; thenumber of plants in a row \u2013 10; row length \u2013 3 m; distancebetween the rows \u2013 0.75 m; distance between the plants inrows \u2013 0.30 m; planting method \u2013 manually (by hand) on furrows,filling furrows with harrows; landing date is the thirddecade of May.Agrochemical characteristics of the soil: the content ofexchanged potassium 110.00 mg/kg; the amount of exchangedbases 24.19 mg-eq/100 g; hydrolytic acidity 3.23 mg-eq/100 g;exchanged acidity 5.60 mg-eq/100 g; humus content 2.67 %;the content of mobile phosphorus 5.14 mg/kg; the degree ofsaturation with bases (V) 88.20 %.Most of the data on resistance to PCN and potato wart weretaken from references, namely from the database of the StateRegister of Selection Achievements Authorized for Use , and from the EuropeanCultivated Potato Database (https://www.europotato.org/).Some of the samples and hybrids for which there were nopublished data on resistance were evaluated under experimentalconditions. Determination of resistance to PCN wascarried out in accordance with the methodology recommendedby OEPP/EPPO (2006) at the All-Russian Institute of PlantProtection. Potato wart resistance was evaluated accordingto the Glynn\u2013Lemmerzahl method as described in the EPPODiagnostic protocol for S. endobioticum at the Russian Potato Research Center.DNA isolation and PCR analysis. DNA was isolated fromthe skin of potato tubers using the DNeasy Plant Mini kit according to the protocol. The concentrationand purity of the tested samples were determined using gelelectrophoresis and a Nanodrop 2000 apparatus.Several diagnostic markers most often used in breedingprograms were selected for genotyping (Table 1). These markerswere associated with R-genes that determine resistanceto race 1 of potato wart (S. endobioticum) and Ro1 pathotypeof potato cyst nematode (G. rostochiensis).Two markers, 57R and CP113, associated with the H1 resistancegene, and the Gro1-4 marker, associated with theGro1-4 resistance gene, were selected to identify PCN resistancegenes (see Table 1). The SCAR PCR marker CP113-5\u20192/CP113-3\u20192 was proposed by J. Niew\u00f6hner et al. (1995) basedon the RFLP marker CP113. Amplification of DNA of resistantgenotypes using this marker formed product with a 760 bplength. The 57R marker was proposed by L. Schultz et al.(2012). Amplification of DNA of resistant genotypes formedproduct with a 450 bp length. SCAR PCR marker Gro1-4 wasdeveloped by J. Paal et al. (2004) based on the RFLP markerGro1. Amplification of DNA of resistant genotypes formedproduct with a 602 bp length.The NL25 marker was proposed by R. Hehl et al. (1999)when mapping the Sen1 gene. C.A. Bormann et al. (2004)and C. Gebhardt et al. (2006) used this marker for markerassistedselection (see Table 1). Amplification produces oneor two fragments of 1200 or 1400 bp lenght. The presenceof the dominant Sen1 allele is determined by the presence ofa 1400 bp fragment.PCR was carried out in a 20 \u03bcL reaction mixture containing100 ng of DNA, 67 mM Tris-HCl (pH 8.8), 1.8 mM MgCl2,0.01 % Tween 20, 0.2 mM each dNTP, 0.25 \u03bcM forward andreverse specific primers, 1 unit Taq DNA polymerase.Two types of amplification programs (SSR55 and SSR60)represented the time-temperature profile of PCR. SSR55:(1) first cycle: 94 \u00b0C \u2013 2 min; (2) the next 45 cycles: 94 \u00b0\u0421 \u20131 minute, 55 \u00b0\u0421 \u2013 1 minute and 72 \u00b0\u0421 \u2013 2 minutes; (3) onecycle of 5 minutes at 72 \u00b0C (Gro1-4). SSR60: (1) first cycle:94 \u00b0C \u2013 2 min; (2) the next 45 cycles: 94 \u00b0\u0421 \u2013 1 minute, 60 \u00b0\u0421 \u20131 minute and 72 \u00b0\u0421 \u2013 2 minutes; (3) one cycle of 5 minutesat 72 \u00b0C .The analysis of the obtained PCR products was carriedout by electrophoresis in a 2 % agarose gel. The results weredocumented using a Molecular Imager Gel Doc XR System(BioRad) using UV light.Statistical processing of the data was carried out usingSpearman\u2019s correlation coefficient; for calculations, theSTATISTICA program was used. The diagnostic efficiency,sensitivity, specificity and predictive value were calculatedusing the MedCalc softwarehttps://www.medcalc.org/Diagnostic efficiency was defined as the proportion of correcttest results in the total number of test results, or the sum oftrue positive and true negative test results divided by the totalnumber of test results. The sensitivity was calculated as thenumber of resistant samples identified using a DNA markerdivided by the total number of resistant samples. Specificityis the number of susceptible samples identified by the DNAmarker divided by the total number of susceptible samples.Positive predictive value was defined as the proportion ofcorrect positive diagnostic test results.Among 73 samples selected for genotyping, 35 were resistantto PCN, 37 samples were susceptible, and in one sample,resistance to nematodes was unknown (Table 2). 69 sampleswere resistant to wart, 3 samples were susceptible to disease,the resistance of one sample was unknown (see Table 2).Genotyping of varieties and hybridsusing markers designed for resistance to PCNThe 57R marker is found in 85.7 % of resistant samples, aswell as in 13.5 % of susceptible ones . Some mismatches can be observeddue to the absence of linkage of the 57R marker with the H1resistance gene in a number of samples. The second reason forthe mismatches can be explained by the presence of other resistancegenes in samples that do not carry the 57R marker. Thediagnostic efficiency of the 57R marker, which is expressedas the percentage of true (both positive and negative) testresults to the total number of results obtained, was 86.11 %.The diagnostic sensitivity of the used marker, which shows thenumber of resistant samples identified using the DNA marker divided by the total number of resistant samples, was 85.71 %.The diagnostic specificity, which is the number of susceptiblesamples identified by the DNA marker divided by the totalnumber of susceptible samples, was 86.48 %. The predictivevalue of a positive result, showing the proportion of correctpositive diagnostic test results, was 85.71 %. Calculation ofthe Spearman correlation coefficient showed a significant correlation betweenresistance and the 57R marker.The CP113 marker is found in only 48.6 % of resistant accessions,while the marker is present in 62.9 % of susceptiblegenotypes .These results can be regarded as the absence of linkage of themarker with the H1 resistance gene in many samples of the potatocollection. The diagnostic efficiency of the CP113 markerwas only 44.44 %. Diagnostic sensitivity was 48.57 %. Diagnosticspecificity accounted for 40.54 %. The predictive valueof a positive result, indicating the probability of resistancepresence if the test shows a positive result when CP113 markerwas used, was equal to 43.58 %. Spearman\u2019s correlation coefficient inthis case showed no significant correlation between resistanceand DNA marker. The use of such a marker when screeninga population to search for resistant samples is not advisable.29 samples were analyzed using the Gro1-4 marker. Thediagnostic fragment was amplified in only 5 samples. Correspondenceof the presence of the marker in the resistantsample was observed only in 1 case out of 5. In other cases,the marker was found in the samples susceptible to the disease.The data obtained show that when screening populationsfor resistance to PCN, it is advisable to use the 57R marker.Genotyping of varieties and hybridsusing markers linked to resistance to potato wart The NL25 marker is found in 62.3 % of resistant samples,however, the marker is present in two of the three susceptiblegenotypes . This can be explainedby the processes of crossing over and by the fact that in a numberof samples the linkage of the marker and the resistancegene is not observed; however, the small number of sensitivesamples does not allow sufficiently assessing the applicabilityof the marker for breeding. The marker is absent in 27 samplesand only in one case we observe the absence of a marker in thesusceptible sample, in the other cases the marker is absent inthe resistant samples. This can be explained by the presence ofanother resistance gene that is not linked to the NL25 marker.The diagnostic efficiency of resistance using the NL25 markerwas 61.11 %. The diagnostic sensitivity turned out to beat 62.31 %. The diagnostic specificity was only 33.33 %.However, the predictive value of a positive result, showingthe proportion of correct positive diagnostic test results, whenusing the NL25 marker was equal to 95.55 %. It should benoted that such results are associated with the fact that the setof samples contained only three sensitive samples, and twoof them showed the presence of the NL25 marker. Spearman\u2019scorrelation coefficient in such situation showed the absenceof significant correlations.Despite the fact that the NL25 marker is often used inscreening and marker selection, a study in our set of samplesshowed that its use does not guarantee a reliable result.In our study, 13 resistant to golden potato nematode samplesthat had both markers (57R and CP113) linked to the H1nematode resistance gene were found. In addition, there are8 genotypes resistant to nematodes and wart and carryingboth the 57R and CP113 markers linked to the H1 nematoderesistance gene and the NL25 marker linked to the Sen1 wartresistance gene. There is also one sample (Safo) in the populationthat is resistant to wart and nematodes and carries all threemarkers 57R, CP113, Gro1-4, linked to nematode resistance,and marker NL25, linked to wart resistance.The NL25 marker linked to the Sen1 gene, which providesresistance to pathotype 1 of potato wart, is successfully usedin the practice of marker-oriented selection. So, C. Gebhardtand colleagues reported that after screening 17 plants in twofamilies of segregating populations using the NL25 marker, 14 genotypes with the marker were identified. All these plantswere found to be resistant to pathotype 1 S. endobioticum.Some were also resistant to pathotype 2 and/or pathotype 6.The effectiveness of this marker is also reported by O.Y. Antonovaand colleagues who analyzed 98 varieties using theNL25 marker. A diagnostic component was found in 95 studiedwart-resistant varieties, while it was not found in threesusceptible varieties. This shows a high level of correlationbetween the presence or absence of the marker and the resistanceand sensitivity of the genotype to wart, respectively.However, A. Khiutti and colleagues, when screening 52 genotypesusing the NL25 marker, found that 39 samples (bothsensitive and resistant genotypes) had the same nondiagnosticfragment, 12 genotypes did not have amplification of theNL25 marker fragments. Only 5 out of 52 genotypes hada diagnostic fragment indicating the presence of a resistancegene. Four of these five accessions were resistant, but onegenotype was found to be sensitive; most resistant genotypesdid not have a 1400 bp diagnostic fragment predicting a resistantphenotype .Our analysis also did not allow us to speak about the reliabilityof using the NL25 marker for screening resistantvarieties.Using the Gro1-4 marker in a segregating population, C. Gebhardtand colleagues found that all 45 plants carrying thismarker linked to the Gro1 gene were resistant to the Ro1 pathotypeof G. rostochiensis .C. Gebhardt and colleagues in 1993 found in a segregatingpopulation that the CP113 marker is linked to the H1 geneso strongly that it has zero recombination . However, D. Milczarek and colleagues (2011) reportedthat the CP113 marker was amplified for all tested varieties,resistant and sensitive, and was unsuitable for the selectionof resistant clones. A similar picture is observed in our work.The 57R SCAR marker was tested in a mapping population,where it was linked to the H1 locus and nematoderesistance . Later L. Schultzand colleagues reported that they analyzed two independentpopulations of 281 and 122 potato samples with knownresistance/sensitivity using the 57R SCAR marker. Whenscreening the first population, the 57R marker revealed a correspondencebetween genotype and phenotype, 89 out of90 resistant varieties had an allele associated with resistance.Only one resistant variety, in which no marker amplificationwas observed, became an exception. None of the 191 PCNsusceptible varieties had an allele predicting resistance. Thenanother independent population of 122 varieties was screened.All varieties showed complete correspondence between resistanceto G. rostochiensis and the presence/absence of the57R allele, corresponding to the presence of the resistancegene .O.Y. Antonova et al. (2016) identified the 57R markerin 33 (30.3 %) of 109 breeding varieties they studied. Theoverwhelming majority of the varieties with the diagnosed57R fragment were resistant or weakly affected by the nematode.The correspondence between resistance and the presenceof a diagnostic fragment was high \u2013 93.5 %. At the same time,only four genotypes with the Gro1-4 marker were identified:two resistant varieties, one weakly affected variety and onesusceptible. All these four varieties, along with the Gro1-4marker, also possessed the H1 gene markers \u2013 57R, TG689,N146, N195 .In the work of N.S. Klimenko et al. (2017) showed the presenceof the 57R marker in 24 out of 103 samples, while themarker was found in 15 resistant and 2 susceptible samples.It was shown that the correlation between the presence of atleast one marker of the H1 gene and the data on the nematoderesistance of varieties was +0.92 .T.A. Gavrilenko et al. (2018) showed that out of 39 samplesof the studied set of samples, 15 had a dominant allele ofthe H1 gene (based on a number of DNA markers), and twovarieties had dominant alleles of both H1 and Gro1-4 genes.At the same time, none of the markers was identified in theremaining 22 genotypes. Comparison of these results withresistance to G. rostochiensis (pathotype Ro1) showed thatall accessions with H1 gene markers are nematode resistant,while varieties affected by G. rostochiensis did not have thesemarkers . This high correlation shows the reliability of the markers used in the study, which can beused to select resistant samples.It should be noted that the saturation of the genotype withgenes of resistance to the nematode does not affect its economicallyvaluable traits. At the same time, there is a stronglink between the presence of the marker and resistance. So, inthe study of D. Milczarek and colleagues in 2014, the relationshipbetween the presence of markers TG689 and 57R linkedto the H1 gene, which determines resistance to the nematodeG. rostochiensis, and valuable agricultural traits is presented.Clones with these markers had a higher total yield of tubersand total starch yield than clones without markers. There wasno negative association between marker presence and quality.All 347 seedlings obtained after three crosses were genotypedusing both markers and phenotypically evaluated for resistanceto the Ro1 pathotype of G. rostochiensis. Of these, 316 (i. e.91 %) and 325 (94 %) clones were resistant and carried theTG689 or 57R markers .In general, our data on the 57R marker are quite close to theresults described above and confirm the high reliability ofthe work of this marker, which suggests the need to use thismarker when selecting samples resistant to PCN.The authors declare no conflict of interest.Antonova O.Y., Shvachko N.A., Novikova L.Y., Shuvalov O.Y., KostinaL.I., Klimenko N.S., Shuvalova A.R., Gavrilenko T.A. Geneticdiversity of potato varieties bred in Russia and its neighboring countriesbased on the polymorphism of SSR-loci and markers associatedwith resistance R-genes. Russ. J. Genet. Appl. Res. 2017;7(5):489-500. DOI 10.1134/S2079059717050021.Asano K., Kobayashi A., Tsuda S., Nishinaka M., Tamiya S. DNAmarker-assisted evaluation of potato genotypes for potential resistanceto potato cyst nematode pathotypes not yet invading into Japan.Breed. Sci. 2012;62(2):142-150. DOI 10.1270/jsbbs.62.142.Baayen R.P., Cochius G., Hendriks H., Meffert J.P., Bakker J., BekkerM., van den Boogert P.H.J.F., Stachewicz H., van LeeuwenG.C.M. History of potato wart disease in Europe \u2013 a proposalfor harmonisation in defining pathotypes. Eur. J. Plant Pathol.2006;116(1):21-31. DOI 10.1007/s10658-006-9039-y.Bakker E., Achenbach U., Bakker J., van Vliet J., Peleman J., Segers B.,van der Heijden S., van der Linde P., Graveland R., Hutten R., vanEck H., Coppoolse E., van der Vossen E., Bakker J., Goverse A.A high-resolution map of the H1 locus harbouring resistance to thepotato cyst nematode Globodera rostochiensis. Theor. Appl. Genet.2004;109(1):146-152. DOI 10.1007/s00122-004-1606-z. Epub 2004Feb 25.Ballvora A., Flath K., Lubeck J., Strahwald J., Tacke E., HofferbertH.- R., Gebhardt C. Multiple alleles for resistance and susceptibilitymodulate the defense response in the interaction of tetraploidpotato (Solanum tuberosum) with Synchytrium endobioticum pathotypes1, 2, 6 and 18. Theor. Appl. Genet. 2011;123(8):1281-1292.DOI 10.1007/s00122-011-1666-9. Epub 2011 Aug 6.Ballvora A., Hesselbach J., Niew\u00f6hner J., Leister D., Salamini F., GebhardtC. Marker enrichment and high-resolution map of the segmentof potato chromosome VII harbouring the nematode resistancegene Gro1. Mol. General Genet. 1995;249:82-90. DOI 10.1007/BF00290239.Barone A., Ritter E., Schachtschabel U., Debener T., Salamini F., GebhardtC. Localization by restriction fragment length polymorphismmapping in potato of a major dominant gene conferring resistanceto the potato cyst nematode Globodera rostochiensis. Mol. GeneralGenet. 1990;224(2):177-182. DOI 10.1007/BF00271550.Bartkiewicz A., Chilla F., Terefe-Ayana D., L\u00fcbeck J., Strahwald J.,Tacke E., Hoferbert H.-R., Flath K., Linde M., Debener T. Improvedgenetic resolution for linkage mapping of resistance to potato wartin monoparental dihaploids with potential diagnostic value in tetraploidpotato varieties. Theor. Appl. Genet. 2018;131:2555-2566.DOI 10.1007/s00122-018-3172-9.Bormann C.A., Rickert A.M., Ruiz R.A.C., Paal J., L\u00fcbeck J., StrahwaldJ., Buhr K., Gebhardt C. Tagging quantitative trait loci formaturity-corrected late blight resistance in tetraploid potato withPCR-based candidate gene markers. Mol. Plant-Microbe Interact.2004;17(10):1126-1138. DOI 10.1094/MPMI.2004.17.10.1126.Brugmans B., Hutten R.G.B., Rookmaker N., Visser R.G.F., vanEck H.J. Exploitation of a marker dense linkage map of potato forpositional cloning of a wart disease resistance gene. Theor. Appl.Genet. 2006;112(2):269-277. DOI 10.1007/s00122-005-0125-x.Finkers-Tomczak A., Bakker E., Boer J., Vossen E., Achenbach U.,Golas T., Suryaningrat S., Smant G., Bakker J., Goverse A. Comparativesequence analysis of the potato cyst nematode resistance locusH1 reveals a major lack of co-linearity between three haplotypesin potato (Solanum tuberosum ssp.). Theor. Appl. Genet. 2011;122:595-608. DOI 10.1007/s00122-010-1472-9.Finkers-Tomczak A., Danan S., van Dijk T., Beyene A., Bouwman L.,Overmars H., van Eck H., Goverse A., Bakker J., Bakker E. A highresolutionmap of the Grp1 locus on chromosome V of potato harbouringbroad-spectrum resistance to the cyst nematode speciesGlobodera pallida and Globodera rostochiensis. Theor. Appl. Genet.2009;119(1):165-173. DOI 10.1007/s00122-009-1026-1.Flor H.H. Current status of the gene-for-gene concept. Annu. Rev.Phytopathol. 1971;9:275-296. DOI 10.1146/annurev.py.09.090171.001423.Food and Agriculture Organization of the United Nations. World Foodand Agriculture \u2013 Statistical pocketbook 2019. Rome: FAO, 2019.Available at: http://www.fao.org/3/ca6463en/ca6463en.pdf.Galek R., Rurek M., De Jong W.S., Pietkiewicz G., Augustyniak H.,Sawicka-Sienkiewicz E. Application of DNA markers linked to thepotato H1 gene conferring resistance to pathotype Ro1 of Globoderarostochiensis. J. Appl. Genet. 2011;52(4):407-411. DOI 10.1007/s13353-011-0056-y.Gavrilenko \u0422.\u0410., Klimenko N.S., Antonova O.Yu., Lebedeva V.A.,EvdokimovaZ.Z., Gadjiyev N.M., Apalikova O.V., Alpatyeva N.V.,Kostina L.I., Zoteyeva N.M., Mamadbokirova F.T., Egorova K.V.Molecular screening of potato varieties bred in the northwesternzone of the Russian Feder\u0430tion. Vavilovskii Zhurnal Genetiki i Selektsii= Vavilov Journal of Genetics and Breeding. 2018;22(1):35-45.DOI 10.18699/VJ18.329. (in Russian)Gebhardt C., Ballvora A., Walkemeier B., Oberhagemann P., Sch\u00fcler K.Assessing genetic potential in germplasm collections of crop plantsby marker-trait association: a case study for potatoes with quantitativevariation of resistance to late blight and maturity type. Mol. Breed.2004;13:93-102. DOI 10.1023/B:MOLB.0000012878.89855.df.Gebhardt C., Bellin D., Henselewski H., Lehmann W., SchwarzfischerJ., Valkonen J. Marker-assisted combination of major genesfor pathogen resistance in potato. Theor. Appl. Genet. 2006;112(8):1458-1464. DOI 10.1007/s00122-006-0248-8. Epub 2006Mar 15.Gebhardt C., Mugniery D., Ritter E., Salamini F., Bonnel E. Identificationof RFLP markers closely linked to the H1 gene conferringresistance to Globodera rostochiensis in potato. Theor. Appl. Genet.1993;85:541-544. DOI 10.1007/BF00220911.Gebhardt C., Valkonen J.P.T. Organization of genes controlling diseaseresistance in the potato genome. Annu. Rev. Phytopathol. 2001;39:79-102. DOI 10.1146/annurev.phyto.39.1.79.Groth J., Song Y., Kellermann A., Schwarzfischer A. Molecular characterisationof resistance against potato wart races 1, 2, 6 and 18 ina tetraploid population of potato (Solanum tuberosum subsp. tuberosum).J. Appl. Genet. 2013;54(2):169-178. DOI 10.1007/s13353-013-0141-5. Epub 2013 Feb 24.Hampson \u041c.\u0421. History, biology and control of potato wart disease inCanada. Can. J. Plant Pathol. 1993;15(4):223-244. DOI 10.1080/07060669309501918.Hehl R., Faurie E., Hesselbach J., Salamini F., Whitham S., Baker B.,Gebhardt C. TMV resistance gene N homologues are linked to Synchytriumendobioticum resistance in potato. Theor. Appl. Genet.1999;98:379-386. DOI 10.1007/s001220051083.Jacobs J.M.E., Eck H.J., Horsman K., Arens P.F.P., Verkerk-Bakker B.,Jacobsen E., Pereira A., Stiekema W.J. Mapping of resistance to thepotato cyst nematode Globodera rostochiensis from the wild potatospecies Solanum vernei. Mol. Breed. 1996;2:51-60. DOI 10.1007/BF00171351.Janssen R., Bakker J., Gommers F.J. Mendelian proof for a gene-forgenerelationship between virulence of Globodera rostochiensisand the H1 resistance gene in Solanum tuberosum ssp. andigenaCPC 1673. Rev. de Nematol. 1991;14(2):207-211.Jones F.G.W., Parrott D.M., Perry J.N. The gene-for-gene relationshipand its significance for potato cyst nematodes and their solanaceoushosts. In: Zuckerman B.M., Rohde R.A. (Eds.). Plant Parasitic Nematodes.Vol. 3. New York: Acad. Press, 1981;23-36.Khiutti A., Afanasenko O., Antonova O., Shuvalov O., Novikova L.,Krylova E., Chalaya N., Mironenko N., Spooner D., Gavrilenko T.Characterization of resistance to Synchytrium endobioticum in cultivatedpotato accessions from the collection of Vavilov Institute ofPlant Industry. Plant Breed. 2012;131(6):744-750. DOI 10.1111/j.1439-0523.2012.02005.x.Khiutti \u0410.V., Antonova O.Yu., Mironenko N.V., Gavrilenko T.A.,Afanasenko O.S. Potato resistance to quarantine diseases. Russ. J.Genet. Appl. Res. 2017;7(8):833-844. DOI 10.1134/S2079059717050094.Klimenko N.S., Antonova O.Yu., Kostina L.I., Mamadbokirova F.T.,Gavrilenko T.A. Marker-assisted selection of Russian potato varietieswith markers of genes for resistance to potato golden nematode(pathotype Ro1). Trudy po Prikladnoy Botanike, Genetike i Selektsii= Proceedings on Applied Botany, Genetics, and Breeding.2017;178(4):66-75. DOI 10.30901/2227-8834-2017-4-66-75. (inRussian)Koretsky P.M. Harmfulness of potato wart in household plots in areasof widespread of the disease in Ukraine. Mikologiya i Fitopatologiya= Mycology and Phytopathology. 1970;4(4):366-369. (in Russian)Kort J., Stone A.R., Rumpenhorst H.J., Ross H. An international schemefor identifying and classifying pathotypes of potato cyst-nematodesGlobodera rostochiensis and G. pallida. Nematologica. 1977;23(3):333-339. DOI 10.1163/187529277x00057.Kreike C.M., De Koning J.R.A., Vinke J.H., Van Ooijen J.W., StiekemaW.J. Mapping of loci involved in quantitatively inherited resistanceto the potato cyst-nematode Globodera rostochiensis pathotypeRo1. Theor. Appl. Genet. 1993;87:464-470. DOI 10.1007/BF00215092.Kreike C.M., Kok-Westeneng A.A., Vinke J.H., Stiekema W.J. Mappingof QTLs involved in nematode resistance, tuber yield and rootdevelopment. Theor. Appl. Genet. 1996;92:463-470. DOI 10.1007/BF00223694.Kuhl J.C. Mapping and tagging of simply inherited traits. In: BradeenJ.M., Chittaranjan K. (Eds.). Genetics, Genomics and Breedingof Potato. Enfield, New Hampshire: Sci. Publishers, 2011;90-112.Leister D., Ballvora A., Salamini F., Gebhardt C. A PCR based approachfor isolating pathogen resistance genes from potato with potentialfor wide application in plants. Nat. Genet. 1996;14:421-429.DOI 10.1038/ng1296-421.Limantseva L., Mironenko N., Shuvalov O., Antonova O., Khiutti A.,Novikova L., Afanasenko O., Spooner D., Gavrilenko T. Characterizationof resistance to Globodera rostochiensis pathotype Ro1in cultivated and wild potato species accessions from the VavilovInstitute of Plant Industry. Plant Breed. 2014;133(5):660-665. DOI10.1111/pbr.12195.Lopez-Pardo R., Barandalla L., Ritter E., de Galarreta J.I.R. Validationof molecular markers for pathogen resistance in potato. Plant Breed.2013;132:246-251. DOI 10.1111/pbr.12062.Milczarek D., Flis B., Przetakiewicz A. Suitability of molecular markersfor selection of potatoes resistant to Globodera spp. Am. J.Potato Res. 2011;88:245-255. DOI 10.1007/s12230-011-9189-0.Milczarek D., Przetakiewicz A., Kaminski P., Flis B. Early selection ofpotato clones with the H1 resistance gene \u2013 the relation of nematoderesistance to quality characteristics. Czech J. Genet. Plant Breed.2014;50(4):278-284. DOI 10.17221/114/2014-CJGPB.Mori K., Sakamoto Y., Mukojima N., Tamiya S., Nakao T., Ishii T., HosakaK. Development of a multiplex PCR method for simultaneousdetection of diagnostic DNA markers of five disease and pest resistancegenes in potato. Euphytica. 2011;180:347-355. DOI 10.1007/s10681-011-0381-6.Niew\u00f6hner J., Salamini F., Gebhardt C. Development of PCR assaysdiagnostic for RFLP marker alleles closely linked to alleles Gro1and H1, conferring resistance to the root cyst nematode Globoderarostochiensis in potato. Mol. Breed. 1995;1:65-78. DOI 10.1007/BF01682090.Obidiegwu J.E., Flath K., Gebhardt C. Managing potato wart: a reviewof present research status and future perspective. Theor. Appl. Genet.2014\u037e127(4):763-780. DOI 10.1007/s00122-014-2268-0.Obidiegwu J.E., Sanetomo R., Flath K., Tacke E., Hoferbert H.-R.,Hofmann A., Walkemeier B., Gebhardt C. Genomic architecture ofpotato resistance to Synchytrium endobioticum disentangled usingSSR markers and the 8.3 k SolCAP SNP genotyping array. BMCGenet. 2015;16:38. DOI 10.1186/s12863-015-0195-y.OEPP/EPPO Standards PM 7/28. Diagnostic protocols for regulatedpests: Synchytrium endobioticum. Bulletin OEPP/EPPO Bulletin.2004;34:213-218. DOI 10.1111/j.1365-2338.2004.00722.x.OEPP/EPPO Testing of potato varieties to assess resistance to Globoderarostochiensis and Globodera pallida. Bulletin OEPP/EPPO Bulletin. 2006;36:419-420. DOI 10.1111/j.1365-2338.2006.01032.x.Paal J., Henselewski H., Muth J., Meksem K., Men\u00e9ndez C.M., SalaminiF., Ballvora A., Gebhardt C. Molecular cloning of the potatoGro1-4 gene conferring resistance to pathotype Ro1 of theroot cyst nematode Globodera rostochiensis, based on a candidategene approach. Plant J. 2004;38(2):285-297. DOI 10.1111/j.1365-313X.2004.02047.x.Pajerowska-Mukhtar K., Stich B., Achenbach U., Ballvora A., L\u00fcbeckJ., Strahwald J., Tacke E., Hofferbert H.-R., Ilarionova E., BellinD., Walkemeier B., Basekow R., Kersten B., Gebhardt C. Singlenucleotide polymorphisms in the allene oxide synthase 2 geneare associated with field resistance to late blight in populations oftetraploid potato cultivars. Genetics. 2009;181(3):1115-1127. DOI10.1534/genetics.108.094268.Pineda O., Bonierbale M.W., Plaisted R.L., Brodie B.B., Tanksley S.D.Identification of RFLP markers linked to the H1 gene conferringresistance to the potato cyst nematode Globodera rostochiensis.Genome. 1993;36(1):152-156. DOI 10.1139/g93-019.Plich J., Przetakiewicz J., \u015aliwka J., Flis B., Wasilewicz-Flis I., Zimnoch-Guzowska E. Novel gene Sen2 conferring broad-spectrumresistance to Synchytrium endobioticum mapped to potato chromosomeXI. Theor. Appl. Genet. 2018;131:2321-2331. DOI 10.1007/s00122-018-3154-y.Prodhomme C., Esselink D., Borm T., Visser R.G.F., van Eck H.J.,Vossen J.H. Comparative Subsequence Sets Analysis (CoSSA) isa robust approach to identify haplotype specific SNPs; mappingand pedigree analysis of a potato wart disease resistance gene Sen3.Plant Methods. 2019;15:60. DOI 10.1186/s13007-019-0445-5.Prodhomme C., Peter G.V., Paulo M.J., Visser R.G.F., Vossen J.H.,van Eck J.H. Distribution of P1(D1) wart disease resistance in potatogermplasm and GWAS identification of haplotype-specific SNPmarkers. Theor. Appl. Genet. 2020;133:1859-1871. DOI 10.1007/s00122-020-03559-3.Ramakrishnan A.P., Ritland C.E., Blas Sevillano R.H., Riseman A. Reviewof potato molecular markers to enhance trait selection. Am. J.Potato Res. 2015;92(4):455-472. DOI 10.1007/s12230-015-9455-7.Rouppe van der Voort J., Lindeman W., Folkertsma R., Hutten R., OvermarsH., van der Vossen E., Jacobsen E., Bakker J. A QTL for broadspectrumresistance to cyst nematode species (Globodera spp.) mapsto a resistance gene cluster in potato. Theor. Appl. Genet. 1998;96:654-661. DOI 10.1007/s001220050785.Rouppe van der Voort J., van der Vossen E., Bakker E., Overmars H.,van Zandvoort P., Hutten R., Klein Lankhorst R., Bakker J. Two additiveQTLs conferring broadspectrum resistance in potato to Globoderapallida are localized on resistance gene clusters. Theor. Appl.Genet. 2000;101:1122-1130. DOI 10.1007/s001220051588.Schultz L., Cogan N.\u041e.I., McLean K., Dale M.F.B., Bryan G.J., ForsterJ.W., Slater A.T. Evaluation and implementation of a potentialdiagnostic molecular marker for H1-conferred potato cyst nematoderesistance in potato (Solanum tuberosum L.). Plant Breed. 2012;131:315-321. DOI 10.1111/j.1439-0523.2012.01949.x.Skupinov\u00e1 S., Vejl P., Sedl\u00e1k P., Domk\u00e1\u0159ov\u00e1 J. Segregation of DNAmarkers of potato (Solanum tuberosum ssp. tuberosum L.) resistanceagainst Ro1 pathotype Globodera rostochiensis in selected F1progeny. Rostlinn\u00e1 V\u00fdroba. 2002;48(11):480-485. DOI 10.17221/4399-PSE.State Register of Selection Achievements Authorized for Use for ProductionPurposes. Vol. 1. Plant Varieties . Moscow:Rosinformagrotech Publ., 2019. (in Russian)Toxopeus H.J., Huijsman C.A. Breeding for resistance to potato rooteelworm. I. Preliminary data concerning the inheritance and thenature of resistance. Euphytica. 1953;2(3):180-186. DOI 10.1007/BF00053725."} +{"text": "Over 600,000 COVID-19 cases, including >7000 deaths reported to MN Dept of Health (MDH) by June 1, 2021. Clinical trials demonstrated high effectiveness of COVID vaccines. We assessed COVID-19 cases among fully vaccinated residents [vaccine breakthrough (VB) cases]. COVID-19 VB cases were MN residents with completed COVID-19 vaccination series \u226514 days prior to symptom onset or positive for SARS-CoV-2 by nucleic acid amplification or antigen test. COVID-19 cases were reported to MDH and COVID-19 vaccinations reported to the MN Immunization Information Connection (MIIC). COVID-19 cases were matched to MIIC to identify VB and interviewed; medical records of hospitalized cases were reviewed. Available VB case specimens underwent whole genome sequencing (WGS) at MDH or collaborating lab.Jan 19 \u2013 June 1, 2021, 2765 VB cases were reported among >2.45 million fully vaccinated residents and 147,445 COVID-19 cases. VB case median (MED) age was 52 y , 83% white, 65% female; MED age of fully vaccinated was 55 y , 77% white, 54% female. Of VB cases, 273 (10%) were hospitalized and 32 (1%) died . 2212 (80%) VB cases were interviewed; 60% reported symptoms; most common were fatigue (53%), rhinorrhea (49%), cough (42%), headache (41%). 35% reported a comorbidity.Of hospitalized VB cases, 120 had completed record reviews. 64 were admitted for COVID-19 related illness including 27 admitted to ICU . 90% (108) reported a comorbidity, most common being chronic metabolic conditions (46%), obesity (45%), renal disease (31%) and chronic lung disease (26%); 27 were immunocompromised , including immunosuppressive therapy (15), hematological malignancy (9), other cancer (11), and organ transplant recipients (8).Of 604 VB case specimens, 79% were B.1.1.7, 9% B.1.427/429, 3% P.1, and 2% B.1.351; lineage distribution was similar to overall 24,157 MN SARS-CoV2 WGS data.Identified VB cases were 0.1% of those vaccinated and < 2% of total cases reported in the time period. COVID-19 vaccines are an important tool in preventing COVID-19. Additional surveillance, including WGS and case characteristics will be useful to monitor VB.Ruth Lynfield, MD, Nothing to disclose"} +{"text": "Salmonella enterica serovar Typhi ISP2825, isolated in 1983 from a Chilean patient, is one of the major S. Typhi strains used for research, along with strains Ty2, CT18, and H58. The complete genome sequence of ISP2825, consisting of a 4,774,014-bp circular chromosome, will help us understand typhoid pathogenesis and evolution. Salmonella enterica serovar Typhi is the causative agent of the life-threatening systemic disease typhoid fever, which is a major cause of infection-mediated morbidity and mortality in countries of endemicity. Humans are the only known host of S. Typhi. Despite its narrow host specificity, S. Typhi has remained a highly successful pathogen since its emergence and extensively drug-resistant (XDR) strains have become the dominant S. Typhi variants overnight at 37\u00b0C, and its genomic DNA was extracted using the DNeasy blood and tissue kit , without processing additional fragmentation and size selection. The genomic DNA quality and quantity were monitored using a NanoDrop 2000 spectrophotometer and a Qubit 4 fluorometer (Thermo Fisher Scientific). A genomic DNA library was prepared using a SQK-LSK110 ligation sequencing kit , followed by sequencing with two MinION Flongle flow cells (R9.4.1) using MinKNOW v21.06.0 (ONT). The combined raw reads from two Flongle flow cells were used for base calling using Guppy v5.0.11 (ONT). Fastq files having Q scores of \u22658 were collected, filtered using NanoLyse v1.2.0 (https://github.com/lh3/bwa) and polished sequentially using Racon v1.4.22 (-m 8 -x -6 -g -8 -w 500) (https://github.com/nanoporetech/medaka) (-m r941_min_hac_g507), and Homopolish v0.2.3 (-s bacteria.msh -m R9.4.pkl) (https://github.com/b-brankovics/fasta_tools) was used to set the start position of the polished assembly according to that of S. Typhi CT18 (GenBank accession number GCF_000195995.1) and Ty2 (GCF_000007545.1). The complete genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) , Medaka 9.4.pkl) . Fasta_se (PGAP) , and itse (PGAP) and AMRFe (PGAP) , respecte (PGAP) . Defaulte (PGAP) . OverallS. Typhi ISP2825 has been deposited at GenBank under accession number GCF_019645915.1 or CP080960.1, BioProject accession number PRJNA753482, BioSample accession number SAMN20695325, and Sequence Read Archive (SRA) accession number SRR15411315.The complete genome sequence of"} +{"text": "Escherichia coli sequence type 1193 (ST1193) is an important cause of multidrug-resistant extraintestinal infections. Here, we report the complete genome sequence of strain AVS0096, isolated from river water in Switzerland in 2020. The genome consists of a chromosome (4.9\u2009Mbp), a multidrug resistance plasmid (101\u2009kb), and two small plasmids. Escherichia coli lineages sequence type 131-H30 (ST131-H30) and ST1193 are major causative agents of fluoroquinolone-resistant E. coli infections in humans (\u2013blaCTX-M-27-carrying ST1193 isolate (AVS0096) obtained from river water in Switzerland.The pandemic (ESBLs) \u20136. Where(ESBLs) \u2013, 6, few Enterobacteriaceae enrichment (EE) broth (BD) at 37\u00b0C for 24\u2009h. One loopful of the enrichment broth was spread onto Brilliance ESBL agar (Oxoid) and incubated at 37\u00b0C for 24\u2009h. Matrix-assisted laser desorption ionization\u2013time of flight mass spectrometry was used for species identification. Susceptibility testing against 13 antimicrobial agents was performed using the disk diffusion method according to CLSI protocols (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and LongQC v1.2.0 and 274\u2009Mbp short-read data using Unicycler v0.4.8 (AVS0096 was isolated in August 2020 from the river Lorze. The water sample 100\u2009ml) was filtered through a 0.45-\u03bcm membrane filter (Millipore). The filter was incubated in 10\u2009ml rotocols and Pore0\u2009ml was r v0.4.8 and annor v0.4.8 . Resistar v0.4.8 and Plasr v0.4.8 databaseH64 clade, as determined using https://pubmlst.org/ and FimTyper v1.0 from E. coli WP3-W18-CRE-03 (ST1193), isolated from wastewater in Japan. According to the CLSI criteria, AVS0096 showed resistance against azithromycin (macrolide), ampicillin, cefazolin, and cefotaxime (\u03b2-lactams), ciprofloxacin (fluoroquinolone), streptomycin (aminoglycoside), tetracycline, and trimethoprim-sulfamethoxazole, confirming genotypically identified resistances.The complete genome of AVS0096 consisted of a 4,944,762-bp chromosome and the three plasmids pAVS0096-a , pAVS0096-b , and pAVS0096-c . AVS0096 belonged to the ST1193-per v1.0 , and carVS0096-a . A near-CP076344.1 (chromosome), CP076345.1 (plasmid pAVS0096-a), CP076346.1 (plasmid pAVS0096-b), and CP076347.1 (plasmid pAVS0096-c). The raw data were deposited in the NCBI Sequence Read Archive (SRA) under BioSample accession number SAMN19493560 and BioProject accession number PRJNA734472.The complete genome sequence of AVS0096 has been deposited in GenBank under the accession numbers"} +{"text": "Candidemia is the second most common cause of healthcare-associated bloodstream infections in the US with mortality of approximately 25%. Studies demonstrate lower candidemia mortality with infectious diseases consultation (IDC). We evaluated effects of IDC on mortality and guideline-adherence at our institution to determine if mandatory IDC was warranted.Candida) between 1/1/2016-12/31/2019. Exclusion criteria included age < 19 years, polymicrobial blood culture, or death or hospice within 48 hours. Primary outcome was all-cause 30-day mortality. Secondary outcomes included guideline-adherence and treatment choice. Guideline-adherence was assessed with a modified EQUAL Candida score (Table 1). Descriptive statistics were performed.We retrospectively reviewed adults hospitalized with candidemia were present in 66 (71.7%) patients and were the most common infection source (N=38 [41.3%]) followed by intra-abdominal (N=23 [25%]). The most isolated species were Candida glabrata (40/94 [42.6%]) and C. albicans/dublienensis (35/94 [37.2%]). 30-day mortality was 21.7%. IDC was performed in 84 (91.3%) cases. Outcomes are in Table 3. Mortality was not different between IDC vs no IDC (18 [21.4%] vs 2 [25%]); other comparisons were numerically different but not significant: repeat blood culture (98.8% vs 87.5%), echocardiography (70.2% vs 50%), CVC removal (91.7% vs 83.3%), and initial treatment echinocandin (67.9% vs 50%). All patients received antifungal therapy. IDC resulted in more ophthalmology consultations . Mean modified EQUAL Candida score was higher with IDC .Of 187 patients reviewed, 92 episodes of candidemia with 94 species of Table 2. Patient CharacteristicsAbbreviations. TPN: total parenteral nutrition, ICU: intensive care unit, AIDS: acquired immunodeficiency syndromeTable 3. OutcomesAbbreviations. NS: non-significant, CVC: central venous catheterIDC was common in candidemic patients and not associated with significant differences in outcomes. Current antimicrobial stewardship and consultation practices at our center do not warrant mandated IDC for candidemia.Trevor C. Van Schooneveld, MD, FACP, BioFire Involved: Self): Consultant, Scientific Research Study Investigator; Insmed Involved: Self): Scientific Research Study Investigator; Merck Involved: Self): Scientific Research Study Investigator; Rebiotix Involved: Self): Scientific Research Study Investigator"} +{"text": "Analysis of 16S rRNA databases showed the preferences of Binatota to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges, supporting their potential role in mitigating methanol and methane emissions, breakdown of alkanes, and their association with sponges. Our results expand the lists of methylotrophic, aerobic alkane-degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades undescribed. Here, we present a global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, and chloromethanes as the substrates. Methylotrophy in Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e., the utilization of diverse sets of genes, pathways, and combinations to achieve a specific metabolic goal. The genomes also encoded multiple alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids production. Further, the majority of genes involved in bacteriochlorophyll Distinct strategies are employed for the analysis of the deluge of obtained genomes. Site- or habitat-specific studies focus on spatiotemporal sampling of a single site or habitat of interest. Function-based studies focus on genomes from single or multiple habitats to identify and characterize organisms involved in a specific process, e.g., cellulose degradation or sulfa efforts , 10. The efforts , as well efforts , 13. As Candidate phylum UBP10 has originally been described as one of the novel lineages recovered from a massive binning effort that reconstructed thousands of genomes from publicly available metagenomic data sets . UBP10 hn\u2009=\u20092), Binatales (n\u2009=\u200948), HRBin30 (n\u2009=\u20097), UBA1149 (n\u2009=\u20099), UBA9968 (n\u2009=\u200934), UBA12105 (n\u2009=\u20091), and UTPRO1 (n\u2009=\u20097), encompassing 12 families and 24 genera and 22 high-quality genomes, as defined by MIMAG standards . Binatot4 genera . 16S rRN classes . RDP II-bacteria .10.1128/mBio.00985-21.7TABLE\u00a0S1Table\u00a0S1, XLSX file, 0.02 MB.Binatota genomes used in this study number, their GTDB classification, and the corresponding classification in Silva and RDP databases, the source from which they were obtained, and the calculated Binatota abundances in metagenomes with available contig coverage data. Download Copyright \u00a9 2021 Murphy et al.2021Murphy et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 10.1128/mBio.00985-21.8TABLE\u00a0S2Table\u00a0S2, XLSX file, 0.02 MB.Sequencing statistics for the genomic bins used in this study. Download Copyright \u00a9 2021 Murphy et al.2021Murphy et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 10.1128/mBio.00985-21.9TABLE\u00a0S3Table\u00a0S3, XLSX file, 0.02 MB.General genomic features of the studied genomes. Download Copyright \u00a9 2021 Murphy et al.2021Murphy et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the mno), typically associated with Gram-positive methylotrophic bacteria (Actinobacteria and Bacillus methanolicus) , was thecyclales , was enccyclales . All latcyclales .mau) was more common, with mauA and mauB enzyme subunits encoded in Binatales, HRBin30, UBA1149, UBA12105, and UTPRO1 (mauC) is the most probable electron acceptor for methylamine dehydrogenase (mau cluster) carried the full complement of genes for methylamine oxidation via the indirect glutamate pathway involved in the degradation of dimethyl sulfone to MSA with the concomitant release of formaldehyde. Three of these nine genomes also encoded alkane sulfonic acid monooxygenase (ssuD), which will further degrade the MSA to formaldehyde and sulfite. Degradation of DMS via DMS monooxygenase (dmoA) to formaldehyde and sulfide was encountered in 13 genomes . Further, one Binatales genome encoded the dso system (enzyme class [EC]: 1.14.13.245) for DMS oxidation to dimethyl sulfone, which could be further degraded to MSA as explained above , and dimethyl sulfide (DMS). Nine genomes encoded dimethyl sulfone monooxygenase (S-transferase (dcmA) capable of converting dichloromethane to formaldehyde.One Bin18 genome encoded the specific dehalogenase/glutathione Proteobacteria, Verrucomicrobia, and \u201cCandidatus Methylomirabilis\u201d (NC10) methanotrophs (bmoA sequences (putative butane monooxygenase gene A) from Actinobacteria and SAR324 (\u201cCandidatus Lambdaproteobacteria\u201d) (Nocardioides sp. strain CF8 demonstrated its capacity to oxidize short-chain (C2 to C4) hydrocarbons, but not methane, via its CuMMO, and its genome lacked methanol dehydrogenase homologues 3D model (Protein Data Bank ID: 3RGB) revealed a heterotrimeric structure (\u03b13\u03b23\u03b33) with the 7, 2, and 5 alpha helices of the PmoA, PmoB, and PmoC subunits, respectively, as well as the beta sheets characteristic of PmoA and PmoB subunits , thought to coordinate the Cu cofactor, were identified in all TUSC-affiliated and SAR324/Actinobacteria-affiliated Binatota CuMMO sequences (Actinobacteria/SAR324-type Binatota genomes using Methylococcus capsulatus (Bath) PmoB subunit (Protein Data Bank [PDB] ID: 3RGB) predicted the binding pockets for Cu in Binatota sequences (Genes encoding copper membrane monooxygenases (CuMMOs), a family of enzymes that includes particulate methane monooxygenase (pMMO), were identified in orders Bin18 (2/2 genomes) and Binatales (9/48 genomes) (\u201d (NC10) \u201323 \u2013. In addiive site , 25. Phynotrophs (2 Binatcteria\u201d) , 28 . Memberscteria\u201d) . Previoucteria\u201d) . Binatotmologues . Such dasubunits . Recentlsubunits . There hsubunits \u201333. Regaequences . Modelinequences .10.1128/mBio.00985-21.2FIG\u00a0S1Methylococcus capsulatus (PDB ID: 3RGB). The alignment is showing conserved residues (red highlight). Of particular importance are the three conserved histidine residues His33, His137, and His139 (shown with a blue rectangle), thought to coordinate the Cu cofactor. Numbering follows the Methylococcus capsulatus strain Bath PmoB subunit (PDB: 3RGB). Alignment was created using the ENDscript webserver (http://espript.ibcp.fr/ESPript/ESPript/). (B and C) Predicted Cu methane monooxygenase (PmoABC) 3D structure (grey) from a cluster 2 TUSC-affiliated Binatota genome and an Actinobacteria/SAR324-affiliated Binatota genome , both superimposed on CuMMO from the model methanotroph Methylococcus capsulatus strain Bath (PDB: 3RGB) (green) with a global model quality estimate of 0.7 and 0.62, respectively, and a quaternary structure quality score of 0.57 and 0.55, respectively. Download FIG\u00a0S1, PDF file, 1.4 MB.(A) Alignment of the PmoB subunit of the 11 copper membrane monooxygenases predicted in Binatota genomes to PmoB from Copyright \u00a9 2021 Murphy et al.2021Murphy et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the 1 oxidation to formaldehyde, formaldehyde oxidation to CO2, and formaldehyde assimilation. Formaldehyde generated by C1 substrates oxidation is subsequently oxidized to formate and eventually CO2. Multiple pathways for formaldehyde oxidation to formate were identified in all Binatota orders , the H4F-linked pathway , the glutathione-independent formaldehyde dehydrogenase (fdhA), and the glutathione-dependent formaldehyde . Also shown is the distribution of the NAD-dependent formate dehydrogenase (EC: 1.17.1.9) (fdh) for formate oxidation. (B) Overview of the pathways for formaldehyde assimilation via the serine cycle (left) and glyoxylate regeneration via the ethylmalonyl-CoA pathway and the glyoxylate shunt (GS) (right). Names of enzymes are shown in red and their distribution in the Binatota genomes from different orders is shown in the heatmap in panel C. glyA, glycine hydroxymethyltransferase [EC: 2.1.2.1]; sgaA, serine-glyoxylate transaminase [EC: 2.6.1.45]; hprA, glycerate dehydrogenase [EC: 1.1.1.29]; gck, glycerate 2-kinase [EC: 2.7.1.165]; ppc, phosphoenolpyruvate carboxylase [EC: 4.1.1.31]; pckA, phosphoenolpyruvate carboxykinase; mdh, malate dehydrogenase [EC: 1.1.1.37]; mtkA/B, malate-CoA ligase [EC: 6.2.1.9]; mcl, malyl-CoA/(S)-citramalyl-CoA lyase [EC: 4.1.3.24 4.1.3.25]; aceA, isocitrate lyase [EC: 4.1.3.1]; aceB, malate synthase [EC: 2.3.3.9]; phbB, acetoacetyl-CoA reductase [EC: 1.1.1.36]; croR, 3-hydroxybutyryl-CoA dehydratase [EC: 4.2.1.55]; ccr, crotonyl-CoA carboxylase/reductase [EC: 1.3.1.85]; epi, methylmalonyl-CoA/ethylmalonyl-CoA epimerase [EC: 5.1.99.1]; ecm, ethylmalonyl-CoA mutase [EC: 5.4.99.63]; mcd, (2S)-methylsuccinyl-CoA dehydrogenase [EC: 1.3.8.12]; mch, 2-methylfumaryl-CoA hydratase [EC: 4.2.1.148]; mut, methylmalonyl-CoA mutase [EC: 5.4.99.2]; mcmA1/A2, methylmalonyl-CoA mutase [EC: 5.4.99.2]. Abbreviations: PEP, phosphoenol pyruvate; OAA, oxaloacetate. Download FIG\u00a0S2, PDF file, 0.2 MB.Formaldehyde oxidation and assimilation capabilities encoded by Binatota genomes. (A) Heatmap of the distribution of formaldehyde oxidation genes in Binatota genomes from different orders. The heatmap colors (as explained in the key) correspond to the percentage of genomes in each order encoding a homologue of the gene in the column header. Shown are the different routes of formaldehyde oxidation, including the (myco)thiol-dependent formaldehyde dehydrogenase Copyright \u00a9 2021 Murphy et al.2021Murphy et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Actinobacteria/SAR324-affiliated CuMMO to oxidize C1 to C5 alkanes and C1 to C4 alkenes as described above, some Binatota genomes encoded propane-2-monoxygenase (prmABC), an enzyme mediating propane hydroxylation in the 2-position yielding isopropanol. Several genomes also encoded medium-chain-specific alkane hydroxylases, e.g., homologues of the nonheme iron alkB (ladA homologues (enzyme class [EC]: 1.14.14.28) known to have a broad substrate specificity for medium-chain-length (C3 to C10) mono- and dihaloalkanes, resulting in the production of their corresponding primary alcohol and haloalcohols, respectively [EC: 1.1.1.80]; acmA, acetone monooxygenase (methyl acetate-forming) [EC: 1.14.13.226]; acmB, methyl acetate hydrolase [EC: 3.1.1.114]; aldehyde dehydrogenase (NAD+) [EC: 1.2.1.3]; acetaldehyde dehydrogenase (acetylating) [EC: 1.2.1.10]; acdAB, acetate-CoA ligase (ADP-forming) [EC: 6.2.1.13]; acs, acetyl-CoA synthase [EC: 2.3.1.169]; atoAD, acetate-CoA/acetoacetate CoA-transferase [EC: 2.8.3.8 2.8.3.9]; medium-chain acyl-CoA synthetase [EC: 6.2.1.2]; fadD, long-chain acyl-CoA synthetase [EC: 6.2.1.3]; pccA, propionyl-CoA carboxylase alpha chain [EC: 6.4.1.3]; epi, methylmalonyl-CoA/ethylmalonyl-CoA epimerase [EC: 5.1.99.1]; mut, methylmalonyl-CoA mutase [EC: 5.4.99.2]; mcl, malyl-CoA/(S)-citramalyl-CoA lyase [EC: 4.1.3.24 4.1.3.25]; mch, 2-methylfumaryl-CoA hydratase [EC: 4.2.1.148]; mct, 2-methylfumaryl-CoA isomerase [EC: 5.4.1.3]; meh, 3-methylfumaryl-CoA hydratase [EC: 4.2.1.153]; smtAB, succinyl-CoA:(S)-malate-CoA-transferase subunit A [EC: 2.8.3.22]; prpB, methylisocitrate lyase [EC: 4.1.3.30]; prpC, 2-methylcitrate synthase [EC: 2.3.3.5]; prpD, 2-methylcitrate dehydratase [EC: 4.2.1.79]; bcd, butyryl-CoA dehydrogenase [EC: 1.3.8.1]; acd, acyl-CoA dehydrogenase [EC: 1.3.8.7]; paaF, enoyl-CoA hydratase [EC: 4.2.1.17]; crt, enoyl-CoA hydratase [EC: 4.2.1.17]; paaH, 3-hydroxybutyryl-CoA dehydrogenase [EC: 1.1.1.157]; phbB, acetoacetyl-CoA reductase [EC: 1.1.1.36]; atoB, acetyl-CoA C-acetyltransferase [EC: 2.3.1.9]; fadJ, 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase/3-hydroxybutyryl-CoA epimerase [EC: 1.1.1.35 4.2.1.17 5.1.2.3]; fadA, acetyl-CoA acyltransferase [EC: 2.3.1.16]; dehH, 2-haloacid dehalogenase [EC: 3.8.1.2]; haloacetate dehalogenase [EC: 3.8.1.3]; glcDEF, glycolate oxidase [EC: 1.1.3.15]; (S)-2-hydroxy-acid oxidase [EC: 1.1.3.15]. Download FIG\u00a0S3, PDF file, 0.3 MB.(A) Heatmap of the distribution of various chain-length fatty acid and haloacid degradation genes in Binatota genomes. The heatmap colors (as explained in the key) correspond to the percentage of genomes in each order encoding a homologue of the gene in the column header. (B) Propionyl-CoA degradation pathways encoded by the Binatota genomes. The methylmalonyl-CoA (MMCoA) pathway is shown in blue, while the 2-methylcitrate pathway is shown in green. In some genomes, the MMCoA pathway seems to be functional but with a slight modification (shown in purple) that includes glyoxylate assimilation and regeneration. Copyright \u00a9 2021 Murphy et al.2021Murphy et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the actABCDEFG), and complex IV, as well as an F-type H+-translocating ATP synthase , 1f (22 sequences), 1i (1 sequence), and 1h (4 sequences) (2-tolerant hydrogenases) and methane (via pMMO) has been shown to occur in methanotrophic Verrucomicrobia to maximize proton-motive force generation and subsequent ATP production . Simultaoduction . As well by pMMO 10.1128/mBio.00985-21.5FIG\u00a0S4cytb/cyt1) and/or alternate cytochrome III , while genes encoding cytochrome c oxidase activities (complex IV) belonged to different families, including family A , family C , and/or cytochrome bd (cydAB). Possible electron transfer proteins between complex III and complex IV belonging to different cytochrome c families are shown. Also shown in panel A is the distribution of the three subunits of the type I respiratory O2-tolerant H2-uptake [NiFe] hydrogenase (hyaABC) in Binatota genomes. (B) Maximum-likelihood phylogenetic tree showing the classification of the hyaA genes carried by the Binatota genomes (magenta) in relation to other [NiFe] hydrogenases. The [Fe-Fe] hydrogenase of Methanobacterium formicicum was used as the outgroup. Bootstrap support (from 100 bootstraps) is shown for branches with >50% support. Download FIG\u00a0S4, PDF file, 0.3 MB.Electron transport chain in the Binatota. (A) Heatmap of the distribution of electron transport chain components in the Binatota genomes and electrons entry points from various substrates. The heatmap colors (as explained in the key) correspond to the percentage of genomes in each order carrying a homologue of the gene in the column header. All subunits of complexes I (NADH-quinone oxidoreductase [EC: 7.1.1.2]) and II (succinate dehydrogenase/fumarate reductase [EC: 1.3.5.1 1.3.5.4]) were encoded in all genomes but are shown here as single components for ease of visualization. Genes encoding quinone-cytochrome C reductase activities belonged to complex III and oxygenated (xanthophyll) carotenoid biosynthesis capabilities. Carotenoids biosynthetic machinery in the Binatota included crtB for 15-cis-phyotene synthesis from geranylgeranyl pyrophosphate (PP), crtI, crtP, crtQ, and crtH for neurosporene and all-trans lycopene formation from 15-cis-phytone, crtY or crtL for gamma- and beta-carotene formation from all-trans lycopene, and a wide range of genes encoding enzymes for the conversion of neurosporene to spheroidene and 7,8-dihydro \u03b2-carotene, as well as the conversion of all-trans lycopene to spirilloxanthin, gamma-carotene to hydroxy-chlorobactene glucoside ester and hydroxy-\u03b3-carotene glucoside ester, and beta-carotene to isorenieratene and zeaxanthins , third bchE (magnesium-protoporphyrin IX monomethyl ester cyclase [EC: 1.21.98.3]), and fourth bchLNB steps were identified in the Binatota genomes (bchM (magnesium-protoporphyrin O-methyltransferase [EC: 2.1.1.11]) and the fifth bciA or bicB or bchXYZ (chlorophyllide a reductase [EC 1.3.7.15]) steps were absent (a (BChl a) formation from chlorophyllide a (bchXYZ (chlorophyllide a reductase [EC 1.3.7.15]) and bchF (chlorophyllide a 31-hydratase [EC 4.2.1.165]) were not identified, while genes encoding bchC (bacteriochlorophyllide a dehydrogenase [EC 1.1.1.396]), bchG (bacteriochlorophyll a synthase [EC: EC: 2.5.1.133]), and bchP (geranylgeranyl-bacteriochlorophyllide a reductase [EC 1.3.1.111]) were present in most genomes (c (BChl c) and d (BChl d) formation from chlorophyllide a (bciC (chlorophyllide a hydrolase [EC: 3.1.1.100]) and bchF (chlorophyllide a 31-hydratase [EC: 4.2.1.165]) or bchV (3-vinyl bacteriochlorophyllide hydratase [EC: 4.2.1.169]) were not identified, while genes for bchR [bacteriochlorophyllide d C-12(1)-methyltransferase (EC: 2.1.1.331)], bchQ [bacteriochlorophyllide d C-8(2)-methyltransferase (EC: 2.1.1.332)], bchU (bacteriochlorophyllide d C-20 methyltransferase [EC: 2.1.1.333]), and bchK (bacteriochlorophyll c synthase [EC: 2.5.1.-]) were identified and 1,213 (IMG/M) 16S rRNA genes affiliated with the Binatota orders were identified are shown on the y axis (B). Further subclassifications for each environment are shown for (C) terrestrial, (D) freshwater, (E) marine, (F) host-associated, and (G) engineered environments. Details, including GenBank accession number of hit sequences, are shown in Extended Data 3. Download FIG\u00a0S5, PDF file, 0.4 MB.(A) Maximum-likelihood phylogenetic tree based on the 16S rRNA gene representatives from six Binatota orders with representative hit sequences (number of sequences in parentheses following the order name) from the IMG and NCBI-nt databases identified by Blastn. Orders are color coded following the color scheme in Copyright \u00a9 2021 Murphy et al.2021Murphy et al.https://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the In addition to the 16S rRNA-based analysis, we queried the data sets from which a Binatota MAG was binned using the sequence of their ribosomal protein S3 and estimating the Binatota relative abundance as the number of reads mapped to contigs with a Binatota ribosomal protein S3 as a percentage of the number of reads mapped to all contigs encoding a ribosomal protein S3 gene. Results showed relative abundances ranging between 0.1 and 10.21% (average 3.84 \u00b1 3.21%) .Aplysina aerophoba. Analysis of the 16S rRNA data set suggests a notable association between Bin18 and sponges, with relatively high host-associated sequences , suggesting its widespread distribution beyond a single sponge species. The absolute majority of order Binatales sequences were of a terrestrial origin in Bin18 and Binatales , Firmicutes (Verrucomicrobia (Candidatus Methylomirabilis\u201d (NC10) is especially notable, given the global magnitude of methane emissions and the relatively narrower range of organisms , Verrucomicrobia , and \u201cCa\u201d (NC10) . Further\u201d (NC10) , 44, for\u201d (NC10) , and met\u201d (NC10) , in the [NC10]) capable chanisms . All 11 1 oxidation to formaldehyde, formaldehyde oxidation to CO2, and formaldehyde assimilation. Within the world of methylotrophs, a wide array of functionally redundant enzymes and pathways have been characterized that mediate various reactions and transformations in such modules. In addition, multiple combinations of different modules have been observed in methylotrophs, with significant variations existing even in phylogenetically related organisms. Our analysis demonstrates that such metabolic versatility indeed occurs within the methylotrophic modules of Binatota. While few phylum-wide characteristics emerged, e.g., utilization of serine pathway for formaldehyde assimilation, absence of H4MPT-linked formaldehyde oxidation, and potential utilization of PEP carboxykinase (pckA) rather than PEP carboxylase (ppc) for CO2 entry to the serine cycle, multiple order-specific differences were observed, e.g., XoxF-type methanol dehydrogenase encoded by Bin18 and Binatales genomes, MDH2-type methanol dehydrogenase encoded by UBA1149 genomes, absence of methanol dehydrogenase homologues in HRBin30 genomes, absence of methylamine oxidation in order UBA9968, and potential utilization of the ethylmalonyl-CoA pathway for glyoxylate regeneration by the majority of the orders versus the glyoxylate shunt by UBA9968.As previously noted , methyloprmABC, propane monooxygenase), medium- , and long-chain alkanes (ladA) identified for their activation and conversion to central metabolites as well as order-specific habitat preferences ; Fig.\u00a0S5osystems , and we Within the phylum Binatota, it appears that orders HRBin30 and UBA1149 are abundant in thermal vents, thermal springs, and thermal soils, suggesting a specialization to high-temperature habitats . The preThe recovery of Binatota genomes from certain lakes could be a reflection of the high gaseous load in such lakes. Multiple genomes and a large number of Binatota-affiliated 16S rRNA sequences were binned and identified from Lake Kivu, a meromictic lake characterized by unusually high concentrations of methane . Biotica57\u201362\u2013Finally, the occurrence and apparent wide distribution of members of the Binatota in sponges, particularly order Bin18, are notable and could possibly be viewed in terms of the wider symbiotic relationship between sponges and their microbiome. Presence of hydrocarbon degraders , 67, incAlphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria (including methano- and methylotrophs) and Bacteroidetes, Deinococcus, Thermus, Deltaproteobacteria, Firmicutes, Actinobacteria, Planctomycetes, and Archaea, e.g., Halobacteriaceae and Sulfolobus. Here, carotenoids could serve as antioxidants are not pigmented. Indeed, root-associated facultative methylotrophs of the genus Methylobacterium have traditionally been referred to as \u201cpink-pigmented facultative methylotrophs\u201d and are seen as an integral part of root ecosystems . While such a pattern is tempting to propose phototrophic capacities in the Binatota, the consistent absence of critical genes , coupled with our inability to detect reaction center-encoding genes, prevents such a proclamation. Identification of a single or few gene shrapnel from the chlorophyll biosynthesis pathway in microbial genomes is not unique. Indeed, searching the functionally annotated bacterial tree of life AnnoTree could possibly be encoded by general methyltransferases (EC: 2.1.1.-), the missing bciC (EC: 3.1.1.100) could possibly be encoded by general hydrolases (EC: 3.1.1.-), and the missing bchF (EC: 4.2.1.165) or bchV (EC: 4.2.1.169) could possibly be encoded by general hydratases (EC: 4.2.1.-).Accordingly, we put forward three scenarios to explain the proposed relationship between Binatota and phototrophy. The most plausible scenario, in our opinion, is that members of the Binatota are pigmented nonphotosynthetic organisms capable of carotenoid production but incapable of chlorophyll production and lack a photosynthetic reaction center. The second scenario posits that members of the Binatota are indeed phototrophs, possessing a complete pathway for chlorophyll biosynthesis and a novel type of reaction center that is bioinformatically unrecognizable. A minimal photosynthetic electron transport chain, similar to that of antiacus , with thantiacus , it has species . A third12. Such auxotrophies are common in the microbial world and could be alleviated by nutrient uptake from the outside environment were downloaded as assemblies from NCBI. In addition, 128 metagenome-assembled genomes with the classification \u201cBacteria;UBP10\u201d were downloaded from the IMG/M database (April 2020). These genomes were recently assembled from public metagenomes as part of a wider effort to generate a genomic catalogue of Earth\u2019s microbiome (n\u2009=\u2009108) were retained for further analysis (All genomes classified as belonging to the Binatota in the Genome Taxonomy Database (GTDB) database , with the arbitrary cutoffs 56% and 68% for family and genus, respectively.Taxonomic classifications followed the Genome Taxonomy Database (GTDB) release r89 , 87 and 1, alkanes, and fatty acids metabolism, C1 assimilation, [NiFe] hydrogenases, electron transport chain complexes, and carotenoid and chlorophyll biosynthesis. To build the HMM profiles, Uniprot reference sequences for all genes with an assigned KO number were downloaded and aligned using Clustal-omega were obtained from the pfam database . Additionally, HMM profiles were built for PscABCD (Chlorobia-specific), PshA/B (Heliobacteria-specific) and reaction center type 2 , and theoflexota . The HMMoflexota , 99 was oflexota to checkoflexota , 102, weoflexota . All ide2-tolerant H2-uptake [NiFe] hydrogenase large subunit (HyaA) were classified using the HydDB web tool (All sequences identified as belonging to the respiratory Oweb tool .Methylococcus capsulatus strain Bath (PDB: 3RGB) and to predict tertiary structure models. Predicted models were superimposed on the template enzyme in PyMol . Modeling of the active site was conducted similarly. The dicopper-binding site proposed for Methylococcus capsulatus strain Bath pMMO (3RGB) was used. Alignment of Binatota PmoB sequences with reference Methylococcus capsulatus strain Bath PmoB was performed with Clustal-omega . Two databases were searched: (i) GenBank nucleotide (nt) database (accessed in July 2020) using a minimum identity threshold of 90%, \u226580% subject length alignment for near full-length query sequences or \u226580% query length for non-full-length query sequences, and a minimum alignment length of 100\u2009bp and (ii) The IMG/M 16S rRNA public assembled metagenomes using a cutoff E value of 1e\u221210, percentage similarity\u2009of \u226590%, and either \u226580% subject length for full-length query sequences or \u226580% query length for non-full-length query sequences. Hits satisfying the above criteria were further trimmed after alignment to the reference sequences from each order using Clustal-omega and inserted into maximum-likelihood phylogenetic trees in FastTree . The ecological distribution for each of the Binatota orders was then deduced from the environmental sources of its hits. All environmental sources were classified according to the GOLD ecosystem classification scheme . We alsohttps://github.com/ChelseaMurphy/Binatota. Maximum-likelihood trees (https://itol.embl.de/shared/1WgxEjrQfEYWk. Maximum-likelihood trees for chlorophyll biosynthesis genes are available at https://itol.embl.de/shared/34y3BUHcQd7Lh.Genomic bins, predicted proteins, and extended data for od trees can be a"} +{"text": "OBJECTIVES/GOALS: Using multi-state discharge data, to identify predictors of frequent emergency department (ED) use among the homeless patients seen in emergent care, and to compare frequent versus less frequent homeless ED users for their risk of serious health services utilization outcomes. METHODS/STUDY POPULATION: Based on the State Emergency Department Database and the State Inpatient Database, homeless individuals who made at least one ED visit in four states in 2014. In this retrospective cross-sectional analysis, patient-level demographic and clinical factors were assessed as predictors for increased ED use. Risks of opioid overdose, opioid-related hospital admission/ED visit, in-hospital mortality, mechanical ventilation, and number of hospitalizations were compared between individuals with 4 or more vs. 2-3 vs. 1 ED visit(s), adjusting for potential confounders including hospital fixed effects . RESULTS/ANTICIPATED RESULTS: Higher rates of ED use were associated with Medicare coverage <65; primary diagnosis of alcohol abuse, asthma, or abdominal pain; and co-morbidity of alcohol abuse, psychoses, or chronic pulmonary disease. Individuals with \u22654 visits had significantly higher adjusted risk of opioid overdose (3.7% vs. 1.2% vs. 1.0%), opioid-related hospitalizations/ED visits (17.9% vs. 8.5% vs. 6.6%), mechanical ventilation (9.8% vs. 7.0% vs. 4.7%), and greater # of hospitalizations (3.2 vs. 1.3 vs. 0.8) compared to individuals with 2-3 or 1 ED visit. Individuals with \u22654 and 2-3 ED visits had similar but increased risks of in-hospital mortality compared to individuals with 1 ED visit (2.8% vs. 2.8% vs. 2.3%). DISCUSSION/SIGNIFICANCE OF IMPACT: Homeless patients who were high ED users were more likely to be hospitalized and have other adverse outcomes. These findings encourage targeted interventions (i.e. housing) for the high-utilizer homeless population to reduce the burden of serious outcomes and costs for the patient and society."} +{"text": "BCOR and BCORL1. We report a distinct co-mutational pattern that suggests a role in disease progression rather than initiation, especially affecting mechanisms of DNA-methylation. Further, we found loss-of-function mutations of BCOR to be independent markers of poor outcomes in multivariable analysis. Therefore, loss-of-function mutations of BCOR need to be considered for AML management, as they may influence risk stratification and subsequent treatment allocation.Acute myeloid leukemia (AML) is a genetically heterogeneous disease. Clinical phenotypes of frequent mutations and their impact on patient outcome are well established. However, the role of rare mutations often remains elusive. We retrospectively analyzed 1529 newly diagnosed and intensively treated AML patients for mutations of BCL6 corepressor (BCOR) and its homolog, the BCL6 corepressor-like 1 (BCORL1), have been reported to be rare but recurrent mutations in AML. Previously, smaller studies have reported conflicting results regarding impacts on outcomes. Here, we retrospectively analyzed a large cohort of 1529 patients with newly diagnosed and intensively treated AML. BCOR and BCORL1 mutations were found in 71 (4.6%) and 53 patients (3.5%), respectively. Frequently co-mutated genes were DNTM3A, TET2 and RUNX1. Mutated BCORL1 and loss-of-function mutations of BCOR were significantly more common in the ELN2017 intermediate-risk group. Patients harboring loss-of-function mutations of BCOR had a significantly reduced median event-free survival : 1.005\u20132.134), p = 0.047), relapse-free survival (HR = 1.904 (95%-CI: 1.163\u20133.117), p = 0.01), and trend for reduced overall survival (HR = 1.495 (95%-CI: 0.990\u20132.258), p = 0.056) in multivariable analysis. Our study establishes a novel role for loss-of-function mutations of BCOR regarding risk stratification in AML, which may influence treatment allocation.Acute myeloid leukemia (AML) is characterized by recurrent genetic events. The Acute myeloid leukemia (AML) is a genetically heterogeneous disease . In the BCOR) gene, and its homolog, the BCL6 corepressor-like 1 (BCORL1) gene, are located on chromosomes Xp11.4 and Xq26.1, respectively [The BCL6 corepressor syndrome in heterozygous females, and prenatal death in hemizygous males [BCOR (mBCOR) and BCORL1 (mBCORL1) both occur in 4\u20136% of patients, and an association with poor outcomes has been suggested [Since BCOR is vital in ectodermal and mesenchymal differentiation, germline loss-of-function mutations in us males . Somaticus males ,16,17,18us males . It has us males ,20, chrous males , clonal us males , myelodyus males ,23,24,25us males ,26,27,28We retrospectively analyzed a multi-center cohort of 1529 AML patients. Eligibility criteria were newly diagnosed AML according to WHO definitions , AML200330). Remission and survival criteria were defined according to ELN2017 recommendations [AML was defined as de novo when neither previous malignancy nor previous treatment with chemo- and/or radiotherapy was reported. When myeloid neoplasms were documented prior to AML diagnosis, AML was defined as secondary (sAML). Prior exposure to chemo- and/or radiotherapy before the initial diagnosis defined therapy-associated AML (tMN). Early death was defined as death by any cause within 30 days of the initial diagnosis using a TruSight Myeloid Sequencing Panel was performed on pre-treatment bone marrow or peripheral blood, targeting 54 genes associatn detail ,35. A DNWe compared categorical variables between groups using the chi-squared test, while continuous variables were compared using the Kruskal\u2013Wallis test. The Kaplan\u2013Meier method was used to estimate survival probabilities. The logrank test was used to compare survival time distributions between groups. Cox regression was used to estimate univariate and adjusted hazard ratios. For the binary endpoint of complete remission, logistic regression models were fitted to estimate univariate and adjusted odds ratios. A significance level of 0.05 was used to determine statistical significance. Calculations were performed in R 4.0.3.n = 1529), we found mBCOR in 71 (4.6%) and mBCORL1 in 53 (3.5%) patients. Twelve patients (0.8%) concomitantly harbored both mBCOR and mBCORL1. The median age for the entire cohort was 55 years (Interquartile range (IQR): 44\u201364). Median variant allele frequency (VAF) for mBCOR and mBCORL1 was 48% (range: 7\u2013100%) and 47% (range: 5\u2013100%), respectively (BCOR (87%) and mBCORL1 (83%) carried two or more additional mutations in other driver genes, while only one patient in each group had no other co-mutations detected by the panel , RUNX1 (30%), TET2 (23%), NRAS (20%), BCORL1 (17%), and STAG2 (17%). Low mutation frequencies were detected for other genes frequently mutated in AML, such as FLT3 , NPM1 (11%), and TP53 (4%). Similar to mBCOR, in mBCORL1 AML the majority of mutations had a loss-of-function effect , RUNX1 (34%), FLT3-ITD (25%), BCOR (23%), and TET2 (23%).However, due to the unknown effect of protein function, these mutations were classified as UFs (unknown functions) for sub-analysis. The co-mutational landscape of mBCOR AML F was chaect 60%, D and werect 60%, E were DNBCORL1 were more prevalent in females than in males , while for mBCOR no such association was observed. For both mBCOR and mBCORL1 no statistically significant associations were detected for age at diagnosis, the presence of a complex karyotype, hemoglobin levels, or platelet counts. With respect to disease status, the rate of sAML was significantly higher amongst patients harboring mBCOR than amongst wtBCOR patients , while no specific association with mutation type (LOF or UF) or mBCORL1 was found regarding AML type. Outcomes did not differ for patients with sAML and mBCOR or mBCORL1 compared to patients with de novo AML. In the ELN2017 intermediate-risk group we found a higher proportion of LOF of mBCOR compared to UF mBCOR and wtBCOR , as well as mBCORL1 compared to wtBCORL1 . Median white blood cell (WBC) counts in LOF mBCOR AML were significantly lower compared to UF mBCOR and wtBCOR (p < 0.001), while mBCORL1 showed no significant association with WBC. BCOR (LOF and UF) and mBCORL1, respectively.Mutations of BCOR and mBCORL1 were not associated with the rate of complete remission (CR) (mBCOR: OR = 0.781 (95%-CI: 0.469\u20131.301), p = 0.342 and mBCORL1: OR = 0.795 (95%-CI: 0.442\u20131.432), p = 0.445) or with ED30 (mBCOR: OR = 0.679 (95%-CI: 0.209\u20132.199), p = 0.518 and mBCORL1: OR = 1.288 (95%-CI: 0.454\u20133.649), p = 0.634). In contrast, mBCOR was associated with lower median measures of event-free survival (EFS) (2.8 months (95%-CI: 1.7\u20138.5) vs. 7.6 months (95%-CI: 6.8\u20138.5), HR = 1.485 (95%-CI: 1.147\u20131.922), p = 0.003; p = 0.026; p = 0.095; BCOR in general was not independently associated with EFS (HR = 1.243 (95%-CI: 0.89\u20131.736), p = 0.202), RFS (HR = 1.407 (95%-CI: 0.93\u20132.129), p = 0.106), and OS (HR = 1.216 (95%-CI: 0.846\u20131.748), p = 0.292).With respect to clinical outcomes, mBCOR, compared to UF mBCOR and wtBCOR, we found in both univariate and multivariable analysis significantly reduced median EFS (LOF mBCOR: 1.9 months (95%-CI: 1.4\u20138.0) vs. UF variant of mBCOR: 4.9 months (95%-CI: 1.676\u2013n.a.) vs. wild-type BCOR: 7.5 months (95%-CI: 6.8\u20138.5), multivariable HR of LOF compared to wtBCOR = 1.464 (95%-CI: 1.005\u20132.134), p = 0.047, BCOR: 8.8 months (95%-CI: 7.3\u201324.0) vs. UF variant of mBCOR: 17.7 months (95%-CI: 8.317\u2013n.a.) vs. wild-type BCOR: 18.7 months (95%-CI: 16.3\u201323.3), multivariable HR of LOF compared to wtBCOR = 1.904 (95%-CI: 1.163\u20133.117), p = 0.01, BCOR variants in univariate analysis (LOF mBCOR: 11.6 months (95%-CI: 8.5\u201333.2) vs. UF variant of mBCOR: 14.2 months (95%-CI: 11.045\u2013n.a.) vs. wild-type BCOR: 18.4 months (95%-CI: 16.7\u201321.4), HR of LOF compared to wtBCOR = 1.409 (95%-CI: 1.010\u20131.965), p = 0.044), and a strong trend for reduced median OS in a multivariable analysis (HR = 1.495 (95%-CI: 0.990\u20132.258), p = 0.056, DNMT3A, TET2, and RUNX1 did not significantly affect HR. However, in order to precisely account for multiple interactions, an even larger cohort is needed, due to the rarity of LOF BCOR.For patients harboring LOF mBCORL1 in general compared to wtBCORL1, median EFS (3.6 months (95%-CI: 1.9\u20139.8) vs. 7.5 months (95%-CI: 6.7\u20138.3), HR = 1.204 (95%-CI: 0.885\u20131.639), p = 0.236; p = 0.263; p = 0.654; BCORL1 showed significantly reduced EFS (LOF mBCORL1: 3.5 months (95%-CI: 1.1\u201310.1) vs. UF mBCORL1: 6.2 months (95%-CI: 1.9\u2013not reached) vs. wtBCORL1: 7.5 months (95%-CI: 6.7\u20138.3), HR = 1.521 (95%-CI: 1.045\u20132.213), p = 0.028); however, in a multivariable analysis adjusting for age, AML type, and ELN2017 risk, this was not statistically significant.In AML with mBCOR and mBCORL1 regarding outcomes in different ELN2017 risk groups. Since few patients with mBCOR and mBCORL1 were in the ELN2017 favorable or ELN2017 adverse-risk groups , we focused on the ELN2017 intermediate-risk group . In ELN2017 intermediate-risk AML with mBCOR, median EFS and OS did not differ compared to wtBCOR, while there was a trend of lower median RFS in a univariate model (11.9 months (95%-CI: 7.0\u201324.0) vs. 14.8 months (95%-CI: 12.5\u201320.3), HR = 1.446 (95%-CI: 0.977\u20132.139), p = 0.065), as well as in a multivariable model adjusted for age and AML type (HR = 1.637 (95%-CI: 0.995\u20132.693), p = 0.052). In ELN2017 intermediate-risk AML with mBCORL1, median EFS and RFS did not differ, but there was a trend of lower median OS in a univariate model (14.9 months (95%-CI: 7.3\u201324.4) vs. 17.0 months (95%-CI: 14.0\u201320.6), HR = 1.401 (95%-CI: 0.954\u20132.058), p = 0.086), while in a multivariable model adjusted for age and AML type this difference was not statistically significant. There was no significant association between LOF of mBCOR or mBCORL1 and ELN2017 risk groups regarding outcomes.We did not find statistically significant differences in mBCOR and BCORL1. The respective proportions of mBCOR and mBCORL1 in the cohort were comparable to those reported in recent studies [BCOR with LOF and mBCORL1 to be more prevalent in patients in the ELN2017 intermediate-risk group [BCOR was significantly higher than in their wild-type counterparts, confirming previous reports [BCORL1 were significantly more prevalent in females than in males, as has been previously suggested [BCOR with LOF had significantly lower WBC, and a trend for lower peripheral blood blast counts. Mutations of BCOR frequently co-occurred with mutations of DNMT3A, RUNX1, TET2, NRAS, and BCORL1. Since both BCOR and DNMT3A function as epigenetic modifiers [BCOR and mutations of TET2, another epigenetic modifier [BCOR in our cohort, has been reported to induce MDS [BCOR and other essential regulators of normal myeloid development appears to be a factor that may promote leukemogenesis. Recent studies suggest, however, that perturbations of BCOR function alone do not suffice to induce malignant transformation [BCOR following an oncogenic event, e.g., MDS driver mutation triggers disease progression towards AML, as suggested by the higher frequency of sAML among mBCOR patients. Accordingly, in our cohort of patients with mBCOR AML, the majority had at least two co-mutations, while only one patient harbored no other co-mutations targeted by our panel (BCOR, co-mutations of mBCORL1 were RUNX1, DNMT3A, and TET2, as well as BCOR and FLT3-ITD, which were only rarely co-mutations of mBCOR. Again, the majority of patients harboring mBCORL1 had at least two other co-mutations, and only one patient had no other co-mutations revealed by our panel (BCOR, this suggests a potential interplay of impaired BCORL1 function with other dysfunctional mechanisms of DNA methylation, cell differentiation, and signal transduction in leukemogenesis.We analyzed a large cohort of newly diagnosed and intensively treated AML patients according to their mutational status of studies ,21,26,27sk group . The pro reports . Mutatioodifiers , a synerodifiers ,40. In mmodifier frequentduce MDS ,42. Thisduce MDS ,43. Therormation ,21,44, aur panel B. Similaur panel B. As forBCOR and mBCORL1 regarding CR rate and ED30, compared to wild-type patients. Interestingly, while we observed lower median EFS, RFS, and OS for both mBCOR and mBCORL1 in general, only LOF mutations of mBCOR were associated with significantly reduced EFS and RFS and a trend of reduced OS in multivariable testing adjusted for age, AML type, and ELN2017 risk. In MDS, Abuhadra et al. [BCOR, while general mutation status did not affect OS. Previous studies of mBCOR in AML have reported poorer outcomes to often be associated with distinct co-mutations; however, a significant association of LOF mutations of BCOR as independent markers of poor outcomes has not yet been reported in AML. Terada et al. [FLT3, and had intermediate-risk cytogenetics. Grossmann et al. [BCOR and a trend of reduced OS in normal-karyotype AML with no mutations in NPM1, FLT3-ITD, CEBPA, or MLL-PTD. However, in a validation cohort no association between mBCOR and OS was observed. Nevertheless, in both cohorts reduced EFS was detected [BCOR or SETBP1. Our findings underline the complexity of the mutational landscape of AML, where even mutational variants of rare mutations have to be considered in order to determine their clinical and prognostic effects. Future work needs to focus on the implementation of LOF mutations of BCOR in risk stratification tools for AML management.Regarding outcomes, we found no statistically significant differences between patients with ma et al. recentlya et al. reportedn et al. reporteddetected . Recentldetected reportedBCOR and mBCORL1 are rare but recurrent mutations in AML. While previous studies suggested poor outcomes for mBCOR in AML, especially in the context of co-occurring mutations, we found loss-of-function mutations of mBCOR to be independent markers of poor outcomes in AML, while mBCORL1 was not significantly associated with outcomes in multivariable testing.In conclusion, both m"} +{"text": "Trimethoprim-sulfamethoxazole (TMP-SMX) is a high-bioavailability antibiotic associated with potentially serious adverse drug events (ADE). The objective of this study was to evaluate the safety of intravenous (IV) and oral (PO) high-dose TMP-SMX.\u2265 18 years old and > 72 hours of renally adjusted high-dose TMP-SMX defined as \u2265 5 mg/kg/day of TMP. Exclusion: prophylaxis. Endpoints during treatment: hyponatremia with sodium < 135 mmol/L, hyperkalemia with potassium > 5 mmol/L, serum creatinine increase of \u2265 0.3 mg/dL or 1.5-1.9 times from baseline, and fluid overload on physical exam. Descriptive and bivariate statistics were performed.IRB-approved retrospective cohort of hospitalized patients from January 2016 to November 2020. Inclusion: Stenotrophomonas maltophilia (52% IV and 18% PO) and Pneumocystis jiroveci (16.3% IV and 62% PO). Median (IQR) days of inpatient therapy: 6 (5-7.5) PO vs. 7.5 (6-11.3) IV. Median (IQR) days of total duration: 9 (6-21.5) PO vs. 12 (7.8-14) IV (p=0.93). IV group: 88% of patients received >1 liter of D5W daily. Median (IQR) liters of D5W daily was 1 (1-1.5). 56% had a diuretic added, and 38% had a diuretic dose increase. Majority of patients (78%) on IV were taking other oral medications. 100% patients experienced any adverse event with IV vs. 70% with PO . Most common ADE in both groups: hyponatremia, hyperkalemia, and elevated creatinine. Hyponatremia: 92% with IV and 32% with PO . Edema on physical exam, an ADE specific to IV TMP-SMX, was the third most common side effect in the IV group. Relative changes from baseline in sodium, potassium, and creatinine from those who experienced hyponatremia, hyperkalemia and elevated creatinine were listed in Table 2.Each group included 50 patients (Table 1). Intensive care unit patients comprised 82% IV TMP-SMX compared to 32% PO. Most common infection: respiratory tract 86% IV and 68.1% PO. Most common organisms were Table 1. Baseline and Clinical CharacteristicsTable 2. Adverse EffectsPatients on IV TMP-SMX therapy were more likely to experience an ADE compared to PO, likely driven by the high volume of free water. Most patients on IV TMP-SMX were on other PO medications, suggesting a missed stewardship opportunity for IV to PO conversion to reduce patient harm.Susan L. Davis, PharmD, Nothing to disclose Michael P. Veve, Pharm.D., Cumberland (Grant/Research Support)Paratek Pharmaceuticals (Research Grant or Support) Rachel Kenney, PharmD, Medtronic, Inc."} +{"text": "Microbacterium foliorum NRRL B-24224. The 41,958-bp double-stranded DNA genome has 71 predicted protein coding genes and 1 tRNA. The lytic actinobacteriophage was extracted from soil samples collected in Stephenville, TX, and is related to cluster EB bacteriophages Didgeridoo and Lahqtemish.Microbacteriophage IndyLu was isolated from Microbacterium foliorum NRRL B-24224 is a rod-shaped Gram-positive aerobic bacterium from the order Actinomycetales that contains no intact prophages or apparent antibacteriophage restriction-modification or CRISPR systems (MH045566) and Lahqtemish (GenBank accession number MT889392). Auto-annotation using GLIMMER v3.02 (http://phagesdb.org/DNAMaster/), and PECAAN. Microbacteriophage IndyLu is predicted to contain 70 protein-coding genes and 1 tRNA coding for glutamine, identified using ARAGORN v1.2.38 showed gER v3.02 , 11 was ER v3.02 , DNA Mas v1.2.38 and tRNA v1.2.38 . Putativ v1.2.38 , 16 and OK318958. The raw reads are available in the SRA under accession number SRX12683423.The actinobacteriophage IndyLu genome sequence is available in GenBank under accession number"} +{"text": "Theshort answer is to administer alpha-2 agonists slowly from admission orendotracheal intubation up to stabilized cooperative sedation. The \u201ctake home\u201dmessage is as follows: a) alpha-2 agonists are jointly sympathetic deactivatorsand sedative agents; b) sympathetic deactivation implies maintaining the strokevolume and iterative assessment of volemia. Evidence-based medicine shoulddocument our propositions.Cardiac, ventilatory and kidney management in the critical care setting has beenoptimized over the past decades. Cognition and sedation represent one of thelast remaning challenges. As conventional sedation is suboptimal and as thesedation evoked by alpha-2 adrenergic agonists represents a valuable alternative,this manuscript covers three practical topics for which evidence-based medicineis lacking: a) Switching from conventional to cooperative sedation(\u201cswitching\u201d): the short answer is the abrupt withdrawal of conventionalsedation, immediate implementation of alpha-2 agonist infusion and the use of\u201crescue sedation\u201d (midazolam bolus[es]) or \u201cbreakthrough sedation\u201d to stabilize cooperative sedation. b) Switching from conventional tocooperative sedation in unstable patients (e.g., refractory Given the circulatory drawbacks in hypovolemic patients, only nicheindications are to be considered , which contradicts the\u201cone size fits all\u201d approach. Circulation is a major concern. In the setting ofsystolic15,16)( or diastolic17)( failure or cardiogenic pulmonary edema and a lowleft ventricular (LV) ejection fraction,18)( the sympathetic deactivation of capacitance(veins) and resistance vessels is beneficial. Venous return is reduced, and ejectionimproves. In the hypovolemia scenario, alpha-2 agonists further reduce venous return and stroke volume (SV) and worsencirculatory distress .Alpha-2 adrenergic agonists evoke \u201ccooperative\u201d, rousable sedation6,22-25)( or sleep26)( anti-inflammation31-35)$( and a reduced CCU stay.36), problems arise: a) how to switch from conventionalsedation to alpha-2 agonists (\u201cswitching\u201d), e.g., in agitated or unstable patients,refractory delirium tremens (DT), circulatory/ventilatory distress,etc.; and b) how can alpha-2 agonists be prescribed as first-line sedatives de novoupon admission? This manuscript addresses the parasympathetic vs. sympatheticsystems, circulation, and ventilation.As alpha-2 agonists interfere with the autonomic system 46-48). Our clinical practice spanning the period of 1980 -2020 in several countries is summarized . Physiol49)emergence delirium is encountered following deep sedation. However,is this delirium related to the pathology itself, the CCUenvironment, or conventional sedation? Moreover, b) deep sedation, bordering GA (1),is used in clinical practice for ARDS or increased intracranialpressure49)( without evidence.50), paralysis and proning.51,52)( is missing.50)the absence of a control group under adequate spontaneous breathing50)( and b) the tendency toshorten57,58)( without strong evidence50), traumatic brain injury,As most groups use cooperative sedation after conventional sedation, i.e., only whenthe patient is recovering and ready for tracheal extubation (\u201cextubation\u201d),switching from conventional to cooperative sedation is examined first.- Hypovolemia: See below.&), sick sinus syndrome,atrioventricular block II or III without a pacemaker.- Bradycardia (- Liver failure (Child-Pugh C): Clonidine and dexmedetomidine areexcreted through the kidney and liver, respectively. Moreover,clonidine and dexmedetomidine are useful in the scenarios of liverand kidney failure, respectively. Nevertheless, a) clonidine can beadministered in the setting of acute renal failure if renalreplacement therapy (RRT) is used, and b) dexmedetomidine can beused in the setting of liver cirrhosis.Dexmedetomidine and clonidine are sympathetic inhibitors in healthy restingsupine volunteers. In the CCU, given the increased sympathetic activity, theynormalize sympathetic hyperactivity back toward baseline, i.e., sympatheticdeactivators, with the following contraindications: no clinical relevance but is only an invitro finding.63). In contrast, clonidine p.o.allows for convenient oral administration (nonintubated patient with DT),transitioning alpha-2 agonists from i.v. dexmedetomidine to p.o. clonidine toavoid alpha-2 agonist withdrawal, etc. Sedation is achieved within 30 - 60minutes in healthy volunteers after clonidine 300\u00b5g p.o.5,12) < +1 occursimmediately before initiation of dexmedetomidine infusion23). Rescue sedation is used to achieve-2 1.5\u00b5g.kg-1.h-1.7) or propofol (25mg) to berepeated if necessary.65)( thesympathetic inhibition evoked by propofol68), blood pressure (BP) and cardiac output(CO).69) or a bolus of clonidine/dexmedetomidine. Consequently,severe bradycardia and hypotension may occur. To avoid such sideeffects, we used abrupt withdrawal. Abrupt withdrawal is performedduring the day shift only, starting in the earlymorning\u00a3. The prescription specifies the target (-2 =80), Mini-Mental Status Exam (MMSE >25 or <=25) and interactions. To evaluate the influence of Caregiver participation, #newFPBs reported by 115 non-demented clinical trial participants (no Caregiver- FT-ClTrNoCG) were compared with the Caregiver outcomes. Dyads using technology reported significantly more #newFPBs (MeanFTCGnoTech=5.34(SEM=0.68), MeanFTCGTech=8.46(SEM=0.76); p=.004) during the intervention month. A significant interaction was observed whereby Dyads with MMSE<=25 using technology, reported significantly more #newFPBs than the non-technology group (MeanFTCGnoTech=4.23(SEM=0.72), MeanFTCGTech=9.01(SEM=0.90); p=.047). Caregiver (n=34) involvement substantially increased #newFPBs (MeanFT-ClTrNoCG=1.39(SEM=0.15), MeanCaregiver=7.21(SEM=0.49); p<.0001), independent of technology. Across studies, participants or Caregivers for those with MMSE<=25 and <80yo reported significantly more #newFMBs (Mean=4.38(SEM=0.55) than those 80+yo (Mean=2.06(SEM=0.30); p=.0026). FallsTalk Caregiver provides an effective means to promote new Dyad FP strategies. The influence of Caregiver involvement and technology show promise in encouraging behavioral change to prevent falls."} +{"text": "Escherichia coli and Klebsiella pneumoniae, as compared to 3GC-susceptible isolates of either species.Carbapenems are considered the drugs of choice for first-line treatment of severe infections caused by carbapenem-susceptible, extended-spectrum \u03b2-lactamases (ESBL)-producing Enterobacterales, while piperacillin-tazobactam has been recommended as an alternative for treatment of non-severe infections. Temocillin is stable to ESBL and AmpC enzymes and may thus represent another treatment option. This study assessed the in vitro activity of piperacillin-tazobactam and temocillin against third-generation cephalosporin (3GC)-resistant One hundred and nine isolates from hospitalized patients with bloodstream and urinary tract infections were tested. All isolates were collected during the resistance surveillance study of the Paul-Ehrlich-Society for Chemotherapy in 2016/17. Minimum inhibitory concentrations (MICs) were determined by broth microdilution according to the standard ISO 20776-1 and interpreted using EUCAST clinical breakpoints (version 11.0).E. coli, n=58; K. pneumoniae, n=21) were 3GC-resistant and 30 were 3GC-susceptible. Susceptibility to piperacillin-tazobactam was detected in 93.3% of 3GC-susceptible isolates (for both E. coli and K. pneumoniae) and in 79.3% and 57.1% of the 3GC-resistant E. coli and K. pneumoniae, respectively. In contrast, 3GC-susceptible isolates were 100% susceptible to temocillin as were 94.8% and 90.5% of the 3GC-resistant E. coli and K. pneumoniae, respectively.Seventy-nine isolates (E. coli and K. pneumoniae from bloodstream and urinary tract infection samples, with susceptibility rates exceeding those of piperacillin-tazobactam.In conclusion, temocillin demonstrated potent in vitro activity against carbapenem-susceptible, 3GC-resistant Escherichia coli and Klebsiella pneumoniae is most commonly mediated by extended-spectrum \u03b2-lactamases (ESBLs), but also occurs through other mechanisms like plasmid-encoded AmpC-type enzymes . Mo enzymes , [2], ) and two were ceftazidime-resistant only (cefotaxime-susceptible [S+I]).Meropenem inhibited all isolates at the lowest concentration tested . Seventy-nine isolates were 3GC-resistant and the number and percentage of isolates classified as susceptible (S or I) or resistant were calculated.MIC distribution data of temocillin and piperacillin-tazobactam are presented in Table 1 E. coli and K. pneumoniae. MIC50/90 values of piperacillin-tazobactam and temocillin were \u22641/4 mg/L and 4/16 mg/L, respectively, for E. coli, and \u22641/8 mg/L and 2/8 mg/L, respectively, for K. pneumoniae. One isolate each of E. coli and K. pneumoniae had a piperacillin-tazobactam MIC of \u2265128 mg/L. MICs of ceftazidime for both isolates were 1 mg/L as compared to MICs of \u22640.25\u20130.5 mg/L for the other 28 3GC-susceptible isolates.Susceptibility to piperacillin-tazobactam (MIC\u22648 mg/L) and temocillin (MIC\u226416 mg/L) among the 30 3GC-susceptible isolates was 93.3% and 100%, respectively, for both E. coli and K. pneumoniae to the other antibiotics tested are displayed in E. coli were observed for ampicillin (53.3%), cotrimoxazole (26.7%), and amoxicillin-clavulanic acid (20%), while the highest level of drug resistance in 3GC-susceptible K. pneumoniae, except for ampicillin, was observed for fosfomycin (33.3%). Two 3GC-susceptible K. pneumoniae were colistin-resistant.Susceptibility data of the 3GC-susceptible E. coli was 79.3% (95% CI: 68.9\u201389.7%) versus 94.8% (95% CI: 89.1\u2013100%), respectively, and among 3GC-resistant K. pneumoniae 57.1% (95% CI: 44.4\u201369.8%) versus 90.5% (95% CI: 83.0\u201398.0%), respectively. MIC50/90 values of piperacillin-tazobactam and temocillin were 2/32 and 8/16 mg/L mg/L, respectively, for E. coli, and 8/\u2265128 mg/L and 8/16 mg/L, respectively, for K. pneumoniae. Seventeen 3GC-resistant isolates were resistant to piperacillin-tazobactam, but susceptible to temocillin, while one E. coli isolate was temocillin-resistant, but susceptible to piperacillin-tazobactam. Two isolates of either species were resistant to both antimicrobials were detected for levofloxacin, tobramycin and fosfomycin in 3GC-resistant K. pneumoniae. One 3GC-resistant isolate each of E. coli and K. pneumoniae was colistin-resistant, and two 3GC-resistant E. coli were fosfomycin-resistant.Susceptibility data of the 3GC-resistant, carbapenem-susceptible E. coli and K. pneumoniae has become widespread in all parts of the world. According to data of the European Antimicrobial Resistance Network (EARS-Net), investigating invasive isolates, resistance to 3GC in E. coli rose from 1.7% in 2002 to 15.1% in 2019. 3GC resistance also increased in K. pneumoniae. EARS-Net reported an overall resistance rate of 31.3% for 2019, with extremely large differences in the level of resistance between individual countries (to >60%) and one temocillin-resistant [MICs 32\u201364 mg/L]) without resistance to other \u03b2-lactams, found mutations in several genes, including a porin-encoding gene (ompD-like) and genes encoding for transport/membrane proteins . T. TE. coleumoniae . Temocillsewhere , 15], [, [E. col Table 2 , but the Table 2 . Seventy Table 2 . Thus, oic shock . It musthttps://doi.org/10.5061/dryad.931zcrjkc [Data for this article are available from the Dryad Repository: 31zcrjkc The investigation of the susceptibility of the test organisms to temocillin was supported by a grant from Eumedica S/A, Manage, Belgium, to Antiinfectives Intelligence GmbH.MK is a partner and CEO of Antiinfectives Intelligence GmbH, a research organization providing services to pharmaceutical companies. YP and GW declare that they have no competing interests."} +{"text": "Streptomyces (68%), Micromonospora (6%), and Nocardiopsis (3%) are dominant producers of secondary metabolites. Additionally, alkaloids (37%), polyketides (33%), and peptides (15%) comprise the largest proportion of natural products with mostly antimicrobial activity and cytotoxicity. Furthermore, the data analysis and clinical information of SMs have been summarized in this article, suggesting that some of these actinomycetes with multiple host organisms deserve more attention to their special ecological status and genetic factors.The actinomycetes have proven to be a rich source of bioactive secondary metabolites and play a critical role in the development of pharmaceutical researches. With interactions of host organisms and having special ecological status, the actinomycetes associated with marine animals, marine plants, macroalgae, cyanobacteria, and lichens have more potential to produce active metabolites acting as chemical defenses to protect the host from predators as well as microbial infection. This review focuses on 536 secondary metabolites (SMs) from actinomycetes associated with these marine organisms covering the literature to mid-2021, which will highlight the taxonomic diversity of actinomycetes and the structural classes, biological activities of SMs. Among all the actinomycetes listed, members of Actinomycetes are Gram-positive bacteria with a GC-rich linear genome and have proven to be a rich source of secondary metabolites (SMs) of broad structural diversity and biological properties . The oceThe objective of this article is to provide an overview of the natural products from actinomycetes associated with marine animals, marine plants, macroalgae, cyanobacteria, and lichens. The present review was not only summarizing the structural classes and biological activities of SMs but also highlighted the taxonomic diversity of actinomycetes, as well as the data analysis of integrated above information. Some of these metabolites with excellent activity are expected to become new drugs such as antibiotics, antineoplastic drugs, or anticancer drugs. Therefore, actinomycetes with multiple host organisms deserve more attention to their special ecological status and genetic factors.Streptomyces, Micromonospora, Microbacterium, and Nocardiopsis were abundant , respectively indole, another known compound indole-3-acetic acid (S16) was discovered from this strain indole (tnam Sea . In addis strain .73) and isoquinocycline B (74) showed good antibiotic activity not only against the Gram-positive strain S. aureus SH1000, but also the Gram-negative strains efflux knockout (KO) mutant strains of K. pneumoniae ATCC10031 and A. baumannii ATCC 17978. It was also active against the human liver cancer cell line HepG2 with an IC50 of 13.3 \u00b5M ..Callyspo79) (S38), and aerugine (80) (S39) and furan-2-carboxamide (S40) from Streptomyces sp. OUCMDZ-1703 associated with a soft coral sample collected from the South China Sea. Thiazole derivatives 79 and 80 displayed moderate antibacterial activity against S. aureus and three methicillin-resistant strains MRSA082, MRSA111, and MRSA234 anthraquinone derivatives, urdamycinone E (in (134) were ide E (135) , the pos50 \u03bcg/mL ,95.136\u2013141) (Streptomyces sp. CMS JV M18_3 [136\u2013139) has great antibacterial activities against MRSA and vancomycin-resistant Enterococcus faecium (VREF). In addition, compounds 136\u2013139 were active against HCT-116 human colon carcinoma [141) displayed anti-biofilm activity inhibiting Staphylococcus aureus biofilm formation, and compound 140 exhibited antimicrobial activities against some Gram-positive bacteria [Six dihydroquinone derivatives 136\u2013141) were iso6\u2013141 wearcinoma . SF2415Bbacteria ,98.142) and B (143) (Nocardiopsis sp. KMF-002 was cultivated from an unidentified dark purple marine sponge. Nocatrione A (142) showed a significant protective effect against UVB irradiation in both NHDF cell lines, whereas nocatrione B (143) was active against UVB only in a specific NHDF cell line [In 2014, Min Cheol Kim et al. reported isolation and identification of two novel tetracenedione derivatives nocatriones A ( B (143) from Nocell line .Actinokineospora sp. EG49 cultivated from the marine sponge Spheciospongia vagabunda afforded two new actinosporin analogs actinosporins C (144) and D (145) (146) and B (147) ( D (145) . At 1.25 B (147) were als148) [Microluside A (148) is a uniectively . In 2015in (S72) .149) (S73), and a related analog (\u2212)-BE-52440A (150) -BE-52440A (150) showed cytotoxicity against NB4 and HL-60 cells with IC50 values of 1.7 and 1.8 \u03bcM, respectively. Naquihexcin A (149) bears a rare unsaturated hexuronic acid moiety and could inhibit the proliferation of an adriamycin-resistant human breast cancer cell line MCF-7 ADM with IC50 = 16.1 \u03bcM, indicating that the unsaturated hexuronic acid moiety could enhance the activity against the cancer cells [Three S-bridged pyranonaphthoquinone dimers naquihexcins A (149) and B (S0A (150) were proer cells .S74, identified as 3-hydroxy-2-methyl-4H-pyran-4-one , was isolated both from the Streptomyces sp. SBT348 and Rhodococcus sp. UA13 [S75 was discovered from the co-culture of sponge-derived Saccharomonospora sp. UR22 and Dietzia sp. UR66 [151\u2013153) (Nocardiopsis sp. HB-J378 associated with Theonella sp. Nocardiopsistin B showed the best anti-MRSA activity with the same MIC (3.12 \u03bcg/mL) as that of chloramphenicol, whereas nocardiopsistins A and C have a moderate anti-MRSA activity (MIC = 12.5 \u03bcg/mL) [151\u2013153), it was found that the ketone functional group at C-4 could enhance the anti-MRSA activity, while the hydroxyl group at C-3 weakened activity.Compound sp. UA13 ,45. Compsp. UR66 . In 2018151\u2013153) separate5 \u03bcg/mL) . On compS76) was first isolated from Streptomyces rochei MB037 associated with marine sponge Dysidea arenaria collected at Yongxin Island in the South China Sea. And the co-culture with fungus Rhinocladiella similis 35 derived from gorgonian could enhance its production [154), together with three known actinosporins C, D, and G exhibited potent antitrypanosomal activity and growth inhibitory activity towards Trypanosoma brucei strain TC221 [7-methoxy-2,3-dimethylchromone-4-one were obtin TC221 .156 and 157) were pro[158\u2013160 were iso and 162 showed iectively .146, 144) were isolated from the axenic cultures of strain EG49. Actinosporin A showed anti-trypanosomal activity and actinosporin C exhibited antioxidant activity. New actinosporins E\u2013H (165) (S78) [Actinosporins A and C were pro4) (165) and the B (166) (plant g167) (S79) with fully saturated eight-membered lactone ring were reported in 1991 from Streptomyces sp. PG-19 collected on the surface of Cortez gorgonian octocoral Pacifigorgia sp. Octalactin A demonstrated significant in vitro cytotoxicity toward B-16-F10 murine melanoma (IC50 = 7.2 \u00d7 10\u22123 \u00b5g/mL) and HCT-116 human colon tumor (IC50 = 0.5 \u00b5g/mL) [Isolation of two novel compounds Octalactins A (167) and B (S5 \u00b5g/mL) .S80) was produced by a marine actinomycete Micromonospora sp. strain A5-1 obtained from soft coral Scleronephthya sp. in the East China Sea [Streptomyces sp. OUCMDZ-1703\u2020 associated with a soft coral collected from the South China Sea led to the discovery of two new chlorinated polyketides strepchloritides A and B (168 and 169) (S41). Polyketides 168 and 169 showed moderate cytotoxicity against MCF-7 tumor cells [A novel analog of jadomycin B, 7b,13-dihydro-7-O-methyl jadomycin B (hina Sea . Streptoand 169) , togetheor cells .S81) and two known anthracycline derivatives were produced by coral-associated Streptomyces sp. SCSIO 41399. Compound 170 (Aranciamycin K (ound 170 exhibite171) and anthracimycin (172) with MIC values less than 0.03 \u00b5g/mL. And anthracimycin B was also active against these four Gram-positive bacteria. In addition, anthracimycin displayed anti-tubercular activity against Mycobacterium tuberculosis [A novel gram-positive antibiotic anthracimycin B (in (172) were isorculosis .173) and HePG2 (hepatic carcinoma) in vitro [1-hydroxy-1-norresistomycin (HNM) (173) was prodin vitro .174\u2013176) were rep25 \u03bcg/mL .177) was isolhrocytes ,110.178) was founlomerase ,111.Streptomyces sp. #N1-78-1 from sea squirt Ecteinascidia turbinata in Puerto Rico led to the purification of bisanthraquinones 1 and 2 , as well as derivative 3 (181) (Staphylococcus aureus) and VRE , and these three compounds displayed cytotoxic activity against HCT-116 cells [The isolation of 3 (181) , the deh16 cells ,112.182, 183, S83, and S84) were produced by a strain of Micromonospora sp. derived from a Brazilian endemic ascidian Eudistoma vannamei. Compounds 182 and 183 . Halomadurones C (184) and D (185) (186) showed p5) (186) was also strains .187\u2013190) and nahuoic acid A (191) with an unprecedented carbon skeleton was the first natural product inhibiting the SETD8 lysine methyltransferase and the first selective SETD8 inhibitor. Compounds 187\u2013191 showed weak antibiofilm activity against Shewanella onedensis MR-1 biofilm [S87, S88, 192\u2013194). Compounds E-G (192\u2013194) were sep biofilm . In 2017192\u2013194) had weaksubtilis .Streptomyces coelicoflavus strain HQA809, which is isolated from sea squirt Styela clava, produced germicidin (195) and 6-isopropyl group-3-ethyl-4-hydroxy-2-pyrone (196) . Both twa salina .Streptomyces sp. PTY087I2 associated with styela canopus collected from Bastimentos Park, Bocas del Toro, Panama produced three naphthoquinone derivatives granaticin (197), granatomycin D (198), and dihydrogranaticin B (199) . Co-cultathogens ,118.200\u2013204) suppressed the proliferation of cancer cell lines, and metabolites 203 is the most active compound with IC50 values ranging from 0.59 to 3.39 mM. The 11-hydroxycurvularins 200 and 201 also showed antibacterial activity inhibiting the growth of Escherichia coli [205 . And the known metabolite 301 (Five curvularin macrolides (200\u2013204) were isohia coli . Compounoli [205 , which wlite 301 with ant206), ochromycinone (207), and X-14881 C (208), together with a new angucyclines saccharothrixmicine A (209) (Saccharothrix espanaensis An 113 obtained from a marine mollusk specimen (Anadara broughtoni), which was collected from Peter the Great Bay, Sea of Japan, Russia. Compounds 206\u2013208 showed significant activity against C. albicans, B. subtilis, E. faecium, S. aureus, and Xanthomonas sp. pv. badrii. And Compound 209 exhibited activity towards Candida albicans and Xanthomonas sp. pv. Badrii [S89) and F (S90), together with gilvocarcins M (S91) and V (S92), have been isolated from an unidentified tunicate-associated Saccharopolyspora sp. SS081219 JE-28 [Three known analogs X- 14881 E ( A (209) , were pr. Badrii ,121. Mac19 JE-28 ,77.210) and I (211) were reported together with known violapyrones B (212) and C (213) showed growth inhibitory activity against cancer cell lines at concentrations less than 26.12 \u03bcg/mL. Wherein compound 210 showed the highest cytotoxic activity against the HCT-15 cell line with a GI50 value of 1.10 \u03bcg/mL. Additionally, violapyrones B and C were demonstrated to have antibacterial activities. Therefore, it may be noteworthy that each compound has structural similarities, but showed different activities. The results suggested that the length of the aliphatic side chain and the position of the methyl group affected the activity. Furthermore, violapyrones having an isomethyl group in the alkyl side chain showed better activity than others [Isolation of two novel 3,4,6-trisubstituted \u03b1-pyrone derivatives violapyrones H ( C (213) , from Stn others .214) and PM100118 (215) from StrTCC10231 .216, 217) (S93\u2013S97) were produced by the sea anemone-derived Streptomyces sp. ZZ406. New compounds 216 and 217 showed potent activity in inhibiting the proliferation of different glioma cells and downregulating the expressions of glioma metabolic regulators. Compound 216 was active against the proliferation of different glioma cells with IC50 values of 4.7 to 8.1 \u03bcM, high selectivity index (>12.3 to 21.3), and good stability in human liver microsomes [S98) and the known angucyclinone PD116740 (126) were isolated from the sea urchin-derived Streptomyces sp. HDa1 [Two new compounds and fivecrosomes . A novelsp. HDa1 .11 (218) and Q12 (219) were separated from the marine gastropod mollusk Batillaria zonalis-associated Streptomyces sampsonii SCSIO 054. In addition, four known anthraquinones chrysophanol (S101), 4-acetylchrysophanol (S102), islandicin (S103), and huanglongmycin A (S104) were also discovered. Julichrome Q12 (219) was found to display antibacterial activity against Micrococcus luteus and Bacillus subtilis with MICs of 2.0 and 8.0 \u03bcg/mL. What\u2019s more, compounds 218, 220\u2013222 , along w 220\u2013222 also sho64 \u03bcg/mL .223\u2013225) (50 0.63 \u03bcg/mL), and all three novel metabolites exhibited significant cytotoxicity against the 39 human cancer cell lines [Further investigation for metabolites of this strain has led to the isolation of three additional novel cytotoxic metabolites designated as halichoblelide A\u2013C (223\u2013225) . Halicholl lines ,126.226) [Ochoa et al. reported the isolation of a new glycosylated polyketide phocoenamicin (226) in 2017, 2.6 \u03bcM) .Most peptides from actinomycetes are circular and contain further rare structural elements, such as chromophore or unusual amino acids.Streptomyces sp. DA18 was separated from marine sponge Craniella australiensis collected at Sanya Island in the South China Sea, from which diketopiperazines (DKPs) were disactivity .230) and Trypanosoma brucei brucei (IC50 = 0.0032 \u03bcM). Additionally, it was active against 293T kidney epithelial cells (IC50 11.24 \u00b5M) and J774.1 macrophages (IC50 < 0.10 \u00b5M) [The cyclic depsipeptide valinomycin (230) was isol0.10 \u00b5M) .231) (Nocardiopsis strain HB383 [232) . The compound displayed weak cytotoxic activity against human cervical carcinoma HeLa cells with an IC50 value of 49 \u03bcM [A diketopiperazine (231) with weain HB383 . The new83 [232) was puriof 49 \u03bcM .233) and JBIR-35 (234) from Strd 2.5 mM .S106) and JBIR-57 (S107) were reported in 2011 from the new isolate Streptomyces sp. SpD081030SC-03, which was obtained from an unidentified sponge collected in Ishigaki, Okinawa, Japan [Isolation of two new peptides JBIR-56 were discovered in 2011 from Verrucosispora sp. strain WMMA107, which was separated from Chondrilla caribensis f. caribensis . 22\u2032-Deoxythiocoraline (236), thiochondrilline C (237), and 12\u2032 -sulfoxythiocoraline (238) , which wne (238) showed sectively .Streptomyces sp. strain RV15 was reported to produce four new cyclic lipopeptides cyclodysidins A\u2013D (S110\u2013S113) in 2012 [239 and 240) (S114), were isolated from Streptomyces M1087 associated with an unidentified sponge. The new compounds 239\u2013240 exhibited weak inhibition against the recombinant enzyme sortase B with EC50 values of 88.3 and 126.4 \u00b5g/mL [A sponge-derived in 2012 ,133. Twoand 240) , along w.4 \u00b5g/mL .Streptomyces sp. NIO 10068 derived from a sponge collected from the western coast of India produced linear dipeptides proline\u2013glycine (S115) and N-amido-\u03b1- proline (S116) [241) with MIC values of 0.25\u20130.5 \u03bcg/mL [e (S116) . Kocurin6) [241) , a new m.5 \u03bcg/mL ,137.242) (S117) in 2015, from sponge-associated Streptomyces sp. LS298. Quinomycin G (242) with a terminal double bond in one of the Ser groups exhibited moderate antibacterial activities against Staphylococcuse pidermidis, S. aureus, Enterococcus faecium, and E. faecalis with MIC values ranging from 16 to 64 \u03bcg/mL. In addition, it showed potent anti-tumor activities and the highest activity was observed against the Jurkat cell line (human T-cell leukemia) with an IC50 value of 0.414 \u03bcM [Xin Zhen et al. reported isolation and identification of two new metabolites quinomycin G (242) and cycl0.414 \u03bcM .243) (Streptomyces sp. SBT348 exhibited significant cytotoxicity towards the human promyelocytic HL-60 and the human colon adenocarcinoma HT-29 cell lines [244) (S118) were isolated from Streptomyces sp. GKU 220 is associated with a marine sponge sample collected in Andaman sea, Ranong, Thailand. Rakicidin F (244) showed growth inhibitory activity against B. subtilis and E. coli at the dosage of 25 \u03bcg per disk [A new cyclic dipeptide petrocidin A (243) was discll lines . New cyces [244) and knowper disk .245) was repo \u03bcg/disk . Four disp. G246 . And thr246 [246 and S120sp. G248 .247\u2013250) and actinomycin D (251) (Streptomyces sp. LHW52447 associated with Phyllospongia foliascens obtained from the Xisha Islands in the South China Sea. Actinomycins D1 (247) and D2 (248) introduced an oxazole unit into the central phenoxazinone chromophore and exhibited more potent activities against three strains of MRSA with MIC values of 0.125\u20130.25 \u03bcg/mL than that of actinomycins D3\u2013D4 (MIC = 0.5\u20131.0 \u03bcg/mL), which indicated that the incorporation of the oxazole unit would enhance the antibacterial activity. In addition, the cytotoxicity evaluation against human lung WI38 embryonal fibroblasts suggested that the incorporation of oxazole unit could decrease the cytotoxicity of actinomycins on human normal cells [Four new D-type actinomycin analogs actinomycins D1-D4 ( D (251) were disal cells . The SARal cells ,142.Streptomyces sp. Call-36 isolated from sponge Callyspongia sp. collected in the Red Sea was reported to produce a new diketopiperazine actinozine A (252), cyclo(2-OH-D-Pro-L-Leu) (253), cyclo(D-Pro-L-Phe) (254) (L-Pro-L-Phe) (S123). Compounds 252 and 253 displayed potent activity against S. aureus and were moderately active against C. albicans. Compound 254 exhibited moderate and selective activity against HCT-116 with an IC50 of 32.7 \u00b5M, while cyclo (L-Pro-L-Phe) (S123) was inactive, indicating that the D/L configuration of Pro had an important effect on the activity [e) (254) , and cycactivity .255) (Nesterenkonia sp. MSA31 and active against multidrug-resistant Pseudomonas aeruginosa by inhibiting the phenotypic expression of virulence factors [256\u2013258) was isol factors . Three a256\u2013258) were obt235) is a thiodepsipeptide antitumor antibiotic isolated from Micromonospora sp. L-13-ACM2-092 is associated with a soft coral collected in the Indian Ocean off the coast of Mozambique. Thiocoraline had an inhibitory effect on DNA polymerase \u03b1. In addition, it displayed potent cytotoxicity and strong activity against Gram-positive bacteria [Thiocoraline (229), bacillusamide B (261) (L-Pro-L-Leu) (246), and cyclo (L-Pro-L-Ile) (262) from a sand MSSA ,147. Fou B (261) , cyclo (e) (262) , were send MCF-7 ,72.263\u2013265) (263\u2013265) was repoell line .266, 267) (S127\u2013S129) were discovered from Streptomyces sp. CNB-091 obtained from the surface of jellyfish Cassiopeia xamachana collected in the Florida Keys. Salinamides A and B exhibited moderate antibiotic activity against Gram-positive bacteria. Additionally, the results of phorbol ester-induced mouse ear edema assay showed that salinamides A and B displayed significant topical anti-inflammatory activity using [268) and sality using ,150. In ng [268) , a new b269\u2013271 was separated from Micromonospora sp. ML1 isolated from a mollusk collected from the Indian Ocean coast of Mozambique [272) and H (273) inhibitory activity with IC50 values of 7.50 and 7.37 \u03bcmol/L, respectively [Three known diketopiperazines 269\u2013271 producedolyticus . Thiocorzambique . Limazep H (273) were disectively .S130 and the known valinomycin (230) in 2018, from sea anemone-associated Streptomyces sp. ZZ406. Valinomycin (230) was active against the proliferation of different glioma cells and downregulating the expressions of glioma metabolic regulators [Streptomyces sp. strains 22 and 34 that have been mentioned above. Compound 274 was sepaof 31 \u03bcM ,154.276, 277, S131\u2013S133) were isolated from Streptomyces sp. (ZJG1) cultivated from stony corals collected in the South China Sea. Compound 277 (276 (Five sesquiterpenes (ound 277 showed g277 (276 exhibiteS134) and B (278) was repos aureus .Streptomyces sp. RKBH-B7 is associated with octocoral Eunicea. Guanahanolide A (279) showed m280) (S135), two novel eunicellin diterpenoids, were reported in 2020 from the culture of Streptomyces albogriseolus SY67903 associated with the gorgonian Muricella sibogae collected at the South China Sea. Microeunicellol A exhibited cytotoxicities against several human cancer cell lines [Microeunicellols A (280) and B (Sll lines .281\u2013283) were disof 30 \u03bcM .284) , a novel2 \u03bcmol/L .285) (S136) were isolated from sponge-associated Streptomyces sp. RM66. Manadoperoxide H exhibited antitrypanosomal activity against Trypanosoma brucei rhodesiense with an IC50 value of 0.375 \u03bcg/mL [Manadoperoxide H (285) and acan75 \u03bcg/mL .S137) was purified from Micrococcus luteus R-1588-10 associated with sponge Xestospongia sp. collected at Noumea, New Caledonia. Additionally, the previously known synthetic 2,4,4\u2032-trichloro-2\u2032-hydroxydiphenylether (286) was alsoalbicans ,160.287) (Streptomyces sp. (LA3L2). Two known compounds montagnetol (S138) and erythrin (S139) were also isolated from Streptomyces sp. (LA3L2) that is the first reported actinomycete to produce these lichen-related compounds. In addition, chromomycin A2 (S140), chromomycin A3 (S141), and chromomycin 02-3D (S142) were reported to be separated from Streptomyces sp. (LA3L1) [Isolation of a new cytotoxic metabolite (287) characte (LA3L1) .290), B (291), and C (292), together with two known analogs X-14881 A (288) and X-14881 B (289) , were pr B (293) was alsoy modest ,121.Streptomyces sp. strain T03 derived from the sponge Tethya sp. led to the identification of butenolide (294) (trypanosoma activity against Trypanosoma brucei brucei (IC50 = 31.77 \u03bcM) [295) (Actinomadura sp associated with a sea squirt Ecteinascidia turbinate. It showed potent activity against Clostridium difficile NAP1/B1/027 [de 294) , which e4 , which1.77 \u03bcM) . EcteinaM) [295) was obta1/B1/027 ,115.S143) and two known compounds S144 and S145 were isolated from Streptomyces microflavus strain No. HVG29 is associated with the marine sponge Hymeniacidon perlevis collected from the coast of Dalian (China). Compounds S143\u2013S145 were the first time to isolate deoxyuridine structures from S. microflavus associated with sponges [New nucleoside derivative ( sponges .Streptomyces sp. NIO 10068 derived from a marine sponge produced cinnamic acid (296) , which wnt study .297, 298) (S146) from Solwaraspora sp. WMMB329 is associated with ascidian Trididemnum orbiculatum. The two novel compounds demonstrated antibacterial activity against MRSA and MSSA [In 2014, Ellis et al. reported isolation and identification of two novel trialkyl-substituted aromatic acids, solwaric acids A and B , togetheand MSSA ,162.299, S147\u2013S149) and diphosphatidylglycerol (S150) were produced by Microbacterium sp. HP2 associated with sponge Halichondria panacea collected at the Adriatic coast, Rovinj, Croatia. The major compound 299 was reported in 2017 from Streptomyces griseorubens sp. ASMR4 is associated with an unidentified soft coral collected in the Red Sea at the Hurghada coast, Egypt. Additionally, along with metabolite S144, seven other known metabolites S152\u2013S158 were also discovered from the strain ASMR4 [Isolation of a new oxaphenalene derivative (in ASMR4 .S159) and tryptophan (S160) were produced by Rhodococcus sp. UA13 [S161) and 1,4-dihydroxy-2-naphthoic acid (S162) were isolated from the axenic culture of Saccharomonospora sp. UR22 [S160) and L-phenylalanine (S163) were produced by the sponge-associated Streptomyces sp. G246 [300 was produced by the sea anemone-derived Streptomyces sp. ZZ406 [Phenylacetic acid methyl ester (sp. UA13 . Two knosp. UR22 . In addisp. G246 . The kno246 [300 isolatedactivity . GTRI-02p. ZZ406 .S165) and thymidine-3-thioamine (S166) from sponge-associated Streptomyces sp. Call-36 [302) transcriptional activation effect [In 2019, Shaala et al. reported the discovery of two new nucleosides thymidine-3-mercaptocarbamic acid was prodE,8Z)/-5-oxo-6,8-tetradecadienoic acids and the fish pathogen Tenacibaculum maritimum (preferred 304). In addition, compounds 303 and 304 displayed agonistic activity against peroxisome proliferator-activated receptors (PPARs) with an isoform specificity towards PPAR\u03b1 and PPAR\u03b3 [A pair of geometrically isomeric unsaturated keto fatty acids were idend PPAR\u03b3 .305) (S167), actinopolysporin B (S168), and acanthosterol G (S169) was reported in 2021 from sponge-associated Streptomyces sp. RM66. Peroxidessethyl plakortide Z was active against solid tumor and L-1210 leukemia cell lines in vitro [Isolation of four metabolites ethyl plakortide Z (305) , seco-plin vitro .306, 109) were produced by an unidentified actinomycete strain CNC-837 obtained from the surface of the Caribbean brown alga Lobophora variegate. The new compounds, distantly related to antibiotics of the kijanimicin class, are potent inhibitors of topical PMA-induced edema in the mouse ear assay when administered either topically or IP [Two new anti-inflammatory compounds lobophorins A and B from the central Cantabrian Sea. Streptomyces cyaneofuscatus M-27 produced several antitumor antibiotics of the anthracycline family, of which two antibiotics were identified as daunomycin (307) and cosmomycin B (308) (309) (310) . And it 8) (309) . In addi9) (310) was sepaoperties .311) was repoes T\u00fc 57 .312) (S170) were separated from the seaweed-associated Streptomyces sp. HZP-2216E obtained from sea lettuce Ulva pertusa, a traditional Chinese medicine. They are both existing as zwitterion and streptopertusacin A showed moderate activity against the growth of MRSA [A unique indolizinium alkaloid streptopertusacin A (312) and a no312) S were sep of MRSA .S171\u2013S173), together with the known benzamides 2-acetamido-3-hydroxybenzamide (S174), 2-amino-3-hydroxybenzamide (S175), and 2-aminobenzamide (S176), were isolated from the Streptomyces sp. ZZ502 is associated with the seaweed Ulva conglobatea collected in the East China Sea [Three new compounds (hina Sea .S177 was reported in 2013 from Streptomyces cavourensis YY01-17 separated from the lichens grown in the Antarctic area [Isolation of a novel metabolite tic area .313 (S178\u2013S180) from Streptomyces sundarbansensis strain WR1L1S8 associated with brown algae Fucus sp. collected in Bejaia coastline, Algeria. Compound 313 stood out as the most active of the series, showing a selective antibacterial activity against MRSA with a MIC of 6 \u03bc\u039c [Polyketide 313 [2-hydro of 6 \u03bc\u039c .314) and B (315) produced by Streptomyces cyaneofuscatus M-27 associated with Fucus spiralis was first isolated from Streptomyces or marine environments [Germicidins A ( B (315) , discoveronments .316) , a 28-me0\u22125\u00b5g/mL .317), together with bafilomycin D(320), 9-hydroxybafilomycin D (321), and bafilomycin A1(322) and 21,22-en-9-hydroxybafilomycin D (319) (S182) were separated. Compounds 318 and 319 had potent activity against the proliferation of glioma U251 and C6 cells with IC50 values of 0.12\u20131.08 \u03bcM. In addition, they were active against MRSA with MIC values of 12.5 mg/mL. The four bafilomycins of compounds 320\u2013322 and 317 showed potent activity in suppressing the proliferation of the four tested glioma cell lines with IC50 values of 0.35 to 2.95 \u00b5M. In addition, compounds 320\u2013322 were reported to have antibacterial, antifungal, insecticidal, and herbicidal activities. Bafilomycins D and A1 also exhibited potent activity in inhibiting vacuolar-type ATPase [A new compound of 23-O-butyrylbafilomycin D( A1(322) , was iso D (319) , togethee ATPase ,171.323) and colon carcinoma (DLD-1), but not normal mammary fibroblasts [Desertomycin G (323) was separoblasts .S183, S184) and Germicidins K, L , together with six previously reported metabolites wailupemycin D (S187), wailupemycin E (S188), enterocin/vulgamycin (324), 5-deoxy-enterocin (325), germicidin A (314) and germicidin B (315) , was rep griseus .326\u2013328) was repoor cells .329) from Strectively .330) and imDKP (331) (Streptomyces praecox strain 291-11 separated from the rhizosphere of Undaria pinnatifida. The two compounds inhibited zoospores with a therapeutic ratio (LC50/EC50) of 17.7 and 21 and inhibited diatoms with a therapeutic ratio of 17.7 and 21, respectively [Two antifouling diketopiperazines bmDKP (KP (331) were isoectively .S189) and cholest-4-en-3-one (S190) were discovered from Streptomyces sp. FX-58 is associated with marine plant Salicornia herbacea [332\u2013335) produced.2 \u03bcg/mL .336) and 2-hepta-1,5-dienyl-3,6-dihydroxy-5-(3-methylbut-2-enyl) benzaldehyde (337) benzaldehyde (de (337) were repus iniae .S191) in 2013 together with a known compound (S192) from lichen-derived Streptomyces cavourensis YY01-17 [338) , hydrocinnamic acid (S193), and (E)-cinnamic acid(S194) were separated from Streptomyces ambofaciens BI0048 associated with red alga Laurencia glandulifera [Shan-Shan Su et al. reported the discovery of a novel compound ( YY01-17 . And a n17 [338) was prodbacteria . Three kdulifera .S195), the compound responsible for the \u201cearth smell\u201d and beta-patchoulene (S196) used as a fragrance agent in the perfume industry, were two major metabolites of Streptomyces carnosus M-40 [339) and Linoleic acid (340) , which wes T\u00fc 57 .Streptomyces (68%), Micromonospora (6%), and Nocardiopsis (3%) are the dominant producers , polyketides (33%), and peptides (15%) comprise the largest proportion of secondary metabolites, while roducers . Figure roducers .Approximately 64% of the SMs displayed various biological activities, especially antimicrobial activity and cytotoxicity . Interes9) is the earliest rifamycin antibiotic used in clinical application. Tetrodotoxin (105) has been widely used as an analgesic, sedative, antispasmodic, and local anesthetic in clinics. And daunomycin (307) has a good effect on acute myeloid leukemia. In addition, for these drugs already in clinical use, more clinical trials are underway for new diseases or new usages. .Molecules with excellent activities, which have been in clinical applications or have entered clinical trials, were listed in Metabolites from actinomycetes associated with marine organisms have proven to be an abundant source for the isolation of multiple potent bioactive metabolites with diverse structures. In this review, we attempt to discuss the significance of the special ecological status and genetic factors of these actinomycetes with multiple hosts. The chemical ecology underlying hosts\u2013actinomycetes interactions provide a great opportunity for the discovery of novel drugs. During the co-evolution, these actinomycetes and their specific hosts constructed a coordinated and relatively independent micro-ecological environment, in which SMs can be tolerated by the host and are the active inhibiting specific external invasion. Therefore, actinomycetes associated with various marine hosts play an important ecological role in producing novel medicinal active compounds. Currently, there are relatively few studies on these actinomycetes, but many secondary metabolites have been isolated with excellent bioactivities. Some of these metabolites have been used in clinical applications or have entered clinical trials where they are expected to become new drugs. There is no doubt that further exploration can be a useful strategy for discovering novel marine natural products. These actinomycetes, however, are difficult to be cultured under experimental conditions. Therefore, in-depth exploration of the ecology of these actinomycetes to continuously optimize culture conditions is crucial for further research. Meanwhile, the use of advanced bioinformatics technology for gene detection of uncultured actinomycetes and heterologous expression of the collected biosynthetic gene clusters will be another important pathway for research on SMs of marine organism-associated actinomycetes."} +{"text": "The cave biodiversity of continental Portugal faces tremendous conservation challenges, mostly linked to their direct destruction and contamination infiltrating from the surface. Beetles are the most diverse insects and one of the most diverse arthropod groups in caves of Portugal.Carabidae) are the most diverse family of cave-adapted beetles in continental Portugal, followed by rove beetles (Staphylinidae). Beetles in caves of Portugal are mostly terrestrial and only one species is known to have evolved to live in groundwater. Trechus is the most diverse genus with four species, followed by Domene with three species and by Speonemadus and Iberoporus, both with one cave-adapted species. The aim of this contribution is to assess all endemic cave-adapted species of beetles from continental Portugal and to support their specific protection, to promote adequate management of surface habitats and the establishment of priority areas for conservation. The main biodiversity erosion drivers that are impacting the conservation of the studied species are pollution infiltrating from the surface, urbaniation, modifications of the natural habitat for touristic purposes and mining, quarrying and energy production infrastructures.We present the IUCN Red List profiles for the cave-adapted beetles from continental Portugal, all endemic to their respective geological units and massifs. Ground beetles (This document can be used in spatial planning and territory management in karst, based on the current scientific knowledge. Cave fauna has relatively low specific richness, but high conservation value for the global biodiversity of our planet . SubterrInsecta, Coleoptera) stand out, as a group that presents the greatest animal specific richness worldwide (Coleoptera (Carabidae (mostly Trechinae) and Leiodidae (mostly Cholevinae) .Portugal is located in the western part of the Iberian Peninsula, has more than 2000 caves identified and is considered a hotspot of subterranean biodiversity . More thTrechusfulvus Dejean, 1831, captured by M.L.W. Schaufuss; the caves then explored remain unknown consists of a matrix of unaggregated rock that can be found in scree slopes. Most of this sampling was performed under the framework of Master and Doctoral studies and all 2) and the maps were created in the open source software QGIS 3.14.16, with the natural protected areas of Portugal layer (Extent of occurence (EOO) and area of occupancy (AOO) were calculated using the Geospatial Conservation Assessment Tool (GeoCAT) with an approximation to the standard IUCN 2 km \u00d7 2 km cells or Photo(s): Fig. 1Region for assessment: EuropeBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 2Basis of EOO and AOO: Known habitat extentBasis (narrative): The extent of occurrence (EOO) and area of occupancy (AOO) are both 4 km\u00b2.Min Elevation/Depth (m): 218Iberoporuspluto is a groundwater-adapted beetle known from a stream in a single cave, located in north-eastern Sic\u00f3 karst area. The cave stream, where it was found, flows in a subterranean system of approximately 15 km of horizontal implementation (Range description: entation .EOO (km2): 4Trend: Decline (observed)Justification for trend: A decline in EOO is inferred due to the degradation of the cave by anthropogenic impact as Soprador do Carvalho Cave is subject to recreational visitation and direct trampling on the subterranean stream.Causes ceased?: NoCauses understood?: YesCauses reversible?: YesExtreme fluctuations?: UnknownTrend: Decline (projected)Justification for trend: No decline in AOO has been observed, but it is inferred due to the decline and vulnerability of the habitat.Causes ceased?: NoCauses understood?: YesCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Iberoporuspluto occurs in a single cave, Soprador do Carvalho, in the Sic\u00f3 karst area in central Portugal and it is under moderate disturbance : Only one specimen of this species is known from a single location in central Portugal.Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: FreshwaterHabitat specialist: YesHabitat (narrative): The specimen was collected in the bottom of a clay pool connected to a subterranean stream .Trend in extent, area or quality?: Decline (observed)Justification for trend: Soprador do Carvalho Cave is located in the vicinity of a village, agricultural fields and a quarry . It is aHabitat importance: Major ImportanceHabitats: 5.1. Wetlands (inland) - Permanent Rivers/Streams/Creeks 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 5.1. Wetlands (inland) - Permanent Rivers/Streams/Creeks 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 2.8 mmGeneration length (yr): 1Dependency of single sp?: UnknownIberoporus Castro & Delgado, 2001 is endemic to the Iberian Peninsula and exclusively stygobiont (Iberoporuspluto has extreme troglomorphic traits (eyeless and depigmentation) and unusually elongated legs not adapted for swimming (Ecology and traits (narrative): The genus ygobiont . Iberoposwimming .Justification for threats: The cave is explored for tourism and visitors step over the habitat where the species was found . Other tThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas3.2. Energy production & mining - Mining & quarrying6.1. Human intrusions & disturbance - Recreational activities9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas3.2. Energy production & mining - Mining & quarrying6.1. Human intrusions & disturbance - Recreational activities9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: Measures should be taken to prevent infiltration of wastewaters from the village into the cave stream. The nearby quarry has been reported in the national media to be the source of the infiltration of small particles of quarry dust that have been deposited all over the gallery of Algarinho Cave by flood events. This type of slurry is known to perniciously impact groundwater quality and AlgaConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management2.3. Land/water management - Habitat & natural process restoration4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management2.3. Land/water management - Habitat & natural process restoration4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Further investigation is needed about the distribution, ecology and life cycle of the species. Developing a management plan for this species is crucial. This plan will aid the conservation of the cave-adapted species of the Sic\u00f3 karst area.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Further investigation is needed about the distribution, ecology and life cycle of the species. Developing a management plan for this species is crucial. This plan will aid the conservation of the cave-adapted species of the Sic\u00f3 karst area.TrechusmachadoiScientific name: Species authority: Jeannel, 1941AnimaliaKingdom: ArthropodaPhylum: InsectaClass: ColeopteraOrder: CarabidaeFamily: T.fulvus-group of species.Taxonomic notes: This species belongs to the Figure(s) or Photo(s): Fig. 2Region for assessment: EuropeBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 3Basis of EOO and AOO: Known habitat extent2.Basis (narrative): The extent of occurrence (EOO) and the maximum estimated area of occupancy (AOO) are both 4 kmMin Elevation/Depth (m): 389Max Elevation/Depth (m): 400Trechusmachadoi is a troglobiont beetle known only in the Alcobertas Cave and in a countinuous mesovoid shallow substratum (MSS) located in the Serra dos Candeeiros subunit of the Estremenho karst massif, central Portugal. The cave extends horizontally for approximately 210 m (Range description: ly 210 m and the ly 210 m .EOO (km2): 4Trend: Decline (observed)Justification for trend: Despite intensive sampling in the type locality (cave), no specimens have been found in there since the species description. Only recent sampling in the MSS contiguous to the cave retrieved specimens.Causes ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: Decline (observed)Justification for trend: AOO decline has been inferred due to the vulnerability of the habitat.Causes ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 2Trechusmachadoi is known only from the Alcobertas Cave and from the adjacent MSS, located approximately 80 m from each other. Its distribution is likely to be confined to the subterranean habitats of the Serra dos Candeeiros subunit : So far, only one population is known from the Alcobertas Cave, which is also dispersed in the contiguous mesovoid shallow substratum at 0.5 m depth in scree slopes .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: NoSystem: TerrestrialHabitat specialist: YesTrechusmachadoi population to other parts of the subterranean network in scree slopes close to the type locality (Habitat (narrative): The Alcobertas Cave was subject of a large anthropogenic intervention at the beginning of the 1970s, with the intention to transform it to receive mass tourism. During that process, a second entry was opened near the end of the gallery which induced significant changes in the climatology of the cave . Many ex network . The Alclocality . These slocality .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - Caves7.2. Caves and Subterranean Habitats (non-aquatic) - Other Subterranean HabitatsHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - Caves7.2. Caves and Subterranean Habitats (non-aquatic) - Other Subterranean HabitatsSize: 4.85 mm (lectotype)Generation length (yr): 1Dependency of single sp?: UnknownTrechusmachadoi is a troglobiont with reduced eyes and body depigmentation. It lives exclusively in subterranean habitats and is only known from a single cave and from scree slopes habitats in the Serra dos Candeeiros subunit of the Estremenho karst massif in central Portugal (Ecology and traits (narrative): Portugal .Justification for threats: Since the 1970s, this cave has been intensively explored for touristic activities. During that period, a second entrance has been opened, drastically changing the environment . The scrThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas3.2. Energy production & mining - Mining & quarrying3.3. Energy production & mining - Renewable energy6.1. Human intrusions & disturbance - Recreational activitiesThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas3.2. Energy production & mining - Mining & quarrying3.3. Energy production & mining - Renewable energy6.1. Human intrusions & disturbance - Recreational activitiesJustification for conservation actions: The habitats are protected under the EU \u201cRede Natura 2000\u201d , but theConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Further investigation is needed about the population size, extent of distribution, ecology and life cycle. It is urgent to develop a management plan for this species, which will consequently improve the conservation of further cave-adapted species of Serra dos Candeeiros subunit of the Estremenho massif.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Further investigation is needed about the population size, extent of distribution, ecology and life cycle. It is urgent to develop a management plan for this species, which will consequently improve the conservation of further cave-adapted species of Serra dos Candeeiros subunit of the Estremenho massif.TrechusgamaeScientific name: Species authority: Ribeira & Reboleira, 2009AnimaliaKingdom: ArthropodaPhylum: InsectaClass: ColeopteraOrder: CarabidaeFamily: T.fulvus-group\u201d species complex.Taxonomic notes: This species belongs to the \u201cFigure(s) or Photo(s): Fig. 3Region for assessment: EuropeBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 4Basis of EOO and AOO: Known habitat extentBasis (narrative): The extent of occurrence (EOO) is 73.4 km\u00b2 and the maximum estimated area of occupancy (AOO) is 24 km\u00b2.Min Elevation/Depth (m): 250Max Elevation/Depth (m): 485Trechusgamae is a troglobiont beetle, known from five caves and from the mesovoid shallow substrate (scree slopes), all located in the Santo Ant\u00f3nio Plateau, the central subunit of the Estremenho karst massif (Range description: t massif .EOO (km2): 73.4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 24Number of locations: 6Trechusgamae was found in five caves: Algar de Marradinhas II, Algar das Gralhas VII, Algar do Pena, Algar da Arroteia and Algar do Ladoeiro, all located in the Santo Ant\u00f3nio Plateau, the central subunit of the Estremenho karst massif. Recently, a single specimen was found in the mesovoid shallow substrate at 0.5 m depth in scree slopes of F\u00f3rnea, which is also located in the Santo Ant\u00f3nio Plateau, showing that this species may also disperse through more superficial subterranean habitats : Amongst the six known localities with populations of eia Cave . Algar deia Cave . All theNumber of subpopulations: 6Trend: Decline (inferred)Justification for trend: All the subpopulations face threats derived from intensive quarrying activity, which changes land use and disturbs the natural processes of the habitat. The subpopulations from Algar do Ladoeiro, Algar das Marradinhas II, Algar da Arroteia and F\u00f3rnea face threats of pollution and land use disturbance due to the proximity of urbanised areas.Extreme fluctuations?: UnknownSevere fragmentation?: NoSystem: TerrestrialHabitat specialist: YesTrechusgamae was found in the deepest parts of the caves, from 50 to 95 m depth, all with high humidity levels (> 98%) and temperatures ranging from 13.5\u00baC (in Algar do Pena) to 17\u00baC (in Algar de Marradinhas II) (Habitat (narrative): nhas II) . The cavnhas II) . More renhas II) .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - Caves7.2. Caves and Subterranean Habitats (non-aquatic) - Other Subterranean HabitatsHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - Caves7.2. Caves and Subterranean Habitats (non-aquatic) - Other Subterranean HabitatsSize: 4.83\u20135.38 mm , 3.94\u20135.44 mm Generation length (yr): 1Dependency of single sp?: UnknownTrechusgamae was the only cave-adapted beetle collected in the caves and MSS of the Santo Ant\u00f3nio Plateau and it shows a strict subterranean lifestyle (Ecology and traits (narrative): ifestyle . Both adifestyle .Justification for threats: The distribution area of the species is all covered by the Natural Park of Serras d'Aire e Candeeiros. However, intense quarry activity is currently ongoing in the surrounding areas of the known localities. Algar do Pena is located 300 m from a quarry and Algar das Gralhas VII 168 m from the same quarry. Algar do Ladoeiro's entrance is 840 m from the closest urban areas, Algar das Marradinhas II is located 1.5 km from the nearest village and Algar da Arroteia is located 112 m from the closest house and 1.3 km from a quarry. Algar do Pena Cave hosts a laboratory and is open for visits upon previous booking. F\u00f3rnea is located 595 m from the closest house and 1.9 km from a quarry. The distribution area faces severe groundwater contamination , due to Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas3.2. Energy production & mining - Mining & quarrying6.1. Human intrusions & disturbance - Recreational activities9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas3.2. Energy production & mining - Mining & quarrying6.1. Human intrusions & disturbance - Recreational activities9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: Although the habitat is protected by law under the \u201cRede Natura 2000\u201d , the speConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Additional investigation about the population size, extent of distribution, ecology and life cycle is required. The development of a management plan that will improve the conservation of this cave-adapted species in the Santo Ant\u00f3nio Plateau subunit of the Estremenho karst massif is fundamental to ensure its conservation and protection.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Additional investigation about the population size, extent of distribution, ecology and life cycle is required. The development of a management plan that will improve the conservation of this cave-adapted species in the Santo Ant\u00f3nio Plateau subunit of the Estremenho karst massif is fundamental to ensure its conservation and protection.TrechuslunaiScientific name: Species authority: Ribeira & Reboleira, 2009AnimaliaKingdom: ArthropodaPhylum: InsectaClass: ColeopteraOrder: CarabidaeFamily: T.fulvus-group\u201d species complex.Taxonomic notes: This species belongs to the \u201cFigure(s) or Photo(s): Fig. 4Region for assessment: EuropeBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 5Basis of EOO and AOO: Known habitat extent2 and the maximum estimated area of occupancy (AOO) is 12 km\u00b2.Basis (narrative): The extent of occurrence (EOO) is 4 kmMin Elevation/Depth (m): 95Max Elevation/Depth (m): 307Trechuslunai is a troglobiont Carabidae known from three horizontal caves, located in Serra de Aire/S\u00e3o Mamede Plateau (Range description: Plateau .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 12Number of locations: 3Trechuslunai was found in three caves of the Serra de Aire/S\u00e3o Mamede Plateau subunits. The southernmost distribution is the Almonda Cave, but this species is also known from the Contenda and Moinhos Velhos Caves' system : Three populations are known exclusively from the Serra d'Aire/S\u00e3o Mamede Plateau subunit of the Estremenho karst massif .Number of subpopulations: 3Trend: Decline (inferred)Justification for trend: The subpopulation in Almonda cave is subject to wastewater and pollution infiltration and the subpopulations of the Contenda and Moinhos Velhos Caves face heavy contamination derived from the village under which they are located.Extreme fluctuations?: UnknownSevere fragmentation?: NoSystem: TerrestrialHabitat specialist: YesTrechuslunai only occurs in the deepest parts of the caves, from 50 to 80 m depth. The three caves have high humidity levels and average temperature of 18\u00baC (Habitat (narrative): of 18\u00baC . In Moin of 18\u00baC . The oth of 18\u00baC .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 3.55\u20134.73 mmGeneration length (yr): 1Dependency of single sp?: UnknownTrechuslunai was the only troglobiont species captured in these caves. All known localities are caves that flood seasonally (Ecology and traits (narrative): asonally .Justification for threats: Almonda Cave is located 50 m from a factory that conducts the subterranean river into the building for industrial use of the water and at 420 m from the village centre. The surrounding village is also heavily populated by agricultural fields. Contenda and Moinhos Velhos caves are heavily contaminated, as their subterranean network extends below the village of Mira d'Aire. The entrance of Moinhos Velhos Cave is located in the village centre and it has been explored for tourism since the 1960s with several complementary touristic infrastructures built .Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.3. Agriculture & aquaculture - Livestock farming & ranching9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.3. Agriculture & aquaculture - Livestock farming & ranching9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: The Contenda and Moinhos-Velhos caves develop below the village of Mira d'Aire and infiltration of sewage is observed in the underground. Therefore an effort to improve sewage treatment is necessary in order to prevent wastewater run-off into subterranean gealleries and groundwaters. Almonda Cave is classified as Property of Public Interest (IIP) since 1993 and protected due to archaeological heritage . The arcConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Information about the population size, extent of distribution, ecology and life cycle of this species is scarce, therefore, further investigation is required. It is also necessary to develop a management plan that will improve the conservation of the species in the Serra de Aire/S. Mamede Plateau subunits of the Estremenho karst massif.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Information about the population size, extent of distribution, ecology and life cycle of this species is scarce, therefore, further investigation is required. It is also necessary to develop a management plan that will improve the conservation of the species in the Serra de Aire/S. Mamede Plateau subunits of the Estremenho karst massif.TrechustataiScientific name: Species authority: Reboleira & Ortu\u00f1o, 2010AnimaliaKingdom: ArthropodaPhylum: InsectaClass: ColeopteraOrder: CarabidaeFamily: T.fulvus-group\u201d species complex. It is recognisable by the shape of the aedeagus and has a slim body, rudimentary wings, reduced eyes and depigmentation. This species is the most troglomorphic ground-beetle known from Portugal or Photo(s): Fig. 5Region for assessment: EuropeBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 6Basis of EOO and AOO: Known habitat extentBasis (narrative): The extent of occurrence (EOO) and the maximum estimated area of occupancy (AOO) are both of 4 km\u00b2.Min Elevation/Depth (m): 380Trechustatai is a cave-adapted hygrophilous Carabidae known only from one small cave, located in Serra do Montejunto (Range description: ntejunto .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Trechustatai only occurs in one cave, Algar do Javali, located in Serra do Montejunto. This species is geographically isolated : Only one population is known from Algar do Javali Cave, in Montejunto karst massif.Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: NoSystem: TerrestrialHabitat specialist: YesTrechustatai was only collected in the deep oligotrophic areas of the cave. It was never found in areas with high organic material content (bat guano accumulation zones). The cave is 10 m deep and extends for 80 m. Temperatures in the deepest zone of the cave ranged from 14.2 \u00baC in winter to 15 \u00baC in summer (Habitat (narrative): n summer .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 5.2\u20135.9 mm , 4.8\u20136 mm Generation length (yr): 1Dependency of single sp?: UnknownTrechustatai is the most troglomorphic carabid beetle from continental Portugal. Other caves of the area were sampled, but T.tatai was never collected elsewhere. The seasonal activity pattern of the beetle was studied during one year in the deepest zone of the cave and specimens were collected during winter, autumn and spring : d spring . The abshumidity .Eucalyptus intensive plantation, with direct impact on land use at the surface, pollution and groundwater depletion.Justification for threats: Algar do Javali Cave is located 1.6 km from a quarry with intensive extraction activity and 2.9 km from the closest village, which induces deep changes in land use at the surface and potential biotic exchange, such as introduction of invasive alien species. The cave entrance is located 50 m from a road and surrounded by Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas2.2. Agriculture & aquaculture - Wood & pulp plantations3.2. Energy production & mining - Mining & quarrying4. Transportation & service corridorsThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas2.2. Agriculture & aquaculture - Wood & pulp plantations3.2. Energy production & mining - Mining & quarrying4. Transportation & service corridorsJustification for conservation actions: Although this cave is protected by law through the \u201cRede Natura 2000\u201d , the speConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Some crucial steps necessary for the protection of the species are the development of a management plan for the conservation of this cave-adapted species in Serra do Montejunto and the promotion of further studies regarding population size, extent of distribution, ecology and life cycle.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Some crucial steps necessary for the protection of the species are the development of a management plan for the conservation of this cave-adapted species in Serra do Montejunto and the promotion of further studies regarding population size, extent of distribution, ecology and life cycle.SpeonemadusalgarvensisScientific name: Species authority: Reboleira, Fresneda & Salgado, 2017AnimaliaKingdom: ArthropodaPhylum: InsectaClass: ColeopteraOrder: LeiodidaeFamily: Speonemadusescalerai-group\" and is recognisable by the equal/subequal length of the 2nd, 4th, 5th and 7th antennomeres and a slightly transverse and hexagonal pronotum : Suppl. materials 7Basis of EOO and AOO: Known habitat extent2 and the maximum estimated area of occupancy (AOO) is 12 km2. The three caves are located along a 48 km straight line, with Algar\u00e3o do Remexido Cave being 23 km from Vale Telheiro and Vale Telheiro Cave being 25 km from Senhora Cave.Basis (narrative): The extent of occurrence (EOO) is 7.4 kmMin Elevation/Depth (m): 72Max Elevation/Depth (m): 269Speonemadusalgarvensis was collected in three caves in the southermost province of Portugal in the Algarve, being most likely endemic to the central and eastern parts of the Algarve karst massif, a region also known as Barrocal Algarvio (Range description: Algarvio .EOO (km2): 7.4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 12Number of locations: 3Speonemadusalgarvensis is known from three caves in the Algarve karst massif : There are three populations known from Portugal, all from caves in the Algarve karst massif. The largest number of individuals was collected in Vale Telheiro Cave, followed by Senhora Cave and Algar\u00e3o do Remexido Cave .Number of subpopulations: 3Trend: Decline (inferred)Justification for trend: All populations are under risk due to wastewater infiltration derived from the urbanised areas in the region. The subpopulation of Algar\u00e3o do Remexido cave is threatened by agricultural pollution infiltration and the subpopulation from Senhora cave is threatened by industrial residue pollution.Extreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): Specimens were collected in three caves, 15 to 30 m deep, with high humidity levels and average temperatures of 17.8\u00baC , 18.8\u00baC (Senhora Cave) and 19.3\u00baC (Algar\u00e3o do Remexido Cave). This species is endemic to the Algarve karst massif .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 4\u20134.9 mmGeneration length (yr): 1Dependency of single sp?: UnknownSpeonemadusalgarvensis occurs exclusively in the Algarve and does not exhibit the typical troglomorphism found in other cave-adapted species, such as evident eye reduction, severe depigmentation and extreme body and appendages elongation, although it has only been collected in caves and never at the surface. This species was found to carry the ectoparasitic fungus of the order Laboulbeniales attached to the cuticle and foresic acari (Ecology and traits (narrative): ic acari .Justification for threats: Algar\u00e3o do Remexido is located under agricultural lands, 370 m from the closest house and 1.7 km from the closest village. Vale Telheiro is located 290 m from the closest house and 745 m from the closest urbanisation. Senhora Cave is located 168 m from the closest house and 900 m from an industrial complex.Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.3. Agriculture & aquaculture - Livestock farming & ranching9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.3. Agriculture & aquaculture - Livestock farming & ranching9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: Although the habitat is protected under legislation by the \u201cRede Natura 2000\u201d , the speConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: The development of a management plan for the conservation of this cave-adapted species in the Algarve karst massif and the encouragement of more studies regarding population size, extent of distribution, ecology and life cycle are essential measures for the protection of the species.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: The development of a management plan for the conservation of this cave-adapted species in the Algarve karst massif and the encouragement of more studies regarding population size, extent of distribution, ecology and life cycle are essential measures for the protection of the species.DomenelusitanicaScientific name: Species authority: Reboleira & Orom\u00ed, 2011AnimaliaKingdom: ArthropodaPhylum: InsectaClass: ColeopteraOrder: StaphylinidaeFamily: Taxonomic notes: Individuals display troglomorphism, such as microphthalmia, lack of wings and body elongation .Figure(s) or Photo(s): Fig. 6Region for assessment: EuropeBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 8Basis of EOO and AOO: Known habitat extentBasis (narrative): The extent of occurrence (EOO) and the maximum estimated area of occupancy (AOO) are both of 4 km\u00b2.Domenelusitanica was found in a single cave located in the Sic\u00f3 karstic massif (Range description: c massif .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Domenelusitanica was collected in Cer\u00e2mica Cave, located in the Sic\u00f3 karst area in central Portugal . This Ccave extends for 355 m : This species is known from a single population in central Portugal .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): Specimens were exclusively collected in the deepest zones of the cave (10 m deep), in high humidity levels and with average temperatures of 16.4\u00baC .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 9\u20139.48 mmGeneration length (yr): 1Dependency of single sp?: UnknownDomenelusitanica is included in the subgenus Lathromene, together with the other two Portuguese species of cave-adapted Domene: D.viriatoi and D.darinkae. This species is a predator troglobiont rove beetle, with reduced eyes, apterous, depigmented and elongated body and appendages : pendages . It is oel, 1946 .Eucalyptus plantations.Justification for threats: Cer\u00e2mica Cave is located 550 m from an animal farm, 3.5 km from the nearest village and 3.6 km from a quarry. It is surrounded by agricultural lands and Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas2.3. Agriculture & aquaculture - Livestock farming & ranching3.2. Energy production & mining - Mining & quarryingThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas2.3. Agriculture & aquaculture - Livestock farming & ranching3.2. Energy production & mining - Mining & quarryingJustification for conservation actions: The habitat is located in an \u201cRede Natura 2000\u201d area . PopulatConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: In order to build a sustainable conservation plan for the species in the Sic\u00f3 karst area, more information about population size, extent of distribution, ecology and life cycle is needed. The threats also need to be addressed and minimised, if possible, in order to improve the habitat quality.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: In order to build a sustainable conservation plan for the species in the Sic\u00f3 karst area, more information about population size, extent of distribution, ecology and life cycle is needed. The threats also need to be addressed and minimised, if possible, in order to improve the habitat quality.DomeneviriatoiScientific name: Species authority: Serrano & Boieiro, 2015AnimaliaKingdom: ArthropodaPhylum: InsectaClass: ColeopteraOrder: StaphylinidaeFamily: Taxonomic notes: This species displays body, leg and antennae elongation, microphthalmia and lack of wings .Region for assessment: EuropeBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 9Basis of EOO and AOO: Known habitat extent2.Basis (narrative): The extent of occurrence (EOO) and the maximum estimated area of occupancy (AOO) are both 4 kmDomeneviriatoi was collected in two galleries of the Buraco da Moura Cave, located in the Serra da Estrela Mountain foothills (Range description: oothills .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Domeneviriatoi was collected from the Buraco da Moura Cave at the edge of the Estrela Mountain chain : This species is known from a single population in the western border of the Estrela Mountain chain, the highest mountain of continental Portugal .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): The cave is formed by granite blocks in the margins of the Cani\u00e7a stream at an elevation of 677 m. It extends for 150 m of underground passages .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 6.9\u20128.2 mm , 6.3\u20128.8 mm Generation length (yr): 1Dependency of single sp?: UnknownDomeneviriatoi is included in the subgenus Lathromene. Both adults and larvae of this species were observed foraging for preys in bat guano on the cave substrate : ubstrate . The cavJustification for threats: The cave entrance is located 127 m from the closest house, 530 m from a hydroelectric power station and 1.2 km from the closest village and is under anthropogenic disturbance due to tourism.Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas6.1. Human intrusions & disturbance - Recreational activities7.2. Natural system modifications - Dams & water management/use9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas6.1. Human intrusions & disturbance - Recreational activities7.2. Natural system modifications - Dams & water management/use9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: Buraco da Moura Cave was classified as a \u201cNational Important Underground Shelter for Bats\u201d therefore a decrease in human disturbance is expected . HoweverConservation action type: In PlaceConservation actions: 1.1. Land/water protection - Site/area protection5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 2.1. Land/water management - Site/area management4. Education & awarenessConservation action type: In PlaceConservation actions: 1.1. Land/water protection - Site/area protection5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 2.1. Land/water management - Site/area management4. Education & awarenessUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.1. Conservation Planning - Species Action/Recovery Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: A sustainable conservation plan for the species is only possible if more information about population size, extent of distribution, ecology and life cycle is collected.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.1. Conservation Planning - Species Action/Recovery Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: A sustainable conservation plan for the species is only possible if more information about population size, extent of distribution, ecology and life cycle is collected.DomenedarinkaeScientific name: Species authority: Magrini & Carotti 2019AnimaliaKingdom: ArthropodaPhylum: InsectaClass: ColeopteraOrder: StaphylinidaeFamily: Region for assessment: EuropeBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 10Basis of EOO and AOO: Known habitat extent2.Basis (narrative): The extent of occurrence (EOO) and the maximum estimated area of occupancy (AOO) are both 4 kmDomenedarinkae is a cave-adapted rove beetle known from an abandoned mine in northern Portugal : 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Domenedarinkae is known from a single horizontal artificial cave, Santa Isabel mine, located in the Mar\u00e3o Mountain chain in north Portugal : Only one specimen of this species is known from a single location in northern Portugal .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): The only known specimen was collected in the rocky debris along the main tunnel of the Santa Isabel mine . The geoTrend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 6.93 mm Generation length (yr): 1Dependency of single sp?: UnknownDomenedarinkae is included in the subgenus Lathromene. It is a predator and exhibits troglomorphisms, such as depigmentation, elongation of body and antennae and accentuated microphthalmia (Ecology and traits (narrative): hthalmia .Threat type: PastThreats: 6.3. Human intrusions & disturbance - Work & other activities7.3. Natural system modifications - Other ecosystem modificationsThreat type: PastThreats: 6.3. Human intrusions & disturbance - Work & other activities7.3. Natural system modifications - Other ecosystem modificationsJustification for conservation actions: Undisturbed areas in the surface of the mine need to be defined and established.Conservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awarenessConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awarenessUse type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Further information about population size, extent of distribution, ecology and life cycle is needed to better protect the species and the habitat. The mine, where the species was found, is an anthropogenic construction that clearly adversely affected the natural habitat of the species that should be the deep fissures and the mesovoid shallow substrate of the area. Therefore, it is recommended to sample these habitats in the area to understand the distribution of this species and to define new conservation priorities.Use type: InternationalEcosystem service type: Very importantResearch needed: 1.2. Research - Population size, distribution & trends1.3. Research - Life history & ecology2.2. Conservation Planning - Area-based Management Plan3.1. Monitoring - Population trends3.4. Monitoring - Habitat trendsJustification for research needed: Further information about population size, extent of distribution, ecology and life cycle is needed to better protect the species and the habitat. The mine, where the species was found, is an anthropogenic construction that clearly adversely affected the natural habitat of the species that should be the deep fissures and the mesovoid shallow substrate of the area. Therefore, it is recommended to sample these habitats in the area to understand the distribution of this species and to define new conservation priorities.http://iyck2021.org), an event organised by the International Union of Speleology to promote the awareness for the importance of caves and their habitats. Under this framework, a global initiative created the International Cave Animal of the Year devoted to cave beetles. Within this initiative, different countries selected their own endemic species as a flag for advocating the conservation of subterranean ecosystems. Here, we offer information about the distribution beetle from Portugal, was described, based on a female specimen and no further specimens have been found in a cave that has been constantly monitored for more than a decade. Its habitat, the Soprador do Carvalho Cave is under serious anthropogenic threats, such as groundwater contamination and touristic pressure ; 2: T.gamae (yellow circle); 3:T.lunai (pink circle); 4: T.tatai (red circle); 5: Iberoporuspluto (blue star); 6: Domenelusitanica (yellow diamond); 7: D.viriatoi (pink diamond); 8: D.darinkae (blue diamond); and 9: Speonemadusalgarvensis (pink triangle). (A) Detail of northern distribution, (B) Detail of central distribution and (C) Detail of southern distribution. In green are protected areas.1: File: oo_528602.tifhttps://binary.pensoft.net/file/528602A.S.P.S. Reboleira, R.P. Eus\u00e9bio0F7E68E8-AAD0-50EE-B880-0CEFA740227D10.3897/BDJ.9.e67426.suppl2Supplementary material 2Iberoporuspluto.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionIberoporuspluto distribution: Soprador do Carvalho Cave, Penela, Coimbra District.File: oo_560421.tifhttps://binary.pensoft.net/file/560421A.S.P.S. Reboleira, R.P. Eus\u00e9bioD7DABAF2-3B19-5E93-BD25-C30939739EB610.3897/BDJ.9.e67426.suppl3Supplementary material 3Trechusmachadoi.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionTrechusmachadoi distribution: Alcobertas Cave and mesovoid shallow substratum, Rio Maior.File: oo_560428.tifhttps://binary.pensoft.net/file/560428A.S.P.S. Reboleira, R.P.Eus\u00e9bioF33828A8-DED8-539A-8ADB-E01A34FF86B110.3897/BDJ.9.e67426.suppl4Supplementary material 4Trechusgamae.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionTrechusgamae distribution: (1) Algar da Arroteia Cave; (2) F\u00f3rnea (MSS); (3) Algar do Ladoeiro Cave; (4) Algar de Marradinhas II Cave; (5) Algar do Pena Cave; and (6) Algar das Gralhas VII Cave. All caves and MSS are located in the Santo Ant\u00f3nio Plateau, the central subunit of the Estremenho karst massif. (A) Detail of distribution.File: oo_560430.tifhttps://binary.pensoft.net/file/560430A.S.P.S. Reboleira, R.P. Eus\u00e9bio50F0176B-32A1-5094-B243-043C8F72D14210.3897/BDJ.9.e67426.suppl5Supplementary material 5Trechuslunai.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionTrechuslunai distribution: (1) Contenda and Moinhos Velhos Cave system; and (2) Almonda Cave, both located in the Estremenho karst massif.File: oo_560431.tifhttps://binary.pensoft.net/file/560431A.S.P.S. Reboleira, R.P. Eus\u00e9bio8999FE89-5F39-5920-80EA-13A029878CF110.3897/BDJ.9.e67426.suppl6Supplementary material 6Trechustatai.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionTrechustatai distribution: Algar do Javali Cave, Montejunto karst massif.File: oo_560436.tifhttps://binary.pensoft.net/file/560436A.S.P.S. Reboleira, R.P. Eus\u00e9bio3044C8C3-6105-508F-AB09-06C452FC863710.3897/BDJ.9.e67426.suppl7Supplementary material 7Speonemadusalgarvensis.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionSpeonemadusalgarvensis distribution: (1) Algar\u00e3o do Remexido Cave; (2) Vale Telheiro Cave; and (3) Senhora cavea, all located in the Algarve karst massif.File: oo_560437.tifhttps://binary.pensoft.net/file/560437A.S.P.S. Reboleira, R.P. Eus\u00e9bio2C303E65-CCAC-500D-B815-0FAE2AEA3BFE10.3897/BDJ.9.e67426.suppl8Supplementary material 8Domenelusitanica.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionDomenelusitanica distribution: Cer\u00e2mica Cave, Sic\u00f3 karst area.File: oo_560438.tifhttps://binary.pensoft.net/file/560438A.S.P.S. Reboleira, R.P. Eus\u00e9bio081BE9A5-9F66-5DA2-8DF0-7B8416C9E0E110.3897/BDJ.9.e67426.suppl9Supplementary material 9Domeneviriatoi.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionDomeneviriatoi distribution: Buraco da Moura Cave, Estrela Mountain chain.File: oo_560439.tifhttps://binary.pensoft.net/file/560439A.S.P.S. Reboleira, R.P. Eus\u00e9bio6A5B9DF4-9ACF-5EC2-B7F1-3228812F5DEC10.3897/BDJ.9.e67426.suppl10Supplementary material 10Domenedarinkae.Distribution of cave-adapted beetle Data typeSpecies distribution mapBrief descriptionDomenedarinkae distribution: Santa Isabel mine, Mar\u00e3o Mountain chain.File: oo_560442.tifhttps://binary.pensoft.net/file/560442A.S.P.S. Reboleira, R.P. Eus\u00e9bio"} +{"text": "Ebola Virus Disease (EVD) outbreaks primarily occur in the HIV endemic setting of Sub-Saharan Africa. Transient increases in HIV viral load (VL), or blips, have been described following routine vaccinations. We characterized VL blips among PLWH enrolled in a phase 2 trial of a heterologous two-dose EVD vaccine.In EBL2003, adult participants with and without HIV were randomized 1:4 to receive placebo or vaccine. Part A in the US studied MVA-BN-Filo followed by Ad26.ZEBOV 14 days later. Part B in Africa evaluated this MVA/Ad26 regimen and also a schedule of Ad26.ZEBOV followed by MVA-BN-Filo 29 days later. VL was assessed at screening, pre-vaccination, and 21, 42, 180, and 365 days post dose 2. Participants with VL < 20 copies/mL at the first 2 visits who received both doses and had complete VL data through 42 days post dose 2 were evaluated. Blips were defined as a post-injection VL \u2265 20 copies/mL no later than 42 days post dose 2, with subsequent return to VL < 20 copies/mL.A total of 277 PLWH on antiretroviral therapy (ART) were assessed; 73.3% (203) had baseline virologic suppression, and 89.2% (181) of those received both doses with complete VL data for inclusion in the analysis. Overall, 19.9% (36) experienced blips: 20.0% (29) of vaccinees vs 19.4% (7) of placebo recipients (p=1.0). All baseline suppressed participants with post-injection viremia subsequently regained suppression. Among vaccinees, the mean blip VL was 192 copies/mL, and the mean blip duration was 56 days, which was not significantly different from placebo. Of all blips, only 2 were > 1,000 copies/mL. Blips occurred in 24.0% (25) of Ad26/MVA recipients, and 9.7% (4) of MVA/Ad26 recipients (p=0.07). A dose of Ad26 was associated with a blip in 6.9% (10) of recipients vs 13.1% (19) for MVA recipients (p=0.12). Regardless of regimen, dose 1 was associated with a blip in 8.3% (12) of vaccinees, compared to 11.7% (17) of vaccinees for dose 2 (p=0.43).Among successfully treated PLWH, we observed low magnitude post-dose HIV blips that were not more common in vaccine vs. placebo recipients and did not result in loss of virologic suppression. This data is favorable for the deployment of the EVD vaccines in this trial in areas of high HIV endemicity.Benjamin L. Custer, M.D., Alexion Pharmaceuticals (Shareholder)Armata Pharmaceuticals (Shareholder)Biomarin Pharmaceutical (Shareholder)Crispr Therapeutics (Shareholder)CVS Health Corp (Shareholder)Editas Medicine (Shareholder)Gilead (Shareholder)Glaxo Smith Kline (Shareholder)Hologic Inc (Shareholder)Merck (Shareholder)Mesoblast LTD (Shareholder)Pfizer (Shareholder)Sanofi (Shareholder)Unitedhealth Group (Shareholder)Vertex Pharmaceuticals (Shareholder) Georgi Shukarev, MD, Janssen (Employee) Auguste Gaddah, PhD, Janssen Pharmaceutica N.V (Employee) Kerstin Luhn, PhD, Janssen Vaccines and Prevention Macaya Douoguih, MD, MPH, Janssen (Employee) Cynthia Robinson, MD, Janssen Vaccines (Employee)"} +{"text": "Once-daily oral tenofovir-based combinations as pre-exposure prophylaxis (PrEP) have shown to be an effective biomedical HIV prevention strategy for populations at-risk of acquiring HIV-1. However, low adherence can lead to poor effectiveness. This study described the characteristics of commercially-insured US PrEP users.This retrospective study used IQVIA\u2122 PharMetrics Plus data (1/1/2015\u20133/31/2020) to identify adults newly initiated (index date) on emtricitabine/tenofovir disoproxil fumarate (FTC/TDF) or emtricitabine/tenofovir alafenamide (FTC/TAF) as daily PrEP. Users had \u22656 months of continuous enrollment pre-index (baseline); those diagnosed with HIV or with antiretroviral therapy (ART) use during baseline were excluded. User characteristics were described during the baseline period. For FTC/TDF users, proportion of days covered (PDC), persistence, treatment breaks, and switching were described during the follow-up period, which spanned from index to the earliest of disenrollment or end of data. Non-persistence was defined as a >90-day gap from last day of supply, with re-initiation after this gap indicating treatment break. For PDC and persistence, follow-up was censored at HIV infection, defined by both multi-class ART initiation and HIV diagnosis. In total 24,232 FTC/TDF and 1,187 FTC/TAF users were identified. Overall, mean age was 35.1 years and 94.5% were male (Table 1). Mean [median] length of follow-up was longer for FTC/TDF (504 [390] days) than FTC/TDF users (77 [70] days). On average, FTC/TDF users had 9.0 dispensings with 38.3 days of supply per dispensing over follow-up; 11.1% had \u22651 treatment break . Among those initiated on FTC/TDF, 10.8% switched to FTC/TAF. The mean PDC for FTC/TDF users at 6 and 12 months was 0.74 and 0.67, respectively, corresponding to 63.7% and 57.9% of patients with PDC \u22650.70 . Persistence to FTC/TDF at 6 and 12 months was 70.2% and 57.4%, respectively .Table 1. Baseline Demographics and Clinical Characteristics of PrEP Users by RegimenFigure 1. Proportion of Days Covered of FTC/TDF UsersFigure 2. Kaplan-Meier Persistence Rates of FTC/TDF UsersPatient characteristics of PrEP users are broadly similar between regimens, though switching from FTC/TDF to FTC/TAF is common. FTC/TDF users had lower real-world PDC and persistence than in recent clinical trials (DISCOVER and HPTN 083).Alan Oglesby, MPH, GlaxoSmithKline (GSK) Guillaume Germain, MSc, ViiV Healthcare Francois Laliberte, MA, Viiv (Research Grant or Support) Staci Bush, NP, GlaxoSmithKline (GSK) Heidi Swygard, MD, ViiV Healthcare (Employee) Sean MacKnight, MScPH, Analysis Group (Employee) Annalise Hilts, BA, Analysis Group, Inc. (Employee) Mei Sheng Duh, MPH, ScD, ViiV Healthcare (Grant/Research Support)"} +{"text": "The innate immune system is the first to respond to invading pathogens. It is responsible for invader recognition, immune-cell recruitment, adaptive-immunity activation, and regulation of inflammation intensity. Previously, two single-nucleotide polymorphisms of innate-immunity genes \u2013 rs5743708 (Arg753Gln) of the TLR2 geneand rs8177374 (Ser180Leu) of the TIRAP gene \u2013 have been shown to be associated with both pneumonia and tuberculosis in humans, but the data are contradictory among different ethnic groups. It has also been reported thatrs10902158 at the PKP3-SIGGIR-TMEM16J genetic locus belongs to a haplotype race-specifically associated with tuberculosis. Meanwhile, a gradient of its frequency is observed in Asia. The aim of this work was to assess the effect ofselection for the genotypes of the above-mentioned SNPs on the gene pools of populations living in harsh climaticconditions that contribute to the development of infectious lung diseases. We estimated the prevalence of thesevariants in white and Asian (Chukchis and Yakuts) population samples from Northern Asia and among patients withcommunity-acquired pneumonia (CAP). Carriage of the rs5743708 A allele was found to predispose to severe CAP, whereas the GG/CT genotype of rs5743708/rs8177374 proved to be protective againstit in white patients. No association of rs10902158 with CAP was foundamong whites. Stratification of CAP by causative pathogen may help eliminate the current discrepancies betweendifferent studies. No significant difference in rs5743708 or rs8177374 was found between adolescent and long-livedwhite samples. Carriage of the alleles studied is probably not associated with predisposition to longevity amongwhites in Siberia. Both white and Asian populations studied were different from Western European and East Asianpopulations in the variants\u2019 prevalence. The frequency of the rs8177374 T (Ser180Leu) variant was significantly higherin the Chukchi sample relative to the East Asian populations. This result may confirm the hypothesisabout the selection of this allele in the course of human migration into areas with unfavorable climatic conditions. Innate immunity constitutes the first barrier against microorganisms and viruses by destroying infected cells and activatingadaptive immunity. Nonetheless, an excessive nonspecificimmune reaction (inflammation) may be life threatening because it can completely disrupt the functioning of vital organs.Community-acquired pneumonia (CAP) and pulmonary tuberculosis(PTB) are infectious diseases characterized by highmortality, and according to WHO, are ranked consistentlyamong the top 10 leading causes of death in the world (https://www.who.int/en/news-room/fact-sheets/detail/the-top-10causes-of-death).Pneumonia is an inflammatory lower-respiratory-tractdisease caused by viruses, bacteria, fungi, and parasites. Inaddition, it may be due to noninfectious processes or have acombined cause. For a long time, Streptococcus pneumoniaeinfection has been considered the main cause of CAP; however, it was shown recently that CAP develops mainly as aresult of viral infections . Streptococcus pneumoniae, Haemophilus inf\u200aluenzae,Staphylococcus aureus, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila and othermicrobes may be causative agents of bacterial pneumonia. Afterinvasion of the airway epithelium by pathogens, these cellsstart to produce reactive oxygen species, cytokines, and othermediators to recruit immune cells. Being most abundant inlungs, alveolar macrophages ingest bacteria and apoptoticcells and can present antigens on MHC II to other immunecells. Proinflammatory M1 macrophages produce cytokinesTNF\u03b1, IL-6, IL-1\u03b2, IL-12, and IL-23 to enhance inflammationfor elimination of the invaders. Anti-inflammatory M2 macrophages produce cytokines IL-4, IL-13, and TGF-\u03b2 to inducecompletion of the inflammatory reaction and remodeling ofdamaged tissue .Depending on the set of present chemokines and cytokines,different cells responsible for humoral and cellular immunityare attracted to the site of infection . Severepneumonias are more likely to develop in coinfections; ithas been demonstrated that a viral infection (in particularinfluenza) facilitates the development of pneumococcal infection by damaging the epithelium and reducing the amount ofa surfactant . Humanrespiratory syncytial virus, metapneumovirus, adenovirus, andinfluenza viruses A and B prefer a cold season . The seasonal increase in the incidence of pneumococcalpneumonia coincides with seasonal outbreaks of influenza;S. pneumoniae, H. inf\u200aluenzae, and S. aureus infections havebeen reported to be associated with significant influenzapandemics . PTB is a pulmonary infectious disease caused mainly byMycobacterium tuberculosis (Mtb). According to the WHO,approximately one-quarter of the world\u2019s population is estimated to be infected by Mtb, and 5\u201315 % of these peoplewill fall ill with active tuberculosis. In Russia, most of thesepatients (95 %) have PTB . The pathogenesisof pulmonary tuberculosis is based on Mtb survival afterphagocytosis by alveolar macrophages. These bacteria canmodulate a host immune response to protect the infectedcells, change their metabolism, induce IL-10, suppress IL-12and TNF\u03b1 synthesis, and to inhibit MHC II expression andantigen presentation. Mtb makes macrophages unresponsiveto interferon (IFN) \u03b3 and inhibits autophagy. It allows themycobacteria to establish a persistent or latent infection inmacrophages. Mycobacteria are believed to use the generalmechanism of negative feedback regulation that restrictsexcessive inflammation . With the lossof immunity-driven control over mycobacterial reproduction, foamy macrophages accumulate in granulomas, andlung tissue necrosis begins . Vitamin Ddeficiency is known to negatively affect the effectiveness ofthe immune response in tuberculosis .These data suggest that in Northern Asia, a region with lowtemperature and reduced insolation during most of the year, signs of purifying selection for genes associated with lunginfections may be noticeable. For many genes of innate immunity, an association with viral, bacterial, and autoimmune diseases has been proven. Despite differences in the pathogenesisbetween CAP and PTB, it has been shown that minor allelesof rs5743708 (the TLR2 gene) and of rs8177374 (the TIRAPgene) can have a pathogenic and protective effect, respectively, in both of these lung diseases in humans. Nevertheless,data obtained by different research groups are contradictory.Toll-like receptors (TLRs) play a pivotal role in host defense. Being membrane-anchored orendosomal (TLRs 3 and 7\u22129) in human immune cells , they are involved in the recognition of structurallyconserved surface molecules of microorganisms and viruses aswell as viral nucleic acids . TLR2 participates in the recognition ofa large number of diverse lipoproteins and peptidoglycansof gram-positive and gram-negative bacteria, fungi, andvirus-infected cells. After ligand binding to the receptor, TIR(Toll-interleukin 1 receptor) domains of TLR2 and TLR1 orTLR2 and TLR6 dimerize via the formation of an extensivehydrogen-bonding network and hydrophobic interactions. Homodimerizationof the cytoplasmic domains of TLR2 does not induce TNF\u03b1production in vitro in murine macrophages, and the formation of the TLR2\u2013TLR2 dimer is not detectable even in thepresence of an agonist . Therefore, the existence of TLR2\u2013TLR2 homodimersin vivo is being questioned. After ligand binding, reorientationof the TIR domains and triggering of a cascade of intracellularreactions lead to the activation of proinflammatory NF-\u03baB andMAPK pathways, synthesis and a release of proinflammatorycytokines and various chemokines into extracellular space, and the development of aninflammatory response at the pathogen entry site . In inflammatory monocytes,TLR2 induces type I IFN production in response to a viralligand . It is reported that prolongedstimulation of TLR2 (more than 24 h) causes PI3K/Aktpathway activation in alveolar macrophages. It limits theproduction of NF-\u03baB, TNF-\u03b1, and IL-12 and activates thesynthesis of anti-inflammatory IL-10. This mechanism is assumed to prevent excessive inflammation .The TLR2 gene is located in 4q31.3, has five exons, andexpresses few splicing isoforms, but all of the coding sequences are contained within exon 3. The protein consistsof 784 amino acid residues (aa) and includes extracellularleucine-rich repeat domains, which are primarily responsiblefor ligand recognition (aa 54\u2013524), followed by the leucinerich repeat C-terminal domain (aa 525\u2013579) and intracellularTIRdomain (aa 639\u2013782), which mediates downstream signaling (https://www.uniprot.org/uniprot/O60603). It is expressedconstitutively on macrophages and dendritic cells and can beinduced in epithelial cells or B-cells. Its overexpression inpatients with pneumococcal disease had been documentedSingle-nucleotide polymorphism (SNP) rs5743708 (of theTLR2 gene) causing the Arg753Gln substitution is locatedin the TIR domain of the protein. This SNP is associatedsimultaneously with resistance to Lyme disease and with predisposition to tuberculosis , whereas the association withpredisposition to PTB is race-specific . It is believed that TLR2 signalingmay be nonessential to control acute tuberculosis but important during chronic tuberculosis . Ameta-analysis has shown the TLR2 rs5743708 minorallele to be associated with CAP, Legionnaires\u2019 disease, andpneumococcal disease; however, the data obtained in differentstudies are contradictory .The TIRAP (TIR domain-containing adaptor protein) genealso known as Mal (MyD88 adapter-like) encodes one of thefive adapter proteins that are involved in signal transductionfrom activated TLRs to protein kinases at the plasma membrane . It is located in 11q24.2, consistsof six exons, and encodes a protein of 221 aa. The TIRAPprotein includes an N-terminal PEST domain (aa 15\u201335) responsible for binding to special sites in the plasma membrane,followed by an AB-loop mediating MyD88 and TLR4 binding.A binding site for TRAF6 (TNF receptor-associated factor 6)is located within the region aa 188\u2013193 . TIRAP is expressed in many cell types , and its isoforms resulting from alternative splicing have unknown functions. There are different opinionsabout whether TIRAP forms a complex with the TIR domainof TLR6 for signal transmission; however, it has been proventhat TIRAP mediates TLR2 and TLR4 signaling by facilitating the recruitment of the MyD88 adaptor protein to theTLRs .Activation of NF-\u03baB, MAPK1, MAPK3, and JNK resultsin cytokine secretion and an inflammatory response. SNPrs8177374 (the TIRAP gene) is located in exon 5 and represents the Ser180Leu substitution in the encoded protein. It islocated close to the TLR-binding site of TIRAP. In carriersof this substitution, modulation of TLR1, TLR2, TLR4, andTLR6 but not TLR9 signaling has been shown . Ser180Leuin a heterozygous state has a protective effect against PTB andinvasive pneumococcal disease in white and African samplesand against malaria in African and Asian samples . Carriage of heterozygous Ser180Leuprotects children from pneumococcal lower-respiratory-tractinfections, whereas carriers of the homozygous 180Leu polymorphism alone or in combination with some TLR1 and TLR6polymorphisms may be susceptible to recurrent pneumococcal infections . Simultaneous carriage ofthe TIRAP 180Leu variant and some SNPs in the TLR4 geneas well as 180Leu homozygosity increases susceptibility tosevere hospital-acquired infections .The opposite results have been obtained as well. Thers8177374 T allele (180Leu) increases the risk of PTB in asample of Iranian population . A metaanalysis of nine published case-control studies did not reveal asignificant association of 180L with tuberculosis risk . There are controversial opinions about the mechanism behind the observed protective effect of Ser180Leuheterozygosity. They are based on differences in observed effects of the SNP at the level of proinflammatory cytokines.Depending on the model used, some research groups showedan increased level and others a decreased level of cytokines after their induction in180 Leu/Leu carriers. Accordingly, homozygosity of the minorvariant of rs8177374 is thought to cause either an excessiveinflammatory reaction or the absence of an adequate immuneresponse. It is supposed that selection pressure on the TIRAPgene provides a balance between protection against excessiveinflammation and effective defense during infectious diseases.Besides the polymorphisms in genes TLR2 and TIRAP,in this paper, we focused on the PKP3-SIGGIR-TMEM16Jgene region. An association of its haplotypes with different types of tuberculosis has been shown among childrenin Vietnam and South Africa . It is believed that the impact of the haplotypes onimmunity is determined by SIGIRR , which is a negativeregulator of TLR signaling . Carriageof rs10902158 GG and rs7111432 AA in introns of PKP3and TMEM16J, respectively, acts additively with a vitamin Ddeficiency and \u201cpathogenic\u201d genotypes of rs5743708 (TLR2)and rs8177374 (TIRAP) on tuberculosis predisposition . rs10902158 located in intron 2of the PKP3 gene has been analyzed. Encoded desmosomalplaque protein plakophilin 3 is involved in intracellular adhesion . Of note, rs10902158 has a frequency gradient in Asia; according to the Genome Aggregation Database (GnomAD) (https://gnomad.broadinstitute.org/), it is absent in South Asia and is found with a frequency of~50 % in Southeast Asia. Nonetheless, functional significanceof genetic variants in noncoding parts of the PKP3-SIGGIRTMEM16J gene region, including rs10902158, is not clear.In this work, we analyzed the frequencies of rs5743708,rs8177374, and rs10902158 (for which conflicting data onthe association with respiratory infections have been reportedpreviously) in white and Asian samples from Northern Asiaand among CAP patients. According to the statistics of theMinistry of Health of the Russian Federation, NovosibirskOblast and Yakutia are characterized by an increased incidence of PTB, whereas Chukotka Autonomous Okrug isthe leader in both pneumonia and PTB morbidity in Russia . According to the WHO, thehighest death rate from pneumonia is observed before the ageof 5 and after 75\u201380 years (https://www.who.int/medicines/areas/priority_medicines/Ch6_22Pneumo.pdf). Therefore, weassumed that long-lived people of the Siberian Federal Districtmay differ from adolescents in the frequency of rs5743708 andrs8177374, and we assessed the prevalence of the pathogenicvariants in the sample of long-lived people.The study protocol was approved by the local Ethics Committee of the Institute of Internal and Preventive Medicine . Written informed consentto be examined and to participate in the study was obtainedfrom each patient. For individuals younger than 18 years, theinformed consent was signed by a parent or legal guardian.The white sample consisted of 451 adolescents from Oktiabr\u2019skiidistrict of Novosibirsk (55\u00b001\u2032 N 82\u00b055\u2032 E) and 289 Russiansettlers in towns Tommot (58\u00b058\u203200\u2033 N 126\u00b016\u20320\u2033 E), Neryungri(56\u00b039\u203230\u2033N 124\u00b043\u203230\u2033 E), Ust-Nera (64\u00b034\u203205\u2033 N143\u00b014\u203210\u2033 E), and Yakutsk (62\u00b001\u203238\u2033 N 129\u00b043\u203255\u2033 E), wholived in Yakutia for more than 16 years or were born there.The adolescent sample was described previously . Asian samples consisted of130Chukchis from the Kanchalan village (65\u00b010\u203241\u2033 N 176\u00b044\u203252\u2033 E) ofChukotka Autonomous Okrug and 132 \u00adYakuts from the Kylayy village(63\u00b013\u203234\u2033 N 132\u00b008\u203206\u2033 E) and towns Tommot, Neryungri,and Ust-Nera of Yakutia. The sample of long-lived peoplewas collected in cities Novosibirsk, Tomsk, and Tumen andconsisted of 188 individuals aged 90\u2013105, mean age 92.Ethnicity of individuals was identified using questionnaires and additional cross-examination with elucidation ofthe nationality of ancestors (at least in three generations).Persons of mixed origin were excluded from the analysis.The CAP patient sample (406 whites) was collected in offices of pulmonary hospitals of Novosibirsk and Yakutskin 2003\u20132005 before the COVID-19 outbreak. The sampleconsists of 120 patients with severe CAP and 286 patients with nonsevere (mild to moderateseverity) CAP . The diagnosis ofpneumonia was made on the basis of radiologically confirmed\u201cfresh\u201d lung tissue infiltration and clinical data in theabsence of an obvious diagnostic alternative. CAP of variousetiologies was regarded as severe if the CURB65 rating scaleindex was 4\u20135 points .Genomic DNA was extracted from peripheral blood leucocytes by the standard phenol\u2013chloroform method . Genotyping was performed using polymerasechain reaction (PCR) with an analysis of restriction fragmentlength polymorphism by electrophoresis in a 5 % polyacrylamide gel after visualization with an ethidium bromide solution.The rs5743708 SNP (TLR2) was identified by amplification of DNA with primers 5\u2032-GCCATTCTCATTCTTCTGG*AGC-3\u2032 and 5\u2032-GGGAACCTAGGACTTTATCGCA-3\u2032 (* denotes a nucleotide changed for restriction site creation). The168-bp PCR product was digested with the Pst I restrictionendonuclease for 2 h at 37 \u00b0C. Thers5743708 A (753Q) allele was revealed by the presence offragments of 20, 45, and 103 bp, whereas the rs5743708 Gallele by fragments of 20 and 148 bp.The detection of rs8177374 (TIRAP) was performed byamplification of genomic DNA with primers 5\u2032-GGCTGCACCATCCCCCA*GC-3\u2032 and 5\u2032-CCGTTCCCCTTCTCCCT CCTGTAG-3\u2032 (* denotes a nucleotide changed for restrictionsite creation). The 162-bp PCR product was digested with theAccB7 I restriction endonuclease for 2 h at 37 \u00b0C. The rs8177374 T (180L) allele was identifiedby the presence of fragments of 21 and 141 bp, whereas incase of rs8177374 C, the PCR product was not cut.Primers 5\u2032-TGGCAAGGATTGGAGAACTC*C*TGTC-3\u2032and 5\u2032-CAGGGCCAGTGCCTCCCC-3\u2032 (* denotes nucleotides changed for restriction site creation) were used forthe amplification of the PKP3 intron 2 sequence containingrs10902158. The resulting 192-bp amplicon was digested withthe BstEN I restriction endonuclease for 2 h at 65 \u00b0C. In the presence of the rs10902158 \u0410allele, the PCR product was not cut, whereas in the case ofthe rs10902158 G allele, fragments of 24 and 168 bp wereobserved.Statistical analysis was performed in the SPSS 16.0 software.Genotype distributions were consistent with the Hardy\u2013Weinberg equilibrium among all the population samples (data notshown). Minor allele frequencies for rs5743708, rs8177374,and rs10902158 are represented in Table 1.In the sample of Novosibirsk adolescents, allele frequenciesof rs5743708, rs8177374, and rs10902158 differed from thoseof the non-Finnish European sample in GnomAD .p = 0.013; \u03c72 = 19.541, p = 0; \u03c72 = 54.554, p = 0, respectively).For the frequency of the rs5743708 A (Arg753Gln) allele, there was a tendency for a decrease in Russian settlersin Yakutia and among long-lived people compared with theNovosibirsk sample.The rs8177374 T (Ser180Leu) frequency did not differamong the studied white samplesIn the sample of Russian settlers of Yakutia, males andfemales differed in the frequency of rs10902158 . Moreover, the frequency of this SNP among maleswas closer to that observed in non-Finnish Europeans according to GnomAD data, and the frequency among females wascloser to that observed in the Novosibirsk sample. Perhapsthere were sex differences during recent migration to Yakutiafrom different regions of Russia. Genetic analysis of a largersample and estimation of this SNP\u2019s frequency in westernregions of Russia are required for explaining the observeddifferencesThe two analyzed Asian samples differed from each otherand from GnomAD East Asian cohorts. Among Yakuts, thers5743708A (Arg753Gln) variant, which is very rare in otherAsian populations, was found at a frequency of 0.015\u00b10.007(mean\u00b1SD). Chukchis differed significantly from GnomADEast Asians in rs10902158 allele frequency (see Table 1).Frequencies of polymorphisms rs5743708, rs8177374, andrs10902158 were not different among adolescents and totalwhite CAP patient samples. By contrast, after the samplewas divided into patients with severe and nonsevere CAP,differences were found for rs5743708 .Next, genotype frequencies were estimated for rs5743708,rs8177374, and rs10902158 in the examined samples (exceptfor long-lived people regarding rs10902158). For the latterSNP (in the PKP3 gene), no difference in frequency wasdetectable within any group (data not shown). The observeddistribution of rs5743708 and rs8177374 genotypes amongthe studied samples is presented in Table 2.The frequencies of genotypes of rs5743708 and rs8177374did not differ among the following samples: adolescents ofNovosibirsk, long-lived people of Siberia, all patients withCAP, and all Russians in Yakutia. Possibly, the carriage of thestudied alleles is not associated with predisposition to longevity in Siberia and does not significantly affect the probabilityof resettling of migrants in more unfavorable climatic conditions at present. This notion is consistent with WHO findingsthat in Eastern Europe, in contrast to Western and CentralEurope, the pneumonia mortality rate does not increase significantly after age 80 (https://www.who.int/medicines/areas/priority_medicines/Ch6_22Pneumo.pdf). As for pneumonia,carriage of the rs5743708 A allele predisposed to severe CAP. The heterozygous genotype of rs8177374 in combination with the GG genotype ofrs5743708 had a protective effect against severe CAP .It was shown here that carriage of none of the three studiedSNPs, rs5743708, rs8177374, and rs10902158, is associatedwith the predisposition to CAP in total. By contrast, we foundthat the Arg753Gln variant of TLR2 predisposes to severeCAP, and the heterozygous Ser180Leu variant of TIRAP incombination with the 753 Arg/Arg variant of TLR2 has aprotective effect against it in the white population. These datapartially explain the contradictions in the data from differentresearchers. Most likely, the contribution of the alleles ofgenes TLR2 and TIRAP to CAP predisposition is determinedby pneumonia etiology. A substantial proportion of severepneumonia cases are known to be caused by combined viraland bacterial infections . TLR2 is responsible mainly forthe recognition of bacteria-associated molecular patterns;Ser180Leu of the TIRAP gene modulates signal transductiononly from TLR2 and TLR4 recognizing molecular patterns ofbacteria as well . Most likely, combinedand bacterial but not viral pneumonias are associated withTLR2 and TIRAP gene variants.The studied Asian ethno-geographical groups showed an increased frequency of the protective rs8177374 T (Ser180Leu)variant of TIRAP relative to neighboring East Asian populations. In the Chukchi sample, the difference was significant. It may be a consequence of the naturalselection that has promoted protection from excessive inflammation during pulmonary diseases. The hypothesis about theselection of the Ser180Leu variant along with the out-ofAfrica migration to a harsh environment has been advancedearlier . An increasedfrequency of the Arg753Gln variant of TLR2 and a decreasedfrequency of Ser180Leu of TIRAP as compared to non-Finnish Europeans may indicate higher genetic predispositionof the Siberian white population to PTB and severe CAP.Nevertheless, there are a lot of genes associated with CAPand PTB independently. Apparently, during the settlement ofpeoples in Northern Eurasia, the formation of gene pools hadbeen determined by the selection that facilitated adaptationto specific infections (Lime disease among them), parasites,and the climate. It would be interesting to determine why twomutations changing the same TLR2 signaling have oppositeeffects on the predisposition to severe CAP. One possible explanation is the difference in the structure and functions ofheterodimers TLR2\u2013TLR1 and TLR2\u2013TLR6 .Existing data on the roles of TLRs 1, 2, and 6 in the activation of proinflammatory and anti-inflammatory signaling areconflicting. Overexpression of TLR2 carrying the Arg753Glnvariant has been demonstrated to cause a significantly strongerimpairment of cytokine induction by TLR2/TLR1 ligands ascompared with TLR2/TLR6 ligands in the HEK293 cell line. In later papers, it has been shown thatthe Arg-to-Gln substitution at position 753 of TLR2 changesthe size, charge, and hydrophobic properties of this site andreduces the ability of TLR2 to form a heterodimer with TLR6. This SNP significantlyalters agonist-inducible association of TLR2 with adaptorproteins TIRAP and MyD88 and impairs NF-\u03baB signaling andIL-8 mRNA expression in the HEK293 cell line . Genes TLR1 and TLR2 have different expression activators . In the TLR2\u2013TLR1 dimer, TLR1and TLR2 are responsible for NF-\u03baB and MAPK pathways and for PI3K pathway activation, respectively; therefore, upregulation of proinflammatory cytokines is TLR1-dependent,whereas upregulation of type I IFN is TLR2-dependent . TLR2\u2013TLR6 binding disruption possibly causesan increase in the number of TLR2\u2013TLR1 dimers in whichTLR1 drives the activation of the NF-\u03baB inflammatory signaling cascade. On the contrary, the Ser180Leu variant of TIRAPweakens proinflammatory signal transmission. Besides,TIRAP acts as an adaptor protein for TLR4 homodimers.This receptor is primarily responsible for the recognitionof lipopolysaccharides of gram-negative bacteria and fungi. It is believed that TLR4 takes part notonly in MyD88-dependent proinf\u200alammatory signaling but alsoin MyD88-independent anti-inf\u200alammatory signaling. Weakening of TLR4 signaling through TIRAP probably enhances thesignaling through adapter proteins TRIF and TRAM, causingthe secretion of anti-inf\u200alammatory cytokines .It remains unclear why the SNPs in TLR2 and TIRAP havesimilar effects on the predisposition to or protection againstacute (CAP) and chronic (PTB) lung infections. Perhaps thisphenomenon is due to an impact on inflammation in both diseases. The severity of CAP is determined by life-threateningacute inflammation; in PTB, the development of chronic inflammation masks the infection from the host immune system.In Northern Asian populations, the observed difference inrs8177374 frequency may reflect consequences of naturalselection during the settlement of peoples on territories withunfavorable climatic conditions. As for pneumonia, carriage ofthe rs5743708 A allele (the TLR2 gene) predisposes to severeCAP; the heterozygous genotype of rs8177374 (the TIRAPgene) in combination with the GG genotype of rs5743708 (theTLR2 gene) has a protective effect against it. Stratification ofCAP by causative pathogen may help to eliminate the currentdiscrepancies among research groups. Regional differencesin a set of pathogens along with the genetic characteristics ofethno-geographical groups can determine the associations ofvarious genetic variants of innate immunity with the prevalence and severity of pneumonia.The authors declare no conflict of interest.Aguilera E.R., Lenz L.L. Inflammation as a modulator of host susceptibility to pulmonary influenza, pneumococcal, and co-infections.Front. Immunol. 2020;11:105. DOI 10.3389/fimmu.2020.00105.Aibana O., Huang C.C., Aboud S., Arnedo-Pena A., Becerra M.C., Bellido-Blasco J.B., Bhosale R., Calderon R., Chiang S., Contreras C.,Davaasambuu G., Fawzi W.W., Franke M.F., Galea J.T., Garcia-Ferrer D., Gil-Fortu\u00f1o M., Gomila-Sard B., Gupta A., Gupte N., Hussain R., Iborra-Millet J., Iqbal N.T., Juan-Cerd\u00e1n J.V., Kinikar A.,Lecca L., Mave V., Meseguer-Ferrer N., Montepiedra G., Mugusi F.M., Owolabi O.A., Parsonnet J., Roach-Poblete F., Romeu-Garc\u00eda M.A., Spector S.A., Sudfeld C.R., Tenforde M.W., Togun T.O.,Yataco R., Zhang Z., Murray M.B. Vitamin D status and risk of incident tuberculosis disease: a nested case-control study, systematicreview, and individual-participant data meta-analysis. PLoS Med.2019;16(9):e1002907. DOI 10.1371/journal.pmed.1002907.Arango Duque G., Descoteaux A. Macrophage cytokines: involvementin immunity and infectious diseases. Front. Immunol. 2014;5:491.DOI 10.3389/fimmu.2014.00491.Barbalat R., Lau L., Locksley R.M., Barton G.M. Toll-like receptor 2on inflammatory monocytes induces type I interferon in responseto viral but not bacterial ligands. Nat. Immunol. 2009;10(11):12001207. DOI 10.1038/ni.1792.Basith S., Manavalan B., Govindaraj R.G., Choi S. In silico approachto inhibition of signaling pathways of Toll-like receptors 2 and 4 byST2L. PLoS One. 2011;6(8):e23989. DOI 10.1371/journal.pone.0023989.Bernard N.J., O\u2019Neill L.A. Mal, more than a bridge to MyD88. IUBMBLife. 2013;65(9):777-786. DOI 10.1002/iub.1201.Bonham K.S., Orzalli M.H., Hayashi K., Wolf A.I., Glanemann C.,Weninger W., Iwasaki A., Knipe D.M., Kagan J.C. A promiscuous lipid-binding protein diversifies the subcellular sites of tolllike receptor signal transduction. Cell. 2014;156(4):705-716. DOI10.1016/j.cell.2014.01.019.Bystritskaya E.V., Bilichenko T.N. An analysis of pneumonia morbidity in adults and children at Russian Federation, 2010\u20132014.Pulmonologiya = Russian Pulmonology. 2017;27(2):173-178. DOI10.18093/0869-0189-2017-27-2-173-178. (in Russian)Caws M., Thwaites G., Dunstan S., Hawn T.R., Lan N.T., Thuong N.T.,Stepniewska K., Huyen M.N., Bang N.D., Loc T.H., Gagneux S.,van Soolingen D., Kremer K., van der Sande M., Small P., Anh P.T.,Chinh N.T., Quy H.T., Duyen N.T., Tho D.Q., Hieu N.T., Torok E.,Hien T.T., Dung N.H., Nhu N.T., Duy P.M., van Vinh Chau N., FarrarJ. The influence of host and bacterial genotype on the developmentof disseminated disease with Mycobacterium tuberculosis. PLoSPathog. 2008;4(3):e1000034. DOI 10.1371/journal.ppat.1000034.Choi S.H., Hong S.B., Ko G.B., LeeY., Park H.J., Park S.Y., Moon S.M.,Cho O.H., Park K.H., Chong Y.P., Kim S.H., Huh J.W., Sung H.,Do K.H., Lee S.O., Kim M.N., Jeong J.Y., Lim C.M., Kim Y.S.,Woo J.H., Koh Y. Viral infection in patients with severe pneumoniarequiring intensive care unit admission. Am. J. Respir. Crit. CareMed. 2012;186(4):325-332. DOI 10.1164/rccm.201112-2240OC.Ferwerda B., Alonso S., Banahan K., McCall M.B.B., GiamarellosBourboulis E.J., Ramakers B.P., Mouktaroudi M., Fain P.R., Izagirre N., Syafruddin D., Cristea T., Mockenhaupt F.P., Troye-Blomberg M., Kumpf O., Maiga B., Dolo A., Doumbo O., Sundaresan S.,Bedu-Addo G., van CrevelR., Hamann L., Oh D.-Y., SchumannR.R.,Joosten L.A.B., de la R\u00faa C., Sauerwein R., Drenth J.P.H., Kullberg B.-J., van der Ven A.J.A.M., Hill A.V., Pickkers P., van derMeer J.W.M., O\u2019Neill L.A.J., Netea M.G. Functional and geneticevidence that the Mal/TIRAP allele variant 180L has been selectedby providing protection against septic shock. Proc. Natl. Acad. Sci.USA. 2009;106(25):10272-10277. DOI 10.1073/pnas.0811273106.Gopalakrishnan A., Salgame P. Toll-like receptor 2 in host defenseagainst Mycobacterium tuberculosis: to be or not to be \u2013 that is thequestion. Curr. Opin. Immunol. 2016;42:76-82. DOI 10.1016/j.coi.2016.06.003.Guo X.G., Xia Y. The rs5743708 gene polymorphism in the TLR2gene contributes to the risk of tuberculosis disease. Int. J. Clin. Exp.Pathol. 2015;8(9):11921-11928.Gupta A., Montepiedra G., Gupte A., Zeldow B., Jubulis J., Detrick B.,Violari A., Madhi S., Bobat R., Cotton M., Mitchell \u0421., Spector S.,IMPAACT NWCS113 and P1041 Study Team. Low vitamin-Dlevels combined with PKP3-SIGIRR-TMEM16J host variants is associated with tuberculosis and death in HIV-infected and -exposedinfants. PLoS One. 2016;11(2):e0148649. DOI 10.1371/journal.pone.0148649.Gurjar M., Raychaudhuri K., Mahadik S., Reddy D., Atak A., Shetty T.,Rao K., Karkhanis M.S., Gosavi P., Sehgal L., Gupta S., Dalal S.N.Plakophilin3 increases desmosome assembly, size and stability byincreasing expression of desmocollin2. Biochem. Biophys. Res.Commun. 2018;495(1):768-774. DOI 10.1016/j.bbrc.2017.11.085.Harding C.V., Boom W.H. Regulation of antigen presentation by Mycobacterium tuberculosis: a role for Toll-like receptors. Nat. Rev.Microbiol. 2010;8(4):296-307. DOI 10.1038/nrmicro2321.Hong H.L., Hong S.B., Ko G.B., Huh J.W., Sung H., Do K.H.,Kim S.H., Lee S.O., Kim M.N., Jeong J.Y., Lim C.M., Kim Y.S.,Woo J.H., Koh Y., Choi S.H. Viral infection is not uncommon inadult patients with severe hospital-acquired pneumonia. PLoS One.2014;9(4):e95865. DOI 10.1371/journal.pone.0095865.Horne D.J., Randhawa A.K., Chau T.T., Bang N.D., Yen N.T., Farrar J.J., Dunstan S.J., Hawn T.R. Common polymorphisms in thePKP3-SIGIRR-TMEM16J gene region are associated with susceptibility to tuberculosis. J. Infect Dis. 2012;205(4):586-594. DOI10.1093/infdis/jir785.Hu L., Tao H., Tao X., Tang X., Xu C. TLR2 Arg753Gln gene polymorphism associated with tuberculosis susceptibility: an updatedmeta-analysis. Biomed. Res. Int. 2019;2628101. DOI 10.1155/2019/2628101.Jin M.S., Kim S.E., Heo J.Y., Lee M.E., Kim H.M., Paik S.G., Lee H.,Lee J.O. Crystal structure of the TLR1\u2013TLR2 heterodimer inducedby binding of a tri-acylated lipopeptide. Cell. 2007;130(6):10711082. DOI 10.1016/j.cell.2007.09.008.Kawai T., Akira S. The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors. Nat. Immunol. 2010;11(5):373-384. DOI 10.1038/ni.1863.Khor C.C., Chapman S.J., Vannberg F.O., Dunne A., Murphy C.,Ling E.Y., Frodsham A.J., Walley A.J., Kyrieleis O., Khan A.,Aucan C., Segal S., Moore C.E., Knox K., Campbell S.J., Lienhardt C., Scott A., Aaby P., Sow O.Y., Grignani R.T., Sillah J.,Sirugo G., Peshu N., Williams T.N., Maitland K., Davies R.J.,Kwiatkowski D.P., Day N.P., Yala D., Crook D.W., Marsh K.,Berkley J.A., O\u2019Neill L.A., Hill A.V. A Mal functional variant isassociated with protection against invasive pneumococcal disease,bacteremia, malaria and tuberculosis. Nat. Genet. 2007;39(4):523528. DOI 10.1038/ng1976.Kumar V. Inflammation research sails through the sea of immunologyto reach immunometabolism. Int. Immunopharmacol. 2019;73:128145. DOI 10.1016/j.intimp.2019.05.002.Kumpf O., Giamarellos-Bourboulis E.J., Koch A., Hamann L., Mouktaroudi M., Oh D.Y., Latz E., Lorenz E., Schwartz D.A., Ferwerda B., Routsi C., Skalioti C., Kullberg B.J., van der Meer J.W.,Schlag P.M., Netea M.G., Zacharowski K., Schumann R.R. Influenceof genetic variations in TLR4 and TIRAP/Mal on the course of sepsisand pneumonia and cytokine release: an observational study in threecohorts. Crit. Care. 2010;14(3):R103. DOI 10.1186/cc9047.Lancioni C.L., Li Q., Thomas J.J., Ding X., Thiel B., Drage M.G., Pecora N.D., ZiadyA.G., Shank S., Harding C.V., Boom W.H., Rojas R.E.Mycobacterium tuberculosis lipoproteins directly regulate humanmemory CD4+ T cell activation via Toll-like receptors 1 and 2.Infect. Immun. 2011;79(2):663-673. DOI 10.1128/IAI.00806-10.Li J., Lee D.S., Madrenas J. Evolving bacterial envelopes and plasticity of TLR2-dependent responses: basic research and translationalopportunities. Front. Immunol. 2013;4:347. DOI 10.3389/fimmu.2013.00347.Lim W.S., van der Eerden M.M., Laing R., Boersma W.G., Karalus N.,Town G.I., Lewis S.A., Macfarlane J.T. Defining community acquired pneumonia severity on presentation to hospital: an international derivation and validation study. Thorax. 2003;58:377-382.DOI 10.1136/thorax.58.5.377.Liu C.H., Liu H., Ge B. Innate immunity in tuberculosis: host defensevs pathogen evasion. Cell Mol. Immunol. 2017;14(12):963-975.DOI 10.1038/cmi.2017.88.Liu Y., Li J.Y., Chen S.T., Huang H.R., Cai H. The rLrp of Mycobacterium tuberculosis inhibits proinflammatory cytokine production anddownregulates APC function in mouse macrophages via a TLR2mediated PI3K/Akt pathway activation-dependent mechanism. Cell.Mol. Immunol. 2016;13(6):729-746. DOI 10.1038/cmi.2015.58.McCullers J.A. The co-pathogenesis of influenza viruses with bacteriain the lung. Nat. Rev. Microbiol. 2014;12(4):252-262. DOI 10.1038/nrmicro3231.Miao R., Li J., Sun Z., Xu F., Shen H. Meta-analysis on the associationof TIRAP S180L variant and tuberculosis susceptibility. Tuberculosis (Edinb.). 2011;91(3):268-272. DOI 10.1016/j.tube.2011.01.006.Moens L., Verhaegen J., Pierik M., Vermeire S., De Boeck K., Peetermans W.E., Bossuyt X. Toll-like receptor 2 and Toll-like receptor 4polymorphisms in invasive pneumococcal disease. Microbes Infect.2007;9(1):15-20. DOI 10.1016/j.micinf.2006.10.002.Moldoveanu B., Otmishi P., Jani P., Walker J., Sarmiento X., Guardiola J., Saad M., Yu J. Inflammatory mechanisms in the lung.J. Inf\u200alamm. Res. 2009;2:1-11.Molgora M., Barajon I., Mantovani A., Garlanda C. Regulatory role ofIL-1R8 in immunity and disease. Front. Immunol. 2016;7:149. DOI10.3389/fimmu.2016.00149.Morris D.E., Cleary D.W., Clarke S.C. Secondary bacterial infectionsassociated with influenza pandemics. Front. Microbiol. 2017;8:1041.DOI 10.3389/fmicb.2017.01041.Naderi M., Hashemi M., Pourmontaseri Z., Eskandari-Nasab E., Bahari G., Taheri M. TIRAP rs8177374 gene polymorphism increasedthe risk of pulmonary tuberculosis in Zahedan, southeast Iran.Asian Pac. J. Trop. Med. 2014;7(6):451-455. DOI 10.1016/S19957645(14)60073-0.Nagpal K., Plantinga T.S., Wong J., Monks B.G., Gay N.J., Netea M.G.,Fitzgerald K.A., Golenbock D.T. A TIR domain variant of MyD88 adapter-like /TIRAP results in loss of MyD88 binding and reduced TLR2/TLR4 signaling. J. Biol. Chem. 2009;284(38):2574225748. DOI 10.1074/jbc.M109.014886.Narayanan K.B., Park H.H. Toll/interleukin-1 receptor (TIR) domainmediated cellular signaling pathways. Apoptosis. 2015;20(2):196209. DOI 10.1007/s10495-014-1073-1.Ozinsky A., Underhill D.M., Fontenot J.D., Hajjar A.M., Smith K.D.,Wilson C.B., Schroeder L., Aderem A. The repertoire forpattern recognition of pathogens by the innate immune system is defined bycooperation between Toll-like receptors. Proc. Natl. Acad. Sci. USA.2000;97:13766-13771. DOI 10.1073/pnas.250476497.Panda A.K., Das B.K., Panda A., Tripathy R., Pattnaik S.S., Mahto H.,Pied S., Pathak S., Sharma S., Ravindran B. Heterozygous mutantsof TIRAP (S180L) polymorphism protect adult patients with Plasmodium falciparum infection against severe disease and mortality.Infect. Genet. Evol. 2016;43:146-150. DOI 10.1016/j.meegid.2016.04.035.Patar\u010di\u0107 I., Gelemanovi\u0107 A., Kirin M., Kol\u010di\u0107 I., Theodoratou E., Baillie K.J., de Jong M.D., Rudan I., Campbell H., Pola\u0161ek O. Therole of host genetic factors in respiratory tract infectious diseases:systematic review, meta-analyses and field synopsis. Sci. Rep. 2015;5:16119. DOI 10.1038/srep16119.Price R.H.M., Graham C., Ramalingam S. Association between viralseasonality and meteorological factors. Sci. Rep. 2019;9(1):929.DOI 10.1038/s41598-018-37481-y.Raieli S., Trichot C., Korniotis S., Pattarini L., Soumelis V. TLR1/2 orchestrate human plasmacytoid predendritic cell response to gram +bacteria. PLoS Biol. 2019;17(4):e3000209. DOI 10.1371/journal.pbio.3000209.Richardson E.T., Shukla S., Sweet D.R., Wearsch P.A., Tsichlis P.N.,Boom W.H., Harding C.V. Toll-like receptor 2-dependent extracellular signal-regulated kinase signaling in Mycobacterium tuberculosis-infected macrophages drives anti-inflammatory responses andinhibits Th1 polarization of responding T cells. Infect. Immun. 2015;83(6):2242-2254. DOI 10.1128/IAI.00135-15.Sambrook J., Russell D.W. Purification of nucleic acids by extractionwith phenol:chloroform. Cold Spring Harbor Protoc. 2006;2006(1):4455. DOI 10.1101/pdb.prot4455.Schr\u00f6der N.W.J., Diterich I., Zinke A., Eckert J., Draing C., vonBaehr V., Hassler D., Priem S., Hahn K., Michelsen K.S., Hartung T., Burmester G.R., G\u00f6bel U.B., Hermann C., Schumann R.R.Heterozygous Arg753Gln polymorphism of human TLR-2 impairsimmune activation by Borrelia burgdorferi and protects from latestage Lyme disease. J. Immunol. 2005;175(4):2534-2540. DOI10.4049/jimmunol.175.4.2534.Self W.H., Balk R.A., Grijalva C.G., Williams D.J., Zhu Y., Anderson E.J., Waterer G.W., Courtney D.M., Bramley A.M., Trabue C.,Fakhran S., Blaschke A.J., Jain S., Edwards K.M., Wunderink R.G.Procalcitonin as a marker of etiology in adults hospitalized withcommunity-acquired pneumonia. Clin. Infect. Dis. 2017;65(2):183190. DOI 10.1093/cid/cix317.Shukla S., Richardson E.T., Drage M.G., Boom W.H., Harding C.V.Mycobacterium tuberculosis lipoprotein and lipoglycan bindingto Toll-like receptor 2 correlates with agonist activity and functional outcomes. Infect. Immun. 2018;86(10). pii: e00450-18. DOI10.1128/IAI.00450-18.Siebert J.N., Hamann L., Verolet C.M., Gameiro C., Grillet S.,Siegrist C.A., Posfay-Barbe K.M. Toll-interleukin 1 receptor domain-containing adaptor protein 180L single-nucleotide polymorphism is associated with susceptibility to recurrent pneumococcallower respiratory tract infections in children. Front. Immunol. 2018;9:1780. DOI 10.3389/fimmu.2018.01780.Smelaya T.V., Belopolskaya O.B., Smirnova S.V., Kuzovlev A.N.,Moroz V.V., Golubev A.M., Pabalan N.A., Salnikova L.E. Geneticdissection of host immune response in pneumonia development andprogression. Sci. Rep. 2016;6:35021. DOI 10.1038/srep35021.Takeda K., Akira S. Toll-like receptors. Curr. Protoc. Immunol. 2015;109:14.12.1-14.12.10. DOI 10.1002/0471142735.im1412s109.Tapader R., Bose D., Dutta P., Das S., Pal A. SslE (YghJ), a cell-associated and secreted lipoprotein of neonatal septicemic Escherichia coli, induces Toll-like receptor 2-dependent macrophageactivation and proinflammation through NF-kB and MAP kinasesignaling. Infect. Immun. 2018;86(9):e00399-18. DOI 10.1128/IAI.00399-18.Wilkinson R.J., Llewelyn M., Toossi Z., Patel P., Pasvol G., Lalvani A., Wright D., Latif M., Davidson R.N. Influence of vitamin Ddeficiency and vitamin D receptor polymorphisms on tuberculosis among Gujarati Asians in west London: a case-control study.Lancet. 2000;355(9204):618-621. DOI 10.1016/S0140-6736(99)02301-6.Xiong Y., Song C., Snyder G.A., Sundberg E.J., Medvedev A.E. R753Qpolymorphism inhibits Toll-like receptor (TLR) 2 tyrosine phosphorylation, dimerization with TLR6, and recruitment of myeloiddifferentiation primary response protein 88. J. Biol. Chem. 2012;287(45):38327-38337. DOI 10.1074/jbc.M112.375493.Zavyalova L.G., Denisova D.V., Simonova G.I., Orlov P.S., Voevoda M.I. Association of polymorphisms of genes FTO and TCF7L2with cadiometabolic parameters of the adolescents in Siberia. Bulleten SO RAMN = Bulleten SB RAMS. 2011;31(5):5-13. (in Russian)."} +{"text": "Correction to: Borderline Personal Disord Emot Dysregul 7, 19 (2020).https://doi.org/10.1186/s40479-020-00132-8Following publication of this article , it is rThe correct reference 35 should be:35. Green A, Charles K. Voicing the Victims of Narcissistic Partners: A Qualitative Analysis of Responses to Narcissistic Injury and Self-Esteem Regulation. SAGE Open. 2019;9(2). 10.1177/2158244019846693.The original article has been updated."} +{"text": "The construction of a nanoimmune controlled-release system that spatiotemporally recognizes tumor lesions and stimulates the immune system response step by step is one of the most potent cancer treatment strategies for improving the sensitivity of immunotherapy response.Here, a composite nanostimulator (CNS) was constructed for the release of second near-infrared (NIR-II) photothermal-mediated immune agents, thereby achieving spatiotemporally controllable photothermal-synergized immunotherapy. CNS nanoparticles comprise thermosensitive liposomes as an outer shell and are internally loaded with a NIR-II photothermal agent, copper sulfide (CuS), toll-like receptor-9 (TLR-9) agonist, cytosine-phospho-guanine oligodeoxynucleotides, and programmed death-ligand 1 (PD-L1) inhibitors (JQ1). Following NIR-II photoirradiation, CuS enabled the rapid elevation of localized temperature, achieving tumor ablation and induction of immunogenic cell death (ICD) as well as disruption of the lipid shell, enabling the precise release of two immune-therapeutical drugs in the tumor region. Combining ICD, TLR-9 stimulation, and inhibited expression of PD-L1 allows the subsequent enhancement of dendritic cell maturation and increases infiltration of cytotoxic T lymphocytes, facilitating regional antitumor immune responses.CNS nanoparticle-mediated photothermal-synergized immunotherapy efficiently suppressed the growth of primary and distant tumors in two mouse models and prevented pulmonary metastasis. This study thus provides a novel sight into photo-controllably safe and efficient immunotherapy.The online version contains supplementary material available at 10.1186/s12951-021-01197-5. Tumor immunotherapy that mobilizes immune cells to fight malignant tumors is a promising therapeutic approach , 2. Dive. recently developed an activatable engineered immune device, which can be remotely controlled by near-infrared (NIR) light. In this scenario, NIR light excitation was used to break the photoresponsive linker, releasing active CpG oligonucleotides (ODNs) and precisely activating local intratumoral inflammation without obvious systemic side effects in the primary tumors compared with the CNS0\u2009+\u2009L, CNSC\u2009+\u2009L, and CNSJ\u2009+\u2009L groups , CRT, and expression of high mobility group box 1 protein (HMGB1) were used to facilitate the uptake, processing, and presentation of tumor antigens in DCs. One day after treatment, the intratumoral ATP levels of various CNS nanoparticles plus laser irradiation were elevated and compared with the single PBS-treated and CNSely Fig.\u00a0a. MoreovPBS Fig.\u00a0b. In conals Fig.\u00a0c. These +CD80+CD86+) via flow cytometric analysis to investigate the CNS-mediated synergized antitumor immune response in the CNSD\u2009+\u2009L group were 1.6, 1.2, and 1.2-fold higher than those in the CNS0\u2009+\u2009L, CNSC\u2009+\u2009L, and CNSJ\u2009+\u2009L groups, respectively , is a key indicator of an antitumor immune response = 100 \u00b5g mL-1) under the NIR-II laser irradiation for 5 min. Fig. S3. The time constant for heat transfer from the system is determined by applying the linear time data from the cooling period of (a) versus the negative natural logarithm of driving force temperature. Fig. S4. Release of CpG from CNSD with or without laser irradiation for 5 min . Fig. S5. Schematic illustration of the synthesis of ICG-loaded CNS nanoparticles for tracing the nanoparticle trajectory. Fig. S6. UV-vis absorption spectrums of CNS0@ICG, CNSC@ICG, CNSJ@ICG, and CNSD@ICG. Fig. S7. Fluorescence intensity of 4T1 cells treated with PBS (control) or various ICG-loaded CNS nanoparticles ([ICG] = 20 \u00b5g mL\u22121) for 24 h via flow cytometry. Fig. S8. Relative mean fluorescence intensity (MFI) of CRT in Panc02 cells after different treatments. Fig. S9. The NIR fluorescence imaging of xenograft Panc02tumor-bearing C57BL/6 living mice at 0, 8, 24, and 36 h after systemic administration of CNS@ICG through tail-vein administration . The fluorescence images were collected with excitation at 710 nm and emission at 790 nm, and the tumors were marked by white circles. (b) The fluorescence intensity of tumor regions of mice at different post-injection times of (n = 3). Fig. S10. (a) NIR thermal photos of 4T1 tumor-bearing mice under laser irradiation at 24 h post-injection of PBS, CNS0, CNSC, CNSJ, and CNSD through tail-vein injection ; (b) Temperature elevation curves of tumors in 4T1 tumor-bearing mice after administration of Control (PBS), CNS0, CNSC, CNSJ and CNSD under NIR-II laser illumination . Fig. S11. Gating strategies for flow cytometry assay of matured CD80+CD86+ DCs in tumor-draining lymph nodes of Panc02 tumor-bearing C57BL/6 mice. Fig. S12. Western-blot analysis of JQ1-induced downregulation of PD-L1 in Panc02 cells (200 nM of JQ1 and 100 ng/ml of IFN-\u03b3). Fig. S13. Gating strategy for flow cytometry assay of CD4+ T cells and CD8+ T cells in distant tumors of Panc02 tumor-bearing C57BL/6 mice. Fig. S14. A volcano plot showing the up-regulated or insignificantly expressed or down-regulated genes when comparing the CNSD-treated group with the Control (PBS) group. Fig. S15. Body weights of Panc02 tumor-bearing C57BL/6 mice in different groups within 14 days of treatment (Control (PBS), CNS0, CNSC, CNSJ and CNSD, 0.2 mL, [CuS] = 300 \u03bcg/mL, n = 5). Fig. S16. Body weights of 4T1 tumor-bearing Balb/c mice in different groups within 14 days of treatment (Control (PBS), CNS0, CNSC, CNSJ and CNSD, 0.2 mL, [CuS] = 300 \u03bcg/mL, n = 5). Fig. S17. Representative histological H&E staining images of major organs were collected from Panc02 tumor-bearing C57BL/6 mice in different treatment groups at the end of treatment (Control (PBS), CNS0, CNSC, CNSJ and CNSD, 0.2 mL, [CuS] = 300 \u03bcg/mL). The scale bar represents 50 \u03bcm. Fig. S18. Representative histological H&E staining photos of major organs in healthy C57BL/6 mice before treatment (Control) and after tail-intravenous injection of CNSD for 15 (Day 15) and 30 days (Day 30). The scale bar represents 50 \u03bcm. Fig. S19. The levels of (a) alanine aminotransferase (ALT), (b) aspartate aminotransferase (AST), (c) \u03b3-glutamyl transpeptidase (GGT), (d) urea, (e) creatinine (CREA), (f) red blood cells (RBC), (g) hemoglobin (HGB), (h) mean corpuscular hemoglobin (MCH), (i) hemoglobin concentration (MCHC), (j) red cell distribution width (RDW-SD), (k) red cell volume distribution width (RDW-CV), (l) platelet (PLT), (m) plateletcrit (PCT), (n) mean platelet volume (MPV), and (o) platelet distribution width (PDW) in the blood of healthy C57BL/6 mice before treatment (D0) and after tail-intravenous administration of CNSD for 15 (D15), and 30 days (D30) (n = 3)."} +{"text": "Vision loss is associated with restricted physical activity (PA), yet the relationship between multiple domains of vision measures and objectively measured PA, especially activity patterns, in mid-to-late life remains unclear. In 603 BLSA participants , best-corrected and presenting visual acuity (VA), contrast sensitivity, visual fields (VF), stereo acuity were assessed from 2015 to 2019. Free-living PA was assessed using a wrist-worn ActiGraph accelerometer for 7 days. Linear regression models showed that participants with vs. without best-corrected VA impairment had 29.3 fewer active minutes/day (p=0.03) and trended towards fewer activity counts (p=0.05), adjusting for sociodemographic and health characteristics. VF impairment was associated with 268,636 fewer activity counts (p=0.02), 46.2 fewer active minutes/day (p=0.02), and a 3% greater activity fragmentation (p=0.009). Older adults with visual impairment have restricted and more fragmented activity patterns. Longitudinal studies are warranted to examine causality between visual impairment and PA decline."} +{"text": "The risk of cervical cancer is caused by persistent human papillomavirus (HPV) infection. Cervical cancer is the most frequent cancer among women. Our purpose was to investigate the association between TP53 215C>G (Pro72Arg), MDM2 -410T>G, and NQO1 609C>T gene polymorphisms with a high HPV load and the inf luence of gene-gene interactions on prolonged HPV infection. Eighty-nine women with a high HPV viral load and 114 healthy women were involved in a case\u2013control study. Genotyping for TP53 215C>G (Pro72Arg) and MDM2 -410T>G SNPs was carried out by allele-specif ic PCR and genotyping for NQO1 609C>T was performed by a TaqMan assay. Quantitative analysis of HPV DNA was performed by AmpliSens\u00ae HPV HCR screen-titer-FRT test system. Gene-gene interactions were analyzed using the multifactor dimensionality reduction (MDR) method. The study of separate SNPs of MDM2 -410T>G and NQO1 609C>T genes did not reveal any statistically signif icant difference in genotype and allele frequencies among women within the two groups. The frequency of the 215G (72Arg) allele and 215GG (72Arg/ Arg) genotype of the TP53 gene was signif icantly higher in the case group than in the control group . MDR analysis showed the signif icance of intergenic interactions of the three studied loci TP53 (rs1042522) \u2013 MDM2 (rs2279744) \u2013 NQO1 (rs1800566) for the formation of a high HPV load . Human papillomavirus (HPV) is implicated in the developmentof cervical cancer. A key critical step in papillomavirusrelatedcarcinogenesis is a persistent viral infection . There is heterogeneity in the development of humanpapillomavirus infection due to genetic variations, ethnicity,viral types involved in infection, viral load, and oncogenicexpression, as well as environmental, and hormonal, physiological,and nutritional factors . After HPV-infection, especially with high-riskHPV types ,HPV oncoproteins induce mutations in oncogenes, epigeneticmodifications, and chromosomal rearrangements . A disequilibrium in the relationship betweenvirus and host results in a decrease in the effectiveness of theimmune system, the imbalance between cellular and humoralimmune processes, as well as alteration in pro- and antiinflammatorycytokine levels, which increases the replicativeability of the virus . In addition, modifications that alter the stability of cellcycle proteins such as retinoblastoma protein (pRb), tumorsuppressor p53, result in uncontrolled cell cycle progressionand induce oncogenic transformation of cells .The TP53 tumor suppressor gene plays a crucial role inregulating DNA repair, apoptosis, and cell cycle control. Ithas been observed that most human tumors contain mutatedp53, with about 50 % of those mutations causing a reductionin DNA repair ability, irregular cell growth, and, eventually,progression to malignancy . Polymorphismsin the TP53 gene change p53 protein conformation,which leads to p53 degradation through a process mediatedby ubiquitin . The most widely studiedof the non-synonymous SNP TP53 Pro72Arg (rs1042522)replaces proline (Pro) with arginine (Arg) in the p53 proteindue to a substituted C to G base in the TP53 gene. Both variantshave the same binding affinity for DNA while their ability tobind components of the transcription factor is different. So, thetwo variants of the p53 protein are not functionally equivalent. The p53 is ubiquitinated in the proteasome,which is regulated by MDM2 via a ubiquitin-dependentdegradation pathway and NAD(P)H quinone oxidoreductase 1via a ubiquitin-independent degradation pathway . As a result, the levelof p53 is affected by MDM2 and NQO1 activity.Oncoprotein MDM2 is a negative regulator of the p53 tumorprotein . A functional SNP in theMDM2 gene promoter (-410T>G rs2279744) regulates MDM2protein expression. When T is replaced with G, this increasesthe affinity of the transcriptional activator Sp1, resulting inhigher MDM2 expression and subsequent suppression of thep53 pathway .The NQO1 enzyme can catalyze the reduction of variousquinones to hydroquinones by a two-electron reductionmechanism (NADH or NADPH) as a reducing cofactor. Thistwo-electron reduction prevents the formation of free radicals(semiquinones) that protect the cells from oxidative stress. The SNP of NQO1 at nucleotideposition 609C>T in exon 6 (rs1800566) with the proline toserine amino acid substitution at codon 187 induces a changeof enzyme activity. The homozygotes (TT ) genotype gives riseto an inactive enzyme NQO1, heterozygotes (CT ) have theenzyme displays mild activity, while the wild homozygotes(CC) have the highest activity of the NQO1 . Wild type NQO1 partially inhibits HPV E6-mediatedp53 degradation, although this does not occur with the mutanttype NQO1 .Thus, the efficiency of the cell cycle repair and controlsystem depends not only on the p53 protein. Also, the levels ofMDM2 and NQO1 proteins in the cell can affect the stabilityof the p53 protein and the activity of its degradation processes.However, human papillomavirus, as an exogenous factor, canbe an additional cause affecting the work of the repair system.Most of the studies on the association of SNPs of genes withHPV infection and cervical cancer are devoted to the analysisof individual nucleotide substitutions. There is practically nodata in the literature on the combined effect of polymorphicvariants of these three genes in the presence of HPV load.Our work aims to analyze the distribution of the polymorphismsof the TP53 gene (rs1042522), MDM2 gene(rs2279744), and NQO1 gene (rs1800566) in patients withHPV load versus HPV-negative women.Two hundred and three samples of epithelial cells scraped fromthe urogenital tract of women were used for molecular geneticstudies. The study equipment has been provided by the clinicaldiagnostic laboratory, Nauka . Thewomen were divided into two groups: women with a highHPV load (above 3 log of HPV genomes per 100 thousandhuman cells) (n = 89), and HPV-negative women (n = 114).All the women included in the study were over thirty yearsold. Criteria for women being included in the control group:a normal result of colposcopy, HPV-negative PCR-test. Thecomparative group of cases included women with symptomssuch as vaginal discharge, bleeding menstrual abnormalities,and HPV-positive PCR-test with an HPV load of morethan 3 log of HPV genomes per 105 human cells. The ethniccomposition of the women involved in the study groups was asfollows: Russians accounted for 86 %, Armenians accountedfor 9 %, and other nationalities of the Caucasian race \u2013 5 %.All women have given formal written consent to take partin the study. The study was approved by the Bioethics Committeeof the Academy of Biology and Biotechnology of theSouthern Federal University . All the tests for clinical experimentation were carriedout in line with the standards and ethical guidelines of theWorld Medical Association (Helsinki Declaration).The total DNA was isolated from scraping epithelial cells ofthe cervical canal of women according to the DNA-sorb-AM reagent kit protocol. The quantification ofDNA for high-risk HPV types in biological material was analyzed accordingto the AmpliSens-HPV HCR screen-titre-FRT PCRkit protocol. According to the kitmanufacturer\u2019s instructions and clinical reports, the viral loadis interpreted as follows: log \u2264 3 per 105 human cells \u2013 lowclinical significance, 3\u20135 log per 105 human cells \u2013 clinicallysignificance, risk of dysplasia; and > 5 log per 105 humancells \u2013 clinically significance, strongly probable dysplasia.Genotyping was performed for the SNP of TP53 215C>G(Pro72Arg) (rs1042522), MDM2 -410T>G (rs2279744) genesby allele-specific PCR and the SNP-express reagent according to the kit protocol. NQO1 609C>T(rs1800566) was genotyped by a TaqMan genotyping assay.The amplification was carried out in a 25-ml reaction containing2 \u03bcl 25 mM MgCl2, 1 \u03bcl 10 mmol/L of the forward primer(5\u2032-CAG AGT GGC ATT CTG CAT TTC T-3\u2032) and reverse(5\u2032-CTG GAG TGT GCC CAA TGC TA-3\u2032) primers and0.5 \u03bcl mmol/L NQO1 wild-type (5\u2032-6FAM-CTT AGA ACCTCA ACT GA-MGBNFQ-3\u2032) and mutant (5\u2032-VIC-CTT AGAATC TCA ACT GAC A-MGBNFQ-3\u2032) probes, 0.5 \u03bcl Taqpolymerase(5 U/\u03bcl), 2.5 \u03bcl 2.5 \u043c\u041c of dNTP, 2 \u03bcl 10 \u00d7 PCRbuffer B, 12 \u03bcl ddH2O and 3 \u03bcl DNA. Cyclingconditions were as follows: initial denaturation at 95 \u00b0C for10 min, followed by 40 cycles consisting of denaturationat 95 \u00b0C for 15 sec, then annealing at 54 \u00b0C for 60 sec. ThePCR products for NQO1 609C>T (rs1800566) were analyzedin real-time using RotorGene thermocycler. PCR productsfor the TP53 Pro72Arg and MDM2 -410T>G genes wereanalyzed by 3 % agarose gel horizontal electrophoresis andvisualized under the ultraviolet (UV) transilluminator GelDoc.To calculate the statistical data, the \u03c72 test was used to comparethe allele and genotype frequencies of the TP53 215C>G(Pro72Arg) (rs1042522), MDM2 -410T>G (rs2279744), andNQO1 609C>T (rs1800566) genes in the case group andcontrol group. The Hardy\u2013Weinberg equilibrium test wasperformed to determine the goodness-of-fit of the \u03c72 test withone degree of freedom by comparing the observed genotypefrequencies with the expected genotype frequencies. The SNPgenetic association was assessed by the \u03c72 test, odds ratio(OR), and its confidence interval (CI). A p-value <0.05 wasconsidered statistically significant. Statistical analyses wereperformed using GraphPad InStat 3.05 software.The analysis of intergenic interactions was performed usingthe MDR software and by using the exhaustive search algorithm.All potential combinations of genotypes were evaluated withrespect to the risk of developing an HPV infection. Multilocusgenotypes are summed up in the MDR program into groups ofincreased and reduced disease risk, which reduces the dimensionof the number of calculated parameters. Using multiplecross-recalculations of the input primary data, the optimalmodel is selected for intergenic interaction, with the highestaccuracy and, accordingly, with the least error, to predict thepresence or absence of predisposition to the studied pathology.In 89 HPV-positive women, the average age was 40.1 \u00b1 7.3 yearsand 41.1 \u00b1 7.6 years in 114 HPV-negative women. Among 89HPV-infected women the minimum, middle, and maximumHPV DNA load were 3.2, 5.1, and 8.6 log of HPV genomesper 100 thousand human cells, respectivelyFrequency distributions for the three investigated TP53,MDM2, and NQO1 gene polymorphisms are given in Table 1.The polymorphic variants of MDM2 -410T>G and NQO1609C>T were not associated with a high HPV load. At thesame time females with a high HPV load had a significantlyhigher frequency of TP53 215G (72Arg) allele and 215GG (72ArgArg)genotype than healthy controls. The existence of multiple allelic variationsin genes that encode for protein molecules can lead to severalrelated changes in the genome and proteome function. Therefore,an analysis of intergenic interactions of allelic variantswas conducted.An analysis of intergenic interactions showed that the threelocusmodel of gene interaction has a prediction accuracy of64 % and cross-validation consistency (10/10) (Table 2). Interactionof TP53 (rs1042522) \u2013 MDM2 (rs2279744) \u2013 NQO1(rs1800566) genes is associated with the risk of high HPV loadamong women .A radial diagram demonstrates the contribution of polymorphismof each gene, both individually and in combination withothers for the three-loci. In the vertices of the diagram, thevalues of information for individual genes are indicated, onthe edges \u2013 the information value of the interaction of a pair ofgenes. The studied SNPs affect the formation of the viral loadto varying degrees. According to the model of loci interaction, the highest predictive potential is possessedby the SPN of the TP53 gene (2.26 %). The TP53 and MDM2loci have the greatest effect by intergenic interaction. A pronouncedsynergism was revealed between these loci \u2013 the totaleffect of the combination is 2.87 %. Its information value ishigher than the sum of its individual effects.Cervical cancer is the most common gynecological canceramong women and the high-risk HPV genotypes play a majorrole in abnormal lesion development and cervical malignant neoplasms . The presenceof a high viral load in HPV-positive women indicates that thevirus has not been entirely removed and will likely continueto replicate in the body cells for a long time. Long-term viruspersistence contributes to the incorporation of HPV DNAinto the human genome, the expression of E6/E7 oncogenicproteins, and the development of cancer .Human papillomatosis appears to be a polygenic disease,suggesting that recurrent, small-effect genetic variations canhave consequences for disease susceptibility . Tumor development is largely attributed to geneticvariations in the host\u2019s cell cycle control .The relationships between the TP53 gene (rs1042522), MDM2gene (rs2279744), NQO1 gene (rs1800566), and the risk ofhigh HPV load have been investigated in this studyIn our study, 43.8 % of women (89 out of 203) were positivefor high-risk HPV types. Our analysis revealed an associationof high viral load formation risk with 215G (72Arg)allele carriage and 215GG (72Arg/Arg) genotype of TP53 gene . On the contrary, 215C (Pro72)allele and 215CC(72ProPro) genotype showed protective effect compared to the controlgroup. The polymorphic variants of the p53 protein with Proor Arg in codon 72 have been shown to vary in the efficiencyof interaction with the E6 oncoprotein of HPV . The Arg variant is degraded by the E6 oncoproteinmore readily than the Pro variant. Therefore, the carriers ofthe Arg/Arg genotype have p53 protein more vulnerable toviral protein-induced degradation . Our resultsare consistent with several other studies suggesting that HPVpositivewomen are more vulnerable to cervical malignantneoplasms when having \u0422\u042053 72Arg/Arg genotype and \u0422\u04205372Arg allele .MDM2 promotes cell cycle progression through the activationof S-phase, via interaction with the retinoblastoma tumorsuppressor protein and the transcriptional factor E2F . MDM2 is one of the central nodes in the p53pathway regulation. It has been shown that even a small changein MDM2 level may affect the p53 pathway and, subsequently,cancer development . Our analysisshowed no statistically significant difference in the genotypes( p = 0.86) and allele frequencies ( p = 0.68) distribution ofMDM2 -410T>G gene polymorphism in two women groups.Our analysis showed no statistically significant differencein the genotypes ( p = 0.29) and allele ( p = 0.18) distributionof NQO1 609C>T gene polymorphism in the two groups ofwomen. In agreement with our results, J. Chansaenroj andhis coworkers showed no association of the NQO1 609C>Tpolymorphism with the risk of cervical cancer . At the same time, several studies reported arelationship between NQO1 609TT genotypes and the riskof cervical cancer . TheNQO1 gene (rs1800566) TT genotype is associated with nullenzyme activity and could influence cancer progression byreducing cytotoxic agents containing the quinone moiety.Favorable conditions for HPV persistence include multiplegenetic substitutions which result in gene expressionchanges. In our work, the analysis of gene-gene interactions(MDR) showed significant interaction of the polymorphic loci for increasedviral load (see Table 2). The interaction of the polymorphicvariantsfor the three loci of the genes TP53 215C>G (Pro-72Arg), MDM2 -410T>G, and NQO1 609C>T are associatedwith HPV viral load increase.A synergistic effect was revealed between the studied loci.That is, the combined effect of these loci is more pronouncedthan individual effects. Thus, we revealed an increased risk ofa high viral load in HPV infection in the case of a combinationof polymorphic variants of the TP53, MDM2, and NQO1genes. The risk may be due to disturbances in the work ofthe checkpoints of the cell cycle due to the activation of theprocesses of degradation of the p53 protein.The current study has several limitations. First, the smallsample size: our results should be verified in larger populationsas well as in other ethnic groups. Second, women with cervicalcancer were not included in our research. Comparison of thedifferent histological types of cervical cancer may also be warrantedfor future studies to determine whether the frequencyof TP53, MDM2, and NQO1 gene polymorphisms differ basedon the histological types of cervical cancer. Third, the influenceof epidemiologic risk factors such as smoking, alcoholintake, and sexual behavior or pathogenic factors like bacteriawith the risk of HPV infection was not included. It would beinteresting to analyze if TP53, MDM2, and NQO1 productionis associated with environmental or pathogenic factors.Our results demonstrate that the risk of high viral load formationis associated with TP53 215G (72Arg) allele andTP53 215GG (72ArgArg) genotype in HPV-positive women.Although the individual SNPs of MDM2 -410T>G andNQO1 609C>T genes did not reveal a statistically significantfrequency difference in our study, intergenic interactionsanalysis revealed significant interaction for all polymorphicvariants. This demonstrated that the infection developmentdepends on the synergistic effect of several polymorphismsthat induce changes in gene expression and represent an allelicload for HPV-positive cells. However, the role of thegenetic susceptibility to HPV infections and high HPV loadwith TP53 rs1042522, MDM2 rs2279744, NQO1 rs1800566polymorphisms requires further investigationThe authors declare no conflict of interest.Atia A., Abdullah A. NQO1 enzyme and its role in cellular protection;an insight. Iberoam. J. Med. 2020;2(4):306-313. DOI 10.5281/zenodo.3877528.Aubrey B.J., Strasser A., Kelly G.L. Tumor-suppressor functions ofthe TP53 pathway. Cold Spring Harb. Perspect. Med. 2016;6(5):a026062. DOI 10.1101/cshperspect.a026062.Balasubramaniam S.D., Balakrishnan V., Oon C.E., Kaur G. Key molecularevents in cervical cancer development. Medicina (Kaunas).2019;55(7):384. DOI 10.3390/medicina55070384.Basyar R., Saleh A.Z., Sastradinata I., Yuwono Y. p53 gene codon72 polymorphisms among cervical carcinoma patients. Indones.J. Obstet. Gynecol. 2016;3(3):165-169. DOI 10.32771/inajog.v3i3.48.Bond G.L., Hu W., Bond E.E., Robins H., Lutzker S.G., Arva N.C.A single nucleotide polymorphism in the MDM2 promoter attenuatesthe p53 tumor suppressor pathway and accelerates tumor formationin humans. Cell. 2004;119(5):591-602. DOI 10.1016/j.cell.2004.11.022.Bordignon V., Di Domenico E., Trento E., D\u2019Agosto G., Cavallo I.,Pontone M. How human papillomavirus replication and immuneevasion strategies take advantage of the host DNA damage repairmachinery. Viruses. 2017;9(12):390. DOI 10.3390/v9120390.Chansaenroj J., Theamboonlers A., Junyangdikul P., Swangvaree S.,Karalak A., Chinchai T. Polymorphisms in TP53 (rs1042522), p16(rs11515 and rs3088440) and NQO1 (rs1800566) genes in Thai cervicalcancer patients with HPV 16 infection. Asian Pac. J. Cancer.Prev. 2013;14(1):341-346. DOI 10.7314/APJCP.2013.14.1.341.Diao J., Bao J., Peng J., Mo J., Ye Q., He J. Correlation betweenNAD(P)H: quinone oxidoreductase 1 C609T polymorphism and increasedrisk of esophageal cancer: evidence from a meta-analysis.Ther. Adv. Med. Oncol. 2017;9(1):13-21. DOI 10.1177/1758834016668682.Fernandes J.V., De Medeiros T.A.A., De Azevedo J.C.V., CobucciR.N.O., De Carvalho M.G.F., Andrade V.S. Link between chronicinflammation and human papillomavirus-induced carcinogenesis(Review).Oncol. Lett. 2015;9(3):1015-1026. DOI 10.3892/ol.2015.2884.Gheit T. Mucosal and cutaneous human papillomavirus infections andcancer biology. Front. Oncol. 2019;9:355. DOI 10.3389/fonc.2019.00355.Hu X., Zhang Z., Ma D., Huettner P.C., Massad L.S., Nguyen L. TP53,MDM2, NQO1, and susceptibility to cervical cancer. Cancer Epidemiol.Biomarkers Prev. 2010;19(3):755-761. DOI 10.1158/1055-9965.EPI-09-0886.Karni-Schmidt O., Lokshin M., Prives C. The roles of MDM2 andMDMX in \u0441ancer. Annu. Rev. Pathol. 2016;11:617-644. DOI10.1146/annurev-pathol-012414-040349.Khoury R., Sauter S., Butsch Kovacic M., Nelson A., Myers K.,Mehta P. Risk of human papillomavirus infection in cancer-proneindividuals: What we know. Viruses. 2018;10(1):47. DOI 10.3390/v10010047.Litwin T., Clarke M., Dean M., Wentzensen N. Somatic host cell alterationsin HPV carcinogenesis. Viruses. 2017;9(8):206. DOI 10.3390/v9080206.Malag\u00f3n T., Louvanto K., Ramanakumar A.V., Koushik A., Coutl\u00e9eF., Franco E.L. Viral load of human papillomavirus types16/18/31/33/45 as a predictor of cervical intraepithelial neoplasia andcancer by age. Gynecol. Oncol. 2019;155(2):245-253. DOI 10.1016/j.ygyno.2019.09.010.McBride A.A., Warburton A. The role of integration in oncogenicprogression of HPV-associated cancers. PLoS Pathog. 2017;13(4):e1006211. DOI 10.1371/journal.ppat.1006211.Mendoza M., Mandani G., Momand J. The MDM2 gene family. Biomol.Concepts. 2014;5(1):9-19. DOI 10.1515/bmc-2013-0027.Mittal S., Banks L. Molecular mechanisms underlying human papillomavirusE6 and E7 oncoprotein-induced cell transformation. Mutat.Res. Rev. Mutat. Res. 2017;772:23-35. DOI 10.1016/j.mrrev.2016.08.001.Moschonas G.D., Tsakogiannis D., Lamprou K.A., Mastora E., DimitriouT.G., Kyriakopoulou Z. Association of codon 72 polymorphismof p53 with the severity of cervical dysplasia, E6-T350G andHPV16 variant lineages in HPV16-infected women. J. Med. Microbiol.2017;66(9):1358-1365. DOI 10.1099/jmm.0.000563.Niwa Y., Hirose K., Nakanishi T., Nawa A., Kuzuya K., Tajima K.Association of the NAD(P)H: quinone oxidoreductase C609T polymorphism and the risk of cervical cancer in Japanese subjects. Gynecol.Oncol. 2005;96(2):423-429. DOI 10.1016/j.ygyno.2004.10.015.Oliner J.D., Saiki A.Y., Caenepeel S. The role of MDM2 amplificationand overexpression in tumorigenesis. Cold Spring Harb. Perspect.Med. 2016;6(6):a026336. DOI 10.1101/cshperspect.a026336.Rampias T., Sasaki C., Psyrri A. Molecular mechanisms of HPV inducedcarcinogenesis in head and neck. Oral. Oncol. 2014;50(5):356-363. DOI 10.1016/j.oraloncology.2013.07.011.Ross D., Siegel D. NAD(P)H:quinone oxidoreductase 1 ,functions and pharmacogenetics. Methods Enzymol.2004;382:115-144. DOI 10.1016/S0076-6879(04)82008-1.Roura E., Travier N., Waterboer T., de Sanjos\u00e9 S., Bosch F.X., PawlitaM. The influence of hormonal factors on the risk of developingcervical Cancer and pre-Cancer: results from the EPIC cohort. PLoSOne. 2016;11(1):e0147029. DOI 10.1371/journal.pone.0147029.Saadatzadeh M., Elmi A., Pandya P., Bijangi-Vishehsaraei K., Ding J.,Stamatkin C. The role of MDM2 in promoting genome stabilityversus instability. Int. J. Mol. Sci. 2017;18(10):2216. DOI 10.3390/ijms18102216.Sen P., Ganguly P., Ganguly N. Modulation of DNA methylation by humanpapillomavirus E6 and E7 oncoproteins in cervical cancer (Review).Oncol. Lett. 2017;15(1):11-22. DOI 10.3892/ol.2017.7292.So K.A., Lee I.H., Lee K.H., Hong S.R., Kim Y.J., Seo H.H. Humanpapillomavirus genotype-specific risk in cervical carcinogenesis.J. Gynecol. Oncol. 2019;30(4):e52. DOI 10.3802/jgo.2019.30.e52.Storey A., Thomas M., Kalita A., Harwood C., Gardiol D., MantovaniF. Role of a p53 polymorphism in the development of humanpapillomavirus-associated cancer. Nature. 1998;393(6682):229-234.DOI 10.1038/30400.Tasic D., Lazarevic I., Knezevic A., Tasic L., Pikula A., Perisic Z. Theimpact of environmental and behavioural cofactors on the developmentof cervical disorders in HR-HPV-infected women in Serbia.Epidemiol. Infect. 2018;146(13):1714-1723. DOI 10.1017/S0950268818001668.Thomas M., Kalita A., Labrecque S., Pim D., Banks L., MatlashewskiG. Two polymorphic variants of wild-type p53 differ biochemicallyand biologically. Mol. Cell Biol. 1999;19(2):1092-1100. DOI10.1128/MCB.19.2.1092.Tsvetkov P., Reuven N., Shaul Y. Ubiquitin-independent p53 proteasomaldegradation. Cell Death Differ. 2010;17(1):103-108. DOI10.1038/cdd.2009.67.Vonsky M., Shabaeva M., Runov A., Lebedeva N., Chowdhury S.,Palefsky J.M. Carcinogenesis associated with human papillomavirusinfection. Mechanisms and potential for immunotherapy.Biochemistry. 2019;84(7):782-799. DOI 10.1134/S0006297919070095.Yang S., Zhao J., Li L. NAD(P)H: quinone oxidoreductase 1 geners1800566 polymorphism increases the risk of cervical cancer in aChinese Han sample. Medicine . 2020;99(20):e19941.DOI 10.1097/MD.0000000000019941."} +{"text": "In this study, we investigated the protective potential of B-LAP against diabetic nephropathy in streptozotocin (STZ) induced diabetic mice. Diabetes induction in mice was carried out by a single intraperitoneal injection of STZ. 2.5 mg/kg/day and 5 mg/kg/day doses of B-LAP were administered orally for twelve weeks and renal histoarchitecture, caspase-3, tumor necrosis factor-alpha (TNF-\u03b1), malondialdehyde (MDA), glutathione peroxidase (GPX), as well as urinary nephrin and neutrophil gelatinase-associated lipocalin (NGAL) were evaluated. Additionally, kidney levels of PI3K, phosphorylated (p)-Akt, p-mTOR, p-CREB, and SIRT1 were assessed in the present investigation. 5 mg/kg B-LAP significantly decreased urinary excretions of nephrin and NGAL. It also mitigated renal TNF-\u03b1 and MDA levels and simultaneously improved GPX activities. 5 mg/kg B-LAP improved renal function in diabetic mice as indicated by elevated values of creatinine clearance. While B-LAP elevated renal levels of SIRT1, it alleviated PI3K, p-Akt, p-mTOR, and p-CREB levels in the kidneys of diabetic mice.Collectively, these findings suggest B-LAP as a potential renoprotective agent in STZ-induced diabetic mice probably via modulating the PI3K/Akt/mTOR pathway. Diabetic nephropathy (DN) is the main cause of end-stage renal disease (ESRD) across the world, which develops in one-third of both type 1 and type 2 diabetic patients , IL-6, and tumor necrosis factor-alpha (TNF-\u03b1) levels via modulating NF-\u03baB and MAPK/ERK signaling pathways in vitro (\u03b2-LAPachone (B-LAP), the natural agent derived from the Lapacho tree, in vitro . Newer cin vitro -10. Morein vitro .The present investigation aimed to examine potential renoprotective effects of B-LAP in streptozotocin (STZ)-induced diabetic mice and to evaluate its impact on the PI3K/Akt/mTOR pathway in the kidneys.ChemicalsThe following commercially available chemicals were obtained: B-LAP and STZ .Experimental designThirty male C57BL/6 mice were obtained from the Pasteur Institute of Iran. Diabetes induction was done by injecting a 50 mg/kg dose of STZ dissolved in citrate buffer (pH: 4.5) . InductiMice were assigned into 5 groups of 6 animals per each; 1- sham receiving B-LAP vehicle, i.e., 0.05% DMSO; 2- diabetic control mice (Diab); 3- Diab + low dose B-LAP (2.5 mg/kg/day); 4- Diab + high dose B-LAP (5 mg/kg/day); 5- Normal mice receiving 5 mg/kg/day B-LAP. Treatment doses of B-LAP were adopted according to a previously conducted similar study and the agent was administered via intra-gastric gavage . After 1Measurement of systolic blood pressureThe systolic blood pressure (SBP) readings were recorded a day before placing the mice in the metabolic cages using a non-invasive tail-cuff method . Animals were placed in a heated restrainer at 37 \u00b1 1 \u00b0C for 10 min during measurements. For each mouse, 3 blood pressures were measured and their average was taken as the SBP.Biochemical and immunochemical assessmentsIn order to calculate Ccr, first serum and urinary levels of creatinine were assayed via commercially available kits . Creatinine clearance (Ccr) was then calculated using the values for urinary creatinine, urine volume, serum creatinine, and body weight :Ccr (mL/min/kg) = (urine creatinine (mg/dL) \u00d7 urine volume (mL)) / (serum creatinine (mg/dL) \u00d7 1440 (min)) \u00d7 1000 / (body weight (g))Renal malondialdehyde (MDA) and glutathione peroxidase (GPX) activities were measured spectrophotometrically using the commercially available kits . Obtained values were normalized by renal total protein levels measured by the Lowry method.Tumor necrosis factor-alpha (TNF-\u03b1), nephrin, and neutrophil gelatinase-associated lipocalin (NGAL) levels were assayed by using enzyme-linked immunosorbent assay (ELISA) kits .Histopathological examinationsRenal tissue specimens were fixed in 10% neutral buffered formalin (NBF) and processed for paraffin sections of five-\u03bcm thickness. Sections were stained with hematoxylin and eosin (H&E) and were qualitatively examined under a light microscope .For immunofluorescence analysis, five-\u00b5m kidney tissue sections were cut and incubated with antibodies raised against caspase-3 after the antigens were retrieved enzymatically using 0.05% trypsin solution (Sigma) for 10 min. Subsequent to incubation with fluorescein isothiocyanate (FITC)-conjugated secondary antibody solution, the slides were visualized using an immunofluorescence microscope . ImageJ software (version 1.41) was utilized to semiquantitatively analyze the data. For normalization, pixel intensities obtained from the treatment groups were divided by the corresponding pixel intensities recorded for the sham mice.Western blottingSodium dodecyl sulfate-polyacrylamide gel electrophoresis was performed to electrophoretically separate the proteins. After the transfer of the separated proteins onto the PVDF membranes via electro-blotting, blocking was performed using a 5% skimmed milk solution for 60 min. Then, the membranes were incubated in caspase-3 , phosphoinositide 3-kinase (PI3K) , phosphorylated Akt (p-Akt) , phosphorylated mammalian target of rapamycin (p-mTOR) , phosphorylated cAMP response element-binding protein 1 (p-CREB-1) , Sirtuin 1 (SIRT1) , and \u03b2-actin primary antibodies at 4 \u00b0C overnight. Blots were then incubated by the horseradish peroxidase-labeled secondary antibody solution at room temperature for 45 min and were visualized by Western Blotting Luminol Reagent (Santa Cruz). ImageJ software (version 1.41) was implemented to measure the pixel intensities of the visualized bands from the X-ray films. The band density of each protein was first divided by the band density of its respective \u03b2-actin loading control and the obtained values for study groups were then normalized by the values for the sham group.Statistical analysispost hoc comparisons using Statistical Package for the Social Sciences, . The statistical significance level was set at\u00a0P<0.05.Data were descriptively expressed as mean \u00b1 SD. The variables were analyzed by one-way analysis of variance followed by Tukey\u2019s test for General characteristics of the study groups have been presented in P<0.01)]. TNF-\u03b1 levels in the kidneys were declined by 23.4% after treatment with 5 mg/kg B-LAP (P<0.05) .P<0.01), and 5 mg/kg B-LAP significantly reduced renal MDA levels to 11.62 \u00b1 1.19 nmol/mg protein (P<0.05) compared with sham mice (4.42 \u00b1 0.92 nmol/mg protein) ((P<0.05) .P<0.01); and 5 mg/kg B-LAP significantly elevated its values to 15.62 \u00b1 1.36 U/mg protein (P<0.05) in diabetic mice. It should be underlined that healthy mice receiving 5 mg/kg B-LAP had higher activities of GPX in their kidneys (7.46 \u00b1 1.12 U/mg protein) compared with sham mice (5.21 \u00b1 1.06 U/mg protein) (P<0.05) were significantly higher than in sham mice (5.21 \u00b1 1.06 U/mg protein) ((P<0.05) .P<0.01)]. Treatment with 5 mg/kg B-LAP reduced urinary levels of nephrin by 23.56% compared with diabetic mice (P<0.05). Urinary NGAL levels were significantly increased in diabetic mice (0.64 \u00b1 0.073 ng/mg Cr) compared with the sham group (0.23 \u00b1 0.042 ng/mg Cr) (P<0.01); and 5 mg/kg B-LAP reduced urinary NGAL levels to 0.53 \u00b1 0.055 ng/mg Cr (P<0.05) .P<0.01). Its values were increased to 1.44 \u00b1 0.18 mL/min/kg after treatment with 5 mg/kg B-LAP (P<0.05) in comparison with sham mice (2.21 \u00b1 0.23 mL/min/kg) ((P<0.05) .P<0.01) and 5 mg/kg B-LAP slightly, albeit statistically significantly, attenuated its levels compared with control diabetic mice (P<0.05) .P<0.01) (P<0.05) . PI3K anP<0.01) ; on the P<0.01) . Convers(P<0.05) .The current study showed that B-LAP, a plant-derived\u00a0naphthoquinone\u00a0with potential anti-inflammatory activity, protected the kidneys against the deleterious effects of STZ-induced diabetes. In addition to improving renal function as demonstrated by elevated creatinine clearance values, B-LAP successfully declined renal and urinary levels of tubular injury markers, including nephrin and NGAL. Ameliorating renal histoarchitecture, B-LAP reduced renal levels of p-mTOR as well as p-CREB and at the same time increased SIRT1 levels in the kidneys of diabetic mice. +; thereby, restored cellular NAD+ activates NAD+-dependent enzymes, including SIRT1 deacetylase. Deacetylated p65 subunit of NF-\u03baB protein complex is prone to degradation by the ubiquitin-proteasome system (UPS); therefore, increased activity of SIRT1 suppresses inflammation by reducing the expression of cytokines that are downstream to NF-\u03baB (B-LAP functions as the activator of NAD(P)H quinone dehydrogenase (NQO1), the enzyme that regenerates cellular NADH into NADto NF-\u03baB , 16. B-Lto NF-\u03baB . In lineto NF-\u03baB .et al., Huang Kui capsule (HKC) alleviates glomerular and tubular pathological changes associated with DN and simultaneously represses renal levels of p-Akt and p-mTOR in mice , in addition to repressing renal levels of PI3K and p-AKT, down-regulates transforming growth factor-beta (TGF-\u03b2) expressions in the kidneys and ameliorates albuminuria in type 2 diabetic rats (Our findings showed that B-LAP especially at 5 mg/kg attenuated elevated levels of PI3K, p-Akt, p-mTOR, and p-CREB in the kidneys of diabetic mice. The induction of the PI3K/Akt/mTOR signaling pathway contributes significantly to the pathogenesis of DN as it initiates the pathways involved in kidney fibrosis and inflammation . In agre in mice . Likewistic rats .CREB is a transcription factor that after phosphorylation is translocated into the nuclei of the renal cells and functions as the regulator of the expression of genes encoding several pro-fibrotic and antiDemonstration of reduced MDA levels and elevated GPX activities in the renal tissues by B-LAP treatment is an indication of ameliorations in oxidative stress, the indispensable feature of DN both in mice and in humans . LikewisGlomerular basement membrane disintegration, as well as podocyte detachment, are two principal pathogenic features of DN . 5 mg/kgOur findings underline the protective actions of B-LAP on the renal complications of STZ-induced diabetic mice. Apart from reductions in the urinary indices of glomerular and tubular injury, creatinine clearance values, the indicators of renal function, were significantly improved in diabetic mice by one-month B-LAP treatment. Moreover, 5 mg/kg B-LAP confers protection against renal inflammation and oxidative stress in STZ-induced diabetic mice probably via modulating the activities of PI3K/Akt/mTOR and SIRT1 levels in the kidneys."} +{"text": "We examined the in vitro activity of CAZ-AVI and comparators against presumed community-acquired and hospital-acquired isolates collected from pediatric patients as part of the ATLAS surveillance program.Ceftazidime-avibactam (CAZ-AVI) is a \u03b2-lactam/non-\u03b2-lactam \u03b2-lactamase inhibitor combination with Escherichia coli, Klebsiella spp., Proteus mirabilis) or meropenem MICs \u22652 \u00b5g/mL or \u22654 \u00b5g/mL (Psa) were screened for \u03b2-lactamase genes.6654 non-duplicate isolates were collected in 52 countries in Europe (n=3423), Latin America (n=1323), Middle East/Africa (n=1177), and Asia/Pacific from patients (newborn to 17 y) with lower respiratory tract , urinary tract , bloodstream , skin and soft tissue , and intra-abdominal infections. Susceptibility testing was performed by CLSI broth microdilution and values were interpreted using CLSI 2021 breakpoints. CAZ-AVI was tested at a fixed concentration of 4 \u00b5g/mL AVI. Isolates with CAZ or aztreonam MICs \u22652 \u00b5g/mL (in vitro activity of CAZ-AVI exceeded that of meropenem and other tested \u03b2-lactams against Ent (97.8% susceptible (S)) and Psa (92.1% S) collected globally from pediatric patients (Table). Percentages of susceptibility to CAZ-AVI ranged from 95.4-99.2% among CA Ent from different infection types and were reduced 0.6-1.3% among HA isolates from LRTI, UTI, SSTI, and IAI. Susceptibility to CAZ-AVI was also similar (92.6-95.8% S) among CA Psa from different infection types and was reduced 1.2-7.0% among HA isolates. Larger differences in susceptibility were typically seen for the tested comparator \u03b2-lactams. For Ent, the lowest percentages of susceptibility to the tested \u03b2-lactams were observed among isolates from BSI, while the pattern was less clear for Psa.The Results TablePsa in pediatric patients.CAZ-AVI could provide a valuable therapeutic option for treatment of CA and HA infections caused by Ent and Krystyna Kazmierczak, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Sibylle Lob, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Gregory Stone, PhD, AztraZeneca Pfizer, Inc. (Employee) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)"} +{"text": "Two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants associated with increased transmission and immune evasion, P.1 and P.2, emerged in Brazil and spread throughout South America. Here, we report genomes corresponding to these variants that were recently detected in Uruguay. These P.1 and P.2 genomes share all substitutions that are characteristic of these variants. Betacoronavirus (family Coronaviridae) and the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic (Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel member of the genus pandemic . VOCs hapandemic , 5. Thespandemic , and theThe research described in this study was performed in adherence to the Declaration of Helsinki; no specific authorization was required, because the activities were conducted as part of a routine virological surveillance by the Uruguayan official Institution for Surveillance of Influenza and Other Respiratory Viruses of the Ministry of Public Health (DLSP-MSP).The variants P.1 and P.2, which emerged in Brazil, have spread to other parts of South America , 8. HereTC) value of\u2009<18. RNA was extracted with a QIAmp viral minikit . Genome amplification was achieved using ARTIC 3 primers (https://artic.network/ncov-2019). First, cDNA strand analysis, Nextera DNA Flex library preparation, and 2\u2009\u00d7\u2009150-bp sequencing on an Illumina MiniSeq platform were performed following a previous report (http://cov-glue.cvr.gla.ac.uk/). Lineages refer to those assigned using the pangolin tool (https://cov-lineages.org). All tools were run with default parameters unless otherwise specified.Nasopharyngeal swab samples were collected in March 2021 in the Uruguayan Rivera department bordering Brazil and came from two symptomatic cases. The samples tested positive for SARS-CoV-2 using a standard quantitative PCR (qPCR) procedure ; both pas report . AdapterSample SARS-CoV-2/human/URY/374/2021 (P.1) has a sequence length of 29,835 nucleotides (nt), 1,240,211 total reads, 3,920\u00d7 mean coverage, and a 38.0% G+C content. Sample SARS-CoV-2/human/URY/380/2021 (P.2) has a sequence length of 29,858 nt, 1,007,202 total reads, 5,877\u00d7 mean coverage, and a 37.9% G+C content. Their genome sequences lack the outermost nucleotides (<20 nt) of the 5\u2032 and 3\u2032 untranslated regions (UTRs), which are not usually sequenced with the ARTIC protocol.nsp6 that is considered a P.1 genetic signature and MW988205 . The raw reads and metadata were deposited under the BioProject accession number PRJNA634396 and SRA accession numbers SRX10652818 (SARS-CoV-2/human/URY/374/2021) and SRX10652819 (SARS-CoV-2/human/URY/380/2021).These genome sequences were deposited in GenBank under accession numbers"} +{"text": "Dear Editor,TNFRSF8, is a transmembrane cytokine receptor of the tumor necrosis factor receptor (TNFR) superfamily and expressed on ~20% of DLBCL. To better understand the underlying mechanism of CD30 expression in DLBCL, we performed clinical, genomic and transcriptomic analysis in a cohort of 1048 patients with de novo DLBCL. A flow chart describing the cohort selection was displayed in Supplementary Fig. P\u2009<\u20090.001, Supplementary Fig. P\u2009=\u20090.002), as compared to CD30-DLBCL. In terms of IPI, 39% of CD30\u2009+\u2009DLBCL and 48% of CD30-DLBCL were categorized into low-risk group, 21% and 19% into low-intermediate risk group, 25% and 17% into intermediate-high risk group, and 16% and 16% into high-risk group, respectively (P\u2009=\u20090.040). Pathologically, CD30\u2009+\u2009DLBCL was significantly associated with increased percentage of non-GCB subtype (P\u2009=\u20090.042) and EBER positivity (P\u2009<\u20090.001), as previously reported [Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma with heterogeneous clinical, immunophenotypic, and genetic features. Surface antigens, such as CD20, CD22, CD79B, and CD19 are important accessible parts of lymphoma cells with immunotherapeutic potential. CD30, encoded by TNFAIP3 (P\u2009=\u20090.002), TNFRSF14 (P\u2009=\u20090.045), SOCS1 (P\u2009=\u20090.010), STAT6 (P\u2009=\u20090.007), CIITA (P\u2009=\u20090.007), CD58 (P\u2009=\u20090.037), KMT2C (P\u2009=\u20090.016), but lower mutation frequency in CD79B (P\u2009=\u20090.026) and MYD88 , cytotoxic T-cells (P\u2009=\u20090.030), exhausted T-cells (P\u2009=\u20090.004), T-helper 17 (Th17) cells (P\u2009=\u20090.001), regulatory T (Treg)-cells (P\u2009=\u20090.001), dendritic cells , and macrophages , with worst prognosis in JA subtype and follicular helper T (Tfh) cells (P\u2009=\u20090.001), with a positive correlation between the signature genes for immune cell recruitment such as CCR6, CCL21, and CXCR4 , in parallel with immune checkpoint genes, such as PD-L1, TIM3, and LAG3 and CD8\u2009+\u2009T-cells and CIITA (CIITAkd), were transfected into OCI-LY10. Meanwhile, SOCS1wt, SOCS1Q175H, CIITAwt, CIITAL807R, as well as a shRNA to knockdown TNFAIP3 (TNFAIP3kd), were transfected into SU-DHL-4. Quantitative real-time PCR and western blot were used to confirm the transfection efficiency , an anti-CD30 monoclonal antibody-drug conjugate has shown remarkable responses in first-line treatment of HL and CD30\u2009+\u2009peripheral T-cell lymphoma in combination with chemotherapy [TNFAIP3L147Q versus TNFAIP3wt OCI-LY10 , and TNFAIP3kd versus scramble SU-DHL-4 , and SOCS1Q175H versus SOCS1wt SU-DHL-4 , and CIITAL807R versus CIITAwt SU-DHL-4 . There are currently no plans to share data not included in this paper.Sequencing data is available at the National Omics Data Encyclopedia (NODE, Supplemental Materials"} +{"text": "Drug-resistant tuberculosis (DR-TB), obesity, and malnutrition are growing public health problems in the world. However, little has discussed the impact of different BMI status on the emergence of TB drug resistance. We aimed to explore the drug-resistant profiles of DR-TB and its clinical predictors among underweight, overweight or obesity population.8957 newly diagnosed TB cases with drug susceptibility results and BMI data in Shandong China, from 2004 to 2019 were enrolled. Multivariable and univariable logistic regression models were applied to investigate the impact of BMI on different drug-resistance. Clinical predicators and drug-resistant profiles of DR-TB among obesity, underweight, normal TB group were also described.P\u2009<\u20090.05.Among 8957\u00a0TB cases, 6417 (71.64%) were normal weight, 2121 (23.68%) were underweight, 373 (4.16%) were overweight, and 46 (0.51%) were obese. The proportion of drug resistance and co-morbidity among normal weight, underweight, overweight, obese TB groups were 18.86%/18.25%/20.38%/23.91% (DR-TB), 11.19%/11.74%/9.65%/17.39% , 3.41%/3.06%/5.36%/0.00% , 4.21%/3.39%/5.36%/6.52% , 10.57%/8.44%/19.57%/23.91% (co-morbidity), respectively. Compared with normal weight group, underweight were associated with lower risk of streptomycin-related resistance , but contributed to a higher risk of MR-TB (isoniazid) (odds ratio (OR) 1.347, 95% CI 1.049\u20131.730; adjusted OR (aOR) 1.31, 95% CI 1.017\u20131.686), P\u2009<\u20090.05. In addition, overweight were positively associated with MDR-TB , isoniazid\u2009+\u2009rifampicin\u2009+\u2009streptomycin resistance : 1.061\u20133.577; aOR 2.113, 95% CI 1.141\u20133.912), Any isoniazid\u2009+\u2009streptomycin resistance , The higher risk of MDR-TB, isoniazid\u2009+\u2009rifampicin\u2009+\u2009streptomycin resistance, Any isoniazid\u2009+\u2009streptomycin resistance, and co-morbidity among overweight population implies that routine screening for drug sensitivity and more attention on co-morbidity among overweight TB cases may be necessary. In addition, underweight TB cases have a higher risk of isoniazid resistance. Our study suggests that an in-depth study of the interaction between host metabolic activity and infection of DR-TB may contribute more to novel treatment options or preventive measures, and accelerate the implementation of the STOP TB strategy. Mycobacterium tuberculosis (MTB), contributes to a largest number of deaths from infectious diseases (more than HIV/AIDS) [Tuberculosis (TB), is caused by IV/AIDS) , 2. AccoIV/AIDS) . AdditioIV/AIDS) . Nine peIV/AIDS) .Multidrug-resistant tuberculosis (MDR-TB) is defined as TB with resistance to at least isoniazid (INH) and rifampin (RFP), which is usually associated with longer hospitalization, more expensive treatment, and higher mortality . The bac2 was independent risk factor of latent tuberculosis infection 1.17, 95% CI 1.04\u20131.33) [The critical influences of diverse nutritional status on TB infection have been recognized for decades . Recent 04\u20131.33) . In summThis research intended to explore the association between BMI and primary DR-TB in the aspects as follows: (1) to describe the clinical characteristics of TB cases with four different BMI status ; (2) to illustrate the drug resistant profiles of TB cases subgroups stratified by BMI; (3) to analyze the relative risk of DR-TB including DR-TB , MDR-TB , mono-resistant tuberculosis , polydrug resistant tuberculosis , RFP-related resistance, INH-related resistance, streptomycin (SM)-related resistance, MR-TB (INH), INH\u2009+\u2009RFP\u2009+\u2009SM resistance (MDR3), INH\u2009+\u2009SM resistance (PDR2), Any INH\u2009+\u2009SM resistance among subgroups with different BMI; (4) to investigate the risk factors of DR-TB among TB cases subgroups stratified by BMI.The Ethics Committee of Shandong Provincial Hospital (SPH) and Shandong Provincial Chest Hospital (SPCH) approved for our study. Personal information of TB patients such as names were erased before data analysis and reporting. All methods were performed in accordance with relevant guidelines and regulations. Informed consent was obtained from all participants or, if participants are under 18, from a parent and/or legal guardian.2 [2) was 3.5% (95% CI 3.4\u20133.6) [Our study was conducted in Shandong, a coastal province in eastern China (36\u00b024\u2032N latitude and 118\u00b0 24\u2032 E longitude), with 100 million inhabitants and an area of 157,100\u00a0km2 . A large2 . The rat2 . As estiNontuberculosis mycobacteria (NTM) infection; (3) BMI information missing; (4) extra-pulmonary cases , meanwhile their basic demography and clinical characteristics were collected. Information of BMI, age, sex , drinking (yes or no), smoking (yes or no), cavity (yes or no), and co-morbidity were collected through questionnaire. Nutritional status indicators except BMI were not routinely collected. Exclusion criteria: (1) cases with previous TB history; (2) 2 were in the underweight range, between 18.5 and 24.9\u00a0kg/m2 were in normal weight range, between 25 and 29.9\u00a0kg/m2 were in the overweight range,\u2009\u2265\u200930\u00a0kg/m2 were in the obese range [BMI below 18.5\u00a0kg/mse range . Mono-rese range . Multidrse range . Polydruse range . MR-TB of SPCH. Initially, at least two sputum specimens of each eligible patient were collected. Then, isolates were cultured in L\u00f6wenstein-Jensen (L-J) medium according to the standard protocol, and then these growing colonies were used for strain identification and phenotypic DST . DST forP value\u2009<\u20090.05. All data analyses were conducted in SPSS software (version 20.0).Categorical baseline demographic and clinical features of 8957\u00a0TB cases including age , sex (men or women), smoker or non-smoker, drinker or non-drinker, cavity (yes/no), co-morbidity (yes/no), and drug resistant profiles in four subgroups with different BMI status were compared by Pearson Chi-square test or Fisher\u2019s exact test. The age subgroups were divided according to previous publications , 22. BinAs shown in Table P\u2009<\u20090.05. Underweight TB cases had a higher proportion of asthma (0.85% vs 0.37%) and COPD (2.55% vs 1.78%) but with a lower rate of diabetes (3.58% vs 7.03%) than normal group, P\u2009<\u20090.05. There were no significant differences in sex, cavity, smoking and drinking between lower and normal BMI cases. Both these two groups have more males, but less drinkers, smokers, and cavity or\u2009>\u200965 (34.64% vs 22.98%) age group, and they had a lower rate of co-morbidity (8.44% vs 10.57%), P\u2009<\u20090.05. In addition, overweight TB cases are less likely to be in 15\u201324 age group (6.18% vs 15.63%), P\u2009<\u20090.05. There were no significant differences in 0\u201314 age group, 65\u2009+\u2009age group, sex, smoking and drinking between overweight and normal cases (Table The proportions of 25\u201344 age group (33.33% vs 15.63%), 45\u201364 age group (39.78% vs 34.21%), cavity (51% vs 43.66%), co-morbidity (19.57% vs 10.57%), COPD (3.22% vs 1.78%), diabetes (13.94% vs 7.03%), hypertension (3.75% vs 1.82%), and cancer (0.80% vs 0.16%) were higher in The rates of females (32.61% vs 17.19%), co-morbidity (23.91% vs 10.57%), diabetes (19.57% vs 7.03%) were higher in obese TB cases than in normal cases, P\u2009<\u20090.05. There were no significant differences in age, smoking, drinking and cavity between obese and normal cases or MDR3 (INH\u2009+\u2009RFP\u2009+\u2009SM) (3.22% vs 1.68%) cases among overweight group than normal group, P\u2009<\u20090.05. There were no significant differences in other drug resistant sub-types between abnormal weight groups and normal group.As shown in Table P\u2009=\u20090.028), but contributed to a higher risk of MR-TB (INH) . In addition, overweight was positively associated with MDR-TB , INH\u2009+\u2009RFP\u2009+\u2009SM resistance , Any INH\u2009+\u2009SM resistance . However, there were no statistical differences on drug resistance between obese group and normal weight group. In univariable and multivariable multinomial logistic regression models, we also found that overweight may be a risk factor for MDR-TB and overweight cases . In addition, co-morbidity except COPD, diabetes, hypertension were positively associated with DR-TB in underweight cases. Among normal weight group, male or cavitary pulmonary tuberculosis were more likely to have anti-TB resistance and overweight (BMI\u2009=\u200924\u201326.9\u00a0kg/m2) contributed to a lower risk of TB infection [2 was observed to be independently associated with LTBI [Obesity has become a global public health problem, and it\u2019s reported that approximately 46% of adults and 15% of children China are overweight or obese . Plenty 04\u20131.33) . Interes04\u20131.33) , 26. Fur04\u20131.33) . Therefo04\u20131.33) , 30. The04\u20131.33) , and theOverweight TB cases had a higher possibility of suffering from co-morbidity including COPD, hypertension, diabetes, and cancer. Actually, previous studies have figured out that BMI was a reliable predictor of prevalent diabetes, hypertension, and COPD \u201333. A stPeople have found a significant association between underweight and higher risk of active TB, adverse TB treatment outcomes, tuberculosis-related mortality , 37\u201339. It has been observed that males were more likely to be affected with DR-TB among normal, underweight, or overweight population. However, there were inconsistent results in the previous literature about the influence of gender differences on vulnerability to MDR-TB \u201344. A stThis study had some strengths. Firstly, it\u2019s the first study to investigate the effect of BMI on drug resistance among newly diagnosed pulmonary TB cases. Secondly, the relative risk of numerous drug-resistant sub-types including DR-TB , MDR-TB , MR-TB , PDR-TB , RFP-related resistance, INH-related resistance, SM-related resistance, IMR-TB (INH), INH\u2009+\u2009RFP\u2009+\u2009SM resistance (MDR3), INH\u2009+\u2009SM resistance (PDR2), Any INH\u2009+\u2009SM resistance among underweight, overweight, obese were analyzed, and could provide clinical reference for future pathologic and molecular studies on different resistant MTB strains. Thirdly, the large amount (DST results from a province of 100 million people) and long time span (from 2004 to 2019) of our data guaranteed the reliance of our findings.This study also had some limitations. Firstly, drug resistance of second-line anti-TB drugs were not routinely examined in China unless at the initiative requirements of patients. Thus, the association between BMI and second-line anti-TB resistance remains to be discovered in future. Secondly, this was a retrospective study, and may have information bias. Thirdly, some obese patients can also be malnourished, since BMI is only one of prognostic factors for assessing malnutrition , 29, 45.Our study has important implications on the global triple epidemics of underweight, obesity, and DR-TB. The positive effect of overweight on MDR-TB, INH\u2009+\u2009RFP\u2009+\u2009SM resistance, Any INH\u2009+\u2009SM resistance, and co-morbidity implies that routine screening for drug sensitivity and more attention on co-morbidity among overweight TB cases may be necessary. Although patients with normal weight had a lower proportion of drug-resistance than overweight or obese patients in Shandong, screening for drug resistance cannot be ignored either because patients with normal weight accounted for 74.64%. In addition, we found underweight TB cases have a higher risk of INH resistance, which provides a reference for clinical rational use of drugs. Our study suggests that an in-depth study of the interaction between host metabolic activity and infection of DR-TB may contribute more to novel treatment options or preventive measures, and accelerate the implementation of the STOP TB strategy."} +{"text": "In December 2020, B.1.1.7 lineage of SARS-CoV-2 was first detected in the United States and has since become the dominant lineage. Previous investigations involving B.1.1.7 suggested higher rates of transmission relative to non-B.1.1.7 lineages. We conducted a household transmission investigation to determine the secondary infection rates (SIR) of B.1.1.7 and non-B.1.1.7 SARS-CoV-2 lineages. From January\u2013April 2021, we enrolled members of households in San Diego County, CA, and Denver, CO metropolitan area (Tri-County), with a confirmed SARS-CoV-2 infection in a household member with illness onset date in the previous 10 days. CDC investigators visited households at enrollment and 14 days later at closeout to obtain demographic and clinical data and nasopharyngeal (NP) samples on all consenting household members. Interim visits, with collection of NP swabs, occurred if a participant became symptomatic during follow-up. NP samples were tested for SARS-CoV-2 using TaqPath\u2122 RT-PCR test, where failure to amplify the spike protein results in S-Gene target failure (SGTF) may indicate B.1.1.7 lineage. Demographic characteristics and SIR were compared among SGTF and non-SGTF households using two-sided p-values with chi-square tests; 95% confidence intervals (CI) were calculated with Wilson score intervals.552 persons from 151 households were enrolled. 91 (60%) households were classified as SGTF, 57 (38%) non-SGTF, and 3 (2%) indeterminant. SGTF and non-SGTF households had similar sex distribution and age and 31 years (IQR 15\u201345), respectively). Hispanic people accounted for 24% and 32% of enrolled members of SGTF and non-SGTF households, respectively (p=0.04). At least one secondary case occurred in 61% of SGTF and 58% of non-SGTF households (P=0.66). SIR was 52% (95%[CI] 46%-59%) for SGTF and 45% (95% CI 37%-53%) for non-SGTF households (P=0.18). SIRs were high in both SGTF and non-SGTF households; our findings did not support an increase in SIR for SGTF relative to non-SGTF households in this setting. Sequence confirmed SARS-CoV-2 samples will provide further information on lineage specific SIRs.All Authors: No reported disclosures"} +{"text": "The elevated plus maze test was employed to evaluate anxiety-like behavior in rats, and in vivo microdialysis was used to measure the extracellular NE level in the BNST. In elevated plus maze tests, EtOHW rats but not EtOH-naive rats exhibited anxiety-like behavior when challenged with 7-minute mild restraint stress, which was, respectively, mitigated by prior intra-NTS infusion of the nitric oxide scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (carboxy-PTIO), nonselective NOS inhibitor NG-nitro-L-arginine methyl ester (L-NAME), or selective neuronal NOS (nNOS) inhibitor 7-nitroindazole (7-NI). Each of these agents also decreased the plasma corticosterone levels in EtOHW rats. In in vivo microdialysis, prior intra-NTS infusion of carboxy-PTIO, L-NAME, or 7-NI attenuated the mild stress-induced NE release in the BNST of EtOHW rats. Additionally, EtOHW rats showed increased solitary nNOS gene and protein expression. Moreover, the anxiolytic effect of intra-NTS administration of 7-NI was abolished by subsequent intra-NTS administration of sodium nitroprusside. These results suggest that elevation of solitary nitric oxide signaling derived from nNOS mediates stress-precipitated anxiety and norepinephrine release in the BNST during protracted EtOHW.Ethanol withdrawal (EtOHW) alters the pattern of neurohormonal and behavioral response toward internal and external stimuli, which mediates relapse to alcohol use even after a long period of abstinence. Increased noradrenergic signaling from the nucleus tractus solitarius (NTS) to the bed nucleus of the stria terminalis (BNST) during EtOHW underlies withdrawal-induced anxiety, while nitric oxide synthase (NOS) inhibitors injected into the periaqueductal area attenuate EtOHW-induced anxiety. Therefore, this study investigated the involvement of NOS within the NTS in anxiety and increased norepinephrine (NE) release in the BNST during protracted EtOHW in rats exposed to a mild stress. Rats were intraperitoneally administered 3\u2009g/kg/day EtOH for 21 days followed by 28 days of withdrawal, and on the 28 Relapse is a major barrier in alcoholism therapy . EthanolElevated anxiety during EtOHW is the major negative emotional component for alcoholism relapse , and sev\u03b2-adrenergic antagonists reduced the withdrawal-associated conditioned place aversion . However, as also seen in Figures into open arms: F = 9.22, p < 0.001, EtOH/vehicle/non-AMRS group (n = 8) versus EtOH/vehicle/AMRS group (n = 8), p < 0.001, EtOH/vehicle/AMRS group versus EtOH/carboxy-PTIO/AMRS group (n = 8), p < 0.01; EtOH/vehicle/AMRS group versus EtOH/L-NAME/AMRS group (n = 8), p < 0.01; EtOH/vehicle/AMRS group versus EtOH/7-NI/AMRS group (n = 8), p < 0.01; EtOH/vehicle/AMRS group versus EtOH/L-NIO/AMRS group (n = 8), p > 0.05; %timespent in open arms: F = 8.05, p < 0.001, EtOH/vehicle/non-AMRS group versus EtOH/vehicle/AMRS group, p < 0.001, EtOH/vehicle/AMRS group versus EtOH/carboxy-PTIO/AMRS group, p < 0.01; EtOH/vehicle/AMRS group versus EtOH/L-NAME/AMRS group, p < 0.01; EtOH/vehicle/AMRS group versus EtOH/7-NI/AMRS group, p < 0.01; EtOH/vehicle/AMRS group versus EtOH/L-NIO/AMRS group, p > 0.05]. Moreover, at the same dose, intra-NTS 7-NI alone did not produce any significant behavioral changes in rats (data not shown).As shown in Figures F(drug) = 19.92, p < 0.001, F(stress) = 32.25, p\u2009<\u20090.001, F(drug \u00d7 stress) = 13.96, p < 0.01; saline/non-AMRS group (n = 6) versus EtOH/AMRS group (n = 6), p < 0.001; EtOH/non-AMRS group (n = 6) versus EtOH/AMRS group, p < 0.001; saline/AMRS group versus EtOH/AMRS group, p < 0.001]. However, as shown in F = 11.71, p < 0.001; EtOH/vehicle/non-AMRS group (n = 6) versus EtOH/vehicle/AMRS group (n = 6), p < 0.001, EtOH/vehicle/AMRS group versus EtOH/carboxy-PTIO/AMRS group (n = 6), p < 0.01], L-NAME , or 7-NI , but not L-NIO , inhibited the increased CORT secretion.Consistent with the results of the behavioral, as seen in n = 7): 4.25 \u00b1 0.32 (pg/15 uL); saline/vehicle/AMRS group (n = 7): 4.75 \u00b1 0.48; EtOH/vehicle/non-AMRS group (n = 7): 4.64 \u00b1 0.41; EtOH/vehicle/AMRS group (n = 7): 5.19 \u00b1 0.44; EtOH/carboxy-PTIO/AMRS group (n = 7): 4.38 \u00b1 0.37; EtOH/L-NAME/AMRS group (n = 7): 4.23 \u00b1 0.38; EtOH/7-NI/AMRS group (n = 7): 5.25 \u00b1 0.37; EtOH/L-NIO/AMRS group (n = 7): 4.81 \u00b1 0.37]. As seen in Figures F(treatment) = 0.07, p > 0.05, F(time) = 2.25, p > 0.05, F(treatment \u00d7 time) = 0.70, p > 0.05; in F(treatment) = 16.79, p < 0.001; F(time) = 25.63, p < 0.001, F(treatment \u00d7 time) = 9.55, p < 0.001; 15\u2009min: saline/vehicle/AMRS group versus EtOH/vehicle/AMRS group, p < 0.001; 30\u2009min saline/vehicle/AMRS group versus EtOH/vehicle/AMRS group, p < 0.05]. However, as shown in F(treatment) = 9.62, p < 0.001, F(time) = 87.92, p < 0.001, F(treatment \u00d7 time) = 4.53, p < 0.001; 15\u2009min: EtOH/vehicle/non-AMRS group EtOH/vehicle/AMRS group, p < 0.001, EtOH/vehicle/AMRS versus EtOH/carboxy-PTIO/AMRS group, p < 0.001; 30\u2009min: EtOH/vehicle/non-AMRS group versus EtOH/vehicle/AMRS group, p < 0.01, EtOH/vehicle/AMRS group versus EtOH/carboxy-PTIO/AMRS group, p < 0.01], L-NAME , or 7-NI , but not L-NIO , prevented these increases. In addition, intra-NTS L-NIO alone did not significantly affect NE release in naive rats (data not shown).No significant differences in the basal extracellular NE level in the vBNST were found between the groups , whereas the AMRS did not alter nNOS protein expression . However, the AMRS markedly enhanced phospho-nNOS levels in EtOHW rats but not in saline-treated controls . Additionally, neither EtOHW nor AMRS significantly affected eNOS or phospho-eNOS protein expressions .As shown in F(drug) = 84.40, p < 0.001, F(stress) = 0.04, p > 0.05, F(drug\u00d7stress)\u2009=\u20090.06, p > 0.05; saline/non-AMRS group (n = 6) versus EtOH/non-AMRS group (n = 6), p < 0.001; saline/AMRS group (n = 6) versus EtOH/AMRS group (n = 6), p < 0.001]. The AMRS did not alter nNOS mRNA expression .In agreement with the Western blot data, as seen in into open arms: F = 15.87, p < 0.001; saline/vehicle/AMRS/vehicle group (n = 6) versus EtOH/vehicle/AMRS/vehicle group (n = 6), p < 0.001; EtOH/vehicle/AMRS/vehicle group versus EtOH/7-NI/AMRS/vehicle group (n = 6), p < 0.001; EtOH/7-NI/AMRS/vehicle group versus EtOH/7-NI/AMRS/SNP group (n = 6), p < 0.01; saline/vehicle/AMRS/vehicle group versus EtOH/7-NI/AMRS/SNP group, p < 0.001; %timespent in open arms: F = 11.17, p < 0.001; saline/vehicle/AMRS/vehicle group versus EtOH/vehicle/AMRS/vehicle group, p < 0.001; EtOH/vehicle/AMRS/vehicle group versus EtOH/7-NI/AMRS/vehicle group, p < 0.01; EtOH/7-NI/AMRS/vehicle group versus EtOH/7-NI/AMRS/SNP group, p < 0.05; saline/vehicle/AMRS/vehicle group versus EtOH/7-NI/AMRS/SNP group, p < 0.01].To further determine the involvement of solitary nNOS in AMRS-induced anxiety during protracted EtOHW, another cohort of EtOHW rats was sequentially treated with 7-NI and SNP and then tested in the EPM . As showThe results of the present study showed that 7-minute AMRS provoked anxiety-like behaviors, enhanced plasma CORT secretion, and sensitized NE release in the vBNST in rats treated with EtOH but not saline, at 28 days after the final dose of EtOH or saline. However, all of these behavioral, hormonal, and neurochemical abnormalities were attenuated by prior intra-NTS infusion of carboxy-PTIO, L-NAME, or 7-NI, but not by L-NIO. EtOHW elevated nNOS, but not eNOS, protein expression in the NTS, concomitant with an increased nNOS mRNA level, and the AMRS increased the phosphorylation rate of nNOS in the NTS of EtOHW rats. Moreover, intra-NTS injection of SNP after 7-NI administration abolished the expected anxiolytic action of 7-NI. Taken together, these results suggest a critical role of solitary nNOS in anxiety and vBNST NE release induced by acute mild stress during protracted EtOHW.The susceptibility to stress during protracted EtOHW alters neurotransmission responses to certain stimuli that are normally innocuous to provoke pathophysiological consequences , 27. To Both anxiety and plasma CORT secretion are closely associated with increased noradrenergic transmission in the BNST , 33. In The NTS primarily integrates and transmits visceral and external information to the forebrain, forming the autonomic-affective functional basis for the body. The gaseous molecule NO serves as both a neurotransmitter and neuromodulator, and is synthesized by three isoforms of NOS, i.e., nNOS, iNOS, and eNOS. We reported previously that systemic nicotine administration increased hypothalamic NE release via activation of both nNOS and eNOS in the NTS . HoweverIn summary, prior intra-NTS infusion of carboxy-PTIO, L-NAME, or 7-NI, but not L-NIO, attenuated the anxiety and vBNST NE release induced by 7-minute AMRS during EtOHW. EtOHW enhanced both nNOS protein and mRNA expression in the NTS but did not affect the eNOS protein level. These observations suggest that nNOS activity is promoted in the NTS during protracted EtOHW, which sensitizes the NTS-BNST noradrenergic response to stress and results in anxiety-like behavior in rats ."} +{"text": "Long term sequelae across multiple medical domains, including the respiratory, psychiatric, and neurocognitive have been reported after COVID-19. Studies evaluating the impact of this symptom burden, however, are lacking. We aimed to describe the self-reported occurrence of symptoms and their effect on patient functioning six months after their acute hospitalization for COVID-19. From a historical cohort study of patients hospitalized for COVID-19 between March 8, and June 14, 2020, we identified patients discharged home. The purpose of the study was explained, and they were asked to consent to a telephone questionnaire. We used a modified version of a previously validated general symptom questionnaire (GSQ-30) to assess multi-system symptom burden. The Patient Health Questionnaire-2 (PHQ-2) was used to screen for major depression. Of the original 565 patients, 258 patients were discharged home (45%). Of these, 57 (22%) patients were able to be contacted and agreed to participate in the survey. The mean (SD) age of the respondents was 55.1 (14.8) years, and 37 (64.9%) were female. The most common symptoms at follow-up were fatigue (60.0%), dyspnea (57.1%), feeling irritable, sad or decreased pleasure (56.4%), and memory difficulty (56.4%). Females had a significantly higher GSQ score (0.02) than males. Patients ages < 60 years tended to experience similar, if not greater, impaired functioning (p=0.07) compared with those ages \u2265 60 years (Table 1). Females were more likely to be irritable or sad (p=0.007), not feel rested on awakening (p=0.04), have shooting, stabbing and burning pain (p=0.02), have discomfort with normal light and sound (p=0.04), and have memory difficulty (p=0.04) than males (Table 2). Table 1. Self-Reported Post-Acute Sequelae of COVID syndrome in adults younger than 60 versus adults at or older than 60 Years. SD: Standard deviation, ICU: Intensive care unit, ED: Emergency department, GSQ - General symptom questionnaire, PHQ-2: Patient Health Questionnaire-2Table 2. Self-Reported Post-acute Sequelae of COVID syndrome in female versus male adults. SD: Standard deviation, ED: Emergency department, GSQ - General symptom questionnaire, PHQ-2: Patient Health Questionnaire-2Our study describes the clinical burden of post-acute sequelae of COVID-19 (PASC) in four core domains: fatigue, neurologic, neuro-psychiatric and viral-like symptoms. Over 45% of patients ages < 60 years suffered impaired functioning, compared with 21.1% of patient\u2019s ages 60 years and above. Females had significantly higher GSQ scores than men which strongly corelates with the functional impairment among the females. Larger studies are needed to further validate our findings.All Authors: No reported disclosures"} +{"text": "Caseins are major milk proteins that have an evolutionarily conserved role in nutrition. Sequence variations in thecasein genes affect milk composition in livestock species. Regulatory elements of the casein genes could be used to directthe expression of desired transgenes into the milk of transgenic animals. Dozens of casein alleles have been identified forgoats, cows, sheep, camels and horses, and these sequence variants are associated with altered gene expression and milkprotein content. Most of the known mutations affecting casein genes\u2019 expression are located in the promoter and 3\u2019-untranslated regions. We performed pronuclear microinjections with Cas9 mRNA and sgRNA against the first coding exon ofthe mouse Csn1s1 gene to introduce random mutations in the \u03b1-casein (Csn1s1) signal peptide sequence at the beginningof the mouse gene. Sanger sequencing of the founder mice identified 40 mutations. As expected, mutations clusteredaround the sgRNA cut site (3 bp from PAM). Most of the mutations represented small deletions (1\u201310 bp), but we detectedseveral larger deletions as well (100\u2013300 bp). Functionally most mutations led to gene knockout due to a frameshift or astart codon loss. Some of the mutations represented in-frame indels in the first coding exon. Of these, we describe a novelhypomorphic Csn1s1 (Csn1s1c.4-5insTCC) allele. We measured Csn1s1 protein levels and confirmed that the mutation has anegative effect on milk composition, which shows a 50 % reduction in gene expression and a 40\u201380 % decrease in Csn1s1protein amount, compared to the wild-type allele. We assumed that mutation affected transcript stability or splicing by anunknown mechanism. This mutation can potentially serve as a genetic marker for low Csn1s1 expression. Caseins are major milk proteins that have an evolutionaryconserved role in nutrition . Casein locushas been studied for a long time to understand the principleof gene regulation and hormone-induced expression . At thesame time, regulatory elements of the casein genes could beused to direct the expression of desired transgenes into milkof transgenic animals .This strategy is frequently employed to create \u201cenriched\u201dmilk with improved composition , or to achieve large scale productionof recombinant human proteins in mouse models and in livestockspecies . Milk-specific signal peptidesare used in biotechnology to enhance recombinant proteinsecretion during lactation . During breeding, casein genes acquired many sequencevariations that can lead to altered gene expression and arecharacteristic of some goat and cow breeds . Many of thesesequence variants could be used as markers for breeding. Indairy industry casein composition is an important milk traitdirectly influencing quality of dairy products . Hypomorphic casein mutationare also associated with other traits such as litter size . For example, K. Wang with colleagues showedthat 11 bp del in the intron 8 of the goat Csn1s1 negativelyaffects the expression of the gene . Otherknown hypomorphic mutations are located in the promoterand 3\u2032-untranslated regions (UTRs) of casein genes . Novel CRISPR methods greatly facilitate genome editing infarm animals , including targeted transgeneintegration and mutation modeling . The latter approach has potential toexplain the molecular mechanism of how hypomorphic mutations affect milk proteins. In this report, we used CRISPR/Cas9to create a set of mutations within a signal peptide sequenceof the \u03b1-casein (Csn1s1) gene in mice. One of the mutantswas chosen to study effects of a small in-frame insertion onthe Csn1s1 expression during lactation.Generation and genotyping of the Csn1s1 mutant mice.In vitro transcription and purification of the gRNA wereperformed with MEGAshortscript\u2122 T7 Transcription Kit(Thermo Fisher Scientific) and MEGAclear\u2122 TranscriptionClean-Up Kit (Thermo Fisher Scientific) according to themanufacturer\u2019s protocol. Cas9 mRNA (GeneArt\u2122 CRISPRNuclease mRNA) was purchased from Thermo Fisher Scientific. 50 ng/\u03bcL Cas9 mRNA and 25 ng/\u03bcL gRNA (5\u2032-GTGAGGATGAGGAGTTTCA-3\u2032) were mixed in RNase-free water,backfilled into an injection needle with positive balancingpressure and injected into thecytoplasm of zygotes (C57BL/6 \u00d7 CBA background). Afterinjections, the embryos were cultured for 1 hour in drops ofM16 medium at 37 \u00b0C and an atmosphere of 5 % CO2. Theviable microinjected zygotes were transplanted the same day into oviducts of pseudopregnant CD-1 females (0.5 days aftercoitus). Isoflurane inhalation anesthesia was applied in theseexperiments.1.Primers for PCR were as follows: 5\u2032-GCGCATAACTAAGCATCTTATGCT-3\u2032 (forward primer), 5\u2032-TGACTTGGAGTTTTAGATTTGGACA-3\u2032 (reverse primer). Selected malemice founders were crossed with C57BL/6 females. Formutation c.4-5insTCC described in this paper, founder malewas crossed with two F1 heterozygous daughters. Offspringwas genotyped and two sibling females were selected foreach group forfurther analysis.Mutations were detected using PCR and Sanger sequencingof the target region of the Csn1s1 exon 2 (Supplementary 1)http://www.bionet.nsc.ru/vogis/download/pict-2021-25/appx8.pdfSupplementary materials 1 and 2 are available at: All experiments were conducted at the Centre for Genetic Resources of Laboratory Animals at the Institute ofCytology and Genetics, SB RAS (RFMEFI61914X0005 andRFMEFI61914X0010). All experiments were performed inaccordance with protocols and guidelines approved by theAnimal Care and Use Committee Federal Research Centreof the Institute of Cytology and Genetics, SB RAS operatingunder standards set by regulations documents Federal HealthMinistry (2010/708n/RF), NRC and FELASA recommendations. Experimental protocols were approved by the BioethicsReview Committee of the Institute of Cytology and Genetics,SB RAS.Droplet digital PCR analysis. Total cellular RNA wasextracted from mouse mammary glands at day 8 of lactationusing TRI Reagent (Sigma-Aldrich). 1 \u03bcg of total RNA wasused to generate cDNA in a 20 \u03bcl reaction using RevertAidRT Kit (Thermo Fisher Scientific) with random hexamerprimers according to the manufacturer\u2019s instructions. DropletDigital PCR (ddPCR) was performed using a QX100 system(Bio-Rad) with primers and probes specific for the Csn1s1and Csn2 mouse transcripts (Supplementary 2). The primersand probes sequences were as follows: 5\u2032-TGTAGTGGATCAGGCACTGG-3\u2032 (Csn1s1 forward primer), 5\u2032-TCCTTGGAGACAATGGGCTT-3\u2032 (Csn1s1 reverse primer), 5\u2032-HEXCCAGTTCTCTGTTCAGCCCTTCCCACA-BHQ2\u20133\u2032(Csn1s1 probe), 5\u2032-AGGACTTGACAGCCATGAAGG-3\u2032(Csn2 forward primer), 5\u2032-ATGTTCAACAGATTCCTCACTGGA-3\u2032 (Csn2 reverse primer), 5\u2032-FAM-ATCCTCGCCTGCCTTGTGGCCCTTGC-BHQ1\u20133\u2032 (Csn2 probe). ddPCRreactions were set in 20 \u03bcl volumes containing 1\u00d7 ddPCR\u2122Supermix for Probes (no dUTP), 900 nM primers and 250 nMprobes, and 1 \u03bcl of 5000-fold diluted cDNA. ddPCR reactionsfor each sample were performed in duplicates. PCR was conducted according to the following program: 95 \u00b0C for 10 min,then 40 cycles of 95 \u00b0C for 30 s and 61 \u00b0C for 1 min, witha ramp rate of 2 \u00b0C per second, and a final step at 98 \u00b0C for5 min. The results were analyzed using QuantaSoft software(Bio-Rad). Concentrations of cDNA copies of Csn1s1 andCsn2 were derived from ddPCR and relative expression ofCsn1s1 to Csn2 was calculated for each animal.Milk and mammary gland protein analysis. Milk wasobtained from narcotized female mice at day 8 of lactationafter oxytocin administration . Themilk was collected with a pipette attached to an aspiration device, transferred into a microcentrifuge tube and stored at\u201380 \u00b0C. Inguinal mammary glands (MGs) were extracted fromthe same (euthanized) mice and stored at \u201380 \u00b0C. For protein extraction MGs were minced in Dounce homogenizers,resuspended in RIPA buffer with protease inhibitor cocktail (1x Complete ULTRA(Roche), 1x PhosSTOP (Roche), 5 mM NaF (Sigma)). Thelysates were incubated on ice for 30 min and then centrifugedat 4 \u00b0C for 10 min at 10\u200a000 g. Supernatant was sonicatedand stored at \u201380 \u00b0C. Total protein concentrations for milkand MG lysates were determined with Pierce\u2122 BCA Protein Assay Kit (Thermo Fisher Scientific), according to themanufacturer\u2019s instructions. To prepare samples for SDSPAGE, milk or MG protein samples were mixed with RIPAand SDS-PAGE loading buffer (Bio-Rad) to a final concentration of 1 \u03bcg/\u03bcl and heated at 65 \u00b0C for 20 minutes. Thesamples (25 \u03bcg) were separated on a 12 % polyacrylamidegel and stained with Coomassie Blue G-250. ThermoFisherPageRuler\u2122 Prestained Protein Ladder (10 to 180 kDa) wasused as a protein molecular weight marker. Csn1s1, albuminand total protein concentrations were evaluated using QuantityOne (Bio-Rad) and ImageJ software.Coomassie-stained gel was used for wet transfer of theproteins to PVDF membrane .The membrane was blocked with 5 % milk in TBST for 2 hoursand incubated with primary mouse anti-Csn1s1 antibodies(1:1000) overnight at4 \u00b0C. Next day membrane was repeatedly washed with TBSTand incubated with secondary mouse HRP-antibodies (1:1000) at 25 \u00b0C for 2 hours.Immunodetection was performed with ECL substrate solution, according tothe manufacturer\u2019s instructions.Generation of the Csn1s1 mutant miceWe performed pronuclear microinjections with Cas9 mRNAand sgRNA against the first coding exon of the mouse Csn1s1gene . Cas9-induced mutations in this region couldpotentially affect signal peptide coding sequence and leadto altered milk composition. We screened founder mice by Sanger sequencing and identified multiple random mutations at the Cas9 cut site (presented in Supplementary 1).The sgRNA targeted the Csn1s1 site with high efficiencyas we detected 41 mutant alleles, 4\u20135 mosaic alleles and only 4\u20135 wild-type allelesin 20 founder mice . Asexpected, mutations clustered around the sgRNA cut site(3 bp from PAM). Most of the mutations represented smalldeletions (1\u201310 bp), but we detected several larger deletionsas well (100\u2013300 bp). Of note, some of the unique mutationvariants had increased incidence rate. For example, 12 bpdeletion (GAAACTCCTCAT) arose independently four timesand another 10 bp deletion (CCATGAAACT) \u2013 three times(see Supplementary 1). We suspect this bias towards somevariants is caused by microhomology-mediated end-joining(MMEJ), since these two mutations are flanked with 3 and 2similar nucleotides (see Supplementary 1). Although mutations were mostly deleterious forthe gene expression and led to a Csn1s1 knockout (KO) byframeshift, several in-frame mutation variants resulted insubtle changes in signal peptide coding sequence withoutKO (see Supplementary 1). We selected one of the mutants,tagged Csn1s1c.4-5insTCC, which had a 3 bp insertion followingthe start codon . To study gene expression andmilk composition we chose 6 female siblings from the Csn1s1c.4-5insTCCline for milk and mammary glands collection. Mutation c.4-5insTCC leads to reducedexpression of the Csn1s1 geneWe estimated the Csn1s1 gene expression in mammary glandsof wild-type and mutant mice at day 8 of lactation usingdroplet digital PCR (ddPCR). We selected Csn2 (\u03b2-casein) asa reference gene as it has a similar expression profile in mammary gland (see Supplementary 2). ddPCR analysis revealedthat Csn1s1:Csn2 ratio was roughly 1:3 (0.338) in wild-typesiblings , which is in agreement with publisheddata . Heterozygous and homozygousCsn1s1c.4-5insTCC siblings showed lower Csn1s1 expressionwith ratios around 1:4 (0.248) and 1:6 (0.168), respectively, compared to wild-type siblings. We also usedfemales from the parental strains C57BL/6 and CBA as controls for normal caseins level . In rare cases, Cas9activity can provoke rearrangements near the target locus.We sequenced mutation-flanking regions, including theCsn1s1 promoter and surrounding introns (2.3 kb+1.1 kb)from homozygous mice (data not shown). We also sequencedtop two off-targets for the Csn1s1 sgRNA in the F0 founder. No mutations werefound in the examined sequences. Thus, we could confirmthat the 3 bp in-frame insertion in the first coding exon led toa 30\u201350 % decrease in the Csn1s1 gene expression. Milk protein composition in c.4-5insTCC mice We measured Csn1s1 protein levels and confirmed that mutation has a negative effect on milk composition. We collectedmilk and mammary glands from lactating females at the day 8of lactation. Csn1s1 knockout mouse was taken from anotherexperiment (\u201cKO\u201d) as additional control for the Csn1s1 levels.Separation of milk proteins on 12 % SDS\u2010PAGE resulted ina typical band pattern for mouse milk . In wildtype mice, Csn1s1 represents a major protein fraction andcorresponds to approx. 30 % of total milk protein . In homozygous mutants, loss of Csn1s1 could beobserved both at the Coomassie-stained gel andafter western blotting . Csn1s1 levels fell down to30 % in homozygotes, both for milk and for mammary glandlysates . However, exact ratios varied depending on the control protein band used for calculations. For instance, we performed the following calculations for the milkCsn1s1: Csn1s1 (gel) vs total protein (gel) \u2013 40 % reduction; Csn1s1 (gel) vs albumin (gel) \u2013 70 % reduction; Csn1s1(western blot membrane) vs total protein (gel) \u2013 80 % reduction. This effect was even more pronounced in mammarygland lysates (intracellular casein levels): Csn1s1 (westernblot membrane) vs total gel \u2013 80 % reduction.We report a novel in-frame Csn1s1 hypomorphic mutationthat leads to a 50 % gene expression decrease in mice. Inmost cases, mutation effect is tied to disruption of a regulatory element . Frame-shifting indels in the coding sequencecould initiate transcript surveillance pathway called nonsense-mediated mRNA decay (NMD) . Alternatively, in-frame mutationscan lead to exon removal by alternative splicing . Essentially, exon skipping could be promoted by internal exon splicing enhancersand suppressors (ESEs and ESSs) which are hard to predict, unliketypical splice site mutations . In ourmutant mice, promoter had no alterations as the mutationhappened in the coding sequence, quite far from a transcription start site. We assumed that it affected transcript stabilityor splicing by unknown mechanism. It should also be notedthat mutated Csn1s1 protein was still secreted in milk, thusthe function of N-terminal signal peptide was not criticallyaffected by the mutation. We demonstrated that CRISPR/Cas9 approach could be conveniently exploited to induce a spectrum of mutations in theCsn1s1 gene either by random mutagenesis, or, ideally, by aset of single-stranded oligo DNA nucleotides (ssODNs). Ourresults warn that careful examination of the gene\u2019s expressionis required in addition to protein analysis. The authors declare no conflict of interest.An L.Y., Yuan Y.G., Yu B.L., Yang T.J., Cheng Y. Generation of human lactoferrin transgenic cloned goats using donor cells with dualmarkers and a modified selection procedure. Theriogenology. 2012;78:1303-1311. DOI 10.1016/j.theriogenology.2012.05.027.Burkov I.A., Serova I.A., Battulin N.R., Smirnov A.V., Babkin I.V.,Andreeva L.E., Dvoryanchikov G.A., Serov O.L. Expression of thehuman granulocyte-macrophage colony stimulating factor (hGMCSF) gene under control of the 5\u2032-regulatory sequence of the goatalpha-S1-casein gene with and without a MAR element in transgenicmice. Transgenic Res. 2013;22:949-964. DOI 10.1007/s11248-013-9697-4.Cartegni L., Chew S.L., Krainer A.R. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev.Genet. 2002;3(4):285-298. DOI 10.1038/nrg775. PMID 11967553.Cieslak J., Wodas L., Borowska A., Pawlak P., Czyzak-Runowska G.,Wojtowski J., Puppel K., Kuczynska B., Mackowski M. 5\u2032-flankingvariants of equine casein genes and their relationship with gene expression and milk composition.J. Appl. Genet. 2019;60(1):71-78. DOI 10.1007/s13353-018-0473-2.Dos Santos C.O., Dolzhenko E., Hodges E., Smith A.D., Hannon G.J.An epigenetic memory of pregnancy in the mouse mammary gland.Cell Rep. 2015;11:1102-1109. DOI 10.1016/j.celrep.2015.04.015.Fomichev K.A., Sazanova A.L., Malewski T., Kaminski S., Sazanov A.A. Associations between two novel rSNPs in 5\u2032-flanking region of the bovine casein gene cluster and milk performance traits.Gene. 2012;496:49-54. DOI 10.1016/j.gene.2011.12.038.Guan D., M\u00e1rmol-S\u00e1nchez E., Cardoso T.F., Such X., Landi V., Tawari N.R., Amills M. Genomic analysis of the origins of extantcasein variation in goats. J. Dairy Sci. 2019;102:5230-5241. DOI10.3168/jds.2018-15281.Hogg D.R., Harries L.W. Human genetic variation and its effect onmiRNA biogenesis, activity and function. Biochem. Soc. Trans. 2014;42(4):1184-1189. DOI 10.1042/BST20140055. PMID 25110023.Houdebine L.M. Production of pharmaceutical proteins by transgenicanimals. Comp. Immunol. Microbiol. Infect. Dis. 2009;32:107-121.DOI 10.1016/j.cimid.2007.11.005.Huang W., Pe\u00f1agaricano F., Ahmad K.R., Lucey J.A., Weigel K.A.,Khatib H. Association between milk protein gene variants and protein composition traits in dairy cattle. J. Dairy Sci. 2012;95:440-449.DOI 10.3168/jds.2011-4757.Kalds P., Zhou S., Cai B., Liu J., Wang Y., Petersen B., Sonstegard T.,Wang X., Chen Y. Sheep and goat genome engineering: from random transgenesis to the CRISPR Era. Front. Genet. 2019;10:750.DOI 10.3389/fgene.2019.00750. eCollection2019.Kim J.J., Yu J., Bag J., Bakovic M., Cant J.P. Translation attenuationvia 3\u2032 terminal codon usage in bovine csn1s2 is responsible for thedifference in \u03b1s2- and \u03b2-casein profile in milk. RNA Biol. 2015;12:354-367. DOI 10.1080/15476286.2015.1017231.Kolb A.F., Huber R.C., Lillico S.G., Carlisle A., Robinson C.J., Neil C.,Petrie L., Sorensen D.B., Olsson I.A., Whitelaw C.B. Milk lacking\u03b1-casein leads to permanent reduction in body size in mice. PLoSOne. 2011;6:e21775. DOI 10.1371/journal.pone.0021775.Lee H.K., Willi M., Wang C., Yang C.M., Smith H.E., Liu C., Hennighausen L. Functional assessment of CTCF sites at cytokinesensing mammary enhancers using CRISPR/Cas9 gene editing inmice. Nucleic Acids Res. 2017;45:4606-4618. DOI 10.1093/nar/gkx185.Li W.R., Liu C.X., Zhang X.M., Chen L., Peng X.R., He S.G., Lin J.P.,Han B., Wang L.Q., Huang J.C., Liu M.J. CRISPR/Cas9-mediatedloss of FGF5 function increases wool staple length in sheep. FEBS J.2017;284:2764-2773. DOI 10.1111/febs.14144.Lindeboom R.G.H., Vermeulen M., Lehner B., Supek F. The impactof nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy. Nat. Genet. 2019;51(11):1645-1651. DOI 10.1038/s41588-019-0517-5. Epub 2019 Oct 28. PMID31659324. PMCID PMC6858879.Liu H.C., Pai S.Y., Chen H.L., Lai C.W., Tsai T.C., Cheng W.T.,Yang S.H., Chen C.M. Recombinant Derp5 allergen with \u03b1S1-caseinsignal peptide secreted in murine milk protects against dust miteallergen-induced airway inflammation. J. Dairy Sci. 2014;97:6792-6803. DOI 10.3168/jds.2014-8484.Lu R., Zhang T., Song S., Zhou M., Jiang L., He Z., Yuan Y., Yuan T.,Lu Y., Yan K., Cheng Y. Accurately cleavable goat \u03b2-lactoglobulinsignal peptide efficiently guided translation of a recombinant humanplasminogen activator in transgenic rabbit mammary gland. Biosci.Rep. 2019;39:6. DOI 10.1042/BSR20190596.Mucaki E.J., Shirley B.C., Rogan P.K. Expression changes confirmgenomic variants predicted to result in allele-specific, alternativemRNA splicing. Front. Genet. 2020;11:109. DOI 10.3389/fgene.2020.00109. PMID 32211018. PMCID PMC7066660.Noce A., Pazzola M., Dettori M.L., Amills M., Castell\u00f3 A., Cecchinato A., Bittante G., Vacca G.M. Variations at regulatory regions ofthe milk protein genes are associated with milk traits and coagulation properties in the Sarda sheep. Anim. Genet. 2016;47:717-726.DOI 10.1111/age.12474.Park K.E., Powell A., Sandmaier S.E., Kim C.M., Mileham A., Donovan D.M., Telugu B.P. Targeted gene knock-in by CRISPR/Cas ribonucleoproteins in porcine zygotes. Sci. Rep. 2017;7:42458. DOI10.1038/srep42458.Popp M.W., Maquat L.E. Leveraging rules of nonsense-mediatedmRNA decay for genome engineering and personalized medicine.Cell. 2016;165(6):1319-1322. DOI 10.1016/j.cell.2016.05.053.PMID 27259145. PMCID PMC4924582.Qian X., Kraft J., Ni Y., Zhao F.Q. Production of recombinant humanproinsulin in the milk of transgenic mice. Sci. Rep. 2014;4:6465.DOI 10.1038/srep06465.Rijnkels M., Elnitski L., Miller W., Rosen J.M. Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins. Genomics. 2003;82:417-432. DOI 10.1016/s0888-7543(03)00114-9.Rijnkels M., Freeman-Zadrowski C., Hernandez J., Potluri V., Wang L.,Li W., Lemay D.G. Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation. PLoS One. 2013;8:e53270. DOI 10.1371/journal.pone.0053270.Sanchez M.P., Wolf V., El Jabri M., Beuvier E., Rolet-R\u00e9p\u00e9caud O.,Ga\u00fcz\u00e8re Y., Min\u00e9ry S., Brochard M., Michenet A., Taussat S., Barbat-Leterrier A., Delacroix-Buchet A., Laithier C., Fritz S., Boichard D. Short communication: Confirmation of candidate causativevariants on milk composition and cheesemaking properties in Montb\u00e9liarde cows. J. Dairy Sci. 2018;101:10076-10081. DOI 10.3168/jds.2018-14986.Sterne-Weiler T., Sanford J.R. Exon identity crisis: disease-causing mutations that disrupt the splicing code. Genome Biol. 2014;15(1):201.DOI 10.1186/gb4150. PMID 24456648. PMCID PMC4053859.Thompson B.A., Walters R., Parsons M.T., Dumenil T., Drost M.,Tiersma Y., Lindor N.M., Tavtigian S.V., de Wind N., Spurdle A.B.,InSiGHT Variant Interpretation Committee. Contribution of mRNAsplicing to mismatch repair gene sequence variant interpretation.Front. Genet. 2020;11:798. DOI 10.3389/fgene.2020.00798. PMID32849802. PMCID PMC7398121.Tuladhar R., Yeu Y., Tyler Piazza J., Tan Z., Rene Clemenceau J., Wu X.,Barrett Q., Herbert J., Mathews D.H., Kim J., Hyun Hwang T.,Lum L. CRISPR-Cas9-based mutagenesis frequently provokeson-target mRNA misregulation. Nat. Commun. 2019;10(1):4056.DOI 10.1038/s41467-019-12028-5. PMID 31492834. PMCIDPMC6731291.Uusi-Oukari M., Hyttinen J.M., Korhonen V.P., V\u00e4sti A., Alhonen L.,J\u00e4nne O.A., J\u00e4nne J. Bovine alpha s1-casein gene sequences directhigh level expression of human granulocyte-macrophage colonystimulating factor in the milk of transgenic mice. Transgenic Res.1997;6:75-84. DOI 10.1023/a:1018461201385.Wan Y.J., Zhang Y.L., Zhou Z.R., Jia R.X., Li M., Song H., Wang H.Z.,Wang L.Z., Zhang G.M., You J.H., Wang F. Efficiency of donor cellpreparation and recipient oocyte source for production of transgeniccloned dairy goats harboring human lactoferrin. Theriogenology.2012;78:583-592. DOI 10.1016/j.theriogenology.2012.03.004.Wang K., Yan H., Xu H., Yang Q., Zhang S., Pan C., Chen H., Zhu H.,Liu J., Qu L., Lan X. A novel indel within goat casein alpha S1 geneis significantly associated with litter size. Gene. 2018;671:161-169.DOI 10.1016/j.gene.2018.05.119.Wu X., Lin Y., Xiong F., Zhou Y., Yu F., Deng J., Huang P., Chen H.The extremely high level expression of human serum albumin in themilk of transgenic mice. Transgenic Res. 2012;21:1359-1366. DOI10.1007/s11248-012-9612-4.Yamaji D., Kang K., Robinson G.W., Hennighausen L. Sequential activation of genetic programs in mouse mammary epithelium duringpregnancy depends on STAT5A/B concentration. Nucleic Acids Res.2013;41:1622-1636. DOI 10.1093/nar/gks1310.Yu Z., Meng Q., Yu H., Fan B., Yu S., Fei J., Wang L., Dai Y., Li N.Expression and bioactivity of recombinant human lysozyme in themilk of transgenic mice. J. Dairy Sci. 2006;89:2911-2918. DOI10.3168/jds.S0022-0302(06)72563-2.Yuan Y.G., An L., Yu B., Song S., Zhou F., Zhang L., Gu Y., Yu M.,Cheng Y. Expression of recombinant human alpha-lactalbuminin the milk of transgenic goats using a hybrid pomoter/enhancer.J. Anal. Method. Chem. 2014;281031. DOI 10.1155/2014/281031.Yue X.P., Zhang X.M., Wang W., Ma R.N., Deng C.J., Lan X.Y.,Chen H., Li F., Xu X.R., Ma Y., Lei C.Z. The CSN1S1 N and F alleles identified by PCR-SSCP and their associations with milk yieldand composition in Chinese dairy goats. Mol. Biol. Rep. 2011;38:2821-2825. DOI 10.1007/s11033-010-0428-0.Zhou S., Cai B., He C., Wang Y., Ding Q., Liu J., Liu Y., Ding Y.,Zhao X., Li G., Li C., Yu H., Kou Q., Niu W., Petersen B., Sonstegard T., Ma B., Chen Y., Wang X. Programmable base editing of thesheep genome revealed no genome-wide off-target mutations. Front.Genet. 2019;10:215. DOI 10.3389/fgene.2019.00215."} +{"text": "The kidneys are among the organs most affected by leukemic involvement in chronic lymphocytic leukemia (CLL) patients in postmortem autopsy series 63%-90%) ,2. Howev%-90% ,2.9/L (lymphocytes: 60%); platelets, 247x109/L. The blood \ufb01lm appearances were suggestive of CLL. The following biochemical tests were abnormal: blood urea nitrogen, 44 mg/dL ; serum creatinine (sCr), 6.16 mg/dL ; CKD-EPI estimated-glomerular filtration rate, 8 mL/min/1.73 m2 . His urine had no leukocytes or casts, with 3 erythrocytes/field and proteinuria in the non-nephrotic range (1779 mg/24 h). Serological tests for hepatitis B, hepatitis C, HIV, and autoimmune kidney disorders were negative. Serum-free light chain (sFLC) kappa was 317.5 mg/dL and sFLC lambda was 22.2 mg/dL , but no monoclonal bands in serum or urine immunofixation were detected. Renal ultrasound showed normal-sized kidneys with no evidence of obstructive nephropathy. A renal biopsy was performed, which demonstrated heavy infiltration of diffuse monomorphic neoplastic lymphocytes in the interstitium (9/L). After a year of follow-up, his renal function had improved to sCr of 2.04 mg/dL, and a complete blood count revealed hemoglobin of 14.7 g/dL, leukocytes of 9.15x109/L, and platelets of 294x109/L.A 72-year-old white male without any renal disease presented with general malaise and weight loss. He had been diagnosed with stage B(1) B-CLL four years before and was treated with a bendamustine and rituximab protocol. Physical examination revealed general lymphadenopathy and hepatomegaly. Complete blood count findings were as follows: hemoglobin, 11.3 g/dL; leukocytes, 411.4x10rstitium . Six of rstitium and 1C wBesides LI, renal impairment in CLL patients can be associated with prerenal azotemia, thrombotic microangiopathy, acute tubular necrosis, acute interstitial nephritis, uric acid nephropathy, light chain nephropathy, amyloidosis, obstructive nephropathy, glomerulonephritis, and cryoglobulinemia . LI of t"} +{"text": "Correction to: J Foot Ankle Res 14, 15 (2021)https://doi.org/10.1186/s13047-020-00435-7Following publication of the original article , we wereThe original article has been corrected.\u00a0Additional file 2 has been replaced.Additional file 2. Development of the systematic podiatry protocol."} +{"text": "A total of 50 neonates participated in this study. LBW-VLBW neonates were further stratified as those with and without structural MRI (sMRI) abnormalities. TRUST and PC MRI studies were undertaken to determine OEF, CBF, and CMRO2. Ultimately, CMRO2 proved significantly lower (p = 0.01) in LBW-VLBW (vs term) neonates, both LBW-VLBW-a and LBW-VLBW-n subsets showing significantly greater physiologic deficits than term controls . CMRO2 and CBF in LBW-VLBW-a and LBW-VLBW-n subsets did not differ significantly (p > 0.05), although OEF showed a tendency to diverge (p = 0.15). However, OEF values in the LBW-VLBW-n subset differed significantly from those of term controls (p = 0.02). Compared with brain volume or body weight, these physiologic parameters yield higher area-under-the-curve (AUC) values for distinguishing neonates of the LBW-VLBW-a subset. The latter displayed distinct cerebral metabolic and hemodynamic, whereas changes were marginal in the LBW-VLBW-n subset by comparison. Physiologic imaging may therefore be useful in identifying LBW-VLBW newborns at high risk of irreversible brain damage.Low birth-weight (LBW) and very low birth-weight (VLBW) newborns have increased risks of brain injuries, growth failure, motor difficulties, developmental coordination disorders or delay, and adult-onset vascular diseases. However, relatively little is known of the neurobiologic underpinnings. To clarify the pathophysiologic vulnerabilities of such neonates, we applied several advanced techniques for assessing brain physiology, namely T2-relaxation-under-spin-tagging (TRUST) magnetic resonance imaging (MRI) and phase-contrast (PC) MRI. This enabled quantification of oxygen extraction fraction (OEF), global cerebral blood flow (CBF), and cerebral metabolic rate of oxygen (CMRO Preterm newborns of low birth weight or very low birth weight present a substantial public health problem. In 2015, the worldwide prevalence was 14.6%, with 91% confined to low- and middle-income countries [primarily Southern Asia (24%) and sub-Saharan Africa (48%)]. More than 80% of perinatal deaths occur in LBW neonates .Although most LBW and VLBW preterm infants show catch-up gains in height and weight, they are still at increased risk of brain injuries , growth 133Xenon clearance technologies have allowed noninvasive and quantitative measurements of critical neurophysiologic parameters, without need of contrast agents. The oxygen extraction fraction (OEF) of the brain is assessable using T2-relaxation-under-spin-tagging (TRUST) MRI technique , and glo2 using T2 prepared tissue relaxation inversion recovery (T2-TRIR) pulse sequences and ASL (2 and CBF in asphyxiated newborns with severe HIE (r = 0.88) is another valuable means of perfusion MRI for this purpose. However, its signal-to-noise ratio (SNR) tends to be lower, the scan times lengthier, and there is a potential for confounding factors . In an earlier effort, infants with hypoxic ischemic encephalopathy (HIE) showed lower CBF and CMRO and ASL . Newborn = 0.88) . Our pre = 0.88) . Tortora = 0.88) . There h2 in a mixed group of LBW and VLBW newborns, comparing outcomes with those of term neonates.In the present study, we used TRUST MRI and PC MRI to determine OEF, CBF, and CMROn = 41) at birth weights >1,000 g but <2,500 g. Term neonates serving as controls (n = 9) had birth weights \u22652,500 g, were \u226537 weeks at birth, and showed no sMRI abnormalities. Population characteristics and results of blood gas analysis were listed in Our investigational protocol received approval from the Ethics Committee at Shengjing Hospital of China Medical University. Between June 2016 and December 2018, a total of 50 newborns accrued for study. The structural MRI pulse sequences performed included axial and sagittal T1-weighted imaging (TIWI), axial T2-weighted imaging (T2WI), and diffusion-weighted imaging (DWI). Congenital malformations, severe infections, or unusable MRI studies were grounds for exclusion. Subjects qualified as LBW-VLBW obtained from all infants (LBW-VLBW and term) were viewed as Picture Archiving and Communication Systems (PACS) files by two neuroradiologists (YQ and XYS) with 10 years of experience, each blinded to group data. They independently scored MRI abnormalities for each infant, using a method similar to one already described that focA 3T MRI system equipped with a phased-array head coil was used for all MR scans. Prior to imaging procedures, a pediatrician sedated infants through nasal feedings of chloral hydrate (50 mg/kg). This is standard clinical practice at our institution. All newborns were well fed, visually monitored, and hearing protected during scans.2; and scan time, 30 s.Axial T1-weighted spin-echo images were acquired at the following settings: repetition time/echo time (TR/TE), 200 ms/2.3 ms; section thickness, 5 mm; field of view (FOV), 180 mm \u00d7 150 mm \u00d7 89 mm; matrix size, 224 \u00d7 162; and scan time, 34.4 s. For sagittal T1-weighted spin-echo images, the following settings were used: TR/TE, 250 ms/2.3 ms; section thickness, 5 mm; FOV, 230 mm \u00d7 230 mm \u00d7 107 mm; matrix size, 256 \u00d7 250; and scan time, 33.0 s. Axial T2WI used the following settings: TR/TE, 5,000 ms/80 ms; section thickness, 5 mm; FOV, 180 mm \u00d7 150 mm \u00d7 90 mm; matrix size, 112 \u00d7 112; and scan time, 40.9 s. Axial echo-planar imaging (EPI) DWI was performed as follows: TR/TE, 3,500 ms/63 ms; section thickness, 5 mm; FOV, 180 mm \u00d7 180 mm \u00d7 89 mm; b values, 0 and 1,000 s/mmOxygen extraction fraction was calculated as follows:where Ya and Yv signify arterial and venous oxygenation, respectively. Ya was measured peripherally, via pulse oximeter applied to neonatal toes. Yv was measured by TRUST MRI technique, given that blood T2 has a calibrationable relation with oxygenation level. This sequence utilizes a spin-labeling module to isolate pure venous blood signals, thereafter applying a series of T2-preparation pulses to modulate the MRI signal, the monoexponential fitting of which yields blood T2 . A T2-YvFor measuring CBF, PC MRI employed bipolar gradients to encode flow velocities of blood supplying major feeding arteries of the brain, specifically left and right internal carotid arteries (LICA and RICA) and left and right vertebral arteries (LVA and RVA), allowing quantitation of total blood flow to the brain. Flow values were then normalized to brain volume, expressing CBF in units of mL/100 g/min. Time-of-flight MR angiograms (TOF-MRAs) were first performed to allow visualization of above-referenced feeding arteries. Imaging slabs were positioned at center of epistropheus, with 60-mm saturation slabs placed above to suppress venous signals. Settings of TOF MRA were as follows: TR/TE, 20 ms/3.45 ms; flip angle, 18\u00b0; FOV, 90 mm \u00d7 90 mm \u00d7 20 mm; voxel size, 0.8 mm \u00d7 0.8 mm \u00d7 2 mm; and scan duration, 23.7 s.Based on MRA images, four PC MRI scans were performed by orienting imaging slices perpendicular to and centered on respective target arteries, as previously described . Scans oProcessing of PC MRI data again followed existing procedures . Manual 2 was calculated according to Fick\u2019s principle on scan age, sex, and diagnostic group (independent variables). In regression analyses, paired groups were encoded as follows: LBW-VLBW (0) vs term (1) neonates; LBW-VLBW-a (1) vs LBW-VLBW-n (0) subsets; LBW-VLBW-a neonates (1) vs term controls (0); and LBW-VLBW-n neonates (0) vs term controls (1). LBW-VLBW newborns underwent MRI scans once their vital signs had stabilized, and ventilators were no longer required (3 weeks old on average). Term infants had good vital signs and were amenable to scanning at any time (1 week old on average). There were distinct chronologic differences in scan ages of these pairings. Due to remarkable disparities , it was 1 and b2 were based on results of an age- and sex-adjusted regression model similarly reported and term neonates (n = 9), LBW-VLBW-a (n = 24) and LBW-VLBW-n (n = 17) subsets, LBW-VLBW-a neonates (n = 24) and term controls (n = 24), and LBW-VLBW-n neonates (n = 17) and term controls (n = 24). We also analyzed birth weight, brain volume, and cerebral physiologic parameters independently, generating receiver operating characteristic (ROC) curves to distinguish the LBW-VLBW-a subset from all other neonates and from the LBW-VLBW group overall. Inter-rater variations in MRI scores determined by YQ and XYS were assessed via intraclass correlation coefficient (ICC), rated as follows: 1.0\u20130.81, excellent; 0.80\u20130.61, very good; 0.60\u20130.41, good; 0.40\u20130.21, reasonable; and 0.20\u20130.00, poor. All computations were driven by standard software , setting significance at p < 0.05.where coefficients breported . Correctp = 0.89); CMRO2, 29.9 \u00b1 11.4 \u03bcmol/100 g/min vs 48.9 \u00b1 12.4 \u03bcmol/100 g/min (p < 0.001); CBF, 13.6 \u00b1 5.0 mL/100 g/min vs 19.5 \u00b1 3.8 mL/100 g/min (p = 0.002); and brain volume, 265.2 \u00b1 74.5 mL vs 354.1 \u00b1 52.0 mL (p = 0.001). Only OEF proved similar, the other parameters differing significantly by group.In LBW-VLBW and term neonates, measured parameters were as follows: OEF, 31.3 \u00b1 10.5% vs 30.8 \u00b1 6.2% (n = 41), including both LBW-VLBW-a and LBW-VLBW-n subsets, are detailed in p > 0.05). Fifteen LBW-VLBW newborns had required mechanical ventilation.Population characteristics and diagnostic outcomes of the LBW-VLBW group (2 was significantly lower (p = 0.01) in LBW-VLBW (vs term) newborns, CBF (p = 0.06) and OEF (p = 0.67) did not differ significantly. Furthermore, CMRO2 (p = 0.48) and CBF (p = 0.63) failed to show scan age-related increases during this period of early development; and despite significant differences in birth weight, LBW-VLBW and term neonates did not differ significantly in brain volume.We first compared physiologic measures of LBW-VLBW and term neonates . Althoug2 rates relative to controls . Contrary to expectations, no significant differences in CMRO2 (p = 0.30), CBF (p = 0.50), or OEF (p = 0.15) recordings were evident across subsets upon linear regression analysis. Relative to term neonates, OEF was significantly lower (p = 0.02) in the LBW-VLBW-n subset.Next, we compared the two subsets of LBW-VLBW neonates (LBW-VLBW-a and LBW-VLBW-n) with term newborns, both displaying lower CMRO1, scan age; b2, sex), with 95% confidence interval (CI) of coefficients and respective p-values. Once corrected for scan age and sex, group comparisons of birth weight, CMRO2, CBF, OEF and brain volume produced similar results , the LBW-VLBW-a subset vs term controls , and the LBW-VLBW-n subset vs term controls . This suggests that observed differences in physiologic parameters (CMRO2 and CBF) of the LBW-VLBW-a subset and term controls stemmed from brain injuries and did not reflect scan age or sex. Corrected OEF values in the LBW-VLBW-n subset did differ significantly (p < 0.001) from those of term controls. There were no significant differences in corrected values of LBW-VLBW-a and LBW-VLBW-n subsets (p > 0.05). results . Correctp = 0.25], OEF , CMRO2 , CBF , and brain volume in distinguishing the LBW-VLBW-a subset from term and LBW-VLBW neonates are shown in 2 demonstrated fair diagnostic performance in this regard.Receiver operating characteristic curves for birth weight . Some term neonates were also discounted due to abnormal laboratory results or MRI findings. Presently, the potential for neurocognitive deficits in these infants and the relevance of CMRO2 reductions on neurocognitive deficits. We will also bolster subject recruitment, further stratifying by birth weight and sex, and foster a multicenter approach to ascertain neurocognitive thresholds for reductions in CMRO2. Owing to brain immaturity, especially in VLBW infants, there is exceptional vulnerability to injuries undermining the microstructural integrity and tract connectivity of periventricular white matter (a vascular watershed territory) . Knut harritory) . We must2 at brain level. Finally, the image quality in It is unclear at this point whether administering an anesthetic, such as chloral hydrate, has any cerebrovascular hemodynamic ramifications. There is no direct evidence in studies of humans and animals that it increases CBF or lowers glucose metabolism . However2, and higher OEF tended to show minimal structural abnormalities. Physiologic imaging may be a useful means of identifying those LBW-VLBW newborns at high risk of developing irreversible brain damage.In the present study, we have demonstrated that structural damage in LBW-VLBW-a neonates is associated with metabolic and hemodynamic deficits of the brain. LBW-VLBW-n neonates with lower CBF and CMROThe raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The study protocol had ethical approval from the Ethics Committee of Shengjing Hospital of China Medical University (IRB2015PS28K). Written informed consent from the participants\u2019 legal guardian/next of kin was not required to participate in this study in accordance with the national legislation and the institutional requirements.YQ contributed study concepts and design, and providing post-processing assistance. Both authors participated in analysis of experiment results, drafting and editing of the manuscript, and have read and approved the final manuscript for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Clostridioides difficile infection (CDI) is the leading cause of life-threatening health care-related gastrointestinal illness worldwide. Phylogenetically appropriate closed reference genomes are essential for studies of C. difficile transmission and evolution. Here, we provide high-quality complete hybrid genome assemblies for the three most prevalent C. difficile strains causing CDI in Australia. Clostridioides difficile causes life-threatening diarrhea and health care-related gastrointestinal infections globally (C. difficile population distinct from that of the rest of the world (C. difficile strains causing C. difficile infection (CDI) in Australia, PCR ribotype 014 (RT014) , RT002 (11.8%), and RT056 (5.4%) were selected from >1,500 isolates recovered from patients with symptomatic CDI, part of the ongoing nationwide longitudinal surveillance of CDI in Australia, the C. difficile Antimicrobial Resistance Surveillance (CDARS) study for 48\u2009h . ONT sequencing was performed on a MinION Mk1C device using an R9 generation flow cell following a DNA by ligation protocol (SQK-LSK109). Filtlong v0.2.0 (https://github.com/rrwick/Filtlong) was used to filter the low-quality reads , resulting in 2.28 (S-0352), 2.59 (S-0253), and 6.66 (S-0942) Gb of sequence data, respectively. The hybrid assembly of ONT and Illumina reads was performed using Unicycler v0.4.8 and annotated using the NCBI Prokaryotic Genome Annotation Pipeline v5.2 and at the ENA under BioProject accession number PRJEB41588 (Illumina sequence data); see The genome data are available at GenBank under BioProject accession number"} +{"text": "Scientific Reports 10.1038/s41598-021-81366-6, published online 19 January 2021Correction to: The original version of this Article contained extensive errors in the Reference list.Reference 26 was incorrectly split into Reference 26 and Reference 27.\u201cTrainer, M. N. & Freud, P. J. High-Concentration Submicron Particle Size Distribution by Dynamic Light Scattering Power spectrum development with heterodyne technology advances biotechnology and nanotechnology measurements.\u201dnow reads:\u201cTrainer, M. N. & Freud, P. J. High-Concentration Submicron Particle Size Distribution by Dynamic Light Scattering Power spectrum development with heterodyne technology advances biotechnology and nanotechnology measurements. Microtrac, Inc. Application Note SL-AN-05 Rev B. (2009).\u201dAs a result, References 27\u201347 were incorrectly listed as References 28\u201348.The original Article has been corrected."} +{"text": "The chemokine receptor 4 (CXCR4) and 7 (CXCR7) are G-protein-coupled receptors (GPCRs) activated through their shared ligand CXCL12 in multiple human cancers. They play a key role in the tumor/tumor microenvironment (TME) promoting tumor progression, targeting cell proliferation and migration, while orchestrating the recruitment of immune and stromal cells within the TME. CXCL12 excludes T cells from TME through a concentration gradient that inhibits immunoactive cells access and promotes tumor vascularization. Thus, dual CXCR4/CXCR7 inhibition will target different cancer components. CXCR4/CXCR7 antagonism should prevent the development of metastases by interfering with tumor cell growth, migration and chemotaxis and favoring the frequency of T cells in TME. Herein, we discuss the current understanding on the role of CXCL12/CXCR4/CXCR7 cross-talk in tumor progression and immune cells recruitment providing support for a combined CXCR4/CXCR7 targeting therapy. In addition, we consider emerging approaches that coordinately target both immune checkpoints and CXCL12/CXCR4/CXCR7 axis. Chemokines are small chemoattractant molecules that control cell migration, proliferation and survival in physiological and pathological processes including cancer . They ar\u2212/\u2212 knock-out mice die before birth -dependent phosphorylation and interaction with \u03b2 \u2013arrestin GPCRs encoded on chromosome 2.1 , 17. CXCre birth . CXCR4 \u2212ogenesis . CXCL12 ogenesis . CXCL12-ogenesis . In addiogenesis . When CXarrestin . CXCR7 parrestin , angiogearrestin , neurogearrestin and cardarrestin . Althougarrestin . Initialarrestin . Withoutarrestin . CXCR7, arrestin . CXCR7 carrestin . Studiesarrestin or in hearrestin . CXCR4/Carrestin . Overallvia Epidermal Growth Factor Receptors (EGFRs) and Matrix Metallopeptidase 9 (MMP-9) (via angiogenesis (An active CXCL12/CXCR4 pathway is considered a feature of aggressive tumors as it po (MMP-9) . Also CX (MMP-9) . CXCR7 a (MMP-9) . The pro (MMP-9) , 48. CXC (MMP-9) \u201351. In o (MMP-9) while CX (MMP-9) . CXCR7 m (MMP-9) . In cerv (MMP-9) . In lung (MMP-9) . Accordi (MMP-9) . Convers (MMP-9) . CXCL12 (MMP-9) . In addi (MMP-9) . In neur (MMP-9) . In breaogenesis . Hence, ogenesis , EGFR , myeloid derived suppressor cells (MDSCs), and dendritic cells (DCs) to the tumor niche . CXCL12 via Raf-ERK pathway , CXCR4 is expressed in tumor endothelium sprouting tumor vessels and CXCR pathway . CXCR7 e pathway or IL-1b pathway , by lipo pathway or durin pathway . CXCR7 i pathway and surv pathway . It is s pathway , 84 and pathway . CXCL12 and TECs . Thus, Celopment .DCs are the most potent antigen presenting cells (APCs) in the immune system . Immatur+CD25high FoxP3+) are CD4+ T cells with predominantly suppressive activity (5\u201310% of circulating CD4+ T cells in humans). Tregs impair immune effector cells function via cytokines, direct lysis, inhibitory receptors, metabolic disruption, IL-2 depletion or inducing an immunosuppressive microenvironment potentiates migration toward vascular-associated CXCL12-positive cells in the BM. In lymphoma-bearing mice, TCXCR4 potentiates the effector function increasing tumor protection -\u03b3 respectively, particularly in macrophages (The only approved drug CXCR4 inhibitor is AMD3100 (known as Plerixafor or Mozobil) while muin vivo . In prosin vivo . Other ain vivo or CCX73in vivo . The antin vivo . Recentlin vivo . It bindrophages . Some anrophages . The cycrophages . A CXCR4rophages . Peptide+CD25\u2013Foxp3+IL2+CD40L+ helper-like cells (-L1) small interfering RNA (siPD-L1). The nanocomplex promotes T cell infiltration, decreases alpha-smooth muscle actin (\u03b1-SMA) and collagen, reduces MDSCs and Tregs recruitment (Recently, CXCR4 antagonists have been coupled to ICIs with the intent to remodel TME improving ICIs efficacy . Since tke cells . Inhibitke cells while take cells . A nanocruitment . Thus, cImmuno-resistance and vascularization are acquired tumor features that contribute to cancer growth and metastasis. Among the different signaling pathways, directly or indirectly involved in cancer immune-resistance and angiogenesis, CXCR4/CXCR7/CXCL12 is crucial for participating in cancer migration, angiogenesis and immunosuppressive cell recruitment. Thus, the inhibition of the CXCR4/CXCL12 or CXCR7/CXCL12 axis is attractive in cancers overexpressing both receptors such as colorectal cancer , renal cSSa, CI, and SSc contributed in conception and design of the study. AMT, AC, FA, and GG supervised the study. SSa, CI, and SSc wrote and edited the manuscript. SSa and CI equally contributed. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Staphylococcus aureus (CA-MRSA) has become a major cause of S. aureus infections globally. We report the complete genome sequences of three of the earliest CA-MRSA strains isolated from remote Australian Indigenous communities in the Kimberley region of Western Australia.Initially reported in Western Australia in the 1980s, community-associated methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of health care-associated infections worldwide and has emerged as a major cause of infections in the community . Each genome was also sequenced with the Illumina NextSeq 500 platform using the Nextera XT DNA library preparation kit (150-bp paired-end chemistry) and the NextSeq 500/550 kit v2.5 . Nesoni clip (github.com/Victorian-Bioinformatics-Consortium/nesoni) was used to remove adaptor sequences and to quality filter the reads. Illumina reads were mapped to the genome assembly with Minimap2 v2.17-r941 . The ONT SQK-RAD004 kit was used to create DNA sequencing libraries, which were loaded onto an ONT FLO-MIN106 flow cell and sequenced using ONT MinKNOW v20.10.3 and MinKNOW Core v4.1.2. Base calling was performed with Guppy v4.4.1+1c81d62 (ONT), using the dna_r9.4.1_450bps_hac.cfg model. NanoFilt . Unfilte.17-r941 was used.17-r941 . Genome .17-r941 . DefaultPRJNA703734 and PRJNA703736 and Sequence Read Archive (SRA) accession numbers SRX11246052, SRX11246051, SRX11247745, SRX11247744, SRX11246056, and SRX11246055, as indicated in GenBank accession numbers for the genome assemblies are provided in"} +{"text": "First-generation COVID-19 vaccines are matched to spike protein of the Wuhan-H1 (WT) strain. Convalescent and vaccinee samples show reduced neutralization of SARS-CoV-2 variants of concern (VOC). Next generation DNA vaccines could be matched to single variants or synthetically designed for broader coverage of multiple VOCs.The synthetic consensus (SynCon\u00ae) sequence for INO-4802 SARS-CoV-2 spike with focused RBD changes and dual proline mutations was codon-optimized . Sequences for wild-type (pWT) and B.1.351 (pB.1.351) were similarly optimized. Immunogenicity was evaluated in BALB/c mice. Pre-clinical efficacy was assessed in the Syrian Hamster model.Figure 1. Design Strategy for INO-4802INO-4802 induced potent neutralizing antibody responses against WT, B.1.1.7, P.1, and B.1.351 VOC in a murine model. pWT vaccinated animals showed a 3-fold reduction in mean neutralizing ID50 for the B.1.351 pseudotyped virus. INO-4802 immunized animals had significantly higher (p = 0.0408) neutralizing capacity (mean ID50 816.16). ID50 of pB.1.351 serum was reduced 7-fold for B.1.1.7 and significantly lower (p = 0.0068) than INO-4802 (317.44). INO-4802 neutralized WT (548.28) comparable to pWT. INO-4802 also neutralized P.1 (1026.6) . pWT, pB.1.351 or INO-4802 induced similar T-cell responses against all variants. INO-4802 skewed towards a TH1-response. All hamsters vaccinated with INO-4802 or pB.1.351 were protected from weight loss after B.1.351 live virus challenge. 4/6 pWT immunized hamsters were completely protected. pWT immunized hamsters neutralized WT (1090) but not B.1.351 (39.16). INO-4802 neutralized both WT (672.2) and B.1.351 (1121) . We observed higher increase of binding titers following heterologous boost with INO-4802 (3.6 \u2013 4.4 log2-fold change) than homologous boost with pWT (2.0 \u2013 2.4 log2 fold change) .Figure 2. INO-4802 Induces Functional Humoral Immune Response Against SARS-CoV-2 Variants of ConcernFigure 3. INO-4802 Protects Hamsters Against Challenge With B.1.351 Live VirusFigure 4. Heterologous Boost with INO-4802 Induces Humoral Immune Response Against SARS-CoV-2 VariantsVaccines matching single VOCs, like pB.1.351 and pWT, elicit responses against the matched antigen but have reduced cross-reactivity. Presenting a pan-SARS-CoV-2 approach, INO-4802 may offer substantial advantages in terms of cross-strain protection, reduced susceptibility to escape mutants and non-restricted geographical use.Katherine Schultheis, MSc, Inovio Pharmaceuticals (Employee) Charles C. Reed, PhD, Inovio Pharmaceuticals Viviane M. Andrade, PhD, Inovio Pharmaceuticals Inc. (Employee) Richa Kalia, MS, Inovio Pharmaceuticals Jared Tur, PhD, Inovio (Employee) Blake Schouest, PhD, Inovio Pharmaceuticals (Employee) Dustin Elwood, PhD, Inovio Pharmaceuticals (Employee) Arthur Doan, n/a, Inovio (Employee) Patrick Pezzoli, BS, Inovio (Employee) Dinah Amante, BS, Inovio (Employee) David Weiner, PhD, Inovio J Joseph Kim, PhD, Inovio (Employee) Laurent Humeau, PhD, Inovio Pharmaceuticals (Employee) Stephanie Ramos, PhD, Inovio Pharmaceuticals (Employee) Trevor R. F. Smith, PhD, Inovio Kate Broderick, PhD, Inovio (Employee)."} +{"text": "S. aureus (MRSA), vancomycin-resistant Enterococcus (VRE), ESBL- and carbapenemase-producing Enterobacteriaceae (E). We assessed T2R performance in detecting these resistant bacteria in whole blood (WB) and analyzed possible impact on time to appropriate Ab. Appropriate antibiotic (Ab) therapy of bloodstream infections (BSI) is often delayed by time to blood culture (BC) positivity, species (sp) identification and Ab sensitivity (sensi). The T2Resistance (T2R) Panel is a direct-from-blood (culture-independent) diagnostic that detects 13 genetic markers associated with methicillin-resistant We performed T2R using WB samples obtained from patients (pts) on the same day as BCs from July 2019-2020. Receipt of appropriate Ab was assessed at time of empiric, Gram stain-directed, MALDI-directed (sp identification) and sensi-directed therapy. T2R results were not available to care teams. Teams were notified of positive BCs. Stewardship optimized Abs based on sensi. S. aureus , Enterococcus , P. aeruginosa and others (n=10). 12 ESBL-E produced CTX-M 14/15. T2R sensitivity and specificity was 78% and 99%, respectively, compared to sequencing of resistance markers. Sensitivity was excellent for vanA/B, KPC (100% each), and CTX-M14/15 (92%); sensitivity was 58% for mecA/C. T2R detected resistance determinants in 3-7h. Median time to appropriate Ab was 16.3h, which was significantly longer for VRE (25.6h) and ESBL- or KPC-E (50.9h) BSIs than for T2R marker-negative bacteria . Pts with VRE or ESBL-/KPC-E BSI were less likely to received appropriate empiric Ab than pts with T2R marker-negative BSI . Median times to achieve \u226580% appropriate Ab therapy of marker-negative, VRE and CTX-M/KPC-E BSIs were 15.5h (after Gram stain), 43.9h (after MALDI) and 63.5h (after sensi), respectively.BC from 103 pts grew 114 bacterial sp: E , Antibiotic TherapyThere was a significant delay in appropriate Ab therapy of BSIs, especially in pts infected with VRE and ESBL/KPC-E. T2R rapidly and accurately detected BSI caused by VRE and ESBL/KPC-E, and has the potential to significantly shorten time to appropriate Ab.Cornelius J. Clancy, MD, Merck (Grant/Research Support) Ryan K. Shields, PharmD, MS, Shionogi Minh-Hong Nguyen, MD, Merck (Grant/Research Support)"} +{"text": "NC_045512.2).We report a coding-complete genome sequence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain SARS-CoV-2/BGD/GC001, isolated from a Bangladeshi patient with respiratory symptoms. Phylogenetic analysis assigned this strain to lineage B.1.1.7, which presented a total of 36 mutations in the spike and other genomic regions compared to strain Wuhan Hu-1 (GenBank accession number Coronaviridae and genus Betacoronavirus (Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the family onavirus . Lineagehttp://www.sanger.ac.uk/science/tools/smalt-0) and SAMtools v1.9 from the symptomatic patient was processed for nucleic acid isolation utilizing a QIAamp viral RNA minikit . SARS-CoV-2 was confirmed using a TaqMan real-time PCR (RT-PCR) assay . A cDNA ols v1.9 . De novo v3.11.1 . RATT wa45512.2) . The Nex45512.2) and MEGA45512.2) software45512.2) . DefaultNC_045512.2) . Strain 45512.2) . MoreovePRJNA702998, BioSample accession number SAMN17993365, and GenBank accession number MW624725.1. The Illumina raw reads have been deposited in the NCBI Sequence Read Archive under accession number SRR13744683.The genome sequence of SARS-CoV-2/BGD/GC001 was deposited in the NCBI database under the BioProject accession number"} +{"text": "Chimeric antigen receptor (CAR-T) T-cell therapy is a novel immunotherapy for cancer treatment in which patients are treated with targeted, genetically-modified T-cells. Common side effects include cytokine release syndrome, neurotoxicity, hypogammaglobulinemia, and increased susceptibility to infections. Long-term infectious outcomes are poorly characterized.We retrospectively examined patients who received CAR-T therapy at BIDMC & MGH from July 2016 to March 2020 and evaluated bacterial, fungal, viral, and parasitic infections at 3 months intervals to 1 year following cell infusion. The incidence, timing, and outcomes of the infectious complications were evaluated.In total, there were 47 patients; averaging 61.4 years of age (\u00b112 years). Primary indications for CAR-T therapy included diffuse large b-cell lymphoma (65%) and multiple myeloma (25%), chronic lymphocytic leukemia (2%) and mantle cell lymphoma (2%). Patients had received an average 4 \u00b1 2.9 lines of chemotherapy prior to CAR-T infusion; 19 subjects (40%) had a history of prior autologous stem cell transplant. All patients received acyclovir for antiviral prophylaxis and most received either trimethoprim-sulfamethoxazole or atovaquone for pneumocystis prophylaxis. In the first year, 35/47 (74.5%) of subjects experienced at least one infection with an infection rate of 84.4/10,000 person days. Median time to first infection was 59 days (range 1-338 patient days). 31/47 (66.0%) subjects had at least one bacterial infection, with pulmonary sources being the most common site of infection. 13/47 (27.7%) of patients had a viral infection and 6/47 (12.8%) had a proven or probable fungal infection. Death attributed to infection was noted in 2 subjects (4.3%), both related to COVID-19. Baseline IgG levels were significantly lower in the group with infections (p=0.028), while white blood cell count and absolute neutrophil counts were comparable.Table 1. Baseline Demographic, Clinical Characteristics, and Outcomes of 47 Recipients of CAR-T Cell Therapy by Infection StatusBMI: body mass index; DLBCL: diffuse large B-cell lymphoma; CLL: chronic lymphocytic leukemia; Flu/Cy: Fludarabine/cyclophosphamide; IVIG: intravenous immunoglobulin; WBC: white blood cell count; ANC: absolute neutrophil count; ALC: absolute lymphocyte count.Table 2. Characteristics of the 113 Infections in the 35 Subjects Who Developed InfectionsInfectious complications, particularly of bacterial etiology, are common in the first year following CAR-T therapy. These data may inform future prophylactic strategies in this patient population.Matthew Frigault, MD, Arcellx (Consultant)BMS (Consultant)Iovance (Consultant)Kite (Consultant)Novartis (Consultant) Jay A. Fishman, MD, Nothing to disclose Jon Arnason, MD, BMS/Juno (Advisor or Review Panel member)Regeneron (Advisor or Review Panel member)"} +{"text": "Lung cancer is one of the most common types of cancer in the world. Although the mechanism of lungcancer is still unknown, a large number of studies have found a link between gene polymorphisms and the risk of lungcancer. The tumor suppressor p53 plays a crucial role in maintaining genomic stability and tumor prevention. MDM2is a critical regulator of the p53 protein. Despite the importance of p53 pathway in cancer, data on the contributionof SNPs of TP53 (rs1042522) and MDM2 (rs2279744) to the development of lung cancer are very contradictory. A metaanalysisthat collects quantitative data from individual studies and combines their results has the advantage of improvingaccuracy, providing reliable estimates, and resolving those issues in which studies on individual associationsare not effective enough. The aim of this study was to determine whether the TP53 (rs1042522) and MDM2 (rs2279744)polymorphisms confer susceptibility to lung cancer. A meta-analysis was conducted on the associations between theTP53 (rs1042522) and MDM2 (rs2279744) polymorphisms and lung cancer. A total of 51 comparison studies including25,366 patients and 25,239 controls were considered in this meta-analysis. The meta-analysis showed no associationbetween lung cancer and MDM2 (rs2279744) under any model. A noteworthy association of TP53 (rs1042522) withsusceptibility to lung cancer in overall pooled subjects was observed under three different models and dominant). Stratification by ethnicity indicated an association between the TP53(rs1042522) and lung cancer in Asians and Caucasians. This meta-analysis demonstrates that the TP53 (rs1042522), butnot MDM2 (rs2279744) polymorphism may confer susceptibility to lung cancer. Cancerincidence rate varies in different regions of our planet, so thehighest incidence of lung cancer is observed in Eastern Europeand Central and East Asia .Lung cancer remains one of the most common forms of cancerin the world. Every year World Health Organization (WHO)includes lung cancer in the lists of the leading cause of deathworldwide. Thus, there were 2.1 million cases of lung cancerand 1.8 million deaths in 2018 (http://www.ensembl.org/).A large number of researches have been conducted tostudy the molecular base of lung cancer. One of the riskfactorsfor the development of pulmonary neoplasms isgenes polymorphisms. The main cause of carcinogenesis isdisordersin the regulation of cell cycle control. The tumorsuppressorgene TP53 plays an important role in regulatingthe cell cycle. p53 protein is known as the \u201cguardian of thegenome\u201d. p53 regulates many genes expression in responseto cellular stress induced by various adverse environmentalfactors . This protein plays a key rolein processes such as DNA repair, cell cycle arrest, apoptosisand senescence . MDM2 is a key regulatorof p53 protein activity and degradation. Polymorphicvariantsof the TP53 and MDM2 genes have been found invarious types of cancer, including lung cancer. Analysis ofthe literature data showed that polymorphisms of the TP53Arg72Pro (rs1042522) and MDM2 SNP309 (rs2279744) genescause an increased predisposition to tumor development.The TP53 (rs1042522) gene polymorphism is localized onchromosome 17 position 7676154 Genotype frequency in theCaucasian population GG: 0.074, CC: 0.503, CG: 0.423. Inthe East Asian population, GG: 0.173, CC: 0.345, CG: 0.482, bladder , colorectalcancer and acute lymphocytic leukemia. However, no association was found betweenTP53 Arg72Pro and the risk of acute myeloid leukemia, oral squamous cell carcinoma , and esophagus cancer .http://www.ensembl.org/).The MDM2 SNP309polymorphism was also found to increase the risk of colorectalcancer , breast cancer andliver cancer . But there was no associationwith prostate, urinary tract and stomach.The polymorphic allele of the MDM2 gene rs2279744 islocated at 68808800 position on chromosome 12 Genotypefrequency in the Caucasian population TT: 0.404, GG: 0.113,GT: 0.483. In the East Asian population TT: 0.200, GG: 0.276,GT: 0.524 and MDM2 SNP309 (rs2279744) on the predisposition tothe development of pulmonary neoplasia. It was shown thatthe polymorphism of the TP53 Arg72Pro gene is associatedwith a high risk of small cell lung cancer among Spaniards. Similar data were found fornon-small cell lung cancer in Norwegians and Poles , squamous cell lung cancer in German residents , and lungadenocarcinoma in the Chinese population .Data on the contribution of MDM2 SNP309 to the developmentof lung cancer are very contradictory. Most studies haveshown an association of the MDM2 (rs2279744) mutant allelewith a high risk of lung tissue carcinogenesis . However, Pine et al.(2006) did not find that MDM2 SNP309 is associated withlung neoplasia in the European population.The data on the association of polymorphisms of the TP53genes Arg72Pro (rs1042522) and MDM2 SNP309 (rs2279744)with the development of tumors as a whole are very contradictory.Therefore, it would be interesting to perform a metaanalysison the association of TP53 Arg72Pro (rs1042522)and MDM2 SNP309 (rs2279744) with a risk of developinglung cancer in Asian and European populations.Search strategy. Search for relevant studies was conductedusing online databases, such as Scopus, PubMed and Web ofScience. The search strategy was performed using a combinationof the following keywords: \u201cTP53\u201d, \u201cMurine double minute2\u201d or \u201cMDM2\u201d, \u201cpolymorphism\u201d, \u201cSNP\u201d, \u201crs1042522\u201d,\u201crs2279744\u201d, \u201cArg72Pro\u201d, \u201ccodon 72 Arg\u201d, \u201cc.215C > G\u201d,\u201cSNP309\u201d, \u201cc.291 T > G\u201d \u201clung cancer\u201d, \u201cnon-small cell lungcancer\u201d, \u201cassociation\u201d.Inclusion and exclusion criteria. The eligible inclusioncriteria for the meta-analysis were (i) case-control study,(ii) identification of different histological types of lungcancer which was confirmed histologically or pathologically,(iii) having an available genotype for estimating anodds ratio (OR) with 95 % confidence interval (95 % CI),(iv) genotype frequencies in controls were consistent withthose expected from Hardy\u2013Weinberg equilibrium ( p > 0.05).The studies were excluded when (i) they were not casecontrolstudies, (ii) with duplicated data from previous articles,(iii) they were not original articles, e. g. review, (iv) inadequategenotype data were available.Data extraction and quality assessment. Two researchers(O.B. and A.K.) evaluated the eligibility of all retrieved studiesand extracted the pertinent data from the specified publicationsin standardized tables. The extracted data included:(i) the first author name, (ii) publication year, (iii) ethnicity,(iv) lung cancer patients and healthy controls sample size foreach studied polymorphism. Disagreement was resolved byconsulting with a third investigator (R.B.). The study qualitywas assessed in accordance with the Newcastle\u2013OttawaScale (NOS) .Statistical analysis. Hardy\u2013Weinberg equilibrium (HWE)in control population was assessed utilizing the \u201cCalculationof Chi-square test for deviation from Hardy\u2013Weinbergequilibrium\u201donline software (http://www.husdyr.kvl.dk/htm/kc/popgen/genetik/applets/kitest.htm). The statistical analysiswas performed using Comprehensive Meta Analysis version2.2.064 . Estimates weresummarized as ORs with 95 % CIs for each study. The heterogeneitywas evaluated by using the I2 index. An I2 valueof > 50 % was considered to indicate high heterogeneity . The random effects model for analysis was used in case high heterogeneity . Otherwise, the fixed-effectsmodel was used. Publication bias was measured via \u201cBegg\u2019sfunnel plot\u201d and \u201cEgger\u2019s linear regression\u201d method . A two-tailed p-value < 0.05 implied a statisticallysignificant publication bias.Studies included in the meta-analysis1.A total of 531 potential articles were identified from the databasessearch. After 236 duplicate records were removed, atotal of 295 potential articles were reviewed. Amongst thesearticles, 216 were excluded after titles and abstracts review.Afterwards, we excluded 28 studies for no case-control design.Finally, 51 studies with a total of 25,239 controls and25,366 cases that met the inclusion criteria were included inthis meta-analysis 1Supplementary Materials are available in the online version of the paper:http://www.bionet.nsc.ru/vogis/download/pict-2020-24/appx13.pdfCharacteristics of studies included in this meta-analysisA total of 37 articles that examined TP53 (rs1042522) associationwith lung cancer risk were determined. Two of thesearticles included data of two different sets (TP53 (rs1042522)and MDM2 (rs2279744)) and these sets were examined autonomously. Thus,the identified 37 articles encompassed case-controls studiesinvolving 16,229 lung cancer patients and 14,897 controls(Table 1). Among 37 articles, 20 studies were establishedin Asian populations and 17 in Caucasian populations. The genotype frequencies in controls of all studies were consistentwith those expected from HWE ( p > 0.05).Another 14 articles identified MDM2 (rs2279744) associationwith increased lung cancer risk were retrieved (Table 2).These 14 articles encompassed case-controls studies involving9,137 lung cancer patients and 10,342 controls. Among14 articles, 7 studies were established in Asian populationsand 7 in Caucasian populations. The genotype frequenciesin controls of all studies were consistent with those expectedfrom HWE ( p > 0.05).All estimated published articles were executed under accreditedgenotyping methods.Meta-analysis of the relationship betweenthe TP53 (rs1042522) polymorphism and lung cancer risksociatedwith lung cancer . And the association was statisticallysignificant under allele model (G versus C), homozygotemodel (GG versus CC) and dominant model(GG+GC vs. CC) ( p < 0.05). A summary ofmeta-analysis findings concerning associations between theTP53 (rs1042522) polymorphism and lung cancer risk isshown in Table 3.Further subgroup analysis was conducted on the associationbetween TP53 (rs1042522) polymorphism and the risk of lungcancer (see Table 3). After stratifying by ethnicity, this metaanalysisindicated an obvious association of TP53 (rs1042522)and lung cancer risk among Caucasians and among Asians .Meta-analysis of the relationship betweenthe MDM2 (rs2279744) polymorphism and lung cancer riskIn this meta-analysis was shown no association MDM2(rs2279744) polymorphism with lung cancer . A summary ofmeta-analysis findings concerning associations between theMDM2 (rs2279744) polymorphism and lung cancer risk isshown in Table 4. Subgroup analysis detected no associationMDM2 (rs2279744) polymorphism with lung cancer.Between-study heterogeneities were found in all subjectsfor both polymorphisms TP53 (rs1042522) and MDM2(rs2279744) . Because of this the meta-analysiswas designed using \u201ca random effect model\u201d to establishpooled OR and corresponding 95 % CI for all models. Weperformed the meta-regression to explore the potential sourceof between-study. A big problem for meta-analysis is the disproportionatenumber of positive studies that leads to a biasin the publication. The funnel plot indicated some evidence ofpublication bias for Caucasians, but not for Asians in analysisof TP53 (rs1042522) and MDM2 (rs2279744) gene polymorphisms. The publication bias was observedfrom Egger\u2019s test ( p \u2264 0.05) also for Caucasian population.The tumor suppressor gene TP53 (previously named p53),is key regulator of a cell cycle network, apoptosis and DNArepair pathway. TP53 is one of the most carcinogenesis-associatedgenes. There were several studies assessing the effectsof TP53 polymorphisms on the risk of lung cancer, but theresults are very contradictory. For example, no associationsof the TP53 (rs1042522) polymorphism with lung cancerwere found in Jung et al.\u2019s (2008) article. But, increased risk to develop lung cancer was observed in association with thePro/Pro genotype variant in Chowdhury et al.\u2019s (2015) research.Mostaid et al. (2014) found that TP53 Arg72Pro andPro72Pro genotype significantly associated with increasedrelative risk of lung cancer. Our previous study also demonstratedthe association of genotype Arg72Pro of TP53 genewith lung cancer risk . Papadakis etal. (2002) demonstrated that subjects with Arg72Arg genotypeof rs1042522 had significantly increased lung cancer risk. Wecomprehensively searched the up-to-date electronic databasesto reveal the associations between TP53 genetic polymorphisms (rs1042522) and risk of lung cancer. The genome-wideassociation study (GWAS) is very popular method to detect avariation in SNPs with variation in common diseases. In 2017,data from a study of new loci of susceptibility to lung cancerwere published. The study identified RNASET2, SECISBP2L,NRG1, CHRNA2, OFBC1 and RTEL1 as candidate genes associatedwith lung cancer . The polymorphismsof TP53 (rs1042522) and MDM2 (rs2279744) weren\u2019tdetected in this GWAS .A total of 37 case-control comparisons for TP53 (rs1042522) were investigated in this meta-analysis. A noteworthy associationof TP53 (rs1042522) with susceptibility to lung cancer inoverall pooled subjects was observed under three differentmodels: the allele contrast, homozygote contrast (additive)and dominant model. Also, stratification analysis explained astrong evidence of this variant with risk of lung cancer amongAsians and Caucasian under allelic, homozygote (only forCaucasian) and dominant models. Moreover, the Arg72Arggenotype was associated with the obvious protective effect.Compared to TP53, whose role has been widely discussed inlung cancer developing, its main negative modifier \u2013 MDM2,has not been sufficiently studied. The data on the associationof polymorphism of MDM2 (rs2279744 or 309T > G) withthe risk of developing lung cancer as well as in the case ofTP53 (rs1042522) are contradictory. Thus, Enokida et al.(2014) did not found any association between polymorphismof MDM2 (rs2279744) and lung cancer risk. Chua et al. (2010)demonstrated that the MDM2 (rs2279744) TT rather than theGG genotype is associated with increased risk of lung cancerin Asian. But, the MDM2 TT genotype was associated witha decreased risk of developing NSCLC compared with thatof the MDM2 GG genotypes in Li G. et al.\u2019s (2006) research.A total of 14 case-control comparisons for MDM2 (rs2279744) wereinvestigated in this meta-analysis. There were no significantassociations between MDM2 (rs2279744) polymorphisms andlung cancer with regard to G allele vs. T allele: OR = 0.86,95 % CI 0.71\u20131.03, p = 0.1; homozygote model: OR = 0.86,95 % CI 0.71\u20131.03, p = 0.1; dominant model: OR = 0.90, 95 %CI 0.79\u20131.02, p = 0.5 and recessive model: OR = 1.10, 95 %CI 0.94\u20131.22, p = 0.276. The stratification analysis also didnot demonstrate the association of this polymorphism withrisk of lung cancer among Asians and Caucasian under allmodels. Thus, MDM2 (rs2279744) polymorphism does notaffect the risk of developing lung cancer.This meta-analysis has some limitations. First, heterogeneitylevel was high. But we tried to eliminate this effect usinga random effects model rather than a fixed effects model.Publication bias could also have biased the results, as studiesthat produced negative results may not have been published.Despite our use of Egger\u2019s regression test, we cannot eliminatethe possibility of bias. Second, the relative importance of theMDM2 (rs2279744) polymorphism during the developmentof lung cancer may vary between ethnic groups, but we wereonly able to perform ethnic-specific meta-analysis in Asiansand Europeans. Thus, our results are applicable to only theseethnic groups. Therefore, additional studies with other ethnicpopulations are warranted to assess the association betweenMDM2 (rs2279744) polymorphism and the risk of lung cancer.But, the present meta-analysis has also several strengths.We used a strong comprehensive search strategy, and had awell-defined inclusion and exclusion criteria. Reviewers performedthe study selection and extracted data independently.Moreover, we assessed the quality of the included studies bypredefined criteria and the score of included studies was high.Finally, all genotype data extracted from the studies werereported in the study. The advantage of this study over othermeta-analyzes is a more complete review of literature and theinclusion of recent data.In summary, this meta-analysis study indicated evidence ofassociation for TP53 (rs1042522), but not MDM2 (rs2279744)variants with lung cancer based on 51 case-control publishedstudies. Additionally, stratified analysis based on ethnicityobserved an obvious association of TP53 (rs1042522) bothamong Asian and European subjects under allelic, homozygoteand dominant models. However, polymorphism MDM2(rs2279744) may not impart susceptibility to lung cancer ineither Asians or Europeans.The authors declare no conflict of interest.Birgander R., Sjalander A., Rannug A., Alexandrie A.K., SundbergM.I., Seidegard J. P53 polymorphisms and haplotypes in lungcancer. Carcinogenesis. 1995;16(9):2233-2236. DOI 10.1093/carcin/16.9.2233.Bray F., Ferlay J., Soerjomataram I., Siegel R.L., Torre L.A., Jemal A.Global cancer statistics 2018: GLOBOCAN estimates of incidenceand mortality worldwide for 36 cancers in 185 countries. CA CancerJ. Clin. 2018;68:394-424. DOI 10.3322/caac.21492.Bulgakova O., Kussainova A., Kakabayev A., Kausbekova A., BersimbaevR. Association of polymorphism TP53 Arg72Pro with radoninducedlung cancer in the Kazakh population. Vavilovskii ZhurnalGenetiki i Selektsii = Vavilov Journal of Genetics and Breeding.2019;23(5):594-599. DOI 10.18699/VJ19.530.Buyru N., Altinisik J., Isin M., Dalay N. p53 codon 72 polymorphismand HPV status in lung cancer. Med. Sci. Monit. 2008;14(9):CR493-497.Cheng H., Ma B., Jiang R., Wang W., Guo H., Shen N., Li D., Zhao Q.,Wang R., Yi P., Zhao Y., Liu Z., Huang T. Individual and combinedeffects of MDM2 SNP309 and TP53 Arg72Pro on breast cancer risk:an updated meta-analysis. Mol. Biol. Rep. 2012;39(9):9265-9274.DOI 10.1007/s11033-012-1800-z.Chowdhury M.K., Moniruzzaman M., Emran A.A., Mostafa M.G.,Kuddus R.H., Uddin M.A. TP53 codon 72 polymorphisms and lungcancer risk in the Bangladeshi population. Asian Pac. J. CancerPrev. 2015;16(8):3493-3498. DOI 10.7314/apjcp.2015.16.8.3493.Chua H.W., Ng D., Choo S. Effect of MDM2 SNP309 and p53 codon72 polymorphisms on lung cancer risk and survival among nonsmokingChinese women in Singapore. BMC Cancer. 2010;10:88.DOI 10.1186/1471-2407-10-88.Ding H., Dai Y., Ning Zh., Fan N., Wang Zh., Li P., Zhang L., Tao Y.,Wang H. Murine double minute 2 SNP T309G polymorphism andurinary tract cancer risk: a meta-analysis. Medicine .2016;95(12):e2941. DOI 10.1097/MD.0000000000002941.Egger M., Smith G., Schneider M., Minder C. Bias in meta-analysisdetected by a simple, graphical test. BMJ. 1997;315(7109):629\u2010634.DOI 10.1136/bmj.315.7109.629.Enokida Y., Shimizu K., Kakegawa S., Atsumi J., Takase Y., MiyamaeY., Nagashima T., Ohtaki Y., Kaira K., Sunaga N., Yanagitani N.,Yoshino R., Tsunekawa K., Igai H., Kamiyoshihara M., Usui K.,Lezhava A., Tomizawa Y., Ishikawa T., Murakami M., HayashizakiY., Takeyoshi I. Single-nucleotide polymorphism (c.309T > G)in the MDM2 gene and lung cancer risk. Biomed. Rep. 2014;2(5):719-724. DOI 10.3892/br.2014.305.Fan R., Wu M.T., Miller D., Wain J.C., Kelsey K.T., Wiencke J. Thep53 codon 72 polymorphism and lung cancer risk. Cancer Epidemiol.Biomarkers Prev. 2000;9:1037-1042.Fern\u00e1ndez-Rubio A., L\u00f3pez-Cima M.F., Gonz\u00e1lez-Arriaga P., Garc\u00eda-Castro L., Pascual T., Marr\u00f3n M.G., Tard\u00f3n A. The TP53 Arg72Propolymorphism and lung cancer risk in a population of NorthernSpain. Lung Cancer. 2008;61(3):309-316. DOI 10.1016/j.lungcan.2008.01.017.Giuliani L., Jaxmar T., Casadio C., Gariglio M., Manna A., D\u2019Antonio D.Detection of oncogenic viruses SV40, BKV, JCV, HCMV, HPV and p53 codon 72 polymorphism in lung carcinoma. Lung Cancer. 2007;57(3):273-281. DOI 10.1016/j.lungcan.2007.02.019.Haronikova L., Olivares-Illana V., Wang L., Karakostis K., Chen S.,F\u00e5hraeus R. The p53 mRNA: an integral part of the cellular stressresponse. Nucleic Acids Res. 2019;47(7):3257-3271. DOI 10.1093/nar/gkz124.Hiraki A., Matsuo K., Hamajima N., Ito H., Hatooka S., Suyama M.,Mitsudomi T., Tajima K. Different risk relations with smoking fornonsmall-cell lung cancer: comparison of TP53 and TP73 genotypes.Asian Pac. J. Cancer Prev. 2003;4:107-112.Hu Z., Ma H., Lu D. Genetic variants in the MDM2 promoter and lungcancer risk in a Chinese population. Int. J. Cancer. 2006;118:1275-1278.Javid J., Mir R., Julka P.K., Ray P.C., Saxena A. Association of p53 andmdm2 in the development and progression of non-small cell lungcancer. Tumour. Biol. 2015;36(7):5425\u20105432. DOI 10.1007/s13277-015-3208-6.Jiang D.K., Yao L., Wang W.Zh., Peng B., Ren W.H., Yang X.M., Yu L.TP53 Arg72Pro polymorphism is associated with esophageal cancerrisk: a meta-analysis. World J. Gastroenterol. 2011;17(9):1227-1233. DOI 10.3748/wjg.v17.i9.1227.Jun H.J., Park S.H., Lee W.K. Combined effects of p73 and MDM2polymorphisms on the risk of lung cancer. Mol. Carcinog. 2007;46:100-105. DOI 10.1002/mc.20279.Jung H.Y., Whang Y.M., Sung J.S., Shin H.D., Park B.L., Kim J.S.,Shin S.W., Seo H.Y., Seo J.H., Kim Y.H. Association study of TP53polymorphisms with lung cancer in a Korean population. J. Hum.Genet. 2008;53:508-514. DOI 10.1007/s10038-008-0278-y.Kawajiri K., Nakachi K., Imai K. Germ line polymorphisms of p53and CYP1A1 genes involved in human lung cancer. Carcinogenesis.1993;14:1085-1089. DOI 10.1093/carcin/14.6.1085.Kiyohara C., Horiuchi T., Miyake Y., Takayama K., Nakanishi Y. Cigarettesmoking, TP53 Arg72Pro, TP53BP1 Asp353Glu and the riskof lung cancer in a Japanese population. Oncol. Rep. 2010;23(5):1361-1368. DOI 10.3892/or_00000772.Kohno T., Kunitoh H., Mimaki S. Contribution of the TP53, OGG1,CHRNA3, and HLA-DQA1 genes to the risk for lung squamous cellcarcinoma. J. Thorac. Oncol. 2011;6:813-817. DOI 10.1097/JTO.0b013e3181ee80ef.Lee Y.H. Meta-analysis of genetic association studies. Ann. Lab. Med.2015;35(3):283\u2010287. DOI 10.3343/alm.2015.35.3.283.Li G., Zhai X., Zhang Z., Chamberlain R.M., Spitz M.R. MDM2 genepromoter polymorphisms and risk of lung cancer: a case-controlanalysis. Carcinogenesis. 2006;27:2028-2033. DOI 10.1093/carcin/bgl047.Li W., Wang S.S., Deng J., Tang J.X. Association of p73 gene G4C14-A4T14 polymorphism and MDM2 gene SNP309 with non-smallcell lung cancer risk in a Chinese population. Oncol. Lett. 2017;14(2):1817-1822. PMID: 28789416. PMCID: PMC5529775. DOI10.3892/ol.2017.6327.Li Y., Chang S.-C., Niu R., Li Y., Chang S.-C., Niu R., Liu L., Crabtree-Ide C.R., Zhao B., Shi J., Han X., Li J., Su J., Cai L., Yu S.,Zhang Z.-F., Mu L. TP53 genetic polymorphisms, interactions withlifestyle factors and lung cancer risk: a case control study in a Chinesepopulation. BMC Cancer. 2013;13:607. DOI 10.1186/1471-2407-13-607.Lind H., Ekstr\u00f8m P.O., Ryberg D., Skaug V., Andreassen T. Frequencyof TP53 mutations in relation to Arg72Pro genotypes in non-smallcell lung cancer. Cancer Epidemiol. Biomarkers Prev. 2007;16(10):2077-2081. DOI 10.1158/1055-9965.EPI-07-0153.Lind H., Zienolddiny S., Ekstrom P.O., Skaug V., Haugen A. Associationof a functional polymorphism in the promoter of the MDM2gene with risk of nonsmall cell lung cancer. Int. J. Cancer. 2006;119:718-721. DOI 10.1002/ijc.21872.Liu D., Wang F., Guo X., Wang Q., Wang W., Xu H., Xu G. Associationbetween p53 codon 72 genetic polymorphisms and tobacco useand lung cancer risk in a Chinese population. Mol. Biol. Rep. 2013;40(1):645-649. DOI 10.1007/s11033-012-2103-0.Liu G., Miller D.P., Zhou W., Thurston S.W., Fan R., Xu L.L. Differentialassociation of the codon 72 p53 and GSTM1 polymorphisms onhistological subtype of non-small cell lung carcinoma. Cancer Res.2001;61(24):8718-8722.Liu G., Wheatley-Price P., Zhou W. Genetic polymorphisms of MDM2,cumulative cigarette smoking and nonsmall cell lung cancer risk.Int. J. Cancer. 2008;122:915-918. DOI 10.1002/ijc.23178.Ma Y., Bian J., Cao H. MDM2 SNP309 rs2279744 polymorphism andgastric cancer risk: a meta-analysis. PLoS One. 2013;8(2):e56918.DOI 10.1371/journal.pone.0056918.McKay J.D., Hung R.J., Han Y., Zong X., Carreras-Torres R., ChristianiD.C., Caporaso N.E., \u2026 Boss\u00e9 Y., Chanock S., Brennan P.,Landi M.T., Amos C.I. Large-scale association analysis identifiesnew lung cancer susceptibility loci and heterogeneity in geneticsusceptibility across histological subtypes. Nat. Genet. 2017;49(7):1126-1132. DOI 10.1038/ng.3892.Mechanic L.E., Bowman E.D., Welsh J.A., Khan M.A., Hagiwara N.,Enewold L. Common genetic variation in TP53 is associated withlung cancer risk and prognosis in African Americans and somaticmutations in lung tumors. Cancer Epidemiol. Biomarkers Prev.2007;16(2):214-222. DOI 10.1158/1055-9965.EPI-06-0790.Miller D.P., Liu G., De Vivo I., Lynch T.J., Wain J.C., Su L., ChristianiD.C. Combinations of the variant genotypes of GSTP1, GSTM1,and p53 are associated with an increased lung cancer risk. CancerRes. 2002;62:2819-2823.Mittelstrass K., Sauter W., Rosenberger A. Early onset lung cancer,cigarette smoking and the SNP309 of the murine double minute-2(MDM2) gene. BMC Cancer. 2008;8:113. DOI 10.1186/1471-2407-8-113.Mostaid M.S., Ahmed M.U., Islam M.S., Bin Sayeed M.S., Hasnat A.Lung cancer risk in relation to TP53 codon 47 and codon 72 polymorphismin Bangladeshi population. Tumour Biol. 2014;35(10):10309-10317. DOI 10.1007/s13277-014-2285-2.Murata M., Tagawa M., Kimura M., Kimura H., Watanabe S., Saisho H.Analysis of a germ line polymorphism of the p53 gene in lung cancerpatients: discrete results with smoking history. Carcinogenesis.1996;17(2):261-264. DOI 10.1093/carcin/17.2.261.Nadji S.A., Mahmoodi M., Ziaee A.A., Naghshvar F., Torabizadeh J.,Yahyapour Y. An increased lung cancer risk associated with codon72 polymorphism in the TP53 gene and human papillomavirusinfection in Mazandaran province, Iran. Lung Cancer. 2007;56(2):145-151. DOI 10.1016/j.lungcan.2006.12.006.Nicolai S., Rossi A., Daniele N., Melino G., Annicchiarico-PetruzzelliM., Raschell\u00e0 G. DNA repair and aging: the impact of the p53family.Aging (Albany NY ). 2015;7(12):1050-1065. DOI 10.18632/aging.100858.Papadakis E.D., Soulitzis N., Spandidos D.A. Association of p53 codon72 polymorphism with advanced lung cancer: the Arg alleleis preferentially retained in tumours arising in Arg/Pro germlineheterozygotes.Br. J. Cancer. 2002;87(9):1013-1018. DOI 10.1038/sj.bjc.6600595.Piao J.M., Kim H.N., Song H.R., Kweon S.S., Choi J.S., Yun W.J.p53 codon 72 polymorphism and the risk of lung cancer in a Koreanpopulation. Lung Cancer. 2011;73(3):264-267. DOI 10.1016/j.lungcan.2010.12.017.Pierce L.M., Sivaraman L., Chang W., Lum A., Donlon T., Seifried A.Relationships of TP53 codon 72 and HRAS1 polymorphisms withlung cancer risk in an ethnically diverse population. Cancer Epidemiol.Biomarkers Prev. 2000;9:1199-1204.Pine S.R., Mechanic L.E., Bowman E.D., Welsh J.A., Chanock S.C.,Shields P.G., Harris C.C. MDM2 SNP309 and SNP354 are notassociatedwith lung cancer risk. Cancer Epidemiol. BiomarkersPrev. 2006;15(8):1559-1561. DOI 10.1158/1055-9965.EPI-06-0217.Popanda O., Edler L., Waas P., Schattenberg T., Butkiewicz D., MuleyT., Dienemann H., Risch A., Bartsch H., Schmezer P. Elevatedrisk of squamous-cell carcinoma of the lung in heavy smokers carryingthe variant alleles of the TP53 Arg72Pro and p21 Ser31Arg polymorphisms. Lung Cancer. 2007;55(1):25-34. DOI 10.1016/j.lungcan.2006.09.006.Qin X., Peng Q., Tang W., Lao X., Chen Zh., Lai H., Deng Y., Mo C.,Sui J., Wu J., Zhai L., Yang Sh., Li Sh., Zhao J. An updated metaanalysison the association of MDM2 SNP309 polymorphism withcolorectal cancer risk. PLoS One. 2013;8(9):e76031. DOI 10.1371/journal.pone.0076031.Ren Y.W., Yin Zh., Wan Y., Guan P., Wu W., Li X., Zhou B. P53Arg72Proand MDM2 SNP309 polymorphisms cooperate to increaselung adenocarcinoma risk in Chinese female non-smokers:a case control study. Asian Pac. J. Cancer Prev. 2013;14(9):5415-5420. DOI 10.7314/apjcp.2013.14.9.5415.Saikia B.J., Das M., Sharma S.K., Sekhon G.S., Zomawia E.,Singh Y.M., Mahanta J., Phukan R.K. Association of a p53 codon 72gene polymorphism with environmental factors and risk of lung cancer:a case control study in Mizoram and Manipur, a high incidenceregion in North East India. Asian Pac. J. Cancer Prev. 2014;15:10653-10658. DOI 10.7314/apjcp.2014.15.24.10653.Sakiyama T., Kohno T., Mimaki S., Ohta T., Yanagitani N., Sobue T.,Kunitoh H., Saito R., Shimizu K., Hirama C., Kimura J., Maeno G.Association of amino acid substitution polymorphisms in DNA repairgenes TP53, POLI, REV1 and LIG4 with lung cancer risk. Int. J.Cancer. 2004;114:730-737. DOI 10.1002/ijc.20790.Sobti R.C., Kaur P., Kaur S., Janmeja A.K., Jindal S.K., Kishan J.Impact of interaction of polymorphic forms of p53 codon 72 andN- acetylation gene (NAT2) on the risk of lung cancer in the NorthIndianpopulation. DNA Cell Biol. 2009;28(9):443-449. DOI10.1089/dna.2008.0797.Souto-Garc\u00eda A., Fern\u00e1ndez-Somoano A., Pascual T., \u00c1lvarez-Avell\u00f3nS.M., Tard\u00f3n A. Association of p21 Ser31Arg and p53 Arg72Propolymorphisms with lung cancer risk in CAPUA study. Lung Cancer(Auckl ). 2012;3:69-78. DOI 10.2147/LCTT.S35287.Sreeja L., Syamala V., Raveendran P.B., Santhi S., Madhavan J., AnkathilR. p53 Arg72Pro polymorphism predicts survival outcome inlung cancer patients in Indian population. Cancer Invest. 2009;26:41-46. DOI 10.1080/07357900701638459.Su L., Sai Y., Fan R., Thurston S.W., Miller D.P., Zhou W., Wain J.C.,Lynch T.J., Liu G., Christiani D.C. P53 (codon 72) and P21 (codon31) polymorphisms alter in vivo mRNA expression of p21. LungCancer. 2003;40(3):259\u2010266. DOI 10.1016/s0169-5002(03)00081-3.Sun Zh., Gao W., Cui G.T. Effect of TP53 rs1042522 on the susceptibilityof patients to oral squamous cell carcinoma and oral leukoplakia:a meta-analysis. BMC Oral Health. 2018;18(1):143. DOI 10.1186/s12903-018-0603-6.Szymanowska A., Jassem E., Dziadziuszko R., Borg A., Limon J.,Kobierska-Gulida G., Rzyman W., Jassem J. Increased risk of nonsmallcell lung cancer and frequency of somatic TP53 gene mutationsin Pro72 carriers of TP53 Arg72Pro polymorphism. Lung Cancer.2006;52(1):9-14. DOI 10.1016/j.lungcan.2005.12.007.Tang T., Song X., Yang Zh., Huang L., Wang W., Tan H. Associationbetween murine double minute 2 T309G polymorphism and risk ofliver cancer. Tumour Biol. 2014;35(11):11353-11357. DOI 10.1007/s13277-014-2432-9.Tian X., Dai Sh., Sun J., Jiang Sh., Jiang Y. Association between TP53Arg72Pro polymorphism and leukemia risk: a meta-analysis of14 case-control studies. Sci. Rep. 2016;6:24097. DOI 10.1038/srep24097.Tian X., Dai Sh., Sun J., Jiang Sh., Jiang Y. The association betweenthe TP53 Arg72Pro polymorphism and colorectal cancer: an updatedmeta-analysis based on 32 studies. Oncotarget. 2017;8(1):1156-1165. DOI 10.18632/oncotarget.13589.To-Figueras J., Gene M., Gomez-Catalan J., Galan C., Firvida J., FuentesM. Glutathione-S-Transferase M1 and codon 72 p53 polymorphismsin a northwestern Mediterranean population and their relationto lung cancer susceptibility. Cancer Epidemiol. BiomarkersPrev. 1996;5(5):337-342.Wang X., Jin L., Cui J., Ma K., Chen X., Li W. Mouse double minute-2homolog (MDM2)-rs2279744 polymorphism associated with lungcancer risk in a Northeastern Chinese population. Thorac. Cancer.2015;6(1):91-96. DOI 10.1111/1759-7714.12153.Wang Y.C., Chen C.Y., Chen S.K., Chang Y.Y., Lin P. p53 codon 72polymorphism in Taiwanese lung cancer patients: association withlung cancer susceptibility and prognosis. Clin. Cancer Res. 1999;5:129-134.Wells G.A., Shea B., O\u2019Connell D., Peterson J., Welch V., Losos M.,Tugwell P. The Newcastle\u2013Ottawa Scale (NOS) for assessing thequality if nonrandomized studies in meta-analyses. Available online:http://www.ohri.ca/programs/clinical_epidemiology/oxford.htm(Accessed on 19 October 2009).Wu X., Zhao H., Amos C.I., Shete S., Makan N., Hong W.K., KadlubarF.F., Spitz M.R. p53 genotypes and haplotypes associated withlung cancer susceptibility and ethnicity. J. Natl. Cancer Inst. 2002;94:681-690. DOI 10.1093/jnci/94.9.681.Xiang B., Mi Y.Y., Li T.F., Liu P.F. Updated meta-analysis of the TP53Arg72Pro polymorphism and gastric cancer risk. Asian Pac. J. CancerPrev. 2012;13(5):1787-1791. DOI 10.7314/apjcp.2012.13.5.1787.Xu T., Xu Z.Ch., Zou Q., Yu B., Huang X.E. P53 Arg72Pro polymorphismand bladder cancer risk \u2013 meta-analysis evidence for a link inAsians but not Caucasians. Asian Pac. J. Cancer Prev. 2012;13(5):2349-2354. DOI 10.7314/apjcp.2012.13.5.2349.Zhang F., Li D., Li Y., Li H., Sun J., Li X., Li X. Quantitative assessmentof the association between TP53 Arg72Pro polymorphism andrisk of glioma. Tumour Biol. 2014;35(1):747-751. DOI 10.1007/s13277-013-1101-8.Zhang X., Miao M., Guo Y., Tan W., Zhou Y., Sun T., Wang Y., Lin D.Genetic polymorphisms in cell cycle regulatory genes MDM2 andTP53 are associated with susceptibility to lung cancer. Hum. Mutat.2006;27(1):110-117. DOI 10.1002/humu.20277.Zhuo W., Zhang L., Zhu B., Ling J., Chen Z. Association of MDM2SNP309 variation with lung cancer risk: evidence from 7196 casesand 8456 controls. PLoS One. 2012;7:e41546. DOI 10.1371/journal.pone.0041546."} +{"text": "Complete characterization of bis(1H-indazol-1-yl)methane is given with 1H and 13C NMR, UV/Vis, FTIR, high resolution mass spectrometry and for the first time, single crystal X-ray diffraction. This simple, inexpensive pathway to yield exclusively bis(1H-indazol-1-yl)methane provides synthetic access to further investigate the coordination and potential applications of the family of bis(indazolyl)methanes.Synthetic access to poly(indazolyl)methanes has limited their study despite their structural similarity to the highly investigated chelating poly(pyrazolyl)methanes and their potentially important indazole moiety. Herein is presented a high yielding, one-pot synthesis for the 3 UV/Vis \u03bbmax (log \u03b5): 251 (3.54), 260 (3.51), 288 (3.52), 293 (3.52), 299 (3.50). IR (cm\u22121): 3106 (w), 3060 (m), 2957 (w), 2921 (w), 1617 (m), 1499 (m), 1463 (m), 1439 (w), 1353 (m), 1279 (m), 1197 (s), 1150 (w), 1005 (m), 906 (m), 828 (m), 758 (s), 736 (s).Formation of 2.2.2.2.1.H-indazole and 0.31 mmol of trans-dichlorotetrakis(pyridine)cobalt(III) chloride Cl was synthesized from the previous literature Cl. Complete characterization of 1L is presented including 1H and 13C NMR, UV/Vis, FTIR, high resolution mass spectrometry, and for the first time single crystal X-ray diffraction. Creating synthetic access and diffraction data will allow for expansion of our knowledge on the bis(1H-indazol-1-yl)methane family of ligands to be utilized in future synthetic, mechanistic, chelating and pharmaceutical applications.This article presents on a simple, high yielding one-pot synthesis producing exclusively bis(1Supplementary Information"} +{"text": "Oncogene 10.1038/s41388-021-01973-5, published online 3 August 2021Correction to: In this article two text marking errors on the Fig. 3F and Supplementary Fig. The correct figures are given below.The original article has been corrected.Supplementary Fig. 3"} +{"text": "Plasmodium parasite fertilization. A recombinant Plasmodium vivax P48/45 (Pvs48/45) protein expressed in Escherichia coli (E. coli) was highly antigenic and immunogenic in experimental animals and elicited specific transmission-blocking (TB) antibodies in a previous pilot study. Here, a similar Pvs48/45 gene was expressed in Chinese Hamster Ovary (CHO) cells and we compared its immunoreactivity with the E. coli product. Specific antibody titers were determined using plasma from Colombian individuals (n=227) living in endemic areas where both P. vivax and P. falciparum are prevalent and from Guatemala (n=54) where P. vivax is highly prevalent. In Colombia, plasma seroprevalence to CHO-rPvs48/45 protein was 46.3%, while for E. coli-rPvs48/45 protein was 36.1% (p<0.001). In Guatemala, the sero prevalence was 24.1% and 14.8% (p<0.001), respectively. Reactivity index (RI) against both proteins showed an age-dependent increase. IgG2 was the predominant subclass and the antibody avidity index evaluated by ELISA ranged between 4-6 mol/L. Ex vivo P. vivax mosquito direct membrane feeding assays (DMFA) performed in presence of study plasmas, displayed significant parasite transmission-blocking (TB), however, there was no direct correlation between antibody titers and oocysts transmission reduction activity (%TRA). Nevertheless, DMFA with CHO rPvs48/45 affinity purified IgG showed a dose response; 90.2% TRA at 100 \u03bcg/mL and 71.8% inhibition at 10 \u03bcg/mL. In conclusion, the CHO-rPvs48/45 protein was more immunoreactive in most of the malaria endemic places studied, and CHO-rPvs48/45 specific IgG showed functional activity, supporting further testing of the protein vaccine potential.P48/45 is a conserved gametocyte antigen involved in P. falciparum is highly prevalent in sub-Saharan Africa, both P. falciparum and P. vivax coexist in vast regions of Latin America, Asia, and Oceania, with many countries displaying greater P. vivax prevalence during the fertilization phase in the mosquito midguts . These antigens have shown the capacity to elicit specific antibodies capable of blocking parasite transmission to mosquitoes and therefore have been identified as potential TB vaccine candidates , 11. Othndidates . Among tclinical , 14, 15 clinical \u201319.Pvs48/45 is a cysteine-rich conserved protein expressed on the gametocyte surface of several Plasmodium species, and is involved in parasite fertilization analyses. These antibodies also reduce parasite transmission to mosquitoes in ex-vivo direct DMFA and Guatemala (GUA). Additionally, TB activity of anti-CHO-rPvs48/45 specific IgG was determined by ex-vivo DMFA.lization . A full-t manner . Additioect DMFA . Despiteproteins , 22, andP. vivax and P. falciparum are endemic at the Centro Internacional de Vacunas in June 2017 (code CECIV 1506-2017) as well as by the Ethics Committee of the GUA Ministry of Health (CNES-dq-005-2015). Additional approval was obtained in GUA from local community leaders before data collection. Written informed consent (IC) was obtained from each volunteer at enrollment. Minors with ages between 7-18 years signed an informed assent (IA) form, and parents or legal guardians gave the corresponding consent. Donors of P. vivax or P. falciparum infections as determined microscopically and confirmed by qPCR. Whole blood samples (5-15mL) were collected in heparin vacutainer tubes by arm venipuncture, and plasma immediately separated by centrifugation. In GUA, 54 patients with ages between 1-70 years of age (38.9% men) with P. vivax infections diagnosed by thick blood smears and confirmed by qPCR, were recruited by active case surveillance, and blood samples were collected as described above. Plasma samples were kept and stored at -80\u00b0C until used for serological characterization and for specific CHO-rPvs48/45 antibody affinity purification.In COL, 227 patients, men (56.8%) and women between 6-84 years of age, were recruited by passive surveillance and included in the study. Subjects were randomly selected among a larger group of patients harboring rPvs48/45 gene was expressed in E. coli, as described before with sufficient viable cell culture biomass of suspension adapted CHO-Express\u2122 cells . All production cultures (post-transfection) were performed in serum-free, animal protein-free medium (low protein content). A non-malaria related protein, expressed in parallel during the production of the CHO-rPvs48/45 protein, was used as a control production to ensure cell culture and methods accuracy. Each production vessel was verified for critical parameters such as cell culture dynamics and recombinant protein production on samples from day 7 and/or day 14, to confirm the appropriate protein cultures. A total of 150 mg of this antigen was produced after a single purification step on IMAC-FPLC. Two buffer exchanges were performed: one to optimize binding of the protein construct to the IMAC column, and the other one, after elution, to remove excess imidazole. SDS-PAGE analysis of both E. coli- and CHO-rPvs48/45 proteins under both reducing (0.05 mol/L dithiothreitol) and non-reducing conditions together with immunoblot and mass spectrometry (LC-MS/MS) confirmed the protein identity. Immunoblot analysis was carried out using sera (1:200 dilution) of P. vivax semi-immune subjects, plasma from Aotus monkeys previously immunized with the E. coli-rPvs48/45 protein (1:200 dilution), and a E. coli-rPvs48/45 monoclonal antibody; normal human serum was used as control and LC/MS/MS analysis was performed using peptides generated by trypsin digestion. Peptides were separated and analyzed using a Qexactive-HFX coupled to U3000 RSLC (Thermofisher). Mass spectra were processed with MaxQuant (v1.6.10.43) using a database consisting of Uniprot entries of Cricetulus griseus , 250 classical contaminants and the sequence of the construction.The CHO-s\u2122 cells . BrieflyrPvs48/45 proteins\u2019 immunoreactivity, as described before , pH 7.4 at 4\u00b0C overnight. After plates were blocked with milk solution 5%, plasma samples diluted at 1:200 were added and incubated for 1 hour followed by incubation with alkaline phosphatase (1:1000) conjugated goat anti-human IgG antibody for 1 hour. Reactions were revealed with para-nitrophenyl phosphate substrate (p-NPP) (Sigma Aldrich) and read at 405 nm wavelength . Cut-off points for ELISA were calculated as three SD above the mean absorbance value at 405 nm of sera from healthy adult volunteers who had never been exposed to malaria (n=60). The results were also expressed as reactivity index (RI) defined as OD values of tested samples divided by the cut-off value. P-value < 0.05 was considered significant.ELISA was used to determine the two d before , 26. BriP. vivax CHO-rPvs48/45 antibodies with ELISA reactive index > 5.0, as described elsewhere , followed by anti-CHO-rPvs48/45-specific antibodies purification using an NHS-activated Sepharose column coupled with CHO-rPvs48/45 protein, as described previously. Affinity adsorption was performed using the purified total IgG, and elution fraction was neutralized by 1 mol/L Tris, pH 9.0. Specific IgG was then dialyzed against 1x PBS using an Amicon Ultra-4 Centrifugal Filter Unit (30 kDa membrane EMD Millipore). The final protein concentration of specific IgG was measured by DS-11FX+ and adjusted to 0.5 mg/mL (rPvs48/45-specific antibodies (Elisa Units - EU) as described before of the CHO-rPvs48/45 recombinant protein competitor. The reaction was incubated for 30\u00a0min at RT and the reactivity of the antibody preparation was determined by ELISA as previously described displaying ELISA reactivity indices (RI) > 5.0 and four plasma sera from the same regions with RI between 2.0-3.0 were selected to determine antibody avidity. Polystyrene microplates were coated with 1 \u03bcg/mL of the CHO-rPvs48/45 protein in duplicates. After overnight incubation plates were washed and blocked with 100 \u03bcL of PBS with 0.5% Tween (PBS-T) per well, 5% skim milk for 2\u00a0h at room temperature (RT). Specific IgG at 10 \u03bcg/mL or plasma samples diluted at 1:200 in PBS-T 2.5% skim milk was added to the plates and incubated for 2h at RT. After washing, plates were incubated with different urea concentrations (from 0 to 7 mol/L) in duplicates for 15\u00a0min to determine antibody avidity. The reaction was revealed using an anti-human IgG alkaline phosphatase conjugate as described above. The urea concentration resulting in 50% of the original ELISA units (IC50) was calculated using linear regression and anti-IgG2 . Then a peroxidase-conjugated goat anti-mouse IgG antibody was added, and the reaction read at 450 nm.The lsewhere . BrieflyrPvs48/45 specific IgG antibodies at 10, 40, and 100 \u03bcg/mL was measured by a DMFA using P. vivax gametocyte-infected blood obtained from malaria patients, as previously described were subsequently reconstituted with a pool of heat-inactivated male AB+\u00a0sera obtained from healthy donors purchased from Sigma (H5667 Sigma-Aldrich Inc) or with test samples. A total of ~100\u00a0Anopheles\u00a0albimanus\u00a0mosquitoes previously subjected to overnight fasting were fed for 15-20 minutes/cage with this mixture. Mosquito midguts were stained with 2% mercurochrome on day 7 post-feeding, and the number of oocysts per mosquito midgut counted.The TB activity of 143 plasma samples (1:2 dilution), and affinity-purified CHO-escribed . Brieflyp-values <0.05 were considered significant. Antibody responses for both CHO-rPvs48/45 and E. coli- were compared by Fisher\u2019s exact test. Differences of RI between age groups were analyzed by Kruskal-Wallis, followed by Dunn\u2019s multiple comparison test. Correlation between %TRA of human sera and RI by Spearman test. Avidity (IC50) of P. vivax plasma samples and affinity-purified CHO-rPvs48/45 specific IgG were compared by Mann-Whitney tests , and ey tests .p-value for TRA was calculated using a zero-inflated negative binomial model as previously described (The percentage reduction in mean oocyst count/mosquitoes (TRA) was calculated using the following formula: [(Xc \u2212 Xa)/Xc)] \u00d7 100, where X is the arithmetic mean oocysts in control (c) and test (a) plasma or IgG. The 95% confidence interval and escribed .E. coli-rPvs48/45 gene without the signal peptide and GPI anchor was sub-cloned in the E. coli system as described elsewhere inserted to\u00a0avoid inclusion bodies formation (rPvs48/45 has a shorter thioredoxin fragment (42aa), and a theoretical mass of 51,766.22 of samples and in 32% (n=90) to the E. coli-rPvs48/45 product (p<0.001) . In COL plasmas (n=227) the prevalence of specific antibodies was 46.3% and 36.1% to the CHO and E. coli products, respectively. In contrast, in GUA plasmas (n=54) it was 24.1% and 14.8%, respectively, indicating significant regional differences for both proteins (CHO and E. coli p<0.001). Also, samples from Tierralta, (COL), where P. vivax is highly prevalent , presented an immunoreactivity of 58.8% and 34.3% against the CHO and E. coli proteins, respectively. In contrast, samples from Tumaco, where P. falciparum is more prevalent than P. vivax , ELISA showed 27.3% and 41.7%, respectively. Significant differences in prevalence among both proteins in samples from COL and GUA samples (p<0.001) was observed. In contrast, in Tumaco (COL) E. coli was better recognized than CHO (p<0.001) (E. coli protein (p<0.001). In GUA, people with > 2.0 RI were 8% (n=1) and 0% (n=0) to CHO and E. coli protein, respectively. Fisher tests indicated that plasma samples with RI > 2 were significantly more frequent in Colombia than in GUA (p=0.0042) to CHO protein. In contrast, there was no difference between both countries to E. coli protein. To determine the impact of age on the RI, in both COL and GUA, samples were stratified into three groups: 0-14 years/old n=41 (14.6%); 15-30 year/old n=118 (42%); and more than >30 years/old, n=122 (43.4%). The mean RI presented an age-dependent increasing trend (rPvs48/45 protein (p<0.05). Individuals >30 years/old presented a RI to CHO mean of 1.45 whereas to E. coli, the mean was 1.13. Significant differences (p<0.05) were observed in the RI values between children (<15 years/old) and adults (>30) when the E. coli - rPvs48/45 protein was used . Regarding TRA activity, 93 of the 143 (65.03%) plasma samples examined by DMFA displayed >80% TRA; 51samples (54.83%) were reactive to the CHO- and 29 (31.18%) reactive to E. coli-rPvs48/45 protein (p>0.28 and E. coli p>0.63).From the total plasma samples studied (n= 281), ELISA assays indicated the presence of specific antibodies to the full-length CHO-p<0.001) Table\u00a01.Pvs48/45 protein. A total of 40 mg/mL of total IgG was obtained after protein G column purification and 500ug/mL of anti-CHO-rPvs48/45-specific antibodies after Sepharose column purification with specific antibody titers of 62.163 EU (E.\u00a0coli-rPvs48/45 proteins (n=22) using the CHO r2.163 EU . SpecifiE. coli-rPvs48/45 specific IgG and sera samples from malaria-endemic regions were incubated with different concentrations of urea. All data sets fitted into the linear regression model (R2>0.94), and the anti-rPvs48/45 specific IgG presented a similar IC50 (4.1 and 4.5 mol/L respectively) with plasma samples with RI between 2-4 and a slightly higher avidity with the HPV-3031 (5.5 mol/L), P-137 (5.6 mol/L), and P-72 (4.9 mol/L) of plasma samples with RI>5.0, except with the sample MPV-139 (3.9 mol/L) in studies conducted in several countries in Africa where this species is almost exclusively transmitted and malaria transmission intensity is significantly higher than in Latin America than in GUA in the year 2017 . In this regard, in COL, immunoreactivity was higher and more prevalent in areas with the relatively higher transmission, e.g., in Tierralta , Department of Cordoba the conformational differences between the 3D structures of the two proteins and, thus, recognition of different epitopes, 2) by the additional thioredoxin fragment added to the E. coli protein to improve its expression, 3) by potential glycosylation in the CHO protein.Although both proteins were highly immunoreactive, CHO was significantly better recognized by all age groups, except in Tumaco (COL) where Pvs48/45and nor the additional fragment are recognized by control sera.None of the constructs were recognized by sera from na\u00efve individuals indicating that neither full-length P. falciparum is significantly higher that P. vivax, yet, the response to rPvs48/45 was similar than in Tierralta (COL) and GUA suggesting a parasite cross-reactivity between the orthologous proteins in natural conditions. To better understand the sero-epidemiology of the rPvs48/45, we are currently studying malaria-endemic regions with different P. vivax/P. falciparum proportions.Another intriguing observation is that in Tumaco (COL) the prevalence of rPvs48/45 antibodies which confirmed the important role of this parasite antigen in TB immunity under natural conditions and a low (~25kDa) molecular weight in the pattern , 41. HerrPvs48/45 activity is independent of the classical complement; this issue requires further analyses.Although several IgG subclasses may contribute to the overall TB activity, the high prevalence of IgG2 suggests that anti-Pfs48/45 vaccine candidate at the Centro Internacional de Vacunas (code CECIV 1506-2017) Ethics Committee of the GUA Ministry of Health (CNES-dq-005-2015). Written informed consent to participate in this study was provided by the participants\u2019 legal guardian/next of kin.rPvs48/45 analysis: AK and GC. Contributed reagents/materials/analysis tools: MA-H, NC, and SH. Wrote the paper: MA-H, NC, GC, CL, and AK. All authors contributed to the article and approved the submitted version.Conceived and designed the experiments: MA-H and SH. Performed the experiments: NC, CE, KM, ES, AC, JR, and AM. Analyzed the data: MA-H, SH, GC, and CL. LC/MS/MS CHO-NIH/NIAID 1R01AI121237-01 sponsored this study and in part by the Intramural Research Program of NIAID, NIH.https://www.frontiersin.org/articles/10.3389/fimmu.2021.634738/full#supplementary-materialThe Supplementary Material for this article can be found online at: Click here for additional data file.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Pickering S, Batra R, Merrick B, et al. Comparative performance of SARS-CoV-2 lateral flow antigen tests and association with detection of infectious virus in clinical specimens: a single-centre laboratory evaluation study. Lancet Microbe 2021; published online June 30. https://doi.org/10.1016/ S2666-5247(21)00143-9\u2014This Article should have been published under a CC BY Open Access license. This correction has been made as of Aug 3, 2021."} +{"text": "Mutant alleles of the Rht-B1 and Rht-D1 (Reduced height) genes are widely used in bread wheat breeding for the development of intensive-type cultivars. These genes and their f lanking regions have been sequenced and the point mutations leading to the nonsense codons and various insertions associated with a change in plant height have been described. DNA-markers based on the allele-specif ic PCR have been developed to identify single-nucleotide changes. However, the use of such technique imposes stringent PCR conditions, and the resulting data are not always unambiguous. An alternative can be found in the CAPS technology: it detects differences in sequences by digesting PCR products. In the absence of restrictases capable of digesting DNA at the point mutation site, restriction sites can be introduced into the primer sequence (derived CAPS). The aim of this study was to propose a system of CAPS-, dCAPS- and STS-markers for identifying alleles of the reduced height genes frequently used in breeding programs. Three CAPS have been developed to identify the Rht-B1b, Rht-D1b, Rht-B1p alleles, as well as two dCAPS for Rht-B1b, Rht-B1e. STS-markers for the insertion-containing alleles Rht-B1c, Rht-B1h and Rht-B1i-1 have been selected from publications. The proposed markers were tested during the genotyping of 11 bread wheat accessions from the VIR collection with the abovementioned mutant alleles and the wild-type Rht-B1a and Rht-D1a. The presence of nonsense mutations was also conf irmed by the resultsof allele-specif ic PCR. This marker system, along with the existing ones, can be used to identify dwarf ing alleles ofthe Rht-B1 and Rht-D1 genes in bread wheat for genetic screening of accessions from ex situ collections and/or formarker-assisted selection. The development of intensive-type short-stemmed wheat cultivarsis considered one of the key success factors in breadwheat breeding, primarily in implementing the Green Revolutioninitiative in the world\u2019s developing countries . The decrease in plant height notonly entailed higher resistance to lodging, with its favorableeffect on the efficiency of mechanized harvesting, but alsoincreased the number of grains per ear and their number per1 m2, which aggregately led to higher yields .At least 25 genes controlling plant height in bread wheat(Triticum aestivum L.) and related species were described: theyare known as Reduced height \u2013 Rht1\u2013Rht25. All these genesare in one way or another associated with the growth hormonegibberellin . Some of them,the so-called GA-sensitive genes Rht4\u2013Rht9, Rht12\u2013Rht20 andRht25, are apparently involved in the synthesis or degradationof gibberellic acid (GA). Other genes, GA-insensitive ones,such as Rht-A1, Rht-B1, and Rht-D1, determine the responseto this acid. For some genes , thenature of their response has not yet been clarified .The most widespread among GA-sensitive genes is Rht8,transferred in the early 20th century, together with the closelylinked photoperiod insensitivity allele Ppd-D1a of the Ppdgene (response to photoperiod ), from the Japanese cultivarAkakomugi first to Italian and later to many East and SouthEuropean cultivars . Thisgene does not exert any significant reducing effect on thecoleoptile length and, as a consequence, makes it possibleto sow seeds to a greater depth, which plays a decisive rolein maintaining the viability of seedlings under water deficitsor high temperatures .GA-insensitive genes were studied in more detail; they arelocated on the short arms of chromosomes of homeologousgroup 4 . Dominantalleles of these genes (wild-type) encode DELLA proteins,belonging to the family of GRAS proteins (transcription regulators);at their C-terminus, there is a conservative domainthat can bind to other transcription factors and thereby blocktheir function. That is why large amounts of DELLA proteinsin cells decelerate plant growth. There is a DELLA domain atthe variable N-terminus: it is capable of forming the GA\u2013GID1complex . Thiscomplex undergoes polyubiquitination and degradation inducedby proteasomes. Accordingly, a decrease in the amountof DELLA proteins in cells in the presence of GA reduces theirnegative effect on plant growth .A fairly large number of recessive and semi-dominant mutantalleles altering the stem length in different ways havebeen described for the Rht-B1 and Rht-D1 genes. These alleleshave been sequenced; the most thoroughly studied sequencesare presented by us in Supplementary material 11. The allelesRht- B1b (=Rht1), Rht-B1e ,Rht-B1p (=Rht17) and Rht-D1b (=Rht2) were shown to beassociated with single-nucleotide substitutions that lead tothe formation of premature stop codons . The phenotypic effectof such nonsense mutations varies from moderate to strong .http://vavilov.elpub.ru/jour/manager/files/Suppl_Porotnikov_Engl.pdfSupplementary materials 1 and 2 are available in the online version of the paper:The alleles Rht-B1h and Rht-B1i-1 have large (over 100 bp)insertions in the 5\u2032 flanking region, while Rht-B1c (=Rht3)is characterized by the presence of an insertion in the 5\u2032 untranslatedregion identical to that in Rht-B1h and, at the sametime, the presence of the Veju retrotransposon in the codingregion . Such insertions can lead to the formationof nondegradable proteins, so the growth of mutant plants isconstitutively repressed,more significantly than in the caseof nonsense mutations in the N-terminal coding region . For example, the Rht-B1c allelereduces plant height approximately by 60 % . However, insertions can not onlyreduce but also increase the height of plants as, for example, in the case ofRht-B1i-1 . Besides, the alleles of \u201cstrongdwarfing\u201d, Rht-D1c (Rht10) and Rht-D1d (Rht Ai-bian 1a),reducing the height by 60\u201370 %, were identified in the Rht-D1gene; they turned out to be multiple copies of the mutant alleleRht-D1b . There are also other known allelesof the Rht-B1h\u2013o and Rht-D1e\u2013j genes, associated witheither nucleotide changes (missense mutations) or indels. Theyare identified in a large number of Chinese cultivars using theEcoTILLING method; however, their phenotypic effect hasnot yet been described. Mutant alleles of the Rht-A1 genewere also identified for the first time in Chinese cultivars .The alleles most frequently used in breeding programs areRht-B1b and Rht-D1b. Their source was the Japanese cultivarNorin 10. At the end of the 20th century, more than 70 % ofthe world\u2019s bread wheat cultivars contained these alleles . Later, however, it was shown thattheir occurrence depended on the region of the world. Rht-B1b was detected in 36.2 % of bread wheat cultivars from China,and Rht-D1b in 53.4 % . Meanwhile,the genotyping of 247 cultivars from the United States andCanada helped to identify these alleles in more than 90 %of them . Rht-D1b predominates in thegenotypes of European cultivars, while its occurrence in thecultivars registered after 1990 is 49 % .Widespread in Russia are cultivars with the Rht-B1e allele,obtained by mutagenesis in cv. Bezostaya 1; the mutantform is Krasnodarsky Karlik 1 . At present, semi-dwarf cultivars , homozygous for Rht-B1e alleles,are cultivated both in Russia and the ex-USSR countries onan area of more than 4 million hectares .The allele Rht-B1p is also promising for breeding: a stopcodon emerges in its DELLA domain due to the substitutionof cytosine for thymine at position 178 from the start codon.This mutation causes an up to 30 cm decrease in the heightof bread wheat plants, especially as far as the lower internodeis concerned, but it does not reduce the length of the ear .The sequencing of Rht-B1 and Rht-D1 alleles in variousbread wheat cultivars have led to the development of molecularmarkers for their identification. For example, STS markerswere obtained to identify the insertion-containing allelesRht-B1c, Rht-B1h and Rht-B1i-1 . Markers based on allele-specific PCR(AS-PCR), including real-time AS-PCR, are used to identifythe alleles Rht-B1b, Rht-B1e, Rht-B1p and Rht-D1b, carryingsingle-nucleotide substitutions .The widespread alleles Rht-B1b and Rht-D1b as well asthose of the Rht24 gene are identified on the basis of competitiveallele-specific PCR (KASP-markers), offering a possibilityto evaluate large numbers of bread wheat accessions atlow time costs .It should also be mentioned that AS-PCR results strongly dependon the reaction conditions, require several replicationsof the analysis, and call for strict observance of the author\u2019sprotocol, which is not always possible. The KASP analysis,in its turn, requires sophisticated equipment and expensivereagents, which are often unaffordable to small practice-orientedlaboratories.The use of CAPS (cleaved amplified polymorphic sequence)markers can be an alternative to AS-PCR: they are based onthe presence of a restriction site in the region with a singlenucleotidemutation (the site is absent in the wild type) or,contrariwise, on the disappearance of the site typical of thewild type in the mutant version . If restrictionsites are absent at the locations of the analyzed mutations,they can be produced purposefully through designing modifiedprimers, i. e., by the derived CAPS method, or dCAPS .Unlike AS-PCR, the CAPS and dCAPS marker techniquesare effortlessly reproducible and do not require stringentPCR conditions, while the results of such analysis are easilyinterpreted in agarose gels. It is possible to generate markersusing the basic PCR equipment. Previously, such markers weredeveloped for the Rht24 dwarfing gene .The objective of the present study was to develop CAPS anddCAPS markers for the analysis of single-nucleotide changesin Rht-B1 and Rht-D1, test STS markers for identification ofinsertions in these genes and, as a result, propose a markersystem for identifying the alleles most frequently used inbread wheat breeding.Plant material. Eleven bread wheat accessions from the VIRcollection with known alleles of the Rht-B1 and Rht- D1 dwarfinggenes (Table 1) served as the material for this study. Thecultivars Chinese Spring and Hongdongmai with wild-typealleles Rht-B1a and Rht-D1a were used as controls. Eachof the studied accessions was represented in the genotypingprocess by two or three individual plants as well as by bulkDNA sample, which was isolated from a total of 10\u201320 genotypes(seedlings).DNA extraction. DNA was extracted from 10-day-oldseedlings using a modified CTAB extraction technique .Sequences alignment. The sequences of different allelesof the Rht-B1 and Rht-D1 genes were aligned using MEGA X(https://www.megasoftware.net/), Unipro UGENE , and BioEdit Sequence Alignment Editor. Restriction sites were searched for using theGenScript Restriction Enzyme Map Analysis Tools .Primers development. Primers for the nested PCR andCAPS analysis were developed with the Primer3Plus software. Primer quality was monitored using OligoAnalyzerTool, a web resource from Integrated DNA Technologies, Inc.. Primers for dCAPSmarkers were generated using the dCAPS Finder 2.0 software. The primers developed in the courseof this study and those supplied from published sources arepresented in Tables 2 and 3, and their locations are shown inFig. 1, a, b.PCR procedure: a) nested PCR. The nested PCR methodwas applied to enhance the specificity of the dCAPS analysis:the first PCR was performed with primers BF/VIR.B1R flankingthe region of point mutations in the Rht-B1 gene; afterthat, the resulting PCR product was used as a template for thesecond PCR with dCAPS and CAPS(B1epF/B1pR) primers. The first round of nested PCR wascarried out in 25 \u03bcl of the reaction mixture containing 40 ngof total wheat DNA; 1\u00d7 reaction buffer; 1.5 mM of MgCl2;0.6 mM of each dNTP; 0.25 \u03bcM of both forward and reverseprimer, and 1 unit of Taq DNA polymerase . For higher specificity, the PCR programcontained the Touchdown function: the initial annealing temperaturewas 4 degrees higher than the design temperature anddecreased by 0.5 degrees per cycle for 8 cycles (see Table 3).Samples of the resulting amplification products (2 \u03bcl ofeach) were transferred into clean tubes, diluted 50 times withwater, and used as a template in the second stage of PCR.Another 10 \u03bcL of each PCR product was taken to control the success of PCR by agarose gel electrophoresis .The remainder (approximately 12 \u03bcl) was treated with therestriction enzyme BstV1I to generate the CAPS marker for theRht- B1b allele.The second round of nested PCR was performed in 20 \u03bclof the reaction mixture containing 4 \u03bcl of the template; 1\u00d7reaction buffer; 2.5 mM of MgCl2; 0.3 mM of each dNTP;0.25 \u03bcM of both forward and reverse primer, and 1 unit of TaqDNA polymerase . The programs for each pair of primersare also presented in Table 3. Approximately 12 \u03bcl of theamplification mixture were taken for restriction analysis, andthe remainder was used for PCR control by electrophoresis;b) standard PCR. In the cases of CAPS markers for theRht-D1b allele and the markers detecting retrotransposonin the gene\u2019s coding region and insertions in the 5\u2032 flankingregion, PCR was performed under standard conditions. Thereaction mixture (20 \u03bcl) contained 40 ng of DNA; 1\u00d7 reactionbuffer; 2.5 mM of MgCl2; 0.3 mM of each dNTP; 0.25 \u03bcMof each primer, and 1 unit of Taq DNA polymerase ;the programs are presented in Tables 2 and 3;\u0441) allele-specific PCR. The conditions and the programs forAS-PCR corresponded to those recommended by the authorsof the primers .Restriction analysis. PCR products were treated with restrictionenzymes produced by SibEnzyme, using the manufacturer\u2019sprotocol (http://russia.sibenzyme.com).Fragment separation was done in horizontal agarosegels in the 1\u00d7 TBE buffer under the voltage of 5 V/cm. Thegels were stained with ethidium bromide and visualized inUV light.For the development of CAPS and dCAPS markers, thesequences from the NSBI databases were analyzed (https://www.ncbi.nlm.nih.gov/) for the following alleles of the dwarfinggenes: Rht-B1b, Rht-B1e, Rht-B1p and Rht-D1b. Also,the sequences of the wild-type alleles Rht-A1a, Rht-B1a andRht-D1a were retrieved as controls. The Genbank accessionnumbers for used sequences are given in Supplementary material1. Sequence alignment confirmed the presence of nonsensemutations in these allelic forms, which made it possible to startthe development of CAPS and dCAPS markers .A search was made for each nonsense mutation to identifyrestriction sites that would distinguish the target allele fromall others, including wild-type ones. The BstV1I (GCAGC)restriction enzyme, unable to digest the mutant GTAGC site,was selected for Rht-B1b. Similarly, BstHHI (GCGC) becamethe restriction enzyme for the Rht-B1p detection (mutantsite GCGT). On the contrary, the BstSFI restriction enzyme(CTRYAG) exclusively digested the mutant site (CTGTAG)contained in Rht-D1b. Thus, it was possible to develop suchCAPS markers as CB1b/BstV1I, CB1p/BstHHI and CD1b/BstSFI to identify the alleles Rht-B1b, Rht-B1p and Rht-D1b,respectively.We failed to identify restriction sites at the location of thenonsense mutation in the Rht-B1e allele. Hence, the dCAPSmarker dCB1e/HinfI was developed for it: the sequence of thereverse primer was modified so that the analyzed nucleotide,together with the 3\u2032 end of the primer, formed a GATTC restrictionsite, providing an opportunity to distinguish this mutationfrom all other alleles by means of the HinfI restriction. ThedCAPS marker dCB1b/Acc36I was additionally constructedto identify Rht-B1b .When performing PCR under standard conditions, with thegenomic DNA of bread wheat used as a template, we wereunable to obtain specific fragments for the dCAPS markers andthe CAPS marker CB1p/BstHHI (the data are not presented).We therefore applied the nested PCR method: the amplificationproducts of the BF/VIR.B1R primers, flanking the regionof localization of all analyzed point mutations in the Rht-B1gene, were used as a template for the second round .The developed markers were tested on a set of bread wheataccessions with known alleles of the dwarfing genes, and all of them demonstrated high efficiency in differentiating thewild-type Rht-B1a, Rht-D1a and mutant versions Rht-B1b,Rht-B1e, Rht-B1p and Rht-D1b .Concurrently, allele-specific primers retrieved from publishedsources were used to identify nonsense mutations inRht-B1b, Rht-B1e, Rht-B1p and Rht-D1b compared to thewild type . For this purpose, two pairs of primers were usedfor identification of each mutation: one of them detected themutant version, while the other spotted the wild type andall other alleles. It was shown for Rht-B1b, Rht-B1e andRht-D1b that the results of allele-specific PCR on the wholeagreed with the data of CAPS and dCAPS analyses. However,identification of the wild-type Rht-B1a and Rht-D1a alleleswith the primers BF/WR and DF2/WR2, respectively , involved certain difficulties: poor reproducibilityof results, and generation of weakly expressed fragments informs with Rht-B1b and/or Rht-D1b . In the case of Rht-B1p, allele-specific PCR under theconditions of this study turned out to be ineffective: afteramplification with the Rht-B1p-F/R1 primers , a specific product was generated both in the formswith mutant alleles and in those with the wild-type ones .The study also employed five pairs of STS primers as a tool for identifyingmutations associated with the presence of a retrotransposonin the coding region (Rht-B1c) as well as with insertionsin the promoter region (Rht-B1i-1) and the 5\u2032 flanking region(Rht-B1h). The locations of these insertions are marked in thescheme of the Rht-B1 gene; it also shows primers for theirdetection .Two pairs of primers were used for the Rht-B1i-1 allele : one of them (B1i-MF1/MR1) in the presence ofan insertion produced a specific 330 bp fragment, while theother (B1i-MF2/MR2) amplified fragments of different sizesin genotypes with or without an insertion . Similarly, to detect the Rht-B1h allele, the Rht-B1h.F/R1 primers were used, resulting in a specific productof 247 bp, as well as the Rht-B1h.F/R2 primers, generatingfragments of different sizes . Since Rht-B1h has a common insertion in the5\u2032 flanking region with Rht-B1c, the Rht-B1c-F1/R1 primer,specific for the retrotransposon sequence, was also used fortheir differentiation . Additional evidence of the presence of a retrotransposonmay be found in the fact that no PCR productsare generated in genotypes with this insertion during the firstround of nested PCR with the BF/VIR.B1R primers: it can beexplained by a big distance between the primers .Our testing of STS markers showed a complete concordancebetween the presence of their diagnostic fragments and thecomposition of alleles present in the studied genotypes . The accessions Atlas 66 and Zheng 9023 containingRht-B1h yielded amplification products pointing to the presenceof an insertion in the 5\u2032 flanking region. In the accession Triumph carrying the Rht-B1i-1 allele, which increasesplant height, an insertion in the promoter region was detectedusing molecular markers, and in Tom Thumb (Rht-B1c), aretrotransposon in the coding sequence and an insertion inthe 5\u2032 flanking region were found. It should be mentionedthat when a retrotransposon was identified using the Rht-B1c-F1/ R1 primers, in addition to the formation of a fragment ofthe expected size, the emergence of nonspecific products ofa larger size was observed in Tom Thumb (Rht-B1c) and inall other genotypes .Assessing the system of the proposed molecular markersin its entirety, it should be kept in mind that it can be used togenerate a marker profile for each of the studied alleles of theRht-B1 and Rht-D1 genes, i. e., to get an unambiguous answerwhether one of the abovementioned alleles of the Rht-B1 andRht-D1 dwarfing genes is present in one or another genotype.Marker profiles for the alleles are presented in Table 4.As a result of this study, a system of molecular markers wasproposed for the Rht-B1 and Rht-D1 dwarfing genes to identifythe alleles most often used in bread wheat breeding. Thesystem is based on the developed CAPS and dCAPS markersof nonsense mutations in these genes, which were previouslydetected by allele-specific PCR . Five STS markersretrieved from published sources were used to identify insertions.The CAPS and dCAPS markers were tested during the genotypingof bread wheat accessions from the VIR collection,containing the mutant Rht-B1b, Rht-B1c, Rht-B1e, Rht-B1h,Rht-B1i-1, Rht-B1p and Rht-D1b alleles as well as those ofthe wild-type. The tests showed complete concordance ofthe obtained results with the expected ones. The presenceof Rht- B1b, Rht-B1e, Rht-B1p and Rht-D1b was also confirmedby allele-specific PCR with the primers widely usedin research and breeding programs .The main advantage of our molecular marker system liesin good reproducibility of results and their unambiguous interpretation.The CASP/dCAPS analysis faces no problemswith controlling the PCR reaction success, because amplificationproducts are formed in all genotypes, and differencesbetween alleles are pinpointed after treatment with restrictionenzymes. Besides, notwithstanding the high cost of restrictionenzymes, CASP/dCAPS analysis is less expensive, sincethere is no need to perform two independent PCRs in severalreplications to detect each allele. The procedure is conductedemploying standard PCR equipment and using agarose gel electrophoresis, so it can be carried out by small practiceorientedlaboratories. When any new point mutations in theRht-B1 and Rht-D1 dwarfing genes become known, a similarapproach to the development of CAPS/dCAPS markers canbe applied to identify them.The authors declare no conflict of interest.Antonova O.Yu., Klimenko N.S., Rybakov D.A., Fomina N.A., ZheltovaV.V., Novikova L.Yu., Gavrilenko T.A. SSR analysis of modernrussian potato varieties using DNA samples of nomenclatural standards.Biotekhnologiya i Selektsiya Rasteniy = Plant Biotechnologyand Breeding. 2020;3(4):77-96. DOI 10.30901/2658-6266-2020-4- o2. (in Russian)Bazhenov M.S., Divashuk M.G., Amagai Y., Watanabe N., Karlov G.I.Isolation of the dwarfing Rht-B1p (Rht17) gene from wheat and thedevelopment of an allele-specific PCR marker. Mol. Breed. 2015;35(11):1-8. DOI 10.1007/s11032-015-0407-1.Bazhenov M.S., Nazarova L.A., Chernook A.G., Divashuk M.G. Improvedmarker for the Rht-B1p dwarfing allele in wheat. In: CurrentChallenges in Plant Genetics, Genomics, Bioinformatics, andBiotechnology: Proc. of the Fifth International Scientific ConferencePlantGen2019 June 24\u201329, 2019. Novosibirsk, Russia. Novosibirsk:ICG SB RAS. 2019;190-192. DOI 10.18699/ICG-PlantGen2019-61Borojevic K., Borojevic Ks. The transfer and history of \u201creduced heightgenes\u201d (Rht) in wheat from Japan to Europe. J. Hered. 2005;96(4):455-459. DOI 10.1093/jhered/esi060.B\u00f6rner A., Plaschke J., Korzun V., Worland A.J. The relationships betweenthe dwarfing genes of wheat and rye. Euphytica. 1996;89(1):69-75. DOI 10.1007/BF00015721.Divashuk M.G., Bespalova L.A., Vasilyev A.V., Fesenko I.A., PuzyrnayaO.Y., Karlov G.I. Reduced height genes and their importance inwinter wheat cultivars grown in southern Russia. Euphytica. 2013;190(1):137-144. DOI 10.1007/s10681-012-0789-7.Divashuk M.G., Vasilyev A.V., Bespalova L.A., Karlov G.I. Identity ofthe Rht-11 and Rht-B1e reduced plant height genes. Russ. J. Genet.2012;48(7):761-763. DOI 10.1134/S1022795412050055Ellis M.H., Rebetzke G.J., Chandler P., Bonnett D., Spielmeyer W.,Richards R.A. The effect of different height reducing genes on theearly growth of wheat. Funct. Plant Biol. 2004;31(6):583-589. DOI10.1071/FP03207Ellis M.H., Spielmeyer W., Gale K., Rebetzke G., Richards R. \u201cPerfect\u201dmarkers for the Rht-B1b and Rht-D1b dwarfing genes inwheat. Theor.Appl. Genet. 2002;105(6-7):1038-1042. DOI 10.1007/s00122-002-1048-4.Evans L.T. Feeding the Ten Billion: Plants and Population Growth.Cambridge: Cambridge University Press, 1998.Flintham J.E., Gale M.D. The Tom Thumb dwarfing gene Rht3 inwheat. Theor. Appl. Genet. 1983;66(3-4):249-256. DOI 10.1007/BF00251155.Gale M.D., Marshall G.A. The chromosomal location of Gai 1 andRht 1, genes for gibberellin insensitivity and semi-dwarfism, in aderivative of Norin 10 wheat. Heredity. 1976;37(2):283-289. DOI10.1038/hdy.1976.88Gale M.D., Youssefian S., Russell G.E. Dwarfing genes in wheat. In:Russel G.E. (Ed.). Progress in Plant Breeding. London: Butterworths-Heinemann, 1985;1-35.Grover G., Sharma A., Gill H.S., Srivastava P., Bains N.S. Rht8 geneas an alternate dwarfing gene in elite Indian spring wheat cultivars.PLoS One. 2018;13(6):e0199330. DOI 10.1371/journal.pone.0199330.Guedira M., Brown-Guedira G., Van Sanford D., Sneller C., Souza E.,Marshall D. Distribution of Rht genes in modern and historic winterwheat cultivars from the Eastern and Central USA. Crop Sci. 2010;50(5):1811-1822. DOI 10.2135/cropsci2009.10.0626Hall T. BioEdit: a user-friendly biological sequence alignment editorand analysis program for Windows 95/98/NT. Nucleic Acids Symp.Ser. 1999;41:95-98.Hedden P. The genes of the green revolution. Trends Genet. 2003;19(1):5-9. DOI 10.1016/S0168-9525(02)00009-4.Korzun V., R\u00f6der M.S., Ganal M.W., Worland A.J., Law C.N. Geneticanalysis of the dwarfing gene (Rht8) in wheat. Part I. Molecularmapping of Rht8 on the short arm of chromosome 2D of bread wheat(Triticum aestivum L.). Theor. Appl. Genet. 1998;96(8):1104-1109.DOI 10.1007/s001220050845.Kurkiev K.U., Tyryshkin L.G., Kolesova M.A., Kurkiev U.K. Identificationof Rht2 and Rht8 genes for semidwarfness in hexaploidtriticale with use of DNA markers. Vavilovskii Zhurnal Genetikii Selektsii = Vavilov Journal of Genetics and Breeding. 2008;12(3):372-377. (in Russian)Li A., Yang W., Guo X., Liu D., Sun J., Zhang A. Isolation of a gibberellin-insensitive dwarfing gene, Rht-B1e, and development ofan allele-specific PCR marker. Mol. Breed. 2012;30(3):1443-1451.DOI 10.1007/s11032-012-9730-y.Li A., Yang W., Lou X., Liu D., Sun J., Guo X., Wang J., Li Y., Zhan K.,Ling H.Q., Zhang A. Novel natural allelic variations at the Rht-1loci in wheat. J. Integr. Plant Biol. 2013;55(11):1026-1037. DOI10.1111/jipb.12103Lou X., Li X., Li A., Pu M., Shoaib M., Liu D., Sun J., Zhang A.,Yang W. The 160 bp insertion in the promoter of Rht-B1i plays avital role in increasing wheat height. Front. Plant Sci. 2016;7(307):1-13. DOI 10.3389/fpls.2016.00307Lukyanenko P.P., Zhogin A.F. Use of induced dwarf mutants in winterwheat breeding. Selektsiya i Semenovodstvo = Breeding and SeedIndustry. 1974;1:13-17. (in Russian)McIntosh R.A., Dub\u0441ovsky J., Rogers W.J., Morris C., Appels R.,Xia X.C. Catalogue of gene symbols for wheat: 2015\u20132016 supplement.2016. Available at: https://shigen.nig.ac.jp/wheat/komugi/genes/macgene/supplement2015.pdf.McIntosh R.A., Dub\u0441ovsky J., Rogers W.J., Xia X.C., Raupp W.J. Catalogueof gene symbols for wheat: 2018 supplement. 2018. Availableat: https://wheat.pw.usda.gov/GG3/sites/default/files/Catalogue%20of %20Gene %20Symbols %20for %20Wheat %20- %20supplement2018-2019.pdf.McIntosh R.A., Yamazaki Y., Dub\u0441ovsky J., Rogers J., Morris C., AppelsR., Xia X.C. Catalogue of gene symbols for wheat. 2013. Availableat: https://shigen.nig.ac.jp/wheat/komugi/genes/download.jsp.Neff M.M., Neff J.D., Chory J., Pepper A.E. dCAPS, a simple techniquefor the genetic analysis of single nucleotide polymorphisms:experimental applications in Arabidopsis thaliana genetics. Plant J.1998;14(3):387-392. DOI 10.1046/j.1365-313X.1998.00124.x.Neff M.M., Turk E., Kalishman M. Web-based primer design for singlenucleotide polymorphism analysis. Trends Genet. 2002;18(12):613-615. DOI 10.1016/s0168-9525(02)02820-2.Okonechnikov K., Golosova O., Fursov M. Unipro UGENE: a unifiedbioinformatics toolkit. Bioinformatics. 2012;28(8):1166-1167. DOI10.1093/bioinformatics/bts091.Pearce S., Saville R., Vaughan S.P., Chandler P.M., Wilhelm E.P.,Sparks C.A., Al-Kaff N., Korolev A., Boulton M.I., Phillips A.L.,Hedden P., Nicholson P., Thomas S.G. Molecular characterizationof Rht-1 dwarfing genes in hexaploid wheat. Plant Physiol. 2011;157(4):1820-1831. DOI 10.1104/pp.111.183657Peng J., Richards D.E., Hartley N.M., Murphy G.P., Devos K.M.,Flintham J.E., Beales J., Fish L.J., Worland A.J., Pelica F., SadhakarD., Christou P., Snape J.W., Gale M.D., Harberd N.P. \u2018Greenrevolution\u2019 genes encode mutant gibberellin response modulators.Nature. 1999;400(6741):256-261. DOI 10.1038/22307.Pestsova E., Korzun V., B\u00f6rner A. Validation and utilisation of Rhtdwarfing gene specific. Cereal Res. Commun. 2008;36(2):235-246.DOI 10.1556/CRC.36.2008.2.4Rabinovich S.V. The breeding value of the Krasnodarskiy karlik 1mutant. In: Chemical Mutagenesis in the Creation of Varietieswith New Properties. Moscow: Nauka Publ., 1986;88-92. (in Russian)Rasheed A., Wen W., Gao F., Zhai S., Jin H., Liu J., Guo Q., Zhang Y.,Dreisigacker S., Xia X., He Z. Development and validation of KASP assays for genes underpinning key economic traits in breadwheat. Theor. Appl. Genet. 2016;129(10):1843-1860. DOI 10.1007/s00122-016-2743-x.Shavrukov Y.N. CAPS markers in plant biology. Russ. J. Genet. Appl.Res. 2016;6(3):279-287. DOI 10.1134/S2079059716030114.Sukhikh I.S., Vavilova V.Y., Blinov A.G., Goncharov N.P. Diversityand phenotypical effect of the allele variants of dwarfing Rhtgenes in wheat. Russ. J. Genet. 2021;57(2):127-138. DOI 10.1134/S1022795421020101Thomas S.G. Novel Rht-1 dwarfing genes: tools for wheat breedingand dissecting the function of DELLA proteins. J. Exp. Bot. 2017;68(3):354-358. DOI 10.1093/jxb/erw509.Tian X., Wen W., Xie L., Fu L., Xu D., Fu C., Wang D., Chen X.,Xia X., Chen Q., He Z., Cao S. Molecular mapping of reduced plantheight gene Rht24 in bread wheat. Front. Plant Sci. 2017;8:1-9. DOI10.3389/fpls.2017.01379.Untergasser A., Nijveen H., Rao X., Bisseling T., Geurts R., LeunissenJ.A. Primer3Plus, an enhanced web interface to Primer3. NucleicAcids Res. 2007;35(2):71-74. DOI 10.1093/nar/gkm306.Wen W., Deng Q., Jia H., Wei L., Wei J., Wan H., Yang L., Cao W.,Ma Z. Sequence variations of the partially dominant DELLA geneRht-B1c in wheat and their functional impacts. J. Exp. Bot. 2013;64(11):3299-3312. DOI 10.1093/jxb/ert183.Wilhelm E.P., Mackay I.J., Saville R.J., Korolev A.V., Balfourier F.,Greenland A.J., Boulton M.I., Powell W. Haplotype dictionary forthe Rht-1 loci in wheat. Theor. Appl. Genet. 2013;126(7):1733-1747.DOI 10.1007/s00122-013-2088-7.Wu J., Kong X., Wan J., Liu X., Zhang X., Guo X., Zhou R., Zhao G.,Jing R., Fu X., Jia J. Dominant and pleiotropic effects of a GAIgene in wheat results from a lack of interaction between DELLAand GID1. Plant Physiol. 2011;157(4):2120-2130. DOI 10.1104/pp.111.185272.W\u00fcrschum T., Langer S.M., Longin C.F.H., Tucker M.R., Leiser W.L.A modern Green Revolution gene for reduced height in wheat.Plant J. 2017;92(5):892-903. DOI 10.1111/tpj.13726.Youssefian S., Kirby E.J.M., Gale M.D. Pleiotropic effects of theGA- insensitive Rht dwarfing genes in wheat. 2. Effects on leaf, stem,ear and floret growth. Field Crops Res. 1992;28(3):191-210. DOI10.1016/0378-4290(92)90040-G.Zhang X., Yang S., Zhou Y., He Z., Xia X. Distribution of the Rht-B1b,Rht-D1b and Rht8 reduced height genes in autumn-sown Chinesewheats detected by molecular markers. Euphytica. 2006;152(1):109-116. DOI 10.1007/s10681-006-9184-6."} +{"text": "Novel coronavirus 2019 (Covid19) caused by SARS-CoV2 can lead to significant morbidity and mortality. There is unclear association between Covid19 and bacteremia. Patient characteristics and outcomes are not well defined. This retrospective cohort study assessed this in patients with Covid19 and bacteremia.Patients with Covid-19 admitted to a tertiary care suburban academic medical center (UH) were assessed retrospectively by EMR chart review for co-morbidities, pre and in hospital factors, and outcomes as defined below. Bacteremias grouped into gram-negative or gram-positive with collation of each unique bacterial species (Table 1).Total 1398 patients with Covid19 hospitalized at UH during local peak of pandemic of whom 238 (17.02%) developed 264 bacteremias with gram-positive and gram-negative organisms . Relevant characteristics (Table 2) 53% with immunomodulator therapy (steroids/Tocilizumab), mean length of stay 21.04days (SEM \u00b1 1.67) with day SARS-CoV2 PCR positivity -1.15days from hospitalization (SEM \u00b1 0.49) and day initial bacteremia 6.38 (SEM \u00b1 0.77), 55.4% required ICU admission, with 89% ICU admissions requiring mechanical ventilation. Most common co-morbidity Hypertension 56.3% followed by Obesity (BMI >30) 45.8% and CAD/CHF 40.3%. Laboratory parameters (Table 3)significant for average difference (date bacteremia- date admission) for Procalcitonin 4.15ng/mL , CRP -0.934mg/dL , WBC 7.027 K/uL . These analyses excluded difference of 0 from hospital day 1 bacteremia. Average antibiotic number (1+ dose per antibiotic) 3.24 (SEM \u00b1 0.16) and total C difficile cases 3 (1.26%). Mortality rate34.45%.Relevant hospitalization characteristics, Covid19 and bacteremia co-infectionsRelevant laboratory parameters for patients with Covid19 and bacteremia co-infectionPatients with Covid19 and bacteremia had high mortality , 53% received immunomodulator therapy, possibly contributing to bacteremia development. With bacteremia increase in WBC and Procalcitonin, not CRP, noted. Most organisms CoNS, likely contaminants, gram positive bacteremias likely from indwelling lines. Only 3 C difficile infections identified. Trends noted in Procalcitonin rise, immunomodulator therapy, and low C difficile infection rates warrant further studies.Post-hospitalization OutcomesAll Authors: No reported disclosures"} +{"text": "Staphylococcus aureus (MRSA), but there are limited patient outcomes in the setting of cystic fibrosis pulmonary exacerbation (CFPE). The study objective was to compare the efficacy and safety of TLV to vancomycin (VAN) in CFPE.Telavancin (TLV) is an advanced generation lipoglycopeptide with activity against methicillin-resistant Retrospective cohort conducted from 1/2011-6/2020. Inclusion criteria were: i) age \u226516 years, ii) hospitalized for CFPE with documented signs/symptoms of infection, iii) confirmed or suspected MRSA lower respiratory tract infection, iv) receipt of \u226548 hours of TLV or VAN. The primary outcome was 30-day CFPE-related readmission: infection recurrence, clinical worsening on treatment, or ADE requiring readmission. Secondary outcomes included adverse drug events (ADE) on therapy: acute kidney injury (AKI), rash, thrombocytopenias, cardiac abnormalities. P< 0.001). The median (IQR) time to TLV initiation from admission was 1 (0.8-1.4) days. 13 patients were readmitted within 30-days due to CFPE; 8 (15)% TLV vs. 5 (10%) VAN . Reasons for 30-day CFPE: TLV: 7 infection recurrence, 1 clinical worsening; VAN: 2 clinical worsening, 2 infection recurrence, 1 treatment-related ADE. When accounting for confounders, TLV was not associated with 30-day CFPE-related readmission . Patients who received VAN more commonly experienced an ADE while hospitalized (18%), most notably AKI101 patients were included: 52 (52%) TLV, 49 (49%) VAN. The median (IQR) age was 22 (21-27) years, 50% were women, and 86% were Caucasian. The majority (84%) of patients had some federal health insurance; 19% had private health insurance. 93% of patients used a maintenance cystic fibrosis (CF) medication, and 35% had previous CF-therapy compliance concerns. 62% had a previous positive culture for MRSA; 22 (43%) TLV patients had documented MRSA infection on admission compared to 41 (84%) VAN ghassan wadi, MD, Cumberland (Grant/Research Support) Michael P. Veve, Pharm.D., Cumberland (Grant/Research Support)Paratek Pharmaceuticals (Research Grant or Support)"} +{"text": "Yang LiuBJU Int. 2020 Jul;126(1):168-176.Percutaneous nephrolithotomy (PCNL) is the gold standard surgical treatment for large renal kidney stones >2.0 cm) according to EUA and AUA guidelines , 2. Howe.0 cm accSeveral authors have already reported favorable outcomes of mini-PCNL when compared to RIRS -6. A sim"} +{"text": "Cited2 deletion has a minor impact on steady-state hematopoiesis, Cited2-deficient HSCs are severely depleted in young mice and fail to expand upon aging. Moreover, although they home normally to the bone marrow, they fail to reconstitute hematopoiesis upon transplantation. Mechanistically, CITED2 is required for expression of key HSC regulators, including GATA2, MCL-1, and PTEN. Hematopoietic-specific expression of anti-apoptotic MCL-1 partially rescues the Cited2-deficient HSC pool and restores their reconstitution potential. To interrogate the Cited2\u2192Pten pathway in HSCs, we generated Cited2;Pten compound heterozygous mice, which had a decreased number of HSCs that failed to reconstitute the HSC compartment. In addition, CITED2 represses multiple pathways whose elevated activity causes HSC exhaustion. Thus, CITED2 promotes pathways necessary for HSC maintenance and suppresses those detrimental to HSC integrity.Hematopoietic stem cells (HSCs) reside at the apex of the hematopoietic differentiation hierarchy and sustain multilineage hematopoiesis. Here, we show that the transcriptional regulator CITED2 is essential for life-long HSC maintenance. While hematopoietic-specific \u2022Unperturbed hematopoiesis can be sustained long term while the HSC pool is depleted\u2022CITED2 promotes HSC survival but not quiescence under homeostatic conditions\u2022Mcl1 and Pten expressionCITED2 maintains the HSC pool by controlling Cited2 deletion causes a progressive HSC loss under steady-state conditions without perturbing normal hematopoiesis. The authors show that CITED2 maintains HSCs by regulating the expression of Mcl1 and Pten. Finally, they indicate that CITED2 promotes multiple pathways necessary for HSC maintenance and suppresses those detrimental to HSC integrity to coordinate HSC function.Kranc, Guitart, and colleagues demonstrate that Hematop humans) . The strCITED2 (CBP/p300-interacting-transactivator-with-an ED-rich-tail 2) is a transcriptional regulator that co-activates or represses multiple transcription factors, including AP-2 , HIF-1alMx1-Cre-mediated deletion of Cited2 (in which Mx1-Cre is induced by poly(I:C)-stimulated IFN-\u03b1 production) results in a rapid loss of HSCs via apoptosis and a resultant BM failure or Trp53 (encoding p53) rescues depletion of Cited2-deficient HSCs. Another study -inducible Mx1-Cre-mediated Cited2 deletion results in loss of HSCs , compromises their reconstitution potential, and leads to a rapid BM failure upon myelotoxic stress. In this study, loss of quiescence, but not increased apoptosis, upon inducible Cited2 deletion is mediated at least in part by HIF-1alpha, as Hif1a deletion partially restores impaired quiescence of HSCs lacking Cited2 and improves their ability to reconstitute the HSC compartment upon transplantation cells, LSKCD48\u2212CD150+ HSCs, Lin\u2212Sca-1\u2212c-Kit+ (LK) myeloid progenitors, and more-mature Lin\u2013 and differentiated Lin+ hematopoietic cell populations, and performed qRT-PCR. Cited2 was expressed in all compartments, with significantly higher expression in the HSC population compared with myeloid progenitors and more mature hematopoietic cell populations (Cited2 in long-term HSCs (LSKCD34\u2212CD135\u2212), MPP1 (LSKCD34+CD135\u2212CD150+CD48\u2212), MPP2 (LSKCD34+CD135\u2212CD150+CD48+), and MPP3 (LSKCD34+CD135\u2212CD150\u2212CD48+) populations, lymphoid-primed multipotent progenitors (LSKCD34+CD135+), which correspond to the MPP4 population, and CMP (LKCD34+Fc\u03b3RII/IIIlow), GMP (LKCD34+Fc\u03b3RII/IIIhigh), and MEP (LKCD34\u2212Fc\u03b3RII/IIIlow) compartments, we analyzed our SMART2-seq single-cell expression data in these populations mice analyses of 8- to 12-week-old Cited2CKO mice revealed unaffected WBC counts, with mild anemia and thrombocythemia mice D, where CKO mice E. Surpricythemia F. Furthelularity G and unalularity H, as wellularity and 1I. numbers J. Notabl numbers F, mice lgenitors K. FinallBM cells L and 1M.or cells M. Taken Cited2 deletion on HSCs and primitive progenitor cells. We found that the total number of LSK cells was not affected in young 8- to 12-week-old Cited2CKO mice , with an increase in MPP2 population and unchanged numbers of the MPP3-4 populations. Thus, despite a select reduction in absolute HSC and MPP1 cell numbers, Cited2CKO mice sustain largely unaffected unperturbed steady-state multilineage hematopoiesis.We next determined the impact of CKO mice A. MarkedCited2 deficiency on long-term HSC maintenance during unperturbed hematopoiesis. We aged mouse cohorts for 52\u00a0weeks and found that Cited2 deficiency had no impact on mouse survival (data not shown). Consistent with physiological HSC aging, during which the HSC pool undergoes expansion and found that they also dramatically failed to reconstitute hematopoiesis resulted in a partial rescue of the HSC and MPP1 cell pools compared with Cited2CKO mice is a pro-survival BCL-2 protein family member, whose failure , thus redeletion . Moreovedeletion . Given tnic mice , which oelements B. IntereCKO mice C. To invent mice D. Signifcl1 mice E and 4F.cl1 mice E and 4F.cipients G. Finallcolonies H, and whol cells I. TherefPten expression was decreased in Cited2-deficient HSCs , Cited2Het, PtenHet, and control mice did not rescue HSC depletion -inducible ectively . Howevertor Mcl1 , whose hotential . Consistntenance . These dactivity . Indeed,Mx1-Cre deletion of Cited2 results in loss of quiescence of HSCs, a phenotype that is partially mediated by HIF-1alpha is known to transiently alter HSCs , unlike Vav-iCre, which is constitutively expressed, and as such more accurately allows for gene deletion under steady-state conditions. Thus, it is possible that concurrent poly(I:C) administration and Cited2 deletion in the Mx1-Cre-mediated model may exhibit exacerbated phenotypes not seen in the Vav-iCre model.Poly(I:C)-inducible F-1alpha , 2014. NWhile in this study we focused on functional interrogation of the CITED2\u2192MCL-1 and CITED2\u2192PTEN axes, our work suggests that CITED2 is also likely to control other diverse pathways to coordinate HSC biology. Our analyses indicate that CITED2 represses multiple pathways downstream of c-MYC, E2F, and RUNX1 transcription factors and K-RAS and proinflammatory signaling pathways, whose upregulation has detrimental consequences for HSC integrity . FinallyCited2fl/fl , anti-CD4; biotin conjugated (cat. no. 553649), anti-CD5; biotin conjugated (cat. no. 553019), anti-CD8a; biotin conjugated (cat. no. 553029), anti-CD11b; biotin conjugated (cat. no. 553309), anti-CD45R/B220; biotin conjugated (cat. no. 553086), anti-Ter119; biotin conjugated (cat. no. 553672), anti-Gr-1/Ly-6G/C; biotin conjugated (cat. no. 553125), anti-CD34; FITC conjugated (cat. no. 553733), and streptavidin; BV421 conjugated (cat. no. 563259). BioLegend antibodies used were anti-c-Kit/CD117; APC conjugated (cat. no. 105812), anti-c-Kit/CD117; APC-Cy7 conjugated (cat. no. 105826), anti-Sca-1; APC-Cy7 conjugated (cat. no. 122520), anti-Sca-1; PB conjugated (cat. no. 108125), anti-CD48; PE conjugated (cat. no. 103406), anti-CD150; PE-Cy7 conjugated (cat. no. 115914), anti-CD135; APC conjugated (cat. no. 135310), anti-CD135; PE conjugated (cat. no. 135305), anti-CD16/32; APC-Cy7 conjugated (cat. no. 101328), anti-CD41; APC conjugated (cat. no. 133914), anti-CD105; PE conjugated (cat. no. 120408), anti-CD127; BV421 conjugated (cat. no. 135023), anti-TER-119; FITC conjugated (cat. no. 116206), streptavidin; PerCp conjugated (cat. no. 405213), anti-CD19; APC-Cy7 conjugated (cat. no. 115530), anti-CD45R/B220; APCCy7 conjugated (cat. no. 103224), anti-CD11b; APC conjugated (cat. no. 101211), anti-Gr-1/Ly-6G/C; PE-Cy7 conjugated (cat. no. 108416), anti-CD4; PE conjugated (cat. no. 130310), anti-CD8a; PE conjugated (cat. no. 100708), anti-CD45.1; FITC conjugated (cat. no. 110706), anti-CD45.2; PB conjugated (cat. no. 109820), anti-Ki67; FITC conjugated (cat. no. 652410). Annexin V; FITC conjugated (cat. no. 640906), and 7-AAD (cat. no. 420403) were purchased from BioLegend. DAPI was purchased from Life Technologies (cat. no. D1306).Mice received 30\u00a0mg/mL of NAC (Sigma) in drinking water for 4\u00a0weeks. The water bottles containing NAC were changed twice a week.6 BM cells stained first for LSK were resuspended in X-Vivo 15 medium (without phenol red) supplemented with 10% FCS, loaded with 5\u00a0\u03bcM MitoSox red (Invitrogen) for 20\u00a0min at 37\u00b0C and analyzed using FACS.For detection of mitochondrial super oxide, 3\u00a0\u00d7 10CFC assays were performed using MethoCult M3434 (STEMCELL Technologies). Colonies were tallied at day 10. For CFC replating, CFC1 cells were washed with IMDM then seeded in M3434.+/CD45.2+ recipient mice was achieved using a split dose of 11\u00a0Gy (two doses of 5.5\u00a0Gy administered 4\u00a0h apart) at an average rate of 0.58 Gy/min using a Cesium 137 GammaCell 40 irradiator. For transplantations 100 HSCs or 2,000 LSK sorted from BM of 8- to 10-week old adult mice mixed with 200,000 support CD45.1+ wild-type BM cells were injected into lethally irradiated CD45.1+/CD45.2+-recipient mice.Lethal irradiation of CD45.1+ BM were injected into CD45.1+ lethally irradiated recipients . After 18 h, recipients were sacrificed and BM CD45.2+ chimerism was analyzed by FACS.LSK cells sorted from CD45.2Actb expression.Gene expression analyses were performed as described previously . DiffereStatistical analyses were performed using GraphPad Prism software. p values were calculated using a Mann-Whitney U test.Cited2CKO and Cited2CTL animals (n\u00a0= 5 per genotype). On average, 6,200 cells per sample were collected and 53.7 million single-ended 85-bp reads per sample were sequenced. Reads were aligned to the GRCm38 mouse genome using HISAT2 v.2.1.0 were mapped to gene loci using the basic set of ENCODE genomic annotation from Ensembl v.91. Next, proximal promoters were defined as the region from 200\u00a0bp upstream to 100\u00a0bp downstream of the transcription start site. Proximal promoter coordinates were shuffled within chromosomes using the bedtools shuffle tool with the \u2013chrom flag to generate control DNA regions for motif analysis. Finally, DNA motifs overrepresented in promoters compared with control regions were identified by Homer v.4.10.in\u00a0vivo experiments, and data analyses and interpretation. L.N.L. and M.B. analyzed gene expression. K.J.C. and S.C. produced VavP-Mcl1 transgenic mice. A.T., J.D., A.V., A.B., C.M., E.G., C.M.-C., C.S., L.A., and J.C. helped with in\u00a0vivo experiments, FACS, and data analyses. D.O., B.G., and N.P.R. provided significant expertise to this study. K.R.K. and A.V.G. contributed equally to this work.K.R.K., A.V.G., and H.L. designed the experiments and wrote the paper. A.V.G. and H.L. performed The authors declare no competing interests."} +{"text": "A terrible disease of the cardiovascular system, atherosclerosis, develops in the areas of bends andbranches of arteries, where the direction and modulus of the blood flow velocity vector change, and consequentlyso does the mechanical effect on endothelial cells in contact with the blood flow. The review focuses on topicalresearch studies on the development of atherosclerosis \u2013 mechanobiochemical events that transform the proatherogenicmechanical stimulus of blood flow \u2013 low and low/oscillatory arterial wall shear stress in the chains of biochemicalreactions in endothelial cells, leading to the expression of specific proteins that cause the progressionof the pathological process. The stages of atherogenesis, systemic risk factors for atherogenesis and its importanthemodynamic factor, low and low/oscillatory wall shear stress exerted by blood flow on the endothelial cells liningthe arterial walls, have been described. The interactions of cell adhesion molecules responsible for the developmentof atherosclerosis under low and low/oscillating shear stress conditions have been demonstrated. The activationof the regulator of the expression of cell adhesion molecules, the transcription factor NF-\u03baB, and the factorsregulating its activation under these conditions have been described. Mechanosensitive signaling pathways leadingto the expression of NF-\u03baB in endothelial cells have been described. Studies of the mechanobiochemical signalingpathways and interactions involved in the progression of atherosclerosis provide valuable information for thedevelopment of approaches that delay or block the development of this disease.Key words: atherogenesis; shear stress; transcription factor NF-\u03baB; RelA expression; mechanosensitive receptors;cell adhesion molecules; signaling pathways; mechanotransduction. Nowadays, cardiovascular disease is a major public healthissue. Moreover, atherosclerosis is one of the most commonpathologies of the cardiovascular system. The systemic riskfactors for the development of atherosclerosis include age,hypertension, diabetes mellitus, smoking, low physical activity,fatty diet, renal failure, increased level of fibrinogen, lowdensitylipoproteins, cholesterol and blood plasma C-reactiveprotein . The level of low-density lipoproteins(LDLs) is classified into a separate group of factorsthat account for the atherogenicity of the subfraction profileof apo-B-containing lipoproteins . The penetration of blood plasma LDLs throughthe endothelium in athero-susceptible areas of the arteries andtheir retention and accumulation in the extracellular matrix(ECM) of the subendothelial space initiates atherogenesis.LDLs are retained in the intima (mainly due to interaction withproteoglycans), undergo oxidation (formation of oxLDLs) andcause an inflammatory response \u2013 the infiltration of circulatingblood monocytes into the intima. In the intima, monocytesdifferentiate into macrophages, uptake oxLDLs and becomefoam cells .The development of atherosclerosis occurs in the followingstages: (i) adaptive intimal thickening, (ii) formation of fattystreaks, (iii) pathological intimal thickening (PIT), (iv) earlyfibroatheroma and (v) late fibroatheroma. In stage (i), smoothmuscle cells (SMCs) of the media migrate to the intima and secreteproteoglycans. The formation of fatty streaks in stage (ii)is accompanied by the accumulation of foamy cells (macrophagesloaded with lipids) in the intima. Lipid-loaded SMCsare less represented. The PIT process (iii) occurs with andwithout the infiltration of macrophages. In both cases, SMCsand extracellular lipid pools are present in the intima. The accumulationof SMCs occurs towards the lumen of the artery,and lipid pools accumulate close to the media. The formationof a fibrous cap that covers the necrotic core occurs in the laterstages of development of the atherosclerotic lesions, includingearly and late fibroatheroma . The cap includes SMCs,infiltrated macrophages, T-lymphocytes, as well as collagensand proteoglycans of the extracellular matrix. Programmedcell death, via apoptosis and necroptosis, plays an essentialrole in early fibroatheroma (iv) with the formation of foci ofnecrosis and cholesterol crystals. In late fibroatheroma (v),an extensive necrotic core that consists of cellular debris anda large number of crystals of free cholesterol and its esters isformed .The molecular and genetic processes of atherogenesis remainunclear. Numerous haemodynamic studies have shownthat, based on systemic risk factors, atherosclerosis developsmainly in the bends and branching of the arteries, where thereis a change in the nature of the blood flow . The haemodynamiccharacteristics of the effect of blood flow on the vessel wallsare wall shear stress (WSS), hydrostatic pressure and cyclicdeformation. WSS is the friction force that occurs whenflowing blood comes into contact with the inner wall of the artery. WSS on the arterial wall is described by :where \u03bc is the blood viscosity index, \u2192V(t) is the blood flowrate parallel to the vessel wall at time t and r is the radial coor-dinate.Studies conducted on animal models and observing patientsrevealed a regular maximum thickening of the intima and theformation of atherosclerotic plaques in areas with low WSS(< 10 dyn/cm2 in humans) and low/oscillatory WSS (with adeviation of the instantaneous WSS vector from its averagedirection). Such damage was minimal in areas of high WSS(>25 dyn/cm2 in humans). High values of WSS were realizedin the rectilinear sections of the arteries with laminar bloodflow. In the areas of branching and bending of the arteries nearthe walls, vortex flows were formed, leading to mechanicalstress on the walls, which was accompanied by pathologicaleffects. These flows were characterised by low and low/oscillatoryWSS .A study conducted on isolated segments of blood vesselsthrough which LDLs flowed demonstrated that the transport ofLDLs into the vascular wall increased with a decrease in WSSand, on the contrary, decreased with an increase in WSS . Patient-specific modelling of the subendothelialaccumulation of LDLs in the stenotic right coronary arteryalso showed an inverse relationship between the distribution ofWSS and the accumulation of LDLs .The zone of recirculating flow and low WSS correspondedto the maximum accumulation of LDLs, and in areas of highWSS, the accumulation of LDLs was low.To localise the segments of arteries with low and low/oscillatoryWSS and monitor the transformation of atheroscleroticplaques into a stable or unstable phenotype, computer modellingof blood flow in the vessels is being developed. Thiswill facilitate the identification of patient-specific fields andgradients of blood flow rates depending on the geometry ofthe vessels . To solve these issues, the Navier\u2013Stokesequations for an incompressible viscous fluid are used. Toreconstruct the geometric shape of the vessels, intravascularultrasound methods are used as well as X-ray microcomputertomography with the use of contrast agents . The ANSYS Fluent, OpenFOAM,FLUENT 6.0 and other software packages are widely used toconduct calculations via mathematical models of stationaryand unsteady blood flows in various areas of the arteries. Computermodelling of the distribution of WSS, which accountsfor patient-specific data on the geometry of blood vessels, isof high value for clinical practice.The molecules of cell adhesionand their interactions in the early stageof atherogenesisOxLDLs in the subendothelial space as well as low and low/oscillatory WSS cause pro-inflammatory activation of endothelialcells (ECs), which leads to the rolling of leukocytes inthe circulating blood flow to the endothelium, their adhesion and transendothelial migration (TEM). The mediators of thesecritical events of the early stage of atherogenesis are cell adhesionmolecules. These molecules are expressed on the surfaceof ECs and circulating blood cells (monocytes or leukocytesand platelets) and include platelet endothelial cell adhesionmolecule-1 (PECAM-1); intercellular adhesion molecule-1and -2 ; vascular cell adhesion molecule-1(VCAM-1); E-, L- and P-selectins; vascular endothelial (VE)cadherin; \u03b21 and \u03b22 integrins; proline-rich glycoprotein CD99and junctional adhesion molecule-A (JAM-A).Selectins (transmembrane glycoproteins) are expressed onthe surface of ECs , leukocytes(L-selectin) and platelets (P-selectin) . Early experiments conducted in a flow chamber with alaminar flow of monocytes on an EC monolayer showed that the rolling of the monocytes to theECs, weak, reversible contact of the monocytes with ECs and slowing down of the rate along theendothelium determine the interactions of the L-selectin ofthe monocytes with glycoprotein ligands of the ECs and, to alesser extent, the P-selectin of the ECs with the glycoproteinligand PSGL-1 of the monocytes. E-selectin is not involvedin the process . Firm, irreversibleadhesion of the leukocytes to the ECs occurs during theinteraction of the leukocyte \u03b14\u03b21 (VLA-4) integrin with theendothelial immunoglobulin VCAM-1 and the interaction of the leukocyte\u03b1L\u03b22 integrinswith the endothelial immunoglobulin ICAM-1 .OxLDLs and lysophosphatidylcholine (a component ofoxLDLs) induce the expression of ICAM-1 and VCAM-1 onthe surface of cultured ECs and stimulate monocyte adhesion. A physiologicallylow WSS, created by the flow of leukocytes on the EC monolayer,generates upward docking structures on the endothelium thatcontain ICAM-1 and VCAM-1 clusters within 1\u20132 minutes.These clusters surround the leukocytes and function as ananchor for them .In turn, the structures of VCAM-1 and ICAM-1 that surroundthe leukocytes stimulate the formation of lateral linear tracksof leukocyte \u03b21 (VLA-4) and \u03b22 (LFA-1) integrins that areoriented parallel to the ICAM-1 and VCAM-1 clusters . Moreover, 90% of the leukocytes thatare surrounded by the VCAM-1 and ICAM-1 clusters transmigrateto the subendothelial space, and the suppression ofVCAM-1 and ICAM-1 via inhibitors significantly suppresses TEM. Regardless of theTEM pathway , the TEM process isassociated with the formation of a cupped traction structureby the VCAM-1/VLA-4 and ICAM-1/LFA-1 interactions ofendothelial and leukocyte cells, which guide and facilitateTEM .VE-cadherin plays an important role in the TEM of leukocytes.VE-cadherin is only expressed in ECs, localised mainlyin the intercellular contacts and plays an important role in the intercellular adhesion and barrier functions of the ECs . The adhesion of leukocytes to the endothelium inthe lateral intercellular contacts, preceding TEM, induces theformation of gaps in the intercellular distribution of VE-cadherinand the components of the VE-cadherin complex at the sites of adhesion or transmigrationof the leukocytes. The gaps are formed as a result of lateraldisplacement of VE-cadherin in the membrane and facilitatethe TEM of the leukocytes. Following the completion of TEM,VE-cadherin moves in the opposite direction and closes thegaps (curtain opening and closing effect) . The lateral displacement of VE-cadherinin the membrane most likely occurs due to the destabilisationof the VE-cadherin bond with the actin cytoskeleton by thefollowing mechanism: the ICAM-1 and VCAM-1 clusters inthe sites of intercellular adhesion of the leukocytes to the ECsinduce the intracellular activation of the Src and Pyk2 tyrosinekinases and the phosphorylation of Tyr658 and Tyr731 of thecytoplasmic domain of VE-cadherin, which are involved in thelow-affinity binding of VE-cadherin to p120- and \u03b2-catenin,respectively. The weakening of these interactions disrupts theVE-cadherin bond with the actin cytoskeleton, destabilises theVE-cadherin or VE-cadherin cell-cell interactions and facilitatesthe lateral movement of the phosphorylated VE-cadherinin the membrane . p120-catenin regulatesthe phosphorylation of VE-cadherin and the paracellularTEM of leukocytes via a competition mechanism with theactivated Src and Pyk2 tyrosine kinases: the overexpressionof p120-catenin in the ECs leads to the absence of gaps in thedistribution of VE-cadherin and the blocking of the TEM ofthe leukocytes .The glycoprotein PECAM-1 (CD31) plays an importantrole in the TEM of leukocytes. In ECs, PECAM-1 is mainlylocalised in the intercellular contacts. The homophilic interactionsof this protein with adjacent ECs occur through theextracellular Ig-like domains IgD1 and IgD2 . PECAM-1 is also present in a distinct membranevesicularrecycling compartment adjacent to the lateral bordermembrane of the ECs . In the restingendothelium (in the absence of adhesive leukocytes), there isconstitutive membrane traffic between the lateral cell borderand the membrane-vesicular compartment . In the presence of adhesive leukocytes onthe endothelium, directed kinesin-dependent migration of thePECAM-1-bearing LBRC membrane along the microtubulesof the ECs to the sites of para- and transmigration of the leukocytesoccurs, in addition to the surrounding of the leukocytesby the LBRC membrane. The LBRC provides non-ligatedPECAM-1 and CD99 in the ECs to interact with the homophilicligands in the leukocytesand initiates the signals for further recruitment of theLBRC as the leukocytes move through the endothelial layer.The antibodies to PECAM-1 and CD99 block the TEM of theleukocytes . The recruitment ofthe LBRC to paracellular TEM sites precedes the formationof gaps in the intercellular distribution of VE-cadherin andis necessary for the formation of these gaps . In ApoE\u2013/\u2013 PECAM-1\u2013/\u2013 mice, the load of plaques inthe areas of the carotid artery with a low and low/oscillatory WSS was significantly less than in the control ApoE\u2013/\u2013 mice. A study on the relationship of singlenucleotide polymorphisms in functionally important domainsof PECAM-1 in patients who were at risk of developingcoronary heart disease and myocardial infarction showed thatArg670Gly substitution can be a homozygous protector forthe development of myocardial infarction. This substitution islocalised close to Tyr663, the phosphorylation of which, underlow WSS conditions, initiates the signaling pathway of activationof the key transcription factor NF-\u03baB for the expressionof cell adhesion molecules . Val125Leuand Asn563Ser substitutions are not associated with the riskof coronary heart disease .Integrins also play an important role in cell adhesion. Theintegrins are a large family of receptors that are localised inthe plasma membrane and consist of 18 \u03b1 and 8 \u03b2 subunitsthat form 24 different heterodimers. The extracellular domainsof the integrins interact with ECM proteins and ligands on the surface of other typesof cells, causing cell-substratum or cell-cell adhesion. Theintegrin-ligand interactions induce the activation of a variety ofsignaling pathways that modulate cellular behaviour, includingproliferation, shape, motility, survival or apoptosis, differentiation,protein phosphorylation, cytoskeleton organisation andgene expression. Many integrins are expressed in an inactivestate on the cell surface since the membrane-proximal highlyconserved sequences of the cytoplasmic domains of the \u03b1and \u03b2 subunits form a structural constraint that locks the conformationof integrins in an inactive, low-affinity state. Theactivation of integrins is often induced by intracellular signalsand regulatory factors that act on the cytoplasmic domains, aswell as phosphorylation. This alters the affinity of integrins forligands through conformational changes in their extracellulardomains, as well as clustering .The adhesion of leukocytes to the endothelium and theirinfiltration into the subendothelial space is enhanced bycytokines, chemokines and other factors. Thus, monocyticchemotactic protein-1 (MCP-1) and interleukin-8 (IL-8) (producedby macrophages) are involved in the delay of peripheralcirculation monocytes and their adhesion and migration intothe arterial intima via interaction with monocyte receptors belongingto the CCR2 and CXCR2 types, respectively . IL-9, secreted mainly byCD45+CD3\u2013CD19\u2013 leukocytes in \u0410\u043f\u043e\u0415\u2013/\u2013 mice, stimulates theexpression of VCAM-1 in the ECs of the aorta of mice throughinteraction with the IL-9 receptor (IL-9R) and activation(phosphorylation) of the signaling protein and transcriptionactivator STAT3 . In the atheroscleroticaortas of \u0410\u043f\u043e\u0415\u2013/\u2013 mice, a high level of IL-17A expressionwas observed, as well as numerous IL-17A-producing CD4+T helper 17 (Th17) and \u03b3\u03b4+ T cells. IL-17A initiates the productionof several cytokines and chemokines by aortic cells,in particular, the pro-inflammatory chemokine CXCL1, whichactivates peripheral circulation monocytes and stimulates theiradhesion and migration to the aortic wall .Pro-atherogenic IL-17C, expressed mainly by aortic SMCsin \u0410\u043f\u043e\u0415\u2013/\u2013 mice, is involved in the recruitment of T cells and macrophages into the aortic wall .TGF-\u03b2-(H2O2-) inducible clone 5 (His-5), expressed on thesurface of ECs and SMCs, is involved in the formation ofstructures that are similar to the microvilli on the surface ofECs, which enhance the adhesion of monocytes to the ECs.Transcription factor NF-\u03baB is a key regulatorof the gene expression of cell adhesion moleculesunder conditions of physiologicallylow and low/oscillatory wall shear stressThe transcription factor NF-\u03baB positively regulates the expressionof cell adhesion molecules with the participation ofother transcription factors and coactivators. The VCAM-1 genepromoter has two NF-\u03baB sites that are required for transcriptionactivation . The C/EBP and NF-\u03baBsites were identified in the ICAM-1 gene promoter, and mutationsin the latter completely suppress the activation of theICAM-1 promoter . The ELAM-1 genepromoter includes a CRE/ATF site, three NF-\u03baB sites and threeHMGI(Y) sites; two of the HMG I(Y) sites are located withinthe NF-\u03baB sites (the interaction of HMG I(Y) and NF-\u03baBwith small and large DNA grooves, respectively). All threeNF-\u03baB sites are required for promoter activation and enhancethe affinity of NF-\u03baB and ATF-2 for the promoter . The promoter of the MCP-1 gene (monocytechemoattractant protein-1) contains the NF-\u03baB site and theAP-1 site, which are necessary for maximum induction of thepromoter . The core element GAGACC(SSRE) was identified in the pro-atherogenic platelet growthfactor (PDGF) promoter that stimulates the proliferation andmigration of SMCs ; it was found tointeract with NF-\u03baB .In ECs, the most common p50/p65 (RelA) heterodimer isNF-\u03baB. It is well known that, in the cytoplasm, latent NF-\u03baBis associated with an inhibitor of I\u03baB (mainly I\u03baB\u03b1) and isinactive. When ECs are stimulated by cytokines TNF\u03b1, IL-1 orbacterial lipopolysaccharide (LPS) that interact with specificEC receptors, signaling pathways are activated, leading to theactivation of the I\u03baB kinase (IKK complex), which specificallyphosphorylates I\u03baB. After the ubiquitination of I\u03baB and itsproteasomal degradation, free NF-\u03baB is translocated into cellnuclei (factor activation), interacts with elements of the DNAmajor groove and activates the expression of genes involved inthe immune response, cell survival, carcinogenesis and inflammation(with the participation of other transcription factorsand coactivators) .Early studies demonstrated that active NF-\u03baB and ICAM-1were present in ECs, macrophages and SMCs in atheroscleroticplaques of arteries of deceased patients but were absentin the intima or media of the healthy arteries of those patients. OxLDL triggers in the ECs in vitro andin vivo signaling pathways for IKK complex activation; thisincludes the activation of focal adhesion kinase (FAK) andribosomal S6 kinase (RSK) and leads to NF-\u03baB activation,VCAM-1 expression and monocyte adhesion to ECs . Using the model flow channel system that is created by a laminar pulsating flow of theculture medium containing monocytes, in which an averagephysiologically low and uniformly distributed WSS acts on the EC monolayer, it was shown that a mechanical stimulus activates the IKK complex andNF-\u03baB and stimulates VCAM-1 expression and monocyteadhesion to the ECs . A model spatialgradient of averaged low/oscillatory WSS, close to the gradientof WSS in arterial branchings and bends, resulted in amore efficient activation of NF-\u03baB compared to uniformlydistributed low WSS .High activation of NF-\u03baB was observed in ECs that werecultivated based on a model of the calculated WSS profile in asite of the human carotid sinus compared with a model of the calculatedWSS profile in the distal segment of the carotid arterybifurcation orcells at rest . A study of the transcriptionalexpression of the VCAM-1 endothelium from the nature ofhaemodynamics and calculated profiles of WSS in the segmentsof the left and right coronary arteries showed that low/oscillatory WSS at the outer wall of the bifurcation of theleft anterior descending artery (atherogenic region) inducesa significantly higher expression of VCAM-1 compared to astraight region of the right artery , inwhich atherosclerotic plaques are largely unformed . The mapping of the endothelial expression ofNF-\u03baB/I\u03baB and the activation of NF-\u03baB in areas of the aorticarch of mice with high and low probability of atherosclerotic plaque formationdemonstrated that in the HP region with low/oscillatory WSS, the expression of NF-\u03baB/I\u03baB and the activationof NF-\u03baB significantly exceeded those in the LP region. S. Cuhlmann et al. (2011) also detectedincreased expression of the RelA subunit NF-\u03baB and a highernuclear localisation compared with the LP region in the HPregion of the aortic arch of mice. Moreover, this was correlatedwith increased expression of VCAM-1 and the accumulationof CD68+ macrophages in the HP regionThe gap-junction protein connexin 40 (Cx40), expressedin ECs under low WSS conditions, whose cytoplasmic C-terminusinteracts with I\u03baB\u03b1 and inhibits its phosphorylation,is a negative regulator of NF-\u03baB activation in areas with lowWSS . Conversely, mechanosensitive phosphatidicacid phosphatase (PPAP2B) regulates NF-\u03baB activity,expression of adhesion proteins, monocyte adhesion and TEMunder high WSS. PPAP2B shows increased expression inECs under atheroprotective flow characteristics and shows decreased expression under atherogeniccharacteristics . PPAP2Bhydrolyses lysophosphatidic acid (LPA), a pro-atherogenicand thrombogenic glycerophospholipid in the blood and,thereby, blocks signaling pathways activated by the interactionof LPA with cellular LPA receptors (LPAR). LPA-LPAR1interaction activates the Rho kinase-NF-\u03baB signaling pathwayand the subsequent transcriptional expression of ICAM-1,VCAM-1 and E-selectin in ECs .LPA-LPAR1/2 interaction leads to an increase in the contractilityof ECs and the permeability of the endothelial monolayer. LPA is an extracellular signalingmolecule that is capable of interacting with at least six G protein LPA-LPAR1/2 interaction leads to an increase in the contractilityof ECs and the permeability of the endothelial monolayer. LPA is an extracellular signalingmolecule that is capable of interacting with at least six G protein-coupled cellular receptors, initiating intracellular signalingcascades and exerting multiple effectson blood cells and vascular wall cells. Therefore, in platelets, LPA induces a changein the shape, aggregation, and formation of platelet-monocyteaggregates. In ECs, LPA induces cell migration, expressionof VCAM-1, ICAM-1, E-selectin, chemokines (CXCL1),formation of actin stress fibres and cell contraction. In SMCs,LPA induces cell contraction, migration and proliferation.Additionally, LPA accumulates in the lipid-rich core of atheroscleroticplaques, and, when ruptured, enters the bloodstreamand activates platelets, leading to the formation of blood clots. Endothelial NO synthase (eNOS) isalso expressed under physiologically high WSS. Under theseconditions, the eNOS promoter is activated through the interactionof NF-\u03baB with the GAGACC element . eNOS produces NO, an inducer of I\u03baB\u03b1 expression.NO stabilises the NF-\u03baB\u2219I\u03baB\u03b1 heterotrimer in the cytoplasmand induces I\u03baB\u03b1 translocation into cell nuclei, leading to theinactivation of NF-\u03baB and the termination of NF-\u03baB-mediatedtranscription . Moreover, NO inhibitsI\u03baB kinase (IKK complex), a positive regulator of NF-\u03baBactivation .Mechanosensitive signaling pathwaysthat control the transcriptional expressionof the RelA subunit of NF-\u03baB in endothelial cellsThe WSS, created by the blood flow to the walls of the arteries,activates mechanosensitive signaling pathways in the ECs.Amechanosensor localised in the cell membrane perceives amechanical stimulus (WSS) and triggers intracellular signalingthat activates specific transcription factors, which regulatethe transcriptional expression of proteins. The internal bendof the aortic arch and the areas of arterial bifurcation, wherelow and low/oscillatory WSS are realized, are associated withthe localisation of atheroma. In the same areas, increased expressionof active c-Jun N-terminal kinase 1 (JNK1), whichbelongs to mitogen-activated protein kinases (MAPK), wasrevealed , as well as increased expres-sionand nuclear localisation of the RelA subunit of NF-\u03baB. The hypothesis that physiologicallylow WSS regulates the expression of RelA and NF-\u03baB targetgenes (VCAM-1 and others) through the JNK1-dependentpathway was proved by modelling the haemodynamics ofthe carotid artery in mice. The implantation of a tapered cuffaround the mouse carotid artery generates a laminar bloodflow with a low velocity and low WSS upstream of the cuffand disturbed, low velocity and low/oscillatory WSS downstreamof the cuff .This approach demonstrated that increased expression ofRelA and activated JNK1 is realised in regions with lowand low/oscillatory WSS. The transcription factor ATF2 isactivated by JNK1 (phosphorylation) and interacts with theRelA promoter sites to activate the promoter. Thus, in areaswith low/oscillatory WSS, the JNK-ATF2-RelA signalingpathway is implemented, which stimulates the expression ofRelA and NF-\u03baB target genes (VCAM-1). The pathway alsostimulates the accumulation of CD68+ macrophages, whichare an indicator of the development of arterial inflammation.The signaling pathway for the transcriptional expressionof RelA upstream of JNK1 includes the activation ofintegrins, which is initiated by the stimulation of the cellsurface mechanosensory complex and an integrin-dependentsignaling cascade, leading to the activation of JNK1. The cellsurface mechanosensory complex includes the PECAM-1 andVE-cadherin receptors and the vascular endothelial growthfactor 2 receptor (VEGFR2), which belongs to the receptortyrosine kinase subfamily . In this complex,PECAM-1 is a key mechanosensitive signaling moleculethat perceives a mechanical signal and converts it into a chainof intracellular biochemical reactions. WSS, acting on theextracellular domain of PECAM-1, affects the conformationof the cytoplasmic domain of PECAM-1 and the availabilityof Tyr663 and Tyr686 of this domain for phosphorylation.Phosphorylation is conducted by membrane-bound Fyn tyrosinekinase (family of Src tyrosine kinases), which is localisedin intercellular contacts near PECAM-1 . PECAM-1/PECAM-1 intercellular EC interactionsthrough the extracellular domains of PECAM-1 are required for efficient phosphorylation and thetriggering of intracellular mechanosensitive signaling . Activated PECAM-1 andVE-cadherin (which functions as an adapter and is associatedwith VEGFR2) facilitate the phosphorylation of VEGFR2 atTyr801 and Tyr1175 by the Src tyrosine kinase. In turn, thephosphorylated VEGFR2, through direct interaction withthe regulatory p85 subunit of the phosphatidylinositol-3-OHkinase (PI(3)K), phosphorylates PI(3)K .The activated PI(3)K stimulates the conformational activationof integrins through the conservative pathway of theassociation of phosphatidylinositol-3,4,5 triphosphate (PI(3)Kproduct) with pleckstrin homology (PH) domains of cytohesin-1 or cytohesin-like proteins. This is followed by the translocationof these proteins to the plasma membrane and theirassociation with the cytoplasmic domains of the \u03b2 subunitsof integrins, which is realized in various types of cells. Thisinteraction leads to conformational changes in the extracellulardomains of the \u03b1 and \u03b2 subunits of integrins and an increase intheir affinity for specific ECM proteins, as well as clustering. In athero-resistant areasof arteries, the ECM is rich in CL (IV) and LN. However, inatherogenic regions (low/oscillatory WSS conditions), theECM is enriched in the pro-inflammatory proteins FN andFG .Antibodies specific to ligated \u03b21 and \u03b23 integrins were usedto show that, under conditions of low/oscillatory WSS, thereis an increase in the binding of \u03b15\u03b21 integrin to FN and of \u03b1v\u03b23 integrin to VN.Thus, the conformational activation of integrins and thedynamic formation of new bonds of integrins with specificligands occur \u2013 ECM proteins are realized .The composition of the ECM and the ligation of integrinsby the ECM proteins activate many intracellular signalingcascades \u2013 in this case, the Shc-Grb\u2219Sos-Ras-MAPKsignaling pathway. The cellular adapter protein Shc, activatedunder conditions of low/oscillatory WSS by tyrosinekinases Src and VEGFR2 close to the EC contacts (phosphorylationof Tyr239/240), forms an early unstable complex Shc\u2219VEGFR2\u2219VE-cadherin . Next, a stablecomplex Shc with an \u03b1v\u03b23 integrin that is ligated with FN orVN is formed . Additionally, Shc associates with the \u03b21 and \u03b25 integrinsthat are ligated with FN and VN . In this manner, Shc coordinates the intercellularcontact proteins (VE-cadherin) and integrin-ECM interactionsunder low/oscillatory WSS conditions. Membrane-associatedsmall G proteins Ras function cyclicallybetween active Ras\u2219GTP and inactive Ras\u2219GDP forms, whichare a molecular switch of an intracellular signal in response toan extracellular stimulus . The complexesof phosphorylated Shc with the \u03b1v\u03b23, \u03b21 and \u03b25 integrinsformed on the cytoplasmic side of the plasma membrane areaccompanied by the association of Shc with the cytoplasmicGrb2\u2219Sos complex of the growth factor receptor-bound protein2 (Grb2) and the guanine nucleotide exchange factor Sos.This complex stimulates the rate of exchange of the GDPassociated with Ras, on the GTP . In turn, activated Rasstimulates cytoplasmic Raf kinase and recruits Raf to the inner surfaceof the plasma membrane through direct interaction with itsregulatory domains and the subsequent phosphorylation offour sites of the kinase domain . Raf,activated via a MAP kinase cascade, activates MAPK (JNK).However, the activation of Shc and membrane-associatedheterotrimeric G proteins leads to the stimulation of Ras under the conditionsof the action of WSS on the cells. In the absence of WSS,G proteins are activated via association with ligand-activatedreceptors: the \u03b1 subunit exchanges the GDP bound to it forGTP and dissociates from the \u03b2\u03d2 dimer. The \u03b1\u2219GTP and \u03b2\u03d2complexes become mediators of cellular event signaling untilthe \u03b1 subunit restores its inactive GDP-bound state (since ithas GTPase activity.) The reassociation of \u03b1\u2219GDP with the \u03b2\u03d2dimer provides an inactive G\u03b1\u03b2\u03d2 heterotrimer that is capableof entering a new activation cycle . Alterationsin the physical properties of membranes under WSSconditions affect the conformation and functions of membrane-associatedproteins and, as a result, the signaling pathways activated bythese proteins .Purified heterotrimeric G proteins in phospholipid liposomesloaded with [\u03d2-32P]GTP were shown to be activatedby the action of physiological levels of WSS on liposomes. Within 1 second, a physiologically lowWSS activated the G\u03b1q/11 and G\u03b1i3/0 subunits of G proteins inECs . The activated G\u03b1q and G\u03b2\u03d2 subunitsdissociated from them under conditions of a WSS gradientin a physiologically low range and initiated Ras activationand downstream MAPK signaling .Moreover, two primary basic mechanosensors, G\u03b1q/11 andPECAM-1, establish a mechanosensitive G\u03b1q/11\u2219PECAM-1complex, which is formed under conditions of laminar flow in vivo (atheroprotective straight region of the descending aorta of mice) and in vitro. Underoscillatory flow conditions (low/oscillatory WSS), leading tothe activation of G proteins, this complex is rapidly (within30 seconds) destroyed . The formation ofthe G\u03b1q/11\u2219PECAM-1 complex involves PECAM-1 extracellularIg-like domains 2 and 3, as well as a G\u03b1q/11 interactingreceptor that associates with G\u03b1q/11 and PECAM-1 Ig-likedomains 2 and 3 and serves as a bridge in the formation of thecomplex . The PECAM-1\u2219G\u03b1q/11 complexalso includes heparan sulfate proteoglycan, which associateswith the Ig-like domain 3 of PECAM-1 and mediates theformation of the PECAM-1\u2219G\u03b1q/11 complex .Computer modelling of the blood flow in the arteries makesit possible to determine the most atherogenic areas of thearteries, which are characterised by low and low/oscillatoryWSS. The transcription factor NF-\u03baB and the cell adhesionmolecules ICAM-1, VCAM-1 and E-selectin are the earliestmarkers of atherogenesis. Therefore, the processes involved inthe expression of these proteins under the conditions inducedby a mechanical stimulus (low and low/oscillatory WSS) onendothelial cells are of great interest. This review presents ananalysis of numerous studies that demonstrated how the activationof membrane-bound proteins that perceive a mechanicalstimulus (low and low/oscillatory WSS) triggers a cascadeof biochemical reactions that lead to the transcriptional expressionof NF-\u03baB, a key regulator of the expression of celladhesion molecules. This review also describes in detail themechanisms of interaction between the endothelial cell adhesionmolecules and blood leukocytes that are responsible foradhesion and the subsequent TEM of leukocytes during the initialstage of atherogenesis. Studying the molecular processesinvolved in the initiation and development of atherosclerosisis extremely important for the development of an effectivedefence against this disease.The authors declare no conflict of interest.Alcaide P., Newton G., Auerbach S., Sehrawat S., Mayadas T.N., GolanD.E., Yacono P., Vincent P., Kowalczyk A., Luscinskas F.W.p120-Catenin regulates leukocyte transmigration through an effecton VE-cadherin phosphorylation. Blood. 2008;112(7):2770-2779.DOI 10.1182/blood-2008-03-147181.Allingham M.J., van Buul J.D., Burridge K. ICAM-1-mediated, SrcandPyk2-dependent vascular endothelial cadherin tyrosine phosphorylationis required for leukocyte transendothelial migration.J. Immunol. 2007;179(6):4053-4064. DOI 10.4049/jimmunol.179.6.4053.Allport J.R., Muller W.A., Luscinskas F.W. Monocytes induce reversiblefocal changes in vascular endothelial cadherin complex duringtransendothelial migration under flow. J. Cell. Biol. 2000;148(1):203-216. DOI 10.1083/jcb.148.1.203Amberger A., Maczek C., J\u00fcrgens G., Michaelis D., Schett G., Trieb K.,Eberl T., Jindal S., Xu Q., Wick G. Co-expression of ICAM-1,VCAM-1, ELAM-1 and Hsp60 in human arterial and venous endothelialcells in response to cytokines and oxidized low-density lipoproteins.Cell Stress Chaperones. 1997;2(2):94-103. DOI 10.1379/1466-1268(1997)002<0094:ceoive>2.3.co;2.Arita-Okubo S., Kim-Kaneyama J.R., Lei X.F., Fu W.G., Ohnishi K.,Takeya M., Miyauchi A., Honda H., Itabe H., Miyazaki T., MiyazakiA. Role of Hic-5 in the formation of microvilli-like structuresand the monocyte-endothelial interaction that accelerates atherosclerosis Cardiovasc. Res. 2015;105(3):361-371. DOI 10.1093/cvr/cvv003.Barreiro O., Yanez-Mo M., Serrador J.M., Montoya M.C., Vicente-Manzanares M., Tejedor R., Furthmayr H., Sanchez-Madrid F.Dynamic interaction of VCAM-1 and ICAM-1 with moesin and ezrinin a novel endothelial docking structure for adherent leukocytes.J. Cell Biol. 2002;157(7):1233-1245. DOI 10.1083/jcb.200112126.Brand K., Page S., Rogler G., Bartsch A., Brandl R., Knuechel R.,Page M., Kaltschmidt C., Baeuerle P.A., Neumeier D. Activatedtranscription factor nuclear factor-kappa B is present in the atheroscleroticlesion. J. Clin. Invest. 1996;97(7):1715-1722. DOI 10.1172/JCI118598.Butcher M.J., Waseem T.C., Galkina E.V. Smooth muscle cell-derivedinterleukin-17C plays an atherogenic role via the recruitment ofproinflammatory interleukin-17A+ T cells to the aorta. Arterioscler.Thromb. Vasc. Biol. 2016;36(8):1496-1506. DOI 10.1161/ATVBAHA.116.307892Carlos T.M., Harlan J.M. Leukocyte-endothelial adhesion molecules.Blood. 1994;84(7):2068-2101. DOI 10.1111/j.1582-4934.2009.00811.x.Carman C.V., Jun C.D., Salas A., Springer T.A. Endothelial cells proactivelyform microvilli-like membrane projections upon intercellularadhesion molecule 1 engagement of leukocyte LFA-1. J. Immunol.2003;171(11):6135-6144. DOI 10.4049/jimmunol.171.11.6135.Carman C.V., Springer T.A. A transmigratory cup in leukocyte diapedesisboth through individual vascular endothelial cells and betweenthem. J. Cell Biol. 2004;167(2):377-388. DOI 10.1083/jcb.200404129.Cecchi E., Giglioli C., Valente S., Lazzeri C., Gensini G.F., Abbate R.,Mannini L. Role of hemodynamic shear stress in cardiovascular disease.Atherosclerosis. 2011;214(2):249-256. DOI 10.1016/j.atherosclerosis.2010.09.008.Chang C.T., Shen M.Y., Lee A.S., Wang C.C., Chen W.Y., Chang C.M.,Chang K.C., Stancel N., Chen C.H. Electronegative low-density lipoproteinincreases the risk of ischemic lower-extremity peripheralartery disease in uremia patients on maintenance hemodialysis. Sci.Rep. 2017;7(1):4654-4662. DOI 10.1038/s41598-017-04063-3.Charo I.F., Taubman M.B. Chemokines in the pathogenesis of vasculardisease. Circ. Res. 2004;95(9):858-866. DOI 10.1161/01.RES.0000146672.10582.17Chen K.D., Li Y.S., Kim M., Li S., Yuan S., Chien S., Shyy J.Y. Mechanotransductionin response to shear stress. Roles of receptor tyrosinekinases, integrins, and Shc. J. Biol. Chem. 1999;274(26):18393-18400. DOI 10.1074/jbc.274.26.18393.Cheng C., Tempel D., van Haperen R., van der Baan A., Grosveld F.,Daemen M.J., Krams R., de Crom R. Atherosclerotic lesion size andvulnerability are determined by patterns of fluid shear stress. Circulation.2006;113(23):2744-2753. DOI 10.1161/CIRCULATIONAHA.105.590018.Chiu Y.J., McBeath E., Fujiwara K. Mechanotransduction in an extractedcell model: Fyn drives stretch- and flow-elicited PECAM-1phosphorylation. J. Cell Biol. 2008;182(4):753-763. DOI 10.1083/jcb.200801062.Colic M., Pantovic S., Jeremic M., Jokovic V., Obradovic Z., Rosic M.Transport of low-density lipoprotein into the blood vessel wallduring atherogenic diet in the isolated rabbit carotid artery. Circ. J.2015;79(8):1846-1852. DOI 10.1253/circj.CJ-14-1316.Collins C., Osborne L.D., Guilluy C., Chen Z., O\u2019Brien E.T. 3rd,Reader J.S., Burridge K., Superfine R., Tzima E. Haemodynamicand extracellular matrix cues regulate the mechanical phenotype andstiffness of aortic endothelial cells. Nat. Commun. 2014;5:3984. DOI10.1038/ncomms4984.Cuhlmann S., Van der Heiden K., Saliba D., Tremoleda J.L., Khalil M.,Zakkar M., Chaudhury H., Luong le A., Mason J.C., Udalova I.,Gsell W., Jones H., Haskard D.O., Krams R., Evans P.C. Disturbedblood flow induces RelA expression via c-Jun N-terminal kinase 1:a novel mode of NF-\u03baB regulation that promotes arterialtion. Circ. Res. 2011;108(8):950-959. DOI 10.1161/CIRCRESAHA.110.233841.Dai G., Kaazempur-Mofrad M.R., Natarajan S., Zhang Y., Vaughn S.,Blackman B.R., Kamm R.D., Garc\u00eda-Carde\u00f1a G., Gimbrone M.A. Jr.Distinct endothelial phenotypes evoked by arterial waveforms derivedfrom atherosclerosis-susceptible and -resistant regions of humanvasculature. Proc. Natl. Acad. Sci. USA. 2004;101(41):14871-14876. DOI 10.1073/pnas.0406073101Davis M.E., Grumbach I.M., Fukai T., Cutchins A., Harrison D.G.Shear stress regulates endothelial nitric-oxide synthase promoter activitythrough nuclear factor kappaB binding. J. Biol. Chem. 2003;279(1):163-168. DOI 10.1074/jbc.M307528200.Davis R.J. Signal transduction by the JNK group of MAP kinases. Cell.2000;103:239-252. DOI 10.1016/S0092-8674(00)00116-1.Denis J.F., Scheckenbach K.E.L., Pfenniger A., Meens M.J., Krams R.,Miquerol L., Taffet S., Chanson M., Delmar M., Kwak B.R. Connexin40controls endothelial activation by dampening NF\u03baB activation.Oncotarget. 2017;8(31):50972-50986. DOI 10.18632/oncotarget.16438.Dumaz N., Marais R. Integrating signals between cAMP and the RAS/RAF/MEK/ERK signalling pathways. FEBS J. 2005;272(14):3491-3504. DOI 10.1111/j.1742-4658.2005.04763.x.Erbel C., Akhavanpoor M., Okuyucu D., Wangler S., Dietz A., Zhao L.,Stellos K., Little K.M., Lasitschka F., Doesch A., Hakimi M., DenglerT.J., Giese T., Blessing E., Katus H.A., Gleissner C.A. IL-17Ainfluences essential functions of the monocyte/macrophage lineageand is involved in advanced murine and human atherosclerosis.J. Immunol. 2014;193(9):4344-4355. DOI 10.4049/jimmunol.1400181.Feaver R.E., Gelfand B.D., Wang C., Schwartz M.A., Blackman B.R.Atheroprone hemodynamics regulate fibronectin deposition tocreatepositive feedback that sustains endothelial inflammation.Circ. Res. 2010;106(11):1703-1711. DOI 10.1161/CIRCRESAHA.109.216283.Frangos J.A., Eskin S.G., McIntire L.V., Ives C.L. Flow effects on prostacyclinproduction by cultured human endothelial cells. Science.1985;227(4693):1477-1479. DOI 10.1126/science.3883488Garrett J.P., Lowery A.M., Adam A.P., Kowalczyk A.P., Vincent P.A.Regulation of endothelial barrier function by p120-catenin\u0387VE-cadherininteraction. Mol. Biol. Cell. 2017;28(1):85-97. DOI 10.1091/mbc.E16-08-0616.Gonzalez A.M., Cyrus B.F., Muller W.A. Targeted recycling of the lateralborder recycling compartment precedes adherens junction dissociationduring transendothelial migration. Am. J. Pathol. 2016;186(5):1387-1402. DOI 10.1016/j.ajpath.2016.01.010Gudi S.R., Clark C.B., Frangos J.A. Fluid flow rapidly activates G proteinsin human endothelial cells. Involvement of G proteins in mechanochemicalsignal transduction. Circ. Res. 1996;79(4):834-839.DOI 10.1161/01.RES.79.4.834Gudi S., Huvar I., White C.R., McKnight N.L., Dusserre N., Boss G.R.,Frangos J.A. Rapid activation of Ras by fluid flow is mediated byGalpha(q) and Gbetagamma subunits of heterotrimeric G proteinsin human endothelial cells. Arterioscler. Thromb. Vasc. Biol. 2003;23(6):994-1000. DOI 10.1161/01.ATV.0000073314.51987.84.Gudi S., Nolan J.P., Frangos J.A. Modulation of GTPase activity ofG proteins by fluid shear stress and phospholipid composition. Proc.Natl. Acad. Sci. USA. 1998;95(5):2515-2519. DOI 10.1073/PNAS.95.5.2515.Hajra L., Evans A.I., Chen M., Hyduk S.J., Collins T., Cybulsky M.I.The NF-kappa B signal transduction pathway in aortic endothelialcells is primed for activation in regions predisposed to atheroscleroticlesion formation. Proc. Natl. Acad. Sci. USA. 2000;97(16):9052-9057. DOI 10.1073/pnas.97.16.9052Harrison M., Smith E., Ross E., Krams R., Segers D., Buckley C.D.,Nash G.B., Rainger G.E. The role of platelet-endothelial cell adhesionmolecule-1 in atheroma formation varies depending on the sitespecifichemodynamic environment. Arterioscler. Thromb. Vasc.Biol. 2013;33(4):694-701. DOI 10.1161/ATVBAHA.112.300379.Hughes P.E., Pfaff M. Integrin affinity modulation. Trends. Cell Biol.1998;8(9):359-364. DOI 10.1016/s0962-8924(98)01339-7.Hung O.Y., Molony D., Corban M.T., Rasoul-Arzrumly E., Maynard C.,Eshtehardi P., Dhawan S., Timmins L.H., Piccinelli M., Ahn S.G.,Gogas B.D., McDaniel M.C., Quyyumi A.A., Giddens D.P., SamadyH. Comprehensive assessment of coronary plaque progressionwith advanced intravascular imaging, physiological measures, andwall shear stress: a pilot double-blinded randomized controlled clinicaltrial of nebivolol versus atenolol in nonobstructive coronary arterydisease. J. Am. Heart. Assoc. 2016;5(1):e002764. DOI 10.1161/JAHA.115.002764.Huo Y., Ley K. Adhesion molecules and atherogenesis. Acta Physiol.Scand. 2001;173(1):35-43. DOI 10.1046/j.1365-201X.2001.00882.x.Hynes R.O. Integrins: bidirectional, allosteric signaling machines. Cell.2002;110(6):673-87. DOI 10.1016/s0092-8674(02)00971-6.Jalali S., del Pozo M.A., Chen K., Miao H., Li Y., Schwartz M.A.,Shyy J.Y., Chien S. Integrin-mediated mechanotransduction requiresits dynamic interaction with specific extracellular matrix (ECM) ligands.Proc. Natl. Acad. Sci. USA. 2001;98(3):1042-1046. DOI10.1073/pnas.98.3.1042.Johnson D.S., Chen Y.H. Ras family of small GTPases in immunity andinflammation. Curr. Opin. Pharmacol. 2012;12(4):458-463. DOI10.1016/j.coph.2012.02.003.Ku D.N., Giddens D.P., Zarins C.K., Glagov S. Pulsatile flow and atherosclerosisin the human carotid bifurcation. Positive correlation betweenplaque location and low oscillating shear stress. Arteriosclerosis.1985;5(3):293-302. DOI 10.1161/01.ATV.5.3.293.Kume N., Cybulsky M.I., Gimbrone M.A.Jr. Lysophosphatidylcholine,a component of atherogenic lipoproteins, induces mononuclear leukocyteadhesion molecules in cultured human and rabbit arterial endothelialcells. J. Clin. Invest. 1992;90(3):1138-1144. DOI 10.1172/JCI115932Ledebur H.C., Parks T.P. Transcriptional regulation of the intercellularadhesion molecule-1 gene by inflammatory cytokines in human endothelialcells. Essential roles of a variant NF-kappa B site and p65homodimers. J. Biol. Chem. 1995;270(2):933-943. DOI 10.1074/jbc.270.2.933Libby P., Buring J.E., Badimon L., Hansson G.K., Deanfield J., BittencourtM.S., Tokg\u00f6zo\u011flu L., Lewis E.F. Atherosclerosis. Nat. Rev.Dis. Primers. 2019;5(1):56. DOI 10.1038/s41572-019-0106-zLiu Y., Sweet D.T., Irani-Tehrani M., Maeda N., Tzima E. Shc coordinatessignals from intercellular junctions and integrins to regulateflow-induced inflammation. J. Cell Biol. 2008;182(1):185-196. DOI10.1083/jcb.200709176.Luscinskas F.W., Ding H., Tan P., Cumming D., Tedder T.F., GerritsenM.E. L- and P-selectins, but not CD49d (VLA-4) integrins, mediatemonocyte initial attachment to TNF-alpha-activated vascularendothelium under flow in vitro. J. Immunol. 1996;157(1):326-335.Luscinskas F.W., Kansas G.S., Ding H., Pizcueta P., SchleiffenbaumB.E., Tedder T.F., Gimbrone M.A. Jr. Monocyte rolling, arrestand spreading on IL-4-activated vascular endothelium under flow ismediated via sequential action of L-selectin, beta 1-integrins, andbeta 2-integrins. J. Cell Biol. 1994;125(6):1417-1427. DOI 10.1083/jcb.125.6.1417.Mamdouh Z., Chen X., Pierini L.M., Maxfield F.R., Muller W.A. Targetedrecycling of PECAM from endothelial surface-connectedcompartments during diapedesis. Nature. 2003;421(6924):748-753.DOI 10.1038/nature01300.Mamdouh Z., Kreitzer G.E., Muller W.A. Leukocyte transmigrationrequires kinesin-mediated microtubule-dependent membrane traffickingfrom the lateral border recycling compartment. J. Exp. Med.2008;205(4):951-966. DOI 10.1084/jem.20072328.Mamdouh Z., Mikhailov A., Muller W.A. Transcellular migration ofleukocytes is mediated by the endothelial lateral border recyclingcompartment. J. Exp. Med. 2009;206(12):2795-2808. DOI 10.1084/jem.20082745.Martin T., Cardarelli P.M., Parry G.C., Felts K.A., Cobb R.R. Cytokineinduction of monocyte chemoattractant protein-1 gene expression in human endothelial cells depends on the cooperative action of NFkappaB and AP-1. Eur. J. Immunol. 1997;27(5):1091-1097. DOI10.1002/eji.1830270508.McCormick F. Signal transduction. How receptors turn Ras on. Nature.1993;363(6424):15-16. DOI 10.1038/363015a0.Mohan S., Mohan N., Valente A.J., Sprague E.A. Regulation of lowshear flow-induced HAEC VCAM-1 expression and monocyte adhesion.Am. J. Physiol. 1999;276(5):C1100-1107. DOI 10.1152/ajpcell.1999.276.5.C1100.Morbiducci U., Kok A.M., Kwak B.R., Stone P.H., Steinman D.A.,Wentzel J.J. Atherosclerosis at arterial bifurcations: evidence forthe role of haemodynamics and geometry. Thromb. Haemost. 2016;115(3):484-492. DOI 10.1160/TH15-07-0597.Nagel T., Resnick N., Dewey C.F. Jr., Gimbrone M.A. Jr. Vascular endothelialcells respond to spatial gradients in fluid shear stress byenhanced activation of transcription factors. Arterioscler. Thromb.Vasc. Biol. 1999;19(8):1825-1834. DOI 10.1161/01.ATV.19.8.1825Nebuloni L., Kuhn G.A., M\u00fcller R. A comparative analysis of watersolubleand blood-pool contrast agents for in vivo vascular imagingwith micro-CT. Acad. Radiol. 2013;20(10):1247-1255. DOI10.1016/j.acra.2013.06.003Neish A.S., Williams A.J., Palmer H.J., Whitley M.Z., Collins T. Functionalanalysis of the human vascular cell adhesion molecule 1 promoter.J. Exp. Med. 1992;176(6):1583-1593. DOI 10.1084/jem.176.6.1583.Oeckinghaus A., Hayden M.S., Ghosh S. Crosstalk in NF-\u03baB signalingpathways. Nat. Immunol. 2011;12(8):695-708. DOI 10.1038/ni.2065.O\u2019Keeffe L.M., Muir G., Piterina A.V., McGloughlin T. Vascular celladhesion molecule-1 expression in endothelial cells exposed tophysiological coronary wall shear stresses. J. Biomech. Eng. 2009;131(8):081003. DOI 10.1115/1.3148191.Orr A.W., Sanders J.M., Bevard M., Coleman E., Sarembock I.J.,Schwartz M.A. The subendothelial extracellular matrix modulatesNF-kappaB activation by flow: a potential role in atherosclerosis.J. Cell Biol. 2005;169(1):191-202. DOI 10.1083/jcb.200410073.Otsuka F., Kramer M.C., Woudstra P., Yahagi K., Ladich E., Finn A.V.,de Winter R.J., Kolodgie F.D., Wight T.N., Davis H.R., Joner M.,Virmani R. Natural progression of atherosclerosis from pathologicintimal thickening to late fibroatheroma in human coronary arteries:a pathology study. Atherosclerosis. 2015;241(2):772-782. DOI10.1016/j.atherosclerosis.2015.05.011.Otte L.A., Bell K.S., Loufrani L., Yeh J.-C., Melchior B., Dao D.N.,Stevens H.Y., White C.R., Frangos J.A. Rapid changes in shearstress induce dissociation of a G alpha(q/11)-platelet endothelial celladhesion molecule-1 complex. J. Physiol. 2009;587(Pt.10):2365-2373. DOI 10.1113/jphysiol.2009.172643.Ozerova I.N., Metelskaya V.A., Gavrilova N.E. Atherogenic normolipidemiain men with coronary atherosclerosis: some peculiarities ofsubfractional distribution of apo B-containing lipoproteins. Ateroscleroz= Atherosclerosis. 2018;14(3):5-11. DOI 10.15372/ATER20180301. (in Russian)Paddock C., Zhou D., Lertkiatmongkol P., Newman P.J., Zhu J. Structuralbasis for PECAM-1 homophilic binding. Blood. 2016;127(8):1052-1061. DOI 10.1182/blood-2015-07-660092.Paz dela N.G., Melchior B., Shayo F.Y., Frangos J.A. Heparan sulfatesmediate the interaction between platelet endothelial cell adhesionmolecule-1 (PECAM-1) and the G\u03b1q/11 subunits of heterotrimericG proteins. J. Biol. Chem. 2014;289(11):7413-7424. DOI 10.1074/jbc.M113.542514.Peters W., Charo I.F. Involvement of chemokine receptor 2 and its ligand,monocyte chemoattractant protein-1, in the development ofatherosclerosis: lessons from knockout mice. Curr. Opin. Lipidol.2001;12(2):175-180. DOI 10.1097/00041433-200104000-00011.Resnick N., Collins T., Atkinson W., Bonthron D.T., Dewey C.F. Jr.,Gimbrone M.A. Jr. Platelet-derived growth factor B chain promotercontains a cis-acting fluid shear-stress-responsive element Proc. Natl. Acad. Sci. USA. 1993;90(10):4591-4595. DOI 10.1073/pnas.90.10.4591.Sahebkar A., Morris D.R., Biros E., Golledge J. Association of singlenucleotide polymorphisms in the gene encoding platelet endothelialcell adhesion molecule-1 with the risk of myocardial infarction: a systematicreview and meta-analysis. Thromb. Res. 2013;132(2):227-233. DOI 10.1016/j.thromres.2013.07.007.Sakellarios A.I, Papafaklis M.I., Siogkas P., Athanasiou L.S., ExarchosT.P., Stefanou K., Bourantas C.V., Naka K.K., Michalis L.K.,Parodi O., Fotiadis D.I. Patient-specific computational modeling ofsubendothelial LDL accumulation in a stenosed right coronary artery:effectof hemodynamic and biological factors. Am. J. Physiol.Heart Circ. Physiol. 2013;304(11):H1455-70. DOI 10.1152/ajpheart.00539.2012.Schober A., Siess W. Lysophosphatidic acid in atherosclerotic diseases.Br. J. Pharmacol. 2012;167(3):465-482. DOI 10.1111/j.1476-5381.2012.02021.x.Shaw S.K., Bamba P.S., Perkins B.N., Luscinskas F.W. Real-time imagingof vascular endothelial-cadherin during leukocyte transmigrationacross endothelium. J. Immunol. 2001;167(4):2323-2330. DOI10.4049/jimmunol.167.4.2323.>Shimada H., Rajagopalan L.E. Rho kinase-2 activation in human endothelialcells drives lysophosphatidic acid-mediated expression ofcell adhesion molecules via NF-kappaB p65. J. Biol. Chem. 2010;285(17):12536-12542. DOI 10.1074/jbc.M109.099630.Sigal A., Bleijs D.A., Grabovsky V., van Vliet S.J., Dwir O., FigdorC.G., van Kooyk Y., Alon R. The LFA-1 integrin supports rollingadhesions on ICAM-1 under physiological shear flow in a permissivecellular environment. J. Immunol. 2000;165(1):442. DOI10.4049/jimmunol.165.1.442.Simon M.I., Strathmann M.P., Gautam N. Diversity of G proteins in signaltransduction. Science. 1991;252(5007):802-808. DOI 10.1126/science.1902986.Snyder J.L., McBeath E., Thomas T.N., Chiu Y.J., Clark R.L., FujiwaraK. Mechanotransduction properties of the cytoplasmic tailof PECAM-1. Biol. Cell. 2017;109(8):312-321. DOI 10.1111/boc.201600079.Soulis J.V., Farmakis T.M., Giannoglou G.D., Louridas G.E. Wall shearstress in normal left coronary artery tree. J. Biomech. 2006;39(4):742-749. DOI 10.1016/j.jbiomech.2004.12.026.Spiecker M., Peng H.B., Liao J.K. Inhibition of endothelial vascularcell adhesion molecule-1 expression by nitric oxide involves the inductionand nuclear translocation of IkappaBalpha. J. Biol. Chem.1997;272(49):30969-30974. DOI 10.1074/jbc.272.49.30969.Suo J., Ferrara D.E., Sorescu D., Guldberg R.E., Taylor W.R., GiddensD.P. Hemodynamic shear stresses in mouse aortas \u2013 implicationsfor atherogenesis. Arterioscler. Thromb. Vasc. Biol. 2007;27:346-351. DOI 10.1161/01.ATV.0000253492.45717.46.Timmins L.H., Molony D.S., Eshtehardi P., McDaniel M.C., OshinskiJ.N., Giddens D.P., Samady H. Oscillatory wall shear stress isa dominant flow characteristic affecting lesion progression patternsand plaque vulnerability in patients with coronary artery disease.J. R. Soc. Interface. 2017;14(127):20160972. DOI 10.1098/rsif.2016.0972.Timmins L.H., Molony D.S., Eshtehardi P., McDaniel M.C., OshinskiJ.N., Samady H., Giddens D.P. Focal association between wallshear stress and clinical coronary artery disease progression. Ann.Biomed. Eng. 2015;43(1):94-106. DOI 10.1007/s10439-014-1155-9.Tzima E., del Pozo M.A., Shattil S.J., Chien S., Schwartz M.A. Activationof integrins in endothelial cells by fluid shear stress mediatesRho-dependent cytoskeletal alignment. EMBO J. 2001;20(17):4639-4647. DOI 10.1093/emboj/20.17.4639.Tzima E., Irani-Tehrani M., Kiosses W.B., Dejana E., Schultz D.A.,Engelhardt B., Cao G., DeLisser H., Schwartz M.A. A mechanosensorycomplex that mediates the endothelial cell response to fluidshear stress. Nature. 2005;437(7057):426-431. DOI 10.1038/nature03952.Virani S.S., Alonso A., Benjamin E.J., Bittencourt M.S., CallawayC.W., Carson A.P., Chamberlain A.M., Chang A.R., Cheng S.,Delling F.N., ..., Stokes A., Tirschwell D.L., VanWagner L.B.,Tsao C.W., American Heart Association Council on Epidemiologyand Prevention Statistics Committee and Stroke Statistics Subcommittee.Heart disease and stroke statistics-2020 update: a report fromthe American Heart Association. Circulation. 2020;141(9):e139-e596. DOI 10.1161/CIR.0000000000000757.Whitley M.Z., Thanos D., Read M.A., Maniatis T., Collins T. A strikingsimilarity in the organization of the E-selectin and beta interferongene promoters. Mol. Cell Biol. 1994;14(10):6464-6475. DOI10.1128/mcb.14.10.6464.Wu C., Huang R.T., Kuo C.H., Kumar S., Kim C.W., Lin Y.C.,Chen Y.J., Birukova A., Birukov K.G., Dulin N.O., Civelek M.,Lusis A.J., Loyer X., Tedgui A., Dai G., Jo H., Fang Y. MechanosensitivePPAP2B regulates endothelial responses to atherorelevanthemodynamic forces. Circ. Res. 2015;117(4):e41-e53. DOI 10.1161/CIRCRESAHA.117.306457.Xia T., Liu X., Du C.J., Jin X., Kong X.Q., Li G. Association of Leu125Valpolymorphisms in the PECAM-1 gene with the risk of coronaryheart disease: a meta-analysis. Int. J. Clin. Exp. Med. 2015;8(2):2219-2225.Xing R., De Wilde D., McCann G., Ridwan Y., Schrauwen J.T., van derSteen A.F., Gijsen F.J., Van der Heiden K. Contrast-enhanced micro-CT imaging in murine carotid arteries: a new protocol for computingwall shear stress. Biomed. Eng. Online. 2016;15(Suppl.2):156. DOI10.1186/s12938-016-0270-2Yamamoto K., Ando J. Emerging role of plasma membranes in vascularendothelial mechanosensing. Circ. J. 2018;82(11):2691-2698. DOI10.1253/circj.CJ-18-0052.Yeh J.-C., Otte L.A., Frangos J.A. Regulation of G protein-coupled receptoractivities by the platelet-endothelial cell adhesion molecule,PECAM-1. Biochemistry. 2008;47(34):9029-9039. DOI 10.1021/bi8003846.Yu X.H., Zheng X.L., Tang C.K. Nuclear factor-\u03baB activation as apathological mechanism of lipid metabolism and atherosclerosis.Adv. Clin. Chem. 2015;70:1-30. DOI 10.1016/bs.acc.2015.03.004.Yung Y.C., Stoddard N.C., Chun J. LPA receptor signaling: pharmacology,physiology, and pathophysiology. J. Lipid Res. 2014;55(7):1192-1214. DOI 10.1194/jlr.R046458.Yurdagul A.Jr., Chen J., Funk S.D., Albert P., Kevil C.G., Orr A.W.Altered nitric oxide production mediates matrix-specific PAK2 andNF-\u03baB activation by flow. Mol. Biol. Cell. 2013;24(3):398-408. DOI10.1091/mbc.E12-07-0513.Yurdagul A.Jr., Sulzmaier F.J, Chen X.L., Pattillo C.B., SchlaepferD.D., Orr A.W. Oxidized LDL induces FAK-dependent RSK signalingto drive NF-\u03baB activation and VCAM-1 expression. J. CellSci. 2016;129(8):1580-1591. DOI 10.1242/jcs.182097.Zakkar M., Chaudhury H., Sandvik G., Enesa K., Luong le A.,Cuhlmann S., Mason J.C., Krams R., Clark A.R., Haskard D.O.,Evans P.C. Increased endothelial mitogen-activated protein kinasephosphatase-1 expression suppresses proinflammatory activationat sites that are resistant to atherosclerosis. Circ. Res. 2008;103(7):726-732. DOI 10.1161/CIRCRESAHA.108.183913Zhang W., Tang T., Nie D., Wen S., Jia C., Zhu Z., Xia N., Nie S.,Zhou S., Jiao J., Dong W., Lu B., Xu T., Sun B., Lu Y., Li Y.,Cheng L., Liao Y., Cheng X. IL-9 aggravates the development ofatherosclerosis in ApoE-/- mice. Cardiovasc. Res. 2015;106(3):453-464. DOI 10.1093/cvr/cvv110.Zou Y., Huang X., Feng L., Hou J., Xing L., Yu B. Localization ofin-stent neoatherosclerosis in relation to curvatures and bifurcationsafter stenting. J. Thorac. Dis. 2016;8(12):3530-3536. DOI 10.21037/jtd.2016.11.108."} +{"text": "Senegalia pennata subsp. insuavis (Lace) Maslin, Seigler & Ebinger, Citrus hystrix DC. and Solanum melongena \u2018Kermit\u2019 extracts exhibited high antioxidant activities. Moreover, Citrus hystrix DC. extract was a potent inhibitor against lipase, angiotensin-converting enzyme and butyrylcholinesterase, while Coriandrum sativum L. and Psophocarpus tetragonolobus (L.) DC. were potent anti-diabetic agents and Senegalia pennata subsp. insuavis (Lace) Maslin, and Seigler & Ebinger was a potent anti-glycation agent. Our data provide a comparative analysis of ten vegetables to encourage healthy food consumption and development to control NCDs in Thailand in the future.Non-communicable diseases (NCDs) are the leading global cause of death. The World Health Organization (WHO) has endorsed the consumption of fruits and vegetables because they are rich in phytochemicals that sustainably ameliorate the occurrence of NCDs. Thai food contains many spices and vegetables with recognized health benefits. Quality control of plant samples encountered a bottleneck in the field and comparative studies of plant control origins including species or cultivar identification, growing area and appropriate harvesting time are limited. To address this issue, all plant samples used in this study were cultivated and controlled by the Department of Agriculture, Ministry of Agriculture and Cooperatives, Thailand. The samples were phytochemically screened and determined their health-promoting bioactivities via antioxidant activities and inhibition of NCD-related enzymes including lipase (obesity), \u03b1-amylase and \u03b1-glucosidase (diabetes), angiotensin-converting enzyme (hypertension), as well as acetylcholinesterase, butyrylcholinesterase and \u03b2-secretase (Alzheimer\u2019s disease). The non-enzymatic reaction toward glycation was also evaluated. The results showed that Non-communicable diseases (NCDs) including cancer, diabetes mellitus (type II), cardiovascular diseases, hypertension, and Alzheimer\u2019s disease (AD) are the leading cause of death worldwide. In 2012, the World Health Organization (WHO) reported that NCDs accounted for 68% of morbidity (38 million deaths from 56\u2009million deaths), while over 16 million 40%) were early deaths (<70 years) [0% were eFruits and vegetables are rich in fiber, vitamins, minerals, and phytochemicals including alkaloids, anthocyanins, glucosinolates, flavonoids, phytosterols, phenolic acids and terpenoids that are secondary plant metabolites, with pharmacological effects toward a wide range of ailments including NCDs . PhytochAllium cepa Aggregatum Group, Allium fistulosum L., Allium sativum L., Citrus hystrix DC., Coriandrum sativum L., Cymbopogon citratus (DC.) Stapf, Eryngium foetidum L., Psophocarpus tetragonolobus (L.) DC., Senegalia pennata subsp. insuavis (Lace) Maslin, Seigler & Ebinger, and Solanum melongena \u2018Kermit\u2019 against NCDs. Despite having nothing in common , these plants have been selected based on their regular and frequent usages in most Thai cuisines. All plant samples were vetted for their origin and quality by the Department of Agriculture, Ministry of Agriculture and Cooperatives, Thailand. Thailand is renowned for its mouthwatering cuisine, consisting of a wide variety of textures and aromas emanating from local vegetable ingredients. Scientific reports have identified the health benefits of vegetables used in Thai dishes including antioxidant , anti-inAllium cepa Aggregatum Group (A. cepa), Allium fistulosum L. (A. fistulosum), Allium sativum L. (A. sativum), Citrus hystrix DC. (Ci. hystrix), Coriandrum sativum L. (Co. sativum), Cymbopogon citratus (DC.) Stapf (Cy. citratus), Eryngium foetidum L. (E. foetidum), Psophocarpus tetragonolobus (L.) DC. (P. tetragonolobus), Senegalia pennata subsp. insuavis (Lace) Maslin, Seigler & Ebinger (Se. pennata), and Solanum melongena \u2018Kermit\u2019 (So. melongena). Seven flavonoids were detected: quercetin, kaempferol, hesperidin, luteolin, apigenin, delphinidin, and cyanidin contained two flavonoids at different concentrations. Four extracts possessed only one flavonoid: A. fistulosum (kaempferol), Cy. citratus (luteolin), E. foetidum (kaempferol), and Se. pennata (apigenin). Interestingly, no flavonoids were detected in A. sativum and So. melongena extracts. An aqueous ethanolic extract of Co. sativum was rich in quercetin (166.16 mg/100 g dry weight (DW)), followed by A. cepa and Ci. hystrix , while kaempferol (4.44\u201347.97 mg/100 g DW) was detected in A. fistulosum, Co. sativum, and E. foetidum extracts, with A. fistulosum extract exhibiting the highest (47.97 mg/100 g DW). Hesperdin (453.47 mg/100 g DW) was solely detected in Ci. hystrix extract, luteolin (4.57 mg/100 g DW) in Cy. citratus extract, apigenin (3.46 mg/100 g DW) in Se. pennata extract, and delphinidin (15.77 mg/100 g DW) in P. tetragonolobus extract. Cyanidin was also found in P. tetragonolobus (43.02 mg/100 g DW) and A. cepa (13.35 mg/100 g DW).High-performance liquid chromatography (HPLC) was employed to determine the specific phytochemical profiles covering the flavonoids and phenolic acids of vegetable extracts including cyanidin . Among tp-coumaric acid, and ferulic acid were detected. Caffeic acid and p-coumaric acid were general phenolics as they were observed in six extracts with different concentrations. The highest content of caffeic acid (246.99 mg/100 g DW) was detected in So. melongena extract that also contained minute amounts of p-coumaric acid (2.16 mg/100 g DW). The highest content of p-coumaric acid (68.13 mg/100 g DW) was detected in Cy. citratus extract, which also possessed the highest content of ferulic acid (123.34 mg/100 g DW) and marginal amounts of caffeic acid (15.65 mg/100 g DW). The second most abundant caffeic acid (52.69 mg/100 g DW) was detected in E. foetidum extract, which also contained minute amounts of p-coumaric acid and ferulic acid . An aqueous ethanolic extract of P. tetragonolobus contained the most varieties of phenolic acids including caffeic acid (16.13 mg/100 g DW), vanillic acid (15.71 mg/100 g DW), 4-hydroxybenzoic acid (10.80 mg/100 g DW), and p-coumaric acid (3.85 mg/100 g DW), while 4-hydroxybenzoic acid was only detected in P. tetragonolobus extract. Other than being observed in P. tetragonolobus extract, vanillic acid was also found in Co. sativum but in lower amounts (3.73 mg/100 g DW). This extract also contained caffeic acid (23.81 mg/100 g DW) and p-coumaric acid (5.20 mg/100 g DW). An aqueous ethanolic extract of A. fistulosum was found to possess ferulic acid (23.13 mg/100 g DW) and p-coumaric acid (7.12 mg/100 g DW), while Se. pennata contained only one phenolic acid: caffeic acid (14.92 mg/100 g DW). Interestingly, no phenolic acids were observed in A. cepa, A. sativum, and Ci. hystrix extracts.For phenolic acid determination , five phSe. pennata exhibited the highest TPC, followed by Ci. hystrix, So. melongena, Cy. citratus, A. fistulosum, P. tetragonolobus, E. foetidum, A. cepa, and Co. sativum, respectively, while A. sativum exhibited the lowest (twelve times lower than Se. pennata). A spectrophotometric analysis indicated that TPCs of all vegetable extracts ranged from 1.23 to 15.33 mg gallic acid equivalent (GAE)/g DW . The aquSe. pennata extract exhibiting the highest DPPH radical scavenging activity and A. sativum extract the lowest. For the FRAP assay, results were consistent with the DPPH radical scavenging activities. Se. pennata exhibited the highest reducing ability (62.33 \u03bcmol TE/g DW) of ferric iron (Fe3+) to ferrous iron (Fe2+), while A. sativum exhibited the lowest reducing activity (3.25 \u03bcmol TE/g DW). On the other hand, Ci. hystrix and So. melongena possessed the highest ORAC activities (415.92\u2013418.32 \u03bcmol TE/g DW), while A. cepa exhibited the lowest (15.12 \u03bcmol TE/g DW) at approximately 27-fold lower than Ci. hystrix and So. melongena. Phenolics contribute to a wide range of health benefits, including being antioxidants. Antioxidant activities were investigated covering both hydrogen atom transfer (HAT) and single electron transfer (SET) mechanisms . The ferAll the vegetable extracts contained phenolic acids and flavonoids that contributed to their therapeutic potential, specifically against some NCDs. Therefore, all the extracts were tested for their therapeutic potential against critical enzymes involved in NCDs and non-enzymatic reactions involving anti-glycation properties. Ci. hystrix exhibited the highest lipase inhibition, while A. cepa exhibited the lowest.Lipase is a lipid-degradation enzyme, and lipase inhibitors prevent fatty acid accumulation as one characteristic of obesity . The resCo. sativum (58.4%), E. foetidum (31.2%), and Ci. hystrix (26.6%) showed inhibitory activities of more than 25% converts angiotensin I to angiotensin II, leading to vasoconstriction and increased blood pressure ; therebyA. sativum, inhibited AChE activities in the range of 8.3\u201358.6% using extract concentration of 1 mg/mL , one type of dementia, have been attributed to (i) degradation of the neurotransmitter acetylcholine by acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), or (ii) accumulation of amyloid plaque formed during amyloidogenesis by \u03b2-secretase (BACE-1) . Therefo 1 mg/mL . Among tntration . The hig 1 mg/mL . Among tSe. pennata provided the most potent anti-glycation activities induced by both D-glucose and MG, while A. sativum and A. cepa exhibited poor ability to inhibit glycation reactions.The glycation reaction is a non-enzymatic reaction involving interaction between monosaccharides and amino acids, lipids, or nucleotides. Methylglyoxal (MG), as a by-product of glycolysis, can act as a potent protein-glycation inducing agent. Finally, glycation induced by either D-glucose or MG as advanced glycation end products (AGEs) contributed to several ailments including premature aging and diabetes . The resRelationships between vegetable extracts and TPCs, antioxidant activities, enzyme inhibitory activities and anti-glycation properties were investigated using principal component analysis (PCA) and hierarchical cluster analysis (HCA) to determine the particular characteristics of each vegetable extract. Information gained from these statistical analyses will be helpful to classify Thai vegetables according to their unique health-promoting characteristics. PCA results showed that TPCs, antioxidant activities, enzyme inhibitory activities, and anti-glycation properties of Thai vegetable extracts could be easily classified. . A. cepa and A. sativum (blue letters) were separated from others (red letters). A. cepa and A. sativum (Cluster 1) were separated from the others (cluster 2) and located far away from the centroid , while cluster 2 consisted of A. fistulosum, Ci. hystrix, Co. sativum, Cy. citratus, E. foetidum, P. tetragonolobus, Se. pennata, and So. melongena (red color). The outcome of HCA supported the PCA results , Allium fistulosum L. (A. fistulosum), Allium sativum L. (A. sativum), Citrus hystrix DC. (Ci. hystrix), Coriandrum sativum L. (Co. sativum), Cymbopogon citratus (DC.) Stapf (Cy. citratus), Eryngium foetidum L. (E. foetidum), Psophocarpus tetragonolobus (L.) DC. (P. tetragonolobus), Senegalia pennata subsp. insuavis (Lace) Maslin, Seigler & Ebinger (Se. pennata), and Solanum melongena \u2018Kermit\u2019 (So. melongena) were comparatively analyzed regarding their phenolic profiles (phenolic acids and flavonoids) and in vitro inhibitory activities against some NCDs. The health-promoting activities involved the inhibition of the key enzymes that control NCDs including lipase (obesity), \u03b1-amylase, and \u03b1-glucosidase (diabetes), angiotensin-converting enzyme (hypertension) and acetylcholinesterase, butyrylcholinesterase, and \u03b2-secretase (Alzheimer\u2019s disease) as well as the non-enzymatic anti-glycation reaction (premature aging). Results showed that among these ten plant extracts, A. cepa exhibited the strongest angiotensin-converting enzyme (ACE) inhibition, while A. fistulosum could effectively fight against \u03b2-secretase (BACE-1). Nevertheless, A. sativum seemed to be the least active extract against these NCDs-related enzymes, in which no inhibitory activities against \u03b1\u2013glucosidase, acetylcholinesterase (AChE), and BACE-1 were observed. However, high ACE inhibitory activity was observed in this plant extract, while other enzyme inhibitory activities were quite low (less than 50% inhibition). On the other hand, Ci. hystrix was the most active extract, which exhibited the strongest antioxidant activity and inhibitory activities against lipase, ACE and butyrylcholinesterase (BChE). Co. sativum was highly effective against \u03b1-amylase, while P. tetragonolobus exhibited the highest \u03b1-glucosidase inhibitory activity. Cy. citratus seemed to exhibit low to moderate enzyme inhibitory activities, with the exception of ACE inhibitory activity, which was more than 50% inhibition. E. foetidum exhibited the highest AChE inhibitory activity, while Se. pennata exhibited strong antioxidant activity and ACE inhibitory activity. Similarly, So. melongena was also a good source of antioxidants. From these results, it is of interest to group these plants according to their bioactivities and discuss the following topics in more detail; (i) Se. pennata exhibited the highest reducing and free radical scavenging abilities, while Ci. hystrix and So. melongena possessed the highest oxygen radical absorbance capacity; (ii) Ci. hystrix exhibited the highest lipase inhibition; (iii) Co. sativum and P. tetragonolobus were potential anti-diabetic agents with high inhibitions against carbohydrate-degrading enzymes; (iv) A. cepa, Ci. hystrix, and Se. pennata had the three highest ACE inhibitory activities; (v) Ci. hystrix and E. foetidum were potential anti-Alzheimer\u2019s disease (AD) agents with high inhibitions against acetylcholine degrading enzymes, whereas A. fistulosum acted against amyloid generating enzyme, and (vi) Se. pennata was a potential anti-glycation agent.Interest in indigenous plants for their health benefits in terms of disease prevention beyond nutritional benefits is increasing. Thai cuisine consists of various spices and herbs with unique aromas and flavors that also have health-promoting bioactivities. Copious literature exists on plant beneficial health characteristics, but control of plant origins is lacking, leading to the absence of a comparative analysis of these vegetables. Here, ten vegetables used in Thai cuisine including Se. pennata, Ci. Hystrix, and So. melongena exhibited high antioxidant capacities with the highest total phenolic contents (TPCs). Our results concurred with previous literature suggesting that TPCs and antioxidant activities in various plant extracts were strongly correlated [Se. pennata (or Cha-om in Thai) exhibit strong odor (some define as stinky) and are normally consumed as a blanched vegetable or mixed in an omelet and eaten with spicy sauce. In our study, Se. pennata exhibited high ferric reducing antioxidant power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities, suggesting that antioxidants in this vegetable extract likely possess an ability to transfer one electron to any potential electron acceptors. A previous report suggested that methanolic extract of Se. pennata leaves exhibited high TPCs of 45.3 \u00b5g gallic acid equivalent (GAE)/mg dry extract with half maximal effective concentration (EC50) of 3.6 mg extract/mg DPPH [50) of 2.0 mg/mL [Ci. hystrix and So. melongena exhibited high oxygen radical absorbance capacity (ORAC), suggesting that the antioxidants in these vegetable extracts likely donate hydrogen atoms to free radicals. The fruit peel of Ci. hystrix is commonly used in many Thai recipes (such as chili paste and curry) for its strong and unique aroma. Eggplants in Thailand can be classified into 22 species of Solanum, with 10 cultivars commercially available [So. melongena can be consumed as fresh or blanched vegetables and are the main ingredient in curry. Previous literature also reported high TPCs and antioxidant activities of these two vegetables. Ethanolic extracts of Ci. hystrix fruit peel were previously reported to exhibit TPCs of 0.32 mg GAE/mg extract and DPPH radical scavenging activity with IC50 of 0.09 mg/mL [So. melongena exhibited DPPH radical scavenging activities of 17.52\u201346.13% [Among the vegetable extracts, rrelated ,28. Youn/mg DPPH , while i.0 mg/mL . Our stuvailable . Fruits 2\u201346.13% .Ci. hystrix but not on its anti-obesity property. Interestingly, in this study, fruit peel extract of Ci. hystrix was found to exhibit the highest lipase inhibition, an activity that retards lipid absorption and, thus, is related to the control of obesity. As the most abundantly found flavonoid in fruit peel of Ci. hystrix, hesperidin exhibited IC50 activity of 52.4 \u00b5M against porcine pancreatic lipase [50 of 6.1 \u00b5M [50 of 4 \u00b5M [Ci. hystrix, it was previously found that phenolic acids were generally less active against lipase inhibition than flavonoids [Ci. hystrix with the highest content of hesperidin and moderate amounts of quercetin possessed a potential bioactivity against lipase. Many authors have reported on the biological activities of c lipase , while af 6.1 \u00b5M . Compare of 4 \u00b5M , quercetavonoids ,35. TherCo. sativum and P. tetragonolobus effectively inhibited \u03b1-amylase and \u03b1-glucosidase, respectively. Leaves and young shoots of Co. sativum (coriander) are added to many Thai dishes including soup or stir fry meat as a decorated vegetable with a strong unique aroma. However, recently, coriander has become popular consumed as a fresh side dish vegetable along with other main dishes. Oral administration of the ethanolic leaf extract to mice under induced insulin deficiency resulted in lowered blood glucose [50 value 2.5-times lower than acarbose, a synthetic anti-diabetic drug [Co. sativum leaves inhibited \u03b1-amylase with 19% inhibition using extract concentration of 1 mg/mL [50 of 14.60 \u00b5M against pancreatic \u03b1-amylase, the most abundant flavonoid in Co. sativum leaves as quercetin exhibited IC50 of 12.7 \u00b5M [50 of 20.4 \u00b5M [Co. sativum is a good candidate as an anti-diabetic agent, even its seeds [P. tetragonolobus (or winged bean) is a Thai local vegetable normally consumed as boiled or blanched young bean pod with many spicy sauces. At present, no report on young bean pod of P. tetragonolobus regarding its anti-diabetic property is available. Nevertheless, major phenolics in P. tetragonolobus such as cyanidin and delphinidin effectively inhibited Saccharomyces cerevisiae \u03b1-glucosidase with IC50 values of 17.0 and 4.1 \u00b5M, respectively, compared to acarbose with IC50 of 0.53 \u00b5M [P. tetragonolobus also contained moderate contents of phenolic acids including 4-hydroxybenzoic acid, vanillic acid, caffeic acid and p-coumaric acid, while phenolic acids generally inhibited \u03b1-glucosidase with a lesser effect than flavonoids [As vegetable extracts with potential anti-diabetic properties, glucose ,35,36. T 1 mg/mL . Compare 12.7 \u00b5M , while t 20.4 \u00b5M . With hits seeds ,40,41. L 0.53 \u00b5M . P. tetravonoids ,43,44. Cavonoids . A. cepa, Ci. hystrix and Se. pennata had the three highest ACE inhibitory activities. These results concurred with previous reports indicating that quercetin-rich onion skin extract decreased ambulatory blood pressure in patients under metabolic syndrome (overweight/obese/hypertension) [A. cepa as quercetin exhibited IC50 of 43 \u00b5M against rabbit lung ACE [Ci. hystrix, exhibited half inhibitory activity of quercetin using a concentration of 0.5 mM [Se. pennata (but in low amounts compared to other vegetables) with IC50 of 5.7 mM [Interestingly, all vegetable extracts effectively inhibited ACE at more than 50% inhibition using extract concentration of 1 mg/mL. Among these, tension) . The prelung ACE , while hf 0.5 mM . Caffeicf 5.7 mM .Ci. hystrix and E. foetidum acted as inhibitors for acetylcholine-degrading enzymes, while A. fistulosum showed promise as a potential extract inhibiting amyloid production. Ci. hystrix and E. foetidum were rich in hesperidin and caffeic acid, respectively, while the consumption of hespiridin-rich extract or caffeic acid avoided cognitive dysfunction and learning deficit in vivo [50 against AChE and BChE at 22.8 and 48.9 \u00b5M, respectively, and caffeic acid at 23.36 and 29.19 \u00b5M, respectively [E. foetidum, usually used in the famous sour soup called \u201cTom Yum\u201d was available; thus, future studies on the anti-AD properties of the caffeic acid rich extract of E. foetidum are required. When considering anti-AD via the inhibition of amyloid production, all extracts displayed mild to low BACE-1 inhibition. A. fistulosum and A. cepa gave the two highest anti-BACE-1 activities, albeit carrying different phytochemicals. A. cepa showed high quercetin, while A. fistulosum was high in kaempferol. Quercetin and kaempferol are well-known flavonoids exhibiting anti-BACE-1 properties with IC50 values at 5.4 and 14.7 \u00b5M, respectively [Co. sativum also possessed high quercetin (2.5-fold higher than A. cepa); however, the anti-BACE-1 activity was lower, indicating that multi-interaction of phytochemicals within the extract may display antagonist effects. For anti-AD properties, our data showed that using an extract concentration of 1 mg/mL, in vivo ,49. Hespectively . Thus, hectively . Leaves Se. pennata may be a potential anti-glycation agent for both reactions. Se. pennata is typically fried with egg or with \u201cTom Yum\u201d soup. The glycation reaction and its AGEs relate to free radical productions [Se. pennata exhibited high antioxidant activity covering the SET mechanism due to its high phenolics content. It remains unclear which phytochemicals in Se. pennata exhibit this property because only trace amounts of caffeic acid and apigenin were observed, even though these two compounds were documented for their anti-glycation properties [The glycation reaction leads to the formation of advanced glycation end products (AGEs) that contribute to diseases such as diabetes, AD, and premature aging . The reaductions . Hence, operties ,55.Ci. hystrix). However, ACE inhibitory activity was different from other bioactivities since it was located in a different axis (PC3). Moreover, ACE inhibitory activities of all vegetable extracts were higher than 50%, even though the extract concentration used in this enzyme inhibitory assay was lower (0.2 mg/mL) than others (1 mg/mL in other enzyme inhibitory assays and 0.63 mg/mL in glycation reactions). It was previously reported that other than phenolics that could act as ACE inhibitors, small peptides could also act as effective ACE inhibitors as well [A. cepa and A. sativum exhibited low TPCs, antioxidant activities, and anti-glycation properties. Cluster 2 consisted of A. fistulosum, Ci. hystrix, Co. sativum, Cy. citratus, E. foetidum, P. tetragonolobus, Se. pennata, and So. melongena exhibited high TPCs, antioxidant activities, and enzyme inhibitory activities. Additionally, the principal component analysis (PCA) suggested that the activities that lied in the same axis were closely related to each other. For example, TPCs, antioxidant activities, \u03b1-glucosidase inhibitory activities, AChE inhibitory activities, and anti-glycation properties were on the same axis (PC1). The extract with relatively high TPCs and antioxidant activities would potentially exhibit relatively high anti-\u03b1-glucosidase, AChE, or glycation activities as well , Allium fistulosum L. (A. fistulosum), Allium sativum L. (A. sativum), Citrus hystrix DC. (Ci. hystrix), Coriandrum sativum L. (Co. sativum), Cymbopogon citratus (DC.) Stapf (Cy. citratus), Eryngium foetidum L. (E. foetidum), Psophocarpus tetragonolobus (L.) DC. (P. tetragonolobus), Senegalia pennata subsp. insuavis (Lace) Maslin, Seigler & Ebinger (Se. pennata), and Solanum melongena \u2018Kermit\u2019 (So. melongena) were collected following the recommendation of the Department of Agriculture, Ministry of Agriculture and Cooperatives, Thailand. The samples were deposited at the Bangkok Herbarium (BK), Bangkok, Thailand. Physical appearance of the edible part, harvesting time and the herbarium voucher specimen are provided in A. cepa (bulps), A. fistulosum (leaves), A. sativum (bulps), Ci. hystrix (fruit peel), Co. sativum (leaves), Cy. citratus , E. foetidum (leaves), P. tetragonolobus (whole fruits), Se. pennata (young leaves), and So. melongena (whole fruits) were cleaned with deionized (DI) water before freeze-drying using a Heto PowerDry PL9000 Freeze Dryer for 3 days. The dry samples were then ground into fine powder using a Philips 600W Grinder and expressed as CIELAB units (L* represented dark (0) to white (100), a* represented green (\u2212) to red (+), while b* represented blue (\u2212) to yellow (+)) as shown in Ten vegetables including v/v) aqueous ethanol (1:10 ratio) at 37 \u00b0C for two hours. The mixture was centrifuged at 3800 g for 15 min using a Hettich\u00ae ROTINA 38R centrifuge . The supernatant was collected, while the residue was repeatedly extracted with the same procedure twice. The supernatants from three extractions were pooled, and ethanol was removed by a rotary evaporator . The dried extracts were re-dissolved in DMSO, filtered through a 0.45 \u00b5M polytetrafluoroethylene (PTFE) membrane syringe filter, and kept at \u221220 \u00b0C until analysis. The dry samples were extracted using 80% (v/v) aqueous methanol (40 mL), 6 N HCl (10 mL) and 0.5 g/L tert-butylhydroquinone (tBHQ). Prior to injection into the HPLC system, the extract (10 mg/mL) was filtered through a 0.22 \u03bcM PTFE membrane. Milli-Q water (18.2 M\u2126.cm resistivity at 25 \u00b0C), HPLC-grade methanol, and HPLC-grade acetonitrile containing 0.05% (v/v) trifluoroacetic (TFA) were used as gradient mobile phases with a constant flow rate of 0.6 mL/min [p-coumaric acid , sinapic acid , and syringic acid (>97.0% T) were received from Tokyo Chemical Industry , while vanillic acid (\u226597% HPLC) and gallic acid (97.5\u2013102.5% T) were received from Sigma-Aldrich . The authentic flavonoid standards including quercetin , kaempferol (>97.0% HPLC), luteolin (>98.0% HPLC), hesperidin , naringenin , myricetin (>97.0% HPLC), and apigenin (>98.0% HPLC) were obtained from Tokyo Chemical Industry , while isorhamnetin (\u226599.0% HPLC), cyanidin (\u226596.0% HPLC), and delphinidin (\u226597.0% HPLC) were from Extrasynthese . The phenolic acids were detected at 280 nm and 325 nm, while flavonoids were detected at 338 nm and 368 nm. HPLC chromatograms were shown in To determine the phenolic profile, high-performance liquid chromatography (HPLC) was employed using an Agilent 1100 HPLC system equipped with a photodiode array detector and a Zorbax Eclipse XDB\u2013C18 column as previously described . In brie6 mL/min . The auty is an area under the peak, a is a y-intercept, b is a slope of the calibration curve, and x is a standard concentration. LOD and LOQ were calculated using the following equation:aS is a standard deviation of the response (y-intercept), and b is a slope of the calibration curve. The intra-day precision was presented as a percentage of the relative standard deviation (%RSD) and calculated using the following equation:tRS is a standard deviation of the retention time, and tRMean is the mean of the retention time measured at all concentrations of each standard.Linear range, linear regression, correlation coefficients, limit of quantitation (LOQ), limit of detection (LOD), and relative standard deviation (RSD) of the standards were analyzed according to the protocol of Srinuanchai et al. 2019 as shownTotal phenolic contents (TPCs) were investigated using Folin\u2019s phenol reagent as formerly described . Gallic Antioxidant activities of the extracts were determined using 2,2-diphenyl-1-picrylhydrazyl (DPPH) together with ferric reducing antioxidant power (FRAP) and oxygen radical absorbance capacity (ORAC) assays as previously described . Trolox,TM HT 96-well UV-visible microplate reader and Gen5 data analysis software . To determine the enzyme inhibitory activities of the extracts against some NCDs, key enzymes that control obesity (lipase), diabetes (\u03b1-amylase and \u03b1-glucosidase), hypertension (angiotensin-converting enzyme), and Alzheimer\u2019s disease were chosen for inhibitory reactions using the well-established protocols as previously described ,12,13,22Candida rugosa lipase , 50 \u00b5L of 0.2 mM 5-5\u2032-dithiobis, 10 \u00b5L of 16 mM 5,5\u2032-dithiobis(2-nitrobenzoic acid) (DTNB) and 40 \u00b5L of the extract (5 mg/mL). The inhibitory activity was visualized as a decline in enzyme kinetics at 412 nm.Briefly, the lipase inhibitory reaction consisted of 100 \u00b5L of 0.01 mg/mL p-nitrophenyl-\u03b1-D-maltopentaoside and 50 \u00b5L of the extract (4 mg/mL), while the \u03b1-glucosidase inhibitory reaction consisted of 100 \u00b5L of 0.1 U/mL Saccharomyces cerevisiae \u03b1-glucosidase , 50 \u00b5L of 2 mM p-nitrophenyl-\u03b1-D-glucopyranoside and 50 \u00b5L of the extract (4 mg/mL). The inhibitory activity was visualized as a decline in enzyme kinetics at 405 nm.The \u03b1-amylase inhibitory reaction consisted of 100 \u00b5L of 30 mg/mL porcine pancreatic \u03b1-amylase , 50 \u00b5L of 30 mM o-phthaldialdehyde and 50 \u00b5L of the extract (0.4 mg/mL). The inhibitory activity was evaluated using an excitation wavelength of 360 nm and an emission wavelength of 485 nm as an end-point assay.The angiotensin-converting enzyme (ACE) inhibitory reaction consisted of 3 \u00b5L of 0.5 U/mL rabbit lung ACE (\u22652 unit/mg), 30 \u00b5L of 3 mM hippuryl-histidyl-leucine, 15 \u00b5L of 20 mg/mL Electrophorus electricus AChE (1000 units/mg), 40 \u03bcL of 0.8 mM acetylthiocholine, 10 \u00b5L of 16 mM DTNB and 40 \u00b5L of the extract (5 mg/mL), while the butyrylcholinesterase (BChE) inhibitory reaction consisted of 100 \u00b5L of 0.5 \u00b5g/mL equine serum BChE (\u226510 units/mg), 40 \u00b5L of 0.4 mM butyrylthiocholine, 10 \u00b5L of 16 mM DTNB and 40 \u00b5L of the extract (5 mg/mL). The inhibitory activity was visualized as a decline in enzyme kinetics at 412 nm. The \u03b2-secretase (BACE-1) inhibitory reaction was studied using a BACE-1 fluorescence resonance energy transfer (FRET) assay kit according to the manufacturer\u2019s recommendations. The inhibitory activity of the extract (20 \u00b5L of 5 mg/mL) was evaluated using an excitation wavelength of 320 nm and an emission wavelength of 405 nm as an end-point assay. The acetylcholinesterase (AChE) inhibitory reaction consisted of 100 \u03bcL of 20 ng The anti-glycation reaction induced by D-glucose consisted of 50 \u00b5L of 20 mg/mL bovine serum albumin in 100 mM potassium phosphate buffer (pH 7.4) containing 0.02% (w/v) sodium azide, 25 \u00b5L of 1 M D-glucose and 25 \u00b5L of extract (2.52 mg/mL). For the anti-glycation reaction induced by methylglyoxal (MG), 25 \u00b5L of 4 mM MG was used instead of D-glucose. The reaction mixture was incubated at 37 \u00b0C for 2 weeks in the dark. The inhibitory activity was evaluated using an excitation wavelength of 330 nm and an emission wavelength of 410 nm as an end-point assay.A is the initial velocity of the control reaction with enzyme (control), a is the initial velocity of the control reaction without enzyme (control blank), B is the initial velocity of the enzyme reaction with extract (sample) and b is the initial velocity of the reaction with extract but without enzyme (sample blank). The percentage of enzyme inhibition using an end-point assay and anti-glycation reaction was evaluated using the same equation but changing from initial velocity to absorbance at a particular wavelength.The percentage of enzyme inhibition using enzyme kinetics was calculated using the following equation:\u00ae to create a biplot. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) of TPCs, antioxidant activities and enzymatic and non-enzymatic inhibitory activities of Thai vegetable extracts were performed using XLSTATn = 3), with data expressed as mean \u00b1 standard deviation (SD). Statistical analysis was performed using the statistical package for the social sciences . Significant difference at p < 0.05 of more than two data was calculated using one\u2013way analysis of variance (ANOVA), followed by Duncan\u2019s multiple comparison test, while significantly difference at p < 0.05 of two data was calculated by Student\u2019s t-test. All experiments were evaluated in triplicate ("} +{"text": "Ornithine aminotransferase (OAT) catalyzes transfer of the delta-amino group from L-ornithine to oxo-glutarate.In plants, this reaction biochemically connects urea cycle, proline cycle, and polyamine biosynthesis pathway.OAT activity is shown to be associated with biotic and abiotic stress responses and nitrogen metabolism, but itsphysiological role is still unclear. In our study, we decided to investigate transcriptional regulation of the OAT gene inArabidopsis thaliana under normal conditions and in response to various growth regulators. In the present work, thereporter gene construct containing the Escherichia coli \u03b2-glucuronidase gene (gus) under control of the A. thaliana OATgene promoter was introduced into the genome of A. thaliana ecotype Columbia plants using the floral dip method;GUS activity was assayed in different experimental conditions including hormone treatment, low and high nitrogen andsalinity. The GUS activity was analyzed histochemically. Plants were incubated with staining solution containing X-Gluc.We show that under standard growth conditions, the promoter is active during germination and in developing floralorgans. OAT promoter activity specifically activates in response to different forms of auxin , cytokinin(6- BAP), ethylene precursor (ACC), high nitrogen and salinity. Analysis of the OAT expression by qRT-PCR confirmed thepattern observed using the GUS reporter system. The OAT gene showed a significantly elevated expression in fourday-old seedlings and in plant roots in response to auxins and cytokinins. The analysis of the OAT promoter structurereveals cis-acting regulatory DNA elements associated with auxin regulation and abiotic stresses. The results of thestudy indicate that the OAT gene is involved in developmental processes and is regulated by auxin and cytokinins. The ornithine-\u03b4-aminotransferase (OAT) is a mitochondrialpyridoxal-5-phosphate (PLP)-dependent enzyme that transfersan amino group from ornithine to oxo-glutarate with formationof glutamate-1-semialdehyde (GSA) and glutamate . Although the biochemical function ofOAT is known, its biological role in plants is not fully understood.On the one hand, OAT is involved in metabolism of ornithine,which takes part in numerous biochemical processes inplants, such as arginine metabolism, synthesis of polyaminesand alkaloids . Onthe other hand, one of the products of the reaction mediated byOAT, namely GSA, is involved in proline production. It readilyinterconverts into the cyclic 1-pyrroline-5-carboxylate (P5C),an intermediate in the proline biosynthesis, in a non-enzymaticfashion . Proline is involved in plantstress response anddevelopment . It has already beenshown in various experiments on several plant species thatoverexpression of the OAT gene is associated with increasedproline content and resistance to abiotic stresses . It is tempting to assume thatOAT might link biological processes related to proline, ornithineand P5C metabolism, such as nitrogen recycling, stressresponse, secondary metabolism, growth and development.We have previously shown that OAT overexpression in tobaccoincreases salt stress resistance. Interestingly, the levelof proline accumulation in OAT overexpressing lines did notdiffer from that of WT plants under both normal and stressconditions, suggesting that OAT might contribute to stressresistance through processes not related to proline synthesis. On a model of transgenic tobaccoplants expressing GUS under the control of putative Arabidopsisthaliana OAT promoter we showed that the promoter activityis associated with meristems and zones of active growth. This observation suggests that theOAT gene might be involved in developmental processes. Thepresent study aims to investigate transcriptional regulation ofthe OAT gene in A. thaliana under normal conditions and inresponse to various growth regulators.Development of transgenic Arabidopsis harboring AtOATpromoter construct. The 1844 bp region upstream of theOAT gene translation start was clonedin the promoterless vector pBI101 with the formation of theP1844 construct . The resultingvector contains the expression cassette harboring the \u03b2-glucuronidase(gus) reporter gene under the control of putativeA. thaliana OAT promoter. A. thaliana plants ecotype Columbiawere grown at 22 \u00b0C in a long-day growth conditions (16 hof light and 8 h of dark). Construct P1844 was transformedinto Agrobacterium tumefaciens strain AGL0, which was usedto transform A. thaliana by floral dip method . T1 transformants were screened on 1/2 MS agar platescontaining 50 mg/L kanamycin, transferred to pots and grownto maturity until the T2 generation seeds were harvested.T2 seeds were germinated on 1/2 MS agar plates containing50 mg/L kanamycin and resistant plants were tested for thepresence of GUS activity by histochemical assay. Six independenttransgenic T2 lines showing the presence of GUS activityin seedlings were selected for further experiments. Plants fromthe selected lines were grown to maturity and T3 generationseeds were harvested. Thus, six independent T3 transgeniclines have been obtained.GUS staining. The histochemical staining method was used to visualize GUS (Escherichia coli\u03b2-glucuronidase) activity in seedlings grown on agar platesand plant parts grown in soil (5-week-old plants). Wholeseedlings and different plant parts were incubated in X-Glucsolution Triton-X) for 24 h at 37 \u00b0C. Chlorophyll was removed byrepeated washing in 70 % (v/v) ethanol. GUS activity wasobserved using a ZEISS Stemi 2000-C microscope coupledwith an AxioCam HRc cameraExperimental treatments. Surface-sterilized seeds of sixindependent transgenic A. thaliana lines (T3) were germinatedon MS plates supplemented with 1 % sucrose, 0.7 % agar. Todetect promoter activity during germination, histochemicalassay was performed for seedlings at 3rd, 5th, 6th and 14th dayafter sowing (DAS) on plates. For experimental treatments,one-week-old seedlings were transferred to the same mediumsupplemented with the following growth regulators (fromSigma-Aldrich): auxins , cytokinins , gibberellic acid (10 \u03bc\u041c GA3),100 \u03bc\u041c abscisic acid, 1 m\u041c methyl jasmonate, ethyleneprecursor (50 \u03bc\u041c ACC), high nitrogen (10 mM NH4NO3),high salinity (200 mM NaCl). For low nitrogen treatment,MS NH4NO3-free medium (Duchefa Biochemie) was used.GUS activity was assayed after 1, 4, 6 and 8 days of treatment.For cold and heat treatment, two-week-old transgenicplants were used. For cold treatment, plates with seedlingswere incubated at +4 \u00b0C for 4 h, then for 2 h at 22 \u00b0C; forheat treatment, plates were incubated at +50 \u00b0C for 15 min,then 6 h at 22 \u00b0C.Gene expression analysis (RNA isolation and qRT\u2011PCR).Wild type Col-0 seed was surface sterilized with 12.5 %bleach and 70 % ethanol and germinated on 1/2 MSmedium . To measure expression ofthe OAT gene during germination and early development,total RNA was isolated from whole seedlings at 4th, 7th and14th DAS. For experimental treatments, one-week seedlingswere transferred to 1/2 MS medium supplemented with differentgrowth regulators , and control, to 1/2 MSmedium. For each treatment, experiment was performed inthree biological replicates. There were 30 seedlings per eachbiological replicate. Total RNA was isolated from roots ofseedlings after 6 days of treatment with the RNeasy PlantMini Kit (Qiagen). RNA was treated with DNAse (QIAGENRNase-Free DNase Set). The concentration of RNA wasmeasured by NanoDrop 2000 (Thermo Scientific). The qualityof RNA was evaluated using Bioanalyzer 2100 (Agilent).First strand cDNA was synthesized from 1 \u03bcg of total RNAusing BIORAD iScript\u2122 Reverse Transcription Supermixfor RT-qPCR. For qRT-PCR analysis, cDNA was diluted tentimes. PCR was performed in a final volume of 15 \u03bcL: 3 \u03bcLof 5\u0445 Low Rox buffer (SibEnzyme), 0.15 \u03bcL of each primer(10 \u03bcM) and the taqman probe solution, 3 \u03bcL of diluted cDNA. The primers and probes were designed using IDT\u2019sPrimerQuest Tool (https://eu.idtdna.com/PrimerQuest/). Thecomparative threshold cycle method was used to determinerelative gene expression, with the expression of EF1-alfa andF-box (accession no. At1g13320 and At5g15710) serving asan internal control. The structures of primers and probes aregiven in Suppl. Table 11. The relative expression levels ofOAT mRNA in all the treated samples were quantified usingan Applied biosystems 7500 Real Time PCR System. Eachreaction was performed in three technical replicates usingthe following program of the qRT-PCR; 95 \u00b0C for 10 min;45 cycles of 95 \u00b0C for 15 s, 68 \u00b0C for 60 s. Statistical analysiswas performed using Student\u2019s t-test. p-values < 0.05 wereconsidered significant.http://www.bionet.nsc.ru/vogis/download/pict-2022-26/appx4.pdfSupplementary Tables 1\u20134 are available in the online version of the paper:Web tools used for cis-acting regulatory DNA elementssearch and expression data analysis. Search of cis-actingregulatory elements was performed using the PLACE database. Gene expression data from different microarray and RNA-seq experiments were extracted fromExpression Atlas and Arabidopsis eFP Browser Web tools.Tissue-specific promoter activation at different developmentalstages and under experimental treatments. StrongGUS staining was detected in hypocotyls and cotyledons ofseedlings at 3\u20134th DAS. At later stages, the GUS activity wasobserved only in cotyledons. In 6- and 14- DAS seedlings, theGUS activity was found only in the distal parts of cotyledons. During flower development, the GUS activity wasobserved in anthers, carpels and developing seeds of growingsiliques .To get a deeper insight into the transcriptional regulationof OAT, transgenic seedlings were subjected to experimentaltreatments including different concentrations of growth regulatorsand phytohormones auxins, cytokinins, gibberellin, ABA,methyl jasmonate, ethylene precursor (ACC), low and highnitrogen, high salinity, cold and heat stress . We observed tissue-specific OAT promoter activity inresponse to different forms of auxin ,cytokinin (6-BAP), and ACC. The strongest GUS activity wasobserved in response to 2,4-D in whole plant. Treatment withIAA and NAA caused GUS activation in root tips; treatmentwith 6-BAP \u2013 in the zone of root hairs. Treatment with ACC,salinity and nitrogen activated promoter along the whole root.OAT gene expression analysis. The qRT-PCR resultsshowed that transcript levels of the OAT gene are significantlyhigher in four-day-old seedlings, than at later developmentalstages . In experimental treatments, the OATgene showed significantly ( p \u2264 0.05) elevated expression inresponse to different forms of auxin andcytokinin (6-BAP) in comparison to control conditions. Treatmentwith synthetic auxin 2,4-D led to 3-fold increase in OATexpression level in roots .Cis-acting regulatory DNA elements search and transcriptomicdata analysis. \u0421is-acting regulatory DNA elementssearch revealed putative transcription factors bindingsites, corresponding to different physiological processes, includinghyperosmotic and hypoosmotic stress response, auxinresponse, axillary bud dormancy control, specific regulation inontogenesis (Suppl. Table 3). Meta-analysis of microarray andRNA-seq data shows that the OAT expression level changes in responseto cold, drought, heat, wounding, osmotic and salt stress. Expressionincreases in response to pathogens Botrytis cinerea,Pseudomonas syringae, Phytophthora infestans and someother infections. Altered OAT gene expression was observedin response to different hormones: it increased in response to3 h of treatment with ABA, methyl jasmonate, and decreasedin response to 3 h of treatment with brassinosteroids. The OATgene demonstrates high expression in seeds, siliques, embryos,senescent leaves, floral organs in A. thaliana (Suppl. Table 4).For more than a decade OAT has been considered an enzymeinvolved in metabolic response to different stress conditions,such as osmotic stress, pathogen attack and ROS production,nitrogen starvation, etc. . This enzyme belongs to the networkof nitrogen-metabolizing pathways in plants, affected byvarious environmental stimuli. It has been shown that plantsaccumulate proline during stress conditions . The results of Funck et al. (2008) and ourprevious study did not support the hypothesis of OAT contributionto proline accumulation. Instead, a specific role of the OATgene in plant developmental and growth processes under bothnormal and stress conditions is hypothesized . This study provides a deeper insight intothe role of the OAT gene in plant development.The important metabolic role of the OAT was clearly shownin an experiment where OAT-deficient plants failed to developwith arginine or ornitine as the sole nitrogen source . This result demonstrated that OAT is requiredfor utilization of arginine and ornithine. The present studydemonstrates high OAT promoter activity and elevated OATtranscript level during seed germination. These results are inagreement with available transcriptomic data . In arginine catabolism, OAT acts downstream ofarginase . Arginine is regarded as a majornitrogen storage compound in seeds. Urease and arginaseactivities increase sharply during germination in A. thaliana and other plant species . Taken together, these data provide evidence for OATinvolvement in nitrogen reorganization during seed germinationtogether with other enzymes of arginine catabolism.Our work also shows that the OAT gene promoter is activeduring inflorescence development. This observation isin accordance with recent findings showing that the OATenzymeplays a role in flower development and seed settingin rice . It has been reported that rice plantswith a mutated OAT gene (OsOAT mutants) have differentabnormalities in inflorescence and seed development. Themutant phenotype of the OsOAT mutant could be rescued byapplication of urea . Authors assumed thatOAT mediates arginase activity and plays a role in regulationof nitrogen reutilization, which is critical for developing tissues.Taking into account the association between the OAT geneexpression and proline accumulation , it can be assumed that OAT enzyme activity may also play a role in control of proline level duringinflorescence development. It has been reported that someproline metabolic enzymes can regulate a number of developmentalprocesses including flowering time , pollen development and root growth . Prolineis known to be accumulated in reproductive organs of manyplant species . Ornithine to prolineconversion is mediated by the plant oncogene RolD , the overexpression of which stimulates floweringand affects inflorescence architecture in transgenic tobaccoplants . This study shows that the OATpromoter is active in inflorescences on different developmentalstages , suggesting that the OAT enzyme canconvert ornithine to proline directly or indirectly via argininecatabolism and glutamate production and might serve as aregulator of proline level during inflorescence development.Tissue-specific activation of the OAT transcription in rootsin response to auxin and cytokinin treatments, as well as thepresence of the auxin-responsive element in the OAT promoter(see Suppl. Table 3) allow us to assume specific regulation ofthe OAT gene during root growth and development. Recentfindings show the importance of nutrient and especially nitrogensignaling for root development and its interplay with hormoneregulation. Thus, cytokinins negatively regulate uptakeof nitrogen, but enhance nitrate distribution and translocation. Auxin level was shown to be elevated in rootsof plants growing on a low-nitrogen medium, while in roots ofplants growing on a medium with high nitrate concentrationthe auxin level was decreased. The reduction of auxin contentcorrelated with the degree of inhibition of root growth andlateral root development . The root growthregulation is associated with local reorganization of nitrogenmetabolism . Thereby, OAT may play animportant role in hormone-dependent fine-tuning of nitrogenmetabolism during the process of root development.The data regarding the OAT transcription activation in a widespectrum of experimental conditions, which was shown inour experiment and other studies, support the hypothesis thatornithine aminotransferase provides a link between differentbiochemical pathways of nitrogen conversion and contributesto the complicated signaling network regulating plantdevelopment.The authors declare no conflict of interest.Ballas N., Wong L.M., Theologis A. Identification of the auxin-responsiveelement, AuxRE, in the primary indoleacetic acid-inducible gene,PS-IAA4/5, of pea (Pisum sativum). J. Mol. Biol. 1993;233:580-596.DOI 10.1006/jmbi.1993.1537.Biancucci M., Mattioli R., Forlani G., Funck D., Costantino P., TrovatoM. Role of proline and GABA in sexual reproduction of angiosperms.Front. Plant Sci. 2015a;6:680. DOI 10.3389/fpls.2015.00680.Biancucci M., Mattioli R., Moubayidin L., Sabatini S., Costantino P.,Trovato M. Proline affects the size of the root meristematic zone inArabidopsis. BMC Plant Biol. 2015b;15:263. DOI 10.1186/s12870-015-0637-8.Clough S.J., Bent A.F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J.1998;16:735-743. DOI 10.1046/j.1365-313X.1998.00343.x.Funck D., Stadelhofer B., Koch W. Ornithine-delta-aminotransferaseis essential for arginine catabolism but not for proline biosynthesis.BMC Plant Biol. 2008;8:40. DOI 10.1186/1471-2229-8-40.Gerasimova S.V., Gorelova V.V., Dorogina O.V., Zhmud E.V., KovalV.S., Romanova A.V., Kochetov A.V., Shumny V.K. Analysis oftranscriptional activity of the Arabidopsis thaliana ornithine-deltaaminotransferasegene promoter. Russ. J. Genet. 2011a;47:625-628.DOI 10.1134/S1022795411050073Gerasimova S.V., Kochetov A.V., Ibragimova S.S., Shumnyi V.K.Functions of delta-ornithine aminotransferase in plants. UspekhiSovremennoi Biologii = Advances in Current Biology. 2011b;131:531-542. (in Russian)Gerasimova S.V., Kolodyazhnaya Y.S., Titov S.E., Romanova A.V.,Koval\u2019 V.S., Kochetov A.V., Shumnyi V.K. Tobacco transformantsexpressing the Medicago truncatula ornithine aminotransferasecDNA. Russ. J. Genet. 2010;46(7):890-893. DOI 10.1134/S102279541007015X.Gilles L., Bluteau D., Boukour S., Chang Y., Zhang Y., Robert T.,Dessen P., Debili N., Bernard O.A., Vainchenker W., Raslova H.MAL/ SRF complex is involved in platelet formation and megakaryocytemigration by regulating MYL9 (MLC2) and MMP9. Blood.2009;114(19):4221-4232. DOI 10.1182/blood-2009-03-209932.Ginguay A., Cynober L., Curis E., Nicolis I. Ornithine aminotransferase,an important glutamate-metabolizing enzyme at the crossroadsof multiple metabolic pathways. Biology. 2017;6(1):18. DOI10.3390/biology6010018.Gu J., Li Z., Mao Y., Struik P.C., Zhang H., Liu L., Wang Z., Yang J.Roles of nitrogen and cytokinin signals in root and shoot communicationsin maximizing of plant productivity and their agronomicapplications. Plant Sci. 2018;274:320-331. DOI 10.1016/j.plantsci.2018.06.010.Hayat S., Hayat Q., Alyemeni M.N., Wani A.S., Pichtel J., Ahmad A.Role of proline under changing environments. Plant Signal. Behav.2012;7:1456-1466. DOI 10.4161/psb.21949.Higo K., Ugawa Y., Iwamoto M., Korenaga T. Plant cis-acting regulatoryDNA elements (PLACE) database: 1999. Nucleic Acids Res.1999;27:297-300. DOI 10.1093/nar/27.1.297.Jefferson R.A., Kavanagh T.A., Bevan M.W. GUS fusions: beta-glucuronidaseas a sensitive and versatile gene fusion marker in higherplants. EMBO J. 1987;6:3901-3907. DOI 10.1073/pnas.1411926112.Kavi Kishor P.B., Kumari P.H., Sunita M.S.L., Sreenivasulu N. Role ofproline in cell wall synthesis and plant development and its implicationsin plant ontogeny. Front. Plant Sci. 2015;6:544. DOI 10.3389/fpls.2015.00544.Kiba T., Krapp A. Plant nitrogen acquisition under low availability:regulation of uptake and root architecture. Plant Cell Physiol. 2016;57:707-714. DOI 10.1093/pcp/pcw052.Kiba T., Kudo T., Kojima M., Sakakibara H. Hormonal control of nitrogenacquisition: roles of auxin, abscisic acid, and cytokinin. J. Exp.Bot. 2011;62:1399-1409. DOI 10.1093/jxb/erq410.Kochetov A.V., Titov S.E., Kolodyazhnaya Y.S., Komarova M.L.,Koval V.S., Makarova N.N., Ilyinskyi Y.Y., Trifonova E.A., ShumnyV.K. Tobacco transformants bearing antisense suppressor of prolinedehydrogenase gene are characterized by higher proline contentand cytoplasm osmotic pressure. Russ. J. Genet. 2004;40:216-218.DOI 10.1023/B:RUGE.0000016999.53466.e1.Liu C., Xue Z., Tang D., Shen Y., Shi W., Ren L., Li Y., Cheng Z. Ornithine\u03b4-aminotransferase is critical for floret development and seedsetting through mediating nitrogen reutilization in rice. Plant J.2018;96:842-854. DOI 10.1111/tpj.14072.Majumdar R., Minocha R., Minocha S.C. Ornithine: at the crossroadsof multiple paths to amino acids and polyamines. In: D\u2019Mello J.P.F.(Ed.) Amino Acids in Higher Plants. Ch. 9. Osfordshire, UK: CABI,2015;156-176.Mattioli R., Biancucci M., Lonoce C., Costantino P., Trovato M. Prolineis required for male gametophyte development in Arabidopsis.BMC Plant Biol. 2012;12:236. DOI 10.1186/1471-2229-12-236.Mattioli R., Marchese D., D\u2019Angeli S., Altamura M.M., Costantino P.,Trovato M. Modulation of intracellular proline levels affects floweringtime and inflorescence architecture in Arabidopsis. Plant Mol.Biol. 2008;66:277-288. DOI 10.1007/s11103-007-9269-1.Mauro M.L., Trovato M., De Paolis A., Gallelli A., Costantino P., AltamuraM.M. The plant oncogene rolD stimulates flowering in transgenictobacco plants. Dev. Biol. 1996;180:693-700. DOI 10.1006/dbio.1996.0338.Papatheodorou I., Fonseca N.A., Keays M., Tang Y.A., Barrera E., BazantW., Burke M., F\u00fcllgrabe A., Fuentes A.M.-P., George N., HuertaL., Koskinen S., Mohammed S., Geniza M., Preece J., JaiswalP.,Jarnuczak A.F., Huber W., Stegle O., Vizcaino J.A., Brazma A.,Petryszak R. Expression Atlas: gene and protein expression acrossmultiple studies and organisms. Nucleic Acids Res. 2018;46:D246-D251. DOI 10.1093/nar/gkx1158.Qamar A., Mysore K.S., Senthil-Kumar M. Role of proline and pyrroline-5-carboxylate metabolism in plant defense against invadingpathogens. Front. Plant Sci. 2015;6:503. DOI 10.3389/fpls.2015.00503.Roosens N.H., Al Bitar F., Loenders K., Angenon G., Jacobs M.Overexpression of ornithine-\u03b4-aminotransferase increases prolinebiosynthesis and confers osmotolerance in transgenic plants. Mol.Breed. 2002;9:73-80. DOI 10.1023/A:1026791932238.Roosens N.H., Thu T.T., Iskandar H.M., Jacobs M. Isolation of theornithine-\u03b4-aminotransferase cDNA and effect of salt stress on itsexpression in Arabidopsis thaliana. Plant Physiol. 1998;117:263-271. DOI 10.1104/pp.117.1.263Satoh R., Nakashima K., Seki M., Shinozaki K., Yamaguchi-ShinozakiK. ACTCAT, a novel cis-acting element for proline-and hypoosmolarity-responsive expression of the ProDH gene encoding prolinedehydrogenase in Arabidopsis. Plant Physiol. 2002;130:709-719.DOI 10.1104/pp.009993.Suzuki M., Ketterling M.G., McCarty D.R. Quantitative statistical analysisof cis-regulatory sequences in ABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis. Plant Physiol. 2005;139:437-447.DOI 10.1104/pp.104.058412.Tatematsu K., Ward S., Leyser O., Kamiya Y., Nambara E. Identificationof cis-elements that regulate gene expression during initiation ofaxillary bud outgrowth in Arabidopsis. Plant Physiol. 2005;138(2):757-766. DOI 10.1104/pp.104.057984Trovato M., Maras B., Linhares F., Costantino P. The plant oncogenerolD encodes a functional ornithine cyclodeaminase. Proc. Natl.Acad. Sci. USA. 2001;98:13449-13453. DOI 10.1073/pnas.231320398Verbruggen N., Hermans C. Proline accumulation in plants: a review.Amino Acids. 2008;35(4):753-759. DOI 10.1007/s00726-008-0061-6.Verslues P.E., Sharma S. Proline metabolism and its implications forplant-environment interaction. Arabidopsis Book. 2010;8:e0140.DOI 10.1199/tab.0140.Winter D., Vinegar B., Nahal H., Ammar R., Wilson G.V., Provart N.J.An \u201cElectronic Fluorescent Pictograph\u201d browser for exploring andanalyzing large-scale biological data sets. PLoS One. 2007;2(8):e718. DOI 10.1371/journal.pone.0000718.Winter G., Todd C.D., Trovato M., Forlani G., Funck D. Physiologicalimplications of arginine metabolism in plants. Front. Plant Sci.2015;6:534. DOI 10.3389/fpls.2015.00534.Wu L., Fan Z., Guo L., Li Y., Zhang W., Qu L.J., Chen Z. Over-expressionof an Arabidopsis \u03b4-OAT gene enhances salt and droughttolerance in transgenic rice. Chinese Sci. Bull. 2003;48:2594-2600.DOI 10.1360/03wc0218.Zonia L.E., Stebbins N.E., Polacco J.C. Essential role of urease ingermination of nitrogen-limited Arabidopsis thaliana seeds. PlantPhysiol. 1995;107:1097-1103. DOI 10.1104/pp.107.4.1097."} +{"text": "Estrogen receptor beta signaling in CD8+ T cells boosts T cell receptor activation and antitumor immunity through a phosphotyrosine switch. J Immunother Cancer 2021;9:e001932. doi:10.1136/jitc-2020-001932Yuan B, Clark CA, Wu B, This article has been corrected since it first published. The provenance and peer review statement has been added."} +{"text": "DTG/3TC is a complete 2-drug regimen (2DR) for the treatment of HIV-1 infection. Non-inferior virologic efficacy has been proven over 3 years in treatment-naive people living with HIV (PLWH) and 2 years in a stable switch setting. TANGO, a randomized, open-label, non-inferiority study, evaluates efficacy and safety of switching to DTG/3TC in PLWH who are virologically suppressed vs remaining on a 3- or 4-drug TAF-based regimen (TBR), stratified by baseline 3rd agent class. Week 144 analyses assessed non-inferiority (NI) with a 4% NI margin for Snapshot virologic failure (VF) and 8% for virologic success .P=0.044 (2-sided). Snapshot VS was high in both arms and demonstrated non-inferiority (Table). Zero pts on DTG/3TC and 3 (0.8%) on TBR met confirmed virologic withdrawal criteria with no resistance observed. Zero pts on DTG/3TC and 6 (1.6%) on TBR discontinued for lack of efficacy. Overall AE rates were similar between arms (Table). TC, LDL-C, and triglycerides improved with DTG/3TC, HDL-C improved with TBR, with no difference in TC/HDL-C ratio between arms. Changes in eGFR (cystatin C) and proximal tubular function marker were similar across arms. Adjusted mean change from BL in weight was 2.2 and 1.7 kg in the DTG/3TC and TBR arms, respectively, and proportion of pts with > 10% weight increase was similar across arms .Of 741 randomized/exposed pts , most pts entered the study on EVG/c (66%). For Week 144 Snapshot VF, switching to DTG/3TC was non-inferior to continuing TBR in the ITT-E analysis: 0.3% vs 1.3%; adjusted difference (95% CI): \u22121.1% and superior to TBR in the per-protocol analysis: 0% vs 1.1%; adjusted difference: \u22121.1% ; Table. Efficacy and Key Safety Results for the ITT-E and Safety PopulationSwitching to the 2-drug regimen of DTG/3TC from a TAF-based 3- or 4-drug regimen resulted in high, non-inferior efficacy with zero confirmed virologic withdrawals and good tolerability over 3 years of treatment. DTG/3TC 2DR is a robust switch option with durable efficacy, good safety and tolerability, and a high barrier to resistance.Olayemi Osiyemi, M.D, Gilead Merck (Advisor or Review Panel member)ViiV Healthcare Fiona Bisshop, MBBBS, Gilead (Grant/Research Support)ViiV Healthcare (Grant/Research Support) St\u00e9phane De Wit, MD, Gilead (Grant/Research Support)Janssen (Grant/Research Support)Merck Sharpe & Dohme (Grant/Research Support)ViiV Healthcare (Grant/Research Support) Joaqu\u00edn Portilla, MD, AbbVie Gilead Janssen Merck Sharpe & Dohme ViiV Healthcare Jean-Pierre Routy, MD, FRCPC, ViiV Healthcare (Grant/Research Support) Mounir Ait-Khaled, PhD, ViiV Healthcare (Employee) Keith Pappa, PharmD, Glaxo Smith Kline (Shareholder)ViiV Healthcare (Employee) Ruolan Wang, Master of Science, ViiV Healthcare (Employee) Peter Leone, MD, viiv healthcare (Employee) Jonathan Wright, MSc, GlaxoSmithKline Brian Wynne, MD, ViiV Healthcare Jean A. van Wyk, MB,ChB, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Michael Aboud, MBChB, MRCP, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Kimberly Smith, MD, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee)"} +{"text": "The gut microbiota is associated with diverse age-related disorders. Several rejuvenation methods, such as probiotic administration and faecal microbiota transplantation, have been applied to alter the gut microbiome and promote healthy ageing. Nevertheless, prolongation of the health span of aged mice by remodelling the gut microbiome remains challenging.Akkermansia and the butyrate biosynthesis pathway in the rejuvenated mouse group. Furthermore, oral administration of Akkermansia sufficiently ameliorated the senescence-related phenotype in the intestinal systems in aged mice and extended the health span, as evidenced by the frailty index and restoration of muscle atrophy.Here, we report the changes in gut microbial communities and their functions in mouse models during ageing and three rejuvenation procedures including co-housing, serum-injection and parabiosis. Our results showed that the compositional structure and gene abundance of the intestinal microbiota changed dynamically during the ageing process. Through the three rejuvenation procedures, we observed that the microbial community and intestinal immunity of aged mice were comparable to those of young mice. The results of metagenomic data analysis underscore the importance of the high abundance of Akkermansia. Our results provide a rationale for developing therapeutic strategies to achieve healthy active ageing.In conclusion, the changes in key microbial communities and their functions during ageing and three rejuvenation procedures, and the increase in the healthy lifespan of aged mice by oral administration of Video abstractThe online version contains supplementary material available at 10.1186/s40168-021-01189-5. Health span is determined by the interactions between genetic and environmental factors , 2. In pAkkermansia muciniphila (AK) induces mucus production in the gut, which is critical for supporting intestinal integrity and other beneficial symbioses or aged mice were systemically treated with serum (100 \u03bcL per mouse) isolated from young mice by intravenous injection into the tail vein eight times (for 3 weeks) or sixteen times (for 6 weeks).Young ; (ii) hetero-chronic including hetero-young and hetero-aged ; and (iii) iso-aged . After the suturing procedure, the mice were monitored daily for 6 weeks for signs of pain and distress. Body weight was recorded once per week. Circulatory exchange between parabiotic pairs was confirmed by injecting Evans blue dye /), and filtered through a strainer. Antibodies were purchased from BD Biosciences or BioLegend. BM cells were stained as previously described ; DAT, D-alanine transaminase [EC:2.6.1.21]; glutaryl-CoA dehydrogenase [EC:1.3.8.6]; lysine 2,3-aminomutase [EC:5.4.3.2]; beta-lysine 5,6-aminomutase [EC:5.4.3.3]; trans-2-enoyl-CoA reductase [EC:1.3.1.38]; acyl-CoA thioesterase YciA [EC:3.1.2.-]; PRPP, phosphoribosyl pyrophosphate; phosphoribosyl-ATP pyrophosphohydrolase [EC:3.6.1.31]; phosphoribosyl-AMP cyclohydrolase [EC:3.5.4.19]; phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase [EC:5.3.1.16]; imidazoleglycerol-phosphate dehydratase [EC:4.2.1.19]; histidinol-phosphate aminotransferase [EC:2.6.1.9]; histidinol-phosphatase (PHP family) [EC:3.1.3.15]; histidinol dehydrogenase [EC:1.1.1.23]; histidine ammonia-lyase [EC:4.3.1.3]; urocanate hydratase [EC:4.2.1.49]; imidazolonepropionase [EC:3.5.2.7]; GAD, glutamate decarboxylase [EC:4.1.1.15]; pectinesterase [EC:3.1.1.11]; pectate lyase [EC:4.2.2.2]; pectate disaccharide-lyase [EC:4.2.2.9]; oligogalacturonide lyase [EC:4.2.2.6]; glucuronate isomerase [EC:5.3.1.12]; tagaturonate reductase [EC:1.1.1.58]; altronate hydrolase [EC:4.2.1.7]; mannonate dehydratase [EC:4.2.1.8]; fructuronate reductase [EC:1.1.1.57]; L-xylulokinase [EC:2.7.1.53]; 3-dehydro-L-gulonate-6-phosphate decarboxylase [EC:4.1.1.85]; L-xylulokinase [EC:2.7.1.53]; L-ribulokinase [EC:2.7.1.16]; L-arabinose isomerase [EC:5.3.1.4]; xylulokinase [EC:2.7.1.17]; L-xylulose reductase [EC:1.1.1.10]; aldehyde reductase [EC:1.1.1.21]; D-xylulose reductase [EC:1.1.1.9]; rhamnulokinase [EC:2.7.1.5]; rhamnulose-1-phosphate aldolase [EC:4.1.2.19]; FabD, [acyl-carrier-protein] S-malonyltransferase [EC:2.3.1.39]; FabH, 3-oxoacyl-[acyl-carrier-protein] synthase III [EC:2.3.1.180]; FabG, 3-oxoacyl-[acyl-carrier protein] reductase [EC:1.1.1.100]; FabZ, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase [EC:4.2.1.59]; FabK, enoyl-[acyl-carrier protein] reductase II [EC:1.3.1.-]; FabL, enoyl-[acyl-carrier protein] reductase III [EC:1.3.1.-]; FabF, 3-oxoacyl-[acyl-carrier-protein] synthase II [EC:2.3.1.179]; FabB, 3-oxoacyl-[acyl-carrier-protein] synthase I [EC:2.3.1.41]; YciA, acyl-CoA thioesterase [EC:3.1.2.-]; GSR, glutathione reductase (NADPH) [EC:1.8.1.7]; phospholipid-hydroperoxide glutathione peroxidase [EC:1.11.1.12]; PepA, leucyl aminopeptidase [EC:3.4.11.1]; PepD; dipeptidase D [EC:3.4.13.-]; PepN; aminopeptidase N [EC:3.4.11.2]; glutamate--cysteine ligase [EC:6.3.2.2]; GAD, glutamate decarboxylase [EC:4.1.1.15]; 2-hydroxyglutarate dehydrogenase [EC:1.1.99.2]; glutaconate CoA-transferase [EC:2.8.3.12]; ptb; phosphate butyryltransferase [EC:2.3.1.19]; buk; butyrate kinase [EC:2.7.2.7]; trans-2-enoyl-CoA reductase [EC:1.3.1.38]; acyl-CoA thioesterase YciA [EC:3.1.2.-]. h, Schematic summary shows key metabolic differences between young and aged group based on relative gene abundance profiles. Host metabolism is influenced by \u03b3-aminobutyric acid (GABA) neurotransmitter, affecting the brain (inducing satiety) GABA modulates inflammation. Fermentation of pectin by intestinal-specific bacteria produces butyrate. It affects host metabolism in several ways by acting on the G protein-coupled receptor (GPR) expressed by intestinal endocrine cells. Butyrate stimulates the release of glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), affecting the pancreas (inducing insulin secretion) and brain (inducing satiety). Lipopolysaccharides (LPS) derived from the membrane of Gram-negative bacteria are pro-inflammatory compounds. AMUC_1100 derived from Akkermansia muciniphila improves intestinal barrier function by increasing goblet cell density and stimulating Toll-like receptor 2 (TLR2). AMUC_1100 exerts the beneficial effect on mucus layer regeneration, inflammation, and insulin sensitivity. Arrow heads indicate stimulation and bar heads indicate inhibition. Fig. S5. Parabiosis experiments restores intestinal function, canonical Wnt signalling target genes, and genes regulating ISC function. a, Verification of blood sharing between the parabiotic pairs using Evans blue. Representative photographs of the mice were taken at 0.5 and 24 h after the injection of Evans blue into the tail vein of one parabiont in a pair a week after surgery. The serum concentration of Evans blue in both mice in each pair was measured at 620 nm by spectrophotometry at 0, 0.5, 1, 24, and 48 h after injection. b, Gene expression profile of mucin in the colon. c, Gene expression profile of barrier-forming tight junction proteins in the colon. d\u2013g, Quantitative real-time PCR analyses for expression of canonical Wnt signalling target genes and genes regulating ISC function in ageing, cage model, serum injection model and parabiosis model. Data are means \u00b1 SEMs . ab means not sharing a common letter are significantly different at P < 0.05. h, Representative Ki67-stained pictures. Scale bar, 25 \u03bcm. i, quantification of Ki-67 positive cells per crypt base columnar cell in the colon. Data are means \u00b1 SEM. . Fig. S6. Dynamics of \u03b1-diversity indices including (a) Shannon diversity, (b) observed OTU, (c) Faith's phylogenetic diversity, (d) Pielou's evenness indices among samples of the co-housing, parabiosis, and serum injection groups. Statistical analysis was performed using Kruskal-Wallis test, young (week 20) versus rejuvenated mice group ; aged (W100) versus rejuvenated mice group . Abbreviations: Co-Y, young mice from co-housing experiments; Co-A, aged mice from co-housing experiments; Hetero-Y, young mice from heterochronic pairs; Hetero-A, aged mice from heterochronic pairs; Iso-Y, young mice from isochronic young pairs; Iso-A, aged mice from isochronic aged pairs; iv 8 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 8 times; iv 16 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 16 times; iv 8 (Y\u2192A), aged mice treated with serum isolated from young mice by intravenously into the tail vein 8 times; iv 16 (Y\u2192A), aged mice treated with serum isolated from young mice by intravenously into the tail vein 16 times. Fig. S7. Gut microbiome alteration in several rejuvenation models. a\u2013b, Principal coordinate analysis (PCoA) of \u03b2-diversity based (a) Jaccard distances, and (b) Bray-Curtis dissimilarity metric among samples of the co-housing (left), parabiosis (middle) and serum injection (right) groups of mice analysed . Each dot represents an individual mouse. c, Heatmap presenting the relative abundance (%) of the key prevalent bacterial taxa found in young and aged-mice. The red and blue genus indicates enriched bacterial taxa in young mice (W20) and aged mice (W100), respectively. Fig. S8. LEfSe analysis showing microbial genus that was significantly different in abundance between (a) young mice (W20) and Co-Y, (b) young mice and Hetero-Y, (c) Hetero-Y mice and Iso-Y, (d) Hetero-A and Iso-A, (e) aged mice and iv 16 (Y\u2192A), (f) young mice and iv 8 (Y\u2192Y), and (g) young mice and iv 16 (Y\u2192Y). Abbreviations: Co-Y, young mice from co-housing experiments; Hetero-Y, young mice from heterochronic pairs; Hetero-A, aged mice from heterochronic pairs; Iso-Y, young mice from isochronic young pairs; Iso-A, aged mice from isochronic aged pairs; iv 8 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 8 times; iv 16 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 16 times; iv 16 (Y\u2192A), aged mice treated with serum isolated from young mice by intravenously into the tail vein 16 times. Abbreviations: Co-Y, young mice from co-housing experiments; Co-A, aged mice from co-housing experiments; Hetero-Y, young mice from heterochronic pairs; Hetero-A, aged mice from heterochronic pairs; Iso-Y, young mice from isochronic young pairs; Iso-A, aged mice from isochronic aged pairs; iv 8 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 8 times; iv 16 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 16 times; iv 8 (Y\u2192A), aged mice treated with serum isolated from young mice by intravenously into the tail vein 8 times; iv 16 (Y\u2192A), aged mice treated with serum isolated from young mice by intravenously into the tail vein 16 times. Fig. S9. Parabiosis experiments induce corticosterone levels in plasma. Plasma corticosterone levels in (a) na\u00efve mice (young and aged mice) and (b) heterochronic parabiotic paired mice. All data are means \u00b1 SEMs . Fig. S10. Taxonomic composition and difference during rejuvenation process determined by metagenomic sequencing. Several microbial genera were significantly different in abundance between (a) Co-A and aged, (b) Co-Y and young, (c) Hetero-A and aged, (d) Hetero-A and Iso-A, (e) Hetero-Y and Young, (f) iv 8 (Y\u2192A) and aged, (g) iv 16 (Y\u2192A) and aged, (h) iv 8 (Y\u2192Y) and young, and (i) iv 16 (Y\u2192Y) and young. Bacterial taxon showing a significant abundance of change was only shown with average fold-change value at the genus level. Red and blue indicate significantly increased bacterial taxa in young mice of 16s rRNA sequencing data and mice of 16s rRNA sequencing data, respectively. The Benjamini and Hochberg's FDR control method was used to correct for multiple comparisons. Abbreviations: Co-Y, young mice from co-housing experiments; Co-A, aged mice from co-housing experiments; Hetero-Y, young mice from heterochronic pairs; Hetero-A, aged mice from heterochronic pairs; Iso-Y, young mice from isochronic young pairs; Iso-A, aged mice from isochronic aged pairs; iv 8 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 8 times; iv 16 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 16 times; iv 8 (Y\u2192A), aged mice treated with serum isolated from young mice by intravenously into the tail vein 8 times; iv 16 (Y\u2192A), aged mice treated with serum isolated from young mice by intravenously into the tail vein 16 times. Fig. S11. Rejuvenation-associated changes in microbial functional potential and metabolism. a, LEfSe analysis of metabolic pathways in colon microbiota during each rejuvenation procedure. The two columns on the left indicate logarithmic LDA scores categorised by KEGG pathways, comparing young group, Co-A, Iso-A, Hetero-A, iv 8 (Y\u2192A), and iv 16 (Y\u2192A) to the aged group. The last column on the right shows logarithmic LDA scores categorised by KEGG pathways, comparing Co-Y, Iso-Y, Hetero-Y, iv 8 (Y\u2192Y), and iv 16 (Y\u2192Y) to the young group. The red and blue names of pathways indicate enriched metabolic pathways in young mice and in aged mice, respectively. Only KEGG pathways differ significantly during each rejuvenation procedure. b\u2013e, Shown horizontal bar plots indicate the fold-change of each enzyme involved in (b) pentose and glucuronate interconversions, (c) lysine degradation, (d) glutathione metabolism, and (e) fatty acid biosynthesis in young, Co-A, Hetero-A, iv8 (Y\u2192A), iv16 (Y\u2192A), Co-Y, Hetero-Y, iv8 (Y\u2192Y), and iv16 (Y\u2192Y). Red and blue KEGG reactions indicate high abundance in young mice and in aged mice, respectively. Abbreviations: Co-Y, young mice from co-housing experiments; Hetero-Y, young mice from heterochronic pairs; Hetero-A, aged mice from heterochronic pairs; Iso-Y, young mice from isochronic young pairs; Iso-A, aged mice from isochronic aged pairs; iv 8 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 8 times; iv 16 (Y\u2192Y), young mice treated with serum isolated from young mice by intravenously into the tail vein 16 times; iv 16 (Y\u2192A), aged mice treated with serum isolated from young mice by intravenously into the tail vein 16 times. The following genes are represented by enzyme name and EC number: OADH, 2-oxoglutarate dehydrogenase (OADH) [EC:2.3.1.61]; DAT, D-alanine transaminase [EC:2.6.1.21]; glutaryl-CoA dehydrogenase [EC:1.3.8.6]; lysine 2,3-aminomutase [EC:5.4.3.2]; beta-lysine 5,6-aminomutase [EC:5.4.3.3]; trans-2-enoyl-CoA reductase [EC:1.3.1.38]; acyl-CoA thioesterase YciA [EC:3.1.2.-]; GAD, glutamate decarboxylase [EC:4.1.1.15]; pectinesterase [EC:3.1.1.11]; pectate lyase [EC:4.2.2.2]; pectate disaccharide-lyase [EC:4.2.2.9]; oligogalacturonide lyase [EC:4.2.2.6]; glucuronate isomerase [EC:5.3.1.12]; tagaturonate reductase [EC:1.1.1.58]; altronate hydrolase [EC:4.2.1.7]; mannonate dehydratase [EC:4.2.1.8]; fructuronate reductase [EC:1.1.1.57]; L-xylulokinase [EC:2.7.1.53]; 3-dehydro-L-gulonate-6-phosphate decarboxylase [EC:4.1.1.85]; L-xylulokinase [EC:2.7.1.53]; L-ribulokinase [EC:2.7.1.16]; L-arabinose isomerase [EC:5.3.1.4]; xylulokinase [EC:2.7.1.17]; L-xylulose reductase [EC:1.1.1.10]; aldehyde reductase [EC:1.1.1.21]; D-xylulose reductase [EC:1.1.1.9]; rhamnulokinase [EC:2.7.1.5]; rhamnulose-1-phosphate aldolase [EC:4.1.2.19]; FabD, [acyl-carrier-protein] S-malonyltransferase [EC:2.3.1.39]; FabH, 3-oxoacyl-[acyl-carrier-protein] synthase III [EC:2.3.1.180]; FabG, 3-oxoacyl-[acyl-carrier protein] reductase [EC:1.1.1.100]; FabZ, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase [EC:4.2.1.59]; FabK, enoyl-[acyl-carrier protein] reductase II [EC:1.3.1.-]; FabL, enoyl-[acyl-carrier protein] reductase III [EC:1.3.1.-]; FabF, 3-oxoacyl-[acyl-carrier-protein] synthase II [EC:2.3.1.179]; FabB, 3-oxoacyl-[acyl-carrier-protein] synthase I [EC:2.3.1.41]; YciA, acyl-CoA thioesterase [EC:3.1.2.-]; GSR, glutathione reductase (NADPH) [EC:1.8.1.7]; phospholipid-hydroperoxide glutathione peroxidase [EC:1.11.1.12]; PepA, leucyl aminopeptidase [EC:3.4.11.1]; PepD; dipeptidase D [EC:3.4.13.-]; PepN; aminopeptidase N [EC:3.4.11.2]; glutamate--cysteine ligase [EC:6.3.2.2]; GAD, glutamate decarboxylase [EC:4.1.1.15]; trans-2-enoyl-CoA reductase [EC:1.3.1.38]; acyl-CoA thioesterase YciA [EC:3.1.2.-]. Fig. S12. Administration of AK restores the expression of the canonical Wnt signalling target genes and ameliorates the senescence-related phenotype in haematopoietic system. a, Quantitative reverse transcription PCR (qRT-PCR) analyses for the expression of canonical Wnt signalling target genes and genes regulating ISC function. Data are presented as means \u00b1 SEMs . b, A representative fluorescence-activated cell sorting plot showing the frequencies of LT-HSCs, ST-HSCs, and MPPs among LSKs in the bone marrow of AK-treated and untreated aged mice. c, Percentages of LT-HSCs, ST-HSCs, and MPPs among LSKs. Data are presented means \u00b1 SEMs . d, Representative images and e, frequencies of neutrophils, T cells, and B cells in the blood of AK-treated and untreated aged mice. Data are presented as means \u00b1 SEMs . f, qRT-PCR analysis of the Icam1 mRNA purified from bone niches and lineage-negative and -positive cells of the aged mice treated with AK. Data are presented as means \u00b1 SEMs . Fig. S13. Effect of AK treatment in aged mice. a, Principal coordinate analysis (PCoA) of \u03b2-diversity based Jaccard distances and Bray-Curtis dissimilarity metric between AK-treated and untreated aged mice . The gut microbiome of AK-treated aged mice shows significant differences with control (Table S2). b, Taxonomic composition and difference determined by metagenomic sequencing. Microbial genera were significantly different in abundance between aged-AK and aged-vehicle groups. Bacterial taxon showing a significant abundance of change was only shown with average fold-change value at the genus level. Red and blue indicate significantly increased bacterial taxa in young mice of 16s rRNA sequencing data and mice of 16s rRNA sequencing data, respectively. The Benjamini and Hochberg's FDR control method was used to correct for multiple comparisons. c, Analysis of differentially abundant microbial genus between AK-treated and untreated aged mice were analysed by LEfSe . d, LEfSe analysis of KEGG enzymes in colon microbiota between AK-treated and untreated aged mice. No metabolic pathway is enriched between aged-AK and aged-vehicle groups. e, Survival rate and f, body weight change of AK-treated and untreated aged mice. g, Schematic summary shows TLR 2 and Wnt signalling pathways can be activated via the high abundance of Akkermansia in the aged-AK group compared to the aged-vehicle group. Lipopolysaccharides (LPS) derived from the membrane of Gram-negative bacteria are pro-inflammatory compounds. AMUC_1100 derived from Akkermansia muciniphila improves intestinal barrier function by increasing goblet cell density and stimulating Toll-like receptor 2 (TLR2). AMUC_1100 exerts a beneficial effect on mucus layer regeneration, inflammation, and insulin sensitivity. Wnt signalling is involved in the development and renewal of intestinal epithelium and hematopoietic stem cells. Arrow heads indicate stimulation and bar heads indicate inhibition.Additional file 2: Table S1. Read statistics of 16s rRNA and metagenome sequencing.Additional file 3: Table S2. Alpha and beta diversity analysis of the analysed groups in this study.Additional file 4: Table S3. Taxa identified by LEfSe analysis in this study. \"LogMaxMean\" indicates the log of the highest-class average. \"Enriched in\" indicates the class with the highest mean if the taxa are discriminative. \"LDA\" indicates the logarithmic of the linear discriminant analysis (LDA) score. \"P-value\" indicates p-value of the pairwise Kruskal-Wallis test performed by LEfSe.Additional file 5: Table S4. Effect of parabiotic pairing on blood parameters.Additional file 6: Table S5. Relative abundance of phylotypes detected in ageing and rejuvenation samples.Additional file 7: Table S6. Relative abundance of phylotypes detected in AK administration samples.Additional file 8: Table S7. Frailty score used to develop a clinical frailty index in mice.Additional file 9: Table S8. Sequences of PCR primers used in this study."} +{"text": "The corrected table is shown here.Page 5: cas type IIA system and the type II restriction-modification system LmoJ3 (24) were negatively associated with nonpersistence\u201d should read \u201cIn contrast, genes associated with the CRISPR-cas type IIA system and the type II restriction-modification system LmoJ3 (24) were associated with nonpersistence.\u201dPage 11, line 10: \u201cIn contrast, genes associated with the CRISPR-Page 15: References 24 and 32 are interchanged. The correctly numbered references are as follows:Listeria monocytogenes strains. Appl Environ Microbiol 78:2623\u20132630. https://doi.org/10.1128/AEM.07203-11.24. Lee S, Ward TJ, Siletzky RM, Kathariou S. 2012. Two novel type II restriction-modification systems occupying genomically equivalent locations on the chromosomes of Listeria monocytogenes clones with enhanced virulence. Appl Environ Microbiol 83:e01189-17. https://doi.org/10.1128/AEM.01189-17.32. Lee S, Ward TJ, Jima DD, Parsons C, Kathariou S. 2017. The arsenic resistance-associated Listeria genomic island LGI2 exhibits sequence and integration site diversity and a propensity for three"} +{"text": "Cladosporium species have attracted considerable interest because of their ability to produce a wide array of metabolites, including alkaloids, macrolides, diketopiperazines, pyrones, tetralones, sterols, phenolics, terpenes, lactones, and tetramic acid derivatives that possess versatile bioactivities. Moreover, they produce diverse enzymes with biotechnological and industrial relevance. This review gives an overview on the Cladosporium species derived from marine habitats, including their metabolites and bioactivities, as well as the industrial and biotechnological potential of these species. In the current review, 286 compounds have been listed based on the reported data from 1998 until July 2021. Moreover, more than 175 references have been cited.The marine environment is an underexplored treasure that hosts huge biodiversity of microorganisms. Marine-derived fungi are a rich source of novel metabolites with unique structural features, bioactivities, and biotechnological applications. Marine-associated Cladosporium (Cladosporiaceae) is one of the largest genera of dematiaceous hyphomycetes [Cladosporium species are frequent airborne molds, which can be isolated from almost every environment and geographic location, because their small conidia are easily dispersed [C. herbarum, C. cladosporioides, and C. sphaerospermum are its three major species [C. fulvum is the causal agent of tomato leaf mold [C. sphaerospermum isolated from Glycine max roots which can promote its growth [Cladosporium species have the potential to be used in various industrial processes [Cladosporium species have attracted considerable interest because of their ability to produce a wide array of metabolites, including macrolides, pyrones, phenolics, alkaloids, diketopiperazines, terpenes, sterols, quinones, lactones, and tetramic acid derivatives. These metabolites possess versatile bioactivities such as anticancer, antimicrobial, antiviral, insecticidal, antifouling, anti-malarial, anti-hyperlipidemic, and \u03b1-glucosidase and protein tyrosine phosphatase inhibiton [Cladosporium species derived from a marine habitat, including the structures and bioactivities of the reported metabolites, as well as the industrial and biotechnological potential of these species even in a non-marine environment [The polycyclic aromatic hydrocarbons (PAHs) are volatile pollutants that can cause various environmental pollutions such as oceanic and freshwater contamination, which can take place during storage, use, or transportation of crude oil and its products. PAHs inhalation or ingestion through contaminated food and airborne contaminants leads to serious health disorders such as endocrine disruption, cancer, and reproductive and birth problems . Therefoironment .C. cladosporioides using the Buescher and Furmanski procedure after 10-day incubation and precipitation with (NH4)2SO4 and benzoate buffer at pH 4.0 [Pectinases are hydrolytic enzymes that are accountable for the hydrolysis of pectins. They are commonly found in fungi, bacteria, and plants. They have remarkable importance in the food industry such as vegetables and fruits processing, wine production, and olive oil extraction, as well as coffee, cocoa, and tea fermentation. They are utilized in the beverage industry to produce high yields due to improving clarification and pressing of concentrated fruit juices . Bastos t pH 4.0 .Cladosporium sp. isolated from the Antarctic macroalgae Ascoseira mirabilis and Georgiella confuens produced agarase that may have industrial importance in the extraction of agar or its byproducts such as bioactive galactose and oligosaccharides exist in the algal biomass to be utilized as substrates of 3rd generation bioethanol [Agarases and carrageenases can decompose algal biomass, producing carrageenans and agars that are the major components of the red algae cell wall. Furthermore, agarases hydrolyze agar, resulting in oligosaccharides that are employed as food additives with beneficial influences on human health ,105. Addoethanol .Cladosporium sp. isolated from Antarctic marine sponge had high xylanase potential when grown on wheat bran and pure xylans at lower temperatures that is a feature of cold-active enzymes [Cladosporium sp. could be convenient for many biotechnological processes, utilizing moderate- to low-temperature processes, especially those in food industries [Cladosporium sp. derived from Antarctic sponge. XynA is highly active on xylans with high arabinose content. Moreover, it is the most thermolabile endo-xylanase reported from filamentous fungus. Therefore, it could be a good alternative in some biotechnological operations to avoid heating, thereby reducing the costs [Xylan, the main component of hemicelluloses in the plant cell walls, represents about one-third of all renewable organic carbon on earth. Xylanases hydrolyze xylan to oligosaccharides that are further degraded to xylose. The latter is utilized for xylitol and bioethanol production. Xylanases have remarkable biotechnological influence in developing eco-friendly technologies in the pulp and paper industry and in food and feed industries, and for generating chemicals and liquid fuels from lignocellulose ,108,109. enzymes . Therefodustries . Gil-Durhe costs .2O2-dependent glycoprotein that needs Mn2+ for oxidizing aromatic dyes and mono-aromatic phenols [2 reduction to H2O [C. cladosporioides CBMAI 857 isolated from the Brazilian cnidarian Palythoa variabilis produced ligninolytic enzymes with particular response to the various conditions of salinity and carbon sources. It possessed high values of MnP and laccase activities under salinity , indicating the potential use of this fungus for industrial applications and bioremediation of high-salt contaminated sites [The three main lignin-hydrolyzing enzymes that have great potential for industrial applications are LiP (lignin peroxidase), MnP (manganese-dependent peroxidase), and Lac (laccase) . LiP is phenols . Laccasen to H2O . C. claded sites .C. cladosporioides CBMAI-857 associated with the coral Palythoa caribaeorum was tested for its RBBR decolorizing potential. It had efficient dye decolorization potential (93%) after 12 days in both liquid and solid media [Cladosporium sp. associated with the seagrass Posidonia oceanica produced tannases and ligninolytic enzymes at high salt concentrations. Its laccase and peroxidase activity was evident by the degradation of RBBR and Amaranth Red dyes [RBBR (Remazol Brilliant Blue R) and polymeric dyes decolorization has been assigned as an effective screening method for the fungi ability to degrade recalcitrant pollutants, including aromatic compounds such as PAHs. It was demonstrated that marine-derived fungi are often more effective than terrestrial fungi in treating various colored effluents because they are better adapted to perform under extreme conditions such as high salinity . C. cladid media . FurtherRed dyes .C. herbarum ER-25 possessed a high invertase potential and removed melanoidins from molasses through bio-adsorption and biodegradation mechanisms by Lac and MnP in the non-sterilized medium than in sterilized one at 5.5 pH and 20 \u00b0C. Therefore, this cold-adapted fungus can be used for molasses de-colorization [Invertase is a \u03b2-fructo-furanosidase that catalyzes sucrose conversion into fructose and glucose, giving invert syrup. This invert syrup is utilized in the beverage and food industries as a humectant in non-crystallizing creams, candies, artificial honey, and jam preparation . Molasserization .C. sphaerospermum obtained from deteriorated seaweed Ulva through SSF (solid-state fermentation) produced cellulase that had saccharification potential of seaweed biomass using green seaweed Ulva\u00a0fasciata. Therefore, this cellulase can be utilized for saccharification of cellulosic feedstock for bioethanol production from marine macro-algal feedstock [Cellulose is a main component of the plant material that is abundantly utilized for the production of alternative liquid fuels such as bioethanol. eedstock .Cladosporium sp. CBMAI 1237 isolated from Dragmacidon reticulatum, revealing the existence of ene-reductases [C. cladosporioides CBMAI-857 isolated from the Brazilian cnidarian Palythoa caribaeorum catalyzed the asymmetric bio-reduction of 1-(4-methoxyphenyl)ethanone to 1-(4-methoxyphenyl)ethanol [C. cladosporioides CBMAI-857 catalyzed the enantio-selective bio-reduction of different aromatic ketones at pH 7.0 and 32 \u00b0C [Biocatalysis is an eco-friendly process for renewable raw materials and clean energy production and for the remediation of environmental contaminants . Recentlductases . Additiond 32 \u00b0C .Cladosporium species are rich with diverse types of metabolites with varied structural features such as macrolides, fatty acids, pyrones, phenolics, alkaloids, diketopiperazines, terpenes, sterols, quinones, lactones, and tetramic acid derivatives. Their classification was carried out here according to the chemical nature. During our search, it was found that some of the reported metabolites had the same structures and molecular formulae with different nomenclature. On the other hand, some metabolites had the same names with different structures. Moreover, some metabolites did not have names, thus they are named here using the AUPAC system for nomenclature. Herein, the reported secondary metabolites from Cladosporium species, as well as their bioactivities have been discussed of them are from C. sphaerospermum.Tetramic acids are five-membered heterocycles with a pyrrolidine-2,4-dione core that are formed by the fusion of polyketide units and amino acid . The terivatives . These sivatives . They arivatives ,128. Theivatives . Note th1, 2, 4, and 5) biosynthesized by C. sphaerospermum 2005-01-E3 obtained from deep-sea sludge had no activity towards influenza A H1N1 virus (3 exhibited anti-H1N1 activity (IC50 276.0 \u03bcM) in comparison to ribavirin (IC50 131.0 \u03bcM) [Mycobacterium tuberculosis in the disk diffusion method [2), C (3), F (5), and L (11) separated from C. sphaerospermum SW67 associated with Hydractinia echinat hydroid polyp were assessed for protection towards cisplatin-caused cell damage in LLC-PK1 cells [2 and 5 alleviated the LLC-PK1 cells damage induced by cisplatin (Conc. 25 \u00b5M). Compound 2 (Conc. 100 \u00b5M) recovered cell viability with 90.68% that was more than NAC , whereas 5 (Conc. 50 and 100 \u03bcM) increased cell viability by 77.65 and 85.60%, respectively. Thus, 2 may be a candidate for treating cisplatin-produced unwanted effects and/or to prohibited nephrotoxicity induced by anticancer drugs. It was proposed that the existence of the C-8 hydroxy group may be essential for the reno-protective effect towards cisplatin-produced toxicity in LLC-PK1 cells [The tetramic acid derivatives, cladosins A, B, D, and E (N1 virus . While 331.0 \u03bcM) . Moreoven method . MoreoveK1 cells . The co-K1 cells .5 and 6 from C. sphaerospermum 2005-01-E3 that did not have anti-influenza A H1N1, anticancer, and anti-tubercular, as well as no NF-\u03baB inhibitory activities [C. sphaerospermum WBS017 isolated from Fritillaria unibracteata var. wabuensis [7\u201310) and cladodionen (13) were isolated from sediment-derived C. sphaerospermum L3P3 and evaluated for cytotoxic capacity towards PC-3, MGC-803, SH-SY5Y, and HCT-116 cell lines using SRB method and against K562 and HL-60 using MTT method was inactive. The results revealed that the C-8 absolute configuration and aniline moiety were essential for activity [In 2015, by OSMAC (one strain many compounds) technique, Yu et al. separated compounds tivities . Note thabuensis . CladosiT method . Compounactivity , compared to etoposide (IC50 ranged from 1.76 to 2.27 \u03bcM) [, and 30 . Compoun2.27 \u03bcM) .C. sphaerospermum EIODSF 008 isolated from the deep-sea sediment collected from the East Indian Ocean yielded tetramic acid derivatives 13 and 22\u201328 (13 had cytotoxicity (IC50 28.6 \u00b5M) towards the HL-60 cell line [E. coli, M. luteus, and B subtilis [13 showed cytotoxic capacity towards HL-60, HeLa, HCT-116, and MCF-7 cell lines (IC50 ranged from 9.1 to 19.1 \u03bcM), compared to ADR (adriamycin) (IC50 ranged from 0.02 to 0.67 \u03bcM). However, it did not have antibacterial activities (conc. 100 \u03bcg/mL) against B. subtilis, P. aeruginosa, C. perfringens, S. aureus, E. coli, and C. albicans [14\u201321, new tetramic acid derivatives, were purified from the sea-sediment derived Cladosporium sp. acetone extract by Huang et al. in 2018. Compounds 14\u201316 are unusual 3-acyltetramic acids, having at C-3 of the pyrrolidine-2,4-dione core, a six-membered lactone ring, and hexyl-enic alcohol chain. They showed no obvious AchEI activity in the modified Ellman\u2019s enzyme assay [C. albicans and S. aureus in the broth micro-dilution method and no cytotoxic effect towards HL60, HepG-2, and MCF-7 cell lines in the CCK8 assay [nd 22\u201328 . They weell line . Additiosubtilis . Additioalbicans . Compounme assay . MoreoveK8 assay .Diketopiperazines (DKPs) are cyclic dipeptides, consisting of two amino acids with or without extra structural modifications in the DKPs nucleus . Their m32) and cyclo-(Phe-Pro) (33) were separated from the EtOAc extract of Cladosporium sp. F14 isolated from seawater and investigated for their anti-larval activity at conc. 50 \u00b5g/mL towards Bugula neritina and Balanus amphitrite larvae in the settlement inhibition assays [B. neritina settlement and B. amphitrite settlement . Furthermore, 32 and 33 obviously prohibited L. hongkongensis growth , compared to streptomycin (MIC 250 \u00b5g/mL). The MICs of 33 towards Ruegeria sp. and M. luteus were 200 and 100 \u00b5g/mL, respectively, compared to streptomycin [36) and B (37), and haematocin (38) purified from the sediment-derived Cladosporium sp. were moderately cytotoxic towards HepG2 cell line [Cyclo- . On the ctively) .Cladosporium species.Fungal alkaloids are nitrogen-containing metabolites that are derived from amino acid metabolism and the mevalonate pathway . Many st42\u201355, were separated from Cladosporium sp. PJX-41 isolated from mangrove and assessed for anti-H1N1 activity using CPE (cytopathic effect) inhibition assay , compared to ribavirin (IC50 87 \u03bcM), while 42\u201344, 46\u201348, 50, and 54 (IC50 100\u2013150 \u03bcM) had weak activity [Cladosporium sp. associated with Chondria crassicualis red alga afforded 56 that exhibited antioxidant potential (ED50 82.0 \u00b5M) more than oxybenzone as evident by their UV-A protecting potential [S. aureus and S. aureus with MICs 31.0, 62.5, and 62.5, \u00b5g/mL, respectively [58, 68, and 70 separated from C. oxysporum were assessed for anti-plasmodial potential towards chloroquine-sensitive Plasmodium falciparum 3D7 [58 (conc. 3.13 \u00b5g to 25.0 \u00b5g) had an anti-plasmodial effect (EC50 24.8 \u00b5M), while 68 and 70 displayed no activity (EC50 > 25.0 \u00b5M), compared to artesunate (EC50 0.074 \u03bcM) in the SYBR Green I assay. Further, 58 (conc. ranged from 6.25 \u00b5M to 50.0 \u00b5M for 24 h) was investigated for apoptotic effect on 3D7-plasmodia strain by measuring the parasite \u0394\u03a8m . It induced loss of \u0394\u03a8m, leading to the release of cytochrome C from mitochondria to the cytosol resulted in parasite apoptosis. Therefore, it may provide a scaffold to apoptotic death in the stages of P. falciparum development [58, 68, and 70 had no anti-buruli ulcer activity against Mycobacterium ulcerans (IC50 \u02c3 10 \u00b5M), compared to rifampicin (IC50 \u02c2 1 \u00b5M) in the Resazurin microtiter assay [The glyantrypine-type alkaloids, on assay . Compounactivity . The mycotential . Furtherectively . The quiarum 3D7 , compared to curcumin . However, they showed moderate activity versus LNCap and LNCap , in comparison to curcumin in the MTT assay [Cladosporium sp. HNWSW-1 associated with the mangrove plant Ceriops tagal biosynthesized compounds 74\u201376 that were assessed for their cytotoxic and \u03b1-glycosidase inhibitory effects , whereas 76 revealed cytotoxic potential towards BEL-7042 and Hela cell lines in the MTT assay.They had significant activity towards HepG-2 and MCF-7 (ICTT assay . Cladosp effects . Compoun76 exhibited \u03b1-glucosidase inhibitory activity (IC50 78.2 \u00b5M), compared to acarbose (IC50 275.7 \u00b5M) in the glucose oxidase method [77) separated from Cladosporium sp. TPU1507 derived from marine sponge was assessed for its inhibitory effect towards PTP1B (protein tyrosine phosphatase) and TCPTP (T-cell PTP), using an enzyme-based assay [50 48 and 54 \u03bcM, respectively), in comparison to oleanolic acid (IC50 0.9 \u03bcM) [78, from a gorgonian-derived Cladosporium sp. collected from the South China Sea. It (IC50 0.76\u20133.11 \u03bcM) exhibited significant cytotoxicity towards HeLa, P388, HT-29, and A549 cell lines [B. cereus, T. halophilus, S. epidermidis, S. aureus, E. coli, P. putida, N. brasiliensis, and V. parahaemolyticus [Cladosporium sp. SCNU-F0001 isolated from a mangrove plant yielded a novel lactam macrolide named cladospamide A (79) that was evaluated for cytotoxic effect (conc. 50 \u03bcM) versus MDA-MB-435, A549, HCT116, HepG2, and BT549 in the MTT method and for antimicrobial potential (conc. 100 \u03bcg/mL) towards S. aureus, B. subtilis, E. coli, Salmonella ATCC 14028, and P. aeruginosa. Unfortunately, it exhibited no noticeable activity [Additionally, e method . Cladosped assay . It had 0.9 \u03bcM) . Cao et ll lines . On the olyticus . Cladospactivity .80) and B (81) purified from Cladosporium sp. SCSIO z015 broth did not have an obvious anti-biofilm activity towards S. aureus, E. coli, and B. subtilis [The new cyano-containing alkaloids, cladosporins A , compared to ascorbic acid (IC50 4.9 \u00b5M). Besides, they showed moderate toxicity towards brine shrine naupalii , compared with toosendanin (LC50 21.2 \u00b5M) in the brine shrimp lethality assay [84 and 85 from Cladosporium sp. JS1-2 isolated from the mangrove Ceriops tagal collected in the South China Sea. Compound 84 moderately prohibited the growth of Helicoverpa armigera Hubner newly hatched larvae (IC50 100 \u03bcg/mL), compared to azadirachtin (IC50 25 \u03bcg/mL). Further, they showed moderate antibacterial potential versus S. aureus with MICs 12.5 and 25.0 \u03bcg/mL, respectively, compared with ciprofloxacin (MIC 0.39 \u03bcg/mL) [In the DPPH assay, they also had no activity (ICty assay . In 20199 \u03bcg/mL) .91), together with 88 and 89 were separated from Cladosporium sp. FT-0012 was obtained from Pohnpei Island, Federated State of Micronesia, and assessed for antimicrobial activity using paper disks at conc. 10 \u00b5g/disk , while 88 was active (IZD 14.0 mm and IC50 17.0 \u00b5g/mL) towards X. campestris pv. oryzae. Moreover, 91 prohibited P. oryzae and M. racemosus growth [The term \u201cmacrolides\u201d was first used to describe the natural antibiotics that have 12\u201316-membered macrocyclic lactone ring, functionalized by double bonds, and carrying different aminosaccharide and saccharide components . Among t \u00b5g/disk . Compounctively) .Cladosporium sp. F14 isolated from seawater yielded a nine-membered macrolide, 92 that had weak antibacterial potential towards M. smegmatis, E. coli, B. thuringiensis, S. aureus, and B. subtilis and weak cytotoxic potential toward A435, HeLa, K562, and A549 in the MTT method [C. herbarum isolated from Callyspongia aerizusa sponge yielded cladospolide B (89) and pandangolides 2\u20134 (95\u201397) that showed no antimicrobial potential versus S. aureus ATCC 25923, B. subtilis 168, E. coli ATCC 25922, and C. albicans in the agar plate diffusion assay [Cladosporium sp. IFB3lp-2 isolated from the mangrove forest of Hainan province of China yielded 88, 89, 93\u201396, 100, and 116 that had no significant activity against HCT-116, Coxsachievirus A16, A549, MD-MBA-231, HepG2, human enterovirus 71, A375, and SW1116 cell lines (conc. 20 \u00b5M) in the MTT assay [T method . C. herbon assay . MoreoveTT assay , along with 89 that were evaluated for cytotoxic effect (conc. 50 \u03bcM) versus MDA-MB-435, A549, HCT116, HepG2, and BT549 in the MTT method and for antimicrobial potential (conc. 100 \u03bcg/mL) towards S. aureus, B. subtilis, E. coli, Salmonella ATCC 14028, and P. aeruginosa. Unfortunately, none of them exhibited noticeable activity [89 and 117\u2013120 from a gorgonian-derived Cladosporium sp. collected from the South China Sea. They showed no cytotoxicity towards HeLa, P388, HT-29, and A549 cell lines [B. cereus, T. halophilus, S. epidermidis, S. aureus, E. coli, P. putida, N. brasiliensis, and V. parahaemolyticus. Compounds 117\u2013119 exhibited antibacterial potential against all tested bacteria , however 89 and 120 had weak activity (MIC \u02c3 25.0 \u03bcM) [93 and 115 separated from Cladosporium sp. F14 at conc. 50 \u00b5g/mL had no anti-larval activity towards both B. neritina and B. amphitrite larvae in the settlement inhibition assays [98 and 99 and a known analog 93 from the rice culture EtOAc extract of C. cladosporioides associated with Bruguiera gymnorrhiza. Their configuration was established using ECD, modified Mosher\u2019s, and X-ray diffraction methods, as well as optical rotations to be 5R, 11R for 98; 11R for 99; and 3R, 5S, 11S for 93. They had weak AChEI activity (IC50 > 50 \u00b5M), in comparison to tacrine in the modified Ellman\u2019s method [C. cladosporioides MA-299 obtained from the mangrove plant B. gymnorrhiza yielded 12-membered thio-macrolides 96 and 101\u2013104 that were assessed for antimicrobial potential against E. tarda QDIO-2 and E. ictarda QDIO-9 (aquatic pathogens) and C. glecosporioides QDAU-2, B. sorokiniana QDAU-5, P. piricola Nose QDAU-15, and F. oxysporum f. sp. cucumerinum QDAU-8 (plant pathogenic fungi) in the microtiter plates assay. All metabolites revealed activity against C. glecosporioides (MIC 1 or 2 \u03bcg/mL), compared to amphotericin B (MIC 0.5 \u03bcg/mL). Moreover, 101 and 104 showed noticeable activity (MIC 1.0 \u03bcg/mL) towards with E. tarda and E. ictarda, respectively, compared to chloramphenicol (MIC 0.5 \u03bcg/mL), while 102 and 104 exerted obvious effectiveness (MIC 1.0 \u03bcg/mL) versus F. oxysporum f. sp. cucumerinum, compared to amphotericin B (MIC 0.5 \u03bcg/mL). The data revealed that sulfur substituent may influence the macrolides\u2019 bioactivities [107\u2013112 and the related formerly reported 93 and 101 isolated from mangrove-derived C. oxysporum HDN13-314 had no cytotoxic activity versus HCT-116, BEL-7402, HL-60, A549, L-02, HeLa, K562, MGC-803, MCF-7, PC-3, SH-SY5Y, and MDA-MB-231 (IC50 > 50 \u03bcM) [Additionally, activity . Cao et ll lines . Further25.0 \u03bcM) . The metn assays . In 2019tivities . The new> 50 \u03bcM) , whereas 108 had the best effect (MIC 4 \u03bcg/mL) versus E. tarda [106) and G (108) and cladocladosin A (121), a macrolide with bicyclo 5/9-ring, were purified from C. cladosporioides MA-299 by Zhang et al. and assessed for antimicrobial effect versus various plant, human, and aquatic pathogenic microbes in the microtiter plates assay. All metabolites revealed activity (MIC ranging from 1.0 to 4.0 \u03bcg/mL) towards V. anguillarum and E. tarda (aquatic pathogenic bacteria) [Additionally, they exerted antibacterial activities versus the aquatic pathogens E. tarda . In 2020acteria) .108 and 121 exerted activity (MICs 4.0 \u03bcg/mL) towards H. maydis (plant-pathogenic fungus) and P. aeruginosa (aquatic-pathogenic bacterium), respectively [113 and 114, purified from Cladosporium sp. L037 isolated from the Okinawan marine brown alga Actinotrichia fragilis exhibited cytotoxic influence towards L1210 murine lymphoma cells in the MTT assay [113 had antifungal potential against C. albicans, C. neoformans, A. niger, and N. crassa (MICs 8.4\u201316.7 \u00b5g/mL), whereas 114 exhibited antibacterial activity only towards M. luteus and inactive against the other microorganisms [Moreover, ectively . The newTT assay . Moreoverganisms .Butanolides and butenolides are five-membered \u03b3-lactones which may also be regarded as furan derivatives. They are an important class of structural motifs often encountered in various natural metabolites and synthetic targets . They ha122), purified from a soft coral-associated fungus Cladosporium sp. TZP-29, together with the formerly isolated derivative 126 showed no cytotoxic effect towards A-549, SMMC-7721, and HeLa cells in the SRB method [126 isolated from Cladosporium sp. IFB3lp-2 exhibited no significant activity against HCT-116, Coxsachievirus A16, A549, MD-MBA-231, HepG2, human enterovirus 71, A375, and SW1116 cell lines (Conc. 20 \u00b5M) in the MTT assay [B. cereus, T. halophilus, S. epidermidis, S. aureus, E. coli, P. putida, N. brasiliensis, and V. parahaemolyticus [126 displayed no anti-larval activity towards both B. neritina and B. amphitrite larvae in the settlement inhibition assays [E. ictarda and Cytospora mandshurica Miura (MIC 8 \u03bcg/mL) [123, 124, and 127 and the known analog 126 separated from C. cladosporioides were assessed for AChEI activity using modified Ellman\u2019s method [The newly separated C12-macrolide, cladospolide F . Qi et an assays . Additios method . Only 12128, 130, and 141 isolated from Cladosporium sp. IFB3lp-2 EtOAc extract had no noticeable cytotoxicity versus HCT-116, Coxsachievirus A16, A549, MD-MBA-231, HepG2, human enterovirus 71, A375, and SW1116 cell lines (Conc. 20 \u00b5M) in the MTT assay [131 did not show any anti-larval activity towards both B. neritina and B. amphitrite larvae [132 did not have cytotoxic activity towards HCT-116, BEL-7402, HL-60, A549, L-02, HeLa, K562, MGC-803, MCF-7, PC-3, SH-SY5Y, and MDA-MB-231 (IC50 > 50 \u03bcM) [E. ictarda, E. tarda, and Cytospora glecosporioides (MICs ranging from 16 to 32 \u03bcg/mL) [129) separated from a soft coral-associated Cladosporium sp. TZP-29, together with the formerly isolated derivatives 130 and 131 had no cytotoxic effect towards A-549, SMMC-7721, and HeLa cells in the SRB method. Moreover, 129\u2013131 with IC50 ranged from 7.1 to 13.1 \u00b5M remarkably reduced the accumulation of lipid elicited by oleic acid (OA) in the HepG2 liver cells, in comparison to lovastatin as determined by oil-red O staining and intracellular triglyceride (TG) and total cholesterol (TC) quantification (The seco-acids TT assay . Compoune larvae . Moreove> 50 \u03bcM) , while i2 \u03bcg/mL) . Cladospfication .133, 134, and 138 and new fatty acids 135\u2013137, 139, and 140 isolated from C. cladosporioides OUCMDZ-187 obtained from the mangrove plant Rhizophora stylosa collected in Shankou, Guangxi Province of China showed no cytotoxic effects (IC50 > 50 \u03bcM) towards K562, A549, and HeLa cells in the SRB method [S. aureus CGMCC-1.2465, E. coli CGMCC-1.2389, E. aerogenes CGMCC-1.0876, P. aeruginosa CGMCC-1.1785, B. subtilis CGMCC-1.3376, and C. albicans CGMCC-2.2086 in the agar dilution method [Further, they exhibited potent lipid-lowering potential in HepG2 hepatocytes, revealing a promising anti-hyperlipidemic capacity . The newB method . Addition method .Tetralones comprise a bicyclic aromatic hydrocarbon and a ketone and are regarded as benzo-fused cyclohexanone derivatives. They played a substantial role as a starting material for the synthesis of a range of synthetic heterocyclic compounds and pharmaceuticals due to their potential reactivity and suitability . Additio152), a new dimeric tetralone bridged via C-C linkage, was separated from Cladosporium sp. KcFL6 derived from the mangrove plant Kandelia candel, together with 142\u2013144 , in comparison to NS-398 and indomethacin [A. baumannii ATCC-19606, S. aureus ATCC-29213, E. faecalis ATCC-29212, A. hydrophila ATCC-7966, E. coli ATCC-25922, K. pneumonia ATCC-13883, Fusarium sp., F. oxysporum f. sp. cucumeris, F. oxysporum f. sp. niveum, A. niger, and R. solani in the disc diffusion assay [Cladosporone A , compared to trichostatin A in the trypan blue-cell viability assay [142 had a remarkable anti-proliferative potential towards SW480, HT-29, and CaCo-2, in particular towards HT-29. It was revealed that HT-29 cells exposure to 142 produced G1/S phase cell cycle arrest, assisted by a vigorous p21waf1/cip1 expression, a significant down-regulation of CDK4, CDK2, cyclin E, and cyclin D1, and repression of CDK4 and CDK2 kinase activity [waf1/cip1 expression and inducing degradation of \u03b2-catenin, as well as impairing TCF/\u03b2-catenin pathway as evident by reduced cyclin D1 and c-Myc transcription. Finally, it induced the expression of E-cadherin, therefore antagonizing invasion and metastasis [C. cladosporioides HDN14-342 isolated from marine sediments yielded tetralone derivatives 143, 145\u2013147, 154, and 155 that were evaluated for cytotoxic activities towards HCT-116, HeLa, and A549 cell lines by SRB method and towards HL-60 and K562 cell lines by MTT method, in comparison to doxorubicin (IC50 0.2\u20130.8 \u00b5M). Compounds 146 and 147 were active towards K562, HeLa, and HCT-116 cell lines (IC50 ranging from 3.9 to 23.0 \u00b5M), while other metabolites had no activity (IC50 > 50.0 \u00b5M) [143 possessed no anti-allergic effect (IC50 > 200 \u00b5M) on RBL-2H3 cells, in comparison to loratadine (IC50 35.01 \u00b5M) using fluorometric assay [143) and cladosporols F-J (146 and 148\u2013151) from the marine algal-derived C. cladosporioides EN-399 and evaluated their cytotoxic activities towards H446, A549, HeLa, L02, Huh7, LM3, SW1990, and MCF-7 using MTT assay. Note that 143, 148, and 149 displayed cytotoxic activities towards most of the tested cell lines with IC50 ranging from 1.0 to 20.0 \u03bcM. Notably, 149 had cytotoxic effect towards LM3, A549, and Huh7 cell lines , compared to cisplatin (IC50 1.3 \u03bcM for A549 and 9.1 \u03bcM for LM3) and fluorouracil (IC50 6.2 \u03bcM for Huh7), whereas 143 exhibited cytotoxic activity (IC50 4.0 \u03bcM) towards H446 cell line, compared to adriamycin (IC50 4.0 \u03bcM). These results revealed that the existence of dihydro-1,4-naphthoquinone nucleus was important for the activity and C-4 methoxyl strengthened the activity (148 vs. 151) [Compounds activity . It was tastasis . C. clad50.0 \u00b5M) . In 2020vs. 151) .E. coli, A. hydrophila, S. aureus, E. tarda, P. aeruginosa, M. luteus, V. alginolyticus, V. parahemolyticus, V. harveyi, A. brassicae, F. oxysporum, G. graminis, C. gloeosporioides, and P. piricolav using micro-plate assay. Compounds 143, 146, and 148\u2013151 showed inhibitory potential towards M. luteus, E. coli, and V. harveyi (MICs 4\u2013128 \u03bcg/mL). None of them had activity (MIC > 128 \u03bcg/mL) towards other tested microbes [143 and 145 from Cladosporium sp. JS1-2 isolated from the mangrove Ceriops tagal collected in the South China Sea [145 prohibited the growth of Helicoverpa armigera Hubner newly hatched larvae (IC50 150 \u03bcg/mL), compared to azadirachtin (IC50 25 \u03bcg/mL) [S. aureus with MIC 6.25 and 1.56 \u03bcg/mL, respectively, compared with ciprofloxacin (MIC 0.39 \u03bcg/mL) [150 and 153 that exhibited quorum sensing inhibitory potential towards Chromobacterium violaceum CV026 in the well diffusion assay [156 had no observable cytotoxic activity towards SF-268, NCI-H460, MCF-7, and HepG-2 (conc. 100 \u03bcM) in the SRB assay [157, in addition to 156, 158, and 159 isolated Cladosporium sp. JJM22 associated with the mangrove plant C. tagal had no cytotoxic effect (IC50 > 10 \u03bcM) versus HeLa cell line in the MTT assay, compared to epirubicin [158 exhibited noticeable antibacterial potential towards S. aureus, B. cereus, E. coli, V. alginolyticus, V. parahemolyticus, and MR S. aureus (conc. 20 \u03bcM) [160) and previously reported -3,4,8-trihydroxy-1-tetralone (159) were isolated from a sediment-associated Cladosporium sp. HDN17-58 , compared to ciprofloxacin [Moreover, their antimicrobial potential was assessed versus microbes . Bai et hina Sea . Compoun5 \u03bcg/mL) . Further9 \u03bcg/mL) . Cladospon assay . NeverthRB assay . The newirubicin . One newHDN17-58 . Note thfloxacin .Perylenequinones comprise a class of natural products characterized by an oxidized pentacyclic core. They are dark-colored pigments isolated from diverse sources such as mold species, plants, and aphids . They re161\u2013164), were isolated from Cladosporium sp. KFD33 production by LPS (lipopolysaccharide) in RAW264.7 cells [Cladosporium sp. JJM22 yielded new naphthalene-chromane derivatives, cladonaphchroms A (169) and B (170), and related metabolites 165 and 168 that were assessed for antibacterial effectiveness versus S. albus ATCC-8799, E. coli ATCC-25922, B. subtilis ATCC-6633, Micrococcus tetragenus ATCC-13623, and M. luteus ATCC-9341, employing microplate assay. Compound 169 possessed significant potential against S. albus (MIC 1.25 \u00b5g/mL), compared to ciprofloxacin (MIC 0.6 \u00b5g/mL). Moreover, 169 and 170 demonstrated broad-spectrum antifungal activities (MICs 25.0\u2013100.0 \u00b5g/mL) towards P. parasitica var. nicotianae, A. brassicicola, B. oryzae, C. capsici, C. paradoxa Moreau, and D. medusaea Nitschke, compared to pochloraz (MICs 12.5\u201350.0 \u00b5g/mL) [166 had no cytotoxic effect (IC50 > 10 \u03bcM) versus HeLa cell line in the MTT assay and no antibacterial activity towards S. aureus, B. cereus, E. coli, V. alginolyticus, V. parahemolyticus, and MR S. aureus (conc. 20 \u03bcM) in the microplate assay [.7 cells . Wu et ate assay .Xanthones are secondary metabolites commonly reported from plants, fungi, and lichen . They arC. halotolerans GXIMD 02502 associated with the coral Porites lutea yielded compounds 171\u2013177 that were evaluated for their cytotoxicity versus 22RV1 and C4-2B (prostatic cancer cell lines), as well as RWPE-1 . Among them, 171\u2013173, 175, and 176 revealed notable cytotoxicity versus C4-2B and 22RV1 cells (inhibitions ranged from 55.8% to 82.1% at conc. 10 \u00b5M), whereas 176 was the potent one . On the other hand, they exhibited nearly no cytotoxic effect versus RWPE-1 cell (inhibition < 27% at conc. 10 \u00b5M) [. 10 \u00b5M) , along with the new metabolite, malettinin E (181) from Cladosporium sp. strain KF501 isolated from the German Wadden Sea , whereas 179\u2013181 exhibited weak antibacterial effect towards Xanthomonas campestris (IC50 28.3\u201337.9 \u03bcM), compared to chloramphenicol (IC50 2.1 \u03bcM) [Silber et al. reported the isolation of malettinins A\u2013C (dden Sea . These m 2.1 \u03bcM) .Bisnaphthopyrones are dimers, belonging to naphthopyrones. They have C13 basic skeleton (C6-C4-C3) that consists of naphthalene and pyrone cores .182), and the formerly isolated viriditoxin (183) and viriditoxin derivatives (184 and 185) were separated the sediment associated C. cladosporioides (183 was firstly reported from Aspergillus viridinutans [183 was the most potent one (IC50 0.1 \u03bcM), however 182 and 184 had a cytotoxic effect . However, 185 was ineffective [S. aureus ATCC-29213, with 183 being the most effective (MIC 0.023 \u03bcM) [The new binaphthopyrone, cladosporinone (orioides . Note thdinutans . They weffective . Note th.023 \u03bcM) .188\u2013190, 193, 200, 201, and 203 from Cladosporium sp. OUCMDZ-302 isolated from mangrove plant Excoecaria agallocha. They possessed no cytotoxic effect towards BEL-7402, A549, HeLa, K562, HL-60, and H1975 cell lines in the MTT and SRB methods. Whilst 201 and 203 showed radical scavenging activity against DPPH . None of these metabolites exhibited antimicrobial activities against E. coli, E. aerogenes, P. aeruginosa, B. subtilis, and C. albicans [192), had no \u03b1-glycosidase inhibitory effect and no cytotoxic activity towards SGC-7901, K562, Hela, and BEL-7042 cell lines in the MTT assay [186 and 205 displayed no cytotoxic effect (IC50 > 10 \u03bcM) versus HeLa cell line in the MTT assay, as well as no antibacterial potential towards S. aureus, B. cereus, E. coli, V. alginolyticus, V. parahemolyticus, and MR S. aureus (conc. 20 \u03bcM) in the microplate assay [C. halotolerans GXIMD 02502 associated with the coral Porites lutea yielded a new benzopyranone derivative, coniochaetone K (196) with unusual C-8 carboxyl, along with 194, 195, 197, and 198 that were evaluated for their cytotoxicity versus 22RV1, C4-2B, and RWPE-1 cell lines . On the other hand, they exhibited nearly no cytotoxic effect versus RWPE-1 and C4-2B cells [206 prohibited the growth of H. armigera Hubner newly hatched larvae (IC50 100 \u03bcg/mL), compared to azadirachtin (IC50 25 \u03bcg/mL) [S. aureus (MIC 6.25 \u03bcg/mL), compared with ciprofloxacin (MIC 0.39 \u03bcg/mL) [207) did not have obvious anti-biofilm activity towards S. aureus, E. coli, and B. subtilis [50 49.9 \u00b5M), compared to toosendanin (LC50 21.2 \u00b5M) in the brine shrimp lethality assay [210 possessed no anti-allergic effect (IC50 > 200 \u00b5M) on RBL-2H3 cells, in comparison to loratadine (IC50 35.01 \u00b5M) using fluorometric assay [211\u2013213 were separated from C. herbarum isolated from the sponge Aplysina aerophoba with mortality rates 85 and 75% and 80 and 65%, respectively, while 213 did not have any activity. Besides, 213 showed growth inhibitory activity towards Spodoptera littoralis larvae [211\u2013213 did not show any noticeable antimicrobial activity in the agar plate diffusion assay [Among them, 2B cells . Bai et 5 \u03bcg/mL) . Further9 \u03bcg/mL) . Cladospsubtilis . On the ty assay . Furtheric assay . \u03b1-Pyronerophoba . Compoun216 from C. cladosporioides that possessed no anti-allergic effect (IC50 > 200 \u00b5M) on RBL-2H3 cells, in comparison to loratadine (IC50 35.01 \u00b5M) using fluorometeric assay [C. tagal associated-fungus Cladosporium sp. JJM22 produced new cyclohexene derivatives, cladoscyclitols A\u2013D (218\u2013221) (219 (IC50 2.95 \u03bcM) revealed potent \u03b1-glucosidase inhibitory activity, compared to acarbose (IC50 2.35 \u03bcM) in the colorimetric assay [S. aureus ATCC-6538, E. coli ATCC-25922, B. cereu ATCC-6633, V. alginolyticus ATCC-3787, V. Parahemolyticus ATCC-17802, or MRSA CMCC-B-63303 in the micro-plate assay [223) and B (224), representing new azaphilone epimers, together with bicyclic diol (225) were separated from sea sediment-associated C. perangustum FS62 fungus. They had no observable cytotoxic activity towards SF-268, NCI-H460, MCF-7, and HepG-2 (Conc. 100 \u03bcM) in the SRB assay [In 2020, He et al. purified ic assay . The man218\u2013221) . Compounic assay . On the te assay . Perangu233 and 235 showed DPPH radical scavenging activity , in comparison to ascorbic acid (IC50 3.29 \u00b5M). Further, none of these compounds had antimicrobial potential versus P. aeruginosa, E. aerogenes, B. subtilis, E. coli, and C. albicans [232, 238, and 249 were separated from EtOAc extract of Cladosporium sp. F14 isolated from seawater and investigated for their anti-larval activity (conc. 50 \u00b5g/mL) towards B. neritina and B. amphitrite larvae in the settlement inhibition assays [232 had weak larvae settlement inhibition towards B. neritina and B. Amphitrite, respectively, whereas 238 and 249 showed weak inhibitory effects towards B. amphitrite and B. neritina larvae, respectively. In another larval settlement bioassay, 232, 238, and 249 inhibited B. neritina larval settlement and B. amphitrite larval settlement . The larval settlement EC50 values of 249 towards B. amphitrite and 232 towards B. neritina were less than the US Navy program established standard requirement (EC50 25.0 \u00b5g/mL), revealing the potential of 232 and 249 as antifouling agents [232 obviously prohibited L. hongkongensis growth (IZD 8 mm and MIC 80 \u00b5g/mL), compared to streptomycin (MIC 250 \u00b5g/mL) [239 isolated Cladosporium sp. JJM22 associated with the mangrove plant C. tagal had no cytotoxic effect (IC50 > 10 \u03bcM) versus HeLa cell line in the MTT assay, compared to epirubicin [In the DPPH assay, albicans . The metn assays . The ribirubicin .S. aureus, B. cereus, E. coli, V. alginolyticus, V. parahemolyticus, and MR S. aureus (conc. 20 \u03bcM) in the microplate assay [240 (IC50 2.05 \u03bcM) revealed potent \u03b1-glucosidase inhibitory activity, compared to acarbose (IC50 2.35 \u03bcM) in the colorimetric assay [S. aureus ATCC-6538, E. coli ATCC-25922, B. cereus ATCC-6633, V. alginolyticus ATCC-3787, V. Parahemolyticus ATCC-17802, and MRSA CMCC-B-63303 in the microplate assay [Cladosporium sp. associated with Chondria crassicualis red alga resulted in the separation of a phenol derivative, clavatol (241) that exhibited antioxidant capacity (ED50 227.0 \u00b5M) more than oxybenzone as evident by their UV-A protecting potential [S. aureus [242 and 243 exhibited no observable cytotoxic activity towards SF-268, NCI-H460, MCF-7, and HepG-2 (Conc. 100 \u03bcM) in the SRB assay [247) did not have obvious anti-biofilm activity towards S. aureus, E. coli, and B. subtilis [50 16.4 \u00b5M), compared with ascorbic acid (IC50 4.9 \u00b5M). Besides, it showed moderate toxicity towards brine shrine naupalii (LC50 81.4 \u00b5M), comparing with toosendanin (LC50 21.2 \u00b5M) in the brine shrimp lethality assay [Additionally, it exhibited no noticeable antibacterial potential towards te assay . The newic assay . On the te assay . Phytochsubtilis , while ity assay .248 separated from Cladosporium sp. TPU1507 derived from marine sponge and assessed for inhibitory effect towards PTP1B and TCPTP using enzyme-based assay [50 27 \u03bcM) that was 2-fold weaker than on PTP1B (IC50 11 \u03bcM) [250), separated from C. herbarum isolated from Callyspongia aerizusa had no activity towards A. salina and HL-60 human leukemia cell line [251 from Cladosporium sp. OUCMDZ-1635 possessed no cytotoxic effect towards MCF-7, HeLa, HCT-116, HeLa, HCT-116, K562, and HL-60. Furthermore, it did not show antibacterial activity (conc. 100 \u03bcg/mL) against B. subtilis, P. aeruginosa, C. perfringens, S. aureus, E. coli, and C. albicans [252) prohibited the growth of H. armigera Hubner newly hatched larvae (IC50 150 \u03bcg/mL), compared to azadirachtin (IC50 25 \u03bcg/mL) [S. aureus (MIC 25.0 \u03bcg/mL), compared with ciprofloxacin (MIC 0.39 \u03bcg/mL) [253) and acetyl Sumiki\u2019s acid (254) exerted activity towards S. aureus and B. subtilis (IZDs 7 mm at conc. 5 \u00b5g/disk), whereas they had no activity towards C. albicans and E. coli [Compound ed assay . It show0 11 \u03bcM) . The newell line . In addi5 \u03bcg/mL) . Further9 \u03bcg/mL) . The fur E. coli .268) and six sterol derivatives: 256, 258, 260, 262, 263, and 267 from gorgonian-associated Cladosporium sp. WZ-2008-0042 [268 was reported in the same year by Pang et al. as new metabolites with the name cladosporisteroid B from Cladosporium sp. SCSIO41007 associated with Callyspongia sp. [50 values ranging from 0.11 to 0.17 \u00b5M) revealed antiviral activity against RSV with therapeutic ratio (TC50/IC50) values ranging from 5.18 to 9.92, in comparison to ribavirin in the neuraminidase inhibition assay. This could be due to their binding to RSV GREs (glucocorticoid response elements) [268 had no noticeable antibacterial potential towards B. cereus, M. luteus, S. aureus, V. anguillarum E. coli, Shigella dysenteriae, B. subtilis, and V. Parahemolyticus, while 263 was moderately active (MIC 3.13 \u03bcM) towards S. dysenteriae [256, 261, 265, 266, and 268 separated from C. cladosporioides sea sediment-derived fungus possessed no anti-allergic effect on RBL-2H3 cells, in comparison to loratadine using fluorometeric assay [264) and new pregnanes, cladosporisteroid B (268) and cladosporisteroid C (269), along with 259, 265, and 270 from Cladosporium sp. SCSIO41007 isolated from Callyspongia sp. and assessed their antiviral activity towards EV71 and H3N2 using CCK-8 and CPE assays, respectively. Only, 268 (IC50 16.2 \u03bcM) had weak activity towards H3N2 compared to oseltamivir (IC50 34.0 nM). Moreover, they revealed no cytotoxic effect towards K562, MCF-7, and SGC-7901 in the CCK-8 assay [268 was purified from C. sphaerospermum EtOAc fraction by HPLC with the aid of LCMS and assessed for its influence on adipogenesis and lipid metabolism during maturation of adipocyte using 3T3-L1 preadipocytes [Adipsin (adipocyte marker gene) expression. Further, it significantly upregulated ATGL and reduced FASN and SREBP1 expression. Collectively, 268 facilitated lipid metabolism and disrupted adipogenesis via promoting lipolysis and prohibiting lipogenesis [A study conducted by Yu et al. in 2018 led to the separation of a new pregnane; 3\u03b1-hydroxy-7-ene-6,20-dione from the culture of Cladosporium sp. isolated from intertidal marine sediment [E. coli ATCC-25922, B. subtilis ATCC-6633, and C. albicans ATCC-18804 in the agar diffusion method. It is noteworthy that this class of metabolites had been reported formerly from red algae [S,3S,4E)-hepta-4,6-diene-2,3-diol (285) and -Undeca-3,8,10-trien-1,6-diol (286) were assessed for cytotoxic potential versus HeLa, BEL-7402, HL-60, A549, K562, and H1975 cell lines. Compound 286 had a cytotoxic effect versus H1975 cell line (IC50 10.0 \u00b5M), compared to ADR (IC50 0.38 \u00b5M). While both metabolites revealed no antioxidant and antimicrobial capacities [Gallo et al. reported for the first time from fungi the isolation of \u03b1,\u03b2-unsaturated aldehydes ,156. Thepacities .Cladosporium sp. isolate N5 associated with Porphyra yezoensis red alga did not produce any pathogenic symptoms in the reinfection assay. Further, its EtOAc extract displayed no lethality to A. salina and had a moderate antimicrobial activity which indicated that Cladosporium sp. had no toxicity to the aquatic ecosystem and could be applied as a biocontrol agent [Cladosporium sp. EIODSF 008 EtOAc extract exhibited significant antibacterial potential towards E. coli, M. luteus, and B. subtilis (conc. 100 \u00b5g/disc) [Cladosporium sp. EN-S01 isolated from Sargassum cinereum brown algae showed anticancer activity towards MCF-7, HeLa, and DU-145 cell lines . The extract had greater cytotoxic activity and anti-proliferative towards MCF-7 and HeLa cell lines than towards DU-145 [C. cladosporioides KT384175 isolated from the seaweed Sargassum wightii possessed remarkable antioxidant potential that was comparable to ascorbic acid, as well as significant Fe3+ reducing power that could be referred to its phenolic contents. Moreover, it revealed anti-angiogenic potential as evidenced by the decrease in the number and length of blood vessel branches on CAM in-vivo in the CAM assay. Further, C. cladosporioides extract (conc. 1.0 mg/mL) had lower wound healing potential than thalidomide (conc. 1.0 \u00b5g/mL) in the in vitro scratch assay using MCF-7 cells [Cladosporium sp. F14 can produce antifouling and antibiotic metabolites in the existence of xylose or glucose. Significantly, it showed higher antibiotic activity towards M. luteus, P. piscida, Rhodovulum sp., Ruegeria sp., V. fluvialis, and V. harveyi in the existence of a sugar carbon source than in its absence in the disc diffusion assay, even though the fungal cells were well-grown under both conditions. Moreover, it possessed antifouling potential as it reduced the attachment of B. neritina (bryozoan larvae) in the larval settlement assay [C. cladosporioides isolated from the seaweed S. wightii possessed noticeable antimicrobial potential towards E. coli MTCC-118, B. subtilis MTCC-441, S. aureus MTCC-7443, P. aeruginosa MTCC-424, and A. niger MTCC-281 with the highest growth inhibition towards S. aureus (IZD 12 mm) and least activity against B. subtilis (IZD 9.5 mm), compared to ampicillin in the well diffusion method. Furthermore, they also had significant antioxidant potential comparable to ascorbic acid in the DPPH assay and moderate effectiveness in reducing power assay [C. halotolerans biomass isolated from the marine debris collected around Tarout Island showed a significant free radical scavenging effect (%inhibition 78% within 30 min incubation) in the DPPH assay. Moreover, it exhibited cytotoxic potential towards MCF-7 (IC50 34.27 \u00b5L/mL), compared to cisplatin (IC50 17.69 \u00b5L/mL) in the MTT assay, as well as an antifungal effect against A. niger in the broth dilution method [Ding et al. stated that ol agent . In the \u00b5g/disc) . The EtOs DU-145 . Moreove-7 cells . The seant assay . The goler assay . Ameen en method .C. phlei and C. cucumerinum were isolated mainly from plant sources [Cladosporium species [seco-acids, macrolides, diketopiperazines, alkaloids, and tetramic acid derivatives were reported mainly from marine-associated Cladosporium species.From the comprehensive review of the available literature, it was noticed that sources ,164,165. sources ,165. Add species ,169,170.Cladosporium species are of biotechnological and industrial relevance and could be considered as substantial enzyme producers. Their enzymes are active in harsh conditions such as extremely low temperatures and high salinity. Therefore, they can be utilized in various industrial and biotechnological applications. Besides, these species were found to be a wealthy pool covering a wide array of metabolites with various bioactivities. Over the past 22 years, 286 metabolites have been separated from marine-associated Cladosporium species isolated from various marine samples, including mangrove, sediment, sponges, corals, gorgonians, algae, bivalves, hydroids, and others and C. cladosporioides .The results revealed that alkaloids, macrolides, tetramic acid and pyrone derivatives, and phenolics are the major metabolites reported from this marine-associated fungal species . They coAlthough the structural diversity of these metabolites, they were insufficiently evaluated for their bioactivities. Most of them had been assessed for their antimicrobial, cytotoxicity, antiviral, and insecticidal activities .However, there are limited studies that focus on the mechanism of action of these metabolites. Many of the tested metabolites possessed no noticeable efficacy in some of the tested activities. Therefore, estimation of other potential bioactivities and derivatization of these metabolites, as well as the mechanistic and in vivo studies of the active metabolites should clearly be the target of future research.Cladosporium species such as co-cultivation of organisms and elicitors epigenetic, as well as, modifiers can be applied [Growing evidence has revealed that the activation of silent gene clusters has the potential to significantly enhance the discovery of new natural metabolites of high-therapeutic leads. Different strategies to awake the silent biosynthetic gene clusters of applied ,173,174. applied ,175. The applied ,172,173. applied . Challen applied ,172,177. applied ,172,173. applied ,172,178. applied ."} +{"text": "Cytopenias are rare complications of prolonged beta-lactam use; however, incidence and associated risk factors are not well described. Patients aged 18-64 years in the 2010-2016 IBM MarketScan Commercial Database discharged from the hospital on cephalosporin, penicillin, or carbapenem outpatient Parenteral Antimicrobial Therapy (OPAT) were included. The primary endpoint was hospital admission coded for neutropenia, leukopenia, or thrombocytopenia within the first 6 weeks post index discharge and within 7 days of beta-lactam discontinuation. Patients with history of malignancy and those who are on chemotherapy were excluded. Significant factors in univariate analysis were incorporated into a multivariable logistic regression model with sequential exclusion of variables with p > 0.1.A total of 35,102 patients received beta-lactam OPAT; median age was 52 years and 53.6% were male. The primary outcome occurred in 150 (0.43%) patients at a median of 19 days (IQR 10-28 days after index discharge), which included 63 (0.18%) neutropenia, 85 (0.24%) thrombocytopenia, and 23 (0.07%) leukopenia admissions. Factors independently associated with readmission cytopenias included chronic liver disease (OR 4.61 [CI 2.93-7.25]), valvular heart disease (2.69 [1.71-4.24]), receipt of vancomycin (2.10 [1.42-3.12]), or antifungal therapy (4.42 [2.01-9.68]); lower risk was associated with carbapenem therapy (0.49 [0.32-0.75]) and diabetes (0.48 [0.31-0.74]) (Table 1).Readmissions with cytopenias during beta-lactam OPAT were rare and carbapenem use was associated with lower risk compared to other classes of beta-lactams. Combination of beta-lactam with vancomycin was associated with an increased risk of cytopenias, and those patients might benefit from closer monitoring.Table 1. Factors Associated with Cytopenias during Beta-Lactams Outpatient Parenteral Antimicrobial Therapy (OPAT)Margaret A. Olsen, PhD, MPH, Pfizer"} +{"text": "Post COVID Syndrome (PCS) is significant morbidity following COVID-19. This study aims to identify biomarkers that predict PCS in a Gulf Coast cohort known for poor health outcomes.Since March 2020 the study Collection of Serum and Secretions for SARS CoV-2 Countermeasure Development (aka ClinSeqSer) has been enrolling subjects with confirmed acute COVID-19, with initial visit at 1 month and follow up every three months from symptom onset. At follow-up, subjects complete symptom questionnaire, physical examination, nasopharyngeal swab/saliva collection, blood draw. Subjects with >= one symptom new since COVID are PCS, remainder are Non-PCS experienced at initial one month visit and six months or longer. Univariate and bivariate analysis was carried out to study significant associations of currently available dataset (N=60).Figure 1. Post-COVID SymptomsIncluded if \u201cnew since covid\u201d. For 60 subjects consented post-covid with completed questionnaire, results were analyzed. Most common symptoms reported were fatigue/tiredness or exhaustion (52%), muscle aches (38%), difficulty concentrating (33%) and headache (32%) as the most common symptoms during one month prior to their initial follow-up visit. The persistent symptoms experienced for six months or longer were fatigue/tiredness or exhaustion (25%), forgetfulness (22%), muscle aches (18%), and sleep difficulties (18%).Cohort is 36 (60%) female, 24 (40%) male, age group of 49 (82%) 18-64 years, 11 (18%) 65+ years, 33 (55%) African American, 27 (45%) Caucasian. Median follow-up time after symptom onset: 290 days. Study cohort reported fatigue (52%), myalgias (38%), difficulty concentrating (33%), headache (32%) as most common symptoms during first month from initial symptom onset. Persistent symptoms ( >=6 months) are fatigue (25%), forgetfulness (22%), myalgias (18%), sleep difficulties (18%). Bivariate analysis shows that gender , past stroke/transient ischemic attack (P=0.04), deep venous thrombosis (P=0.02), abnormal kidney function (P=0.01) associate with PCS. Convalescent antibodies were measured and percentage inhibition of ACE2 spike interaction was recorded. Plasma inflammatory protein levels were measured using multiplex ELISA and Proximity Extension Assay technology during follow-up visit. Increased antibody ReSARS N IgG response and higher convalescent IL-10 (P=0.04) was associated with PCS. Percent inhibition of ACE2: spike interaction was not associated (P=0.79) with PCS. Nasal swab/saliva SARS-COV-2 sequencing has not identified a specific SARS-CoV-2 virus mutation predictive of PCS. Table 1. Demographic and Clinical CharacteristicsThe bivariate analysis results showed that the gender , history of stroke or transient ischemic attack (P=0.0382), chest pain from narrow heart vessels (P=0.0479), deep venous thrombosis (P=0.0241) and abnormal kidney function (P=0.0142) were associated with Post-COVID syndrome.Table 2. Antibodies and ACE2 spike inhibition.The convalescent antibodies, ReSARS N IgG and S-RBD IgG were measured in U/mL and percentage inhibition of ACE2 spike interaction was recorded during follow-up visit for PCS vs Non-PCS subjects. The increased antibody ReSARS N IgG response was associated with Post-COVID syndrome. Percent inhibition of ACE2: spike interaction was not associated (P=0.7932) with PCS.Table 3. Plasma inflammatory protein levels.Plasma inflammatory protein levels were measured using multiplex ELISA (MSD) and Proximity Extension Assay technology (Olink) recorded during follow-up visit for PCS vs Non-PCS subjects, revealing IL-10 (P=0.0379) was associated with development of PCS.This study identifies initial clinical and biomarker predictors of PCS in a cohort that is 55% African American.Figure 2. Antibody ReSARS N IgGReSARS N IgG measured in post-covid patients is significantly associated with post-COVID syndrome(P=0.0159). X axis: number of months from symptom onset to blood draw. Y axis: N IgG U/mL.Figure 3. Spike amino acid mutationsSpike amino acid mutations detected in SARS-CoV-2 from acute-phase respiratory isolates. Nasal swab/saliva samples were collected from subjects with acute COVID-19 at time of enrollment into ClinSeqSer, stored at -80\u00b0C followed by RNA isolation and SARS-CoV-2 qRT-PCR. Samples with Ct value of \u226430 were then sequenced using NextSeq (Illumina). All sequences are deposited on GISAID and under BioProject (ID PRJNA681020). X axis: subject ID, with ID number increasing chronologically. Y axis: amino acid position of each mutation moving from N- to C-terminus.Robert Garry, PhD, Zalgen Labs (Shareholder)"} +{"text": "Ceftolozane/tazobactam (C/T), a cephalosporin\u2013\u03b2-lactamase inhibitor combination, is approved for treatment of complicated urinary tract infections, complicated intra-abdominal infections (cIAI), and nosocomial pneumonia in adults. Safety and efficacy of C/T in pediatric participants with cIAI was assessed.This phase 2 study (NCT03217136) compared C/T + metronidazole (MTZ) with meropenem (MEM) for treatment of cIAI. Age- and weight-adjusted dosing is summarized in Table 1. The primary objective was to evaluate the safety and tolerability of C/T + MTZ compared with MEM. A key secondary endpoint was clinical cure at end of treatment (EOT) and test of cure (TOC).Table 1. Summary of Dosing and Pharmacokinetic Sampling Schedule by Age CohortA total of 94 participants were randomized 3:1; 91 were treated with C/T + MTZ (n=70) or MEM (n=21) comprising the modified intent-to-treat (MITT) population. The clinically evaluable population included 78 participants at EOT and 77 participants at TOC . The most common diagnosis and pathogen in the MITT population were complicated appendicitis and Escherichia coli . The mean (SD) intravenous therapy/overall treatment duration was 6.4 (2.8)/9.3 (3.6) days and 5.8 (1.8)/9.0 (3.2) days for C/T + MTZ and MEM, respectively. In total, \u22651 adverse events (AE) occurred in 80.0% and 61.9% of participants receiving C/T + MTZ and MEM, respectively (Table 2), of which 18.6% and 14.3% were considered drug related. Serious AE occurred in 11.4% (8/70) and 0% (0/21) of participants receiving C/T + MTZ and MEM, respectively; none were considered drug related. No drug-related study drug discontinuations occurred. In the MITT population, rates of clinical cure for C/T + MTZ and MEM at EOT were 80.0% and 95.2%, and at TOC were 80.0% and 100%, respectively ; 6 of the 14 failures for C/T + MTZ were indeterminate responses scored as endpoint failures per protocol. In the clinically evaluable (CE) population, rates of clinical cure for C/T + MTZ and MEM were 89.8% and 100% at EOT, and 89.7% and 100% at TOC, respectively .C/T + MTZ was well tolerated in pediatric participants with cIAI, and rates of clinical success were high with C/T treatment. C/T is a promising new treatment option for children with cIAI.Carl-Christian A. Jackson, MD, Merck & Co. Inc. (Shareholder) Julia Lonchar, MSc, Merck Sharp & Dohme Corp. Feng-Hsiu Su, MPH, MBA, Merck Sharp & Dohme Corp. Jennifer A. Huntington, PharmD, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA (Employee) Mekki Bensaci, PhD, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA (Employee) Myra W. Popejoy, PharmD, Merck Sharp & Dohme Corp. (Employee) Matthew G. Johnson, MD, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA (Employee) Carisa S. De Anda, PharmD, Merck Sharp & Dohme Corp. Elizabeth G. Rhee, MD, Merck Sharp & Dohme Corp Christopher Bruno, MD, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA (Employee)"} +{"text": "Sarcomas are highly heterogeneous in molecular, pathologic, and clinical features. However, a classification of sarcomas by integrating different types of pathways remains mostly unexplored.We performed hierarchical clustering analysis of sarcomas based on the enrichment scores of 14 pathways involved in immune, stromal, DNA damage repair (DDR), and oncogenic signatures in three bulk tumor transcriptome datasets.TP53 mutations, and the worst survival. We further validated the stability and reliability of our classification method by analyzing a single cell RNA-Seq (scRNA-seq) dataset. Based on the expression levels of five genes in the pathways of T cell receptor signaling, cell cycle, mismatch repair, focal adhesion, and calcium signaling, we built a linear risk scoring model (ICMScore) for sarcomas. We demonstrated that ICMScore was an adverse prognostic factor for sarcomas and many other cancers.Consistently in the three datasets, sarcomas were classified into three subtypes: Immune Class (Imm-C), Stromal Class (Str-C), and DDR Class (DDR-C). Imm-C had the strongest anti-tumor immune signatures and the lowest intratumor heterogeneity (ITH); Str-C showed the strongest stromal signatures, the highest genomic stability and global methylation levels, and the lowest proliferation potential; DDR-C had the highest DDR activity, expression of the cell cycle pathway, tumor purity, stemness scores, proliferation potential, and ITH, the most frequent Our classification method provides novel insights into tumor biology and clinical implications for sarcomas.The online version contains supplementary material available at 10.1186/s12967-022-03248-3. CDK4 and RB1-associated CNAs prognosis among the sarcoma subtypes. Notably, DDR-C was likely to have the worst survival consistently in the three datasets Fig.\u00a0B, while 05) Fig.\u00a0C.Fig. 3CU test, P\u2009<\u20090.001) . These phenotypes are associated with tumor progression, immune evasion, drug resistance, and unfavorable prognosis , 29. Not01) Fig.\u00a0D. Stemne01) Fig.\u00a0E. In add05) Fig.\u00a0F. AltogeP\u2009=\u20090.047; hazard ratio (HR)\u2009=\u20091.72 and its 95% confidence interval (CI) survival analysis by the multivariate Cox\u00a0proportional hazards model. We found that the subtype DDR-C remained a significant risk factor for DFS , while it showed no significant difference between Imm-C and DDR-C , while they were not significantly different between Imm-C and DDR-C and/or increased CNAs . We founR-C Fig.\u00a0A. HomoloR-C Fig.\u00a0B. In addR-C Fig.\u00a0C. The G-R-C Fig.\u00a0D. OveralTP53 had a significantly higher mutation frequency in DDR-C than in Imm-C and Str-C \u2009=\u20092.0) . On the other hand, TP53 mutations were less frequent in Str-C than in DDR-C and Imm-C . This result could explain why Str-C was more genomically stable than the other subtypes because p53 plays an important role in the maintenance of genomic stability [DYNC2H1 and MDN1 were more frequently mutated in DDR-C than in Imm-C and Str-C \u2009<\u20090.05]. In contrast, 124 and 180 genes had significantly higher methylation levels in Str-C and DDR-C, respectively, compared to other subtypes. Notably, most of these genes showed significant inverse correlations of their expression levels with methylation levels . These proteins included Syk, PREX1, Lck, 14-3-3_epsilon, PI3K-p85, Caspase-7_cleavedD198, PRDX1, Annexin-1, G6PD, Bax, ATM, p38, STAT5-alpha, Annexin_VII, Claudin-7, p90RSK, TIGAR, CD31, and GATA3 Fig.\u00a0. These pCD40LG, CDC25A, MSH2, FLT4, and ADCY2. The five genes were involved in five of the 14 pathways for clustering analysis, including T cell receptor signaling (CD40LG), cell cycle (CDC25A), mismatch repair (MSH2), focal adhesion (FLT4), and calcium signaling (ADCY2). ICMScore calculates risk score in a tumor as follows: ICMScore\u2009=\u20090.76\u2009\u00d7\u2009exp(CD40LG)\u2009+\u20090.73\u2009\u00d7\u2009exp(FLT4)\u00a0\u2212\u00a00.20\u2009\u00d7\u2009exp(ADCY2)\u2009+\u20091.97\u2009\u00d7\u2009exp(CDC25A)\u2009+\u20091.50\u2009\u00d7\u2009exp(MSH2), where exp(X) denotes the expression level of gene X in the tumor sample. To prove that ICMScore is an authentic risk factor in sarcomas, we compared ICMScores among the three sarcoma subtypes and analyzed their correlation with survival prognosis in sarcomas. In the three sarcoma datasets, As expected, ICMScores was significantly higher in DDR-C than in Imm-C and Str-C to evaluate the prognostic risk of sarcomas based on the expression levels of five genes, including 05) Fig.\u00a0A. Surviv05) Fig.\u00a0B. These 05) Fig.\u00a0C.Fig. 8AUsing the pathway-based clustering method, we analyzed a scRNA-seq dataset GSE131309), which involved gene expression profiles in 6951 single cells from 12 sarcoma [advanced synovial sarcoma (SyS)] patients. The 6951 single cells included 4371 tumor cells, 90 B cells, 943 macrophages, 185 mastocytes, 102 NK cells, 235 CD4\u2009+\u2009T cells, 659 CD8\u2009+\u2009T cells, 206\u00a0T cells, 79 endothelial cells, and 81 cancer-associated fibroblasts (CAFs). Using the t-distributed stochastic neighbor embedding (tSNE) algorithm , we clus, which iWe performed hierarchical clustering of the 6951 single cells based on the enrichment scores of the 14 pathways identified three subtypes of these cells exhibited the consistent expression pattern: Imm-C\u2009<\u2009Str-C\u2009<\u2009DDR-C were significantly higher in Imm-C than in Str-C and DDR-C Fig.\u00a0D. The raR-C Fig.\u00a0D. It ind01) Fig.\u00a0E, suppor01) Fig.\u00a0F. It is TP53 mutations, and the worst survival. It is interesting to observe that there was no significantly different TMB between DDR-C and Imm-C, while their immune infiltration levels were significantly different. Two possible reasons could explain this observation: (1) DDR-C had more frequent arm-level copy number amplifications and deletions than Imm-C; and (2) DDR-C had higher ITH than Imm-C, since both CNAs [In this study, we proposed a novel classification method for sarcomas based on the enrichment scores of 14 pathways, which were involved in immune, stromal, DDR, and oncogenic signatures. In three datasets for bulk tumors and a scRNA-seq dataset, we reproducibly identified three sarcoma subtypes: Imm-C, Str-C, and DDR-C. Imm-C had the strongest anti-tumor immune signatures and the lowest ITH; Str-C showed the strongest stromal signatures, the highest genomic stability and global methylation levels, and the lowest proliferation potential; DDR-C had the highest DDR activity, expression of the cell cycle pathway, tumor purity, stemness scores, proliferation potential, and ITH, the most frequent oth CNAs and ITH oth CNAs are negaThe TCGA Research Network analyzed six types of adult soft tissue sarcomas: DDLPS, LMS, UPS, MFS, MPNST, and SS . We founBased on the enrichment scores of 14 pathways associated with immune, stromal, and DDR signatures, we classified sarcomas into three subtypes. The three sarcoma subtypes were characterized by different immune infiltration levels, stromal signatures, DDR activity, genome features, tumor progression phenotypes, and clinical outcomes. Our new classification method for sarcomas provides novel insights into tumor biology and clinical implications for this disease.Additional file 1: Table S1. A summary of the datasets analyzed.Additional file 2: Table S2. Pathways, immune signatures, and biological processes and their marker genes.Additional file 3: Fig. S1. Comparisons of the expression levels of human leukocyte antigen\u00a0(HLA) genes among the sarcoma subtypes. The one-way ANOVA test P-values are shown. * P\u2009<\u20090.05, ** P\u2009<\u20090.01, *** P\u2009<\u20090.001.Additional file 4: Table S3. Pearson correlations between the methylation levels and expression levels of the genes having significantly different methylation levels among the sarcoma subtypes.Additional file 5: Fig. S2. Heatmap showing top 30 genes with the most significant upregulation of methylation levels in each of the three subtypes.Additional file 6: Fig. S3. Positive correlations between the expression levels of 19 proteins significantly upregulated in Imm-C and immune signature scores in TCGA-SARC. * P\u2009<\u20090.05, ** P\u2009<\u20090.01, *** P\u2009<\u20090.001.Additional file 7: Fig. S4. Overlaps between our subtyping and other subtyping of sarcoma in TCGA-SARC. (A) Proportions of our subtypes in six types of adult soft tissue sarcomas: DDLPS, LMS (ULMS and STLMS), UPS, MFS, MPNST, and SS. (B) Proportions of our subtypes in the immune subtypes of sarcomas. (C) Proportions of the five subgroups (Clusters A-E) in our subtypes."} +{"text": "Enterobacterales are considered an urgent threat for patients in healthcare facilities, causing infections with significant morbidity and mortality. Most isolates are multidrug resistant with limited treatment options, so combination therapy is an alternative. Recently, synergy with piperacillin/tazobactam (P/T) + meropenem (MP) was demonstrated against 7/10 (70%) KPC-producing Escherichia coli and 9/10 (90%) OXA-48-producing K. pneumoniae using time-kill assay . The aim of the present study was to further evaluate the combination of P/T + MP against KPC-producing Enterobacter cloacae, in addition to OXA-producing K. pneumoniae using our rapid ETEST MIC:MIC synergy method.Carbapenem-resistant K. pneumoniae and 7 KPC-producing E. cloacae were obtained from the CDC and FDA Antibiotic Resistance Isolate Bank. ETEST MICs for P/T and MP and our ETEST synergy method were performed in triplicate for each isolate. The summation fractional inhibitory concentration was calculated, and the mean value was interpreted as: < 0.5 synergy; > 0.5-1 additivity; > 1-4 indifference; and > 4 antagonism.14 carbapenemase-producing isolates: 7 OXA-48-like K. pneumoniae and synergy (6) or additivity (1) against all 7 KPC-producing E. cloacae. No antagonism was detected.MICs (\u00b5g/mL) ranged: MP, 0.5 to > 32 (14% susceptible) and P/T, 96/4 to > 256/4 . The combination of P/T + MP showed synergy (3) or additivity (2) against 5/7 (71%) OXA-producing K. pneumoniae and 7/7 KPC-producing E. cloacae, similar to previously published findings showing synergy in 7/10 KPC-producing E. coli and 9/10 OXA-48-producing K. pneumoniae using time-kill assay. Our ETEST synergy method is simple to use and should be evaluated more extensively. Regardless of the method used, results may or may not correlate in an in vivo setting. In vivo studies are needed.Using our ETEST MIC:MIC method, the combination of P/T + MP demonstrated synergy or additivity in 5/7 OXA-producing All Authors: No reported disclosures"} +{"text": "Annexins as Ca2+/phospholipid-binding proteins are involved in the control of many biological processes essential for plant growth and development. In a previous study, we had shown, using a proteomic approach, that the synthesis of two annexins is induced in pea roots in response to rhizobial inoculation. In this study, phylogenetic analysis identif ied these annexins as PsAnn4 and PsAnn8 based on their homology with annexins from other legumes. The modeling approach allowed us to estimate the structural features of these annexins that might inf luence their functional activity. To verify the functions of these annexins, we performed comparative proteomic analysis, experiments with calcium inf lux inhibitors, and localization of labeled proteins. Essential down-regulation of PsAnn4 synthesis in a non-nodulating pea mutant P56 (sym10) suggests an involvement of this annexin in the rhizobial symbiosis. Quantitative RT-PCR analysis showed that PsAnn4 was upregulated at the early stages of symbiosis development, starting from 1\u20133 days after inoculation to up to 5 days after inoculation, while experiments with the Ca2+ channel blocker LaCl3 revealed its negative inf luence on this expression. To follow the PsAnn4 protein localization in plant cells, it was fused to the f luorophores such as red f luorescent protein (RFP) and yellow f luorescent protein (YFP) and expressed under the transcriptional regulation of the 35S promoter in Nicotiana benthamiana leaves by inf iltration with Agrobacterium tumefaciens. The localization of PsAnn4 in the cell wall or plasma membrane of plant cells may indicate its participation in membrane modif ication or ion transport. Our results suggest that PsAnn4 may play an important role during the early stages of pea-rhizobial symbiosis development. Annexins are of particular research interest due to their abilityto regulate various aspects of plant growth and development.Annexins belong to the evolutionarily conservedsuperfamily of proteins that are involved in Ca2+-dependentor Ca2+-independent binding with membrane phospholipids. Most annexinshave four putative annexin repeats of around 70 amino acids,with the conservative repeat GxGT-(38 residues)-D/E, whichconfers Ca2+/phospholipid-binding activity to these proteins. In addition,some plant annexins have motifs demonstrating F-actin bindingand peroxidase and ATPase/GTPase activities .Despite the general structural similarity of these proteins,the functions of annexins are diverse, and individual annexinsmay have specific activities. Annexins are involved in a widevariety of essential cellular processes, including the regulationof membrane organization, vesicle trafficking, cytoskeletaldynamics, exocytosis, cell cycle control, ion transport, andsignal transduction . Annexins as phospholipid-binding proteinsare being implicated in the fusion of membrane vesicles,as was shown for annexins from bell pepper and cotton . They are also involved inthe regulation of exocytosis, e. g., annexins in Zea mays rootcap cells . Moreover, annexins can functionas cationic channels activated by various stimuli in cells.Annexins can influence the Ca2+ influx in plant cells, as wasdemonstrated for a Capsicum annuum annexin, which hasCa2+-channel activity . The Arabidopsisthaliana annexin AtAnn1, which is expressed in root cells,exhibits pH-dependent cation-channel activity, while Z. maysannexins cause active conductivity of Ca2+ in lipid bilayersat slightly acidic pH . Since annexins can be Ca2+ sensors, these proteins arelikely to be involved in signal transduction; for example, theannexin from Triticum aestivum was suggested to be engagedin low-temperature signaling .Participation of annexins in the responses to cold, oxidative,and saline stresses is well-studied in plants . The annexinAtAnn1 from A. thaliana is involved in plant protectionagainst oxidative stress .The overexpression of AtAnn has been found to confer toleranceto drought and salt stresses and fungal attack in transgenicplants . Similarly,the overexpression of the wild tomato (Solanum pennellii)annexin SpAnn2 in cultivated tomato Solanum lycopersicumenhances drought and salt tolerance through the eliminationof reactive oxygen species (ROS) .Some annexins are also known to be activated in plantsduring interaction with plant-growth promoting bacteria and the development of mutualistic symbioses. During legume-rhizobial symbiosis,physiological changes occur, which are necessary for rhizobialinfection and nodule organogenesis, such as the stimulationof ion fluxes, membrane depolarization, ROS production,cytoplasm alkalinization, perinuclear calcium oscillations,and cytoskeletal rearrangements. In Medicago truncatula, thetranscription of MtAnn1 is activated directly by Nod factorsor inoculation with rhizobia in epidermal cells and later incortical cells . Studies using confocal microscopy showedGFP-labeled MtAnn1 to be localized in the cytoplasm, butprotein accumulation in response to inoculation occurred atthe periphery of the nucleus. MtAnn1 has been shown to beable to bind to the membrane phospholipid phosphatidylserine.Therefore, MtAnn1 is probably related to the eventsoccurring at the early stages of symbiosis, leading to bacterialinfection or nodule organogenesis .Transcriptome profiling of roots inoculated with rhizobiarevealed enhanced expression of MtAnn2, as well as MtAnn1. The expression of the MtAnn2 gene isassociated with cell division in the nodule primordium . Proteomic analysis revealed the MtAnn2protein presence in lipid rafts from root plasma membranepreparations . Another annexin MtAnn3was found to be important for root hair deformations inM. truncatula . The increased expression ofMtAnn1 and MtAnn2 is also associated with the early stagesof AM fungal symbiosis, which corresponds to the stages ofpre-infection and infection in this type of symbiosis . This may indicate the general role of these annexinsin the regulation of signaling pathways that lead to thedevelopment of two types of symbiosis.A protein homologous to MtAnn1 \u2013 PvAnn1 from Phaseolusvulgaris \u2013 is activated at the early stages of symbiosisdevelopment . The stimulation of Ca2+ ion transfer throughthe plasma membrane and ROS production caused by Nodfactors constitute an early response in the signal transductionpathway. Analysis of PvAnn1-RNAi transgenic roots inoculatedwith rhizobia showed a decrease in ROS productionand Ca2+ influx into the cells, which resulted in impairedprogression and decreased numbers of infection threads andnodules . Taken together, thesefindings point to the involvement of PvAnn1 in the regulationof signal transduction at early stages.Previously performed proteomic analysis in pea (Pisumsativum L.) allowed us to reveal two annexins, the synthesisof which was increased in response to inoculation with Rhizobium leguminosarum bv. viciae RCAM1026 in 24 h. In this work, searching in therecently released pea genome database using available codingsequences for annexin genes from M. truncatula andP. vulgaris revealed 15 annexins in pea. Phylogenetic analysisshowed the relationship among members of the annexin superfamilyin other legumes and allowed the identification oftwo previously revealed pea annexins responsive to rhizobialinoculation as PsAnn4 and PsAnn8 based on their homologywith the M. truncatula and P. vulgaris proteins. To verify thefunction of these annexins, we performed comparative proteomicanalysis using pea mutant P56 (sym10) unable to formsymbiosis and wild type cv. Frisson. The approaches employedincluded quantitative RT-PCR, experiments with calciumchannel inhibitors, and localization of labeled proteins.Plant material and bacterial strain. Pea Pisum sativum L.seeds cv. Frisson were sterilized with sulphuric acid for5 min, washed with water 3 times, transferred on 1 % wateragar plates and germinated at room temperature in the dark.4\u20135 days-old seedlings were transferred into pots with vermiculitesaturated with Jensen medium , grown in a growth chamber at 21 \u00b0\u0421 at 16 h light/8 h dark cycles, 60 % humidity. For experiments with inhibitor,the Ca2+ channels blocker LaCl3, the plants were grownin pots saturated with Jensen medium with 100 \u03bcM CaCl2 \u00d72 H2O. The Rhizobium leguminosarum bv. viciae strainRCAM 1026 (WDCM 966) was cultivated at 28 \u00b0\u0421 on TY agar medium with 0.5 mg/ml of streptomycin.Fresh liquid bacterial culture was grown in B\u2013 medium and the optical density of the suspensionat 600 nm (OD600) was adjusted to 0.5. Pea seedlingswere inoculated with 2 ml of R. leguminosarum bv. viciaeper plant. Pea roots were harvested 1 dayafter inoculation (dai).Nicotiana benthamiana seeds were surface sterilized with10 % hypochlorite for 10 min, washed with water 5 timesand left for imbibition on a plate with sterile filter paper at4 \u00b0\u0421. All seeds were germinated in a large plastic box withsoil for seven days, and then transferred into individual potswith soil. Plants were grown at 23 \u00b0\u0421 with 16 h light/8 h darkcycles, 60 % humidity.http://www.clustal.org/omega/. The phylogenetic tree was generatedwith the Maximum Likelihood method using MEGA X https://www.megasoftware.net/ with 1000 bootstrap replicates. Thedomain composition of the corresponding encoded proteinswas assessed using PFAM https://www.sanger.ac.uk/science/tools/pfam.Phylogenetic analysis. Multiple sequence alignments wereperformed using Clustal\u03a9 https://salilab.org/modeller/9.20/release.html. Visualization of the three-dimensional structurewas obtained using the PyMol programhttps://pymol.org/2/. The three-dimensional crystal structure of theGhAnn1 G. hirsutum protein was used asa template for building the model. To refine the model, the (VTFM) and the method of molecular dynamics in vacuum.The reliability of the model was calculated by the formula Protein homology modeling was performed in Modeller9.20 Isolation of total protein from pea roots. A modified methodwas used to isolate proteins from pea roots . 100 mg of the roots were ground in liquid nitrogen,then extraction buffer (0.1 M tris-HCl (pH 8.0), 30 % sucrose,10 mM dithiothreitol (DTT), 2 % sodium dodecyl sulfate(SDS), a mixture of protease inhibitors was added to the material and extraction was performed at+4 \u00b0\u0421. After centrifugation at 12 000 g for 15 min, the supernatantwas mixed in a 1:1 ratio with phenol (pH 8.0) , centrifuged at 12 000 g for 5 min.The upper phase was taken for precipitation of proteins. Fivevolumes of cold 100 mM ammonium acetate in methanol wereadded and incubated for 30 min at \u201320 \u00b0\u0421. After centrifugationat 12 000 g for 5 min, the pellet was washed twice with100 mM ammonium acetate in methanol and twice with 80 %acetone. The precipitate was dried in air and dissolved in thebuffer for isoelectric focusing (25 mM tris-HCl (pH 8.0), 9 Murea, 4 % CHAPS, 50 mm DTT, 0.2 % ampholytes ). Protein concentration was measuredusing Bradford assay .Two-dimensional differential gel electrophoresis. Twodimensionaldifferential gel electrophoresis (DIGE) of proteinswas performed using staining of samples with variousfluorescent dyes . The samples were conjugatedfor 30 min on ice with fluorescent dyes Cyanine 2or Cyanine 5 (Cy2 or Cy5) in various combinations. The incubationsolution contained 400 pM of each dye dissolvedin dimethylformamide for 30 min on ice. The reaction wasstopped by adding 10 mM L-lysine (Sigma-Aldrich), followedby incubation on ice for 10 min. After that, the controland experimental samples were mixed, DTT and ampholyteswere added. Passive in-gel rehydration with immobilizedpH gradient (Bio-Rad Laboratories) was performed overnightat room temperature. The total amount of sample applied to7 cm gel was up to 100 \u03bcg.Isoelectric focusing (IEF) was performed in a Protean IEFsystem (Bio-Rad Laboratories) at a temperature of 20 \u00b0\u0421, thesamples were desalted at 250 V for 15 min, after which thevoltage was linearly increased to 4,000 V for 2 hours, thenIEF was carried out with increasing voltage up to 10 000 V.Before electrophoresis in polyacrylamide gel (PAGE), proteinrecovery was carried out in buffer with DTT for10 min followed by alkylation in iodoacetamide buffer for 15 min. The second direction of two-dimensionalelectrophoresis was carried out in tris-glycine bufferin 15 % polyacrylamide gel using a 4 % stacking gel. Afterseparation of proteins the gels were visualized using a laserscanner Typhoon FLA 9500 .Mass spectrometry. The proteins were rehydrated in trypsinsolution on ice for1 h and then incubated for 1 h at 56 \u00b0\u0421. The peptides wereextracted from the gel with 50 % acetonitrile, 0.1 % formicacid. This solution was evaporated in vacuum concentratorCentriVap (Labconco) at 4 \u00b0\u0421 and dissolved in phase A . Mass spectrometry was performedusing Agilent ESI-Q-TOF 6538 UHD (Agilent Technologies)combined with high performance liquid chromatographAgilent 1260 (Agilent Technologies). Chromatographywas performed in system water \u2013 acetonitrile in the presenceof 0.1 % formic acid in the gradient of acetonitrile (from 5 to 60 % phase Bfor 25 min and to 100 % phase B for 5 min) on Zorbax 300SBC18column 3.5 \u03bcm, 150 mm length (Agilent Technologies)with flow rate 15 \u03bcl/min.RNA extraction and quantitative reverse transcriptionPCR (RT-PCR). RNA extraction and RT-PCR were performedas described previously . Thequantitative RT-PCR analysis was performed on a CFX-96real-time PCR detection system with C1000 thermal cycler(Bio-Rad Laboratories). All primer pairs (Table 1) were designedusing the Vector NTI program and produced by theEvrogen company (www.evrogen.com). PCR amplificationspecificity was verified using a dissociation curve (55\u201395 \u00b0\u0421).mRNA levels were normalized against Ubiquitin and valueswere calculated as ratios relative to non-inoculated root expressionlevels. The data of two-three independent biologicalexperiments were analysed. Statistical analysis was conductedby Student\u2019s test ( p < 0.05) to assess the differences betweenvariants.Mass spectrometry. The proteins were rehydrated in trypsinsolution on ice for1 h and then incubated for 1 h at 56 \u00b0\u0421. The peptides wereextracted from the gel with 50 % acetonitrile, 0.1 % formicacid. This solution was evaporated in vacuum concentratorCentriVap (Labconco) at 4 \u00b0\u0421 and dissolved in phase A . Mass spectrometry was performedusing Agilent ESI-Q-TOF 6538 UHD (Agilent Technologies)combined with high performance liquid chromatographAgilent 1260 (Agilent Technologies). Chromatographywas performed in system water \u2013 acetonitrile in the presenceof 0.1 % formic acid in the gradient of acetonitrile (from 5 to 60 % phase Bfor 25 min and to 100 % phase B for 5 min) on Zorbax 300SBC18column 3.5 \u03bcm, 150 mm length (Agilent Technologies)with flow rate 15 \u03bcl/min.RNA extraction and quantitative reverse transcriptionPCR (RT-PCR). RNA extraction and RT-PCR were performedas described previously . Thequantitative RT-PCR analysis was performed on a CFX-96real-time PCR detection system with C1000 thermal cycler(Bio-Rad Laboratories). All primer pairs (Table 1) were designedusing the Vector NTI program and produced by theEvrogen company (www.evrogen.com). PCR amplificationspecificity was verified using a dissociation curve (55\u201395 \u00b0\u0421).mRNA levels were normalized against Ubiquitin and valueswere calculated as ratios relative to non-inoculated root expressionlevels. The data of two-three independent biologicalexperiments were analysed. Statistical analysis was conductedby Student\u2019s test ( p < 0.05) to assess the differences betweenvariants.Genetic constructs for plant transformation. To obtainthe pBIN19 vector for plant transformation, carrying the geneof interest, the coding sequence of PsAnn4 gene without stopcodonhas been amplified using cDNA as a template withcorresponding primers (see Table 1). Total RNA was isolatedfrom 2 dai pea roots of cv. Frisson. Amplification was doneusing Phusion Flash High-Fidelity PCR Master Mix (ThermoScientific). The amplified products were restricted with XbaIand EcoRI and subcloned in the pMON vector under 35Spromoter in the frame with the sequences encoding RFP orYFP and nopaline synthase terminator (Tnos). The inserts wereverified by sequencing. The cassette composed of the 35Spromoter, gene of interest fused with RFP or YFP and Tnoswas excised from pMON using Hind III, SmaI and cloned inthe pBIN19. All verified constructs were transferred into theAgrobacterium tumefaciens LBA4404.Transient protein expression in N. benthamiana leaves.A. tumefaciens strain LBA4404 was used for infiltration inN. benthamiana leaves. Bacterial culture was grown at 28 \u00b0Covernight, then centrifuged at 3000 g and resuspended in10 mM MES-KOH, 10 mM MgCl2 and 0.5 mM acetosyringoneup to culture density OD600 = 0.5. Bacterial cells wereinfiltrated into the leaves of 3-week-old N. benthamiana.Plants were analyzed 48\u201396 h after infiltration.ResultsPhylogenetic analysis of annexinsin pea and other legumesThe search of the sequences presumably coding for annexinsin legumes was performed using BlastX with 8 previouslyrevealed M. truncatula and 13 P. vulgaris nucleotidesequences encoding these proteins as queries against differentplant sequence databases: https://phytozome.jgi.doe.gov/pz/portal.html for M. truncatula and P. vulgaris, http://www.kazusa.or.jp/lotus/ for L. japonicus, and the URGI databasev. 1 https://urgi.versailles.inra.fr/blast for P. sativum L.. As a result, we were able to identify 18 codingsequences (CDSs) for annexins in M. truncatula, 15 inP. sativum L., and 13 in L. japonicus (Table 2). Twenty-threegenes had been previously found to encode annexins in soybean. The coding sequences for annexinsfrom P. sativum were named based on their phylogeneticrelationships with the corresponding homologous sequencesfrom M. truncatula and P. vulgaris (see Table 2) .The phylogenetic analysis was performed usingthe deduced amino acid sequences of annexins found andannotated for P. sativum along with those of other legumes and non-legumes , whichwere available in the Phytozome database v. 12.1 and otherdatabases.Based on our analysis, the previously found MtAnn1(Medtr8g038210) and PvAnn1 (Phvul.011g209300) clusteredin the subclade with proteins corresponding to P. sativumPsat4g147120 and Psat4g191080, named PsAnn1a andPsAnn1b (see Table 2). Revealed in M. truncatula MtAnn2(Medtr8g038220) and P. vulgaris PvAnn2 (Phvul.011g209200)clustered in the subclade with Psat4g191040, named PsAnn2.Two previously described pea annexins induced in rootsin response to rhizobial inoculation were identified as proteins corresponding to Psat5g217440and Psat2g074960 coding sequences using a new databasehttps://urgi.versailles.inra.fr/blast for P. sativum (see Table 2). The phylogenetic analysis depicted anadditional branch in the phylogenetic group with MtAnn1/PvAnn1 and MtAnn2/PvAnn2, comprising MtAnn4(Medtr3g018780), PvAnn4 (Phvul.005g030100), and theirhomolog Psat5g217440, named PsAnn4 (identified by proteomicscreening) (see Table 2). Another previously foundpea annexin, Psat2g074960, might be closely related toMedtr5g063670 and Phvul.008G173100.1, defined as MtAnn8and PvAnn8 based on phylogenetic analysis (see Table 2).Analysis of the domain composition of pea annexinsand modeling of three-dimensional structureof PsAnn4 and PsAnn8Analysis of the domain composition of the correspondingproteinsin pea showed the presence of four typical domainsof plant annexins . This suggests that the annexin genefamily indeed comprises several members in pea. Althoughplant annexins have four putative annexin repeats, not all Ca2+-binding motifs in these repeats seem to be functional. In plantannexins, the Ca2+-binding site is highly conservative in thefirst (I) repeat but is not conservative in the second (II) andthird (III) repeats, while in the fourth (IV) repeat moderateconservatism is preserved .The crystal structure of the Gossypium hirsutum annexinGhAnn1 bound to calcium was obtained in an earlier study. Since PsAnn4 and PsAnn8 may be involvedin regulation of pea-rhizobial symbiosis, we modeled thethree-dimensional (3D) structure of these two annexins usingGhAnn1, with 50 % sequence identity for PsAnn4 and 78 %sequence identity for PsAnn8 as a template .The resulting 3D structures of PsAnn4 and PsAnn8 proteinsindicated the coordination of calcium ions in the first andfourth annexin repeats. In the first repeat of both proteins, thecalcium-binding site of the type II was coordinated by threecarbonyl oxygen atoms of the residues Phe-23, Gly-25, andGly-27, and carboxylate of Glu-67 in PsAnn4 and PsAnn8, as was shown earlier for GhAnn1.We suppose that the second calcium ion is bound in the loopof the fourth annexin repeat of PsAnn4 and PsAnn8 proteins. Itis coordinated in the binding site of type II by Ile-254, Lys- 256,and Gly-258 in pea annexins . The thirdcalcium ion (in the binding site of type III) is coordinated bytwo oxygen atoms of the residues Val-296 and Thr-299 andcarboxylate of Glu-304 in this protein . However, in thefourth repeat of PsAnn4 protein, the Val-296 is replaced bySer and Glu-304 by Lys . This might potentially obstruct the binding of the calcium ion, as was shown in ourmodeling . Although we cannot rule out that thismight be due to low homology between PsAnn4 and GhAnn1,which was used as a template in the modeling, the results suggestthe potential difference in Ca2+ binding between PsAnn4and PsAnn8 proteins.Comparative analysis of protein patternsin wild-type and non-nodulating pea mutantTo verify whether the stimulation of synthesis of PsAnn4 andPsAnn8 proteins depends on Nod factor perception, the proteinpatterns were analyzed in wild-type pea cv. Frisson anda P56 mutant with a defective sym10 gene (which encodes aputative Nod factor receptor) .Two-dimensional differential in-gel electrophoresis-basedproteomics was used to characterize the pattern of proteindistribution . Two spots corresponding to the locationof the previously characterized annexins were excised from the gel. Mass spectrometric analysisconfirmed their identity to annexins Psat5g217440 (PsAnn4)and Psat2g074960 (PsAnn8). Enhanced level of PsAnn4 wasfound in the inoculated roots of wild type pea plants (cv. Frisson)compared to the inoculated P56 mutant roots.The amount of PsAnn8 protein was also slightly higher inresponse to inoculation in the wild type than in the P56 mutant,but not as essential as for PsAnn4. In accordance with this,low amounts of PsAnn4 and PsAnn8 proteins were found inthe roots of the P56 mutant and didn\u2019t change in response toinoculation. This suggests that the up-regulation of both annexinsmay depend on Nod factor recognition in pea plantsand may be connected with the functioning of these annexinduring symbiotic interaction of plants with rhizobia at earlystages. Since the increase in the amount of PsAnn4 proteinwas more significant in response to inoculation, we focusedon this annexin in our next experimentsPsAnn4 expression pattern in response to rhizobialinoculation and treatment with Ca2+ inhibitorsThe PsAnn4 expression pattern in response to rhizobial inoculationwas analyzed in our experiments . A quantitativeRT-PCR analysis revealed that Rhizobium infectionenhanced the PsAnn4 gene expression at the early stages ofnodulation, starting from 1\u20133 days after inoculation up to5 days after inoculation, but thereafter their transcript levelsdid not significantly change upon nodule development . In our experiments the expression of another annexingene, PsAnn1a, the closest homolog of MtAnn1 genewas also analyzed . As it was expected, thePsAnn1a gene expression was primarily enhanced at theearly stages of symbiosis development and reached the highestlevels in the nodules. Similar pattern had been previouslyfound for MtAnn1 .Therefore, up-regulation of PsAnn4 expression may be relatedto the early stages of nodulation. The upregulation of thePsAnn4 transcription level was not as significant as it wasat the protein level, which implies that the regulation of thisannexin can be mainly achieved at the post-transcriptionaland translational level.To verify the influence of calcium inhibitors on the regulationof PsAnn4 gene, its expression level was estimated after plant treatment with the Ca2+ channel blocker LaCl3 .Two previously described as symbiosis-specific genes PsNINand PsEnod5 were also used in our experiments as a controlfor effective inoculation. In pea roots, the upregulation ofPsAnn4 expression in response to inoculation was revealedin 1 dai, corresponding with experiments on the dynamics ofthis gene expression upon nodulation. The significant decreasein the expression of PsAnn4 was found in our experiments inthe presence of LaCl3. Down-regulation of symbiosis-specificgenes PsEnod5 and PsNIN was also observed, which indicatedthe importance of Ca2+ influx for their regulation. Therefore,the influx of calcium ions into the cell, which is observed atthe early stages of symbiosis development, may affect theexpression level of PsAnn4 in pea roots .Subcellular localization of pea PsAnn4 annexinTo follow the PsAnn4 protein localization in plant cells, itwas fused to the fluorophores such as red fluorescent protein(RFP) and yellow fluorescent protein (YFP) at the C-terminusand expressed under the transcriptional regulation of the 35Spromoter in N. benthamiana leaves by infiltration with A. tumefaciens. The infiltration of constructs for thesynthesis of proteins fused with RFP and YFP allowed us tovisualize the protein in leaf tissues after transformation. In thecells of N. benthamiana leaves, PsAnn4 protein was localizedin the plasma membrane or in the cell wall. In addition, we alsoestimated the presence of PsAnn4 in different cell fractionsby Western-blot hybridization using anti-YFP or anti-RFPantibodies. PsAnn4-YFP was found in insoluble fraction ofleaf tissue pelleted at 36 000 g . It suggests thatPsAnn4 may be involved in cell wall or membrane modificationas well as in ion transport.DiscussionAvailable pea genome information allowedus to determine the composition of the annexin genefamily in this legume. Database searches revealed 15 annexingenes in P. sativum L., 18 in M. truncatula as well as 13 inboth P. vulgaris and L. japonicus. Based on the phylogeneticanalysis of these annexins, close homologs can be identifiedamong these legume species .At present, only one pea annexin, p35, has been functionallycharacterized . The localization of thisannexin in root cells involved in active secretion suggests itsfunction in exocytosis. Subsequently, the use of antibodiesagainst this protein revealed its localization in epidermalcells of the leaf and stem . However,annexins involved in nodulation have not been characterizedin P. sativum. In contrast, in M. truncatula, two annexins,MtAnn1 (Medtr8g038210) and MtAnn2 (Medtr8g038220),demonstrated a high level of expression during nodulationand were found to be involved in controlling bacterial infectionand nodule organogenesis .Another annexin, MtAnn3 (Medtr4g097180), was found to beimportant for root hair deformations in M. truncatula . At the same time, close homologs of MtAnn1 \u2013PvAnn1 (Phvul.011g209300) and LjAnn1 (Lj0g3v0203419),which belong to the same phylogenetic group as MtAnn1, playimportant roles in the symbiotic process in P. vulgaris andL. japonicus .In our earlier work, two annexins activated at the earlystages of symbiosis development in pea were found using theproteomics approach . This approachmight be helpful for the identification of new regulators ofsignal transduction pathways at the initial stages of nodulationin pea. Our present analysis revealed that these two identifiedannexins of pea belong to different phylogenetic groups,defined as homologs of MtAnn4, PvAnn4 and MtAnn8,PvAnn8, respectively. Although PsAnn4, and MtAnn4 andPvAnn4 have high levels of homology with MtAnn1 andPvAnn1, they belong to another group of annexins basedon phylogenetic analysis. PsAnn8 belongs to a less studiedphylogenetic group. Therefore, two previously unknown annexinswere identified in our study. In addition to stimulationduring rhizobial inoculation, the dependence of PsAnn4 andPsAnn8 activation on the LysM-receptor-like kinase SYM10,encoding a putative Nod factor receptor, was revealed in thepresent study , which suggested that rhizobialsignaling molecules Nod factors may be important for theiractivation. It also suggests the participation of these twoannexins in the development of the symbiotic interaction ofplants with rhizobia.Phylogenetic analysis and prediction of the overall 3Dstructure of PsAnn4 and PsAnn8 proteins showed differencesin the Ca2+-binding motif in the fourth annexin repeat of theseproteins, and therefore, in the potential ability to bind calciumions. This can potentially influence the binding of these annexinsto phospholipids by means of a calcium bridge mechanism.It was predicted that three calcium ions were coordinatedin the first and fourth repeats, which is consistent with the dataof the canonical binding of the G. hirsutum annexin GhAnn1and animal annexins to the phospholipids of membranesusingthe mechanism of calcium bridges . Inthe predicted structures of Arabidopsis annexins , the canonicity of the Ca2+-bindingmotif in the first repeat and the presence of modified motifsin the fourth repeats of AtAnn1 and AtAnn3 were also shown,while AtAnn4 had no recognizable Ca2+ \u2013 or phospholipidbindingmotifs .Since the level of PsAnn4 synthesis in response to inoculationwas more significant in the roots of wild type pea plantscompared with mutant defective in symbiosis, we carried outthe analysis of this annexin in more detail. It was shown thatthe regulation of PsAnn4 annexin in pea could be achievedat the transcriptional level as well as post-transcriptionaland translational levels, probably. Significant activation ofMtAnn1 and MtAnn2 gene expression level was found in theroots of M. truncatula treated with Nod factors or inoculated with rhizobia . Meanwhile, theexpression of PvAnn1 in P. vulgaris was slightly upregulatedin developing nodules . However,a phosphoproteomic approach revealed that PvAnn1 wasa phosphorylated protein with enhanced levels of synthesisduring nodulation . Hence, theregulation of annexins involved in nodulation might be differentand is probably connected with different functions thatannexins fulfil in this processLocalization of annexins might differ depending on theirfunction. Some annexins show cytoplasmic and nuclear localization,while other annexins are associated with variousplant membranes, including the plasma membrane, endoplasmicreticulum, and nuclear membrane . Some annexins maybe embedded in the membrane in the form of monomers oroligomers. One of the distinctive characteristics of annexinsis their ability to change their cellular localization in responseto various stimuli. In our experiments, the localization ofannexin 4 (PsAnn4) in the cell wall or plasma membranewas shown, suggesting the participation of this annexin inprocesses associated either with membrane modification orion transport at the early stages of symbiosis establishment inpea. Similarly, the localization of the other annexin, MtAnn2,involved in nodulation in M. truncatula, was revealed to beassociated with the plasma membrane, particularly with lipidrafts from root plasma membrane preparations . In addition, the annexin PvAnn1 is essential forROS-dependent regulation of Ca2+ influx into the cells ofP. vulgaris, which strongly suggests the localization of thisprotein in the plasma membrane. Therefore, specific subcellularlocalization of annexins might be associated with theirfunction signal transduction at the early stages of symbiosis.In this study, phylogenetic analysis of the pea annexinsPsAnn4 and PsAnn8 was performed based on their homologywith annexins from other legumes. The modeling approachallowed us to estimate the structural features of these annexinsthat might influence their functional activity. To verify thefunctions of these annexins, we performed comparative proteomicanalysis, experiments with calcium influx inhibitors,and localization of labeled proteins. Essential down-regulationof PsAnn4 synthesis in a non-nodulating pea mutant P56(sym10) suggests an involvement of this annexin in the rhizobialsymbiosis. The localization of PsAnn4 in the cell wall orplasma membrane of plant cells may indicate its participationin membrane modification or ion transport.The authors declare no conflict of interest.Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-JonesS., Khanna A., Marshall M., Moxon S., Sonnhammer E.L.L.,Studholme D.J., Yeats C., Eddy S.R. The Pfam protein families database.Nucleic Acids Res. 2004;32:D138-D141. DOI 10.1093/nar/gkh121.Bradford M.M. A rapid and sensitive method for the quantitation ofmicrogram quantities of protein utilizing the principle of proteindyebinding. Anal. Biochem. 1976;72(1-2):248-254. DOI 10.1016/0003-2697(76)90527-3.Breakspear A., Liu C., Roy S., Stacey N., Rogers C., Trick M., MorieriG., Mysore K.S., Wen J., Oldroyd G.E.D., Downie J.A., MurrayJ.D. The root hair \u201cInfectome\u201d of Medicago truncatula uncoverschanges in cell cycle genes and reveals a requirement for auxin signalingin rhizobial infection. Plant Cell Online. 2014;26(12):4680-4701. DOI 10.1105/tpc.114.133496Breton G., Vazquez-Tello A., Danyluk J., Sarhan F. Two novel intrinsicannexins accumulate in wheat membranes in response to low temperature.Plant Cell Physiol. 2000;41(2):177-184. DOI 10.1093/pcp/41.2.177.Carrasco-Castilla J., Ortega-Ortega Y., J\u00e1uregui-Z\u00fa\u00f1iga D., Ju\u00e1rez-VerdayesM.A., Arthikala M.K., Monroy-Morales E., Nava N., SantanaO., S\u00e1nchez-L\u00f3pez R., Quinto C. Down-regulation of a Phaseolusvulgaris annexin impairs rhizobial infection and nodulation.Environ. Exp. Bot. 2018;153:108-119. DOI 10.1016/j.envexpbot.2018.05.016.Carroll A.D., Moyen C., Van Kesteren P., Tooke F., Battey N.H.,BrownleeC. Ca2+, annexins, and GTP modulate exocytosis frommaize root cap protoplasts. Plant Cell. 1998;10(8):1267-1276. DOI10.1105/tpc.10.8.1267.Clark G.B., Dauwalder M., Roux S.J. Purification and immunolocalizationof an annexin-like protein in pea seedlings. Planta. 1992;187(1):1-9. DOI 10.1007/BF00201617.Clark G.B., Dauwalder M., Roux S.J. Immunological and biochemicalevidence for nuclear localization of annexin in peas. Plant Physiol.Biochem. 1998;36(9):621-627. DOI 10.1016/S0981-9428(98)80010-7.Clark G.B., Morgan R.O., Fernandez M.P., Roux S.J. Evolutionaryadaptationof plant annexins has diversified their molecular structures,interactions and functional roles. New Phytol. 2012;196(3):695-712. DOI 10.1111/j.1469-8137.2012.04308.x.Clark G.B., Rafati D.S., Bolton R.J., Dauwalder M., Roux S.J. Redistributionof annexin in gravistimulated pea plumules. Plant Physiol.Biochem. 2000;38(12):937-947. DOI 10.1016/S0981-9428(00)01206-7.Clark G.B., Sessions A., Eastburn D.J., Roux S.J. Differential expressionof members of the annexin multigene family in Arabidopsis.Plant Physiol. 2001;126(3):1072-1084. DOI 10.1104/pp.126.3.1072.Dam S., Dyrlund T.F., Ussatjuk A., Jochimsen B., Nielsen K., GoffardN., Ventosa M., Lorentzen A., Gupta V., Andersen S.U., EnghildJ.J., Ronson C.W., Roepstorff P., Stougaard J. Proteome referencemaps of the Lotus japonicus nodule and root. Proteomics.2014;14(2-3):230-240. DOI 10.1002/pmic.201300353.Davies J.M. Annexin-mediated calcium signalling in plants. Plants.2014;3(1):128-140. DOI 10.3390/plants3010128De Carvalho Niebel F., Lescure N., Cullimore J.V., Gamas P. The Medicagotruncatula MtAnn1 gene encoding an annexin is induced byNod factors and during the symbiotic interaction with Rhizobiummeliloti. Mol. Plant Microbe Interact. 1998;11(6):504-513. DOI10.1094/MPMI.1998.11.6.504.De Carvalho-Niebel F., Timmers A.C.J., Chabaud M., Defaux-Petras A.,Barker D.G. The Nod factor-elicited annexin MtAnn1 is preferentiallylocalised at the nuclear periphery in symbiotically activatedroot tissues of Medicago truncatula. Plant J. 2002;32(3):343-352.DOI 10.1046/j.1365-313X.2002.01429.x.Espinoza C., Liang Y., Stacey G. Chitin receptor CERK1 links saltstress and chitin-triggered innate immunity in Arabidopsis. Plant J.2017;89(5):984-995. DOI 10.1111/tpj.13437Feng Y.M., Wei X.K., Liao W.X., Huang L.H., Zhang H., Liang S.C.,Peng H. Molecular analysis of the annexin gene family in soybean.Biol. Plant. 2013;57(4):655-662. DOI 10.1007/s10535-013-0334-0.Gerke V., Moss S.E. Annexins: from structure to function. Physiol. Rev.2002;82(2):331-371. DOI 10.1152/physrev.00030.2001.Gong Z.Y., Song X., Chen G.Y., Zhu J.B., Yu G.Q., Zou H.S. Molecularstudies of the Medicago truncatula MtAnn3 gene involved in roothair deformation. Chinese Sci. Bull. 2012;57(15):1803-1809. DOI10.1007/s11434-011-4937-6.Gorecka K.M., Konopka-Postupolska D., Hennig J., Buchet R., PikulaS. Peroxidase activity of annexin 1 from Arabidopsis thaliana.Biochem. Biophys. Res. Commun. 2005;336(3):868-875. DOI10.1016/j.bbrc.2005.08.181Hofmann A., Proust J., Dorowski A., Schantz R., Huber R. Annexin 24from Capsicum annuum. X-ray structure and biochemical characterization.J. Biol. Chem. 2000;275(11):8072-8082. DOI 10.1074/jbc.275.11.8072.Hu N.J., Yusof A.M., Winter A., Osman A., Reeve A.K., Hofmann A.The crystal structure of calcium-bound annexin Gh1 from Gossypiumhirsutum and its implications for membrane binding mechanismsof plant annexins. J. Biol. Chem. 2008;283(26):18314-18322.DOI 10.1074/jbc.M801051200.Ijaz R., Ejaz J., Gao S., Liu T., Imtiaz M., Ye Z., Wang T. Overexpressionof annexin gene AnnSp2, enhances drought and salt tolerancethrough modulation of ABA synthesis and scavenging ROSin tomato. Sci. Rep. 2017;7(1):1-14. DOI 10.1038/s41598-017-11168-2.J\u00e1uregui-Z\u00fa\u00f1iga D., Ortega-Ortega Y., Pedraza-Escalona M., Reyes-Grajeda J.P., Ruiz M.I., Quinto C. Phosphoproteomic analysis inPhaseolus vulgaris roots treated with Rhizobium etli nodulation factors.Plant Mol. Biol. Report. 2016;34(5):961-969. DOI 10.1007/s11105-016-0978-y.Kirienko A.N., Porozov Y.B., Malkov N.V., Akhtemova G.A., Le SignorC., Thompson R., Saffray C., Dalmais M., Bendahmane A., TikhonovichI.A., Dolgikh E.A. Role of a receptor-like kinase K1 inpea Rhizobium symbiosis development. Planta. 2018;248(5):1101-1120. DOI 10.1007/s00425-018-2944-4.Kodavali P.K., Skowronek K., Koszela-Piotrowska I., Strzelecka-KiliszekA., Pawlowski K., Pikula S. Structural and functional characterizationof annexin 1 from Medicago truncatula. Plant Physiol.Biochem. 2013;73:56-62. DOI 10.1016/j.plaphy.2013.08.010.Konopka-Postupolska D., Clark G. Annexins as overlooked regulatorsof membrane trafficking in plant cells. Int. J. Mol. Sci. 2017;18(4):1-34. DOI 10.3390/ijms18040863.Konopka-Postupolska D., Clark G., Goch G., Debski J., Floras K.,Cantero A., Fijolek B., Roux S., Hennig J. The role of annexin 1in drought stress in Arabidopsis. Plant Physiol. 2009;150(3):1394-1410. DOI 10.1104/pp.109.135228.Konopka-Postupolska D., Clark G., Hofmann A. Structure, functionand membrane interactions of plant annexins: An update. Plant Sci.2011;181(3):230-241. DOI 10.1016/j.plantsci.2011.05.013.Kreplak J., Madoui M.-A., C\u00e1pal P., Nov\u00e1k P., Labadie K., Aubert G.,Bayer P.E., Gali K.K., Syme R.A., Main D., Klein A., B\u00e9rard A.,Vrbov\u00e1I., Fournier C., D\u2019Agata L., Belser C., Berrabah W., Toegelov\u00e1H., Milec Z., Vr\u00e1na J., Lee H., Kougbeadjo A., T\u00e9r\u00e9zol M.,Huneau C., Turo C.J., Mohellibi N., Neumann P., Falque M., GallardoK., McGee R., Tar\u2019an B., Bendahmane A., Aury J.-M., Batley J.,Le Paslier M.-C., Ellis N., Warkentin T.D., Coyne C.J., Salse J., EdwardsD., Lichtenzveig J., Macas J., Dole\u017eel J., Wincker P., BurstinJ. A reference genome for pea provides insight into legume genomeevolution. Nat. Genet. 2019;51(9):1411-1422. DOI 10.1038/s41588-019-0480-1.Kwon Y.S., Lee D.Y., Rakwal R., Baek S.B., Lee J.H., Kwak Y.S.,Seo J.S., Chung W.S., Bae D.W., Kim S.G. Proteomic analyses ofthe interaction between the plant-growth promoting rhizobacteriumPaenibacillus polymyxa E681 and Arabidopsis thaliana. Proteomics.2016;16(1):122-135. DOI 10.1002/pmic.201500196.Laohavisit A., Davies J.M. Annexins. New Phytol. 2011;189(1):40-53.DOI 10.1111/j.1469-8137.2010.03533.x.Laohavisit A., Mortimer J.C., Demidchik V., Coxon K.M., StancombeM.A., Macpherson N., Brownlee C., Hofmann A., Webb A.A.R.,Miedema H., Battey N.H., Davies J.M. Zea mays annexins modulatecytosolic free Ca2+ and generate a Ca2+-permeable conductance.Plant Cell. 2009;21(2):479-493. DOI 10.1105/tpc.108.059550.Lefebvre B., Furt F., Hartmann M.-A., Michaelson L.V., Carde J.-P.,Sargueil-Boiron F., Rossignol M., Napier J.A., Cullimore J., BessouleJ.-J., Mongrand S. Characterization of lipid rafts from Medicago truncatula root plasma membranes: A proteomic study revealsthe presence of a raft-associated redox system. Plant Physiol. 2007;144(1):402-418. DOI 10.18362/bjta.v4.i1-2.59. Leppyanen I.V., Kirienko A.N., Lobov A.A., Dolgikh E.A. Differentialproteome analysis of pea roots at the early stages of symbiosiswith nodule bacteria. Vavilovskii Zhurnal Genetiki i Selektsii =Vavilov Journal of Genetics and Breeding. 2018;22(2):196-204.DOI 10.18699/VJ18.34.7.Limpens E., Moling S., Hooiveld G., Pereira P.A., Bisseling T., BeckerJ.D., K\u00fcster H. Cell- and tissue-specific transcriptome analysesof Medicago truncatula root nodules. PLoS One. 2013;8(5):e64377.DOI 10.1371/journal.pone.0064377.Lizarbe M.A., Barrasa J.I., Olmo N., Gavilanes F., Turnay J. Annexinphospholipidinteractions. Functional implications. Int. J. Mol. Sci.2013;14:2652-2683. DOI 10.3390/ijms14022652.Madsen E.B., Madsen L.H., Radutoiu S., Olbryt M., Rakwalska M.,Szczyglowski K., Sato S., Kaneko T., Tabata S., Sandal N., StougaardJ. A receptor kinase gene of the LysM type is involved in legumeperception of rhizobial signals. Nature. 2003;425(6958):637-640. DOI 10.1038/nature02045Manthey K., Krajinski F., Hohnjec N., Firnhaber C., P\u00fcnler A., PerlickA.M., K\u00fcster H. Transcriptome profiling in root nodules andarbuscular mycorrhiza identifies a collection of novel genes inducedduring Medicago truncatula root endosymbioses. Mol. Plant-Microbe Interact. 2004;17(10):1063-1077. DOI 10.1094/MPMI.2004.17.10.1063.Mortimer J.C., Laohavisit A., Macpherson N., Webb A., Brownlee C.,Battey N.H., Davies J.M. Annexins: multifunctional componentsof growth and adaptation. J. Exp. Bot. 2008;59(3):533-544. DOI10.1093/jxb/erm344.Ordog R. PyDeT, a PyMOL plug-in for visualizing geometric conceptsaround proteins. Bioinformation. 2008;2(8):346-347. DOI 10.6026/97320630002346.Orosz L., Sv\u00e1b Z., Kondorosi A., Sik T. Genetic studies on rhizobiophage16-3. I. Genes and functions on the chromosome. Mol. Gen.Genet. 1973;125(4):341-350. DOI 10.1007/BF00276589.Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., LopezR., McWilliam H., Remmert M., S\u00f6ding J., Thompson J.D., HigginsD.G. Fast, scalable generation of high-quality protein multiplesequence alignments using Clustal Omega. Mol. Syst. Biol. 2011;7(1):539. DOI 10.1038/msb.2011.75.Talukdar T., Gorecka K.M., de Carvalho-Niebel F., Downie J.A., CullimoreJ., Pikula S. Annexins \u2013 calcium- and membrane-binding proteinsin the plant kingdom: potential role in nodulation and mycorrhizationin Medicago truncatula. Acta Biochim. Pol. 2009;56(2):199-210. DOI 20091709.Van Brussel A.A.N., Planque K., Quispel A. The wall of Rhizobium leguminosarumin bacteroid and free-living forms. J. Gen. Microbiol.1977;101(1):51-56. DOI 10.1099/00221287-101-1-51.Van Brussel A.A.N., Tak T., Wetselaar A., Pees E., Wijffelman C. Smallleguminosae as test plants for nodulation of Rhizobium leguminosarumand other rhizobia and agrobacteria harbouring a leguminosarumsym plasmid. Plant Sci. Lett. 1982;27(3):317-325. DOI10.1016/0304-4211(82)90134-1.Voss T., Haberl P. Observations on the reproducibility and matchingefficiency of two-dimensional electrophoresis gels: consequencesfor comprehensive data analysis. Electrophoresis. 2000;21(16):3345-3350. DOI 10.1002/1522-2683(20001001)21:16<3345::AIDELPS3345>3.0.CO;2-Z.Webb B., Sali A. Comparative protein structure modeling using Modeller.Curr. Protoc. Bioinform. 2016;54(1):5.6.1-5.6.37. DOI 10.1002/cpbi.3.Wienkoop S., Saalbach G. Proteome analysis. Novel proteins identifiedat the peribacteroid membrane from Lotus japonicus root nodules.Plant Physiol. 2003;131(3):1080-1090. DOI 10.1104/pp.102.015362."} +{"text": "Background: Coronavirus disease (COVID-19) has spread rapidly since 2019. Approximately 15% of the patients will develop severe complications such as multiple organ disease syndrome related to cytokine release syndrome (CRS). Continuous renal replacement therapy (CRRT) can remove inflammatory cytokines through filtration or adsorption. We evaluated the effectiveness of CRRT in COVID-19 patients with CRS.Methods: This retrospective, multicenter, descriptive study included 83 patients with CRS from three hospitals in Wuhan.Results: In COVID-19 patients with CRS, the fatality rate was even higher in CRRT group (P=0.005). However, inflammatory markers such as C-reactive protein, neutrophil counts, and D-dimer decreased after CRRT (P<0.05). Results of Lasso model showed that tracheotomy (\u03b2 -1.31) and convalescent plasma (\u03b2 -1.41) were the protective factors. In contrast, CRRT (\u03b2 1.07), respiratory failure (\u03b2 1.61), consolidation on lung CT (\u03b2 0.48), acute kidney injury (AKI) (\u03b2 0.47), and elevated neutrophil count (\u03b2 0.02) were the risk factors for death.Conclusions: Our results showed that although CRRT significantly reduced the inflammation, it did not decrease the fatality rate of patients with CRS. Therefore, the choice of CRRT indication, dialysis time and dialysis mode should be more careful and accurate in COVID-19 patients with CRS. An outbreak of coronavirus disease COVID-19) in December 2019 in Wuhan, China, has developed into a global pandemic. COVID-19 is caused by infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus 9 in Dece. AlthougCytokine release syndrome (CRS) plays a vital role in the occurrence and disease progression of the COVID-19 . It has Although there are no standard diagnostic criteria for CRS, some treatments based on managing CRS have been widely applied clinically. These include antagonism at the IL-6 receptor (using the antagonist Tocilizumab), artificial-liver blood-purification therapy that can remove cytokines from the circulation, and continuous renal replacement therapy (CRRT) can remove inflammatory factors such as cytokines from the circulation via filtration and adsorption . TocilizOf the 83 cases included in our study, 67 were classified as critical, and 16 as non-critical. Of the 67 critical patients, 38 cases were treated with CRRT during hospitalization. A total of 45 patients died, and 36 were cured or improved. The outcome of two patients is unknown.The mean age of the patients was 67.3\u00b112.6 years. Almost three-quarters (73.5%) of the patients were male; 67 were critical cases, and 13.3% of the patients had a history of smoking. The underlying medical conditions of the patients included hypertension (55.4%), diabetes (24.1%), tumors (6%), and chronic obstructive pulmonary disease (1.2%). Pulmonary CT revealed that 51.7% of the critical patients had consolidation, and 73.3 % of non-critical patients had ground-glass changes in the lungs. The mean peak creatinine value during hospitalization was 133.2 pg/mL . AKI was present in 60.2%, MODS in 36.1%, and ARDS in 42.2% of the patients. Compared to the non-critical groups, the critical group had more patients with an IL-6 value >4000 pg/mL (29.9% vs.18.8%) .Patients in the critical group had a significantly higher WBC count (P=0.001), neutrophil count (P<0.001), neutrophil percentage (P<0.001), LDH (P<0.001), peak creatinine (P=0.01), high-sensitivity troponin I (P<0.001), CRP (P<0.001), ferritin (P=0.001) and procalcitonin (PCT) (P=0.043) than those in the non-critical group. Patients in the critical group had significantly lower lymphocyte counts (P=0.018) and albumin levels (P=0.015) than patients in the non-critical group .Treatments such as CRRT (P=0.001), antibiotics (P=0.002), hormones (P=0.004), globulin therapy (P<0.001), invasive mechanical ventilation (P<0.001) and non-invasive ventilation (P<0.001), were each more commonly used in critical patients than in non-critical patients. Moreover, critical patients had a higher incidence of AKI (P<0.001), respiratory failure (P<0.001), ARDS (P<0.001), MODS (P<0.001), gastrointestinal bleeding (P=0.004), acute liver dysfunction (P<0.001) and acute myocardial injury (P<0.001) .Over half of the critical patients (38/67) were treated with CRRT. Those who received CRRT had a lower blood platelets (PLT) (P=0.023), and lower albumin (P=0.041), a higher peak creatinine (P=0.018), and a greater incidence of MODS (P<0.001) than those who did not receive CRRT. More patients receiving CRRT also underwent tracheal cannulation (P=0.003) or invasive mechanical ventilation (P=0.002). Most patients who received CRRT (64.7%) had pulmonary consolidations on CT . Unexpec9g/L vs. 0.64 109g/L] followed the same pattern, demonstrating lower values in the CRRT patients. The CRP was higher in the CRRT than in the non-CRRT group [97.7 mg/L vs. 89.16 mg/L)]. Moreover, the incidence of AKI and ARDS in critical patients treated with CRRT was 81.1% and 71.4%, respectively, which was higher than the corresponding figures of non-CRRT . The blood oxygen saturation in patients who received CRRT was lower than in the non-CRRT group [90 % vs.93 %] and the lymphocyte count , and differences between the groups were determined using a two-sample t-test or Wilcoxon rank-sum test. Lasso and accurate logistic analysis were conducted to identify the factors related to death. The explanatory variables included treatments , respiratory failure, consolidation on lung CT, AKI, elevated neutrophil percentage, cough, dyspnea, hormone treatment, invasive mechanical ventilation, acute myocardial injury, White blood cell (WBC) count (x 10The data underlying this article are available in the article and its online supplementary material."} +{"text": "Trichoderma are well-studied filamentous fungi generally observed in nature, which are widely marketed as biocontrol agents. The secondary metabolites produced by Trichoderma have gained extensive attention since they possess attractive chemical structures with remarkable biological activities. A large number of metabolites have been isolated from Trichoderma species in recent years. A previous review by Reino et al. summarized 186 compounds isolated from Trichoderma as well as their biological activities up to 2008. To update the relevant list of reviews of secondary metabolites produced from Trichoderma sp., we provide a comprehensive overview in regard to the newly described metabolites of Trichoderma from the beginning of 2009 to the end of 2020, with emphasis on their chemistry and various bioactivities. A total of 203 compounds with considerable bioactivities are included in this review, which is worth expecting for the discovery of new drug leads and agrochemicals in the foreseeable future. Moreover, new strategies for discovering secondary metabolites of Trichoderma in recent years are also discussed herein.Fungi play an irreplaceable role in drug discovery in the course of human history, as they possess unique abilities to synthesize diverse specialized metabolites with significant medicinal potential. Trichoderma is a fungal genus that was first described in 1794 , and six known trichothecenes, trichodermol (9), trichodermin (10), trichoderminol (11), trichodermarin A (12) and trichodermarin B (13), and 2,4,12-trihydroxyapotrichothecene (14), were isolated from Trichoderma brevicompactum ADL-9-2, which was obtained as an endophyte of marine algae Chondria tenuissima (8), featuring a 2\u2019-N-acetylglucosaminyl moiety, represented the first aminoglycoside-bearing trichothecene. Chemical investigations of the marine fungus Trichoderma cf. brevicompactum TPU199 fermented with NaI afforded three new trichothecenes, trichobreols A\u2013C (15\u201317) , whereas compounds 16 and 17 were found only under NaI-containing culture conditions. Additionally, isolation of the same fungus yielded two new trichothecenes, trichobreols D (18) and E (19) (20) and B (21), two trichothecenes linked with octa-2,4,6-trienedioyl moiety, were isolated from the biofertilizer fungus T. brevicompactum (CGMCC19618) , 8-deoxy-trichothecin (23), and trichothecinol B (24) were yielded . Interesd E (19) . HarzianCC19618) . From a yielded .T. virens Y13-3, eight undescribed carotane sesquiterpenes, trichocarotins A\u2013H (25\u201332), along with the known compounds CAF-603 (33), trichocarane B (34), 7-\u03b2-hydroxy CAF-603 (35), and trichocarane A (36), were discovered (From the marine-derived fungus scovered (Shi et scovered . Carotanscovered .37), containing a previously unrecognized site of an exocyclic olefin functionality at C-10, was obtained from the marine-derived fungus T. virens Y13-3 , and three known ones, i.e., aspergilloid G (41), rhinomilisin E (42), and rhinomilisin G (43), were characterized from the marine sponge-derived fungus Trichoderma sp. SM16 , was produced by the marine fungus T. harzianum (XS-20090075), which was isolated from soft corals -isocyclonerotriol (45) and (10Z)-isocyclonerotriol (46), which were characterized as the first example with an isomerized ring in cycloneranes (47), methyl 3,7-dihydroxy-15-cycloneranate (50), and 10-cycloneren-3,5,7-triol (51), as well as two structurally related cycloneranes, 9-cycloneren-3,7,11-triol (48) and (\u2013)-cyclonerodiol (49), were obtained from T. harzianum X-5, an endophyte of the marine alga Laminaria japonica and 10(E)-cyclonerotriol (52), were obtained from T. longibrachiatum, an endophyte of the highly halophile Suaeda glauca , II (54), and III (55) (56), 3-oxoneomacrophorins I (57) and II (58), neomacrophorin VII (59), 5\u2032-epimacrophorin B (60), and 5\u2032-deoxyneomacrophorin IV (61), as well as four novel premacrophorin congeners, i.e., premacrophorin III (62), premacrophorindiol (63), premacrophorintriols I (64), and II (65), were isolated from the same fungus (56 and 57) or 2,3-epoxybenzosemiquinol substructures (58\u201360 and 62\u201364). Premacrophorins 62\u201365 carried acyclic isoprenoid side chains biosynthetically derived from neomacrophorins in the early stage, rather than the common drimane skeleton.Chemical exploration of an endophyte III (55) (Hirose III (55) . They bee fungus . These mTrichoderma sp. 307 and aquatic pathogenic bacterium Acinetobacter johnsonii B2 afforded two undescribed furan-type isoeremophilane sesquiterpenes, microsphaeropsisins B (66) and C (67) , trichoacorenol (69), and trichoacorenol B (70) were isolated from marine-derived T. harzianum X-5, and they were structurally characterized as acorane sesquiterpenes (71), an unusual norsesquiterpene with a novel tricyclic-6/5/5--decane framework, was characterized to originate from T. longibrachiatum (72) and B (73), were produced by T. atroviride S361, an endophyte of Cephalotaxus fortunei and B (75), were obtained from T. brevicompactum ADL-9-2, which was isolated from marine algae C. tenuissima , were isolated from T. asperellum residing in Panax notoginseng and B (81) . It is bterpenes . Trichodachiatum . Two newfortunei . Compounnuissima . Compounoginseng . The newe C (79) . Chemicad B (81) . InteresTrichoderma species (82\u201386), and three previously reported diterpenes, i.e., 3S-hydroxyharzianone (87), harziandione (88), and harzianol A (89), were isolated from the endophyte T. atroviride B7 of Colquhounia coccinea var. mollis (90), an undescribed harziane lactone, was isolated from an endophyte T. longibrachiatum A-WH-20-2 of marine algae Laurencia okamurai (91), was obtained from the soft coral-sourced T. harzianum (XS-20090075) by chemical epigenetic manipulation strategy , was produced by T. harzianum X-5 -dihydro-harzianone (93) and harzianelactone (94), were produced by Trichoderma sp. Xy24 from mangrove plant Xylocarpus granatum , as well as five new lactones, i.e., harzianones A\u2013D (97\u2013100) and harziane (101) (102), was isolated from Trichoderma erinaceum derived from Acanthaster planci . Finallyr planci .103), a rare norditerpene, was produced by an endophyte T. citrinoviride cf-27 , was characterized from the marine algicolous fungus T. harzianum X-5 , characterized as a novel chlorinated cleistanthane diterpenoid, was isolated from the marine fungal strain T. harzianum (XS-20090075) (Trichoderma for the first time.Citrinovirin (de cf-27 . Compounanum X-5 . 104 and0090075) . TricyclT. harzianum KZ-20 afforded four new cyclodepsipeptides belonging to the destruxin family, i.e., trichodestruxins A\u2013D (106\u2013109), and two previously reported derivative, i.e., destruxin E2 chlorohydrin (110) and destruxin A2 (111) , trichomide B (113), and homodestruxin B (114), characterized as cyclohexadepsipeptides of the trichomide series, were produced by T. longibrachiatum (115) and halobacillin (116) were obtained from the endophyte T. asperellum (Bioassay-guided fractionation of the plant endophytic fungus A2 (111) (Liu Z. A2 (111) . Destruxachiatum . Finallyperellum .Trichoderma sp. TPU199 is a producer of a series of diketopiperazines (117\u2013127) (117), gliovirin (118), and trichodermamide A (119). 117 and 118 possessed an unusual epipolythiodiketopiperazine (ETP) skeleton. Then, this strain with sodium halides added to the culture medium afforded the halogenated gliovirin-type ETPs DC1149B (120), DC1149R (122), and iododithiobrevamide (123). Subsequently, chlorotrithiobrevamide (124), the first trisulfide derivative in the type of ETP, was characterized. Furthermore, a highly modified dipeptide, dithioaspergillazine A (125), was obtained after the long time cultivation. Finally, two undescribed ETPs, i.e., 5-epi-pretrichodermamide A (126) and 5-epi-trithiopretrichodermamide A (127), were characterized under NaI-containing culture conditions. Pretrichodermamide G (128) was established as a 1,2-oxazadecaline ETP, and it was identified from the endophyte T. harzianum of Zingiber officinale (129), and a biogenetically related metabolite aspergillazin A (130) were produced by the marine-sourced T. harzianum D13 (129 and 130 were novel ETP derivatives with the sulfur bridge locating at different positions. Dehydroxymethylbis(dethio)bis(methylthio)gliotoxin (131) and -6-(para-hydroxybenzyl)-1,4-dimethyl-3,6-bis(methylthio)piperazine-2,5-dione (132), which were structurally characterized as two undescribed sulfurated diketopiperazines, were produced by an algicolous isolate of T. virens Y13-3 (133) (The marine fungus 117\u2013127) (Yamazak117\u2013127) . Initialficinale . A rare anum D13 . Notablyns Y13-3 . The funo) (133) .T. virens FKI-7573 generated an undescribed N-containing compound, i.e., trichothioneic acid (134) (134 contained a heptelidic acid and an L-ergothioneine substructure. Ethyl 2-bromo-4-chloroquinoline-3-carboxylate (135) was produced by the soft coral-sourced T. harzianum (XS-20090075) in Czapek\u2019s medium and B (137), isolated as stereoisomers originating from the PKS-NRPS mixed pathway, were isolated from T. gamsii, an endophyte of P. notoginseng (138) and B (139), were identified from Trichoderma sp. strain MF106 from the Greenland Seas (140), a nitrogen heterocyclic siderophore, was isolated from T. harzianum M10 -1-methyl-3,5-dioxopyrrolidin-2-ylmethyl]-3-methyl-butyric acid. Atrichodermone A (141) was a unique compound with a dimeric cyclopentenone framework that was discovered from the endophytic fungal strain T. atroviride and 5\u2032-acetoxy-deoxycyclonerin D (143), were obtained from the marine fungus T. asperellum A-YMD-9-2 (Miyano id (134) . 134 cons medium . 135 wasoginseng . Two rarand Seas . Harziananum M10 . 140 wasroviride . 141 was-YMD-9-2 .144), a natural product, methyl-trichoharzin (145), and the known trichoharzin (146) and eujavanicol A (147) were produced by the marine fungus T. harzianum XS-20090075 was identified from a fungal strain of T. harzianum F031 and B (150) were isolated from an endophytic fungus T. spirale, and characterized as new octahydronaphthalene derivatives , 1,6-di-epi-koninginin A (152), 15-hydroxykoninginin A (153), 10-deacetylkoningiopisin D (154), and koninginin T (155), along with two previously reported derivatives, koninginin L (156) and trichoketide A (157), were produced by Trichoderma koningiopsis QA-3 (151\u2013153 were characterized as tricyclic polyketides with an octahydrochromene skeleton. Koninginins I (158), J (159) and K (160), which were structurally characterized as new koninginin-type compounds, were produced by T. neokongii 8722 and trichodermaketones A\u2013D (162\u2013165) (162 and 163 represented unprecedented tricyclic polyketides having a bistetrafuran skeleton. Trichoketides A (166) and B (167), two undescribed octaketides, were isolated from Trichoderma sp. TPU1237 (herein reported as a new compound) and M (168) were isolated from solid fermentation of T. koningii 8662 and M (168) was an oxygen bridge located between the C-10 and C-7 positions.Five new polyketides, sis QA-3 . Compoungii 8722 . Chemica162\u2013165) . 162 and TPU1237 . 166 andgii 8662 . A serie169) and trichoderone B (170), together with three previously reported cytochalasans, aspochalasins D (171), J (172), and I (173), were obtained from T. gamsii from P. notoginseng and D (175), as well as three known cytochalasans, aspochalasins D (171), M (176), and P (177), were obtained from the abovementioned strain T. gamsii , was isolated from endophytic T. atroviride (179), was produced by the marine-sourced Trichoderma sp. HPQJ-34 and B (181), were found from the marine fungus T. harzianum (XS-20090075) (180 and 181 had a C9 polyketide framework with a \u03b3-lactone moiety. Trichoderpyrone (182), a novel cyclopentenone-pyrone mixed polyketide, was produced by T. gamsii , a new cyclopentenone, was obtained from the marine Trichoderma sp. , which was identified as a new isocoumarin derivative with a 6,8-dihydroxyisocoumarin moiety, was isolated from T. citrinoviride A-WH-20-3 (187) and 4,6-dihydroxy-5-methylphthalide (188), were produced by the fungus T. harzianum F031 (189 and 190) with a 1-hydroxyhepta/methoxyhepta-3,5-dien-2-one moiety were produced in the transformant of Trichoderma afroharzianum (191) and E (192), were obtained from dragonfly associated T. harzianum QTYC77 (193), elucidated as but-2-enoic acid 7-acetoxy-6-hydroxy-2- methyl-10-oxo-5,6,7,8,9,10-hexahydro-2H-oxecin-5-yl ester, was isolated from cultural filtrates of Trichoderma cremeum -7-hydroxy-de-O-methyllasiodiplodin (194) and (3R)-5-oxo-de-O-methyllasiodiplodin (195), were isolated from the cocultivation of Trichoderma sp. 307 and A. johnsonii B2 (196), and the known nafuredin A (197), were produced by marine fungus T. harzianum D13 . Compoun. gamsii . 182 haderma sp. . Compoun Fes1712 . Trichop-WH-20-3 . Previounum F031 . Two strarzianum . Two undm QTYC77 . A new 1 cremeum . Two undsonii B2 . An undeanum D13 .198) and B (199), were produced by a culture broth of T. polypori FKI-7382 and II (201). Notably, both of them were characterized from Trichoderma for the first time (202) and B (203), two new compounds with 4-(2-hydroxyethyl) phenol moieties, were isolated from an endophyte T. gamsii associated with secondary metabolites are cryptic or expressed at very low levels under general laboratory conditions . TherefoTrichoderma sp. TPU199 was found to produce a series of diketopiperazines under different conditions , 122 (Br derivative of 117), and 123 (I derivative of 177) when added with NaCl, NaBr, and NaI in culture medium, respectively. Moreover, TPU199 supplemented with DMSO yielded 124, a new trithio derivative of 120. A continuous study indicated that, with the long time cultivation, an undescribed modified dipeptide 125 was obtained. Finally, two undescribed ETPs 126 and 127 were characterized under NaI-containing culture conditions. It is undoubtedly proven that changing the culture conditions can activate cryptic metabolic pathways.The marine-derived fungus nditions (Yamazaknditions . ChemicaTrichoderma sp. 307 and pathogenic bacterium A. johnsonii B2 yielded two undescribed sesquiterpenes (66 and 67) and de-O-methyllasiodiplodin (194 and 195) . This is the first report of cleistanthane diterpenoids isolated from Trichoderma species. This study provided solid example to show that it is efficient to activate the silent genes of Trichoderma species by chemical epigenetic manipulation.Microorganism coculture based on microbial interspecies competition is an efficient path to stimulate cryptic BGCs. Cocultivation of and 195) . HPLC anabolites . A histoT. afroharzianum, a laeA-like gene overexpression transformant was built (189 and 190). This study indicated that transcriptional control could be a considerable strategy in activating more secondary metabolites and enhancing the silent potential metabolism of Trichoderma species.The transcriptional control has also proven to be an effective approach. To activate the chemical potential of the endophytic fungus as built . Further1\u2013203 are listed in The producing fungus, environmental source, and bioactivities of compounds 1\u201314 were assayed for antifungal activity against Botrytis cinerea, Cochliobolus miyabeanus, Fusarium oxysporum f. sp. cucumerium, F. oxysporum f. sp. niveum, and Phomopsis asparagi among these trichothecenes indicated that the acetoxy and methyl functionalities (compound 10) were necessary, while the epoxide moiety and the ether linkage were other possibilities exhibited potent effect on Staphylococcus aureus, Bacillus subtilis, and Micrococcus luteus, with EC50s of 7.7, 7.7, and 9.9 \u03bcg/mL, respectively was active against B. subtilis , Staphylococcus epidermidis (24.28 \u03bcM), and C. albicans (25.38 \u03bcM) (148) displayed mild activity against Colletotrichum gloeosporioides, with an MIC value of 128 \u03bcg/mL was inactive against C. albicans (MIC > 125 \u03bcg/mL). However, it was active at 125 \u03bcg/mL when treated with 0.05 \u03bcg/mL ketoconazole . Further10 \u03bcg/mL . The nov 8 \u03bcg/mL . The newectively . It seem.4 \u03bcg/mL . Cyclopeectively . The new5.38 \u03bcM) . Trichoh28 \u03bcg/mL . Polyket64 \u03bcg/mL . Trichodconazole . New iso32 \u03bcg/mL . Polyket32 \u03bcg/mL . The newd 7.0 mm . The newa solani . Nafuredectively .Amphidinium carterae, Heterocapsa circularisquama, Heterosigma akashiwo, and Prorocentrum donghaiense) of trichothecene derivatives 1\u201314 was evaluated. Notably, 10 featured the strongest effect, with IC50s of 1.7, 0.82, 0.91, and 1.4 \u03bcg/mL - and (10Z)-cyclonerotriol, the isomerization of the five-membered ring greatly suppressed their antimicroalgal activities , while the new proharziane diterpene 104 potently inhibited with IC50s of 1.2\u20134.3 \u03bcg/mL , H. akashiwo (9.1 \u03bcg/mL), and P. donghaiense (5.9 \u03bcg/mL) .38\u201343 were evaluated against NCIH-460, NCI-H929, and SW620 cell lines showed cytotoxicity against human adenocarcinoma cells (COLO 201) with an IC50 of 46 \u03bcg/mL was observed to exhibit moderate cytotoxicity against NCI-H1975 , HepG2 (60.88 \u03bcM), and MCF-7 (53.92 \u03bcM) cell lines , HepG2 (30.8 \u03bcM), and HeLa (33.9 \u03bcM) , c. The 33.9 \u03bcM) . Cyclopeell line . The sel20) and B (21) decreased the shoot and root lengths of the dicot species Brassica chinensis and induced inhibitory effect of seed germination at 2 \u03bcg/mL . The results indicated that 20 and 21 possess potent herbicidal potential for dicotyledon and/or monocotyledon weeds. All of the isolated harzianes 95\u2013101 exhibited potent phytotoxicity at 200 ppm lethal rates of 38.2 and 42.7% at 200 \u03bcg/mL showed OH radical-scavenging and singlet oxygen-quenching ability in a dose-dependent manner, which was equivalent to those of positive controls (140) as a plant growth promoter was evaluated .Trichoderma from 2009\u20132020. Their chemical structures were classified into terpenoids , cyclopeptides (104\u2013116), diketopiperazines (117\u2013133), alkaloids and other nitrogen-containing compounds (134\u2013143), polyketides , and other compounds (198\u2013203) according to their putative biogenetic sources. As shown in Trichoderma are considerable producing strains of novel terpenoids. It should be pointed out that some terpenoids, such as harzianes, are isolated exclusively from Trichoderma species. This review described 21 harziane diterpenes produced by Trichoderma. Considering their intriguing structures and bioactivities, much more attention should be devoted to this type of terpenoid in subsequent chemical studies.A total of 203 natural products were reported from Trichoderma comprises more than 340 species. Some of them are used as biocontrol agents, while some of them are promising producers of enzymes for industrial purposes. On the other hand, some Trichoderma species possess the unique capacity to synthesize various secondary metabolites with potent biological activities. In this review, a total of 17 identified species, including T. harzianum, T. brevicompactum, T. virens, T. gamsii, T. atroviride, T. longibrachiatum, T. asperellum, T. koningiopsis, T. koningii, T. citrinoviride, T. neokongii, T. spirale, T. afroharzianum, T. polypore, T. polyalthiae, T. erinaceum, and T. cremeum, are reported as the producing strains of the described metabolites. Among them, T. harzianum and T. brevicompactum were the most prolific strains, with 48 (23.76%) and 33 (16.34%) metabolites identified, respectively have been characterized from T. brevicompactum.The genus ectively . The funTrichoderma is widely distributed and has been isolated in soils, decaying wood, and endophytes in the inner tissue of host plants. Previous studies have mainly focused on terrestrial species of Trichoderma. However, Trichoderma from the marine environment are unexploited. It would be useful to examine marine-derived Trichoderma species since they may be induced to produce specific metabolites in hyperhaline environments. Accordingly, in recent years, increasing attention has been devoted to marine Trichoderma. As shown in Trichoderma. From the above analysis, it can be concluded that marine environment and endophytes are more abundant sources of those productive strains.The genus 22 and 23 showed higher antifungal effect on C. lagrnarium than the synthetic fungicide carbendazim , anticancer (20.61%), and antimicroalgal (17.98%) activities were dominant in assessing the pharmacological potential of these metabolites . It shou2 \u03bcg/mL) . Cyclopeell line . The sel effects . These iTrichoderma from the beginning of 2009 to the end of 2020. As a result, a total of 203 metabolites are described herein, including their structural diversity and biological activities. Moreover, new strategies for discovering secondary metabolites of Trichoderma in recent years have also been discussed. Trichoderma has proven to be a treasure house of interesting secondary metabolites with medicinal importance. The biochemical studies of Trichoderma are untapped. Although a mass of metabolites have been isolated from Trichoderma species, the further excavation of those metabolites is worth expecting. By using new approaches to activate their silent gene clusters, including cultivation-based approaches, metabolomic profiling, and genome mining-based molecular approaches, an ever-increasing number of bioactive compounds will be obtained, which will be beneficial for the new drug discovery in the near future.In the present review, we offer a detailed summary of recently isolated metabolites from J-LZ and W-LT wrote this manuscript. Q-RH, Y-ZL, M-LW, L-LJ, CL, XY, H-WZ, and G-ZC collected and reorganized the literature data. X-XZ supervised the research work and revised the manuscript. All authors reviewed the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Uropathogen resistance, Fluoroquinolone-resistance (FQR) and Extended spectrum beta-lactamase (ESBL), has been observed to be emerging worldwide with prevalences above recommended thresholds for routine empirical treatment. We sought to determine recent resistance prevalence from a geographically diverse sample of US Emergency Departments (ED).Escherichia coli. We conducted a multi-center, observational cohort study utilizing a network of 15 geographically diverse US EDs. Patients \u2265 18 years of age with the primary international classification of diseases (ICD-10) diagnosis code of cystitis, pyelonephritis, or urinary tract infection (UTI) and were discharged home from the ED from 2018-2020 were included. We calculated descriptive statistics for uropathogens and susceptibilities. Logistic regression analysis was used to identify antimicrobial resistance risk factors associated with fluoroquinolone (FQ)-resistant E. coli was the most common pathogen (62.9%), followed by Klebsiella pneumoniae (13%) and Enterococcus species (5.8%). Across all sites, overall E. coli FQ-resistance prevalence was 22.1%, ranging from 10.5 to 29.7% by site. The prevalence of ESBL-producing uropathogen was 4.4%, ranging from 2.3% to 8.6% by site. Previous IV or oral antimicrobial use in the last 90-days and complicated vs. uncomplicated UTI were associated with FQ-resistant E. coli . Of the most prescribed oral antibiotics upon patients discharged from the ED, E. coli resistance to nitrofurantoin and cephalexin was 1.8% and 0.9%, respectively.Among 3,779 patients who met inclusion criteria, median age was 62.9 years (IQR: 41-77.6) and 76.3% were female. The most common diagnoses were complicated (40.9%) and uncomplicated cystitis (39.4%). Six hundred and forty-five (17%) patients reported receiving antimicrobials in the previous 90-days. E. coli is widely prevalent and ESBL-mediated resistance appears to be emerging across US sites highlighting the need for ongoing monitoring of antimicrobial resistance and, at some locations, modification of empirical treatments. FQ-resistant Brett Faine, PharmD, Spero Therapeutics (Research Grant or Support) Megan A. Rech, PharmD, MS, BCCCP, FCCM, Spero (Research Grant or Support) David A. Talan, MD, AbbVie (Consultant)GSK (Consultant)SPERO Therapeutics (Grant/Research Support)"} +{"text": "Athelia (Fibularhizoctonia) sp. strain TMB , which forms termite-egg-mimicking sclerotia for which termites care. We further compare its repertoire of psilocybin gene homologs to homologs previously reported for Fibularhizoctonia psychrophila.Atheliales is a diverse order of crust-forming Basidiomycota fungi. Here, we report the draft genome of the \u201ccuckoo fungus,\u201d Athelia (Fibularhizoctonia) sp. TMB strain TB5 , which forms termite-egg-mimicking sclerotia that termites tend. We further compare its repertoire of psilocybin gene homologs to homologs previously reported for Fibularhizoctonia psychrophila.Atheliales is a diverse order of crust-forming Basidiomycota fungi. Here, we report the draft genome of the \u201ccuckoo fungus,\u201d Fibularhizoctonia psychrophila CBS 109695, associated with carrot spoilage psilocybin gene cluster is an ecologically diverse \u20134 order \u2013spoilage , 5, and Athelia (Fibularhizoctonia) sp. TMB produces sclerotia that chemically and structurally mimic Reticulitermes sp. eggs and receive care in over 70% of colonies of some Reticulitermes species . Sclerotia were cultured in potato dextrose broth at room temperature for 14\u2009days with shaking. Tissue was filtered through Miracloth, flash-frozen with liquid nitrogen, and pulverized with a mortar and pestle. Genomic DNA was immediately extracted using the DNeasy plant minikit (Qiagen). Short-read DNA libraries were prepared using the NEBNext Ultra DNA library preparation kit and were sequenced with a 150-bp paired-end format on a NovaSeq 6000 system (Illumina). Long reads were generated by fragmenting genomic DNA with a Covaris g-TUBE, preparing libraries using the SQK-LSK108 ligation sequencing kit, and sequencing the libraries on a MinION system (Oxford Nanopore Technologies) using an R9.4 flow cell. Sequencing generated 62,281,267 Illumina reads with an average coverage of 230.98\u00d7 and 228,721 MinION reads with a mean length of 3,983.38\u2009bp, a median length of 1,834\u2009bp, and a mean coverage of 10.94\u00d7. Coverage was calculated by mapping reads to the assembly with Bowtie 2 v2.4.1-2 data set (F. psychrophila expressed sequence tag (EST) and transcript data , Coniophora olivacea MUCL 20566 (https://mycocosm.jgi.doe.gov/Conol1), Coniophora puteana (https://mycocosm.jgi.doe.gov/Conpu1), Paxillus involutus ATCC 200175 (https://mycocosm.jgi.doe.gov/Paxin1), Pisolithus microcarpus 441 (https://mycocosm.jgi.doe.gov/Pismi1), Pisolithus tinctorius Marx 270 (https://mycocosm.jgi.doe.gov/Pisti1), Rhizopogon vesiculosus Smith (https://mycocosm.jgi.doe.gov/Rhives1), Scleroderma citrinum Foug A (https://mycocosm.jgi.doe.gov/Sclci1), Serpula himantioides MUCL 38935 (https://mycocosm.jgi.doe.gov/Serla_varsha1), and Suillus brevipes Sb2 v2.0 (https://mycocosm.jgi.doe.gov/Suibr2). Gene prediction was finalized using OrthoFiller v1.1.1 , C. olivacea MUCL 20566, F. psychrophila CBS 109695, Galerina marginata , Laccaria bicolor v2.0 (https://mycocosm.jgi.doe.gov/Lacbi2), P. croceum F 1598, Plicaturopsis crispa (https://mycocosm.jgi.doe.gov/Plicr1/Plicr1.home.html), Psilocybe serbica (https://mycocosm.jgi.doe.gov/Psiser1), and S. brevipes Sb2 v2.0.Illumina reads were trimmed using Trimmomatic v0.36 with the v1.0.11 and the v1.0.11 . Genes w v1.0.11 , AUGUSTU v1.0.11 , Glimmer v1.0.11 , and Gen v1.0.11 via the v1.0.11 . We refedata set , F. psycipt data , and pror v1.1.1 with defF. psychrophila and Athelia sp. TMB TB5 was calculated from the BLASTp . Protein domains were aligned (MAFFT v7.467 [Average amino acid identity (AAI) between e BLASTp identitye BLASTp with P. equences were obtequences domains T v7.467 with --aT v7.467 , -automaT v7.467 ). Close Athelia sp. TMB TB5 has a mean AAI of 82.58% with F. psychrophila across 1,727 single-copy orthologs, consistent with substantial divergence time. Multiple copies of psilocybin decarboxylase, hydroxylase, and kinase in Athelia sp. TMB TB5 , and SRR12880627 (Illumina read library).The assembly and annotation of"} +{"text": "Members of the interferon regulatory factor (IRF) gene family are crucial regulators of type I interferon signaling, which may play a role in the resistance of glioma to immune checkpoint blockade. However, the expression profiles, potential functions, and clinical significance of IRF family members remain largely unknown. Here, we examined IRF transcript levels and clinicopathological data from glioma patients using several bioinformatic databases, including ONCOMINE, GEPIA, TCGA, and cBioPortal. We found that IRF1, IRF2, IRF5, IRF8 and IRF9 were significantly upregulated in glioma compared to normal brain tissue. Higher IRF1, IRF2, IRF3, IRF4, IRF5, IRF7, IRF8 and IRF9 mRNA levels correlated with more advanced tumor grades and poorer outcomes. Moreover, although IRFs mutation rates were low (ranging from 0.5% to 2.3%) in glioma patients, genetic alterations in IRFs were associated with more favorable patient survival. Functional analysis showed that IRFs participated in glioma pathology mainly through multiple inflammation- and immunity-related pathways. Additionally, correlations were identified between IRFs and infiltration of immune cells within glioma tissues. Collectively, these results indicate that IRF family members, including IRF1, IRF2, IRF5, IRF8 and IRF9, may serve as prognostic biomarkers and indicators of immune status in glioma patients. Glioma is the most prevalent primary malignancy in the human brain and is characterized by high recurrence and lethality rates . AccordiRecent reports suggest that type I interferon signaling, which is regulated by interferon regulatory factors (IRFs), plays an important role in glioma resistance to immune checkpoint blockade , 6. The Recent advances in gene sequencing technology have enabled comprehensive analysis of IRF family members with existing bioinformatic tools. In this study, we performed an in-depth exploration of the expression patterns of IRF family members in glioma and evaluated their potential as prognostic biomarkers with the goal of improving molecular diagnosis and prognostic prediction for glioma patients.p = 0.008); two additional studies by Liang and Bredel found that IRF1 expression was increased 2.225- and 2.151-fold, respectively, in glioblastoma. IRF2 transcript levels were also higher in glioblastoma than normal brain tissues in two datasets from TCGA . The results of Sun\u2019s study suggested that IRF5 was increased 2.125-fold in diffuse astrocytoma (p = 1.33E-4) and 2.180-fold in anaplastic astrocytoma (p = 3.20E-5). Moreover, studies by Lee, Ramaswamy, and Bredel all found that IRF8 and IRF9 levels were significantly increased in glioblastoma or anaplastic oligoastrocytoma , IRF2 (p = 6.80E-18), IRF3 (p = 1.70E-23), IRF5 (p = 2.30E-08), IRF7 (p = 1.90E-29), IRF8 (p = 0.029), IRF9 (p = 4.80E-05) expression and pathological grade (p = 0.064). No correlation between IRF6 expression and pathological grade was observed (p = 0.49). For all of the identified correlations, expression increased as tumors progressed, suggesting that IRFs may play a role in glioma tumorigenesis and progression.Relationships between IRF family member expression and clinicopathological parameters of glioma patients were examined using data from the TCGA database. Among the 260 grade II, 267 grade III, and 173 grade IV glioma patients, significant correlations were observed between IRF1 , IRF2 (p = 2.22E-16), IRF3 (p = 1.43E-15), IRF4 (p = 0.004), IRF5 p = 5.84E-12), IRF7 (p = 6.85E-28), IRF8 (p = 0.001), and IRF9 (p = 0.000) transcript levels had significantly longer overall survival times to 20.48% (17/83); mutations, deep deletions, and amplification were the most common types of alteration . For eac.237E-6) .We next explored potential co-expression among IRF family genes using data from TCGA glioma dataset. Pearson's correlation results revealed significant positive correlations between the following IRFs: IRF1 with IRF2 (r = 0.48) and IRF7 (r = 0.52); IRF2 with IRF1, IRF5 (r = 0.54), and IRF8 (r = 0.43); IRF3 with IRF7 (r = 0.41); IRF5 with IRF7 (r = 0.41) and IRF8 (R = 0.73); IRF7 with IRF9 (r = 0.74) . Little p < 1.0E-16; Next, we conducted a network analysis to examine potential internal interactions among IRF family genes as well as external interactions with other functionally related genes. PPI network analysis using STRING software revealed close protein-protein associations among the IRF family genes with 9 nodes, 32 edges, and an average node degree of 7.11 and 11 KEGG items were enriched. p < 0.01). Similar results were obtained for GBM. In addition, IRF1, IRF2, IRF6, and IRF9 were positively correlated with CD8+ T cell infiltration in LGG. However, IRF1, IRF5, IRF6, IRF7, IRF8, and IRF9 expression were negatively correlated with CD8+ T cell infiltration in GBM.Since the IRF family may regulate glioma progression and prognosis by participating in a wide range of inflammatory and immune responses, we undertook a comprehensive analysis of tumor immune infiltrates using the TIMER database. The results are shown in p = 0.002), CD8+ T cells (p = 0.042), IRF1 expression (p = 0.001), and IRF8 expression (p = 0.000) were significantly associated with the prognosis of LGG patients, while CD4+ T cells, dendritic cells (p =0.002), IRF1 expression (p = 0.01), IRF7 expression (p = 0.007), and IRF8 expression (p = 0.028) were associated with the prognosis of GBM patients , another online tool that contains RNA sequence expression data from 518 LGG samples, 163 GBM samples, and 207 normal brain samples [t-tests; p < 0.05 and fold change >2 were considered significant.We used a two-step analysis to assess IRF family member expression patterns in glioma patients. First, we examined mRNA level data from ONCOMINE, the largest public microarray database for genome-wide expression analysis . Data we samples . IRF expp-value <0.05 was considered significant.Correlations between IRF family member expression and clinicopathological characteristics and prognosis in glioma patients were evaluated using data derived from The Cancer Genome Atlas (TCGA) database, which contains both sequencing and clinical records for over 30 types of human cancers . A totalThe molecular characteristics and internal/external interactions of IRF family members were explored with multiple tools. Genetic alterations and their associations with patient prognosis were evaluated using cBioPortal, an online tool for visualization and analysis of multidimensional cancer genomics data . Co-exprp < 0.05. Additionally, associations between IRF family members and the activity of cancer pathways, including TSC/mTOR, RTK, RAS/MAPK, PI3K/AKT, hormone ER, hormone AR, EMT, DNA damage response, cell cycle, and apoptosis pathways, were explored with GSCALite, a web-based platform for gene set cancer analysis [To examine biological functions, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted for IRF family members and functionally related genes using DAVID software (version 6.8) . Biologianalysis .The TIMER (Tumor Immune Estimation Resource) database is an immune infiltrate analysis tool for systematic evaluation of the different immune cells that infiltrate tumor tissue and their clinical significance . In our"} +{"text": "In the SIDERO-CR-2014\u20132016 surveillance study, European clinical isolates comprising carbapenem-non-susceptible (CarbNS) Enterobacterales and MDR non-fermenters were tested against cefiderocol and comparators.Many carbapenem-resistant (CR) Gram-negative (GN) pathogens exhibit MDR, meaning few therapeutic options are available for CR-GN infections. Cefiderocol, a siderophore cephalosporin, has demonstrated Cefiderocol MICs were determined using iron-depleted CAMHB, and comparators using CAMHB, per recommended CLSI methodology. Carbapenemase gene profiles were determined using PCR.N\u2009=\u2009870) from 23 European countries comprised CarbNS Enterobacterales (n\u2009=\u2009457), MDR Pseudomonas aeruginosa (n\u2009=\u2009177) and MDR Acinetobacter baumannii (n\u2009=\u2009236). The most common carbapenemases were KPC (52%), OXA-48-like (19%), VIM (14%) and NDM (8%) in Enterobacterales, VIM (41%) in P. aeruginosa and OXA-23-like (57%) and OXA-24/40-like (37%) in A. baumannii. Most carbapenemase-producing isolates (65%) co-carried ESBLs. Approximately half of P. aeruginosa isolates were negative for carbapenemases, compared with 10% of Enterobacterales and 3% of A. baumannii. A similar proportion of Enterobacterales were susceptible to cefiderocol compared with comparator antimicrobial agents, including colistin and ceftazidime/avibactam . Of P. aeruginosa isolates, 98.3% were susceptible to cefiderocol (100% of VIM producers), similar to colistin (100%). Against A. baumannii, 94.9% had cefiderocol MIC \u22642\u2009mg/L and 93.6% of isolates were susceptible to colistin.Isolates (Cefiderocol demonstrated potent activity against CarbNS and MDR GN bacteria, including non-fermenters and a wide variety of MBL- and serine-\u03b2-lactamase-producing strains. Globally, the incidence of carbapenem-resistant (CR) GN bacteria is increasing,Cefiderocol is a novel siderophore cephalosporin, which was developed for the treatment of MDR GN bacteria, including those resistant to carbapenems. Cefiderocol has recently been approved in Europe for the treatment of infections due to aerobic GN organisms in adults with limited treatment options,,,Escherichia coli and Klebsiella pneumoniae, as well as meropenem-resistant Pseudomonas aeruginosa and Acinetobacter baumannii.The structure of cefiderocol is based around a cephalosporin backbone with the addition of a catechol moiety at the 3-position side chain. The cephalosporin core enables cefiderocol to act like other cephalosporins, binding primarily to PBPs and killing bacterial cells by inhibition of peptidoglycan cell wall biosynthesis. Cefiderocol differs from other cephalosporins in that the catechol moiety chelates ferric (Fe-III) iron, mimicking natural siderophores, allowing cefiderocol to exploit the bacteria\u2019s own active receptor-mediated iron transport system to cross the outer membrane.in vitro conditions are essential in order to mimic the hypoferremic conditions encountered by bacteria in the human body during infection.,,in vivo efficacySusceptibility testing of cefiderocol by broth microdilution requires an iron-depleted medium to promote the natural production of siderophores by bacterial cells. Iron-depleted In the SIDERO-CR surveillance study, CR and MDR clinical isolates of GN bacteria collected from patients between 2014 and 2016 were tested against cefiderocol and comparators using recommended CLSI broth microdilution methodology.JAC-AMR Online).,Full methodology for the SIDERO-CR study and molecular characterization using PCR has been published previously (see n\u2009=\u2009457), defined as having a meropenem MIC of \u22652\u2009mg/L. Isolates of P. aeruginosa (n\u2009=\u2009177) and A. baumannii (n\u2009=\u2009236) were included if they demonstrated an amikacin-resistant (MIC \u226532\u2009mg/L), ciprofloxacin-resistant (MIC \u22654\u2009mg/L) and imipenem-resistant (MIC \u226516\u2009mg/L) MDR phenotype.Included in the SIDERO-CR-2014\u20132016 European test set were carbapenem-non-susceptible (CarbNS) phenotypes of Enterobacterales isolates (A. baumannii (CLSI breakpoint \u22648\u2009mg/L),,P. aeruginosa are considered susceptible to cefiderocol at MIC \u22642\u2009mg/L (resistant >2\u2009mg/L).MICs were determined for cefiderocol, cefepime, ceftazidime/avibactam, ceftolozane/tazobactam, ciprofloxacin, colistin and meropenem by broth microdilution according to CLSI guidelines.in vitro samples were anonymized.Ethics approval was not required as all N\u2009=\u2009870) were from Italy [217 (24.9%)], Greece [128 (14.7%)] and Russia [91 (10.5%)].The majority of SIDERO-CR-2014\u20132016 European isolates (A. baumannii [135/385 (35.1%)] and P. aeruginosa (106/385 [27.5%]). K. pneumoniae (120/385 [31.2%]) was the most common Enterobacterales species in RTIs , followed by intra-abdominal infections , surgical site infections and bloodstream infections . K. pneumoniae was the most common pathogen in UTIs [59/157 (37.6%)], SSIs [57/89 (64.0%)] and BSIs [47/85 (55.3%)] while A. baumannii was the most common in IAIs [46/125 (36.8%)].Respiratory tract infections (RTIs) were the most common isolate source [385 (44.3%)]; the majority were non-fermenters [241/385 (62.6%)], consisting of Is Table . Urinaryin vitro activity against a variety of CarbNS-GN bacteria in SIDERO-CR-2014\u20132016 European isolates. Overall, 772/870 (88.7%) had a cefiderocol MIC of \u22642\u2009mg/L; 547/634 (86.3%) of Enterobacterales and P. aeruginosa isolates were susceptible to cefiderocol and 224/236 (94.9%) of A. baumannii isolates had a cefiderocol MIC of \u22642\u2009mg/L.Cefiderocol exhibited 90\u2009=\u20094\u2009mg/L) (TableK. pneumoniae isolates (n\u2009=\u2009332), 82.8% were susceptible to cefiderocol, while 71.7% were susceptible to colistin and 88.9% to ceftazidime/avibactam.Of CarbNS Enterobacterales, 81.6% were cefiderocol susceptible (MIC/L) Table. The pro90 was 1\u2009mg/L against MDR P. aeruginosa and 98.3% of isolates were cefiderocol susceptible (MIC \u22642\u2009mg/L). Colistin demonstrated a similar level of activity (100% susceptible) to cefiderocol, while other comparators were active against <35% of isolates.The cefiderocol MICA. baumannii, the cefiderocol MIC90 was 1\u2009mg/L and 94.9% of isolates had a cefiderocol MIC of \u22642\u2009mg/L. Of the comparators, only colistin demonstrated activity (93.6% susceptible). The MIC ranges for cefiderocol were 0.004\u2009\u2212\u20098\u2009mg/L for P. aeruginosa and 0.03\u2009\u2212\u200932\u2009mg/L for K. pneumoniae, while the range against A. baumannii was somewhat wider (0.015 to >64\u2009mg/L).Against MDR P. aeruginosa isolates non-susceptible to cefiderocol (MIC >2\u2009mg/L) was 13.7% (87/634); these isolates consisted mainly of CarbNS K. pneumoniae (n\u2009=\u200957) and Enterobacter cloacae (n\u2009=\u200918) , Italy (n\u2009=\u20092), Denmark (n\u2009=\u20091), Portugal (n\u2009=\u20091) and Turkey (n\u2009=\u20091)].In total, the proportion of Enterobacterales and ) Figure . There wn\u2009=\u2009107; cefiderocol MIC90\u2009=\u20094\u2009mg/L; range: 0.06\u2009\u2212\u200932\u2009mg/L), as did 97.8% of ceftolozane/tazobactam-resistant P. aeruginosa and all colistin-resistant isolates , 76.9% were cefiderocol susceptible; all 15 colistin-resistant A. baumannii isolates had cefiderocol MICs of \u22642\u2009mg/L.Notably, 66.4% of ceftazidime/avibactam-resistant Enterobacterales remained susceptible to cefiderocol (L) Figure. Of coliP. aeruginosa isolates, VIM (41.2%) was the most common carbapenemase. OXA-23-like (57.2%) and OXA-24/40-like (37.3%) producers accounted for the majority of A. baumannii isolates. Most isolates produced multiple \u03b2-lactamases, e.g. 34/37 (91.9%) NDM-1 Enterobacterales also harboured ESBLs and OSBLs. A proportion of all isolates, phenotypically non-susceptible to meropenem, were negative for carbapenemase genes, with a greater proportion of P. aeruginosa (49.7%) being carbapenemase negative compared with Enterobacterales (9.8%) and A. baumannii (3.4%).In total, 28 subclasses of carbapenemase were identified, along with 37 ESBL (e.g. CTX-M) and older-spectrum \u03b2-lactamase subclasses,n\u2009=\u2009157) and Greece (n\u2009=\u200997) provided the most CarbNS Enterobacterales isolates. Most of these isolates produced KPC or VIM ; however, NDM was less prevalent in Italy (0.6%) than in Greece (5.2%). OXA-48-like carbapenemases ]. NDM-producing P. aeruginosa isolates were only apparent in Serbia, representing 6/10 samples.In countries providing \u22658 isolates, the majority of carbapenemase-producing MDR A. baumannii isolates from countries with \u22658 available isolates established that the majority produced OXA-23-like carbapenemases,Analysis of MDR 90 values were \u22644\u2009mg/L for all carbapenemases across all strains where \u226510 isolates were available for testing and NDM MBL producers. Isolates producing OXA-48-like (n\u2009=\u200985), OXA-23-like (n\u2009=\u2009135) and OXA-24/40-like (n\u2009=\u200988) carbapenemases had cefiderocol MIC90 values of \u22644\u2009mg/L.Cefiderocol MICing Table. Across 90 of KPC-producing isolates was 4\u2009mg/L, with 83.6% being cefiderocol susceptible at the EUCAST breakpoint of \u22642\u2009mg/L, but with 98.3% being cefiderocol susceptible at the CLSI breakpoint of \u22644\u2009mg/L. Ceftazidime/avibactam demonstrated potent activity against 97.9% of KPC-producing Enterobacterales by both EUCAST and CLSI breakpoints. Similarly, against OXA-48-like-producing Enterobacterales, only cefiderocol and ceftazidime/avibactam (both 88.2% susceptible) demonstrated efficacy in >75% isolates. Against VIM-producing Enterobacterales, only cefiderocol (79.0% susceptible) and colistin (93.5% susceptible) demonstrated notable activity. The proportion of susceptible NDM-producing Enterobacterales isolates was higher for cefiderocol (51.4%) and colistin (78.4%) versus all other comparators (<3%).The activity of cefiderocol and comparators by carbapenemase is summarized in TableP. aeruginosa, cefiderocol and colistin demonstrated potent activity, with 100% of isolates being susceptible to both agents. Cefiderocol and colistin were also active against non-carbapenemase-producing MDR P. aeruginosa, with 96.6% of isolates being cefiderocol susceptible and 100% being colistin susceptible.Against both VIM- and GES-producing A. baumannii producing OXA-23-like and OXA-24/40-like carbapenemases.Cefiderocol and colistin also demonstrated potency against P. aeruginosa and A. baumannii isolates is apparent in FigureThe wide variety of carbapenemases produced by European Enterobacterales, n\u2009=\u200939), followed by NDM (n\u2009=\u200919), VIM (n\u2009=\u200913), OXA-48-like (n\u2009=\u200910), OXA-23-like (n\u2009=\u20096) and OXA-24-like (n\u2009=\u20095). Twelve isolates carried either OSBLs/ESBLs or no known \u03b2-lactamase, with eight isolates harbouring the PER-type \u03b2-lactamase.A range of \u03b2-lactamases were identified across 99 isolates with cefiderocol MIC values of >2\u2009mg/L, including isolates with co-carriage of multiple \u03b2-lactamases. The most common carbapenemase was KPC and carbapenemase-producing K. pneumoniae (n\u2009=\u2009107) were cefiderocol susceptible.Similar isolate studies involving cefiderocol have used provisional CLSI breakpoints. In a study including 1086 CR isolates from the USA (737 KPC producers), MICs were higher for isolates of Enterobacterales with \u03b2-lactamases compared with those without, but no clear association was found between the type of \u03b2-lactamase and the MIC.A key limitation of the SIDERO-CR study was the geographical spread and number of collection sites within countries. Isolates were selected by a limited number of sites per country based on the MDR/CR phenotype, therefore the relative frequency observed may not reflect the national prevalence. Additionally, the number of sites and isolates per country were not proportionate to population. Consequently, the isolate collection is not necessarily representative, as there may be considerable heterogeneity in the numbers and types of pathogens and mechanisms of resistance provided by different locales. However, from SIDERO-CR-2014\u20132016 isolate characterization, it is apparent that carbapenem resistance across Europe is associated with a diverse range of \u03b2-lactamases. Of the CR isolates included, 83.8% (729/870) produced at least one carbapenemase, with 65.2% (475/729) of carbapenemase-producing isolates also carrying ESBLs and/or OSBLs.K. pneumoniae with genes encoding for OXA-48 and NDM-1 has recently been reported in the Mecklenburg-Western Pomerania state of Germany.K. pneumoniae was investigated across eight Greek hospitals between 2013 and 2016.K. pneumoniae isolates were of a clonal type (ST11) similar to those identified in Bulgaria in 2015\u201316, indicating that the Balkan region is also at risk of increasing prevalence of MBL-producing Enterobacterales.K. pneumoniae infection has led to a shift in the carbapenemase landscape in Greece, with the incidence of MBLs increasing between 2015\u201317 (12.0%) and 2018 (51.1%), mainly due to VIM-producing K. pneumoniae becoming more prevalent.,,P. aeruginosa isolates resistant to ceftazidime/avibactam and 77.4% of all MDR P. aeruginosa isolates resistant to ceftolozane/tazobactam , recent reports have described an increasing proportion of non-KPC MBL-mediated resistance. A Rapid Risk Assessment report from the ECDC described an increase in NDM-containing carbapenemase-producing Enterobacterales in Italy,tam Table.A. baumannii.,P. aeruginosa and A. baumannii, but particularly in K. pneumoniae , mediated, to some extent, by transmissible mcr-1 resistance.K. pneumoniae) and 6.4% of A. baumannii, with 100% of P. aeruginosa isolates being colistin susceptible. These results do not necessarily reflect the incidence of colistin resistance in specific geographical locations or from specific infection sources; for example, the incidence of colistin-resistant A. baumannii was reported to be 47.7% in a set of A. baumannii RTI isolates from Greece, Italy and Spain (n\u2009=\u200965).In vitro assessment of CR-GN isolates from 18 hospitals in Greece demonstrated that \u223c40% of K. pneumoniae and A. baumannii isolates were resistant to colistin; 100% of these isolates had cefiderocol MICs of \u22644\u2009mg/L.Colistin, often considered a treatment of last resort, has a broad spectrum of GN activity and is frequently used for CR- and MDR-GN infections, particularly for MDR P. aeruginosa. Cefiderocol retained activity against the majority of isolates harbouring MBLs, with only 3.0% (3/99) of MBL-positive CarbNS Enterobacterales isolates having MIC values >4\u2009mg/L. The in vitro activity (MIC \u22642\u2009mg/L) of cefiderocol against a range of serine-\u03b2-lactamases varied from 100% in OXA-58-producing isolates to 83.6% in KPC producers. In addition, 91.5% of isolates with no carbapenemase and 97.5% with no \u03b2-lactamase had a cefiderocol MIC \u22642\u2009mg/L, demonstrating potent cefiderocol activity where the mechanism of resistance was not clear.In this study, the proportions of isolates susceptible to cefiderocol are similar to comparators in Enterobacterales and generally similar to colistin but greater than other comparators in P. aeruginosa isolates (98.3% cefiderocol susceptible), yet half carried no carbapenemase. The low prevalence of carbapenemases in SIDERO-CR-2014\u20132016 P. aeruginosa isolates aligns with recently reported data describing the prevalence of XDR P. aeruginosa; of 1445 P. aeruginosa isolates collected from 51 Spanish hospitals, 252 (17.3%) were classified as XDR and only 3.1% carried either carbapenemases or ESBLs.P. aeruginosa isolates in SIDERO-CR-2014\u20132016 is likely to be due to porin- and efflux pump-mediated mechanisms.in vitro activity against strains with alterations in outer membrane porins or overexpressed efflux pumps.,Cefiderocol demonstrated potency against the MDR in vitro activity against a broad range of CarbNS and MDR pathogens. The isolates tested included \u03b2-lactamase-producing strains from all Ambler classes, with cefiderocol demonstrating activity against the key MBLs VIM and NDM, as well as against clinically important serine-\u03b2-lactamases KPC, GES and OXA, and isolates co-carrying ESBLs and OSBLs. Consequently, cefiderocol represents a key addition to the limited armamentarium available for the treatment of infections caused by CR- and MDR-GN organisms and could be a particularly valuable and timely treatment option for when resistance is apparent but the mechanism is unknown.In conclusion, the SIDERO-CR European dataset, coupled with the rise of resistance to existing agents and the shift towards MBL- from serine-\u03b2-lactamase-producers, demonstrates the diverse and dynamic nature of the European carbapenemase landscape. In SIDERO-CR-2014\u20132016, cefiderocol exhibited potent dlaa060_Supplementary_DataClick here for additional data file."} +{"text": "EGFR) T790M mutation on osimertinib efficacy remains unclear.Seventy-eight patients were studied with EGFR-mutated NSCLC and LM. Case data were collected and EGFR mutation status of circulating cell-free DNA from paired CSF, and plasma of 23 patients with LM was detected using droplet digital PCR. The median overall survival (mOS) was 8.08 months (95% CI: 6.07\u201310.09) in the study. Forty-four osimertinib-treated patients had an improved mOS of 13.15 (95% CI: 5.74\u201320.57) and a median progression-free survival (PFS) of 9.50 months (95% CI: 6.77\u201312.23) when compared with patients treated with first- or second-generation EGFR-TKI (mOS\u2009=\u20093.00 months (95% CI: 1.32\u20134.68) and median PFS\u2009=\u20091.50 months (95% CI: 0.00\u20133.14)). In the osimertinib group, mOS values for CSF with and without T790M mutation were 22.15 months (95% CI: 9.44\u201334.87) and 13.39 months (95% CI: 7.01\u201319.76), respectively, with no statistical differences. Regardless of the CSF T790M mutation status, osimertinib demonstrated significant efficacy against LM associated with NSCLC.Osimertinib has demonstrated promising efficacy against leptomeningeal metastasis (LM) associated with T790M-positive non-small-cell lung cancer (NSCLC). However, the effect of cerebrospinal fluid's (CSF's) epidermal growth factor receptor ( EGFR) is the most important driver gene in NSCLC. EGFR mutations occur in 10\u201320% of Caucasian patients with NSCLC but in 40\u201360% of Asian patients [EGFR mutations [EGFR tyrosine kinase inhibitor (EGFR-TKI) treatments [Leptomeningeal metastasis (LM) is defined as the spread of malignant cells within the leptomeninges and subarachnoid space, resulting in a devastating prognosis with limited treatment options . Non-smautations , 4. ThisEGFR mutation status is a critical prognostic factor in the treatment of NSCLC with LM. A secondary EGFR test is often required to determine the status of T790M drug-resistant mutation. However, it is difficult to obtain a second tumor tissue from most patients. Circulating cell-free DNAs (cfDNAs) are extracellular nucleic acids released by tumor cells that can be useful biomarkers for early diagnosis and prognosis [rognosis . Howeverrognosis , 7.EGFR-TKIs remains dismal [EGFR-TKIs, such as afatinib, could partially penetrate the blood\u2013brain barrier, they exhibit no obvious advantage as a treatment for LM [LM is often associated with an extremely poor prognosis, with a median OS (mOS) of 3\u201310 months after diagnosis . Currents dismal \u201313. AlthEGFR-TKI that selectively inhibits EGFR and EGFR T790M mutations. It is highly effective in both untreated and previously treated patients with EGFR-mutated NSCLC by prolonging OS and progression-free survival (PFS) [EGFR-mutated positive NSCLC [EGFR T790M mutation [Osimertinib is an irreversible third-generation al (PFS) \u201316. Accove NSCLC . In contEGFR T790M mutation status and osimertinib efficacy in patients with NSCLC [EGFR-TKIs and evaluate the factors influencing osimertinib efficacy.Few studies have focused on the relationship between CSF th NSCLC , 18. In EGFR-mutated NSCLC and LM at the People's Hospital of Zhengzhou University, recruited from January 1, 2014, to December 31, 2020. Inclusion criteria were: (1) space-occupying lesions of the lungs detected using computed tomography (CT) or whole-body positron emission tomography/computed tomography (PET/CT) and confirmed as NSCLC using histological biopsy, (2) symptoms and signs of the central nervous system metastases, (3) typical leptomeningeal enhancement on magnetic resonance imaging (MRI), and (4) cytologic identification of malignant cells within the CSF. All patients were scored using the Eastern Cooperative Oncology Group performance status (ECOG PS), CT, or PET/CT. In addition, the patient's histology, metastasis site, imaging, CSF parameters, and molecular profiling were collected. And no patients had complicated organ failure, infection in the central nervous system, and diseases of the autoimmune system or hematological system.This retrospective study involved patients with EGFR-mutated NSCLC and LM, 34 patients were treated with first- or second-generation EGFR-TKIs treatment, and 44 patients were treated with osimertinib analysis or next-generation sequencing.EGFR kit . All protocols of analysis were carried out in strict accordance with the manufacturer's instructions.Secondary T790M mutation analysis was performed using one of the following samples: biopsied tumor tissues, plasma, or CSF samples. Approximately 10\u2009mL of whole blood and 10\u2009mL of CSF (EDTA as the anticoagulant) were collected for the purpose of cfDNA extraction. The retrieved CSF was used for analysis within 4\u2009h of the lumbar puncture procedure. Plasma and CSF were centrifuged at 1,600\u2009\u00d7\u2009g and 10,000\u2009\u00d7\u2009g, respectively, for 10\u2009min at room temperature. CfDNA was extracted using the QiAamp circulating nuclear acid kit . Droplet digital PCR (ddPCR) was used to detect cfDNA using the Sysmex OncoBeam EGFR-TKI treatment to tumor progression. The cutoff date was December 31, 2020.OS for LM was defined as the time from LM diagnosis to death. PFS was calculated from the onset of p values were used for survival analysis at 95% confidence intervals (95% CI). Cox regression analysis was performed to estimate hazard ratios (HRs) and 95% CIs for OS. Statistical significance was set at p < 0.05.Statistical analyses were performed using SPSS software . Chi-square univariate analysis was used for continuous variables, and a non-parametric test was used for non-normal distribution variables. Kaplan\u2013Meier estimation and log rank EGFR-mutated NSCLC and LM were included. The median age was 61 years (range: 28\u201378), and 74.4% (58/78) were non-smokers. The ECOG PS scores at the time of LM diagnosis were: <1 in 23 (29.5%), 2\u20133 in 43 (55.1%), and 4 in 12 patients (15.4%). Twenty-five patients with NSCLC also presented with LM at initial diagnosis. The median time from NSCLC to LM diagnosis of the remaining 53 patients was 21 months (95% CI: 12.0\u201324.5). Statistically significant differences were not observed in age, sex, smoking status, histology, initial ECOG PS scores, and EGFR mutations.As shown in EGFR T790M mutation analysis. Of these samples, EGFR T790M mutation was identified in 28 cases.Among the 78 patients, 66 (84.6%) of them underwent secondary EGFR gene of cfDNA in 23 patients simultaneously, and T790M mutation was detected in 8 patients (Supplementary EGFR mutations in plasma and CSF samples were 56.5% (13/23) and 60.9% (14/23), respectively, but without any statistically significant difference (p=0.765).Plasma and CSF were used to detect the EGFR-TKI: 24 (45.3%) of them received gefitinib, 11/53 (20.8%) received erlotinib, 7/53 (13.2%) received icotinib, 5/53 (9.4%) received afatinib and gefitinib, and 6/53 (11.3%) received osimertinib. Moreover, 35/53 (66.0%) patients received cytotoxic chemotherapy, and 11/53 (20.8%) had undergone whole-brain radiation therapy (WBRT) for brain metastasis prior to LM were treated with osimertinib at the time of LM diagnosis. The median duration of osimertinib treatment was 7.0 months (95% CI: 4.0\u20139.0). Thirty-four patients received first- or second-generation TKI treatment without osimertinib. Eighteen (52.9%) of them received gefitinib; 10 (29.4%) received erlotinib; 3 (8.8%) received icotinib; and 1 (2.9%) received afatinib and gefitinib. Twelve patients (35.7%) received cytotoxic chemotherapy; 4 (12.9%) received WBRT; 2 (6.5%) underwent IT chemotherapy; and 3 (9.7%) had VPS insertion .At the end of follow-up, 58 patients died from the disease, 15 were still alive, and 5 were lost to follow-up (6.4%). The 1-year OS rate in the study was 32.7% (19/73), with a mOS of 8.08 months , with a 1-year OS rate of 12.9%, which was shorter than that of patients treated with osimertinib (HR: 0.58 (95% CI: 0.44\u20130.77) and p \u2264 0.001; Among the 44 patients who received osimertinib treatment, 39 (88.6%) had positive clinical responses. Twenty-eight patients died, and 14 were still alive at the time of follow-up, with a mOS of 13.15 months (95% CI: 5.74\u201320.57). The 1-year OS rate was 53%. Among the patients who were treated with first- or second-generation Compared to the group treated with osimertinib, PFS of the group treated without osimertinib also was significantly shorter (PFS: 1.50 months (95% CI: 0.00\u20133.14) and HR: 0.57 month (95% CI: 0.44\u20130.75); p=0.564). Regardless of T790M status, the survival benefit of the osimertinib treatment group was better than that of the first- or second-generation EGFR-TKI treatment group (mOS\u2009=\u20093.00 months (95% CI: 1.32\u20134.68) and HR: 0.56 (95% CI: 0.41\u20130.78); Furthermore, we further divided the group treated with osimertinib into two subgroups according to T790M mutational status. The mOS for patients with and without T790M mutational status was 15.92 months (95% CI: 7.70\u201324.14) and 9.00 months (95% CI: 5.50\u201312.50), respectively, but without any significant difference (EGFR mutation in CSF cfDNA was detected in 23 patients of the osimertinib treatment group. Seven patients with T790M mutation in CSF had a mOS of 22.15 months (95% CI: 9.44\u201334.87), whereas 16 patients without T790M mutation had a mOS of 13.39 months (95% CI: 7.01\u201319.76). No statistical difference was found according to Kaplan\u2013Meier survival analysis and 13.39 months (95% CI: 3.59\u201323.18), respectively. However, survival analysis revealed no significant differences between the two groups p=0.416; .p=0.001 and multivariate HR: 3.22 (95% CI: 1.74\u20135.95), p=0.021). Osimertinib treatment was identified as a significant independent favorable prognostic factor in patients with NSCLC and LM (univariate HR: 0.59 (95% CI: 0.45\u20130.78), p=0.000 and multivariate HR: 0.65 (95% CI: 0.49\u20130.87), p=0.004). Univariate analysis revealed a statistically significant correlation between WBRT and prognosis (0.45 (95% CI: 0.23\u20130.96), p=0.038). However, no significant associations were observed with concurrent brain metastases, initial EGFR and EGFR T790M mutations, CSF pressure, protein and glucose levels, and systemic and intrathecal cytotoxic chemotherapy , otherapy .EGFR-TKI drugs have resulted in significant survival benefits and improved quality of life for patients with EGFR mutations. Third-generation EGFR-TKIs, such as osimertinib, have also been found to extend the survival of patients with T790M mutation by more than 10 months [The treatment of lung cancer has gradually evolved from traditional therapies to gene-oriented personalized treatments. The first- and second-generation 0 months .EGFR\u2009+\u2009NSCLC, regardless of T790M mutation that confers drug resistance, with a median LM PFS of 9.50 months and a mOS of 13.15 months. Patients treated with only first- or second-generation EGFR-TKI after LM diagnosis had a median PFS of 1.50 months and a mOS of 3.00 months. Compared to first- or second-generation EGFR-TKIs, osimertinib showed a markedly improved survival benefit.Our study found that osimertinib is a clinically effective standard regimen in patients with LM associated with EGFR-TKIs for LM is limited because of the blood\u2013brain barrier. The first- and second-generation EGFR-TKIs have low CSF penetration, with an average CSF penetration of 1\u20133% for gefitinib and 3\u20136% for erlotinib compared to only 1% for afatinib [As mentioned, the efficacy of first-generation afatinib \u201313. Highafatinib . Althougafatinib .EGFR mutation NSCLC [EGFR-TKI therapy failure [Preclinical studies of osimertinib using mouse models of brain metastasis with 19 gene deletions (PC9) have demonstrated that a dose-dependent tumor reduction can be achieved . The AURon NSCLC . Several failure , 23. SimEGFR T790M screening failure in the BLOOM study might be a missed opportunity in revealing osimertinib activity in the CNS [EGFR-TKI-resistant NSCLC and without the T790M mutation should be further investigated.The excluded patients based on the CNS . A recen the CNS . SimilarEGFR mutations detected using CSF cfDNA tended to be higher compared to plasma cfDNA [EGFR mutation rate based on CSF samples [in vivo, in vitro, and/or in silico along with other math tools and models, including meta-analysis [Due to the blood\u2013brain barrier, plasma cfDNA may not accurately reflect the actual state of mutations in intracranial tumors, whereas the rapid CSF circulation within the cerebral ventricle and spinal cord cavity indicates that CSF cfDNA may be a reliable biomarker for intracranial tumors. In patients with LM associated with metastasized lung carcinoma, the proportion of ma cfDNA . A simil samples , which i samples . Howeveranalysis , 26, resanalysis , 28, netanalysis , and molanalysis , 31.This study had several limitations. Firstly, this was a retrospective study involving a small number of patients. All the patients included in our study were confirmed using cytological findings, whereas patients diagnosed via clinical examination and imaging were not included, which may have contributed to selection bias. Secondly, the ddPCR method for detecting plasma and CSF cfDNA had low sensitivity, which could have potentially resulted in a lower detection rate. Therefore, more sensitive cfDNA detection assays, such as NGS, will be employed for further verification analysis.EGFR mutation status of circulating cell-free DNA from paired CSF, and plasma of 23 patients with LM was detected using droplet digital PCR. The median overall survival (mOS) was 8.08 months (95% CI: 6.07\u201310.09) in the study. Forty-four osimertinib-treated patients had an improved mOS of 13.15 months (95% CI: 5.74\u201320.57) and a median progression-free survival (PFS) of 9.50 months (95% CI: 6.77\u201312.23) when compared with patients treated with first- or second-generation EGFR-TKI (mOS\u2009=\u20093.00 months (95% CI: 1.32\u20134.68) and median PFS\u2009=\u20091.50 months (95% CI: 0.00\u20133.14)). In the osimertinib group, mOS values for CSF with and without T790M mutation were 22.15 months (95% CI: 9.44\u201334.87) and 13.39 months (95% CI: 7.01\u201319.76), respectively, with no statistical differences. Regardless of the CSF T790M mutation status, osimertinib demonstrated significant efficacy against LM associated with NSCLC.Case data were collected and"} +{"text": "Kappaphycus alvarezii, Eucheuma denticulatum, Halymenia durvillaei (Rhodophyta), Caulerpa lentillifera, Caulerpa racemosa (Chlorophyta), Dictyota dichotoma and Sargassum polycystum (Ochrophyta). This review aims to highlight the therapeutic potential of North Bornean seaweeds and their nutraceutical profiling. North Bornean seaweeds have demonstrated anti-inflammatory, antioxidant, antimicrobial, anticancer, cardiovascular protective, neuroprotective, renal protective and hepatic protective potentials. The protective roles of the seaweeds might be due to the presence of a wide variety of nutraceuticals, including phthalic anhydride, 3,4-ethylenedioxythiophene, 2-pentylthiophene, furoic acid , eicosapentaenoic acid, palmitoleic acid, fucoxanthin, \u03b2-carotene (E. denticulatum), eucalyptol, oleic acid, dodecanal, pentadecane (H. durvillaei), canthaxanthin, oleic acid, pentadecanoic acid, eicosane (C. lentillifera), pseudoephedrine, palmitic acid, monocaprin (C. racemosa), dictyohydroperoxide, squalene, fucosterol, saringosterol (D. dichotoma), and lutein, neophytadiene, cholest-4-en-3-one and cis-vaccenic acid (S. polycystum). Extensive studies on the seaweed isolates are highly recommended to understand their bioactivity and mechanisms of action, while highlighting their commercialization potential.Malaysia has a long coastline surrounded by various islands, including North Borneo, that provide a suitable environment for the growth of diverse species of seaweeds. Some of the important North Bornean seaweed species are Marine organisms have been widely used as sources of functional bioactive compounds over the years . Among mKappaphycus alvarezii (Doty) Doty, Eucheuma denticulatum (Burman) Collins et Harvey, Halymenia durvillaei Bory de Saint-Vincent, Caulerpa lentillifera J. Agardh, Caulerpa racemosa (Forssk\u00e5l) J. Agardh, Dictyota dichotoma (Huds.) Lamouroux, and Sargassum polycystum C. Agardh [Malaysia is part of the Coral Triangle, a geographical area in Southeast Asia and the Pacific that includes the oceans close to Indonesia, Malaysia, Philippines, Papua New Guinea, Timor-Leste and Solomon Islands. The temperatures of Malaysia\u2019s coastal waters make it ideal for the development and growth of a wide variety of seaweed species. The North Borneo region of Malaysia is one of the main seaweeds growing areas; it has a suitable environment for cultivating a diverse variety of seaweeds and is the only region of Malaysia where seaweeds are farmed commercially . In Nort. Agardh . Brief dSeaweeds are also known as sea vegetables and have been used for the treatment of various disorders ,14,15,16Inflammation is a recognized defensive mechanism evolved in high-level organisms in response to stressors that disrupt bodily homeostasis. Microbial infections, tissue stress and some traumas are examples of hazards that cause inflammation with common symptoms of fever, redness, swelling and pain ,24. OverK. alvarezii has been reported to have anti-inflammatory potential in asthma-induced rats. The extract changed circulating white blood cell levels, reduced mucin synthesis, and downregulated the expression of TNF-\u03b1, IL-4, nuclear factor kappa beta (NF-\u03baB), epidermal growth factor receptor (EGFR) and matrix metalloproteinase (MMP-9). The consumption of seaweed may be useful for asthma patients. The extract decreases bronchiole smooth muscle thickness for airflow facilitation and decreases asthmatic inflammation, lung eosinophil infiltration, and mucin production [oduction .C. lentillifera polysaccharides has been reported to have an inhibitory impact on lipopolysaccharide (LPS)-induced HT29 colorectal carcinoma cells, lowering the overproduction of TNF-\u03b1 and IL-1\u03b2, SIgA and mucin2 (related proteins), as well as decreasing TNF-\u03b1 and IL-1\u03b2 expression [C. racemosa polysaccharides have been reported to have anti-inflammatory potential and activate the hemoxigenase-1 (HO-1) pathway to sustain the production of hemoxigenase-1 enzyme, crucial for the prevention of inflammation [The anti-inflammatory activity of pression . C. raceammation . D. dichotoma extract at a concentration of 25 ug/mL inhibited the production of NO and PGE2, followed by a reduction in the expression of inducible nitric oxide synthase (iNOS) and COX-2 proteins, and iNOS and COX-2 mRNA in a dose-dependent pattern. COX-2 and iNOS are implicated in a variety of pathological processes, including inflammation. The solvent fractions of D. dichotoma extracts also decrease the mRNA expression of other cytokines including TNF-\u03b1, IL-1, and IL-6 in the murine macrophage cell line [In murine macrophage RAW 264.7 cells, the dichloromethane fraction of ell line .S. polycystum has been reported using a mouse model with the paw edema method, where the mouse paw was inflamed and the hexane fraction of seaweed extract at a concentration of 70 mg/kg b.w. was applied. The anti-inflammatory effect was measured by the decreased percentage of edema size. The hexane fractions of S. polycystum extract significantly reduced the edema size compared to untreated mice [Anti-inflammatory and analgesic activity from brown algae ted mice .Antioxidant phytochemical compounds can scavenge the reactive oxygen species (ROS) and reactive nitrogen species (RNS) in the human body, and slow down or prevent the onset of oxidative stress-related diseases including cardiovascular diseases (CVDs), neurological diseases , Parkinson\u2019s disease, multiple sclerosis, amyotrophic lateral sclerosis (ALS), and depression), cancer , respiratory disease (chronic obstructive pulmonary disease (COPD) and asthma), rheumatoid arthritis, delayed sexual maturation, and kidney and liver diseases ,31,32,33K. alvarezii 1.63 and 225.00 TEAC and FRAP mM.mg/dry extract and 22.50 TPC mg PGE/g dry extract, E. denticulatum 1.54 and 153.97 TEAC and FRAP mM.mg/dry extract and 15.82 TP mg PGE/g dry extract, H. durvillaei 1.67 and 182.29 TEAC and FRAP mM.mg/dry extract and 18.90 TP mg PGE/g dry extract, C. lentillifera 2.16 and 362.11 TEAC and FRAP mM.mg/dry extract and 42.85 TP mg PGE/g dry extract, C. racemosa 2.01 and 355.36 TEAC and FRAP mM.mg/dry extract and 40.36 TP mg PGE/g dry extract, D. dichotoma 1.66 and 268.86 TEAC and FRAP mM.mg/dry extract and 35.23 TP mg PGE/g dry extract, S. polycystum 1.86 and 366.69 TEAC and FRAP mM.mg/dry extract and 45.16 TP mg PGE/g dry extract compared to butylated hydroxytoluene (standard) (3.84 and 615.71 TEAC and FRAP mM.mg/dry extract) [C. lentillifera has high antioxidation activities followed by C. racemosa, S. polycystum, H. durvillaei, D. dichotoma, K. alvarezii and E. denticulatum; while in terms of TP, S. polycystum has indicated high values followed by C. lentillifera, C. racemosa, D. dichotoma, K. alvarezii, H. durvillaei and E. denticulatum [Marine seaweeds from North Borneo are a good source of antioxidants ,11,34,35Pathogenic microbes including bacteria, fungi, viruses and parasites are responsible for the development of various diseases that arise in the community . SeaweedK. alvarezii against Staphylococcus aureus (S. aureus) has been examined. Administration of the extract at a concentration of 200 mg/mL resulted in an inhibition zone of 10.03 mm [K. alvarezii was also effective against S. aureus, Staphylococcus epidermidis (S. epidermidis) , Pseudomonas aeruginosa (P. aeruginosa) and Bacillussubtilis (B. subtilis) bacterial strain at a concentration of 30\u201380% (w/v) with an inhibition zone of 11.93\u201314.85 mm, while ethyl acetate fractions of the ethanol extract of K. alvarezii at a concentration of 50% (w/v) inhibited the growth of S. aureus, S. epidermidis, P. aeruginosa and B. subtilis with inhibition zones of 7.14, 19.70, 0.73 and 18.30 mm, respectively. No antifungal activity of K. alvarezii extract and fractions have been published against Candida albicans (C.P. Robin) Berkhout and Aspergillus niger (A. niger) (Tiegh) [K. alvarezii extract have been reported against Lagenidium spp and Haliphthoros fungal strains [Lagenidium thermophilum (L. thermophilum) and Haliphthoros sabahensis (H. sabahensis) are pathogenic to the eggs and larval stages of Scyllaserrata and Scyllatranquebarica (mangrove crabs) [K. alvarezii inhibited the hyphal growths of L. thermophilum IPMB 1401 and H. sabahensis IPMB 1402 [K. alvarezii exhibited strong anti-influenza activity against a wide spectrum of influenza virus strains, including the newly evolving swine-origin H1N1-2009 influenza strain. The mechanism involved the direct binding of ECA-2 to the viral envelope protein hemagglutinin (HA) and inhibited influenza virus propagation [The antibacterial potential of the aqueous extraction of 10.03 mm . The eth (Tiegh) . On the e crabs) ,40. The pagation .E. denticulatum inhibited the growth of S. aureus with inhibition zones of 6.0\u201316.3 mm. Furthermore, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values for E. denticulatum extract against S. aureus were 10% and 15%, respectively. At 10%, minimum bacterial growth was observed, the number of bacteria greatly decreased from 3.0 \u00d7 107 to 1.5 \u00d7 102 CFU/plate, and turbidity levels also decreased; while at 15% of the extract, no bacterial growth was noticed [E. denticulatum extract has been reported against Aspergillus flavus (A. flavus) (Link) [E. denticulatum have been tested for in vitro antiviral activity against human herpes virus type 1 (HHV-1). Carrageenans indicated an antiviral impact by the inhibition of virus attachment and interference in a subsequent stage of the virus replicative cycle. HHV-1 viral DNA synthesis was reduced by 3 folds in cultures treated with sulphated polydigalactosides from E. denticulatum (0.75 mg/mL) [The ethanol extract of noticed . No anti) (Link) . Sulphat5 mg/mL) .H. durvillaei has been reported to have antimicrobial effects. The presence of antimicrobial activities of H. durvillaei extract against pathogenic bacteria was determined using the disc diffusion method. The solvent extract of H. durvillaei inhibited the growth of P. aeruginosa (11.89 mm), S. aureus (12.22 mm), and Streptococcus pyogenes (S. pyogenes) Rosenbach, 1884 (10.67 mm), respectively. However, no fungicidal activity of the solvent extract of H. durvillaei has been reported against C. albicans [The extracts of albicans .C. lentillifera were tested against Methicillin-resistant S. aureus (MRSA) and neuropathogenic Escherichia coli K1 (E. coli K1). Moderate antibacterial activity of 62.17% against MRSA and poor antibacterial impact against E. coli K1 of 12.42% were demonstrated by C. lentillifera extract at a concentration of 250 \u03bcg/mL [C.lentillifera (0\u2013128 \u03bcg/mL) was recorded against the shrimp pathogenic bacteria Vibrio vulnificus Farmer, 1980, V. alginolyticus Sakazaki, 1968, V. parahaemolyticus Sakazaki et al., 1963 or V. harveyi, , as compared with positive and negative controls [C. lentillifera extract was tested against White Spot Syndrome Virus (WSSV) [C. lentillifera extract yielded very good outcomes. Shrimps injected with WSSV and C. lentillifera (1\u201310 mg/mL) preincubated solutions exhibited significantly lower mortality of 0.0\u20136.7%, compared with the positive control (100%) (only WSSV-injected). This inhibitory effect was further confirmed by the reduction in viral loads of WSSV, and C. lentillifera (1\u201310 mg/mL) expressed significantly lower viral loads than the positive control [C. lentillifera against L. thermophilum and H. sabahensis have been reported as well. An ethanol extract of C. lentillifera inhibited hyphal growths of L. thermophilum IPMB 1401, L. thermophilum IPMB 1601 and H. sabahensis IPMB 1603 [The chloroform extracts of 50 \u03bcg/mL . Howevercontrols . The ant genome) ,47. WSSV genome) . The admtal DNA) . FungiciPMB 1603 .C. racemosa demonstrated antibacterial activity against MRSA and E. coli K1. The extract of C. racemosa, at a concentration of 250 \u03bcg/mL, displayed a high antibacterial effect of 97.7% against MRSA, but a weak effect of 19.90% against E. coli K1. A methanol extract of C. racemosa (250 \u03bcg/mL) also showed antibacterial activity of 61.54% and 42.91% against MRSA and E. coli K1 [C. racemosa has been reported to show antifungal activity against A. flavus. An ethanol extract of the seaweed demonstrated the strongest inhibitory power with a 30 mm diameter inhibition zone against A. flavus [C. racemosa was demonstrated against the Chikungunya virus (CHIKV) [Aedes aegypti and Aedes albopictus mosquitoes, which cause high fever, joint pain, back pain, vomiting, headache, kidney, liver, heart disease, etc. [C. racemosa was determined based on inhibition of the cytopathic effect caused by CHIKV on African monkey kidney epithelial (Vero) cells. Chloroform, ethyl acetate, ethanol, and methanol extracts (5 to 640 \u03bcg/mL) of C. racemosa showed a significant inhibition effect [A chloroform extract of coli K1 , respect. flavus . The ant (CHIKV) . The virn effect .D. dichotoma at a concentration of 1.5 mg/disc were investigated for in vitro antibacterial and antifungal activities. The results indicated that the methanol extract inhibited the growth of B. subtilis (6.5 mm) and S. aureus (7.5 mm). The dichloromethane extract inhibited the growth of B. subtilis (7.0 mm), Enterobacter aerogenes (E. aerogenes) (6.5 mm), E. coli (6.5 mm), Proteus vulgaris (P. vulgaris) (11.0 mm) and Salmonella typhimurium (S. typhimurium) (7.0 mm), whereas the hexane extract inhibited the growth of B. subtilis (9.0 mm) and S. aureus (7.5 mm) only [D. dichotoma has been shown against Salmonella typhi (S. typhi), Klebsiella pneumoniae (K. pneumoniae) Trevisan, 1887 and Shigella boydii (S. boydii) [D. dichotoma has been reported against Mucor sp. and A. flavus [D. dichotoma (1.5 mg/disc) has been observed against C. albicans [D. dichotoma extract has been tested against herpes simplex virus (HSV) and coxsackievirus B3 (CVB3) [Methanol, dichloromethane and hexane extracts of mm) only . The antg, 1949) . The ant. flavus , while nalbicans . The ant3 (CVB3) . HSV bel3 (CVB3) ,55. The 3 (CVB3) .S. polycystum was tested against human pathogenic bacteria. The methanol extract of the seaweed resulted in the inhibition of P. aeruginosa (15 mm), K. pneumoniae (16 mm), E. coli (19 mm), and S. aureus (20 mm) [S. polycystum indicated no inhibition against B. subtilis or S. enteritidis. Similarly, no antifungal activity has been observed against A. niger [A solvent extract of (20 mm) . HoweverA. niger .Cancer is one of the main causes of mortality in the world, and many research facilities are now focusing on the development of new anticancer medicines that could improve chemotherapy treatment and reduce mortality rates . The proK. alvarezii has been reported with anti-breast and anti-colorectal cancer potential. The anticancer activities were expressed with inhibitory concentration (IC50) value (\u00b5g/mL). An IC50 value of less than 100 is considered to indicate an active compound with anticancer properties. An ethanolic extract of K. alvarezii exhibited anticancer activity against human breast adenocarcinoma cell line MCF-7 with an IC50 of 75.7 \u00b5g/mL, while ethyl acetate and hexane extracts showed anti-colorectal cancer activity against human colorectal carcinoma cell line HCT-116 with IC50 values of 21.4 and 43.0 \u00b5g/mL, respectively [A solvent extract of ectively .E. denticulatum against Ehrlich carcinoma and Meth-A fibrosarcoma has been reported. Oral administration of the extract (1600 mg/kg b.w.) for 28 days resulted in the inhibition of Ehrlich carcinoma by 25% in tumor-implanted mice. Similarly, intraperitoneal administration of E. denticulatum extract (50 mg/kg b.w.) for 7 days resulted in the inhibition of Meth-A fibrosarcoma by 17% [H. durvelaei was investigated against four cancer cell lines . The results indicated that administration of H. durvelaei extracts reduced the growth of AGS and HT-29 cell lines by 27.17% and 1.47%, respectively [The antitumor activity of a by 17% . The antectively .C. lentillifera have been reported to show antitumor properties against human breast adenocarcinoma cell line MCF-7. Exposure to C. lentillifera oligosaccharides inhibited the growth of MCF-7 cells in a dose-dependent manner and induced apoptosis (triggered chromatin condensation and poly ADP-ribose polymerase degradation) [Oligosaccharides obtained from adation) .C. racemosa have been reported to show antitumor activity in tumor-inoculated mice (H22 tumor). The results indicated that administration of C. racemosa polysaccharide fractions of different doses could significantly inhibit the H22 tumor. After 14 days of transplantation, the weight of tumors in mice without polysaccharide treatment increased to 1.02 g while the tumor weight in mice exposed to the polysaccharide at a dose of 100 mg/kg b.w./day by routine oral passage decreased to 0.47 g, and the tumor inhibition rate reached 53.9% [Polysaccharide fractions (coded as CRP) obtained from ed 53.9% .D. dichotoma were tested against seven different cancer cell lines including HCT-116, MCF-7, HepG2, A-549, PC-3, HeLa, and CACO in 96-well plates. The extract and fractions were applied at concentrations ranging from 0.86 to 100 \u03bcg/mL. The results demonstrated that D. dichotoma extract and fractions displayed significant anticancer effects against several cancer cell lines in a dose-dependent manner but were generally more selective against MCF-7 and PC-3 cell lines. The chloroform fraction was the most effective in MCF-7, PC3, and CACO cells followed by the petroleum ether fraction against MCF-7 and PC-3 and the ethyl acetate fraction against HepG2 and CACO [A methanol extract and fractions of ctively) .S. polycystum at a concentration ranging from 25\u2013150 \u03bcg/mL has been reported against human breast adenocarcinoma cell line MCF-7 via cell viability assay. Treatment with the sulphated polysaccharides indicated the highest percentage of inhibition (90.4%) against the MCF-7 cell line at 150 \u03bcg/mL with an estimated IC50 of 50 \u03bcg/mL [S. polycystum polysaccharide induced apoptosis in colorectal cancer cell lines (HCT-15 cell) [The anticancer activity of sulphated polysaccharides (fucoidan) from 50 \u03bcg/mL . In anot15 cell) .The hypocholesterolemic effects of various marine algae and algal polysaccharides have been reported. The administration of extract significantly reduced serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and triglycerides (TG) ,20.K. alvarezii to the HCF diet dramatically decreased body weight (29.1%), LDL-C (49.3%), plasma TC (11.4%), TG (36.1%), plasma MDA level (10.7%), GSH-Px (13.49%), SOD (9.4%) and CAT (24.48%), and significantly increased HDL-C levels (55%), compared to rats fed the HCF diet only [After 16 weeks on high-cholesterol/high-fat (HCF) diets, male Sprague-Dawley rats weighing 260\u2013300 g had significantly higher body weight (b.w.), lipid peroxidation , end-product of lipid peroxidation), plasma low-density lipoprotein cholesterol (LDL-C), plasma total cholesterol (TC), plasma triglycerides (TG), erythrocyte glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) and catalase (CAT) levels. The addition of 5% iet only . E. denticulatum played a vital role in the reduction of fat absorption by the body via inhibition of pancreatic lipase [E. denticulatum extract at a concentration of 3.8 mg/mL showed pancreatic lipase activity inhibition with an 83% reduction [c lipase . Inhibitc lipase ,66. An Eeduction . C. lentillifera was reported to show anti-obesity and cardiovascular protection activity. Supplementation with 5% C. lentillifera extract for 16 weeks in HCF-diet rats reduced body weight by 39.5%, significantly increased HDL-C levels by 48.7%, reduced plasma TC by 18.4%, LDL-C by 34.6% and TG by 33.7%, and lowered plasma MDA level by 9%, GSH-Px by 31.8% and CAT by 3.14%, compared to the corresponding levels in high-cholesterol-diet rats [Treatment of HCF diet rats with iet rats . S. polycystum significantly reduced body weight gain, plasma antioxidant enzymes and plasma lipid peroxidation to levels closer to those of healthy rats. Supplementation with 5% S. polycystum in rats fed a high-fat diet reduced body weight by 42.6%, significantly increased HDL-C levels by 16.2%, reduced plasma TC by 11.4%, LDL-C by 22% and TG by 7.69%, and decreased the plasma MDA level by 6.8%, GSH-Px by 43.4% and CAT by 15.7%, as compared to the corresponding levels in hypercholesterolemia and hypertriglyceridemia rats [The exposure of induced-hypercholesterolemia and -hypertriglyceridemia rats to mia rats .Millions of people die each year as a result of hepatic diseases across the world ,68. The K. alvarezii ethanolic extract administered for 25 days against lead acetate-induced hepatic injury in mice has been investigated. The extract at a concentration of 800 mg/kg b.w. reduced AST, ALT and ALP levels by 15.79%, 18.52% and 16.11%, respectively, compared to lead acetate-treated mice . Mice administered with ethanol extract of K. alvarezii (800 mg/kg b.w.) also demonstrated a significant (p < 0.05) elevation in SOD and GPx levels by 45.94% and 18.78%, respectively, and a significant (p < 0.05) reduction in MDA level by 22.83%, compared with lead acetate-treated mice. Histological observations of mouse hepatic tissues treated with K. alvarezii ethanolic extract indicated improved hepatic cell structure, blood congestion, and fatty degeneration compared to lead acetate-treated mice [The hepatoprotective activity of ted mice .C. lentillifera demonstrated hepatoprotection against acetaminophen induced hepatic damage in juvenile zebrafish (aged 1\u20133 months). The administration of APAP to the control group at a concentration of 10 \u03bcM caused fish mortality; while the introduction of the methanol extract of C. lentillifera at concentrations of 10, 20 and 30 \u03bcg/l to tanks holding 10 \u03bcM APAP-treated groups reduced fish mortality. Histological observation by hematoxylin and eosin staining of zebrafish hepatic tissues exposed to 10 \u03bcM APAP and concurrently administered C. lentillifera extract indicated a reduction in hepatic necrosis, hepatocyte swelling, hepatocyte vacuolization and leukocyte infiltration in a dose-dependent manner, as compared to the control group treated solely with 10 \u03bcM APAP [A methanol extract of \u03bcM APAP .C. racemosa at a concentration of 200 mg/kg b.w. was administered for 30 days on a daily basis to 40% carbon tetrachloride (CCl4) induced hepatic fibrosis rats . Intoxicated rats treated with water extracts of C. racemosa showed significant (p < 0.05) decreases in their high levels of AST (46.7%), ALT (82.2%), ALP (41.3%), LDH (25.8%) and total bilirubin (69.6%), as compared to CCl4 treated control rats [An aqueous extract of rol rats . S. polycystum was examined in acetaminophen induced hepatic oxidative injured rats. The oral administration of S. polycystum extract in intoxicated rats at a concentration of 200 mg/kg b.w./day for 15 days reduced elevated levels of ALT (27.64%), AST (56.43%), LDH (43.38%), ALP (72.53%) and MDA (31.50%), compared to the levels in an APAP-administered control group [The protective effect of a solvent extract of ol group .Neuroprotection is a strategy for halting the progression of neurodegeneration . NeurodeK. alvarezii might be beneficial as a food supplement or medication for those who are prone to neurological disorders. In primary cultures of hippocampal neurons, the effects of K. alvarezii extracts on the development and complexity of neuronal cytoarchitecture were reported. A solvent extract of K. alvarezii with an optimal concentration of 1 \u03bcg/mL was added to primary cultures of fetal rat hippocampal neurons. The extract significantly elevated axonal length, number of secondary axonal collateral branches, length of primary dendrites and number of secondary dendritic branches by 58%, 8 folds, 68% and 2.6 folds, respectively, as compared to control [It was reported that an extract of control .D. dichotoma has been reported. A methanol extract of D. dichotoma at a concentration of 1.3\u20136.5 mg/mL showed significant (p < 0.05) inhibition of cholinesterase enzyme (54.42%), compared to standard donepezil (cholinesterase inhibitor) (57.57%) at a concentration of 0.40\u20134.15 mg/mL [Alzheimer\u2019s disease is a common neurologic disorder, responsible for brain shrinkage and cell death. It is the most prevalent type of dementia and one of the top four causes of mortality in developed countries . So far,15 mg/mL . C. racemosa and S. polycystum at various concentrations (0.0125\u20130.2 mg/mL) have been determined. Solvent extracts of C. racemosa and S. polycystum indicated anti-acetylcholinesterase activities with IC50 values ranging from 0.086\u20130.115 mg/mL, while C. racemosa extracts indicated anti-butyrylcholinesterase activity with an IC50 value of 0.156 mg/mL [The acetylcholinesterase and butyrylcholinesterase inhibitory activities of 56 mg/mL .A summary regarding the protective nature of the above-mentioned North Bornean seaweeds is shown in Seaweed nutraceutical bioactive compounds have great potential in biomedical and pharmaceutical applications ,90,91,92The information was retrieved from multiple internet databases such as ScienceDirect, PubMed, Wiley, ACS publications, etc., and registers including theses and proceedings. Records were searched with keywords related to seaweed, North Borneo, distribution, taxonomy, bioactivity, secondary metabolites, and diseases. Around 250 records approximately from the year 2000 to 2021 were retrieved and screened. Among these, about 100 records were excluded due to being out of the scope of the review. Eventually, a total of 149 records were adopted for the current review paper, and data from organizations such as the World Health Organization were included as well.K. alvarezii), eicosapentaenoic acid, palmitoleic acid, fucoxanthin, \u03b2-carotene (E. denticulatum), eucalyptol, oleic acid, dodecanal, pentadecane, (H. durvillaei), canthaxanthin, pentadecanoic acid, eicosane (C. lentillifera), pseudoephedrine, palmitic acid, monocaprin (C. racemosa), dictyohydroperoxide, squalene, fucosterol, saringosterol (D. dichotoma) and lutein, neophytadiene, cholest-4-en-3-one, and cis-vaccenic acid (S. polycystum). In the current review, the protective effects of North Bornean seaweeds in terms of anti-inflammatory, antioxidant, antimicrobial, anticancer, anti-obesity and cardiovascular protection, neuroprotection, and renal protection as well as hepatic protection were described and followed by nutraceutical profiling. The protective roles of the seaweeds might be due to the presence of a wide variety of nutraceuticals including phthalic anhydride, 3,4-ethylenedioxythiophene, 2-pentylthiophene, furoic acid (K. alvarezii and E. denticulatum are widely cultivated, developed as a functional food source, and used for carrageenans production. Locally, C. lentillifera and C. racemosa are also consumed as a nutrition source. For future perspectives, studies on functional food development and cultivation techniques are highly recommended. Furthermore, extensive studies on the seaweed isolates are needed to understand their bioactivity and mechanisms of action, while highlighting their commercialization potential.Despite their excellent pharmacological characteristics, only"} +{"text": "Increasing evidence emphasizes the implications of dysregulated apoptosis and autophagy cellular processes in coronary artery disease (CAD). Herein, we aimed to explore apoptosis- and autophagy-related long noncoding RNAs (lncRNAs) in peripheral blood of CAD patients. p value < 0.05, differentially expressed apoptosis- and autophagy-related mRNAs were screened between CAD and healthy blood samples. Also, differentially expressed lncRNAs were identified for CAD. Using the psych package, apoptosis- and autophagy-related lncRNAs were defined with Spearson's correlation analysis. Receiver operating characteristic (ROC) curves were conducted for the assessment of the diagnosed efficacy of these apoptosis- and autophagy-related lncRNAs. The mRNA and lncRNA expression profiles were retrieved from the Gene Expression Omnibus (GEO) database. With \u2223fold\u2009change | >1.5 and adjusted Our results showed that 24 apoptosis- and autophagy-related mRNAs were abnormally expressed in CAD than normal controls. 12 circulating upregulated and 1 downregulated apoptosis- and autophagy-related lncRNAs were identified for CAD. The ROCs confirmed that AC004485.3 (AUC = 0.899), AC004920.3 (AUC = 0.93), AJ006998.2 (AUC = 0.776), H19 (AUC = 0.943), RP5-902P8.10 (AUC = 0.956), RP5-1114G22.2 (AUC = 0.883), RP11-247A12.1 (AUC = 0.885), RP11-288L9.4 (AUC = 0.928), RP11-344B5.2 (AUC = 0.858), RP11-452C8.1 (AUC = 0.929), RP11-565A3.1 (AUC = 0.893), and XXbac-B33L19.4 (AUC = 0.932) exhibited good performance in differentiating CAD from healthy controls. Collectively, our findings proposed that circulating apoptosis- and autophagy-related lncRNAs could become underlying diagnostic markers for CAD in clinical practice. Coronary artery disease (CAD), as a commonly diagnosed heart disease, contributes to the dominant cause of cardiovascular-related deaths . This diApoptosis and autophagy, as two types of programmed cellular deaths, are both involved in the development of CAD . Undue ahttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) according to the following criteria: organism\u2014Homo sapiens; experiment type\u2014noncoding RNA profiling by array; and disease\u2014CAD. As a result, two datasets including GSE113079 and GSE69587 datasets were obtained for this study. The GSE113079 dataset included 93 CAD and 48 healthy blood samples based on the GPL20115 platform [The mRNA and lncRNA expression profiles of CAD patients and healthy controls were searched from the Gene Expression Omnibus | >1.5 and adjusted heatmaps .https://www.kegg.jp/) [Genes in autophagy (entry: map04140) and apoptosis (entry: map04210) were obtained from the Kyoto Encyclopedia of Genes and Genomes database . They wehttp://string-db.org/) [Physical or functional interactions between specified proteins were analyzed via the STRING online tool (db.org/) . Requiredb.org/) . Connectdb.org/) .p value < 0.05 with at least 50% of differentially expressed autophagy- and apoptosis-related mRNAs were considered as differentially expressed autophagy- and apoptosis-related lncRNAs.Spearson's correlation analysis between differentially expressed lncRNAs and differentially expressed autophagy- and apoptosis-related mRNAs was presented via the psych package in R. lncRNAs with correlation The expression of differentially expressed autophagy- and apoptosis-related lncRNAs was externally verified in blood samples from 5 CAD patients and 5 healthy controls in the GSE169256 dataset. Moreover, associations between their expression and clinical features (age) were analyzed by Spearson's correlation tests. Their expression was also compared between male and female patients.Based on the expression profiles of the differentially expressed autophagy- and apoptosis-related lncRNAs, relative operating characteristic curves (ROCs) were conducted via the pROC package in R in the GSE113079 dataset .To explore CAD-related mRNAs, we screened abnormally expressed mRNAs between 93 CAD and 48 healthy blood samples in the GSE113079 dataset. Firstly, we normalized the microarray data via the limma package Figures . 988 up-To find autophagy- and apoptosis-related mRNAs in CAD, we overlapped the abnormally expressed mRNAs and autophagy- and apoptosis-related mRNAs. As a result, 24 mRNAs were identified for CAD , as follCirculating lncRNAs have been considered as diagnosed biomarkers for CAD . Herein,Since the GSE69587 dataset has been standardized, this study no longer standardized the dataset. In total, 430 circulating lncRNAs were upregulated and 305 circulating lncRNAs were downregulated in CAD compared to healthy samples Figures . The topp < 0.05; p < 0.05). Meanwhile, JUN and ITPR3 had positive correlations with downregulated LOC338758 (both p < 0.05). Thus, these lncRNAs could be distinctly related to autophagy and apoptosis in CAD.We analyzed the correlation between 13 abnormally expressed circulating lncRNAs and autophagy- and apoptosis-related mRNAs. Herein, we found that PRKACA, PIK3R2, and NGF were positively related to the 12 upregulated lncRNAs , AJ006998.2 , H19 , RP11-247A12.1 , RP11-288L9.4 , RP11-344B5.2 , RP11-452C8.1 , RP11-565A3.1 , RP5-1114G22.2 , RP5-902P8.10 , and XXbac-B33L19.4 are as follows: AC004485.3 , and XXbac-B33L19.4 (AUC = 0.932) exhibited good performance to differentiate CAD from healthy controls. The above findings concerning circulating lncRNAs might possess effective diagnostic value on CAD, thereby reducing mortality. Among them, circulating H19 is correlated to risk of CAD among a Chinese cohort [On account of the shortcomings of current diagnostic markers on CAD, circulating lncRNAs appear to have attracted close attention. After verification, our data demonstrated that AC004485.3 (AUC = 0.899), AC004920.3 (AUC = 0.93), AJ006998.2 (AUC = 0.776), H19 (AUC = 0.943), RP5-902P8.10 (AUC = 0.956), RP5-1114G22.2 (AUC = 0.883), RP11-247A12.1 (AUC = 0.885), RP11-288L9.4 (AUC = 0.928), RP11-344B5.2 (AUC = 0.858), RP11-452C8.1 (AUC = 0.929), RP11-565A3.1 were distinctly upregulated in CAD compared to healthy controls. More importantly, they had good performance in distinguishing CAD from healthy individuals. Thus, these circulating lncRNAs could be promising diagnostic markers for CAD."} +{"text": "Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted For a long time, Antarctica was considered an inhospitable environment with low biodiversity. Although it is a part of Earth\u2019s cryosphere which covers about 20% of the Earth\u2019s surface , it has Bacteroidetes . Its mem05.2021) . In addic losses .Flavobacterium spp. in Antarctica is supported by their adaptation and coping mechanisms required for survival in harsh conditions including low temperatures, lack of nutrients or intense UV exposure, and freeze-thaw cycles that exert a strong evolutionary pressure on microbial cells . Microbiological sampling is conducted yearly on the James Ross Island (near the north-eastern extremity of the Antarctic Peninsula), Antarctica. Sampling is performed during the summer period when the majority of the island becomes an ice-free area. Antarctic summer season allows sampling of upper soil layers, permafrost, lakes and proglacial streams, which are all areas of intense microbial activities sampled during the years 2010\u20132019 for parallel testing and comparison purposes. All strains were routinely cultivated on R2A agar plates at 20\u00b0C for 48 hrs.The present study describes a taxonomic investigation of eight strains isolatedtivities . Flavoba010\u20132019 . Water s3. The 16S rRNA sequences were submitted to the EzBioCloud server software (v7.0) (Genomic DNA was extracted and purified using High Pure PCR Template Preparation Kit (Roche Diagnostics) according to the manufacturer\u2019s recommendations. The 16S rRNA genes were amplified and sequenced using universal bacterial primers pA (5\u2032-AGAGTTTGATCCTGGCTCAG-3\u2032) and pH (5\u2032-AAGGAGGTGATCCAGCCGCA-3\u2032) . PCR prod server for inite (v7.0) . The maxde novo genome assembly. The MismatchCorrector was run to reduce short indels and the number of mismatches. The read coverage cut-off value was automatically computed by the software resulting in contigs and scaffolds. Quality assessment was performed by the QUAST tool with 7 min of enzymatic fragmentation and final fragments length within the range of 550\u2013650 bp. Sequencing was performed on Illumina MiSeq platform with MiSeq Reagent Kit v2 (500-cycles) . The St. Petersburg genome assembler (SPAdes v3.11.1) was usedAST tool and BowtAST tool .Flavobacterium spp. The WGS data of type strains P4023T and P7388T were submitted to the Type Strain Genome server (TYGS) values were calculated using the ANI calculator on the Kostas Laboratory website5 using reciprocal best hits (two-way ANI) (6 (The whole genome sequence (WGS) data were analyzed for further confirmation of the taxonomic status of the analyzed strains and for comparison with genomes of related r (TYGS) and to tr (TYGS) . To furtpipeline with defway ANI) . Proteinway ANI) and subj ANI) 8 with CARD v3.1.1 database and Operdatabase , NCBI Badatabase , MEGAResdatabase and ARG-database . Furtherdatabase . The enzdatabase .T and P7388T, was also examined by transmission electron microscopy using a Morgagni 268D Philips (FEI Company) electron microscope.The colony morphology was determined on R2A agar after 48 h cultivation at 20\u00b0C. The cellular morphology of all strains was observed by light microscopy after Gram staining. The cellular morphology of the type strains, P40232PO4/0.1 M NaOH; pH 9.0\u201310.0, 0.1 M NaHCO3/0.1 M Na2CO3. The pH value of the TSB was confirmed after autoclaving.The growth at different temperatures and the salt tolerance were determined on R2A agar plates. The pH tolerance was assessed in Trypticase Soya Broth (TSB) inoculated with two drops of cell suspension of concentration as McFarland 2.0 with pH 5\u201310 at intervals of 1.0 pH unit at 20\u00b0C adjusted with the following buffer systems: pH 5.0\u20138.0, 0.1 M KHF. hercynium CCM 9054T, F. branchiicola CCM 9061T, F. chilense CCM 7940T, F. araucananum CCM 7939T, F. psychroterrae CCM 8827T and F. saccharophilum CCM 8770T were phenotypically characterized by the most relevant tests recommended for description of new taxa within the family Flavobacteriaceae (2S on Triple Sugar Iron Agar (HiMedia), hydrolysis of aesculin, starch , phosphoe (ONPG) , nitratee (ONPG) , utilizae (ONPG) and sodie (ONPG) . The pree (ONPG) .2, both on R2A agar plates. All above listed tests were inoculated using cells of analyzed strains grown on R2A agar at 20\u00b0C for 48 hrs. All tests were read daily for up to 7 days with exception of the tyrosine hydrolysis test (up to 10 days). The utilization of carbon sources, enzyme activities and other additional phenotypic characteristics were further tested using identification test kits GEN III MicroPlateTN (Biolog) with the protocol A, API 20 NE and API ZYM (bioM\u00e9rieux) according to the manufacturer\u2019s instructions.Capability of growth on different media was tested on R2A agar (Oxoid), Nutrient agar (Oxoid), Plate Count agar (Oxoid), Tryptone Soya agar (Oxoid), marine agar , MacConkIn vitro antimicrobial susceptibility was assessed using the disk diffusion method. Cell suspensions of concentration as 0.5 McFarland were prepared from cultures cultivated on R2A agar. Suspension containing each strain (100 \u03bcl) was spread on the Mueller-Hinton agar plates. Tested antibiotic disks were as follows: ampicillin (10 \u03bcg), aztreonam (30 \u03bcg), carbenicillin (100 \u03bcg), cefixime (5 \u03bcg), ceftazidime (10 \u03bcg), cephalotin (30 \u03bcg), ciprofloxacin (5 \u03bcg), gentamicin (10 \u03bcg), chloramphenicol (30 \u03bcg), imipenem (10 \u03bcg), kanamycin (30 \u03bcg), co-trimoxazole (25 \u03bcg), piperacillin (30 \u03bcg), polymyxin B (300 U), streptomycin (10 \u03bcg) and tetracycline (30 \u03bcg). CLSI and EUCAST standards were strictly followed for cultivation and inhibition zone diameter reading , F. hercynium DSM 18292T (98.54%) and F. chilense LMG 26360T (98.39%). A proposed type strain for the second cluster, P7388T, showed the highest sequence similarities to the F. branchiicola 59B-3-09T (99.12%), F. araucananum DSM 24704T (99.08%) and F. psychroterrae CCM 8827T (99.04%). The 16S rRNA gene sequence similarities of strain P4023T fell below the cut-off value 98.65%, whereas strain P7388T reached similarities above this threshold. Nevertheless, several studies have already proved that the standard 16S rRNA gene sequence cut-off value is not sufficient for some genera, such as Streptomyces, Streptococcus or Bacillus could not be assigned to a specific class of orthologous genes clusters (COGs) or with specific function . Howeverhnsoniae .T contained 112 scaffolds with a draft genome size of 4,387,206 bp and the genomic G + C content 34.5 mol% . Prediction of PULs found seven putative loci involved in degradation of carrageenan, dextran, hemicellulose, chitin, pectin, starch and xylan, which implies the ability of strain P7388T to degrade various polysaccharide substrates.Functional annotation revealed that 485 genes (12.97%) could not be assigned to any COGs or with specific function . The remT and P7388T. The analysis indicated that these strains harbor four (P4023T) and seven (P7388T) gene clusters potentially related to secondary metabolite production. Out of these, six clusters did not match any known BGCs deposited in the MIBiG database -non-ribosomal peptide synthetase (NRPS) BGC for strain P7388T that did not match any known BGCs , 3. ThisF. hercynium DSM 18292T, F. saccharophilum DSM 1811T and F. pectinovorum DSM 6368T. Genome-mining focused on cold-adaptation confirmed that Flavobacterium spp. are well adjusted to environmental stress and harbor a significant number of genes associated with cold-adaptation regardless of their thermotype , transcription termination/antitermination factor (nusA), translation initiation factors IF1 and IF2 , polynucleotide nucleotidyltransferase (pnp), heat-shock cognate proteins (hsc), recombinase A (recA) and many others , a member of family Flavobacteriaceae, was found to substantially increase tolerance to freezing and thus considered a primary response to ensure freeze-tolerance of its hosts , chromosomal replication initiation ATPase (dnaA), DNA topoisomerases IV , transcription antitermination factor (nusA), translation factors IF-1, 2, 3 along with other cold-inducible genes were present in all genomes in one copy, regardless of the thermotype (rpoD) and sigma factor 24 (rpoE) were present in genomes only in one and two copies, respectively, although psychrotrophic Flavobacterium spp. were previously found to harbor multiple copies of these genes , superoxide-dismutase and peroxidase , or thioredoxin and peroxiredoxin reductases . Although all analyzed strains harbored peroxiredoxin genes in multiple copies , strain P4023T harbored multiple copies of superoxide-dismutase (sodA) and thioredoxin (trxA), which may be explained by its isolation from surface rather than deeper soil layers and therefore exposed to higher oxidative stress and stronger UV radiation. Similarly versatile microorganisms to flavobacteria are pseudomonads that colonize diverse Antarctic areas including soils, fresh or marine waters by Pseudomonas extremaustralis 14-3T (Cold-adaptation is inseparably associated with oxidative stress response as a result of higher oxygen solubility at lower temperatures leading to increased levels of reactive oxygen species (ROS). Notably, e waters . Considee waters . Howeveris 14-3T . None ofT harbored a crtZ gene required for zeaxanthin biosynthesis is a membrane light-driven protein acting as an outward Hon pumps . Both th retinal . PRs wer retinal and inte retinal . Neverth. MED134 , which mFlavobacterium strains, since the type II CRISPR/Cas-system was found to be an adaptive immune system in other cold-adapted flavobacteria were predicted in the P4023T genome likely to provide resistance against 16 different drug classes (T genome (in vitro antibiotic susceptibility testing. Correlation between resistome predictions and in vitro testing was found for resistance to aminoglycosides which is presumably encoded by aadS gene (MBP4138141.1) in the genome of P7388T, a widely spread bacterial adenylyltransferase conferring resistance to aminoglycoside antibiotics (JOHN-1 present in P4023T (MBP4142760.1) and P7388T (MBP4137930.1) genomes. This gene provides resistance to a broad spectrum of \u03b2-lactam antibiotics in Flavobacterium johnsoniae (in vitro susceptibility results. Additive effects on resistance to \u03b2-lactam antibiotics may result from the presence of putative OXA beta-lactamase OXA-29 (MBP4140625.1) in P4023T, known to hydrolyze penams and cephalosporines but is not effective against carbapenems , ciprofloxacin (5 \u03bcg) and chloramphenicol (30 \u03bcg). Disagreement between the phenotypic susceptibility pattern and ARGs computational prediction is a well-known controversy, especially in clinical bacteriology (in vivo vs. in vitro), testing of single strain culture vs. biofilm formation, presence of specific metabolites and growth factors, presence of specific phages or inadequate time/concentration of tested antibiotics that induce expression of resistance genes. Any of above-mentioned factors or even their combination may be also responsible for discrepancies observed among analyzed Antarctic Flavobacterium isolates, in particular considering extreme environment they colonize and presence of phages in their genomes.Although routine screening did not find any resistance genes, RGI prediction of the resistome from draft genomes of P4023 classes . InactivT genome , they maibiotics . All Antibiotics . This wihnsoniae , howeverbapenems . Both steriology . There aT additionally harbors a putative rosA gene (MBP4140897.1) encoding an efflux pump/potassium antiporter system. This efflux transporter has been detected in marine Flavobacterium spp. (Bacteroidetes (rosA gene is related to polymyxin B resistance and represents a part of a two component efflux antiporter system (RosAB) found in Yersinia enterocolitica and confers resistance to cationic antimicrobial peptides including polymyxin B , which is a well-known environment with resistant bacteria . AlthougT and P7388T were aerobic, Gram-negative rods with rounded ends, with average cell size 0.4\u20130.6 \u03bcm \u00d7 1.2\u20132.4 \u03bcm and 0.3\u20130.4 \u03bcm \u00d7 1.5\u20133.0 \u03bcm, respectively , Summed Feature 3 (C16:1 \u03c97c/C16:1 \u03c96c) (9.9%), anteiso-C15:0 (9.8%), iso-C15:0 (9.3%) and iso-C16:0 3OH (9.3%). The major fatty acid of the group comprising strain P7388T were iso-C15:0 (23.4%), Summed Feature 3 (C16:1 \u03c97c/C16:1 \u03c96c) (9.9%), iso-C17:0 3OH (8.5%) and iso-C15:0 3OH (8.4%). The proposed species differ not only qualitatively and quantitatively in the profiles of major fatty acids, but also quantitatively in minor fatty acids, especially iso-C14:0, iso-C16:1 H and Summed Feature 9 (C16:0 10-methyl/iso-C17:1). The overall fatty acids profile of both groups is in agreement with the genus description ] and minor amounts of putrescine [0.7 \u03bcmol (g dry weight\u20131)] and spermidine [0.2 \u03bcmol (g dry weight\u20131)]. The polyamine pattern of strain P7388T was similar with the major polyamine sym-homospermidine [20.5 \u03bcmol (g dry weight\u20131)] and minor amounts of putrescine [0.2 \u03bcmol (g dry weight\u20131)] and spermidine [0.3 \u03bcmol (g dry weight\u20131)]. Quinone systems, polar lipid profile and polyamine pattern are well in agreement with the genus description .L-tyrosine agar. Negative for hydrolysis of Tween 80, aesculin, ONPG, starch, DNA, CMC and agar. Does not produce lecithinase. Does not produce H2S. Positive for arginine dihydrolase, and negative for ornithine and lysine decarboxylases. Does produce acid from glucose and maltose in aerobic conditions. Negative for production of acid from fructose and xylose in aerobic conditions. Positive for utilization of glucose and maltose by API 20 NE. Negative for utilization of arabinose, mannose, N-acetylglucosamine, gluconic acid, capric acid, adipic acid, malic acid, citric acid and phenylacetic acid by API 20 NE. Positive for alkaline phosphatase, leucine arylamidase, valine arylamidase and acid phosphatase by API ZYM. Negative for esterase (C 4), esterase lipase (C 8), lipase (C 14), cystine arylamidase, trypsin, \u03b1-chymotrypsin, naphtol-AS-BI-phosphohydrolase, \u03b1-galactosidase, \u03b2-galactosidase, \u03b2-glucuronidase, \u03b1-glucosidase, \u03b2-glucosidase, N-acetyl-\u03b2-glucosaminidase, \u03b1-mannosidase, and \u03b1-fucosidase by API ZYM. Carbon source utilization ability via respiration determined by Biolog GEN III MicroPlate test panels is positive for D-maltose, \u03b1-D-glucose, D-glucose-6-PO4, gelatine, L-arginine, L-aspartic acid, L-glutamic acid, acetoacetic acid and acetic acid. Negative for D-trehalose, D-cellobiose, gentiobiose, sucrose, stachyose, D-raffinose, \u03b1-D-lactose, D-melibiose, \u03b2-methyl-D-glucoside, D-salicin, N-acetyl-\u03b2-D-mannosamine, N-acetyl neuraminic acid, D-mannose, D-fructose, D-galactose, 3-methyl glucose, D-fucose, L-fucose, L-rhamnose, inosine, D-sorbitol, D-mannitol, D-arabitol, myo-inositol, glycerol, D-fructose-6-PO4, D-aspartic acid, D-serine, L-alanine, L-histidine, L-pyroglutamic acid, L-serine, D-galacturonic acid, D-galactonic acid lactone, D-gluconic acid, D-glucuronic acid, glucuronamide, mucic acid, quinic acid, D-saccharic acid, p-hydroxy phenylacetic acid, methyl pyruvate, D-lactic acid methyl ester, L-lactic acid, citric acid, \u03b1-keto glutaric acid, D-malic acid, L-malic acid, bromo-succinic acid, Tween 40, \u03b3-amino-butyric acid, \u03b1-hydroxy-butyric acid, \u03b2-hydroxy-D,L-butyric acid, \u03b1-keto butyric acid, propionic acid and formic acid.Cells are Gram-stain-negative rods with rounded ends, cell size in range 0.4\u20130.6 \u03bcm \u00d7 1.2\u20132.4 \u03bcm, cells occurring in irregular clusters, occasionally singly or in pairs. Endospores are not formed. Does not produce a capsule. Negative for presence of flexirubin-type pigments. Does not adhere to agar. Yellowish colonies. Motile with gliding-activity. Catalase and oxidase positive. Growth occurs on R2A, PCA, TSA, marine agar NA, blood agar with 5% sheep blood, BHI, Mueller-Hinton and Endo agar. Does not grow on MacConkey agar. Grows in pH range 6\u20139 and temperature range 1\u201330\u00b0C with optimum growth at 20\u00b0C and pH around 7. Cells grow well in presence of 1% NaCl, and 2% NaCl inhibits growth. Does grow in microaerophilic conditions but growth in anoxic conditions is limited. Does not produce fluorescein on King B medium. No utilization of Simmon\u2019s citrate, malonate and acetamide. Negative for reduction of nitrates and nitrites. Negative for production of urease and indole. Positive for hydrolysis of gelatine, casein, and tyrosine. Does not produce brown diffusible pigment on 15:1 \u03c96c, Summed Feature 3 (C16:1 \u03c97c/ C16:1 \u03c96c), anteiso-C15:0, iso-C15:0 and iso-C16:0 3OH. Major respiratory quinone is MK-6 and major polyamine is sym-homospermidine. Polar lipid profile contains major amounts of phosphatidylethanolamine, an ornithine lipid, and two unidentified lipids lacking a functional group, moderate amounts of unidentified lipid L1, unidentified glycolipid GL, minor amounts of an unidentified aminophospholipid (APL), and two unidentified lipids . The DNA G + C content of the type strain is 31.2 mol%.The major fatty acids are iso-CT (= CCM 9062T = LMG 31963T) was isolated in 2011 from the organic material of an abandoned bird nest located at the Lachman Cape . All characteristics listed in the species description are shared by all strains, except for the following strain-dependent test results: motility, production of acid from mannitol, and variable results observed by Biolog GEN III MicroPlate were utilization of dextrin, D-turanose, N-acetyl-D-glucosamine, glycyl-L-proline and pectin. A formal proposal of the species \u201cFlavobacterium flabelliforme sp. nov.\u201d is given in Type strain P4023Flavobacterium flabelliforme sp. nov. P4023T are MW691162 and JAGFBU000000000, respectively.The GenBank/EMBL/DDBJ accession numbers for the near full length 16S rRNA gene sequences and whole genome sequences for Flavobacterium geliluteum .L-tyrosine agar. Negative for hydrolysis of DNA and agar. Does not produce lecithinase. Does not produce H2S. Positive for arginine dihydrolase and negative for ornithine and lysine decarboxylases. Does produce acid from glucose, maltose and xylose in aerobic conditions. Negative for production of acid from mannitol in aerobic conditions. Positive for utilization of glucose, arabinose, mannose, N-acetyl-glucosamine, maltose, and hydrolysis of aesculin by API 20 NE. Negative for utilization of gluconic acid, capric acid, adipic acid, malic acid, citric acid and phenylacetic acid by API 20 NE. Positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, naphtol-AS-BI-phosphohydrolase and \u03b2-glucosidase by API ZYM. Negative for esterase (C 4), esterase lipase (C 8), lipase (C 14), valine arylamidase, cystine arylamidase, trypsin, \u03b1-chymotrypsin, \u03b1-galactosidase, \u03b2-galactosidase, \u03b2-glucuronidase, N-acetyl-\u03b2-glucosaminidase, \u03b1-mannosidase and \u03b1-fucosidase by API ZYM. Carbon source utilization ability via respiration determined by Biolog GEN III MicroPlate test panels is positive for D-trehalose, D-cellobiose, gentiobiose, N-acetyl-D-glucosamine, N-acetyl-D-galactosamine, \u03b1-D-glucose, D-mannose, D-glucose-6-PO4, glycyl-L-proline, L-aspartic acid, L-glutamic acid, D-galacturonic acid, acetoacetic acid and acetic acid. Negative for sucrose, stachyose, D-raffinose, \u03b1-D-lactose, D-melibiose, N-acetyl-\u03b2-D-mannosamine, N-acetyl neuraminic acid, 3-methyl glucose, D-fucose, L-fucose, L-rhamnose, inosine, D-sorbitol, D-mannitol, D-arabitol, myo-inositol, glycerol, D-aspartic acid, D-serine, L-alanine, D-gluconic acid, D-glucuronic acid, glucuronamide, D-saccharic acid, quinic acid, p-hydroxy phenylacetic acid, L-lactic acid, \u03b1-keto glutaric acid, D-malic acid, L-malic acid, bromo-succinic acid, \u03b3-amino-butyric acid, \u03b1-hydroxy-butyric acid, \u03b2-hydroxy-D,L-butyric acid, \u03b1-keto butyric acid, propionic acid, and formic acid.Cells are Gram-stain-negative rods with rounded ends, cell size in range 0.3\u20130.4 \u03bcm \u00d7 1.5\u20133.0 \u03bcm, occurring singly and in irregular clusters, occasionally in pairs. Endospores are not formed. Does not produce a capsule. Dark yellow to orange pigmented colonies. Flexirubin-type pigment present. Does not adhere to agar. Motile with gliding-activity. Catalase positive. Oxidase negative. Growth occurs on R2A, PCA, TSA, NA, blood agar with 5% sheep blood, BHI and Mueller-Hinton agar. Does not grow on marine and MacConkey agar. Grows in pH range 6\u20138 and temperature range 15\u201330\u00b0C with optimum growth at 20\u00b0C and pH around 7. Cells grow in presence of 0.5% NaCl, and 1% NaCl inhibits growth. Does grow in microaerophilic conditions but growth in anoxic conditions is limited. Does not produce fluorescein on King B medium. No utilization of Simmon\u2019s citrate, malonate and acetamide. Negative for reduction of nitrates and nitrites. Negative for production of urease and indole. Positive for hydrolysis of gelatine, aesculin, ONPG, starch, casein, tyrosine and CMC. Does not produce brown diffusible pigment on 15:0, Summed Feature 3 (C16:1 \u03c97c/C16:1 \u03c96c), iso-C17:0 3OH and iso-C15:0 3OH. Major respiratory quinone is menaquinone MK-6 and major polyamine is sym-homospermidine. Polar lipid profile contains major lipids phosphatidylethanolamine, an ornithine lipid, two unidentified lipids lacking a functional group , moderate amounts of unidentified lipid L1, minor amounts of lipids L2 and L6 and an unidentified glycolipid (GL). The DNA G + C content of the type strain is 34.5 mol%.The major fatty acids are iso-CT (= CCM 9064T = LMG 31962T) was isolated from water samples taken in 2016 from a small temporary lake . All characteristics listed in the species description are shared by all strains, except for the following strain-dependent test results: growth at 5 and 10\u00b0C, growth on Endo agar, hydrolysis of Tween 80, production of acid from fructose, presence of \u03b1-glucosidase in API ZYM and variable results observed by Biolog GEN III MicroPlate were utilization of dextrin, D-maltose, pectin, \u03b2-methyl-D-glucoside, D-salicin, D-fructose, D-galactose, D-fructose-6-PO4, gelatine, L-arginine, D-galactonic acid lactone, mucic acid, methyl pyruvate, D-lactic acid methyl ester, citric acid and Tween 40. A formal proposal of the species \u201cFlavobacterium geliluteum sp. nov.\u201d is given in Type strain P7388Flavobacterium geliluteum sp. nov. P7388T are MW691150 and JAGFBV000000000, respectively.The GenBank/EMBL/DDBJ accession numbers for the near full length 16S rRNA gene sequences and whole genome sequences for https://www.ncbi.nlm.nih.gov/genbank/, MW691162; https://www.ncbi.nlm.nih.gov/genbank/, JAGFBU000000000; https://www.ncbi.nlm.nih.gov/genbank/, MW691150; https://www.ncbi.nlm.nih.gov/genbank/, JAGFBV000000000.The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: SK performed phylogenetic, phylogenomic, genomic analysis, analysis of fatty acid-methyl esters, and drafted and finalized the manuscript. H-JB performed chemotaxonomic analyses of polar lipids, menaquinones, and polyamines. MB was responsible for whole-genome sequencing. MS-P was involved in genomic analysis of biosynthetic potential. MN was involved in genome assembly and quality of WGS data. DK performed electron microscopy. ES and IS performed morphological, physiological, and biochemical characterization including antibiotic susceptibility. SK drafted the manuscript with inputs of H-JB, MB, MS-P, and IS. All authors edited the draft manuscript and agreed to the final manuscript version for submission.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Investigation of the frequencies of functionally signif icant gene variants in the context of medical biology and gene geography is a relevant issue for studying the genetic structure of human populations. The transition from a traditional to an urbanized lifestyle leads to a higher incidence of civilizational diseases associated with metabolic disorders, including type 2 diabetes mellitus. The goal of the present paper is to analyze the frequencies of functionally signif icant gene alleles in the metabolic prof iles of indigenous Siberian peoples to identify the gene pool resilience, evaluate the susceptibility of various ethnic groups to metabolic disorders under changing environmental conditions, and predict the epidemiological situation that may occur in the near future. The study was performed in the monoethnic samples of eastern and western Buryats, Teleuts, Dolgans, and two territorial groups of Yakuts. A real-time PCR was used to determine the frequencies of single nucleotide polymorphisms (SNPs) G103894T, rs12255372, and C53341T, rs7903146 in the TCF7L2 gene. The results obtained were compared to the frequencies identif ied for Russians from Eastern Siberia and the values available in the literature. The frequencies of the polymorphic variants studied in the samples from the indigenous Siberian peoples place them in between Caucasian and East Asian populations, following the geographicgradient of polymorphism distribution. A signif icantly lower occurrence of type 2 diabetes risk alleles TCF7L2 (103894T)and TCF7L2 (53341T) in the samples of indigenous Siberian peoples compared to Russians was observed, which agreeswith their lower susceptibility to metabolic disorders compared to the newcomer Caucasian population. Taking intoaccount urbanization, a reduced growth in type 2 diabetes incidence may be predicted in indigenous Siberian peoples,i. e. Buryats, Yakuts, Dolgans, and Teleuts, compared to the newcomer Caucasian population. A further study of populationstructure with respect to different metabolic prof ile genes is required to better understand the molecular geneticfoundations of the adaptive potential of indigenous Siberian peoples Investigation into the peculiarities of the population geneticstructure of ethnic groups in the context of medical biologyand gene geography is a relevant issue in human genetics. Tobetter understand molecular genetic foundations of adaptivepotential that ethnic groups develop as they evolve under specificclimatic and geographic conditions and adapt to specificdietary patterns, it is important to analyze the frequencies ofthe candidate gene alleles proven to be functionally significantbased on studies in individual populations.Type 2 diabetes mellitus (DM2) is among the leading mortalityand disability factors in a working-age population . DM2 is a metabolic syndrome componentand above that is linked to increased risk of multiple associatedpathological states, primarily including cardiovasculardiseases andchronic renal failureIncretin hormone secretion defect, a key element of DM2pathogenesis, is associated with TCF7L2 gene polymorphismsince it is this gene\u2019s product that regulates the production ofpancreatic \u03b2-cells from pluripotent stem cells and is involvedin glucose-stimulated insulin secretion .In addition, the gene also targets the brain, where TCF7L2determines the intensity of the anorexigenic effect and affectsthe central glucose homeostasis mechanism . In the liver, the gene is involved in the regulationof triglycerides and low- and very low-density lipoproteinexchange. It is also involved in gluconeogenesis and acts asan insulin resistance mediator .It was found that SNPs G103894T, rs12255372, andC53341T, rs7903146 in introns 3 and 4 of gene TCF7L2were associated with DM2 . The linkof TCF7L2 (103894T ) and TCF7L2 (53341T ) alleles withincreased risk of DM2 was demonstrated in a number ofpopulations around the world, including Russia . It was shown that the TCF7L2 (53341T )variant was linked to increased risk of DM2 compared toTCF7L2 (103894T ), with homozygous alleles showing highersusceptibility to the disease than heterozygous ones The TCF7L2 polymorphisms are also linked to BMI, totalbody fat volume, as well as subcutaneous and visceral fat. TCF7L2 (53341T )allele is associated with the risk of myocardial ischemia andmyocardial infarction as syntropic diseases with commonpathogenetic elements . Gene TCF7L2 is also linked to renal embryogenesis,i. e. its polymorphisms are associated with variousdegrees of chronic renal failure, a vascular complication ofDM2 . It was proved that TCF7L2 polymorphism inloci rs7903146 and rs12255372 was associated with risks ofgastric, breast, and colorectal cancer . The effect of natural selectionon locus rs7903146 in gene TCF7L2 was discovered and astatistically significant link between 53341\u0422 allele frequencyand several climatic geographic factors was shown .Studies on the frequencies of gene alleles associated withthe risk of DM2 and other metabolic disorders in indigenousSiberian populations have remained relevant throughout therecent decade . However,the distribution of the polymorphic variants of functionallysignificant gene TCF7L2 in Siberian populations remainsunderstudied. Polymorphism frequencies in locus rs7903146for some Siberian peoples, including Buryats and Yakuts,were presented in . Unfortunately, theauthors did not indicate the area where genetic material wascollected, which seems necessary for these large heterogeneousethnic groups populating vast territoriesThe present paper reports the results of a study into thefrequencies of polymorphisms G103894T, rs12255372, andC53341T, rs7903146 in gene TCF7L2 associated with severaldiseases in the populations of indigenous Siberian ethnicgroups, namely Buryats, Teleuts, Yakuts and Dolgans, incomparison to Russians living in Siberia.The genetic material for the present research was collectedin the field in 2000\u20132006. Blood samples were taken fromapparently healthy volunteers under their informed consentand with the approval of the local healthcare authorities andthe Ethics Committee of the Institute of Cytology and Genetics,SB RAS. Before blood sampling, all volunteers filled ina special demographic questionnaire to specify their ancestors\u2019nationalities down to 3 to 4 generations.The data obtained were used to form 7 population samplescovering Southern and Eastern Siberia. Persons of Buryatnationality with no outsider ancestors living in Alkhanay andOrlovsky settlements in the Aginsky Buryat Okrug (ABO) ofZabaykalsky Krai were included in the Eastern Buryat group (N = 132). Ethnic Buryats from settlements of Ekhirit-BulagatskyDistrict of Ust-Ordynsky Buryat Okrug (UOB) ofthe Irkutsk Region (N = 278) were included in the Westernsample. Also included in the study were Teleuts from the BelovoDistrict of the Kemerovo Region (N = 116). Two ethni-callyhomogeneous samples of Yakuts were formed as follows:the Nyurbinsky group included the residents of settlementsNyurbachan and Syultsy of the Nyurbinsky District(N = 109), and the Ust-Aldansky group \u2013 the residents of theDyupsya settlement of the Ust-Aldansky District (N = 100).The residents of the town of Dudinka and settlements Volochankaand Ust-Avam of the Taymyr Dolgan-Nenets Okrugof Krasnoyarsk Krai identifying as ethnic Dolgans were includedin the Dolgan sample (N = 180). The seventh samplecombined Russians from Zabaykalsky Krai and the IrkutskRegion (N = 133).DNA samples were isolated from the leukocyte fractionof venous blood using the BioSilica kits (Russia). Real-timeSNP genotyping in genes TCF7L2 and TCF7L2 was performed applyingcompeting TaqMan-probes complementary to polymorphicDNA segments. Primer and probe designs wereselected using the sequences available in the NCBI database(http://www.ncbi.nlm.nih.gov/) with UGENE and Oligo Analyzer software(Table 1).Amplification was performed in 25-\u03bcl final volume, themaster mix included 300 nM primers, 100 nM TaqMan probes,65 mM TrisHCl (\u0440\u041d 8.9), 16 mM (NH4)2SO4, 2.5 mM MgCl2,0.05 % Tween-20, 0.2 mM dNTP, 0.5\u201310 ng DNA, and 0.5 UTaq DNA polymerase . Reactionconditions were as follows: initial denaturation for 3 min at96 \u00b0\u0421 was followed by 46 cycles including denaturation at96 \u00b0\u0421 for 5 s, primer annealing, and extension at 61 \u00b0\u0421 for 30 s.Allele variant frequencies in the populations were determinedbased on observed genotype frequencies. The matchbetween empirically observed genotype frequency distributionand theoretically expected distribution at the Hardy\u2013Weinbergequilibrium was tested using Pearson\u2019s chi-squared (theequilibrium holds at p > 0.05). The statistical confidence ofallele frequency differences between the studied sampleswas evaluated using the chi-squared test with Yates continuitycorrection; the results were considered statisticallysignificant at p < 0.025 .Genotyping results for TCF7L2 and in samples of Buryats, Teleuts, Yakuts,Dolgans, and Russians from Eastern Siberia are presented inTable 2.The genotype distribution matched the Hardy\u2013Weinbergequilibrium for all polymorphic loci and samples. The frequenciesof alleles TCF7L2 (103894T ) and TCF7L2 (53341T ) inthe studied samples and some ethnic groups described in theliterature , as well as comparisonof populations , are presented in Tables 3\u20134.It was shown that TCF7L2 (103894T ) allele frequency inthe Russians sample (23.1 %) matched that in other Caucasiangroups (22\u201337 %) . The frequencyin the studied samples of indigenous Siberian peoplesvaries from 5.4 % for Western Buryats to 9.5 % for Teleuts,with no statistically significant differences observed. However,the allele frequency in all samples of indigenous populationswas significantly lower than in Russians from Eastern Siberiaand other Caucasian groups described in the literature . At the same time, it was significantlyhigher than in several East Asian populations, i. e. Chinese andVietnamese. We could also see a significant difference betweenTeleuts and Japanese not observed for other studied groups.This in-between position of indigenous Siberian populations,as exemplified by Buryats and Teleuts, had been demonstratedearlier in the polymorphism frequencies of some other metabolicprofile genes .TCF7L2 (53341T ) allele frequency in the Russians sample(25.9 %) matched that in other Caucasian groups (23\u201340 %). The studied samples of indigenouspopulations showed a significantly lower value comparedto Russians varying from 4.5 % in Yakuts from the NyurbinskyDistrict to 11.3 % in Teleuts. Statistically significantdifferences were discovered between Teleuts and the sampleswith the lowest frequency values, namely Eastern Buryats(4.9 %) and Yakuts from the Nyurbinsky District. The data onTCF7L2 (53341T) allele frequency in the samples of Buryats(6.3 %) and Yakuts (4.3 %) resembling the results obtainedin our study were presented by Trifonova et al. (2020). Unfortunately,the authors did not indicate sample sizes and theparticipants\u2019 places of residence, so confidence evaluationwas impossible to perform. The frequency values do not show significant differences between the samples of Eastern Buryatsand Yakuts from the Nyurbinsky District and the samples ofindigenous East Asian populations, namely Chinese, Japaneseand Vietnamese, available in the literature. Yakuts from theUst-Aldansky District demonstrated a significantly higherTCF7L2 (53341T ) allele frequency than Vietnamese, whileDolgans showed differences compared to some Chinesepopulations as well. Western Buryats and Teleuts showedsignificantly higher allele frequencies than all the East Asiansamples described in the literature. It was also shown thatthis polymorphism frequency in populations of indigenousSiberian peoples was significantly lower than in the Caucasiangroups described in the literature . Thus, TCF7L2 (53341T ) allele frequencies also confirmthe trend that places samples of indigenous Siberianpeoples in-between East Asian and Caucasian populationsInvestigation of the frequencies of functionally significantgene variants in the context of medical biology and genegeographyis a relevant issue for studying the population geneticstructure of indigenous Siberian peoples. In the presentpaper, we have determined the frequencies of the 103894Tand 53341T alleles in gene TCF7L2 associated with DM2 andother metabolic disorders in the populations of Buryats, Yakuts,Dolgans, and Teleuts, as well as a sample of Russians fromEastern Siberia. It was shown that these frequencies in Russiansfall within the same range as in other Caucasian populations.Meanwhile, the populations of indigenous Siberianethnic groups show significantly lower TCF7L2 (103894T )and TCF7L2 (53341T ) polymorphism frequencies, whichplaces them in-between Caucasian and East Asian populations.It was shown in several papers that indigenous Siberian andFar Eastern ethnic groups, as well as the ethnic groups from theEuropean part of Russia with a mongoloid component in theirgene pool, had lower incidence rates of metabolic syndromeand its DM2 component compared to Caucasians .It is primarily explained by the traditional lifestyle implyinga sufficient amount of physical activity and diet consistingmostly of animal source foods rich in proteins and fats withlimited carbohydrate component .Ethnic peculiarities in DM2 prevalence and manifestationsare also caused by distinctions from the European gene pool,i. e. a unique combination of frequencies of functionallysignificant genes developed as a result of adaptation to localenvironmental conditions . Differences in living conditions between indigenousand newcomer populations are alleviated due to urbanization,centuries-long traditions, and acquired dietary patterns change,and, as a result, civilizational diseases associated with metabolicdisorders, including DM2, become increasingly commonin indigenous populations . Investigation ofthe polymorphism distribution of the functionally significantgenes associated with risks of diseases in indigenous Siberianpopulations makes it possible to identify the gene pool resilience,evaluate the susceptibility of various ethnic groups tometabolic disorders under changing environmental conditions,and predict the epidemiological situation in the near future.Lower prevalence of DM2 among indigenous Siberianpopulations agrees with reduced populational frequencies ofstudied alleles TCF7L2 (103894T ) and TCF7L2 (53341T )associated with DM2 and several syntropic diseases, discoveredin the present paper. The reduced frequencies ofthese polymorphisms may affect the incidence rates of thediseases in the studied populations. With urbanization takeninto account, one might predict reduced growth in incidencerates of DM2 and other pathological states associated withstudied polymorphisms in indigenous Siberian ethnic groupscompared to newcomer Caucasians.The high frequency of TCF7L2 (53341T ) polymorphismin Teleuts from the Kemerovo Region compared to Buryatsand Yakuts may be attributed to a Caucasian component thatthis ethnic group adopted in their gene pool in the process offormation . With more comfortableliving conditions close to cities of Prokopyevsk, Kemerovo,and Novokuznetsk and a richer European-type diet, Teleutsmay face an increased risk of DM2 and associated diseases.Increased incidence of cardiovascular diseases has been observedin this ethnic group in recent decades . However, polymorphism frequencies of otherfunctionally significant genes are to be investigated to drawbetter-grounded conclusions.Ethnic peculiarities in the frequency distribution of polymorphismsin gene TCF7L2 and in the populations of Buryats, Yakuts,Dolgans, and Teleuts, as well as a sample of Russians fromEastern Siberia, have been studied in the present paper. Locusrs12255372 has been studied in various territorial groups ofBuryats and Yakuts for the first time, and the same goes forloci rs12255372 and rs7903146 in the Dolgan and Teleutpopulations. It has been shown that the samples of indigenousSiberian populations fall in-between Caucasian and East Asianpopulations with respect to studied polymorphism frequencies,following the geographic polymorphism distributiongradient.Significantly lower occurrence of TCF7L2 (103894T ) andTCF7L2 (53341T ) alleles associated with DM2 and othermetabolic disorders in the samples of indigenous Siberianpeoples compared to Russians was demonstrated, which agreeswith their lower susceptibility to metabolic disorders, includingDM2, compared to the newcomer Caucasian populationdescribed in the literature. With the transition to urbanizedlifestyle taken into account, one might predict reduced growthin incidence rates of DM2 and other pathological states associatedwith the studied polymorphisms in indigenous Siberianethnic groups, namely Buryats, Yakuts, Dolgans, and Teleuts,compared to newcomer Caucasians.To better understand the nature of ethnic differences, furtherinvestigation into population structure with respect to othermetabolic profile genes is required.The authors declare no conflict of interest.Ametov A.S., Kamynina L.L., Akhmedova Z.G. The clinical aspectsof effectiveness of incretin therapy (Wnt-pathogenic path and polymorphismof gene TCF7L2). Rossiyskiy Meditsinskiy Zhurnal =Medical Journal of the Russian Federation. 2016;22(1):47-51. DOI10.18821/0869-2106-2016-22-1-47-51. (in Russian)Anjum N., Jehangir A., Liu Y. Two TCF7L2 variants associated withtype 2 diabetes in the Han nationality residents of China. J. Coll.Physicians Surg. Pak. 2018;28(10):794-797.Asfandiyarova N.S. A review of mortality in type 2 diabetes mellitus.Sakharnyi Diabet = Diabetes Mellitus. 2015;18(4):12-21. DOI10.14341/DM6846. (in Russian)Avzaletdinova D.S., Sharipova L.F., Kochetova O.V., Morugova T.V.,Erdman V.V., Somova R.S., Mustafina O.E. The association ofTCF7L2rs7903146 polymorphism with type 2 diabetes mellitusamong Tatars of Bashkortostan. Sakharnyi Diabet = Diabetes Mellitus.2016;19(2):119-124. DOI 10.14341/DM2004138-45. (in Russian)Bairova T.A., Dolgikh V.V., Kolesnikova L.I., Pervushina O.A. Nutriciogeneticsand risk factors of cardiovascular disease: associated researchin Eastern Siberia populations. Byulleten\u2019 VSNTs SO RAMN =Bulletin of the East Siberian Scientific Center SB RAMS. 2013;4(92):87-92. (in Russian)Baturin A.K., Sorokin\u0430 E.Yu., Pogozheva A.V., Keshabyants E.E., KobelkovaI.V., Kambarov A.O., Elizarova E.V., Tutelyan V.A. The associationof rs993609 polymorphisms of gene FTO and rs659366polymorphisms of gene UCP2 with obesity among Arctic Russianpopulation. Voprosy Pitaniya = Problems of Nutrition. 2017;86(3):32-39. (in Russian)Bennett C.N., Ross S.E., Longo K.A., Bajnok L., Hemati N., JohnsonK.W., Harrison S.D., MacDougald O.A. Regulation of Wntsignaling during adipogenesis. J. Biol. Chem. 2002;277(34):30998-31004. DOI 10.1074/jbc.M204527200.Bondar\u2019 I.A., Filipenko M.L., Shabel\u2019nikova O.Yu., Sokolova E.A.Rs7903146 variant of TCF7L2 gene and rs18012824 variant ofPPARG2 gene (Pro12Ala) are associated with type 2 diabetes mellitusin Novosibirsk population. Sakharnyi Diabet = Diabetes Mellitus.2013;4:17-22. DOI 10.14341/DM2013417-22. (in Russian)Cauchi S., El Achhab Y., Choquet H., Dina C., Krempler F., WeitgasserR., Nejjari C., Patsch W., Chikri M., Meyre D., Froguel P.TCF7L2 is reproducibly associated with type 2 diabetes in variousethnic groups: a global meta-analysis. J. Mol. Med. 2007;85(7):777-782. DOI 10.1007/s00109-007 0203-4.Cygankova D.P., Mulerova T.A., Ogarkov M.Yu., Saarela Ye.Yu., BarbarashO.L. Traditional lifestyle change as a reason for metabolicdisorders risk increase in residents of Gornaya Shoriya. ConsiliumMedicum. 2018;20(5):66-70. DOI 10.26442/2075-1753_2018.5. 66-71. (in Russian)Franceschini N., Shara N.M., Wang H., Voruganti V.S., Laston S.,Haack K., Lee E.T., Best L.G., MacCluer J.W., Cohran B., Dyer T.D., Howard B.V., Cole S.A., North K.E., Umans J.G. The association ofgenetic variants of type 2 diabetes with kidney function. Kidney Int.2012;82(2):220-225. DOI 10.1038/ki.2012.107.Hallmark B., Karafet T.M., Hsieh P.H., Osipova L.P., Watkins J.C.,Hammer M.F. Genomic evidence of local adaptation to climate anddiet in indigenous Siberians. Mol. Biol. Evol. 2018;36(2):315-327.DOI 10.1093/molbev/msy211.Han X., Luo Y., Ren Q., Zhang X., Wang F., Sun X., Zhou X., Ji L.Implication of genetic variants near SLC30A8, HHEX, CDKAL1,CDKN2A/B, IGF2BP2, FTO, TCF2, KCNQ1, and WFS1 in type 2diabetes in a Chinese population. BMC Med. Genet. 2010;11:81.DOI 10.1186/1471-2350-11-81.Haupt A., Thamer C., Heni M., Ketterer C., Machann J., Schick F.,Machicao F., Stefan N., Claussen C.D., H\u00e4ring H.U., Fritsche A.,Staiger H. Gene variants of TCF7L2 influence weight loss and bodycomposition during lifestyle intervention in a population at risk fortype 2 diabetes. Diabetes. 2010;59(3):747-750. DOI 10.2337/db09-1050.Ievleva K.D., Bairova T.A., Sheneman E.A., Ayurova Zh.G.,Bal\u2019zhieva V.V., Novikova E.A., Bugun O.V., Rychkova L.V.,Kolesnikova L.I. The protective effect of the G-allele of PPARG2rs1801282 polymorphism against overweight and obesity in Mongoloidadolescents. Zhurnal Mediko-Biologicheskikh Issledovaniy =Journal of Medical and Biological Research. 2019;7(4):452-463.DOI 10.17238/issn2542-1298.2019.7.4.452. (in Russian)Katsoulis K., Paschou S.A., Hatzi E., Tigas S., Georgiou I., Tsatsoulis A.TCF7L2 gene variants predispose to the development of type 2diabetes mellitus among individuals with metabolic syndrome.Hormones(Athens). 2018;17(3):359-365. DOI 10.1007/s42000-018-0047-z.Kaya E.D., Ariko\u011flu H., Kayi\u015f S.A., \u00d6zt\u00fcrk O., G\u00f6nen M.S. Transcriptionfactor 7-like 2 (TCF7L2) gene polymorphisms are strong predictorsof type 2 diabetes among nonobese diabetics in the Turkishpopulation. Turk. J. Med. Sci. 2017;47(1):22-28. DOI 10.3906/sag-1507-160.Kichigin V.A., Kochemirova T.N., Akimova V.P. Ethnic peculiarities inprevalence of cardiovascular risk factors in urban population. ActaMedica Eurasica. 2017;4:16-23. (in Russian)Kurtanov Kh.A., Sydykova L.A., Pavlova N.I., Filippova N.P., DodokhovV.V., Apsolikhova G.A., Solov\u2019eva N.A., D\u2019yakonova A.T.,Neustroeva L.M., Varlamova M.A., Borisova N.V. Polymorphismof the adiponutrin gene (PNPLA3) in the indigenous inhabitantsof the Republic of Sakha (Yakutia) with type 2 diabetes mellitus.Al\u2019manakh Klinicheskoy Meditsiny = Almanac of Clinical Medicine.2018;46(3):258-263. DOI 10.18786/2072-0505-2018-46-3-258-263.(in Russian)Mel\u2019nikova E.S., Rymar O.D., Ivanova A.A., Mustafina S.V., ShapkinaM.Ju., Bobak M., Maljutina S.K., Voevoda M.I., MaximovV.N. Association of polymorphisms of genes TCF7L2, FABP2,KCNQ1, ADIPOQ with the prognosis of the development of type 2diabetes mellitus. Terapevticheskiy arkhiv = Therapeutic Archive.2020;92(10):40-47. DOI 10.26442/00403660.2020.10.000393. (inRussian)Melzer D., Murray A., Hurst A.J., Weedon M.N., Bandinelli S., CorsiA.M., Ferrucci L., Paolisso G., Guralnik J.M., Frayling T.M.Effects of the diabetes linked TCF7L2 polymorphism in a representativeolder population. BMC Med. 2006;4:34. DOI 10.1186/1741-7015-4-34.Nobrega M.A. TCF7L2 and glucose metabolism: time to look beyondthe pancreas. Diabetes. 2013;62(3):706-708. DOI 10.2337/db12-1418.Orlov P.S., Kulikov I.V., Ustinov S.N., Gafarov V.V., Malyutina S.K.,Romashchenko A.G., Voyevoda M.I., Maksimov V.N. Associationanalysis of some single nucleotide polymorphism markers of thesecond type of diabetes with myocardial infarction. Byulleten\u2019 SORAMN = Bulletin of Siberian Branch of Russian Academy of MedicalSciences. 2011;31(5):19-24. (in Russian)Ostaptseva A.V., Shabaldin A.V., Akhmatianova V.R., Minina V.I.,Glushkov A.N., Druzhinin V.G., Zorkoltseva I.V., Shabaldin E.V.,Glushkova O.A., Makarchenko O.S., Ageyeva T.N. Molecular geneticanalysis of interleukin 4 gene polymorphism among Teleutians,Shorians, and Caucasians of Kemerovo region. MeditsinskayaImmunologiya = Medical Immunology. 2006;8(5-6):737-740. (inRussian)Ovsyannikova O.V., Podkhomutnikov V.M., Kolbasko A.V., LuzinaF.A., Gus\u2019kova E.V. Cardiovascular disease in rural Kuzbass aborigines\u2013 Teleut. Rossiyskiy Kardiologicheskiy Zhurnal = RussianJournal of Cardiology. 2007;6:59-62. (in Russian)Potapov V.A., Nosikov V.V., Shamkhalova M.N., Shestakova M.V., SmetaninaS.A., Bel\u2019chikova L.N., Suplotova L.A. TCF7L2 rs12255372and SLC30A8 rs13266634 confer susceptibility to type 2 diabetes ina Russian population. Russ. J. Genet. 2010;46(8):1001-1008. DOI10.1134/S1022795410080132.Rosales-Reynoso M.A., Arredondo-Valdez A.R., Ju\u00e1rez-V\u00e1zquez C.I.,Wence-Chavez L.I., Barros-N\u00fa\u00f1ez P., Gallegos-Arreola M.P., Flores-Mart\u00ednez S.E., Mor\u00e1n-Moguel M.C., S\u00e1nchez-Corona J. TCF7L2and CCND1 polymorphisms and its association with colorectal cancerin Mexican patients. Cell Mol. Biol. 2016;62(11):13-20. DOI10.14715/cmb/2016.62.11.3.Saxena R., Gianniny L., Burtt N.P., Lyssenko V., Giuducci C., Sj\u00f6grenM., Florez J.C., Almgren P., Isomaa B., Orho-Melander M.,Lindblad U., Daly M.J., Tuomi T., Hirschhorn J.N., Ardlie K.G.,Groop L.C., Altshuler D. Common single nucleotide polymorphismsin TCF7L2 are reproducibly associated with type 2 diabetes and reducethe insulin response to glucose in nondiabetic individuals. Diabetes.2006;55(10):2890-2895. DOI 10.2337/db06-0381.Sladek R., Rocheleau G., Rung J., Dina C., Shen L., Serre D., Boutin P.,Vincent D., Belisle A., Hadjadj S., Balkau B., Heude B., CharpentierG., Hudson T.J., Montpetit A., Pshezhetsky A.V., Prentki M.,Posner B.I., Balding D.J., Meyre D., Polychronakos C., Froguel P.A genome-wide association study identifies novel risk loci fortype 2 diabetes. Nature. 2007;445(7130):881-885. DOI 10.1038/nature05616.Smetanina S.A. Molecular-genetic and hormonal-metabolic associationsamong women of the Russian population of reproductive agewith obesity and early menarche. Meditsinskaya Nauka i ObrazovaniyeUrala = Medical Science and Education in Ural. 2015;2(1):126-129. (in Russian)Tabikhanova L.E., Osipova L.P., Voronina E.N., Bragin A.O., FilipenkoM.L. Polymorphism of lipid exchange genes in some populationsof South and East Siberia. Vavilovskii Zhurnal Genetiki i Selektsii =Vavilov Journal of Genetics and Breeding. 2019;23(8):1011-1019.DOI 10.18699/VJ19.578The 1000 Genomes Project Consortium. An integrated map of geneticvariation from 1,092 human genomes. Nature. 2012;491(7422):56-65. DOI 10.1038/nature11632.Timpson N.J., Lindgren C.M., Weedon M.N., Randall J., OuwehandW.H., Strachan D.P., Rayner N.W., Walker M., Hitman G.A.,Doney A.S., Palmer C.N., Morris A.D., Hattersley A.T., Zeggini E.,Frayling T.M., McCarthy M.I. Adiposity-related heterogeneity inpatterns of type 2 diabetes susceptibility observed in genome-wideassociation data. Diabetes. 2009;58(2):505-510. DOI 10.2337/db08-0906.Trifonova E.A., Popovich A.A., Bocharova A.V., Vagaitseva K.V.,Stepanov V.A. The role of natural selection in the formation of thegenetic structure of populations by SNP markers in association withbody mass index and obesity. Mol. Biol. 2020;54(3):349-360. DOI10.1134/S0026893320030176.Tsyretorova S.S., Bardymova T.P., Protasov K.V., Donirova O.S.,Mistyakov M.V. Ethnic features of diabetes mellitus and coronaryheart disease. Sibirskiy Meditsinskiy Zhurnal (Irkutsk) = SiberianMedical Journal (Irkutsk). 2015;136(5):15-21. (in Russian)Vikulova O.K., Zheleznyakova A.V., Lebedeva N.O., Nikitin A.G.,Nosikov V.V., Shestakova M.V. Genetic factors in the developmentof kidney chronic disease in patients with diabetes mellitus. Russ.J. Genet. 2017;53(4):420-432. DOI 10.1134/S1022795417030140.Xi B., Takeuchi F., Meirhaeghe A., Kato N., Chambers J.C., MorrisA.P., Cho Y.S., Zhang W., Mohlke K.L., Kooner J.S., Shu X.O.,Pan H., Tai E.S., Pan H., Wu J.Y., Zhou D., Chandak G.R., DIAGRAMConsortium, AGEN-T2D Consortium, SAT2D Consortium.Associations of genetic variants in/near body mass index-associatedgenes with type 2 diabetes: a systematic meta-analysis. Clin. Endocrinol.(Oxf .). 2014;81(5):702-710. DOI 10.1111/cen.12428.Zhang M., Tang M., Fang Y., Cui H., Chen S., Li J., Xiong H., Lu J.,Gu D., Zhang B. Cumulative evidence for relationships betweenmultiple variants in the VTI1A and TCF7L2 genes and cancer incidence.Int. J. Cancer. 2018;142(3):498-513. DOI 10.1002/ijc.31074."} +{"text": "Scientific Reports 10.1038/srep11362, published online 12 June 2015Retraction of: Fig. 1e HFD/p-Src lane 1 and 3;Fig. 4c NCD/Ve-cadherin lane 1 and 3Fig. 5e HFD+\u2009APN/ICAM-1 lane 1 and 2Fig. 5f HFD/beta-catenin lane 2 and HFD+\u2009APN/beta-catenin lane 1Fig. S1d HFD/beta-catenin all lanesFig. S4c NCD/beta-catenin lane 1 and 3.The Authors have retracted this Article. After publication of this Article, concerns have been raised about irregularities in the western blot data. In particular, the following bands appear to be duplicated:Additionally, the beta-catenin subpanel in Fig. 5f was subsequently reused in another study and descDilip Shah, Nadan Wang, Benjamin T. Suratt, Jianxin Sun, Ying Zhu, Kenneth Walsh and Ross Summer agree to this retraction. Freddy Romero, Bishnuhari Paudyal and Caleb B. Kallen have not responded to any correspondence from the editor or publisher about this retraction. The Publisher has not been able to obtain a current email address for Michelle Duong."} +{"text": "Scientific Reports 10.1038/s41598-021-84517-x, published online 04 March 2021Correction to: The original version of this Article contained an error in Reference 32, which was incorrectly given as:et al.\u00a0Exogenic basalt on asteroid (101955) Bennu.\u00a0Nat. Astron.\u00a0https://doi.org/10.1038/s41550-020-1195-z\u00a0(2020).DellaGiustina, D. N.\u00a0The correct reference is listed below:et al. Variations in color and reflectance on the surface of asteroid (101955) Bennu. Science370, abc3660. https://doi.org/10.1126/science.abc3660 (2020).DellaGiustina, D. N. The original Article has been corrected."} +{"text": "T and H16/1AT, of Gram-stain-positive, coagulase-negative staphylococci were isolated from separate healthy domestic dogs in Scotland. Both strains were genome sequenced and their inferred DNA\u2013DNA hybridisation indicates that H8/1T and H16/1AT represent two novel species of the genus Staphylococcus. On the basis of the results of genome sequence analysis H8/1T is most closely related to Staphylococcus devriesei and H16/1AT most closely related to Staphylococcus felis. Also, average nucleotide identity distinguished H8/1T and H16/1AT from S. devriesei and S. felis as did minor phenotypic differences. On the basis of these results, it is proposed that H8/1T and H16/1AT represent novel species with the respective names Staphylococcus caledonicus and Staphylococcus canis. The type strain of S. caledonicus is H8/1T (=NCTC 14452T=CCUG 74789T). The type strain of S. canis is H16/1AT (=NCTC 14451T=CCUG 74790T)Two strains, H8/1 Staphylococcus before plating onto mannitol salt agar (Oxoid) and then incubation at 37\u2009\u00b0C for 24\u2009h. Both isolates are Gram-stain-positive, catalase-positive cocci and were whole-genome sequenced using HiSeq technology (Illumina) with 2\u00d7250\u2009bp paired-end reads, read trimming and assembly . Reads were trimmed using Trimmomatic version 0.30 [de novo using SPAdes version 3.7 [https://tygs.dsmz.de/) [Staphylococcus. The TYGS phylogenetic tree generated by the Genome blast Distance Phylogeny approach (GBDP) indicated that H8/1T is most closely related to, but distinct from Staphylococcus devriesei CCUG 58238T with H16/1AT most closely related to, but distinct from Staphylococcus felis DSM 7377T values calculated with the Type (Strain) Genome Server using the recommended settings of the Genome-to-Genome Distance Calculator (GGDC) 2.1 [blast (ANIb) [S. caledonicus H8/1T with S. devriesei CCUG 58238T. Divergence between ANI and tetranucleotide signature correlation index has been described previously with a possible explanation being that evolutionary or environmental forces may impede modifications in this genome signature despite genetic drift occurring [Staphylococcus was generated using CSI Phylogeny 1.4 [Staphylococcus aureus DSM 20231T as the reference genome, this analysis produced a single-nucleotide polymorphism tree comprising 19637 nucleotide positions Genome Server (TYGS) (smz.de/) . The resSM 7377T . A 16S rS. felis . Althougparisons . Indeed,GDC) 2.1 and by At (ANIb) , MUMmer t (ANIb) and the t (ANIb) (Table 1t (ANIb) . With ont (ANIb) according to the manufacturer\u2019s instructions alongside the type strains of S. devriesei DSM 25293T and S. felis DSM 7377T and for DNAse activity using DNAse agar (Oxoid). In each case, both H8/1T and H16/1AT tested negative for these activities.Phenotypic characterisation of H8/1SM 7377T . H8/1T i. felis, . AdditioT and H16/1AT were susceptible to all the antimicrobials tested, which were as follows: amoxicillin/clavulanic acid, benzylpenicillin, cefovecin, cefoxitin (screen), ceftiofur, chloramphenicol, clindamycin, doxycycline, enrofloxacin, erythromycin, gentamicin, inducible clindamycin resistance, kanamycin, marbofloxacin, neomycin, nitrofurantoin, oxacillin, pradofloxacin, tetracycline and trimethoprim/sulfamethoxazole. No known antimicrobial resistance genes (perfect and strict hits) were identified in either H8/1T and H16/1AT on using The Comprehensive Antibiotic Resistance Database (CARD) (https://card.mcmaster.ca/) [Antimicrobial sensitivity testing was performed using the Vitek2 system (bioM\u00e9rieux) according to the manufacturer\u2019s instructions. Using the AST-GP80 card and applying the CLSI 2017 interpretations for coagulase-negative staphylococci, both H8/1ter.ca/) .Staphylococcus caledonicus , the country where the type strain was isolated).d-glucose, d-fructose, maltose, trehalose, d-mannitol and sucrose but not from d-mannose, lactose, xylitol, melibiose, raffinose, d-xylose, methyl \u03b1-d-glucopyranoside or N-acetylglucosamine. Has arginine dihydrolase activity and is able to reduce nitrates to nitrites. Catalase-positive and negative for clumping factor, coagulase and DNAse.Gram-stain-positive, non-spore forming, facultative anaerobe, forms non-pigmented, smooth, circular colonies about 1\u20132\u2009mm in diameter with entire margins on Columbia horse blood agar after 18\u2009h incubation at 37\u2009\u00b0C. Able to produce acid from S. caledonicus, H8/1T (=NCTC 14452 T=CCUG 74789T), was isolated from a healthy dog in Scotland during 2018. The draft genome of H8/1T is 2\u200a503\u200a367 bases in length with a DNA G+C\u2009content of 33.6\u2009mol%, it comprises 38 contigs with an average coverage of approximately 85-fold. The genome sequence data from H8/1T is available under these accession numbers: BioSample, SAMN15065541; Sequence Read Archive, SRR11909362; and assembly, JABTXV000000000.The type strain of Staphylococcus canis .d-glucose, d-fructose, d-mannose, maltose, lactose, trehalose and d-mannitol but not from xylitol, melibiose, raffinose, d-xylose, sucrose or methyl \u03b1-d-glucopyranoside. Has alkaline phosphatase and urease activity and is able to reduce nitrates to nitrites. Catalase-positive and negative for clumping factor, coagulase and DNAse.Gram-stain-positive, non-spore forming, facultative anaerobe, forms non-pigmented, smooth, circular colonies about 1\u20132\u2009mm in diameter with entire margins on Columbia horse blood agar after 18\u2009h incubation at 37\u2009\u00b0C. Able to produce acid from Staphylococcus canis, H16/1AT (=NCTC 14451T=CCUG 74790T), was isolated from a healthy dog in Scotland during 2018. The draft genome of H16/1AT is 2\u200a229\u200a149 bases in length with a DNA G+C\u2009content of 34.8\u2009mol%, it comprises 143 contigs with an average coverage of approximately 92-fold. The genome sequence data from Staphylococcus canis H16/1AT is available under these accession numbers: BioSample, SAMN14548534; Sequence Read Archive, SRR11498036; and assembly, JABANU000000000.The type strain of Click here for additional data file."} +{"text": "None showed focal spasm that exclusively involved DCB-treated lesions. Among 27 patients with vasospastic features, DCB-treated segments showed less vasoconstriction than spastic counterparts (p < 0.001). A total of 110 DCB-treated lesions were analyzed to assess vasomotor function. Vasomotor function, defined as a combined constrictor and dilator response, was comparable between DCB-treated and angiographically normal segments (p = 0.173), while significant differences were observed against spastic counterparts (p < 0.001). In our study, DCB-treated lesions were not particularly vulnerable to vasospasm and were found to have vasomotor function similar to angiographically normal segments, supporting safety of DCB-only strategy in treating de novo native coronary lesions.Balloon-injured coronary segments are known to harbor abnormal vasomotion. We evaluated whether de novo coronary lesions treated using drug-coated balloon (DCB) are prone to vasospasm and how they respond to ergonovine and nitrate. Among 132 DCB angioplasty recipients followed, 89 patients underwent ergonovine provocation test at 6\u20139 months follow-up. Within-subject ergonovine- and nitrate-induced diameter changes were compared among three different sites: DCB-treated vs. angiographically normal vs. segment showing prominent vasoreactivity (spastic). No patient experienced clinically refractory vasospastic angina or symptom-driven revascularization during follow-up. Ergonovine induced vasospasm in seven patients; all were multifocal spasm either involving ( Drug-coated balloon (DCB) angioplasty is an emerging treatment approach for obstructive coronary artery disease (CAD). It has demonstrated its safety and efficacy in the treatment of in-stent restenosis and small vessel CAD and, currently, many on-going trials are exploring its value in a broader range of lesions ,2,3. ThePercutaneous transluminal coronary angioplasty (PTCA), including plain old balloon angioplasty (POBA) or stenting, unavoidably results in significant vascular injury, leading to a variety of deleterious consequences, such as dissection, thrombus formation, impairment of physiologic vasomotion, and restenosis . In partThis prospective all-comers study evaluated all patients with significant CAD who received percutaneous coronary intervention (PCI) with DCB-only angioplasty, concomitant DCB angioplasty and POBA, or concomitant DCB angioplasty and drug-eluting stent (DES) implantation for de novo lesions in the native coronary arteries at the Korea University Ansan Hospital between July 2019 and December 2020. The patients with a life expectancy shorter than 2 years and those who refused to provide their consent were excluded. DCB angioplasty was performed in accordance with the recent recommendations . SpecifiThe presence of significant vasospasm and coronary artery vasomotor function were assessed via intracoronary injection of ergonovine and isosorbide dinitrate . All par-Constrictor response (%): after ergonovine administration\u2014MLD after nitrate administration)/MLD after nitrate administration \u00d7 100-Dilator response (%): (MLD after nitrate administration\u2014MLD at baseline)/MLD at baseline \u00d7 100Coronary spasm was defined as transient, total, or near-total occlusion (>90%) of a coronary artery as recommended . Spasm wThe reference vessel diameter (RVD), measured at the proximal and distal portions of each segment of interest, was used to calculate the diameter stenosis (DS) for quantitative comparative analysis. Segments with a percent change of >50% after the ergonovine provocation test were considered to have significant vasoconstriction, and patients who had at least one or more coronary segments showing significant vasoconstriction (>50%) were considered to have vasospastic features.Vasomotor response to ergonovine and isosorbide dinitrate was compared among three different segments: DCB-treated segments, angiographically normal arterial segments (control), and segments showing prominent vasoconstrictive response to ergonovine (spastic) . The cont-test. Ergonovine-induced percent diameter changes (constrictor response) between DCB-treated vs. spastic segments were compared using paired t-test or Wilcoxon signed-rank test based on normality test. Differences in combined constrictor and dilator responses across the three segments were analyzed using general linear model two-way repeated measures analysis of variance (ANOVA). Repeated measures ANOVA incorporated the Bonferroni test for pair-wise comparison. Statistical analyses were performed using the SPSS software . Statistical significance was set at p-values of <0.05.Continuous variables are expressed as means \u00b1 standard deviations and dichotomous variables as counts and percentages. Differences in MLD between baseline and after drug administration were analyzed using a paired A total of 132 patients who underwent DCB angioplasty for de novo native coronary lesions were analyzed. Clinical characteristics of the study population is described in During the median follow-up period of 18.5 months, two patients underwent repeated PCI due to recurrent ACS; one patient presented with unstable angina due to a de novo stenotic lesion in the treated vessel (2 months post-PCI); and one patient presented with non-ST elevation myocardial infarction due to post-POBA restenosis of the proximal right coronary artery but whose DCB-treated proximal left anterior descending artery remained patent. Albeit asymptomatic, three patients underwent redo DCB angioplasty owing to post-DCB angioplasty restenosis and one patient underwent DCB angioplasty owing to a newly-developed lesion at the follow-up angiography. One patient complained a sublingual nitroglycerin-responsive, alcohol-related nocturnal chest pain during the follow-up. His symptom was controlled by prescribing calcium channel blocker and oral nitrates, and he later showed ergonovine-induced multifocal vasospasm at the follow-up angiography . In summAmong 132 enrollees, patients who underwent 6\u20139 months of follow-up invasive coronary angiography and those excluded for the ergonovine provocation test are summarized in the CONSORT flow diagram in p = 0.069; DS (%): 27.64 \u00b1 10.07 vs. 31.46 \u00b1 13.64, p = 0.498]. However, ergonovine-induced constrictor response (%) was significantly lower in the DCB-treated segments than in the spastic segments : 24.19 \u00b1 0.97 vs. 24.66 \u00b1 12.53, p = 0.845).In seven patients with documented vasospasm, RVD and DS were similar between eight DCB-treated segments and their spastic counterparts [DCB-treated vs. spastic: RVD (mm): 2.98 \u00b1 0.56 vs. 2.61 \u00b1 0.37, p < 0.001; DS (%): 12.72 \u00b1 7.14 vs. 24.21 \u00b1 8.59 vs. 17.56 \u00b1 10.45, p < 0.001). DCB-treated segments showed similar RVD (p > 0.999), but greater DS compared to spastic segments (p < 0.001).A total of 274 segments from 82 patients were analyzed after excluding those from seven vasospasm cases. Angiographic characteristics of the analyzed segments are presented in p < 0.001; DCB-treated: 1.90 \u00b1 0.42 vs. 1.58 \u00b1 0.41, p < 0.001; spastic: 1.94 \u00b1 0.46 vs. 1.37\u00b1 0.44, p < 0.001, p < 0.001; DCB-treated: 1.90 \u00b1 0.42 vs. 2.06 \u00b1 0.40, p < 0.001; spastic: 1.94 \u00b1 0.46 vs. 2.22 \u00b1 0.47, p < 0.001, After ergonovine administration, most segments showed significant constriction [MLD (mm): baseline vs. ergonovine: control: 2.54 \u00b1 0.57 vs. 2.20 \u00b1 0.57, Intriguingly, some DCB-treated segments were found to be unaffected by ergonovine. 35.5% (39 out of 110) of DCB-treated segments had a diameter of at least 20% greater than the adjacent arterial portions after ergonovine administration . These cp < 0.001, p = 0.173), while these were significantly greater in the spastic segments than in the DCB-treated and control segments (control vs. spastic: p < 0.001; DCB-treated vs. spastic: p < 0.001, Vasomotor function, as comprehensively assessed as a combined constrictor and dilator response, was analyzed using repeated measure ANOVA. Within-subject difference in the ergonovine- and nitrate-induced serial percent diameter changes was statistically significant across the three segments (ergonovine vs. nitrate: control: \u221218.78 \u00b1 10.45 vs. 7.79 \u00b1 8.48; DCB-treated: \u221222.95 \u00b1 15.57 vs. 9.36 \u00b1 10.73; spastic: \u221237.03 \u00b1 17.56 vs. 15.55 \u00b1 15.19, Coronary artery spasm is not only a functional abnormality of the coronary artery, causing transient, reversible myocardial ischemia, but it indeed plays a role in the pathogenesis of ACS . A previThe introduction of metallic stents was a major breakthrough in overcoming the limitations of PTCA, such as abrupt vessel closure, acute recoil, dissection, and vasospasm. However, permanent vessel caging by metallic implants constitutes barriers to physiological vasomotion and expansile vessel remodeling. Further, DESs implantation produces prolonged endothelial dysfunction in stented artery and, as The mechanisms underlying the observed favorable findings may be multifactorial. Ergonovine, an ergot derivative, exerts vasoconstrictive effects by stimulating alpha-adrenergic and serotonin receptors and inhiThis study is limited by a relatively small population. Angiographically normal segments, not evidenced by intravascular imaging, may harbor atherosclerosis. Unlike acetylcholine affecting both the endothelium and vascular smooth muscle, the ergonovine effect primarily represents endothelium-independent constriction . Thus, oAbnormal coronary vasomotion, as invasively assessed using intracoronary vasoactive substances, is an independent prognosticator for adverse cardiovascular events ,30. Thus"} +{"text": "Muti HS, Heij LR, Keller G, et al. Development and validation of deep learning classifiers to detect Epstein-Barr virus and microsatellite instability status in gastric cancer: a retrospective multicentre cohort study. Lancet Digit Health 2021; published online Aug 17. https://doi.org/10.1016/S2589-7500(21)00133-3\u2014In figure 2A of this Article, the colours were missing. This correction has been made as of Aug 19, 2021."} +{"text": "Streptomyces sp. HO1518. A total of ninety-eight aminooligosaccharides, including eighty potential new compounds, were detected mainly based on the characteristic fragment ions originating from quinovosidic bond cleavages in their molecules. Following an LC-MS-guided separation technique, seven new aminooligosaccharides (10\u201316) along with four known related compounds (17\u201320) were obtained directly from the crude extract of strain HO1518. Compounds 10\u201313 represent the first examples of aminooligosaccharides with a rare acarviostatin II02-type structure. In addition, all isolates displayed considerable inhibitory effects on three digestive enzymes, which revealed that the number of the pseudo-trisaccharide core(s), the feasible length of the oligosaccharides, and acyl side chain exerted a crucial influence on their bioactivities. These results demonstrated that the UPLC-QTOF-MS/MS-based metabolomics approach could be applied for the rapid identification of aminooligosaccharides and other similar structures in complex samples. Furthermore, this study highlights the potential of acylated aminooligosaccharides with conspicuous \u03b1-glucosidase and lipase inhibition for the future development of multi-target anti-diabetic drugs.A rapid and sensitive method using ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) was applied for the analysis of the metabolic profile of acarviostatin-containing aminooligosaccharides derived from Acarbose, a typical anti-diabetes drug functioning as an \u03b1-glucosidases inhibitor, potently inhibits the \u03b1-glucosidases in vivo to retard carbohydrate digestion and avoid blood glucose elevation +; HRESIMS: m/z 1273.4938 [M + H]+ .Acarviostatin II02 : White amorphous powder, c 1.01, H2O). UV (H2O) end absorption; IR \u03bdmax 3337, 1726, 1407, 1149, 1026 cm\u22121. 1H (500 MHz) and 13C (125 MHz) NMR spectroscopic data, see m/z 1329 [M + H]+; HRESIMS: m/z 1329.5234 [M + H]+ .D6-O-Isobutyryl-acarviostatin II02 : White amorphous powder, c 1.02, H2O). UV (H2O) end absorption; IR \u03bdmax 3329, 1721, 1365, 1147, 1014 cm\u22121. 1H (500 MHz) and 13C (125 MHz) NMR spectroscopic data, see m/z 1343 [M + H]+; HRESIMS: m/z 1343.5365 [M + H]+ .D6-O-Isovaleryl-acarviostatin II02 : White amorphous powder, c 0.99, H2O). UV (H2O) end absorption; IR \u03bdmax 3305, 1647, 1407, 1150, 1013 cm\u22121. 1H (500 MHz) and 13C (125 MHz) NMR spectroscopic data, see m/z 1357 [M + H]+; HRESIMS: m/z 1357.5520 [M + H]+ .D6-O-Propionyl-acarviostatin II03 : White amorphous powder, c 0.90, H2O). UV (H2O) end absorption; IR \u03bdmax 3304, 1734, 1402, 1148, 1023 cm\u22121. 1H (500 MHz) and 13C (125 MHz) NMR spectroscopic data, see m/z 1491 [M + H]+; HRESIMS: m/z 1491.5727 [M + H]+ .D6-O-Butyryl-acarviostatin II03 : White amorphous powder, c 0.53, H2O). UV (H2O) end absorption; IR \u03bdmax 3324, 1729, 1568, 1149, 1024 cm\u22121. 1H (500 MHz) and 13C (125 MHz) NMR spectroscopic data, see m/z 1505 [M + H]+; HRESIMS: m/z 1505.5872 [M + H]+ .D6-O-2-Methyl-butyryl-acarviostatin II03 : White amorphous powder, c 1.03, H2O). UV (H2O) end absorption; IR \u03bdmax 3303, 1645, 1406, 1149, 1014 cm\u22121. 1H (500 MHz) and 13C (125 MHz) NMR spectroscopic data, see m/z 1519 [M + H]+; HRESIMS: m/z 1519.6039 [M + H]+ .D6-9\u201320 were conducted based on a previously reported method. Commercial \u03b1-amylase inhibitor acarbose was used as the positive control [The PPA inhibitory activities of compounds 9\u201320 was evaluated according to the previously reported method. Acarbose was also used as the positive control [The sucrase inhibition assay of compounds control .9\u201320 was performed according to the method outlined by McDougall et al. with slight modification [The lipase inhibition assay of compounds fication . Orlistax: 4.342 \u00c5; y: 24.299 \u00c5; z: 47.471 \u00c5) and the grid box dimensions (30 \u00d7 30 \u00d7 30 \u00c5) were set. The results of molecular docking were evaluated on the basis of the binding energy, criteria of binding structure, and possible interactions between ligand and the critical catalytic triad of protein 1LPB.The molecular docking simulations were performed by AutoDock Vina software, version 1.5.7 . The cryStreptomyces sp. HO1518. A total of ninety-eight aminooligosaccharides, including eighty new compounds, were detected and characterized from the extract of stain HO1518. Among them, twenty structural intriguing oligomers that ended with the 4-amino-4-deoxy-D-quinovopyranose unit at the non-reducing terminus were reported for the first time. The subsequent MS-guided fractionation method resulted in the isolation of seven new oligosaccharides (10\u201316) and four known analogs (17\u201320). Notably, compounds 10\u201313 are the first reported examples of oligosaccharides with a rarely occurring acarviostatin II02-type structure. All the compounds exhibited significant inhibitory activities against three digestive enzymes, among which compounds 9\u201316, 19 and 20 sharing two pseudo-trisaccharides were the most effective inhibitors of \u03b1-amylase and lipase. Furthermore, primary structure-activity relationships of 9\u201320 revealed that the number of the pseudo-trisaccharide core and acyl side chain play pivotal roles in their biological activity, which was evidenced by molecular docking analysis. These results of this study highlighted the advantages of UPLC-QTOF-MS/MS for the rapid structural identification of oligosaccharides, and this strategy could be extended to other investigations for high-throughput analysis of natural products with similar structures. More importantly, this study not only provided new lead compounds for further scientific research towards anti-diabetic drug discovery, but also shed light on the structural optimization of aminooligosaccharides analogs for medicinal scientists.In summary, the hyphenated system UPLC-QTOF-MS/MS that could provide qualitative retention time and reliable mass spectrometry information was utilized to reveal the metabolic profiling of aminooligosaccharides secreted by"} +{"text": "Burkholderia spp. is an opportunistic pathogen associated with respiratory infections. Cefiderocol (CFDC), a siderophore cephalosporin approved in US and EU, is active in vitro against carbapenem-resistant Gram-negative bacteria including Burkholderia spp. This study examined in vitro and in vivo activity of CFDC against Burkholderia spp.Burkholderia spp. collected in 2014 - 2019 in 13 countries were determined by broth microdilution method according to CLSI guidelines. Only for CFDC, iron-depleted CAMHB was used. In a rat lung infection model, B. cepacia ATCC 25416 was used. Male CD rats were infected by intrabronchial inoculation of the bacterial suspension including 1% nutrient agar. The humanized PK in plasma by administration of CFDC 2 g every 8 h (3-h infusion) and MEM 1 g every 8 h (0.5-h infusion) were recreated via the continuous intravenous infusion for 4 days, and the viable cfu in lungs were counted.MICs of CFDC and 13 marketed antibacterial drugs against 462 clinical isolates of 50/MIC90 of \u2264 0.031/1 \u00b5g/mL, which was the lowest among the tested antibiotics. Among 185 MEM non-susceptible isolates, 94% of the isolates exhibited \u2264 4 \u00b5g/mL of CFDC MIC. In a rat lung infection model, CFDC and MEM showed bactericidal activity with 2.8 and 2.4 log10 CFU/lung decrease compared with non-treated control, respectively. By recreating the humanized PK exposure in this model, 100% and ca.35% of fT >MIC of CFDC and MEM in plasma has been achieved, respectively. The bactericidal activities of both compounds vs B. cepacia ATCC 25416 would be reasonable because the fT >MIC achieved in this model exceeds the target fT >MIC required to cause 1 log10 reduction in murine thigh infection models1,2). Against 462 strains, including 185 MEM non-susceptible isolates, CFDC showed MIC1) M. Sabet. 2019. AAC 2) R. Nakamura. 2019. AACIn vitro activity of CFDC and comparator agents against Burkholderia spp.Burkholderia spp. In critically ill patients, the recommended dosing regimen achieves 100% of fT >MIC of \u2264 4 ug/mL3).3) N. Kawaguchi. 2021. AACCFDC has potential for treating respiratory tract infections caused by Merime Oota, BSc, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Toriko Yoshitomi, -, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Rio Nakamura, BSc, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Miki Takemura, MS, SHIONOGI & CO., LTD. (Employee) Yoshinori Yamano, PhD, Shionogi (Employee) Meredith Hackel, PhD MPH, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)"} +{"text": "Hospitalized COVID-19 patients tend to be older and frequently have hypertension, diabetes or CHD, but whether these co-morbidities are more common than in the general older population is unclear. We estimated associations between pre-existing diagnoses and hospitalized COVID-19 alone or with mortality . In 269,070 UK Biobank participants aged 65+, 507 (0.2%) became COVID-19 hospital inpatients, of which 141 (27.8%) died. Common preexisting co-morbidities in hospitalized inpatients were hypertension (59.6%), history of falls/fragility fractures (29.4%), CHD (21.5%), T2 diabetes (19. 9%) and asthma (17.6%). However, in adjusted models, pre-existing diagnoses of dementia, T2 diabetes, COPD, pneumonia, depression, atrial fibrillation and hypertension emerged as independent risk factors for COVID-19 hospitalization, the first five remaining statistically significant for related mortality. There are specific high risk pre-existing co-morbidities for COVID-19 hospitalization and deaths in community based older men and women."} +{"text": "The dependences of the crystal structure of CrAs on temperature (30\u2013400\u2005K) and on pressure (0\u20139.46\u2005GPa) are reported. The investigation shows twinning accompanying the temperature-induced isosymmetrical phase transition and the existence of a distinct Cr\u2013Cr distance within the structure showing anomalous behavior. TN = 267\u2005K can induce a change in the microstructure by twinning due to a crossing of the orthohexagonal setting of the unit-cell parameter ratio c/b. Within the crystal structure, one particular Cr\u2013Cr distance exhibits anomalous behavior in that it is nearly unaffected by temperature and pressure in the paramagnetic phase, which is stable above 267\u2005K and at high pressures. The distinction of this shortest Cr\u2013Cr distance might be of importance for the superconducting properties of CrAs.The crystal structure of CrAs was investigated using synchrotron X-ray single-crystal diffraction for separate dependences on temperature (30\u2013400\u2005K) and on pressure (0\u20139.46\u2005GPa). The isosymmetrical magnetostructural phase transition at The iderk Fig. 1.aCmcm, with a\u2032 = ahex, b\u2032\u00a0= c\u2032 = chex. A slight displacement of the atomic positions leads to the loss of the C-centering and the symmetry reduction to space group Pmcn following the P63/mmc\u2192Cmcm\u2192Pmcn group\u2013subgroup relation are of second order, the low-temperature transitions in MnP (from the ferro- to the helimagnetic state) and in CrAs are of first order and accompanied by abrupt changes in the unit-cell parameters, though the precise changes in MnP are controversial at about 33\u2005GPa at very low temperatures on the kappa diffractometer equipped with a Pilatus CdTe 1M area detector.For the measurements in the range 35\u2013275\u2005K at ambient pressure, the temperatures were set using a Cryocool G2b-LT helium gas jet cryostat.et al., 1986The high-pressure measurements to 9.5\u2005GPa at room temperature were carried out using several diamond anvil cells, each pre-loaded with a CrAs single crystal, a ruby chip, and a 4:1 methanol\u2013ethanol mixture as pressure-transmitting medium. The pressure during all measurements in diamond anvil cells was determined using the ruby luminescence method showed no significant difference in the overall quality of the fit. However, refinement of the parameters yCr and yAs, which are fixed to \u00bc in Pnma but free in Pn21a, show that within the errors they do not deviate from the centrosymmetric value \u00bc in the whole temperature range. This observation is similar to the findings of Selte & Kjekshus , the observed diffraction patterns exhibit extinction rules that are in accordance with space groups us 1973b regardin3.2.aTN, the structural phase transition is clearly visible from the large abrupt changes of all unit-cell parameters. The relative changes on cooling \u0394a/a \u2243 \u22120.40%, \u0394b/b \u2243 +3.51%, \u0394c/c \u2243 \u22120.83% and \u0394V/V \u2243 +2.25% confirm the previous observations from the literature. Below the transition temperature, the unit-cell parameters change smoothly; a and c decrease in a comparable way, b first increases and eventually stays nearly constant below about 200\u2005K, where due to the lack of further change in b, the volume V is dominated by the behavior of a and c \u2005\u00c5, b = 3.467\u2005(2)\u2005\u00c5, c = 6.200\u2005(3)\u2005\u00c5 and V = 121.4\u2005(1)\u2005\u00c53. The fitted unit-cell volume at zero pressure, the bulk modulus and the first derivative of the bulk modulus are V0 = 121.3\u2005(2)\u2005\u00c53, B0 = 28\u2005(4)\u2005GPa and B0\u2032 = 36\u2005(5), respectively. Compared to other MnP-type compounds [e.g. MnP: B0 = 116\u2005(12)\u2005GPa, B0\u2032 = 4.2\u2005(8) \u2005GPa, B0\u2032 = 4 \u2005GPa, B0\u2032 = 8.8\u2005(33) . In addition to the standard refinements with harmonic atomic displacement parameters (ADPs), refinements with anharmonic ADPs were carried out, as this was suggested by a visual inspection of the Fobs density maps. The resulting parameters show consistently that around the transition temperature the displacement parameters of the atoms show a significant anharmonicity, indicating that around and during the phase transition, the atoms show increased and anharmonic movement around their mean positions or that there is an increased degree of static disorder of the atoms which are slightly moved away from their highly symmetrical special positions.This formation of twin domains during the phase transition is furthermore coupled to increased displacement parameters of the atoms , as the Cr atoms carry the magnetic moment and they and their interactions are of particular importance for the magnetic and eventually superconducting properties. Above the phase transition, the distances CrI\u2013CrI and CrI\u2013CrIV follow the general trend and increase with temperature. However CrI\u2014CrII, the strongest covalent Cr\u2014Cr bond and strongest homoatomic interaction, is remarkable as it shows anomalous behavior in that it stays constant above TN. At the phase transition, the same distinction between the three Cr\u2013Cr distances is seen. Here, CrI\u2013CrI and CrI\u2013CrIV increase (upon cooling) due to the phase transition, while CrI\u2013CrII, the shortest Cr\u2013Cr distance, decreases even further. CrI\u2013CrI directly determines the length of the b axis of the unit cell, so that its increase is equivalent to the observed discontinuity in the temperature dependence of the b unit-cell parameter. CrI\u2013CrIV, lying almost in the bc plane, increases as well. The decrease in CrI\u2013CrII, which is oriented approximately along the a axis, leads to the abrupt shortening of this axis. Besides this decrease in the distance CrI\u2013CrII, the transition is also accompanied by a slight straightening of the CrI\u2013CrII\u2013CrI chains and the \u2220CrI\u2013CrII\u2013CrI angle gets closer to the ideal value of 180\u00b0. CrI\u2013CrII thus shows two distinctions: decreasing at TN and staying constant above TN. Below the transition, CrI\u2013CrII and CrI\u2013CrIV decrease with temperature, while CrI\u2013CrI increases and is eventually constant below about 200\u2005K.The most interesting distances in the CrAs structure are the Cr\u2013Cr distances \u2013 which decrease during the phase transition .In CrAs on compression, all Cr\u2013As and Cr\u2013Cr distances decrease with the exception of CrII Fig. 7, which ins Fig. 8 and the 4.et al. and also in good agreement with those reported by Selte et al. with the MnP-type structure shows that at least the behavior of the relevant interatomic T\u2013T distances on compression are similar global, Synchrotron-275K, Synchrotron-270K, Synchrotron-260K, Synchrotron-250K, Synchrotron-240K, Synchrotron-220K, Synchrotron-200K, Synchrotron-185K, Synchrotron-170K, Synchrotron-155K, Synchrotron-140K, Synchrotron-125K, Synchrotron-110K, Synchrotron-95K, Synchrotron-80K, Synchrotron-65K, Synchrotron-50K, Synchrotron-35K, Synchrotron-1.03GPa, Synchrotron-2.53GPa, Synchrotron-3.13GPa, Synchrotron-4.45GPa, Synchrotron-6.05GPa, Synchrotron-7.32GPa, Synchrotron-8.09GPa, Synchrotron-9.46GPa, Lab-400K, Lab-390K, Lab-380K, Lab-370K, Lab-360K, Lab-350K, Lab-340K, Lab-330K, Lab-320K_02, Lab-320K_01, Lab-310K_02, Lab-310K_01, Lab-300K_02, Lab-300K_01, Lab-290K, Lab-280K_02, Lab-280K_01, Lab-275K, Lab-270K, Lab-250K, Lab-240K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-275Ksup2.hklStructure factors: contains datablock(s) Synchrotron-275K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-270Ksup3.hklStructure factors: contains datablock(s) Synchrotron-270K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-260Ksup4.hklStructure factors: contains datablock(s) Synchrotron-260K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-250Ksup5.hklStructure factors: contains datablock(s) Synchrotron-250K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-240Ksup6.hklStructure factors: contains datablock(s) Synchrotron-40K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-220Ksup7.hklStructure factors: contains datablock(s) Synchrotron-220K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-200Ksup8.hklStructure factors: contains datablock(s) Synchrotron-200K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-185Ksup9.hklStructure factors: contains datablock(s) Synchrotron-185K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-170Ksup10.hklStructure factors: contains datablock(s) Synchrotron-170K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-155Ksup11.hklStructure factors: contains datablock(s) Synchrotron-155K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-140Ksup12.hklStructure factors: contains datablock(s) Synchrotron-140K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-125Ksup13.hklStructure factors: contains datablock(s) Synchrotron-125K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-110Ksup14.hklStructure factors: contains datablock(s) Synchrotron-110K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-95Ksup15.hklStructure factors: contains datablock(s) Synchrotron-95K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-80Ksup16.hklStructure factors: contains datablock(s) Synchrotron-80K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-65Ksup17.hklStructure factors: contains datablock(s) Synchrotron-65K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-50Ksup18.hklStructure factors: contains datablock(s) Synchrotron-50K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-35Ksup19.hklStructure factors: contains datablock(s) Synchrotron-35K. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-1.03GPasup20.hklStructure factors: contains datablock(s) Synchrotron-1.03GPa. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-2.53GPasup21.hklStructure factors: contains datablock(s) Synchrotron-2.53GPa. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-3.13GPasup22.hklStructure factors: contains datablock(s) Synchrotron-3.13GPa. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-4.45GPasup23.hklStructure factors: contains datablock(s) Synchrotron-4.45GPa. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-6.05GPasup24.hklStructure factors: contains datablock(s) Synchrotron-6.05GPa. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-7.32GPasup25.hklStructure factors: contains datablock(s) Synchrotron-7.32GPa. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-8.09GPasup26.hklStructure factors: contains datablock(s) Synchrotron-8.09GPa. DOI: 10.1107/S2052520621005655/xk5084Synchrotron-9.46GPasup27.hklStructure factors: contains datablock(s) Synchrotron-9.46GPa. DOI: 10.1107/S2052520621005655/xk5084Lab-400Ksup28.hklStructure factors: contains datablock(s) Lab-400K. DOI: 10.1107/S2052520621005655/xk5084Lab-390Ksup29.hklStructure factors: contains datablock(s) Lab-390K. DOI: 10.1107/S2052520621005655/xk5084Lab-380Ksup30.hklStructure factors: contains datablock(s) Lab-380K. DOI: 10.1107/S2052520621005655/xk5084Lab-370Ksup31.hklStructure factors: contains datablock(s) Lab-370K. DOI: 10.1107/S2052520621005655/xk5084Lab-360Ksup32.hklStructure factors: contains datablock(s) Lab-360K. DOI: 10.1107/S2052520621005655/xk5084Lab-350Ksup33.hklStructure factors: contains datablock(s) Lab-350K. DOI: 10.1107/S2052520621005655/xk5084Lab-340Ksup34.hklStructure factors: contains datablock(s) Lab-340K. DOI: 10.1107/S2052520621005655/xk5084Lab-330Ksup35.hklStructure factors: contains datablock(s) Lab-330K. DOI: 10.1107/S2052520621005655/xk5084Lab-320K_02sup36.hklStructure factors: contains datablock(s) Lab-320K_02. DOI: 10.1107/S2052520621005655/xk5084Lab-320K_01sup37.hklStructure factors: contains datablock(s) Lab-320K_01. DOI: 10.1107/S2052520621005655/xk5084Lab-310K_02sup38.hklStructure factors: contains datablock(s) Lab-310K_02. DOI: 10.1107/S2052520621005655/xk5084Lab-310K_01sup39.hklStructure factors: contains datablock(s) Lab-310K_01. DOI: 10.1107/S2052520621005655/xk5084Lab-300K_02sup40.hklStructure factors: contains datablock(s) Lab-300K_02. DOI: 10.1107/S2052520621005655/xk5084Lab-300K_01sup41.hklStructure factors: contains datablock(s) Lab-300K_01. DOI: 10.1107/S2052520621005655/xk5084Lab-290Ksup42.hklStructure factors: contains datablock(s) Lab-290K. DOI: 10.1107/S2052520621005655/xk5084Lab-280K_02sup43.hklStructure factors: contains datablock(s) Lab-280K_02. DOI: 10.1107/S2052520621005655/xk5084Lab-280K_01sup44.hklStructure factors: contains datablock(s) Lab-280K_01. DOI: 10.1107/S2052520621005655/xk5084Lab-275Ksup45.hklStructure factors: contains datablock(s) Lab-275K. DOI: 10.1107/S2052520621005655/xk5084Lab-240Ksup46.hklStructure factors: contains datablock(s) Lab-240K. DOI: 10.1107/S2052520621005655/xk5084Lab-250Ksup47.hklStructure factors: contains datablock(s) Lab-250K. DOI: 10.1107/S2052520621005655/xk5084Lab-270Ksup48.hklStructure factors: contains datablock(s) Lab-270K. DOI: 10.1107/S2052520621005655/xk5084sup49.pdfTables S1-S12 , Appendix A and Figs. S1-S4. DOI: 2087357, 2087358, 2087359, 2087360, 2087361, 2087362, 2087363, 2087364, 2087365, 2087366, 2087367, 2087368, 2087369, 2087370, 2087371, 2087372, 2087373, 2087374, 2087375, 2087376, 2087377, 2087378, 2087379, 2087380, 2087381, 2087382, 2087383, 2087384, 2087385, 2087386, 2087387, 2087388, 2087389, 2087390, 2087391, 2087392, 2087393, 2087394, 2087395, 2087396, 2087397, 2087398, 2087399, 2087400, 2087401, 2087402, 2087403CCDC references:"} +{"text": "The model reflects age, platelet count, hepatitis B e antigen positivity, serum albumin and total bilirubin levels, cirrhosis development, and liver stiffness values measured by transient elastography. Our new model showed better performance for predicting hepatocellular carcinoma development (Harrell\u2019s p < 0.05). Our nomogram showed acceptable performance in predicting HCC in Asian HBV-infected patients receiving potent antiviral therapy.Hepatocellular carcinoma (HCC) risk prediction is important to developing individualized surveillance approaches. We designed a novel HCC prediction model using liver stiffness on transient elastography for patients receiving antiviral therapy against hepatitis B virus (HBV) infection. We recruited 2037 patients receiving entecavir or tenofovir as first-line antivirals and used the Cox regression analysis to determine key variables for model construction. Within 58.1 months (median), HCC developed in 182 (8.9%) patients. Patients with HCC showed a higher prevalence of cirrhosis (90.7% vs. 45.9%) and higher liver stiffness values (median 13.9 vs. 7.2 kPa) than those without. A novel nomogram (score 0\u2013304) was established using age, platelet count, cirrhosis development, and liver stiffness values, which were independently associated with increased HCC risk, along with hepatitis B e antigen positivity and serum albumin and total bilirubin levels. Cumulative HCC probabilities were 0.7%, 5.0%, and 22.7% in the low- (score \u226487), intermediate- (88\u2013222), and high-risk (\u2265223) groups, respectively. The c-index value was 0.799 , higher than that of the PAGE-B (0.726), modified PAGE-B (0.756), and modified REACH-B (0.761) models (all Globally, approximately 240 million individuals are chronically infected with hepatitis B virus (HBV), which remains a major etiology of hepatocellular carcinoma (HCC) and cirrhosis, especially in endemic areas, including the Republic of Korea ,2,3. A hSeveral efforts were made to evaluate HCC development in patients with CHB. Several models, such as the GAG-HCC, CU-HCC, and REACH-B, were designed with sufficiently good prognostic performance ,14,15. AIn the current era of potent AVT, we aimed to establish a novel prediction model for HCC development optimized for patients with CHB receiving ETV and TDF based on liver stiffness on transient elastography, one of the most reliable fibrosis markers, and validate its role in comparison with that of other prediction models.Between 2007 and 2018, patients who started AVT with ETV or TDF against chronic HBV infection at Yonsei University Severance Hospital were consecutively screened for eligibility. The inclusion criteria were as follows: (1) age \u226519 years, (2) patients who received ETV or TDF in first-line AVT, (3) reliable liver stiffness values available, (4) no previous history of HCC at enrollment, (5) no previous history of decompensated cirrhosis with Child-Pugh class C at enrollment, and (6) no history of previous organ transplant. The exclusion criteria were as follows: (1) co-infection with other hepatitis viruses, (2) HCC development within 6 months since AVT initiation, (3) death or orthotropic liver transplant within 6 months since AVT initiation, (4) uncontrolled advanced malignancy at enrollment, and (5) other significant medical illnesses.3/\u03bcL and imaging findings suggestive of cirrhosis, including a blunted, nodular liver edge accompanied by splenomegaly (>12 cm), or (2) clinical signs of portal hypertension, such as gastroesophageal varices ), intermediate- ), and high-risk groups according to the 25th (87 points) and 75th percentiles (223 points) of the risk score distribution of the nomogram. The 2-, 3-, and 5-year cumulative probabilities of HCC development in the low- (scores: \u226487), intermediate- (88\u2013222), and high-risk (\u2265223) groups were 0%, 0.2%, and 0.7%; 1.1%, 2.9%, and 5.0%; and 7.5%, 13.3%, and 22.7%, respectively , together with categorized serum albumin levels , total bilirubin levels (<2.0 and \u22652.0 mg/dL), and HBeAg positivity, which were reported to be closely associated with the HCC risk among subjects with chronic HBV infection ,13,15. Tc-index was 0.805 (95% CI: 0.777\u20130.834), and the 2-, 3-, and 5-year TDAUCs were 0.809 (95% CI: 0.783\u20130.834), 0.808 (95% CI 0.782\u20130.834), and 0.805 (95% CI 0.779\u20130.831), respectively.Harrell\u2019s c-index value of the prediction model was 0.799 (95% CI: 0.769\u20130.829), and the 2-, 3-, and 5-year TDAUCs were 0.802 (95% CI: 0.776\u20130.827), 0.802 (95% CI: 0.776\u20130.828), and 0.799 (95% CI 0.773\u20130.826), respectively . Calibrap < 0.001), mPAGE-B , and mREACH-B models. The 2-, 3-, and 5-year TDAUCs of the new nomogram were also significantly higher than those of the PAGE-B , mPAGE-B , and mREACH-B models (p < 0.001).The c-index value of the new nomogram for predicting HCC development (0.799) was significantly higher than that of the PAGE-B models . Furthern = 324, 36.0%).For external validation, we recruited 901 patients from Gangnam Severance Hospital and Yongin Severance Hospital using the same criteria. During follow-up (median: 51.8 [IQR 34.4\u201373.1] months), HCC developed in 56 (6.2%): 10 patients without cirrhosis and 46 patients with cirrhosis in this cohort. The c-index value and 2-, 3-, and 5-year TDAUC of the nomogram were also acceptable: 0.785 (95% CI: 0.729\u2013 0.840) and 0.782 (95% CI: 0.722\u20130.841), 0.777 (95% CI: 0.719\u20130.835), and 0.771 (95% CI: 0.714\u20130.827), respectively, in overall patients. In subgroup analysis, Harrell\u2019s C-index, 2-, 3-, and 5-year TDAUC values were 0.749 (95% CI: 0.692\u20130.806), 0.649 (95% CI: 0.522\u20130.775), 0.651 (95% CI: 0.524\u20130.779), and 0.651 (95% CI: 0.525\u20130.776), respectively, in patients without cirrhosis and 0.668 (95% CI: 0.585\u20130.750), 0.653 (95% CI: 0.571\u20130.736), 0.651 (95% CI: 0.570\u20130.732), and 0.653 (95% CI: 0.573\u20130.733), respectively, in patients with cirrhosis during the long-term follow-up period of approximately 60 months, allowed for statistical reliability and adequate power [Our study has several strengths. Firstly, our nomogram showed consistently superior c-index and TDAUC values for predicting HCC development during the long-term follow-up period, compared with that of other conventional risk prediction models, including the PAGE-B, mPAGE-B, and mREACH-B models, which showed high performance in previous literature ,16,30. Cte power . The higte power . Finallyn = 571, 28.0%), HCC surveillance can be mitigated safely, until the value calculated by our nomogram reaches more than 87. Accordingly, repeated assessment of HCC risk at every visit is required in routine practice. Contrary, because the intermediate- and high-risk groups had significantly higher annual incidence rates of HCC , a more sensitive imaging study of detecting HCC rather than abdominal ultrasonography, for example, magnetic resonance imaging with or without contrast, is required. Further prospective studies on personalized surveillance strategies according to individual risk and cost-effectiveness are required.The 5-year cumulative incidence of HCC was <1% in the low-risk group (score: \u226487). Generally, the currently recommended bi-annual surveillance strategy is cost-effective when the annual incidence rate of HCC ranges \u22650.2% in patients with chronic HBV infection and \u22651.5% in those with cirrhosis ,34. TherThe type of AVT does not seem to influence the risk of HCC development. Our study included similar proportions of patients who first started AVT with ETV (45.0%) and TDF (55.0%), and the type of AVT was not associated with HCC development in univariate analysis. There is controversy on whether TDF is more advantageous than ETV in reducing HCC risk ; howeverUnsolved issues remain in our study. Firstly, the findings of this study were potentially subject to selection bias. Considering that our institute is the second largest tertiary hospital with approximately 2500 beds in the Republic of Korea, our study population was more likely to cover patients with advanced liver disease and a high prevalence of cirrhosis in comparison with the nationwide cohort . HoweverThis study developed a novel nomogram to predict HCC using baseline information readily available among treatment-na\u00efve patients with chronic HBV infection who started their first-line AVT with potent nucleos(t)ide analogs. The nomogram consistently showed better prognostic performance over that of conventional models. Further studies are required to validate our results among independent cohorts, including Western populations."} +{"text": "Agastache foeniculum (Pursch) Kuntze (Lamiaceae), Gaultheria procumbens L. (Ericaceae), Heliopsis helianthoides (L.) Sweet (Asteraceae), Liatris spicata (L.) Willd. (Asteraceae), Pycnanthemum incanum (L.) Michx. (Lamiaceae), Smallanthus uvedalia (L.) Mack. ex Mack. (Asteraceae), and Verbena hastata L. (Verbenaceae) by hydrodistillation. The essential oils were analyzed by gas chromatographic techniques. The essential oil of A. foeniculum was dominated by estragole (88\u201393%), while methyl salicylate (91%) dominated the G. procumbens essential oil. Germacrene D was the major component in H. helianthoides (42%) and L. spicata (24%). 1,8-Cineole (31%) and \u03b1-terpineol (17%) were the main compounds in P. incanum essential oil. The essential oil of S. uvedalia showed \u03b1-pinene (24%), perillene (15%), and \u03b2-caryophyllene (17%) as major components. Verbena hastata essential oil was rich in 1-octen-3-ol (up to 29%) and palmitic acid (up to 22%). Four of these essential oils, H. helianthoides, L. spicata, P. incanum, and V. hastata, are reported for the first time. Additionally, the enantiomeric distributions of several terpenoid components have been determined.As part of our evaluation of essential oils derived from Native American medicinal plants, we have obtained the essential oils of Plants have been used in traditional medicine since prehistoric times. The therapeutic properties of medicinal plants are generally attributed to secondary metabolites produced by the plants as protection against pathogens and herbivory. As with many other aboriginal peoples, Native North Americans have used plants as medicines throughout their history. Although not as extensively documented as traditional Chinese medicine or Ayurvedic medicine, there are several sources of information regarding Native American ethnopharmacology ,2,3. As Agastache foeniculum (Pursch) Kuntze (Lamiaceae) is native to north central United States and southern Canada, but has been recorded in southern Alabama [A. foeniculum as a cold medicine [A. foeniculum have been extensively studied, and the oils are typically dominated by methyl chavicol (estragole) with smaller amounts of (E)-anethole [A. foeniculum include flavonoids , polyphenolics , pentacyclic triterpenoids , and sterols [ Alabama . The pla Alabama . Cheyennmedicine . Essentianethole . Nonvolaastanol) .Gaultheria procumbens L. (Ericaceae) naturally ranges in eastern North America from Canada, south through Alabama and Georgia [G. procumbens to treat headaches, colds or to treat arthritis, rheumatism, and lumbago [G. procumbens along with the roots of Epigaea repens for chronic indigestion, and they also chewed the leaves as a substitute for chewing tobacco [Gaultheria fragrantissima Wall., the essential oil of G. procumbens is dominated by methyl salicylate. Commercial G. fragrantissima essential oil has 99.7% methyl salicylate, while methyl salicylate in G. procumbens essential oil typically ranges 96.6\u201399.8% [ Georgia . Severalawatomi) . The Che tobacco . Much li.6\u201399.8% .Heliopsis helianthoides (L.) Sweet (Asteraceae) is native to North America from Saskatchewan, Canada east to the Atlantic coast of Newfoundland and south to the Gulf of Mexico, with the western range extending as far as New Mexico [H. helianthoides, ssp. helianthoides, generally occurring east of the Mississippi River; ssp. occidentalis, found in the Great Plains region; and ssp. scabra, which is predominant in the Ozark region [H. helianthoides as a stimulant [Scutellaria incana \u201cfor young women\u201d, presumably for menstruation-related discomforts, and sore feet were relieved by soaking in an infusion of what was called \u201cswamp sunflower\u201d [N-alkylamides [H. helianthoides.w Mexico ,11,12. Tnflower\u201d . Guaianonflower\u201d , N-alkylylamides , and ligylamides have beeLiatris spicata (L.) Willd. (Asteraceae) is the eastern United States and Canada, east of the Mississippi River, from the south along the Gulf of Mexico including southern Alabama and northern Florida areas, north to Ontario and Quebec [L. spicata [The natural range of d Quebec ,16,17. Td Quebec . The gua spicata .Pycnanthemum incanum (L.) Michx. (Lamiaceae) ranges naturally in the eastern United States from the Mississippi River east to the Atlantic coast and from southern Ontario, Canada south to the Gulf of Mexico, though it is primarily found from the Appalachian mountain region beginning in north Georgia north into Ontario, Canada [P. incanum externally to treat headaches [P. incanum to be \u03b2-ionone, myrcene, linalool, and pulegone [, Canada ,19. The eadaches . Dein anpulegone .Smallanthus uvedalia (L.) Mack. ex Mack. (Asteraceae) is the southeastern United States, from the Ohio river basin south to the Gulf of Mexico [Smallanthus uvedalia was reportedly used internally by Native American Indians for laxative properties as well as a stimulant and also to treat swollen glands, especially mastitis [ent-kaurane diterpenoids have been isolated and characterized from S. uvedalia [S. uvedalia from several locations in north Alabama have been analyzed previously [The natural range of f Mexico . Smallanmastitis . The Chemastitis . Interesmastitis . A numbeuvedalia . The leaeviously ,24.Verbena hastata L. (Verbenaceae) ranges throughout North America [V. hastata has shown antiplasmodial [V. hastata [ America . The Che America . The ethasmodial , antinocasmodial , and antasmodial . The iri hastata .The purpose of this study was to extend our understanding of the volatile phytochemistry of Native American aromatic medicinal plants by examination of the essential oils of these seven plant species, to determine their chemical compositions as well as the enantiomeric distributions of terpenoid constituents.The essential oils of each species were obtained by hydrodistillation of dried plant material .A. foeniculum were collected from cultivated plants in Newville, Alabama. Hydrodistillation gave pale yellow essential oils in yields ranging from 1.48% to 2.30% yield. The essential oil compositions are compiled in The aerial parts of three different plant samples of A. foeniculum essential oil was dominated by the phenylpropanoid methyl chavicol (=estragole). There are apparently five different chemotypes of A. foeniculum based on essential oil chemical profiles: (1) methyl chavicol, (2) spathulenol/bornyl acetate, (3) \u03b3-cadinene/\u03b1-cadinol, (4) limonene, and (5) isomenthone [A. foeniculum essential oils belong to the methyl chavicol chemotype, however [The menthone ,34. Most however ,40,41,42A. foeniculum and has shown anti-inflammatory and anti-edematogenic [Methyl chavicol contributes to the anise-like aroma of atogenic ,44, cytoatogenic , and antatogenic ,47. Unfoatogenic ,49.G. procumbens was obtained in 4.25% yield and the major component was methyl salicylate (91.1%) . Methyl 1.1% . Meo 99.96% ,50,51,52G. procumbens essential oil, methyl salicylate, is well-known as an anti-inflammatory, antipyretic, analgesic agent [The major component of ic agent , and accic agent ,55,56.H. helianthoides was obtained in 0.95% yield. The major component in the essential oil was germacrene D (42.4%), with a lesser amount of 4-vinylguaicol (5.5%) . As far Centaurea hadimensis Wagenitz, K. Ertugrul & H. Dural (44.3%) [Centaurea pseudoscabiosa Boiss. & Buhse (36.0%) [Eupatorium cannabinum L. (33.5%) [Polymnia canadensis L. (63.6%) [Rudbeckia fulgida Aiton (30.1%) [Rudbeckia hirta L. (23.6%) [Solidago canadensis L. (64.1%) [Symphyotrichum novae-angliae (L.) G.L. Nesom (25.5%) [Verbesina macrophylla (Cass.) F.S. Blake (37.3%) [Verbesina turbacensis Kunth (36.9%) [Liatris spicata . Germacrene D has shown antimicrobial and cytotoxic activities [Although not necessarily a phytochemical marker of the family, germacrene D has been found to be a major component in several members of the Asteraceae. For example, germacrene D is the dominant compound in the essential oils of (44.3%) , Centaur (36.0%) , Eupator (33.5%) , Polymni 63.6%) , Rudbeck (30.1%) , Rudbeck (23.6%) , Solidag 64.1%) , Symphyo (25.5%) , Verbesi (37.3%) , Verbesi (36.9%) , and Lia.6% , Rud.1% , SymL. spicata essential oil is presented in L. spicata.The essential oil composition of P. incanum growing wild in South Carolina. The essential oil was rich in oxygenated monoterpenoids, including 1,8-cineole (30.7%), \u03b1-terpineol (16.9%), borneol (8.2%), and cis-sabinene hydrate (5.6%). The sesquiterpene hydrocarbons (E)-\u03b2-caryophyllene (11.0%), and germacrene D (5.0%) were also relatively abundant. To our knowledge, this is the first reported analysis of P. incanum essential oil. Volatiles obtained from a diethyl ether extract have been analyzed by gas chromatography-olfactometry to determine the key odorants [P. incanum essential oil and the volatiles from the previously published diethyl ether extract [odorants . Althoug extract . ConcentS. uvedalia from South Carolina is summarized in S. uvedalia essential oil were \u03b1-pinene (23.9%), (E)-\u03b2-caryophyllene (16.9%), perillene (14.5%), germacrene D (12.2%), and limonene (6.1%). In comparison, S. uvedalia from northern Alabama (collected in September 2018) contained \u03b1-pinene (62.6%), limonene (11.4%), and \u03b2-pinene (6.0%), with lesser concentrations of (E)-\u03b2-caryophyllene (3.8%) [S. uvedalia samples collected in February, 2016, from northern Alabama were rich in (E)-\u03b2-caryophyllene (24.5% and 16.5%) and caryophyllene oxide (19.8% and 14.2%) [S. uvedalia may be attributed to geographical location and/or seasonal variation.The essential oil composition of e (3.8%) . Neither\u03b1-pinene .9%, (E)-Erechtites hieracifolia (L.) Raf. [S. uvedalia (this work). Likewise, (+)-\u03b2-pinene was the only enantiomer in Coreopsis capillacea Kunth (syn. C. triloba S.F. Blake) [Achillea ligustica All. [S. uvedalia (this work) and Solidago canadensis L. [E. hieracifolia [C. capillacea [There does not seem to be a trend in the major enantiomers for essential oils of the Asteraceae see . For exaL.) Raf. , but (\u2013). Blake) , while (ica All. . (+)-Limensis L. , whereasacifolia and C. cpillacea .V. hastata were collected and investigated (E)-\u03b2-ionone, and (E)-nerolidol were the same for the three samples, however. As far as we know, this is the first report on the essential oil composition of V. hastata.Three different specimens of stigated . AlthougVerbena essential oil compositions to compare. However, several Verbena officinalis L. essential oils have been reported, and these samples also show wide variation in composition. The major components in V. officinalis essential oil from Morocco were spathulenol (10.8%), limonene (7.5%), 1,8-cineole (7.5%), caryophyllene oxide (7.3%), and ar-curcumene (6.0%) [V. officinalis from Italy was rich in geranial (45.5%) and isobornyl formate (41.4%) [Verbena officinalis from Algeria, on the other hand, showed limonene (17.7%), geranial (14.8%), carvone (14.2%), and caryophyllene oxide (12.4%) as major components [There are few e (6.0%) . In cont (41.4%) . Verbenamponents .V. hastata essential oils as it was in P. incanum essential oil (above). Notably, (\u2013)-1-octen-3-ol is the major enantiomer, generally greater than 97%, in mushrooms [The (\u2013)-enantiomer of 1-octen-3-ol was the only stereoisomer observed in ushrooms , and is ushrooms . Interesushrooms .V. hastata. (\u2013)-Linalool also dominated in the essential oil of Lantana camara L. (Verbenaceae) from Madagascar [Lippia alba (Mill.) N.E. Brown (Verbenaceae) from Uruguay was dominated by the (+)-enantiomer [A racemic mixture was observed for \u03b1-terpineol, but there was a higher concentration of (\u2013)-linalool over (+)-linalool in dagascar . In contantiomer .A. foeniculum, G. procumbens, and H. helianthoides were obtained from plants cultivated in at Kirkland Gardens, in Newville, Alabama , tubers , or young plants . All the plants were grown in full sun, except the G. procumbens, which was located in a partially shaded location (4 h/day average sunlight), and all were watered at least once a week. The plants were cultivated directly in the ground, which was clayey-loamy sand, which was amended with composted chicken manure, worm castings, kelp meal, and bone meal at time of planting. Pycnanthemum incanum and S. uvedalia were collected in the wild from a fully shaded forest understory roadside location near a small waterfall in northern South Carolina. The plants were located beside highway 276 near the North Carolina\u2013South Carolina border , S. uvedalia (SKL31820), and V. hastata (SKL51321) were deposited in the University of Alabama in Huntsville Herbarium (HALA); cultivated plants were not vouchered. For each species, the plant material was air-dried in the laboratory (around 23 \u00b0C) for 10 days. The dried plant materials of each species were chopped and hydrodistilled using a Likens\u2013Nickerson apparatus with continuous extraction with dichloromethane for 4 h. The dichloromethane was evaporated using a stream of dry nitrogen to give the essential oils , gas chromatography-flame ionization detection (GC-FID), and chiral GC-MS as previously described .GC-MS: Shimadzu GCMS-QP2010 Ultra, electron impact (EI) mode (electron energy = 70 eV), scan range = 40\u2013400 atomic mass units, scan rate = 3.0 scans/s, and GC-MS solution software; ZB-5ms fused silica capillary column (30 m length \u00d7 0.25 mm inner diameter) with a (5% phenyl)-polymethylsiloxane stationary phase and a film thickness of 0.25 \u03bcm; He carrier gas with a column head pressure of 552 kPa and flow rate of 1.37 mL/min; injector temperature = 250 \u00b0C, ion source temperature = 200 \u00b0C; GC oven temperature 50\u2013260 \u00b0C (2 \u00b0C/min), 1-\u03bcL injection of 5% solution of EO in dichloromethane . The essential oil components were identified by MS fragmentation, and retention indices compared with those in the databases ,30,31,322 carrier gas, and flow rate = 1.0 mL/min. The composition percentages were calculated from raw peak areas without standardization.GC-FID: Shimadzu GC 2010 equipped with flame ionization detector, a split/splitless injector, and Shimadzu autosampler AOC-20i, with a ZB-5 capillary column (30 m length \u00d7 0.25 mm inner diameter) with a (5% phenyl)-polymethylsiloxane stationary phase and a film thickness of 0.25 \u03bcm; oven temperature was programmed the same as above for GC-MS; injector temperature = 250 \u00b0C, detector temperature = 280 \u00b0C, NChiral GC-MS: Shimadzu GCMS-QP2010S, EI mode (electron energy = 70 eV) with scan range of 40\u2013400 amu and scan rate of 3.0 scans/s; Restek B-Dex 325 capillary column (30 m \u00d7 0.25 mm ID \u00d7 0.25 \u03bcm film); GC oven temperature program, 50\u2013120 \u00b0C (1.5 \u00b0C/min), 120\u2013200 \u00b0C (2 \u00b0C/min), and kept at 200 \u00b0C for 5 min; He carrier gas, flow rate = 1.8 mL/min; 0.1-\u03bcL injection of 3% solution of EO in dichloromethane . The monoterpenoid enantiomers were identified by comparison of retention times with authentic samples obtained from Sigma-Aldrich . Relative enantiomer percentages were determined based on peak areas. Chiral GC-MS chromatograms are available as Heliopsis helianthoides, Liatris spicata, Pycnanthemum incanum, and Verbena hastata, were reported for the first time. Additionally, the enantiomeric distributions of several terpenoid components have been determined. The chemical compositions presented add to our knowledge of the phytochemistry of the medicinal plants.This report presented the essential oil compositions of seven aromatic medicinal plants used by Native Americans. Four of these essential oils,"} +{"text": "MUC1-C integrates activation of the IFN-\u03b3 pathway with suppression of the tumor immune microenvironment in triple-negative breast cancer. J Immunother Cancer. 2021;9:e002115. doi: 10.1136/jitc-2020-002115.Yamashita N, Long M, Fushimi A, This article has been corrected since it first published. The provenance and peer review statement has been added."} +{"text": "Correction to: Microbiome 9, 241 (2021)https://doi.org/10.1186/s40168-021-01195-7Supplementary Data was missing from this article and has now been uploaded.The original article has been updated.Additional file 1: Supplementary Table S1. Details of the search terms used in the respective databases. Supplementary Table S2a. Additional summary of African Gut Microbiome studies. Supplementary Table S2b. Additional summary of African Urogenital Microbiome studies. Supplementary Table S2c. Additional summary of African Microbiome studies (Other body sites)."} +{"text": "The DISC1 (disrupted in s\u0441hizophrenia 1) gene is associated with brain dysfunctions, which are involvedin a variety of mental disorders, such as schizophrenia, depression and bipolar disorder. This is the first study toexamine the immune parameters in Disc1-Q31L mice with a point mutation in the second exon of the DISC1 genecompared to mice of the C57BL/6NCrl strain . A flow cytometry assay has shown that intact Disc1-Q31L mice differ from the WT strain by an increase in the percentage of CD3+ T cells, CD3+CD4+ \u0422 helper cellsand CD3+CD4+CD25+ T regulatory cells and a decrease in CD3+CD8+ T cytotoxic/suppressor cells in the peripheralblood. A multiplex analysis revealed differences in the content of cytokines in the brain structures of Disc1-Q31Lmice compared to WT mice. The content of pro-inflammatory cytokines was increased in the frontal cortex and striatum (IFN\u03b3), and decreased in the hippocampus and hypothalamus. At the same time, thelevels of IL-1\u03b2 were decreased in all structures being examined. In addition, the content of anti-inflammatory cytokinesIL-4 was increased in the frontal cortex, while IL-10 amount was decreased in the hippocampus. Immuneresponse to sheep red blood cells analyzed by the number of antibody-forming cells in the spleen was higher inDisc1-Q31L mice at the peak of the reaction than in WT mice. Thus, Disc1-Q31L mice are characterized by changes inthe pattern of cytokines in the brain structures, an amplification of the peripheral T-cell link with an increase in thecontent of the subpopulations of CD3+CD4+ T helpers and CD3+CD4+CD25+ T regulatory cells, as well as elevatedimmune reactivity to antigen in the spleen. Animal models have provided valuableopportunities to study the impact of immune dysfunctions andrelated alterations in neurotransmitter and hormonal systemsin the pathogenesis of neuropsychiatric disorders caused bymultiple risk factors, including genetic background. As shownpreviously, animals with genetic predisposition to depressiveor aggressive behavior are characterized by changes in thedistribution and ratio of the main subpopulations of T-cells inthe blood and spleen, immune responsiveness to T-dependentantigen, as well as cytokine variations in the periphery andbrain structures .It is now well established that a variety of social, environmentaland genetic factors may cause inflammatory responses that,over time, may result in development of multiple diseases,including neuropsychiatric disorders . The inflammatory processesare closely associated with alterations in the productionof cytokines , the compositionof T-cell subsets with different functional activities . Analysis of emotional,social and cognitive behaviors of this mice line showeda range of behavioral abnormalities that may be considered asa depression-like endophenotype . TheQ31L mutation in DISC1 gene is also known to be associatedwith changes in the dopaminergic (DA) activity and other neuromediator systems, which are involvedin the neurobiological mechanisms of psychiatric disordersand in the control of immune function .Disrupted-in-Schizophrenia-1 (DISC1) gene has beenfunctionally linked to brain dysfunctions associated with impairedneurodevelopment processes and intracellular signalingpathways that predispose to schizophrenia, major depression,and bipolar disorder . Several mouse models based on DISC1 dysfunctionhave been generated to date, including a homozygousDisc1-Q31L\u2013/\u2013 mice remain to be elucidated. Given a roleof the immune system both in the development of differentpsychoemotional states and in neuroimmunomodulation was also determined.2019), the aim of this study was to analyze the basal contentof T- and B-cells in the peripheral blood and spleen, as wellas the level of pro- and anti-inflammatory cytokines in thebrain structures of Disc1-Q31LAnimals. The experiments were performed in adult (3.0\u20133.5 months old) homozygous male mice of the Disc1-Q31L\u2013/\u2013strain (n = 23) and there wild type (WT) littermates of theC57BL/6NCrl strain (n = 23) weighing 27\u201330 g. Mice werebred in the animals facility of the Scientific Research Instituteof Physiology and Basic Medicine .Mice were kept in standard cages in groups for 5 animals per cage under standardvivarium conditions and free access to food and water.All experimental procedures were performed in accordancewith the requirements of the European Community Directive(86/609/EC) and approved by Local Ethical Committeeof the Scientific Research Institute of Physiology and BasicMedicine, protocol No. 10 (17.12.2015).Design of experiments. The levels of T- and B-lymphocytesand their subpopulations in the peripheral blood andspleen, as well as the content of proinflammatory and anti-inflammatory (IL-4and IL-10) cytokines in the brain structures were assessed in intactmice of the Disc1-Q31L and WT strains . The immune reactivity to sheep red blood cells (SRBC)was analyzed by measuring the number of antibody-formingcells (AFC) in the spleen of mice of both strains (n = 13 ofeach strain). SRBC were suspended in saline and injectedonce, intravenously into the tail vein at a dose of 5 \u00b7 108.Blood was immediately collected after the animals weredecapitated into tubes containing K3EDTA . Spleens were removed on ice on day 4 afterSRBC injection and placed in tubes with cooled RPMI-1640medium . Brain structures were dissectedon ice; brain samples were frozen in liquid nitrogenand stored at \u201370 \u00b0C until analysis.Determination of cell subpopulation. To analyze cellsubsets, 25 \u03bcl of blood was incubated for 30 minutes ina dark place with 1.5 \u03bcl (0.2\u20130.5 \u03bcg/\u03bcl) labeled rat anti-mousemonoclonal antibodies (MoAB) against surface markers:\u0421D3 , \u0421D4 , \u0421D8 , \u0421D25 (BrilliantViolet 421), \u0421D19 . Erythrocytes of theblood were lysed with Lysing Solution BD FASC . After a 10-minute incubation, the cells werewashed once with phosphate buffered saline (PBS), the cellpellet was resuspended in 100 \u03bcl of PBS.6/100 \u03bcl of the suspension and placed intoplates in a volume of 100 \u03bcl in each well. The cell suspensionwas incubated with the same MoAB as the blood cellsfor 20 minutes, and fixed by adding 1 % paraformaldehyde toeach tube. Isotypic antibodies were used as a control.The spleen was cut into several pieces, and then disaggregatedmechanically into single-cell suspension, which waspassed through a 50 \u03bcm cell strainer. The suspension waswashed twice with RPMI-1640 medium at 200 g for 5 minutes.The cell pellet was resuspended in RPMI-1640 medium,adjusted to 1 \u00b7 10+ T-lymphocytes, CD3+CD4+T-helpers, CD3+CD8+ cytotoxic/suppressor T-lymphocytes,CD3+CD4+CD25+ T-regulatory cells, CD19+ B-lymphocytesas a percentage of the total number of cells were determined.Immunoregulatory index was measured as a ratio of the contentof CD4+ to CD8+ \u0422-cells.The study of cell populations was performed on a FACSCANTO\u2122 II flow cytometer usingmulti-stage gating. At least 50 000 cells were analyzed in eachsample. Data analysis was performed using the FACSDivasoftware. The contents of CD3Determination of cytokines in the brain structures.For the analysis of cytokines, detergent-soluble fractions ofbrain tissues were prepared. The samples were thawed on ice,homogenized in lysis buffer cooled to +4 \u00b0C containing PBS(pH 7.4), 0.1 % Triton X-100, 1 mM EDTA, and 1 mM PMSFusing plastic pestles. The homogenates were incubated on icefor 30\u201340 minutes. The tissue extracts were centrifuged (Centrifuge5415 R) at 4500 rpm for 20 minutes at +4 \u00b0C. Cytokineconcentrations were determined in the supernatants. Theconcentration was normalized to tissue weight (pg/g tissue)The content of cytokines in brain homogenates was determinedaccording to the manufacturer\u2019s protocol by multipleximmunoassay on a multiplex protein and nucleic acid analyzer using a kit . The resultswere analyzed using the xPONENT and Analist software.Determination of antibody-forming cells. The immuneresponse was assessed by the relative (per 106 spleen cells)and absolute numberof IgM-AFC using the standard method .Statistical analysis. The data were analyzed using Statistica10.0 software. To verify whether data were normallydistributed, the Kolmogorov\u2013Smirnov and Shapiro\u2013Wilktests were used. Normally distributed data were assessedby one-way ANOVA. The Mann\u2013Whitney test was used forabnormally distributed data (cytokine content and AFC number).Data are presented as mean and mean error (M \u00b1 m) withsignificance set at a level of p < 0.05.Content of T-cells, their subpopulations, and B-cells in theperipheral blood and spleen of Disc1-Q31L mice. Therewere differences in the content of all analyzed immunocompetentblood cells between nonimmunized Disc1-Q31L andWT mice. The percentage of CD3+ T-lymphocytes in mice of the Disc1-Q31L strain was significantly higher than inWT mice (F(1.18) = 45.2, p < 0.001). Analysis of T-lymphocytesubpopulations showed an increase in the content ofCD3+CD4+ \u0422-helpers (F(1.17) = 15.5, p < 0.01) in Disc1-Q31Lmice compared to WT strain, while the number of CD3+CD8+T-cytotoxic/suppressor cells was decreased (F(1.17) = 12.6,p < 0.01). As a result, the immunoregulatory index, determinedas the ratio of the content of CD4+ to CD8+ T-lymphocytes, inmutant mice was 1.3 times higher (F(1.18) = 27.5, p < 0.01)than in WT mice. The content of T-regulatory cells with theCD3+CD4+CD25+ phenotype in Disc1-Q31L mice was alsohigher than in WT mice (F(1.17) = 5.3, p < 0.05). The numberof CD19+ B-lymphocytes was decreased in the peripheralblood of mutant mice compared to WT mice (F(1.17) = 5.7,p < 0.05) (see the Table).Cytokines in the brain structures in mice of the Disc1-Q31L strain. Analysis of the cytokine profile in brain structuresof intact Disc1-Q31L mice revealed regional differencesin the content of cytokines between mutant and WT mice.In the frontal cortex, levels of the three pro-inflammatorycytokines IL-6 ( p < 0.01), IL-17 ( p < 0.01) and IFN\u03b3( p < 0.01) were higher in Disc1-Q31L mice than in WT mice,while the level of IL-1\u03b2 ( p < 0.05) decreased. IL-2 and TNF\u03b1levels were similar between the mutant and WT strains( p < 0.05). As to the content of anti-inflammatory cytokines,the level of IL-4 in Disc1-Q31L mice was higher than inWT mice ( p < 0.01), while the level of IL-10 did not change( p > 0.05) .In the striatum, the content of IFN\u03b3 ( p < 0.01) was foundto be increased in Disc1-Q31L mice compared to WT animals.The levels of other pro-inflammatory cytokines \u2013 IL-1\u03b2( p < 0.01), IL-2 ( p < 0.001) in the mutant mice were lowerthan in WT mice, while the levels of IL-6, IL-17 and TNF\u03b1remained unchanged ( p > 0.05). Similarly, there were nosignificant strain differences in the levels of anti-inflammatorycytokines IL-4 and IL-10 ( p > 0.05) .When compared to WT mice, Disc1-Q31L mice showedlower levels of IL-1\u03b2 ( p < 0.01), IL-2 (p < 0.01) and IL-17( p < 0.05) in the hypothalamus, while the levels of the restcytokines were unchanged ( p > 0.05) .The levels of proinflammatory cytokines IL-1\u03b2, IL-2,IL-17, TNF\u03b1 ( p < 0.05) were significantly lower in the hippocampusof Disc1-Q31L mice than in WT mice, with morepronounced decrease in IFN\u03b3 content ( p < 0.001). The levelsof IL-6 were equivalent between Disc1-Q31 and WT mice( p > 0.05). The content of anti-inflammatory cytokine IL-10in the hippocampus of Disc1-Q31 mice was also decreased ( p < 0.05), while the level of IL-4 did not differ from that ofWT mice ( p > 0.05) .Immune reaction of Disc1-Q31L mice to the antigen.Immunization of Disc1-Q31L mice with SRBC produced anincrease of the immune response at the peak of its developmentin the spleen of WT mice. The relative ( p < 0.001) andabsolute ( p < 0.001) numbers of AFC in Disc1-Q31L micewere significantly higher than in WT mice .+ T-helpers, and the ratio of CD4+to CD8+ T-cells . Aggressive behavior, asobserved in a variety of animal models, is also associated withan increase in T-helpers and the CD4+/CD8+ ratio, as well asa higher immune response generated by an antigen .Changes in DISC1 protein activities caused by mutations inthe DISC1 gene are known to be involved in multiple mentaldisorders, such as schizophrenia, depression, bipolar disorder. Alterations in immune variables associated withthese disorders may differentially contribute to disease development.Schizophrenia has been found to be accompanied byelevated serum numbers of B-cells, along with a decrease inthe content of T-cells, CD4+CD8+ T-suppressor/cytotoxic cells, adecrease in the immunoregulatory index and the immuneresponse suppression .On the other hand, depression is characterized by increasingnumbers of CD3+ T-lymphocytes, and their subpopulations, such asCD3+CD4+ T-helpers and CD3+CD4+CD25+ T-regulatorycells, with a consequent increase of the immunoregulatoryindex. At the same time, the mutant mice showed lower percentageof CD3+ T-lymphocytes in the spleen, that might leadto a predominance of CD19+ B-cells, thereby suggesting aredistribution of these cell subsets within the immune system.The present study demonstrates that, compared to WT mice,intact mice of the Disc1-Q31L strain have raised blood levelsof CD3Redistribution of T- and B-lymphocytes, which are knownto produce specific sets of cytokines, and the ratio of thesecells in the immunocompetent organs may significantly affectinflammatory and immune processes characteristic of geneticallydetermined behaviors and psychopathology . It seems, thus, possiblethat higher ability of Disc1-Q31L mice to respond to antigenchallenge, as measured by the numbers of AFC in the spleen,may be related to changes in immune cell distribution amongdifferent compartments of the immune system.Our results have also shown that the pattern of cytokinevariations over brain structures differ in Disc1-Q31L andWT mice and depends on the brain area, in which thesecytokines are localized. The levels of IL-6, IL-17 and IFN\u03b3were found to be simultaneously increased only in the frontalcortex of Disc1-Q31L mice compared to WT animals. Thesepro-inflammatory cytokines has long been known as verypotent signaling molecules of neuroinflammation implicatedin the pathophysiology of depression, bipolar disorder, andschizophrenia .Moreover, the frontal cortex has also been associated withthe development of various psychiatric diseases .Only the IFN\u03b3 level was increased in the striatum of Disc1-Q31L mice compared to WT mice, whereas the concentrationsof other cytokines decreased. Levels of pro-inflammatory cytokineswere also lower in the hippocampus and hypothalamusof mutant mice than in WT mice. Changes in the distributionof brain cytokines found in Disc1-Q31L mice suggest thatthis mutation may contribute to neuroinflammation, whichis an important etiological factor for affective disorders. Theobserved increase in the level of anti-inflammatory cytokineIL-4 in the frontal cortex of Disc1-Q31L mice could reflecta compensatory response to the elevations of pro-inflammatorycytokines that occurred in this brain area. These findings areconsistent with previous reports, showing that various formsof depression-like behavior or aggression are associatedwith impaired balance between pro- and anti-inflammatorycytokines in a number of brain regions including the frontalcortex and hippocampus .DISC1 has been found to form a complex with other intranucleartranscription factors, which mediate the expression ofseveral genes implicated in behavioral changes resembling human psychiatric disorders . A wide rangeof studies on behavioral phenotype of Disc1-Q31L producedconflicting results. Some data indicate that mice with Q31Lmutation in Disc1 have a depressive-like enodophenotype, while others did not show significant behavioral differencesin this strain compared with the WT control in any of thetests . Recent evidence suggests that Disc1-Q31L mice may also display aggressive behavior . In contrast to the data obtained in other models, inwhich animals developing depression-like responses showedimmunosuppression , our results revealed higher immunereactivity in Disc1-Q31L mice compared to WT control. Atthe same time, immune parameters characteristic of Disc1-Q31L mice are more relevant to those observed in aggressiveanimals. It may be due to the diverse behavioral phenotype ofthese mice displaying not only depression, but also aggressivebehavior that is associated with increasedimmune function and specific pattern of cytokines.However, the mechanisms underlying alterations in peripheralimmune parameters and the profile of brain cytokines areunknown. There is growing evidence that immune mediatorssuch as cytokines are involved in the interactions betweenthe immune and neuroendocrine systems and can change theactivity of central neuromediator systems that contribute tocognitive, behavioral, and brain structure abnormalities seenin affective disorders . It is possible that the immune status of Disc1-Q31Lmice could be related to the neurochemical pattern of thebrain characteristic of this strain. Disc1-Q31L mice have beenshown to have decreased levels of DA combined with DOPACincrease in the nucleus accumbens , knownto implicate in neuroimmunomodulation . There is also data thatthe DOPAC/DA ratio, which may reflect the metabolic rate ofDA and synaptic activity, increases under immunostimulationobserved in animals experienced excessive aggression associatedwith elevated activity of the DA system . Taking into account changing DAergicactivity in the brain structures of Disc1-Q31 mice and the critical role of this system in the control ofaggression and neuroimmunomodulation , it is likely that DA maycontribute to the enhancement of immune function found inthe Disc1-Q31 strain.However, it remains unclear whether variations of centralcytokines are related to brain alterations of monoamines specificfor Disc1-Q31L mice or the Q31L mutation determinestheir profile. Moreover, it has been found that not only neurotransmitterscan affect the production of cytokines , but also cytokines can modulate mediator neurotransmissionand promote changes in the neurochemicalpattern of the brain .+CD4+CD25+ T-regulatory cell subpopulations, as wellas elevated immune reactivity in the spleen induced by theantigen. Alterations in the peripheral immune variables areaccompanied with changes in the distribution of pro- andanti-inflammatory cytokines within brain structures, whichare involved both in the control of different forms of behaviorand in immune function. The Disc1-Q31L mouse strain is apromising model for further study of the relationships betweengenetic factors and neuroimmunological mechanismsand their implication in the development of psychoemotionaldisorders.Our data indicate that the Q31L point mutation in the DISC1gene leading to the substitution of glutamine to leucineat amino acid 31 has a significant influence on immunity and may result in an amplification of peripheral T-cell linkwith an increase in the content of CD3+CD4+ T-helpers andCD3The authors declare no conflict of interest.Al\u2019perina E.L. Involvement of the dopaminergic system in the mechanismsof immunomodulation. Uspekhi FiziologicheskikhNauk = Advances in Physiological Sciences. 2014;45(3):45-56.Available at: https://elibrary.ru/item.asp?id=22265117. (in Russian)Alperina E., Idova G., Zhukova E., Zhanaeva S., Kozhemyakina R.Cytokine variations within brain structures in rats selected for differencesin aggression. Neurosci. Lett. 2019;692:193-198. DOI10.1016/j.neulet.2018.11.012.Alperina E.L., Kulikov A.V., Popova N.K., Idova G.V. Immune responsein mice of a new strain ASC .Bull. Exp. Biol. Med. 2007;144(2):221-223. DOI10.1007/s10517-007-0294-5.Clapcote S.J., Lipina T.V., Millar J.K., Mackie S., Christie S., OgawaF., Lerch J.P., Trimble K., Uchiyama M., Sakuraba Y., KanedaH., Shiroishi T., Houslay M.D., Henkelman R.M., Sled J.G.,Gondo Y., Porteous D.J., Roder J.C. Behavioral phenotypes ofDisc1 missense mutations in mice. Neuron. 2007;54(3):387-402.DOI 10.1016/ j.neuron.2007.04.015.Dantzer R. Neuroimmune interactions: from the brain to the immunesystem and vice versa. Physiol. Rev. 2018;98(1):477-504. DOI10.1152/physrev.00039.2016.Devoino L.V., Idova G.V., \u0410lperina E.L. Psychoneuroimmunomodulation:Behavior and Immunity. A Role of \u201cNeuromediator Patternof the Brain\u201d, Novosibirsk: Nauka Publ., 2009. Available at:https://elibrary.ru/item.asp?id=19548477 (in Russian)Dubrovina N.I., Khrapova M.V., Lipina T.V. Characteristics of theformation of memories relating to fear in mice with depressionandschizophrenia-like phenotypes: effects of gender and age.Neurosci. Behav. Physiol. 2018;48(4):488-495. DOI 10.1007/s11055-018-0590-8.Dunn A.J. Effects of cytokines and infections on brain neurochemistry.Clin. Neurosci. Res. 2006;6(1-2):52-68. DOI 10.1016/j.cnr.2006.04/002.Felger J.C., Lotrich F.E. Inflammatory cytokines in depression:neurobiological mechanisms and therapeutic implications. Neuroscience.2013;246:199-229. DOI 10.1016/neuroscience.2013.04/060.Grigor\u2019ian G.A., Dygalo N.N., Gekht A.B., Stepanichev M.Iu., GuliaevaN.V. Molecular and cellular mechanisms of depression. Roleof glucocorticoids, cytokines, neurotransmitters, and trophic factorsin genesis of depressive disorders. Uspekhi FiziologicheskikhNauk = Advances in Physiological Sciences. 2014;45(2):3-19. (inRussian)Haroon E., Raison C.L., Miller A.H. Psychoneuroimmunology meetsneuropsychopharmacology: translational implications of the impactof inflammation on behavior. Neuropsychopharmacology.2012;37(1):137-162. DOI 10.1038/npp.2011.205.Hikida T., Gamo N.J., Sawa A. DISC1 as a therapeutic target formental illnesses. Expert Opin. Ther. Targets. 2012;16(12):1151-1160. DOI 10.1517/14728222.2012.719879.Idova G., Alperina E., Gevorgyan M., Zhukova E., Kulikov A.,Yur\u2019ev D. T-lymphocyte subpopulation composition and the immuneresponse in depression-like behavior in ASC mice. Neurosci.Behav. Physiol. 2013;43(8):946-950. DOI 10.1007/s11055-013-9833-x.Idova G., Alperina E., Plyusnina I., Gevorgyan M., Zhukova E., KonoshenkoM., Kozhemyakina R., Wang S.W. Immune reactivityin rats selected for the enhancement or elimination of aggressivenesstowards humans. Neurosci. Lett. 2015;609:103-108. DOI10.1016/ j.neulet.2015.10.027.Idova G.V., Al\u2019perina E.L., Zhanaeva S.Ya., Gevorgyan M.M.,Rogozhnikova A.A. Cytokine content in the hypothalamus andhippocampus of C57BL/6J mice with depressive-like behavior.Bull. Exp. Biol. Med. 2019;167(1):11-16. DOI 10.1007/s10517-019-04450-y.Idova G., Gevorgyan M., Alperina E., Zhanaeva S.Ya., Markova E.V.Cytokine production by splenic cells in C57BL/6J mice with depressive-like behavior depends on the duration of social stress.Bull. Exp. Biol. Med. 2018;164(5):645-649. DOI 10.1007/s10517-018-4050-9.Kawano M., Takagi R., Saika K., Matsui M., Matsushita S. Dopamineregulates cytokine secretion during innate and adaptiveimmune responses. Int. Immunol. 2018;30(12):591-606. DOI10.1093/intimm/dxy057.Ladics G.S. Primary immune response to sheep red blood cells(SRBC) as the conventional T-cell dependent antibody response(TDAR) test. J. Immunotoxicol. 2007;4(2):149-152. DOI 10.1080/15476910 701337357.Lesh T.A., Careaga M., Rose D.R., McAllister A.K., Van de WaterJ., Carter C.S. Ashwod P. Cytokine alterations in first-episodeschizophrenia and bipolar disorder: relationships to brain structureand symptom. J. Neuroinf lammation. 2018;15:165. DOI 10.1186/s12974-018-1197-2s.Lipina T.V., Fletcher P.J., Lee F.H., Wong A.H., Roder J.C. Disrupted-in-schizophrenia-1 Gln31Leu polymorphism results insocial anhedonia associated with monoaminergic imbalance andreduction of CREB and \u03b2-arrestin-1,2 in the nucleus accumbens ina mouse model of depression. Neuropsychopharmacology. 2013;38(3):423-436. DOI 10.1038/npp.2012.197.Lipina T.V., Niwa M., Jaaro-Peled H., Fletcher P.J., Seeman P.,Sawa A., Roder J.C. Enhanced dopamine function in DISC1-L100P mutant mice: implications for schizophrenia. Brain Behav.2010;9:777-789. DOI 10.1111/j.1601-183X.2010.00615.x.Lipina T.V., Roder J.C. Disrupted-in-Schizophrenia-1 (DISC1) interactomeand mental disorders: impact of mouse models. Neurosci.Biobehav. Rev. 2014;45:271-294. DOI 10.1016/j.neubiorev.2014.07.001.Mathieson I., Munaf\u00f2 M.R., Flint J. Meta-analysis indicates thatcommon variants at the DISC1 locus are not associated withschizophrenia. Mol. Psychiatry. 2012;17(6):634-641. DOI 10.1038/mp.2011.41.Ottaway \u0421.A., Husband A. The influence of neuroendocrine pathwayson lymphocyte migration. Immunol. Today. 1994;5(11):511-571. DOI 10.1016/0167-5699(94)90206-2.Saurer T.B., Carrigan K.A., Ijames S.G., Lysle D.T. Suppression ofnatural killer cell activity by morphine is mediated by the nucleusaccumbens shell. J. Neuroimmunol. 2006;173(1-2):3-11. DOI10.1016/j.jneuroim.2005.11.009Serykh A., Khrapova M.V., Dubrovina N.I., Petrova E.S., MikhnevichN., Starostina M.V., Amstyslavskaja T.G., Lipina T.V. Theincreased density of the habenular neurons, high impulsivity, aggressionand resistant fear memory in Disc1-Q31L genetic mousemodel of depression. Behav. Brain Res. 2020;392:112693. DOI10.1016/ j.bbr.2020.112693.Shoji H., Toyama K., Takamiya Y., Wakana S., Gondo Y., MiykawaT. Comprehensive behavioral analysis of ENU-induced Disc1-Q31L and -L100P mutant mice. BMC Res. Notes. 2012;5:108.DOI 10.1186/1756-0500-5-108.Steiner J., Jacobs R., Panteli B., Brauner M., Schiltz K., Bahn S.,Herberth M., Westphal S., Gos T., Walter M., Bernstein H.G.,Myint A.M., Bogerts B. Acute schizophrenia is accompanied byreduced T cell and increased B cell immunity. Eur. Arch. PsychiatryClin. Neurosci. 2010;260(7):509-518. DOI 10.1007/s00406-010-0098-x.Takahashi A., Flanigan M.E., McEwen B.S., Russo S.J. Aggression,social stress, and the immune system in humans and animalmodels.Front. Behav. Neurosci. 2018;12:56. DOI 10.3389/fnbeh.2018. 00056."} +{"text": "The SARS-CoV-2 B.1.617 lineage variants, Kappa (B.1.617.1) and Delta emerged during the second wave of infections in India, but the Delta variants have become dominant worldwide and continue to evolve. Here, we compared B.1.617 variants for neutralization resistance by convalescent sera, mRNA vaccine-elicited sera, and therapeutic neutralizing antibodies using a pseudovirus neutralization assay. B.1.617.1, B.1.617.2, and AY.1 pseudoviruses showed a modest 1.5- to 4.4-fold reduction in neutralization by convalescent sera and vaccine-elicited sera. In comparison, similar modest reductions were also observed for C.37, P.1, R.1, and B.1.526 pseudoviruses, but 7- and 16-fold reductions for vaccine-elicited and convalescent sera, respectively, were seen for B.1.351 pseudoviruses. Among twenty-three therapeutic antibodies tested, four antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses and six antibodies showed either complete or partial loss of neutralization against B.1.617.1 and AY.1 pseudoviruses. Our results indicate that the current mRNA-based vaccines will likely remain effective in protecting against B.1.617 variants. Finally, the P681R substitution confers efficient cleavage of B.1.617 variants\u2019 spike proteins and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants. SARS-CoV-2 trimeric spike (S) glycoprotein on the virion surface binds the angiotensin-converting enzyme (ACE2) to facilitate cellular entry and is the target of therapeutic neutralizing antibodies and vaccines [685|S686 into S1 and S2 subunits, which facilitates subsequent cleavage at the S2\u2032 site (R815|S816) by TMPRSS2 for viral entry into respiratory cells. The S1 subunit spans the N-terminal domain (NTD) and the receptor-binding domain (RBD) within the C-terminal domain (CTD) whereas the S2 subunit spans the fusion peptide and a linker region flanked by heptad repeat regions that drive virus-cell membrane fusion [Since its origin in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally to cause a coronavirus disease 2019 (COVID-19) pandemic that recorded more than 263 million infections and has claimed 5.2 million lives thus far ,9,10,11.Several key substitutions in the RBD of spike were demonstrated to either enhance affinity towards ACE2 or contribute to immune escape. The E484K substitution in the RBD of B.1.351, P.1, R.1, and B.1.526 variants was previously identified among in vitro escape mutants selected against single antibody and antibody cocktails ,14. SeveThe spike protein of the B.1.617.2 variant contains nine substitutions and deletions compared to the early D614G variant used here as wild type (WT or D614G). The three substitutions and two deletions in NTD occur in the NTD antigenic supersite spanning between residues 14\u201320, 140\u2013158, and 245\u2013264 . In addiThe global dominance and ongoing evolution of B.1.617 lineage variants require continuing assessment of the neutralization potency of convalescent sera, vaccine-elicited sera, and therapeutic neutralizing antibodies against emerging B.1.617 variants. Here, we measured the neutralization potency of convalescent sera, vaccine-elicited sera, and therapeutic neutralizing antibodies against two independent variants each in the Kappa (B.1.617.1) and Delta lineages and assessed the contribution of the RBD substitutions in conferring resistance. We found that resistance to convalescent and vaccine-elicited sera was predominantly conferred by RBD substitutions E484Q, T478K, and L452R. Furthermore, out of 23 therapeutic neutralizing antibodies tested, Kappa and Delta pseudoviruses displayed complete resistance to five neutralizing antibodies and partial resistance to one antibody. Finally, we showed that the P681R substitution confers enhanced furin processing in spike protein of B.1.617 lineage variants that corresponded to enhanced cell-cell fusion activity. However, only Delta spike protein exhibited greater sensitivity to soluble ACE2 inhibition, implying enhanced ACE2 affinity. This feature along with enhanced cell-cell fusion activity may contribute to the dominance of the B.1.617.2 variant.Use of de-identified sera in this study was approved by the U.S. Food and Drug Administration Research in Human Subjects Committee. Vaccine-elicited sera were collected at the U.S. Food and Drug Administration with written consent under an approved Institutional Review Board (IRB) protocol (FDA IRB Study # 2021-CBER-045).Codon-optimized full-length open reading frames of the S genes of SARS-CoV-2 variants were cloned into pcDNA3.1(+) or pVRC8400 by GenScript . The codon optimization for gene expression in human cell was performed by GenScript\u2019s OptimumGene algorithm system to optimize the following parameters: codon usage bias, GC content, CpG dinucleotides content, mRNA secondary structure, internal chi sites and ribosomal binding sites, negative CpG islands, cryptic splicing sites, premature PolyA sites, PolyT sites, RNA instability motif (ARE), and repeat sequences . The codon-optimized sequence of Wuhan-Hu-1 S gene is shown in n = 10) collected 6\u201361 days after symptom onset were purchased from Bocabiolistics . Donors were 18\u201373 years old with six males/four females. The information about the convalescent sera is shown in n = 15) or Moderna mRNA-1273 vaccinated individuals (n = 14) obtained two weeks after the second vaccination were used in this study. Vaccinated individual donors were 21\u201365 years old with six males/nine females for Pfizer BNT162b2 vaccination and eight males/six females for Moderna mRNA-1273 vaccination. All sera were tested negative for non-specific neutralization using amphotropic murine leukemia enveloped pseudovirus. Vaccinated donors were prescreened for absence of both history of SARS-CoV-2 infection and SARS-CoV-2 neutralizing antibodies prior to vaccination. Twenty-three therapeutic neutralizing antibodies against SARS-CoV-2 spike protein were donated by different pharmaceutical companies for the U.S. government COVID-19 response Therapeutics Research Team efforts to define neutralization profiles against existing and emerging SARS-CoV-2 variants [Convalescent sera from SARS-CoV-2-infected donors as described previously .6 relative luminescence units (RLU)/mL of luciferase activity were incubated with serially diluted sera or antibodies for two h at 37 \u00b0C. Pseudovirus and serum or antibody mixtures (100 \u03bcL) were then inoculated onto the plates pre-seeded one day earlier with 3.0 \u00d7 104 cells/well. Pseudovirus infectivity was scored 48 h later for luciferase activity. The antibody concentration or inverse of the sera dilutions causing a 50% reduction of RLU compared to control was reported as the neutralization titer. Titers were calculated using a nonlinear regression curve fit . The mean titer from at least two independent experiments each with intra-assay duplicates was reported as the final titer. WT(D614G) pseudovirus was run as a control for every assay.HIV-based lentiviral pseudoviruses with spike proteins were generated as previously described . The B.16 RLU/mL) for one hour at 37 \u00b0C and 100 \u03bcL of pseudovirus and soluble ACE2 mixture was added to 293T-ACE2.TMPRSS2 cells. Luciferase activity was measured 48 h later. The soluble ACE2 concentration causing a 50% reduction of RLU compared to control was reported as the 50% inhibitory concentration or IC50.For ACE2 neutralization assay, serially diluted recombinant human soluble ACE2 was incubated with indicated pseudovirus .4 cells per well on a 96-well plate. The cells were co-cultivated for 24 h at 37 \u00b0C. The culture supernatants were then removed, and cell-cell fusion was scored by determination of the \u03b2-gal activity in co-cultured cell lysates using a Galacto-Star kit according to the manufacturer\u2019s instructions.For measuring spike-protein-mediated cell-cell fusion, \u03b2-gal complementation assay was performed as described previously . BrieflyTo ensure equivalent amount of spike cell surface expression levels among treatments, spike-transfected \u03b2-gal \u03c9 subunit-expressing 293T cells were quantified for cell surface spike levels by flow cytometry. Spike-transfected 293T cells employed in cell-cell fusion assay were concurrently stained with SARS-CoV-2 positive human polyclonal sera at 1:20 dilution, washed twice, and then incubated with FITC-conjugated goat anti-human . The cells were washed twice and then fixed with 2% paraformaldehyde. The results were acquired using BD LSRFortessa\u2122 X-20 Cell Analyzer . The mean fluorescence intensities of spike positive cells were recorded.https://github.com/acorg/Racmacs, accessed on: 15 October 2021) [We created a geometric interpretation of neutralization titers against the tested SARS-CoV-2 pseudoviruses using Racmacs antigenic cartography software (Sam Wilks (2021), Racmacs: R Antigenic Cartography Macros. R package version 1.1.16. er 2021) ,37. The http://www.cbs.dtu.dk/services/ProP/ (accessed on: 15 July 2021) and the PiTou V3 software hosted at http://www.nuolan.net/reference.html (accessed on: 15 July 2021).The prediction of furin-specific cleavage site in spike proteins was computed using the ProP 1.0 Server hosted at p values of less than 0.05 were considered statistically significant. All neutralization titers were log2 transformed for analyses.One-way analysis of variance (ANOVA) with Dunnett\u2019s multiple comparisons tests (variants compared to WT(D614G)), Mann\u2013Whitney test for the comparison of two groups with unmatched pairs (Pfizer BNT162b2 compared to Moderna) and geometric mean titers (GMT) with 95% confidence intervals were performed using GraphPad Prism software. The We first investigated the cross-neutralization potency of convalescent sera from individuals infected with SARS-CoV-2 in the U.S. against pseudoviruses bearing spikes of B.1.617.1 and B.1.617.2 variants and their corresponding RBD mutations A. TitersThe C.37 variant also has a substitution at L452 residue (L452Q instead of L452R) along with F490S in the RBD. A modest 1.8-fold reduction in titers against C.37 pseudoviruses was observed compared to WT(D614G) pseudoviruses . A 1.4-fold reduction in titers was observed for pseudoviruses with only the L452Q and F490S substitutions, indicating that these RBD substitutions contribute to C.37 resistance. These findings are in agreement with a prior report showing a 3.3-fold reduction of convalescent sera neutralization titer for C.37 pseudoviruses compared to WT(D614G), as well as L452Q and F490S single substitutions contributing to neutralization resistance . In compBecause the convalescent sera came from individuals who were previously infected by different variants , we alsoSera from the group infected by variants that had the L452R substitution showed similar fold changes in neutralization titers as the group infected by WT(D614G) variants without the L452R except against B.1.617.1 (B) and AY.1 pseudoviruses. Fold changes in neutralization titers against B.1.617.1 (B) and AY.1 variants were 3.3 and 1.3, respectively, for the L452 group, compared to 5.2 and 2.5, respectively, for the WT(D614G) group B,C. The p = 0.1225, Mann\u2013Whitney test). The Moderna mRNA-1273 vaccine-elicited sera trended towards higher neutralization titers against most variants compared to Pfizer/BioNtech BNT162b2, possibly due to higher vaccine mRNA content and greater interval between priming and boosting for Moderna mRNA-1273 (4 weeks vs. 3 weeks for Pfizer/BioNtech BNT162b2) [We next assessed the neutralization potency of mRNA vaccine-elicited sera against WT(D614G) and B.1.617 variant pseudoviruses. Sera from fourteen individuals who received two doses of Moderna mRNA-1273 vaccine and fifteen individuals who received two doses of Pfizer/BioNtech BNT162b2 vaccine were collected approximately two weeks after the second immunization. Each vaccine-elicited serum had high neutralization titers against WT(D614G) pseudoviruses, ranging between 578 and 3935 for Pfizer/BioNtech BNT162b2 and 651 and 5853 for Moderna mRNA-1273 A,B (PfizNT162b2) . CompareNT162b2) ,39.We also investigated the contribution of individual RBD substitutions of B.1.617.1 and B.1.617.2/AY.1 on the D614G background. Titers against L452R (GMT 935 for Pfizer and 1781 for Moderna) and E484Q (GMT 798 for Pfizer and 1429 for Moderna) alone trended slightly lower. Likewise, titers against K417N (GMT 1208 for Pfizer and 2070 for Moderna) and T478K (GMT 1046 for Pfizer and 2113 for Moderna) alone or in L452R + T478K combination (GMT 964 for Pfizer and 1796 for Moderna) remained comparable to GMTs of WT(D614G) .Similarly, GMTs against B.1.1.7 (955 for Pfizer and 1917 for Moderna) and B.1.429 variant with the L452R substitution (1063 for Pfizer and 1799 for Moderna) were comparable to those against WT(D614G). Consistent with previous observations, the B.1.351 variant (GMT 169 for Pfizer and 306 for Moderna) displayed ~7-fold lower titers compared to WT(D614G), whereas C.37, P.1, R.1, and B.1.526 variants displayed modestly reduced titers that are similar to the titers against B.1.617 pseudoviruses (GMT 452\u2013707 for Pfizer and GMT 824\u20131332 for Moderna). Overall, the trends in neutralization titers for the vaccine-elicited sera against a large panel of variant pseudoviruses were similar to those for convalescent sera, though the GMTs were approximately 3- to 5-fold higher for vaccine-elicited sera.A prior study showed that convalescent sera and vaccine-elicited antibody neutralization titers against pseudoviruses bearing spikes containing L452R-E484Q-P681R substitutions displayed 2\u20135-fold reduction, compared to the neutralization titers against WT(D614G) pseudoviruses . In thisn = 10,000 antigenic maps were made by resampling sera with replacement pseudovirus and the WT(D614G) sera and L452R sera, including K417N, L452R, T478K, L452Q + F490S, and B.1.429 (0.25 to 0.72 antigenic units (AU) from WT . B.1.617The antigenic map of the same SARS-CoV-2 variant pseudoviruses for vaccine-elicited sera showed similar patterns to the convalescent sera map but with some notable differences. Again, pseudoviruses K417N, L452R, T478K, L452Q + F490S, and B.1.429 were close to WT(D614G) (0.05\u20130.51 AU). However, E484Q and C.37 were both closer to WT(D614G) but were poorly coordinated and extended in elongated shapes around WT(D614G). B.1.617.1 was also slightly closer to WT(D614G) at 1.55 AU and was positioned adjacent to the other variants. Unexpectedly, AY.1 was between B.1.617.2 and B.1.351 and was further away from WT(D614G) (1.89 AU) than in the convalescent sera map (1.60 AU), being positioned only slightly closer to WT(D614G) than B.1.351 was from WT(D614G) (3.02 AU). These antigenic maps reinforce what was observed in terms of neutralizing antibody titers. Compared to the convalescent sera map, there was a larger antigenic difference between AY.1 and WT(D614G) on the vaccine-elicited sera map.Notably, given that the vaccine-elicited sera had much higher titers than convalescent sera across variants, the titers against AY.1 were still higher in vaccinated individuals, meaning the antigenic difference may not translate into loss of vaccine protection. Furthermore, vaccine-elicited sera saw a smaller difference between B.1.351 and WT(D614G) than the convalescent sera, which may have aligned AY.1 and B.1.351 closer together. Overall, while these antigenic maps provide meaningful information on the relative positions of antigens, they are limited by the sera being so tightly clustered. Future antigenic maps with sera against distinct variants would enable more accurate evaluation of antigenic variation among the variants.We next evaluated 23 clinical-stage therapeutic neutralizing antibodies for potency against the B.1.617 variants. These antibodies were evaluated as part of the U.S. Government COVID-19 response effort to inform the clinical testing and use of these antibodies [B.1.617.1 pseudoviruses displayed complete resistance (>50-fold) to five nAbs and partial resistance (10\u201350-fold) to one nAb (H) . The E48B.1.617.2 pseudoviruses displayed complete resistance (>50-fold) to three nAbs and partial resistance (10\u201350-fold) to one nAb (H) B. The L4Prior reports indicated increased infectivity of pseudoviruses containing the L452R substitution in spike in 293T-ACE2.TMPRSS2 cells due to L452R conferring enhanced RBD affinity to ACE2 ,27. We t50) of sACE2 against B.1.617.2 was 4.2-fold lower, compared to WT(D614G) (IC50: 2.88 \u00b5g/mL) and L452R + T478K displayed 2.4- and 2.3-fold higher sensitivity to inhibition by sACE2. However, pseudoviruses with only spike RBD substitutions , as well as the B.1.617.1 (IC50:2.03 \u00b5g/mL) and AY.1 (IC50:1.97 \u00b5g/mL) spikes, displayed comparable IC50 to WT(D614G) (0.5\u20131.5-fold change) . In agre change) . These fSince P681H enhanced proteolytic processing of B.1.1.7 spike ,49, we nTo gain further insight into the furin processing efficiency at the S1/S2 site of the B.1.617 S, we undertook a bioinformatic approach utilizing the PiTou and ProP furin cleavage prediction tools, comparing B.1.617 to the Wuhan-Hu-1 (D614) prototype spike and B.1.1.7 spike, as well as spike proteins of several lineage-specific mammalian and animal CoVs. The PiTou algorithm combines a hidden Markov model and knowledge-based cumulative probability score functions for the functional characterization of a 20 amino acid cleavage motif from P14 to P6\u2032 for furin binding and cleavage, whereas ProP predicts furin cleavage sites based on experimental data-derived networks ,54. Both679- R685 and E661- R685 have been reported to have host neuropilin-1 attachment [While SARS-CoV-2 S1/S2 P\u2212R\u2212R\u2212A\u2212R furin cleavage site conforms to a minimal furin recognition motif, R\u2212X\u2212X\u2212R, the presence of H/R instead of P increases the total number of basic residues to four. This presence of basic residue H/R results in additional electrostatic and intramolecular hydrogen bonding to gain substrate turnover . In facttachment and staptachment .Furin cleavage score analysis of CoV S1/S2 cleavage sites. CoV spike and influenza hemagglutinin (HA) sequences were analyzed using the ProP 1.0 and PiTou 3.0 furin prediction algorithms, generating a score with bold numbers indicating predicted furin cleavage. \u201c|\u201d denotes the position of the furin cleavage site. Sequences corresponding to the S1/S2 region of NL63 (APF29063.1), 229E (ABB90529.1), SARS-CoV-2 (QHD43416.1), SARS-CoV (AAT74874.1), MERS-CoV (AFS88936.1), HCoV-HKU1 (AAT98580.1), HCoV-OC43 (APU51936) Bat-SL-CoVZC45 (AVP78031.1) BatCoV-HKU4 (YP_001039953.1), Influenza A/Chicken/Hong Kong/822.1/01/H5N1 HA (AF509026.2), Influenza A virus HA (A/Wisconsin/67/2005(H3N2) (ACF54576.1), infectious bronchitis virus (QIV13719.1), CoV-HKU9 (YP_001039971), BatCoV-PML (AGY29650), BatCoV-HKU5 (YP_001039962.1), Bat-CoV RaTG13 (QHR63300.2), and Bat-SL-CoVZXC21 (AVP78042.1) were obtained from GenBank. Sequences corresponding to the S1/S2 region of SARS-CoV-2 B.1.1.7 (EPI_ISL_1374509), B.1.617.1 (EPI_ISL_1841346), B.1.617.2 (EPI_ISL_2229775), B.1.617.3 (EPI_ISL_2157058), Bat CoV RmYN02 (EPI_ISL_412977), as well as HA of Influenza A virus ) (EPI1859607) were obtained from GISAID.To quantify whether higher ACE2 binding and furin cleavage of B.1.617.2 spike augments fusion between virus and/or cell membranes, we performed cell-cell fusion assays by complementing \u03b2-galactosidase subunits in spike-transfected effector cells and 293T-ACE2.TMPRSS2 target cells. Compared to WT(D614G), both B.1.617.1 and B.1.617.2 spikes induced significantly higher cell-cell fusion activity when controlled for spike cell surface expression (4000 MFI of spike protein on cell surface) B. Our fiHere we show that pseudoviruses bearing B.1.617.1 spike with L452R and E484Q substitutions, and B.1.617.2 spike with K417N, L452R and T478K substitutions, have modestly reduced susceptibility to neutralization by Pfizer/BioNtech BNT162b2 or Moderna mRNA-1273 vaccine-elicited sera and convalescent sera compared to pseudoviruses bearing WT(D614G) spike. The individual L452R, T478K, E484Q, and dual L452R + T478K substitutions accounted for most but not all of the reduction in neutralization potency of the sera, suggesting contributions from substitutions in the NTD/CTD. Neutralization titers, as well as antigenic maps, indicated that the full set of RBD substitutions in combination with substitutions outside the RBD contributes to antigenic differences of B.1.617.1, B.1.617.2, and C.37 variants. Antigenic distances between the variants also tended to be more spaced apart in the map generated by the convalescent sera compared to the vaccine-elicited sera. Limitations in our study include the small number of sera samples in the convalescent and vaccine cohorts. Potential differences in COVID-19 severity in the convalescent sera cohort and time of sera collection could also affect neutralization titers. Nonetheless, most sera from convalesced and vaccinated individuals neutralized the B.1.617.1, B.1.617.2, and AY.1 variants. Furthermore, 17 of 23 therapeutic neutralizing antibodies retained complete neutralization against B.1.617 variants. Resistance to the remaining therapeutic neutralizing antibodies is due to RBD substitutions, K417N, L452R, and E484Q, but not T478K. These findings suggest that the two-dose immunization with current mRNA vaccines will likely induce protective immunity against the tested B.1.617 variants. However, as B.1.617.2 variants continue to evolve, it will be important to continue to monitor how new substitutions in spike impact their resistance to therapeutic neutralizing antibodies and vaccine efficacy."} +{"text": "With an aging population and increasing healthcare utilization, the frequency of hospital-acquired pneumonia (HAP) is expected to increase. Since HAP is life threatening, appropriate diagnosis and treatment are required; however, large-scale Japanese data focusing on patient profiles and treatment patterns is lacking.The demographics and treatment patterns of HAP were examined using a large-scale Japanese claims database from Jan. 2016 to Apr. 2018. The HAP population included patients who received injection antibiotics \u22673 consecutive days after admission, but not within 2 days after admission, and those whose reason for hospitalization was not pneumonia but had a diagnosis of pneumonia after hospitalization (based on ICD-10 codes).2,968 HAP patients contributing 2,979 total HAP episodes were included. The 12-month pre-index mean Charlson Comorbidity Index (CCI) score was 4.0\u00b13.1 (mean\u00b1SD), CCI scores \u22674 comprised 44.0%. Most HAP episodes (77.6%) occurred \u22675 days after hospitalization. During the 12month pre-index period including outpatients, 84.9% of patients had some type of pneumonia record, 9.1% had VAP (ventilator associated pneumonia) records, and 7.4% had anti-MRSA prescription records. For post-index HAP treatment, ampicillin/sulbactam and piperacillin/tazobactam were frequently prescribed as the first antibiotic prescription. Ceftriaxone (19.4%) and meropenem (9.8%) were also frequently prescribed. Examinations prescribed during HAP: 30.5% blood culture tests, 28.2% sputum examinations and 29.2% urine antigen tests. The overall mortality rate of HAP in overall hospitalization post-index was 22.0%, in which 14.4% of deaths occurred within 30 days. The mean (\u00b1SD) length of overall hospital stay was 49.9 (\u00b134.2) days (11.3 days for HAP period), with 12.4% ICU use and 17.6% ventilator use. The median total cost during hospitalization was \u00a51,924,848.18 .The data revealed patient characteristics, treatment patterns, mortality rates and healthcare costs in Japanese HAP patients. This database approach should prove useful for discussing antibiotics usage trends in highly aging Japan.Masahiro Kimata, PhD, MSD K.K., Tokyo, Japan (Employee) Yosuke Aoki, MD, PhD, MSD K.K., Tokyo, Japan SHIONOGI & Co., Ltd Adachi Noriaki, n/a, MSD K.K., Tokyo, Japan (Employee) Takeshi Akiyama, MSc, MSD K.K., Tokyo, Japan (Independent Contractor) Akiko Harada, n/a, MSD K.K., Tokyo, Japan (Employee)"} +{"text": "The phase IIIb ATLAS-2M study demonstrated non-inferiority of long-acting (LA) cabotegravir (CAB) + rilpivirine (RPV) dosed every 8 weeks (Q8W) compared with every 4 weeks (Q4W) for maintenance of virologic suppression. Hepatitis C virus (HCV) co-infection occurs in ~6% of people with HIV due to shared modes of transmission. We report efficacy and safety of CAB + RPV LA in participants with HIV/HCV co-infection in ATLAS-2M.Participants with HIV-1 RNA < 50 c/mL receiving CAB + RPV LA Q4W (transitioned from ATLAS [NCT02951052]) or oral comparator ART were randomized 1:1 to receive CAB + RPV LA Q4W or Q8W. Baseline HCV RNA was assessed by polymerase chain reaction. Participants with symptomatic chronic HCV infection requiring treatment within 12 months or liver enzymes not meeting entry criteria were excluded. Week 48 assessments included proportion with HIV-1 RNA \u226550 and < 50 c/mL , general and hepatic safety, and pharmacokinetics.HIV/HCV co-infection was present in 10 (1%) of 1045 participants, 60% of whom were female at birth. At Week 48, 9/10 (90%) and 972/1035 (94%) participants with HIV/HCV co-infection and HIV mono-infection, respectively, had HIV-1 RNA < 50 c/mL . No participants with HIV/HCV co-infection had HIV-1 RNA \u226550 c/mL (vs 14/1035 [1%] with HIV mono-infection) or confirmed virologic failure through Week 48 (vs 10 [1%] with HIV mono-infection); 1/10 (10%) discontinued for reasons other than adverse events (AEs). Excluding injection site reactions (ISRs), AEs and serious AEs were reported in 4 (40%) and 0 participants with HIV/HCV co-infection, respectively; the only AE reported in >1 participant was injection site pain . In participants with HIV/HCV co-infection, all ISRs were grade 1/2; none led to withdrawal. No hepatic laboratory abnormalities were reported in participants with HIV/HCV co-infection through Week 48; rates were low in those with HIV mono-infection (Table). Plasma CAB and RPV concentrations were similar between groups.CAB + RPV LA was effective and well tolerated in this small cohort of participants with HIV and asymptomatic HCV co-infection.Ronald D\u2019Amico, DO, MSc, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Paul Benn, MB ChB FRCP, ViiV Healthcare (Employee) Shanker Thiagarajah, MB ChB, GlaxoSmithKline Susan L. Ford, PharmD, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Eileen Birmingham, MD, MPH, Janssen Research and Development Ojesh R. Upadhyay, MPH, MBA, GlaxoSmithKline (Employee) Louise Garside, PhD, GlaxoSmithKline (Employee) Rodica Van Solingen-Ristea, MD, Janssen Research and Development (Employee)ViiV Healthcare (Employee) Kati Vandermeulen, M.SC., Janssen Research and Development (Employee) William Spreen, PharmD, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee)"} +{"text": "Scientific Reports 10.1038/s41598-021-99672-4, published online 11 October 2021Correction to: The Preprint section in the original version of this Article was omitted. The Preprint section now reads:58.\u201d\u201cThis article was submitted to an online preprint archiveAs a result Reference 58 was omitted, which is listed below.et al. Host Genetics Underlying Pathological Outcomes to Mycobacterium Avium Subsp. Paratuberculosis Infection is Governed by Distinct Genetic Variants. Preprint at 10.21203/rs.3.rs-668666/v1 (2021).58. Canive, M., The original Article has been corrected."} +{"text": "This study examined physical activity (FITNESS) and social relationships (FRIENDS) on social engagement among community older adults. Members from two Florida aging-in-village programs participated. Three five-Likert scales were used: A 5-item FITNESS , 4-item FRIEND , and a 3-item social engagement scales . Among the 96 participants, 79% were females, 91% were whites, 56% were married, 86% had college education, and 46% living alone. Mean age was 70.7 (SD=10.10). Participants reported at least 30-min. physical activity about 4.2 days per week. Overall social engagement was high (mean=4.38), FITNESS was median (mean=3.46), and FRINED was high (mean=4.19). FITNESS was significant to more 30-min. physical activity. Yet, higher FITNESS, FRIENDS, age, and volunteers were all significant to social engagement. Results has implications on promoting social engagement among older adults participating in aging-in-community programs."} +{"text": "Staphylococcus aureus bacteremia (pMRSAB) is unclear. Vancomycin plus ceftaroline (V/C) has demonstrated potent in vitro synergistic activity against MRSA; however, clinical data is limited. Thus, we sought to evaluate V/C salvage therapy for pMRSAB.The preferred antibiotic salvage regimen for persistent methicillin-resistant \u2265 72 hours, received anti-MRSA monotherapy initially, and subsequently received V/C \u2265 24 hours. Patients were excluded if they received other anti-MRSA antibiotics within 72 hours of V/C initiation. The primary outcome was time to BC clearance following V/C initiation. Secondary outcomes included 90-day all-cause mortality, microbiological cure, 90-day MRSAB recurrence, and length of stay (LOS). Microbiological cure was defined as BC clearance.This was a single-center, retrospective cohort study of patients with MRSAB who received V/C salvage therapy between 1/1/2016-3/10/2021. Adult patients were included if blood cultures (BC) were positive for MRSA for Of 178 patients identified, 20 were evaluated after inclusion and exclusion criteria were applied. Mean (SD) age and Pitt Bacteremia score were 38.5 (14.5) years and 4.2 (3.1), respectively. Most patients were male (70%), intravenous drug users (65%), and admitted to the intensive care unit (65%). The most common source was intravenous drug use (55%) and the majority had infective endocarditis (70%). All patients received infectious disease consultation and median (IQR) vancomycin AUC:MIC was 527 . Source control, if possible, was obtained in most patients (55%). Median (IQR) time to bloodstream clearance from first positive BC and from when ceftaroline was initiated was 9.7 and 2.4 days, respectively. 90-day all-cause mortality, microbiological cure, and 90-day MRSAB recurrence occurred in 35%, 95%, and 5% of patients, respectively. Median (IQR) LOS was 25 days.To our knowledge, this is the largest cohort to evaluate V/C for pMRSAB. Patients were medically complex; however, median time to MRSAB clearance following ceftaroline initiation was < 2.5 days and microbiological cure was obtained in nearly all patients. V/C may represent a potential salvage regimen for pMRSAB.Wesley D. Kufel, PharmD, Melinta (Research Grant or Support)Merck (Research Grant or Support)Theratechnologies, Inc. (Advisor or Review Panel member) Jeffrey Steele, Pharm.D., Paratek Pharmaceuticals (Advisor or Review Panel member)"} +{"text": "In this study, we characterized blaNDM-carrying plasmids in Enterobacterales isolated in Vietnam, and identified several possible cases of horizontal transfer of plasmids both within and among species of bacteria. Twenty-five carbapenem-nonsusceptible isolates from a medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 13 blaNDM-positive isolates, including isolates of Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii, Morganella morganii, and Proteus mirabilis, were further sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. Almost identical 73 kb IncFII(pSE11)::IncN hybrid plasmids carrying blaNDM-1 were found in a P. mirabilis isolate and an M. morganii isolate. A 112 kb IncFII(pRSB107)::IncN hybrid plasmid carrying blaNDM-1 in an E. coli isolate had partially identical sequences with a 39 kb IncR plasmid carrying blaNDM-1 and an 88 kb IncFII(pHN7A8)::IncN hybrid plasmid in a C. freundii isolate. 148\u2013149 kb IncFIA(Hl1)::IncA/C2 plasmids and 75\u201376 kb IncFII(Yp) plasmids, both carrying blaNDM-1 were shared among three sequence type 11 (ST11) isolates and three ST395 isolates of K. pneumoniae, respectively. Most of the plasmids co-carried genes conferring resistance to clinically relevant antimicrobials, including third-generation cephalosporins, aminoglycosides, and fluoroquinolones, in addition to blaNDM-1. These results provide insight into the genetic basis of CRE in Vietnam, and could help control nosocomial infections.Carbapenem-resistant Enterobacterales (CRE) represent a serious threat to public health due to the lack of treatment and high mortality. The rate of antimicrobial resistance of Enterobacterales isolates to major antimicrobials, including carbapenems, is much higher in Vietnam than in Western countries, but the reasons remain unknown due to the lack of genomic epidemiology research. A previous study suggested that carbapenem resistance genes, such as the carbapenemase gene The same integron cassette was observed on E. coli pHPA isolated from a human in Japan in 2002 , which had partially identical sequences with two plasmids, pMH17-012N_1 and pMH17-012N_2 , both found in C. freundii MH17-012N (isolated in 2017) (E. coli pMH13-051M_1 [IncFII(pRSB107)::IncN plasmid] and C. freundii pMH17-012N_1 commonly carried blaNDM-1 and blaTEM-1b, and pMH13-051M_1 further carried blaCTX-M-55 and rmtB. C. freundii pMH17-012N_2 [larger IncFII(pHN7A8)::IncN plasmid] carried no known AMR genes, but did have a set of conjugation-associated type IV secretion system (T4SS) genes, which shared identical sequences with E. coli pMH13-051M_1. The genetic structures surrounding blaNDM-1 in E. coli pMH13-051M_1 and C. freundii pMH17-012N_1 contained MGEs, including ISAba125, ISCR21, and two IS26, and shared identical sequences with Tn125 (in 2017) . E. colith Tn125 : 98.6% ablaNDM-1\u2013carrying plasmids identified in Vietnam with those reported in other countries. A set of conjugation-associated T4SS genes in P. mirabilis pMH13-009N_1 [72.6 kb plasmid with IncFII(pSE11)::IncN replicons] was partially identical with Salmonella enterica FDAARGOS_70 plasmid unnamed1 isolated from a human in the United States in 2013, which carried blaTEM-1b (S. enterica FDAARGOS_70 plasmid unnamed1 did not carry blaNDM-1 as P. mirabilis pMH13-009N_1 did. C. freundii pMH17-012N_2 [87.6 kb plasmid with IncFII(pHN7A8)::IncN replicons and no AMR genes] was highly identical with E. coli p103-2-4 from a goose farm in China in 2018 and with S. enterica serovar Enteritidis p12367A isolated from a human in China in 2013 shared nearly identical blaNDM-1-carrying plasmids, pMH15-289M_1, pMH16-398D_1, and pMH15-258M_1 , and all of these plasmids carried other AMR genes, such as blaCTX-M-15, blaOXA-1, rmtC, and qnrB9 ::IncA/C2 replicons, accession: CP021952, 99.8% identity in 82% region of pMH15-289M_1] in the United States and with E. coli pK71-77-1-NDM isolated from a human in Norway in 2010. The plasmids tig00000169_pilon and pK71-77-1-NDM had identical sequences in the T4SS region of pMH15-289M_1, and carried blaNDM-1, blaCMY-6, and rmtC, and the plasmid tig00000169_pilon further carried blaSHV-11 and qnrB58. K. pneumoniae MH16-398D had 235 sequence variants , and K. pneumoniae MH15-258M had six sequence variants (five SNVs and one replacement) relative to K. pneumoniae MH15-289M.Furthermore, three nd qnrB9 . blaNDM-K. pneumoniae isolates belonging to ST395 shared nearly identical blaNDM-1-carrying plasmids, pMH15-208H_1, pMH15-191M_1, and pMH13-055M_1 , and all plasmids carried another AMR gene, rmtB replicon, accession: CP043383, 99.9% identity in 98% region of pMH15-208H_1] isolated from a human in China in 2018 and with K. pneumoniae pSECR18-2374C isolated from a human in South Korea in 2018. E. hormaechei pNDM1_045001 and K. pneumoniae pSECR18-2374C had a partially identical sequence of conjugation-associated T4SS genes with pMH15-208H_1. E. hormaechei pNDM1_045001 carried blaNDM-1, blaTEM-1b, and rmtB, and K. pneumoniae pSECR18-2374C carried blaNDM-4, blaTEM-1b and rmtB. K. pneumoniae MH15-191M had three sequence variants (two SNVs and one MNV) and K. pneumoniae MH13-055M had only one SNV relative to K. pneumoniae MH15-208H.Another three ne, rmtB . blaNDM-th Tn125 : 99.5\u201310E. coli, C. freundii pMH17-012N_1 (39.2 kb plasmid with IncR replicon), pMH17-012N_2 [87.6 kb plasmid with IncFII(pHN7A8)::IncN replicons], E. coli pMH13-051M_1 [111.5 kb plasmid with IncFII(pRSB107)::IncN replicons], K. pneumoniae pMH15-258M_1 [148.8 kb plasmid with IncFIA(Hl1)::IncA/C2 replicons], and K. pneumoniae pMH15-208H_1 [75.4 kb plasmid with IncFII(Yp) replicon] were not transferred to recipient E. coli under our experimental conditions though a set of T4SS-associated genes were detected in C. freundii pMH17-012N_2, E. coli pMH13-051M_1, K. pneumoniae pMH15-258M_1, and K. pneumoniae pMH15-208H_1.In bacterial conjugation experiments with K. pneumoniae to third-generation cephalosporins, carbapenems, aminoglycosides, and fluoroquinolones were 66.4%, 17.1%, 29.5%, and 53.0%, respectively, in Vietnam according to the following protocol. The same amount of Luria-Bertani (LB) broth cultures of each donor bacteria and the recipient azide\u2013resistant E. coli J53 , were mixed and spotted onto Mueller-Hinton agar and then incubated at 37\u00b0C overnight. The mixed cells were recovered and suspended into PBS buffer, plated onto LB agar after 10-fold serial dilution, and incubated at 37\u00b0C overnight. Transconjugants were selected on LB agar containing 2 \u03bcg/mL of meropenem and 100 \u03bcg/mL of sodium azide.Bacterial conjugation was performed using six S1 TableAlso, sequence types of multilocus sequence typing (MLST) analysis determined from genomes, carbapenemase genes detected by ResFinder in genomes, sizes and contigs of genomes, coverages in short-read sequencing, Illumina sequencing platforms, and accession numbers of genomes are shown. According to the CLSI 2020 guidelines, Breakpoints of meropenem and imipenem are as follows: \u22641 \u03bcg/mL, susceptible; 2 \u03bcg/mL, intermediate; \u22654 \u03bcg/mL, resistant (R).(TIFF)Click here for additional data file.S2 TableAlso, replicon types detected by PlasmidFinder and antimicrobial resistance genes (ARGs) detected by ResFinder in plasmids, sizes of plasmids, and coverages in long-read sequencing, and accession numbers of plasmids are shown.(TIFF)Click here for additional data file."} +{"text": "It has come to our attention that figures 1 and 3 in this article have been reproduced by the authors without first obtaining permission from the original publishers or authors:Figure 1: Akerfelt M, Morimoto RI, Sistonen L:\u00a0https://dx.doi.org/10.1038/nrm2938?utm_medium=email&utm_source=transaction Heat shock factors: integrators of cell stress, development and lifespan. Nat Rev Mol Cell Biol. 2010, 11:545-55.\u00a0https://dx.doi.org/10.1038/nrm2938 10.1038/nrm2938\u00a0Figure 3:\u00a0Pockley AG. https://www.cambridge.org/core/journals/expert-reviews-in-molecular-medicine/article/abs/heat-shock-proteins-in-health-and-disease-therapeutic-targets-or-therapeutic-agents/21095BFDB742E7876E4D1FDBF33E971C Heat shock proteins in health and disease: therapeutic targets or therapeutic agents? Expert Rev Mol Med. 2001, 3:1-21.\u00a0https://dx.doi.org/10.1017/S1462399401003556 10.1017/S1462399401003556.In addition, Figure 3 was also not properly attributed to the original source. This was later fixed via correction. After confirming with the publisher of Figure 1 that permission to republish was not obtained, and receiving no response from the authors despite multiple attempts, we have made the decision to retract this article and completely remove Figures 1 and 3 from the online and PDF versions of the article."} +{"text": "Coronaviruses (CoVs) belong to the subfamily Orthocoronavirinae of the family Coronaviridae. CoVs are enveloped (+) RNA viruses with unusually long genomes. Severe acute respiratory syndrome CoV (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV), and the novel coronavirus have been identif ied as causing global pandemics. Clinically tested vaccines are widely used to control rapidly spreading, acute, and often severe infections; however, effective drugs are still not available. The genomes of SARS-CoV-2 and SARS-CoV are approximately 80 % identical, while the genomes of SARS-CoV-2 and MERS-CoV are approximately 50 % identical. This indicates that there may be common mechanisms of coronavirus pathogenesis and, therefore, potential therapeutic targets for each virus may be the same. The enzymes and effector proteins that make up the replication-transcription complex (RTC) of coronaviruses are encoded by a large replicase gene. These enzymes and effector proteins represent promising targets for potential therapeutic drugs. The enzyme targets include papain- and 3C-like cysteine proteinases that process two large viral polyproteins, RNA-dependent RNA polymerase, RNA helicase, viral genome-modifying enzymes, and enzymes with 3\u2019\u20135\u2019 exoribonuclease or uridylate-specif ic endonuclease activity. Currently, there are many studies investigating the complex molecular mechanisms involved in the assembly andfunction of the RTC. This review will encompass current, modern studies on the properties and complexes of individualnon-structural subunits of the RTC, the structures of individual coronavirus RTC subunits, domain organizationand functions of subunits, protein-protein interactions, properties and architectures of subunit complexes, the effectof mutations, and the identif ication of mutations affecting the viability of the virus in cell culture.Key words: non-structural proteins CoVs; subunits of replicase CoVs; replication-transcription complex of CoVs; architectureof non-structural protein complexes CoVs. The 2019 coronavirus infection has spread globally, oftencausing severe respiratory, intestinal, and systemic illnesses.Coronaviruses (CoVs) belong to the Orthocoronavirinaesubfamily of the Coronaviridae family. The subfamily isfurther divided into \u03b1-, \u03b2-, \u03d2-, and \u03b4-coronaviruses. Severeacute respiratory syndrome CoV (SARS-CoV), Middle Eastrespiratory syndrome CoV (MERS-CoV), novel coronavirus, mouse hepatitis virus (MHV),and bovine coronavirus (BCoV) are all \u03b2-coronaviruses . Coronaviruses are enveloped viruses with an unusuallylong, single-stranded (+) RNA genome (26\u201332 kb).The SARS-CoV-2 genome is similar to the SARS-CoVgenome (sequence identity ~80 %), while the SARS-CoV-2and MERS-CoV genomes are less similar (sequence identity~50 %) . The structure and function of proteinsare preserved at levels as low as 30 % of amino acid sequenceidentity . This indicates that there may be commonmechanisms of pathogenesis among the CoVs and, therefore,the viruses may have the same potential therapeutic targets.The 5\u2032 proximal region of each CoV genome includes a cap,a 5\u2032 untranslated region (UTR) and a long replicase gene encoding16 non-structural proteins (comprising two-thirds ofthe genome). The 3\u2032 regions encode structural proteins, includingS (spike), E (surface), M (membrane), and N (nucleocapsid),auxiliary proteins (the number of these varies amongCoVs), a 3\u2032 UTR, and a poly(A) tract.The replication-transcription complex (RTC) of CoVs is acomplex consisting of viral and, probably, cellular proteins.The RTC produces the (+) RNA genome and a set of subgenomicCoVs RNA in infected cells. The CoV replicase genehas two overlapping open reading frames, ORF1a and ORF1b,which encode the viral components of the RTC. Expression ofthe gene leads to the formation of the pp1a polyprotein, whichis encoded by ORF1a. A ribosomal frameshift of \u20131 before theORF1a translation termination codon and ORF1b are requiredfor the formation of the pp1ab polyprotein, which is a continuationof pp1a. Polyproteins pp1a and pp1ab are processed bytwo viral cysteine proteinases, papain-like proteinase PLpro(PLP) and 3C-like proteinase 3\u0421Lpro (Mpro), which results inthe release of intermediate precursors and 16 mature highlyconserved non-structural proteins (nsps) capable of associatingwith each other and being subunits of the RTC. The pp1apolyprotein includes nsp1\u2013nsp11, while pp1ab includes allpp1a nsps, as well as nsp12\u2013nsp16 .The molecular mechanisms of the assembly and function ofthe RTC has not been studied. However, the structural andfunctional properties of conserved non-structural RTC subunitsand their complexes have been extensively researchedand are extremely important for the identification of key drugtargets against CoVs:nsp1 interacts with the 40S ribosome subunit and inhibitstranslation initiation of host proteins, including interferonresponse factors. Interaction of nsp1 with ribosomes alsoleads to the degradation of host RNA. Thus, nsp1 suppressescellular defence antiviral mechanisms ;nsp2 is not part of the RTC in cell culture. However, theabsence of nsp2 in cells infected with the MHV\u0394nsp2 orSARS-CoV\u0394nsp2 deletion mutants reduces the productionof the virus and viral RNA ;nsp3 and nsp5 are proteinases that process the pp1a andpp1ab polyproteins, resulting in the release of individual RTCcomponents. The PLP nsp3 domain(s) process the N-proximalregions of pp1a and pp1ab. The MHV nsp3 has two domains,PL1pro (PL1P) and PL2pro (PL2P). The PL1P domain cleavesthe nsp1/nsp2 and nsp2/nsp3 sites, while the PL2P domaincleaves the nsp3/nsp4 site . The SARS-CoV nsp3 has a single PL2Pdomain that cleaves all three nsp sites .The SARS-CoV PLP is an intracellular immune responseantagonist. PLP blocks the activation of transcription factorsIRF3 and NF-\u03baB, which induces the expression of IFN(I)and antiviral genes. It does this by indirectly inhibiting IKKiand TBK1 kinases that activate IRF3 and stabilizing I\u03baB\u03b1, aninhibitor of NF-\u03baB . PLP also hydrolyzeselements of ubiquitin and the product of interferon-stimulatinggene 15 of the ubiquitin-like protein, thereby blocking thecellular mechanism of post-translational ubiquitination and,in turn, enhancing viral replication .However, nsp3 stabilizes the host E3 ubiquitin ligase RCHY1through the interaction of its SUD and PLP domains withRCHY1. This activates the RCHY1-mediated degradation ofp53, a cellular inhibitor of SARS-CoV replication . SARS-CoV nsp3 interacts with nsp5, nsp6,nsp12, nsp13, nsp14, and nsp16 in the yeast two-hybrid (Y2H)system and is thought to serve as a scaffold for RTC assembly;nsp5 is a 3CLpro (Mpro). Mpro plays a key role in the processingof pp1a and pp1ab polyproteins, cleaving the centraland C-proximal regions of pp1ab at 11 highly conserved sites,which releases mature nsp4\u2013nsp16 proteins . Mpro isonly active as a dimer. Self-elimination of MERS-CoV Mproat the nsp4/nsp5 and nsp5/nsp6 sites occurs as a result of theligand-induced formation of an \u201cimmature dimer\u201d during theconvergence of Mpro III domains within two polyproteins. Structural analysis of the SARS-CoV-2Mpro complexes with known antiviral inhibitors, Boceprevir(peptidomimetic NS3/4A protease of hepatitis C virus) and GC376 (inhibitor of CoV replication), revealed atomic-levelinteractions between Mpro and these inhibitors. Such studiesare important for the optimization and design of effectivedrugs against CoVs ;nsp6 interacts with nsp2, nsp8, and nsp9 in the Y2H system. Six of the predicted hydrophobic domainsof MHV nsp6 and SARS-CoV nsp6 are transmembrane domains. MHV nsp6 and SARS-CoV nsp6are localized in the membranes of the endoplasmic reticulum(ER) and induce the formation of autophagosomes from ERmembranes and activate autophagy .Co-transfection of nsp3, nsp4, and nsp6 induces a change inthe internal membranes of the host cell through the formationof double-membrane vesicles (DMVs), similar to the DMVsinduced by SARS-CoV ;and nsp8 co-crystallize to form the nsp7/8 hexadecamericsupercomplex. The assembly of the supercomplex involvesthe formation of two different nsp7/8 heterodimers, D1 andD2, which differ in nsp8 conformation. D1 and D2 eachdimerize to form the heterotetramers T1 and T2. The interactionof two T1 with two T2, in the order T1\u2013T2\u2013T1\u2032\u2013T2\u2032 andwith ring closure through the T1\u2013T2\u2032 interaction, leads to theconstruction of the full supercomplex. The supercomplex hasa unique architecture: 16 molecules (8 nsp7 molecules and8 nsp8 molecules) interact tightly with each other, forminga hollow cylindrical structure in which two nsp8 conformationscoexist. The positive charge of the inner channel of thecylinder and its diameter (30 \u00c5) indicates the ability of thensp7/8 supercomplex to surround and interact with doublestrandedRNA (dsRNA) . The SARS-CoVnsp7/8 hexadecameric supercomplex can be formed in solutionat an equimolar nsp7: nsp8 ratio .In solution, hexadecameric SARS-CoV nsp7/8 associateswith dsRNA (Kd ~1.2 \u03bcM). The association of nsp7/8 withdsRNA is mediated by nsp8 and enhanced by nsp7 . On its own, SARS-CoV nsp8 possesses primerindependentRNA-dependent RNA polymerase (RdRp)activity and initiates, with low fidelity, the de novo synthesisof short (less than 6 nucleotides) complementary oligomers(primers) on single-stranded RNA (ssRNA) templates . SARS-CoV nsp8 and nsp7/8 complex also exhibitprimer-dependent RdRp activity . TheFCoV (feline coronavirus) nsp7/8 complex is a 2 : 1 heterotrimerformed by the association of two nsp7 molecules and onensp8 molecule. This complex does not form a hollow structure,either in crystalline form or in solution. FCoV nsp7/8has primer-independent RdRp activity ;nsp9 is an ssRNA-binding protein . Both monomeric and dimeric forms ofPDCoV (porcine \u03b4 coronavirus) nsp9 and PEDV (porcineepidemic diarrhoea virus related to \u03b1 coronaviruses) nsp9, as well as the dimeric form of SARSCoVnsp9 , have been found in solutionduring in vitro experiments. Studies of the crystal structuresof SARS-CoV nsp9 ,PDCoV nsp9, and PEDV nsp9 haverevealed dimeric forms of nsp9. The monomer SARS-CoVnsp9 is characterized by a different structure compared toother proteins involved in the replicative complexes of RNAviruses, the features of which are similar to the structures ofoligosaccharide/oligonucleotide-binding proteins . Mutations affecting the dimerization of SARS-CoVnsp9 weaken its interaction with ssRNA, which is lethal forSARS-CoV replication in cell culture ;nsp10 interacts with dsRNA, dsDNA, and ssRNA withmicromolar affinity . Crystal structurestudies of SARS-CoV nsp10 showed that the monomerstructure includes two zinc fingers, a new discovery amongzinc finger protein structures. Motifs of zinc-binding nsp10sequences have been identified. Twelve identical monomersform a unique spherical dodecameric architecture, which ishypothesized to be the functional form of nsp10 . Through two-hybrid analysis in mammaliancells, interactions of SARS-CoV nsp10 with nsp14and nsp16 have been revealed ;nsp11 is a short peptide resulting from the cleavage of thepp1a polyprotein by the 3CLpro/Mpro proteinase at the nsp10/nsp11 site. Nsp11 is encoded by the region of genomic RNAwhere the translational reading frame shift occurs (ORF1a toORF1b). This shift results in the formation of nsp12\u2013nsp16proteins from the pp1ab polyprotein. SARS-CoV-2 nsp11contains 13 amino acid residues and has a disordered conformation,the dynamics of which have been studied in thepresence of lipid-membrane mimetics. In the presence of SDSmicelles, the disordered conformation of nsp11 is transformedinto an \u03b1-helix ;nsp14 is bifunctional. The N-terminal domain of nsp14has 3\u2032\u20135\u2032 exoribonuclease activity (ExoN), and its C-terminaldomain has (guanine-N7) methyltransferase activity(N7-MTase). ExoN corrects the low fidelity of synthesis ofthe complementary RNA strand by viral RdRp nsp12 andcatalyzes the removal of 3\u2032-terminal erroneous nucleotidesin dsRNA. N7-MTase catalyzes the methylation of the viralRNA cap at the N7 guanine position in the presence of S- adenosylmethionine(methyl group donor). N7-MTase has anS- adenosylmethionine binding motif which recognizes the capof viral GpppRNA and methylates guanine N7 GpppRNA toform 7MeGpppRNA (cap-0). Cap-0 plays an important role inblocking the degradation of viral RNA by 5\u2032\u20133\u2032 exoribonucleases,translation initiation, and immune system controlescape . Mutants of the catalyticmotif MERS-CoV ExoN and SARS-CoV-2 ExoN arenot viable in cell culture . SARS- CoVnsp10 associates with the ExoN domain of SARS-CoV nsp14,increasing the ExoN activity of nsp14 by more than 35 timeswithout affecting its N7-MTase activity .Structural studies of the SARS-CoV nsp10/14 complexshowed that one nsp10 molecule associates with the ExoNdomain of nsp14, stabilizing and enhancing the activity ofthe ExoN. The architecture of the nsp10/14 complex has beenstudied and has been found to include two regions of contactbetween the nsp10 molecule and the ExoN domain of nsp14;nsp16 has (nucleoside-2\u2032O) methyltransferase activity(2\u2032O-MTase). 2\u2032O-MTase recognizes the cap-0 of viralRNA and catalyzes the transfer of the methyl group fromS-adenosylmethionine to the 2\u2032OH group of the first nucleotide\u2019sribose after N7-methylated guanine, resulting in the formation of 7MeGpppN2\u2032OMe-RNA (conversion of cap-0 intocap-1). SARS-CoV nsp10 associates with nsp16 and stimulatesthe 2\u2032O-MTase activity of nsp16 .Mutagenesis mapping of the surface amino acid residues ofSARS-CoV nsp10 involved in nsp10\u2013nsp14 interaction andstructural analysis of the nsp10/16 complex revealed overlappingsurfaces of nsp10 interacting with nsp14 and nsp16.Nsp10 can serve as a platform that recruits nsp14 or nsp16to the RTC, stimulating the ExoN activity of nsp14 or the2\u2032O- MTase activity of nsp16. Therefore, nsp10 is an importantregulator of the RTC. Mutations have been identified thatdisrupt the nsp10\u2013nsp14 and nsp10\u2013nsp16 interactions, someof which lead to a nonviable viral phenotype in cell culture;nsp12, an RdRp, catalyzes the synthesis of complementaryRNA strands on (+) and (\u2013) viral RNA templates and is a keyCoV RTC enzyme. CoVs nsp12 initiates de novo synthesisfrom the 3\u2032 end of the viral genome of the full-length (\u2013) RNAstrand, as well as for subgenomic (\u2013) RNA transcripts, whichhave differing 3\u2032 end lengths. In turn, the full-length (\u2013) RNAstrands and subgenomic (\u2013) RNA strands serve as templatesfor the synthesis of the new RNA genome and subgenomic(+) RNA transcripts. Subgenomic (+) RNA is important forthe expression of structural and accessory proteins encodedby genes in the 3\u2032 proximal region of the viral genome, whichis inaccessible to ribosomes that translate the viral genome. Full-length recombinant SARS-CoVnsp12 associates with short (20\u201330 nucleotides long) dsRNAand ssRNA , and initiatesprimer-dependent RNA synthesis on both homo- and heteropolymericRNA templates of the same length . However, the recombinant SARS-CoV nsp12 does notassociate with a primer-template that mimics the 3\u2032-terminal40 nucleotides of the SARS-CoV UTR and does not exhibitRdRp activity on this primer-template .Cryo-electron microscopy determined the structure of themonomer SARS-CoV-2 nsp12, which includes the nidovirusspecificN-terminal domain of the RdRp-associated nucleotidyltransferase (NiRAN), the interface domain, and theC- terminal RdRp domain. The C-terminal RdRp domain hasa conserved right-hand-like architecture, which includes threesubdomains: fingers, palm, and thumb. The active centre isformed by conservative motifs of amino acid residues localizedin the palm subdomain. The motifs of the channel ofentry for nucleotide triphosphates and the primer-template andthe exit of the resulting RNA strand converge in the centralcavity,where these motifs carry out matrix-dependent RNAsynthesis have been determined .The association of the nsp7/8 complex with nsp12 leadsto the formation of the nsp7/8/12 complex. This complexpossesses high RNA-binding capacity, polymerase activity,and processivity. It is also capable of initiating de novo RNAsynthesis on the 3\u2032 UTR template of the SARS-CoV genome,resulting in the elongation of the RNA product by over300 nucleotides. For nsp7/8/12 complex-mediated initiationof processive RNA synthesis, three amino acid residues fromnsp7 and one amino acid residue from nsp8(K58) are required for the interaction of nsp7/8/12 with theRNA template, while four amino acid residues from nsp8 interact with nsp12 . Moreover, nsp7/8/12 is able to associate with nsp14to form the nsp7/8/12/14 multicomplex. This ensemble ofnon-structural proteins possesses high RNA polymeraseactivity and is involved in 5\u2032 RNA capping; however, it doesnot have ExoN activity . The structure ofthe SARS-CoV-2 and SARS-CoV nsp7/8/12 complexes wasdetermined by cryo-electron microscopy. These complexes,including the nsp12 monomer, nsp8 monomer, and nsp7/nsp8heterodimer, have similar architecture: the nsp8-1 subunitinteractswith the RdRp finger subdomain, while the nsp7and nsp8-2 subunits interact with the RdRp thumb subdomain;nsp13 possesses helicase and nucleoside-triphosphatase(NTPase) activities; nsp13 interacts with nsp7, nsp8, andnsp12 in the Y2H system .The crystal structure of MERS-CoV nsp13 was determined.The structure includes an N-terminal zinc-binding domain(ZBD) rich in Cys/His residues that coordinate three zinc ions,as well as C-terminal helicase RecA1 and RecA2 domainswhich contain parallel \u03b2-chains . The nsp13helicase separates dsRNA and dsDNA strands with overhanging(5\u201320 nucleotides long) 5\u2032 ends; nsp13 interacts with thesingle-stranded 5\u2032 end of the partial nucleic acid duplex ofdsRNA and dsDNA and unwinds it in the 5\u2032\u20133\u2032 direction, usingthe hydrolysis energy of the 5\u2032-deoxy- and ribonucleotidetriphosphates .The RNA 5\u2032-triphosphatase activity of nsp13 catalyzes thecleavage of the \u03d2 phosphate from the 5\u2032-terminal nucleotideof RNA and is thought to be involved in the capping of viralRNA . Studies of SARS-CoV nsp13 haveshown that the unwinding of DNA duplexes occurs in discreteintervals of ~9.3 base pairs (bp) at a rate of 30 intervals persecond. Therefore, the unwinding speed of DNA duplexes isapproximately 280 bp/s.The helicase activity of nsp13 increases approximately2-fold when nsp13 interacts with nsp12, suggesting theinteractionof these proteins is involved in the function ofthe RTC . When SARS-CoV-2 nsp13interacts with the RTC, specifically with nsp7/2nsp8/nsp12:RNA, the stable complexes 2nsp13\u2013RTC (67 %) and nsp13\u2013RTC (20 %), as well as the dimer (2nsp13\u2013RTC)2 (13 %) areformed. Using cryo-electron microscopy, the architecture ofthe dominant 2nsp13\u2013RTC complex has been determined.This involves the interaction of the ZBD on the first nsp13molecule with the N-terminus of nsp8b and the nsp12 thumbsubdomain, as well as the interaction of the ZBD of the secondnsp13 molecule with the N-terminus of nsp8a. The catalyticRecA1 helicase domain of the first nsp13 molecule is fixedagainst nsp7 and the nsp8b head ;nsp15 is a nidovirus uridylate-specific endoribonuclease(NendoU). It cleaves RNA at the 3\u2032 uridylate in unpaired,single-stranded, and looped regions . The crystal structures of SARS-CoV-2,SARS-CoV, and MERS-CoV nsp15 are homologous, functionallyactive hexamers formed by the dimerization of trimers.Each of the hexamer protomers includes three domains: theN- terminal, middle, and C-terminal catalytic NendoU domains.During trimer assembly, the N-terminal domain ofone protomer is packed into a gap between the central andC-terminal domains of the neighbouring protomer. During assembly of the hexamer, the N-terminal domains of the protomersof the two trimers are packed back-to-back and are inthe centre of the hexamer structure. The C-terminal domainscontaining active centres are located outward at the verticesof the cloverleaf. This architecture provides nsp15 with sixfunctionally active centres .The uridylate content in RNA, Mn+2 and, to a lesser extent,Mg+2 increase the affinity of nsp15 for RNA. The hexamericstructure of SARS-CoV and MERS-CoV nsp15 is criticalfor its substrate and catalytic activity. The study of a seriesof mono-, tri- and hexameric protein mutants revealed weakinteractions with RNA (rU16\u201320) and low catalytic activity inmonomers and trimers compared to hexamers and wild-typensp15 . Nsp8 andthe nsp7/8 complex interact with MERS-CoV nsp15, enhancingthe binding ability of the nsp15 hexamer for RNA and itscatalytic activity . The NendoU activity ofnsp15 is an antagonist of the IFN-induced cellular antiviralresponse and stimulates the initiation of viral RNA translation.A large number of non-structural subunits and their respectivecomplexes within the RTC is a defining feature of CoVs.An important feature is that some subunits have domains withdifferent enzymatic activities. For example, nsp14 has bothExoN and N7-MTase activity, while nsp13 has helicase andnucleoside triphosphatase activity. Non-structural proteinshave a set of activities universal for (+) RNA viruses: proteinases, RNA-dependent RNA polymerases (nsp12),RNA helicases (nsp13). There are also unique domains involvedin mRNA capping, cap modification .Some proteins possess 3\u2032\u20135\u2032 exoribonuclease activity (nsp14),which regulate the reliability of RNA genome replication,while some possess uridylate-specific endonuclease activity(nsp15). Many proteins serve as cofactors for importantenzymes and affect cellular processes.In particular, some proteins suppress the antiviral cellularresponse . The nsp9 and nsp10structures are unique among the protein structures of the replicativecomplexes of RNA viruses. Many CoVs subunits andtheir complexes have a complex architecture. For example,nsp7 and nsp8 form a functional and unique hexadecamericsupercomplex, the nsp10 architecture includes 12 identicalsubunits, and the nsp15 architecture is a functionally activehexamer. The complex architecture of the RTC is defined bythe 2 nsp13/2 nsp8/1 nsp7/1 nsp12 model.The lack of effective drugs against the novel coronavirus infectionis a current global challenge. The RTC of CoVs replicates(+) RNA and determines the production of the virusin infected cells; however, the molecular mechanisms of thisremain unexplored. Currently, great efforts are being undertakenaimed at creating a structural or functional network ofinteractions within the CoV proteome, as well as its interactionswith the host cell. This would identify a large-scale panelof therapeutic targets. The determination of the structures ofindividual non-structural RTC subunits and their complexesand the identification of key interacting amino acid residuesand types of bonds between them will enable the design ofselective and effective inhibitors. Investigations employingbiochemical methods and mutational analyses can identifyfactors that affect the efficiency of viral genomic RNA productionand the virus in an infected cell, the multiple effects ofviral proteins on the host cell, and potential key drug targets.The authors declare no conflict of interest.Adedeji A.O., Lazarus H. Biochemical characterization of Middle Eastrespiratory syndrome coronavirus helicase. mSphere. 2016;1(5):e00235-16. DOI 10.1128/mSphere.00235-16.Adedeji A.O., Marchand B., Velthuis A.J.W., Snijder E.J., Weiss S.,Eoff R.L., Singh K., Sarafianos S.G. Mechanism of nucleic acid unwindingby SARS-CoV helicase. PLoS One. 2012;7(5):e36521. DOI10.1371/journal.pone.0036521.Angelini M.M., Akhlaghpour M., Neuman B.W., Buchmeier M.J.Severe acute respiratory syndrome coronavirus nonstructural proteins3, 4, and 6 induce double-membrane vesicles. mBio. 2013;4(4):e00524-13. DOI 10.1128/mBio.00524-13.Bhardwaj K., Sun J., Holzenburg A., Guarino L.A., Kao C.C. RNA recognitionand cleavage by the SARS coronavirus endoribonuclease.J. Mol. Biol. 2006;361(2):243-256. DOI 10.1016/j.jmb.2006.06.021.Bouvet M., Debarnot C., Imbert I., Selisko B., Snijder E.J., Canard B.,Decroly E. In vitro reconstitution of SARS-coronavirus mRNA capmethylation. PLoS Pathog. 2010;6(4):e1000863. DOI 10.1371/journal.ppat.1000863.Bouvet M., Imbert I., Subissi L., Gluais L., Canard B., Decroly E. RNA3\u2032-end mismatch excision by the severe acute respiratory syndromecoronavirus nonstructural protein nsp10/nsp14 exoribonucleasecomplex. Proc. Natl. Acad. Sci. USA. 2012;109(24):9372-9377. DOI10.1073/pnas.1201130109.Bouvet M., Lugari A., Posthuma C.C., Zevenhoven J.C., Bernard S.,Betzi S., Imbert I., Canard B., Guillemot J.-C., L\u00e9cine P., PfefferleS., Drosten C., Snijder E.J., Decroly E., Morelli X. CoronavirusNsp10, a critical co-factor for activation of multiple replicative enzymes.J. Biol. Chem. 2014;289(37):25783-25796. DOI 10.1074/jbc.M114.577353Brunn A., Teepe C., Simpson J.C., Pepperkok R., Friedel C.C., ZimmerR., Roberts R., Baric R., Haas J. Analysis of intraviral proteinproteininteractions of the SARS coronavirus ORFeome. PLoS One.2007;2(5):e459. DOI 10.1371/journal.pone.0000459.Chen J., Malone B., Llewellyn E., Grasso M., Shelton P.M.M., OlinaresP.D.B., Maruthi K., Eng E.T., Vatandaslar H., Chait B.T., KapoorT.M., Darst S.A., Campbell E.A. Structural basis for helicasepolymerasecoupling in the SARS-CoV-2 replication-transcriptioncomplex. Cell. 2020;182(6):1560-1573.e13. DOI 10.1016/j.cell.2020.07.033Chen Y., Cai H., Pan J., Xiang N., Tien P., Ahola T., Guo D. Functionalscreen reveals SARS coronavirus nonstructural protein nsp14as a novel cap N7 methyltransferase. Proc. Natl. Acad. Sci. USA.2009;106(9):3484-3489. DOI 10.1073/pnas.0808790106.Cottam E.M., Maier H.J., Manifava M., Vaux L.C., Chandra-SchoenfelderP., Gerner W., Britton P., Ktistakis N.T., Wileman T. Coronavirusnsp6 proteins generate autophagosomes from the endoplasmicreticulum via an omegasome intermediate. Autophagy. 2011;7(11):1335-1347. DOI 10.4161/auto.7.11.16642.Daczkowski C.M., Dzimianski J.V., Clasman J.R., Goodwin O., MesecarA.D., Pegan S.D. Structural insights into the interaction ofcoronavirus papain-like proteases and interferon-stimulated geneproduct15 from different species. J. Mol. Biol. 2017;429(11):1661-1683. DOI 10.1016/j.jmb.2017.04.011.Deng X., Baker S.C. An \u201cOld\u201d protein with a new story: Coronavirusendoribonuclease is important for evading host antiviral defenses.Virology. 2018;517:157-163. DOI 10.1016/j.virol.2017.12.024.Deng X., Geelen A., Buckley A.C., O\u2019Brien A., Pillatzki A., LagerK.M., Faaberg K.S., Baker S.C. Coronavirus endoribonucleaseactivity in porcine epidemic diarrhea virus suppresses type I andtype III interferon responses. J. Virol. 2019;93(8):e02000-18. DOI10.1128/JVI.02000-18.Egloff M.-P., Ferron F., Campanacci V., Longhi S., Rancurel C., DutartreH., Snijder E.J., Gorbalenya A.E., Cambillau C., Canard B. Thesevere acute respiratory syndrome-coronavirus replicative proteinnsp9 is a single-stranded RNA-binding subunit unique in the RNAvirus world. Proc. Natl. Acad. Sci. USA. 2004;101(11):3792-3796.DOI 10.1073/pnas.0307877101.Frieman M., Ratia K., Johnston R.E., Mesecar A.D., Baric R.S. Severeacute respiratory syndrome coronavirus papain-like proteaseubiquitin-like domain and catalytic domain regulate antagonism ofIRF3 and NF-kappaB signaling. J. Virol. 2009;83(13):6689-6705.DOI 10.1128/JVI.02220-08.Fu L., Ye F., Feng Y., Yu F., Wang Q., Wu Y., Zhao C., Sun H., Huang B.,Niu P., Song H., Shi Y., Li X., Tan W., Qi J., Gao G.F. Both Boceprevirand GC376 efficaciously inhibit SARS-CoV-2 by targetingits main protease. Nat. Commun. 2020;11(1):4417. DOI 10.1038/s41467-020-18233-x.Gadhave K., Kumar P., Kumar A., Bhardwaj T., Garg N., Giri R. Conformationaldynamics of 13 amino acids long NSP11 of SARS-CoV-2under membrane mimetics and different solvent conditions. Microb.Pathog. 2021;158:105041. DOI 10.1016/j.micpath.2021.105041.Gao Y., Yan L., Huang Y., Liu F., Zhao Y., Cao L., Wang T., Sun Q.,Ming Z., Zhang L., Ge J., Zheng L., Zhang Y., Wang H., Zhu Y.,Zhu C., Hu T., Hua T., Zhang B., Yang X., Li J., Yang H., Liu Z.,Xu W., Guddat L.W., Wang Q., Lou Z., Rao Z. Structure of theRNA-dependent RNA polymerase from COVID-19 virus. Science.2020;368(6492):779-782. DOI 10.1126/science.abb7498.Goyal B., Goyal D. Targeting the dimerization of the main protease ofcoronaviruses: a potential broad-spectrum therapeutic strategy. ACSComb. Sci. 2020;22(6):297-305. DOI 10.1021/acscombsci.0c00058.Graham R.L., Sims A.C., Brockway S.M., Baric R.S., Denison M.R.The nsp2 replicase proteins of murine hepatitis virus and severeacute respiratory syndrome coronavirus are dispensable for viralreplication. J. Virol. 2005;79(21):13399-13411. DOI 10.1128/JVI.79.21.13399-13411.2005.Hao W., Wojdyla J.A., Zhao R., Han R., Das R., Zlatev I., Manoharan M.,Wang M., Cui S. Crystal structure of Middle East respiratory syndromecoronavirus helicase. PLoS Pathog. 2017;13(6):e1006474.DOI 10.1371/journal.ppat.1006474.Hughes S.A., Bonilla P.J., Weiss S.R. Identification of the murinecoronavirus p28 cleavage site. J. Virol. 1995;69(2):809-813. DOI10.1128/JVI.69.2.809-813.1995.Imbert I., Guillemot J.-C., Bourhis J.-M., Bussetta C., Coutard B., EgloffM.-P., Ferron F., Gorbalenya A.E., Canard B. A second, noncanonicalRNA-dependent RNA polymerase in SARS coronavirus.EMBO J. 2006;25(20):4933-4942. DOI 10.1038/sj.emboj.7601368.Imbert I., Snijder E.J., Dimitrova M., Guillemot J.-C., L\u00e9cine P., CanardB. The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein. Virus Res. 2008;133(2):136-148. DOI 10.1016/j.virusres.2007.11.017.Ivanov K.A., Thiel V., Dobbe J.C., Meer Y., Snijder E.J., Ziebuhr J.Multiple enzymatic activities associated with severe acute respiratorysyndrome coronavirus helicase. J. Virol. 2004;78(11):5619-5632.DOI 10.1128/JVI.78.11.5619-5632.2004Joseph J.S., Saikatendu K.S., Subramanian V., Neuman B.W., BroounA.,Griffith M., Moy K., Yadav M.K., Velasquez J., Buchmeier M.J.,Stevens R.C., Kuhn P. Crystal structure of nonstructural protein 10from the severe acute respiratory syndrome coronavirus reveals anovel fold with two zinc-binding motifs. J. Virol. 2006;80(16):7894-7901. DOI 10.1128/JVI.00467-06.Kamitani W., Narayanan K., Huang C., Lokugamage K., Ikegami T.,Ito N., Kubo H., Makino S. Severe acute respiratory syndromecoronavirus nsp1 protein suppresses host gene expression by promotinghost mRNA degradation. Proc. Natl. Acad. Sci. USA. 2006;103(34):12885-12890. DOI 10.1073/pnas.0603144103.Kanjanahaluethai A., Baker S.C. Identification of mouse hepatitis viruspapain-like proteinase 2 activity. J. Virol. 2000;74(17):7911-7921.DOI 10.1128/jvi.74.17.7911-7921.2000.Kim Y., Jedrzejczak R., Maltseva N.I., Wilamowski M., Endres M.,Godzik A., Michalska K., Joachimiak A. Crystal structure of Nsp15endoribonuclease NendoU from SARS-CoV-2. Protein Sci. 2020;29(7):1596-1605. DOI 10.1002/pro.3873.Lu R., Zhao X., Li J., Niu P., Yang B., Wu H., Wang W., Song H.,Huang B., Zhu N., Bi Y., Ma X., Zhan F., Wang L., Hu T., Zhou H.,Hu Z., Zhou W., Zhao L., Chen J., Meng Y., Wang J., Lin Y., Yuan J.,Xie Z., Ma J., Liu W.J., Wang D., Xu W., Holmes E.C., Gao G.F.,Wu G., Chen W., Shi W., Tan W. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus originsand receptor binding. Lancet. 2020;395(10224):565-574. DOI10.1016/S0140-6736(20)30251-8.Ma Y., Wu L., Shaw N., Gao Y., Wang J., Sun Y., Lou Z., Yan L.,Zhang R., Rao Z. Structural basis and functional analysis of theSARS coronavirus nsp14\u2013nsp10 complex. Proc. Natl. Acad. Sci.USA. 2015;112(30):9436-9441. DOI 10.1073/pnas.1508686112.Ma-Lauer Y., Carbajo-Lozoya J., Hein M.Y., M\u00fcller M.A., Deng W.,Lei J., Meyer B., Kusov Y., von Brunn B., Bairad D.R., H\u00fcnten S.,Drosten C., Hermeking H., Leonhardt H., Mann M., Hilgenfeld R.,von Brunn A. p53 down-regulates SARS coronavirus replication andis targeted by the SARS-unique domain and PLpro via E3 ubiquitinligase RCHY1. Proc. Natl. Acad. Sci. USA. 2016;113(35):E5192-E5201. DOI 10.1073/pnas.1603435113.Malik Y.S., Sircar S., Bhat S., Sharun K., Dhama K., Dadar M., TiwariR., Chaicumpa W. Emerging novel coronavirus (2019-nCoV) \u2013current scenario, evolutionary perspective based on genome analysisand recent developments. Vet. Q. 2020;40(1):68-76. DOI 10.1080/01652176.2020.1727993.Miknis Z.J., Donaldson E.F., Umland T.C., Rimmer R.A., Baric R.S.,Schultz L.W. Severe acute respiratory syndrome coronavirus nsp9dimerization is essential for efficient viral growth. J. Virol. 2009;83(7):3007-3018. DOI 10.1128/JVI.01505-08.Naqvi A.A.T., Fatima K., Mohammad T., Fatima U., Singh I.K.,Singh A., Atif S.M., Hariprasad G., Hasan G.M., Hassan M.I. Insightsinto SARS-CoV-2 genome, structure, evolution, pathogenesisand therapies: Structural genomics approach. Biochim. Biophys.Acta Mol. Basis Dis. 2020;1866(10):165878. DOI 10.1016/j.bbadis.2020.165878.Narayanan K., Huang C., Lokugamage K., Kamitani W., Ikegami T.,Tseng C.-T.K., Makino S. Severe acute respiratory syndrome coronavirusnsp1 suppresses host gene expression, including that oftype I interferon, in infected cells. J. Virol. 2008;82(9):4471-4479.DOI 10.1128/JVI.02472-07.Ogando N.S., Zevenhoven-Dobbe J.C., Meer Y., Bredenbeek P.J., PosthumaC.C., Snijder E.J. The enzymatic activity of the nsp14 exoribonucleaseis critical for replication of MERS-CoV and SARS-CoV-2.J. Virol. 2020;94(23):e01246-20. DOI 10.1128/JVI.01246-20.Oostra M., Hagemeijer M.C., Gent M., Bekker C.P.J., Lintelo E.G.,Rottier P.J.M., Haan C.A.M. Topology and membrane anchoring ofthe coronavirus replication complex: not all hydrophobic domainsof nsp3 and nsp6 are membrane spanning. J. Virol. 2008;82(24):12392-12405. DOI 10.1128/JVI.01219-08.Pan J., Peng X., Gao Y., Li Z., Lu X., Chen Y., Ishaq M., Liu D., DediegoM.L., Enjuanes L., Guo D. Genome-wide analysis of proteinproteininteractions and involvement of viral proteins in SARS-CoVreplication. PLoS One. 2008;3(10):e3299. DOI 10.1371/journal.pone.0003299.Pasternak A.O., Spaan W.J.M., Snijder E.J. Nidovirus transcription:how to make sense...? J. Gen. Virol. 2006;87(6):1403-1421. DOI10.1099/vir.0.81611-0.Rost B. Twilight zone of protein sequence alignments. Protein Eng.1999;12(2):85-94. DOI 10.1093/protein/12.2.85.Su D., Lou Z., Sun F., Zhai Y., Yang H., Zhang R., Joachimiak A.,Zhang X.C., Bartlam M., Rao1 Z. Dodecamer structure of severeacute respiratory syndrome coronavirus nonstructural protein nsp10.J. Virol. 2006;80(16):7902-7908. DOI 10.1128/JVI.00483-06.Subissi L., Posthuma C.C., Collet A., Zevenhoven-Dobbe J.C., GorbalenyaA.E., Decroly E., Snijder E.J., Canard B., Imbert I. One severeacute respiratory syndrome coronavirus protein complex integratesprocessive RNA polymerase and exonuclease activities. Proc.Natl. Acad. Sci. USA. 2014;111(37):E3900-E3909. DOI 10.1073/pnas.1323705111.Tahir M. Coronavirus genomic nsp14-ExoN, structure, role, mechanism,and potential application as a drug target. J. Med. Virol. 2021;93(7):4258-4264. DOI 10.1002/jmv.27009.Thiel V., Ivanov K.A., Putics \u00c1., Hertzig T., Schelle B., Bayer S., Wei\u00dfbrichB., Snijder E.J., Rabenau H., Doerr H.W., Gorbalenya A.E.,Ziebuhr J. Mechanisms and enzymes involved in SARS coronavirusgenome expression. J. Gen. Virol. 2003;84(9):2305-2315. DOI10.1099/vir.0.19424-0.Tomar S., Johnston M.L., John S.E.St., Osswald H.L., Nyalapatla P.R.,Paul L.N., Ghosh A.K., Denison M.R., Mesecar A.D. Ligand-induceddimerization of Middle East respiratory syndrome (MERS)coronavirus nsp5 protease (3CLpro): implications for nsp5 regulationand the development of antivirals. J. Biol. Chem. 2015;290(32):19403-19422. DOI 10.1074/jbc.M115.651463.Velthuis A.J.W., Arnold J.J., Cameron C.E., Worm S.H.E., Snijder E.J.The RNA polymerase activity of SARS-coronavirus nsp12 is primerdependent. Nucleic Acids Res. 2010;38(1):203-214. DOI 10.1093/nar/gkp904.Velthuis A.J.W., Worm S.H.E., Snijder E.J. The SARS-coronavirusnsp7+nsp8 complex is a unique multimeric RNA polymerase capableof both de novo initiation and primer extension. Nucleic AcidsRes. 2012;40(4):1737-1747. DOI 10.1093/nar/gkr893Xiao Y., Ma Q., Restle T., Shang W., Svergun D.I., Ponnusamy R.,Sczakiel G., Hilgenfeld R. Nonstructural proteins 7 and 8 of felinecoronavirus form a 2:1 heterotrimer that exhibits primer-independentRNA polymerase activity. J. Virol. 2012;86(8):4444-4454. DOI10.1128/JVI.06635-11.Zeng Z., Deng F., Shi K., Ye G., Wang G., Fang L., Xiao S., Fu Z.,Peng G. Dimerization of coronavirus nsp9 with diverse modesenhances its nucleic acid binding affinity. J. Virol. 2018;92(17):e00692-18. DOI 10.1128/JVI.00692-18.Zhai Y., Sun F., Li X., Pang H., Xu X., Bartlam M., Rao Z. Insights intoSARS-CoV transcription and replication from the structure of thensp7\u2013nsp8 hexadecamer. Nat. Struct. Mol. Biol. 2005;12(11):980-986. DOI 10.1038/nsmb999.Zhang L., Li L., Yan L., Ming Z., Jia Z., Lou Z., Rao Z. Structural andbiochemical characterization of endoribonuclease nsp15 encodedby Middle East respiratory syndrome coronavirus. J. Virol. 2018;92(22):e00893-18. DOI 10.1128/JVI.00893-18.Ziebuhr J., Snijder E.J., Gorbalenya A.E. Virus-encoded proteinasesand proteolytic processing in the Nidovirales. J. Gen. Virol. 2000;81(4):853-879. DOI 10.1099/0022-1317-81-4-853."} +{"text": "Rescue ECMO has been used worldwide in patients (pts) with ARDS caused by COVID-19. Bacterial super-infections affect 3.5-14.3% of hospitalized pts with COVID-19. Pts requiring ECMO may be at an increased risk of infection due to their severity of illness, gut translocation and ECMO impact on host immunity.This was a retrospective review of pts requiring ECMO for COVID-19 from April 2020-2021 at a single center. Strict definitions of infections were in accordance with CDC criteria. S. aureus (25%) and P. aeruginosa (16%) . Only 2% of all organisms were multi-drug resistant. 3 pts had fungal infections . Duration of ECMO was significantly longer for infected pts vs , p=.01. 95% of infected pts had received steroids vs. 67% of uninfected pts, p=0.09. Treatment success at 1 week was 50%, and 24% and 40% of pts had recurrent infections and persistent/recurrent organisms in clinical cultures, respectively. S. aureus (54%) and Enterobacterales (26%) were associated with persistent or recurrent clinical cultures, requiring prolonged antimicrobial therapy. Mortality rate at 30 days was 65% and was significantly higher for pts with infection than those without . 43 ECMO pts with 1065 ECMO days were evaluated. Median age was 53 yrs (range: 21-62) and median BMI was 36.2 (range: 19.4-75.8). 70% were men and 65% were white. 37 patients (86%) experienced a total of 40 infectious episodes with a median onset from ECMO cannulation to first infection of 10.5d (range: 4-50). Median SOFA and SAPSII scores at time of infection were 12 (6-20) and 63 (30-90), respectively. PNA was the most common infection . The most common organisms isolated were Enterobacterales (37%), S. aureus. Super-infection and mortality rates of ARDS pts on ECMO for COVID-19 were worse than for ARDS pts on ECMO for influenza at our center.Super-infection (most commonly PNA) occurred in almost all COVID-19 pts requiring ECMO for >4 days, and was a significant risk factor for death. Recurrent infections among survivors were common, especially when caused by Enterbacterales or Ryan K. Shields, PharmD, MS, Shionogi Fernanda P. Silveira, MD, MS, FIDSA, Ansun Involved: Self): Grant/Research Support; Novartis Involved: Self): Grant/Research Support; Qiagen Involved: Self): Grant/Research Support; Shire Involved: Self): Advisor or Review Panel member, Grant/Research Support; SlieaGen Involved: Self): Grant/Research Support; Whiscon Involved: Self): Grant/Research Support Cornelius J. Clancy, MD, Merck (Grant/Research Support)"} +{"text": "Brachypodium distachyon are still unclear.Mitogen-activated protein kinase (MAPK) cascades are involved with signal transduction in almost every aspect of plant growth and development, as well as biotic and abiotic stress responses. The evolutionary analysis of MAPKs and MKKs in individual or entire plant species has been reported, but the evolutionary patterns in the diverse inbred lines of B. distachyon. A total of 799 MAPKs and 618 MKKs were identified from 53 B. distachyon inbred lines. Remarkably, only three inbred lines had 16 MPKs and most of those inbred lines lacked MPK7-2 members, whereas 12 MKKs existed in almost all B. distachyon inbred lines. Phylogenetic analysis indicated that MAPKs and MKKs were divided into four groups as previously reported, grouping them in the same branch as corresponding members. MPK21-2 was the exception and fell into two groups, which may be due to their exon-intron patterns, especially the untranslated regions (UTRs). We also found that differential evolution patterns of MKK10 paralogues from ancient tandem duplicates may have undergone functional divergence. Expression analyses suggested that MAPKs and MKKs likely played different roles in different genetic contexts within various tissues and with abiotic stresses.We conducted the systematical molecular evolutionary analysis of MPK21-2 genes and the differential evolution of MKK10 paralogues with ancient tandem duplication might have functional divergences. Our findings provide new insights into the functional evolution of genes in closely inbred lines.Our study revealed that UTRs affected the structure and evolution of They are divided into three highly-conserved subfamilies that continuously act in a sequential manner in evolution and fundamental signaling transduction pathways . The MAPion loop . Activation loop .Brachypodium distachyon (2n = 10) is an annual temperate grass with a close phylogenetic relationship to other temperate cereals and an intermediate position within the Pooideae subfamily clade, a mostly Spanish (S+) clade, and a Turkish (T+) clade, based on their flowering phenotype and geographical substructure (BrachyPan (https://brachypan.jgi.doe.gov/) (B. distachyon inbred lines. Collected sequences were only accepted for scanning using InterPro software (5-S/T within the activation loop for MKKs. The gene identifier information of these sequences was collected and is listed in We downloaded gene information for /plaza/) . BLASTP /plaza/) searchesoe.gov/) to identsoftware if they MAPKs and MKKs was performed using Gene Structure Display Server 2.0 (GSDS 2.0) software (http://gsds.gao-lab.org/). All of the full-length amino acid sequences were initially aligned using Clustal Omega with default parameters . The domains and motifs of MAPKs and MKKs were scanned using InterProScan software (http://www.ebi.ac.uk/interpro/) (http://weblogo.threeplusone.com/).The exon/intron structure of identified terpro/) . The strB. distachyon inbred lines were generated in the BrachyPan project and visualized with the CorelDRAW X3 program. Phylogenetic trees were created based on the alignment of all MAPKs or MKKs using the maximum likelihood (ML) method with the Jones\u2013Taylor\u2013Thornton (JTT) model, 2,000 bootstrap values, and partial deletion by the MEGA 6.0 software, respectively (http://pdgd.njau.edu.cn:8080/) .B. distachyon were collected at the early flowering stages according to their different flowering times /10 h dark (18 \u00b0C) photoperiods. We harvested the root, stem, leaf blade, and leaf sheath at the eight-to-nine leaf stage. Spikelet samples from ng times . For the\u2019s instructions. The quality of total RNA was detected using Nanodrop1000 and its integrity was estimated by electrophoresis in 1.5% (w/v) agarose gel. The real-time quantitative polymerase chain reaction (RT-qPCR) was carried out in 10 \u00b5l reactions with 5\u201350 ng of first-stand cDNA products (four \u00b5l), five pmol of each primer (0.4 \u00b5l), five \u03bcl SYBR green master mix (2X), 0.2 \u00b5l ROX as a passive reference standard to normalize the SYBR fluorescent signal. The conditions for RT-qPCR were: initial activation at 95 \u00b0C for 5 min followed by 45 cycles of 95 \u00b0C for 30 s, and 60 \u00b0C for 30 s. Subsequently, the specificity of PCR products was monitored using a melting curve analysis (61\u201395 \u00b0C with fluorescence read every 0.5 \u00b0C). The B. distachyon actin (gene locus: Bradi2g24070) gene was used as an internal control for all RT-qPCR analyses; specific primers for MAPK and MKK were listed in MAPK and MKK genes was calculated using the 2\u2212\u0394\u0394Ct method.Total RNA was extracted from samples using Trizol reagent and 1\u20132 \u03bcg was reverse-transcribed into cDNA using PrimeScript RT Master Mix Perfect Real Time according to the manufacturerBrachyPan database , Bd3-1 (7), Adi-10 (10), Gaz-8 (5), ABR5 (11), Foz1 (11), and Jer1 (11) . The incer1 (11) . Furtherf Adi-10 . We alsof Adi-10 and S2.B. distachyon inbred lines, the phylogeny of all identified 799 MPK protein sequences were performed using ML and NJ methods, respectively. As expected, all homologues for each of the 16 Bd21 MPKs (BdMPKs) were divided into four groups and clustered on the corresponding branch except Tek-4MPK16 had similar clustering patterns with corresponding branches and fell into four groups: A, B, C, and D and S5. B. distachyon inbred lines consistently contained 5, 10, and 8 introns, respectively domain , the TXYectively , suggested lines and S9. EY motif . MAPKs hEY motif that binEY motif . MPK7-2sed lines . Moreoveed lines . Specified lines . Furtherinal end and 5B. inal end . This muinal end . Remarkaeudicots .5-S/T motif (2\u20133X1\u20135L/IXL/I) in the N-terminal domain had a part mutation in the phosphorylation site which coincided with a wide range of plant species (5-S/T), which were the most crucial amino acids in B. distachyon inbred lines, were 7.2 and 3.32, respectively, while the same results were 7.2 and 3.32 in Bd21 synthase gene was observed between two MKK members presented tandem duplication in the canonical form of the MKK-DMRL-MKK model with occasional variations (PNN (pinin) gene instead of the DMRL gene between two MKK gene members model in Mur1, MKK-DMRL-MKK-ChaC-MKK (ChaC: ChaC-like protein) model in BdTR12c, and MKK-DMRL-PK-PK-MKK (PK: protein tyrosine kinase) model in Sig2 and abiotic stresses of erformed to explo0-4 gene and 8, wresearch . Among tn Bd30-1 . MPK3s hreatment . MKK10-3d Bd30-1 . Moreove in root . MKK4s hd Bd30-1 . MPK3s hopposite . Express tissues . Almost tissues . We furtthe root and BdTRstresses . The strMPKs and MKKs. Our results showed that the exon-intron architecture, including lengths and numbers of intron, intron phase, and lengths of UTR, was generally conserved in corresponding orthologs instead of the DMRL gene (MKK10s may have contributed to gene expansion and function conservation and/or divergence during the evolution process of monocots.Our analysis suggested that occurred . These roccurred , indicatMRL gene . This maMRL gene and prefMRL gene , 2012. TMAPK and MKK genes have been characterized with corresponding functions in plant growth and development. For instance, the expression levels of AtMKK10 are high in pollen but do not appear in shoot apices, mesophyll cells, or mature leaves (CaMPK19-2 genes are highly expressed in roots and stems in pepper, while CaMPK1 is highly expressed in in leaves (B. distachyon inbred lines. The result indicated that most MPK and MKK genes had quantitative distinct expression patterns among the three different genetic contexts in different tissues and various abiotic stresses. For example, MPK17 had higher expression levels in the root, stem, leaf blade, and salt treatment in Bd30-1 compared with Bd21 and BdTR8i (MPK17s, which may result from the nonsynonymous substitutions at some pivotal amino acid sites in EF-hand CBP motif in their C-terminal extensions (MKK10-3 and MKK10-5 had similar expression patterns in the leaf blade in Bd30-1 and BdTR8i and distinct profiles in Bd21 (MKK3-2 gene had similar patterns under heat and salt condition (MAPKs and MKKs had an expression divergence which was correlated with the differential evolution in B. distachyon inbred lines.Tissue-specific expression patterns of e leaves , indicate leaves . CaMPK19n leaves , which in leaves . We inved BdTR8i and 8. Ttensions as descrtensions . Moreove in Bd21 . These r in Bd21 and are in Bd21 . Furtherondition . Taken tMPK and 618 MKK genes were retrieved from 53 kinds of B. distachyon inbred lines based on their conserved TXY or S/T-X5-S/T domain, respectively, using bioinformatics approaches. Phylogenetic analyses showed that most MAPKs and MKKs clustered into same branch, with the exception of MPK21-2s, which was divided into two groups, designated as type I and II. Further analysis found that the divergence of MPK21-2 may be involved with the presence of UTRs. MKK10s expanded during the evolutionary process by ancient tandem duplications with a differential model. This may have resulted in expression differences and functional divergence. We discovered that the expression of the MPK and MKK gene members varied in different tissues and across abiotic stresses in three different genetic contexts, suggesting that these genes may have diverse biological functions. Taken together, our results revealed a more comprehensive understanding of the function and evolutionary patterns of MAPKs and MKKs in diverse B. distachyon inbred lines.A total of 799 10.7717/peerj.11238/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj.11238/supp-2Supplemental Information 2Click here for additional data file.10.7717/peerj.11238/supp-3Supplemental Information 3Five MPKs including Gaz-8MPK4, Kah-1MPK20-4, Mon3MPK7-1, Tek-4MPK16, Tek-4MPK20-1, were excluded from entire sequences for reconstructing NJ tree.Click here for additional data file.10.7717/peerj.11238/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.11238/supp-5Supplemental Information 5Nine MKKs including Adi-10MKK5, Bd3-1MKK4, BdTR10cMKK10-5, Bd29-1MKK4, BdTR12cMKK3-1, BdTR5iMKK5, BdTR9kMKK10-5, Tek-4MKK3-1, Tek-4MKK3-3, were excluded from entire sequences for reconstructing NJ tree.Click here for additional data file.10.7717/peerj.11238/supp-6Supplemental Information 6Click here for additional data file.10.7717/peerj.11238/supp-7Supplemental Information 7Click here for additional data file.10.7717/peerj.11238/supp-8Supplemental Information 8Click here for additional data file.10.7717/peerj.11238/supp-9Supplemental Information 9Click here for additional data file.10.7717/peerj.11238/supp-10Supplemental Information 10Click here for additional data file.10.7717/peerj.11238/supp-11Supplemental Information 11Click here for additional data file.10.7717/peerj.11238/supp-12Supplemental Information 12Click here for additional data file.10.7717/peerj.11238/supp-13Supplemental Information 13Click here for additional data file.10.7717/peerj.11238/supp-14Supplemental Information 14Click here for additional data file.10.7717/peerj.11238/supp-15Supplemental Information 15Click here for additional data file.10.7717/peerj.11238/supp-16Supplemental Information 16Click here for additional data file.10.7717/peerj.11238/supp-17Supplemental Information 17Click here for additional data file.10.7717/peerj.11238/supp-18Supplemental Information 18Click here for additional data file.10.7717/peerj.11238/supp-19Supplemental Information 19Click here for additional data file."} +{"text": "Dear Editor,With increased survival of patients with multiple myeloma (MM), therapy-related myelodysplastic syndrome (t-MDS) and t-acute myeloid leukemia (AML) may occur more frequently , 2. We pIn June 2015, a 64-year-old female was diagnosed with IgG kappa (\u03ba) MM. IgG levels were 46g/L, \u03ba-serum-free light chains (SFLC) 75.4mg/L and \u00df2-microglobulin 8.2mg/L Fig. . Anemia 6/L). BM assessment did not reveal increased PCs or MDS, and serological parameters indicated stable disease.First-line therapy with bortezomib, cyclophosphamide, and dexamethasone was followed by autologous stem cell transplantation and maintenance therapy with lenalidomide Fig. . After 16/L, platelets 12x106/L) and \u03ba-SFLCs increased .Due to frailty at that time, she was ineligible for intensive AML induction therapy. Therefore, treatment with decitabine/venetoclax was started in February 2019. A BM biopsy in March 2019 confirmed CR of the t-AML Fig. , right; ted Fig. . This inIn June 2019, after worsening pancytopenia re-emerged and myeloid blasts were detectable in PB smears, decitabine/venetoclax was re-initiated. The BM biopsy in August 2019 showed persisting (30%) immature myeloid blasts ."} +{"text": "Correction to: J Exp Clin Cancer Res 41, 18 (2022)https://doi.org/10.1186/s13046-021-02203-2Fig.\u00a07i: plotting errors in the histogram; the histogram has been correctedFig. S8d: western blots (right hand side) replaced with correct blotsFig. S11: raw western blots presented for Fig.S8d have been replaced with correct blotsFollowing publication of the original article , the autThe corrected figure is given here. The correction does not have any effect on the final conclusions of the paper. The original article has been corrected.Additional file 1: Fig. S8 mTORC1\u2019s inhibitory effect on HuD. A. Comparison between mouse neuroblastoma and neurons under stress; Akt-mTOR pathway examined by Western blot assay. Full-length blots are presented in Supplementary Figure S11. B. Viability assay (control or miR375 mimic or miR375 inhibitor) in IMR-32 cells. C. Relative mRNA expression quantified by RT-qPCR (control or miR375 inhibitor and/or active mTOR via Rheb S16H construct and/or inactive mTOR via rapamycin-25 nM) in IMR-32 cells. D. Western blot analysis of HuD and pS6 in IMR-32 cells. Full-length blots are presented in Supplementary Figure S11. Data are presented as mean \u00b1 SEM; t test: *p < 0.05, **p < 0.01, ***p < 0.001. Fig. S11 Raw Western blot images for Fig. S5, S6 and S8."} +{"text": "On January 30, 2020, the World Health Organization (WHO) declared the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic a worldwide emergency.\u00a0Worldwide there have been 170 million cases of the resulting disease coronavirus 2019 (COVID-19), of those, 3.53 million have resulted in death. The Food and Drug Administration (FDA) with Mayo Clinic as the lead institution authorized COVID-19 convalescent plasma (CCP) for treatment of SARS-CoV-2 infection. Effective therapeutic window for CCP administration had yet to be defined. We addressed this gap by characterizing longitudinal biologic response and clinical outcomes of COVID-19 patients treated with CCP. Primary outcome was discharged to home/home health. On January 30, 2020, the World Health Organization (WHO) declared the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic a worldwide emergency.\u00a0Worldwide there have been 114 million cases of the resulting disease coronavirus 2019 (COVID-19) of those, 2.54 million have resulted in death. At pandemic debut, available treatment was limited to supportive care as no approved therapy or vaccination was available. This treatment vacuum motivated the utilization of convalescent plasma infusion to complement the antibody response.Passive immunization has been successfully used to treat infectious diseases since the 1890s . ConvaleResults from small case series conducted during the prior Middle East Respiratory Syndrome (MERS) and SARS-CoV documented CP to be safe, well-tolerated and promoted faster viral clearance, particularly when given early in the disease course . The priThe Food and Drug Association (FDA) with Mayo Clinic as the lead institution authorized COVID-19 convalescent plasma (CCP) for treatment of CoV-2 infection. Effective therapeutic window for CCP administration had yet to be defined. We addressed this gap by characterizing longitudinal biologic response and clinical outcomes of COVID-19 patients treated with CCP.\u00a0\u00a0Study design and populationThis retrospective longitudinal study analyzed electronic medical record data, including but not limited to characteristics and laboratory test findings from 197 patients consecutively admitted between March 28 and August 5, 2020. Among those, 92 and 105, respectively, received CCP infusion within 48h of versus 48h after hospitalization. Primary outcome was discharged to home/home health and secondary outcome was longitudinal CRP levels post CCP infusion.\u00a0Sarasota Memorial Hospital Institutional Review Board authorized consenting COVID-19 inpatients to participate in the national CCP protocol. Written informed consent was obtained from every CCP recipient or their legal guardian. Internal medicine resident physicians identified, contacted, and facilitated logistical pathways for CCP donation in collaboration with the community blood bank.Enrolled patients were at least 18 years old with laboratory confirmed SARS-CoV-2 infection admitted for treatment of severe or life-threatening COVID-19. Severe disease was defined as the presence of at least one of the following characteristics: dyspnea, respiratory rate of 30 breaths per minute or more, oxygen saturation (SpO2) equal to or less than 93%, partial pressure of arterial oxygen to fraction of inspired oxygen less than 300 or development of lung infiltrates with more than 50% involvement within 24-48 hours (h). Life-threatening disease was defined as the development of at least one of the following: respiratory failure, septic shock or multiple organ dysfunction or failure.Data analysisAnalyses contrasted patients who underwent CCP infusion within or more than 48h after admission. Primary outcome was discharged to home/home health. Continuous data summarized as median (interquartile range\u00a0[IQR]) were compared using Kruskal-Wallis test or two-way analysis of variance (ANOVA). Discrete data were compared with Pearson\u2019s chi-square test. Two-tailed p < 0.05 was significant.2, p < 0.0001) (32.7 (27-40)) vs. (29.4 (26-37) kg/mInitial admission vital signs and laboratory test results were not different between groups (p>.05) including temperature (98.4 (98.0-99.0) \u00b0F); SpO2 %); C-reactive protein (CRP) (2.6 (0.3-2.7) mg/dL); D-dimer (1.01 (0.69-2.03) mg/L); and ferritin (624 (281-1228) ng/mL) vs. 81.7 (61.3-130.0) hours who respectively received CCP infusion within vs after 48h, p < 0.0001. Admission lactate dehydrogenase (LDH) was (366 (301-469) U/L) vs. (326 (274-428) U/L, p = 0.02) vs. 29/105 (28%), p = 0.34. Days of mechanical ventilation were 8.0 (5.0-11.8) vs. 11.3 (4.5-17.9), p = 0.16. Hospital length of stay was 8.5 (4.9-15.2) vs. 13.0 (6.5-18.9) days, p = 0.03 vs. 49/105 (46%), p = 0.005.Between March 28 and August 5, 2020, Sarasota Memorial Hospital participated in the Mayo Clinic-led national FDA expanded access program providing access to convalescent plasma protocol. Throughout this period, data from 197 participants were analyzed and contrasted among those who received CCP infusion within or more than 48h after admission with a confirmed COVID-19 infection. We observed a post-CCP reduction in C-reactive protein, lower hospital length of stay and increase in discharge directly from hospital to home/home health in patients who received CCP within 48h of admission rather than later in hospitalization. Moreover, earlier CCP treatment resulted in 7% fewer patients who died or were discharged to hospice.In December 2019, a new member of Coronaviridae family, SARS-CoV-2 was detected in Wuhan, China primarily manifesting as a respiratory illness . Since tInitial evidence demonstrated CCP to be most beneficial when administered soon after SARS-CoV-2 infection. A randomized, double-blinded, placebo-controlled trial evaluated disease progression in 80 patients who received convalescent plasma within 72h after onset of mild COVID-19 symptoms vs. placebo ,11,12. ACCP transfusion is associated with a reduction in inflammatory markers, such as CRP ,10,14. IOur data should be interpreted with some caveats. We conducted a monocenter pragmatic investigation. CCP was administered before FDA required titer labeling. Therefore, we couldn\u2019t establish if antibody titers in CCP transfused across patient groups were equivalently distributed. In addition, SARS-CoV-2 serologic testing was unreliable restricting the assessment of whether a patient exhibited an impaired humoral response.Our study was conducted while no anti-viral treatment was approved by the FDA for patients hospitalized with COVID-19. We evince CCP treatment within 48h of admission was associated a reduction in hyperinflammation and hospital length of stay in patients more obese with higher LDH levels\u00a0with greater benefit for discharge to home/home health benefit and reduction in composite outcome of hospital mortality or discharge to hospice. Convalescent plasma has shown to be an effective treatment when given soon after SARS-CoV-2 infection. Unfortunately, in hospitalized patients with COVID-19, infusion of CCP late in the course of illness provides no observed benefit, as reported with other anti-viral agents."} +{"text": "Listeria monocytogenes strains that were isolated from the invasive alien snail species Arion vulgaris in Austria in 2019.We report the draft genomes of two Listeria monocytogenes is widespread in the environment, living as a saprophytic organism in the plant-soil compartment DNA kit . Paired-end sequencing (2 \u00d7 300 bp) was performed with a MiSeq platform as described . LibraryDefault parameters were used for all software unless otherwise specified. Raw reads were quality controlled using FastQC v0.11.9. Trimmomatic v0.36 . ContigsL. monocytogenes isolates, S-01 and S-02, generated 1,212,448 and 1,407,694 reads, respectively, with mean coverages of 101- to 113-fold and GC contents of 37.9% (L. monocytogenes. Strains were characterized by multilocus sequence typing (MLST) (https://www.cgmlst.org), respectively (Whole-genome sequencing (WGS) of the two of 37.9% . The NCBof 37.9% . Mash diectively .Listeria monocytogenes WGS project has been deposited in DDBJ/ENA/GenBank under BioProject no. PRJNA716154 and accession no. JAGGDY000000000 (S-01) and JAGGDX000000000 (S-02) (first versions). The raw sequence reads have been deposited in the Sequence Read Archive (SRA) under accession no. SRR14027493 (S-01) and SRR14027492 (S-02).The"} +{"text": "Next-generation sequencing (NGS) of whole genomes has become more accessible to biomedical researchers as the sequencing price continues to drop, and more laboratories have NGS facilities or have access to a core facility. However, the rapid and robust development of practical bioinformatics pipelines partly depends on convenient access to data for the testing of algorithms. Publicly available data sets constitute a part of this strategy.Here, we provide a triplicate whole-genome paired-end sequencing data set, consisting of 1.38 billion raw sequencing reads derived from saliva DNA from a single anonymous male Caucasian donor, with the average sequencing depths aimed at 30x for two of the samples and 4x for a low-coverage sample. The raw number of single nucleotide variants were 3.3\u20134 million and the median variant read depth of GATK4-passed variants in three samples was 22, 18, and 10. 81% of all variants were found in two or three of the samples, whereas 19% were singletons. The karyotype was evaluated as 46,XY with no apparent copy-number variation.The data set is provided without restrictions for research, educational or commercial purposes. Specifications TableValue of the Data\u2022The data set provided here is relevant for the continued development and testing of bioinformatics pipelines as whole-genome sequencing become more important in biomedical research.\u2022Data access is provided by simple download and without restrictions. The triplicate sequencing of a Caucasian male may benefit bioinformaticians, biomedical researchers for testing or as control samples. The data may also be used for educational purposes.\u2022The raw sequencing data consists of biological replicates of low, medium, and higher coverage, which thus may be used for testing different workflow setups.1stats), and approximately 93.4% paired and mappable reads (GRCh37). The combined theoretical mean coverage was estimated to be 63\u201367x, depending on whether the unadjusted or mapped percentage was implemented, using the Lander and Watermann approach C\u00a0=\u00a0L*N/G . Calculations were based on an average read length of 144, 146, and 148 bp. The median GATK-passed variant read depths of the three were 22, 18, and 10 with 3.3\u20134 million variants over the time span of approximately one year from replicate 1 to 3. For the assessment shown here, alignment implemented Burrows-Wheeler Aligner Used commandline workflowfn=${1%_L001_R1_001.fastq.gz}bwa mem -M -R ``@RG\\tID:group1\\tSM:$1\\tPL:illumina\\tLB:lib1\\tPU:unit1'' -t 23 hg38/Homo_sapiens_assembly38.fasta $1 ${1%_L001_R1_001.fastq.gz}_L001_R1_001.fastq.gz | samtools view -@23 -m 1G -Sb -> ${1%_L001_R1_001.fastq.gz}.bamgatk MarkDuplicatesSpark \\-I $fn.bam \\-O $fn.dedup.bam \\\u2013remove-sequencing-duplicatesgatk BaseRecalibrator \\-I $fn.dedup.bam \\-R hg38/Homo_sapiens_assembly38.fasta \\\u2013known-sites hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \\\u2013known-sites hg38/Homo_sapiens_assembly38.dbsnp138.vcf \\\u2013known-sites hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \\-O $fn.recal1.tablegatk ApplyBQSR \\-I $fn.dedup.bam \\-R hg38/Homo_sapiens_assembly38.fasta \\\u2013bqsr-recal-file $fn.recal1.table \\-O $fn.dedup.recal.bamgatk HaplotypeCaller \\\u2013native-pair-hmm-threads 23 \\-R hg38/Homo_sapiens_assembly38.fasta \\-I $fn.dedup.recal.bam \\\u2013dbsnp hg38/Homo_sapiens_assembly38.dbsnp138.vcf \\-O $fn.mnvs.vcfgatk SelectVariants \\-R hg38/Homo_sapiens_assembly38.fasta \\-V $fn.mnvs.vcf \\\u2013select-type-to-include SNP \\-O $fn.SNP.vcfgatk VariantRecalibrator \\-R hg38/Homo_sapiens_assembly38.fasta \\-V $fn.SNP.vcf \\\u2013resource:hapmap,known=false,training=true,truth=true,prior=15.0 hg38/hapmap_3.3.hg38.vcf \\\u2013resource:omni,known=false,training=true,truth=true,prior=12.0 hg38/1000G_omni2.5.hg38.vcf \\\u2013resource:1000G,known=false,training=true,truth=false,prior=10.0 hg38/1000G_phase1.snps.high_confidence.hg38.vcf \\\u2013resource:dbsnp,known=true,training=false,truth=false,prior=2.0 hg38/Homo_sapiens_assembly38.dbsnp138.vcf \\-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP \\-mode SNP \\-O $fn.output.recal \\\u2013tranches-file $fn.output.tranches \\\u2013rscript-file $fn.output.plots.Rgatk ApplyVQSR \\-R hg38/Homo_sapiens_assembly38.fasta \\-V $fn.SNP.vcf \\-O $fn.SNP.filtered.vcf \\\u2013truth-sensitivity-filter-level 99.5 \\\u2013tranches-file $fn.output.tranches \\\u2013recal-file $fn.output.recal \\-mode SNPInformed consent was obtained concerning the donation of biological material and genomic information. Sequencing was part of a technology assessment using anonymous donor material and does not involve any clinical evaluations or trials. Data is made freely available in order to contribute to the continued development of NGS bioinformatics and for educational purposes.Marcus H\u00f8y Hansen: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data Curation, Writing, Editing, Visualization, Supervision, Project administration, Funding acquisition; Charlotte Guldborg Nyvold: Writing, Editing, Supervision.It is not a regular scientific paper.The authors declare that they have no known competing financial interests or personal relationships which have or could be perceived to have influenced the work reported in this article. Funding was provided by the first author. Disclaimer: The provided data presentation is deliberately descriptive."} +{"text": "Klebsiella pneumoniae, especially the hypervirulent blaKPC-positive K. pneumoniae (Hv-blaKPC(+)-KP).To investigate the overall distributions of key virulence genes in K. pneumoniae from GenBank were collected and analyzed. Multilocus sequence typing, molecular serotyping, antibiotic-resistance, virulence genes and plasmid replicon typing were investigated.A total of 521 complete genomes of c-rmpA/A2) to 99.6% (entB). Totally 207 strains presented positive fimH, mrkD, entB and wzi and 190 showed positive fimH, mrkD, entB, irp2 and wzi, which were the two primary modes. A total of 94, 165 and 29 strains were denoted as hypervirulent K. pneumoniae (HvKP), blaKPC(+)-KP and Hv-blaKPC(+)-KP. ST11 accounted for 17 among the 29 Hv-blaKPC(+)-KP strains; Genes iucA, p-rmpA2 and p-rmpA were positive in 28, 26 and 18 Hv-blaKPC(+)-KP strains respectively. Among the 29 Hv-blaKPC(+)-KP strains exhibiting four super clusters from GenBank, IncHI1B plasmids carrying virulence genes and IncFII ones with blaKPC were responsible for both 23 strains respectively.Positive rates of virulence genes highly varied, ranging from 2.9 -KP. IncHI1B plasmids carrying virulence genes and IncFII ones with blaKPC constitute the primary combination responsible for Hv-blaKPC(+)-KP. The making of Hv-blaKPC(+)-KP is mostly via blaKPC(+)-KP acquiring another plasmid harboring virulence genes.Positive rates of virulence genes vary remarkably in Klebsiella pneumoniae, a ubiquitous and an opportunistic pathogen, can induce both nosocomial and community-acquired infections (K. pneumoniae inducing such \u201cinvasive syndrome\u201d is termed as hypervirulent K. pneumoniae (HvKP), which is more virulent than \u201cclassical\u201d K. pneumoniae (cKP) typically responsible for nosocomial infections , New Delhi metallo-\u03b2-lactamase gene (blaNDM), and oxacillinases-48 gene (blaOXA-48), which are predominantly carried on the mobile genetic elements \u00a0has now become a great public health threat worldwide gained more and more prevalence with its positive rate reaching 7.4\u201315.0% among CRKP in recent years -KP), was rarely reported. Here, we collected 521\u00a0K. pneumoniae strains from GenBank. Upon the yielded data, we could get insight into the distributions of key virulence genes in K. pneumoniae, particularly Hv-blaKPC(+)-KP.In the past decades, hypervirulence and drug-resistance advance separately in virulent . Howevervirulent . Not surortality . Due to nt years . To dateK.\u00a0pneumoniae from the GenBank Database were analyzed in this study. Those draft genomes (contigs and scaffolds) were not included. The 521 strains included 28.4% (148 strains) from Mainland China, 4.4% (23 strains) from Taiwan of China, 1.5% (eight strains) from Hong Kong of China, 25.7% (134 strains) from USA, 9.6% (50 strains) from Australia, 6.7% (35 strains) from UK, 3.8% (20 strains) from Germany, 2.7% (14 strains) from Korea, 2.3% (12 strains) from India, 2.1% (11 strains) from France, 1.5% (eight strains) from Japan and 11.1% (58 strains) from other countries.A total of 521 complete whole genomes Table S1K. pneumoniae MLST database and the STs were yielded.The DNA fasta sequences of the 521 genomes were compared with the database containiK. pneumoniae from GenBank, the accession numbers were directly used to determine the capsular types via the database of Institute Pasteur (https://bigsdb.pasteur.fr/klebsiella/klebsiella.html). The potential beta-lactamase genes were determined using the Resfinder software version 3.2 (https://cge.cbs.dtu.dk/services/ResFinder/) with thesupports Table S2peg-344), colonization , assembling channel protein for capsular polysaccharides or macromolecular exopolysaccharides , regulator of mucoid phenotype , Type 1 fimbriae (fimH), Type 3 fimbriae (mrkD), enterobactin (entB), yersiniabactin (irp2), salmochelin (iroN), and aerobactin (iucA) and capsular polysaccharide-anchor (wzi).For virulence genes in this study, they could be classified as the following categories: metabolism , EPS (by wzy-K1) and excessive siderophores , or \u22651 positive capsule-regulating genes . Non-HvKP is termed as cKP. Hv-blaKPC(+)-KP is defined as HvKP carrying blaKPC.The factors responsible for HvKP include hypercapsule . Chi-square test was used to analyze comparisons between groups; c-rmpA/A2) to 99.6% (entB) among the 521\u00a0K. pneumoniae strains. Four genes exhibited prevalence rates of > 90.0%, 1 (irp2) > 50.0% and the others < 25.0%. For the rmpAs, the order was: p-rmpA2 (12.5%), p-rmpA (10.6%) and c-rmpA/A2 (2.9%). For the four siderophore genes, the order was: entB (99.6%), irp2 (53.4%), iucA (15.7%) and iroN (9.2%). Positive rates of iroN and iucA were both lower than that of irp2 and entB . K. pneumoniae: each \u22652 strains. Totally 207 strains presented positive fimH, mrkD, entB and wzi and 190 showed positive fimH, mrkD, entB, irp2, and wzi simultaneously, which were the two primary modes and accounted for 39.7% and 36.5% respectively.wzy-K1, p-rmpA, p-rmpA2 or c-rmpA/A2, 49 (53.8%) possessed p-rmpA and p-rmpA2, 18 (19.8%) possessing wzy-K1, p-rmpA and p-rmpA2, 15 (16.5%) possessing merely p-rmpA2. wzy-K1/p-rmpA or p-rmpA/p-rmpA2. In the 520 strains positive in entB, irp2, iroN or iucA, 278 (53.5%) harbored entB and irp2, 241 (46.3%) harboring only entB, 35 (6.7%) harboring all the four genes. iucA/iroN and irp2. Other relationships were also shown in: peg-344, allS and ST23), p-rmpA, p-rmpA2 and c-rmpA/A2), peg-344, allS and ST14), irp2, iroN and iucA) and irp2, iroN and iucA). Gene wzy-K1 was completely restricted to K1 serotype (31/31), vice versa. High prevalence of peg-344 and allS was found in K1 strains , but rarely in K2 ones . Gene allS was mainly found in K1 strains (28/33), contrary to peg-344 (22/65). K1 strains mostly belonged to ST23 (23/31) while less than a half (17/38) of K2 ones belonged to ST14. K1 strains showed higher rates of rmpAs (p-rmpA/p-rmpA2/c-rmpA/A2) and siderophore genes (iroN/iucA) than K2 ones: 23/31 vs 10/38 (p < 0.0001), 23/31 vs 9/38 (p < 0.0001), which \u201cconfirmed\u201d hypervirulence in K1 strains.Among the 91 strains harboring K. pneumoniae (HvKP), blaKPC(+)-KP and Hv-blaKPC(+)-KP, as shown in blaKPC(+)-KP shared 17.6% (29/165) among blaKPC(+)-KP. For the blaKPC(+)-KP, ST11 accounted for 34.5% (57/165) while clonal group 258, including ST11, ST258, ST340 and ST437, was positive for 65.5% (108/165), indicating the focus of blaKPC(+)-KP.According to the aforementioned criteria, 94 (18.0%), 165 (31.7%) and 29 (5.6%) strains were denoted as hypervirulent blaKPC(+)-KP strains, ranging from fimH (100.0%), mrkD (100.0%), entB (100.0%), wzi (100.0%) to c-rmpA/A2 (6.9%). Genes iucA, p-rmpA2 and p-rmpA were positive in 28 (96.6%), 26 (89.7%) and 18 (62.1%) Hv-blaKPC(+)-KP strains respectively. A sum of 28 (96.6%) strains presented \u2265 3 siderophores and 29 (100.0%) carried p-rmpA/p-rmpA2 (p\u00a0> 0.9999).blaKPC(+)-KP strains, as shown in A total of nine modes of virulence genes were found among the 29 Hv-blaKPC(+)-KP strains, ST11 accounted for the majority although more than 10 STs were found in total (Among the 29 Hv-blaKPC(+)-KP infections revealed that the prevalence of Hv-blaKPC(+)-KP significantly increased between 2018 and 2020, mainly from China, especially Mainland China , suggesting that Hv-blaKPC(+)-KP strains were mainly induced by two different plasmids (blaKPC(+)-KP strains. ST11 accounted for 17 (58.6%) among the 29 Hv-blaKPC(+)-KP strains. Those Hv-blaKPC(+)-KP strains with ST11 typically corresponded to K47 (9/17) and K64 (8/17) serotypes and were divided into four super subgroups. Those with ST86 were all K2 serotype (4/4).Trends in virulence among Hv-K. pneumoniae, in particular Hv-blaKPC(+)-KP.This study investigated the general distributions of key virulence genes in peg-344, of which 63 were denoted as HvKP. A sensitivity of 96.9% was therefore yielded, similar as the report (p = 0.5791) , corresponding to K1 serotype, vice versa, could help K. pneumoniae yield macromolecular EPS, which confers hypervirulence . Gene aldocument . The reairulence . Wzi is capsular . Acapsulrobactin . Intrigurobactin .p-rmpA, p-rmpA2 or c-rmpA/A2 genes. Hypercapsule played an equal role with excessive siderophores in hypervirulence of K. pneumoniae. The reason lies in the same pLVPK-like plasmids harboring rmpAs and siderophore genes concurrently.Except for macromolecular EPS and excessive siderophores, hypercapsule could also contribute to hypervirulence , which iblaKPC was first reported from USA in 1996 (blaKPC-2(+)-KP strain was reported in mainland China in 2007 strains while blaKPC-3 was found in 30 (5.8%) strains. Our study also showed clonal group 258 but not ST11 made up the majority of blaKPC(+)-KP -KP ; The reablaKPC(+)-KP worldwide. Different prevalence of iucA, p-rmpA2 and p-rmpA in Hv-blaKPC(+)-KP strains suggested their different roles in hypervirulence. The modes of virulence genes were rather diverse in Hv-blaKPC(+)-KP. Similar prevalence of \u2265 3 siderophores and p-rmpA/p-rmpA2 (p > 0.9999) indicated their equal roles in hypervirulence of Hv-blaKPC(+)-KP strains, which also originated from the same pLVPK-like plasmids harboring rmpAs and siderophore genes simultaneously. The proportion of K64 was , lower than another report (p < 0.0001). Further, IncHI1B plasmids carrying virulence genes and IncFII ones with blaKPC were responsible for both 23 strains, suggesting IncHI1B and IncFII plasmids jointly constitute the most successful combination. Furthermore, the phylogenetic trees revealed that the 29 Hv-blaKPC(+)-KP strains belonged to four super clusters although three clusters all possessed ST11 strains.The first Hv-CRKP, belonging to K2 and ST65, was unveiled in mainland China in 2015, which was isolated from blood in Wuhan City in March 2013 . Armed wr report (p < 0.0blaKPC(+)-KP evolution may occur through two mechanisms. The first pathway is via HvKP acquiring a plasmid carrying drug-resistance determinants (via multidrug-resistant/extreme drug-resistant cKP acquiring a pK2044- or pLVPK-like virulence plasmid or integrated virulence genes into drug-resistance plasmids (blaKPC(+)-KP mainly evolved through the second pathway, i.e. via blaKPC(+)-KP acquiring another plasmid harboring virulence genes. blaKPC entering ST11 strains; IncHI1B plasmids are different from IncFII ones: rare protospacers were found and they lacked Type IV secretion systems, e.g. traM gene. Therefore, the mechanisms behind IncHI1B plasmids entering ST11 strains would be sophisticated and intriguing.Hv-rminants or by thrminants . The secplasmids . Our datK. pneumoniae strains are not well known. Second, some\u00a0positive virulence genes do not inevitably mean \u201cexact\u201d hypervirulence.This study has some limitations. First, the specimen types of\u00a0521\u00a0K. pneumoniae. Hypercapsule plays an equal proportion with excessive siderophores in hypervirulence of K. pneumoniae. Virulence genes iucA, p-rmpA2 and p-rmpA are primary ones inducing Hv-blaKPC(+)-KP. IncHI1B plasmids carrying virulence genes and IncFII ones with blaKPC constitute the primary combination responsible for Hv-blaKPC(+)-KP. Hv-blaKPC(+)-KP urges more insightful investigations.Taken together, positive rates of virulence genes vary overwhelmingly in https://pan.baidu.com/s/1sbsl_phsx8IRoQeeY87e-w (password: xf5l).Publicly available datasets were analyzed in this study. This data can be found here: DH, YL and PR conceived the study. DT, WC, PF, WW and XJ collected the 521 genomes. DH, YL, PR and XL did bioinformation analysis. DH and YL wrote the manuscript, which was revised by XL and XJ. All authors contributed to the article and approved the submitted version.This work was funded by research grants from the National Natural Science Foundation of China and the Shanghai Municipal Science and Technology Commission (grant number 19JC1413002).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Previous studies have demonstrated that obesity is associated with pulmonary fibrosis. We attempted to identify whether regular aerobic exercise (AE) can protect against high-fat diet (HFD)-associated pulmonary fibrosis.Forty-eight C57BL/6 mice were randomly assigned to four groups: chow group (Ch), chow plus exercise group (CE), obesity group (Ob), and obesity plus exercise group (OE). The mice were fed either an HFD or a chow diet for 16 weeks, and low-intensity aerobic exercise (AE) was performed in the last 8 weeks. We measured the degree of pulmonary fibrosis; pulmonary inflammation; oxidative stress parameters; insulin resistance-related indicators; the number of inflammatory cells in bronchoalveolar lavage fluid (BALF); the mRNA expression levels of IL-10, IL-1\u03b2, TGF-\u03b2, TNF-\u03b1, CXCL-1, IL-17, MMP-9, MPO, NE, and sirt-1; and the BALF levels of CXCL-1, IL-17, TGF-\u03b2, IL-10, IL-1\u03b2, and TNF-\u03b1 in lung tissue.AE in obese mice protected against obesity-associated pulmonary fibrosis, chronic inflammation, pro-oxidative/antioxidative imbalance, and insulin resistance. AE ameliorated the HFD-induced inflammatory response and neutrophil infiltration in the lung. AE downregulated BALF levels of CXCL-1, IL-1\u03b2, TNF-\u03b1 IL-17, and TGF-\u03b2 but upregulated BALF levels of IL-10. AE decreased IL-1\u03b2, TGF-\u03b2, TNF-\u03b1, CXCL-1, IL-17, MMP-9, MPO, and NE mRNA expression levels but upregulated IL-10 and sirt-1 mRNA expression levels in the lung.AE protects against HFD-induced pulmonary fibrosis by improving obesity-associated insulin resistance, chronic low-grade inflammation, and pro-oxidative/antioxidative imbalance. AE improved HFD-induced pulmonary fibrosis by suppressing IL-17, TGF-\u03b2, NE, and MMP-9 expression and activating IL-10 and sirt-1 expression. The prevalence of obesity is increasing drastically and its prevalence markedly upregulates the incidence of many complications such as chronic obstructive pulmonary disease (COPD), asthma, and pulmonary fibrosis . At presvia the TGF-\u03b2 pathway .All protocols used in this study were approved the Animal Experimental Welfare of the Institute of Animal Science, Chinese Academy of Agricultural Sciences . All experiments were performed in accordance with the Animal Experimental Welfare of the Institute of Animal Science, Chinese Academy of Agricultural Sciences and the Guide for the Care and Use of Laboratory Animals published by the US National Institutes of Health. The mice were anaesthetized Forty-eight male C57BL/6 mice were randomly divided into four groups: (1) chow (Ch) group, where the mice were fed a chow diet for 16 weeks; (2) chow diet plus exercise (CE) group, where the mice were fed a chow diet for 16 weeks and forced to train in the last 8 weeks; (3) the obesity (Ob) group, where the mice were fed a HFD for 16 weeks; and (4) the obesity plus exercise (OE) group, where the mice were fed a HFD for 16 weeks and forced to train in the last 8 weeks. Each group included 12 mice.\u00b0 incline, 18 m/min).OE mice were forced to train using a treadmill. Treadmill aerobic training lasted for 8 weeks and was performed once a day for 60 min per session Biotech, CO., LTD, Hangzhou, China).Following the manufacturer\u2019s specifications, superoxide dismutase (SOD), malondialdehyde (MDA), myeloperoxidase (MPO), and glutathione (GSH) levels in the mice were detected using spectrophotometry as previously described . We measTotal RNA was extracted from DNase I-treated cells using TRIzol as previously described . Total RAccording to the reagent manufacturer\u2019s specifications, plasma glucose levels were detected with a glucometer . The plasma insulin and adiponectin levels were detected using commercial kits .post hoc test was utilised to analyse the data in this study. The significance threshold was set at P < 0.05. GraphPad Prism 9 software was utilised to analyse the data and draw figures.All data were expressed as the mean \u00b1 SEM. Two-way ANOVA and Tukey\u2019s P < 0.001), net body weight gains (P < 0.001), abdominal fat weights (P < 0.001), and subcutaneous fat weights (P < 0.001) than did Ch mice. OE mice had lower body weights (P < 0.001), net body weight gains (P < 0.001), abdominal fat weights (P < 0.001), and subcutaneous fat weights (P < 0.001) than did Ob mice.As In the Ch group and the CE group, no inflammatory cell infiltration was observed in the lung. HFD markedly increased the number of neutrophils in the lung, while AE markedly decreased the number of neutrophils in obese mice .P < 0.001) in BALF was markedly upregulated. Regular AE markedly downregulated the number of neutrophils in obese mice (P = 0.0301).As shown in P < 0.001) and CXCL-1 (P < 0.001), profibrogenic factors TGF-\u03b2 (P < 0.001) and IL-17 (P < 0.001), and proinflammatory factor IL-1\u03b2 (P < 0.001) but significantly lower levels of the anti-inflammatory factor IL-10 (P < 0.001) in BALF than did Ch mice. AE markedly decreased BALF levels of IL-1\u03b2 (P = 0.033), IL-17 (P = 0.009), TGF-\u03b2 (P = 0.013), and TNF-\u03b1 (P = 0.025) but markedly increased BALF levels of IL-10 (P = 0.004) compared with Ob mice.As shown in Masson staining showed the degree of pulmonary fibrosis. Compared with those in the Ch group and the CE group, the magnitude of pulmonary fibrosis increased after 16 weeks of HFD administration, but AE decreased the magnitude of pulmonary fibrosis in obese mice .Sirius Red staining showed collagen fibre deposition in lung tissue. In the Ch group and the CE group, no obvious collagen fibre deposition was noted in the airway wall, while collagen fibre deposition in the airway wall increased after 16 weeks of HFD administration. AE decreased collagen fibre deposition in the airway wall in obese mice .P = 0.024) and IL-17 (P = 0.0031) in BALF. Regular AE downregulated BALF levels of TGF-\u03b2 (P = 0.013) and IL-17 (P = 0.003) in obese mice.As shown in P < 0.001), Ashcroft fibrosis (P < 0.001), lung fibrotic score (P < 0.001), and airway collagen (P < 0.001) in the lung, whereas AE markedly downregulated hydroxyproline levels (P = 0.019), Ashcroft fibrosis (P = 0.024), lung fibrotic score (P = 0.031), and airway collagen (P = 0.005) in obese mice.As P < 0.001), IL-1\u03b2 (P < 0.001), IL-17 (P = 0.0034), MMP-9 (P = 0.0089), MPO (P < 0.001), NE (P < 0.001), TGF-\u03b2 (P < 0.001), and TNF-\u03b1 (P = 0.0072) mRNA expression levels but decreased IL-10 (P = 0.013) and sirt-1 (P = 0.011) mRNA expression levels compared with the Ch group. AE for 8 weeks markedly downregulated CXCL-1 (P < 0.001), IL-1\u03b2 (P < 0.001), IL-17 (P = 0.024), MMP-9 (P = 0.0029), MPO (P = 0.013), NE (P = 0.011), TGF-\u03b2 (P = 0.0125), and TNF-\u03b1 (P < 0.001) mRNA expression levels in obese mice.The mRNA expression levels of CXCL-1 , IL-1\u03b2 , IL-10 , IL-17 , MMP-9 , MPO Fi, NE Fig, sirt-1 P = 0.0063) and SOD (P = 0.0047) and increased expression levels of MDA (P = 0.0092) and MPO (P = 0.0025) in lung tissue compared with the Ch group. Significant downregulation of MPO (P = 0.0396) and MDA (P = 0.0412) expression and significant upregulation of GSH (P = 0.0037) and SOD (P = 0.0268) expression were detected after 8 weeks of AE compared with the Ob group.The levels of GSH , MDA Fi, MPO Fi, and SODP < 0.001) and plasma insulin levels (P < 0.001) but markedly upregulated blood glucose levels (P < 0.001) compared with Ch treatment. Significant downregulation of blood glucose levels (P = 0.0164) and significant upregulation of plasma adiponectin levels (P = 0.0386) and plasma insulin levels (P = 0.0441) were detected after AE for 8 weeks. The results of the GTT (HFD feeding markedly downregulated plasma adiponectin levels ( the GTT , ITT (Fi the GTT , and IRT the GTT demonstrPrevious studies demonstrate that obesity was closely associated with pulmonary fibrosis . HoweverMorphological analysis demonstrated that AE in obese mice reduced hydroxyproline levels and collagen fibre deposition in lung tissue. Our data demonstrated that HFD administration dramatically increased the levels of the profibrogenic factors NE, MMP-9, TGF-\u03b2, and IL-17 in BALF. Similarly, HFD administration dramatically increased NE, MMP-9, TGF-\u03b2, and IL-17 mRNA expression levels in lung tissue, which was reversed by the end of the 8-week AE programme. Thus, AE protected against pulmonary fibrosis by repressing the expression of NE, MMP-9, TGF-\u03b2, and IL-17. In addition, sirt-1 was a negative regulator of MMP-9 . TherefoNeutrophils play an important role in the pathogenesis of pulmonary fibrosis . We founHFD administration led to pro-oxidative/antioxidative imbalance, and the antioxidant effects of exercise were identified in this study. Our data identified that regular AE in obese mice significantly downregulated MDA and MPO levels but significantly upregulated SOD and GSH levels in the lung. AE in obese mice modulated the oxidative/antioxidative balance in lung tissue. Previous studies have demonstrated that sirt-1 has therapeutic effects in lung diseases because sirt-1 modulates the pro-oxidative/antioxidative balance . Our datPrevious studies identified that obesity-associated insulin resistance enhanced TGF-\u03b2 expression, which played an important role in the pathogenesis of pulmonary fibrosis . We founThe results of this study provide insight into pulmonary fibrosis and indicate that AE is a novel tool to treat pulmonary fibrosis. HFD administration leads to pulmonary fibrosis by causing insulin resistance, a chronic inflammatory response, pro-oxidative/antioxidative imbalance, and increased levels of profibrogenic factors, including TGF-\u03b2, IL-17, NE, and MMP-9. AE improves HFD-induced pulmonary fibrosis by counteracting obesity-associated insulin resistance, chronic inflammatory responses, and pro-oxidative/antioxidative imbalance and shows an antifibrogenic effect by suppressing TGF-\u03b2, IL-17, NE, and MMP-9 production in obese mice.The original contributions presented in the study are included in the article/The animal study was reviewed and approved by Animal Experimental Welfare and Ethical Inspection Form of Institute of Animal Science, Chinese Academy of Agricultural Sciences.XW: conceptualisation, methodology, software, validation, writing\u2014original draft preparation, and project administration. XY and DT: formal analysis, investigation, resources, supervision, and funding acquisition. XW, XY, and DT: writing\u2014review and editing. All authors have read and agreed to the published version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "The ts3agn mutation drastically increases the frequency ofectopic contacts (FEC) in specific regions of intercalary heterochromatin, suppresses learning/memory and affectslocomotion. As is shown in this study, the polytene X chromosome bands in reciprocal hybrids between ts3agn and thewild type strain Berlin are heterogeneous in modes of FEC regulation depending either on maternal or paternal geneorigin. Bioinformatic analysis reveals that FEC between X:11AB and the other X chromosome bands correlates with theoccurrence of short (~30 bp) identical DNA fragments partly homologous to Drosophila 372-bp satellite DNA repeat.Although learning acquisition in a conditioned courtship suppression paradigm is similar in hybrids, the middle-termmemory formation shows patroclinic inheritance. Seemingly, this depends on changes in miR-974 expression. Severalparameters of locomotion demonstrate heterosis. Our data indicate that the ts3agn locus is capable of trans-regulatinggene activity via POEs on the chromatin nuclear organization, thereby affecting behavior.Prognosis of neuropsychiatric disorders in progeny requires consideration of individual (1) parent-of-origineffects (POEs) relying on (2) the nerve cell nuclear 3D chromatin architecture and (3) impact of parent-specific miRNAs.Additionally, the shaping of cognitive phenotypes in parents depends on both learning acquisition and forgetting,or memory erasure. These processes are independent and controlled by different signal cascades: the first is cAMPdependent,the second relies on actin remodeling by small GTPase Rac1 \u2013 LIMK1 (LIM-kinase 1). Simple experimentalmodel systems such as Drosophila help probe the causes and consequences leading to human neurocognitive pathologies.Recently, we have developed a Drosophila model for Williams\u2013Beuren Syndrome (WBS): a mutant Genome plasticity is ensured by the architecture of specificnuclear loci and nuclear localization of transcriptional machinerywhere the chromatin organization is the priority-driven factor. The outcome of recent achievements in systems biologyis the notion that the plasticity of 3D chromatin architectureof nervous cell nuclei plays the leading role in cognitionand neuropsychiatric disorders . The epigeneticcomponent is still an underestimated source of psychomotordisturbances and neuronal diversity . Therefore, a new field of human biomedical researchnamed molecular cytogenetics and cytogenomics , or chromosomics has evolved. Themain goal of chromosomics is the study of chromosomes,their 3D architecture in the interphase nucleus, the outcomesof chromosomal sub-region plasticity and gene interactions forshaping interindividual and intercellular genomic variationsin normal behavior and disease.Recently, this topical problem has turned out to be thepursuit of understanding the concomitant role of activeforgetting, since the antithesis to learning acquisition is theforgetting or memory erasure . Bothprocesses are independent and controlled by different signalcascades: learning acquisition and memory consolidationoccurs via cAMP cascade, its components being CREB andC/EBP. Active forgetting relies on actin remodeling cascaderesponsible for structural alterations of neurons and synapses:small GTPase Rac1 \u2013 LIMK1 (the key enzyme of actin remodelingLIM-kinase 1) and its phosphorylation substrate\u0441ofilin. The absence of Rac1-dependent forgetting causesthe autistic spectrum disorders. Expression changes (activeor non-active state) of LIMK1 and cofilin lead to differentneuro pathologies. The most studied example embracing allthe aforementioned facets of manifestations is Microdeletion(Deletion) Williams\u2013Beuren Syndrome, or WBS in 7q11.23.WBS deletion leads to cardiovascular pathology, cognitivedeficit in visuospatial construction and hypersociability. This isbecause long-term synaptic plasticity and depression determinesuccessfulness of learning and memory, as well as oflocomotor behavior, and depend on epigenetic regulation of LIM-kinase 1 (LIMK1) gene, one of approximately 28 genesuncovered by WBS deletion. Epigenetic regulation of LIMK1activity involves DNA methylation, chromatin remodeling andthe noncoding RNA-mediated process .LIMK1, a member of serine/threonine (Ser/Thr) familykinases regulated by the Rho-GTPase pathway, is the keyenzyme of actin remodeling cascade. Dendritic spines areactin-rich structures, and spine dynamics is driven mainly byactin remodeling, thus sharing several molecular pathwayswith dendrite growth . Increasing sets ofevidence suggest that nuclear actin also plays a pivotal rolein transcriptional regulation and DNA repair. Interestingly,monomeric actin is a stoichiometric subunit of a variety ofchromatin remodeling complexes. Ashift between monomericand polymeric states modifies activity of histone deacetylases.agnostic locus harboringLIMK1 gene (X:11AB). This region possesses theproperties of intercalary heterochromatin. Being a hotspot ofchromosome breaks, ectopic contacts, underreplication andrecombination, the region attains strain-specific architecturemarked by single base changes and small insertion/deletions.The EMS-induced temperature-sensitive (ts) mutationts3agn carries the insertion of transposable element (TE) fromTc1/mariner superfamily ~460 bp downstream 3\u2032UTR ofDrosophila LIMK1 gene (dlimk1), as well as A/T-rich 28 bpinsertion within intron 1 of dlimk1 capable of pairing with5\u2032 TIR of the TE.Recently, we have developed a simple and appropriateDrosophila model for chromosomics using the properties of the ts3agn shows a temperaturesensitivelethality at all stages of development except for theimaginal stage. At normal temperature, the adult flies showdrastic learning acquisition and memory retention defects, aswell as locomotor impairments and amyloid-like inclusions. Stressexposure (heat shock for 30 min at 37 \u00b0C) suppresses thesemanifestations . Also, ts3agnmutationleads to: (1) LIMK1 and p-cofilin increase in the adultbrain and salivary glands of 3rd instar larvae at 22\u201325 \u00b0C anda fall down to the level of the wild type strain Canton S at29\u201337 \u00b0C; (2) high level of ts-induced recombination withints3agn region; (3) 3-fold increase in frequency of non-allelicectopic contacts (FEC) within 2L arm of the chromosome 2 and in the 11\u0412 X chromosome region . Additionally, miRNAs expression including the biomarkersfor human neuropathologies is drastically reducedin ts3agn relative to the wild type strains .When maintained at 29 \u00b0C, ts3agn-specific nuclear organization is shaped in early embryogenesisalongside with formation of chromosomal heterochromatinregions. Intrinsic ts3agn FEC is maternally inherited. Therefore, ts3agn is a promisingmodel for studies on parent-of-origin effects (POEs) on progenyconsidered as significant causative factors of psychiatricdisorders . For instance, a 1.5 Mb WBSdeletion recurrently arises de novo and depends on POEs: maternalorigin leads to more severe developmental abnormalitiesand microcephaly . Moreover,when WBS deletion has a paternal origin, expression levels ofa number of genes within the WBS deletion decrease. Amongthese genes crucial for the brain development is a gene for generaltranscription factor II-I (GTF2I). It regulates transcriptionby binding to DNA and histone deacetylase (HDAC) . The main goal of the study is the analysisof POEs role in shaping quantitative traits, namely learningacquisition, memory retention, locomotion, and miRNAs expressionwhile using the advantages of the Drosophila modelfor POEs in progeny from reciprocal crosses between ts3agnand the wild type strain Berlin .To meet the requirements of chromosomics, FECs betweenthe region X:11AB and the other bands of the X chromosomemay be estimated as an indicator of chromosomal spatialorganization. This approach is justified by the existence oflate-replicating genomic territories including the underreplicatedregions of polytene chromosomes. These regions overlapwith late-replicating regions of mitotically dividing cells. Suppression of SUUR gene responsiblefor underreplication of intercalary heterochromatin and, as aconsequence, for the ectopic pairing leads to death in early embryogenesis. Additionally, to elucidatethe contribution of DNA sequence homology as componentsof epigenetic regulation in the ectopic chromatin pairing wehave developed the special software package Homology SegmentAnalysis.Drosophila stocks. The fly stocks used belong to Biocollectionof Pavlov Institute of Physiology of the Russian Academyof Sciences:\u2022 Berlin, a wild type strain;\u2022 Canton S, a wild type strain;\u2022 ts3agn, a temperature-sensitive mutation on Canton Sgenetic background within agnostic locus (X:11AB) affectingdlimk1 activity.ts3agn and Berlin were usedbecause Berlindlimk1 sequence is closer to FlyBase referencesequence . At the same time,the reciprocal hybrids ts3agn\u00d7Canton S (the genetic backgroundfor ts3agn) and Canton S\u00d7ts3agn demonstrate exactlythe same cognitive behavior as reciprocal hybrids with Berlin approving the usage of Berlin.The reciprocal hybrids between Berlin and ts3agn female and male parents and F1 female and male progeny from reciprocal crosses with theaccent on the putative hairpin formed in the X chromosomeby 28 bp A/T rich insertion within intron 1 of dlimk1 geneand 3\u2032 end of Tc1/mariner element.Figure 1 shows the X chromosome and autosomes architecturein Flies were maintained on standard Drosophila yeast-raisinmedium at +22 \u00b1 0.5 \u00b0\u0421 under a 12-h light/dark cycle. Forthe memory and locomotion tests, males were collected uponeclosion without narcotization and kept individually in culturevials till the behavioral experiments on the 5th dayEstimation of frequency of ectopic contacts (FECs).The aceto-orcein squash preparations were prepared fromsalivary glands of III instar D. melanogaster female larvae.20 to 30 animals were examined, therefore the number ofanalyzed chromosomes varied from 300 to 500. The examplesof ectopic contacts are presented on Fig. 2. The number ofnon-homologous contacts between the region X:11AB anddifferent bands of the X chromosome was calculated and expressedas per cent of the total number of the examined nuclei.FECs in parents and F1 reciprocal hybrids were comparedusing Student\u2019s t-test. Identification of genes localized in theX chromosome bands forming contacts with the 11AB regionwas performed using NCBI Genome Data Viewer databasehttps://www.ncbi.nlm.nih.gov/genome/gdv/ and molecularfunction of identified genes was derived from FlyBase https://flybase.org analysis of DNA segments homology.D. melanogaster genome sequence (release 6) was taken from. Special software package HomologySegment Analysis searching the matches of short singlestrandedDNA fragments within the chromosome areasinvolved in the ectopic pairing in Drosophila has been developed.The software written in Python 3 can be freely downloadedfrom . Software version from git(commit 41719cddc6283edbd79c5bf2aee237cde48d4b7d)was used. The algorithm of the program is described in brief in. The exact run parameters for 11AB region are following: segmentanalysis.py -v -s 30 dm6.nounmapped.fa.gz :X:11982050:12772070 DmelMapTable.160615c.bedHere, dm6.nounmapped.fa.gz is Drosophila genome canonicalsequence (Ensembl release 6) and DmelMapTable.160615c.bed is chromosome bands location from Ensembldatabase converted to BED format. Both files are included insoftware repository.For other tested regions, all parameters were the sameexcept for the regions location.Preparation of miRNAs libraries and bioinformaticanalysis. The detailed description of the procedure is givenin . Extract RNA reagent was used for total RNA extraction fromadult 5 days old males. To obtain the fraction of small RNA,25 \u03bcg of total RNA were separated using 15 % polyacrylamidegel electrophoresis in the presence of Urea (8 M) followingexcision of small RNA fraction corresponding to 21\u201329 nts.Illumina TruSeq Small RNA prep kit wasused for small RNA libraries preparation. Sequencing wasperformed on an Illumina HiSeq 2000 platform.The amount of mapped miRNAs reads was counted byBEDTools (v. 2.22) and mirbase annotation (r. 19) . Analysis of differentially expressed miRNAs wasperformed using edgeR (v. 3.10.2) package in R environment(v. 3.2.2) . miRNA functions werederived from miRBase . Small RNAlibraries were deposited in NCBI SRA under the numberPRJNA633483.Locomotor activity. Computer-aided automatic device forsimultaneous registration of 20 animals is described in . The experiment lasted for 1 h. Spontaneouslocomotor activity of flies was detected in a plate witheight chambers and transparent cover using high-resolutionvideo camera. Software used for locomotor activity analysisis freely available at .The following parameters of locomotion were assessed:activity index (%); run frequency (the number of run boutsin 100 seconds); running speed (mm/s). The full record wasdivided into 1 s quanta, and the mean speed of fly movementin each quantum was calculated. If the result was less thanthe threshold value (5 mm/s), the fly was considered to beresting during this time quantum; otherwise, it was considered moving. Neighboring quanta with similar movement patternwere merged in intervals of moving and resting. Activity indexis determined as a time spent in movement. Running speedis an average fly speed, determined using only intervals ofmovement. The Kruskal\u2013Wallis analysis of variance with themultiple comparison of mean ranks was used to compare allthe experimental groups.Learning acquisition and middle-term memory formationin Drosophila males. Detailed description of learning/memory assessments in conditioned courtship suppressionparadigm (CCSP) and specially designed software for observationand statistical analysis (randomization test) of learningindices based on courtship indices is given in . CCSP employs the natural stimuli of Drosophilacourtship. Both virgin and fertilized females emit an aphrodisiacpheromone, attracting a na\u00efve male without courtshipexperience. However, a fertilized female rejects a male atthe courtship stage of attempted copulation via emitting anaversive pheromone. Repetitive rejections during 30 mintraining provoke a kind of learned helplessness when a malestops courting another female. This courtship suppressionmight last for one hour when test female is virgin and foreight hours when fertilized. Males with defective memoryformation continue to court after such a training as vigorously,as na\u00efve males.The courtship index was calculated for each male. The learning index (LI)was computed according to the formula:Analysis of spatial nuclear organizationdelimited to FECs formedby the X chromosome region 11ABBerlin, ts3agn and their hybrids are presented in Table 1. Thecolumns 1\u20134 show the pattern of FECs between the 11AB regionand other X chromosome regions pertinent to listedstrains. The absence of significant differences of FECs betweencolumns, i.e. 1 vs 2 and 3 vs 4 indicates matroclinicinheritance, 2 vs 3 indicates hybrid-specific frequencies, 2 vs 4and 1 vs 3 pinpoints the patroclinic inheritance. The polytenechromosome bands in hybrids demonstrate differences inFECs, a part of them showing either matroclinic propertiesor properties of the father strain. In certain bands, FECs aresimilar in reciprocal hybrids or depend on the direction of a cross, but significantly differfrom that of parents.Spatial nuclear organization was analyzed using microscopicimages of polytene chromosomes in larvae salivaryglands. The results of comparative analysis of FECs betweenthe 11AB region and the other X chromosome regions in Berlin, ts3agn and their hybrids are presented in Table 1. Thecolumns 1\u20134 show the pattern of FECs between the 11AB regionand other X chromosome regions pertinent to listedstrains. The absence of significant differences of FECs betweencolumns, i.e. 1 vs 2 and 3 vs 4 indicates matroclinicinheritance, 2 vs 3 indicates hybrid-specific frequencies, 2 vs 4and 1 vs 3 pinpoints the patroclinic inheritance. The polytenechromosome bands in hybrids demonstrate differences inFECs, a part of them showing either matroclinic propertiesor properties of the father strain. In certain bands, FECs aresimilar in reciprocal hybrids or depend on the direction of a cross, but significantly differfrom that of parents.NCBI Genome Data Viewer software helped to reveal thegenes located in the X chromosome bands forming the ectopiccontacts. Based on the assumption that shared location ofgenes determines their functional features ,it was worth elucidating what biological processes are underthe influence of epigenetic factors related to allelic parentof-origin. Therefore, the grouping of genes implied theirinvolvement in control of a certain biologic process .ts3agn\u00d7Berlin relative to the reciprocalhybrid are genes for motor proteins and sensoryreceptors . Genes involved in neurodevelopment,oxidative-reduction process and proliferation do not present inBerlin\u00d7ts3agn progeny. Heterosis, when the number of genesinvolved in hybrid-specific contacts is more than 2-fold higherthan in both parents, is manifested for oxidative-reductionprocess (3), signal transduction (4), proliferation (9) and noncodingRNAs (13).Figure 3, a presents provisional definition of the biologicalprocesses controlled by genes within bands forming contactswith 11AB region either in matroclinic or in reciprocal hybridspecificmanner. Among the functional groups of genes havingincreased number in ts3agn\u00d7Berlin relative to thereciprocal hybrid), reactive oxygen species metabolic process, and metabolism . Sensory perception andsignal transduction groups do not present in Berlin\u00d7ts3agn.The biological processes and genes involved in ectopiccontacts with 11AB in a mode of father strain are shown inFig. 3, b. Among them are the genes responsible for chromatinremodeling ; metabolism ; cell proliferation ); chromatine remodeling . Reparation/recombination group does not present in Berlin\u00d7ts3agn.Data on biological processes and the number of genes involvedin contacts with 11AB region exclusively in hybridsor with FECs prevailing those of parents (FEC heterosis), areshown on Fig. 3, c. The ratio of gene numbers for Profiles of the localized fragment frequencies (LFFs)Using our specially designed software Homology SegmentAnalysis, we analyzed correlation between ectopic pairingand distribution of small identical fragments within contactingregions.The region X:11AB (~790 kb) involved in DrosophilaX \u2013 X:11AB ectopic pairing was selected as the source ofsmall 30 nt fragments, and the profile of X:11AB localizedfragment frequencies (LFFs) was constructed for the X chromosome. The region X:14B\u201315B was selected asa control region having almost equal length (~790 kb).ts3agn\u00d7Berlin FEC (X:11AB). Probably,20 nt fragments are too short to display DNA homologyspecifically associated with ectopic pairing. The increasein fragments length from 20 to 50 nt leads to decrease inLFF (X:14B\u201315B) \u2013 FEC (X \u2013 X:11AB) unspecific correlation and simultaneous increase in LFF \u2013 FEC (X:11AB) specificcorrelation. However, there is a lack of LFF (50 nt) \u2013 ECFcorrelation for ts3agn. Hence, 30 nt fragment length seems tobe optimal in search for the identical fragments within thecandidate chromosomal regions involved in ectopic pairing.Both LFF and the FEC (X \u2013 X:11AB) distributions significantlydiffer from normal. Therefore, we calculated Spearman\u2019srank-order correlation coefficients (rS) for LFF andthe strain-specific FEC (X \u2013 X:11AB) (Table 2). A positivecorrelation between LFF and FEC is observed within the region of interest X:11AB. The influence of the fragment lengthon rS value has been tested. For 30 nt fragments, rS is highlysignificant for all Drosophila strains ( p < 0.001). As to LFF(X:14B\u201315B), there is no significant correlation with FEC(X \u2013 X:11AB) ( p \u2265 0.01) pointing to specificity of analysisof DNA homology within the region of ectopic pairing. For 20 nt fragments, there is a false-positive correlation betweenLFF (X:14B\u201315B) and Berlin FEC and thelocalization frequencies for the several specific X:11AB 30 ntfragments having the highest number of occurrences (NO)in the X chromosome (Table 3). The maximal correlation isevident in the part of 372 bp middle repetitive DNA sequence). The majorityof fragments with significant positive rS values appear to bethe parts of a ~50 bp repeat (marked with #) having significantself-complementarity. This sequence also shows an almostcomplete identity to another part of 372 bp repeat. Such repeatswith slight sequence variations occur in both DNA strands ofthe X chromosome. rS is much lower for (-at-)15 repeat and isnearly absent for (-gt-)15 (-tc-)15 and (-ca-)15 repeats, althoughtheir NO can be higher. Noteworthy, all rS values for 372 bprepeat fragments are lower compared to rS for the whole setof the localized fragments (see Table 2), hence all of themseemingly impact ectopic pairing.To find out what DNA sequences impact the ectopic pairingthe most, we calculated rS between miRNAs expression profileBerlin, ts3agn and their reciprocalhybrids demonstrates significant differences betweenmales of parent strains and hybrids in content of 44 miRNAs.For the reciprocal hybrids, the heat maps of miRNAs expressionare presented in Fig. 5. Among 44 miRNAs 10 miRNAsbelong to the same cluster of testis-specific miRNAs . However, only miR-980 and miR-974are involved in memory processes. Expression of miR-980suppresses Drosophila memory ,while lowered expression of miR-974 impairs memory formationAnalysis of miRNAs expression in The heat map represents the RPM-normalized and log2-transformed counts of miRNAs reads with z-scale normalizationof the rows. Thirty percent of low-expressed miRNAswere removed from further analysis. Only the miRNAs withaltered content in a hybrid compared to at least one parentare shown. analysis of parent strainsand their reciprocal hybridsLocomotor behavior. Figure 6 presents the parameters oflocomotion. As to activity indices, they are significantly differentin ts3agn and Berlin, both hybrids differ from ts3agn andBerlin\u00d7ts3agn differs from Berlin. Running speed and runfrequency in ts3agn and Berlin are similar. Both hybrids differfrom ts3agn and Berlin\u00d7ts3agn from Berlin. However, thehybrid running speed exceeds that of parents, demonstratingheterosis. Comparatively to parents, run frequency in hybridsis intermediate. At the same time, any alterations in locomotorparameters in hybrids are similar and unidirectional.Learning acquisition and memory formation.In all strains,CIs of males decrease after training with fertilized femalescompared to na\u00efve flies . Learning/memory scoresin reciprocal hybrids show that memory formation (3 hoursafter training), but not learning acquisition (0 hours aftertraining), demonstrates patroclinic inheritance .Berlin strain in crossests3agn\u00d7Berlin, learning and 3-hour memory do not differfrom LIs of Berlin, but do differ from LIs of ts3agn. Patroclinicinheritance is evident in the reciprocal hybrid Berlin\u00d7ts3agn.In this case, 3-hour LIs in Berlin\u00d7ts3agn and ts3agn are similar.The patroclinic inheritance cannot be associated with theY chromosome, as it is likely to be similar in Berlin, ts3agnand Canton S . Also, it cannot be attributed to the X chromosomes,since they are different in Berlin and ts3agn\u00d7Berlin.Seemingly, this may be caused by some paternal epigeneticfactors, such as miRNAs in cytoplasm of male sperm.When male parent originates from Discussionts3agn gene and epigenetic factors (POEs) in spatial nucleararchitecture, learning/memory formation and spontaneouslocomotor activityStudies of genome-wide associations between DNA polymorphismsand phenotypic traits have revealed genetic variantspredisposing to different mental diseases. Findings pinpointingthe role of POEs in genetic risk for neuropathology opennew possibilities for therapy and preventive medicine . In this study, we estimated FECs in reciprocalhybrids considering an impact both of genetic variants ofdlimk1 gene.Our assumption was that FE\u0421s partly reflect the restrictedhomology of short DNA sequences in different, seemingly\u201cnon-homologous\u201d regions.To exploit the advantages given by the model, we delimitedthe analysis of spatial nuclear organization to FECs formedby the X chromosome region 11AB harboring As shown in this study for the short identic fragments withinthe contacting regions, FECs correlate with LFFs. Althoughthe correlation is rather moderate (~0.35), it is highly specificfor 30 nt fragments. Many factors affect ectopic pairing,such as DNA homology, the distance between the interactingregions and epigenetic factors causing the interstrainFECs differences . Our computationalalgorithm concerns only fragments aligned with the X chromosomewithout gaps. This reveals the partial homology ofinteracting bands. Thus, the interacting chromosomal areasmay be significantly larger than 30 or 50 nts. Although differentmechanisms are involved in ectopic pairing, includingPOEs, our data indicate the significant role of DNA sequenceitself. However, as FEC\u2013LFF correlation is mainly observedfor specific DNA fragments, their pairing mediated by someproteins or non-coding RNAs cannot be ruled out.Most of the found 30\u201350 nt fragments are similar to theD. melanogaster dispersed 372 bp A/T-rich noncoding repeat. This moderately repeated sequence islocated in the euchromatin of the X chromosome between theregions 4 and 14A in ~300\u2013400 copies per haploid genome.The 372 bp repeat is a part of 1.688 g/cm3 class of satelliteDNA (1.688X repeats) . siRNAfrom the 1.688X repeats is involved in dosage compensationin recognition of the X and autosomal chromatin, therebydelimiting activities of male-specific lethal (MSL) complexto sex chromosomes through up-regulation of the X chromosome.ts3agn, FECs in thesebands significantly decrease. In this case maternal control ofspatial localization and therefore, of gene expression is geneticallydetermined. These are genes controlling membranereceptor regulation (PPYR1) and signal transduction (gce),chromatin remodeling , axon guidance andchemosensory jumping behavior (acj6 ).The data obtained consider the common mechanisms ofectopic contacts formation and dosage compensations. Seemingly,POEs might influence the spatial chromatin organization,thereby affecting behavioral performances.This indicates that each Drosophila strain possesses itsown pattern of ectopic contacts with the region 11AB. Thepolytene chromosome bands are heterogeneous in their modesof regulation of ectopic pairing. Apart of them is regulated bygenes of either maternal, or paternal origin. A separate classis comprised of regions manifesting only hybrid properties.Similar \u0420\u041e\u0415s were observed for the pattern of methylation andnucleosome distribution within the imprinted loci in humansand plants .In both reciprocal crosses, bands 7A, 9A and 13B displaythe maternal properties. When mother is This indicates that each Drosophila strain possesses itsown pattern of ectopic contacts with the region 11AB. Thepolytene chromosome bands are heterogeneous in their modesof regulation of ectopic pairing. Apart of them is regulated bygenes of either maternal, or paternal origin. A separate classis comprised of regions manifesting only hybrid properties.Similar \u0420\u041e\u0415s were observed for the pattern of methylation andnucleosome distribution within the imprinted loci in humansand plants .ts3agn, FECs in thesebands significantly decrease. In this case maternal control ofspatial localization and therefore, of gene expression is geneticallydetermined. These are genes controlling membranereceptor regulation (PPYR1) and signal transduction (gce),chromatin remodeling , axon guidance andchemosensory jumping behavior (acj6 ).In both reciprocal crosses, bands 7A, 9A and 13B displaythe maternal properties. When mother is ts3agn\u00d7Berlin, the number of genes with knownfunctions contacting with 11AB with maternal-specific frequencyis 2-fold higher than in reciprocal cross. Possibly, thisis due to the ts3agn-specific miRNAs pattern of expression.The role of miRNAs in maternal inheritance and expressionin embryogenesis is sparsely studied. As we have shownearlier, the expression level of miR-9, miR-34 and miR-124differs in ts3agn from that in Berlin, Canton S and Oregon-R. miR-9 and miR-124 are alsoexpressed in early development (0\u201312 hrs) , miR-34 is detected in embryos till zygotic reduction. As known, the switch from maternal tozygotic development program occurs between the second andthe third hours of embryonic stage, hence miRNA found inearly development have maternal origin . ThesemiRNAs targets are Swi/Snf-like complex, neural-progenitorspecificnpBAF, repressor-element-1-silencing transcriptionfactor (REST belonging to 1 class of histone deacetylases(HDAC1/2) and silent information regulator 1 (SIRT1) \u20133 class of NAD+-dependent histone deacetylases involved inheterochromatin formation, Bourassa, Ratan, 2014). They areinvolved in neurogenesis, dendrite morphogenesis and axonguidance which depend on global chromatin remodeling.In the cross ts3agn\u00d7Berlinectopic contacts between 11AB and regions containing genesinvolved in chromosome remodeling are formed with frequencycharacteristic for the maternal genome. The products ofthese genes are: Tip60 \u2013 histone acetyltransferase, HDAC6 \u2013histone deacetylase; mxc \u2013 regulator of histone synthesis ofPolycomb group; Top1 \u2013 DNA topoisomerase. However, onlytwo regions containing genes HDAC6 and Top1 are presentin cross Berlin\u00d7ts3agn.Therefore, it is not surprising that in cross ts3agn-like matroclinicmode of inheritance is pertinent to genes responsible for actinand microtubules-binding proteins with motor function andneurodevelopment. Noteworthy, the state of actin remodelingdetermining neurologic manifestations is a diagnostic featureof ts3agn .Noteworthy, new knowledge about topologically associatingdomains (TADs) indicates that polytene, diploid, andembryonic TADs condensation along the chromosome axisis just the same everywhere . Moreover,comparison of TADs with 3D chromatin organization revealedby the Hi-C method confirms that the interphase nucleusspatial organization into TADs is directly represented by bandingpattern of polytene chromosomes .Therefore, this allows to bridge the ratio of genes forming ectopic contacts in a mode of either maternal, or paternal strainin reciprocal crosses and their physiologic manifestations.The later might result from alterations in the 11AB regionarchitecture. As shown in Fig. 3, a, the The regions with FECs similar in reciprocal hybrids, butdiffering from parents, i. e. manifesting hybrid properties,contain a large set of genes responsible for motor functions.ts3agn:meiosis, reparation, recombination; transcription factors; metabolism;proliferation; actin-binding proteins, microtubuleassociatedproteins.Figure 3, c shows genes and biological processes for chromosomalregions forming ectopic contacts with X:11AB onlyin hybrids or mainly in hybrids compared to parents. Theseprocesses are pertinent to main manifestations of ts3agn the chromosomalbands 8D, 12E, and 19D demonstrate FECs significantly exceedingthese of parents. These bands contain genes involvedin taste and odor perception and neurodevelopment, in particularof the mushroom bodies of the brain. The other examplesof father strain manifestations might result from activities oftrans-acting factors, such as miRNAs .Interestingly, in the cross Berlin\u00d7ts3agn and in progenyof Berlin\u00d7ts3agn (impaired 3-hour memory) and is similar towild type in the ts3agn\u00d7Berlin cross . Likely,miR-974 might act as trans-acting factor presumed to regulategenes in patroclinic mode. The prevailing role of the paternalgenome in memory formation is evident in Canton S and ts3agnreciprocal hybrids .miR-974 is involved in memory processes: its loweredexpression impairs memory formation .Decrease in its content in olfactory neurons and the mushroombody V2 neurons promotes 3-hour memory. Noteworthy, thecontent of miR-974 is decreased both in agnostic locusmight belong to the class of quantitative trait loci (QTL) .Taken together, our data indicate that the agnostic LIMK1 gene is a good candidate for linkingthe neuronal activity and genetic apparatus . Additionally, quite recent andunexpected findings reveal a new targetof intellectual disabilities: learning acquisition and memory erasure (forgetting) are governed by different signal cascades,correspondently cAMP-dependent and actin remodeling cascadesmall GTPase Rac1 \u2013 LIMK1 (the key enzyme of actinremodeling LIM-kinase 1) and its phosphorylation substrate\u0441ofilin. The absence of Rac1-dependent forgetting causesthe autistic spectrum disorders. Expression changes (activeor non-active state) of LIMK1 and cofilin lead to differentneurological disorders. Therefore, in the tradition of Russiangenetic school , the agnostic genemight be a functional link between genetic and cytogeneticprocesses within the nervous system and serve as a model forelucidating both the maternal and paternal modes of transgenerationalinheritance.One of the requirements of predictive and personalizedmedicine is consideration of POEs for prognosis of clinicalphenotype of many multifactorial neuropsychiatric disorders.These different and individual manifestations of cognitiveabilities and motor functions in patients with the same disease,i. e. behavioral plasticity, results from genome plasticity provokedby 3D chromatin architecture of the nerve cells nuclei.The evolutionary gene conservation approves the usage ofsimple low cost, fast and efficient models as Drosophila toprobe the causes, consequences and mechanisms of pathologyleading to human disease . The DrosophilaThe authors declare no conflict of interest.Belyaeva E.S., Zhimulev I.F., Volkova E.I., Alekseyenko A.A., MoshkinY.M., Koryakov D.E. Su(UR)ES: a gene suppressing DNAunderreplication in intercalary and pericentric heterochromatin ofDrosophila melanogaster polytene chromosomes. Proc. Natl. Acad.Sci. USA. 1998;95(13):7532-7537. DOI 10.1073/pnas.95.13.7532.Belyakin S.N., Christophides G.K., Alekseyenko A.A., KriventsevaE.V., Belyaeva E.S., Nanayev R.A., Makunin I.V., Kafatos F.C.,Zhimulev I.F. Genomic analysis of Drosophila chromosome underreplicationreveals a link between replication control and transcriptionalterritories. Proc. Natl. Acad. Sci. USA. 2005;102(23):8269-8274. DOI 10.1073/pnas.0502702102.Bourassa M.W., Ratan R.R. The interplay between microRNAs andhistone deacetylases in neurological diseases. Neurochem. Int. 2014;77:33-39. DOI 10.1016/j.neuint.2014.03.012.Busto G.U., Guven-Ozkan T., Fulga T.A., Van Vactor D., Davis R.L.microRNAs that promote or inhibit memory formation in Drosophilamelanogaster. Genetics. 2015;200(2):569-580. DOI 10.1534/genetics.114.169623.Collette J.C., Chen X.N., Mills D.L., Galaburda A.M., Reiss A.L.,Bellugi U., Korenberg J.R. William\u2019s syndrome: gene expression isrelated to parental origin and regional coordinate control. J. Hum.Genet. 2009;54(4):193-198. DOI 10.1038/jhg.2009.5.Davis R.L., Zhong Y. The biology of forgetting \u2013 a perspective. Neuron.2017;95(3):490-503. DOI 10.1016/j.neuron.2017.05.039.Dong X., Chen J., Li T., Zhang X., Zhang M., SongW., Zhao H., Lai J.Parent-of-origin-dependent nucleosome organization correlates withgenomic imprinting in maize. Genome Res. 2018;28(7):1020-1028.DOI 10.1101/gr.230201.117.Eagen K.P., Hartl T.A., Kornberg R.D. Stable chromosome condensationrevealed by chromosome conformation capture. Cell. 2015;163(4):934-946.Guven-Ozkan T., Busto G.U., Schutte S.S., Cervantes-Sandoval I.,O\u2019Dowd D.K., Davis R.L. MiR-980 is a memory suppressor microRNAthat regulates the autism-susceptibility gene A2bp1. CellRep. 2016;14(7):1698-1709. DOI 10.1016/j.celrep.2016.01.040.Iourov I.Y., Vorsanova S.G., YurovY.B. Molecular cytogenetics and cytogenomicsof brain diseases. Curr. Genomics. 2008;9(7):452-465.DOI 10.2174/138920208786241216.Iourov I.Y., Vorsanova S.G., Yurov Y.B. Pathway-based classificationof genetic diseases. Mol. Cytogenet. 2019;12:4. DOI 10.1186/s13039-019-0418-4.Ito S., Magalska A., Alcaraz-Iborra M., Lopez-Atalaya J.P., Rovira V.,Contreras-Moreira B., Lipinski M., Olivares R., Martinez-HernandezJ., Ruszczycki B., Lujan R., Geijo-Barrientos E., WilczynskiG.M., Barco A. Loss of neuronal 3D chromatin organizationcauses transcriptional and behavioural deficits related to serotonergicdysfunction. Nat. Commun. 2014;5:4450. DOI 10.1038/ncomms5450.Jagannathan M., Warsinger-Pepe N., Watase G.J., Yamashita Y.M.Comparative analysis of satellite DNA in the Drosophila gaster species complex. G3 (Bethesda). 2017;7(2):693-704. DOI10.1534/g3.116.035352Kaiser-Rogers K., Rao K. Structural chromosome rearrangements. In:Gersen S.L., Keagle M.B. (Eds.). The Principles of Clinical Cytogenetics.Humana Press, Totowa, NJ., 2005;165-206. DOI 10.1385/1-59259-833-1:165.Kaminskaya A.N., Nikitina E.A., Medvedeva A.V., Gerasimenko M.S.,Chernikova D.A., Savvateeva-Popova E.V. The influence of thelimk1 gene polymorphism on learning acquisition and memory formation,pCREB distribution and aggregate formation in neuromuscularjunctions in Drosophila melanogaster. Russ. J. Genet. 2015;51(6):582-590. DOI 10.1134/S1022795415060071.Kamyshev N.G., Iliadi K.G., Bragina J.V. Drosophila conditionedcourtship: two ways of testing memory. Learn. Mem. 1999;6:1-20.DOI 10.1101/lm.6.1.1.Kim S., Yu N.K., Shim K.W., Kim J.I., Kim H., Han D.H., Choi J.E.,Lee S.W., Choi D.I., Kim M.W., Lee D.S., Lee K., Galjart N.,Lee Y.S., Lee J.H., Kaang B.K. Remote memory and cortical synapticplasticity require neuronal CCCTC-binding factor (CTCF).J. Neurosci. 2018;38(22):5042-5052. DOI 10.1523/JNEUROSCI.2738-17.2018.Klages-Mundt N.L., Kumar A., Zhang Y., Kapoor P., Shen X. The natureof actin-family proteins in chromatin-modifying complexes.Front. Genet. 2018;9:398. DOI 10.3389/fgene.2018.00398.Kolesnikova T.D. Banding pattern of polytene chromosomes as a representationof universal principles of chromatin organization intotopological domains. Biochemistry. (Mosc). 2018;83(4):338-349.Kozomara A., Birgaoanu M., Griffiths-Jones S. miRBase: from microRNAsequences to function. Nucleic Acids Res. 2019;47(D1):D155-D162. DOI 10.1093/nar/gky1141.Li K.L., Zhang L., Yang X.M., Fang Q., Yin X.F., Wei H.M., Zhou T.,Li Y.B., Chen X.L., Tang F., Li Y.H., Chang J.F., Li W., Sun F.Histone acetyltransferase CBP-related H3K23 acetylation contributesto courtship learning in Drosophila. BMC Dev. Biol. 2018;18(1):20. DOI 10.1186/s12861-018-0179-z.Liehr T. From human cytogenetics to human chromosomics. Int. J. Mol.Sci. 2019;20(4):826. DOI 10.3390/ijms20040826.Liu L., Li Q.Z., Jin W., Lv H., Lin H. Revealing gene function andtranscription relationship by reconstructing gene-level chromatininteraction. Comput. Struct. Biotechnol. J. 2019;17:195-205. DOI10.1016/j.csbj.2019.01.011.Lobashev M.E., Ponomarenko B.B., Polyanskaya G.G., Tsapygina R.I.The role of nervous system in the regulation of genetic and cytogeneticprocesses. Zh. Evol. Biokhim. Phiziol. 1973;9:398-405. (inRussian)Medrano-Fern\u00e1ndez A., Barco A. Nuclear organization and 3D chromatinarchitecture in cognition and neuropsychiatric disorders. Mol.Brain. 2016;9(1):83. DOI 10.1186/s13041-016-0263-x.Medvedeva A., Zhuravlev A., Savvateeva-Popova E. LIMK1, the keyenzyme of actin remodeling bridges spatial organization of nucleusand neural transmission: from heterochromatin via non-coding RNAsto complex behavior. In: Cytoskeleton: Cell Movement, Cytokinesisand Organelles Organization. Nova Science Publishers, Inc., 2010;1:37-67.Menon D.U., Coarfa C., Xiao W., Gunaratne P.H., Meller V.H. siRNAsfrom an X-linked satellite repeat promote X-chromosome recognitionin Drosophila melanogaster. Proc. Natl. Acad. Sci. USA. 2014;111(46):16460-16465. DOI 10.1073/pnas.1410534111.Mohammed J., Bortolamiol-Becet D., Flynt A.S., Gronau I., Siepel A.,Lai E.C. Adaptive evolution of testis-specific, recently evolved,clustered miRNAs in Drosophila. RNA. 2014;20(8):1195-1209. DOI10.1261/rna.044644.114.Nikitina E.A., Kaminskaya A.N., Molotkov D.A., Popov A.V., Savvateeva-Popova E.V. Effect of heat shock on courtship behavior, soundproduction, and learning in comparison with the brain content ofLIMK1 in Drosophila melanogaster males with altered structure ofthe LIMK1 gene. J. Evol. Biochem. Physiol. 2014a;50(2):154-166.DOI 10.1134/S0022093014020082.agnostic locus: involvement in the formation of cognitivedefects in Williams Syndrome. Acta Naturae. 2014b;6(2):53-61.Nikitina E., Medvedeva A., Zakharov G., Savvateeva-Popova E. TheDrosophila Nikitina E., Medvedeva A., Zakharov G., Savvateeva-Popova E. Williamssyndrome as a model for elucidation of the pathway genes \u2013the brain \u2013 cognitive functions: genetics and epigenetics. Acta Naturae.2014c;6(1):9-22.Nikitina E.A., Medvedeva A.V., Dolgaya Yu.F., Korochkin L.I., PavlovaG.V., Savvateeva-Popova E.V. Involvement of GDNF andLIMK1 and heat shock proteins in Drosophila learning and memoryformation. J. Evol. Biochem. Physiol. 2012;48:529-539. DOI10.1134/S0022093012050076.Peffer S., Cope K., Morano K. Unraveling protein misfolding diseasesusing model systems. Future Sci. OA. 2015;1(2). DOI 10.4155/fso.15.41.P\u00e9rez Jurado L.A., Peoples R., Kaplan P., Hamel B.C., Francke U. Moleculardefinition of the chromosome 7 deletion in Williams syndromeand parent-of-origin effects on growth. Am. J. Hum. Genet.1996;59(4):781-792.Qin H., Niu T., Zhao J. Identifying multi-omics causers and causal pathwaysfor complex traits. Front. Genet. 2019;10:110. DOI 10.3389/fgene.2019.00110. PMID: 30847004. PMCID: PMC6393387.Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparinggenomic features. Bioinformatics. 2010;26(6):841-842. DOI10.1093/bioinformatics/btq033.Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductorpackage for differential expression analysis of digital gene expressiondata. Bioinformatics. 2010;26(1):139-140. DOI 10.1093/bioinformatics/btp616.Savvateeva-Popova E.V., Zhuravlev A.V., Br\u00e1zda V., ZakharovG.A., Kaminskaya A.N., Medvedeva A.V., Nikitina E.A., TokmatchevaE.V., Dolgaya J.F., Kulikova D.A., Zatsepina O.G., FunikovS.Y., Ryazansky S.S., Evgen\u2019ev M.B. Drosophila model forthe analysis of genesis of LIM-kinase 1-dependent Williams\u2013BeurenSyndrome cognitive phenotypes: INDELs, transposable elements ofthe Tc1/mariner superfamily and microRNAs. Front. Genet. 2017;8:123. DOI 10.3389/fgene.2017.00123.Schier A.F. The maternal-zygotic transition: death and birth of RNAs.Science. 2007;316(5823):406-407. DOI 10.1126/science.1140693.PMID: 17446392.Sempere L.F., Sokol N.S., Dubrovsky E.B., Berger E.M., Ambros V.Temporal regulation of microRNA expression in Drosophila melanogastermediated by hormonal signals and Broad-Complex geneactivity. Dev. Biol. 2003;259(1):9-18. DOI 10.1016/s0012-1606(03)00208-2. PMID: 12812784.Smrt R.D., Zhao X. Epigenetic regulation of neuronal dendrite and dendriticspine development. Front. Biol. (Beijing). 2010;5(4):304-323.DOI 10.1007/s11515-010-0650-0.Soni K., Choudhary A., Patowary A., Singh A.R., Bhatia S., SivasubbuS., Chandrasekaran S., Pillai B. miR-34 is maternally inheritedin Drosophila melanogaster and Danio rerio. Nucleic AcidsRes. 2013;41(8):4470-4480. DOI 10.1093/nar/gkt139.Tokmacheva E.V. The mitotic activity of the cells in the head neuralganglion in larvae of the Drosophila ts mutant with an altered capacityfor learning and augmented calmodulin activation properties.Zh. Vyssh. Nerv. Deiat. Im. I.P. Pavlova. 1995;45(3):565-571. (inRussian)Vasiljeva S., Tokmacheva E., Medvedeva A., Ermilova A., Nikitina E.,Shchegolev B., Surma S.V., Savvateeva-Popova E.V. Parent-of-origineffect in genetic instability of somatic brain\u2019s cells of Drosophilaand memory formation under normal and stress conditions. Tsitologiia.2019;61(12):951-963. DOI 10.1134/S0041377119120071.(in Russian)Waring G.L., Pollack J.C. Cloning and characterization of a dispersed,multicopy, X chromosome sequence in Drosophila melanogaster.Proc. Natl. Acad. Sci. USA. 1987;84(9):2843-2847. DOI 10.1073/pnas.84.9.2843.Wittkopp P.J., Haerum B.K., Clark A.G. Parent-of-origin effects onmRNA expression in Drosophila melanogaster not caused by genomicimprinting. Genetics. 2006;173(3):1817-1821. DOI 10.1534/genetics.105.054684.Zakharov G. Locotrack. https://github.com/GennadiyZakharov/locotrack. 2017. .Zakharov G.A., Zhuravlev A.V., Payalina T.L., Kamyshov N.G., Savvateeva-Popova E.V. The effect of mutations of the kynureninepathway of tryptophan metabolism on locomotor behavior and geneexpression in glutamatergic and cholinergic systems of D. melanogaster.Russ. J. Genet. Appl. Res. 2012;2:197-204. DOI 10.1134/S2079059712020141.Zayats T., Johansson S., Haavik J. Expanding the toolbox of ADHDgenetics. How can we make sense of parent of origin effects inADHD and related behavioral phenotypes? Behav. Brain Funct.2015;11(1):33. DOI 10.1186/s12993-015-0078-4.Zerbino D.R., Achuthan P., Akanni W., Amode M.R., Barrell D.,Bhai J., Flicek P. Ensembl 2018. Nucleic Acids Res. 2018;46:D754-D761. DOI 10.1093/nar/gkx1098.Zhuravlev A. Homology Segment Analysis. Available at: https://bitbucket.org/beneor/homology-segment-analysis/src/master/ 2019a..Zhuravlev A. Homology Segment Analysis protocol. protocols.io.2019b. DOI 10.17504/protocols.io.bakyicxw.Zink F., Magnusdottir D.N., Magnusson O.T., Walker N.J., Morris T.J.,Sigurdsson A., Halldorsson G.H., Gudjonsson S.A., Melsted P., IngimundardottirH., Kristmundsdottir S., Alexandersson K.F., HelgadottirA., Gudmundsson J., Rafnar T., Jonsdottir I., Holm H.,Eyjolfsson G.I., Sigurdardottir O., Olafsson I., Masson G., GudbjartssonD.F., Thorsteinsdottir U., Halldorsson B.V., Stacey S.N., StefanssonK. Insights into imprinting from parent-of-origin phasedmethylomes and transcriptomes. Nat. Genet. 2018;50(11):1542-1552. DOI 10.1038/s41588-018-0232-7.Zykova T.Y., Levitsky V.G., Belyaeva E.S., Zhimulev I.F. Polytenechromosomes \u2013 a portrait of functional organization of the Drosophilagenome. Curr. Genomics. 2018;9(3):179-191. DOI 10.2174/1389202918666171016123830."} +{"text": "Antenatal care is a unique opportunity to assess SARS-CoV-2 seroprevalence and antibody response in pregnant people, including those with previously unknown infection. Pregnant people were screened for SARS-CoV-2 IgG during antenatal care or delivery in Seattle, Washington with Abbott Architect chemiluminescent immunoassay which provides quantitative index (positive \u22651.4). Participants with IgG+ results or identified with RT-PCR+ results via medical records were invited to enroll in a longitudinal evaluation of antibody responses. We report preliminary results of an ongoing seroprevalence and longitudinal study with planned 18-month follow-up.\u2264280 days after first RT-PCR+ result for those with and \u2265104 days after first IgG detection for those without prior RT-PCR+ results), while 5/14 (26%) had a negative Abbott IgG test at a median of 81 days (IQR 75\u2013112) since initial testing.Between September 9, 2020\u2013May 7, 2021, we screened 1304 pregnant people; 62 (4.8%) tested SARS-CoV-2 IgG+, including 28 (45%) with known prior SARS-CoV-2 infection. Among participants testing IgG+, median age was 32 years (interquartile range [IQR] 26\u201335) and median gestational age was 21 weeks (IQR 12\u201338) at screening; median IgG index was 3.2 , including 3.9 (IQR 2.3\u20135.8) among those with vs. 2.7 (IQR 1.9\u20134.2) among those without prior RT-PCR+ results (p=0.05 by Wilcoxon rank-sum). Of 30 longitudinal study participants enrolled, 24 tested IgG+ at baseline (75% with prior RT-PCR+ result) and 6 tested IgG- on enrollment but were identified as previously RT-PCR+ via medical records; 24/30 (80%) reported previous symptoms. Of 24 participants testing IgG+ at baseline, 14 (58%) had first follow-up IgG results at median of 66 days (IQR 42\u2013104) since initial testing, with median IgG index of 2.0 (IQR 1.0\u20133.8). 9/14 (64%) participants with repeat IgG testing remained IgG+ at first follow-up Alisa Kachikis, MD, MS, GlaxoSmithKline (Consultant)Pfizer (Consultant) Alexander L. Greninger, MD, PhD, Abbott (Grant/Research Support)Gilead (Grant/Research Support)Merck (Grant/Research Support) Janet A. Englund, MD, AstraZeneca GlaxoSmithKline (Research Grant or Support)Meissa Vaccines (Consultant)Pfizer (Research Grant or Support)Sanofi Pasteur (Consultant)Teva Pharmaceuticals (Consultant) Alison Drake, PhD, MPH, Merck (Grant/Research Support)"} +{"text": "The cirrhosis-associated abnormalities of ACE, IL-6, VWF antigen, and antiplasmin parallel those observed in severe COVID-19.(1) Background: Cirrhotic patients have an increased risk for severe COVID-19. We investigated the renin-angiotensin-aldosterone system (RAS), parameters of endothelial dysfunction, inflammation, and coagulation/fibrinolysis in cirrhotic patients and in COVID-19 patients. (2) Methods: 127 prospectively characterized cirrhotic patients (CIRR), along with nine patients with mild COVID-19 (mild-COVID), 11 patients with COVID-19 acute respiratory distress syndrome , and 10 healthy subjects (HS) were included in the study. Portal hypertension (PH) in cirrhotic patients was characterized by hepatic venous pressure gradient (HVPG). (3) Results: With increased liver disease severity (Child\u2212Pugh stage A vs. B vs. C) and compared to HS, CIRR patients exhibited higher RAS activity (angiotensin-converting enzyme (ACE), renin, aldosterone), endothelial dysfunction (von Willebrand-factor (VWF) antigen), inflammation (C-reactive protein (CRP), interleukin-6 (IL-6)), and a disturbed coagulation/fibrinolysis profile . Increased RAS activity (renin), endothelial dysfunction (vWF), coagulation parameters and inflammation were significantly altered in COVID patients and followed similar trends from mild-COVID to ARDS-COVID. In CIRR patients, ACE activity was linked to IL-6 (\u03c1 = 0.26; Severe acute respiratory distress syndrome-coronavirus-2 (SARS-CoV-2) causes substantial morbidity and mortality worldwide . CoronavPatients with ARDS due to COVID-19 exhibit severe endothelial damage, pulmonary microangiopathy, and thrombosis ,5, indicSimilarly, coagulation imbalance, inflammation, and RAS activation also represent well-known hallmarks of advanced chronic liver disease (ACLD) ,12,13. CPatients with ACLD are at particularly high risk for severe courses of COVID-19 ,17; howeACLD patients undergoing hepatic venous pressure gradient (HVPG) measurement at the Vienna General Hospital between February 2019 and December 2020 with portal hypertension (CIRR) were included in this study. Hemodynamic parameters including mean arterial pressure (MAP) were assessed at the time of HVPG measurement. Blood samples were withdrawn after the patients had rested for at least 30 min in supine position.Patients with intake of non-selective beta-blockers, antithrombotic or antiplatelet therapy, with active malignancy, portal vein thrombosis, porto-sinusoidal vascular disease or cardiac cirrhosis, as well as patients after liver transplantation were excluded from the study. If multiple HVPG measurements were performed in the same patient, only the baseline measurement was used for this study. The ACLD patients were stratified by Child\u2212Turcotte\u2212Pugh (CTP) stage A, B, and C and by HVPG . Etiology of ACLD, comorbidities , age, and intake of concomitant medication were recorded.Moreover, inpatients at the General Hospital of Vienna with COVID-19 (mild-COVID), inpatients with ARDS due to COVID-19 (ARDS-COVID), as well as outpatients without ACLD or COVID-19 willing to participate in the study were included.For HVPG measurement, the right jugular vein was accessed via Seldinger technique using a catheter introducer set . A balloon catheter was subsequently used for liver vein cannulation . HVPG waA colorimetric assay was used to determine ACE activity. Plasma concentrations of renin and aldosterone were measured by chemiluminescence-immunoassay. VWF antigen was measured by latex agglutination assay . Prothrombin fragment F1,2 and plasminogen activator inhibitor (PAI) were assessed by ELISA , plasminogen activity, and \u03b1-2 antiplasmin (antiplasmin) activity by chromogenic assay . Routine laboratory parameters including D-dimer, C-reactive protein (CRP), and interleukin-6 (IL-6) were assessed by standard laboratory methods.Categorical variables were presented as number (n) of patients and % of these patients with the characteristic of interest, while continuous data was reported as median and interquartile range (IQR). D\u2019Agostino and Pearson and Shapiro\u2013Wilk normality tests were used to test for normal distribution. Mann-Whitney U test was implemented for comparing non-normally distributed continuous variables between two groups, and Kruskal-Wallis test for comparison of non-normally distributed continuous variables in three or more groups. Dunn\u2019s multiple comparisons test was used as post-hoc test. Group comparisons of categorical variables were computed using Pearson\u2019s Chi-squared or Fisher\u2019s exact test.p < 0.100) were included in the multivariate model. Multicollinearity was investigated via variance inflation factor (VIF). GraphPad Prism 8 and IBM SPSS 22.0 statistic software were used for statistical analysis. A two-sided p-value of <0.05 was considered as being statistically significant.Factors associated with ACE plasma levels were assessed using linear regression models including either VWF antigen, prothrombin fragment F1,2, or antiplasmin activity. Parameters that showed a trend (NCT03267615).The study was approved by the ethics committee (EC) of the Medical University of Vienna (study number: 1461/2020 and 1262/2017). It was performed according to the current version of the Helsinki Declaration. All patients were prospectively included in the study and gave their informed consent before the blood withdrawal. The cirrhotic cohort of this study is part of the Vienna Cirrhosis Study registry, registered under p < 0.001).In total, 127 CIRR patients with male predomination were included in the study. Median age was 56.6 (IQR 15.5) years. Alcoholic (49.6%), viral (15.0%), and cholestatic liver disease (8.7%) were the main etiologies . There wThe mild-COVID cohort consisted of nine patients with COVID-19, who were admitted to the Vienna General Hospital due to the viral infection , while the ARDS-COVID cohort included 11 patients and the HS cohort included 10 subjects .p < 0.001) and VWF antigen (A: 223.4 (IQR 114.0)% vs. B: 307.0 (IQR 133.0)% vs. C: 396.0 (91.0)%; p < 0.001) significantly increased with decreasing liver function, while there was a trend for PAI levels (A: 0.89 (1.60) IU/mL vs. B: 0.92 (2.06) IU/mL vs. C: 2.68 (1.73) IU/mL; p = 0.149) (p < 0.001), plasminogen activity (A: 75.0 (21.0)% vs. B: 59.0 (12.0)% vs. C: 42.0 (9.0)%; p < 0.001), and in tendency prothrombin fragment F1,2 (A: 287.0 (292.0) pmol/L vs. B: 292.5 (241.0) pmol/L vs. C: 176.0 (194.0) pmol/L; p = 0.079) decreased with increasing CTP stage (D-dimer (A: 0.48 (IQR 0.41) \u00b5g/mL vs. B: 1.40 (IQR 2.90) \u00b5g/mL vs. C: 3.19 (3.08) \u00b5g/mL; = 0.149) . AntiplaTP stage . SimilarTP stage .p < 0.001) (p < 0.001). Similarly, more pronounced RAS activation was observed in patients with more advanced hepatic dysfunction: ACE (A: 41.3 (35.9) U/L vs. B: 54.4 (45.6) U/L vs. C: 71.3 (66.9) U/L; p = 0.006), as well as plasma renin (A: 12.4 (26.7) \u00b5IU/mL vs. B: 55.1 (115.9) \u00b5IU/mL vs. C: 594.1 (949.8) \u00b5IU/mL; p < 0.001) and aldosterone concentrations (A: 84.5 (442.0) pg/mL vs. B: 240.0 (442.0) vs. C: 397.0 (238.0) pg/mL; p < 0.001).With increasing CTP stage, there was increased inflammation, as indicated by rising CRP (A: 0.18 (0.29) mg/dL vs. B: 0.47 (0.67) mg/dL vs. C: 0.47 (1.23) mg/dL; < 0.001) and IL-6p = 0.009), vWF antigen (mild-COVID: 247.5 (73.0) vs. ARDS-COVID: 420.0 (99.0)%; p = 0.007), D-dimer (mild-COVID: 0.54 (0.58) \u00b5g/mL vs. ARDS-COVID: 2.94 (4.75) \u00b5g/mL; p < 0.001), prothrombin fragment F1,2 (mild-COVID: 151.5 (252.0) pmol/L vs. ARDS-COVID: 429.0 (2687.0) pmol/L; p = 0.006), CRP (mild-COVID: 0.50 (1.42) mg/dL vs. ARDS-COVID: 15.10 (14.69) mg/dL; p < 0.001), and IL-6 (mild-COVID: 7.66 (14.74) pg/mL vs. ARDS-COVID: 65.70 (357.90) pg/mL; p < 0.001), indicating an increased RAS activation, endothelial dysfunction, coagulation/fibrinolysis activation, and inflammation \u00b5IU/mL vs. ARDS-COVID: 62.7 (107.1) \u00b5IU/mL; ammation .Compared to healthy control subjects, cirrhotic patients and COVID-19 patients exhibited markedly increased VWF antigen, while the highest median VWF antigen level occurred in ARDS-COVID patients . Both ciMoreover, compared to healthy subjects, cirrhotic and COVID-19 patients had higher levels of CRP and IL-6.On the other hand, cirrhotic patients exhibited significantly lower antiplasmin activity and plasminogen activity than COVID-19 patients, while ACE activity and plasma aldosterone concentration were higher.p < 0.001), D-dimer , prothrombin fragment F1,2 , antiplasmin activity , IL-6 , and HVPG .p = 0.001), coagulation , and of fibrinolysis , but not with parameters of inflammation .In this study, we thoroughly characterized the state of components of the RAS, coagulation, and inflammation in cirrhotic patients of different disease severity and compared the findings to patients with mild COVID-19 and with COVID-ARDS. Importantly, we identified profound abnormalities of the coagulation system and upregulated systemic inflammation linked to cirrhosis-associated RAS activation that followed similar trends in COVID-19.By stratifying our ACLD cohort by hepatic dysfunction , as well as for portal pressure (by the diagnostic gold-standard HVPG), we observed marked endothelial dysfunction and dysbalanced coagulation state with increasing ACLD severity. At the same time, inflammatory markers , along with RAS components, were elevated with more severe ACLD, indicating a state of coagulation/fibrinolysis activation linked to RAS activity\u2014that reportedly is upregulated in cirrhosis ,22.COVID-19 patients exhibited very similar levels of endothelial dysfunction, coagulation/fibrinolysis, and inflammation parameters, compared to cirrhotic patients, as well as RAS activation, indicated by increased plasma renin concentration. Interestingly, these parameters were also the most important factors differing between mild-COVID and ARDS-COVID. This suggests that cirrhotic patients are in a disadvantageous position when contracting SARS-CoV-2 infection. Importantly, the pronounced RAS activation causing associated coagulation imbalance and a proinflammatory state in Child\u2212Pugh B/C patients may explain why cirrhotic patients have been reported to be particularly susceptible to severe courses of COVID-19 ,17.The RAS is intricately involved in cirrhosis development and progression . ImportaIn COVID-19, especially the non-classical RAS is subject of scientific interest, as SARS-CoV-2 uses the ACE2 receptor for cell entry and it hCOVID-19 is strongly linked to thromboembolic complications, including microvascular thrombosis, but also macrovascular events such as stroke or pulmonary embolism ,30. EndoSimilarly, D-dimer and prothrombin fragment F1,2 were also increased both in cirrhosis and COVID-19, signifying an activation of coagulation and fibrinolysis, with the highest values in ARDS-COVID patients. Interestingly, prothrombin fragment F1,2 levels were highest in Child-A patients, indicating coagulation dysregulation already in an early stage of cirrhosis. Elevated D-dimer was identified as a marker of poor prognosis in patients with COVID-19 . The higFurthermore, high plasmin levels are observed in liver cirrhosis, likely due to decreased antiplasmin and elevated tissue-type plasminogen activator activity . ImportaFinally, both liver cirrhosis and COVID-19 were associated with increased systemic inflammation. As an infectious disease, COVID-19 triggers a complex immune response, leading to a pronounced (and sometimes excessive) inflammatory reaction . Again, Elevation of inflammatory parameters in cirrhosis may be due to gut-derived bacterial translocation ; howeverOur study has limitations: The cohorts were not age- and sex-matched. While cirrhotic patients were mainly male, the COVID-19 cohort was mainly female. Moreover, the healthy control group was significantly younger than the other groups, which may have impacted laboratory tests such as VWF, which increases with age . HoweverIn conclusion, we comprehensively investigated the role of the RAS, endothelial dysfunction, coagulation, and inflammation both in patients with cirrhosis and with COVID-19. Importantly, we found striking similarities between cirrhotic patients and COVID-19 patients, as both groups suffer from endothelial dysfunction, coagulation/fibrinolysis activation, and a systemic pro-inflammatory state. The \u201cbaseline-upregulation\u201d of the RAS in the setting of advanced cirrhosis may facilitate SARS-CoV-2 cell entry due to decreased antiplasmin activity and consecutively elevated plasmin levels. The molecular mechanisms driven by cirrhosis-associated RAS activation\u2014including the induction of an imbalanced coagulation profile, endothelial dysfunction, and systemic inflammation\u2014may mechanistically explain a susceptibility to severe COVID-19 in cirrhotic patients."} +{"text": "Correction to: BMC Health Serv Res 21, 733 (2021)https://doi.org/10.1186/s12913-021-06757-x7,8 to D. Laplanche7.Following publication of the original article , the affThe author affiliation list has been updated above and the original article has been"} +{"text": "Cohort studies suggest higher rates of discontinuations (DCs) and adverse events (AEs) with integrase inhibitors (INSTIs) than is reported in clinical trials. Here, we assess DC of different INSTIs in combination with one of two tenofovir prodrugs in the first year following initiation defined as \u201cearly DC\u201d in a real-world cohort of treatment-na\u00efve patients.This analysis evaluated treatment-na\u00efve patients at a single center initiating raltegravir (RAL), elvitegravir/cobicistat (EVG/c), dolutegravir (DTG) or bictegravir (BIC) in combination with emtricitabine/tenofovir alafenamide (F/TAF) or emtricitabine/tenofovir disoproxil fumarate (F/TDF) between 10/2007-1/2020. Eligible patients had a minimum follow-up of 1 year. The primary endpoint was incidence of early INSTI DC. Secondary endpoints included AEs and risk factors for early INSTI DC and treatment-related AEs.331 patients were included. Median age was 32 years, 89% were male, 43% were non-White, 8% started RAL-based therapy, 46% started EVG/c-based therapy, 22% started DTG-based therapy and 24% started BIC/F/TAF. 36 discontinued INSTI-based therapy early yielding an incidence rate of 0.17 DCs per person-years (PPY) among RAL patients, 0.14 DCs PPY among EVG/c patients, 0.22 DCs PPY among DTG patients, and 0 DCs PPY among BIC patients, p=0.006. Treatment-related AEs occurred in 27% of RAL patients, 42% of EVG/c patients, 50% of DTG patients, and 43% of BIC patients p=0.607; and were responsible for early DC rates of 0.022 in 3 EVG/c patients and 0.075 in 5 DTG patients. No treatment-related early DCs occurred among RAL or BIC patients. No evaluated factor was significantly associated with early INSTI DC, however DTG use was significantly associated with treatment-related AEs .Table 1. Risk factors for early integrase inhibitor discontinuation and treatment-related adverse eventsIn this cohort, early DCs occurred in 11% initiating INSTI-based therapy, however of these only 2% were treatment-related. These data support use of INSTI-based regimens as preferred options for treatment-na\u00efve patients living with HIV due to their favorable safety and tolerability profiles.Charlotte-Paige M. Rolle, MD MPH, Gilead Sciences Janssen Infectious Disease ViiV Healthcare Kiran Patel, PharmD, Gilead Sciences (Employee) Federico Hinestrosa, MD, AbbVie (Speaker\u2019s Bureau)Gilead Sciences Theratechonologies (Advisor or Review Panel member)ViiV Healthcare Edwin DeJesus, MD, Gilead Sciences"} +{"text": "Klebsiella pneumoniae is an increasingly important hospital pathogen. Classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp) are two distinct evolutionary genetic lines. The recently ongoing evolution of K. pneumoniae resulted in the generation of hybrid hvKP-MDR strains. K. pneumoniae distinct isolates (n = 70) belonged to 20 sequence types with the prevalence of ST395 (27.1%), ST23 (18.6%), ST147 (15.7%), and ST86 (7.1%), and 17 capsular types with the predominance of K2 (31.4%), K57 (18.6%), K64 (10.0%), K1 (5.7%) were isolated from patients of the Moscow neurosurgery ICU in 2014\u20132019. The rate of multi-drug resistant (MDR) and carbapenem-resistant phenotypes were 84.3% and 45.7%, respectively. Whole-genome sequencing of five selected strains belonging to cKp (ST395K47 and ST147K64), hvKp (ST86K2), and hvKp-MDR (ST23K1 and ST23K57) revealed blaSHV, blaTEM, blaCTX, blaOXA-48, and blaNDM beta-lactamase genes; acr, oqx, kpn, kde, and kex efflux genes; and K. pneumoniae virulence genes. Selective pressure of 100 mg/L ampicillin or 10 mg/L ceftriaxone induced changes of expression levels for named genes in the strains belonging to cKp, hvKp, and hybrid hvKp-MDR. Obtained results seem to be important for epidemiologists and clinicians for enhancing knowledge about hospital pathogens. Klebsiella pneumoniae is an increasingly important hospital pathogen causing a wide range of infections including urinary tract infections, pneumonia, bacteremia, and liver abscesses. In severe clinical cases, it can also lead to multiple organ failure, or even death [K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp), were described and are both global pathogens [K. pneumoniae strains belong to particular clones producing beta-lactamases in combination with other functional classes of resistance determinants [K. pneumoniae were attributed to sequence types ST23, ST86, ST65, etc., and capsular types K1, K2, K57, K20, etc. [en death . Two difathogens . Most muK. pneumoniae resulting in the generation of hybrid hvKp-MDR strains. Mechanisms for the emergence of such strains can be a result of acquiring hypervirulent plasmids by cKp [Recent studies have shown the ongoing evolution of s by cKp , acquiris by cKp , and acqs by cKp . HoweverK. pneumoniae strains collected in Moscow neurosurgery ICU in 2014\u20132019, to identify resistance and virulence genes in their cells, and to estimate relative expression levels of such genes in selected strains belonging to epidemiology significant genetic lines cKp (ST395K47 and ST147K64), hvKp (ST86K2), and hybrid hvKp-MDR (ST23K1 and ST23K57).This study aimed to determine the genetic lines of K. pneumoniae caused about 28% among the agents of nosocomial infections in neurosurgery ICU during the period from January 2014 to May 2019. The incidence rates of K. pneumoniae infections were 8.0 per 100 patient infections of the central nervous system, 4.3/100 of bloodstream infections, 26.3/100 of respiratory infections, and 25.3/100 of urinary tract infections [K. pneumoniae clinical isolates were collected from 283 patients in this period, including those isolated from the respiratory system (n = 271), urine (n = 166), the nervous system (n = 41), blood (n = 36), surgical wounds (n = 27), and other (n = 4).n = 34), urine (n = 19), the nervous system (n = 8), blood (n = 6), and surgical wounds (n = 3). As a result, 20 sequence types were identified, the majority of them were ST395, ST23, ST147, and ST86, and a total of 17 capsular types were identified. Predominant K-types were K2, K57, K64, and K1 , ampicillin-sulbactam (90.0%), cefuroxime (86.8%), cefoxitin (68.8%), ceftriaxone (77.8%), ceftazidime (72.8%), cefoperazone-sulbactam (82.7%), cefepime (69.2%), ertapenem (48.1%), tetracycline (80.7%), ciprofloxacin (81.2%), chloramphenicol (77.0%), gentamicin (67.1%), tobramycin (83.0%), trimethoprim-sulfamethoxazole (69.2%), and nitrofurantoin (82.2%). Fewer resistant isolates were found for imipenem (33.8%), tigecycline (37.2%), and amikacin (31.8%) (It was shown that major (31.8%) .K. pneumoniae isolates carried beta-lactamase genes blaSHV (100.0%), blaCTX-M (74.2%), blaTEM (51.4%), blaOXA-48 (40.0%), blaNDM (11.4%), class 1 (37.6%) and 2 (2.1%) integrons, and porin protein gene ompK36 (91.5%). Both blaOXA-48 and blaNDM carbapenemase genes were detected in four (5.7%) isolates. Beta-lactamase genes blaKPC, blaVIM, and blaIMP were not detected (The frequency of the multi-drug resistant (MDR) phenotype was 84.3%, with the carbapenem-resistant phenotype consitituting 45.7%. detected .K. pneumoniae isolates: rmpA (34.2%), aer (21.4%), kfu (17.1%), uge (85.7%), wabG (100.0%), fimH (97.1%), allS (94.3%), and allR (5.7%). Twelve virulence gene combinations were identified. The most prevalent combination was uge+wabG+fimH+allS (51.4% isolates), followed by rmpA+aer+uge+wabG+fimH+allS (11.4%), uge+wabG+kfu+fimH+allS (7.1%), rmpA+wabG+fimH+allS (5.7%), and rmpA+aer+ +uge+wabG+kfu+fimH+allR (5.7%). The rarest combinations were wabG+fimH+allS (4.3%), rmpA+uge+wabG+fimH+allS (4.3%), uge+wabG+allS (2.8%), rmpA+aer+wabG+fimH+allS (2.8%), rmpA+wabG+kfu+fimH+allS (1.4%), rmpA+aer+uge+wabG+kfu+fimH+allS (1.4%), and rmpA+wabG+kfu+fimH+allS (1.4%) (Eight virulence genes were detected in 70 S (1.4%) .n = 9) and urine (n = 2), belonging to genetic lines ST23K1 (n = 4), ST86K2 (n = 3), ST23K57 (n = 2), ST65K2 (n = 1), and ST218K57 (n = 1). Isolates of ST23K1 carried rmpA+aer+uge+wabG+kfu+fimH+allR; isolates of ST86K2 and ST218K57 harbored rmpA+aer+uge+wabG+fimH+allS; isolates of ST23K57 carried two combinations, rmpA+uge+wabG+fimH+allS and rmpA+wabG+kfu+fimH+allS; and isolates of ST65K2 carried rmpA+aer+uge+wabG+kfu+fimH+allS virulence gene combinations. All 11 hypermucoviscous isolates carried rmpA, wabG, and fimH genes. Major isolates of hypermucoviscousity-positive isolates were MDR (n = 6), resistant to 3\u20137 antimicrobial functional groups . Among them, two isolates were CR. The remaining isolates were resistant to ampicillin only. As a result, there was no revealed correlation between the hypermucoviscousity phenotype and genetic line or the antimicrobial phenotype or virulence gene profiles (Phenotype of hypermucoviscousity was detected for 11 of 70 isolates (15.7%) collected from the respiratory system , hvKp (ST86K2), and hvKp-MDR (ST23K1 and ST23K57), were analyzed by whole-genome sequence and quantitative analyses of antimicrobial resistance and virulence gene expression. One of these strains (B2523/18) was resistant to AMP and carried only one beta-lactamase gene of the blaSHV type. In contrast, the other four strains that belonged to the MDR category were resistant to 10\u201318 antimicrobials. The latter strains carried beta-lactamase genes of blaSHV, blaTEM, blaCTX-M, blaOXA-48, and blaNDM types and the resistance determinants for other antimicrobial groups in the genomes: aminoglycosides, fosfomycin, streptogramins, phenicols, quinolones, sulfonamide, tetracyclines, sulfonamides, macrolides, and rifamycins, as well as genes coding 4\u20135 efflux pumps and 1\u20134 genes of heavy metal resistance. The following genetic determinants of K. pneumoniae virulence were identified in the genomes: peg-344 (n = 3), rmpA (n = 3), rmpA2 (n = 1), iroB (n = 2), iroN (n = 2), iroD (n = 2), uge (n = 5), wabG (n = 5), kfu (n =1 ), fimH (n = 5), allR (n = 1), irp (n = 4), iuc (n = 3), entB (n = 3), iut (n = 4), mrk (n = 5), ybt (n = 4), fyu (n =4 ), treC (n = 5), celB (n = 5), and ureA (n = 5) .K. pneumoniae strains during growth without selective pressure of antimicrobials were different: the chromosomal beta-lactamase genes blaSHV were transcribed significantly lower compared with those of the reference gene rpoD. In contrast, other beta-lactamase genes , as well as porin gene ompK36 were transcribed at higher levels compared with the reference gene, with the exception of blaTEM in the hvKp-MDR strain of ST23K1 which exhibited lower expression. The efflux pump genes and the virulence genes were expressed mostly at the same or lower levels compared with the rpoD gene, with the exception of two virulence genes: treC in the strains of ST395K47, ST147K64, ST23K1, and ST23K57; and celB in the strain of ST86K2 gene, and downregulation of the blaTEM (5.5-fold), acrA (2.4-fold), acrB (2.8-fold), oqxB (4.8-fold), kpnE (3.5-fold), kpnF (2.0-fold), and kdeA (3.0-fold) genes. Another MDR strain of ST147K64 was characterized by the upregulation of the blaTEM (2.2-fold), kpnE (3.2-fold), kdeA (2.7-fold), fimH (2.3-fold), and ureA (14.0-fold) genes, and downregulation of the blaOXA-48 (5.3-fold) gene. The hvKp strain of ST86K2 demonstrated upregulation of only one gene, iroN (4.1-fold), and downregulation of 13 genes: blaSHV (2.6-fold), acrA (9.0-fold), acrB (10.0-fold), oqxB (10.1-fold), kpnE (9.9-fold), kpnF (5.0-fold), kexD (4.9-fold), kdeA (4.8-fold), iroD (4.0-fold), uge (3.2-fold), wabG (6.2-fold), treC (4.8-fold), and ureA (5.3-fold). The hybrid hvKp-MDR strain of ST23K1 showed upregulation of the acrB (3.4-fold), oqxA (2.1-fold), oqxB (2.1-fold), wabG (6.2-fold), fimH (3.2-fold), celB (8.0-fold), and ureA (8.9-fold) genes. The second hvKp-MDR strain of ST23K57 expressed upregulation of the blaTEM (4.1-fold), blaCTX-M (5.3-fold), ompK36 (2.9-fold), acrB (2.3-fold), oqxA (2.9-fold), oqxB (4.6-fold), kpnE (2.3-fold), kpnF (2.0-fold), kexD (3.2-fold), kdeA (11.7-fold), uge (3.4-fold), wabG (14.5-fold), fimH (2.9-fold), celB (3.7-fold), and ureA (3.1-fold) genes genes .K47 demonstrated downregulation of the blaTEM (3.3-fold) and acrA (2.4-fold) genes. The MDR strain of ST147K64 was characterized by upregulation of the oqxB (2.7-fold), kpnE (7.0-fold), kpnF (4.4-fold), kdeA (2.3-fold) genes, and downregulation of the blaOXA-48 (2.1-fold) gene. The hybrid hvKp-MDR strain of ST23K1 showed upregulation of the fimH (2.1-fold) gene, and downregulation of the blaTEM (2.1-fold), kdeA (5.1-fold), and ureA (2.7-fold) genes. The second hybrid hvKp-MDR strain of ST23K57 expressed upregulation of the blaSHV (2.3-fold), blaTEM (2.4-fold), blaCTX-M (6.3-fold), acrB (3.0-fold), oqxB (3.8-fold), kpnE (2.1-fold), kdeA (8.6-fold), wabG (14.8-fold), and ureA (4.2-fold) genes, and no genes were downregulated [(16\u201320%) , and sig(16\u201320%) .K. pneumoniae isolates collected from 62 patients were attributed to specific genetic lines, virulence, and antimicrobial resistance genotypes. Single isolates were collected from 54 patients and two isolates from eight patients. Double isolates were studied from one patient in a case of their differences in ST , K-type (Patient 35), and antimicrobial resistance genes profiles (Patients 4 and 39) (K64 carried (blaTEM+blaSHV+blaCTX-M+blaOXA-48+blaNDM) and (blaSHV+blaOXA-48) beta-lactamase genes, respectively. Two isolates obtained from the trachea of Patient 39 belonged to ST23K57 (blaTEM+blaSHV+blaCTX-M) and (blaSHV+blaCTX-M+blaOXA-48) beta-lactamase genes, respectively. Different antimicrobial resistance gene profiles of K. pneumoniae named isolates possibly indicate the evolution events in the patient\u2019s body as described previously [Non-duplicate 70 and 39) . Two isoeviously .K. pneumoniae genetic lines common for classical K. pneumoniae (cKp) (ST395 and ST147) and hypervirulent K. pneumoniae (hvKp) (ST23 and ST86). ST395 was reported as prevalent for cKp-MDR strains in studies from Poland, France, Italy, and Russia [K. pneumoniae of ST23 and ST86 were described previously as hvKp causing bacteremia, sepsis, and liver abscess in India, France, Taiwan, and Russia [K. pneumoniae isolates of K64 commonly were recognized as cKp, but recently some isolates of K64 were described as hybrid hvKp-MDR due to acquiring the hvKp virulence plasmids [K20/K64, ST395K2, as well as hvKp ST23K1 and ST86K2 [K. pneumoniae isolates in our study were MDR with resistance to carbapenems for 45.7% isolates. Such high MDR rates were reported from China and Iran [blaCTX-M in our study was 74.2%, carbapenemase genes blaOXA-48 and blaNDM at 40.0% and 11.4%, respectively, similar to the prevalence of these genes published previously [n = 11) were attributed to ST23K1, ST86K2, ST23K57, ST65K2, and ST218K57 genetic lines. All of them carried the rmpA gene coding the major virulence-associated factor in hvKP isolates [rmpA-positive isolates in this study were hypermucoviscousity-positive, which is in agreement with a previously published report [K. pneumoniae among hypermucoviscousity-positive isolates in this study was 6/11, which is consistent with the modern trend for the appearance of hybrid hvKp-MDR genetic lines [Twenty STs and 17 K-types were identified. The most prevalent sequence types were ST395 27.1%), ST23 18.6%), ST147 15.7%), and ST86 (7.1%). The remaining 16 STs were each represented at \u2264 4.3%. The dominant STs were described previously as .7%, and .6%, ST14d Russia ,20,21,22plasmids . Moreoved ST86K2 ,27,28,29.1%, ST23and Iran ,31. The isolates , althougic lines ,34.K. pneumoniae strains belonging to prevalent STs and K-types were selected for further comparative study of whole-genome sequences, antimicrobial resistance phenotypes, hypermucoviscosity, and altered expression levels of virulence and resistance genes in response to beta-lactams effect (AMP and CRO). It was shown that K. pneumoniae isolates belonging to ST86K2, ST23K1, and ST23K57 demonstrated hypermucoviscosity phenotype in contrast with isolates of ST395K47 and ST147K64, which confirmed the virulent phenotype of three isolates. All K. pneumoniae isolates carried blaSHV genes, including extended-spectrum beta-lactamase (ESBL) variant blaSHV-12, broad-spectrum variants blaSHV-28 and blaSHV-33, and narrow-spectrum variants blaSHV-67 and blaSHV-190. These alleles of blaSHV genes were previously described in Portugal, Turkey, China, Russia, and Spain [K. pneumoniae isolates carried the blaTEM-1B, blaCTX-M-15, and blaOXA-1 genes. It was reported that these genes were horizontally transferred by the IncFIA-FIB-FII and IncHI2 plasmids [K57) carried the blaCTX-M-55 and blaOXA-1 genes; such gene combination was reported previously from China [K47 and ST147K64 additionally carried two carbapenemase genes, i.e., blaOXA-48 and blaNDM-1. Previously, it was reported that K. pneumoniae clinical isolates of ST395 and ST147 harbored blaNDM-5 and blaOXA-181/232 in Nepal and that ST11 harbored blaNDM-1 and blaOXA-48 in Greece [K. pneumoniae isolates belonging to the hvKp evolutionary branch, which acquired the resistance genes and became a hybrid hvKp-MDR. In our study, a hvKp-MDR isolate of ST23K1 carried simultaneously blaCTX-M-15 and blaOXA-48 genes, similar to a recently published study [K57 carried not only the blaCTX-M-55 and blaOXA-48 genes but additionally the blaNDM-1 gene. This is the first report describing K. pneumoniae of ST23K57 genetic-line-acquired cefalosporinase gene blaCTX-M-55, and two carbapenemase genes blaOXA-48 and blaNDM-1, which is particularly alarming. The incidence of high-risk clone ST383 carrying blaCTX-M-14b gene and two carbapenemase genes blaNDM-1 and blaOXA-48 combining both resistance and virulence elements was recently published [blaCTX-M-15, blaNDM, and blaOXA-181 genes [acrA, acrB, oqxA, oqxB, kpnE, kpnF, kdeA, and kexD) because of their clinical significance for K. pneumoniae beta-lactam resistance presented recently [K1 carried four efflux pump genes: acr and oqx of RND-type systems, kde of MATE-type, and kpn of SMF-type. The rest of the four strains carried five efflux pumps: acr, oqx, kde, kpn, and additionally the kex gene of the RND-type efflux system. The same efflux pump genes were detected recently in K. pneumoniae clinical isolates, which exhibited co-resistance to beta-lactams and aminoglycosides, glycopeptides, fluoroquinolones, and tetracyclines in India [Five nd Spain ,35,36. Tplasmids ,38. One n Greece . Of greaed study . Moreove81 genes . Additiorecently . In our in India . Interesin India .peg-344, iroB, iucA, plasmid-encoded rmpA, and rmpA2 and quantitative siderophore production (entB and ybtS) [K2, ST23K1, and ST23K57. In contrast, K. pneumoniae virulence genes , common for both hvKp and cKp, were detected in all five isolates. This is in agreement with recently published data [K1 and ST23K57 are characterized as hybrid hvKp-MDR. Thus, the data obtained in this study indicate the ongoing formation of hybrid K. pneumoniae on the base of the ST23 genetic line, which was already defined in the last decade [It is known that multiple biomarkers have been shown to predict hvKp isolates: nd ybtS) . In thist decade ,35,45.K. pneumoniae resistance and virulence genes at non-selective conditions in vitro and the fold change of expression levels in presence of AMP and CRO. It was shown that ESBL gene blaSHV-12 expressed ~4-fold higher in the MDR strain of ST395K47 than blaSHV-type genes coding broad-spectrum and narrow-spectrum beta-lactamases in the remaining K. pneumoniae strains. This is in agreement with previously reported data that ESBL variants of the blaSHV-12 gene expressed higher than non-ESBL variants [We estimated the basal expression levels of variants . These gblaTEM,blaCTX-M, blaOXA-48, and blaNDM and porin gene ompK36 were expressed at higher levels, with the exception of blaTEM in the hvKp-MDR strain of ST23K1. Notably, the expression levels of the beta-lactamase (blaTEM and blaCTX-M) and carbapenemase genes were higher in cKp-MDR strains than those in hybrid hvKp-MDR strains. Possibly, the reason for this observation is the higher metabolic load in Klebsiella cells producing resistance and virulence factors simultaneously. Growing at AMP conditions for 90 min induced upregulation of blaTEM gene expression in cKp-MDR of ST147K64 (2.1-fold), as well as the blaCTX-M (5.3-fold) and ompK36 (2.8-fold) genes in hvKp-MDR of ST23K57, but downregulation of blaTEM gene expression in cKp-MDR of ST395K47 and the blaOXA-48 gene in cKp-MDR of ST147K64. In contrast, growing at CRO conditions induced upregulation of the blaCTX-M gene in hvKp-MDR of ST23K57 (6.5-fold) and downregulation of the blaTEM gene in cKp-MDR of ST395K47 (3.3-fold), in hvKp-MDR of ST23K1 (2.1-fold), and the blaOXA-48 gene in cKp-MDR of ST147K64 (2.1-fold).Beta-lactamase genes ropD, and 2\u20133 genes were lower than the reference. In the hvKp strain, one efflux gene expression was higher, three genes were expressed at the same level, and four genes were lower than the reference gene. In contrast, major efflux genes in hybrid hvKp-MDR strains were expressed lower than the rpoD gene, and one gene in the strain of ST23K57 was expressed on the same level as the reference. Interestingly, the previously described expression of the arcB efflux gene showed upregulation of this gene in carbapenem-resistant K. pneumoniae strains compared with non-resistant ones [Klebsiella evolutionary branches that are consistent with previous reports [K. pneumoniae genetic lines may reflect differences in bacterial surface structures in particular K-types: downregulation in the strains of K47 and K2, and upregulation in the strains of K1 and K57 in response to AMP; and upregulation in the strains of K64 and K57 in response to CRO were present at higher levels in the cKp strains of ST395K47, ST147K64, and hvKP ST86K2 than in the hybrid hvKp-MDR strains of ST23K1 and ST23K57. In conditions containing 100 mg/L AMP, these genes were upregulated in cKp and hybrid hvKp-MDR strains (fimH 2.3-4.6-fold) and wabG in hvKp-MDR strains (6.1\u201314.9-fold), while downregulated in the hvKp strain . In conditions with 10 mg/L CRO, only the wabG gene was upregulated in hybrid hvKp-MDR strains (2.3-14.9-fold). The expression levels of the remaining virulence genes common for cKp and hvKp (celB and ureA), as well as common for only hvKp , were approximately equal in all studied strains at non-selective conditions. The celB gene expression at AMP medium was upregulated in hvKp-MDR strains (3.7\u20138.0-fold); the ureA gene expression was upregulated in the cKp strain of ST147K64 (13.9-fold) and hvKp-MDR strains of ST23K1 (9.2-fold) and ST23K57 (3.2-fold). It was detected that CRO induced upregulation of the ureA gene in a hvKp-MDR strain of ST23K57 (4.3-fold) and downregulation of this gene in a hvKp-MDR strain of ST23K1 (2.6-fold). Expression levels of virulence genes common for hvKp strains were not changed under selective pressure generated by AMP or CRO in the growth media in a specialized Neurosurgical Hospital in Moscow, Russia. Following the requirements of the Russian Federation Bioethical Committee, each patient signed informed voluntary consent to treatment and laboratory examination. The materials used in the study did not contain the personal data of patients.K. pneumoniae isolates were collected from the respiratory system, blood, urine, cerebrospinal fluid, and wounds of 62 patients of the neuro-ICU. Bacteria identification was performed using by a Vitek-2 Compact instrument and a MALDI-TOF Biotyper . Bacteria were grown at 37 \u00b0C with agitation on Luria-Bertani broth and Muller-Hinton broth . Bacterial isolates were stored in 20% glycerol at minus 80 \u00b0C.Seventy n-101 and AST n-102 cards . The results were interpreted according to the European Committee on Antimicrobial Susceptibility Testing . E. coli strains ATCC 25922 and ATCC 35218 were used for quality control. Strains non-susceptible to \u22651 agent in \u22653 antimicrobial categories were identified as multi-drug resistant (MDR), according to Magiorakos et al., 2012 [Minimal inhibitory concentrations (MICs) of ampicillin (AMP), ampicillin-sulbactam (SAM), cefuroxime (CXM), cefoxitin (FOX), ceftriaxone (CRO), ceftazidime (CAZ), cefoperazone-sulbactam (CSL), cefepime (FEP), ertapenem (ETP), imipenem (IPM), tetracycline (TET), tigecycline (TGC), ciprofloxacin (CIP), chloramphenicol (CHL), gentamicin (GEN), tobramycin (TOB), amikacin (AMK), trimethoprim-sulfamethoxazole (SXT), and nitrofurantoin (NIT) were determined using a Vitek-2 instrument with VITEK-2 using AST l., 2012 .K. pneumoniae strains growing on the plates with Luria-Bertani broth overnight at 37 \u00b0C [K. pneumoniae formed viscous strings >5 mm length using a standard bacteriological loop.The string test was used for the identification of hypermucoviscous at 37 \u00b0C . The posK. pneumoniae isolates were determined by the Multilocus Sequence Typing (MLST) scheme of Pasteur Institute using the previously published primers [K. pneumoniae isolates was performed using specific primers for the wzy gene associated with K serotypes K1, K2, K20, and K57 [wzi gene sequencing for identification of capsular types K23, K27, K28, K31, K47, K60, K62, and K64 [Sequence types (STs) of primers ,51. The and K57 and by w and K64 . BacteriblaSHV, blaCTX-M, blaTEM, blaOXA-48, blaKPC, blaVIM, blaIMP, and blaNDM, class 1 and 2 integrons, and porin protein gene ompK36, as well as 8 genes associated with K. pneumoniae virulence, rmpA (hypermucoid phenotype regulator), aer (aerobactin), kfu (ferric absorption system), uge , wabG (glucosyltransferase), fimH (fimbria type I), allS and allR , were detected by PCR using specific primers as was described previously [Beta-lactamase genes eviously .http://www.generunner.net/, accessed on 1 November 2021) and in silico analysis by insilico.ehu.eus [K. pneumoniae virulence genetic determinants and antibacterial resistance genes were detected by RT-PCR using qPCRmix-HS SYBR and the CFX96 Real-Time PCR system with the following program: 95\u00b0 for the 20s, 61\u00b0 for 20s, 72\u00b0 for 30 s, repeat 40 times. Bacterial thermolysates were used as DNA templates.Oligonucleotides for RT-PCR were des.ehu.eus was perfhttps://github.com/ncbi/pgap, accessed on 1 November 2021). Antimicrobial resistance genes, STs, plasmids, and restriction-modification systems were identified using the web resource of the Center for Genomic Epidemiology . Virulence genes, capsular type, genes conferring resistance to heavy metals, and efflux pumps were identified by the Institut Pasteur, Paris, France, BIGS database web-resource of .WGS was carried out on the Illumina MiSeq platform using Nextera DNA Library Preparation Kit and MiSeq Reagent Kits v3 . The obtained single reads were collected into contigs using the SPAdes 3.9.0 software . De novo assembled genomes were annotated in the GenBank database containing/not containing antimicrobials (100 mg/L AMP or 10 mg/L CRO) and incubated at 37 \u00b0C with agitation for 90 min. Each experiment was represented by three independent repeats. All following steps for RNA isolation were performed at 4 \u00b0C to limit RNase activity. Total RNA was isolated by phenol-chloroform extraction using kit RNA-extran , following manufacturer protocol. After isolation, RNA was treated with TURBO DNase to remove traces of genomic DNA.proC, recA, and rpoD expression. Three technical replicates per each of the three biological samples were used for statistical validity. The relative transcript levels of antimicrobial resistance and virulence genes were calculated using the 2\u2212\u0394\u0394Ct method [www.graphpad.com accessed on 1 November 2021). Gene expression levels of each gene at present of AMP and CRO were compared to those in conditions without antimicrobials.One \u00b5g of isolated total RNA was used for cDNA synthesis with RevertAid RT Reverse Transcription Kit . qPCR was performed using qPCRmix-HS SYBR and the CFX96 Real-Time PCR system with the following program: 40 cycles of 20 s at 95 \u00b0C for denaturation, 20 s at 61 \u00b0C for annealing, 30 s at 72 \u00b0C for extension and SYBR Green detection. The melting curve analysis in the temperature range from 60 \u00b0C to 94 \u00b0C, with a fluorescence estimation step of 0.2 \u00b0C, was performed to confirm the specificity of the reaction. Relative quantification of the target gene expression was normalized with reference genes t method . A heat"} +{"text": "Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family . RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio, which are themselves required for invasion. Both the filamin and the tetraspanin enhance the cortical activity of Rho1 and the formin Diaphanous and thus the assembly of cortical actin, which is a critical function since expressing a dominant active form of Diaphanous can rescue the Dfos macrophage invasion defect. In vivo imaging shows that Dfos enhances the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the properties of the macrophage nucleus from affecting tissue entry. We thus identify strengthening the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.The infiltration of immune cells into tissues underlies the establishment of tissue-resident macrophages and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here, we find that the tissue invasion of The infiltration of immune cells into tissue underlies the establishment of tissue-resident macrophages, and responses to infections and tumors, but how do they overcome tissue barriers? This study shows that macrophages upregulate the proto-oncogene Fos, increasing the density and crosslinking of cortical actin, thereby counteracting the tension of surrounding tissues and protecting the macrophage nucleus. The classical model of cell migration on a surface postulated in the 1980s by Abercrombie has been extended . Much ofMigration in 2D and 3D environments requires actin polymerization to power forward progress. The assembly of actin at the leading edge, when coupled to Integrin adhesion to anchor points in the surrounding extracellular matrix (ECM), can allow the front of the cell to progress . This anDrosophila macrophage migration into the embryonic germband (gb) to investigate mechanisms of immune cell tissue invasion. Macrophages, also called plasmatocytes or hemocytes, are the primary phagocytic cell in Drosophila and share striking similarities with vertebrate macrophages (control), UAS-cher RNAi KK107451, UAS-TM4SF RNAi KK102206, UAS-Lam RNAi1 GD45636, UAS-Lam RNAi2 KK107419 lines were obtained from the Vienna Drosophila Resource Center (Austria).SF, USA) . Oregon Here, we list the lines used in each figure; we state first the name from FlyBase; in parentheses, the name used in the figure panels is provided.Oregon R. srpHemo-GAL4, UAS-GFP (control). srpHemo-Gal4, srpHemo-H2A::3xmCherry/P{CaryP}attP2 (control). srpHemo-GAL4, UAS-GFP; kay1(Dfos1). srpHemo-GAL4, UAS-GFP::nls/+ (control 1). srpHemo-GAL4, UAS-GFP/+; kay1(Dfos1). srpHemo-GAL4, UAS-GFP::nls/+; kay2(Dfos2). srpHemo-GAL4, UAS-GFP::nls/(UAS-Fra)2; kay2. 10XUAS-IVS-myr::GFP/+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/+ (control 2 and control). UAS-DfosDN/+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/+ (mac>DfosDN). srpHemo-Gal4, srpHemo-H2A::3xmCherry/ UAS GFP::nls (ctrl). srpHemo-Gal4, srpHemo-H2A::3xmCherry/UAS-fbz (mac>DfosDN). srpHemo-Gal4, srpHemo-H2A::3xmCherry /+ (ctrl). srpHemo-Gal4, srpHemo-H2A::3xmCherry/UAS-DfosDN (mac>DfosDN). UAS-GFP; srpHemo-Gal4, srpHemo-H2A::3xmCherry (ctrl). UAS-Dfos RNAi HMS00254/srpHemo-Gal4, srpHemo-H2A::3xmCherry (mac>DfosRNAi1). UAS-Dfos RNAi JF02804/srpHemo-Gal4, srpHemo-H2A::3xmCherry (mac>DfosRNAi2). srpHemo-GAL4, UAS-GFP::nls/+ or /(UAS-Fra)2 (mac>Dfos). UAS-GFP; UAS-Dfos RNAi HMS00254/ srpHemo-Gal4, srpHemo-H2A::3xmCherry (mac>DfosRNAi1+ GFP). UAS-GFP; UAS-Dfos RNAi JF02804/srpHemo-Gal4, srpHemo-H2A::3xmCherry (mac>DfosRNAi2+ GFP).srpHemo-H2A::3xmCherry/+ (control). srpHemo-Gal4, srpHemo-H2A::3xmCherry/+ (3 movies) and Resille::GFP/+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/+ and Resille::GFP/+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/+ (3 movies) and Resille::GFP/+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/UAS-DfosDN . srpHemo-Gal4, srpHemo-H2A::3xmCherry/UAS-fbz (mac>DfosDN). srpHemo-GAL4, UAS-GFP.nls/+ (control). srpHemo-GAL4, UAS-GFP.nls/+; kay2(Dfos2).UAS-Dicer2;; srpHemo-Gal4, srpHemo-H2A::3xmCherry/w1118 (control). UAS-Dicer2; UAS-TM4SF RNAi KK10220/+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/+ (mac>TM4SF RNAi). UAS-Dicer2; UAS-cher RNAi KK107451/+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/+ (mac>cher RNAi). UAS-Dicer2; UAS-cher RNAi KK107451/UAS-TM4SF RNAi KK102206; srpHemo-Gal4, srpHemo-H2A::3xmCherry/+ . srpHemo-GAL4, UAS-mCherry::nls/UAS-mCD8::GFP (control). srpHemo-GAL4, UAS-mCherry::nls/UAS-mCD8::GFP; UAS-fbz/+ (mac>DfosDN). srpHemo-GAL4,UAS-mCherry::nls/UAS-cheerio::FLAG; UAS-fbz/+ . srpHemo-GAL4,UAS-mCherry.nls/UAS-TM4SF; UAS-fbz/+ . srpHemo-GAL4, UAS-mCherry::nls/ UAS-TM4SF (mac>TM4SF). srpHemo-GAL4, UAS-mCherry::nls/UAS-cher (mac>cher). srpHemo-Gal4, srpHemo-3xmCherry/+ (control). srpHemo-Gal4, srpHemo-3xmCherry/UAS-fbz (mac>DfosDN).srpHemo-3xmCherry; kay1 (Dfos1) and srpHemo-3xmCherry; +. srpHemo-Gal4, srpHemo-moe::3xmCherry/+;UAS-mCD8::GFP/+(Control). srpHemo-Gal4, srpHemo-moe::3xmCherry/UAS-fbz (mac>DfosDN). w118. srpHemo-Gal4, srpHemo-moe::3xmCherry/w118 (Control). srpHemo-Gal4, srpHemo-moe::3xmCherry/UAS-cher RNAi KK107451 (mac>cher RNAi). srpHemo-Gal4, srpHemo-moe::3xmCherry/UAS-TM4SF RNAi KK102206 (mac>TM4SF RNAi). srpHemo-GAL4, UAS-mCherry.nls/UAS-mCD8::GFP (control). srpHemo-GAL4, UAS-mCherry.nls/UAS-Dia\u0394Dad::EGFP; UAS-fbz/+ . srpHemo-GAL4, UAS-mCherry.nls/UAS-mCD8::GFP; UAS-fbz/+ (mac>DfosDN). srpHemo-GAL4, UAS-mCherry.nls/ UAS-Dia\u0394Dad::EGFP (mac>diaCA). UAS-GFPnls; srpHemo-Gal4, srpHemo-H2A::3xmCherry. #2: UAS-GFPnls/srpHemo-Gal4, srpHemo-H2A::3xmCherry; Dfos1. #3: UAS-GFPnls/ srpHemo-Gal4, srpHemo-H2A::3xmCherry; Dfos2. #4: UAS-Dia\u0394Dad::EGFP/srpHemo-Gal4, srpHemo-H2A::3xmCherry; Dfos1. #5: UAS-Dia\u0394Dad::EGFP/srpHemo-Gal4, srpHemo-H2A::3xmCherry; Dfos2. UAS-Dicer2;; srpHemo-Gal4, srpHemo-H2A::3xmCherry/P{CaryP}attP40 (control). UAS-Dicer2;+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/ UAS-dia RNAi HM05027 (mac>dia RNAi1). UAS-Dicer2;+; srpHemo-Gal4, srpHemo-H2A::3xmCherry/UAS-dia RNAi HMS00308 (mac>dia RNAi2). UAS-dia::EGFP/+; UAS-nlacz/ srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato. UAS-dia::EGFP/+; UAS-Rho1N.19)/srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato (mac>Rho1DN). UAS-dia::EGFP/+; UAS-fbz/srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato (mac>DfosDN). UAS-dia::EGFP/+; UAS-cher RNAi KK107451/srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato (mac>cher RNAi). UAS-dia::EGFP/+; UAS-TM4SF RNAi KK102206/srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato (mac>TM4SF RNAi). UAS-diaRBD::GFP/+; srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato/UAS-nlacZ (control). UAS-diaRBD::GFP/+; srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato/UAS-Rho1N.19 (mac>Rho1DN). UAS-diaRBD::GFP/UAS-fbz; srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato/+ (mac>DfosDN). UAS-diaRBD::GFP/UAS-cher RNAi KK107451; srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato/+ (mac>cher RNAi). UAS-diaRBD::GFP/UAS-TM4SF RNAi KK102206; srpHemo-Gal4, 10XUAS-IVS-myr::tdTomato/+ (mac>TM4SF RNAi).srpHemo-Gal4 UAS-LifeActGFP UAS-RedStinger (control); srpHemo-Gal4 UAS-LifeActGFP UAS-RedStinger; UAS-DfosDN (mac>DfosDN). srpHemo-Gal4, UAS-CLIP::GFP, UAS-RedStinger (control). srpHemo-Gal4, UAS-CLIP::GFP, UAS-RedStinger; UAS-fbz (mac>DfosDN). srpHemo-GAL4, UAS-mCherry.nls/UAS-mCD8::GFP (control). srpHemo-GAL4, UAS-mCherry.nls/UAS-Lamin RNAi GD45636, KK107419 . srpHemo-GAL4, UAS-mCherry.nls/UAS-LaminC RNAi TRIP JF01406 (mac>LamC RNAi). srpHemo-GAL4, UAS-mCherry.nls/UAS-mCD8::GFP; UAS-fbz/+ (mac>DfosDN). srpHemo-GAL4, UAS-mCherry.nls/UAS-Lam RNAi ; UAS-fbz/+ . srpHemo-GAL4, UAS-mCherry.nls/UAS-LaminC RNAi TRIP JF01406; UAS-fbz/+ . e22c-Gal4,srpHemo-H2A::3xmCherry/+ (control). srpHemo-QF/ srpHemo-H2A::3xmCherry; QUAS-fbz/UAS-Rho1.N12 (mac<>DfosDN). e22c-Gal4, srpHemo-H2A::3xmCherry/srpHemo-QF; +/ UAS-Rho1.N12 (ecto>Rho1DN). srpHemo-QF/ e22c-Gal4, srpHemo-H2A::3xmCherry; UAS-Rho1.N12/QUAS-fbz . +;UAS-GFP::nls, srpHemo-GAL4 (control). +;UAS-GFP::Lamin, srpHemo-GAL4 (mac>Lam).UAS-fbz (UAS-Dfos DN) line [The fragment was amplified from genomic DNA of the published DN) line using pry1M{vas-int.Dm}ZH-2A w*; M{3xP3-RFP.attP}ZH-51D, BL 24483), to produce second chromosome inserts. All male survivors were crossed to w; Sp/CyO; PrDr/TM3Ser virgins. Transformants were recognized by eye color and crossed again to w; Sp/CyO; PrDr/TM3Ser virgins to get rid of the X chromosomal integrase.The TM4SF open reading frame was amplified from the DGRC GH07902 cDNA clone , using primers acagcgGAATTCATGGCATTGCCGAAGAAAAT and acagcgTCTAGATTAAAAGCTAATCGTCTGTCATT. The PCR product and the pUASt-aTTB vector (DGRC plasmid #1419) were digested with EcoRI and XbaI, and ligated. After sequencing, the construct was injected into the landing site line, against the C-terminal end of g. Then 10 \u03bcg of the cleared lysate were separated by SDS-PAGE using 4% to 15% Mini-PROTEAN TGX Precast Protein gels and blotted onto a Amersham Protran Premium western blotting nitrocellulose membrane . The nitrocellulose membrane was blocked with Pierce Clear Milk blocking buffer and incubated in blocking buffer with anti-mCherry at 1:1,000, and anti-Profilin [Cages were prefed on fresh yeast plates for 2 days. Late stage 11/early stage 12 embryos were handpicked using a Leica M205 fluorescent microscope on ice-cold apple juice plates. They were transferred to RIPA buffer with a Halt Protease/Phosphatase inhibitor cocktail and lysed. After a 30-minute incubation on ice, they were centrifuged 15 minutes at 4\u00b0C at 15,000#chi 1J) at 1:50 Dfos2 for which the setting was 25\u00b0C.Embryos were dechorionated in 50% bleach for 5 minutes, washed with water, and mounted in halocarbon oil 27 (Sigma) on a 24 \u00d7 50 mm high precision coverslip between 2 bridges (approximately 0.5 cm high) of coverslips glued on top of each other or mounted in halocarbon oil 27 (Sigma) between an 18 \u00d7 18 mm coverslip and an oxygen permeable membrane (YSI). The embryo was imaged on an upright multiphoton microscope equipped with a W Plan-Apochromat 40X/1.4 oil immersion objective (Olympus). GFP and mCherry were imaged at 860 nm and 1,100 nm excitation wavelengths, respectively, using a Ti-Sapphire femtosecond laser system (Coherent Chameleon Ultra) combined with optical parametric oscillator technology (Coherent Chameleon Compact OPO). Excitation intensity profiles were adjusted to tissue penetration depth and Z-sectioning for imaging was set at 1 \u03bcm for tracking. For long-term imaging, movies were acquired for 60 to 150 minutes with a frame rate of 25 to 45 seconds. A temperature control unit set to 29\u00b0C was utilized for all genotypes except Dfos RNAi, embryos with 70% gb retraction (Stage 13) were used for vnc counts. The pre-gb zone was defined based on embryo and yolk autofluorescence as an area on the yolk sac underneath the amnioserosa with borders defined posteriorly by the gb ectoderm and anteriorly by the head. Macrophages were visualized using confocal microscopy with a Z-stack step size of 2 \u03bcm, and macrophage numbers within the gb or the segments of the vnc were calculated in individual slices (and then aggregated) using the Cell Counter plugin in FIJI. Total macrophage numbers were obtained using Imaris (Bitplane) by detecting all the macrophage nuclei as spots.Autofluorescence of the embryo revealed the position of the gb for staging of fixed samples. Embryos with 40% (\u00b15%) gb retraction (Stage 12) were analyzed for macrophage numbers in the pre-gb, within the gb, along the vnc, and in the whole embryo. For the srpHemo-H2A::3xmCherry and the surrounding tissues with Resille::GFP, or with only macrophages labeled by srpHemo-H2A::3xmCherry, or srpHemo>GFP::nls were imaged, and 250 \u00d7 250 \u00d7 40 \u03bcm3 3D stacks were typically acquired with approximately 0.2 \u00d7 0.2 \u00d7 1 \u03bcm3 voxel size every 39 to 41 seconds for approximately 2 hours. For imaging macrophages on vnc, frames were acquired at every 40 to 43 seconds for 30 minutes after macrophages started spreading into abdominal segment 2 are its instantaneous velocities. Only trajectories with a minimal duration of 15 time frames were used. Calculated persistence values were averaged over all trajectories to obtain a persistence index (I) for the duration of measurement (with \u22121 being the lowest and 1 the maximum). From 3 to 6 embryos were recorded and analyzed for each genotype; numbers of control and perturbed embryos are equal in each pairwise comparison.Cell speed and persistence were calculated from nuclei positions using custom Python scripts as described elsewhere . Briefly2 in each embryo. Analyses were carried out using standard Fiji software. From 4 to 5 embryos were analyzed per genotype. Macrophages in the pre-gb or gb entry zones were analyzed.The junctional intensity of F-actin was calculated using linescan analysis as previously described with thesrpHemo-moe::3xmCherry reporter line [DfosDN, cher RNAi, or TM4SF RNAi. Embryos were collected for 5 hours 30 minutes at 29\u00b0C, dechorionated in 50% bleach for 5 minutes, rinsed thoroughly with water, and aligned laterally side by side under a stereomicroscope using a fluorescence lamp to check for the presence of mCherry. Aligned embryos were then mounted as described in the live imaging section above. To image Moe::3xmCherry, a Zeiss LSM800 inverted microscope was used with the following settings: Plan-APOCHROMAT 40x/1.4 Oil, DIC, WD = 0.13 objective, 1.5\u00d7 zoom, 1,025 \u00d7 1,025 pixel, speed 8, heating chamber set to 29\u00b0C, z-interval 1 \u03bcm. Laser settings were kept constant in all experiments. Images were acquired during macrophage invasion into the gb (St 12). Pseudo-coloring was conducted for the mCherry red channel. Each pixel in the image has a color ascribed to it via the fire \u201cLook Up Table\u201d translating the level of intensity of the mCherry channel into a defined amount of each color. The highest intensity of the image is represented as very bright yellow, and all other gray values are depicted as colors on the scale accordingly.To quantify cortical F-actin intensity in living embryos, a ter line was crost test with Welch\u2019s correction for DfosDN and one way-ANOVA for cher RNAi and TM4SF RNAi.For quantification of Moe::3xmCherry intensity, an ROI was drawn in Fiji software around macrophages at the gb entry site in 20 z-stacks for each embryo. The area mean intensity was measured in all ROIs, and the average/embryo was calculated. To normalize fluorescence intensities per batch, the average intensity/embryo of all ROIs in each sample was divided by the arithmetic mean of the average intensity/embryo of all ROIs in the control per batch. The normalized average intensities/embryo were then compared to each other using a https://github.com/Axmasha/Image_analysis_scripts.Methanol-fixed St 11 embryos were mounted either after staining with GFP antibody (Dia::GFP) or without staining (DiaRBD::GFP) and imaged with a Zeiss Inverted LSM800, Plain-Apochromat 63X/1.4 Oil Objective at an XY-resolution of 0.1 \u03bcm and a Z-resolution of 1 \u03bcm . All macrophages within 40 \u03bcm of the gb were analyzed. For the quantification of the levels of DiaRBD or the complete Dia protein at the plasma membrane versus the cytoplasm, confocal images were processed using Fiji and MATLAB-R2017b (MathWorks). Individual focal planes were used to segment a profile corresponding to an 8-pixel wide line drawn across the single outer membrane of individual macrophages chosen such that the extracellular portion of the line extended into surrounding tissue or space and not another macrophage. The corresponding intensity profiles of the Myr::Tomato and Dia::GFP or DiaRBD::GFP channels were extracted in Fiji using a custom macro and analyzed further using a custom MATLAB script. The membrane region was defined by finding the maximal value in the Tomato intensity profile and centering a 0.8-\u03bcm interval around it. The background was calculated for each GFP profile as the mean intensity in the 2 \u03bcm outside the cell, flanking the membrane region, and substracted from the entire profile. The integrated Dia::GFP or DiaRBD::GFP intensity at the membrane was calculated within the 0.8-\u03bcm interval defined above. The integrated cytoplasmic Dia::GFP or DiaRBD::GFP level was calculated as the mean intensity of 2 \u03bcm of the GFP profile inside the cell flanking the membrane region. Image analysis scripts are publicly available at UAS-CLIP::GFP under the control of srpHemo-Gal4. Briefly, 3D-stacks with 1 \u03bcm Z resolution were acquired every 35 to 45 seconds for approximately 1 hour. As the strength of the GAL4 expression increased over time, laser power was adjusted during acquisition to reach the best possible quality of visualization. Images acquired from mutiphoton microscopy were initially processed with ImSpector software (LaVision Bio Tec) to compile channels from the imaging data.Laterally oriented embryos were used to measure the maximal length and width of macrophages expressing We started measuring from the time the cell body of the first macrophage fully appeared at the interface between the ectoderm and mesoderm and yolk sac until it had moved 30 \u03bcm along the ectoderm mesoderm interface. At each time frame, a line was drawn in Fiji along the longest dimension of the macrophage in the direction of its front-rear polarization axis, denoted the maximal cell length, and along the orthologonal longest dimension, which was considered maximal cell width. We did not observe long CLIP::GFP protrusions, but when a small protrusion was present, it was not included in the length measurement; within this gb region, the front of the first macrophage was clearly outlined with CLIP::GFP. The border between the first and second entering macrophages was drawn based on the uninterrupted intense line of CLIP::GFP at the base of the first macrophage; only cells with a clearly visible border were measured. The length-to-width ratio was quantified for each time frame, and a probability density function was plotted: 5 embryos were recorded for each genotype.srpHemo-Gal4 UAS-LifeAct::GFP were used to image macrophage actin live with a 3D-stack resolution of 1 \u03bcm. See above description of CLIP::GFP labeled macrophage imaging for laser power and image compilation. Laser power was also increased further in the DfosDN samples to enhance actin visualization. We measured the length of the filopodia-like protrusion of the first entering macrophage with Imaris software (Bitplane) from the time when the protrusion was inserted into the ectoderm, mesoderm, and yolk sac interface until the macrophage started to translocate its cell body into that location.Laterally oriented embryos expressing w; +; srpHemo-Gal4, srpHemo-3xmCherry/+ or w; +; srpHemo-Gal4, srpHemo-3xmCherry/ UAS-DfosDN genotypes were placed into plastic cages closed with apple juice plates with applied yeast to enhance egg laying. Collections were performed at 29\u00b0C for 1 hour, then kept at 29\u00b0C for additional 5 hours 15 minutes to reach stage 11 to early stage 12. Embryos were harvested for 2 days with 6 to 7 collections per day and stored meanwhile at +4\u00b0C to slow down development. Collected embryos were dissociated and the macrophages sorted as previously described [5 macrophages were sorted within 30 minutes.Adult flies of either escribed . About 15 macrophages. RNA sequencing was performed by the CSF facility of Vienna Biocenter according to standard procedures (https://www.vbcf.ac.at/facilities/next-generation-sequencing/) on 3 replicates. Briefly, the cDNA library was synthesized using QuantSeq 3\u2032 mRNA-seq Library Prep kit and sequenced on the Illumina HiSeq 2500 platform. The reads were mapped to the Drosophila melanogaster Ensembl BDGP6 reference genome with STAR (version 2.5.1b). The read counts for each gene were detected using HTSeq (version 0.5.4p3). Flybase annotation (r6.19) was used in both mapping and read counting. Counts were normalized to arbitrary units using the TMM normalization from edgeR package in R. Prior to statistical testing, the data were voom transformed, and then the differential expression between the sample groups was calculated with limma package in R. The functional analyses were done using the topGO and gage packages in R [Total RNA was isolated from FACS-sorted macrophages using Qiagen RNeasy Mini kit (Cat No. 74104). The quality and concentration of RNA was determined using Agilent 6000 Pico kit (Cat No. 5067\u20131513) on an Agilent 2100 Bioanalyzer: on average about 100 ng of total RNA was extracted from 1.5 \u00d7 10ges in R ,109. RNARNA isolation and qPCR was performed from bones of wild-type C57BL/6 mice and from bones and OS of H2-c-fosLTR as previously described with the primers in p-value <0.05 was considered statistically significant .Mouse experiments: Data are shown as mean \u00b1 SEM. One-way ANOVA followed by Tukey multiple comparisons posttest was applied to compare experimental groups. Statistical analysis was performed using GraphPad Prism 6.0 software. A Drosophila experiments: Statistical tests as well as the number of embryos, cells, tracks, or contacts assessed are listed in the figure legends. All statistical analyses were performed using GraphPad PRISM or R Studio, and significance was determined using a 95% confidence interval. No statistical method was used to predetermine sample size.Dfos mutant analyses in Representative images of Dfos antibody staining were analyzed per replicate per genotype and in situ hybridization are from experiments that were repeated 2 times with many embryos with reproducible results. S1 TableComparison of TF mRNA expression in macrophages at stages 11\u201312 and 13\u201316, based on data in . TFs exp(TIF)Click here for additional data file.S2 TableGenes are ordered according to the adjusted p-value from the RNA sequencing. Function is based on Flybase assignments . The mur(TIF)Click here for additional data file.S1 Raw imagessrpHemo-moe::3xmCherry expressing either CD8::GFP (ctrl) or DfosDN in macrophages. Rightmost western blot also contains a w- lane. Top row shows blots probed with an mCherry antibody, bottom row the same blots probed with a profilin antibody as a loading control. Cropped versions of the blots are shown in Three original uncropped western blots of St 11 embryo extracts from (PDF)Click here for additional data file.S1 DataThis Excel file contains the raw data of the quantification of embryo macrophage counts and linescan analyses along with movie outputs. Each tab in the file names the figure panel whose graph is based on the data shown in that chart.(XLSX)Click here for additional data file.S2 DatasrpHemo-3xmCherry control embryos and those expressing DfosDN in macrophages. The mean from 3 samples is shown for each genotype, organized by Flybase IDs (Fbgn), along with statistical analyses.Compendium of the RNA sequencing data obtained from FACSed macrophages from Stages 11\u201312 (XLSB)Click here for additional data file.S1 Fig2Dfos mutant embryos compared to the control (p = 0.37) SD: 6, 7. (C) The total number of macrophages (see schematic at left) was not altered from that in the control embryos expressing DfosDN in macrophages (p = 0.12). SD: 60, 120. The number of macrophages (green) along the vnc (outlined by black dotted line in the schematic on the left) shows no significant difference between the control and (D) macrophages that express DfosDN or (E) either of 2 RNAi lines against Dfos. (D) DfosDN p = 0.88, 0.99, >0.99. 1Dfos RNAi (TRiP HMS00254) p = 0.21, 0.06, 0.11, 0.072, 0.033, 0.30, 0.56. 2Dfos RNAi (TRiP JF02804) p = 0.34, 0.15, 0.83, 0.27, 0.47, 1.0, 0.45. (D) SD: Ctrl 3, 3, 3, 0.8; DfosDN 6, 3, 0.7. (E) SD: Ctrl 6, 3, 3, 3, 2, 0.3; 1Dfos RNAi 6, 3, 3, 3, 2, 2, 0.3; 2Dfos RNAi 6, 2, 3, 2, 3, 1, 0.4. Macrophage numbers in the pre-gb (see schematic at left) are increased compared to the control for lines expressing (F) DfosDN or (G) one of 2 different UAS-Dfos RNAi constructs in macrophages under srpHemo-GAL4 control. (F) p = 0.04, SD: 19, 29. (G) 1Dfos RNAi p < 0.0009, 2Dfos RNAi p < 0.0001. SD: 12, 9, 14. (H) Macrophage numbers in the gb are not significantly altered compared to the control upon overexpression of Dfos in macrophages (p = 0.14). SD: 22, 14. (I) Macrophage numbers in the gb for lines expressing one of 2 different UAS-Dfos RNAi constructs in macrophages under srpHemo-GAL4 control and lines, which additionally express UAS-GFP. Control vs. 1mac>Dfos RNAi (TRiP HMS00254) or Control vs. 2mac>Dfos RNAi (TRiP JF02804), p < 0.0001. 1mac>Dfos RNAi vs. 1 + GFPmac>Dfos RNAi or 2mac>Dfos RNAi vs. 2 + GFPmac>Dfos RNAi, p > 0.99. SD: 33, 47, 34. The effect of each Dfos RNAi was eliminated upon simultaneous expression of another UAS construct. Macrophages are labeled using either srpHemo-Gal4 driving UAS-GFP or srpHemo-H2A::3xmCherry. \u201cmac>\u201d indicates srpHemo-GAL4 driver expressing UAS constructs specifically in macrophages. Histograms show mean \u00b1 SEM ***p < 0.005, **p < 0.01, *p < 0.05. Unpaired t test was used for statistics, except for G, I, which used one-way ANOVA. The number of embryos analyzed for that genotype is shown within each column in the graphs. In D, n = 6 embryos for the control and n = 9 for Dfos DN. In E, n = 9 embryos for control, 15 and 11 for Dfos RNAis. Scale bar in A: 10 \u03bcm. The data underlying the graphs can be found in (A) Dfos protein (green) is detected with an antibody in macrophages (magenta) in embryos from the stages as indicated. (B-I) Quantification in mid St 12 embryos. (B) The number of macrophages (green) in the pre-gb zone (outlined by a black dotted line in the schematic on the left) showed no significant change in (TIF)Click here for additional data file.S2 Fig2Dfos macrophages entering the gb (outlined by the dashed line). Time in minutes shown in the top right corner of each image. (C) Quantification of macrophage speed shows a significant reduction in the speed of 2Dfos macrophages in the pre-gb zone and at gb entry, but none in the head. Regions analyzed indicated in left schematic. Speed in head: control = 2.59 \u03bcm/min, 2Dfos = 2.68 \u03bcm/min, p = 0.40; speed in pre-gb = 3.38 \u03bcm/min, 2Dfos = 2.47 \u03bcm/min, p = 2.38e-06; speed in gb entry: control = 2.35 \u03bcm/min, 2Dfos = 1.62 \u03bcm/min, p = 0.0003. Macrophages are labeled using srpHemo-H2A::3xmCherry. Histograms show mean \u00b1 SEM. ****p < 0.0001, ***p < 0.005, **p < 0.01, *p < 0.05. Unpaired t test was used for statistics. The number of analyzed macrophages for each genotype shown within each graph column. Tracks were obtained from movies of 3 embryos each for control and mac>DfosDN for pre-gb entry in A, 4 each for gb entry in A, 3 each for the vnc in A, 4 each of control and 4 2Dfos embryos for head and pre-gb in C, and 3 embryos each for gb entry in C. Scale bars: 10 \u03bcm. The data underlying the graphs can be found in (A) Quantification reveals that the directional persistence of macrophages expressing DfosDN (0.58) is unchanged (0.56) in the pre-gb area (p = 0.66) but decreased during gb entry (0.65) (0.72), p = 0.038 and along the vnc (0.54) compared to the control (0.61), p = 0.00026. Left schematic shows pre-gb area in yellow, gb entry outlined in solid line. Boxed area in right schematic shows analyzed area of vnc. (B) Movie stills showing wild-type and (TIF)Click here for additional data file.S3 FigDhc36C 0.02, CG14204 0.03, CG42402 0.04, CR43767 0.046, TM4SF 0.03, CG42260 0.0011, cher 0.046, GstT4 0.018, Xrp1 0.0011, Tspo 0.046, CG31337 0.046. Frl, DAAM, dia, capu all >0.99. Quantification of the macrophage numbers in (D) the pre-gb zone and (E) along the vnc from embryos expressing RNAi against cher (KK 107451), or TM4SF in macrophages (KK 102206) driven by srpHemo-Gal4 shows no significant alteration. The number in the column in (D) corresponds to the number of embryos analyzed. Control vs. cher RNAi p = 0.33. Control vs. TM4SF RNAi p = 0.05. Control vs. cher/TM4SF RNAi p = 0.67. (D) SD: 20, 20, 19, 13. For (E), n = 13 embryos for control and n = 15 for each cher RNAi and TM4SF RNAi. Control vs. cher RNAi p = 0.97 for T1, p = 0.33 for T2, p = 0.88 for T3. Control vs. TM4SF RNAi p = 0.52 for T1, p = 0.76 for T2, p = 0.35 for T3. SD: ctrl 6.5, 5.4, 0.6; cher RNAi 5.0, 3.3, 0.8; TM4SF RNAi 4.4, 4.9, 1.9. (F-I) q-PCR analysis of mRNA extracted from the bones of mice that are wild type, tg for MHC c-fos, viral 3\u2032 UTR, and those in which c-fos transgenesis has led to an OS. Analysis of mRNA expression shows that (F) higher Fos levels in OS correlate with higher levels of (G) the glutathione S transferase Gstt3, and (H) the slit receptor Eva1c, but not (I) Tspo. Bone and OS RNA isolated from the same transgenic mouse, n = 4 mice per group, age 5 to 6 months. p-values = 0.86, 0.0028, 0.0013 in (F), 0.79, 0.0001, 0.0003 in (G), 1.0, 0.054, 0.049 in (H), 0.37, 0.33, 0.040 in (I). SD: 0.7, 0.6, 2.6 in (F); 0.2, 0.3, 1.1 in (G); 0.4, 0.2, 1.5 in (H); 0.1, 0.2, 0.2 in (I). Histograms show mean \u00b1 SEM ***p < 0.005, **p < 0.01, *p < 0.05. Unpaired t test or one-way ANOVA with Tukey post hoc were used for statistics of quantifications. Significance is based on adjusted p-values. The data underlying the graphs can be found in (A-C) Comparative mRNA expression levels as determined from RNA sequencing analysis of FACS-sorted wild-type macrophages and those expressing DfosDN, n = 3 biological replicates. Genes down-regulated in macrophages expressing DfosDN are shown, separated into those with (A) strong and (B) moderate expression in wild-type macrophages. (C) Expression levels of Drosophila formin family genes are unchanged. Fold enrichment is normalized. p-values: (TIF)Click here for additional data file.S4 FigsrpHemo-moe::3xmCherry expressing either CD8::GFP (ctrl) or DfosDN in macrophages. Left western blot also contains w- lane. Original uncropped western blots can be found in 1Dfos or 2Dfos embryos completely rescued the macrophage gb invasion defect. p-values: Control vs. 1Dfos or vs. 2Dfos p = 0.0004 or p = 0.0055, respectively; Control vs. 1 mac>DiaCADfos or vs. 2 mac>DiaCADfos p > 0.999; 1Dfos vs. 1 mac>DiaCADfos p = 0.0005; 2Dfos vs. 2 mac>DiaCADfos p = 0.035. SD: 20, 23, 18, 19, 7.8. There was no significant change in the number of macrophages in (C) the pre-gb zone or (D) along the vnc in embryos expressing either of 2 different RNAi lines against dia expressed in macrophages. Pre-gb: Control vs. 1dia RNAi p = 0.54, Control vs. 2dia RNAi p = 0.77. vnc: Control vs. 1dia RNAi p = 0.99, Control vs. 2dia RNAi p = 0.95. RNAi1 = TRiP HMS05027, RNAi2 = TRiP HMS00308. (C) SD: 9, 12, 13. (D) SD: Ctrl 5.2, 6.4, 2.5, 0.4; 1dia RNAi 5.6, 6.8, 1.7, 0.2; 2dia RNAi 5.1, 4.9, 2.1, 0.6. Two further examples of line profiles used for the determination of the membrane-to-cytoplasmic ratios in cher RNAi, or TM4SF RNAi as shown in the schematic in E. Line length approximately 8 \u03bcm. Blue lines indicate mean GFP intensity on the membrane and in cytoplasm. Histograms show mean \u00b1 SEM ***p < 0.005, **p < 0.01, *p <0.05. One-way ANOVA with Tukey post hoc was used for statistics of quantification. The number in each column corresponds to the number of analyzed embryos. \u201cmac>\u201d indicates srpHemo-GAL4 driver expressing UAS constructs in macrophages. Macrophages are labeled using srpHemo-H2A::3xmCherry. The data underlying the graphs can be found in (A) Three western blots probed with an mCherry antibody of St 11 embryo extracts from (TIF)Click here for additional data file.S5 FigsrpHemo-Gal4 (\u201cmac>\u201d) driving UAS-LifeActGFP. White stars indicate the tip of each actin protrusion. Scale bar 5 \u03bcm. (B) Microtubules are labeled with srpHemo-Gal4 driving UAS-CLIP::GFP. Spatially matched stills of the first macrophage expressing DfosDN and control extending protrusions into the gb slightly before entering with the body of the cell. As DfosDN macrophages have a delay in entry, the stills from the DfosDN movie are from a later developmental time point than the control. (C) Quantification of macrophage maximum length and maximum width shows that DfosDN expressing macrophages are 23% longer and 12% thinner than wild-type macrophages inside the gb (indicated in schematic above by dashed box). Control vs. DfosDN maximum length p = 0.0005, SD: 3.4, 5.7; control vs. DfosDN maximum width p = 0.0025, SD: 1.3, 1.0. (D) Quantification of the maximum length and maximum width of macrophages in the pre-gb zone (indicated in schematic by dashed box) shows that macrophages expressing DfosDN are 9% shorter and 9% thinner than wild-type macrophages. Control vs. DfosDN maximum length p = 0.0095, SD: 2.2, 2.0; control vs. DfosDN maximum width p = 0.005, SD: 2.3, 1.9. (E) Overexpression of UAS-Lam in macrophages through srpHemo-Gal4 (mac>) causes no change in their number in the gb compared to the control. p = 0.65, SD: 15, 18. Histograms show mean \u00b1 SEM ***p < 0.005, **p < 0.01, *p < 0.05. Unpaired t test was used for statistics of quantification. The number of measurements per genotype is shown in each columns. The data underlying the graphs can be found in (A) Representative image showing actin protrusions of the first macrophage entering the gb in the control and in lines expressing DfosDN in macrophages. Actin was visualized by (TIF)Click here for additional data file.S6 FigProposed interactions of proteins at the cell cortex in wild-type macrophages during gb infiltration as shown in (TIF)Click here for additional data file.S1 MoviesrpHemo-H2A::3xmCherry are imaged while entering the gb in control embryos (left) and embryos in which macrophages express DfosDN (right). Time in minutes is indicated in the upper right corner. Scale bar: 10 \u03bcm. DfosDN, dominant negative version of Dfos; DN, dominant negative; gb, germband.Movies corresponding to stills shown in (AVI)Click here for additional data file.S2 MoviesrpHemo-Gal4 driving UAS-GFP::nls are imaged during their migration along the segments of the vnc in control embryos (left) and embryos in which DfosDN is expressed in macrophages (right). Time in minutes is indicated in the upper right corner. Scale bar: 10 \u03bcm. DfosDN, dominant negative version of Dfos; vnc, ventral nerve cord.Movies corresponding to stills shown in (AVI)Click here for additional data file.S3 MoviesrpHemo-Gal4 driving UAS-GFP::nls are imaged while entering the gb in control embryos (left) and 2Dfos mutant embryos (right). Time is indicated in minutes. Scale bar: 10 \u03bcm. gb, germband.Movies corresponding to stills shown in (AVI)Click here for additional data file.S4 MoviesrpHemo-Gal4 driving UAS-LifeAct::GFP is imaged during gb entry in control embryos (left) and embryos with macrophages expressing DfosDN (right). Note the extended protrusion of the DfosDN expressing macrophages. Time is indicated in minutes. Scale bar: 10 \u03bcm. DfosDN, dominant negative version of Dfos; gb, germband.Movies corresponding to stills shown in (AVI)Click here for additional data file.S5 MoviesrpHemo-Gal4 driving UAS-CLIP::GFP. They are imaged during gb entry in control embryos (left) and embryos with macrophages expressing DfosDN (right). Note the extended shape of the DfosDN expressing macrophages. Time is indicated in minutes. Scale bar: 10 \u03bcm. DfosDN, dominant negative version of Dfos; gb, germband.Movies corresponding to stills shown in (AVI)Click here for additional data file."} +{"text": "Amycolatopsis sp. CA-230715, a potentially interesting producer of natural products. The genome of CA-230715 was sequenced using PacBio, Illumina, and Nanopore technologies. It consists of a circular 10,363,158-nucleotide (nt) chromosome and a circular 12,080-nt plasmid.We report the sequencing, assembly, and annotation of the genome of Amycolatopsis is a recognized source of secondary metabolites . The original colony was isolated from a serial dilution of a soil suspension plated onto HANOB medium after incubation for 5\u2009weeks at 28\u00b0C/70% relative humidity. For DNA isolation, the strain was grown in liquid yeast extract-malt extract (YEME) medium . Subread generation and adapter removal were performed using SMRT Analysis v2.3 software. A KAPA HyperPlus library was sequenced on an Illumina MiSeq instrument , yielding 4,477,879 read clusters (2\u2009\u00d7\u2009150\u2009nt), totaling 1,273,625,221\u2009nt. Nanopore data were generated on a MinION device using the SQK-RBK004 kit and a FLO-MIN106D R9.4 Rev-D flow cell . Default software parameters were used except where otherwise noted. The Illumina reads were adapter and quality trimmed using AdapterRemoval2 v2.1.7 similarity to Amycolatopsis nigrescens CSC17Ta-90, and GTDB-tk v1.5.1, R202 , SRR12367305 (PacBio), and SRR12367307 (Nanopore). The GenBank accession numbers are CP059997.1 (chromosome) and CP059998.1 (plasmid).All data are available under BioProject accession number"} +{"text": "Legionella pneumophila secretes toxins into the host cell that induce the non-canonical processing and activation of the ER stress sensor and transcription factor ATF6 via a mechanism that is distinct from the canonical pathway activated by unfolded protein buildup. Legionella pneumophila (L.p.) secretes \u223c330 effector proteins into the host cell to sculpt an ER-derived replicative niche. We previously reported five L.p. effectors that inhibit IRE1, a key sensor of the homeostatic unfolded protein response (UPR) pathway. In this study, we discovered a subset of L.p. toxins that selectively activate the UPR sensor ATF6, resulting in its cleavage, nuclear translocation, and target gene transcription. In a deviation from the conventional model, this L.p.\u2013dependent activation of ATF6 does not require its transport to the Golgi or its cleavage by the S1P/S2P proteases. We believe that our findings highlight the unique regulatory control that L.p. exerts upon the three UPR sensors and expand the repertoire of bacterial proteins that selectively perturb host homeostatic pathways.The intracellular bacterial pathogen Legionella pneumophila (L.p.), expertly manipulate host cell function to create their replicative niche. L.p. uses the specialized Dot/Icm Type IVB secretion system (T4SS) to translocate roughly 300 bacterial effector proteins into the host cytosol with the host endosomal machinery. Instead these effectors facilitate the remodeling of the LCV into a compartment that supports pathogen replication to allow for the antibody-mediated opsonization of L.p. Surprisingly, and in contrast to DTT treatment, infecting these cells with wild type L.p. (WT L.p.) resulted in the near complete processing of endogenous ATF6-FL into two distinct fragments\u2014a major fragment of \u223c75 kD that we designate as ATF6-P did not affect ATF6-FL protein levels is processed upon cleavage into an \u223c55 kD N-terminal fragment (ATF6-N) that translocates to the nucleus and activates transcription . Both threatment . ImportaL.p. infection has been shown to influence the IRE-1 branch of the UPR . HEK293-Fc\u03b3R cells were pre-treated for 3 h with the proteasome inhibitor MG-132 or control media. ER stress induction using DTT led to rapid ATF6 processing after 1 h, whereas prolonged exposure to DTT for 3 h resulted in recovery of ATF6 signal due to autoregulatory feedback from UPR induction . In contnfection . When cet impact . Previout impact . It was epletion . To testwith CHX . Similared cells . Howevercontrols . As L.p.ynthesis , we consynthesis . Consist WT L.p. . Taken tL.p. induced ATF6-FL processing into the ATF6-P (\u223c75 kD) and ATF6-LMW (\u223c30 kD) fragments affected its distal function as a nuclear transcription factor. To address this question, we used the N-terminal tagged GFP fusion protein of ATF6-FL (GFP-ATF6-FL) domain, whereas GFP-ATF6 1-331, GFP-ATF6 1-343, and GFP-ATF6 1-355 possessed partial bZIP domains (WT L.p. (WT L.p. but not \u0394dotA L.p. (WT L.p. migrated on a reducing SDS\u2013PAGE gel in a manner similar to the GFP-ATF6 1-331 truncation mutant (L.p. 5 h lane at high exposure). Significantly, an in vitro transcription and translation product of the DNA encoding the ATF6 1-331 protein migrated as a sharp band at a MW of \u223c30 kD on a reducing SDS\u2013PAGE and was detected by an antibody raised against ATF6 (Chen etATF6-FL) . During ATF6-FL) Indeed, ATF6-FL) . After 1ATF6-FL) . We thene JF-644 . Analyseme point . Strikinreatment . These r domains . We coll and GalT-RFP (red) and stained with Hoechst solution (blue). DTT was added to cells at t = 0. Still frame images were taken every 5 min over 2 h 30 min. Video 2Halo-tag WT-L.p. Infected cells were imaged directly after spin-fection with no more than 30 min elapsed time between centrifugation and image acquisition at t = 0. Still frame images were taken every 10 min over 12 h. Download videoTime-lapse wide-field microscopy movie of HeLa-Fc\u03b3RII cells expressing GFP-ATF6 (green) and stained with Hoechst solution (blue). Cells were infected with JF-646 stained L.p. infection, we monitored the mRNA levels of ATF6 target genes by quantitative real time PCR (qRT-PCR), including UPR regulator/ER chaperone BiP (HSPA5), in HEK293-Fc\u03b3R cells. As expected, UPR induction with DTT increased expression of ER quality control genes BiP and HERPUD1 by greater than fivefold in comparison to control (DMSO-treated) cells cells . Interespression . To gainreatment . When thL.p. infection was dependent on the ATF6-LMW. As the ATF6-LMW resembled the sequence architecture of the ATF6 1-331 mutant protein .We then undertook two orthogonal approaches to determine if the transcriptional program induced during tein see , we firstein see Fig 3D)L.p. infe3T cells . To compficiency . Indeed,L.p. demonstrate the activation of the ATF6 pathway during L.p. infection.In sum, the gene expression changes in concomitance with ATF6 processing induced by L.p. infection, ATF6-FL is processed into a ATF6-P fragment and a ATF6-LMW fragment that retains transcriptional activity During activity and 3A\u2013Epparatus . It is wpathways . Howeverhe Golgi . Treatmehe Golgi and S3A,A levels and S3B.A levels and S3A pression and S3B.93 cells , along wmRNA see . In macrragments . Yet sur and on both the ATF6 S1P and S2P cleavage sites that have both overlapping and distinct specificities. Pre-treatment of cells with this protease inhibitor cocktail did not affect the loss of ATF6-FL activated by WT L.p. , Legionella wadsworthii (L. wad), and Legionella longbeachae (L. lon)\u2014were tested in addition to L. pneumophila strains\u2014Philadelphia str. (WT L.p. Phila or \u0394dotA L.p. Phila), Paris str. (L.p. Paris), Lens str. (L.p. Lens), and Serogroup 6 str. (L.p. SG6). The Legionella species and strains were used to infect HEK293-Fc\u03b3R and RAW264.7 macrophage cells and endogenous ATF6-FL levels were monitored by immunoblotting. Whereas most of the species and strains tested recapitulated the loss of ATF6-FL as seen with wild type L.p. (see above), infecting cells with either L. wadsworthii or the L. pneumophila Paris str. did not result in an efficient processing of ATF6-FL L.p. PhilL.p. effectors lpg0519 and lpg2131 for further characterization. We generated GFP tagged fusion constructs of lpg0159 and lpg2131 and transiently expressed them in U2OS and HEK293 Fc\u03b3R cells. Unfortunately, the ectopic expression of tagged Lpg2131 in cells resulted in toxicity and confounded our interpretation of the results obtained (data not shown). We thus excluded this effector from further analyses. In contrast, GFP-Lpg0519, when expressed in U2OS cells, was relatively non-toxic and localized to the ER as observed by colocalization with the ER marker mCherry-KDEL ATF6-FL is processed into two fragments, a higher MW ATF6-P fragment (\u223c75 kD) and a lower MW ATF6-LMW fragment (\u223c30 kD) . Analysi(\u223c30 kD) and 2. I(\u223c30 kD) and S2B;(\u223c30 kD) ; and (3) fashion . These fL.p. infected cells that activates the ERSE reporter in cells that presumably evolved from the same species of L. pneumophila process ATF6 differently in their mammalian hosts due to a small but significant divergence in their effector repertoires Lpg0519 folds and functions as an atypical protease; or (b) Lpg0519 promotes the activity of an ER localized host protease. In either scenario, the answers to these questions using molecular tools derived from L. pneumophila, will enhance our understanding of ATF6 regulation in physiology and pathology.The primary targets of the amoebae . It is wan hosts . Examplean hosts . In this enzymes . Homologertoires . One of o the ER . Bioinfoo the ER , did not-FL loss . This suLegionella strains were gifts from Craig Roy\u2019s laboratory at Yale University. Legionella strains used in this study were routinely cultivated on Charcoal Yeast Extract agar. The \u0394dotA, \u0394sidC-sdcA, and IPTG-inducible Halo-expressing strains were derived from the parental Lp01 strain. The \u03942,3,4,6,7, \u03942,3,6,7, and \u03942,3,6 L.p. strains (7-translation L. pneumophila strain (L. pneumophila serogroup 1 Lp02 (L. pneumophila Paris B1 strain was purchased from ATCC (ATCC 700833). Chloramphenicol (10 \u03bcg/ml), IPTG (0.1 mM), and thymidine (100 \u03bcg/ml) were added to Charcoal Yeast Extract agar plates as needed. L.p. were harvested from 2-d heavy patches and used to infect cells.All strains , and thea strain was a gip 1 Lp02 . L. pneulpg0519 was amplified from L.p. (Lp01) genomic DNA and cloned into the pEGFP-C2 vector.GFP-ATF6, HA-ATF6, and HA-ATF6 1\u2013373 were kind gifts from Ron Prywes . The GFP-ATF6 truncation mutants were cloned from the GFP-ATF6 backbone and generated by Genscript Inc. For in vitro transcription and translation, the ATF6 1\u2013331 fragment was sub-cloned between HindIII and SalI sites on the pGEM3Z vector carrying an SP6 promoter. GFP-ATF6 S1P mutant and GFP-ATF6 S1P/S2P mutant constructs were generated by site directed mutagenesis using the Q5 Site-Directed Mutagenesis Kit (NEB). For the effector screen, Myc-tagged effector proteins were amplified from a plasmid effector library that was a kind gift from Russell Vance, University of California, Berkeley. To generate N-terminal GFP tagged Lpg0519, 2. RAW264.7 macrophages were cultured in Roswell Park Memorial Institute media (RPMI) (Corning) supplemented with 10% FBS at 37\u00b0C and 5% CO2. Cells were placed in poly-L-lysine\u2013treated plates and grown to 90% confluency. Drug treatments were performed at final concentration, 200 nM Tg (Enzo Life Sciences), 1 mM DTT , protease inhibitor cocktail (100 \u03bcM 4-(2-aminoethyl)benzenesulfonyl fluoride [AEBSF] [Sigma-Aldrich], 10 \u03bcM Tosyl phenylalanyl chloromethyl ketone [TPCK] [Sigma-Aldrich], 10 \u03bcM Calpain Inhibitor I [Sigma-Aldrich], 10 \u03bcM E 64 Protease inhibitor [EMD Millipore], 100 \u03bcM phenylmethylsulfonyl fluoride [PMSF] [Sigma-Aldrich]), 5 nM Bafilomycin A1 (Sigma-Aldrich), 1 \u03bcM PF-429242 (Sigma-Aldrich), 5 \u03bcM/20 \u03bcM MG-132 (Enzo Life Sciences), 25 \u03bcM Cycloheximide (Sigma-Aldrich), 10 \u03bcM Ceapin A7 supplemented with 10% FBS at 37\u00b0C and 5% COeapin A7 . Ceapin-For transient transfections, cells were grown to 70% confluency and transfected with 2 \u03bcg of plasmid for 60 and 35 mm dishes, or 1 \u03bcg per well for 24-well plates using JetPRIME (Polyplus-transfection) according to the manufacturer\u2019s instructions. Cells were incubated with transfection reagent for 4 h, then media replaced with fresh DMEM supplemented with 10% FBS. For siRNA transfections, cells were grown to 30\u201350% confluency and transfected using Oligofectamine (Thermo Fisher Scientific) according to the manufactures protocol. Cells were grown for 72 h before application of treatment conditions. The following siRNA oligos used were purchased from Sigma-Aldrich: SEL1L-TTAACTTGAACTCCTCTCCCATAGA, Scramble-GCATACTCAACTACTTCGCATACTT; ATF6- GAACAGGGCTCAAATTCTC, Scramble-GCTAGTGCACAAGTACCTA.Legionella polyclonal antibody was used at 1:2,000 and incubated for 20 min at room temperature. Immediately after infection, cells were centrifuged for 5 min at 100g. After centrifugation, cells were left at 37\u00b0C for an additional 60 min. After 1 hour, cells were washed with 1\u00d7 PBS to remove extracellular bacteria. DMEM supplemented with 10% FBS or the same media supplemented with treatment reagent was replaced after the washes in PBS. Infected cells were harvested at the designated times.Cells were infected at a MOI of 100, 50, 25 or 5. If cells required opsonization, BiP (Human) forward- CATCACGCCGTCCTATGTCG, reverse- CGTCAAAGACCGTGTTCTCG; HERPUD1 (Human) forward- AACGGCATGTTTTGCATCTG, reverse- GGGGAAGAAAGGTTCCGAAG; SEL1L (Human) forward- AAACCAGCTTTGACCGCCAT, reverse- GTCATAGGTTGTAGCACACCAC; HYOU1 (Human) forward- GAGGAGGCGAGTCTGTTGG, reverse- GCACTCCAGGTTTGACAATGG; ATF6 (Human) forward- AGAGAAGCCTGTCACTGGTC, reverse- TAATCGACTGCTGCTTTGCC; DNAJB11 (human) forward- AACCTGAGCACCTTTTGCCT, reverse- GGTTCCGGTCGGGATGAAG, BiP (mouse) forward- ACTTGGGGACCACCTATTCCT, reverse- GTTGCCCTGATCGTTGGCTA; Dnajb11 (mouse) forward- TTGGAGGAACCCCTCGTCA, reverse- CTCTTGCCGACAGTTGCATTT; Hsp90B1 (mouse) forward- GTTCGTCAGAGCTGATGATGAA, reverse- GCGTTTAACCCATCCAACTGAAT; Atf6 (mouse) forward- TCGCCTTTTAGTCCGGTTCTT, reverse- GGCTCCATAGGTCTGACTCC; Actin (mouse) forward- GGCTGTATTCCCCTCCATCG, reverse- CCAGTTGGTAACAATGCCATGT.HEK-293 FC\u03b3 cell mRNA was harvested and isolated using Direct-zol RNA Miniprep Plus (Zymo Research) according to the manufacturer\u2019s protocol. cDNA synthesis was performed using QuantiTect Reverse Transcription Kit (QIAGEN) and cDNA reactions were primed with poly dT. Relative quantitative PCR was performed using iTaq Universal SYBR Green Supermix (Bio-Rad). GAPDH or HPRT mRNA (for human cells) or Actin mRNA (for RAW264.7) was used for normalization. Uninfected and untreated HEK-293 FC\u03b3RII and RAW264.7 macrophage cells were used as the endogenous control for each qRT-PCR analysis. The following qRT-PCR primers were used: Mammalian cells were lysed in radioimmunoprecipitation assay buffer (RIPA) buffer with the addition of protease (Roche cOmplete), and phosphatase inhibitors (GB Sciences). Protein levels of lysates were determined using the Bio-Rad DC/RC assay. Equal amounts of protein lysate were boiled with SDS load buffer, and equal amounts of protein were loaded. Immunoblotting was performed with the following antibodies: GAPDH , ATF6 rabbit polyclonal , ATF6 mouse monoclonal , \u03b2-Actin , \u03b1-Tubulin , SEL1L , ABCD3 , GFP tag , BiP , ATF4 .L.p. as needed. For ubiquitin recruitment assays, HEK293 Fc\u03b3R cells were infected with L.p. at MOI = 5. 1 h after infection, cells were washed twice with PBS to remove extracellular bacteria and incubated for 2 h more. For co-localization assays, Cos7 cells were co-transfected with pcDNA-Fc\u03b3RII and GFP-ATF6\u03b1, then infected with L.p. at MOI = 10 and infected for 1, 4, or 8 h. For 4- and 8-h time points, cells were washed with PBS after 1 h to remove extracellular bacteria. Coverslips were mounted with ProLong Diamond Antifade Mountant (Thermo Fisher Scientific) incubated at 37\u00b0C for 10 min, then imaged directly. For immunofluorescence, coverslips were washed with cold 1\u00d7 PBS, fixed with 4% paraformaldehyde in PBS for 10 min at room temperature, permeabilized in 0.1% saponin in PBS, and blocked in 3% BSA in PBS, and then incubated with the appropriate primary and secondary antibodies diluted in 3% BSA. Nuclei were stained with Hoechst 33342 dye for 10 min before mounting on microscope slides. Coverslips were imaged using an inverted Nikon Eclipse Ti-E spinning disk confocal microscope equipped with a Prime 95B 25mm CMOS camera (Photometrics) camera. Antibodies used were Ubiquitin , and Secondary Antibody, Alexa Fluor 546 or Alexa Fluor 488 (Thermo Fisher Scientific).Cells were plated on 12 mm glass coverslips in 24-well plates. After 24 h, cells were fixed, treated with drugs, or infected with WT- or \u0394dotA L.p. that were previously stained with HaloTag-Janelia Fluor 646 conjugates to facilitate HaloTag-JF646 conjugation. After 15 min incubation with ligand in the dark, L. pneumophila were washed 1\u00d7 with water. Stained bacteria were resuspended in 2 ml of DMEM lacking phenol red (Gibco) and used for infection of cells. Imaging of cells took place in a controlled chamber maintaining 37\u00b0C with 5% CO2. A random selection of cells was imaged at 60\u00d7 magnification at 5- or 10-min intervals for 12 h using a Nikon Eclipse Ti2 microscope with a Nikon DS-Qi2 camera. Cells that died or lost focus over the time course were omitted from analysis.HeLa Fc\u03b3RII cells expressing GFP-ATF6 were plated on 35 mm poly-lysine\u2013coated imaging dishes (Cellvis). Cells were infected at MOI = 5 with njugates . For staIn vitro transcription and translation of luciferase and the ATF6 1\u2013331 fragment were performed using the TnT coupled Reticulocyte Lysate Systems kit from Promega. Briefly, 1 \u03bcg of DNA encoding for luciferase or the ATF6 1\u2013331 fragment downstream of an SP6 promoter were incubated with TnT reaction buffer, RNA polymerase, amino acids, RNAsin ribonuclease inhibitor (Promega), Magnesium actetate (0.25 mM) and rabbit reticulocyte lysate as a source of ribosomes and translation machinery in a test tube at 30\u00b0C for 90 min. 20% of the total reaction mixture was then boiled with Lammeli buffer and run on a 4\u201315% reducing SDS\u2013PAGE gel before immunoblotting with an ATF6 antibody .Legionella effectors as previously described (2 with 1 s exposure. Background signal was subtracted from untreated untransfected cells. Treatment conditions were normalized to control cells and represented as fold change in relative luminiscence.ONE-Glo Luciferase assay system was purchased from Promega. HEK-293T ERSE-Luciferase cells, provided as a gift from the Peter Walter laboratory at UC San Francisco and described previously , were seescribed for 24 ht test was performed using three biological replicates. Statistical significance: *P-value < 0.05; **P-value<0.01, ***P-value <0.001. Image analysis was performed using ImageJ.GraphPad Prism 6 software was used for statistical analysis. Where statistical analysis was performed an unpaired"} +{"text": "Rumex madaio Makino. The bacteriostatic rate of the extract was 75% against 23 species of common pathogenic bacteria. The extract was further purified using the preparative high-performance liquid chromatography (Prep-HPLC) technique, and five separated componential complexes (CC) were obtained. Among these, the CC 1 significantly increased cell surface hydrophobicity and membrane permeability and decreased membrane fluidity, which damaged cell structure integrity of Gram-positive and -negative pathogens tested. A total of 58 different compounds in the extract were identified using ultra-HPLC and mass spectrometry (UHPLC-MS) techniques. Comparative transcriptomic analyses revealed a number of differentially expressed genes and various changed metabolic pathways mediated by the CC1 action, such as down-regulated carbohydrate transport and/or utilization and energy metabolism in four pathogenic strains tested. Overall, the results in this study demonstrated that the CC1 from R. madaio Makino are promising candidates for antibacterial medicine and human health care products.Outbreaks and prevalence of infectious diseases worldwide are some of the major contributors to morbidity and morbidity in humans. Pharmacophageous plants are the best source for searching antibacterial compounds with low toxicity to humans. In this study, we identified, for the first time, antibacterial components and action modes of methanol-phase extract from such one edible herbaceous plant R. madaio Makino is an edible, perennial and herbaceous plant that belongs to the Dicotyledoneae class, Polygonaceae family, and Rumex genus. According to the National Compilation of Chinese Herbal Medicine (1996 Edition), leaf and root tissues of R. madaio Makino can be used as medicine such as clearing heat and detoxification, removing blood stasis, and defecating and killing insects. Nevertheless, current studies on the antibacterial activity of R. madaio Makino are rare.China is one of the richest countries in biodiversity, with very high levels of plant endemism . PharmacR. madaio Makino were for the first time identified. The objectives of this study were: (1) to extract bioactive substances from R. madaio Makino using the methanol and chloroform extraction (MCE) method, and determine their inhibition activity against 23 species of pathogenic bacteria; (2) to purify the methanol-phase extract from R. madaio Makino by preparation high-performance liquid chromatography (Prep-HPLC) analysis, and identify bioactive compounds in componential complex 1 (CC 1) using an ultra-HPLC and mass spectrometry (UHPLC-MS) technique; (3) to determine cell surface hydrophobicity, cell membrane permeability, fluidity, and the damage of four representative pathogenic strains treated with the CC 1; (4) to decipher possible molecular mechanisms underlying antibacterial activity by comparative transcriptomic analysis. The results of this study meet the increasing need for novel antibacterial agent candidates against common pathogenic bacteria.In this study, antibacterial components and action modes of methanol-phase extract from R. madaio Makino were extracted using the MCE method. The results showed that the water loss rate of the plant material was 93.32%, and extraction rates of the methanol phase and chloroform phase were 32.10% and 29.60%, respectively. Antibacterial activity of the crude extracts against 23 species of pathogenic bacteria was determined, most of which are common foodborne pathogens, and the results are presented in R. madaio Makino showed a bacteriostatic rate of 39%, inhibiting 2 species of Gram-positive and 11 species of Gram-negative pathogens showed weak or no antibacterial activity, indicating that bioactive compounds in the methanol-phase extract from V. alginolyticus ATCC17749 and V. parahaemolyticus ATCC17802; 128 \u03bcg/mL against B. cereus A1-1; and 256 \u03bcg/mL against V. parahaemolyticus B4-10.MIC values of the CC 1 were also determined, which was 64 \u03bcg/mL against B. cereus A1-1, the 2 h treatment by the CC 1 resulted in the bacterial cell surface shrinking seriously, the flagella breaking, and some contents leaking. After being treated for 4 h, cell surface shrinkage was intensified, and more cells were ruptured. After being treated for 6 h, the cell structure was seriously damaged, a large number of contents exuded, and only a few cells still maintained rod shape analysis. As shown in od shape A. For th for 6 h C. These p < 0.05) when compared with the control groups (V. parahaemolyticus ATCC17802 (1.47-fold), V. parahaemolyticus B4-10 (1.62-fold) and B. cereus A1-1 (1.42-fold) after being treated with the CC1 for 2 h (p < 0.05), whereas a similar change was observed in the treatment group of V. alginolyticus ATCC17749 (1.48-fold) after being treated for 4 h. Moreover, the highest increase in cell surface hydrophobicity was observed in B. cereus A1-1 (3.75-fold) after being treated with the CC1 for 6 h . However, a significant decrease in membrane fluidity of these three strains was observed after the treatment for 4 h. Additionally, cell membrane fluidity significantly declined in B. cereus A1-1 (1.20-fold) treated with the CC 1 for 2 h, and sharply lost for 6 h (8.11-fold) B. The chd-galactopyranoside (o-nitrophenyl)-\u03b2-d-galactopyranoside (ONPG) was used as a probe to monitor the inner cell membrane permeability of the four bacterial strains, and the results were illustrated in R. madaio Makino on inner cell membrane permeability was observed among the four treatment groups. For example, V. alginolyticus ATCC17749 did not change significantly in the inner cell membrane permeability after the treatment for 2 h (p > 0.05), whereas a significant increase was observed after being treated for 4 h (1.15-fold) and 6 h (1.18-fold), respectively (p < 0.05) (The o-nitrophenyl-\u03b2- < 0.05) .N-Phenyl-1-naphthylamine (NPN) was used as a probe to monitor the bacterial outer membrane permeability. As shown in p < 0.01). The highest increase was found in B. cereus A1-1 (6.06-fold) after being treated for 6 h, whereas an opposite pattern was observed in V. parahaemolyticus ATCC17802 (1.77-fold).p < 0.05), which raised with the increase in treatment time. Significant damage was observed in B. cereus A1-1 (2.95-fold) and V. parahaemolyticus B4-10 (2.21-fold) after being treated for 2 h, whereas a similar change was found in the other two strains treated for 4 h. Moreover, cell membrane damage of B. cereus A1-1 was the most severe among the four strains after being treated for 6 h (8.54-fold).As shown in R. madaio Makino significantly increased bacterial cell surface hydrophobicity and membrane permeability and decreased membrane fluidity of V. parahaemolyticus ATCC17802, V. parahaemolyticus B4-10, V. alginolyticus ATCC17749, and B. cereus A1-1, consistent with the observed bacterial surface structure by the TEM analysis. The damaged cell surface and membrane structure integrity were beneficial for the CC1 to penetrate bacterial cell envelope to target intracellular processes.Taken together, these results demonstrated that the CC 1 from 2O was subjected to UHPLC-MS analysis. As shown in R. madaio Makino.The obtained CC 1 resolved in HR. madaio Makino, we determined transcriptomes of the four bacterial strains treated for 6 h using Illumina RNA sequencing technology. A complete list of DEGs in the four strains was available in the NCBI SRA database under the accession number PRJNA767551. To validate the transcriptome data, we examined 32 representative DEGs , and 78 genes were down-regulated (FC \u2264 0.5). Based on the comparative transcriptomic analyses, 11 significantly changed metabolic pathways were identified, including valine, leucine and isoleucine degradation; nitrogen, histidine, tryptophan, glyoxylate and dicarboxylate metabolisms; quorum sensing (QS); lysine degradation; fatty acid degradation; amino sugar and nucleotide sugar metabolism; ABC transporters; and mitogen-activated protein kinase (MAPK) signal pathway (Approximately 6.73% (316/4698) of pathway .V. alginolyticus ATCC17749 (2.002- to 87.807-fold) (p < 0.05) (p < 0.05); six DEGs encoding key enzymes in the histidine metabolism were also significantly up-regulated (2.001- to 3.187-fold) (p < 0.05); similarly, in the tryptophan metabolism, expression of three DEGs were significantly enhanced (2.123- to 5.154-fold) (p < 0.05); additionally, in the lysine degradation, expression of a transcriptional regulator (N646_3623) and an arginine/lysine/ornithine decarboxylase (N646_1979) were significantly up-regulated (2.972- to 3.332-fold) (p < 0.05). These four pathways are related to amino acid degradation metabolisms.Remarkably, approximately 60 DEGs involved in 10 changed metabolic pathways were significantly up-regulated in < 0.05) . For exap < 0.05), in which, specifically, one DEG encoding a hydroxylamine reductase (N646_0236) was greatly enhanced to express (87.807-fold).Meanwhile, eight DEGs in the nitrogen metabolism were also significantly up-regulated (2.193- to 87.807-fold) (p < 0.05) . ABC trap < 0.05) ( < 0.05) , which lV. parahaemolyticus ATCC17802 genes were expressed differently in the experimental group compared with the control group. Among these, 128 genes showed higher transcription levels (FC \u2265 2.0), and 789 genes were down-regulated (FC \u2264 0.5). Comparative transcriptome analyses revealed 20 significantly changed metabolic pathways, including methane, nitrogen, glycerolipid, propanoate, sulfur, starch and sucrose, taurine and hypotaurine, phosphonate and phosphinate, and biotin metabolisms; glucagon, and hypoxia inducible factor-1 (HIF-1) signaling pathway; benzoate and ethylbenzene degradation; glycolysis/gluconeogenesis; flagellar assembly; apoptosis; bacterial chemotaxis; cationic antimicrobial peptide (CAMP) resistance; necroptosis, and RNA transport of ransport .p < 0.05) (VP_RS18295), the other seven DEGs were significantly down-regulation (0.087- to 0.433-fold) (p < 0.05); in the propanoate metabolic pathway, express of four DEGs were significantly depressed (0.051- to 0.240-fold) (p < 0.05); in the starch and sucrose metabolisms, except for a 4-alpha-glucono transfer (VP_RS22910), the other five DEGs were significantly down-regulated (0.206- to 0.499-fold) (p < 0.05). These three metabolic pathways were related to carbohydrate metabolisms. Their overall down-regulation trend indicated inactive carbon source transportation and/or utilization, which likely resulted in insufficient energy supply.Notably, approximately 77 DEGs involved in 12 changed metabolic pathways were significantly down-regulated (0.05- to 0.491-fold) ( < 0.05) . For exaV. parahaemolyticus ATCC17802 were also significantly inhibited (p < 0.05). For example, the DEG encoding a pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase (VP_RS12210) was significantly down-regulated (0.331-fold), which connects glycolysis with tricarboxylic acid cycle (TCA) and plays a key role in glucose metabolism [Approximately 44 DEGs involved in six energy metabolism pathways in tabolism . The dowtabolism , which cV. parahaemolyticus ATCC17802 (0.055- to 0.49-fold) (p < 0.05), which indicated the depressed flagellum assembly that led to inactive motility of V. parahaemolyticus ATCC17802. The 17 down-regulated DEGs in the bacterial chemotaxis [p < 0.05) provided indirect evidence for this result.The bacterial flagellum is a complex mobility machine with a diversity of roles in pathogenesis, including attachment, colonization, invasion, maintenance and post-infection dispersal in the host ,22. In temotaxis (0.101- p < 0.05). T3SS enables pathogenic bacteria to directly inject effector proteins into host cells, facilitating bacterial colonization in the host [V. parahaemolyticus ATCC17802 was significantly reduced after being treated with the CC 1 from R. madaio Makino.Interestingly, 23 DEGs encoding type III secretory system (T3SS) components were also significantly down-regulated (0.055- to 0.490 -fold) (the host . This reVP_RS00200), a thiol: disulfide interchange protein DsbA/DsbL (VP_RS21260), an ATP-binding cassette domain-containing protein (VP_RS05670), a multidrug efflux RND transporter periplasmic adaptor subunit VmeC (VP_RS00205), and a phosphoethanolamine-lipid A transferase (VP_RS21300) resistance system, five DEGs were significantly inhibited (0.120- to 0.489-fold), including a multidrug efflux RND transporter permease subunit VmeD (RS21300) . These rVP_RS14060) and an envelope stress sensor histidine kinase CpxA (VP_RS14065) , e.g., a response regulator (RS14065) .V. parahaemolyticus B4-10 genes were expressed differently in the experimental group when compared with the control group. Among these genes, 204 showed higher transcription levels (FC \u2265 2.0), and 579 genes were down-regulated (FC \u2264 0.5). Based on the comparative transcriptome analysis, five significantly changed metabolic pathways were identified, including styrene degradation, nitrogen metabolism, QS, folate biosynthesis, and histidine metabolism (Approximately 16.75% (783/4674) of tabolism .V. alginolyticus ATCC17749, the expression of 10 DEGs in the nitrogen metabolism were significantly up-regulated (2.129- to 107.754-fold) (p < 0.05) (VP_RS05780) was greatly up-regulated (107.754-fold). This enzyme can reduce hydroxylamine analogs such as methylhydroxylamine and hydroxyquinone as a scavenger of potentially toxic by-products of nitrate metabolism [V. parahaemolyticus B4-10 after being treated by the CC 1.Similar to < 0.05) . Notablytabolism . MoreoveB. cereus A1-1 genes were expressed differently in the experimental group. Among these genes, 178 showed higher transcription levels (FC \u2265 2.0), and 542 genes were down-regulated (FC \u2264 0.5). The comparative transcriptome analysis revealed 17 significantly changed metabolic pathways, including flagellar assembly; bacterial chemotaxis; two-component system (TCS); thiamine and nitrogen metabolisms; ABC transporters; arginine biosynthesis; fatty acid degradation; alanine, aspartate and glutamate metabolism; riboflavin metabolism; HIF-1 signaling pathway; glycolysis/gluconeogenesis; butanoate, pyrimidine, and propanoate metabolisms; benzoate degradation; and inositol phosphate metabolism (Approximately 12.57% (720/5730) of tabolism .B. cereus A1-1 (3.325- to 150.780-fold) (p < 0.05) (BCN_RS16540) was also greatly enhanced to express in B. cereus A1-1 (150.780-fold).Similar to the other bacterial strains tested, expression of 12 DEGs involved in the nitrogen metabolism and riboflavin metabolism were significantly up-regulated in < 0.05) . SpecifiB. cereus A1-1 (0.038- to 0.487-fold) (p < 0.05) (p < 0.05); 9 DEGs in bacterial chemotaxis were significantly down-regulated (0.063- to 0.474-fold); and expression of 33 DEGs in ABC transporters were significantly inhibited (0.051- to 0.487-fold).Conversely, 69 DEGs involved in the flagellar assembly, bacterial chemotaxis, ABC transporters, and TCS were significantly down-regulated at the transcription level in < 0.05) , similarBCN_RS24725) was also significantly down-regulated (0.191-fold). These results indicated the inhibited signal transduction systems in B. cereus A1-1.Approximately eight DEGs in the TCSs were significantly down-regulated. TCSs are widespread regulatory systems that can help bacteria to control their cellular functions and respond to a diverse range of stimuli . In thisp < 0.05) ( < 0.05) , which sVibrio strains were inoculated in media (pH 8.4\u20138.5) with 3.0% NaCl, while non-Vibrios in media (pH 7.0\u20137.2) with 1% NaCl [Bacterial strains and culture media used in this study are listed in 1% NaCl .R. madaio Makino was collected in Lishui City , Zhejiang Province, China in September of 2020. A 500 g of fresh leaf and stem tissues of R. madaio Makino was washed clean, dried at room temperature, and then freeze-dried using ALPHA 2-4 LD Plus Freeze Dryer at \u221280 \u00b0C for 48 h. The freeze-dried material was crushed using FW-135 High-Speed Crusher and passed through 300 mesh screen. Then, 10.0 g of the powder was mixed with 99-mL chloroform: methanol at a solid to liquid ratio of 1.10 (m/v) for 5 h [2O was then added, fully mixed, and then sonicated using Scientz IID ULtrasonic Cell Crusher at the following parameters: power: 300 W; ultrasonic on time: 1 s; ultrasonic off time: 1 s; working time: 20 min; and probe size: 6 mm. The sonicated mixture was filtered through 20\u201325 \u03bcm membrane , and the filtration was collected for the secondary extraction. The methanol phase was separated from the chloroform phase and then individually evaporated, concentrated on pasting using Rotary Evaporator . for 5 h . A 60 mLR. madaio Makino was determined according to the method issued by Clinical and Laboratory Standards Institute (CLSI) using Mueller-Hinton (M-H) agar (CM337) and Mueller-Hinton broth (M391) . Briefly, a 10 \u03bcL of crude extracts (500 \u03bcg/mL) was added onto each blank disc on MH ager plates. The gentamicin disc was used as a positive control, while the methanol-phase with water and chloroform-phase with ethanol was a negative control, respectively. The plates were incubated at 37 \u00b0C for 12 h. Bacteriostatic activity was evaluated by measuring diameters of bacteriostatic circles.Susceptibility of bacterial strains to the e6 colony-forming unit (CFU)/mL), and then incubated at 37 \u00b0C for 12 h [Broth dilution testing (microdilution) was used to determine MICs of the extracts. Briefly, a 100 \u03bcL/well of the extracts (1024 \u03bcg/mL) was serially diluted, mixed with 100 \u03bcL/well of Mueller-Hinton broth (CM337) and 10 \u03bcL/well of bacteria strain were centrifuged at 12,000 rpm for 20 min. The supernatant was filtered through 0.22 \u00b5m membrane , and the filtration was collected for further analysis. Prep-HPLC was run using Waters 2707 linked with UPLC Sunfire C18 column at the following parameters: column temperature, 40 \u00b0C; injection volume, 100 \u03bcL; and mobile phase of methanol (eluent A) and water (eluent B) at a flow rate of 4 mL/min . Photo-diode array (PDA) spectra were measured in the wavelength ranging from 200 to 600 nm.Aliquots (10 mg/mL) of freeze-dried samples resolved in H2O (v/v), and mobile phase B was acetonitrile ; column temperature: 40 \u00b0C; auto-sampler temperature: 4 \u00b0C; injection volume: 2 \u03bcL. Typical ion source parameters were: IonSpray voltage: +5500/\u22124500 V; curtain gas: 35 psi; temperature: 400 \u00b0C; ion source Gas 1:60 psi; ion source Gas 2: 60 psi; and declustering potential (DP): \u00b1100 V. The SCIEX Analyst Work Station Software (Version 1.6.3) was employed for multiple reaction monitoring (MRM) data acquisition and processing. In-house R program and database were applied for peak detection and annotation .The UHPLC\u2013MS analysis was carried out using EXIONLC System by Shanghai Hoogen Biotech, Shanghai, China using the parameters as described previously . The mobR. madaio Makino was added in bacterial culture (5 mL) at middle logarithmic growth phase (mid-LQP), and incubated at 37 \u00b0C for 2 h, 4 h and 6 h, respectively. A 1.5 mL of the cell suspension were collected, washed, fixed, and observed using SU5000 transmission electron microscope [Samples for TEM analysis were prepared according to the method described previously . Briefly\u00d730,000) .600 nm values of 0.55 to 0.60) and rotated for 1 min and then stood at room temperature for 30 min. The absorbance of the aqueous phase was measured at OD600 nm using BioTek Synergy 2 . To measure the membrane fluidity, a 200 \u03bcL/well of bacterial suspension was mixed with 2 \u03bcL of 10 mM 1,6-diphenyl-1,3,5-hexatriene (DPH) , and the change of fluorescence intensity of each well was measured at excitation light wavelength of 362 nm and emission light wavelength of 427 nm using BioTek Synergy 2 .Bacterial cell surface hydrophobicity and membrane fluidity were measured according to the methods by Krausova et al. and KuhrCell membrane damage was examined according to the method described previously . BrieflyR. madaio Makino and then incubated at 37 \u00b0C for 2 h, 4 h and 6 h. Outer membrane permeability was measured according to the method described previously [Bacterial culture at the mid-LGS was mixed with 1 \u00d7 MIC concentration of the CC 1 from eviously . Brieflyeviously .415 nm using BioTek Synergy 2 every 30 min for 5 h, which was marked as OD1, while OD2 generated from the untreated bacterial suspension was used as a negative control [Inner membrane permeability was measured according to the method described previously . Briefly control .R. madaio Makino for 6 h. Total RNA was prepared using RNeasy Protect Bacteria Mini Kit and QIAGEN RNeasy Mini Kit (QIAGEN). DNA was removed from the samples using RNase-Free DNase Set (QIAGEN). Three independently prepared RNA samples were used for each Illumina RNA-sequencing analysis. Illumina sequencing was conducted by Shanghai Majorbio Bio-pharm Technology Co. Ltd. using Illumina HiSeq 2500 platform . High quality reads that passed the Illumina quality filters were used for sequence analyses [Bacterial culture at the mid-LGP was treated with 1 \u00d7 MIC concentration of the CC 1 from analyses .\u2212\u0394\u0394Ct method was used to calculate relative expression of genes. Oligonucleotide primers used for the RT-qPCR were synthesized by Sangon, Shanghai, China.Total RNA extraction, reverse transcription reactions, and relative quantitative PCR reactions were performed using the same kits and instrument according to the method described previously . The 16Shttp://deweylab.github.io/RSEM/, accessed on 17 October 2021). Genes with the criteria, fold-changes \u2265 2.0 or \u22640.5, and p-values < 0.05 relative to the control were defined as DEGs. These DEGs were used for gene set enrichment analysis (GSEA) against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database . Significantly changed GSEA were identified when the enrichment test p-value fell below 0.05 [Expression of each gene was calculated using RNA-Seq by Expectation-Maximization . The methanol-phase extract was further purified using the Prep-HPLC technique, and five separated CCs were obtained. Among these, the CC 1 from R. madaio Makino significantly increased bacterial cell surface hydrophobicity and membrane permeability and decreased membrane fluidity of Gram-positive and Gram-negative pathogens, such as V. parahaemolyticus ATCC17802, V. parahaemolyticus B4-10, V. alginolyticus ATCC17749, and B. cereus A1-1. The damaged cell surface and membrane structure integrity facilitated the CC1 to penetrate bacterial cell envelope to target intracellular processes. A total of 58 different compounds in the extract were identified using UHPLC\u2013MS technique. Comparative transcriptomic analyses revealed a number of differentially expressed genes (DGEs) and various changed metabolic pathways mediated by the CC1 action, such as down-regulation of carbohydrate transport and/or utilization, and energy metabolism; upward regulation of amino acid and fatty acid degradation, and nitrogen metabolism; and inactive flagellar assembly and mobility in the four bacterial strains. Taken, the results in this study demonstrated that the CC1 from R. madaio Makino are promising candidates for antibacterial medicine and human health care products.In this study, we identified, for the first time, antibacterial components and action modes of methanol-phase extract from one edible herbaceous plant"} +{"text": "Frailty, a clinical syndrome characterized by vulnerability to stressors resulting from multisystemic loss of physiological reserve, predicts future cognitive decline. However, frailty has also been proposed as a dementia risk factor, predicting future cognitive impairment. The study aim was to determine frailty in older veterans and its association with risk of dementia. Community-dwelling Veterans \u226550 years completed a mailed socio-demographic questionnaire and Self-Administered Gerocognitive Examination (SAGE), July 2019-May 2020. The information was complemented with EHR data. We calculated the CAIDE score, a validated tool predicting dementia (\u22656 points= high risk 20 years later) and the 31-item VA frailty index data . After adjusting for socio-demographic characteristics, smoking, alcohol/substance abuse, OSA and anticholinergic use, odds ratio (OR) and 95% CI were calculated using BLR to assess the cross-sectional association between frailty and dementia risk (CAIDE \u22656 points and MCI). The survey response rate was 19.75% . Participants mean age was 68.38 (SD=8.49) years, 57.50% (n=617) Caucasian, 69.34% (n=744) non-Hispanic, 95.81% male, and 36.72% (n=394) frail. 11.84%(n=127) screened positive for MCI and 15.38% (n=165) for dementia. 689 (75.88%) veterans were at high risk for dementia of whom 426 (61.83%) were non-frail and 263 (38.17%) were frail. Frailty was cross-sectionally associated with higher risk for dementia in older Veterans, adjusted OR:1.45 (95%CI:1.016-2.070), p=.041. The mailed screening was a feasible and practical approach to screen for dementia risk. Early identification of patients with frailty can help in the implementation of interventions aimed at preventing or delaying dementia."} +{"text": "Excessive sedentary behavior (SB) is related to deleterious health outcomes. Understanding the patterns and contexts in which SB accumulates can promote healthy aging. Daily sitting time and mean sitting bout duration (MBD) were measured by triaxial accelerometers. Participants self-reported how much time they spent sitting while: watching TV, reading, using the computer, driving, working, or taking phone calls. Data were compared across aging-related characteristics. Age-adjusted sitting time (minutes/day) for 5,838 diverse , older women (mean age 78.7\u00b16.7) were 577.2 for Hispanic women, 630.3 for Black women, and 632.0 for White women. Those in the lowest vs. highest physical function category had the longest MBD (16.1 vs. 11.7 minutes/bout). Watching television was the most common self-reported sedentary activity. The highest vs. lowest quartile of MBD spent, on average, 30.6 and 22.3 minutes/day watching television, respectively. This presentation will illuminate critical factors associated with sitting patterns in older adults."} +{"text": "This study reports on the E. coli and 344 S. saprophyticus isolates were collected between 2019 and 2020 from 92 medical centers located in 25 countries. Most isolates (68%) tested were cultured from urine specimens collected from patients seen in ambulatory, emergency, family practice, and outpatient medical services. Bacterial identifications were confirmed by MALDI-TOF. Isolates were tested for susceptibility by CLSI methods at a central laboratory (JMI Laboratories). MIC results for oral antibiotics licensed for the treatment of uUTI and drug-resistant subsets were interpreted per CLSI guidelines. A total of 3,562 50/90, 2/2 mg/L) displayed good activity against 3,562 E. coli isolates, with 98.0% of all observed gepotidacin MICs \u22644 mg/L (Table). Susceptibility (S) rates for the other oral agents tested against these isolates were: amoxicillin-clavulanate (79.6% S), ampicillin (45.6% S), ciprofloxacin (72.5%S), fosfomycin (99.0% S), mecillinam (94.1%S), nitrofurantoin (97.3% S), and trimethoprim-sulfamethoxazole (68.2% S). When tested against the drug-resistant subsets, gepotidacin maintained similar MIC50/90 values (2/4 mg/L), except against isolates resistant to fosfomycin (2/8 mg/L). Against S. saprophyticus isolates, gepotidacin inhibited all isolates at \u22640.25 mg/L. Most oral agents showed S results of >97% against S. saprophyticus isolates, except for penicillin (3.5%S).Gepotidacin (Research Grant or Support)GlaxoSmithKline, LLC (Research Grant or Support)Melinta Therapeutics, LLC (Research Grant or Support)Nabriva Therapeutics (Research Grant or Support)Spero Therapeutics (Research Grant or Support) Deborah Butler, n/a, GlaxoSmithKline, LLC (Employee) Nicole Scangarella-Oman, MS, GlaxoSmithKline, LLC (Employee) Lindsey Paustian, BS (ASCP), GlaxoSmithKline, LLC (Research Grant or Support) Jennifer M. Streit, BS, GlaxoSmithKline, LLC (Research Grant or Support)Melinta Therapeutics, LLC (Research Grant or Support)Shionogi (Research Grant or Support)Spero Therapeutics (Research Grant or Support) Rodrigo E. Mendes, PhD, AbbVie (Research Grant or Support)AbbVie (formerly Allergan) (Research Grant or Support)Cipla Therapeutics (Research Grant or Support)Cipla USA Inc. (Research Grant or Support)ContraFect Corporation (Research Grant or Support)GlaxoSmithKline, LLC (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, LLC (Research Grant or Support)Nabriva Therapeutics (Research Grant or Support)Pfizer, Inc. (Research Grant or Support)Shionogi (Research Grant or Support)Spero Therapeutics (Research Grant or Support)"} +{"text": "Here, we describe BIOVERA-Tree, a database on tree diversity, community composition, forest structure and functional traits collected in 120 forest plots, distributed along an extensive elevational gradient in Veracruz State, Mexico. BIOVERA-Tree includes information on forest structure from three levels of forest-use intensity, namely old-growth, degraded and secondary forest, replicated across eight elevations from sea-level to near the tree line at 3500 m and on size and location of 4549 tree individuals with a diameter at breast height \u2265 5 cm belonging to 216 species, 154 genera and 80 families. We also report measurements of eight functional traits, namely wood density for 143 species, maximum height for 216 species and leaf traits including: specific leaf area, lamina density, leaf thickness, chlorophyll content and leaf area for 148 species and leaf dry matter content for 145 species.BIOVERA-Tree is a new database comprising data collected in a rigorous sampling design along forest-use intensity and elevational gradients, contributing to our understanding of how interactive effects of forest-use intensity and elevation affect tree diversity, community composition and functional traits in tropical forests. Mountains are fascinating ecosystems and natural laboratories for evolutionary and ecological research as they encompass a wide variety of different climatic conditions over short distances . MountaiLand-use change and intensification are occurring at rapid rates and are strongly impacting mountain ecosystems . For ins> 5 cm and tree height (metres) of 4548 and 4549 individuals, respectively. BIOVERA-Tree also includes functional traits for the common tree species, with data for wood density of 143 species calculated, based on 483 individuals, maximun height for 216 species calculated, based on 4549 individuals and leaf traits for 148 species, specific leaf area (n = 3148 leaves), lamina density (n = 3194 leaves), chlorophyll content (n = 3280 leaves), leaf area (n = 3214 leaves), leaf thickness (n = 3299) and leaf dry matter content for 145 species (n = 3081 leaves).BIOVERA-Tree originated from the interdisciplinary research project BIOVERA, which aims at documenting and understanding biodiversity patterns along gradients of altitude, climate, soil and disturbance along an elevational transect at the Cofre de Perote in central Veracruz, Mexico . BIOVERAThe study area is located along an elevational gradient from sea level close to the Gulf of Mexico to near the tree line at 3545 m on the eastern slopes of the Cofre de Perote volcano, in the central part of the State of Veracruz, Mexico Fig. . This reWe selected eight sites along the elevational gradient, separated by about 500 m in elevation Fig. . At each> 5 cm and identified individual trees to the highest taxonomic resolution possible. For each individual, we measured its DBH (in cm) and tree height (in m), which was measured with a Leica laser to close to the treeline at 3545 m elevation along the eastern slopes of Cofre de Perote volcano (4282 m) in Veracruz State, Mexico . Individuals were identified to the species level by specialists , while some individuals could only be identified to the family or genus level or could not be identified. Vouchers of specimens were deposited at the Herbarium XAL of Instituto de Ecolog\u00eda, A.C. at Xalapa, Mexico.Tree diversity and community compositionThe database contains information of 216 tree species Data package title BIOVERA-Tree: community, functional traits and forest structure along forest-use intensity and elevational gradients in Veracruz, Mexico.6BIOVERA-Tree forest plots description13Location of the 120 plots along the elevational gradient at the eastern slopes of Cofre de Perote in Veracruz, Mexico. Available as Suppl. material BIOVERA-Tree scientific name3List of tree species along the elevational gradient and different levels of forest-use intensity. Available as Suppl. material BIOVERA-Tree community matrix2Tree community matrix composition along eight elevational sites and three different forest-use intensity levels of 216 tree species (n = 5 plots per forest-use intensity within elevation). The numbers within the matrix are the number of individuals. Available as Suppl. material BIOVERA-Tree forest structure5> 5 cm and tree height (metres) for 216 species along the elevational gradient and different levels of forest-use intensity. Available as Suppl. material Diameter at breast height (DBH) BIOVERA-Tree functional traits7Plant functional traits measured along the elevational gradient and different levels of forest-use intensity; including leaf traits, wood density and maximum height. Available as Suppl. material BIOVERA Tree metadata3metadataDefinition and categories according with Darwin Core, Functional Diversity thesaurus and this research.https://doi.org/10.5061/dryad.ngf1vhhvb.The data underpinning the analysis reported in this paper are deposited in the Dryad Data Repository at 1BCEFC74-C760-5C41-BC74-77C909F237EB10.3897/BDJ.9.e69560.suppl1Supplementary material 1BIOVERA-Tree forest plots descriptionData typeLocation DataFile: oo_549009.csvhttps://binary.pensoft.net/file/549009Mar\u00eda Leticia Monge-Gonz\u00e1lez, Patrick Weigelt, Nathaly Guerrero-Ram\u00edrez, Dylan Craven, Gonzalo Castillo-Campos, Thorsten Kr\u00f6mer, Holger Kreft.297517E1-0C9F-5503-B9D1-6B484B74C9E710.3897/BDJ.9.e69560.suppl2Supplementary material 2BIOVERA-Tree scientific nameData typeTaxonomyFile: oo_549044.csvhttps://binary.pensoft.net/file/549044Mar\u00eda Leticia Monge-Gonz\u00e1lez, Patrick Weigelt, Nathaly Guerrero-Ram\u00edrez, Dylan Craven, Gonzalo Castillo-Campos, Thorsten Kr\u00f6mer, Holger Kreft.42D688AD-8284-53B7-8D58-28F37D03F2EF10.3897/BDJ.9.e69560.suppl3Supplementary material 3BIOVERA-Tree community matrixData typeSpecies community dataBrief descriptionTree community matrix with abundancesFile: oo_549021.csvhttps://binary.pensoft.net/file/549021Mar\u00eda Leticia Monge-Gonz\u00e1lez, Patrick Weigelt, Nathaly Guerrero-Ram\u00edrez, Dylan Craven, Gonzalo Castillo-Campos, Thorsten Kr\u00f6mer, Holger Kreft.1B6E2702-97B7-5634-BDC4-A09F03A3709210.3897/BDJ.9.e69560.suppl4Supplementary material 4BIOVERA-Tree forest structureData typeForest structure, DBH, tree heightFile: oo_549014.csvhttps://binary.pensoft.net/file/549014Mar\u00eda Leticia Monge-Gonz\u00e1lez, Patrick Weigelt, Nathaly Guerrero-Ram\u00edrez, Dylan Craven, Gonzalo Castillo-Campos, Thorsten Kr\u00f6mer, Holger Kreft.8880BA0C-CC51-5419-83D8-EA722FAC054510.3897/BDJ.9.e69560.suppl5Supplementary material 5BIOVERA-Tree functional traitsData typeFunctional trait dataFile: oo_549015.csvhttps://binary.pensoft.net/file/549015Mar\u00eda Leticia Monge-Gonz\u00e1lez, Patrick Weigelt, Nathaly Guerrero-Ram\u00edrez, Dylan Craven, Gonzalo Castillo-Campos, Thorsten Kr\u00f6mer, Holger Kreft.BB3E33BB-DDFE-53F9-976F-4676697DF15D10.3897/BDJ.9.e69560.suppl6Supplementary material 6BIOVERA-Tree metadataData typemetadataBrief descriptionDefinition and categories according with Darwin Core, Functional Diversity thesaurus and this research.File: oo_549022.csvhttps://binary.pensoft.net/file/549022Mar\u00eda Leticia Monge-Gonz\u00e1lez, Patrick Weigelt, Nathaly Guerrero-Ram\u00edrez, Dylan Craven, Gonzalo Castillo-Campos, Thorsten Kr\u00f6mer, Holger Kreft."} +{"text": "Patients (pts) with newly diagnosed acute myeloid leukemia (AML) undergoing induction chemotherapy are at increased risk for invasive fungal infections (IFI). Guidelines recommend posaconazole prophylaxis (ppx), but use is precluded by interactions and adverse effects. Micafungin (MCF) is an alternative, but data is limited by small prospective and retrospective studies. Primary objective: describe incidence of probable/proven IFI until neutrophil recovery (ANC \u2265 500 cells/\u00b5L) or 28 days after induction start date, whichever occurred first, in pts receiving MCF ppx. Secondary objective: describe incidence of clinical failure to MCF prophylaxis. Retrospective review (January 2017 to January 2020) of newly diagnosed AML adult pts undergoing 7 + 3 using idarubicin (7 + 3-ida), 7 + 3 using daunorubicin (7 + 3-dau), venetoclax/decitabine (VEN/DEC), or venetoclax/azacitadine (VEN/AZA) receiving MCF ppx for at least 7 days included. Diagnosis of IFI < 30 days prior to induction, liver function tests (LFT) 5x ULN at start of induction, or evidence of refractory disease after induction excluded. Probable/proven IFI defined by EORTC criteria. Clinical failure: changing to a different antifungal class for any reason until ANC recovery or 28 days after induction start date.Ninety-five pts included. Baseline characteristics: mean (\u00b1SD) age 57.8 (\u00b113.0) years; 53.6% males. 62% (59/95) 7 + 3-ida, 13.7% (13/95) 7 + 3-dau, 15.8% (15/95) VEN/DEC, 8.4% (8/95) VEN/AZA. Mean (\u00b1SD): 32.5% (\u00b126) blasts, WBC 13.2 (\u00b123.8), ANC 2.4 (\u00b14.6), ALC 1.9 (\u00b11.6), platelets 92.6 (\u00b1123.2). Incidence of probable IFI 2/95 (2.1%). No proven IFI cases identified. Clinical failure occurred in 37/95 (39%): 8 persistent febrile neutropenia, 29 due to suspected IFI. No MCF discontinuation due to adverse events. Our findings suggest that prophylactic MCF is safe and effective in pts with newly diagnosed AML undergoing induction chemotherapy. Outcomes were similar to those of prophylactic posaconazole studies, indicating MCF may be considered as an alternative when interactions and adverse effects preclude use of posaconazole. Our study was limited by small numbers, retrospective, single-center design. Future opportunities include prospective trials of prophylactic MCF in this setting. All Authors: No reported disclosures"} +{"text": "Hospitalized patients with COVID-19 have created increased demands on health care infrastructure and resources. Bacterial and fungal infections have been reported and have increased the need for antimicrobial utilization. We performed a retrospective chart review to characterize bacterial infections and antibiotic utilization during the COVID-19 surge at our tertiary care center. All patients diagnosed with COVID-19 using SARS-CoV-2 PCR admitted to MedStar Georgetown University Hospital from 01Mar2020 through 31Aug2020 were included in the analysis. Data was collected on hospital-wide antimicrobial utilization [mean days of therapy per 1000-patient-days (DOT)] during the 6-month surge and was compared to antimicrobial utilization during a 6-month period that preceded the COVID-19 surge. Clinical and microbiological data and patient outcomes were also collected and analyzed.A total of 238 patients met eligibility criteria during the observation period, of which 25.6% (n = 61) developed a bacterial, fungal, or viral co-infection. Culture-positive bacterial complications were seen in 21.8% (n = 52) with 32.8% (n = 20) having a multidrug resistant organism (MDRO). There was a statistically significant difference between COVID-19 patients with co-infection and those without for intubation (p < 0.001), vasopressor use (p < 0.001), and renal replacement therapy (p = 0.001). COVID-19 patients with co-infections had a longer mean length of stay and greater mortality compared to those without a co-infection, respectively.Mean antimicrobial utilization for the entire hospital population was 790.6 DOT during the COVID surge compared to 928.7 DOT during a 6-month period preceding the COVID surge (p < 0.001). For all COVID-19 patients, antimicrobial utilization was 846.9 DOT; however, this increased to 1236.4 DOT for COVID-19 patients with co-infections.Table 1. DemographicsTable 2. Antimicrobial Utilization in COVID-19 PatientsAlthough hospital-wide antimicrobial utilization had decreased during the COVID surge, COVID-19 patients with co-infections demonstrated a disproportionate use of antimicrobial agents as well as ICU resources. As MDRO infections were relatively common, antimicrobial stewardship should be prioritized in the COVID-19 population.Lan Duong, Pharm.D., Astra Zeneca (Shareholder)Eli Lilly & Co. (Shareholder)Gilead Sciences, Inc. (Shareholder)Merck & Co. (Speaker\u2019s Bureau)Moderna, Inc. (Shareholder)Novavax, Inc. (Shareholder)Sarepta Therapeutics (Shareholder)Thermo Fisher Scientific (Shareholder) Princy N. Kumar, MD, AMGEN Eli Lilly (Grant/Research Support)Gilead GSK Merck & Co., Inc."} +{"text": "The stromal elements of a malignant tumor can promote cancer progression and metastasis. The structure of the tumor stroma includes connective tissue elements, blood vessels, nerves, and extracellular matrix (ECM). Some of the cellular elements of the tumor stroma are cancer-associated f ibroblasts (CAFs). The origin and function of CAFs have been actively studied over the past thirty years. CAFs produce collagen, the main scaffold protein of the extracellular matrix. Collagen in the tumor stroma stimulates f ibrosis, enhances the rigidity of tumor tissue, and disrupts the transmission of proliferation and differentiation signaling pathways. CAFs control tumor angiogenesis, cell motility, tumor immunogenic properties, and the development of resistance to chemo- and immunotherapy. As a result of metabolic adaptation of rapidly growing tumor tissue to the nutrients and oxygen deprivation, the main type of energy production in cells changes from oxidative phosphorylation to anaerobic glycolysis. These changes lead to sequential molecular alterations, including the induction of specif ied transcriptional factors that result in the CAFs activation. The molecular phenotype of activated CAFs is similar to f ibroblasts activated during inf lammation. In activated CAFs, alpha-smooth muscle actin (\u03b1-SMA) is synthetized de novo and various proteases and f ibronectin are produced. Since CAFs are found in all types of carcinomas, these cells are potential targetsfor the development of new approaches for anticancer therapy. Some CAFs originate from resident f ibroblastsof the organs invaded by the tumor, while others originate from epithelial tumor cells, which are undergoing anepithelial-mesenchymal transition (EMT). To date, many molecular and metabolic inducers of the EMT have beendiscovered including the transforming growth factor-beta (TGF-\u03b2), hypoxia, and inf lammation. This review classifies modern concepts of molecular markers of CAFs, their functional features, and discusses the stages of epithelial-mesenchymal transition, and the potential of CAFs as a target for antitumor therapy Modern concept of tumor morphology postulates that solidtumors are formed by epithelial and stromal cells, such asfibroblasts, endothelial cells, and immune cells . Stromal cells with a fibroblast-like phenotype, theso-called cancer-associated fibroblasts (CAFs), in contrast tonormal fibroblasts, contain various chromosomal abnormalities,such as duplications, multiple rearrangements, and eventhe loss of entire chromosomes . CAFscontrol tumor angiogenesis, motility and metastasis of cancercells, tumor immunogenic properties, and the developmentof resistance to chemotherapy and immunotherapy .A meta-analysis of the clinical relevance of the tumorstroma has demonstrated the association of high CAFs contentwith the advanced stages of tumor progression, as wellas with the high risk of local recurrence after tumor resection.In 1995, a heterogeneous origin of CAFs was hypothesizedby R\u00f8nnov-Jessen and colleagues, who showed that breastcancer CAFs can originate from resident fibroblasts, vascularsmooth muscle cells, and pericytes .To date, it has been shown that precursors of mesenchymalcells from the red bone marrow, endothelial and epithelialcells, resident fibroblasts of the affected tissue, adipocytesand vascular adventitia cells can be sources of CAFs . For the initiation of theCAFs phenotype in some progenitor cells, additional stimulationwith cytokines and growth factors, such as transforminggrowth factor beta (TGF-\u03b2), fibroblast growth factor (FGF),and other signaling molecules is required (Table 1) .Tumor epithelial cells can undergo transformation intoCAFs via the epithelial-mesenchymal transition (EMT). EMT is a dynamic process of transdifferentiation ofepithelial cells into fibroblast-like cells. The EMT plays animportant role not only in cancer, but also in embryogenesisand regeneration. In particular, EMT occurs in embryonic stemcells producing mesoderm and neural crest, and in skin cellsduring wound healing . Dynamic changesin cell morphology during EMT are caused by changes inthe regulatory genes\u2019 expression with production of certainproteins. These proteins are considered as EMT markers. Among these markers, the most significant areN-cadherin and vimentin, which are responsible for the rearrangementof the cytoskeleton and the change in the shapeof the cell, as well as the change in cell-to-cell and cell-toextracellularmatrix (ECM) interactions .In addition to molecular inducers of EMT, the importantrole of hypoxic conditions has been shown. Hypoxia activatesEMT via the binding of the hypoxia-inducible factor (HIF-1)to the promoters of genes responsible for EMT activation.HIF-1 has been shown to increase the expression of the transcriptionfactors genes of the zinc finger motif family such asZEB1, Snail and SLUG. Overexpression of these factors isassociated with the mesenchymal phenotype and a decreasein the abundance of epithelial cell markers \u2013 E-cadherin andtype 1 tight junction protein (TJP1 or ZO-1) .Endothelial cells of tumor vessels can undergo an endothelial-mesenchymal transition (EndMT) and acquire thephenotype and functional features of CAFs with the loss ofendothelial cells molecular markers, such as the endothelialcell/platelet adhesion molecule (CD31), and the acquisition ofmarkers specific for mesenchymal cells, such as \u03b1-SMA andfibroblast specific protein 1 (FSP-1) .An important component of breast cancer stroma areadipose cells, which can transform into tumor-associatedadipocytes, and then into CAFs. Such changes are accompaniedby an increase in the expression of molecular markersof mesenchymal cells, including, PPARG (receptors inducedby peroxisome activators gamma), RUNX-2 (transcriptionfactor containing the Runt type 2 DNA-binding domain), andSOX9 (transcription factor of the HMG family DNA-bindingproteins) .Using the model of prostate cancer, it was shown thatmesenchymal stem cells (MSCs) can differentiate into CAFsafter the activation of the chemokine receptor type 6 (CXCR6)by its ligand CXCL16. Moreover, the activation of CXCR6results in the secretion of stromal factor-1 (CXCL12) involvedin EMT . Weber and colleagues also showedthat the extracellular structural protein osteopontin (OPN),which plays a key role in bone formation, activates TGF-\u03b2gene expression in integrin-dependent MSCs to maintain thephenotype of CAFs in breast cancer. Interestingly, even specializedcells such as Ito cells in the liver, pancreatic stellatecells, and mammary myofibroblasts can acquire the phenotypeof CAFs . These examples illustrate a widerange of cells that, responding to the molecular changes ina tumor, are able to acquire the CAFs\u2019 phenotype and, as aconsequence, be involved in tumor homeostasis.The involvement of CAFs in carcinogenesis and tumor progressionmakes them a potential target for the developmentof novel therapeutic approaches. A potentially clinicallysignificant marker of CAF is the transmembrane mucin-likeprotein podoplanin (PDPN) (Table 2); to date, PDPN has beendescribed as a marker of lymphoid capillary progenitor cellsand CAFs in lung cancers. Expression of podoplanin wasshowed in 54 (30.5 %) out of 177 CAFs\u2019 populations studied inthe work of Yurugi et al. Interestingly, all podoplanin-positiveCAFs correlated with invasiveness of adenocarcinomas, whilea podoplanin-negative phenotype was shown only in noninvasiveadenocarcinomas .Platelet-derived growth factor receptors \u03b1/\u03b2 are importantmarkers of CAFs. PDGFR\u03b1/\u03b2 belong to the 3rd class oftyrosine kinases and are activated by interaction with thePDGF ligand. PDGFR regulates the organogenesis of varioussystems during embryogenesis; however, the significanceof the PDGFR\u03b1 and -\u03b2 receptors activation in tumors is stillpoorly understood. It has been shown that the expression ofthe PDGFR\u03b2 receptor is increased in the tumor microenvironmentcells, where platelet growth factor activates CAFsand, probably, stimulates cancer progression . PDGFR\u03b1-positive CAFs have been found in thestroma of melanoma, suggesting that these CAFs originatefrom resident fibroblasts as a result of their activation . Serum amyloid A (SAA-1) protein is one of thepotential targets of CAFs; its expression and involvementin tumor progression has been shown in CAFs from gastrictumors .In the search for specific markers of the tumor stroma cells,among the CAFs of prostate adenocarcinoma, an increasedcontent of the surface protein with a single V-domain of immunoglobulin(CD90), initially found on T cells and neurons,was identified as a specific marker. The high level of CD90 onthe cell surface differentiates the tumor-associated stroma and \u201cbenign\u201d stroma. Since CD90 expression was shown only intumor associated fibroblasts, this marker is a potential targetfor therapy .Certain CAFs proteins can be prognostic markers of tumorinvasiveness. One of these markers is a protein from the familyof low molecular weight calcium-binding proteins ofthe S100 \u2013 S100A4 family . S100 familyproteins have both intracellular and extracellular activitydue to maintaining the calcium balance and Ca2+-dependentprocesses. S100A4 activates a cascade of reactions associatedmainly with the secretion of pro-inflammatory cytokines andthe expression of growth factors, extracellular matrix proteins,metalloproteinases, and others. Intracellular activity ofS100A4 is of particular interest, and is associated with theenhancement of the invasive capabilities of tumor cells, theirescape from apoptosis, and the stem phenotype of the cells. During the study of the role ofS100A4 in tumor progression, it was shown that suppressionof S100A4 decreased tumor growth . The role of stromal cells thatsecrete S100A4 was shown in the MMTV-PyVmT mousemodel with the S100A4 knocked-out gene during orthotopicco-transplantation of CSML100 mouse mammary adenocarcinomacells and MEF mouse embryonic fibroblasts. MEFcell lines were obtained by spontaneous immortalization ofprimary embryonic fibroblasts from mouse embryos with theS100A4+ and S100A4\u2013 phenotypes. Upon co-transplantationof tumor cells and fibroblasts with the S100A4\u2013 phenotypein syngeneic mice, no metastases were formed, however,upon transplantation of S100A4+ fibroblasts, the metastaticpotential of tumor cells returned. S100A4+ fibroblasts werecharacterized by increased mobility and invasiveness comparedto S100A4\u2013 fibroblasts, as well as the ability to secreteS100A4 into the tumor microenvironment .To date, it is clear that the expression of certain CAFsmarkers does not unambiguously predict the aggressivenessof the tumor. For example, the loss of caveolin-1 in breastcancer CAFs has been shown to be associated with a poorprognosis because the population of these cells stimulates thegrowth of triple negative (ER-/PR-/HER2-) breast cancer cells. In a parallel study, the expression ofcaveolin-1 in the breast cancer CAFs stimulated the remodelingof the tumor microenvironment, thereby facilitating theinvasion of malignant cells and an increased invasiveness levelcorrelated with the metastatic potential of the tumor . These contradictingresultsindicate the diverse role of caveolin-1 in histologicallydifferent tumors. More studies should be made to determinecaveolin-1 as a tumor prognostic marker.CAFs-dependent stimulation of the tumor cells proliferationand their invasion is of particular interest in the study oftumor. This interest is primarily due to the fact that even inthe precancerous phenotype of epithelial cells, some residentfibroblasts are already transformed into CAFs . Fibroblasts from intestinal tumors and polyps werea good model to confirm the contribution of stromal cells totumor growth and progression. These fibroblasts were shownto stimulate the proliferation of tumor and polyp cells .The interaction of tumor epithelial cells with CAFs wasanalyzed by comparing the histological picture of varioustypes of gastric cancer. In a study by Orimo and Weinberg,it was demonstrated that in the case of diffuse gastric cancer,CAFs and epithelial cells are more closely spaced, while inthe intestinal type, CAFs form a stroma-like matrix, due towhich tumor epithelial cells retain their glandular structure.Using the model of heterogeneous 3D spheroids, consistingof breast cancer epithelial cells and fibroblasts, Dang and colleaguesshowed that CAFs stimulated the migration of tumorcells of basal breast cancer (ER-/PR-/HER2-). Interestingly,this effect was not observed in the models of luminal breastcancer types . These data are consistent with clinical observationsindicating a higher percentage of metastasis in triplenegativebreast cancer compared with other types of breast tumors. However, which factors make cells of basal breastcancer sensitive to CAFs stimulation remain undiscovered.In order to reach the blood and lymphatic streams, tumorcells should pass through the basement membrane (BM), separatingthem from connective tissue and vessels. Thus, CAFsare able to synthesize metalloproteinases \u2013 endopeptidasescapable of destroying proteins of all types of the BM extracellularmatrix . In 2017, Glentis andcolleagues revealed a metalloproteinase-independent CAFssupportedovercome of BM by tumor cells. They demonstratedthe ability of CAFs to stretch BM with the formation of pores,and through these pores, epithelial tumor cells and CAFs canmigrate into the bloodstream and form metastases in distantorgans. Interestingly, BM regions with low expression oflamininand type IV collagen exhibited the highest tendencyfor stretching . This alternative CAFsdependentmigration pathway explains the ineffectiveness ofthe metalloproteinase inhibitors application in patients withhead and neck tumors.The paracrine secretion of IL-1\u03b1 by CAFs in bladder cancerwith further activation of the Wnt pathway in tumor cells isthe perfect illustration of the pro-carcinogenic role of CAFs. Moreover, bladder cancer \u0421AFs secretingIL-8 are able to stimulate the secretion of neuropilin-1,which enhances the proliferation of tumor cells and is oneof the potential prognostic markers of malignancy . Interestingly, recent studies have shown thatneuropilin-1 may be a co-factor in the induction of EMT.Paracrine stimulation of the epithelial-mesenchymal transitionin tumor epithelial cells by CAFs is an important factorcontributing to tumor progression. The central mechanism ofEMT in the tumor is the TGF-\u03b2/Smad pathway activation,induced by TGF-\u03b2 from stromal fibroblasts . The Smad factor is a transcription factor that controlsthe expression of EMT genes. Vered and colleagues showedthat cells with EMT markers are found in primary foci ofsquamous cell carcinoma of the tongue as well as in regionallymph nodes metastases. This confirms the importance of CAFs in the induction of metastasis and in the formation ofa secondary tumor node .The central mechanism of the EMT activation in ovariancancer is the induction of the CXCR4/Wnt/\u03b2-catenin pathwayin tumor epithelial cells. CAFs secreting stromal growth factor-1 (SDF-1 or CXCL12) have been shown to be the majorplayers in this process. Moreover, SDF-1 is also interlinkedwith the resistance of tumor cells to chemotherapeutic agentssuch as cisplatin .In 2020, Franz\u00e8 and colleagues demonstrated the activationof CAFs phenotype in normal fibroblasts from rectal polypsco-cultured with CAFs. They showed that CAFs derivedfrom colorectal tumors can secrete IL-34, which in normalfibroblasts activates the expression of CAFs markers suchas \u03b1-SMA, vimentin, and fibroblast activating protein (FAP).Even though most of the described functions of \u0421AFs areassociated with the stimulation of tumor progression, someauthors also describe \u0421AFs as tumor-suppressing players. Forexample, the subpopulation of CAFs expressing the melanomaadhesion molecule (CD146) in breast tumors correlated witha retarded cell proliferation in estrogen-dependent types ofbreast cancer . Since CAFs secretecytokines involved in the recruitment and maturation ofmacrophages, T-lymphocytes and natural killer cells , they increase the availabilityof the tumor to immune cells and promote antitumor immuneresponse . In the study of oral cancer,it was also shown that CAFs can suppress the proliferationof tumor cells. In particular, the population of CAFs secretingBone Morphogenetic Protein 4 (BMP4) and expressing\u03b1-SMA inhibited the proliferation of cancer stem cells (CSC). Using the mice model with a predispositionfor the development of pancreatic cancer, Rhim and colleaguesexhibited the role of CAFs in cancer progression. They excludedthe \u03b1-SMA-positive population of CAFs or CAFs withinhibited Hedgehog signaling pathway. These modificationssuppress the growth of pancreatic ductal adenocarcinoma.Histological analysis of tumors revealed abnormalities in thevessel\u2019s formation .These examples demonstrate the tumor-suppressing functionof CAFs only in high differentiated cancers with nosimilarity in undifferentiated ones. It can be assumed thatapart from origin and tissue of the affected organ, the functionof CAFs is determined by the differentiation stage of cancercells .Cell cultures obtained from patients\u2019 tumors after surgery aremost often used to study the properties of CAFs. It is necessaryto establish new CAFs cell cultures, since in vitro CAFs tendto age rapidly, and the possibilities of their use are limitedby early passages . Moreover, in commerciallyavailable cell collections American Type CultureCollection (ATCC), European Collection of AuthenticatedCell Cultures (ECACC), Russian collection of cell cultures,etc. cell lines with the CAFs phenotype are limited. For instance,in ATCC, only one CAFs cell line is available. Thiscell culture originates from the prostate adenocarcinoma and ismodified by the introduction of the telomerase transgene underthe control of the constitutive promoter of the polyoma virusSV40 hTERT PF179T CAF. This modification of fibroblastsis aimed at maintaining the proliferative properties of CAFs.To obtain cell cultures from tumor tissue, mechanical disaggregation,enzymatic dissociation, chelation and their combinationare used. Trypsin and type IV collagenase are mostoften used to destroy the stroma of tumor tissue. The choice ofwhat technique to use should consider the histological originof the tissue of interest. When tissue disaggregated, CAFs canrepresent a small population of cells and obtaining a monoculturerequires an additional stage of their separation fromthe total cell mass. In order to isolate a particular populationof CAFs, magnetic separation, or FACS of cells with immunostainingof specific CAFs markers such as FAP or \u03b1-SMAare used . The main difficulty in isolating CAFs lies in adaptingprotocols for vital staining of intracellular markers such as\u03b1-SMA, FAP, and vimentin. Therefore, it is highly desirableto include surface markers such as CD90 in the analysis.Clear understanding the tumor microenvironment role iscrucial for the development of new approaches in cancer diagnosticsand treatment. The multifaceted influence of CAFson tumor progression makes them an important object for thestudy of carcinogenesis and the development of new antitumoragents. The use of drugs targeted to the components of thetumor microenvironment has not demonstrated efficacy foranti-metalloproteinase compounds and angiogenesis inhibitorsas well as T-cell immunity checkpoints inhibitors in sometypes of cancer . The heterogeneity ofthe molecular phenotypes of CAFs can be an important factorin the failure of CAF-targeted cancer treatment. The scientificcommunity should develop more detailed classifications ofvarious subtypes of CAFs considering their involvement intumor progression.Thus, a detailed classification of CAFs and a study of thefunctions of each phenotypic subgroup may provide importantknowledge for the development of new methodsfor the CAF-related treatment and diagnosis of oncologicaldiseases.The authors declare no conflict of interest.Alkasalias T., Moyano-Galceran L., Arsenian-Henriksson M., Lehti K.Fibroblasts in the tumor microenvironment: shield or spear? Int. J.Mol. Sci. 2018;19(5):1532. DOI 10.3390/ijms19051532.Al-Mahmood S., Sapiezynski J., Garbuzenko O.B., Minko T. Metastaticand triple-negative breast cancer: challenges and treatment options.Drug Deliv. Transl. Res. 2018;8(5):1483-1507. DOI 10.1007/s13346-018-0551-3.Ambartsumian N., Klingelh\u00f6fer J., Grigorian M. The multifacetedS100A4 protein in cancer and inflammation. In: Heizmann C. (Ed.).Calcium-Binding Proteins of the EF-Hand Superfamily: From Basicsto Medical Applications. (Ser. Methods in Molecular Biology).New York: Humana Press, 2019;1929:339-365. DOI 10.1007/978-1-4939-9030-6_22.Anderberg C., Li H., Fredriksson L., Andrae J., Betsholtz C., Li X.,ErikssonU., Pietras K. Paracrine signaling by platelet-derivedgrowth factor-CC promotes tumor growth by recruitment of cancer-associated fibroblasts. Cancer Res. 2009;69(1):369-378. DOI10.1158/0008-5472.CAN-08-2724.Bochet L., Lehuede C., Dauvillier S., Wang Y.Y., Dirat B., Laurent V.,Dray C., Guiet R., Maridonneau-Parini I., Le Gonidec S., CoudercB., Escourrou G., Valet P., Muller C. Adipocyte-derived fibroblastspromote tumor progression and contribute to the desmoplasticreaction in breast cancer. Cancer Res. 2013;73(18):5657-5668. DOI10.1158/0008-5472.CAN-13-0530.Bordignon P., Bottoni G., Xu X., Popescu A.S., Truan Z., Guenova E.,Kofler L., Jafari P., Ostano P., R\u00f6cken M., Neel V., Dotto G.P. Dualismof FGF and TGF-\u03b2 signaling in heterogeneous cancer-associatedfibroblast activation with ETV1 as a critical determinant. CellRep. 2019;28(9):2358-2372.e6. DOI 10.1016/j.celrep.2019.07.092.Brechbuhl H.M., Finlay-Schultz J., Yamamoto T.M., Gillen A.E., CittellyD.M., Tan A.-C., Sams S.B., Pillai M.M., Elias A.D., RobinsonW.A., Sartorius C.A., Kabos P. Fibroblast subtypes regulate responsivenessof luminal breast cancer to estrogen. Clin. Cancer Res.2017;23(7):1710-1721. DOI 10.1158/1078-0432.CCR-15-2851.Bu L., Baba H., Yoshida N., Miyake K., Yasuda T., Uchihara T., Tan P.,Ishimoto T. Biological heterogeneity and versatility of cancer-associatedfibroblasts in the tumor microenvironment. Oncogene. 2019;38(25):4887-4901. DOI 10.1038/s41388-019-0765-y.Calon A., Tauriello D.V.F., Batlle E. TGF-beta in CAF-mediated tumorgrowth and metastasis. Semin. Cancer Biol. 2014;25:15-22. DOI10.1016/j.semcancer.2013.12.008.Chen C., Zhang R., Ma L., Li Q., Zhao Y., Zhang G., Zhang D., Li W.,Cao S., Wang L., Geng Z. Neuropilin-1 is up-regulated by cancerassociatedfibroblast-secreted IL-8 and associated with cell proliferationof gallbladder cancer. J. Cell. Mol. Med. 2020;24(21):12608-12618. DOI 10.1111/jcmm.15825Chen Z., Gao H., Dong Z., Shen Y., Wang Z., Wei W., Yi J., Wang R.,Wu N., Jin S. NRP1 regulates radiation-induced EMT via TGF-\u03b2/Smad signaling in lung adenocarcinoma cells. Int. J. Radiat. Biol.2020;96(10):1281-1295. DOI 10.1080/09553002.2020.1793015.Dang T.T., Prechtl A.M., Pearson G.W. Breast cancer subtype-specificinteractions with the microenvironment dictate mechanisms of invasion.Cancer Res. 2011;71(21):6857-6866. DOI 10.1158/0008-5472.CAN-11-1818.Fei F., Qu J., Zhang M., Li Y., Zhang S. S100A4 in cancer progressionand metastasis: a systematic review. Oncotarget. 2017;8(42):73219-73239. DOI 10.18632/oncotarget.18016.Franz\u00e8 E., Di Grazia A., Sica G.S., Biancone L., Laudisi F., MonteleoneG. Interleukin-34 enhances the tumor promoting function ofcolorectal cancer-associated fibroblasts. Cancers. 2020;12(12):3537.DOI 10.3390/cancers12123537.Glentis A., Oertle P., Mariani P., Chikina A., El Marjou F., Attieh Y.,Zaccarini F., Lae M., Loew D., Dingli F., Sirven P., SchoumacherM., Gurchenkov B.G., Plodinec M., Vignjevic D.M. Cancer-associatedfibroblasts induce metalloprotease-independent cancer cellinvasion of the basement membrane. Nat. Commun. 2017;8(1):924.DOI 10.1038/s41467-017-00985-8.Goetz J.G., Minguet S., Navarro-L\u00e9rida I., Lazcano J.J., Samaniego R.,Calvo E., Tello M., Osteso-Ib\u00e1\u00f1ez T., Pellinen T., Echarri A., CerezoA., Klein-Szanto A.J.P., Garcia R., Keely P.J., S\u00e1nchez-Mateos P.,Cukierman E., Del Pozo M.A. Biomechanical remodeling of themicroenvironment by stromal caveolin-1 favors tumor invasion andmetastasis. Cell. 2011;146(1):148-163. DOI 10.1016/j.cell.2011.05.040.Gonzalez-Avila G., Sommer B., Mendoza-Posada D.A., Ramos C.,Garcia-Hernandez A.A., Falfan-Valencia R. Matrix metalloproteinasesparticipation in the metastatic process and their diagnostic andtherapeutic applications in cancer. Crit. Rev. Oncol. Hematol. 2019;137:57-83. DOI 10.1016/j.critrevonc.2019.02.010Grantham J. The molecular chaperone CCT/TRiC: an essential componentof proteostasis and a potential modulator of protein aggregation.Front. Genet. 2020;11:172. DOI 10.3389/fgene.2020.00172.Grum-Schwensen B., Klingelh\u00f6fer J., Beck M., Bonefeld C.M., HamerlikP., Guldberg P., Grigorian M., Lukanidin E., AmbartsumianN. S100A4-neutralizing antibody suppresses spontaneoustumor progression, pre-metastatic niche formation and alters T-cellpolarization balance. BMC Cancer. 2015;15(1):44. DOI 10.1186/s12885-015-1034-2.Grum-Schwensen B., Klingelhofer J., Berg C.H., El-Naaman C., GrigorianM., Lukanidin E., Ambartsumian N. Suppression of tumor developmentand metastasis formation in mice lacking the S100A4(mts1)gene. Cancer Res. 2005;65(9):3772-3780. DOI 10.1158/0008-5472.CAN-04-4510.Hosein A.N., Wu M., Arcand S.L., Lavall\u00e9e S., H\u00e9bert J., Tonin P.N.,Basik M. Breast carcinoma-associated fibroblasts rarely containp53 mutations or chromosomal aberrations. Cancer Res. 2010;70(14):5770-5777. DOI 10.1158/0008-5472.CAN-10-0673.Huang Yingying, Zhou S., Huang Yong, Zheng D., Mao Q., He J.,Wang Y., Xue D., Lu X., Yang N., Zhao Y. Isolation of fibroblast-activationprotein-specific cancer-associated fibroblasts. BioMed Res.Int. 2017;2017:4825108. DOI 10.1155/2017/4825108.Jansson S., Aaltonen K., Bendahl P.-O., Falck A.-K., Karlsson M., PietrasK., Ryd\u00e9n L. The PDGF pathway in breast cancer is linked totumour aggressiveness, triple-negative subtype and early recurrence.Breast Cancer Res. Treat. 2018;169(2):231-241. DOI 10.1007/s10549-018-4664-7.Joyce J.A., Pollard J.W. Microenvironmental regulation of metastasis.Nat. Rev. Cancer. 2009;9(4):239-252. DOI 10.1038/nrc2618.Jung Y., Kim J.K., Shiozawa Y., Wang Jingcheng, Mishra A., JosephJ., Berry J.E., McGee S., Lee E., Sun H., Wang Jianhua, Jin T.,Zhang H., Dai J., Krebsbach P.H., Keller E.T., Pienta K.J., TaichmanR.S. Recruitment of mesenchymal stem cells into prostate tumourspromotes metastasis. Nat. Commun. 2013;4(1):1795. DOI10.1038/ncomms2766.Kim D., Xing T., Yang Z., Dudek R., Lu Q., Chen Y.-H. Epithelial mesenchymaltransition in embryonic development, tissue repair andcancer: a comprehensive overview. J. Clin. Med. 2017;7(1):1. DOI10.3390/jcm7010001.Knops A.M., South A., Rodeck U., Martinez-Outschoorn U., HarshyneL.A., Johnson J., Luginbuhl A.J., Curry J.M. Cancer-associatedfibroblast density, prognostic characteristics, and recurrence in headand neck squamous cell carcinoma: a meta-analysis. Front. Oncol.2020;10:565306. DOI 10.3389/fonc.2020.565306.Liotta L.A., Kohn E.C. The microenvironment of the tumour\u2013host interface.Nature. 2001;411(6835):375-379. DOI 10.1038/35077241Liu B., Pan S., Liu J., Kong C. Cancer-associated fibroblasts and the relatedRunt-related transcription factor 2 (RUNX2) promote bladdercancer progression. Gene. 2021;775:145451. DOI 10.1016/j.gene.2021.145451.Lobba A.R.M., Carreira A.C.O., Cerqueira O.L.D., Fujita A., DeOcesano-Pereira C., Osorio C.A.B., Soares F.A., Rameshwar P., SogayarM.C. High CD90 (THY-1) expression positively correlates withcell transformation and worse prognosis in basal-like breast cancertumors. PLoS One. 2018;13(6):e0199254. DOI 10.1371/journal.pone.0199254.Lynch M.D., Watt F.M. Fibroblast heterogeneity: implications for humandisease. J. Clin. Investig. 2018;128(1):26-35. DOI 10.1172/JCI93555.Madar S., Brosh R., Buganim Y., Ezra O., Goldstein I., Solomon H.,Kogan I., Goldfinger N., Klocker H., Rotter V. Modulated expressionof WFDC1 during carcinogenesis and cellular senescence. Carcinogenesis.2009;30(1):20-27. DOI 10.1093/carcin/bgn232Marlow R., Strickland P., Lee J.S., Wu X., Pebenito M., Binnewies M.,Le E.K., Moran A., Macias H., Cardiff R.D., Sukumar S., Hinck L.SLITs suppress tumor growth in vivo by silencing Sdf1/Cxcr4within breast epithelium. Cancer Res. 2008;68(19):7819-7827. DOI10.1158/0008-5472.CAN-08-1357.Massagu\u00e9 J. TGF\u03b2 in cancer. Cell. 2008;134(2):215-230. DOI 10.1016/j.cell.2008.07.001.Mossahebi-Mohammadi M., Quan M., Zhang J.-S., Li X. FGF signalingpathway: a key regulator of stem cell pluripotency. Front. CellDev. Biol. 2020;8:79. DOI 10.3389/fcell.2020.00079.Mukaida N., Sasaki S. Fibroblasts, an inconspicuous but essential playerin colon cancer development and progression. World J. Gastroenterol.2016;22(23):5301. DOI 10.3748/wjg.v22.i23.5301.Nushtaeva A.A., Karpushina A.A., Ermakov M.S., Gulyaeva L.F., GerasimovA.V., Sidorov S.V., Gayner T.A., Yunusova A.Y., TkachenkoA.V., Richter V.A., Koval O.A. Establishment of primary humanbreast cancer cell lines using \u201cpulsed hypoxia\u201d method and developmentof metastatic tumor model in immunodeficient mice. CancerCell Int. 2019;19(1):46. DOI 10.1186/s12935-019-0766-5.Nushtaeva A.A., Stepanov G.A., Semenov D.V., Juravlev E.S., BalahonovaE.A., Gerasimov A.V., Sidorov S.V., Savelyev E.I., KuliginaE.V., Richter V.A., Koval O.A. Characterization of primary normaland malignant breast cancer cell and their response to chemotherapyand immunostimulatory agents. BMC Cancer. 2018;18(1):728. DOI10.1186/s12885-018-4635-8.Orimo A., Weinberg R.A. Stromal fibroblasts in cancer: a novel tumor-promoting cell type. Cell Cycle. 2006;5(15):1597-1601. DOI10.4161/cc.5.15.3112Patel A.K., Vipparthi K., Thatikonda V., Arun I., Bhattacharjee S.,Sharan R., Arun P., Singh S. A subtype of cancer-associated fibroblastswith lower expression of alpha-smooth muscle actin suppressesstemness through BMP4 in oral carcinoma. Oncogenesis. 2018;7(10):78. DOI 10.1038/s41389-018-0087-x.Pur\u00e9 E., Hingorani S.R. Mesenchymal cell plasticity and perfidy inepithelialmalignancy. Trends Cancer. 2018;4(4):273-277. DOI10.1016/j.trecan.2018.02.007.Rhim A.D., Oberstein P.E., Thomas D.H., Mirek E.T., Palermo C.F.,Sastra S.A., Dekleva E.N., Saunders T., Becerra C.P., Tattersall I.W.,Westphalen C.B., Kitajewski J., Fernandez-Barrena M.G., Fernandez-Zapico M.E., Iacobuzio-Donahue C., Olive K.P., Stanger B.Z.Stromal elements act to restrain, rather than support, pancreaticductal adenocarcinoma. Cancer Cell. 2014;25(6):735-747. DOI10.1016/j.ccr.2014.04.021.R\u00f8nnov-Jessen L., Petersen O.W., Koteliansky V.E., Bissell M.J. Theorigin of the myofibroblasts in breast cancer. Recapitulation of tumorenvironment in culture unravels diversity and implicates convertedfibroblasts and recruited smooth muscle cells. J. Clin. Invest.1995;95(2):859-873. DOI 10.1172/JCI117736.Scherz-Shouval R., Santagata S., Mendillo M.L., Sholl L.M., Ben-Aharon I., Beck A.H., Dias-Santagata D., Koeva M., Stemmer S.M.,Whitesell L., Lindquist S. The reprogramming of tumor stroma byHSF1 is a potent enabler of malignancy. Cell. 2014;158(3):564-578.DOI 10.1016/j.cell.2014.05.045.Sha M., Jeong S., Qiu B., Tong Y., Xia L., Xu N., Zhang J., Xia Q.Isolation of cancer-associated fibroblasts and its promotion to the progression of intrahepatic cholangiocarcinoma. Cancer Med. 2018;7(9):4665-4677. DOI 10.1002/cam4.1704.Sharon Y., Alon L., Glanz S., Servais C., Erez N. Isolation of normaland cancer-associated fibroblasts from fresh tissues by FluorescenceActivated Cell Sorting (FACS). J. Vis. Exp. 2013;71:4425. DOI10.3791/4425.Taddei M.L., Cavallini L., Comito G., Giannoni E., Folini M., MariniA., Gandellini P., Morandi A., Pintus G., Raspollini M.R., ZaffaroniN., Chiarugi P. Senescent stroma promotes prostate cancerprogression: the role of miR-210. Mol. Oncol. 2014;8(8):1729-1746.DOI 10.1016/j.molonc.2014.07.009Tam S.Y., Wu V.W.C., Law H.K.W. Hypoxia-induced epithelial-mesenchymaltransition in cancers: HIF-1\u03b1 and beyond. Front. Oncol.2020;10:468. DOI 10.3389/fonc.2020.00486.Tripathi M., Billet S., Bhowmick N.A. Understanding the role of stromalfibroblasts in cancer progression. Cell Adh. Migr. 2012;6(3):231-235. DOI 10.4161/cam.20419.True L.D., Zhang H., Ye M., Huang C.-Y., Nelson P.S., von Haller P.D.,Tjoelker L.W., Kim J.-S., Qian W.-J., Smith R.D., Ellis W.J., LiebeskindE.S., Liu A.Y. CD90/THY1 is overexpressed in prostate cancerassociatedfibroblasts and could serve as a cancer biomarker. Mod.Pathol. 2010;23(10):1346-1356. DOI 10.1038/modpathol.2010.122.Vered M., Dayan D., Yahalom R., Dobriyan A., Barshack I., Bello I.O.,Kantola S., Salo T. Cancer-associated fibroblasts and epithelial- mesenchymaltransition in metastatic oral tongue squamous cell carcinoma.Int. J. Cancer. 2010;127(6):1356-1362. DOI 10.1002/ijc.25358Wang M., Zhao J., Zhang L., Wei F., Lian Y., Wu Y., Gong Z., Zhang S.,Zhou J., Cao K., Li X., Xiong W., Li G., Zeng Z., Guo C. Roleof tumor microenvironment in tumorigenesis. J. Cancer. 2017;8(5):761-773. DOI 10.7150/jca.17648.Wang-Gillam A. Targeting stroma: a tale of caution. J. Clin. Oncol.2019;37(13):1041-1043. DOI 10.1200/JCO.19.00056.Weber C.E., Kothari A.N., Wai P.Y., Li N.Y., Driver J., Zapf M.A.C.,Franzen C.A., Gupta G.N., Osipo C., Zlobin A., Syn W.K., Zhang J.,Kuo P.C., Mi Z. Osteopontin mediates an MZF1\u2013TGF-\u03b21-dependenttransformation of mesenchymal stem cells into cancer-associatedfibroblastsin breast cancer. Oncogene. 2015;34(37):4821-4833.DOI 10.1038/onc.2014.410.Witkiewicz A.K., Dasgupta A., Sotgia F., Mercier I., Pestell R.G., SabelM., Kleer C.G., Brody J.R., Lisanti M.P. An absence of stromalcaveolin-1 expression predicts early tumor recurrence and poor clinicaloutcome in human breast cancers. Am. J. Pathol. 2009;174(6):2023-2034. DOI 10.2353/ajpath.2009.080873.Yang F., Guo Z., He C., Qing L., Wang H., Wu J., Lu X. Cancer-associatedfibroblasts promote cell proliferation and invasion via paracrineWnt/IL1\u03b2 signaling pathway in human bladder cancer. Neoplasma.2021;68(1):79-86. DOI 10.4149/neo_2020_200202N101.Yasukawa Y., Hattori N., Iida N., Takeshima H., Maeda M., Kiyono T.,Sekine S., Seto Y., Ushijima T. SAA1 is upregulated in gastric cancer-associated fibroblasts possibly by its enhancer activation. Carcinogenesis.2021;42(2):180-189. DOI 10.1093/carcin/bgaa131.Ye X., Weinberg R.A. Epithelial\u2013mesenchymal plasticity: a central regulatorof cancer progression. Trends Cell Biol. 2015;25(11):675-686. DOI 10.1016/j.tcb.2015.07.012Yin Z., Dong C., Jiang K., Xu Z., Li R., Guo K., Shao S., Wang L.Heterogeneity of cancer-associated fibroblasts and roles in the progression,prognosis, and therapy of hepatocellular carcinoma. J. Hematol.Oncol. 2019;12(1):101. DOI 10.1186/s13045-019-0782-x.Yoshida G.J. Regulation of heterogeneous cancer-associated fibroblasts:the molecular pathology of activated signaling pathways.J. Exp. Clin. Cancer Res. 2020;39(1):112. DOI 10.1186/s13046-020-01611-0.Yu Y., Xiao C.-H., Tan L.-D., Wang Q.-S., Li X.-Q., Feng Y.-M. Cancer-associated fibroblasts induce epithelial\u2013mesenchymal transitionof breast cancer cells through paracrine TGF-\u03b2 signalling. Br. J.Cancer. 2014;110(3):724-732. DOI 10.1038/bjc.2013.768.Yurugi Y., Wakahara M., Matsuoka Y., Sakabe T., Kubouchi Y., HarukiT., Nosaka K., Miwa K., Araki K., Taniguchi Y., Shiomi T., NakamuraH., Umekita Y. Podoplanin expression in cancer-associatedfibroblasts predicts poor prognosis in patients with squamous cellcarcinoma of the lung. Anticancer. Res. 2017;37(1):207-214. DOI10.21873/anticanres.11308.Zeisberg E.M., Potenta S., Xie L., Zeisberg M., Kalluri R. Discoveryof endothelial to mesenchymal transition as a source for carcinomaassociatedfibroblasts. Cancer Res. 2007;67(21):10123-10128. DOI10.1158/0008-5472.CAN-07-3127.Zhang F., Cui J., Gao H., Yu H., Gao F., Chen J., Chen L. Cancerassociatedfibroblasts induce epithelial-mesenchymal transition andcisplatin resistance in ovarian cancer via CXCL12/CXCR4 axis.Future Oncol. 2020;16(32):2619-2633. DOI 10.2217/fon-2020-0095."} +{"text": "Metabolic comorbidities including diabetes (DM) and dyslipidemia pose challenges to the long-term care of people with HIV (PWH). Incidence of cardiovascular disease and DM are reported at higher rates in PWH than the general population. Obesity is broadly prevalent in both the general population and PWH, and higher body mass index (BMI) can contribute to metabolic complications. Here we present longer-term follow up on incidence of DM, hypertension (HTN), BMI categorical shifts, and lipid changes over 144 weeks of blinded treatment from two trials of PWH initiating antiretroviral therapy.We assessed incidence of metabolic complications in adult PWH in Study 1489: bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF) vs dolutegravir/abacavir/ lamivudine (DTG/ABC/3TC) and Study 1490: B/F/TAF vs DTG+F/TAF. Treatment-emergent (TE) metabolic comorbidities were defined by standard MedDRA search lists. CDC-defined BMI categories were compared from baseline (BL) to Week 144. Analyses by sex at birth and race were performed, as well as for lipid changes.Among 1,274 total participants, median (range) age was 33 years (18-77), 90% men, 33% black. In study 1489, BL prevalence of DM and HTN was 4.5 and 12.1% with TE DM and HTN in B/F/TAF being 0.7% and 10%, and for DTG/ABC/3TC 1.3% and 6.9%, respectively. In study 1490, BL prevalence of DM and HTN was 6.8 and 18.8% with TE DM and HTN in B/F/TAF being 2.1 and 5.8%, and for DTG+F/TAF 2.3 and 6.5%, respectively. BMI shift from Normal to Obese: B/F/TAF 0%, DTG/ABC/3TC 3.2%, p=0.12 (1489) (Table 1); B/F/TAF 2.5%, DTG+F/TAF 2.9% p=1.00 (1490) (Table 2). Subgroup analyses by gender/race showed similar findings for TE DM, HTN, and BMI changes. Median changes from BL fasted lipids were small (Table 1).Table 1\u00a7. Studies 1489 and 1490: Metabolic Outcomes from Baseline to Week 144Table 2\u00b1. Shift Table of BMI Category at Week 144 by Baseline BMI Category \u2013 OverallThrough over 144 weeks of follow up, PWH randomized to initiate B/F/TAF, DTG/ABC/3TC or DTG+F/TAF had low rates of incident DM or HTN-related AEs, with no statistically significant differences by treatment group. BMI changes/categorical shifts from BL did not significantly differ by regimen, and no clinically significant change or difference by regimen in lipids were observed. While data are limited by three years of follow up, they are strengthened by randomized study design of three widely used initial ART regimens.Eric Daar, MD, Bristol-Myers Squibb (Consultant)Gilead Sciences Inc. Janssen Merck Teva ViiV Healthcare Chloe Orkin, MD, Gilead Sciences Inc. Janssen Merck ViiV Healthcare Paul Sax, MD, Gilead Sciences Janssen (Consultant)Merck ViiV Jeffrey L. Stephens, MD, Gilead Sciences Inc. Ellen Koenig, MD, Gilead Sciences Inc. (Scientific Research Study Investigator) Amanda Clarke, MD, Gilead Sciences Inc. ViiV Healthcare Axel Baumgarten, MD, AbbVie Bristol-Myers Squibb Gilead Sciences Inc. Janssen (Speaker\u2019s Bureau)Merck (Advisor or Review Panel member) Cynthia Brinson, MD, Abbvie (Scientific Research Study Investigator)BI (Scientific Research Study Investigator)Gilead Sciences Inc. GSK (Scientific Research Study Investigator)Novo Nordisk (Scientific Research Study Investigator)ViiV Healthcare Moti Ramgopal, MD FIDSA, Abbvie Gilead Janssen Merck ViiV Hailin Huang, PhD, Gilead Sciences Inc. Terry Farrow, MD, Gilead Sciences Inc. Jared Baeten, MD, PHD, Gilead Sciences Inc. Jason Hindman, PharmD, Gilead Sciences Inc. Hal Martin, MD, MPH, Gilead Sciences Inc. Kimberly Workowski, MD, Nothing to disclose"} +{"text": "Cabotegravir (CAB) plus rilpivirine (RPV) is the first complete long-acting (LA) regimen recommended by treatment guidelines for the maintenance of HIV-1 virologic suppression. CAB+RPV LA dosed every 4 weeks (Q4W) or every 8 weeks (Q8W) demonstrated noninferior efficacy in multinational Phase 3/3b trials. This This analysis focuses on data for US/CAN participants naive to CAB+RPV (n=376) from the larger pooled population of the ATLAS, FLAIR, and ATLAS-2M Phase 3/3b studies (N=1245). Endpoints included the proportion of participants with plasma HIV-1 RNA \u2265 50 and < 50 c/mL at W48 , incidence of confirmed virologic failure , safety, and treatment preference through W48.2) previously associated with CVF. Among the US/CAN participants with a single baseline factor, none met CVF. Overall, archived RPV RAMs were observed in 3.2% (12/376), HIV subtype A6/A1 in 1.1% (4/376), and BMI \u2265 30 kg/m2 in 26.3% (99/376) of participants. Safety and injection site reaction findings were similar to the overall pooled population (Table 2). Most participants preferred LA over oral dosing . 376 US/CAN participants received CAB+RPV LA Q4W or Q8W. Median (range) age was 39y (20\u201374); 14.9% were female, 66.0% were White. At W48, 93.1% (350/376) maintained virologic suppression (HIV-1 RNA < 50 c/mL), 1.9% (7/376) had HIV-1 RNA \u2265 50 c/mL, and 0.8% (3/376) met the CVF criterion, consistent with the overall global pooled population (Table 1). Two of the three participants with CVF had \u2265 2 of the three baseline factors Table 2. Safety summary through Week 48 following CAB+RPV LA Q4W and Q8W or comparator ART in participants naive to CAB+RPV from ATLAS, FLAIR, and ATLAS-2MIn US/CAN Phase 3/3b trial participants, CAB+RPV LA was highly effective and well tolerated, with outcomes consistent with the overall pooled population. Baseline prevalence of archived RPV RAMs and subtype A6/A1 was low and aligned with regional prevalence/surveillance data. CAB+RPV LA provides a tolerable and effective injectable LA treatment option for virologically suppressed US/CAN individuals with HIV.Babafemi O. Taiwo, MBBS, Gilead (Consultant)Merck (Consultant)ViiV Healthcare (Consultant) Darrell Tan, MD PhD, Abbvie (Grant/Research Support)Gilead (Grant/Research Support)GlaxoSmithKline (Scientific Research Study Investigator)ViiV Healthcare (Grant/Research Support) Parul Patel, PharmD, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Paula Teichner, PharmD, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Joseph Polli, PhD, FAAPS, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Louise Garside, PhD, GlaxoSmithKline (Employee) Ronald D\u2019Amico, DO, MSc, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Christine L. Talarico, M.S., GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Rodica Van Solingen-Ristea, MD, Janssen Research and Development (Employee)ViiV Healthcare (Employee) Bryan Baugh, MD, Janssen, Johnson & Johnson William Spreen, PharmD, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Michael Aboud, MBChB, MRCP, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Matthew Bosse, DO, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee)"} +{"text": "Dengue fever is a mosquito-borne viral disease endemic in 128 countries. An unmet clinical need remains for an effective vaccine that can be used more broadly than the vaccine presently available. A clinical development program has evaluated the long-term safety, immunogenicity, and vaccine efficacy (VE) of TAK-003, a live attenuated tetravalent dengue vaccine with a DENV-2 backbone engineered to elicit immune responses to all 4 dengue serotypes. nd dose, and for another 25 months after a booster dose. Data up to 3 years after the second vaccination are currently available.18 clinical trials in 13 countries have involved 28,175 seropositive/seronegative participants aged from 1.5-60 years from endemic/non-endemic regions. In the ongoing pivotal phase III study, 4\u201316-year-old healthy children were randomized 2:1 to receive two doses of TAK-003 or placebo, 3 months apart for an evaluation of VE and safety over a multi-year period stratified pre-vaccination dengue serostatus. Active surveillance throughout the trial detected symptomatic dengue. The trial will continue up to 4\u20134.5 years post 2nd dose. At 18 months, VE was 66.2% (95% CI: 49.1\u201377.5) in dengue-naive and 76.1% (95% CI: 68.5\u201381.9) in dengue pre-exposed participants, with VE of 90.4% (95% CI: 82.6\u201394.7) and 85.9% (95% CI: 31.9\u201397.1) for prevention of hospitalized VCD and dengue hemorrhagic fever, respectively. Cumulative VE against VCD from first dose to 3 years post 2nd dose was 62.0% (95% CI: 56.6\u201366.7) and 83.6% (95% CI: 76.8\u201388.4) in prevention of hospitalized VCD. Some decline in VE was observed over time mainly driven by outpatient dengue. Two doses of TAK-003 3 months apart were well-tolerated with no important safety risks identified up to 3 years after completion of the vaccination schedule. Safety and immunogenicity data from Phase I/II studies established the final formulation and dosing schedule. Overall VE in the pivotal phase III study was 80.2% [95% CI: 73.3\u201385.3] against virologically confirmed dengue (VCD) at 12 months post 2TAK-003 is immunogenic against all 4 dengue serotypes and continues to be efficacious, well-tolerated, and with no evidence of disease enhancement in seronegative population up to 3 years post-vaccination.Vianney Tricou, D Phil, Takeda Pharmaceuticals International (Employee) Shibadas Biswal, MD, Takeda Vaccines, Inc (Employee) Sanjay S. Patel, PhD, Takeda Pharmaceuticals International AG (Employee) Olaf Zent, MD, Takeda Pharmaceuticals International AG (Employee) Martina Rauscher, PhD, Takeda Pharmaceuticals International AG (Employee) Gonzalo Perez, MD, Takeda group companies (Employee) Walid Kandeil, MD, Takeda Pharmaceuticals International AG (Employee) Nicolas Folschweiller, PhD, Takeda (Employee)"} +{"text": "KBP-7072 was active against Staphylococcus aureus , methicillin-resistant S. aureus , S. lugdunensis , and other coagulase-negative staphylococci . KBP-7072 was active against Enterococcus faecalis and vancomycin-susceptible and -nonsusceptible E. faecium ; Streptococcus pneumoniae , including penicillin- and tetracycline-resistant strains; S. agalactiae , including macrolide-resistant strains; S. pyogenes ; and viridans group streptococci, including S. anginosus group isolates. KBP-7072 inhibited 90.2% of all Enterobacterales isolates, including expanded-spectrum \u03b2-lactamase-phenotype strains at \u22642\u2009mg/liter. KBP-7072 demonstrated potent activity against Acinetobacter baumannii-calcoaceticus species complex and Stenotrophomonas maltophilia isolates , Haemophilus influenzae , and Moraxella catarrhalis . Based on MIC90 values, KBP-7072 in vitro activity was generally superior to that the other tetracycline class comparators tested. The potent activity of KBP-7072, including resistant organism groups, merits further clinical investigation in infections where these organisms are likely to occur.KBP-7072 is a novel broad-spectrum tetracycline (aminomethylcycline) antibacterial in clinical development for the treatment of acute bacterial skin and skin structure infections, community-acquired bacterial pneumonia, and complicated intra-abdominal infections. KBP-7072 is active against many of the World Health Organization priority pathogens. In this study, KBP-7072 and tetracycline class comparators were susceptibility tested against 1,057 geographically diverse surveillance isolates from 2019 according to Clinical and Laboratory Standards Institute (CLSI) guidelines. KBP-7072 demonstrated potent The effectiveness of tetracycline antibacterials has declined since their initial discovery and introduction in the late 1940s, primarily due to the emergence of resistance caused by efflux and ribosomal protection mechanisms . This re1\u20135\u2013KBP-7072 has comp10\u2013in vitro antibacterial activity against many of the organisms listed on the World Health Organization (WHO) priority pathogen list, including methicillin-resistant Staphylococcus aureus, penicillin-nonsusceptible Streptococcus pneumoniae, vancomycin-resistant Enterococcus faecium, ampicillin-resistant Haemophilus influenzae, and carbapenem-resistant Acinetobacter baumannii , percent intermediate (I), and percent resistant (R) according to CLSI or FDA breakpoint interpretive criteria, are presented in 90 values, KBP-7072 was the most active agent tested against S. aureus, including methicillin-resistant S. aureus (MRSA) , tetracycline-resistant S. aureus , and enterococci , including vancomycin-nonsusceptible strains , S. agalactiae , S. pyogenes , and S. pneumoniae , including penicillin-resistant, tetracycline-resistant, and macrolide-resistant strains at \u22640.12\u2009mg/liter was comparable in activity to tigecycline , 8-fold more active than omadacycline and minocycline , 16-fold more active than doxycycline , and >32-fold more active than tetracycline was 4-fold more active than tigecycline , 8-fold more active than omadacycline and minocycline , >32-fold more active than doxycycline , and >64-fold more active than tetracycline (H. influenzae isolates (100.0%) were inhibited by \u22640.25\u2009mg/liter KBP-7072 (Cumulative percent inhibition and MIC strains and 2. Kmg/liter . Againstg/liter) . When teg/liter) . All H. KBP-7072 .50/90, 0.06/0.12\u2009mg/liter; 100.0% inhibited at \u22640.5\u2009mg/liter) demonstrated potent in vitro activity against 104 S. aureus isolates, including methicillin-susceptible S. aureus (MSSA) and MRSA organism subsets was 2-fold more active than minocycline , omadacycline , and tigecycline , 8-fold more active than doxycycline , and 128-fold more active than tetracycline (KBP-7072 (MIC subsets and 2. Sas 11.5% . Based oeptible) .50/90, 0.03/0.03\u2009mg/liter; 100.0% inhibited at \u22640.03\u2009mg/liter) demonstrated potent in vitro activity against 20 Staphylococcus lugdunensis isolates where resistance to tetracycline was 5.0% was comparable in activity to minocycline , 2-fold more active than doxycycline , omadacycline , and tigecycline and 4-fold more active than tetracycline (KBP-7072 (MICwas 5.0% . Based oeptible) and 2.50/90, 0.06/0.25\u2009mg/liter, 100% inhibited at \u22640.5\u2009mg/liter) and tigecycline were comparable in activity against 22 other coagulase-negative staphylococci (CoNS) isolates was 2-fold more active than minocycline , 4-fold more active than omadacycline , 32-fold more active than doxycycline , and 256-fold more active than tetracycline against other CoNS isolates isolates was 2-fold more active than omadacycline and tigecycline , minocycline , and tetracycline demonstrated limited activity against E. faecalis isolates (KBP-7072 was highly active against 51 isolates . Based oeptible) . Doxycycisolates .E. faecium isolates, and its activity was not adversely affected by susceptibility or nonsusceptibility to vancomycin was 2-fold more active than tigecycline and 4-fold more active than omadacycline , minocycline , and tetracycline demonstrated reduced activity against E. faecium isolates . Doxycycisolates .S. pneumoniae isolates (n\u2009=\u2009127) were highly susceptible to KBP-7072 , and its activity was not adversely affected by resistance to erythromycin , penicillin , or tetracycline was comparable in activity to tigecycline , 2-fold more active than omadacycline , 256-fold more active than doxycycline and minocycline , and 2,048-fold more active than tetracycline , and 27.6%, respectively , 22.0% for clindamycin, and 18.1% for trimethoprim-sulfamethoxazole (data not shown).g/liter) and 2. Beptible) . Resistaectively . ResistaS. agalactiae and 51 S. pyogenes isolates , were inhibited by \u22640.06\u2009mg/liter of KBP-7072 regardless of erythromycin (macrolide) resistance was comparable in activity to tigecycline , 4-fold more active than omadacycline , 256-fold more active than doxycycline , 512-fold more active than minocycline , and 1,024-fold more active than tetracycline was 2-fold more active than tigecycline , 4-fold more active than omadacycline , 256-fold more active than doxycycline and minocycline , and 1,024-fold more active than tetracycline . Similareptible) .Streptococcus anginosus group isolates (n\u2009=\u200917) were inhibited by low concentrations of KBP-7072 and tigecycline , 256-fold more active than doxycycline (MIC90 8\u2009mg/liter), 512-fold more active than minocycline , and 1,024-fold more active than tetracycline .All eptible) . Based oeptible) . Resista50/90, 0.25/2\u2009mg/liter; 90.2% inhibited at \u22642\u2009mg/liter) and tigecycline were the most active tetracycline class compounds tested against 410 Enterobacterales isolates was 8-fold more active than omadacycline and minocycline , 16-fold more active than doxycycline , and >32-fold more active than tetracycline against Enterobacterales isolates was comparable in activity to tigecycline against 133 tetracycline-resistant Enterobacterales isolates and meropenem (data not shown).KBP-7072 and tigecycline were the most active tetracycline class agents tested against 22 Citrobacter freundii species complex isolates was 8-fold more active than omadacycline and 16-fold more active than doxycycline, minocycline, and tetracycline (KBP-7072 (MICisolates . Based oeptible) .Citrobacter koseri isolates (n\u2009=\u200921) were susceptible (100.0%) to doxycycline, minocycline, tetracycline, and tigecycline. KBP-7072 and tigecycline were the most active tetracycline class agents against C. koseri, with MIC90 values of 0.25\u2009mg/liter.All 90, 0.5\u2009mg/liter; 100.0% inhibited at \u22644\u2009mg/liter) and tigecycline were the most active tetracycline class agents tested against 50 Enterobacter cloacae species complex isolates was 4-fold more active than doxycycline and 8-fold more active than minocycline , omadacycline , and tetracycline was equally active against ceftazidime-susceptible and ceftazidime-nonsusceptible (AmpC-derepressed phenotype) E. cloacae species complex isolates (KBP-7072 (MICisolates and 3. Beptible) . KBP-707isolates and 3.50/90, 0.12/0.5\u2009mg/liter; 100.0% inhibited at \u22642\u2009mg/liter) was active against 77 Escherichia coli isolates, including a subset of 26 expanded-spectrum \u03b2-lactamase (ESBL)-phenotype E. coli isolates was comparable in activity to tigecycline , 4-fold more active than omadacycline , 8-fold more active than minocycline , 32-fold more active than doxycycline , and >64-fold more active than tetracycline (KBP-7072 (MICg/liter) and 3. Aeptible) .90, 0.5\u2009mg/liter; 100.0% inhibited at \u22644\u2009mg/liter) and tigecycline were the most active tetracycline class agents tested against 21 Klebsiella aerogenes isolates was 4-fold more active than minocycline and omadacycline , 8-fold more active than doxycycline , and 16-fold more active than tetracycline (KBP-7072 (MICisolates . Based oeptible) .90, 0.5\u2009mg/liter; 100.0% inhibited at \u22642\u2009mg/liter) and tigecycline were comparable in activity against 53 K. oxytoca isolates was 4-fold more active than omadacycline , 8-fold more active than minocycline , and 16-fold more active than doxycycline and tetracycline (KBP-7072 (MICisolates . Based oeptible) .50/90, 0.25/1\u2009mg/liter; 100.0% inhibited at \u22644\u2009mg/liter) was active against 80 K. pneumoniae isolates, including a subset of 27 ESBL-phenotype K. pneumoniae isolates was comparable in activity to tigecycline , 8-fold more active than omadacycline , 16-fold more active than doxycycline , >16-fold more active than minocycline , and >32-fold more active than tetracycline (KBP-7072 (MICg/liter) and 3. Aeptible) .50/90, 1/2\u2009mg/liter; 95.0% inhibited at \u22642\u2009mg/liter) and tigecycline were the most active tetracycline class agents tested against 20 Morganella morganii isolates , minocycline , doxycycline , and tetracycline (KBP-7072 (MICisolates and 3. Reptible) .Proteus mirabilis isolates, including KBP-7072 , doxycycline , minocycline , omadacycline , tetracycline , and tigecycline (All tetracycline class agents demonstrated reduced or limited activity against 22 eptible) and 3.90, 4\u2009mg/liter; 95.5% inhibited at \u22644\u2009mg/liter) and tigecycline were the most active tetracycline class agents tested against 22 Providencia species isolates , minocycline , omadacycline , and tetracycline (KBP-7072 (MICisolates and 3. Oeptible) .90, 1\u2009mg/liter; 95.5% inhibited at \u22641\u2009mg/liter) and tigecycline were the most active tetracycline class agents tested against 22 Serratia marcescens isolates was 4-fold more active than minocycline , 8-fold more active than omadacycline , 16-fold more active than doxycycline , and >64-fold more active than tetracycline (KBP-7072 (MICisolates and 3. Beptible) .in vitro activity, KBP-7072 was the most potent tetracycline class agent tested against 22 A. baumanniicalcoaceticus species complex isolates was 4-fold more active than tigecycline , 8-fold more active than minocycline and omadacycline , >32-fold more active than doxycycline , and >64-fold more active than tetracycline .Based on isolates . KBP-707eptible) . Compara50/90, 8/16\u2009mg/liter) and all tetracycline class agents was limited against 22 Pseudomonas aeruginosa isolates and minocycline demonstrated potent in vitro activity against 22 Stenotrophomonas maltophilia isolates was 2-fold more active than tigecycline , 8-fold more active than omadacycline , and 64-fold more active than tetracycline .KBP-7072 , doxycycline , minocycline , omadacycline , tetracycline , and tigecycline (All tetracycline class agents were very active against 52 eptible) .50/90, 0.25/0.5\u2009mg/liter; 100.0% inhibited at \u22640.5\u2009mg/liter) was active against 12 H. parainfluenzae isolates was comparable in activity to tigecycline , 2-fold more active than tetracycline , and 4-fold more active than doxycycline , minocycline , and omadacycline (KBP-7072 (MICisolates and 3. Beptible) .50/90, 0.06/0.06\u2009mg/liter; 100.0% inhibited at \u22640.06\u2009mg/liter), were active against 21 Moraxella catarrhalis isolates pathogens, vancomycin-resistant E. faecium and MRSA were identified as priority 2 (high) pathogens, and ampicillin-resistant H. influenzae and penicillin-nonsusceptible S. pneumoniae were identified as priority 3 (medium) pathogens at a dose level of 200\u2009mg. The therapeutic dose for KBP-7072 is projected to be lower than the current daily oral dose for another aminomethylcycline class antibacterial (omadacycline) in community-acquired bacterial pneumonia and acute bacterial skin and skin structure infection ; tetracycline-resistant S. aureus (8-fold); E. faecium (4-fold); S. pneumoniae (2-fold), including penicillin-nonsusceptible strains; beta-hemolytic streptococci (4-fold); Enterobacterales (8-fold), including ESBL-phenotype and tetracycline-resistant strains; A. baumannii (8-fold); S. maltophilia (8-fold); and H. influenzae (4-fold).KBP-7072 has demonstrated dose-proportional pharmacokinetic/pharmacodynamic (PK/PD) properties in both animal models and phase I clinical studies supporting once-daily oral or intravenous administration 1013, 18\u20132018\u2013nfection . A lowerin vitro activity of KBP-7072 was unaffected by isolates displaying resistance to tetracycline. KBP-7072 remained active against isolates displaying resistance to other antibacterial agents, including ampicillin, ceftazidime, erythromycin, penicillin, and vancomycin.The in vitro activity of KBP-7072 against A. baumannii is also supported by a prior study using 531 isolates that included carbapenem-resistant, colistin-resistant, ESBL-positive, metallo-\u03b2-lactamase-producing, and tetracycline-resistant strains were collected from 117 medical centers located in 35 countries, including the United States , Europe , Latin America , and the Asia-Pacific region as part of the SENTRY Surveillance Program. The surveillance isolates utilized in this study were randomly selected from patients with skin and skin structure infections , pneumonia in hospitalized patients , and community-acquired respiratory tract infections and included only 1 isolate/patient/infection episode. The percentage of tetracycline-resistant isolates in this study generally mimicked the 2019 worldwide SENTRY Surveillance Program distributions for A. baumannii (54.5% versus 60.3% in SENTRY), Enterobacterales (32.4% versus 34.6% in SENTRY), H. influenzae (1.9% versus 1.4% in SENTRY), S. aureus (11.5% versus 6.0% in SENTRY), S. agalactiae (80.8% versus 79.6% in SENTRY), S. pneumoniae (27.6% versus 24.7% in SENTRY), and S. pyogenes (19.6% versus 21.2% in SENTRY). Organism identifications were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy .Geographically diverse, recent (2019) bacterial clinical isolates (KBP-7072 and omadacycline (KBP-3039) powders were supplied by KBP Biosciences Co., Ltd. . Doxycycline, tetracycline, and tigecycline powders were obtained from the United States Pharmacopeial Convention . Minocycline powder was obtained from Sigma-Aldrich .E. coli and K. pneumoniae isolates, MRSA, vancomycin-susceptible and -nonsusceptible E. faecium, penicillin-susceptible, -intermediate, -resistant , and tetracycline-resistant S. pneumoniae, erythromycin (macrolide)-resistant S. agalactiae and S. pyogenes, ceftazidime-susceptible and -nonsusceptible E. cloacae, carbapenem (meropenem)-resistant A. baumannii, and ampicillin-resistant H. influenzae phenotype for fluenzae . Most ESanalysis .Broth microdilution susceptibility testing was conducted at JMI Laboratories according to Clinical and Laboratory Standards Institute M07 and M100E. faecalis ATCC 29212, E. coli ATCC 25922, E. coli ATCC 35218, P. aeruginosa ATCC 27853, and S. aureus ATCC 29213. All (100.0%) of the doxycycline (18/18), minocycline (15/15), omadacycline (18/18), tetracycline (25/25), and tigecycline (18/18) MIC values obtained were within CLSI-approved quality control ranges (JMI Laboratories followed current CLSI quality assurance practices when performing susceptibility tests. MIC values were validated by concurrently testing the CLSI-recommended American"} +{"text": "Scientific Reports 10.1038/s41598-021-84500-6, published online 23 March 2021Correction to: The original version of this Article contained errors in References 27, 43 and 44, where hyperlinks to external data were omitted and as a result were incorrectly given as:27. Kramarenko, A. V. Demo of non-contac polatimetric cardiograph testing, 43. Kramarenko, A. V. Demo of an industrial application (pump work control) of a non-contact rf registration device .44. Kramarenko, A. V. Demo of a car driver monitoring system .The correct references are listed below:https://www.youtube.com/watch?v=gOGvGjJ2QnI (Accessed 23 Jul 2020a).27. Kramarenko, A. V. Demo of non-contac polatimetric cardiograph testing, https://www.youtube.com/watch?v=z-1pzf3iUyM (Accessed 3 Nov 2020b).43. Kramarenko, A. V. Demo of an industrial application (pump work control) of a non-contact rf registration device, https://www.youtube.com/watch?v=yB9uKd3MNxU (Accessed 13 Oct 2020c).44. Kramarenko, A. V. Demo of a car driver monitoring system, The original Article has been corrected."} +{"text": "TB meningitis is the most severe form of tuberculosis (TB), associated with high morbidity and mortality. High-dose rifampin (35mg/kg/day) is safe in adults and substantially improves the bactericidal activity of standard TB regimen. However, there is conflicting data regarding its benefit in TB meningitis where outcomes may also be associated with intracerebral inflammatory responses. Mycobacterium tuberculosis infections were used for these studies . Animals received high-dose (35 mg/kg/day) or standard-dose (10 mg/kg/day) rifampin in combination with isoniazid, pyrazinamide and dexamethasone at human equipotent dosing. Bacterial burden, multi-modality positron emission tomography (PET) imaging, tissue drug concentrations, markers of neuroinflammation, and vascular leak were measured. Imaging data from a patient with TB meningitis was analyzed and correlated with the findings in animals.A novel mouse and a validated rabbit model of TB meningitis utilizing intracranial Figure 1. Mouse model of TB meningitis replicates human histopathology hallmarks. (A) Scheme of infection. (B) Histopathology hematoxylin-eosin (H&E) and acid-fast bacilli (AFB) staining in a representative M. tuberculosis-infected mouse shows regions of meningitis, ventriculitis, choroiditis, necrotizing and non-necrotizing granulomas. The bar represents 100\u00b5m. (C) Images show immunofluorescence of microglia activation in red (Iba-1) and nuclear stain in blue (DAPI). The rabbit model of TB meningitis has been described previously . Animal studies were approved by the Johns Hopkins Animal Care and Use Committee.P < 0.01) . There were no differences in intracerebral microglial activation (124I-DPA-713 PET and iDISCO) and pro-inflammatory cytokines during treatment in animals receiving high- or standard-dose rifampin regimens . Whole-brain PET and immunolabeling demonstrated spatially compartmentalized inflammation, vascular leak and rifampin exposures . Longitudinal imaging in the same animals showed a 40% decrease in vascular leak after two weeks of TB treatment. Spatially compartmentalized brain rifampin exposures and decreases in vascular edema over TB treatment were also noted in the TB meningitis patient.Administration of the high-dose rifampin regimen achieved four times higher brain concentration than the standard-dose regimen and displayed higher bactericidal activity in both mice and rabbits Experimental scheme. R10 (rifampin 10mg/kg), R35 (rifampin 35mg/kg), H (isoniazid), Z (pyrazinamide), D (dexamethasone). (B) Bactericidal activity of high-dose rifampin and standard-dose rifampin regimens in mice. (C) Grouped colony forming units (CFU) and (D) rifampin brain concentration in mice after 42 days of TB treatments. (E) Bactericidal activity of high-dose rifampin and standard-dose rifampin regimens in rabbits. Data from untreated rabbits is also shown. (F) Grouped CFU and (G) rifampin brain concentration in rabbits after 14 days of TB treatments. Tissues were assayed using validated ultra-high-performance liquid chromatography and tandem mass spectrometry (LC-MS/MS) for rifampin at the Infectious Diseases Pharmacokinetics Laboratory of the University of Florida. The bacterial burden is represented as CFU per gram of tissue and presented on a logarithmic scale. CFU and mass spectrometry data are represented as mean \u00b1 SD. *P < 0.05, **P < 0.01 and ***P < 0.001 calculated using a two-way ANOVA test.Figure 3. Neuroinflammatory responses during TB treatment. (A) Iba-1 and DAPI immunofluorescence in a representative untreated, high-dose and low-dose-treated mouse. (B) Quantification of Iba-1 immunofluorescence before treatment and after 6 weeks of treatment (n = 3 mice per group). Sections were imaged at 40X with Nikon A1+ confocal microscope. HALO was used for visualization and quantification. Quantification of intraparenchymal (C) INF-\u03b3, (D) TNF and (E) MCP-1 in untreated and treated mice (Milliplex Multiplex Luminex assay). (F) Coronal CT and 124I-DPA-713 PET/CT of a representative mouse with TB meningitis before treatment initiation. (G) 124I-DPA-713 PET quantification before treatment and after 2 and 6 weeks of TB treatment. PET data is represented as median \u00b1 IQ. *P < 0.05, **P < 0.01 and ***P < 0.001 were calculated using a two-way ANOVA test.Figure 4. Changes in vascular leakage and rifampin penetration during TB treatment. (A) Experimental scheme in mice. (B) Whole-brain immunolabeling (iDISCO) of a representative M. tuberculosis-infected mouse prior to treatment initiation. Images show immunolabeling of \u03b1-smooth muscle actin in grey and microglia activation in red (Iba-1). Asterix represents the areas of vascular amputation. (C) Coronal 18F-py-Albumin PET/CT and quantification (tissue to plasma ratio) in untreated and 2 weeks-treated mice . (D) Serial imaging in a patient with TB meningitis. (E) Transverse T2 post-contrast section and maximal intensity projection (MIP) showing vasogenic edema. (F) Co-registered T2 post-contrast MIP with transverse 11C-rifampin area under the curve (AUC) heat-map, and 11C-rifampin tissue to plasma ratio quantification of the areas with and without vasogenic edema, and unaffected brain. (G) T2 post-contrast MIP at 3 and 45 months after treatment initiation. The patient with TB meningitis was recruited as part of a 11C-rifampin PET research study performed under the U.S. FDA Radioactive Drug Research Committee program for investigational drugs . Human studies were approved by the Johns Hopkins University Institutional Review Board Committee. M = moxifloxacin. PET data is represented as median \u00b1 IQ. *P < 0.05, **P < 0.01 and ***P < 0.001 calculated using a two-way ANOVA test.Our cross-species findings suggest that an intensified high-dose rifampin regimen is more efficacious than the standard treatment for TB meningitis without an increase in neuroinflammation. Vascular leak decreases during TB treatment and may account for decreases in rifampin permeability over time. These studies have important implications for antimicrobial development for TB meningitis.Charles A. Peloquin, Pharm.D., Nothing to disclose Alvaro A. Ordonez, MD, Cubresa (Consultant)Fujirebio Diagnostics (Research Grant or Support) Sanjay K. Jain, MD, Fujirebio Diagnostics, Inc., USA (Research Grant or Support)Novobiotic LLC, USA (Research Grant or Support)T3 Pharma, Switzerland (Research Grant or Support) Sanjay K. Jain, MD, Fujirebio Diagnostics, Inc., USA Involved: Self): Research Grant or Support; Novobiotic LLC, USA Involved: Self): Research Grant or Support; T3 Pharma, Switzerland Involved: Self): Research Grant or Support"} +{"text": "CLSI broth microdilution was used to determine MICs for Enterobacterales , Pseudomonas aeruginosa , Acinetobacter baumannii complex , Stenotrophomonas maltophilia , and Burkholderia cepacia complex (n\u2009=\u2009425). MICs were interpreted by CLSI-approved clinical breakpoints (February 2021). Cefiderocol inhibited 99.8, 96.7, 91.6, and 97.7% of all Enterobacterales, meropenem-nonsusceptible, ceftazidime-avibactam-nonsusceptible, and ceftolozane-tazobactam-nonsusceptible isolates, respectively, at \u22644\u2009\u03bcg/mL (susceptible breakpoint). Cefiderocol inhibited 99.9, 99.8, 100, and 99.8% of all P. aeruginosa, meropenem-nonsusceptible, ceftazidime-avibactam-nonsusceptible, and ceftolozane-tazobactam-nonsusceptible isolates, respectively, at \u22644\u2009\u03bcg/mL (susceptible breakpoint). Cefiderocol inhibited 96.0% of all A. baumannii complex isolates and 94.2% of meropenem-nonsusceptible isolates at \u22644\u2009\u03bcg/mL (susceptible breakpoint) and 98.6% of S. maltophilia isolates at \u22641\u2009\u03bcg/mL (susceptible breakpoint). B. cepacia complex isolates were tested with a MIC50 of \u22640.03\u2009\u03bcg/mL and MIC90 of 0.5\u2009\u03bcg/mL. Annual cefiderocol percent susceptible rates for Enterobacterales and P. aeruginosa were unchanged from 2014 to 2019. Annual percent susceptible rates for A. baumannii complex demonstrated sporadic, nondirectional differences ; the wider range for Europe (\u223c7%) was due to isolates from Russia. Annual percent susceptible rates for S. maltophilia showed minor, nondirectional differences . We conclude that clinical isolates of Enterobacterales (99.8% susceptible), P. aeruginosa (99.9%), A. baumannii (96.0%), and S. maltophilia (98.6%) collected in North America and Europe from 2014 to 2019 were highly susceptible to cefiderocol.We report Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii as pathogens of the highest priority for development of new antibacterial agents when limited or no other treatment options exist , P. aeruginosa, and Acinetobacter baumannii complex. Clinical development of cefiderocol continues for the treatment of serious infections attributable to resistant Gram-negative bacilli, including infections caused by carbapenem-resistant Gram-negative bacilli , and difficult-to-treat Gram-negative bacilli is increasing worldwide, and therapeutic options for infected patients are often limited \u20133. The W\u2013l agents . Cefiderns exist . In Aprins exist . In Sept bacilli .Cefiderocol possesses a unique mechanism of bacterial cell entry, making it an important addition to the antimicrobial armamentarium. The optimized chloro-catechol moiety within the C-3 side chain of cefiderocol facilitates formation of chelated complexes with ferric iron and expedites its transport across the outer membrane of Gram-negative bacilli using constitutive iron transport systems . Followi7\u2013in vitro activities for recently approved and investigational agents is critical to establishing and supporting treatment decisions and expanding the role of these agents in patient care, particularly for patients where unmet medical need exists , 8\u2009\u03bcg/mL (intermediate), and \u226516\u2009\u03bcg/mL (resistant) and for Stenotrophomonas maltophilia of \u22641\u2009\u03bcg/mL (susceptible) and >1\u2009\u03bcg/mL (nonsusceptible) . The updeptible) and the eptible) collected over five consecutive annual SIDERO-WT surveillance studies (from November 2014 to December 2019) conducted in North America and Europe using the recently approved (February 2021) CLSI MIC clinical breakpoints and 90% (MIC90) of the 31,896 isolates of Enterobacterales tested from North America and Europe from 2014 to 2019 were 0.12 and 1\u2009\u03bcg/mL, respectively isolates of Enterobacterales; 96.7% of meropenem-nonsusceptible isolates were susceptible to cefiderocol. Cefiderocol demonstrated a higher percent susceptible rate against meropenem-nonsusceptible isolates (\u226520% higher) than ceftazidime-avibactam (77.0%), cefepime (8.7%), ceftolozane-tazobactam (7.8%), and ciprofloxacin (7.8%). A total of 91.6% of 263 isolates of ceftazidime-avibactam-nonsusceptible Enterobacterales and 97.7% of 2,658 isolates of ceftolozane-tazobactam-nonsusceptible Enterobacterales were susceptible to cefiderocol. In comparison, only 3.8% of ceftazidime-avibactam-nonsusceptible Enterobacterales isolates were susceptible to ceftolozane-tazobactam and 90.5% of ceftolozane-tazobactam-nonsusceptible Enterobacterales isolates were susceptible to ceftazidime-avibactam. MIC90 values for colistin and ciprofloxacin were 1 and >8\u2009\u03bcg/mL, respectively, for all isolates of Enterobacterales tested.The minimal inhibitory concentrations of cefiderocol that inhibited 50% demonstrated a rightward shift (of 1 to 3 doubling dilutions) to higher cefiderocol MICs compared to each respective antimicrobial-susceptible subset; however, as mentioned earlier, most meropenem (96.7%)-, ceftazidime-avibactam (91.6%)-, and ceftolozane-tazobactam (97.7%)-nonsusceptible isolates remained susceptible to cefiderocol, with MICs of \u22644\u2009\u03bcg/mL.Cefiderocol MICs for meropenem-nonsusceptible , ceftazi50 and MIC90 were 0.12 and 0.5\u2009\u03bcg/mL for 7,700 isolates of P. aeruginosa collected in North America and Europe from 2014 to 2019 P. aeruginosa were 0.25 and 1\u2009\u03bcg/mL, respectively, and 99.9% of meropenem-nonsusceptible isolates were susceptible to cefiderocol. Ceftazidime-avibactam, ceftolozane-tazobactam, and cefepime were all tested with MIC90 values of 32 or >64\u2009\u03bcg/mL against isolates of meropenem-nonsusceptible P. aeruginosa and exhibited percent susceptible rates of 76.1% (ceftolozane-tazobactam), 75.0% (ceftazidime-avibactam), and 49.0% (cefepime). MIC90 values for ciprofloxacin (31.2% susceptible) and colistin were >8\u2009\u03bcg/mL and 1\u2009\u03bcg/mL, respectively, for meropenem-nonsusceptible P. aeruginosa. A total of 100% of 477 isolates of ceftazidime-avibactam-nonsusceptible and 99.8% of 463 isolates of ceftolozane-tazobactam-nonsusceptible P. aeruginosa, respectively, were susceptible to cefiderocol. In comparison, only 24.3% of ceftazidime-avibactam-nonsusceptible P. aeruginosa isolates were susceptible to ceftolozane-tazobactam, and only 22.0% of ceftolozane-tazobactam-nonsusceptible P. aeruginosa isolates were susceptible to ceftazidime-avibactam.The cefiderocol MIC to 2019 . CefiderP. aeruginosa (both North American and European isolates combined) demonstrated a rightward shift (of 1 doubling dilution) to higher cefiderocol MICs compared to each respective antimicrobial-susceptible subset; however, almost every nonsusceptible isolate (99.8 to 100%) remained susceptible to cefiderocol, with a MIC of \u22644\u2009\u03bcg/mL.Cefiderocol MICs for meropenem-nonsusceptible , ceftazi50 and MIC90 of cefiderocol for isolates of A. baumannii complex from both North America and Europe were 0.12 and 1\u2009\u03bcg/mL; 96.0% of isolates demonstrated cefiderocol MICs of \u22644\u2009\u03bcg/mL and MIC90 values (1\u2009\u03bcg/mL) for the meropenem-nonsusceptible subset of isolates and Europe (99.3 to 99.9% susceptible) varied over very narrow ranges (0.4 to 0.6%) than for isolates from Europe (90.4 to 97.5%). In total, there were 171 isolates of A. baumannii with cefiderocol MICs of \u22658\u2009\u03bcg/mL (nonsusceptible) collected in Europe from 2014 to 2019. Of these isolates, 74.3% (127/171) were from one country (Russia); 127/437 (29.1%) of isolates from Russia were cefiderocol nonsusceptible, with annual rates of 28.2% (11/39) in 2014, 41.2% (7/17) in 2015, 24.1% (19/79) in 2016, 42.7% (50/117) in 2017, 31.9% (36/113) in 2018, and 5.6% (4/72) in 2019. Other European countries contributing >10 isolates over the study period submitted isolates with cefiderocol-nonsusceptible MICs at rates ranging from zero (no cefiderocol-nonsusceptible isolates) to 7.3% (8/109 isolates [United Kingdom]). Annual cefiderocol MIC distributions for Enterobacterales, P. aeruginosa, A. baumannii complex, S. maltophilia, and B. cepacia complex are provided in Tables S2 to S6 in the supplemental material.Annual cefiderocol percent susceptible rates for isolates of to 0.6%) . Even leEnterobacterales from North America (99.7 to 100%) and Europe (98.2 to 98.8%) were similar , while annual percent susceptible rates for ceftolozane-tazobactam were higher in isolates from North America (93.8 to 94.9%) than in those from Europe (87.3 to 90.6%) (P. aeruginosa from North America were higher for both ceftazidime-avibactam (96.0 to 99.6%) and ceftolozane-tazobactam (96.7 to 99.6%) than for isolates from Europe .Annual percent susceptible rates for ceftazidime-avibactam for isolates of o 90.6%) . Annual Enterobacterales, P. aeruginosa, A. baumannii complex, S. maltophilia, and B. cepacia complex collected in 2019 were also tested against meropenem-vaborbactam and imipenem-relebactam . Meropenem-vaborbactam demonstrated in vitro activity similar to that of ceftazidime-avibactam against Enterobacterales (98.9% of isolates susceptible); <70% of meropenem-nonsusceptible Enterobacterales isolates were susceptible to meropenem-vaborbactam and imipenem-relebactam, compared to 93.2% susceptible for cefiderocol. Imipenem-relebactam was less active (83.9% susceptible) than ceftazidime-avibactam against P. aeruginosa, compared to 99.9% susceptible for cefiderocol. Meropenem-vaborbactam and imipenem-relebactam were largely inactive in vitro against clinical isolates of A. baumannii complex and S. maltophilia .Isolates of Enterobacterales (99.8%), P. aeruginosa (99.9%), A. baumannii complex (96.0%), and S. maltophilia (98.6%) collected across North America and Europe from 2104 to 2019 were susceptible to cefiderocol. Data in the current study confirm and expand upon data presented in earlier studies. Cefiderocol was previously reported to demonstrate potent in vitro activity against key Gram-negative pathogens but only limited activity against Gram-positive and anaerobic bacteria , P. aeruginosa (\u226597%), and A. baumannii complex (\u226591%) isolates, as well as MDR Enterobacterales (\u226597%), P. aeruginosa (\u226597%), and A. baumannii complex (\u226590%) isolates and P. aeruginosa (>99%), with ceftazidime-avibactam-, ceftolozane-tazobactam-, cefepime-, ciprofloxacin- and colistin-resistant phenotypes at MICs of \u22644\u2009\u03bcg/mL , S. maltophilia , and B. cepacia complex .Data in the current study clearly demonstrate that the large majority of isolates of bacteria , 10, 15.cteria 2023 and rerales 99.%, P. aercteria 20\u201314, 24 hrales 99.%, P. aerrales 99.%, P. aerEnterobacterales, P. aeruginosa, and A. baumannii have not been identified, although the addition of avibactam, a \u03b2-lactamase inhibitor, to cefiderocol has been shown to lower the MICs for some cefiderocol-resistant isolates, primarily A. baumannii possessing various ESBLs. or PiuA (not PirA) (P. aeruginosa) can also elevate cefiderocol MICs or Acinetobacter spp. , and the FDA has not published breakpoints for S. maltophilia , P. aeruginosa (99.9%), A. baumannii complex (96.0%), and S. maltophilia (98.6%) in North America and Europe are susceptible to cefiderocol by the recently approved CLSI MIC breakpoints and P. aeruginosa were negligible. Annual percent susceptible rates for A. baumannii complex demonstrated sporadic, nondirectional differences , primarily due to isolates from Russia. Annual percent susceptible rates for S. maltophilia also showed minor, nondirectional fluctuation . In vitro susceptibility testing of cefiderocol may be of benefit when cefiderocol is being considered for treatment of patients infected with carbapenem-nonsusceptible, ceftazidime-avibactam-nonsusceptible, or ceftolozane-tazobactam-nonsusceptible isolates of Enterobacterales and P. aeruginosa, carbapenem-nonsusceptible isolates of A. baumannii complex, and MDR isolates of S. maltophilia.We conclude that most current (2014 to 2019) clinical isolates of akpoints . ImportaEnterobacterales, 7,700 isolates of P. aeruginosa, 5,225 isolates of A. baumannii complex, 2,030 isolates of S. maltophilia, and 425 isolates of B. cepacia complex were collected in North America and Europe from 2014 to 2019. All isolates were shipped to IHMA , where their identities were confirmed using matrix-assisted laser desorption ionization\u2013time of flight mass (MALDI-TOF) mass spectrometry .SIDERO-WT surveillance studies, sponsored by Shionogi & Co., Ltd., , were run annually from November 2014 to December 2019. In those studies, predefined quotas of isolates of specific Gram-negative bacilli cultured from patients with intra-abdominal, urinary tract, lower respiratory tract, skin and soft tissue, or bloodstream infections were collected from clinical laboratories in North America and Europe as previously described , 15, 20.Enterobacterales, P. aeruginosa, and Acinetobacter species of \u22644\u2009\u03bcg/mL for susceptible, 8\u2009\u03bcg/mL for intermediate, and \u226516\u2009\u03bcg/mL for resistant and MIC breakpoints for S. maltophilia of \u22641\u2009\u03bcg/mL for susceptible and >1\u2009\u03bcg/mL for nonsusceptible (CLSI-defined broth microdilution susceptibility testing was performed at IHMA using custom in-house-prepared broth microdilution panels , 16, 30.ceptible ."} +{"text": "DRIVE-FORWARD is a phase 3 trial with a completed double-blind period comparing doravirine (DOR) 100 mg with ritonavir-boosted darunavir (DRV/r) 800/100 mg, both administered with two nucleos(t)ide reverse transcriptase inhibitors , and an ongoing open-label extension. At Week (W) 48, DOR demonstrated non-inferior efficacy to DRV/r, with a superior lipid profile. Those results were sustained at W96. Here we present efficacy and safety results through W192.Participants who completed the 96-week double-blind phase and met inclusion criteria were eligible to receive open-label DOR plus two NRTIs in a 96-week extension. Efficacy and safety at W192 were assessed in two groups: participants initially randomized to DOR and maintained on DOR (n=259) and those who switched from DRV/r to DOR at W96 (n=233).3) and those switched from DRV/r (53 cells/mm3). Protocol-defined virologic failure occurred in 3.1% and 5.6% of participants maintained on DOR and switched from DRV/r, respectively, and development of genotypic resistance was low in both groups (Table 1). Discontinuation due to adverse events was also low (Table 1). Fasting LDL-cholesterol, non-HDL-cholesterol, and triglycerides showed minimal increase in participants maintained on DOR and were reduced in those switched from DRV/r to DOR (Table 1). Participants maintained on DOR had minimal weight gain after W96 (median 1 kg), and a small increase overall ; participants who switched to DOR had a small increase after W96 (median 1.5 kg), similar to the median weight gain in the base study .HIV-1 RNA < 50 copies/mL were maintained through W192 in 81.1% of participants who continued DOR and 80.7% of those who switched from DRV/r to DOR. The mean increase in CD4 T-cell counts from W96 to W192 was similar for participants maintained on DOR ViiV Healthcare Kathleen Squires, MD, Merck (Employee) Sushma Kumar, PhD, Merck (Employee) Hong Wan, PhD, Merck (Employee) Valerie Teal, MS, Merck (Employee) Ernest Asante-Appiah, PhD, Merck (Employee) Peter Sklar, MD, Merck (Employee) Elizabeth A. Martin, DO, MPH, MBA, Merck (Employee) Rima Lahoulou, n/a, Merck (Employee)"} +{"text": "African Americans (AA) and Latinos, compared with Whites, experience disproportionately higher rates of morbidity and mortality in COVID-19. Exuberant inflammatory responses may explain, in part, the differences in disease severity in COVID-19 observed among different demographic groups.In a retrospective cohort study, we analyzed data from patients aged \u226518 years hospitalized for COVID-19 (confirmed by positive SARS-CoV-2 PCR) from 3/1/2020 \u2013 12/31/2020 at Emory Healthcare hospitals. Patient demographics, clinical characteristics, and peak levels of high-sensitivity C-reactive protein (hs-CRP) during hospitalization were abstracted from electronic medical record. Comorbidity burden was defined as the number of six total comorbidities assessed per patient. Multivariable logistic regression assessed the effects of race and comorbidity burden on peak hs-CRP level.3,860 patients, median age 60 [18-108] years, 51% female, 57% AA, 28% White, 6% Latino and 9% other races were enrolled. Median comorbidity burden per patient was 2 , with prevalent comorbidities distributed as follows: 68% had hypertension, 43% renal disease, 42% diabetes, 16% cardiovascular disease, 12% lung disease, and 5% cancer. Unadjusted peak hs-CRP (mg/L) levels were highest among Latino patients (144.9) followed by other races (137), AA (130.3), and Whites (122.2). In adjusted models (including race), the mean difference in peak hs-CRP (mg/L) compared with patients who had no comorbidities was 18.7 (p=0.108), 56.7 (p< 0.001), and 78.2 mg/L (p< 0.001) for 1, 2, and \u22653 comorbidities, respectively. In adjusted models (including comorbidity burden), the mean level of peak hs-CRP, compared with Whites, was 34.2 (p< 0.001), 38.4 (p=0.003), and 36.0 mg/L (p=0.06) higher in AA, Latinos, and other races, respectively.Among patients hospitalized with COVID-19, non-White race and comorbidity burden were associated with significantly higher levels of inflammation. These findings suggest that exuberant inflammatory responses may be driving, in part, the differences in COVID-19 disease severity observed across different demographic groups. Lauren F. Collins, MD, MSc, Nothing to disclose"} +{"text": "Ceftolozane/tazobactam (C/T) is an antipseudomonal cephalosporin combined with a \u03b2-lactamase inhibitor approved by FDA and EMA for complicated urinary tract (cUTI) and complicated intraabdominal infections (cIAI), as well as hospital-acquired/ventilator-associated bacterial pneumonia (HABP/VABP) in patients \u226518 years. Clinical trials studying the use of C/T for pediatric patients with cUTI and cIAI are completed, and HABP/VABP pediatric studies are underway. We evaluated the antimicrobial activity of C/T against gram-negative isolates collected from patients \u226417 years in the United States (US) as part of the global SMART surveillance program.P. aeruginosa were screened for genes encoding \u03b2-lactamases.In 2017-2019, 27 US clinical labs each collected up to 250 consecutive gram-negative pathogens per year. A total of 1336 isolates were collected from pediatric patients. MICs were determined using CLSI broth microdilution and breakpoints. C/T-nonsusceptible Enterobacterales (Ebact) and P. aeruginosa isolates, 40.7% and 76.4%, respectively, were collected from patients with respiratory tract infections, 37.0% and 10.0% from UTI, 13.7% and 8.2% from IAI, and 8.3% and 5.0% from bloodstream infections. The table shows antimicrobial susceptibility of Ebact, P. aeruginosa, and select phenotypes. C/T was active against 98% of Ebact, including 50 of 51 and 12 of 13 ESBL-non-CRE phenotype E. coli and K. pneumoniae, respectively. Among P. aeruginosa, C/T was active against 95% of isolates, 9-21 percentage points higher than the comparator \u03b2-lactams, and it maintained activity against 71-75% of P. aeruginosa isolates nonsusceptible to commonly used \u03b2-lactams. Among the 21 C/T-nonsusceptible Ebact, 2 isolates carried KPC and ESBL and 3 isolates carried only ESBL; in 16 isolates no \u03b2-lactamases were detected, of which 15 were species with intrinsic AmpC. Among 12 C/T-nonsusceptible P. aeruginosa, no acquired \u03b2-lactamases were detected, likely indicating chromosomally-mediated resistance mechanisms.Among the 944 collected Ebact and 220 Results TableP. aeruginosa, including resistant phenotypes.C/T could be a potential new treatment option for US pediatric patients with infections caused by Ebact and Sibylle Lob, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Meredith Hackel, PhD MPH, IHMA (Employee)Pfizer, Inc. (Independent Contractor) C. Andrew DeRyke, PharmD, Merck & Co., Inc. Kelly Harris, PharmD, BCPS, Merck & Co. Inc (Employee) Katherine Young, MS, Merck (Employee) Mary Motyl, PhD, Merck & Co., Inc. Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)"} +{"text": "Dear Editors,We and others have shown that kidney transplant recipients (KTR) exhibit a reduced immune response with a seroconversion (SC) rate <50% after a regular 2-dose mRNA SARS-CoV-2 vaccination regimen , 2. Very\u00ae SARS-CoV-2-TrimericS IgG chemiluminescent immunoassay, Diasorin S.p.A., Saluggia, Italy; cut-off value for seroconversion: \u226533.8\u00a0BAU/mL). After double mRNA vaccination the SC rate was 48%. Following heterologous triple vaccination an additional 54% of the initial non-responders achieved SC. Altogether, 97 out of 122 KTR (80%) achieved SC after either double mRNA vaccination or the heterologous triple vaccination. Forty-eight of the 142 KTR showed high-level SC after double mRNA vaccination. Twenty patients developed low antibody concentrations (arbitrary threshold <350\u00a0BAU/mL). After a third heterologous dose all these 20 patients significantly boosted their humoral response (1391.9 (SD 687.2) vs. 144.8 (SD 94.6) BAU/mL, p < 0.001). Non-responders after heterologous triple vaccination were significantly older , were more often treated with prednisolone or belatacept and had a shorter median transplantation vintage . They showed a trend of lower mean eGFR and being treated more often with mycophenolic acid . Higher mycophenolic acid doses did not correlate with inferior antibody response (p = 0.299). As a limitation, our study lacks cellular immune response and neutralizing antibody data. But anti-spike IgG antibodies are highly correlated with neutralizing antibodies, and a level >264\u00a0BAU/mL has been found to be associated with 80% vaccine efficacy against primary symptomatic Covid-19, although limited to the B.1.177 and B.1.1.7 SARS-CoV-2 variant (vs. 4.6\u00a0years) and extended interval between second and third dose (109 vs. 80\u00a0days) in our cohort compared to the study by Reindl-Schwaighofer et al. after double mRNA and triple heterologous vaccination . Patient"} +{"text": "While the second wave of COVID-19 pandemic almost reached its climax, unfortunately, new viral strains are rapidly spreading, and numbers of infected young adults are rising. Consequently, chest high-resolution computed tomography (HRCT) demands are increasing, regarding patients\u2019 screening, initial evaluation and follow up. This study aims to evaluate the detection accuracy of ultra-low-dose chest CT in comparison with the routine low-dose chest CT to reduce the irradiation exposure hazards.-4.This study was prospectively conducted on 250 patients during the period from 15th December 2020 to 10th February 2021. All of the included patients were clinically suspected of COVID-19 infection. All patients were subjected to routine low-dose (45 mAs) and ultra-low-dose (22 mAs) chest CT examinations. Finally, all patients had confirmatory PCR swab tests and other dedicated laboratory tests. They included 149 males and 101 females (59.6%:40.4%). Their age ranged from 16 to 84 years (mean age 50 \u00b1 34 SD). Patients were divided according to body weight; 104 patients were less than 80 kg, and 146 patients were more than 80 kg. HRCT findings were examined by two expert consultant radiologists independently, and data analysis was performed by other two expert specialist and consultant radiologists. The inter-observer agreement (IOA) was excellent (96\u2013100%). The ultra-low-dose chest CT reached 93.53\u201396.84% sensitivity and 90.38\u201393.84% accuracy. The signal-to-noise ratio (SNR) is 12.8:16.1; CTDIvol (mGy) = 1.1 \u00b1 0.3, DLP (mGy cm) = 42.2 \u00b1 7.9, mean effective dose (mSv/mGy cm) = 0.59 and absolute cancer risk = 0.02 \u00d7 10Ultra-low-dose HRCT can be reliably used during the second wave of COVID-19 pandemic to reduce the irradiation exposure hazards. Real-time polymerase chain reaction (PCR) remains the gold standard tool for the diagnosis of the Novel coronavirus disease COVID-19) since it was first described in December 2019 and announced as a pandemic in February 2020 9 since i, 4.On the other hand, high-resolution computed tomography (HRCT) expressed more availability and more rapid results. Besides, HRCT sensitivity exceeded 90% in comparison with PCR sensitivity which could not exceed 75% \u20138. Low-dIn September 2019, the American Association of Physicists in Medicine (AAPM) suggested certain criteria for efficient low-dose CT during lung cancer screening among standard-sized persons (70\u201390 kg), including CTDIvol \u2264 3.0 mGy, DLP \u2264 75 mGy cm and effective dose \u2264 1.0 mSv . A dose While the second wave of COVID-19 pandemic almost reached its climax, unfortunately, new viral strains are rapidly spreading, and numbers of infected young adults are rapidly rising. Hence, chest HRCT demands are increasing.This study aims to evaluate the detection accuracy of ultra-low-dose chest CT in comparison with the routine low-dose chest CT during the assessment of COVID-19 patients in order to reduce the irradiation exposure hazards.This study was prospectively conducted on 250 patients who were clinically suspected of COVID-19 infection during the period from 15th December 2020 to 10th February 2021. The study was approved by the Ethics Committee of our University hospital. Patient verbal consent was accepted by the Ethics Committee respecting absolute safety of non-invasive non-therapeutic procedure without additional personal risk or burden to the public health, also assuring full respect of both patient and medical record confidentiality. The authors emphasize on the fact that the overall radiation dose in both low- and ultra-low-dose CT examinations together remains much lower than single routine chest CT examination.Patients included 149 males and 101 females (59.6%:40.4%). Their age ranged from 16 to 84 years (mean age 50 \u00b1 34 SD). By definition of the American Association of Physicists in Medicine (AAPM), the standard bodyweight for an adult ranges from 70 to 90 kg [2) [ of air] . The staair] [2) . By defiair] [2) .Fig. 1IThe prevalence rate of each HRCT finding (isolated or mixed) was estimated as the percentage of patients with each abnormal CT finding. This was done by each observer for both groups of patients regarding both low-dose and ultra-low-dose CT examinations.Similarly, the prevalence rate of the maximum attenuation of the pathological lesions was also estimated.Cohen\u2019s Kappa test was utilized to calculate the \u201cInter-Observer Agreement\u201d (IOA) coefficient regarding each HRCT characteristic and lung attenuation.https://www.medcalc.org/calc/diagnostic_test.php) was utilized to detect the mean value and 95% confidence interval (95% CI) regarding the sensitivity, specificity, positive predictive value (PPV), negative predictive value, positive likelihood ratio, negative likelihood ratio, and accuracy of both low-dose and ultra-low-dose CT protocols.An online calculator in the ultra-low-dose CT was lower than that in the low-dose CT (12.8\u201316.1 compared with 17.5\u201324.4 respectively). This almost did not impact the diagnostic efficacy of CT as detailed later on.Ground-glass opacities were the most common findings among our patients. They were found alone in 173 patients (69.2%). They were found also surrounding a solid nodule among 49 patients (19.6%) and associated with interlobular septal thickening (crazy paving pattern) also among 49 patients (19.6%). Consolidative changes with or without ground-glass opacities were detected among 84 patients (33.6%). The CT attenuation of these pathological CT findings ranged from + 40 to \u2212 750 HU. The predominant CT attenuation among these CT findings ranged from \u2013 300 to \u2212 400 HU (157 patients/62.8%).In comparison with the low-dose CT, the ultra-low-dose CT protocol similarly detected all HRCT findings of COVID-19 , as well as their ranges of CT attenuation (+ 40 to \u2212 750 HU). The inter-observer agreement was excellent (100%) Figs. and 3.FIn comparison with the low-dose CT, the ultra-low-dose CT protocol only showed lower efficacy regarding detection of small GG nodules < 1 cm and nodules with ground-glass halo sign (ranging from 77 to 94% and 91 to 96% among both observers respectively). The CT attenuation of these lesions ranged from \u2212 300 to \u2212 600 HU. Otherwise, no absolute differences were found regarding the detection of the rest of the HRCT findings and their ranges of CT attenuation. Finally, the inter-observer agreement was collectively excellent (96\u2013100%) Figs. and 6.FA multi-compartmental flow chart Fig. is summaCollectively the ultra-low-dose chest CT reached 93.53\u201396.84% sensitivity and 90.38\u201393.84% accuracy in comparison with the low-dose CT which showed 96.84\u201397.84% sensitivity and 90.38\u201395.21% accuracy.No differences were found between both observers at both low-dose and ultra-low-dose CT protocols regarding the final diagnosis. Ninety-two patients (88.5%) were truly positive and confirmed by PCR to have COVID-19. On the other hand, only 3 patients (3%) were false negative. Consequently, both CT protocols showed same statistical results: sensitivity (mean = 96.84% and CI 95% = 91.05 to 99.34%) and accuracy (mean = 90.38% and CI 95% = 83.03 to 95.29%).CT specificity was equally low (22.22%) for both low-dose and ultra-low-dose CT as 7/99 patients showed false-positive CT results with negative PCR swab tests and alternative diagnoses .Observer 1 truly detected 130 patients using ultra-low-dose CT compared with 136 patients using low-dose CT. Six cases were furtherly missed using the ultra-lose-dose CT. Consequently the low-dose CT showed sensitivity (mean = 97.84% and CI 95% = 93.82 to 99.55%) and accuracy (mean = 95.21% and CI 95% = 90.37 to 98.05%), while the ultra-low-dose CT showed sensitivity (mean = 93.53% and CI 95% = 88.06 to 97.00%) and accuracy (mean = 91.10% and CI 95% = 85.26 to 95.17%).Meanwhile, observer 2 truly detected 134 patients using ultra-low-dose CT compared with 136 patients using low-dose CT, while only two cases were furtherly missed using the ultra-low-dose CT. Consequently the low-dose CT showed sensitivity (mean = 97.84% and CI 95% = 93.82 to 99.55%) and accuracy (mean = 95.21% and CI 95% = 90.37 to 98.05%), while the ultra-low-dose CT showed sensitivity (mean = 96.40% and CI 95% = 91.81 to 98.82%) and accuracy (mean= 93.84% and CI 95%= 88.62 to 97.14%).CT specificity was equally low (42.86%) for both low-dose and ultra-low-dose CT as 4/146 patients showed false-positive CT results with negative PCR swab tests and alternative diagnoses .Comparison with other CT protocols is demonstrated in Table The second wave and even further crisis of COVID-19 pandemic are striking the world with increased demands for chest CT imaging .Similar to Chung et al. and Song-4. These estimated radiation doses are 12.5:13.3 and 18.1:20 times more than that of the low-dose and the ultra-low-dose CT protocols in this study respectively. Additionally, the DLP and absolute cancer risk of the ultra-low-dose CT in this study were lower than those provided by Tabatabaei et al. [According to Kubo et al. , the DLPi et al. and Bahri et al. and iterative dose reduction (IDR).Ultra-low-dose HRCT can be reliably used during the second wave of COVID-19 pandemic to reduce irradiation exposure hazards."} +{"text": "Scientific Reportshttps://doi.org/10.1038/s41598-019-51090-3, published online 10 October 2019Correction to: The original version of this Article omitted Supplementary Table S1, Supplementary Table S2, and Supplementary Table S3.These Supplementary Information files now accompany the original Article."} +{"text": "The prognostic value of bile duct invasion (BDI) remains controversial. We aimed to investigate the prognostic value of BDI and the stage of BDI in different staging systems.Patients with hepatocellular carcinoma (HCC) from nine hepatobiliary medical centers who underwent R0 resection were included. Overall survival (OS) was assessed using the Kaplan\u2013Meier method and tested using the log-rank test. The prognostic effect of BDI was analyzed using univariate and multivariate Cox proportional hazard regression analyses. The predictive performance of these models was evaluated using the concordance index and time-dependent receiver operating characteristic curve (tdAUC).Of 1021 patients with HCC, 177 had BDI. OS was worse in the HCC with BDI group than in the HCC without BDI group (p<0.001); multivariate analysis identified BDI as an independent risk factor for OS. After adjustment for interference of confounding factors using the Cox proportional hazard regression model, HCC with BDI and without macrovascular invasion was classified as Barcelona Clinic Liver Cancer (BCLC) B, eighth edition American Joint Committee on Cancer (AJCC) IIIA, and China Liver Cancer (CNLC) IIb, respectively, whereas HCC with BDI and macrovascular was classified as BCLC C, AJCC IIIB, and CNLC IIIA, respectively. C-indexes and tdAUCs of the adjusted staging systems were superior to those of the corresponding current staging systems.We constructed adjusted staging systems with the BDI status, improved their predictive performance and facilitate clinical use. Hepatocellular carcinoma (HCC) is the sixth common cancer and fourth cancer-specific cause of death globally . HCC is th AJCC) staging system .HCC patients with microscopic or macroscopic BDI admitted to one of the nine Chinese hepatobiliary medical centers between March 1, 2007 and March 1, 2018 were included. HCC patients without BDI were from the Mengchao Hepatobiliary Hospital of Fujian Medical University and Eastern Hepatobiliary Surgery Hospital of Second Military Medical University during the same period.The inclusion criteria were as follows: 1) both HCC and BDI were histopathologically confirmed, 2) tumors were treated with R0 resection, and 3) complete clinical data and postoperative follow-up records. The exclusion criteria were as follows: 1)\u00a0recurrent or metastatic HCC, 2) combined HCC-intrahepatic cholangiocarcinoma, 3) other accompanying cancers, and 4) clinical data or survival data are missing. R0 resection was defined as the removal of all macroscopic tumors with a microscopically negative margin. The decision of treatment depends on the discussion of the multidisciplinary team in each center, whether perform surgical resection mainly considering the liver function, residual liver volume, tumor related factors such as if complicated with portal vein main trunk tumor thrombus or vena cava tumor thrombus or distant metastasis, and whether tumor and tumor thrombus can be completely removed.All patients were regularly followed up after discharge from the hospital. Follow-up visits were scheduled once every 2\u20133 months in the first 2 years, once every 6 months from 2 to 5 years, and once every year after 5 years. Follow-up examinations were conducted using laboratory tests , abdominal ultrasonography, and/or contrast-enhanced computed tomography magnetic resonance imaging. Overall survival (OS) was defined as the time of resection to the date of either death or the latest follow-up. Data including baseline and clinical characteristics and follow-up information were extracted and censored on September 31, 2020.via clinical diagnosis. PS (performance status) score refer to ECOG PS score. Tumor differentiation was classified according to the Edmonson\u2013Steiner grade. MVI was vascular invasion of small vessels only identifiable histologically. Major vascular invasion was defined as invasion of the branches of the main portal vein , one or more of the three hepatic veins , or the main branches of the proper hepatic artery (right or left hepatic artery) , major vascular invasion, macrovascular invasion (MaVI), preoperative serum gamma-glutamyltransferase (GGT), alkaline phosphatase (ALP), total bilirubin (TBil), AFP, Child\u2013Pugh grade, MELD (model for end-stage liver disease) score, BCLC stage, AJCC stage, and CNLC stage. Underlying liver diseases were categorized as viral liver disease (hepatitis B virus or hepatitis C virus), non-alcoholic fatty liver disease, alcoholic liver disease, and no underlying liver disease. Cirrhosis was confirmed histopathologically or artery) . Major vhttp://www.r-project.org/); the R packages of \u201creadxl,\u201d \u201ctable1,\u201d \u201crms,\u201d \u201csurvminer,\u201d \u201csurvival,\u201d \u201cggplot2,\u201d \u201cCsChange,\u201d and \u201ctimeROC\u201d were used.Continuous variables are reported as medians with interquartile ranges and were compared using Student\u2019s t-test or the Mann\u2013Whitney test. Categorical data, presented as frequencies (%), were compared using the chi-square test or Fisher\u2019s exact test. Kaplan\u2013Meier survival curves were used to assess OS. Univariate and multivariate analyses were performed using the Cox proportional hazard regression model, and a backward stepwise selection method was used to identify independent prognostic factors and adjust for confounding factors. The Harrell\u2019s concordance index (C-index) and timeOf 1021 patients with HCC who were included, flowchart was shown in The median follow-up time of the whole cohort was 49.03 months . The median OS times (mOST) of patients without BDI and with BDI were 59.27 months (95%CI 50.7-67.17 months) and 23.3 months (95%CI 19.67-26.23 months), respectively (P<0.001) Figure\u00a01The respective mOST of the BDI- and BDI+ groups were 76.87 months (95%CI 76.87- Not Available [NA] months) and 28.98 months (95%CI 18.53-NA months) in BCLC stage 0 (P=0.05), 75.53 months (95%CI 70.37-NA months) and 26.73 months (95%CI 20.27-35.9 months) in BCLC stage A (P<0.001), 40.33 months (95%CI 27.43-67.6 months) and 26.2 months (95%CI 23.07-NA months) in BCLC stage B (P=0.12), and 16.2 months (95%CI 12.67-20.87 months) and 16.3 months (95%CI 13.17-22.73 months) in BCLC stage C (P=0.45) D.The respective mOST of the BDI- and BDI+ groups were 76.87 months (95%CI 73.53-NA months) and 28.98 months (95%CI 23.43-NA months) in AJCC stage IA (P=0.03), 75.53 months (95%CI 70.07-NA months) and 31.8 months (95%CI 25.44-NA months) in AJCC stage IB (P<0.001), 44.97 months (95%CI 29.7-57.9 months) and 23.07 months (95%CI 19.67-26.53 months) in AJCC stage II (P<0.001), 26.93 months (95%CI 21.4-31.97 months) and 26.21 months (95%CI 12.6-NA months) in AJCC stage IIIA (P=0.35), 9.76 months (95%CI 7.57-12.63 months) and 10.23 months (95%CI 6.2-16.36 months) in AJCC stage IIIB (P=0.73) I.The mOST of the BDI- and BDI+ groups were 80.83 months (95%CI 76.87-NA months) and 28.98 months (95%CI 20.2-NA months) in CNLC stage Ia (P<0.001), 52.6 months (95%CI 48.27-67.13 months) and 24.17 months (95%CI 19.67-30.97 months) in CNLC stage Ib (P<0.001), 30.47 months (95%CI 22.93-NA months)and 26.53 months (95%CI 17.07-NA months) in CNLC stage IIa (P=0.43), 26.2 months (95%CI 19.0-40.33 months) and 24.77 months (95%CI 7.57-NA months) in AJCC stage IIIA (P=0.6), 11.77 months (95%CI 9.7-17.7 months) and 13.96 months (95%CI 7.54-16.37 months) in AJCC stage IIIB (P=0.27) N.OS curves stratified by different stages obtained from the multivariate Cox proportional hazard regression model adjusted for other covariates are shown in The BDI+ group was restaged according to the HR of each stage. BCLC stage 0/A/B BDI+ was integrated into BDI+MaVI- and classified as BCLC stage B, and BCLC stage C BDI+ was classified as BCLC stage C , Key Clinical Specialty Discipline Construction Program of Fuzhou, Fujian, P.R.C (Grant number: 201912002) and Fujian Provincial Medical Center of Hepatobiliary.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Patients with lymphoid malignancies are at high risk of severe COVID-19 disease and were not included in the phase 3 mRNA vaccine trials. Many patients with lymphoid malignancies receive immunosuppressive therapies, including B-cell depleting agents, that may negatively impact humoral response to vaccination.We recruited patients with lymphoid malignancies and healthy participants who planned to receive two doses of SARS-CoV-2 mRNA vaccine (BNT162b2 or mRNA-1273). Blood was drawn at baseline, prior to second dose of vaccine, and 28 days after last vaccination. Disease characteristics and therapies were extracted from patients\u2019 electronic medical record. An ultrasensitive, single molecule array (Simoa) assay detected anti-Spike (S), anti-S1, anti-receptor binding domain (RBD), and anti-Nucleocapsid (N) IgG from plasma at each timepoint.23 healthy participants and 37 patients with lymphoid malignancies were enrolled (Table 1). Low titers of anti-N demonstrate no prior exposure or acquisition of COVID-19 before vaccination or during the study. 37.8% of the lymphoid malignancy cohort responded to the vaccine, using an internally validated AEB cutoff of 1.07. A significantly higher magnitude of anti-S (p< 0.0001), anti-S1 (p< 0.0001) and anti-RBD (p< 0.0001) are present in the healthy as compared to lymphoid malignancy cohort at the second dose and day 28 post-series . Anti-S IgG titers were compared between the healthy cohort, treatment na\u00efve, and treatment experienced groups . The treatment na\u00efve cohort had high titers by series completion which were not significantly different from the healthy cohort (p=0.2259), although the treatment experienced group had significantly decreased titers (p< 0.0001). Of the 20 patients who had received CD20 therapy, there was no clear correlation of anti-S IgG response with time from CD20 therapy, although most patients who received CD20 therapies within 12 months from the vaccine had no response . Table 1. DemographicsFigure 1. Anti-N, Anti-S, Anti-S1, Anti-RBD and Anti-N Ig G for healthy v. lymphoid malignancy cohortThe dotted line at 1.07 marks in an internally validated threshold to mark anti-S IgG response. The black bars denote median with 95% CI.Figure 2: Anti-S IgG for healthy v. treatment na\u00efve v. treatment experiencedThe dotted line at 1.07 marks in an internally validated threshold to mark antibody response. The black bars denote median with 95% CI.The vaccine-induced immune response was poor among treatment-experienced patients with lymphoid malignancies, especially among those who received CD20 therapies within 12 months.Figure 3. Months from CD20 therapy v. anti-S IgG titersThe dotted line at 1.07 marks in an internally validated threshold to mark antibody response.Jennifer Crombie, MD, AbbVie (Grant/Research Support)Bauer (Grant/Research Support)Karyopharm (Consultant)MorphoSys (Consultant) Philippe Armand, MD PhD, ADCT, Celgene, Morphosys, Daiichi, Miltenyi, Tessa, C4, Genmab, Enterome, Regeneron, Genentech, Epizyme, Astra Zeneca Affimed, Adaptive, BMS, Merck, Kite, IGM, Genentech David Walt, PhD, Quanterix Corporation Nicolas C. Issa, MD, AiCuris (Scientific Research Study Investigator)Astellas (Scientific Research Study Investigator)GSK (Scientific Research Study Investigator)Merck (Scientific Research Study Investigator)"} +{"text": "The 2017 IDSA CDI guideline update phased out metronidazole (MTZ) and recommended vancomycin (VAN) or fidaxomicin (FDX) for first-line use. This study examined changes in CDI antibiotic use and clinical outcomes among Medicare beneficiaries with CDI pre- vs. post- the guideline update.This retrospective claims analysis used 2016-2018 national Medicare claims data. The two study samples included continuously eligible fee-for-service Medicare beneficiaries aged \u226566 years with a new CDI diagnosis followed by an antibiotic fill in the pre-period (04/01/2017-09/30/2017) and post-period (04/01/2018-09/30/2018), respectively. Outcomes included type of CDI antibiotic received; sustained response and CDI recurrence. Multivariable regressions compared pre- vs. post-period outcomes while controlling for sociodemographic and clinical factors.The pre-period and post-period samples had similar characteristics . Post-guideline update, absolute rates of MTZ use declined 27.7% and VAN use increased 26.9% . While FDX use increased 0.8% , overall use remained low (1.63%). Surprisingly, clinical outcomes did not improve between the pre- and post-period (Table 1). Even after adjustment, overall sustained response rates decreased and overall CDI recurrence rates increased slightly in the post- vs. pre-period. Additional analyses by type of antibiotic showed that VAN (55.0% and 35.1%) was similar in outcomes to MTZ (54.2% and 33.0%), whereas FDX (71.4% and 20.9%) had higher sustained response and lower CDI recurrence rates, respectively .Figure 1. First-line use of CDI treatments, pre- vs. post- the guideline update, among Medicare beneficiaries with CDITable 1. Clinical outcomes, pre- vs. post- the guideline update, among Medicare beneficiaries with CDIFigure 2. Clinical outcomes* by type of index CDI treatment among Medicare beneficiaries with CDIPooled rates among patients on each index CDI treatment across the pre- and post-index periods.The 2017 IDSA guideline update was associated with a substantial increase in VAN use and decrease in MTZ use. FDX use rates remained low (< 2%). Overall CDI outcomes did not improve post guideline update despite the shift to guideline-indicated VAN. This may be because VAN was not associated with meaningfully improved outcomes relative to MTZ. However, improved outcomes seen with FDX relative to VAN and MTZ suggest potential benefits from its greater use in Medicare patients.Erik R. Dubberke, MD, MSPH, Ferring (Grant/Research Support)Merck (Consultant)Pfizer Seres (Consultant)Summit (Consultant) Justin T. Puckett, BA, COVIA Health Solutions (Employee) Engels N. Obi, PhD, Merck & Co. Sachin Kamal-Bahl, PhD, AbbVie (Consultant)Arena Pharmaceuticals, Inc. (Consultant)COVIA Health Solutions (Employee)Janssen, Inc. (Consultant)Merck Novartis (Consultant)Pfizer, Inc. PhRMA (Consultant) Kaushal Desai, PhD, AstraZeneca Pharmaceuticals (Shareholder)Merck & Co. Inc. (Employee) Bruce Stuart, PhD, COVIA Health Solutions (Consultant) Jalpa A. Doshi, PhD, Acadia Allergan (Advisor or Review Panel member)Biogen (Grant/Research Support)Boehringer Ingelheim Catabasis (Consultant)Humana (Grant/Research Support)Janssen, Inc. MeiraGTX (Consultant)Merck Novartis (Grant/Research Support)Otsuka (Advisor or Review Panel member)Regeneron (Grant/Research Support)SAGE Therapeutics (Consultant)Sanofi (Grant/Research Support)Shire (Advisor or Review Panel member)The Medicines Company (Advisor or Review Panel member)"} +{"text": "Here, we present 36 metagenomes, 59 metatranscriptomes, and 373 metagenome-assembled genomes (MAGs) from Chesapeake and Delaware Bay water samples. This data set will be useful for studying microbial biogeochemical cycling in estuaries. Sharp. Surface (\u223c1.5 m below the seafloor [mbsf]) water samples were collected using a rosette sampler with associated conductivity-temperature-depth (CTD) profiles. The sampling scheme (\u2013\u2013https://www.bco-dmo.org/dataset/565451).Estuaries are productive aquatic environments harboring diverse flora, fauna, and microbial communities important for global carbon and nutrient cycling , 2. Omicg scheme , environg scheme \u20137 were d scheme \u2013\u20137 and arhttps://doi.org/10.6084/m9.figshare.14173664 (metatranscriptomes).Cells were separated as large- and small-cell-size fractions by passing water samples through 0.8- and 0.22-\u03bcm-pore-size filters. Nucleic acids were extracted from size-fractionated cells using the Allprep DNA/RNA minikit . A totalPrior to assembly, Cutadapt v1.11 and Sickle v1.33 were used to remove adapters from and quality trim (Q\u2009=\u200930) Illumina-sequenced reads . Nanoporhttps://doi.org/10.6084/m9.figshare.14179448) with >80% completion and <5% contamination were taxonomically annotated using Anvi\u2019o and Microbial Genome Atlas (MiGA) v0.7.26.2 , Burkholderiales (n = 31), Flavobacteriales (n = 55), Microtrichales (n = 39), Nanopelagicales (n = 11), Pelagibacterales (n = 31), Pseudomonadales (n = 26), Rhodobacterales (n = 28), and Synechococcales (n = 13), as well as the archaeal phyla Crenarchaeota (n = 5) and Euryarchaeota (n = 2).For binning, trimmed reads from each Illumina-sequenced library were mapped to contigs \u22652,000\u2009bp in the corresponding metagenome using the default parameters (end-to-end mode) of Bowtie 2 v2.2.7 . Alignme17\u20130.7.26.2 . They bePRJNA432171.The metagenomes, metatranscriptomes, and MAGs are available on NCBI under the umbrella project"} +{"text": "Complicated urinary tract infections (cUTI) are one of the most common bacterial infections and represent substantial burden to the health care system. Here, we examine the epidemiology and treatment patterns associated with cUTI in a large US database containing longitudinal inpatient (IP) and outpatient (OP) patient-level data.We conducted a retrospective cohort study of adult patients in the IBM MarketScan\u00ae Commercial or Medicare Supplemental Databases with at least 1 IP or non-diagnostic OP claim with a diagnosis for cUTI between January 1, 2017 and June 30, 2019. Patients meeting the following criteria were included for analysis: (1) \u226518 years of age on the index date, (2) \u22656 months of continuous enrollment (CE) with medical and pharmacy benefits prior to the index date, (3) \u226512 months of CE following the index date or evidence of death, and (4) no evidence of a prior cUTI during the 6-month baseline period. Demographics and clinical characteristics were quantified. Patients were classified as IP if they were hospitalized during 30-day post index date; remaining patients were classified as OP. Antibiotics received in the OP setting in the 12-months post index date were examined. 95,423 patients met study criteria. Most (86.4%) patients were Commercially insured, mean (SD) age was 53.6 (18.1) and 70.4% were female. Mean baseline Charlson Comorbidity Index was 0.77. During the 30-day post index date, 22.2% were treated as IP and 77.8% were strictly treated as OP. In the 12-month OP follow-up period among index IP, 78.2% required \u2265 2 antibiotics, 38.2% required \u22654 antibiotics, and 41.6% received an IV antibiotic. In the 12-month OP follow-up period among index OP, 81.8% required \u22652 antibiotics, 38.2% required \u22654 antibiotics, and 46.8% received an IV antibiotic. For both IP and OP, fluoroquinolones were the most common oral antibiotic class (57.7%), followed by cephalosporins (39.2%), penicillins (30.3%), trimethoprim-sulfamethoxazole (29.8%), and nitrofurantoin (25.2%). Cephalosporins were the most common IV antibiotic class (38.5%).Regardless of index treatment setting, approximately 40% of all cUTI patients required \u22654 antibiotic therapy and almost half with receive an IV antibiotic in the outpatient setting in the 12-months post index date.Thomas Lodise, Jr., PharmD, PhD, Astra-Zeneca (Consultant)Bayer (Consultant)DoseMe ferring (Consultant)genentech (Consultant)GSK (Consultant)Melinta (Consultant)merck nabriva (Consultant)paratek shionogi Spero (Consultant)tetraphase (Consultant)Venatrox (Consultant) Thomas Lodise, Jr., PharmD, PhD, Melinta Therapeutics Involved: Self): Consultant; Merck Involved: Self): Consultant, Scientific Research Study Investigator; Paratek Involved: Self): Consultant; Shionogi Involved: Self): Consultant, Speakers\u2019 bureau; Spero Involved: Self): Consultant; Tetraphase Pharmaceuticals Inc. Involved: Self): Consultant Janna Manjelievskaia, PhD, MPH, IBM Watson Health (Employee)Spero Therapeutics (Consultant) Matthew Brouillette, MPH, Spero Therapeutics, Inc. Kate Sulham, MPH, Spero Therapeutics (Consultant)"} +{"text": "Communications Biology 10.1038/s42003-021-02971-9, published online 10 January 2022.Correction to: The original version of this Article contained errors in Fig. 1 and Supplementary Fig.\u00a0Updated Supplementary Information"} +{"text": "Early bacterial co-infection is rare in hospitalized COVID-19 patients, yet antibiotics are commonly prescribed. Antibiotic stewardship (AS) intervention is needed, especially in small community hospitals (SCHs), which often lack access to AS expertise.We implemented daily remote multidisciplinary tele-COVID rounds (synchronous case review between SCH providers and ID clinicians) and tele-stewardship surveillance (ID pharmacist review of COVID patients on antibiotics) on 6/24/2020 in 17 SCHs. We retrospectively included adult symptomatic COVID-19 admissions between 3/2020 and 4/2021. The primary outcome was early use of antibiotics for pneumonia (started within 48 hours of admission); mean monthly days of therapy per 1,000 patient days (DOT) were compared pre- (3/2020-6/2020) and post-intervention (7/2020-4/2021). Secondary outcomes were early use of antibiotics for any indication, estimated days of antibiotics avoided (comparing pre- and post-intervention DOT), and in-hospital mortality. Analyses were conducted using a two-tailed unpaired t-test (antibiotic use) or Fisher\u2019s exact test .Of the 1,976 patients included (124 pre- vs. 1852 post-intervention), 55.4% were male and 85.5% were white. Patients in the pre-intervention group were more likely to require hospital transfer [21.8% vs 8.8% (p< 0.001)] and ICU admission [18.5% vs. 9.7% (p=0.003)]. We observed a significant decrease in mean use of early antibiotics for pneumonia [656.9 vs. 240.1 DOT (p< 0.001)], including among non-ICU patients only [603.6 vs 240.2 DOT (p< 0.001)]. Early antibiotic use for any indication also decreased [686.2 vs. 359.3 DOT (p< 0.001)]. An estimated 3,697 days of unnecessary antibiotics for pneumonia were avoided in the 10-months post-intervention [370 days per month (95% CI 304 \u2013 435)]. Unadjusted in-hospital mortality was not different pre- vs post-intervention , but was higher among those prescribed early antibiotics .A significant, sustained reduction in antibiotic use among COVID-19 patients at 17 SCHs was observed after implementation of tele-COVID rounds and tele-stewardship surveillance without an observed difference in mortality.All Authors: No reported disclosures"} +{"text": "In Cohort A, baseline NT-proBNP > 3000 ng/L and cTnT-HS > 50 ng/L and a relative increase of NT-proBNP > 50% during follow-up were independent prognostic factors of EFS. The slopes of logs NT-proBNP and cTnT-HS increased with time before and stabilized after tafamidis. Conclusion: ATTR-CA patients with increasing NT-proBNP had an increased risk of EFS. Tafamidis stabilize NT-proBNP and cTnT-HS increasing, even if initial NT-proBNP levels were >3000 ng/L. Thus suggesting that all patients, irrespective of baseline NT-proBNP levels, may benefit from tafamidis.Background: We assesse the evolution and prognostic value of N-terminal pro-brain natriuretic peptide (NT-proBNP) and high-sensitivity troponin T (cTnT-HS) in transthyretin amyloid cardiomyopathy (ATTR-CA) before and after tafamidis treatment. Methods and Results: 454 ATTR-CA patients without tafamidis (Cohort A) and 248 ATTR-CA with tafamidis (Cohort B) were enrolled. Event-free survival (EFS) events were death, heart transplant, or acute heart failure. In Cohort A, 27% of patients maintained NT-proBNP < 3000 ng/L and 14% cTnT-HS < 50 ng/L at 12 months relative to baseline levels. In Cohort B, the proportions were 49% and 29%, respectively. In Cohort A, among the 333 patients without an increased NT-proBNP > 50% relative to baseline EFS was extended compared to the 121 patients with an increased NT-proBNP > 50% (HR: 0.75 ; Transthyretin amyloid cardiomyopathy (ATTR-CA) is a systemic life-threatening disease characterized by amyloid fibrils accumulating in the heart . There aIn the blood, TTR, mainly produced in the liver, transports the retinol-binding protein-vitamin A complex and to a lesser extent thyroxine. However, when TTR tetramer dissociates and the monomers misfolds TTR aggregates resulting in amyloidogenesis. Mutation of TTR (in ATTRv-CA) or aging (in ATTRwt-CA) destabilizers the tetramers and accelerate their dissociation into monomers. The TTR amyloid fibrils formed by the misfolding deposit in several tissues and organs in the body.Prior to the development of TTR stabilizers, ATTRv was treated by liver transplantation: replacing mutant TTR, in the liver, with wild-type TTR . CurrentThe phase III, double-blinded, placebo-controlled ATTR-ACT trial NCT01994889) assessed the benefit of tafamidis in ATTR patients. The all-cause mortality after 30 months was significantly lower in patients treated with tafamidis (30%) compared to those treated with placebo (43%), hazard ratio (HR): 0.70 (95% CI: 0.51\u20130.96) (p < 0.0001) and log (cTnT-HS) levels during follow up are shown in 0.0001) .n = 192/385) after 6 months, 30.6% (45/147) after 12 months, and 23.4% (30/128) after 18 months and 14.5 months (95% CI: 10.9\u201319.0) in those with non-increased NT-proBNP (n = 333), HR: 0.75 (95% CI: 0.57\u20130.98); p = 0.032 (log-rank test) (p = 0.09) and 0.78 , respectively (figure not shown).At the cut-off date and after a median follow-up of 14.2 months (IQR: 3.1\u201340.4), 234 patients (52%) had reported EFS events (25 deaths and 209 acute heart failure). Among the 209 acute heart failures, 33 patients died after acute heart failure for a total number of deaths of 58 patients. 220 patients have not reported an EFS event: 176 had initiated tafamidis including 28 patients enrolled in the ATTR-ACT study (NCT01994889), and 44 (9.7%) were without an EFS event . The median EFS was 8.8 months (95% CI: 6.2\u201314.2) in patients with 50% relative increased NT-proBNP levels (nk test) A. The sen = 48) and 12.6 months (95% CI: 8.3\u201316.6) in those with non-increased levels (n = 260), HR: 0.86 (95% CI: 0.60\u20131.25); p = 0.43 (log-rank test) (p = 0.40) and 0.91 , respectively (figure not shown).We also analysed median EFS in the 308 patients with at least two cTnT-HS assessments, according to whether patients had a 50% relative increased cTnT-HS levels. The median EFS was 12.2 months (95% CI: 5.1\u201315.4) in patients with 50% relative increased levels (nk test) B. Simila2) to be significantly associated with an extended EFS at a 5% level. Of these, the multivariate analysis, identified non-50% relative increased NT-proBNP levels , as well as baseline levels of NT-proBNP \u2264 3000 ng/L and cTnT-HS \u2264 50 ng/L to be significantly and independently associated with extended EFS , cTnT-HS (\u226450 ng/L), and eGFR (>45 mL/min/mnded EFS .n = 248) was 17.5 months (IQR: 10.9\u201318.2).Among the 248 patients assessed in Cohort B, 63 (25%) had ATTRv and 185 (75%) had ATTRwt . The popn = 248), 194 patients (78.2%) were still being treated with tafamidis and 54 (21.8%) had discontinued tafamidis. In patients who discontinued tafamidis, 27 patients had died (including 25 before 18-month timepoint), 15 had aggravated disease, 8 had been enrolled in the ATTR-ACT study (NCT01994889), 1 had been enrolled in the APOLLO study (NCT01960348), 1 did not support the treatment, 1 refused to continue treatment, and 1 was non-compliant. In Cohort B (n = 248) the following proportions of patients had baseline levels of NT-proBNP maintained \u22643000 ng/L or decreased from >3000 ng/L to \u22643000 ng/L: 139/223 (62.3%) after 6 months, 89/162 (54.9%) after 12 months, and 80/145 (55.2%) after 18 months. At 18 months, 17% (25/145) of the patients were dead (In Cohort B (ere dead C.n = 248) the following proportions of patients had baseline levels of cTnT-HS maintained \u226450 ng/L or decreased from >50 ng/L to \u226450 ng/L: 90/204 (44.1%) after 6 months, 48/147 (32.7%) after 12 months, and 57/134 (42.5%) after 18 months. 19% (25/134) of the patients had died . We also generated the scatterplots for the subpopulations of patients that initiated tafamidis with NT-proBNP levels >3000 ng/L (p = 0.03). Similarly, for patients with NT-proBNP levels \u22643000 ng/L, the slope was 0.0007 (95% CI: \u22120.0070 to \u22120.0084) before tafamidis and 0.0080 (95% CI: 0.0025\u20130.0135) after tafamidis (p = 0.15). However, despite a stable positive slope of NT-proBNP levels after tafamidis, in patients with initial NT-proBNP levels \u22643000 ng/L, most of the individual NT-proBNP levels remain within a narrow logarithmic range (8 logs corresponding to 3000 ng/L).The scatterplots for log (NT-proBNP) before and after tafamidis treatment, are shown in 000 ng/L B and tho000 ng/L C. For pap < 0.01. In addition, we plotted the log (cTnT-HS) levels of patients with cTnT-HS levels >50 ng/L (p < 0.001). Similarly, for patients with cTnT-HS levels \u226450 ng/L, the slope was 0.0071 (95% CI: 0.0025\u20130.0118) before tafamidis and 0.0025 (95% CI: \u22120.0045\u20130.0094) after tafamidis (p = 0.35).The scatterplots for log (cTnT-HS) levels before and after tafamidis treatment, are shown in >50 ng/L E and tho>50 ng/L F. For paOur study is the first to describe the natural history of cardiac biomarkers in ATTR and their evolution after tafamidis treatment in a real-life cohort. Our results show that NT-proBNP and cTnT-HS levels increase in ATTR-CA natural history and that 50% relative increases in NT-proBNP levels significantly increases the risk of death, heart transplant, or acute heart failure in ATTR-CA patients. In contrast, increases in cTnT-HS levels were not associated with an increased risk of these events. Baseline levels of NT-proBNP \u2264 3000 ng/L and cTnT-HS \u2264 50 ng/L were found to be independently associated with extended EFS. Furthermore, our results show that tafamidis slows the increasing of NT-proBNP levels associated with amyloidosis evolution in ATTR-CA patients with NT-proBNP levels > 3000 ng/L when tafamidis is initiated. Similarly, tafamidis also slows the increasing of cTnT-HS levels in patients with cTnT-HS levels > 50 ng/L. The proportion of patients who maintained their baseline levels of NT-proBNP \u2264 3000 ng/L or decreased their NT-proBNP levels from >3000 ng/L to \u22643000 ng/L at 12 months was 31% for untreated patients and 55% for those treated with tafamidis.Amyloid formation is a progressive and dynamic process with cardiac biomarkers reflecting the pathophysiology of the disease. Our results show that cTnT-HS and NT-proBNP levels increase during the natural evolution of ATTR-CA.NT-proBNP is a cardiac biomarker indicative of cardiac wall stress and levels increase when heart ventricles become overloaded. NT-proBNP levels are used to diagnose congestive heart failure ,12,13,14In cardiac amyloidosis, fibrillogenesis is a dynamic process. An increase in biomarker levels may be linked to cardiomyopathy evolution, emphasizing the need to slow down their progression. Thus, increasing NT-proBNP levels may be linked with cardiac wall stress associated with amyloid infiltration. While, increasing troponin levels may be linked with the toxicity of amyloid fibrils .The prognostic value of baseline NT-proBNP and cardiac troponin levels in cardiac amyloidosis patients are well established ,21,22,23In our analysis of the cohort of patients treated with tafamidis we found that NT-proBNP levels continued to increase after initiating tafamidis but at a constant or reduced rate. We also found that tafamidis had a similar effect on cTnT-HS levels. The activity of tafamidis is reportedly due to its capacity to stabilise the TTR tetramer, reducing the build-up of amyloid fibrils in the heart . This meInteresting, our results correspond with an exploratory endpoint of the ATTR-ACT study showing a slightly higher NT-proBNP levels in patients, at 12 and 30 months and one assessment before and another after tafamidis (Cohort B). However, a comparison of the patients included and those not included in the cohorts did not show any major imbalance. Secondly, the time intervals between NT-proBNP assessments were not control and varied. Our data were analysed using piecewise regression random model that generates slope models before and after treatment despite this variability in the time intervals. Thirdly, the cTnT-HS levels used for our analyses are different from the troponin assay usually used in cardiac amyloidosis literature. Recently, cTnT-HS assays have replaced the more traditional assays. These new assays detect the same proteins but with a much lower detection limit . It has Finally, this study was not designed to compare patients treated with tafamidis with those not treated. The patients in the two cohorts were not included during the same time period. Thus, untreated patients from Cohort A that were included in the Cohort B (tafamidis treated patients) may have less severe ATTR-CA. Indeed, a patient included in Cohort A with an EFS event would not have been included in Cohort B. Comparisons of the baseline characteristics of the cohorts support this hypothesis with lower level of NT-proBNP, cTnT-HS, Gillmore stage, and Grogan stage in treated patients. However, the sensitivity analyses that we performed gave results consistent with the results and conclusions herein reported. Nevertheless, this indirect comparison was not an objective of this study. We are currently indirectly comparing these cohorts using an adapted methodology, including the use of propensity scores and matching analysis.NT-proBNP and cTnT-HS are biomarkers for cardiac dysfunction that increase as ATTR-CA evolves. Increasing NT-proBNP levels, but not cTnT-HS levels, signal increasing cardiac dysfunction with an increased risk of death, heart transplant, or acute heart failure, in ATTR-CA patients. Our results seem to indicate that tafamidis slows disease evolution in ATTR-CA patients by stabilizing NT-proBNP and cTnT-HS levels."} +{"text": "Achillea santolinoides and Achillea aleppica aeral parts and root were extracted with ethyl acetate, methanol, and water. Detailed phytochemical profiles were obtained using UHPLC-MS, yielding the identification of hydroxybenzoic and hydroxycinnamic acids, phenolic acid glycosides and sugar esters, acylquinic acids, O-glycosyl flavones and flavonols, and flavonoid aglycons, among others. The antioxidant properties and enzyme inhibitory activities of the extracts were assayed with in vitro tests. The phenolic content of the water extracts was significantly higher as compared to the ethyl acetate and methanol ones. A. aleppica aerial parts methanol extract possessed highest flavonoid content . Antioxidant properties assessment revealed that the methanol extract of A. santolinoides roots actively scavenged DPPH (54.11 mg TE/g) and ABTS radicals (112.53 mg TE/g) and possessed highest reducing potential . The ethyl acetate extracts of aerial parts and roots of both species showed highest inhibition against BuCHE (6.07\u20136.76 mg GALAE/g). The ethyl acetate extract of A.santolinoides aerial part showed highest inhibition against tyrosinase (73.00 mg KAE/g). These results showed that the tested Achillea species might represent novel phytotherapeutic avenues for the management of Alzheimer\u2019s disease and epidermal hyperpigmentation conditions, which are both associated with oxidative stress. This paper could shed light into future potential industrial applications using the tested Achillea species.In the current study, Achillea genus, one of the most important genera of the Asteraceae family with ethnopharmacological significance, consists of approximately 85 species mainly distributed in Middle East regions, such as Iran, Turkey, and Serbia and Eastern regions of Europe \u2212 at m/z 357.084) were obtained (m/z 195.050 (C6H11O7\u2212) corresponding to the [gluconic acid-H]\u2212 supported by the fragment ions at m/z 177.040 [GA-H-H2O]\u2212, 87.007 [GA-H-C3H8O4]\u2212 and 59.012 [GA-H-C3H8O4-CO]\u2212 and four hydroxycinnamic acids together with extracts . In addiobtained . They yi8O4-CO]\u2212 .O-(6-caffeoyl)-hexoside (32) was deduced from the loss of vanillic acid (168 Da) at m/z 323.077 and a subsequent transition 323.077\u2192221.046 [M-H-102]\u2212 arising from the hexose cross ring cleavage . The latter ion points out to the caffeoyl moiety at Hex C-6. Regarding 42, the prominent ion at m/z 323.077 [M-H-C7H6O3]\u2212 and a base peak at m/z 137.023 [salicylic acid-H]\u2212 together with m/z 93.033 [salicylic acid-H-CO2]\u2212 were in accordance with caffeic acid-O--hexoside (Tanacetum vulgare [Vanillic acid-4-hexoside . Both 32 vulgare .A. santolinoides. Syringic acid-hexoside (6) was presented mainly in A. allepica roots afforded prominent ions at m/z 353.088 and 191.055 indicating the subsequent losses of a caffeoyl moiety (diCQA 33 and 37 were witnessed by the \u201cdehydrated\u201d ion of quinic acid at m/z 173.044 (100%) supported by the diagnostic ions at m/z 335.0771 [CQA-H-H2O]\u2212 and 135.044 [caffeic acid-H-CO2]\u2212 in 3,4-diCQA (33) (diCQA as suggested by the lack of ion at m/z 335 and the chromatographic behavior on the reverse phase (the most lipophilic diCQA isomer). The base peak at m/z 191.055 evidenced 1,3-diCQA (24a), 1,5-diCQA (34) and 3,5-diCQA (35) supported by the relative abundance of the ions at m/z 179.034 and m/z 135.044: 73.2% and 58.7% (24a), 6.2% and 6.6% (34), and 53.1% and 52.7% (35), respectively.Five peaks 24, 33\u201335, and 37 ([M-H]l moiety . The vicCQA (33) . The secp-coumaroyl-caffeoylquinic acids (p-CoCQA) isomers 41 and 44 at m/z 499.122 (C25H23O11) were deduced from the distinctive fragments at m/z 337.093 [M-H-caffeoyl]\u2212, m/z 163.039 [p-CoA-H]\u2212 and m/z 119.049 [p-CoA-H-CO2]\u2212 for p-coumaric acid (m/z 337.093 (83.6%) indicating a loss of caffeoyl residue before the p-coumaroyl one. This assignment was also supported by the base peak at m/z 163.039 as was registered in 3-p-CoQA \u2212 and m/z 353.270 [M-H-feruloyl]\u2212 for feruloyl-caffeolylquinic acids (FCQA). The fragment ion at m/z 335.0754 [M-H-FA]\u2212 accompanied by the \u201cdehydrated\u201d form of quinic acid suggested 3F-4CQA (40) [m/z 193.050 together with the abundant ion at m/z 134.036 (74.4%) as was registered in 3-FQA (m/z 161.023 [CA-H-H2O]\u2212 accompanied by the abundant ions at m/z 179.034 [CA-H]\u2212 (42.3%) and 367.104 (34.1%) \u2212 at m/z 327.051 (54) and 311.056 (57) supported by the relevant ions at m/z 299.056 0,2X/CO\u2212 [(M-H)-120\u201328]\u2212 and m/z 283.061, respectively. This fragmentation pathway was consistent with C-8 hexosyl luteolin/apigenin [C-6 hexosyl isomers 52 and 58 was shown by the ions at m/z 447.094 [M-H]\u2212 (100%) and 431.099, as well as 0,3X\u2212 at m/z 357.062 and 341.067, and 0,2X\u2212 at m/z 327.051 and 311.056. The aglycones luteolin and apigenin were discernable by the RDA ions 1,3A\u2212 (m/z 151.022), 0,4A\u2212 (m/z 107.012), 1,3B\u2212 at m/z 133.028 and 117.033 . Based on the comparison with reference standards, compounds 52, 54, 57, and 58 were identified as homoorientin, orientin, vitexin, and isovitexin, respectively.MS/MS spectra of the acquired . In the apigenin . In cont\u2212 at m/z 593.152 (C-glycosyl flavon pathway were produced at m/z 473.109 [(M-H)-120]\u2212, 383.077 [(M-H)-90\u2013120]\u2212 and 353.067 [(M-H)-2 \u00d7 120]\u2212 suggesting the presence of two C-hexosyl moieties on the flavonoid skeleton \u2212 at m/z 413.088 [(M-H)-60\u2013120]\u2212 and \u2212 at 323.057 [(M-H)-120-150]\u2212 suggesting the presence of both C-pentosyl (X0) and C-hexosyl (X1) moieties. Additionally, methylluteolin was assigned on the basis of specie at m/z 299.560 [MeLu-H]\u2212 and 298.048 Y0/0,2X1/\u2022CH3/CO [m/z 323.057 ([(M-H)-(132 + H2O)-120]\u2212 and 443.097 ([(M-H)-(132 + H2O)]\u2212 suggesting O-pentosyl unit at 2\u2033 of the primary hexose 593.152 . Concerny hexose . Diagnos\u2212 at 609.147, 47 was annotated as 6, 8-diC-hexosyl-luteolin, while 48 was assigned to O, C-dihexosyl-luteolin. The latter structure was shown by a series of diagnostic ions at m/z 447.093 [M-H-Hex]\u2212, 357.062 [M-H-Hex-90]\u2212 and 327.051 [M-H-Hex-120]\u2212. Additionally, ions at m/z 298.048 , 175.039 and 133.028 1,3A\u2212 indicated luteolin. The sugar chain of 56 was consistent with rutinose (308 Da); aglycone quercetin was witnessed by a series of fragments including RDA ions at m/z 178.998 \u2212, 163.003 \u2212, 151.002 \u2212, 121.028 \u2212, 107.012 \u2212. Based on comparison with reference standard, 56 (rutin), 60 (luteolin-7-glucoside), 65 (kaempferol-3-glucoside), 66 (isorhamnetin-3-glucoside), 67 (apigenin-7-glucoside), luteolin (50), quercetin (72), apigenin (75), kaempferol (77) and chrysoeriol (78) were unambiguously identified , 299.056 and 329.067 (71) [(M-H)-HexA]\u2212, respectively, indicating flavonoid hexuronides was deduced from the fragment ions at m/z 243.030 [(M-H)-HexA-CH3-HCO\u2022-CO]\u2212, 227.035 [(M-H)-HexA-CH3-HCO\u2022-CO2]\u2212 as well as RDA ions at m/z 133.028 . Compound 69 was ascribed to chrysoeriol-O-hexuronide , while 70 was consistent with jaceosidin-O-hexuronide flavones . In (\u2212) llea sp. .1,3A\u2212) at m/z 165.990 , 139.039 , 136.986 and 1,2 B\u2212 at m/z 121.028. Within this group, compounds 73 (patuletin), 74 (axillarin), and quercetagetin-3,6,3\u2032(4\u2032)-trimethyl ether (80) were quercetagetin derivatives, while compounds 77 (hispidulin) and 81 (cirsimaritin) were scutellarein derivatives , 164.981 , 163.002 , 136.987 . Moreover, at m/z 132.020 indicated 2 methoxy groups either in C-3, C-4\u2032 or C-3\u2032, C-4\u2032, as was observed in santin and eupatilin, respectively + and 243.101 [M + H-2H2O]+ and a base peak at m/z 237.111 [M + H-H2O-CH2]+. This fragmentation pathway could be associated with the presence of peroxide group and 84 was tentatively ascribed to tanaparthin-peroxide, previously isolated from Achillea nobilis (+ at m/z 307.153 gave a base peak at m/z 247.132 [M + H-CH3COOH]+ which is in accordance with the structure of achillicin/matricin. Compound 87 differs from 85 for 60 Da (CH3COOH) and revealed the same fragmentation patterns as 85. Thus, compound 87 was tentatively annotated as achillin/leucodin , 2xH2O (\u221236 Da), CO (\u221228 Da), as well as concomitant loss of H2O + CO (\u221246 Da), 2H2O + CO (\u221264 Da), 88 and 89 were ascribed to artabsin and dihydrosantamarin, respectively, and were previously isolated from Achillea collina [MS/MS spectrum of 84 [M + H] nobilis 44]. Co. Co+ at leucodin . Similarm/z 280.263 (C18H33NO) together with distinctive fragments at m/z 263.236 [M + H-NH3]+ and m/z 245.225 [M + H-NH3-H2O]+, suggesting amide of octadecadienoic acid. Additionally, the suggested structure was supported by the fragments at m/z 81.070 (C6H9), 69.070 (C5H9), 57.070 (C6H9) . Thus, 9ectively 46]..m/z 280.A. aleppica aerial parts (55.15 mg TE/g) and A. santolinoides roots (54.11 mg TE/g) showed highest scavenging activity against DPPH. In contrast A. aleppica roots water extract (101.88 mg TE/g) and A. santolinoides roots methanol extract (112.53 mg TE/g) were most potent in scavenging ABTS. Protocatechuic acid and its derivatives identified in the A. aleppica roots water extract, A. aleppica aerial parts methanol extract, and A. santolinoides roots methanol extract, has been reported to exhibit radical scavenging activity [A. aleppica aerial parts and A. santolinoides roots showed highest reducing capabilities and ethyl acetate and water extract of the aerial parts of A. santolinoides (27.37 and 26.06 mg EDTAE/g), respectively possessed strong chelating ability. Caffeic acid, chlorogenic acid, and protocatechuic acid were identified in aerial parts of A. aleppica water and A. santolinoides ethyl acetate extracts. Interestingly, a study conducted by Andjelkovi\u0107, et al. [A.santolinoides was previously reported to possess antioxidant effect on brain tissues in pentylenetetrazole-induced seizures Wistar rat models [A.santolinoides was also found to exhibit antioxidant potential against DPPH radical (IC50 = 129\u2013372 mg/mL) [The total antioxidant capacity of the extracts was determined using the phosphomolybdenum assay. As shown in activity ,48. Neocactivity . The redbilities . The che, et al. has asset models . The ess2 mg/mL) .Achillea species against enzymes targeted in the management of diabetes mellitus type II, Alzheimer\u2019s disease, and skin hyperpigmentation problems was investigated. Alzheimer\u2019s disease has escalated to epidemic proportions and the need for complementary therapeutic agents to effectively manage this debilitating condition is of paramount importance. From A. aleppica aerial parts ethyl acetate extract and A. santolinoides roots methanol exhibited highest inhibition against AChE. A previous molecular docking study confirmed the interaction of orientin with AChE which showed least binding energy and highest binding affinity [A. aleppica roots and A. santolinoides aerial parts was previously reported to inhibit BuChE in an in silico study. On the other hand, the ethyl acetate extracts of A. aleppica aerial parts and roots (6.07 and 6.73 mg GALAE/g) and as well as that of A. santolinoides aerial parts (6.76 and 6.70 mg GALAE/g) were most active against BuChE. The inhibition of BuChE has been advocated in the later stage of Alzheimer\u2019s disease. During the progression of the disease, BuChE level increases, exacerbating the conditions of the patient [A. aleppica and A. santolinoides aerial parts and roots possessed weak anti-diabetic properties. Tyrosinase, a rate limiting enzyme responsible for the biosynthesis of melanin, is considered to be a key therapeutic strategy for the management of skin hyperpigmentation conditions. In the present study, methanol extracts of A. aleppica aerial parts and roots showed the highest inhibitory activity against tyrosinase. In other side, ethyl acetate and methanol extracts of both studied parts of A. santolinoides displayed strongest anti-tyrosinase activity. Hispidulin, isolated from Phyla nodiflora and identified in extracts which actively inhibited tyrosinase was previously reported to exhibit inhibitory action against tyrosinase with an IC50 value of 146 \u00b5M [The inhibitory ability of extracts prepared from the aerial parts and roots of the selected affinity . Vitexinaffinity . Acacetiaffinity . However patient . The abif 146 \u00b5M .A. aleppica roots EA and MeOH and A. santolinoides roots EA were grouped together. Similarly, in PC1 vs PC2 and PC1 vs. PC3, A. A. santolinoides roots MeOH and A. aleppica aerial parts MeOH were close together. Following PCA, a hierarchical classification was done to obtain a clearer picture of the different group. Based on the scores of samples on the three PCs, the hierarchical analysis revealed two principal clusters, each of which was divided into two sub-clusters were characterized by higher antioxidant activity while samples of the second cluster were marked by stronger enzyme inhibitory activity.Subsequent to comparison of the bioactivities of the samples of each species, principal component analysis (PCA) was used in order to uncover the similarities/differences among the extracts of both species, in light of assessed antioxidant and enzyme inhibitory activities. The results of PCA were displayed in clusters B. The sa2X) and biological activities (R2Y) respectively, indicating the good performance of the model.The relationship between the metabolites and biological activities Partial was assessed and result was reported in Achillea species. In respect of the genes modulation, 73, 122, 280, 122, 113, 122, 57, 57, 254, 287 and 272 mRNA were found to be up-regulated and down-regulated by artabsin, dehydroleucodin, dihydrosantamarin, leucodin, matricin, tanaparthin peroxide, neochlorogenic acid, chlorogenic acid, homoorientin, vitexin and isovitexin respectively (Artemisia capillaries, it has been demonstrated that leucodin dose dependently enhances phosphorylation of AMPK in alcohol-exposed HepG2 cells [After the phytochemical screening and in vitro evaluation of biological properties of the samples, we have been engaged in the investigation of KEGG pathway enrichment analysis of identified sesquiterpene lactones and derivatives and five of the main phenolics of ectively . As regaectively . StructuG2 cells . FurtherG2 cells . While tG2 cells . This fiA.aleppica and A. santolinoides roots and aerial part. Chlorogenic acid was the main derivative in aerial parts of both the species. 3,5-diCQA was the most important diCQA derivative in A. aleppica while 1,3diCQA was the most significant in A santolinoides. Sesquiterpene lactone and fatty acid amides have been also detected showing large chemical diversity in the constituents of the plant. The extraction with ethyl acetate, methanol and water allowed to prepare samples with different composition that were used to assess their in vitro bioactivity on several antioxidant and enzyme inhibition assays. The methanol extract of A. santolinoides roots possessed significant antioxidant activities. The ethyl acetate extracts of the aerial parts and roots of both Achillea species showed significant inhibition against butyrylcholinesterase while the ethyl acetate extract of A. santolinoides aerial part actively inhibited tyrosinase. The detailed phytochemical investigation, the evaluation of in vitro bioactivity, of the two Achillea species indicate these plants as valuable starting point for potential future studies and possible applications extracts in cosmetic, pharmaceuticals and nutraceuticals products. KEGG mapping using some of the phenolics and sesquiterpenes of the plants allowed to predict some of the possible molecular targets for significant bioactivities. This information opens new opportunities of research and application for A. aleppica and A. santolinoides extracts and isolated compounds.This study allowed obtaining a detailed phytochemical fingerprint of"} +{"text": "Staphylococcus aureus (MRSA) SCCmec IV[2B] has become one of the most common community-associated MRSA clones in Australia. We report the complete genome sequence of one of the earliest isolated Australian S. aureus ST1-MRSA-IV strains, WBG8287, isolated from an Indigenous Australian patient living in the remote Kimberley region of Western Australia.Sequence type 1 (ST1) methicillin-resistant Staphylococcus aureus (CA-MRSA) first emerged in Australia in the 1980s . WBG8287 was additionally sequenced using the Illumina NextSeq 500 platform, the Nextera XT DNA library preparation kit (paired-end format) , and the NextSeq 500/550 kit v2.5 (300-cycle format) (Illumina). The Illumina sequencing produced 2,083,742 reads, with a maximum read length of 151\u2009bp and a mean read length of 147\u2009bp. The Nesoni clip tool (github.com/Victorian-Bioinformatics-Consortium/nesoni) was used to remove adaptor sequences and quality filter reads. The assembly was polished with the Illumina reads 5\u00d7 using Minimap2 v2.17-r941 , using MinKNOW v20.10.3 and MinKNOW Core v4.1.2 software. Base calling was performed using Guppy v4.4.1\u2009+\u20091c81d62 (ONT) with the dna_r9.4.1_450bps_hac.cfg model. Sequencing produced 470,277 reads and a read-length CP070986.1 (chromosome), CP070987.1 (pWBG750), and CP070988.1 (pWBG751). The sequencing reads have been deposited in the Sequence Read Archive under accession numbers SRX11246054 and SRX11246053.The WBG8287 sequences are deposited in NCBI GenBank under accession numbers"} +{"text": "Macrolides are a significant family of natural products with diverse structures and bioactivities. Considerable effort has been made in recent decades to isolate additional macrolides and characterize their chemical and bioactive properties. The majority of macrolides are obtained from marine organisms, including sponges, marine microorganisms and zooplankton, cnidarians, mollusks, red algae, bryozoans, and tunicates. Sponges, fungi and dinoflagellates are the main producers of macrolides. Marine macrolides possess a wide range of bioactive properties including cytotoxic, antibacterial, antifungal, antimitotic, antiviral, and other activities. Cytotoxicity is their most significant property, highlighting that marine macrolides still encompass many potential antitumor drug leads. This extensive review details the chemical and biological diversity of 505 macrolides derived from marine organisms which have been reported from 1990 to 2020. Lamellomorpha strongylata (La. strongylata) [Symbiodinium sp. [The term \u201cmacrolide\u201d was coined by Woodward in 1957 ,3,4. Thengylata) , and thenium sp. . MacroliThis literature review from 1990 to 2020 highlights 505 new macrolides derived from marine organisms . CompareTheonella sp. (T. sp.) sponges produced a series of dimeric macrolides called swinholides A\u2013G (1\u20137) and isoswinholide A (8) [9), isobistheonellide A (10), and bistheonellic acids A (11) and B (12)\u2014are also produced by Okinawan T. sp. sponges [13), which is weakly cytotoxic and obtained from Japanese sponge Polyfibrospongia sp., was elucidated by X-ray single crystal diffraction [14) was isolated from Mycale adhaerens (M. adhaerens) and identified by spectroscopic analysis [The Okinawan de A (8) ,17,18,19 sponges . The strfraction . 13-Deoxanalysis . 15) and halistatin 2 (16) were isolated from Phakellia carteri from the Comoros Islands and Axinella cf. carteri (Dendy) from the Western Indian Ocean [17) was produced in extremely small quantities by Phakellia sponges collected at Chuuk [The antimitotic macrolides halistatin 1 , 2 (19), and 3 (20), which were isolated from Spongia sp. in the Republic of Maldives and identified via spectral data without stereochemistry [21), 5 (22), 6 (23), 7 (24), 8 (25), and 9 (26) from Spirastrella spinispirulfera (S. spinispirulfera) on the southeast coast of Africa [Independent groups have reported the potent antitumor macrolides spongiastatins 1 , C (28), and D (29) have been isolated from the Caledonian sponge Neosiphoniu superstes [Three macrolides sphinxolides B (uperstes . 30), B (31), and C (32), were reported without stereochemical data in an Okinawan Juspis sponge [Three new trisoxazole macrolides, jaspisamides A (30), B , and C (33) was isolated from a Republic of Maldives Spongia sponge and exhibited significant cytotoxicity towards murine P388 lymphocytic leukemia [34) and B (35), have been produced by the marine sponge Reidispongia coerulea (R. coerulea) [A new 22-membered macrocyclic lactone named dictyostatin 1 (leukemia . The rel4) and B , have beoerulea) . The reloerulea) . 36) and superstolide B (37) have been isolated from the deep-water marine sponge Neosiphonia superstes (N. superstes) [38), was produced by the shallow-water Caribbean sponge Forcepia sp. [39), belonging to the halichondrin family, was isolated from the New Zealand deep-water sponge Lissodendoryx sp. (Li. sp.) [40) and B (41) have an unprecedented scaffold and were isolated from the Indian Ocean sponge Phorbas sp. (P. sp.), with complete stereochemistry and absolute configuration determined by spectroscopy and partial synthesis [42) and laulimalide B (43) isolated from Okinawan sponge Fasciospongia rimosa were determined by X-ray analysis [44), neolaulimalide (45) and zampanolide (46), have been produced by the F. rimosa genus [47), isolated from the marine sponge Halichodria okadai, exhibited significant inhibition of vascular cell adhesion molecule 1 (VCAM-1) [Cytotoxic superstolide A (perstes) ,39. Anotepia sp. . IsohomoLi. sp.) . Phorboxynthesis ,43. The analysis . Other climalide and zamppanolide , have be48), exhibiting antifungal and cytotoxic activities, was obtained from the sponge Leucascandra caveolata (Le. caveolata) [Callipelta sp. contains the first member of a new class of marine-derived macrolides, callipeltoside A (49), which incorporates an unusual chlorocyclopropyl group and an amino sugar [50\u201352) and 5-desacetylaltohyrtin A (53) were isolated from the sponge Hyrtios altum and their absolute stereochemistries were determined by spectroscopy [La. strongylata for cytotoxicity towards the P388 cell line yielded swinholide H (54) [Leucascandrolide A , exhibittoside A , which ino sugar ,51,52. Chyrtin A were isotroscopy . Screenie H (54) .Li. produced the antitumor macrolides neonorhalichondrin B (55), neohomohalichondrin B (56), 55-methoxyisohomohalichondrin (57), 53-methoxyneoisohomohalichondrin B (58a) and 53-epi-53-methoxyneoisohomohalichondrin B (58b) [Another deep-water (> 100 m) sponge of the genus ondrin B , neohomo59) and B (60) were isolated from the Haliclona sponge, representing a potentially important new class of antitumor leads [61) and C (62), two members of a novel class of marine glycoside macrolides, were isolated from the sponge Cal. sp. [Macrolide salicylihalamides A and B were iso63\u201366), were isolated from an Okinawan marine sponge, Halichondria sp. [Four new oxazole-containing compounds, halishigamides A\u2013D , showing modest cytotoxicity [68), 32-hydroxymycalolide A (69), and 38-hydroxymycalolide B (70), were isolated from the marine sponge M. magellanica and showed cytotoxicity towards L1210 cells [A Palau toxicity . Three m10 cells . 71), a thiazole-containing macrolide with an unique dilactone functionality, was isolated from M. sp. sponge [72\u201375), were produced by the marine sponge Amphimedon spp. collected in the Great Australian Bight [Pateamine 1 (. sponge . Four nean Bight . 76), NB (77), NC (78), ND (79) and NE (80) were isolated from the New Caledonian Litbistida sponges N. superstes and R. Coerulea [81\u201383) and reidispongiolide C (84) are new cytotoxic macrolides from Okinawan species of Ircinia [85) is a 16-membered macrolide from the calcareous sponge Le. caveolata from the northeastern waters of New Caledonia [M. sp. contained the polyoxygenated, pyranose ring-containing, 16-membered macrolide peloruside A (86) [Cytotoxic macrolides haterumalides NA , which we A (86) . 87) has been isolated from the Vanuatu marine sponge Spongia sp. [88), was isolated from a marine sponge of the genus Dactylospongia. This has been synthesized and the relative stereochemistry of the acyloxymethine and the absolute configuration of the whole molecule have been determined [Ha. sp. was found to contain the cyclic metabolite haliclamide (89) [Cytotoxic spongidepsin (ngia sp. . A new ctermined . The Vanide (89) .90\u201393) have been found in sponge Myriastra clavosa [94\u2013100) are antimitotic macrolides isolated from the Caribbean marine sponge S. coccinea [Clavosolides A\u2013D and (19Z)-halichondramide (102), and the open ringed secohalichondramide. Neohalichondramide and (19Z)-halichondramide exhibited significant cytotoxicity and antifungal activity toward the human leukemia cell-line K562 and Candida albicans [The sponge lbicans) .103), 32-hydroxymycalolide A (104) and 38-hydroxymycalolide B (105), have been isolated from a Japanese M. magellanica [106\u2013110) were isolated from Forcepia sponge collected in the U.S. Gulf of Mexico [111), isolated from the marine sponge Geodia exigua, was reported to inhibit fertilization of sea urchin (Hemicentrotus pulcherrimus) gametes but not embryogenesis [Three cytotoxic mycalolides, 30-hydroxymycalolide A (ellanica . The fivf Mexico . Exiguologenesis . The absogenesis .112) and B (113) were obtained from a deep-water (>200 m) Leiodermatium sponge [114), isolated from Ircinia sp. (Papua New Guinea), was found to be potently cytotoxic, causing S-phase arrest, suggestive of protein synthesis inhibition [115\u2013118) were produced by Pachastrissa nux (P. nux) (Gulf of Thailand) [Cytotoxic macrolides leiodolides A . 119), was isolated from P. nux sponge [120) and the related hurghadolide A (121), with cytotoxicity towards human colon cancer cells, were produced by T. swinhoei [An antiplasmodial macrolide, kabiramide L .122) was isolated from Red Sea sponge Negombata corticata and showed significant antifungal and anticancer activities, suggesting it as a potential member of the bioactive latrunculin family [123) with potential cytotoxic and antifungal activities. This compound was synthesized to determine its absolute configuration and the relative stereochemistry of C-13 [124), a complex mixture of acyl esters of a macrolide related to tedanolide, was isolated from Candidaspongia sp. (Can. sp.) (Papua New Guinea) and Can. flabellata [125\u2013130) were produced by sponge Cacospongia mycofijiensis (Cac. mycofijiensis) [131\u2013135) are chlorocyclopropane macrolides isolated from marine sponge P. sp. [Oxalatrunculin B . FijianoVanuatu) . Phorbase P. sp. ,97. 136\u2013138), 18-epi-latrunculol (139) and latrunculones A (140) and B (141), were obtained from Cac. mycofijiensis [142), salarin B (143) and tulearin A (144) were obtained from repeated collections of the Madagascan sponge Fascaplysinopsis sp. (F. sp.) [Latrunculin analogs, latrunculol A\u2013C . 145), which was considered to be the precursor of salarins A and B [Siliquariaspongia mirabilis contained an antitumor macrolide lactam named mirabilin (146) [147) was isolated from the Madagascar sponge F. sp. and was found to inhibit proliferation of K562 leukemia cells [148), containing a rare hexahydro-1H-isoindolone and trichlorocarbinol ester, was isolated from marine sponge of the genus Phorbas [A further collection led to the isolation of salarin C ( A and B . Marine in (146) . The nitia cells . Muirono Phorbas . 149), B-1092 (150), B-1020 (151) and B-1076 (152), were extracted from the Poecilosclerid sponge Li. sp. in microgram quantities and their structures were elucidated by capillary NMR spectroscopy [Four variants of halichondrin B, B-1140 (troscopy . 153) and two analogs, 15-O-methylenigmazole A (154) and 13-hydroxy-15-O-methylenigmazole A (155), were extracted from the marine sponge Cinachyrella enigmatica collected in Papua New Guinea [Cytotoxic phosphate-containing macrolide enigmazole A (w Guinea and theiw Guinea .156\u2013162) were obtained from the Madagascan F. sp. sponge. Scalarins D, E, H, and J inhibited cell proliferation in a dose- and time-dependent manner [163\u2013165) were obtained from the Okinawan marine sponge T. sp. and absolute configurations were determined by combining a JBCA method, a universal NMR database, and a 13C-acetonide method [Seven scalarin analogs D\u2013J and swinholide K (167) [168), with strong cytotoxicity towards human Jurkat J16 T and Ramos B lymphocytes, was isolated from marine sponge Cal. sp. [169) and C (170) were isolated from Petrosiidae sponge with stereochemical assignment via enantioselective synthesis of the macrocyclic core [171), F (172), and G (173) were isolated from the marine sponge Poecillastra sp. [The Indonesian sponge K (167) . An unusCal. sp. . Cytotoxlic core . Cytotoxstra sp. .Periconia byssoides (Per. byssoides), obtained from the sea hare Aplysia kurodai (Ap. sp.), was reported to produce the cytotoxic triols pericosides A and B, and four new macrolides, macrosphelides E\u2013H (174\u2013177) [178) and macrosphelides E\u2013H from Per. byssoides isolated from Ap. kurodai were also reported elsewhere [179) and H produced by Per. byssoides from Ap. kurodai, and the cytotoxic macrosphelide M (180) [Penicillum verruculosum (IMI352119) was reported to produce three macrolides with antifungal activity: BK223-A (181), BK223-B (182) and BK223-C (183) [Varicosporina ramulosa has been reported to produce -colletodiol (184), -colletodiol (185) and colletoketol (186) [187) and pandangolide 2 (188) were extracted from an unidentified fungus isolated from marine sponge collected in Indonesia [The fungus 174\u2013177) . Macrosplsewhere . Macrosplsewhere . The synlsewhere ,118. Abs M (180) ,119,120.-C (183) . The mitol (186) ,123. Thendonesia . 189), macrolide dimer pandangolide 4 (190), and a new acetyl derivative of 5-hydroxymethylfuran-2-carboxylic acid were produced by the fungus Cladosporium herbarum (Cla. herbarum), associated with the sponge Callyspongia aerizusa and collected in Bali [191) was obtained from an extract of the marine fungus Myrothecium roridum (M. roridum) [192\u2013196) were isolated from the mangrove fungus Aigialus parvus BCC 5311 [197) and 15G256\u0461 (198) were obtained from the marine fungus Hypoxylon oceanicum LL-15G256 [199) and B (200), were produced by the fungus Cladosporium isolated from the brown alga Actinotrichia fragilis [Pandangolide 3 . The 14-BCC 5311 . PotentiL-15G256 . Two cyt, Japan) . Sargassum sp. was the source of two 12-membered ring lactones (201\u2013202) [203), roridin Q (204) and 2,3-deoxyroritoxin D (205) were obtained from M. roridum on submerged wood in Palau [Gliocladium sp. isolated from the alga Durvillaea antarctica yielded 4-ketoclonostachydiol (206) [An unidentified endophytic fungus from the brown alga 201\u2013202) . 12-Hydrin Palau . Glioclaol (206) . 207) and 2\u2032-hydroxyzearalanol (208) were isolated from the marine-derived fungus Penicillium sp. (Pen. sp.) [209) was obtained from the culture broth of the fungus Fusarium sp. 05ABR26 [210\u2013212) were isolated from the culture broth of the marine sponge-derived fungus Aspergillus ostianus (As. ostianus) [The 14-membered resorcylic acid lactone derivatives 8\u2032-hydroxyzearalanone (en. sp.) . \u03b2-resor 05ABR26 . The cytronesia) .As. sp. SCSGAF 0076 was reported to produce the 16-membered macrolide aspergillide D (213) [214) and enantiomers of curvularin (215\u2013220) were isolated from Curvularia sp. (Cur. sp.) [221) was produced by Cur. sp. isolated from the marine alga Gracilaria folifera and inhibited the growth of B. subtilis, Microbotryum violaceum, Septoria tritici, and Chlorella fusca [The marine-derived fungus D (213) . Apralacur. sp.) ,138. Thela fusca . 222\u2013224), were purified from an ethyl acetate extract of Corynespora cassiicola isolated from leaf tissues of the Chinese mangrove medicinal plant Laguncularia racemose [225) and B (226) (as the diacetate) were isolated from the fungus Pestalotiopsis spp., which is associated with mangrove twigs of Rhizophora mucronata [227\u2013229), 15G256\u03b1 (230), and 15G256\u03b2 (231) were obtained from crude extracts of the fungus Calcarisporium sp. KF525 isolated from German Wadden Sea water samples [Three decalactones, xestodecalactones D\u2013F , were obtained from the fungus Dendrodochium sp. derived from sea cucumber Holothuria nobilis Selenka in the South China Sea [Thirteen new 12-membered macrolides, dendrodolides A\u2013M was produced by the gorgonian-derived fungus Cochliobolus lunatus (Coc. lunatus) [Cochliomycin C (lunatus) , its abslunatus) .Pen. sumatrense MA-92, associated with the mangrove Lumnitzera racemose, yielded the sulfur-containing curvularin derivatives sumalarins A\u2212C (246\u2013248) [Coc. lunatus (TA26-46) with histone deacetylase inhibitors led to the elucidation of two 14-membered resorcylic acid lactones: 5-bromozeaenol (249) and 3,5-dibromozeaenol (250) [251\u2013255) were obtained from a sponge-derived fungus Gliomastix sp. ZSDS1-F7-2, their structures being determined by spectroscopy and single crystal X-ray diffraction [256\u2013257) were isolated from the marine-derived fungus Pen. meleagrinum var. viridiflavum [Penicillium sp. DRF2 led to the isolation of cyclothiocurvularins (258\u2013260) and cyclosulfoxicurvularins (261\u2013262) [263) was produced by the mangrove endophytic fungus Cladosporium sp. (Cla. sp.) SCNU-F0001 and its absolute configuration was determined by X-ray diffraction [264\u2013268) were isolated from another mangrove-derived endophytic fungus species in the same Cla. genus [269) was isolated from endophytic fungus Aplosporella javeedii [270\u2013271), were obtained from the endophytic fungus Paramyrothecium roridum isolated from the medicinal plant Morinda officinalis [The fungus 246\u2013248) . Chemicaol (250) . Gliomasfraction . Two 13-diflavum . Applica261\u2013262) . Thioclafraction . Thioclaa. genus . The macjaveedii . Two triicinalis .272) was isolated from a marine bacterium in the order Actinomycetales [273) was produced by Streptomyces hygroscopicus (S. hygroscopicus) isolated from the marine fish Halichoeres bleekeri [O-Succinyl macrolactin F (274) and 7-O-succinyl macrolactin A (275) were isolated from a culture of marine Bacillus sp. (B. sp.) Sc026 [The 24-membered macrolide maduralide Sc026 .276) was obtained from marine actinomycete L-25-ES25-008 [277) was isolated from marine Streptomycete isolate B7064 and was bioactive in both microorganisms and microalgae [278\u2013279) have been extracted from culture broths of bacteria isolated from the surface of the Caribbean brown alga Lobophora variegata [280\u2013282) were produced by Micromonospora sp. (M. sp.) and demonstrated inhibition of gastrulation in starfish embryos [Cytotoxic macrolide IB-96212 . Micromo embryos ,164. 283\u2013286) were isolated from actinomycete \u201cMarinispora\u201d. These marinomycins showed antibacterial activity towards methicillin-resistant S. aureus (MRSA), while marinomycin A inhibited vancomycin-resistant S. faecium (VREF) and C. albicans (weakly). Marinomycins A\u2013C demonstrated cytotoxic activity against a panel of 60 tumor cell lines, including six of the eight melanoma cell lines [Marinomycins A\u2013D , with arenicolides A showing moderate cytotoxicity [290) has been reported in a culture of marine Bacillus sp. [Marinispora\u201d yielded polyene macrolides marinisporolides A (291) and B (292), which photoisomerized to the geometric isomers marinisporolides C\u2013E, suggesting that they may be artefacts [S. hygroscopicus produced halichoblelides B (293) and C (294), which are cytotoxic to tumor cells [Marine actinomycete toxicity . Macrolallus sp. . The actrtefacts . S. hygror cells .295\u2013296), were obtained from the culture of a marine actinomycete S. sp. isolated from a sediment sample collected at North Cat Cay in the Bahamas [Two 36-membered macrolides, bahamaolides A and B ( Bahamas . B. subtilis isolated from marine sediment collected at Gageocho (Republic of Korea) was a source of three new glycosylated methoxy-macrolactins (297\u2013299) [300\u2013302), featuring an oxetane, an epoxide, and a tetrahydropyran ring, were isolated from an ethyl acetate extract of a marine B. sp. [303) was produced by a marine-derived actinomycete strain (CNJ-878) [M. strain FIM07-0019 isolated from shallow coastal waters near the island of Chiloe (Chile) produced a 20-membered macrolide, levantilide C (304) [297\u2013299) . Three ne B. sp. . CytotoxCNJ-878) . The M. C (304) . S. sp. in sediment from Heishijiao Bay yielded 11\u2032,12\u2032-dehydroelaiophylin (305) and 11,11\u2032-O-dimethyl-14\u2032-deethyl-14\u2032-methylelaiophylin (306)\u2014both 6-deoxyhexose-containing antibiotics\u2014with the former exhibiting inhibition of MRSA and vancomycin-resistant Enterococci pathogens [307), was produced by a marine-derived filamentous sulfur bacteria, Thioploca sp. [308), was isolated from marine sediment-derived actinomycete S. sp. [309) and B (310) were identified in marine-derived bacteria of the genus Nocardiopsis and demonstrated inhibition towards TNF-\u03b1-induced NF\u03baB activation (fijiolide A to a greater extent than fijiolide B) [311) and B (312) were obtained from S. hygroscopicus in the alkaline soil of the Saratov region of Russia. They exhibited significant cytotoxicity towards doxorubicin-resistant human leukemia cells [313) and B (314), were isolated from the actinobacterium Catenulispora sp. KCB13F192 [Investigation of a athogens . A rare loca sp. . A poten U.S.A.) . Fijioliolide B) . Astolidia cells . Two hygCB13F192 . Scytonema mirabile BY-8-1, S. burmanicum DO-4-1, and S. ocellatum DD-8-1, FF-65-1 and FF-66-3 have been reported to produce tolytoxin (315). S. burmanicum DO-4-1 also yielded scytophycin B (316), 6-hydroxyscytophycin B (317), 19-O-demethylscytophycin C (318), 6-hydroxy-7-O-methylscytophycin E (319), and scytophycin E (320) [321), was isolated from Japanese Oscillatoria sp. and demonstrated inhibition towards fertilized echinoderm eggs [Lyngbya bouillonii (L. bouillonii) collected on Laing Island (Papua New Guinea) produced lyngbyaloside (322) [323), madangolide (324), and laingolide A (325) [326), for which the configuration of C-11 was later revised [Cyanobacteria E (320) . A macroerm eggs . The marde (322) in addit A (325) ,185, and revised ,187.327) and B (328), together with swinholide A previously obtained from the marine sponge T. swinhoei [Geitlerinema sp. collected in Madagascar [329), demonstrating significant molluscicidal activity towards the snail vector Biomphalaria glabrata, was also isolated from L. bouillonii from Papua New Guinea [330) was isolated from L. sp. and showed strong apoptosis-inducing activity in HeLa S3 and HL60 cells [331\u2013333), were produced by another L. cyanobacterium sampled on Tokunoshima Island (Japan) [2+ concentration in HeLa S3 cells [Two glycosylated swinholides, ankaraholides A . BiselynS3 cells . 334) [335\u2013338), have been isolated from Leptolyngbya sp. collected in Okinawa [The Caribbean Okeania cyanobacterium VQR28MAR11-2 has been reported to produce polycavernoside D (334) , while f Okinawa .339) was isolated from the Okinawan flatworm Amphiscolops sp. (Amphis. sp.) and exhibited cytotoxicity towards murine leukemia cells L1210 and L5178Y [340), G (341) and H (342) were produced by dinoflagellate Amphidinium sp. (Amphid. sp.) associated with the Okinawan flatworm Amphis. breviviridis [Amphidinolide E and K (344) were isolated from symbiotic dinoflagellate Amphid. sp. and later synthesized [345), B2 (346) and B3 (347) were also isolated from Amphid. sp. [348), M (349) and N (350) [Amphidinolides G and H were elucidated by X-ray diffraction analysis and interconversion . Amphidithesized ,200. Amphid. sp. ,202,203, N (350) ,205,206.351) and P (352), were also isolated from Amphis. sp. [353), showing moderate cytotoxicity towards murine lymphoma L1210 cells in vitro (IC50 6.4 \u03bcg/mL), was obtained from the symbiotic flatworm Amphis. sp. of dinoflagellate Amphid. sp. [R, 7R, 9S, 11R, and 13R on the basis of NMR analysis and a modified Mosher\u2019s method [354) and S (355) were also isolated from Amphid. sp. [356) was obtained from a cultured Amphid. sp. Y-56 isolated from the flatworm Amphis. sp. in Okinawa [357), was also obtained from the Y-56 dinoflagellate strain and exhibited cytotoxicity towards P388, L1210 and KB cells [358) [A. sp. Y-5 produced the 14-membered polyene amphidinolide V (359) [360), T3 (361), T4 (362), and T5 (363) were produced by Amphid. sp. [364), H3 (365), H4 (366), H5 (367), G2 (368), and G3 (369) were produced by Amphid. sp. strain Y-42 isolated from marine acoel flatworms Amphis. sp. The absolute configurations of these compounds were determined by coupling constant data, distance geometry calculations, and chemical means [S)-lactate via a 16-step linear sequence [370) was isolated from an Amphid. sp. and the absolute stereochemistry determined by a combination of J-based configuration analysis and modified Mosher\u2019s method [371) and Y (372) were produced by symbiotic dinoflagellate Amphid. sp. strain Y-42 from Okinawan Amphis. species. Amphidinolide Y exists as a 9:1 equilibrium mixture of the 6-keto- and 6(9)-hemiacetal forms (373). Both amphidinolides X and Y showed significant cytotoxicity against murine lymphoma L1210 and human epidermoid carcinoma KB cells in vitro [374) and B7 (375), were isolated from a culture of a symbiotic dinoflagellate Amphid. sp. from Amphis. sp. and demonstrated cytotoxicity against human B lymphocyte DG-75 cells [376) was isolated from dinoflagellate Amphid. sp. (Y-71 strain) [The structure of amphidinolide N was later revised and stereochemistry assigned . Cytotoxhis. sp. . The abshis. sp. . The 12-hid. sp. . The abss method . Cytotoxhid. sp. . The 20- Okinawa . A 25-meKB cells . Y-56 hals [358) , while t V (359) . Total s V (359) . Analogshid. sp. ,220. Ampal means . Amphidisequence . Amphidis method . Total ss method . Amphidiin vitro ,226. Two75 cells . Amphidi strain) . Amphid. strain S1-36-5 yielded the highly cytotoxic 26-membered caribenolide I (377) [The I (377) .378) and a 26-membered macrolide amphidinolactone B (379) have been isolated from cultures of Amphid. sp. Amphidinolactone A was synthesized totally via a ring-closing metathesis reaction and the absolute configuration was elucidated [380) and B (381) were isolated from a symbiotic dinoflagellate Symbiodinium sp. (Y-6 strain), which was associated with Amphis. sp. [Prorocentrum maculosum Faust yielded the fast-acting toxin prorocentrolide B (382) [383) was identified in the marine dinoflagellate P. hoffmannianum [384), -1b (385) and -1c (386) were isolated from a marine benthic dinoflagellate Amphid. sp. (strain HYA024) [The 13-membered macrolide amphidinolactone A 37 and a 26ucidated ,231. Thehis. sp. ,233. Bio B (382) . Hoffmanannianum . The 20- HYA024) ,237. 387) was also obtained from Amphid. sp. [388) containing an allyl epoxide was obtained from Amphid. sp. strain HYA024 and was potently cytotoxic to human B lymphocyte DG-75 cells and Epstein\u2013Barr virus (EBV)-infected Raji cells [389) and -5a (390) were isolated from a benthic dinoflagellate Amphid. sp. (strain HYA024) and showed moderate cytotoxicity towards human B lymphocytes DG-75 [391) and -11a (392) were cytotoxic towards human cervix adenocarcinoma HeLa and murine hepatocellular carcinoma MH134 cells [The cytotoxic 23-membered iriomoteolide-2a (hid. sp. . The 15-ji cells . Iriomotes DG-75 . The 15-34 cells .393) and -12a (394) were isolated from a marine dinoflagellate Amphid. sp. (KCA09053 strain) with iriomoteolide-10a being cytotoxic to human cervix adenocarcinoma HeLa and murine hepatocellular carcinoma MH134 cells [395) was isolated from the symbiotic dinoflagellate Symbiodinium sp. (S. sp.) and showed significant voltage-dependent N-type Ca2+ channel-opening activity at 7 nM and immediately ruptured the surface tissue of the acoel flatworm Amphis. sp. at 2.5 mM [S,18R,21R) configurations were determined by synthesis [S,40S) and (C-1\u2032\u2013C-25\u2032) [396) caused potent stimulation of actomyosin ATPase activity [397) was isolated from cultures of the marine dinoflagellate Prorocentrum belizeanum [398) was extracted and purified from a culture of dinoflagellate Alexandrium ostenfeldii from the Baltic Sea [399) was isolated from a culture of the symbiotic marine dinoflagellate S. sp. [Iriomoteolide-10a ,244,245.activity . The 25-lizeanum . Gymnodiltic Sea . Symbiode S. sp. .Polycavernosa tsudai (Gracilaria edulis) contained the macrolide polycavernoside A (400), which led to human illness and death in Guam [401), A3 (402), B (403) and B2 (404) were also obtained from Polycavernosa red algae [ in Guam . The rel in Guam ,252. Its in Guam . Polycaved algae . 405) and C2 (406), were isolated from the red alga Gracilaria edulis (G. edulis) [407\u2013409) were isolated from extracts of red alga G. coronopifolia [410) and manauealide C were extracted from Hawaiian G. coronopifolia [Callophycus serratus (C. serratus) led to the isolation of three diterpene-benzoate natural products: bromophycolides A (411) and B (412), and a nonhalogenated compound (413). Bromophycolides A and B exhibited moderate antibacterial and antifungal properties while bromophycolides A demonstrated potent anti-HIV and moderate cytotoxic activities [414\u2013420) were also isolated from extracts of C. serratus. All the bromophycolides exhibited modest antineoplastic activity towards a range of human tumor cell lines while bromophycolides F and I showed weak antifungal activity [Two analogs of polycavernosolide A, polycavernosides C ( edulis) . Manaueaopifolia . Anhydroopifolia . Investitivities . Bromophactivity . C. serratus extract yielded a series of unusual antimalarial diterpene-benzoate macrolides, bromophycolides J\u2013Q (421\u2013428), with a range of moderate to strong antimicrobial and anticancer properties [C. serratus was also a source of the diterpene-benzoate macrolides bromophycolides R\u2013U (429\u2013432). These demonstrated modest cytotoxicity toward selected human cancer cell lines while bromophycolide S was active (at submicromolar concentrations) against the human malaria parasite Plasmodium falciparum [Further investigation of the operties . C. serrciparum) . 433) and B (434) were obtained from the Fijian red alga Neurymenia fraxinifolia [Ecklonia stolonifera produced ecklonialactones C (435) and D (436) containing a 14-membered lactone moiety, and ecklonialactones E (437) and F (438), with a 16-membered moiety [439\u2013446) with a macrolide scaffold and one cymathere-type oxylipin with an open ring were isolated from the brown alga Eisenia bicyclis. The absolute configurations of compounds 439\u2013443 and 446 were determined by NMR spectroscopy with the relative stereochemistry at C-9 in 446 remaining unassigned [447) was isolated from the crustose coralline alga Hydrolithon reinboldii and its absolute relative configuration was determined by NMR spectroscopy with the relationships of the two side chains to the macrolide ring remaining unassigned [The \u03b1-pyrone macrolides neurymenolides A and B1e (449), exhibiting moderate antifouling activity were obtained from Anthrogorgia caerulea collected in the South China Sea [Two avermectin congeners, avermectins B1c (hina Sea .450) from the marine bryozoan Bugula neritina (L.) was carried out to provide material for clinical study [451) has been converted to bryostatin 1 and bryostatin 12 (452) by selective protection and deprotection involving the C-26 hydroxyl group [p-bromobenzoate (453) [1H- and 13C-NMR were later revised [B. neritina and reinvestigation of 2D NMR spectroscopic data revised the structure of bryostatin 3 to structure 454 [Large-scale isolation of bryostatin 1 , while t revised . Bryostature 454 .B. neritina led to the identification of bryostatins 14 (455) and 15 (456) [457) have been elucidated by NMR spectroscopy [458) was determined to be the major cytotoxic component of B. neritina [459), 17 (460), and 18 (461), were isolated in trace amounts from B. neritina from the Gulf of Mexico [462) was isolated from B. neritina collected from the South China Sea [463), was produced by the larvae of B. neritina and its structure determined by spectral comparison with previously described bryostatins [464), which was cytotoxic towards the P388 lymphocytic leukemia cell line [Further investigation of 15 (456) . The strtroscopy ,273,275.troscopy . Bryostaneritina . Three af Mexico . Antineohina Sea . A furthostatins . Bioassaell line .465) was isolated from an extract of the sea hare Stylocheilus longicauda and synthesized [Aplysia kurodai Baba contained the novel and potently cytotoxic macrolides aplyronines A (466), B (467) and C (468). The absolute configuration of aplyronine A was assigned following enantioselective synthesis of its degradation products and total synthesis was also reported [469\u2013473), were also isolated from the Japanese sea hare Aplysia kurodai [474) and the diacetyl derivative dolabelide B (475), both cytotoxins, were obtained from the Japanese sea hare Dolobella auricularia [476) and D (477) were also isolated from Dolabella auricularia, the originally assigned structure of dolabelide D being confirmed by total synthesis [478\u2013482) were found in the skin of the marine mollusk Aplysia depilans, and were ichthyotoxic to the mosquito fish Gambusia affinis [483) and 7 (484) were isolated from Patinopecten yessoensis scallops [485) as a pectenotoxin accumulating in Norwegian blue mussels (Mytilus edulis) and cockles (Cerastoderma edule) [486), containing a 14-membered macrocyclic lactone linked to a 2,4-di-O-methyl-L-R-rhamnopyranoside, was found in the Gulf of California in the shell-less mollusk Dolabella auricularia [Aplysiatoxin . Dolastaicularia . The steicularia .487) and D (488), were isolated from the Okinawan tunicate Eudistoma cf. rigida [489) and B (490), were reported in the tunicate Aplidium lobatum [A. lobatum from shallow waters in Australia, A. sp. from deep water, and an unidentified Philippine ascidian have been reported as sources of a series of macrolides, lobatamides C\u2013F (491\u2013494), demonstrating cytotoxicity towards human tumor cell lines [495) was obtained from an Okinawan ascidian L. sp. by bioassay-guided isolation and was shown to inhibit the first cleavage of fertilized sea urchin eggs at 0.01 \u03bcg/mL [Didemnidae sp. was the source of the macrolides biselides A (496) and B (497) [D. sp. led to the isolation of biselides C (498), D (499) and E (500) which exhibited cytotoxicity against human cancer cells NCI-H460 and MDA-MB-231 [501) was obtained from the Antarctic tunicate Synoicum adareanum [Two 24-membered macrolide sulfates showing antineoplastic activity, iejimalides C . FurtherA-MB-231 . Cytotoxdareanum and its dareanum ,307. 502\u2013505) were isolated from Lissoclinum ascidian collected in Algoa Bay near Port Elizabeth and the surrounding Nelson Mandela Metropole in South Africa [Glycosylated macrolides mandelalides A\u2212D (h Africa .The biological activities of marine-derived macrolides have been studied extensively. As listed in This review presents a summary of 505 marine-derived macrolides reported from 1990 to 2020 and highlights their chemical and biological diversity. As shown in For macrolides with larger macrocyclic rings, such as reidispongiolides A and B , symbiod"} +{"text": "ADG20 is a fully human IgG1 monoclonal antibody engineered to have potent and broad neutralization against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-like CoVs with pandemic potential as well as an extended-half-life. ADG20 is administered intramuscularly (IM). A QSP/PBPK model was constructed to support dose selection for a COVID-19 Phase 2/3 prevention trial (EVADE: NCT04859517).90]) for authentic SARS-CoV-2 were also evaluated.A QSP/PBPK model and a CDC reference adult body weight distribution (45\u2013150 kg) were used to simulate 1000 concentration-time profiles for candidate single-dose regimens of ADG20 (150\u2013450 mg IM). As serum virus neutralizing antibody (sVNA) titers are reportedly a key correlate of protection from COVID-19, a regression equation between time-matched serum ADG20 concentrations (following a 300 mg IM dose) and sVNA titers was developed using measured titers against authentic SARS-CoV-2 determined by a plaque reduction neutralization assay. Projected ADG20 serum concentrations relative to neutralization potency in vitro .The measured 50% neutralization titer was 1382 (32.7%) 13 days after a single 300 mg IM dose of ADG20. This was within the range of peak sVNA titers reported for COVID-19 vaccine recipients. Using the linear equation relating serum ADG20 concentration to time matched individual MN50 titers and the QSP/PBPK median PK prediction, the anticipated median MN50 exceeded the threshold for protection from SARS-CoV-2 infection established in a non-human primate adoptive transfer model for up to 52 weeks. Based on the QSP/PBPK median PK prediction, median ADG20 serum concentrations are projected to remain >100-fold above the ADG20 ICFollowing administration of a single 300 mg IM dose, sVNA titers and concentrations of ADG20 are projected to remain above thresholds anticipated to be required for protection against COVID-19 for up to 52 weeks. These data support the evaluation of a single ADG20 300 mg IM dose for the prevention of COVID-19.Figure. QSP/PBPK model forecast of ADG20 300 mg IM in adults.Predicted median serum ADG20 concentration is shown with the dotted line representing 100\u00d7 in vitro IC90 of 0.011 mg/L or 1.1 mg/L; the solid black line represents the simulated median; the shaded area represents the 90% prediction interval. The predicted median half-life of ADG20 300 mg IM exceeded 74 days. PBPK model inputs include Ln-normal Kd,FcRn of 9.55 nM (10% IIV); IM bioavailability of 100%; 15% IIV on muscle lymph RC; and Centers for Disease Control and Prevention weight distribution of 45\u2013150 kg. FcRn, neonatal Fc receptor; IIV, inter-individual variability; Kd, dissociation constant; Ln, log-normal; RC, reflection coefficient.Scott A. Van Wart, PhD, Adagio Therapeutics, Inc. (Independent Contractor) Evan D. Tarbell, PhD, Adagio Therapeutics, Inc. (Independent Contractor) Kristin Narayan, PhD, Adagio Therapeutics, Inc. (Employee) Laura M. Walker, PhD, Adagio Therapeutics, Inc. Lynn E. Connolly, MD, PhD, Adagio Therapeutics, Inc. (Employee) Paul G. Ambrose, PharmD, Adagio Therapeutics, Inc. (Employee)"} +{"text": "Integrase inhibitor (INSTI)-based antiretroviral therapies (ART) are first-line for HIV infection. Recent studies have identified metabolic complications of INSTI regimens, especially when TAF is included. The objective of this study was to assess lipid changes associated with INSTI-based ART.This was a retrospective, observational, single-center study. Patients age \u2265 18 with HIV infection, receiving care Jan 2004 to Jul 2019, and prescribed the same ART for \u2265 6 consecutive months were randomly selected from a computer-generated list. Unique ART regimens prescribed per patient were considered \u201cexposures\u201d. Patients were followed up to 2 years per exposure. INSTI-based exposures included an INSTI plus one or more NRTI. Non-INSTI-based exposures included a PI or NNRTI plus one or more NRTI. Lipid panel results were recorded before and during exposures. Lipid changes with INSTI and non-INSTI exposures were compared. Other metabolic outcomes were recorded.2, respectively. 72 (37.5%) were ART-na\u00efve. 53.5% INSTI recipients received BIC or DTG. Hypertriglyceridemia (HTG) occurred more often during INSTI exposures . Mean change in TG concentration was +10.1 and -15.0 mg/dL for INSTI and non-INSTI regimens, respectively (p = 0.105). Patients receiving INSTIs were more commonly prescribed a new lipid-lowering therapy (LLT) or an increase in dose of preexisting LLT . Of those that received an INSTI-regimen and either TAF, TDF, or no tenofovir, 17.4%, 10.3%, and 8.3% developed HTG, respectively (p = 0.49). There was no difference between groups in HDL or LDL changes. Among INSTI and non-INSTI groups, weight increased by +3.8 and +2.1 kg, respectively (p = 0.129). Mean weight change was less in INSTI recipients whose regimen included TDF .192 exposures were identified among 132 patients. The majority were Black (69.3%) and male (61.9%). Mean age and BMI were 42.0 \u00b1 11.3 and 26.2 \u00b1 5.5 kg/mTreatment with INSTI-based ART was associated with HTG. LLTs were utilized more often among INSTI recipients, and this limited our ability to fully characterize lipid changes in this real-world study. Weight gain among INSTI recipients may be attenuated if TDF is included in the regimen.James Johnson, PharmD, FLGT (Shareholder) Caryn Morse, MD, Chimerix (Scientific Research Study Investigator)Covis Pharma (Scientific Research Study Investigator)Gilead Sciences Inc. (Scientific Research Study Investigator)Ridgeback Biotherapeutics (Scientific Research Study Investigator)Roche (Scientific Research Study Investigator)SCYNEXIS, Inc. (Scientific Research Study Investigator)Theratechnologies (Advisor or Review Panel member)Viiv (Advisor or Review Panel member)"} +{"text": "Staphylococcus lugdunensis and determine its association with sequence types (STs) determined by multilocus sequence typing (MLST) and oxacillin susceptibility. Primers were designed to detect and sequence types IIIA and IIC CRISPR-Cas in 199 S. lugdunensis isolates. MLST and oxacillin susceptibility tests were also performed on the isolates. We found that 84 S. lugdunensis isolates had type IIIA CRISPR-Cas, while 46 had type IIC. The results showed a strong association between STs and CRISPR-Cas types. The ST1, ST6, ST12, and ST15 isolates had type IIIA CRISPR-Cas systems, and the ST4, ST27, and ST29 isolates had type IIC CRISPR-Cas. Interestingly, of 83 isolates containing type IIIA CRISPR-Cas, 17 (20.5%) were oxacillin-resistant S. lugdunensis (ORSL), and all of these ORSL isolates belonged to ST6 cluster 1. Moreover, spacers 23 and 21 were found in 16 and 17 ORSL isolates, respectively. In contrast, all 46 isolates with type IIC CRISPR-Cas were susceptible to oxacillin. Our results showed that 41.3% of CRISPR-Cas IIIA spacers were homologous to plasmids and 20.2% were homologous to phages. However, in type IIC CRISPR-Cas, 11.8% and 39.9% of spacers showed sequence homology with plasmids and phages, respectively. In conclusion, we found that the distribution and composition of the CRISPR-Cas system in S. lugdunensis was associated with STs and oxacillin susceptibility.Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) genes (CRISPR-Cas) are present in many bacterial genomes with functions beyond adaptive immunity. We aimed to characterize the CRISPR-Cas system in the pathogenic Gram-positive bacterium IMPORTANCE CRISPR-Cas systems have been characterized as playing several biological roles in many bacterial genomes. Moreover, CRISPR-Cas systems are useful for epidemiological, diagnostic, and evolutionary studies of pathogenic bacteria. However, the characteristics of CRISPR-Cas systems in Staphylococcus lugdunensis have been rarely reported. In this study, we revealed that type IIIA CRISPR-Cas was dominant in S. lugdunensis isolates, followed by type IIC CRISPR-Cas. Moreover, the composition of CRISPR-Cas spacers was strongly associated with multilocus sequence typing and oxacillin susceptibility of S. lugdunensis. These results advance our understanding of the evolution of CRISPR-Cas systems; however, the biological functions of CRISPR-Cas systems in S. lugdunensis remain to be further characterized. Staphylococcus lugdunensis is a Gram-positive, catalase-positive, and coagulase-negative Staphylococcus (CoNS) bacterium. Staphylococcus lugdunensis has emerged as an important pathogen, implicated in clinically invasive infections such as endocarditis and bacteremia in recent years has been frequently reported over the last decade (Staphylococcus lugdunensis expressing penicillin-binding protein 2a (PBP2a), encoded by the mecA gene, shows a lower affinity for \u03b2-lactams and is responsible for \u03b2-lactam resistance , 5.S. lugdunensis isolates from different clinical and geographic sources, using DNA sequence analysis of seven housekeeping genes: aroE, dat, ddl, gmk, ldh, recA, and yqiL (S. lugdunensis isolates could be defined into 20 sequence types (STs) and 5 clonal complexes and CRISPR-associated (Cas) genes (CRISPR-Cas) are present in many bacterial and archaeal genomes . CRISPR-lococcus \u201313. Rossococcus \u2013, 15. HowS. lugdunensis isolates and determined the distribution of CRISPR-Cas in the isolates. The PCR results showed that 130/199 (65.3%) of the S. lugdunensis isolates had CRISPR-Cas systems, including 84 (42.2%) with type IIIA and 46 (23.1%) with type IIC . Most ST1 and ST6 clusters (clusters 1 to 5) had spacers 1 and 2, which showed homology with Campylobacter phage CP220 and Clostridium botulinum strain CDC_67071 plasmid pNPD7, respectively. All ST15 cluster 7 isolates had spacers 94, 95, 96, and 97, of which 94 and 96 showed homology with phages in the S. lugdunensis genome . We were unable to determine the homologs of spacers 12 and 81.To further validate the association between CRISPR-Cas types and STs, we performed a phylogenetic analysis based on the sequences of seven housekeeping genes for MLST. The results revealed a strong association between ST1, ST6, ST12, and ST15 , which had type IIIA CRISPR-Cas systems . Among tisolates . Spacer s genome . Spacer S. lugdunensis isolates containing type IIIA CRISPR-Cas systems was 10.2 (818 spacers/80 isolates) (S. lugdunensis chromosome (The mean number of spacers in solates) . We founsolates) . Moreoveromosome . Overallromosome .S. lugdunensis isolates with type IIC CRISPR-Cas comprised 8 clusters and 33 CTs (S. lugdunensis genome (Table\u00a0S5). All ST29 isolates had spacers 55 and 56 (Secundilactobacillus paracollinoides strain TMW 1.1979 plasmid pL11979-2 (Table\u00a0S5). We were unable to determine the homologs of spacer 56. Spacers 20, 21, 29, 31, 32 to 36, 44 to 46, and 53 were highly conserved in ST4 isolates, but ST4 cluster 1 lacked spacer 53 (Staphylococcus genomes (Table\u00a0S5).Forty-three d 33 CTs . Three id 33 CTs and 3B. d 33 CTs . Howeverd 33 CTs . Spacers5 and 56 . Spacer pacer 53 . Among tS. lugdunensis containing type IIC CRISPR-Cas systems was 13.7 (591 spacers/43 isolates) (S. lugdunensis containing type IIIA CRISPR-Cas systems (mean 10.2 spacers/strain) (S. lugdunensis chromosome (All isolates with type IIC CRISPR-Cas were susceptible to oxacillin. The mean number of spacers in solates) , higher /strain) . Our res/strain) . Moreoveromosome . Overallromosome . Of spacromosome .S. lugdunensis. We found 84 S. lugdunensis isolates with type IIIA CRISPR-Cas and 46 isolates with type IIC and related IncF epidemic plasmids . Surprisingly, spacer 23 showed homology with a S. aureus strain 16405 plasmid that expressed PBP2A encoded by mecA. Therefore, the activity of CRISPR-Cas systems in plasmid acquisition and their association with oxacillin susceptibility of S. lugdunensis merits further investigation.Our results demonstrated that CRISPR-Cas spacer sequences were strongly associated with MLST and oxacillin susceptibility. Previous studies have shown that pandemics caused by multidrug-resistant plasmids . The absplasmids , 16. In isolates . In addiisolates . The homS. lugdunensis typing, including a classical length-based multiple loci VNTR analysis (MLVA) method and a sequence-based MLVA method known as the tandem repeat sequence typing (TRST) method (fbl-typing) has also been used for S. lugdunensis typing method . Sequenc) method . DNA seqs typing . Among tdunensis , 9. CompAcinetobacter baumannii global clone 1 (GC1) isolates were included in the study. All information associated with the 199 isolates was collected. Staphylococcus lugdunensis isolates were initially identified by Gram staining, biochemical methods , and rapid PCR detection . The isolates were stored in tryptic soy broth containing 20% glycerol at \u221280\u00b0C until use.A total of 199 etection . All thecas1 gene for CRISPR-Cas types IIIA and IIC, respectively database, including sequences for type IIIA-positive strain VISLISI_33 (accession no. CP020769.1) and type IIC-positive strain C_33 (accession no. CP020768.1). The PCRs were carried out in a total volume of 20\u2009\u03bcl containing 2\u00d7 master mix , 10\u2009pmol of each primer, and 1\u2009\u03bcl DNA template. The PCR cycling conditions for CRISPR-Cas system detection were 95\u00b0C for 3\u2009min; 30 cycles of 30 s at 95\u00b0C, 30 s of annealing at 50\u00b0C, and 1\u2009min of extension at 72\u00b0C; and a final extension for 3\u2009min at 72\u00b0C.The Crispr-IIIA-F/Crispr-IIIA-R and Crispr-IIC-F/Crispr-IIC-R primers were designed to specifically detect the The primers Crispr-IIIA-F/Crispr-IIIA-R and Crispr-IIC-F/Crispr-IIC-R were designed for also determining type IIIA and type IIC CRISPR-Cas spacer sequences, respectively for ST type determination. Sequence types were identified based on the allele profiles. Further analysis was performed using eBURST (http://eburst.mlst.net) to identify clonal complexes (CCs) and founders, as well as to determine the overall population structures. A minimum-evolution (ME) tree of the concatenated sequences (aroE-dat-ddl-gmk-ldh-recA-yqiL) for each ST shared by the S. lugdunensis isolates was generated using Mega X and the Kimura two-parameter model to estimate genetic distances. Statistical support of the nodes in the ME tree was assessed by performing 1,000 bootstrap resamplings.MLST was performed for all us study . Seven hS. lugdunensis isolates to oxacillin was determined using an agar dilution assay and interpreted according to the Clinical and Laboratory Standards Institute guidelines (Staphylococcus lugdunensis isolates with a MIC\u2009\u2265\u20094\u2009\u03bcg/mL were defined as resistant. Staphylococcus aureus ATCC 29213 was used as a control strain. Antimicrobial susceptibility testing was performed in duplicate to ensure reproducibility.Susceptibility of the idelines . StaphylS. lugdunensis isolates were subjected to SCCmec typing and mecA detection using a multiplex PCR assay to amplify the ccr and mec complexes according to a previous study (All us study ."} +{"text": "Arabidopsis thaliana, Gossypium herbaceum (A1), Gossypium arboreum (A2), Gossypium raimondii (D5), and Gossypium hirsutum (AD1) genomes demonstrated that four HSF genes were inherited from a common ancestor, A0, of all existing cotton A genomes. Members of the HSF gene family in G. herbaceum (A1) genome indicated a significant loss compared with those in G. arboretum (A2) and G. hirsutum (AD1) A genomes. However, HSF genes in G. raimondii (D5) showed relative loss compared with those in G. hirsutum (AD1) D genome. Analysis of tandem duplication (TD) events of HSF genes revealed that protein-coding genes among different cotton genomes have experienced TD events, but only the two-gene tandem array was detected in Gossypium thurberi (D1) genome. The expression analysis of HSF genes in G. hirsutum (AD1) and Gossypium barbadense (AD2) genomes indicated that the expressed HSF genes were divided into two different groups, respectively, and the expressed HSF orthologous genes between the two genomes showed totally different expression patterns despite the implementation of the same abiotic stresses. This work will provide novel insights for the study of evolutionary history and expression characterization of HSF genes in different cotton genomes and a widespread application model for the study of HSF gene families in plants.Heat shock transcription factors (HSFs) are involved in environmental stress response and plant development, such as heat stress and flowering development. According to the structural characteristics of the HSF gene family, HSF genes were classified into three major types in plants. Using conserved domains of HSF genes, we identified 621 HSF genes among 13 cotton genomes, consisting of eight diploid and five tetraploid genomes. Phylogenetic analysis indicated that HSF genes among 13 cotton genomes were grouped into two different clusters: one cluster contained all HSF genes of HSFA and HSFC, and the other cluster contained all HSF genes of HSFB. Comparative analysis of HSF genes in Gossypium) is one of the most important economic crops worldwide, which provides the major resource of natural fiber for human beings over the past decades. The genus Gossypium contains over 45 diploid (designated as A to G and K) and 7 tetraploid (designated as AD1 to AD7) species (Gossypium herbaceum (A1) (Gossypium arboreum (A2) (Gossypium thurberi (D1) (Gossypium raimondii (D5) (Gossypium turneri (D10) (Gossypioides kirkii (K) (Gossypium hirsutum (AD1) (Gossypium barbadense (AD2) (Gossypium tomentosum (AD3) (Gossypium mustelinum (AD4) (Gossypium darwinii (AD5) (Bombax ceiba at approximately 24 million years ago (Mya). Subsequently, cotton A0 and D5 genome species diverged from their ancestor at approximately 4.8 Mya. After the split of their ancestor, cotton A0 and D5 genome species crossed and generated cotton allotetraploid AD genome species at approximately 1.6 Mya (G. hirsutum (AD1) and G. barbadense (AD2) (G. herbaceum (A1) and G. arboreum (A2) (Cotton (genus species . To facieum (A1) , Gossypieum (A2) , Gossypieri (D1) , Gossypidii (D5) , Gossypiri (D10) , Gossypilyx (F1) , Gossypiale (G2) , and Gosrkii (K) , and fivum (AD1) , Gossypise (AD2) , Gossypium (AD3) , Gossypium (AD4) , and Gosii (AD5) . Previou 1.6 Mya . Later, se (AD2) . Less theum (A2) . A cleareum (A2) .Solanum lycopersicum (24) (Oryza sativa (25) (Zea mays (25) (Glycine max (26) (Brassica oleracea (35) (Brassica rapa (36) (Brassica napus (64) (Sesamum indicum (30) (Prunus mume (18) (Fagopyrum tataricum (29) (Cicer arietinum (20) (Vitis vinifera (19) (Capsicum annuum (25) (Brassica juncea (60) (G. hirsutum (AD1) D genome using EST assembly and genome-wide analyses (Heat shock transcription factors (HSFs) serve as the major activators of heat shock proteins (HSPs) with the help of binding to the promoter regions of HSP genes in plants. This enables HSP genes to regulate transcription in response to heat stress for adapting to various environmental dynamic changes . HSF procum (24) , Arabidoana (21) , Oryza siva (25) , Zea mayays (25) , Glycinemax (26) , Brassiccea (35) , Brassicapa (36) , Brassicpus (64) , Sesamumcum (30) , Prunus ume (18) , Fagopyrcum (29) , Cicer anum (20) , Vitis vera (19) , Capsicuuum (25) , and Bracea (60) . For theanalyses .G. herbaceum (A1), G. arboreum (A2), G. raimondii (D5), and G. hirsutum (AD1), we detected the formation of the HSF gene family and traced the evolution of HSF genes in G. hirsutum (AD1) genome. According to the genome-wide analysis of TD events, we investigated the influence of TD events on the generation of HSF genes among 13 cotton genomes. However, we used the expression analysis to reveal the functional differences of HSF genes under the same abiotic stresses in G. hirsutum (AD1) acc. TM-1 and G. barbadense (AD2) acc. Hai7124. This project will provide novel insights for understanding the evolutionary history and expression characterization of the HSF gene family, paving the way for genetic breeding and molecular improvement of cotton diploid and tetraploid species.In this project, we performed genome-wide comparative genomics analysis for the HSF gene family among 13 cotton genomes. Based on the evolutionary relationship among G. herbaceum , G. arboreum , G. thurberi , G. raimondii , G. turneri , G. longicalyx , G. australe , and G. kirkii , and tetraploid genomes, G. hirsutum , G. barbadense , G. tomentosum , G. mustelinum , and G. darwinii , are downloaded from CottonGen1 acc. TM-1 and G. barbadense (AD2) acc. Hai7124 are retrieved from the Sequence Read Archive (SRA) database with accession number PRJNA490626 program with \u201ctrusted cutoff\u201d as threshold . All proA. thaliana and Gossypium species followed the same procedures.ClustalW2 was employed to perform MSA with protein sequences of target HSFs from 13 different cotton species. Then, the MSA file with \u201cmeg\u201d format were used to construct the phylogenetic tree through MEGA 7 with maximum likelihood (ML) statistical method and 1,000 bootstrap replications . The phyFollowing the identification of tandemly duplicated genes in PTGBase, all-against-all BLAST of protein sequences in 13 cotton species was employed to identify the paralogous gene pairs within single cotton species with E-value cut-off \u22641e-20 . After cG. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genomes, as well as between G. raimondii (D5) and G. hirsutum (AD1) D genomes, were detected by the MCscanX software and validated by phylogenetic analysis (G. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genomes and between G. raimondii (D5) and G. hirsutum (AD1) D genomes. So, phylogenetic analysis of these four cottons and A. thaliana genomes was used to validate collinear relationships among cotton genomes. The collinear analysis of G. hirsutum (AD1) and G. barbadense (AD2) A genomes, as well as G. hirsutum (AD1) and G. barbadense (AD2) D genomes, follows the above procedures.Orthologous gene pairs between analysis . First, G. hirsutum (AD1) and G. barbadense (AD2) reference genome sequences through HISAT (version 2.2.1) , and alln 2.2.1) . The Strn 2.2.1) . The hien 2.2.1) .G. herbaceum , with 17 in G. arboreum , 29 in G. thurberi , 33 in G. raimondii , 36 in G. turneri , 38 in G. longicalyx , 36 in G. australe , 29 in G. kirkii , 78 in G. hirsutum , 78 in G. barbadense , 84 in G. tomentosum , 79 in G. mustelinum , and 80 in G. darwinii genomes (G. herbaceum (A1) has the least number of HSF genes and G. australe (G2) has the greatest number of HSF genes in cotton diploid genomes. Out of five cotton tetraploid genomes, G. hirsutum (AD1) and G. barbadense (AD2) have the least number of HSF genes, and G. tomentosum (AD3) has the greatest number of HSF genes.With the development of genome sequencing technology, more and more cotton genome sequences were released for the community, which facilitate the analysis of key gene families within plant whole genomes. Totally, 13 latest cotton genomics data, consisting of eight diploid and five tetraploid genomes, were downloaded from CottonGen , G. tomentosum (AD3), G. mustelinum (AD4), and G. darwinii (AD5) genomes, respectively. Finally, we obtained 78 representative HSF genes in G. barbadense (AD2) genome, with 84, 79, and 80 HSF genes in G. tomentosum (AD3), G. mustelinum (AD4), and G. darwinii (AD5) genomes, respectively.To identify accurately the members of the HSF gene family, we used the entire available protein sequences in different cotton genomes. After curation, we found that several cotton tetraploid genomes released multiple protein sequences for one gene due to an alternative splice in genomes. Using the profile HMMs of HSF_DNA-bind, we identified 120, 135, 122, and 106 HSF protein sequences in Based on the characteristics of conserved domains of HSF genes, we obtained 621 target HSF genes among 13 cotton genomes. With protein sequences of the identified HSF genes, we constructed a phylogenetic tree to investigate the evolutionary relationship of all HSF genes among 13 cotton genomes. Following the phylogenetic tree, all HSF genes were grouped into two different clusters, including I and II clusters, among 13 cotton genomes . A previG. hirsutum (AD1), was generated from hybridization between G. raimondii (D5) and the common progenitor, A0 genome, of G. herbaceum (A1) and G. arboreum (A2). However, out of four HSF genes in G. herbaceum (A1) genome, two HSF genes belonged to HSFA, with one HSF gene belonging to HSFB and one HSFC gene belonging to HSFC. For HSF genes in G. arboreum (A2) genome, six HSF genes were classified into HSFA, with eight HSF genes belonging to HSFB and three HSF genes belonging to HSFC. These HSF genes in G. herbaceum (A1) and G. arboreum (A2) originated from a common progenitor of all existing A genomes, including A genome in G. hirsutum (AD1). So, different types of HSF genes in G. herbaceum (A1) genome indicated a significant loss compared with G. arboreum (A2) and G. hirsutum (AD1) A genomes. However, different types of HSF genes in G. raimondii (D5) experienced relative loss compared with those in G. hirsutum (AD1) D genome.Upland cotton, Arabidopsis thaliana is an important model plant, and its genomic data were released more than 20 years, which brings opportunity for studying HSF genes in A. thaliana , G. arboreum (A2), G. raimondii (D5), and G. hirsutum (AD1) genomes to perform comparative genomics analysis of HSF genes in A. thaliana and cotton genomes. Through phylogenetics analysis of HSF genes in A. thaliana and cotton genomes, all HSF genes among five species were clustered into two different groups, namely the I and II groups has two orthologous genes (Ghe05G03320 and Ghe08G31530) in G. herbaceum (A1) genome, two orthologous genes (Gar05G03090 and Gar08G31350) in G. arboreum (A2) genome, two orthologous genes (D5.v1.pred_00000361-RA and D5.v1.pred_00033482-RA) in G. raimondii (D5) genome, and three and two (Ghi_D05G01481 and Ghi_D07G00601) orthologous genes in G. hirsutum (AD1) A and D genomes, respectively (G. arboreum (A2) genome, three orthologous genes in G. raimondii (D5) genome, and three and three orthologous genes in G. hirsutum (AD1) A and D genomes, respectively , two genes (Gar02G18780 and Gar10G10520) in G. raimondii (D5) genome, three genes in G. raimondii (D5) genome, and three and three genes in G. hirsutum (AD1) A and D genomes were clustered together and divided into two groups following the divergence from the common ancestor of A. thaliana and Gossypium lineage was identified to belong to HSFC. Through the analysis of phylogeny, AT3G24520.1 has one orthologous gene (Ghe06G07640) in G. herbaceum (A1) genome, three orthologous genes in G. arboreum (A2) genome, three orthologous genes in G. raimondii (D5) genome, and three and three in G. hirsutum (AD1) A and D genomes, respectively (In ectively . AT3G029ectively . This re lineage . In A. tectively .G. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genomes and between G. raimondii (D5) and G. hirsutum (AD1) D genomes. This result will help to trace the evolution of HSF genes in G. hirsutum genome clearly. In G. hirsutum (AD1) genome, 78 HSF genes were identified, namely 40 and 38 HSF genes distributed into A and D genomes, respectively. From the comparisons between G. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genomes, we got 11 and 64 all-against-all HSF gene pairs, respectively , G. arboreum (A2), G. raimondii (D5), and G. hirsutum (AD1), four HSF genes in G. herbaceum (A1) genome were investigated to get four HSF orthologous genes in G. hirsutum (AD1) A genome, and 17 HSF genes in G. arboreum (A2) genome and 17 HSF orthologous genes in G. hirsutum (AD1) A genome (G. hirsutum (AD1) A genome were detected to have orthologous genes in G. herbaceum (A1) and G. arboreum (A2) genomes, which represented 42.5% of the total HSF genes in G. hirsutum (AD1) A genome. A previous study indicated that all existing A genomes in Gossypium lineage originated from a common progenitor, A0 genome, and G. herbaceum (A1) and G. arboreum (A2) genome experienced independent evolution after the split of the A0 genome (G. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genome existed in ancestral genome A0 and remained in G. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genomes although they experienced independently long-term evolutionary history, but HSF genes in G. herbaceum (A1) genome missed more according to orthologous analysis between G. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genomes.To trace the evolutionary history of HSF genes in the Upland cotton genome, we combined the MCscanX software and validation of phylogeny to confirm HSF orthologous gene pairs between ectively . CombineA genome were obt0 genome . FollowiG. hirsutum (AD1) D genome, 33 of 38 HSF genes were detected to have orthologous genes in G. raimondii (D5) genome, representing 86.8% of the total HSF genes in G. hirsutum (AD1) D genome. For G. raimondii (D5) genome, all HSF genes were detected to have orthologous genes in G. hirsutum (AD1) D genome. These results meant that members of the HSF gene family in G. raimondii (D5) genome and G. hirsutum (AD1) D genome kept excellent collinear relationships after the formation of G. hirsutum (AD1), but HSF genes in G. hirsutum (AD1) D genome showed significant expansion compared with those in G. raimondii (D5) genome.In G. herbaceum, G. arboreum, G. thurberi, G. raimondii, G. turneri, G. longicalyx, G. australe, G. kirkii, G. hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii, representing 12.9, 11.83, 19.79, 14.76, 12.49, 21.03, 14.71, 13.44, 10.27, 34.66, 33.94, 35.23, and 27.75% of total protein-coding genes in G. herbaceum, G. arboreum, G. thurberi, G. raimondii, G. turneri, G. longicalyx, G. australe, G. kirkii, G. hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii genomes (G. thurberi (D1) genome were identified following the identification of tandemly duplicated genes in plants. However, for the remaining 12 cotton genomes, we did not get any tandemly duplicated genes of the HSF gene family in these cotton genomes. So, the TD events brought an increase of the members of the HSF gene family in G. thurberi (D1) genome, but the HSF gene family in 12 cotton species did not experience TD event, which meant that members of the HSF gene family were discretely distributed into 12 cotton genomes.In this part, we investigated this important mechanism that occurred in different cotton genomes to get more evidence for the expansion of the HSF gene family. With the method implemented in PTGBase, we obtained 5,672, 5,118, 6,237, 6,013, 4,956, 8,070, 5,630, 4,930, 7,635, 25,877, 26,570, 26,306, and 21,726 tandemly duplicated genes in genomes . ThroughG. hirsutum (AD1) acc. TM-1 and G. barbadense (AD2) acc. Hai7124. These treatments of different periods (hours) include control , heat , and cold in G. hirsutum (AD1) and G. barbadense (AD2), respectively. After curation, we got 32 treatments in total. Using all available RNA-seq short-reads data of different samples of G. hirsutum (AD1) and G. barbadense (AD2), we implemented an expression analysis of total protein-coding genes in G. hirsutum (AD1) and G. barbadense (AD2) genome and further retrieved expression values of 78 and 78 HSF genes from different G. hirsutum (AD1) and G. barbadense (AD2) samples, respectively (G. hirsutum (AD1) genome, 76 HSF genes were detected to have expression in 16 samples, with 2 HSF genes (Ghi_A01G06131 and Ghi_D01G05506) having no expression in any of the samples. In G. barbadense (AD2) genome, 76 HSF genes have expression among 16 samples and two HSF genes (Gobar.A01G125400.1 and Gobar.D01G132500.1) were not detected to have expression in any of the samples. In G. hirsutum (AD1) genome, the 76 expressed HSF genes were divided into two different groups, I and II, and the I group contained 35 HSF genes, with the II group containing 41 HSF genes (G. barbadense (AD2) genome, 76 expressed HSF genes also were divided into two different groups, I and II, but the I group contained 46 HSF genes and the II group contained 30 HSF genes (G. hirsutum (AD1) and G. barbadense (AD2) indicated different expression patterns despite the implementation of identical experimental materials with identical heat and cold stresses.To investigate the expression differences of cotton HSF genes for heat stress tolerance, we analyzed the expression profiling of HSF genes in leaves under different treatments of ectively . Out of SF genes . In G. bSF genes . These rG. hirsutum (AD1) and G. barbadense (AD2), we obtained 61 HSF orthologous gene pairs between the two genomes. In G. hirsutum (AD1) genome, 31 and 30 HSF genes from 61 orthologous gene pairs were located on G. hirsutum (AD1) A and D genomes, respectively, with one HSF gene locating on unknown pseudomolecular in G. hirsutum (AD1) D genome. In G. barbadense (AD2) genome, there were 61 HSF genes from 61 orthologous gene pairs and one HSF gene was not detected on any chromosome, with 30 HSF genes locating on A genome and 30 HSF genes locating on D genome. The no expression HSF genes, Ghi_A01G06131 versus Gobar.A01G125400.1 and Ghi_D01G05506 versus Gobar.D01G132500.1, were orthologous gene pairs between G. hirsutum (AD1) and G. barbadense (AD2) genomes. After removing the no expression HSF genes, 59 HSF orthologous gene pairs between G. hirsutum (AD1) and G. barbadense (AD2) genomes were selected to investigate the difference of expression patterns (G. herbaceum (A1), G. hirsutum (AD1), and G. barbadense (AD2), four HSF genes in G. herbaceum (A1) were detected to have four and four orthologous HSF genes in G. hirsutum (AD1) and G. barbadense (AD2), respectively. Only three of four HSF orthologous gene pairs between G. hirsutum (AD1) and G. barbadense (AD2) were expressed in different abiotic stress treatments and demonstrated different downregulated expression patterns regardless of control, cold, or heat stresses (According to the collinear relationship between patterns . Throughstresses .G. hirsutum (AD1) genome, we collected five genome-sequenced plant species, including the model plant A. thaliana, three cotton diploid species and one tetraploid species [G. hirsutum (AD1)]. The allotetraploid cotton, G. hirsutum (AD1), named Upland cotton, is one of the most economically important crops which dominates over 98% of cotton production worldwide. Previous reports illustrated that G. hirsutum (AD1) was generated from hybridization between cotton A-genome progenitor and D-genome ancestor by chromosome doubling. Upland cotton D genome originated from G. raimondii (D5), and the A genome originated from the common progenitor, A0 genome, of all existing A genomes in Gossypium lineage. Furthermore, the formation of G. hirsutum (AD1) has preceded the split of G. herbaceum (A1) and G. arboreum (A2). These two cotton A genomes were shown to evolve independently from their common ancestor (G. hirsutum (AD1) genome, we got 40 and 38 HSF genes in G. hirsutum (AD1) A and D genomes, which meant that the D genome in G. hirsutum (AD1) missed two HSF genes compared with G. hirsutum (AD1) A genome. Through comparative genomic analysis between G. raimondii (D5) and G. hirsutum (AD1) D genome, we got 33 HSF orthologous gene pairs between the two genomes, which meant that G. raimondii (D5) missed five HSF genes after independent evolution. For the comparisons of G. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genomes, we got 17 HSF orthologous gene pairs between G. arboreum (A2) and G. hirsutum (AD1) A genomes, containing four HSF orthologous gene pairs, which meant that G. herbaceum (A1) and G. arboreum (A2) missed more HSF genes after the split of their common ancestor, but they kept four HSF orthologous genes inherited from their common ancestor, A0 genome. These four common conserved HSF genes in G. herbaceum (A1), G. arboreum (A2), and G. hirsutum (AD1) A genome might experience stronger natural selection pressures and performed a key biological function for resisting heat stress tolerance for adapting to the changing environment. From the evolutionary history of cotton diploid and tetraploid genomes, we knew that ancestral cotton genomes experienced loss of the members of the HSF gene family, but the current cotton tetraploid genomes kept more members of the HSF gene family.To trace the evolutionary history of HSF genes in ancestor . ThroughHeat shock transcription factor gene family analysis among different cotton diploid and tetraploid genomes showed significant differences in number variation of the members of the HSF gene family. Apparently, members of the HSF gene family in cotton tetraploid genomes indicated a larger family size of the HSF gene family than those in cotton diploid genomes. Members of the HSF gene family in subgenomes of cotton tetraploid genomes showed expansion compared with those in cotton diploid genomes. These results demonstrated that HSF genes in cotton diploid genomes experienced weaker selection pressures leading to fast loss of HSF genes during the evolutionary history, but the HSF genes in subgenomes of cotton tetraploid genomes experienced stronger selection pressures after hybridization. The analysis of number variation of the members of the HSF gene family illustrated that the cotton tetraploid species may indicate stronger ability for the resistance of heat stress tolerance than diploid species.G. hirsutum (AD1) and G. barbadense (AD2) diverged after the formation of cotton allotetraploid AD genome at approximately 0.96 Mya, suggesting that these two genomes kept many orthologous gene pairs (G. hirsutum (AD1) and G. barbadense (AD2) genomes, respectively. From collinear analysis, 122 HSF genes from 61 orthologous gene pairs in G. hirsutum (AD1) and G. barbadense (AD2) were used to detect the expression pattern of HSF orthologous genes in cotton tetraploid species. After the analysis of difference expression, 61 and 61 HSF genes in G. hirsutum (AD1) and G. barbadense (AD2), respectively, indicated totally different expression pattern, which meant the functional divergence of HSF orthologous genes between the two genomes. These results provided novel insights for functional studies and molecular breeding for the cotton community.A previous study illustrated that ne pairs . Based oG. thurberi (D1), G. raimondii (D5), G. turneri (D10), G. longicalyx (F1), G. australe (G2), and G. kirkii (K) compared with those in G. herbaceum (A1) and G. arboreum (A2). As expected, cotton tetraploid genomes have more members of the HSF gene family than diploid genomes. Phylogenetic analysis revealed that 621 HSF genes in 13 cotton genomes were clustered into two different groups, and the I group contained all HSF genes of HSFA and HSFC, with the II group containing all HSF genes of HSFB according to the conserved domains and phylogeny of HSF genes. Comparing A. thaliana, G. herbaceum (A1), G. arboreum (A2), G. raimondii (D5), G. herbaceum (A1), and G. arboreum (A2), four HSF genes were inherited from the common progenitor, A0, of all existing cotton A genomes, and members of the HSF gene family indicated a significant expansion in G. arboreum (A2) and G. hirsutum (AD1) A genome compared with G. herbaceum (A1). However, HSF genes in G. hirsutum (AD1) D genome experienced a significant expansion compared with those in G. raimondii (D5). Analysis of TD events of HSF genes revealed that the HSF gene family in G. thurberi (D1) genome has experienced TD event, but not in the remaining 12 cotton genomes. Expression analysis revealed that HSF orthologous gene pairs between G. thurberi (D1) and G. barbadense (AD2) showed a totally different expression trend under identical heat and cold stresses, which is beneficial for cotton molecular breeding and directed screening. This study is the first to trace the evolutionary history and expression features of the HSF gene family in 13 cotton genomes and provides more biological evidence to study the HSF gene family in response to abiotic stress tolerance in cotton genomes, particularly expression diversity of HSF genes in different treatments of leaves among different G. hirsutum (AD1) and G. barbadense (AD2) accessions. We hope this work will provide novel insights for the study of HSF genes under environmental stress in different cotton genomes and a widespread application model for the study of HSF gene families in plants.According to the conserved domains of HSF gene family in plants, we identified 621 HSF genes among 13 genome-sequenced cotton species distributed into eight diploid and five tetraploid species. Comparative genomics analysis demonstrated that members of the HSF gene family in cotton diploid genome showed a significant expansion in The original contributions presented in the study are included in the article/YL and QC conceived and designed the experiments. YL analyzed the data and prepared the manuscript. JW and JZ performed the experiments and analyzed the data. ZG performed phylogenetic analysis and revised the manuscript draft. ZL collected genomic data, performed comparative analysis of HSF genes, and revised the manuscript draft. XA and XL performed the tandem duplication analysis of HSF genes and revised the manuscript draft. QC revised the manuscript. All authors read and approved the final manuscript.ZL was employed by company Adsen Biotechnology Corporation. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Rapid antigen tests are cheaper and faster than nucleic acid amplification tests for SARS-CoV-2 infection, with variable reported sensitivity. A horse racetrack in California experienced a COVID-19 outbreak among staff and used BinaxNOW to supplement RT-PCR. Utility of BinaxNOW in detecting SARS-CoV-2 infection in a workplace outbreak was assessed.t) < 30.Between November 25\u2013December 22, 2020, anterior nasal swabs were collected from racetrack staff for six rounds of paired BinaxNOW and RT-PCR tests. BinaxNOW tests were interpreted according to manufacturer instructions. RT-PCR was performed at the state public health lab using the ThermoFisher TaqPath COVID-19 Combo Kit. Staff with positive results on either test were isolated and removed from subsequent testing. Viral cultures were attempted on specimens with cycle threshold (17.8 vs. 28.5) (p < 0.001). In dual positive pairs, median time from specimen collected to RT-PCR result reported was 4 days (range 1-6), compared to the 15-minute BinaxNOW reporting time. Of 100 Ct < 30 specimens, 51 resulted in positive virus isolation, 45 (88.2%) of which were BinaxNOW-positive.Overall, 769 paired results from 342 staff were analyzed. Most were of Hispanic ethnicity (62.0%) and ages ranged from 18 to 92 years (median 52). BinaxNOW performance compared to RT-PCR (95% CI) was as follows: positive percent agreement (PPA) 43.3% (34.6%\u201352.4%); negative percent agreement (NPA) 100% (99.4%\u2013100%); positive predictive value (PPV) 100% (93.5%\u2013100%); negative predictive value 89.9% (87.5%\u201392.0%). Among 127 RT-PCR-positive specimens, those with paired BinaxNOW-positive results (n = 55) had a lower mean Ct value and positive viral cultures, which could suggest that among RT-PCR-positive specimens, those that are BinaxNOW-negative may be less likely to contain infectious virus than those that are BinaxNOW-positive.High NPA and PPV support immediate isolation of BinaxNOW-positive individuals, while low PPA supports confirmatory testing following BinaxNOW-negative results. BinaxNOW performed better in paired specimens with lower CDavid Seftel, M.D., M.D., M.B.A., Enable Biosciences, Inc"} +{"text": "Authors would like to correct the errors in their publication.The original article has been corrected.Incorrect Supplementary Information (ESM2) deleted now.The line \u201cA color version of this figure is available online\u201d to be deleted from all figure captions since the color figures in print version is not charged now.Missing references for the text citations were updated hereAlongi, 2002Alongi DM (2002) Present State and Future of the World\u2019s Mangrove Forests. Environ Conserv 29:331\u2013349. 10.1017/S0376892902000231Alongi and Dixon, 2000Alongi DM, Dixon P (2000) Mangrove primary production and above-and below-ground biomass in Sawi Bay, southern Thailand. Phuket Mar Biol Cent Spec Publ 22:31-38.Arfi et al. 2012Avicennia marina and Rhizophora stylosa. FEMS Microbiol Ecol 79:433\u2013444. 10.1111/j.1574-6941.2011.01236.xArfi Y, Bu\u00e9e M, Marchand C, et al (2012) Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Krishna and Mohan, 2017Krishna MP, Mohan M (2017) Litter decomposition in forest ecosystems: a review. Energy, Ecol Environ 2:236\u2013249. https://doi.org/10.1007/s40974-017-0064-9Murdiyarso et al. 2015Murdiyarso D, Purbopuspito J, Kauffman JB, et al (2015) The potential of Indonesian mangrove forests for global climate change mitigation. Nat Clim Chang 5:1089\u20131092. 10.1038/nclimate2734Quadros et al. 2019Quadros AF, Nordhaus I, Reuter H, Zimmer M (2019) Modelling of mangrove annual leaf litterfall with emphasis on the role of vegetation structure. Estuar Coast Shelf Sci 218:292\u2013299. 10.1016/j.ecss.2018.12.012"} +{"text": "We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extent of gene expression changes was dependent on hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation of LIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia-inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene, PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitising might require additional approaches to a simple HIF inhibition.Glioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair-related genes in four classical glioblastoma cell lines exposed to 5 days of normoxia (21% O Surviva options . Alterna options . Despite options .2 components leading to reduced HRR capacity . Also, cWe adopted a NanoString transcriptomic approach to assess the impact of chronic hypoxia on DNA repair genes in glioblastoma cell lines. We found that hypoxia specifically affects mismatch repair (MMR), non-homologous end-joining (NHEJ) and homologous recombination repair (HRR). Additionally, we provide evidence that the hypoxia inducible factor (HIF) play a role in downregulation of some, but not all, key DNA repair genes. Downregulation of DNA repair genes by hypoxia will have significant clinical impact for cancer management and should be considered when designing new treatment methods and protocols.Cell culture reagents were from Gibco Life Technologies and Foetal Calf Serum from Harlam Seralab (UK). Acriflavin was purchased from Sigma Aldrich. \u03b2-Actin (Ab8226), PMS2 (Ab110638) and anti-mouse HRP (Ab6808) antibodies were from abcam. HIF-1\u03b1 (20960-1-AP) and HIF-2\u03b1 (A700-003) were from Bethyl. Anti-rabbit HRP (7074S) antibody was from Cell Signalling.2. For hypoxic experiments, cells were incubated in a Don Whitley H35 Hypoxystation for 1% O2 or a New Brunswick Galaxy 48R incubator for 0.1% O2. Cells were routinely tested for mycoplasma infection.U87-MG and T98G were purchased from ATCC. U251-MG were purchased from CLS. D566-MG cells were a kind gift from Prof. DD Bigner . U87-MG and T98G were cultured in modified Eagle\u2019s Medium (EMEM) with 10% FCS, 1% Sodium pyruvate. D566-MG and U251-MG were cultured using EMEM, 10% FCS, 1% sodium pyruvate and 1% non-essential amino acids. Cells were maintained at 37 \u00b0C in 5% CO2. RNA was extracted using High Pure RNA Extraction kit . A total of 100 ng of total RNA was used in the NanoString assay. The expression of 180 DNA repair genes, plus 12 housekeeping genes, were assessed using the NanoString nCounter Vantage\u2122 RNA Panel for DNA Damage and Repair (LBL-10250-03) following the manufacturer\u2019s protocol. Analysis of the NanoString data was conducted using nSolver\u2122 Analysis Software (3.0) with nCounter\u00ae Advanced Analysis plug-in (2.0.115). Data are available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139250 and inCells were cultured in 6 cm dishes for 5 days at 21%, 1% or 0.1% O\u00ae VILO following the manufacturer\u2019s guidelines. RT-PCR experiments were performed and analysed as described in LIG4 Forward: TCCCGTTTTTGACTCCCTGG Reverse: GGCAAGCTCCGTTACCTCTG, ABL Forward: TGGGGCATGTCCTTTCCATC Reverse: GATGTCGGCAGTGACAGTGA, ERCC4 Forward: CTCCCTCGCCGTGTAACAAA Reverse: ACACCAAGATGCCAGTAATTAAATC, FEN1 Forward: GTTCCTGATTGCTGTTCGCC Reverse: ATGCGAATGGTGCGGTAGAA, MSH5 Forward: GTTTGCGAAGGTGTTGCGAA Reverse: GTCTGAGACCTCCTTGCCAC, PARP1 Forward: GCCCTAAAGGCTCAGAACGA Reverse: CTACTCGGTCCAAGATCGCC, UBE2T Forward: ATGTTAGCCACAGAGCCACC Reverse: ACCTAATATTTGAGCTCGCAGGT, WRN Forward: TCACGCTCATTGCTGTGGAT Reverse: CAACGATTGGAACCATTGGCA, PMS2 Forward: AGCACTGCGGTAAAGGAGTT Reverse: CAACCTGAGTTAGGTCGGCA, CYCLOA Forward: GCTTTGGGTCCAGGAATGG Reverse: GTTGTCCACAGTCAGCAATGGT. Cyclophillin A was used as a housekeeping gene.RNA was extracted using High Pure RNA Extraction kit . Reverse transcription was conducted using SuperScriptLIG4 (NM_001352604.1) and PMS2 (NM_000535.7) was obtained through the UCSC Genome Browser using human genome assembly h38 , and GLUT1 or VEGFA levels assessed by RT-PCR to confirm hypoxia had indeed resulted in hypoxia-induced gene expression changes , D566-MG (0.1% = 2.6-fold) and U87-MG (0.1% = 1.6-fold) at 0.1% O2 and MutL\u03b1 actively translocates along the DNA in search of discontinuity . EXO1 is 0.1% O2 , yet litsistance , was als.6-fold) and 3B, .6-fold) . However studies . Other c 0.1% O2 . MSH5 is 0.1% O2 , therefo 0.1% O2 , potentiXRCC6, Ku80-XRCC5, DNA-PK-PRKDC) remain largely unaffected by hypoxia. However, in all cell lines tested, LIG4 (DNA Ligase IV) was downregulated at least 1.5-fold in hypoxia (1% and 0.1% O2.), although, this was only statistically significant in U87-MG complex recognises the DSB . The endn U87-MG and 3D. hypoxia and 3D. in XRCC4 .PMS2 and LIG4, essential components of their respective repair pathways, are involved in chemoresistance , resulti2 (PHD2) . To testactivity . Treatmeget gene . In bothnificant . In contreatment , suggestPMS2 (MMR) and LIG4 (NHEJ), essential components of their respective pathways, were downregulated across multiple cell lines after chronic and acute hypoxic exposure, providing potential targets for re-sensitisation of hypoxic tumour cells to DNA damaging therapies.Tumour hypoxia plays an essential role in tumour progression, metastasis and drug resistance, leading to poor patient outcome, particularly for GBM patients. Hypoxia has been shown to impact numerous signalling pathways including the cell cycle, metabolism and apoptosis, yet additionally, hypoxia can have a significant impact on DNA repair mechanisms. We have shown here that several key DNA repair pathways were downregulated by hypoxia, including MMR and NHEJ, both essential pathways for the repair of modified/mismatch bases and double strand breaks respectively. Further analysis determined that PMS2 , and siRNA of LIG4 enhanced cell lethality of both chemotherapeutics U87-MG, (B) U251-MG and (C) D566-MG was utilised in RT-PCR experiments to assess the expression levels of selected genes. Data are expressed as logClick here for additional data file.10.7717/peerj.11275/supp-3Supplemental Information 32 and treated with 0\u201310 \u00b5M Acriflavin for 24 h. Control cells remained in 21% O2. RT-PCR was performed to assess GLUT1 expression levels. Data represent the fold change in GLUT1 expression relative to 21% O2. Data are from a single experiment. (B) HIF inhibition does not restore PMS2 mRNA levels in hypoxia. D566\u2011MG and U87-MG cells were incubated in 21% and 1% O2 for 24 h with and without 5 \u00b5M Acriflavin, the plots show the log2 fold change in mRNA levels with respect to levels for the 21% O2 samples. Data are the mean of at least two independent experiment.(A) D566-MG cells were incubated in 0.1% OClick here for additional data file.10.7717/peerj.11275/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.11275/supp-5Supplemental Information 5The data for each figures are on separate tabs.Click here for additional data file.10.7717/peerj.11275/supp-6Supplemental Information 62 for 5 days before examination of gene expression using the NanoString nCounter Vantage\u2122 RNA Panel for DNA Damage and Repair. Differential gene expression analysis was performed using nSolver\u2122.U87-MG, D566-MG, U251-MG and T98G were exposed to 21%, 1% or 0.1% OClick here for additional data file."} +{"text": "P. aeruginosa is a common infection among hospitalized patients, with increased levels of morbidity and mortality. This pathogen exhibits multiple resistance mechanisms to antibiotics. We analyzed the molecular epidemiology and activity of the main therapeutic options against P. aeruginosa isolated from RTI in Latin America (LATAM).Respiratory Tract Infection (RTI) caused by Isolates were collected from 36 sites in 10 countries during 2017-2019. Non-duplicate samples were consecutively collected. MICs were determined by broth microdilution and interpreted by CLSI criteria. A subset of imipenem non-susceptible isolates was selected for characterization of carbapenemase encoding genes via multiplex PCR and DNA sequencing. \u03b2-lactamase genes encoding ESBLs, carbapenemases, and plasmid-mediated AmpCs were investigated.P. aeruginosa were collected from RTI. Overall C/T [87.8% susceptible (S)] was the most active antimicrobial tested against P. aeruginosa isolates followed by amikacin (85.8% S) and imipenem/relebactam . Other antimicrobials had less than 80% susceptibility. C/T remained the most active agent including activity against imipenem and piperacillin/tazobactam non-susceptible isolates . 583 imipenem non-susceptible P. aeruginosa were selected for molecular analysis (Table 1). Thirty isolates were confirmed to be producers of serine-carbapenemases , while 83 (14.2%) were MBL producers. KPC-2 was found in Colombia (9), Chile (6), Puerto Rico (4), Guatemala (3), and Brazil (2). GES-5 was identified in Mexico (3), Argentina (2) and Brazil (1). VIM-2 was the most common MBL encoding gene identified. IMP variants were observed in Brazil , Ecuador (IMP-13), Mexico (IMP-18), Panama (IMP-18) and Puerto Rico (IMP-18). SPM-1 was only encountered in Brazil. The production of ESBLs was low in most LATAM countries, except for Guatemala (80%) . A total of 2,044 Figure 1. Activities of selected antimicrobial agents against 2,044 P. aeruginosa isolated from respiratory tract infections in Latin America (2017 to 2019).TABLE 1. Molecular analysis of imipenem non-susceptible P. aeruginosa isolates in Latin America (LATAM) from Respiratory Tract Infection (N=583).Figure 2. Carbapenemases identified in 583 imipenem non-susceptible P. aeruginosa isolated from patients with respiratory tract Infections in Latin America (LATAM).P. aeruginosa infections. The prevalence of carbapenemases-encoding genes varied geographically in LATAM.CT, amikacin and IMI/REL showed good activity against RTI isolates and could represent effective treatment options for Leandro Cardinal, PharmD, PhD, MSD (Employee) Cicera P. Marcelino, n/a, MSD (Employee) Aline Okuma, n/a, MSD (Employee)MSD Brazil (Employee) Gustavo Mizuno, PharmD, Merck Sharp Dohme (Employee) Felipe Tuon, PhD, Merck Sharp Dohme Brazil (Scientific Research Study Investigator) Ana C. Gales, MD, MSD Pfizer Marina Della Negra, Medical Doctor, MSD Brazil (Employee) Thales Polis, Medical Doctor, MSD Brazil (Employee)"} +{"text": "OBJECTIVES/GOALS: We compared the validity of an International Classification of Diseases, Clinical Modification (ICD) algorithm for identifying high-grade cervical intraepithelial neoplasia and adenocarcinoma in situ (together referred to as CIN2+) from ICD 9th revision (ICD-9) and 10th revision (ICD-10) codes. METHODS/STUDY POPULATION: Using Tennessee Medicaid data, we identified cervical diagnostic procedures in 2008-2017 among females aged 18-39 years in Davidson County, TN. Gold-standard cases were pathology-confirmed CIN2+ diagnoses validated by HPV-IMPACT, a population-based surveillance project in catchment areas of five US states. Procedures in the ICD transition year (2015) were excluded to account for implementation lag. We pre-grouped diagnosis and procedure codes by theme. We performed feature selection using least absolute shrinkage and selection operator (LASSO) logistic regression with 10-fold cross validation and validated models by ICD-9 era and ICD-10 era . RESULTS/ANTICIPATED RESULTS: Of 7864 cervical diagnostic procedures, 880 (11%) were true CIN2+ cases. LASSO logistic regression selected the strongest features of case status: Having codes for a CIN2+ tissue diagnosis, non-specific CIN tissue diagnosis, high-grade squamous intraepithelial lesion, receiving a cervical treatment procedure, and receiving a cervical/vaginal biopsy. Features of non-case status were codes for a CIN1 tissue diagnosis, Pap test, and HPV DNA test. The ICD-9 vs ICD-10 algorithms predicted case status with 68% vs 63% sensitivity, 95% vs 94% specificity, 63% vs 64% positive predictive value, 96% vs 94% negative predictive value, 92% vs 89% accuracy, and C-indices of 0.95 vs 0.92, respectively. DISCUSSION/SIGNIFICANCE OF IMPACT: Overall, the algorithm\u2019s validity for identifying CIN2+ case status was similar between coding versions. ICD-9 had slightly better discriminative ability. Results support a prior study concluding that ICD-10 implementation has not substantially improved the quality of administrative data from ICD-9."} +{"text": "The article presents the results of studying the biodiversity and biotechnological potential of halophilicmicroorganisms from the thermal highly mineralized Berikey Lake, the salty Lake Tarumovskoye and saline soils ofthe Peri-Caspian Lowland (Republic of Daghestan). Denitrifying halophilic bacteria of the genus Halomonas andVirgibacillus were identified using microbiological methods and 16S rRNA gene analysis. A new species Halomonas sp. G2 (MW386470) with a similarity of the nucleotide sequences of the 16S rRNA genes is 95 %. Strain G2 isan extreme halophile capable of growing in the range of 5\u201325 % NaCl (optimum 25 %) and forming a carotenoidpigment. Mesophil, 30\u201337 \u00b0\u0421 (optimum 30 \u00b0\u0421); neutrophil, pH 6\u20138 (optimum 7.2\u20137.4). Strain G2 chemolithotroph;reduces nitrate or nitrite as electron donors; catalase-, amylase-, protease- and \u03b2-galactosidase-positive; lipase-,oxidase- and urease-negative. Not able to hydrolyze inositol, indole; produces lysine, gelatin, ectoine; uses citrateand sodium malate as a source of carbon and energy; does not produce ornitin, H2S or acid from d-mannose, sucrose, glycerol, cellobiose, except for lactose and d-glucose. Susceptible to trimethoprim, ciprofloxacin, ofloxacin,kanamycin, vancomycin, rifampicin, cefuroxime, ampicillin, ceftazidime, fosfomycin, clarithromycin, cefepime, cefaclor. The G+C content in DNA is 67.3 %. A distinctive characteristic of the isolate was the production of industrially significant hydrolytic enzymes such as amylase, protease, \u03b2-galactosidase, and oxidoreductase at aNaCl concentration of 25 % in the medium. Habitat: saline soils on the territory of the Tersko-Kumskaya lowland. The rest of the halophilic isolates of H. ventosae G1 (MW386469), H. elongata G3(MW386471), V. salinarius B2 (MW386472), and V. salinarius B3 (MW386473) had a high degree of similarity (100 %)with the type strains of H. elongata DSM 2581\u0422and V. salarius DSM 18441\u0422; the content of G+C in DNA was 65.8,66.5, 42.8 and 37.3 %, respectively. The strains had a high biotechnological potential at NaCl concentrations of 5 and25 % in the medium. The data obtained expanded the understanding of the diversity and ecological significanceof denitrifying bacteria in the functioning of arid ecosystems and make it possible to identify strains producingenzymes of industrial importance. The interest in extremophilic microorganisms is relativelyhigh due to their biological uniqueness. Agreat contributionto the study of natural microbial communities was made bythe school of Russian scientists . Archaeaand highly-specialized bacteria of the genera Alcaligenes,Bacillus, Halobacillus, Virgibacillus, Micrococcus, andPseudomonas occupy a dominant place in ecologicalniches with a high salt content and anthropogenic ecosystems with an increasedlevel of mineralizationThe largest ecosystems on the planet are saline and hypersaline environments . Daghestan isa unique natural province of Russia that has a variety ofnatural landscapes due to the influence of tectonic processes,the erosive activity of flowing waters, transgressive andregressive dynamics of the Caspian Sea, and arid climate.There are a number of works on the study of microbial communities of various ecological niches of the region: lithotrophic sulfur-oxidizing representatives of sulfide sources,hydrocarbon-oxidizing bacteria of the geothermal sourceof the Kizlyar field .The highly mineralized lakes of the Tersko-Kumskayalowland with high salinity form conditions for the existence of halophilic bacteria. Microorganisms from extremehabitats are the producers of valuable industrially importantenzymes, antibiotics; they can participate in soil biodegradation, and are highly resistant to contamination by foreignmicroflora .The study considers the spatial distribution of halophilicmicrobial communities of halophyte plants, saline soils, and highly mineralized lakes in arid regions of the Peri-CaspianLowland . Chemoorganoheterotrophic bacteria of the genera Virgibacillus, Bacillus,Halomonas and Salimicrobium from the phylum Firmicutesand Proteobacteria have proved to be the main componentsof the microbial flora of the Tersko-Kumskaya and TerskoSulakskaya provinces. A major correlation was revealedbetween isolated microbial communities and concentrationsof chemicals Na, K, Ca, Mg, Cl, Cu, Sr, SO4, Cl, and HCO3,as one of the main regulators of microbiological activity insoils and lakes.The aim of the paper is a molecular taxonomic studyof isolated halophilic bacteria and their biotechnologicalpotential.The objects of research are natural microbial communitiesof saline reservoirs and soils in the territory of the PeriCaspian Lowland of the Republic of Daghestan (Table 1). Samples were taken in July\u2013September 2014.Cultivation. For the cultivation of halophilic bacteria,a modified medium of the following composition (g/l) wasused: bacto yeast extract \u2013 10.00, Na3C6H5O7 \u22195.5H2O \u20133.0, NaCl \u2013 50, 100, 250, KCl \u2013 2.0, MgSO4 \u2219 7H2O \u201320.0, glycerin \u2013 4.0 . Bacto-peptone \u2013 5 g/lwas used as a substrate; the pH of the medium was adjustedto 7.2\u20137.4 by 1N HCl or 4M KOH (Russia) using a HannaInstrumentals pH 211 pH meter (Germany). The cultureswere incubated in a Binder-115 microbiological incubator(USA) at an operating temperature of (30\u201337)\u00b11 \u00b0C for3\u201320 days.Morphology of bacterial cells was studied using a light microscope CX21 FS1 and thePowerShot A640 digital camera at a working magnification of \u00d7600.Ecological and physiological characteristics of growth. Effect of NaCl concentration in an amount of 2 % ofthe medium volume for cell growth in liquid and solid mediawas determined at 30\u201337 \u00b0C in the Binder-115 incubator(USA). The growth was monitored at 24-hour intervals for7 days by measuring turbidity using a Genesys-20 spectrophotometer . The effect of temperature (30 and 37 \u00b0C) on the growth rate was determinedby cultivation under the same conditions.The use of growth substrates was studied using standard methods.The use of electron acceptors. The ability to use nitrateas an electron acceptor was determined using the BD BBLTaxo Differentiation Discs Nitrate , in compliance with the manufacturer\u2019sinstructions. The discs were impregnated with a solutioncontaining 40 % potassium nitrate and 0.1 % sodium molybdate. The reduction of nitrate to nitrite was detected by theaddition of sulfanilic acid and N,N-dimethyl-\u03b1-naphthylamine, which reacts with nitrite to form a red-colored substance-n-sulfobenzenazo-\u03b1-naphthylamine (positive result).In the absence of a change in color after the addition ofreagents (negative result), zinc dust was added to determinethe presence of unrecoverable nitrate or products other thannitriteDetermination of enzymatic activity. Hydrolase-producing bacteria were screened for amylase, proteinase,\u03b2-galactosidase, lactase, lipase, urease, and oxidoreductases on dishes of starch, tributyrin, andgelatin agar, depending on the concentrations of NaCl.Amylase activity \u2013 on the elective medium . The isolateswere incubated at 45 \u00b0C for 24\u201336 hours, tested with Lugolsolution . Potential amylase producers were selected based onthe ratio of the clearance zone diameter to the colony diameter. Protease was determined on media with agar and 10 %skimmed milk; \u03b2-galactosidase (lactase) \u2013 using indicatordisks impregnated with a special reagent-ortho-nitrophenyl\u03b2-d-galactopyranoside ; urease \u2013 using CLOtest ; lipase \u2013 tested on dishes with1 % tributyrin. Isolates showing clear zones of tributyrinhydrolysis were identified as lipase-producing bacteria.Determination of oxidoreductases: catalase \u2013 using 3 %H2O2 as a substrate in the medium for 24\u201348 hours, oxidase \u2013 by Kovac\u2019s method . All screening testsfor enzymatic activity were performed in three repetitions.The bacteria were incubated at 37 \u00b0C for seven days.Antibiotic resistance was determined by the intensity of bacterialgrowth on the basic agarized medium \u201cB\u201d in Petri dishesusing standard disks \u201cIndicator paper systems for identifyingmicroorganisms\u201d of NPO Microgen of Natsimbio Holding(Russia) with 10\u201330 \u03bcg of antimicrobial agent .G+C content and phylogenetic analysis. Genomic DNAwas isolated according to Marmur (1961) and Thomas methods. The DNA nucleotide compositionwas determined by thermal denaturation (0.5 \u00b0C\u2219min\u20131)using a Cary-100 Bio UV-VIS spectrophotometer . The GC content in the composition of DNA \u2013according to the method . Escherichiacoli K-12 DNA (51.7 %) was used as the standard.For phylogenetic analysis, the DNA was isolated fromsamples using the modified Birnboim\u2013Doly alkaline DNA method and the Wizard technologyof Promega (USA) . The concentration of the resulting DNA sample when using this methodwas 30\u201350 \u03bcg /ml. RNA in the resulting preparation is present in trace amounts .For polymerase chain reaction (PCR) and further sequencing of PCR fragments of the 16S rRNA gene for each ofthe studied samples, universal primer systems were usedto detect both eubacteria (11f-1492r) and archaea (8fa-A915R) . The volumeof the amplification mixture was 50 \u03bcl with the followingcomposition: 1\u00d7 buffer of BioTaq DNA polymerase (17 mM(NH4)2SO4, 67 mM Tris-HCl, pH 8.8, 2 mM MgCl2);12.5 nmol of each dNTP, 50 ng of the DNA matrix; 5 pmolof the corresponding primers and 3 units of BioTaq DNApolymerase . The temperature-timeprofile of the PCR was as follows: the first cycle \u2013 94 \u00b0C\u00d79 min, 55 \u00b0C\u00d71 min, 72 \u00b0C\u00d72 min; the next 30 cycles \u201394 \u00b0C\u00d71 min, 55 \u00b0C\u00d71 min, 72 \u00b0C\u00d72 min; the final cycle \u201372 \u00b0C\u00d77 min. The PCR products were analyzed by electrophoresis in 2 % agarose gel at an electric field strengthof 6 V/cm. Isolation and purification of PCR products werecarried out from low-melting agarose using a set of reagentsby WizardPCRPreps , according to themanufacturer\u2019s recommendations.Sequencing of PCR products was carried out at the Centerof \u201cBioengineering\u201d of the Russian Academy of Sciences,Moscow, by the method of using a setof BigDyeTerminatorv.3.1 reagents on the ABIPRIZM 3730genetic analyzer . Standardprimers were used for sequencing .Analysis of 16S rRNA sequences. The primary analysisof the similarity of the nucleotide sequences of the 16S rRNAgenes of the studied strains was performed using the BLASTprogram on the following web-site: https://blast.ncbi.nlm.nih.gov .The 16S rRNA gene sequences of all studied strains aredeposited in GenBank: G1 \u2013 MW386469, G2 \u2013 MW386470,G3 \u2013 MW386471, B2 \u2013 MW386472, B3 \u2013 MW386473.Strains of halophilic bacteria G1, G2, G3, B2 and B3,isolated from salt lakes and salt marshes of the TerskoKumskaya and Tersko-Sulakskaya lowlands, grew at atemperature of 30\u201337 \u00b0C and pH 6.4\u20137.4. The culturesshowed steady growth in the agarized elective mediumin the presence of 5\u201325 % NaCl with an optimum of 5,10, 25 %, which indicated that they belonged to moderateand extreme halophiles following the known classification.The analysis of the 16S rRNA gene sequence allowed usto determine their phylogenetic position. The 16S rRNAgene sequences of the new halophilic strains were analyzedand compared with the 16S rRNA sequences of the validlydescribed bacterial species. The analysis has shown that thenew isolates belong to two genera of bacteria containing halophilic microorganisms Halomonas and Virgibacillus. Table 2 and Figure 1 demonstrate that theG2 strain represents a new species in the genus Halomonas.The H. ventosae G1 (MW386469) and H. elongata G3(MW386471) strains seem to belong to the species H. ventosae and H. elongata, respectively, while the V. salinariusB2 (MW386472) and V.salinarius B3 (MW386473) strainsbelong to the group of species related to V. salinarius.Characteristics of the Halomonas sp. G2 strainThe main object of further research is the strain Halomonas sp. G2. The GC content in the G2 strain DNA was67.3 %.Morphology of cells and colonies. Rod-shaped, gramnegative, mobile bacillus of the size of 0.8\u20131.0\u00d71.5\u20133.0 \u00b5m.The cells were observed singly, in pairs, or in short chains. Cell mobility was ensured by one or two lateralflagella located on one side of the cell, forming endospores.On an elective solid medium, the strain formed an activegrowth of colonies of a round shape with a wavy edge, yellow and pale-yellow color with a gloss. With an increase inthe concentration of NaCl in the culture medium, a brightcarotenoid pigment appeared in the beige-colored colonies.On meat-peptone agar (MPA) \u2013 small colonies located closeto each other in a chain, rounded shape with a wavy edge,turning into a solid growth; smooth, shiny, light beige witha pinkish tinge. In all variants, a smearing consistency wasobserved .Physiology of strain growth . When determining the optimal growth parameters, theG2 strain was assigned to mesophiles and moderate alkalophiles . As a representative of the genus Halomonas, it cangrow in a wide range of NaCl concentrations from 10 to25 % with an optimum of 25 %; an extreme halophileThe substrates and electron acceptors used. Oxygenratio. The G2 strain is capable of denitrification by usingnitrates as an electron acceptor, reducing them to nitrites.The differentiating characteristics of the G2 strain arepresented in Table 3. The strain had a positive reaction tolysine, gelatin, ectoine, lactose, and d-glucose; utilized citrate and Na malonate. Tests for \u03b2-galactosidase, amylase,protease, and catalase are positive; for oxidase, lipase, andurease \u2013 negative. Growth does not occur under anaerobicconditions.Antibiotic sensitivity. The G2 culture differed in sensitivity to trimethoprim of the sulfanilamide group; fluoroquinolones of the 1st and 2nd generations ; vancomycin of the macrolide group;rifamycins of the rifampin group; cefuroxime and ampicillin of the penicillin group; antibiotics of the 3rd generationcephalosporins of the macrolides ; antibiotics of the 4th generation cephalosporins .Characteristics of isolates G1, G3, B2, B3Rod-shaped, mobile cells of strains G1, G3 have the following sizes: 0.6\u20130.8 \u00d7 1.6\u20131.9 \u00b5m (G1), 0.7\u20131.0 \u00d7 1.5\u20132.5 \u00b5m (G3) . Single cells and chains ofthem were observed. Mobility was provided by flagellalocated on one side of the cell. The cells of the B2 andB3 strains were mobile, in the form of rods, with sizes:0.5\u20130.7\u00d71.0\u20132.5 \u00b5m (B2) and 0.2\u20130.7\u00d71.0\u20135.0 \u00b5m (B3);formed endospores. The biomass of isolated strains on theMPA medium is represented by a chain of colonies locatedone after another, differing in shape, color, size, pigment andmorphology . On an elective agar mediumwith 5\u201325 % NaCl and 5\u201310 % NaCl , thecultures formed colonies with lipochromic pigment.The results of phylogenetic analysis of 16S rRNA genesequences indicated that the closest type strains (100 %) forG1 and G3 are the type strain of H. elongata DSM 2581T,and for B2 and B3 \u2013 V. salarius DSM 18441T. On thedendrogram, the cultures formed a common cluster withthe typical strains, making it possible to classify isolated cultures as these species. Related cultures for G1 and G3 areH. ventosae GQ903443, H. elongata NR 074782; for B2 andB3 \u2013 V. salarius MK785132, B. brevis JF802177, V. olivaeNR 043572, H. arcis MK063873, V. salarius NR 041270,which combined the typical features of moderate and extreme halophiles.The distinctive characteristics differentiating the culturesof H. ventosae G1 and H. elongata G3 were: optimumgrowth at 5\u201325 % NaCl vs. 32 %; pH 7.2\u20137.4 vs. 7\u20139; noutilization of sucrose, glycerol, d-mannose, cellobiose,lactose, and production of urease, oxidase, and protease(except G3) at a concentration of 5\u201325 % NaCl in themedium (see Table 3). At the same time, such traits forV.salarius B2 and B3 strains in comparison with the typicalV. salarius DSM 18441T were: no need for d-mannose, theability to produce amylase, protease, and \u03b2-galactosidaseenzymes at a concentration of 5\u201310 % NaCl in the medium(Table 4).Characteristics of genera Halomonas and VirgibacillusThus, based on phenotypic and genetic studies, we providea brief description of the strain of the new species Halomonas sp. G2 and halophilic strains of H. ventosa G1, H. elongata G3, V. salinarius B2, V. salinarius B3.Currently, the genus Halomonas includes 91 species,where H. elongata acts as the type species . The Halomonadaceaefamily was first described in 1988 by combining moderatelyhalophilic and marine bacteria of the genera Deleya andHalomonas . Over the past threedecades, many species have been assigned to the genusHalomonas, the domain Bacteria, the phylum Proteobacteria, the class Gammaproteobacteria, the order Oceanospirillales, and the family Halomonadaceae; however, at the timeof writing, 7 species have been reclassified. Representativesof the genus \u2013 gram-negative, facultative anaerobes, aerobes,prototrophs, mesophiles, denitrifying, produce exopolysaccharides; they mainly utilize oxygen, nitrate or nitrite as anelectron acceptor; under conditions of saline stress, theysynthesize ectoine, which protects cells from adverse environmental influences .The genus Virgibacillus was created as a result of thereclassification of Bacillus pantothenticus, Virgibacilluspantothenticus and, subsequently, established as a speciesof Virgibacillus . At the moment, the genus consists of 27 species,representatives of which are gram-positive, obligate aerobesor facultative anaerobes, moderate halophiles, chemotaxonomic; the main fatty acid is C15:0 .Description of the strain of the new species Halomonas sp. G2. The G2 strain cells are encapsulated, motile,aerobic, gram-negative bacillus 0.8\u20131.0 \u00d7 1.5\u20133.0 \u00b5m;observed singly or in a chain of 2 to 4 interlocked cells.The G2 strain is an extreme halophile, capable of growingin the range of 10\u201325 % NaCl (25 % optimum) and forming a carotenoid pigment. On an elective solid mediumwith 25 % NaCl, it forms colonies of a round shape with awavy edge, beige color with a gloss; forms areas of brightcarotenoid pigment. The strain grows on meat-peptonebroth. The species is mesophile, the temperature range is30\u201337 \u00b0C (30 \u00b0C optimum). Neutrophil, pH 6\u20138 (7.2\u20137.4optimum). Denitrifying strain; chemolithotrophic; reducesnitrate or nitrite as electron donors; catalase-, amylase-,protease-, and \u03b2-galactosidase-positive; lipase-, oxidase-,and urease-negative. Unable to hydrolyze inositol, indole;produces lysine, gelatin, ectoine; uses sodium citrate andmalate as a source of carbon and energy; does not produceornithine; H2S and acid from d-mannose, sucrose, glycerol,cellobiose, except lactose and d-glucose. Susceptible to trimethoprim, ciprofloxacin, ofloxacin, kanamycin, vancomycin, rifampicin, cefuroxime, ampicillin, ceftazidime, fosfomycin, clarithromycin, cefepime, cefaclor. The GC contentin DNA is 67.3 %.Based on its physiological, biochemical, and phylogeneticproperties, the G2 strain represents a new species, calledHalomonassp. G2. Adistinctive characteristic of the isolateis the production of hydrolytic enzymes protease, amylase,\u03b2-galactosidase, and oxy-reductase-catalase at a concentration of 25 % NaCl in the medium.Habitat: soil on the territory of theTersko-Kumskaya lowland .Tersko-Kumskaya lowland .Description of the strains Halomonas ventosae G1(MW386469), and Halomonas elongata G3 (MW386471).Halomonas G1 and G3 strains are aerobes, gram-negative,denitrifying; mesophiles, prototrophs, chemolithotrophs,and extreme halophiles (5 to 25 % NaCl). Unable to hydrolyze inositol; produce lysine, ornithine, gelatin, ectoine;reduce nitrate or nitrite as electron donors; utilize citrate(excluding G3) and sodium malonate as a source of carbonand energy; do not produce H2S and acid from d-mannose,sucrose, glycerol, cellobiose, except for d-glucose. TheGC content in the DNA for G1 and G3 are 65.8 and 66.5 %,respectively. On the basis of phenotypic and genotypic characteristics, isolated bacteria are classified as H. ventosae G1(MW386469), and H. elongata G3 (MW386471).Habitat: saline soils and Lake Tarumovskoe on the territoryof the Tersko-Kumskaya lowland . The type strain of H. elongata DSM 2581\u0422 wasisolated from equipment for extraction of salt from brine.Description of V. salinarius B2 (MW386472) andB3 (MW386473) strains. The strains are gram-positive;mesophiles, neutrophils, chemolithotrophs, moderate halophiles . The cultures are unable tohydrolyze inositol, sodium malonate; they do not producelysine (except for B3), indole, H2S and acid from d-mannose,sucrose, except for d-glucose, reduce nitrate to nitrite andare capable of utilizing the polypeptide substrate gelatin andsodium citrate as a carbon source. The GC content in theDNA of strains B2 andB3 was 42.8 and 37.3 %, respectively.Based on the phenotypic and genotypic characteristics, theisolated cultures have been classified as V. salinarius B2(MW386472) and V. salinarius B3 (MW386473) strains.Habitat: waters of technogenic, highly mineralizedBerikey Lake . The type strain Virgibacillus salarius DSM 18441\u0422isolated from the salt crust of the Gharsah Salt Lake in Shattal Gharsah (Sahara) in Tunisia .Biotechnological potentialof halophilic microorganismsHalophilic bacteria are increasingly being studied for theirbiotechnological potential for the production of biochemically active and resistant enzymes to alkaline pH, hightemperature and salt concentration . These multifaceted properties are useful fora variety of industries , suchas fermented food, textiles, pharmaceuticals, cosmetics,and leather production .Most producers of extracellular hydrolytic enzymes lipase,amylase, protease, inulinase, xylanase, cellulase, DNase,and pectinase are halophilic bacteria, including strains ofthe genera Halomonas and Virgibacillus .Isolation of natural strains in these studies made it possibleto discover a new species Halomonas sp. G2 (MW386470)and new strains Halomonas G1 (MW386469) and G3(MW386471), Virgibacillus B2 (MW386472) and B3(MW386473), capable of producing hydrolytic enzymesand oxidoreductase .The study confirms the biotechnological and scientific importance of halophilic denitrifying bacteria inhabiting theextremophilic ecological niches of the Peri-Caspian Lowland in the Republic of Daghestan. The strains of bacteriaof the genera Halomonas and Virgibacillus isolated provedto be not strictly confined to the salt lakes and soils of thePeri-Caspian Lowland ,having a wide distribution area, including the ecologicalniches of Bonaire Island (Netherlands Antilles) and Tunisia.Isolation and study of natural strains have revealed a newspecies Halomonassp. G2 that complement the collection ofthe already known strains \u2013 producers of industrially usefulenzymes such as amylase, protease, lactase, lipase, urease,\u03b2-galactosidase, catalase, and oxidase.The authors declare no conflict of interest.Banciu H.L., Enach M., Rodriguez R.M., Oren A., Ventosa A. Ecology and physiology of halophilic microorganisms \u2013 Thematic issuebased on papers presented at Halophiles 2019 \u2013 12th InternationalConference on Halophilic Microorganisms, Cluj-Napoca, Romania,24\u201328 June, 2019. FEMS Microbiol. Lett. 2020;366(23):1-4. DOI10.1093/femsle/fnz250.\u0412aumann P., Baumann L. The marine gram-negative Eubacteria. In:Starr M.P., Stolp H., Tr\u00fcper H.G., Balows A., Schlegel H.G. (Eds.).The Prokaryotes. A handbook on habitats, isolation nd identificationof bacteria. Berlin: Springer-Verlag, 1986;2:1302-1331.Begmatov Sh.A., Selitskaya O.V., Vasileva L.V., Berestovskaja Yu.Yu.,Manucharova N.A., Drenova N.V. Morphophysiological features ofsome cultivable bacteria from saline soils of the Aral Sea region.Eur. J. Soil Sci. 2020;53(1):90-96. DOI 10.1134/S1064229320010044.Birnboim H.C., Doly J. A rapid alkaline extraction procedure forscreening recombinant plasmid DNA. Nucleic Acids Res. 1979;7(6):1513-1523.Bonch-Osmolovskaya E.A., Atomi H. Editorial overview: Extremophiles: from extreme environments to highly stable catalysts. Curr.Opin. Microbiol. 2015;25:88-96.Bulygina E.S., Kuznetsov B.B., Marusina A.I., Kravchenko I.K., Bykova S.A., Kolganova T.V., Galchenko V.F. Study of nucleotide sequences of nifH genes in methanotrophic bacteria. Mikrobiologiya =Microbiology. 2002;71(4):425-432.Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. BLAST+: architecture and applications. BMCBioinform. 2009;10(421):1-9. DOI 10.1186/1471-2105-10-421.Chernousova E.Yu., Akimov V.N., Gridneva E.V., Dubinina G.A.,Grabovich M.Yu. Phylogenetic in situ/ex situ analysis of a sulfurmat microbial community from a thermal sulfide spring in the NorthCaucasus. Mikrobiologiya = Microbiology. 2008;77(2):219-223.DOI 10.1134/S002626170802015X.Cira-Ch\u00e1vez L.A., Guevara-Luna J., Soto-Padilla M.Y., Rom\u00e1nPonce B., V\u00e1squez-Murrieta M.S., Estrada-Alvarado M.I. Kineticsof halophilic enzymes. In: Rajendran L., Fernandez C. (Eds.). Kinetics of Enzymatic Synthesis. IntOpen, 2018;1-25. DOI 10.5772/intechopen.81100.Corral P., Amoozegar M.A., Ventosa A. Halophiles and their biomolecules: recent advances and future applications in biomedicine.Marine Drugs. 2020;18:2-33. DOI 10.3390/md18010033.Delgado-Garc\u00eda M., Valdivia-Urdiales B., Aguilar-Gonzalez C.N.,Contreras-Esquivel J.C., Rodriguez-Herrera R. Halophilic hydrolases as a new tool for the biotechnological industries. J. Sci. FoodAgric. 2012;92(13):2575-2580. DOI 10.1002/jsfa.5860.De Lourdes Moreno M., P\u00e9rez D., Garc\u00eda M.T., Mellado E. Halophilicbacteria as a source of novel hydrolytic enzymes. Life. 2013;3(1):38-51. DOI 10.3390/life3010038.Di Donato P., Buono A., Poli A., Finore I., Abbamondi R.G., Nicolaus B., Lama L. Exploring marine environments for the identification of extremophiles and their enzymes for sustainable and greenbioprocesses. Sustainability. 2019;11:149-169. DOI 10.3390/su11010149.Franzmann P.D., Wehmeyer U., Stackebrandt E. Halomonadaceaefam. nov., a new family of the class Proteobacteria to accommodatethe genera Halomonas and Deleya. Syst. Appl. Microbiol. 1988;11:16-19.Ghosh S., Kumar S., Kumar Khare S. Microbial diversity of salinehabitats: an overview of biotechnological applications. In: Giri B.,VarmaA. (Eds.). Microorganisms in Saline Environments: Strategiesand Functions (Ser. Soil Biology. 56). Cham: Springer, 2019;65-92.DOI 10.1007/978-3-030-18975-4_4.Gordon R.E., Smith M.M. Rapidly growing, acid fast bacteria. I. Species descriptions of Mycobacterium phlei Lehmann and Neumannand Mycobacterium smegmatis (Trevisan) Lehmann and Neumann.J. Bacteriol. 1953;66(1):41-48.Gridneva E.V., Grabovich M.Yu., Dubinina G.A., Chernousova E.Yu.,Akimov V.N. Ecophysiology of lithotrophic sulfur-oxidizing Sphaerotilus species from sulfide springs in the Northern Caucasus. Mikrobiologiya = Microbiology. 2009;78(1):76-83.Heyndrickx M., Lebbe L., Kersters K., De Vos P., Forsyth G., Logan N.A. Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus. Int. J. Syst. Bacteriol. 1998;48(1):99-106.DOI 10.1099/00207713-48-1-99.Heyrman J., Logan N.A., Busse H.-J., BalcaenA., Lebbe L., RodriguezDiaz M., Swings J., De Vos P. Virgibacillus carmonensis sp. nov.,Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov.,three novel species isolated from deteriorated mural paintings,transfer of the species of the genus Salibacillus to Virgibacillus, asVirgibacillus marismortui comb. nov. and Virgibacillus salexigenscomb. nov., and emended description of the genus Virgibacillus.Int. J. Syst. Evol. Microbiol. 2003;53(2):501-511. DOI 10.1099/ijs.0.02371-0.Holt J.R., Corey D.P., Eatock R.A. Mechanoelectrical transduction andadaptation in hair cells of the mouse utricle, a low-frequency vestibular organ. J. Neurosci. 1997;17:8739-8748.Hua N.P., Hamza-Chaffai A., Vreeland R.H., Isoda H., Naganuma T.Virgibacillus salarius sp. nov., a halophilic bacterium isolated froma Saharan salt lake. Int. J. Syst. Evol. Microbiol. 2008;58:2409-2414.DOI 10.1099/ijs.0.65693-0.Kaitouni L.B.D., Anissi J., Sendide K., Hassouni M.E. Diversity ofhydrolase-producing halophilic bacteria and evaluation of their enzymatic activities in submerged cultures. Annals Microbiol. 2020;70:33. DOI 10.1186/s13213-020-01570-z.Khalilova E.A., Kotenko S.Ts., Islammagomedova E.A., Hasanov R.Z.,Abakarova A.A., Aliverdiyeva D.A. Extremophilic microbial communities of saline soils and their diversity in the regions of the Caspian depression. Aridnye Ekosistemy = Arid Ecosystems. 2017;7(2):116-120. DOI 10.1134/S2079096117020068.Khalilova E.A., Kotenko S.Ts., Islammagomedova E.A., Hasanov R.Z.,Abakarova A.A., Aliverdiyeva D.A. Halophilic microbial communities and their biodiversity in the arid regions of the Caspian Lowland. Aridnye Ekosistemy = Arid Ecosystems. 2020;10(1):79-85.DOI 10.1134/S2079096120010084.Khalilova E.A., Nuratinov R.A., Kotenko S.Ts., Islammagomedova E.A. Hydrocarbon-oxidizing microorganisms of hot springs andtheir significance in the assessment of the biodiversity of microbialcommunities. Aridnye Ekosistemy = Arid Ecosystems. 2014;4(1):25-30. DOI 10.1134/S2079096114010028.Kindzierski V., Raschke S., Knabe N., Siedler F., Scheffer B., Grau K.P.,Pfeiffer F., Oesterhelt D., Marin-Sanguino A., Kunte H.J. Osmoregulation in the halophilic bacterium Halomonas elongata: a casestudy for integrative systems biology. PLoS One. 2017;12(1):1-22.DOI 10.1371/journal.pone.0168818.Kolganova T.V., Kuznetsov B.B., Turova T.P. Designing and testingof oligonucleotide primers for amplification and sequencing of 16SrRNA genes of archaea. Mikrobiologiya = Microbiology. 2002;71(2):243-246.Kushner D.J., Kamekura M. Physiology of halophilic eubacteria. In:Rodr\u00edguez-Varela F. (Ed.). Halophilic Bacteria. Boca Raton, FL,USA: CRC Press, 1988;1:109-138.Kuznetsov A.E., Kalenov S.V. Russian Federation Patent RU 2323226.Method for preparing halophilic bacterium biomass. Bull. No. 12.2008;6. (in Russian)Lalov V.V., Osokina N.V., Piorunskij D.A., Chizhikov M.A. RussianFederation Patent RU 2115722 C1. Method of halophilic microorganism culturing. 1998;5 (in Russian)Lane D.J. 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics. In: Stackebrandt E., Goodfellow M. (Eds.). NewYork: John Wiley & Sons, 1991;115-175.Lee S.-Y., Kang C.-H., Oh T.K., Yoon J.H. Virgibacillus campisalissp. nov., from a marine solar saltern. Int. J. Syst. Evol. Microbiol.2012;62:347-351. DOI 10.1099/ijs.0.033084-0.Liu C., Baffoe D.K., Zhang M. Halophile, an essential platform for bioproduction. J. Microbiol. Methods. 2019;166:105704. DOI 10.1016/j.mimet.2019.105704.Marmur J. A procedure for the isolation of deoxyribonucleic acidfrom microorganisms. J. Mol. Biol. 1961;3:208-218. DOI 10.1016/S0022-2836(61)80047-8.Namsaraev Z.B., Babasanova O.B., Dunaevsky Y.E., Akimov V.N.,Barkhutova D.D., Gorlenko V.M., Namsaraev B.B. Anoxybacillus mongoliensis sp. nov., a novel thermophilic proteinase producing bacterium isolated from alkaline hot spring, Central Mongolia.Microbiology. 2010;79(4):491-499.Netrusov A.I., Egorova M.A., Zakharchuk L.M. Laboratory Manualon Microbiology for college students. Moscow: Akademiya Publ.,2005. (in Russian)Owen R.J., Hill L.R., Lapage S.P. Determination of DNA base composition from melting profiles in dilute buffers. Biopolimers. 1969;7:503-516.Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chainterminating inhibitors. Pro\u0441. Natl. Acad. Sci. USA. 1977;84:5463-5467.Schwibbert K., Marin-SanguinoA., Bagyan I., Heidrich G., Lentzen G.,Seitz H., Rampp M., Schuster S.C., Klenk H.P., Pfeiffer F., Oesterhelt D., Kunte H.J. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T.Environ. Microbiol. 2011;13:1973-1994. DOI 10.1111/j.1462-2920.2010.02336.Steel K.J. The oxidase reaction as a taxonomic tool. J. Gen. Microbiol.1961;25:297-306.Tamura K., Nei M. Estimation of the number of nucleotide substitutionsin the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993;10:512-526.Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. MEGA6:Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol.Evol. 2013;30:2725-2729.Thomas J.C., Khour R., Neeley C.K., Akroush A.M., Davies E.C.A fast CTAB method of human DNA isolation for polymerase chainreaction applications. Biochem. Educ. 1997;25(4):233-235. DOI10.1016/S0307-4412(97)00122-2.Van de Peer Y., De Wachter R. TREECON for Windows: a softwarepackage for the construction and drawing of evolutionary trees forthe Microsoft Windows environment. Comput. Appl. Biosci. 1994;10:569-570. DOI 10.1093/bioinformatics/10.5.569.Varrella S., Tangherlini M., Corinaldesi C. Deep hypersaline anoxicbasins as untapped reservoir of polyextremophilic prokaryotes ofbiotechnological interest. Mar. Drugs. 2020;18(2):91. DOI 10.3390/md18020091.Vreeland R.H., Litchfield C.D., Martin E.L., Elliot E. Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria.Int. J. Syst. Bacteriol. 1980;3(2):485-495. DOI 10.1099/00207713-30-2-485.Wang T., Zhang L., Bo L., Zhu Y., Tang X., Liu W. Simultaneous heterotrophic nitrification and aerobic denitrification at high concentrations of NaCl by Halomonas nacteria. IOP Conf. Ser: Earth.Environ. Sci. 2019;237(5):052033. DOI 10.1088/1755-1315/237/5/052033.Zavarzin G.A. Microbial diversity studies at the Winogradsky Instituteof Microbiology. Mikrobiologiya = Microbiology. 2004;73(5):509-522. DOI 10.1023/B:MICI.0000044242.93603.00."} +{"text": "Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae, the causative agent of gonorrhea, is a global public health concern with increasing transmission and development of antimicrobial resistance (AMR) (ce (AMR) . The incce (AMR) . This trce (AMR) . In 2020ce (AMR) . Nonethece (AMR) . Furtherce (AMR) and the ce (AMR) .N. gonorrhoeae, there are many different molecular AMR determinants, for example, target mutations in: penA, encoding penicillin-binding protein 2 (PBP2), associated with resistance and decreased susceptibility to ESCs and penicillins; 23S rRNA associated with macrolide resistance; gyrA and parC, encoding subunits of DNA gyrase and DNA topoisomerase IV, respectively, associated with fluoroquinolone resistance; and 16S rRNA associated with spectinomycin resistance result in decreased influx and increased efflux of antimicrobials, respectively. These mutations decrease the antimicrobial susceptibility further is, due to its high resolution and accuracy, an ideal method for molecular epidemiology and enables collection of comprehensive data on gonococcal population characteristics and AMR determinants internationally in Sweden in 2016, representing 72.0% of all reported gonorrhea cases (n = 1777) in the year, were included. When multiple isolates from the same gonorrhea episode were available, isolates from extragenital sites were prioritized. Accordingly, the examined gonococcal isolates were cultured from the urethra (n = 521), rectum (n = 291), pharynx (n = 150), or other/not reported (n = 65) in men and from cervix (n = 119), pharynx (n = 44), urethra (n = 34), rectum (n = 21), vaginal swabs (n = 14), or other/not reported (n = 20) in women. Multiple gonococcal infections of the same patient were considered separate episodes if the infections were > 3 weeks apart. AMR testing was conducted using Etest, according to the instructions of the manufacturer . Minimum inhibitory concentrations of ceftriaxone, cefixime, ciprofloxacin and spectinomycin were interpreted according to the clinical breakpoints recommended by the European Committee on Antimicrobial Susceptibility Testing. For azithromycin, no clinical breakpoints are recommended and the epidemiological cut-off value of 1 mg/L (1 v11.0) was applied (isolates with azithromycin MIC > 1 mg/L are referred to as resistant hereafter). Additionally, isolates with MIC values of 0.064 to 0.125 mg/L for ceftriaxone and cefixime were interpreted to have a decreased susceptibility , and country of infection were extracted.2 was used to calculate significance and significance was set at p < 0.05.Statistical analysis was performed using logistic regression in IBM SPSS Statistics (version 25) with calculation of a 95% confidence interval and odds ratio (OR). Pearson\u2019s \u03c7Ethical approval for the study was obtained from the Swedish Ethical Review Authority .Genomic DNA was extracted using the QIASymphony DSP virus/pathogen kit according to the manufacturer\u2019s instructions, including RNase treatment and elution with Tris-HCl (pH 8), on the QIASymphony instrument (Qiagen). All DNA extractions were paired-end sequenced using Illumina HiSeq X platform . DNA extractions and sequencing libraries were quality controlled using Qubit BR/HS assays and appropriate assays on the TapeStation according to manufacturer\u2019s instructions .N. gonorrhoeae genomes (n = 1279) were sequenced with 50-100-fold coverage and initially quality controlled for contamination using Kraken (v1.1.1) (N. gonorrhoeae multi-antigen sequence typing (NG-MAST) (All (v1.1.1) . All rea(v1.1.1) ], geneti(v1.1.1) , N. gonoNG-STAR) and N. gNG-MAST) sequenceNG-MAST) . The NG-NG-MAST) based onv3.14.1) with theN. gonorrhoeae reference strain FA1090 (accession number LT591897) to obtain a multiple sequence alignment using multiple_mappings_to_bam pipeline3 with BWA-MEM visualized using Microreact .All WGS sequence reads are available from the ENA (PRJEB47922).n = 21) except one (V\u00e4sterbotten) were represented. Regarding origin of infection, 68.4% and 29.6% were reported as domestic (n = 875) and foreign (n = 379), respectively (n = 70), Germany (n = 32), Spain (n = 31), Denmark (n = 25), and Turkey (n = 18) (The study population included 252 women and 1027 men with median (mean) age of 24 (27.4) years and 30 (32.1) years, respectively . In totaectively . The mos(n = 18) . A highe4 and The phenotypic antimicrobial susceptibility of all gonococcal isolates by regional council is summarized in Figure 1n = 119) of all isolates (n = 1279) showed a decreased susceptibility. Cefixime resistance was found in 1.7% of isolates , and the highest resistance levels were in \u00d6sterg\u00f6tland (4.0%), Stockholm (2.4%), and Sk\u00e5ne (2.3%) (n = 134) of isolates had a decreased susceptibility to cefixime. Eighty (6.3%) isolates had a decreased susceptibility to both ceftriaxone and cefixime. One of these 80 isolates was also resistant to azithromycin, i.e., a high-level azithromycin-resistant (MIC > 256 mg/L) strain cultured from a heterosexual male with a sexual contact in Thailand. Based on the WGS sequences, 20 (90.9%) of the cefixime-resistant isolates (n = 22) had mosaic penA alleles [penA-10.001 (n = 18) and penA-34.001 (n = 2)] cefixime-resistant isolates did not contain any mosaic penA, however, these isolates harbored PBP2 A501V and P551S alterations (penA-13.001) as well as mtrR and porB1b mutations. Overall, 44 penA alleles were found among the 1279 isolates, of which the most common were penA-2.001 (n = 325), penA-2.002 (n = 232), penA-19.001 (n = 101), penA-44.001 (n = 98), and penA-14.001 (n = 94). Ninety-two isolates (7.2%) had mosaic penA alleles: penA-34.001 (n = 60), penA-10.001 (n = 23), penA-34.008 (n = 6), penA-72.001, penA-105.001, and penA-180.001 (n = 1 each) resulting in ceftriaxone MICs < 0.002-0.125 mg/L and cefixime MICs < 0.016-0.5 mg/L. The combination of mosaic penA with mtrR and/or porB1b mutations, which further decrease the ESC susceptibility, was found in 81 isolates, of which 49 (60.5%) isolates had decreased susceptibility to ceftriaxone and 17 (21.0%) and 60 (74.1%) isolates had resistance and decreased susceptibility to cefixime, respectively. PBP2 A501V/T, P551S and G542S alterations were found in 162 (12.7%), 56 (4.4%), and 45 (3.5%) isolates, respectively. The ceftriaxone and cefixime MIC range (mean) was 0.004-0.125 (0.035) mg/L and < 0.016-0.125 (0.040) mg/L for A501V/T, 0.004-0.064 (0.034) mg/L and < 0.016-0.064 (0.029) mg/L for P551S, and 0.004-0.032 (0.016) mg/L and < 0.016-0.032 (0.020) mg/L for G542S, respectively. The combination of PBP2 A501V/T and P551S alterations was present in 48 isolates (3.8%) with ceftriaxone and cefixime MIC range (mean) of 0.004-0.125 (0.07) mg/L and < 0.016-0.25 (0.07) mg/L, respectively. The combination of PBP2 A501T and G542S alterations was present in six isolates (0.5%) with ceftriaxone and cefixime MIC range (mean) of 0.016-0.064 (0.051) mg/L and 0.016-0.064 (0.045) mg/L, respectively.No resistance to ceftriaxone was found, however, 9.3% (e (2.3%) . FurthermtrR -35 A-deletion was found in all of them, two isolates had additionally a mosaic mtrD and the remaining three isolates had porB1b mutations. Mosaic mtrR was found in 1.1% (n = 14) of isolates, mosaic mtrC in 1.1% (n = 14), mosaic mtrD in 8.4% (n = 107), and mosaic mtrE in 1.0% (n = 13). The combination of mosaic alleles in all genes of the mtrRCDE operon was found in 1.0% (n = 13) of isolates with azithromycin MICs of 0.032-1.0 mg/L. One isolate harbored mosaic alleles in all genes except mtrE (azithromycin MIC = 1.0 mg/L). Notably, one isolate, which lacked known azithromycin resistance determinants, contained the previously described GC deletion in mtrC (Azithromycin resistance was found in 16 (1.3%) isolates, and the highest resistance levels were found in Dalarna (11.1%) and Stockholm (1.8%) . High-le in mtrC (azithroparC was found in 451 (35.3%) isolates, all except one had the GyrA S91F mutation, consisting of the amino acid substitutions D86N (n = 137), S87I/N/R (n = 311), S88P (n = 27), and E91K (n = 10).Ciprofloxacin resistance was found in 653 (51.1%) isolates . All isorpsE genes.No resistance was found to spectinomycin, including no spectinomycin resistance determinants in the 16S rRNA or mtrR and porB1b mutations were found in 540 (42.2%) and 356 (27.8%) isolates, respectively.In total, n = 133), ST7363 (n = 125), ST1901 (n = 93), ST1588 (n = 89), and ST7359 (n = 67). Fifty-five MLST STs represented by single isolates were found. Using NG-MAST, 422 STs were identified and the five most prevalent STs were ST5441 (n = 89), ST5793 (n = 56), ST2992 (n = 41), ST11461 (n = 39), and ST387 (n = 35). In total, 260 NG-MAST STs were found in only one isolate. With NG-STAR, 280 STs were observed and the five most prevalent ones were ST442 (n = 133), ST55 (n = 63), ST158 (n = 63), ST231 (n = 61), and ST520 (n = 52). One hundred and forty-eight NG-STAR STs were represented by single isolates. Lastly, 92 NG-STAR CCs were found and 19 isolates were ungroupable. The five most common CCs were CC442 (n = 134), CC158 (n = 100), CC63 (n = 91), CC42 (n = 70), and CC390 (n = 69). Twenty-six NG-STAR CCs were represented by single isolates.Based on the WGS sequences, the most common MLST, NG-MAST, NG-STAR STs and NG-STAR CCs by sex and sexual orientation is summarized in penA types in sublineages A1 and A2 and linage B are summarized in n = 133) and ST1901 (n = 90); NG-MAST ST5441 (n = 89) and ST2992 (n = 41); NG-STAR ST442 (n = 133) and ST90 (n = 51); and NG-STAR CCs 442 (n = 134) and 63 (n = 91). The sexual orientation of the patients in A2 was homosexual male (57.9%), bisexual male (2.6%), heterosexual male (23.4%), women (14.5%), and not reported (1.7%) (penA (49/81) predominantly belonged to A2. The isolates with decreased susceptibility to ceftriaxone (n = 89) were cultured from MSM , heterosexual men , women and not reported . The majority of these infections were domestic and 73.0% (n = 65) were diagnosed in Stockholm. The most common molecular types among the isolates with decreased susceptibility to ceftriaxone were MLST ST1901 (n = 34), NG-MAST ST1407 (n = 25), NG-STAR ST90 (n = 33), and NG-STAR CC90 (n = 35). The 21 (95.5%) cefixime-resistant isolates in A2 were cultured from infections acquired heterosexually or MSM (3/21). Furthermore, 14 isolates were from domestic and seven from foreign infections, in six different countries. The majority were diagnosed in Stockholm, however, all cefixime-resistant isolates were from patients in larger metropolitan areas. The most common molecular types among the cefixime-resistant isolates were MLST ST7363 (n = 16), NG-MAST ST13876 (n = 9), NG-STAR ST232 (n = 10), and NG-STAR CC348 (n = 15).Phylogenomic analysis revealed two main lineages (A and B), of which one (A) was subdivided into two main sublineages (A1 and A2) (d (1.7%) . Isolaten = 11), or mtrR -35 A-deletion plus mosaic mtrD (n = 2). Sexual orientation of these patients was homosexual male (46.2%), heterosexual male (15.4%) and women (38.5%). These azithromycin-resistant isolates did not belong to any predominant ST nor did they cluster together in the phylogenomic tree also belonged to A2, and contained 23S rRNA gene mutations (n = 90), NG-MAST ST1407 (n = 33), NG-STAR ST90 (n = 51), and NG-STAR CC90 (n = 61).Resistance to ciprofloxacin was also prevalent (53.2%) in A2. The most common molecular types among the ciprofloxacin-resistant isolates in A2 were MLST ST1901 (n = 101) and ST1588 (n = 89); NG-MAST ST12001 (n = 21), ST9184 (n = 19), and ST18710 (n = 19); NG-STAR ST158 (n = 63) and ST426 (n = 22); and NG-STAR CC158 (n = 100) and CC309 (n = 48). The sexual orientation of the patients in A1 was homosexual male (32.8%), bisexual male (1.9%), heterosexual male (40.0%), women (22.5%), and not reported (2.8%) (penA). The remaining three azithromycin-resistant isolates also belonged to A1 and appeared to represent the same gonococcal strain . All these isolates were also lacking 23S rRNA mutations and mosaic mtrD, but had mtrR -35 A-deletion plus porB1b mutations (azithromycin MICs of 2 mg/L). Furthermore, ciprofloxacin resistance was very common in A1 (90%). The most common molecular types among the ciprofloxacin-resistant isolates in A1 were MLST ST7363 (n = 101), NG-MAST ST12001 (n = 21), NG-STAR ST158 (n = 63), and NG-STAR CC158 (n = 100) (In lineage A1 (360 isolates), the most common molecular types were MLST ST7363 (d (2.8%) . A1 incln = 100) .n = 67) and ST1599 (n = 53), NG-MAST ST5793 (n = 56) and ST11461 (n = 39), NG-STAR ST55 (n = 63) and ST231 (n = 61), and NG-STAR CC42 (n = 69) and CC390 (n = 64). The sexual orientation of the patients was homosexual male (52.4%), bisexual male (0.8%), heterosexual male (22.8%), women (22.9%), and not reported (1.4%) (penA but no isolates comprised mosaic mtrD. The majority (93.3%) of isolates were ciprofloxacin susceptible.In lineage B (359 isolates), the most frequent molecular types were MLST ST7359 (d (1.4%) . Lineagen = 5) and epidemiological data were diagnosed in metropolitan areas, especially in the capital city Stockholm. In 2016, resistance to ceftriaxone and cefixime remained low nationally; i.e., no resistance to ceftriaxone and 1.7% to cefixime. Resistance to azithromycin was also low (1.3%). The cefixime resistance was caused by penA-10.001 (n = 18), penA-34.001 (n = 2), or PBP2 A501V and P551S alterations in combination with mtrR and porB1b mutations (n = 2). The azithromycin resistance was caused by 23S rRNA A2059G (n = 1), 23S rRNA C2611T (n = 10) or mtrR -35 A-deletion plus mosaic mtrD (n = 2) or mtrR -35 A-deletion plus porB1b mutations (n = 3). None of the cefixime-resistant isolates was resistant to azithromycin. Prior to 2019, the Swedish gonorrhea guideline recommended ceftriaxone 500 mg, plus azithromycin 2 g if pharyngeal infection, for treatment of uncomplicated gonorrhea. However, from 2019, ceftriaxone 1 g monotherapy is the recommended treatment and A1 contained the lowest proportion of MSM. Lineage B harbored most of the antimicrobial-susceptible isolates.Phylogenomic analysis showed that the isolates grouped into two main lineages as previously described , of whicpenA alleles in MLST ST1901 and ST7363 was originally documented in Japan of the 21 Swedish regions, making preventions targeted on single sexual networks or risk group and in general gonorrhea control very challenging.The most prevalent MLST STs found in the present study have been described in previous studies. A national genomic Norwegian study described 21 STs with \u2265 10 isolates , all of in Japan and thesin Japan , 2021. Iectively . The majd Europe . In SwedN. gonorrhoeae, NG-STAR CC due to the lack of phylogenomic similarity of the isolates. NG-STAR with CC designation, which clusters based on AMR determinants and the closest alleles, appeared to correspond relatively well with the genome-based phylogeny and can also inform regarding resistance or decreased susceptibility to cefixime and ceftriaxone and presence of associated AMR determinants.The newly proposed classification method for -STAR CC , assigne-STAR CC , where iN. gonorrhoeae population in 2016 had a low prevalence of resistance to cefixime and no resistance to ceftriaxone. However, the limited cefixime resistance and especially the high level of decreased susceptibility to ESCs, predominantly domestically transmitted, remain worrisome and is a risk for development of resistance to ceftriaxone. The prevalence of azithromycin resistance was also low. Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were mainly found in the phylogenomic sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.In conclusion, the Swedish https://www.ebi.ac.uk/ena, PRJEB47922.The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: The studies involving human participants were reviewed and approved by the Swedish Ethical Review Authority . Written informed consent for participation was not required for this study in accordance with the national legislation and the institutional requirements.MU and RH designed, initiated, and coordinated the study. RH, DG, and LE were involved in the laboratory work, WGS, and/or bioinformatic analysis. A-KO, E-LE, and YL provided gonococcal isolates. IV and HF contributed with epidemiological data. RH, DG, and MU analyzed and interpreted all the data. RH and MU wrote the first draft of the manuscript. All authors read, commented, and approved the submitted manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Inflammatory osteolysis after total joint replacement (TJR) may cause implant failure, periprosthetic fractures, and be a severe threat to global public health. Our previous studies demonstrated that melatonin had a therapeutic effect on wear-particles induced osteolysis. Gut microbiota is closely related to bone homeostasis, and has been proven to be affected by melatonin. However, whether melatonin could play its anti-osteolysis effects through reprogramming gut microbiota remains elusive.Here, we demonstrated that melatonin could alleviate Ti-particles induced osteolysis, while this therapeutic effect was blocked by antibiotic cocktail treatment. Interestingly, transplantation of fecal microbiota from mice treated with melatonin reappeared the same beneficial effect. Analysis of the 16S rRNA revealed that melatonin could reverse dysbacteriosis triggered by osteolysis, and elevate the relative abundance of some short chain fatty acid (SCFA) producing bacteria. Moreover, butyrate was enriched by exogenous melatonin administration, while acetate and propionate did not show an evident difference. This was consistent with the results of the metagenomic approach (PICRUSt2) analysis, which revealed a general increase in the synthetic enzymes of butyrate. More importantly, direct supplementation of butyrate could also recapitulate the anti-osteolysis effect of melatonin. Further analysis identified that butyrate alleviated osteolysis via activating its receptor GPR109A, and thus to suppress the activation of NLRP3 inflammasome triggered by Ti-particles.Taken together, our results suggested that the benefits of melatonin mainly depend on the ability of modulating gut microbiota and regulating butyrate production.The online version contains supplementary material available at 10.1186/s12951-021-00915-3. As the essential treatment for end-stage arthritis, total joint replacement (TJR) could effectively relieve joint pain, stiffness, and improve joint function . However. ** p < .01). Figure S3. Principle coordinate analysis (PCoA) plot between Ti-trans and MT-trans groups based on the Bray Curits distance. n = 6. Figure S4. Ti-particles induced osteolysis could be blocked by the treatment of either NLRP3 or caspase-1 inhibitor. (A) Representative view of calvarium from sham, Ti, MCC950, and Ac-YVAD-CMK groups via Micro-CT 3D reconstruction. (B-D) Quantification of bone erosion parameters (BV/TV) bone volume to tissue volume ratio, (BMD) bone mineral density, and total porosity. n=6. (E) Percentage of osteoclasts surface per bone surface . n = 5.(F) H&E and (G) TRAP staining of calvarial slices from each group. (H) H&E and (I) TRAP staining of calvarial slices from Sham, Ti and Butyrate group. Results are expressed as mean \u00b1 SEM (One-way ANOVA[post hoc:SNK] *** p < .001). Figure S5. Quantification of NLRP3, Caspase-1, IL-1\u03b2 and GPR109A staining. (A) Quantification of NLRP3 immunohistochemical staining using integrated optical density/specimen area (IOD/Area). n=5. (B) Quantification of Caspase-1 immunofluorescence staining using mean density (integrated density/specimen area). n=5. (C) Quantification of IL-1\u03b2 immunohistochemical staining using integrated optical density/specimen area (IOD/Area). n=5. (D) Quantification of GPR109A immunohistochemical staining. n=5. Results are expressed as mean \u00b1 SEM ."} +{"text": "Anxiety Disorder (AD) is common in inpatient pediatric burn patients and likely related to pain/stress associated with acute care. This study ascertained if burn survivors reported higher anxiety levels based on sex, visibility of scars, or TBSA \u2265 50%.Burn-injured youth completed the Screen for Child Anxiety Related Disorders (SCARED) with parental consent. This 41 item self-report measures DSM-IV pediatric anxiety disorder symptoms: panic disorder (PD), separation anxiety (SA), generalized anxiety disorder (GAD), social phobia (SP) school phobia (SCP) and total anxiety (TA). The percentage of respondents above threshold for each disorder was calculated.112 survivors, mean age of 13, included boys (51%) & girls (49%). 83 reported visible scars. Females had higher percentages for TA (53%) vs. males (21%) (p < 0.001), PD (47%) vs. (7%) (p< 0.001), GAD (40%) vs. (16%) (p < 0.005), & SA (51%) vs. (21%) (p < 0.001). Youth with TBSA \u2265 50% (n=22) had higher precents for GAD (46%) vs. < 50% (24%) (p < 0.01). The visibly scarred had higher percent for GAD (38%) vs. hidden (7%) (p< .01).Female, visibly scarred, and patients with burns > 50% revealed increased AD symptoms. AD may be chronic, interfere with a child\u2019s home & school function and lead to chronic distress, substance abuse, and isolation. Screening for anxiety in burn-injured youth is recommended."} +{"text": "The primary analysis of the STAT study demonstrated the feasibility, efficacy, and safety of using DTG/3TC as a first-line regimen in a test-and-treat setting through 24 weeks, with therapy adjustments for baseline resistance or hepatitis B virus (HBV) co-infection. Here we present secondary analyses through Week 48 of virologic outcomes in participants by baseline viral load (VL). 2, then antiretroviral therapy (ART) was potentially adjusted and participants remained on study. Efficacy analyses included proportion of participants with HIV-1 RNA < 50 c/mL regardless of ART regimen at Week 48, among all participants and among participants with available HIV-1 RNA data at Week 48 . STAT is a single-arm study of treatment-naive adults with HIV-1 infection who initiated DTG/3TC \u2264 14 days after HIV-1 diagnosis without availability of screening/baseline laboratory results. If baseline testing indicated DTG or 3TC resistance, HBV co-infection, or creatinine clearance < 30 mL/min/1.73 mOf 131 enrolled, DTG/3TC treatment was adjusted in 10 participants, and of those with available data (n=7), all (100%) achieved HIV-1 RNA < 50 c/mL at Week 48. At Week 48, 82% (107/131) of all participants and 97% (107/110) of those with available data achieved HIV-1 RNA < 50 c/mL. Of participants with baseline VL \u2265 500,000 c/mL, 89% (17/19) achieved HIV-1 RNA < 50 c/mL at Week 48; the remaining 2 withdrew from study. Of participants with baseline VL \u2265 1,000,000 c/mL, 90% (9/10) achieved HIV-1 RNA < 50 c/mL at Week 48 (Table); the remaining participant withdrew consent. Of the 17 participants with baseline VL \u2265 500,000 c/mL with available data through Week 48, 76% (13/17) achieved virologic suppression by Week 24. One participant with baseline VL \u2265 500,000 c/mL switched from DTG/3TC before the Week 48 assessment. Of the 9 participants with baseline VL \u2265 1,000,000 c/mL with available data through Week 48, most participants were suppressed by Week 24.Figure 1. Virologic outcomes at Week 48, overall and by baseline VL and CD4+ cell count: ITT-E missing = failure analysis.Figure 2. Virologic outcomes at Week 48, overall and by baseline VL and CD4+ cell count: observed analysis.Table. Viral Load by Study Visit Among Participants with Baseline HIV-1 RNA \u22651,000,000 c/mLThese data provide evidence for the efficacy and feasibility of using DTG/3TC as a first-line regimen in a test-and-treat setting, including among participants with very high baseline VL.Charlotte-Paige M. Rolle, MD MPH, Gilead Sciences Janssen Infectious Disease ViiV Healthcare Tulika Singh, MD MS AAHIVS, Gilead ViiV Moti Ramgopal, MD FIDSA, Abbvie Gilead Janssen Merck ViiV Dushyantha Jayaweera, MD, mrcog(uk), face, Gilead (Research Grant or Support)Janssen (Research Grant or Support)viiv (Research Grant or Support) Peter Leone, MD, viiv healthcare (Employee) Jessica Matthews, BS, ViiV Healthcare (Employee) Michael Cupo, Ph.D., GlaxoSmithKline (Employee) Mark Underwood, PhD, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Kostas Angelis, PhD, GSK Brian Wynne, MD, ViiV Healthcare Deanna Merrill, PharmD, MBA, AAHIVP, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Christopher T. Nguyen, MD, ViiV Healthcare (Employee) Jean A. van Wyk, MB,ChB, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee) Andrew Zolopa, MD, GlaxoSmithKline (Shareholder)ViiV Healthcare (Employee)"} +{"text": "Due to antiretroviral treatment success, individuals with HIV are living longer. People aging with HIV may be more likely to experience nutritional risk compared to their HIV-negative counterparts due to biopsychosocial factors. The DETERMINE checklist measure accounts for social and economic factors as well as aspects of the aging process that are not typically considered when examining nutritional risk and are important for PAWH. The current study examined nutritional risk and health-related quality of life (HRQoL) in PAWH using the DETERMINE checklist and PROMIS t-scores through secondary analyses of 158 participants in the Strengthening Therapeutic Resources in Older patients agiNG with HIV (STRONG) study. DETERMINE nutritional risk scores (0-21) were separated into 4 groups . The sample was 55% male, 94% Black/African American and had a mean age=59 (SD=5.5). Most of the sample (74%) were at high or very high nutritional risk and low HRQoL t-score: physical M=43.7 (SD=9.5), and mental M=45.7 (SD=10.1). Mental and physical HRQoL were significantly (p<.001) associated with nutritional risk group as tested through linear regressions. Means were as follows: physical HRQoL low-risk M=53.4 (SD=10.6), moderate-risk M=47.4 (SD=8.9), high-risk M=43.5 (SD=8.1), very high-risk M=38.4 (SD=8.9); mental HRQoL low-risk M=54.0 (SD=8.9), moderate-risk M=49.1(SD=7.9), high-risk M=46.1(SD=9.5), and very high-risk M=39.5 (SD=9.7). These associations remained significant after controlling for age and sex. Higher nutritional risk as measured by the DETERMINE checklist in PAWH was associated with poorer physical and mental HRQoL."} +{"text": "In a Phase 3 trial, the Janssen COVID-19 vaccine, Ad26.COV2.S, showed robust efficacy against severe\u2013critical COVID-19 in countries where different SARS-CoV-2 variants were circulating. We evaluated Ad26.COV2.S-elicited antibody neutralizing activity against variants of concern (VOC) B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta) in sera from participants in clinical trials following a single dose of Ad26.COV2.S.10 viral particles [vp]) against VOC were assessed by wild-type virus neutralizing (wtVNA) and pseudovirion neutralization (psVNA) assays in sera from participants in Phase 1/2a and Phase 3 clinical trials, respectively. Geometric mean titers (GMTs) were determined at Days 29 and 71 after vaccination.Neutralizing activities of Ad26.COV2.S . Day 71 titers against the Delta variant were maintained for at least 8 months following a single dose of Ad26.COV2.S (5 x 1010 vp). In serum samples from Phase 3 participants (n = 8), psVNA titers against VOC were lower than the original strain at Day 71 after vaccination, with the lowest titers observed for the Beta variant . Smaller reductions in Nab titers for VOC were observed in the psVNA assay compared to wtVNA.In serum samples from Phase 1/2a participants (n = 6), at Day 29 after 1 dose of Ad26.COV2.S, wtVNA titers against VOC were lower than for the original strain (GMT = 573), with GMT = 65, 14, and 15 for Alpha, Beta, and Delta, respectively, representing 8.8-, 40.9-, and 37.7-fold decreases. By Day 71 after vaccination (n = 14), fold differences between the original strain (GMT = 375) and VOC were smaller than at Day 29, suggestive of B-cell maturation , B.1.351 (Beta), and B.1.617.2 (Delta) lineages in serum samples from participants who received Ad26.COV2.S. n = 6 samples at Day 29 and n = 14 samples at Day 71 after vaccination with a single dose of Ad26.COV2.S (5 x 10^10 vp dose level) were analyzed in wild-type virus neutralization assays against the SARS-CoV-2 Victoria strain , the B.1.1.7 the B.1.351 , and the B.1.617.2 lineages. Dots represent the IC50 (inhibitory concentration) titers per participant. Geometric mean titers (GMTs) and fold decrease in neutralizing activity between the original Victoria strain and each lineage are shown.Ad26.COV2.S-elicited serum neutralizing activity against VOC showed an overall decrease in titers relative to the original strain that was largest for the Beta variant, even though vaccine efficacy against severe\u2013critical COVID-19 was maintained in countries where these variants were circulating versus in countries where they were not circulating. Over time, titers against variants increased, suggesting B-cell affinity maturation leading to increasing coverage of VOC.Mathieu Le Gars, n/a, Johnson & Johnson Jerald Sadoff, MD, Johnson & Johnson Mandy Jongeneelen, n/a, Johnson & Johnson Dirk Heerwegh, n/a, Janssen Research and Development (Employee) Georgi Shukarev, MD, Janssen (Employee) Carla Truyers, n/a, Janssen Research and Development (Employee) Anne Marit de Groot, n/a, Johnson & Johnson (Employee) Gert Scheper, n/a, Johnson & Johnson Jenny Hendriks, n/a, Johnson & Johnson Boerries Brandenburg, n/a, Johnson & Johnson Frank Struyf, n/a, Johnson & Johnson Johan Van Hoof, n/a, Johnson & Johnson Macaya Douoguih, MD, MPH, Janssen (Employee) Hanneke Schuitemaker, PhD, Johnson & Johnson"} +{"text": "BRCA. In this study, we investigated the somatic mutation of DNA damage response genes in epithelial ovarian cancer patients using a multiple-gene panel with next-generation sequencing. In all, 69 serous, 39 endometrioid and 64 clear cell carcinoma patients were enrolled. Serous carcinoma patients (69.6%) had higher percentages of DDR gene mutations compared with patients with endometrioid (33.3%) and clear cell carcinoma (26.6%) . The percentages of DDR gene mutations in patients with recurrence or cancer-related death were higher than those without recurrence or living patients. In endometrioid carcinoma, patients with \u22652 DDR gene mutations had shorter PFS and OS than those with one mutation or none. In clear cell carcinoma, patients with \u22652 DDR gene mutations had significantly shorter PFS and OS than those with 1 DDR mutation or none. In the EOC patients, somatic DDR gene mutations were associated with advanced-stage tumor recurrence and tumor-related death. Type I EOC patients with DDR mutations had an unfavorable prognosis, especially for clear cell carcinoma.DNA damage response (DDR) is important for maintaining genomic integrity of the cell. Aberrant DDR pathways lead to accumulation of DNA damage, genomic instability and malignant transformations. Gene mutations have been proven to be associated with epithelial ovarian cancer, and the majority of the literature has focused on Epithelial ovarian carcinoma (EOC) is a major cause of death in women worldwide, and patients are usually diagnosed at an advanced stage with a 5-year survival of less than 50% ,2,3,4. CBRCA mutations or homologous recombination deficiency (HRD) status is critical for selecting potential patients, but both positive and negative patients as defined by current HRD assays benefited from PARPi [Precision medicine is the current direction for cancer management depending on the specific genetic or molecular features of cancer. There are several subtypes of EOC\u2014high-grade serous, clear cell, endometrioid, mucinous and low-grade serous\u2014that could be viewed as distinct diseases for their differences in clinical course and pathological features ,7. To daom PARPi ,13,14,15BRCA 1/2 genes participating in HR and maintaining PARPi therapy for BRCA-mutated EOC is a good example of synthetic lethality [DNA damage response (DDR) is important for maintaining a cell\u2019s genomic integrity, and the DDR pathway is composed of various molecules that detect DNA damage, activate cell-cycle checkpoints, trigger apoptosis, and coordinate DNA repair ,17,18. Sethality . Severalethality ,17. UndeThe study protocol was approved by the National Taiwan University Hospital Research Ethics Committee . Informed consent from all participants was obtained and the methods were performed in accordance with the guidelines and regulations. From December 2015 to October 2018, 172 women diagnosed with epithelial ovarian cancer who had received debulking surgery and adjuvant chemotherapy were enrolled. The cancerous tissue specimens collected during debulking surgery were immediately frozen in liquid nitrogen and stored at \u221270 \u00b0C. A portion of the tissue specimens were sent for pathological examinations to confirm the diagnosis and ensure tumorous tissue sufficient for the following experiments. Clinical data were obtained from medical records, including age, cancer stage, the findings during debulking surgery, treatment course and recurrence. Optimal debulking surgery was defined as a maximal residual tumor size <1 cm following surgery. The tumor grade based on International Union Against Cancer criteria, and cancer stage was based on International Federation of Gynecology and Obstetrics (FIGO) criteria . All patWe selected 60 genes involved in DNA damage response (DDR) for the gene panel , includi260/280 ratio.Genomic DNA was isolated using a QIAGEN Genomic DNA extraction kit according to the manufacturer\u2019s instructions . The purity and concentration of the genomic DNA were checked by agarose gel electrophoresis and the ODThe genomic DNA was fragmented with Covaris fragmentation protocol . The size of the fragmented genomic DNA was checked by Agilent Bioanalyzer 2100 and NanoDrop spectrophotometer . The target gene library was generated with NimblGen capture kits . The samples were sequenced by Illumina MiSeq with paired-end reads of 300 nucleotides.The analysis algorithm was conducted according to our previous protocol . BrieflyThe sequence variants were classified according to the IARC variant classification . The patp value of less than 0.05.All statistical analyses were performed using the Statistical Package for Social Sciences software package and R . One-way ANOVA was used to compare continuous variables and a chi-squared test was used for categorical variables. Survival curves were generated using the Kaplan\u2013Meier method, and differences were calculated using the log-rank test. A multivariate Cox\u2019s regression model was used to evaluate the prognostic factors for progression-free survival (PFS) and overall survival (OS). Statistical significance was set as a There were 172 EOC patients enrolled: 69 serous, 39 endometrioid and 64 clear cell carcinomas . There whttp://www.ncbi.nlm.nih.gov/snp, accessed on 28 September 2021) and bioinformatic analyses , MUTYH (6.4%) and BRCA2 (5.8%) for all patients. Serous carcinoma\u2014TP53 (56.5%), BRCA2 (5.8%) and RAD51C (5.8%); endometrioid carcinoma\u2014TP53 (15.4%), ATM (12.8%) and MSH2 (7.7%); clear cell carcinoma\u2014MUTYH (9.4%), TP53 (4.7%), BRCA2 (3.1%) and ERCC8 (3.1%). The top three prevalent mutated subgroups of DDR genes were CCR (30.8%), HR (10.5%) and BER (7.0%) for all patients. Serous carcinoma\u2014CCR (58.05%), HR (15.9%) and BER (5.8%); endometrioid carcinoma\u2014CCR (23.1%), MMR (15.4%) and HR (7.7%); clear cell carcinoma\u2014BER (9.4%), CCR (6.3%) and HR (6.3%). For detailed information, please refer to The pattern of prevalent mutated DDR genes was different among the histological subtypes . The prop = 0.048, chi-squared test). Endometrioid carcinoma (15.38%) had a higher percentage of MMR mutations than those of serous carcinoma (2.90%) and clear cell carcinoma (4.69%) . Low-grade tumors had a higher percentage of MMR mutations compared with high-grade tumors . Type II tumors had a higher percentage of DSBR mutations than type I tumors . Serous carcinoma (57.97%) had a higher percentage of CCR mutations than those of endometrioid carcinoma (23.08%) and clear cell carcinoma (6.25%) . Type II tumors had higher percentage of CCR mutations than those of type I tumors . The advanced-stage patients had a higher percentage of CCR mutations than the early-stage patients . The recurrent patients had a higher percentage of CCR mutations than those without recurrence . Patients who died of EOC had higher percentages of CCR mutations than living patients . Serous carcinoma (69.57%) had higher percentage of DDR mutations than those of endometrioid carcinoma (33.33%) and clear cell carcinoma (26.56%) . Type II tumors had a higher percentage of DDR mutations than type I tumors . The advanced stage patients had higher percentage of DDR mutations than the early-stage patients . Recurring patients had a higher percentage of DDR mutations than those without recurrence . Patients who died of EOC had a higher percentage of DDR mutations than living patients .We evaluated the correlations between the mutation of DDR genes, the clinicopathologic parameters and outcome of the EOC patients. As shown in p = 0.0072, log-rank test, p = 0.022, log-rank test, p = 0.56, log-rank test, p = 0.47, log-rank test, p = 0.0035, log-rank test, p = 0.015, log-rank test, p = 0.0056, log-rank test, p = 0.0046, log-rank test, EOC patients without DDR gene mutation had longer progression-free survival (PFS) (p = 0.011), 1 DDR gene mutation (HR: 1.71 (1.12\u20132.60), p = 0.013), endometrioid carcinoma (HR: 0.17 (0.08\u20130.37), p < 0.001), type II tumor (HR: 2.69 (1.81\u20134.00), p < 0.001), advanced-stage carcinoma (HR: 5.29 (3.16\u20138.85), p < 0.001), high-grade tumor (HR: 5.57 (2.26\u201313.70), p < 0.001) and optimal debulking surgery (HR: 0.28 (0.18\u20130.41), p < 0.001) were significant in the univariate Cox regression model (p = 0.001) and optimal debulking surgery (HR: 0.51 (0.32\u20130.80), p = 0.004) were important prognostic factors in the multivariate analysis. Cancer-related death with TLS gene mutation (HR: 33.76 (3.95\u2013289.00), p = 0.001), 1 DDR gene mutation (HR: 1.96 (1.20\u20133.20), p = 0.007), endometrioid carcinoma (HR: 0.12 (0.04\u20130.38), p < 0.001), type II tumor (HR: 1.88 (1.19\u20132.96), p = 0.007), advanced-stage carcinoma (HR: 6.84 (3.28\u201314.25), p < 0.001), high-grade tumor (HR: 17.97 (2.50\u2013129.29), p = 0.004) and optimal debulking surgery (HR: 0.26 (0.16\u20130.41), p < 0.001) were significant in the univariate Cox regression model. Type II tumor (HR: 0.35 (0.20\u20130.60), p < 0.001), TLS gene mutation (HR: 9.57 (1.08\u201384.83), p = 0.042), advanced-stage carcinoma (HR: 4.82 (2.09\u201311.09), p < 0.001) and optimal debulking surgery (HR: 0.38 (0.22\u20130.64), p < 0.001) were important prognostic factors in the multivariate analysis.Tumor recurrence with CCR gene mutation (HR: 1.68 (1.12\u20132.50), on model . AdvanceATM, BRCA1/2, BRIP1, MLH1, MSH2, MSH6, PALB2, RAD51C and RAD51D [BRCA test alone. The percentage of BRCA 1/2 somatic mutation in serous carcinoma was 7.2, which was compatible with the 6\u20137% in previous studies [BRCA HR somatic mutation of our study was more than 10% in serous and endometrioid carcinomas, and the MMR somatic mutation was around 15% in endometrioid carcinomas, which was compatible with the previous study [Our study showed that nearly half of the epithelial ovarian cancer (EOC) patients had DNA damage response (DDR) gene mutations with varied proportions of histological subtypes. Two-thirds of serous adenocarcinoma patients, one-third of endometrioid adenocarcinoma patients and one-fourth of clear cell carcinoma patients had DDR gene mutations. Our DDR gene panel consisted of the genes involved in single-strand break repair, double-strand break repair and cell cycle regulation, including the genes recommended by National Comprehensive Cancer Network (NCCN) guidelines as cost-effective tools for assessing the lifetime risk of EOC, such as d RAD51D . The maj studies ,35,36,37us study .ARID1A, PIK3CA, KRAS and PPP2R1A) might be related to chromatin remodeling, cell proliferation, cell cycle checkpointing and cytoskeletal organization [ARID1A, PIK3CA, PPP2R1A or TP53 in ovarian clear cell carcinoma did not correlate well with the prognosis [ARID1B, ARID3A, CREBBP, CSMD3, CTNNB1, LPHN3, LRP1B, MAGEE1, MLH1, MLL3, MUC4, PIK3R1, PTEN and TP53 [Our study showed that ovarian clear cell carcinoma patients with DDR gene mutations had an unfavorable survival prognosis. Those who had somatic DDR mutations were significantly associated with advanced-stage carcinomas, tumor recurrence and tumor-related death. The trend was different in histological subtypes as serous carcinomas or type II tumors with DDR mutation showed a better survival trend. Non-serous or type I EOC patients with DDR mutations had a poor prognosis, especially in clear cell carcinoma. Ovarian clear cell carcinoma is an aggressive drug-resistant subtype of EOC in association with endometriosis and glycogen accumulation. It accounts for about 5\u201313% of all EOCs in Western populations, but up to 20\u201325% in East Asia, including Taiwan [nization ,47,48,49rognosis . Other iand TP53 ,46,48,49BRCA gene tests or companion HRD assays are currently suggested for PARPi, but there are unmet problems that need to be resolved [BRCA (tBRCA) mutations, including germline (gBRCA) or somatic (sBRCA), derived the greatest benefit from PARPi maintenance therapy [BRCA mutation, and another 6\u20137% patients had an sBRCA mutation with a negative gBRCA test [BRCA mutated patients tested negative for tBRCA [BRCA HR gene mutations were usually pooled together to interpret the association with clinical outcomes in previous studies because of their relatively low prevalence [BRCA somatic mutations derived benefit from olaparib in study 19 [BRCA HR gene mutations , but the sensitivity in discriminating a rucaparib response was only 11% [BRCA wild type EOC patients still benefitted from PARPi, which indicated that a BRCA test by itself was inadequate for selecting EOC patients for PARPi [BRCA HR genes could be used to predict a PARPi response, especially in non-serous EOC patients.Our DDR gene panel could provide a scientific rationale for patient selection in future clinical trials that target DNA damage repair response pathways, especially in clear cell carcinoma. resolved ,14,15,20resolved ,50,51. G therapy ,13,14,15RCA test ,35,36,37or tBRCA ,53,54. Tevalence ,56,57. Tstudy 19 . In ARIEonly 11% . HoweverATM, BRCA1/2, BRIP1, MLH1, MSH2, MSH6, PALB2, RAD51C, RAD51D and STK11 to assess the lifetime risk of EOC [BRCA gene, there is a difference among laboratories in the VUS reporting rate (3\u201350%), detection protocols and management strategies [There were limitations to our study. First, germline gene mutations were not investigated. These not only inform the patients but also identify family members of the possible risk of malignancy ,53,54. Tk of EOC , but howk of EOC ,61,62. Tk of EOC . Even inrategies . FurtherOur study found that nearly half of the EOC patients had DDR gene mutations of varying proportions in the histological subtypes. Patients with somatic DDR mutations were significantly associated with advanced-stage carcinoma, tumor recurrence and tumor-related death. Type I EOC patients with DDR mutations had an unfavorable prognosis, especially for clear cell carcinoma. A broad multiple-gene DDR panel would provide not only comprehensive information of gene mutations but also a rationale for a future study of a novel therapy target for DNA damage response pathways."} +{"text": "Correction to: BMC Pharmacol Toxicol 20, 5 (2019)https://doi.org/10.1186/s40360-018-0280-8After publication of the original article , an erroThe incorrect sentence is:P < 0.0001).SIB peak plasma concentrations were 207.1 mg/L for SPC and 12.6 mg/L for SM tablets. All pharmacokinetic parameters differed significantly between formulations (The correct sentence is:P < 0.0001).SIB peak plasma concentrations were 207.1 ng/L for SPC and 12.6 ng/L for SM tablets. All pharmacokinetic parameters differed significantly between formulations (The original article has been corrected."} +{"text": "Breast cancer is the most common cancer in women . Triple-First, we generated a cisplatin (DDP)-resistant TNBC cell line, MDA-MB-231/DDP, which is 5-fold more resistant to cisplatin than its parental line MDA-MB-231 Fig.\u00a0a. IntereP\u2009=\u20090.005). Consistently, in both validation cohort of 128 samples . Likewise, low-SNORD33 group showed significantly reduced overall survival (OS) compared with high-SNORD33 group , validation group and combined cohorts patients who received first-line platinum-based chemotherapy Fig. f. In theles Fig. a, low-SN38) Fig. revealedROC test was used to evaluate the value of SNORD33 in predicting PFS in mTNBC patients treated with platinum-based regimens in the combined cohort. SNORD33 signature showed the strongest predictive value (AUC\u2009=\u20090.652) for PFS, compared with other single clinicopathological risk factors , suggesting better performance of SNORD33 signature as a surrogate predictor for platinum-based chemotherapy outcome Fig. m. Based P\u2009=\u20090.023) than high-SNORD33 group [RPL13A (host gene), DICER enzyme (an endoribonuclease), or SNORD32a (homologue to SNORD33 modifying 18S rRNA during cell proliferation) in MDA-MB-231 cells . It part(RPL13A) . Does SNlls Fig.\u00a0a. The insis Fig. b. We obssis Fig. b. We thenes Fig. c. Down-rnes Fig. . ConsistTogether, we identified plasma SNORD33 signature as a predictor for the sensitivity of platinum-based chemotherapy in mTNBC patients. Furthermore, we showed that MeCP2 could convey SNORD33 associated platinum resistance. Our findings may have immediate translational relevance for precision platinum-based chemotherapy.Additional file 1. Methods.Additional file 2: Supplementary Figure 1. Aberrantly expressing RNA in 231/DDP cells. Supplementary Figure 2. SNORD33 knockdown increases proliferation and decreases apoptosis of TNBC cells. Supplementary Figure 3. Reduced SNORD33 level is correlated with poor prognosis of mTNBC patients who received first-line platinum-based chemotherapy. Supplementary Figure 4. Increased cell viability was observed in cisplatin treated cell lines with SNORD33 knockdown. Supplementary Figure 5. Reduced SNORD33 level correlates with poor prognosis of non-small cell lung cancer (NSCLC) patients who received first-line platinum-based chemotherapy. Supplementary Figure 6. MeCP2 is a candidate protein binding with SNORD33. Supplementary Figure 7. Down-regulation of MeCP2 partially rescues SNORD33 knockdown increased cell colony formation. Supplementary Figure 8. Down-regulation of MeCP2 rescues SNORD33 knockdown decreased cell apoptosis and induced alteration of apoptotic markers.Additional file 3: Supplementary Table 1. Baseline characteristics in mTNBC patients received first-line platinum-containing regimens. Supplementary Table 2. Univariate and multivariate analysis of prognostic factors associated with progression-free survival and overall survival in the combined cohort. Supplementary Table 3. Baseline characteristics in mTNBC patients received first-line non-platinum-containing regimens. Supplementary Table 4. Baseline characteristics in lung adenocarcinoma patients received first-line platinum-containing regimens. Supplementary Table 5. Univariate and multivariate analysis of prognostic factors associated with progression-free survival in lung adenocarcinoma patients.Additional file 4."} +{"text": "CMV infection is common post-kidney transplant (KT). Valganciclovir (VGC) prophylaxis (Px) has lessened CMV infection among high-risk (CMV D+/R-) KT recipients (KTRs), but VGC can induce neutropenia. We quantified the burden of CMV infection among CMV D+/R- KTRs and healthcare resources required to manage these patients (pts).Retrospective study of pts undergoing KT between Jan 2014-Dec 2018. Study and control groups (gps) were CMV D+/R- and R+ KTRs, respectively. Standard post-KT immunosuppression was tacrolimus and mycophenolate mofetil (MMF). D+/R- and R+ KTRs received VGC Px (900 mg/day) for 6 and 3 months (mos), respectively.Clinical characteristics did not differ between D+/R- (n=131) and R+ (n=140) pts. Median VGC Px duration was longer for D+/R- . Within the first 6 mos post KT, a higher proportion of D+/R- KTRs received \u22651-course of granulocyte-stimulating factor (G-CSF) . VGC Px was stopped prematurely/intermittently in 20% and 10% of D+/R- and R+, respectively, due to neutropenia (p=0.02); corresponding data for stopping MMF for \u22651 mos were 32% and 21% (p=.05). 50% of D+/R- pts received < 3 mos Px. Leukopenia prompted hospitalization in 3% of D+/R- vs 0% of R+ pts (p=.05). CMV infections did not differ between gps ; however, VGC-resistant CMV was higher in D+/R- gp . Between 6-12 mos post-KT, D+/R- KTRs had higher rates of CMV infection , VGC resistance , hospitalization due to CMV , MD intervention , and infectious disease (ID) referral . 57% of CMV resistance was observed in pts who prematurely stopped VGC. Hospitalizations were longer for CMV infections in D+/R- KTRs . There was a trend toward higher rejection for D+/R- KTRs .Universal VGC Px in D+/R- KTR remains challenging and requires significant resources for monitoring and intervention for neutropenia, including MD involvement and ID referral. Intermittent/premature stop of VGC may have led to VGC-resistant CMV,and stop of MMF may have led to a trend of higher cellular rejection at 1 yr. There is critical need for new CMV agents with a better safety profile.Amit D. Raval, PhD, Merck and Co., Inc. (Employee) Yuexin Tang, PhD, JnJ Merck & Co., Inc. Cornelius J. Clancy, MD, Merck (Grant/Research Support) Minh-Hong Nguyen, MD, Merck (Grant/Research Support)"} +{"text": "Carbapenem (Carb) minimum inhibitory concentration (MIC) breakpoints were lowered by CLSI in 2010 and recognized by FDA in 2012. Adoption of revised breakpoints is often slow, which may lead to under-reporting of Carb non-susceptibility (NS) by facilities. We compare facility-reported rates of Carb-NS ENT to the CLSI MIC breakpoints for a large nationwide collection of isolates in the United States (US) from 2016-2019.All adults with a positive non-contaminant ENT culture in ambulatory/inpatient settings from up to 300 US hospitals from 2016-2019 were evaluated (BD Insights Research Database). Facility-reported Carb-NS was defined as: susceptible (S), intermediate (I) or R to ertapenem (ETP), imipenem (IPM), meropenem (MEM) and/or doripenem (DOR) per commercial panels. Where available, MICs were interpreted using CLSI 2010 MIC breakpoints (\u00b5g/ml): \u2264 0.5 (S), 1 (I), \u2265 2 (R) for ETP and \u22641 (S), 2 (I), and \u2265 4 (R) for IPM/MEM/DOR. For evaluable ENT isolates we compared susceptibility results as reported by the facility to CLSI MIC breakpoints.Overall, 77.4% and 90.6% non-duplicate ENT isolates with facility-reported susceptibility results also had interpretable MIC results for ETP and IPM/MEM/DOR, respectively (Tables). ETP S rates were 99.3% and 99.1% as reported by facilities and using CLSI criteria, respectively. S rates of other Carbs were 98.9% and 98.4% by facility reporting and CLSI criteria, respectively. Systematic application of CLSI breakpoints under-reported EPT-I and \u2013R isolates by 24.2% and 16.4%, respectively, and identification of IPM/MEM/DOR-I and \u2013R isolates by 31.3% and 22.7%, respectively.Systematic application of CLSI breakpoints in 2016-19 would have had minimal impact on ENT S rates in the US. However, facility reporting failed to identify 18.8% of ETP I or R and 26.5% of IPM/MEM/DOR I or R isolates. The clinical implications of this observation are unknown. Facilities should know their local epidemiology, decide if under-reporting might be an issue, and assess if there is any impact on their patients.Vikas Gupta, PharmD, BCPS, Becton, Dickinson and Company Kalvin Yu, MD, BD (Employee) Jason M Pogue, PharmD, BCPS, BCIDP, Merck (Consultant)QPex (Consultant)Shionogi (Consultant)Utility Therapeutics (Consultant)VenatoRX (Consultant) Janet Weeks, PhD, Becton, Dickinson and Company (Employee) Cornelius J. Clancy, MD, Merck (Grant/Research Support)"} +{"text": "Scientific Reports 10.1038/s41598-021-98868-y, published online 30 September 2021Correction to: The original version of this Article contained an error in the order of the References 16 and 17, which was incorrectly given as:et al. Vitamin D increases glucocorticoid efficacy via inhibition of mTORC1 in experimental models of multiple sclerosis. Acta Neuropathol. 10.1007/s00401-019-02018-8 (2019).16. Hoepner, R. FASEB J23, 3649\u20133658 (2009).17. Ayroldi E, Riccardi C. Glucocorticoid\u2010induced leucine zipper (GILZ): a new important mediator of glucocorticoid action. The correct order of the References is listed below:FASEB J23, 3649\u20133658 (2009).16. Ayroldi E, Riccardi C. Glucocorticoid\u2010induced leucine zipper (GILZ): a new important mediator of glucocorticoid action. et al. Vitamin D increases glucocorticoid efficacy via inhibition of mTORC1 in experimental models of multiple sclerosis. Acta Neuropathol. 10.1007/s00401-019-02018-8 (2019).17. Hoepner, R. The original Article has been corrected."} +{"text": "Effective treatment of glioma requires a nanocarrier that can cross the blood\u2013brain barrier (BBB) to target the tumor lesion. In the current study, elemene (ELE) and cabazitaxel (CTX) liposomes were prepared by conjugating liposomes with transferrin (Tf) and embedding the cell membrane proteins of RG2 glioma cells into liposomes , which exhibited effective BBB infiltration to target glioma.The findings showed that Tf-ELE/CTX@BLIP was highly stable. The liposomes exhibited highly significant homologous targeting and immune evasion in vitro and a 5.83-fold intake rate compared with classical liposome (ELE/CTX@LIP). Bioluminescence imaging showed increased drug accumulation in the brain and increased tumor penetration of Tf-ELE/CTX@BLIP in orthotopic glioma model nude mice. Findings from in vivo studies indicated that the antitumor effect of the Tf-ELE/CTX@BLIP led to increased survival time and decreased tumor volume in mice. The average tumor fluorescence intensity after intravenous administration of Tf-ELE/CTX@BLIP was 65.2, 12.5, 22.1, 6.6, 2.6, 1.5 times less compared with that of the control, CTX solution, ELE solution, ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP groups, respectively. Histopathological analysis showed that Tf-ELE/CTX@BLIP were less toxic compared with administration of the CTX solution.These findings indicate that the active-targeting biomimetic liposome, Tf-ELE/CTX@BLIP, is a promising nanoplatform for delivery of drugs to gliomas.The online version contains supplementary material available at 10.1186/s12951-021-01048-3. P-gp) occurs on the BBB, which further increases clearance of chemotherapy drugs \u2009=\u200920\u00a0\u03bcg/mL) and incubated for 2\u00a0h. In addition, RG2 cells were seeded into a 6-well plate (3\u2009\u00d7\u2009105 cells/well) and incubated with ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP and Tf-ELE/CTX@BLIP (Rho B\u2009=\u200920\u00a0\u03bcg/mL) for 2\u00a0h. The medium was removed and cells were fixed with 4% paraformaldehyde, stained with DAPI and washed thrice with PBS. The cellular uptake was determined by confocal laser scanning microscope imaging and flow cytometry [Tf-ELE/CTX@BLIP was incubated with SPC-A-1 cells, A549 cells, MDA-MB-231 cells, LM-3 cells, U251 cells, C6 cells, and RG2 cells, separately. Cells were inoculated into 6-well plates for 2\u00a0h. Effect on immune evasion was then determined by CLSM and flow cytometry .Cytotoxicity effects of ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP and Tf-ELE/CTX@BLIP on RG2 cells were determined using a CCK-8 kit. RG2 cells (3000\u00a0cells/well) were inoculated in 96-well plates and incubated for 24\u00a0h. After incubation, cells were exposed to ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP and Tf-ELE/CTX@BLIP (CTX concentrations ranging from 0.4 to 200\u00a0ng/mL) for 48\u00a0h. Non-treated cells were used as negative controls. Medium was evaluated as the blank control. Cytotoxicity was quantitatively determined by measuring the absorbance at 450\u00a0nm using a Spark multi-functional microporous plate testing platform .Furthermore, apoptotic cells were determined by FACS analysis . RG2 cells were incubated with ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP and Tf-ELE/CTX@BLIP and 50\u00a0ng/mL CTX for 48\u00a0h then treated with the apoptosis detection kit for 10\u00a0min. Percentage of apoptotic cells was determined using a FACS Calibur System. Non-treated cells were used as the negative control .5\u00a0cells/well) and incubated for 24\u00a0h. Rhodamine 123 was preconditioned with ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP, Tf-ELE/CTX@BLIP (50\u00a0ng/mL) and verapamil (0.625\u00a0\u03bcg/mL) separately for 30\u00a0min then it was exposed to bEnd.3 for 2\u00a0h. The medium was removed and bEnd.3 cells were fixed with 4% paraformaldehyde for 30\u00a0min and washed thrice with PBS. Cells were then analyzed using fluorescence microscope and flow cytometry. Relative expression level of P-gp in bEnd.3 cells was determined by WB assay. bEnd3 cells in 6-well plates were conditioned with medium and verapamil, ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP, Tf-ELE/CTX@BLIP were added [bEnd.3 cells were cultured as described in the \u201cre added .Female nude mice were obtained from Shanghai Slack Laboratory Animal Co. LTD. Mice were allowed to acclimatize at room temperature for 7\u00a0days prior to the performing animal studies. Animals were housed under the animal care facility and allowed free access to food/water. All animal experiments were approved by the animal ethics committee of Hangzhou Normal University .7 glioma-luc cells in medium were injected slowly into the brain right striatum of nude mice . The needle was maintained at the injection point for 1\u00a0min after injection and then pulled out slowly. Alcohol cotton swabs were used to disinfect the skin, the skin was sewn with a needle and thread. The mice were then placed back to the cage to wake up naturally. Rate of growth of intracranial tumor was monitored by magnetic resonance imaging (MRI) and fluorescence imaging.Glioma-luc cells were injected into the right striatum of nude mice to develop a orthotopic glioma-bearing model. Nude mice were anesthetized through administration of 10% chloral hydrate and the head was immobilized on a stoelting . Approximately 2.5\u2009\u00d7\u200910Cypate\u2009=\u20090.1\u00a0mg/mL) were injected into normal mice and glioma-bearing mice through the tail vein. Bioluminescence imaging was performed at fixed times using a small animals in vivo 3D bioluminescence imaging system .The nude mice were then sacrificed, and brains, liver, heart, spleen, lung, and kidney were collected for quantitative biodistribution analysis and ex vivo bioluminescence imaging [Orthotopic glioma-bearing model was established by injecting RG2 cells into the brain striatum as described above. Cypate, Cypate@LIP, Cypate@BLIP, Tf-Cypate@LIP and Tf-Cypate@BLIP (CP-gp.Orthotopic glioma-bearing model nude mice were randomly assigned into seven groups (6 mice/group) as follows: (1) control ; (2) CTX solution; (3) ELE solution (25\u00a0mg/kg ELE); (4) ELE/CTX@LIP; (5) ELE/CTX@BLIP; (6) Tf-ELE/CTX@LIP; (7) Tf-ELE/CTX@BLIP, to explore the anti-tumor effect in vivo. Treatments were administered by intravenous injection through the tail at day 1, 3, 5, 7, 9 and 11. Group 2, 4, 5, 6, 7 was administered with 2.5\u00a0mg/kg (CTX) on the first time and 0.625\u00a0mg/kg for the subsequent 5 injections. Bioluminescence imaging was performed at day 1, 5, 10, and 15 to explore tumor growth. Body weight and survival time were recorded every 3\u00a0days. Nude mice were euthanized 2\u00a0h post-treatment and their brains were collected for H&E staining, TUNEL immunofluorescence staining and detection of glioma Glioma-bearing nude mice were assigned into seven groups and were administered with (1) control ; (2) CTX solution; (3) ELE solution; (4) ELE/CTX@LIP; (5) ELE/CTX@BLIP; (6) Tf-ELE/CTX@LIP; (7) Tf-ELE/CTX@BLIP, 6 times and every other day. Whole blood samples were collected from retro-orbital sinus of glioma-bearing nude mice 2\u00a0h post-treatment. A portion of the complete blood samples was used for complete blood count analysis. The supernatant (serum) of the portion of blood obtained after centrifugation was used for determination of biochemical indexes of liver and kidney, including total bilirubin, blood urea nitrogen, uric acid, alanine transaminase, creatinine and aspartate transaminase level. Liver, heart, spleen, lung and kidney sections were stained with H&E to evaluate effects of free ELE, CTX solution and liposomes toxicity .t test for comparison between two groups and ANOVA for comparison among multiple groups. Statistical difference was defined as significant for *p\u2009<\u20090.05 and highly significant for **p\u2009<\u20090.01.GraphPad Prism 8.0.2.263 software was used for statistical analysis. Data were expressed as mean\u2009\u00b1\u2009SD. Experimental data were analyzed using two-tailed Student Additional file 1: Table S1. Encapsulation efficiency stability of the drug in 4 liposomes at 3 months\u00a0(n = 3). Fig. S1. Diameter and \u03b6-potential of Tf-ELE/CTX@BLIP, Tf-ELE/CTX@LIP, ELE/CTX@BLIP and ELE/CTX@LIP. Fig. S2. 7-days stability of TF-ELE/CTX@BLIP diameter in different medium. Fig. S3. Flow cytometry analysis of RG2 glioma cells after incubation with Tf-ELE/CTX@BLIP, Tf-ELE/CTX@LIP, ELE/CTX@BLIP and ELE/CTX@LIP for 2 h. Rho B = 20 \u03bcg/mL. Fig. S4. CLSM images of RG2, U251 and C6 glioma cells treated with Tf-ELE/CTX@BLIP for 2 h. Scale bar = 50 \u03bcm. Fig. S5. Flow cytometry analysis of RAW264.7 cells treated with Tf-ELE/CTX@BLIP, Tf-ELE/CTX@LIP, ELE/CTX@BLIP and ELE/CTX@LIP for 2 h. Rho B = 20 \u03bcg/mL. Fig. S6. WB analysis of P-gp in bEnd.3 cells. Relative protein expression was calculated. Cells preconditioned with (1) control; (2) verapamil; (3) ELE/CTX@LIP; (4) ELE/CTX@BLIP; (5) Tf-ELE/CTX@LIP; (6) Tf-ELE/CTX@BLIP. . Fig. S7. Corresponding quantitative fluorescent analysis of brain, liver, heart, spleen, lung and kidney at 48 h post-injection in glioma-beard mice. *p < 0.05. Fig. S8. In vivo fluorescence imaging of Tf-Cypate@BLIP, Tf-Cypate@LIP, Cypate@BLIP and Cypate@LIP in normal mice. Cypate = 0.5 mg/kg. Fig. S9. Averaged fluorescent intensity of saline, free CTX, free ELE, ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP and Tf-ELE/CTX@BLIP in nude mice bearing orthotopic glioma brain within 15 days of treatments. Fig. S10. H&E staining of brain sections of orthotopic glioma-bearing mice in different formulation groups. Fig. S11. Biochemical parameter analysis after treated with saline, free CTX, free ELE, ELE/CTX@LIP, ELE/CTX@BLIP, Tf-ELE/CTX@LIP and Tf-ELE/CTX@BLIP. (A) BLI-T: total bilirubin, (B) BUN: blood urea nitrogen, (C) URIC: uric acid, (D) ALT: alanine transaminase, (E) CRE: creatinine, (F) AST: aspartate transaminase."} +{"text": "Compared with WT mice, S\u2212/\u2212tat1 had reduced neutrophils, Th1, and Th17 cell infiltration. To evaluate corticosteroid sensitivity, mice were treated with either vehicle, 1 or 3 mg/kg fluticasone propionate (FP). Corticosteroids significantly reduced eosinophil infiltration and cytokine levels in both c-di-GMP + MA-challenged WT and \u2212/\u2212Stat1 mice. However, histological and functional analyses show that corticosteroids did not reduce airway inflammation, epithelial mucous cell abundance, airway smooth muscle mass, and AHR in c-di-GMP + MA-challenged WT or \u2212/\u2212Stat1 mice. Collectively, our data suggest that increased Th1 inflammation is associated with a decrease in corticosteroid sensitivity. However, increased airway pathology and AHR persist in the absence of STAT1 indicate corticosteroid insensitivity in structural airway cells is a STAT1 independent process.Corticosteroid insensitivity in asthma limits the ability to effectively manage severe asthma, which is characterized by persistent airway inflammation, airway hyperresponsiveness (AHR), and airflow obstruction despite corticosteroid treatment. Recent reports indicate that corticosteroid insensitivity is associated with increased interferon-\u03b3 (IFN-\u03b3) levels and T-helper (Th) 1 lymphocyte infiltration in severe asthma. Signal transducer and activator of transcription 1 (STAT1) activation by IFN-\u03b3 is a key signaling pathway in Th1 inflammation; however, its role in the context of severe allergic airway inflammation and corticosteroid sensitivity remains unclear. In this study, we challenged wild-type (WT) and Corticosteroids have broad anti-inflammatory effects that contribute to the effective management of asthma symptoms and exacerbations. In contrast to the corticosteroid-sensitive mild asthma, people with severe asthma exhibit greater airway inflammation, remodeling, airway hyperresponsiveness (AHR), and more frequent exacerbations despite treatment with higher doses of corticosteroids , 2. Alth+ T lymphocytes in bronchoalveolar lavage samples levels . Studies samples , 9. Alth samples . These o samples , 11\u201313. samples , 11, imp\u2212Stat1/\u2212 mice exhibit reduced Th1 responses and IFN-\u03b3 production is a transcription factor that is activated by IFN-\u03b3 and mediates proinflammatory responses in immune and airway structural cells . Given toduction , 16. Preoduction . Given t\u2212Stat1/\u2212 mice using a chronic mixed allergen (MA) model augmented with c-di-GMP. We hypothesized that ablation of STAT1 would disrupt Th1 inflammation and increase corticosteroid sensitivity in chronic severe allergic airway inflammation. However, our data demonstrate reduced corticosteroid sensitivity in both WT and \u2212Stat1/\u2212 mice. Examination of immunological, functional, and structural aspects of chronic allergic airway inflammation shows that persistent airway remodeling remains increased in \u2212Stat1/\u2212 mice despite treatment with corticosteroids. Our studies demonstrate that corticosteroid insensitivity remains in the absence of STAT1 signaling during severe allergic airway inflammation.In this study, we examined corticosteroid sensitivity in wild-type (WT) and \u2212Stat1/\u2212 (Stock No. 012606) mice were procured from Jackson Laboratory . Mice were maintained in Research Building III at the Abigail Wexner Research Institute and provided food and water ad libitum. Adult male and female mice were mated to generate pup litters that were randomly assigned a treatment group. Newborn male and female mice were intranasally (in) sensitized and challenged with PBS or mixed allergens (MA), which consists of 10 \u00b5g Alternaria alternata , 10 \u00b5g Aspergillus fumigatus , 10 \u00b5g Dermatophagoides pteronyssinus , and 10 \u00b5g ovalbumin (OVA) plus 0.5 \u00b5g c-di-GMP , three times per week for 7 wk. During the last 2 wk, mice were intraperitoneally (ip) injected with vehicle (PBS containing 0.015% DMSO) or 1 mg/kg or 3 mg/kg FP on the same day as MA challenge. Necropsy was performed \u223c24 h after last allergen challenge and hallenge A. Mice wg for 5 min. Supernatant was collected and stored at \u221280\u00b0C for further analyses. Cellular pellets were resuspended in PBS for total and differential cell count analysis. Total counts were performed using a hemocytometer. Cytospins were generated on microscope slides and differentially stained using a modified Wright-Giemsa Stain . Cells were imaged on a bright-field microscope and counted by a blinded investigator until a total of 200 cells had been counted.Bronchoalveolar lavage fluid (BAL) was harvested as previously described . BrieflyOnce anesthetized, the trachea was exposed and cannulated with a 19-gauge blunt tip cannula. The mouse was placed on a 37\u00b0C heating pad and attached to Y-tubing on the Flexivent . A series of measurements including Snapshot maneuvers were performed following nebulization with PBS, 6.25, 12.5, 25, and 50 mg/mL methacholine . Airway hyperresponsiveness is reported as total resistance in response to methacholine.Lung tissue was homogenized in RIPA buffer, processed, and protein concentration measured using Bradford assay. Each well in custom Meso scale U-Plex Multiplex ELISA plates was coated with antibodies against IL-4, IL-17A, and IFN-\u03b3. Analytes were measured in whole lung homogenates following manufacturer instructions. IL-13 levels in BAL were measured using ELISA according to the manufacturer\u2019s instructions.Samples were quantified by BCA assay (Pierce) and 25 \u00b5g of protein was analyzed per sample. Samples were separated on a 14% SDS-PAGE gel and transferred to nitrocellulose membrane (Bio-Rad). Membranes were blocked for 1 h at room temperature in 1% milk/TBS-T and then incubated in primary antibody overnight at 4\u00b0C. Primary antibodies were purchased from Cell Signaling : monoclonal rabbit anti-Stat1 antibody at 1:1,000 dilution, Cat. No. 14994S; polyclonal rabbit antiphospho-Stat1 (Ser727) antibody at 1:500 dilution, Cat. No. 9177S; monoclonal rabbit anti-Stat6 at 1:500, Cat. No. 5397S; and monoclonal rabbit anti-phospho-Stat6 (Tyr641) at 1:500, Cat. No. 56554S. The following day, samples were washed in Tris-buffered saline-Tween 20 (TBST), incubated with secondary antibodies for 1 h at room temperature, washed with TBST, and imaged on an Odyssey Clx (LI-COR). Protein quantification was performed using ImageStudio Software (LI-COR).2O. Lungs were processed, paraffin embedded, cut into 6 \u00b5m sections, and stained with hematoxylin and eosin . H&E slides were analyzed and scored for inflammation and bronchial-associated lymphoid tissues (BALTs) were quantified by a blinded investigator. Inflammation scores are based on the degree of immune cell infiltration/aggregation around peribronchiolar and perivascular spaces. To quantify BALTs, compact lymphoid nodules were counted in proximal and distal regions. To quantify abundance of mucous cells in the airway epithelium, left lung lobe sections were stained with Alcian Blue-Periodic Acid Schiff (AB-PAS) and photomicrographs of four different airways were taken at \u00d7100 using an Olympus BX-40 light microscope and digital camera . PAS-positive and -negative cells were quantified by a blinded investigator using ImageJ (NIH) and reported as a percentage of total airway epithelial cells counted.Left lung lobes were inflated with 10% neutral-buffered formalin at 25 cm HFormalin-fixed, paraffin embedded left lung lobe sections (6 \u00b5m) were used for immunohistochemical staining for \u03b1-smooth muscle actin (\u03b1-SMA). Sections were deparaffinized with xylene (2 \u00d7 5 min each) and rehydrated with graded ethanol . Antigen retrieval was performed with 10 mM sodium citrate at 100\u00b0C for 1 h. The slides were blocked for 1 h in TBS containing 4% goat serum and 0.04% Triton X-100. After washing, slides were incubated overnight in monoclonal mouse anti-\u03b1-SMA at 1:100 dilution . After incubation, slides were washed and incubated with anti-mouse-FITC secondary antibody at 1:1,000 dilution. Negative control slides followed the same protocol but without addition of a primary antibody. Slides were counterstained with DAPI, and images taken at \u00d7100 using Lionheart . Smooth muscle actin area was analyzed using ImageJ (NIH). Data were normalized to length of airway basement membrane to report as airway smooth muscle (ASM) mass per \u00b5m basement membrane.12\u201318 primers and Superscript IV (Thermo Fisher Scientific Applied Biosystems). Quantitative real-time PCR with TaqMan using Muc5ac (Mm0127618_m1), Muc5b (Mm00466391_m1), and GAPDH (Mm99999915_g1) primer sets was performed (Life Technologies) according to the manufacturer\u2019s instructions. Samples were run on a QuantStudio 3 96-well Real-Time PCR system (Thermo Fisher Scientific Applied Biosystems). Results were analyzed using the comparative Ct method for TaqMan assays.RNA (300\u20131000 ng) from profiled samples was cDNA transcribed using Oligo dTg for 10 min, and resuspended in 10 mL of DMEM medium. Cells were counted using a hemocytometer. For Th stimulation, two million cells were incubated in DMEM medium containing leukocyte activation cocktail with Golgi plug , protein transported inhibitor containing Monensin , and 10% FBS for 37\u00b0C for 4 h. Cells were collected and permeabilized/fixed using fixation/permeabilization buffer and 1\u00d7 permeabilization/wash buffer and resuspended in 200 \u03bcL of PBS. Single cell suspensions were used in flow cytometry analysis.Lungs were perfused with 5 mL of PBS through right ventricle of the heart, and then placed in C-tubes and digested for 30 min in 432 U/mL Collagenase Type IV and 64 U/mL DNAase I in DMEM medium. Lung tissue was homogenized using Gentlemacs octo dissociator (Miltenyi Biotec), strained through 70 \u03bcm nylon cell strainer, centrifuged at 300 1 isotypes were used. All antibodies were purchased from BioLegend. Data were acquired using a BD LSRII flow cytometer and analyzed using FlowJo software (v. 10.7.1).Single cell suspensions were stained with various fluorochrome conjugated anti-mouse monoclonal antibodies for cellular phenotyping as follows: FITC-conjugated anti-CD45 (30-F11), BV421-conjugated anti-CD3 (17A2), PE-conjugated anti-CD4 (A161A1), Alexa 700-conjugated anti-IFN\u03b3 (XMG1.2), APC-conjugated anti-IL-4 (11B11), and APC-conjugated anti-IL-17A (TC11-18H10.1). To control for intracellular cytokine staining, APC (RTK2071) and Alexa fluor 700 (RTK2071) IgGP < 0.05.Data were analyzed by performing two-way ANOVA with Bonferroni post hoc analysis for multiple comparisons. Data were analyzed and graphed using GraphPad Prism 9 Software . Values are presented a means \u00b1 standard error and significant differences indicated by \u2212Stat1/\u2212 mice challenged with c-di-GMP + MA exhibited increased total BAL immune cells compared with PBS-challenged WT mice and WT mice B. BAL to WT mice C. Differ WT mice D. In con\u2212/\u2212 mice E. Treatm WT mice B, wherea\u2212/\u2212 mice D and E. \u2212/\u2212 mice C.+CD4+ T cell numbers were significantly increased in c-di-GMP + MA-challenged WT and \u2212Stat1/\u2212 and IL-4 and IL-13 expression. Th2 lymphocytes were increased in c-di-GMP + MA-challenged WT and \u2212Stat1/\u2212 mice and were not reduced with 1 or 3 mg/kg FP treatment cells and IL-17A levels were significantly higher in c-di-GMP + MA-challenged WT and \u2212Stat1/\u2212 mice nodules quantified. Compared with PBS challenge, c-di-GMP + MA challenge significantly increased airway inflammation in WT and \u2212/\u2212 mice A and B. \u2212/\u2212 mice B. To anagenotype C. In regcontrols D. A signmg/kg FP C.\u2212Stat1/\u2212mice exhibited significant increases in mucous cells compared with PBS-challenged mice mass in lung sections stained for \u03b1-smooth muscle actin. C-di-GMP + MA-challenged WT and mg/kg FP .\u2212Stat1/\u2212 mice showed significantly increased AHR compared with PBS-challenged mice. Treatment with 1 mg or 3 mg/kg fluticasone propionate did not significantly reduce AHR in WT and \u2212Stat1/\u2212 mice was measured using forced oscillation maneuvers following administration of methacholine (0\u201350 mg/mL). C-di-GMP + MA-challenged WT and \u2212/\u2212 mice . To analcontrols .\u2212Stat1/\u2212 mice that exhibit dysfunctional Th1 signaling and c-di-GMP exhibited reduced AHR even in the absence of corticosteroids, implicating Th1 inflammation in increased AHR . Although we observed that corticosteroids significantly reduced IL-4 and IL-13 expression levels in \u2212Stat1/\u2212 mice, their levels did not return to baseline. IL-4 and IL-13 at relatively low levels have been shown to induce mucus production, AHR, and remodeling expression and mucus production are associated with increased Th2-associated inflammation model, Ifn\u03b3\u2212/\u2212 and \u2212Irf5/\u2212 mice exhibited evidence of increased Th2 inflammation with greater eosinophil infiltration than allergen-challenged WT mice , and persistent airway remodeling could be contributing factors in the lack of reduced airway inflammation and corticosteroid sensitivity in \u2212Stat1/\u2212 mice.Our findings in WT mice . However\u2212Stat1/\u2212 mice, persistent airway inflammation and corticosteroid insensitivity may involve enhanced Th2 inflammation. Negative regulation of Th2 inflammatory responses by Th1 inflammation is an established and important immune regulatory mechanism , R01 HL155095 (to R. D. Britt), R01 AI121405 (to M. Guerau-de-Arellano), R03 AI151769 (to M. Guerau-de-Arellano), and startup funds from the Abigail Wexner Research Institute at Nationwide Children\u2019s Hospital.No conflicts of interest, financial or otherwise, are declared by the authors.B.W.L., M.H.G., and R.D.B.J. conceived and designed research; B.W.L., D.J., S.A.A., J.W., M.G., S.G., E.C., A.V.B., and R.D.B.J. performed experiments; B.W.L., D.J., S.A.A., J.W., M.G., S.G., E.C., A.V.B., M.G.-d.-A., and R.D.B.J. analyzed data; B.W.L., M.G.-d.-A., M.H.G., and R.D.B.J. interpreted results of experiments; B.W.L. and R.D.B.J. prepared figures; B.W.L., M.G.-d.-A., M.H.G., and R.D.B.J. drafted manuscript; B.W.L., D.J., S.A.A., J.W., M.G., S.G., E.C., A.V.B., M.G.-d.-A., M.H.G., and R.D.B.J. edited and revised manuscript; B.W.L., D.J., S. A.A., J.W., M.G., S.G., E.C., A.V.B., M.G.-d.-A., M.H.G., and R.D.B.J. approved final version of manuscript."} +{"text": "Chalara sp. is able to biotransform the epigenetic modifier vorinostat to form unique, aniline-containing polyketides named chalanilines. Here, we sought to expand the chemical diversity of chalaniline A-type molecules by changing the aniline moiety in the precursor vorinostat. In total, twenty-three different vorinostat analogs were prepared via two-step synthesis, and nineteen were incorporated by the fungus into polyketides. The highest yielding substrates were selected for large-scale precursor-directed biosynthesis and five novel compounds, including two fluorinated chalanilines, were isolated, purified, and structurally characterized. Structure elucidation relied on 1D and 2D NMR techniques and was supported by low- and high-resolution mass spectrometry. All compounds were tested for their bioactivity but were not active in antimicrobial or cell viability assays. Aminofulvene-containing natural products are rare, and this high-yielding, precursor-directed process allows for the diversification of this class of compounds.The plant endophyte Tolypocladium sp. which results from highly reactive intermediates that can detoxify various synthetic and naturally derived antifungals via nucleophilic substitutions + and an m/z value of 416.0904 [M + Na]+ , resulting in a molecular formula of C22H16FNO5. The UV spectrum showed maxima at 380, 308, and 244 nm, representing the chalaniline A-type backbone. The 1H NMR spectrum exhibited a broad hydroxyl peak (\u03b4H 13.75), an N-H resonance (\u03b4H 11.84) with a large coupling constant (14.5 Hz) to one methine (\u03b4H 8.74), seven aromatic/olefinic hydrogens, one methoxy, and one methyl group , 2J (26.2 and 21.4 Hz), and 3J (9.4 Hz) C-F coupling constants in the carbon spectrum, and the proton spectrum revealed two 3J (10.7 and 8.0 Hz) H-F coupling constants , as well as the correlation between H-11 and C-2\u2032 supported the structural assignment. The placement of the fluorine at C-3\u2032 was confirmed by C-F coupling constant analysis was isolated as a yellow amorphous solid and the HRESIMS provided an m/z value of 394.1088 [M + H] + and m/z value of 416.0909 [M + Na]+ for the sodium adduct . The 1H NMR spectrum of 2 was very similar to the spectrum of 1, the only differences can be found in the number of aromatic signals and the coupling and integration pattern for the fluoro-benzene moiety. Two sets of aromatic signals, with each an integration of ~2H, supported the symmetric, para-substituted fluoro-aniline incorporation , 2J C-F coupling of 23.0 Hz for C-3\u2032/5\u2032, 3J C-F coupling of 8.3 Hz for C 2\u2032/6\u2032, and 4J C-F coupling (2.6 Hz) for C-1\u2032 and the 4-fluoro anilino ring C-2\u2032/6\u2032, and also from the H-11 to C-2\u2032 was isolated as an amorphous yellow solid. The HRESIMS gave an m/z value of 406.1284 [M + H] + and m/z value of 428.1102 [M + Na]+ for the sodium adduct . The 1H NMR spectrum of 3 showed a similar pattern of signals as previously reported for chalaniline A + , indicative of a regioisomer of 3. The para-substitution in the 4-methoxy aniline moiety became evident in the proton NMR with two doublets each with an integration of ~2H , as well as the correlation between bridging methine (H-11) to the fulvene assisted in the structure assembly was isolated as a yellow amorphous solid and the HRESIMS gave an m/z value of 426.1341 [M + H]+ , and an m/z value of 448.1160 [M + Na]+ for the sodium adduct supporting a molecular formula of C26H19NO5. The 1H and 13C NMR spectra were similar to chalaniline A with additional signals for the naphthyl moiety instead of the phenyl in the aromatic region and melanoma (SK-MEL-5) cancer cell models by measuring the reduction of the tetrazolium salt MTT -2,5-diphenyltetrazolium bromide) by metabolically active cells + , m/z 416.0904 [M + Na]+ 3-Fluoro chalaniline A (2): yellow amorphous solid; IR (ATR): \u03bdmax = 3430, 2925, 2853, 1712, 1651, 1589, 1508, 1466, 1365, 1209, 1098 cm\u22121; UV (MeCN) \u03bbmax: 380, 308, 244 nm; 13C NMR and 1H NMR see m/z 394.1088 [M + H]+ , m/z 416.0909 [M + Na]+, 4-Fluoro chalaniline A (3): yellow amorphous solid; IR (ATR): \u03bdmax = 3290, 2924, 2850, 1703, 1647, 1601, 1510, 1470, 1252, 1190, 1050, 840, 735 cm\u22121; UV (MeCN) \u03bbmax = 383, 310, 246 nm; 13C NMR and 1H NMR see m/z 406.1284 [M + H]+ , m/z 428.1102 [M + Na]+ 3-Methoxy chalaniline A (4): yellow amorphous solid; IR (ATR): \u03bdmax = 3290, 2924, 1703, 1647, 1510, 1490, 1252, 1050, 820, 745 cm\u22121; UV (MeCN) \u03bbmax: 382, 308, 244 nm; 13C NMR and 1H NMR see m/z 406.1286 [M + H]+, 4-Methoxy chalaniline A (5): yellow amorphous solid; IR (ATR): \u03bdmax = 3410, 2926, 2852, 1737, 1647, 1614, 1465,1372, 1307, 1207, 1098, 830, 767 cm\u22121; UV (MeCN) \u03bbmax: 374, 305, 242, 214 nm; 13C NMR and 1H NMR see m/z 426.1341 [M + H]+ , m/z 448.1160 [M + Na]+ Naphthyl chalaniline A (Staphylococcus aureus (ATCC 25923), methicillin-resistant Staphylococcus aureus (ATCC BAA-41), multidrug-resistant Staphylococcus aureus (ATCC BAA-44), Pseudomonas aeruginosa (ATCC 15442), Candida albicans (ATCC 90027), Candida krusei (ATCC 34135), and Mycobacterium smegmatis (ATCC 14468) in microbroth assays performed following an established protocol [Antimicrobial Assays. Extracts and fractions were tested for inhibitory activity against protocol ,31. FracCell proliferation assay. Cytotoxic activities of extracts and pure compounds were evaluated against colon (HCT-116) and melanoma (SK-MEL-5) cancer models by measuring the reduction of the tetrazolium salt MTT -2, 5-diphenyltetrazolium bromide) by metabolically active cells following standard procedures ,33."} +{"text": "P. aeruginosa from bloodstream infections (BSI) to those from other infection types.Ceftolozane/tazobactam (C/T), an antipseudomonal cephalosporin combined with a \u03b2-lactamase inhibitor, was approved for treatment of complicated urinary tract (cUTI) and intraabdominal infections (cIAI), and hospital-acquired/ventilator-associated bacterial pneumonia (HAP/VAP). Imipenem/relebactam (IMI/REL) is a combination of imipenem/cilastatin with relebactam, an inhibitor of class A and C \u03b2-lactamases. IMI/REL was approved for HAP/VAP and for infections due to aerobic gram-negative organisms in adults with limited treatment options . We compared the activity of C/T and IMI/REL against Pa isolates were collected. MICs were determined using CLSI broth microdilution and breakpoints.As part of the SMART program, 24 hospitals in the US and 8 in Canada each collected up to 250 consecutive gram-negative isolates per year in 2018-2019 from patients with BSI, lower respiratory tract infections (LRTI), IAI, and UTI. A total of 2351 Pa isolates from BSI tended to show higher susceptibility than IAI, UTI, and especially LRTI isolates (Table). Susceptibility to the tested comparator \u03b2-lactams was 11-12 percentage points lower among LRTI than BSI isolates, while C/T and IMI/REL susceptibility was only 2-5% lower. Even among BSI isolates, the comparator \u03b2-lactams were active against only 75-88% of isolates, while C/T and IMI/REL were active against >95%. Only amikacin showed higher activity. Analyzing coverage by either C/T or IMI/REL, 98.7% of Pa isolates from BSI were susceptible to one or both agents. C/T and IMI/REL maintained activity against 89% and 69% of meropenem-nonsusceptible (MEM-NS) Pa isolates from BSI (n=36), respectively, and 87% and 76% of piperacillin/tazobactam (P/T)-NS Pa (n=38).Results TablePa susceptibility to commonly used \u03b2-lactams like MEM and P/T was < 90%, 7-23% lower than C/T and IMI/REL. Given the desirability of \u03b2-lactams among clinicians and the >98% coverage by either C/T or IMI/REL of Pa isolates from BSI, both agents represent important options in the treatment of patients with BSI.Even among BSI isolates, which were generally more susceptible than those from other infection types, Sibylle Lob, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Meredith Hackel, PhD MPH, IHMA (Employee)Pfizer, Inc. (Independent Contractor) C. Andrew DeRyke, PharmD, Merck & Co., Inc. Kelly Harris, PharmD, BCPS, Merck & Co. Inc (Employee) Katherine Young, MS, Merck (Employee) Mary Motyl, PhD, Merck & Co., Inc. Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)"} +{"text": "Lactococcus lactis may represent a potential approach for IBD therapy.Inflammatory bowel diseases (IBDs) are generally characterized by persistent abdominal pain and diarrhea caused by chronic inflammation in the intestine. Cathelicidins are antimicrobial peptides with pleiotropic roles in anti-infection, wound healing, and immune modulation. However, the sensitivity to the acidic environment and short half-life of cathelicidins limit their application in IBD treatment. Recombinant cathelicidin-related antimicrobial peptide (CRAMP)-producing L. lactis NZ9000 and explore the role and mechanism of recombinant L. lactis NZ9000 expressing CRAMP in colitis.The aim of this study was to develop recombinant CRAMP-producing L. lactis NZ9000 with different plasmids pMG36e (L.L-pMU45CR) or pNZ8148 (L.L-pNU45CR), which use a Usp45 secretion signal to drive the secretion of CRAMP. Bacterial suspensions were orally supplemented to mice with a syringe for 4 days after dextran sodium sulfate (DSS) treatment. Body weight change, disease active score, colon length, and colonic histology were determined. The expression of tight junction and cytokines in colon was performed by qPCR. The expression of p-ERK, p-p38, and p-p65 was determined by Western blot analysis.We constructed two strains of CRAMP-producing L. lactis NZ9000 strains protected against colitis, as shown by reduced weight loss and disease activity score, improved colon shortening, and histopathological injury. In addition, CRAMP-producing L. lactis NZ9000 restored gut barrier by upregulating ZO-1, ZO-2, and occludin. Moreover, CRAMP-producing L. lactis NZ9000 regulated the colonic cytokines profile with reduced IL-6, IL-1\u03b2, and TNF-\u03b1 production, and increased IL-10 production. By further analysis, we found that CRAMP-producing L. lactis NZ9000 reduced the expression of p-p38 and p-p65.Both CRAMP-producing L. lactis NZ9000 attenuated dextran sulfate sodium-induced colitis by colonic colonization and inhibiting p38/NF-\u03baB signaling. Orally administered recombinant CRAMP-secreting L. lactis NZ9000 represents a potential strategy for colitis therapy.Together, our data suggested that CRAMP-secreting Lactococcus lactis NZ9000 were constructed with different plasmids pMG36e (L.L-pMU45CR) or pNZ8148 (L.L-pNU45CR), which use a Usp45 secretion signal to drive the secretion of CRAMP.Two strains of recombinant CRAMP-producing L. lactis NZ9000 strains protected mice from colitis via suppressed activation of p-p38/NF-\u03baB signaling, thus resulting in a restored cytokines profile and an improved gut barrier integrity.CRAMP-producing L. lactis NZ9000 represents a novel intervention strategy for colitis treatment.CRAMP-producing Inflammatory bowel diseases (IBDs) are inflammatory conditions in the intestine, which generally include ulcerative colitis (UC) and Crohn\u2019s disease (CD) . Both UCCathelicidins are antimicrobial peptides found in humans and mice, which includes LL-37 and cathelicidin-related antimicrobial peptide (CRAMP), that are homologous in nature, . These hLactococcus lactis (L. Lactis) is widely used in food fermentation and oral delivery of therapeutic proteins (Lactococcus lactis NZ9000 (L. Lactis NZ9000) plays a key role in industrial fermentation or pNZ8148 (L.L pNU45CR) plasmids, respectively. We also evaluated the role and mechanism of CRAMP-secreting L. lactis NZ9000 in experimental colitis.In this study, we constructed two recombinant Lactococcus lactis NZ9000 was grown in M17 medium containing 0.5% (w/v) glucose at 30\u00b0C. CRAMP gene (Lactococcus lactis NZ9000 was transformed with pMG36e-Usp45-CRAMP (L.L-pMU45CR) and pNZ8148-Usp45-CRAMP (L.L-\u200bpNU45CR) by electroporation (Lactococcus lactis NZ9000 was transformed with empty pMG36e (L.L-pMVectro) and empty pNZ8148 (L.L-pNVector) as controls. Nisin was used for 4 h to induce gene expression in L.L-pNU45CR and L.L-pNVector as controls (AMP gene containiAMP gene was syntAMP gene (pMG36e-AMP gene (pNZ8148poration . Lactococontrols . Bacterin = 5) as follows: [1] control (without DSS), [2] 3% DSS + sterilized water, [3] 3% DSS + L.L-pMVector, [4] 3% DSS + L.L-pNVector, [5] 3% DSS + L.L-pMU45CR, and [6] 3% DSS + L.L- pNU45CR. After 7 days of DSS treatment, bacterial suspensions (1010 CFU) were orally administrated with syringe once daily for 4 days. Bacterial suspensions were prepared as described below. The bacterial cells were centrifuged at 3,000 g at 4\u00b0C for 20 min and washed twice with PBS. These bacterial cells were resuspended at concentrations of 5 \u00d7 1010 CFU/mL based on optical density (OD600). Mice were gavaged with 200 \u00b5L of bacterial suspension (1010 CFU) with syringe. To check the number of CFUs, plate counts were performed on M17 agar supplemented with 0.5% glucose at 30\u00b0C without agitation. After 24 h, the plates were observed.Male C57BL/6 mice (7\u20138 weeks old) were purchased from Su Pu Si Biotechnology Co. Ltd and were randomly divided into six groups according to the manufacturer\u2019s instructions.Colon tissues were fixed and embedded in paraffin via standard methods , and sec-\u2206\u2206ct method was used for calculation and normalized to \u03b2-actin. All primers were synthesized by Thermo Fisher Scientific . Primers were designed with Primer 5 software . To check the specificity of primers, blast program was used for colonic RNA isolation. SuperRT cDNA synthesis kit was used for reverse transcription. SYBR Green was used for quantitation. The 2 program was usedL. Lactis cultures at a given optical density of 600 nm (OD600) were harvested by centrifugation at 3,000\u00b4g for 20 min at 4\u00b0C. The equivalent of 1 mL of 1 OD600 unit of culture (cell or supernatant) was concentrated in a 100 \u03bcL final volume as described below, and 10 \u03bcL was loaded for SDS-PAGE. Supernatants were precipitated by the addition of 10% trichloroacetic acid, harvesting by centrifugation at 10,000\u2005\u00d7\u2005g at 4\u00b0C. The resulting pellet was dissolved in a 1:20 volume of 50 mM NaOH. Cell pellets were resuspended in 70 \u03bcL of TES containing lysozyme (1 mg/mL). After 30 min of incubation at 37\u00b0C, cells were lysed with 30 \u03bcL of 20% SDS. Equal volumes of 2\u00d7 loading buffer were added to all samples. RIPA buffer with phosphatase and protease inhibitors was purchased from Songon Biotech and used in the preparation of colon samples. Electrophoresis and transfer were performed as described before and statistically analyzed by GraphPad Prism software using one-way analysis of variance followed by Tukey\u2019s post-hoc test. L.L-pMU45CR or L.L-pNU45CR. As shown in L.L-pMU45CR and L.L-pNU45CR expressed CRAMP, and the levels of CRAMP were higher in supernatants than in bacterial cells to confirm whether CRAMP with secretion signal peptides (Usp45 + CRAMP) were expressed in al cells . CollectL. lactis NZ9000 on colitis, we treated mice with recombinant L. lactis NZ9000 for 4 days after dextran sodium sulfate (DSS)-induced colitis. We found that both L.L-pMU45CR and L.L-pNU45CR attenuated colitis in DSS-treated mice, as shown by reduced weight change L. lactis, which transit with diet, could survival through acidic conditions in gastric juice (L. lactis NZ9000 is able to colonize the colon and has been used to express bioactive molecules in the treatment of colitis, such as theme oxygenase-1 and insulin-like growth factor I (L. lactis are varied due to the characteristics of heterologous proteins. Usp45 is a signal peptide widely applied in driving protein secretion (L. lactis NZ9000 with Usp45 signal peptides.ic juice . Recombifactor I , 19. Theecretion . We achiL. Lactis-treated mice. However, the recombinant CRAMP producing L. lactis may not have a direct effect on serum CRAMP, because bioactive peptides were not able to cross the gut wall intact, except dipeptides and tripeptides (Cathelicidins have multifunctional roles, such as anti-microbial, anti-inflammation, anti-apoptosis activities, and wound healing. Serum LL-37 levels are positively correlated with recovery in IBD patients . We obsepeptides , 39. Conpeptides , 41.L. lactis increased the expression of IL-10. Similarly, cathelicidins increased the expression of IL-10 in human mononuclear cells (L.L-pMU45CR and L.L-pNU45CR reduced IL-6, TNF-\u03b1, and IL-1\u03b2 expression by suppressing the expression of p-p38 and p-p65. These results revealed that recombinant CRAMP-producing L. lactis regulates proinflammatory cytokine expression by p-p38/NF-\u03baB p-p65 signaling.Cytokines exert major impacts on intestinal inflammation and related clinical symptoms in IBD. The unbalanced cytokines profile between proinflammatory and regulatory cytokines promotes mucosal inflammation. IL-10 regulates intestinal homeostasis, and its deficiency leads to spontaneous colitis in mice . We founar cells , 44. Bloar cells , 45, 46.Escherichia coli is increased in IBD patients and can disrupt tight junctions (L. lactis restored the expression of tight junctions by regulating the cytokines profile in colitis, although it is unclear whether recombinant CRAMP-producing L. lactis regulates adherent-invasive E. coli.Epithelial tight junctions are crucial in regulating intestinal barrier and permeability. Disruption of intestinal barrier results in the transfer of intestinal bacteria and antigens into submucosa, thus subsequently leading to inflammatory response, such as transcription factor activation and immune cell infiltration. Tight junctions are regulated by intestinal microbes and cytokines in IBD. Adherent-invasive unctions . Severalunctions . Previouunctions and epidunctions . TogetheL. lactis NZ9000 strains protected mice from colitis via suppressed activation of p-p38/NF-\u03baB p-p65 signaling, thus resulting in a restored cytokines profile and improved gut barrier integrity (L. lactis NZ9000 may represent a potential strategy for IBD therapy.Our data revealed that two CRAMP-secreting ntegrity . Our dat"} +{"text": "Correction to: BMC Public Health 22, 354 (2022)https://doi.org/10.1186/s12889-022-12776-yThe original publication of this article contained an incorrect Fig. 1. The incorrect and correct Fig. 1 are included in this correction article .The original article has been updated.Fig. 1 Incorrect version of figure 1 as originally publishedFig. 2 Correct version of figure 1 as corrected"} +{"text": "We investigated the infectivity of 128 severe acute respiratory disease coronavirus 2\u2013associated deaths and evaluated predictive values of standard diagnostic procedures. Maintained infectivity (20%) did not correlate with viral RNA loads but correlated well with anti-S antibody levels. Sensitivity >90% for antigen-detecting rapid diagnostic tests supports their usefulness for assessment. Deaths associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have raised concerns that contact with the corpses of deceased persons might pose a risk for transmitting infection , panel Apies/mL) , panel B7 copies/mL, IQR 3.7 \u00d7 104\u20133.3 \u00d7 108) among culture-positive corpses did not differ significantly from PMI and RNA loads among culture-negative corpses (4 copies/mL), in contrast with previous findings among living patients , indicative of potentially decreased infectivity.Virus isolation proved infectivity was maintained in 26/128 (20%) corpses . PMI (We confirmed seroconversion in 18/44 (41%) blood samples, 15/43 (35%) anti-nucleocapsid positive and 17/44 (39%) anti-spike positive , panel C = 0.23) , panel Chttps://www.abbott.com), sensitivity was 80.3% (95% CI 72.3%\u201386.4%) and specificity 100.0% (95% CI 95.0%\u2013100.0%); for the SARS-CoV-2 Rapid Antigen Test (Roche https://www.roche.com), sensitivity was 86.4% (95% CI 79.1%\u201391.9%) and specificity 98.6% (95% CI 93.0%\u2013100.0%); and for the SARS-CoV-2 Antigen Rapid Test (MEDsan https://www.medsan.eu), sensitivity was 84.1% (95% CI 76.6%\u201390.0%) and specificity 95.8% (95% CI 88.0%\u201399.0%) .Antigen-detecting rapid diagnostic tests (Ag-RDTs) are considered adequate alternative swift diagnostic tools in living patients (6 RNA copies/mL (n = 74) revealed 100% (95% CI 95.1%\u2013100.0%) sensitivity in Abbott (n = 74) and Roche and MEDsan (n = 73 each) assays. In contrast, neither PMI (p = 0.34) nor putrefactive changes (p = 0.90) were predictive for testing positive in Ag-RDTs . Ag-RDT sensitivity in infectious corpses was 92.3% (95% CI 74.9%\u201399.1%) for Abbott, 96.2% (95% CI 80.4%\u201399.9%) for Roche, and 96.2% (95% CI 80.4%\u201399.9%) for MEDsan. We detected 2 SARS-CoV-2 variants of concern despite relatively low viral RNA loads (4.83 log10); the 2 samples tested positive by Abbott and Roche but were missed by MEDsan.We found SARS-CoV-2 RNA load correlated with Ag-RDT positivity in univariate and multivariate analyses (p<0.001), thereby confirming their predictive value (The first limitation of our study is that blood was not available from all corpses, and the serologic assays and Ag-RDTs used are not approved for cadaveric samples. Furthermore, because of a shortage of reagents and supplies, we had to use different tests to quantify RNA, and slight deviations cannot be ruled out.In summary, we show that cadavers from SARS-CoV-2\u2013associated deaths remain infectious long after death in a considerable proportion of cases. Postmortem infectivity does not correlate with PMI or viral RNA load but correlates with the absence of virus-specific antibodies. Ag-RDTs performed well, enabling rapid on-site detection. Because previous studies among living patients indicate that Ag-RDTs reliably detect all SARS-CoV-2 variants (Additional information about study of infectivity of cadavers from SARS-COV-2 deaths"} +{"text": "Klebsiella pneumoniae (hvKp), unlike classical K. pneumoniae (cKp), are often responsible for community-acquired infections in otherwise healthy individuals. The acquisition of hypervirulence genes by sequence type 11 (ST11) carbapenem-resistant (CR) Kp endemic in Asia is a grave threat. Aztreonam-avibactam (ATM-AVI) is a monobactam combined with a \u03b2-lactamase inhibitor for the treatment of infections caused by Enterobacterales isolates that carry Class A, B, C and some Class D \u03b2-lactamases.Hypervirulent K. pneumoniae isolates were collected from 17 sites in China in 2019 as a part of the ATLAS global surveillance study. 220 isolates with MICs >1 \u00b5g/ml to meropenem (MEM), ceftazidime or ATM were selected for whole genome sequencing (Illumina Hiseq 2x150 bp reads). Analyses were carried out using the CLC Genomics Workbench (Qiagen). Presence of the aerobactin synthesis locus differentiated hvKp and cKp. Antimicrobial susceptibility was determined by CLSI broth microdilution.487 90 values for ATM-AVI were lower than those for any comparator tested, with only two isolates testing with MIC >4 \u00b5g/ml. Of the isolates sequenced, 82/220 (37.3%) were ST11. 53/82 (64.6%) of these ST11 isolates were hvKp and showed percentages of susceptibility < 90% to three last-line agents (0% MEM-susceptible (S); 18.9% amikacin (AMK)-S; 88.7% tigecycline (TGC)-S). Isolates of other STs (Non-ST11) were less frequently identified as hvKp and more Non-ST-11 hvKp and cKp alike were S to MEM and AMK relative to isolates of ST11 . Likewise, the ATM-AVI MIC90 value (0.25 \u00b5g/ml) was 4-fold lower for Non-ST11 isolates.Of the 487 isolates, MICResults Tablein vitro activity against these isolates which displayed resistance to a range of last-line agents. CST and TGC also displayed some activity but are limited in utility due to nephrotoxicity and poor accumulation in blood, respectively. The spread of virulence factors leading to the complicated clinical presentation of hvKp infection into multidrug-resistant lineages warrants continued surveillance.CR ST11 hvKp represented at least 10.9% of the collected Kp isolates. ATM-AVI retained potent Mark Estabrook, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Krystyna Kazmierczak, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Francis Arhin, PhD, Pfizer, Inc. (Employee) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)"} +{"text": "During the COVID-19 pandemic, a task force was assembled to collect data on patient characteristics and treatment exposures to assess what factors may contribute to patient outcomes, and to help develop institutional treatment guidelines. apriori. Covariates of interest included baseline comorbidities, admission level-of-care, vital signs, mortality outcomes, need for intubation, and specific pharmacological treatment exposures. Logistic regression was performed on our final model and reported as OR +/- 95% CI. A retrospective study was performed on COVID-19 inpatient admissions within a four-hospital community health system over a six-month period from April-October 2020. Positive COVID-19 immunology results and/in conjunction with an inpatient admission was criteria for inclusion. Covariates for age, gender, race were added A total of 349 patients met inclusion criteria. Pharmacotherapies were not associated with a difference in mortality in a four-hospital system. Corticosteroids (p = 0.99); Remdesivir (p = 0.79); hyrdroxychloroquine (p = 0.32); tocilizumab (p = 0.91); were not associated with mortality. ACE-inhibitor or angiotensin II receptor blockers OR 0.29 (0.09-0.93) (p = 0.03); convalescent plasma OR 7.85 (1.47-42.1) (p = 0.02); neuromuscular blocking agents (NMBA) OR 5.51 (1.28-23.8) (p = 0.02); vasopressors OR 17.6 (5.62-54.9) (p = 0.00) were associated with in-hospital mortality. Covariates that were associated with a difference in mortality were: age > 60 years OR 2.73 (1.04-7.14) (p = 0.04); structural lung disease OR 3.02 (1.28-7.10) (p = 0.01). Covariates not associated with mortality included African American race (p = 0.30); critical care admission (p = 0.19); obesity (p = 0.06); cardiovascular disease (p = 0.89); diabetes (p = 0.28).The use of corticosteroids, remdesivir, tocilizumab, and hydroxychloroquine, and admission to a critical care bed was not associated with a difference of in-hospital mortality. Patients who required vasopressors or NMBA were associated with in-hospital mortality. Despite national trends reporting increased mortality in patients with obesity, diabetes, cardiovascular disease, and of African American race, this was not observed in our health system safety net hospitals. All Authors: No reported disclosures"} +{"text": "Achromobacter spp. is intrinsically resistant to multiple antibiotics, and the treatment options are limited. Cefiderocol (CFDC), a siderophore cephalosporin approved in US and EU, is active against a wide variety of aerobic Gram-negative bacteria, including carbapenem-resistant strains. In this study, in vitro and in vivo antibacterial activity of CFDC against Achromobacter spp. was evaluated.In vivo efficacy of CFDC was compared with meropenem (MEM), piperacillin-tazobactam (PIP/TAZ), ceftazidime (CAZ), and ciprofloxacin (CIP) in a neutropenic murine lung infection model (n=5), and compared with MEM in a immunocompetent rat lung infection model (n=3-7) caused by 2 A. xylosoxydans. In the murine model, treatment was given 2, 5, and 8 hours post-infection, and the numbers of viable cfu in lungs were determined 24 hours post-infection. In the rat model, the humanized PK in plasma resulting from CFDC 2 g every 8 h (3-h infusion) or meropenem 1 g every 8 h (0.5-h infusion) were recreated via continuous intravenous infusion for 4 days, following which cfu in lungs were determined.A total of 334 global isolates collected by IHMA from 39 countries in 2015-2019 were used. Minimum inhibitory concentrations (MICs) of CFDC and comparators were determined by broth microdilution method using iron-depleted CAMHB or CAMHB, respectively, as recommended by CLSI guidelines. in vitro activity with MIC50/90 of 0.06/0.5 \u00b5g/mL against 334 Achromobacter spp. Only 7 isolates (2.1%) had MICs > 4 \u00b5g/mL. These were the lowest values among all compound tested (Table). In the murine model, CFDC caused > 1.5 log10 decrease of viable cfu in lungs at 100 mg/kg dose (%fT >MIC: < 50%) from baseline control against both of strains (CFDC MIC: 0.5 and 2 \u00b5g/mL) (P< 0.05). No decrease of cfu in lungs was observed for the comparators at 100 mg/kg . In the rat model, humanized CFDC dosing reduced the viable cfu by >1 log10 CFU/lung compared with baseline controls (P< 0.05). MEM showed no significant activity.CFDC showed In vitro activity of CFDC and comparator agents against Achromobacter spp.334 Achromobacter spp. isolates collected from 2015 and 2019. The majority of isolates tested were A. xylosoxidans , followed by A. insolitus , Achromobacter sp. , A. denitrificans , and A. piechaudii .in vivo efficacy reflecting in vitro activity against A. xylosoxidans. The results suggested that CFDC has the potential to be an effective therapeutic option for Achromobacter spp. infections.CFDC showed potent Ryuichiro Nakai, MSc, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Ayaka makino, BSc, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Toriko Yoshitomi, -, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Rio Nakamura, BSc, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Meredith Hackel, PhD MPH, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Miki Takemura, MS, SHIONOGI & CO., LTD. (Employee) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Yoshinori Yamano, PhD, Shionogi (Employee)"} +{"text": "Pseudomonas aeruginosa isolated from cystic fibrosis sputum. Short reads were de novo assembled into 190 contigs and scaffold assembled to a length of 6.26\u2009Mbp. PhiSpy predicts that PA291 is free of prophages.Here, we report the genome sequence of PA291, a nonmucoid, multidrug-resistant strain of Pseudomonas aeruginosa causes difficult-to-treat and often multidrug-resistant (MDR) infections, which severely impacts individuals with cystic fibrosis (CF) (sis (CF) , 2. CF psis (CF) . Phage tsis (CF) , 5; in pP. aeruginosa. The strain was named PA291 and found to have a nonmucoid phenotype, and a broth microdilution assay revealed strong antibiotic resistance to ceftazidime (MIC\u2009>\u200916\u2009\u03bcg/ml) and intermediate resistance to aztreonam , gentamicin , and meropenem . Moreover, PA291 was lysed by phages PAK_P1, E215, and E217, which are under investigation to treat P. aeruginosa infections was cultured overnight on blood agar at 37\u00b0C, and matrix-assisted laser desorption ionization\u2013time of flight (MALDI-TOF) mass spectrometry identified it as belonging to the species de novo assembled using SPAdes v3.14.1 (AE004091.2), W16407 (CP008869.2), VA-134 (CP013245.1), DVT779 (CP050330.1), SE5357 (CP054844.1), H47921 (CP008861.1), SE5443 (CP046405.1), PAO1161 (CP032126.1), PABL048 (CP039293.1), and PAC6 (CP053705.1). The quality and metrics were analyzed using QUAST v5.02 and alginate biosynthesis genes , a polymyxin resistance gene (arnC), and a fosfomycin resistance gene (fosA). PhiSpy v4.2.6 (PA291 DNA extraction and purification was performed after overnight growth in Lennox broth (LB) at 37\u00b0C using the phenol-chloroform method . The DNA v3.14.1 into 190 v3.14.1 with the161 CP0326.1, PABLg, kinB) were useP. aeruginosa strain isolated from CF sputum. The size of PA291 is consistent with that of other P. aeruginosa genomes, between 5.5 and 7\u2009Mbp under accession number SRR14436913. The RAST annotation of the genome is available on Zenodo (https://zenodo.org/record/5114517#.YPXHVehKguV). The genome sequence of P. aeruginosa PA291 was deposited in GenBank under accession number JAGYWJ000000000, where the Prokaryotic Genome Annotation Pipeline (PGAP) annotation is also available.Data for"} +{"text": "Nosocomial pneumonia (NP) remains associated with excess morbidity and mortality. The effect of NP on other measures of outcome and quality, such as re-admission at 30 days, remains unclear. Moreover, differing types of NP may have varying impacts on re-admissions.We conducted a multicenter retrospective cohort study within the Premier Research database, a source containing administrative, pharmacy, and microbiology data. The rate of rehospitalization at 30 days following the index discharge served as our primary endpoint. We compared NP patients readmitted with pneumonia (RaP) as the principal diagnosis to those readmitted for other reasons (RaO). We also compared readmission rates as function of the type of NP: ventilator-associated bacterial pneumonia (VABP), ventilated hospital-acquired bacterial pneumonia (vHABP), and non-ventilated HABP (nvHABP).Among 17,819 patients with NP, 14,123 (79.3%) survived to discharge, of whom 2,151 (15.2%) required an acute readmission within 30 days of index discharge. Of these, 106 (4.9%) were RaP, and the remainder were RaO. At index hospitalization, RaP patients were older (mean age (SD) 67.4 (13.9] vs. 63.0 (15.2) years), more likely medical (44.3% vs. 36.7%), and less chronically ill (median [IQR] Charlson scores (3 [2-5] vs. 4 [2-5]) than persons with RaO. Bacteremia (10.4% vs. 17.5%), need for vasopressors (15.1% vs. 20.0%), dialysis (9.4% vs. 16.5%), and/or sepsis (9.4% vs. 16.5%) or septic shock 14.2% vs. 17.1%) occurred less frequently in the RaP group. With respect to NP type, nvHABP was most common in RaP (47.2%) and VABP in RaO (38.1%). One in seven survivors of a hospitalization complicated by NP requires an acute rehospitalization within 30 days. However, few of these readmissions had a principal diagnosis of pneumonia, irrespective of NP type. This suggests that short-term readmission does not capture the quality of care initially delivered to patients for their NP. Of the 5% of NP subjects with RaP, the plurality initially suffered from nvHABP. Marya Zilberberg, MD, MPH, Cleveland Clinic (Consultant)J&J (Shareholder)Lungpacer Merck (Grant/Research Support)scPharma (Consultant)Sedana Spero (Grant/Research Support) Brian Nathanson, PhD, Lungpacer (Grant/Research Support)Merck (Grant/Research Support)Spero (Grant/Research Support) Laura A. Puzniak, PhD, Merck & Co., Inc. (Employee) Andrew F. Shorr, MD, MPH, MBA, Merck (Consultant)"} +{"text": "Children infected with SARS-CoV-2 often have mild or no symptoms, making symptom screening an ineffective tool for determining isolation precautions. As an infection control measure, universal pre-procedural and admission SARS-CoV-2 testing for pediatric patients was implemented in April and August 2020, respectively. Limited data exist on the utility screening programs in the pediatric population. We performed a retrospective cohort study of pediatric patients (birth to 18 years) admitted to a tertiary care academic medical center from April 2020 to May 2021 that had one or more SARS-CoV-2 point-of-care or polymerase chain reaction tests performed. We describe demographic data, positivity rates and repeat testing trends observed in our cohort.A total of 2,579 SARS-CoV-2 tests were performed among 1,027 pediatric inpatients. Of these, 51 tests (2%) from 45 patients (4.3%) resulted positive. Community infection rates ranged from 4.5-60 cases/100,000 persons/day during the study period. Hispanic patients comprised 16% of the total children tested, but were disproportionately overrepresented (40%) among those testing positive . Of 654 children with repeated tests, 7 (0.1%) converted to positive from a prior negative result. Median days between repeat tests was 12 (IQR 6-45), not necessarily performed during the same hospital stay. Five of these 7 patients had tests repeated < 3 days from a negative result, of which only 2 had no history of recent infection by testing performed at an outside facility. Pre-procedural tests accounted for 35% of repeat testing, of which 0.9% were positive. Repeated tests were most frequently ordered for patients in hematology/oncology (35%) and solid organ transplant/surgical (33%) wards, each with < 3% positive conversion rate. Notably, no hematopoietic stem cell transplant patients tested positive for SARS-CoV-2 during the study period.Pediatric SARS-CoV-2 Testing Distributed by Race/EthnicityThe positivity rate of universal pre-procedural and admission SARS-CoV-2 testing in pediatric patients was low in our inpatient cohort. Tests repeated < 3 days from a negative result were especially low yield, suggesting limited utility of this practice. Diagnostic testing stewardship in certain populations may be useful, especially as community infection rates decline.Michael J. Smith, MD, M.S.C.E, Merck (Grant/Research Support)Pfizer (Grant/Research Support) Rebekah W. Moehring, MD, MPH, UpToDate, Inc."} +{"text": "Staphylococcus aureus (MRSA) is a prominent colonizer in cystic fibrosis (CF) patients that causes acute pulmonary exacerbation (APE). Vancomycin is the first line treatment for APE of CF; however, optimal alternatives remain poorly defined. The goal of this study was to determine the safety and efficacy of ceftaroline in CF patients presenting with an APE caused by MRSA.Methicillin-resistant > 10% lower than the patient\u2019s baseline. A positive MRSA culture within 90 days before or 21 days after hospital admission and receipt of > 7 days of either vancomycin or ceftaroline was required for inclusion. Patients were excluded for receipt of a lung transplant, > 48 hours of alternative MRSA therapy, renal replacement therapy, or an APE secondary to fungal or mycobacterium infection. The primary outcome was the return to > 90% of baseline lung function measured by discharge %FEV1 in comparison to baseline %FEV1.This study was a single-center, retrospective cohort study from January 1, 2011 to January 1, 2020. The study included adult CF patients admitted for APE with %FEV1 Clostridioides difficile infection 0 (0%) vs. 1 (3%), P = >0.99; or acute kidney injury 2 (9%) vs. 5 (15%), P = 0.69. Fifty-six patients were included in the analysis . There were no differences in baseline characteristics (Table 1). Eleven (50%) patients in the ceftaroline group and 19 (56%) in the vancomycin group met the primary outcome (P = 0.79) . FEV1 measurements at baseline, admission, and discharge were not different between treatments . Patients treated with ceftaroline had a longer length of stay during hospital admission, 14 days (IQR 13-14) vs.10 days (IQR 7-14), P = 0.01. Other secondary outcomes were similar between the ceftaroline and vancomycin groups, respectfully, including 30-day readmission rate, 6 (27%) vs. 12 (35%), P = 0.57; 30-day mortality, 0 (0%) vs. 2 (6%), P = 0.51; neutropenia 3 (12%) vs. 1 (3%), P = 0.29; Table 1. Baseline characteristics for ceftaroline and vancomycin treated patients1Lumacaftor/ivacaftor, tezacaftor/ivacaftor; 2Piperacillin/tazobactam, aminoglycoside, furosemide, contrast dye, lisinopril, NSAIDs, colistin, phenylephrine; 3Methimazole, sulfasalazine, trimethoprim/sulfamethoxazole; 4Albuterol, hypertonic saline, dornase alpha, azithromycin, ibuprofen, inhaled aminoglycoside, inhaled colistin, corticosteroid; 5Azithromycin, aminoglycoside, fluroquinolone, cephalosporin, carbapenem, piperacillin/tazobactam. Data represents n (%) unless noted. CFTR=cystic fibrosis transmembrane conductance regulator.Figure 1. %FEV1 trend from baseline to discharge in patients treated with ceftaroline or vancomycin(A) Percentage (%) of patients who met the primary outcome in each group; (B) Mean %FEV1 change between ceftaroline (square) and vancomycin (circle) with error bars representing standard deviationsThis study found no difference in safety and efficacy outcomes between vancomycin and ceftaroline. Our small cohort supports ceftaroline as an alternative agent for the treatment of MRSA mediated APE of CF. All Authors: No reported disclosures"} +{"text": "Bambusa oldhamii Munro, known as \u201cgreen bamboo\u201d, is famous for its edible bamboo shoots and fast-growing timber. The green and yellow striped-culm B. oldhamii variety, named B. oldhamii f. revoluta W.T. Lin & J. Y. Lin, is an attractive system for researching the culm color variation of B. oldhamii.The clumping bamboo 1, GA3, GA4, and GA7 was performed using HPLC\u2013MS/MS platforms.Millions of clean reads were generated and assembled into 604,900 transcripts, and 383,278 unigenes were acquired with RNA-seq technology. The quantification of ABA, IAA, JA, GAB. oldhamii f. revoluta. Phytohormone contents, especially GA1 and GA7, were higher in B. oldhamii. Approximately 21 transcription factors (TFs) were differentially expressed between the two groups: the bZIP, MYB, and NF-YA transcription factor families had the most DEGs, indicating that those TFs play important roles in B. oldhamii culm color variation. RNA-seq data were confirmed by quantitative RT-PCR analysis of the selected genes; moreover, phytohormone contents, especially those of ABA, GA1 and GA7, were differentially accumulated between the groups. Our study provides a basal gene expression and phytohormone analysis of B. oldhamii culm color variation, which could provide a solid fundamental theory for investigating bamboo culm color variation.Differential expression analysis showed that 449 unigenes were differentially expressed genes (DEGs), among which 190 DEGs were downregulated and 259 DEGs were upregulated in Dendrocalamus latiflorus, Bambusa oldhamii, and Bambusa chungii; and running bamboos , such as Phyllostachys edulis and fast-growing culm timber (Paeonia suffruticosa (Rosa chinensis (m timber . B.\u00a0oldholorata) , Paeoniaruticosa , and Roshinensis .Basidiomycota phylum; they comprise red to red-violet betacyanins and yellow-orange betaxanthins and jasmonic acid (JA) could promote anthocyanin biosynthesis, while auxin and gibberellin (GA) could inhibit anthocyanin biosynthesis . Abscisike genes . JA treake genes . JA treake genes . The accke genes . The plake genes . GA3 incing time . Treatmeotenoids .MdDFR and MdUFGT and influence fruit coloration were labeled LZ_1, LZ_2, and LZ_3, and those from B.\u00a0oldhamii f. revoluta W.T. Lin & J. Y. Lin (HLZ) were labeled HLZ_1, HLZ_2, and HLZ_3, representing three biological replicates of each type of bamboo. The culm skin samples were frozen in liquid nitrogen immediately for further phytohormone detection, RNA-seq, and relative gene expression. Total RNA was isolated using plant RNA isolation kits .The middle and lower culm internode epidermis samples that were removed from https://www.illumina.com) at Wuhan Metware Biotechnology Co., Ltd. . The output data contained raw reads in fastq format, that were then processed for quality control, including filtering and trimming of low confidence bases, biased nucleotide composition, adapters, duplicates and low-quality reads to acquire clean reads. Trinity (2.6.6) (Library construction and sequencing steps were performed based on the Illumina HiSeq platform for RNA-seq protocols ( (2.6.6) and Cors (2.6.6) were usee-value = 1e\u22125, and the Pfam annotation was performed using the hmmscan command of the HMMER 3.2 package with e-value = 0.01. Transcription factor annotation was performed with iTAK (1.7a) (Nr (NCBI nonredundant protein sequences), Pfam (Protein family), KOG (Protein family), Swiss-Prot, Trembl, KEGG (Kyoto Encyclopedia of Genes and Genomes), and GO (Gene Ontology) were used for gene annotation. The Nr, KOG, Swiss-Prot, Trembl, KEGG, and GO annotations were performed using BLAST (v2.7.1) with an K (1.7a) with defWe used the assembled transcriptome of Trinity as a reference and then mapped the clean reads of each sample to the reference with RSEM software. FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values were calculated to estimate gene expression and abundance after normalization of the mapped reads and transcript lengths. The R package Pheatmap was used to draw a heatmap with normalized log2(FPKM+1) data and clusters of expression patterns with kmeans_k = 10. The color from red to blue indicates gene expression from high to low.After acquiring the abundance information and performing normalization, gene expression between the groups was compared. DESeq2 (1.22.2) was used to calculate the differentially expressed genes between the LZ and HLZ groups, which were corrected with FDR by Benjamini\u2013Hochberg methods. Differentially expressed genes were filtered with the condition of \u2014log2(Fold Change)\u2014 \u2265 1 and FDR <\u00a00.05.\u00ae II Q RT SuperMix for qPCR . Quantitative Real-Time PCR (qRT-PCR) was performed on a LightCycler\u00ae 480 II Real-Time PCR system using the Unique Aptamer\u2122\u00a0qPCR SYBR\u00ae Green Master Mix. The components of the qRT-PCR were as follows: SYBR Premix Ex Taq (2x) (10 \u00b5l), forward primers (0.5 \u00b5M), reverse primers (0.5 \u00b5M), cDNA template (2 \u00b5l), and ddH2O to 20\u00a0\u00b5l. Then, qRT-PCR was performed as follows: initial denaturation at 95\u00a0\u00b0C for 5 min; 40 cycles of denaturation at 95\u00a0\u00b0C for 10 s and annealing at 72\u00a0\u00b0C; and finally, steps for melt-curve analysis . Actin was used as the internal control was performed by Genepioneer Biotechnologies Co., Ltd. using an HPLC\u2013MS/MS platform.The quantification of endogenous abscisic acid (ABA), auxin , jasmonic acid (JA), and gibberellic acid (GAn\u00a0=\u00a09) with a significant difference (p\u00a0<\u00a00.05) according to unpaired t-tests.The enrichment of up- and downregulated genes was determined using GOseq and KOBAS . The corB.\u00a0oldhamii (LZ) is a species of clumping bamboo (B.\u00a0oldhamii variety referred to as B.\u00a0oldhamii f. reboluta W.T. Lin & J. Y. Lin (HLZ) has green culms with yellow stripes of random widths. The culm skin was removed from LZ and HLZ to research the correlation of culm color variation on the phytohormone contents and gene expression levels.g bamboo and it hB.\u00a0oldhamii with three biological replicates marked LZ_1 - LZ_3 and from B.\u00a0oldhamii f. revoluta with three biological replicates marked HLZ_1 - HLZ_3. After the cDNA library was constructed and sequenced, approximately 282 million raw sequence reads were obtained from the RNA-seq experiment, and 267 million clean sequence reads remained after filtering with a Q20 above 98% after quality control was performed. The error correction and GC content are shown as follows . The annotation results produced 38.64%, 70.18%, 44.92%, 69.23%, 40.03%, 57.24%, and 47.26% unigenes annotated in the KEGG, NR, SwissProt, Trembl, KOG, GO, and Pfam databases, respectively. Approximately 274,681 unigenes were annotated in at least one database.All of the unigenes were annotated using seven databases (https:/The unigenes annotated with GO functions were assigned to three main ontologies: molecular function (MF), cellular component (CC), and biological process (BP). The terms cellular process (GO:0009987), metabolic process (GO:0008152), biological regulation (GO:0065007), and response to stimulus (GO:0050896) were the most common BP ontologies; the terms cell (GO:0005623), cell part (GO:0044464), and organelle (GO:0043226) were the most common CC ontologies; and binding (GO:0005488), catalytic activity (GO: 0003824), transporter activity (GO:0005215), and transcription regulator activity (GO:0140110) were the most common MF ontologies . The uniunigene-21666.123476) annotated with metallothionein that was highly expressed in all six samples, and cluster 1 included 8 genes that were more highly expressed in LZ samples. unigene-21666.69211 (mitogen-activated protein kinase kinase kinase ANP1), unigene-21666.134631 (SAUR family protein), unigene-21666.128797 (EREBF-like factor), and others without a specific annotation were included. The upregulated genes in HLZ were classified into 10 clusters , unigene-21666.90795 ; unigene-21666.169778 (serine/threonine-protein kinase PBS1), unigene-21666.167280 (granule-bound starch synthase), unigene-21666.149531 (acyl-[acyl-carrier-protein] desaturase), unigene-21666.125526 (anthranilate O-methyltransferase), unigene-21666.107961 (serine/threonine-protein kinase PBS1), and others without specific annotations , metabolic process (GO:0008152), response to stimulus (GO:0050896), and biological regulation (GO:0065007) terms were the most common BP ontologies; cell (GO:0005623), cell part (GO:0044464), organelle (GO:0043226), and membrane (GO:0016020) were the most common CC ontologies; and binding (GO:0005488) and catalytic activity (GO:0003824) were the most common MF ontologies . For theDifferential expression analysis between the LZ and HLZ groups showed that 190 and 259 DEGs were down- and upregulated in the HLZ culm skin samples. The GO functional enrichment revealed that the downregulated DEGs were more enriched in monocarboxylic acid transport (GO:0008028), transporter complex (GO:1990351), transmembrane transporter complex (GO:1902495), replication fork (GO:0005657), organelle envelope lumen (GO:0031970), lipid transporter activity (GO:0005319), and monocarboxylic acid transmembrane transporter activity (GO:0008028) .The upregulated DEGs were more enriched in biological processes and molecular functions. In particular, the top three terms were L-phenylalanine metabolic process (GO:0006558), L-phenylalanine catabolic process (GO:0006559), and entrainment of the circadian clock (GO:0009649), followed by photoreceptor activity (GO:0009881), phenylalanine ammonia-lyase activity (GO:0045548), NAD(P)H dehydrogenase (quinone) activity (GO:0003955), and carbon-nitrogen lyase activity (GO:0016840) .The downregulated DEGs were enriched in the alpha-linolenic acid metabolism pathway (ko00592) , and theB. oldhamii, the content of endogenous abscisic acid (ABA), auxin , jasmonic acid (JA), and gibberellic acid was detected and gene expression was analyzed with corresponding samples. There were 18 genes whose expression was significantly related to ABA accumulation patterns (1 (7 (1 and GA7 were more enriched in the GO terms of chloride channel complex (GO:0034707), ion channel complex (GO:0034702), protein kinase complex (GO:1902911), transporter complex (GO:1990351), anion channel activity (GO:0005253), chloride channel activity (GO:0005254), phosphatidylinositol bisphosphate binding (GO:1902936), and phosphatidylinositol-3,5-bisphosphate binding (GO:0080025) pathway (ko04712) (unigene-21666.126192 and unigene-21666.239597) and protein FLOWERING LOCUS T (FT) (unigene-54902.0) were up-regulated. Moreover, the expression of genes significantly related to ABA, GA1 and GA7 showed that unigene-21666.90795 was relatively highly expressed in HLZ . All theko04712) . In the d in HLZ . The genunigene-21666.57044 (bHLH), unigene-21666.218036 (MYB-related), and unigene-21666.41135 (SBP) were not detected in the HLZ samples and were only detected in the LZ samples. bHLH transcription factors can interact with MYB transcription factors to regulate anthocyanin biosynthesis (unigene-21666.194872 (FAR1), unigene-21666.98709 (MADS-M-type), unigene-21666.139384 (MYB), and unigene-21666.212035 (TRAF) were not detected in the LZ samples and were only detected in the HLZ samples. MADS-box transcription factors are involved in flower promotion and development, and simultaneous death usually follows after mass production of bamboo flowers were annotated as the transcription factor HY5. The target genes of HY5 participate in many biological signaling processes, such as light signaling, circadian clock, anthocyanin biosynthesis, and chlorophyll biosynthesis , CHI , and FLS (flavonol synthase) to regulate anthocyanin biosynthesis that were members of the MYB transcription factor family. MYB transcription factors could regulate anthocyanin biosynthesis . The psbP protein is required for the photosystem II complex and normal thylakoid architecture in Arabidopsis thaliana (unigene-54902.0 (FT) gene is upregulated in the circadian rhythm (plant) pathway. The FT gene (FLOWERING LOCUS T), a mobile stimulus expressed in leaves and then translocated to the shoot apex, is essential for floral induction in Arabidopsis (unigene-21666.98709 (MADS-M-type) is relatively highly expressed in HLZ. MADS-box genes are essential for flower induction, promotion, and maturation . These proteins are usually divided into four classes: (1) R2R3-MYB, (2) 1R-MYB, MYB-related, and others, (3) 3R-MYB, and (4) 4R-MYB . Among tis genes .unigene-21666.57044, was differentially expressed. These results demonstrate that MYB and bHLH transcription factors could regulate the color variation of bamboos. However, how the crosstalk among the transcription factors and hormone regulation influences color variation still needs further investigation.The family of Basic Helix-Loop-Helix (bHLH) transcription factors contains approximately 60 conserved amino acid domains that bind to the promoter of E-box cis-elements to regulate downstream genes , and theB. oldhamii via combined RNA-seq and endogenous phytohormone content variation analyses. The results showed that bZIP, MYB, HY5, and other differentially expressed transcription factors play a role in B. oldhamii culm color variation. Moreover, phytohormone contents, especially GA1 and GA 7, were more highly accumulated in LZ, but many flower-regulated genes were more highly expressed in HLZ, which indicates that HLZ may flower more rapidly than LZ and that the senescence pathways may be involved in bamboo culm color variation. The transcription factors HY5, MYB, and bHLH participate in culm color variation by regulating pigment biosynthesis pathways to cause bamboo culm color variation, but how the regulatory pathways between transcription factors and phytohormones influence culm color variation still needs to be deeply investigated.This paper focused on investigating the culm color variation of the clumping bamboo 10.7717/peerj.12796/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj.12796/supp-2Supplemental Information 2Click here for additional data file.10.7717/peerj.12796/supp-3Supplemental Information 3Click here for additional data file.10.7717/peerj.12796/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.12796/supp-5Supplemental Information 5Click here for additional data file.10.7717/peerj.12796/supp-6Supplemental Information 6Click here for additional data file.10.7717/peerj.12796/supp-7Supplemental Information 7Click here for additional data file.10.7717/peerj.12796/supp-8Supplemental Information 8Click here for additional data file.10.7717/peerj.12796/supp-9Supplemental Information 9Click here for additional data file.10.7717/peerj.12796/supp-10Supplemental Information 10Click here for additional data file.10.7717/peerj.12796/supp-11Supplemental Information 11Click here for additional data file.10.7717/peerj.12796/supp-12Supplemental Information 12Click here for additional data file.10.7717/peerj.12796/supp-13Supplemental Information 13Click here for additional data file.10.7717/peerj.12796/supp-14Supplemental Information 14Click here for additional data file.10.7717/peerj.12796/supp-15Supplemental Information 15Click here for additional data file.10.7717/peerj.12796/supp-16Supplemental Information 16Click here for additional data file.10.7717/peerj.12796/supp-17Supplemental Information 17Click here for additional data file.10.7717/peerj.12796/supp-18Supplemental Information 18Click here for additional data file.10.7717/peerj.12796/supp-19Supplemental Information 19Click here for additional data file.10.7717/peerj.12796/supp-20Supplemental Information 20Click here for additional data file.10.7717/peerj.12796/supp-21Supplemental Information 21Click here for additional data file.10.7717/peerj.12796/supp-22Supplemental Information 22Click here for additional data file."} +{"text": "Helicobacter pylori (H.pylori) may cause dyspepsia and/or unexplained functional nonspecific, gastrointestinal complaints of the irritable bowel syndrome (IBS) spectrum. Hitherto, in H. pylori infected patients with symptoms of the IBS spectrum the occurrence of additional food intolerance/malabsorption is not evaluated. We used a retrospective analysis of charts from 548 patients who presented with gastrointestinal complaints of the irritable bowel syndrome spectrum. An enzyme-linked IgA immunosorbent assay or histologic evaluation of gastric mucosa were used to detect H. pylori infection. A hydrogen breath (H2) test was performed to evaluate fructose malabsorption (FM) and lactose intolerance (LIT). Serum diamine oxidase value of <10 U/ml and a response to a histamine-reduced diet was used to identify histamine intolerance (HIT). We found 293 patients infected with H. pylori, within these were 58 H. pylori patients with LIT, 23 H. pylori LIT patients with FM and 46 H. pylori LIT patients with HIT. Additionally, 13 H. pylori, lactose- and histamine intolerance patients also had FM. The Kruskal Wallis test and pairwise comparison were used to analyze differences of the area under the curve of expiratory hydrogen. In lactose H2 breath tests compared with LIT-only patients, LIT with H. pylori, LIT and H. pylori with HIT, LIT and H. pylori with FM showed significantly higher exhaled H2 levels (p=0.022). Pairwise comparison demonstrated H. pylori infected patients with LIT exhaled more H2 compared to LIT-only (p=0.029). H. pylori with lactose- and histamine intolerance, and H. pylori with lactose-, histamine intolerance and FM compared to H. pylori-only patients indicated a significantly higher occurrence of stomach pain during lactose H2 breath tests . We demonstrate that LIT patients with high expiratory H2 levels in lactose breath tests may have H. pylori infection and possibly additional food intolerance/malabsorption. Subsequently, besides H. pylori eradication, a dietician is necessary for an individually tailored reduction- or exclusion diet of symptom triggering food components.Infection with AUC, Area under the curve; DAO, diamine oxidase; FM, fructose malabsorption; GI, gastrointestinal; HIT, histamine intolerance; IBS, irritable bowel syndrome; LIT, lactose intolerance.Helicobacter pylori (H. pylori) infection is the most prevalent human pathogen and is present in more than 50 % of worldwide populations. If H. pylori is detected, then an eradication therapy is mandatory. Some association of H. pylori infection and dyspepsia and/or unexplained functional, nonspecific, non-allergic gastrointestinal (GI) complaints of the irritable bowel syndrome (IBS) spectrum is documented. Reduction of these symptoms due to H. pylori eradication has been shown . Based al., 2019).Unexplained functional, nonspecific, non-allergic GI complaints and dyspepsia, including IBS and IBS-like syndromes, are widespread and costly, and a main reason for consultations in primary care settings . GeneraH. pylori-infected patients for additional food intolerance/malabsorption, including CD, FM, HIT and LIT. All included patients presented with dyspepsia/unexplained functional, nonspecific, non-allergic GI complaints of the IBS spectrum. Compared to LIT-only, patients with LIT and H. pylori combined with or without additional food intolerance/malabsorption demonstrated significantly higher expiratory hydrogen (H2) values during lactose tolerance breath tests. In this study we have evaluated H. pylori infection. 293 were infected with H. pylori and in 255 H. pylori was not found. Eradication therapy was started after performance of H2 breath tests and included in this evaluation were only patients who took part in all tests. Patients with alarming symptoms, such as vomiting, rectal bleeding or unintentional weight loss were excluded.During the retrospective evaluation, we found 548 patients who presented with dyspepsia/unexplained functional, nonspecific, non-allergic GI complaints of the IBS spectrum. Main symptoms included abdominal pain, diarrhea, loose stools, bloating, constipation and postprandial fullness. They were examined for additional food intolerance/malabsorption, including CD, FM, HIT, and LIT. In evaluated patients, either an enzyme-linked IgA immunosorbent assay or a histologic evaluation of gastric mucosa was used to detect 2 breath tests were used for LIT and FM testing as described earlier .Hal., 2020). After A thorough anamnesis, concerning abdominal complaints, and a timely relation to the ingestion of food or drinks, including pharmaceutical treatments that might influence dyspepsia/unexplained functional, nonspecific, non-allergic GI complaints of the IBS spectrum was performed. A registered dietitian was consulted to implement and monitor an individualized diet to reduce and/or eliminate symptom-triggering foods. For screening of celiac disease, antibodies against tissue transglutaminase were measured with the anti-tTG IgA ELISA method. The study follows the ethical guidelines of the Declaration of Helsinki and was approved by the Ethical Committee of the Johannes Kepler University in Linz, Austria (No. K-107-16).2 breath tests were calculated and compared with the Kruskal-Wallis test, and pairwise comparison. The Chi-square and the Fisher's exact test were applied for evaluation of symptoms. The level of significance was set to 5 %. The Bonferroni correction was used for multiple testing.Descriptive statistics are presented as medians with interquartile ranges (IQR). The data distribution was assessed with a Shapiro Wilk test. For not normally distributed data non-parametric tests were applied. The areas under the curve (AUC) of exhaled hydrogen during HStatistical analyses were performed with IBM SPSS statistics version 25.0 , and GraphPad Prism version 9.0.0. was used for the generation of figures. H. pylori, male/female 93/200, median age 50 years (IQR 21), age range 17-93 years. We identified 68 patients with H. pylori infection only (12.4 %) - male/female 25/43, median age 56 years (IQR 22), age range 25-93 years. Hydrogen breath tests neither showed LIT nor FM in these patients, and serum DAO values were within normal >10 IU/mL (median 17.9 IU/mL (IQR 12.1), range 10.1-63.4 IU/mL). 58 patients with H. pylori had additional LIT (10.6 %) - male/female 20/38, median age 50 years (IQR 17), age range 22-84 years. Hydrogen breath tests did not show FM in these patients, and DAO values were >10 IU/mL (median 17 IU/mL (IQR 9.5), range 10.5-80 IU/mL). 17 H. pylori patients had only additional FM (3.1 %), male/female 3/14, median age 57 years (IQR 15), age range 23-78 years. Hydrogen breath tests did not show LIT in these patients, and DAO values were >10 IU/mL (median 14.7 IU/mL (IQR 5.6), range 10.7-30.6 IU/mL). However, 47 H. pylori patients had additional HIT (8.6 %), male/female 12/35, median age 50 years (IQR 22), age range 24-91 years. Their DAO values were <10 IU/mL (median 5 IU/mL (IQR 5.2), range 1.5-9.7 IU/mL). Moreover, hydrogen breath tests did show neither LIT nor FM in this group. For this retrospective evaluation, we used 548 patients with IBS spectrum symptoms. We found 293 infected withH. pylori combined with LIT and FM (4.2 %) - male/female 6/17, median age 45 years (IQR 21), and age range 17-82 years. Their DAO values were >10 IU/mL (median 16.6 IU/mL (IQR 9.5), range 12.4-71 IU/mL). In 46 patients we found H. pylori combined with LIT and HIT (8.4 %) - male/female 17/29, median age 43 years (IQR 21), age range 22-83 years. Accordingly, their DAO values were <10 IU/mL (median 6.6 IU/mL (IQR 3.0), range 1.5-9.9 IU/mL) and hydrogen breath tests did not show FM. In 17 H. pylori patients we found additional FM combined with HIT (3.1 %) - male/female 6/11, median age 54 years (IQR 22), age range 28-79 years. Their DAO values were <10 IU/mL (median 4.1 IU/mL (IQR 6.7), range 1.5-10 IU/mL). Hydrogen breath tests did not show LIT in these patients. 13 patients with H. pylori had LIT and FM combined with HIT (2.4 %). Their DAO values were <10 IU/mL (median 7.8 IU/mL (IQR 3.5), range 2.1-9.9 IU/mL). Antibodies against tissue transglutaminase were not detectable in 289 H. pylori patients. Four patients with H. pylori infection demonstrated celiac disease (0.8 %) with elevated tissue transglutaminase antibodies and following histologic diagnosis of the duodenal mucosa as shown in Table 1Additionally, 23 patients showed 2 breath tests. 102 patients (18.6 %) were positive for FM , range 19-91 years). Their DAO values were > 10 IU/mL, with median 16.9 IU/mL (IQR 7.9) and range 10.2-62.5 IU/mL and they did not show LIT in lactose H2 breath tests. In all of these 255 patients neither antibodies against H. pylori nor tissue transglutaminase were detected.In 153 (27.9 %) patients , age range 16-84 years, LIT only was diagnosed. Their DAO values were >10 IU/mL (median 16.6U/ml (IQR 10.2), range 10.2-80 IU/mL) and they did not show FM in fructose HH. pylori, to H. pylori, LIT with HIT and, to H. pylori, LIT with FM demonstrated significantly higher exhaled hydrogen values (p=0.022) , corrected for multiple testing (test statistic 35.206 and standard error 12.48). Due to the low number of H. pylori patients with LIT, FM and HIT these were not included in Figure 1The Kruskal Wallis test for the comparison of the AUCs of LIT-only, to patients with LIT and Figure 1. PairwisH. pylori and LIT patients were abdominal pain, bloating, diarrhea, and increased bowel movements. Other GI symptoms included nausea, heartburn, belching, fullness, and excessive mucus in the throat. Extra-intestinal symptoms were headache, fatigue, vertigo and one eczema. Various double and few triple combinations of these symptoms were indicated. GI-symptoms were indicated by 160 of 279 LIT patients (57 %) during H2 breath tests. As shown in Figure 2H. pylori with LIT and FM, and H. pylori with LIT, FM and HIT compared to H. pylori-only patients demonstrate significantly higher occurrence of stomach pain . Patients with H. pylori-only infection did specify symptoms, although neither bloating nor diarrhea were mentioned during lactose breath tests. All patients >50 years old were screened by colonoscopy and no pathology was present.During performed lactose breath tests patients specified their GI and extra-intestinal symptoms on paper. Indicated GI symptoms by H. pylori in 262 patients, male/female 84/178, median age 51 years (IQR 22), age range 17-93 years, with mean 77.2 IU/mL (range 21-200 IU/mL) IgA antibodies. 63 patients had H. pylori only, male/female 25/38, median age 53 years (IQR 24), age range 25-93 years, and they had mean 73.9 IU/mL (range 21-200 IU/mL) IgA antibodies. 45 patients had H. pylori combined with LIT, male/female 17/28, median age 49 years (IQR 16), age range 26-86 years, with mean 63.8 IU/mL (range 21-200 IU/mL) IgA antibodies. 46 were H. pylori and HIT patients male/female 9/37, median age 49.5 years (IQR 24), age range 24-91 years, they had IgA antibodies mean 65.3 IU/mL (range 22-200 IU/mL). 19 were H. pylori and FM patients, male/female 3/16, and median age 56 years (IQR 17), age range 23-78 years, with mean 74.1 IU/mL (range 21-200 IU/mL) IgA antibodies. 44 were H. pylori and LIT with HIT patients, male/female 17/27, median age 43 years (IQR 18), age range 22-83 years, IgA antibodies with mean 84.9 IU/mL (range 21-200 IU/mL). 19 were H. pylori patients with LIT and FM male/female 6/13, median age 51 years (IQR 21), age range 17-79 years, with mean 111 IU/mL (range 34-200 IU/mL) IgA antibodies. 15 were H. pylori, FM and HIT patients male/female 5/10, median age 54 years (IQR 28), age range 28-58 years, IgA antibodies with mean 95.3 IU/mL (range 24-200 IU/mL). 11 H. pylori, LIT, HIT with FM patients, male/female 2/9, median age 41 years (IQR 32), age range 24-83 years, with mean 92.8 IU/mL (range 25-200 IU/mL) IgA antibodies.The enzyme-linked IgA immunosorbent assay detected IgA antibodies against H. pylori significant different among all groups (p=0.044). Patients with H. pylori, LIT and FM had the highest quantity of IgA antibodies. Pairwise comparisons showed significantly lower antibody values comparing H. pylori, LIT and FM to H. pylori and LIT (p=0.005), to H. pylori and HIT (p=0.005), to H. pylori with FM (p=0.034) and, to H. pylori only (p=0.016). However, correction for multiple testing showed no significance.As shown in Figure 32 (p=0.39) comparing all groups (data not shown). Fructose malabsorption breath tests (n=159), using the Kruskall-Wallis test for evaluation of AUCs, showed no differences of exhaled HSee also the Supplementary data.From a clinical perspective, considerable overlap exists between food intolerance/ malabsorption and unexplained dyspepsia/ functional, nonspecific, non-allergic GI complaints and disorders, including IBS and IBS-like disorders. Currently, IBS is classified as a functional gastrointestinal disorder, according to Rome IV criteria, but new disease models are being proposed continuously Talley, 2020). Food i020. FoodH. pylori, the hormone gastrin and the biogenic amine histamine are main stimulants of gastric acid secretion . In patal., 2018). Due toal., 2018), we useal., 2020).H. pylori infection and its association with deficiencies of micronutrients, minerals and vitamins was reported . A relaley, 2020). Succesal., 2000). Additial., 2020). Severakas, 2020). FinallH. pylori patients with dyspepsia/functional, nonspecific, non-allergic GI complaints of the IBS spectrum, besides a thorough anamnesis, it seems useful to include examinations for food intolerance/malabsorption with FM- and lactose intolerance H2 breath tests, serum DAO determination and screening for celiac disease . 2 production. Therefore, the clinical diagnosis of LIT and FM is primarily performed with H2 breath tests. Impaired degradation of ingested histamine due to an anticipated gastrointestinal DAO deficiency, promotes HIT. So far, serum DAO is not established to reflect GI histamine-degrading DAO activity , fermen al. 2021). Noneth al. 2021; Mu\u0161i\u010d e al. 2021). Althou al. 2021).Generally, only few studies have reported on combined occurrence of food intolerance/malabsorption. Nonetheless, more than 30 % of patients with dyspepsia/ unexplained functional, nonspecific, non-allergic GI complaints and carbohydrate intolerance/malabsorption may have combinations of these . Next tH. pylori, the presence of additional food intolerance/ malabsorption induced significantly increased expiratory H2 values . In thikas, 2020).H. pylori patients when this infection is combined with LIT and FM or with LIT, FM and HIT . HoweveH. pylori infection may have additional food intolerance/malabsorption. Moreover, we show that in LIT the presence of H. pylori infection causes significantly higher expiratory H2 values in lactose tolerance breath tests. Subsequently, besides eradication, a registered and experienced dietician is essential for the development of an individually tailored reduction- or exclusion diet of symptom triggering food components.In conclusion, we describe, that patients with dyspepsia/unexplained functional, nonspecific, non-allergic GI complaints of the IBS spectrum having LIT and We are indebted to Mrs. Katharina Schnedl, Cardiff University, Cardiff, UK, who performed English language corrections.Wolfgang J. Schnedl received speaking honoraria from Sciotec. The other authors have no conflict of interest."} +{"text": "Mycobacterium smegmatis mc2 155 host. The genome of JeTaime is 75,099 bp (142 predicted genes), and that of Luna22 is 53,730 bp (87 predicted genes). Both phages exhibit Siphoviridae morphology.The mycobacteriophages JeTaime (E cluster) and Luna22 (Q cluster) were isolated from soil in Providence, Rhode Island, and Charleston, South Carolina, respectively, using a Mycobacterium smegmatis mc2 155, as described in the SEA-PHAGES Phage Discovery Guide program through the Howard Hughes Medical Institute (HHMI) . The phale tails .de novo into a single contig using Newbler v2.9 (https://cpt.tamu.edu/computer-resources/pause), genome termini with 3\u2032 cohesive overhangs were identified, as follows: JeTaime, 5\u2032-CGCTTGTCA-3\u2032; Luna22, 5\u2032-TAAGCCGCGCGGTA-3\u2032. The Promega Wizard DNA cleanup system was used to extract DNA from phage lysates, and sequencing libraries were prepared with a NEBNext Ultra II DNA library prep kit v3). Libraries for each phage were independently generated, and genomes were sequenced separately. Sequencing was performed at the Pittsburgh Bacteriophage Institute on an Illumina MiSeq system (MiSeq reagent kit v3) , TOPCONS v2 (https://phagesdb.org/DNAMaster). All programs used default settings.Each genome was annotated on PECAAN using GLPCONS v2 , and thePCONS v2 . tRNAs aPCONS v2 and tRNAPCONS v2 , and comKT222941) genomes. The other 103 published E-cluster members typically contain endonuclease VII and/or DNA methylase in that genome region. Also, the JeTaime gp89 (unidentified function) is rare, occurring in only one other E-cluster bacteriophage, 244 (GenBank accession number DQ398041). Whole-genome BLASTn alignment (NC_004681.1) (99.24% identity and 96% coverage), Phrux (GenBank accession number NC_021309.1) (99.20% identity and 95% coverage), and ShereKhan (GenBank accession number MH513983.1) (99.10% identity and 95% coverage).JeTaime is an E-cluster phage with 142 predicted protein-coding genes (54 assigned functions), while Luna22 is a Q-cluster phage with 87 predicted protein-coding genes (42 assigned functions) . Intereslignment revealedMT114159) and New Zealand (GenBank accession number MK494095) retain >98% nucleotide sequence identity to the Luna22 genome. Also, the genome of Giles (GenBank accession number EU203571) is nearly identical to that of Luna22 (99.96% identity and 100% coverage) \u201321; the Individual GenBank and SRA numbers are listed in"} +{"text": "Defining the metabolic syndrome (MetS) in children remains challenging. Furthermore, a dichotomous MetS diagnosis can limit the power to study associations. We sought to characterize the serum metabolite signature of the MetS in early childhood using high-throughput metabolomic technologies that allow comprehensive profiling of metabolic status from a biospecimen.In the Family Atherosclerosis Monitoring In earLY life (FAMILY) prospective birth cohort study, we selected 228 cases of MetS and 228 matched controls among children age 5 years. In addition, a continuous MetS risk score was calculated for all 456 participants. Comprehensive metabolite profiling was performed on fasting serum samples using multisegment injection-capillary electrophoresis-mass spectrometry. Multivariable regression models were applied to test metabolite associations with MetS adjusting for covariates of screen time, diet quality, physical activity, night sleep, socioeconomic status, age, and sex.Compared to controls, thirteen serum metabolites were identified in MetS cases when using multivariable regression models, and using the quantitative MetS score, an additional eight metabolites were identified. These included metabolites associated with gluconeogenesis (glucose (odds ratio (OR) 1.55 [95% CI 1.25\u20131.93]) and glutamine/glutamate ratio (OR 0.82 [95% CI 0.67\u20131.00])) and the alanine-glucose cycle ), amino acids metabolism (tyrosine (OR 1.33 [95% CI 1.10\u20131.63]), threonine (OR 1.24 [95% CI 1.02\u20131.51]), monomethylarginine (OR 1.33 [95% CI 1.09\u20131.64]) and lysine (OR 1.23 [95% CI 1.01\u20131.50])), tryptophan metabolism (tryptophan (OR 0.78 [95% CI 0.64\u20130.95])), and fatty acids metabolism (carnitine (OR 1.24 [95% CI 1.02\u20131.51])). The quantitative MetS risk score was more powerful than the dichotomous outcome in consistently detecting this metabolite signature.A distinct metabolite signature of pediatric MetS is detectable in children as young as 5\u2009years old and may improve risk assessment at early stages of development.The online version contains supplementary material available at 10.1186/s12916-021-02162-7. Obesity and related metabolic sequelae such as type 2 diabetes are increasingly prevalent among children in high-income countries , 2. The N-oxide or TMAO) Additional file 2. Supplemental Methods [IDEFICS MetS definitions and MSI-CE-MS data processing]Additional file 3: Table S1. [Serum metabolites characteristics]Additional file 4: Table S2. [Unadjusted and intermediate adjusted models]Additional file 5: Table S3. [Pathway analysis]Additional file 6: Fig. S2. [Clustering of MetS cases]"} +{"text": "Orgyia postica. The complete mitochondrial genome was a circular molecule with 15,258\u2009bp in full-length, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes (rRNAs). The nucleotide composition of O. postica mitogenome was A: 37.6%, C: 7.9%, G: 14.8%, T: 39.7%. In addition, the results of the phylogenetic analysis indicate that O. postica had the closest relationship with Laelia suffusa. Our study will contribute to further research on the evolution of Lymantriidae and the identification of larva species.The high-throughput sequencing method was used for the first time to determined complete mitochondrial genome of Orgyia postica Walker, 1855 (Lepidoptera: Lymantriidae) is a crop pest that mainly damages stamens and leaves, It mainly damages more than 70 crops such as tea, cotton, strawberries, loofah, asparagus, radishes, peaches, grapes, pears, citrus, mangoes, causing poor growth, reduced production and even death . The specimen was deposited at the Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety (Voucher specimen number: FDSW202318382-1r) and identified by the head of herbarium Mr Li (Email: lijunlijun1981@163.com). Genomic DNA was extracted using Genomic DNA Kit and constructed the libraries with an average length of 350\u2009bp using the NexteraXT DNA Library Preparation Kit . Then the libraries were sequenced on Illumina Novaseq 6000 platform, 9.23\u2009Gb clean data was assembled by SPAdes (version 3.11.0) . The original sequencing data were uploaded to the NCBI database (https://www.ncbi.nlm.nih.gov/sra/) with the accession number SRR15041082. The complete mitochondrial genome was assigned Genbank accession number MW355619.The sample of O. postica is a closed circular molecule of 15,258\u2009bp, consisting of complex I (NADH dehydrogenase), complex IV (cytochrome C oxidase), ATP synthase, transfer RNAs, ribosomal RNAs and other genes, with the base content of A 37.6%, C 7.9%, G 14.8%, and T 39.7%. The A\u2009+\u2009T content is 77.3%, showing a strong AT skew. The genome encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). With the gene rrnS as a starting point, the gene order of complete mitochondrial is rrnS, trnV-TAC, rrnL, trnL-TAG, ND1, trnS-TGA, CYTB, ND6, trnP-TGG, trnT-TGT, ND4L, ND4, trnH-GTG, ND5, trnF-GAA, trnE-TTC, trnS-GCT, trnN-GTT, trnR-TCG, trnA-TGC, ND3, trnG-TCC, COX3, ATP6, ATP8, trnD-GTC, trnK-CTT, COX2, trnL-TAA, COX1, trnY-GTA, trnC-GCA, trnW-TCA, ND2, trnQ-TTG, trnI-GAT, trnM-CAT. Among these genes, the shortest and longest were 62 (trnR-TCG) and 1692\u2009bp (ND5), and the average gene length was 390.78\u2009bp.The mitochondrial genome of O. postica within lepidoptera. 21 published complete mitochondrial genome sequences from lepidoptera including Euproctis pseudoconspersa (KJ716847.1), Euproctis cryptosticta (KY996558.1), Anarta trifolii (MN715147.1), Sesamia inferens (JN039362.1), Spodoptera littoralis (MT816470.1), Spodoptera litura (JQ647918.1), Spodoptera frugiperda (KM362176.1), Spodoptera exigua (JX316220.1), Spodoptera exempta (MT906792.1), Parasa consocia (KX108765.1), Aglaomorpha histrio (KY800518.1), Spilarctia subcarnea (KT258909.1), Lemyra melli (KP307017.1), Hyphantria cunea (GU592049.1), Amata formosae (KC513737.1), Euproctis similis (KT258910.1), Euproctis seitzi (MN916588.1), Lymantria dispar (FJ617240.1), Laelia suffusa (MN908152.1), Lymantria umbrosa (KY923066.1) and Lymantria sugii (MT265380.1) species were collected and aligned with O. postica by MAFFT7.037 (Katoh and Standley, L. suffusa has the closest relationship with O. postica.To confirm the phylogenetic position and understand the relationship of"} +{"text": "Women aged 65 and older experience nearly three-fourths of the 2 million osteoporotic fractures annually in the US, yet whether accelerometer-measured volumes and intensities of physical activity and sedentary behavior (SB) are associated with reduced fracture risk is understudied. We investigated associations of accelerometer-measured light physical activity (LPA), moderate-to-vigorous physical activity (MVPA), sedentary time (ST), and mean sedentary bout duration (MBD) with incident clinical fractures in the WHI OPACH cohort. Participants without prior hip fracture wore the ActiGraph GT3X+ for 7 days between May 2012-April 2014 and were followed through March 2020 for incident clinical fracture (N=711). Cox models estimated hazard ratios (HR) and 95% confidence intervals (CI), adjusting for age, race-ethnicity, education, alcohol, smoking, height, weight, falls history, RAND-36 physical function, diabetes, thiazide use, prescription osteoporotic therapy, and age at menopause. The HR(95% CI) across MVPA quartiles was 1.00(reference), 1.15(0.93-1.41), 0.90(0.72-1.13), and 0.79(0.61-1.02); p-trend=0.01. The HR(95% CI) for a one-interquartile range increment in MVPA (42 minutes/day) was 0.86(0.76-0.97). Associations were modified by prescription osteoporotic therapy and varied in magnitude by age, BMI , and race-ethnicity . LPA, ST, or MBD were not associated with incident fractures. These data suggest that MVPA may reduce and not increase fracture risk and that LPA and SB do not increase fracture risk."} +{"text": "Scientific Reports 10.1038/s41598-021-81257-w, published online 18 January 2021Correction to: This Article contains an error, where Supplementary Data files Supplementary Data 1.Supplementary Data 2.Supplementary Data 3."} +{"text": "Monarda (family Lamiaceae) contains 22 species of which three are native to southern Alabama, M. citriodora, M. fistulosa, and M. punctata. Several species of Monarda have been used in traditional medicines of Native Americans, and this present study is part of an ongoing project to add to our understanding of Native American pharmacopeia. Plant material from M. citriodora, M. fistulosa, and M. punctata was collected in south Alabama and the essential oils obtained by hydrodistillation. The essential oils were analyzed by gas chromatographic techniques to determine the chemical compositions as well as enantiomeric distributions. The compounds thymol, carvacrol, p-cymene, and their derivatives were the primary terpenoid components found in the essential oils. The known biological activities of these compounds are consistent with the traditional uses of Monarda species to treat wounds, skin infections, colds, and fevers.The genus Monarda L. (Lamiaceae) species, 18 of which occur in the United States [Monarda species native to south Alabama, namely Monarda citriodora Cerv. ex Lag., Monarda fistulosa L., and Monarda punctata L. and carvacrol (RIdb = 1296). The other major components were p-cymene (RIdb = 1024) and thymol methyl ether (RIdb = 1239).The M. citriodora essential oils revealed the (+)-enantiomers to be the major stereoisomers for \u03b1-thujene, \u03b1-pinene, \u03b2-pinene, \u03b1-phellandrene, \u03b4-3-carene, \u03b1-terpinene, cis-sabinene hydrate, trans-sabinene hydrate, \u03b1-terpineol, \u03b1-copaene, (E)-\u03b2-caryophyllene, and germacrene D. On the other hand, the (\u2212)-enantiomer was dominant for \u03b2-phellandrene, borneol, carvone, and \u03b4-cadinene. Limonene showed variation in the enantiomeric distributions with (+)-limonene in 26.7%, 63.3%, and 57.3% for aerial parts #1, #2, and roots essential oils, respectively. Likewise, linalool also showed variation with (+)-linalool of 71.9%, 49.7%, and 50.1%. (+)-Terpinen-4-ol was the predominant enantiomer in the aerial parts essential oils (60.2% and 58.5%), but (\u2212)-terpinen-4-ol (79.1%) was dominant in the root essential oil.Chiral gas chromatography\u2013mass spectrometry (GC-MS) analysis of the Monarda fistulosa essential oils were obtained in 2.66\u20134.83% yields as bright orange oils. The chemical compositions of the essential oils from the aerial parts of M. fistulosa are summarized in db = 1289) dominated the compositions with lesser quantities of p-cymene , limonene , carvacrol , and thymoquinone . Curiously, sample #3, although qualitatively similar, had a very different quantitative composition with thymoquinone as the most abundant constituent (41.3%) followed by p-cymene (21.9%), but with lower concentrations of thymol (8.9%) and carvacrol (1.6%).M. citriodora essential oils, in M. fistulosa essential oils, the (+)-enantiomer was the major for \u03b1-thujene, \u03b1-pinene, \u03b2-pinene, \u03b1-phellandrene, \u03b4-3-carene, \u03b1-terpinene, cis-sabinene hydrate, trans-sabinene hydrate, \u03b1-terpineol, \u03b1-copaene, (E)-\u03b2-caryophyllene, and germacrene D, while the (\u2212)-enantiomer was predominant for \u03b2-phellandrene and borneol. (\u2212)-Limonene (97.4\u201399.5%) and (\u2212)-linalool (62.1\u201362.5%) dominated in all three M. fistulosa samples. (+)-Camphene (100%), (+)-sabinene (58.4\u201359.0%), and (+)-terpinen-4-ol (63.2\u201363.3%) were also dominant.As was observed in M. punctata aerial parts gave bright orange essential oils in 0.781% and 0.658% yield. The most abundant components in the essential oils were thymol , p-cymene , \u03b3-terpinene , and carvacrol (see Hydrodistillation of two samples of wild-growing .1%) see .M. punctata essential oils were analogous to those observed for M. citriodora and M. fistulosa oils with the exception of limonene, which was virtually racemic in sample #1, but 100% (\u2212)-limonene in sample #2.The enantiomeric distributions of terpenoids in Monarda citriodora and M. fistulosa have been introduced throughout temperate regions of the world as popular herbal medicines as well as ornamentals [M. citriodora in the present study were rich in both thymol and carvacrol, whereas essential oils from Europe and Asia were dominated by thymol with much lower concentrations of carvacrol. Monarda fistulosa, in particular, showed wide variation with at least three different chemotypes in this study fit into the thymol-rich chemotype. Interestingly, there was a high concentration of thymoquinone in M. fistulosa sample #3, with concomitant lower concentrations of thymol and carvacrol. Thymol was reported as the major component of M. punctata in two old reports [M. punctata from China was rich in thymol (75.2%), which is in agreement with the aerial parts essential oils from Alabama.amentals ,5,6. The reports ,12. Consp-cymene are consistent with the traditional uses of Monarda spp. to treat skin infections, wounds, fevers, and respiratory problems. Thymol [p-cymene [The high concentrations of thymol, carvacrol, and . Thymol , carvacr. Thymol , and p-cp-cymene have demp-cymene ,35, as wp-cymene . Thymol p-cymene and carvp-cymene , in addip-cymene , have shp-cymene . Furtherp-cymene and carvp-cymene have shop-cymene .Monarda species. Several investigations on the enantiomeric distributions in other members of the Lamiaceae have been reported in the literature, however. There seems to be much variation in the enantiomeric distribution of monoterpenoids across the family. Consistent with what was observed in Monarda essential oils, (+)-\u03b1-pinene was the major enantiomer found in Coridothymus capitatus [Rosmarinus officinalis [Lepechinia heteromorpha [Ocimum canum, and Ocimum kilimandscharicum [C. capitatus [Monarda essential oils. On the other hand, (\u2212)-\u03b2-pinene dominates in R. officinalis [Lepechinia mutica [Mentha \u00d7 piperita) and spearmint (Mentha spicata) have shown nearly racemic mixtures of \u03b1- and \u03b2-pinenes [Monarda essential oils. In marked contrast, however, (\u2212)-\u03b1-phellandrene and (+)-\u03b2-phellandrene predominated in L. mutica essential oil [M. fistulosa essential oil, peppermint (M. piperita) and spearmint (M. spicata) essential oils [C. capitatus [O. canum, and O. kilimandscharicum [R. officinalis) essential oil [C. capitatus [Salvia schimperi [Pycnanthemum incanum [O. canum, and O. kilimandscharicum [Lavandula angustifolia [R. officinalis [As far as we are aware, this work presents the first chiral analysis of terpenoid constituents of apitatus , Rosmariicinalis , Lepechiromorpha , Ocimum charicum . Likewisapitatus as well icinalis and Lepea mutica . The ess-pinenes . (+)-\u03b1-Ptial oil . (\u2212)-Limial oils whereas apitatus , O. canucharicum , and a ntial oil . (+)-Linapitatus , Salvia chimperi , Pycnant incanum , O. canucharicum , whereasstifolia and R. oicinalis .Monarda citriodora was cultivated in Kirkland Gardens, Newville, AL, USA from seeds . The cultivated Monarda spp. were grown in loamy clayey-sand and fertilized with chicken manure, kelp meal, and bone meal at planting in full sun. The aerial parts of M. citriodora were collected from separate plants on separate occasions . The roots of M. citriodora were obtained from plant #2.Monarda fistulosa was cultivated in Kirkland Gardens, Newville, AL, USA from seedlings as above. The aerial parts of three different plant samples were collected on 25 June 2020.Monarda punctata was collected from wild-growing plants near Newville, AL, USA ; the edge of a planted pine forest, disturbed grassland, full/partial sun, sandy-clay soil that had been intentionally burned (prescribed burn) 1.5 years before collection. The aerial parts of two different plants were collected on 1 June 2020.M. citriodora (SKL61820), M. fistulosa (SKL72020), and M. punctata (SKL9620). The Monarda plant materials were allowed to dry in the shade for several days, the air-dried plant materials were pulverized and subjected to hydrodistillation using a Likens-Nickerson apparatus with continuous extraction with dichloromethane (Plants were identified by S.K. Lawson and a voucher specimen of each plant was deposited in the University of Alabama in Huntsville Herbarium (HALA); voucher numbers for omethane .The essential oils were analyzed by gas chromatography\u2013mass spectrometry (GC-MS), gas chromatography with flame ionization detection (GC-FID), and chiral GC-MS as previously reported .n-alkanes. Compounds identified by comparison of the MS fragmentation and retention indices with those in the databases [Shimadzu GCMS-QP2010 Ultra, ZB-5ms GC column, GC oven temperature 50 \u00b0C\u2013260 \u00b0C (2 \u00b0C/min), 1-\u03bcL injection of 5% solution of EO in dichloromethane . Retention indices (RIs) were determined with reference to a homologous series of atabases ,8,9,10.Shimadzu GC 2010, FID detector, ZB-5 GC column, GC oven temperature 50 \u00b0C\u2013260 \u00b0C (2.0 \u00b0C/min). The percent compositions were determined from raw peak areas without standardization.Shimadzu GCMS-QP2010S, Restek B-Dex 325 column, GC oven temperature 50 \u00b0C\u2013120 \u00b0C (1.5 \u00b0C/min) then 120 \u00b0C\u2013200 \u00b0C (2.0 \u00b0C/min), 0.1 \u03bcL injection of 5% solution of EO in dichloromethane . The enantiomeric distributions were determined by comparison of retention times with authentic samples obtained from Sigma-Aldrich . Relative enantiomer percentages were calculated from peak areas.Monarda growing in south Alabama. In addition, the enantiomeric distribution of terpenoids was also carried out. This work illustrates the wide variation in essential oil compositions based on geographical location as well as variations in enantiomeric distribution. It would be interesting to compare enantiomeric distributions for Monarda essential oils from other geographical locations and for other Monarda species. Nevertheless, the phenolic monoterpenoids thymol and/or carvacrol were found to dominate the compositions of M. citriodora, M. fistulosa, and M. punctata and support the traditional medicinal uses of these plants.This study presents, for the first time, analyses of the essential oils of three species of"} +{"text": "Ferrigenium kumadai An22T (= JCM 30584T = NBRC 112974T = ATCC TSD-51T) is a microaerophilic iron oxidizer isolated from paddy field soil and belongs to the family Gallionellaceae. Here, we report the complete genome sequence of F. kumadai An22T, which was obtained from the hybrid data of Oxford Nanopore long-read and Illumina short-read sequencing. Ferrigenium kumadai, isolated from paddy soil has been described (F. kumadai An22T (= JCM 30584T = NBRC 112974T = ATCC TSD-51T).Microaerophilic iron-oxidizing bacteria, which are capable of oxidizing ferrous iron (Fe) under circumneutral pH and microoxic conditions, are a key player in the Fe redox cycle in environments . Howeverescribed . Here, wT and DNA preparation were described previously were removed with Sickle v1.33 (https://github.com/najoshi/sickle). Short ONT reads were filtered out with Filtlong v0.2.0 (https://github.com/rrwick/Filtlong), and then error correction of the reads was carried out on FMLRC v0.1.2 (Betaproteobacteria. Genes were annotated with DFAST v10 (Sideroxydans lithotrophicus ES-1 (GenBank accession number CP001965.1), Rhodopseudomonas palustris TIE-1 (CP058907.1), Mariprofundus ferrooxydans PV-1T (DS022294.1), and Acidithiobacillus ferrooxidans ATCC 23270T (CP001219.1). An orthologous gene cluster table among the genome sequences used was created was found as a sole candidate gene of Fe(II) oxidation.The genome size of strain An22F. kumadai An22T was deposited to the DDBJ database under the accession number AP019536.1. The raw sequencing data were deposited under BioProject accession number PRJDB7995 and SRA accession numbers DRR168795 and DRR168796.The genome sequence of"} +{"text": "Elevated resistance rates have been reported in ICUs. Aztreonam (ATM) combined with avibactam (AVI) is being developed for use against drug-resistant Enterobacterales (Ebact), including metallo-\u03b2-lactamase (MBL)-positive isolates. We examined the activity of ATM-AVI and comparators against Ebact isolates collected from geriatric patients in ICU and non-ICU wards as part of the ATLAS surveillance program.Escherichia coli, Klebsiella spp. and Proteus mirabilis with ATM or ceftazidime MIC >1 \u00b5g/mL.23754 non-duplicate Ebact isolates were collected in 53 countries in Asia/Pacific (excluding mainland China and India), Europe, Latin America, and Middle East/Africa from patients \u226565 years with lower respiratory tract (LRTI), urinary tract (UTI), skin and soft tissue (SSTI), intra-abdominal (IAI), and bloodstream (BSI) infections. Susceptibility testing was performed by CLSI broth microdilution and values interpreted using CLSI 2021 breakpoints. PCR and sequencing were used to determine the \u03b2-lactamase genes present in isolates with meropenem MIC >1 \u00b5g/mL, and 90 values were up to 32-fold higher. ATM-AVI MIC90 values were within one doubling-dilution across all studied strata (0.12-0.25 \u00b5g/mL), were comparable to or lower than for meropenem in all strata, and were 2 to \u22659 dilutions lower than all other tested comparators. MBL-positive Ebact were found in 1.5% of LRTI (n=91), 1.2% of UTI (n=70), 1.1% of SSTI (n=52), 1.3% of BSI (n=49), and 0.7% of IAI isolates (n=22). MBL-positive rates were higher among ICU than non-ICU isolates . ATM-AVI MIC90 values were 0.5 \u00b5g/mL against MBL-positive isolates from all ward and infection types except SSTI (MIC90 0.25 \u00b5g/mL) and BSI (MIC90 1 \u00b5g/mL), 2-4 dilutions lower than tigecycline and at least 5-10 dilutions lower than the other comparators.Susceptibility of the studied comparator agents was generally slightly lower among Ebact from BSI than other infection types (Table). Susceptibility was also generally lower among Ebact from ICU than non-ICU wards by up to 10 percentage points, and MICResults TableATM-AVI could provide a valuable therapeutic option for treatment of infections caused by Ebact in patients \u226565 years old in both ICU and non-ICU wards.Sibylle Lob, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Krystyna Kazmierczak, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Francis Arhin, PhD, Pfizer, Inc. (Employee) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)"} +{"text": "Rhizopus species is the primary fungi responsible for 70% of mucormycosis cases.During the second wave of the COVID-19 pandemic, an unusual increase in cases of mucormycosis was observed in India, owing to immunological dysregulation caused by the SARS-CoV-2 and the use of broad-spectrum antibiotics, particularly in patients with poorly controlled diabetes with ketoacidosis to have contributed to the rise, and it has been declared an epidemic in several states of India. Because of the black colouring of dead and dying tissue caused by the fungus, it was dubbed \"black fungus\" by several Indian media outlets. In this study, attempts were taken to unmask novel therapeutic options to treat mucormycosis disease. Rhizopus delemar such as CotH3, Lanosterol 14 alpha-demethylase and Mucoricin which plays a crucial role in the virulence of Mucorales. Initially, we explored the physiochemical, structural and functional insights of proteins and later using AutoDock Vina, we applied computational protein\u2013ligand binding modelling to perform a virtual screening around 300 selected compounds against these three proteins, including FDA-approved drugs, FDA-unapproved drugs, investigational-only drugs and natural bioactive compounds. ADME parameters, toxicity risk and biological activity of those compounds were approximated via in silico methods. Our computational studies identified six ligands as potential inhibitors against Rhizopus delemar, including 12,28-Oxamanzamine A, vialinin B and deoxytopsentin for CotH3; pramiconazole and saperconazole for Lanosterol 14 alpha-demethylase; and Hesperidin for Mucoricin. Interestingly, 12,28-Oxamanzamine A showed a maximum binding affinity with all three proteins .We chose three important proteins from the In summary, our investigation identified 12,28-Oxamanzamine A, vialinin B, deoxytopsentin, pramiconazole, saperconazole and hesperidin as potent bioactive compounds for treating mucormycosis that may be considered for further optimisation techniques and in vitro and in vivo studies.The online version contains supplementary material available at 10.1186/s42269-022-00704-4. Rhizopus species are the most common fungi in the order of Mucorales responsible for over 70% of mucormycosis cases and diabetic ketoacidosis. SARS-Cov-2, in addition to mucormycosis, is a fatal combination that has caused a considerable number of deaths, particularly in India acts as a fungal ligand for host cell GRP78 and mediates pathogenic host-cell interactions. The presence of CotH3 in Mucorales also explained why DKA patients with high GRP78 levels are more susceptible to mucormycosis require a thorough examination of their structure and function, which will bring unique insights into the development of an effective, low-cost medicine with minimal side effects. Therefore, the current study aims to collect 300 compounds that exhibit antiviral, antifungal, antibacterial and antimicrobial properties have been identified through different literature reviews, and it was screened against CotH3, Lanosterol 14 alpha-demethylase and Mucoricin by applying several in silico tools, viz., protein modelling, binding pocket prediction, molecular docking, ADME and drug-likeness screening, bioactivity prediction and toxicity prediction , cytochrome P450 enzyme Lanosterol 14 alpha-demethylase (ACCESSION: EIE87079) and ricin-like toxin Mucoricin (ACCESSION: EIE81863) . Various physicochemical properties of the CotH3, Lanosterol 14 alpha-demethylase and Mucoricin were calculated using ExPasy's ProtParam tool NPS@ .All three proteins were subjected to 3D modelling. CotH3 was modelled via SWISS-MODEL 3.0 was used to predict probable binding pockets of the proteins , part of MGLTools program alpha helix, 13.95% (36 residues) extended strand, 2.71% (7 residues) beta turn and 43.02% (111 residues) random coil, while Lanosterol 14 alpha-demethylase showed to have 49.80% (254 residues) alpha helix, 10.78% (55 residues) extended strand, 3.14% (16 residues) beta turn and 36.27% (185 residues) random coil. Similarly, Mucoricin exhibited 5.44% (8 residues) alpha helix, 40.14% (59 residues) extended strand, 14.97% (22 residues) beta turns and 39.46% (58 residues) random coil.Bacillus cereus CotH kinase (PDB ID: 5JD9) \u2009=\u20090.02\u00a0nM) and acts as a promising anti-allergic agent . The compound displayed potent low nanomolar inhibitory activity against MRSA PK with significant concomitant selectivity over human PK orthologues -dien-3, \u03b2-6\u03b1-diol and 14\u03b1-methylergosta-5,7,22,24(28)-tetraenol , Parsiguine (B), Haliclonacyclamine B (C), Vialinin B (D), 6-Deoxymanzamine X (E), Natamycin (F), Olorofim (G), Deoxytopsentin (H), Manzamine E (I), Fascioquinol A (J). Figure S2. 2D visualisation of docking analysis of Lanosterol 14 alpha-demethylase binding with Pramiconazole (A), 12,28-Oxamanzamine A (B), Fascioquinol D (C), Saperconazole (D), Nakadomarin A (E), Plakinamine A (F), Fascioquinol C (G), Parsiguine (H), Hesperidin (I), Epoxyazadiradione (J). Figure S3. 2D visualisation of docking analysis of Mucoricin binding with 12,28-Oxamanzamine A (A), Manzamine A (B), Parsiguine (C), Halicyclamine A (D), Tetrahydrohaliclonacyclamine A (E), Phaeosphenone (F), 6-Deoxymanzamine X (G), Goniodomin A (H), Hesperidin (I), Stelletin A (J).Additional file 2: Table S1. The variants of mucormycosis and the symptoms associated with the disease .Additional file 3: Data 1. Binding affinities of all bioactive compunds with our three target proteins."} +{"text": "Literature on SARS-CoV-2 infection in cancer patients is scarce in Latin America. This population seems to have a higher risk for adverse outcomes. This study aims to correlate clinical characteristics with outcomes in patients with cancer in a referral center in Mexico.We included patients with cancer and confirmed SARS-CoV-2 infection, from April, 19 to December 30, 2020, at the Instituto Nacional de Cancerolog\u00eda, Mexico. Clinical information was obtained from medical and epidemiological records. We conducted a descriptive analysis. For the association between variables with hospitalization, invasive mechanical ventilation (IMV), and mortality; univariate and multivariate logistic regression was performed; odds ratios and 95% confidence intervals were calculated.Four hundred thirty-three patients were included; 268 (62%) were female, the median age was 55 years. One hundred thirty-five (31%), 130 (30%), and 93 (21%) patients had obesity, hypertension, and diabetes mellitus (DM), respectively. Three hundred forty-one (79%) had solid cancer; 82 (19%) hematological malignancy (HM), and 10 (2%) were under evaluation for cancer diagnosis. One hundred seventy (39%) had advanced or metastatic cancer. One hundred ninety-eight (46%) patients were hospitalized. Risk factors were: age (p= 0.001); woman (p=0.019); HM (p=0.050) and advanced or metastatic cancer (p= 0.041). Fourty-five (10%) patients required IMV. Age (p=0.018); DM (p=0.041); C-Reactive Protein (p= 0.002), and LDH (p= 0.033) were associated with invasive mechanical ventilation. Mortality within 30-days after diagnosis was 19% (82 cases). Associated characteristics were: age (p=0.041); lymphocytes (p=0.049); creatinine (p=0.005) and albumin (p=0.001).In this study, patients with cancer showed higher mortality, need of hospitalization, and invasive mechanical ventilation compared with groups of patients without cancer. We did not find an increased risk in mortality for hematological malignancies. Although our cohort was younger than others previously reported, age was a strong predictor of adverse outcomes. Variables associated with IMV and death were similar to those previously described in cancer patients with COVID-19.All Authors: No reported disclosures"} +{"text": "Despite well-established guidelines for urinary tract infection (UTI) treatment, prescribing practices vary. We examined the association between inappropriate (IA) or suboptimal (SO) antibiotic (AB) prescribing (RX) and hospitalization, healthcare resource use (HRU), and costs among patients with uncomplicated UTI (uUTI) in the US.Table 1) were assessed from Optum claims data during index episode (within 28 days of index) and 12-month follow-up.This retrospective cohort study used linked Premier Healthcare/Optum claims data from female outpatients (\u2265 12 years old) with a uUTI diagnosis . Patients with complicated UTIs were excluded. HRU and costs between patients with IA/SO and appropriate and optimal (AP&OP) AB RX (defined in Table 1. Definitions of appropriateness of AB RXTable 2). During index episode, mean ambulatory care and pharmacy claims were significantly higher for IA/SO versus AP&OP AB RX , and total HRU cost per patient was higher for IA/SO (&2616) versus AP&OP AB RX . During follow-up, 267 (9.7%) patients with IA/SO AB RX had a UTI-related emergency department (ED) visit versus 202 (6.5%) patients with AP&OP AB RX (p < 0.001). Mean UTI-related HRU costs were significantly higher for IA/SO (&5048) versus AP&OP AB RX . After adjusting for patient characteristics, patients with IA/SO AB RX were 40% more likely than those with AP&OP AB RX to have a UTI-related ED visit during follow-up (Table 3). Adjusted HRU costs for IA/SO AB RX (vs AP&OP) were numerically higher for index uUTI episode (by &1772), and UTI-related (by &1102) and all-cause (by &1528) charges during follow-up .Of 5870 patients, 1856 (31.6%) had IA and 1255 (21.4%) had SO AB RX. Patients with IA/SO AB RX (47.1%) were older and more likely to have a Charlson Comorbidity Index score > 0 than those with AP&OP AB RX , stratified by appropriateness of AB RX at index and during follow-upIA/SO AB RX was associated with higher overall and UTI-related HRU and costs during index episode and 12-month follow-up, highlighting a need for education on applying prescription guidelines and the use of culture-based RX.Rena Moon, MD, Premier Applied Sciences, Premier Inc. (Employee) Alen Marijam, MSc, GlaxoSmithKline plc. Fanny S. Mitrani-Gold, MPH, GlaxoSmithKline plc. Daniel C. Gibbons, PhD, GlaxoSmithKline plc. Alex Kartashov, PhD, Premier Applied Sciences, Premier Inc. (Employee) Ning Rosenthal, MD, Premier Applied Sciences, Premier Inc. Ashish V. Joshi, PhD, GlaxoSmithKline plc."} +{"text": "Oncogene (2020) 39:5616\u20135632, 10.1038/s41388-020-01388-8, published online 13 July 2020Correction to: Following the publication of the above article, the authors noted two errors in Fig. p\u2009<\u20090.05, ** p\u2009<\u20090.01.Supplemental Fig. 2: Overexpression of LINC01503 promotes NPC cell growth, migration, and invasion in vitro. (a) Relative expression of LINC01503 in 5-8F and HONE1 cells transfected with LINC01503-expressing plasmid and empty vector. (b) LINC01503 overexpression promoted cell growth of 5-8F and HONE1 cells as shown by CCK-8 assays. (c) LINC01503 overexpression facilitated cellular survival effects as evaluated by colony formation assays. (d) LINC01503 overexpression accelerated the movement of 5-8F and HONE1 cells as assessed by wound healing assays. Scale bar, 100 \u03bcm. (e) LINC01503 overexpression promoted the migration and invasion ability of 5-8F and HONE1 cells as determined by transwell assays. Scale bar, 100\u2009\u03bcm. * The original article has been corrected.Supplementary Fig. 2"} +{"text": "Hemophagocytic lymphohistiocytosis (HLH) is a disease that can affect both children and adults. HLH can be categorized as primary or secondary. Secondary HLH (sHLH) may be secondary to various viral infections. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infection is a pandemic with multi-system involvement. HLH in COVID-19 positive patients is a recognized entity. However, in post-COVID-19 patients who have recovered and are negative by serological tests and reverse transcription-polymerase chain reaction test may present with sHLH due to dysregulation of the immune system. We highlight this unusual finding of post-COVID-19 sHLH in two cases, who were diagnosed by the new revised H-score. Hemophagocytic lymphohistiocytosis (HLH) is a lethal disorder of varying etiology and encompasses a wide range of diseases. Familial HLH (FHLH) and immune-related HLH constitute the primary HLH spectrum whereas infections, drug-related and transplantation, malignancies, and macrophage activation syndrome (MAS) constitute the secondary HLH (sHLH) spectrum . LaboratCase 12 was 88%, and the temperature was 40\u030aC. On examination, pallor was present. Bilateral crepitations and rhonchi were present in respiratory system auscultation. The cardiovascular system was unremarkable and central nervous system examination showed no focal neurological deficit. Ultrasonography of the whole abdomen revealed hepatosplenomegaly. High-resolution computed tomography (HRCT) thorax showed CO-RADS category 6 and CT severity of 15/25. Bone marrow aspirate showed evidence of hemophagocytosis and was hospitalized for 1.5 months. At presentation, the patient was conscious, alert, and oriented.\u00a0Her blood pressure was 96/58 mmHg, pulse rate was 118 beats per minute, respiratory rate was 33/min and SPO3 /\u00b5L with differential leukocyte count (DLC) of N87L10M03E0, and platelet count of 20x103 /\u00b5L. Biochemical investigations revealed serum urea of 61 mg/dL (reference range [RR]: 17-45 mg/dL), serum creatinine of 0.9 mg/dL (RR: 0.6-1.4 mg/dL), D-dimer of 1.58 mg/L (RR: 0-0.5 mg/L), aspartate aminotransferase (AST) of 76 IU/L (RR: 5-40 IU/L), alanine aminotransferase (ALT) of 98 IU/L (RR: 5-55 IU/L), alkaline phosphatase (ALP) of 137 IU/L (RR: 20-140 IU/L), total bilirubin of 2.5 mg/dL (RR: up to 1.2 mg/dL), direct bilirubin of 1.3 mg/dL (RR: 0-0.2 mg/dL), IL-6 of 11.56 pg/mL (RR: 5-15 pg/mL), fibrinogen of 2.3 g/L (RR: 2-4 g/L), vitamin B12 of 489.5 pg/mL (RR: 160-950 pg/mL), ferritin of 170.2 ng/L (RR:12-250 ng/L), and C-reactive protein of 77mg/L (RR: 0-10 mg/L). Direct Coombs test was negative and indirect cold antibodies titer was more than 256 (RR: less than 164). All viral markers, anti-nuclear antibody (ANA), and glucose-6-phosphate dehydrogenase (G6PD) were negative. The H-score estimated as per the H-score of 2014 was 213 points with a probability of sHLH to be 93% to 96% of 3.3 g%, total leukocyte count (TLC) of 18.3x10According to the protocols of our institute, the patient was isolated and started on intravenous steroids (dexamethasone acetate 10 mg/day), low molecular weight heparin (LMWH), antibiotics, and oxygen support. Considering the deranged kidney function, strict monitoring and adequate hydration were provided along with four units of whole blood transfusion. The patient developed congestive cardiac failure during the hospital stay and oral diuretics were initiated. The patient responded to treatment without the addition of etoposide and was hemodynamically stable. She was discharged after four weeks of hospital stay. The patient was reviewed after 14 days and was stable.Case 23 /\u00b5L with DLC N86L10M02E02, and platelet count of 60x103 /\u00b5L. Biochemical investigations showed serum ferritin of 188.0 ng/mL (RR: 7-140 ng/mL), IL-6 of 1,057 pg/mL (RR: 1-5 pg/mL), D-dimer of 1.76 mg/L (RR: 0-0.5 mg/L), AST of 182 IU/L (RR:10-40 IU/L), ALT of 77 IU/L (RR:10-40 IU/L), ALP of 77 IU/L (RR: <350 IU/L), C-reactive protein of 62.1 mg/L (RR: 0.02-14.5 mg/L), and fibrinogen of 2.13 g/L (RR: 2-4 g/L). Malaria, scrub typhus, HBsAg, anti-HCV were negative. Bone marrow aspirate revealed features of hemophagocytosis with increased iron , diarrhea, and vomiting for two days. The patient had no previous episodes in the past and developmental milestones were achieved at his age normally. On examination of muscle tone, neck control was decreased. A possible diagnosis of post-viral encephalitis was considered. The patient was positive for SARS-CoV-2 virus by RT-PCR and was admitted to COVID-19 designated hospital. He was discharged after testing negative for the SARS-CoV-2 virus.\u00a0After two weeks of discharge, he presented with the above symptoms but was negative for COVID-19 by RAT and RT-PCR. MRI brain showed features suggestive of viral encephalitis with atrophy of cerebral hemispheres and peritrigonal white matter hyperintensities. Laboratory findings revealed Hb of 7.1 g%, TLC of 7.3x10The H-score estimated as per the H-score of 2014 was 239 points with a probability of sHLH to be 98% to 99%\u00a0, laboratory , and histological parameters , which was modified in 2004 . The HLHThe optimal cut-off for a diagnosis of HLH was considered to be 169 by Fardet et al. with 93% sensitivity and 86% specificity . In our HLH in COVID-19 positive patients is reported in various case reports ,15. HoweSARS-CoV-2 infection is a recent pandemic with important complications inherent to its multisystemic affections.\u00a0Recent information\u00a0about etiopathogenesis, clinical signs\u00a0and symptoms, and treatment protocols are getting highlighted. sHLH is a condition primarily occurring in COVID-19 positive patients; however, sHLH in post-COVID-19\u00a0patients is rare. Immune dysregulation following infection by the SARS-CoV-2 virus may be the prime reason for sHLH in such patients. We highlighted two such post-COVID-19\u00a0patients who were negative for COVID-19 at the time of presentation but were diagnosed as cases of sHLH based on the H-score."} +{"text": "Otostigmus (O.) lewisiO. (O.) beroni Lewis, 2001. The latter was also recorded from Jilong County by O. (O.) beroni from Jilong County with new materials of O. (O.) lewisi from Jiacha County, we reaffirm that O. (O.) lewisi is a valid species. Otostigmus Porat, 1876 currently comprises about 56 species (O. (O.) aculeatus Hasse, 1887, O. (O.) astenus , O. (O.) beroni Lewis, 2001, O. (O.) lewisi Song, Gai, Song & Zhu, 2005, O. (O.) martensi Lewis, 1992, O. (O.) politus Karsch, 1881, O. (O.) scaber Porat, 1876, and O. (O.) xizangensis Niu, Li & Di, 2021.The subgenus species . Among t species : O. (O.)Otostigmus (O.) lewisi was identified as a synonym of O. (O.) beroni (O. (O.) lewisi has complete paramedian sutures on sternites 4\u201319, sternite 21 has a shallow medial longitudinal depression, and the coxopleural process is short. However, the sternite paramedian sutures in O. (O.) beroni are incomplete, and the coxopleural process is long. These differences were not shown in the corresponding figures of O.lewisi is a junior subjective synonym of O.beroni\u201d. We would also like to highlight that all type materials used in the O. (O.) lewisi were sub-adults.) beroni . AccordiMHBU .Studied materials were collected by hand and preserved in 75% ethanol. All studied materials in this paper were examined under a stereomicroscope (Motic K700). Photographs and measurements were taken using a Leica Stereomicroscope (M205 A). The standard terminology followed Otostigminae Kraepelin, 1903Subfamily Otostigmus Porat, 1876Genus Taxon classificationAnimalia\ufeffLewis, 200160ED176E-3416-5BCE-9AFD-79035CE69070Otostigmusberoni Lewis, 2001: 22; MHBU-SoJL1608050101\u2013Ar.-MHBU-SoJL1608050120: Jilong Town, Jilong (Gyirong) County, Xizang (Tibet), China, 28.4370\u00b0N, 85.2568\u00b0E, 5/8/2016, leg. Zhiyong Di. Ar.-MHBU-SoJL21080101: Jilong Town, Jilong (Gyirong) County, Xizang (Tibet), China, 28.4350\u00b0N, 85.2570\u00b0E, 1/8/2021, leg. Zhiyong Di. Housed in MHBU.Ar.-Maximum length 57 mm. Antennae 18 articles, the basal 2.25 to 2.40 glabrous dorsally Fig. . With 4 MHBU-SoJL1608050101). Length.Pigmentation : body color yellow-brown; legs and antennae yellow; cephalic plate, tergites 1\u20132, tergites 20\u201321 and penultimate and ultimate legs blue-green : cephalic plate blue-green, tergites blue-brown, penultimate legs and ultimate legs yellow with blue middle part in each segment, the other legs yellow : with complete paramedian sutures from 3 to 20, marginate from 7 to 21 : smooth, with incomplete paramedian sutures from 5 to 19 : L1\u201316 and L18\u201319 with 2 tarsal spurs, L1\u20134, left L5 and right L6 with 1 tibial spur and L1 with 1 femoral spur.Ultimate prefemur with 4 ventro-lateral, 2 ventro-medial, 3 medial, 2 dorso-medial spines and 1 corner spine Fig. .There are multiple differences among individuals as addressed below. The number of teeth of forcipular tooth plates 4+4 (11 specimens), 5+5 (6 specimens), 3+3 (2 specimen) or 3+4 (2 specimens). Coxopleural process with 4\u20137 spines . One tibial spur on L1\u20134 (8 specimens), L1\u20135 (5 specimens), L1\u20132 (2 specimens), L1\u20133 (3 specimens), or L1\u20136 (2 specimens). Two tarsal spurs on 1 to 18 or 19 pairs of legs; 1 tarsal spur on subsequent to penultimate legs. Ultimate legs without tarsal spur. Ultimate legs prefemur with 11\u201314 spines and Nepal Fig. .Taxon classificationAnimalia\ufeffSong, Gai, Song & Zhu, 2005 80F267B0-9D5B-5FC6-A29B-D11CC060ACBEOtostigmuslewisiMHBU-SoJC1908060301\u2013 Ar.-MHBU-SoJC1908060307: Jiacha County (Gyaca County), Xizang (Tibet), China, 29.0857\u00b0N, 92.3430\u00b0E, 6/8/2019, leg. Zhiyong Di. Ar.-MHBU-SoJC1608DX01: Jiacha County, Xizang, China, 29.1188\u00b0N, 92.6969\u00b0E, 12/8/2016, leg. Zhiyong Di. Ar.-MHBU-SoJC1608120401: Jiacha County, Xizang, China, 29.1387\u00b0N, 92.6880\u00b0E, 12/8/2016, leg. Zhiyong Di. Housed in MHBU.Ar.-Maximum length 77 mm. Antennae 17\u201320 articles, basal 2.2\u20133 glabrous dorsally Fig. . With 3 O. (O.) lewisi holotype described in The O. (O.) lewisi and O. (O.) beroni; however, the description and figures of O. (O.) lewisi were not consistent in O. (O.) martensi (O. (O.) lewisi (O. (O.) lewisi (O. (O.) martensi (Following O. (O.) lewisi is similar to O. (O.) beroni, and distinguished O. (O.) lewisi from the latter by the length of coxopleural process and the shape of the ultimate sternite. Because O. (O.) lewisi in O. (O.) lewisi is a junior subjective synonym of O. (O.) beroni beroni .O. (O.) lewisi reported by O. (O.) lewisi described previously were sub-adults.The characteristics of the holotype of MHBU-SoJC1908060301). Length.Pigmentation : cephalic plate and tergites yellow with light green; antennae and legs yellow; penultimate legs and ultimate legs green : antennae light blue mainly, cephalic plate and tergites brownish, penultimate legs and ultimate legs yellow with blue middle part in each segment, the rest of the legs yellow : with complete paramedian sutures from 4 to 20; marginate from 6 to 21 : smooth, with incomplete paramedian sutures from 3 to 4, complete paramedian sutures from 5 to 19 : L2\u20139, right L11 and left L12 with 2 tarsal spurs; 1 tarsal spur on subsequent to penultimate legs; L1 and left L2 with 1 tibial spur and right L1 with 1 femoral spur.The left prefemur with 1 corner spine, 3 ventro-lateral spines, 1 ventro-medial spines, 2 medial spines, 1 dorso-medial spine; the right prefemur with 2 corner spines, 5 ventro-lateral spines, 2 ventro-medial spines, 7 medial spines, 3 dorso-medial spines Fig. .Adult and juvenile individuals differ primarily in body length and pigmentation Figs , 3A, B. Found under stones in arid mountain bush Fig. .China (Xizang) Fig. .Otostigmus, namely, O. (O.) beroni, O. (O.) lewisi, O. (O.) martensi and O. (O.) xizangensis, were reported in Xizang, China lewisi can be easily distinguished from O. (O.) beroni using the following characteristics: (1) larger average body length: 73 mm in O. (O.) lewisi (average of 2 adults), versus 48 mm in O. (O.) beroni (average of 5 adults); (2) body color (live): primarily brownish cephalic plate and tergites in O. (O.) lewisi, and blue-green cephalic plate and blue-brown tergites in O. (O.) beroni lewisi 3+3 in 5 specimens or 4+4 in 4 specimens versus O. (O.) beroni 4+4 in 11 specimens or 5+5 in 6 specimens; (4) the number of tibial spurs on legs: O. (O.) lewisi with one tibial spur on legs 1\u20132 in 6 specimens or on legs 1 in 3 specimens. In contrast, O. (O.) beroni with one tibial spur on legs 1\u20134 in 8 specimens or 1\u20135 in 5 specimens; (5) the number of tarsal spurs on legs: O. (O.) lewisi with 2 tarsal spurs on legs 1(2)\u20139(13), with no regularity. In O. (O.) beroni, however, 2 tarsal spurs on legs 1\u201318(19); (6) the length of coxopleural process: coxopleural process of O. (O.) lewisi is shorter than that of O. (O.) beroni. The specimens described by Only four species of the genus ina Fig. , geograponi Fig. ; (3) theO. (O.) beroni and O. (O.) martensi. The main difference between O. (O.) beroni and O. (O.) martensi are as follows: (1) the number of teeth of tooth plates: O. (O.) martensi 3+3, whereas, O. (O.) beroni 4+4 or 5+5; (2) the number of spines on the coxopleural process: O. (O.) martensi coxopleural process with 1 apical spine, 1 lateral spine and 1 dorsal spine. In contrast, O. (O.) beroni coxopleural process with 2\u20133 apical spines, 1\u20132 lateral spines, and 1\u20132 dorsal spines; (3) spurs on legs: O. (O.) martensi L1\u20134 or 5 with 2 tarsal spurs, whereas O. (O.) beroni L1\u201319 with 2 tarsal spurs, L20 with 1 tarsal spur (O. (O.) lewisi and O. (O.) martensi are obviously different species.The most geographically close species of this genus in Xizang, China are sal spur . Given tO. (O.) beroni in China) and Zhangmu Town martensi in China)) is about 78 km, and the distance between Jilong Town and Jiacha County lewisi in China) is about 714 km. No species of the genus Otostigmus was found in the area between Jilong Town (or Zhangmu Town) and Jiacha County. The habitat of O. (O.) beroni in Jilong Town is more humid than the habitat of O. (O.) lewisi in Jiacha County lewisi is a valid species.The distance between Jilong Town (the locality of nty Fig. . Based o"} +{"text": "Oniscidea) are the most diverse group of troglobionts in caves of continental Portugal. They occur in all karst regions of Portugal, play a major role in decomposition of organic matter in caves and may act as umbrella species for the conservation of all other cave-adapted invertebrates.Terrestrial isopods (We present the IUCN Red List profiles for the cave-adapted terrestrial isopods from continental Portugal, based on recent distribution data from caves. Cave-adapted fauna have a high and global conservationist interest . Cave-adOniscidea) evolved to be the only truly terrestrial crustaceans . The maps were generated in the open source software QGIS 3.14.16, with the layer of the natural protected areas of Portugal (Extent of occurence (EOO) and area of occupancy (AOO) were calculated using the Geospatial Conservation Assessment Tool (GeoCAT) with an approximation to the standard IUCN 2 km \u00d7 2 km cells : Suppl. materials 2Basis of EOO and AOO: Known habitat extent2.Basis (narrative): Both the extent of occurrence (EOO) and area of occupancy (AOO) are 4 kmMin Elevation/Depth (m): 380Trichoniscoidesbellesi is known from Algar do Javali Cave in the Montejunto karst massif (Range description: t massif .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Trichoniscoidesbellesi occurs in a single cave : A total of three specimens have been collected in the type locality .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesTrichoniscoidesbellesi was found in the deepest and most thermally insulated parts of the cave, at 10 m depth (Habitat (narrative): m depth .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 1.7 mm , 1.8 mm Generation length (yr): 1Dependency of single sp?: UnknownTrichoniscoidesbellesi is a blind and depigmented troglobiont species : species . It shara, 2012) and Roncra, 2013 ; an unde\u00f1o, 2010 and a neEucalyptus intensive plantations, which substituted the original native vegetation and is located 50 m from a road, 1.6 km from a quarry and 2.9 km from the closest village.Justification for threats: The cave entrance is surrounded by Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas2.2. Agriculture & aquaculture - Wood & pulp plantations3.2. Energy production & mining - Mining & quarrying4. Transportation & service corridorsThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas2.2. Agriculture & aquaculture - Wood & pulp plantations3.2. Energy production & mining - Mining & quarrying4. Transportation & service corridorsJustification for conservation actions: Even though this cave is protected under legislation by the \u201cRede Natura 2000\u201d , this raConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelTrichoniscoidesbroteroiScientific name: Species authority: Vandel, 1946AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: TrichoniscidaeFamily: Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 3Basis of EOO and AOO: Known habitat extent2.Basis (narrative): The extent of occurrence (EOO) and area of occupancy (AOO) are both 4 kmMin Elevation/Depth (m): 100Trichoniscoidesbroteroi is a troglobiont isopod known from Alqueves Cave, located in the Sic\u00f3 karst area (Range description: rst area . This carst area .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Trichoniscoidesbroteroi is known from a single cave : Alqueves Cave is considered a pre- and proto-historic site. It is a natural funerary cave as bone fragments and other human artifacts were there found, testifying to its human occupation at the end of the Neolithic period, beginning of the Chalcolithic . This caTrend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 4 mm , 4.5 mm Generation length (yr): 1Dependency of single sp?: UnknownTrichoniscoidesbroteroi is a blind and depigmented troglobiont species and a single cave endemic (Porcelliocavernicolus (Ecology and traits (narrative): endemic . It sharrnicolus .Justification for threats: The entrance to the cave is located within a fully urbanised area, more specifically in the middle of a roundabout . This caThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.3. Residential & commercial development - Tourism & recreation areas4. Transportation & service corridors9.1. Pollution - Domestic & urban waste water9.5. Pollution - Air-borne pollutantsThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.3. Residential & commercial development - Tourism & recreation areas4. Transportation & service corridors9.1. Pollution - Domestic & urban waste water9.5. Pollution - Air-borne pollutantsTrichoniscoidesbroteroi : Suppl. materials 4Basis of EOO and AOO: Known habitat extent2 and the area of occupancy (AOO) is 40 km2.Basis (narrative): The extent of occurrence (EOO) is 217.7 kmMin Elevation/Depth (m): 95Max Elevation/Depth (m): 485Trichoniscoidesmeridionalis is recorded from 10 caves distributed along the Estremenho karst massif: Algar do Vale da Pena, Algar do Z\u00e9 de Braga, Alcobertas, Lapa da Ch\u00e3 de Cima, Moinhos Velhos, Almonda, Papagaio, Algar do Burro, Algar do Pena and Algar do Ladoeiro (Range description: Ladoeiro .EOO (km2): 217.7Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 40Number of locations: 10Trichoniscoidesmeridionalis occurs in ten caves : A total of 43 specimens have been collected: six in Moinhos Velhos cave, five in Algar do Vale do Pena, five in Algar do Burro, one in Algar do Z\u00e9 de Braga, fifteen in Algar do Ladoeiro, ten in Almonda and one in Papagaio Caves .Number of subpopulations: 10Trend: Decline (inferred)Extreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): The caves are located at an altitude ranging from 95 to 485 m a.s.l. . Amonda Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 2 mm , 2.5 mm Generation length (yr): 1Dependency of single sp?: UnknownTrichoniscoidesmeridionalis is a blind, depigmented troglobiont that is adapted to life in the underground (Ecology and traits (narrative): erground . This sperground .Justification for threats: Almonda Cave is located 50 m from a factory that extracts water from a subterranean river and 420 m from a village, which has many agricultural fields. Algar do Ladoeiro's Cave entrance is 840 m from the closest urbanisation. The Moinhos Velhos Cave is the largest show cave of Portugal with around 140,000 visitors per year. Alcobertas Cave has also been subject to structural alterations with the intention to transform it into a show cave during the last century and it is exploited for tourism by a local association . The subThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.1. Agriculture & aquaculture - Annual & perennial non-timber crops3.2. Energy production & mining - Mining & quarrying3.3. Energy production & mining - Renewable energy6.1. Human intrusions & disturbance - Recreational activities9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.1. Agriculture & aquaculture - Annual & perennial non-timber crops3.2. Energy production & mining - Mining & quarrying3.3. Energy production & mining - Renewable energy6.1. Human intrusions & disturbance - Recreational activities9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: Almonda Cave is classified, since 1993, as a Property of Public Interest (IIP) and protected due to its archaeological heritage . The arcConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelTrichoniscoidesouremensisScientific name: Species authority: Vandel, 1946AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: TrichoniscidaeFamily: Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 5Basis of EOO and AOO: Known habitat extent2.Basis (narrative): Both the extent of occurrence (EOO) and area of occupancy (AOO) are 4 kmTrichoniscoidesouremensis is only recorded from Lapa da Salgada Cave, located in the F\u00e1tima Plateau, in the eastern part of the Estremenho karst massif (Range description: t massif .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Trichoniscoidesouremensis is recorded from a single cave : Lapa da Salgada Cave is composed of a main underground gallery and the floor is mostly covered by flowstone and clay, with a few bat guano deposits.Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 3.5 mm Generation length (yr): 1Dependency of single sp?: UnknownTrichoniscoidesouremensis is classified as a troglobiont species, being blind and depigmented. It is a single cave endemic (Ecology and traits (narrative): endemic .Justification for threats: The cave entrance is located 270 m from a road in which trucks transport goods from warehouses 600 m away. The cave is also located 1 km away from the closest town.Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas4. Transportation & service corridors9.1. Pollution - Domestic & urban waste water9.2. Pollution - Industrial & military effluentsThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas4. Transportation & service corridors9.1. Pollution - Domestic & urban waste water9.2. Pollution - Industrial & military effluentsJustification for conservation actions: Measures need to be put in place in order to protect the habitat and species from the disturbances caused by truck movements and proximity to the urban areas.Conservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelTrichoniscoidesserraiScientific name: Species authority: Cruz, 1993AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: TrichoniscidaeFamily: Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 6Basis of EOO and AOO: Known habitat extent2.Basis (narrative): Both the extent of occurrence (EOO) and area of occupancy (AOO) are 4 kmMin Elevation/Depth (m): 577Trichoniscoidesserrai is only recorded from Santo Adri\u00e3o Cave, located in the palaeokarst of Vimioso in north-eastern Portugal : 4Trend: UnknownCauses ceased?: UnknownCauses understood?: YesCauses reversible?: YesExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Trichoniscoidesserrai occurs in a single cave : Santo Adri\u00e3o mines are located at 580 m a.s.l. in the Municipality of Miranda do Douro, District of Bragan\u00e7a . The cavTrend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 3.6 mm ; 4.2 mm Generation length (yr): 1Dependency of single sp?: UnknownTrichoniscoidesserrai is classified as a blind, depigmented troglobiont, adapted to life in the underground (Ecology and traits (narrative): erground .Justification for threats: The cave entrance is in the border of an active quarry, very close to a road .Threat type: OngoingThreats: 3.2. Energy production & mining - Mining & quarrying4.1. Transportation & service corridors - Roads & railroads9.2. Pollution - Industrial & military effluentsThreat type: OngoingThreats: 3.2. Energy production & mining - Mining & quarrying4.1. Transportation & service corridors - Roads & railroads9.2. Pollution - Industrial & military effluentsJustification for conservation actions: Even though this cave is protected under legislation by the \u201cRede Natura 2000\u201d , this spConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelTrichoniscoidessicoensisScientific name: Species authority: Reboleira & Taiti 2015AnimaliaKingdom: ArthropodaPhylum: Class: MalacostraIsopodaOrder: TrichoniscidaeFamily: Trichoniscoidessicoensis is blind and depigmented and it can be distinguished from all species of the genus because the male pereopod 7 merus has a lobe on the mid-sternal margin, the male pleopod 1 exopod has a broadly rounded outer margin and two unequal setae, the endopod has a fusiform distal article with a distinct circular suture in the middle and the male pleopod 2 endopod has a thickset distal article bearing two short triangular lobes and two setae at the apex or Photo(s): Fig. 1Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 7Basis of EOO and AOO: Known habitat extentBasis (narrative): The extent of occurrence (EOO) is 129.2 km\u00b2 and the maximum estimated area of occupancy (AOO) is 20 km\u00b2.Min Elevation/Depth (m): 20Max Elevation/Depth (m): 380Trichoniscoidessicoensis is recorded from six caves located in the Sic\u00f3 karst area: Cer\u00e2mica, Santa Maria da Estrela, Soprador do Carvalho, Algarinho, Arrifana and S\u00e3o Sim\u00e3o (Range description: \u00e3o Sim\u00e3o .EOO (km2): 129.2Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 20Number of locations: 6Trichoniscoidessicoensis is known from six caves : The largest population was found in the type locality Cer\u00e2mica Cave, where a higher number of specimens has been collected, followed by Santa Maria da Estrela Cave and then Soprador do Carvalho, Algarinho, Arrifana and S\u00e3o Sim\u00e3o Caves .Number of subpopulations: 6Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesTrichoniscoidessicoensis inhabits the deepest and isolated parts of caves of the Sic\u00f3 karst area, found up to a maximum altitude of 380 m a.s.l. The easternmost locality is Soprador do Carvalho Cave and the westernmost is Santa Maria da Estrela Cave, its distribution being limited at the north by the Arrifana Cave and at the south by the Cer\u00e2mica Cave. Cer\u00e2mica Cave opens at 355 m a.s.l., it has a horizontal development of 120 m, a depth of 21 m : of 21 m and is t of 21 m . Santa M of 21 m . Sopradoalleries .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 3.5 mm , 3.9 mm Generation length (yr): 1Dependency of single sp?: UnknownTrichoniscoidessicoensis is classified as a troglobiont species, blind and depigmented. It is endemic to the Sic\u00f3 karst area (Ecology and traits (narrative): rst area . Most ofrst area .Eucalyptus intensive plantations. It is located 270 m from a road, 550 m from an animal farm, 1.6 km from the closest village and 3.6 km from a quarry. Santa Maria da Estrela Cave is located 86 m from a touristic site called Monstro das Bolachas, 230 m from the Nossa Senhora da Estrela viewpoint, 250 m from the closest urbanised area, 80 m from the road, 220 m from agricultural fields and 2.6 km from two quarries. Soprador do Carvalho Cave is surrounded by agricultural lands distances and is located 67 m from the closest house and 1.4 km from a quarry. This cave is also affected by touristic activities, as people who visit the cave walk all over the habitat : Suppl. materials 8Basis of EOO and AOO: Known habitat extent2.Basis (narrative): Both the extent of occurrence (EOO) and area of occupancy (AOO) are 4 kmMin Elevation/Depth (m): 122Trichoniscoidessubterraneus is only recorded from Alta do Cabe\u00e7o dos Mosqueiros Cave, located in Carvalhal de Aljubarrota, the western part of the Estremenho karst massif (Range description: t massif .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Trichoniscoidessubterraneus occurs in a single cave : This cave is currently part of the Geocaching network; therefore, it is subject to human disturbance without regulation.Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 3 mmGeneration length (yr): 1Dependency of single sp?: UnknownTrichoniscoidessubterraneus is classified as a blind and depigmented troglobiont species (Ecology and traits (narrative): species .Justification for threats: This cave is frequently visited by geocachers looking for the geocache installed inside the cave.Threat type: OngoingThreats: 6.1. Human intrusions & disturbance - Recreational activitiesThreat type: OngoingThreats: 6.1. Human intrusions & disturbance - Recreational activitiesJustification for conservation actions: Measures to limit the number of visits to the cave should be implemented in order to ensure the integrity of the habitat and the survival of this species.Conservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelMetatrichoniscoidessalirensisScientific name: Species authority: Reboleira & Taiti 2015AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: TrichoniscidaeFamily: Metatrichoniscoidessalirensis can be distinguished from all species of the genus because the pleopod 1 exopod of the male has two long distal setae of subequal length and its pleopod 2 endopod has a thickset distal article, ending in a thinner sinuous part with a beak-like small lobe medially directed : Suppl. materials 9Basis of EOO and AOO: Known habitat extentBasis (narrative): Both the extent of occurrence (EOO) and area of occupancy (AOO) are 4 km\u00b2Min Elevation/Depth (m): 60Metatrichoniscoidessalirensis is only known from Salir Cave, a single isolated cave located in the western border of Caldas da Rainha Typhonic Valley : 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Metatrichoniscoidessalirensis is only recorded from one cave : A total of seven specimens have been collected in the type locality .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): Salir Cave was discovered in the 1960s by the labour force of a quarry. It is located near the sea, at an altitude of 60 m a.s.l. The substrate is mostly composed of flowstone, clay and marine sand that can be found in the deepest parts of the cave .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 2.2 mm Generation length (yr): 1Dependency of single sp?: UnknownMetatrichoniscoidessalirensis is classified as a troglobiont species, blind and depigmented and is hitherto the only troglobiont species known from this cave and from this karst area (Ecology and traits (narrative): rst area . The meaJustification for threats: The cave entrance is located in a former quarry, at 400 m from the closest house and 1 km from the village centre. Salir Cave has an easy access and mostly horizontal development, which attracts casual visitors. It has suffered recurrent episodes of vandalism, which include paintings inside the first chamber and breakage of many lithological formations. This cave is currently listed in the Geocaching network and subject to human disturbance without regulation.Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: The cave should be a protected site, as it is the only locality known for this species; therefore, a site of maximum priority for biodiversity conservation. The entrance should be closed and the access regulated in order to prevent the recurrent vandalism and human disturbance to the ecosystem.Conservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelTroglonethesolissipoensisScientific name: Species authority: Reboleira & Taiti 2015AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: TrichoniscidaeFamily: Taxonomic notes: Antennae have five flagellar articles, the male pleopod 1 exopod is triangular, as wide as long and the male pleopod 2 endopod distal article has a basal and a distal hook-like process .Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 10Basis of EOO and AOO: Known habitat extentBasis (narrative): Both the extent of occurrence (EOO) and area of occupancy (AOO) are 4 km\u00b2.Min Elevation/Depth (m): 42Troglonethesolissipoensis is only recorded from Alvide Cave, located in Cascais Municipality in the Lisbon metropolitan area (Range description: tan area .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Troglonethesolissipoensis occurs in a single cave : A total of 25 specimens have been collected in the type locality .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): The entrance to Alvide Cave is through a house currently serving as headquarters of Den\u00edvel Association. Part of the cave's ceiling has concrete that serves as the base of a residential building. This cave is in the margin of a small canyon and it is composed of three levels of horizontal galleries connected by pits, it has a horizontal development of 708 m and total depth of 28 m.Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 3.5 mm , 4.2 mm Generation length (yr): 1Dependency of single sp?: UnknownTroglonethesolissipoensis is a troglobiont species, being blind and depigmented. It is endemic and the only cave-adapted species known from this cave (T.olissipoensis were collected in the deepest parts of the cave (Ecology and traits (narrative): his cave . The avethe cave .Justification for threats: Alvide Cave is located below an over-urbanised area .Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: Measures should be taken to minimise the pernicious effects due to the cave's close proximity to the urbanisation on the habitat.Conservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelTroglonethesarrabidaensisScientific name: Species authority: Reboleira & Taiti 2015AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: TrichoniscidaeFamily: Taxonomic notes: Antennae have three flagellar articles, the male pereopod 7 carpus is enlarged in the basal part, the male pleopod 1 exopod is triangular and as wide as long and the male pleopod 2 endopod has the distal article with an apical hook-like process .Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 11Basis of EOO and AOO: Known habitat extentBasis (narrative): Both the extent of occurrence (EOO) and area of occupancy (AOO) are 4 km\u00b2.Min Elevation/Depth (m): 0Troglonethesarrabidaensis is only recorded from Frade Cave, located in the Arr\u00e1bida karst massif (Range description: t massif .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Troglonethesarrabidaensis occurs in a single cave : A total of 17 specimens have been collected in Frade Cave .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): Frade Cave is located near the seashore, with several anchialine lakes inside, which are influenced by the sea tides with a slight delay period . The cavTrend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 2.7 mm Generation length (yr): 1Dependency of single sp?: UnknownTroglonethesarrabidaensis is classified as a troglobiont, depigmented, blind and with an elongated body (Ecology and traits (narrative): ted body . It is aJustification for threats: The cave entrance is located 600 m from a very touristic beach, mainly accessed by boat; therefore, fuel residues brought in by the tidal movement might be a concerning pollutant inside the cave. Contamination of groundwater should be evaluated.Threat type: OngoingThreats: 9. Pollution6.1. Human intrusions & disturbance - Recreational activitiesThreat type: OngoingThreats: 9. Pollution6.1. Human intrusions & disturbance - Recreational activitiesJustification for conservation actions: Even though this cave is protected under legislation by the \u201cRede Natura 2000\u201d , this siConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelMiktoniscuslongispinaScientific name: Species authority: Reboleira & Taiti 2015AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: TrichoniscidaeFamily: Taxonomic notes: The male pereopod 7 has a long and stout seta on the distal corner of the ischium and a triangular male pleopod 1 exopod . The speFigure(s) or Photo(s): Fig. 2Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 12Basis of EOO and AOO: Known habitat extentBasis (narrative): The extent of occurrence (EOO) is 137.96 km\u00b2 and the area of occupancy (AOO) is 12 km\u00b2.Min Elevation/Depth (m): 145Max Elevation/Depth (m): 355Miktoniscuslongispina is recorded from three caves with disjunt distribution. Bolhos Cave, also known as Casal da Lebre Cave, located in the Cesaredas Plateau and Ervilha and Cer\u00e2mica Caves located in the centre of the Sic\u00f3 karst area (Range description: rst area .EOO (km2): 137.96Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 12Number of locations: 3Miktoniscuslongispina can be found in three caves : A total of 12 specimens were collected in the three localities: two in Bolhos Cave, eight in Cer\u00e2mica Cave and two in Algar da Ervilha Cave .Number of subpopulations: 3Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: YesSystem: TerrestrialHabitat specialist: YesHabitat (narrative): Bolhos Cave has a horizontal development of 130 m and is located in Cesaredas Plateau, 93 km away from the other localities in the Sic\u00f3 karst area. Cer\u00e2mica Cave has a horizontal development of 120 m and is the richest cave in troglobiont species in central Portugal. Algar da Ervilha Cave has a depth of 52 m and a horizontal development of 150 m . The cavTrend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 3.5 mm Generation length (yr): 1Dependency of single sp?: UnknownMiktoniscuslongispina is a troglobiont, with a depigmented and elongated body. All specimens, except for the ones collected in Bolhos Cave, are blind.Ecology and traits (narrative): Eucalyptus intensive plantations. It is located 270 m from a road, 550 m from an animal farm, 1.6 km from the closest village and 3.6 km from a quarry. Algar da Ervilha Cave is located in the border of a road in the westernmost access to Ereiras Village, at 90 m from the closest house and 3.5 km from the same quarry as Cer\u00e2mica Cave.Justification for threats: Bolhos Cave is located 130 m from an energy windmill and 700 m from the closest village, in an area of extensive agricultural fields. Cer\u00e2mica Cave is surrounded by agricultural fields and Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas2.2. Agriculture & aquaculture - Wood & pulp plantations2.3. Agriculture & aquaculture - Livestock farming & ranching3.2. Energy production & mining - Mining & quarrying3.3. Energy production & mining - Renewable energy4. Transportation & service corridors9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas2.2. Agriculture & aquaculture - Wood & pulp plantations2.3. Agriculture & aquaculture - Livestock farming & ranching3.2. Energy production & mining - Mining & quarrying3.3. Energy production & mining - Renewable energy4. Transportation & service corridors9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: The caves located in the Sic\u00f3 karst area are protected under the \u201cRede Natura 2000\u201d . Bolhos Conservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelMoseriusinexpectatusScientific name: Species authority: Reboleira & Taiti 2015AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: TrichoniscidaeFamily: Moserius species due to the peculiar shape of the male pleopod 1 exopod, with a truncate and sinuous, rather than triangular, distal point : Suppl. materials 13Basis of EOO and AOO: Known habitat extent2.Basis (narrative): Both the extent of occurrence (EOO) and area of occupancy (AOO) are 4 kmMin Elevation/Depth (m): 95Moseriusinexpectatus is only recorded from Almonda Cave, also known as Olho do Moinho da Fonte, located in the easternmost subunit of the Estremenho karst massif (Range description: t massif .EOO (km2): 4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 4Number of locations: 1Moseriusinexpectatus is endemic to a single cave : Only one specimen was collected from the type locality .Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesHabitat (narrative): Almonda Cave, the type locality for this species, is the largest cave in Portugal .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 1.5 mm Generation length (yr): 1Dependency of single sp?: UnknownMoseriusinexpectatus is a troglobiont blind and depigmented isopod. This is the third species described from the genus Moserius, previously known from Slovenia and Italy (Ecology and traits (narrative): nd Italy .Justification for threats: Almonda Cave is located 50 m from a factory that extracts and uses water from a subterranean stream and 420 m from a village, which has many agricultural fields.Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.1. Agriculture & aquaculture - Annual & perennial non-timber crops9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.1. Agriculture & aquaculture - Annual & perennial non-timber crops9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: In 1993, Almonda Cave was classified as a Property of Public Interest (IIP) and protected due to its archaeological heritage . The arcConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelCordioniscuslusitanicusScientific name: Species authority: Reboleira & Taiti 2015AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: StyloniscidaeFamily: Taxonomic notes: The male pereopod 7 ischium has a rounded hyaline basal lobe, the triangular male pleopod 1 exopod is as long as the endopod and the male pleopod 2 endopod has a complex apical part .Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 14Basis of EOO and AOO: Known habitat extent2 and the area of occupancy (AOO) is 16 km2.Basis (narrative): The extent of occurrence (EOO) is 5,893.93 kmMin Elevation/Depth (m): 10Max Elevation/Depth (m): 370Cordioniscuslusitanicus is recorded from five caves, located in two isolated karst areas: Algar de Santo Ant\u00f3nio from the Estremoz-Cano karst massif and Ibne Ammar, Algar\u00e3o do Remexido, Vale Telheiro and Senhora Caves from the Algarve karst massif (Range description: t massif .EOO (km2): 5,893.93Trend: UnknownJustification for trend: The four caves, located in the Algarve karst massif, are at 200 km distance from the cave in the Estremoz-Cano karst massif.Causes ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 16Number of locations: 5Cordioniscuslusitanicus occurs in five caves : A total of 26 specimens have been collected: nine from Algar de Santo Ant\u00f3nio, six from Ibne Ammar, six from Algar\u00e3o do Remexido and four from Senhora and one Number of subpopulations: 5Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: UnknownCordioniscuslusitanicus was collected in two karst areas, Estremoz-Cano and Algarve, located more than 200 km apart, which are isolated from each other by the dry and flat areas of the Alentejo Province. In Algar de Santo Ant\u00f3nio, the specimens were collected in deep layers of soil at the bottom of an entrance pit of the cave (Habitat (narrative): the cave .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 3 mm , 5 mm Generation length (yr): 1Dependency of single sp?: UnknownCordioniscuslusitanicus is classified as a troglobiont and endogean species. It is blind, depigmented and has an elongated body (Ecology and traits (narrative): ted body .Justification for threats: Algar de Santo Ant\u00f3nio is located in the middle of an urbanised area of a village. Algar\u00e3o do Remexido is located under agricultural lands, 370 m from the closest house and 1.7 km from the closest village. Senhora Cave is located 168 m from the closest house and 900 m from an industrial complex. Ibne Ammar Cave is located right in the flooding zone of the Arade river, 380 m from the national road IC4 and 1.4 km from the nearest town. Vale Telheiro Cave is located 50 m from a road and 150 m from the closest house.Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.2. Agriculture & aquaculture - Wood & pulp plantations4. Transportation & service corridors9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.2. Agriculture & aquaculture - Wood & pulp plantations4. Transportation & service corridors9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: Of the five caves, only Ibne Ammar Cave is protected under legislation by the \u201cRede Natura 2000\u201d and thisConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelPorcelliocavernicolusScientific name: Species authority: Vandel, 1946AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: PorcellionidaeFamily: Figure(s) or Photo(s): Fig. 3Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 15Basis of EOO and AOO: Known habitat extent2 and the area of occupancy (AOO) is 24 km2.Basis (narrative): The extent of occurrence (EOO) is 713 kmMin Elevation/Depth (m): 20Max Elevation/Depth (m): 380Porcelliocavernicolus is recorded from seven caves located in two isolated massifs, Gruta d\u2019el Rey in the Cantanhede-Outil karst massif and Santa Maria da Estrela, Soprador do Carvalho, Algarinho, Cer\u00e2mica, Abrigo Tomar I and Furjaca caves, located in the Sic\u00f3 massif (Range description: \u00f3 massif .EOO (km2): 713Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 24Number of locations: 7Porcelliocavernicolus occurs in seven caves : More than 63 specimens have been collected: 28 from Gruta d\u2019el Rey, 16 from Santa Maria da Estrela, seven from Soprador do Carvalho, three from Cer\u00e2mica, four from Abrigo Tomar I and five from Furjaca. The specimens, collected from Algarinho Cave, are simply described as \u201cmany\u201d .Number of subpopulations: 7Trend: UnknownExtreme fluctuations?: UnknownSevere fragmentation?: UnknownSystem: TerrestrialHabitat specialist: YesPorcelliocavernicolus inhabits the most superficial parts of caves and it occurs on roots that hang from the ceiling. Specimens are easily distinguishable due to their whitish colouration (Habitat (narrative): ouration .Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 10 mm Generation length (yr): 1Dependency of single sp?: UnknownPorcelliocavernicolus is classifid as a troglobiont, endemic to seven caves from central Portugal, distributed in two isolated karst massifs (Ecology and traits (narrative): massifs .Eucalyptus intensive plantations. It is located 270 m from a road, 550 m from an animal farm, 1.6 km from the closest village and 3.6 km from a quarry. Abrigo Tomar I Cave is located in a quite pristine location and it is a local protected area by the ONG Quercus. Furjaca Cave is located in an abandoned quarry which, after closure, was used as a trash dumping site.Justification for threats: Gruta d\u2018el Rey is located in the middle of an urbanised area, 1 km from a quarry and 1.2 km from highway A14. Santa Maria da Estrela Cave is located 86 m from a touristic site called Monstro das Bolachas, 230 m from the Nossa Senhora da Estrela viewpoint, 250 m from the closest house, 80 m from the closest road, 220 m from agricultural fields and 2.6 km from two quarries. Soprador do Carvalho is surrounded by agricultural lands and is located 67 m from the closest house and 1.4 km from a quarry. This cave is also affected by touristic activities, as people who visit the cave walk all over the habitat . The subThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.2. Agriculture & aquaculture - Wood & pulp plantations3.2. Energy production & mining - Mining & quarrying4. Transportation & service corridors6.1. Human intrusions & disturbance - Recreational activities9.1. Pollution - Domestic & urban waste water9.4. Pollution - Garbage & solid wasteThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.2. Agriculture & aquaculture - Wood & pulp plantations3.2. Energy production & mining - Mining & quarrying4. Transportation & service corridors6.1. Human intrusions & disturbance - Recreational activities9.1. Pollution - Domestic & urban waste water9.4. Pollution - Garbage & solid wasteJustification for conservation actions: Of the seven locations, only three are protected under legislation by the \u201cRede Natura 2000\u201d . Almost Conservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelTroglelumamachadoiScientific name: Species authority: AnimaliaKingdom: ArthropodaPhylum: MalacostracaClass: IsopodaOrder: ArmadillidiidaeFamily: Figure(s) or Photo(s): Fig. 4Region for assessment: EuropeReviewers: ReviewersEditor: EditorReviewers: ReviewersEditor: EditorBiogeographic realm: PalearcticCountries: PortugalMap of records (Google Earth): Suppl. materials 16Basis of EOO and AOO: Known habitat extent2 and the area of occupancy (AOO) is 16 km2.Basis (narrative): The extent of occurrence (EOO) is 356.4 kmMin Elevation/Depth (m): 10Max Elevation/Depth (m): 260Troglelumamachadoi is recorded from six caves, located in the Algarve karst massif: Ibne Ammar, Algar\u00e3o do Remexido, Vale Telheiro, Senhora, Algar\u00e3o do Paulino and Abismo Novo (Range description: smo Novo .EOO (km2): 356.4Trend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownTrend: UnknownCauses ceased?: UnknownCauses understood?: UnknownCauses reversible?: UnknownExtreme fluctuations?: UnknownAOO (km2): 16Number of locations: 6Troglelumamachadoi occurs in six caves : Trend in extent, area or quality?: Decline (inferred)Habitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesHabitat importance: Major ImportanceHabitats: 7.1. Caves and Subterranean Habitats (non-aquatic) - CavesSize: 8 mmGeneration length (yr): 1Dependency of single sp?: UnknownTroglelumamachadoi is a blind and depigmented species, classified as a troglobiont. Specimens are found in the most deep and well isolated parts of of caves, they have the integument covered with clay, while some others were found walking on cave walls and completely clean of clay, probably recently moulted : moulted . The temicamagna , the relgmaticus , the dyslitoides , the milocalense , the dipamendesi , the giagharbica and the arvensis .Justification for threats: Ibne Ammar Cave is located right in the flooding zone of the Arade River, 380 m from the national road IC4 and 1.4 km from the nearest town. Algar\u00e3o do Remexido is located under agricultural lands, 370 m from the closest house and 1.7 km from the closest village. Senhora Cave is located 168 m from the closest house and 900 m from an industrial complex. Abismo Novo Cave is located 100 m from the closest house and 500 m from the village centre and is also located 1 km from Senhora Cave. Algar\u00e3o do Paulino is located near a road, 90 m from the closest house and 800 m from the closest village. Vale Telheiro Cave is located 50 m from a road and 150 m from the closest house.Threat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.1. Agriculture & aquaculture - Annual & perennial non-timber crops4. Transportation & service corridors9.1.2. Pollution - Domestic & urban waste water - Run-offThreat type: OngoingThreats: 1.1. Residential & commercial development - Housing & urban areas1.2. Residential & commercial development - Commercial & industrial areas2.1. Agriculture & aquaculture - Annual & perennial non-timber crops4. Transportation & service corridors9.1.2. Pollution - Domestic & urban waste water - Run-offJustification for conservation actions: Of the five locations, only three are protected under legislation by the \u201cRede Natura 2000\u201d . MeasureConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelConservation action type: NeededConservation actions: 1.1. Land/water protection - Site/area protection1.2. Land/water protection - Resource & habitat protection2.1. Land/water management - Site/area management4. Education & awareness5.1.3. Law & policy - Legislation - Sub-national levelCave-adapted terrestrial isopods are key species for cave ecosystem conservation: i) they are the most diverse group of cave-adapted species in continental Portugal, ii) they have several single cave endemics that are under threat and require specific protection measures, iii) they are basal in the trophic chains in caves and serve as a food source for several other zoological groups; iv) they play a vital role on the decomposition of organic matter in caves; and v) they are very sensitive to contaminants and climate change .Almost all cave-adapted terrestrial isopod species face direct anthropogenic threats, such as point or diffuse pollution, direct habitat destruction by mining and quarry activities or excess cave visitation . With thOniscidea . So far,niscidea . Therefod groups .It is a priority to establish concrete protection strategies for cave-adapted species in continental Portugal. We need to improve the knowledge about population size and dynamics, real extent of subterranean distribution, improve our knowledge on the functional ecology, understand species life cycle and evaluate their sensitivity to disturbance. This contribution may be used as a support for decision-making for territory management and to define conservation measures for cave endemic species. Cave-adapted terrestrial isopods have the potential to be used as umbrella species for the conservation of other cave-adapted species sharing the same subterranean habitats.Discussion2F1C3046-2169-5E36-AB53-F8D02E3A9E1410.3897/BDJ.10.e78796.suppl1Supplementary material 1Distribution of cave-adapted terrestrial isopods in continental PortugalData typeSpecies distribution mapBrief description(A) Overview of the distribution of cave-adapted terrestrial isopods in continental Portugal; (B) Sic\u00f3 karst area distribution detail; (C) Estremenho and Montejunto karst massifs, Caldas da Rainha Typhonic Valley and Cesaredas Plateau distribution detail; (D) Algarve karst massif distribution detail; (E) Lisbon Peninsula and Arr\u00e1bida karst massif and Estremoz-Cano karst massif distribution detail; and (F) Vimioso paleokarst distribution detail.Species:Trichoniscoidesbroteroi (orange circle), T.ouremensis (pink circle), T.serrai (dark blue circle), T.subterraneus (yellow circle), T.meridionalis (purple circle), T.bellesi (forest green circle), T.sicoensis (light blue circle), Metatrichoniscoidessalirensis (dark blue diamond), Troglonethesolissipoensis (dark blue star), T.arrabidaensis (pink star), Miktoniscuslongispina (yellow cross), Moseriusinexpectatus (light blue hexagon), Cordioniscuslusitanicus (dark blue triangle outline), Porcelliocavernicolus (pink triangle) and Troglelumamachadoi (pink circle outline).File: oo_607434.pnghttps://binary.pensoft.net/file/607434A.S.P.S. Reboleira, R.P. Eus\u00e9bioDD91E314-7C4E-5774-8FF0-6086CE34BF8A10.3897/BDJ.10.e78796.suppl2Supplementary material 2TrichoniscoidesbellesiDistribution of Data typeSpecies distribution mapBrief descriptionTrichoniscoidesbellesi distribution: Algar do Javali Cave, Montejunto karst massif.File: oo_607707.tifhttps://binary.pensoft.net/file/607707A.S.P.S. Reboleira, R.P.Eus\u00e9bio5914DE8F-D8BC-5B98-9A9F-9D4D7A6E1EE910.3897/BDJ.10.e78796.suppl3Supplementary material 3TrichoniscoidesbroteroiDistribution of Data typeSpecies distribution mapBrief descriptionTrichoniscoidesbroteroi distribution: Alqueves Cave, Sic\u00f3 karst area.File: oo_607708.tifhttps://binary.pensoft.net/file/607708A.S.P.S. Reboleira, R.P. Eus\u00e9bio5FB36EF8-919B-5348-86EF-333B2BE58A3510.3897/BDJ.10.e78796.suppl4Supplementary material 4TrichoniscoidesmeridionalisDistribution of Data typeSpecies distribution mapBrief descriptionTrichoniscoidesmeridionalis distribution. (A) Detail of distribution: Algar do Vale do Pena; Alcobertas Cave; Algar do Z\u00e9 de Braga Cave; Lapa da Ch\u00e3 de Cima Cave; Algar do Ladoeiro Cave; Algar do Pena Cave; Moinhos Velhos Cave; Papagaio Cave; Algar do Burro Cave; and Almonda Cave.File: oo_607711.tifhttps://binary.pensoft.net/file/607711A.S.P.S. Reboleira, R.P. Eus\u00e9bio597F809C-3090-5016-9767-C3E76CCD0A1610.3897/BDJ.10.e78796.suppl5Supplementary material 5TrichoniscoidesouremensisDistribution of Data typeSpecies distribution mapBrief descriptionTrichoniscoidesouremensis distribution: Lapa da Salgada Cave, F\u00e1tima Plateau.File: oo_607712.tifhttps://binary.pensoft.net/file/607712A.S.P.S. Reboleira, R.P. Eus\u00e9bioF92DCDAA-FA35-5326-85D4-F63245509A6C10.3897/BDJ.10.e78796.suppl6Supplementary material 6TrichoniscoidesserraiDistribution of Data typeSpecies distribution mapBrief descriptionTrichoniscoidesserrai distribution: Santo Adri\u00e3o Cave, Vimioso karst area.File: oo_607713.tifhttps://binary.pensoft.net/file/607713A.S.P.S. Reboleira, R.P. Eus\u00e9bio48CB91A0-5194-5E31-94A2-A512AA8133E510.3897/BDJ.10.e78796.suppl7Supplementary material 7TrichoniscoidessicoensisDistribution of Data typeSpecies distribution mapBrief descriptionTrichoniscoidessicoensis distribution. (A) Detail of the distribution: Arrifana Cave; Santa Maria da Estrela Cave; Cer\u00e2mica Cave; S\u00e3o Sim\u00e3o Cave; Algarinho Cave; and Soprador do Carvalho Cave.File: oo_607714.tifhttps://binary.pensoft.net/file/607714A.S.P.S. Reboleira, R.P.Eus\u00e9bio774C7847-3F7C-544E-81E9-48B9C9A29AFE10.3897/BDJ.10.e78796.suppl8Supplementary material 8TrichoniscoidessubterraneusDistribution of Data typeSpecies distribution mapBrief descriptionTrichoniscoidessubterraneus distribution: Alta do Cabe\u00e7o dos Mosqueiros Cave, Aljubarrota Plateau.File: oo_607720.tifhttps://binary.pensoft.net/file/607720A.S.P.S. Reboleira, R.P. Eus\u00e9bio71845157-2E1F-5082-AAA4-DDC0924AFDBD10.3897/BDJ.10.e78796.suppl9Supplementary material 9MetatrichoniscoidessalirensisDistribution of Data typeSpecies distribution mapBrief descriptionMetatrichoniscoidessalirensis distribution: Salir Cave, Caldas da Rainha.File: oo_607721.tifhttps://binary.pensoft.net/file/607721A.S.P.S. Reboleira, R.P. Eus\u00e9bio425A22BF-FE18-5FDB-B23D-8937DEED57B610.3897/BDJ.10.e78796.suppl10Supplementary material 10TroglonethesolissipoensisDistribution of Data typeSpecies distribution mapBrief descriptionTroglonethesolissipoensis distribution: Alvide Cave, Lisbon.File: oo_607722.tifhttps://binary.pensoft.net/file/607722A.S.P.S. Reboleira, R.P. Eus\u00e9bio85C91C9B-5B83-533D-AB14-9F6ABE3F8A6B10.3897/BDJ.10.e78796.suppl11Supplementary material 11TroglonethesarrabidaensisDistribution of Data typeSpecies distribution mapBrief descriptionTroglonethesarrabidaensis distribution: Frade Cave, Arr\u00e1bida karst massif.File: oo_607723.tifhttps://binary.pensoft.net/file/607723A.S.P.S. Reboleira, R.P.Eus\u00e9bioBC5A499B-29AA-5FBE-B1CE-77CC7E4752A510.3897/BDJ.10.e78796.suppl12Supplementary material 12MiktoniscuslongispinaDistribution of Data typeSpecies distribution mapBrief descriptionMiktoniscuslongispina distribution. (A) Detail of distribution: Casal da Lebre Cave; Algar da Ervilha Cave; and Cer\u00e2mica Cave.File: oo_607725.tifhttps://binary.pensoft.net/file/607725A.S.P.S. Reboleira, R.P. Eus\u00e9bioDB2A85A3-79E9-53CC-AC9E-E2C21922CF6F10.3897/BDJ.10.e78796.suppl13Supplementary material 13MoseriusinexpectatusDistribution of Data typeSpecies distribution mapBrief descriptionMoseriusinexpectatus distribution: Almonda Cave, Estremenho karst massif.File: oo_607726.tifhttps://binary.pensoft.net/file/607726A.S.P.S. Reboleira, R.P. Eus\u00e9bioC9060AAB-01F8-5426-86EE-22A80F48CE2110.3897/BDJ.10.e78796.suppl14Supplementary material 14CordioniscuslusitanicusDistribution of Data typeSpecies distribution mapBrief descriptionCordioniscuslusitanicus distribution. (A) Detail of distribution: Ibne Ammar Cave; Algar\u00e3o do Remexido Cave; Vale Telheiro Cave; Senhora Cave; and Algar de Santo Ant\u00f3nio Cave.File: oo_607729.tifhttps://binary.pensoft.net/file/607729A.S.P.S. Reboleira, R.P. Eus\u00e9bio9A58FB28-25DF-5F94-842E-3D0690437F8C10.3897/BDJ.10.e78796.suppl15Supplementary material 15PorcelliocavernicolusDistribution of Data typeSpecies distribution mapBrief descriptionPorcelliocavernicolus distribution. (A) Detail of distribution: Gruta d\u2019el Rey; Furjaca Cave; Santa Maria da Estrela Cave; Cer\u00e2mica Cave; Algarinho Cave; Soprador do Carvalho Cave; and Abrigo Tomar I Cave.File: oo_607732.tifhttps://binary.pensoft.net/file/607732A.S.P.S. Reboleira, R.P. Eus\u00e9bioF77EA613-7319-514F-BCF6-CF2EFDC4F8E210.3897/BDJ.10.e78796.suppl16Supplementary material 16TroglelumamachadoiDistribution of Data typeSpecies distribution mapBrief descriptionTroglelumamachadoi distribution. (A) Detail of distribution: Ibne Ammar Cave; Algar\u00e3o do Remexido Cave; Vale Telheiro Cave; Algar\u00e3o do Paulino Cave; Abismo Novo Cave; and Senhora Cave.File: oo_607736.tifhttps://binary.pensoft.net/file/607736A.S.P.S. Reboleira, R.P. Eus\u00e9bio"} +{"text": "Monocyte derived dendritic cells were generated from these peripheral blood mononuclear cells (PBMC), loaded with SARS-CoV-2 peptides, and used to induce autologous CD4+ and CD8+ T cell activation. The SARS-CoV-2 peptides demonstrated antigenicity against the T-cells from individuals with previous SARS-CoV-2 infection indicating that this approach holds promise as a method to activate anti-SAR-CoV-2 T-cell responses from conserved regions of the virus which are not included in vaccines utilising the Spike protein.The pandemic caused by SARS-CoV-2 has led to the successful development of effective vaccines however the prospect of variants of SARS-CoV-2 and future coronavirus outbreaks necessitates the investigation of other vaccine strategies capable of broadening vaccine mediated T-cell responses and potentially providing cross-immunity. In this study the SARS-CoV-2 proteome was assessed for clusters of immunogenic epitopes restricted to diverse human leucocyte antigen. These regions were then assessed for their conservation amongst other coronaviruses representative of different alpha and beta coronavirus genera. Sixteen highly conserved peptides containing numerous HLA class I and II restricted epitopes were synthesized from these regions and assessed NC_045512.2, MN996532.2, MT072864.1, MT040333.1, KC881005.1, KY417144.1, KT444582.1, KF367457.1, KC881006.1, KY417152.1, MK211376.1, AY572034.1, AY572035.1, AY572038.1, AY686864.1, AY686863.1, NC_004718.3, AY390556.1, KY352407.1, NC_014470.1, GU190215.1, MG772933.1, MG772934.1, MK211374.1, JX993987.1, MK211377.1, DQ084199.1, GQ153539.1, DQ084200.1, DQ022305.2, KJ473815.1, KJ473813.1, KJ473812.1, KP886808.1, DQ648857.1, DQ412043.1, KY417147.1, DQ648856.1, JX993988.1, FJ588686.1, MK211378.1, KJ473816.1, KJ473811.1, MG596802.1, MG596803.1, NC_009020.1, MG021452.1, MK129253.1, JX869059.2, MT576585.1, NC_038294.1, DQ648794.1, KJ473821.1, KJ473822.1, KX442564.1, EF065505.1, NC_009019.1, KC869678.4, NC_039207.1, KC545386.1, KJ473806.1, NC_026011.1, NC_017083.1, FJ647223.1, KF686343.1, AY391777.1, NC_030886.1, NC_009021.1, HM211098.1, MK211375.1, KY770860.1, KU182964.1, MT430884.1, LC469308.1, NC_048212.1, MF593268.1, NC_034440.1, NC_028814.1, JQ989273.1, NC_018871.1, AF304460.1, JQ410000.1, NC_048216.1, AY567487.2, NC_046964.1, NC_028833.1, KJ473820.1, NC_028811.1, NC_022103.1, EF203064.1, NC_028824.1, DQ648858.1, EU420138.1, KJ473795.1, EU420137.1.The pandemic caused by the novel coronavirus, SARS-CoV-2, has prompted a global response to produce effective vaccines. A number of vaccines have been approved for use having demonstrated varying levels of efficacy in clinical trials . These vin vitro.T-cell responses to SARS-CoV-1 demonstrate greater durability than those of neutralising antibody and are https://www.ncbi.nlm.nih.gov/labs/virus/vssi/), alignment using Clustal Omega with default settings and analysis of conservation using Microsoft Excel. Accession numbers of coronaviruses strains can be found in the supplementary material file.Analysis of SARS-CoV-2 and other coronaviruses protein sequences from proteins harbouring epitope rich regions was performed using FASTA sequences deposited in the NCBI database (https://www.iedb.org/).Identification of SARS-CoV-2 HLA restricted epitopes using prediction algorithms and experimentally validated epitopes deposited in the Immune epitope database and by using the NetMHCpan EL 4.1 (2020.09) prediction algorithm against an HLA allele reference set (Selection of conserved immunogenic regions between 15\u201330 amino acids in length (synthetic long peptides) was determined by assessing their suitability for synthesis based upon the physiochemical properties of the amino acids in the sequence and potential as CPP (cell penetrating peptides) defined by a net positive charge. Selected peptides were synthesized .Peripheral blood mononuclear cells (PBMC) were purchased from the national blood service prior to the distribution of SARS-CoV-2 vaccines. PBMC demonstrating responses to a SARS-CoV-2 consensus peptide pool and serum antibody responses to the SARS-CoV-2 spike protein were defined as having been previously infected with SARS-CoV-2 whilst PBMC and sera lacking detectable responses were defined as SARS-CoV-2 na\u00efve.\u22121 IL-4 and 50 ng ml\u22121 GM-CSF . These mDDC were subsequently co-cultured with the T-cells enriched from the CD14- fraction of PBMC using anti-CD3 magnetic beads in the presence of SARS-CoV-2 peptides individual and in groups, and control peptides including CEF , CEFT SARS-CoV-2 reference group (1 \u00b5g ml\u22121 for each peptide) for antigenicity assays.The generation of mDDC (monocyte-derived dendritic cells) was performed using established protocols. CD14+ cells were isolated by positive selection using anti-CD14 conjugated magnetic beads . The CD14+ cells were cultured for 6 days in RPMI 10% foetal calf serum and 5% streptomycin/penicillin of 10 ng ml4 mDDC: 2\u00d7105 T-cells) were incubated in IFN-\u03b3 ELISPOT plates for 48 h in order to assess antigen specific T-cell activation. After 48 h ELISPOT plates were processed according to the manufacturers protocol. Briefly, plates were washed in PBS \u00d73 prior to the incubation with detection anti-IFN-\u03b3 antibody for 2 h. Plates were washed \u00d73 in PBS wash buffer and Strep-Biotin reagent was added for 1 h. Plates were washed \u00d73 prior to the addition of substrate solution. Spot formation was observed and the plates were washed once in distilled H2O and left to dry before enumeration using a CTL Immunospot entry ELISPOT plate reader. Positive responses compared to the no peptide control were defined as >1.5-fold change and statistical significance using Student\u2019s t-test.IFN-\u03b3 ELISPOT (enzyme-linked immunosorbent spot) assays using peptide pulsed mDDC-T-cell co-cultures since the physiochemical properties of the peptides may make them unsuitable for synthesis or for targeting toward antigen presenting cells or homology between the peptides and human proteins may make them unsuitable for vaccination. Amino acid modifications were made outside of epitope containing regions in order to improve synthesis, stability and internalisation. Each of the peptides was differently conserved between other coronaviruses and contained a different number of epitopes restricted to different HLA. A total of 16 of these candidate SLP were selected as an immunogenic pool for The selected peptides were assessed for their ability to activate T-cell responses. PBMC from seven individuals with previous SARS-CoV-2 infection and four individuals seronegative for SARS-CoV-2, without selection for specific HLA expression, were used to generate monocyte derived dendritic cells , loaded 4895-915 which demonstrated a CD4+ T cell response from the PBMC of one individual but no CD8+ T cell responses. This pattern of responses was consistent with other reports studying anti-SARS T-cell responses [Next a flow cytometry-based activation induced marker (AIM) assay was used to gain a greater insight into the T-cell responses raised by the peptides and CD8+esponses . Interesesponses .in vitro T-cell antigenicity of SARS-CoV-2 derived SLP containing epitopes restricted to multiple HLA and conserved between SARS-CoV-2 variants and other coronaviruses.Taken together these data demonstrate the SARS-CoV-2 vaccines based upon the Spike protein have demonstrated between 60\u201395% efficacy in phase three trials and are now in widespread use. Although these vaccines are highly efficacious numerous issues remain unresolved. These include supply, cost and the requirement of some vaccines for a cold chain. From an immunological perspective there remains concern that variation in the Spike protein may evolve against which antibodies raised by vaccination are less effective, demonstrated to some degree by the Gamma and DeltThe broad therapeutic activation of SARS specific T-cell immune responses may resolve or ameliorate a number of these issues. T-cell responses are more stable than humoral responses whilst pIn this study, immunogenic regions from SARS-CoV-2 proteins other than the spike were identified and their conservation amongst selected alpha and beta coronaviruses was assessed. The selected peptides contain multiple epitopes restricted to the most common HLA class I molecules and which have previously demonstrated induction of T-cell activation in response to SARS-CoV-2 . ImportaThe peptides are derived from the immunodominant viral proteins other than the spike so couldin vitro experiments DC-T-cell co-cultures generated from the PBMC of individuals with previous SARS-CoV-2 infection responded with IFN-\u03b3 expression to an average of five peptides derived from an average of four proteins. Previous studies have demonstrated that broad T-cell responses against multiple epitopes are more effective than narrow responses targeting fewer epitopes [A recent study showed that CD8+ T cell responses against SARS-CoV-2 were raised against approximately 17 epitopes derived from between 1\u20136 viral proteins (average 2.7) [epitopes and lessepitopes indicatiAnalysis of T-cell responses to the ChAdOx1 spike-based vaccine showed that nearly 30% of unique TCRs raised by the vaccine mapped to a single region of the spike protein which is mutated in the Beta variant of SARS-CoV-2 . This maSynthetic long peptides of the kind studied here have been used in numerous therapeutic vaccines for both infectious disease and cancer and demonstrated an ability to induce efficacious T-cell responses . PeptideClick here for additional data file."} +{"text": "People admitted to a skilled nursing facility (SNF) for post-acute care undergo comprehensive evaluation and rehabilitation, potentially enabling prediction of future functional recovery. We identified the first SNF admission per beneficiary between 07/01/2014 \u2013 06/30/2016 in a 5% Medicare sample, using the Minimum Data Set (MDS) and the Outcome and Assessment Information Set (OASIS). Episodes were excluded for non-community discharge or no OASIS admission assessment within 14 days of SNF discharge . A deficit accumulation Frailty Index (FI) was measured on admission MDS assessment and categorized into robust (MDS-FI<0.15), pre-frailty (MDS-FI0.15-0.24), mild frailty (MDS-FI0.25-0.34), and moderate or worse frailty (MDS-FI\u22650.35). Outcomes were functional decline obtained from OASIS, readmission, or death after initiation of home care. Functional status was measured by activities of daily living from OASIS assessments. A total of 135,310 SNF episodes were matched to OASIS episodes. Of these, there were 6,472 (4.8%) robust patients, 38,923 (28.8%) pre-frail, 63,727 (47.1%) mildly frail and 26,053 (19.3%) moderately frail or worse. In a logistic regression after adjustment for OASIS admission function, compared to robust status, frailty was associated with hospital readmission or death within 30 days of OASIS admission, (mild frailty OR1.33 [95%CI 1.23-1.45] and moderate or worse OR1.81 [95%CI 1.66-1.97]). Frailty was also associated with functional decline at OASIS discharge, after adjustment for OASIS admission function (mild frailty OR1.50 [95%CI 1.38-1.63] and moderate or worse OR2.30 [95%CI 2.11-2.50]). Among those discharged from SNF with home services, a SNF-based MDS-FI is associated with increased likelihood of poor community outcomes."} +{"text": "Tracheal, bronchus, and lung (TBL) cancer is the leading cause of cancer death globally, but trends in TBL mortality attributable to tobacco, ambient particulate matter pollution (APMP), and household air pollution (HAP) were unequally distributed within global population subgroups over the last three decades. We used data from the Global Burden of Disease 2019 study to quantify the impact of sex, time, sociodemographic development index (SDI), and age for each exposure from 1990\u20132019. During that interval, tobacco dominated the TBL cancer mortality landscape, with its minimum global age-adjusted death rate of 16.71 deaths/100,000 : 15.27\u201318.13) outstripping maximums of 3.85 deaths/100,000 (UI: 2.82\u20134.83) and 2.54 deaths/100,000 (UI: 1.69\u20133.54) for APMP and HAP, respectively. In 2019, tobacco male TBL death rates exceeded female rates by a factor of 4.4:1. Ratios of 1.9:1 for APMP and 2.1:1 for HAP were seen. Our analysis indicates that both-sex middle SDI and female low, low-middle, and high-middle SDI populations are suffering increasing tobacco TBL burden. Efforts producing successful global reductions in HAP-associated TBL mortality should continue, with attention to low SDI female death rate increases. Finally, except for high SDI populations, global APMP-attributable TBL cancer burden is increasing and represents a major health concern. Lung cancer is the leading cause of cancer death globally , with trRecent studies have shed light on TBL incidence, DALYs, and mortality trends in the GBD 2017 and GBD 2019 data ,11,12. WAnnual TBL cancer deaths and death rate estimates attributable to environmental exposures were extracted from the GBD 2019 dataset . Death rt-tests of the 95% confidence interval of the difference between a given subgroup\u2019s 1990 and 2019 death rates, at a significance level of p < 0.05 . Statistically significant findings are termed \u201csignificant\u201d in the Results section; non-significant findings are not preceded by a word modifier. Lastly, using Microsoft Excel software, we generated heat maps for each exposure using death rate stratification by sex, SDI, and age between 1990 and 2019 to highlight granular trends among subpopulations. Other visualizations were generated using the GBD Compare tool [Specific considerations for each stratifying variable were as follows: (1) Time: TBL deaths and age-standardized death rate estimates were available for all years between 1990\u20132019; (2) SDI: The GBD 2019 authors created SDI as a country\u2019s \u201ccomposite indicator of socio-demographic development status\u201d utilizing \u201ctotal fertility rate in those under 25 years old, mean education for those 15 years or older, and lag-distributed income per capita\u201d to give each country an index value from 0 to 100 [are tool .From 1990\u20132019, tobacco dominated the TBL cancer mortality landscape. Tobacco-attributed global age-adjusted death rates ranged from 16.71 deaths/100,000 (UI: 15.27\u201318.13) to 19.99 deaths/100,000 (UI: 19.10\u201320.86), which outstripped interval maximum rates of 3.85 deaths/100,000 (UI: 2.82\u20134.83) and 2.54 deaths/100,000 (UI: 1.69\u20133.54) for APMP and HAP, respectively c. Globalp < 0.01). Males in the global population experienced a large, significant decrease (p < 0.01), while the female trend was a non-significant increase (p = 0.80). Exploring these trends by SDI highlighted significant decreases of 30% in HSDI (p < 0.01) and 14% in HMSDI (p = 0.01) both-sex populations (p < 0.01) (p = 0.06) (p = 0.10); MSDI females saw a 31% increase (p = 0.07) (p = 0.02) and LMSDI females a non-significant increase, while male subgroups saw non-significant decreases . The global male rate increased 12% to 5.78 deaths/100,000 (UI: 4.19\u20137.18), while the female rate increased 60% (p = 0.06) to 2.08 deaths/100,000 (UI: 1.49\u20132.71) (p = 0.11), with similar decreases in the male and female rates during this period (p = 0.01) and 133% (p < 0.01) for MSDI populations (p = 0.01), 263% in LMSDI (p < 0.01), 178% in MSDI (p < 0.01), and 81% in HMSDI (p = 0.02). LMSDI and MSDI males additionally saw a significant increase of 157% (p = 0.01) and 119% (p = 0.01), respectively, while LSDI and LMSDI males also saw non-significant increases to 3.78 deaths/100,00 (UI: 2.79\u20134.86) between 1990\u20132019 (49\u20132.71) a\u2013c. HSDIp = 0.01) from 2.54 deaths/100,000 (UI: 1.69\u20133.54) to 0.97 deaths/100,000 (UI: 0.55\u20131.93). The decrease in males was larger than that in females, with significant reductions of 66% (p = 0.01) in the former and a 54% reduction (p = 0.03) in the latter and, more recently, China (HMSDI) do offer some indication that implementing regulations aimed at improving APMP levels can reduce related TBL mortality . HMSDI fHAP trends offered the most universally positive outlook among the three exposures studied. HAP-attributable TBL mortality reductions across almost every global subpopulation can be taken as a sign that international efforts to reduce the burden of disease associated with these exposures, such as indoor stove interventions ,23, haveOur findings further characterize the complex, dynamic, exposure-related trends in TBL cancer mortality from 1990\u20132019. Our analysis indicates that the most urgent areas for tobacco-related intervention are both-sex MSDI populations and female LSDI, LMSDI, and HMSDI populations suffering from increasing tobacco-attributable TBL burden. Successful efforts that have brought about global reductions in HAP-associated TBL burden should continue, with special attention to LSDI female populations, where death rate increases were seen. Finally, except for both-sex HSDI and younger male HMSDI populations, the TBL cancer burden attributed to APMP is increasing and represents an urgent threat to the health of many global populations. With these targeted insights, global leaders, policy makers, and health care professionals will be better able to address the contribution of TBL cancer to the global burden of disease."} +{"text": "We externally validated the recently suggested FSAC prediction model for hepatocellular carcinoma (HCC) in treatment-na\u00efve Asian chronic hepatitis B patients starting potent antiviral therapy (AVT). The model reflects age, sex, presence of cirrhosis, and on-therapy changes in non-invasive fibrosis markers (NFMs) after 12 months of antiviral therapy, such as APRI and FIB-4. Our results highlighted better predictive performance for the FSAC model for HCC (Harrell\u2019s c-index: 0.770) than the PAGE-B, modified PAGE-B, modified REACH-B, LSM-HCC, and CAMD models, which only use baseline parameters. A simplified version of FSAC score ), including only NFMs at 12 months, also showed a high c-index value (0.763). Our retrospective study suggests that the accurate measurement of intra-hepatic fibrotic burden during adequate AVT is necessary for predicting HCC development.n = 3026; median age, 50.0 years; male predominant (61.3%); cirrhosis in 1391 (46.0%) patients) receiving potent AVTs for >18 months between 2007 and 2018. During follow-up (median 64.0 months), HCC developed in 303 (10.0%) patients. Patients with low FIB-4 or APRI levels at 12 months showed significantly lower HCC risk than those with high NFM levels at 12 months . Cumulative 3-, 5-, and 8-year HCC probabilities were 0.0%, 0.3% and 1.2% in the low-risk group (FSAC \u2264 2); 2.1%, 5.2%, and 11.1% in the intermediate-risk group (FSAC 3\u22128); and 5.2%, 15.5%, and 29.8% in the high-risk group (FSAC \u2265 9) (both p < 0.001 between each adjacent pair). Harrell\u2019s c-index value for FSAC score (0.770) was higher than those for PAGE-B (0.725), modified PAGE-B (0.738), modified REACH-B (0.737), LSM-HCC (0.734), and CAMD (0.742). Our study showed that the FSAC model, which incorporates on-therapy changes in NFMs, had better predictive performance than other models using only baseline parameters.Antiviral therapy (AVT) induces the regression of non-invasive fibrosis markers (NFMs) and reduces hepatocellular carcinoma (HCC) risk among chronic hepatitis B (CHB) patients. We externally validated the predictive performance of the FSAC prediction model for HCC using on-therapy NFM responses. Our multicenter study consecutively recruited treatment-na\u00efve CHB patients ( Chronic hepatitis B virus (HBV) infection is a major public health problem affecting approximately more than 250 million people worldwide; it remains a leading cause of hepatocellular carcinoma (HCC), especially in endemic areas such as Korea ,2,3,4,5.Many models have been developed to help with predicting the risk of HCC development among HBV patients with or without AVT. Since the prognostic role of baseline serum HBV-DNA levels has been substantially attenuated in the present era of potent nucleos(t)ide analogues, models established within one decade have adopted the presence of baseline cirrhosis rather than virological factors ,14,15. MHere, we aimed to externally validate the predictive performance of the newly developed FSAC model in comparison with other risk prediction models assessed at one time-point in an independent HBV cohort treated with ETV, TDF, or TAF.\u00ae at the time of AVT initiation, as described in previous reports. Cirrhosis was histologically or clinically diagnosed as follows: (1) platelet count of <150/\u00d7103/\u03bcL and imaging findings suggestive of cirrhosis, including a blunted, nodular liver edge accompanied by splenomegaly (>12 cm) or (2) clinical signs of portal hypertension, such as gastroesophageal varices ) and were compared using Student\u2019s The predictive performances of the risk scoring models for HCC development were assessed using Harrell\u2019s C-index, time-dependent area under the receiver operating characteristic curve (TDAUC) at 3-, 5-, and 8-years from the index date and integrated area under the receiver operating characteristic curve (iAUC). Furthermore, lower values for the Akaike information criterion (AIC) were considered reflective of a better discriminatory ability for each model. Model performance was presented graphically using calibration plots, which compared the model prediction probability with the actual probability of HCC development. Discrimination and calibration were evaluated using the bootstrap method with re-sampling 1000 times.Statistical differences in parameters of predictive performance between FSAC and the other HCC-risk prediction models were evaluated using the bootstrap method with re-sampling 1000 times. If 95% CIs contained zero, there was deemed to be no significant difference in the parameters of predictive performance between the two models.http://cran.r-project.org/, accessed on 10 August 2021). Two-sided p-values < 0.05 were considered to indicate statistical significance.All statistical analyses were conducted using R package ; and higher median values of liver stiffness (14.3 vs. 7.7 kPa), FIB-4 (3.38 vs. 2.11), and APRI , compared to those without HCC months, HCC developed in 303 (10.0%) patients (1.82 per 100 patient-years), and the cumulative probabilities of HCC development at 3-, 5-, and 8-years were 2.5%, 7.5%, and 15.3%, respectively. Patients who developed HCC were predominantly male (73.3% vs. 60.0%) and showed a significantly older age (median: 55.0 vs. 49.0 year); higher prevalence of cirrhosis (79.5% vs. 42.2%), diabetes mellitus (31.0% vs. 16.6%), hypertension (42.5% vs. 22.1%), and HBeAg negativity . Likewisp = 0.001) and D , whose FIB-4 values at 12 months were \u22651.45, compared to those without , 952 (31.5%), 87 (2.9%), and 852 (28.2%) were classified into groups A, B, C, and D, respectively. Patients who developed HCC showed a higher prevalence of being classified into groups B and D , whose APRI values at 12 months were \u22650.5, compared to those without , 733 (24.2%), 402 (13.3%), and 490 (16.2%) were classified into groups A, B, C, and D, respectively. Patients who developed HCC showed a higher prevalence of being classified into groups B . Subsequent multivariable analysis revealed that older age , male sex , presence of cirrhosis , higher liver stiffness values , hypertension , and lower platelet counts were independently associated with an increased risk of HCC development , 0.769 (95% CI 0.745\u20130.791), 0.768 (95% CI 0.745\u20130.790), 0.768 (95% CI 0.743\u20130.789), and 0.769 (95% CI 0.744\u20130.791), respectively. The calibration plots for predicting 3-, 5-, and 8-year HCC development showed that the predicted probabilities were very close to the observed incidences .Harrell\u2019s c-index values for PAGE-B, modified PAGE-B, modified REACH-B, LSM-HCC, and CAMD were 0.725 (95% CI 0.699\u20130.750), 0.738 (95% CI 0.712\u20130.764), 0.737 (95% CI 0.710\u20130.763), 0.734 (95% CI 0.706\u20130.762), and 0.742 (95% CI 0.715\u20130.768), respectively, whereas their iAUC values were 0.718 (95% CI 0.693\u20130.741), 0.722 (95% CI 0.701\u20130.744), 0.724 (95% CI 0.699\u20130.748), 0.731 (95% CI 0.705\u20130.755), and 0.743 (95% CI 0.717\u2013 0.768), respectively . The FSAHarrell\u2019s c-index and iAUC values of FSAC (2) model were 0.763 (95% CI 0.737\u20130.787) and 0.763 (95% CI 0.739\u20130.784), respectively .n = 1391, 46.0%) showed that the Harrell\u2019s c-index and the iAUC value of the FSAC model were 0.668 (95% CI 0.633\u20130.701) and 0.661 (95% CI 0.627\u20130.694), respectively : scores 0\u20132); intermediate- (n = 1172 (38.2%): scores 3\u20138); and high-risk groups (n = 1009 (33.3%): scores 9\u201312), according to a previous study [p < 0.001, n = 0), 0.3% (n = 2), and 1.2% (n = 5) in the low-risk group; 2.1% (n = 23), 5.2% (n = 48), and 11.1% (n = 75) in the intermediate-risk group; and 5.2% (n = 49), 15.5% (n = 126), and 29.8% (n = 196) in the high-risk group, respectively (both p < 0.001 between each adjacent pair).Using FSAC score, we stratified patients into the three risk groups: low- occurred during the median follow-up period of 64.0 months, allowing for highly acceptable statistical power. Second, among the low-risk group defined according to FSAC score (n = 845), only 6 patients developed HCC, with an annual incidence of 0.15%. Considering that current surveillance strategies to detect early-stage HCC may be cost-effective when annual risk exceeds at least 0.2% in patients without cirrhosis and 1.5% in patients with cirrhosis, the 27.9% of individuals in the low-risk group could likely avoid biannual abdominal ultrasonography-based HCC surveillance safely. Conversely, the intermediate- and high-risk groups, accounting for the remaining 72.1% of this study population, may require more delicate surveillance, given the suboptimal diagnostic sensitivity of abdomen ultrasonography and the overall poor prognosis of HCC detected at advanced stages. Thus, in order to achieve higher detection rates of HCC at early stages and greater cost-effectiveness, further studies on how to implement individualized surveillance strategies based on optimal visit intervals and the adoption of novel diagnostic modalities using radiology and/or serum biomarkers are warranted.Our study had several clinical implications. First of all, the prognostic performance of the FSAC model over other HCC-risk prediction models was reproduced. The large sample of >3000 patients with long-term follow-up enhanced the statistical reliability of the results. Moreover, a sufficient number of HCC cases ) which included only NFMs assessed at 12 months, also showed a Harrell\u2019s c-index value similar to the FSAC model . The observations in this study are consistent with reports of excellent predictive performance for the CAGE-B and SAGE-B models that incorporate liver stiffness values on transient elastography after 5 years of AVT.n = 1102, 36.4%) [p < 0.001). Hence, further large-scale study with the serial follow-up of transient elastography during long-term AVT should be required.Although the predictive performance of FSAC model among our study population was acceptable, further research using novel biomarkers that can exclude the overestimation caused by active necro-inflammation before starting AVT should be required in the near future , in orde, 36.4%) , we confOur study has several limitations. First, although liver stiffness values by transient elastography were available in all patients at the baseline, approximately two thirds of patients did not undergo transient elastography during long-term AVT, primarily because it is not reimbursed by the National Health Insurance Service in Korea. Since the predictive performances might vary depending on the sample size and HCC incidence, further studies are required in the setting of paired transient elastography tests. Second, when the HCC prediction models were assessed among a subgroup with cirrhosis, their prognostic performances were generally attenuated. This is most likely because the discriminatory power of the variables constituting the models might become considerably attenuated in the relatively \u201chomogenous\u201d cirrhotic subgroup. Given that the majority of HCC rises in the setting of cirrhosis, especially among patients in Western countries, further studies concerning development of novel biomarkers should be required, allowing the optimized prognostication in a subgroup with cirrhosis.In this external validation study of a large-scale cohort, the FSAC model exhibited more robust predictive performance for HCC development, compared to other HCC-risk prediction models that use only baseline characteristics. For predicting HCC development, accurate measurement of fibrotic burden during long-term AVT is necessary."} +{"text": "Pseudomonas aeruginosa. The activity of the investigational combination cefepime-taniborbactam (FTB) and comparator agents was evaluated against clinical isolates of Enterobacterales from a 2018-2020 global surveillance study.Taniborbactam (formerly VNRX-5133) is a novel cyclic boronate-based broad-spectrum \u03b2-lactamase inhibitor with potent and selective direct inhibitory activity against both serine- and metallo-\u03b2-lactamases . Taniborbactam restores the activity of cefepime against many difficult to treat organisms, including cephalosporin- and carbapenem-resistant Enterobacterales and MICs of cefepime with taniborbactam fixed at 4 \u00b5g/mL and comparators were determined following CLSI M07-A11 guidelines against 10,543 Enterobacterales. Isolates were from community and hospital infections collected from 259 sites in 56 countries in 2018-2020. Resistant phenotypes were based on 2021 CLSI breakpoints. A set of 827 isolates with meropenem MIC \u22654 \u00b5g/mL (n=421) or with cefepime and/or ceftazidime MIC \u22652 \u00b5g/mL (n=406) was evaluated for the presence of MBLs, KPC, ESBLs, and OXA-48 group genes via PCR and sequencing. Forty-eight isolates with FTB MIC values of 16 \u00b5g/mL or greater were interrogated by WGS.50/90 values of 0.06/0.25 \u00b5g/mL and 99.5% inhibited at \u22648 \u00b5g/mL. FTB maintained activity against MBL-, KPC-, OXA-48 group, and ESBL-positive isolates . Isolates with elevated FTB MICs had IMP-type enzymes, variation in the cefepime target (penicillin binding protein 3), permeability defects in combination with acquired \u03b2-lactamases, and/or possible up-regulated efflux.Overall, 23.0% and 15.9% of isolates were nonsusceptible (NS) to cefepime and piperacillin-tazobactam (TZP), respectively (Table). FTB had potent activity against all Enterobacterales, with MICResults Tablein vitro activity of cefepime against Enterobacterales, including isolates nonsusceptible to recently-approved BL/BLI combinations and expressing serine and metallo-\u03b2-lactamases. This support the continued development of FTB as a potential new treatment option for challenging infections due to resistant Gram-negative pathogens.Taniborbactam significantly restored the Meredith Hackel, PhD MPH, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Mark G G. Wise, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)"} +{"text": "Mycobacterium kansasii\u2014termed rBCG-Mkan85B\u2014which was used together with a booster immunization with plasmid DNA expressing the same M. kansasii Ag85B gene (DNA-Mkan85B). We reported that rBCG-Mkan85B/DNA-Mkan85B prime\u2013boost immunization elicited various NTM strain-specific CD4+ and CD8+ T cells and induced Mycobacterium\u00a0tuberculosis-specific immunity. In this study, to investigate the protective effect against M. kansasii infection, we challenged mice vaccinated with a rBCG-Mkan85B or rBCG-Mkan85B/DNA-Mkan85B prime\u2013boost strategy with virulent M. kansasii. Although BCG and rBCG-Mkan85B immunization each suppressed the growth of M. kansasii in the mouse lungs, the rBCG-Mkan85B/DNA-Mkan85B prime\u2013boost vaccination reduced the bacterial burden more significantly. Moreover, the rBCG-Mkan85B/DNA-Mkan85B prime\u2013boost vaccination induced antigen-specific CD4+ and CD8+ T cells. Our data suggest that rBCG-Mkan85B/DNA-Mkan85B prime\u2013boost vaccination effectively enhances antigen-specific T cells. Our novel rBCG could be a potential alternative to clinical BCG for preventing various NTM infections.The incidence of infections with nontuberculous mycobacteria (NTM) has been increasing worldwide. The emergence of multidrug-resistant NTM is a serious clinical concern, and a vaccine for NTM has not yet been developed. We previously developed a new recombinant Bacillus Calmette\u2013Gu\u00e9rin (rBCG) vaccine encoding the antigen 85B (Ag85B) protein of Mycobacterium tuberculosis complex and Mycobacterium leprae, such as Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium kansasii. Recently, the incidence of NTM infection has been increasing worldwide [Nontuberculous mycobacteria (NTM) are mycobacterium species other than the orldwide ,2,3. Altorldwide ,5,6,7,8.Since NTM pathogens are intracellular, cell-mediated immunity plays a major role in protecting against NTM. Previous reports have indicated that protective immunity against tuberculosis (TB) and NTM infection might overlap . EpidemiM. kansasii\u2014termed rBCG-Mkan85B\u2014which we used with a booster vaccination with plasmid DNA expressing the same M. kansasii Ag85B gene (DNA-Mkan85B) [M. tuberculosis and M. leprae [+ T cells and CD8+ T cells [d)-restricted epitopes that induced cross-reactive responses to M. tuberculosis and other related mycobacteria, including M. kansasii, in both BALB/c (H2d) mice and CB6F1 (H2b/d) mice [d-restricted peptide epitopes elicited polyfunctional CD8+ T cell responses that were also highly cross-reactive with those of other proteins in the Ag85 complex [M. kansasii, we challenged rBCG-Mkan85B/DNA-Mkan85B-prime\u2013boost-vaccinated CB6F1 mice with M.kansasii and evaluated the protective effect and cellular immunity in this study.Previously, we developed a new recombinant BCG (rBCG) vaccine encoding the antigen 85B (Ag85B) protein of Mkan85B) . The Ag8Mkan85B) . The Ag8. leprae ,16. We r. leprae . We also T cells . Moreove/d) mice . The H2- complex . TherefoSpecific pathogen-free female CB6F1 mice, aged between 6 and 8 weeks, were purchased from Japan SLC Inc. . All animal studies were carried out under institutional guidelines approved by the Nihon University Animal Care and Use Committee (AP19MED029-3), the institutional committee for gene recombination experiments (2018MED21), and biorisk management and control (30-10-4). The institutional animal experimental guidelines are in accordance with the ILAR Guide. Mice were allowed free access to sterile water and standard mouse food, and their physiological conditions were assessed every few days.We used the previously prepared rBCG-Mkan85B strain and DNA-Mkan85B plasmid in this BCG was cultured in Middlebrook 7H9 broth (Difco) supplemented with albumin dextrose complex (ADC) enrichment (Difco) and 0.05% Tween 80 at 37 \u00b0C. rBCG-Mkan85B was cultured in Middlebrook 7H9 broth (Difco) supplemented with ADC enrichment (Difco), 0.05% Tween 80, and 10 mg/mL kanamycin at 37 \u00b0C. Bacterial culture density was monitored by measuring the absorbance at 470 nm and 600 nm.6 CFU or 0.1 mg of bacilli intradermally (i.d.), and 100 \u00b5g of plasmid DNA in saline intramuscularly (i.m.) three times [Mice were immunized with the BCG vaccine or rBCG-Mkan85B at a concentration of 4 \u00d7 10ee times . The bacteriological experiment was carried out under institutional guidelines approved by Nihon University biorisk management and control (30-10-4). M. kansasii was grown in Middlebrook 7H9 broth (Difco) supplemented with ADC enrichment (Difco) with 0.05% Tween 80 at 37 \u00b0C and harvested during the exponential growth stage. Infection of mice with M. kansasii was conducted intratracheally. Mice were anaesthetized with isoflurane and inoculated with 50 \u00b5L of a bacterial suspension containing 1 to 10 \u00d7 104 CFU of M. kansasii using a yellow pipet tip.At 6 weeks after infection, the mice were sacrificed, and the numbers of viable bacilli in their lungs were estimated. Lung tissues were homogenized with sterilized water. Tenfold serial dilutions of homogenate were inoculated onto duplicate 7H10-OADC agar plates (Difco) to determine bacterial loads. Colonies were counted after incubation for 3 weeks at 37 \u00b0C.Fractioned lung samples from each mouse were fixed with 10% neutral-buffered formalin and embedded in paraffin wax. The sections from these tissues were 4 mm thick and stained with hematoxylin and eosin (H&E) or with the Ziehl-Neelsen stain for acid-fast bacilli.+ epitope peptide (peptide-25: FQDAYNAAGGHNAVF) [M. kansasii. A seven-color flow cytometry panel was used to simultaneously analyze multiple cytokines at the single-cell level. The gating strategy used to identify cytokine-producing CD8+ and CD4+ T cells in mouse splenocytes is shown in Splenocytes and immune cells isolated from the lung were stimulated with a 9-mer Ag85B CD8 epitope peptide (YYQSGLSIV) (Pep8) , 15-mer GGHNAVF) , or tubeGGHNAVF) ,17. PPD All comparisons among recombinant and control groups and among immunization groups were conducted using one-way ANOVA tests with the Tukey-Kramer test using the JMP program (SAS Institute) and R version 4.0.3 (R core team 2020). Data are expressed as the mean \u00b1 SD.M. avium and M. abscessus [M.kansasii infection.According to previous epidemiological reports, BCG vaccination can reduce the risk of NTM infection in humans ,20,21. Ibscessus . TherefoM.kansasii strain for infection for another 6 weeks. The immunization schedule is shown in 4 (\u00b11.5 \u00d7 104) pulmonary CFU per animal. Although BCG and rBCG-Mkan85B vaccination both reduced the pulmonary CFU (p < 0.01) (The CB6F1 (H2b/d) mice were either left unimmunized or immunized with BCG or rBCG-Mkan85B for 6 weeks, followed by a nasal exposure to a virulent < 0.01) , the eff < 0.01) A,D. Acid < 0.01) G,J. Alth < 0.01) B,C, the < 0.01) H,I.M.kansasii infection. The CB6F1 mice were either left unimmunized or immunized with BCG or rBCG-Mkan85B/DNA-Mkan85B and then challenged with a virulent M.kansasii strain for another 6 weeks. The immunization schedule is shown in Next, we evaluated the efficacy of the rBCG-Mkan85B/DNA-Mkan85B prime\u2013boost vaccination against To analyze the adaptive immune responses induced by BCG, rBCG-Mkan85B, and rBCG-Mkan85B/DNA-Mkan85B vaccination, we examined the induction of antigen-specific polyfunctional T cells using an intracellular cytokine staining (ICS) method.M. kansasii infection [M. malmoense, M. marinum, or M. kansasii [M. avium and M. abscessus cross-reactive T cells in humans [+ T cell epitopes of the mycobacterial Ag85 complex elicited similar levels of cytokine production by polyfunctional T cells in mice vaccinated with an rBCG-Mkan85B/DNA-Mkan85B prime\u2013boost strategy [Generally, NTM patients are considered to have been infected by environmental NTM, not by NTM from other patients. In other words, NTM do not cause airborne or droplet infections, unlike TB and SARS-CoV-2, the latter of which is responsible for coronavirus disease 2019 (COVID-19). However, increases in NTM incidence rates have been reported recently [ex (MAC) , M. malmn humans . Previoustrategy .M. kansasii. We showed that both BCG and rBCG-Mkan85B could protect the mice from virulent M. kansasii infection. However, contrary to our expectation, the efficacy of rBCG-Mkan85B vaccination was not superior to that of BCG vaccination. An ICS analysis revealed that M. kansasii antigen-specific polyfunctional CD4+ T cells were equally induced by BCG and rBCG-Mkan85B vaccination. However, similar to previous reports [M. kansasii peptides could not induce antigen-specific polyfunctional CD8+ T cells. Moreover, the present study demonstrated that rBCG-Mkan85B vaccination alone was not sufficient to induce M. kansasii Ag85B-specific polyfunctional CD8+ T cells. Therefore, we immunized mice with rBCG-Mkan85B and boosted them with DNA-Mkan85B three times. BCG and recombinant BCG prime\u2013boost immunization were reported to be beneficial strategies for inducing antigen-specific CD8+ T cells [+ and CD4+ T cells. Regarding antigen-specific CD4+ T cells, several critical roles for eliminating mycobacteria have been reported [+ T cell counts have a high risk of developing NTM infection. In addition to that of CD4+ T cells, the importance of CD8+ T cells to protecting against mycobacterial infection was revealed by previous studies by other researchers. For instance, the airborne infection of mice [M. avium induced the activation of both CD4+ T cells and CD8+ T cells. However, the significance of CD8+ T cells in protection against NTM infection, especially M. avium infection, has been controversial. Although the depletion or genetic elimination of CD8+ T cells significantly decreases immunological responses to TB and increases susceptibility to M. tuberculosis [+ T cells was reported to be unrelated to M. avium infection [+ T cells occurred during experimental M. avium infection [+ T cells in M. kansasii infection has not been investigated thoroughly. In the present study, although BCG or rBCG-Mkan85B immunization could activate only M. kansasii-specific polyfunctional CD4+ T cells, rBCG-Mkan85B/DNA-Mkan85B prime-boost vaccination was able to elicit M. kansasii-specific polyfunctional CD8+ T cells. Nevertheless, the BCG- or rBCG-Mkan85B-immunized mice were shown to be protected against M. kansasii infection, and the rBCG-Mkan85B/DNA-Mkan85B prime-boost strategy drastically reduced the bacterial burden in the lungs of the mice. The results suggest a role for antigen-specific polyfunctional CD8+ T cells in protecting against M. kansasii infection.In the present study, we first challenged unvaccinated and BCG- or rBCG-Mkan85B-vaccinated mice with virulent reports ,22,23,25 T cells ,17,24. Ireported ,26,27. I of mice , calves of mice , and rherculosis ,31, the nfection . Gilbertnfection . On the + and CD8+ T cells [Since the end of 2019, COVID-19 has been a serious public health concern worldwide. Looking back on history, human beings have suffered from many kinds of infections. We have to continue to fight various pathogenic microorganisms and infectious diseases. Vaccines are the gold standard for protecting against infectious diseases. One of the aims of a vaccine is to induce effective neutralizing antibodies against the target pathogen. To protect against several pathogenic microbes, such as mycobacteria, the activation of cellular immunity is required in addition to the induction of humoral immunity. BCG has been used globally as a live attenuated vaccine against TB for a century. Various recombinant BCG strains have been designed, developed, and evaluated as novel vaccines against various infectious diseases. For instance, several rBCG strains expressing HIV antigens, such as HIV gag and env, have been reported to induce anti-HIV neutralizing antibodies and antigen-specific CD4 T cells ,33,34. W T cells ,36,37. MM. kansasii infection by inducing M. kansasii-specific polyfunctional CD4+ T cells. Furthermore, rBCG-Mkan85B/DNA-Mkan85B prime\u2013boost vaccination induced antigen-specific CD4+ and CD8+ T cells and drastically reduced the CFU of M. kansasii in the lungs of vaccinated mice. Our data suggest that the combination of rBCG expressing Ag85B derived from M. kansasii with DNA that also expresses Ag85B derived from M. kansasii may be effective in enhancing antigen-specific T cells, resulting in more efficient control of M. kansasii infection.In conclusion, we demonstrated that BCG and rBCG-Mkan85B immunization protected CB6F1 mice from"} +{"text": "The Centers for Disease Control and Prevention (CDC) estimated direct healthcare costs of &271 million in 2018. CDC 2015 guidelines recommended cephalosporin plus azithromycin for GC. We used real-world data to assess patterns of inappropriate Table 1) during the first uUGG episode . Generalized linear models were used for multivariate analysis.A retrospective cohort study of IBM MarketScan data in patients \u2265 12 years old with uUGG. Eligible patients had an AB prescription \u00b15 days of uUGG diagnosis (index date) and continuous health-plan enrollment with \u2265 6 months\u2019 baseline/\u2265 12 months\u2019 follow-up data. Patients with complicated urogenital GC were excluded. Patients were stratified by AB prescription , 77.1% had an IA/SO prescription (mostly due to IA AB class [~82.0%] and duration [24.0%]), while only 22.9% had an AP&OP prescription; uUGG episodes were more frequent with IA/SO (n=2386) than AP&OP (n=714) prescriptions during follow-up. Patients with IA/SO prescriptions had higher GC-related total adjusted costs per patient (PP) per index episode (&196) vs those with AP&OP prescriptions . Patients with IA/SO prescriptions also had higher GCrelated total adjusted costs PP during follow-up (&220) vs those with AP&OP prescriptions , mostly driven by higher outpatient ambulatory and emergency room (ER) adjusted costs with IA/SO vs AP&OP prescriptions . ER visits PP at index and during follow-up were higher with IA/SO vs AP&OP prescriptions .Figure. GC-related costs per patient with uUGG, stratified by appropriateness of AB prescription*Table 2. GC-related HRU per patient with uUGG, stratified by AB prescriptionMost patients with uUGG were not prescribed treatments in accordance with CDC 2015 guidelines. High IA/SO AB prescriptions and associated healthcare costs suggest an unmet need for improved prescribing practices for uUGG in the US.Madison T. Preib, MPH, STATinMED Research Fanny S. Mitrani-Gold, MPH, GlaxoSmithKline plc. Ziyu Lan, MSc, STATinMED Research Xiaoxi Sun, MA, STATinMED Research Ashish V. Joshi, PhD, GlaxoSmithKline plc."} +{"text": "The predictive value of silver stained nucleolar organiser regions (AgNORs) was assessed in 229 patients with transitional cell bladder cancer followed up for over 10 years. The AgNORs were enumerated in pretreatment biopsy specimens. The AgNORs were related to clinical stage (T) (P = 0.0111), papillarity (P less than 0.0001), WHO grade (P less than 0.0001), DNA ploidy (P = 0.0010) and S-phase fraction (P less than 0.0001). Tumours presenting with pelvic lymph node involvement (P = 0.0085) or metastasis (P = 0.0780) at the time of diagnosis had more AgNORs than tumours confined to the bladder wall. Progression in T-, N- and M-categories (P = 0.0010-0.0030) was related to AgNORs and consequently they predicted bladder cancer related survival (P = 0.0005). The diploid tumours could be regrouped according to survival by AgNORs (P = 0.0001). In papillary tumours AgNORs predicted progression (P = 0.0110) and survival (P = 0.0038). In Ta-T1 tumours AgNORs predicted progression (P = 0.11) and survival (P = 0.0751) and also in T2-T3 tumours AgNORs contributed to survival significantly (P = 0.0039). The AgNORs subdivided WHO grade III tumours according to their ability to progress during the follow-up time (P = 0.0711). In a multivariate analysis AgNORs predicted progression independently in Ta-T1 category (P = 0.0165). AgNORs predicted recurrence free period like SPF (P = 0.0010). In conclusion, AgNORs are inferior to classic prognostic factors or DNA flow cytometric variables in muscle invasive bladder cancers whereas they have independent predictive value in superficial cancers."} +{"text": "The role of cholecystokinin (CCK) has been explored in pancreatic carcinogenesis following pancreatobiliary diversion (PBD), using the specific CCK receptor antagonist CR-1409. Male Wistar rats (n = 80) weighing 70-100 g were given weekly i.p. injections of azaserine (30 mg kg-1 week-1) for 3 consecutive weeks. One week later animals were randomised to receive either PBD or sham PBD and thereafter to receive s.c. injections of either saline or CR-1409 . Six months after operation surviving rats were killed as follows: sham + saline 20, PBD + saline 19, sham + CR-1409 14, PBD + CR-1409 11. Cardiac blood was taken for CCK assay and the pancreas was excised for wet weight measurement and quantitative estimation of atypical acinar cell foci (AACF), the precursor of carcinoma. PBD reduced median body weight (3-20% less than shams) but trebled the absolute and relative pancreatic weights (P < 0.001). CR-1409 blunted this adaptive response to PBD, reducing absolute pancreatic weight by 35% (P < 0.005). PBD quadrupled circulating CCK concentrations, regardless of the antagonist treatment. Acidophilic AACF occurred only in rats with PBD. CR-1409 markedly reduced the number of observed acidophilic AACF by 90% (P < 0.001) and the number of foci per pancreas by 93% (P < 0.001). Moreover, CR-1409 reduced the mean focal diameter of each lesion by 18% (P < 0.005), the mean focal volume by 58% (P < 0.05) and the percentage of pancreas occupied by acidophilic foci by 95% (P < 0.001). PBD enhances pancreatic carcinogenesis by causing hypercholecystokininaemia, and CR-1409 largely inhibits this enhancement."} +{"text": "Cytokines are small proteins that regulate immunity in vertebrate species. Marsupial and eutherian mammals last shared a common ancestor more than 180 million years ago, so it is not surprising that attempts to isolate many key marsupial cytokines using traditional laboratory techniques have been unsuccessful. This paucity of molecular data has led some authors to suggest that the marsupial immune system is 'primitive' and not on par with the sophisticated immune system of eutherian mammals.IFN-\u03b3, IL-2, IL-4, IL-6, IL-12 and IL-13, in the genome of the grey short-tailed opossum (Monodelphis domestica). Many of these genes were not predicted in the publicly available automated annotations.The sequencing of the first marsupial genome has allowed us to identify highly divergent immune genes. We used gene prediction methods that incorporate the identification of gene location using BLAST, SYNTENY + BLAST and HMMER to identify 23 key marsupial immune genes, including The power of this approach was demonstrated by the identification of orthologous cytokines between marsupials and eutherians that share only 30% identity at the amino acid level. Furthermore, the presence of key immunological genes suggests that marsupials do indeed possess a sophisticated immune system, whose function may parallel that of eutherian mammals. The marsupial and eutherian lineages diverged approximately 180 million years ago. Marsupials are chiefly distinguished from other mammals by their unique reproductive strategies, with young born in an immature state with only the most rudimentary neurological and immunological systems , T Cell However, conventional experimental strategies using degenerate primers for reverse-transcriptase polymerase chain reaction (RT-PCR) and heterologous probes for screening genetic libraries have only identified the most phylogenetically conserved immune molecules, with cytokines proving particularly difficult to isolate . To datein vitro Mixed Lymphocyte Response -x(3)-L) is conserved . Inverted triangles indicate cysteine residues that are conserved across species. Dots represent identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (Q9HBE4), Mus musculus (NP_068554.1), Gallus gallus (NP_001020006.1), Canis familiaris (NP_001003347.1), Sus scofa (Q76LU6), Bos taurus (Q76LU5).Click here for fileSyntenic region between human chromosome 4q27 and opossum chromosome 5, illustrating the gene cluster of interleukin 2 and 21. Transcriptional directions are indicated by arrows.Click here for fileIL-2R\u03b3 amino acid sequences. Conserved cysteine residues are marked with an inverted triangle. Dots represent identity to Monodelphis domestica sequence. Completely conserved residues are shaded. Sequences used for alignment: Homo sapiens (NP_000197.1), Mus musculus (NP_038591.1), Gallus gallus (NP_989858.1), Rattus norvegicus (NP_543165.1), Canis familiaris (NP_001003201.1), Sus scrofa (NP_999248.1), Bos taurus (NP_776784.1).Click here for fileAlignment of IL-5 amino acid sequences. Dots represent identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_000870.1), Macaca mulatta (NP_001040598.1), Bos taurus (NP_776347.1), Canis familiaris (NP_001006951.1), Mus musculus (NP_034688.1), Macropus eugenii (AAD37462.1), Gallus gallus (NP_001007085.1).Click here for fileSyntenic region between human chromosome 5q23.3 and opossum chromosome 1, illustrating the gene cluster of interleukin 5, 4 and 13. Transcriptional directions are indicated by arrows.Click here for fileAlignment of IL-6 amino acid sequences. Residues involved in receptor binding in human IL-6 are denoted with diamonds. Cysteine residues conserved among all species are marked with an inverted triangle. PROSITE family motif is boxed. Dots represent identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_000591.1), Mus musculus (NP_112445.1), Oryctolagus cuniculus (Q9MZR1).Click here for fileAlignment of IL-12\u03b1 amino acid sequences. Cysteine residues conserved among all species are marked with an inverted triangle. Dots represent identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_000873.2), Mus musculus (NP_032377.1), Gallus gallus (NP_998753.1), Rattus norvegicus (NP_445842.1), Ovis aries (NP_001009736.1) Canis familiaris (NP_001003293.1).Click here for fileAlignment of IL-10 amino acid sequences. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_000563.1), Mus musculus (NP_034678.1), Gallus gallus (NP_001004414.1), Trichosurus vulpecular (AAD01799), Canis familiaris (NP_001003077.1), Sus scofa (Q29055), Cervus elaphus(P51746).Click here for fileAlignment of IL-19 amino acid sequences. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_037503.2), Mus musculus (NP_001009940.1).Click here for fileAlignment of IL-20 amino acid sequences. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_061194.2), Mus musculus (NP_067355.1), Tetraodon nigroviridis (AAP57416.1).Click here for fileAlignment of IL-24 amino acid sequences. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_006841.1), Mus musculus (NP_444325.1), Rattus norvegicus (NP_579845.1), Tetraodon nigroviridis (AAP57418.1).Click here for fileAlignment of IL-26 amino acid sequences. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_060872.1), Danio rerio (NP_001018635.1).Click here for fileAlignment of IL-22 amino acid sequences. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_065386.1), Mus musculus (NP_058667.1), Sus scofa (AAX33671.1), Rattus norvegicus (ABF82262.1), Danio rerio (NP_001018628.1).Click here for fileNeighbour-Joining tree of IL-10 family ligand protein sequences rooted by midpoint. JTT amino acid substitution matrix was used and 500 bootstrap replicates performed. Branches supported by bootstrap values over 70 are in bold. Opossum sequences are marked by triangles. Sequences used for this analysis were Homo sapiens IL-10 (NP_000563.1), IL-19 (NP_715639.1), IL-20 (NP_061194.2), IL-22 (NP_065386.1), IL-24 (NP_006841.1), IL-26 (NP_060872.1); Mus musculus IL-10 (NP_034678.1), IL-19 (NP_001009940.1), IL-20 (NP_067355.1), IL-22 (NP_058667.1), IL-24 (NP_444325.1); Rattus norvegicus IL-24 (NP_579845.1); Sus scofa IL-10 (Q29055); Bos taurus IL-10 (P43480); Trichosurus vulpecular IL-10 (AAD01799); Gallus gallus IL-10 (NP_001004414.1); Cyprinus carpio IL-10 (BAC76885.1); Tetraodon nigroviridis IL-10 (CAD67786.1); Takifugu rubripes IL-10 (CAD62446.1) Danio rerio IL-26 (NP_001018635.1) and Monodelphis domestica. Sequences labels in the tree are abbreviated by the first letter from the genus with the first two letters from the specific name followed by the gene name.Click here for fileAlignment of CD4 amino acid sequences. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_000607.1), Mus musculus (NP_038516.1), Macaca mulatta (BAA09671.1) Felis cattus (NP_001009250.1), Rattus norvegicus (NP_036837.1) Oncorhynchus mykiss (AAY42068.1).Click here for fileAlignment of CD8 amino acid sequences. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_001759.3), Mus musculus (Q60965), Gallus gallus (NP_990566.1), Canis familiaris (NP_001002935.1), Sus scofa (NP_001001907.1), Rattus norvegicus (AAH88126.1).Click here for fileAlignment of IFNGR-2 amino acid sequences. Cysteine residues conserved among all species are marked with an inverted triangle. Dots indicate identity to Monodelphis domestica sequence. Sequences used for alignment: Homo sapiens (NP_005525.2), Mus musculus (NP_032364.1), Gallus gallus (NP_001008676.1).Click here for file"} +{"text": "Animals were inoculated either with 10(6) or 10(7) MAT-LyLu cells, or with saline to serve as controls. Carcass weight in tumour-bearing (TB) animals decreased despite similar food and water intake in both groups. Absence of metastatic tumour cells from HL of all TB animals was confirmed by histological examination. Twenty-one days after inoculation, 31P MRS showed a 2.5-fold increase in [Pi]/[ATP] ratios in HL in vivo (P < 0.001) which was confirmed by 31P MRS of liver extracts in vitro (P < 0.005). Phosphodiester to ATP ratios were significantly increased (P < 0.05) in HL in vivo, but absolute PDE levels were similar in both groups. Phosphomonoester to ATP ratios did not change, although absolute phosphomonoester levels in HL were reduced by -41% (not significant). In HL extracts in vitro, sharp reductions in the levels of glucose-6-phosphate (P < 0.05), fructose-6-phosphate (P = 0.05), phosphocholine (P < 0.001), glycerophosphocholine (P < 0.001), and glycerophosphoethanolamine (P < 0.001) were observed. Electron microscopy revealed increased amounts and altered distribution of rough endoplasmic reticulum in HL. These findings show that experimental prostate cancer significantly affects hepatic phosphorylation status, phospholipid metabolism, and gluconeogenesis in the host animal, and demonstrate the value of combined MRS in vivo and in vitro in monitoring HL metabolism in cancer."} +{"text": "A longitudinal study of iron status markers (haemoglobin (Hb), serum (S-) iron, S-transferrin, transferrin saturation, S-ferritin) was performed in 31 chemotherapy treated patients with small cell lung cancer. At discovery, eight patients were anaemic (Hb less than 121 g l-1). Hb, S-iron and transferrin saturation were lower (P less than 0.01), and S-ferritin higher (P less than 0.01) than in healthy subjects. Chemotherapy induced an immediate fall in Hb (P less than 0.003), increase in S-iron (P less than 0.003) and transferrin saturation (P less than 0.001). Later in the disease a fall in S-transferrin (P less than 0.006) and an increase in S-ferritin (P less than 0.02) occurred. Thirty patients died during the 2 years observation. S-ferritin at discovery was correlated to performance status score and to survival . Patients with S-ferritin less than or equal to 400 micrograms l-1 (n = 13) had longer survival than those with S-ferritin greater than 400 micrograms l-1 (n = 18) (P = 0.004)."} +{"text": "Sequential exposure to these factors , however, resembling the order of secretion during liver embryogenesis, induced both glycogen-storage and cytokeratin (CK)18 expression. Additional exposure of the cells to trichostatin A (TSA) considerably improved endodermal differentiation, as evidenced by acquisition of an epithelial morphology, chronological expression of hepatic proteins, including hepatocyte-nuclear factor (HNF)-3\u03b2, alpha-fetoprotein (AFP), CK18, albumin (ALB), HNF1\u03b1, multidrug resistance-associated protein (MRP)2 and CCAAT-enhancer binding protein (C/EBP)\u03b1, and functional maturation, i.e. upregulated ALB secretion, urea production and inducible cytochrome P450 (CYP)-dependent activity.hMSC are able to undergo mesenchymal-to-epithelial transition. TSA is hereby essential to promote differentiation of hMSC towards functional hepatocyte-like cells. By utilizing in vitro models, pharmaceutical companies attempt to reduce clinical failure rates by accurately evaluating efficacy and safety much earlier in the drug discovery process , CD45-PE (DAKO), CD105-FITC , CD73-PE, CD90-PE, CD166-PE and analyzed using a flow cytometer . Mesodermal differentiation was verified by means of different stainings (described below). To exclude spontaneous differentiation, hMSC were cultivated in regular MSCGM medium (Cambrex) and analyzed in parallel.3 cells/cm2 on 1 mg/ml collagen gel type I (BD) in basal medium supplemented with 2% (v/v) foetal bovine serum . Basal medium consisted of 60% (v/v) DMEM and 40% (v/v) MCDB-201 supplemented with 100 IE/ml penicillin , 100 \u03bcg/ml streptomycin, 1 mg/ml linoleic-acid bovine serum albumin, 0.1 mM L-ascorbic acid, 0.03 mM nicotinamide, 0.25 mM sodium pyruvate and 1.623 mM glutamine . At 100% confluence, cells were exposed to hepatogenic cytokines and growth factors, added either simultaneous as a cocktail ('referred to as 'cocktail-condition/-set-up/-exposure' or a derivative thereof) or sequentially . Differentiation media were changed every 3 days. From day 6 onwards, 1 \u03bcM TSA (Sigma) was added. The cocktail- and sequential-conditions, supplemented with 1 \u03bcM TSA will be further referred to as 'cocktail TSA-condition/-set-up/-exposure', and 'sequential TSA condition/-set-up/-exposure, respectively, or a derivative hereof.hMSC were plated at 21.5 10Cells were fixed with 10% (w/v) formalin for 10 min at room temperature or with methanol for 2 min at -20\u00b0C (osteogenic differentiation). After fixation, adipocytes were identified as red-colored lipid droplets upon staining with Oil-red O (from Sigma) . MineralChondrocytic differentiation was determined using rabbit polyclonal anti-collagen II antibody .Cells were fixed either with ethanol (Merck) for 10 min at -20\u00b0C or with 4% (w/v) paraformaldehyde for 10 min at 4\u00b0C (nuclear and cytoplasmic markers). After fixation, liver-specific protein expression was analysed using primary antibodies against AFP (goat), (HNF3\u03b2 (goat), HNF1\u03b1 (rabbit), C/EBP\u03b1 (rabbit), MRP2 , CK18 and ALB . HDAC inhibition was assessed using anti-acetyl histone H4 antibody . Respective secondary antibodies came from Jackson Immunoresearch, Cambridgeshire, UK. As a negative control, cells were incubated with appropriate gamma immunoglobulines (Jackson Immunoresearch) and immunostained under the same conditions. Cells were analysed using fluorescence microscopy with a Zeiss Axiovert scope.Cell morphology was analysed using phase-contrast light-microscopy (Nikon).ALB concentrations, secreted into the culture media, were analysed by ELISA .4Cl (Sigma), were measured colometrically in the culture media according to the manufacturer's instructions . Fresh culture media supplemented with 6 mM NH4Cl (Sigma) and 4 hours-cultured adult hepatocytes were used as negative and positive controls, respectively.Urea concentrations produced, after 24 hours-exposure of the cells to 6 mM NHEROD- and PROD-activities were assessed as previously described with somTo evaluate the inducibility of CYP2B6 and CYP1A1/2, cells were, after 18 days of differentiation, exposed to PB and MC , respectively. Media, supplemented with either PB or MC, were daily renewed. Fresh culture media and 4 hours-cultured adult hepatocytes were used as negative and positive controls, respectively.Results are expressed as mean \u00b1 SD. Statistical analyses were performed using Oneway Anova and Student's t-test. The significance level was set at 0.05.Albumin (ALB); alpha-fetoprotein (AFP); CCAAT-enhancer binding protein (C/EBP); cytochrome P450 (CYP); cytokeratin (CK); dimethylsulfoxide (DMSO); ethoxyresorufin-O-deethylase (EROD); fibroblast growth factor-4 (FGF-4); hepatocyte growth factor (HGF); hepatocyte nuclear factor (HNF); histone deacetylase inhibitor (HDAC-I); human adipose tissue-derived stromal cells (hADSC); human mesenchymal stem cells (hMSC); insulin-transferrin-sodium-selenite (ITS); lactate dehydrogenase (LDH); multidrug resistance-associated protein (MRP); multipotent adult progenitor cells (MAPC); methylcholantrene (MC); new chemical entities (NCEs); oncostatin M (OSM); pentoxyresorufin-O-dealkylase (PROD); Periodic-acid-Schiff (PAS) staining; phenobarbital (PB); trichostatin A (TSA).SS: Differentiation of expanded hMSC under hepatocyte-specific conditions. Analysis of multilineage differentiation by means of staining, functionality assays, microscopic analysis. Preparation of the manuscript.TV, PP and MV: Optimization of the concentration of TSA and onset of exposure to TSA. Critical revision of the manuscript. ADB and IVR: Isolation, expansion and routine characterization of hMSC . Critical revision of the manuscript. VR: Head of department of Toxicology and promotor of the hereby associated PhD thesis. Microscopic analysis. Critical revision of the manuscript.All authors read and approved the final manuscript.3H] thymidine incorporation into trichloroacetic acid precipitated-DNA was measured using a scintillation counter . Graphs shown are representative for 3 independent experiments.DNA synthesis of sequentially (+/-1 \u03bcM TSA) and cocktail (+/-1 \u03bcM TSA)-exposed hMSC. hMSC, plated on 1 mg/ml collagen gel type I, were at 100% confluence treated with either the cocktail- or sequential-condition. From day 6 onwards, 1 \u03bcM TSA was added . Differentiation media were changed every 3 days. Samples for DNA synthesis were taken 2, 4, 6, 12 and 18 hours upon media change. [Methyl-Click here for fileCell viability analysis of sequentially (+/-1 \u03bcM TSA) and cocktail (+/-1 \u03bcM TSA)-exposed hMSC. hMSC, plated on 1 mg/ml collagen gel type I, were at 100% confluence treated with either the cocktail- or sequential-condition. From day 6 onwards, 1 \u03bcM TSA was added . LDH leakage into culture media was measured throughout culture time according to the Bergmeyer procedure using a commercial kit . Graphs shown are representative for at least 3 independent experiments.Click here for fileCell death analysis of sequentially (+/-1 \u03bcM TSA) and cocktail (+/-1 \u03bcM TSA)-exposed hMSC. hMSC, plated on 1 mg/ml collagen gel type I, were at 100% confluence treated with either the cocktail- or sequential-condition. From day 6 onwards, 1 \u03bcM TSA was added . Differentiation media were changed every 3 days. Cells were, 12 hours upon media change, incubated with Alexa Fluor 488 annexin V (green fluorescent), propidiumiodide (red fluorescent) and the nuclear counterstain DAPI (blue fluorescent). The red, green, and both red and green-stained cells represent necrotic, apoptotic and death cells, respectively. 20 \u00d7 10 original magnification, phase contrast. Stainings shown are representative for at least 3 separate experiments.Click here for file"} +{"text": "PLoS Genetics, vol 2, issue 4, DOI: 10.1371/journal.pgen.0020053In http://www.ncbi.nlm.nih.gov) accession numbers for the sequence discussed in this paper are HVS1 (AY72095-AY721592)\u201d should be \u201cThe GenBank (http://www.ncbi.nlm.nih.gov) accession numbers for the sequence discussed in this paper are HVS1 (AY720957-AY721592).\u201dIn the Supporting Information section, the sentence \u201cThe GenBank ("} +{"text": "The expression of oestrogen receptor protein (ER) was examined in 151 cases of symptomatic or screening detected pure ductal carcinoma in situ (DCIS) of the breast by immunocytochemical assay (ERICA), in formalin-fixed paraffin-embedded tissue, with the monoclonal antibody H 222 (Abbott). Forty-eight tumours (31.8%) of cases were ER positive. Twenty-seven (17.9%) of cases showed high level ER expression and 21 (13.9%) of cases showed low level ER immunoreactivity. Significant associations of positive tumour ER immunoreactivity and non-comedo architecture chi 2 = 6.76; (d.f. = 1): P < 0.001, small cell size chi 2 = 4.49; (d.f. = 1): P = 0.034, higher S-phase fraction chi 2 = 4.71; (d.f. = 1): P = 0.03 and lack of c-erbB-2 protein overexpression chi 2 = 7.96; (d.f. = 1): P < 0.01 were identified. No significant associations of ER expression and patient age, histological grade of necrosis in DCIS, or DNA ploidy were found. ER expression is detectable in less than one third of symptomatic and screening detected cases of DCIS, implying that endocrine therapy of DCIS may be a more appropriate form of management for morphological subtypes of DCIS which show higher rates of oestrogen receptor expression, particularly those of non-comedo and small cell type."} +{"text": "Scientific Reports 10.1038/s41598-018-20137-2, published online 29 January 2018Correction to: This Article contains errors in References 8 and 9 which are incorrectly given as:et al. Colistin hetero-resistance in multidrug-resistant Acinetobacter baumannii clinical isolates from the Western Pacific region in the SENTRY antimicrobial surveillance programme. J Infection58, 138\u2013144, 10.1016/j.jinf.2008.11.002 (2009).\u2019\u2018Yau, W. et al. Synergistic killing of NDM-producing MDR Klebsiella pneumoniae by two \u2018old\u2019 antibiotics-polymyxin B and chloramphenicol. J Antimicrob Chemoth70, 2589\u20132597, 10.1093/jac/dkv135 (2015).\u2019\u2018Rahim, N. A. 2.The correct references are listed below as refs"} +{"text": "Microbacterium paludicola CC3 exhibits the capability to produce polysaccharide bioflocculants. Here, we report the whole-genome sequence of M.\u00a0paludicola CC3, which may be helpful in understanding the genetic basis of the biosynthesis of polysaccharide bioflocculants as well as in promoting its production and application in industrial fields. Paenibacillus shenyangensis, Agrobacterium tumefaciens F2, and Paenibacillus wulumuqiensis RSII platform using P6-C4 chemistry. The resulting sequencing reads with 320.4-fold coverage were then de novo assembled using Hierarchical Genome Assembly Process (HGAP) (http://www.ncbi.nlm.nih.gov/COG/), and the Gene Ontology (GO) Consortium (http://www.geneontology.org/). The metabolic pathways were predicted using the KEGG Automatic Annotation Server (KAAS) (http://www.genome.jp/tools/kaas/). rRNAs and tRNAs were identified using Barrnap 0.4.2 (http://www.vicbioinformatics.com/software.barrnap.shtml) and tRNAscan-SE version 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/), respectively. The clustered regularly interspaced short palindromic repeat (CRISPR) elements were detected using PILER-CR , 9. Genes (HGAP) . FunctioPILER-CR .M.\u00a0paludicola CC3. No plasmid sequences were detected. The chromosome was composed of 3,410,829\u00a0bp, with an average G+C content of 70.10%, which comprised 3,390 predicted genes, of which 3,209 were protein coding genes (CDSs), 32 were tRNA genes, 146 were rRNA genes, and 3 were microRNA genes. Pseudogenes and prophage genes were not identified, whereas 14 CRISPR candidates were detected in the genome of strain CC3. A series of genes encoding polysaccharide biosynthesis/modification proteins, such as mannose-1-phosphate guanylyltransferase .The sequence data for the genome of"} +{"text": "AbstractPhlaeothripinae, Mystrothripslevissp. n. and Urothripslancangensissp. n., are described from China. Pentagonothripsantennalis Haga & Okajima and Plectrothripsbicolor Okajima are newly recorded in China.Two new species of fungivorous Phlaeothripinae belong to Phlaeothrips lineage, which are usually taken from dead branches or leaf-litter and feed on fungal hyphae .All thrips specimens were extracted by using Tullgren funnels from leaf litter, and then sorted and preserved in 90% alcohol. Examined specimens were mounted into Canada balsam using the method outlined by Taxon classificationAnimaliaThysanopteraPhlaeothripidaehttp://zoobank.org/5399B364-0B5C-4B37-A2F5-896C751EF8A6. Holotype. Female aptera: CHINA, Guangdong: Guangzhou City, South China Botanical Garden (23Guangdong: Guan), in leaf litter of bamboo, 9.viii.2014 (Chao Zhao).Paratypes. 8 females 2 males, collected with holotype; 5 females 1 male, the same locality but collected on 20.xi.2015 (Chao Zhao).Female aptera . Distended body length 2030. Head length 190, width 185; eyes length 50; postocular setae length 75. Antennae length 470, segments I\u2013VIII length (width) as follows: 49(43); 53(41); 68(32); 67(34); 65(34); 61(30); 54(24); 52(12). Pronotum median length 140, width across median part 310; length of major setae: pronotum anteromarginal setae 48, anteroangular setae 68, midlateral setae 90, posteroangular setae 85, epimeral setae 80. Metanotum median setae 40. Pelta length 100, width at base 170. Abdominal tergite IX S1 setae length 190, intermediate setae length 85, S2 length 190. Tube length 155, width at base 93, at apex 42; anal setae length 135.Male aptera . Distended body length 1620. Head length 160, width 155; eyes length 35; postocular setae length 70. Antennae length 375, segments I\u2013VIII length (width) as follows: 34(36); 44(29); 50(32); 50(31); 55(28); 50(25); 45(20); 45(13). Pronotum median length 125, width across median part 260; length of major setae: pronotum anteromarginal setae 60, anteroangular setae 45, midlateral setae 73, posteroangular setae 66, epimeral setae 63. Metanotum median setae 30. Pelta length 65, width at base 110. Abdominal tergite IX setae S1 length 145, intermediate setae length 60, S2 length 45. Tube length 130, width at base 80, at apex 32; anal setae length 110.China (Guangdong).levis, is from the Latin adjective, meaning \u201csmooth\u201d, and refers to the dorsal surface of head and pronotum which are largely smooth. In contrast, most species of this genus are sculptured with distinct polygonal reticulation on head and pronotum.The specific epithet, Mystrothrips to Japan head and pronotum largely smooth ; (2) antennae uniformly brown (versus antennae segments I and II distinctly lighter than remaining segments in M.flavidus); (3) pelta semicircular with short lateral lobes ; (4) S1 and S2 setae on abdominal tergite IX much longer than tube (vs shorter than tube in M.flavidus).Of the seven species worldwide listed in the genus rothrips , two areto Japan . The newPageBreakTaxon classificationAnimaliaThysanopteraPhlaeothripidaeHaga & OkajimaPentagonothripsantennalis Haga & Okajima, 1979: 147.CHINA, Hunan: 2 females and 1 male, Zhuzhou City, Yanling County, Shennong Valley , in leaf litter, 16. ix. 2014 (Chao Zhao). Hubei: 1 male, Huanggang City, Yingshan County, Taohuachong , in leaf litter, 23.iv.2014 (Chao Zhao).Dorsal surface of body entirely reticulate; head longer than width, cheeks distinctly incut behind eyes; postocular setae well-developed with expanded at apex. Antennae 7-segmented, morphological segments VII and VIII fused with an incomplete suture, segments III and IV with two and three sense cones, respectively. Maxillary stylets short, wide apart. Pronotum with five pairs of well-developed major setae, strongly expanded at apex. Basantra absent. Fore tarsal tooth present in both sexes. Pelta transverse, shaped as a squashed ellipse, with distinctly polygonal reticulation. Sternite VIII with pair of stout or leaf-like posteromarginal setae submedially. Tube short than head. Pore plate of male absent.China ; Japan.Pentagonothrips, was originally established from Japan ; mesothoracic furcae closely fused together medially as well as metathoracic furcae joined together medially (but metathoracic furcae separated in Mystrothrips).The monobasic genus, om Japan . P.anteTaxon classificationAnimaliaThysanopteraPhlaeothripidaeOkajimaPlectrothripsbicolor Okajima, 1981: 313.CHINA, Guangdong: 1 female, Guangzhou City, Arboretum of South China Agricultural University , in leaf litter, 20.xi.2004 (Jun Wang); 1 male, Guangzhou City, Dafushan Forest Park , in leaf litter of Litchichinensis,17.iv.2016 (Chao Zhao).Body bicolored, yellow and brown. Head, thorax and tube brown, abdomen yellowish brown; all legs yellow; antennal segments II and III yellow, remaining segments brown. Head longer than broad, dorsal surface smooth except weakly sculptured posterolaterally. Antennal segments III and IV with two and three sense cones, respectively, segment VI with two sense cones. Maxillary stylets short, maxillary bridge developed and arched. Pronotum smooth, surrounded by stippled membrane with a distinct median longitudinal line. Metanotum with longitudinal striae medially. Mid tibia and hind tibia with one and two apical spur-like stout setae, respectively. Forewing parallel-sided with seven duplicated cilia. Pelta irregularly triangular with slender lateral lobes and a pair of campaniform sensilla. Abdominal tergites II\u2013VII each with a pair of wing retaining setae; sternites V\u2013VII with a pair of worm-like reticulate areas in both sexes; tergite IX S1 and S2 setae pointed, S1 setae longer than S2 but shorter than tube; tergite IX in male with a small median projection on posterior margin.China (Guangdong); Japan; Indonesia.P.bicolor, originally described from Japan and Indonesia . Holotype. Female aptera, CHINA, Yunnan province, Pu\u2019er City, Lancang County, Nuozhadu Nature Reserve , 5.xi.2016 (Chao Zhao).Paratypes. 6 females, 3 males, collected with holotype.Female aptera . Body length 1400. Head length 180; maximum width 190. Pronotum length 110; median width 250; epimeral setae 20. Metathoracic epimeral setae 20. Abdominal tergite IX length 120, basal width 75, distal width 40. Tube length 130, basal width 22, apical width 25; anal setae 430. Antennal segments I\u2013VIII length (width) as follows: 20(36), 28 (31), 37 (23), 39 (24), 45 (20), 40 (15), 47 (12).Male aptera. . Body length 1050. Head length 160; maximum width 160. Pronotum length 90; median width 185; epimeral setae 13. Metathoracic epimeral setae 13. Abdominal tergite IX length 105, basal width 55, distal width 40. Tube length 115, basal width 20, apical width 22; anal setae 370. Antennal segments I\u2013VIII length (width) as follows: 22(33), 23 (31), 32 (19), 29 (22), 33 (20), 31(17), 39(13).China (Yunnan).The specific epithet is named after the type locality, Lancang County, Yunnan Province, China.Urothripstarai , particularly in the shape of antennae, but it can be differentiated from the latter by the following diagnostic characters: (1) head broadly rounded in front (vs slightly produced in U.tarai); (2) dorsal surfaces of head and pronotum largely sculptured with polygonal reticulation (vs head and pronotum distinctly tuberculate and without reticulation in U.tarai); (3) major body setae on head, pronotum, especially on abdominal tergites are stout, dilated and fan-shaped at apex ; (4) fore femora brown (while fore femora yellow in U.tarai).There are ten species recognized in this genus , of whicPageBreak"} +{"text": "Negative, cognitive and depressive symptoms, as well as physical comorbidities, have a great impact on the real-world functioning in patients with schizophrenia (SZ) . However, not all the studies have employed accurate psychometric instruments to assess these symptoms, nor have all these factors been studied simultaneously.The aim of the current study is to analyze the determinants of functionality in SZ measured by the Personal and Social Performance (PSP) scale, and considering not exclusively psychopathological and cognitive variables, but also aspects related to physical health and inflammation.Sample: 73 outpatients with SZ, duration of illness \u226410 years, under stable maintenance treatment .Clinical variables: PANSS, CGI-Severity, Clinical Assessment Interview of Negative Symptoms (CAINS) -Motivation/Pleasure (MAP) & Expression (EXP) domains-, Brief Negative Symptom Scale (BNSS), Calgary Depression Scale (CDS), MATRICS Consensus Cognitive Battery (MCCB), PSP.Biological variables: Glucose, cholesterol, LDL, HDL, triglycerides, TSH, prolactin, insulin, uric acid, alkaline phosphatase (APh), C-reactive protein (CRP), TNF-\u03b1, interleukin(IL)-6, IL-2, IL-1\u03b2, IL-1RA, homocysteine, HT (% hemolysis), lipid peroxidation (LPO), catalase.Pearson correlations were performed to select variables significantly related to PSP scores which were later included in stepwise multiple linear regression analyses. Age, sex, education, smoking, alcohol use, BMI, antipsychotic equivalent doses and other confounding factors were considered.Final model for PSP total score identified that CGI-Severity (\u03b2= -0.279), PANSS-NM (negative Marder Factor) (\u03b2 = -0.218), Asociality subscale of BNSS (\u03b2= -0.383) and IL-2 (\u03b2= -0.269) were significant predictors.Predicting variables included in regression models for specific PSP domains:- Self-care : PANSS-NM (\u03b2=0.458), Avolition subscale of BNSS (\u03b2=0.248), IL-2 (\u03b2=0.221), APh (\u03b2=0.201).- Useful activities : CGI-S (\u03b2=0.245), Avolition (\u03b2=0.557).- Social relationships : Asociality (\u03b2=0.578), PANSS-GP (\u03b2=0.276), CAINS-EXP (\u03b2=0.178).- Aggresive behaviour : PANSS-P (\u03b2=0.408), CDS (\u03b2=0.273).1.Negative symptoms are the most important determinants of a deficit in the real-world functioning in SZ, especially \u201casociality.\u201d2.\u201cApathy\u201d has a negative impact on self-care and useful activities domains.3.Proinflammatory cytokine IL-2 marks poor functionality.1. Harvey (2014). Assessing disability in schizophrenia: tools and contributors. J Clin Psychiatry.2. Strassnig et al. (2015). Determinants of different aspects of everyday outcome in schizophrenia: The roles of negative symptoms, cognition, and functional capacity. Schizophr Res.3. Menendez-Miranda et al. (2015). Predictive factors of functional capacity and real-world functioning in patients with schizophrenia. Eur Psychiatry."} +{"text": "Marinomonas fungiae strain AN44T was isolated from mucus of the coral Fungia echinata. Optimum growth occurs at 3 to 5% NaCl. The draft genome is 4.2\u2009Mb, with 3,776 protein-coding genes. It harbors genes for the degradation of aromatic compounds, such as quinate, ferulate, p-coumarate, protocatechuate, and p-hydroxyphenylacetate. Marinomonas fungiae strain AN44T (JCM 18476T) is an aerobic, Gram-negative, motile, and rod-shaped bacterium belonging to the class Gammaproteobacteria and was isolated from mucus of the coral Fungia echinata from the Andaman Sea (N44T JCM 8476T is aman Sea .M. fungiae strain AN44T was generated at the DOE Joint Genome Institute (JGI) using the Illumina HiSeq 2000 platform (https://github.com/lh3/wgsim), and AllPaths-LG , respectively. The draft genome contains a total of 3,776 CDSs, 78 pseudogenes, 53 tRNAs, 16 rRNAs , 5 noncoding RNAs (ncRNAs), and 1 clustered regularly interspaced short palindromic repeat (CRISPR). Based on COG functional categories, the CDSs of the M. fungiae genome were distributed into categories of amino acid transport and metabolism (9.84%), carbohydrate transport and metabolism (5.92%), cell cycle control, cell division, and chromosome partitioning (1.08%), cell motility (3.51%), cell wall/membrane/envelope biogenesis (5.06%), chromatin structure and dynamics (0.09%), coenzyme transport and metabolism (5.47%), defense mechanisms (2.18%), energy production and conversion (6.61%), extracellular structures (0.44%), function unknown (5.41%), general function prediction only (7.31%), inorganic ion transport and metabolism (5.19%), intracellular trafficking, secretion, and vesicular transport (1.55%), lipid transport and metabolism (3.35%), mobilome prophages and transposons (1.08%), nucleotide transport and metabolism (2.47%), posttranslational modification, protein turnover, and chaperones (4.15%), RNA processing and modification (0.03%), replication, recombination, and repair (3.83%), secondary metabolite biosynthesis, transport, and catabolism (2.12%), signal transduction mechanisms (8.13%), transcription (7.97%), translation, ribosomal structure, and biogenesis (7.18%), and unassigned (28.88%).The genome was annotated using the JGI Microbial Genome Annotation Pipeline . Genes wp-coumarate, along with a single operonic gene cluster for central aromatic compound degradation via the protocatechuate meta-cleavage pathway, were found in the genome. Additionally, a single operonic gene cluster for the degradation of p-hydroxyphenylacetate was found.Further, putative genes or gene clusters for peripheral aromatic compound degradation pathways of quinate, ferulate, and LIQF00000000. The version described in this paper is the first version, LIQF01000000, and consists of sequences LIQF01000001 to LIQF01000036.This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number"} +{"text": "Nucl. Acids Res. (04 January 2016) 44 (D1): D447\u2013D456. doi: 10.1093/nar/gkv1145.3Medizinisches Proteom Center (MPC), Ruhr-Universit\u00e4t Bochum, D-44801 Bochum, Germany.The authors wish to correct the affiliation of one of the authors. Gerhard Mayer's only affiliation should be 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.He does NOT have a second affiliation at: The authors apologise to the readers for this error."} +{"text": "With limited and low-genetic barrier drugs used for the prevention of mother-to-child transmission (PMTCT) of HIV in sub-Saharan Africa, vertically transmitted HIV-1 drug-resistance (HIVDR) is concerning and might prompt optimal pediatric strategies.The aim of this study was to ascertain HIVDR and viral-tropism in majority and minority populations among Cameroonian vertically infected children.A comparative analysis among 18 HIV-infected children (7 from PMTCT-exposed mothers and 11 from mothers without PMTCT-exposure) was performed. HIVDR and HIV-1 co-receptor usage was evaluated by analyzing sequences obtained by both Sanger sequencing and ultra-deep 454-pyrosequencing (UDPS), set at 1% threshold.10 copies/mL, and 526 (282\u2013645) cells/mm3, respectively. All children had wild-type viruses through both Sanger sequencing and UDPS, except for 1 PMTCT-exposed infant harboring minority K103N (8.31%), born to a mother exposed to AZT+3TC+NVP. X4-tropic viruses were found in 5 of 15 (33.3%) children (including 2 cases detected only by UDPS). Rate of X4-tropic viruses was 0% (0/6) below 5 years , and became relatively high above 5 years versus CD4 >15% ; similarly for CD4 \u2264200 (3/4 [75%]) versus CD4 >200 age, viremia, and CD4 count were 6 (4\u201310) years, 5.5 (4.9\u20136.0) logNGS has the ability of excluding NRTI- and NNRTI-mutations as minority species in all but 1 children, thus supporting the safe use of these drug-classes in those without such mutations, henceforth sparing ritonavir-boosted protease inhibitors or integrase inhibitors for the few remaining cases. In children under five years, X4-tropic variants would be rare, suggesting vertical-transmission with CCR5-tropic viruses and possible maraviroc usage at younger ages. From these observations, we postulated that minority DRMs in HAART-na\u00efve children might grow-up through selective drug-pressure and populate plasma in a short-frame, herein justifying the rapidly emerging DRMs we observed at failure. Although not yet clinically endorsed, pediatric minority DRMs might be more concerning in the context of PMTCT, henceforth underscoring an unmet clinical need.,11 Coupled to previous knowledge on the detection of DRMs by next-generation sequencing (NGS),\u201314 we thus hypothesized that using NGS to assess DRMs in vertically infected HAART-na\u00efve children would contribute in designing long-term HAART strategies for SSA-children.As the footprint of long-term HAART depends largely on the effectiveness of first-line drugs in sustaining viral suppression, establishing adequacy between pediatric HAART and DR-mutations (DRMs) would be clinically relevant. As HAART would be reaching 1.5 million children by 2020, as high as 20% virological failure (VF) is expected, favored by high-viremia and poor adherence in children.,16 Without optimal strategies, VF would quickly overcome HAART success, maintaining children vulnerable.Current pediatric HAART-regimens consist of lamivudine (3TC), abacavir (ABC), or zidovudine (AZT), associated to ritonavir-boosted lopinavir (LPV/r) or NVP. LPV/r is recommended to overcome PMTCT-resulting non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance, whereas NVP matches with postnatal prophylaxis.,8 Although not yet approved for under 16 years, the CCR5 antagonist\u2014maraviroc\u2014might represent a suitable antiretroviral alternative for children, pending proof-of-concept towards relevant pediatric clinical trials. Particularly, there are limited evidence on the potential effectiveness of maraviroc for SSA-children in PMTCT, initial-HAART and/or following treatment-failure.\u201321 With rising concerns of minority variants on response to several classes of antiretrovirals, a genuine delineation of HIV-1 tropism, considering both minority and majority quasi-species,,23 could rationalize maraviroc suitability for pediatric HAART-policies in SSA.Moreover, pediatric HAART options are limited in SSA, urging the quest for a wider therapeutic portfolio.Based on these assumptions, we aimed to ascertain DRMs and HIV-1 co-receptor usage, in majority and minority viral populations, from children according to maternal PMTCT-exposure in a resource-limited setting (RLS).22.1A comparative study was conducted in 2015 among 18 HIV-1 vertically infected Cameroonian children, all HAART-na\u00efve, stratified according to maternal antiretroviral exposure during pregnancy: control-group versus case-group (7 children from mothers exposed to reverse transcriptase inhibitors [RTIs]). For each child, a plasma sample was collected to perform both Sanger- and 454 ultra-deep pyrosequencing (UDPS).2.2 Briefly, viral RNA was extracted from plasma using QIAamp Viral RNA minikit , following manufacturer's instructions. PR/RT-containing region was then reverse-transcribed and amplified using SuperScript One-Step for long templates reverse transcriptase polymerase chain reaction (RT-PCR) of Invitrogen kit , with an eventual second-round seminested PCR. Direct sequencing was then performed using 7 overlapping primers.Protease (PR)/RT Sanger sequencing was performed as previously described. Briefly, viral RNA containing the V3-loop region was reverse-transcribed and amplified using an RT/Taq mix, with an eventual second-round seminested PCR. Direct sequencing was then performed using 4 overlapping primers.V3 loop Sanger sequencing was performed as previously described.2.32O DNase RNase free, 1\u200a\u03bcL forward primer (10\u200a\u03bcmol/L), 1\u200a\u03bcL reverse primer (10\u200a\u03bcmol/L), 1\u200a\u03bcL RNase Out (40\u200aU/\u03bcL Invitrogen) and 1.2\u200a\u03bcL RT/TAQ, for a final volume of 50\u200a\u03bcL. RT-PCR conditions were the following: 1 cycle 50\u00b0C, 30 minutes; 1 cycle 94\u00b0C, 2 minutes; 40 cycles ; a final extension 68\u00b0C, 10 minutes. Forward and reverse primers were respectively 5\u2019GACAGGCTAATTTTTTAGGG3\u2019 and 5\u2019GATAAATTTGATATGTCCATTG3\u2019 . Nested-mid PCR was then performed with the Fast Start HiFi PCR system using 5 pairs of barcoded-modified forward and reverse primers for each amplicon , 8\u200a\u03bcL MgSO4 (5\u200ammol/L), 2.8\u200a\u03bcL H2.4Ten microliters viral RNA were reverse transcribed with 1-step RT-PCR system using forward and reverse primers, under the following conditions: 1 cycle 50\u00b0C, 30 minutes; 1 cycle 94\u00b0C, 2 minutes; 35cycles ; a final extension 68\u00b0C, 10 minutes. A nested mid-PCR was then performed with the Fast Start HiFi PCR system as previously described.2.5PR/RT PCR products and V3 loop (one fragment of 367 bps) were purified using Agencourt AMPure PCR purification beads and quantified with Quant-iT PicoGreen double-stranded DNA assay kit on a GloMax multidetection system . Phylogenetic analyses excluded any possible sample contamination (data not shown).Pooled purified PCR products were clonally amplified by emulsion PCR and pyro-sequenced on the 454 GS junior platform as previously described.2.6The entire PR (amino acid position: 1\u201399), RT (1\u2013251) and the entire V3 loop (1\u201335) sequences obtained after 454-pyrosequencing were de-multiplexed and then quantified using the SFF tool Roche. Using a home-made Perl script and SHORAH package 0.5.1, sequences were filtered and corrected for homopolymeric region-associated errors and aligned against HIV-1 consensus B. Final alignments were manually checked for insertion or deletion in homopolymeric regions that could result in a frame shift. Nucleotidic/aminoacidic variants were evaluated and quantified by a home-made pearl script, and sequences were considered reliable when showed an intra-patient frequency \u22651% in both forward and reverse strands.2.7http://hivdb.stanford.edu/pages/download/resistanceMutations_handout.pdf) and geno2pheno.v2.5 (http://coreceptor.geno2pheno.org/), respectively. Using a quantitative interpretation, viruses were considered CXCR4-tropic (X4-variants) by UDPS when \u22652% viral species had a false-positive rate (FPR) \u22643.5%, or by Sanger sequencing when FPR was \u226410%, describing the probability of classifying an R5-virus falsely as an X4-variant.PR/RT DRMs and HIV-1 co-receptor usage were interpreted using Stanford HIVdb list available at 2.9HIV-1 DRMs and coreceptor usage were compared between the two PMTCT-groups. Coreceptor results by Sanger sequencing and UDPS were considered concordant if viral-tropism was identical from both sequencing technologies. Viral-tropism was explored according to age and CD4 count.P values <.05 were considered statistically significant.All statistical analyses were performed using the statistical open source environment R.v.3.1.1. 2.10Ref.\u200aN\u00b0034/NEC/SE), proxy-informed consent was provided, unique identifiers were used for privacy and confidentiality, and a material transfer agreement was established.Ethical clearance was obtained from the Cameroon National Ethics Committee cells/mm3, respectively, without any significant difference between the 2 groups (data not shown). In the control, neither children nor their mothers had any antiretroviral exposure. Antiretroviral history of children belonging to the case-group, considered at higher risk of HIVDR, is described in Table Overall, median (interquartile range [IQR]) age, viremia, and CD4 count were 6 (4\u201310) years, 5.5 (4.9\u20136.0) log3.2HIV-1 subtyping revealed 50% CRF02_AG (9/18), 33.3% F (6/18), 11.1% CRF01_AE (2/18), and 5.6% CRF11.cpx (1/18).3.3PR/RT sequences were successfully obtained both through Sanger sequencing and UDPS for 17/18 children. The median UDPS coverage was of 1642 (IQR: 1269\u20135193) reads. In the entire covered PR/RT regions, the 2 sequencing technologies showed total concordance in variants detection, and all UDPS variants with frequencies <20% were not detected by Sanger sequencing , an accessory polymorphism weakly selected under etravirine (ETR) and rilpivirine (RPV), was found in a child aged 8 years from the control group.By using UDPS, 1 (aged 1 year) of 7 children 14.3%) from the case-group harbored viruses with K103N , a nonpolymorphic mutation causing high-level resistance to NVP and efavirenz (EFV). This infant was born from an RTI-treated mother (AZT\u200a+\u200a3TC\u200a+\u200aNVP). Thus, Sanger sequencing and UDPS were performed also for the mother (ID-18613). UDPS revealed a virus harboring 2 major DRMs: L74\u200aV at minority-level (2.5%), causing high- and intermediate-level resistance respectively to didanosine and to ABC; Y181C at population-level (96.7%), causing high- and intermediate-level resistance respectively to NVP and to EFV, ETR, and RPV , a polymorphic accessory mutation selected under EFV, in a child aged 6 years Table .Other variants, found even at RTI-associated drug resistance positions, were with minimal or no effect on drug susceptibility or virological response. Of note, in either group, no major DRMs to ritonavir-boosted protease inhibitors (PI/r) were found by both Sanger sequencing and UDPS.3.4V3 loop sequencing was successful by both Sanger sequencing and UDPS for 15 of 18 children and the mother ID-18613, with an overall viral-tropism concordance of 87.5% 14/16) between Sanger sequencing and UDPS (Table /16 betweX4-tropic viruses were found in 5 of 15 (33.3%) children (including 2 cases detected only by UDPS), all aged above 5 years. Specifically, in 1 child (ID-11621) UDPS provided an added value in tropism-determination compared to Sanger sequencing. Indeed, a clinically relevant quantity of minority X4-tropic variants (frequency: 3.9%) was detected by UDPS in this child . In another child (ID-10196), despite an R5-tropism (FPR\u200a=\u200a79.7%) determined by Sanger sequencing, a discordant tropism was observed through UDPS with a high percentage of X4-tropic variants , because of insertions detected only at minority levels.P\u200a=\u200a.040). As expected, X4-tropic viruses were higher with CD4 \u226415% (4/9 [44.4%]) versus CD4 >15% ; similarly for CD4 \u2264200 (3/4 [75%]) versus CD4 >200 . No statistical difference was found in X4-variants between the 2 PMTCT-groups: 2 of 7 (28.6%) case group versus 3 of 8 (37.5%) control group, P\u200a=\u200a1.000.Of relevance, the rate of X4-tropic viruses was 0% (0/6) among children under 5 years , and became significantly higher as from 5 years and above , known to be associated with resistance to NNRTIs used both for PMTCT and first-line HAART in SSA, was found in a PMTCT-exposed infant, thus suggesting NNRTI-sparing regimens for such children.,30,34 Discrepancy in DRMs between mother and infant would be due to sample collection later after delivery (at the moment of infant HIV diagnosis), with possible selection following prophylaxis/breastfeeding; as previously reported in similar RLS . This infant (aged 1 year), compared to the median age of the study population (6 years), suggests that circulating DRMs might have fade-up with increasing age.,33 NNRTI mutations (E138A and V179D), found in children without PMTCT-exposure, are known as polymorphisms with little or no effect on drug susceptibility or virological response. The ability of NGS in excluding minority RTI-mutations supports the safe use of NNRTIs/NRTIs in those without such mutations, thus sparing from inappropriate switch to PI/r- or integrase inhibitor-containing regimens.,17,33\u201335In this high CRF02_AG-infected population,,37 as well as a baseline FPR <60 as previously demonstrated.,39 Further investigations might help in establishing novel public health strategies for an eventual usage of maraviroc in children.,40 As current PMTCT-practice might not be an independent factor for viral-tropism , CCR5-antagonist (maraviroc) could be a useful therapeutic weapon for pediatric HAART.,18,40Coreceptor usage in these children provides a clue for clinical application. Indeed, X4-variants appeared to be associated with older ages and lower CD4 cells, suggesting limited vertical transmission by CXCR4-tropic viruses, and later appearance of X4-variants with chronicity, immunological impairment,,39 Interestingly, by detecting minority insertions associated with a complete discrepant result on Sanger sequencing, UDPS appears very useful in validating tropism determination for non-B subtypes.Of the two children showing discordant results between the two sequencing techniques, the added value of UDPS in detecting X4-tropic minority variants is in accordance with previous reports.,22,41Therefore, UDPS might provide additional information in detecting DRMs and viral-tropism, confirming the added value of this technology for both clinical diagnostics and management of non-B HIV-infected children.,43In spite of this added value of UDPS, implementing NGS is more challenging in RLS , suggesting the need for simpler and affordable approaches integrating minority variants (point-of-care or pragmatic sequencing).,13,44\u201346 This study therefore provides relevant data to be used as base for further/enlarged studies.A potential study limitation could be the relatively small sample size, which makes the study probability relatively large. Also, in the PMTCT-exposed group, only 3 of 7 were exposed to triple ART, calling for subsequent investigations with scale-up of option B+. Moreover, HIV-1 variants were investigated only in plasma compartment, suggesting the need for exploring HIV variability in several compartments and the impact on treatment and monitoring strategies in SSA.In a nutshell, NGS could help in identifying PMTCT-exposed children harboring minority NNRTI-DRMs, therefore serving for a timely switch of treatment and limiting failure rate. NGS also reveals a possible absence of X4-variants among children below 5 years, thus suggesting possible public health approaches using maraviroc. These preliminary evidences, generated on a small sample of mainly CRF02_AG-infected individuals, merit further investigations for improved pediatric-HAART strategies in RLS.Conceptualization: A. Nanfack, C-F. Perno, C. Fokunang, C. Tangimpundu, D. Armenia, D. Takou, E. Temgoua, F. Ceccherini-Silberstein, G. Cappelli, J. Fokam, M-M. Santoro, P. Koki, V. Colizzi.Data curation: D. Armenia, F. Ceccherini-Silberstein, J. Fokam, L. Carioti, M. Bellocchi, M-M. Santoro.Formal analysis: D. Armenia, F. Ceccherini-Silberstein, J. Fokam, L. Carioti, M. Bellocchi, M-M. Santoro.Funding acquisition: C-F. Perno, J. Fokam, V. Colizzi.Investigation: A. Ndjolo, A. Nanfack, C-F. Perno, C. Fokunang, C. Tangimpundu, D. Takou, E. Temgoua, F. Ceccherini-Silberstein, G. Cappelli, J. Fokam, J. Torimiro, M-M. Santoro, P. Koki, V. Colizzi.Methodology: D. Armenia, D. Takou, F. Continenza, F. Ceccherini-Silberstein, J. Fokam, L. Carioti, M. Bellocchi, M-M. Santoro.Project administration: A. Ndjolo, C-F. Perno, C. Fokunang, F. Ceccherini-Silberstein, G. Cappelli, J. Fokam, J. Torimiro, P. Koki, V. Colizzi.Resources: A. Ndjolo, C-F. Perno, J. Fokam, V. Colizzi.Software: D. Armenia, D. Takou, F. Continenza.Supervision: A. Ndjolo, C-F. Perno, C. Fokunang, F. Ceccherini-Silberstein, G. Cappelli, M-M. Santoro, P. Koki, V. Colizzi.Validation: A. Ndjolo, C-F. Perno, C. Fokunang, C. Tangimpundu, D. Armenia, E. Temgoua, F. Continenza, F. Ceccherini-Silberstein, G. Cappelli, J. Fokam, J. Torimiro, L. Carioti, M. Bellocchi, M-M. Santoro, P. Koki, V. Colizzi.Visualization: A. Nanfack, C-F. Perno, C. Tangimpundu, D. Takou, E. Temgoua, F. Continenza, J. Fokam, M-M. Santoro.Writing \u2013 original draft: C-F. Perno, F. Ceccherini-Silberstein, J. Fokam, M-M. Santoro.Writing \u2013 review & editing: A. Ndjolo, A. Nanfack, C. Fokunang, C. Tangimpundu, D. Armenia, D. Takou, E. Temgoua, F. Continenza, G. Cappelli, J. Torimiro, L. Carioti, M. Bellocchi, P. Koki, V. Colizzi.We are appreciative to our institutional staff that participated locally in the enrolment and in sample processing. We thank Domenico Di Carlo for statistical analyses."} +{"text": "Halopteris filicina (Grateloup) K\u00fctzing, Dictyota dichotoma (Hudson) J. V. Lamouroux, Posidonia oceanica (L.) Delile and Flabellia petiolata (Turra) Nizamuddin from the Adriatic Sea (single point collection). VOCs were investigated by headspace solid-phase microextraction (HS-SPME) and analysed by gas chromatography and mass spectrometry (GC-MS/FID). H. filicina headspace contained dimethyl sulfide , C8-compounds ), benzaldehyde , alkane C17, dictyopterene D and C , tribromomethane (V), 1-iodopentane, others. F. petiolata headspace was characterized by DMS (22.2%), 6-methylhept-5-en-2-one (9.5%), C17 (9.1%), II (6.5%), compounds I-V. DMS (59.3%), C15 (14.5%), C17 (7.2%) and C19 (6.3%) dominated in P. oceanica headspace. Sesquiterpenes were found in D. dichotoma, predominantly germacrene D (28.3%) followed by other cadinenyl (abundant), muurolenyl and amorphenyl structures. Determined VOCs may be significant for chemosystematics and chemical communications in marine ecosystem.Performed phytochemical study contributes to the knowledge of volatile organic compounds (VOCs) of The research on the algae VOCs has been continued by different teams cyclohepta-1,4-diene). Proposed biogenesis of dictyopterenes starts from (3S)-1,cis-5-undecadien-3-ol and (3S)-1,cis-5,cis-8-undecatrien-3-ol by dehydration and cyclization.Carotenoid cleavage dioxygenases (CCDs) catalyze oxidative cleavage of carotenoids, resulting in the production of norisoprenoids\u2014apocarotenoids via glycso occur . The bre2-unit, which can potentially occur via either the \u03b2-oxidative pathway or non-oxidatively [Benzenoid and phenylpropanoid volatile compounds, primarily derived from phenylalanine require shortening of the carbon skeleton side chain by a Cdatively .P. oceanica followed by F. petiolata and H. filicina indicating those plants as source of sulfur compounds in marine ecosystem. Their headspace contained individually variety of C8-compounds (e.g. fucoserratene), benzaldehyde, alkanes C15, C17 and C19, dictyopterene D and C, others. Sesquiterpenes were found in D. dichotoma, predominantly germacrene D indicating similarity to terrestrial aromatic plants. Identified VOCs contain different types of organic compounds that may be significant for chemosystematics and ecology .Considering limited data available on the chemical composition of marine plants from the Adriatic Sea, the present research is contribution toward their better chemical characterization. Significant differences were found among the headspace VOCs from 3 seaweeds and 1 seagrass. High abundance of DMS was found in"} +{"text": "In t test) .S1 Fign = 8 biological replicates per genotype. (B) Percent of male only Spen KD larvae floating. (C) Percent of female only Spen KD larvae floating. (D) FB-specific Spen KD with different insertion site as Spen KD in Fig 1A compared to KD control (dcg>iw). (E) Genetic background controls (iSpen/+ and iw/+) for (D). (F) As the Spen hairpin insertion site appears to result in a lean phenotype, KD animals were normalized to their genetic background. (G) As in (A), three additional independent Spen hairpin constructs (dcg>iSpen) tested in different density solutions and compared to KD control (dcg>iw). (H) Genetic background controls (iSpen/+\u2019s and iw/+) for (G). P value obtained by ANOVA. *P < 0.05, ** P < 0.01, ***P < 0.001, **** P < 0.0001. Error bars represent SEM.(A) Percent of floating larvae in different density solutions. FB-specific Spen KD as in Fig 1A with additional dcg/+ background control. Fifty larvae per genotype per experimental replicate, (TIF)Click here for additional data file."} +{"text": "Klebsiella\u00a0pneumoniae infections. Herein, we report the draft genome sequences of two colistin-resistant K.\u00a0pneumoniae isolates (BA41763 and B6753). The sequence data indicate that BA41763 and B6753 contain genomes of ~5.9 and 5.7\u00a0Mb in size with several plasmids.Resistance to colistin is a major threat that limits therapeutic choices for treating carbapenem-resistant Klebsiella pneumoniae (CRKP) infections are difficult to manage, with very few remaining treatment options, such as colistin and tigecycline with 49\u00d7 and 23\u00d7 coverage, respectively. Assembled genome sequences were annotated in PATRIC, the bacterial bioinformatics database and analysis resource (http://www.patricbrc.org) (http://rast.nmpdr.org/) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).To further understand the molecular mechanism behind colistin resistance, we determined their whole-genome shotgun sequences in Ion Torrent PGM using 400-bp chemistry. https://www.patricbrc.org). Similarly for B6753, 5,754,328\u00a0bp with 6,248 CDS were identified. Also identified were 13 rRNAs, 72 tRNAs with 34 and 82 ARDB and CARD antimicrobial resistance genes and 72 and 181 virulence factors from the VFDB and Victors database, respectively.The genome of BA41763 had 5,944,266\u00a0bp with 6,678 coding sequences (CDS), 10 rRNAs, and 66 tRNAs. The annotation revealed 32 and 85 ARDB and CARD antimicrobial resistance genes, respectively. In addition, 74 and 183 virulence factors from VFDB and the Victors database, respectively, were identified (https://cge.cbs.dtu.dk//services/MLST/) (https://cge.cbs.dtu.dk//services/ResFinder/) (rmtf and aacA4), beta-lactam , fluoroquinolones lb-cr, oqxA, qnrB66), fosfomycin (fosA), macrolide (mph(A)), rifampin (ARR-2), and sulfonamide (sul2) resistance genes. Similarly, for B6753, we found aminoglycoside -Vla), beta-lactam , fluoroquinolone (aac(6\u2032)lb-cr), fosfomycin (fosA), macrolide (mph(E), msr(E)), phenicol (catB3), sulfonamide (sul1), tetracycline (tet(D), and trimethoprim . However, plasmid-mediated colistin resistance genes mcr-1 and mcr-2 were absent. B6753 had a mutation in the mgrB gene with a premature stop codon resulting in a truncated protein of 27\u00a0amino acids, but there were no mutations in the mgrB gene of BA41763.Next-generation sequencing (NGS) also revealed that BA41763 and B6753 were of sequence types (STs) ST147 and ST14, respectively, as analyzed by the MLST 1.8 tool (https://cge.cbs.dtu.dk//services/PlasmidFinder/) (PlasmidFinder 1.3 (Finder/) revealedLZYN00000000 and MEBR00000000, respectively. The versions described in this paper are the first versions, LZYN01000000 and MEBR01000000.This whole-genome shotgun project of both the isolates BA41763 and B6753 has been deposited at DDBJ/ENA/GenBank under the accession numbers"} +{"text": "EditorThe following manuscript has been retracted from our November \u2013 December, 2016 issue. It has been retracted on a request from the authors as they forgot to properly acknowledge the source of their data. The authors are grateful to those who pointed out this mistake. - Retraction in: Pak J Med Sci 2016;32(6):1500-1505. doi: https://doi.org/10.12669/pjms.326.11460Link: http://pjms.com.pk/index.php/pjms/article/view/11460/4800Effective role of lady health workers in immunization of children in Pakistan1, Azka Naeem2, Unaiza Shahid3, Wajiha Noor Syed4, Urva Khan5, Nayyar Misal Zaidi6Saira AfzalRetracted on February 7, 2017"} +{"text": "A 24-year-old male from Wangdue Phodrang district, Bhutan, presented with a history of unexplained intermittent low-grade fever and cough for 8 months. He also complained of weight loss, abdominal discomfort, and one episode of hemoptysis and convulsion. He was a cow herder by profession. A computed tomography scan showed hepatosplenomegaly with mesenteric lymphadenopathy. Biochemical evaluation showed elevated alkaline phosphatase 1096 IU/L), lactate dehydrogenase 330 IU/L), and C-reactive protein (40.8 mg/dL) and reverse albumin/globulin ratio. Complete blood count showed pancytopenia confirmed by peripheral smear. In addition, left shift of neutrophils and giant platelets were observed. Erythrocyte sedimentation rate (26 mm/h) was increased. Prothrombin time (20 s) and activated partial thromboplastin time (51 s) were prolonged. The bone marrow aspirate smear revealed intracellular and extracellular Leishman-Donovan bodies . In view096 IU/L,30 IU/L,"} +{"text": "C. elegans cell divisions that produce an apoptotic daughter cell exhibit Daughter Cell Size Asymmetry (DCSA), producing a larger surviving daughter cell and a smaller daughter cell fated to die. Genetic screens for mutants with defects in apoptosis identified several genes that are also required for the ability of these divisions to produce daughter cells that differ in size. One of these genes, ham-1, encodes a putative transcription factor that regulates a subset of the asymmetric cell divisions that produce an apoptotic daughter cell. In a survey of C. elegans divisions, we found that ham-1 mutations affect primarily anterior/posterior divisions that produce a small anterior daughter cell. The affected divisions include those that generate an apoptotic cell as well as those that generate two surviving cells. Our findings suggest that HAM-1 primarily promotes DCSA in a certain class of asymmetric divisions. Caenorhabditis elegans somatic development is essentially invariant. Almost all of the somatic divisions are asymmetric, generating two daughter cells that differ in fate [4p::gfp] .LG II. ynIs25 [flp-12p::gfp] [2p::gfp] , 19.LG III. nIs107[tbh-1p::gfp + lin-15(+)] [rdvIs1 [egl-17p::mCherry:his-24 + egl-17p::myristolated mCherry + pRF4] [n-15(+)] , rdvIs1 + pRF4] .LG IV. ham-1(gm279) [ ham-1gm29 [7].LG V. zuIs178 [-119(+)] .LGX. gmIs81 [7p::gfp] .ltIs44[pie-1p-mCherry::PH(PLC1delta1) + unc-119(+)] [lqIs80[scmp::gfp::CaaX] [Unmapped: -119(+)] , leIs270-119(+)] , lqIs80[p::CaaX] .kyEx581[ocr-4p::gfp + lin-15(+)] , Ex [Extra-chromosomal arrays: ::dsRed] .C. elegans promoter. The A/PVM, SDQR/L, A/PQR and URXR/L neurons were detected using the gmIs81 reporter. The SMB, OLQ, ASK, MC and RIC neurons were detected using the reporters flp-12p::gfp, ocr-4p::gfp, srbc-66p::gfp, ceh-19p::gfp and tbh-1p::gfp, respectively. When an extra neuron was detected in a ham-1 mutant, its position was in close proximity to the normal position of the single neuron found in wild-type animals. Missing neurons were only scored when using integrated transgenes, since extra-chromosomal arrays can be lost during cell divisions. Statistical analysis was performed using the two-sample Z-test for proportions.All neurons were detected with transcriptional reporters that express fluorescent proteins under control of the indicated lqIs80[scmp::gfp::CaaX]. V5.pa lineage analysis was performed by compiling and reordering images of rdvIs1[egl-17p::myr mcherry + egl-17p::H2B::mcherry] L2 larvae. The mcherry markers are upregulated in all cells of the V5.pa lineage. V5.paa daughter cells size measurements were performed at the 3- and early 4-cell stages, before V5.paap and V5.paaa migrations occurred. T.pp and V5.pa neuroblast daughter cell sizes measurements were performed as previously described for the Q neuroblasts' daughters , which labels the cells of the P3-8 lineage. Ratios are indicated in the text \u00b1 standard deviation.T.p lineage analysis was performed in early L2 larvae using aughters , 12. TheFor embryonic neuroblasts, automated lineaging was performed as described . After nFor each genotype and ACD, the measured daughter cells size ratio was plotted on graphs where horizontal dotted lines indicate 1:1 ratios, and horizontal grey bars indicate the median of each ratio distribution. Statistical analysis was performed using the Mann-Whitney U-test.ham-1 mutants produce abnormal numbers of neurons in specific lineages . The cells boundaries are indicated by dotted lines and the name of each cell is indicated. Right panels are schematic representations of the corresponding cells. Black arrows describe cell displacements. Colored arrows indicate the direction of neurite extensions. Upon V5.pa division, the anterior daughter V5.paa moves to a more dorsal position above its sister V5.pap. The V5.paa neuroblast divides asymmetrically before V5.pap to produce the smaller anterior daughter V5.paaa, which will become the PDE neuron, and the larger posterior daughter V5.paap. The V5.pap glioblast's division produces daughter cells of equal size, the anterior daughter V5.papa, which will become the PDE socket cell, and the posterior daughter V5.papp, which will become the PDE sheath cell. Before the V5.paap division, both V5.paap and V5.paaa migrate anteriorly and ventrally, respectively. V5.paap then divides to generate the larger anterior daughter V5.paapa which will become the PVD neuron, and the smaller posterior daughter V5.paapp, which dies. After completion of all cell divisions, PDE and PVD neurons extend their neurites. Abbreviations: so: socket cell; sh: sheath cell. Scale bars: 10 \u03bcm.(A) Schematic diagram of the V5.pa lineage, which produces two neurons (PDE and PVD), two neuron-associated support cells (PDE socket cell and PDE sheath cell) and one apoptotic cell (V5.paapp). V5.paa and V5.paap daughters are unequal in size, whereas V5.pap division is symmetric in size. (B) Description of the cell division sequence and cell movements that occur during posterior deirid development. Left panels are representative fluorescent labeling of the left V5.pa lineage at all stages of development by (TIF)Click here for additional data file."} +{"text": "Objectives. In this study, we assessed the extra-articular symptoms in constellation with selected serum cytokines and disease activity in spondyloarthritis (SpA). Patients and Methods. We studied 287 SpA patients: 131 had AS, 110 had PsA, and 46 had SAPHO. We assessed extra-articular symptoms in all cases. In 191 SpA patients, we measured serum interleukin-6 (IL-6), interleukin-18 (IL-18), interleukin-23 (IL-23), endothelin-1 (ET-1), vascular endothelial growth factor (VEGF), and epidermal growth factor (EGF). Results. Patients with acute anterior uveitis (AAU) had higher VAS (P = 0.0008), BADSDAI (P = 0.0001), ASDAS-ESR (P = 0.04), CRP (P = 0.006), IL-6 (P = 0.02), and IL-18 (P = 0.03) levels. Patients with inflammatory bowel disease (IBD) had higher VAS (P = 0.03), CRP (P = 0.0009), and IL-6 (P = 0.0003) levels. Patients with skin psoriasis had lower VAS (P = 0.001) and BASDAI (P = 0.00007) levels. Patients with psoriatic onycholysis had lower VAS (P = 0.006), BASDAI (P = 0.00001), and CRP (P = 0.02) and higher IL-23 (P = 0.04) levels. Patients with PPP had lower BASDAI (P = 0.04) and higher ET-1 (P = 0.001) levels. Conclusions. SpA patients with increased serum IL-18 and decreased serum ET-1 had an increased risk of extra-articular symptoms. In SpA patients, increased disease activity was associated with an increased risk of AAU and IBD and a decreased risk of skin psoriasis, psoriatic onycholysis, and PPP. Ankylosing spondylitis (AS), psoriatic arthritis (PsA), and SAPHO syndrome (SAPHO) are seronegative spondyloarthropathies (SpA) which are connected with the presence of HLA-B27 antigen \u20133. In thSeveral proinflammatory cytokines such as interleukin-6 (IL-6), interleukin-18 (IL-18), interleukin-23 (IL-23) are considered to play a role in pathogenesis of SpA \u201314. AlsoThere are data that development of different extra-articular symptoms is connected with elevated levels of different markers of inflammatory process , 6, 13. The aim of our study was to assess extra-articular symptoms in constellation with selected serum cytokines and disease activity in SpA. We selected cytokines that play a role in the pathogenesis of SpA and are involved in angiogenesis and endothelial function.This study was approved by the Ethics Committee of the Pomeranian Medical University in Szczecin . Informed consent was obtained from all patients. We studied 287 SpA patients: 131 had AS, 110 had PsA, and 46 had SAPHO. All patients were Caucasian. The following data were recorded: age, sex, disease duration, and extra-articular symptoms: acute anterior uveitis (AAU), inflammatory bowel disease (IBD), skin psoriasis, psoriatic onychopathy, and positivity for HLA B27. The diagnosis of AS was made according to modified New York criteria . The patWe also assessed the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI). This index has a possible score of 0\u201310, with a higher score indicating greater disease activity. We regarded patients as active if the BASDAI score was > 4 .The Ankylosing Spondylitis Disease Activity Score (ASDAS) was assessed using ESR. The ASDAS-ESR was calculated, in AS patients and PsA patients with axial joint involvement, using online calculator available at the Assessment of Spondyloarthritis International Society website.Disease activity score calculation, in PsA patients, were made use of free online Disease Activity Score 28 (DAS28) calculator.In the first 191 SpA patients, 81 had AS, 76 had PsA, and 34 had SAPHO; we studied serum levels of selected cytokines: IL-6, IL-23, IL-18, endothelin-1(ET-1), VEGF, and EGF. Additionally, we studied CRP and ESR. The controls were 30 healthy volunteers. The methods of assessment of these cytokines were presented in our previous paper .R values of correlations were determined and corresponding P values <0.05 were considered significant. The groups were compared using Student's t-test, Mann\u2013Whitney U test, and Kruskal-Wallis test. To assess parameters Pearson's chi-squared test (\u03c72), logistic regression analysis, and step-wise analysis were performed. The level of significance was set at P < 0.05. The statistical analysis was performed using STATISTICA version 8.0, StatSoft, Inc., Tulsa, United States.Data distributions were assessed using the Kolmogorov\u2013Smirnov test. Data are described as mean \u00b1 standard deviation and median (Q1 and Q3). The The clinical characteristics of SpA patients and the prevalence of extra-articular symptoms are presented in P < 0.000001) and in AS than in SAPHO (P = 0.0001). We compared SpA patients with AAU to those without AAU. SpA patients with AAU had longer disease duration (P = 0.0002) and higher prevalence of HLA-B27 antigen (P = 0.0001). SpA patients with AAU had higher disease activity as assessed using the VAS (P = 0.0008), BADSDAI (P = 0.0001), ASDAS-ESR (P = 0.04), and CRP (P = 0.006). Additionally, they had lower disease activity as assessed using the DAS28 (P < 0.0001) .P = 0.01) and BASDAI (P = 0.005) were associated with increased risk of AAU (P = 0.02) and IL-18 (P = 0.03) levels (P = 0.02). SpA patients with AAU compared to healthy controls had higher serum IL-18 levels (P = 0.00009). In SpA patients as compared to healthy controls, increased serum levels of IL-6 (P = 0.02), IL-23 (P = 0.03), and Il-18 (P = 0.0006) were associated with increased risk of AAU (P = 0.0007) were associated with increased risk of AAU (In SpA patients increased CRP (k of AAU . SpA pat) levels . SpA patk of AAU . In SpA k of AAU .P = 0.004). We compared SpA patients with IBD to those without IBD. SpA patients with IBD had higher prevalence of HLA-B27 antigen (P = 0.04) and higher disease activity as assessed using the VAS (P = 0.03), CRP (P = 0.0009), and IL-6 (P = 0.0003). Additionally, they had lower disease activity as assessed using the DAS28 (P < 0.0001) (P = 0.007). When SpA patients were compared to controls, increased serum levels IL-18 (P = 0.03) were associated with an increased risk of IBD (IBD was present in 3.5% SpA patients and in 7.6% AS patients. No one patient with PsA or SAPHO had IBD . The pre 0.0001) . SpA patk of IBD .P = 0.004), lower prevalence of HLA-B27 antigen (P = 0.00004), and lower disease activity as assessed using the VAS (P = 0.001), and BASDAI (P = 0.00007) (P = 0.003) and BASDAI (P = 0.002) were associated with decreased risk of skin psoriasis . In SpA soriasis .P > 0.05). In SpA patients as compared to healthy controls, increased serum levels of IL-18 (P = 0.0002) and decreased serum levels of ET-1 (P = 0.006) were associated with increased risk of skin psoriasis , lower prevalence of HLA-B27 antigen (P = 0.0004), and lower disease activity as assessed using the VAS (P = 0.006), BASDAI (P = 0.00001), CRP (P = 0.02), and IL-23 (P = 0.04) (We compared SpA patients with psoriatic onychopathy to those without psoriatic onychopathy. SpA patients with psoriatic onychopathy had shorter disease duration ( = 0.04) .P = 0.02).SpA patients with psoriatic onychopathy compared to healthy controls had higher IL-23 level (P = 0.002) had lower risk of psoriatic onychopathy (SpA patients with increased BASDAI (chopathy .P = 0.0002) and decreased serum levels of ET-1 (P = 0.008) were associated with increased risk of psoriatic onychopathy , lower prevalence of HLA-B27 antigen (P = 0.0008), and lower disease activity as assessed using the BASDAI (P = 0.04). They had higher ESR (P = 0.004) and higher serum ET-1 (P = 0.001) (P = 0.4). In SpA patients compared to healthy controls increased serum levels of IL-18 (P = 0.01) were associated with increased risk of PPP (PPP was present in 14.6% SpA patients and in 91.3% SAPHO patients . We comp= 0.001) . There wk of PPP .We presented extra-articular symptoms in constellation with disease activity and selected serum cytokines which are involved in disease activity, angiogenesis, and endothelial function in SpA patients.The percentage of AAU in SpA patients and AS patients in our study was similar to those presented by other authors \u20136, 9.The most important genetic factor associated with AAU is HLA-B27 . We confIn our study AAU was the most frequent in AS patients. Additionally, SpA patients with AAU had higher levels of ASDAS-ESR and lower DAS28. These confirm observations of other authors that AAU is more frequent in axial SpA , 8, 9. TWe also confirmed as other authors that patients with AAU had longer disease duration and higher disease activity , 8.IL-6 plays role in arthritis but its role in SpA pathogenesis is controversial. Kramer et al. presenteIL-18 is considered as one of proinflammatory cytokine which also activate and deregulate endothelial function. In our previous study we confirmed higher levels of IL-18 in SpA patients and AS patients . In currThe percentage of IBD in SpA patients in our study was similar to those presented by other authors , 5. PatiThe percentage of SpA patients with skin psoriasis in our study was similar to the results presented by others , 9. PeluWe also found that SpA patients with skin psoriasis, compared to SpA group without that symptom, had lower levels of proinflammatory cytokines such as IL-6, IL-23, IL-18, VEGF, and EGF. Nevertheless, we confirmed that increased serum IL-18 levels were associated with increased risk of skin psoriasis in SpA. These foundlings suggest that some markers of disease activity did not influence on prevalence of psoriatic skin changes. On the other hand it can confirm the role of IL-18 in pathogenesis of skin psoriasis by influence on disease activity and endothelial function.IL-23 is produced by keratinocytes and is considered to play a role in SpA pathogenesis. In our previous study by Przepiera-B\u0119dzak et al. we showePsoriatic onychopathy was observed only in PsA group. Peluso et al. have presented psoriatic onychopathy in 89.2% PsA patients . In SpA The axis IL-17/ILK-23 is considered to play the crucial role in SpA pathogenesis. In our study we presented association between psoriatic onychopathy and serum IL-23. SpA patients with psoriatic onychopathy had higher serum IL-23 than healthy controls. In our previous study by Przepiera-B\u0119dzak et al. we confiThere were data which confirmed increased serum IL-18 in SAPHO. These suggested role of IL-18 in pathogenesis of SAHO , 13. In ET-1 plays a role in inflammation and vasculopathy. Kuryliszyn-Moskal et al. presentepatients with AAU had higher serum IL-6 and IL-18;patients with IBD had higher levels of IL-6;patients with nail psoriasis had higher levels of IL-23;patients with PPP had higher levels of ET-1.In SpA patients, increased serum IL-18 and decreased serum ET-1 were associated with an increased risk of extra-articular symptoms. Additionally, increased serum IL-6 and IL-23 increased the risk of AAU. Among SpA patients, increased disease activity was associated with an increased risk of AAU and IBD and a decreased risk of skin psoriasis, psoriatic onycholysis, and PPP.The analysis of serum levels of selected cytokines in SpA patients with and without extra-articular symptoms and healthy controls confirmed the following:"} +{"text": "AbstractSciaroidea) are a globally species rich group of lower Diptera. In Europe, Fennoscandian peninsula in particular holds a notable diversity, ca. 1000 species, of which 10 % are still unnamed. Fungus gnats are predominantly terrestrial insects, but some species dwell in wetland habitats.Fungus gnats and Mycetophilidae , are described. Four of the species are known from Fennoscandia only whilst two are supposed to have boreo-alpine disjunct ranges, i.e. having populations in Fennoscandia and the Central European Alps. One of the species probably has a boreal range . Type material of Boletinacurta Sasakawa & Kimura from Japan was found to consist of two species, and a further species close to these taxa is described from Finland. Phroniaelegantula Hackman is redescribed and reported for the first time from Norway. DNA barcodes are provided for the first time for five species.Eight new fungus gnat species, belonging to the families Sciaroidea are lower Diptera traditionally classified to the infraorder Nematocera, thread-horned flies , black-winged fungus gnats (Sciaridae) and gall midges (Cecidomyiidae) (ed flies . Nematocfamilies . Sciaroimyiidae) . In thismyiidae) .Fungus gnats are a highly diverse group of flies, having over 5000 known species globally , and butDNA barcoding has become a standard procedure in biodiversity surveys and taxonomic studies e.g. . The metOrfelia Costa, Sciophila Meigen, Boletina Staeger and Phronia Winnertz. Orfelia is a keroplatid genus with 36 Holarctic species, of which 25 are known from the Palaearctic region .Images of male hypopygia were taken using an Olympus SZ61 stereomicroscope equipped with a Canon 650D camera and a LM Digital SLR Adapter. Habitus photos of the new Sciaroidea specimens. Legs or 2\u20133 abdominal segments of the specimens were placed in 96% ethanol in a 96-well lysis microplate and dispatched to the Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario where DNA was extracted and sequenced using standard protocols and primers was sequenced from a total of 10 primers . The frahttp://v4.boldsystems.org/index.php/IDS_OpenIdEngine) in order to search for conspecific taxa and to assess the COI divergence between the new species and the taxa available in the BOLD database. We used \u201ccurrent database\u201d and \u201cAll Barcode Records on BOLD\u201d as options in the queries. The queries were made during October 2016 and at that time the BOLD database held 4,708,558 sequences (with a minimum sequence length of 500 bp), of which 46206 belonged to the family Mycetophilidae and 3665 to the Keroplatidae. Genetic similarities presented here are based on K2P distances and were calculated by the BOLD identification engine.Barcodes of the Finnish specimens were submitted to the BOLD identifiSalmelasp. n.urn:lsid:zoobank.org:act:B5A81F63-3F71-4A8F-B23B-ADF5CA4211D3Type status:Holotype. Occurrence: catalogNumber: DIPT-JS-2014-0233; recordedBy: M. M\u00e4kil\u00e4; individualCount: 1; sex: M; lifeStage: adult; Taxon: phylum: Arthropoda; class: Insecta; order: Diptera; Location: country: Finland; stateProvince: Lapponia kemensis pars orientalis; municipality: Savukoski; locality: T\u00f6rm\u00e4oja Conservation Area; decimalLatitude: 67.823; decimalLongitude: 29.439; Identification: identifiedBy: Jukka E. Salmela; Event: eventDate: 2014-08-07; Record Level: institutionCode: ZMUTType status:Paratype. Occurrence: catalogNumber: BIOUG08366-D12; recordNumber: bayw.17; recordedBy: G. Sellmayer; individualCount: 1; sex: female; Location: country: Germany; stateProvince: Bavaria; locality: Nationalpark Bayerischer Wald, 11.3 km N of Grafenau; decimalLatitude: 48.9509; decimalLongitude: 13.422; Event: eventDate: 2012-09-13/22; Record Level: institutionCode: ZSMMale. Head bicolored, vertex with a triangular dark area, laterally yellowish brown Fig. a, b, c. 1Scutum yellowish with three longitudinal brown stripes; median stripe consisting of two stripes that are largely merged, a narrow anterior gap between the stripes is present Fig. b, c. DarWings yellowish, with a faint subapical dark band extending from C to M2. Veins dark brown except bm\u2013cu and bRs that are lighter. Veins R1 and bCuA with dorsal setae, R5 setose both ventrally and dorsally. Sc ending in C before bRs. R4 very short, about 0.12 times longer than apical portion of R5. Wing length 4.1 mm.Coxae yellowish brown - brown, bearing short dark setae, legs yellowish. Ratio of femur to tibia for fore, mid and hind legs: 0.79, 0.68, 0.63. Ratio of tibia to basitarsus for fore, mid and hind legs: 1.67, 1.0, 1.0. Anterior spur of mid-tarsus about 0.5 times longer than posterior spur.Abdominal tergites and sternites brown, bearing dark setae. Hypopygium brown. 9th tergite widest medially, apex rounded. Gonocoxites dorsally with an outgrowth, bearing a few long apical setae and having a mesial protrusion Fig. a. Cerci 22222Female.The paratype female is lacking all legs except right fore leg and right hind femur. The specimen is slightly paler than the holotype male. The specimen may be somewhat teneral or it has bleached in the Malaise trap or later in the ethanol. Otherwise the specimen is very similar to the holotype. Antennal flagellomeres, except first and last, are wider than long (length:width ratio of 4th segment is 0.78). Cerci short, apically truncated, gonocoxite 8 short and rounded. Wing length 3.9 mm.O.nigricornis (Fabricius) and O.subnigricornis Zaitzev & Menzel have a bunch of setae.The new species is characterised by the short and dark antennae, a yellow scutum with contrasting scutellar stripes, brown pleural sclerites of the thorax, brown, unicolorous abdomen and a short R4 vein. The dorsal lobe of gonostylus is strongly curved. The ventral lobe of gonostylus has only two black apical setae, while The name of the new species refers to its putative boreo-alpine, disjunct range in Europe. The name is a noun in apposition.O.boreoalpina sp.n. has a disjunct European range, having populations in the northern Fennoscandia and the Central European mountains dominated boreal forest. Bavarian site is a conifer-dominated mountain forest . If using the key provided by O.boreoalpina sp.n. has an orange scutum and brown pleura, thus dropping out already in the first couplet. In the key provided by O.nigricornis, that has elongated palpal segments and one pointed outgrowth on the dorsal side of gonocoxites. Orfelianigricornis, however, has a tuft of setae on the apex of dorsal lobe of the gonostylus while O.boreoalpina has only two dark setae. Other more or less similar species are 1) O.subnigricornis, that is characterized by the yellow scape and pedicel and median flagellomeres that are 1.4 times longer than wide , 2) O.sachalinensis (Matsumura) has a yellow abdomen and indistinct scutal stripes and 3) O.minima (Giglio-Tos) that has a yellowish scape, pedicel and a yellowish abdomen .The new species is rather distant to all other Holarctic species, but it may be closest to han wide shared by no other members. The nearest specimens are rather distant: 97 closest sequences have similarity values between 88.25 and 86.35, being assigned to O.nemoralis (Meigen) (54 specimens), O.nigricornis (2), Keroplatidae (40) and Mycetophilidae (1). DNA barcode and associated data of the paratype is available from the BOLD Public data portal.The DNA barcode of the paratype specimen is almost identical to the holotype, their similarity is 99.54 %. The type specimens belong to the same BIN old-growth boreal forest, dominated by birch , black. Scape:pedicel length ratio 1.30; scape with a rounded, a bit depressed sensory field in its lateral base, having 7 minute setae. Flagellomeres cylindrical, length:width ratio of 1st flagellomere 1.51, 4th flagellomere 1.76 and apical flagellomere 3.13. Flagellomeres covered by dense light setosity, setae slightly curved, their length shorter than width of respective flagellomere; polygon-like (reticulate) pattern present, especially so in apical flagellomeres.Thorax black. Scutum covered by pale setae. Anepimeron bare, other sclerites setose. Scutellum with eight setae in a curved row. Halteres light brown with pale setae; apical part of stem and base of knob infuscated.Wings hyaline, lamina covered by both macro and microtrichia. Base of Rs, R4 and r-m bare, other veins setose, veins light brown to dark brown. C exceeding tip of R5 25 % of the distance between R5 and M1. Sc2 situated between base of Rs and R4. Furcation point of median fork at the level of bRs. M1+M2 very short. Length ratio of M1+2:r-m = 0.53. Wing length 3.2 mm.Fore coxae light brown, mid and hind coxae dark brown, with pale setae, trochanters dark-brown. Legs yellowish brown, femora basoventrally darkened; apices of mid and hind coxae infuscated, the latter more clearly so. Setae on femora mostly dark, tibial and tarsal setae dark. Length ratio of femur to tibia for fore, mid and hind legs: 0.93, 1.03, 0.89. Length ratio of tibia to basitarsus for fore, mid and hind legs: 1.36, 1.57, 1.89. Anteroapical depressed area of the fore tibia with two rows of pale setae, proximal row curved with ca. 17 setae and distal row almost straight with ca. 20 setae. Ratio of apical width of tibia:length of longest tibial spur for fore, mid and hind legs: 0.52, 0.33, 0.33.Abdominal tergites and sternites dark brown - almost black, covered by dark setae. Distal margin of 9th tergite rounded Fig. a. Gonoco44444This is a very dark species with the head, antennae, thorax, and abdomen black or dark brown. The 9th tergite is apically rounded. The ventral lobe of the gonostylus has a prominent apical outgrowth. The aedeagus is about as long as the parameres with the apex truncated. The parameres are rather thin with their apices contorted.The new species is named after Mr. Tuomas Holopainen, the founder, songwriter and keyboardist of a Finnish metal band, \"Nightwish\". The name is a genitive.The new species is so far known only from eastern Finnish Lapland, the north boreal ecoregion Fig. .The type locality in T\u00f6rm\u00e4oja Conservation Area was a sloping birch forest in a river canyon, close to a spring brook.Sciophila. The number of large setae on the small median appendage of gonostylus is varying, it may be two or three, thus making the use of Zaitzev's , but is otherwise very different, having e.g. a high number of comb-like megasetae on the large median lobe of the gonostylus (63\u201365 vs. 19 in S.holopaineni sp.n.). If three setae, the species runs to the couplet 79 and thereafter to 95, 99, 109 and finally to 114, but the new species does not fit either S.kashmirensis Zaitzev or S.stackelbergi Zaitzev. Holotype male had two and three setae, paratype male had two in both gonostyli.The new species seems to be rather distant from the known Holarctic species of aitzev's key probSciophila. JS checked a few specimens in his collection (JES), and the character was present in S.buxtoni Freeman, S.curvata sp.n., Leptomorphusforcipatus Landrock, Polyleptaborealis Lundstr\u00f6m and Allocotocerapulchella (Curtis), but it was absent among Anaclileiadziedzickii (Landrock). In Acnemiatrifida Zaitzev there was an ventroapical sensory field at the scape, with hyaline cover. It is possible, that this trait is symplesiomorphic amongst Sciophilinae and is lost in some genera.We were not able to find any notes in the literature on the presence of a sensory field at the base of scape among Salmelasp. n.urn:lsid:zoobank.org:act:1B97183D-C325-46CA-9E12-AA1E98678CFEType status:Holotype. Occurrence: catalogNumber: DIPT-JS-2015-0252; recordedBy: J. Salmela; individualCount: 1; sex: male; Location: country: Finland; stateProvince: borealis pars borealisOstrobothnia ; verbatimLocality: Kemij\u00e4rvi, Pyh\u00e4-Luosto National Park, Karhunotko; verbatimLatitude: 67.001; verbatimLongitude: 27.133; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 2014-6-10/7-11; habitat: old-growth boreal forest with an intermittent brook; Record Level: institutionCode: ZMUTType status:Other material. Occurrence: recordedBy: A. Polevoi; individualCount: 1; sex: male; Location: country: Russia; stateProvince: Karelia; verbatimLocality: Kivach Nature Reserve; verbatimLatitude: 62.272; verbatimLongitude: 33.986; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 1990-8-13/9-11; habitat: Myrtillus pine forest; Record Level: institutionCode: FRIPMale. Head dark, almost black. Ocelli arranged in a shallow triangle, approximately on the median part of vertex; ratio of distance of lateral ocellus from median ocellus: distance of lateral ocelli from eye = 0.59. Vertex covered by dark setae, face covered by small setae and clypeus by longer setae. Eyes pubescent. Palpi pale, covered by pale setae. Length ratio of palpal segments 3\u20135: 3:4=0.81, 4:5=0.52. Penultimate segment 4.3 times as long as wide, last segment 11.0 times as long as wide. Antennae 16-segmented , brown, first flagellomere light brown. Scape:pedicel length ratio 1.38. Scape with a slightly depressed sensory field in its base, having 5-6 minute setae. Flagellomeres cylindrical, length:width ratio of 1st flagellomere 1.54, 4th flagellomere 1.3 and apical flagellomere 2.90. Flagellomeres covered by dense light setosity, setae slightly curved, their length shorter than width of respective flagellomere. Polygonal (reticulate) pattern not present in basal and median flagellomeres, and either unclearly present or absent on the apical flagellomeres; apical flagellomeres of the holotype are slightly wrinkled.Thorax dark brown. Scutum covered by pale setae. Anepimeron bare, other sclerites setose. Scutellum with eight setae in a curved row. Halteres light brown with pale setae.Wings hyaline, both macro and microtrichia present on lamina. Base of Rs and R4 bare, other veins setose, veins brown to dark brown. C exceeding tip of R5 22 % of the distance between R5 and M1. Sc2 situated above R4. Furcation point of median fork slightly before the level of R4. Length ratio of M1+2:r-m = 0.71. Wing length 2.6 mmCoxae yellow, with pale setae, trochanters infuscated. Legs yellow, femora ventrobasally darkened, setae on femora pale, tibial and tarsal setae darker. Length ratio of femur to tibia for fore, mid and hind legs: 0.98, 0.92, 0.83. Length ratio of tibia to basitarsus for fore, mid and hind legs: 1.81, 1.64, 2.20. Anteroapical depressed area of the fore tibia with ca. 16 pale setae in a row. Ratio of apical width of tibia:length of longest tibial spur for fore, mid and hind legs: 0.65, 0.27, 0.26.Abdominal tergites and sternites dark brown, covered by pale setae. 9th tergite triangular, apex pointed Fig. a. Gonoco66666S.californiensis Zaitzev; the 9th tergite of the latter species is medially constricted, in the former the outline of the 9th tergite is triangular.The new species is characterised by the presence of three setae on the small median lobe of the gonostylus, very narrow dorsal lobe of the gonostylus and strongly curved parameres. The new species is closest to curvata Latin, curved, an adjective) refers to the curved parameres of the male hypopygium.The name of the new species and having 18 comb-like megasetae . Although not mentioned in the description and improperly figured Boletinacurta Zaitzev 1994: 209 Type status:Paratype. Occurrence: recordedBy: M. Sasakawa; individualCount: 1; sex: male; Location: country: Japan; stateProvince: Honsu; verbatimLocality: Otsu, Mt. Hiei; verbatimLatitude: 35.06; verbatimLongitude: 135.83; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: eventDate: 1974-5-3; Record Level: institutionCode: OSAKABoletinacurta is a poorly known East Palaearctic species, hitherto recorded from Japan, Honshu range between April 27 and May 3. However, Russian specimens reported by , Honshu and Russ, Honshu . BoletinBoletinacurta was described from Honshu, the main island of Japan .of Japan . The typcription . The secBoletinacurta can be separated from the closely related B.sasakawai sp.n. and B.norokorpii sp.n. based on the following characters: 1) two stout setae present on the ventral lobe of the gonostylus and 3) the proximal row of stout setae on cerci (comb-like rows) is wider than apical row and the first flagellomere of B.curta is yellowish ; pedicel:first flagellomere length ratio of B.curta is 0.32 (0.24 in B.sasakawai sp.n. and 0.36 in B.norokorpii sp.n.). For the details of the male hypopygium of B.curta, please see Fig. ow Fig. 7b, 9b. FuBoletina species, such as B.trivittata Staeger, occur in both early and late season . Hence, it might be possible in theory that B.sasakawai sp.n. is just a late summer/autumn morph of B.curta, likewise the butterfly species Araschnialevana (Linnaeus), that has two distinct colour morphs within a season , elongated . Scape yellowish and brownish, pedicel yellow and first flagellomere basally yellowish. Length ratio of pedicel:first flagellomere 0.24. Flagellomeres dark, palpus yellow.Thorax dark-brown with pale setosity. Scutum shining, pleural sclerites with weak microtrichosity. Antepronotum yellow. Halter yellow. Femora yellow, bearing pale setae. Trochanters infuscated. Femora yellow, but mid and hind femora ventrobasally infuscated. Legs gradually darkening toward tarsi. Tibial spurs brownish. Length ratio of femur to tibia for fore, mid and hind legs: 0.77, 0.66, 0.66. Length ratio of tibia to basitarsus for fore, mid and hind legs: 1.06, 1.68, 1.68.Apex of wing slightly infuscated. Bases of M1 and M2, M1+2, r-m, bM1+2, Rs, A1 and Sc bare, other veins setose. C exceeding tip of R5 36 % of the distance between R5 and M1. Sc ending in C at the level of Rs. Length ratio of M1+2:r-m = 1.19. Cu forking slightly beyond M end of r-m. Wing length 5.0 mm.Abdomen dark-brown, tergites 2\u20134 laterodistally yellowish. 9th tergite elongated; cerci bearing two rows of combs, that are about equally wide, having ca. 45 stout setae Fig. b. Ventra8888B.curta it is curved and bearing two stout setae. The apices of parameres with a conspicuous pair of horn-like outgrowths.A large species with a vaguely infuscated wing apex, abdominal tergites 2\u20134 laterally yellowish and relatively long first flagellar segment (about 4-times the length of the pedicel). The ventral lobe of gonostylus bare, sinuous; in the closely related The new species is named after Dr. Mitsuhiro Sasakawa, Japanese entomologist and the collector of the holotype. The name is a genitive.Known only from the type locality (Yoshino in Japan). The holotype male was collected at the end of October.Boletinacurta.See above Salmela & Kolcs\u00e1rsp. n.urn:lsid:zoobank.org:act:D906B0FD-0C14-4FDC-9FF7-EADF472C4476Type status:Holotype. Occurrence: catalogNumber: DIPT-JS-2016-0044; recordedBy: J. Salmela; individualCount: 1; sex: male; Location: country: Finland; stateProvince: borealis pars borealisOstrobothnia ; verbatimLocality: Ylitornio, Tuorerommas Mire Conservation Area; verbatimLatitude: 66.479; verbatimLongitude: 24.757; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 2012-7-2/8-6; habitat: old-growth boreal forest with a spring brook; Record Level: institutionCode: ZMUTMale. Head black, vertex covered by pale setae, frons glabrous and face with scattered setae. Ocelli in a shallow triangle, median ocellus smallest. Clypeus not much longer than wide . Scape and pedicel brownish, first and second flagellomeres yellowish, base of third flagellomere yellowish. Length ratio of pedicel:first flagellomere 0.36. Flagellomeres dark, palpus yellow.Thorax dark-brown with pale setosity. Antepronotum yellow. Halter yellow. Femora yellow, bearing pale setae. Trochanters infuscated. Femora yellow. Legs gradually darkening toward tarsi. Tibial spurs brownish. Length ratio of femur to tibia for fore and hind legs: 0.93, 0.76. Length ratio of tibia to basitarsus of hind leg: 1.68.Apex of wing slightly infuscated. Bases of M1 and M2, M1+2, r-m, bM1+2, Rs, A1 and Sc bare, other veins setose. C exceeding tip of R5 16 % of the distance between R5 and M1. Sc ending in C at the level of Rs. Sc2 present. Length ratio of M1+2:r-m = 1.14. Cu forking slightly beyond M end of r-m. Wing length 4.1 mm.Abdomen dark-brown, tergites 2-4 laterodistally yellowish. 9th tergite elongated; cerci bearing two rows of combs, that are about equally wide, having 18 stout setae . The caudal and proximal combs of the cerci are equally wide, having relatively a small number (18) of stout setae (over 40 in both B.curta and B.sasakawai sp.n.)A species very close to The new species is named after Dr. Yrj\u00f6 Norokorpi, Finnish forest researcher and former area manager at Parks & Wildlife Finland. The name is a genitive.So far known from SW Finnish Lapland only Fig. .Parisquadrifolia and Calypso bulbosa.The Finnish trapping site was an old-growth boreal forest characterised by vascular plants typical for base-rich soils, such as B.curta and B.sasakawai sp.n. It is likely, however, that the eastern species are more related to each other than to B.norokorpii sp.n. For example, presence of Sc2 (absent in other species), shorter basal flagellar segments and the small number of stout setae of combs in the cerci separate the new species from the eastern Palaearctic taxa. We assume that both eastern Palaearctic species have restricted ranges in Japan, Far East Russia and neighbouring areas, whereas B.norokorpii sp.n. might have a widespread boreal range.The new species is very close to the eastern Palaearctic species SCFI744-16. GenBank accession number: KY062991.Holotype: BOLD Sample ID: DIPT-JS-2016-0044. BOLD Process ID: AATATTATATTTTATTTTTGGAGCTTGATCAGGAATAATTGGTACATCATTAAGAATTCTTATTCGTGCTGAATTAGGACACCCTGGAGCATTAATTGGAGATGATCAAATTTATAATGTTATTGTAACAGCTCATGCATTTGTAATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAATCCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCTCGAATAAATAATATAAGATTTTGACTACTTCCTCCTTCATTAATATTACTTTTATCCAGAAGTTTAGTTGAAACAGGGGCTGGTACAGGTTGAACAGTGTACCCACCATTATCCTCAACAATTGCTCATGCAGGAGCATCTGTTGATTTAGCAATTTTTTCATTACATTTAGCAGGAATTTCTTCTATTTTAGGAGCTGTAAATTTTATTACTACAATTATTAATATACGAGCTCCTGGAATTACTTTTGAACGAATACCTCTTTTTGTATGATCAGTTTTAATTACAGCTATTTTATTATTATTATCTCTCCCAGTTTTAGCTGGAGCTATTACTATACTTTTAACAGACCGTAATTTAAATACATCATTTTTTGATCCTGCTGGAGGAGGAGATCCTATTTTATATCAACACTTATTCBOLD:ADD1952, shared by no other specimens. In BOLD database the closest matches to this specimen are three Boletinalundbecki Lundstr\u00f6m and four Boletina unassigned to taxonomic species .The new species is assigned to the BIN Salmelasp. n.urn:lsid:zoobank.org:act:B3FBE538-6CFA-451B-AB4F-F62698CC3E27Type status:Holotype. Occurrence: catalogNumber: DIPT-JS-2014-0011; recordedBy: J. Salmela; individualCount: 1; sex: male; Location: country: Finland; stateProvince: Regio kuusamoensis; verbatimLocality: Salla, V\u00e4rri\u00f6 Strict Nature Reserve, Kuntasjoki; verbatimLatitude: 67.749; verbatimLongitude: 29.616; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 2013-6-4/29; habitat: old-growth boreal riparian forest with seepages; Record Level: institutionCode: ZMUTType status:Paratype. Occurrence: catalogNumber: DIPT-JS-2015-0101; recordedBy: J. Salmela; individualCount: 1; sex: male; Location: country: Finland; stateProvince: Regio kuusamoensis; verbatimLocality: Salla, V\u00e4rri\u00f6 Strict Nature Reserve, Kuntasjoki; verbatimLatitude: 67.750; verbatimLongitude: 29.620; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 2013-6-29/7-29; habitat: riparian forest with lush vegetation and large amount of decaying trees,; Record Level: institutionCode: JESType status:Paratype. Occurrence: catalogNumber: DIPT-JS- 2014-0404; recordedBy: J. Salmela; individualCount: 1; sex: male; Location: country: Finland; stateProvince: Lapponia kemensis pars orientalis; verbatimLocality: Savukoski, Urho Kekkonen National Park, Tyyroja; verbatimLatitude: 68.143; verbatimLongitude: 28.574; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 2014-7-1/8-5; habitat: riparian meadow, spring brook with abundant Palustriella mosses; Record Level: institutionCode: JESMale. Head brown, vertex covered by pale setae, frons glabrous. Ocelli in a line, central ocellus smallest, lateral ocelli close to eyes, their distance from eye less than their own width. Eyes pubescent. Palpi brown, bearing light setae. Length ratio of palpal segments 3-5: 3:4=0.88, 4:5=0.61. Penultimate segment 2.62 times as long as wide, last segment 4.67 times as long as wide. Third palpomere with a sensory pit in its base. Antennae brown, 16-segmented , pedicel and base of first flagellomere yellowish brown. Scape:pedicel length ratio 1.47. Flagellomeres cylindrical, length:width ratio of 1st flagellomere 2.27, 4th flagellomere 1.67 and apical flagellomere 1.90. Flagellomeres covered by dense light setosity, setae slightly curved, their length shorter than width of respective flagellomere.Thorax generally brown, except scutum that has yellowish brown anterior corners. Scutum with mainly pale setosity, two stout and long posterodorsal setae are present just above scutellum. Mediotergite bare, other sclerites bearing setae. Scutellum with four stout marginal setae. Halteres pale, bearing weak light setae and setulae.Wings hyaline, veins light brown. Bases of M1 and M2, M1+2, base of r-m, bM1+2, bRs and Sc bare, other veins setose. C slightly exceeding tip of R5. Sc ending free. Length ratio of M1+2:r-m = 1.03. Wing length 1.8 mm.Coxae yellow, bearing dark setae, legs yellowish. Length ratio of femur to tibia for fore, mid and hind legs: 1.02, 1.0, 0.84. Length ratio of tibia to basitarsus for fore, mid and hind legs: 1.28, 1.6, 1.63. Anteroapical depressed area of the fore tibia ovate, having ca. 20 light setae arranged in a curved row. Ratio of apical width of tibia:length of longest tibial spur for fore, mid and hind legs: 0.37, 0.30, 0.29.Abdominal tergites and sternites brown, bearing light setae. 9th tergite and cerci without peculiar characteristics. Ventroapical margin of gonocoxite with a marked median emargination Fig. b. Ventra10101010A small species that is different from the known member of the genus. The male hypopygium has the following diagnostic characters: the ventroapical margin of the gonocoxites has a deep notch; the mesial projection of the gonostylus lacks comb-like structures but bears a prominent finger-like projection and a rounded, hyaline protrusion; the aedeagal complex is about as long as broad and is apically notched.Lapponia kemensis pars orientalis, abbreviated as Lkor, is in Finnish \"Sompion Lappi\". The name is a noun in apposition.The name of the new species refers to the old Forest Sami name of the region, Sompio, meaning large area bordered by aapamires. The biogeographical province of The species has been collected so far from three localities, all of these from eastern Finnish Lapland close to the Russian border. In fact, all of the collecting sites belong to the River Tuuloma catchment area east of the Maanselk\u00e4 divide, so the waters finally flow to the Barents Sea in Russia.Collecting sites are small waterbodies surrounded by old-growth boreal forests.The new species stands apart from all other Holarctic members of the genus.SCFI001-15.BOLD Sample ID: DIPT-JS-2014-0011. BOLD Process ID: SCFI164-15.BOLD Sample ID: DIPT-JS-2015-0101. BOLD Process ID: SCFI102-15.BOLD Sample ID: DIPT-JS-2014-0404. BOLD Process ID: Barcoding of the holotype and paratypes failed.Salmelasp. n.urn:lsid:zoobank.org:act:082AAF64-6B68-438B-991A-9C42736838A3Type status:Holotype. Occurrence: catalogNumber: DIPT-JS-2015-0272; recordedBy: J. Salmela; individualCount: 1; sex: male; Location: country: Finland; stateProvince: Regio kuusamoensis; verbatimLocality: Salla, Iso Pyh\u00e4tunturi; verbatimLatitude: 66.776; verbatimLongitude: 28.810; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 2013-7-19/8-8; habitat: poor - intermediate rich sloping fen; Record Level: institutionCode: ZMUTType status:Paratype. Occurrence: catalogNumber: 1386 (3); recordedBy: G.P. Ostroverkhova; individualCount: 1; sex: male; preparations: slide mounted; Location: country: Russia; stateProvince: Krasnoyarsk region; verbatimLocality: Tungussko-Chunsky District, village Vanavary; verbatimLatitude: 60.33; verbatimLongitude: 102.30; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: sweep net; eventDate: 1972-7-26; habitat: swampy forest; Record Level: institutionCode: TSUMale. Head dark-brown, vertex covered by pale setae, frons glabrous. Ocelli in a line, central ocellus slightly smaller than laterals; lateral ocelli close to eyes, their distance from eye less than their own width. Eyes pubescent. Palpi brown, bearing light setae. Length ratio of palpal segments 3\u20135: 3:4=0.83, 4:5=0.69. Penultimate segment 3.6 times as long as wide, last segment 5.3 times as long as wide. Third palpomere with a sensory pit in its base. Antennae brown, 16-segmented , base of pedicel and base of first flagellomere yellowish brown. Scape:pedicel length ratio 1.60. Flagellomeres cylindrical, length:width ratio of 1st flagellomere 2.86, 4th flagellomere 1.75 and apical flagellomere 3.0. Flagellomeres covered by dense light setosity, setae slightly curved, their length shorter than width of respective flagellomere.Thorax generally dark-brown, except scutum that has yellowish anterior corners. Scutum with mainly pale setosity. Mediotergite bare, other sclerites bearing setae. Scutellum with four stout setae. Halteres pale, bearing weak light setae and setulae.Wings hyaline, veins brown. Bases of M1 and M2, M1+2, base of r-m, bM1+2, base of Rs and Sc bare, other veins setose. C exceeds tip of R5 very slightly. Sc ending free. Length ratio of M1+2:r-m = 1.18. Wing length 3.1 mm.Coxae yellow, bearing pale setae, legs yellowish, except femora ventrobasally and apices of hind femora infuscated. Length ratio of femur to tibia for fore, mid and hind legs: 0.95, 0.99, 0.82. Length ratio of tibia to basitarsus for fore, mid and hind legs: 1.03, 1.34, 1.60. Anteroapical depressed area of the fore tibia ovate, having ca. 19 light setae arranged in a slightly curved row. Ratio of apical width of tibia:length of longest tibial spur for fore, mid and hind legs: 0.39, 0.27, 0.24.Abdominal tergites and sternites brown, bearing light setae. 9th tergite and cerci normal for the genus Fig. a. Ventro11111111111111P.braueri Dziedzicki but differs in the following features; the apices of the parameres are non-setose (the setae here are long in P.braueri), the internal outgrowth of the ventral lobe of the gonostylus is curved and apically notched (not curved or notched in P.braueri), and the ventral lobe of the gonostylus also has a narrow club-like basal projection .The new species is close of reducta, reduced, an adjective) is referring to the non-setose apices of the male parameres.The name of the new species was close to a pine and spruce dominated pristine boreal forest.P.annulata, (= P.braueri). These two taxa are indeed closely related, but due to differences in the male hypopygia and DNA barcodes are considered as distinct species .The holotype male is the only member of the BIN Salmelasp. n.urn:lsid:zoobank.org:act:3A162039-F1B7-458E-BEBC-0317C31C25B7Type status:Holotype. Occurrence: catalogNumber: DIPT-JS-2015-0215; recordedBy: E. Rundgren; individualCount: 1; sex: male; Location: country: Finland; stateProvince: Lapponia inarensis; verbatimLocality: Inari, Muotkatunturi Wilderness Area, Kielajoki; verbatimLatitude: 69.146; verbatimLongitude: 26.292; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 2014-6-26/8-5; habitat: lush and swampy riparian birch forest; Record Level: institutionCode: ZMUTType status:Paratype. Occurrence: catalogNumber: MYCFI183-11; recordedBy: Finnmarksprosjektet; individualCount: 1; sex: male; Location: country: Norway; stateProvince: Finnmark; verbatimLocality: Alta, Goppaelva; verbatimLatitude: 70.027; verbatimLongitude: 23.394; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela, G. S\u00f6li; Event: samplingProtocol: sweep net; eventDate: 2010-6-13; Record Level: institutionCode: NHMOType status:Paratype. Occurrence: catalogNumber: MYCFI184-11; recordedBy: Finnmarksprosjektet; individualCount: 1; sex: male; Location: country: Norway; stateProvince: Finnmark; verbatimLocality: Alta, Goppaelva; verbatimLatitude: 70.027; verbatimLongitude: 23.394; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela, G. S\u00f6li; Event: samplingProtocol: sweep net; eventDate: 2010-6-13; Record Level: institutionCode: NHMOType status:Paratype. Occurrence: catalogNumber: BC-ZSM-DIP-22552-E10; recordedBy: D. Doczkal, S. Schmidt & J. Voith; individualCount: 1; sex: male; Location: country: Germany; stateProvince: Bavaria; verbatimLocality: Allg\u00e4u, Oberstdorf, Schochen; verbatimElevation: 2032 m; verbatimLatitude: 47.3936; verbatimLongitude: 10.3692; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: J. Salmela; Event: samplingProtocol: Malaise trap; eventDate: 2014-6-6/21; habitat: Blaugras-Horstseggenrasen; Record Level: institutionCode: ZSMType status:Other material. Occurrence: catalogNumber: BIOUG21868-H06; recordedBy: BIObus; individualCount: 1; sex: female; Location: country: Canada; stateProvince: British Columbia; verbatimLocality: Vancouver Island; verbatimLatitude: 49.044; verbatimLongitude: -125.684; verbatimCoordinateSystem: decimal degrees; verbatimSRS: WGS84; Identification: identifiedBy: BOLD ID engine; Event: samplingProtocol: sweep net; eventDate: 2014-6-30; habitat: old growth temperate rain forest; Record Level: institutionCode: BIOUGMale. Head brown, vertex covered by pale setae, frons glabrous. Ocelli arranged in a very shallow triangle, central ocellus slightly smaller than laterals; lateral ocelli close to eyes, their distance from eye less than their own width. Eyes pubescent. Palpi brown, bearing light setae. Length ratio of palpal segments 3\u20135: 3:4=0.92, 4:5=0.62. Penultimate segment 3.51 times as long as wide, last segment 10.0 times as long as wide. Third palpomere with a sensory pit in its base. Antennae brown, 16-segmented . Scape:pedicel length ratio 1.28. Flagellomeres cylindrical, length:width ratio of 1st flagellomere 3.0, 4th flagellomere 2.58 and apical flagellomere 3.2. Flagellomeres covered by dense light setosity, setae slightly curved, their length shorter than width of respective flagellomere.Thorax generally brown, scutum dorsally dark-brown. Scutum with mainly pale setosity, including the two stout and long dorso-posterior setae above scutellum. Mediotergite bare, other sclerites bearing setae. Scutellum with four stout marginal setae. Halteres pale, bearing weak light setae and setulae.Wings hyaline, veins light brown. Bases of M1 and M2, M1+2, r-m, bM1+2, bRs and apex of Sc bare, other veins setose. C slightly exceeding tip of R5. Sc ending free. Length ratio of M1+2:r-m = 1.29. Wing length 3.2-3.5 mm.Coxae and legs yellowish brown, bearing dark setae. Length ratio of femur to tibia for fore and mid legs : 0.93, 0.9, 0.76. Length ratio of tibia to basitarsus for fore and mid legs: 0.96, 1.21, 1.5. Anteroapical depressed area of the fore tibia ovate, having numerous light setae over the area. Ratio of apical width of tibia:length of longest tibial spur for fore and mid legs: 0.67, 0.33, 0.23.Abdomen. 9th tergite and cerci as in Fig. 141414141414Female. In general, similar to male. Antennae dark except scape, pedicel and base of 1st flagellomere yellowish brown. Scape:pedicel length ratio 1.54. Length:width ratio of 1st flagellomere 3.1, 4th flagellomere 2.14 . Length ratio of M1+2:r-m = 1.58. Wing length 3.5 mm.Phroniaprolongata sp.n. is a closely related species of P.exigua , the aedeagus is evenly curved along its length (less curved in P.exigua) and the parameres are very long, about as long as the aedeagus .prolongata, an adjective) of the new species refers to the elongated, prolonged parameres of the male hypopygium.The name , Norway, Finland and Germany Fig. . FennoscThe Finnish collecting site was a swampy riparian birch forest and in Germany the species was collected from an alpine meadow.P.exigua, all sharing a beaked, setose ventral lobe of the gonostylus and a row of ventral setae on the hind tibia .The new species belongs to a group of species clastered with nd tibia . The newsee e.g. c. The clSCFI251-15. GenBank accession number: KY062993.BOLD Sample ID: DIPT-JS-2015-0215. BOLD Process ID: AATTTTATACTTTATTTTTGGTGCTTGATCTGGAATAGTAGGAACTTCCCTAAGAATTATTATTCGTGCTGAACTTGGTCATCCAGGAGCATTGATTGGAAATGATCAAATTTATAATGTAATTGTTACTGCTCATGCTTTCATTATAATTTTTTTTATAGTTATGCCCATTATAATTGGTGGGTTTGGTAACTGACTTGTCCCATTGATATTGGGGGCCCCTGATATAGCTTTTCCTCGAATAAATAATATAAGTTTCTGATTATTGCCTCCCTCATTAACACTTCTTCTTTCAAGAAGTTTAGTCGAAGCTGGGGCTGGTACAGGTTGAACTGTTTATCCCCCTCTTTCTTCTACTATTGCTCACGCAGGATCTTCTGTTGATCTAGCTATTTTTTCTCTTCATTTAGCTGGTATTTCTTCAATTTTAGGGGCGGTAAATTTTATCACAACTATTATTAATATACGAGCTCCAGGAATTTCCTTTGATCGTTTACCTTTATTTGTTTGATCTGTTCTTATTACTGCTGTATTGCTTCTTTTATCGCTACCAGTTTTAGCTGGGGCTATTACTATACTTTTAACTGATCGAAATTTAAACACATCTTTCTTTGACCCTGCCGGAGGGGGGGACCCTATTCTTTATCAACATTTATTTP.exigua range between 95.57 and 94.8, and between the new species and P.egregia 89.98-87.86. The new species displays a notable intraspecific variation: the Canadian non-type female has 97.06 similarity compared to the holotype and the two Norwegian specimens have 96.6 similarity. Interestingly the similarity of the holotype and German paratype is 98.94, and these two are classified to the same Barcode index number (BIN) by the BOLD (BOLD:ACW2188), shared by no other specimens. The new species is, however, monophyletic Brachypogonsociabilis (Goetghebuer) and Bezziarhynchostylata Remm in Finnmark, Norway, were characterised by relatively high intraspecific distances (4.0-3.8 %) and were classified to four and three BINs, respectively ; scape, pedicel and basal half of first flagellomere yellowish. Scape with a prominent dorsal seta, about as long as first flagellomere. Scape:pedicel length ratio 1.33. Flagellomeres cylindrical, length:width ratio of 1st flagellomere 2.98, 4th flagellomere 1.75 and apical flagellomere 2.95. Flagellomeres covered by dense light setosity, setae slightly curved, their length shorter than width of respective flagellomere.Thorax generally brown. Scutum dorsally with three dark stripes, that are almost confluent; the stripes are separated by very narrow yellowish gaps; anterolateral corners yellowish. Scutum with mainly pale setosity. Mediotergite bare, other sclerites bearing setae. Scutellum with four stout setae. Halteres pale, bearing weak light setae and setulae.Wings hyaline, veins light brown. Bases of M1 and M2, M1+2, r-m, bM1+2, base of Rs and apex of Sc bare, other veins setose. C very slightly exceeding tip of R5. Sc ending free. Length ratio of M1+2:r-m = 1.29. Wing length 2.2 mm.Coxae and legs yellow, apices of mid and hind femora sligthly infuscated, bearing dark setae. Length ratio of femur to tibia for fore, mid and hind legs: 0.99, 0.97, 0.79. Length ratio of tibia to basitarsus for fore, mid and hind legs: 1.08, 0.97, 0.8. Anteroapical depressed area of the fore tibia ovate, having ca. 20 light in a row. Ratio of apical width of tibia:length of longest tibial spur for fore, mid and hind legs: 0.35, 0.28, 0.25.Abdomen mostly dark brown, but first, second and third tergites caudolaterally yellowish; these yellow areas are most extensive in second and third tergite. Sternum of second and third segments yellowish. Hypopygium dark brown. Ventroapical margin of gonocoxite with a wide and shallow median emargination, with a moderate median peak Fig. b. Ventra17171717Female. Similar to male. Antennae dark except scape, pedicel and base of 1st flagellomere yellowish brown. Scape:pedicel length ratio 1.32. Length:width ratio of 1st flagellomere 3.9, 4th flagellomere 2.80, apical flagellomere 2.5. Length ratio of M1+2:r-m = 1.84. Wing length 2.2 mm.Phronia species with a yellowish pattern on the abdominal tergites 1\u20133. The ventral lobe of the gonostylus is rounded and at its widest basally. The mesial projections are finger-like and the inner lamella of the ventral lobe of the gonostylus bears a tuft of setae. The species is somewhat close to P.elegans Dziedzicki and P.signata Winnertz, that have similarly shaped ventral lobe of the gonostylus; P.elegantula can be distinguished from these due to differences in the structure of the aedeagus, the ventral lobe of gonostylus and the mesial portion of the gonostylus.A A European species. The species was described from eastern Finland (Ok: Sotkamo and Ks: Kuusamo) and has been later recorded from southern and northern parts of the country . The species has been found from Russian Karelia and MurmSampling sites are coniferous forests, mixed forests and wetlands.Phroniaelegantula is somewhat similar to P.signata and P.elegans, and has the same yellowish anterolateral corners to the scutum as well as a rotund ventral lobe of the gonostylus. However the abdomen of P.elegans is dark brown as opposed to some yellowish colouration on abdominal tergites 1\u20133 of P.elegantula. Phroniasignata have only moderately emarginated ventroapical margins of the gonocoxites, whereas this character is much more conspicuous in P.elegantula. Phroniasignata has ca. 14 setae on the ventral edge of the ventral lobe of gonostylus . The nearest specimens in BOLD database belong to P.disgrega Dziedzicki, being 90.98 % similar to P.elegantula. DNA barcode and associated data of the German paratypes and female specimens is available from the BOLD Public data portal.All studied specimens belong to the BIN"} +{"text": "Edwardsiella ictaluri is a Gram-negative bacillus that has recently been implicated in disease outbreaks in tilapia and zebrafish. We report here the complete and annotated genome sequence of an isolate from a Nile tilapia (Oreochromis niloticus), which contains a chromosome of 3,630,639\u00a0bp and two plasmids. Ictalurus punctatus) was first detected in the late 1970s, predominantly in pond-reared fingerling channel catfish . Raw data 754\u00a0Mb) were error-corrected and trimmed to a total of 129\u00a0Mb in 8,795 sequences and assembled using Canu version 1.3 .The circularized and completed genome was submitted to the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) for annotation and submission to GenBank. The genome was also submitted for Rapid Annotations using Subsystems Technology (RAST) analysis , 11, empE.\u00a0ictaluri RUSVM-1 genome consists of one circular chromosome with 3,630,639\u00a0bp (57.4% G+C content). PGAP annotation predicted 3,377 genes encoding 3,254 proteins and 93 tRNAs. The RUSVM-1 genome is 5% smaller than that of E.\u00a0ictaluri 93-146, isolated from catfish, which contains 3,783 predicted genes. RNAmmer ( E.\u00a0ictaluri isolate 93-146 (E. anguillarum isolate LADL05-105 (E. piscicida isolate S11-285 (E. tarda isolate FL95-01 (E.\u00a0hoshinae isolate ATCC 35051 (E. ictaluri isolated from tilapia will be useful for future investigations into host-pathogen interactions and comparative Edwardsiella analyses.The e 93-146 , 92.4% (DL05-105 , 92.1% ( S11-285 , 83.0% ( FL95-01 , and 82.CC 35051 . Two plaCC 35051 . This coEdwardsiella ictaluri isolate RUSVM-1 has been deposited in GenBank under the accession no. CP020466.The complete genome sequence for"} +{"text": "D. Adams) A. Rich., Erythrina sigmoidea Hua (Fabaceae), Imperata cylindrical Beauv. var. koenigii Durand et Schinz, Nauclea pobeguinii (Pob\u00e9g. ex Pellegr.) Merr. ex E.M.A., Piper capense L.f., Polyscias fulva (Hiern) Harms., Uapaca togoensis Pax., Vepris soyauxii Engl. and Xylopia aethiopica A. Rich. Prominent antiproliferative compounds include: isoquinoline alkaloid isotetrandrine (51), two benzophenones: guttiferone E (26) and isoxanthochymol (30), the isoflavonoid 6\u03b1-hydroxyphaseollidin (9), the naphthyl butenone guieranone A (25), two naphthoquinones: 2-acetylfuro-1,4-naphthoquinone (4) and plumbagin (37) and xanthone V1 (46). However, only few research activities in the African continent focus on cytotoxic drug discovery from botanicals. The present review is expected to stimulate further scientific efforts to better valorize the African flora.Cancer remains a major health hurdle worldwide and has moved from the third leading cause of death in the year 1990 to second place after cardiovascular disease since 2013. Chemotherapy is one of the most widely used treatment modes; however, its efficiency is limited due to the resistance of cancer cells to cytotoxic agents. The present overview deals with the potential of the flora of Central, Eastern and Western African (CEWA) regions as resource for anticancer drug discovery. It also reviews the molecular targets of phytochemicals of these plants such as ABC transporters, namely P-glycoprotein (P-gp), multi drug-resistance-related proteins (MRPs), breast cancer resistance protein as well as the epidermal growth factor receptor (EGFR/ErbB-1/HER1), human tumor suppressor protein p53, caspases, mitochondria, angiogenesis, and components of MAP kinase signaling pathways. Plants with the ability to preferentially kills resistant cancer cells were also reported. Data compiled in the present document were retrieved from scientific websites such as PubMed, Scopus, Sciencedirect, Web-of-Science, and Scholar Google. In summary, plant extracts from CEWA and isolated compounds thereof exert cytotoxic effects by several modes of action including caspases activation, alteration of mitochondrial membrane potential (MMP), induction of reactive oxygen species (ROS) in cancer cells and inhibition of angiogenesis. Ten strongest cytotoxic plants from CEWA recorded following Cancer is a term for a series of malign diseases characterized by abnormal cell proliferation, leading to invasion and metastasis, the ultimate causes of deaths by cancer. The burden of neoplastic diseases affects the entire world population. Over the past two decades, there has been a slight improvement in cancer statistics due to diagnostic and therapeutic progresses and a better understanding of tumor biology -binding cassette (ABC) proteins are amongst the largest protein families found in all living organisms from microbes to humans . Additionally, other ABC transporters such as ABCC1/MRP1 , a signal transducer for cell growth and differentiation, is the cell-surface receptor belonging to the ErbB family of receptors. This family consists of four closely related receptor tyrosine kinases, namely EGFR/HER1/ErbB-1, HER2/c-neu/ErbB-2, HER3/ErbB-3, and HER4/ErbB-4. Mutations affecting the activity or expression of EGFR can contribute to carcinogenesis . They can be classified into three main types, that are initiator caspase , executioner or effector caspases and inflammatory caspases are generated. In many cancer cells, mitochondria appear to be dysfunctional , with a shift in energy metabolism from oxidative phosphorylation to active glycolysis and an increase in the generation of ROS pathway or Ras-Raf-MEK-ERK pathway is one of the most important signal transduction pathways. The MAPK/ERK pathway regulates growth, proliferation, differentiation and survival of the cells. Its deregulation is observed in various diseases such as cancer, degenerative syndromes, immunological and inflammatory diseases, making it an important drug target will be discussed. According to the criteria of the American National Cancer Institute, 20 \u03bcg/mL is the upper IC50 limit to be considered as promising for cytotoxic crude extracts from Garcinia punctata Oliv. and isobavachalcone (27) isolated from Dorstenia barteri Bureau isolated from Dorstenia mannii Hook.f. from Morus mesozygia Stapf. from Dorstenia angusticornis Engl. from Erythrina sigmoidea Hua from Erythrina excelsa Baker from Milicia excelsa Welw C.C. Berg. from Vismia laurentii De Wild. Engl. et Diels. A. Rich. Harms. K.Schumex.Engl. A. Rich. M\u00fcll.-Arg. and damnacanthol (20) from Pentas schimperi (Hook f.) Verde from Maesa lanceolata Forssk., Myrsine africana L., Embelia keniensis R.E.Fr., Embelia schimperi Vatke and Rapanea pulchra Gilg & Schellenb. and the naphthoquinone, plumbagin (37) from Plumbago and Diospyros species isolated Xylopia aethiopica A.Rich. from Polygonum limbatum Meisn from Erythrina sigmoidea Hua from Ficus chlamydocarpa Mildbr. & Burret from Dorstenia mannii Hook.f. from Dorstenia poinsettifolia Engl. and sophorapterocarpan A (45) from Pycnanthus angolensis (Welw.) Ward from Milicia excelsa Welw C.C. Berg. M\u00fcll.-Arg. Engl. et Diels. Harms. Hochst (Anacardiaceae) and isoquinoline alkaloid isotetrandrine (51), anthraquinones 19 and 20 and the xanthone 46 . Plants and compounds inducing hypersensitivity in these cell lines are summarized in Tables Some botanicals and phytochemicals from CEWA were screened against ABC transporters-expressing cell lines. The most investigated cell lines included the P-gp-overexpressing CEM/ADR5000 leukemia cell line, the MRP1-expressing HL60/AR leukemia cell line and BCRP-expressing MDA-MB-231/Aframomum arundinaceum (Oliver & Hanbury) K. Schum (Zingiberaceae) Merr. ex E.M.A. (Rubiaceae) from Polygonum limbatum Meisn from Dorstenia barteri from Erythrina sigmoidea Hua from Aframomum arundinaceum (Oliver & Hanbury) K. Schum from Uapaca togoensis Pax. Merr. ex E.M.A. isolated from Aframomum arundinaceum (Oliver & Hanbury) K. Schum from Hypericum lanceolatum Lam. from Aframomum arundinaceum (Oliver & Hanbury) K. Schum from Erythrina sigmoidea Hua from Garcinia nobilis Engl. . They included: Albizia adianthifolia (Schum.) and Alchornea cordifolia (Schum. & Thonn.) M\u00fcll.-Arg. Stapf. (Euphorbiaceae) Merr. ex E.M.A. A.Rich. (Annonaceae) from Hypericum lanceolatum Lam. compared to its sensitive counterpart HCT116 (p53+/+) cell line included: Beilschmiedia acuta Kosterm (Lauraceae) A. Rich. (Compositae) Merr. ex E.M.A. Harms. from Erythrina senegalensis DC Robyns & Wilczek or Tylostemon acutifolius Engl. & K. Krause] belongs to the family Lauraceae. The plant is mainly found in Cameroon and Central African Republic, where it is traditionally used to treat cancer and gastrointestinal infections , CEM/ADR5000 cells (IC50: 7.96 \u03bcg/mL) and HL60AR cells (IC50: 9.24 \u03bcg/mL), MDA-MB-231-pcDNA cells (IC50: 8.61 \u03bcg/mL), MDA-MB-231-BCRP cells (IC50: 6.52 \u03bcg/mL), colon carcinoma HCT116 (p53+/+) cells (IC50: 3.58 \u03bcg/mL), HCT116 (p53\u2212/\u2212) cells (IC50: 3.29 \u03bcg/mL), gliobastoma U87MG cells (IC50: 13.55 \u03bcg/mL) and U87MG.\u0394EGFR cells (IC50: 11.15 \u03bcg/mL), hepatocarcinoma HepG2 cells (IC50: 14.32 \u03bcg/mL) is a tree of 3\u20136 m, or 10\u201320 m belonging to the Fabaceae family. The plant is mainly found in Cameroon and Chad, where it is used as antidote , diuretic, febrifuge and to treat arthritis, rheumatism, pulmonary troubles, stomach troubles, infectious diseases and kidney diseases , atalantoflavone (15), bidwillon A (16), neobavaisoflavone (35), neocyclomorusin (36), and sigmoidin I (44) , CEM/ADR5000 cells (IC50: 20.06 \u03bcg/mL), MDA-MB-231-pcDNA cells (IC50: 22.37 \u03bcg/mL), MDA-MB-231-BCRP cells (IC50: 27.42 \u03bcg/mL), HCT116 (p53+/+) cells (IC50: 19.63 \u03bcg/mL), HCT116 (p53\u2212/\u2212) cells (IC50: 16.22 \u03bcg/mL), U87MG cells (IC50: 45 \u03bcg/mL), U87MG.\u0394EGFR cells (IC50: 29.80 \u03bcg/mL), and HepG2 cells (IC50:22.34 \u03bcg/mL) and CEM/ADR5000 cells (IC50: 7.18 \u03bcg/mL), pancreatic MiaPaca-2cells (IC50: 12.11 \u03bcg/mL) , HL60AR cells (IC50: 30.60 \u03bcg/mL), MDA-MB-231-pcDNA cells (IC50: 5.19 \u03bcg/mL), MDA-MB-231-BCRP cells IC50: 10.04 \u03bcg/mL), HCT116 (p53+/+) cells (IC50: 4.37 \u03bcg/mL), HCT116 (p53\u2212/\u2212) cells (IC50: 4.60 \u03bcg/mL), U87MG cells (IC50: 19.99 \u03bcg/mL), U87MG.\u0394EGFR cells (IC50: 10.68 \u03bcg/mL), and HepG2 cells (IC50: 18.28 \u03bcg/mL) is a deciduous, small to medium-sized tree growing up to 30 m tall, sometimes a shrub. In CEWA, the plant is distributed in South Tropical Africa especially in Angola, Zambia, West Tropical Africa: Burkina, Ghana, Guinea, Guinea-Bissau, Ivory Coast, Nigeria, Senegal, Sierra Leone, West-Central Tropical Africa: Cameroon, Central African Republic, Congo, DR Congo, Gabon. The plant is used in traditional medicine as abortive and to treat stomach ache and infectious diseases , CEM/ADR5000 cells , HCT116 (p53+/+) cells and HCT116 (p53\u2212/\u2212) cells , CEM/ADR5000 (IC50: 6.56 \u03bcg/mL) and MiaPaca-2 cells (IC50: 8.92 \u03bcg/mL) , HL60AR cells (IC50: \u03bcg/mL), MDA-MB-231-pcDNA cells (IC50:4.17 \u03bcg/mL), MDA-MB-231-BCRP cells (IC50: 19.45 \u03bcg/mL), HCT116 (p53+/+) cells (IC50: 4.64 \u03bcg/mL), HCT116 (p53\u2212/\u2212) cells (IC50: 4.62 \u03bcg/mL), U87MG cells (IC50: 13.48 \u03bcg/mL), U87MG.\u0394EGFR cells (IC50: 7.44 \u03bcg/mL), HepG2 cells (IC50: 16.07 \u03bcg/mL) , 22.63 \u03bcg/mL (CEM/ADR5000 cells), 3.27 \u03bcg/mL (MDA-MB-231 cells), 16.67 \u03bcg/mL (MDA-MB-231/BCRP cells), 14.66 \u03bcg/mL (HCT116 p53+/+cells), 5.98 \u03bcg/mL (HCT116 p53\u2212/\u2212cells), 4.15 \u03bcg/mL (U87MG cells), 16.35 \u03bcg/mL (U87MG.\u0394EGFR cells), and 12.99 \u03bcg/mL (HepG2 cells) against the above cancer cell lines Hutch., Uapaca perrotii Beille Uapaca somon Aubr\u00e9v. & Leandri) is an evergreen tree. The plant grows in tropical Africa, from Senegal to southern Chad and Central African Republic and from Gabon to DR Congo and northern Angola. In traditional medicine, the plant is used as antiemetic, lotion for skin disorders , CEM/ADR5000 cells (IC50: 4.44 \u03bcg/mL), MDA-MB-231-pcDNA cells (IC50: 25.85 \u03bcg/mL), MDA-MB-231-BCRP cells (IC50: 4.17 \u03bcg/mL), HCT116 (p53+/+) cells , HCT116 (p53\u2212/\u2212) cells (IC50: 3.09 \u03bcg/mL), U87MG cells (IC50: 8.01 \u03bcg/mL), U87MG.\u0394EGFR cells (IC50: 8.68 \u03bcg/mL), and HepG2 cells (IC50: 19.90 \u03bcg/mL) and an alkaloid,arborinin (49) is a plant of the family Rutaceae mostly found throughout West Africa, from Sierra Leone, Liberia, Ivory Cost, Mali, Ghana to Nigeria, and Cameroon. In traditional medicine, the plant is used as anti-fibriomyoma and to treat stomachache, malaria , CEM/ADR5000 cells (IC50: 11.72 \u03bcg/mL), MDA-MB-231-pcDNA cells (IC50: 7.52 \u03bcg/mL), MDA-MB-231-BCRP cells (IC50: 12.93 \u03bcg/mL), HCT116 (p53+/+) cells (IC50: 8.59 \u03bcg/mL), HCT116 (p53\u2212/\u2212) cells (IC50:9.70 \u03bcg/mL), U87MG cells (IC50: 8.75 \u03bcg/mL), U87MG.\u0394EGFR cells (IC50: 4.09 \u03bcg/mL) and HepG2 cells (IC50: 13.60 \u03bcg/mL) , CEM/ADR5000 cells (IC50:7.4 \u03bcg/mL)and Mia PaCa-2 cells (IC50: 6.86 \u03bcg/mL) , breast adonocarcinoma MCF7 cells (IC50: 60.2 \u03bcg/mL), human oral squamous carcinoma KB cells (IC50: 62.5 \u03bcg/mL) , HL60AR cells (IC50: 30.60 \u03bcg/mL), MDA-MB-231-pcDNA cells (IC50: 5.19 \u03bcg/mL), MDA-MB-231-BCRP cells (IC50: 10.04 \u03bcg/mL), HCT116 (p53+/+) cells (IC50: 4.37 \u03bcg/mL), HCT116 (p53\u2212/\u2212) cells (IC50: 4.60 \u03bcg/mL), U87MG cells (IC50: 19.99 \u03bcg/mL), U87MG.\u0394EGFR cells (IC50: 10.68 \u03bcg/mL) and HepG2 cells (IC50: 18.28 \u03bcg/mL) and trans-tiliroside isolated from Xylopia aethiopica was amongst the most active alkaloids reported in CEWA plants. This compound displayed interesting cytotoxic effects with IC50 values below 10 \u03bcM toward a panel of sensitive and MDR cancer cell lines. These cell lines included: CCRF-CEM cells (IC50: 1.53 \u03bcM), CEM/ADR5000 cells (IC50: 2.36 \u03bcM), MDA-MB-231-pcDNA cells (IC50: 7.28 \u03bcM), MDA-MB-231-BCRP cells IC50:6.70 \u03bcM), HCT116 (p53+/+) cells (IC50: 2.39 \u03bcM), HCT116 (p53\u2212/\u2212) cells(IC50: 4.55 \u03bcM), U87MG cells (IC50: 3.89 \u03bcM), U87MG.\u0394EGFR cells (IC50: 1.45 \u03bcM) and HepG2 cells (IC50: 3.28 \u03bcM) and isoxanthochymol (30) isolated from Garcinia punctata Oliv. (Guttiferae) , CEM/ADR5000 cells, HL60 cells , HL60AR cells , MDA-MB-231-pcDNA cells , MDA-MB-231-BCRP cells , HCT116 (p53+/+) cells , HCT116 (p53\u2212/\u2212) cells , U87MG cells , U87MG.\u0394EGFR cells and HepG2 cells , isobavachalcone (27), neocyclomorusin (36), poinsettifolin B (38), 6\u03b1-hydroxyphaseollidin (9), isoneorautenol (29), neobavaisoflavone (35), sigmoidin I (44) and sophorapterocarpan A (45) , CEM/ADR5000 cells (IC50: 5.51 \u03bcM), MDA-MB-231-pcDNA cells (IC50: 5.70 \u03bcM), MDA-MB-231-BCRP cells (IC50: 5.87 \u03bcM), HCT116 (p53+/+) cells (IC50: 5.68 \u03bcM), HCT116 (p53\u2212/\u2212) cells (IC50: 4.60 \u03bcM), U87MG cells (IC50: 4.91 \u03bcM), U87MG.\u0394EGFR cells (IC50: 4.91 \u03bcM) and HepG2 cells (IC50: 6.44 \u03bcM), a major component of the leaves of Guiera senegalensis displayed good cytotoxic effects on a panel of human cancer cell lines. The cytotoxicity of 25 was documented toward CCRF-CEM cells (IC50: 2.31 \u03bcM), CEM/ADR5000 cells (IC50: 3.19 \u03bcM), MiaPaCa-2 cells (IC50: 12.39 \u03bcM), Capan-1 cells (IC50: 29.08 \u03bcM), MCF-7 cells (IC50: 3.42\u03bcM), 786-0 cells (IC50: 11.32 \u03bcM), U87MG cells (IC50: 7.78 \u03bcM), lung carcinoma A549 cells (IC50: 2.28 \u03bcM), skin melanoma Colo-38 cells (IC50: 7.69 \u03bcM), cervical carcinoma HeLa cells (IC50: 1.61 \u03bcM), and Caski cells (IC50: 3.73 \u03bcM) and plumbagin (37), showed remarkable cytotoxic effects (Table 4 showed good cytotoxicity toward PF-382 cells (IC50: 2.36 \u03bcM), MiaPaCa-2 cells (IC50: 7.48 \u03bcM), MCF-7 cells (IC50: 6.68 \u03bcM), U87MG cells (IC50: 8.02 \u03bcM), Colo-38 cells (IC50: 2.77 \u03bcM), HeLa cells (IC50: 1.65 \u03bcM), and Caski cells (IC50: 0.70 \u03bcM) , 786-0 cells (IC50: 9.62 \u03bcM), U87MG cells (IC50: 9.64 \u03bcM), A549 cells (IC50:10.13 \u03bcM), Colo-38 cells (IC50: 3.02 \u03bcM), HeLa cells (IC50: 0.58 \u03bcM), and Caski cells (IC50: 0.61 \u03bcM) Table is one oThe present review paper aimed at compiling and summarizing relevant data on the potential of medicinal plant and isolated natural products from Central, Eastern and Western Africa to combat cancer with emphasis on their possible cellular targets. This report could not deliver medical results on the therapeutic capacities of the flora of these three African Regions as anticancer drugs. Nonetheless, in phytochemical and pharmacological basic sciences it clearly shows that efforts are being made by African scientists and their international collaborators to achieve this goal in the future. However, few research teams in the continent are already involved in the cytotoxic drug discovery from botanicals and it is expected that this review will stimulate other laboratories to undertake similar research projects to better valorize the African flora.AM and VK wrote the manuscript; VK and TE designed and corrected the work. All authors read and approved the final version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "In this review, a comprehensive overview about the antifouling compounds from marine invertebrates is described. In total, more than 198 antifouling compounds have been obtained from marine invertebrates, specifically, sponges, gorgonian and soft corals. Biofouling includes microfouling (mainly by bacteria and diatoms) and macrofouling in the marine environment . BiofoulMarine invertebrates have developed prominent chemical defense systems against biofouling in the course of evolution. Lots of AF compounds have been isolated from marine invertebrates. Several books ,7 and reMarine invertebrates, specifically, sponges, gorgonian and soft corals, are rich sources of novel and bioactive secondary metabolites. Studies of the natural chemistry of these interesting groups of marine invertebrates began in the late 1950s. They are recognized to mainly produce novel diterpenoids, sesquiterpenoids, prostanoids, alkaloids, and highly functionalized steroids that are largely unknown from terrestrial sources. Most of these compounds showed AF activity.Terpenoids, especially isocyanoterpenoids, were the typical AF metabolites of marine sponges.l\u20133) dipodazine (162) and other four dipodazine analogs (163\u2013166) with a dipodazine group significantly inhibited the settlement of B. improvisus larvae with EC50 values of 0.034, 5.8, 1.5, 2.4 and 6.7 \u03bcM [167) from the sponge G. barrette inhibited the settlement of B. improvisus larvae with EC50 value of 15 nM [AF indole alkaloids : Alkaloitoxicity . Barettiectively . In 2006d 6.7 \u03bcM , respectof 15 nM .168), isoaaptamine (169), and demethylated aaptamine (170) isolated from the sponge Aaptos aaptos showed AF activity against zebra mussel attachment [Haliclona exigua was rich in bis-1-oxaquinolizidine alkaloid (171), exhibiting significant AF activity against the growths of seven fouling bacterial strains and against the settlement of B.amphitrite larvae [Other AF alkaloids : Aaptamiptamine 1 isolatedlkaloid 1, exhibitBesides the above characteristic terpenoids, alkaloids and steroids, there were many other kinds of AF compounds isolated from marine invertebrates, such as polyacetylenes, butenolides, phenol derivatives, and peptides.172), callypentayne (173), callytriols A-E (174\u2013178) and callyspongins A-B (179\u2013180) from the sponge Callyspongia truncate showed potent metamorphosis-inducing activity towards the ascidian Halocynthia roretzi larvae with ED100 values of 0.13\u20131.3 \u00b5g/mL, and 174\u2013180 also showed AF activity against B. amphitrite larvae with ED50 values of 0.24\u20134.5 \u00b5g/mL [AF polyacetylene derivatives : Callyte181\u2013183) from a soft coral Sinularia sp. showed moderate AF activity against the barnacle B. amphitrite [R)-5-(1-ethoxypropyl)-5-hydroxy-3,4-dimethylfuran-2(5H)-one (184) as a pair of inseparable epimers, along with (S)-5-hydroxy-3,4-dimethyl-5-propylfuran-2(5H)-one (185) and (S)-5-hydroxy-3,4-dimethyl-5-pentylfuran-2(5H)-one (186) were obtained from the gorgonian S. suberosa. Compounds 184\u2013186 exhibited moderate AF activity against the settlement of B. amphitrite larvae [AF butenolides : Sinularphitrite . Butenole larvae . The strDyside. It was believed that this type of compound was biosynthesised by the symbiotic cyanobacteria of the sponge. Five polybrominated diphenyl ethers including 187 from a sponge Callyspongia sp., 188 from Dysidea granulosa, and 189\u2013191 from D. herbacea were investigated against several taxa of prominent fouling organisms including marine bacteria, the diatom A. coffeaeformis, the barnacle B. amphitrite and the mussel Mytilus edulis. All of these compounds exhibited significant antibacterial and AF activity. Compound 187 was the strongest in all the bioassays with non-toxicity. It inhibited the growth of all of the tested bacterial strains with MIC \u00bc 0.02\u20131.52 \u00b5M, and inhibited the larval settlement of A. coffeaeformis, B. amphitrite and M. edulis larvae with EC50 values of 0.24, 0.66 and 1.26 \u00b5M, respectively [AF brominated phenol derivatives : Brominaectively .1c and B1e (192 and 193), avermectin B2a (194) and ivermectin A1a (195) from the gorgonian Anthogorgia caerulea exhibited potent antilarval activity towards B. amphitrite larvae with low-toxicity [O-palmityl-sn-glycero-3-phosphocholine (196) from the sponge Crella incrustans showed strong inhibition against the settlement of B. amphitrite larvae [197) and B (198) from the sponge Geodia barrette showed significant antilarval activity against the settlement of B. improvises larvae at concentrations of 0.6 and 6 \u03bcM, respectively [Other AF compounds : Four avtoxicity . 1-O-pale larvae . Two novectively .50 < 15 \u03bcg/mL, and AF compounds having high LC50/EC50 ratios (>15) are potentially good candidate antifoulants [Totally, over 198 AF compounds have been obtained from marine invertebrates, especially, sponges, gorgonian and soft corals. These compounds covered isocyanoterpenoids, sesquiterpenes, diterpenes, sesterterpenes, triterpenoids, alkaloids , steroids, polyacetylenes, butenolides, peptides, and phenol derivatives, which played important chemical defense roles in the marine invertebrates. In here, the AF activities of 198 compounds towards microfouling and macrofouling were summarized in foulants . From Ta"} +{"text": "AbstractKSA) was published in 2013 and contained a total of 582 species; an addendum to this list was published in 2015 adding 142 species and bringing the total number recorded from the province to 724 insect species representing 17 orders. The previous two studies excluded Jabal Shada al-A\u2019la Nature Reserve (SANR), so the present study in SANR, as belonging to Al-Baha Province, are complementary to the previous two. The present study presents a preliminary list of Diptera (Insecta) in SANR, with remarks on their zoogeography, and is the first of a series of planned ecological and systematic studies on different insect orders as one of the outputs of a project proposed to study the entire insect fauna of SANR.The first list of insects of Al-Baha Province, Kingdom of Saudi Arabia ; Saropogon sp. [Asilidae]; Spogostylumtripunctatum [Bombyliidae]; Phycus sp. [Therevidae]; Hemeromyia sp.; Meoneurapalaestinensis Hennig, 1937 [Carnidae]; Desmometopainaurata Lamb, 1914 [Milichiidae]; Stomoxysniger Macquart, 1851 [Muscidae]; and Sarcophagapalestinensis [Sarcophagidae].A total number of 119 PageBreakZoogeographic affinities of recorded fly species suggest a closer affiliation to the Afrotropical region (46%) than to the Palearctic region (23.5%) or the Oriental region (2.5%). This supports the previous studies\u2019 conclusions and emphasizes the fact that parts of the Arabian Peninsula, including Al-Baha Province, ought to be a part of the Afrotropical Region rather than of the Palaearctic Region or the Eremic Zone. KSA) between the Holy Makkah and Asir provinces. It is the smallest province in KSA , situated at 41\u201342 \u00b0E and 19\u201320 \u00b0N. It is characterized by natural tree cover (SANR) lies between latitudes 19.8149N\u201319.8763N and longitudes 41.2855E\u201341.3501E ], striped hyaena [Hyaenahyaenasultana ], Arabian wolf , sand cat , and reportedly the Arabian leopard , makes this small protected area a unique PageBreaktreasure of biological diversity. Small communities on the mountain grow a distinctive variety of coffee and other crops in terraced fields (d fields .Diptera (Insecta) in SANR, Al-Baha Province, KSA, with remarks on their zoogeography. This is not the final list of Diptera that occur at SANR with the study serving as a basis for further investigations as many additional collected species are still unidentified and further studies are planned to be carried out at SANR. Also, this is the first of a series of planned ecological and systematic studies on different insect orders as one of the outputs of a project proposed to study the entire insect fauna of SANR.The purpose of this paper is to present a preliminary list of SANR, so the present study and other future studies in SANR are complementary to the previous two studies. Studies on the fauna of SANR are of particular interest as this area lies in a part of the Arabian Peninsula which is thought by many authors to touch three of the main zoogeographical regions: the Palaearctic, the Afrotropical, and the Oriental Vahl, Blepharisciliaris (L.) B.L.Burtt and Hypoestesforskaolii (Vahl) R.Br. (Acanthaceae); Aloeofficinalis Forssk. (Aloeaceae), Aervajavanica (Burm.f.) Juss. ex Schult., Aervalanata (L.) A. L. Juss. ex Schultes and Celosia spp. (Amaranthaceae); Adeniumobesum (Forssk.) Roem. & Schlt. and Carissaedulis (Forssk.) Vahl (Apocynaceae); Commiphoraquadricinta Schweinf. and Cappariscartilaginea Decne. (Burseraceae); Commelinaforskaolii Vahl (Commelinaceae); Conyzastricta Willd., Echinops sp., Psiadiapunctulata (DC.), Pulicariaundulata (DC.), Rhamnusdispermus (L.), Tagetesminuta L. and Vernoniaschimperi DC. (Compositae); Sansevieriaehrenbergii Schweinf. ex Baker (Dracaenaceae); succulent Euphorbia spp. (Euphorbiaceae); Acaciaasak (Forssk.), Acaciaetbaica Schweinf and Indigoferaspinosa Forssk. (Fabaceae); Asparagusafricanus Lam. (Liliaceae); Hibiscusmicranthus L. and Hibscusdeflersii Schweinf. ex Cufod. ; Ficusingens (Miq.) (Moraceae); Commicarpus spp. (Nyctaginaceae); Aristidaadscensionis L., Cenchrusciliaris L., Eragrostistenella (L.) P. Beauv. ex Roemer & Schultes and Pennisetumdivisum (Gmel.) Henr. (Poaceae); Solanumincanum L. (Solanaceae); Grewiatembensis Fresen and Grewiatenax (Forssk.) (Tiliaceae); Cissusrotundifolius (Forssk.) Vahl (Vitaceae); in addition to semi-evergreen PageBreaksclerophyllous woodlands of the Afromontane vegetation .SANR over two successive years, 2014 and 2015 by the authors. Twelve collecting trips were made, six in 2014 in February, April, June, August, October and December, and six in 2015 in January, March, May, July, September and November. Collections were made in 6 different localities representing different altitudinal levels and habitats in SANR .Images of newly recorded species were made using a Leica MZ 125 stereo-binocular microscope fitted with a digital camera at Many studies and keys have been consulted in order to identify, classify and estimate the zoogeographical affiliation of collected specimens and such studies are indicated after each taxon in the list, in addition to the following: Unidentified specimens (or photos of specimens)were sent to experts for identification, as indicated after each of these taxa in the list.Nematocera were examined and preserved in alcohol, while other flies were glued to pinned stiff paper points, and all are deposited at the King Saud University Museum of Arthropods, Riyadh, Saudi Arabia (KSMA).Flies of suborder Abbreviations used: Afrotropical AF Bait trap BT Hand-collecting HP King Saud University Museum of Arthropods, Riyadh, Saudi Arabia KSMAPageBreak Light trap LT Malaise trap MT Nearctic NE Oriental OR Palaearctic PA Pitfall trap PT Jabal Shada al-A\u2019la Nature Reserve SANR Sweeping and areal nets SW Vacuuming VCSANR through the present study. Some species have been identified only to genus and listed herein as the genera were not previously recorded from KSA.A total of 119 fly species belonging to 87 genera, 31 tribes, 42 subfamilies, and representing 30 families was recorded from Most of the recorded fly species are characteristic of the Afrotropical region. Table (2) indicates the zoogeographic affinities of recorded species suggesting a closer affiliation to the Afrotropical region (46%) than to the Palearctic region (23.5%) or the Oriental region (2.5%).PageBreakDipteraOrder NematoceraSuborder BibionidaeFamily Dilophustridentatus Walker, 184815 February 2014 (MT1), 5 May 2015 (SW1).Identification: AF.Known distribution: CeratopogonidaeFamily CeratopogoninaeSubfamily CulicoidiniTribe Culicoideskingi 23 August 2014 .Identification: AF.Known distribution: ForcipomyiinaeSubfamily Forcipomyiasahariensis Kieffer, 192323 August 2014 (LT1).Identification: AF. First record from KSA.Known distribution: CulicidaeFamily AnophelinaeSubfamily Anophelesmulticolor Cambouliu, 190223 August 2014 (LT2), 15 February 2014 (LT3).Identification: PA.Known distribution: CulicinaeSubfamily Aedescaspius 15 February 2014 .Identification: PA.Known distribution: Culexpipiens Linnaeus, 175823 August 2014 (PT4).Identification: Known distribution: Cosmopolitan.SciaridaeFamily Chaetosciara sp. Fig. 715 February 2014 (MT1), 23 August 2014 (LT2).Remark: This seems to be the first record of Sciaridae from KSA..Identification: Known distribution: Undetermined.PageBreakPageBreakBrachyceraSuborder AsilomorphaInfraorder AsiloideaSuperfamily AsilidaeFamily AsilinaeSubfamily AsiliniTribe Neolophonotus sp1. Fig. 414-15 February 2014 , 21 April 2014 (LT3), 27 January 2015 , 5 May 2015 (SW1), 27 July 2015 (LT2).Remark: This seems to be the first record of this genus from KSA.Identification: Dr. Jason G.H. Londt, from photos .Known distribution: Undetermined.Neolophonotus sp2. Fig. 615 February 2014 (MT3), 15 November 2015 (MT3).Remark: This seems to be the first record of this genus from KSA.Identification: Dr. Jason G.H. Londt, from photos .Known distribution: Undetermined.ApocleinaeSubfamily Promachussinaiticus Efflatoun, 1934 Fig. 320 April 2014 (LT6), 3 June 2014 , 3-5 June 2014 (SW2), 15 November 2015 (MT6).Identification: PA. First record of the species from the KSA.Known distribution: DasypogoninaeSubfamily DasypogoniniTribe Saropogonlongicornis Fig. 53 June 2014 (MT3).Identification: PA. First record from KSA.Known distribution: Saropogon sp.15 November 2015 (MT6).Remark: This seems to be the first record of this genus from KSA.Identification: Known distribution: Undetermined.LaphystiinaeSubfamily Trichardisleucocomus 3 June 2014 (MT5), 5 May 2015 (MT5).Identification: Dr Torsten Dikow, from photos .PA.Known distribution: PageBreakBombyliidaeFamily BombyliinaeSubfamily BombyliiniTribe Bombylelladelicata Wiedemann, 18305 June 2014 (SW6), 28 July 2015 (SW3).Identification: Magdi El-Hawagry using AF.Known distribution: Bombyliuspallidipilus Greathead, 196715 February 2014 (MT1), 23 August 2014 (LT2).Identification: Magdi El-Hawagry using AF.Known distribution: Systoechushorridus Greathead, 198021 April 2014 (LT2), 3 May 2015 (LT5), 14 November 2015 (LT6).Identification: Magdi El-Hawagry using PA.Known distribution: AnthracinaeSubfamily AnthraciniTribe Anthraxsticticus Klug, 1832LT).22 April 2015 4 June 2014 (SW6).Identification: Magdi El-Hawagry using OR, PA.Known distribution: Spogostylumisis 29 July 2015 (PT5).Identification: Magdi El-Hawagry using PA.Known distribution: Spogostylumtripunctatum 4-5 June 2014 (SW2), 2 September 2015 (LT6).Identification: Magdi El-Hawagry using PA. First record from KSA.Known distribution: ExoprosopiniTribe Defilippianigrifimbriata 17 October 2014 (MT5).Identification: Magdi El-Hawagry using AF.Known distribution: Exoprosopadisruptatihamae Greathead, 1980 Fig. 93 June 2014 (SW1).Identification: Magdi El-Hawagry using PageBreakPageBreakAF.Known distribution: Heteraloniabisecta Greathead, 198829 July 2015 (PT5).Identification: Magdi El-Hawagry using AF.Known distribution: Pterobateschalybaeus 3 November 2014 (HP6).Identification: Magdi El-Hawagry using PA.Known distribution: VilliniTribe Exhyalanthraxtriangularis Bezzi, 192427 January 2015 (MT5), 5 May 2015 , 15 November 2015 (MT4).Identification: Magdi El-Hawagry using AF.Known distribution: Pachyanthraxcirce 5 May 2015 (MT4).Identification: Magdi El-Hawagry using AF.Known distribution: Villa bivirgata Austen, 19373 June 2014 (SW4), 5 May 2015 (SW4).Identification: Magdi El-Hawagry using PA.Known distribution: Villa paniscoides Bezzi, 19123 June 2014 (SW4), 27-28 July 2015 (SW1), 15 November 2015 (MT4).Identification: Magdi El-Hawagry using AF.Known distribution: XeramoebiniTribe Desmatoneura sp.4 June 2014 (SW4).Identification: Magdi El-Hawagry using Known distribution: Undetermined.Petrorossiaalbula Zaitzev, 19625 June 2014 (SW2), 27 July 2015 (SW1).Identification: Magdi El-Hawagry using PA.Known distribution: Petrorossialetho 5 June 2014 (SW4), 27 July 2015 (SW1).PageBreakIdentification: Magdi El-Hawagry using PA.Known distribution: Petrorossiatropicalis Bezzi, 19213-5 June 2014 , 5 May 2015 (MT3), 27 July 2015 (SW4).Identification: Magdi El-Hawagry using AF.Known distribution: TherevidaeFamily Phycus sp.1 June 2014 (LT5), 24 August 2014 (LT6).Remark: This seems to be the first record of the genus from KSA.Identification: Dr Martin Hauser .AF.Known distribution: EmpidoideaSuperfamily DolichopodidaeFamily DiaphorinaeSubfamily Asyndetusalbifacies Parent, 1929SW).27 July 2015 (Identification: AF.Known distribution: DolichopodinaeSubfamily Dolichopus sp.23 August 2014 (LT4), 10 December 2014 (LT6), 26 January 2015 (PT4), 27 July 2015 (LT6).Identification: Known distribution: Undetermined.Tachytrechusplanitarsis Becker, 190723 August 2014 (LT2).Identification: PA.Known distribution: NemestrinoideaSuperfamily NemestrinidaeFamily Trichopsideacostata Loew, 185810 December 2014 (LT6).Identification: AF.Known distribution: PageBreakTabanoideaSuperfamily TabanidaeFamily Haematopotapluvialis 15 November 2015 (LT6).Identification: PA.Known distribution: MuscomorphaInfraorder AschizaSection PlatypezoideaSuperfamily PhoridaeFamily Megaseliascalaris 23 April 2014 , 5 June 2014 (PT4), 2 March 2015 (PT4), 29 July 2015 (PT5), 23 August 2015 (LT3).Identification: Magdi El-Hawagry.Known distribution: Cosmopolitan.SchizophoraSection AcalyptrataeSubsection CarnidaeFamily Hemeromyia sp. 23 August 2014 (LT1).Remark: This seems to be the first record of the genus from KSA.Identification: Known distribution: Undetermined.Meoneurapalaestinensis Hennig, 193723 August 2014 .Identification: PA.Known distribution: ChloropidaeFamily ChloropinaeSubfamily Pachylophuspellucidus Becker, 191024 August 2014 (MT6).Identification: AF.Known distribution: Thaumatomyianotata 27 January 2015 (LT1).Identification: AF, PA.Known distribution: OscinellinaeSubfamily Anatrichuspygmaeus Lamb, 191827 July 2015 (VC5).Identification: AF.Known distribution: PageBreakAphanotrigonumsubfasciellum Collin, 19494 June 2014(SW4), 24 August 2014 (LT6).Identification: PA.Known distribution: Lasiochaetavulgaris 15 February 2014 (MT1), 8 December 2014 , 5 May 2015 (MT4).Identification: AF.Known distribution: Polyodaspisrobusta 15 February 2014 , 17 October 2014 (LT1), 27 July 2015 (VC2).Identification: AF.Known distribution: Scoliophthalmusmicantipennis Duda, 19355 May 2015 (MT6).Identification: Identification: AF.Known distribution: Scoliophthalmustrapezoides Becker, 19035 May 2015 (MT6).Identification: Identification: AF.Known distribution: SiphonellopsinaeSubfamily Apotropinagregalis 23 August 2014 , 17 October 2014 (LT5), 8 December 2014 (VC4), 2-3 March 2015 , 17 July 2015 , 15 November 2015 (LT6).Identification: Identification: AF.Known distribution: ChyromyidaeFamily ChyromyinaeSubfamily Somatiosomaeremicolum Ebejer, 200815 February 2014 (MT4).Identification: AF.Known distribution: ConopidaeFamily MyopinaeSubfamily ZodioniniTribe Zodioncinereum 5 May 2015 (MT6).Mei & Stuke J-H (2008) has been consulted to identify this species.Identification: PA.Known distribution: PageBreakDiopsidaeFamily Diopsisapicalis Dalman, 18175 May 2015 .Identification: AF.Known distribution: Sphyracephalabeccarii 2 June 2014 (LT6), 3 June 2014 , 3 June 2014 (MT2), 27 January 2015 (LT4), 5 May 2015 , 15 November 2015 (LT6).Identification: AF.Known distribution: DrosophilidaeFamily DrosophilinaeSubfamily DrosophiliniTribe Drosophilamelanogaster Meigen, 183017-18 October 2014 , 8 December 2014 (PT2), 26-27 January 2015 , 2 March 2015 .Identification: Magdi El-Hawagry.Known distribution: Cosmopolitan.Zaprionusindianus Gupta, 19702 March 2014 (PT5), 23 August 2014 (LT2), 18 October 2014 .Identification: OR.Known distribution: EphydridaeFamily DiscomyzinaeSubfamily DiscomyziniTribe Actocetorindicus , 17 October 2014 (LT4).Identification: AF.Known distribution: Actocetormargaritatus Wiedemann, 1830 Fig. 828 February 2014 (PT3), 23 August 2014 , 10 December (2014 (LT6), 5 May 2015 .Identification: AF.Known distribution: PsilopiniTribe Psilopanilotica 15 February 2014 , 4 June 2014 (SW4), 29 July 2015 .Identification: AF, PA.Known distribution: PageBreakHydrelliinaeSubfamily Notiphilaignobilis Loew, 186229 July 2015 (MT6).Identification: AF.Known distribution: LonchaeidaeFamily LonchaeinaeSubfamily LonchaeiniTribe Silbavirescens Macquart, 185115 February 2014 (SW6).Identification: AF.Known distribution: MilichiidaeFamily MadizinaeSubfamily Desmometopainaurata Lamb, 1914 Fig. 1027 January 2015 (LT2), 29 July 2015 (PT4).Identification: AF. First record from KSA.Known distribution: Desmometopavaripalpis Malloch, 19275 May 2015 (PT5), 29 July 2015 (PT6).Identification: Identification: AF.Known distribution: PhyllomyzinaeSubfamily Phyllomyza sp.15 February 2014 (LT2), 27 July 2015 (LT2).Identification: Known distribution: Undetermined.PyrgotidaeFamily Campyloceraferruginea Macquart, 184315 November 2015 (LT6).Identification: Dr Valery Korneyev, from photos .AF.Known distribution: Eupyrgotalatipennis 3 June 2014 (LT2), 14 November 2015 (LT2).Identification: Dr Valery Korneyev, from photos .AF.Known distribution: PageBreakSphaeroceridaeFamily Rachispodafuscipennis 15 February 2014 , 23 August 2014 (PT6), 18 October 2014 , 8-11 December 2014 .Identification: Magdi El-Hawagry, compared with museum specimens.PA.Known distribution: TephritidaeFamily DacinaeSubfamily DaciniTribe Bactrocerazonata 23 August 2014 (LT2), 5 May 2015 (SW1), 27 July 2015 (SW1).Identification: OR.Known distribution: TephritinaeSubfamily TephritiniTribe Acanthiophilushelianthi 23 August 2014 (LT2).Identification: AF, OR, PA.Known distribution: Dioxynasororcula 15 February 2014 (MT4), 3 June 2014 (MT4), 8 December 2014 .Identification: AF.Known distribution: Goniurelliatridens 23 August 2014 (LT2).Identification: PA.Known distribution: Trupaneastellata 3 June 2014 (LT2).Identification: PA.Known distribution: UlidiidaeFamily UlidiinaeSubfamily UlidiiniTribe Physiphoraalceae 15 February 2014 , 21 April 2014 (LT1), 6 June 2014 (LT1), 23 August 2014 (LT1), 17-18 October 2014 , 27 January 2015 , 5 May 2015 (LT1), 27 July 2015 , 15 November 2015 .Identification: Known distribution: Cosmopolitan.PageBreakCalyptrataeSubsection AnthomyiidaeFamily AnthomyiinaeSubfamily AnthomyiiniTribe Anthomyiapluvialis 15 February 2014 (MT1), 27 January 2015 (MT3), 4-5 May 2015 , 15 November 2015 (LT5).Identification: PA.Known distribution: HydrophoriiniTribe Deliaplatura 15 February 2014 , 23 August 2014 (LT2), 17 October 2014 , 27 January 2015 .Identification: Known distribution: Cosmopolitan.CalliphoridaeFamily CalliphorinaeSubfamily Calliphoracroceipalpis Jaennicke, 186715 February 2014 (MT4).Identification: AF.Known distribution: Calliphoravicina 3 June 2014 (SW6).Identification: Known distribution: Cosmopolitan.ChrysomyinaeSubfamily Chrysomyaalbiceps 4 June 2014 (SW1), 2 September 2015 (LT6), 15 November (LT3).Identification: AF.Known distribution: Chrysomyaputoria 3 June 2014 (SW4).Identification: AF.Known distribution: Chrysomyaregalis Robineau-Desvoidy, 183015 February 2014 (MT3), 4 June 2014 (MT6), 10 December 2014 (LT6).Identification: AF.Known distribution: PageBreakLuciliinaeSubfamily Luciliasericata 16 February 2014 (HP6), 21 February 2014 (LT3), 10 December 2014 (LT6).Identification:Known distribution: Cosmopolitan.PolleniinaeSubfamily Polleniahungarica Rognes, 198717 October 2014 (LT6).Identification: PA.Known distribution: Polleniarudis 17 October 2014 (LT5).Identification: PA.Known distribution: MuscidaeFamily AtherigoninaeSubfamily AtherigoniniTribe Atherigonahumeralis Wiedemann, 183015 November 2015 (SW5).Identification: AF.Known distribution: Atherigonalaevigata 15 February 2014 (MT1), 8 December 2014 (VC4).Identification: AF.Known distribution: Atherigonareversura Villeneuve, 193615 February 2014 (MT3), 23 August 2014 , 17 October 2014 , 5 May 2015 (MT2), 15 November 2015 (MT4), 2 September 2015 (LT6).Identification: OR.Known distribution: CoenosiinaeSubfamily CoenosiiniTribe Coenosiaattenuata Stein, 190315 February 2014 , 23 April 2014 (PT1), 23 August 2014 (LT2), 17 October 2014 , 18 October 2014 (PT5), 5 May 2015 (MT4), 15 November 2015 (MT4).Identification: Known distribution: Cosmopolitan.Coenosiahumilis Meigen, 1826PageBreak5 May 2015 (MT6).Identification: Known distribution: Cosmopolitan.LimnophoriniTribe Lispenivalis Wiedemann, 183015 February 2014 (LT6).Identification: AF.Known distribution: Lispepectinipes Becker, 190323 August 2014 , 17 October 2014 (LT5), 5 May 2015 , 14-15 November 2015 .Identification: PA.Known distribution: MuscinaeSubfamily MusciniTribe Muscaalbina Wiedemann, 18305 May 2015 (MT6).Identification: AF, OR, PA.Known distribution: Muscaautumnalis De Geer, 177623 August 2014 (LT2), 5 May 2015 (MT2).Identification: Known distribution: Cosmopolitan.Muscacalleva Walker, 184914 November 2015 (LT4).Identification: AF.Known distribution: Muscadomestica Linnaeus, 175815 February 2014 , 3 June 2014 , 23 August 2014 , 5 May 2015 (MT6), 2 September 2015 (LT5), 15 November 2015 (LT6).Identification: Known distribution: Cosmopolitan.Muscalucidula 3 June 2014 (MT6).Identification: AF, PA.Known distribution: Muscasorbens Wiedemann, 18305 May 2015 (MT1), 15 November 2015 (LT5).Identification: AF.Known distribution: PageBreakStomoxyiniTribe Stomoxysniger Macquart, 1851 Fig. 1115 February 2014 (MT4), 17 October 2014 (LT5).Identification: AF. First record from KSA.Known distribution: PhaoniinaeSubfamily DichaetomyiiniTribe Dichaetomyialuteiventris 2 March 2015 (PT5).Identification: AF.Known distribution: PhaoniiniTribe Helinaconiformis 15 February 2014 , 21 April 2014 (LT2), 17 October 2014 , 27 January 2015 , 14-15 November 2015 .Identification: AF.Known distribution: Helinalucida 21 April 2014 (LT5).Identification: AF.Known distribution: RhiniidaeFamily Cosminaviridis Townsend, 191715-16 February 2014 , 17 October 2014 (LT5), 27 January 2015 , 4-5 May 2015 .Identification: AF.Known distribution: Isomyiaterminata 15 February 2014 .Identification: AF.Known distribution: Rhiniaapicalis 15 February 2014 (MT5), 3 June 2014 (SW4), 17 October 2014 , 14-15 November 2015 .Identification: AF.Known distribution: PageBreakSarcophagidaeFamily MiltogramminaeSubfamily Taxigrammaheteroneura 15 February 2014 (MT5), 3 June 2014 (SW4), 27 January 2015 (MT4), 5 May 2015 , 27-29 July 2015 (PT5).Identification: Thomas Pape and the first author.NE, PA.Known distribution: ParamacronychiinaeSubfamily Wohlfahrtiaerythrocera Villeneuve, 191028 July 2015 (PT6).Identification: Thomas Pape and the first author.AF.Known distribution: Wohlfahrtianuba Wiedemann, 18303 May 2015 (PT5).Identification: Thomas Pape and the first author.AF.Known distribution: SarcophaginaeSubfamily Blaesoxiphaalgeriensis 23 August 2014 (LT5).Identification: Thomas Pape and the first author.PA.Known distribution: Blaesoxipharufipes 3 June 2014 (SW4).Identification: Thomas Pape and the first author.Known distribution: Cosmopolitan.Sarcophagaadhamae 21 April 2014 (BT6).Identification: AF.Known distribution: Sarcophagaafrica 5 May 2015 (SW4).Identification: Thomas Pape and the first author.Known distribution: Cosmopolitan.Sarcophagababiyari 3 June 2014 (LT6).Identification: Thomas Pape and the first author.AF.Known distribution: Sarcophagadux Thompson, 186915 February 2014 (MT1).Identification: Thomas Pape and the first author.Known distribution: Cosmopolitan.PageBreakSarcophagapalestinensis Fig. 1221 February 2014 (LT1).Identification: Thomas Pape and the first author.PA.Known distribution: TachinidaeFamily ExoristinaeSubfamily EryciiniTribe Drinolota 15-16 February 2014 , 17 October 2014 , 14-15 November 2015 .Identification: AF, PA.Known distribution: ExoristiniTribe Exoristalarvarum 3 June 2014 .Identification: NE, PA.Known distribution: GoniiniTribe Goniacapitata 5 May 2015 (MT1).Identification: PA.Known distribution: Sturmiabella 15 February 2014 (MT1), 21 April 2014 (LT1), 3 June 2014 (SW4), 27-30 January 2015 , 27 July 2015 (LT5).Identification: OR, PA.Known distribution: PhasiinaeSubfamily CylindromyiiniTribe Cylindromyiabicolor 7 June 2014 (SW4).Identification: PA.Known distribution: TachininaeSubfamily TachininiTribe Dejeaniabombylans 10 December 2014 (LT6).Identification: AF.Known distribution: PageBreakKSA, including Al-Baha Province, is considered to be the most important part of the country and the Arabian Peninsula in general. Floristically and ecologically, this area is similar to the high altitude mountains of north-eastern and eastern parts of Africa, and like other areas in the south-western part of the Arabian Peninsula, contains montane woodlands and evergreen shrub lands, with strong Afromontane affinities as shown in the present results which obviously emphasize the fact that Al-Baha Province, as lying in the south-western part of the Arabian Peninsula, should be included in the Afrotropical Region rather than in the Palaearctic Region or the Eremic Zone.The authors would like to extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for its funding this research group NO (RGP-1437-009)."} +{"text": "Enterobacter sp. strain EA-1 is an electrochemically active bacterium isolated from tropical sediment in Singapore. Here, the annotated draft genome assembly of the bacterium is reported. Whole-genome comparison indicates that Enterobacter sp. EA-1, along with a previously sequenced Enterobacter isolate from East Asia, forms a distinct clade within the Enterobacter genus. Enterobacter belong to the class Gammaproteobacteria and are rod-shaped, Gram-negative, motile, facultative anaerobes. They are commonly found in soil, water, sewage, and the intestines of animals and humans and have been associated with nosocomial infections broth at room temperature and with shaking at 150\u2009rpm. The Wizard genomic DNA purification kit was used according to the protocol for Gram-negative bacteria supplied by the manufacturer.The draft genome sequence was determined by shotgun sequencing on a MinION Mk1B sequencer using R9 chemistry and library protocol SQK-LSK108. Raw sequencing data were assembled using Canu version 1.3 , manuallEnterobacter cloacae ATCC 13047, Enterobacter cloacae SBP-8, and Enterobacter sp. strain FY-07. However, a whole-genome comparison indicated an average nucleotide identity (E. cloacae ATCC 13047 (NCBI accession number CP001918), 78.09% compared to E. cloacae SBP-8 (NCBI accession number CP016906), and 93.38% compared to FY-07 (NCBI accession number CP012487), suggesting that EA-1 forms, together with FY-07, a distinct clade within the Enterobacter genus related to but separate from E. cloacae.The draft genome of EA-1 is composed of 5,145,523 bp, with an average G+C content of 54.56%, and it contains 81 tRNAs, 22 rRNAs organized in 7 operons, and 1 transfer-messenger RNA (tmRNA). A comparison of the 16S rRNA gene sequence revealed >98% identity to the 16S rRNA genes of http://www.ebi.ac.uk/Tools/psa/) using the EMBOSS Needle tool . In FY-07, these genes are arranged in three BC-producing operons: bcsI, bcsII, and bcsIII , AKI40_0197 (CWS02_01215), AKI40_0198 (CWS02_01220), AKI40_0199 (CWS02_01225), AKI40_0200 (CWS02_01230), AKI40_0201 (CWS02_01235), and AKI40_0202 (CWS02_01240). For bcsII, the FY-07 and corresponding EA-1 locus tags (in parentheses) are AKI40_0206 (CWS02_01260), AKI40_0207 (CWS02_01265), AKI40_0208 , AKI40_0209 (CWS02_01285), AKI40_0210 (CWS02_01290), and AKI40_0211 (CWS02_01295). In the case of the EA-1 locus tag corresponding to FY-07\u2019s AKI40_0208, multiple ORFs were stitched together during nucleotide alignment in order to identify the complete homologous gene sequence which was interrupted due to frameshifting errors associated with the sequencing technology used. For bcsIII, the FY-07 and corresponding EA-1 locus tags (in parentheses) are AKI40_0894 (CWS02_05060), AKI40_0893 (CWS02_05055), AKI40_0892 (CWS02_05050), and AKI40_0891 (CWS02_05045). For other BC-related genes (not operon-associated), the FY-07 and corresponding EA-1 locus tags are AKI40_0203 (CWS02_01245), AKI40_0204 (CWS02_01250), and AKI40_0205 (CWS02_01255).In-detail genome alignments between EA-1 and FY-07 using the Artemis Comparison Tool , are alsd bcsIII . In bcsICP025776.The whole-genome shotgun project was deposited in NCBI under the accession number"} +{"text": "Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) strain CRJJGF_00165 , isolated from ground beef in 2007.Here, we report a 4.78-Mb draft genome sequence of the Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) strain CRJJGF_00165 distinguishes it from the phylogenetically distinct monophasic S. enterica subsp. IIIa serovar 61:k:1,5,(7) is mostly associated with reptiles strain CRJJGF_00165 was isolated from ground beef using standard microbiology techniques. SMART-PCR was used to serotype this isolate and tRNAs were predicted with Prodigal . DNA libraries were constructed using the Nextera XT DNA preparation kit, and paired-end sequencing was performed on the Illumina HiSeq2500 platform using a 500-cycle MiSeq reagent kit. A total of 3,848,000 reads were generated. Reads were g Velvet into 108Prodigal and ARAGProdigal , respectProdigal , CRISPRFProdigal , and PHAProdigal , respectRG-ANNOT . The genS. enterica subsp. IIIb serovar 61:k:1,5,(7) strain CRJJGF_00165 has been deposited in GenBank (NCBI) under the accession number JQYQ00000000. The version described here is the first version.The genome sequence of"} +{"text": "Addendum to: Translational Psychiatry (2017) 7, e1001;doi:10.1038/tp.2016.263; published online 17 January 2017post hoc tests for clarifying the direction of the three MANOVA results thatfound significant associations between functional connectivity changes and long-termclinical outcomes. In each of the three regression tests, greater increases infunctional connectivity were associated with improved long-term clinical outcomes, asascertained by positive beta weights for the following regressors: longitudinal positivepsychotic symptoms =2.79;P=0.015), longitudinal affective symptoms =2.36; P=0.035) and subjective long-termrecovery =2.56;P=0.024). These tests replace the correlation tests originally reportedin the article.After publication, the authors determined that regression tests are the appropriate"} +{"text": "In sub-Saharan Africa, 20%\u201325% of people starting antiretroviral therapy (ART) have severe immunosuppression; approximately 10% die within 3 months. In the Reduction of EArly mortaLITY (REALITY) randomized trial, a broad enhanced anti-infection prophylaxis bundle reduced mortality vs cotrimoxazole. We investigate the contribution and timing of different causes of mortality/morbidity.Participants started ART with a CD4 count <100 cells/\u00b5L; enhanced prophylaxis comprised cotrimoxazole plus 12 weeks of isoniazid + fluconazole, single-dose albendazole, and 5 days of azithromycin. A blinded committee adjudicated events and causes of death as tuberculosis, cryptococcosis, severe bacterial infection (SBI), other potentially azithromycin-responsive infections, other events, and unknown.P < .05) but not tuberculosis, SBI, potentially azithromycin-responsive infections, or other causes (P > .3); and reduced nonfatal/fatal tuberculosis and cryptococcosis (P < .05), but not SBI, other potentially azithromycin-responsive infections, or other events (P > .2).Median pre-ART CD4 count was 37 cells/\u00b5L. Among 1805 participants, 225 (12.7%) died by week 48. Fatal/nonfatal events occurred early (median 4 weeks); rates then declined exponentially. One hundred fifty-four deaths had single and 71 had multiple causes, including tuberculosis in 4.5% participants, cryptococcosis in 1.1%, SBI in 1.9%, other potentially azithromycin-responsive infections in 1.3%, other events in 3.6%, and unknown in 5.0%. Enhanced prophylaxis reduced deaths from cryptococcosis and unknown causes (Enhanced prophylaxis reduced mortality from cryptococcosis and unknown causes and nonfatal tuberculosis and cryptococcosis. High early incidence of fatal/nonfatal events highlights the need for starting enhanced-prophylaxis with ART in advanced disease.ISRCTN43622374. In sub-Saharan Africa, 20%\u201325% of human immunodeficiency virus (HIV)\u2013infected individuals starting antiretroviral therapy (ART) have a CD4 count <100 cells/\u00b5L . In the The REALITY trial ISRCTN43622374) recruited 1805 HIV-infected ART-naive adults and children \u22655 years (98% aged \u226513 years) from Zimbabwe, Uganda, Malawi, and Kenya with a CD4 count <100 cells/\u00b5L. In brief, participants were randomized 1:1 to enhanced prophylaxis vs standard prophylaxis (cotrimoxazole) ), other events (n = 63 [3.6%]), SBI (n = 33 [1.9%]), other potentially azithromycin-responsive infections (n = 23 [1.3%]), and cryptococcosis (n = 20 [1.1%]). Sixty-seven (29.8%) deaths were adjudicated as compatible with IRIS. Enhanced prophylaxis reduced all-cause mortality by 24 weeks by 27% log-rank 8.4% wereP = .06) . There w4 and 48 .P = .007), cryptococcosis , and IRIS-compatible events (P = .26), potentially azithromycin-responsive infections (P = .34), or other events (P = .81). Although occurring at much higher rates events of each category occurred in 674 (37.3%) participants. The most common were other events (n = 479 participants [27.0%]) , followe = .001) , but noter rates , similarer rates . Rates fAt 48 weeks post\u2013ART initiation, rates of fatal/nonfatal events were lowest and participants with lower baseline CD4 count (P = .02) or self-reported vomiting (P = .005) (P = .03); those with lower baseline CD4 count (P = .05), creatinine clearance (P < .001), or albumin (P = .01); higher bilirubin (P = .05); without previous healthcare contact (P = .04); or with wasting/severe weight loss (P = .02), participant-reported fever (P = .08), or problems with mobility (P = .05) or self-care (P = .05). There was no effect of water source or household toilet type on either cause of death (P > .3).Given the impact of enhanced prophylaxis on deaths from cryptococcosis and unknown causes, we considered whether predictors of these 2 categories of death were similar, suggesting unascertained cryptococcal disease could be driving these effects. Deaths from cryptococcosis were more common in standard prophylaxis ( = .005) . Deaths Considering the 1716 participants alive and in follow-up at week 4, median last postbaseline VL before death was 95 copies/mL , with reIn the REALITY trial of patients starting ART with severe immunosuppression in sub-Saharan Africa, morbidity/mortality rates were high in the first month after starting ART, regardless of type of event, and dropped exponentially thereafter. However, even within a randomized trial with intensive follow-up, structured clinical narratives, and independent endpoint review, causes of death were difficult to ascertain and the commonest category was unknown. Furthermore, multiple causes were identified in almost one-third of deaths, highlighting the complexity of clinical presentations in patients starting ART with advanced immunosuppression.REALITY showed that enhanced prophylaxis reduces mortality by 27% , due to Of note, 62.7% of participants had no serious morbidity/mortality during their first 48 weeks on ART, despite very low pre-ART CD4 and high VL. Nevertheless, their low CD4 put them at substantially increased risk of impaired short- and long-term immunological response, reinforcing the importance of undertaking baseline CD4 to identify these patients. Where CD4 is becoming less available, our data reinforce the need to further develop CD4 point-of-care tests which at least qualitatively identify the most immunosuppressed individuals. Alternatively, total lymphocyte counts could be used to identify at least some of those at greatest risk , 21.Given current WHO guidance focusing on diagnostic tools to rule out opportunistic infections before ART initiation , our praClinical Infectious Diseases online. Consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author.Supplementary materials are available at Supplementary Material 1Click here for additional data file."} +{"text": "Juniperus phoenicea (Arar), Anastatica hierochuntica (Kaff Maryam), and Citrullus colocynthis with a set of reference compounds with established modes of action. Cluster analyses of the cytological profiles of the tested compounds suggested that these plants contain possible topoisomerase inhibitors that could be effective in cancer treatment. Using histone H2AX phosphorylation as a marker for DNA damage, we discovered that some of the compounds induced double-strand DNA breaks. Furthermore, chemical analysis of the active fraction isolated from Juniperus phoenicea revealed possible anti-cancer compounds. Our results demonstrate the usefulness of cell-based phenotypic screening of natural products to reveal their biological activities.Natural products have been used for medical applications since ancient times. Commonly, natural products are structurally complex chemical compounds that efficiently interact with their biological targets, making them useful drug candidates in cancer therapy. Here, we used cell-based phenotypic profiling and image-based high-content screening to study the mode of action and potential cellular targets of plants historically used in Saudi Arabia\u2019s traditional medicine. We compared the cytological profiles of fractions taken from Cancer is a leading cause of morbidity and mortality worldwide, exceeding the number of cases of illness and death due to HIV/AIDS, malaria, and tuberculosis . In 2012High-content screening (HCS) optimizes the discovery of biologically active small molecules and their subsequent development into therapeutic compounds by the use of automated microscopy in conjunction with image analysis. A high-throughput platform based on image-processing software that reviews images from automated fluorescence microscopy \u201310, HCS Anastatica hierochuntica (Kaff Maryam), Juniperus phoenicea (Arar), and Citrullus colocynthis , that have been used in traditional medicine in Saudi Arabia. Previous reports reported anti-cancer activity in Juniperus phoenicea and Citrullus colocynthis .\u201331.1H NM 4 and 5 , 33. TheThis study demonstrates the capability of HCS for cytological profiling for drug discovery in natural products. In recent years, HCS has developed from a promising concept into an efficient methodology and indispensable tool. HCS now can be implemented during the early drug discovery process as a result of its recent technological advances , 34.C. colocynthis, J. phoenicea, and A.hierochuntica. We used a library of known small molecules with assigned modes of action as reference compounds. We compared their cytological profiles with profiles retrieved from the fractionated plant extracts. We were able to predict the mode of action of pure compounds as well as fractionated extracts -\u03b2Dgalactopyranoside triacetate and Estra-1,3,5(10)-triene-3,6beta,17beta-triol triacetate. Estra-1,3,5(10)-triene-3,6beta,17beta-triol triacetate (PubChem CID: 5756) is used as anti-inflammatory drug but no anti-inflammatory activity has been reported for Methyl6-O--\u03b2-Dgalactopyranoside triacetate compound.The 2,2-dimethoxybutane (PubChem CID: 137941) found in the JUN_C2_60% fraction was found to be toxic to microbial membranes \u201361, but polymers . This mae needed . 3-Trifl effects , 67. It effects , in agre Tunisia . Anti-in Tunisia . Ethyl 4 Tunisia . Of the Tunisia \u201375. SphiOur results demonstrate the power of HCS for drug discovery. HCS allows traditionally used medicinal plants to be assessed for the presence of bioactive compounds. Cytological profiles allow us to identify topoisomerase II inhibitor activity in the plant fractions that we tested to verify the presence of anti-cancer compounds in the plants. Further studies are needed to evaluate and better characterize the active compounds identified in our study. This can be done by guided fractionation using HPLC to isolate and eliminate the active from the non-active compounds and to retest the active compounds with HCS. Furthermore, active compounds can be synthesized and tested in vivo.S1 Table(DOCX)Click here for additional data file.S2 TableThis figure were adapted from the cited publication.(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file.S5 Table(DOCX)Click here for additional data file.S6 Table(DOCX)Click here for additional data file.S1 FigEight peaks were identified from the LC-MS chromatogram: (1) 185.98322 m/z, (2) 144.98225 m/z, (3) 144.98225 m/z, (4) 288.28995 m/z, (5) 256.26364 m/z, (6) 387.18086 m/z, (7) 415.21219 m/z, and (8) 637.30585 m/z.(TIFF)Click here for additional data file.S2 Fig4H5NO4S.Acesulfame-K, Chemical Formula: C(TIFF)Click here for additional data file.S3 Fig2H6ClO3P.Ethephon, Chemical Formula: C(TIFF)Click here for additional data file.S4 FigSphinganine, Chemical Formula: C17H37NO2.(TIFF)Click here for additional data file.S5 Fig16H33NO.Palmitic amide, Chemical Formula: C(TIFF)Click here for additional data file.S6 Fig22H26O6.Burseran or (+)Eudesmin, Chemical Formula: C(TIFF)Click here for additional data file.S7 Fig24H30O6.Estra-1,3,5(10)-triene-3,6beta,17beta-triol triacetate. Chemical Formula: C(TIFF)Click here for additional data file.S8 Fig29H48O15.Methyl 6-O--\u03b2-D-galactopyranoside. Chemical Formula: C(TIFF)Click here for additional data file.S9 FigThe spectrum was recorded at room temperature using a 600-MHz NMR spectrometer.(TIFF)Click here for additional data file.S10 FigThe spectrum was recorded at room temperature using a 600-MHz NMR spectrometer. This figure verifies the MS finding of the -6-methyl-\u03b2-D-glucopyranuronosyl]-\u03b2-D-galactopyranoside) molecules with signals of several CH3 groups around 1 ppm in (TIFF)Click here for additional data file.S11 FigA) Estra-1,3,5(10)-triene-3,6beta,17beta-triol triacetate B) Burseran C) (+)Eudesmin D) Extended aromatic region of the NMR spectrum.(TIFF)Click here for additional data file.S12 Fig(TIFF)Click here for additional data file.S13 Fig(TIFF)Click here for additional data file.S14 Fig(TIFF)Click here for additional data file."} +{"text": "Magnetospirillum sp. 15-1. This strain was isolated from a planted fixed-bed reactor based on its ability to degrade toluene under anaerobic conditions. The genome assembly consists of 5.4\u00a0Mb in 28 contigs and 5,095 coding sequences containing the genes involved in anaerobic toluene degradation.Here, we report the draft genome sequence of Betaproteobacteria strains, represented by Thauera aromatica and Azoarcus sp. continuously fed with toluene (De novo assembly was conducted with the A5-miseq pipeline (http://www.geneious.com) (coding percentage 98.82%). The assembled sequences were functionally annotated using the RAST online service , generat (M.\u00a0magnetotacticum MS-1 (86%) (Magnetospirillum sp. XM-1 (Magnetospirillum sp. SO-1 (89%) (M. bellicus VDY (77%) (Magnetospirillum sp. WD (77%) , M.\u00a0magn-1 (86%) , Magnetosp. XM-1 (88%), M-1 (89%) , and M.\u00a0-1 (76%) than to DY (77%) and MagnWD (77%) . This fibss, bbs, and bam), as observed for Thauera aromatica K172 (bss operon of strain 15-1 against other anaerobic toluene degraders were performed through BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Results showed similarities of 99% to Magnetospirillum sp. TS-6 and 80% to both T.\u00a0aromatica K172 (Azoarcus sp. (Magnetospirillum strains (excluding strain 15-1) showed that none of these strains contain genes related to aromatic compound degradation pathways.The genes for degradation of toluene under anaerobic conditions were found to be organized in three operons on the chromosome under the accession no."} +{"text": "Globally, endometrial cancer is the sixth leading cause of female cancer-related deaths. Non-atypical endometrial hyperplasia (EH), has a lifetime progression rate to endometrial cancer ranging from less than 5%, if simple without atypia, to 40%, if complex with atypia. Site specific, long-acting intrauterine devices (IUDs) provide fertility sparing, progestin-based EH medical management. It is unclear which IUD is most beneficial, or if progesterone sensitizing metformin offers improved outcomes. For resolution, PubMed searches for \u201cMirena\u201d or \u201cMetformin,\u201d \u201ctreatment,\u201d \u201cendometrial hyperplasia,\u201d or \u201cstage 1 endometrial cancer,\u201d were performed, yielding 33 articles. Of these, 19 articles were included. The 60 mg high-dose frameless IUD/20 mcg levonorgestrel has achieved sustained regression of Grade 3 endometrial intraepithelial neoplasia for 14 years. Case series on early stage endometrial cancer (EC) treatment with IUDs have 75% or greater regression rates. For simple through complex EH with atypia, the 52 mg-IUD/10\u201320 mcg-LNG-14t has achieved 100% complete regression in 6-months. Clearly, IUDs have an outcome advantage over oral progestins. However, studies on metformin for EH, and of progestins or metformin for early stage EC management are underpowered, with inadequate dose ranges to achieve significant differences in, or optimal outcomes for, the treatment modalities. Therefore, outcomes from the feMMe trial for the 52 mg-IUD/10\u201320 mcg-LNG-14t and metformin will fill a gap in the literature. Endometincrease . Therefoincrease . Insulinincrease . Based on unopposed estrogen driving malignant endometrial proliferation, progestins have been the mainstay for fertility sparing medical management of EH and Stage I, grade I EC ,8,12,13.p < 0.04, after adjusting for age, clinical stage, grade, chemotherapy treatment, radiation treatment and presence of hyperlipidemia [Metformin has been successfully used in a few cases of progestin nonresponsive atypical EH . Cell liipidemia . With inipidemia . This waipidemia . Progestipidemia . As metfIt will be shown that oral continuous or intermittent progestin has lower regression rates (higher progression rates), than do progestin containing IUDs. In other words, the locally- long-acting intrauterine progestin delivery provided by the 52 mg-IUD/10\u201320 mcg-LNG-14t, the 60 mg-IUD/14 mcg-LNG, the 60 mcg-HD-frameless-IUD/20 mcg-LNG and the 60 mcg-LD-frameless-IUD/14 mcg-LNG more effectively medically manages EH than does continuous or intermittent oral progestin. PubMed searches on June 3, 2017, search terms \u201cMirena treatment endometrial hyperplasia\u201d and \u201cmetformin treatment endometrial hyperplasia\u201d with the parameters English language, free full text, published from 2012 onwards yielded 25 articles. Of these, 1 was on contraception, 1 was redundant, 1 was concerned with diagnosis, 1 focused on PCOS, 1 focused on hysterectomy in obese patients, 1 included hysteroscopic resection, 1 explored progestin resistance, and 18 were included. PubMed searches on February 11, 2017, search terms \u201cMirena treatment stage 1 endometrial cancer\u201d and \u201cmetformin treatment stage 1 endometrial cancer\u201d with the parameters English language, free full text, published from 2012 onwards, yielded 8 articles. Of these, 3 were excluded as a duplicate, 2 were concerned with hysteroscopic resection as treatment or pretreatment followed by progestin treatment, 1 was concerned with ovarian cancer and 1 was concerned with advanced EC, leaving 1 inclusion. From the four PubMed searches, 19 articles were included, 14 articles were excluded. Hand search yielded seven additional included articles as shown in Progestins modulate endometrial glands\u2019 secretory differentiation, inhibit estrogen receptor function and endometrial cell mitosis, and are pro-apoptotic . ProgestGrade 2 endometrial endometrioid adenocarcinoma in an 18-year old nullipara with Class III obesity, NIDDM and PCOS was treated with a 52 mg-IUD/10\u201320 mcg-LNG-14t . CompletA multi-center randomized controlled trial (RCT) with 170 participants compared the 52 mg-IUD/10\u201320 mcg-LNG-14t to 10 mg MPA for 10 days monthly or continuously for EH treatment . Patholop = 0.001 [p = 0.001 [p = 0.30 [For further surveillance, 153 participants from the above trial participated in a national, multicenter RCT of the 52 mg-IUD/10-20 mcg-LNG-14t compared to cyclic MPA 10 mg for 10 days per cycle, and continuous MPA 10 mg daily for 6-month\u2019s treatment followed by reevaluation at 6, 12, 18, and 24 months . Of the = 0.001 . Consist = 0.001 . Howeverp = 0.30 . It is ip = 0.30 .p = 0.013, this study, which did not use intent to treat analysis, was underpowered for the 18.9 percentage-point regression rate difference to achieve statistically significance [A RCT of 60 participants in total, compared EH treatment with the 52 mg-IUD/10\u201320 mcg-LNG-14t to MPA 10 mg orally daily for 12 days monthly for 3-months [p < 0.01) and 55.7% cyclic NET for simple hyperplasia respectively at 12 months [At 1-year follow up, a randomized controlled trial (RCT) with 59 patients assigned to the 52 mg-IUD/10\u201320 mcg-LNG-14t versus 61 patients assigned to cyclic norethindrone (NET) 15 mg daily for 3-week cycles, indicated that the 52 mg-IUD/10\u201320 mcg-LNG-14t was more effective than cyclic NET medical management of non-atypical EH ,21. InteA single case series of 20 women with non-atypical and atypical EH, achieving sustained, complete regression for an average of 32-months with the 60mg-IUD/14 mcg-LNG or 60 mg-HD-frameless-IUD/20 mcg-LNG has been reported . A 44-yep < 0.0001 [p < 0.00001), however, this was predominantly spotting which resolved in 1-year [p = 0.08) [p = 0.28), or cancer-induced death, [Meta-analysis of three RCT with a total of 359 participants found that the 52 mg-IUD/10\u201320 mcg-LNG-14t prevented tamoxifen-induced endometrial polyp formation, odds ratio (OR) 0.18, 95% confidence interval (CI): 0.13 to 1.02, < 0.0001 . Interesn 1-year . The 52 = 0.08) . The 52 = 0.71) .Clearly the 52 mg-IUD/10\u201320 mcg-LNG-14t\u2019s 1 in 1000 uterine perforation risk and invasive placement in the uterus are limitations that oral medications lack. Studies with IUDs cannot be completely blinded, and cannot have an innocuous a placebo control as other RCT can have. Normally an IUD string is left palpable in the vagina for IUD removal. The presence of the IUD string alerts the participant to the in utero IUD. Furthermore, any object placed in utero can exert a mass effect on the endometrium and uterus, therefore, a plastic IUD lacking hormonal or metallic active component is not inert. Incomplete participant and trial personnel blinding contributes to a performance bias . The 52 Clearly, the 52 mg-, 60 mg-, and frameless-IUD have long acting reservoir adherence advantages over daily oral progesterone for endometrial protection. While depo progestin precludes immediate treatment discontinuation, IUDs can be removed and progestin diffusion immediately halted. Oral progestin must be continuous to assure EH regression . NeverthLike progestins, metformin is anti-proliferative on the endometrium ,13,17. MPhosphoinositide 3-kinase (P13K) proto-oncogene serine/threonine protein kinase B (Akt) mammalian target of rapamycin signaling pathway inhibition, mitogen-activated protein kinase (MAPK) inhibition, and glucose metabolism changes form part of metformin\u2019s anti-proliferative effect ,11. MetfMetformin upregulates GLUT4 mRNA and protein which are normally decreased in PCOS in comparison to non-PCOS . Like prp = 0.002 [A case-controlled trial of 28 participants taking 850 mg twice daily for 7 to 30 days versus 12 participants not taking metformin found an average daily dose dependent 17.2% reduction in atypical EH and endometrioid EC Ki-67, 95% confidence interval (CI) \u22127.0%, \u221227.4%, = 0.002 . This st = 0.002 . 2, p = 0.004 [p = 0.25 [A case series of five insulin resistant PCOS patients diagnosed by the Rotterdam criteria, who had Stage 1A Grade 1 EC treated with metformin 1000 mg daily and Cyproterone/Ethinyl Estradiol 2 mg/35 mcg 21 days per month for 6 months achieved 100% complete regression . This tr = 0.004 . HOMA-IRp = 0.25 . Cyprotep = 0.25 . Cyprotep = 0.25 . TherefoA pilot study compared megestrol acetate 160 mg daily to metformin 500 mg trice daily with megestrol acetate 160 mg daily for treatment of atypical EH . Only 16Metformin use is limited by its gastrointestinal adverse effect profile. Metformin is associated with abdominal pain, diarrhea, lactic acidosis, nausea and vomiting, and taste changes . MetformConsideration should be given to head-to-head trials of the 52 mg-IUD/10\u201320 mcg-LNG-14t and metformin combined with oral progesterone for EH and EC medical management. In vivo dose-escalation studies on metformin are needed to establish the optimal dose for EH treatment . MetformAromatase inhibitors that would reduce estrogen concentrations, gonadotrophin-releasing hormone agonists, and selective estrogen receptor modulators could be investigated for efficacy in preventing and/or treating EH and early stage EC . GLUT1 aProgestins have least three anti-proliferative mechanisms: anti-angiogenesis, estrogen receptor inhibition and IGF-1 inhibition . HoweverCyclic progestin has a 55.7 to 72% regression rate for EH, whereas continuous progestin has an 88 to 100% regression rate ,21. The p = 0.001 [p = 0.30 [Of note, with oral and intrauterine progestin therapy, premenopausal status and higher mean estrogen level are associated with EH recurrence, = 0.001 . Conversp = 0.30 . While bHopefully, the feMMe trial, an international, phase II, RCT of the 52 mg-IUD/10\u201320 mcg-LNG-14t, metformin with the 52 mg-IUD/10\u201320 mcg-LNG-14t, and weight loss with metformin and the 52 mg-IUD/10\u201320 mcg-LNG-14t, for atypical EH and early stage EC patients will provide clarity on the effective of metformin concurrent with a progestin IUD . It is bIf the feMMe trial supports metformin use with progestin IUDs for medical management of EH and early stage EC, a combined metformin and LNG IUD may become a reasonable treatment modality. A combined metformin\u2013LNG IUD may also have contraceptive and antiglycemic benefits for female, reproductive age diabetics. However, as the feMMe trial excludes oral progestins, unanswered questions will remain after the feMMe trial. The comparative effectiveness of oral progestins combined with metformin versus that of the IUDs combined with metformin for EH or early stage EC medical management remains to be answered."} +{"text": "Brucella species are the etiological agent of brucellosis in humans and animals. Here, we report the whole-genome sequence of Brucella melitensis strain CIIMS-BH-2, belonging to biovar 2. The draft assembly of CIIMS-BH-2 is 3.31\u2009Mb in size, with 57.2% G+C content. Brucella species. Brucella spp. are Gram-negative, nonmotile, and facultative intracellular coccobacilli. Brucellosis in humans is characterized by undulant fever, arthritis, and gastrointestinal complications. It also causes a negative impact on livestock and public health , B. abortus (cattle), B. suis (swine), B. canis (dogs), B. ovis (sheep), B. neotomae (wood rats), B. ceti , B. pinnipedialis , B. microti (voles and foxes), B. inopinata (humans), B. papionism (baboons), and B. vulpis (foxes) .Brucella spp. lack classical virulence factors, they have the ability to adapt to various environmental conditions using version 2 chemistry. The sequencing of the isolate was performed on an Illumina HiSeq 2500 platform. The de novo assembly was carried out using SPAdes (version 3.10.1) . The seqBrucella melitensis 16M. As predicted by RAST, the CIIMS-BH-2 genome consists of 3,216 open reading frames (ORFs), including 3,113 protein-coding sequences with 67 RNAs (The 16S rRNA gene sequence of CIIMS-BH-2 revealed 100% similarity to that of 67 RNAs . FurtherBrucella melitensis CIIMS-BH-2 genome sequence was deposited in the GenBank database under accession numbers CP025680 and CP025681.The"} +{"text": "Volume 29, no. 3, Page 326\u2013328, 2014Page 327, Legend for Fig. 1IncorrectFig. 1. Changes in viability (black line) and ATP levels (gray line) during carbon-starvation conditions.CorrectFig. 1. Changes in viability (gray line) and ATP levels (black line) during carbon-starvation conditions."} +{"text": "Bevacizumab addiction to triplet chemotherapy, according to FIr-B/FOx schedule, as first-line treatment in young-elderly metastatic colorectal CANCER (MCRC) patients may be more effective. Tailored treatments show worse clinical outcome in unfit patients.Elderly patients were clinically evaluated according to age and comorbidity to select FIr-B/FOx regimen in fit or tailored treatments in unfit elderly. Limiting toxicity syndromes (LTS) were evaluated.KRAS genotype. G3-4 toxicities were diarrhea 21%, mucositis 11%, neutropenia 11%. LTS were 46%, significantly more multiple than single site. At 8 months follow-up, in 37 unfit patients: ORR 37%, PFS 7 months, OS 13 months. PFS was significantly different in KRAS wild-type compared to mutant patients, while not OS. PFS and OS were significantly worse in KRAS c.35 G > A compared to wild-type and/or other mutant.At 17 months follow-up, in 28 young-elderly patients treated with first line FIr-B/FOx: objective response rate (ORR) 79%, progression-free survival (PFS) 11 months, overall survival (OS) 21 months. Clinical outcome was not significantly different according to KRAS, and specifically c.35 G > A mutant genotype, may significantly affect clinical outcome in patients unfit for FIr-B/FOx.Careful decision-making process including evaluation of patient's fitness, and individual safety should be included to select FIr-B/FOx intensive first line regimen in young-elderly MCRC patients. RAS genotype [KRAS wild-type patients [KRAS genotype) represents a major challenge in clinical management of MCRC patients.Different treatment options and lines of medical treatment in metastatic colorectal cancer (MCRC) patients are currently tailored according to fitness , comorbidities), metastatic extension (liver-limited (L-L) or other/multiple metastatic (O/MM)), and genotype \u20137. Firstgenotype , 7, 8, 1genotype , 10, 6. patients , 6. The MCRC patients are prevalently elderly but often under-treated in clinical practice, and usually underrepresented in clinical trials. They require a decision-making process combining the evaluation of fitness, according to co-morbidity, functional, and nutritional status , and selNo impact on PFS and OS was observed by age and/or comorbidities in patients treated with FOLFOX or FOLFIRI added or not to cetuximab . AdditioRecent retrospective analyses reported by our group, evaluating clinical outcome and safety of first-line FIr-B/FOx intensive regimen in fit young-elderly MCRC patients , 33, or et al. [2/w), OXP (32.5 mg/m2/w), associated to bolus plus continuous infusion 5-FU 880 mg/m2/w (88%)) failed to confirm significantly improved clinical efficacy compared to FOLFIRI in unresectable MCRC patients [HORG-FOLFOXIRI schedule proposed by Soug-lakos et al. , charact, OXP 32. mg/m2/w,patients , 5.In an unplanned subgroup evaluation of the phase III study, prognostic relevance of elderly status in both FOLFIRI and FOLFOXIRI treated patients was evaluated , and cliHORG/FOLFOXIRI intensive regimen showed a worse safety profile compared to FOLFIRI, with significantly more dose reductions and treatment delays; in elderly compared with younger patients, significantly more dose reductions , treatment delays , particularly due to toxicity were reported . In the FOLFIRI arm, dose reductions and treatment delays were not different. However, there was no significantly different rDI of drugs in elderly compared with younger patients, in both FOLFOXIRI and FOLFIRI arms.Grade 3-4 diarrhea was significantly more prevalent in elderly, compared to younger patients, in both chemotherapy regimens . Moreove2, 12h-timed-flat-infusion, 2 days weekly; CPT-11 160 mg/m2/BEV 5 mg/kg or OXP 80 mg/m2, weekly alternating. Cumulative Index Rating Scale (CIRS) was used to evaluate the comorbidity status, and only patients with primary and intermediate CIRS stage were enrolled [We retrospectively evaluated consecutive young-elderly patients 65 to 75 years enrolled in the previously reported phase II trial and in tenrolled . Primaryenrolled . LTS werKRAS wild-type patients, ORR was 92%, liver metastasectomies 23% (50% in L-L patients), median PFS 14 months (4-78+ months), median OS 38 months (8-78+ months). Among 13 KRAS mutant patients, ORR was 77%, liver metastasectomies 15%, (20% in L-L patients), median PFS 7 months (3-69+ months), median OS 19 months (6-69+ months). Neither PFS nor OS were significantly different in KRAS wild-type compared with mutant patients, according to log-rank test. No BRAF mutations were detected.Young-elderly patients were 28 (42%) among overall MCRC patients enrolled fitting for FIr-B/FOx intensive treatment, according to inclusion criteria, WHO PS 0 89%, CIRS primary/intermediate. At a median follow-up of 17 months, ORR was 79%, liver metastasectomies 18% (37.5% in L-L patients), median PFS 11 months (3-78+), median OS 21 months (6-78+) . Patients\u2019 distribution according to age and comorbidities was: young-elderly 22%, old-elderly 54%; CIRS stage primary 11%, intermediate 40%, secondary 42%. Medical treatment regimens were tailored according to age and comorbidity status in the individual patients. Eighteen patients (49%) were treated with triplet regimens; 15 patients (40%) with doublet regimens; 4 patients (11%) with mono regimens; 3 underwent up-front surgery.At a median follow-up of 8 months, ORR was 37%, median PFS was 7 months (1-13+), median OS 13 months (1+-23+). Among patients treated with triplet regimens, ORR was 37.5%, median PFS 8 months (3-12), median OS 12 months (3-23+ months) , median OS 13 months (1+-23+ months). Among 12 KRAS mutant patients evaluable for activity, ORR was 25%, median PFS 6 months (1-11 months), median OS 8 months (3-18 months). A significantly different PFS (p = 0.043), but not OS, was reported in KRAS wild-type compared with mutant patients. Significantly worse PFS and OS were reported in c.35 G > A KRAS mutant compared to wild-type , and to other mutant patients .Among 14 KRAS wild-type patients, demonstrated clinical outcome and safety profile equivalent to younger patients [Fit young elderly patients, PS<2, treated with triplet regimens consisting of chemotherapeutic drugs, or BEV addiction to doublets, or doublets plus EGFR-inhibitors in patients , 5, 8, 1patients , 34 obtaRetrospective analysis of randomized clinical trials showed that doublets CPT-11, or OXP, added to fluoropyrimidin in older patients eligible for clinical study reported ORR 18-59.4%, PFS 4.9-10.0 months and OS 8.5-20.7 months , 32, 30.Published studies showed that limiting toxicities were not significantly different in elderly patients treated with 5-FU or CPT-11 \u201316, sligKRAS wild-type compared to mutant patients. More, significantly worse clinical outcome (PFS and OS) may be influenced by KRAS c.35 G > A mutant genotype, compared to wild-type and/or other mutant, confirming that KRAS genotype, and specifically c.35 G > A mutant, confers different biological aggressiveness [KRAS genotype may significantly explain different PFS, and c.35 G > A KRAS mutant a significantly worse PFS and OS, compared to wild-type and other mutant.In clinical practice, selection of patients eligible for intensive medical treatment and to achieve optimal activity and clinical outcome could be performed by the evaluation of age, PS, CIRS and careful monitoring of individual safety using LTS Table . Patientsiveness \u201341, lessKRAS genotype, and specifically the prevalent KRAS c.35 G > A mutant status, that can discriminate significantly different clinical outcome particularly in unfit MCRC patients.We revised intensive medical treatment consisting of triplet chemotherapy regimens or more intensive triplet chemotherapy plus anti-angiogenic drug, bevacizumab, in elderly MCRC patients, that we previously developed, discussed compared with tailored medical regimens selected for unfit MCRC in clinical practice , 7, 32,"} +{"text": "The correct name is: Victor W. M. van Hinsbergh. The correct citation is: Nauta TD, Duyndam MCA, Weijers EM, van Hinsbergh VWM, Koolwijk P (2016) HIF-2\u03b1 Expression Regulates Sprout Formation into 3D Fibrin Matrices in Prolonged Hypoxia in Human Microvascular Endothelial Cells. PLoS ONE 11(8): e0160700. doi:"} +{"text": "Primulina cardaminifolia Yan Liu & W.B. Xu (Gesneriaceae), a distinct new species with imparipinnate leaves, is described and illustrated from a limestone valley in Guangxi Zhuangzu Autonomous Region, China. To assure its generic placement and phylogenetic affinity, phylogenetic analyses were performed using DNA sequences of nuclear ITS and chloroplast trnL-F intron spacer region. Additionally, somatic chromosome number was counted and pollen stainability was tested.Primulina; however, two phylogenetically distinct ITS sequence types were detected, suggesting a probable hybrid origin. Its pollen stainability is 100% and its chromosome number, 2n = 36, is congruent with all known counts of diploid species of the genus.Phylogenetic analyses support its placement in Primulina cardaminifolia and suggest that it could have derived from homoploid hybrid speciation. Color plates, line drawings and a distribution map are provided to aid in identification.All available data support the recognition of the new species The online version of this article (doi:10.1186/1999-3110-54-19) contains supplementary material, which is available to authorized users. Chirita D. Don Mich. M\u00f6ller & A. Weber] made without support from molecular data by Weber et al. .Although the new generic circumscription reflects better the evolutionary relationships and ecological preferences of the genus, diagnostic characters of rosette and the r et al. was recePrimulina, which is described and illustrated here. Chromosome count of the new species is in agreement with those reported for Primulina in Christie et al. has been deposited in HAST. Root tips were gathered and pretreated in 2 mM 8-hydroxyquinoline at 15\u201318\u00b0C for about 6 h and fixed overnight in an ethanol-acetic acid solution (3:1) below 4\u00b0C. The chromosomes were stained and macerated in 2% acetic orcein with 1 N hydrochloric acid (10:1). Classification of chromosome complement based on centromere position at mitotic metaphase followed Levan et al. and cycle-sequenced using the T7 and SP6 promoter primer pairs.DNA sequences of the nuclear ribosomal internal transcribed spacers (ITS) and the chloroplast u et al. . BecausetrnL-F regions as separated matrices. Primulina pinnata (W.T. Wang) YinZ. Wang, which was not included in Xu et al. YinZ. Wang, and Didymocarpus podocarpus C.B. Clarke chosen as outgroups based on recent phylogenetic analyses and maximum likelihood (ML) criteria implemented in MEGA5. MP trees were searched using the Tree-Bisection-Reconnection (TBR) search option with the initial trees setting at 50, MP search level setting at 5, and maximum number of trees setting at 2000. Clade supports were calculated based on 100 bootstrap resamplings . ML trees were reconstructed using the nearest-neighbor-interchange (NNI) method with all site used and the initial tree automatically selected under the model(s) selected by MEGA5. Clade supports of ML analysis were evaluated based on 100 bootstrap resamplings .For phylogenetic analyses, matrices of Xu et al. were adou et al. because Wei-Bin Xu & Yan Liu 08050 . \u788e\u7c73\u85ba\u8449\u5831\u6625\u82e3\u82d4 Figures\u00a0Yan Liu & W.B. Xu, sp. nov.\u2014TYPE: CHINA. Guangxi Zhuangzu Autonomous Region, Laibin Shi (City), Fenghuang Zhen (Township), alt. 280\u00a0m, on moist limestone rock face in a valley, 14 July 2008, Primulina cardaminifolia Yan Liu & W.B. Xu resembles Primulina pinnata (W.T. Wang) YinZ. Wang in having imparipinnate leaves, but is clearly distinct from this species by the ovate-cordate terminal leaflet of 3\u20137 \u00d7 3\u20136.5 cm, 1 or 2 pairs of broadly ovate to sub-ovate lateral leaflets, 1\u20133-branched cymes with 3 to 10-flowers, and the entire-margined calyx lobes with acuminate apex.Herbs perennial. Rhizome subterete, 3\u20135 mm across. Leaves 5\u20137, in basal rosette, imparipinnate, 10\u201320 cm long, papery when dry; petiole subterete, 6\u201312.5 cm long, densely pubescent; terminal leaflet ovate-cordate, 3\u20137 \u00d7 3\u20136.5 cm, apex obtuse, base cordate, margin repand to irregularly pinnately lobed, densely pubescent on both surfaces; lateral leaflets 1 or 2 pairs, opposite or alternate, broadly ovate to rotund, 1\u20133 \u00d7 1\u20133 cm, margin repand to irregularly pinnately lobed, densely pubescent on both surfaces, petiolules short, 2\u201310 mm long. Cymes 2\u20134, axillary, 1\u20133-branched, 3\u201310-flowered; peduncle 4\u20138 cm long, 1\u20132 mm in diam., densely pubescent; bracts 2, opposite, linear-lanceolate, 7\u20138 \u00d7 2\u20133 mm, margin entire, pubescent; pedicel 4\u20137 mm long, densely pubescent. Calyx 5-parted to base, lobes lanceolate-linear, 8\u201312 \u00d7 2\u20133 mm, apex acuminate, outside pubescent, inside glabrous, margins entire. Corolla white to pale purple, 3.2\u20133.5 cm long, outside glandular-pubescent, inside sparsely puberulent, with 2 pale-yellow stripes; corolla tube 2.1\u20132.3 cm long, 8\u201312 mm in diam. at the mouth, 2.5\u20133 mm in diam. at the base; limb pale purple, distinctly 2-lipped; adaxial lip 2-parted to over the middle, lobes oblong, 8\u201310 \u00d7 6\u20137 mm; abaxial lip 3-lobed to over the middle, lobes oblong, 12\u201313 \u00d7 4\u20135 mm; stamens 2, adnate to 1.5 cm above the corolla tube base; filaments linear, ca. 1.2 cm long, geniculate above the base, sparsely glandular-puberulent; anthers ca. 3 mm long, ca. 1.5 mm wide, dorsifixed, glabrous; staminodes 2, ca. 5 mm long, apex capitate, glabrous, adnate to ca. 6 mm above the base of corolla tube. Disc ring-like, ca. 1 mm in height, margin repand, glabrous. Pistil 2.5\u20132.8 cm long, ovary 7\u20138 mm long, ca. 1.5 mm across, puberulent; style 1.5\u20131.8 cm long, ca. 0.6 mm across, puberulent; stigma obtrapeziform, ca. 2 mm long, apex 2-lobed. Capsules not seen.CHINA. Guangxi Zhuangzu Autonomous Region, Laibin Shi, Fenghuang Zhen, 3 July 2008, Wei-Bin Xu & Yan Liu 08040 (IBK); same locality, 8 Sep 2008, Wei-Bin Xu & Kuo-Fang Chung 08472 (IBK), Shin-Ming Ku et al. 2035 (HAST); same locality, 28 June 2007, Hong-Jin Wei & Wei-Bin Xu 07244 (IBK).Primulina cardaminifolia is extremely rare, currently known only from the type locality in Laibin Shi, Guangxi Zhuangzu Autonomous Region, China .The specific epithet is derived from the leaves resembling those of the genus Primulina cardaminifolia resembles Primulina pinnata (W.T. Wang) YinZ. Wang YinZ. Wang and 634 (P. cardaminifolia-B) bp, respectively, while only one cpDNA sequence type was detected in the species. With the addition of these two ITS sequences, the ITS matrix contained 28 accessions of 675 aligned positions, of which 182 (26.96%) were parsimoniously informative. Based on the Kimura 2-parameter model using a discrete Gamma distribution (K2\u2009+\u2009G) with 5 rate categories selected by the corrected Akaike Information Criterion (AICc) implemented in MEGA5, a single ML tree (log likelihood\u2009=\u2009\u22124114.9869) was recovered and low supports in ITS and cpDNA datasets, respectively . Primulina cardaminifolia was collected from the type locality [S.M. Ku 2035(HAST)].GenBank accession numbers: Species: (ITS/Didymocarpus podocarpus C.B. Clarke: (DQ912688/FJ501514); Petrocodon dealbatus Hance: (FJ501358/FJ501537); Petrocodon scopulorum (Chun) YinZ. Wang [=Tengia scopulorum Chun]: (GU350637/GU350669); Primulina bipinnatifida (W.T. Wang) Yin Z. Wang [=Chiritopsis bipinnatifida W.T. Wang]: (DQ872842/DQ872806); Primulina cardaminifolia Yan Liu & W.B. Xu: ; Primulina cordifolia (D. Fang & W.T. Wang) YinZ. Wang [=Chiritopsis cordifolia D. Fang & W.T. Wang]: (DQ872845/DQ872803); Primulina dryas (Dunn) Mich. M\u00f6ller & A. Weber [=Chirita sinensis Lindl.]: (FJ501348/FJ501524); Primulina gemella (D. Wood) YinZ. Wang [=Chirita gemella D. Wood]: (FJ501345/FJ501523); Primulina glandulosa Yin Z. Wang : (DQ872841/DQ872804); Primulina heterotricha (Merr.) YinZ. Wang [=Chirita heterotricha Merr.]: (DQ872826/DQ872816); Primulina linearifolia (W.T. Wang) YinZ. Wang [=Chirita linearifolia W.T. Wang]: (DQ872834/DQ872810); Primulina longgangensis (W.T. Wang) YinZ. Wang [=Chirita longgangensis W.T. Wang]: (FJ501347/AJ492290); Primulina luochengensis (Yan Liu & W.B. Xu) Mich. M\u00f6ller & A. Weber [=Wentsaiboea luochengensis Yan Liu & W.B. Xu]: (HQ633046/HQ632949); Primulina minutimaculata (D. Fang & W.T. Wang) YinZ. Wang [=Chirita minutimaculata D. Fang & W.T. Wang]: (DQ872828/DQ872815); Primulina multifida B. Pan & K.F. Chung: (JX507031/JX506756); Primulina ophiopogoides (D. Fang & W.T. Wang) YinZ. Wang [=Chirita ophiopogoides D. Fang & W.T. Wang]: (DQ872829/DQ872814); Primulina pinnata (W.T. Wang) YinZ. Wang [Chirita pinnata W.T. Wang]: (FJ501349/FJ501526); Primulina pinnatifida (Hand.-Mazz.) Yin Z. Wang [=Chirita pinnatifida (Hand.-Mazz.) B.L. Burtt]: (FJ501350/FJ501527); Primulina pseudomollifolia W.B. Xu & Yan Liu: (JX506869/JX506759); Primulina pteropoda (W. T. Wang) Yan Liu [=Chirita pteropoda W.T. Wang]: (DQ872827/DQ872817); Primulina repanda var. guilinensis (W.T. Wang) Mich. M\u00f6ller & A. Weber [=Chiritopsis repanda var. guilinensis W.T. Wang]: (DQ872846/DQ872808); Primulina spadiciformis (W.T. Wang) Mich. M\u00f6ller & A. Weber [=Chirita spadiciformis W.T. Wang]: (FJ501346/AJ492291); Primulina spinulosa (D. Fang & W.T. Wang) YinZ. Wang [=Chirita spinulosa D. Fang & W.T. Wang]: (DQ872830/DQ872813); Primulina tabacum Hance: (FJ501352/AJ492300); Primulina weii Mich. M\u00f6ller & A. Weber : (DQ872832/DQ872811); Primulina wentsaii (D. Fang & L. Zeng) YinZ. Wang [=Chirita wentsaii D. Fang & L. Zeng]: (DQ872831/DQ872812)."} +{"text": "Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium which is an important foodborne bacterial pathogen for humans worldwide with high mortality rates. Here, we report a 2,964,284-bp draft genome sequence of Listeria monocytogenes strain ATCC 7644 (American Type Culture Collection). Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium and an important foodborne bacterial pathogen for humans worldwide with high mortality rates isolated from a human was obtained from ATCC and stored at \u221280\u00b0C. Genomic DNA was isolated from overnight cultures grown at 37\u00b0C on brain and heart infusion agar using the Qiagen DNeasy blood and tissue DNA purification kit . Three sequencing libraries were constructed from three independent cultures/DNA extractions using the Nextera XT DNA sample preparation kit , and library quality was analyzed using a BioAnalyzer . Libraries were sequenced with the Illumina MiSeq platform using v3 reagent kits. A total of 2,889,385 300-bp paired-end reads were generated.http://jgi.doe.gov/data-and-tools/bbtools/). Preprocessed reads were assembled using SPAdes v3.10.1 , and overlapping pairs were merged (bbmerge) using the bbtools software suite ( v3.10.1 and poli v3.10.1 . Assemblh v1.1.1 , which ph v1.1.1 . Two of NGZM00000000. The version described in this paper is the first version, NGZM01000000.This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no."} +{"text": "P = 0.03, I2 = 0%; CC vs. GG: OR = 0.59, 95% CI = 0.36\u20130.97, P = 0.04, I2 = 0%; GC+CC vs. GG: OR = 0.61, 95% CI = 0.37\u20130.99, P = 0.05, I2 = 0%). In summary, current evidence indicates that the microRNA-608 rs4919510 G>C polymorphism maybe an important factor of DSCs susceptibility, especially in Caucasian population.Previous epidemiologic studies have revealed a possible association between microRNA-608 rs4919510 G>C polymorphism and digestive system cancers (DSCs) risk, but the results were not consistent. We therefore performed an updated meta-analysis to explore the association between microRNA-608 rs4919510 G>C polymorphism and DSCs risk. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the relationship between the microRNA-608 rs4919510 G>C polymorphism and DSCs risk. Heterogeneity, cumulative analyses, sensitivity analyses, and publication bias were also conducted to examine the statistical power. Eight published articles with nine independent case-control studies involving 10,836 individuals were included in this meta-analysis. Overall, no significant association was found between microRNA-608 rs4919510 G>C polymorphism and DSCs risk in general populations. But some significant protective effects were observed in the subgroup of Caucasian population group in three genetic models (C vs. G: OR = 0.82, 95% CI, 0.68\u20130.99, Digestive system cancers (DSCs), which comprise esophageal cancer (EC), gastric cancer (GC), hepatocellular cancer (HC), pancreatic cancer (PC) colorectal cancer (CRC) and other solid carcinoma, is one of the most common malignancies with increasing incidence and mortality worldwide are the most common type of genetic variation in people. SNPs alter gene function and/or expression, consequently affecting downstream biologic pathways and increasing cancer risk statement were searched for relevant studies that focused on the association between microRNA-608 rs4919510 G>C polymorphism and DSCs risk from inception up to January 1, 2018. Only studies that were written in English and Chinese were included. Moreover, the bibliographies of the collected studies and relevant reviews were retrospected to identify additional articles. The following search terms and strategy was used :#1 microRNA 608#2 microRNA-608#3 mir 608#4 mir-608#5 rs4919510#6 #1 OR #2 OR #3 OR #4 OR #5#7 polymorphism#8 variant#9 mutation#10 #7 OR #8 OR #9#11 cancer#12 tumor#13 neoplasm#14 #11 OR #12 OR #13#15 #6 AND #10 AND #14Studies were included based on the following criteria: (1) only case-control studies that focusing on the association between the microRNA-608 rs4919510 G>C polymorphism and DSCs risk; and (2) studies had to provided sufficient frequency data on the genotype distribution to evaluate the crude odds ratios (ORs) and 95% confidence intervals (CIs); and; (3) studies had to be published only in English and Chinese; and (4) only publications with the largest or most recently updated sample data were included when there were some overlapping or duplicate publications on the same theme.Two researchers (Li and Song) independently reviewed and extracted relevant information from all included studies, including name of the first author, publishing date, country or region where the study was conducted, race, control design, sample sizes of the cases and controls, frequency data of genotype distribution, genotyping method, Hardy-Weinberg equilibrium (HWE) assessment in controls, and cancer type. Quality evaluation of the included studies was performed by the two researchers using the modified Newcastle-Ottawa scale (NOS). The scores ranged from 0 points (worst) to 11 points (best) Table ; studiesQ-test and I2 statistical method , co-dominant models (GC vs. GG and CC vs. GG), dominant model (GC+CC vs. GG), and recessive model (CC vs. GG+GC). Heterogeneity between the included studies was calculated using Cochran's A total of 164 articles were collected. The study selection process was presented in Figure P = 0.98, I2 = 53.4%; GC vs. GG: OR = 1.07, 95% CI = 0.93\u20131.24, P = 0.35, I2 = 43.0%; CC vs. GG: OR = 1.01, 95% CI = 0.83\u20131.24, P = 0.90, I2 = 56.4%; GC+CC vs. GG: OR = 1.05, 95% CI = 0.89\u20131.23, P = 0.58, I2 = 56.4%, .Publication bias was examined with Begg's test and no apparent asymmetry of the funnel plot was found Figure . These rMicroRNAs is a family of small, noncoding, evolutionarily conserved endogenous RNAs consisting of 22 nucleotides that can regulate gene expression through a post-transcriptional pathway binding to the 3\u2032-UTR of target mRNAs , and the results were calculated without gene-gene and gene-environment risk factors, leading to a failure to interpret the potential interaction mechanisms. Third, almost all of the included studies focused on Asian and Caucasian populations, which would restrict the application of our results to other populations.In summary, our meta-analysis demonstrated that the microRNA-608 rs4919510 G>C polymorphism might play an important role in DSCs susceptibility. Further studies in different races and regions with larger population sizes are needed to confirm our findings.X-FL, J-KS, and Y-MN conceived the study. X-FL, J-KS, and J-WC searched the databases and extracted the data. J-KS, Y-QZ, and ML analyzed the data. X-FL, J-KS, and J-WC wrote the draft of the paper. JZ and Y-MN reviewed the manuscript. All the authors approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Molecular classifications of breast cancer have resulted in improved treatments. However, treatments for triple negative breast cancer (TNBC) are lacking. Analysis of molecular targets for TNBC is a priority. One potential candidate is androgen receptor (AR) phosphorylation. This study assessed the role of AR phosphorylation at ser81/ser515 and their two upstream effectors, cyclin-dependent kinase 1 (pCDK1) and extracellular-regulated kinase 1/2 (pERK1/2) in 332 ductal breast cancer patients by immunohistochemistry.p = 0.038), decreased size (p = 0.001), invasive grade (p < 0.001), necrosis (p = 0.003), b-lymphocytes (p = 0.020), molecular subtype (p < 0.001) and estrogen receptor (ER)/progesterone receptor (PR)-status (p < 0.001). The cohort was therefore stratified into ER+ve and ER-ve patients. In ER+ve tumours, pERK1/2 combined with AR-515 associated with improved CSS (p = 0.038), smaller size (p = 0.004), invasive grade (p = 0.001), decreased b-lymphocytes (p = 0.013) and increased plasma cells (p = 0.048). In contrast, in TNBC patients, phosphorylation of AR-515 associated with poorer CSS (p = 0.007). pERK1/2 combined with AR-515 associated with decreased inflammation (p = 0.003), increased tumour stroma (p = 0.003) and tumour budding (p = 0.011), with trends towards decrease CSS (p = 0.065) and macrophage levels (p = 0.093).pERK1/2 combined with AR-515 associated with improved cancer-specific survival (CSS, In Conclusions, AR-515 may be an important regulator of inflammation in breast cancer potential via ERK1/2 phosphorylation. AR-515 is a potential prognostic marker and therapeutic target for TNBC. Approximately 1.7 million cases of breast cancer are diagnosed every year. About 522,000 die of breast cancer yearly making it the 5th most common cause of cancer death globally . In the The majority of breast cancers comprise of luminal A and luminal B subtypes. These subtypes display oestrogen (ER) and/or progesterone receptors (PR) rendering these cancer cells susceptible to endocrine therapies e.g. anti-oestrogen therapies (Tamoxifen) , 8. In HIt has been shown that TNBC patients displaying pathological complete response (pCR) had better outcomes in terms of progression-free survival than patients who had not achieved pCR . pCR is Although numerous studies on AR have been published, the exact role of AR as tumour-promoting or anti-tumorigenic remains undecided. It is known that AR signalling plays a role in regulating cancer cell proliferation and apoptosis \u201319. AR aIt was also reported that when Tamoxifen-resistant breast cancer cells that expressed high levels of AR were exposed to bicalutamide (anti-androgen), cell growth was shown to decrease as well as reversing Tamoxifen resistance , indicatThe MAPK/ERK signalling cascade is heavily involved in the regulation of cancer cell proliferation, growth and differentiation. The stimulation of this pathway leads to the activation of a cascade of kinases , which ultimately leads to the activation of ERK1/2, which is associated with poor prognosis in breast cancer . One funin vitro kinase assays demonstrated an increase in ser-308 phosphorylation by CDK1 is responsible for Serine\u201381 phosphorylation [In contrast, AR phosphorylation at ser-81 is the prototypical site for dihydrotestosterone (DHT) activation, which is thought to be facilitated by activated Cdk1, as observed by Chen et al where Cdk1 inhibitors decreased ser-81 phosphorylation of AR in LNCaP cells and similarly decreased AR protein expression and transcriptional activity. Whereas transfected Cdk1 stimulated AR phosphorylation at ser-81 and increased AR protein expression . This surylation . Cdk1 phrylation .This study aims to further understand the role of androgens and AR activation in breast cancer by determining its effect on patient survival. This is followed by the determination of the role of upstream pathways (i.e. Cdk1 and ERK1/2 pathways) on AR activation and their effects on cancer specific survival (CSS). We aim to confirm that the phosphorylation of AR at either ser-515 or ser-81 is a surrogate for AR activation and assess if the pathways responsible for this phosphorylation are potential targets for therapeutic intervention.n = 332, Figure Only patients with staining for AR, AR-81 and AR-515 were included in the analysis (p = 0.842) nor AR-515 (p = 0.563) were associated with CSS alone. Therefore, upstream effectors of AR phosphorylation were investigated. AR-81 significantly correlated with nuclear CDK1 (p < 0.001) and AR-515 correlated with nuclear pERK1/2 (p < 0.001) as expected. However, AR-81 still showed no associations even when combined with CDK1 in the nucleus (p = 0.344). In contrast, AR-515 was significantly associated with improved CSS when combined with ERK1/2 phosphorylation in the nucleus . When nuclear pERK1/2 was assessed alone it was also significantly associated with improved CSS (p = 0.004). Therefore, further analysis was confined to nuclear pERK1/2 and AR-515.The relationship between nuclear AR activation and CSS is shown in Table p = 0.001), lower grade (p < 0.001), ER/PR+ve tumours (p < 0.001), molecular subtype (p < 0.001), lower necrosis (p = 0.003), weak Klintrup-Makinen (KM) grade (p = 0.004) and lower b-lymphocyte levels (p = 0.020). There was also a trend towards decreased HER2 (p = 0.096) and lower lymphovascular invasion (p = 0.099). When pERK1/2 was combined with AR-515 significant associations were still seen with smaller size (p = 0.017), lower grade (p < 0.001), ER+ve tumours (p = 0.013), PR+ve tumours (p = 0.008), decreased HER2 (p = 0.041), molecular subtype (p < 0.001), lower necrosis (p = 0.006), weak KM grade (p = 0.005) and lower b-lymphocytes (p = 0.023). Significant associations were now also seen with decreased proliferation (p = 0.009), lymphovascular invasion (p = 0.017) and increased tumour budding (p = 0.047).The relationship between pERK1/2, AR-515, clinicopathological characteristics, and local inflammatory response is presented in Table p = 0.008). As pERK1/2 and AR-515 strongly correlated in ER+ve patients (p < 0.001) they were combined. However, when combined the survival effect was weakened (p = 0.038), suggesting that pERK can also act independently of AR-515 in ER+ve breast cancers. When ER+ve patients where stratified further, there was no difference in CSS between luminal A and luminal B subtypes for pERK1/2 alone or combined with AR-515 therefore further analysis was carried out in all ER+ve tumours (n = 228).As pERK1/2 plus AR-515 associated with molecular subtype, we firstly stratified patients into ER+ve and ER-ve tumours . pERK1/2p = 0.004), lower grade (p = 0.001), molecular subtype (p = 0.024), decreased proliferation (p = 0.006), lower b-lymphocytes (p = 0.013) and increased plasma cells (p = 0.048). There was also a trend towards decreased necrosis (p = 0.096). When pERK1/2 was combined with AR-515 significant associations where still seen with lower grade (p = 0.002), molecular subtype (p = 0.001), decreased proliferation (p = 0.001), lower b-lymphocytes (p = 0.006) and increased plasma cells (p = 0.023). Significant associations were now also seen with decreased necrosis (p = 0.009) and lymphovascular invasion (p = 0.029).The relationship between pERK1/2, AR-515, clinicopathological characteristics, and local inflammatory response in ER+ve tumours is presented in Table p = 0.023) may be due to differences between the two ER-ve subtypes. Therefore, ER-ve patients were stratified into HER2-type and TNBC to further investigate these effects (p = 0.010), however no significant effect on CSS was observed for pERK1/2 alone (p = 0.534) and only a trend towards poorer outcome was seen when combined with AR-515 (p = 0.065). However, high levels of AR-515 combined with total AR, representing full AR activation, associated with a significantly poorer outcome and no significant associations were seen in these patients. However, there was a trend towards improved patient survival with AR-515 phosphorylation (p = 0.056) alone and when combined with pERK1/2 (p = 0.076), confirming our hypothesis that these two ER-ve subtypes respond differently to AR-515 phosphorylation.It was observed in patients with ER-ve breast cancer that high pERK1/2 plus AR-515 had a trend towards an effect on survival rate. It was hypothesised that the loss of significance and weaker correlation between pERK1/2 and AR-515 in ER-ve patients ( effects . In patip = 0.033), lower KM grade (p = 0.004), increased tumour-stroma percentage (TSP) (p = 0.033) and increased tumour budding (p = 0.007). When combined with pERK1/2 associations were still seen with lower KM grade (p = 0.003), increased TSP (p = 0.003) and increased tumour budding (p = 0.011). Trends towards association were also seen for increased age (p = 0.075) and decreased macrophages (p = 0.093).Due to the detrimental effect of AR-515 phosphorylation in TNBC, associations with clinicopathological characteristics were assessed Table . Full acp = 0.002), invasive grade (p = 0.013), lymph node involvement (p = 0.009), necrosis (p < 0.001), proliferation index (p < 0.001), lymphatic invasion (p < 0.001), cytotoxic t-lymphocytes (p = 0.005), TSP (p = 0.009), tumour budding (p = 0.001) and angiogenesis (p = 0.043) were significantly associated with poorer CSS. Lymphovascular invasion (p = 0.054) and b-lymphocytes (p = 0.064) trended towards significance.For ER+ve tumours, since pERK1/2 plus AR-515 had significant associations with improved patient survival, these factors were taken into univariate and multivariate analysis (Table p = 0.036), proliferation index (p = 0.014), cytotoxic t-lymphocytes (p = 0.001), and TSP (p = 0.033) were independent prognostic factors, with lymphatic invasion (p = 0.060), tumour budding (p = 0.084), angiogenesis (p = 0.051) and pERK1/2 (p = 0.073) showing trends towards independence. However, pERK1/2 plus AR-515 does not appear to be independently prognostic in these patients (p = 0.682).On multivariate survival analysis including pERK1/2 plus AR-515; necrosis (p = 0.022), lymph node involvement (p < 0.001), necrosis (p = 0.030), lymphatic invasion (p = 0.001), lymphvascular invasion (p < 0.001), macrophages (p = 0.011) and cytotoxic t-lymphocytes (p = 0.047) were significantly associated with poorer CSS. Age (p = 0.055) and plasma cells (p = 0.055) trended towards significance.For TNBC, since AR-51 plus total AR had significant associations with poorer patient survival, these factors were taken into univariate and multivariate analysis (Table 7). On univariate analysis, size (p = 0.006), lymphovascular invasion (p = 0.002), and macrophages (p = 0.002) were independent prognostic factors. However, AR-515 plus total AR (p = 0.957) nor AR alone (p = 0.801) appear to be independently prognostic in these patients.On multivariate survival analysis including AR-515 plus total AR; lymph node involvement . The study was approved by the Research Ethics Committee of the West Glasgow University Hospitals NHS Trust.Patients presenting with invasive ductal breast cancer at Glasgow Royal Infirmary, Western Infirmary and Stobhill Hospital between 1995 and 1998 with formalin-fixed paraffin embedded blocks of the primary tumour available for evaluation were studied were retrieved from the routine reports. Tumour grade was assigned according to the Nottingham Grading System. ER and PR status were assessed on tissue microarrays (TMAs) using immunohistochemistry (IHC) with Dako ER antibody and Leica PR antibody and scored according to the American Society of Clinical Oncology and College of American Pathologists guidelines with a cut-off value of 1% positive tumour nuclei . Her2 stFull-section haematoxylin and eosin (H&E) slides for the 474 patients were used to score local inflammatory infiltrate according to Klintrup-Makinen (KM) criteria. KM scoring of slides was carried out as previously described. Briefly, tumours were scored on four-point scores based on appearances at the tumour invasive margin. A score of 0 signified that there were no inflammatory cells at tumour's invasive margin; score 1 indicated a mild and patchy inflammatory cells; score 2 denoted a prominent band-like inflammatory reaction at the invasive margin; and score 3 revealed a florid cup-like inflammatory infiltrate at the invasive edge , 44. IndFull-section H&E slides were also used to score the tumour stroma percentage (TSP) as previously reported . BrieflyLymphatic and blood vessel (lymphovascular) invasion were assessed, on 2.5-\u03bcm thick sections, using IHC staining with the lymphatic endothelial marker D2-40 diluted 1:100 and vascular endothelial marker Factor VIII diluted 1:100 as previously described . Ki67 prThe molecular subtypes were defined as follows: Luminal A: oestrogen (ER) and/or progesterone receptor (PR) positive, Her-2 negative or low proliferative index (< 15%); Luminal B: hormone receptor positive, Her-2 positive or high proliferative index (> 15%); Her-2 subtype: Her-2 positive and hormone receptor negative, any proliferative index; and triple negative: Her-2 negative, hormone receptor negative, any proliferative index.2O2. Sections were further blocked using 5% horse serum (10% casein for pERK1/2) in Tris-buffered saline (TBS). Antibodies for pCdk1 (Abcam), pERK1/2 , AR-81 , AR-515 were incubated overnight at 4\u00b0C diluted in Dako antibody diluent at 1:150 (Dako UK Ltd.) Total AR antibody (Dako UK Ltd.) was incubated overnight at 4C at 1:4000. Bound antibody complex was visualised using EnVision plus kit (Dako UK Ltd.) followed by 3,3-diaminobenzidine tetrahydrochloride . Nuclei were counterstained with haematoxylin and blued with Scots Tap Water Substitute, dehydrated through graded alcohol and xylene and mounted with Di-N-Butyl Phthalate in xylene (DPX).Antibody validation for AR-81, AR-515, pERK1/2 and pCDK1 was carried out as previously described , 26. ImmTMAs were scanned using the Hamamatsu NanoZoomer at \u00d7 20 magnification, and visualization was carried out using Slidepath Digital Image Hub, version 4.0.1 .Only nuclear expression was scored as this represents the active form of each protein. Tissue staining intensity was scored by two blinded independent observers using a weighted histo-score (H-score) method , 49. Then = 332). Cut-off values for high or low protein expression were determined by the median of the average values of the intensity of staining. The relationships between variables were assessed using contingency table analysis with the X2 test for linear trend. Correlations coefficients were analysed using a Spearman's rho. Kaplan\u2013 Meier curves with log rank analysis was used to examine the effect of protein expression on CSS. Univariate survival analysis was performed using Cox proportional hazards regression. Variables with P-value of < 0.05 were entered into a multivariable model using a backwards conditional method for all patients and triple negative patients. All statistical analyses were two-sided and significance defined as P-value < 0.05. All statistical analysis was performed using the SPSS software version 22 .Only patients with a score for AR, AR-81 and AR-515 were included in the analysis ("} +{"text": "The absolute configurations of four terpenes were determined based on their optical rotary powers. Incubation experiments with R)-(+)-limonene is found in citrus fruits. Cineol is one of the main constitutents of eucalyptus oil and (+)-carvone is present in caraway. Some famous sesquiterpenes are \u03b1-humulene from hops, \u03b1-patchoulene from patchouli oil, and \u03b2-cedrene from juniper D = +120) , wh, whStrepades ago , the fultructure . The sig carbons . The HMB = +120) , while i2+ cofactor to which in turn the substrate\u2019s diphosphate portion is bound D24 = +7.1 . This points to the same enantiomer as reported from the heartwood of Cryptomeria japonica D22 = \u221251.3 . The opposite enantiomer was reported from Eucalyptus macarthuri ([\u03b1]D = +30.5) + calcd for C15H24+, 204.1873; found, 204.1872; IR (diamond ATR) : 2964 (m), 2925 (m), 2873 (m), 1670 (w), 1447 (w), 1412 (w), 1377 (w), 1259 (s), 1090 (s), 1016 (s), 866 (w), 797 (s), 700 (w), 662 (w) cm\u22121.I = 1483 ); MS (EI(+)-T-Muurolol (2): GC (HP 5): I = 1640 (literature (HP 5): I = 1640 + calcd for C15H26O+, 222.1978; found, 222.1982; IR (diamond ATR) : 3353 , 2956 (m), 2925 (m), 2869 (m), 1722 (m), 1639 (w), 1446 (m), 1376 (s), 1319 (m), 1258 (w), 1180 (m), 1081 (s), 955 (m), 910 (w), 837 (m), 802 (w) 614 (w), 539 (w) cm\u22121.I = 1493 ); MS (EI(\u2212)-7-epi-\u03b1-Eudesmol (4): GC (HP 5): I = 1661 (literature (HP 5): I = 1662 + calcd for C15H26O+, 204.1873, found. 204.1870; IR (diamond ATR) : 3388 , 2966 (s), 2910 (s), 2850 (s), 1662 (w), 1440 (s), 1376 (w), 1281 (m), 1260 (m), 1220 (s), 1139 (m), 1101 (m), 1021 (s), 937 (w), 873 (m), 841 (s) 798 (w), 755 (w), 707 (w), 649 (w), 568 (w) cm\u22121.(\u2212)-\u03b3-Cadinene (5): GC (HP 5): I = 1514 (literature (HP 5): I = 1513 + calcd for C15H24+, 204.1873; found, 204.1865; IR (diamond ATR) : 2925 (s), 2850 (s), 1525 (m), 1458 (s), 1366 (s), 1302 (s), 1192 (w), 1087 (s), 1030 (s), 963 (m), 921 (w), 823 (s), 691 (m) 608 (s) cm\u22121.I = 1513 ); MS (EI(\u2212)-(E)-\u03b2-Caryophyllene (6): GC (HP 5): I = 1429 (literature (HP 5): I = 1428 + calcd for C15H24+, 204.1873; found, 204.1868; IR (diamond ATR) : 3066 (w), 2924 (s), 2856 (s), 1670 (m), 1631 (m), 1449 (s), 1382 (s), 1367 (s), 1276 (m), 1257 (w), 1227 (w), 1182 (m), 1106 (w), 1067 (w); 1019 (w), 936 (m), 885 (s), 842 (m), 813 (m), 764 (w) 742 (s), 641 (w), 544 (m) cm\u22121.I = 1428 ); MS (EIE. coli BL 21 transformants was inoculated from an overnight preculture. The cells were grown to an OD600 = 0.4 before IPTG (0.4 mM) was added. The cultures were incubated at 18 \u00b0C and 160 rpm overnight. E. coli cells were harvested by centrifugation at 4 \u00b0C and 8000 rpm for 10 min. Protein purification was performed by Ni2+-NTA affinity chromatography with Ni2+-NTA superflow (Novagen) as reported above. For the incubation experiment in 2H2O with 7-epi-\u03b1-eudesmol synthase and (6-13C)FPP, the soluble enzyme fraction was washed with binding buffer and then eluted twice with 10 mL elution buffer . Each pure protein fraction from 0.5 L 2YT liquid culture was concentrated with a Vivaspin20 concentration tube for 0.5 to 1.5 h at 6000 rpm to 2 mL enzyme fraction. Incubation experiments were performed with the pure protein (2 mL) and the 13C-labeled substrate (0.8 mg to 3.0 mg in 2 mL 2H2O or H2O) at 28 \u00b0C overnight. The reaction mixture was extracted with 2 \u00d7 0.4 mL (2H6)benzene and directly measured by NMR.For each incubation experiment a 0.5 L 2YT liquid culture (containing kanamycin (50 mg/L)) of File 11\u20135.Gas chromatograms of extracts from enzyme reactions and NMR spectra of compounds"} +{"text": "GNB3) gene has been implicated in obesity risk; however, the molecular mechanism of GNB3-related disease is unknown. GNB3 duplication is responsible for a syndromic form of childhood obesity, and an activating DNA sequence variant (C825T) in GNB3 is also associated with obesity. To test the hypothesis that GNB3 overexpression causes obesity, we created bacterial artificial chromosome (BAC) transgenic mice that carry an extra copy of the human GNB3 risk allele. Here we show that GNB3-T/+ mice have increased adiposity, but not greater food intake or a defect in satiety. GNB3-T/+ mice have elevated fasting plasma glucose, insulin, and C-peptide, as well as glucose intolerance, indicating type 2 diabetes. Fasting plasma leptin, triglycerides, cholesterol and phospholipids are elevated, suggesting metabolic syndrome. Based on a battery of behavioral tests, GNB3-T/+ mice did not exhibit anxiety- or depressive-like phenotypes. GNB3-T/+ and wild-type animals have similar activity levels and heat production; however, GNB3-T/+ mice exhibit dysregulation of acute thermogenesis. Finally, Ucp1 expression is significantly lower in white adipose tissue (WAT) in GNB3-T/+ mice, suggestive of WAT remodeling that could lead to impaired cellular thermogenesis. Taken together, our study provides the first functional link between GNB3 and obesity, and presents insight into novel pathways that could be applied to combat obesity and type 2 diabetes.The G-protein beta subunit 3 ( LEP) as the first obesity gene [delta]Ct method using Inguinal WAT (iWAT) and BAT were dissected, weighed and immediately homogenized on ice in CelLytic MT Mammalian Tissue Lysis/Extraction Reagent with protease inhibitor cocktail. Total protein concentration was determined using Pierce BCA Protein Assay Kit .Citrate synthase activity for iWAT and BAT extracts were measured using the Citrate Synthase Assay Kit following the manufacturer\u2019s instructions.t-test was used to compare two groups, and one-way ANOVA was used to compare more than two groups. Comparisons with p-values <0.05 were considered significant.Statistical analyses were performed using GraphPad Prism version 6 for Mac . Data are presented as mean \u00b1 SD (or SEM where indicated). Unpaired Student\u2019s GNB3-T/+. To determine the expression levels of human GNB3 and endogenous Gnb3 we performed quantitative RT-PCR in RNA from whole brain, olfactory bulb, hypothalamus, and cerebellum of 5-week-old GNB3-T/+ and WT mice. As expected, we did not detect human GNB3 in WT mice. Notably, human GNB3 expression was much greater than endogenous Gnb3 in whole brain, olfactory bulb, hypothalamus and cerebellum of GNB3-T/+ mice as calculated by delta cycle threshold values , and 50-fold greater than endogenous Gnb3 in iWAT and BAT were not significantly different in WT mice . At 20 wther sex . Inflamm obesity . Growth ale mice . It is iGNB3-T/+ mice could be due to greater food intake, lack of activity, or a metabolic defect in energy expenditure. To investigate these possibilities, we measured food consumption at ages 5, 10, 15, 20 and 25 weeks in male mice. At 5 weeks old, VO2, heat and RER measurements are similar in GNB3-T/+ and WT mice , this difference was not significant.In our transgenic model, GNB3-T/+ mice, indicated by elevated fasting plasma glucose levels and GTT response. Though GNB3-T/+ mice did not have glucose intolerance prior to obesity, 5-week old female GNB3-T/+ mice had elevated fasting blood glucose, and both female and male GNB3-T/+ mice had elevated fasting plasma insulin. This could indicate the beginning stage of impaired glucose metabolism prior to obesity. However, GNB3-T/+ mice do not respond to the ITT like other mouse models of type 2 diabetes, indicating a milder phenotype.Glucose intolerance and type 2 diabetes are apparent at 20 weeks in GNB3-T/+ mice, consistent with lower circulating GH in obese humans [GNB3-T/+ mice at 20 weeks. Thyroid hormones control multiple physiological systems and have an important role in regulating basal metabolic rate, lipolysis, as well as the differentiation process in the adipose tissue [GNB3-T/+ mice at 20 weeks, which could indicate hypogonadotropic hypogonadism [GH was reduced in obese e humans . Anothere tissue . FSH, LHgonadism .GNB3-T/+ mice could be due to increased calorie intake, reduced activity, or a defect in metabolism that results in lower energy expenditure. Our results from food intake measurements and levels of fasting ghrelin, PYY, and amylin hormones revealed that hyperphagia or a satiety defect are not responsible. Novelty suppressed feeding tests also show no significant difference in the amount of sucrose eaten, latency to feed, or total feeding time between the GNB3-T/+ and WT mice, indicating that anxiety-like feeding behaviors are not involved in GNB3-related obesity. GNB3-T/+ and WT mice do not have a statistically significant difference in locomotor activity or oxygen consumption. However, it is possible that subtle differences in locomotion and/or oxygen consumption could contribute to increased adiposity. Future energy expenditure experiments conducted at thermoneutrality and/or brown fat induction experiments could shed light on the effects of GNB3 overexpression. Further, behavioral assessments indicate that there are no substantial anxiety- or depressive-like phenotypes in GNB3-T/+ mice, and that these affective phenotypes are unlikely to add to the relationship between GNB3 overexpression and obesity.Obesity is caused by an energy imbalance between calories consumed and calories expended. The increased adiposity in GNB3-T/+ mice. Ucp1 in mitochondria dissipates chemical energy in the form of heat, mainly in BAT, through a process called nonshivering thermogenesis [+ cells [+ adipose tissue which has a gene expression pattern more similar to beige cells than to classic brown cells in the mouse [GNB3 overexpression alters the gene expression profiles of both BAT and WAT, GNB3 appears to have the greatest effect in beige-cell containing iWAT.Ucp1 expression in adipose tissues provides a clue to the underlying defect in ogenesis . Recentlogenesis . In addi[+ cells \u201348 known[+ cells or brown[+ cells . Beige c[+ cells and deve[+ cells . Adult hhe mouse . Though GNB3-T/+ mice has lower expression of beige and brown adipocyte markers. Additionally, GNB3-T/+ mice showed markedly worsened beige adipocyte function in subcutaneous fat pads as indicated by lower levels of Ucp1 in iWAT. Subcutaneous adipose tissue in GNB3-T/+ mice acquired properties of visceral fat indicated by elevated expression of adipogenic markers, Pparg and adiponectin. Overall, GNB3 overexpression stimulates a conversion of subcutaneous WAT, particularly in the inguinal depot, into a less UCP1+ and a less beige but whiter tissue. We show that this white-like remodeling of iWAT and loss of brown and beige properties in BAT is accompanied by increased adiposity in mice fed normal chow. Together, these data implicate GNB3 overexpression in impaired WAT and BAT, and for the first time provide a functional link between GNB3 and obesity pathogenesis. However, the specific causes of GNB3-related obesity remain to be determined. Future studies of GNB3 overexpression are needed to dissect the molecular mechanisms by which GNB3 alters adipose tissue metabolism, signaling, and energy expenditure.BAT in S1 Fign = 8\u201311 mice per group in A, C, and D; n = 1\u20138 mice per group in B; n = 14\u201322 mice per group in E, F. Data are \u00b1 SD. No significant difference between GNB3-T/+ and WT of same sex by unpaired Student\u2019s t-test.A. gWAT weight/body weight (gWAT%), B. iWAT weight/body weight (iWAT%), C. BAT weight/body weight (BAT%), D. liver weight/body weight (liver%), E. DXA lean mass and F. DXA fat mass of 5-week-old mice. (TIF)Click here for additional data file.S2 Fign = 8\u201311 mice per group in A, n = 7 mice per group in B-D, n = 9\u201313 mice per group in E-H, n = 10\u201314 mice per group in I, n = 11\u201315 mice per group in J. Data are \u00b1 SD. *P < 0.05, **P < 0.01 vs. WT of same sex by unpaired Student\u2019s t-test.A. Fasting blood glucose, B. fasting plasma insulin, C. C-peptide, D. leptin, E. triglycerides, F. cholesterol, G. phospholipids and H. non-esterified fatty acids. I. GTT and AUC of female and J. male mice. All mice are 5 weeks old. (TIF)Click here for additional data file.S3 FigGNB3-T/+ mice have elevated fasting plasma resistin during obesity.Male A,B. Fasting plasma glucagon; C,D. resistin; E,F. GIP; G,H. IL-6; I.J., TNF-a; and K,L. MCP-1 in 5-week and 20-week-old mice, respectively. n = 7 mice per group in A, C, E, G, I, K; n = 10\u201313 mice per group in B, n = 11\u201320 mice per group in D, F, H, J, L. Data are \u00b1 SD. *P < 0.05 vs. WT of same sex by unpaired Student\u2019s t-test.(TIF)Click here for additional data file.S4 FigGNB3-T/+ male mice have lower GH, TSH, FSH, LH and prolactin during obesity. A,B. Fasting plasma growth hormone (GH); C,D. thyroid-stimulating hormone (TSH); E,F. follicle-stimulating hormone (FSH); G,H. luteinizing hormone (LH); I,J. prolactin; K,L. adrenocorticotropic hormone (ACTH) levels of 5 week and 20 week old mice, respectively. n = 7 mice per group in A, C, E, G, I, K; n = 11\u201320 mice per group in B, D, F, H, J, L. Data are \u00b1 SD. *P < 0.05, **P < 0.01, ***P < 0.001 vs. WT of same sex by unpaired Student\u2019s t-test.(TIF)Click here for additional data file.S5 Fign = 7 mice per group in A-C, n = 19\u201321 mice per group in D-F. Data are \u00b1 SD in A-C, and \u00b1 SEM in D-F. *P < 0.05, **P < 0.01, ***P < 0.001 vs. WT of same sex by unpaired Student\u2019s t-test.A. Fasting plasma ghrelin, B. PYY and C. amylin. D. Total movement in X-plane, E. horizontal ambulatory activity, and F. vertical activity averaged over a 72-hour period. All mice are 5 weeks old. (TIF)Click here for additional data file.S6 Fig2, B. heat produced normalized over body weight, and C. RER (VCO2/VO2) averaged over a 72-hour period. D. Acute cold stress at 4\u00b0C. All mice are 5 weeks old. n = 19\u201321 mice per group in A-C, n = 5\u20138 mice per group in D. Data are \u00b1 SEM in A-C; and \u00b1 SD in D-F. ****P < 0.0001 vs. WT of same sex by unpaired Student\u2019s t-test.A. VO(TIF)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 TableGNB3-T/+ mice and WT littermates were subjected to behavioral tests in order to evaluate anxiety/depressive-like behaviors and learning and memory.(DOCX)Click here for additional data file."} +{"text": "Nature Communications7: Article number: 11929; DOI: 10.1038/ncomms11929 (2016); Published 06222016; Updated 03172017In this Article, residues D128 and D132 of ASC are consistently referred to incorrectly as D130 and D134, respectively. These errors appear in the Results, Methods, Fig. 2, Fig. 3 and Supplementary Fig. 1."} +{"text": "Enterobacter cloacae is a major nosocomial pathogen causing bloodstream infections. We retrospectively conducted a study to assess antimicrobial susceptibility and phylogenetic relationships of E. cloacae bloodstream isolates in two tertiary university-affiliated hospitals in Shanghai, in order to facilitate managements of E. cloacae bloodstream infections and highlight some unknowns for future prevention.E. cloacae bloodstream isolates were consecutively collected from 2013 to 2016. Antimicrobial susceptibility was determined by disk diffusion. PCR was performed to detect extended-spectrum \u03b2-lactamase (ESBL), carbapenemase and colistin resistance (MCR-1) gene. Plasmid-mediated AmpC \u03b2-lactamase (pAmpC) genes were detected using a multiplex PCR assay targeting MIR/ACT gene and other plasmid-mediated genes, including DHA, MOX, CMY, ACC, and FOX. eBURST was applied to analyze multi-locus sequence typing (MLST).Fifty-three non-duplicate E. cloacae isolates, 8(15.1%) were ESBL producers, 3(5.7%) were carbapenemase producers and 18(34.0%) were pAmpC producers. ESBL producers bear significantly higher resistance to cefotaxime (100.0%), ceftazidime (100.0%), aztreonam (100.0%), piperacillin (87.5%), tetracycline (75.0%), and trimethoprim-sulfamethoxazole (62.5%) than non-producers (p<0.05). PAmpC- and non-producers both presented low resistance rates (<40%) to all antibiotics (p>0.05). SHV and MIR/ACT predominated in ESBL and pAmpC producers respectively. Moreover, 2 isolates co-carried TEM-1, SHV-12, IMP-26 and DHA-1. MLST analysis distinguished the 53 isolates into 51 STs and only ST414 and ST520 were assigned two isolates of each (2/53).The rates of resistance to all tested antibiotics were <40%. Among 53 E. cloacae bloodstream isolates in the two hospitals. Multiclonality disclosed no evidence on spread of these isolates in Shanghai. The simultaneous presence of ESBL, carbapenemase and pAmpC detected in 2 isolates was firstly reported in Shanghai, which necessitated active ongoing surveillances and consistent prevention and control of E. cloacae.The antimicrobial resistance rates were low among 53 Enterobacter cloacae is an important emerging pathogen, causing various nosocomial infections, including respiratory infections, bloodstream infections (BSIs) and surgical site infections ). Escherichia coli ATCC 25922 was used for quality control.Antimicrobial susceptibility of the by CLSI . The ant Edition). For tig Edition); for polblaTEM, blaSHV, blaCTX-M , blaOXA , blaVEB, blaGES, and blaPER), carbapenemase genes and plasmid-mediated colistin resistance gene (mcr-1), using primers previously described [http://blast.ncbi.nlm.nih.gov/BLAST).Polymerase chain reaction (PCR) was performed to confirm the existence of ESBL genes as described by Miyoshi-Akiyama et al.[http://pubmlst.org/ecloacae/). STs not found in the database were submitted. The eBURST version 3.0 was used to analyze the clustering of related STs. The eBURST algorithm can group strains according to their allelic profiles by employing a user-specified group definition, as well as drawing a rough sketch to show the genetic relationship[A multilocus sequence typing (MLST) scheme was used to assign ma et al.. The comationship. In thisP value of <0.05.SAS 8.2 was used for statistical analysis. Continuous variables were presented as median and interquartile range. The chi-square or Fisher\u2019s exact test was used to compare the disparity between different groups for categorical variables. Differences were considered statistically significant at a two-tailed The age of the 53 patients ranged from 23 to 86 years . Male patients (37/53) were more than females (16/53). Near half of the episodes were derived from the surgery (22/53), and where most patients suffered from malignant tumor (10/22) .E. cloacae isolates, 8(15.1%) were ESBL producers, 3(5.7%) were carbapenemase producers and 18(34.0%) were pAmpC producers (P<0.05). Of note, pAmpC- and non-producers both presented low resistance rates (<40%) to all antibiotics, which did not differ significantly in the two groups (p>0.05) (As summarized in roducers . The hig(p>0.05) .E. cloacae isolates were positive for pAmpC genes, of which 15 (83.3%) isolates were detected with MIR/ACT gene and the other 3 (16.7%) were detected with DHA-1 gene , blaVEB, blaGES, blaPER, blaVIM, blaKPC, blaOXA-48 and blamcr-1 were detected.Of the 8 ESBL producers, SHV enzymes predominated with all identified as SHV-12, and CTX-M enzymes followed, including CTX-M-15 and CTX-M-65 . A totalA-1 gene . Of the A-1 gene . Besideshttps://pubmlst.org/bigsdb?db=pubmlst_ecloacae_seqdef). It was indicated in MLST analysis distinguished 51 different STs, clustered into 3 non-overlapping clonal complexes (CCs) and 43 singletons . Only STE. cloacae was frequently implicated in nosocomial infections[E. cloacae isolates[E. cloacae worsening clinical outcome and prolonging hospitalization duration have been alarmingly increasing since 21st century[E. cloacae bloodstream isolates harboring resistant genes were mostly associated with elderly patients from the surgery or Intensive Care Unit produced ESBL, which was higher than that in north-eastern USA (10.1%)[Enterobacter spp. collected from all sites[E. cloacae [E. cloacae isolates due to various modes of transmission.Of all 15.1% 8/5 producedall sites. Unlike all sites, SHV wasall sites, and simall sites. SHV-12, cloacae . What\u2019s cloacae , 26, whiE. cloacae was once reported in Taiwan[PAmpC can preferentially hydrolyze all \u03b2-lactams except fourth-generation cephalosporins and carbapenems and may serve as the reservoir for the emergence of antibiotic resistance . The higin Taiwan, but firPseudomonas aeruginosa isolate in Singapore [E. cloacae isolates, but interestingly, the two IMP-producers in our study were both detected as IMP-26. It was still noted that IMP-producing E. cloacae had caused several outbreaks or possible spread in other countries [E. cloacae. NDM-1 was the dominant carbapenemase of carbapenems-resistant E. cloacae in Henan China, and in contrast to VIM-1 the most prevalent in Spain and other southern Europe [Carbapenemase spread has been increasingly reported worldwide over the last decade. We founingapore and few ountries , 33, 34,n Europe , 36; whiE. cloacae has once denoted the association of distinct clonal groups with genetic lineages of higher prevalence and/or wider geographical spread [E. cloacae bloodstream isolates did not evolve from a unique ancestral background with 51 STs distinguished from 53 isolates and 8 isolates (15.1%) assigned to 3 CCs Click here for additional data file."} +{"text": "VOLUME 104104(3) July, page 242http://dx.doi.org/10.3163/1536-5050.104.3.014.Bramer WM, Giustini D, de Jonge GB, Holland L, Bekhuis T. De-duplication of database search results for systematic reviews in EndNote. J Med Libr Assoc. 2016 Jul;104(3):240\u20133. DOI: Page 242: Table 1, row C3, should state:Review the top references without page numbers and those with page numbers starting with the number 1 for equivalent author names.Only articles without page numbers or page numbers starting with 1 should be reviewed."} +{"text": "Correction to:The ISME Journal (2017) 11, 932\u2013944; doi:10.1038/ismej.2016.172Updated online 28 February 2017: This article was originally published under a CC BY-NC-SA 4.0 license, but has now been made available under a CC-BY 4.0 license. The PDF and HTML versions of the paper have been modified accordingly."} +{"text": "In the original article, there was a mistake in the published supplementary material. The literature search string as mentioned in the section \u201cLiterature Search and Selection Strategy\u201d never appeared in the published material. The search string as applied in Medline appears below. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way.Ovid Technologies, Inc. Email ServiceDatabase: Epub Ahead of Print, In-Process & Other Non-Indexed Citations, Ovid MEDLINE(R) Daily and Ovid MEDLINE(R)<1946 to Present>Search Strategy:1 Hyperparathyroidism, Primary/dt [Drug Therapy] (99)2 Hyperparathyroidism, Primary/(2211)3 Parathyroid adenom*.mp. (4188)4 (Primary adj2 Hyperparathyr*).mp. (9043)5 2 or 3 or 4 (11256)6 exp Diphosphonates/(22931)7 bisphosphonate*.mp. (14211)8 diphosphonat*.mp. (17321)9 bisphosphonic*.mp. (152)10 clodron*.mp. (2326)11 alendron*.mp. (4714)12 etidron*.mp. (3123)13 ibandron*.mp. (1063)14 incadron*.mp. (78)15 medron*.mp. (4405)16 minodron*.mp. (104)17 neridron*.mp. (94)18 olpadron*.mp. (77)19 pamidron*.mp. (2920)20 risedron*.mp. (1775)21 tiludron*.mp. (156)22 zoledron*.mp. (4145)23 cinacalcet.mp. (1071)24 Cinacalcet Hydrochloride/(735)25 \"amg 073\".mp. (24)26 amg073.mp. (0)27 krn 1493.mp. (3)28 krn1493.mp. (4)29 mimpara.mp. (20)30 parareg.mp. (0)31 regpara.mp. (1)32 sensipar.mp. (30)33 exp Isoflavones/(15928)34 ipriflavone.mp. (268)35 Denosumab/(925)36 denosumab.mp. (1712)37 amg 162.mp. (33)38 amg162.mp. (3)39 amgiva.mp. (0)40 prolia.mp. (32)41 xgeva.mp. (16)42 blosozumab.mp. (14)43 ly 2541546.mp. (0)44 ly2541546.mp. (1)45 romosozumab.mp. (45)46 amg 785.mp. (27)47 amg785.mp. (0)48 cdp 7851.mp. (0)49 cdp7851.mp. (3)50 odanacatib.mp. (156)51 (\"mk 0822\" or mk0822 or mk822 or mk 822).mp. (5)52 etelcalcetide.mp. (5)53 (amg 416 or amg416).mp. (12)54 (kai 4169 or kai4169).mp. (1)55 (ono 5163 or ono5163).mp. (0)56 telcalcetide.mp. (0)57 velcalcetide.mp. (4)58 or/6-57 (49081)59 5 and 58 (459)60 1 or 59 (491)The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "We report here the first complete genome sequences of genotype GI.3, GI.4, GI.6, GI.7, and GII.7 sapovirus strains, detected from fecal samples of acute gastroenteritis patients. Complete or nearly complete genome sequences of all 18 genotypes of human sapoviruses are now available for phylogenetic analysis and primer design. Genetically diverse sapovirus (SaV) strains have been detected in fecal specimens from patients with acute gastroenteritis \u20134. We ha\u20136\u2013de novo assembly of consensus SaV genome sequence were performed first, as described ((AY237420), GII.3 (AY603425), GII.5 (LC190463), and GII.6 (AY646855) SaV genomes in combination with two primers designed in the previously determined VP1-encoding-region sequence or QIAamp viral RNA minikit (Qiagen). Library preparation from the purified RNA for sequencing on an Illumina MiSeq platform (Illumina) and escribed , 10. Forescribed using thsequence . FurtherGII.5 LC10463, andsequence 11. The 5GII.5 LC10463, andThe genomes of GI.3 Hu/OH08021/2008/JP, GI.4 Hu/SV/Chiba/000496/2000, GI.6 Hu/SV/Chiba/000764/2000, GI.7 Hu/D1714-B/2008/JPN, and GII.7 Hu/20072248/2008/JP SaV strains consist of 7,442, 7,436, 7,443, 7,452, and 7,462\u2009nt, respectively, excluding the poly(A) tail. All of these SaV genomes were predicted to encode two ORFs, a short 5\u2032 untranslated region (UTR) (12 or 13\u2009nt long) and a 3\u2032-UTR 78 to 112\u2009nt long). The 5\u2032 terminal sequence was conserved as GTG, similarly to those of other SaVs , 11.2\u2009nt longThe new sequence data determined in this study will be useful in designing more broadly reactive primers and probes for human SaV detection PCR, as well as establishment of a nonstructural protein coding region typing scheme like that recently established for norovirus .AB623037, AJ606693, AJ606694, AB522390, and AB630067, respectively.The genome sequences of GI.3 Gu/OH08021/2008/JP, GI.4 Hu/SV/Chiba/000496/2000, GI.6 Hu/SV/Chiba/000764/2000, GI.7 Hu/D1714-B/2008/JPN, and GII.7 Hu/20072248/2008/JP SaV strains have been deposited in GenBank under the accession no."} +{"text": "Nature Communications8: Article number: 15110; DOI: 10.1038/ncomms15110 (2017); Published: 04272017; Updated: 0613201752\u2019 and \u2018pSANG10-3F-BG4 (Addgene 55756)52 was transformed into\u2026.\u2019 The correct citation is given below.In this Article, the antibody \u2018BG4\u2019 is consistently referred to incorrectly as \u2018hf2\u2019. These errors appear in the Results and Methods. Additionally, the Article incorrectly cites reference 52 in the sentences \u2018A recent study described hf2, an engineered single-chain antibody specific for G4 DNANat. Chem.5, 182\u2013186 (2013).Biffi, G., Tannahill, D., McCafferty, J. & Balasubramanian, S. Quantitative visualization of DNA G-quadruplex structures in human cells."} +{"text": "The impact of MMP-1 , MMP-3 Lys45Glu (A/G), MMP-7 -181A/G, and MMP-12 -82A/G variants and plasma MMP levels on obesity and microvascular reactivity in Tunisians. Our population included 202 nonobese and 168 obese subjects. Anthropometric, biochemical, and microvascular parameters were determined according to standard protocols. PCR-RFLP and ELISA were used to determine the genetic variants and levels of MMPs, respectively. 2): 30\u2009\u00b1\u20090.51 versus 27.33\u2009\u00b1\u20090.8, P = 0.004; MMP-3 levels: 7.45 (4.77\u201311.91) versus 5.21 (3.60\u201310.21) ng/ml, P = 0.006). The MMP-12 -82G allele was also associated with higher BMI values when compared to subjects carrying the AA genotype . Individuals carrying the MMP-3 45G or MMP-12 -82G variants were also associated with a higher risk for severe forms of obesity . Similarly, the MMP-7 -181G allele was associated with a higher MMP-7 level and an increased risk for morbid obesity when compared to AA genotype carriers (0.32 (0.31\u20130.60) versus 0.18 (0.17\u20130.24) ng/ml, P = 0.01; OR\u2009=\u20091.67, P = 0.02, resp.). The MMP-3 45Glu (G) allele associates with higher anthropometric values and MMP-3 levels compared to AA genotype carriers (BMI (kg/m MMP-3, MMP-7, and MMP-12 polymorphisms associate with obesity risk and its severity. Obesity is a pathological condition that is closely related to genes with environmental modulators, including sedentary life and positive energy balance . It is cUntil now, SNPs in MMP genes have been described to alter their expression . As an eUp to now, only a few studies have determined the impact of MMP variants and plasma MMP levels on obesity-related phenotypes and microvascular reactivity. The goals of the current report were to explore the impact of MMP-1 , MMP-3 Lys45Glu (A/G), MMP-7 -181A/G, and MMP-12 -82A/G SNPs on the development of obesity and its severity among Tunisians. We also determined whether these SNPs affect biochemical and microvascular reactivity, as well as plasma levels of the corresponding proteins.2) while 168 subjects were obese (BMI\u2009\u2265\u200930\u2009kg/m2). Obese individuals were categorized according to the WHO classification as class I with 30\u2009\u2264\u2009BMI\u2009<\u200935\u2009kg/m2, class II with 35\u2009\u2264\u2009BMI\u2009<\u200940\u2009kg/m2, and class III (morbidly obese) with 40\u2009kg/m2\u2009\u2264\u2009BMI [2 were excluded from the study. Diabetic individuals and subjects with a history of cardiovascular disease, smoking habits, malignancy, and renal, thyroid, and liver diseases were also excluded from the study. Other exclusion criteria were subjects using medications that might alter the endothelial or smooth muscle-dependent responses. All participants signed a written informed consent, and the study was approved by the Farhat Hached Hospital Ethics Committee.370 randomly selected Tunisian subjects (181 men and 189 women) with a mean age of 38 years were selected for the current study. 202 individuals were classified as nonobese subjects (18.5\u2009\u2264\u2009BMI\u2009<\u200925\u2009kg/mm2\u2009\u2264\u2009BMI . Overwei2), waist circumference (WC) (cm), and hip circumference (HC) (cm) were determined according to standard protocols. Waist-to-height ratio (WHtR) and waist-to-hip ratio (WHR) were also measured by WC/height ratio and WC/HC ratio, respectively. The fasting glucose (FG), total cholesterol (TC), and triglycerides (TG) were determined by the corresponding oxidase methods . The immune-inhibition method was used to measure high-density lipoprotein cholesterol concentration (HDL-C) while LDL-C was determined with the Friedwald formula [For all participants, weight (kg), height (m), BMI (kg/m formula . The senmax) represented the endothelium-dependent response, registered after three cumulative doses of acetylcholine (ACh) (arbitrary unit). The forearm flow response to heating the skin (FSBFRHS) represented the endothelium-independent response registered after the increase in skin temperature (44\u00b0C) without ACh infusion (arbitrary unit). Data were also presented as cutaneous vascular conductance (CVC) that represents the cutaneous blood flow (CBF)/mean arterial pressure (MAP) ratio. The MAP was determined as 1/3 SBP\u2009+\u20092/3 DBP. The difference between the peak CVC upon ACh stimulation (after three doses of ACh) and the baseline CVC was considered as the endothelium-dependent response (\u0394ACh-CVC). The difference between the peak CVC following RHS-induced vasodilation and the baseline was considered as the endothelium-independent response (\u0394RHS-CVC) [Endothelial function was determined in all subjects by assessing the forearm microvascular cutaneous vasoreactivity using laser Doppler flowmetry coupled with iontophoresis . The maxRHS-CVC) .\u03bcl) contained 100\u2009ng of genomic DNA, 25\u00a0\u03bcM of each deoxynucleotide triphosphate , 50\u2009pmol of each primer, 2.5\u2009mM of MgCl2, and 0.5 units of Taq polymerase . Details of primers and PCR-RFLP conditions are reported in DNA was isolated as previously described . AllelicMMP-1 and MMP-3 levels were determined by enzyme-linked immunosorbent assays (ELISA) using commercially available kits . MMP-7 and MMP-12 plasma levels were evaluated by Magnetic Luminex .t-test or the Mann\u2013Whitney U test as appropriate. Comparison of categorical variables including calculation for deviation from the Hardy\u2013Weinberg equilibrium (HWE) was performed using the chi-square (\u03c72) test. The evaluation of odds ratios (ORs) and 95% confidence intervals (CIs) was carried out using an unconditional logistic regression model adjusted for age and sex. Haplotypes and linkage disequilibrium (LD) were analyzed with SNPstats (http://bioinfo.iconcologia.net/SNPstats). Results were considered statistically significant if the P value <0.05. The Bonferroni correction (Pc) was applied to adjust for multiple comparisons.SPSS\u00ae 17.0 software and GraphPad Prism (version 6.04) were used for statistical analyses. Comparisons of quantitative variables were carried out using a 2\u2009\u00b1\u20090.44. In this study, we used a BMI cutoff point of 30\u2009kg/m2 for obesity status. As expected, higher BMI and abdominal obesity values were associated with obesity status. SBP, DBP, MAP, and hs-CRP were increased in obese subjects. As indicated in max as well as the FSBF dose-response to ACh expressed as area under the curve (AUC) was decreased in the obese group (P < 0.001). Basal CVC, as well as peak ACh-CVC and \u0394ACh-CVC values, was also decreased in obese subjects (P < 0.001). BMI and central adiposity (WC and WHR) were inversely correlated with the FSBFmax response to ACh . Additionally, basal CVC and peak ACh-CVC were inversely associated with BMI and WC values . The abdominal obesity marker (WHtR) was inversely associated with peak ACh-CVC .Anthropometric, biochemical, and microvascular values are indicated in 2\u2009\u00b1\u20090.61 versus 28.5\u2009kg/m2\u2009\u00b1\u20090.63, For the MMP-1 (-519A/G) polymorphism, no significant variation in BMI values was observed in individuals carrying the dominant model (AG+GG) genotype in comparison to AA genotype carriers ; WC ; WHtR , 2\u2009\u00b1\u20090.49 versus 27.19\u2009kg/m2\u2009\u00b1\u20090.49, P = 0.04) ; WC ; WHtR , Regarding the MMP-3 Lys45Glu (A/G) SNP, individuals carrying the (AG/GG) genotype showed increased BMI, WC, and WHtR values when compared to AA genotype carriers (BMI (30\u2009kg/m = 0.04) ). HigherP = 0.06). No significant correlation was observed between MMP-1, MMP-3, MMP-7, and MMP-12 polymorphisms, FG, and hs-CRP levels. No significant association was also found between MMP-1 and MMP-7 polymorphisms and TG, TC, LDL-C, and HDL-C levels. Regarding the MMP-3 polymorphism, a higher amount of LDL-C was found in subjects carrying the AG or GG genotypes compared to AA genotype carriers . A significant increase in LDL-C was also found among obese subjects carrying the AG or GG genotypes when compared to AA genotype carriers . Investigation of the MMP-12 (-82A/G) SNP also revealed that individuals carrying the AG or GG genotypes present higher LDL-C levels when compared to AA genotype carriers . Analysis of endothelial function in the sampled population revealed, however, no significant relationships between the MMP-1, MMP-7, MMP-3, and MMP-12 variants and microvascular reactivity parameters (data not shown).The SBP, DBP, and MAP revealed no significant association with MMP-1, MMP-3, and MMP-7 polymorphisms. Regarding the MMP-12 (-82A/G) SNP, there was an increase in DBP among subjects carrying the AG or GG genotypes compared to AA genotype carriers . When subjects were categorized according to severity of obesity, a higher level of MMP-7 was observed in morbidly obese subjects carrying the -181G variant (AG+GG: 0.32 (0.31\u20130.6), AA: 0.18 (0.17\u20130.24), P = 0.01, Pc = 0.04).We also determined whether the MMP polymorphisms affect plasma levels of the corresponding proteins. For the MMP-1 SNPs, there was no significant impact on MMP-1 levels in the sampled population ng/ml, AG+GG: 2 (0.75\u20134.16) ng/ml; \u20131607 1G/2G), 1G1G: 2.53 (0.75\u20134.17) ng/ml, 1G2G+2G2G: 1.66 (0.66\u20133.81) ng/ml). For the MMP-3 Lys45Glu (A/G) polymorphism, subjects carrying the AG or GG genotypes present higher MMP-3 levels compared to individuals having the AA genotype (7.45 (4.77\u201311.91) ng/ml versus 5.21 (3.6\u201310.21) ng/ml, P = 0.03, Pc = 0.24; OR\u2009=\u20091.61, P = 0.02, Pc = 0.08, resp., P = 0.01; OR\u2009=\u20092.4, P = 0.006; OR\u2009=\u20092.04, P = 0.004, resp., P = 0.004, Pc = 0.016). When subjects were categorized according to severity of obesity, the frequency of the Lys45Glu (G) allele was more frequent in nonmorbidly obese (48.58%) compared to nonobese subjects . For the MMP-12 (-82A/G) SNP, the frequencies of AA, AG, and GG genotypes were 76.4%, 23%, and 0.6% in obese participants and 88.6%, 11.4%, and 0% in nonobese participants. We found a significant association between the AG genotype, the combined genotypes AG+GG, and the development of obesity . The frequencies of A and G alleles were 94.28% and 5.72% in nonobese subjects and 87.88% and 12.12% in obese individuals. The G allele was associated with enhanced obesity when compared to A allele carriers . The G allele was also associated with nonmorbid obesity when compared to the A allele . Similarly, the AG genotype alone or in combination with the GG variant was associated with a higher risk for severe forms of obesity when compared to AA genotype carriers . The G allele was also significantly associated with morbid obesity when compared to the A allele .Analyses were carried out to study the distribution of the different SNPs according to obesity status and severity based on BMI Tables and 4. F, resp.) . BesidesD\u2032 = 0.42, r = 0.13). Haplotypes follow this order: MMP-1 (-1607 1G/2G), MMP-1 (-519A/G), MMP-7 (-181A/G), MMP-3 Lys45Glu (A/G), MMP-12 (-82A/G). Comparison of the haplotype frequencies between obese and nonobese groups revealed an increased risk for obesity for the haplotype s1G\u22121607:G\u2212519:G\u2212181:GLys45Glu:A\u221282 (Supplementary File 1 available online at https://doi.org/10.1155/2017/6198526).We further determined the haplotype frequencies of the different polymorphisms in obese and nonobese subjects. Linkage disequilibrium analysis revealed that MMP-3 and MMP-12 SNPs were in mild linkage disequilibrium . Several studies reported an enhanced expression of MMP-1 in preadipocytes from obese subjects suggesting a role in ECM remodeling in obesity . MMP-1 hMMP-3 (stromelysin I) is a proteoglycanase and a key player in ECM degradation and remodeling . MMP-3 wMMP-7 (matrilysin-1) is another metalloproteinase with an inflammatory regulatory role that displays a proteolytic activity against various kinds of ECM components . Previouin vitro adipogenesis decreases adipocyte expansion by increasing endostatin levels and inhibiting adipose tissue vascularity. Up to now, several SNPs were reported in the MMP-12 locus. Among these, the -82A/G SNP was found to affect both AP-1 binding affinity and MMP-12 promoter activity [MMP-12 is a macrophage metalloelastase that has a role in ECM remodeling processes . A previactivity . A reporactivity revealedactivity revealedactivity , 54. WitIn the current report, when individuals were stratified by BMI, the MMP-3 45Glu (G) and MMP7 (-181G) variants were more frequent in individuals with severe forms of obesity. Although further studies are required, these results may highlight that the contribution of MMP-3 and MMP-7 SNPs in the development of the morbid phenotype can be substantially higher than in lower classes of BMI and could, therefore, be valuable markers to predict the risk for the development of extreme classes of obesity. Consistently, previous studies provided evidence of a weak population-related risk for common obesity for several genetic variants. As an example, Villalobos-Compar\u00e1n et al. found thThe limitations of this study should be considered. A first limitation is the small sample size of the screened population. Our findings need, therefore, to be replicated in a larger population or an independent severe obesity cohort. A second limitation is the lack of measures of MMP activities in serum, as well as in adipose tissue.MMP-3 Lys45Glu (A/G), MMP-7 (-181A/G), and MMP-12 (-82A/G) variants were associated with obesity and its anthropometric indicators. The current findings also highlight a significant correlation between the MMP-3Lys45Glu (A/G) and MMP-7 (-181A/G) variants and severe forms of obesity among Tunisians. Our results also revealed significant alterations in microvascular reactivity in obese subjects. MMP variants may not, however, be determinant factors of endothelial dysfunction in the studied population.Supplementary file 1. Estimated haplotype frequencies of MMP-1, MMP-3, MMP-7 and MMP-12 polymorphisms in obese and non-obese subjects."} +{"text": "Scientific Reports7:1110; doi:10.1038/s41598-017-01016-8; Article published online 24 April 2017The original version of this Article contained errors. In the Abstract,\u201cThe use of SC79, an Akt1/2 inhibitor\u201dnow reads:\u201cThe use of SC79, an Akt1/2 activator\u201dIn the Introduction,\u201cwildlife and animal exposure including fetal growth\u201dnow reads:\u201cwildlife and animal exposure including reduced fetal growth\u201dIn addition,\u201cinducing Sertoli cell injury and Leydig cell steroidogenic function\u201dnow reads:\u201cinducing Sertoli cell injury and disrupting Leydig cell steroidogenic function\u201dFinally,\u201cThis mechanistic study thus provides additional insight on the molecular mechanism by which PFOS mediates reproductive\u201dnow reads:\u201cThis mechanistic study thus provides additional insight on the molecular mechanism by which PFOS causes reproductive\u201dThe original version of this Article omitted Xiang Xiao and Wing-yee Lui as corresponding authors. Correspondence and request for materials should also be addressed to X.X. (xxiao@zjams.com) or W.Y.L. (wylui@hku.hk)In the Results section, under the sub-heading \u2018PFOS perturbs Sertoli cell TJ-barrier function through changes in the spatial expression of actin binding and regulatory proteins\u2019,\u201cPalladin also no longer stretched across the Sertoli cell cytosol to organize actin filaments into bundles, instead, paladin retracted from cell cytosol and found closer to the cell nuclei .\u201dnow reads:\u201cPalladin also no longer stretched across the Sertoli cell cytosol to organize actin filaments into bundles as seen in controls, instead, palladin retracted from cell cytosol and found closer to the cell nuclei following PFOS treatment \u201dThe Results section contains an error in a sub-heading, where:\u201cRescue of PFOS-induced Sertoli cell TJ-barrier disruption by SC79, an activator of Akt through changes in the re-distribution of BTB-associated proteins.\u201dnow reads:\u201cRescue of PFOS-induced Sertoli cell TJ-barrier disruption by SC79, an activator of Akts through changes in the re-distribution of BTB-associated proteins.\u201dThere were also errors in the Figure legends. In Figure 2 legend,\u201cInstead, palladin was retraced from the cell peripheries but concentrated to cell nuclei after PFOS treatment.\u201dnow reads:\u201cInstead, palladin was retracted from the cell peripheries but concentrated to cell nuclei after PFOS treatment.\u201dIn Figure 3(c) legend6 cells/cm2 for 3 days were pre-treated with 2\u2009\u03bcg/ml SC79 for 30\u2009min, and then cells were rinsed and treated with 20\u2009\u03bcM PFOS for 24 hr. Thereafter, cells were then fixed and examined by immunofluorescence microscopy. SC79 treatment was found to block PFOSinduced mis-localization of TJ proteins CAR and ZO-1, as well as basal ES proteins N-cadherin and \u03b2-catenin, apparently through enhanced endocytosis. BTB-associated proteins at the Sertoli cell-cell interface in control and treated cells were annotated by corresponding white and yellow brackets, respectively\u201d\u201c(C) Sertoli cells cultured at 0.04\u2009\u00d7\u200910now reads:6 cells/cm2 for 3 days were pre-treated with 2\u2009\u03bcg/ml SC79 for 30\u2009min, and then cells were rinsed and treated with 20\u2009\u03bcM PFOS for 24 hr. Thereafter, cells were then fixed and examined by immunofluorescence microscopy. SC79 treatment was found to block PFOS-induced mis-localization of TJ proteins CAR and ZO-1, as well as basal ES proteins N-cadherin and \u03b2-catenin. BTB-associated proteins at the Sertoli cell-cell interface in control and PFOS-treated cells were annotated by corresponding white and yellow brackets, respectively\u201d\u201c(C) Sertoli cells cultured at 0.04\u2009\u00d7\u200910In Figure 4 legend\u201cyellow rectangles in FOS-treated cells\u201dnow reads:\u201cyellow rectangles in PFOS-treated cells\u201dIn Figure 5 legend, Figure 1A now reads Figure 1BIn Figure 6 legend,\u201cThereafter, cells were fixed with ice-cold methanol and visualized byimmunofluorescence microscopy.\u201dnow reads:\u201cThereafter, cells were fixed with ice-cold methanol and visualized by immunofluorescence microscopy using corresponding antibodies (Table 1)\u201dIn addition, the Acknowledgments section now reads:We wish to thank Dr. Ben Margolis and Dr. Shuling Fan who kindly provided us with some anti-CRB3 antibody to validate some experiments in this report. This work was supported by grants from the National Institutes of Health ; National Natural Science Foundation of China (NSFC) (31371176 to X.X.), Qianjiang Talents Program (QJD1502029 to X.X.), Zhejiang Province Funding ; Hong Kong Research Grants Council (RGC) General Research Fund (GRF) , NSFC/RGC Joint Research Scheme (N_HKU 717/12 to W.M.L.), and University of Hong Kong CRCG Seed Funding (to W.M.L.)The Author Contributions statement now reads:C.Y.C., Y.G. and H.C. designed research; Y.G., H.C. and C.Y.C. performed research; X.X., W.Y.L., W.M.L., D.D.M. and C.Y.C. contributed new reagents/analytic tools; Y.G., H.C. and C.Y.C. analyzed data; Y.G. and C.Y.C. wrote the paper; Y.G., H.C. and C.Y.C. prepared all figures. All authors reviewed the manuscript.There were also errors in References 43 and 76, which now read:in vitro a useful model to study molecular mechanisms in spermatogenesis? Semin Cell Dev Biol59, 141\u2013156, doi:10.1016/j.semcdb.2016.01.003 (2016).43. Li, N., Mruk, D. D., Lee, W. M., Wong, C. K. C. & Cheng, C. Y. Is toxicant-induced Sertoli cell injury et al. SC79 protects retinal pigment epithelium cells from UV radiation via activating Akt-Nrf2 signaling. Oncotarget7, 60123\u201360132, doi:10.18632/oncotarget.11164 (2016).76. Gong, Y. These errors have now been corrected in the HTML and PDF versions of this Article."} +{"text": "Bariatric surgery has emerged as a competitive strategy for obese patients. However, its comparative efficacy against non-surgical treatments remains ill-defined, especially among nonseverely obese crowds. Therefore, we implemented a systematic review and meta-analysis in order for an academic addition to current literatures.Literatures were retrieved from databases of PubMed, Web of Science, EMBASE and Cochrane Library. Randomized trials comparing surgical with non-surgical therapies for obesity were included. A Revised Jadad's Scale and Risk of Bias Summary were employed for methodological assessment. Subgroups analysis, sensitivity analysis and publication bias assessment were respectively performed in order to find out the source of heterogeneity, detect the outcome stability and potential publication bias.P > 0.05). The pooled results of primary endpoints (weight loss and diabetic remission) revealed a significant advantage among surgical patients rather than those receiving non-surgical treatments (P < 0.05). Furthermore, except for certain cardiovascular indicators, bariatric surgery was superior to conventional arms in terms of metabolic secondary parameters (P < 0.05). Additionally, the pooled outcomes were confirmed to be stable by sensitivity analysis. Although Egger's test (P < 0.01) and Begg's test (P<0.05) had reported the presence of publication bias among included studies, \u201cTrim-and-Fill\u201d method verified that the pooled outcomes remained stable.25 randomized trials were eligibly included, totally comprising of 1194 participants. Both groups displayed well comparability concerning baseline parameters (Bariatric surgery is a better therapeutic option for weight loss, irrespective of follow-up duration, surgical techniques and obesity levels. Emerging as a costly burden of global healthcare system, obesity has currently attracted worldwide attentions due to its uncontrollably rising incidence, especially in industrialized countries . EconomiAccording to SAGES and NICEBariatric surgery, initially reported in 1995 , has beeversus non-surgical interventions is rarely described, especially lacking of a well summarized evidence. Additionally, the clinical value of bariatric surgery for nonseverely obese patients requires further analysis. Hence we performed this systematic review and meta-analysis in order to comprehensively make comparisons between both strategies, aiming to provide novel evidences for future guidelines.Nevertheless, long-term (3-year or more) efficacy of surgical The preliminary 1076 entries were rigorously screened to generate 25 eligible studies for pooling analysis, with a total amount of 1194 participants and individually ranging from 16 to 150 Figure . Merely According to Revised Jadad's Scale, 13 trials were appraised as high-quality in methodology, while DSS, Heindorff 1997 and Mingrone 2002 were identified as low-quality investigations , 2-year (P < 0.00001) or long-term (3 years or more) follow-up duration (P < 0.00001) , Roux-en-Y gastric bypass (P < 0.00001), laparoscopic adjustable gastric banding (P < 0.00001) and biliopancreatic diversion (P < 0.00001) and severe obesity , metabolic surgery was a more effective tool for losing weight against non-surgical treatments .P < 0.0001), 2-year (P = 0.004) and long-term follow-up (P < 0.0001) .P < 0.00001), Roux-en-Y gastric bypass (P < 0.00001), laparoscopic adjustable gastric banding (P = 0.0008) and biliopancreatic diversion (P = 0.001) .P = 0.0004) and severely obese (P < 0.0001) sufferers significantly benefited from surgical remedies, compared with non-surgical patients .P < 0.00001), 2-year (P < 0.00001) or long-range follow-up (P = 0.006), bariatric surgery was far more efficient to eliminate excessive weight than non-surgical interventions (Regardless of 1-year (ventions .P < 0.00001), Roux-en-Y gastric bypass (P < 0.00001), laparoscopic adjustable gastric banding (P = 0.0008) and biliopancreatic diversion (P < 0.00001) was performed and severe obesity (P < 0.00001) .P < 0.00001) .P = 0.0005), 2-year (P = 0.0003) or long-term follow-up (P = 0.02), surgical management was significantly effective in decreasing fasting glucose compared to non-surgical interventions (Regardless of 1-year (ventions .P = 0.0005), Roux-en-Y gastric bypass (P < 0.00001) and laparoscopic adjustable gastric banding (P < 0.0001) fell behind in fasting glucose reduction against conserved therapeutics, except for biliopancreatic diversion, which was statistically equivalent to contrastive group (P = 0.05) (None of sleeve gastrectomy ( = 0.05) .P = 0.001) and severely obese (P < 0.00001) patients obtained greater downregulation on fasting glucose following the surgical interventions .P < 0.00001), 2-year (P = 0.02) and long-term follow-up (P < 0.00001), rather than those with conservative interventions , Roux-en-Y gastric bypass (P < 0.00001), laparoscopic adjustable gastric banding (P = 0.002) and biliopancreatic diversion (P = 0.03), bariatric surgery was significantly superior to non-surgical approaches in terms of reducing elevated glycated hemoglobin (Irrespective of sleeve gastrectomy (moglobin .P < 0.00001) and severely obese patients (P < 0.00001) .P < 0.00001) .P < 0.00001), 2-year (P < 0.00001) and long-term follow-up (P < 0.00001), patients that were surgically treated obtained larger decline on waist circumference than those were conventionally cured (Among the three subgroups of 1-year (ly cured .P < 0.0001), Roux-en-Y gastric bypass (P < 0.00001), laparoscopic adjustable gastric banding (P < 0.00001) and biliopancreatic diversion (P < 0.00001) .P < 0.00001) and severely obese sufferers (P < 0.00001), more reduction on waist circumference was observed following surgical management in contrast to traditional treatments (Based on the pooled outcomes featuring nonseverely (eatments .P < 0.00001) .P = 0.30), while bariatric surgery was a superior option among sufferers with 1-year (P = 0.001) and long-range follow-up (P = 0.02) .P = 0.36), laparoscopic adjustable gastric banding (P = 0.36) and biliopancreatic diversion (P = 0.90) was statistically comparable with non-surgical strategies in terms of reduction on systolic pressure, except for the dominant efficacy of Roux-en-Y gastric bypass (P = 0.007) (Bariatric surgery featuring sleeve gastrectomy (= 0.007) .P < 0.00001) and severely obese patients (P = 0.41) respectively, in terms of reduction on systolic pressure .P = 0.26) and 2-year (P = 0.55). However, surgical interventions were inferior to non-invasive remedies amid patients with long-term follow-up (P = 0.03) .P = 0.03) were in a significantly superior status, the remaining techniques were statistically comparable to conservative regimens concerning the decrease on diastolic pressure, inclusive of sleeve gastrectomy (P = 0.67), laparoscopic adjustable gastric banding (P = 0.57) and biliopancreatic diversion (P = 0.52) (Although Roux-en-Y gastric bypass ( = 0.52) .P = 0.23) and severe obesity (P = 0.73) (Patients undergoing both interventions exhibited comparable efficacy on diastolic pressure reduction regardless of nonsevere obesity ( = 0.73) .P < 0.00001) .P < 0.0001) and 2-year (P < 0.0001) follow-up had a greater decline on triglycerides level than those being conventionally treated, except for the comparable efficacy among patients with long-term follow-up (P = 0.06) .P = 0.0005) and laparoscopic adjustable gastric banding (P = 0.004) exerted a more evident influence among enrolled patients, while sleeve gastrectomy (P = 0.08) and biliopancreatic diversion (P = 0.14) was therapeutically comparable with conventional remedies and severe obesity (P < 0.0001) .P = 0.13) .P = 0.18) and 2-year (P = 0.07), there was no therapeutic difference between both interventions. However, patients with long-term follow-up achieved more reduction on total cholesterol following non-surgical managements, in contrast to bariatric surgery (P = 0.03) (Among obese sufferers being followed up for 1-year ( = 0.03) .P = 0.004), patients receiving bariatric surgery gained comparable efficacy of total cholesterol reduction against non-surgical enrollees, including sleeve gastrectomy (P = 0.67), Roux-en-Y gastric bypass (P = 0.78) and laparoscopic adjustable gastric banding (P = 0.62) (Besides the preponderant role of biliopancreatic diversion ( = 0.62) .P = 0.01), while nonseverely obese counterparts reported no significant difference between surgical and non-surgical interventions (P = 0.76) .P < 0.00001) .P < 0.00001), 2-year (P = 0.0005) and long-term follow-up (P = 0.001), metabolic surgery led to more increase on high density lipoprotein among included patients, compared to non-surgical recipients (Despite of 1-year (cipients .P = 0.003) and Roux-en-Y gastric bypass (P < 0.00001) displayed a higher increase on high density lipoprotein. However, the increase on high density lipoprotein was identically obtained between non-surgical treatments and bariatric surgery of laparoscopic adjustable gastric banding (P = 0.19) and biliopancreatic diversion (P = 0.27) (The recipients of sleeve gastrectomy ( = 0.27) .P < 0.00001) or severe obesity (P < 0.00001), bariatric surgery was a more capable pattern of elevating high density lipoprotein than traditional modes .P = 0.24) and 2-year follow-up (P = 0.14), recipients of conventional strategies exceled those with long-term postoperative follow-up duration, with regard to the reduction on low density lipoprotein (P < 0.00001) .P = 0.34), Roux-en-Y gastric bypass (P = 0.71) and laparoscopic adjustable gastric banding (P = 0.46), it was mathematically comparable between surgical and non-surgical patients regarding the decrease on low density lipoprotein. Nevertheless, patients undergoing biliopancreatic diversion had an advantage over those were conventionally cured (P < 0.00001) (Based on subgroup statistics of sleeve gastrectomy (0.00001) .P = 0.76) and severely obese patients (P = 0.09) .Firstly, by interchanging random-effects and fixed-effects models, the overall as well as subgroup outcomes of primary endpoints (weight loss and diabetic remission) were confirmed to be statistically stable Table .Secondly, by eliminating four low-quality trials of DSS, Heindorff 1997, Mingrone 2002 along with O'Brien 2013, the stability of primary endpoints were numerically verified, irrespective of overall or subgroup analysis and 6 added for diabetic remission and diabetic remission , Egger's test and Begg's test consistently confirmed the presence of publication bias among the included studies . However 0.0001) .Although Golomb et al had retrospectively doubted the dominant role of bariatric surgery at 5-year follow-up , its conIt is empirically regarded that compared to severe obesity, patients suffering from nonsevere obesity manifest with better general conditions which makes it more economical to be conventionally cured. However, deriving from our pooled evidence, nonseverely obese patients should rather receive bariatric surgery than conservative managements, which is similar to those featuring morbid obesity and is a vital addition to current literatures.Adolescent obesity and overweight crowds have been targeted as further research highlights of bariatric surgery. Uncontrollable weight increase has severer impacts on pubescents than adults, simultaneously damaging their sexual development and intelligence growth . O'BrienNotwithstanding the statistical outcomes are of great strength in both methodology and statistics, there are still some limitations within. First of all, the internal heterogeneity is still in a considerable level despite the subgroup analyses have been additionally performed. Difference from chemical examination methods, surgical manipulation techniques and diversified non-surgical interventions (life-style and medications) may contribute to inerasably internal heterogeneity. More accurate grouping on different confounding factors may benefit the source seeking of heterogeneity. Secondly, raw data of life-quality and survival prognostication are inadequate for meta-analyzing, making it less valuable in terms of comparisons on life expectancy. Moreover, mutual comparison of financial burdens is still lacking, blockading a more comprehensive appraisal of both strategies.Taken together, despite of the shortcomings of surgical therapeutics , bariatrIn line with the PRISMA Checklist and CochIn order to guarantee the integrity of literature retrieval, databases of PubMed, Web of Science, EMBASE and Cochrane Library were electronically searched with a search term \u201cbariatric randomized OR bariatric randomised OR obesity surgery\u201d. Both abstracts and full-texts were elaborately examined for fear of omission or ineligible inclusion. Additionally, citation lists of formerly published meta-analysis were screened as well.versus non-surgical interventions among obese patients (body mass index > 30); 3. Adequate raw data of interested endpoints including metabolic and cardiovascular indicators;Studies were eligibly included because of the following criteria: 1. English-written and officially published trials until December 2015; 2. Randomized controlled trials evaluating the comparative efficacy of surgical Studies were eventually eliminated due to the following reasons: 1. Duplicated publications; 2. Inadequate sample-size (< 10); 3. Lack of follow-up materials;With regard to baseline, primary and secondary parameters , a well-prepared electronic form was designed to facilitate date extraction from tables, figures, text contents and supplementary information within the eligible trials. Overlapped data deriving from a single registered trial was mathematically combined to prevent repetitive counting. All continuous variables were rounded to one decimal place.Firstly, a Revised Jadad's Scale was emplSecondly, as an addition to Revised Jadad's Scale, Review Manager 5.3 assisted us to summarize the risk of bias amid the qualified literatures. The symbol of green, yellow and red represented low risk of bias, unclear risk of bias and high risk of bias respectively, in terms of seven constituted categories . The higher proportion that green occupies, the lower risk of bias there is .2) [2 < 25%. Otherwise a random-effects model was preferred under the remaining circumstances [via eliminating low-quality trials, exclusion of controversial studies and comparing the outcome variation between fixed-effects and random-effects models. Moreover, the incorporated outcomes were additionally classified into various subgroups for purpose of more specific and instructive discoveries. With aid of STATA 12.0, publication bias was numerically examined by Begg's test and Egger's test [P < 0.05.Review Manager 5.3 was employed as a statistical platform for our quantitative analysis. The effect-sizes of dichotomous and continuous variable were calculated by models of odds ratio and weighted mean difference respectively, along with 95% confidence interval. If the source data on endpoints were not offered explicitly, median was statistically regarded as mean while standard deviation was derived from range, interquartile range or 95% confidence interval as appropriate , 49. A d2) . Revealimstances , in order's test . A \u201cTrim"} +{"text": "SmC5-MTase genes were identified from the genome of Salvia miltiorrhiza, a well-known traditional Chinese medicine material and an emerging model medicinal plant. Based on conserved domains and phylogenetic analysis, eight SmC5-MTase genes were divided into four subfamilies, including MET, CMT, DRM and DNMT2. Genome-wide comparative analysis of the C5-MTase gene family in S. miltiorrhiza and Arabidopsis thaliana, including gene structure, sequence features, sequence alignment and conserved motifs, was carried out. The results showed conservation and divergence of the members of each subfamily in plants. The length of SmC5-MTase open reading frames ranges widely from 1,152 (SmDNMT2) to 5,034\u00a0bp (SmMET1). The intron number of SmC5-MTases varies between 7 (SmDRM1) and 20 (SmCMT1 and SmCMT2b). These features were similar to their counterparts from Arabidopsis. Sequence alignment and conserved motif analysis showed the existence of highly conserved and subfamily-specific motifs in the C5-MTases analyzed. Differential transcript abundance was detected for SmC5-MTases, implying genome-wide variance of DNA methylation in different organs and tissues. Transcriptome-wide analysis showed that the transcript levels of all SmC5-MTase genes was slightly changed under yeast extract and methyl jasmonate treatments. Six SmC5-MTases, including SmMET1, SmCMT1, SmCMT2a, SmCMT2b, SmCMT3 and SmDRM1, were salicylic acid-responsive, suggesting the involvement of SmC5-MTases in salicylic acid-dependent immunity. These results provide useful information for demonstrating the role of DNA methylation in bioactive compound biosynthesis and Dao-di herb formation in medicinal plants.Cytosine DNA methylation is highly conserved epigenetic modification involved in a wide range of biological processes in eukaryotes. It was established and maintained by cytosine-5 DNA methyltransferases (C5-MTases) in plants. Through genome-wide identification, eight putative Cytosine DNA methylation, a dominating epigenetic modification mechanism, plays vital roles in gene expression regulation, transposon silencing, gene imprinting, and X chromosome inactivation . It is wde novo through distinct mechanisms (De novo methylation is mainly established by RNA-directed DNA methylation (RdDM), in which domains-rearranged methyltransferases (DRMs) are guided to target locus to direct methylation of all three sequence contexts via 24-nucleotide short interfering RNAs , another CMT subfamily member . Arabidopsis AtC5-MTase proteins were blast-analyzed against the S.\u00a0miltiorrhiza 99-3 whole genome sequence using tBLASTn algorithm using the BLASTx and BLASTn program, respectively (http://www.ncbi.nlm.nih.gov/blast/). Obtained raw genomic sequences, open reading frame (ORF) sequences and deduced protein sequences were listed in Sequences of 11 lgorithm . S.\u00a0milthttp://gsds.cbi.pku.edu.cn/index.php) using the coding sequences and the corresponding genomic sequences as inputs. Protein amino acid number, molecular weight (Mw) and theoretical isoelectric point (pI) were analyzed using the EXPASY PROTOPARAM tool (http://www.expasy.org/tools/protparam.html). Multiple sequence alignment was carried out using ClustalW plants grown in a field nursery at the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, were collected in August and stored in liquid nitrogen until use. Total RNA was extracted from three biological replicates for each tissue using the Quick RNA isolation kit . Each biological replicate represents independent single plant. RNA integrity and quantity were analyzed using agarose gel and NanoDrop 2000C Spectrophotometer , respectively. Total RNA was reverse-transcribed using the PrimeScript\u2122\u00a0 RT reagent kit . qRT-PCR primers listed in http://frodo.wi.mit.edu/primer3/). qRT-PCR analysis was conducted in triplicate on the CFX96\u2122 real-time PCR detection system for each biological replicate using SYBR premix Ex Taq\u2122\u00a0kit as described (S. miltiorrhiza hairy roots treated with yeast extract (YE) and methyl jasmonate (MeJA) were downloaded from SRA database under the accession number SRP111399 were downloaded from SRA database under the accession number SRX1423774 . RNA-seqRP111399 . RNA-seqX1423774 . DiffereX1423774 . Heat maX1423774 .Arabidopsis cytosine DNA methyltransferase proteins against the whole S.\u00a0miltiorrhiza 99-3 genome sequence resulted in the identification of eight SmC5-MTase genes. The number of SmC5-MTase genes in S.\u00a0miltiorrhiza is comparable with that in other plants, such as Arabidopsis varies from 4.89 (SmCMT3) to 8.03 (SmCMT2a) and the molecular weight (Mw) varies from 43.7 kDa (SmDNMT2) to 189.4 kDa (SmMET1) . These sterparts . Gene stse genes . The undS. miltiorrhiza and Arabidopsis. Four highly conserved motifs, including I, IV, VI and X and methyl jasmonate (MeJA) are effective elicitors for tanshinone and phenolic acid production in iorrhiza . The resry roots . The trary roots . CompareSmC5-MTases in plant defense, RNA-seq data from SA-treated S.\u00a0miltiorrhiza cell cultures was analyzed -dependent immunity . In ordeanalyzed . The trareatment , suggestS. miltiorrhiza. Understanding the regulatory mechanism of their biosynthesis and metabolism is important for S. miltiorrhiza quality improvement. Most of the studies about S. miltiorrhiza gene function concentrate on key enzyme genes and transcription factors associated with secondary metabolism through regulating SA-dependent defense genes in trans or cis (S. miltiorrhiza.Recent studies suggest that DNA methylation is involved in regulation of secondary metabolism . Consistnd xylem . Althougreatment . Dynamiced by SA . Analysis or cis . SimilarSmC5-MTase genes were identified using whole genome sequence and RNA-seq data from S. miltiorrhiza. Based on phylogenetic tree and conserved domain distribution, SmC5-MTase genes were divided into four subfamilies, including SmMET, SmCMT, SmDRM and SmDNMT2. Comparative analysis of SmC5-MTases and AtC5-MTases revealed the conservation and divergence of plant C5-MTases. The transcript abundance analysis of SmC5-MTase genes suggests functional importance of SmC5-MTases in secondary metabolism and stress response in S. miltiorrhiza. The results provide useful information for understanding the role of DNA methylation in medicinal plant development and bioactive compound biosynthesis.Eight 10.7717/peerj.4461/supp-1Table S1Click here for additional data file.10.7717/peerj.4461/supp-2Table S2Click here for additional data file.10.7717/peerj.4461/supp-3Table S3Click here for additional data file.10.7717/peerj.4461/supp-4Figure S1Click here for additional data file.10.7717/peerj.4461/supp-5Figure S2Click here for additional data file.10.7717/peerj.4461/supp-6Figure S3Click here for additional data file.10.7717/peerj.4461/supp-7Figure S4Click here for additional data file.10.7717/peerj.4461/supp-8Figure S5Click here for additional data file.10.7717/peerj.4461/supp-9Data S1Raw data.Click here for additional data file."} +{"text": "Protective effects of boswellic acid (BA) against acetaminophen (APAP)-induced hepatotoxicity in Balb/ cA mice were examined. BA, at 0.05 or 0.1%, was supplied for 4 weeks. Acute liver injury was induced by APAP treatment. Results showed that BA intake increased hepatic BA bioavailability. APAP treatment decreased glutathione (GSH) level, increased reactive oxygen species (ROS) and oxidized glutathione (GSSG) production; and lowered activity and protein expression of glutathione reductase (GR) and heme oxygenase (HO)-1 in liver. BA intake at both doses alleviated subsequent APAP-induced oxidative stress by retaining GSH content, decreasing ROS and GSSG formations, reserving activity and expression of GR and HO-1 in liver, and lowering hepatic cytochrome P450 2E1 activity and expression. APAP treatment enhanced hepatic levels of interleukin-6, tumor necrosis factor-alpha and monocyte chemoattractant protein-1. BA pre-intake diminished APAP-induced release of those inflammatory cytokines and chemokines. APAP up-regulated hepatic protein expression of toll-like receptor (TLR)-3, TLR-4, MyD88, nuclear factor kappa B (NF-\u03baB) p50, NF-\u03baB p65 and JNK. BA pre-intake at both doses suppressed the expression of NF-\u03baB p65 and p-JNK, and only at 0.1% down-regulated hepatic TLR-3, TLR-4 and MyD88 expression. APAP led to obvious foci of inflammatory cell infiltration in liver, determined by H&E stain. BA intake at both doses attenuated hepatic inflammatory infiltration. These findings support that boswellic acid is a potent hepato-protective agent. It is metabolized by hepatic cytochrome P450 system, especially CYP2E1, which leads to the overproduction of reactive free radicals and n-acetyl-p-benzoqui- noneimine (NAPQI) , 4. In aet al. [et al. [Toll-like receptors (TLRs) are pattern recognition receptors mainly responsible for immunomodulation. The activation of TLR-3 and TLR-4 has been implicated in APAP-induced hepatic damage because both TLRs could stimulate the production of adaptor proteins including MYD88 and nuclear factor kappa B (NF-\u03baB), which in turn promote the generation of oxidants and inflammatory cytokines and chemokines , 8. Furtet al. reportedBoswellia species including Boswellia carteri, Boswellia serrata and Boswellia sacra [via its anti-oxidative and anti-inflammatory activities [et al. [Boswellic acid BA, , a pentaia sacra . It is rtivities . The stu [et al. revealed [et al. . Thus, i\u03baB, TLR-3 and TLR-4 was evaluated. Furthermore, histological analysis was processed in order to provide more solid evidence to support the benefit of using BA as a hepatic protective agent.The purpose of this animal study was to examine the protective effects and action modes of BA at various doses upon liver of acetaminophen treated mice. The influence of this compound upon GSH, ROS and cytokines variation, CYP2E1 activity and protein expression of associated factors such as NF-2.2.1.Boswellic acid was synthesized and provided by Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China. APAP (98%) was purchased from Sigma Chemical Co. .2.2.Five-to six-week-old male Balb/cA mice were obtained from National Laboratory Animal Center . Mice were housed on a 12-h light-12-h dark schedule, and fed with water and mouse standard diet . Use of the mice was reviewed and approved by the China Medical University animal care committee (104-305).2.3.BA at 0.05 or 0.1 g was mixed with 99.95 or 99.9 g powder diet to prepare 0.05 and 0.1% BA diets. Mice were divided into five groups: normal group ; BA group (0.1% BA diet), APAP group ; BA-low-APAP group (0.05% BA diet plus APAP treatment); BA-high-APAP group (0.1% BA diet plus APAP treatment). After 4 weeks supplement, normal and BA groups were sacrificed, and the other three groups were treated by a single intraperitoneal injection of APAP (400 mg/kg body weight). APAP was dissolved in phosphate-buffered saline (PBS). Mice were killed with carbon dioxide after 24 h. The mortality of mice due to APAP injection was zero. After sacrificed, liver from each mouse was collected and weighted. There was no mice die before sacrificed. Blood was also collected, and serum was separated from erythrocyte immediately. Liver tissue, 0.2 g, was homogenized on ice in 2 ml phosphate buffer (pH 7.2), and the filtrate was collected. The protein concentration of serum and liver filtrate was determined by a commercial assay kit with bovine serum albumin as standard.2.4.et al. [g for 5 min at 4\u00b0C. Agilent 1100 series HPLC system equipped with a C18 reversed-phase column was used. BA quantification was performed using the external standard method. The limit of detection was 0.1 mg/g tissue. The relative standard deviations of precision and accuracy were less than 5.2%.The HPLC method of Lozano-Mena et al. was used2.5.Serum activities of ALT and AST were determined by using commercial assay kits . CRP level (mg/l) was measured by an ELISA kit .2.6.Liver tissue was homogenized with cold PBS containing 0.05% Tween 20 and 1 mM EDTA. After centrifuging, supernatants were used for measurements. GSH and GSSG concentrations (nmol/mg protein) in liver were determined by commercial colorimetric GSH and GSSG assay kits . ROS level was quantified by using 2\u2019, 7\u2019-dichlorofluores- cein diacetate. Fluorescence value was measured by using a fluorescence microplate reader at excitation and emission wavelengths of 485 and 530 nm, respectively. Relative fluorescence unit (RFU) was the difference in fluorescence values obtained at time 0 and 5 min. Results are expressed as RFU/mg protein. The activity (U/mg protein) of GPX and GR was assayed by using commercial kits purchased from EMD Biosciences Co. .2.7.Hepatic levels of IL-6, TNF-alpha and MCP-1 were measured by using cytoscreen immunoassay kits . The sensitivity of assay with the detection limit was 5 pg/ml for IL-6, and 10 pg/ml for TNF-alpha and MCP-1.2.8.The activity of CYP2E1 in freshly prepared liver microsome was estimated by colorimetrically measuring the formation of 4-nitrocatechol, a product from p-nitrophenol hydroxylation catalyzed specifically by CYP2E1. The protein concentration of CYP2E1 was measured by ELISA, and a rabbit anti-CYP2E1 antibody was used for detection. The formed 4-nitrocatechol was expressed as nmol/mg protein.2.9.Hepatic tissue, 40 mg, was homogenized in buffer containing protease-inhibitor cocktail purchased from Sigma-Aldrich Chemical Co. and 0.5% Triton X-100. Homogenate was then mixed with buffer , and followed by boiling for 5 min. Protein sample at 40 was electrophoresed on 10% SDS-polyacrylamide gel, and further transferred onto nitrocellulose membranes for 1 h. After blocking with a protein solution containing 5% skim milk for 1 h, membranes were treated with monoclonal antibody against heme oxygenase (HO)-1, CYP2E1 (1:1000), NF-\u03baB p50, NF-\u03baB p65, JNK (1:500), TLR-3, TLR-4, MyD88 (1:2000) at 4\u00b0C overnight, and followed by incubating with horseradish peroxidase-conjugated antibody at room temperature for 3.5 h. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a loading control, and the bands were quantified by an ATTO image analyzer .2.10.Partial liver tissue from each mouse was fixed in 10% phosphate-buffered formalin, and embedded in paraffin. Paraffin section at 5 mm thickness was cut and processed with hematoxylin-eosin (H&E) stain, and followed by examining under a light microscope for histological analysis. The severity of hepatic inflammatory injury was assayed according to the Ishak scoring system . The inj2.11.P < 0.05.The effect of each treatment was analyzed from 10 mice (n = 10) in each group. Data were reported as means \u00b1 standard deviation (SD), and subjected to analysis of variance. Differences among means were determined by the Least Significance Difference Test with significance defined at 3.3.1.. The intake of BA at both doses alleviated subsequent APAP-induced elevation of ALT, AST and CRP levels in serum (P < 0.05).BA intake at 0.1% increased hepatic BA content, and did not affect body weight, feed intake, water intake and liver weight 3.2.P < 0.05); but BA pre-intake attenuated APAP-induced GSH depletion and decreased hepatic GSSG and ROS production (P < 0.05). APAP raised GPX activity and reduced GR activity in liver (P < 0.05). BA intake failed to change hepatic GPX activity (P > 0.05); but significantly maintained hepatic GR activity (P < 0.05). As shown in P < 0.05). BA intake did not affect GPX protein expression (P > 0.05); but significantly retained protein expression of GR and HO-1 in liver (P < 0.05). APAP treatment enhanced CYP2E1 activity and expression (P < 0.05); however, BA intake significantly suppressed subsequent APAP-induced elevation of CYP2E1 activity and protein expression (P < 0.05). APAP treatment also significantly increased hepatic release of TNF-alpha, IL-6 and MCP-1 (P < 0.05). BA intake lowered APAP-induced hepatic production of these cytokines (P < 0.05).As shown in 3.3.P < 0.05). BA pre-intake at both doses down-regulated the expression of NF-\u03baB p65 and p-JNK (P < 0.05), and only at high dose suppressed hepatic TLR-3, TLR-4 and MyD88 expression (P < 0.05).APAP up-regulated hepatic protein expression of TLR-3, TLR-4, MyD88, NF-\u03baB p50, NF-\u03baB p615, JNK and p-JNK (\u03baB p50 expression (P > 0.05).BA did not alter NF-3.4.P < 0.05). BA intake at 0.05 and 0.1% decreased hepatic infiltration by inflammatory cells and lowered Ishak inflammation scores (P < 0.05), in which 0.1% BA treatment exhibited greater anti-inflammatory effects than 0.05% BA (P < 0.05).Histological data revealed that BA intake at 0.1% only (without APAP) did not cause inflammatory stress and showed similar Ishak inflammation score as normal groups . APAP tr4.Boswellia species, increased its deposit in liver and protected liver against subsequent APAP induced oxidative and inflammatory injury. Besides increasing GSH retention, we found that BA effectively decreased CYP2E1 activity and expression, lowered ROS, TNF-alpha and MCP-1 production, as well as suppressed HO-1, TLR-3, TLR-4, NF-\u03baB p65 and p-JNK expression. In addition, our histological results indicated that BA improved diffuse ballooning degeneration and lobular inflammation caused by APAP These findings support that BA is a potent hepatic protective agent.Our present study revealed that the pre-intake of BA, an active compound of APAP at high dose led to GSH depletion and GSSG accumulation . Our datvia its anti-oxidative activities, which definitely led to less stimulation for hepatic NF-\u03baB activation and JNK phosphorylation. Our western blot data regarding hepatic protein expression of NF-\u03baB p65 and p-JNK agreed that BA intake at both doses limited the activation of these two signal pathways. Consequently, it is reasonable to observe lower hepatic levels of IL-6, TNF-alpha and MCP-1 in BA treated mice. The decrease in serum levels of ALT, AST and CRP in BA treated mice also agreed that BA intake declined APAP caused liver inflammatory stress. In addition, our histological data further supported that BA pre-intake effectively improved hepatic inflammatory injury.APAP overdose activated NF-\u03baB and JNK pathways through stimulating ROS generation , 23. Theet al. [et al. [in vivo anti-inflammatory data of BA, and extended BA\u2019s mediating activity to TLRs and MyD88.TLRs play crucial roles in the pathological progression of inflammatory liver diseases because TLRs recognize endogenous damage-associated molecular patterns during inflammatory reactions . TLR-3 iet al. reported [et al. reportedBA is naturally present in many edible plants including vegetables and herbs , 30. The5.via maintaining hepatic GSH content, retaining activity and expression of GR and HO-1, decreasing inflammatory cytokines and suppressing protein expression of CYP2E1, NF-\u03baB p65, JNK, TLR-3 and TLR-4. These findings support that boswellic acid was a potent hepatic protective agent.Boswellic acid pre-intake protected mice liver against subsequent acetaminophen-induced oxidative and inflammatory injury All authors claimed that no Conflict of Interest."} +{"text": "Pochazia shantungensis adults and nymphs, newly recorded pests, were evaluated. The LC50 values of Thymus vulgaris, Ruta graveolens, Citrus aurantium, Leptospermum petersonii and Achillea millefolium oils were recorded as 57.48, 84.44, 92.58, 113.26 and 125.78\u2009mg/L, respectively, against P. shantungensis nymphs using the leaf dipping bioassay, and 75.80, 109.86, 113.26, 145.06 and 153.74\u2009mg/L, respectively, against P. shantungensis adults using the spray bioassay method. Regarding volatile components identified in T. vulgaris oil, the LC50 values of carvacrol and thymol using the leaf dipping bioassay against P. shantungensis nymphs were 56.74 and 28.52\u2009mg/L, respectively. The insecticidal action of T. vulgaris oil against P. shantungensis could be attributed to carvacrol and thymol. Based on the structure-toxicity relationship between thymol analogs and insecticidal toxicities against P. shantungensis nymphs similar to the LC50 values against P. shantungensis adults, the LC50 values of thymol, carvacrol, citral, 2-isopropylphenol, 3-isopropylphenol, and 4-isopropylphenol were 28.52, 56.74 and 89.12, 71.41, 82.49, and 111.28\u2009mg/L, respectively. These results indicate that the insecticidal mode of action of thymol analogs may be largely attributed to the methyl functional group. Thymol analogues have promising potential as first-choice insecticides against P. shantungensis adults and nymphs.The insecticidal toxicities of five essential oils against Pochazia shantungensis Chou & Lu. is a hemipterous insect that belongs to the Ricaniidae insect family, which includes about 400 described species in over 40 generaP. shantungensis is a newly recorded pest that is economically devastating for various trees including apple, blueberry, peach and persimmon, mainly in Wanjugun, KoreaP. shantungensis was first recorded in Chungcheongnamdo in 2010P. shantungensis has subsequently occurred sporadically in several other provinces across Korea2P. shantungensis adults and nymphs, despite the urgent demandP. shantungensis.Cynanchum paniculatum oilMentha piperita oilMentha spicata oil3789Plant oil is a very complex mixture that can contain approximately 30\u201365 constituents at various concentrations35Thymus vulgaris oil-derived constituents against P. shantungensis. Therefore, the aims of the present study were first to investigate the insecticidal properties of T. vulgaris oil-derived components against P. shantungensis adults and nymphs, and then to determine the structure-activity relationship between thymol analogs and insecticidal toxicities.So for no report has been received about the insecticidal toxicities of P. shantungensis adults and nymphs. Essential oils of Achillea millefolium flowers, Citrus aurantium fruits, Leptospermum petersonii leaves, Ruta graveolens leaves and T. vulgaris leaves were analyzed of P. shantungensis adults and nymphs. Differences in the insecticidal toxicities of plant-derived oils may be explained on the basis of species-specific responses to plant species, phytochemicals, and the weight and size of P. shantungensis adults and nymphsThis study was undertaken within the framework of a more general study involving the natural products for insecticidal toxicities against analyzed . The yieexposure . From thP. shantungensis adults and nymphs, the components of A. millefolium, C. aurantium, L. petersonii, R. graveolens, and T. vulgaris oils were investigated by GC-MS analysis. The identified components, together with the percentages present in the essential oils are displayed in A. millefolium oil; limonene (87.75%), citral (3.21%), limonene oxide (2.29%), and (\u2212)-carveol (1.75%) in C. aurantium oil; citral (48.12%), \u03b2-citronellal (19.50%), isopulegol (8.14%), geraniol (4.64%), and linalool (3.33%) in L. petersonii oil, and thymol (23.34%), undecyl trichloroacetate (18.52%), methyltridecyl pentanoate (16.18%), and 2,2-dimethylpropanoic acid (7.03%), 2-acetoxytetradecane (6.98%), palmitic acid (5.07%), and methyl linolenate (4.78%) in R. graveolens oil. The major components in T. vulgaris oil were thymol (40.04%), \u03c1-cymene (29.97%), \u03b3-terpinene (8.17%), linalool (4.99%), terpinolene (3.26%), \u03b1-pinene (2.84%), \u03b2-caryophyllene (2.50%), carvacrol (2.45%), limonene (1.25%), \u03b1-phellandrene (1.20%), myrcene (0.91%), camphene (0.89%), and caryophyllene oxide (0.21%). Together, thymol, \u03c1-cymene and \u03b3-terpinene made up 78.18% of T. vulgaris oil. The volatile components consisted of 8 monoterpene hydrocarbons , 1 monoterpene alcohol , 2 monoterpene phenols (carvacrol and thymol) and 2 sesquiterpene hydrocarbons (\u03b2T. vulgaris oil were borneol (0.98%), camphene (0.60%), carvacrol (2.81%), \u03b2-caryophyllene (2.39%), 1,8-cineol (0.96%), p-cymene (25.2%), myrcene (1.93%), linalool (2.86%), \u03b1-pinene (1.16%), 1-octen-3-ol (1.19%), \u03b1-terpinene (1.02%), \u03b3-terpinene (6.37%), \u03b1-thujene (1.50%) and thymol (42.27%). The fact that the essential oil of T. vulgaris leaves dried more at 45\u2009\u00b0C than at 30\u2009\u00b0C can be explained mainly by the increase of thymol by 8% and carvacrol by 12%, while the quantity of \u03b3-terpinene was decreased by 4.9%T. vulgaris were affected by the environmental conditions, including harvest time, genotype, storage period, handling method and intraspecific variability, and the experimental conditions, which included the extraction method, extracted plant parts, and plant tissue drying temperatureTo further explore the insecticidal toxicities of the five essential oils against oxide 2.2%, and derived from the five essential oils were evaluated using spray and leaf dipping bioassays against P. shantungensis adults and nymphs -carveol, geraniol, and bornyl acetate) did not exhibit any insecticidal toxicity against P. shantungensis adults and nymphs (data not shown). The insecticidal toxicities of the essential oils appear to be connected to their chemical composition. The insecticidal toxicities of T. vulgaris and R. graveolens oils could be due to the existence of thymol and carvacrol, which exhibited the greatest insecticidal toxicities. The essential oils of C. aurantium and L. petersonii contain citral, which showed insecticidal toxicities against P. shantungensis adults and nymphs, however its toxicity was weaker than thymol and carvacrol. Furthermore, P. shantungensis nymphs were more susceptible to T. vulgaris oil, carvacrol and thymol, when compared to P. shantungensis adults -carveol, (+)-carvone, \u03b2-caryophyllene, caryophyllene oxide, \u03b2-citronellal, citral, 1,8-cineole, d nymphs . Based os adults . In a prP. shantungensis adults and nymphs, thymol, carvacrol, 2-isopropylphenol, 3-isopropylphenol, and 4-isopropylphenol were selected as thymol analogs for testing , decyl chloroformate (97%), dodecanoic acid (98%), \u03b2-farnesene (90%), geranyl acetate (97%), geraniol (98%), isopulegol (98%), linalool (97%), limonene (97%), limonene oxide (97%), methyl linolenate (99%), myrcene (90%), myristic acid (99%), palmitic acid (99%), \u03b1-phellandrene (85%), \u03b1-pinene (98%), pivalic acid (99%), sabinene (75%), \u03b1-terpineol (90%), \u03b3-terpinene (97%), 4-terpineol (95%), terpinolene (90%), and tymol (99%) were obtained from Sigma-Aldrich . Achillea millefolium L. flowers, Citrus aurantium L. fruits, Leptospermum petersonii F. M. Bailey leaves, Ruta graveolens L. leaves, and Thymus vulgaris L. leaves were collected from a local store in Chonju, Korea. Sample specimens were authenticated by Jeongmoon Kim at Chonbuk National University, Korea. Essential oils of the five plants were obtained by steam distillation extraction, and finally dried over Na2SO4 to extract the pure essential oils (Bornyl acetate (99%), camphene (95%), camphor (96%), carvarol (98%), (\u2212)-carveol (95%), (+)-carvone (96%), \u03b2-caryophyllene (98.5%), caryophyllene oxide (95%), \u03b2-citronellal (95%), citral (95%), 1,8-cineole (99%), ial oils .P. shantungensis adults and nymphs were collected from persimmon trees in Wanjugun, Korea and classified the fourth instar stages of P. shantungensis nymphs and adults as detailed elsewhere2P. shantungensis adults and nymphs were assessed and were separated with HP-Innowax capillary column and DB-5 column . The conditions of the column were as follows: Helium at 0.75\u2009mL/min; column temperature (51 to 201\u2009\u00b0C) at 2\u2009\u00b0C/min; injector temperature (211\u2009\u00b0C); split ration (48:1); ion source temperature (231\u2009\u00b0C); ionization potential (70e\u2009V); and mass spectra range (50\u2013800\u2009amu). The components of T. vulgaris oils were evaluated according to retention times, retention indices, and mass spectra and were identified by comparison with a spectrum library (T. vulgaris oil constituent (%) was measured by comparison with internal standards.The components of the essential oil extracted from library . The rel50) value and the slope of the regression lines were calculated using the statistical package SPSS, version 12.0 for Windows.Data obtained for each dose response bioassay were subjected to probit analysis. The median lethal concentration .Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations."} +{"text": "MiR-486 was found to be associated with cancer\u2019s diagnosis and prognosis. This meta-analysis aimed to investigate the potential effect of miR-486 on cancer detection and prognosis.We searched PubMed, Cochrane library, Embase, Chinese National Knowledge Infrastructure (CNKI) and Wanfang databases to find all correlated articles. The STATA 11.0 was applied to estimate the pooled effects, heterogeneity and publication bias.The pooled sensitivity (SEN), specificity (SPE) and Area under the curve (AUC) were 82% (95% CI: 78\u201385%), 88% (95% CI: 83\u201392%) and 0.91 (95% CI: 0.88\u20130.93). Subgroup analysis indicated miR-486 from circulating samples exhibited higher diagnostic accuracy with the AUC was 0.90 (95% CI: 0.87\u20130.92) than miR-486 from other specimen with the AUC of 0.78 (95% CI: 0.75\u20130.82) and miR-486 obtained a better diagnostic value in the Asian population with the AUC of 0.94 (95% CI: 0.91\u20130.95) than the Caucasian and Caucasian/African population with the AUC of 0.80 (95% CI: 0.76\u20130.83) and 0.89 (95% CI: 0.86\u20130.91) respectively. MiR-486 obtained high value for the diagnosis of non-small cell lung cancer with SEN, SPE and AUC were 0.82 (95% CI: 0.0.77\u20130.87), 0.90 (95% CI: 0.84\u20130.94) as well as 0.92 (95% CI: 0.89\u20130.94) respectively. For the 7 prognostic tests, the pooled hazard ratio (HR) was 0.48 (95% CI: \u20130.13\u20131.08) for low versus high miR-486 expression.This meta-analysis indicated that miR-486 can be used as ideal biomarkers in the cancer\u2019s diagnosis. However, Low miR-486 expression did not increase the risk of poor outcome. MicroRNA is a group of 19\u201322 nucleotide, small, single-stranded and conserved non-coding RNA that acts as a regulator of gene expression at both the post-transcriptional and the translational levels through acting on the 3\u2019-untranslated region (UTR) of messenger RNA (mRNA) , SPE [TN/ (FP+TN)], the positive likelihood ratio (PLR) [(SEN/ (1-SEN)], the negative likelihood ratio (NLR) [(1-SPE)/SPE)], the diagnostic odds ratio (DOR) [PLR/ NLR] and the pooled HR with its 95% Confidence Interval (95% CI) respectively. We also constructed the SROC curve and calculated the AUC value. Simultaneously, we assessed the heterogeneity among the selected studies through the I2 value . The P vnificant . As for This was the first meta-analysis to confirm the potential value of miR-486 on cancer diagnosis and prognosis. The expression of miR-486 might be an effective biomarker for detection of human cancer."} +{"text": "A new recombinant norovirus GII.P16-GII.2 outnumbered pandemic GII.4 as the predominant GII genotype in the winter of 2016\u20132017 in Hong Kong, China. Half of hospitalized case-patients were older children and adults, including 13 young adults. This emergent norovirus targets a wider age population compared with circulating pandemic GII.4 strains. Noroviruses are leading causes of acute gastroenteritis (http://www.rivm.nl/mpf/norovirus/typingtool).Since August 2012, we have conducted an ongoing molecular surveillance of norovirus genotype distribution in all hospitalized gastroenteritis patients in our teaching hospital in Hong Kong . The female-to-male ratio was 1.04:1. We successfully genotyped 357 (90.8%) samples. The top 3 circulating VP1 genotypes during the study period were GII.4 (n = 214 [54.5%]), GII.2 (n = 86 [21.9%]), and GII.3 (n = 16 [4.1%]). Before this season, GII.2 had been a rare genotype, accounting for <1% of total strains circulating locally , panel Ahttp://www.megasoftware.net) from the samples of 20 case-patients as previously described (are.net) , panel AThe GII.2 strains we identified clustered most closely with the recombinant GII.P16-GII.2 strains from Germany during the same period . SubsequU-test) , panel CU-test) , panel CU-test) Figure. We noted a gradual narrowing in the age distribution of GII.4 infections to young children <5 years of age in the past 5 seasons , presumaWe report the emergence of a recombinant norovirus GII.P16-GII.2 variant that surpassed the previously predominant genotype GII.4 in hospitalized acute gastroenteritis case-patients in the winter of 2016\u20132017 in Hong Kong. However, unlike the recently emerged epidemic GII.17 Kawasaki variant that predominated only in part of Asia (China and Japan) during 2014\u20132016 apart from causing outbreaks. Collectively, these findings might have important implications for norovirus vaccine formulation and vaccination strategy. Close monitoring of the global spread of GII.P16-GII.2 is warranted.Incidence of hospitalization in case-patients with GII.4 and GII.2 infections, Hong Kong, China, July 2016\u2013February 2017."} +{"text": "Mycobacterium porcinum is a rapidly growing environmental mycobacterium responsible for opportunistic infections. The 7,025,616-bp draft genome of M. porcinum strain CSURP1564 exhibits a 66.71% G+C content, 6,687 protein-coding genes, and 65 predicted RNA genes. In silico DNA-DNA hybridization confirms its assignment to the Mycobacterium fortuitum complex. Mycobacterium porcinum, a member of the Mycobacterium fortuitum third biovariant complex, is a nontuberculous mycobacterium primarily recovered from swine with lymphadenitis oleic acid-albumin-dextrose-catalase under a 5% CO2 atmosphere. Colonies were confirmed by matrix-assisted laser desorption ionization\u2013time of flight mass spectrometry (M. porcinum CSURP1564 genome was incorporated into in silico DNA-DNA hybridization (DDH) (M. porcinum IP141460001 (GenBank accession number MVIG00000000), 49.5% with M. boenickei CIP 107829 (FUWC00000000), 34.5% with M. conceptionense D16 (CTEF00000000), 34.4% with M. farcinogenes DSM 43637 (CCAY000000000) and M. neworleansense ATCC 49404 (CWKH00000000), 31.40% with M. fortuitum CT6 (NCBI reference sequence number NZ_CP011269), and 20.5% with M. avium 104 (NCBI reference sequence NC_008595).trometry . Reads itrometry , and contrometry , GapFilltrometry , and mantrometry yielded on (DDH) using GGon (DDH) , with reM. porcinum strain CSURP1564 differs from M. conceptionense in the M. fortuitum complex. This is the first report of MinION technology applied to the genome sequencing of a nontuberculous Mycobacterium species , European Nucleotide Archive (ENA), under the accession number OLMG00000000 (OLMG01000001 to OLMG01000005).The draft genome sequence of"} +{"text": "Lactobacillus plantarum Oregon-R-modENCODE strain BDGP2 was isolated from the gut of Drosophila melanogaster for functional host microbial interaction studies. The complete genome comprised a single circular genome of 3,407,160\u00a0bp, with a G+C content of 44%, and four plasmids. Lactobacillus plantarum increases amino acid metabolism and promotes larval growth in Drosophila melanogaster under nutrient-scarce conditions (L.\u00a0plantarum strains include one derived from a laboratory fly strain (KP) and one from wild-caught flies (DF) . Here, wL. plantarum Oregon-R-modENCODE strain BDGP2 was isolated from a fecal swab. Bacteria were streaked onto Difco de Man, Rogosa, and Sharpe (MRS) agar agar agar (BDRS) agar and sequRS) agar . DNA wasRS) agar , and whoRS) agar . A singlsion 2.0 , 9. The sion 2.0 and the sion 2.0 .L.\u00a0plantarum strains, ours contains integrated likely prophages . There are seven copies, six ranging in size from 36,225 to 46,235\u00a0bp and in sequence similarity from 45 to 70% and a partial copy of only 13,544 kb. Together they constitute 7.5% of the genome. Two cornerstone proteins highly conserved in prophages are the large terminase subunit and the portal protein (L. plantarum strain DF plasmid unnamed1 (GenBank accession number CP013754) and L. plantarum strain TMW 1.277 plasmid pL1277-4 (accession number CP017367), respectively.The chromosomal genome annotation predicts 3,148 protein-coding genes, 131 pseudogenes, 5 rRNA operons, a single 5S rRNA, and 85 tRNAs . Of the 3,148 protein-coding genes, 328 are contained within candidate prophages. Like other protein . These cL. plantarum Oregon-R-modENCODE strain BDGP2 have been deposited in GenBank under the accession numbers CP023174 (chromosome) and CP023175 (pLtBDGP2A), CP023176 (pLtBDGP2B), CP023177 (pLtBDGP2C), and CP023178 (pLtBDGP2D) (plasmids).The complete genome sequences of the chromosome and four plasmids of"} +{"text": "Both spontaneous hepatitis C virus (HCV) clearance and the achievement of sustained virological response (SVR) by anti-viral therapy greatly reduce the incidence of hepatocellular carcinoma (HCC). The current study aimed to compare the risk of HCC between the two patient groupsA total of 313 subjects with spontaneous HCV clearance (SC) and 564 age- and sex-matched patients in the treatment-induced SVR group were enrolled for analysis.Nineteen (2.2%) of the 877 patients developed HCC during 6,963 person-years of follow-up. Fourteen (2.5%) SVR patients and 5 (1.6%) SC patients developed HCC (P=0.004). Cox regression analysis of factors predictive of HCC included SVR , diabetes (HR/CI:3.41/1.21-9.58), and age (HR/CI: 1.07/1.01-1.14). Of the 564 SVR patients, eleven (5.9%) of the 187 patients with fibrosis stage 2-4 (F2-4) and 2 (0.9%) of the 226 patients with F01 developed HCC (P=0.01). Compared to SC subjects, only SVR patients with F2-4 (P<0.001) but not F0-1(P=0.60) had a higher risk of HCC development. Cox-regression analysis using liver fibrosis as a variable demonstrated that factors associated with HCC included SVR with F2-4 (versus SC: HR/CI: 10.06/2.20-45.98), diabetes (HR/CI:3.23/1.14-9.19), and age (HR/CI: 1.08 1.02-1.15).Compared to subjects with spontaneous viral clearance, subjects with antiviral treatment-induced HCV viral clearance remain at high risk for HCC development, especially if they have significant hepatic fibrosis. These results may provide important information for decision-making regarding the prioritization of current direct antiviral agents in resource-limited countries. Spontaneous hepatitis C virus (HCV) seroclearance occurs in 20-30% of patients after acute infection \u20133. SubjeA total of 313 subjects in the SC group (participants who had anti-HCV seropositivity and undetectable HCV RNA at baseline (n = 291) and those who had anti-HCV seropositivity and detectable HCV RNA levels at baseline, but HCV RNA became undetectable after more than one-year follow-up (n = 22)) and 564 age- and sex-matched patients in the SVR group were enrolled for analysis with a follow-up period of 4,224and 2,739 person-years, respectively. The baseline characteristics are shown in Table Nineteen 2.2%) of the 877 patients developed HCC over 6,963 person-years of follow-up, including fourteen (2.5%) SVR patients and 5 1.6%) SC patients with an incidence of 0.51% and 0.12% per person-year, respectively (P=0.004) of the 564 SVR patients had liver histology available within six months of initiating the antiviral therapy. Of them, eleven (5.9%) of the 187 patients with F2-4 and two (0.9%) of the 226 patients with F0-1 developed HCC (Log-Rank test P=0.01). Compared to SC subjects, only SVR patients with F2-4 (Log-Rank test P<0.001), but not F0-1(Log-Rank test P=0.60), had significantly higher risk of HCC development HCV cohort. The R.E.V.E.A.L-HCV study is a community-based cohort and enrolled participants from seven townships in Taiwan during 1991-1992. The details of the study participants, interview, blood collection and laboratory examinations have been described previously in detail. , 23 Sex-Interleukin 28B (IL-28B) rs8099917 was selected as the single-nucleotide polymorphism (SNP) to be tested for its association with HCC. The genetic testing was determined using methods that have been described previously , 25\u201327.The baseline characteristics of the clinical cohort and R.E.V.E.A.L.-HCV cohort were compared by chi-squared tests. The cumulative risk of the incidence of HCC among patients who occurred spontaneous HCV RNA clearance (R.E.V.A.E.L.-HCV cohort) and treatment-induced RNA clearance was estimated by Kaplan-Meier method, and the statistical significance of the difference was examined by log-rank tests. Cox proportional hazards models were used to estimate multivariate-adjusted hazard ratios (HR) with 95 percent confidence intervals (95% CI) for HCC risk for various groups with RNA clearance after adjustment for other risk factors. Statistical significance levels were determined by a 2-sided P-value of 0.05. The proportionality assumption (non-changing HRs over time) of Cox models was examined, and the assumption was not violated. All analyses were performed using the SAS statistical software package ."} +{"text": "ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116\u00a0bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.133510.1601/strainfinder?urlappend=%3Fid%3DIAM+12611T, 10.1601/nm.1334 A 321T and 10.1601/nm.1783110.1601/strainfinder?urlappend=%3Fid%3DORS+1407T, based on 16S rRNA gene sequences. gANI values of \u226598.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares \u226598% sequence identity with nodC of M. laciniata-nodulating 10.1601/nm.1328 strains, but \u226493% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.10.1601/nm.1335 Mlalz-1 (INSDC = The online version of this article (10.1186/s40793-017-0270-2) contains supplementary material, which is available to authorized users. Medicago spp.) are some of the most important and extensively grown pasture legumes and their specific symbiosis with strains of rhizobia belonging to either 10.1601/nm.1328 (synonym 10.1601/nm.1339) meliloti or the closely related species 10.1601/nm.1334 [Symbiotic nitrogen fixation by pasture legumes and their associated root nodule bacteria provides a critical contribution to sustainable animal and plant production, and the maintenance of soil fertility in agricultural systems \u20133. As su/nm.1334 , 6 has b/nm.1334 .Medicago laciniata (L.) Miller (cut leaf medic), an annual native of southern and eastern Mediterranean and Saharo-Sindian countries, is of importance because of its ability to grow in comparatively arid habitats and marginal cropping areas [Medicago sativa L. or Medicago truncatula Gaertn. [nod genes, in particular a specific nodC allele [M. truncatula and M. laciniata shared chromosomal identity, but differed in their nodC alleles [M. laciniata and bv. meliloti for the classical 10.1601/nm.1335 group that efficiently nodulates M. sativa. However, in subsequent studies the diversity observed within bv. medicaginis strains indicate that this group is certainly heterogeneous [ng areas \u201311. It i Gaertn. , 13. ThiC allele . For exa alleles . Based oM. laciniata is native to the Canary Islands and is present on all of the islands of this archipelago, growing in environments that range from arid to subhumid. 10.1601/nm.1335 strain Mlalz-1 was isolated from a N2-fixing nodule of M. laciniata grown in alkaline soil (pH\u00a09.0) collected in Guatiza, in the arid Northeast of Lanzarote Island, in 2007. This strain was one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 GEBA-RNB project proposal [proposal , 18. HerLeft and Center). It is fast growing, forming colonies after 3\u20135\u00a0days when grown on \u00bdLA, TY, or a modified yeast-mannitol agar [Right). Minimum Information about the Genome Sequence (MIGS) for strain Mlalz-1 is provided in Table\u00a010.1601/nm.1335 Mlalz-1 is a motile, non-sporulating, non-encapsulated, Gram-negative strain in the class 10.1601/nm.809. The rod shaped form has dimensions of approximately 0.5\u00a0\u03bcm in width and 1.0\u20132.0\u00a0\u03bcm in length [T (= 10.1601/strainfinder?urlappend=%3Fid%3DLMG+19920T) [T [T, 99.7% to 10.1601/nm.1334 A 321T and 99.5% to 10.1601/nm.1783110.1601/strainfinder?urlappend=%3Fid%3DORS+1407T. In contrast, 10.1601/nm.133510.1601/strainfinder?urlappend=%3Fid%3DIAM+12611T and 10.1601/nm.133710.1601/strainfinder?urlappend=%3Fid%3DLMG+7834T [Previous studies using multilocus sequence typing showed that al group . Phyloge+6133T) , 10.160120T) [T . The avaG+7834T were onlM. laciniata, which is suited for cultivation in arid environments [10.1601/nm.1335 Mlalz-1 was selected for sequencing at the U.S. Department of Energy funded Joint Genome Institute as part of the GEBA-RNB project , 18. Theronments . The 10.ronments and a hironments . Sequenc600nm of 0.6 was reached. DNA was isolated from 50\u00a0ml of cells by Peter van Berkum according to the method described by van Berkum [\u22121.10.1601/nm.1335 Mlalz-1 (= 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+1984) was cultured on MAG solid media for thren Berkum . The finThe draft genome of 10.1601/nm.1335 Mlalz-1 was generated at the DOE Joint genome Institute (JGI) using Illumina technology . An IlluUniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. The tRNAScanSE tool [Walnut Creek, CA, USA.Genes were identified using Prodigal , as partnSE tool was usednSE tool . Other nnSE tool . AdditionSE tool developeThe genome is 6,664,116\u00a0bp with 62.16% GC content Table\u00a0 and compT (= 10.1601/strainfinder?urlappend=%3Fid%3DLMG+6133T), 10.1601/nm.1334 A 321T (= 10.1601/strainfinder?urlappend=%3Fid%3DLMG+19920T) and 10.1601/nm.1783110.1601/strainfinder?urlappend=%3Fid%3DORS+1407T. As the genomes of these type strains have not been sequenced or are not publically available, gANI values [repC, which is present as a single copy on 10.1601/nm.1335 pSymA and pSymB. The 10.1601/nm.1335 Mlalz-1 genome carried 2 repC loci (A3CADRAFT_00120 and A3CADRAFT_01676) with highest encoded protein identity to RepC proteins of 10.1601/nm.1335 strains. Mlalz-1 A3CADRAFT_00120 RepC1 had highest identity (98.10%) to the RepC1 protein encoded by SMb20044 on pSymB of 10.1601/nm.1335 1021. 10.1601/nm.1335 Mlalz-1 A3CADRAFT_01676 RepC2 had highest identity (99.00%) to the RepC2 protein encoded by SMa2391 on pSymA of 10.1601/nm.1335 1021. This indicated the presence of two megaplasmids in strain Mlalz-1, and revealed that strain Mlalz-1 has a similar genome architecture to that of 10.1601/nm.1335 1021.10.1601/nm.1335 Mlalz-1 is one of seven strains of 10.1601/nm.1335 that have been sequenced from the GEBA-RNB genome sequencing projects . On the I values had to bI values . The totgspDOGLMCKEFHIJ necessary for a functional T2SS, but lacks the gspS gene found only in certain genera [.All 29 10.1601/nm.1335 strains within the gANI clique share a core set of 4948 orthologous genes, using cut off values of 1e-5 and 30% minimum protein identity. 10.1601/nm.1335 Mlalz-1 contains 176 unique genes, 96 (54.5%) of which encode hypothetical proteins. The unique genes include those encoding the components of a T2SS, located on scaffold A3CADRAFT_scaffold_5.6 Fig.\u00a0, as welln genera , actP, actR, actS, phrR, exoR, exoH, lpiA, acvB, degP1, mdh3, fbaB, groS, kdpB, kdpC, fixN2 and fixO2 [lpiA-acvB operon. One operon (A3CADRAFT_01189-A3CADRAFT_01190) is found on scaffold A3CADRAFT_scaffold_3.4, in a gene region that is conserved in other 10.1601/nm.1335 (sequence similarity >98%) and is located on the chromosome of the fully sequenced 10.1601/nm.1335 1021. The second version of the lpiA-acvB operon (A3CADRAFT_05694-A3CADRAFT_05695) is located on A3CADRAFT_scaffold_47.48, in a gene region that is conserved in 10.1601/nm.1334 genomes (sequence similarity >96%) and is located on the pSMED02 symbiotic plasmid of the fully sequenced 10.1601/nm.133410.1601/strainfinder?urlappend=%3Fid%3DWSM+419. The regulatory gene fsrR, required for the acid activated expression of lpiA in 10.1601/nm.133410.1601/strainfinder?urlappend=%3Fid%3DWSM+419 [lpiA-acvB gene regions of all other 10.1601/nm.1335 sequenced genomes. These findings suggest that 10.1601/nm.1335 Mlalz-1 acquired the plasmid-borne lpiA-acvB operon and associated fsrR regulatory gene by lateral transfer from an 10.1601/nm.1334 strain.The Mlaz-1 genome also contains acid-tolerance or acid-responsive genes that are orthologous to the genes identified in the comparatively acid tolerant strain 10.1601/nm.133410.1601/strainfinder?urlappend=%3Fid%3DWSM+419. Acid-tolerance or acid-responsive genes identified in Mlaz-1 include nd fixO2 \u201352 genes identified in the 10.1601/nm.1335 Mlalz-1 genome with nodC of other M. laciniata-nodulating 10.1601/nm.1328 strains in the NCBI database, whereas there is a lower sequence identity (\u2264 93%) with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Nodulation of Medicago hosts requires Nod factors that are sulfated at the reducing terminus and acylated at the non-reducing terminus, with a polyunsaturated fatty acyl tail [Medicago species since the nodEF, nodL and nodHPQ genes that are required for these specific decorations of the Nod factor are present in the genome. 10.1601/nm.1335 Mlalz-1 also possesses the three nodD genes that mediate host-specific activation of nodABC in the symbiotic interactions of 10.1601/nm.1335 with Medicago [Essential symbiotic with that of sequenced 10.1601/nm.1334 strains, which infers horizontal gene transfer of this region from 10.1601/nm.1334.10.1601/nm.1335 Mlalz-1 is a rhizobial strain that is able to nodulate and fix nitrogen with the highly specific host strains . HoweverAdditional file 1: Table S1.Ensifer meliloti Mlalz-1. (DOCX 52\u00a0kb)Associated MIGS record for Additional file 2: Table S2-S4.Table S2. Acid responsive gene orthologs present in Ensifer strains. Table S3. The nodulation genes of Ensifer meliloti Mlalz-1. Table S4. The nitrogen fixation genes of Ensifer meliloti Mlalz-1. (DOCX 65\u00a0kb)"} +{"text": "In the Local score development subsection of the Results section, there is an error in the model equation following the second paragraph. The correct equation is:Log odds of in-hospital mortality = -4.67 + (moderate hypoxemia x 0.43) + (severe hypoxemia x 1.62) + + + + (wheeze x -0.35) + (unconsciousness x 1.74)"} +{"text": "Since 2005, anti-hepatitis B virus (anti-HBV) vaccine is part of the Expanded Program on Immunization (EPI) for infants born in Cameroon, with 99% anti-HBV coverage. In a context of generalized HIV epidemiology, we assessed paediatric anti-HBV vaccine response according to HIV status, feeding option and age in a tropical context.Prospective, observational and cross-sectional study conducted among 82 children , after complete anti-HBV vaccination (Zilbrix Hepta: 10\u03bcg AgHBs) at the Essos Health Centre in Yaounde, Cameroon, classified as group-A: HIV unexposed (28), group-B: HIV-exposed/uninfected (29), group-C: HIV-infected (25). Quantitative anti-HBs ELISA was interpreted as \u201cno\u201d, \u201clow-\u201d or \u201cprotective-response\u201d with <1, 1\u201310, or \u226510 IU/L respectively; with p-value<0.05 considered significant.95% 0.933\u20137.500], p = 0.041. According to feeding option during first six months of life, 47.67% (21/45) developed a protective-response on exclusive breastfeeding vs. 43.24% (16/37) on mixed or formula feeding, OR: 1.148 [CI95% 0.437\u20133.026], p = 0.757. According to age, protective-response decreased significantly as children grow older: 58.33% (28/48) <24 months vs. 26.47% (9/34) \u226524 months, OR: 3.889 [CI95% 1.362\u201311.356], p = 0.004; and specifically 67.65% (23/34) \u22646 months vs. 0%, (0/5) 33\u201341 months, p = 0.008.Children were all HBV-unexposed (AcHBc-negative) and uninfected (HBsAg-negative). Response to anti-HBV vaccine was 80.49% (66/82), with only 45.12% (37/82) developed a protective-response (\u226510IU/L). According to HIV status, 60.71% (17/28) developed a protective-response in group-A, vs. 51.72% (15/29) and 20% (5/25) in group-B and group-C respectively, Odds Ratio (OR): 2.627 [CIAnti-HBV vaccine provides low rate of protection (<50%) among children in general, and particularly if HIV-exposed, infected and/or older children. Implementing policies for early vaccination, specific immunization algorithm for HIV-exposed/infected children, and monitoring vaccine response would ensure effective protection in tropical settings, pending extensive/confirmatory investigations. Viral hepatitis B (HBV) and C are globally known as prevailing agents in hepatocellular carcinoma (HCC) and associated mortality . As the Out of 36.7 million of HIV-infected individuals (including 2.6 million children) worldwide, ~70% are living in SSA, with consistent risks of mother-to-child transmission ,5. FurthIn HBV-endemic settings like SSA, anti-HBV vaccination is strongly recommended to every newborn ,11. Of nIn contrast to the high vaccine-induced HBV-protection rate (90\u201395%) observed among children living in western countries , childreIn a tropical context with highly prevalent HIV/HBV coinfection and consistent MTCT like Cameroon ,7,14, inWe herein sought to ascertain the overall post-vaccination response against HBV in children, compare the degree of HBV protection according to HIV vertical exposure and infection, evaluate the impact of infant feeding option and age on vaccine response.th May\u2013 04th August in 2014 among HBV-vaccinated children at the Essos Health Centre (EHC) in Yaounde, Cameroon; stratified according to HIV profile, feeding option and age range.A prospective, observational and cross-sectional study was conducted from 052 featuring a tropical wet and dry climate with constant temperature (22.9\u201325.7\u00b0C mean daily temperature); the population is over 2.5 million inhabitants, for a density of 14,000/km2. EHC currently has a large accommodation capacity of ~250 beds, innovative technical equipment and a very high-performance within a wide range of specialised services: general medicine, emergency, anaesthesiology, reanimation, surgery and sub-specialities, gynaecology, ophthalmology, dentistry, medical imaging, laboratories (including molecular biology), pharmacy, neonatology, paediatrics, etc. Specifically, EHC is a reference antiretroviral treatment (ART) centre for both adults and children since 2005, with ~450 HIV-infected children on ART to date. This performance ranked the EHC as the four national reference center for paediatric ART in Cameroon.EHC is a reference health facility based in the capital city of Cameroon, a township of 180 kmAt the EHC, PMTCT of HBV at the study site follows national guidelines, and starts with antenatal screening for HBV infection for all pregnant women during antenatal care. For positive-HBsAg mothers, early neonatal administration of anti-HBV immunoglobulin is strongly recommended within 48 hours after birth. Both for HBV vertically exposed and unexposed infants, anti-HBV vaccine (Zilbrix Hepta) is administered at a series of three monthly doses. Assessing antibody response consists of anti-HBs serological testing recommended at least 1\u20134 months after the final (third) vaccine dose.Based on a convenient sampling, the sample size was calculated using the following formula: (42.9%) , and \u201cD\u201d3) for HIV-infected children. Four children had received the third vaccine dose \u22654 months ago prior to enrolment, while two others had insufficient samples for laboratory analysis. Final sampling therefore had 82 study participants. The HIV status of the 82 participants, as well as the CD4 count of HIV-infected children, was confirmed from their medical records at EHC.At the vaccination unit of the EHC paediatric service, mothers and their children attending the routine immunization program were provided with information on the study objectives. Then, 200 mothers of potentially eligible children received the written information sheet and the study informed consent form. Of these 200 women, 34% (88) mothers returned with a signed informed consent form, and their children were enrolled. Vaccination charts of the 88 children were then checked by retrieving information to confirm eligibility to study criteria, mainly based on age (6\u201359 months), on complete anti-HBV vaccination , and on the absence of advanced stage of immunodeficiency , HIV-exposed but uninfected (group-B), and HIV-exposed and infected (group-C).As per the study secondary outcomes, participants were furthered stratified according to feeding option and age in the frame of anti-HBV vaccine response.Evaluation of post-vaccination response was based on a component of three different HBV-specific biomarkers, among which anti-HBs, anti-HBc and HBsAg tests.0.10 for the mean negative control and of \u22650.80 for the mean positive control. Cut-off value was calculated using the mean negative control x 2.1. Samples were considered Anti HBS positive if D.O \u22651.00, Anti HBS negative or \u201cno vaccine response\u201d if D.O <1.00. \u201cProtective response\u201d was defined as Anti HBS titer >10 UI/ml; \u201clow response\u201d as Anti HBS titer: 1\u20139 UI/ml; and \u201cno response\u201d Anti HBS titer <1 UI/ml.Levels of anti-HBs antibody titer was measured to determine the threshold of effective protection in HBV vaccinated children, using the quantitative anti-HBs Sandwich enzyme-linked immunosorbent assay (ELISA) of CTK Biotech, USA (lot: E0604K3), as per the manufacturer\u2019s instructions. Briefly, reagents were brought at room temperature (18\u201325\u00b0c), wash solutions were prepared with phosphate buffer saline (1/30), and 50 \u03bcl of controls (negative and positive) and samples were added in respective wells. 50 \u03bcl of conjugate was added in each well (except for the blank), followed by incubation at 37\u00b0c for 60 min. Wells were washed and 50 \u03bcl of substrates A and B added in every well (including the blank), then incubated for 30 min at room temperature in a back room. 100\u03bcl of stop solution was then added to each well and reading of optical densities performed at 450 nm wave length, with reference to 630\u2013690 nm. Assay validation was performed with optical density of \u2264 This anti-HBs ELISA kit is coupled to the systematic detection of anti-HBc marker, irrespective of anti-HBs present or absent in the analysed serum .\u00ae, USA), with 50\u03bcl of serum. Validated results were reported as Anti-HBc \u201cresponse\u201d or \u201cno response\u201d. Both Anti-HBc results were all concordant, confirming HBV unexposed status.Anti-HBc marker was used to qualitatively detect any child with past/on-going exposure with HBV. In addition to aforementioned testing of anti-HBc, anti-HBc was also tested using the lateral flow chromatographic immunoassay HBV-5 Rapid Test of BioSino Biotechnology & Science Inc , with 100\u03bcl of serum. Validated results were reported as HBsAg reactive (HBV-positive) or non-reactive (HBV-negative).S) \u201clow-response\u201d (1\u20139 UI/ml anti-HBS), or \u201cno response\u201d (<1 UI/ml anti-HBS).Vaccine response was defined by a profile of anti-HBs positive, anti-HBc negative and HBsAg negative; further stratified as \u201cprotective-response\u201d were performed using Chi-square and Fisher Exact test where appropriate, with corresponding 95% CI. P-values, generated by SAS, SPSS, R software, were considered statistically significant if p<0.05.Administrative authorisation (Reference: N\u00b0005/14/DCHE/DA/CE/CHE/CNPS) was issued and ethical clearance for the study obtained from the Institutional Review Board (IRB) of the Essos Health Centre (Reference: N\u00b02014/001/EC-CHE). Mothers of potential participating children received detailed information on the study (with provision of an information sheet). Compliant mothers then provided each a signed written proxy-informed consent; this consent procedure was approved by the IRB. Laboratory results were freely offered for participant clinical benefits, data management was under strict confidentiality by using specific identifiers and restricted access.Study dataset is provided as supporting information .In total, 82 eligible children were enrolled in the study, all being anti-HBc and HBsAg negative. Sex ratio was similar (F/M: 5/4), median age was 27 [IQR: 9\u201347] months, min-max: 6\u201359 months. According to maternal HBV status, 22 children were born to HBV-negative mothers (of whom 7 were HBV-vaccinated), four from HBV-positive mothers, and 56 from mothers with unknown HBV-status.All HIV-infected children were normal clients attending the routine immunization program; all were receiving antiretroviral therapy and the majority were asymptomatic without any event of advanced immunodeficiency .According to feeding option of the 82 children during the first six months of life, 54.87% experienced exclusive-breastfeeding, 26.83% formula feeding, and 18.30% mixed feeding. All these children were not exposed to HBV, reported by a negative result both to anti-HBc and HBsAg testing.Overall assessment of anti-HBV post-vaccine response showed that: 80.49% (66/82) of children responded to anti-HBs testing (positive anti-HBsAb), indicating an immune response following anti-HBs vaccination, while 19.51% (16/82) did not responded to vaccination (negative anti-HBsAb).Analysis on the level of protective vaccine response revealed that only 45.12% (37/82) developed a protective immune response against HBV (anti-HBsAb \u226510IU/L) against 35.37% (29/82) who developed a low post-vaccine response.95% 0.933\u20137.5], p = 0.041), as shown in In group-A (HIV unexposed children), 82.14% (23/28) responded to HBV-vaccination and 60.71% (17/28) had a protective response. In the group of HIV-vertically exposed children, 79.63% (43/54) responded to HBV-vaccination and only 37.03% (20/54) had a protective response. Compared to HIV-unexposed children, the level of anti-HBV protection dropped significantly (~two fold) in HIV-exposed children as compared to : 2.627 [CI95%1.099\u201317.602], p = 0.065).Among HIV-exposed/uninfected children, 82.76% (24/29) responded to HBV-vaccination and 51.72% (15/29) had a protective response. Among HIV-exposed/infected children, 76.00% (19/25) responded to HBV-vaccination and only 20.00% (5/25) developed a protective response. Compared to HIV-exposed/uninfected children, the level of anti-HBV protection dropped in HIV-exposed/infected children , as shown in Among HIV-infected children, 76.00% (19/25) responded to HBV-vaccination and only 20.00% (5/25) had a protective response. Among all HIV-uninfected children (exposed or unexposed), 82.46% (47/57) responded to HBV-vaccination and 56.14% (32/57) had a protective response. Compared to HIV-uninfected children, the level of anti-HBV protection dropped significantly (~three fold) in HIV-infected children on exclusive breastfeeding, against 43.24% (16/37) on mixed (15) or formula feeding (22), OR: 1.079 [CI = 0.757 .95% 1.362\u201311.356], p = 0.004; with specifically 67.65% (23/34) \u22646 months vs. 0%, (0/5) 33\u201341 months, p = 0.008.Evaluation of vaccine efficacy according to the age ranges of children revealed that protective-response decreased from 67.65% (23/34) for age 6\u201314 months, 35.71% (5/14) for age 15\u201323 months, 20% (1/5) for age 24\u201332 months, 0% (0/5) for age 33\u201341 months . Most imFurthermore, among all HIV-exposed children (n = 54), age \u226412 vs. >12 months, respectively, confirmed the decreasing protection with higher age and HIV-infection: uninfected and infected .In highly endemic HBV and HIV settings like Cameroon, considering paediatric HIV-exposure when monitoring paediatric anti-HBV vaccine response might be of great clinical and public health relevance, and supports optimal performance of the EPI ,7,10\u201312.Though the majority (80.49%) of children were showed a response to anti-HBs testing, a non-negligible rate 19.51%) failed completely, highlighting the necessity for routine evaluation of post-vaccination to either confirm efficacy or determine eligibility for re-vaccination .51% fail. This inHaemophilus influenzae type b, etc) as earlier addressed [et al. in Kenya [Levels of anti-HBV protection dropped significantly for HIV-vertically exposed and/or infected children. This reflects the potential impact of maternal immunodeficiency on the child protectiveness ,9, and cddressed ,20,24. Tddressed ,22,25. Tin Kenya ,22,26.Though feeding options, especially exclusive breastfeeding, had no significant impact on anti-HBV vaccine response (p = 0.757) in our dataset, further investigations with higher sample size are needed on the impact of feeding option on anti-HBV vaccine response. This is because breast-feeding is generally known to positively modulate response to vaccines through significant developmental changes in Th-1 pipeline response , as compared to formula-fed infants . This isThe quality of response appears to be decreasing, as children grow older, thus supporting the fact that anti-HBV immunization stimulates higher production of Th2-type cytokines and higher levels of antigen-specific type 2 immunoglobulins in newborns than in adults . Though The high rate of non-consenting mothers is the major limitations to our study, as this is directly related to the statistical power in the three arms. Non-consenting were due to (a) believe that vaccination automatically provide the required protection, (b) fear that the child sample could be used for other purpose beside informed research goals, (c) fear of phlebotomy, (d) undisclosed or unknown motivations. These indicate needs for counselling parents on the importance of controlling vaccine efficacy, as well as sensitizing health staff on implementing such measures in routine care, for programmatic effectiveness .Higher sampling would have allowed closer age-match, gender-match, and wider immune status analysis with respect to anti-HBV vaccine response . Lack ofDespite high response to anti-HBV vaccination among Cameroonian children, protectiveness is poor in general (<50%), worse with HIV-exposure, and even worst with HIV-infection; and a decreasing response as children grow older. Strategies supporting early-age vaccination as well as implementing policies to monitoring post-vaccination response and cost-effective analysis of specific immunization algorithms for HIV vertically exposed- or infected-children would be of high public health benefit in resource-limited settings. These observations therefore merit wider sampling for confirmation towards a stronger policy-implementation.S1 File(ZIP)Click here for additional data file."} +{"text": "Correction to:Leukemia (2017) 31, 2717\u20132725; doi:10.1038/leu.2017.143; published online 23 May 2017This article was originally published under a CC BY-NC-ND 4.0 license, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the paper have been modified accordingly."} +{"text": "SALL4 and ZNF217 have been widely acknowledged as pivotal effectors stimulating embryonic immortalization as well as oncogenicity. Nevertheless, their prognostic worthiness towards solid tumors remains obscure. Hence we performed this comprehensive meta-analysis aiming to unveil the survival significance of both aberrantly expressed proteins.Overall we included 22 eligible entries comprising of 3093 participants. Over-expression of SALL4 and ZNF217 were negatively correlated with clinical prognosis of 3-year, 5-year, 10-year and disease-free survival in solid malignancies, irrespective of cancer types, source regions, mean-age and sex predominance. Results of sensitivity analysis additionally verified the stability of the pooled outcomes. No publication bias was observed on the basis of Egger's test and Begg's test.Studies were eventually included via database searching and rigorous eligibility appraisal. Data extraction and methodological assessment were implemented under a standard manner. Review Manager 5.3 and STATA 12.0 were utilized as statistical platforms following the recommendations by Cochrane Collaboration protocols.Aberrant amplification of SALL4 and ZNF217 serve as unfavorable predictors of survival expectancy among cancer sufferers, revealing great potential as targeted spots in future therapeutics. Over the past decade, the global healthcare system has been heavily burdened by soaring amount of solid malignancies . Includiin vivo and in vitro, SALL4 was first described as an oncoprotein in leukemia carcinogenesis [SALL4, expressively silenced in mature entities, is constitutively enriched in embryonic tissue and serves to maintain self-renewal capability , 4. Aberogenesis . Similarogenesis . NeverthAs a novel zinc finger transcription factor, ZNF217 was initially identified as a tumorigenic stimulator in breast carcinoma and was frequently amplified in diverse malignancies . HoweverTherefore, as representatives of zinc-finger transcriptional factors with independent performances, we performed this comprehensive meta-analysis aiming to clarify the prognostic roles of SALL4 and ZNF217 in solid malignancies and provide promising targeted spots.Deriving from 742 preliminarily retrieved entries, 22 observational cohorts were eventually selected (13 for SALL4 and 9 for ZNF217), with a total sample-size of 3093 participants (2111 for SALL4 and 982 for ZNF217). The selection flow chart was depicted in Figure n = 5) and liver cancer (n = 9) respectively. The wide spectrum of sample-size ranged from 38 to 337, with a median value of 144. Baseline parameters were statistically comparable between both contrastive groups. Additional details were demonstrated in Table Among the studies featuring SALL4 expression, the chief source region and cancer type were Japan (n = 4). Meanwhile, China (n = 3) became the major source region of literatures, followed by USA (n = 2) and France (n = 2). The median sample-size was 84, with a wide range from 44 to 319 . However, a poorer prognosis of cancer patients was observed concerning 5-year (P = 0.008) and 10-year disease free survival (P = 0.003) (Other types: P = 0.01). Meanwhile, its unfavorable impact on overall survival was similarly observed among patients with 5-year follow-up duration (Liver cancer: P < 0.00001) (Other types: P = 0.0003) .P = 0.004) (Mean-age < 60: P < 0.0001) and 5-year overall survival (Mean-age > 60: P = 0.04) (Mean-age < 60: P < 0.00001) disclosed a prognostic disadvantage among solid cancer patients, irrespective of 3-year (Mean-age > 60: 0.00001) .P < 0.00001) and 5-year survival expectancy (P < 0.00001). Similar outcomes were obtained in non-Asian subgroup (3-year: P < 0.00001) (5-year: P < 0.00001) .P < 0.0001) and 5-year overall prognosis .P = 0.0001) , 5-year (P = 0.003) and 10-year disease frees survival (P = 0.006) (Others types: P = 0.02) and 5-year prognosis respectively (Breast cancer: P = 0.01) (Others types: P = 0.0004) .P = 0.04) and 5-year follow-up duration (P < 0.00001). Nevertheless, there was no significant correlation between ZNF217 overexpression and long-term prognosis among patients with mean-age < 50 (3-year:P = 0.06) (5-year: P = 0.06) .P = 0.02) (Non-Asian: P = 0.005) and 5-year overall survival in solid malignancies (Asian: P = 0.002) (Non-Asian: P = 0.002) .P = 0.03) and 5-year overall survival in solid malignancies .P < 0.0001) and 5-year (P < 0.00001) overall survival rate, despite that Han et al. [P = 0.0002) and 5-year (P < 0.00001) overall survival in solid malignancies.Firstly, we performed sensitivity analysis by elimination of low-quality trials (NOS = 6). Outcomes remained stable in terms of 3-year or 5-year overall survival (P < 0.00001).Secondly, we implemented another sensitivity analysis by excluding studies with cytoplasmic staining. Nguyen et al. and Li eP = 0.125; ZNF217: P = 0.790) and Begg's test jointly confirmed that there was no publication bias among the included studies in both groups expression and clinical prognosis in solid malignancies; 3. The expression of SALL4 or ZNF217 was detected by immunohistochemistry (IHC).Studies were ruled out due to the following reasons: 1. Inadequate survival data for further quantification or the follow-up duration was shorter than 3 years; 2. Overlapped or duplicated studies; 3. Inappropriate article types such as reviews and case-reports; 4. Studies involving less than 10 participants as its sample-size.Two investigators independently implemented the selection process and any disagreement was settled by mutual discussion.Standardized extraction forms were applied for data extraction. Concerning the classification standards of SALL4 and ZNF217 expression, we generally recognized low-expression as < 25% of cell positivity while high-expression as > 25% of cell positivity. However, this criterion was adaptively adjusted if necessary, mainly based on original subgroups within individual trials. Two authors collaboratively extracted prognostic materials from main texts or Kaplan-Meier curves.Owing to the observational properties of included studies, a Newcastle-Ottawa Scale (NOS) was employed for methodological evaluation. The scale consisted of three categories including selection, comparability and outcome, with a maximum score of nine. Studies graded with more than six scores were identified as high quality trials in methodology. Each study was appraised by two evaluators in an independent way. Any disapproval was resolved by mutual discussion.I2 as a heterogeneity indicator with its value < 25%, 25%\u201350% and > 50% defined as low, moderate and significant heterogeneity respectively. A moderate or significant heterogeneity was adjusted by a random-effects model, otherwise a fix-effects model was preferred. The statistical significance within all comparisons was mathematically signified as P < 0.05. Moreover, sensitivity analysis was applied to examine the stability of pooled outcomes. Publication bias was statistically analyzed via Egger's test and Begg's test, based on the results from STATA 12.0.Our quantitative calculation was performed on Review Manager 5.3 under Cochrane Collaboration protocols. Odds ratio (OR) along with Mantel-Haenszel model were adopted for dichotomous variables. We acknowledged"} +{"text": "Visceral adiposity is associated with higher productions of C-reactive protein (CRP) and interleukin-6 (IL-6). Inflammation of obese adipose tissues could contribute to systemic metabolic dysregulation, especially thermogenic activity of white adipose tissues, namely, beige adipogenesis, characterized by altered irisin expression. Thus, we investigated the roles of inflammation and adipocyte beiging in Chinese centrally obese (CO) adults with metabolic syndrome (MetS). This cross-sectional study was conducted on 54 CO and 58 non-CO subjects drawn from 1492 Chinese people with age and sex matched during November 2010 and August 2013. Twenty (37.0%) of the CO subjects fulfilled the IDF worldwide definition of MetS. Serum CRP, IL-6, and irisin levels were examined. Higher CRP and IL-6, but lower irisin, levels were manifested in MetS versus non-MetS subjects with or without CO. Multiple linear regression identified high-density lipoprotein cholesterol level as the only independent risk factor for irisin level. Categorized by median of CRP and IL-6 levels, a lower irisin level was only observed in high CRP group. Under the condition of central obesity, chronic inflammation and impaired beige adipogenesis are associated with MetS in Chinese adults. People with metabolic syndrome (MetS) are at a heightened risk for overt diabetes and cardiovascular events . RelativC-reactive protein (CRP), an established marker of inflammation, is an acute phase protein secreted from liver, playing a key role in the underlying causes of endothelial dysfunction as indicated by decreased nitric oxide and increased endothelin-1, as well as reduced plasminogen activator inhibitor-1 (PAI-1) levels . Moreove\u03b3 coactivator-1 \u03b1/uncoupling protein-1 signaling cascades to elicit beige adipogenesis, muscular mitochondrial biogenesis, and fibre-type switching, resulting in loss of body weight Low level of HDL-C Raised blood glucose This case-matched, cross-sectional study was conducted on 112 subjects drawn from 1492 Hong Kong Chinese people aged from 24 to 86 years with age and sex matched during November 2010 and August 2013 , 28. AllWaist circumference and blood pressure were measured by a trained researcher (Yu AP) . Waist ct- or Mann\u2013Whitney U tests. Univariate and stepwise multiple linear regressions were employed to estimate the correlations of each clinical characteristic with serum CRP, IL-6, and irisin levels. A two-tailed test with P \u2264 0.05 was considered significantly different. All statistical analyses were conducted using SPSS Statistics 24.0.Data were presented as mean\u2009\u00b1\u2009SD (standard deviation) or median (25th and 75th percentiles) for continuous variables and assessed for normality by Shapiro-Wilk test. Either one-way analysis of variance or Kruskal-Wallis test was used for comparing differences across MetS, CO, and non-CO groups. Group differences were compared using either Student's P < 0.01 and P < 0.001), systolic BP (P < 0.001), diastolic BP (P < 0.001), plasma triglyceride (P < 0.001), and fasting blood glucose (P < 0.001), but lower HDL-C (P < 0.001) in MetS compared with non-MetS subjects with or without CO, respectively, whereas there was no significant difference between CO and non-CO, non-MetS subjects, except waist circumference (P < 0.001).The clinical characteristics of our subjects were categorized by the presence of CO in P < 0.01) and non-CO, non-MetS subjects (P < 0.01) (P < 0.05) and non-CO, non-MetS subjects (P < 0.01).There were significantly higher serum levels of CRP and IL-6 in MetS versus CO ( < 0.01) . On the P < 0.001), diastolic BP (P = 0.04), and triglycerides (P < 0.001), but negatively correlated with HDL-C levels (P < 0.001). Serum IL-6 levels were positively associated with waist circumference (P = 0.03), systolic BP (P = 0.008), diastolic BP (P = 0.04), triglycerides (P < 0.001), and fasting plasma glucose (P = 0.002) and also negatively correlated with HDL-C levels (P = 0.002). More importantly, serum irisin levels were negatively correlated with systolic BP (P = 0.04) and fasting plasma glucose (P = 0.03), but positively associated with HDL-C levels (P = 0.001) (P < 0.001) and irisin (P = 0.005) levels, respectively, whereas systolic BP was found to be the only independent risk factor for serum IL-6 levels (P = 0.006).The correlations of clinical characteristics with serum levels of CRP, IL-6, and irisin were analyzed using univariate and stepwise multiple linear regression models. Serum CRP levels were shown to be positively correlated with systolic BP (= 0.001) . StepwisP < 0.001] and IL-6 levels (Tables P < 0.001) and triglycerides (P = 0.01), but lower HDL-C (P = 0.001) and irisin (P = 0.05) levels in high versus low CRP groups (P = 0.003) and fasting plasma glucose (P = 0.009), but lower HDL-C (P = 0.02), were observed , serum irisin levels were also negatively correlated with waist circumference (R = \u22120.15). In addition, stepwise multiple linear regression determined HDL-C as the only independent predictor for serum irisin levels, substantiating circulating irisin as a surrogate marker of improved lipid profile as previously described [Adipose tissue is metabolically active in nature and a highly secretory endocrine organ that is capable of modulating signals in appetite, energy expenditure, immune responses, inflammation, insulin sensitivity, and so forth . In enerescribed \u201333.\u03b2 levels [P = 0.28). This phenomenon could be attributed to dual functions of IL-6 in both pro- and anti-inflammation, and its conflicting roles are largely dependent on (1) its expression levels of which lower extent exerts anti-inflammatory actions and vice versa, (2) different cell contexts as exemplified by its varying roles in hepatocytes, endothelial cells, skeletal muscle, and macrophages, and (3) its selective involvement in either classic or alternative transsignaling, where components of the transsignaling were positively associated with MetS, endothelial dysfunction, and arterial stiffness in male subjects at high risk of cardiovascular disease, and effective blockade of this signaling has been experimentally proven to attenuate innate immunity-triggered inflammatory responses in phenotypically IL-6-transsignaling knockout-like mice [It is known that in obesity, inflamed adipose tissues could cause impaired beige adipogenesis and hence less efficient energy metabolism through complex interactions between macrophages and adipocytes , yet the\u03b2 levels . In contike mice . HoweverThe present study provides a novel insight on how chronic inflammation affects the thermogenic activity of adipose tissue possibly through altered circulating levels of irisin in Chinese adults. Future studies are warranted to further delineate the exact mechanism(s) underlying the interplay among a spectrum of inflammatory mediators and irisin."} +{"text": "Scientific Reports5: Article number: 16768; 10.1038/srep16768 published online: 11252015; updated: 10202017.This Article contains errors in the legend of Figure 5.A) Systemic zinc chloride significantly inhibited NaHS-induced scratching. (B) Local application of ZnCl2 (i.d. 5\u2009nmol) significantly inhibited NaHS-induced scratching in both RTX- and vehicle-treated mice. (C) ZnCl2 (i.d. 5\u2009nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (D) ZnCl2(i.pl. 5\u2009nmol) significantly inhibited NaHS-induced flinching. (E) Systemic ascorbic acid significantly inhibited NaHS-induced scratching. (F) Asc (i.d. 1\u2009nmol) significantly inhibited NaHS-induced scratching in both RTX- and vehicle-treated mice. (G) Asc (i.d. 1\u2009nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (H) Asc (i.pl. 1\u2009nmol) significantly inhibited NaHS-induced flinching. (I) Local application of mibefradil (Mib) (i.d. 5\u201325\u2009nmol) dose-dependently inhibited NaHS-induced scratching in mice. (J) Mib (i.d. 10\u2009nmol) significantly inhibited NaHS-induced scratching in RTX-treated mice. (K) Mib (i.d. 10\u2009nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (L) Mib (i.d. 10\u2009nmol) significantly inhibited NaHS-induced flinching. All data are expressed by means\u2009\u00b1\u2009SEM. n\u2009=\u20096\u20138 mice per group. *P\u2009<\u20090.05; **P\u2009<\u20090.01, ***P\u2009<\u20090.001 vs. vehicle control, Student\u2019s t test\u201d.\u201c(should read:A) Local application of mibefradil (Mib) (i.d. 5\u201325 nmol) dose-dependently inhibited NaHS-induced scratching in mice. (B) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced scratching in RTX-treated mice. (C) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (D) Mib (i.d. 10 nmol) significantly inhibited NaHS-induced flinching. (E) Systemic zinc chloride significantly inhibited NaHS-induced scratching. (F) Local application of ZnCl2 (i.d. 5 nmol) significantly inhibited NaHS-induced scratching in both RTX- and vehicle-treated mice. (G) ZnCl2 (i.d. 5 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (H) ZnCl2 (i.pl. 5 nmol) significantly inhibited NaHS-induced flinching. (I) Systemic ascorbic acid significantly inhibited NaHS-induced scratching. (J) Asc (i.d. 1 nmol) significantly inhibited NaHS-induced scratching in both RTX- and vehicle-treated mice. (K) Asc (i.d. 1 nmol) significantly inhibited NaHS-induced both forelimb wiping and hindpaw scratching in cheek model. (L) Asc (i.pl. 1 nmol) significantly inhibited NaHS-induced flinching. All data are expressed by means\u2009\u00b1\u2009SEM. n\u2009=\u20096\u20138 mice per group. *P\u2009<\u20090.05; **P\u2009<\u20090.01, ***P\u2009<\u20090.001 vs. vehicle control, Student\u2019s t test\u201d.\u201c("} +{"text": "This E.\u00a0coli is serotype O25b and sequence type 131, a pandemic clonal group, causing worldwide antimicrobial-resistant infections.The draft genome sequence has been determined for an extended-spectrum-\u03b2-lactamase (ESBL)-producing ( Escherichia coli sequence type 131 (ST131) has emerged as a globally dispersed pathogen, the predominant lineage causing extraintestinal infections, and is often resistant to antibiotic treatment . The ESBL-producing E.\u00a0coli strain E10394 (= CCUG 62462) was isolated from a urinary tract infection (UTI) sample as part of an outbreak of ESBL-producing Enterobacteriaceae in a neonatal postsurgery ward at Sahlgrenska University Hospital, Gothenburg, Sweden, in 2008 with command line arguments \u201c\u2014stringency 3\u2014retain_unpaired.\u201d After quality filtering, 1,424,760 paired reads and 2,356/75 unpaired forward/reverse reads were retained for analysis. The high-quality reads were assembled de novo with SPAdes version 3.7.0 -IIa on contig LZET01000076, and aadA5, mph(A), sul1, and dfrA17 on contig LZET01000047. PlasmidFinder (IncFIA (nucleotide accession no. AP001918) on contig LZET01000040, IncFIB (accession no. AP001918) on contig LZET01000042, and IncFII (accession no. AY458016) on contigs LZET01000050, LZET01000068, and LZET01000072. In addition, genes involved in type IV secretion systems (T4SS) were identified, using CONJscan (F), relaxases , and type IV coupling proteins (T4CP). Three small plasmids were completely assembled. First, a 5,627-bp plasmid (contig LZET01000060), which was 99% identical to the pJJ1886_3 plasmid previously described in E.\u00a0coli strain JJ1886 (accession no. CP006787.1), was found. Second, a 5,166-bp plasmid (contig LZET01000063), and last, a 1,718-bp plasmid (contig LZET01000087), which was 99% identical to plasmid pEC648 previously described in E.\u00a0coli strain ST648 (accession no. CP008716.1), were found.The = CCUG 6462 was iLZET00000000. The version described in this paper is version LZET00000000.1.This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no."} +{"text": "Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect. Ventricosa Baum ex Romero-Zarco and Avena sect. Avena) were estimated to be in the early to middle Miocene, and the A. sativa lineages were dated to the late Miocene to Pliocene. These periods coincided with the mild seasonal climatic contrasts and the Mediterranean climate established in the Mediterranean Basin. Our results suggest that polyploidy, lineage divergence, and complex reticulate evolution have occurred in Avena, exemplifying the long-term persistence of tetraploids and the multiple origins of hexaploids related to paleoclimatic oscillations during the Miocene-Pliocene interval in the circum-Mediterranean region. This newly-resolved infrageneric phylogenetic framework represents a major step forward in understanding the origin of the cultivated oat.Understanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of Genome duplication following hybridization is common among flowering plants, and is found in nearly a quarter of Poaceae that provide crops and fuel worldwideAvena L. (Poaceae) contains ca. 29 species exhibiting considerable morphological and ecological diversity in the Mediterranean Basin, Eastern Africa, Europe, Asia, and the Americas4Avena: Avenotrichon (Holub) Baum, Ventricosa Baum ex Romero-Zarco, Agraria Baum, Tenuicarpa Baum, Ethiopica Baum, Pachycarpa Baum, and Avenax\u2009=\u200914), AB- and A\u2019C (DC)-genome tetraploids (4x\u2009=\u200928), to ACD-genome hexaploids (6x\u2009=\u200942)9The genus ds 4x\u2009=\u20092, to ACD-A. clauda DurA. canariensis Baum & Raj. & SampA. insularis Ladiz., A. maroccana Grand., and A. murphyi Ladiz. may contain the D genome found in hexaploid oat11Avena.Molecular data support a close relationship between D and A genomes12A. strigosa Schreb. DNA was homologous to the A-genome sequences of the cultivated oatA. canariensisA. longiglumis DurA. weistii SteudA. damascena Rajah & Baum, A. hirtula Lag., and A. wiestii Steud. rather than from one particular species9812Cultivated oat offers a model for unraveling the dynamic evolutionary process of polyploid crops in the Mediterranean BasinA. sativa21A. clauda)Given chromosome structural differentiation, the C-genome origin of cultivated oat has been under intense scientific scrutiny. Eighteen chromosomes were involved in intergenomic translocations between C and A genomes of Avena with 28 (96.55%) species 3 polyploid cool-season grasses, e.g., fodder ryegrassesThe Mediterranean Basin, encompassing an area between 28\u00b0\u201348\u00b0N and 10\u00b0\u201339\u00b0E, is one of the 34 global biodiversity hotspots with c. 24,000 plant speciesth 28 96.5% specieAvena species parsimony-informative characters. The maximum likelihood (ML) analyses and the Bayesian inference (BI) showed an identical topology for Avena . Three clades and two nodes were observed in the ppcB1 phylogram: A\u2019C-PPI , and A- and A\u2019-type sequences hexaploids ] and hexaploids ] (A. wiestii and A\u2019(D)-type sequences of hexaploids (without A. fatua and A. nuda)] (PP\u2009=\u20090.80) , and A\u2019 and C-type sequences of tetraploids and hexaploids (without A. nuda)] (PP\u2009=\u20090.54) (Avena (The monophyly of \u2009=\u20090.98) ; node A\u2019erilis)] ; node ABntalis)] ; A-PPI -types of \u2009=\u20091.00) . C-type \u2019C-PPIII . As for in Avena .GBSSI matrix had 1352 characters, including exons 9, 10, 11, 12, 13, and 14, and introns 8, 9, 10, 11, 12, 13, and 14, with the lengths of 53\u2009bp, 81\u2009bp, 194\u2009bp, 88\u2009bp, 129\u2009bp, 22\u2009bp, 47\u2009bp, 148\u2009bp, 153\u2009bp, 127\u2009bp, 154\u2009bp, 152\u2009bp, and 4\u2009bp, respectively (GBSSI data provided 434 (32.1%) parsimony-informative characters. The ML and BI analyses generated different topologies for Avena ] were observed in the GBSSI tree: A\u2019C-GBI and hexaploid A. fatua] , A\u2019-type sequences of A. maroccana and A. murphyi and hexaploids] (Avena (The monophyly of \u2009=\u20091.00) and 4. I\u2009=\u20091.00) ; AB-GBI \u2009=\u20090.93) ; and AB&aploids] . The cla] ] were observed in the GBSS1 tree: A\u2019C-GBI , and A\u2019-type sequences of A. maroccana and A. murphyi)] (PP\u2009=\u20090.50) and hexaploids (without A. nuda and A. sterilis)] (PP\u2009=\u20090.66) (A. sterilis). Clade AB-GBI was sister to clade AB-GBII, and this group (PP\u2009=\u20090.66) plus clade A\u2019C-GBII (PP\u2009=\u20090.50) was assigned to a single monophyletic lineage (PP\u2009=\u20090.98), which was sister to clade A\u2019C-GBI. This large clade received strong support in Avena -type sequences of tetraploids \u2009=\u20091.00) ; A\u2019C-GBI\u2009=\u20090.50) ; AB-GBI \u2009=\u20090.50) ; and AB-\u2009=\u20090.66) . Clades in Avena .GBSSI sequences were identified in four accessions of A. sativa , consistent with its hexaploid origin. These sequences fell into three distinct groups. In clade A\u2019C-GBI, C-type sequences of A. sativa clustered with C-genome diploids, C-type sequences of tetraploids and hexaploids (without A. nuda) , and C]-types of \u2009=\u20091.00) . A-type AB-GBII , respectanalysis , and conanalysis .gpa1 matrix had 1034 characters, including exons 10, 11, 12, introns 10, 11, and 12; with the lengths of 22\u2009bp, 94\u2009bp, 60\u2009bp, 681\u2009bp, 92\u2009bp, and 85\u2009bp, of which 137 (13.25%) were parsimony-informative. ML and BI analyses had an identical topology for Avena . Seven clades were observed for the gpa1 tree and five hexaploids (without A. nuda)] ; A\u2019C-GPII ; A-GPI (A. canariensis and A-type sequence of A. hybrida) ; AB-GPI ; A\u2019C-GPIII (A. hirtula and A\u2019-type sequences of A. maroccana) ; and AB-GPII . Clades A-GPII, A-GPI, AB-GPI, A\u2019C-GPIII, and A\u2019C-GPII formed one monophyletic lineage , and this lineage in turn was sister to clade A\u2019C-GPI with strong support , then the large group was sister to clade C-GPI with strong support (The monophyly of pa1 tree : C-GPI (\u2009=\u20091.00) .gpa1 sequences were identified in a single accession of A. sativa (Liu 310). These sequences fell into two distinct groups, with A\u2019(D)-type sequence of A. sativa nested within clade AB-GPII, and C-type sequences of A. sativa nested within clade A\u2019C-GPI (Two [A\u2019(D)- and C-] types of A\u2019C-GPI .Avena ; A\u2019C-NRR \u2009+\u2009AB-NRR . Clade A\u2019C-NRR\u2009+\u2009AB-NRR was sister to clade C-NRR in Avena were parsimony-informative. The BEAST analysis generated a well-supported tree, which was identical to the topologies obtained from ML and BI analyses of Avena . Two clain Avena . Here weAvena was 20.04 [95% highest posterior density (HPD) 3.56\u201335.06] mya (node 1). This was also the stem ages for clades C-NRR and A\u2019C-NRR\u2009+\u2009AB-NRR, whose crown ages were 10.71 (HPD: 1.62\u201320.25) and 14.54 (HPD: 2.68\u201325.02) mya, respectively (nodes 2 and 3). The crown age of clade A\u2019C-NRR\u2009+\u2009AB-NRR was also the divergence time for nodes A\u2019C-NRR and AB-NRR (nodes 4 and 8). The crown ages of the A. sativa lineages were 2.43, 2.46, and 2.97 mya , respectively (The uncorrelated-rate relaxed molecular clock suggests that the crown age of ectively .Avena were identified by the plastid data: the C-genome diploid lineage (Avena sect. Ventricosa) containing A. clauda, A. eriantha, and A. ventricosa in clade C-NRR; and the A-genome diploid-polyploid lineage (Avena sect. Avena) containing other congeneric species in clade AB-NRR\u2009+\u2009A\u2019C-NRR -genome tetraploids and hexaploids.Two strongly supported infrageneric lineages within \u2009A\u2019C-NRR . Members\u2019C-PPIII and A\u2019C-\u2019C-PPIII . In the Avena sect. Avena was proposed for the A-genome diploid-polyploid lineage including nodes with low support in the plastid tree , A. damascena (Ad-genome), and A. longiglumis (Al-genome) clustered with three A\u2019C(DC)-genome tetraploids in node A\u2019C-PPII , A. canariensis (Ac-genome), A. damascena (Ad-genome), and A. prostrata (Ap-genome) clustered with AB-genome tetraploids in node AB-PPI , A. damascena (Ad-genome), and A. longiglumis (Al-genome) clustered with AB-genome tetraploids in clade AB-GBII -genome tetraploids originated from different A-genome diploid ancestors 5gpa1 tree showed specific genetic divergence from A. hirtula and A. hispanica (group 3) in high-density GBS analysis6) and the genome size (9.08\u2009\u00b1\u20090.1112), A. hirtula can be easily differentiated from the two As-genome diploids, that have a similar genome size to the smallest Ad-genome diploid A. damasceneAvena lusitanica and A. hispanica might represent ecotypes of A. hirtula found in the circum-Mediterranean, western Asia, and EuropeWithin the As-genome diploids, tid tree . Howeverca group showed sAvena sect. Ventricosa and the C-copy sequences of A\u2019C-genome tetraploids plus hexaploids was a novel discovery which suggested their C-genome donor to be the ancestor of Avena sect. Ventricosa. This was consistent with the hypothesis that the paleotetraploidy events pre-dated and potentially triggered divergence of the extant A\u2019C(DC)-genome tetraploids in narrow ranges of the Mediterranean Basingpa1 tree, A\u2019C(DC)-genome tetraploids together with hexaploids comprised the clade A\u2019C-GPI - and C-genome diploid ancestors to form A\u2019C -genome tetraploids. The second step includes subsequent recent allohexaploidy events involving hybridization between DC-genome tetraploids and the more recent A-genome diploid progenitors to form the extant ACD-genome hexaploids A\u2019C-GPI . TherefoppcB1 tree, i.e., A. atlantica, A. longiglumis, and A. wiestii were embedded within the A\u2019C-PPII-A1, A\u2019C-PPII-A2, and A-PPI subclades located in node A\u2019C-PPII and clade A-PPI (FL intron2 clones (CIav 9053)A. wiestii is certainly different from other As-genome diploids. Although the different genome forms of A. wiestii were close in genome sizeA wiestii deserves further investigation. Two plausible explanations can be proposed for the ploidy level of allelic variation found in A. wiestii. First, the three diploids may have arisen by allopolyploidy and subsequent unequal diploidization led to heterozygotes. Second, introgression may have brought about very subtle morphological and genetic changes in Avena and 10.71 (HPD: 1.62\u201320.25) mya, respectively seem to correlate with highly seasonal climatic oscillation. Geographic isolation might have contributed to genetic differentiation in the progenitor-derivative species pair, the presumed D(or A\u2019)-genome progenitors having disjunct distributions in the Mediterranean region A. wiestii (eastern-most) from A. atlantica (western-most). Therefore, the independent hexaploidy events of cultivated oat were modulated by harsh climatic oscillation, thus A. sativa was able to adapt to new habitats.Cultivated oat may have arisen multiple times in response to selection pressure such as geographic isolation. The long-term aridity of the Mediterranean Basin summer became more severe along a south-eastern to north-western gradient during the late Miocene to PlioceneAvena represents a remarkable model to study because its history of polyploidy, lineage divergence, and complex reticulate evolution. The complex evolution of cultivated oat and its close relatives involved paleotetraploidy events between the ancient A(or A\u2019)- and C-genome diploid ancestors and subsequent recent allohexaploidy events between A\u2019C(DC)-genome tetraploids and the more recent A-genome diploid progenitors. The pattern of recurrent polyploidizations in Avena and their temporal relationships with paleoclimatic oscillations is unparalleled among polyploid crops occurring in the circum-Mediterranean region4AvenaSupplementary Table S1Eighty-nine accessions of 27 species were sampled to represent the morphological diversity and geographic range of six sections in phosphoenolpyruvate carboxylase B1 (ppcB1), granule-bound starch synthase I (GBSSI) and G protein alpha subunit 1 (gpa1), were used. The ppcB1 gene encodes PEPC enzyme for the oxaloacetate replenishment of the tricarboxylic acid cycle in C3 plantsGBSSI gene encodes GBSSI enzyme for the amylose synthesis in plantsgpa1 gene encodes a G-protein \u03b1 subunit for signal transduction in flowering plants247448Three low-copy nuclear genes, et alppcB1, GBSSI, and gpa1) and plastid fragments, which were amplified using designed or published primers and protocols listed in Table S2Escherichia coli TOP10 competent cells following the protocol of TOPO TA Cloning Kit . The resulting sequences were edited using Sequencher v.5.2.3 and aligned with MUSCLE v.3.8.31http://tree.bio.ed.ac.uk/software/seal/). All sequences were deposited in GenBank .Genomic DNA was extracted following Liu Phylogenetic analyses were performed using maximum likelihoodhttp://tree.bio.ed.ac.uk/software/tracer). All resulting trees were then combined with LogCombiner v.1.6.1 (http://beast.bio.ed.ac.uk/) with 25% burn-ins. The remaining trees were used to calculate the Bayesian posterior probabilities (PP) for internal nodes. Data sets and phylogenetic trees are available at TreeBase based on a likelihood ratio testAvena. Three plastid markers were partitioned using BEAUTI v.1.8.2 (within BEAST) with the best fit model determined by Modeltest v.3.7 of three runs was obtained using TreeAnnotator v.1.8.2 (within BEAST) with a PP limit of 0.5 and mean lineage heights. The convergence between two runs was checked using the \u201ccumulative\u201d and \u201ccompare\u201d functions in AWTYHow to cite this article: Liu, Q. et al. Unraveling the evolutionary dynamics of ancient and recent polypoidization events in Avena (Poaceae). Sci. Rep.7, 41944; doi: 10.1038/srep41944 (2017).Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations."} +{"text": "The first author is listed incorrectly in the citation. Please view the correct citation here:https://doi.org/10.1371/journal.pone.0186602Guardo AC, G\u00f3mez CE, D\u00edaz-Brito V, Pich J, Arnaiz JA, Perdiguero B, et al. (2017) Safety and vaccine-induced HIV-1 immune responses in healthy volunteers following a late MVA-B boost 4 years after the last immunization. PLoS ONE 12(10): e0186602."} +{"text": "Leishmania but not found in mammals, is considered a potentially useful target for chemotherapy against leishmaniasis. Leishmania (Viannia) braziliensis is endemic in Latin America and causes American tegumentary leishmaniasis. We demonstrated that IPCs are localized internally in parasites, using a specific monoclonal antibody. Treatment with 5 \u03bcM myriocin rendered promastigotes 8-fold less infective than controls in experimental hamster infection, as determined by number of parasites per inguinal lymph node after 8 weeks infection, suggesting the importance of parasite IPC or sphingolipid derivatives in parasite infectivity or survival in the host. IPC was isolated from promastigotes of three L. (V.) braziliensis strains and analyzed by positive- and negative-ion ESI-MS. The major IPC ions were characterized as eicosasphinganine and eicosasphingosine. Negative-ion ESI-MS revealed IPC ion species at m/z 778.6 (d20:1/14:0), 780.6 (d20:0/14:0), 796.6 (t20:0/14:0), 806.6 (d20:1/16:0), and 808.6 (d20:0/16:0). IPCs isolated from L. (V.) braziliensis and L. (L.) major showed significant differences in IPC ceramide composition. The major IPC ion from L. (L.) major, detected in negative-ion ESI-MS at m/z 780.6, was composed of ceramide d16:1/18:0. Our results suggest that sphingosine synthase in L. (V.) braziliensis is responsible for synthesis of a long-chain base of 20 carbons (d20), whereas SPT in L. (L.) major synthesizes a 16-carbon long-chain base (d16). A phylogenetic tree based on SPT proteins was constructed by analysis of sequence homologies in species of the Leishmania and Viannia subgenera. Results indicate that SPT gene position in L. (V.) braziliensis is completely separated from that of members of subgenus Leishmania, including L. (L.) major, L. (L.) infantum, and L. (L.) mexicana. Our findings clearly demonstrate sphingoid base differences between L. (V.) braziliensis and members of subgenus Leishmania, and are relevant to future development of more effective targeted anti-leishmaniasis drugs.Inositol phosphorylceramide (IPC), the major sphingolipid in the genus Leishmania. The prevalence of leishmaniasis worldwide was recently estimated as 12 million cases, with ~1.5\u20132 million new cases per year and Leishmania (Viannia), species of which are responsible for various clinical pathologies and related biological, molecular, and biochemical features has received considerable research attention during the past three decades because of their biological relevance as structural cell membrane components, and as bioactive compounds involved in cell-cell recognition, cell adhesion, cell growth, and signal transduction , with condensation by serine palmitoyltransferase (SPT) of L-serine and palmitoyl-CoA (16:0) to form 3-ketosphinganine, followed by reduction of this intermediate to produce sphinganine in a reaction that involves NADPH that contain two hydroxyl groups, and are denoted by the letter \u201cd\u201d (di) followed by the number of carbons in the chain. SLs in plants and fungi are derived from dihydroxylated or trihydroxylated sphingoid bases, and are denoted respectively by the letter \u201cd\u201d or \u201ct.\u201d Trihydroxylated sphingoid bases in plants and fungi are later acylated to form phytoceramide, a precursor of inositol phosphorylceramides (IPCs) and glycosyl inositol phosphorylceramides (GIPCs) donovani promastigotes , sphingomyelin (SM), IPCs, and GIPCs braziliensis promastigotes are present in fractions enriched in membrane microdomains resistant to non-ionic detergent at 4\u00b0C mexicana major braziliensis contain mainly C14:0 fatty acid braziliensis, one of the major etiologic agents of cutaneous and mucocutaneous leishmaniasis in South America. In cutaneous leishmaniasis, parasites spread from the skin to the naso-oropharyngeal mucosa. The causative factors for such mucosal dissemination and resulting mucosal disease are poorly understood. Effective systemic treatment of cutaneous leishmaniasis caused by L. (V.) braziliensis will presumably reduce the risk of mucosal disease development. We focused on characterization of IPCs from L. (V.) braziliensis mainly because these molecules, and enzymes involved in their specific biosynthetic pathways, are promising targets for anti-Leishmania drug development tandem MS with electrospray ionization (ESI) in both negative-ion mode [M-H]Stock solutions of 2 mM myriocin (a SL synthesis inhibitor) were prepared in dimethyl sulfoxide and stored at \u221270\u00b0C for a maximum of 1 month.L. (V.) braziliensis strains MHOM/BR/1987/M11272, MHOM/BR/2001/BA778 and MHOM/BR/1975/M2903 were cultured at 23\u00b0C by several passages of log-phase parasites in Medium 199 supplemented with 10% heat-inactivated fetal calf serum , 2 mM L-glutamine (Sigma-Aldrich), 0.02 mg ml\u22121 bovine hemin, 100 U ml\u22121 penicillin, 100 \u03bcg ml\u22121 streptomycin, and 2% sterile male human urine (complete medium). The starting inoculum (0.4 \u00d7 107 cells ml\u22121) consisted of parasites isolated from early stationary phase. Parasites were collected either in log-phase or after 48 h (stationary phase). L. (V.) major strain MRHO/SU/59/P (LV39) was also cultured at 23\u00b0C in complete Medium 199.Promastigotes of Leishmania (Viannia) braziliensis MHOM/BR/2001/BA778 promastigotes were cultured (starting inoculum 0.4 \u00d7 107 cells ml\u22121) in complete medium in the presence of myriocin (5 \u03bcM) or equivalent vehicle concentration for 6 days. Cell growth was estimated by counting cells with a hemocytometer (Improved Double Neubauer). Parasite viability was determined by SYTOX\u00ae Blue staining as per the manufacturer's protocol, and shown to be >85% in control and myriocin-treated cultures. Parasite cultures were washed with PBS, cells were resuspended in PBS, and 1 \u00d7 106 parasites (0.05 ml) were inoculated subcutaneously in footpads of female golden hamsters (Mesocricetus auratus) (groups of four). Eight weeks after inoculation (infection), inguinal lymph nodes were removed and homogenized in 3 ml culture medium. Parasite suspension from each node was plated in complete Medium 199, and parasites were quantified by limiting dilution in 96-well plates containing 120 \u03bcl well\u22121. Plates were kept at 23\u00b0C for 7 days. Parasite number (PN) per lymph node was estimated based on the highest dilution at which parasites were detected after 7 days \u00d7 3 . Experiments were performed in triplicate. All animal procedures were conducted in accordance with the recommendations of the Guide for the Care and Use of Laboratory Animals of the Brazilian National Council of Animal Experimentation (www.cobea.org.br). The protocol was approved by the Research Ethical Committee of Federal University of S\u00e3o Paulo .Leishmania IPC; Godoy et al., MS in prep) and SST-1 .Parasites were fixed with 2% formaldehyde in 10 mM phosphate buffer, pH 7.2, containing 150 mM NaCl (PBS), for 10 min. Some fixed cells were permeabilized with 0.1% saponin. Cells were washed, resuspended in 1 ml PBS, and 100 \u03bcl of the solution was added to coverslips pretreated with 0.1% poly-L-lysine. Coverslips were blocked for 3 h with 0.1% gelatin in PBS and for 1 h with 10% skimmed milk and 1% bovine serum albumin (BSA) in PBS. Parasites were incubated sequentially with primary antibody LST-1 and with chloroform/methanol (CM) 20 psi, and nebulizing gas (N2) 40 psi. Each MS2 individual ion fragmentation was optimized with regard to capillary and collision energy to minimize variations in relative ion abundance resulting from differences in dissociation rates. The CID gas was argon at 2 mTorr. The inlet system consisted of a direct infusion pump (Harvard Apparatus), and methanol/ water with 5 mM ammonium formate as mobile phase, flow rate 30 \u03bcl min\u22121. Precursor ion scan (PREIS) for detection of ion containing phosphoinositol derivative m/z 259 (inositol monophosphate anion) and m/z 241 was performed in negative ion mode with capillary energy -110 V and collision energy 40 V. Typically, 20 scans were used for accumulation of non-targeted scan range, and 30 scans for analysis of precursor ions. Ion characterization was performed by CID in negative and positive ion mode with collision energy 15, 30, or 45 V with ESI source. Data acquisition was performed using the Varian MS Workstation program, V. 6.9. Sample analysis was conducted in positive-ion and negative-ion ESI modes with respective needle voltages 5.8 and 5 kV infantum, L. (L.) donovani, L. (L.) mexicana, L. (L.) major, L. (V.) braziliensis, L. (V.) guyanensis, L. (V.) panamensis, T. brucei, and T. cruzi CL Brener. Sequences were chosen by homology search using BLAST software with annotated yeast and/or human proteins as baits. Sequences were retrieved from GenBank or GeneDB (TriTrypDB) .Phylogenetic analysis was performed using gene data from SPT enzymes from many distinct species of the family Trypanosomatidae: B) Table . ID sequt-test, using GraphPad Prism software program V. 5.0 . Differences between means were considered statistically significant for p < 0.01. All experiments were performed in triplicate.Quantitative data were analyzed by Student's Leishmania surface, parasites were double-labeled with monoclonal antibodies (mAbs) directed to L. (V.) braziliensis glycolipids (mAb SST-1), and to Leishmania IPC (mAb LST-1). Representative images from a z-stack confocal series are shown in Figure To determine whether IPCs are expressed on the mAb SST-, and to mAb SST-, and to L. (V.) braziliensis IPC expression, growth rate, and cytokinesis , and at m/z 241, corresponding to inositol-1,2-cyclic phosphate anion (InsP-H2O). ESI-MS of [M-H]\u2212 ions of IPC fractions purified from three L. (V.) braziliensis strains were performed, and similar spectral profiles were observed for all strains. In full scan of IPC fraction from negative-ion ESI-MS of L. (V.) braziliensis (M11272), major ions were detected at m/z 778.6 and 780.6, and minor components were detected at m/z 796.6, 806.6, and 808.6 major IPC fraction showed a distinctive profile: the major IPC ion was at m/z 778.6, relative abundance of m/z 780.6 was significantly reduced, and minor IPC ions were detected at m/z 796.6 and 806.6 braziliensis, and at m/z 780.6, 782.6, 798.6, and 808.6 for L. (L.) major braziliensis and L. (L.) major braziliensis and L. (L.) major braziliensis and 241 (InsP-H2O).CID was performed for major IPC ions detected in Figures and at ms Figure , phosphoL. (V.) braziliensis [M+H]+ ions at m/z 780.6, using collision energy of 15V, yielded expected fragments at m/z 762 (M-H2O), 520 (M-InsP), and 502 (M-InsP-H2O) . Application of higher collision energy (45 V) for the ion at m/z 780.6 , suggesting that this compound was d20:1/14:0-IPC. Figure L. (V.) braziliensis [M+H]+ ion at m/z 780.6.Ceramide moieties were characterized by CID in positive-ion mode using various collision energies. MS/MS product ion spectra of ) Figure . We also6 Figure , in addiL. (L.) major [M+H]+ ion at m/z 780.6, using collision energies 15 and 30V, gave rise as expected to ions at m/z 762 (M-H2O), 520 (M-InsP), and 502 (M-InsP-H2O) braziliensis. The ion profile, in terms of LCB and fatty acid composition, was distinct from that of L. (V.) braziliensis. Ions were detected at m/z 236 (indicating the presence of d16:1 sphingoid base), and fragments at m/z 308 and 284 , identifying the 18:0-fatty acyl substituent, as described by Hsu et al. braziliensis [M+H]+ ion at m/z 782.6 using collision energies 15 and 45 V , 522 (M-InsP), 504 (M-InsP-H2O), 294 , 252, and 228 , indicating that this compound is d20:0/14:0-IPC.ESI-MS/MS spectra of Figures generateL. (V.) braziliensis. ESI-MS/MS spectra of [M-H]\u2212 ions at m/z 796.6, 806.6, and 808.6 are shown in Figures m/z 259 (InsP) and 241 (InsP-H2O) were detected in all IPC ions.We also characterized minor IPC ions of + ion at m/z 798.6 allowed us to characterize the ceramide moiety. Using collision energy 45V , 520 (M-InsP-H2O), 328, 310, 292 (characteristic products of phytosphingosine t20:0), 252, and 228 . These findings suggest that this ion (m/z 798.6 in positive-ion mode) corresponds to t20:0/14:0-IPC.Analysis of ESI-MS/MS spectra of the [M+H]V Figure , the spe+ ion at m/z 808.6 using collision energy 45 V , 530 (M-InsP-H2O), 292 (characteristic of sphingoid base d20:1), 280, and 256 (corresponding to fatty acid 16:0 acyl substituent) , suggesting that this compound is d20:1/16:0-IPC.Analysis of ESI-MS/MS spectra of the [M+H]V Figure generate+ ion at m/z 810.6 using collision energy 45 V , 532 (M-InsP-H2O), 294 (characteristic of d20:0), 280, and 256 (corresponding to fatty acid 16:0 acyl substituent) , suggesting that this compound is d20:0/16:0-IPC.Analysis of ESI-MS/MS spectra of the [M+H]V Figure generateL. (V.) braziliensis are summarized in Table L. major braziliensis display predominantly 20-carbon LCBs , and C14:0 and C16:0 fatty acids. Positive-ion ESI-CID-MS/MS of IPC ions from L. (V.) braziliensis did not detect product ions related to d16:0 (m/z 238) or d16:1(m/z 236). Positive-ion ESI-CID-MS/MS of L. (L.) major IPC ion at m/z 780.6 did not detect sphingoid base product related to d20:1 (m/z 292) braziliensis strains M11272, BA778, and M2903.IPC proposed structures and positive- and negative-ion ESI-CID-MS/MS fragments of IPC ions from ) Figure , Table 2L. (V.) braziliensis is responsible for synthesis of 20-carbon LCB (d20), whereas L. (L.) major presents mainly 16-carbon LCB (d16), and T. brucei and T. cruzi SLs present mainly 18-carbon sphingoid bases (d18) braziliensis, L. (V.) guyanensis and L. (V.) panamensis) were completely separated from those of the Leishmania subgenus (L. (L.) infantum, L. (L.) mexicana, and L. (L.) major), and comprised two distinct clades. SPTs of T. brucei and T. cruzi also represented different clades.SPT in Leishmania SPTs, we also analyzed N-terminal and catalytic portions of SPTs of L. (V.) braziliensis and L. (L.) major to determine whether sequence homologies refer specifically to the catalytic portion. Phylogenetic results were similar for sequences of SPT whole proteins, N-terminal regions, and catalytic regions braziliensis showed that IPCs and GIPLs are not co-localized in L. (V.) braziliensis promastigotes; GIPLs are found on the parasite surface whereas IPCs are localized internally. Labeling of IPCs was observed only when parasites were permeabilized with 0.1% saponin, confirming the internal localization of IPCs. Previous studies have demonstrated the involvement of Leishmania SLs in a variety of biological processes, including differentiation, replication, trafficking, and virulence braziliensis promastigotes treated with the SPT inhibitor myriocin displayed reduced IPC accumulation and incomplete cytokinesis braziliensis infectivity. Golden hamsters were infected by subcutaneous footpad injection of promastigotes treated (or not) with 5 \u03bcM myriocin for 6 days. After 8 weeks of infection, PN was counted in inguinal lymph nodes, and found to be ~8-fold lower for myriocin-treated parasites in comparison with controls. Our findings suggest that IPCs (and/or their intermediate SLs) are important for L. (V.) braziliensis infectivity, for their survival during the first few hours inside macrophages, for differentiation to amastigotes, and for amastigote proliferation. We obtained similar results in a previous study of L. (L.) amazonensis mouse experimental infection, in which parasite burden was reduced by infection of mouse footpads with promastigotes pretreated with a different SL inhibitor: the IPC synthase inhibitor aureobasidin A major displayed defective membrane trafficking events in extracellular promastigotes, thus delaying promastigote infection in BALB/c mice braziliensis contain mainly C14:0 fatty acid major and L. (L.) donovani contain mainly C18:0 fatty acids braziliensis strains, isolated from patients living in different regions of Brazil: reference strain MHOM/BR/1975/M2903 from a subject in Par\u00e1 (Northern Brazil), strain MHOM/BR/01/BA788 from a cutaneous leishmaniasis patient in Bahia State (Northeastern Brazil), and strain MHOM/BR/1987/M11272 from a cutaneous leishmaniasis patient in Paran\u00e1 State (Southern Brazil). IPC molecules were detected by negative-ion ESI-MS, as described by Hsu et al. braziliensis, and to identify novel IPC structures. The major IPC ions detected by negative-ion ESI-MS were at m/z 778 and 780 for all three strains, regardless of whether ions were isolated at logarithmic or stationary growth phase. These two ions accounted for >70% of IPCs expressed in the parasites. In negative-ion mode, the full scan profile of IPC fractions isolated from the three strains showed ions at m/z 778.6, 780.6, 796.6, 806.6, and 808.6 major and L. (L.) donovani major donovani braziliensis IPC [M+H]+ ions at m/z 780.6 and 782.6 displayed fragments at m/z 292 (20:1-LCB), 294 (20:0-LCB), and 228 (C14:0-fatty acyl substituent). IPC ions with the same mass in positive-ion mode (m/z 780 and 782) from L. (L.) major presented d16:1 and d16:0 LCBs, respectively, with C18:0-fatty acid. IPCs are the major SLs in Leishmania; these findings therefore suggest strongly that L. (V.) braziliensis preferentially synthesizes sphingoid bases through condensation of L-serine and stearoyl-CoA (18:0) to produce d20:0 in LCBs and ceramide, whereas L. (L.) major and L. (L.) donovani (subgenus Leishmania) preferentially synthesize d16:0 sphingoid base through condensation of L-serine and myristoyl-CoA (14:0) braziliensis showed that the SPT protein sequence of L. (V.) braziliensis is completely separated from those of species in the Leishmania subgenus, suggesting that L. (V.) braziliensis and the Leishmania subgenus species represent different clades. The constructed trees suggest that genetic factors are involved in SPT separation. More precise studies are needed to clarify this issue. The two Leishmania subgenera may have differentiated at different times, as evidenced by the SPT protein data, and this separation may be responsible for observed differences in enzyme functions and specificities. The overall conclusion from the SPT phylogenetic tree is that neither L. major nor L. braziliensis is closer to T. cruzi or T. brucei. It appears that the common SPT ancestor of L. braziliensis and L. major separated from the Trypanosomatidae prior to the separation of Leishmania.In the present study, we investigated the role of SLs in u et al. , who dem6 Figure . PredomiL. (V.) braziliensis vs. L. major, in addition to differences in LCBs, show distinctive fatty acid compositions. In L. (V.) braziliensis IPCs, the major fatty acid is C14:0, and there are only trace amounts of fatty acid 16:0, as detected in positive-ion mode ESI-MS/MS at m/z 808.6 and 810.6. In contrast, the major fatty acid in L. (L.) major and L. (L.) donovani IPCs is stearic acid (C18:0) braziliensis, preferentially use d20:0 and myristoyl-CoA (14:0) or palmitoyl-CoA (16:0), whereas members of the Leishmania subgenus, e.g., L. (L.) major and L. (L.) donovani, preferentially use d16:0 and stearoyl-CoA (18:0) amino)hexanoyl)sphingosine C6-ceramide.The existence of o et al. reporteda et al. showed tLeishmania enzyme specificities in LCB synthesis and concurrent ceramide synthesis will contribute to the development of more effective drugs having high ligand efficiency indices against L. (V.) braziliensis, L. (L.) major, or L. (L.) donovani, but low (or zero) ligand efficiency to mammalian host cells.Future studies on ED and AS conceived and designed the experiments, and wrote the manuscript. ED performed the experiments. ED and MT performed mass spectrometric analysis. RW and DB performed phylogenetic studies. ED and RM performed confocal microscopy and image analysis. HT critically reviewed and revised the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR). Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC) format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A\u221702:02g (0.096), B\u221707:02g (0.082), C\u221707:02g (0.180), DQB1\u221706:02 (0.157), and DRB1\u221715:01 (0.072). The most common haplotype was A\u221703:01g~B\u221707:02g~C\u221707:02g~DQB1\u221706:02~DRB1\u221715:01 (0.067), which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies. The ~4\u2009Mb human leukocyte antigen (HLA) complex on chromosome 6 in humans is amongst the most polymorphic gene regions in the genome . SeventeBone Marrow Donors Worldwide (BMDW) is a centralized databank of HLA phenotypes and other relevant data of unrelated stem cell donors which aims to support HSCT programmes . The SouDonor registries continuously try to improve their recruitment strategies through increasing donor numbers , recruitIn this study, we describe HLA allele and haplotype frequency data from 237 donors registered with the SABMR, which serves as the source of unrelated marrow donors in South Africa. Frequencies of HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 alleles and haplotypes were analyzed with the aim of developing a resource for disease association, anthropology, and evolutionary studies. Furthermore, these data will support models for population-specific vaccine development and willhttps://hml.nmdp.org/MacUI/.Two hundred and thirty-seven (237) SABMR-registered-consenting volunteer bone marrow donors HLA typed at varying resolutions were included in this study. This subset was accessed following an extensive reconsenting procedure of donors in the SAMBR. The self-reported ethnic grouping of the study population was Asian, Black, Chinese, Coloured, White, and some unknown. High-resolution typing has recently been adopted by SABMR, with most donors having low-resolution typing (two digit) , 21 whichttp://www.ebi.ac.uk/ipd/imgt/hla/) [Allele and haplotype frequencies were estimated by resolving phase and allelic ambiguities using the expectation-maximization (EM) algorithm , 37 in Hgt/hla/) , 3 and rgt/hla/) . Global gt/hla/) . MAC codSelf-reported ethnicity was not considered for analysis in this study owing to redundancy and simplicity of this classification as previously discussed , 42. Onep < 0.05), with HLA-C and HLA-DQB1 having insignificant (p > 0.05) differences between expected and observed heterozygosity (p < 0.001), as summarized in In this donor subset, HLA-A, HLA-B, and HLA-DRB1 genotypes deviated from the expected HWE proportions (zygosity . No signzygosity . In addi\u221702:01g (0.096), A\u221703:01g (0.093), and A\u221701:01g (0.057); B\u221707:02g (0.082), B\u221708:01g (0.049), and B\u221758:02 (0.048); C\u221707:02g (0.180), C\u221707:01g (0.104), and C\u221704:01g (0.091); DRB1\u221715:01 (0.072), DRB1\u221715:03 (0.065), and DRB1\u221707:01 (0.057); and DQB1\u221706:02 (0.157), DQB1\u221703:01 (0.139), and DQB1\u221705:01 (0.118).The full list of alleles including those derived from MACs and their frequencies are listed in \u221733:95~B\u221707:231N (1.08725E-06), A\u221703:01g~C\u221707:02g~DQB1\u221703:02 (1.03519E-06), and A\u221711:01g~C\u221701:02g~DRB1\u221701:01~DQB1\u221705:01 (2.8507E-06) were less frequent two, three, and four locus haplotypes, respectively (\u221703:01g~B\u221707:02g~C\u221707:02g~DRB1\u221715:01~DQB1\u221706:02 being the most frequent (0.067).All two, three, four, and five (extended) haplotype frequencies are detailed in Supplementary ectively . The twehttps://hml.nmdp.org/MacUI) were analyzed using a robust Hapl-o-Mat [Although this study had a limited sample size of 237, we provide an in-depth analysis of HLA diversity in a subset of donors in the SABMR. Mixed resolution HLA typing data with multiple allele codes (pl-o-Mat package pl-o-Mat . Althougp < 0.001 in p > 0.05), which contrasts to the significant deviation (p < 0.05) observed in the current study encoded alleles [The main thrust of our study has been the ability to estimate, with high confidence, haplotype frequencies from mixed resolution typings including MAC , despitAlthough results reported here are from a small subset of SABMR registered donors, allele and haplotype frequencies generated by Hapl-o-Mat tool could be"} +{"text": "Bacillus velezensis YJ11-1-4 is a strain that exhibits broad-spectrum antimicrobial activity against various pathogens. It was isolated from doenjang, a traditional Korean fermented soybean paste. The genome comprises a single circular chromosome of 4,006,637\u00a0bp with 46.42% G+C content without plasmids. Bacillus velezensis was first proposed by Ruiz-Garc\u00eda et al. which has revealed good antimicrobial activities against various foodborne pathogens, including Bacillus\u00a0cereus, Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, and Aspergillus flavus subsp. Flavus, was isolated from homemade doenjang, and its complete genome was sequenced.a et al. as a surdization . Recentldization suggesteB. velezensis YJ11-1-4 was sequenced using a Pacific Biosciences RS II platform with a 20-kb SMRTbell template library at Macrogen . It generated a total of 969,934,944\u00a0bp (about 198-fold coverage) with 112,837 reads. The sequencing reads were assembled using the Hierarchical Genome Assembly Process version 2.0 (HGAP2.0). The assembled genome of strain YJ11-1-4 comprises a single circular chromosome of 4,006,637\u00a0bp with a 46.42% G+C content without plasmids. The complete genome sequence was annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The tRNA and rRNA genes were detected using tRNAscan-SE encoded by bacABCDE (AAV30_01545 to AAV30_01565) (acnABCDEF (AAV30_04380 to AAV30_04405) (fenEDCBA (AAV30_10135 to AAV30_10160), bacillomycin D (targeting yeast) encoded by bmyDABC (AAV30_10275 to AAV30_10290), surfactin (targeting virus) encoded by srfABCD (AAV30_17390 to AAV30_17405), and an LCI gene (targeting some Gram-negative bacteria) (AAV30_17550) . Strain B.\u00a0velezensis YJ11-1-4 was deposited in NCBI under GenBank accession number CP011347.The genome information for"} +{"text": "The genetic basis for biofilm formation among nontyphoidal salmonellae (NTS) remains poorly understood. This draft genome submission provides initial insights on the genetic differences between biofilm-forming and non-biofilm-forming clinical and environmental NTS serovars. Nontyphoidal salmonellae (NTS) are pathogens of global importance with varSalmonella enterica serovars , which possess diametrically opposed biofilm phenotypes (biofilm formers and non-biofilm formers) as assessed by the crystal violet binding assay , and S.\u00a0Dublin MN-12 (D15-051537) were isolated from a poultry barn, bovine lymph node, and porcine lung, respectively. The three non-biofilm-forming strains S.\u00a0Heidelberg MN-618, S.\u00a0Typhimurium variant 5 MN-62 (D15-043619), and S.\u00a0Dublin MN-69 (D15-009047) were isolated from a poultry barn, bovine brain, and porcine lung, respectively.The NTS isolates sequenced in this study include pairs of strains from each of three ng assay . The thrde novo assembled by the A5-miseq pipeline (http://rast.nmpdr.org), and PGAP, of the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The occurrence of antibiotic resistance genes, clustered regularly interspaced short palindromic repeat (CRISPR) regions, prophages, Salmonella pathogenicity islands (SPIs), and number of plasmids on assembled sequences were predicted using ResFinder version 2.1 (http://crispr.i2bc.paris-saclay.fr/Server/), PHAST (https://cge.cbs.dtu.dk/services/SPIFinder), and PlasmidFinder version 1.3 and processed on the MiSeq platform . Paired-end reads were pipeline . The asssion 2.1 , CRISPRF), PHAST , SPI Finsion 1.3 , respectsion 1.3 .S.\u00a0Heidelberg MN-714 , S. Typhimurium variant 5 MN-74 (D15-052810) , and S.\u00a0Dublin MN-D12 (D15-051537) possessed a higher number of plasmids than the non-biofilm-forming strains S.\u00a0Heidelberg MN-618 (ColpVC and IncX1), S.\u00a0Typhimurium variant 5 MN-62 (D15-043619) (no plasmid), and S.\u00a0Dublin D MN-69 (D15-009047) (IncA/C2). Biofilms provide an ideal niche for plasmid exchange and also promotes plasmid stability relative to non-biofilm formers. A larger genome size would favor increased functional gene content and could enhance the ability of organisms to form biofilms under stressful conditions. It is also noteworthy that the biofilm-forming strains D15-04361 , S.\u00a0Dublin MN-12 (D15-051537), S.\u00a0Heidelberg MN-618, S.\u00a0Typhimurium variant 5 MN-62 (D15-043619), and S.\u00a0Dublin MN-69 (D15-009047) have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Whole-genome sequences of the six NTS isolates"} +{"text": "In the article titled \u201cChitosan Prevents Gentamicin-Induced Nephrotoxicity via a Carbonyl Stress-Dependent Pathway\u201d , the namhttps://www.doi.org/10.1016/j.toxlet.2013.01.024. Additionally, the same picture of Figure 2(e) was presented as Figure 2(c). The corrected Also, there was an error in Figure 2. Figures 2(b) and 2(e) were inadvertently reused from Yi-Chieh Li, Yi-Min Shih, and Jen-Ai Lee, \u201cGentamicin caused renal injury deeply related to methylglyoxal and N\u025b-(carboxyethyl)lysine (CEL),\u201d Toxicology Letters, Volume 219, Issue 1,"} +{"text": "Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze proteins and cold-shock proteins, genes involved in bioremediation of xenobiotic compounds including naphthalene, and genes with chitinolytic and N-acetylglucosamine utilization properties and also plant-growth-influencing properties. In this genome report, we present a complete genome sequence of A. alpinus strain R3.8 and its annotation data, which will facilitate exploitation of potential novel cold-active enzymes.The online version of this article (doi:10.1186/s40793-017-0264-0) contains supplementary material, which is available to authorized users. Antarctica. The optimum growth temperature range of this bacterium is 10\u201316 \u00b0C, which rendered it a promising source for discovery of novel cold-adapted enzymes. The complete genome sequence of 10.1601/nm.20084 strain R3.8 was generated using Single Molecule Real Time sequencing technology to provide a rapid and complete insight into its biotechnological potential. Here, we highlight various genome features that indicate the potential biotechnological value of 10.1601/nm.20084 strain R3.8 in the context of xenobiotic biodegradation and metabolism, chitin utilization, and as a potential component in bio-fertilizers.The production of cold-adapted enzymes by psychrotolerant bacteria has important scientific and industrial interest due to their highly specific activity and catalytic efficiency at low and moderate temperatures . The useArea No.129 . Strain R3.8 was isolated using basal medium supplied with C6-HSL as sole carbon source. An isolation temperature of 4\u00a0\u00b0C was used to select for psychrophilic or psychrotolerant bacteria maintained on Luria Bertani (LB) agar and urease gamma subunit [AOC05_18490]). Urease is important in catalyzing one of the metabolic pathways involved in microbial-induced calcite precipitation. MICP is a promising approach in the containment of heavy metals such as lead and cadmium in contaminated soils , 24.Various other xenobiotic biodegradation genes and pathways of 10.1601/nm.20084 strain R3.8 are available from the PATRIC server.Chitinase is a biotechnologically-important enzyme widely used in waste management industries for the degradation of chitinous waste into simpler depolymerized substances , in agriN-acetylglucosamine utilization being identified, including beta-hexosaminidase (EC 3.2.1.52) , eukaryotic type N-acetylglucosamine kinase (EC 2.7.1.59) [AOC05_12050], PTS system, N-acetylglucosamine (EC 2.7.1.69) [AOC05_12345], N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) [AOC05_15120], eukaryotic type N-acetylglucosamine kinase (EC 2.7.1.59) [AOC05_15120], chitinase (EC 3.2.1.14) [AOC05_02965], N-acetyl-glucosamine kinase 2, ROK family (EC 2.7.1.59) [AOC05_03295], transcriptional regulator of N-acetylglucosamine utilization, GntR family [AOC05_07215] and glucosamine-6-phosphate deaminase (EC 3.5.99.6) [AOC05_10045].The full chitinolytic potential of 10.1601/nm.20084 strain R3.8 was also identified here, with various genes involved in chitin and N-(5\u2032-phosphoribosyl) anthranilate isomerase [AOC05_12350] were identified. Production of bacterial IAA is important to assist plants to overcome abiotic stresses and inhibitory compounds, and thus contributes to plant growth stimulation [Application of psychrotrophic PGP bacteria to vegetation can promote growth and improve cold tolerance of crops . From thmulation . SeveralAntarctica. The strain was sequenced to explore its biotechnological potential. By analyzing the complete genome of 10.1601/nm.20084 strain R3, we identified genes involved in xenobiotic biodegradation and metabolism, and chitin utilization, as well as genes that potentially promote plant growth. Further comparative genomic studies with related isolates together with functional studies will provide better understanding of the potential biotechnological value of this strain.We report the complete genome sequence of 10.1601/nm.20084 strain R3.8 that was originally isolated from the soil collected from Rothera Point, Adelaide Island, maritime"} +{"text": "Delineation of high-risk LTBI can, however, allow for chemoprophylaxis and curtail majority cases of active tuberculosis (ATB). There is epidemiological evidence to support the view that LTBI in context of HIV-1 co-infection is high-risk for progression to ATB relative to LTBI among HIV-ve persons. We recently showed that assays of M.tb thymidylate kinase (TMKmt) antigen and host specific IgG can differentiate ATB from LTBI and or no TB . In this study, we aimed to expose the differential levels of TMKmt Ag among HIV+ve co-infected LTBI relative to HIV-ve LTBI as a strategy to advance these assays for designating incipient LTBI.Precise designation of high risk forms of latent Mycobacterium TMKmt host specific IgM and IgG detection Enzyme Immuno-Assays (EIA) were conducted on 40 TB exposed house-hold contacts (22 LTBI vs. 18 no TB (NTB) by QunatiFERON-TB GOLD\u00ae); and TMKmt Ag detection EIA done on 82 LTBI (46 HIV+ve vs 36 HIV-ve) and 9 NTB (American donors). Purified recombinant TMKmt protein was used as positive control for the Ag assays.IgM levels were found to be equally low across QuantiFERON-TB GOLD\u00ae prequalified NTB and TB exposed house-hold contacts. Higher TMKmt host specific IgG trends were found among TB house-hold contacts relative to NTB controls. TMKmt Ag levels among HIV+ve LTBI were 0.2676 \u00b1 0.0197 (95% CI: 0.2279 to 0.3073) relative to 0.1069 \u00b1 0.01628 (95% CI: 0.07385 to 0.14) for HIV-ve LTBI (supporting incipient nature of LTBI in context of HIV-1 co-infection). NTB had TMKmt Ag levels of 0.1013 \u00b1 0.02505 (5% CI: 0.0421 to 0.1606) (intimating that some were indeed LTBI).TMKmt Ag levels represent a novel surrogate biomarker for high-risk LTBI, while host-specific IgG can be used to designate NTB from LTBI.The online version of this article (10.1186/s12879-018-3007-y) contains supplementary material, which is available to authorized users. Mycobacterium tuberculosis (M. tb) as per our prior work ) relative to HIV-ve LTBI (<0.14: 0.1069 \u00b1 0.01628[95% CI: 0.07385 to 0.14]) (see Table On one hand:(a) for n=128 and prevalence of 80.0 , the sensitivity, specificity, PPV and NPV of pre-set TMKmt Ag capture-EIA-OD cut-off for differentiating ATB from NTB alone at 95% CI were respectively: 99.0 , 68.0 , 92.7 , and 94.4 [yielding a ROC-area of 83.5 ] compared to 96.6 , 21.1 , 78.9 and 66.7 [ROC-area 58.8 ] obtained using pre-set TMKmt host-specific IgG-EIA-OD cut-offs on n=154 participants and prevalence of 74.0 . On the other hand, (b) for n=220 and prevalence of 63.0 , the sensitivity, specificity, PPV and NPV of pre-set TMKmt Ag capture-EIA-OD cut-off for differentiating ATB from both LTBI & NTB at 95% CI were respectively: 73.9 , 90.2 , 92.7 and 67.3 [ ROC-area of 82.1 ] compared to 92.6 , 34.8 , 78.9 and 64.0 [ROC-area 63.7 ] obtained using pre-set TMKmt host-specific IgG-EIA-OD cut-offs for n=167 participants and prevalence of 72.0 as a surrogate for disease progression. Although several M.tb targets inclusive of lip-arabinomannose (LAM), IP-10, early secretory antigen 6(ESAT-6) and colony filtrate protein 10 (CFP-10) have previously been developed for the purpose of detecting TB, none meets the criteria for designating delineating high-risk LTBI [tb targets [A key limitation of our work\u2014as is the case for all projects that aim to advance novel biomarkers for LTBI, is the absence of a gold standard for precisely designating LTBI and NTB \u201319. As nisk LTBI \u20137. On pa targets , 51. It targets \u201319.In conclusion, TMKmt Ag and host specific IgG antibodies offer us novel surrogate biomarkers for LTBI in-context of HIV-1 co-infection. Precisely, Levels of TMKmt\u00a0Ag represent a novel surrogate biomarker for high-risk LTBI, while host-specific IgG can be used to designate NTB from LTBI. TMKmt host specific IgM levels might be relevant towards evaluating TB exposure among residents of low TB endemic areas (NTB) who recently travelled to a high TB endemic area.Additional file 1:This file shows processing of the duplicate EIA readings for TMKmt Ag capture among the 46 HIV+ve LTBI and 36 HIV-ve LTBI relative to the 9 NTB controls and 2 rTMKmt positive controls. Overall, readings of blanks were subtracted from the average ODs of the test wells to obtain a corrected average ODs used to draw the graphs. (XLSX 29 kb)"} +{"text": "Drosophila wing imaginal discs. We used genetic tools to ablate the wing primordium to induce regeneration, and carried out transcriptional profiling of the regeneration blastema by fluorescently labeling and sorting the blastema cells, thus identifying differentially expressed genes. Importantly, by using genetic mutants of several of these differentially expressed genes we have confirmed that they have roles in regeneration. Using this approach, we show that high expression of the gene moladietz (mol), which encodes the Duox-maturation factor NIP, is required during regeneration to produce reactive oxygen species (ROS), which in turn sustain JNK signaling during regeneration. We also show that JNK signaling upregulates mol expression, thereby activating a positive feedback signal that ensures the prolonged JNK activation required for regenerative growth. Thus, by whole-genome transcriptional profiling of regenerating tissue we have identified a positive feedback loop that regulates the extent of regenerative growth.Regenerating tissue must initiate the signaling that drives regenerative growth, and sustain that signaling long enough for regeneration to complete. How these key signals are sustained is unclear. To gain a comprehensive view of the changes in gene expression that occur during regeneration, we performed whole-genome mRNAseq of actively regenerating tissue from damaged Drosophila imaginal discs, the epithelial structures in the larva that will form the adult animal during metamorphosis, have been an important model system for tissue repair and regeneration for over 60 years. Here we show that damage-induced JNK signaling leads to the upregulation of a gene called moladietz, which encodes a co-factor for an enzyme, NADPH dual oxidase (Duox), that generates reactive oxygen species (ROS), a key tissue-damage signal. High expression of moladietz induces continuous production of ROS in the regenerating tissue. The sustained production of ROS then continues to activate JNK signaling throughout the course of regeneration, ensuring maximal tissue regrowth.Regenerating tissue must initiate the signaling that drives regenerative growth, and then sustain that signaling long enough for regeneration to complete. The capacity to regenerate damaged or lost organs or limbs is significantly greater in some animals than others. The use of model organisms with varying degrees of regenerative capacity, from whole-body regeneration in planaria and hydra, to limb regeneration in amphibians, organ and fin regeneration in zebrafish, and the limited tissue regeneration that occurs in mammalian models, has advanced our understanding of this process , antz (mol) , AdoR (F0039747) , and kay0001297) , Nlaz (FE FBgn00117 activi0003900) , and zfh0004606) showed u (corto) . Some offeration ,73, and % were dipuckered, can be observed . Vari. VariDroresponse , during response ,85 and aresponse . After acontrols . A seconneration . Additio (Alp-4) , the 4E-4) , an89) /TM6B (gift from M. Uhlirova)[nlaZ:GFP[R2] (gift from M. Ganfornina)[w1118; P{10xStat92E-GFP}1 (BL26197)[cn1P{PZ}dve01738/CyO; ry506 (BL11073)[cn1P{PZ}sm05338/CyO; ry506 (BL11403)[y1w*; P{PTT-GB}LamCCB04957ttvCB04957/SM6a (BL51528)[y1w*; Mi{PT-GFSTF.1}AdoRMI01202-GFSTF.1/TM6C, Sb1Tb1 (BL60165)[y1w*; P{lacW}Thork13517 (BL9558)[y1w*; Mi{PT-GFSTF.0}kayMI05333-GFSTF.0 (BL63175)[w1118; PBac{corto-GFP.FPTB}VK00037 (BL42268), w1118; PBac{Hr78-GFP.FLAG}VK00037 (BL38653), w1118;PBac{NC2\u03b2-GFP.FPTB}VK00033 (BL56157), y1 w*; Mi{PT-GFSTF.0}CatMIO4522-GFSTF.0 (BL60212)[Hml\u0394RFP (gift from K. Bruckner)[TRE-red and gstD-GFP (gifts from D. Bohmann)[Ets21Cf0369 (BL18678)[y1w*; Mi{MIC}CG9336MI03849 (BL36397)[y1w67c23; P{lacW}Col4a1K00405/CyO (BL10479)[y1w67c23; P{lacW}vkgk00236 (BL10473)[P{PZ}Thor06270cn1/CyO; ry506 (BL11481)[w1; P{UAS-Sod1.A}B36 (BL24754), w1; P{UAS-CatA}2 (BL24621), w1; P{UAS-Sod2.M}UM83 (BL24494), w1118; PBac{RB}mole02670/CyO (BL18073)[y1sc*v1; P{TRiP.HMS02560}attP40 (UAS-molRNAi) (BL42867), y1v1; P{TRiP.GL00678}attP40 (UAS-DuoxRNAi) (BL38907), y1v1; P{TRIP.GL00678}attP40 (UAS-NoxRNAi) (BL32902), y1w*; Mi{MIC}NoxMI15634/SM6a (BL61114)[pucE69 [UAS-JNKDN [w* hepr75/FM7C (BL6761)[w*; P{neoFRT}82B p38a1 (BL8822)[Flies were reared on standard molasses medium at 25\u00b0 C except during regeneration experiments. The following (BL37920), y1,w67c(BL10440), y1, w* (BL56274), P{PZ}Al(BL12285), w1118; BL11515), y1w67c(BL12173), ry506PS (BL684), w;;pBACUhlirova), nlaZ:GFnfornina), w1118; (BL26197), cn1P{P(BL11073), cn1P{PBL11403), y1w*; (BL51528), y1w*; (BL60165), y1w*; (BL63175), w1118; (BL60212), Hml\u0394RFP15, y1w603, y1w*(BL36397), y1w67c(BL11481), w1; P{U(BL61114), pucE69 AS-JNKDN , w* hepr (BL6761), w*; P{n (BL8822).Immunostaining was carried out as previously described .Anitbodies and dilutions used were Anti-Nubbin (1:500) (gift of S. Cohen) , mouse aAlexa Fluor (AF) secondary antibodies from Molecular Probes were AF488, AF555 and AF633 (used at 1:500). Nuclei were labeled with DAPI (Sigma)(1:5000).EdU incorporation was carried out using the click-it EdU Alexa Fluor 594 Imaging kit (Molecular Probes) as previously described . SamplesImmunostained samples were imaged on a Zeiss LSM 700 confocal microscope and images were processed using ZenLite, Adobe Photoshop, and Image J software. Bright-field imaging of adult wings was done on an Olympus SZX10 microscope using the CellSens Dimension software, and images were processed using Image J.ROS were detected in imaginal discs using Dihydroethidium (DHE) using the protocol described in Owusu-Ansah et al. , with slgstD-GFP, whose expression was not uniform and thus was quantified by measuring GFP intensity in the entire pouch area. Average intensities of multiple wing discs were combined to calculate the final average intensity plotted in the graphs. For measuring the pouch area, a maximum projection of all the confocal slices was taken and the Nubbin-expressing area measured in Image J. Graphs were plotted in Excel, R, and GraphPad Prism 7.0.Fluorescence intensity analysis was performed using single confocal slices. Average intensity was calculated by measuring intensity values in three equal-sized boxes in the pouch region of the wing disc in Image J, except for the For imaginal disc measurements and immunofluorescence quantifications, the Welch\u2019s t-test was performed using R and GraphPad Prism 7.0. For the adult wing size assay, chi-squared tests were performed using GraphPad online tools. Statistical analyses for adult wing measurements were performed using Welch\u2019s t-test.nub-GFP/+; rn-Gal4, GAL80ts, UAS-rpr /+, while the mock-ablated controls had the genotype nub-GFP/+; rn-Gal4, GAL80ts/+. Cells were isolated for the transcriptional profile as previously described [The ablated regenerating discs had the genotype escribed . Brieflyescribed . RNA quaDrosophila melanogaster genome with a maximum of 2 mismatches permitted. Intron length was set between 20 and 150,000, and a gene model was provided as GTF . FPKM estimation was done using Cufflinks (v.0.0.7) [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101797).Fastq reads were trimmed using FASTQ Quality Trimmer (v.1.0.0) and adaptor sequences were removed using Clip (v.1.0.1) in Galaxy . Reads wv.0.0.7) , and botv.0.0.7) , geometrv.0.0.7) . All biov.0.0.7) . The datv.0.0.7) and are S1 Fig(A) Variation in the size of the wing pouch as marked by anti-Nub immunostaining in undamaged and ablated wing discs. Note the minimal variation in pouch size at R0, indicating consistency of ablation. Undamaged n = 8, regenerating n = 28. Error bars are SEM. (B) Quantification of percentage of regenerating animals that had pupariated by each day, showing the asynchronous progression to pupariation that occurred after tissue damage. Undamaged animals were w1118;; rnGAL4, Gal80TS/+, regenerating animals were w1118;; rnGAL4, UAS-reaper, Gal80TS/+, and both experienced the 24-hour temperature shift. Three independent experiments, total undamaged n = 144 pupae, regenerating n = 176 pupae. (C) Percentage of wings of different sizes on w1118;; rnGAL4, UAS-reaper, Gal80TS/+ animals that eclosed on different days after egg laying due the asynchronous development induced by tissue damage. Note that the animals that eclosed first (day 18) had smaller wings than those that eclosed on day 19, and those that eclosed on day 20 had the largest wings. Thus, variation in wing size after disc regeneration is partly determined by length of time for regeneration. Three independent experiments, total n = 371 wings.(TIF)Click here for additional data file.S2 Fig(A) Venn diagrams showing genes at least 1.3-fold upregulated or downregulated in three transcription profiles of r(TIF)Click here for additional data file.S3 FigAdoR-GFP MiMIC enhancer trap. (B-B\u2019) Kayak-GFP protein trap. (C-C\u2019) Thor-lacZ enhancer trap. (D-D\u2019) Corto-GFP protein trap. (E-E\u2019) NLaz-GFP MiMIC enhancer trap. (F-F\u2019) anti-Twist. (G-G\u2019) zfh1-lacZ enhancer trap. Blue dashed line outlines the wing primordium. Scale bars are 100 \u03bcm. (H) Quantification of upregulation of mol, Nox, and Ets21C expression using qPCR. Four biological replicates each. Error bars are SEM, *p<0.05.Undamaged (A-G) and regenerating (R24) (A\u2019-G\u2019) wing discs. (A-A\u2019) (TIF)Click here for additional data file.S4 Figfru3/+ males had larger wings after regeneration than controls. Three independent experiments, w1118 n = 112 wings, fru3/+ n = 95 wings, p<0.001 by a chi-squared test. (B) Adult htlAB42/+ animals had larger wings after regeneration than controls. Three independent experiments, w1118 n = 316 wings, htlAB42/+ n = 223 wings, p<0.001 by a chi-squared test. Error bars are SEM.(A) Adult (TIF)Click here for additional data file.S5 Fig(A-D) Hemolectin-RFP (Hml-RFP) (green) showing hemocytes near undamaged and R24 wing discs. Anti-Nimrod (green) also showing hemocytes near an R24 wing disc, confirming the Hml-RFP results. (B), (D), and (F) are orthogonal slices with the columnar epithelium or the disc proper (DP) toward the bottom and the peripodial epithelium (PE) toward the top of the images. (G) Schematic of an undamaged and a regenerating epithelium showing the location of a hemocyte outside the PE.(TIF)Click here for additional data file.S6 FigmolRNAi caused smaller adult wings after regeneration of the imaginal discs than controls. Three independent experiments, w1118 n = 402 wings, UAS-molRNAi n = 221 wings, p<0.0001 by a chi-squared test. (B-C) Cellular debris is visually distinct from the regenerating epithelium. Regenerating w1118 (B) and mole02670/+ (C) discs at R24, expressing the nub-GFP enhancer trap and stained with DHE. The speckled, grainy GFP tissue is cellular debris, outlined with yellow. The smooth GFP tissue is the intact epithelium, outlined with blue. The side panels are zoomed-in views of debris and epithelium, to show that they are easily distinguished. Undamaged and R24 w1118 discs stained with DAPI and the ROS detector H2DCFDA. (F-J) gstD-GFP expression in undamaged w1118 (F), and regenerating w1118 and mole02670/+ wing discs at R24 and R48 . (K-O) Anti-Myc immunostaining in w1118 and mole02670/+ regenerating wing discs at R24 and R48 . (O) Quantification of immunofluorescence in Myc staining. R24 w1118 n = 14 discs, mole02670/+ n = 12 discs. R48 w1118 n = 11 discs, mole02670/+ n = 14 discs. Scale bars are 100 \u03bcm. Error bars are SEM except where noted. *p<0.02.(A) Expression of (TIF)Click here for additional data file.S7 Figw1118 and UAS-DuoxRNAi animals. Three independent experiments. w1118 n = 390 wings, UAS-DuoxRNAi n = 200 wings, p = 0.0005 using a chi-squared test. (B) Sizes of adult wings after disc regeneration in w1118 and UAS-NoxRNAi animals. Two independent experiments, thus error bars are SD. w1118 n = 299 wings, UAS-NoxRNAi n = 257 wings, p<0.0001 using a chi-squared test. (C) Sizes of adult wings after disc regeneration in w1118 and NoxMI15634/+ animals. Three independent experiments. w1118 n = 349 wings, NoxMI15634/+ n = 180 wings, p<0.0001 using a chi-squared test. qPCR showing effectiveness of Duox (D) and Nox (E) RNAi. The RNAi was expressed under rn-GAL4 control in the pouch of normally developing wing discs for 24 hours before collecting for qPCR. Three biological replicates each, *p<0.05. (F) Total number of mitotic cells as identified by anti-phospho-Histone H3 staining in the wing pouch as identified by anti-Nub staining in the indicated genotypes. R0 w1118 n = 14 discs, NoxMI15634/+ n = 15 discs, UAS-NoxRNAi n = 15 discs, R24 w1118 n = 12 discs, NoxMI15634/+ n = 17 discs, UAS-NoxRNAi n = 15 discs, R48 w1118 n = 11 discs, NoxMI15634/+ n = 18 discs, UAS-NoxRNAi n = 19 discs. (G) Area of the wing pouch as marked by anti-Nub staining was measured at R0, R24 and R48 for the indicated genotypes. R0 w1118 n = 14 discs, NoxMI15634/+ n = 15 discs, UAS-NoxRNAi n = 15 discs, R24 w1118 n = 12 discs, NoxMI15634/+ n = 17 discs, UAS-NoxRNAi n = 15 discs, R48 w1118 n = 11 discs, NoxMI15634/+ n = 18 discs, UAS-NoxRNAi n = 19 discs. (H) Pupariation timing for regenerating animals of the indicated gentoypes. Three independent experiments. w1118 n = 204, NoxMI15634/+ n = 113, UAS-NoxRNAi n = 206 (I) Pupariation timing for normally developing animals that did not experience the thermal shift and so did not ablate and regenerate the wing primordia. Note that because these animals did not experience the thermal shift, the pupariation timing cannot be compared directly to the pupariation timing in panel H, in which the animals did experience the thermal shift. w1118 n = 97, NoxMI15634/+ n = 49, UAS-NoxRNAi n = 122. Error bars are SEM.Regeneration assays using adult wing size to assess extent of regenerative growth in the imaginal discs. (A) Sizes of adult wings after disc regeneration in (TIF)Click here for additional data file.S8 Figmol-lacZ reporter (green) in w1118 undamaged discs (A), and in regenerating wing discs at R0 (B), R24 (C) and R48 (D). (E) Quantification of mol-lacZ expression changes. Undamaged n = 3, R0 n = 7, R24 n = 10, R48 n = 10. Anti-\u03b2-galacosidase immunostaining showing expression of the mol-lacZ reporter (green) in w1118 (F) and p38a1/+ (G) R24 discs. (H) Quantification of the fluorescence from the immunostaining. Two independent experiments, for a total w1118 n = 10 discs, p38a1/+ n = 12 discs. Scale bars are 100 \u03bcm. Error bars are SEM.(A-E) Anti-\u03b2-galacosidase immunostaining showing expression of the (TIF)Click here for additional data file.S1 Table(PDF)Click here for additional data file.S2 Table(PDF)Click here for additional data file.S1 Text(DOCX)Click here for additional data file."} +{"text": "Staphylococcus aureus , including methicillin-resistant S. aureus (MRSA); streptococci , including Streptococcus pneumoniae, viridans group streptococci, and beta-hemolytic streptococci; Enterobacteriaceae, including Escherichia coli ; Haemophilus influenzae ; and Moraxella catarrhalis . Omadacycline merits further study in serious infections where resistant pathogens may be encountered.Omadacycline was tested against 21,000 bacterial isolates collected prospectively from medical centers in Europe and the United States during 2016. Omadacycline was active against Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), Enterobacteriaceae that produce extended-spectrum \u03b2-lactamases (ESBLs) and carbapenemases, and multidrug-resistant (resistant to \u22653 classes of agents) strains of Acinetobacter spp. and Stenotrophomonas maltophilia were collected prospectively from hospitalized patients in 68 medical centers in the United States and Europe for the 2016 SENTRY Antimicrobial Surveillance Program. Isolate identifications were established by the participating medical centers and confirmed at JMI Laboratories , when necessary. Omadacycline MIC values were determined using the reference Clinical and Laboratory Standards Institute (CLSI) broth microdilution method (Enterobacteriaceae isolates were classified as susceptible (S) to ceftazidime , nonsusceptible (NS) to ceftazidime , R to imipenem , R to tetracycline , and NS to tigecycline . Other resistant phenotypes included MRSA (oxacillin MIC \u2265 4 mg/liter or cefoxitin MIC > 8 mg/liter), vancomycin-NS enterococci (MIC \u2265 8 mg/liter), tetracycline-R A. baumannii, staphylococci, enterococci , and Streptococcus pneumoniae (MIC \u2265 4 mg/liter), macrolide-R S. pneumoniae (erythromycin MIC \u2265 1 mg/liter and azithromycin MIC \u2265 2 mg/liter), and macrolide-R \u03b2-hemolytic streptococci (BHS) (erythromycin MIC \u2265 1 mg/liter). Haemophilus influenzae isolates were divided into \u03b2-lactamase-positive and -negative groups. QC strains were tested concurrently and included Escherichia coli ATCC 25922 and ATCC 35218, S. aureus ATCC 29213, Pseudomonas aeruginosa ATCC 27853, Enterococcus faecalis ATCC 29212, and S. pneumoniae ATCC 49619. All QC results, including all omadacycline MIC values, were within published ranges.Bacterial isolates isolates were methicillin R, 40.0% of Enterococcus faecium isolates were vancomycin NS, 11.6% of S. pneumoniae isolates were penicillin R, 31.4% of S. pneumoniae isolates were macrolide R, 14.4% of E. coli isolates were ceftazidime NS, 28.6% of Klebsiella pneumoniae isolates were ceftazidime NS, 27.9% of Enterobacter cloacae species complex (SC) isolates were ceftazidime NS, and 8.1% of K. pneumoniae isolates were imipenem R , 43.6% of BHS, 32.8% of Enterobacteriaceae, 66.4% of Acinetobacter baumannii, 0.2% (data not shown) of H. influenzae, and 11.1% (data not shown) of Haemophilus parainfluenzae , omadacycline inhibited 99.9% of isolates at \u22642 mg/liter, including 100.0% of methicillin-S S. aureus (MSSA) and 99.7% of MRSA isolates . Tetracycline resistance had little effect on omadacycline MIC values against S. aureus or CoNS isolates than against E. faecalis and was not adversely affected by vancomycin or tetracycline resistance , VGS , and BHS isolates, regardless of species and susceptibility to penicillin, macrolides, or tetracycline , indole-positive Proteus spp. , and tigecycline-NS K. pneumoniae and K. pneumoniae (50/MIC90 2/4 mg/liter) against ceftazidime-NS E. cloacae isolates as it was against ceftazidime-S E. cloacae isolates , K. pneumoniae , Klebsiella oxytoca , E. cloacae SC , and Citrobacter spp. inhibited 71.2% of isolates at \u22644 mg/liter at \u22644 mg/liter (data not shown). Omadacycline demonstrated good in vitro activity against S. maltophilia (Table 2). Omadacycline was equally active against \u03b2-lactamase-negative and -positive isolates of H. influenzae and was also very active against Moraxella catarrhalis isolates (Omadacycline MIC distributions are shown in isolates . All CoNsistance and S1. acycline and S1. g/liter) except Pg/liter) and S2. g/liter) and S2. ctively) and S2. isolates and S2. olates]) and S2. mg/liter . Omadacyg/liter) and S2.Compared to older tetracyclines, omadacycline has advantages that include a low propensity for selection of resistance, enhanced binding to the 30S ribosomal subunit, the ability to overcome common tetracycline resistance mechanisms, a lack of effect of other resistance mechanisms, availability as intravenous or oral formulations, a prolonged half-life, and once-daily administration . Omadacyin vitro activity of omadacycline against bacterial isolates (United States and Europe) from the 2016 SENTRY survey. Overall, omadacycline provided broad coverage against Gram-positive and fastidious Gram-negative bacteria (S. pneumoniae isolates (E. coli and somewhat less active against ESBL-producing K. pneumoniae and ceftazidime-NS E. cloacae strains. Tetracycline-R Enterobacteriaceae were slightly less susceptible to omadacycline than tetracycline-S strains. Imipenem and amikacin were the most active agents against Enterobacteriaceae, including the resistant subsets. Omadacycline was the only agent with useful activity against A. baumannii, and omadacycline and trimethoprim-sulfamethoxazole were the only agents with useful activity against S. maltophilia isolates.This study documents the isolates and S1. These data build on previous SENTRY surveillance surveys and indi"} +{"text": "However, IDH mutations make classification of gliomas according to the WHO2007 edition controversial. Here, we characterized IDH-1R132H mut status in a cohort of 670 adult patients with different WHO2007 grades of diffuse glioma. Patient characteristics, clinical data and prognoses were obtained from medical records. Patients with IDH-1R132H mut were younger and had better clinical outcomes than those without mutations. Differences in age among patients with astrocytomas of different WHO2007 grades were eliminated after patients were grouped based on IDH-1R132H status. IDH-1R132H mut was present more often in patients with lower Ki-67 and MGMT protein levels and higher mutant p53 levels. Ki-67 was also strongly associated with WHO2007 grade independently of IDH-1R132H mut status. Moreover, patients with Ki-67<30 survived longer than those with Ki-67\u226530, regardless of IDH-1R132H mut status. Patients in the IDH-1R132H mut group with lower MGMT protein levels also had better clinical outcomes than those in other groups. Our results indicate that to better treat gliomas, IDH mutation status should be included when determining WHO2007 grade in glioma patients.WHO The median OS of 36.230 months (95% CI 31.103\u201341.357) in patients with Ki-67<30 was higher than the OS of 15.370 months (95% CI 12.842\u201317.898) in patients with Ki-67\u226530 . We subdivided IDH-1R132H mut or IDH-1R132H wt gliomas based on Ki-67<30, and found differences in mOS among the four groups vs. 19.000 months (95% CI 13.754\u201324.246); p<0.001, Breslow test, Figure R132H wt [median 17.400 months (95% CI 13.627\u201321.173) vs. 13.270 months (95% CI 11.141\u201315.399); p=0.039, Breslow test, Figure R132H mut/Ki-67\u226530 and IDH-1R132H wt /Ki-67<30 patients .IDH-1s Figure . Patientp<0.001, Breslow test). Furthermore, mOS differed among IDH-1R132H-mut-MGMTneg , IDH-1R132H mut-MGMTpos , IDH-1R132H wt-MGMTneg and IDH-1R132H-WT-MGMTpos patients .The mOS of 15.670 months (95% CI 13.273\u201318.067) in MGMT-positive patients was shorter than the mOS of 32.500 months (95% CI 22.439\u201342.561) observed in MGMT-negative patients and IDH wt (median OS=355 days) groups. The median OS in our study was closer to that found by Zeng et al. These results indicate that Ki-67 index is a reliable candidate for determining prognosis in glioma patients in addition to IDH-1 status. Although the prognostic value of MGMT protein levels is controversial [Recent data suggests that IDH-1 mutations, Ki-67 index, and MGMT protein levels are prognostic factors for diffuse gliomas , 30\u201332. oversial , we founR132H mut in a large cohort of glioma patients. IDH-1R132H mut was associated with specific WHO2007 histological grades and younger age. Age differences between different WHO2007 grades of astrocytoma were strongly influenced by IDH-1R132H mutation status. Low Ki-67 index values occurred much more often in patients with lower WHO2007 grades and IDH-1R132H mutation. Finally, our study indicated that Ki-67 index and MGMT protein levels, together with IDH mutation status, were predictive of prognosis in different glioma subtypes.In summary, we characterized the expression of IDH-1Tumor samples were obtained from Sanbo Brain Hospital. Informed consent was obtained from all patients prior to the study. All experiments using human tissues were approved by the Institutional Review Board of Sanbo Brain Hospital. 670 adult patients with diffuse supratentorial gliomas were involved in the study. WHO classification of all specimens was performed by two independent neuropathologists . In the R132H (Dianova 1:100), p53 (1:100 Invitrogen), MGMT (1:150 Invitrogen), and Ki-67 (1:200 Invitrogen) were used. The cutoff values were 10% for IDH-1R132H mut, 10% for mutant p53, 10% for MGMT, and 30% for Ki-67. Representative images of high and low IDH-1R132H mut was considered statistically significant.SPSS 22.0 was used for all statistical analyses. The \u03c7"} +{"text": "Nature Communications8:312 doi:10.1038/s41467-017-00390-1; Article pubilshed online: 22 Aug 2017Nat. Commun.7, 12374 (2016).\u201dWe regretfully omitted to give credit to a previous figure upon which the surface-tension scheme in Fig. 1b is based. The caption to Fig. 1 should have included the following: \u201cThe surface-tension scheme in Fig. 1b is adapted from Fig. 1a in Noh, J., Jeong, S. & Lee, J.-Y. Ultrafast formation of air-processable and high-quality polymer films on an aqueous substrate."} +{"text": "Xiphinema includes a remarkable group of invertebrates of the phylum Nematoda comprising ectoparasitic animals of many wild and cultivated plants. Damage is caused by direct feeding on root cells and by vectoring nepoviruses that cause diseases on several crops. Precise identification of Xiphinema species is critical for launching appropriate control measures. We make available the first detailed information on the diversity and distribution of Xiphinema species infesting wild and cultivated olive in a wide-region in southern Spain that included 211 locations from which 453 sampling sites were analyzed. The present study identified thirty-two Xiphinema spp. in the rhizosphere of olive trees, ten species belonging to Xiphinema americanum-group, whereas twenty-two were attributed to Xiphinema non-americanum-group. These results increase our current knowledge on the biodiversity of Xiphinema species identified in olives and include the description of four new species , and two new records for cultivate olives . We also found evidence of remarkable prevalence of Xiphinema spp. in olive trees, viz. 85.0% (385 out of 453 sampling sites), and they were widely distributed in both wild and cultivated olives, with 26 and 17 Xiphinema spp., respectively. Diversity indexes were significantly affected by olive type. We also developed a comparative morphological and morphometrical study together with molecular data from three nuclear ribosomal RNA genes . Molecular characterization and phylogenetic analyses allowed the delimitation and discrimination of four new species of the genus described herein and three known species. Phylogenetic analyses of Xiphinema spp. resulted in a general consensus of these species groups. This study is the most complete phylogenetic analysis for Xiphinema non-americanum-group species to date.The genus Soil is most likely one of the more species-rich habitats of terrestrial ecosystems because over one quarter of all living species on Earth are inhabiting the soil , 2. One Meloidogyne spp.) and cyst nematodes (Heterodera spp. and Globodera spp.), likewise the ectoparasitic nematodes belonging to the family Longidoridae Thorne, 1935 [Xiphinema Cobb, 1913 [Nepovirus, family Comoviridae) that cause significant damage to a wide range of crops [Xiphinema was divided into two different species groups [Xiphinema americanum-group comprising a complex of about 60 species [Xiphinema non-americanum-group which comprises a complex of more than 215 species [Xiphinema is based mainly on classical diagnostic features; however, due to a high degree of intraspecific morphometric variability can lead to overlapping among Xiphinema species and increase the risk of species miss-identification [The most important nematodes economically include endoparasitic species such as the root-knot species , 17, 18.fication .Xiphinema species have been characterized molecularly by ribosomal genes , constituting a useful tool for molecular-based species identification [Xiphinema species identification becomes difficult when dealing with morphological closely species that co-occur in a sample or region, as often detected in the Iberian Peninsula [Xiphinema spp. detected in the Iberian Peninsula [Xiphinema have been reported in Spain, mainly associated with woody, ornamental and vegetable plant species [Recently, 96 fication \u201333. Xipheninsula , 28. Seveninsula \u201336. In p species , 38.Xiphinema spp.) [Xiphinema spp. associated with olive trees, except for the recent contributions of Archidona-Yuste et al. [Xiphinema macrodora Archidona-Yuste et al., 2016, Xiphinema oleae Archidona-Yuste et al., 2016, Xiphinema plesiopachtaicum Archidona-Yuste et al. 2016, and Xiphinema vallense Archidona-Yuste et al. 2016 [Xiphinema spp. infecting wild and cultivated olives in southern Spain, we surveyed a total of 211 localities at the eight provinces of Andalusia where both olive forms were present. This survey raised 385 populations of Xiphinema species, apparently morphologically related to other known Xiphinema spp. This prompted us to carry out an integrative taxonomic study to identify the species within this complex genus.Olive, in wild and cultivated forms, is widely distributed in the Mediterranean Basin, and particularly in southern Spain , 39\u201341. ma spp.) , 42. Howe et al. , 18, 28 al. 2016 , 18, 28.Xiphinema species and to test the resemblance between morphological and molecular data within Xiphinema species, and the specific objectives were: i) to identify the 385 Spanish populations of Xiphinema spp. detected in wild and cultivate olives; ii) to carry out a molecular characterisation of these Xiphinema populations based on sequences of the D2-D3 expansion segments of the 28S nuclear ribosomal RNA gene, the ITS1 of rRNA, and partial 18S rRNA sequences; and iii) to study the phylogenetic relationships of Xiphinema spp.The general objectives of this research was to study the occurrence and abundance of No specific permits were required for the described fieldwork studies. Permission for sampling the olive orchards was granted by the landowner. The samples from wild olives were obtained in public areas, forests, and other natural areas studied and do not involve any species endangered or protected in Spain. The sites are not protected in any way.et al. [Nematodes were surveyed from 2012 to 2015 during the spring season in wild and cultivate olives growing in Andalusia, southern Spain , Fig 1. et al. .3 sub-sample of soil by a modification of Cobb\u00b4s decanting and sieving method [et al. [Xiphinema.Nematodes were extracted from a 500-cmg method . Since rg method , 44, theg method . The nem [et al. . PPN froXiphinema spp. populations detected infesting soils from olives in Andalusia, conventional ecological and diversity indexes were performed in order to evaluate the distribution and changes in the diversity in wild and cultivated olives. In this regard, abundance and prevalence of each Xiphinema species identified were estimated. For each sampling site, abundance was calculated as the mean number of Xiphinema nematodes per 500 cm3 of soil for all samples. The prevalence was computed by dividing the number of samples in which a Xiphinema species was detected by the total number of samples and expressed as a percentage.Based on the P \u2264 0.05 using the general model procedure of SAS .Several diversity indexes including Hill\u00b4s diversity, Hill\u00b4s reciprocal of D (Simpson\u00b4s dominance index) and Hill\u00b4s evenness indexes were calXiphinema specimens for light microscopy were killed by gentle heat, fixed and examined Xiphinema specimens as described by Archidona-Yuste et al. and Seinhorst [viz. Xiphinema cadavalense Bravo & Roca 1995 [viz. Xiphinema conurum Siddiqi, 1964 [Xiphinema species already described were analysed morphologically and molecularly in this study and proposed as standard and reference populations for each species given until topotype material becomes available and molecularly characterized. Voucher specimens of these described species have been deposited in the nematode collection of Institute for Sustainable Agriculture, IAS-CSIC, C\u00f3rdoba, Spain.einhorst , 50. Theeinhorst , 27, 51.oca 1995 , and Dr.qi, 1964 . NematodXiphinema. Following morphological confirmation, the specimens were removed from the slides and DNA extracted.For molecular analyses, in order to avoid mistakes in the case of mixed populations, two live nematodes from each sample were temporary mounted in a drop of 1M NaCl containing glass beads (to avoid nematode crushing/damaging specimens) to ensure specimens conformed to the unidentified populations of et al. [et al. [Detailed protocols for nematode DNA extraction, PCR and sequencing were applied as described by Castillo et al. . The D2-et al. , 55\u201358. [et al. . The newXiphinema spp. from GenBank were used for phylogenetic reconstruction. Outgroup taxa for each dataset were chosen according to previous published data [http://molevol.cmima.csic.es/castresana/Gblocks_server.html) using the less stringent option . Percentage similarity between sequences was calculated using a sequence identity matrix in BioEdit. For that, the score for each pair of sequences was compared directly and all gap or place-holding characters were treated as a gap. When position of both sequences has a gap they do not contribute as a difference. Phylogenetic analyses of the sequence data sets were performed based on Bayesian inference (BI) using MrBayes 3.1.2 [6 generations, respectively. The Markov chains were sampled at intervals of 100 generations. Two runs were performed for each analysis. After discarding burn-in samples and evaluating convergence, the remaining samples were retained for further analyses. The topologies were used to generate a 50% majority rule consensus tree. Posterior probabilities (PP) are given on appropriate clades. Trees were visualised using TreeView [D2-D3 expansion segments of 28S rRNA, ITS1, and partial 18S rRNA sequences of different hed data , 17, 18.hed data , strateghed data and edithed data in Castres 3.1.2 . The beses 3.1.2 with theTreeView .http://zoobank.org/. The LSID for this publication is: urn:lsid:zoobank.org:pub:CE945C7D-7B14-46DD-8A17-A93A05750590. The electronic edition of this work was published in a journal with an ISSN, and has been archived and is available from the following digital repositories: PubMed Central, LOCKSS.The electronic edition of this article conforms to the requirements of the amended International Code of Zoological Nomenclature (ICZN), and hence the new names contained herein are available under that Code from the electronic edition. This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix Xiphinema spp. found in this study including specimens of sampling sites used in morphological and/or molecular analyses, are shown in Xiphinema spp. and sampling sites are presented in Xiphinema spp. were detected in the rhizosphere of olive trees, ten species belonging to X. americanum-group, whereas 22 were attributed to X. non-americanum-group Kirjanova 1951 [X. parachydermum Guti\u00e9rrez-Guti\u00e9rrez et al., 2012 [X. turcicum Luc, 1963 [X. vallense), while the remaining 21 identified species where present either in wild or cultivated olives only.All um-group . From aled olive ; Fig 1. l., 1992 , X. coxian, 1964 , X. duril., 1993 , X. incel., 1983 , X. italyl, 1953 , X. macrl., 1992 , X. pachova 1951 , 71, X. l., 2012 , X. turcuc, 1963 and X. vXiphinema spp. were present in low to high densities in both wild and cultivated olives, being observed in cultivated olives in higher densities than in wild olives (X. americanum-group species was significantly higher (P < 0.01) in cultivated than wild olives in both olive types in the Xiphinema non-americanum-group (P < 0.001) for X. americanum group than X. non-americanum-group species (Xiphinema species with the highest nematode density was X. pachtaicum (414 nematodes per 500 cm3 of soil), which showed a higher average density in cultivated than wild olives , both belonging to X. non-americanum-group, showing lower average density in cultivated than in wild olives , which r species . On the d olives . Howeverd olives .Xiphinema spp. in olive was 85.0% (385 out of 453 sample sites) in Andalusia than cultivated olives that was detected in both olive types in the most of the Andalusia provinces, at exception of Almer\u00eda , that was found in both olive types in Almer\u00eda, C\u00e1diz, Huelva and M\u00e1laga provinces, but only in wild olive in C\u00f3rdoba, Granada, Ja\u00e9n and Seville provinces . In addive types . As indie sites) . The sub Almer\u00eda . Anotherrovinces .Xiphinema spp. in wild and cultivated olive (Xiphinema spp. detected in each sampling site (Richness index) was significantly affected (P < 0.05) by olive type (P < 0.001) in wild than cultivated olives (X. non-americanum-group species were significantly higher (P < 0.05) in wild than in cultivated olive (X. americanum-group species (P < 0.001) in X. americanum-group than in X. non-americanum-group (P < 0.05) for both diversity indexes were observed when Xiphinema species groups were considered separately than X. americanum-group (Tables P < 0.01) among them when it was considered both olive types (P < 0.01) than that of wild olives (P < 0.05) detected in cultivated than wild olives (X. americanum-group was significantly higher (P < 0.001) than that of X. non-americanum-group species , and Hill\u00b4s evenness ), and teed olive . Overallive type , showingd olives . Similared olive , but the species . Overallum-group . Diversium-group . Thus, sparately . On the P < 0.00 in wild p Tables resultedve types . Evennesd olives accordind olives . On the species .Nematoda Linnaeus, 1758 Dorylaimida Pearse, 1942 Longidoridae Thorne, 1935 [Longidorinae Thorne, 1935 [Xiphinema Cobb, 1913 [bb, 1913 Xiphinema andalusiense Archidona-Yuste, Navas-Cort\u00e9s, Cantalapiedra-Navarrete, Palomares-Rius & Castillo, sp. nov.urn:lsid:zoobank.org:act:95E9BE47-B822-4AAF-A11C-50EF7A016137Figs 5Olea europaea subsp. silvestris (Miller) Lehr) , at Belmez, C\u00f3rdoba province, Spain; collected by G. Leon Ropero, March 14, 2015; mounted in pure glycerine and deposited in the nematode collection at Institute for Sustainable Agriculture (IAS) of Spanish National Research Council (CSIC), C\u00f3rdoba, Spain (collection number AR093-2).Adult female, collected from the rhizosphere of wild olive of Spanish National Research Council (CSIC), C\u00f3rdoba, Spain (collection numbers AR093-5-AR093-7); two females at Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), Bari, Italy (AR093-8); and one female at USDA Nematode Collection, Beltsville, MD, USA (T-6774p); collected by G. Leon Ropero, March 14, 2015.Xiphinema andalusiense sp. nov. is an apparently parthenogenetic species belonging to morphospecies Group 5 from the Xiphinema non-americanum-group species [pars dilatata uteri, and small spiniform structures and crystalloid bodies in low number; female tail short, convex-conoid to conical shape with distinctly digitate terminus, and bearing three pairs of caudal pores; c\u00b4 ratio (1.0\u20131.3); and specific D2-D3, ITS1 rRNA and partial 18S rRNA sequences . According to the polytomous key of Loof & Luc [ species . It is cof & Luc , the newThe species epithet refers to the autonomous community from Spain, Andalusia, where the species was detected and moderately distributed.ca 76\u201388% of lip region diam. and located at ca two-thirds of lip region height. Odontostyle long, 1.6\u20131.9 times longer than odontophore, and the latter with moderate-developed flanges 9.5\u201312.5 \u03bcm wide. Guiding ring with average guiding sheath length of 16.0 \u03bcm. Pharynx occupying about 8\u201315% of body length, consisting of an anterior slender narrow part 346\u2013541 \u03bcm long and extending to terminal pharyngeal bulb occupying ca 19\u201327% of total pharyngeal length, 112\u2013139 \u03bcm long and 22.5\u201329.5 \u03bcm wide. Glandularium 99.5\u2013119.0 \u03bcm long. Nucleus of dorsal pharyngeal gland (DN) located at beginning of basal bulb (10.4\u201314.3%), ventrosublateral nuclei (SVN) situated ca halfway along bulb (46.9\u201359.4%) similar to that of female, including almost conoid tail shape ending in a digitate terminus were identified using morphological characters such as body length, length of replacement and functional odontostyle , Fig 5 , 76. Speterminus , becominXiphinema andalusiense sp. nov. was collected from the rhizosphere of wild olive (Olea europaea subsp. silvestris (Miller) Lehr) of two localities belonging to C\u00f3rdoba and Ja\u00e9n provinces, being one of the new species described in this work which has a broader distribution in Andalusia, concretely on North of Andalusia , slightly lower c\u00b4 ratio (1.0\u20131.3 vs 1.1\u20131.8), the presence of spiniform structures or crystalloid bodies along tubular portion of uterus vs absent, and the absence vs presence of males [X. andalusiense sp. nov. mainly differs from X. cadavalense in having a shorter odontostyle and odontophore length resulting in a shorter stylet length (215.5\u2013239.5 vs 244.5\u2013278.5 \u03bcm), a narrower lip region (12.0\u201315.5 vs 14.0\u201319.5 \u03bcm), and higher a and c\u00b4 ratios [X. andalusiense sp. nov. differs from X. turdetanense in having a slightly longer odontostyle length (137.0\u2013151.0 vs 121.0\u2013142.0 \u03bcm), a slightly narrower lip region (11.5\u201315.5 vs 14.0\u201316.0 \u03bcm), higher number of globular bodies present in the Z-differentiation (11\u201316 vs 6\u20138), size and number of spiniform structures presents along tubular part of uterus , presence of crystalloid bodies along uterus vs absence, and the absence vs presence of males [According to the polytomous key by Loof & Luc and sortl., 2013 , X. cadal., 2013 . Xiphineof males . On the ctively) . Finallyof males .X. andalusiense sp. nov. is molecularly related to X. macrodora, but it can be clearly differentiated in having a smaller nematode body and odontostyle length [In addition, ctively) .X. andalusiense sp. nov. (KX244884-KX244888) was 97% similar to X. baetica , X. macrodora and X. cadavalense (KX244900); sequence variation among these species was from 24 to 34 nucleotides and from 3 to 8 indels in relation to the ITS1 region were also X. baetica , X. cadavalense , and X. macrodora . Intraspecific variation for this marker was 44 nucleotides and 23 gaps amongst the five studied populations , with several Xiphinema spp. such as X. baetica (KC567148-KC567149), X. cadavalense (KX244932), X. macrodora (KU171050) and X. coxi europaeum (KC567153).D2-D3 region of 8 indels . Xiphineulations . FinallyXiphinema celtiense Archidona-Yuste, Navas-Cort\u00e9s, Cantalapiedra-Navarrete, Palomares-Rius & Castillo, sp. nov.urn:lsid:zoobank.org:act:17E565E4-18E8-4D60-AA57-55253F3E257EFigs 7Olea europaea subsp. silvestris (Miller) Lehr) , at Pe\u00f1aflor, Seville province, Spain; collected by A. Archidona-Yuste, April 22, 2014; mounted in pure glycerine and deposited in the nematode collection at Institute for Sustainable Agriculture (IAS) of Spanish National Research Council (CSIC), C\u00f3rdoba, Spain (collection number AR083-01).Adult female, collected from the rhizosphere of wild olive of Spanish National Research Council (CSIC), C\u00f3rdoba, Spain (collection numbers AR083-03-AR083-06); two females and one juvenile at Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), Bari, Italy (AR083-22); two females and two juveniles at Royal Belgian Institute of Natural Sciences, Brussels, Belgium (RIT 852); and two females and two juveniles at USDA Nematode Collection, Beltsville, MD, USA (T-6775p); collected by A. Archidona-Yuste, April 22, 2014.Xiphinema celtiense sp. nov. is a Xiphinema non-americanum-group species belonging to morphospecies Group 5 sensu Loof & Luc [of & Luc . It is aof & Luc , the newCelti\u2019, where the type specimens were collected.The species name is derived from originating Roman city of Pe\u00f1aflor, \u2018ca 58\u201378% of lip region diam. Guiding ring with average guiding sheath length of 15.5 \u03bcm. Odontostyle long, 1.4\u20131.8 times longer than odontophore, and the latter with well-developed flanges 13.0\u201316.5 \u03bcm wide. Pharynx very long occupying about 10\u201314% of body length, consisting of an anterior slender narrow part 379\u2013510 \u03bcm long and extending to pharyngeal bulb, 126.0\u2013168.0 \u03bcm long and 22.5\u201336.0 \u03bcm wide. Glandularium 110\u2013155 \u03bcm long. Nucleus of dorsal pharyngeal gland (DN) located at beginning of basal bulb (11.5\u201316.1%), ventrosublateral nuclei (SVN) situated ca halfway along bulb (50.5\u201362.3%) \u03bcm wide and 7.2 \u00b1 1.4 (4.5\u20139.5) \u03bcm high. Amphidial fovea aperture extending for Coomans . Vestigiize Figs . Small cExtremely rare, only one male specimen was found in type locality. Male genital tract diorchic with testes containing multiple rows of different stages of spermatogonia. Tail short, convex-conoid with a broadly rounded terminus and thickened outer cuticular layer. Spicules moderately long and slightly curved ventrally; lateral guiding pieces more or less straight or with curved proximal end. One pair of adanal and 4 mid-ventral supplements.ca 75 \u03bcm. Tail morphology of second-stage juvenile similar to J1 expect to absence of knob-like expansion, and tail conoid and subdigitate with rounded terminus for third-stage juvenile. In J4 tail conoid with a short bulge rounded terminus were identified using morphological characters such as body length, length of replacement and functional odontostyle , Fig 5 , 76. Speterminus . All juvterminus , Fig 7.Xiphinema celtiense sp. nov. was found in the rhizosphere soil of wild olive (Olea europaea subsp. silvestris (Miller) Lehr) in one additional locality belonging to C\u00f3rdoba province. , posterior vulva position (50.0\u201355.0 vs 46.0\u201351.0%), a longer odontostyle and odontophore resulting in a longer stylet length (241.0\u2013263.05 vs 213.0\u2013234.0 \u03bcm), a narrower lip region (13.5\u201316.0 vs 15.5\u201317.0 \u03bcm), frequency of males (extremely rare vs frequent), and the female and J1 tail shape , posterior vulva position (50.0\u201355.0 vs 47.1\u201351.8%), and presence vs absence of crystalloid bodies along uterus [X. turcicum by slightly higher a and c ratios , presence vs absence of crystalloid bodies in the tubular portion of uterus, and different shape of J1 tail although in both species the tail ends in a knob-like expansion more or less separated from the anterior part of tail , and female tail shape [X. cohni it mainly differs by the presence vs absence of Z-differentiation containing numerous granular bodies, and female tail shape , 65. AndX. celtiense sp. nov. (KX244889-KX244890) differed with the closest related species, X. hispanum (GU725074) by 24 nucleotides and 3 gaps (97% similarity) and from X. cohni from 27 nucleotides and 1 indel (97% similarity). Intraspecific variation of D2-D3 segments detected between the two studied population of X. celtiense sp. nov. consisted of 7 nucleotides (99% similarity), and no indels (X. hispanum (GU725061) and 86% (141 nucleotides and 34 indels) with X. cohni (KX244933). Intraspecific variation of the ITS1 for these sequences (KX244926-KX244927) was 44 nucleotides and 18 gaps, 95% similarity (X. celtiense sp. nov. (KX244943) showed a high level of similarity (99%) with several sequences deposited in GenBank such as X. hispanum (GU725083), X. adenohystherum (GY725084), and X. nuragicum (GU725080).D2-D3 sequences from o indels . ITS1 , at Izn\u00e1jar, C\u00f3rdoba province, Spain; collected by J.E. Palomares-Rius, December 3, 2014; mounted in pure glycerine and deposited in the nematode collection at Institute for Sustainable Agriculture (IAS) of Spanish National Research Council (CSIC), C\u00f3rdoba, Spain (collection number JAO-25-1).Adult female, collected from the rhizosphere of cultivated olive of Spanish National Research Council (CSIC), C\u00f3rdoba, Spain (collection numbers JAO-25-2-JAO-25-7); one female and one male at Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), Bari, Italy (JAO-25-12); two females and one juvenile at Royal Belgian Institute of Natural Sciences, Brussels, Belgium (RIT 853); and two females, one male, and one juvenile at USDA Nematode Collection, Beltsville, MD, USA (T-6777p); collected by J.E. Palomares-Rius, December 3, 2014.Xiphinema iznajarense sp. nov. is an amphimictic species belonging to morphospecies Group 5 from X. non-americanum-group species sensu Loof & Luc [ca 71 \u03bcm), and one pair of adanal supplement plus 4\u20135 pairs of ventromedian supplements; and specific D2-D3, ITS1 rRNA and partial 18S rRNA sequences . According to the polytomous key of Loof & Luc [of & Luc . It is cof & Luc , the newThe species epithet refers to the type locality, Izn\u00e1jar, where the species was detected.ca 63\u201374% of lip region diam. and located at ca two-thirds of lip region height. Guiding ring with average guiding sheath length of 12.0 \u03bcm. Odontostyle moderately long, 1.5\u20131.8 times longer than odontophore, and the latter with well-developed flanges in the most of specimens studied, 11.5\u201322.0 \u03bcm wide. Pharynx consisting of an anterior slender narrow part 265\u2013414 \u03bcm long, extending to a cylindrical, terminal pharyngeal bulb occupying ca 23\u201336% of total pharyngeal length, cylindrical, 117\u2013153 \u03bcm long and 20\u201329 \u03bcm wide. Glandularium 101\u2013135 \u03bcm long. Nucleus of dorsal pharyngeal gland (DN) located at beginning of basal bulb (11.6\u201312.6%), ventrosublateral nuclei (SVN) situated ca halfway along bulb (50.5\u201357.8%) , a reflexed oviduct with well-developed pars dilatata oviductus separated from uterus by a well-developed sphincter. Uteri tripartite, comprising a developed pars dilatata uteri continuing into a narrower, muscular tube-like portion, and a well-developed Z-differentiation with weakly muscularised wall and containing numerous small granular bodies. Uterine wall wrinkles present along uterus, being more numerous in the proximal part of pars dilatata uteri and ovejector . Ovejector well-developed 35.5\u201356.0 \u03bcm wide, vagina perpendicular to body axis, 18.0\u201324.0 \u03bcm long in lateral view. Vulva slit-like, pre-equatorial. Tail conoid and short, dorso-ventrally convex, ending in a rounded and broadly terminus, bearing in four to five pairs of caudal pores on each side.Habitus in specimens killed by gentle heat usually almost straight anterior to the vulva, more curved behind the vulva, occasionally open C-shaped. Cuticle 2.0\u20134.0 \u03bcm thick at mid-body, more thickened in the lip region (4.0\u20136.0 0 \u03bcm wide) and tail tip region (5.5\u201310.0 \u03bcm wide). Lateral hypodermical chords occupying about 26\u201346% of the corresponding maximum body diameter. Lip region hemispherical, broadly rounded frontally, usually low and offset from body contour by a shallow constriction; 15.5\u201317.0 \u03bcm wide and 5.5\u20137.5 \u03bcm high. Amphidial fovea aperture extending for vejector . Small svejector . In someFrequent but less abundant than female (ratio = 1: 2). Morphologically similar to female except for genital system and more curved posterior part of body. Male genital tract diorchic with testes containing multiple rows of different stages of spermatogonia. Tail short, convex-conoid with short bulge rounded terminus and thickened outer cuticular layer Figs . Spiculeca 63 \u03bcm. Tail morphology in second-stage juvenile similar to J1 expect for the presence a slightly depression at the level of the hyaline region in both sides. On the other hand, the tail was conoid and subdigitate with a rounded terminus for J3, while for fourth-stage juvenile was conoid with rounded terminus and short bulge were identified using morphological characters such as body length, length of replacement and functional odontostyle , Fig 5 , 76. In rt bulge . All juvrt bulge .Xiphinema iznajarense sp. nov. was only found in type locality, Izn\u00e1jar (C\u00f3rdoba province), being extracted from the rhizosphere of cultivated olive (Olea europaea subsp. europaea L.) (Morphometric variability is described in paea L.) , Fig 1.X. iznajarense sp. nov. closely resembles with X. celtiense sp. nov., X. coronatum and X. turcicum. Xiphinema iznajarense sp. nov. can be differentiated from X. celtiense sp. nov. by the characters discussed above. From X. coronatum it differs in having a longer body (4.5\u20135.8 vs 3.8\u20134.6 mm), higher a ratio (75.2\u2013106.3 vs 65.5\u201375.5), a shorter odontophore and lower oral aperture-guiding ring distance , frequency of males (frequent vs extremely rare), presence vs absence of crystalloid bodies in the tubular portion of uterus, female tail shape , and shape of J1 tail (conoid elongate with rounded terminus vs a long clavate peg) , a shorter odontostyle length (132.0\u2013151.0 vs 152.0\u2013182.0 \u03bcm), the presence vs absence of crystalloid bodies along uterus, the frequency of males (frequent vs rare), the female tail shape , and shape of J1 tail , lower c\u00b4 ratio (0.7\u20131.1 vs 1.4\u20132.2), a longer odontostyle (132.0\u2013151.0 vs 107.0\u2013131.0 \u03bcm), and the presence vs absence of crystalloid bodies along uterus was 97% similar (26 nucleotides and 1 indel) to X. adenohystherum (GU725075), X. hispidum (KC567181) and 95% similar (36 nucleotides and 2 indels) to X. hispanum (GU725074). No intraspecific variation of D2-D3 segments was detected amongst the studied individuals (100% similarity) (X. hispanum (GU725061), X. adenohystherum (GU725063) and X. hispidum (HM921367) with similarity values of 88% (131 nucleotides and 31 indels), 87% (145 nucleotides and 29 indels) and 84% (175 nucleotides and 52 indels), respectively (X. iznajarense sp. nov. (KX244944) closely matched with several species of Xiphinema, some of them were X. adenohystherum (GU725084), X. hispanum (GU725083), X. gersoni Roca & Bravo, 1993 [X. sphaerocephalum Lamberti, Castillo, G\u00f3mez Barcina & Agostinelli, 1992 [D2-D3 region of ilarity) . Similarectively . ITS1 alvo, 1993 , at Meng\u00edbar, Ja\u00e9n province, Spain; collected by J. Mart\u00edn-Barbarroja, March 25, 2012; mounted in pure glycerine and deposited in the nematode collection at Institute for Sustainable Agriculture (IAS) of Spanish National Research Council (CSIC), C\u00f3rdoba, Spain (collection number O3C4-01).Adult female, collected from the rhizosphere of cultivated olive of Spanish National Research Council (CSIC), C\u00f3rdoba, Spain (collection numbers O3C4-02-O3C4-08); one female, one male and one juvenile at Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), Bari, Italy (O3C4-19); one female and one male at Royal Belgian Institute of Natural Sciences, Brussels, Belgium (RIT 854); and one female and one male at USDA Nematode Collection, Beltsville, MD, USA (T-6776p); collected by J. Mart\u00edn-Barbarroja, March 25, 2012.Xiphinema mengibarense sp. nov. belongs to the X. non-americanum Group 5 in Loof and Luc [Xiphinema non-americanum Group 5 and has the following specific alphanumeric codes (codes in parentheses are exceptions): A4-B2+3-C5a-D6(5)-E6(5)-F45-G32-H2-I2-J6-K2-I2. and Luc ; and it and Luc , the speThe species epithet refers to the type locality, Meng\u00edbar, where the species was detected.ca 64\u201378% of lip region diam. and located at ca two-thirds of lip region height. Guiding ring and guiding sheath variable in length depending on degree of protraction/retraction of stylet. Odontostyle moderately long, 1.5\u20131.7 times longer than odontophore, in the most specimens the latter with moderate-developed flanges, but in some specimens it was observed weaker, 8.5\u201314.0 \u03bcm wide. Pharynx composed by an anterior slender narrow flexible part 317\u2013417 \u03bcm long, and a posterior muscular expanded part with three nuclei. Terminal pharyngeal bulb variable in length, 120\u2013173 \u03bcm long and 19.5\u201329.5 \u03bcm wide. Glandularium 104\u2013148 \u03bcm long. Nucleus of dorsal pharyngeal gland (DN) located at beginning of basal bulb (9.2\u201315.0%), ventrosublateral nuclei (SVN) situated ca halfway along bulb (45.7\u201358.0%) , with slightly bulging rounded terminus with a distinct terminal blind canal. Three to four caudal pores present on each side.Body cylindrical in an open C-shape when heat relaxed. Cuticle 3.1 \u00b1 0.3 (2.0\u20134.5) \u03bcm thick at post-lip region, 2.8 \u00b1 0.5 (2.0\u20134.0) \u03bcm wide at mid-body, but thicker just posterior to anus, 6.4 \u00b1 1.8 (5.0\u201310.0) \u03bcm thick. Lateral chord 13.0 \u00b1 4.8 (8.0\u201320.0) \u03bcm wide, occupying 17\u201342% of corresponding body diam. Lip region flatly rounded, slightly offset from body contour by a depression, 13.9 \u00b1 0.7 (12.5\u201315.5) \u03bcm wide and 6.9 \u00b1 0.8 (5.5\u20138.5) \u03bcm high. Amphidial fovea aperture extending for Coomans ). CardiaFunctional, less abundant than females (ratio = 1: 2). Reproductive system diorchic with testes occupying 45\u201357% of body length, and spindle-shaped sperm. Spicules dorylaimoid, massive, well sclerotised, 57.5\u201366.0 \u03bcm long, ventrally curved with tubular lateral guiding pieces 13.5\u201318.0 \u03bcm long. One pair of adanal supplements located at 16.6 \u00b1 1.2 (15.5\u201319.0) \u03bcm from cloacal opening and a series of four to five ventromedian supplements. Tail similar to that of female, dorsally more convex than female, and ending in a rounded terminus with short bulge.ca 53 \u03bcm, and shorter distance from anterior end to stylet guiding-ring than that in adult stages. Tail morphology in second and third juvenile stages similar to J1, becoming progressively shorter and stouter in each progressively moult. However, tail shape in fourth-stage similar into that of female, broadly dorsally convex-conoid with slightly bulging rounded terminus , being extracted from the rhizosphere of cultivated olive (Olea europaea subsp. europaea L.) (Morphometric variability is described in paea L.) , Fig 1.X. mengibarense sp. nov. groups with X. herakliense Tzortzakakis et al., 2015 [X. hispanum, and X. lanceolatum Roca & Bravo, 1993 [Xiphinema mengibarense sp. nov. can be differentiated from X. herakliense by higher a and c ratios , a shorter odontostyle (120.0\u2013131.5 vs 127.0\u2013157.0 \u03bcm), shorter spicules (57.5\u201366.0 vs 70.0\u201381.0 \u03bcm) [X. mengibarense sp. nov. mainly differs from X. hispanum in having higher a ratio (80.0\u201398.2 vs 73.1\u201383.9), a shorter odontostyle (120.0\u2013131.5 vs 131.2\u2013142.3 \u03bcm), the number of spiniform structures present in the Z-differentiation (lower vs abundant), the presence vs absence of crystalloid bodies in the tubular portion of uterus, and the frequency of males (frequent vs rare) , a shorter odontostyle and odontophore resulting in a shorter stylet (194.5\u2013215.0 vs 255.5\u2013283.0 \u03bcm), a slightly narrower lip region (12.5\u201315.5 vs 14.5\u201318.0 \u03bcm), posterior vulva position (48.5\u201357.0 vs 43.5\u201350.0%), the presence vs absence of males, and the number of spiniform structures and crystalloid bodies (lower vs very abundant) was 94% similar to several Xiphinema species such as X. italiae , X. pyrenaicum Dalmasso, 1969 [X. sphaerocephalum . Xiphinema mengibarense sp. nov. showed a high homogeneity for the D2-D3 region in the three sampled populations (X. hispanum (GU725061) and X. cohni (KC567159), with a similarity of 84% (X. mengibarense sp. nov. (KX244945) closely matched (99% similarity) those for X. italiae (FJ713154), X. pyrenaicum (GU725085) and X. gersoni (KC567154).D2-D3 region of so, 1969 (GU72507ulations . The cloctively) . Low intX. adenohystherum, X. baetica, X. cohni, X. coxi europaeum, X. duriense, X. hispanum, X. hispidum, X. incertum, X. index Thorne & Allen, 1950 [X. italiae, X. lupini Roca & Pereira, 1993 [X. macrodora, X. madeirense Brown, Faria, Lamberti, Halbrendt, Agostinelli & Jones, 1993 [X. nuragicum, X. oleae, X. opisthohysterum Siddiqi, 1961 [X. pachtaicum, X. parapachydermum, X. plesiopachtaicum, X. rivesi Dalmasso, 1969 [X. santos Lamberti, Lemos, Agostinelli & D\u2019Addabbo, 1993 [X. sphaerocephalum, X. turcicum, X. turdetanense, and X. vallense have been previously recorded within studies of dagger and needle nematodes infesting olives and vineyards in southern Spain [viz. X. cadavalense, X. conurum and X. pseudocoxi Sturhan, 1985 [Morphological and morphometrical data, and molecular delineation (rDNA) of en, 1950 , X. italra, 1993 , X. macres, 1993 , X. nuraqi, 1961 , X. pachso, 1969 , X. santbo, 1993 , X. spharn Spain , 18, 28.an, 1985 ), a brieXiphinema collected from the rhizosphere of cultivated olive (Olea europaea subsp. europaea L.) at Espiel (C\u00f3rdoba province) corresponds fairly well with studied paratypes and original description of X. cadavalense. This population was characterised by a long body; lip region hemispherical, rounded both anteriorly and laterally and set off from body contour by slightly depression; long odontostyle and odontophore; reproductive system didelphic-amphidelphic with both branches about equally developed with a well-developed Z-differentiation with weakly muscularised wall and comprising 9\u201315 sclerotized bodies of variable size and petal shape, each one consisting of a large portion, irregularly spherical surrounded by a variable number of refractive pieces; spiniform structures and crystalloid bodies in very small size and low number present along the narrower and muscular tube-like of uterus; tail dorsally convex-conoid ending in a terminal peg with blind canal , posterior guiding ring position from oral aperture (149.5\u2013167.0 vs 126.5\u2013148.5 \u03bcm) [X. cadavalense has the following specific alphanumeric codes (codes in parentheses are exceptions): A4-B2+3-C5a-D65-E56-F5-G4-H2-I3-J-K-L1.The amphimictic population of nd canal . The obs and Luc , which aavalense . In addi48.5 \u03bcm) . These d48.5 \u03bcm) , this SpX. cadavalense (KX244900) was 98% similar (14 nucleotides and no indels) to X. baetica (KC567168), 97% similar (24 nucleotides and 3 indels) to X. andalusiense sp. nov. (KX244884-KX244888) and 96% similar (30 nucleotides and 10 indels) to X. macrodora . ITS1 sequence (KX244932) region also agrees with results obtained from D2-D3, this sequence was 90% similar (105 nucleotides and 28 indels) to X. baetica (KC567157), 89% (121 nucleotides and 35 indels) to X. andalusiense sp. nov. (KX244921-KX244925) and 86% (157 nucleotides and 70 indels) to X. macrodora (KU171048). The partial 18S region of X. cadavalense (KX244946), was very similar to several sequences of Xiphinema spp., including X. diversicaudatum Thorne, 1939 [X. baetica (KC567149) and X. bakeri Williams, 1961 [D2-D3 segments of nse KX2440 was 98%et al. [The Spanish population of this species from the rhizosphere of olive was characterised by a lip region rounded offset from the rest of the body by a conspicuous depression, two equally developed female genital branches, vulva slightly anterior to mid-body, uterus with uterine differentiation, presence of Z-differentiation with small granular bodies plus small spines (in low number), female tail conical, ventral profile nearly straight, dorsal profile regularly curved with rounded terminus . The moret al. . Up to oX. conurum (KX244902) matched well, 99% similar with former sequences from Tunisia deposited in GenBank (KX062671-KX062673); and ITS1 (KX244934) was 95\u201396% similar with former sequences from Tunisia deposited in GenBank (KX062696-KX062697). And partial 18S (KX244947) was provided for the first time in this research, being 99% similar to several Xiphinema spp. such as X. nuragicum (GU725081) or X. israeliae Luc, Brown & Cohn, 1982 [D2-D3 sequence for TS1 KX2444 was 95\u2013Xiphinema collected from the rhizosphere of wild olive (Olea europaea subsp. silvestris (Miller) Lehr) at Alcaracejos (C\u00f3rdoba province) agrees fairly well with original description of X. pseudocoxi. This population was characterised by a moderately long body in an open C-shaped after fixation; lip region distinct from the body contour by a depression, frontally rounded; female reproductive system didelphic-amphidelphic having both branches about equally developed; Z-differentiation with weakly muscularised wall formed by 6\u201310 globular bodies similar in size, and irregularly spherical surrounded by a variable number of refractive pieces; no spiniform structures and, crystalloid bodies nor sperm cells observed along uterus; female tail convex-conoid, varying slightly in shape, and ending in a terminal peg with a blind canal : A4-B2-C5a-D45-E4(5)-F4(5)-G2-H2-I3-J-K-L1.The amphimictic population of nd canal , Table 9 and Luc , which ieudocoxi . Additioeudocoxi , 94, 95.eudocoxi , the newX. pseudocoxi (KX244915-KX244916) were obtained for the first time in this study. The closet species regarding D2-D3 segments of X. pseudocoxi (KX244915-KX244916) were X. globosum Sturhan, 1978 [X. diversicaudatum and X. coxi europaeum . Similarly, ITS1 region (KX244939-KX244940) also showed some similarity with X. globosum , X. diversicaudatum and X. coxi europaeum . Finally, the partial 18S of X. pseudocoxi (KX244948) matched closely (99%) with several Xiphinema spp., such as X. globosum (GU549476), X. diversicaudatum (EF538761), X. bakeri (AY283173), X. vuittenezi Luc, Lima, Weischer & Flegg, 1964 [X. index (AY687997).Sequences for an, 1978 were used for further phylogenetic studies. Sequences for X. andalusiense sp. nov., X. cadavalense, X. celtiense sp. nov., X. duriense, X. iznajarense sp. nov., X. mengibarense sp. nov., X. opisthohysterum and X. pseudocoxi were obtained for these species in this study. On the other hand, sequences from X. adenohystherum, X. cohni, X. conurum, X. hispanum, X. hispidum, X. incertum, X. index, X. italiae, X. nuragicum, X. parapachydermum, X. turcicum and X. turdetanense matched well with former sequences deposited in GenBank, and spread out the molecular diversity of these species to the newly studied areas.The amplification of D2-D3 expansion segments of 28S rRNA, ITS1 rRNA, and partial 18S rRNA yielded a single fragment of approximately 800 bp, 1000 bp, and 1800 bp, respectively, based on gel electrophoresis. Sequences from other species of Xiphinema non-americanum-group species inferred from analyses of D2-D3 expansion segments of 28S, ITS1, and the partial 18S rDNA gene sequences using BI are given in Figs X. non-americanum-group spp. based in a multiple edited alignment including 103 sequences and 753 total characters showed two clearly separated (PP = 1.00) major clades with X. cohni and X. hispanum , this clade was related (PP = 1.00) with another subclade which was formed by X. iznajarense sp. nov. (KX244891-KX244892), X. adenohystherum , X. hispidum and X. gersoni (KC567180). Finally, X. mengibarense sp. nov. formed a low-supported subclade (PP = 0.76) with X. italiae , X. pyrenaicum (GU725073), and X. meridianum Heyns, 1971 [X. bakeri and X. index which belong to Groups 7 and 8, respectively. This clade grouped sequences from the new species X. andalusiense sp. nov. (KX244884-KX244888) and the new accessions from X. cadavalense (KX244900), X. conurum (KX244902), and X. pseudocoxi (KX244915-KX244916). Xiphinema andalusiense sp. nov. (KX244884-KX244888) from wild olive occupied a superior position within the clade II forming a well-supported subclade (PP = 1.00) with X. cadavalense (KX244900) from cultivated olive, X. baetica and X. macrodora . Finally, X. pseudocoxi (KX244915-KX244916) was phylogenetically related to X. globosum (GU549474) forming a well-supported clade (PP = 0.99).Phylogenetic relationships among r clades . Clade IX. non-americanum-group species, was 1113 characters after discarding ambiguously aligned regions from the alignment. Two new accessions were used as outgroup, X. duriense (KX244935) and X. opisthohysterum (KX244938). The 50% majority rule consensus BI tree of X. non-americanum-group spp. showed two major clades (PP = 1.00) similar to those obtained for D2-D3 region , X. pseudocoxi (KX244939-KX244940) and X. cadavalense (KX244932). Xiphinema andalusiense sp. nov. (KX244921-KX244925) and X. cadavalense (KX244932) clustered with X. baetica (KC567156-KC567157) and X. macrodora (KU171048) in a well-supported subclade (PP = 1.00), these results agree with the results obtained with D2-D3 region. Xiphinema pseudocoxi and X. globosum were also phylogenetically related to this marker and they were placed in a well-supported subclade (PP = 1.00) which was related (PP = 0.96) at the same time with X. turdetanense (KC567163). Clade II grouped thirteen species from different morphospecies Groups 1, 4, 5 and 7, including X. celtiense sp. nov., X. iznajarense sp. nov. and X. mengibarense sp. nov. Xiphinema iznajarense sp. nov. (KX244928-KX244929), and X. celtiense sp. nov. (KX244926-KX244927) clustered together with X. cohni (KX244933), X. adenohystherum (GU725063), X. hispanum (GU725061) and X. hispidum (HM921367) as occurred in the D2-D3 tree. Finally, X. mengibarense sp. nov. (KX244930-KX244931) formed a low-supported subclade with X. barense Lamberti, Roca, Agostinelli & Bleve-Zacheo, 1986 [X. pyrenaicum (GU725060) although this relation also was poorly supported. The new accessions for X. duriense (KX244935) and X. opisthohysterum (KX244938) clustered together with X. pachtaicum (AY430178) as an outgroup, all of them from the X. americanum-group clustered with X. cadavalense, X. macrodora and X. baetica within the same well-supported subclade (PP = 1.00). Phylogenetic inferences based on 18S also suggest that X. pseudocoxi and X. globosum are related species, although this relation was poorly supported (X. iznajarense sp. nov. (KX244944), X. celtiense sp. nov. (KX244943) and X. mengibarense sp. nov. (KX244945) clustered in this case with X. cohni (KC567151), X. hispanum (GU725083), X. adenohystherum (GU725084), X. italiae , X. barense (KM199695), X. gersoni (KC567154), X. sphaerocephalum (GU725082), and X. pyrenaicum (GU725085) within a well-supported subclade (PP = 1.00).The 50% majority rule BI tree of a multiple alignment including 60 18S sequences and 1647 bp long showed several major clades . Additioupported . FinallyXiphinema associated with wild and cultivated olives in southern Spain, as well as their distribution and molecular phylogeny. This was conducted in an extensive and systematic nematological survey that included 211 locations and 453 sampling sites. We found 385 Spanish populations of Xiphinema spp. infesting olive soils. We described four new Xiphinema species, enlarging the diversity of Xiphinema species in the Iberian Peninsula which is in agreement with previous data obtained for the phylogeny and biogeography of the genus Xiphinema and Longidorus in the Euro-Mediterranean region [Xiphinema based on nuclear rDNA markers.This study aimed to get knowledge and a better understanding on the occurrence, abundance and biodiversity of dagger nematodes of the genus n region , 101. ToXiphinema is one of the most diverse PPN associated with olive, with twenty species reported in various countries of the Mediterranean Basin [Xiphinema species detected in olive worldwide, including four new species from the X. non-americanum-group. All these species were new records for olive with the exception of X. pachtaicum, X. index, X. italiae, X. nuragicum and X. turcicum [Xiphinema spp. observed in both olive types, our study showed a great species diversity, that was mainly associated with the X. non-americanum-group species [X. non-americanum-group, i.e. X. italiae found in all provinces, X. nuragicum in 7 out of 8 provinces, and X. coxi europaeum in 5 out of 8 provinces. In this sense, the presence of a high number of frequent species belonging to X. non-americanum-group explains the higher value observed in Hill\u00b4s 2 (Dominance diversity) index with respect to X. americanum-group . Other sXiphinema cause damage to olive by feeding on unmodified plant root cells and causing cell necrosis and galling in root apex [X. diversicaudatum and X. vuittenezi [Xiphinema spp. were responsible for 5 to 10% of loss production resulting in an estimated $39 million loss [Xiphinema spp. in both olive types studied because of their sensitivity to fast desiccation, large body size, and the absence of survival-resistance forms\u201d. Unfortunately, little is known about the ecological requirements of Xiphinema nematodes and further research is needed [Longidorus spp. showed evidence of some geographic species associations in Andalusia [Xiphinema spp. in southern Spain and other wider areas.Overall, nematode diversity decreases rapidly to agricultural management including plant-parasitic nematodes . Our resin areas . Althoug species , the geoe et al. for Longs needed . Some prndalusia . ConsequX. cadavalense, X. pseudocoxi, and X. conurum) and for ITS1 . D2-D3 expansion region was more useful for establishing phylogenetic relationships among Xiphinema species than ITS1 or 18S. Phylogenetic analyses based on D2-D3, ITS1, and partial 18S using BI resulted in a consistent position for the newly described species of X. non-americanum-group species from Spain, which grouped in two separated clades, and mostly agree with the clustering obtained by other authors [X. andalusiense sp. nov., X. baetica, and X. cadavalense. In the case of X. andalusiense sp. nov. vs X. baetica, only lower a and c\u2019 ratios, the absence of spines in the uterus, the absence of males and different ribosomal genes could separate X. baetica from X. andalusiense sp. nov. These species probably evolved in the Iberian Peninsula as they occur only there. The Iberian Peninsula has been suggested as a possible center of recent speciation for PPN nematode genera such as Longidorus, Trichodorus or Rotylenchus species [Xiphinema celtiense sp. nov., X. iznajarense sp. nov. and X. mengibarense sp. nov. could be clearly separated morphologically and molecularly from the other Xiphinema species. The majority of the species showed congruence in the phylogenetic relationships within D2-D3, ITS1, and partial 18S using the DNA from the same individual and these markers matched very well with the sequences deposited in the GenBank. This result is in contrast with the close related genus Longidorus found in a similar sampling scheme and localities in which the diversity of species was lower and all the species occupies two major positions in the phylogenetic clade [Sequences of nuclear ribosomal RNA genes, particularly D2-D3 and ITS1, are useful molecular markers for providing accurate species identification of Longidoridae , 30, 127 authors , 18. The species . Xiphineic clade .X. americanum-group and the non-americanum group species. This research provides molecular markers for precise and unequivocal diagnosis of some species of Xiphinema in order to differentiate virus vector or quarantine species. Furthermore, it reflects that similar intensive and extensive integrative studies on Xiphinema species based on widest areas may help to elucidate the evolutionary origin of Xiphinema species. In this sense, further studies based on widespread species (i.e. X. pachtaicum) could also help to clarify if the main speciation occurred in Africa leading to many apomictic species in tropical and subtropical environments as hypothesised by Coomans [In summary, this study provides new insights into the diversity of this genus associated with the olive in Mediterranean conditions with important differences related to the species within the Coomans , or in SS1 Table(DOCX)Click here for additional data file."} +{"text": "Alchornea cordifolia and Canthium subcordatum were obtained by hydrodistillation and analyzed by gas chromatography-mass spectrometry (GC-MS). The essential oils were subjected to in vitro antibacterial, antifungal and cytotoxic activity screening. Thirty-eight compounds comprising 97.7% of A. cordifolia oil and forty-six constituents representing 98.2% of C. subcordatum oil were identified. The major components in A. cordifolia oil were methyl salicylate (25.3%), citronellol (21.4%), \u03b1-phellandrene (7.4%), terpinolene (5.7%) and 1,8-cineole (5.5%). Benzaldehyde (28.0%), \u03b2-caryophyllene (15.5%), -\u03b1-farnesene (5.3%) and methyl salicylate (4.5%) were the quantitatively significant constituents in C. subcordatum fruit essential oil. A. cordifolia essential oil demonstrated potent in vitro antibacterial activity against Staphylococcus aureus (MIC = 78 \u03bcg/mL) and marginal antifungal activity against Aspergillus niger (MIC = 156 \u03bcg/mL). C. subcordatum showed antibacterial activity against Bacillus cereus and S. aureus (MIC = 156 \u03bcg/mL) and notable antifungal activity against A. niger (MIC = 39 \u03bcg/mL). However, no appreciable cytotoxic effects on human breast carcinoma cells (Hs 578T) and human prostate carcinoma cells (PC-3) were observed for either essential oil. The antimicrobial activities of A. cordifolia and C. subcordatum fruit essential oils are a function of their distinct chemical profiles; their volatiles and biological activities are reported for the first time.Bacterial resistance has been increasingly reported worldwide and is one of the major causes of failure in the treatment of infectious diseases. Natural-based products, including plant secondary metabolites , can be exploited to ameliorate the problem of microbial resistance. The fruit essential oils of Antimicrobial resistance is one of the most serious public health threats that results mostly from the selective pressure exerted by antibiotic use and abuse ,2. DurinAlchornea cordifolia (Schumach. and Thonn.) M\u00fcll. Arg. (Euphorbiaceae) is a shrub found along the coastal regions of West Africa. It has multipurpose utilization as fodder, food and medicine. The leaves, roots and stem bark extracts are used extensively in traditional medicine in the preparation of drugs for urinary, respiratory and gastro intestinal disorders [A. cordifolia has been a subject of scientific studies: anti-microbial, antioxidant and anticancer activities, etc. [A. cordifolia has been reported [A. cordifolia has demonstrated antibacterial activity against 21 bacterial strains tested and showed the highest levels of antibacterial activity with MICs against methicillin-resistant Staphylococcus aureus (MRSA) in the range of 1.6\u20133.1 mg/mL and MBCs in the range of 6.3\u201312.5 mg/mL among 24 other plant species studied [A. cordifolia leaf [isorders . A slurrisorders . The leaisorders . Hithertes, etc. ,11,12,13reported . The aqu studied . Phyto-clia leaf ,17,18,19Canthium subcordatum DC. is a tree that grows in central and western Africa and reaches a height of more than 10 m [C. subcordatum [S,9R)-roseoside [C. subcordatum and their structures deduced. GC-MS analysis and anticancer activity of ethanol leaf extract of C. parviflorum have also been reported [A. cordifolia and C. subcordatum.han 10 m . Its roohan 10 m and the han 10 m . Recentlcordatum . A numbeoseoside and shanoseoside have beereported ,27. As pA. cordifolia and C. subcordatum were collected in the month of July 2004, from the campus of the University of Ibadan, Nigeria. Plant samples were authenticated by F. Usang of the Herbarium Headquarters, Forest Research Institute of Nigeria (FRIN), Ibadan, Nigeria, where voucher specimens were deposited.The mature fresh fruits of The fruit essential oils were obtained by hydrodistillation (4 h) of the pulverized air-dried plant samples (500 g) in an all glass Clevenger-type apparatus following the British Pharmacopoeia specifications . The fruhttp://www.agilent.com/en-us/products/software-informatics/massspec-workstations/gc-msd-chemstation-software). The GC column was an HP-5ms fused silica capillary with a (5% phenyl)-methyl polysiloxane stationary phase (30 m \u00d7 0.25 \u03bcm film thickness). The carrier gas was helium with a column head pressure of 7.07 psi and flow rate of 1.0 mL/min. Inlet temperature was 200 \u00b0C and MSD detector temperature was 280 \u00b0C. The GC oven temperature program was used as follows: 40 \u00b0C initial temperature, held for 10 min; increased at 3 \u00b0C/min to 200 \u00b0C; increased 2 \u00b0C/min to 220 \u00b0C. The sample was dissolved in CH2Cl2, and 1 \u03bcL was injected using a splitless injection technique.The essential oils were subjected to GC-MS analysis on an Agilent system consisting of a model 6890 gas chromatograph, a model 5973 mass selective detector (MSD) , and an Agilent ChemStation data system and by comparison of their mass spectral fragmentation patterns and with the literature .A. cordifolia and C. subcordatum essential oils were screened for antibacterial activity against Bacillus cereus (ATCC No. 14579), Staphylococcus aureus (ATCC No. 29213), Pseudomonas aeruginosa (ATCC No. 27853), and Escherichia coli (ATCC No. 10798). Minimum inhibitory concentrations (MICs) were determined using the micro broth dilution technique [w/w solutions of samples in DMSO plus 50 \u03bcL CAMHB. The sample solutions were serially diluted (1:1) in CAMHB in 96-well plates to give concentrations of 2500, 1250, 625, 313, 156, 78, 39, and 19.5 \u03bcg/mL. Organisms at a concentration of approximately 1.5 \u00d7 108 colony-forming units (CFU)/mL were added to each well. Plates were incubated at 37 \u00b0C for 24 h; the minimum inhibitory concentration (MIC) was determined as the lowest concentration without turbidity. Gentamicin was used as a positive antibiotic control; DMSO was used as a negative control .echnique . Dilutioi.e., serial dilution, concentrations of 2500, 1250, 625, 313, 156, 78, 39, and 19.5 \u03bcg/mL) using Candida albicans (ATCC No. 10231) in a yeast-nitrogen base growth medium with approximately 7.5 \u00d7 107 CFU/mL. Amphotericin B was used as the positive control. An additional test for antifungal activity against Aspergillus niger (ATCC No. 16888) was determined as above using yeast mold (YM) broth inoculated with A. niger hyphal culture diluted to a McFarland turbidity of 1.0. Amphotericin B was the positive control.Antifungal activity was determined, as described above for bacteria (2 environment at 37 \u00b0C in Dulbecco\u2019s modified Eagle medium (DMEM) with 4500 mg glucose per liter of medium, supplemented with 10% fetal bovine serum, 10 \u03bcg bovine insulin, 100,000 units penicillin and 10.0 mg streptomycin per liter of medium, and buffered with 44 mM NaHCO3, pH 7.35.Human Hs578T breast ductal carcinoma cells (ATCC No. HTB-129) were gro2 environment at 37 \u00b0C in RPMI-1640 medium with l-glutamine, supplemented with 10% fetal bovine serum, 100,000 units penicillin and 10.0 mg streptomycin per liter of medium and buffered with 15 mM Hepes and 23.6 mM NaHCO3, pH 7.30.Human PC-3 prostatic carcinoma cells (ATCC No. CRL-1435) were gro5 cells per well and PC-3 cells at 1.9 \u00d7 104 cells per well. The volume in each well was 100 \u03bcL for both cell types. After 48 h, supernatant fluid was removed by suction and replaced with 100 \u03bcL growth medium containing either 2.5 or 1.0 \u03bcL of dimethylsulfoxide (DMSO) solution of oils (1% w/w in DMSO), giving a final concentration of 250 or 100 \u03bcg/mL, respectively, for each oil. Hs 578T cells were tested with final concentrations at 250 \u03bcg/mL and PC-3 at final concentration of 100 \u03bcg/mL. Solutions were added to wells in four replicates. Medium controls and DMSO controls (25 or 10 \u03bcL DMSO/mL) were used. Tingenone (250 or 100 \u03bcg/mL) was used as a positive control [\u00aeAQueous Non-Radioactive Cell Proliferation assay was performed [oil/% killDMSO) were calculated.Hs 578T cells were plated into 96-well cell culture plates at 1.0 \u00d7 10 control . After terformed . After cA. cordifolia and C. subcordatum fruits, according to their elution order on HP-5ms capillary column are presented in w/w) yield. Thirty-eight compounds comprising 97.7% of A. cordifolia oil and forty-six constituents representing 98.2% of C. subcordatum oil were identified. The fruit essential oil of A. cordifolia consisted of oxygenated monoterpenoids and aromatic esters (52.9% and 26.5%), monoterpene and sesquiterpene hydrocarbons (17.2% and 14.6%) and low amounts of aliphatic alcohol and aldehyde (3.7%). The major components identified in this sample include methyl salicylate (25.3%), citronellol (21.4%), \u03b1-phellandrene (7.4%), terpinolene (5.7%) and 1,8-cineole (5.5%). Other minor constituents detected in considerable quantities were p-cymene (3.6%), \u03b1-humulene (3.0%), \u03b2-caryophyllene (2.8%) (E)-\u03b2-damascenone (2.0%) and 1-octen-3-ol (2.0%). Two uncommon essential oil constituents were identified as (Z)-rose oxide and geosmin in A. cordifolia essential oil. (Z)-Rose-oxide (isobutenyl-4-methyl tetrahydropyran) is a perfumery ingredient and a constituent of Pelargonium essential oils and secretions of Aromia moschata [Actinomycetes, Streptomyces riseus and Streptomyces odourifer) are reported to be present on some fruits, grapes for example, and are known for their ability to produce geosmin during metabolism [et al. [A. cordifolia reported by Okoye et al. [E)-\u03b1-bergamotene (4.54%). Twenty-five constituents consisting 90.3% of the composition of the leaf essential oil were identified in 0.13% w/w yield.The relative concentrations of the volatile components in moschata . This cymoschata . Geosmintabolism . Accordi [et al. , geosmin,EE)-\u03b1-farnesene (5.3%) and methyl salicylate (4.5%) were the quantitatively significant constituents in C. subcordatum fruit essential oil. C. subcordatum fruit oil is comprised of 41.3% hydrocarbons and 56.9% oxygen-containing compounds. The five classes of organic compounds identified and reported are twenty-four hydrocarbons (41.3%), twelve alcohols (18.6%), three aldehydes (28.7%), four aromatic esters (5.8%), one ketone and one ether (3.8%). The fruit volatile oil is dominated by sesquiterpenoid compounds (50.8%), followed by aromatic compounds (33.8%), monoterpenoid compounds (7.3%), simple aldehydes and alcohols (6.3%). The monoterpenoid profile consisted of two monoterpene hydrocarbons (2.8%) and six oxygenated monoterpenes (4.5%). Twenty-two sesquiterpene hydrocarbons and seven oxygenated sesquiterpenes made up the sesquiterpenoid profile of the oil. Two unusual sesquiterpenoids, \u03b1-calacorene and longiborneol were identified in C. subcordatum fruit oil. The sesquiterpene alcohol, longiborneol is a constituent of Juniperus, Pinus, Cupressus, Dacrydium species and Cedrus deodara. It is reported to be a plant growth regulator (inhibits cress root growth and promotes wheat germination) [Canthium species. The high concentration of benzaldehyde in essential oil samples has been reported by other workers. Lei et al. [Cerasus subhirtella and C. serrulata contain 31.2% and 42.1% benzaldehyde, respectively as major constituents. Benzaldehyde (96.96%) was also indicated as a major component in the leaf essential oil of Prunus myrtifolia [Benzaldehyde (28.0%), \u03b2-caryophyllene (15.5%), (ination) . A literi et al. showed trtifolia .A. cordifolia and C. subcordatum showed promising antimicrobial activity and moderate antifungal activity against A. niger (MIC = 156 \u03bcg/mL); C. subcordatum oil exhibited moderate antibacterial activity against B. cereus and S. aureus (MIC = 156 \u03bcg/mL) and good antifungal activity (MIC = 39 \u03bcg/mL) against A. niger. It has been documented that Gram-positive bacteria are more sensitive to chemical compounds than Gram-negative bacteria due to differences in the structures of their cell walls; Gram-negative bacteria are less susceptible to hydrophobic small molecules such as essential oil components due to hydrophilic lipopolysaccharides in their outer membrane [A. cordifolia essential oil, Laportea aestuans essential oil, rich in methyl salicylate (54.50%), has been shown to exhibit antimicrobial activity against S. aureus, B. subtilis, P. aeruginosa, E. coli and C. albicans at 200 mg/mL compared to the standard drug; however, it was more active against the fungi Rhizopus stolon and A. niger at 25 mg/mL [Pelargonium graveolens essential oil, dominant in citronellol (26.7%), inter alia, and citronellol, also demonstrated strong inhibitory activity against S. aureus and E. coli [P. myrtifolia and apricot, Prunus armeniaca, seed essential oils) exhibited antimicrobial activity against S. aureus, S. epidermidis, B. subtilis, P. aeruginosa, E. coli and C. albicans [Stachys cretica essential oil and \u03b2-caryophyllene are reported to exhibit strong antimicrobial activity, particularly against P. aeruginosa and B. subtilis [The antibacterial and antifungal activities of the fruit volatile oils of activity . Alchornmembrane . This is25 mg/mL ; Pelargo E. coli ,44. Simity MIC = \u03bcg/mL agalbicans . Additiosubtilis .A. cordifolia and C. subcordatum fruit essential oils were screened for in vitro cytotoxic activity against Hs 578T human breast adenocarcinoma and PC-3 human prostatic carcinoma cells. Neither oil showed activity, however, with 0% kill at the concentrations tested.Both A. cordifolia and C. subcordatum essential oils are a function of their distinct chemical profiles. The fruit essential oil of A. cordifolia, rich in methyl salicylate and citronellol, showed antibacterial activity against S. aureus and antifungal activity against A. niger. The antimicrobial activity can be attributed to these two major components, which have shown antimicrobial activities [C. subcordatum fruit oil was active against B. cereus, S. aureus, and A. niger, but the activity is not likely due to the major component benzaldehyde, which is generally not antimicrobial [A. cordifolia and C. subcordatum essential oils are consistent with traditional uses of these medicinal plants.The antimicrobial activities of tivities ,47,48. Cicrobial , but rat"} +{"text": "Triticosecale Wittmack) is an important feed crop which suffers severe yield, grade and end-use quality losses due to Fusarium head blight (FHB). Development of resistant triticale cultivars is hindered by lack of effective genetic resistance sources. To dissect FHB resistance, a doubled haploid spring triticale population produced from the cross TMP16315/AC Ultima using a microspore culture method, was phenotyped for FHB incidence, severity, visual rating index (VRI), deoxynivalenol (DON) and some associated traits followed by single nucleotide polymorphism (SNP) genotyping. A high-density map consisting of 5274 SNPs, mapped on all 21 chromosomes with a map density of 0.48 cM/SNP, was constructed. Together, 17 major quantitative trait loci were identified for FHB on chromosomes 1A, 2B, 3A, 4A, 4R, 5A, 5R and 6B; two of incidence loci (on 2B and 5R) also co-located with loci for severity and VRI, and two other loci of VRI (on 1A and 4R) with DON accumulation. Major and minor loci were also identified for all other traits in addition to many epistasis loci. This study provides new insight into the genetic basis of FHB resistance and their association with other traits in triticale.Triticale (x Triticosecale Wittmack; 2n = 6 \u00d7 = 42) crop suffers severe losses in yield, grade and end-use quality due to Fusarium head blight (FHB) caused by Fusarium graminearum, Fusarium avenaceum, Fusarium poae and other spp. of genus Fusarium , five main effect QTL for Type-II resistance , seven main effect QTL for VRI and seven main effect QTL for Type-III resistance (R2) and were considered major QTL ; Table 4ajor QTL . The totIn addition to the above main effect QTL, epistasis QTL were also identified for DS and VRI on chrs 1A, 2A, 3A and 3B ; Table 5QErg.lrdc-4A), 5R (QErg.lrdc-5R) and 7A (QErg.lrdc-7A)) (R2) and were considered major QTL ) ; Table 6ajor QTL ; Table 6In addition to above main effect QTL, epistasis QTL were also identified for reduced ERG incidence on chrs 6B and 6R ; Table 7QGpc.lrdc-2A), 2B (QGpc.lrdc-2B), 4R (QGpc.lrdc-4R), 5R (QGpc.lrdc-5R), 6R (QGpc.lrdc-6R) and 7B (QGpc.lrdc-7B)) (R2) and were considered major QTL ) ; Table 6QTwt.lrdc.1R), 4R (QTwt.lrdc.4R), 5A and 5R (QTwt.lrdc.5R)) (R2) and were considered major QTL ) ; Table 6ajor QTL ; Table 7QYld.lrdc-4A), 4R (QYld.lrdc-4R.2), 6A (QYld.lrdc-6A) and 6R (QYld.lrdc-6R)) (R2) and were considered major QTL ) ; Table 6ajor QTL ; Table 7QPht.lrdc-5A), 5R (QPht.lrdc-5R), 6R (QPht.lrdc-6R) and 7R (QPht.lrdc-7R)) (QLdg.lrdc-2R), 4R , 6R (QLdg.lrdc-6R), 7B (QLdg.lrdc-7B) and 7R (QLdg.lrdc-7R)) (R2) explained by these QTL ranged from 6.0 to 38.0%. One of the above identified QTL on chr 5R (QPht.lrdc-5R) for reduced PHT was commonly shared with reduced Type-II and -III resistance and interestingly favorable allele for these, reduced PHT, DS and DON content, were contributed by TMP16315 ) ; Table 6rdc-7R)) ; Table 6Additionally, epistasis QTL were identified for PHT but not for LDG ; Table 7QFhb.lrdc-1A) and DON (QDon.lrdc-1A), also harbored QTL for TWT (QTwt.lrdc-1A) (QFhs.lrdc-2A) harbored a QTL for PHT (QPht.lrdc-2A), a 2B region for DI (QFhi.lrdc-2B), DS (QFhs.lrdc-2B) and VRI (QFhb.lrdc-2B) harbored QTL for GPC (QGpc.lrdc-2B), a 4R region for VRI (QFhb.lrdc-4R) and DON harbored QTL for TWT (QTwt.lrdc.4R) and LDG (QLdg.lrdc-4R), another 4R region for GPC (QGpc.lrdc-4R) harbored QTL for YLD (QYld.lrdc-4R.2), a 5A region for DON (QDon.lrdc-5A) harbored QTL for PHT (QPht.lrdc-5A), a 5R region for DI (QFhi.lrdc-5R), DS (QFhs.lrdc-5R.1) and VRI (QFhb.lrdc-5R.1) harbored QTL for TWT (QTwt.lrdc-5R), another 5R region for DON (QDon.lrdc-5R) and PHT (QPht.lrdc-5R) also harbored QTL for DS (QFhs.lrdc-5R.2) and a 6R region for GPC (QGpc.lrdc-6R) and YLD (QYld.lrdc-6R) harbored QTL for PHT (QPht.lrdc-6R) and LDG (QLdg.lrdc-6R) QTL listed above, fifteen more QTL were also co-localized with other QTL. One region on chr 1A, which harbored QTL for VRI (lrdc-1A) . Similarlrdc-6R) .Fusarium head blight (then scab) in England in 1884, many scientific studies have been conducted in wheat, barley and other cereals. The genetic factors, their chromosomal locations and sources for FHB resistance have been identified and well-studied in wheat [After the first report of in wheat . Howeverin wheat . Previouin wheat , predomiin wheat and possin wheat ,12. In ain wheat ,55, diffin wheat and theiin wheat was subjParents to make this DH population were selected for commercial breeding program and neither of the parents was highly susceptible for FHB, ERG and both parents shared many other favorable characters . This inSecale cereale L. genome, which is a mosaic of various progenitor genomes [Gene associated SNPs, high-throughput genotype calling and low cost per data point of recently developed SNP assays for wheat (Infinium iSelect 90K SNP assay) and rye genomes . Around genomes also obs genomes to 5.2 c genomes , however genomes to 4907. genomes cM. On t genomes also obs genomes construc genomes . We also genomes and can genomes or previ genomes and use R2) (R2) another FHB/DON resistance QTL. Interestingly 1A QTL region was never identified in any of the previous triticale studies. This region also harbored an important QTL for TWT and was derived from AC Ultima, where most of the other important QTL were derived from TMP16315. This 5A QTL seems to be common with one of the three QTL of widely used Chinese cv. Sumai-3. However, phenotypic data indicate that AC Ultima possess low level of resistance in comparison to Sumai-3. This is obvious since AC Ultima may not have 3B and 6B QTL. However, effect of 5A QTL on FHB resistance can be validated in multiple environments for its further use in breeding programs. These observations suggest that while TMP16315 possess quantitative inheritance of minor additive genes/QTLs, AC Ultima carries a major QTL for FHB resistance along with some minor QTL. Since both parents, AC Ultima and TMP16315, contribute favorable QTL alleles, they can be utilized to pyramid and obtain a high level of FHB resistance in triticale. In this study, a few of the DH lines showed significantly better phenotype for FHB resistance than both parents. Phenotypic data largely showed continuous variation for FHB-DI, -DS, -VRI and DON traits . These oR2) which inR2) though QQPht.lrdc-5R); most likely this region was flanked by markers Xiac130 and Xiac128 in Kalih et al. [rPt509721 and wPtm8731 in Kalih et al. [QErg.lrdc-7A which had an additive effect of 34.0 and LOD score 8.1 (QPht.lrdc-5R) on chr 5R, which have also been most likely identified in earlier studies, Kalih et al. [Previous studies showed negative relationship of FHB resistance with plant height ,19,20,22h et al. . Howevercore 8.1 . Though,core 8.1 . Similarh et al. . Since, The understanding of genetic architecture of FHB resistance and some related traits like ERG, GPC, TWT, YLD, PHT and LDG in spring triticale is important for developing superior cultivars. Therefore, for the first time, a high-density spring triticale SNP genetic map was generated and several new major and minor effects and epistasis QTL were mapped for FHB resistance and other related traits. These QTL includes both specific (such as a 3A QTL for reduced DON content) and common/pleotropic QTL . On the other hand, both parents contributed favorable QTL alleles and identified QTL expressed either across environments or specifically in an environment (such as 2B QTL for VRI and 1A QTL for DON). Most of the identified FHB resistance QTL were also co-localized with one or more agronomic traits such as a QTL on interstitial region of chr 5R for reduced DS, VRI and DON was found pleotropic for reduced PHT. At many pleotropic QTL regions, such as those mentioned above, the favorable alleles were contributed by same parent and these QTL can efficiently be used for marker-assisted selection (MAS) without any disadvantageous results to improve FHB resistance and other agronomic traits simultaneously. The high-density spring triticale SNP map also promises a starting platform for the fine mapping and map-based cloning of major stable QTL identified during the present study."} +{"text": "Among the variants, the homozygote variant CC genotype of mTOR rs17036508 C>T were associated with higher PCa risk than the wild TT genotypes (adjusted OR = 3.73 (95% CI = 1.75-7.94), P = 0.001). The GT genotype of mTOR rs2295080 G>T was more protective than the TT genotypes (adjusted OR=0.54 (95% CI=0.32-0.91), P=0.020). The distributions of Raptor rs1468033 A>G genotypes differed between cases and controls, especially in subgroups defined by age, BMI, smoking status, and ethnicity. The CT/CC genotypes of AKT2 rs7250897 C>T were associated with an increased risk of PCa, particularly in subgroups of age >71 and BMI >24 kg/m2. These findings suggest that SNPs in the PI3K/AKT/mTOR pathway may contribute to the risk of PCa in Chinese men.In this hospital-based case-control study of 413 prostate cancer (PCa) cases and 807 cancer-free controls, we investigated the role of functional single nucleotide polymorphisms (SNPs) of pivotal genes in the PI3K/AKT/mTOR pathway. We genotyped 17 SNPs in For Raptor variants, heterozygote genotypes AG of polymorphism rs1468033 A>G were associated with PCa risk compared to genotypes GG (adjusted OR=1.61 (95% CI =1.25-2.06), P <0.001). We also found that rs1468033 A>G was associated with PCa risk . Further analysis of the combined genotypes of these three SNPs and AKT2 rs7250897 C>T showed enhanced PCa susceptibility with increasing numbers of putative high-risk genotypes (Ptrend<0.001) , P = 0.006). Further, the mTOR rs17036508 CC genotypes were associated with increased PCa risk by recessive genetic model for subgroups of age \u226471(adjusted OR=4.75 (95%CI =1.78-12.71), P = 0.002), age >71 (adjusted OR=4.88 (95%CI =1.65-14.38), P = 0.004), BMI \u226424 kg/m2 (adjusted OR=3.20 (95%CI =1.2-8.53), P = 0.02), BMI >24 kg/m2 (adjusted OR=8.11 (95%CI =2.62-25.11), P< 0.001), ever smokers (adjusted OR=6.39 (95%CI =2.46-16.6), P< 0.001), and Uygur population (adjusted OR=5.09 (95%CI =2.2-11.78), P< 0.001). On the contrary, the mTOR rs2295080 GT/GG genotypes were associated with decreased PCa risk by a dominant genetic model in BMI >24 kg/m2 and ever smokers subgroups. However, the mTOR rs2295080 GG genotypes were associated with PCa risk among age subgroups according to the recessive genetic model. For Raptor rs1468033 A>G, AG/AA genotypes were associated with increased PCa risk by the dominant genetic model, particularly in subgroups of age >71(adjusted OR=1.81 (95%CI =1.31-2.48), P = 0.003), BMI >24kg/m2 (adjusted OR=2.02 (95%CI =1.42-2.87), P< 0.001), never smokers (adjusted OR=1.61 (95%CI =1.21-2.30), P = 0.009), ever smokers (adjusted OR=1.58 (95%CI =1.13-2.19), P = 0.068), and Uygur population (adjusted OR=1.66 (95%CI =1.26-2.20), P< 0.001). Furthermore, increased PCa risk was observed by recessive genetic model for the BMI >24 kg/m2 subgroup (adjusted OR=5.13 (95% CI=1.94-13.59), P = 0.001). Increased PCa risk was observed for AKT2 rs7250897 C>T by the dominant genetic model, particularly in subgroups of age >71(adjusted OR=1.83 (95%CI =1.33-2.52), P = 0.002) and BMI >24kg/m2 (adjusted OR=1.58 (95%CI =1.12-2.24), P = 0.010). However, further homogeneity tests showed no difference in risk estimates between subgroups for most strata except age group by mTOR rs17036508 CT/CC genotypes (P=0.032), mTOR rs2295080 GG genotypes (P=0.002), AKT2 rs7250897 CT/CC genotypes (P<0.001) and BMI group by Raptor rs1468033 AA genotypes (P<0.001). The details are shown in Table The mTOR rs17036508 CC and rs2295080 TT, Raptor rs1468033 AG/AA, and AKT2 rs7250897 TT/CT) and four environmental risk factors . Among all 8 factors, the Raptor rs1468033 A>G variant was the best one-factor model. Likewise, interactions between mTOR rs17036508 CC, rs2295080 TT and Raptor rs1468033 AG/AA represented the best three-factor model. Age was the most promising environmental risk factor associated with the four genetic factors. The details are presented in Table We performed the multifactor dimensionality reduction (MDR) analysis by including the genotypes of four significant genetic factors values at variant prior probability levels for all positive findings Table . Some himTOR rs17036508 CC, mTOR rs2295080 GG/GT, Raptor rs1468033 AG/AA, and AKT rs7250897 TT/CT genotypes were associated with PCa risk, especially in age, BMI, smoker-status, and ethnic subgroups. To the best of our knowledge, this is the first post-GWAS study analyzing associations of these six pivotal genes of PI3K/AKT/mTOR pathway with PCa risk.In the current single institution based case-control study, functional SNPs of six pivotal genes of PI3K/AKT/mTOR pathway were associated with PCa risk. Briefly, the mTOR gene is a critical cellular protein with more than 2651 SNPs reported across the whole region [mTOR rs2295080 GT/GG genotypes protected against PCa risk in Han Chinese populations [mTOR rs2295080 GT/GG genotypes were also observed in esophageal squamous cell carcinoma, gastric carcinoma, and renal cell carcinoma [In vitro and in vivo studies suggested that mTOR rs2295080 T allele probably increased the affinity of special transcription factors to this promoter region and contributed to enhanced mTOR activity [mTOR rs2295080 was linked to eight potential functional variants of mTOR with higher linkage disequilibrium (LD) coefficient >0.8, including rs1064261, rs1074078, rs1135172, rs1883965, rs4845860, rs6540965, and rs6671083. Among these, the variant rs1064261 probably interrupted the exonic splicing enhancer or silencer motif and correlated with neuroendocrine tumors [mTOR, variant rs1883965 was associated with esophageal carcinoma, gastric cancer, and hepatocellular carcinoma [mTOR was located within a miRNA binding site and an exonic splicing enhancer or silencer motif, thereby affecting pre-RNA splicing. The association between rs17036508 and PCa was also observed previously [ANGPTL7), resulting in upregulation of ANGPTL7 by hypoxia in cancer cells, which exerts a pro-angiogenesis effect [mTOR and ANGPTL7 simultaneously.The e region . Howeverulations , 19. Thearcinoma \u201322. In vactivity . Variante tumors , gastrice tumors , and esoe tumors . Similars effect . Taken tRaptor gene, located in 17q25.3 with 34 exons, regulates responses to nutrient and insulin levels [in vitro and in vivo studies have shown that Raptor acts as a scaffold protein that regulates mTOR-dependent signaling [Raptor gene polymorphisms were associated with increased risk for bladder cancer; physical activity, energy balance and genetic variants in the mTOR pathway co-coordinately influenced bladder cancer risk [Raptor rs1468033 was associated with PCa risk, particularly in subgroups of age, BMI, and smoking status, similar to previous findings. Silico analysis indicated that rs1468033 was found with several potential functional polymorphisms of Raptor gene, including rs2292639, rs499609, rs6565500, and rs9899178. Among these, rs2292639, rs4999609, and rs6565500 were predicted as transfactor binding sites, whereas rs9899178 was predicted as splicing site. It is plausible that these variants modulate the expression of Raptor gene, and affect mTOR activity.The n levels . The Rapignaling . One of cer risk . In thisAKT2 was not known. The different AKT isoforms play contradictory regulatory roles; for example, AKT1 activation inhibits cell migration whereas AKT2 promotes it [et al. reported that AKT2 rs7254617 increased prostate cancer risk [AKT2 rs7250897 was associated with increased PCa risk by a dominant genetic model in subgroups of age >71and BMI >24kg/m2, indicating that rs7250897 altered AKT2 expression, which subsequently affected synthesis of adipose-related proteins. Since the three variants were far from each other, we postulated that they were associated with carcinogenesis by different mechanisms. These findings need to be further validated.Although mTOR activity was previously implicated in promoting PCa cell invasion, the role of motes it , 32. Manmotes it . Additiomotes it . Recentlcer risk . Also, ain vitro and in vivo experiments are necessary to unravel molecular mechanisms for the genetic associations that we have postulated in this study.There were few limitations in the present study that need to be addressed. First, the limited sample size in our study may have decreased detection of weaker genetic effects in carcinogenesis. Second, information regarding predisposition to PCa was not collected for the analysis and might confuse the stratified positive associations. Third, the case-control study may have inherent selection and information biases. Because of insufficient medical records, we could not perform correlative analyses between stages of PCa and variants of AKT pathway that may have provided more information in PCa carcinogenesis. Moreover, further mTOR leading to PCa susceptibility.In summary, we showed that variants of PI3K/AKT/mTOR signal pathway genes may associate with PCa risk. The combined genotypes of these variants enhanced PCa risk with increasing numbers of putative high-risk genotypes. Moreover, the three-factor model was the best model to predict PCa risk. In conclusion, our study postulated that the genetic variants may alter the expression and activity of We recruited 413 newly diagnosed PCa cases and 807 frequency-matched cancer-free controls from genetically unrelated Chinese Han and Uygur participants in Xinjiang province between January 2003 and January 2015. The cases were histopathologically confirmed as primary prostate adenocarcinoma at the First Affiliated Hospital of Xinjiang medical University (XJMU). Pathological grades of the PCa were determined by Gleason scores from the radical prostatectomy specimens according to the latest WHO criteria . The recAll subjects were interviewed with a written informed consent. Response rate was 92% and 90% for cases and controls, respectively. The experimental and research protocols were approved by the Institutional Review Board of XJMU.http://www.ncbi.nlm.nih.gov/projects/SNP) and SNPinfo web server (http://snpinfo.niehs.nih.gov/snpfunc.htm). The criteria were: 1) minor allele frequency (MAF) was at least 5% in Chinese populations; 2) SNPs were potentially functional according to SNPinfo prediction platform. Ultimately, 17 potentially functional variants were selected involving mTOR , Raptor , AKT1 , AKT2 , PTEN (rs701848 C>T), and K-ras (rs7312175 A>G) based on the bioinformatics analysis performed with HaploView software 4.2. All these SNPs were genotyped by the TaqMan real-time PCR method as described previously [For the six pivotal genes in PI3K/AKT/mTOR pathway, selection strategy for the potentially functional SNPs was based on the NCBI dbSNP database to identify the best n-factor interaction model [The multifactor dimensionality reduction (MDR) analysis was conducted by the MDR V2.0 beta 8.2 software (on model . We furt"} +{"text": "Pseudomonas resinovorans strain MO-1, which possesses a high ability to oxidize Mn(II), has been isolated from oligotrophic pond sediment. The draft genome sequence consists of 6,252,942 bp and has a G+C content of 63.4%. Strain MO-1 has 5,694 coding sequences, including 13 putative Mn(II) oxidation genes. The extracted DNA was sequenced using a 101-bp paired-end sequencing method with an Illumina HiSeq 2500 platform at Hokkaido System Science Co., Ltd. , obtaining 22,074,708 reads, with approximately 350-fold genome coverage. After the adaptors were trimmed using the Trimmomatic program version 0.36 (mnxG (locus tag PputGB1_2447 under GenBank accession no. CP000926), mcoA (locus tag PputGB1_2665 under GenBank accession no. CP000926) and mopA (locus tag PputGB1_3353 under GenBank accession no. CP000926) of Pseudomonas putida GB-1 (\u221250) oxidation genes, much more than the 3 annotated Mn(II) oxidation genes in P. putida GB-1.Two gene families encoding multicopper oxidase (MCO) and heme peroxidase oxidase domains play an important role in Mn(II) oxidation in several MnOB. Of our 5,694 CDSs, 1, 8, and 4 CDSs were identified as being related to Mn(II) oxidation; these were homologous to ida GB-1 , respect-1 (\u221250) . The higlgorithm are 82.2P. resinovorans strain MO-1 genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession no. BDMA00000000. The version described in this paper is the first version, BDMA01000000.The"} +{"text": "Escherichia coli J53, which is used as a recipient in conjugation experiments and is a laboratory strain derived from E. coli K-12. This genome sequence will help in the development of a comprehensive genetic analysis of conjugative elements.We report here the complete genome sequence of Escherichia coli J53 is a laboratory mutant of E. coli K-12 and Oxford Nanopore Technologies MinION (R9.4 flow cell) systems. A circular chromosome was obtained by a http://mlst.warwick.ac.uk/mlst/dbs/Ecoli), similar to other E. coli K-12 strains. A genomic comparison against the K-12 reference genome for substrain MG1655 (GenBank accession no. U00096) using progressiveMauve (1A (2 copies), IS5, proB, proA, four tRNAs, a part of prophage CP4-6, and a part of a repetitive extragenic palindromic sequence (REP321) in 7 segments. A total of 57,947 bp of insertions included IS10R (6 copies), rtT small RNA (sRNA), and the lambda prophage (GenBank accession no. J02459), in 8 segments. J53 contained an 825,667-bp inversion block flanked by 2 copies of IS5 between nucleotide positions 3652638 and 4476957 of the MG1655 genome.The complete genome contains a 4,682,574-bp chromosome with a GC content of 50.8%, 4,530 coding sequences, 82 tRNA-coding genes, and 22 rRNA-coding operons. The strain belongs to sequence type 10, as per the Achtman multilocus sequence typing scheme (E. coli K-12 genomes available on the NCBI Assembly resource (https://www.ncbi.nlm.nih.gov/assembly/) as of 9 April 2018 and the J53_AICK draft genome sequence, we made a phylogenetic tree based on core single nucleotide polymorphisms (SNPs) with kSNP3.0 (secA gene, which is associated with azide resistance (Using the 39 kSNP3.0 . The J53E. coli J53 has been deposited in GenBank under accession no. CP028702.The complete sequence of the chromosome of"} +{"text": "AbstractGammarus are described and illustrated from Tibetan Plateau. Gammarusaltussp. n. and G.limosussp. n. are characterized by pereopods III\u2013IV with a few short setae and uropod III with marginal spines accompanied by short setae. Gammaruskangdingensissp. n. and G.gonggaensissp. n. are characterized by pereopods III\u2013IV with long straight setae on posterior margins and inner ramus of uropod III 0.4 times as long as outer ramus. Detailed morphological comparisons with related species are discussed. A key to 15 Gammarus species from the Tibetan Plateau and a map of their distributions are provided.Four new species of the genus PageBreakunderstood, except fishes , Beijing.The specimens were collected along the bank of streams flowing from high mountains with a fine-meshed hand net. Samples were preserved in 95% ethanol in the field and deposited in a -20\u00b0C refrigerator for long-term preservation. The body length of each amphipod was recorded by holding the specimen straight and measuring the distance along the dorsal side of the body from the base of the first antenna to the base of the telson. All dissected appendages were mounted in glycerol on slides. Appendages were drawn using a Leica DM2500 compound microscope equipped with a drawing tube. The specimens are lodged in the Taxon classificationAnimaliaORDOFAMILIAGenusFabricius, 1775Gammaruspulex .PageBreakTaxon classificationAnimaliaORDOFAMILIAhttp://zoobank.org/B32F6C92-AEAB-4A62-BD6F-4916FCC73377IZCAS-I-A0061-1), 11.6 mm, Maniganggo Town , Dege County, Sichuan Province, altitude 4000 m, August 12, 2001, collected by Xianjin Peng. Paratype: female (IZCAS-I-A0061-2), 10.1 mm; paratypes: five males and five females (IZCAS-I-A0061-3), same data as holotype.Holotype: male , 11.6 mm., 10.1mm.: second article of palp with two groups of B-setae (a group of B-setae); bases of pereopods V\u2013VII elongated (broad), narrowing distally (posterior margin of pereopods V and VI nearly straight); uropod III with spines accompanied by simple setae on inner margin (uropod III with spines accompanied by plumose setae); and telson with no medial spines on surface .G.sichuanensis Hou, Li & Zheng, 2002 in peduncle of antenna I and II with two or three groups of setae along anterior and posterior margins, and pereopod IV with a few setae on posterior margin. It differs from G.sichuanensis (G.sichuanensis in parentheses) by pereopod III with short setae on posterior margins PageBreakPageBreakof merus and carpus (with long setae on posterior margins of merus and carpus); bases of pereopods V\u2013VII elongated (broad in G.sichuanensis); uropod III with no plumose setae (both rami with plumose setae on inner and outer margins).This species is similar to Taxon classificationAnimaliaORDOFAMILIAhttp://zoobank.org/2883210F-54D8-4945-95C0-9C9DEE5D0DA2IZCAS-I-A0059-1), 11.8 mm, Erdaohe, Kangding County , altitude 2470 m, August 19, 2001, collected by Xianjin Peng. Paratype: female (IZCAS-I-A0059-2), 8.5 mm; paratypes: two males and three females (IZCAS-I-A0059-3), same data as holotype.Holotype: male , 11.8 mm, slender., 8.5 mm. in antenna II peduncle having short setae along anterior and posterior margins, and calceoli ; uropod III inner ramus 0.4 times the length of outer ramus (inner ramus 0.7 times the length of outer ramus); uropod III terminal article of outer ramus longer than adjacent spines .Gamamruskangdingensis sp. n. is similar to G.altus sp. n. in the shape of gnathopods I and II. It differs from G.altus sp. n. in having pereopods III and IV with long setae on posterior margins (with a few short setae on posterior margins); and inner ramus of uropod III 0.4 times the length of outer ramus (0.3), inner margins of inner and outer rami with a row of plumose setae (with no plumose setae).Taxon classificationAnimaliaORDOFAMILIAhttp://zoobank.org/ED25CC10-321D-44B1-98F3-E2E30CC99286IZCAS-I-A0065-1), 10.0 mm, Hepinggou, Baoxing County , Gongga Mountains, altitude 2110 m, June 15, 2001, collected by Jinzhong Fu and Yuezhao Wang. Paratype: female (IZCAS-I-A0065-2) 8.6 mm; paratypes: two males (IZCAS-I-A0065-3), same data as holotype.Holotype: male , 10.0 mm., 8.6 mm. by antenna II peduncle having long setae along anterior and posterior margins, calceoli absent ; outer ramus of uropod III with a few plumose setae on inner margin, inner ramus with no plumose marginal setae (with a row of plumose setae on inner margins of inner and outer rami); terminal article of uropod III shorter than adjacent spines (longer than adjacent spines).The new species of Gammarusgonggaensis sp. n. is similar to G.emeiensis Hou, Li & Koenemann, 2002 in antenna II peduncle with long setae along anterior and posterior margins, calceoli absent, and pereopods III and IV with long setae on posterior margins. It differs from G.emeiensisG.emeiensis.Gammarusgonggaensis sp. n. differs from G.altus sp. n. by anternna II peduncle with long setae, calceoli absent ; pereopods III and IV with long setae on posterior margin (with a few short setae); uropod III with plumose setae on inner margin of inner ramus (with no plumose setae), terminal article shorter than adjacent spines (longer than adjacent spines).Taxon classificationAnimaliaORDOFAMILIAhttp://zoobank.org/9ACD4C39-16EC-47AF-A3B0-C32C3BA8EAC3IZCAS-I-A0063-1), 8.6 mm, Baxoi County , Tibet, altitude 4400 m, August 21, 2001, collected by Xianjin Peng. Paratype: female (IZCAS-I-A0063-2), 5.5 mm; paratypes: five males and five females (IZCAS-I-A0063-3), same data as holotype.Holotype: male , 8.6 mm., 5.5 mm. by pereopod III with few setae on posterior margin (merus with four groups of setae on posterior margin); epimeral plate III acute on posterodistal corner (blunt); and uropod III inner ramus longer than half of outer ramus length (inner ramus 0.3 times the length of outer ramus).Gammaruslimosus sp. n. is very similar to G.balcanicus Sch\u00e4ferna, 1922 (widespread in Europe). It differs from the latter by pereopods III\u2013IV and uropod III having few setae; bases of pereopods VI and VII slender.Gammarus recorded from the Tibetan Plateau can be classified into four groups based on morphological comparison: (1) G.lacustris group, is characterized by uropod III inner ramus longer than half of outer ramus length, both rami fringed with plumose setae, and includes five species: G.lacustris Sars, 1863, G.lasaensis Barnard & Dai, 1988, G.hongyuanensis Barnard & Dai, 1988, G.frigidus Hou & Li, 2004, and G.jaspidus Hou & Li, 2004; (2) cave species with no eyes, including G.abstrusus Hou, Platvoet & Li, 2006, and G.praecipuus Li, Hou & An, 2013; (3) G.sinuolatus Hou & Li, 2004 with long simple setae on uropod III; and (4) G.kangdingensis group is characterized by uropod III having a few simple or plumose setae, and includes G.emeiensis Hou, Li & Koenemann, 2002, G.sichuanensis Hou, Li & Zheng, 2002, G.glaber Hou, 2017, Gammarusaltus sp. n., G.kangdingensis sp. n., G.gonggaensis sp. n., and G.limosus sp. n. A key to these species is presented as follows.The species of the genus"} +{"text": "MLL) gene produce fusion proteins such as MLL-AF4 that disrupt epigenetic pathways and cause poor-prognosis leukemias. Here, we find that at a subset of gene targets, MLL-AF4 binding spreads into the gene body and\u00a0is associated with the spreading of Menin binding, increased transcription, increased H3K79 methylation (H3K79me2/3), a disruption of normal H3K36me3 patterns, and unmethylated CpG regions in the gene body. Compared to other H3K79me2/3 marked genes, MLL-AF4 spreading gene expression is downregulated by inhibitors of the H3K79 methyltransferase DOT1L. This sensitivity mediates synergistic interactions with additional targeted drug treatments. Therefore, epigenetic spreading and enhanced susceptibility to epidrugs provides a potential marker for better understanding combination therapies in humans.Understanding the underlying molecular mechanisms of defined cancers is crucial for effective personalized therapies. Translocations of the mixed-lineage leukemia ( \u2022MLL-AF4 binding requires an unmethylated CpG (uCpG) island and Menin\u2022MLL-AF4 and Menin can spread into the gene body of some targets\u2022Spreading targets are highly transcribed and have an aberrant chromatin signature\u2022Spreading of MLL-AF4 is a predictor of sensitivity to DOT1L inhibitors Translocations of the MLL gene produce fusion proteins such as MLL-AF4 that cause poor-prognosis leukemias. Kerry et\u00a0al. show that MLL-AF4 can spread into the gene body of some target genes. Spreading targets have an aberrant chromatin signature and are sensitive to DOT1L inhibitors. MLL) gene produce over 120 different MLL fusion proteins (MLL-FPs) that cause aggressive acute leukemias, the most common one being the MLL-AF4 fusion at target genes, an epigenetic mark associated with gene activation . H3K79MeHere, we reveal a strong co-dependent relationship between MLL-AF4 and Menin binding at a small number of target genes containing uCpGs. At a subset of these gene targets, we observe MLL-AF4 and Menin spreading that is bookended by uCpGs. These spreading targets are distinct from super-enhancers, are associated with high levels of gene transcription, have an aberrant H3K79me2/H3K36me3 signature, and are predictive of a poor overall survival in patients with acute lymphoblastic leukemia (ALL). These gene targets also display a remarkable dependence on H3K79me2 and the fusion protein for their sustained expression in leukemia. Together, this work shows that MLL-FP spreading occurs at genes important in MLL leukemogenesis and has the potential to act as a biomarker for therapeutic response.Using MLL(N) and AF4(C) chromatin immunoprecipitation sequencing (ChIP-seq) in the human MLL-AF4 SEM cell line C, we ideIf the CXXC domain is essential for MLL-AF4 recruitment, we would expect all MLL-AF4 binding sites to occur at regions of uCpGs. To test this, we used a biotinylated CXXC affinity purification (Bio-CAP) assay for highTo determine whether other CXXC domain-containing proteins (\u201cCXXC proteins\u201d from now on) are also restricted to only a proportion of uCpG sites, we performed ChIP-seq for CFP1 (a CXXC protein member of the SET1 complex associated with gene activation), and KDM2B (a CXXC protein involved in the recruitment of the polycomb group repressive complex [PRC] ), in SEM2\u00a0= 0.96) I, wherea\u00a0= 0.96) J and S1HChIP-seq on two members of PAFc, PAF1 and LEO1 C, overlaLedgf siRNA system see A legend gf siRNA F and S2GNA level F.HOXA9 locus gene target isoforms ChIP-seq in the MLL-AF6 cell line ML-2 detects the fusion protein unambiguously due to a deletion of the wild-type isoforms , and simisoforms B. The hiisoforms . ER-taggisoforms , biotin-isoforms , MLL-AF4isoforms , MLL-AF4, at wild-type MLL binding sites in SEM cells C and 4D,ARID2, JMJD1C, MBNL1, MEF2C, or RUNX2 alone is associated with at least one indicator of poor prognosis in ALL patients .Cell lines, culture methods, and drug treatment protocols used in this study are listed in Western blot analysis was performed as previously described . AntibodChIP and ChIP-seq experiments were performed as described in MLL-AF4, Menin, and PAF1 cDNA were inserted downstream of the FS2-TetR coding sequence in the original pCAGFS2TetR vector, by ligation-independent cloning (LIC). Plasmids were transfected into TetO mESCs using Lipofectamine 2000, and clones stably expressing TetR fusions were selected using puromycin (1\u00a0\u03bcg/mL), or MLL-AF4 cDNA was transiently transfected into mESCs at 60%\u201370% confluency using Lipofectamine 2000. Cells were collected 24\u00a0hr after transfection.For the TetR recruitment assay, we used the previously engineered Tet-operon (TetO) mESC line . MLL-AF4ChIP-seq peaks were called as described in Nascent RNA-seq and gene expression analysis was performed as described in Clinical datasets and survival analyses are detailed in GSE13313, GSE28460, GSE29130, GSE34861, GSE73528, GSE74812, and GSE84116; and ArrayExpress: E-MTAB-3593 (for a detailed list of datasets, see Data were analyzed using Fisher\u2019s exact test, Wilcoxon test, and Mann-Whitney U test, where appropriate. Results were deemed significant if p\u00a0< 0.05. Unless otherwise indicated, data are shown as mean \u00b1 SD. This paper analyzed datasets from GEO: Conceptualization, T.A.M. and J.K.; Formal analysis, J.K., E.R., H.G., and H.M.; Investigation, J.K., L.G., M.T., N.P.B., H.M., E.B., T.A.M.; Resources, S.O., F.P., O.H., A.R., I.R.; Writing \u2013 Original draft, T.A.M. and J.K.; Writing \u2013 Review & Editing, T.A.M., J.K., O.H., A.R., I.R., M.K., R.J.K., H.G.; Visualization, T.A.M. and J.K.; Supervision, T.A.M., M.K., and R.J.K.; Funding Acquisition, T.A.M., O.H., A.R., I.R., R.J.K., M.K."} +{"text": "Riemerella anatipestifer, the tetracycline susceptibility of 212 R. anatipestifer isolates from China between 2011 and 2017 was tested. The results showed that 192 of 212 (90.6%) R. anatipestifer isolates exhibited resistance to tetracycline (the MICs ranged from 4 to 256 \u03bcg/ml). The results of PCR detection showed that, 170 of 212 (80.2%) R. anatipestifer isolates possessed the tet(X) gene. Other genes, including tet(A), tet(M), tet(Q), tet(O), tet(B), and tet(O/W/32/O), were found at frequencies of 20.8, 4.7, 1.4, 0.9, 0.9, and 0.5%, respectively. However, tet(C), tet(E), tet(G), tet(K), and tet(W) were not detected in any isolate. In these tet gene positive strains, 31 (14.6%), 2 (0.9%), 5 (2.4%), 1 (0.5%), 3 (1.4%) were detected containing tet(A)/tet(X), tet(M)/tet(O), tet(M)/tet(X), tet(O)/tet(X), and tet(Q)/tet(X) simultaneously, respectively. One isolates, R131, unexpectedly contained three tet genes, i.e., tet(M), tet(O), and tet(X). Sequence analysis of the tet gene ORFs cloned from R. anatipestifer isolates confirmed that tet(A), tet(B), tet(M), tet(O), tet(Q) and an unusual mosaic tet gene tet(O/W/32/O) were present in R. anatipestifer. The MIC results of R. anatipestifer ATCC 11845 transconjugants carrying tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), tet(Q), and tet(X) genes exhibited tetracycline resistance with MIC values ranging from 4 to 64 \u03bcg/ml. Additionally, the tet(X) gene could transfer into susceptible strain via natural transformation (transformation frequencies of ~10\u22126). In conclusion, the tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), tet(Q), and tet(X) genes were found and conferred tetracycline resistance in R. anatipestifer isolates. Moreover, the tet(X) is the main mechanism of tetracycline resistance in R. anatipestifer isolates. To our knowledge, this is the first report of tet(A), tet(B), tet(M), tet(O), tet(Q), and mosaic gene tet(O/W/32/O) in R. anatipestifer.To investigate tetracycline resistance and resistant genotype in In addition, an unknown gene tet(U) was reported to be located on the pKq10 plasmid in Enterococcus faecium gene was reported to be located on the pRA0511 plasmid in R. anatipestifer was reported to be the main mechanism of tetracycline resistance in R. anatipestifer isolates , tet(B), tet(O), tet(O/W/32/O), tet(Q) in R. anatipestifer and their resistant function were confirmed by transferring into tetracycline-susceptible R. anatipestifer ATCC 11845.To determine the tetracycline resistance mechanisms of R. anatipestifer field isolates were isolated from 58 large-scale duck farms in different regions of China between 2011 and 2017, including Sichuan, Jiangsu, Guizhou, Anhui, Guangdong, Chongqing, Guangxi, Hainan, Jiling, Henan and Beijing provinces. Under sterile conditions, the brains, hearts or livers were collected from infected or died ducks, and samples were streak-inoculated on tryptic soybean agar plates supplementary with 10% sheep-blood. A single colony from one duck was purified and cultured repeatedly. A total of 212 isolates were identified as R. anatipestifer by PCR amplifying 16S rRNA and sequencing and biochemical analyses. R. anatipestifer strains were cultured at 37\u00b0C in GC broth (GCB) or on GC agar (GCA) plates strains DH5\u03b1 and S17-1 were grown at 37\u00b0C in Luria-Bertani broth or on LB agar. When required, antibiotics were added as follows: 5 \u03bcg/ml tetracycline (TET); 2 \u03bcg/ml cefoxitin (FOX); 40 \u03bcg/ml kanamycin (KAN) or 100 \u03bcg/ml ampicillin (AMP). All antibiotics were obtained from Dalian Meilun Biotech Co., Ltd. .The bacteria and plasmids used in this study are listed in Table 6 CFU/ml (100 \u03bcl/well). The inoculated micro-plates were incubated at 37\u00b0C for 24 h. E. coli ATCC 25922 was used as a quality control strain. The experiments were repeated at least three times. Due to the lack of CLSI-approved tetracycline breakpoints applicable to R. anatipestifer in 96-well microtiter-plates according to Clinical and Laboratory Standards Institute (CLSI) guideline specific for bacteria isolated from animals CLSI, . The finp. CLSI, , i.e., stet) characterized previously in other bacteria were determined in all R. anatipestifer field isolates by PCR , tet(B), tet(C), tet(E), tet(G), tet(K)], 4 ribosomal protection genes , enzymatic inactivation gene tet(X), and a mosaic tetracycline resistance gene tet(O/W/32/O). The primers and protocols described previously was used as positive control. Since the absence of available positive controls for other tet genes, all PCR products were size-confirmed by electrophoresis on a 1.5% agarose gel. All amplicons of tet(B), tet(M), tet(O), tet(O//W/32/O), and tet(Q) from R. anatipestifer isolates were verified by sequencing , while only 12 amplicons of tet(A) were sequenced.The PCR templates were prepared by treating the bacteria with lysis buffer and boiled for 10 min. The presence of the tetracycline resistance genes (tet(X) gene was amplified by PCR from R. anatipestifer CH-2 using the primer sets tet(X)-F2/tet(X)-R2, listed in Table tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), and tet(Q) gene were also amplified from tet-positive isolates confirmed above using the additional primers that were designed based on the previously described tet sequences in other bacteria (Table tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), and tet(Q) genes, respectively. The purified amplicons were sequenced and digested with restriction enzymes, and then ligated to the same digested shuttle vector pLMF03 and KAN (40 \u03bcg/ml) and identified by PCR. At the same time, the negative control empty vector pLMF03 was transferred into ATCC 11845, resulting in the transconjugant ATCC 11845 (pLMF03). The MICs of tetracycline for the wild-type and transconjugants were measured as described above.The correct recombinant plasmids were transferred into tet(X) gene was verified by natural transformation as described previously were respectively used as donor DNA and transferred into the recipient strain R. anatipestifer ATCC 11845. The transformants, designated ATCC 11845 [tet(X)], were screened using GCB plates supplemented with TET (5 \u03bcg/ml). The insertion of the transferred tet(X) genes was verified by PCR and sequencing. The tetracycline resistance phenotypes of transformant was determined as described above.The transferability of the tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), and tet(Q) genes in R. anatipestifer isolates R100, R98, R131, R96, and R159 in this study have been deposited in GenBank under the accession numbers from MF969099 to MF969104, respectively.The sequences of All animals studies were conducted in strict accordance with the recommendations of the Guide for the Care and Use of Laboratory Animals, National Research Council. The animal-use procedures were approved by the Animal Ethics Committee of the Sichuan Agricultural University .R. anatipestifer field isolates were resistance to tetracycline by susceptibility test. The MICs of tetracycline in 212 R. anatipestifer field isolates ranged from 0.25 to 256 \u03bcg/ml was detected in 170 of 212 isolates, exhibiting the highest rate of occurrence among tet genes (80.2%). The detected frequency of other tet genes was as followed: tet(A) (20.8%), tet(M) (4.7%), tet(Q) (1.4%), tet(O) (0.9%), tet(B) (0.9%), and tet(O/W/32/O) (0.5%). However, tet(C), tet(E), tet(G), tet(K), and tet(W) were not detected in any of 212 tested R. anatipestifer field isolates (Table tet genes simultaneously (Table tet(X) was detected simultaneously along with tet(A), tet(M), tet(O), and tet(Q) in 31(14.6%), 5 (2.4%), 1 (0.5%), and 3 (1.4%) isolates, respectively. Two isolates (0.9%) carried tet(M) and tet(O) genes simultaneously. Moreover, one isolate (0.5%) had three commensal tet genes, tet(M), tet(O), and tet(X), respectively. The R. anatipestifer field isolates containing one or more tet genes exhibited tetracycline resistance with MICs ranging from 4 to 256 \u03bcg/ml, while no tet genes were detected in 19 tetracycline-susceptible isolates and 1 intermediately resistant isolate. Although several isolates carried more than one tet genes in this study, they did not display higher MIC values. Thus, the positive rate of genotype was in line with that of tetracycline resistance phenotype.To assess the prevalence of the R. anatipestifer isolates selected for ORFs sequencing were listed in Table tet(A) gene cloned from six different R. anatipestifer isolates shared 99\u2013100% identity (Table MF969099) showed 99% sequence identity with the tet(A) gene from transposon Tn1721 gene cloned from R. anatipestifer isolates showed 99% identity each other. The one in R98 isolate (GenBank accession no. MF969100) showed 100% identity with tet(B) gene from transposon Tn10 genes from five different R. anatipestifer isolates shared 99\u2013100% sequence homology. The one in R133 isolate (GenBank accession no. MF969101) exhibited 96 and 95% sequence identity with tet(M) genes from Streptococcus pneumoniae genes cloned from R. anatipestifer isolates were 100% identity. The tet(O) gene in R131 isolate (GenBank accession no. MF969102) exhibited 99% sequence identity with the tet(O) genes from Streptococcus mutans DL5 from R. anatipestifer isolate R96 (GenBank accession no. MF969103) was a mosaic tetracycline resistance gene derived from tet(O) and tet(W) genes. Sequence alignment result showed that it had 97 and 99% sequence identity with the tet(W/32/O) gene from Bifidobacterium thermophilum (GenBank accession no. AM710601) gene from Streptococcus suis integrative conjugative element ICESsu32457 (GenBank accession no. FR823304) gene from three different R. anatipestifer isolates shared 100% identity. The tet(Q) gene in R159 isolate (GenBank accession no. MF969104) exhibited 97% sequence identity with the tet(Q) gene from Bacteroides thetaiotaomicron gene in R. anatipestifer CH-2 gene previously reported on the pRA0511 plasmid in R. anatipestifer , tet(B), tet(M), tet(O), tet(O/W/32/O), tet(Q), and tet(X) genes were responsible for tetracycline resistance in R. anatipestifer, recombinant plasmids carrying these genes amplified from different R. anatipestifer isolates were transferred into the tetracycline-susceptible R. anatipestifer ATCC 11845 by conjugative transfer. The tetracycline MICs for all transconjugants ranged from 4 to 64 \u03bcg/ml (Table tet(A), tet(B), or tet(O) genes showed low-level tetracycline resistance, and their MIC values were 4\u20138 \u03bcg/ml. The transconjugants containing tet(M), tet(O/W/32/O), or tet(X) genes exhibited tetracycline resistance of 32 \u03bcg/ml. The tetracycline resistance of ATCC 11845 [pLMF03-R159-tet(Q)] was the highest among all transconjugants .To further verify whether the identified tet(X) gene, we transferred the tet(X) gene from R. anatipestifer CH-2 to ATCC 11845 by natural transformation. The results showed that the tet(X) gene could be successfully transferred into tetracycline-susceptible ATCC 11845. The maximum transformants were obtained with transformation frequency about ~10\u22126 for 5 \u03bcg R. anatipestifer CH-2 genome. Compared with wild-type strain ATCC11845, the transformant ATCC 11845 [tet(X)] exhibited 128-fold increased tetracycline resistance gene could confer tetracycline resistance and be easily transferred by natural transformation in R. anatipestifer.To study the transferability of the R. anatipestifer isolates in China. The results of antimicrobial susceptibility showed that tetracycline resistance in R. anatipestifer was widespread in China between 2011 and 2017, although the usage of this antibiotic treatment was decreased in the avian industry. By PCR detection, the genotypes of tetracycline resistance were abundant in our investigated R. anatipestifer isolates, including efflux genes [tet(A) and tet(B)], ribosomal protection genes , enzymatic gene tet(X), and mosaic tetracycline resistance gene tet(O/W/32/O). The total rate of positive resistance genes was as high as 90.6%. The tet(X) gene had the highest occurrence frequency and was the dominant mechanism conferring tetracycline resistance in R. anatipestifer isolates. Unexpectedly, this conclusion was in contrast to previous reports that ribosomal protection and efflux pumps were the classical tetracycline resistance mechanisms in other bacteria detected in this study was also in contrast to the previous conclusion that tet(C) was the main mechanism of tetracycline resistance in R. anatipestifer isolates , tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), and tet(Q) genes were detected in R. anatipestifer.Tetracyclines have been widely used for disease treatment and growth promotion in livestock Roberts, . In thistet genes or an isolate may contain different tet genes on different plasmids or some tet genes on plasmid and other tet genes in the chromosome or tet(S) gene was reported to accompany with tet(M) gene /tet(B), tet(A)/tet(C), and tet(A)/tet(D)] /tet(C), and tet(C)/tet(M)]. In this study, multiple tet genes were also found in one R. anatipestifer isolate, such as tet(A)/tet(X), tet(M)/tet(O), tet(M)/tet(X), tet(O)/tet(X), tet(Q)/tet(X), and tet(M)/tet(O)/tet(X). This phenomenon might be due to strong selective pressure and horizontal gene transfer among the various bacteria , the tet(X), tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), and tet(Q) genes were most likely located in the chromosome of R. anatipestifer. We confirmed that the tet(X) gene could be transferred by natural transformation, and this transferability might contribute to its wide dissemination in R. anatipestifer.The Roberts, . In genetet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), tet(Q), and tet(X) genes to susceptible strain, we verified that all tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), tet(Q), and tet(X) genes were functional and conferred tetracycline resistance in R. anatipestifer. Interestingly, tet genes detected in this study have high identities with others reported previously, while they exhibited comparatively lower tetracycline resistance in R. anatipestifer , tet(B), and tet(O) conferred the tetracycline resistance with the MIC values from 4 to 8 \u03bcg/ml. We speculated that the low-level of resistance in R. anatipestifer might result from the low-level of tet gene expression, which needed to be further illustrated.Finally, through transferring the tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), and tet(Q) tetracycline resistance genes in R. anatipestifer. We confirmed that all the tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), tet(Q), and tet(X) confer the tetracycline resistance in R. anatipestifer. The predominant tetracycline resistance mechanism in R. anatipestifer is conferred by tet(X) gene.To the best of our knowledge, this is the first report of the presence of tet genes in R. anatipestifer isolates. D-KZ, X-XZ, and R-YJ cloned and sequenced the tet genes. SC, K-FS, and QY analyzed the sequences of tet genes. H-YL, YW, and X-YC transferred the shuttle vectors. D-KZ, H-YL, and M-SW performed the natural transformation of tet(X) gene. HL, D-KZ, and A-CC drafted and revised the manuscript. All authors have read and approved the final version of the manuscript.D-KZ, M-SW, and A-CC conceived and designed the project. H-YL, M-FL, and M-SW performed the tetracycline susceptibility test and prevalence of The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Case Reports in Psychiatry has retracted the article titled \u201cCombined Case of Blood-Injury-Injection Phobia and Social Phobia: Behavior Therapy Management and Effectiveness through Tilt Test\u201d . The artHeimberg RG et al.: Psychometric properties of the Liebowitz Social Anxiety Scale. Psychological Medicine, 1999, 29, 199\u2013212 (not cited);Ayala ES, Meuret AE, Ritz T: Treatments for blood-injury-injection phobia: a critical review of current evidence. J Psychiatr Res. 2009 Oct; 43(15):1235-42. doi: 10.1016/j.jpsychires.2009.04.008;Lars-G\u00f6ran \u00d6st, Ulf Sterner: A specific behavioral method for treatment of blood phobia. Behaviour Research and Therapy Volume 25, Issue 1, 1987, Pages 25\u201329 doi: 10.1016/0005-7967(87)90111-2;Lars-G\u00f6ran \u00d6st, Anita Jerremalm, Jan Johansson: Individual response patterns and the effects of different behavioral methods in the treatment of social phobia. Behaviour Research and Therapy. Volume 19, Issue 1, 1981, Pages 1\u201316 doi: 10.1016/0005-7967(81)90107-8;Ryan C. Shorey and Gregory L. Stuart: Manualized Cognitive-Behavioral Treatment of Social Anxiety Disorder: A Case Study. Clin Case Stud. 2012 Feb 1; 11(1): 35\u201347. doi: 10.1177/1534650112438462 (not cited)."} +{"text": "Spiroplasma citri causes stubborn disease in Citrus spp. and diseases in other plants. Here, we report the nucleotide sequence of the 1,599,709-bp circular chromosome and two plasmids of S. citri strain R8-A2T. This information will facilitate analyses to understand spiroplasmal pathogenicity and evolutionary adaptations to lifestyles in plants and arthropod hosts. Sympt\u2013coplasma \u201313. Onlyoplasma \u2013, 15, fors coined , was thema citri , 17.Spiroplasma kunkelii CR2-3X (S.\u00a0citri strain R8-A2T (Morocco-R8-A2 [ATCC 27556T]), which was originally isolated from stubborn diseased citrus [Citrus sinensis (L.) Osbeck var. Washington navel] , CP013198 (plasmid pSCI26), and CP013199 (plasmid pSCI15). The sequence versions described in this paper are CP013197.1, CP013198.1, and CP013199.1, respectively.This genome project has been deposited in GenBank under BioProject ID PRJNA296877, BioSample accession number SAMN04110376, and GenBank accession numbers"} +{"text": "Psammomys obesus as an animal model of diet-induced type 2 diabetes when subjected to a hypercaloric regimen.Type 2 diabetic retinopathy is the main cause of acquired blindness in adults. The aim of this work was to examine the retinal function of the sand rat Psammomys obesus by high caloric diet . The visual function of control (n = 7) and diabetic (n = 7) adult rodents were followed up during 28 consecutive weeks with full-field electroretinogram(ERG) recordings evoked to flashes of white light according to the standard protocol of the International Society for Clinical Electrophysiology of Vision protocol (ISCEV).Hyperglycemia was induced in Twenty-eight weeks following the induction of diabetes, results revealed significantly reduced and delayed photopic and scotopic ERG responses in diabetic rats compared to control rats. More specifically, we noted a significant decrease in the amplitude of the dark-adapted 0.01ERG (62%), a- and b-wave amplitudes of the dark-adapted 3.0 ERG and the four major oscillatory potentials components (OP1-OP4) . In photopic conditions, diabetic rats showed a significant decrease in a- and b-wave , photopic negative response (55.3%), 30 Hz flicker (63.7%), OP1-OP4 and S-cone (34.7%). Significantly delayed implicit times were observed for all ERG components in the diabetic animals. Results obtained are comparable to those characterizing the retinal function of patients affected with advanced stage of diabetic retinopathy.Psammomys obesus is a useful translational model to study the pathophysiology of diabetic retinopathy in order to explore new therapeutic avenues in human patients. Diabetic retinopathy (DR), which can lead to blindness in severe cases, is reported to affect more than 90% of diabetic patients . The patPsammomys obesus (P.obesus) fed with a high caloric diet will spontaneously develop type 2 diabetes, with accompanying retinopathy, thus making them a valid translational model of this retinal disorder . Of interest, in the present study, all P.obesus which developed DR after 28 weeks of high-fat treatment also developed a retinal dysfunction as measured with the ERG.Electrophysiological evaluation after the morphological assessment in diabetic P.obesus was needinopathy , 32, 33.inopathy on the msubjects , making P.obesus. These functional changes suggest that photoreceptor function, as well as synaptic transmission from the photoreceptors to bipolar cells, were affected in vivo by the high-fat induced hyperglycemia [P.obesus showed a decreased expression of both PKC \u03b1 and \u03b6 isoforms that are Ca2+ independent and co-localized in rod bipolar cells[P.obesus retina. Another alteration detected in diabetic retina in our previous study affecting the synaptic terminals by an increase in synaptic proteins such as synaptophysin [P.obesus viewed as an indicator of retinal cell stress [in vitro by Baccouche et al. [P.obesus were present for both scotopic (rod-mediated) and photopic (cone-mediated) conditions, indicating that both retinal systems are affected in our animal model of diabetic retinopathy. Based on ERG abnormalities and histologic findings in advanced human DR, a significant decrease in amplitudes of scotopic a- and b- waves from pre-proliferative DR [P.obesus at 28 weeks after diabetes induction. A calculation of b-/a-wave amplitude ratios in the present study revealed a declined in scotopic condition, suggesting that bipolar cells are more affected than photoreceptors. However, in photopic condition the unchanged ratio showed that the decrease of b-wave amplitude was correlated to the photoreceptoral response.Our results demonstrated that the amplitude of a- and b- waves ERG of diabetic rodents at 28weeks were significantly reduced, and the implicit times were considerably delayed compared to control glycemia , 34. Thelar cells. This detophysin . The uprl stress . These ce et al. . ERG abnative DR indicateative DR . The darative DR is reporative DR \u201341. Thusative DR . Chung eative DR reportedative DR \u201346 and iP.obesus may be explained by the loss of amacrine cells numbers at different cell retinal layers including retinal ganglion cells [P.obesus ERG were comparable to what is reported in human patients at the proliferative stage in diabetic retinopathy [P.obesus.Our results also provide evidence of retinal impairments beyond the level of the photoreceptors in rodents with diabetes, given that OPs were shown to signal inner retinal activity, particularly the amacrine cells , 48. Alton cells . These con cells , 49\u201351, inopathy \u201354. Thisinopathy , 55\u201357, P.obesus model mimics several of the DR features observed in human diabetes and should therefore be considered as a valid alternative to test therapeutic pharmacological molecules on type 2 DR functions.Currently available diabetic rodent models can be used to study the initial (acute) or latent phase of diabetic retinopathy and several studies have reported a concurrent change in OPs , 58, 59.P.obesus after 7 months of diabetic induction.The i-wave of the human full-field photopic ERG response is a relatively small positive deflection following the b-wave and is thought to originate in an off-circuitry in the inner retina . AlthougP.obesus were previously reported by our laboratory showing a reduction by 44% of RGCs in diabetic P.obesus retina after 7 months of diabetes progression [Degeneration of the retinal ganglion cells (RGC) and deterioration of the inner nuclear layer in the retinas of diabetic gression . In the gression , 69. In gression , 70, 71.P.obesus was reduced in amplitude and delayed in timing, similar to what was previously reported in human diabetes [P.obesus. Recognition of these defects will enhance our understanding of the pathophysiology of diabetic retinopathy.Our results also showed that the photopic flicker ERG of our diabetic diabetes , 72, 73.diabetes . The timdiabetes describeP.obesus was significantly reduced in amplitude and delayed in timing. The cone short-wavelength opsin staining was detectably reduced in P.obesus diabetic retinas and this was confirmed by Western blot analysis in our previous study [Finally, as previously shown in diabetic human subjects , 76, theus study .P.obesus and the corresponding changes in human DR and support the notion that it represents a valid translational model to study the retinal pathophysiological processes involved in the onset and progression of type 2 diabetic retinopathy.\u201dIn summary, the totally of our findings regarding ERG presented in this report further confirms the similarity between the characteristics of retina changes in diabetic P.obesus. Such studies should include fundus photography, optical coherence tomography and fluorescein angiography in order to clarify to what extent the ERG findings correlate (precede or follow) with morphological changes in the retina.Clearly, more studies are needed to better correlate structural and functional changes in the diabetic retina of The present study clearly demonstrated for the first time that long-lasting and significant alterations in visual function detected by full-field ERG take place after 28 weeks of diet-induced type 2 diabetes in the retina of the sand rat. Thus, the diabetic sand rat appears to be an animal model that mimics several important features of the human form of diabetic retinopathy.P.obesus as a useful translational model to study diet-induced type 2 diabetic retinopathy . We strongly believe that adding this new model to the researchers\u2019 armamentarium will not only be instrumental in increasing our understanding of the pathophysiology of human diabetic retinopathy but also help in the development of new therapeutic strategies.Our results confirm the validity of the S1 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S2 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S3 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S4 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S5 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S6 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S7 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S8 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S9 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S10 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S11 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file.S12 Fig2 flash. (B) Mixed response using 3 cd.s/m2 flash. (C) Photopic responses using 3 cd.s/m2 flash. (D) Photopic 30 Hz flicker response. (E) Photopic S-cone response using 0.0045cd.s/m2 blue flash on an orange background.Representative traces indicating: (A) Rod responses using 0.01 cd.s/m(TIF)Click here for additional data file."} +{"text": "Microbacterium hominis 84-0209T and M.\u00a0laevaniformans 91-0039 were studied. Genome sizes were 3,506,522 (70.96%) and 2,999,965 (69.51%), respectively. Annotation revealed: (M.\u00a0hominis) three rRNA sequences, 45 tRNA genes, and 3,218 coding sequences; (M.\u00a0laevaniformans) three rRNA sequences, 49 tRNA genes, and 2,874 coding sequences.Draft genomes for Microbacterium are environmentally derived, Gram stain-positive bacilli which infrequently cause opportunistic infections in humans (T (CDC group A-4) and LCDC 91-0039 (CDC group A-5) were shared by Health Canada\u2019s Laboratory Centre for Disease Control with European and Japanese colleagues as part of an effort to assign provisionally named bacteria to validly published genera. Many CDC group A-4 and A-5 isolates were assigned to the genus Microbacterium in 1995 after 16S rRNA gene sequencing analysis as well as M.\u00a0laevaniformans LCDC 91-0039 (T and LCDC 91-0039.Members of the genus n humans . Some ofn humans . LCDC 84DNA was extracted using the TruseqR DNA HT sample preparation kit. Paired-end whole-genome shotgun libraries were constructed using TruseqR Nano DNA HT library preparation kit and mate-pair libraries for each strain were prepared using the Nextera mate-pair sample preparation kit (Illumina). Sequencing was performed using a MiSeq sequencer (Illumina).M.\u00a0hominis and M.\u00a0laevaniformans generated 2,296,026 and 1,583,940 reads; mate-pair libraries gave rise to 2,272,076 reads and 2,768,080 reads, respectively. Overlapping paired-end reads were merged using FLASH (fast length adjustment of short reads) predicted three rRNA sequences, 45 tRNA genes, and 3,218 coding sequences. Data was highly consistent (>99% symmetric identity [SI]) with an unpublished genome of M.\u00a0hominis NBRC 15708T (Genbank [GB] accession no. NZ_BCW100000000.1); both genomes were not closely related (63% SI) to GB NZ_JWSZ00000000.1. Annotation of M.\u00a0laevaniformans using Prokka and repeat sequences; mate-pair reads were added to contigs using Sspace (v2.0.0) to produce scaffolds . This reM.\u00a0hominis LCDC 84-0209T and M.\u00a0laevaniformis LCDC 91-0039 have been deposited at DDBJ/EMBL/GenBank under accession no. LRYC00000000 and LRAD00000000.Draft whole-genome projects for"} +{"text": "Escherichia coli (ETEC) is a major cause of diarrhoea in children below 5 years of age in endemic areas, and is a primary cause of diarrhoea in travellers visiting developing countries. Epidemiological analysis of E. coli pathovars is traditionally carried out based on the results of serotyping. However, genomic analysis of a global ETEC collection of 362 isolates taken from patients revealed nine novel O-antigen biosynthesis gene clusters that were previously unrecognized, and have collectively been called unclassified. When put in the context of all isolates sequenced, one of the novel O-genotypes, OgN5, was found to be the second most common ETEC O-genotype causing disease, after O6, in a globally representative ETEC collection. It\u2019s also clear that ETEC OgN5 isolates have spread globally. These novel O-genotypes have now been included in our comprehensive O-genotyping scheme, and can be detected using a PCR-based and an in silico typing method. This will assist in epidemiological studies, as well as in ETEC vaccine development.Enterotoxigenic CF, colonization factor; ETEC, enterotoxigenic Escherichia coli; LT, heat-labile toxin; O-AGC, O-antigen biosynthesis gene cluster; OgUT, O-genotype untypeable; ST, heat-stable toxin; STEC, Shiga toxin-producing Escherichia coli.Escherichia coli isolates were deposited in GenBank/EMBL/DDBJ under the accession numbers shown in Table S1 .1. Assembled draft genomes for 55 enterotoxigenic wzy genes from positive control strains were deposited in GenBank/EMBL/DDBJ under the accession numbers LC177546\u2013LC177554 and LC223608\u2013LC223610, respectively.2. Sequences of nine annotated O-antigen biosynthesis gene clusters and three Escherichia coli (ETEC) isolates. The novel O-genotype OgN5 was found to be the second most common ETEC O-genotype globally, with no prior information regarding the contribution to the burden of disease. To gain more information about trends in ETEC OgN epidemiology, further studies of global OgN isolates are needed. The PCR method described in this study and an in silico typing method may help the surveillance and monitoring of the OgN groups.We identified nine novel O-genotypes (OgN) in a global collection of enterotoxigenic Escherichia coli (ETEC) [The first diarrhoeal illness that infants often experience in endemic areas is caused by enterotoxigenic i (ETEC) . In 2010i (ETEC) . The majE. coli isolates, especially pathogenic E. coli, for taxonomical and epidemiological studies. Most of what we know about E. coli prevalence, outbreaks and surveillance is described in terms of the O-serogroup. Recently, sequence analyses show that phenotypic O-serogroup diversification can be correlated with differences in the gene content and genetic diversity of the O-antigen biosynthesis gene cluster (O-AGC) located on the chromosome [wzx (encoding the O-antigen flippase), wzy (encoding the O-antigen polymerase), and the wzm and wzt genes (encoding components of the ABC transporter pathway) located on the O-AGCs are highly variable in sequence, and can be used as gene markers for the identification of O-serogroups via molecular approaches [in silicoblast analysis using a wzx/wzy and wzm/wzt sequence set extracted from O1 to O187 O-AGCs, we subtyped our 362 global ETEC isolates [n=38), O25 (n=24), O27 (n=18), O114 (n=17), O115 and O159 . In addition to the ETEC isolates classified into 48 known O-genotypes, 55 isolates carried wzx/wzy genes that showed <50\u200a%\u2009or no sequence identity to the previously defined sequences. These ETEC isolates were categorized as O-genotype untypeable (OgUT), but carried novel O-AGCs.O-serogrouping remains the gold standard for the subtyping of romosome . In partproaches . By applIn this study, we focused on characterizing the OgUT ETEC isolates detected in our previous study . Such ETwzx and wzy sequences were extracted from each O-AGC. The known wzx/wzy sequences from typical E. coli O-serogroups [Shigella O-serogroups [E. coli OX serogroups [E. coli [wzy genes of OX25 and S. dysenteriae type 6, which are not found in the O-AGCs). A complete set of fliC sequences [ETEC O-AGC sequences were obtained from draft genomes used in a previous study . The wzx groups) , Shigell sonnei) , E. coliwzx and wzy were constructed by using the neighbour-joining algorithm using mega5 software [clustal W program [Phylogenetic trees of software , followi program .wzy sequences. PCR was performed as follows: the 30\u2009\u00b5l reaction mixture contained 2\u2009\u00b5l genomic DNA, 6\u2009\u00b5l 5\u00d7 Kapa Taq buffer, dNTP mix , MgCl2 , primers and 0.8 U Kapa Taq DNA polymerase (Kapa Biosystems). The thermocycling conditions were: 25 cycles of 94\u2009\u00b0C for 30\u2009s, 58\u2009\u00b0C for 30\u2009s and 72\u2009\u00b0C for 1 min. The PCR products were visualized following agarose gel (1.5\u200a%) electrophoresis in 0.5x TBE and staining with ethidium bromide (1 mg/ml). Three strains were used as positive-control strains for PCR.OgN-specific PCR primers targeting OgN3, OgN5 and OSB16 were designed based on each alignment of wca) (upstream) and the histidine biosynthesis (his) (downstream) extracted from OgUT ETEC genomes contained nine novel O-AGCs, OgN2, OgN3, OgN4, OgN5, OgN13, OgN14, OgN15, OgN16 and OgN17 (wzx and wzy were highly conserved within each O-genotype (99.8\u2013100\u200a%\u2009sequence identity). ETEC OgN5 strains were isolated in five countries, Guatemala (n=12), Argentina (n=5), Egypt (n=4), Mexico (n=4) and Indonesia (n=4), between 1989 and 2003. All ETEC OgN5 isolates carried the ST-encoding gene, except for a single isolate (E1542) that carried the LT-encoding gene, and all OgN5 isolates were confirmed negative for all known CFs by dot-blot and PCR-based analyses in our previous study [fliC-based H-typing showed that the OgN5 isolates were classified into eight H-types: H5, H9, H10, H16, H18, H19, H32 and H39 (see Table S1). Phylogenetic analysis showed OgN5 isolates were spread across phylogenetically distinct lineages where most/some isolates grouped based on their H-types . The major groups were OgN5\u200a:\u200aH10 and OgN5\u200a:\u200aH16 belonging to a phylogenetic lineage L14 [E. coli phylogroup A and a lineage L22 (designed in this study) of phylogroup B, respectively . Additionally, OgN5\u200a:\u200aH18 , OgN5\u200a:\u200aH9 , OgN5\u200a:\u200aH32 , OgN5\u200a:\u200aH19 , OgN5\u200a:\u200aH34 , OgN5\u200a:\u200aH16 and OgN5\u200a:\u200aH5 were observed. No significant association between lineages and geographical origins was observed (see Table S1).Comparative analyses revealed that chromosomal O-AGC sequences flanked by gene clusters of the colanic acid biosynthesis . Among t (OSB16) . A summafliC of H45, and were confirmed positive for STh and two CFs, CFA/I (a fimbria) and CS21 (a type IV pilus) (see Table S1). All OgN3\u2009:\u2009H45 isolates were phylogenetically grouped into L6 of phylogroup A, and originated from Central and South America, including Mexico, Guatemala and Argentina . Six of eight OSB16 strains carried the fliC of H32, and were confirmed positive for LT, LT+STh or LT+STp, and negative for all known CFs (see Table S1). All OSB16\u200a:\u200aH32 and OSB16\u200a:\u200aH2 isolates were phylogenetically grouped into L13 of phylogroup A, and originated from Guatemala and Argentina . Additionally, three OgN13, two OgN15 and single OgN2, OgN4, OgN14, OgN16 and OgN17 strains were observed in our ETEC collection (see Table S1).Six of eight OgN3 strains carried the wzy genes associated with diarrhoeal patients in Egypt , Boliviawzx/wzy from O-AGCs were highly conserved within each O-genotype, indicating that these O-AGCs have been spread across this species by horizontal gene transfer. Phylogenetic analysis in our previous study [Novel O-genotype ETEC isolates were found in several distinct phylogenetic lineages, and sequences of us study showed tin silico-based serotyping web tool, SerotypeFinder, of the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/SerotypeFinder) [E. coli O-antigen associated genes from O1 to O187 and H-antigen associated genes (fliC and its homologues) from H1 to H56 can be used to estimate E. coli O\u2009:\u2009H serotypes of sequenced isolates. If it is possible to organize and update the database with new wzx and wzy sequences, it becomes possible to meet the requirements for broader O-genotypes, including OgN5, OgN3 and OSB16 in the in silico typing.Recently, we have been able to access whole-genome sequencing data due to the appearance of next-generation sequence technologies. A publicly available eFinder) , which hin silico typing method.In conclusion, by using detailed whole genome sequence-based analyses, it is clear that there is a hidden diversity of ETEC O-genotypes for which there is no prior information regarding their contribution to the burden of disease. It should be noted that even from our global collection, ETEC isolates from Africa are underrepresented. Hence, it is possible and perhaps likely that additional novel ETEC O-types and their associated lineages will continue to be discovered. These novel O-genotypes identified in this study have now been included in our comprehensive O-genotyping scheme and can be detected using the PCR-based method described in this study and by the rfb) cluster of Escherichia coli O111. Gene 1995;16:17\u201323. GenBank/EMBL/DDBJ accession no.: AF078736.Bastin DA, Reeves PR. Sequence and analysis of the O antigen gene . Appl Environ Microbiol 2005;71:7995\u20138001. GenBank/EMBL/DDBJ accession no.: AY220982.Guo H, Yi W, Shao J, Lu Y, Zhang W, Escherichia coli O59 and O155 O-antigen gene clusters: the atypical wzx genes are evolutionary related. FEMS Microbiol Lett 2005;15:153\u2013161. GenBank/EMBL/DDBJ accession nos: AY654590, AY657020.Guo H, Kong Q, Cheng J, Wang L, Feng L. Characterization of the et al. DNA microarray-based identification of serogroups and virulence gene patterns of Escherichia coli isolates associated with porcine postweaning diarrhea and edema disease. Appl Environ Microbiol 2007;73:4082\u20134088. GenBank/EMBL/DDBJ accession nos: DQ868764\u2013DQ868766.Han W, Liu B, Cao B, Beutin L, Kr\u00fcger U et al. Structural and genetic evidence for the close relationship between Escherichia coli O71 and Salmonella enterica O28 O-antigens. FEMS Immunol Med Microbiol 2010;59:161\u2013169. GenBank/EMBL/DDBJ accession no.: GU445927.Hu B, Perepelov AV, Liu B, Shevelev SD, Guo D Escherichia coli O serogroup cross-reacting with Shigella boydii type 10. J Clin Microbiol 2011;49:3678\u20133680. GenBank/EMBL/DDBJ accession no.: AB627352.Iguchi A, Iyoda S, Seto K, Ohnishi M, EHEC Study Group. Emergence of a novel Shiga toxin-producing et al. A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster. DNA Res 2015;22:101\u2013107. GenBank/EMBL/DDBJ accession nos: AB811596\u2013AB811624, AB812020\u2013AB812085, AB972413\u2013AB972424.Iguchi A, Iyoda S, Kikuchi T, Ogura Y, Katsura K et al. Six novel O genotypes from Shiga toxin-producing Escherichia coli. Front Microbiol 2016;7:765. GenBank/EMBL/DDBJ accession nos: LC125927\u2013LC125932.Iguchi A, Iyoda S, Seto K, Nishii H, Ohnishi M et al. Expression of the O9 polysaccharide of Escherichia coli: sequencing of the E. coli O9 rfb gene cluster, characterization of mannosyl transferases, and evidence for an ATP-binding cassette transport system. J Bacteriol 1995;177:2178-2187. GenBank/EMBL/DDBJ accession no.: D43637.Kido N, Torgov VI, Sugiyama T, Uchiya K, Sugihara H et al. A multiplex PCR method to detect 14 Escherichia coli serogroups associated with urinary tract infections. J Microbiol Methods 2010;82:71-77. GenBank/EMBL/DDBJ accession nos: GU299791, GU299792, GU299795.Li D, Liu B, Chen M, Guo D, Guo X et al. Structural and genetic characterization of the O-antigen of Escherichia coli O161 containing a derivative of a higher acidic diamino sugar, legionaminic acid. Carbohydr Res 2010;345:1581\u20131587. GenBank/EMBL/DDBJ accession nos: GU220361, GU220362.Li X, Perepelov AV, Wang Q, Senchenkova SN, Liu B et al. Structural and genetic relationships of two pairs of closely related O-antigens of Escherichia coli and Salmonella enterica: E. coli O11/S. enterica O16 and E. coli O21/S. enterica O38. FEMS Immunol Med Microbiol 2011;61:258\u2013268. GenBank/EMBL/DDBJ accession no.: HQ388393.Li Y, Perepelov AV, Guo D, Shevelev SD, Senchenkova SN et al. Structural and molecular characterization of Shigella boydii type 16 O antigen. Gene 2006;380:46\u201353. GenBank/EMBL/DDBJ accession no.: DQ371800.Liu B, Senchenkova SN, Feng L, Perepelov AV, Xu T et al. Structure and genetics of Shigella O antigens. FEMS Microbiol Rev 2008;32:627\u2013653. GenBank/EMBL/DDBJ accession nos: EU294162\u2013EU294178, EU296402\u2013EU296404, EU296406\u2013EU296418, EU296421.Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN et al. Development of a serogroup-specific DNA microarray for identification of Escherichia coli strains associated with bovine septicemia and diarrhea. Vet Microbiol 2009;142:373-378. GenBank/EMBL/DDBJ accession nos: FJ940774, FJ940775, GQ499368.Liu B, Wu F, Li D, Beutin L, Chen M et al. Structure of the O-antigen of Salmonella O66 and the genetic basis for similarity and differences between the closely related O-antigens of Escherichia coli O166 and Salmonella O66. Microbiology 2010;156:1642\u20131649. GenBank/EMBL/DDBJ accession no.: GU299794.Liu B, Perepelov AV, Li D, Senchenkova SN, Han Y Escherichia coli serogroup O117, O126, and O146 O-antigen gene clusters and development of PCR assays targeting serogroup O117-, O126-, and O146-specific DNA sequences. Mol Cell Probes 2007;21:295\u2013302. GenBank/EMBL/DDBJ accession no.: DQ465247-DQ465249.Liu Y, DebRoy C, Fratamico P. Sequencing and analysis of the Escherichia coli VW187 (O7:K1). Microbiology 1999;145:2485\u20132495. GenBank/EMBL/DDBJ accession no.: AF125322.Marolda CL, Feldman MF, Valvano MA. Genetic organization of the O7-specific lipopolysaccharide biosynthesis cluster of Shigella flexneri. J Bacteriol 1994;176:733\u2013747. GenBank/EMBL/DDBJ accession no.: X71970.Morona R, Mavris M, Fallarino A, Manning PA. Characterization of the rfc region of Escherichia coli serotype O113. Infect Immun 1999;67:5930\u20135937. GenBank/EMBL/DDBJ accession no.: AF172324.Paton AW, Paton JC. Molecular characterization of the locus encoding biosynthesis of the lipopolysaccharide O antigen of Escherichia coli O91 and development of a O91 PCR serotyping test. J Appl Microbiol 2002;93:758\u2013764. GenBank/EMBL/DDBJ accession no.: AY035396.Perelle S, Dilasser F, Grout J, Fach P. Identification of the O-antigen biosynthesis genes of et al. Structural and genetic characterization of the closely related O-antigens of Escherichia coli O85 and Salmonella enterica O17. Innate Immun 2008;17:164\u201373. GenBank/EMBL/DDBJ accession no.: GU299798.Perepelov AV, Li D, Liu B, Senchenkova SN, Guo D et al. Structural and genetic characterization of Escherichia coli O99 antigen. FEMS Immunol Med Microbiol 2009;57:80\u201387. GenBank/EMBL/DDBJ accession no.: FJ940773.Perepelov AV, Li D, Liu B, Senchenkova SN, Guo D et al. Structure and gene cluster of the O-antigen of Escherichia coli O109; chemical and genetic evidences of the presence of L-RhaN3N derivatives in the O-antigens of E. coli O109 and O119. FEMS ImmunolMed Microbiol 2010;61:47\u201353. GenBank/EMBL/DDBJ accession no.: HM485572.Perepelov AV, Ni Z, Wang Q, Shevelev SD, Senchenkova SN et al. Characterization of Escherichia coli O3 and O21 O antigen gene clusters and development of serogroup-specific PCR assays. J Microbiol Methods 2008;75:329\u2013334. GenBank/EMBL/DDBJ accession no.: EU694097, EU694097.Ren Y, Liu B, Cheng J, Liu F, Feng L et al. Structural and genetic characterization of the Shigella boydii type 10 and type 6 O antigens. J Bacteriol 2005;187:2551-2554. GenBank/EMBL/DDBJ accession no.: AY693427.Senchenkova SN, Feng L, Yang J, Shashkov AS, Cheng J et al. Structural and genetic characterization of Shigella boydii type 17 O antigen and confirmation of two new genes involved in the synthesis of glucolactilic acid. Biochem Biophys Res Commun 2006;349:289\u2013295. GenBank/EMBL/DDBJ accession no.: DQ875941.Senchenkova SN, Feng L, Wang Q, Perepelov AV, Qin D Escherichia coli O128 antigen biosynthesis cluster and functional identification of an alpha-1,2-fucosyltransferase. FEBS Lett 2003;553:99\u2013103. GenBank/EMBL/DDBJ accession no.: AY217096.Shao J, Li M, Jia Q, Lu Y, Wang PG. Sequence of Shigella boydii O11 and functional identification of its wzy gene. FEMS Microbiol Lett 2004;234:125\u2013132. GenBank/EMBL/DDBJ accession no.: AY529126.Tao J, Feng L, Guo H, Li Y, Wang L. The O-antigen gene cluster of et al. Molecular analysis of Shigella boydii O1 O-antigen gene cluster and its PCR typing. Can J Microbiol 2005;51:387\u2013392. GenBank/EMBL/DDBJ accession no.: AY630255.Tao J, Wang L, Liu D, Li Y, Bastin DA Escherichia coli O157 O antigen gene cluster and identification of its specific genes. Infect Immun 1998;66:3545\u20133551. GenBank/EMBL/DDBJ accession no.: AF061251.Wang L, Reeves PR. Organization of Shigella boydii O-antigen loci: implication for Escherichia coli and Shigella relationships. Infect Immun 2001;69:6923\u20136930. GenBank/EMBL/DDBJ accession no.: AF402312\u2013AF402315.Wang L, Qu W, Reeves PR. Sequence analysis of four et al. Sequence of the E. coli O104 antigen gene cluster and identification of O104 specific genes. Gene 2001;30:231\u2013236. GenBank/EMBL/DDBJ accession no.: AF361371.Wang L, Briggs CE, Rothemund D, Fratamico P, Luchansky JB Escherichia coli O55:H7 and identification of a new UDP-GlcNAc C4 epimerase gene. J Bacteriol 2002;184:2620\u20132625. GenBank/EMBL/DDBJ accession no.: AF461121.Wang L, Huskic S, Cisterne A, Rothemund D, Reeves PR. The O-antigen gene cluster of et al. Molecular markers for detection of pathogenic Escherichia coli strains belonging to serogroups O 138 and O 139. Vet Microbiol 2005;111:181\u201390. GenBank/EMBL/DDBJ accession nos: DQ109551, DQ109552.Wang L, Liu B, Kong Q, Steinr\u00fcck H, Krause G et al. Genetic and structural analyses of Escherichia coli O107 and O117 O-antigens. FEMS Immunol Med Microbiol 2009;55:47\u201354. GenBank/EMBL/DDBJ accession no.: EU694095.Wang Q, Perepelov AV, Feng L, Knirel YA, Li Y et al. Development of a DNA microarray for detection and serotyping of enterotoxigenic Escherichia coli. J Clin Microbiol 2010;48:2066\u20132074. GenBank/EMBL/DDBJ accession nos: GU014554, GU014555.Wang Q, Wang S, Beutin L, Cao B, Feng L et al. Development of a serogroup-specific multiplex PCR assay to detect a set of Escherichia coli serogroups based on the identification of their O-antigen gene clusters. Mol Cell Probes 2010;24:286\u2013290. GenBank/EMBL/DDBJ accession nos: GU068041, GU068044\u2013GU068046.Wang Q, Ruan X, Wei D, Hu Z, Wu L et al. Molecular cloning and characterization of genes for Shigella sonnei form I O polysaccharide: proposed biosynthetic pathway and stable expression in a live salmonella vaccine vector. Infect Immun 2002;70:4414\u20134423. GenBank/EMBL/DDBJ accession no.: AF294823.Xu DQ, Cisar JO, Ambulos Jr N, Burr DH Shigella dysenteriae serotype 1 O-antigen in live Salmonella Typhi vaccine vector Ty21a: preclinical evidence of immunogenicity and protection. Vaccine 2007;25:6167\u20136175. GenBank/EMBL/DDBJ accession no.: AY585348.Xu DQ, Cisar JO, Osorio M, Wai TT, Kopecko DJ. Core-linked LPS expression of"} +{"text": "Corynebacterium CDC group F-1 were assembled and studied. Genome sizes ranged between 2.3 and 2.44\u00a0Mb, with G+C content between 60.4% and 60.7%.Three draft and one complete genome sequence from strains isolated from urine and consistent with Corynebacterium based on biochemical results and other phenotypic traits published an identification scheme for isolates consistent with the genus roup F-1 . Here, fDNA was extracted using the TruSeq DNA high-throughput (HT) sample preparation kit. Paired-end whole-genome shotgun libraries were constructed using TruSeq Nano DNA HT library preparation kit. A mate-pair library for strain NML 98-0116 was prepared using the Nextera mate-sample prep kit (Illumina). Sequencing was performed using a MiSeq sequencer (Illumina), and assembly was performed with SPAdes version 3.1.1) . Contigs.1.1 . Cohttps://www.ncbi.nlm.nih.gov/genome/annotation_prok). Assembled whole genomes demonstrated essentially identical G+C contents, genome sizes, and number of coding regions , with a G+C content of 56.72% (Corynebacterium species (ermX gene (associated with resistance to erythromycin and clindamycin) homologous to that found in Corynebacterium urealyticum, Corynebacterium\u00a0jeikeium, and Corynebacterium\u00a0striatum. This was consistent with published antibiograms for these strains Prokaryotic Genome Annotation Pipeline (PGAP) ( regions . The gen regions . Using t regions . NML 140 strains , consist strains .Corynebacterium CDC group F-1 isolates have been deposited in GenBank under accession numbers shown in Complete or draft genome sequences of four"} +{"text": "The publisher apologizes for the error. The correct citation is: Zou W, Yadav S, DeVault L, Jan YN, Sherwood DR (2015) RAB-10-Dependent Membrane Transport Is Required for Dendrite Arborization. PLoS Genet 11(9): e1005484. doi:10.1371/journal.pgen.1005484This article was republished on October 21, 2015, to correct an XML error causing the 4S1 File(PDF)Click here for additional data file.S2 File(PDF)Click here for additional data file."} +{"text": "Plasmodium parasites to bind and invade target cells. Hence, characterising molecules that participate in reticulocyte interaction is key to understanding the molecular basis of Plasmodium vivax invasion. This study focused on predicting functionally restricted regions of the P. vivax GPI-anchored micronemal antigen (PvGAMA) and characterising their reticulocyte binding activity.Adhesin proteins are used by pvgama gene was initially found in P. vivax VCG-I strain schizonts. According to the genetic diversity analysis, PvGAMA displayed a size polymorphism very common for antigenic P. vivax proteins. Two regions along the antigen sequence were highly conserved among species, having a negative natural selection signal. Interestingly, these regions revealed a functional role regarding preferential target cell adhesion.The PvGAMA reticulocyte binding properties for the first time. Conserved functional regions were predicted according to natural selection analysis and their binding ability was confirmed. These findings support the notion that PvGAMA may have an important role in P. vivax merozoite adhesion to its target cells.To our knowledge, this study describes The online version of this article (doi:10.1186/s13071-017-2183-8) contains supplementary material, which is available to authorized users. Plasmodium vivax is a human malaria-causing parasite whose eradication is a priority on the international health agenda C[G/C]C[A/T]AA[C/T][C/G][A/G/C][G/A]AC[G/C/A] repeat which was not present in P. cynomolgi, P. inui, P. fragile, P. knowlesi or P. coatneyi , P\u2009>\u20090.1). However, synonymous divergence was greater than non-synonymous divergence (P\u2009<\u20090.0001) when comparing pvgama sequences to each related species: KN-KSP. vivax/P. cynomolgi\u2009=\u2009-0.041 (0.006); KN-KSP. vivax/P. inui\u2009=\u2009-0.062 (0.008); KN-KSP. vivax/P. fragile\u2009=\u2009-0.030 (0.006); KN-KSP. vivax/P. knowlesi\u2009=\u2009-0.072 (0.009); KN-KSP. vivax/P. coatneyi\u2009=\u2009-0.049 (0.007). The evolutionary rate \u03c9 (dN/dS and KN/KS) sliding window showed that two highly conserved regions amongst species (codons 80\u2013320 and 514\u2013624) might be under negative selection (\u03c9\u2009<\u20090.5). Furthermore, 308 negatively-selected codons were observed amongst species whilst 67.5% of them recognised rPvGAMA-Ct (0.47 cut-off point). These data agreed with a study of the profile of the humoral immune response for P. vivax in which rPvGAMA was recognised by 54.5% of the sera used in the array AN[A/G][N/D] was predicted. This RR was common in different ce Pv12 ) or in tce . DN. DNP. vi or in t regions , 53. Thimsp4 showed higher rosetting activity, unlike the F1 region (aa 22 to 344) (amino fragment) : percentage of sites evolving under positive selection. P-value corrected for multiple tests using the Holm-Bonferroni method. (TIF 470\u00a0kb)Lineage-specific positive selection. Branches under positive episodic selection were identified by using the REL-site branch method. Episodic selection acts very quickly and involves a switch from negative to positive natural selection and back to negative and might enable adaptation to a new host. Phylogeny was inferred in MEGA v6 by the maximum likelihood method using the GTR\u2009+\u2009G evolutionary model. \u03c9Additional file 3: Figure S3.PvGAMA-Nt and -Ct stained with Coomassie blue or analysed by western blot using anti-polyhistidine antibodies, respectively. c Purifying conserved (CR1 and CR2) and variable (VR1 and VR2) PvGAMA regions. Lanes 2, 4, 6 and 8 show purified recombinant proteins and lanes 3, 5, 7 and 9 show western blot detection. The proteins\u2019 molecular markers are indicated in Lane 1 on all figures. (TIF 5327\u00a0kb)Obtaining recombinant proteins. a, b Recombinant GAMA protein expression and purification. Lanes 2\u20133 show non-induced and induced cell lysate, respectively. Lanes 4\u20135 show purified rAdditional file 4: Figure S4.Selection strategy for immature and mature erythrocyte populations. The doublets were excluded by plotting FSC-H against FSC-A. Cells were then selected by their granularity, using an SSC-A vs FSC-A cytogram. The CD45 vs CD71 signal was plotted for selecting reticulocyte (CD71\u2009+\u2009CD45-) and mature erythrocyte (CD71-CD45-) populations and omitting activated lymphocytes (CD71\u2009+\u2009CD45+). The percentage of cells having bound protein was calculated using the PE signal (CD71\u2009+\u2009CD45-PE+). A representative histogram from three independent experiments analysing the PE signal for the CR2 binding assay compared to control is also shown. (TIF 10448\u00a0kb)"} +{"text": "During 2000\u20132013, among adults aged 50\u201375 years, the use of colorectal cancer tests or procedures increased for all racial and ethnic groups shown. Non-Hispanic Asian adults had the largest increase; the percentage more than doubled from 20.6% in 2000 to 51.2% in 2013. Although increases were observed among all groups, in 2013 the prevalence of colorectal cancer screening remained higher among non-Hispanic white (60.4%) and non-Hispanic black (58.2%) adults and lower among non-Hispanic Asian (51.2%) and Hispanic (41.5%) adults.Source: Health, United States, 2014 . Available at http://www.cdc.gov/nchs/data/hus/hus14.pdf.Reported by: Hashini Khajuria, MPA, hwq6@cdc.gov, 301-458-4253."} +{"text": "Acute myocarditis (AM) is an inflammatory disease of the heart muscle. Clinical presentation and outcome are variable, ranging from asymptomatic to fulminant myocarditis (FM), presenting with decompensated heart failure or cardiogenic shock needing inotropic or mechanical circulatory support. Cardiac magnetic resonance (CMR) is increasingly employed in the diagnosis and follow-up (f.u.) of AM. We investigated the differences in functional parameters evaluated with CMR between patients (pts) presenting with FM versus non fulminant AM (NFM), at baseline and f.u.We retrospectively analyzed consecutive pts with AM who underwent CMR within 30 days from clinical presentation. Cine, STIR T2-weighted and late-enhancement images were acquired on matching planes. CMR diagnosis of AM was based on Lake Louise Criteria. Indexed LV end-diastolic (LVEDVi) and end-systolic (LVESVi) volumes, LV ejection fraction (LVEF), indexed LV mass (LVmi), indexed RV end-diastolic (RVEDVi) and end-systolic (RVESVi) volumes and RV ejection fraction (RVEF) were calculated for each patient. F.u. scans were similarly analyzed, if available.2, p=0.028) and LVEF improved from 56% to 66% (p=0.028); in NFM LVEDVi and LVEF were unchanged at f.u. . F.u. LVEF and RVEF did not differ significantly between FM and NFM, 66% (60-69) vs 65% (61-69), p=0.79 and 62% (57-68) vs 63% (59-68),p=0.69 respectively. In both FM and NFM LVmi significantly decreased from baseline . There was a trend towards a more pronounced reduction of LVmi in FM, but the difference fell short of statistical significance .Four pts with FM died and 3 were heart transplanted before performing CMR and thus were excluded from the analysis; none of the pts with NFM died or were transplanted before CMR. In total, 68 pts were included: 11 (16%) with FM and 57 (84%) with NFM underwent CMR. Baseline scans were obtained earlier in the NFM group, 5 (3-9) vs 12 (7-21) days after presentation, p = 0.0035. Baseline LVEF was significantly lower in FM compared to NFM, 56% (43-65) vs 64% (59-68),p=0.026. RVEF was lower in FM than in NFM pts, 56% (52-58) vs 63% (58-66),p=0.0024. F.u. scans were available in 47 pts and were obtained after a median of 169 (110-203) days from baseline scan in FM and 148 (93-242) days in NFM (p=0.78). In FM, LVEDVi was increased at f.u. (from 75 to 77 mL/mPts with FM achieved normal LVEF at f.u., despite a lower baseline LVEF, even if a mild LV remodeling was observed at f.u. This might in part be due to a more pronounced decrease in LVmi, likely secondary to more severe myocardial edema in FM, but this observation warrants further investigation and longer f.u. to better understand long term consequences of FM on ventricular remodeling and prognosis."} +{"text": "Talaromyces produce useful biomass-degrading enzymes and secondary metabolites. However, these enzymes and secondary metabolites are still poorly understood and have not been explored in depth because of a lack of comprehensive genetic information. Here, we report a 36.51-megabase genome assembly of Talaromyces pinophilus strain 1\u201395, with coverage of nine scaffolds of eight chromosomes with telomeric repeats at their ends and circular mitochondrial DNA. In total, 13,472 protein-coding genes were predicted. Of these, 803 were annotated to encode enzymes that act on carbohydrates, including 39 cellulose-degrading and 24 starch-degrading enzymes. In addition, 68 secondary metabolism gene clusters were identified, mainly including T1 polyketide synthase genes and nonribosomal peptide synthase genes. Comparative genomic analyses revealed that T. pinophilus 1\u201395 harbors more biomass-degrading enzymes and secondary metabolites than other related filamentous fungi. The prediction of the T. pinophilus 1\u201395 secretome indicated that approximately 50% of the biomass-degrading enzymes are secreted into the extracellular environment. These results expanded our genetic knowledge of the biomass-degrading enzyme system of T. pinophilus and its biosynthesis of secondary metabolites, facilitating the cultivation of T. pinophilus for high production of useful products.Species from the genus Talaromyces pinophilus, formerly designated Penicillium pinophilum, is a fungus that produces biomass-degrading enzymes such as \u03b1-amylase1, cellulase2, endoglucanase3, xylanase2, laccase4 and \u03b1-galactosidase2. In one study, a blended enzyme cocktail produced by T. pinophilus and Chrysoporthe cubensis improved the efficiency of hydrolysis of glucan and xylan in sugarcane bagasse for glucose and xylose production, compared with enzymes from a single strain2. A relatively high level of \u03b2-glucosidase activity is observed in T. pinophilus under solid state fermentation5. Therefore, T. pinophilus is considered a potential alternative to Trichoderma reesei for cellulase production and efficient biomass hydrolysis. T. pinophilus produces a variety of medically useful metabolites such as 3-O-methylfunicone, which is used to inhibit mesothelioma cell motility6, and talaromycolides 1\u20133, 5 and 11, which inhibit the growth of the human pathogen methicillin-resistant Staphylococcus aureus7.T. pinophilus 1\u201395 was isolated from the soil of a dried, ploughed field in Wuzhou, China. This strain produces a highly efficient, calcium-independent \u03b1-amylase1. Application of calcium-independent \u03b1-amylase in starch conversion avoids problems caused by addition of calcium ions8. Additionally, we found that T. pinophilus 1\u201395 produces 1.21\u2009\u00b1\u20090.30\u2009U/mL of filter-paper cellulase, 10.72\u2009\u00b1\u20090.74\u2009U/mL of carboxymethylcellulose cellulase, 0.71\u2009\u00b1\u20090.02\u2009U/mL of p-nitrophenyl-\u03b2-cellobioside cellulase, 0.27\u2009\u00b1\u20090.01\u2009U/mL of p-nitrophenyl-\u03b2-glucopyranoside cellulase and 41.93\u2009\u00b1\u20092.84\u2009U/mL of xylanase activities in submerged flask cultivation (data not shown). However, a comprehensive understanding of the biomass-degrading enzyme system in this fungus is still lacking.The fungal strain de novo whole-genome assembly of T. pinophilus strain 1\u201395, a nearly complete genome sequence of a high biomass-degrading enzyme-producing species in the genus Talaromyces. Carbohydrate-active enzyme (CAZyme) genes and secondary metabolism gene clusters were observed in the sequenced genome. Comparative genomic analysis suggested that T. pinophilus harbors more biomass-degrading enzymes and secondary metabolites than other related filamentous fungi. In addition, the predicted secretory protein patterns of T. pinophilus 1\u201395 were analyzed.We describe the T. pinophilus 1\u201395 (CGMCC No. 2645), isolated from soil in a dried, ploughed field in Wuzhou, China, was performed using a combination of single molecule real-time (SMRT) DNA sequencing and next generation sequencing technology. A high-quality genome sequence of T. pinophilus 1\u201395 was generated on the PacBio RS II platform. Approximately 1.94\u2009Gb of clean subreads, with sequences from a single pass of a polymerase on a single strand of an insert within a SMRTbell template and no adapter sequences with an N50 size of 10,045\u2009bp and average length 8,102\u2009bp were generated. Additionally, a paired-end (PE) library with a 500-bp average insert size was constructed using the Illumina HiSeq 4000 platform, and 3.88\u2009Gb clean, short-sequence PE reads were generated with a length of 125\u2009bp. Reads were used to correct wrong bases in the assembled genome sequence on the PacBio RS II platform. Finally, a 36.51-Mb genome of T. pinophilus 1\u201395 was generated with 159-fold coverage. This size was in accordance with the estimated genome size of 28\u201336\u2009Mb for three Talaromyces species11. The genome was covered by nine scaffolds, including eight large scaffolds (accession number CP017344-CP017351 in GenBank) without gaps , GeneMark-ES (http://exon.gatech.edu/GeneMark/), Genewise (http://www.ebi.ac.uk/Tools/psa/genewise/), SNAP14 and an unsupervised learning system program Glean version 1 (https://sourceforge.net/projects/glean-gene/). The number of coding genes was significantly higher than other filamentous fungi that produce biomass-degrading enzymes , were annotated in the Gene Ontology (GO) database (http://geneontology.org/), 12,828 (95.21%) in the UniProt database (http://www.uniprot.org/), 12,946 (96.09%) in the NCBI non-redundant (NR) protein sequences database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) and 4437 (32.93%) in the Clusters of Orthologous Groups of proteins database (http://www.ncbi.nlm.nih.gov/COG/). A total of 6817 (50.6%) genes belonging to 331 pathways were also annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (http://www.kegg.jp/) search of all-vs.-all findings showed that T. pinophilus 1\u201395 and T. cellulolyticus Y-94 shared 10,260 orthologous proteins, accounting for 76.16% of the total proteome, with an average amino acid sequence identity of 98.28%. In contrast, low identity was observed to other sequenced Talaromyces species17, Trichoderma sp.18, Penicillium sp.20 and Aspergillus sp.22, ranging from 70% to 88% , 35 families of glycosyl transferases (GTs), 13 families of carbohydrate esterases (CEs), 10 families of auxiliary activities (AAs), 5 families of polysaccharide lyases (PLs) genes and 19 families of carbohydrate-binding modules (CBMs) Fig.\u00a0. FurtherMs) Fig.\u00a0.Figure 3T. cellulolyticus Y-94 and P. oxalicum HP7-1, larger numbers of BGLs were classified into GH families 1 and 3 in the T. pinophilus 1\u201395 genome , 8 \u03b2-1,4-endoglucanases and 29 \u03b2-glucosidases were included as cellulases. Of these, the known cellulases included Cel7A-2 (TP09412), Cel5A (TP03457), Cel5B (TP07499), Cel7B (TP08514) and Bgl3A (TP09042). Compared with known filamentous fungi used for cellulase production, i.e., T. pinophilus 1\u201395 genome was rich in hemicellulose-degrading enzymes (97 genes) assigned into 29 predicted CAZyme families; this finding was compared to 77 genes in T. cellulolyticus Y-94 and 80 genes in P. oxalicum HP7\u20131, which includes Xyn11A (TP00436) and Xyn10A (TP06900), encoding the important \u03b2-1,4-endoxylanases. This result supports the high xylanase activity of T. pinophilus 1\u201395. The predicted hemicellulases in T. pinophilus 1\u201395 were divided into 19 types by substrate specificities. The large differences among T. pinophilus 1\u201395, T. cellulolyticus Y-94 and P. oxalicum HP7\u20131 broadly covered most of the listed hemicellulase types (see Supplementary Table\u00a0T. pinophilus 1\u201395 possessed more \u03b2-D-xylosidases (EC 3.2.1.37), acetyl xylan esterases (EC 3.1.1.72) and feruloyl esterases (EC 3.1.1.73) than the two others. \u03b2-D-xylosidases hydrolyze xylobiose or linear xylooligosaccharides to the monomer xylose. Acetyl xylan esterases liberate acetic acid esterifying position 2 and 3 on mono- and di-O-acetylated \u03b2-1,4-linked D-xylopyranosyl residues in xylan chains. Feruloyl esterases liberate trans-ferulic acid from 5-O-feruloylated L-arabinofuranosyl residues. These enzymes facilitate the hydrolysis of hemicellulose26. In contrast, the T. pinophilus 1\u201395 genome possessed a similar number of pectin-degrading enzymes as T. cellulolyticus Y-94 and P. oxalicum HP7\u20131 , which mainly hydrolyze \u03b1-1,4-glucosidic linkages from the nonreducing ends of starch chains with the release of \u03b2-D-glucose28; and a 1,4-\u03b1-glucan branching enzyme (EC 2.4.1.18) that cleave \u03b1-1,4 glucosidic linkages of glucan chain, and then transfer the cut end to 6-position of glucose residue within the cleaved or another glucan chain, resulting the generation of an \u03b1-1,6 glucosidic linkage29. Comparative analysis indicated that T. pinophilus 1\u201395 had more \u03b1-glucosidases and glucoamylases than the other investigated fungi containing zinc-finger structures, such as the Zn2Cys6 type, the C2H2 type and CCHC type, followed by the winged helix repressor DNA-binding family (97 members) , the cellulase transcription activator CLR-2 (TP10486), the starch degradation regulator AmyR (TP09286) and the xylan degradation regulator XlnR (TP02627) (Table\u00a0T. pinophilus 1\u201395.Transcription factors (TFs) are essential for modulating diverse biological processes by regulating gene expression. In total, 943 TFs were found in the predicted proteome of T. pinophilus 1\u201395 had a wealth of secondary metabolites using the AntiSMASH web service30. A total of 68 secondary metabolism gene clusters harboring 401 putative genes were identified. The predicted products of 52 secondary metabolism gene clusters were classified into 8 different types: 28 T1 polyketide synthase (T1PKS) gene clusters, 9 non-ribosomal peptide synthase (NRPS) gene clusters, 9 terpene gene clusters, 2 Nrps-T1pks gene clusters, 1 phosphonate gene cluster, 1 T1pks-Indole gene cluster, 1 T1pks-Nrps gene cluster and 1 Terpene-T1pks gene cluster; the remaining 16 gene clusters synthesized other unknown secondary metabolites , comprising 831 classical and 372 nonclassical secretory proteins , Cel7B (TP08415), Cel5A (TP13457), Cel5B (TP07499), Cel5C (TP08784), Cel45A (TP06957) and Bgl3A (TP09042). We also identified 62 hemicellulose-degrading enzymes and 6 pectin-degrading enzymes, including eight \u03b2-1,4-endoxylanases, nine acetyl xylan esterases, four \u03b1-galactosidases, 10 \u03b1-L-arabinofuranosidases, five \u03b1-L-fucosidases, one endo-1,4-\u03b2-mannanase and four feruloyl esterases, as well as two pectin esterases, two tannases, one pectate lyase and one pectin lyase , glucoamylases (5 coding genes) and \u03b1-glucosidases (13 coding genes) among species we compared. BGLs are important for releasing inhibition of cellulase activity36. Furthermore, the predicted secretome of T. pinophilus 1\u201395 showed that approximately 50% of CWDEs and starch-degrading enzymes were secreted into the extracellular region, including major cellulases, hemicellulases and amylases. This result indicated a promising application of T. pinophilus in biorefining. These results also demonstrated that T. pinophilus 1\u201395 is more excellent cellular machinery for biomass-degrading enzymes than that of P. oxalicum HP7\u20131 and T. cellulolyticus Y-94 as previously observed35, meriting further study.Comparative genome analysis indicated that the most closely related species to Talaromyces, Trichoderma, Penicillium and Aspergillus, indicated that T. pinophilus 1\u201395 possessed the most secondary metabolism gene clusters except for A. niger and A. oryzae. T. pinophilus 1\u201395 had more T1PKs than Trichoderma sp., Penicillium sp. and Aspergillus sp., and fewer NRPS than Aspergillus species. These results suggested that T. pinophilus 1\u201395 has potential for producing bioactive secondary metabolites. Although thus far, several bioactive secondary metabolites have been extracted and characterized from T. pinophilus7, according to the genomic data, additional secondary metabolites could be generated using this species.Comparative analysis to 10 filamentous fungi from four genera, Talaromyces. The result provided new insights for a comprehensive understanding of the biomass-degrading enzyme system of Talaromyces at the genome level. Detailed comparative genomic analysis revealed a complex biomass-degrading enzyme system in T. pinophilus, indicating its promising application in biomass biorefineries. This study provides a genome-sequence basis for developing strategies that use T. pinophilus as a microbial cell factory for production of high-value enzymes and secondary metabolites.In summary, this study provided a nearly complete genome sequence for the genus T. pinophilus 1\u201395 was isolated from soil in a dried, ploughed paddy field in Wuzhou, China1 and was deposited at the China General Microbiological Culture Collection Center (CGMCC) under accession number CGMCC No. 2645. Total DNA extraction from mycelia was performed using a phenol-chloroform method with some modifications37. Mycelia were ground in liquid nitrogen and put in 1\u2009mL lysate reagent per 100\u2009mg mycelia powder. Genomic DNA was collected by centrifugation at 11,300\u2009\u00d7\u2009g for 10\u2009min.T. pinophilus strain 1\u201395 genome was sequenced using a PacBio RS II platform and Illumina HiSeq 4000 platform at the Beijing Genomics Institute . Four SMRT cells zero-mode waveguide arrays of sequencing, were used by the PacBio platform to generate the subreads set. PacBio subreads (length\u2009<\u20091\u2009kb) were removed. The program Pbdagcon (https://github.com/PacificBiosciences/pbdagcon) was used for self-correction. Draft genomic unitigs, which are uncontested groups of fragments, were assembled using the Celera Assembler38 against a high-quality corrected circular consensus sequence subreads set. Order, distance and orientation of unitigs and combined scaffolds were generated using software SSPACE39. An upgraded draft genome was obtained after filling or reducing as many captured gaps as possible using software PBJelly40. To improve the accuracy of the genome sequences, GATK (https://www.broadinstitute.org/gatk/) and SOAP tool packages 42 were used to make single-base corrections.The 43 used reasonable PE sequence data from Illumina libraries to perform comprehensive variant detection and improve genome assembly.A DNA library of 500\u2009bp inserts was constructed and PE sequenced. For generated HiSeq reads, Q20, representing the probability of the incorrectness of the corresponding base call, was detected. If Q20 reads accounted for less than 60%, they were discarded. Software PilonT. pinophilus 1\u201395 genome were predicted independently with the gene prediction programs Augustus , GeneMark-ES (http://exon.gatech.edu/GeneMark/), Genewise (http://www.ebi.ac.uk/Tools/psa/genewise/), SNAP14, and the unsupervised learning system program Glean (https://sourceforge.net/projects/glean-gene/) version 1. Augustus and SNAP, using default parameters, were trained on gene models for A. oryzae, P. oxalicum, T. marneffei and T. stipitatus and Swiss-Prot and TrEMBL databases (http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pres/swiss2.htm) and KEGG database (http://www.kegg.jp/) version 76, were used to assign general protein function profiles. We used cut-off E-value\u2009\u2264\u20091e-5, overlap 0.4 and identity 30. InterProScan5 (http://www.ebi.ac.uk/interpro/), stand-alone version 55, and GO (http://geneontology.org/) were also used to annotate the predicted proteome. TFs were predicted based on InterPro IDs in the Fungal Transcription Factor Database (http://ftfd.snu.ac.kr/). The hmmsearch program in the HMMER 3.1b2 package (http://hmmer.org/), was used to search all predicted proteomes with the family-specific hidden Markov model profiles of CAZymes from the dbCAN database26. Primary results were processed with an E-value threshold of 1E-7. Protein kinases and phosphatases were detected using hmmsearch based on the Eukaryotic Kinase and Phosphatase Database (http://ekpd.biocuckoo.org/). Membrane transport proteins were classified and identified by a BLASTp search against the transport classification database44, with E-value threshold 1E-10, overlap 0.4 and identity of 30. AntiSMASH30 was used to annotate secondary metabolism gene clusters.For functional annotation of translated proteins in the 45. We selected 2,082 single-copy genes from 118,099 genes in 11 fungal genomes. MUSCLE (http://www.ebi.ac.uk/Tools/msa/muscle/) version 3.7 with default parameters was used to perform multiple sequence alignment of single-copy genes. A neighbor-joining tree was calculated using TreeBeST46 with bootstrapping set to 100. The phylogenetic tree was visualized using SVGKit (http://svgkit.sourceforge.net/) and PERL scripts.An all-against-all pairwise BLASTp similarity search was performed using proteomes from 11 filamentous fungi and for glycosylphosphatidyl inositol anchors use web server PredGPI (http://gpcr.biocomp.unibo.it/predgpi/). Software tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/) version 1.3 was used for transfer RNA prediction using the T. pinophilus 1\u201395 genome with option C and other default parameters.The total set of 13,472 proteins of Supplementary Infromation for SREP-16-39329Dataset 1Dataset 2Dataset 3"} +{"text": "Bradyrhizobium canariense, isolated from root nodules of Lupinus microanthus and Lupinus angustifolius, and 1 strain of Bradyrhizobium japonicum isolated from root nodules from Lupinus angustifolius in Algeria. These sequences add to the known diversity of this agronomically important genus.We report here the whole-genome sequences of 14 strains of Bradyrhizobium canariense , mungbean (Vigna radiata), cowpea (Vigna unguiculata), and siratro (Macroptilium atropurpureum) is rather recent (Lupinus angustifolius and Lupinus micranthus (Papilionoideae: Genisteae), collected at 2 sites in the National Park El-Kala . For whole-genome sequencing, DNA libraries were generated with a Nextera XT kit . Sequencing was performed on a MiSeq sequencer (Illumina) in three different runs generating 2 \u00d7 250-bp paired-end reads (version 2 chemistry) and 2 \u00d7 250-bp and 2 \u00d7 300-bp paired-end reads (version 3 chemistry). Quality control of the reads was assessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Genome assemblies were computed with SPAdes genome assembler 3.10 and 8,379,024\u00a0bp (UBMAN05), with G+C contents from 62.94% to 63.06% (UBMA122), and Bradyrhizobium japonicum UBMA197 had a larger genome, at 10,442,239\u00a0bp, with 63.3% G+C content. Genome coverage varied from 46-fold (UBMA510) to 255-fold (UBMA060). PlasmidFinder , 4. Bactrpureum) , 2, 5. Brpureum) , Bradyrhs Poland , 7, Itals Poland , and Mors Poland . While dr recent . The 15 ler 3.10 and analler 3.10 . For BraidFinder and PlasidFinder detectedidFinder identifiAll genome sequences have been deposited at GenBank under the accession numbers reported in"} +{"text": "The effect of degradable starch microspheres (DSM) on the intrahepatic distribution of a low molecular weight marker, 99Tcm-labelled methylene diphosphonate (MDP), was studied in rats with hypovascular HSN liver tumours. MDP was injected regionally, via the hepatic artery, alone or co-administered with DSM, with or without subsequent occlusion of either the hepatic artery or the portal vein. Tumour vascularity was measured with 57Co-labelled microspheres. Co-injection with DSM immediately significantly increased hepatic retention of marker in both tumour (T) (median 22.40 (range 16.82-39.58)% injected dose) and normal liver (N) (9.08 (4.85-12.59) %ID) the greater effect seen in T (P < 0.01). After DSM degradation, very little MDP remained in N (0.61 (0.28-1.40) %ID) but there was significant retention in T (10.01 (6.73-20.28) %ID, P < 0.01). Clamping the hepatic artery had minimal effect on the retention of MDP when administered alone. Regional injection of 16.5 microM 57Co microspheres resulted in a N:T ratio of 2.25:1. Concomitant injection of the 40 microM DSM was 57Co microspheres reversed this ratio to 1:2. The results indicate that DSM selectively enhances the retention of MDP to a hypovascular hepatic tumour, not by causing intra-tumour stasis, but by directing a greater arterial flow to hypovascular areas in the liver."} +{"text": "Primary chemotherapy in operable breast invasive carcinoma enables tumour reduction and conservative surgery. In order to search for one or more biological factors capable of predicting tumour behaviour under primary chemotherapy, and subsequent patient survival, an immunohistochemical study was performed with specific antibodies to p53, c-erbB-2 (Her-2/neu), Mib1 (antiKi-67), pS2, GST pi, oestrogen receptors (ERs) and progesterone receptors (PRs). Core biopsies, obtained before primary chemotherapy, were available from a series of 128 breast invasive carcinomas treated between January 1985 and April 1989, with a median follow-up of 93.3 months. Univariate statistical analysis showed that negative ER detection by immunohistochemistry (IHC) was highly correlated with chemosensitivity (P = 0.001). A high percentage of Mib1-positive tumour cells (> 40%), as well as initial tumour size less than 4 cm, were also correlated with tumour responsiveness to chemotherapy (P = 0.009 and P = 0.03). By multivariate analysis IHC-ER, Mib1 and initial tumour size were independent predictors, the last parameter being the most important. Concerning subsequent patient survival, c-erbB-2 overexpression, as detected by IHC, was significant with respect to overall survival (OS) (P = 0.0006), disease-free interval (DFI) (P = 0.03) and metastasis-free interval (MFI) (P = 0.008) by univariate analysis. Furthermore, c-erbB-2 was the major independent prognostic factor for OS and MFI by multivariate analysis."} +{"text": "A sentence was omitted from Section 2.2 of the Methods . The corrected paragraph should read: DMEM, bovine serum and penicillin/streptomycin were purchased from Hyclone . Nilotinib (TasignaR) was obtained as a gift from Novartis pharmaceuticals . Imatinib and dasatinib were purchased from ChemieTeck Inc. . Paclitaxel, vincristine, doxorubicin, colchicine, p-aminophenylmethylsulfonyl fluoride, bovine serum albumin, dimethyl sulfoxide (DMSO) and 1--3,5-diphenylformazan (MTT), the monoclonal mouse antibody against P-gp (P7965), the secondary horseradish peroxidase-labeled anti-goat or anti-mouse IgG were purchased from Sigma-Aldrich Chemical Co. . A polyclonal goat antibody against human MRP7 (D-19) was purchased from Santa Cruz Biotech Inc.
. A polyclonal antibody against human MRP1/ABCC1 was kindly provided by Dr. Akiyama [21]. A monoclonal antibody BXP-34 against BCRP was acquired from Signet Laboratories Inc. . [3H]-paclitaxel was purchased from Moravek Biochemicals ."} +{"text": "Two tris-chelated water-coordinated units are bridged by a 2,4-dihydroxy\u00adpyrimidine-5-carboxyl\u00adate dianion, which is disordered about a center of inversion. The metal center has a monocapped square-anti\u00adprismatic coordination.The water-coordinated neodymium(III) atom in the centrosymmetric title compound, [Nd DOI: 10.1107/S1600536808001499/ci2552Isup2.hkl Structure factors: contains datablocks I. DOI: crystallographic information; 3D view; checkCIF report Additional supplementary materials:"} +{"text": "B. microti infection (7).\u201dIn \u201cTransfusion-Associated Babesiosis after Heart Transplant\u201d by Joseph Z. Lux et al., errors occurred in the text. On page 118, left column, lines 20\u201322, the sentence should read \u201che became symptomatic during the typical 2- to 8-week incubation period for transfusion-transmitted http://www.cdc.gov/ncidod/eid/vol8no12/02-0149.htm.The corrected text appears online at"} +{"text": "The 4,4\u2032-bipyridine ligands bridge the metal ions, forming one-dimensional chains along different directions, which are further connected by formate ligands into a topologically (1010.124.14)(10)3 three-dimensional network.In the title compound, [Cd(HCOO) DOI: 10.1107/S1600536809009969/jh2074Isup2.hkl Structure factors: contains datablocks I. DOI: crystallographic information; 3D view; checkCIF report Additional supplementary materials:"} +{"text": "From January 1983 to December 1986 seventy-six previously untreated children with non-Hodgkin's lymphoma (NHL) were treated by combination chemotherapy. Burkitt's lymphoma patients were ineligible. The treatment regimens include intermittent chemotherapy and for non-localized patients, prophylactic central nervous system chemotherapy. Intrathoracic non-Hodgkin's lymphoma patients also had cranial prophylactic radiotherapy. Sixty-six patients (86.8%) achieved complete remission. Two year failure-free survival rate was 82.1% for localized (stage I and II) NHL and 53.3% for non-localized (stage III and IV) NHL patients. Failure-free survival did not differ significantly for the two major histologic diagnoses, but two year survival rate was lower in diffuse poorly differentiated lymphoblastic than undifferentiated non-Burkitt's lymphoma (50% versus 66.8% respectively). Failure-free survival rate was 53.7% in mediastinal disease and, 73.2% in abdominal disease at 24 months. Relapse rate was higher in mediastinal cases (46.1%) than primary abdominal cases (24.3%) at 24 months. Eleven (13.5%) died of treatment related sepsis. Although the overall survival rate was 72.4% at 2 years we need novel or more intensive programmes for mediastinal and non-localized disease."} +{"text": "Correction for:10.1371/journal.pmed.0030184Wagstaff SC, Laing GD, Theakston RDG, Papaspyridis C, Harrison RA (2006) Bioinformatics and multiepitope DNA immunization to design rational snake antivenom. PLoS Med 3(6): e184. doi:In the Supporting Information section of this paper, Figure S1 and Figure S2 were incorrectly linked. Figure S1 and Figure S2 labeled and in the order originally intended are provided here.Figure S1(48 KB PDF).Click here for additional data file.Figure S210.1371/journal.pmed.0050209.sg002 (32 KB PDF).Found at doi:Click here for additional data file."} +{"text": "Drosophila wing growth by fueling a wave front of Fat-Dachsous signaling that recruits new cells into the wing primordium.The secreted morphogen Wingless promotes Drosophila wing primordium undergoes a dramatic increase in cell number and mass under the control of the long-range morphogens Wingless and Decapentaplegic . This process depends in part on the capacity of wing cells to recruit neighboring, non-wing cells into the wing primordium. Wing cells are defined by activity of the selector gene vestigial (vg) and recruitment entails the production of a vg-dependent \u201cfeed-forward signal\u201d that acts together with morphogen to induce vg expression in neighboring non-wing cells. Here, we identify the protocadherins Fat (Ft) and Dachsous (Ds), the Warts-Hippo tumor suppressor pathway, and the transcriptional co-activator Yorkie as components of the feed-forward signaling mechanism, and we show how this mechanism promotes wing growth in response to Wg. We find that vg generates the feed-forward signal by creating a steep differential in Ft-Ds signaling between wing and non-wing cells. This differential down-regulates Warts-Hippo pathway activity in non-wing cells, leading to a burst of Yki activity and the induction of vg in response to Wg. We posit that Wg propels wing growth at least in part by fueling a wave front of Ft-Ds signaling that propagates vg expression from one cell to the next.During development, the Drosophila, wings develop at the larval stage from wing primordia. Recently, we discovered that the morphogen Wingless promotes growth of the Drosophila wing by inducing the recruitment of neighboring cells into the wing primordium. Wing cells are defined by the expression of the \u201cselector\u201d gene vestigial. Recruitment depends on the capacity of wing cells to send a short-range, feed-forward signal that allows Wingless to activate vestigial in adjacent non-wing cells. Here, we identify the molecular components and circuitry of the recruitment process. We define the protocadherins Fat and Dachsous as a bidirectional ligand-receptor system that is controlled by vestigial to generate the feed-forward signal. Further, we show that the signal is transduced by the conserved Warts-Hippo tumor suppressor pathway via activation of its transcriptional effector Yorkie. Finally, we propose that Wingless propels wing growth by fueling a wave front of Fat-Dachsous signaling and Yorkie activity that propagates vestigial expression from one cell to the next.Under normal conditions, animals and their various body parts grow until they achieve a genetically predetermined size and shape\u2014a process governed by secreted organizer proteins called morphogens. How morphogens control growth remains unknown. In Growth is a fundamental property of animal development. Under normal conditions, animals of a given species, as well as their various body parts, achieve a characteristic size, shape, and pattern under tight genetic control. However, the basis of this control is poorly understood.Drosophila wing, the morphogens Wingless and Decapentaplegic drive a rapid \u223c200-fold increase in cell number and mass that occurs during larval life Morphogens, such as secreted factors of the Wingless/Int (Wnt), Bone Morphogenetic Protein (BMP), and Hedgehog (Hh) families, control growth. For example, in the classic paradigm of the Another system involved in growth is the evolutionarily conserved Warts-Hippo tumor suppressor pathway Drosophila, two protocadherins, Dachsous (Ds) and Fat (Ft), have been implicated as a ligand-receptor pair that acts, via the atypical myosin Dachs (D), to regulate Wts kinase activity In Ft and Ds are also important for planar cell polarity (PCP), in which cells within epithelial sheets adopt a common orientation, e.g. as manifest by their secreting hairs that point in the same direction Drosophila wing growth by morphogen vestigial (vg), the selector gene that defines the wing state vg expressing cells to send a feed-forward (FF) signal that induces neighboring cells to activate vg in response to Wg vg expression from cell to cell in response to Wg spreading from the border cells.Recently, we defined a new mechanism for the control of vg expression and initiate a new cycle of FF signaling. Based on these findings, we posit that Wg (and likely Dpp) promote wing growth by fueling the propagation of a wave front of Ft-Ds signaling that transiently suppresses the Wts-Hpo pathway and elevates Yki activity to recruit new cells into the wing primordium.In our initial analysis of the recruitment process, we speculated that Ft and Ds might be involved in the FF mechanism vg Boundary Enhancer (BE) to generate a stripe of vg expressing \u201cborder cells\u201d vg expression in surrounding cells via the vg Quadrant Enhancer (QE) [4],[5],apterous (ap) in D, but not V, cells ap null discs (henceforth oap discs), the D-V segregation fails, vg and wg expressing border cells are not specified, and the nascent wing primordium is subsequently lost and ds, itself, are expressed at peak levels in complementary domains that abut at the wing periphery, fj in the vgON domain . Such clones express moderate levels of exogenous Vg, a few fold lower than the peak endogenous level observed in wild type discs, and rescue wing development cell-autonomously fj-lacZ and repress ds-lacZ . Hence, prospective wing cells in these discs behave as if they have constitutively activated the FF signal transduction pathway but can mount only a weak QE response owing to the low levels of cryptic Wg available As described above, imordium and 2B [o apoft discs is Wg dependent. First, the QE response is abolished in clones of o Dfz2ofz cells, which are unable to transduce Wg (UAS.Nrt-wg clones) drive peak levels of Vg and 5XQE.DsRed expression in o apoft discs, both within the clones and in abutting cells . These results confirm that ods clones serve as ectopic sources of FF signal, capable of inducing QE-dependent vg expression in neighboring cells, provided that the responding cells also receive Wg.In the presence of Nrt-Wg, ame disc . In the F signal : they inoft clones elicited a strictly cell autonomous response, both in Nrt-Wg expressing oap discs and hence should be potent sources of FF signal; nevertheless they behave as if devoid of the capacity to signal. Note that this failure cannot be attributed to a generic inability of oft cells to send intercellular signals. First, oft clones repolarize their neighbors, whereas o ftods clones do not, indicating that they have the capacity to send the Ds PCP signal oft clones in the wing primordium can also send DSL-Notch, Wg, and Dpp signals and generate ectopic FF signal in oap discs, as monitored by the induction of 5XQE.DsRed expression in adjacent wild type cells that wing cells require Ft to generate FF signal and (ii) that non-wing cells require both Ft and Ds to receive the signal.Although wing cells require Ft, but not Ds, to send the FF signal, cells undergoing recruitment are also in position to receive an opposing Ds signal coming from non-wing cells on the other side, raising the possibility that this Ds input may also contribute to activating the QE and recruiting cells into the wing primordium.oap discs and asked if the resulting disparity in Ds signaling across the clone border is sufficient to induce the QE response in surrounding cells.To assess this, we generated Ds over-expressing clones in UAS.ds cells in oap discs generate levels of Ds that are several fold higher than endogenous Ds . In the absence of exogenous Wg, such UAS.ds clones had little effect on surrounding cells, only occasionally inducing 5XQE.DsRed expression just outside the clone (unpublished data). However, when supplemented with exogenous Wg (using co-expression of a UAS.wg transgene), most UAS.ds clones induced 5XQE.DsRed expression both within the clone and in surrounding cells . Hence, if the FF signal is transduced by the Wts-Hpo pathway, manipulations that promote Yki action , as expected if D is not available to block Wts activity in the absence of Ds and/or Ft.First, we examined the consequences of generating ods and od clones in oUAS.wg ap discs. Under these conditions, the ods clones both expressed Vg and induced Vg expression in neighboring wild type cells but failed to induce detectable expression in abutting cells belonging to the od clone, resulting in their exclusion from the rescued wing pouch . In this context, Ds and Ft are thought to function as a ligand-receptor pair, with tissue-wide gradients of Ds signal serving to activate Ft to appropriate levels within each cell To date, Ft-Ds signaling has been studied in two contexts: the control of Yki target genes in tissue growth and the orientation of cell structures in PCP. Most work on tissue growth has focused on Yki target genes that control basic cell parameters, such as survival, mass increase, and proliferation and non-wing (vgOFF) cells. Further, we posit that these differentials are transduced in cells undergoing recruitment that work in conjunction with FF propagation see also . And thiDrosophila wing, Wts-Hpo activity and YAP appear to function in these contexts in a manner that is distinct from their generic roles in the regulation of cell survival, growth, and proliferation, namely as part of an intercellular signaling mechanism that specifies cell type. We suggest that this novel employment of the pathway constitutes a new, and potentially general, mechanism for regulating tissue and organ size.Our identification of Ft-Ds signaling, the Wts-Hpo pathway, and Yki as key components of the FF recruitment process provides a striking parallel with the recently discovered involvement of the Wts-Hpo pathway and Yki/YAP in regulating primordial cell populations in vertebrates, notably the segregation of trophectoderm and inner cell mass in early mammalian embryos (i) Flp/FRT mediated mitotic recombination Hsp70.flp transgene . Wing discs from mature third instar larvae were dissected, fixed, and processed for immuno-fluorescence by standard methods, using anti-Vg, anti-Wg, anti-HA, and anti-\u03b2Gal antisera by heat shock induced expression of an vg QE activity was monitored by expression of 1XQE.lacZ and 5XQE.DSRed reporter transgenes as well as by the expression of Vg protein in the absence of DSL-Notch signaling fj-lacZ enhancer trap allele P1fjvg expression. All four assays gave similar results, with the 5XQE.DSRed and fj-lacZ reporters showing the greatest sensitivity.http://flybase.bio.indiana.edu/) The following amorphic mutant alleles and transgenes were employed Exel6006, UA071ds, 2D60bds, E1ex, P1fj, 15ft, P21fz, C1Dfz2 , 83b27Rvg, and X1wts.Mutant alleles: apintraUAS.N, UAS.Nrt-wg, UAS.wg, Tub\u03b11>GFP,y+>vg, C765.Gal4, nub.Gal4, Tub\u03b11>Gal80>Gal4, GSUAS.ds, UAS.ft, UAS.d, UAS.yki, Hsp70.GFP.Transgenes: Exact genotypes, by Figure panel:56f fjP1/+.y w 5XQE.DsRed/y w Hsp70.flp; FRT39 ap(2A) 56f fjP1/FRT39 ap56f.y w 5XQE.DsRed/y w Hsp70.flp; FRT39 ap(2B) 2D60b FRT39 ap56f vg83b27R/+.y w 5XQE.DsRed/y w Hsp70.flp; ds(2C) 2D60b FRT39 ap56f vg83b27R/FRT39 ap56f.y w 5XQE.DsRed/y w Hsp70.flp; ds(2D) 56f vg83b27R 5XQE.DsRed/FRT39 ap56f vg83b27R fjP1; Tub\u03b11>flu-GFP,y+>vg/+.y w Hsp70.flp/y w Hsp70.flp; ap(2E) 56f vg83b27R 5XQE.DsRed/ds2D60b FRT39 ap56f vg83b27R; Tub\u03b11>flu-GFP,y+>vg/+.y w Hsp70.flp/y w Hsp70.flp; ap(2F) 56f/Hsp70.flu-GFP FRT39 ap56f fjP1; Tub\u03b11>flu-GFP,y+>vg UAS.Nrt-flu-wg/C765.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; FRT39 ap(2G) 56f/ds2D60b FRT39 ap56f vg83b27R; Tub\u03b11>flu-GFP,y+>vg UAS.Nrt-flu-wg/C765.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; FRT39 ap(2H) UA071 FRT39 ap56f/dsUA071 FRT39 ap56f; UAS.wg/+.y w 5XQE.DsRed/y w Hsp70.flp; ds(3A) 15 FRT39 ap56f/dsUA071 ft15 FRT39 ap56f fjP1.y w 5XQE.DsRed/y w 5XQE.DsRed; ft(3B) UA071 ft15 FRT39 ap56f/dsUA071 ft15 FRT39 ap56f fjP1; Tub\u03b11>CD2,y+>Gal4/+.y w 5XQE.DsRed/y w 5XQE.DsRed; ds(3C) 15 FRT39 ap56f/ft15 FRT39 ap56f; fzP21 Dfz2C1 FRT2A/Hsp70.CD2 Hsp70.flu-GFP FRT2A.y w 5XQE.DsRed/y w Hsp70.flp; ft(3D) 15 FRT39 ap56f/ft15 FRT39 ap56f; UAS>CD2,y+>Nrt-flu-wg C765.Gal4/+.y w 5XQE.DsRed/y w Hsp70.flp; ft(3E) UA071 FRT39 ap56f/Hsp70.flu-GFP Tub\u03b11.Gal80 FRT39 ap56f fjP1.y w 5XQE.DsRed/y w Hsp70.flp Tuba1.Gal4 UAS.GFPnls; ds(4A) 15 FRT39 ap56f/Hsp70.flu-GFP Tub\u03b11.Gal80 FRT39 ap56f fjP1; UAS.wg/+.y w 5XQE.DsRed/y w Hsp70.flp; ft(4B) UA071 ft15 FRT39 ap56f fjP1/Hsp70.flu-GFP Tub\u03b11.Gal80 FRT39 ap56f; C765.Gal4/+.y w 5XQE.DsRed/y w Hsp70.flp; ds(4C) UA071 FRT39 ap56f/Hsp70.flu-GFP FRT39 ap56f; UAS.Nrt-flu-wg/C765.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; ds(4D) 15 FRT39 ap56f/Hsp70.flu-GFP FRT39 ap56f; UAS.Nrt-flu-wg/C765.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; ft(4E) UA071 FRT39 ap56f/Hsp70.flu-GFP FRT39 ap56f; UAS>CD2,y+>Nrt-flu-wg C765.Gal4/1XQE.lacZ.y w Hsp70.flp/y w Hsp70.flp; ds(4F) UA071 Tub\u03b11.Gal80 FRT39 ap56f vg83b27R/Hsp70.flu-GFP FRT39 ap56f fjP1; UAS.ft/Tuba1.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; ds(5A) 15 Tub\u03b11.Gal80 FRT39 ap56f/Hsp70.flu-GFP FRT39 ap56f fjP1; UAS.ft/Tub\u03b11.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; ft(5B) 56f fjP1/FRT39 ap56f UAS.flu-wg; UAS.ft/Tub\u03b11>Gal80,y+>Gal4.y w 5XQE.DsRed/y w Hsp70.flp UAS.GFPnls; FRT39 ap(5C) 56f 1XQE.lacZ/dsUA071 FRT39 ap56f; UAS.ds/Tub\u03b11>Gal80,y+>Gal4 UAS.wg.y w 5XQE.DsRed/y w Hsp70.flp UAS.GFPnls; ap(5D) 56f/Hsp70.flu-GFP Tub\u03b11.Gal80 FRT39 ap56f fjP1; UAS.d/UAS.wg.y w 5XQE.DsRed/y w Hsp70.flp Tuba1.Gal4 UAS.GFPnls; FRT39 ap(6A) 56f UAS.flu-wg/FRT39 ap56f fjP1; Tub\u03b11>Gal80,y+>Gal4 UAS.yki/+.y w 5XQE.DsRed/y w Hsp70.flp UAS.GFPnls; FRT39 ap(6B) 56f/ap56f UAS.flu-Nrt-wg; FRT82 wtsx1/FRT82 Hsp70.flu-GFP.y w Hsp70.flp/y w Hsp70.flp; nub-Gal4 FRT39 ap(6C) e1 FRT39 ap56f/Hsp70.flu-GFP FRT39 ap56f fjP1; UAS.wg/C765.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; ex(6D) UA071 Hsp70.flu-GFP FRT39 ap56f/dGC13 FRT39 ap56f fjP1; UAS.wg/C765.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; ds(7A) GC13 FRT39 ap56f fjP1/dGC13 FRT39 ap56f; Tub\u03b11>flu-GFP,y+>vg UAS.Nrt-flu-wg/C765.Gal4.y w 5XQE.DsRed/y w Hsp70.flp; d(7B) UA071 dGC13 FRT39 ap56f/Hsp70.flu-GFP Tuba1.Gal80 FRT39 ap56f fjP1; UAS.wg/+.y w 5XQE.DsRed/y w Hsp70.flp Tuba1.Gal4 UAS.GFPnls; ds(7C) UA071 FRT39 ap56f/dsUA071 FRT39 ap56f; UAS.Nrt-flu-wg/Tub\u03b11>Gal80,y+>Gal4.y w 5XQE-DsRed/y w Hsp70.flp; ds(S1A) 56f UAS>CD2,y+>Nrt-flu-wg/nub-Gal4 FRT39 ap56f; FRT82 wtsx1/FRT82 Hsp70.flu-GFP.y w Hsp70.flp/y w Hsp70.flp; ap(S1B) 56f 1XQE.lacZ/FRT39 ap56f; UAS>CD2,y+>Nrt-flu-wg C765.Gal4/UAS.yki.y w Hsp70.flp/y w Hsp70.flp; ap(S1C) (S2A) as (4E).15 FRT39 ap56f/Df(2L)Exel6006 Hsp70.flu-GFP FRT39 ap56f; UAS.Nrt-flu-wg/C765.Gal4.y w 5XQE-DsRed/y w Hsp70.flp; ft(S2B) 15 Tuba1.Gal80 FRT39 ap56f/Hsp70.flu-GFP FRT39 ap56f; UAS>CD2,y+>Nrt-flu-wg C765.Gal4/1XQE.lacZ.y w Hsp70.flp/y w Hsp70.flp; ft(S2C) cx4 FRT39 ap56f/Hsp70.flu-GFP Tub\u03b11.Gal80 FRT39 ap56f; UAS.Nintra/1XQE.lacZ.y w Hsp70.flp Tub\u03b11.Gal4 UAS-GFPnls/y w Hsp70.flp; wg(S3A) 15 wgcx4 FRT39 ap56f/Hsp70.flu-GFP Tub\u03b11.Gal80 FRT39 ap56f; lqf1227 Hsp70-CD2 FRT2A UAS.Nintra/+.y w 5XQE-DsRed/y w Hsp70.flp Tub\u03b11.Gal4 UAS-GFPnls; ft(S3B) 15 FRT39 ap56f/Tub\u03b11.Gal80 FRT39; UAS.wg/+.y w Hsp70.flp Tub\u03b11.Gal4 UAS-GFPnls/y w Hsp70.flp; ft(S3C) 15 FRT39 ap56f/Tub\u03b11.Gal80 FRT39; UAS.dpp/+.y w omb-lacZ/y w Hsp70.flp Tub\u03b11.Gal4 UAS-GFPnls; ft(S3D) Figure S1Quadrant enhancer activity is Wingless dependent in oap discs that lack either Dachsous or Warts or that over-express Yorkie. (A) A UAS.Nrt-wg clone in a o apods disc. Both Vg and 5XQE.DsRed are expressed at peak levels in the clone and in surrounding cells that abut the clone, as observed for UAS.Nrt-wg clones in o apoft discs , Vg is strongly up-regulated in the UAS.Nrt-wg clones and abutting cells. (C) UAS.Nrt-wg clones generated in an oUAS.yki ap disc; same outcome as in (A), except a 1XQE.lacZ transgene was used instead of the 5XQE.DsRed transgene.po discs . (B) UAS(3.99 MB TIF)Click here for additional data file.Figure S2Exceptional cases of local non-autonomous Quadrant enhancer activity associated with oft clones can be attributed to induction by their sibling 2\u00d7+ft clones. (A) A oft clone (marked by the absence of GFP) associated with local, non-autonomous activity of the 5XQE.DsRed transgene (appears yellow in A') in an o UAS.Nrt-wgap disc. Note that this non-autonomous expression is associated with a sibling 2\u00d7+ft clone . In this experiment, 26/43 oft clones were associated with strictly cell-autonomous QE activity , and in the remaining 10/17 cases, 9/10 had no detectable twin, and 1/10 had a twin clone located elsewhere. Thus, the majority of oft clones analyzed in this experiment showed a strictly cell-autonomous response, and in 7/8 cases in which local, non-autonomous 5XQE.DsRed expression was observed and a 2\u00d7+ft twin survived, the twin spot was associated with the 5XQE.DsRed expression. Based on these results, we attribute the exceptional cases of non-autonomous 5XQE.DsRed expression associated with oft clones to signaling by their 2\u00d7+ft sibling clones, a conclusion further supported by experiments in panels (B) and (C). (B) A oft clone generated and marked as in (A), except under conditions in which its sibling 2\u00d7+ft clone died, owing to homozygosity for Df(2L)Exel6006. Note the strictly cell-autonomous expression of the 5XQE.DsRed transgene. 39/45 clones generated in this experiment behaved in this way; 6/45 showed local non-autonomy. We have not determined how quickly the sibling 2\u00d7+ Df(2L)Exel6006ft clones die after being generated in this experiment; it is possible that rare 2\u00d7+ Df(2L)Exel6006ft clones survive long enough to induce self-sustaining vg and 5XQE.DsRed expression in neighboring cells prior to their loss. (C) A UAS.Nrt-wg 2\u00d7+ft clone and its oft sibling clone (marked by the absence of GFP) in an oap disc. Note the association of the 2\u00d7+ft clone with ectopic Vg expression as well as the local induction of Vg expression by Nrt-Wg in neighboring cells . This result corroborates the evidence shown in (A) and (B), that 2\u00d7+ft clones generated in 1\u00d7+ apoft discs have the capacity to induce 5XQE-DsRed and vg expression.ty as in : of thesft+ twin , and the(2.19 MB TIF)Click here for additional data file.Figure S3oft clones can send Delta/Serrate/Lag2 (DSL), Wingless, and Decapentaplegic signals. (A) A intra wgoUAS.N clone generated in an oap disc. intraN encodes a constitutively active form of Notch; clones of intra wgoUAS.N cells in oap discs up-regulate the expression of the Notch ligands Delta and Serrate and activate Notch in adjacent cells, as visualized by the induction of a ring of ectopic, Wg-expressing D-V border cells encircling the clone . These ectopic border cells suffice to initiate the long-range propagation of QE-dependent vg expression in surrounding cells, as indicated by the broad halo of 1XQE-lacZ expression. (B) A intra wgo ftoUAS.N clone generated an oap disc. Essentially the same experiment shown in (A), except that the clones are also oft. The result is the same (except that a 5XQE-DsRed reporter was used in place of the 1XQE-lacZ reporter), indicating that cells in the clone can send DSL signals to the surround, even though they are devoid of Ft. (C) A oUAS.wg ft clone generated in a wild type disc. QE-dependent vg expression depends on the level of Wg input. As a consequence UAS.wg clones up-regulate Vg expression in surrounding cells within the wing pouch, as seen in this example, even though the clone is also oft. (D) A oUAS.dpp ft clone generated in a wild type disc. Ectopic Dpp expressed by the clone has induced ectopic omb-lacZ expression in the surround, even though the clone is oft.(3.03 MB TIF)Click here for additional data file."} +{"text": "The expression of retinoblastoma (Rb), c-Myc and Bcl-2 proteins was studied by immunohistochemical methods in 104 cases of renal adenocarcinoma. One tumour was completely negative for Rb protein and altered expression pattern was detected in 36% of cases. A low fraction of Rb-positive nuclei was related to high grade (P = 0.016) and high mitotic index (P = 0.012). Twenty-eight per cent of the tumours expressed c-Myc in cancer cell nuclei and 87% showed cytoplasmic positivity. Cytoplasmic expression of c-Myc was related to high grade (P = 0.002), while nuclear expression of c-Myc was related to small tumour diameter (P = 0.034), low T category (P = 0.04), low mitotic index (P = 0.019) and expression of c-ErbB-2 (P = 0.0007). Overexpression of c-myc predicted favourable outcome in M0 tumours (P = 0.0157). Bcl-2 was expressed in 20% of tumours and it was related to small tumour size (P < 0.0001), low T category (P < 0.0001), lack of venous invasion (P = 0.008), node negativity (P = 0.015) and absence of metastasis (P = 0.017). In multivariate analysis the expression of Rb, Bcl-2 and c-Myc had no independent prognostic value over T category (P < 0.001), mitotic index (P = 0.008) and combined nuclear grade (P = 0.056)."} +{"text": "P= 0.08). A negative association was found between ARs and cell proliferative activity: MIB-1 scores were higher (25.4%) in AR-negative than in AR-positive cases . A strong positive association (P= 0.0001) was found between ARs and oestrogen receptors (ERs). In univariate analysis, ARs (as well as ERs and PGRs) were not correlated with overall survival; tumour histological grade (P= 0.02), size (P= 0.01), p53 expression (P= 0.0008) and MIB-1 scores (P= 0.0003) had strong prognostic value. In multivariate survival analysis, only p53 expression (P= 0.002) and histological grade (P= 0.02) retained independent prognostic significance. In conclusion, the lack of association between AR and most clinicopathological features and survival, together with the absence of prognostic value for ER/PGR status, suggest that MBCs are biologically different from female breast carcinomas and make it questionable to use antihormonal therapy for patients with MBC. \u00a9 1999 Cancer Research CampaignAndrogen receptor (AR) expression was retrospectively analysed in 47 primary male breast carcinomas (MBCs) using a monoclonal antibody on formalin-fixed, paraffin-embedded tissues. AR immunopositivity was detected in 16 out of 47 (34%) cases. No association was found with patient age, tumour stage, progesterone receptor (PGR) or p53 protein expression. Well-differentiated MBCs tended to be AR positive more often than poorly differentiated ones ("} +{"text": "P for trend = 0.022, adjusted odds ratio 1.20, 95% confidence interval 1.07\u20131.33 respectively. No association was found between HHV-6 and ALL, CML or RAEB. \u00a9 1999 Cancer Research CampaignThe relationships between acute myeloid leukaemia (AML), acute lymphocytic leukaemia (ALL), chronic myeloid leukaemia (CML) and refractory anaemia with excess of blasts (RAEB) and human herpes virus (HHV)-6 antibody level were investigated in a multicentre case-control study. An association between increased HHV-6 seropositivity and geometric mean titre ratio with AML was shown:"} +{"text": "We have studied the cytotoxicity of bleomycin (4--10 u/kg/day for 6 days) given by continuous i.p. infusion (using an osmotic minipump) compared to daily i.p. bolus administration, against P388 leukaemic spleen colony-forming-units(LCFU-S). Continuous i.p. bleomycin at 8 u/kg/day caused a 0.5 log greater reduction of LCFU-S than did an identical dose given by intermittent bolus administration. The infusion minipump provided constant bleomycin plasma levels of 0.62 +/- 0.03 mu/ml and a total plasma AUC (area under the plasma decay curve) of 89.0 mu.h/ml for 6 days at 8 u/kg/day. Intermittent bolus bleomycin at 8 u.kg/day had a terminal-phase plasma t1/2 of 15 min and a total 6-day plasma AUC of 90.8mu.h/ml. These pharmacokinetic data validate the osmotic minipump as a constant drug-delivery system, and suggest that the two administration schedules resulted in equal total bleomycin dosages. Although high peak bleomycin plasma levels (i.e. 32 mu/ml) were achieved with the intermittent bolus administration, continuous-infusion bleomycin's greater inhibition of LCFU-S was probably related to the drug's schedule-dependent cell-killing characteristics. The results of this study provide further rationale for the continuing use of infusion bleomycin schedules in cancer patients."} +{"text": "P < 0.0001), 100 nM NPY (P < 0.0001), 100 nM VIP (P < 0.001), 100 nM CGRP (P < 0.001), 100 nM SP (P < 0.01), and 0.1 mM histamine (P < 0.01), whereas 0.1 mM 5-HT, mM acetylcholine, and 1 \u03bcM isoproterenol (\u03b2-adrenergic agonist) had no effect. Proliferation(incorporation of tritiated thymidine) was increased by CGRP (P = 0.004) and histamine (P < 0.02), but decreased by isoproterenol (P = 0.002), 5-HT (P = 0.003), and acetylcholine (P < 0.05). The percentage of multinucleate cells was decreased after isoproterenol (2.5%), and increased after 5-HT (21.3%), GABA (15%), and histamine (15.1%). Compared to controls, thymulin in the supernatant was decreased after challenge with acetylcholine (52%), isoproterenol (71%), 5-HT (73%), and histamine (84%). This study demonstrates direct effectsof neuropeptides and neurotransmitters on functional aspects of cultured thymic epithelial cells.To determine if major thymic neuropeptides and neurotransmitters can directly influence the functional activity of cultured rat thymic epithelium, neuropeptides and neurotransmitters were applied, and intercellular communication, proliferation, and thymulin secretion assessed. After injections of a mixture of lucifer yellow dextran (too large to pass gap junctions) and cascade blue (which does) into single cells, some neuropeptides decrease dye coupling: 0.1 mM GABA ("} +{"text": "The atomic arrangement consists of an infinite long-chain polyphosphate organization. Chains, with a period of four PO4 tetra\u00adhedra, run along the a-axis direction. Two other polymorphs of this phosphate are known, in space groups P21/n and C2/c.The title compound, potassium yttrium polyphosphate, KY(PO DOI: 10.1107/S1600536808013925/br2073Isup2.hkl Structure factors: contains datablocks I. DOI: crystallographic information; 3D view; checkCIF report Additional supplementary materials:"} +{"text": "The 4,6-dihydroxy\u00adbenzene-1,3-disulfonate anion, acting as a counter-ion, is also located on the mirror plane. The crystal packing is stabilized by O\u2014H\u22efO hydrogen bonds, forming a three-dimensional supra\u00admolecular network.In the title compound, [Zn(CH DOI: 10.1107/S1600536810006525/hy2283Isup2.hkl Structure factors: contains datablocks I. DOI: crystallographic information; 3D view; checkCIF report Additional supplementary materials:"} +{"text": "Since 1997, the largest epidemic of highly pathogenic avian influenza (H5N1) ever recorded has caused 172 human and several billion bird deaths. Recently administered questionnaires determined that live poultry exposures have declined by \u224863% in Hong Kong since 2004 and that, in Vietnam, domestic backyard exposures to poultry are likely more important than retail exposures. MappingIn Hong Kong, random household telephone interviewing of 1 adult >17 years of age selected by Kisch grid (which randomizes selection of persons within households) was conducted from December 2005 through 2006 from a list of 5,000 numbers. Simultaneously in Vietnam, stratified cluster sampling was carried out throughout 2 districts in each of 5 northern provinces. Within 3 of these provinces, 1 district with and 1 without an HPAI epidemic history were selected. Within each district, 1 urban and 1 rural commune each provided 100 households randomly selected from electoral rolls. Kisch grid selected 1 adult from each household for face-to-face interviews.Respondents estimated their live poultry purchase frequency and touching at purchase ; 64% of respondents were women and 36% were men; their median age, 44 years . VietnamIn Hong Kong in 2006, 18,586 standardized purchases averaged 10.56 chickens/household/year . This is a territory-wide gender-adjusted rate of 11.05 chickens/household/year, which indicated that 22,673,000 live chickens were purchased during the preceding year, 41% fewer than in 2004. Households buying poultry bought an average of 15.6 chickens/household/year. Among respondents personally buying, 7.5% touched the poultry during purchasing (compared with 11% in 2004), giving \u22481,700,500 exposures/year. Adjustment for touching frequency and gender differences in reported touching gave \u22481,110,900 contacts for Hong Kong in 2006, or 0.76 exposures/buying household/year . Applied retrospectively to Hong Kong 2004 data, this gave an adjusted exposure rate of 8.6% (95% CL 6.8\u201310.3), \u22483,311,300 contacts, and exposure frequency of 2.07 exposures/buying household/year (0.62/person/year) in 2004. These adjusted estimates indicate an absolute exposure decline of 3.7% (95% CL 2.25%\u20134.91%), a relative decline of 43% between 2004 and 2006. Less purchasing and touching reduced annualized buying exposures by 63% overall.2 = 45.57, df = 4, p<0.001), after adjustment for gender proportion and reported touching, was 63% (62%\u201364%). Estimated exposures in the surveyed provinces from buying were \u224813,097,000 \u00d7 0.63 = \u22488,251,000 exposures/year. When these rates were used, national per capita exposure estimates (assuming 4.49 persons/household) from touching when buying are \u224862,479,000 exposures/year, 2.24 exposures/person/year in buying households, 0.76 exposures/person/year overall.In Vietnam, respondents reported 10,659 standardized purchases, averaging 5.36 chickens/household/year, giving a gender-adjusted rate of 5.43 chickens/household/year. Estimated number of live birds purchased in the sampled provinces was 13,097,000 chickens per year. Buying households buy on average 15.97 chickens per year, comparable to the Hong Kong 2006 purchase rate. Touching frequency during purchasing that raised poultry, 92 (5%) ceased keeping poultry from February 2005 through February 2006 . HousehoWhile 34% (32%\u201336%) of households buy live chickens, 53% (52%\u201354%) raise live poultry at home, and 12% (10%\u201313%) do both. Assume a 53% national average and, conservatively, that all persons within households rearing backyard poultry have at least weekly physical contact with their birds, bird eggs, or feces. Household size in the surveyed districts averages 3.38 persons . Thus, 224,685,500 exposures/year would occur from backyard poultry in surveyed districts, an average exposure within backyard poultry raising households of \u2248175 exposures/person/year. Households buying live poultry have 8,251,000 /820,080 = 10.1 exposures/household/year (2.99 exposures/person/year) from these purchases. Total purchase-related plus backyard exposure events then equal + 224,685,500 = 232,968,300 exposures/year. Average household exposure is therefore \u224896 exposures/household/year (28 exposures/person/year) in sampled districts. If daily backyard exposure occurs, then there are \u22481,581,081,300 total exposures, \u2248655 exposures/household/year (194 exposures/person/year). Nationally, average household size is 4.49 persons. Hence, between \u22482,322,546,000 (weekly contact) and \u224815,882,953,000 (daily contact) exposures/year, \u2248127\u2013869 exposures/household/year occur nationally. If multiple contacts occur daily, these figures would be much higher.Epidemic and nonepidemic district-buying frequency CL overlapped (exposure 3.4 [1.9\u20134.8] chickens/household/year vs. nonexposure 5.8 [4.5\u20137.0] chickens/household/year). Dual adjusted touching frequencies were 69% (62%\u201376%) in epidemic and 60% (57%\u201363%) in nonepidemic districts, respectively. Backyard poultry were more common in epidemic districts (71% [67%\u201375%] vs. 45% [42%\u201348%]), where keeping poultry declined 17% (14%\u201320%) compared with 8% (6%\u201310%) in nonepidemic districts. Epidemic and nonepidemic districts had comparable average incomes .In Hong Kong, government import restrictions have reduced poultry availability by 41% from 2004 to 2006. Purchase and touching declines prompted by health education messages have together reduced exposure by \u224860%.www.worldbank.org/data/quickreference/quickref.html), live chickens costs $16.6\u2013$18.0 and $21.8\u2013$31.0 each in Hong Kong and in Vietnam, respectively. Hence, temptation to use sick, dying, or dead poultry is high, increasing the risk for human influenza (H5N1) infection (Fewer Vietnamese households bought live chickens, but those that did so bought at comparable frequencies to Hong Kong 2006 households. Chickens are relatively more expensive in Vietnam. Adjusted for purchasing power parity (Limitations include generalizing from 5 northern Vietnamese provinces to the country as a whole and using arbitrary estimates for backyard exposure frequency. Nonetheless, valuable data are presented on differential exposure patterns."} +{"text": "Objective: Octreotide, a somatostatin analogue, hasbeen shown to prevent angiogenesis in diverse invitro models. We evaluated its effect on retinal neovascularizationin vivo, using a neonatal rat retinopathymodel. Methods: We used, on alternating days, hypoxia(10% O2) and hyperoxia (50% O2) during the first 14days of neonatal rats, to induce retinal neovascularization.Half of the rats were injected subcutaneouslywith octreotide 0.7 \u03bcg/g BW twice daily. Atday 18 the eyes were evaluated for the presence ofepiretinal and vitreal hemorrhage, neovascularizationand epiretinal proliferation. Octreotide pharmacokineticsand its effect on serum growth hormone(GH) and insulin-like growth factor I (IGF-I) wereexamined in 28 rats. Results: Serum octreotide levels were 667 \u03bcg/1 twohours after injection, 26.4 \u03bcg/1 after nine hours and3.2 \u03bcg/1 after 14 hours. GH levels were decreasedby 40% (p = 0.002) two hours after injection butthereafter returned to baseline. IGF-I levels were unchangedtwo hours after injection and were elevatedby 26% 14 hours after injection (p = 0.02). Epiretinalmembranes were highly associated with epiretinalhemorrhages (p < 0.001), while retinal neovascularizationwas notably associated with vitreal hemorrhages (p < 0.001). Conclusions: Twice-daily injections of octreotidefailed to produce sustained decrease in serum GH,but produced rebound elevation of serum IGF-I.Accordingly, no statistically significant effect of injectionson retinal pathology was noted. This finding,however, does not contradict our assumptionthat GH suppression may decrease the severity ofretinopathy."} +{"text": "The crystal structure contains six sites in the asymmetric unit: two sites are statistically occupied by rare-earth atoms with Gd:Sc ratios of 0.967\u2005(4):0.033\u2005(4) and 0.031\u2005(3):0.969\u2005(3), one site (.m. symmetry) is occupied by Sc atoms, and three distinct sites (two of which with .m. symmetry) are occupied by Ge atoms. The rare-earth atoms form two-dimensional slabs with Ge atoms occupying the trigonal-prismatic voids.Gd DOI: 10.1107/S1600536809007211/mg2062Isup2.hkl Structure factors: contains datablocks I. DOI: crystallographic information; 3D view; checkCIF report Additional supplementary materials:"} +{"text": "We looked for associations between spontaneous apoptosis, p53 gene mutation, p53 protein accumulation, growth fraction, bcl-2 expression and histological parameters in 64 ovarian, four tubal and three peritoneal carcinomas. Apoptotic cells were detected with the TUNEL method. p53 gene variants were detected by the single-strand conformation polymorphism and were sequenced directly. P53, Ki-67 and bcl-2 protein expressions were detected immunohistochemically. A weighed multiple logistic regression model was applied. Apoptotic index (Al) ranged 0.02\u20130.18 (mean 0.11); proliferation index (PI) ranged 3\u201390% (mean 54%). p53 gene mutations were present in 51, p53 protein accumulation in 46, and diffuse bcl-2 expression in 29 of 71 tumours. The AI was positively associated with the presence of p53 gene mutation (P = 0.011). However, the PI included into the analysis did positively influence the AI (P = 0.02) and diminished the association with p53 gene mutation (P = 0.082). The AI was negatively associated with good histological differentiation (P = 0.0006), the serous tumour type (P = 0.002), and diffuse bcl-2 expression (P = 0.025). Strong bcl-2 expression was associated with endometrioid tumour type (P = 0.002). FIGO stage and p53 protein accumulation were the only parameters that influenced overall survival time. Thus, our results suggest that histological tumour type and grade are major determinants of spontaneous apoptosis in ovarian carcinomas;p53 alterations do not adversely but rather positively affect spontaneous apoptosis by increasing growth fraction. This, in turn, suggests p53-independency of spontaneous apoptosis in ovarian carcinomas. \u00a9 2000 Cancer Research CampaignChanges in cell survival contribute to tumour development, influence tumour biology and its response to chemotherapy."} +{"text": "Lactobacillus plantarum LQ80 is a strain isolated from liquid feed for pigs. We determined the complete genome sequence of this strain using the PacBio RS II platform. LQ80 contained a single circular chromosome of 3,230,192 bp, with 44.66% G+C content and seven plasmids. Lactobacillus plantarum is found in various environmental niches, e.g., vegetable pickles (https://www.qiagen.com/us/resources/resourcedetail?id=8b1b2b4f-3dca-4447-8d21-f6fd64c3a729), and a 5-kb library was constructed with shearing. One SMRT cell was used for sequencing on the PacBio RS II platform with a 360-min movie time. The result of 362,945 reads with a mean length of 1,519 bp was assembled with HGAP3, and five circular contigs were obtained, representing five plasmids . From this analysis, another four smaller plasmids were constructed.Strain LQ80 was cultured with de Man-Rogosa-Sharpe medium at 37\u00b0C. For the genome sequencing of LQ80, DNA was isolated at the early log phase. DNA was purified using a PowerClean DNA cleanup kit , followed by 20-kb library construction for P6-C4 chemistry with shearing. Five single-molecule real-time (SMRT) cells were used for sequencing on the PacBio RS II platform with a 180-min movie time. We obtained 320,152 reads with a mean length of 5,268 bp. (HGAP3) . Four ciThe LQ80 chromosome was 3,230,192 bp in length, with a G+C content of 44.66%. In addition, LQ80 had seven plasmids: pLQ801 , pLQ802 , pLQ803 , pLQ804 , pLQ805 10,218 bp), pLQ806 , and pLQ807 . The complete genome was annotated using NCBI Prokaryotic Genome Annotation Pipeline (PGAP) and Micr bp, pLQ8L. plantarum LQ80 have been deposited in GenBank under accession numbers CP028977 (chromosome), CP028978 (pLQ801), CP028979 (pLQ802), CP028980 (pLQ803), CP028981 (pLQ804), CP028982 (pLQ805), CP028983 (pLQ806), and CP028984 (pLQ807).The complete genome sequences of the chromosome and seven plasmids of"} +{"text": "Salmonella typhimurium (S. typhimurium) A1-R, a facultative anaerobe that is an auxotroph of leucine and arginine. The tumor-targeting efficacy of S. typhimurium A1-R was demonstrated in vivo and vitro using several malignant cell lines including melanoma, sarcoma, glioma, breast, pancreatic, colon, cervical, prostate, and ovarian cancers. Our laboratory also developed a patient-derived orthotopic xenograft (PDOX) model by implanting patient-derived malignant tumor fragments into orthotopic sites in mice. We reviewed studies of S. typhimurium A1-R against recalcitrant cancers. S. typhimurium A1-R was effective against all PDOX tumor models tested and showed stronger efficacies than chemotherapy or molecular-targeting therapy against some tumors. Furthermore, the synergistic efficacy of S. typhimurium A1-R when combined with chemotherapeutic agents, molecular-targeting agents, or recombinant methioninase was also demonstrated. We suggest potential clinical uses of this S. typhimurium A1-R treatment.We developed tumor-targeting Streptococcus pyogenes (S. pyogenes). He then developed Coley\u2019s toxin, a mixture of killed S. pyogenes and Serratia marcescens, achieving clinical responses for many malignant tumors [Dr. William B. Coley began bacterial therapy of cancer using t tumors .Live bacteria can actively penetrate tumors to reach lesions distant from blood vessels, where chemotherapeutic drugs cannot be delivered, and damage malignant cells by several cytotoxic mechanisms . ObligatClostridium. butyricum (C. butyricum) M-55 resulted in oncolysis and accumulation in treated tumors [C. novyi-NT induced intratumor infection and necrosis [Salmonella typhimurium (S. typhimurium) VNP20009 attenuated by msbB and purI mutations, showed bacterial colonization of treated melanomas [S. typhimurium showed bacterial colonization in treated tumors after local or systemic administration [In clinical studies, limited antitumor efficacy has been shown thus far. d tumors ,7. Intraelanomas ,9. ObjecS. typhimurium is a facultative anaerobe. Green fluorescence protein (GFP)-labeled S. typhimurium A1-R developed by our laboratory has high tumor-targeting efficacy, due to the leucine\u2013arginine auxotroph, resulting in broad antitumor efficacy and limited adverse effects [S. typhimurium A1-R was quickly eliminated from normal organs including the liver and spleen seven days after intravenous administration [S. typhimurium A1-R remained at high density in CT26 tumors. In addition, tumors treated with S. typhimurium A1-R were significantly smaller than those treated with S. typhimurium VNP20009. The efficacy of S. typhimurium A1-R was demonstrated in orthotopic nude mouse models of prostate [S. typhimurium A1-R was also effective in metastatic cancer models [ effects . In a CTstration . In contprostate , breast prostate ,14, pancprostate ,16, and prostate , as wellprostate and glioprostate ,20. S. tr models ,22.S. typhimurium A1-R against malignancies in patient-derived orthotopic xenograft (PDOX) nude mouse models, in which human tumors are orthotopically implanted in mice, to examine future clinical applicability.We review in the present report the therapeutic efficacy of We established PDOX tumors as follows: when the original tumors derived from primary sites, the PDOX tumors were implanted into the same primary sites in mice; when the original tumors derived from recurrent or metastatic sites, the PDOX tumors were implanted into original, recurrent, or metastatic sites in mice.S. typhimurium A1-R in PDOX models were identified. All of the 17 studies of human cancer of different histological types were evaluated and the efficacy of S. typhimurium A1-R was compared with the efficacy of chemotherapy [S. typhimurium A1-R ranged from 5 \u00d7 105 colony-forming units (CFUs) to 1.5 \u00d7 108 CFUs. Intravenous injection twice weekly with a dose of 5 \u00d7 107 CFUs was used in most experiments. S. typhimurium A1-R treatment was performed either as a monotherapy or a polytherapy in combination with chemotherapeutic or molecular-targeting agents, or recombinant methioninase (rMETase), which reduces the plasma methionine on which cancer cells are addicted [s (i.v.) ,37,38,39s (i.v.) ,25, intrs (i.v.) ,28, or is (i.v.) . A singladdicted . PolytheS. typhimurium A1-R was evaluated via culture of resected specimens. A fluorescent microscope was used to detect GFP-expressing S. typhimurium A1-R in tumors grown in PDOX models treated with S. typhimurium A1-R i.t., i.p., i.v., or i.a. injection [S. typhimurium A1-R grown from a Ewing\u2019s sarcoma PDOX tumor [S. typhimurium A1-R were present in STS PDOX tumors, including undifferentiated STS [S. typhimurium A1-R were not detectable in adjacent muscles, suggesting selective tumor-targeting efficacy [The tumor-targeting efficacy of njection ,34,37,38OX tumor . Abundanated STS , pleomorated STS , follicuated STS , melanomated STS ,29,30,34ated STS , a GIST ated STS , and a Cefficacy ,37. The treatment efficacy of S. typhimurium A1-R was confirmed in all PDOX models . SignifiS. typhimurium A1-R showed stronger antitumor efficacy than gemcitabine, cisplatinum, or fluorouracil treatment in the pancreatic PDOX model [S. typhimurium A1-R was more effective than cisplatinum [S. typhimurium A1-R resulted in greater tumor growth inhibition compared to doxorubicin treatment [S. typhimurium A1-R showed stronger efficacy than imatinib in the GIST PDOX model [OX model . In the platinum ,32. In treatment ,35,39. MOX model .S. typhimurium A1-R with chemotherapy [S. typhimurium A1-R had additional efficacy when combined with gemcitabine or gemcitabine plus bevacizumab [S. typhimurium A1-R with temozolomide or vemurafenib significantly reduced tumor growth compared to monotherapy with these agents [S. typhimurium A1-R, rMETase, and cisplatinum was more effective than double therapy using S. typhimurium A1-R with rMETase, or monotherapy of these agents [Synergistic treatment efficacy was observed with combination of otherapy ,36, moleotherapy ,26,29,30otherapy ,35. In pacizumab ,36. Addie agents .S. typhimurium A1-R-treated tumors showed extended necrosis compared to untreated tumors. As an example, S. typhimurium A1-R caused central tumor necrosis to a large extent in the Ewing\u2019s sarcoma PDOX model, while the untreated tumors grew without necrosis (S. typhimurium A1-R treatment resulted in changes in sarcoma cell shape but not necrosis [S. typhimurium A1-R treatment in combination with cisplatinum and rMETase resulted in tumor necrosis. Moreover, S. typhimurium A1-R showed more extensive necrosis when combined with chemotherapy or molecular-targeting agents than S. typhimurium A1-R monotherapy on undifferentiated STS and melanoma PDOX models [S. typhimurium A1-R induced a higher degree of necrosis in several PDOX models including pancreatic cancer, STS, osteosarcoma, and GIST [S. typhimurium A1-R led to more extensive necrosis than intravenous administration in the osteosarcoma PDOX model [Established tumors in the PDOX model had a similar morphologic appearance to the original patient tumor A,B. S. tnecrosis C\u2013G. In anecrosis . S. typhX models ,29,30. Wand GIST ,32,33,37OX model . These rS. typhimurium A1-R compared to the untreated control.None of the PDOX experiments showed adverse effects, in terms of significant weight loss, in mice treated with S. typhimurium A1-R against recalcitrant-caner PDOX models, indicating advantages that S. typhimurium A1-R may have over chemotherapy. Therefore, for rare malignancies or cancers of unknown primary origin, for which effective treatments have not been established, S. typhimurium A1-R treatment can be a good candidate. Moreover, for highly aggressive malignancies such as pancreatic cancer or melanomas, S. typhimurium A1-R was highly effective when combined with chemotherapy or molecular-targeting therapy. In addition, adverse effects were shown to be limited. Therefore, S. typhimurium A1-R treatment has clinical potential. PDOX models are theoretically better at mimicking the human disease than heterotopic tumors, increasing the robustness of drug discovery studies. The present review demonstrates the strong antitumor efficacy of S. typhimurium penetrated the cancer cells in vitro by being attracted to small molecules such as ribose and serine [S. typhimurium A1-R targeted tumors in several PDOX mouse models. The antitumor efficacy of S. typhimurium A1-R against many kinds of cancer cell lines was demonstrated and suggested that S. typhimurium A1-R kills cancer cells directly [S. typhimurium A1-R expanded and burst, resulting in loss of viability [S. typhimurium A1-R, a facultative anaerobe, can grow under anaerobic condition [S. typhimurium A1-R induces central tumor necrosis (Salmonella plays the role of inducing antitumor immune responses in an immunocompetent model [Salmonella enhances both innate and adaptive immunity. Salmonella induces cytokine production, including interferon-\u03b3, via Toll-like receptor 4 signaling [S. typhimurium resulted in recruitment of CD8+ lymphocytes, CD4+ lymphocytes and B lymphocytes as well as macrophages and granulocytes in the tumor [S. typhimurium A1-R was correlated with CD8+ lymphocyte infiltration into treated tumors in a pancreatic cancer syngeneic immunocompetent mouse model [S. typhimurium A1-R acts as a decoy. It induces the cancer cells to leave the chemo-sensitive state of the cell cycle, making the cancer cells highly sensitive to chemotherapy [S. typhimurium A1-R. d serine ,42. The directly ,43,44. Uiability . Importaondition ,44. As anecrosis . In addint model . Salmoneignaling . Upregulignaling ,47. Avogse model . Moreoveotherapy . These fS. typhimurium A1-R against recalcitrant cancer PDOX models. Pre-clinical efficacy studies of S. typhimurium A1-R were completed and only a toxicity test needs to be performed to enable S. typhimurium A1-R to begin phase I clinical studies.The present review discusses the antitumor efficacy of"} +{"text": "Siphoviridae bacteriophage, characterized by an unusual prolate capsid, containing a 72,658-base-pair double-stranded DNA genome with 132 predicted protein-coding genes. Conserved among cluster O bacteriophages, the Ryadel genome contains 31 copies of a unique 17-bp sequence with dyad symmetry.Mycobacteriophage Ryadel is a newly isolated cluster O Siphoviridae bacteriophage, characterized by an unusual prolate capsid, containing a 72,658-base-pair double-stranded DNA genome with 132 predicted protein-coding genes. Conserved among cluster O bacteriophages, the Ryadel genome contains 31 copies of a unique 17-bp sequence with dyad symmetry.Mycobacteriophage Ryadel is a newly isolated cluster O Mycobacterium smegmatis mc2155 at 37\u00b0C for 48 hours and resulted in small-sized lytic plaques. Ryadel was purified by collecting virus from well-isolated plaques from the direct isolation and two successive rounds of serial dilutions. Negative-staining transmission electron microscopy . Soil samples were placed in 7H9 liquid medium, and the supernatant was passed through a 0.22-\u00b5m filter for direct isolation of bacteriophages. Filtered supernatant was incubated with croscopy of isolahttps://blast.ncbi.nlm.nih.gov/) whole-genome alignment (MG099943) and Catdawg (GenBank accession number KF017002) (http://phagesdb.org/DNAMaster/), and PECAAN (https://pecaan.kbrinsgd.org/). Mycobacteriophage Ryadel was predicted to contain 132 protein-coding genes, and no tRNA genes were identified by ARAGORN v1.2.38 encode DNA polymerase III sliding clamp beta, Ku-like double-stranded DNA (dsDNA) break-binding protein, and ParB-like dsDNA partitioning protein.Glimmer v3.02 , 7 and Gor.org/) , DNA Mas v1.2.38 or tRNAs v1.2.38 . Putativ v1.2.38 and NCBI v1.2.38 . SimilarMH590592. Raw reads are available in the SRA under accession number SRX4721442.The mycobacteriophage Ryadel genome is available at GenBank under accession number"} +{"text": "Few studies have compared the effectiveness of brief training courses on point-of-care ultrasound (POCUS) skill acquisition of novice attending physicians vs. trainees. The purpose of this study was to evaluate the change in POCUS image interpretation skills and confidence of novice attending physicians vs. trainees after a 1-day POCUS training course.A 1-day POCUS training course was held in March 2017 in Japan. A standardized training curriculum was developed that included online education, live lectures, and hands-on training. The pre-course assessment tools included a written examination to evaluate baseline knowledge and image interpretation skills, and a physician survey to assess confidence in performing specific ultrasound applications. The same assessment tools were administered post-course, along with a course evaluation. All learners were novices and were categorized as trainees or attending physicians. Data were analyzed using two-way analysis of variance.p\u2009<\u20090.001). The post-course physician confidence scores in using ultrasound significantly increased in all skill categories for both groups. Both trainees and attending physicians demonstrated similar improvement in their post-course test scores and confidence with no statistically significant differences between the groups. The course evaluation scores for overall satisfaction and satisfaction with faculty members\u2019 teaching skills were 4.5 and 4.6 on a 5-point scale, respectively.In total, 60 learners attended the course, and 51 learners (85%) completed all tests and surveys. The 51 novice learners included 29 trainees and 22 attending physicians . The mean pre- and post-course test scores of novice trainees improved from 65.5 to 83.9% while novice attending physicians improved from 66.7 to 81.5% contains supplementary material, which is available to authorized users. Point-of-care ultrasound (POCUS) is defined as ultrasonography at the patient\u2019s bedside that is performed in real-time by a physician caring for the patient . In contMultiple studies have demonstrated the effectiveness of POCUS training courses on knowledge and skills acquisition by different learner groups. These courses have varied in duration, content, delivery, and target audience , 8, 12. Even though POCUS ultrasound training courses have been proven to be effective, , 8, 12 tAs a preparatory step, a 2-day train-the-trainer course was conducted in November 2016 to standardize the educational curriculum for a future POCUS training course in March 2017. The train-the-trainer course curriculum was based on the principles shown to be effective for POCUS skills training \u201315. The The same twelve POCUS faculty that participated in the train-the-trainer course in November 2016 served as the faculty for a 1-day POCUS training course in March 2017 at the 14th Japanese Society of Hospital General Medicine Semi-Annual Meeting. The 1-day POCUS course was a separate session from the main conference and the enrollment cap was 60 participants. The 1-day POCUS course was geared toward novices learners and included pre-course internet-based modules, live lectures 3.5\u00a0h), and hands-on skills training with live models (1.5\u00a0h) and included three focused cardiac ultrasound (FOCUS) sessions, and one session each for deep vein thrombosis, lung/diaphragm, and abdominal ultrasound. The faculty-to-learner ratio was 1:3 during these hands-on sessions. Learning objectives were displayed, and faculty used standardized printed materials as teaching aids at each station . We analyzed differences in examination and survey scores between the trainees and attending physicians. Data analyses were performed using R statistical software (R version 3.1.3.)In total, 60 learners attended the course, and 51 learners (85%) completed all tests and surveys. The 51 novice learners included 29 trainees and 22 attending physicians (Table\u00a0p\u2009<\u20090.001). However, there was no statistically significant difference between the pre-course examination scores (p\u2009=\u20090.80) nor the post-course examination scores (p\u2009=\u20090.43) between trainees vs. attending physicians. Descriptive statistics and an ANOVA table of the examination scores for each application are shown in Additional\u00a0file\u00a0The mean pre- and post-course written examination scores for all learners were 66.0% (standard deviation [SD] 12.9) and 82.8% (SD 9.0), respectively. The mean pre-course examination scores of trainees vs. attending physicians were 65.5% (SD 13.0) and 66.7 (SD 13.0), respectively. The mean post-course examinations scores of trainees vs. attending physicians were 83.9% (SD 9.0) and 81.5% (SD 9.0), respectively. Post-course examination scores were significantly improved compared with pre-course examination scores in both groups (es p\u2009=\u20090.3 betweenp\u2009<\u20090.001). However, there were no significant differences in improvement of post-course confidence scores between the trainees vs. attending physicians in all categories . The pre- and post-course self-evaluation survey results are shown in Additional\u00a0files\u00a0The mean confidence scores for all learners in the pre-course vs. post-course self-evaluation surveys were: general ultrasound skills, 2.37 (SD 0.90) vs. 3.32 (SD 0.71); focused cardiac ultrasound, 2.56 (SD 0.84) vs. 3.60 (SD 0.71); vascular diagnostics, 1.94 (SD 0.90) vs. 3.55 (SD 0.70); lung/diaphragm ultrasound, 1.77 (SD 0.76) vs. 3.30 (SD 0.70); and abdominal ultrasound, 2.95 (SD 0.97) vs 3.81 (SD 0.75). Post-course confidence scores were significantly higher compared with pre-course scores in all categories for both groups Additional file 2:Pre- and post-course physicians survey. (DOCX 17 kb)Additional file 3:Post-course satisfaction surveys. (DOCX 15 kb)Additional file 4:Descriptive statistics and an ANOVA table of the test scores for pre- and post-course written examinations. (DOCX 19 kb)Additional file 5:Descriptive statistics for the pre- and post-course self-evaluation survey. (DOCX 19 kb)Additional file 6:Analysis of variance table for pre- and post-course self-evaluation survey. (DOCX 22 kb)"} +{"text": "Using the Meikirch model as a theoretical underpinning, the present study aimed to examine population health disparities by discerning age variations within and across rural urban areas. Secondary data analysis was conducted using the CDC\u2019s 2017 Behavioral Risk Factor Surveillance System. The study\u2019s outcome variables included physical health and mental health burden . A total sample of 96,568 adults were included with a mean age of 66.05 years (SD = 9.91). Individuals were classified in the following age groups: 43% middle-aged (45-64 years), 33% young-old (65-74 years), and 25% old-old adults (75+ years). The sample was largely female (61%), Non-Hispanic White (86%), and urban (67%). A series of chi-square tests of independence \u2013 post hoc tests when applicable \u2013 were completed. Overall, rural residents reported a higher prevalence of severe physical and mental health symptom burden. Regarding physical health burden, a significant difference was found within urban settings (X2(4) = 50.74, p < .001), where, unexpectedly, young-old adults reported the best physical health. Regarding mental health burden, a significant difference was found for both urban (X2(4) = 1661.72, p < .001)) and rural settings (X2(4) = 820.65, p < .001), with middle-aged adults reporting greater mental illness and the old-old adults reporting greater mental health resiliency. Findings suggest that a multidimensional framework of health usefully informs public health and clinical service interventions, identifying populations and locations in need ."} +{"text": "Bacillus sp. strain YSP-3 was isolated from a salt lake.The halophilic, alkaliphilic bacterium Bacillus sp. strain YSP-3 was isolated from a salt lake. It grows optimally at 8% (wt/vol) NaCl (pH 9.0). The draft genome is composed of 4,006 predicted genes. Genomic analysis showed that various genes are potentially involved in the adaptation mechanisms for osmotic stress and pH homeostasis.The halophilic, alkaliphilic bacterium Bacillus sp. strain YSP-3 was isolated from a salt lake in Jilin, China. In sodium bicarbonate-buffered medium (Bacillus aurantiacus K1-5T (97.9 \u200a%) and Bacillus populi FJAT-45347T (97.01%). A phylogenetic tree was reconstructed by a neighbor-joining (B. aurantiacus K1-5T and B. populi FJAT-45347T (data not shown), which revealed that YSP-3 belonged to the genus Bacillus. To understand the adaptive strategies for survival under hypersaline conditions, draft genome sequencing of Bacillus sp. YSP-3 was performed using an Illumina platform.The halophilic and alkaliphilic bacterium d medium , growth d medium . The resde novo assembled using MicrobeTrakr plus v. 0.9.1 (http://microbetracker.org/). Genome annotation was processed using NCBI PGAP (www.ncbi.nlm.nih.gov/genome/annotation_prok). The total length of the draft genome sequence was 4,047,843\u2009bp and yielded 12 contigs, with a G+C content of 48.26%. Among the predicted 4,006 genes, 3,910 putative protein-coding genes (CDSs) were identified. Furthermore, 87 complete RNAs, including 10 rRNAs , 72 tRNAs, and 5 noncoding RNAs (ncRNAs) were found.Total genomic DNA (2\u2009\u03bcg) was isolated using a DN12 microbial DNA isolation kit according to the manufacturer\u2019s instructions. A library for genome sequencing was constructed using the NEBNext Ultra DNA library prep kit for Illumina . The genBacillus sp. YSP-3 contains 1 gene cluster for ectoine biosynthesis from aspartate semialdehyde, 1 glnA gene for l-glutamine biosynthesis from l-glutamate, 9 genes of glycine/betaine ABC transporter, 3 genes of Na+/solute symporter, 3 genes of Na+/alanine symporter, and 2 genes of Na+/proline symporter, indicating that Bacillus sp. YSP-3 may resist osmotic stress when salinity increases by taking up compatible solute into the cell from the extracellular environment (+ uptake system also implies that strain YSP-3 possibly gains isosmotic cytoplasm though K+ as an osmolyte via a \"salt-in strategy\" when coping with a rapid osmotic shock (Bacillus sp. YSP-3 contains nine Na+/H+ antiporter genes (+ antiporter gene (+/H+ antiporter gene (Bacillus sp. YSP-3 survival in alkaline environments (+ homeostasis under salinity stress.Analysis of the genome sequence revealed that ironment , 7. The ic shock . Alkalipter gene , and a Kter gene , which mronments . These pBacillus sp. YSP-3 has been deposited at DDBJ/ENA/GenBank under the accession number PDOF00000000.The draft genome assembly of"} +{"text": "Verticillium nonalfalfae, a soilborne vascular fungus, shows promise for biocontrol of highly invasive Ailanthus altissima strains. This announcement provides draft genome sequences of the aggressive isolate G1/5 (wild-type strain), the highly aggressive isolate Vert56 (improved strain), and the mildly aggressive isolate I3/2, all obtained from symptomatic A. altissima trees in Austria. Verticillium nonalfalfae, a soilborne vascular fungus, shows promise for biocontrol of highly invasive Ailanthus altissima strains. This announcement provides draft genome sequences of the aggressive isolate G1/5 (wild-type strain), the highly aggressive isolate Vert56 (improved strain), and the mildly aggressive isolate I3/2, all obtained from symptomatic A. altissima trees in Austria. Verticillium nonalfalfae is an important vascular wilt pathogen on several dicotyledonous crops as well as on tree of heaven \u20133. This issima) \u2013\u20137. For telection and resuKT223526 and WGLJ00000000) (WGLK00000000), and another less pathogenic isolate, I3/2 (GenBank accession numbers KT223527 and SPUV00000000) with Milli-Q water for elution. Whole-genome sequencing was performed by Vienna BioCenter Core Facilities GmbH using an Illumina HiSeq 2500 system with a single-end 100-bp setup. Sequencing libraries were prepared according to the Westburg next-generation sequencing (NGS) DNA library prep kit protocol v3.1 . A total of 60.09 million (Vert56), 54.24 million (I3/2), and 57.87 million (G1/5) reads were received, representing in total 6,008.9 million, 5,423.5 million, and 5,786.7 million bases, respectively. Default parameters were used for all software, unless otherwise noted. A read quality check was performed using FastQC v0.11.4) (.4 (11) we strain , and theV. nonalfalfae strains Vert56, I3/2, and G1/5, respectively.Sequencing completeness was estimated using BUSCO (v3.0.2) based onWGLJ00000000 , SPUV00000000 , and WGLK00000000 . The versions described in this paper are the first versions, WGLJ01000000, SPUV0100000000, and WGLK01000000, respectively. Sequence reads were deposited under SRA project accession numbers SRR8271219, SRR8271218, and SRR8271217, respectively, and BioProject accession number PRJNA507541.These whole-genome shotgun projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers"} +{"text": "Dictyostelium discoideum forms a fruiting body consisting of spores and a multicellular stalk. Originally, the chlorinated alkylphenone differentiation-inducing factors (DIFs) -1 and -3 were isolated as stalk cell inducers in D. discoideum. Later, DIFs and their derivatives were shown to possess several biologic activities including antitumor and anti-Trypanosoma properties. In this study, we examined the antibacterial activities of approximately 30 DIF derivatives by using several bacterial species. Several of the DIF derivatives strongly suppressed the growth of the Gram-positive bacteria Staphylococcus aureus, Bacillus subtilis, and Enterococcus faecalis and Enterococcus faecium, at minimum inhibitory concentrations (MICs) in the sub-micromolar to low-micromolar range. In contrast, none of the DIF derivatives evaluated had any noteworthy effect on the growth of the Gram-negative bacterium Escherichia coli . Most importantly, several of the DIF derivatives strongly inhibited the growth of methicillin-resistant S. aureus and vancomycin-resistant E. faecalis and E. faecium. Transmission electron microscopy revealed that treatment with DIF derivatives led to the formation of distinct multilayered structures consisting of cell wall or plasma membrane in S. aureus. The present results suggest that DIF derivatives are good lead compounds for developing novel antimicrobials.At the end of its life cycle, the cellular slime mold Dictyostelium discoideum has long been studied as an excellent model system in the fields of cell and developmental biology; at the end of its developmental process, this organism forms fruiting bodies, each consisting of spores and a multicellular stalk [D. discoideum [D. discoideum [The cellular slime mold ar stalk ,2,3. Difar stalk ,5 and moscoideum . DIF-3 [Trypanosoma drugs [In addition to these developmental roles, DIF-1, DIF-3, and several of their derivatives B,C exertomiasis) . Importaomiasis) ,26,27,28ma drugs . MoreoveStaphylococcus aureus, Bacillus subtilis, Enterococcus faecalis and, Enterococcus faecium. In addition, several of the DIF derivatives evaluated strongly inhibited the growth of methicillin-resistant S. aureus and vancomycin-resistant enterococci . Our results support the investigation of such DIF derivatives as candidate lead compounds for developing novel antimicrobials.In this study, we investigated the antibacterial activities of DIF derivatives in vitro and show that several of them exert strong antibacterial effects against Gram-positive bacteria, including S. aureus , methicillin-resistant S. aureus , vancomycin-susceptible E. faecalis , vancomycin-resistant E. faecalis , vancomycin-resistant E. faecium , and B. subtilis (ATCC6633) and the Gram-negative bacteria Escherichia coli (NIHJ) and Mycobacterium bovis were used in this study. DIF derivatives (The Gram-positive bacteria methicillin-susceptible ivatives were synS. aureus suspension (109 CFU/mL) in Mueller\u2013Hinton broth (MHB) (0.2% (w/v) beef extract, 1.75% (w/v) casein hydrolysate, 0.15% (w/v) starch) into 10 mL of MHB agar (MHB containing 1.7% (w/v) agar; final bacterial density, 107 CFU/mL) and spread this suspension in a plastic culture dish . Paper discs impregnated with 2 \u00b5L of EtOH, DMSO, a 10 mM solution of the DIF or DIF derivative of interest in EtOH or DMSO (approx. 5.5\u20138 \u00b5g DIF/disc), or the purchased penicillin\u2013streptomycin solution (10 units penicillin and 10 \u00b5g streptomycin/disc) were placed on the bacterial agar plate. In addition, paper discs containing minomycin (30 \u00b5g/disc), imipenem (10 \u00b5g/disc), gentamicin (10 \u00b5g/disc), levofloxacin (5 \u00b5g/disc), or clindamycin (2 \u00b5g/disc) were placed on a MHB bacterial agar plate as controls. The plates were incubated for 20 h at 37 \u00b0C, after which the bacterial growth-inhibition zones around each disc was noted.We mixed 0.1 mL of S. aureus in MHB (107 CFU/mL) was spread on an MHB agar plate , after which 2 \u00b5L of each 10 mM DIF solution was dropped directly on the agar surface. The plates were incubated for 20 h at 37 \u00b0C, after which the bacterial growth-inhibition zones around the discs were noted.In addition, a diffusion assay without paper discs was performed for comparison. Briefly, 10 mL of 5 CFU/mL; 0.1 mL/well) were incubated for 20 to 24 h at 37 \u00b0C in 96-well plates in the presence of vehicle, various concentrations of serially diluted DIF derivatives, or known antibiotics; MIC was defined as the lowest concentration of the additives that inhibited visible bacterial growth.Gram-positive and Gram-negative bacteria in MHB (5 \u00d7 10M. bovis was grown in Hayflick modified PPLO (pleuropneumonia-like organisms) broth (0.5% (w/v) glucose, 5% (w/v) beef heart infusion, 2.5% (w/v) yeast extract, 1% (w/v) peptone, 0.5% (w/v) NaCl, 15% (v/v) heat-inactivated horse serum, 50 \u00b5g/mL of ampicillin) and used at concentrations of 104 to 107 CFU/mL for the minimum inhibitory concentration (MIC) assay as described; tiamulin and enrofloxacin (Sigma-Aldrich) were used as positive-control antibiotics.S. aureus (strain ATCC29213) in MHB was incubated for 1.5 h at 37 \u00b0C in 6-well plates (Corning) in the presence of 0.2% DMSO (vehicle) or 4 \u00b5M DIF derivative. After incubation, the bacteria were transferred to centrifuge tubes, collected by centrifugation , fixed overnight at 4 \u00b0C in 0.5 mL of 2.5% (v/v) glutaraldehyde in 100 mM phosphate buffer (pH 7.4) , and postfixed in 1% (w/v) OsO4 in 100 mM phosphate buffer. Fixed specimens were dehydrated through a graded series of ethanol and embedded in Epon812 . Ultrathin sections were cut by using an ultramicrotome and stained with uranyl acetate and lead citrate. These sections were examined under a transmission electron microscope .Specimens for transmission electron microscopy were prepared according to standard procedures . BrieflyS. aureus (MSSA: strain 209P) (S. aureus (MRSA: strain MS29202) from those of the known antibiotics that we used.We first examined the effects of DIF-1, DIF-3 A, and thin 209P) A and metMS29202) B by usinMS29202) A, a largMS29202) B, peniciMS29202) C. These B. subtilis (ATCC6633) and on the Gram-negative bacterium E. coli (NIHJ), and MIC values of DIF derivatives were determined and enrofloxacin (0.7 \u00b5M).We next examined the effects of DIF derivatives on the growth of the Gram-positive bacteria MSSA (strain 209P), MRSA (MS29202), and termined . Several>100 \u00b5M) ; M. boviNote that the MIC values of DIF-3 against MSSA and MRSA were comparable to those of DIF-1 , even thvanB and vanA, respectively . Transmission electron microscopy revealed distinct multilayered structures consisting of cell wall and/or plasma membrane in the DIF-treated MSSA cells . This fiD. purpureum [S. aureus (strain IID671), MRSA (IID1677), E. faecalis (ATCC29212), and B. subtilis (ATCC6633) are 1.56 \u00b5g/mL (3.4 \u00b5M), 3.13 \u00b5g/mL (6.8 \u00b5M), 50 \u00b5g/mL (109 \u00b5M), and 0.78 \u00b5g/mL (1.7 \u00b5M), respectively [Polysphondylium filamentosum [The antibacterial substance AB0022A, a chlorinated dibenzofuran A, was isurpureum and is sectively , and thumentosum , but theWhen we assessed the MIC values of these dichlorinated dibenzofurans in MRSA (strain MS29202), neither AB0022A nor Pf-2 had any noteworthy inhibitory effect on the growth of this strain B. In conPenicillium notatum have been isolated from fungi and Actinobacteria [Most of the many antibiotics identified since the discovery of penicillin in the fungus bacteria ,34,35,36bacteria ,35,36,37D. discoideum has long been used as a model organism in the study of cell and developmental biology. However, slime molds have recently been identified as excellent sources of potential lead compounds for drug discovery and the development of novel medicines [D. discoideum-derived DIFs and their derivative compounds in various types of eukaryotic cells [The cellular slime mold edicines ,38. In tic cells ,16,29.D. discoideum DIF derivatives possess antibacterial activity against Gram-positive bacteria, including S. aureus, E. faecalis, E. faecium, and B. subtilis. In contrast, these DIF derivatives did not inhibit the growth of Mycoplasma or the Gram-negative bacterium E. coli and E. faecium (containing vanA) were resistant to both vancomycin and ampicillin (E. faecalis and E. faecium cause the great majority of enterococcal infections, and isolates that carry drug-resistance genes such as vanA or vanB can cause serious infections [In the present study, we showed that several E. coli . Most im E. coli . Note th E. coli B but als E. coli C, wherea E. coli . In addipicillin . Althougfections ,40. OverAlthough the antibacterial activities of the DIF derivatives varied among the Gram-positive strains of bacteria examined in this study , the strS. aureus, Ph-DIF-1, Ph-DIF-3, and Bu-DIF-3 induce the formation of distinct multilayered structures composed of cell wall or membrane (Regarding the mechanism through which DIF derivatives exert their antibacterial effects, DIF derivatives have mitochondrial uncoupling activity in mammalian cells ,18. Givemembrane . AlthougD. discoideum possess strong antimicrobial activities against Gram-positive bacteria including MRSAs and VREs. Our results suggest that the DIF derivatives are good lead compounds for developing novel antimicrobials.In this study, we showed that several derivatives of DIF-1 and DIF-3, chlorinated polyketides found in The following authors hold a patent related to this article:Kubohara, Y.; Kikuchi, H.; Oshima, Y. Antibacterial drugs. Japanese Patent No. 6478378, 15 February 2019."} +{"text": "Haematobia irritans irritans , a hematophagous external parasite of cattle, causes considerable economic losses to the livestock industry worldwide. This pest is mainly controlled with insecticides; however, horn fly populations from several countries have developed resistance to many of the products available for their control. In an attempt to better understand the adult horn fly and the development of resistance in natural populations, we used an Illumina paired-end read HiSeq and GAII approach to determine the transcriptomes of untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males from a Louisiana population of horn flies with a moderate level of pyrethroid resistance. A total of 128,769,829, 127,276,458, 67,653,920, and 64,270,124 quality-filtered Illumina reads were obtained for untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males, respectively. The de novo assemblies using CLC Genomics Workbench 8.0.1 yielded 15,699, 11,961, 2672, 7278 contigs (\u2265 200\u202fnt) for untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males, respectively. More than 56% of the assembled contigs of each data set had significant hits in the BlastX (UniProtKB/Swiss-Prot database) (E <0.001). The number of contigs in each data set with InterProScan, GO mapping, Enzyme codes and KEGG pathway annotations were: Untreated Control Adult Females \u2013 10,331, 8770, 2963, 2183; Untreated control adult males \u2013 8392, 7056, 2449, 1765; Permethrin-treated surviving adult males \u2013 1992, 1609, 641, 495; Permethrin + PBO-treated killed adult males \u2013 5561, 4463, 1628, 1211.The horn fly, Specifications TableValue of the data\u2022Haematobia irritans irritans.Resource for investigations of the molecular basis of insecticide resistance in the horn fly, \u2022Provides candidate protein coding regions for the development of control strategies targeting adult flies.1https://www.ncbi.nlm.nih.gov/sra/SRP131897 or through SRA accession number SRP131897. The adult horn fly transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GGLM00000000. The version described in this paper is the first version, GGLM01000000. The overall BioProject ID is PRJNA429442 and the BioSample accessions are SAMN08355023, SAMN08355024, SAMN08355025, and SAMN08355026.RNA was isolated from unfed, newly emerged adult horn flies, including untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males. Subsequently, a single lane of 2 \u00d7 54\u202fbp paired end RNASeq reads were obtained, de novo assembled and annotated. The raw reads are accessible at NCBI\u05f3s SRA through the direct link 22.12, ~LD25) or permethrin + 1% piperonyl butoxide (PBO) by the impregnated filter paper assay Adult flies were collected with aerial sweep hand nets from pastured cattle at the St. Gabriel Research Station, Saint Gabriel, Louisiana, and incubated in large inverted Erlenmeyer flasks to collect eggs that were immediately seeded into manure to allow adult fly emergence. The unfed, newly emerged flies were sexed and either immediately frozen at \u221280\u202f\u00b0C for sequencing or exposed to low doses of permethrin and the FastRNA Pro Green Kit .2.3https://www.qiagenbioinformatics.com/) or Trimmomatic programmable-0.33 https://de.cyverse.org/de/?type=apps&app-id=8cb5c088-6b3e-11e7-a22d-008cfa5ae621&system-id=de) followed by Sickle-quality-based-trimming_version_1.0\u00a0\u00a0https://de.cyverse.org/de/?type=apps&app-id=9f5710c6-3424-11e7-9a58-008cfa5ae621&system-id=de) and Illumina adaptor sequences and low quality bases were removed. Trimmomatic and Sickle were both run on CyVerse/Discovery Environment https://de.cyverse.org/de/?type=apps&app-id=trinity-wrangler-2.5.1u2&system-id=agave) or version 11.10.13 (https://de.cyverse.org/de/?type=apps&app-id=trinity-stmpde-11.10.13u2&system-id=agave) and SoapdenovoTrans version 1.0.3 https://de.cyverse.org/de/?type=apps&app-id=Soaptrans-1.0.3u1&system-id=agave). Both Trinity versions and SoapdenovoTrans were run on CyVerse/Discovery Environment Sequencing was performed at the National Center for Genome Research using the standard Illumina RNAseq library preparation protocol and a single lane of the RNAseq. 2 \u00d7 54 paired-end approach. A total of 134,671,818, 132,374,494, 68,856,572, 65,427,160 paired-end Illumina raw reads were produced for untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + PBO-treated killed adult males, respectively . The rawhttps://pods.iplantcollaborative.org/wiki/display/DEapps/Compute+Contig+Statistics), rnaQUAST_1.2.0 (de novo based) https://de.cyverse.org/de/?type=apps&app-id=980dd11a-1666-11e6-9122-930ba8f23352&system-id=de) and BUSCO-v3.0\u00a0\u00a0https://de.cyverse.org/de/?type=apps&app-id=7f948668-7a53-11e7-a680-008cfa5ae621&system-id=de) (The assembled transcriptomes were then compared using three tools on CyVerse/Discovery Environment m-id=de) . Assemblm-id=de) and were-3) using Blast2GO PRO version 5.0.21 The transcriptomes were BlastX aligned against the UniProtKB/SwissProt database (E-value = 1.0 e"} +{"text": "AbstractSinocentrus Yuan, S.brevicornis Li & Chen, sp. nov. from China, is described and illustrated. A checklist and key to species of the Sinocentrus are provided.A new species of the treehopper genus Sinocentrus was established by Yuan , 1 r-m and 1 m-cu crossveins present, apical limbus broad, with wrinkles. Metathoracic trochanter without spines, tibia with 3 rows of cucullate setae.Large sized. Frontoclypeus distinct. Suprahumeral horns narrow, acuminate, horizontally extended laterally, width between their apex ca 0.5 to 1.0 times body length. Pronotum highly developed, with anterior part strongly inflated and evenly rounded in profile, metopidium vertical, glabrous and minutely punctate without obvious pubescence. Posterior pronotal process strongly elevated above scutellum at base, slender, elongate, evenly tapered toward apex, straight or slightly sinuate, lateral and dorsal carina well developed, apex extended beyond forewing clavus. Scutellum entirely exposed, posterior margin emarginate. Basal one-fifth of forewing with opaque sclerotization, veins M and Cu fused basally to approximately one-fifth to one-fourth of wing length then strongly divergent, veins M+Cu and R fused basally, with 1 m-cu, 2 r-m, and 1 s crossveins. Hindwing vein R branched into RCentrotinae genera by the following characters: pronotum highly developed, strongly inflated with anterior part evenly rounded, glabrous with minute punctures and no obvious pubescence, suprahumeral horns extended laterad, posterior pronotal process elevated far above scutellum, scutellum emarginate.This genus can be distinguished from other oriental China Fig. .S.brevicornis Li & Chen, sp. nov.; China (Hainan)S.sinensis Yuan, 2002; China (Yunnan); elevation: 1600 m.Taxon classificationAnimaliaHemipteraMembracidaeLi & Chensp. nov.0F416316-4D26-546E-8578-BDD13EA0550Dhttp://zoobank.org/73BE02FB-C98E-4D45-AC88-D597817F3597Holotype: \u2642, CHINA: Hainan, Bawangling, 29 April 2017, Hong-Xing Li. Paratypes: 2\u2640\u2640, same data as holotype.N = 1), female 8.9\u20139.3 mm (N = 2); forewing length: male 7.3 mm (N = 1), female 7.3\u20137.9 mm (N = 2); width between humeral angles apices: male 3.3 mm (N = 1), female 3.5\u20133.8 mm (N = 2); width between suprahumeral horns apices: male 4.6 mm (N = 1), female 4.6\u20135.2 mm (N = 2).Body length: male 8.1 mm . Humeral angles triangular with apices somewhat blunt. Suprahumeral horns short, width between horns apices nearly half length of body. Scutellum humped basally, large punctures present, longer than wide, apex extended antero-dorsally male, curved ventrally in female .brevicornis\u201d is derived from the Latins words \u201cbrevi-\u201d and \u201ccornu\u201d, referring to having the short suprahumeral horns.The word \u201cS.sinensis Yuan, 2002, but differs from the latter in: (1) forewing veins black and apical limbus black (2) suprahumeral horns short, width between suprahumeral horns apices shorter than body length (as long as body length in S.sinensis); (3) posterior pronotal process nearly straightly ; (4) scutellum longer than wide (wider than long in S.sinensis); (5) apex of posterior pronotal process not reaching M3+4 veins (exceeding M3+4 veins in S.sinensis).This species is similar to Taxon classificationAnimaliaHemipteraMembracidaeYuan, 2002074481DF-471C-5038-857A-48AFE38F7BD3Sinocentrussinensis Yuan, 2002: 170, by original designation.Coloration. General color reddish-brown with golden setae .While holotype was not examined, an online image of the holotype Fig. and detaCentrotinae, Sinocentrus and treated the genus as Centrotinae, incertae sedis.In their phylogeny and genus-level revision of Sinocentrus: (1) frontoclypeus distinct (indistinct in Centrotypini); (2) posterior pronotal process elevated far above the scutellum, entirely exposed ; (3) male lateral plate with short dorsoapical lobe extending dorsally, style clasp angled ventrally; style shank with arch at central section ; (4) mesothoracic femur without ablateral and adlateral cucullate setae; metathoracic leg cucullate setae row II irregular. Although the above characteristics can suggest that the genus is related to Leptocentrini, the shape of the female second valvulae closely align S.brevicornis with the tribe Centrotypini. Given these mixed affinities, we follow Wallace and Deitz, in treating Sinocentrus as Centrotinae, incertae sedis. Proper tribal placement may be affirmed by future phylogenetic analyses of combined morphological and molecular data.We provide the following additional details on"} +{"text": "Lower physical activity is cross-sectionally associated with greater fatigability; whether such a relationship holds for longitudinal changes in fatigability is under-studied. We examined this question in offspring enrolled in the Long Life Family Study, a two-generation cohort enriched for exceptional longevity and their spousal controls. At Visit 2 (2014-2017), we measured self-reported physical activity (PA) with the Framingham Physical Activity Index . Perceived physical fatigability was assessed using the Pittsburgh Fatigability Scale at Visit 2 and repeated during a follow-up contact 2.7\u00b10.92 years later. We constructed a repeated-measures linear mixed-effect model to examine the effect of PA on longitudinal change in PFS by median age adjusted for family structure, field center, follow-up time, sex, and self-rated health. We found a strong dose-response relationship of PFS scores across the four age/PA groups (ptrend<0.001). Specifically, older/less active (N=310) participants had the highest annual PFS increases of 0.37 points/yr (p<0.001) while those older/more active (N=340) had annual increases of 0.17 points/yr (p=0.03). Younger/less active (N=371) participants had annual PFS increases of 0.09 points/yr (p=0.008); those younger/more active (N=341) had annual decreases (improvement) of 0.18 points/yr (p<0.001). Although annual PFS changes were modest, our findings indicate physical activity attenuated age differences in these trajectories. Physical activity is emerging as a potential target for intervention aimed at reducing fatigability - an important risk factor in the disability pathway."} +{"text": "Their structures were elucidated on the basis of extensive 1D and 2D NMR spectroscopic data analyses. Significant antifeedant activity of 1, 3 and 10 against the beet armyworm (Spodoptera exigua) was found, indicating that these diterpenoids might also be involved in the plant defense against insect herbivores.Three new grayanane diterpenoids, pierisoids C\u2012E ( Pieris, Rhododendron, Kalmia, Craibiodendron and Leucothoe +; HR-ESI-MS: m/z 507.2567 [M + Na]+ ; 1H- and 13C-NMR data: see Pierisoid D (2): Colorless oils;c = 0.1, MeOH); UV (MeOH) \u03bbmax (log \u03b5): 202 (2.48) nm; IR (KBr) \u03bdmax: 3441, 3432, 2971, 2939, 1735, 1730, 1630, 1382, 1179, 1049, 1025 cm\u22121; ESI-MS: m/z 463 (88) [M + Na]+; HR-EI-MS: m/z 440.2420 ; 1H- and 13C-NMR data: see Pierisoid E (3): Colorless crystals; mp 271\u2013272 \u00b0C;c = 0.1, MeOH); UV (MeOH) \u03bbmax (log \u03b5): 202 (2.29) nm; IR (KBr) \u03bdmax: 3441, 2942, 1787, 1734, 1631, 1372, 1264, 1237, 1053 cm-1; ESI-MS: m/z 661 (68) [M + Na]+; HR-EI-MS: m/z 638.2560 ; 1H- and 13C-NMR data: see Spodoptera exigua) were purchased from the Pilot-Scale Base of Bio-Pesticides, Institute of Zoology, Chinese Academy of Sciences. A modified dual-choice bioassay was performed for an antifeedant test as previously described \u00d7 100, where C and T represent the control and treated leaf areas consumed by the insect. The insect antifeedant potency of the test compound was evaluated in terms of the EC50 value, which was determined by probit analysis for each insect species.Beet armyworms , as well as 10 known ones (4\u201213), were identified from the flowers of P. formosa via their extensive 1D and 2D NMR spectroscopic data analyses. Notably, compounds 1, 3 and 10, especially 10, exhibited obvious antifeedant activity against the beet armyworm (S. exigua), suggesting that these diterpenoids were important defensive substances in P. formosa against natural enemies.Terpenoids play an important role in natural product chemistry and biology, such as antifungal and insecticidal activities . Seconda"} +{"text": "Drosophila Hippo pathway maintains NSC quiescence, but its regulation during brain development remains unknown. Here, we show that CRL4Mahj, an evolutionarily conserved E3 ubiquitin ligase, is essential for NSC reactivation (exit from quiescence). We demonstrate that damaged DNA-binding protein 1 (DDB1) and Cullin4, two core components of Cullin4-RING ligase (CRL4), are intrinsically required for NSC reactivation. We have identified a substrate receptor of CRL4, Mahjong (Mahj), which is necessary and sufficient for NSC reactivation. Moreover, we show that CRL4Mahj forms a protein complex with Warts (Wts/large tumor suppressor [Lats]), a kinase of the Hippo signaling pathway, and Mahj promotes the ubiquitination of Wts. Our genetic analyses further support the conclusion that CRL4Mahj triggers NSC reactivation by inhibition of Wts. Given that Cullin4B mutations cause mental retardation and cerebral malformation, similar regulatory mechanisms may be applied to the human brain.The ability of neural stem cells (NSCs) to transit between quiescence and proliferation is crucial for brain development and homeostasis. During the transition from quiescence to reactivation of neural stem cells, the E3 ubiquitin ligase CRL4Mahj promotes their reactivation by inhibiting Wts, a core kinase of Hippo signalling pathway. The ability of stem cells to switch between quiescence and proliferation is crucial for tissue homeostasis and regeneration. Most adult neural stem cells (NSCs) exist in quiescence, a reversible dormant state, without proliferation or differentiation . In respDrosophila NSCs, called neuroblasts, have emerged as a powerful model to study mechanisms underlying NSC reactivation in vivo. Most Drosophila NSCs enter quiescence at the end of embryogenesis and resume proliferation shortly after larval hatching (ALH) #44974) driven by insc-Gal4 at 24 h ALH . Similarly, 31.2% and 26.3% of NSCs extended a cellular process in cul4G1-3 and cul4JJ11 mutants, compared with only 6.1% of NSCs of WT brain lobes . Moreover, at 24 h ALH upon knockdown of cul4 by two different RNAi lines driven by NSC-driver insc-Gal4, significantly more quiescent NSCs, as judged by the lack of EdU incorporation and by the presence of cellular processes, were observed versus 12.4% and 10.3% PH3+ NSCs were observed in cul4RNAi1/VDRC#105668 and cul4RNAi2/VDRC#44829 and ddb1HK-2-3 , ddb15-1 , and cul4G1-3 mutant brains were proliferating at 24 h ALH on food depleted of amino acids, as indicated by their ability to incorporate EdU , overexpression of Cul4KR resulted in a marked decrease of EdU+ NSCs to 57.2% in control MARCM clones were EdU+, only 7.5% (n = 53) and 19.5% (n = 41) of Mira+ NSCs in cul4G1-3 and cul4JJ11 MARCM clones were EdU+ (cul4G1-3 and cul4JJ11 was completely rescued by overexpression of UAS-cul4 transgene (n = 105 and n = 69). By contrast, overexpression of UAS-Cul4KR failed to rescue the quiescent NSC phenotypes of cul4G1-3 and cul4JJ11, as indicated by 3.7% (n = 27) and 3.2% (n = 31) EdU+ NSCs, respectively . Further control . These p mutants . At 96 here EdU+ . The quiectively . These r+ NSCs , whereas overexpression of an active form of InR (InRCA) in NSCs triggered NSC reactivation . By contrast, ddb1 knockdown dramatically suppressed this effect induced by InRCA overexpression . This result suggested that DDB1 likely functions downstream of the InR pathway during NSC reactivation.We next tested whether DDB1 is required for premature reactivation induced by overactivation of InR signaling pathway. Similar to previous reports ,11, in tDrosophila ortholog of human DCAF1/Vpr (HIV-1) Binding Protein (VprBP) #34912 and mahjRNAi2: VDRC#110669) driven by insc-Gal4 led to an increase in proportion of NSCs with a cellular process to 23.1% and 27.1% and 75.1% upon mahj RNAi knockdown, whereas there were 96.6% EdU+ NSCs in the control in mahjRNAi1 and 9.1% in mahjRNAi2, compared with 20.6% in control , as the t = 575) . Consist control . In addi control .mahj1, that was previously generated by imprecise P-element excision , depending on the combinations of constructs) displayed no PLA foci, and the rest of the cells displayed weak PLA foci (1\u201310 foci); on average, there were 0\u20130.4 \u00b1 0.2\u20130.8 PLA foci per cell (n = 281) coexpressing Flag-Wts and Myc-Mahj showed PLA signals: 26.0%, 30.6%, and 41.3% of cell with strong (>20 foci), moderate (11\u201320 foci), and weak (1\u201310 foci) signals, respectively; they resulted in 16.2 \u00b1 14.9 foci per cell (n = 176) expressing Flag-Wts and Myc-DDB1 (n = 176) showed PLA signals: 10.1%, 27.0%, and 60.7% of the cells with strong, moderate, and weak PLA signals; and on average, these cells displayed 10.7 \u00b1 9.94 PLA foci per cell (n = 157) also indicated positive physical interaction: 11.9 \u00b1 10.5 PLA foci per cell and 97.5% cells showed strong, moderate, and weak PLA signals of 56.7%, 26.1%, and 14.6%, respectively . By contn of Wts . These rS2 cells .mahj depletion could aggravate NSC reactivation defects observed upon ddb1 depletion. Whereas 97.2% of control NSCs were positive for EdU, 84.7% of ddb1RNAi and 81.5% of mahjRNAi controls incorporated EdU of NSCs were EdU+ of NSCs were positive for EdU, comparable to that of the control brains of NSCs in mahj knockdown were EdU+ at 24 h ALH, upon simultaneous knockdown of both mahj and wts by insc-Gal4, 97.1% of NSCs incorporated EdU . These data suggest that wts knockdown significantly suppresses NSC reactivation defects observed in mahj RNAi brains. To maintain NSC quiescence, Wts phosphorylates and inactivates the transcriptional coactivator Yki to turn off expressions from Yki target genes XE-2900) transheterozygous mutants were labeled with EdU, Dpn, and Mira. (M-N) Quantification of NSCs that are EdU+ or with process of various genotypes in (L). (O) MB NSC lineages in larval brains from WT and mahj1 at 24 h ALH were labeled with EdU, Dpn, and Dac. The enlarged views of white dotted boxes are shown to the right. Yellow arrowheads, MB NSCs surrounded by Dac-positive MB neurons. (P) At 0 h ALH, larval brains of grh-gal4>UAS-CD8-GFP were labeled with Mahj and a NSC marker (Dpn). Blue arrows, NSCs. (Q) Quantification of number of NSCs in ddb1\u2212, cul4\u2212, and mahj\u2212 mutant brains at 24 h ALH. Data are presented as mean \u00b1 SD. **** for P \u2264 0.0001, *** for P \u2264 0.001, ** for P \u2264 0.01, * for P \u2264 0.05, and ns for P > 0.05. Scale bars: 10 \u03bcm. The data underlying this figure can be found in Drosophila Stock Center; cul4, Cullin 4; Dac, dachshund; Dcr2, Dicer 2; ddb1, damaged DNA-binding protein 1; Dpn, Deadpan; EdU, 5-ethynyl-2\u2032-deoxyuridine; GFP, green fluorescent protein; Mahj, Mahjong; MB, mushroom body; Mira, Miranda; ns, statistically nonsignificant; NSC, neural stem cell; PH3, phospho-Histone H3; ROD, relative of density; UAS, upstream activating sequence; VDRC, Vienna Drosophila Resource Center; WT, wild type.(A-F) At 24 h ALH, larval NSCs in control ((TIF)Click here for additional data file.S4 FigDmMahj and DmDDB1. (A) View of Mahj 1110\u20131441 aa and DDB1 heterodimers. (B) Detail of predicted interaction between residues R1120 and R1123 (red stick) side chains in the HLH motif of Mahj (yellow ribbon) and DDB1 . Relevant residues are depicted in stick models: R1220 and R1123 , D1134 , and D788 . The predicted H-bonds are depicted by black dashed lines. Mahj R1120 and R1123 are corresponding to HsDCAF1 R1053 and R1056, respectively. (C) Detail of predicted interaction between R1307 and R1343 (red stick) side chains in the WD40 domain of Mahj (yellow ribbon) and DDB1 . Relevant residues are depicted in stick models: R1307 and R1342 , E1295 , and E201 . The predicted H-bonds are depicted by black dashed lines. Mahj R1307 and R1343 are corresponding to HsDCAF1 R1247, R1283, respectively. (D) A schematic diagram illustrating different Wts domains and truncated Wts proteins. (E) Wts C-terminal fragment containing kinase domain interacts with Mahj. Co-IP between Myc-Mahj and Flag-Wts or indicated truncated constructs. Anti-Myc were used for IP, followed by western blotting probed with anti-Myc, anti-Flag, or anti-Actin antibodies. Actin served as a loading control. aa, amino acid; DDB1, damaged DNA-binding protein 1; Dm, D. melanogaster; HLH, helix-loop-helix; HsDCAF1, H. sapiens DDB1-Cul4 associated factor 1; IP, immunoprecipitation; Mahj, Mahjong; Wts, Warts.(A-C) A homology model illustrating the interaction between (TIF)Click here for additional data file.S5 Fign = 272), Flag-Wts + Myc-control (n = 247), Flag-control + Myc-Mahj (n = 889), Flag-control + Myc-DDB1 (n = 284), Flag-control + Myc-Cul4 (n = 263), Flag-Wts + Myc-Mahj (n = 281), Flag-Wts + Myc-DDB1 (n = 176), and Flag-Wts + Myc-Cul4 (n = 157). The data underlying this figure can be found in (A) Co-IP between Flag-DDB1 and HA-Wts. S2 cells were cotransfected with Flag-DDB1 and HA-Wts or respective controls. Immunoprecipitation was performed using anti-Flag antibodies, and western blot was performed using anti-Flag or anti-HA antibodies. (B) A schematic illustration for PLA. (C) In situ PLA assay between Flag-Wts and either Myc-Mahj, Myc-DDB1, or Myc-Cul4. S2 cells transfected with the indicated plasmids were stained with Flag, Myc, and DAPI and detected for PLA signal (red). Cell outline was shown by DIC images. Scale bar, 10 \u03bcm. (D) Quantification graph showing the percentage of cells with PLA foci in (B). (E) Quantification for the average number of PLA foci per cell in (C). The number of cells used for quantification in are coexpression of Flag-control + Myc-control ((TIF)Click here for additional data file.S6 FigctrlRNAi: \u03b2-galRNAi), wtsRNAi +\u03b2-galRNAi, ddb1RNAi (VDRC#44974) +\u03b2-galRNAi, and ddb1RNAi + wtsRNAi were labeled with Dpn, Mira, and EdU. (B-C) Quantification of Dpn+ Mira+ NSCs that are EdU+ (B) or with cellular process (C). In (B), control : brain lobes n = 8, total NSCs t = 517; wtsRNAi+\u03b2-galRNAi: n = 11, t = 705; ddb1RNAi+\u03b2-galRNAi: n = 10, t = 647; ddb1RNAi + wtsRNAi: n = 15, t = 955. In (C), control : n = 4, t = 320; wtsRNAi+\u03b2-galRNAi: n = 6, t = 485; ddb1RNAi+\u03b2-galRNAi: n = 6, t = 598; ddb1RNAi + wtsRNAi: n = 16, t = 1,403. (D) Larval NSCs in ctrlRNAi , YkiS168A+\u03b2-galRNAi, ddb1RNAi+ \u03b2-galRNAi, and ddb1RNAi + YkiS168A were labeled with Dpn, Mira, and EdU. (E-F) Quantification of Dpn+ Mira+ NSCs that are EdU+ (E) or with cellular process (F). In (E), control : n = 7, t = 388; YkiS168A+\u03b2-galRNAi: n = 10, t = 645; ddb1RNAi+\u03b2-galRNAi: n = 9, t = 551; ddb1RNAi + YkiS168A: n = 11, t = 809. In (F), control : n = 5, t = 429; YkiS168A+\u03b2-galRNAi: n = 4, t = 255; ddb1RNAi+\u03b2-galRNAi: n = 5, t = 357; ddb1RNAi + YkiS168A: n = 9, t = 755. (G) Larval NSCs in ctrlRNAi , wtsRNAi+\u03b2-galRNAi, cul4RNAi (VDRC#105668)+\u03b2-galRNAi, and cul4RNAi + wtsRNAi were labeled with Dpn and EdU. (H-I) Quantification of Dpn+ NSCs that are EdU+ or with Mira+ cellular process. In (H), control : n = 13, t = 1,179; wtsRNAi+\u03b2-galRNAi: n = 19, t = 1,665; cul4RNAi+\u03b2-galRNAi: n = 14, t = 1,073; cul4RNAi + wtsRNAi: n = 19, t = 1,404. In (I), control : n = 8, t = 702; wtsRNAi+\u03b2-galRNAi: n = 8, t = 696; cul4RNAi+\u03b2-galRNAi: n = 9, t = 772; cul4RNAi + wtsRNAi: n = 10, t = 847. (J) Larval NSCs in ctrlRNAi+\u03b2-galRNAi, YkiS168A+\u03b2-galRNAi, cul4RNAi+\u03b2-galRNAi, and cul4RNAi + YkiS168A were labeled with Dpn and EdU. (K-L) Quantification of Dpn+ NSCs that are EdU+ or with Mira+ cellular process. In (K), control : n = 12, t = 990; YkiS168A+\u03b2-galRNAi: n = 11, t = 917; cul4RNAi+\u03b2-galRNAi: n = 13, t = 1,056; cul4RNAi + YkiS168A: n = 15, t = 950. In (L), control : n = 7, t = 701; YkiS168A+\u03b2-galRNAi: n = 4, t = 344; cul4RNAi+\u03b2-galRNAi: n = 11, t = 974; cul4RNAi + YkiS168A: n = 10, t = 895. Driver is insc-Gal4, tub-Gal80ts (A-F), and insc-Gal4; UAS-Dcr2 (G-L). Note that to balance the number of UAS elements across different genotypes, additional control UAS line, \u03b2-galRNAi for (A-F) or CD8-GFP/BDSC#32186 for (G-L), was added to various RNAi lines, resulting in weaker phenotype in RNAi lines compared with those without additional UAS control shown earlier in this study. Yellow arrows, EdU+ NSCs. White arrows, EdU-negative NSCs. Data are presented as mean \u00b1 SD. **** for P \u2264 0.0001, *** for P \u2264 0.001, ** for P \u2264 0.01, * for P \u2264 0.05, and ns for P > 0.05. Scale bars, 10 \u03bcm. The data underlying this figure can be found in Drosophila Stock Center; CRL4, Cullin4-RING ligase; ddb1, damaged DNA-binding protein 1; Dpn, Deadpan; EdU, 5-ethynyl-2\u2032-deoxyuridine; Mira, Miranda; ns, statistically nonsignificant; NSC, neural stem cell; RNAi, RNA interference; UAS, upstream activating sequence; VDRC, Vienna Drosophila Resource Center; Wts, Warts; Yki, Yorkie.(A) Larval NSCs in control ((TIF)Click here for additional data file.S1 TableC-term, C-terminal fragment; F, forward; FL, full length; HLH+WD40, helix-loop-helix motif and WD40 domain; N-term, N-terminal fragment; R, reverse; sc, with stop codon; wo sc, without stop codon.(XLSX)Click here for additional data file.S2 TableF, forward; R, reverse.(XLSX)Click here for additional data file.S3 TableDDB1, damaged DNA-binding protein 1; F, forward; R, reverse; RNAi, RNA interference; UAS, upstream activating sequence.(XLSX)Click here for additional data file.S1 Text(DOCX)Click here for additional data file.S1 Data(XLSX)Click here for additional data file."} +{"text": "To investigate the diagnostic value of the interferon-\u03b3 release assay (IGRA) for detecting tuberculosis (TB) infection in patients with Beh\u00e7et\u2019s disease (BD).We retrospective analyzed the data collected from 173 BD patients hospitalized between 2010 and 2015. Ninety-nine healthy volunteers were enrolled as a control group. IGRA was performed using T-SPOT.TB. The diagnosis of active TB (ATB) was based on clinical, radiological, microbiological, histopathological information and the response to anti-TB therapy. Latent TB (LTB) infection was defined as asymptomatic patients with positive T-SPOT.TB.6 PBMC was the optimal cutoff for diagnosing ATB, with an area under the curve of 0.891. Furthermore, the median SFCs in ATB group was significantly higher than those in LTB infection or previous TB infection . A significant discrepancy between T-SPOT.TB and tuberculin skin test was noted .TB infection was documented in 59 BD patients (34.1%). The sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio and negative likelihood ratio of T-SPOT.TB for the diagnosis of ATB were 88.9%, 74.8%, 29.1%, 98.3%, 3.53 and 0.15, respectively. The receiver-operating-characteristic curve demonstrated that spot-forming cells (SFCs) of 70/10T-SPOT.TB, an IGRA, may assist in the diagnosis of ATB in BD patients, and the higher SFCs suggest ATB in BD patients. M.tuberculosis may act as a trigger of BD through molecular mimicking. On the other hand, defective cell-mediated immunity in BD patients may increase the susceptibility of TB [Behcet\u2019s disease (BD) is a multi-system inflammatory disorder, characterized by recurrent oral ulcers, genital ulcers, skin lesions, and ocular involvement of unknown etiology. Notably, the clinical manifestation of orogenital ulcers and skin lesions including erythema nodosum could be mimicked by tuberculosis (TB). Additionally, active TB (ATB) is frequently observed in patients with BD, and those symptoms were relieved after anti-TB therapy , 2. BD aty of TB , and thety of TB . Therefo. Given IGRAs do not cross-react with BCG vaccination or nontuberculous mycobacteria infection, IGRAs show higher specificity than TST [Tuberculin skin test (TST), a routine screening test for latent TB (LTB) infection, has limited diagnostic value in BD patients due to cross-reactivity with the bacillus Calmette-Gu\u00e9rin (BCG) vaccine and nontuberculous mycobacteria as well as pathergy reaction . In addithan TST . IGRAs, than TST and rheuthan TST . HoweverM.tuberculosis. Highly-probable TB was defined as highly suggestive clinical and radiological features for TB in combination with the appropriate response to anti-TB treatment [Medical records of the hospitalized BD patients from Peking Union Medical College Hospital between January 2010 and March 2015 were retrospectively reviewed. All patients fulfilled the International Study Group BD criteria or the new International Criteria for BD . T-SPOT.reatment . LTB infreatment .M.tuberculosis. Briefly, peripheral blood mononuclear cells were isolated from whole blood samples by density gradient separation, then stimulated with two TB specific antigens, early secreted antigenic target 6 (ESAT-6) and culture filtrate protein 10 (CFP-10), phytohaemagglutinin (PHA) (positive control) or AIM-V (negative control) in microplate wells (2.5\u2009\u00d7\u2009105 per well) precoated with interferon-\u03b3 (IFN-\u03b3) capture antibodies. The number of spot-forming cells (SFCs) was calculated after 16 to 20\u2009h of incubation. The result was considered positive if the number of SFCs was six or more after subtracting the spot count of negative control [IGRAs were performed using T-SPOT.TB, a simplified enzyme-linked immunospot (ELISPOT) for detection of effector T cells that respond to stimulation by antigens specific for control .TST was performed with an intradermal injection using standardized 0.1\u2009ml (5\u2009U)-purified protein derivative into the ventral surface of the forearm according to the Mantoux method . On the p values <\u20090.05 is considered statistically significant. Statistical analysis was performed by using SPSS and the GraphPad Prism .Numerical data were expressed as mean\u2009\u00b1\u2009standard deviation or median , and categorical data were expressed as frequencies/ percentages. The Mann-Whitney U test and Pearson chi-square test were used to compare differences between two groups. The concordance of TST and T-SPOT.TB results were assessed using \u03baappa coefficient. . The diagnostic performance of T-SPOT.TB on ATB was evaluated by calculation of its sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR), and negative likelihood ratio (NLR). The area under the receiver operating characteristic curve of the T-SPOT.TB on peripheral blood mononuclear cell (PBMC) diagnostic cutoff for ATB was calculated. A two-sided with Among the 173 BD patients performed with TB-SPOT.TB test, 114 (65.9%) were men. The mean age was 37.07\u2009\u00b1\u200914.74\u2009years, and median disease duration of BD was 84\u2009months (range 1\u2013608). The most common clinical manifestation was recurrent oral ulceration (98.3%). Other common findings included fever (81.5%), genital ulcers (58.4%), skin lesions (58.4%), gastrointestinal involvement (39.3%), vascular involvement (28.3%), positive pathergy test (22.5%), ocular involvement (19%), neurologic involvement (15%), cardiac involvement (9.8%) and hematological involvement (5.2%). The median BDCAF2006 score for disease activity was 2 (range 0\u20135). Elevated erythrocyte sedimentation rate (ESR) and high-sensitivity C-reactive protein (hs-CRP) levels were detected in 98 (56.6%) and 118 patients (68.2%), respectively. The median ESR was 21 (range 1\u2013140) mm/first hour and the median hs-CRP was 11.54 (range 0.12\u2013262.77) mg/L. In the past 2 years, 113 patients (65.3%) were treated with glucocorticoids, including 13 patients (7.5%) received glucocorticoid pulse therapy. Ninety-seven patients (56.1%) were under glucocorticoids treatment when T-SPOT.TB assay was performed, and the median daily dose of corticosteroids was 40 (range 5\u2013100) mg. Ninety-four patients received immunosuppressants, including cyclophosphamide (30.1%), leflunomide (5.2%), cyclosporin A (4.6%), azathioprine (4.6%), methotrexate (4.6%) and salazosulfapyridine (2.9%). Sixteen patients (9.2%) received two or more immunosuppressants. Biological agents were used in 12 patients (6.9%), including infliximab injection in six patients, etanercept injection in five patients, etanercept followed by infliximab in one patient , especially erythema nodosa compare to BD-LTB infection patients.TB infection was documented in 59 BD patients 34.1%) in our study, including 18 (10.4%) ATB (BD-ATB), 29 (16.8%) LTB (BD-LTB) infection, and 12 (6.9%) patients with evidence of previous TB. Of the 18 BD-ATB cases, culture-confirmed TB and highly probable TB were diagnosed in 4 and 14 patients, respectively. Of the four culture-confirmed TB patients, pulmonary TB, tuberculous lymphadenitis, tuberculous pleuritis, tuberculous meningitis were diagnosed in one patient, respectively. Among 14 highly-probable TB, highly-probable pulmonary TB was diagnosed in 7 cases based on fever, cough, expectoration or chest pain, and CT-confirmed pulmonary cavity, infiltrating or nodules as well as % in our 6 PBMC (IQR: 108\u2013925). Among patients with evidence of previous TB, ten patients (83.3%) had positive T-SPOT.TB with the median number of SFCs being 96/106 PBMC (IQR: 31.75\u2013187). The median number of SFCs in BD-LTB infection patients was 68/106 PBMC (IQR: 38\u2013208). The median number of SFCs in the BD-ATB group was higher than those in the BD-LTB infection group (p\u2009=\u20090.007) or those in previous TB patients (p\u2009=\u20090.018). The median numbers of SFCs in the BD-ATB group, BD-LTB infection group and previous TB patients were higher than those in the non-TB infection group (p\u2009=\u20090.000) , and the median number of spot-forming cells (SFCs) was 466/10The sensitivity, specificity, PPV and NPV of the T-SPOT.TB test for the diagnosis of ATB were 88.9% (95%CI 63.9\u201398.1%), 74.8% (95%CI 67.1\u201381.3%), 29.1% (95%CI 18\u201343.1%), and 98.3% (95%CI 93.4\u201399.7%), respectively. PLR was 3.53(95%CI 2.57\u20134.85) and NLR was 0.15 (95%CI 0.04\u20130.55).6 PBMC was the optimal cutoff for diagnosing BD-ATB, with an area under the curve of 0.891 (95%CI 0.796\u20130.987) Fig.\u00a0. Accordi6 PBMC (IQR:80\u2013308). There was no significant difference in the proportion of LTB infection and the number of SFCs detected by T-SPOT.TB between BD patients and healthy controls.LTB infection was documented in 27(27.3%) healthy controls, and the median number of SFCs was 192/10p\u2009=\u20090.002).Both T-SPOT.TB and TST results were simultaneously tested in 63 patients. Among these patients, positive results of TST and T-SPOT.TB were presented in 44.4% 28/63) and 46% (29/63) patients, respectively. 30.2% (19/63) of the 63 patients had both positive TST and T-SPOT.TB, and 60.3% (38/63) had positive results on either TST or T-SPOT.TB (Table\u00a08/63 and The sensitivity of TST for detecting ATB was 78.6% (95%CI 48.8\u201394.3%), which was lower than that of the T-SPOT.TB test (92.9%), but there was no significant difference between the two groups. The specificity of TST was similar with T-SPOT.TB test (Table\u00a0p\u2009=\u20090.06). However, there was no difference in the sensitivity between parallel testing and T-SPOT.TB assay alone.We also evaluated the diagnostic values of the combination of T-SPOT.TB and TST for ATB diagnosis in these 63 patients TB report . Patientnfection , but thenfection .M.tuberculosis-specific antigens [In recent years, IGRAs emerges as accurate diagnostic assays for screening of TB infection. IGRAs specifically detect the presence of specific effector T cells which response to antigens . Dai Y. antigens . And Theantigens . Consistantigens .6 PBMC as the cutoff, the specificity and PLR are improved for diagnosing ATB in BD patients. Although, neither T-SPOT.TB nor TST can clearly distinguish between LTB infection, ATB or history of TB infection [In this study, we evaluated T-SPOT.TB and TST for the diagnosis of ATB in BD patients. To our knowledge, this is the first study that reports the diagnostic value of T-SPOT.TB for TB in BD patients. We reported the high sensitivity (88.9%) and specificity (74.8%) of T-SPOT.TB for the diagnosis of ATB in BD patients. Compared to Dai Y\u2019s study , our stunfection , 26, we nfection . Meanwhinfection .It has been reported that the pooled sensitivity of T-SPOT.TB was higher than that of TST for the diagnosis of ATB in culture-confirmed or non-confirmed TB . A discrMycobacterium tuberculosis antigens with no evidence of clinically ATB. Given the risk of LTB infection reactivation increases in patients receiving immunosuppressive therapy or with immune dysfunction [LTB infection is defined as the sustained immune response to function , it is ifunction \u201333 suggefunction \u201336. Alsofunction , 37, andfunction . In ourfunction , 38. A nfunction . SecondlM.tuberculosis bacteriologically confirmed, which might introduce a high risk of bias. Fourth, given no gold standard of LTB infection is available, the precision of the diagnosis of LTB infection by T-SPOT.TB could not be assessed in this study. Nevertheless, this is the first study on the diagnostic value of T-SPOT.TB for TB in BD patients. A large-scale, multi-center study enrolled bacteriologically confirmed TB patients are warranted to confirm our findings.Our study has several limitations. First, our study is a retrospective analysis of a case series, which may have incomplete data of TST. Second, since all BD patients were enrolled from a single-center with relatively small sample sizes, and our center is a national referred center for complicated rheumatic diseases, potential selection bias of BD patients is possible. Third, it is challenging to identify active TB in BD patients based on clinical features since systemic inflammation is a shared feature of both BD and TB. The majority of our ATB patients were diagnosed according to clinical criteria rather than 6 PBMC) strongly suggested ATB. Further study is needed to investigate the diagnostic value of T-SPOT.TB for LTB infection in BD patients.T-SPOT.TB may assist in the diagnosis of ATB in BD patients, and the higher number of SFCs (>\u200970/10"} +{"text": "In this study, resistance spectrum of TA7733 was assayed by using 15 Blumeria graminis f. sp. tritici (Bgt) isolates prevalent in different regions of China. The result indicated that TA7733 was highly resistant to all tested Bgt isolates and the gene(s) on chromosome 2Mb conferred broad-spectrum resistance to powdery mildew. In order to characterize mechanism of powdery mildew resistance by identifying candidates R-genes derived from Ae. biuncialis chromosome 2Mb and develop 2Mb-specific molecular markers, we performed RNA-seq analysis on TA7733 and CS. In total we identified 7,278 unigenes that showed specific expression in TA7733 pre and post Bgt-infection when compared to CS. Of these 7,278 unigenes, 295 were annotated as putative resistance (R) genes. Comparatively analysis of R-gene sequences from TA7733 and CS and integration CS Ref Seq v1.0 were used to develop R-gene specific primers. Of 295 R-genes we identified 53 R-genes were specific to 2Mb and could be involved in powdery mildew resistance. Functional annotation of majority of the 53 R-genes encoded nucleotide binding leucine rich repeat (NLR) protein. The broad-spectrum resistance to powdery mildew in TA7733 and availability of 2Mb-derived putative candidate R-gene specific molecular markers identified in this study will lay foundations for transferring powdery mildew resistance from 2Mb to common wheat by inducing CS-Ae. biuncialis homoeologous recombination. Our study also provides useful candidates for further isolation and cloning of powdery mildew resistance gene(s) from Ae. biuncialis chromosome 2Mb.Powdery mildew is one of the most widespread diseases of wheat. The development and deployment of resistant varieties are one of the most economical and effective methods to manage this disease. Our previous study showed that the gene(s) at 2M Triticum aestivum L., 2n = 6x = 42, AABBDD), one of the most widely planted crops in the world provides 20% of the calories and 25% of its protein consumed by human [Fusarium head blight (FHB) and powdery mildew. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive diseases all over the world, with severe yield losses ranging from 13% to 50% [Common wheat was more than 80 at 54 loci [Pm genes were derived from wild relatives of wheat. However, some Pm genes had been defeated by new virulent Bgt races or by races that were previously present at very low frequencies in the pathogen population [Wild relatives of common wheat contain a large number of 54 loci , of whicpulation ,11, and pulation ,13. TherAegilops biuncialis is a tetraploid wild relative of wheat, belonging to the section Polyeides of the genus Aegilops. The Ub genome of it was derived from Ae. umbellulata , and Mb genome from the diploid Ae. comosa [Aegilops biuncialis owns many desired agronomic traits for wheat improvement, such as resistance to yellow rust [Ae. biuncialis with wheat, develop a series of wheat-Ae. biuncialis addition lines, and transfer desired genes from Ae. biuncialis into wheat [Ae. biuncialis 2Mb disomic addition line TA7733 conferred high resistance to powdery mildew compared with its recipient parent CS [ 14, MM) . Aegiloplow rust , brown rlow rust , powderylow rust , toleranlow rust \u201321, highlow rust , and spelow rust . Successto wheat ,24,25. Iarent CS .Ph) genes in hexaploid wheat backgrounds [Thinopyrum intermedium by RNA-seq analysis [Pm60 from T. urartu by combining genetic mapping and RNA-seq analysis [The isolation and cloning of plant disease resistance genes had great significance for both plant disease resistance breeding and the study on molecular mechanisms of disease resistance. Map-based cloning is currently an important method to isolate novel genes. However, it is very challenging to perform fine mapping and map-based cloning of alien genes derived from wild relatives of wheat due to the strict control of homoeologous recombination by pairing homoeologous from chromosome 2Mb, as well as further understanding of the molecular and genetic mechanisms of disease resistance conferred by Ae. biuncialis chromosome 2Mb.In this study, we report the assays of a broad-spectrum resistance gene(s) on chromosome 2Mn = 6x = 42, AABBDD), Ae. comosa TA2102 , and CS-Ae. biuncialis 2Mb disomic addition line TA7733 (2n = 44) where a pair of 2Mb chromosomes derived from Ae. biuncialis were added into CS genetic background were used in this study. All the materials were kindly provided by the Wheat Genetics Resource Center at Kansas State University, USA and maintained at the experimental station of Henan Agricultural University, China.Common wheat landrace CS . The cytGenomic DNA (gDNA) was extracted from fresh leaves using a modified hexadecyl trimethyl ammonium bromide (CTAB) method . The conin situ hybridization (GISH) was applied to analyze the chromosomal composition of TA7733. Genomic DNA of Ae. comosa accession TA2102 and wheat CS were respectively used for probe labeling with fluorescein-12-dUTP and blocking at a ratio of 1:130 to distinguish Ae. biuncialis 2Mb chromosome. GISH was carried out as described by Liu et al. (2017) [Genomic . (2017) . Hybridiin situ hybridization (ND-FISH) [10. The first six were labeled with 6-carboxytetramethylrhodamine (TAMRA) generating red signals, and the last two being labeled with 6-carboxyfuorescein (FAM) generating green signals. All the oligonucleotides were synthesized at Sangon Biological Technology, Shanghai, China.After GISH, the hybridization signals were washed off with phosphate-buffered saline (PBS). Eight single-strand oligonucleotides were then used as probes for dual-color nondenaturing fluorescence ND-FISH) ,39. The Bgt isolates collected in Henan Province were used to evaluate the resistance of CS and CS-Ae. biuncialis 2Mb disomic addition line TA7733. Fifteen prevalent Bgt isolates collected from different regions of China were chosen to evaluate the resistance spectrum of TA7733 at the seedling stage by using CS as a susceptible control. The 15 Bgt isolates were provided by Prof. Pengtao Ma, Yantai University, China. They were all single-pustule-derived powdery mildew virulent isolates by separate artificial inoculation. The infection type (IT) were scored 7\u201310 days post-inoculation using a 0 to 4 rating scale [A mixture of prevailing ng scale , with 0 Bgt inoculation, the first leaves of TA7733 and CS were cut into 2 cm segments and stained with coomassie brilliant blue following Li et al. (2016) [Bgt development on the leaves.At 10 days post-. (2016) for furtBgt isolates. Leaves at 0, 12, 24, 48 and 72 hours post-inoculation (hpi) were respectively collected, rapidly frozen in liquid nitrogen and stored at -80\u00b0C for RNA extraction.Seeds of CS and TA7733 soaking in water for 24 h at 23\u00b0C were transferred into a mixture of nutrient soil and vermiculite (1:1). Seedlings with full extended first leaf were dusted using fresh conidiophores of Total RNA of ten samples were extracted for transcriptome sequencing. Then equal amounts of RNA samples 12\u201372 hpi from TA7733 and CS were mixed to generate RNA-seq sample RI and SI, respectively. RNA at 0 hpi from TA7733 and CS were accordingly represented as RNA-seq sample RC and SC. Two biological replicates were performed in this study, forming a total of eight RNA samples . The designations 1 and 2 are used to represent replicates 1 and 2, respectively. Libraries with an average insert size of 200 bp constructed from these eight samples were then sequenced using the Illumina HiSeqTM 2500 by the Beijing Genomics Institute.\u22125) against the NCBI non-redundant (NR) protein, SWISSPROT, gene ontology (GO), eukaryotic orthologous groups (KOG), kyoto encyclopedia of genes and genomes (KEGG) and plant resistance gene (PRG) databases.Prior to assembly, sequencing raw reads were pre-processed using a Perl script dynamic-Trim.pl to remove the adaptor sequences, low-quality sequences, low complexity sequences, short reads and empty reads. Reads data with a quality score (Qphred) \u2265 50 (Q50: ratio of an error rate of 0.01%) were then merged and input into the data assembly software Trinity for assembling into transcripts. The generated unigenes were annotated by a Blastx alignment search , 0.25 \u03bcl forward primer (10 \u03bcmol/l), 0.25 \u03bcl reverse primer (10 \u03bcmol/l), 7.5 \u03bcl Taq MasterMix and 5 \u03bcl ddH2O. PCR cycling conditions were as follows: 94\u00b0C for 5 min followed by 35 cycles of 94\u00b0C for 30 s, 50\u201366\u00b0C for 30 s, and 72\u00b0C for 1 min, followed by a final 10-min extension at 72\u00b0C. The PCR products were digested with four base-restriction enzymes. Five microliters of a restriction enzyme mixture containing 2.8 \u03bcl of ddH2O, 2.0 \u03bcl of CutSmart buffer, and 0.2 \u03bcl of an enzyme stock solution was added to 15 \u03bcl of PCR products and incubated for 3.5 h at 65\u00b0C. The PCR or restricted PCR products were separated on a 2.0% agarose gel-electrophoresis stained with ethidium bromide and visualized by UV light.R gene-specific primer sets were designed based on their transcriptome sequences to perform PCR amplification using gDNA from TA7733 and CS as templates to verify 2MAe. biuncialis chromosome 2Mb. Comparative maps of 2Mb-specific R genes were made using MapDraw software referring homoeologous chromosome locations of CS Ref Seq v1.0.Genome sequences of wheat landrace CS (CS Ref Seq v1.0) were used as references in Blastn searches to obtain position information for R genes from Ae. biuncialis 2Mb disomic addition line TA7733 by using fluorescein-labeled gDNA from M genome donor Ae. comosa as a probe and wheat CS DNA as blocker. As shown in Ae. biuncialis 2Mb chromosomes in TA7733, confirming the disomic addition of chromosome 2Mb.GISH and ND-FISH were respectively performed to confirm the chromosome composition of CS-Bgt isolates collected in Henan Province was used to inoculate seedlings with fully-extended first leaves of TA7733 and its recipient parent CS in the greenhouse. Ten days post-inoculation, the leaves of CS were covered with a large number of Bgt hyphae, with ITs of 3\u20134, whereas TA7733 showed only stunted spores, with ITs 0 to 1 to all the 15 Bgt isolates tested, whereas its recipient parent CS was highly susceptible (IT = 4 or 3) to all tested Bgt isolates. These results indicated that the chromosome 2Mb in TA7733 conferred broad-spectrum resistance to powdery mildew of wheat.The resistance spectrum of TA7733 was further assayed at the seedling stage by inoculation of 15 prevalent Ae. biuncialis 2Mb disomic addition line TA7733 and its recipient parent CS were respectively conducted pre and post Bgt-infection. A total of 158,953 unigenes were assembled with a total length of 198,364,757 bp. The average unigene size was 1247.95 bp ranging from 301 to 19,496 bp , 48,724 (30.65%), 40,543 (25.51%), 37,008 (23.28%), 13,414 (8.44%) and 10,969 (6.92%) annotated unigenes, respectively unigenes were assigned to one or more GO term annotations , of whicThe KEGG database was used to systematically describe the pathway where the unigenes involved. Out of a total 158,953 annotated unigenes, 26,589 unigenes were assigned to 23 KEGG pathways . The mosAe. biuncialis chromosome 2Mb, which should be only expressed in TA7733 other than in CS. Based on pairwise comparison of unigenes of TA7733 vs CS, a total of 7,278 genes were uniquely expressed in TA7733, of which 4,382 unigenes were significantly differentially expressed post vs before Bgt-inoculation, and the remaining 2,896 unigenes had insignificantly different expression levels. In consideration of the fact that expression levels of some cloned resistance genes did show no significant difference before and after pathogen infection [b-derived R-genes involved in powdery mildew resistance.One of the objectives of this study was to explore putative R genes specific to nfection , these 2Ae. biuncialis 2Mb chromosome.To analyze the biological pathways of these 4,382 unigenes, the statistical enrichment of differentially expressed genes (DEGs) in KEGG pathways were tested using the KOBAS software. In consequence, 399 out of 4,382 DEGs were allocated to 162 KEGG pathways . The mosBased on transcriptome data analysis, 7,278 unigenes were uniquely expressed in TA7733. Only 295 of 7,278 unigenes were annotated as putative R-genes by Blastx alignment against the PRG and NCBI databases. However, of 295 R-genes sequences when blastn searched against CS Ref Seq v1.0, only 61 (20.68%) R-genes mapped to wheat homoeologous group 2, and the remaining 234 (79.32%) R-genes to none of the homoeologous group 2 chromosome of wheat.Ae. biuncialis chromosome 2Mb, a total of 61 sets of PCR primer pairs were designed based on transcriptome sequences of these R genes. PCR amplification of gDNA of CS and TA7733 confirmed 40 R genes to be specific to chromosome 2Mb, which producing unique amplification in CS-Ae. biuncialis 2Mb disomic addition line TA7733 structures, a central nucleotide-binding (NB) subdomain and a leucine-rich repeat (LRR) domain, 12 in NL class containing NBS and LRR domains, but lack of CC domain, five in class RLP which contains leucine-rich receptor-like repeat, a transmembrane region of 25AA, and a short cytoplasmic region, each one for TNL class which contains a central NB subdomain, a LRR domain, a interleukin-1 receptor (1L-1R) domain, and N class only containing NBS domain . The remAe. biuncialis chromosome 2Mb specificity with those in CS Ref Seq v1.0 on Ae. biuncialis 2Mb chromosome should be a new Pm gene(s).Development of resistant wheat varieties is the most important and environment-friendly way to control programs . Wild re group 2 , 42\u201344. Pm60, a map-based cloned powdery mildew gene, showed no significant differences at various time points after Bgt E09 infection based on qRT-PCR analysis [bsr-d1 in rice were not significantly up-regulated after blast infection [Bgt-resistance related candidate genes from all specifically expressed R genes in TA7733 regardless of significance of their expression level changes post vs before Bgt-infection. After PCR verification by using R gene sequence-based primer sets and integrating transcriptome sequences blastn against CS Ref Seq v1.0, we finally verified 53 R genes candidates of chromosome 2Mb specificity, which included 47 unregulated, four up-regulated and two down-regulated genes.Previous studies have generally focused on the significantly differentially expressed genes in interactions between plant and pathogens to explore disease resistance-related genes by transcriptome sequencing \u201347. Howenfection . So, thePm genes including Pm2 [Pm3 [Pm8 [Pm21 [Pm60 [b-specific R genes were predicted to encode CC-NBS-LRR protein. These 14 R genes should be considered as the most promising candidate genes for further isolating and cloning Pm genes carried by Ae. biuncialis chromosome 2Mb.Isolation of plant resistance (R) gene is greatly helpful to breed resistant varieties and elucidates resistance molecular mechanisms. Conventional map-based cloning proved to be a effective method to clone R genes , howeverding Pm2 , Pm3 [50Pm3 [Pm8 , Pm21 [2m8 [Pm21 ,52 and P21 [Pm60 , have beD. villosum 6V#4S-specifc markers using transcriptome data [Ae. longissima chromosome-specific markers by RNA-seq [D. villosum#4 based on transcriptome data [Ae. biuncialis chromosome 2Mb. These markers will be useful to assist the transfer resistance gene(s) from 2Mb into common wheat by inducing CS-Ae. biuncialis 2Mb homoeologous recombination for wheat disease breeding in the future.GISH is a popular visual method to identify alien chromosome or chromatin in wheat background. Whereas GISH is expensive and time-consuming especially used to screen a large population derived from distant crossing between wheat and its wild relatives . In contome data . Wang et RNA-seq . Li et aome data . Furtherome data . Therefoome data ,58. In tAe. biuncialis chromosome 2Mb was verified to be board-spectrum in this study. It could be a valuable disease-resistance resource for wheat breeding programs. Fifty-three disease resistance gene candidates of 2Mb specificity, which were selected based on transcriptome sequencing analyses, will be greatly helpful to further isolate and clone Pm gene(s) derived from chromosome 2Mb and provide the insights into molecular mechanism of 2Mb-conferred powdery mildew resistance. Furthermore, 53 R gene sequence-based functional molecular markers of 2Mb specificity in this study will facilitate the transfer of resistance gene(s) from 2Mb to common wheat by inducing CS-Ae. biuncialis homoeologous recombination.In summary, powdery mildew resistance gene(s) on S1 Fig(M) 100 bp DNA Ladder. CS. TA7733. (A) CL119404Contig1. (B) CL88277Contig1. (C) CL82670Contig1. (D) 82789Contig1. (E) CL82700Contig1. (F) CL85355Contig1. (G) CL66003Contig1. (H) CL89405Contig1. (I) CL106750Contig1. (J) CL119216Contig1. (K) CL19981Contig2. (L) CL93721Contig1. (M) CL84424Contig1. (N) CL88613Contig1. (O) CL91022Contig1. (P) 96221Contig1. (Q) comp19533_c0_seq1_6. (R) CL85258Contig1. (S) CL113949Contig1. (T) CL86521Contig1. (U) CL105879Contig1. (V) CL90029Contig1. (W) CL84846Contig2. (X) CL87530Contig1. (Y) CL29910Contig1. (Z) CL92547Contig1. (AA) CL75219Contig1. (AB) CL108886Contig1. (AC) CL113652Contig1. (AD) CL80063Contig1. (AE) CL89447Contig1. (AF) CL93169Contig1. (AG) CL114224Contig1. (AH) CL116612Contig1. (AI) CL67241Contig1. (AJ) CL119539Contig1. (AK) CL90483Contig1. (AL) CL91742Contig1. (AM) comp84147_c0_seq1_6. (AN) CL124Contig7. (AO) CL100654Contig1. (AP) CL104996Contig1. (AQ) CL107524Contig1. (AR) CL107607Contig1. (AS) CL465Contig5. (AT) CL66266Contig1. (AU) CL72629Contig1. (AV) CL75868Contig1. (AW) CL86319Contig1. (AX) CL79458Contig1. (AY) comp121700_c0_seq1_5. (AZ) comp80277_c0_seq1_7. (BA) comp93868_c0_seq1_7.(TIF)Click here for additional data file.S1 Raw_imageAegilops biuncialis 2Mb disomic addition line TA77333; 3, common wheat CS; 4, CS-Ae. biuncialis 2Mb disomic addition line TA77333. (A) CL119404Contig1. (B) CL88277Contig1. (C) CL82670Contig1. (D) 82789Contig1. (E) CL82700Contig1. (F) CL85355Contig1. (G) CL66003Contig1. (H) CL89405Contig1. (I) CL106750Contig1. (J) CL119216Contig1. (K) CL19981Contig2. (L) CL93721Contig1. (M) CL84424Contig1. (N) CL88613Contig1. (O) CL91022Contig1. (P) 96221Contig1. (Q) comp19533_c0_seq1_6. (R) CL85258Contig1. (S) CL113949Contig1. (T) CL86521Contig1. (U) CL105879Contig1. (V) CL90029Contig1. (W) CL84846Contig2. (X) CL87530Contig1. (Y) CL29910Contig1. (Z) CL92547Contig1. (AA) CL75219Contig1. (AB) CL108886Contig1. (AC) CL113652Contig1. (AD) CL80063Contig1. (AE) CL89447Contig1. (AF) CL93169Contig1. (AG) CL114224Contig1. (AH) CL116612Contig1. (AI) CL67241Contig1. (AJ) CL119539Contig1. (AK) CL90483Contig1. (AL) CL91742Contig1. (AM) comp84147_c0_seq1_6. (AN) CL124Contig7. (AO) CL100654Contig1. (AP) CL104996Contig1. (AQ) CL107524Contig1. (AR) CL107607Contig1. (AS) CL465Contig5. (AT) CL66266Contig1. (AU) CL72629Contig1. (AV) CL75868Contig1. (AW) CL86319Contig1. (AX) CL79458Contig1. (AY) comp121700_c0_seq1_5. (AZ) comp80277_c0_seq1_7. (BA) comp93868_c0_seq1_7.Lanes: M, 100 bp Ladder DNA Marker; 1, common wheat CS; 2, CS-(PDF)Click here for additional data file.S1 Table(XLS)Click here for additional data file.S2 Table(XLS)Click here for additional data file.S3 Table(XLS)Click here for additional data file.S4 Table(XLS)Click here for additional data file.S5 Table(XLS)Click here for additional data file.S6 Table(XLS)Click here for additional data file."} +{"text": "Scyphiphora hydrophyllacea Gaertn. collected in Hainan Province of China resulted in the isolation of a new iridoid, scyphiphin C (1) and a known iridoid glycoside, shanzhiside methyl ester (2). Their structures were elucidated by a study of their physical and spectral data.Chemical investigation of the ethanol extract of the aerial parts of Scyphiphora hydrophyllacea Gaertn. F. (Rubiaceae), one of the mangrove plants, is distributed from south to southeast Asia, Caroline Islands, Australia, and New Caledonia to give 26 fractions. Fraction 16 (5.02 g) was subjected to column chromatography over silica gel eluted with light petroleum-EtOAc (4:6) to afford nine further fractions. Sub-fraction 4 (624.2 mg) was fractionated by column chromatography (Sephadex LH-20) eluted with 95 % EtOH and then rechromatographed on a silica-gel column with light petroleum-EtOAc (3:7) to afford compound 1 (18.7 mg). Fraction 18 (10.06 g) was subjected to vacuum liquid column chromatography over RP-18 eluted with MeOH-H2O gradually to afford eight further fractions. Sub-fraction 1 (2.18 g) was purified by silica gel CC eluted with CHCl3-MeOH (9:1) to afford compound 2 (290.2 mg).The dried, milled aerial parts of Scyphiphin C (1): White amorphous powder, = - 13.4 . IR (KBr): n = 3875, 3858, 3605, 3308, 2941, 2247, 1482, 865 cm-1. HR-ESI-MS (positive): m/z = 269.0998 . 1H and 13C-NMR: see Shanzhigenin methyl ester (2): White amorphous powder, = - 380.0 . IR (KBr): n = 3922, 3886, 3779, 3654, 3700, 3543, 3112, 3081, 2326, 1583, 891 cm-1. HR-ESI-MS (positive): m/z = 429.1380 .Scyphiphora hydrophyllaceaGaertn., a new iridoid scyphiphin C (1) and a known iridoid glucoside shanzhigenin methyl ester (2) were isolated. Their structures were established on the basis of spectroscopic evidence.As a part of our chemical investigation on"} +{"text": "Open Biol.7, 170165. (Published online 13 September 2017). (doi:10.1098/rsob.170165)A correction is required to The correct version of table 2 is as follows:"} +{"text": "Flammulina rossica (wood-rotting basidiomycete) genome was performed to identify its carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) revealed a total length of 35,646,506 bp (49.79% GC content). In total, 12,588 gene models of F. rossica were predicted using an ab initio gene prediction tool (AUGUSTUS). Orthologous analysis with other fungal species revealed that 7433 groups contained at least one F. rossica gene. Additionally, 12,033 (95.6%) of 12,588 genes for F. rossica proteins had orthologs among the Dikarya, and F. rossica contained 12 species-specific genes. CAZyme annotation in the F. rossica genome revealed 511 genes predicted to encode CAZymes including 102 auxiliary activities, 236 glycoside hydrolases, 94 glycosyltransferases, 19 polysaccharide lyases, 56 carbohydrate esterases, and 21 carbohydrate binding-modules. Among the 511 genes, several genes were predicted to simultaneously encode two different CAZymes such as glycoside hydrolases (GH) as well as carbohydrate-binding module (CBM). The genome information of F. rossica offers opportunities to understand the wood-degrading machinery of this fungus and will be useful for biotechnological and industrial applications.Next-generation sequencing (NGS) of the Flammulina rossica was first identified in 1999 by Redhead and Petersen E) , suggesting that these GHs can be secreted (The GH16 family consists of agarase (EC 3.2.1.81), lichenase (EC 3.2.1.73), \u03ba-carrageenase (EC 3.2.1.83), xyloglucan xyloglucosyltransferase (EC 2.4.1.207), endo-\u03b2-1,3-glucanase (EC 3.2.1.39), endo-\u03b2-1,3-1,4-glucanase (EC 3.2.1.6), and endo-\u03b2-galactosidase (EC 3.2.1.103), and most of these enzymes contain conserved motifs such as Glu-Xaa-Asp-Xaa-(Xaa)-Glu (EXDX[X]E). The first and last glutamic acid (E) residues of the conserved motif are characterized as a nucleophile and Br\u00f8nsted acid/base, respectively, and play an important role in the catalytic activity of GH16 family enzymes ,52,53. AXDX[X]E) . Althougsecreted . F. rossica also contains a series of genes related to cellulase (27 genes), xylanase (6 genes), and chitinase (23 genes) in its genome sequence . Cellulasequence . Cellobis genome .F. rossica with more than 200 genes encoding various GHs showed strong potential for diverse applications, such as biotechnology and industry.Simultaneous actions of several GHs are necessary to effectively degrade plant cell wall complexes composed of cellulose and xylan. Recently, genome sequencing of various bacterial and fungal species has reviewed the various activities of GHs on cellulose, chitin, and xylan degradation and their potential for biotechnological applications and industrial degradation of biopolymers ,59,60,61F. rossica genome based on three different databases searches (PLs EC 4.2.2.-) cleave polymer chains of polysaccharides, essential cellular components of all living organisms, through a \u03b2-elimination mechanism to produce unsaturated polysaccharides ,63. PLs .2.2.- clsearches . Among tsearches . In addisearches . PL20 wasearches 64]..F. rossid-galacturonate) or pectin is an acidic polysaccharide in plant cell walls [F. rossica and other fungal species. However, according to this study, genes encoding PL families 2 and 10 were not found in F. rossica and in other fungal species genomes but not in other fungal species are classified into AA families, which are mainly involved in the depolymerization of non-carbohydrate structural components (lignin) of plants . These Asequence . Among tectively . Interes species . In addiomycetes .3-His-Xaa4-Met/Leu/Phe [18-Glu that interacts with the FAD cofactor [F. rossica was also found to contain 24 genes predicted to encode AA3, and 17 genes contained the \u03b2-\u03b1-\u03b2 dinucleotide binding motif in their amino acid sequences has conserved motifs (copper binding motifs) within its amino acid sequence such as His-Xaa-His, His-Xaa-His-Gly, His-Xaa-Xaa-His-Xaa-His, and His-Cys-His-Xaa/Leu/Phe . Our rescofactor ,71,72. Fequences . These rAmino acid sequence within a carbohydrate-active enzyme with carbohydrate-binding activity is known as CBM ,76. CBM F. rossica genome based on three different database searches. CBM family 13 was prominent, and six families, including CBM18, -20, -22, -35, -48, -63, and -67, were represented by only one CBM in the F. rossica genome genes that simultaneously encode CBM suggest that CBM is required for efficient substrate degradation , trisaccharide (cellotriose), and oligosaccharide (cellotetraose) to ethanol at similar recovery rates to glucose and to convert glucose to ethanol at a similar level as S. cerevisiae [F. velutipes is suitable for consolidated bioprocessing (CBP), which is considered an effective process for bioethanol production from lignocellulosic biomass [F. velutipes, the closest white rot fungus to F. rossica, is a very attractive model for bioethanol production due to the numerous genes associated with lignocellulolytic enzymes such as CAZymes [F. rossica genome to identify genes involved in lignocellulose degradation. As described above, various CAZyme genes were identified in the F. rossica genome including 102 auxiliary activities, 236 glycoside hydrolases, 94 glycosyltransferases, 19 polysaccharide lyases, 56 carbohydrate esterases, and 21 carbohydrate binding-modules. Although further studies on CAZyme genes are needed, this study suggests that F. rossica has great potential for future production of biomaterials such as bioenergy.This study aimed to improve the understanding of lignocellulolytic machinery in revisiae ,80. This biomass ,82,83. P"} +{"text": "Multiple medication use within one year is associated with increased fall injury risk in older adults. However, chronically using multiple medications and treated fall injury have rarely been explored, particularly in cohort studies linked with claims data. We examined using >5 medications in 2 or more consecutive years (chronic medication use) as a risk factor for treated fall injury in 1,898 community-dwelling adults with linked Medicare Fee-For-Service (FFS) claims from the Health, Aging and Body Composition Study since 1997/98 clinic visit. Incident fall injury (N=546) was the first claim from 1998/99 clinic visit to 12/31/08 with an ICD-9 fall code and non-fracture injury code, or fracture code with/without a fall code. Stepwise Cox models with a time-varying predictor of chronic medication use before fall injury or censoring (N=414) vs. not using >5 medications at the same time (N=1008) were adjusted for baseline demographics, lifestyle factors, fall history, quadriceps strength, cardiovascular disease (CVD), diabetes, sensory nerve impairment, and kidney function. Fall injury risk increased for chronic medication users (37%) vs. non-users (29%) (HR=1.25[1.00-1.57]), though was attenuated after adjustment for CVD and diabetes (HR=1.18[0.93-1.51]). Sensitivity analyses excluding fall-risk-increasing drugs (FRIDs) from medication counts (HR=1.32[0.54-3.20]), or including those using >5 medications non-chronically (N=365) in referent groups (HR=1.22[0.96-1.55]) had consistent findings. Unmeasured comorbidity differences may confound associations of chronic medication use and treated fall injury risk in older adults with Medicare FFS. Considering both chronic diseases and medication use in fall risk assessments is needed."} +{"text": "Stenotrophomonas maltophilia is a prevalent nosocomial pathogen with multidrug resistance. Here, we describe the complete genome of S. maltophilia myophage Moby, which shares characteristics with Enterobacteria phage T4 and is closely related to Stenotrophomonas phage IME-SM1. Moby has a 159,365-bp genome with 271 predicted protein-coding genes and 24 predicted tRNAs. Stenotrophomonas maltophilia is a prevalent nosocomial pathogen with multidrug resistance. Here, we describe the complete genome of S. maltophilia myophage Moby, which shares characteristics with Enterobacteria phage T4 and is closely related to Stenotrophomonas phage IME-SM1. Moby has a 159,365-bp genome with 271 predicted protein-coding genes and 24 predicted tRNAs. Stenotrophomonas maltophilia is a multidrug-resistant Gram-negative bacterium with rising prevalence as a nosocomial pathogen was grown aerobically at 30\u00b0C in nutrient broth or agar (BD), and the phage was propagated by the soft-agar overlay method (www.bioinformatics.babraham.ac.uk/projects/fastqc), and trimming was performed using FastX Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). Assembly into a single contig with 673.7-fold coverage was performed using SPAdes v3.5.0 , and, unless otherwise stated, were executed using default parameters (Moby was isolated from filtered (0.2-\u03bcm pore size) wastewater collected in Bryan, TX. The y method . Phage Dy method . An Illust ATCC 1807 was gs v3.5.0 . Rho-inds v3.5.0 . Gene fus v3.5.0 \u201315. Stru v3.5.0 \u2013. progresost ATCC 807 was grameters . Phage mrameters .pac-type headful DNA packaging mechanism used by T4-like phages (Stenotrophomonas phage IME-SM1 (GenBank accession no. KR560069), an unclassified myovirus. No introns were identified in Moby, including in the predicted thymidylate synthase and nrdB genes, which contain introns in phage T4 (GenBank accession no. NC_000866) .MN095772, BioProject accession no. PRJNA222858, SRA accession no. SRR8893605, and BioSample accession no. SAMN11414490.The genome sequence and associated data for phage Moby were deposited under GenBank accession no."} +{"text": "Triticum aestivum L.) through development and cultivation of superior genotypes incorporating yield-related agronomic and physiological traits derived from genetically diverse and complementary genetic pool. Despite significant breeding progress, yield levels in wheat have remained relatively low and stagnant under marginal growing environments. There is a need for genetic improvement of wheat using yield-promoting morpho-physiological attributes and desired genotypes under the target production environments to meet the demand for food and feed. This review presents breeding progress in wheat for yield gains using agronomic and physiological traits. Further, the paper discusses globally available wheat genetic resources to identify and select promising genotypes possessing useful agronomic and physiological traits to enhance water, nutrient-, and radiation-use efficiency to improve grain yield potential and tolerance to abiotic stresses . Finally, the paper highlights quantitative trait loci (QTL) linked to agronomic and physiological traits to aid breeding of high-performing wheat genotypes.Enhanced grain yield has been achieved in bread wheat ( Triticum aestivum L., 2n = 6x = 42) is the world\u2019s third important staple food crop after maize (Zea mays) and rice (Oryza sativa). It is the most widely grown crop globally are discussed. Finally, the paper highlights QTL linked to agronomic and physiological traits to aid breeding of high-performing wheat genotypes.Grain yield response in wheat is influenced by several agronomic and physiological traits . AgronomIndia, Russia, China, and Kazakhstan are currently the leading wheat producers with approximately 30, 27, 24, and 12 million hectares devoted to wheat production, respectively. In terms of total production, China is the world\u2019s leading wheat producer with approximately 131 million tons per year . Other c-1 yr-1), Chile (246 kg ha-1 yr-1), France (123 kg ha-1 yr-1), and Mexico (41.77 kg ha-1 yr-1), whereas relatively lower genetic progress were reported in Spain (24 kg ha-1 yr-1), Australia (25\u2005kg ha-1 yr-1), and Siberia (15.3 kg ha-1 yr-1). Annual yield gains in Egypt, India, and Pakistan were estimated at 27.4 (0.55%), 21.4 (0.62%), 111.6 (1.13%), 32.5 (0.83%), and 18.5 kg ha-1 yr-1 (0.5%), respectively (-1 (0.65%) (Wheat yield gains across the major wheat producing countries are presented in ectively . Genetic (0.65%) . Countri (0.65%) .Genetic progress is relatively lower under low-yielding environments compared to high-yielding environments . TherefoGenetic gains in grain yield have been attributed to development and deployment of high-yielding wheat genotypes with improved agronomic and physiological traits related with high yield potential . For exaGrain yield in wheat is influenced by several agronomic traits which haVrn-A1, Vrn-B1, and Vrn-D1 regulate flowering and maturity in wheat . The effect of Vrn loci on heading and maturity, and grain yield potential are ranked as follows: Vrn-A1 < Vrn-B1 < Vrn- D1 among Chinese wheat cultivars followed by Vrn-A1 , grain yield (23 and 40%), and HI (31 and 50%) from tall and dwarf genotypes, respectively. Canadian spring wheat carrying dominant allele of Vrn-B1, photo-period insensitive allele of Ppd-D1, and height reducing allele Rht-1 produced shorter plants and higher grain yield , Rht2 (Rht-D1b), Rht-D1c, and Rht8 but resulted in reduced grain number per spike and increased 1,000\u2013kernel weight, above-ground biomass and grain yield in wheat have negligible effects on biomass production, whereas some can increase above-ground biomass, kernel weight, and grain yield and 0.3% yr-1 for TKW among Chinese and American wheat genotypes, respectively. Similarly, -1 among Brazilian wheat genotypes. TKW is reportedly linear with moderate to high correlation with grain yield (Grain yield improvement has been significantly associated with increased thousand kernel weight (TKW) . On the in yield suggestiin yield , rather -1 y-1 (0.44% yr-1) between 1980 and 2003 attributed to high number of kernels spike-1 (0.24 kernels spike-1 yr-1) in Spain. Similarly, -2 yr-1 through breeding and selection spanning over 50 years in Iran. Grain number among Brazilian wheat genotypes was increased by 77.89 grains yr-1. In China grain number per spike varied between 26 for landraces developed in 1941 to 38 for improved wheat genotypes released between 2007 and 2011 (The number of grains per spike has been identified as an important trait for improving grain yield . Yield gand 2011 . Among wand 2011 . Althougand 2011 . Therefoand 2011 . The reland 2011 . On the and 2011 .-1 was derived from \u2018Zhoumai 16\u2019 x \u2018Liken 4\u2019. Zhoumai 16 was developed from \u2018Yumai 21\u2019 x \u2018Zhou 8425B\u2019 whereby Zhou 8425B is characterized by large spikes and high TKW (Spike fertility (SF) is a grain yield component that influences the increase in the number of kernels per spike . For inshigh TKW , demonstOther spike characteristics useful for breeding include SL, SPS, and SC . The numTin1 tiller inhibition gene can increase grain number per spike and/or anthesis date genes (e.g. Ppd1) resulted in improvement of WSC. In addition, wheat genotypes with high WSC produce more fertile tillers, reduced days to anthesis, increased biomass, grain number, and grain yield than genotypes with low WSC possess useful source of alleles for enhancing drought tolerance and improving yield and its component traits (Aegilops tauschii) with durum wheat (T. durum Desf.) (T. turgidum L.) is also identified as a useful genetic resource for wheat breeding possessing functional genes that surpass the early maturity effect caused by the early flowering allele Ppd-A1a found in T. turgidum L. . Tetraplamidale) . Wild emamidale) . Wheat gamidale) . Furtheramidale) .QTLs QTn.ipk-5D, QTn.ipk-2D, QTn.ipk-3B, and QTn.ipk-1B which are associated with productive tiller number (QFlt.dms-2D, QFlt.dms-5B, QFlt.dms-2D, QFlt.dms-7A, and QFlt.dms-6B.2 are linked to days to flowering; whereas, QTLs QMat.dms-2D, QMat.dms-2D, QMat.dms-7A.2, and QMat.dms-4A.1 are associated with days to maturity (QTL mapping of agronomic and physiological traits is important for marker-assisted breeding in wheat . Agronomr number . QTL QFlmaturity . About 4maturity . New QTLmaturity . QTLs fomaturity Table 3 maturity . QTL\u2019s fmaturity . The idematurity .2 concentration were co-located with QTL for grain yield and/or yield components (mponents . QTL whimponents . Such plmponents . Marker-mponents . Generalmponents , their imponents . TherefoIn conclusion, genetic improvement can be achieved by either direct selection for primary traits such as grain yield or indirectly through selection of secondary traits related to higher grain yield potential. Breeding high-yielding genotypes incorporating yield-promoting agronomic and physiological traits has accelerated yield gains in wheat. As a result, further grain yield improvement will likely be achieved through in/direct selection targeting yield-related agronomic and physiological attributes. Furthermore, QTL associated with agronomic and physiological traits linked to grain yield are useful for marker-assisted selection of high-performing wheat genotypes.All authors listed have made substantial, direct and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Brassica rapa, an important vegetable cultivated worldwide.Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci.We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3\u2032-end RNA sequencing from B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in The epigenome comprises alternative chromatin states that can affect gene activity . These iArabidopsis thaliana (hereinafter referred to as Arabidopsis) the core PRC2 subunits are well conserved and H3K27me3 is crucial for plant development . Ca. CaB. raRRID:SCR_006989) [P <\u00a00.05; and Plant GO slim ontology type); data were visualized reduced in complexity and redundant GO terms using REViGO [Gene Ontology analysis was performed using agriGO v2.0 (Fisher _005825) with defB. rapa v3.0 gene models was obtained from Zhang et al. [B. rapa genome v3.0 was obtained by blasting coding sequences against B. rapa genome v1.5 and Arabidopsis .Functional annotation of g et al. . Custom B. rapa AGAMOUS genes, we found that BraA.AG.a (BraA01g010430.3C) gene structure annotation was not correct in the recent B. rapa genome v3.0. We curated BraA.AG.a gene structure using AUGUSTUS [B. rapa genome V1.5) gene information at the B. rapa database [During our analyses of H3K27me3 levels on _008417) and Bra0database .Project name: Epigenomics Workflow on Galaxy and Jupyterhttps://github.com/wilkinsonlab/epigenomics_pipelineProject home page: Operating systems: Platform independentProgramming languages: Python, R, BashOther requirements: noneLicense: MITRRID:SCR_017544https://github.com/wilkinsonlab/epigenomics_pipeline; this is associated with a Zenodo release to match the configuration used in this publication [RRID:SCR_017544 and biotools: Epigenomics_Workflow_on_Galaxy_and_Jupyter at SciCrunch and bio.tools databases, respectively. Compiled Docker images are available at https://hub.docker.com/u/mpaya. All supporting data are available in the GigaScience GigaDB database [ChIP-seq and RNA-seq data sets supporting the results of this article are available at NCBI SRA under the accession number PRJNA542357. Latest versions of the components of the REA pipeline, and instructions to deploy the Galaxy/Jupyter containers and run the analysis, can be found in the GitHub repository lication . The REAdatabase .Figure S1: Differences between epic2 and MACS2 peak-calling algorithmsB. rapa inflorescencesFigure S2: ChIP-seq analysis of H3K27me3 regions in B. rapa inflorescencesFigure S3: Comparisons of H3K27me3 ChIP-seq signal in B. rapa H3K27 methyltransferase-coding genesFigure S4: Transcript levels of BraA.clf-1 mutant phenotypesFigure S5: B. rapa plant sampling materialsFigure S6: Pictures of Figure S7. ChIP-seq sample-sample correlation testsFigure S8. RNA-seq sample-sample correlation testsTable S1. Alignment statisticsTable S2. Comparison of Bowtie2 and BWA performanceB. rapaTable S3. H3K27 trimethylated regions identified in B. rapa leavesTable S4. List of H3K27me3 peaks in B. rapa inflorescencesTable S5. List of H3K27me3 peaks in Table S6. 3\u2032RNA-seq resultsTable S7. List of H3K27me3 differentially marked regionsTable S8. H3K27me3-regulated genesTable S9. Primer listgiz147_GIGA-D-19-00256_Original_SubmissionClick here for additional data file.giz147_GIGA-D-19-00256_Revision_1Click here for additional data file.giz147_Response_to_Reviewer_Comments_Original_SubmissionClick here for additional data file.giz147_Reviewer_1_Report_Original_SubmissionDiep Ganguly -- 8/28/2019 ReviewedClick here for additional data file.giz147_Reviewer_1_Report_Revision_1Diep Ganguly -- 11/7/2019 ReviewedClick here for additional data file.giz147_Reviewer_2_Report_Original_SubmissionJingyu Zhang -- 9/1/2019 ReviewedClick here for additional data file.giz147_Supplemental_FilesClick here for additional data file.M: log2 fold-change of the normalized H3K27me3 read densities in leaves relative to inflorescences calculated by MAnorm; MACS: Model-based Analysis of ChIP-Seq; mRNA: messenger RNA; NCBI: National Center for Biotechnology Information; PRC2: Polycomb repressive complex 2; REA: Reproducible Epigenomic Analysis; RNA-seq: RNA sequencing; RT-qPCR: real-time quantitative reverse transcription PCR; s.d: standard deviation; SEA: singular enrichment analysis; SICER: Spatial Clustering for Identification of ChIP-Enriched Regions; SRA: Sequence Read Archive.3\u2032RNA-seq: 3\u2032-end mRNA high-throughput sequencing; AG: AGAMOUS; bp: base pairs; cDNA: complementary DNA; ChIP: chromatin immunoprecipitation; ChIP-seq: ChIP followed by high-throughput sequencing; ChIP-qPCR: ChIP followed by real-time quantitative PCR; CLF: CURLY LEAF; DAG: days after germination; DEG: differentially expressed genes; FAIR: findability, accessibility, interoperability, and reusability; FC: fold change; FDR: false discovery rate; GO: gene ontology; H3K27me3: histone H3 lysine 27 trimethylation; IGV: integrative genomics viewer; kb: kilobase pairs; LOWESS: Locally Weighted Scatterplot Smoothing; The authors declare that they have no competing interests.This work was supported by grants RTI2018-097749-B-100, BIO2015\u201368031-R and RYC-2013\u201314689 to P.C., and BES-2016\u2013078939 fellowship to L.P.V. from the Spanish Ministerio de Economia y Competitividad ; and by the \"Severo Ochoa Program for Centres of Excellence in R&D\u201d from the Agencia Estatal de Investigaci\u00f3n of Spain, grant SEV-2016-0672 (2017\u20132021) to the CBGP. M.P.M. was supported by a Postdoctoral contract associated with the Severo Ochoa Program.P.C. conceived the work; M.P.M. performed computational biology analyses; L.P.V. performed initial bioinformatic analysis and all experimental research. P.M.U. and D.L.A. performed 3\u2032RNA-seq library preparation and sequencing. M.W. contributed analytical tools and metadata generation. P.C. and M.P.M. wrote the first draft of the manuscript, which was completed with the assistance of L.P.V. and M.W. All authors approved the final version of the article."} +{"text": "Scientific Reports 10.1038/s41598-019-50208-x, published online 26 September 2019Correction to: The Acknowledgements section in this Article is incomplete.\u201cWe thank Michael Miller at W.S.I. for discussion.\u201dshould read:\u201cWe thank Michael Miller at W.S.I. for discussion. We gratefully acknowledge Dr. Tyler Maxwell for his contribution to Figure S11c.\u201d"} +{"text": "The publisher apologizes for the error.The fifth author is listed incorrectly in the citation. The correct citation is: Ljones K, Ness HO, Solvang-Garten K, Gaustad SE, H\u00f8ydal MA (2017) Acute exhaustive aerobic exercise training impair cardiomyocyte function and calcium handling in Sprague-Dawley rats. PLoS ONE 12(3): e0173449."} +{"text": "Scientific Reports 10.1038/s41598-019-49575-2, published online 17 October 2019Correction to: This Article contains errors in Reference 46 which was incorrectly given as:Odorico, J. S. et al. Extracellular matrix scaffold and hydrogel derived from decellularized and delipidized human pancreas. Sci. Rep. 8, 1\u201316 (2018)The correct reference is listed below as Reference"} +{"text": "Luminal B cancers show much worse outcomes compared to luminal A. This present study aims to screen key lncRNAs and mRNAs correlated with luminal-B breast cancer.cis nearby-targeted DEmRNAs of DElncRNAs. DElncRNA-DEmRNA co-expression networks were performed. The mRNA and lncRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database to validate the expression patterns of selected DEmRNAs and DElncRNAs.Luminal-B breast cancer tissue samples and adjacent tissue samples were obtained from 4 patients with luminal-B breast cancer. To obtain differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) between luminal-B breast cancer tumor tissues and adjacent tissues, RNA-sequencing and bioinformatics analysis were performed. Functional annotation of DEmRNAs and protein-protein interaction networks (PPI) construction were performed. DEmRNAs transcribed within a 100\u2009kb window up- or down-stream of DElncRNAs were searched, which were defined as A total of 1178 DEmRNAs and 273 DElncRNAs between luminal-B breast cancer tumor tissues and adjacent tissues were obtained. Hematopoietic cell lineage, Cytokine-cytokine receptor interaction, Cell adhesion molecules (CAMs) and Primary immunodeficiency were significantly enriched KEGG pathways in luminal-B breast cancer. FN1, EGFR, JAK3, TUBB3 and PTPRC were five hub proteins of the PPI networks. A total of 99 DElncRNAs-nearby-targeted DEmRNA pairs and 1878 DElncRNA-DEmRNA co-expression pairs were obtained. Gene expression results validated in TCGA database were consistent with our RNA-sequencing results, generally.This study determined key genes and lncRNAs involved in luminal-B breast cancer, which expected to present a new avenue for the diagnosis and treatment of luminal-B breast cancer. Breast cancer is the leading cause of cancer-related death in women, both overall and in less developed countries . It is aWith advances in high-throughput technology, it is discovered that human transcriptome mainly consists of non-coding RNAs (ncRNAs) with limited or no protein-coding capacity , 10. Loncis nearby-targeted DEmRNAs of DElncRNAs and construction of DElncRNA-DEmRNA co-expression networks were performed. In this light, we expect this study could represent a new avenue to improve the understanding of the pathogenesis and be helpful for treatment of luminal B breast cancer.In this study, differentially expressed lncRNAs (DElncRNA) and mRNAs (DEmRNAs) in tumor tissues of patients with luminal-B breast cancer were identified by RNA-sequencing. Subsequently, protein-protein interaction (PPI) networks of DEmRNAs were conducted. Identification of Luminal-B breast cancer tissue samples and adjacent tissue samples were obtained from 4 patients with luminal-B breast cancer in People\u2019s Hospital of Deyang City, which were free of treatment. The detailed characteristics of patients are displayed in Table\u00a0http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), the FASTQ sequence data were acquired from the RNA-sequencing data. Read QC tool in FastQC version 0.11.4 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for the quality control of FASTQ data with Q\u2009>\u200930. Trimming of raw data was performed with cutadapt version 1.16 (http://cutadapt.readthedocs.io). Reads with low quality were removed to obtain the clean reads.According to the manufacturer\u2019s protocol, RNA was extracted with PAXgene blood RNA kit . With Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit), the concentration, integrity and RNA integrity number (RIN) values of RNA were assessed. Sequencing was performed based on the Illumina Hiseq X-ten platform with PE150 bp sequencing mode. The sequencing was done with paired-ends and 10G depth. With Base Calling version 0.11.4 (ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens), HISAT2 version 2.1.0 (https://ccb.jhu.edu/software/hisat2/index.shtml) was applied. Expression of mRNAs and lncRNAs was normalized and outputted with StringTie version 1.3.3b (http://ccb.jhu.edu/software/stringtie/). Fragments per Kilobase of exon per million fragments mapped (FPKM) of lncRNAs and mRNAs were calculated with StringTie. With edgeR version 3.24 (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html), both DEmRNAs and DElncRNAs were obtained with |log2FC|\u2009>\u20091 and p-value <\u20090.05. By using R package \u201cpheatmap\u201d, hierarchical clustering analysis of DElncRNAs and DEmRNAs were conducted.In order to align the clean reads with the human reference genome, Ensemble GRCh38.p7 (http://metascape.org/gp/index.html). A value of p\u2009<\u20090.05 was set as the cut-off for significance.Functional annotation, including Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses was performed with Metascape (http://www.uniprot.org/database/DB-0184). Then, PPI networks were visualized with Cytoscape software .Top 100 up- and down-regulated DEmRNAs were scanned with the BioGrid .A total of 1178 DEmRNAs (666 up-regulated and 512 down-regulated DEmRNAs) and 273 DElncRNAs (181 up-regulated and 92 down-regulated DElncRNAs) were obtained. The top 10 up- and down-regulated DEmRNAs and DElncRNAs were exhibited in Table\u00a0p\u2009=\u20091.14E-50), cytokine-mediated signaling pathway (p\u2009=\u20095.74E-44) and cytokine production (p\u2009=\u20098.78E-38) were significantly enriched GO terms in luminal-B breast cancer , Cytokine-cytokine receptor interaction (p\u2009=\u20098.19E-21), Cell adhesion molecules (CAMs) (p\u2009=\u20093.61E-18) and Primary immunodeficiency (p\u2009=\u20091.17E-14) were significantly enriched KEGG pathways in luminal-B breast cancer , EGFR (degree\u2009=\u200914), JAK3 (degree\u2009=\u200911), TUBB3 (degree\u2009=\u200911) and PTPRC (degree\u2009=\u200910) were five hub proteins of the PPI networks , regulation of cell-cell adhesion (p\u2009=\u20097.86E-12), cytokine binding (p\u2009=\u20093.41E-07), T cell selection (p\u2009=\u20097.75E-07) and negative regulation of secretion (p\u2009=\u20091.38E-06) were significantly enriched GO terms , Cytokine-cytokine receptor interaction (p\u2009=\u20092.81E-03), Primary immunodeficiency (p\u2009=\u20097.71E-03), AMPK signaling pathway (p\u2009=\u20099.30E-03) and Wnt signaling pathway (p\u2009=\u20091.46E-02) were significantly enriched KEGG pathways , cytokine-mediated signaling pathway (p\u2009=\u20099.35E-28), cytokine production (p\u2009=\u20091.68E-27), leukocyte migration (p\u2009=\u20093.20E-22) and alpha-beta T cell activation (p\u2009=\u20094.89E-20) were significantly enriched GO terms , Hematopoietic cell lineage (p\u2009=\u20099.66E-16), Primary immunodeficiency (p\u2009=\u20092.85E-15), Th1 and Th2 cell differentiation (p\u2009=\u20093.38E-13) and Cell adhesion molecules (CAMs) (p\u2009=\u20091.66E-12) were significantly enriched KEGG pathways . During Metastasis-associated lung adenocarcinoma transcript\u00a01 (MALAT1) is a highly conserved lncRNA, and its over-expression in multiple cancerous tissues has been linked to the proliferation and metastasis of tumor cells. It was first identified as being up-regulated in lung tumors, and a prognostic marker for metastasis and patient survival in non-small cell lung cancer (NSCLC), specifically in early stages of lung adenocarcinoma . Subsequ+ T cells promotes metastasis in luminal breast cancer is primarily expressed in heart and fetal brain tissue . DysreguThe Wilms\u2019 tumor 1 (WT1) was first cloned in 1990 as a suppressor in Wilms\u2019 tumor, which was located at chromosome 11p13 . WT1 genWilms tumor 1 Antisense RNA (WT1-AS) is located upstream of the WT1 gene, and these two genes are bi-directionally transcribed from the same promoter region. Down-regulation of WT1-AS was related to a poorer prognosis in ovarian clear cell adenocarcinoma . Lv et aIn conclusion, a total of 1178 DEmRNAs and 273 DElncRNAs between luminal-B breast cancer tumor tissues and adjacent tissues were obtained. We discussed and emphasized the importance role of three DElncRNA-DEmRNA pairs, including MALAT1-S100A7, MIAT-CCL5 and WT1-AS-WT1, involved in luminal B breast cancer, which expected to provide new insight into understanding the mechanism underlying pathogenesis of luminal B breast cancer. The small sample size was a limitation of our study. Although the validation results in TCGA database indicated that our RNA-sequencing results were generally reliable, larger cohorts of patients and further experimental validation studies are needed to conduct to verify this conclusion."} +{"text": "Oriens lacunosum-moleculare (O-LM) interneurons constitute 40% of hippocampal interneurons expressing Somatostatin (SST). Recent evidence has indicated a dual origin for these cells in the medial and caudal ganglionic eminences (MGE and CGE), with expression of Htr3a as a distinguishing factor. This is strikingly different from cortical SST interneurons that have a single origin within the MGE/preoptic area (POA). We reassessed the origin of hippocampal SST interneurons using a range of genetic lineage-tracing mice combined with single-cell transcriptomic analysis. We find a common origin for all hippocampal SST interneurons in NKX2-1-expressing progenitors of the telencephalic neuroepithelium and an MGE/POA-like transcriptomic signature for all SST clusters. This suggests that functional heterogeneity within the SST CA1 population cannot be attributed to a differential MGE/CGE genetic origin. \u2022+ progenitors generate all hippocampal CA1 somatostatin (SST) interneuronsNKX2-1\u2022+ cells generated in the absence of NKX2-1 do not migrate to the hippocampusSST\u2022LHX6 expression maintained in MGE-derived cortical and hippocampal CA1 interneurons\u2022Htr3a is detected in MGE-derived hippocampal CA1 interneuronsLow expression of In this article, Kessaris and colleagues combine genetic lineage tracing and single-cell transcriptomic analysis to identify the embryonic origin of hippocampal CA1 Somatostatin interneurons. They report a common origin in the medial ganglionic eminence/preoptic area from neuroepithelial precursors expressing NKX2-1. The pri the CGE . The pre the CGE .oriens lacunosum-moleculare (O-LM) interneurons, which have their cell bodies within stratum oriens (s.o.) and represent 40% of all SST interneurons in the hippocampus mapping of Sst interneurons in the developing mouse brain suggested that most, if not all, telencephalic Sst cells originate in the diagonal area (or anterior entopeduncular area [AEP]) and not the pallidal neuroepithelium (Recent ithelium . This su (E13.5) .Lhx6 to label MGE-derived interneurons in the cortex and hippocampus B\u20131F. Aro30 (P30) B and 1F.30 (P30) or from 30 (P30) A (Fogart30 (P30) . Analysi30 (P30) C and 1F,30 (P30) D and 1F.with GFP E and 1F.rneurons .Figure\u00a01Sst interneurons in the developing mouse brain suggested that most, if not all, telencephalic Sst cells originate in the AEP and that failure to label 30% of cortical interneurons in Nkx2-1-Cre mice may have been caused by lack of NKX2-1 expression in the AEP at E13.5 embryos for the presence of SST-positive cells. At E13.5, most Sst cells were missing from the telencephalon in Nkx2-1 KO embryos compared with controls \u223c30% of SST cells with typical O-LM characteristics were labeled with GFP in Htr3a-GFP mice; (2) a proportion of s.o. SST O-LM cells were labeled with GFP in Mash1-CreER;RCE transgenic mice following tamoxifen administration; and (3) there was only \u223c10% overlap in expression of tdTomato and GFP in Nkx2-1-Cre;tdTOM;Htr3a-GFP mice 1Wdr (MGI:3761164) ((Nkx6-2-icre)1Kess (MGI:4355562) (JAX 027798), Tg(Lhx6-icre)1Kess (MGI:4355717) (JAX 026555) (tm1(EGFP/cre)Cjt (MGI:3053959) (JAX 005622) (tm2.1(cre)Zjh (MGI:4838416) (JAX 013044) (KI (JAX 006148) (KI reporter mice (JAX 004077) , Tg(Nkx6 026555) , Shhtm1( 005622) , Ssttm2. 013044) , R26R-YF 006148) , and R26 004077) have beed allele . All aniLhx6- and Sst DIG-labeled probes were generated from a plasmid (kind gift from V. Pachnis) and IMAGE clone 4218815 (Source Biosciences), respectively.Tissue processing, immunohistochemistry, and ISH were carried out as previously described . Primary+ cells per animal were counted in order to generate the data shown in Images were captured using a Hamamatsu C4742-95 camera on\u00a0a\u00a0Zeiss Axioplan fluorescence microscope and Digital Pixel software. Confocal images were captured on a Leica CTR6500 confocal microscope or a Zeiss LSM880 with Airyscan. ISH images were captured on a Zeiss Axio Scan.Z1 scanner. Image composites were assembled using Microsoft ICE software and processed with Adobe Photoshop CS6 . Figures were generated in Adobe Illustrator CS6 (Adobe Systems). Quantification was performed as described previously . Three ahttps://github.com/cortexlab/Transcriptomics. To visualize different cell subtypes, we used the negative binomial t-stochastic neighbor-embedding (nbtSNE) algorithm as previously described (The single-cell data presented were obtained by reanalyzing our previously published datasets . The codescribed .Conceptualization, Z.A. and N. Kessaris; Methodology, N. Kessaris and K.D.H.; Investigation, Z.A., L.M., N. Ktena, K.D.H., and N. Kessaris; Writing \u2013 Original Draft, Z.A. and N. Kessaris; Writing \u2013 Review\u00a0& Editing, Z.A., L.M., K.D.H., and N. Kessaris; Funding Acquisition, K.D.H. and N. Kessaris."} +{"text": "We observed that both EBV- and HCMV-specific T cell responses were significantly lower in SLE patients compared with healthy subjects. We reported decreased EBV- and HCMV-specific T cell responses among medium-high immunosuppressed patients compared to low immunosuppressed patients. Immunosuppressive level could exert a role in the control of herpesviruses reactivation, even if the immunosuppressive condition of SLE remains the driving cause of skewed virus-specific T cell response.Systemic lupus erythematosus (SLE) is an autoimmune disease with a complex etiology. Opportunistic viral pathogens, such as human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV), are particularly relevant. The role of the T cell response in SLE has not been deeply studied; we investigated the role of HCMV- and EBV-specific T cell responses in SLE patients also in relation to their pharmacological immunosuppressive status. PBMCs from 70 SLE patients and 50 healthy controls were stimulated with EBV- and HCMV-specific antigens, and IFN- Herpesviridae family, and they may complicate the disease course [\u03b3) is also suggested to play a crucial role in this context [Systemic lupus erythematosus (SLE) is a complex pathological condition which mae course \u201315 or mie course . Furthere course . It has e course , 23, whie course . In this context .\u03b3 ELISPOT assay. By using a novel approach we provided a good estimation of both CD4+ and CD8+ antigen-specific T cell responses, avoiding predepletion assay [+ and CD8+ antigen-specific T cell response, avoiding the intracellular cytokine staining approach that is labor intensive and requires a larger number of cells. However, this approach cannot be considered as precise as flow cytometry strategy, but could represent an easier way for the estimation of antigen-specific T cell response. For comparison, T cell response to the nonspecific mitogen (PHA) was also investigated.The aim of this study was to evaluate and characterize T cell responses to HCMV and EBV in SLE patients using IFN-on assay . In thisSeventy patients 38.0-57.8) fulfilling the 1997 ACR classification criteria for SLE and refeSLE patients had a median age at disease onset of 30 (IQR 23-46) years and a median disease duration of 121.5 (IQR 42.3-228.5) months. In all cases, disease activity was evaluated according to SLEDAI 2k score [For practical purposes, we divided the patients into two groups, according to the degree of pharmacological immunosuppression: patient treatment with hydroxychloroquine and/or with prednisone\u2009\u2264\u20095\u2009mg/day was considered low pharmacological immunosuppression . Patient treatment with mycophenolate mofetil, methotrexate, cyclosporin A, rituximab, belimumab, and/or prednisone\u2009>\u20095\u2009mg/day was considered medium-high pharmacological immunosuppression .\u03bcg/ml streptomycin, 25% human albumin , and 10% DMSO ), and stored in liquid nitrogen (10\u2009\u00d7\u2009106 cells/ml) until analysis. After thawing, about 50-60% of cells were still viable and could be used in the ELISPOT assay.Peripheral blood was collected into vacutainer tubes (BD) containing heparin. Whole blood was used for viral genome quantification and determination of T cell subsets; plasma was separated for serological analyses. Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation , cryopreserved in freezing medium , IgG anti-VCA, and anti-EBNA were quantified using an ELISA kit , according to the manufacturer's instructions. Healthy subjects and SLE patients were considered EBV-seropositive when IgG anti-VCA and anti-EBNA were positive.IgM anti-HCMV and IgG anti-HCMV were quantified using an ELISA kit , according to the manufacturer's instructions. Healthy subjects and SLE patients were considered HCMV-seropositive when IgG anti-HCMV was positive.DNA was purified using NucliSENS\u00aeeasyMAG\u00ae . EBV DNA and HCMV DNA were quantified using real-time PCR (lower limit detection HCMV and EBV DNA 90 copies/ml), as previously described were determined by flow cytometry , using Flow-Count Fluorospheres. Gating strategy was set up on CD45+ and side scatter (SSC).Fresh whole blood was stained with anti-CD3-PC5, anti-CD45-FITC, anti-CD4-RD1, and anti-CD8-ECD monoclonal antibodies . After lysis of red blood cells, absolute CD3\u03bcg/ml streptomycin with 8% of DMSO. Resuspended peptide pools were used after dilution (1\u2009:\u2009100) in RPMI 1640 supplemented with 2\u2009mM L-glutamine, 100\u2009U/ml penicillin and 100\u2009\u03bcg/ml streptomycin, and 10% FBS and then used as antigens. A lytic pool, containing peptides spanning the full length of BZLF-1 (59 peptides) and BMRF-1 (99 peptides) EBV proteins; an Epstein-Barr nuclear antigen (EBNA) pool, containing peptides spanning the full length of EBNA 1 (158 peptides), EBNA3a (234 peptides), EBNA 3b (279 peptides), and EBNA 3c (265 peptides) EBV proteins; and a latent membrane protein (LMP) pool, containing peptides spanning the full length of LMP1 (94 peptides) and LMP2 (122 peptides) EBV proteins, were used as EBV-specific antigens at a final concentration of 0.25\u2009\u03bcg/ml for each individual peptide in the corresponding pool. Peptide pools representative of whole HCMV proteins IE-1 (120 peptides), IE-2 (143 peptides), and pp65 (138 peptides) (JPT Peptide Technologies) were used at a final concentration of 0.25\u2009\u03bcg/ml for each individual peptide in the corresponding pool.Lyophilized peptide pools, 15 amino acids in length with an 11 amino acid overlap, were resuspended in RPMI 1640 supplemented with 2\u2009mM L-glutamine, 100\u2009U/ml penicillin, and 100\u2009\u03b3 ELISPOT kits and Multiscreen-IP membrane-bottomed 96-well plates were used as described [\u03b3 and stored at 4\u00b0C. After washing with PBS, plates were blocked with culture medium (Euroclone)) for 2 hours at room temperature. Cells were plated in duplicate (1 \u00d7 105/100\u2009\u03bcl per well) and stimulated with the corresponding antigens or with phytohemagglutinin or with medium alone (negative control) and incubated at 37\u00b0C in a 5% CO2 humidified atmosphere for 24 hours. After washing, plates were incubated overnight at 4\u00b0C with biotinylated IFN-\u03b3 detection antibody. Plates were washed, streptavidin-alkaline phosphatase conjugate was added, and plates were incubated at 37\u00b0C in a 5% CO2 atmosphere for 1 hour. Plates were then washed, and 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium (BCIP/NBT) was added for 20 minutes at room temperature. Wells were then washed several times under running water and air-dried overnight. Spots were counted by using an automated AID ELISPOT reader system . The mean number of spots from duplicate wells was adjusted to 1 \u00d7 106 PBMCs. The net spots per million PBMCs was calculated by subtracting the number of spots responding to the negative control from the number of spots responding to the corresponding antigenand results were given as net spots/million PBMCs. Furthermore, results were normalized to absolute CD4+ and CD8+ T cell counts, as previously described [Human IFN-escribed \u201331. Briet-test or Mann-Whitney test was used for quantitative variables in order to perform comparison between groups. Spearman's test was used for the correlation analysis. All tests were two-tailed. A P value\u2009<\u20090.05 was considered statistically significant. Analyses were performed using the GraphPad Prism 5 .Descriptive data were reported or considered as absolute and relative frequencies, mean and standard deviation, median, and interquartile range (IQR) based on the type of the variable distribution. For qualitative variables, Fisher's test was used, while + and CD8+ T cells were significantly lower in SLE patients than in healthy controls (P < 0.0001). In SLE patients, the median CD4+ and CD8+ T cell counts were 434.5 (IQR 270.3-620.3) cells/\u03bcl and 287.0 (IQR 196.0-397.3) cells/\u03bcl, respectively, while in healthy subjects, the median CD4+ and CD8+ T cell counts were 1054.0 (IQR 760.5-1361.0) cells/\u03bcl and 532.0 (IQR 376.8-748.8) cells/\u03bcl, respectively. EBV- and HCMV-specific antibodies were analyzed in all enrolled subjects, as well as HCMV and EBV DNAemia. Demographic data are summarized in T cell subsets were analyzed in 70 SLE patients and 50 healthy subjects with homogeneous characteristics. The two groups were not substantially different in terms of age and sex distribution. Both CD4+ and CD8+ T cell responses to all EBNA, LMP, and lytic overlapping 15-mer peptide pools were evaluated in 68 EBV-seropositive SLE patients, 25 EBV-seropositive healthy subjects, and four EBV-seronegative individuals .EBV-specific CD4P = 0.0002) vs 1.140 (IQR 0.5235-2.6180) EBV-specific CD4+ T cells/\u03bcl EBV-specific CD4+ T cells/\u03bcl; P < 0.0001) (+ T cell response was significantly different in the two groups of subjects (0.0905 (IQR 0.0215-0.2148) and 0.5620 (IQR 0.2335-1.231) EBV-specific CD8+ T cells/\u03bcl, respectively, P < 0.0001) (+ and CD8+ T cell responses with the SLEDAI 2k score in SLE patients (data not shown).Median EBV-specific T cell response was significantly lower in EBV-seropositive SLE patients than in EBV-seropositive healthy subjects (340.5 (IQR 75-738.8) vs. 890 (IQR 360-1983) net spots/million PBMCs; 0.0002) . Normali 0.0001) . Similar 0.0001) . There wn = 25, 36.8%) or mhp-IS . The latter had significantly lower EBV-specific T cell response than the other group (170 (IQR 70-530) and 500 (IQR 237.5-905.0) net spots/million PBMCs, respectively; P = 0.0224) (+ and CD8+ T cells. The EBV-specific CD4+ T cell response was lower in mhp-IS than in lp-IS (0.0620 (IQR 0.0170-0.2680) and 0.2420 (IQR 0.1065-0.4515) EBV-specific CD4+ T cells/\u03bcl; P = 0.0124) (+ T cell response in SLE patients receiving mhp-IS was lower than that observed in patients receiving lp-IS (0.1430 (IQR 0.0800-0.3335) and 0.0450 (IQR 0.0180-0.1640) EBV-specific CD8+ T cells/\u03bcl; P = 0.0174) . Results 0.0124) . Similar 0.0174) .+ and CD8+ T cell EBV-specific ELISPOT response in SLE patients with undetectable EBV DNA and detectable EBV DNA . A trend toward statistical significance was observed when we compared the EBV-specific T cell response measured as net spots/million PBMCs in SLE patients with undetectable (median 387.5 (IQR 119.8-953.8)) and detectable EBV DNA (220 (IQR 56.3-538.8); P = 0.0753) (+ T cells/\u03bcl between the two groups (0.202 IQR (0.038-0.450) and 0.072 IQR (0.016-0.236) EBV-specific CD4+ T cells/\u03bcl; P = 0.0773) EBV-specific CD8+ T cells/\u03bcl and 0.0710 IQR (0.0157-0.1565) EBV-specific CD8+ T cells/\u03bcl; P = 0.1070) . Similar 0.0773) , althoug 0.1070) .P = 0.0373) (+ T cell response in mhp-IS patients (median 0.040 IQR (0.013-0.160) EBV-specific CD4+ T cells/\u03bcl) was compared with lp-IS patients (median 0.223 IQR (0.097-0.398) EBV-specific CD4+ T cells/\u03bcl; P = 0.0573) (+ T cell response in mhp-IS (0.034 IQR (0.011-0.120) EBV-specific CD8+T cells/\u03bcl and lp-IS patients (0.097 IQR (0.080-0.210) EBV-specific CD8+ T cells/\u03bcl; P = 0.0394) were receiving mhp-IS and nine (30%) lp-IS. In a comparison of the two groups, EBV-specific T cell response measured as net spots/million PBMCs was higher in lp-IS group (median 110 IQR (37.5-460)) than in mhp-IS (median 380 IQR (313-750); 0.0373) . A trend 0.0573) . A signi 0.0394) . No diffP = 0.3679) vs 0.6065 (IQR 0.1368-1.250) HCMV-specific CD4+ T cells/\u03bcl; P = 0.0004) (+ T cell response was significantly different in the two groups of subjects (0.6490 (IQR 0.1480-1.280) vs 2.279 (IQR 0.7108-3.570) HCMV-specific CD8+T cells/\u03bcl; P = 0.0059). Both groups of HCMV-seropositive subjects had HCMV-specific responses higher than HCMV-seronegative controls (P < 0.0001) . Seventeen out of 55 (30.9%) SLE patients were receiving lp-IS, while the remaining 38 (69.1%) were receiving mhp-IS. The HCMV-specific ELISPOT response measured as net spots/million PBMCs was significantly higher in lp-IS patients (median 2695 (IQR 1003-6525)) than in mhp-IS patients (median 1055 (IQR 271-1810)) (P = 0.0282) (+ T cell response was significantly reduced in this mhp-IS patients (0.271 IQR (0.125-1.083) vs 0.927 IQR (0.611-2.315) HCMV-specific CD4+ T cells/\u03bcl; P = 0.0179) (+ T cell response between mhp- and lp-IS (0.359 IQR (0.071-0.738) vs 0.910 IQR (0.383-2.090) HCMV-specific CD8+ T cells/\u03bcl; P = 0.0111) . HCMV-specific T cell response was lower in HCMV-seropositive SLE patients than in HCMV-seropositive healthy subjects (median 1155 (IQR 415-3925) and 1850 (770-3103) net spots/million PBMCs, respectively), but the difference was not statistically significant ( 0.3679) . Results 0.0004) . Similar 0.0001) . There w 0.0282) . Similar 0.0179) . Finally 0.0111) .We observed that ELISPOT T cell response in the 52 SLE patients with undetectable HCMV DNA was higher than the response observed in the three patients with detectable HCMV DNAemia (data not shown). However, due to the low number of patients in the latter group, the difference was not considered statistically valid.All patients with detectable HCMV DNA were medium-high immunosuppressed. Two of them were also positive for EBV DNA.+ and CD8+ T cells producing IFN-\u03b3 in response to PHA, a nonspecific antigen, were significantly lower in 70 SLE patients than in 41 healthy controls. PHA-specific T cell responses measured as net spots/million PBMCs were 4795 (IQR 2956-7193) and 6915 (5449-8165) (P = 0.0140), respectively, and 6.890 (IQR 4.542-10.89) PHA-specific CD4+ T cells/\u03bcl (P < 0.0001), respectively, and 3.859 (IQR 2.199-5.700) PHA-specific CD8+T cells/\u03bcl (P < 0.0001) . There w+ and CD8+ T cells producing IFN-\u03b3, as previously described [\u03b3 ELISPOT is one of the most widespread assays used to evaluate antigen-specific T cell response. It allows the evaluation of total CD4+ and CD8+ antigen-specific T cell response by detection of IFN-\u03b3-producing T cells. As known, IFN-\u03b3 is a cytokine mainly produced by activated T helper 1 (Th1) and T cytotoxic cells in response to specific antigens, having a crucial role inactivating lymphocytes to enhance antimicrobial and antitumor effects. The traditional ELISPOT assay does not easily distinguish between CD4+ and CD8+ T cell responses unless separate antigens to detect CD4+ and CD8+ T cell responses or lymphocyte subset depletion are used [+ and CD8+ T cells [+ and CD8+ T cell counts, in order to estimate both CD4+ and CD8+ T cells producing IFN-\u03b3, in response to different viral antigens. Even if it does not allow a precise quantification of CD4+ and CD8+ antigen-specific T cell response, our previous results evidenced a good correlation between intracellular cytokine staining and normalized ELISPOT approach [The aim of this study was to evaluate EBV- and HCMV-specific T cell responses by ELISPOT assay. In this setting, we used the normalization on CD4 and CD8 T cells in order to provide an estimation of CD4escribed . As our are used . EBV- an T cells , 34. Resapproach .Among viral pathogens, EBV infection is the most common in patients with SLE, and more importantly, it has been hypothesized that EBV may play a role in SLE disease induction . In a st+ and CD8+ T cell responses to EBV-specific peptide pools were significantly lower in SLE patients compared with controls. Berner et al. demonstrated that the frequency of EBV-specific CD8+ T cells was similar between SLE and healthy subjects when analyzed by using MHC I tetramers with a lytic cycle EBV antigen peptide. However, CD8+ T cell EBV-specific IFN-\u03b3 production was significantly lower in SLE patients than in healthy controls, when assayed by ELISPOT [+ T cell EBV-specific response was provided. In contrast with our results, Kang et al. showed an increased frequency of EBV-specific CD69+ CD4+ T cells producing IFN-\u03b3 in SLE patients compared with controls. However, the frequency of EBV-specific CD69+ CD8+ T cells producing IFN-\u03b3 tended to be lower in SLE patients [Both CD4 ELISPOT . Neverthpatients . These d\u03b3 production upon stimulation with EBNA 1 or EBV early antigen diffuse (EBV-EA/D) in SLE patients, suggesting the decreased control of EBV infection in these subjects [Similarly, Draborg et al. showed a significantly reduced number of activated T cells and IFN-subjects . InteresA few studies \u201339 have + CD4+ T cells producing IFN-\u03b3 and TNF-\u03b1 was similar in SLE patients and healthy controls, while the frequency of HCMV-specific CD69+ CD8+ T cells producing IFN-\u03b3 and TNF-\u03b1 was lower in SLE patients, although the difference was not statistically significant [+ and CD8+ T cell IFN-\u03b3-producing cells.Larsen et al. did not find immune alterations in HCMV-specific T cell responses in SLE patients compared with controls . Anothernificant . On the Analyzing HCMV-specific T cell response in SLE patients according to immunosuppression level, we do not have the evidence of the difference between lp-IS SLE patients and healthy HCMV-seropositive subjects, while mhp-IS patients showed a markedly reduced HCMV-specific T cell response if compared to lp-IS patients as well as to healthy HCMV-seropositive subjects. This could support the role of immunosuppressive treatment in the control of HCMV reactivation.Interestingly, in our study, a significantly lower T cell response to the specific PHA antigen in SLE patients compared with healthy subjects was demonstrated, while other authors have not shown any differences , 38, sug+ and CD8+ T cell responses in SLE patients treated with medium-high immunosuppression. Similarly, HCMV-specific CD4+ and CD8+ T cells had reduced IFN-\u03b3 production in medium-high immunosuppressed SLE patients. On the contrary, there was no difference in terms of PHA-specific T cell response between low and medium-high immunosuppressed SLE patients.In contrast with other studies , 39, we The role of immunosuppressive therapy appears to be crucial mainly to the response to EBV but also to HCMV-specific T cell response. Furthermore, a generally deficient immune response in SLE patients with respect to healthy controls was observed, supporting the hypothesis that SLE disease exerts a general immunosuppressive action regardless of the therapy. To corroborate this hypothesis, virus-specific T cell responses need to be analyzed in a larger number of patients, in order to stratify patients according to immunosuppressive status and iatrogenic risk factors."} +{"text": "The near-complete genome sequence of foot-and-mouth disease virus (FMDV) serotype A potential vaccine strain BAN/CH/Sa-304/2016 is reported here. Its genome revealed antigenic heterogeneity with the current Indian vaccine strain IND40/00, with four amino acid substitutions in antigenically critical sites of the VP1 protein. The near-complete genome sequence of foot-and-mouth disease virus (FMDV) serotype A potential vaccine strain BAN/CH/Sa-304/2016 is reported here. Its genome revealed antigenic heterogeneity with the current Indian vaccine strain IND40/00, with four amino acid substitutions in antigenically critical sites of the VP1 protein. Aphthovirus in the family Picornaviridae. FMDV exists as seven immunologically distinct serotypes with multiple topotypes, lineages, and sublineages (Foot-and-mouth disease (FMD) is a highly contagious disease of domestic and wild cloven-hoofed animals worldwide . Foot-anlineages . Among alineages . All thelineages , 5.r > 0.3) . The serr > 0.3) . The ampr > 0.3) .The near-complete genome of the vaccine candidate BAN/CH/Sa-304/2016 is 8,221 nucleotides (nt) in length, consisting of 53.49% GC content, with a 5\u2032 untranslated region (5\u2032 UTR), coding sequence (CDS), and 3\u2032-UTR region of 1,101, 6,999, and 121 nt, respectively. The CDS codes for a polyprotein 2,332 amino acids (aa) long, containing four structural proteins, VP1 to -4, and eight nonstructural proteins , while the 5\u2032-UTR poly(C) tract and 3\u2032-UTR poly(A) tail are 16 nt and 25 nt long, respectively. Phylogenetically, the isolates BAN/CH/Sa-304/2016 and BAN/CH/Sa-302/2016 clustered in a separate clade closely related to other isolates from Bangladesh and India within genotype VII of the Asia topotype .KJ754939) and 91% with Indian vaccine strain IND40/00 (GenBank accession no. HM854025). The VP1, VP2, and VP3 protein sequences of BAN/CH/Sa-304/2016 had 8%, 6%, and 5% variability, with 16, 12, and 9 aa substitutions compared to the respective regions of vaccine strain IND40/00. Only 4 aa substitutions of VP1 were in antigenically critical sites (59 position of BAN/CH/Sa-304/2016.The homology search in GenBank using BLAST showed that BAN/CH/Sa-304/2016 shares 96% nucleotide similarity with previous serotype A isolate BAN/GA/Sa-197/2013 (GenBank accession no. al sites . One amiWe report here the near-complete genome sequence of FMDV serotype A potential vaccine strain BAN/CH/Sa-304/2016 for FMD control in Bangladesh.MK088171.The near-complete genome sequence of FMDV serotype A strain BAN/CH/Sa-304/2016 has been deposited in the NCBI GenBank database under the accession no."} +{"text": "Trypanosoma equiperdum primarily parasitizes the genital organs and causes dourine in equidae. We isolated a new T. equiperdum strain, T. equiperdum IVM-t1, from the urogenital tract of a horse definitively diagnosed as having dourine in Mongolia. Trypanosoma equiperdum primarily parasitizes the genital organs and causes dourine in equidae. We isolated a new T. equiperdum strain, T. equiperdum IVM-t1, from the urogenital tract of a horse definitively diagnosed as having dourine in Mongolia. Here, we report the whole-genome sequence, the predicted gene models, and their annotations. Trypanosoma equiperdum belongs to the kingdom Protista, phylum Sarcomastigophora, class Zoomastigophorea, order Kinetoplastida, family Trypanosomatidae, genus Trypanosoma, subgenus Trypanozoon together with T. brucei and T. evansi , EthiopiICT2011) , and Ven in 2005 , 2015 (7T. equiperdum strain IVM-t1 isolate was cultivated using Hirumi's modified Isocove's medium-9 (HMI-9) soft-agarose medium at 37\u00b0C in 5% CO2 (T. equiperdum IVM-t1 was extracted and purified using Tris-EDTA (TE)-saturated phenol (Sigma-Aldrich Japan) and phenol-chloroform isoamyl-alcohol solution (Sigma-Aldrich Japan) , a DNA/polymerase binding kit P6 v2, and a DNA sequencing kit 4.0 v2 for PacBio RS II sequencing . The MiSeq sequencer produced 28,337,050 paired-end reads with an average read length of 300\u2009bp, and the PacBio RS II sequencer produced 7,508 reads with an average read length of 8,523\u2009bp . The low-quality reads were trimmed using FastQC v0.11.5 and FASTX-Toolkit v0.0.13.The h Japan) . PurifieT. equiperdum by Metassembler v1.5 (T. equiperdum IVM-t1 were performed using the published genome of T. brucei brucei (T. b. brucei) TREU927 as a reference via the Companion pipeline (https://companion.sanger.ac.uk/) (Whole-genome assembly was performed with ABySS-2.0.2 with parler v1.5 with the.ac.uk/) with defN50 value of 859,849\u2009bp and a cumulative length of 26,988,997\u2009bp (\u224827 Mbp). The T. equiperdum IVM-t1 draft genome contains 7,718 protein-coding genes, 102 noncoding genes, and 2,473 pseudogenes. Following comparison of the predicted genes of T. equiperdum IVM-t1 with the reference gene sets of T. b. brucei TREU927 using OrthoMCL v2.0.7 (T. equiperdum IVM-t1-specific protein-coding genes were identified. Seven short genes that have less than 25 amino acids were not included in the comparison (https://doi.org/10.6084/m9.figshare.7552262.v1).The integrated draft genome consisted of 45 contigs with an L v2.0.7 , 6,831 pT. equiperdum-specific genes.In conclusion, the whole-genome draft assembly produced in the present study provides a resource for future trypanosome genetic studies and identifies some QSBY00000000. The version described in this paper is the first version, QSBY01000000. Raw sequence reads have been deposited in the NCBI SRA database under the accession no. PRJNA477427.This whole-genome project has been deposited in DDBJ/ENA/GenBank under the accession no."} +{"text": "N-methyl-d-aspartate/glutamate receptor (NMDAR) is one of the major voltage-sensitive ligand-gated cation channel. Several noncompetitive NMDAR antagonists contribute to pathophysiology of schizophrenia and mood disorders; however, the effects of inhibition of NMDAR on several transmitter system have not been well clarified. Thus, this study determined the selective NMDAR antagonist, MK801 (dizocilpine), on thalamocortical, mesothalamic, and mesocortical transmissions associated with l-glutamate, GABA, serotonin, norepinephrine, and dopamine using multiprobe microdialysis. Perfusion with MK801 into the medial prefrontal cortex (mPFC) increased and decreased respective regional releases of monoamine and GABA without affecting l-glutamate. The mPFC MK801-induced monoamine release is generated by the regional GABAergic disinhibition. Perfusion with MK801 into the reticular thalamic nucleus (RTN) decreased GABA release in the mediodorsal thalamic nucleus (MDTN) but increased releases of l-glutamate and catecholamine without affecting serotonin in the mPFC. The RTN MK801-induced l-glutamate release in the mPFC was generated by GABAergic disinhibition in the MDTN, but RTN MK801-induced catecholamine release in the mPFC was generated by activation of \u03b1-amino-3-hydroxy-5-methyl-4-isoxazolepropionate/glutamate receptor (AMPAR) which received l-glutamate release from thalamocortical glutamatergic terminals in the mPFC. Perfusion with MK801 into the dorsal raphe nucleus (DRN) decreased GABA release in the DRN but selectively increased serotonin release in the MDTN and mPFC. These DRN MK801-induced serotonin releases in the both mPFC and MDTN were also generated by GABAergic disinhibition in the DRN. These results indicate that the GABAergic disinhibition induced by NMDAR inhibition plays important roles in the MK801-induced releases of l-glutamate and monoamine in thalamic nuclei and cortex. N-methyl-d-aspartate/glutamate receptor (NMDAR) modulation has been a source of scientific discussion in psychiatry and psychopharmacology, since various clinical studies have demonstrated that a noncompetitive NMDAR antagonist, ketamine contributes to pathophysiology of schizophrenia and mood disorders = 20.9 (p < 0.05), FTime = 43.7 (p < 0.05), FMK801*Time = 36.4 (p < 0.05)] = 18.8 (p < 0.05), FTime = 32.0 (p < 0.05), FMK801*Time = 25.9 (p < 0.05)] = 7.4 (p < 0.05), FTime = 56.2 (p < 0.05), FMK801*Time = 22.2 (p < 0.05)] (l-glutamate level in the mPFC (Perfusions with MK801 (1 and 5 \u03bcM) into the mPFC increased regional extracellular levels (mPFC MK801-induced release) of serotonin [F< 0.05)] C, norepi< 0.05)] D and dop< 0.05)] E, but de< 0.05)] B withoutthe mPFC A. Extracthe mPFC C\u2013E; howethe mPFC B. Therefl-glutamate, GABA, serotonin, norepinephrine, or dopamine = 11.4 (p < 0.05), FTime = 74.3 (p < 0.05), FMK801*Time = 17.0 (p < 0.05)]) = 9.1 (p < 0.05), FTime = 65.2 (p < 0.05), FMK801*Time = 12.1 (p < 0.05)] = 7.3 (p < 0.05), FTime = 47.1(p < 0.05), FMK801*Time = 5.3(p < 0.05)] ]) C, norepi< 0.05)] D and dop< 0.05)] E without< 0.05)] B. These l-glutamate release in the mPFC = 16.4 (p < 0.05), FTime = 46.7 (p < 0.05), FMK801*Time = 18.5 (p < 0.05)] = 9.0 (p < 0.05), FTime = 49.2 (p < 0.05), FMK801*Time = 21.3 (p <0.05)] into the RTN increased extracellular levels of < 0.05)] A, norepi< 0.05)] D, and do <0.05)] E without <0.05)] B,C. Extr <0.05)] D,E; howe\u03bcM MK801 A. Therefl-glutamate = 7.2 (p < 0.05), FTime = 21.3 (p < 0.05), FMK801*Time = 7.5 (p < 0.05)] = 9.0 (p < 0.05), FTime = 73.7 (p < 0.05), FMK801*Time = 12.6 (p < 0.05)] into the RTN increased extracellular levels of < 0.05)] A and ser< 0.05)] C, and de< 0.05)] B without< 0.05)] D. The exl-glutamate level was increased by 5 \u03bcM MK801, but not by 1 \u03bcM MK801 and perampanel (AMPAR antagonist) into the MDTN and mPFC on transmitter releases in the mPFC and MDTN induced by 50 \u03bcM MK801 perfusion into the RTN .The specific noradrenergic, dopaminergic and serotonergic terminals from respective LC (locus coeruleus), VTA and DRN project to deeper layers of frontal cortex ,26,33,37A-R agonist) and 1 \u03bcM perampanel (AMPAR antagonist) into MDTN reduced 50 \u03bcM RTN MK801-induced l-glutamate release in the mPFC = 7.5 (p < 0.05), FTime = 65.2 (p < 0.05), FPER*Time = 8.5 (p < 0.05)] and mPFC = 11.6 (p <0.05), FTime = 48.1 (p <0.05), FMus*Time = 17.8 (p <0.05)], but perfusion with 1 \u03bcM muscimol into the mPFC did not affect = 5.0 (p < 0.05), FTime = 107.2 (p < 0.05), FPER*Time = 9.8 (p < 0.05)] and mPFC = 5.3 (p < 0.05), FTime = 87.2 (p < 0.05), FMus*Time = 22.7 (p < 0.05)], but perfusion with muscimol into the mPFC did not affect (Contrary to < 0.05)] D. Perfust affect D. Simila< 0.05)] E. Perfust affect E.l-glutamate release in the mPFC is generated by the GABAergic disinhibition and relatively activation of AMPAR in the MDTN, but is not modulated by these receptors in the mPFC. Contrary to l-glutamate, RTN MK801-induced catecholamine release in the mPFC is regulated by the GABAergic disinhibition in the MDTN, and activation of AMPAR in the MDTN and mPFC, but is not modulated by GABAA-R in the mPFC. Therefore, RTN MK801-induced catecholamine release in the mPFC is activated by AMPAR in the mPFC via activation of thalamocortical glutamatergic transmission.These results suggest that RTN MK801-induced A-R agonist) into MDTN reduced 50 \u03bcM RTN MK801-induced l-glutamate release in the MDTN, whereas perfusion with 1 \u03bcM perampanel (AMPAR antagonist) into the MDTN did not affect was regulated by independent system compared with other catecholamine, since serotonin release in the mPFC is not affected by thalamocortical glutamatergic transmission, but conversely mesothalamic serotonergic transmission possibly affects thalamocortical glutamatergic pathway in the MDTN . To clarMK801 = 16.8 (p < 0.05), FTime = 42.9 (p < 0.05), FMK801*Time = 16.1 (p < 0.05)] into the DRN concentration-dependently increased extracellular serotonin level in the mPFC [F< 0.05)] C withoutdopamine A,B,D,E. dopamine C. TherefMK801 = 41.9 (p < 0.05), FTime = 63.8 (p < 0.05), FMK801*Time = 24.0 (p < 0.05)] ] C withoutdopamine A,B,D,E. MK801 = 11.6 (p < 0.05), FTime = 26.0 (p < 0.05), FMK801*Time = 6.3 (p < 0.05)] into the DRN concentration-dependently increased extracellular serotonin level in the MDTN [F< 0.05)] C withoutdopamine A,B,D. Exdopamine C. Our prMK801 = 21.5 (p < 0.05), FTime = 36.3 (p < 0.05), FMK801*Time = 6.1 (p < 0.05)] ] C. TherefMK801 = 13.6 (p < 0.05), FTime = 53.3 (p < 0.05), FMK801*Time = 15.8 (p < 0.05)] = 9.9 (p < 0.05), FTime = 42.9 (p < 0.05), FMK801*Time = 12.1 (p < 0.05)] into the DRN concentration-dependently increased and decreased extracellular levels of serotonin [F< 0.05)] C and GAB< 0.05)] B in the the DRN A,D,E. Ex the DRN B,C. TherMK801 = 22.0 (p < 0.05), FTime = 42.0 (p < 0.05), FMK801*Time = 6.1 (p < 0.05)] ] C, wherea< 0.05)] B. These The threshold concentration of local administration (perfusion) of MK801 into the mPFC, MDTN, RTN, and DRN on several transmission systems demonstrated by this study and previous reports ,16,17,20l-glutamate, GABA, serotonin, norepinephrine and dopamine in the mPFC, MDTN and DRN. According to the results in this study and published neural circuits [The present study also demonstrated the presence of several regulatory systems in the thalamocortical (RTN-MDTN-mPFC) glutamatergic, mesothalamic (DRN-MDTN), and mesocortical (DRN-mPFC) serotonergic pathways controlling releases of circuits ,38,39,40l-glutamate release [A-R in the mPFC (perfusion with 1 \u03bcM muscimol into the mPFC). Therefore, inhibition of NMDAR in the mPFC increases monoamine release induced by presynaptic GABAergic disinhibition in the mPFC. Indeed, the threshold concentrations of local administration of MK801 into the mPFC on GABA release (1 \u03bcM) is more sensitive compared with that of monoamine (5 \u03bcM) .l-glutamate, norepinephrine and dopamine in the mPFC without affecting those of GABA or serotonin. The threshold concentration of local administration of MK801 into the RTN on releases of l-glutamate and catecholamine (norepinephrine and dopamine) in the mPFC were 1 \u03bcM and 5 \u03bcM, respectively. The RTN MK801-induced l-glutamate release in the mPFC was inhibited by the activation of GABAA-R and inhibition of AMPAR in the MDTN, but was not affected by the activation of GABAA-R or inhibition of AMPAR in the mPFC. These results suggest that an activation of glutamatergic neuronal activity induced by GABAergic disinhibition in the MDTN contributes to RTN MK801-induced l-glutamate release in the mPFC.Contrary to intra mPFC regulation system, local administration of MK801 into the RTN increased releases of l-glutamate release in the mPFC is thalamocortical (from MDTN to mPFC) glutamatergic pathway, but generating mechanisms is GABAergic disinhibition from RTN to MDTN through NMDAR inhibition in the RTN.Various thalamic nuclei, which receive GABAergic inhibition from RTN , projectl-glutamate release, the RTN MK801-induced catecholamine release in the mPFC was inhibited by the activation of GABAA-R in the MDTN, inhibition of AMPAR in the MDTN and mPFC, but was not affected by the activation of GABAA-R in the mPFC. Electrophysiological study demonstrated that electrical stimulation of the MDTN increased the releases of glutamate and catecholamine in the mPFC without affecting those of serotonin [Contrary to erotonin . Other lerotonin ,24,40. Terotonin ,24. TakeThis study indicates the several specific regulation systems of serotonergic transmission in the mPFC and MDTN which are independent upon catecholamine release regulation system. The first, intra mPFC regulation of serotonergic transmission associated with NMDAR is resembling to the regulation systems of catecholaminergic transmission, since the selective noradrenergic, dopaminergic and serotonergic terminals in the deeper layers of mPFC receive GABAergic inhibition. However, the serotonergic terminal in the mPFC from DRN does not contact with thalamocortical glutamatergic afferents, whereas mesothalamic serotonergic transmission activates thalamocortical glutamatergic transmission, since an activation of serotonergic neuronal activities in the DRN increases serotonin release in the MDTN. Recent multiprobe microdialysis studies demonstrated that an activation of serotonergic neuronal activity enhances MDTN glutamatergic neurons through activation of excitatory 5-HT7 receptor in the MDTN ,16. In tA-R predominantly, as indicated by decreased regional serotonin release following local administration of muscimol (GABAA-R agonist) into the DRN; however, GABA release is regulated by excitatory 5-HT7 receptor, reflecting decreased regional GABA release following local perfusions with SB269970 (5-HT7R antagonist) into the DRN [A-R and 5-HT7R predominantly inhibit serotonergic neurons and enhance GABAergic neurons, respectively. In the present study, local administration of MK801 into the DRN, decreased and increased releases of GABA and serotonin in the DRN, respectively. The opposite effects of MK801 between releases of GABA and serotonin were inhibited by local administration of muscimol in the DRN. Therefore, NMDAR in the DRN regulates predominantly GABAergic neurons rather than serotonergic neuronal activity in the DRN.In the DRN, serotonin release is regulated by inhibitory GABA the DRN . Previou the DRN . In cont the DRN . Taken wThe present study demonstrated that inhibition of NMDAR directly inhibited GABAergic transmission, but enhanced indirectly glutamatergic and monoaminergic transmissions induced by GABAergic disinhibition. In other words, during resting stage, MK801 selectively inhibits NMDAR on GABAergic neurons, but cannot affect NMDAR on the glutamatergic or monoaminergic neurons. In generally, GABAergic interneuron is more sensitive to NMDAR antagonist compared with other types of neurons, since the resting membrane potential of GABAergic interneurons are more positive (\u221250 ~\u221260 mV) rather than those of monoaminergic and glutamatergic neurons ,44. NMDAIn this study, the threshold concentrations of local administrations of MK801 into the mPFC, RTN and DRN on regional GABAergic transmission were almost equal to be 1 \u03bcM. Contrary to GABA, the threshold concentrations of local administration of MK801 into the mPFC and RTN on catecholamine release in the mPFC were 5 \u03bcM, whereas those into mPFC and DRN on serotonin release in the mPFC were 5 \u03bcM and 1 \u03bcM, respectively. Therefore, serotonergic transmission is more sensitive to NMDAR antagonist rather than other catecholaminergic transmissions in the mPFC.Subanesthetic doses of ketamine produces transient dissociative and psychotomimetic effects that resemble the positive and negative symptoms of schizophrenia ; howeverR)-ketamine into the infralimbic mPFC and hippocampus also produced antidepressant-like action [R)-ketamine into the prelimbic mPFC nucleus accumbens could not produce [R)-ketamine. Moreover, the binding affinity of (S)-ketamine and (R)-ketamine to NMDAR are 0.7 and 2.6 \u03bcM, respectively [S)-ketamine is potent than that of (R)-ketamine [Neither clinical mechanisms between psychotomimetic and antidepressant effects of ketamine have remained to be clarified. Local administration of ketamine into the infralimbic mPFC reproduced the antidepressant-like actions of systemic ketamine administration . Local ae action , whereas produce . These fectively . Indeed,ketamine . The MK8ketamine . Clinicaketamine ,57. Thesketamine .l-glutamate and secondary catecholamine release in the mPFC, suggests that lower concentration of MK801 affects emotional rather than cognitive disturbances. In the present study, inhibition of AMPAR in the MDTN and mPFC attenuated the MK801-induced glutamatergic and monoaminergic transmissions without affecting GABAergic disinhibition. Several preclinical studies reported the possibility that NMDAR inhibition conversely activates glutamatergic transmission associated with AMPAR through GABAergic disinhibition [The thalamocortical glutamatergic transmission plays important roles in the function of neuro-cognition, including learning, memory, and perceptual integration ,59,60. Thibition ,65. In shibition , whereashibition . The detl-glutamate release in the mPFC activates AMPAR on the regional co-releasing terminals resulting in an increase in releases of norepinephrine and dopamine, but does not affect serotonin release. Inhibition of NMDAR in the DRN enhances serotonin release in the DRN, MDTN and mPFC via GABAergic disinhibition in the DRN. The sensitivities of serotonin release in the mPFC to local administration of MK801 into the DRN is more predominant rather than that of catecholamine release in the mPFC induced by local MK801 administration into the RTN.The present study determined the effects of MK801 on the thalamocortical (RTN-MDTN-mPFC) glutamatergic, mesothalamic (DRN-MDTN), and mesocortical (DRN-mPFC) serotonergic transmissions using multiprobe microdialysis, to clarify the NMDAR associated regulation systems in these three pathways. Inhibition of NMDAR in the RTN activates thalamocortical glutamatergic transmission induced by GABAergic inhibition and secondarily activated AMPAR in the MDTN. The enhanced"} +{"text": "Of note, abdominal fat tissue of obese pre-DM patients treated with metformin therapy presented higher SIRT6 expression and lower NF-\u03baB, PPAR-\u03b3, and SREBP-1 expression levels compared to pre-DM control group. Collectively, results show that SIRT6 is involved in the inflammatory pathway of subcutaneous abdominal fat of obese pre-DM patients and its expression responds to metformin therapy.The role of sirtuin 6 (SIRT6) in adipose abdominal tissue of pre-diabetic (pre-DM) patients is poorly known. Here, we evaluated SIRT6 expression in visceral abdominal fat of obese pre-diabetic patients and the potential effects of metformin therapy. Results indicated that obese pre-DM subjects showed low SIRT6 protein expression and high expression of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-\u03baB), peroxisome proliferator-activated receptor gamma (PPAR-\u03b3), and sterol regulatory element-binding transcription factor 1 (SREBP-1). Obese pre-DM patients showed high values of glucose, insulin resistance (HOMA-IR), C reactive protein (CRP), nitrotyrosine, tumor necrosis factor-\u03b1 (TNF-\u03b1) and interleukin 6 (IL-6), and low values of insulin ( Visceral fat and superficial adipose tissue of obese patients express cytokines cross-talking with the cardiovascular system . It has p < 0.05) (p < 0.05), lower values of insulin (p < 0.05), and higher values of HOMA-IR (p < 0.05) than NG obese patients (group 1) (p < 0.05), inflammatory markers, such as CRP (p < 0.05), IL-6 (p < 0.05), TNF-\u03b1 (p < 0.05), and nitrotyrosine (p < 0.05), than NG obese patients (group 1) (p < 0.05) . Obese pgroup 1) . Moreovegroup 1) . The sam < 0.05) .p < 0.01). Obese pre-DM not-metformin users presented lower values of SIRT6 (p < 0.01 vs. NG) and higher values of NF-\u03baB, PPAR-\u03b3 and SREBP-1 (p < 0.01 vs. NG) (p < 0.05) and lower values of NF-\u03baB, PPAR-\u03b3, and SREBP-1 protein levels (p < 0.05) compared to obese pre-DM not-metformin users . Moreovein users . p < 0.05). However, a regulatory effect on SIRT6 expression might be the main determinant of oxidative stress and nitrotyrosine reduction in pre-DM receiving an anti-oxidative drug therapy with metformin buffer, 30 mM Tris-HCl, pH 8.8. Tissues were homogenized with a Precellys-24 system and centrifuged at 800\u00d7 p < 0.05 was considered significant. Statistical analysis was performed using the SPSS software package for Windows 17.0 .Data were presented as group mean \u00b1 SD. One-way analysis of variance (ANOVA) was used to compare baseline data, followed by Scheffe\u2019s test for pairwise comparisons. Simple and partial correlation were used to evaluate relationships between variables."} +{"text": "Eggerthellaceae within the class Coriobacteriia (phylum Actinobacteria), Adlercreutzia muris WCA-131-CoC-2 (= DSM 29508 = KCTC 15543) and Ellagibacter urolithinifaciens CEBAS 4A (= CCUG 70284 = DSM 104140).Here, we report the annotated draft genome sequences of two type strains belonging to the family Eggerthellaceae within the class Coriobacteriia (phylum Actinobacteria), Adlercreutzia muris WCA-131-CoC-2 (= DSM 29508 = KCTC 15543) and Ellagibacter urolithinifaciens CEBAS 4A (= CCUG 70284 = DSM 104140).Here, we report the annotated draft genome sequences of two type strains belonging to the family Eggerthellaceae are typical members of the mammalian gut and have been isolated from, e.g., humans under anaerobic conditions of N2-CO2 (80:20) in flushed brain heart infusion medium (Merck) supplemented with 0.5% yeast extract, 0.05% l-cysteine monohydrochloride (Roth), 1\u2009mg ml\u22121 resazurin sodium salt, 2.5\u2009mg liter\u22121 heme solution, and 2\u2009\u03bcg ml\u22121 vitamin K1 solution (Sigma-Aldrich). Ellagibacter urolithinifaciens DSM 104140T was cultured (37\u00b0C) under anaerobic conditions of N2-CO2 (80:20) in flushed anaerobe basal broth (Oxoid). DNA extraction was done using a Qiagen blood and tissue kit. DNA was quantified with a double-stranded DNA (dsDNA) high-sensitivity (HS) assay on a Qubit version 2.0 fluorometer (Thermo Fisher Scientific), according to the manufacturer\u2019s instructions, and adjusted to a concentration of 0.2\u2009ng \u03bcl\u22121.The following type strains were obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ): escribed , 13. AdlA. muris DSM 29508T, while 1,067,866 reads were generated for E. urolithinifaciens DSM 104140T. Data processing was done as previously described using a BLASTn search . Whole-genome shotgun sequencing was performed on an Illumina MiSeq benchtop sequencer using a 500-cycle v2 kit . In total, 1,469,853 reads were generated for escribed , 13. Seqescribed , 16. The 2.3.3.1 . To elimn search . All conn search . To calcPipeline . The assPipeline was usedA. muris DSM 29508T and E. urolithinifaciens DSM 104140T, has been deposited at DDBJ/ENA/GenBank under BioProject number PRJNA574580. The versions described in this publication are the first versions and are listed in A. muris DSM 29508T have been deposited under SRA accession number SRX6974936, while the raw reads of E. urolithinifaciens DSM 104140T have been deposited under accession number SRX6974937.This whole-genome shotgun project, including raw reads of"} +{"text": "This study explores associations between frailty and oral health in cross-sectional data of 1,202 community-dwelling older people. Two dichotomous outcomes were used: 1. Potential frailty, using routine primary care data; 2. Self-reported frailty, using a questionnaire. Oral health concerned dental record data and self-reported oral problems. Following exploration of univariate associations, age and sex adjusted multivariate logistic regressions were performed. For potential frailty and self-reported frailty associations were found with dental emergency visit (odds ratio (OR)= 2.0, 95% confidence Interval (CI)=1.33;3.02 respectively OR=1.58, 95% CI=1.00;2.49), experiencing oral problems , making dietary adjustments . Additional associations were found for self-reported frailty with wearing dental prosthesis and missing periodontal information . The cross-sectional data of this study show that in community dwelling older people oral health is associated with frailty."} +{"text": "Scientific Reports 10.1038/s41598-019-38633-4, published online 14 February 2019Correction to: This Article contains an error in the Figure legends of Figures 2 and 3 which have been inadvertently reversed.The correct legend for Figure 2 is:A) Map of specimens CUE JJ_M01-3 showing four-track Minisauripus trackway, and additional isolated fifth track on small unconnected slab. Map based on counterpart cast of track-bearing surface. Red outline shows part of surface preserved as natural impressions. Pterosaur manus tracks, desiccation cracks (stippled areas), raindrop impressions and invertebrate traces also shown. Compare with Fig. 2 and text for details. (B) Shows microstratigraphy of part and counterpart of track-bearing slab. (C) Shows four track-trackway with dashed line to highlight steps and pace angulations. See Table 1 for measurements. Map made by M. G. Lockley and K-S Kim with layout created in Canvas X .\u201d\u201c Counterpart slab CUE JJ_M01 showing trackway with four consecutive Minisauripus track casts TL1-TR2. (B) Natural impression slab (CUE JJ_M02) showing tracks TL2 and TR2. (C) Isolated track specimen (CUE JJ_M03). Compare with Fig. 3. Photographs by K-S Kim and layout created in Canvas X .\u201d\u201c("} +{"text": "Rhodomyrtus tomentosa, which belongs to the Myrtaceae family. In the current study, we investigated the properties of rhodomyrtone as a potential drug candidate for the treatment of stress-caused depression.Rhodomyrtone is one of the main active compounds derived from We assessed the function of rhodomyrtone in chronic unpredictable mild stress, a well-validated depression model in mice. Depression-like behavior tests, including a sucrose performance test, social interaction test, and forced swimming test, were used to validate the antidepressant effects of rhodomyrtone. The Morris water maze was used to evaluate the mice\u2019s learning and memory ability. Spine density, glycogen synthase kinase-3\u03b2, brain-derived neurotrophic factor, postsynaptic density protein 95, and apoptosis-associated protein were detected to reveal the underlying mechanism.Rhodomyrtone was found to prevent source consumption decrease, decreased social behaviors, and increase immobility in the forced swimming test, suggesting a protective effect of rhodomyrtone against depression-like behaviors. Additionally, rhodomyrtone prevented the impairment of spatial memory in mice exposed to chronic unpredictable mild stress. Rhodomyrtone administration also reversed dendritic spine density defects in chronic unpredictable mild stress. Furthermore, rhodomyrtone inhibited the increase of glycogen synthase kinase-3\u03b2 activity and reversed the decrease of brain-derived neurotrophic factor and postsynaptic density protein 95 in chronic unpredictable mild stress mice. Elevated expression of apoptosis-associated protein Bax and cleaved-caspase 3 was also reversed by rhodomyrtone treatment.These results suggested that the antidepressant effect of rhodomyrtone involves the regulation of neurogenesis, neuronal survival, and synaptic plasticity in the hippocampus. We identified a protection effect of rhodomyrtone against depression-like behaviors in a well-validated depression model in mice. Rhodomyrtone administration can prevent increase of depression-like behaviors, impairment of cognitive abilities, and morphological changes in dendritic spines in CUMS model mice. Rhodomyrtone also prevents CUMS-induced changes in depression-related proteins, including GSK3 activity, BDNF expression, Bax activity, and caspase-3 cleavage. These observations indicate that rhodomyrtone exhibits antidepressant activity involving the promotion of neurogenesis and neuronal survival in the hippocampus.As one of the common mood disorders, depression is correlated with stressful events in life . The cliRhodomyrtus tomentosa, belongs to the acylphloroglucinol derivative family. R. tomentosa has been used in traditional medicine for the treatment of many diseases and used in the current study. Standard chow and water were supplied ad libitum. Mice were housed in a temperature-controlled (20\u00b0C\u00b11\u00b0C) room with a normal 12-h-light/-dark cycle, with the lights on at 7:00 Mice in CUMS+vehicle and CUMS+rhodomyrtone groups were exposed to CUMS as described previously . InitialThe SPT wAn adult The mouseSpatial learning and memory were assessed by the Morris water maze (MWM) . The MWMGolgi staining was performed using a GolgiStain kit according to the protocol provided by the manufacturer on ice. Each sample of lysates (20 \u03bcL) was added into SDS-PAGE and electroblotted onto PVDF membranes, blocked by 5% bovine serum albumin, and incubated with primary antibodies overnight at 4\u00b0C, including postsynaptic density protein 95 (PSD-95) , cleaved caspase-3 , caspase3 , brain-derived neurotrophic factor (BDNF) , glycogen synthase kinase-3\u03b2 (GSK3\u03b2) , p-GSK3\u03b2 , Bax (BD), and \u03b2-actin (Sigma). Secondary antibodies were purchased from Sigma.Rhodomyrtone was i.p. injected at 15 mg/kg. The dosages were chosen based on the behavioral results from the 5-mg/kg (low dosage), 15-mg/kg (high dosage 1), and 45-mg/kg (high dosage 2) groups . RhodomyTwo-way ANOVA was used to analyze the effects of exposure to the CUMS protocol and rhodomyrtone treatment, and a posthoc Tukey\u2019s test was conducted. All values were expressed as mean\u00b1SEM.F=10.38, CUMS: F=38, 72, Rho: F=17.21, all P<.05; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.01; F=19.72, CUMS: F=14.23, Rho: F=26.02, all P<.05; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.01; F=12.65, P<.01; F=8.41, P<.01; Rho: F=2.66, P=.11; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.01; To investigate the protective effects of rhodomyrtone on CUMS-induced depression, mice were exposed to CUMS protocol for 35 days, and rhodomyrtone or vehicle saline was i.p. injected daily during the last 3 weeks. Meanwhile, mice from vehicle control and rhodomyrtone control group were group-housed with no stress and were i.p. injected with vehicle or rhodomyrtone . DepressF=10.27, P<.01; day 3 interaction: F=15.47, P<.01; day 4 interaction: F=47.60, P<.001; F=0.49, P=.48; F=2.20, P=.15; CUMS: F=13.36, P<.01; rhodomyrtone: F=7.38, P<.05; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.05; 2-way ANOVA; F=8.45, P<.01; CUMS: F=11.25, P<.01; rhodomyrtone: F=7.2, P<.05; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.01; To investigate whether rhodomyrtone could protect against impaired spatial cognition performance in the CUMS group, the MWM task was performed. The escape latency improved in all 4 groups with trial training. However, mice in the CUMS group spent more time to locate the hidden platform during the training. Interestingly, rhodomyrtone treatment significantly improved the latency time of CUMS mice =4.39, P<.05; CUMS: F=12.93, P<.01; rhodomyrtone: F=4.39, P<.05; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.05; Alterations in synaptic and dendritic structure and function are associated with impaired learning and memory in depressive disorders . We deteF=8.01, P<.01; CUMS: F=25.83, P<.01; rhodomyrtone: F=10.59, P<.01; posthoc Tukey\u2019s tests found CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.01; F=2.12, P=.155; CUMS: F=58.38, P<.01; rhodomyrtone: F=7.08, P<.05; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.05; F=0.48, P=.49; CUMS: F=24.26, P<.01; rhodomyrtone: F=9.02, P<.01; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.01; Numerous studies have shown that abnormal activity of GSK3\u03b2 has multiple effects and is correlated with the severity of depressive symptoms, including neurogenesis defects . Thus, wF=6.21, P<.05; CUMS: F=10.05, P<.01; rhodomyrtone: F=2.23, P>.05; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.05; F=10.75, P<.01; CUMS: F =13.90, P<.01; rhodomyrtone: F=7.59, P<.01; posthoc Tukey\u2019s test CUMS+Veh. vs Control+Veh., P<.01; CUMS+Rho. vs CUMS+Control, P<.01; Volume decrease of the hippocampus in depression is associated with a reduction of neuronal cell body size and increased neural apoptosis in depression patients . AntidepIn the current study, we found that rhodomyrtone exhibited antidepressant activity in a mouse CUMS model. We observed that rhodomyrtone administration protected against CUMS-caused, depression-like behaviors and cognitive defects. Further, CUMS-decreased spine density was reversed by rhodomyrtone treatment. Impairment of neurogenesis and increase of apoptosis are 2 potential mechanisms of depression. We found that rhodomyrtone reversed the CUMS-induced changes in GSK3\u03b2 activity and BDNF expression level, 2 essential regulators of hippocampal neurogenesis. The activation of apoptosis-related protein Bax and caspase-3 was also reversed by rhodomyrtone treatment. Our findings demonstrated the antidepressant-like effects of rhodomyrtone through regulation of neurogenesis and apoptosis in a classic depressive mouse model induced by CUMS. Studies also showed that rhodomyrtone exhibits antibacterial, anticancer, antiinflammatory, and antioxidant activities . Here, tIt has been reported that defects in emotional memory and spatial learning are key characteristics of depression besides depression-like behaviors . The hipHippocampus shrinkage has been observed in both depressive patients and animal models . InteresAnother important explanation for hippocampus shrinkage is increased apoptosis . ChronicIn summary, for the first time to our knowledge, we showed that rhodomyrtone exhibits antidepressant-like activity in a mouse depression model. Rhodomyrtone can prevent CUMS-induced increase of depression-like behaviors, impairment of cognitive abilities, and morphological changes in dendritic spines. Rhodomyrtone also prevents CUMS-induced changes in GSK3 activation, BDNF expression, Bax activation, and caspase-3 cleavage. These observations indicate that rhodomyrtone has antidepressant effects involving the promotion of neurogenesis and neuronal survival in the hippocampus.None.Supplementary Figure 1Click here for additional data file.Supplementary MaterialClick here for additional data file."} +{"text": "Arabidopsis NBS genes revealed a clade-specific nesting pattern in CNLs, with RNLs nested in the CNL-A clade, and species-specific nesting pattern for TNLs. Surprisingly, we found a moderate bootstrap support (BS = 50%) for CNL-A clade being nested within TNL clade making both the CNL and TNL clades paraphyletic. Arabidopsis and sunflower showed 87 syntenic blocks with 1049 high synteny hits between chromosome 5 of Arabidopsis and chromosome 6 of sunflower. Expression data revealed functional divergence of the NBS genes with basal level tissue-specific expression. This study represents the first genome-wide identification of NBS genes in sunflower paving avenues for functional characterization and potential crop improvement.Nucleotide Binding Site\u2014Leucine-Rich Repeat (NBS-LRR) genes encode disease resistance proteins involved in plants\u2019 defense against their pathogens. Although sunflower is affected by many diseases, only a few molecular details have been uncovered regarding pathogenesis and resistance mechanisms. Recent availability of sunflower whole genome sequences in publicly accessible databases allowed us to accomplish a genome-wide identification of Toll-interleukin-1 receptor-like Nucleotide-binding site Leucine-rich repeat (TNL), Coiled Coil (CC)-NBS-LRR (CNL), Resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) and NBS-LRR (NL) protein encoding genes. Hidden Markov Model (HMM) profiling of 52,243 putative protein sequences from sunflower resulted in 352 NBS-encoding genes, among which 100 genes belong to CNL group including 64 genes with RX_CC like domain, 77 to TNL, 13 to RNL, and 162 belong to NL group. We also identified signal peptides and nuclear localization signals present in the identified genes and their homologs. We found that NBS genes were located on all chromosomes and formed 75 gene clusters, one-third of which were located on chromosome 13. Phylogenetic analyses between sunflower and CNL-C (I) clade, sister clade to CNL-C (II) and CNL-D constituted 79 genes. CNL-B clade constituted three genes . The remaining 12 genes did not belong to any clade of Arabidopsis CNL genes. The TNL group formed a species-specific clade, except ten genes that formed a small clade with AT5G36930, named TNL-D clade with strong bootstrap support of 100%. We found a moderate bootstrap support (BS = 50%) for CNL-A clade being nested within TNL clade making both the CNL and TNL clades paraphyletic. Another tree constructed using RNL genes of A. thaliana and H. annuus showed two distinct clades for two lineages: activated disease resistance gene 1 (ADR1) and N-required gene 1 (NRG1) was used in phylogenetic analyses. Phylogenetic relationships among the sunflower NBS sequences are shown in NL group . The nes1 (NRG1) . The Newhomologs . The synbidopsis .H. annuus clone Ha-NTIR11g CC-NBS-LRR gene (Pl8). HanXRQChr13g0425411, HanXRQChr13g0425361, and HanXRQChr13g0425431 showed more than an 80% identity to the Pl8 gene suggesting the probable homologs to that gene. HanXRQChr04g0123041, belonging to the NL group has shown homology to Lycopersicon esculentum EIX receptor 1 (LeEIX1), a gene that encodes receptor-like proteins (RLPs). Similarly, HanXRQChr17g0552491 showed homology to MLA10, HanXRQChr13g0420141 to N, HanXRQChr17g0552491 to both MLA12 and MLA13 and HanXRQChr17g0552491 to Sr33 protein with greater than 60% identity. Sunflower Genome Database with H. annuus r1 annotations was employed to obtain expression data for predicted NBS genes. We compared accessions of H. annuus r1.2 annotations to H. annuus r1 to obtain the expression data for NBS proteins. Since there were many duplicates for H. annuus r1.2 annotations, we used only the sequences with the unique names. The raw Read Per Kilobase Million) (RPKM) values of gene expression were downloaded separately. The expression values were from bract, corolla, leaves, ligule, ovary, pollen, seed, stamen and stem. Only expression data for 9 CNL type, 33 TNL type, 23 NL type and 6 RNL type genes were retrieved from the database and employed to generate heatmap after deseq normalization of the data using MeV package [Arabidopsis (~0.43%) [C. sativus (~0.21%) [Carica papaya (~0.21%) [P. vulgaris (~1.19%) [Manihot esculenta (~0.9%) [V. vinifera (~1.3%) [G. max (~0.73%) [Our findings on the NBS-encoding genes in this study is based on recently sequenced sunflower genome . Previoual. 2004 identifial. 2008 identifi(~0.66%) . This nu(~0.43%) , C. sati(~0.21%) , Carica (~0.21%) and lowe(~1.19%) , Manihot (~0.9%) , V. vini (~1.3%) , and G. (~0.73%) ,24. We p(~0.73%) , Plocik (~0.73%) , and Rad(~0.73%) showed 7A. thaliana (1:2), A. lyrata (1:2), B. rapa (1:2), Eucalyptus grandis (1:1.25), and Thellungiella salsuginea (1:1.5) as numbers of TNLs were higher than CNLs in these species [M. truncatula, A. thaliana, and B. rapa [A. thaliana and B. rapa [Following the classification of NBS genes by Shao et al. 2016 and Yu e species ,65,66,67 species ,57. The B. rapa ,27. HanX B. rapa .S. tuberosum [A. thaliana, P. vulgaris, G. max, and P. trichocarpa [P. trichocarpa [B. rapa [A. thaliana, P. trichocarpa, and O. sativa [NBS-encoding genes also called NBS-LRR genes encode proteins having TIR/CC at the N-terminal, NBS domain in the center and LRR at the C-terminal . Among tuberosum . All TIRchocarpa ,24,63,69chocarpa . All of [B. rapa . Kelch m. sativa .Arabidopsis CLAVATA2 [Cladosporium fulvum in tomato [We further compared our pipeline with another pipeline, RGAugury , for theAtRLP10) is involn tomato .M. esculenta, 143 NBS genes positioned in 39 clusters [C. sativus, 33 NBS genes were located in nine clusters [B. oleracea (3.04), B. rapa (2.7), A. thaliana (2.8) [G. max (4), V. vinifera (6), M. truncatula (5) [Gossypium species such as G. arboretum (3.4), G. raimondii (5.5), G. hirsutum (5.3), and G. barbadense (3.5) [Arabidopsis [aK/sK values of less than one, indicating that these genes are under the influence of purifying selection.A variety of clustering patterns of NBS-encoding genes, frequently observed in almost all plant species, is one of the major reasons for rapid evolution of the NBS genes ,79. The clusters . In C. sclusters , Brassicna (2.8) , Fabaceatula (5) , Gossypise (3.5) . Both sese (3.5) . HoweverC. sativus CNL genes while compared to their respective TNL genes [Arabidopsis, as TNL clades constitute larger numbers of genes than CNL clade [HanXRQChr02g0057361, HanXRQChr02g0057351, and HanXRQChr13g0425771 in the subclade CC (VI) possessed in the range of five to seven. Similarly, subclade TIR (II) possessed gene members with introns in the lowest range (three to five). TIR (I), TIR (III), TIR (IV), TIR (V) and TIR (VI) gene members possessed introns in range of 3 to 17, 2 to 7, 1 to six, 1 to 15, and 1 to 13, respectively. Similar patterns were also observed in the phylogenetic tree of CNL and TNL in C. sativus [Sunflower CNL genes were similar to NL genes . HoweverNL clade . Subclad sativus . The dif sativus . In addi sativus .H. annuus in the analysis as the genome was not available by then. Our results indicate a surprising position of RNLs within TNLs in sunflower making the clades of TNL and CNL potentially paraphyletic. Upon reconstruction of the phylogenetic tree with Arabidopsis NBS genes, RNL genes of sunflower were observed in a CNL-A clade [ADR1 and NRG1, and two ancient lineages separated before the Angiosperms diversified. The RNL genes, ADR1 and NRG1, have been characterized in Arabidopsis and Nicotiana, respectively. A separate tree, constructed to observe the relationships among sunflower RNLs and Arabidopsis RNLs, formed two clades. The sunflower RNL genes HanXRQChr02g0046611 and HanXRQChr05g0129181 were nested with AT4G3330 (ADR1-L1), AT1G33560 (ADR1) and AT5G04720 (ADR1-L2 or PHX21), with bootstrap support of 90%. On the other hand, HanXRQChr02g0048181, HanXRQChr11g0331571, HanXRQChr03g0067681, HanXRQChr0073241, and HanXRQChr04g0095241 were nested with AT5G66630 (RNL) and AT5G66910 (homologous to NRG1), with bootstrap support of 63%. This suggests that the sunflower RNLs mentioned above are orthologous to the ADR1 and NRG1 homologs of Arabidopsis. ADR1 proteins play a role as helper genes for receiving signals from the R genes in downstream signaling of effector-triggered immunity [A. lyrata (2.5%), A. thaliana (4.2%), B. rapa (4.4%), Capsella rubella (4.7%) and T. salsuginea (5.7%) [a/KsK ratios values for the clade. This supports the hypothesis of high conservation and slow evolutionary rates among the RNL genes [We found that RNLs were nested within the clade of TNLs in sunflower (a member of the Asterids lineage) although RNLs in the families Brassicaceae and Fabaceae (Rosids lineage) were found to be related to CNLs ,30. The s study) . The CNLs study) suggesteimmunity . Similarimmunity . Since timmunity . Only 5.NL genes .S. tuberosum nematode resistance protein (Gro1.4) [S. tuberosum subsp. andigena RY-1 (conferring resistance to potato virus Y) [N. glutinosa Tobacco Mosaic Virus resistance (N) gene [A. thaliana RPS2 (Resistant to P. syringae 2) [Cucumis melo VAT (resistance to Aphis gossypii) [H. annuus Pl8 [O. sativa Pi36 (conferring resistance to Blast fungus) [H. vulgare subsp. vulgare RPG1 (conferring resistance to stem rust fungus) [http://www.prgdb.org has shown some of them to be the possible homologs of the reference proteins . The Pl8 gene is involved in conferring resistance to P. halstedii, a causative agent to downy mildew [L. esculentum EIX receptor 2 (Eix2), a gene that encodes receptor-like proteins (RLPs) involved in detecting ethylene-inducing xylanase, a fungus elicitor [MLA locus is highly polymorphic and encode allelic CNL type resistance proteins such as MLA1, MLA2, and MLA3 that confer resistance to barley powdery mildew fungus [Puccinia graminis f. sp. tritici [H. annuus r1.2 annotations compared to H. annuus r1 annotations. From the available expression data, it can be deduced that NBS genes can be expressed at a basal level with tissue specificity in unchallenged conditions [Sunflower NBS proteins identified in this study formed clades with reference proteins such as Pi36, Pl8, Rps2, VAT, RPG1, Gro1.4, RY-1, and N proteins, suggesting their homologous relationships . The sun(Gro1.4) , S. tubevirus Y) , and N. (N) gene . Similaringae 2) , Cucumisossypii) , H. annunuus Pl8 , O. sati fungus) , and H. fungus) . The BLAproteins . Sunflowy mildew . HanXRQCelicitor . Other iei, Bgh) . Another tritici . We werenditions . In the nditions . Thus, dPl8, LeEIX1, MLA10-13, Sr33 resistance genes. Further characterization of the NBS genes will help us to understand resistance pathways and to develop durable resistance necessary for crop improvement in sunflower, one of the major oilseed crops in the world.We identified 352 NBS genes in sunflower and studied their clustering, phylogenetic relationships, gene homology and functional divergence. These genes formed clusters and showed structural conservation in signature domains and exon/intron architecture in CNL, TNL and RNL types of NBS genes. The RNLs belonged to the CNL-A clade, which in turn was found nested within the TNL clade, making both CNL and TNL clades paraphyletic. This warrants further rigorous analysis. All of the NBS-encoding genes have undergone purifying selection and available expression data have revealed their functional divergence. We confirmed homology of sunflower NBS genes to multiple previously characterized"} +{"text": "Histopathological and functional outcomes were evaluated on P10, P18, and P90. Baseline outcome parameters were established in sham-treated and healthy control animals. Gross brain injury did not significantly differ between treatment groups at any time point. On P10, caspase-3 activation and caspase-independent apoptosis were similar between treatment groups; cell proliferation and the number of BrdU-positive vessels did not differ on P18 or P90. Neurobehavioral assessment did not reveal significant differences between treatment groups in accelerod performance, open field behavior, or novel object recognition capacity on P90. Turning behavior was more frequently observed in G-CSF/SCF- and FL-treated animals. No sex-specific differences were detected in any outcome parameter evaluated. In hypoxic-hyperoxic ischemic neonatal brain injury, G-CSF/SCF and FL treatment does not convey neuroprotection. Prior to potential clinical use, meticulous assessment of these hematopoietic growth factors is mandated.Hematopoietic growth factors are considered to bear neuroprotective potential. We have previously shown that delayed treatment with granulocyte colony-stimulating factor (G-CSF)/stem cell factor (SCF) and Fms-related tyrosine kinase 3 ligand (FL) ameliorates excitotoxic neonatal brain injury. The effect of these substances in combined-stressor neonatal brain injury models more closely mimicking clinical conditions has not been investigated. The aim of this study was to assess the short-, mid-, and long-term neuroprotective potential of G-CSF/SCF and FL in a neonatal model of hypoxic-hyperoxic ischemic brain injury. Five-day-old (P5) CD-1 mice were subjected to unilateral common carotid artery ligation and subsequent alternating periods of hypoxia and hyperoxia for 65 minutes. Sixty hours after injury, pups were randomly assigned to intraperitoneal treatment with (i) G-CSF (200\u2009 Neonatal brain injury is a problem of great global concern , 2. AdvaOur research group has recently been able to show that systemic treatment with the hematopoietic growth factors/cytokines granulocyte colony-stimulating factor (G-CSF)/stem cell factor (SCF) and Fms-related tyrosine kinase 3 ligand (FL) starting 60 hours after insult protects against N-methyl-D-aspartate receptor-mediated developmental excitotoxic brain damage by reducing injury extent and apoptotic cell death . WhetherFurthermore, any neuromodulatory intervention taking place during potentially critical or sensitive periods of brain development possibly has not only short-, but also long-term impact . The assThus, the aim of the current study was to investigate short-, mid-, and long-term effects of delayed treatment with G-CSF/SCF and FL in a mouse model of combined hypoxic-hyperoxic ischemic neonatal brain injury. From our previous findings we hypothesised that G-CSF/SCF and FL reduce injury extent and apoptotic cell death, stimulate neuroproliferation, and improve neurobehavioral outcome following hypoxia-hyperoxia ischemia.Heparin (Heparin Immuno 1000\u2009IU/ml) was obtained from Ebewe Pharma , and phenobarbital was obtained from Desitin Arzneimittel GmbH ; murine G-CSF, SCF, and FL were obtained from Peprotech , and 5-bromo-2\u2032-deoxyuridine (BrdU) was obtained from Sigma-Aldrich .\u03bcg/kg bw)/SCF (50\u2009\u03bcg/kg bw) in vehicle , (ii) FL (100\u2009\u03bcg/kg bw) in vehicle, or (iii) vehicle only and received an intraperitoneal (i.p.) injection every 24 hours for three or five consecutive days, depending on timing of endpoint determination. Endpoints were assessed on P10, P18, and P90. Sex was visually determined by assessment of the anogenital distance and confirmed by polymerase chain reaction or was determined by visual assessment alone depending on mouse age as described previously ; 1x PBS: 37.1 (11.1), G-CSF/SCF: 37.3 (5.8), FL: 34.6 (6.3); n=11-12 per group, F=0.377, p=0.689, One-Way ANOVA, two degrees of freedom). Female mice were significantly lighter in 1x PBS and G-CSF/SCF treatment groups, whereas body weight did not differ between male and female experimental animals in FL-treated mice (mean bodyweight (SD) [g]; 1x PBS: male 44.6 (9.6), female 28.0 (2.7), n=5-6, t=3.727, p= 0.005, Student's t-test; G-CSF/SCF: male 41.1 (3.8), female 31.9 (2.8), n=5-7, t=4.528, p=0.001, Student's t-test; FL: male 35.5 (7.2), female 33.0 (5.0), n=4-7, t=0.618, p=0.552, Student's t-test; Bonferroni-adjusted level of significance p<0.025).\u03c72=1.263, p=0.532, Pearson Chi-Square, two degrees of freedom; Turning behavior with counter-clockwise movements and hyperactivity was not observed in healthy control animals, but it occurred in six animals subjected to HHI, indicating severe brain damage (1x PBS: n=1 (9.1%) , G-SCF/SCF: n=2 (16.7%) , FL: n=3 (27.3%) ; With regard to accelerod performance, baseline time until task disruption in healthy control animals was 97.2 \u00b1 46\u2009sec (mean \u00b1 SD).In HHI, accelerod performance did not significantly differ between treatment groups (mean time until task disruption (SD) [sec]; 1x PBS: 107.7 (46.7), G-CSF/SCF: 116.3 (35.6), FL: 146.7 (74.4); n=11-12 per group, F=1.624, p=0.213, One-Way ANOVA, two degrees of freedom). No statistically significant sex-specific differences were detected .With regard to open field assessments, baseline anxiety index in sham-treated animals was 80.6% (median (IQR)), baseline travel distance as an indicator of horizontal activity was 3000.3\u2009cm (median (IQR)), and baseline time spent rearing as an indicator of vertical activity was 68.1\u2009sec (12.9) (mean (SD)).In HHI, anxiety (median anxiety index (IQR) [%]; 1x PBS: 85.0 , G-CSF/SCF: 78.8 , FL: 85.4 ; n=34, H=2.291, p=0.318, Kruskal-Wallis test, two degrees of freedom), horizontal activity (median travel distance (IQR) [cm]; 1x PBS: 2871.6 ; G-CSF/SCF: 3132.2 , FL: 3420.1 ; n=34, H=4.191, p=0.123, Kruskal-Wallis test, two degrees of freedom), and vertical activity (mean time spent rearing (SD) [sec]; 1x PBS: 71.6 (29.4), G-SCF/SCF: 85.0 (33.4), FL: 68.7 (49.3); n=11-12 per group, F=0.603, p=0.554, One-Way ANOVA, two degrees of freedom) did not significantly differ between treatment groups. No statistically significant sex-specific differences were detected .With regard to novel object recognition, baseline discrimination index (DI) in sham-treated animals was 0.16 (median (IQR)) after one hour, 0.29 (median (IQR)) after three hours, and 0.35 (median (IQR)) after five hours.In HHI, no overall differences in DI between treatment groups were observed after one (median DI (IQR); 1x PBS: 0.41 , G-CSF/SCF: 0.47 , FL: 0.22 ; n=34, H=2.269, p=0.322, Kruskal-Wallis test, two degrees of freedom), three (median DI (IQR); 1x PBS: 0.63 , G-CSF/SCF: 0.61 , FL: 0.46 ; n=34, H=1.942, p=0.379, Kruskal-Wallis test, two degrees of freedom), or five hours (median DI (IQR); 1x PBS: 0.40 , G-CSF/SCF: 0.26 , FL: 0.43 ; n=34, H=1.250, p=0.535, Kruskal-Wallis test, two degrees of freedom). Details can be seen in The identification of novel treatment options for brain injury is one of the biggest challenges encountered in neonatal neuroscience , 40, 41.In the study at hand, we used a combined hypoxic-hyperoxic ischemic brain injury model, thought to more adequately reflect the clinical situation in neonatal intensive care units , 34. AlsOn a histomorphological basis, we did not observe statistically significant differences between treatment groups at any time point, either in gross brain injury, or in caspase-dependent or -independent apoptosis as indicated by AIF-positivity. Another mechanism of action described for G-CSF/SCF is its trophic effect on neurons . An incrThis is in discordance with previous neonatal rodent brain injury studies, reporting reduced damage extent, apoptotic cell death, and increased cell proliferation following both single and repetitive G-CSF treatments , 24, 28.\u03bcg/g body weight was chosen, based on previous publications and our own studies, showing a dose response curve [For the present study, a higher dose of G-CSF was selected. The dose of 200\u2009se curve , 30. These curve The diffse curve had no ese curve A directInterestingly, turning behavior as an indicator of severe brain damage was more frequently observed in G-CSF/SCF- and FL-treated animals than in vehicle-treated controls. Even though the finding was not statistically significant, this might still be of relevance as turning behavior has been shown to correlate with histological damage and sensory motor deficit in rodents exposed to cerebral ischemia . CautiouThe importance of evaluating sex-specific differences has been proven by several studies, especially when considering the variable responses of male and female immature rodents to brain injury , 47, 48.To conclude, in this multistressor mouse model of hypoxia-hyperoxia ischemia we cannot confirm the protective effect of G-CSF/SCF and FL on neonatal brain injury previously reported. As adverse effects cannot be ruled out, meticulous assessment of these hematopoietic growth factors in extensive preclinical studies is mandated prior to potential clinical use."} +{"text": "This article has been corrected: Due to a labeling error, the legends for Figures 2 and 3 were accidentally switched. The proper figure legends are given below. The authors declare that these corrections do not change the results or conclusions of this paper.Figure 2: Induction of fibrosis in the mammary gland of NeuT/ATTAC mice following AP21087 treatment for four weeks. Six-week-old NeuT/ATTAC mice were injected i.p. with vehicle (NeuT/ATTAC) or 0.4 mg/kg AP21087 (NeuT/ATTAC+AP) for four weeks. FFPE sections were stained as described in Figure 2. Magnification 400\u00d7.Figure 3: Induction of fibrosis in NeuT/ATTAC mice. Mice at 6 weeks-of-age were injected i.p. with vehicle (NeuT/ATTAC) three times weekly for 5.5 months (NeuT/ATTAC) or with 0.4 mg/kg AP21087 (NeuT/ATTAC+AP) for 4 months. FFPE sections were stained with H&E, for collagen (PicroSirius Red) and with antibodies against Ki-67, CD31, \u03b1-smooth muscle actin (SMA), F4/80, Cxcl1, Foxp3, CD8 and PD-L1. Magnification 400\u00d7.8042-8053. https://doi.org/10.18632/oncotarget.24233Original article: Oncotarget. 2018; 9:"} +{"text": "A post-conflict vaccination campaign, Central African Republic. Bull World Health Organ. 2018 Aug 1;96(8):540\u201347. on page 544,"} +{"text": "Scientific Reports 10.1038/s41598-018-34229-6, published online 31 October 2018Correction to: In this Article the Competing Interests section was omitted. This should read:\u201cT.S. received research funding from Sony IP&S Inc.\u201d"} +{"text": "This article has been corrected: The correct order of authors' names is given below:1,2, Milind Shivajirao Patole1, Punam Vasudeo Nagvenkar1, Sonali Shankar Kamble2 and Rajesh Nivarti Gacche2,3Bhimashankar Gurushidhappa Utage30304-30323. https://doi.org/10.18632/oncotarget.25717Original article: Oncotarget. 2018; 9:"} +{"text": "The correct name is: Ashwani K. Singal. The correct citation is: Axley P, Mudumbi S, Sarker S, Kuo Y-F, Singal AK (2018) Patients with stage 3 compared to stage 4 liver fibrosis have lower frequency of and longer time to liver disease complications. PLoS ONE 13(5): e0197117."} +{"text": "Correction to: J Immuno Therapy Cancer. (2018) 6 (Suppl 1)https://doi.org/10.1186/s40425-018-0422-yhttps://doi.org/10.1186/s40425-018-0423-xAfter publication of this supplement , 2, it wP128Multiplexed immunofluorescent assay development for study of the PD-1/PD-L1 checkpoint in the tumor immune microenvironment (TIME)Sneha Berry, MS, Nicolas Giraldo, MD PhD, Peter Nguyen, MS, Benjamin Green, BS, Haiying Xu, Aleksandra Ogurtsova, Abha Soni, DO, Farah Succaria, MD, Daphne Wang, MS, Charles Roberts, Julie Stein, MD, Elizabeth Engle, MSc, Drew Pardoll, MD, PhD, Robert Anders, MD, PhD, Tricia Cottrell, MD, PhD, Janis M. Taube, MDJohns Hopkins University School of Medicine, Baltimore, MD, USACorrespondence: Sneha Berry (jtaube1@jhmi.edu)Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P128Janis M. Taube, MD is a contributing author and has therefore been added to the author list in this correction article. Contributing author Sneha Berry, MS is listed three times in the original article; this is no longer the case in this correction article.BackgroundMultispectral immunofluorescent (mIF) staining of formalin-fixed paraffin-embedded (FFPE) tissue allows spatially-resolved quantitative analysis of cell position and protein expression. The design and validation of mIF panels is a challenge. Our goal was to develop a 7-plex assay for characterizing PD-1 and PD-L1 expression, with high sensitivity for multiple markers and minimal bleed-through between fluorescent channels, while avoiding steric hindrance among markers occupying the same cellular compartment.MethodsSingle IF slides were stained for PD-1, PD-L1, CD8, FoxP3, CD163, and a tumor marker (e.g. Sox10/S100 for melanoma) using primary antibodies at manufacturer\u2019s recommended concentrations and visualized with an Opal kit (PerkinElmer). Positive signal was compared to chromogenic IHC (n=3 tonsil specimens). In some instances, the kit\u2019s HRP-polymer was substituted for one that provided greater amplification. Primary antibody titrations were performed, and the concentration with comparable signal to chromogenic IHC that showed the highest IF signal to noise ratio was selected. Using the selected primary antibody concentration, TSA dilution series were performed on n=5 tumor specimens to minimize bleed-through. Finally, the optimized single IF stains were combined into multiplex format, which was again validated to ensure no positivity loss. Images were scanned with the Vectra 3.0 and processed using inForm (Ver 2.3).Resultshigh vs. PD-1low lymphocytes.The percent positive pixels for CD163, CD8, and tumor marker expression by IF were comparable to chromogenic IHC with manufacturer\u2019s recommended protocols (p>0.05). However, PD-1, PD-L1, and FoxP3 showed ~50% loss of signal (p<0.05), which was recovered by replacing the Opal kit's secondary HRP polymer with PowerVision (Leica). Unbalanced fluorescence intensities between 540 to 570 Opal dyes resulted in significant bleed-through and led to false positive pixels. This error was minimized >2 fold (2.5% to 1.1%) by concentrating the 570 dye and ensuring that this dye pair was used to study markers in different cellular compartments (nuclear FoxP3 vs. membrane CD8), so any residual bleed-through could be discounted during image analysis. Using the optimized panel, we are able to reliably identify cell types contributing PD-L1 and PD-1 to the TIME, and even resolve populations of PD-1ConclusionsWe demonstrate successful optimization of a 7-color multiplex panel characterizing the PD-1/PD-L1 axis to provide high quality data sets for whole slide or regional analysis of the TIME. With the use of multiparametric assays such as this, we hope to guide improved approaches to patient selection and potentially identify additional tumor types likely to respond to anti-PD-(L)1 immunotherapy.Ethics ApprovalThe study was approved by Johns Hopkins University Institutional Review Board.P308A Phase 1 study of MEDI5752, a bispecific antibody that preferentially targets PD-1 and CTLA-4 expressing T cells, in patients with advanced solid tumors2, Mark Voskoboynik3, James Kuo4, Yung-Lue Bang5, Hyun-Cheo Chung6, Myung-Ju Ahn7, Sang-We Kim8, Ayesh Perera1, Daniel Freeman1, Ikbel Achour1, Raffaella Faggioni1, Feng Xiao1, Charles Ferte1, Charlotte Lemech4Ben Tran1MedImmune, Gaithersburg, MD, USA; 2Peter MacCallum Cancer Center, Melbourne, Australia; 3Nucleus Network, Melbourne, Australia; 4Scientia Clinical Research, Sydney, Australia; 5Seoul National University Hospital, Seoul, Korea, Republic of; 6Yonsei Cancer Center, Yonsei University, Seoul, Korea, Republic of; 7Samsung Medical Center, Seoul, Korea, Republic of; 8Asan Medical Center, Songpa-Gu, Korea, Republic ofCorrespondence: Charles Ferte (fertec@MedImmune.com) Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P308Jeff Brubaker was not a contributing author and has therefore been removed from the author list in this correction article. The credentials as shown on the original article are no longer listed on this correction article.BackgroundBased on demonstrated clinical activity and manageable safety profiles, checkpoint inhibiting antibodies blocking PD 1, PD-L1, or CTLA-4 have received regulatory approvals for the treatment of various malignancies [1-5]. The combination therapy with anti-PD-1 and anti-CTLA-4 agents is approved by FDA for metastatic melanoma, renal cell carcinoma and microsatellite instability-high (MSI-H) or mismatch repair deficient (dMMR) metastatic colorectal cancer, based on improved overall survival versus either agent alone [6-10]. Numerous clinical studies of combination immunotherapy are currently investigating the same combination across a range of solid tumors [11- 15]. Although the efficacy of these drug combinations is dose dependent, the toxicity associated with anti-CTLA-4 agents, in particular, is dose limiting, thereby potentially affecting treatment outcomes with combination therapy.- MEDI5752 is a bispecific humanized IgG1 monoclonal antibody that binds PD-1 and CTLA-4. In contrast to the combination therapy, MEDI5752 exhibits a novel T cell targeting mechanism that could provide a favorable toxicity profile. In addition, we have shown that MEDI5752 can impact cell surface expression of PD-1. Based on these novel mechanisms of action, MEDI5752 may show improved efficacy and safety in comparison to co- administration of conventional anti-PD1/anti-PD-L1 and anti-CTLA-4 antibodies.MethodsThis is a Phase 1, first-time-in-human, multicenter, open-label study in patients with advanced solid tumors. The dose-escalation phase will evaluate approximately six MEDI5752 dose levels to identify a maximum tolerated dose. Dose escalation will be followed by two dose-expansion cohorts in defined setting with patients with advanced or metastatic solid tumor and tested against a control arm. Subjects will remain on treatment until confirmed progressive disease, initiation of alternative cancer therapy, unacceptable toxicity, or other reason for discontinuation. The primary endpoints are safety and efficacy (objective response in the dose-expansion phase). Secondary endpoints include additional efficacy assessment across both phases, pharmacokinetics, and immunogenicity.Trial RegistrationNCT03530397References1. Opdivo Prescribing Information. Princeton, NJ: Bristol-Myers Squibb Company, 2018. [revised 2018 Apr].2. Keytruda Prescribing Information. Whitehouse Station, NJ: Merck Sharp & Dohme Corp, 2018 [revised 2018 Jun].3. Tecentriq Prescribing Information. San Francisco (CA): Genentech, Inc, 2018. [revised 2019 Jul].4. Imfinzi Prescribing Information. Wilmington (DE): AstraZeneca Pharmaceuticals LP, 2018. [revised 2018 Feb].5. Yervoy Prescribing Information. Princeton (NJ): Bristol-Myers Squibb Company, 2018. [revised 2018 Apr].6. Larkin J, Chiarion-Sileni V, Gonzalez R, Grob JJ, Cowey CL, Lao CD, et al. Combined nivolumab and ipilimumab or monotherapy in untreated melanoma. N Engl J Med. 2015;373:23-34.7. Postow MA, Chesney J, Pavlick AC, Robert C, Grossmann K, McDermott D, et al. Nivolumab and ipilimumab versus ipilimumab in untreated melanoma. N Engl J Med. 2015;372:2006-2017.8. Motzer RJ, Tannir NM, McDermott DF, Frontera OA, Melichar B, Choueiri TK, et al. Nivolumab plus ipilimumab versus sunitinib in advanced renalcell carcinoma. N Engl J Med. 2018;378:1277-1290.9. Overman MJ, Lonardi S, Wong KYM, Lenz H-J, Gelsomino F, Aglietta M, et al. Durable clinical benefit with nivolumab plus ipilimumab in DNA mismatch repair\u2013deficient/microsatellite instability\u2013high metastatic colorectal cancer. J Clin Oncol. 2018;36:773-779.https://www.pharmacytimes.com/news/nivolumab-ipilimumabcombo-approved-by-fda-for-msihdmmr-colorectal-cancer. Accessed 18 July, 2018.10. Broderick JM. Nivolumab, ipilimumab combo approved by FDA for MSI-H/dMMR colorectal cancer. Pharmacy Times, 11 July, 2018. Available at: 11. Antonia S, Goldberg SB, Balmanoukian A, Chaft JE, Sanborn RE, Gupta A, et al. Safety and antitumour activity of durvalumab plus tremelimumab in non-small cell lung cancer: a multicentre, phase 1b study. Lancet Oncol. 2016a;17(3):299-308.12. Haddad R, Gillison M, Ferris RL, Harrington K, Monga M, Baudelet C, et al. Double-blind, two-arm, phase 2 study of nivolumab (nivo) in combination with ipilimumab (ipi) versus nivo and ipi-placebo (PBO) as first-line (1L) therapy in patients (patients) with recurrent or metastatic squamous cell carcinoma of the head and neck (R/M SCCHN)\u2014CheckMate 714. Ann Oncol. 2016;27(suppl_6):1017TiP-TiP.13. Kelley RK, Abou-Alfa GK, Bendell JC, Kim T-Y, Borad MJ, Yong W-P, et al. Phase I/II study of durvalumab and tremelimumab in patients with unresectable hepatocellular carcinoma (HCC): Phase I safety and efficacy analyses. J Clin Oncol. 2017;35(15_suppl):4073.14. Janjigian YY, Ott PA, Calvo E, Kim JW, Ascierto PA, Sharma P, et al. Nivolumab \u00b1 ipilimumab in patients with advanced (adv)/metastatic chemotherapy-refractory (CTx-R) gastric (G), esophageal (E), or gastroesophageal junction (GEJ) cancer: CheckMate 032 study. J Clin Oncol. 2017;35(15_suppl):4014.15. Escudier B, Tannir NM, McDermott DF, Frontera OA, Melichar B, Plimack ER, et al. LBA5CheckMate 214: Efficacy and safety of nivolumab + ipilimumab (N+I) v sunitinib (S) for treatment-na\u00efve advanced or metastatic renal cell carcinoma (mRCC), including IMDC risk and PD-L1 expression subgroups. Ann Oncol. 2017;28(suppl_5):mdx440.029- mdx440.029.P309Phase I dose-finding study of MIW815 (ADU-S100), an intratumoral STING agonist, in patients with advanced solid tumors or lymphomas2, Theresa Werner3, Stephen Hodi4, Wells Messersmith, MD5, Nancy Lewis6, Craig Talluto7, Mirek Dostalek6, Aiyang Tao6, Sarah McWhirter8, Damian Trujillo8, Jason Luke, MD, FACP9Funda Meric-Bernstam, MD2MD Anderson Cancer Center, Houston, TX, USA; 3University of Utah, Salt Lake City, UT, USA; 4Dana-Faber Cancer Institute, Boston, MA, USA; 5University of Colorado Cancer Center, Aurora, CO, USA; 6Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA; 7Novartis Institutes for BioMedical Resea, Cambridge, MA, USA; 8Aduro Biotech Inc, Berkeley, CA, USA; 9The University of Chicago Medicine, Chicago, IL, USACorrespondence: Funda Meric-Bernstam (fmeric@mdanderson.org)Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P309Janis Callister was not a contributing author and has therefore been removed from the author list in this correction article. The redundant affiliation Articulate Science as shown on the original article is no longer listed on this correction article.BackgroundMIW815 (ADU-S100) is a novel synthetic cyclic dinucleotide that can activate human STING (STimulator of INterferon Genes) in antigenpresenting cells. In preclinical models, STING pathway activation can induce tumor antigen-specific T-cell priming within the tumor microenvironment, leading to antitumor immunity and tumor destruction.MethodsEligible patients include those with advanced/metastatic solid tumors or lymphomas with progressive disease despite standard of care or for whom there is no standard treatment.MIW815 (ADU-S100) is administered by weekly intratumoral injections (3 weeks on/1 week off) at escalating doses (starting dose: 50\u03bcg) in 28-day cycles. Primary objectives are to characterize safety and tolerability and to identify a recommended dose for future studies.Secondary objectives include preliminary efficacy, pharmacokinetics (PK), and pharmacodynamics (PD). The study is currently in dose escalation.ResultsAs of June 15, 2018, 41 heavily pretreated patients with various solid tumors or lymphomas were enrolled. Thirty-five patients have discontinued from the study for the following reasons: disease progression (n=26), physician/patient decision (n=8), and death (n=1); 6 patients continue to receive treatment. No dose-limiting toxicities (DLTs) were reported during the first cycle at any dose level. The most common (\u226510% of patients) treatment-related AEs (TRAEs) were pyrexia , injection site pain , and headache . Grade 3/4 TRAEs included increased lipase and elevated amylase, tumor pain, dyspnea, respiratory failure, and injection site reaction . Systemic MIW815 (ADU- S100) exposure increased with dose. On-treatment tumor biopsies showed increases in CD8 T cells infiltrating the injected tumors in a subset of patients. Preliminary antitumor activity, PK analysis, and PD data from injected lesions, noninjection lesions, and peripheral blood, will be presented.ConclusionsIntratumoral injection of MIW815 (ADU-S100) was well tolerated in doses tested thus far in patients with advanced solid tumors and lymphoma, with no DLTs reported to date. Trials evaluating combinations of MIW815 (ADU-S100) with anti-PD1 or anti-CTLA4 antibodies are ongoing.Ethics ApprovalThis study was approved by an independent ethics committee or institutional review board at each site.P383Combination therapy with M7824 (MSB0011359C) and NHSmuIL12 enhances antitumor efficacy in preclinical cancer models2, Bo Marelli2, Jin Qi2, Guozhong Qin2, Huakui Yu2, Molly Jenkins2, Kin-Ming Lo2, Joern-Peter Halle2, Yan Lan, MD2Chunxiao Xu, PhD2EMD Serono Research and Development, Belmont,MA, USACorrespondence: Yan Lan (yan.lan@emdserono.com)Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P383Colleen Stanton was not a contributing author and has therefore been removed from the author list in this correction article. The redundant affiliation Nucleus Global as shown on the original article is no longer listed on this correction article.BackgroundPD-1/PD-L1 pathway inhibition is a clinically validated approach in cancer therapy. However, most patients do not respond to the monotherapy due to multiple immunosuppressive mechanisms. Combining anti-PD-1/ PD-L1 with other immunotherapeutic agents targeting additional immunomodulatory pathways in the tumor microenvironment (TME) is one strategy to overcome resistance and improve response rates. M7824 is an innovative first-in-class bifunctional fusion protein composed of two extracellular domains of TGF-\u03b2 receptor II (a TGF-\u03b2 \u201ctrap\u201d) fused to a human anti-PD-L1 IgG1 monoclonal antibody. Through simultaneous blockade of the PD-L1 and TGF-\u03b2 pathways, M7824 demonstrated enhanced anti-tumor activity in preclinical models [1]. NHS-IL12, and the surrogate NHS- muIL12, are immunocytokines designed to target tumor necrotic regions to deliver IL-12 into the TME, where they can activate NK cells and CD8+ T cells to increase their cytotoxic functions. The surrogate NHSmuIL12 has demonstrated antitumor efficacy in preclinical models [2].This study is designed to investigate whether M7824 treatment may further benefit from combination therapy with NHS-muIL12.MethodsMice bearing MC38, EMT-6, or 4T1 tumors were treated with M7824, NHS-muIL12, or combination therapy. Tumor growth and survival were assessed in each model, and tumor recurrence following remission and rechallenge was evaluated in the EMT-6 model. Immune cell populations in the spleens and tumors were evaluated by flow cytometry and the frequency of tumor antigen-reactive IFN\u03b3-producing CD8+ T cells was evaluated by an ELISpot assay in the MC38 model.ResultsCombination of M7824 and NHS-muIL12 enhanced antitumor activity and extended the survival relative to either monotherapy in preclinical tumor models. Combination therapy also enhanced the proliferation, infiltration, and cytotoxicity of CD8+ T cells relative to monotherapies. In addition, the combination therapy increased the frequency of tumor antigenreactive T cells and induced the generation of tumor-specific immune memory, as demonstrated by protection against tumor rechallenge.ConclusionsThese data demonstrate that combination therapy with M7824 and NHS-muIL12 improved anti-tumor efficacy in multiple preclinical tumor models and suggest that combining these therapies may be a promising therapeutic strategy for patients with solid tumors.References1. Lan Y, et al. Enhanced preclinical antitumor activity of M7824, a bifunctional fusion protein simultaneously targeting PD-L1 and TGF-\u03b2. Sci Trans Med. 2018;10(424).2. Fallon J, et al. The immunocytokine NHS-IL12 as a potential cancer therapeutic. Oncotarget 2014;5(7):1869-84.P391A phase 1b/2 trial of lenvatinib in combination with pembrolizumab in patients with advanced melanoma2, Nicholas Vogelzang, MD3, Allen Cohn3, Daniel Stepan4, Robert Shumaker, PhD,4, Corina Dutcus4, Matthew Guo4, Emmett Schmidt, MD PhD5, Drew Rasco6Matthew Taylor, MD2Oregon Health and Science University, Portland, OR, USA; 3McKesson Specialty Health, Las Vegas, NV, USA; 4Eisai Inc., Woodcliff Lake, NJ, USA; 5Merck & Co., Inc., Kenilworth, NJ, USA; 6South Texas Accelerated Research Therape, San Antonio, TX, USACorrespondence: Matthew Taylor (taylmatt@ohsu.edu) Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P391The redundant affiliation 1. Oxford PharmaGenesis, Oxford, UK as shown on the original article is no longer listed on this correction article.BackgroundLenvatinib is a multikinase inhibitor of VEGFR 1\u22123, FGFR 1\u22124, PDGFR\u03b1, RET, and KIT. Pembrolizumab, an anti-PD-1 antibody, is approved for the first-line treatment of patients with advanced melanoma, with objective response rates (ORR) of 21\u201334% . Preclinical studies indicate that lenvatinib decreases the population of tumorassociated macrophages, increases CD8+ T cell infiltration, and augments the activity of PD-1 inhibitors; therefore, lenvatinib is a rational combination partner for pembrolizumab . We report interim results of an ongoing phase 1b/2 trial evaluating lenvatinib in combination with pembrolizumab in patients with solid tumors, focusing on the advanced melanoma cohort.MethodsIn this multicenter, open-label study (NCT02501096), patients with measurable, confirmed, metastatic melanoma and ECOG performance status \u22641 received lenvatinib + pembrolizumab . Patients were not preselected based on PDL1 status. Tumor assessments were performed by study investigators using immune-related RECIST (irRECIST). The phase 2 primary end point was ORR at 24 weeks (ORRWK24). Secondary end points included ORR, progression-free survival (PFS), and duration of response (DOR).ResultsAt the data cutoff of March 1, 2018, 21 patients were enrolled: 14 (67%) patients were PD-L1(+), 4 (19%) were PD-L1(-), 3 (14%) were not tested; and 38% of patients had \u22651 prior anticancer therapy. The primary end point of ORRWK24 was 47.6% . Additional efficacy outcomes are summarized in the table (Table 1). All patients experienced \u22651 treatment-related adverse event (TRAE). Grade 3 and 4 TRAEs occurred in 13 (62%) and 1 patients respectively. There were no fatal TRAEs. The most common any-grade TRAEs were fatigue (52%), decreased appetite (48%), diarrhea (48%), hypertension (48%), dysphonia (43%), and nausea (43%). Dose reduction and interruption due to TRAEs occurred in 13 (62%) and 10 (48%) patients, respectively.ConclusionsThe lenvatinib and pembrolizumab combination regimen was welltolerated and demonstrated encouraging clinical activity. The combination may potentially improve upon the antitumor activity of antiPD-1 monotherapies, supporting further evaluation of this regimen in patients with advanced melanoma.Trial RegistrationNCT02501096References1. Ribas A, et al. Pembrolizumab versus investigator-choice chemotherapy for ipilimumab-refractory melanoma (KEYNOTE-002): a randomised, controlled, phase 2 trial. Lancet Oncology. 2015;16(8):908-18.2. Robert C, et al. Pembrolizumab versus ipilimumab in advanced melanoma. N Engl J Med. 2015;372(26):2521- 2532.3. Kato Y et al. Effects of lenvatinib on tumor-associated macrophages enhance antitumor activity of PD-1 signal inhibitors. Mol Cancer Ther. 2015;14 (12Suppl2):A92.4. Kato Y. Upregulation of memory T cell population and enhancement of Th1 response by lenvatinib potentiate antitumor activity of PD-1 signaling blockade. Cancer Res. 2017;77 (13 Suppl):4614. Ethics Approval This study was approved by all relevant institutional review boards.Table 1 (abstract P391). See text for description.P392A phase 1b/2 trial of lenvatinib in combination with pembrolizumab in patients with non-small cell lung cancer2, Nicholas Vogelzang, MD3, Christopher Di Simone3, Sharad Jain, MD3, Donald Richards3, Carlos Encarnacion3, Drew Rasco4, Robert Shumaker, PhD5, Corina Dutcus5, Daniel Stepan5, Matthew Guo5, Emmett Schmidt, MD PhD6, Matthew Taylor, MD7Marcia Brose2Abramson Cancer Center of the University, Philadelphia, PA, USA; 3McKesson Specialty Health, Las Vegas, NV,USA; 4South Texas Accelerated Research Therape, San Antonio, TX, USA; 5Eisai Inc., Woodcliff Lake, NJ, USA; 6Merck & Co., Inc., Kenilworth, NJ, USA; 7Oregon Health and Science University, Portland, OR, USACorrespondence: Marcia Brose (Brosem@mail.med.upenn.edu) Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P392The redundant affiliation 1. Oxford PharmaGenesis, Oxford, UK as shown on the original article is no longer listed on this correction article.BackgroundLenvatinib is a multikinase inhibitor of VEGFR 1\u22123, FGFR 1\u22124, PDGFR\u03b1, RET, and KIT. Pembrolizumab, an anti-PD-1 antibody, is approved as a monotherapy for previously treated patients with metastatic PD-L1\u2013positive (tumor proportion score [TPS] \u22651%) non-small cell lung cancer (NSCLC), with an objective response rate (ORR) of 18% [1]. We report interim results of an ongoing phase 1b/2 trial evaluating lenvatinib in combination with pembrolizumab in patient with solid tumors, focusing on the metastatic NSCLC cohort.MethodsIn this multicenter, open-label study (NCT02501096), patients with measurable, confirmed metastatic NSCLC and ECOG performance status \u22641 received lenvatinib and pembrolizumab . In the phase 2 portion, patients must have had \u22642 prior lines of systemic therapy; there was no limit for phase 1b. Patients were not preselected based on PD-L1 status. Tumor assessments were performed by study investigators using immune-related RECIST (irRECIST). The phase 2 primary end point was ORR at 24 weeks (ORRWK24). Secondary end points included ORR, progressionfree survival (PFS), and duration of response (DOR).ResultsAt the data cutoff of March 1, 2018, 21 patients were enrolled. 9 (43%) Patients were PD-L1(+) (TPS \u22651%); 5 (24%) were PD-L1(-); 7 (33%) were not tested. 3 (14%) Patients were treatment-na\u00efve; 7 (33%), 10 (48%), and 1 (5%) patients had 1, 2, and \u22653 prior lines of systemic therapy, respectively. The primary end point of ORRWK24 was 33.3% . Additional efficacy outcomes are summarized in the table (Table 1). Grade 3 and 4 treatment-related adverse events (TRAEs) occurred in 10 (48%) and 1 patients, respectively. There was 1 fatal TRAE . The most common grade 3 TRAEs were hypertension (24%), fatigue (14%), diarrhea (14%), proteinuria (10%), and arthralgia (10%).ConclusionsThe combination of lenvatinib and pembrolizumab showed promising clinical activity with a manageable safety profile in previously treated patients with metastatic NSCLC who were not preselected for PD-L1 status. Further study is warranted.Trial RegistrationNCT02501096ReferencesHerbst RS et al. Pembrolizumab versus docetaxel for previously treated, PD-L1-positive, advanced non-small-cell lung cancer (KEYNOTE-010): a randomised controlled trial. Lancet. 2016;387(10027):1540-50.Ethics ApprovalThis study was approved by all relevant institutional review boards.Table 1 (abstract P392). See text for description.P393A phase 1b/2 trial of lenvatinib in combination with pembrolizumab in patients with urothelial cancer2, Carlos Encarnacion2, Allen Cohn2, Christopher Di Simone2, Drew Rasco3, Donald Richards2, Matthew Taylor, MD4, Corina Dutcus5, Daniel Stepan5, Robert Shumaker, PhD5, Matthew Guo5, Emmett Schmidt, MD PhD6, James Mier, MD7Nicholas Vogelzang, MD2McKesson Specialty Health, Las Vegas, NV, USA; 3South Texas Accelerated Research Therape, San Antonio, TX, USA; 4Oregon Health and Science University, Portland, OR, USA; 5Eisai Inc., Woodcliff Lake, NJ, USA; 6Merck & Co., Inc., Kenilworth, NJ, USA; 7Beth Israel Deaconess Medical Center, Boston, MA, USACorrespondence: Nicholas Vogelzang (nicholas.vogelzang@usoncology.com) Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P393The redundant affiliation 1. Oxford PharmaGenesis, Oxford, UK as shown on the original article is no longer listed on this correction article.BackgroundPembrolizumab, an anti-PD-1 antibody, is approved in the secondline setting for patients (objective response rate [ORR] 21%) with advanced/metastatic urothelial cancer and in the first-line setting for patients who are ineligible for cisplatin with combined positive score \u226510 or ineligible for platinum-based chemotherapy, with ORR [1\u20133]. However, there is still an unmet need for effective therapeutic options for advanced urothelial cancer. Lenvatinib is a multikinase inhibitor of VEGFR 1-3, FGFR 1-3, PDGFR\u03b1, RET and KIT. Tyrosine kinase inhibitors, such as lenvatinib, have demonstrated activity in urothelial cancer and may reverse the immunosuppressive environment that leads to immuno-oncology (IO) therapy failure. Here we present a phase 1b/2 trial to determine the safety and efficacy of lenvatinib in combination with pembrolizumab in patients with advanced urothelial cancer.MethodsIn this multicenter, open-label study (NCT02501096), patients with confirmed metastatic urothelial cancer and an ECOG PS of 0 or 1 received lenvatinib 20 mg orally once daily and 200 mg pembrolizumab intravenously every 3 weeks. Patients were not preselected based on PD-L1 status. The phase 2 primary end point was ORR at week 24 (ORRwk24), as assessed by study investigators using immune-related RECIST (irRECIST). Secondary end points included ORR, duration of response (DOR), and progression-free survival (PFS).ResultsAt the time of data cutoff , 20 patients were enrolled. 9 (45%) Patients were PD-L1(+); 5 (25%) were PD-L1(-); 6 (30%) were not tested. 4 Patients (20%) were treatment-na\u00efve, whereas 11 (55%) and 5 (25%) patients had had 1 and 2 lines of prior anticancer therapies, respectively. No patient had received prior IO therapy. The primary end point of ORRwk24 was 25% (95% CI: 8.7\u201349.1). Additional efficacy outcomes are summarized in the table (Table 1). 18 (90%)Patients experienced treatment-related adverse events (TRAEs).Grade 3 and 4 TRAEs occurred in 5 (25%) and 5 (25%) patients, respectively. There was 1 fatal TRAE . The most common any-grade TRAEs were proteinuria (45%), diarrhea (40%), fatigue (30%), hypertension (30%), and hypothyroidism (30%).ConclusionsThe tyrosine kinase inhibitor (lenvatinib) and immunotherapy (pembrolizumab) regimen demonstrated activity in this study, which included patients receiving later-line treatment. The combination of lenvatinib and pembrolizumab deserves further investigation in patients with metastatic urothelial cancer.Trial RegistrationNCT02501096References1. Bellmunt J, et al. Pembrolizumab as second-line therapy for advanced urothelial carcinoma. N Engl J Med. 2017;376(11):1015-26.2. Vuky J et al. Updated efficacy and safety of KEYNOTE-052: A single arm phase 2 study investigating first-line pembrolizumab (pembro) in cisplatin-ineligible advanced urothelial cancer (UC). J Clin Oncol. 2018;36(15 Suppl):4524.3. Keytruda\u00ae (pembrolizumab) [package insert]. Whitehouse Station, NJ: Merck & Co., Inc.; 2017.Ethics ApprovalThis study was approved by all relevant institutional review boards.Table 1 (abstract P393). See text for description.P569Novel Pharmacobiotic approach to enhance the tamoxifen efficacy using bacterial extracellular vesicles as the immunotherapy in breast cancer1, Yeun-yeoul Yang1, Won-Hee Lee2, Jinho Yang2, Jong-kyu Kim1, HyunGoo Kim1, Se Hyun Paek1, Jun Woo Lee1, Joohyun Woo1, Jong Bin Kim1, Hyungju Kwon1, Woosung Lim1, Nam Sun Paik1, Yoon-Keun Kim2, Byung-In Moon1Jeongshin An, MD,PhD1Ewha Womans University, Seoul, Korea, Republic of; 2MD healthcare company, Seoul, Korea, Republic ofCorrespondence: Jeongshin An (rulru81@hanmail.net) Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P569Byung-In Moon is a contributing author and has therefore been added to the author list in this correction article.BackgroundThe anti-cancer effect of bacteria has a long history. According to Bierman et al., spontaneous remission of cancer has been observed in patients with severe bacteremia [1]. The reason was not revealed at that time, but we studied that in breast cancer. There are four main ways in which microbiota affects cancer: probiotics, prebiotics, drugs that target microbial enzymes and microbial products that have anticancer properties [2]. Among them, bacterial extracellular vesicles(EVs) are one of microbial products. In this study, we investigated the effects of bacterial EVs on the growth of breast cancer cells and tamoxifen efficacy.MethodsHere, we analized microbiota of urine samples by NGS to select the target EVs that were expected to affect the growth of breast cancer cells. A total of 347 female urine samples \u2013 from 127 breast cancer patients (cancer group) and 220 normal individuals (control group) \u2013 were collected and analyzed by NGS using a universal bacterial primer of 16S rDNA. Human breast cancer cells were cultured, and the cells were treated with EVs of S. aureus and K.pneumoniae for 72 h. Real-time polymerase chain reaction (PCR) and Western blotting for signalling molecule analysis were performed after treatment of EVs in each breast cancer cell.ResultsThere was a significant difference in the distribution of bacterial EVs between the urine samples from breast cancer patients and from normal controls. Especially, S.aureus EVs were predominant in the normal group, and K.pneumoniae was abundant in the breast cancer group. Therefore, we selected these two bacterial EVs that may have an effect on breast cancer cell growth. We found that S.aureus and K.pneumoniae EVs down-regulated cell growth in MDA-MB-231 cells. We also found that S.aureus or K.pneumoniae EVs had a synergic effect on growth inhibition of while co-treated with tamoxifen. S.aureus EVs down-regulated mRNA expression of cyclin E2 and up- regulated that of TNF-alpha which was related ERK pathway while co-treated with tamoxifen.ConclusionsThe anti-cancer effect of S.aureus and K.pneumoniae was initiated by its bacterial EVs and consequently inhibited the growth of breast cancer cells in triple negative breast cancer cells and improved the efficacy of tamoxifen in ER-positive cells. In the near future, we plan to conduct animal studies which are expected to further clarify the effect of bacterial EV on breast cancer. Ethics ApprovalThe study was approved by Ewha Womans University Medical Center\u2018s Ethics Board.ConsentWritten informed consent was obtained from the patient for publication of this abstract and any accompanying images. A copy of the written consent is available for review by the Editor of this journal.References1. Bierman, H. R. et al. Remissions in leukemia of childhood following acute infectious disease. Staphylococcus and streptococcus, varicella, and feline panleukopenias. Cancer 6, 591-605 (1953).2. Zitvogel, L., Daill\u00e8re, R., Roberti, M. P., Routy, B. & Kroemer, G. Anticancer effects of the microbiome and its products. Nature Reviews Microbiology 15, 465 (2017).Fig. 1 (abstract P569). See text for descriptionFig. 2 (abstract P569). See text for descriptionFig. 3 (abstract P569). See text for descriptionFig. 4 (abstract P569). See text for descriptionFig. 5 (abstract P569). See text for descriptionFig. 6 (abstract P569). See text for descriptionFig. 7 (abstract P569). See text for descriptionP651First-in-human study of FAZ053, an anti-PD-L1 mAb, alone and in combination with spartalizumab, an anti- PD-1 mAb, in patients with advanced malignancies2, David Tan3, Juan Martin-Liberal4, Shunji Takahashi5, Ravit Geva, MD6, Ayca Gucalp7, Xueying Chen8, Kulandayan Subramanian9, Jennifer Mataraza9, Jennifer Wheler9, Philippe Bedard, MD10Filip Janku, MD, PhD2MD Anderson Cancer Center, Houston, TX, USA; 3National University Cancer Institute, Singapore, Singapore 4Vall d\u2019Hebron Institute of Oncology, Barcelona, Spain; 5The Cancer Institute Hospital of JFCR, Tokyo, Japan; 6Tel Aviv Sourasky Medical Center, Tel-Aviv, Israel; 7Memorial Sloan Kettering Cancer Center, New York, NY, USA 8Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA 9Novartis Institutes for BioMedical Resea, Cambridge, MA, USA; 10Princess Margaret Cancer Centre, Toronto, ON, CanadaCorrespondence: Filip Janku (fjanku@mdanderson.org)Journal for ImmunoTherapy of Cancer 2018, 6(Suppl 1):P651Janis Callister was not a contributing author and has therefore been removed from the author list in this correction article. The redundant affiliation Articulate Science as shown on the original article is no longer listed on this correction article.BackgroundFAZ053 and spartalizumab are humanized immunoglobulin G4 monoclonal antibodies (mAbs) that bind anti-programmed death ligand-1 (PD-L1) and programmed death-1 (PD-1), respectively. We report the dose-escalation results from an ongoing Phase I study of FAZ053 \u00b1 spartalizumab in patients with advanced malignancies, enriched for patients with chordoma, a rare subtype of sarcoma.MethodsPatients received escalating doses of single-agent (SA) FAZ053 intravenously once every 3 weeks (Q3W) or 6 weeks (Q6W), or FAZ053 + spartalizumab Q3W. The primary objective was to assess the safety and tolerability of FAZ053 \u00b1 spartalizumab, and determine recommended doses for expansion (RDEs). Dose escalation was guided by an adaptive Bayesian logistic regression model following the escalation with overdose control principle.ResultsAs of the data cutoff of March 30, 2018, 61 patients received SA FAZ053 at doses 80\u20131600 mg Q3W or 800\u20131600 mg Q6W. Most patients received prior treatment; 1 (2%) received prior anti-PD-1. FAZ053 exposure was generally dose proportional, with terminal half-life of ~16\u201318 days. A dose-limiting toxicity occurred in 1 patient . RDE was determined to be 1200 mg Q3W or 1600 mg Q4W. Adverse events (AEs) of all grades assessed as possibly related to treatment were reported for 33 patients (54%); most commonly (\u226510%) fatigue and pruritus ; 4 patients (7%) had Grade 3/4 treatment-related AEs, including elevated amylase (3%), renal failure, elevated lipase, elevated AST, and elevated blood CPK (each 2%). For these patients treated with SA FAZ053, partial responses (PRs) were demonstrated in 4 patients (7%) with chordoma, alveolar soft part sarcoma (ASPS), poorly differentiated carcinoma of scalp, and penile squamous cell carcinoma . Among 5 patients with chordoma treated with SA FAZ053, 1 patient has a PR, treatment ongoing >12 months, and 4 patients have stable disease ongoing (+4% to \u201329%). Data for 57 patients treated with combination FAZ053 (20\u20131200 mg) + spartalizumab 300 mg Q3W are preliminary. Updated results and biomarker data for patients receiving SA and combination treatment, including additional patients with chordoma, will be presented.ConclusionsSA FAZ053 was well tolerated and the RDE was determined to be 1200 mg Q3W. Clinical activity was observed in a range of indications including chordoma, a rare tumor without standard therapy options.Trial Registrationwww.clinicaltrials.gov; NCT02936102"} +{"text": "Scientific Reports 10.1038/s41598-018-25836-4, published online 10 May 2018Correction to: In this Article, the legend of Figure 3 is incorrect:\u201cA flowchart of the rapid (RAP) system for bone staining (RAP-B). The new procedure for bone staining which is rapid, nondestructive, and allowed to obtain high-definition, fine bone-stained specimens, was based on our RAP system. Cartilage staining (RAP-C) can be applied as single staining or optionally added before the bone staining for double staining of bone and cartilage . FIXATIVE: 5% formalin, 5% Triton X-100, 1% potassium hydroxide (KOH); B-STAINING SOLUTION: 0.05% alizarin red S, 20% ethylene glycol, 1% KOH; C-STAINING SOLUTION: 50\u201370% ethanol, 20% acetate, 0.015\u20130.02% alcian blue; CLEARING SOLUTION: 20% Tween 20, 1% KOH; ENHANCEMENT SOLUTION: 20% ethylene glycol, 5% Triton X-100, 1% KOH.\u201dshould read:\u201cA flowchart of the rapid (RAP) system for bone staining (RAP-B). The new procedure for bone staining which is rapid, nondestructive, and allowed to obtain high-definition, fine bone-stained specimens, was based on our RAP system. Cartilage staining (RAP-C) can be applied as single staining or optionally added before the bone staining for double staining of bone and cartilage . FIXATIVE: 5% formalin, 5% Triton X-100, 1% potassium hydroxide (KOH); B-STAINING SOLUTION: 0.05% alizarin red S, 20% ethylene glycol, 1% KOH; C-STAINING SOLUTION: 50\u201370% ethanol, 20% acetic acid, 0.015\u20130.02% alcian blue; CLEARING SOLUTION: 20% Tween 20, 1% KOH; ENHANCEMENT SOLUTION: 20% ethylene glycol, 5% Triton X-100, 1% KOH.\u201d"} +{"text": "Plasmodium vivax infections. Knowledge of the metabolism of PQ is critical for understanding the therapeutic efficacy and hemolytic toxicity of this drug. Recent in vitro studies with primary human hepatocytes have been useful for developing the ultra\u00a0high-performance liquid chromatography coupled with high-resolution mass spectrometric (UHPLC-QToF-MS) methods for simultaneous determination of PQ and its metabolites generated through phase I and phase II pathways for drug metabolism.Primaquine (PQ), an 8-aminoquinoline, is the only drug approved by the United States Food and Drug Administration for radical cure and prevention of relapse in These methods were further optimized and applied for phenotyping PQ metabolites from plasma and urine from healthy human volunteers treated with single 45\u00a0mg dose of PQ. Identity of the metabolites was predicted by MetaboLynx using LC\u2013MS/MS fragmentation patterns. Selected metabolites were confirmed with appropriate standards.Besides PQ and carboxy PQ (cPQ), the major plasma metabolite, thirty-four additional metabolites were identified in human plasma and urine. Based on these metabolites, PQ is viewed as metabolized in humans via three pathways. Pathway 1 involves direct glucuronide/glucose/carbamate/acetate conjugation of PQ. Pathway 2 involves hydroxylation (likely cytochrome P450-mediated) at different positions on the quinoline ring, with mono-, di-, or even tri-hydroxylations possible, and subsequent glucuronide conjugation of the hydroxylated metabolites. Pathway 3 involves the monoamine oxidase catalyzed oxidative deamination of PQ resulting in formation of PQ-aldehyde, PQ alcohol and cPQ, which are further metabolized through additional phase I hydroxylations and/or phase II glucuronide conjugations.This approach and these findings augment our understanding and provide comprehensive view of pathways for PQ metabolism in humans. These will advance the clinical studies of PQ metabolism in different populations for different therapeutic regimens and an understanding of the role these play in PQ efficacy and safety outcomes, and their possible relation to metabolizing enzyme polymorphisms.The online version of this article (10.1186/s12936-018-2433-z) contains supplementary material, which is available to authorized users. Plasmodium vivax malaria + (intense peak), 175.0842 [M\u2009+\u2009H-C5H8O2]+, 101.0593 [M\u2009+\u2009H-C10H10N2O]+, 83.0493 [M\u2009+\u2009H-C10H12N2O2]+ , 260.177 , 243.1523 , 175.0895 , 86.0959 , 160.0619 [M\u2009+\u2009H-C8H16NO2]+, 88.0384 [M\u2009+\u2009H-C14H18N2O]+ , 147.0553 [M\u2009+\u2009H-C6H11NO]+, 86.0970 [M\u2009+\u2009H-C9H6N2O2]+ , 2-Hydroxy PQ (18) and 4-hydroxy PQ (19) with the same retention time (Table\u00a017) could not be established due to non-availability of corresponding synthetic standard.ESI-HRMS of these four metabolites gave identical molecular ion peak at m/z 453.1881 [M\u2009+\u2009H]+ which corresponds to the molecular formula C21H29N2O9. , 161.0751 [M\u2009+\u2009H-C5H11N]+, 86.0966 [M\u2009+\u2009H-C9H8N2O]+, 69.0721 [M\u2009+\u2009H-C9H11N3O]+ , 86.0966 [M\u2009+\u2009H-C12H12N2O2]+ , 175.0884 [M\u2009+\u2009H-C11H16O8]+, 101.0593 [M\u2009+\u2009H-C16H18N2O7]+ (2) and cPQ (m/z 275.1385) (5), only seven additional metabolites of PQ were detected in plasma. These include four phase I metabolites namely, hydroxy-primaquine quinone-imine (m/z 274.1549) (1), carboxyprimaquine lactam (m/z 257.1273) (3), Dihydroxy-carboxyprimaquine methylester (m/z 321.1454) (8) and carboxyprimaquine methyl ester (m/z 289.1560) (6) and three phase II metabolites, namely, glycosylated PQ (m/z 422.2315) (7), PQ N-carbamoyl glucuronide (m/z 480.1992) (4) and PQ methyl carbamate (m/z 318.1789) (9). No hydroxylated metabolites of PQ were detected in plasma.Very limited numbers of PQ metabolites were detected in plasma from the individuals treated with single dose of PQ. Besides PQ (m/z 260.1769) (2) and the major plasma metabolite cPQ (m/z 275.1385) (5) were detected in urine also. Besides these, the carboxy PQ lactam (m/z 257.1273) (3), predictably formed by spontaneous cyclization of carboxy side chain of cPQ and PQ carbamoyl glucuronide (m/z 480.1992) (4), a unique phase II metabolite formed through direct N-carbamoylation of PQ followed by glucuronidation, which were present in plasma, were also detected in urine. Glycosylated PQ (m/z 422.2315) (7), a prominent metabolite detected in plasma, was not detected in urine. Three acetylated metabolites were present in urine namely, PQ acetate (m/z 302.1875) (29), acetylated hydroxyl-PQ glucuronide conjugate (m/z 494.2127) (20) and N-Acetyl-PQ quinone-imine (m/z 316.1676) (35). Two metabolites with different retention times but identical accurate mass and MS/MS fragmentation profile corresponding to PQ glucuronide conjugate (m/z 436.2100) were also detected in urine.The urine from the individuals treated with PQ contained large numbers of PQ metabolites. PQ (m/z 276.1694) correspond to 2-OH (18), 3-OH (21), and 4-OHPQ (14), and the fourth (17) could be 7-OH, 8-N\u2013OH, 1-N-oxide, or 8-N-oxide of PQ. Desmethy-PQ (m/z 246.1606) (19), and desmethyl-PQ glucuronide (m/z 422.1908) (12) were also detected in urine. Two metabolites predicted as PQ-quinone-imine (m/z 274.1549) and PQ-5,6-ortho-quinone (m/z 260.1403) (10), which is spontaneously generated from 5-OH-PQ, were also detected in urine. None of these phase I metabolites were detected in plasma. Further metabolism of hydroxyl-PQ was evident from presence of two dihydroxy-PQ (m/z 292.1647) metabolites and a dihydroxyl PQ quinone-imine (m/z 290.15) (24). Phase II conjugation metabolites, generated from further metabolism of hydroxyl PQ metabolites, detected in urine were two monohydroxy-PQ glucuronides (m/z 452.2011) trihydroxy-PQ glucuronide (m/z 484.1932) (23) and desmethyl-PQ glucuronide (m/z 422.1908) (12).Surprisingly, four mono hydroxylated metabolites of PQ, likely to be formed through CYP mediated pathways, were detected in urine. Three of these metabolites (m/z 451.1722) (32), hydroxyl cPQ glucuronide (m/z 467.1649) (27), trihydroxy-cPQ glucuronide (m/z 499.1545) (26) and dihydroxy cPQ methylester (m/z 321.1454) (8). Hydroxy-PQ alcohol (m/z 277.1559) (33), PQ alcohol glucuronide (m/z 437.1911) (31), hydroxyl-PQ alcohol glucuronide (m/z 453.1881) (15) detected in urine may be generated through further metabolism of PQ alcohol, the metabolite from oxidative deamination of PQ side chain alkyl amine.Further metabolism of cPQ, a major plasma metabolite, through phase I and phase II pathways of drug metabolism was evident from presence of several cPQ metabolites namely, cPQ glucuronide [N-carbamoylation and glucuronidation [2 tension yield N-carbamoyl glucuronide conjugates [N-carbamoyl glucuronide conjugate of PQ as a predominant metabolite, when PQ was incubated in vitro with primary human hepatocytes [S-PQ generated more than two-fold higher levels of the conjugate than (\u2212)-R-PQ [R-PQ to the oxidative deamination pathway [S-PQ than from (\u2212)-R-PQ. In the human hepatocyte study, glycosylated PQ was detected at time zero and thought to be a simple adduct of the primary amine group of PQ and the aldehyde form of glucose via non-enzymatic means. This metabolite could also be formed in plasma by the same mechanism. Predominant metabolism of (+)-S-PQ through these pathways may explain the somewhat lower plasma concentrations of the (+)-S-PQ, despite its negligible metabolism through oxidative deamination to cPQ [Based on the comprehensive LC-ESI-HRMS and MS/MS fragmentation profiles of PQ metabolites identified in plasma and urine of healthy human volunteers treated with single dose of 45\u00a0mg, PQ may be regarded as metabolized broadly through three pathways. Pathway 1 involves direct glucuronide/glucose/carbamate/acetate conjugation of PQ. The presence of s (UGTs) . Althougnidation , 36. Incatocytes . Formati(\u2212)-R-PQ . This ma pathway . Glycosy pathway and was n to cPQ , 20.orthoquinone was only detected in urine but not in plasma. Recent PK and tissue distribution studies in mice showed rapid appearance of PQ-5,6-orthoquinone in high concentrations in the liver and in low concentration in plasma and its fast disappearance from the liver and circulation [orthoquinone PQ. Earlier in vitro studies have indicated the role of multiple CYP isoforms in hemolytic toxicity of PQ with predominant involvement of CYP2D6 and CYP3A4 [orthoquinone metabolite, has been linked to therapeutic efficacy of PQ [orthoquinone through CYP2D6 mediated pathway [The pathway 2 mediated pathways, generates monohydroxylated PQ metabolites. These metabolites have been implicated in therapeutic efficacy and hemolytic toxicity of PQ. Further, extension of these studies to quantitative profiling of key metabolites in malaria infected individuals treated with PQ and their correlation with therapeutic outcomes vis-\u00e0-vis CYP2D6 genotypes may be useful in determining the rational approach for application of PQ in malaria radical cure, the primary application of this drug, as well as malaria control programs.This is the most exhaustive study on identification and characterization of human metabolites of primaquine, the only approved drug for malaria radical cure. Based on overall metabolites\u2019 profile, three pathways were predicted for metabolism by humans, (a) direct glucuronide/glucose/carbamate/acetate conjugation of PQ (b) hydroxylation of PQ at different positions on the quinoline ring and (c) oxidative deamination of PQ at the terminal amine of the aminoalkyl side chain. Metabolism of PQ through direct conjugation and oxidative deamination pathways may determine pharmacokinetics and pharmacodynamics of this important antimalarial drug. Metabolism of PQ through hydroxylations on the quinolone ring, predictably catalyzed by cytochrome PAdditional file 1: Fig. 1S. Key fragments of PQ and other metabolites using LC/ESI-QToF"} +{"text": "This article has been corrected: The authors made a mistake in size of scale bar in captions of Figures 2-5. The authors declare that this correction does not change the results or conclusions of this paper. The authors sincerely apologize for this error. The correct Figure captions are provided below. The correct scale bar size is marked in bold font.Ink4a+/CD34+) in human skeletal muscle after resistance exercise.Figure 2. Senescent endothelial progenitor cells (p16 (A) Representative immunohistochemical co-staining of muscle cross-sections (senescent cells indicated by arrows). Scale bar 55 \u03bcm. (B) Senescent endothelial progenitor cells decreased in human skeletal muscle after a single bout of resistance exercise, and to a greater extends under low protein supplemented condition. * Significant difference against Baseline, P < 0.05; \u2020 Significant difference against Low Protein, P < 0.05. Low protein: 14% protein; High protein: 44% protein in weight.+) in human skeletal muscle after resistance exercise.Figure 3. Phagocytic macrophage (CD68 (A) Representative immuno-histochemical staining of a muscle cross-section (CD68+ macrophage indicated by an arrow). Scale bar 100 \u03bcm. (B) Low protein supplementation before and after resistance exercise enhanced CD68+ macrophage infiltration in skeletal muscle above High protein trial. * Significant difference against Baseline, P < 0.05; \u2020 Significant difference against Low Protein, P < 0.05. Low protein: 14% protein; High protein: 44% protein in weight.+) in human skeletal muscle after resistance exercise.Figure 4. Regenerative macrophage (CD163 (A) Representative immunohistochemical staining of a muscle cross-section (CD163+ macrophage indicated by an arrow). Scale bar 100 \u03bcm. (B) High protein supplementation before and after resistance exercise increased CD163+ macrophage presence in human skeletal muscle 48 h after exercise. * Significant difference against Baseline, P < 0.05; \u2020 Significant difference against Low Protein, P < 0.05. Low protein: 14% protein; High protein: 44% protein in weight.Figure 5. Centrally nucleated fibers in human skeletal muscle after resistance exercise. (A) Representative hematoxylin and eosin staining of a muscle cross-section . Scale bar 100 \u03bcm. (B) (\u2020\u2020) No difference between Low and High protein trials was found. *Significant difference against Baseline, P < 0.05. Low protein: 14% protein; High protein: 44% protein in weight.1356-1365 . https://doi.org/10.18632/aging.101472Original article: Aging. 2018; 10:1356\u20131365."} +{"text": "Streptococcus pneumoniae Serotype 15A-ST63 Clone in Japan, 2012\u20132014 . The article has been corrected online (https://wwwnc.cdc.gov/eid/article/24/2/17-1276_article).Some data were inaccurate in the text and figures in Spread of Meropenem-Resistant"} +{"text": "The Supporting Information files were published with tracked changes. Please view the correct files below.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file.S5 Table(DOCX)Click here for additional data file.S6 Table(DOCX)Click here for additional data file.S7 Table(DOCX)Click here for additional data file.S1 Fig(DOCX)Click here for additional data file.S2 Fig(DOCX)Click here for additional data file.S3 Figvs. progressors using eGFR , Gd-IgA1 biomarkers, and Oxford classification . Area under the curve, AUC = 0.936. b- Receiver operating characteristic (ROC) curve for non-progressors vs. progressors using eGFR and Oxford classification . Area under the curve, AUC = 0.836.a- ROC curve for non-progressors (DOCX)Click here for additional data file.S4 Fig2 at the time of renal-biopsy; group 2 (n = 42), eGFR <60 mL/min/1.73 m2 at the time of renal-biopsy. Prediction equation from logistic regression (predicts probability to choose group 1): Pred(group 1) = 1 / (1 + exp(-(1517.5\u20131.2E-02*AB-IgA-24.9*eGFR))).Area under the curve = 1.00. Accuracy of the discrimination is 100%. Group 1 (n = 35), eGFR \u226560 mL/min/1.73 m(DOCX)Click here for additional data file.S5 FigS-creat, serum creatinine (\u03bcmol/L); eGFR ; serum IgG autoantibody specific for Gd-IgA1 (U/mL). Group 1 (n = 35), eGFR \u226560 mL/min/1.73 m2 at the time of renal biopsy; group 2 (n = 42), eGFR <60 mL/min/1.73 m2 at the time of renal biopsy.(DOCX)Click here for additional data file."} +{"text": "Scientific Reports 10.1038/s41598-018-34127-x, published online 23 October 2018Correction to: This Article contains errors in Figure 1, where 4 microbial diversity patterns were omitted. The correct Fig.\u00a0As a result, the Figure legend,A. mali gut microbiotas. Alpha-diversity in bacterial and fungal gut communities of A. mali gut. Beta-diversity in bacterial (E) and fungal (F) gut communities estimated via principal coordinate analysis (PCoA) based on Bray-Curtis distance.\u201d\u201cMicrobial diversity patterns for should read:A. mali gut microbiotas. Alpha-diversity in bacterial and fungal gut communities of A. mali gut. Beta-diversity in bacterial (E) and fungal (F) gut communities estimated via principal coordinate analysis (PCoA) based on Bray-Curtis distance.\u201d\u201cMicrobial diversity patterns for"} +{"text": "Scientific Reports 10.1038/s41598-019-54905-5, published online 05 December 2019Correction to: This Article contains a typographical error in the Acknowledgements section.\u201cMinistry of Education and Science of Russian Federation (Grant \u2116 12.1223.2017/AP to S.S. and E.R.).\u201dshould read:\u201cMinistry of Education and Science of Russian Federation (Grant No. 18-15-00172 to S.S.and E.R.)\u201d"} +{"text": "Acinetobacter radioresistens strain DD78 (= CCUG 69565) is a soil hydrocarbon-degrading and biosurfactant-producing bacterium isolated from chronically crude oil-polluted soil of the Aconcagua River mouth in Chile. The 3.25-Mb A. radioresistens DD78 genome (41.8% GC content) was completely sequenced, with 4 replicons, 2,970 coding sequences, and 77 tRNAs. Acinetobacter radioresistens strain DD78 (= CCUG 69565) is a soil hydrocarbon-degrading and biosurfactant-producing bacterium isolated from chronically crude oil-polluted soil of the Aconcagua River mouth in Chile. The 3.25-Mb A. radioresistens DD78 genome (41.8% GC content) was completely sequenced, with 4 replicons, 2,970 coding sequences, and 77 tRNAs. Acinetobacter species are aerobic Gram-negative coccobacilli present in soil, freshwater, sediment, polluted environments, and clinical samples , improving hydrocarbon bioavailability (A. radioresistens DD78 (CCUG_69565), a soil hydrocarbon-degrading and biosurfactant-producing bacterium from crude oil-polluted soil of the Aconcagua River mouth in Central Chile, which was isolated using enrichment in diesel (0.1% [vol/vol]) in Bushnell Hass mineral medium . The PacBio reads were trimmed and assembled into 5 contigs using SMRTLink v5 and the Hierarchical Genome Assembly Process v4.0 (HGAP4.0) with default parameters , proteins for osmoprotectant glycine betaine synthesis , and the osmoprotectant transporters osmo-dependent choline transporter, sodium/proline symporter, and aspartate/alanine antiporter were identified (>30% identity) with BLASTP using the Uniprot-KB/Swiss-Prot database. Arsenic and heavy metal resistance genes are in pAr1. Catabolic genes encoding an alkane monooxygenase , a rubredoxin NAD(H) reductase/rubredoxin system (E3H47_10395 and E3H47_10400), and the catechol and benzoate catabolic pathways are chromosomal. Comparative complete 16S rRNA gene sequence analysis showed a close relationship (99.7% identity) with A. radioresistens FO-1T and <97.5% identity with other Acinetobacter species (A. radioresistens CIP 103788T, A. lwoffii ATCC 9957T, and A. tandoii CIP 107469T showed ANIb values of 98.9%, 74.1%, and 73.6%, respectively, indicating that strain DD78 most likely belongs to the species A. radioresistens. The genome sequence of A. radioresistens DD78 provides essential data on alkane degradation, salt resistance, and biosurfactant production. samples , 2. A. b alkanes , 4. A. rlability , 6. Here78 CCUG_6565, a some sizes . The 5 cme sizes . The DD7me sizes identifime sizes identifi isolate . Genes e species with A. Acinetobacter radioresistens DD78 genome sequences have been deposited in DDBJ/ENA/GenBank under the accession number GCA_005519305 and the SRA accession number SRX5548971. The version discussed here is the first version. The BioProject number for the publicly available raw data is PRJNA528312.The"} +{"text": "Blood cultures were negative. Laparoscopic nodal biopsy showed sheets of medium-sized lymphocytes diffusely expressing CD30, TIA-1, granzyme B, and ALK, but not T-cell markers including CD2, CD3, CD4, CD5, CD7, CD8, and \u03b2F1, indicating ALK+ ALCL of null cell phenotype. Bone marrow biopsy showed two small aggregates of tumor cells in a background of normal tri-lineage hematopoiesis. ALK immunostaining revealed singly scattered positive cells (Anaplastic large cell lymphoma (ALCL) frequently involves both nodal and extranodal sites and is rarely leukemic. A 21-year-old male presented with abdominal pain. His complete blood count, which had been normal four months ago, showed increasing white cell counts from 14.9x10ve cells in additve cells . The dis"} +{"text": "Correction: J Intensive Carehttps://doi.org/10.1186/s40560-018-0352-2In the original publication of this article , an AuthSome data concerning specifically ECMO-treatment in patients with septic shock have been published previously in a German journal with respect to a completely different research question: Friedrichson B, Fichte J, Banjas N, Sch\u00fctz M, Hopf H-B. Extrakorporale Membranoxygenierung bei erwachsenen Patienten mit septischem Schock. An\u00e4sthesie und Intensivmed. 2018;59:698\u2013704."} +{"text": "Haemophilus influenzae and Streptococcus pneumoniae has been implicated in the pathogenesis of otitis media, mainly in chronic and recurrent cases. We studied the \u201cin vitro\u201d biofilm production by these 2 species isolated alone or together from the nasopharynx of children with acute otitis media.Biofilm production by H. influenzae and 191\u2009S. pneumoniae strains.The studied strains were from 3 pneumococcal conjugate vaccine (PCV) periods: pre-PCV7, post-PCV7/pre-PCV13 and post-PCV13. A modified microtiter plate assay with crystal violet stain was used to study the biofilm production of 182 H. influenzae and 128/191 (66.8%) S. pneumoniae strains produced biofilm. The proportion of biofilm-producing H. influenzae strains was greater with than without the isolation of S. pneumoniae in the same sample . Conversely, the proportion of biofilm-producing S. pneumoniae strains was not affected by the presence or not of H. influenzae (66.3% vs 67.4%). S. pneumoniae serotypes 6B, 15B/C, 19A, 35F and 35B were the better biofilm producers (80%). Serotypes 11A, 14, 15A, 19F and 19A were more associated with H. influenzae biofilm-producing strains. Overall, 89/94 (94.6%) of cases with combined isolation showed biofilm production by S. pneumoniae or H. influenzae.Overall, 117/181 (64.6%) H. influenzae and S. pneumoniae strains isolated from the nasopharynx of children with acute otitis media, which reinforces the results of studies suggesting the importance of biofilm in the pathogenesis of acute otitis media.This study emphasizes the high proportion of biofilm production by The online version of this article (10.1186/s12879-018-3657-9) contains supplementary material, which is available to authorized users. Acute otitis media (AOM) is the leading cause of bacterial infections in childhood, about 700 million cases each year, and the leading cause of antibiotic prescription . More thStreptococcus pneumoniae and non-typable Haemophilus influenzae (NT-Hi) as well as Moraxella catarrhalis : strong production >\u20091.10, moderate production 0.35\u20131.10, negative <\u20090.35.The cut-offs used to determine the intensity of biofilm production in isolates of S. pneumoniae were classified as strong biofilm producers, 55 (30.2%) moderate producers and 64 (35.1%) non-producers. One strain could not be evaluated. Overall, 117/181 (64.6%) NT-Hi strains produced biofilm were classified as strong biofilm producers, 64 (33.5%) moderate producers and 63 (33%) non-producers. Overall, 128/191 (66.8%) S. pneumoniae strains produced biofilm , whether isolated alone or with S. pneumoniae strains or with S. pneumoniae strains . Overall, the proportion of NT-Hi biofilm-producing strains was greater when isolated with S. pneumoniae or with NT-Hi strains (71.9 and 62.5% in pre-PCV7 and post-PCV13 periods). Overall, the proportion of S. pneumoniae biofilm-producing strains did not differ whether isolated alone or with NT-Hi strains that produced biofilm was similar to that for other serotypes: 57.4% (31/54) versus 70.6% (96/137), p\u00a0=\u20090.09 (data not shown). Moreover, the proportion did not differ between the 6 additional S. pneumoniae serotypes included in PCV13 and other serotypes . Strains of serotypes 6B, 15B/C, 19A, 35F, and 35B produced biofilm in more than 80% of the cases. In contrast, strains of serotypes 23B, 23F,19F were the lowest producers (40% of strains) of the combination. H. influenzae biofilm-producing strains were isolated more often with serotypes 11A, 14, 15A, 19F and 19A. This association did not affect biofilm production by S. pneumoniae.The p\u00a0=\u20090.44.Susceptibility or resistance to penicillin did not differ with and without biofilm production: 64.2% (61/96) versus 69.5% (66/95), -Hi strains produced biofilm when isolated with S. pneumoniae strains. Serotypes of S. pneumoniae were not associated with biofilm production by NT-Hi strains.Overall, 75.5% (72/96) of NTS. pneumoniae or H. influenzae or both produced biofilm in 94.6% (89/94) of cases or fever + otalgia . These relations were not observed for S. pneumoniae .Table -Hi and S. pneumoniae. Among NT-Hi strains, the proportion of \u03b2-lactamase\u2013producing strains decreased from 51.5% (33/64) in the pre-PCV7 period to 17.8% (10/56) and 17.7% (11/62) in the post-PCV7/pre-PCV13 and post-PCV13 periods, respectively (p\u2009<\u20090.001). As well, the proportion of S. pneumoniae strains with decreased susceptibility to penicillin decreased from 65.7% in the pre-PCV7 period to 45.4% (29/64) and 39.7% (25/63) in the post-PCV7/pre-PCV13 and post-PCV13 periods (p\u2009=\u20090.003). Among S. pneumoniae strains, the proportion of those with erythromycin susceptibility increased from 46.8% (30/64) to 81% (51/63) between the post-PCV7/pre-PCV13 and post-PCV13 periods, respectively (p\u2009<\u20090.001).The proportion of resistant strains significantly decreased from the pre-PCV7 to post-PCV13 periods for both NT. pneumoniae serotypes changed according to the study period with no variation in proportion for S. pneumoniae over PCV implementation periods. Of note, the proportion of NT-Hi biofilm-producing strains was greater when H. influenzae strains were isolated with S. pneumoniae, which agreed with the results of Hong et al. : strong production >\u20091.10, moderate production 0.35\u20131.10, negative <\u20090.35. Strains were classified according to agreement of at least 2 of the 3 methods used to calculate biofilm production. (XLS 195 kb)Supplementary Data S1: Different cut-offs used to determine the biofilm production by Additional file 2:H. influenzae: the different cut-offs used were as followed where AB represented the stained wells containing attached bacteria, CW the stained control wells containing bacteria-free medium only and G the bacterial growth control i) AB \u2013 CW: strong production >\u20090.30, moderate production 0.10\u20130.30, negative <\u20090.10 ii) AB / CW: strong production >\u20096, moderate production 2\u20136, negative <\u20092 iii)[(AB \u2013 CW) / G]: strong production >\u20091.10, moderate production 0.35\u20131.10, negative <\u20090.35. Strains were classified according to agreement of at least 2 of the 3 methods used to calculate biofilm production. (XLSX 76 kb)Supplementary Data S2: Different cut-offs used to determine the biofilm production by Additional file 3:. pneumoniae serotypes by study period . (DOCX 15 kb)Supplementary Data S3: Distribution of S"} +{"text": "Scientific Reports 10.1038/s41598-017-01512-x, published online 02 May 2017Correction to: This Article contains an error in Reference 29:PLoS One12(4), e0175267 (2017)\u2019\u2018Jose Carlos Mancera Gracia, Silvie Van den Hoecke, Xavier Saelens, Kristien Van Reeth & Mirco Schmolke. Effect of serial pig passages on the adaptation of an avian H9N2 influenza virus to swine. should read:PLoS One12(4), e0175267 (2017)\u2019\u2018Mancera Gracia, J. C., Van den Hoecke, S., Saelens, X. & Van Reeth, K. Effect of serial pig passages on the adaptation of an avian H9N2 influenza virus to swine."} +{"text": "Ralstonia solanacearum is a major phytopathogenic bacterium that attacks many crops and other plants around the world. In this study, a novel actinomycete, designated strain NEAU-SSA 1T, which exhibited antibacterial activity against Ralstonia solanacearum, was isolated from soil collected from Mount Song and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the strain coincided with those of the genus Streptomyces. The 16S rRNA gene sequence analysis showed that the isolate was most closely related to Streptomyces aureoverticillatus JCM 4347T (97.9%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a cluster with Streptomyces vastus JCM4524T (97.4%), S. cinereus DSM43033T (97.2%), S. xiangluensis NEAU-LA29T (97.1%) and S. flaveus JCM3035T (97.1%). The cell wall contained LL-diaminopimelic acid and the whole-cell hydrolysates were ribose, mannose and galactose. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), hydroxy-phosphatidylethanolamine (OH-PE), phosphatidylinositol (PI), two phosphatidylinositol mannosides (PIMs) and an unidentified phospholipid (PL). The menaquinones were MK-9(H4), MK-9(H6), and MK-9(H8). The major fatty acids were iso-C17:0, C16:0 and C17:1 \u03c99c. The DNA G+C content was 69.9 mol %. However, multilocus sequence analysis (MLSA) based on five other house-keeping genes , DNA\u2013DNA relatedness, and physiological and biochemical data showed that the strain could be distinguished from its closest relatives. Therefore, it is proposed that strain NEAU-SSA 1T should be classified as representatives of a novel species of the genus Streptomyces, for which the name Streptomyces sporangiiformans sp. nov. is proposed. The type strain is NEAU-SSA 1T (=CCTCC AA 2017028T = DSM 105692T). Ralstonia solanacearum is the causal agent of bacterial wilt, one of the most devastating plant pathogenic bacteria around the world [he world , which hhe world , includihe world . TherefoStreptomyces, within the family Streptomycetaceae, is the largest genus of the phylum Actinobacteria, first proposed by Waksman and Henrici (1943) [http://www.bacterio.net/streptomyces.html), which are widely distributed in soils throughout the world. Therefore, members of novel Streptomyces species are in demand as sources of novel, environmentally friendly, commercially significant, naturally bioactive compounds [T with inhibitory activity against phytopathogenic bacterium Ralstonia solanacearum was isolated and subjected to the polyphasic taxonomy analysis. Results demonstrated that the strain represents a novel species of the genus Streptomyces, for which the name Streptomyces sporangiiformans sp. nov. is proposed.The actinobacteria are known to produce biologically active secondary metabolites, including antibiotics, enzymes, enzyme inhibitors, antitumour agents and antibacterial compounds ,5,6. Thei 1943) and currompounds ,9. Durin43 and cT was isolated from soil collected from Mount Song , Dengfeng, Henan Province, China. The soil sample was air-dried at room temperature for 14 days before isolation for actinomycetes. After drying, the soil sample was ground into powder and then suspended in sterile distilled water, followed by a standard serial dilution technique. The diluted soil suspension was spread on humic acid-vitamin agar (HV) [\u22121) and nalidixic acid (20 mg L\u22121). After 28 days of aerobic incubation at 28 \u00b0C, colonies were transferred and purified on the International Streptomyces Project (ISP) medium 3 [v/v) at \u221280 \u00b0C for long-term preservation.Strain NEAU-SSA 1gar (HV) supplemew/v) were tested in GY (Glucose-Yeast extract) medium [2PO4/0.1 M NaOH; pH 9.0\u201310.0, 0.1 M NaHCO3/0.1 M Na2CO3; and pH 11.0\u201312.0, 0.2 M KH2PO4/0.1 M NaOH. Hydrolysis of Tweens and production of urease were tested as described by Smibert and Krieg [2S were examined as described previously [Gram staining was carried out by using the standard Gram stain, and morphological characteristics were observed using light microscopy and scanning electron microscopy using cultures grown on ISP 3 agar at 28 \u00b0C for 6 weeks. Samples for scanning electron microscopy were prepared as described by Jin et al. . Cultura) medium at 28 \u00b0Cnd Krieg . The utieviously ,20.18 Column that had a mobile phase consisting of acetonitrile: 0.05 mol L\u22121 phosphate buffer pH 7.2 at a flow rate of 0.5 mL min\u22121. The peak detection used an Agilent G1321A fluorescence detector with a 365 nm excitation and 455 nm longpass emission filters. The whole-cell sugars were analyzed according to the procedures developed by Lechevalier and Lechevalier [18 Column at 270 nm. The mobile phase was acetonitrile-iso-propyl alcohol . To determine cellular fatty acid compositions, the strain NEAU-SSA 1T was cultivated in GY medium in shake flasks at 28 \u00b0C for 4 days. Fatty acid methyl esters were extracted from the biomass as described by Gao et al. [Biomass for chemotaxonomic studies was prepared by growing the organisms in GY medium in shake flasks at 28 \u00b0C for 5 days. Cells were harvested using centrifugation, washed with distilled water, and freeze-dried. The isomer of diaminopimelic acid (DPA) in the cell wall hydrolysates was derivatized and analyzed using an HPLC (High Performance Liquid Chromatography) method with an hevalier . The polhevalier . Menaquihevalier . Extracto et al. and analT was cultured in GY medium for 3 days to the early stationary phase and harvested using centrifugation. The chromosomal DNA was extracted according to the method of sodium dodecyl sulfate (SDS)-based DNA extraction [T (1412bp) was obtained and compared with type strains available at the EzBioCloud server (https://www.ezbiocloud.net/), retrieved using NCBI BLAST and then submitted to the GenBank database. Phylogenetic trees were constructed based on the 16S rRNA gene sequences of strain NEAU-SSA 1T and related reference species. Sequences were multiply aligned in Molecular Evolutionary Genetics Analysis (MEGA) software version 7.0 using the Clustal W algorithm and trimmed manually where necessary. Phylogenetic trees were constructed with neighbor-joining [T to its closely related strains, phylogenetic relationships of the strain NEAU-SSA 1T were also confirmed using sequences of five individual housekeeping genes for core-genome analysis. The sequences of NEAU-SSA 1T and its related strains were obtained from the genomes or GenBank/EMBL/DDBJ (European Molecular Biology Laboratory/DNA Data Bank of Japan). GenBank accession numbers of the sequences used are given in atpD-gyrB-recA-rpoB-trpB. Phylogenetic analysis was performed as described above. Genome mining for bioactive secondary metabolites was performed using \u201cantibiotics and secondary metabolite analysis shell\u201d (antiSMASH) version 4.0 [For DNA extraction, strain NEAU-SSA 1traction . PCR amptraction ,30. The -joining and maxi-joining algorith-joining . The sta-joining . A dista-joining . All pos-joining . To furtsion 4.0 .T was extracted using the method of SDS-based DNA extraction [\u00ae 2.0 Fluorometer (Thermo Scientific). Whole-genome sequencing was performed on the Illumina HiSeq PE150 platform. A-tailed, ligated to paired-end adaptors, and PCR amplified samples with a 350 bp insert were used for the library construction at the Beijing Novogene Bioinformatics Technology Co., Ltd. Illumina PCR adapter reads and low-quality reads from the paired-end were filtered using a quality control step using our own compling pipeline. All good-quality paired reads were assembled using the SOAP (Short Oligonucleotide Alignment Program) denovo [https://github.com/aquaskyline) into a number of scaffolds. Then, the filter reads were handled by the next step of the gap-closing.For draft genome sequencing and assembly, the genomic DNA of strain NEAU-SSA 1traction . The har) denovo ,39 , then sheared using a JY92-II ultrasonic cell disruptor . The DNA renaturation rates were determined in 2 \u00d7 SSC at 70 \u00b0C. The experiments were performed with three replications and the DNA\u2013DNA relatedness value was expressed as a mean of the three values. Several genomic metrics are now available to distinguish between orthologous genes of closely related prokaryotes, including the calculation of average nucleotide identity (ANI) and digital DNA\u2013DNA hybridization (dDDH) values [T and S. flaveus JCM3035T (JOCU00000000) using the ortho-ANIu algorithm from Ezbiotaxon and the genome-to-genome distance calculator (GGDC 2.0) at http://ggdc.dsmz.de.Because of a lacking number of genome sequences of y et al. under coy et al. , using atraction . The con) values ,43. In tT against two pathogenic bacteria was evaluated using the agar well diffusion method [T, the strain was cultured in tryptone-glucose-soluble starch-yeast extract medium , and the inhibitory activity was tested. Briefly, strain NEAU-SSA 1T was inoculated into MB medium and incubated at 28 \u00b0C for seven days in a rotary shaker. The supernatant (100 mL for this study) was obtained via centrifugation at 8000 rpm and 4 \u00b0C for 10 min and subsequently extracted by using an equal volume of ethyl acetate. Then, the extract was dried in a rotary evaporator at 40 \u00b0C and eluted with proper volume methanol (1 mL used in this study). The cell precipitate was extracted with an equal volume of methanol and also condensed as above. After that, the antibacterial activity was evaluated using the agar well diffusion method, and each well contained 200 \u00b5L of the methanol extract. To examine the effect of temperature on antibacterial activity, the ten-fold dilution methanol extract was placed in a water bath at 40, 60, 80, and 100 \u00b0C for 30 min, and then cooled to room temperature. The antibacterial activity was evaluated using the agar well diffusion method.The antibacterial activity of strain NEAU-SSA 1n method with theT showed that the strain had the typical characteristics of the genus Streptomyces. Observation of 6-week cultures of strain NEAU-SSA 1T grown on ISP 3 medium revealed that it formed well-developed, branched substrate hyphae and aerial mycelia. Sporangia consisted of cylindrical, and rough-surfaced spores (0.6\u20130.8 \u03bcm \u00d7 0.9\u20131.6 \u03bcm) were produced on aerial mycelia, but spore chains were not observed with an optimal level of 0\u20131% (w/v). Detailed physiological characteristics are presented in the species description (29.5%), MK-9(H6) (41.2%), and MK-9(H8) (29.4%). The cellular fatty acid profile of strain NEAU-SSA 1T was composed of iso-C17:0 (30.9%), C16:0 (26.4%), C17:1\u03c99c (19.9%), C15:0 (7.8%), C17:0 (4.4%), C14:0 (3.3%), iso-C16:0 (1.7%), anteiso-C15:0 (1.7%), C18:1\u03c99c (1.7%), C16:0 1-OH (1.2%), and iso-C18:0 (1.1%). The polar lipids of the strain consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), hydroxy-phosphatidylethanolamine (OH-PE), phosphatidylinositol (PI), two phosphatidylinositol mannosides (PIMs), and an unidentified phospholipid (PL) . All theT were affiliated with the genus Streptomyces and most closely related to S. aureoverticillatus JCM 4347T (97.9%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a cluster with S. vastus JCM4524T (97.4%), S. cinereus DSM43033T (97.2%), S. xiangluensis NEAU-LA29T (97.1%), and S. flaveus JCM3035T (97.1%) in the neighbor-joining tree and S. flaveus JCM 3035T (7%); and the strain could grow at pH 11.0, while S. vastus JCM4524T, S. cinereus DSM 43033T, and S. xiangluensis NEAU-LA29T could not. Other phenotypic differences included the production of H2S; decomposition of cellulose; liquefaction of gelatin; growth temperature; hydrolysis of Tweens ; and utilization of L-arabinose, D-galactose, D-fructose, D-maltose, lactose, L-rhamnose, D-ribose, D-sorbitol, D-mannose, raffinose, D-xylose, myo-inositol, L-glutamine, glycine, L-threonine, L-tyrosine, L-serine, L-proline, L-asparagine, and L-arginine.Comparison of phenotypic characteristics between strain NEAU-SSA 1 strains . DiffereT is considered to represent a novel species within the genus Streptomyces, for which the name Streptomyces sporangiiformans is proposed.On the basis of morphological, physiological, chemotaxonomic, and phylogenetic results, strain NEAU-SSA 1Streptomyces sporangiiformans .w/v) NaCl. Growth was observed at temperatures between 15 and 45 \u00b0C, with an optimum temperature of 28 \u00b0C. Positive for decomposition of Tweens (40 and 80) and cellulose, hydrolysis of aesculin and starch, liquefaction of gelatin and production of urease; and negative for coagulation and peptonization of milk, hydrolysis of Tween 20, production of H2S, and reduction of nitrate. D-fructose, D-galactose, D-glucose, inositol, lactose, D-maltose, D-mannose, D-raffinose, L-rhamnose, and D-sucrose were utilized as sole carbon sources, but not L-arabinose, dulcitol, D-ribose, D-sorbitol, or D-xylose. L-alanine, L-arginine, L-asparagine, L-aspartic acid, creatine, L-glutamic acid, L-glutamine, L-proline, L-serine, and L-threonine were utilized as sole nitrogen sources, but not glycine or L-tyrosine. Cell wall contained LL-diaminopimelic acid and the whole-cell hydrolysates were ribose, mannose, and galactose. The polar lipids contained diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), hydroxy-phosphatidylethanolamine (OH-PE), phosphatidylinositol (PI), two phosphatidylinositol mannosides (PIMs), and an unidentified phospholipid (PL). The menaquinones were MK-9(H4), MK-9(H6), and MK-9(H8). Major fatty acids were iso-C17:0, C16:0, and C17:1\u03c99c.Gram-stain-positive, aerobic actinomycete that formed well-developed, branched substrate hyphae and aerial mycelia. Sporangia consisted of cylindrical and rough surfaced spores (0.6\u20130.8 \u03bcm \u00d7 0.9\u20131.6 \u03bcm) were produced on aerial mycelia, but spore chains were not observed. Good growth on ISP 3, ISP 4, ISP 7, and Nutrient agar media; moderate growth on ISP 1, ISP 2, ISP 5, ISP 6, and Czapek\u2019s agar media; and poor growth on Bennett\u2019s agar medium. Growth occurred at pH values between 6.0 and 11.0, the optimum being pH 7.0. Tolerates up to 6.0% NaCl and grows optimally in 0\u20131% (T (=CCTCC AA 2017028T = DSM 105692T), isolated from soil collected from Mount Song, Dengfeng, Henan Province, China. The DNA G+C content of the type strain was 69.9 mol %, calculated from the assembly for the draft genome sequence. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain NEAU-SSA 1T is MH842151. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession VCHX00000000. The version described in this paper is version VCHX00000000.2.The type strain was NEAU-SSA 1T exhibited antibacterial activity against Ralstonia solanacearum with inhibitory zone diameters of 23 mm suggested that strain NEAU-SSA 1T belonged to the genus Streptomyces. Physiology and biochemical characteristics, together with DDH relatedness values and ANI values, clearly indicated that strain NEAU-SSA 1T could be differentiated from the closely related strains S. aureoverticillatus JCM 4347T, S. vastus JCM 4524T, S. cinereus DSM 43033T, S. xiangluensis NEAU-LA29T, and S. flaveus JCM 3035T. Based on the polyphasic analysis, it is proposed that strain NEAU-SSA 1T should be classified as representatives of a novel species of the genus Streptomyces, for which the name Streptomyces sporangiiformans sp. nov. is proposed. The type strain is NEAU-SSA 1T (=CCTCC AA 2017028T = DSM 105692T).A novel strain NEAU-SSA 1"} +{"text": "These articles have been corrected: The Figure 2G in \u2018Upregulation of long non-coding RNA PlncRNA-1 promotes proliferation and induces epithelial-mesenchymal transition in prostate cancer,\u2019 (https://doi.org/10.18632/oncotarget.15318), is a duplication of Figure 3F in the published article \u2018PlncRNA-1 induces apoptosis through the Her-2 pathway in prostate cancer cells,\u2019 (https://doi.org/10.4103/1008-682X.178849). The proper Figure 2G is shown below. The authors declare that these corrections do not change the results or conclusions of this paper.26090-26099.https://doi.org/10.18632/oncotarget.15318Original article: Oncotarget. 2017; 8:26090\u201326099."} +{"text": "Lysinibacillus sp. OL1 and Enterococcus sp. OL5, were isolated from boron fertilizer-amended cauliflower plantation field soils in India. Here, we report the draft genome sequences of OL1 (4.87\u2009Mb) and OL5 (3.93\u2009Mb) to explore the intricacies of boron tolerance in bacteria.Two novel boron-tolerant, arsenic-resistant, Gram-positive bacterial strains, Lysinibacillus sp. OL1 and Enterococcus sp. OL5, were isolated from boron fertilizer-amended cauliflower plantation field soils in India. Here, we report the draft genome sequences of OL1 (4.87\u2009Mb) and OL5 (3.93\u2009Mb) to explore the intricacies of boron tolerance in bacteria.Two novel boron-tolerant, arsenic-resistant, Gram-positive bacterial strains, The enriched culture was dilution plated on boric acid-supplemented tryptone soya agar (TSA) for isolation and screening of boron-tolerant strains, as described previously (3BO3 and sodium arsenite (NaAsO2), respectively, was tested in TSA supplemented with different concentrations of boron or arsenic , following methods described previously (Boron (B) occurs in soil solution as a nonionized molecule (Ht growth . Boron-t arsenic with minhttp://www.usadellab.org/cms/?page=trimmomatic) high-quality data, which were subsequently assembled into 179 scaffolds using SPAdes v3.11.1 with default parameters (http://hannonlab.cshl.edu/fastx_toolkit/download.html). For OL5, a genomic DNA library was constructed using an Ion Xpress Plus fragment library kit and sequenced on a 530 chip of the Ion S5 system (Thermo Fisher Scientific). Before sequence retrieval from Ion S5, low-quality and polyclonal reads were filtered out and the adaptor sequences trimmed using the inbuilt PGM software. A total of 3,993,359\u2009bp of adapter-free, quality-filtered reads were obtained and subsequently assembled into 46 contigs using SPAdes v3.13.0 with default parameters under the accession numbers PRJNA521315 and PRJNA549579.These whole-genome shotgun projects have been deposited at DDBJ/ENA/GenBank under the accession numbers"} +{"text": "HERC family emerged >595 million years ago and has undergone gene duplication and gene loss events throughout its evolution. The structural topology of the RCC1-like domain and HECT domains from all HERC paralogs is highly conserved among evolutionarily diverse vertebrates despite low sequence homology. Functional analyses showed that the human small HERCs exhibit different degrees of antiviral activity toward HIV-1 and that HERC5 provides the strongest inhibition. Notably, coelacanth HERC5 inhibited simian immunodeficiency virus (SIV), but not HIV-1, particle production, suggesting that the antiviral activity of HERC5 emerged over 413 million years ago and exhibits species- and virus-specific restriction. In addition, we showed that both HERC5 and HERC6 are evolving under strong positive selection, particularly blade 1 of the RCC1-like domain, which we showed is a key determinant of antiviral activity. These studies provide insight into the origin, evolution, and biological importance of the human restriction factor HERC5 and the other HERC family members.In humans, homologous to the E6-AP carboxyl terminus (HECT) and regulator of chromosome condensation 1 (RCC1)-like domain-containing protein 5 (HERC5) is an interferon-induced protein that inhibits replication of evolutionarily diverse viruses, including human immunodeficiency virus type 1 (HIV-1). To better understand the origin, evolution, and function of HERC5, we performed phylogenetic, structural, and functional analyses of the entire human small-HERC family, which includes HERC3, HERC4, HERC5, and HERC6. We demonstrated that the IMPORTANCE Intrinsic immunity plays an important role as the first line of defense against viruses. Studying the origins, evolution, and functions of proteins responsible for effecting this defense will provide key information about virus-host relationships that can be exploited for future drug development. We showed that HERC5 is one such antiviral protein that belongs to an evolutionarily conserved family of HERCs with an ancient marine origin. Not all vertebrates possess all HERC members, suggesting that different HERCs emerged at different times during evolution to provide the host with a survival advantage. Consistent with this, two of the more recently emerged HERC members, HERC5 and HERC6, displayed strong signatures of having been involved in an ancient evolutionary battle with viruses. Our findings provide new insights into the evolutionary origin and function of the HERC family in vertebrate evolution, identifying HERC5 and possibly HERC6 as important effectors of intrinsic immunity in vertebrates. Vertebrates possess multiple defense mechanisms to inhibit the replication of viruses. This defense system is largely composed of specialized hematopoietic cells that react nonspecifically to pathogens (innate immunity), an antibody-dependent and cell-mediated response (adaptive immunity), and core cellular effector proteins called restriction factors (intrinsic immunity). Restriction factors are considered to be the front line of defense against viral infection, since their activity typically does not require virus-triggered signaling or intercellular communication . The imp3\u2013Retroviridae, Orthomyxoviridae, Flaviviridae, Togaviridae, Herpesviridae, Poxviridae, Arteriviridae, and Pneumoviridae (\u201328\u201332\u201332\u2013Interferon-stimulated gene 15 (ISG15) and/or its conjugation to newly translated proteins (referred to as ISGylation) exhibits broad antiviral activity toward evolutionarily diverse viruses, including those belonging to the families oviridae \u201331. The idae \u201328\u2013, 32\u201336. By virtue of their RCC1-like domains, HERCs also belong to the phylogenetically widespread RCC1 superfamily of proteins , 39. The32\u2013https://genome.ucsc.edu]) and NCBI gene and protein sequence databases for the presence of small HERC gene members. The oldest small-HERC member is HERC4, which is present in one of the only surviving lineages of jawless fish, sea lampreys (originating \u223c595 million years ago [mya]) , just after the small-HERC family expanded with the duplication and divergence of HERC4 , giving rise to two different chromosomal HERC loci in most vertebrates, where the HERC3-HERC5-HERC6 locus is flanked by FAM13A and PIGY-PYURF and HERC4 by MYPN and SIRT1 . To bettngements . This alngements . A singlof HERC4 . HERC3 and SIRT1 .HERC family expanded further after the divergence of cartilaginous fish (\u223c430 mya), with the emergence of HERC6, which is present in most jawed vertebrates with an apparent absence in platypus and some fish and bird species (HERC family occurred after the divergence of ray-finned fish (\u223c413 mya), with the likely duplication of HERC6, giving rise to HERC5 , metatherian mammals , and rodents 43, 45), 45HERC HERC sequences showed segregation of the small HERC genes into four major clusters consisting of HERC3, HERC4, HERC5, and HERC6 . Notably, coelacanth and lizard HERC5 sequences clustered on their own, showing more sequence similarity to HERC6 genes than to other HERC5 genes, possibly indicating that these genes are actually HERC6 or a hybrid of HERC5 and HERC6. Similar tree topologies regarding the main branching were predicted using several tree-generating algorithms . Consistent with the approximate emergence times of the small-HERC family members shown in HERC4 is the oldest of the HERC paralogs, followed by HERC3, HERC6, and then HERC5.Phylogenetic analysis of nd HERC6 . Most HEH structural measure derived from alignment of the predicted tertiary structures of RCC1-like domains (https://bmm.crick.ac.uk/~populus/) and showed that each of the RCC1-like domains of HERC3 to -6 adopted the characteristic \u03b2-propeller structure of the superfamily, despite their low sequence homology constructs for the ability to knock down endogenous HERC mRNA and protein levels. As shown in HOS-CD4-CXCR4 cells were cotransfected with plasmids carrying HERC shRNA and HIV-1 R9 (a full-length replication-competent NL4-3 derivative). After 72 h of replication (\u223c2 or 3 rounds), quantitative Western blot analysis of cell lysates or virions produced from cells showed that cells knocked down for HERC5 expression exhibited a significant increase in Gag particle production (\u223c8-fold), whereas HERC3, -4, and -6 released modestly more virions into the supernatant than the control cells (\u223c2-fold) . The amo53\u2013To test the effect of increased HERC expression on single-round HIV-1 particle production, human 293T cells, which do not support multiround replication, were cotransfected with plasmids carrying HIV-1 (R9) and either empty vector, HERC3, HERC4, HERC5 or HERC6. As expected, HERC5 potently inhibited HIV-1 particle production . HERC3 oWe previously showed that human HERC5 blocked nuclear export of Rev-dependent HIV-1 RNA . To detecis-acting element called the Rev-response element (RRE) located within an HIV-1 intron and Rev-independent constructs, as previously described , 58. HIV1 intron . HIV-1 m1 intron . Success1 intron and F. THERC5, we tested the ability of coelacanth HERC5 to inhibit HIV-1 virus production. To assess potential virus-specific effects, we also tested the antiviral activity toward another, related nonhuman retrovirus, simian immunodeficiency virus (SIV) , which is thought to be at least 32,000 years older than HIV-1 or blade 1 (H6:H5blade1) from human HERC5 with the corresponding region in human HERC6. We then measured the abilities of these HERC6 mutants to inhibit HIV-1 particle production. As shown in HERC family has an ancient marine origin, where HERC4 emerged at least 595 mya and expansion of the family occurred sometime after the divergence of jawed vertebrates from jawless vertebrates (\u223c476 to 595 mya). Elephant sharks are among the oldest and most slowly evolving jawed vertebrates and have accumulated a small number of chromosomal rearrangements comprise a substantial portion of vertebrate genomes and appear to have an ancient marine origin, with evidence of ERV sequences found in the genomes of elephant shark, coelacanth, and possibly lamprey , resulting in a smaller repertoire of immune genes than in humans . However, HERC3 and HERC4 do exhibit differential tissue-specific expression supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U/ml penicillin, and 100 \u03bcg/ml streptomycin at 37\u00b0C with 5% COHomo sapiens (human) (NP_055421.1), Gorilla gorilla gorilla (gorilla) (XP_004039158.1), Pan troglodytes (chimpanzee) (XP_517337.3), Nomascus leucogenys (gibbon) (XP_003265945.1), Papio anubis (baboon) (XP_003898995.1), Saimiri boliviensis boliviensis (squirrel monkey) (XP_003924058.1), Callithrix jacchus (marmoset) (XP_002745644.1), Bos taurus (cow) (NP_001077132.1), Ovis aries (sheep) (XP_004009758.1), Felis catus (cat) (XP_003985228.1), Canis lupus familiaris (dog) (XP_535653.3), Ailuropoda melanoleuca (giant panda) (XP_002913643.1), Equus caballus (horse) (XP_001496703.3), Callorhinchus_milii (elephant shark) (XM_007902532.1), Danio rerio (zebrafish) (NM_001145624.1), Takifugu rubripes (pufferfish) (XM_011612933.1), Oreochromis niloticus (tilapia) (XM_005456948.2), Latimeria chalumnae (coelacanth) (XM_006005071.2), Xenopus tropicalis (frog) (XM_002938630.3), Anolis carolinensis (lizard) (XM_008111037.2), Geospiza fortis (finch) (XM_005418124.1), Meleagris gallopavo (turkey) (XM_003205471.2), Gallus gallus (chicken) (XM_015276202.1), Monodelphis domestica (opossum) (XM_007495699.2), Mus musculus (mouse) (NM_028705.3), and Dasypus novemcinctus (armadillo) (XM_004480548.2); for HERC4, human (NP_071362.1), gorilla (XP_004049535.1), chimpanzee (XP_001167753.1), gibbon (XP_003258260.1), baboon (XP_003903924.1), squirrel (XP_003928728.1), marmoset (XP_002756356.1), cow (NP_001070362.2), sheep (XP_004021455.1), dog (XP_849808.1), panda (XP_002913788.1), horse (XP_001503636.1), elephant shark (XM_007897346.1), zebrafish (XM_005173035.3), pufferfish (XM_011602912.1), tilapia (XM_005473848.2), coelacanth (XM_005992449.2), frog (NM_001128650.1), lizard (XM_008115175.2), finch (XM_005428501.2), turkey (XM_010714265.1), chicken (XM_015278711.1), Ornithorhynchus anatinus (platypus) (XM_007667149.1), opossum (XM_016421882.1), mouse (NM_030114.2), armadillo (XM_012529817.1), and Petromyzon marinus (lamprey) ENSPMAG00000001626; for HERC5, human (NP_057407.2), chimpanzee (XP_003310459.1), gorilla (XP_004039179.1), marmoset (XP_002745648.1), baboon (XP_003898997.1), squirrel monkey (XP_003924055.1), gibbon (XP_003265940.1), horse (XP_001915115.2), giant panda (XP_002913645.1), sheep (XP_004009762.1), cow (NP_001095465.1), dog (XP_535652.3), cat (XP_003985249.1), coelacanth (XM_014498805.1), lizard (XM_008111035.2), and armadillo (XM_012520464.1); for HERC6, human (NP_060382.3), gorilla (XP_004039178.1), chimpanzee (XP_001160851.1), gibbon (XP_003265938.1), baboon (XP_003899001.1), squirrel (XP_003924053.1), marmoset (XP_002745681.1), cow (NP_001179573.1), sheep (XP_004010096.1), cat (XP_003985250.1), dog (XP_851549.1), horse (XP_001494887.1), pufferfish (XM_011618146.1), tilapia (XM_005474674.1), coelacanth (XM_014498807.1), frog (XM_002938624.2), lizard (XM_008111034.2), opossum (XM_007495704.1), mouse (NM_025992.2), and armadillo (XM_012520459.1).The MEGA 7.0 package was used for phylogenetic analysis . The amiCallorhinchus milii 6.1.3 GCF_000165045.1 (elephant shark), Danio rerio GRCz10 GCF_000002035.5 (zebrafish), Takifugu rubripes FUGU5 GCF_000180615.1 (pufferfish), Oreochromis niloticus Orenil1.1 GCF_000188235.2 (tilapia), Latimeria chalumnae LatCha1 GCF_000225785.1 (coelacanth), Xenopus tropicalis Xtropicalis_v7 GCF_000004195.2 (frog), Anolis carolinensis AnoCar2.0 GCF_0000090745.1 (lizard), Geospiza fortis GeoFor_1.0 GCF_000277835.1 (finch), Meleagris gallopavo Turkey_5.0 GCF_000146605.2 (Turkey), Gallus_gallus-5.0 GCF_000002315.4 (chicken), Ornithorhynchus_anatinus-5.0.1 GCF_000002275.2 (platypus), Monodelphis domestica MonDom5 GCF_000002295.2 (opossum), Dasypus novemcinctus Dasnovv3.0 GCF_000208655.1 (armadillo), Loxodonta africana Loxafr3.0 GCF_000001905.1 (elephant), Mus musculus GRCm38.p3 GCF_000001635.23 (mouse), Rattus norvegivcus Rnor_6.0 GCF_000001895.5 (rat), Elephantulus edwardii EleEdw1.0 GCF_000299155.1 (shrew), Chrysochloris asiatica ChrAsi1.0 GCF_000296735.1 (cape golden mole), Canis lupus familiaris CanFam3.1 GCF_000002285.3 (dog), and Homo sapiens GRCh38.p2 GCF_000001405.28 (human).Synteny maps were derived using the following reference assemblies: http://www.ncbi.nlm.nih.gov/tools/cobalt/) (Homo sapiens (human) (NP_055421.1), Gorilla gorilla gorilla (gorilla) (XP_004039158.1), Pan troglodytes (chimpanzee) (XP_517337.3), Nomascus leucogenys (gibbon) (XP_003265945.1), Papio anubis (baboon) (XP_003898995.1), Saimiri boliviensis boliviensis (squirrel monkey) (XP_003924058.1), Callithrix jacchus (marmoset) (XP_002745644.1), Bos taurus (cow) (NP_001077132.1), Ovis aries (sheep) (XP_004009758.1), Felis catus (cat) (XP_003985228.1), Canis lupus familiaris (dog) (XP_535653.3), Ailuropoda melanoleuca (giant panda) (XP_002913643.1), and Equus caballus (horse) (XP_001496703.3); for HERC4, human (NP_071362.1), gorilla (XP_004049535.1), chimpanzee (XP_001167753.1), gibbon (XP_003258260.1), baboon (XP_003903924.1), squirrel (XP_003928728.1), marmoset (XP_002756356.1), cow (NP_001070362.2), sheep (XP_004021455.1), dog (XP_849808.1), panda (XP_002913788.1), and horse (XP_001503636.1); for HERC5, human (NP_057407.2), chimpanzee (XP_003310459.1), gorilla (XP_004039179.1), marmoset (XP_002745648.1), baboon (XP_003898997.1), squirrel monkey (XP_003924055.1), gibbon (XP_003265940.1), horse (XP_001915115.2), giant panda (XP_002913645.1), sheep (XP_004009762.1), cow (NP_001095465.1), dog (XP_535652.3), and cat (XP_003985249.1); for HERC6, human (NP_060382.3), gorilla (XP_004039178.1), chimpanzee (XP_001160851.1), gibbon (XP_003265938.1), baboon (XP_003899001.1), squirrel (XP_003924053.1), marmoset (XP_002745681.1), cow (NP_001179573.1), sheep (XP_004010096.1), cat (XP_003985250.1), dog (XP_851549.1), and horse (XP_001494887.1). At least 2 independent sequences were available for human, sheep, baboon, marmoset, gibbon, and squirrel monkey. The following sequences were not independently validated: cat, dog, cow, horse, sheep, and giant panda. The identification of site-specific positive selection and purifying selection was generated using the Selecton server (http://selecton.tau.ac.il/index.html). The HERC5 phylogenetic tree was used in the Selecton analysis. Nested pairs of models and a nonnested pair (M8a and MEC) were compared using the likelihood ratio test implemented in the Selecton program.Positive-selection analysis was performed as previously described . HERC secobalt/) . The folPlasmids encoding Flag-tagged HERC3, HERC4, HERC5, and HERC6 were created by first PCR amplifying the various HERC coding regions from their respective templates (as described above) using the following primers: for HERC3, forward, 5\u2032 ACG TGA ATT CCA TGT TAT GTT GGG GAT ATT GG 3\u2032, and reverse, 5\u2032 ACG TGG TAC CTC AGG CCA AAC TAA ACC CTT CAT AGT TGT C 3\u2032; for HERC4, forward, 5\u2032ACG TGA ATT CTA TGT TGT GCT GGG GAA ATG C 3\u2032, and reverse, 5\u2032 ACG TTC TAG ATT ATA TTA AAC TGA AGC CTT CAT TGT G 3\u2032; for HERC5, forward, 5\u2032 AAT CGA GAT CTT ATG GAG CGC CGC AGC 3\u2032, and reverse, 5\u2032 TAT GCG GAT CCT CAG CCA AAT CCT CTG 3\u2032; and for HERC6, forward, 5\u2032 AGA TAA GAT CTT ATG TAC TTC TGT TGG GGC 3\u2032, and reverse, 5\u2032 TAG GAG ATA TCT TAT GAC TGT GTG AGC ATG 3\u2032. The amplified products were then cloned into p3xFLAG-CMV10 using the following restriction enzymes: for HERC3, EcoRI and KpnI; for HERC4, EcoRI and XbaI; for HERC5, BglII and BamHI; and for HERC6, BglIII and EcoRV. The resulting plasmids were named pHERC3, pHERC4, pHERC5, and pHERC6.To generate pH 6:H5RLD, the HERC5 RCC1-like domain was PCR amplified from pHERC5 using the following primers: forward, 5\u2032 GGA TGA CGA TGA CAA GAT GGA GCG CCG CAG CC 3\u2032, and reverse, 5\u2032 TAT GTT CCA GCA AAA ATT ATT AAC TCC TTT TCT GAG GTA TGG CTT TCA AG 3\u2032. The backbone of pHERC6 was PCR amplified using the following primers: forward, 5\u2032 TTT TTG CTG GAA CAT ATG CCA ACT TTG 3\u2032, and reverse, 5\u2032 CTT GTC ATC GTC ATC CTT GTA ATC GAT G 3\u2032. The two amplified fragments were cloned using the fast cloning technique .To generate pH6:H5blade1, blade 1 of HERC5 (amino acids 1 to 100) was PCR amplified from pHERC5 using the following primers: forward, 5\u2032 GGA TGA CGA TGA CAA GAT GGA GCG CCG CAG CCG CCC CAA CAG AAG TAC ATC TTG TCA TCG TCA TCC TTG TAA TCG ATG 3\u2032, and reverse, 5\u2032 GCT CCT TCC CGC AGC TCA CGT GGA TCT TCA TGT TCT TGC CCA GC 3\u2032. The backbone of pHERC6 was PCR amplified using the following primers: forward, 5\u2032 GCT GGG CAA GAA CAT GAA GAT CCA CAG CTG CGG GAA GGA GCA C 3\u2032, and reverse, 5\u2032 GGC TGC GGC GCT CCA TCT TGT CAT CGT CAT CCT TGT AAT CGA TG 3\u2032. The two amplified fragments were cloned using the Gibson cloning technique per the manufacturer's instructions (New England Biolabs).To generate pH6:R10A, site-directed mutagenesis was performed on pHERC6 using the following primers: forward, 5\u2032 TTC TGT TGG GGC GCC GAC TCC GCG GAG CTG CAG CGC CGG AGG 3\u2032, and reverse, 5\u2032 CCT CCG GCG CTG CAG CTC CGC GGA GTC GGC GCC CCA ACA GAA 3\u2032. pH6:E67A was generated similarly using the following primers: forward, 5\u2032 GCA GCG CGG GGA GCT GCC AGC ACC AAT TCA GGC ATT GGA AAC C 3\u2032, and reverse, 5\u2032 GGT TTC CAA TGC CTG AAT TGG TGC TGG CAG CTC CCC GCG CTG C 3\u2032. pH6:R10A/E67A was generated similarly, except pH6:R10A was used as the template with the following primers: forward, 5\u2032 GCA GCG CGG GGA GCT GCC AGC ACC AAT TCA GGC ATT GGA AAC C 3\u2032, and reverse, 5\u2032 GGT TTC CAA TGC CTG AAT TGG TGC TGG CAG CTC CCC GCG CTG C 3\u2032. pR10G was generated similarly, using the following primers: forward, 5\u2032 CGC CGA CTC CGG GGA GCT GCA 3\u2032, and reverse, 5\u2032 TGC AGC TCC CCG GAG TCG GCG 3\u2032. pHERC3-\u0394RLD was generated similarly, using the following primers: forward, 5\u2032 GAC GAT GAC AAG ATG AGC TCA CCA CCA GAT GTT GAA G 3\u2032, and reverse, 5\u2032 CAT CTG GTG GTG AGC TCA TCT TGT CAT CGT CAT CCT TGT AAT CG 3\u2032. pHERC4-\u0394RLD was generated similarly, using the following primers: forward, 5\u2032 ACG ATG ACA AGA TGA ATT GGT ACC CCT ATA ATG GGC AGT G 3\u2032, and reverse, 5\u2032 TAG GGG TAC CAA TTC ATC TTG TCA TCG TCA TCC TTG TAA TCG 3\u2032. pHERC5-\u0394RLD was generated previously . pHERC6-HERC3, HERC4, HERC5, and HERC6 were obtained from the following sources: HERC3 (NM_014606.2), HERC6 (NM_017912.3) (HERC5 (NP_057407.2) (HERC4 (NM_015601.3) was isolated from HeLa cells by first reverse transcribing total RNA and then PCR amplification of cDNA using the following primers: forward, 5\u2032ACG TGA ATT CTA TGT TGT GCT GGG GAA ATG C 3\u2032, and reverse, 5\u2032 ACG TTC TAG ATT ATA TTA AAC TGA AGC CTT CAT TGT G 3\u2032. All the constructs were verified by sequencing. Transfections were performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions unless otherwise indicated. Cotransfections of HERC plasmids with pR9 were performed at a ratio of 10:1 unless otherwise noted. Standard Western blot analyses were performed as previously described , and HER57407.2) . HERC4 (escribed . DensitoSaccharomyces cerevisiae-based cloning of diverse HIV-1 strains (S. cerevisiae Hanson (MYA-906) (MAT\u03b1 ade6 can1 his3 leu2 trp1 URA3) was obtained from the American Type Culture Collection (ATCC). The yeast was grown at 30\u00b0C in appropriate medium , depending on the cloning step. Transformations/recombinations were performed using the lithium acetate (LiAc) method. Briefly, the linearized vector DNA (\u223c1 \u03bcg) and PCR product (\u223c3 \u03bcg) were added to competent cells at a 1:3 ratio, along with 50 \u03bcg of single-stranded salmon sperm carrier DNA and sterile polyethylene glycol (50%)-TE -LiAc (100 mM). Following agitation for 30 min at 30\u00b0C, the yeast was heat shocked at 42\u00b0C for 15 min and plated on C-leu agar plates containing the appropriate selection.For the construction of pSIVmac239 (pREC_nfl_SIV239), the SIVmac239 Spx vector was obtained from the NIH AIDS Reagent Program. We previously constructed pREC_nfl_HIV and pCMV_cplt vectors for strains . We deve strains . For yeaThe following reagents were obtained through the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH: HIV-1 p24 monoclonal antibody (183-H12-5C) from Bruce Chesebro and Kathy Wehrly and anti-SIVmac p17 monoclonal antibody (KK59) from Karen Kent and Caroline Powell. Anti-FLAG and anti-hemagglutinin (HA) (clone 3F10) were purchased from Sigma, anti-myc and anti-\u03b2-actin were purchased from Rockland, anti-eGFP was purchased from Clontech, and anti-GAPDH (clone 6C5) was purchased from EMD/Millipore. Anti-HERC3 (H00008916-B01P), anti-HERC4 (H00026091-A01), anti-HERC5 (H00051191-A01), and anti-HERC6 (H00055008-A01) were purchased from Abnova.TC) for each PCR. The gene-specific forward and reverse primer sets used were as follows: Gag- ; Rev . Quantification of endogenous HERC mRNA was run on the QuantStudio5 qPCR machine (Applied Biosystems) under the following cycling conditions: 2 min at 95\u00b0C and 40 cycles of 5 s at 95\u00b0C, 10 s at 60\u00b0C, and 20 s at 72\u00b0C. QuantStudio design and analysis desktop software (version 1.4) was used to determine the TC for each PCR. The primer pairs were as follows: HERC3 , HERC4 , HERC5 , HERC6 , GAPDH , and eGFP . To ensure no carryover of DNA into each total purified RNA sample, 3 \u03bcg of the purified RNA was used directly as the template without reverse transcription for qPCR, using the primer sets described above.Total RNA was extracted using the PureLink RNA minikit . Three micrograms of RNA was reverse transcribed to cDNA using Moloney murine leukemia virus (MMLV) reverse transcriptase and oligo(dT) primers (Life Technologies). Prior to qPCR, the cDNA samples were diluted 1:5 with water. Each PCR mixture consisted of 10 \u03bcl of SYBR green master mix, 2 \u03bcl of gene-specific primers (1 \u03bcl of 10 \u03bcM forward primer and 1 \u03bcl of 10 \u03bcM reverse primer), 5 \u03bcl of diluted cDNA, and water to a total volume of 20 \u03bcl. For quantification of incompletely and fully spliced HIV RNAs, qPCR was run on the Rotor-Gene 6000 qPCR machine (Corbett Life Science) under the following cycling conditions: 10 min at 95\u00b0C and 40 cycles of 10 s at 95\u00b0C, 15 s at 60\u00b0C, and 20 s at 72\u00b0C. The Rotor-Gene 6000 series software (version 1.7) was used to determine the cycle threshold (P values and statistical tests used are mentioned where appropriate. P values of less than 0.05 were deemed significant.GraphPad Prism v6 was used for all statistical analyses mentioned in the text. The"} +{"text": "Xueshuan Xinmaining Tablet (XXT) is a widely used traditional Chinese medicine for the treatment of stroke, chest pain, coronary heart disease, and angina pectoris caused by blood stasis. Having a multiple-component preparation, it is still far from meeting the requirements of modernization and standardization because its detailed chemical basis and action mechanism have not been clarified. In this work, the different batches of XXT samples were analyzed by HPLC and the typical sample was analyzed by UPLC-ESI-Q-TOF/MS to understand its chemical profiling. As a result, 77 chromatographic peaks were detected, among which 63 constituents were identified or tentatively characterized based on the comparison of retention time and UV spectra with authentic compounds as well as by summarized MS fragmentation rules and matching of empirical molecular formula with those of published components. This is the first systematic report on the chemical profiling of the commercial XXT products, which provides the sufficiently chemical evidence for the global quality evaluation of XXT products. Chuanxiong rhizoma), Huaihua (Sophorae flos), Danshen , Shuizhi (Hirudo), Maodongqing (Hairy holly root), Rengong Niuhuang , Rengong Shexiang (Moschus artifactus), Renshen Jingye Zongzaogan , Bingpian (Borneolum syntheticum), and Chansu (Bufonis venenum) + (ESI+) or [M+HCOO]\u2212 (ESI-) were detected in MS spectrum. In MS/MS spectrum, a series of fragmentation ions were observed due to the neutral loss of glucose, rhamnose, arabinose, or xylose were unambiguously identified as ginsenoside Rg1, ginsenoside Re, ginsenoside Rb2, ginsenoside Rb3, 20S-ginsenoside F1, ginsenoside Rd, 20S-ginsenoside F2, and 20S-ginsenoside Rh2. Unknown ginsenoside saponins followed the similar dissociation pathways. For the ginsenosides of protopanaxadiol, the ions at m/z 407, 425, and 443 could be found in the positive ion mode. Meanwhile the ginsenosides of protopanaxatriol showed the ions at m/z 405, 423, and 441 in the positive ion mode.lose see . These f1 showed [M+Na]+ ion at m/z 823.4824 (C42H72O14Na) in the positive ion mode and [M+HCOO]\u2212 ion at m/z 845.4895 (C43H73O16) in the negative ion mode. The fragmentation ions at m/z 621.4368 and 603.4259 were produced from the protonated ion [M+H]+ by losing glucose and the further loss of H2O. In the negative MS/MS analysis, [M-H]\u2212 at m/z 799.4838 gave the characteristic ion at m/z 637.4307 [M-H-glc]\u2212and 475.3773[M-H-2glc]\u2212. Compounds 23 and 40 showed the quasimolecular ions at m/z 823 [M+Na]+ and 845 [M+HCOO]\u2212 in the full mass spectrum. Compound 23 has the same retention time and MS data as those of reference ginsenoside Rg1 and it was identified as ginsenoside Rg1. As for compound 40, although the fragmentation ions at m/z 405, 423, or 441 could not be detected in the MS/MS spectrum, it was temporarily identified as ginsenoside Rf.Ginsenoside Rg+ ion at m/z 969.5427 (C48H82O18Na) in the positive ion mode and [M+HCOO]\u2212 ion at m/z 991.5482 (C49H83O20) in the negative ion mode. The fragmentation ions at m/z 945.5428 [M-H]\u2212, 799.4845 [M-H-rha]\u2212, 783.4893 [M-H-glc]\u2212, and 637.1430 [M-H-rha-glc]\u2212 were found in MS/MS spectrum in the negative ion mode. Compound 24 showed similar retention time and MS data as those of reference ginsenoside Re and it was identified as ginsenoside Re.Ginsenoside Re showed [M+Na]2, [M+Na]+ ion at m/z 1101.5868 (C53H90O22Na) in the positive ion mode and [M+HCOO]\u2212 ion at m/z 1123.5908 (C54H91O24) in the negative ion mode are shown in the full mass spectrum. The fragmentation ions at m/z 945.5425 [M-H-ara]\u2212 and 783.4889 [M-H-ara-glc]\u2212 were detected in MS2. Reference ginsenoside Rb3 and 683.4375 [M+HCOO]\u2212 (C37H63O11Na). In the negative MS/MS experiment, the fragmentation ion at m/z 475.3785 [M-H-glc]\u2212 was detected. Compound 49 showed similar retention time and MS data as those of reference 20S-ginsenoside F1.20 m/z 969.5379 [M+Na]+ and 991.5495 [M+HCOO]\u2212 in the full mass spectrum. The fragmentation ions at m/z 783.4892 [M-H-glc]\u2212, 621.4368 [M-H-2glc]\u2212, and 459.3842 [M-H-3glc]\u2212 were produced by losing glucose. Compound 53 was identified as ginsenoside Rd by displaying the same retention time and MS information.Reference ginsenoside Rd showed the adduct ions atS-ginsenoside F2, it showed the quasimolecular ions at m/z 807.4890 [M+Na]+ and 829.4949 [M+HCOO]\u2212. The deprotonated ion peak at m/z 783.4881 [M-H]\u2212 produced the fragmentation ion at m/z 621.4355 [M-H-glc]\u2212 in MS2. Compounds 45, 61, 64, and 65 gave the same adduct ions [M+Na]+ in positive MS and [M+HCOO]\u2212 in negative MS, indicating the molecular formula as C42H72O13. Compound 45 was deduced as protopanaxatriol type and the latter three compounds were deduced as protopanaxadiol type on the base of the fragmentation rules described above. Among them, compound 61 has similar ions in full mass spectrum and MS/MS experiment as those of reference 20S-ginsenoside F2 and was unambiguously identified as 20S-ginsenoside F2. The deprotonated ion of 45 at m/z 783.4910 [M-H]\u2212 indicated the ion at m/z 475.3791 [M-H-rha-glc]\u2212, supporting that 45 was ginsenoside Rg2. Compounds 64 and 65 displayed same MS data; however, unfortunately, MS2 information could not be detected and they were tentatively identified as 20R-ginsenoside Rg3 and 20S-ginsenoside Rg3.As for reference 202 showed the ions at m/z 1245.8995 [2M+H]+, 645.4348 [M+Na]+, and 667.4437[M+HCOO]\u2212. Compound 74 was identified as 20S-ginsenoside Rh2 by comparing the retention time and MS data.Reference ginsenoside Rh 35, 36, and 37 have the same molecular formula of C48H82O19 and were tentatively characterized as 20S-glc-ginsenoside Rf, beads ginseng saponin F1, and notoginsenoside R3. They gave [M+Na]+ ions at m/z 985.5332, 985.5319, and 985.5339 in the positive ion mode and [M+HCOO]\u2212 ions at m/z 1007.5457, 1007.5457, and 1007.5459 in the negative ion mode. In their MS/MS experiments, the fragmentation ions of 35 at m/z 799.4843 and 637.4273 were produced from the ion at m/z 961.5391 [M-H]\u2212 by loss of glucose unit. Similarly, the fragmentation ions of 36 and 37 at m/z 799 and 637 were yielded. The retention order of three chromatographic peaks is determined according to the description in the literature [Compounds 42 and 43 are calculated as C41H70O13 based on the ions at m/z 793.4705 [M+Na]+ in the positive ion mode and 815.4818 [M+HCOO]\u2212 in the negative ion mode. Both compounds showed the fragmentation ions at m/z 405, 423, or 441 indicating that they are due to protopanaxatriol type. In MS/MS analysis, the ions at m/z 637.4326 [M-H-xyl]\u2212 and 475.3794 [M-H-xyl-glc]\u2212 for compound 42, as well as 637.4319 [M-H-ara]\u2212 and 475.3788 [M-H-ara-glc]\u2212 for compound 43, were detected from the deprotonated ions at m/z 769.4753 [M-H]\u2212 and 769.4758 [M-H]\u2212, respectively. Compounds 42 and 43 were identified as notoginsenoside R2 and ginsenoside F3.The chemical formulas of compounds 54 showed the quasimolecular ions at m/z 939.5284 [M+Na]+ and 961.5390 [M+HCOO]\u2212, indicating the molecular formula as C47H80O17. The fragmentation ions 783.4901 [M-H-xyl]\u2212 and 621.4363 [M-H-xyl-glc]\u2212 were detected, supporting that 54 was gypenoside IX.Compound 60 showed the quasimolecular ions at m/z 789.4742 [M+Na]+ and 811.4871 [M+HCOO]\u2212 and the molecular formula was calculated as C42H70O12. In the MS/MS analysis, the deprotonated ion at m/z 765.4792[M-H]\u2212 gave the ions at m/z 603.4261 [M-H-glc]\u2212 and 441.3730 [M-H-2glc]\u2212. Further loss of H2O yielded the ions at m/z 423 and 405. It was identified as ginsenoside Rk1.Compound 34 showed [M+Na]+ ion at m/z 1117.5740 and [M+HCOO]\u2212 ion at m/z 1139.5891, suggesting the molecule formula of C53H90O23. Besides, it showed [M-H]\u2212 ion at m/z 1093.5826 and fragment ions at m/z 961 [M-H- xyl/ara]\u2212, 799 [M-H-xyl/ara-glc]\u2212, and 637 [M-H-xyl/ara-2glc]\u2212, concerning consecutive loss of 132, 294, and 456. These data were in accordance with those of floral ginsenoside P, floranotoginsenoside D, notoginsenoside FT3, or yesanchinoside H [Compound 72 showed [M+Na]+ ion at m/z 789.4742 and [M+HCOO]\u2212 ion at m/z 811.4847, indicating the molecule formula as C42H70O12. Besides, the ions at m/z 603.4251 [M-H-162]\u2212 and 471.3466 [M-H-162-132]\u2212 in the MS/MS analysis suggested that the glycoside chain of 72 consisted of a molecule of glucose and a molecule of arabinose or xylose. It could be one of ilexoside A or ilexoside D described in the literature + and deprotonated ion at m/z 609.1461 [M-H]\u2212 as well as the ion at m/z 1219.3008 [2M-H]\u2212. Quercetin, with UV \u03bbmax absorption at 253 and 356 nm, displayed the deprotonated ion at m/z 301.0376 [M-H]\u2212. Four compounds were determined as flavonoid derivatives due to the typical UV absorption. Especially, compound 9 was one of main constituents of XXT. Compounds 9 and 26 were unambiguously identified as rutin and quercetin based on the direct comparison of their UV spectra, and mass spectra with those of the authentic compounds. Compound 10 has UV \u03bbmax absorption at 264 and 343 nm. The molecular formula was calculated as C27H30O15 by the quasimolecular ion at m/z 595.1652 [M+H]+, 617.1472 [M+Na]+, and 593.1505 [M-H]\u2212. Other fragment ions at m/z 449.1083 [M+H-rha]+ and 287.1055 [M+H-rha-glc]+ were detected. Therefore, compound 10 was identified as kaempferol-3-O-rutinoside. Compound 13 has UV \u03bbmax absorption at 252 and 339 nm. The molecular formula was calculated as C28H32O16 by the quasimolecular ion at m/z 625.1754 [M+H]+, 647.1578 [M+Na]+, and 623.1616 [M-H]\u2212, suggesting it was isorhamnetin 3-O-rutinoside \u2212 ion at m/z 395.07949 was found. The MS/MS spectrum of [M-H]\u2212 exhibited an obvious fragment ion, [M-H-H2O]\u2212 at m/z 179.0338, and further loss of COOH obtained ion at m/z 135.0438. Compound 1 was identified as danshensu.Danshensu has UV \u03bbmax absorption at 323 nm. In the full mass spectrum, the deprotonated ion at m/z 353.0869 [M-H]\u2212 was found. The MS/MS spectrum of [M-H]\u2212 showed ions at m/z 191.0548, 179.0336, and 135.0438. Compound 2 was identified as neochlorogenic acid.Neochlorogenic acid has UV \u03bbmax absorption at 325 nm and showed the quasimolecular ion at m/z 353.0872 [M-H]\u2212 and 707.1482 [2M-H]\u2212. The fragment ion at m/z 191.0553 was yielded by losing C9H6O3. Compound 4 was identified as chlorogenic acid.Chlorogenic acid has UV \u03bbmax absorption at 229, 278, and 310 nm. The [M-H]\u2212 ion at m/z 137.0236 was detected. In the MS/MS analysis, the ion at m/z 108.0204 was yielded by losing CHO and further losing oxygen produced from the ion at m/z 92.0256. Compound 5 was identified as protocatechuic aldehyde.Protocatechuic aldehyde has UV \u03bbmax absorption at 238 and 322 nm. It showed [M-H]\u2212 ion at m/z 179.0339 in the full mass spectrum and the ion at m/z 135.0438 by losing CO2 in the MS/MS experiment. Compound 7 was identified as caffeic acid.Caffeic acid has UV 11, 14, and 15) at m/z 515 [M-H]\u2212 and 517 [M+H]+ were easily located in the chromatogram of XXT, suggesting the molecular formula of C25H24O12. They were assigned as dicaffeoylquinic acids by comparison with retention times. Besides, they gave the same fragment ions with those of chlorogenic acid, such as m/z 191, 179, 173, and 135. in MS/MS experiments. The fragmentation pathways are in accordance with those described in the literature terature . Based o 12 has UV \u03bbmax absorption at 244 and 327 nm. The molecular formula was calculated as C27H22O12 on the basis of the quasimolecular ions at m/z 539.1149 [M+H]+ and 537.1031 [M-H]\u2212. In the MS/MS experiment, it indicated the characteristic ion at m/z 339.0500 [M-H-C9H10O5]\u2212, supporting that compound 12 was salvianolic acid H.Compound 17 has UV \u03bbmax absorption at 250 and 306 nm. It showed the ion at m/z 341.0666 [M+H]+. In the MS/MS analysis, the ions at m/z 295.0617 and 279.0659 were yielded by losing CH2O2 and CH2O3. Compound 17 was identified as salvianolic acid G.Compound 18 has UV \u03bbmax absorption at 251 and 317 nm. It showed [M-H]\u2212 ion at m/z 493.1134 and the molecular formula was calculated as C26H22O10. In the MS/MS analysis, the fragment ion at m/z 295.0604 [M-H-C9H10O5]\u2212 was detected, suggesting compound 18 was salvianolic acid A.Compound 32 showed the ions at m/z 567.1498 [M+H]+, 589.1320 [M+Na]+, and 565.1342 [M-H]\u2212 in MS spectrum, revealing molecular formula of C29H26O12. Besides, fragment ion at m/z 369.0971 [M-H-C9H10O5]\u2212 was observed. Compound 32 was identified as ethyl lithospermate.CompoundBufadienolides. The MS/MS behaviors of bufadienolides have been extensively described + ions was triggered by initial loss of 60 Da (HOAc). The elimination of CO was significant for bufadienolides with a 19-formyl group, and the 19-hydroxyl group could be characterized by the loss of 30 Da (HCHO). These fragmentation rules were applied to the identification of bufadienolides in XXT sample. As shown in 19), arenobufagin (25), bufotalin (41), bufalin (50), resibufogenin (55), and cinobufagin (56) by comparison with reference substances isolated from toad venom. The other two bufadienolides were tentatively identified as bufarenogin (20) and hellebrigenin (29) + ion at m/z 403.2486 was found and the fragment ions at m/z 385.2366 [M+H-H2O]+, 367.2262 [M+H-2H2O]+, and 349.2169 [M+H-3H2O]+ were detected in MS2.escribed , 18. BriBile acids. Bile acid derivatives are in lack of conjugated system and their UV absorption is not obvious. However, they always present high sensitivity in the negative ion mode. The deprotonated ion [M-H]\u2212 and adduct ion [M+HCOO]\u2212 were obviously detected in MS spectrum. The loss of side chain was commonly observed in MS2. Four bile acid derivatives were detected from XXT sample, two of which were unambiguously identified as ursodeoxycholic acid and chenodeoxycholic acid based on the direct comparison of reference substances. The other two compounds were tentatively identified as cholanic acid (57) and hyodeoxycholic acid (67). They are derived from the raw material, Rengong Niuhuang [ifactus) . m/z 391.2851 [M-H]\u2212, 437.2916 [M+HCOO]\u2212, and 783.5778 [2M-H]\u2212 in the negative ion mode. In the positive ion mode, the ion at m/z 357.2807 [M+H-2H2O]+ was assigned as the loss of two molecules of H2O. The ion at m/z 321.2587 represented its side chain loss in MS2. Compound 58 was identified as UDCA.Ursodeoxycholic acid showed the ions at m/z 391.2872 [M-H]\u2212, 437.2907[M+HCOO]\u2212, and 783.5798 [2M-H]\u2212 in the negative ion mode. In the positive ion mode, the loss of H2O unit yielded [M+H-2H2O]+ ion at m/z 357.2809. The occurrence of the ion at m/z 321.2586 in MS2 was due to side chain loss. Compound 70 was identified as CDCA.CDCA showed the ions at 57 showed [M+Na]+ ion at m/z 431.2778 in positive mode, and [M-H]\u2212 ion at m/z 407.2803, [M+HCOO]\u2212 ion at m/z 453.2857, and [2M-H]\u2212 ion at m/z 815.5698 in the negative mode. The ions representing a series of H2O loss was observed, such as 373.2749 [M+H-2H2O]+ and 355.2649 [M+H-3H2O]+. It was tentatively characterized as cholanic acid.Compound 67 showed [M-H]\u2212 ion at m/z 391.2852, [M+HCOO]\u2212 ion at m/z 437.2903, and [2M-H]\u2212 at m/z 783.5792 in the full mass spectrum. The molecular formula was calculated as C24H40O4. It was tentatively deduced as hyodeoxycholic acid.CompoundQuinones derivatives. Quinones derivatives are another kind of active constituents from Danshen and they were easily detected in XXT sample. Compounds 63, 71, and 76 were identified as dihydrotanshinone, cryptotanshinone, and tanshinone II A by comparison with reference substances. They displayed similar fragmentation pathways concerning successive eliminations of H2O and CO molecules. Tanshinone IIA was used as an example to illustrate the fragmentation pathway of quinones constituents as shown in 31, 1-oxo tanshinone IIA 59, neotanshinone D 62, tetrahydrotanshinone I 66, methyltanshinonate 69, methylenetanshinquinone 73, and miltirone 77. + ion at m/z 207.1024. The above data were in accordance with those of 4-hydroxyl-3-butylphthalide in the literature [ 21 was tentatively assigned as 4-hydroxyl-3-butylphthalide. It could be derived from individual herb Chuanxiong rhizome [terature . Compoun rhizome .Among the identified compounds, most constituents were derived from the raw materials, Danshen and Renshen Jingye Zongzaogan, and a small proportion of compounds were considered from Huaihua, Maodongqing, Chuanxiong, Chansu, and Rengong Niuhuang. The other ingredients, Rengong Shexiang, Bingpian, and Shuizhi, were not characterized in the present HPLC and UPLC-QTOF/MS condition. This could be related to the prescription of raw materials and the manufacturing process employed. Usually, muscone, one of active constituents in Rengong Shexiang and borneol are detected by GC or GC-MS . They arIn this work, HPLC analysis was employed to find out the common chromatographic peak in various batches of XXT samples and UPLC-Q-TOF/MS was used for the identification of main constituents in the typical XXT sample. As a result, a total of 63 constituents including twenty saponins, four flavonoids, fifteen phenolic acids, eight steroids, four bile acids, ten quinones, and other two compounds were identified or tentatively characterized based on the comparison of retention time and UV spectra with authentic compounds as well as by summarized MS fragmentation rules and matching empirical molecular formula with those of published components. The present investigation clearly understood the nonvolatile constituents in XXT and provided good basis for further study on the active substances and quality control of this preparation."} +{"text": "Scientific Reports 10.1038/s41598-019-42959-4, published online 29 April 2019Correction to: In Figure 5 there is a missing axis label. The y-axis of the bottom graph should be labelled \u201cIntensity (arb. units)\u201d The correct Figure 5 appears below as Figure\u00a0Additionally, this Article contains errors in Reference 44 which is incorrectly given as:Jpn. J. Appl. Phys. 56, 01AC06 (2016)Ito, T., Uchida, G., Nakajima, A., Takenaka, K. & Setsuhara, Y. Selective production of reactive oxygen and nitrogen species in the plasma-treated water by using a nonthermal high-frequency plasma jet. The correct reference is listed below as ref."} +{"text": "Decline in driving skills begins in preclinical AD, when an older adult remains cognitively normal, but the underlying disease process has begun. Preclinical AD is detectable among cognitively normal individuals using molecular biomarkers: positron emission tomography (PET) imaging and cerebrospinal fluid (CSF). The aim of this prospective, longitudinal study is to determine whether naturalistic driving behavior using in-vehicle dataloggers can distinguish older adults with (n=36) and without preclinical AD (n=134). Driving data was calculated as mean/month for several variables for participants followed between one to 46 months. Using stepwise logistic regression, the area under the receiver operating curve (AUC) and 95% confidence interval for these five variables was 0.73 (0.63-0.79) in distinguishing those with and without preclinical AD via amyloid imaging. When age, gender, race, and education were added, the model improved: 0.80 (0.72-0.88). Finally, when apolipoprotein \u03b54 allele (APO\u03b54), obtained via blood or saliva, was added to the model, accuracy improved: 0.84 (0.77-0.89). Similar results were found using CSF biomarker tau/A\u03b242: AUCs (95% CI) were 0.68 (0.58-0.79) for driving variables alone, 0.77 (0.69-0.86) for driving variables and demographics, and 0.87 (0.80-0.94) driving variables, demographics, and apolipoprotein \u03b54 allele. These promising findings suggest that naturalistic driving behavior can predict those with and without preclinical AD. The AUC is further improved with demographics and APO\u03b54, an easily obtainable genetic biomarker. This model may be used in clinical/research settings as a screen or adjunct for diagnostics and prognostics purposes."} +{"text": "Rhodococcus erythropolis X5 is a psychrotrophic (cold-adapted) hydrocarbon-degrading bacterium, as it showed effective n-alkane destruction at low positive temperatures. Here, the genome of strain X5 was completely sequenced; it consists of a 6,472,161-bp circular chromosome (62.25% GC content) and a 526,979-bp linear plasmid, pRhX5-526k (62.37% GC content). Rhodococcus erythropolis X5 is a psychrotrophic (cold-adapted) hydrocarbon-degrading bacterium, as it showed effective n-alkane destruction at low positive temperatures. Here, the genome of strain X5 was completely sequenced; it consists of a 6,472,161-bp circular chromosome (62.25% GC content) and a 526,979-bp linear plasmid, pRhX5-526k (62.37% GC content). Rhodococcus erythropolis X5 (VKM Ac-2532D) was isolated from oil-polluted soil (R. erythropolis X5 is a psychrotrophic (cold-adapted) hydrocarbon-degrading bacterium, as it showed effective n-alkane destruction at low positive temperatures . Sequencing was performed using a MinIon sequencer (Oxford Nanopore Technologies [ONT]) at the Center of Analytical and Genetic Engineering Research . A library was prepared with the ONT ligation sequencing kit . Guppy v3.2.4 software was used for base calling, which yielded a total of 301 Mbp, distributed in 33,708 reads. Reads with a Q score of >10 were used for further analysis. Additionally, the same DNA sample was sequenced with an Illumina MiSeq platform using a MiSeq reagent kit v3 (2\u2009\u00d7\u2009300\u2009bp). A paired-end library for sequencing was prepared with the MuSeek library preparation kit . The Nanopore reads were assembled into 2 contigs using Canu assembler v1.8 (Genomic DNA was isolated from a fresh culture biomass (a colony) of R. erythropolis. For the average nucleotide identity (ANI) analysis, we used all available GenBank data on the R. erythropolis representatives and on Rhodococcus sp. strains. Average nucleotide identity parameter analysis revealed that the closest phylogenetic relatives of strain X5 are Rhodococcus sp. strain 008 (GenBank accession number CP012749), Rhodococcus sp. strain NJ-530 (CP034152), R. erythropolis CCM2595 (CP003761), and Rhodococcus sp. strain YL-1 (CP017299).The X5 genome consists of a 6,472,161-bp circular chromosome (62.25% GC content) and a 526,979-bp linear plasmid, pRhX5-526k (62.37% GC content). Chromosome circularization and plasmid linearity were specified by Canu. Also, there were no reads overlapping with plasmid ends. The strain was previously identified as R. erythropolis X5 bears 5 copies of alkane hydroxylase-encoding gene alkB. These genes are essential for the degradation process of alkanes with a chain length of C12 to C20 v4.6 , which i2 to C20 , 10. In 2 to C20 , 12. ApaCP044283 and CP044284, BioSample number SAMN12818508, BioProject number PRJNA573614, and SRA accession number PRJNA573614.This genome project has been deposited in the NCBI database under GenBank accession numbers"} +{"text": "Elaeagnus macrophylla were analyzed via conserved DNA-derived polymorphism molecular markers. A total of 289 discernible loci were obtained from 102 individuals via fifteen primers, and 100% of the loci were polymorphic. The observed number of alleles was 1.9654, and the effective number of alleles was 1.2604. Nei\u2019s genetic diversity index was 0.1724 on average, and Shannon\u2019s information index was 0.2869, indicating that Elaeagnus macrophylla had lower levels of genetic diversity than those reported for its continental relatives and other continental species. The average percentage of polymorphic loci was 42.1%, and the maximum and minimum were 80.97% and 14.88%, respectively, which were associated with the Nanji Island and Liugong Island populations, respectively. The populations of Elaeagnus macrophylla were highly differentiated. Cluster analysis revealed that the similarity between the tested samples was related to their geographical location, that the samples from the same island tended to cluster together, and that there was no cross-clustering between samples. The Nanji Island and Da Rushan populations differentiated into two subpopulations. Last, we detected no correlation between genetic distance and geographic distance between populations .The genetic diversity and genetic structure of five natural populations of the island and coastal endangered plant species Elaeagnus\u00a0macrophylla is an endangered evergreen shrub species of East Asian coastal areas and islands. It is distributed in the Shandong, Zhejiang, and Jiangsu Provinces of China, mainly on offshore islands and in coastal lowlands molecular markers (Neolitsea sericea based on random amplified polymorphic DNA (RAPD) molecular markers have shown that CDDP markers have many advantages, including convenience, low cost, and rich polymorphism, and can effectively mark sequences of target traits (Solanum dulcamara (Chrysanthemum (Paeonia suffruticosa (Vaccinium\u00a0vitis-idaea (Rosa rugosa (E.\u00a0macrophylla.The conserved DNA-derived polymorphism (CDDP) method is based on a single primer amplification reaction, with primers designed to target conserved sequences of plant functional genes, mostly transcription factors such as WRKYs, MYBs, MADs, ERFs, KNOXs, and ABP1. Because of the strong conservation of some sequences of plant DNA, CDDP molecular marker technology can be used across different species. Studies of rice . Only one individual each was found on Lingshan Island and Putuo Island. After the samples were collected, silica gel was used to quickly dry the specimens, after which they were stored at 20\u00a0\u00b0C.A total of 102 individual leaf samples were collected from 7 islands and offshore sites from AprE. macrophylla via the modified cetyltrimethylammonium bromide (CTAB) method method . The qua2O, 1 \u00b5l of 30 ng/\u00b5l DNA template, and 1.0 \u00b5l of 10 pmol/\u00b5l primers . A standard PCR thermocycler was used and the PCR program was as follows: an initial denaturation step at 94\u00a0\u00b0C for 3 min; 35 annealing cycles of 94 \u00a0\u00b0C for 1 min, 50\u00a0\u00b0C for 1 min and 72\u00a0\u00b0C for 2 min; and a final extension of 72 \u00a0\u00b0C for 5 min. The PCR products were subsequently stored at 4\u00a0\u00b0C. The products were then electrophoresed on a 2% agarose gel (110 V and 110 mA) for 1.5\u20132 h; a DL2000 marker was used as a size marker. The electrophoresis results were imaged and recorded by a gel imaging system. All amplification procedures were repeated at least twice to ensure the repeatability of the experiment.The DNA from one sample per population was selected to screen 21 CDDP primers synthes. PCR wasWe used POPGEN v.1.32 to compuA dendrogram was generated by the unweighted pair group method with arithmetic mean (UPGMA) clustering procedure in NTSYS-pc 2.10e software . The relK values) was set from 1 to 10, with 10 independent runs for each K. The contribution of the accessions to the genotypes was calculated on the basis of a 105 iteration burn-in period and 105 iteration sampling period. The optimal number of K clusters was then identified according to the methods of The genetic structure of populations was further assessed via the Bayesian clustering approach implemented in STRUCTURE v.2.3.4 . The numE. macrophylla was high.The DNA of 102 samples was amplified with 15 primers, yielding 289 bands, and the fragment length was between 500 and 2,000 bp . The numAt the population level, the PPL ranged from 14.88% to 80.28%, with an average of 48.928%, whereas it was 96.54% at the species level. The Na ranged from 1.1488 to 1.8028, while the Ne varied from 1.0739 to 1.2410. H varied from 0.0446 to 0.1580, with an average of 0.1149, and I ranged from 0.0690 to 0.2613, with an average of 0.1848. At the species level, H and I were 0.1724 and 0.2869, respectively . The Na,The Ht and Hs were 0.1706 and 0.1149, respectively, as calculated by POPGEN v.1.32 software. The Gst was 0.3263, indicating that 67.37% of the variation was within the populations and that 32.63% of the variation occurred between the populations. A certain degree of genetic differentiation was observed between the populations. The Nm was 1.0325, indicating that there was some genetic exchange between populations.E. macrophylla, the genetic distance was between 0.0490 and 0.1443 .The applied measure of genetic similarity was used to construct UPGMA dendrograms . The cluThe UPGMA clustering map provided a clear division of the 102 samples . NotablyE. macrophylla best fit three genetic groups, and when K\u00a0=\u00a05, the delta K value was also large (K\u00a0=\u00a03 (K\u00a0=\u00a05 (K\u00a0=\u00a05: a northwestern group (indicated in yellow) and a southeastern group (indicated in blue). The DRS population differentiated into two subpopulations when K\u00a0=\u00a03 and K\u00a0=\u00a05: Nos. 9\u201318 and Nos. 19\u201328, respectively.The results of the Bayesian clustering analysis of the genetic structure showed that the populations of so large . When K\u00a0e (Elaeagnus mollis) and Paeo\u00a00.2682) estimate mollis) , the geniversity . E. macrlination . The Ht is sweet . The frutinction . Island tinction .E. macrophylla were 0.1706 and 0.1149, respectively. Compared with endangered and Chinese secondary protected plants studies . This ge >\u00a00.15) . Furtherulations .E. macrophylla displayed little gene flow (Nm = 1.0325), and the UPGMA clustering analysis of samples revealed no hybridization among individuals from different localities. Structure analysis (K\u00a0=\u00a05) revealed that most of the populations had a simple pedigree, and the genetic exchange between each pair of populations was low. These results were mainly due to the geographical isolation of the islands (mainly barriers posed by seawater), which limited the range of dispersal by pollen- and seed-dispersing birds ; it is difficult for small pollinators to spread pollen across islands separated by vast seas. In addition to pollen, seeds play an important role in the spread of gene flow. One important aspect of seed movement is its role in the initial founding of a population of N. sericea were dispersed within a range of approximately 480 m (Hakdongri on Keojae Island) and 680 m (Naechori on Oenaro Island), respectively, from their maternal plants . After possible causes such as the prevention of gene flow were excluded, the reason may be related to differences in habitats within the population. The NJD nature reserve has numerous islands and reefs with meandering shorelines, headlands, and numerous bays. There are many types of coastal beaches, such as mudflats, gravel beaches, and rocky reefs, and NJD is at the intersection of the Taiwan Warm Current and the Jiangsu and Zhejiang Coastal Currents. The flow system is complex, so the habitat is complex was significantly greater than that of island species with relatively small populations NJD (0.1580)>DRS (0.1290)>DGD (0.1222)>LS (0.1208)>LGD (0.0446), with an average value of 0.1149. The average genetic diversity index of the NJD population is much greater than that of the LGD population. The values of the other three populations are relatively similar. The NJD population is the largest, the DRS, DGD, and LS populations are similar in size, and the LGD population is declining. Human disturbances such as excessive logging, habitat destruction, and the introduction of exotic species are considered to be the main causes endangering island species . The ave species , which a species . NJD is E. macrophylla.Am in situ conservation method was proposed because the conservation of sufficient natural population numbers and sizes to prevent a reduction in genetic diversity is urgently needed. The best strategy for in situ conservation of genetic diversity during an endemic is the preservation of natural habitat . In thisElaeagnus macrophylla using conserved DNA-derived polymorphism markers to investigate the distribution and genetic variation. The results showed that conserved DNA-derived polymorphism markers can be effectively used to study the genetic diversity of Elaeagnus macrophylla populations and revealed that Elaeagnus macrophylla populations have low genetic diversity and high genetic differentiation. The low levels of gene flow between populations are the main cause of the high levels of genetic differentiation. On the basis of these findings, some conservation measures for Elaeagnus macrophylla are proposed.The present study is the first genetic investigation of 10.7717/peerj.8498/supp-1Supplemental Information 10-1 matrix obtained from the results of electropherogram.Click here for additional data file.10.7717/peerj.8498/supp-2Supplemental Information 2It can be seen that the three primer amplification bands are clear and specific and can be used for experiments.Click here for additional data file.10.7717/peerj.8498/supp-3Supplemental Information 3It can be seen that the MYB1, MYB2, ERF1 amplified bands are clear and specific and can be used for experiments.Click here for additional data file.10.7717/peerj.8498/supp-4Supplemental Information 4It can be seen that the WRKY-F1, WRKY-R1 amplified bands are clear and specific and can be used for experiments. Although the WRKY-R2 has a strip, the strip is weak and therefore not used.Click here for additional data file.10.7717/peerj.8498/supp-5Supplemental Information 5It can be seen that the WRKY-R3 amplified band is clear and specific, and can be used for experiments. WRKY-R2B, WRKY-R3B is not effective, so it is not used.Click here for additional data file.10.7717/peerj.8498/supp-6Supplemental Information 6It can be seen that KNOX-2, KNOX-3, MADS-1 amplified bands are clear and specific and can be used for experiments.Click here for additional data file.10.7717/peerj.8498/supp-7Supplemental Information 7It can be seen that the ABP1-1, ABP1-3 amplified bands are clear and specific and can be used for experiments. ABP1-2 did not amplify the band and therefore could not be used.Click here for additional data file.10.7717/peerj.8498/supp-8Supplemental Information 8It can be seen that the MADS-4 amplification band is clear and specific and can be used for experiments. Although the MADS-2 has a band, it is not effective in use, and the MADS-3 does not amplify the band, so it is not used.Click here for additional data file.10.7717/peerj.8498/supp-9Supplemental Information 9Amplification results of WRKY-F1 on LGD1-8 and DRS9-20.Click here for additional data file.10.7717/peerj.8498/supp-10Supplemental Information 10Amplification results of WRKY-F1 on DRS21-28, NJD1-12.Click here for additional data file.10.7717/peerj.8498/supp-11Supplemental Information 11Amplification results of WRKY-F1 on NJD13-NJD32.Click here for additional data file.10.7717/peerj.8498/supp-12Supplemental Information 12Amplification results of WRKY-F1 on NJD 33, LS 1-13, PTD1, LSD1.Click here for additional data file.10.7717/peerj.8498/supp-13Supplemental Information 13Amplification results of WRKY-F1 on DGD1-13.Click here for additional data file.10.7717/peerj.8498/supp-14Supplemental Information 14Amplification results of WRKY-F1 on DGD14-26.Click here for additional data file.10.7717/peerj.8498/supp-15Supplemental Information 15Amplification results of WRKY-R1 on LGD1-8 and DRS9-20.Click here for additional data file.10.7717/peerj.8498/supp-16Supplemental Information 16Amplification results of WRKY-R1 on DRS21-28, NJD1-12.Click here for additional data file.10.7717/peerj.8498/supp-17Supplemental Information 17Amplification results of WRKY-R1 on NJD13-32.Click here for additional data file.10.7717/peerj.8498/supp-18Supplemental Information 18Amplification results of WRKY-R1 on NJD 33, LS1-13, PTD1, LSD1.Click here for additional data file.10.7717/peerj.8498/supp-19Supplemental Information 19Amplification results of WRKY-R1 on DGD1-20.Click here for additional data file.10.7717/peerj.8498/supp-20Supplemental Information 20Amplification results of WRKY-R1 on DGD21-26.Click here for additional data file.10.7717/peerj.8498/supp-21Supplemental Information 21Amplification results of WRKY-R3 on LGD1-8, DRS9-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-22Supplemental Information 22Amplification results of WRKY-R3 on DRS21-28, NJD1-12 samples.Click here for additional data file.10.7717/peerj.8498/supp-23Supplemental Information 23Amplification results of WRKY-R3 on DRS21-28, NJD13-32 samples.Click here for additional data file.10.7717/peerj.8498/supp-24Supplemental Information 24Amplification results of WRKY-R3 on NJD33, LS1-13, PTD1, LSD1 samples.Click here for additional data file.10.7717/peerj.8498/supp-25Supplemental Information 25Amplification results of WRKY-R3 on DGD1-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-26Supplemental Information 26Amplification results of WRKY-R3 on DGD21-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-27Supplemental Information 27Amplification results of MYB1 on LGD1-8, DRS9-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-28Supplemental Information 28Amplification results of MYB1 on DRS21-28, NJD1-12 samples.Click here for additional data file.10.7717/peerj.8498/supp-29Supplemental Information 29Amplification results of MYB1 on NJD13-33 samples.Click here for additional data file.10.7717/peerj.8498/supp-30Supplemental Information 30Amplification results of MYB1 on NJD33, LS1-13, PTD1, LSD1 samples.Click here for additional data file.10.7717/peerj.8498/supp-31Supplemental Information 31Amplification results of MYB1 on DGD1-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-32Supplemental Information 32Amplification results of MYB1 on DGD21-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-33Supplemental Information 33Amplification results of MYB2 on LGD1-8, DRS9-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-34Supplemental Information 34Amplification results of MYB2 on DRS21-28, NJD1-12 samples.Click here for additional data file.10.7717/peerj.8498/supp-35Supplemental Information 35Amplification results of MYB2 on NJD13-32 samples.Click here for additional data file.10.7717/peerj.8498/supp-36Supplemental Information 36Amplification results of MYB2 on NJD33, LS1-13, PUD1, LSD1 samples.Click here for additional data file.10.7717/peerj.8498/supp-37Supplemental Information 37Amplification results of MYB2 on DGD1-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-38Supplemental Information 38Amplification results of MYB2 on DGD21-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-39Supplemental Information 39Amplification results of ERF1 on LGD1-8, DRS9-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-40Supplemental Information 40Amplification results of ERF1 on DRS21-28, NJD1-12 samples.Click here for additional data file.10.7717/peerj.8498/supp-41Supplemental Information 41Amplification results of ERF1 on NJD13-32 samples.Click here for additional data file.10.7717/peerj.8498/supp-42Supplemental Information 42Amplification results of ERF1 on NJD33, LS1-13, PTD1, LSD1 samples.Click here for additional data file.10.7717/peerj.8498/supp-43Supplemental Information 43Amplification results of ERF1 on DGD1-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-44Supplemental Information 44Amplification results of ERF1 on LS1-6, DGD21-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-45Supplemental Information 45Amplification results of ERF2 on LGD1-8, DRS9-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-46Supplemental Information 46Amplification results of ERF2 on DRS21-28, NJD1-12 samples.Click here for additional data file.10.7717/peerj.8498/supp-47Supplemental Information 47Amplification results of ERF2 on NJD13-32 samples.Click here for additional data file.10.7717/peerj.8498/supp-48Supplemental Information 48Amplification results of ERF2 on NJD33, LS1-13, PTD1, and LSD1 samples.Click here for additional data file.10.7717/peerj.8498/supp-49Supplemental Information 49Amplification results of ERF2 on DGD1-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-50Supplemental Information 50Amplification results of ERF2 on DGD21-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-51Supplemental Information 51Amplification results of ERF3 on LGD1-8, DRS9-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-52Supplemental Information 52Amplification results of ERF3 on DRS21-28, NJD1-12 samples.Click here for additional data file.10.7717/peerj.8498/supp-53Supplemental Information 53Amplification results of ERF3 on NJD13-32 samples.Click here for additional data file.10.7717/peerj.8498/supp-54Supplemental Information 54Amplification results of ERF3 on NJD33, LS1-13, PTU1, LSD1, and DGD24-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-55Supplemental Information 55Amplification results of ERF3 on DGD1-23 samples.Click here for additional data file.10.7717/peerj.8498/supp-56Supplemental Information 56Amplification results of ERF3 on DGD24-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-57Supplemental Information 57KNOX-1 amplification results for LGD1-8, DRS9-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-58Supplemental Information 58KNOX-1 amplification results for DRS21-28, NJD1-12 samples.Click here for additional data file.10.7717/peerj.8498/supp-59Supplemental Information 59KNOX-1 amplification results for NJD13-32 samples.Click here for additional data file.10.7717/peerj.8498/supp-60Supplemental Information 60KNOX-1 amplification results for NJD33, LS1-13, PUD1, LSD1 samples.Click here for additional data file.10.7717/peerj.8498/supp-61Supplemental Information 61KNOX-1 amplification results for DGD1-20 samples.Click here for additional data file.10.7717/peerj.8498/supp-62Supplemental Information 62KNOX-1 amplification results for DGD21-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-63Supplemental Information 63KNOX-2 amplification results for LGD1-8, DRS9-23 samples.Click here for additional data file.10.7717/peerj.8498/supp-64Supplemental Information 64KNOX-2 amplification results for DRS24-28, NJD1-18 samples.Click here for additional data file.10.7717/peerj.8498/supp-65Supplemental Information 65KNOX-2 amplification results for NJD19-33, LS1-6 samples.Click here for additional data file.10.7717/peerj.8498/supp-66Supplemental Information 66KNOX-2 amplification results for LS7-13, PTD1, LSD1and DGD1-13 samples.Click here for additional data file.10.7717/peerj.8498/supp-67Supplemental Information 67KNOX-2 amplification results for DGD14-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-68Supplemental Information 68KNOX-3 amplification results for LGD1-8, DRS9-23 samples.Click here for additional data file.10.7717/peerj.8498/supp-69Supplemental Information 69KNOX-3 amplification results for DRS24-28, NJD1-18 samples.Click here for additional data file.10.7717/peerj.8498/supp-70Supplemental Information 70KNOX-3 amplification results for NJD19-33, PTD1, LSD1, LS1-4 samples.Click here for additional data file.10.7717/peerj.8498/supp-71Supplemental Information 71KNOX-3 amplification results for LS5-13, DGD1-13 samples.Click here for additional data file.10.7717/peerj.8498/supp-72Supplemental Information 72KNOX-3 amplification results for DGD14-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-73Supplemental Information 73Amplification results of MADS-1 on LGD1-8, DRS9-23 samples.Click here for additional data file.10.7717/peerj.8498/supp-74Supplemental Information 74Amplification results of MADS-1 on DRS24-28, NJD1-18 samples.Click here for additional data file.10.7717/peerj.8498/supp-75Supplemental Information 75Amplification results of MADS-1 on NJD19-NJD33, PTD1, LSD1, LS1-4 samples.Click here for additional data file.10.7717/peerj.8498/supp-76Supplemental Information 76Amplification results of MADS-1 on LS5-13, DGD1-13 samples.Click here for additional data file.10.7717/peerj.8498/supp-77Supplemental Information 77Amplification results of MADS-1 on DGD14-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-78Supplemental Information 78Amplification results of MADS-4 on LGD1-8 and DRS9-23 samples.Click here for additional data file.10.7717/peerj.8498/supp-79Supplemental Information 79Amplification results of MADS-4 on DRS24-28, NJD1-18 samples.Click here for additional data file.10.7717/peerj.8498/supp-80Supplemental Information 80Amplification results of MADS-4 on NJD19-33, PUD1, LSD1, LS1-4 samples.Click here for additional data file.10.7717/peerj.8498/supp-81Supplemental Information 81Amplification results of MADS-4 on LS5-13, DGD1-13 samples.Click here for additional data file.10.7717/peerj.8498/supp-82Supplemental Information 82Amplification results of MADS-4 on DGD14-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-83Supplemental Information 83ABP1-1 amplification results for LGD1-8, DRS9-23 samples.Click here for additional data file.10.7717/peerj.8498/supp-84Supplemental Information 84ABP1-1 amplification results for DRS24-28, NJD1-18 samples.Click here for additional data file.10.7717/peerj.8498/supp-85Supplemental Information 85ABP1-1 amplification results for NJD19-33, LS1-4 samples.Click here for additional data file.10.7717/peerj.8498/supp-86Supplemental Information 86ABP1-1 amplification results for LS5-13, DGD1-13 samples.Click here for additional data file.10.7717/peerj.8498/supp-87Supplemental Information 87ABP1-1 amplification results for DGD14-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-88Supplemental Information 88ABP1-3 amplification results for LGD1-8, DRS9-23 samples.Click here for additional data file.10.7717/peerj.8498/supp-89Supplemental Information 89ABP1-3 amplification results of DRS24-28, NJD1-18 samples.Click here for additional data file.10.7717/peerj.8498/supp-90Supplemental Information 90ABP1-3 amplification results for NJD19-33, PTD1, LSD1, LS1-4 samples.Click here for additional data file.10.7717/peerj.8498/supp-91Supplemental Information 91ABP1-3 amplification results for LS5-13, DGD1-13 samples.Click here for additional data file.10.7717/peerj.8498/supp-92Supplemental Information 92ABP1-3 amplification results for DGD14-26 samples.Click here for additional data file.10.7717/peerj.8498/supp-93Supplemental Information 93When K=3, the value of delat K is the largest and best fit three genetic groups. When K=5, the value of delat K is also large, so we analyze the cases of K=3 and K=5.Click here for additional data file.10.7717/peerj.8498/supp-94Supplemental Information 94Nm represents the gene flow, and Gst represents the genetic differentiation coefficient.Click here for additional data file.10.7717/peerj.8498/supp-95Supplemental Information 95Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-96Supplemental Information 96Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-97Supplemental Information 97Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-98Supplemental Information 98Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-99Supplemental Information 99Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-100Supplemental Information 100Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-101Supplemental Information 101Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-102Supplemental Information 102Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-103Supplemental Information 103Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-104Supplemental Information 104Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-105Supplemental Information 105Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-106Supplemental Information 106Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-107Supplemental Information 107Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-108Supplemental Information 108Two repetitions per sample.Click here for additional data file.10.7717/peerj.8498/supp-109Supplemental Information 109Raw data format when generating a sample cluster map.Click here for additional data file.10.7717/peerj.8498/supp-110Supplemental Information 110Generate raw data for population clustering analysis.Click here for additional data file."} +{"text": "Xanthomonas sp. strain ATCC PTA-13101, which was isolated from rice. The 44-kbp Pagan genome contains direct terminal repeats and contains 59 genes, 27 of which have a predicted function. Pagan is most closely related to Xanthomonas phage phi Xc10 and Xylella phage Prado.The T7-like podophage Pagan infects Xanthomonas sp. strain ATCC PTA-13101, which was isolated from rice. The 44-kbp Pagan genome contains direct terminal repeats and contains 59 genes, 27 of which have a predicted function. Pagan is most closely related to Xanthomonas phage phi Xc10 and Xylella phage Prado.The T7-like podophage Pagan infects Xanthomonas consists of many diverse species of Gram-negative, rod-shaped phytopathogenic gammaproteobacteria , and phages were propagated via the soft agar overlay method described previously (www.bioinformatics.babraham.ac.uk/projects/fastqc). Sequence reads were then trimmed using the FASTX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). The genome was assembled through SPAdes v3.5.0 (using default parameters) with a sequencing coverage of 6.3-fold , mixed freshwater collected in Vidor, TX, and infects the rice-associated eviously , 7. Full6.3-fold . Next, txy-pub/) . Structuxy-pub/) \u201314. Geney-pub/) \u2013\u201317. Like-pub/) \u2013\u2013, 19. Rho-pub/) \u2013\u2013. progres-pub/) \u2013\u2013. Phage m-pub/) \u2013\u2013.Xanthomonas genome average of 64% G+C content (Xanthomonas phage phi Xc10 (GenBank accession number MF375456) and Xylella phage Prado (accession number KF626667), with 93.46% and 69.55% nucleotide sequence identity and 53 and 48 shared proteins, respectively (The 44,448-bp podophage Pagan genome has a coding density of 96.95% and contains 59 predicted genes but no tRNAs. The genome of Pagan displayed a G+C content of 62.3%, near the host content . Pagan iectively . These sMK903278, BioProject accession number PRJNA222858, SRA accession number SRR8892144, and BioSample accession number SAMN11408680.The genome sequence and associated data for phage Pagan were deposited under GenBank accession number"} +{"text": "Klebsiella pneumoniae, a Gram-negative pathogen whose multidrug-resistant strains are a public health issue. Here, we describe the annotation of the 157,741-bp Magnus genome and its similarity to other myophages.Bacteriophage Magnus infects Klebsiella pneumoniae, a Gram-negative pathogen whose multidrug-resistant strains are a public health issue. Here, we describe the annotation of the 157,741-bp Magnus genome and its similarity to other myophages.Bacteriophage Magnus infects Klebsiella pneumoniae is an opportunistic, Gram-negative enteric bacterium. Carbapenemase-producing K. pneumoniae (KPC) strains are resistant to carbapenem antibiotics and are an emerging cause of nosocomial and systemic human infections (fections . Phage tK. pneumoniae strain 39427 (BioSample number SAMN06218024) (www.bioinformatics.babraham.ac.uk/projects/fastqc). Quality-controlled reads were trimmed using the FASTX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/) and then assembled into a single contig of circular assembly at 146-fold coverage using SPAdes v3.5.0 collected at a wastewater treatment facility in Austin, TX, against v3.5.0 68. Termin v3.5.0 6 and BLAS v3.5.0 6, 12. Bioxy-pub/) , 14. Unlxy-pub/) .Magnus is a myophage that has a 157,741-bp genome and a coding density of 92%, with 212 predicted protein-coding genes, 71 of which have a predicted function. The Magnus genome also contains 5 tRNA genes . Its G+C content was determined to be 46.3%. It was predicted by PhageTerm that Magnus uses a headful packaging system .Klebsiella phage 0507KN21 (GenBank accession number AB797215) (Serratia phage vB_Sru_IME250 (GenBank accession number KY073123) and Shigella phage Ag3 (GenBank accession number FJ373894), all classified within the Ackermannviridae. Additionally, Magnus contains at least 27 genes with significant amino acid similarity to type phages T4 (GenBank accession number NC_000866) and K (GenBank accession number KF766114), including core structural and replication proteins. The large terminase gene (NCBI accession number QEG07939) harbors an intein element.By BLASTp and progressiveMauve analyses, Magnus has 75.15% nucleotide identity to, and shares 146 similar proteins with, B797215) . Magnus MN045230, BioProject accession number PRJNA222858, SRA accession number SRR8869229, and BioSample accession number SAMN11360383.The genome sequence and associated data for phage Magnus were deposited under GenBank accession number"} +{"text": "Psychrobacter spp. Analysis of Arctic psychrophilic Psychrobacter sp. DAB_AL32B genome content provided an insight into its overall stress response, and genes conferring protection against various life-limiting factors were recognized and described. Moreover, it was revealed that the strain carries a large plasmid pP32BP2. Its replication system was used for the construction of two novel shuttle vectors (pPS-NR\u2014Psychrobacter-Escherichia coli-specific plasmid and pPS-BR\u2014Psychrobacter-various Proteobacteria-specific plasmid) of an increased carrying capacity, which may be used for genetic engineering of Psychrobacter spp.Cold-active bacteria are currently of great interest in biotechnology, and their genomic and physiological features have been extensively studied. One of the model psychrotolerant bacteria are The online version of this article (10.1007/s00203-018-1595-y) contains supplementary material, which is available to authorized users. Psychrobacter spp. belong to the Moraxellaceae family (Gammaproteobacteria). Bacteria of this genus are frequently isolated from various cold environments, including seawater, ice, permafrost and Arctic and Antarctic ornithogenic soils. Some strains are considered to be opportunistic pathogens, as they are occasionally isolated from human patients, as well as from infected animals , 77 genomes (including 65 drafts) and an additional 65 plasmid sequences of Psychrobacter spp. are available (22nd June 2018). Analysis of the Psychrobacter genomes revealed the presence of various adaptation mechanisms allowing their survival in extremely cold environments. Hence, psychrophilic Psychrobacter strains are model, cold-active bacteria useful for studying bacterial adaptation to extreme conditions a pABW1 vector containing a ColE1-type replication system. Therefore, the broad host range vector pBBR1 MCS-2 with pBBR1-type replication system was tested. Surprisingly, this replication system was also found to be inactive in tested Psychrobacter spp. These negative results encouraged us to construct novel, shuttle Psychrobacter\u2013Escherichia coli-specific vectors.It was previously reported that plasmids carrying ColE1- and p15a-type replication systems were stably maintained in E. coli-specific replication system originating from the pMB1 plasmid, i.e., high copy number replicon) or pWSK29 plasmids, and carrying replication systems of the pP43BP3 and pP43BP4 plasmids originating from psychrophilic Psychrobacter sp. DAB_AL43B, were reported , based on the pBGS18 was obtained. The genome analyses provided brief insights into the stress adaptation mechanisms of the strain. Moreover, we found that the strain carries a large, approximately 60-kb, plasmid. Although this plasmid was not fully assembled during genome drafting, its replication system was used for the construction of two novel Psychrobacter-specific vectors that are suitable for cloning of large DNA fragments.In this study, the draft genome sequence of Psychrobacter spp.) or 37\u00a0\u00b0C (Escherichia coli DH5\u03b1). The medium was solidified by the addition of 1.5% (w/v) agar. Where necessary, the media were supplemented with X-gal, IPTG and antibiotics: kanamycin (20\u00a0\u00b5g/ml for Psychrobacter spp. or 50\u00a0\u00b5g/ml for E. coli) and rifampin (50\u00a0\u00b5g/ml).The bacterial strains and plasmids used in this study are listed in Table\u00a0The CTAB/lysozyme method was used for isolation of genomic DNA .ACCGGTGCGAACCACTGTGAGTATTG-3\u2032 and 32B_REPR\u20145\u2032-ATACCGGTTTAATTCTATCGCCCGCCTG-3\u2032. To obtain the PCR product, the following conditions were applied: 35 cycles preceded by 3-min denaturation at 95\u00a0\u00b0C and followed by 2-min extension at 72\u00a0\u00b0C.Plasmid DNA was isolated using a GeneMATRIX Plasmid Miniprep DNA Purification Kit and alkaline lysis method was specified as taxon separating from other bacterial taxa.Genome completeness was assessed by the presence/absence of bacterial orthologs according to the OrthoDB database using BUSCO available at the Ribosomal Database Project (RDP) website (Nawrocki and Eddy P. adeliensis DSM 15333T (HE654007.1), P. aestuarii SC35 (EU939718.1), P. alimentarius JG-100 (AY513645.1), P. allis E2 (JX122558.1), P. aquaticus CMS 56 (NR_042206.1), P. aquimaris SW-210 (AY722804.1), P. arcticus 273-4 (NR_075054.1), P. arenosus R7T (AJ609273.1), P. celer SW-238 (NR_043225.1), P. ciconiae 176/10 (KM486054.1), P. cryohalolentis K5 (NR_075055.1), P. faecalis DSM 14664 (NR_118025.1), P. fjordensis BSw21516B (GQ358940.1), P. fozii NF23 (NR_025531.1), P. frigidicola DSM 12411 (NR_042222.1), P. fulvigenes KC 40 (NR_041688.1), P. glacialis DD43 (AJ539102.1), P. glaciei BIc20019 (NR_148850.1), P. glacincola DSM 12194 (NR_042076.1), P. halophilus DD2 (AJ539103.1), P. immobilis ATCC 43116 (NR_118808.1), P. jeotgali YKJ-103 (NR_025205.1), P. luti NF11 (NR_025532.1), P. lutiphocae IMMIB L-1110 (NR_044602.1), P. marincola KMM 277 (NR_025458.1), P. maritimus Pi2-20 (NR_027225.1), P. meningitidis SBA4 (KR091838.1), P. muriicola 2pS (NR_114669.1), P. namhaensis SW-242 (AY722805.1), P. nivimaris 88/2\u20137 (AJ313425.1), P. oceani 4k5 (AB910522.1), P. okhotskensis MD17 (NR_024806.1), P. pacificensis NBRC 103191 (NR_114238.1), P. pasteuri CIP110853 (KY292376.1), P. phenylpyruvicus ATCC 23333 (NR_118815.1), P. piechaudii CIP110854 (KY292375.1), P. piscatorii T-3-2 (NR_112807.1), P. piscidermidis 45 (FJ613616.1), P. pocilloporae S6-60 (KT444699.2), P. proteolyticus HAMBI 2948 (LT899990.1), P. psychrophilus BBDP29 (DQ337513.1), P. pulmonis CCUG 46240 (NR_118026.1), P. salsus DD 48 (NR_042166.1), P. sanguinis 13983 (HM212668.1), P. submarinus KMM 225 (AJ309940.1), P. urativorans DSM 14009T (AJ609555.1), P. vallis CMS 39 (AJ584832.1), P. cibarius JG-219 (AY639871.1), Psychrobacter sp. DAB_AL32B (JF714884.1) and Psychrobacter sp. DAB_AL43B (JF714885.1).Phylogenetic analysis was performed based on the comparison of partial 16S rRNA gene sequences of the DAB_AL32B strain, DAB_AL43B strain and strains representing 48 Psychrobacter sp. DAB_AL32B draft genome sequence has been deposited in the GenBank (NCBI) database under accession numbers NEXU01000001-NEXU01000218 and the sequences of vectors constructed in this study under accession numbers MH539767 (pPS-BR) and MH539768 (pPS-NR).The Psychrobacter spp. genomes available in the NCBI database (the average length of the Psychrobacter genome is 3.07\u00a0Mb). An assembly of the DAB_AL32B draft genome resulted in 37 scaffolds composed of 218 contigs. The average GC content is 41.9%, which is typical for Psychrobacter spp. . An automatic annotation of the DAB_AL32B genome performed applying the NCBI Prokaryotic Genome Annotation Pipeline resulted in 2,799 predicted genes with an average length of 973.43\u00a0bp, which covers about 80.08% of the genome. Additionally, 41 tRNA genes were identified .The estimated size of the DAB_AL32B genome is 3,211,529\u00a0bp, which is similar to the size of other Gammaproteobacteria BUSCO set (containing 452 BUSCO groups), was performed. The gene set predicted within the DAB_AL32B genome contains 94.3% of genes present in an applied BUSCO set (92.5% complete and 1.8% fragmented genes), which suggests that the genome assembly is complete or very close to completeness.To estimate the completeness of the obtained draft genome, a BUSCO analysis, using Psychrobacter genomes, with only short fragments homologous to genomes of phylogenetically closely related Moraxella and Acinetobacter. Other two contigs (contig00048 and contig00081) exhibit similarity to Psychrobacter genomes in majority of their fragments, while the remaining fragments are either homologous to Acinetobacter, Moraxella, and other unrelated bacteria, or not homologous to any sequence in the nr database. However, BLASTx search revealed significant similarity to proteins encoded within most of these fragments to Psychrobacter and Acinetobacter proteins. For three other contigs the best BLAST hits were sequences from either Acinetobacter or Moraxella; however, they showed comparable similarity to Psychrobacter genomes. One contig (contig00082) was mistakenly automatically classified as a contaminant, because of a non-significant hit to zebrafish genome in low-complexity region. As a result of above analysis, these 15 contigs were recategorized as non-contaminant sequences. Seven other contigs exhibited no significant homology to sequences available in the GenBank database , therefore it is unclear if these are contaminants or not. Finally, only nine contigs may be considered as potential contaminants, as they do not show similarities to neither Psychrobacter sequences nor closely related bacteria.To examine if obtained draft genome is contaminated with other genomic sequences, an analysis using Taxoblast was performed . This analysis revealed that 30 out of 218 contigs were classified as possible contaminants or did not exhibit significant homology to sequences available in the GenBank database. These contigs were manually examined. Putative prophage was found within contig00038. Seven contigs mostly exhibited homology to Psychrobacter frigidicola DSM 12411. As several new Psychrobacter species have been described since the last analysis, we performed another analysis with dataset extended on 14 new Psychrobacter-type strains in NCBI database . Unfortunately, the genome of P. frigidicola DSM 12411 or some other representative of this species, is not publicly available. The phylogenomic analysis revealed that the DAB_AL32B strain is most related with Psychrobacter sp. DAB_AL43B . However, to predict if these strains may be considered as representatives of novel Psychrobacter species, the calculation of the ANI value with P. frigidicola is needed.For more precise classification of DAB_AL32B at the species level, the ANI analysis, based on whole-genome comparison between various Psychrobacter sp. DAB_AL32B had to cope not only with low temperatures, but also increased ultraviolet (UV) radiation, osmotic pressure and oxidative stress. The genes involved in the response to oxidative, osmotic, and cold shock encoded within the DAB_AL32B genome are listed in Table\u00a0Various adaptive mechanisms enable survival of psychrophilic bacteria in Arctic. Identification and analysis of genes encoding various stress response proteins of psychrophiles is important for studying their biology and adaptation, as well as for proper recognition of their biotechnological potential , lipids cross-linking with proteins and disturbances to membrane structure affecting its fluidity are observed formed in the cell. Increased ROS formation in cells may occur as a result of (i) depletion of the UV-protective ozone layer in the Arctic region , peroxidase (1), superoxide dismutase (1), peroxiredoxin (2), rubredoxin (1) and glutaredoxins (3) Table\u00a0.2+). Hydroxyl radicals are then produced via Fenton reaction (Touati 2+ ions) and formation of very stable complexes with DNA , decreasing gene expression and membrane fluidity from the environment or synthesise them in elevated quantities. Compatible solutes increase the stability of proteins and cell membranes without interfering with cellular function , cryptic plasmid pP32BP1 within the N-terminal part of this protein and winged helix DNA-binding domain (residues 1\u2013136 and 140\u2013233). Upstream to the repA gene, the putative origin of replication (oriV) was found . It is composed of five 20-bp-long direct repeats DR1.1-1.5 (5\u2032-ATAACACTAAATGATGTGGG-3\u2032) followed by a pair of 19-bp long inverted repeats, IR1 and IR2 of pP32BP2 shows 76% identity with RepB protein (GenBank: AFD62164) of pP62BP1 of parS, were found. ParA contains the ParA domain (residues 4-182) and shows 93% identity to ParA-like protein (GenBank: ABE76262) encoded within the plasmid 1 of Psychrobacter cryohalolentis K5. Within the ParB protein, the ParG domain, specific to the ParB-like proteins of, e.g., Salmonella enterica plasmid TP228 and Pseudomonas alcaligenes plasmid pRA2, was found (Hayes Psychrobacter urativorans R10.10B. The putative parS centomer-like sequence is located upstream to the parA gene. It consists of eight direct repeats DR2.1-2.8 (5\u2032-(A/T)ATACTCA-3\u2032) , and centromer-like sequence nd Hayes . The prePsychrobacter-specific cloning vectors. Currently, all available Psychrobacter-specific vectors are based on replication systems of small (not exceeding 6.4\u00a0kb) plasmids, which may exclude their application as molecular tools for cloning of large genetic modules. Since Psychrobacter spp. recently became a model bacterium representing cold-active microorganisms plasmid pP32BP2, encouraged us to use this system for the construction of novel Psychrobacter spp., were constructed . Its functionality was confirmed by introducing it into two Psychrobacter spp. strains, DAB_AL12R and DAB_AL43BR. Vector stability was tested in both these strains, and after approximately 30 generations of growth without antibiotic selection pressure, plasmid pPS-NR was found in 21% and 61% of the host cells, respectively . The vector was successfully introduced via triparental mating into Psychrobacter sp. DAB_AL12R and DAB_AL43BR. To analyse the carrying capacity of the pPS-BR vector, we cloned and successfully introduced to Psychrobacter spp. two relatively large restriction fragments of the DAB_AL32B genome, of a length of 5.8\u00a0kb (approx. the size of the vector) and 12.7\u00a0kb (approx. two times bigger than the vector), respectively.For the construction of this vector, the PCR-amplified (1.8-kb) DNA fragment containing the replication system of the pP32BP2 plasmid was cloned within PfoI site of the pBBR1 MCS-2 vector. This resulted in construction of a unique Psychrobacter spp. and E. coli (pPS-NR) or various Proteobacteria (pPS-BR), (iii) the system enabling mobilization to conjugal transfer, (iv) aphA gene-conferring resistance to kanamycin, (v) multiple cloning site (MCS) and (vi) a selection marker (lacZ\u2019 gene) enabling blue-white screening of clones in E. coli two replication systems, which enable their replication in oli Fig.\u00a0. The obtBelow is the link to the electronic supplementary material.Supplementary material 1 (DOCX 308 KB)Supplementary material 2 (DOCX 50 KB)Supplementary material 3 (DOCX 31 KB)"} +{"text": "In this work, we investigate the self-assembly between Ag(I) and Au(I) centers and pyridyl donors to form hexagonal metallacycles and related linear complexes. The precipitation of hexagonal metallacycles upon assembly in chloroform/methanol mixtures results in high solid-state photo-stability. Whereas, the Ag(I) species have fast kinetics and high formation constants in acetone, this solvent interferes in the formation of the analogous Au(I) complexes. The photophysical properties of this suite of metallacycles was investigated including steady-state absorption, emission, and time-resolved lifetime measurements. All ligands and hexagons exhibited ligand-centered singlet emissions with ground-state absorption and emission perturbed upon coordination. The ligand-based fluorescent photoluminescence was affected by the heavy-atom effect when halide or metals are present, attenuating quantum yields as evidenced by increases in the experimentally measured non-radiative rate constants. The formation of group 11 metallacycles is motivated by their potential applications in mixed-matrix materials wherein metal ions can interact with substrate to facilitate separations chemistry with reduced energy requirements, in particular the isolation of ethylene and light olefins. Existing processes involve cryogenic distillation, an energy intensive and inefficient method. Coordination-driven self-assembly precursors , acetone, dichloromethane (DCM), ethyl acetate (EtOAc), n-hexanes, toluene, diethyl ether, petroleum ether, potassium hydroxide (KOH), sodium sulfate (Na2SO4) and potassium carbonate (K2CO3) were purchased from Fisher Scientific. N,N-dimethylformamide (DMF) was purchased from Macron Fine Chemicals. Tetrahydrofuran (THF), triethylamine (NEt3), and chloroform (CHCl3) were purchased from EMD Millipore. Ethanol was purchased from Decon Labs, Inc. Tetrakis(triphenylphosphine)palladium(0) (Pd(PPh3)4), and bis(triphenylphosphine)palladium(II) chloride (Pd(PPh3)2Cl2), and 1,3-dibromobenzene were purchased from Matrix Scientific. 4-pyridinylboronic acid (pyB(OH)2) was purchased from AK Scientific. Copper (I) iodide (CuI) was purchased from Strem Chemicals. Tetrahydrothiophene (tht) was purchased from Aldrich. Silver(I) hexafluorophosphate (AgPF6) was purchased from Oakwood Chemical. Hydrogen tetrachloroaurate(III) trihydrate (HAuCl4\u00b73H2O) was purchased from J&J Materials Inc. 4-ethynylpyridine hydrochloride and 1,3,5-tribromobenzene were purchased from Ark Pharm Inc. Deionized water was used whenever water was needed. THF was purified and dried through a Pure Process Technology free standing solvent purification system. NEt3 was purified and dried by distillation in KOH. DMF was filtered and dried using activated molecular sieves under N2 and freeze-pump-thawed with water before use for synthesis.All reagents and solvents were reagent grade and used as received without further purification unless noted. Methanol (CH1H Nuclear Magnetic Resonance (NMR) spectra were recorded on either Varian 300 or 400 MHz spectrometer. Chemical shifts (\u03b4) are reported in parts per million (ppm) referenced using the residual protio-solvent peaks as internal standards. Coupling constants (J) are quoted in Hertz (Hz), and the following abbreviations are used to describe the signal multiplicities: s (singlet); d (doublet); t (triplet); q (quartet); m (multiplet). Fourier Transform-Ion Cyclotron Resonance (FT-ICR) mass spectra were acquired using a Bruker Daltonics SolariX 12T FT-ICR Mass Spectrometer that was calibrated with > 90% Angiotensin I purchased from Sigma Aldrich under either Electrospray Ionization (ESI) or Laser Desorption Ionization (LDI) modes. Single Crystal X-ray Diffraction (SC-XRD) Crystallography was performed using a Bruker D8 Venture diffractometer in a fixed-chi geometry, equipped with a Photon-100 CMOS area detector, Oxford Cryosystems cryostat, a molybdenum source , and a graphite monochromator. Fourier Transform Infrared Resonance (FT-IR) spectra were collected from a Perkin Elmer 1760 FT-IR spectrometer equipped with horizontal attenuated total reflectance (HATR) from 4,000 to 500 cm\u22121 wavenumbers (\u03bd). The following abbreviations are used to describe signal intensities: w (weak); m (medium); s (strong). All UV-Vis absorption spectra were acquired from an Agilent Cary 8454 UV-Vis Diode Array system. Blank spectra with pure solvents were acquired before each run. All emission spectra were collected using a Horiba Scientific FluoroMax-4 Spectrofluorometer equipped with Quanta-\u03c6 Integrating light sphere with Spectralon coating for quantum yield (\u03a6) measurements and Delta-Hub DH-HT High Throughput Time-correlated Single Photon Counting (TCSPC) Controller and Nano-LED NL-C2 pulsed-diode controller with N-350 NanoLED Source for lifetime measurements. All solution-state absorbance and emission spectra were collected using a 10-mm rectangular quartz cuvette from Starna Cells Inc.L12 complex was self-assembled using a modified literature procedure AgPF6 was dissolved in 80.0 mL MeOH then layered over the L1 solution. After 48 h, white needle-like crystals form. These crystals were filtered and washed with 10-mL portions of CHCl3 (3x) to afford 1.19 g (100% yield) isolated product. 1H NMR : \u03b4 (ppm) = 8.81 , 7.82 , 7.77 , 7.71 , 7.65 , 7.46 . FT-IR : 3069 (w), 2235 (w), 2187 (w), 1609 (m), 1558 (w), 1506 (w), 1470 (w), 1433 (w), 1405 (w), 1223 (w), 1152 (w), 1070 (w), 1031 (w), 991 (w), 915 (w), 881 (m), 815 (m), 775 (m), 757 (m), 743 (m), 678 (m), 663 (m), 553 (m), 531 (m).AgL2}6 hexagon, was self-assembled using a modified literature procedure AgPF6 was dissolved in 5.0 mL MeOH then layered over the L2 solution. After 48 h, white powdered product formed which was filtered and washed with 10-mL portions of CHCl3 (3x) to afford 0.062 g (73% yield) isolated product. 1H NMR : \u03b4 (ppm) = 8.72 , 7.90 , 7.83 , 7.62 . FT-IR : 3076 (w), 2219 (w), 1613 (m), 1557 (w), 1507 (w), 1435 (m), 1338 (w), 1291 (w), 1221 (m), 1174 (w), 1162 (w), 1136 (w), 1107 (w), 1066 (w), 1028 (w), 993 (w), 964 (w), 864 (m), 821 (s), 748 (w), 736 (w), 663 (m), 573 (w), 552 (s).{AgL3}6 hexagon, was self-assembled using a modified literature procedure AgPF6 was dissolved in 5.0 mL MeOH then layered over the L3 solution. After 48 h, white powdered product formed which was filtered and washed with 10-mL portions of CHCl3 (3x) to afford 0.096 g (100% yield) isolated product. 1H NMR : \u03b4 (ppm) = 8.74 , 7.86 , 7.74 , 7.66 , 7.63 \u2013 7.56 . FT-IR : 3107 (w), 2203 (w), 1615 (m), 1543 (w), 1501 (w), 1431 (w), 1227 (w), 1167 (w), 1064 (w), 1025 (w), 878 (w), 821 (m), 752 (w), 733 (w), 682 (w), 556 (m), 541 (m).{AgL4}6 hexagon, was self-assembled using a modified literature procedure AgPF6 was dissolved in 2.0 mL MeOH then layered over the L4 solution. After 48 h, white powdered product formed which was filtered and washed with 10-mL portions of CHCl3 (3x) to afford 0.052 g (92% yield) isolated product. 1H NMR : \u03b4 (ppm) = 8.76 , 8.25 , 8.00\u20137.87 , 7.80\u20137.71 . FT-IR : 3092 (w), 1618 (m), 1545 (w), 1513 (w), 1478 (w), 1431 (w), 1411 (w), 1314 (w), 1230 (w), 1069 (w), 1031 (w), 1019 (w), 873 (m), 818 (s), 791 (s), 736 (m), 695 (m), 663 (w), 637 (m), 613 (w), 555 (s).{AgL12 complex was self-assembled using a modified literature procedure Au(tht)Cl were dissolved in 6.0 mL acetone. After 6 h, the solution was concentrated in vacuo and the collected solid was washed with 6-mL portions of CHCl3 (3x) to afford 0.007 g (20% yield) isolated product. 1H NMR : \u03b4 (ppm) = 8.84 , 7.89 , 7.80 , 7.68 , 7.50 \u2013 7.40 . FT-IR : 3044 (w), 2918 (w), 2856 (w), 2218 (m), 2187 (w), 1943 (w), 1801 (w), 1614 (m), 1588 (m), 1558 (w), 1496 (w), 1463 (w), 1429 (w), 1404 (w), 1261 (w), 1234 (w), 1217 (w), 1158 (w), 1105 (w), 1088 (w), 1060 (w), 1038 (w), 987 (w), 906 (w), 876 (w), 836 (m), 814 (w), 789 (m), 747 (w), 713 (w), 691 (w), 680 (m), 655 (m), 565 (w), 535 (m).AuL2}6 hexagon was self-assembled using a modified literature procedure Au(tht)Cl were dissolved in 6.0 mL CHCl3. After 24 h, the solution was concentrated in vacuo and the collected yellow solid was washed with 6-mL portions of CHCl3 (3x) to afford 0.025 g (78% yield) isolated product. 1H NMR : \u03b4 (ppm) = 8.84\u20138.71 , 8.09 \u2013 7.82 . FT-IR : 3100 (w), 3044 (w), 2210 (m), 1615 (s), 1553 (w), 1496 (w), 1430 (m), 1336 (w), 1288 (w), 1211 (m), 1171 (w), 1134 (w), 1105 (w), 1063 (m), 1046 (w), 992 (w), 966 (w), 863 (m), 826 (m), 761 (w), 721 (w), 672 (m), 587 (w), 574 (m), 527 (w).{AuL3}6 hexagon was self-assembled using a modified literature procedure Au(tht)Cl were dissolved in 6.0 mL CHCl3. After 24 h, the solution was concentrated in vacuo and the collected yellow solid was washed with 6-mL portions of CHCl3 (3x) to afford 0.026 g (89% yield) isolated product. 1H NMR : \u03b4 (ppm) = 8.76 , 8.08 \u2013 7.70 , 7.66\u20137.57 . FT-IR : 3092 (w), 3029 (w), 2203 (m), 1943 (w), 1609 (s), 1529 (w), 1492 (w), 1427 (w), 1324 (w), 1213 (w), 1162 (w), 1150 (w), 1125 (w), 1093 (w), 1065 (w), 1042 (w), 991 (w), 942 (w), 902 (w), 831 (m), 792 (w), 754 (w), 729 (w), 666 (w), 569 (w), 544 (w).{AuL4}6 hexagon was self-assembled using a modified literature procedure Au(tht)Cl were dissolved in 6.0 mL CHCl3. After 24 h, the solution was concentrated in vacuo and the collected white solid was washed with 6-mL portions of CHCl3 (3x) to afford 0.027 g (100% yield) isolated product. 1H NMR : \u03b4 (ppm) = 8.82 , 8.35 , 8.22 , 8.11 , 7.86 . FT-IR : 3060 (w), 1611 (s), 1546 (w), 1508 (w), 1472 (w), 1443 (w), 1427 (w), 1398 (m), 1340 (w), 1318 (w), 1266 (w), 1231 (m), 1186 (w), 1109 (w), 1076 (m), 1034 (w), 970 (w), 935 (w), 915 (w), 857 (w), 832 (m), 786 (s), 761 (w), 732 (m), 687 (w), 667 (w), 645 (m), 632 (w), 606 (w), 535 (s).{AuL1), 5-bromo-1,3-bis(4-ethynylpyridyl)benzene (L2), 1,3-bis(4-ethynylpyridyl)benzene (L3), and 1,3-bis(4-pyridyl)benzene (L4), were prepared as donors for self-assembly reactions. As illustrated in L1, L2, and L3 were prepared following a typical Sonogashira coupling reaction while L4 was prepared following a typical Suzuki coupling reaction. The 1H NMR spectra of L1, L2, L3, and L4 in acetone-d6 are summarized in L11H spectrum shows the pyridyl-H doublets at 8.63 and 7.49 ppm and the benzyl-H singlet at 7.78 ppm, two doublets at 7.65 and 7.60 ppm, and triplet at 7.42 ppm. The L2 spectrum shows the pyridyl-H doublets at 8.66 and 7.53 ppm and the benzyl-H singlets at 7.87 and 7.82 ppm. The L3 spectrum shows the pyridyl-H doublets at 8.65 and 7.51 ppm and the benzyl-H singlet at 7.83 ppm, doublet at 7.69 ppm, and triplet at 7.56 ppm. The L4 spectrum shows the pyridyl-H doublets at 8.68 and 7.78 ppm and the benzyl-H singlet at 8.17 ppm, doublet at 7.89 ppm, and triplet at 7.70 ppm.Four pyridyl ligands, 1-bromo-3(4-ethynylpyridyl)benzene (L1 was used to synthesize linear Ag(I) and Au(I) complexes, while L2, L3, and L4 were used to self-assemble Ag(I) and Au(I) hexagonal metallacycles. The general method used to self-assemble the complexes and hexagons is shown in L12, was prepared by layering one equivalent of AgPF6 in MeOH over two equivalents of L1 in CHCl3. This resulted in the crystallization of AgL12 after 48 h. Ag(I) hexagons, {AgL}6 where L = L2, L3, and L4, were prepared by layering one equivalent of AgPF6 in MeOH over one equivalent of L in CHCl3. The hexagons precipitated at almost quantitative yields as white powders after 48 h. The gold analogs, Au(I) hexagons, {AuL}6 where L = L2, L3, and L4, were prepared by mixing 1:1 equivalents of Au(tht)Cl and L in CHCl3. After 24 h, powdered metallacycles were isolated upon solvent removal and CHCl3 washing. In the case of the monomeric Au(I) complex, AuL12, previous attempts using pure CHCl3 or 1:1 (v/v) CHCl3/MeOH did not result in any complex formation. However, the complex was isolated at a relatively low yield by mixing 1:1 equivalents of Au(tht)Cl and L1 in acetone.N,N'-dimethylsulfoxide (DMSO), which are typically used in solution-state structural analyses of Ag(I) and Ag(I) complexes proved to be unsuitable for our complexes and hexagons and Au(I) complex and hexagons is their limited solubilities. Coordinating solvents such as acetonitrile (MeCN) and ns Laye, . In all 1H NMR peaks as well as peak integration agreements complexes and hexagons as well reements . In addi1H NMR spectra of {AuL2}6, {AuL3}6, and {AuL4}6. The full spectra of each Au(I) hexagon are shown in 1H NMR peaks, the peak integration agreements, and the similarity in peak splitting patterns indicate the formation of pure Au(I) hexagonal metallacycles. Although the solubility of these species is limited, our identification of NMR-suitable solvents rules out the formation of polymeric species as such coordination polymers are fully insoluble. ESI-MS (see below) further confirms the stoichiometries of self-assembly.For the Au(I) hexagons, ligand dissociation occurs when MeCN, DMSO, and acetone were used as solvents. These hexagons are insoluble in all other solvents except for nitromethane, in which we were able to observe intact Au(I) hexagons. 3 or in CHCl3 mixtures with MeOH. MeCN and DMSO competitively coordinate with the Ag(I) and Au(I) resulting in ligand dissociation. Acetone was a suitable solvent for the building blocks, as well as the final assemblies, enabling the study of complex formation. Using 1H NMR methods, we initially acquired a series of spectra for a solution containing 1:1 equivalents of Ag:L in acetone upon mixing and after 24 h (All of these complexes were synthesized in pure CHClter 24 h . We obseL in acetone to ensure complete ligand coordination. The acquired 1H NMR spectra at 0 (upon mixing), 6, 24, and 48 h were summarized in L12 complex self-assembles within 6 h then partially dissociates thereafter. In the case of both {AuL2}6 and {AuL3}6, an equilibrium was established immediately upon mixing that stays up to at least 48 h. Products of {AuL4}6 hexagon assembly crash out of solution immediately upon mixing such that we only observe uncoordinated L4 and partially dissolved products. In all cases, the initial coordination is fast; however, quantitative analyses of the NMR peaks is not straightforward using a one-step metal-ligand binding model. There are reports on the mechanism and reducing ability of acetone to form Au nanoparticles from Au(III) and Au(I) complex and hexagons. In this case, we prepared solutions containing 1:1, 2:1, and 3:1 equivalents of Au:High-resolution mass spectrometry (HRMS) was used to probe the stoichiometry of our self-assemblies. We used Fourier transform-ion cyclotron mass spectrometry (FT-ICR MS) with electrospray ionization (ESI) for soluble complexes and hexagons, while laser desorption ionization (LDI) was used for hexagons that are unstable in acetone. ESI, as a soft ionization technique, is advantageous and popularly used in detection of intact coordination complexes and cages with high molar masses complex and hexagons and for Au(I) complex and hexagons are shown in complex as well hexagon and + complex (\u2212 counter-ion by ESI-FT-ICR MS. The Au(I) hexagons, which are unstable is acetone were detected by LDI-FT-ICR MS. We were able to detect singly-charged intact [{AuL2}6+AuCl+K]+ hexagon (L3}6+Na]+ hexagon (L4}6+Na]+ hexagon (L}6 fragments (For the Au(I) complex and hexagons, we were able to detect the intact cores that ionized by the loss of counterions.Silver(I) and gold(I) mononuclear complexes and hexagonal rings were self-assembled from AgPFLonger-term photostability of all complexes and hexagons in the solid-state were confirmed by FT-IR. Significant peak shifts to higher wavenumbers were observed upon coordination of the ligands to either Ag(I) or Au(I). No changes to the spectra were observed after storing the compounds at ambient conditions under room light for one week.L3 and L4 were the most and least emissive ligands, respectively. In the solid-state, all complexes and hexagons have diminished emission except for {AgL2}6, {AgL4}6, and {AuL4}6 wherein aggregation-induced emission was observed. In the solution-state, all ligands and hexagons exhibited ligand-centered singlet emissions while AgL12 and AuL12 both exhibited metal-perturbed ligand-centered singlet emissions.Ligand-centered fluorescence emission was observed for many of these complexes. In both the solid- and solution-state, This work establishes that Ag(I) and Au(I) centers are effective linear nodes for self-assembly reactions with dipyridyl ligands and that the resultant materials stabilize these ions with respect to oxidation and photodecomposition. Due to the modular nature of coordination-driven self-assembly, efforts are ongoing to exploit ligand-tuning to incorporate functional groups that will enhance metallacycle solubility to improve their processability for incorporation into mixed-matrix materials.L12 (CCDC No. 1879931) for this study can be found in the Cambridge Crystallographic Data Centre https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/.The dataset AgCF designed and carried out the experiments and wrote the manuscript. SK assisted in ligand synthesis. AF carried out the mass spec characterization. TC designed the project and wrote the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Alcaligenes aquatilis strain QD168 (= CCUG 69566) is a marine hydrocarbon-degrading bacterium isolated from crude oil-polluted sediment from Quintero Bay, Central Chile. Here, we present the 4.32-Mb complete genome sequence of strain QD168, with 3,892 coding sequences, 58 tRNAs, and a 56.3% G+C content. Alcaligenes aquatilis strain QD168 (= CCUG 69566) is a marine hydrocarbon-degrading bacterium isolated from crude oil-polluted sediment from Quintero Bay, Central Chile. Here, we present the 4.32-Mb complete genome sequence of strain QD168, with 3,892 coding sequences, 58 tRNAs, and a 56.3% G+C content. Alcaligenes are Gram-negative, aerobic, and motile bacteria that are frequently isolated from water, soil, and clinical samples, as well as from industrial and contaminated environments , a marine hydrocarbon-degrading bacterium capable of growing on n-hexadecane and diesel in M9 minimal medium agar in Bushnell Hass mineral medium and artificial seawater.Members of the genus ronments \u20136. Alcalg phenol , atrazing phenol , endosulg phenol , phenantg phenol , pyrene,a]pyrene . Here, wium agar at 30\u00b0C.Genomic DNA of QD168 cells cultivated in Luria-Bertani broth was extracted using a Qiagen Genomic-tip 100/G kit . Next-generation sequencing was performed using a PacBio RS II platform with one single-molecule real-time (SMRT) cell and an average 20-kb insert library, obtaining 87,836 reads with an average length of 12,761\u2009bp. PacBio reads were trimmed and assembled using the Hierarchical Genome Annotation Pipeline (HGAP) v3.0 , obtainiectABCD; D3M96_13270, D3M96_13265, D3M96_13260, and D3M96_13255) and the bioplastic polyhydroxyalkanoates were identified. Aromatic catabolic genes encoding catechol 1,2-dioxygenase , catechol 2,3-dioxygenase , homogentisate 1,2-dioxygenase , protocatechuate 4,5-dioxygenase and gentisate 1,2-dioxygenase were identified.Gene functional annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.6 , identifhttps://www.ebi.ac.uk/Tools/psa/emboss_needle/) showed a close relationship (99.9% identity) with A. aquatilis LMG 22996T, while identities with those of the type strains of other Alcaligenes species were <98.5% (species threshold) and A. faecalis DSM 30030T, resulted in ANIb values of 96.8% and 90.5% , respectively.Comparative 16S rRNA gene sequence analyses using EMBOSS Needle (reshold) . MultiloW v.1.81 and manuT (ANIb) , using JT (ANIb) with A. A. aquatilis strain.This is the first complete genome sequence of an Alcaligenes aquatilis strain QD168 has been deposited in DDBJ/ENA/GenBank under the accession number CP032153. The version described in this paper is the first version, CP032153.1. The accession number for the publicly available raw data at NCBI is PRJNA489687.The genome sequence of"} +{"text": "Klebsiella pneumoniae represents an emerging public health issue. Here, we present the draft whole-genome sequences of K. pneumoniae clinical strains KPL0.1 (OXA-48 carbapenemase) and KPL0.2 (NDM-1 carbapenemase).Carbapenemase-producing Klebsiella pneumoniae represents an emerging public health issue. Here, we present the draft whole-genome sequences of K. pneumoniae clinical strains KPL0.1 (OXA-48 carbapenemase) and KPL0.2 (NDM-1 carbapenemase). These genome sequences should help in investigating pathophysiological mechanisms of digestive colonization or infection with these highly resistant bacteria.Carbapenemase-producing Enterobacteriaceae (CPE) are resistant to most beta-lactams, including last-line options such as carbapenems, and are an emerging public health issue , KPL0.1 (producing OXA-48 carbapenemase) and KPL0.2 (producing NDM-1 carbapenemase). Both strains were isolated from blood cultures using the Virtuo automated system and identified by matrix-assisted laser desorption ionization\u2013time of flight (MALDI-TOF) mass spectrometry . KPL0.1 was isolated from a 77-year-old patient following digestive surgery, and KPL0.2 came from an 84-year-old patient with a urinary tract infection.Carbapenemase-producing th issue . Klebsieescribed . In Franescribed . Two strde novo assembled with Unicycler. Genomes were annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) v4.5 , and quality control was performed using a Qubit v3.0 fluorometer . Libraries were prepared using the Nextera XT DNA Library prep kit , followed by paired-end 2 \u00d7 150-bp) sequencing on a HiSeq platform (Illumina). Genome coverage was about 650\u00d7 for each isolate. Paired reads were filtered, and Nextera adapters were removed using Trimmomatic on a Galaxy server using default settings . Process0-bp sequblaOXA-48, blaSHV-28, blaTEM-1B, blaCTX-M-15, blaOXA-1), four aminoglycoside resistance genes , five fluoroquinolone resistance genes , and individual antimicrobial resistance genes .The draft genome of KPL0.1 consists of 5,825,863\u2009bp and has a mean G+C content of 56.70%. A total of 5,628 protein-coding genes were annotated, including 92 RNA-coding genes and 75 tRNAs, and the remaining genes were annotated as hypothetical proteins. KPL0.1 belongs to sequence type 307 (ST-307) and possesses the KL102 capsule locus , four aminoglycoside resistance genes , and individual antimicrobial resistance genes .The draft genome of KPL0.2 consists of 5,741,089\u2009bp with a mean G+C content of 56.94%. A total of 5,570 protein-coding genes were annotated, including 93 RNA-coding genes and 79 tRNAs, and the remaining genes were annotated as hypothetical proteins. KPL0.2 belongs to ST-147 and possesses the KL64 capsule locus. The following resistance genes were predicted: five beta-lactam resistance genes and PYBH00000000 (KPL0.2). The versions described in this paper are QHMA01000000 (KPL0.1) and PYBH01000000 (KPL0.2). The SRA accession number is SRP155589.These two draft whole-genome shotgun projects have been deposited at DDBJ/ENA/GenBank under the accession numbers"} +{"text": "Spodoptera litura, and significantly influences the development and fecundity of S. litura at either lethal or sublethal doses. Herein, Illumina HiSeq Xten (IHX) platform was used to explore the transcriptome of S. litura and to identify genes responding to fluralaner exposure.Fluralaner is a novel isoxazoline insecticide with a unique action site on the \u03b3-aminobutyric acid receptor (GABAR), shows excellent activity on agricultural pests including the common cutworm S. litura transcriptome and annotated according to the COG, GO, KEGG and NR databases. These genes included 156 detoxification enzyme genes and 24 insecticide-targeted genes . There were 3275 and 2491 differentially expressed genes (DEGs) in S. litura treated with LC30 or LC50 concentrations of fluralaner, respectively. Among the DEGs, 20 related to detoxification and 5 were growth-related genes (1 chitin and 4 juvenile hormone synthesis genes). For 26 randomly selected DEGs, real-time quantitative PCR (RT-qPCR) results showed that the relative expression levels of genes encoding several P450s, GSTs, heat shock protein (HSP) 68, vacuolar protein sorting-associated protein 13 (VPSAP13), sodium-coupled monocarboxylate transporter 1 (SCMT1), pupal cuticle protein (PCP), protein takeout (PT) and low density lipoprotein receptor adapter protein 1-B (LDLRAP1-B) were significantly up-regulated. Conversely, genes encoding esterase, sulfotransferase 1C4, proton-coupled folate transporter, chitinase 10, gelsolin-related protein of 125\u2009kDa (GRP), fibroin heavy chain (FHC), fatty acid synthase and some P450s were significantly down-regulated in response to fluralaner.A total of 16,572 genes, including 451 newly identified genes, were observed in the S. litura whilst the DEGs identified sheds further light on the molecular response to fluralaner.The transcriptome in this study provides more effective resources for the further study of Spodoptera litura Fabricius (Lepidoptera: Noctuidae), is a destructive polyphagous pest with a broad host plant range of more than 100 species of crops and vegetables of fluralaner dissolved in acetone. After 24\u2009h, 15 alive and normal S. litura from each treatment were randomly collected, equally divided into three 1.5\u2009mL Eppendorf tubes, respectively, immediately frozen in liquid nitrogen and stored at \u2212\u200980\u2009\u00b0C until use.A laboratory strain of s report . Flurala. (2019) . The 3rdS. litura from each group by TRIzol\u2122 Reagent . The concentration and integrity of total RNA were measured using NanoDrop 2000 and with the RNA Nano 6000 Assay Kit by Agilent Bioanalyzer 2100 system , respectively.Total RNA was isolated from whole body of RNA sequencing libraries were generated from each sample and the sequencing was carried out by BioMarker following the manual of the NEB Next\u00ae Ultra\u2122 RNA Library Prep Kit in Illumina. Briefly, 1\u2009\u03bcg of total RNA from each sample was enriched using magnetic beads with Oligo (dT) and broken into short fragments, which was carried out using divalent cations under elevated temperature by adding NEB Next First Strand Synthesis Reaction Buffer (5x) (NEB). These short fragments of mRNA served as templates for synthesis of the first-strand complementary DNA (cDNA) with random hexamer primers and Moloney Murine Leukemia Virus (M-MuLV) Reverse Transcriptase (NEB). Using buffer, dNTPs, RNase H and DNA Polymerase I, the second-strand cDNA was subsequently synthesized. Remaining overhangs were converted into blunt ends via exonuclease/ polymerase activities. After adenylation of 3\u2032 ends of DNA fragments, NEB Next Adaptor with hairpin loop were ligated for hybridization. The purified cDNAs were subjected to end repair by adding an adenosine triphosphate (A) base to the 3\u2032 end and connected with sequencing adaptor. Suitable fragments of cDNAs were extracted by the AMPure XP system . Three microliter of USER Enzyme (NEB) was used for size selection, and adaptor-ligated cDNAs at 37\u2009\u00b0C for 15\u2009min followed by 5\u2009min at 95\u2009\u00b0C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase (NEB), Universal PCR primers, and Index (X) Primer (NEB). PCR products were purified with the AMPure XP system (Beckman Coulter) and library quality was assessed on the Agilent Bioanalyzer 2100 system (Agilent).The clustering of the index coded samples was carried out on a cBot Cluster Generation System (Illumina) using TruSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer\u2019s instruction. After cluster generation, the prepared libraries were sequenced on an Illumina platform and paired end reads were generated.S. litura . The clean reads with a perfect match or with only one mismatch were mapped to the reference genome of . litura by the H. litura . The map. litura and all . litura accordin. litura , Gene On. litura , Kyoto E. litura and Non-. litura . In addiS. litura transcriptome. Referring to the previous studies [S. litura, B. mori, D. melanogaster and A. mellifera, then the phylogenetic trees were mapped with 1000 bootstrap replications using the neighbor-joining method to evaluate the branch strength of each tree using MEGA 7 [Genes encoding detoxification enzymes including P450s, GSTs, CarEs, and insecticide-targeted genes including ionotropic GABARs, GluCl, VGSCs, nAChRs, RyR and AChEs, were identified from the studies , 21, 62,g MEGA 7 . The phyg MEGA 7 . Referrig MEGA 7 , 48, 65,g MEGA 7 and Treeg MEGA 7 .30- and LC50-treated groups were analyzed using DEGseq method [>\u00a02) and false discovery rate (FDR <\u20090.01) from corrected P-value were used as a judgment standard for the significant differences in gene expression between two samples [Premix Ex Taq\u2122 II (Tli RNaseH Plus) \u2002Co.,\u2002Ltd., Liaoning, China) on a Quant Studio\u2122 6 and 7 Flex Real-Time PCR System according to the procedures from Liu et al. (2018) [-\u25b3\u25b3Ct method [The relative expression levels of genes among the control, LCq method , which p samples . The DEG. (2018) . The hou. (2018) . Three tt method . The priAdditional file 1: Text S1. Gene annotation with COG and GO databases.Additional file 2. All pathways annotated by KEGG database.Additional file 3. Cytochrome P450 nucleotide sequences of the S. litura transcriptome.Additional file 4. Neighbor-joining phylogenetic analysis of the P450s genes from D. melanogaster, H. armigera, P. xylostella,S. litura and B. mori.Additional file 5. Glutathione S-transferase nucleotide sequences of the S. litura transcriptome.Additional file 6. Neighbor-joining phylogenetic analysis of the GST genes from D. melanogaster, A. mellifera,S. litura and B. mori.Additional file 7. Carboxylesterase nucleotide sequence of the S. litura transcriptome.Additional file 8. Neighbor-joining phylogenetic analysis of the CarE genes from D. melanogaster, H. armigera, P. xylostella,S. litura and B. mori.Additional file 9. Nucleotide sequences of annotated insecticide-targeted genes of the S. litura transcriptome.Additional file 10. Neighbor-joining phylogenetic analysis of the cys-loop ligand-gated ion channel superfamily genes from S. litura and other species. The subunits sequence used are as follow: Am-alpha1 (AAY87890.1), Am-alpha2 (AAS48080.1), Am-alpha3 (AAY87891.1), Am-alpha4 (AAY87892.1), Am-alpha5 (AJE70263.1), Am-alpha6 (AAY87894.1), Am-alpha7 (AAR92109.1), Am-alpha8 (NP_001011575.1), Am-alpha9 (AAY87896.1), Am-beta1 (AAY87897.1), Am-beta2 (AAY87898.1), Am-GluCl (ABG75737.1), Am-RDL (AJE68941.1), Am-GRD (AJE68942.1), Am-LCCH3 (AJE68943.1), Am-CG8916 (NP_001071290.1), Am-HisCl (ABG75739.1), Am-pHCl (ABG75741.1), Am-CG6927 (ABG75747.1), Am-CG12344 (ABG75746.1), Dm-alpha1 (AGB96296.1), Dm-alpha2 (NP_524482.1), Dm-alpha3 (NP_525079.3), Dm-alpha4 (NP_001097669.2), Dm-alpha5 (NP_995708.1), Dm-alpha6 (NP_995674.1), Dm-alpha7 (NP_996514.1), Dm-beta1 (NP_523927.2), Dm-beta2 (NP_524483.1), Dm-beta3 (AAF51485.1), Dm-RDL (NP_523991.2), Dm-LCCH3 (NP_996469.1), Dm-GRD (CAA55144.1), Dm-CG8916 (AAF48539.4), Dm-HisCl1 (AAL74413.1), Dm-HisCl2 (AAL74414.1), Dm-NtR (NP_651958.2), Dm-pHCl1 (NP_001034025.2), Dm-pHCl2 (NP_651861.1), Dm-CG6927 (AAF45992.1), Dm-CG7589 (AAF49337.2), Dm-CG12344 (NP_610619.2), Bm-alpha1 (XP_021203289.1), Bm-alpha2 (NP_001103397.1), Bm-alpha3 (NP_001103387.2), Bm-alpha4 (NP_001166816.1), Bm-alpha5 (NP_001166811.1), Bm-alpha6 (NP_001166813.1), Bm-alpha7 (NP_001166818.1), Bm-alpha8 (NP_001166817.1), Bm-alpha9 (ABV72691.1), Bm-beta1 (ABV72692.1), Bm-beta2 (ABV72693.1), Bm-beta3 (ABV45510.1), Bm-RDL1 (ADM88014.1), Bm-RDL2 (NP_001182629.1), Bm-RDL3 (NP_001182630.1), Bm-LCCH3 (BAT57341.1), Bm-GluCl (BAO58781.1), Bm-pHCl (BAX77827.1).Additional file 11. Phylogenetic analysis of the AChE genes.Additional file 12. Functional classification of DEGs according to COG database. Note: A represented the DEGs and all genes after the exposure of LC30 fluralaner, B represented the DEGs and all genes after the exposure of LC50 fluralaner, respectively.Additional file 13. Functional classification of DEGs according to KEGG database.Additional file 14. Changes of DEGs related to detoxification and development of S. litura after exposure of fluralaner.Additional file 15. Primers for RT-qPCR validation."} +{"text": "Pneumonia and influenza (P&I) increase morbidity and mortality among older adults, especially those residing in long-term care facilities (LTCFs). Facility-level characteristics may affect P&I risk beyond resident-level determinants. However, the relationship between facility characteristics and P&I is poorly understood. We therefore identified potentially modifiable facility-level characteristics that might influence the incidence of P&I across LTCFs. We conducted a retrospective cohort study using 100% of 2013-2015 Medicare claims linked to Minimum Data Set 3.0 and LTCF-level data. Short-stay (<100 days) and long-stay (\u2265100 days) LTCF residents aged \u226565 were followed for the first occurrence of hospitalization, LTCF discharge, Medicare disenrollment, or death. We calculated LTCF risk-standardized incidence rates (RSIRs) per 100 person-years for P&I hospitalizations by adjusting for over 30 resident-level demographic and clinical covariates using hierarchical logistic regression. The final study cohorts included 1,767,241 short-stay and 922,863 long-stay residents . LTCFs with lower RSIRs had more Physician Extenders (Nurse Practitioners or Physician\u2019s Assistants) among short-stay and long-stay residents , higher Registered Nurse hours/resident/day among short-stay and long-stay residents (Mean (SD): 0.5 (0.7) vs. 0.4 (0.4), p<0.001), and fewer residents prescribed antipsychotics among short-stay (21.4% (11.6) vs. 23.6% (13.2), p<0.001) and long-stay residents (22.2% (14.3) vs. 25.5% (15.0), p<0.001). LTCF characteristics may play an important role in preventing P&I hospitalizations. Hiring more Registered Nurses and Physician Extenders, increasing staffing hours, and reducing antipsychotic use may be modifiable means of reducing P&I in LTCFs. Funding provided by Sanofi Pasteur."} +{"text": "LncRNA MIR4435-2HG is observed in a variety of cancers, while its role in colorectal cancer is unknown. We aimed to demonstrate the relationship between MIR4435-2HG and colorectal cancer based on The Cancer Genome Atlas (TCGA) database.Patients with colorectal cancer were collected from TCGA. We compared the expression of MIR4435-2HG in colorectal cancer and normal tissues with Wilcoxon rank sum test, and logistic regression was used to evaluate the relationship between MIR4435-2HG and clinicopathological characters. Moreover, Kaplan\u2013Meier and Cox regression was performed to evaluate the correlation between MIR4435-2HG and survival rate. Gene set enrichment analysis (GSEA) was also conducted to annotate biological function of MIR4435-2HG.P-value <0.05). High MIR4435-2HG expression had a poorer progression-free survival (p = 0.048), and overall survival (OS) (P = 0.028), which were validated in the GSE92921 and GSE29621 datasets. MIR4435-2HG expression ) was independently correlated with OS. GSEA demonstrated that the P38/MAPK pathway, the VEGF pathway, the cell adhesion molecules cams, the NOD-like receptor signaling pathway, the cell surface interactions at the vascular wall, and integrin cell surface interactions were differentially enriched in MIR4435-2HG high expression phenotype.MIR4435-2HG level was elevated in colorectal cancer tissues. Increased level of MIR4435-2HG was significantly correlated with TNM stage , stage (OR = 1.66 for stage 1/2 vs. stage 3/4), and carcinoembryonic antigen level before treatment (OR = 1.70 for <5 vs. \u22655) (all Increased MIR4435-2HG might be a potential biomarker for the diagnosis and prognosis of colorectal cancer. Moreover, MIR4435-2HG might participate in the development of colorectal cancer via the P38/MAPK and VEGF pathway. The prevalence of colorectal cancer is increasing worldwide . SurgeryMIR4435-2HG, also known as AGD2, MORRBID, LINC00978, MIR4435-1HG, lncRNA-AWPPH, has been regarded as a new oncogenic lncRNA in many types of cancer, like breast cancer and bladder cancer . A recenTherefore, we aimed to demonstrate the correlation between MIR4435-2HG and colorectal cancer, and analyze the prognostic role of MIR4435-2HG in colorectal cancer based on The Cancer Genome Atlas (TCGA). To achieve this goal, we analyzed the expression level of LncRNA MIR4435-2HG in colorectal cancer and normal tissues based on TCGA. And the correlation between LncRNA MIR4435-2HG and prognostic values was performed. Furthermore, MIR4435-2HG related biological pathways involved in colorectal cancer were detected using Gene set enrichment analysis (GSEA).The present study showed increased MIR4435-2HG was related to poor prognosis of colorectal cancer, and P38/MAPK pathway, VEGF pathway, cell adhesion molecules cams, Nod like receptor signaling pathway, cell surface interactions at the vascular wall, and integrin cell surface interactions were associated with LncRNA MIR4435-2HG expression phenotype using GSEA.n = 9) and with overall survival (OS) less than 30 days (n = 42) were excluded. The related RNA-seq data and clinicopathological data were extracted. The expression of lncRNA MIR4435-2HG in colorectal adenocarcinoma were analyzed and compared with that in adjacent normal tissues. Considering the fact that the relationship between LncRNA MIR4435-2HG expression and the development of a tumor is independent of the follow-up days, we used 622 RNA-seq data for further association analysis, and 580 data for survival analysis. The characteristics of patients including gender, race, differentiation, venous or perineural invasion, preoperative pretreatment, TNM stage, and tumor location were recorded. Some of them were not available, which were treated as missing value. In addition, the Gene Expression Omnibus (GEO) database was used to validate the association between MIR4435-2HG expression and colorectal cancer outcome. Two raw gene expression datasets were downloaded from GEO for further study.In the TCGA database, 459 patients with colonic adenocarcinoma and 172 cases with rectal adenocarcinoma were collected. Finally, 580 cases were included in the further analysis, while cases without RNA-seq data .In this study, GSEA was used to elucidate the significant survival difference between high- and low- MIR4435-2HG groups. The number of gene set permutations were 1,000 times for each analysis. The expression level of lncRNA MIR4435-2HG was used as a phenotype label. The pathways enrichment was analyzed based on nominal Statistical analysis was performed using R (v.3.5.1) . Comparin = 240), and 156 cases (31.52%) had history of colon polyps. Stage I disease was found in 102 patients (18.21%), stage II in 206 (36.79%), stage III in 168 (30.00%), and stage IV in 84 (15.00%). Most tumors were of colonic adenocarcinoma, and 27.07% (n = 157) were rectal adenocarcinoma. The topography distribution included 3.29% T1 (n = 19), 17.82% T2 (n = 103), 68.17% T3 (n = 394), and 10.73% T4 (n = 62). A total of 123 cases (24.50%) had venous invasion, and 57 (26.03%) perineural invasion. A total of 83 cases (16.12%) had distant metastases.The characteristics of patients including gender, race, differentiation, venous or perineural invasion, preoperative pretreatment, TNM stage, and tumor location were collected, as shown in P < 0.001) (P < 0.001) . In addi< 0.001) , indicatP < 0.001), lymph node metastasis (P < 0.001), stage (P < 0.001), and CEA level before treatment (P = 0.013), as shown in A total of 580 colorectal cancer samples with LncRNA MIR4435-2HG expression data were analyzed from TCGA. Increased expression of MIR4435-2HG was correlated significantly with the grade of topography distribution , stage , and CEA level before treatment . Univari= 0.015) . These rP = 0.048) (P = 0.028) was significantly poorer in patients with high LncRNA MIR4435-2HG expression than those with low LncRNA MIR4435-2HG expression (P = 0.044) based on GSE92921 (P = 0.021) based on GSE29621 ), older patients ), higher CEA level ), higher TNM stage ; N: P < 0.001, HR = 2.991 (95% CI [2.027\u20134.414]); M: P < 0.001, HR = 4.737 (95% CI [3.156\u20137.11])), higher disease stage ), and venous invasion ) was significantly poorer in patients with high LncRNA MIR4435-2HG expression than those with low LncRNA MIR4435-2HG expression (= 0.048) \u20133C, simi= 0.028) \u20133F. In aGSE92921 \u2013S1C, andGSE29621 \u2013S1F. We GSE29621 . High Ln3.728])) .P = 0.040, HR = 1.955 (95% CI [1.031\u20133.710])), age ), status ), lymph node metastasis ), and disease stage ) were independently correlated with OS in multivariate analysis in enrichment of MSigDB Collection (c2.cp.v6.2.symbols.gmt).Gene set enrichment analysis was used to identify signaling pathways involved in colorectal cancer between low and high LncRNA MIR4435-2HG expression data sets, and demonstrated significant differences The Kaplan\u2013Meier curve, (B) Number at risk, and (C) Number of censoring of DFS in colorectal cancer based on GSE92921 dataset. (D) The Kaplan\u2013Meier curve, (E) Number at risk, and (F) Number of censoring OS in colorectal cancer based on GSE29621 dataset. DFS: disease-free survival; OS: over survival.Click here for additional data file.10.7717/peerj.6683/supp-3Supplemental Information 3Click here for additional data file.10.7717/peerj.6683/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.6683/supp-5Supplemental Information 5Click here for additional data file."} +{"text": "Healthy People 2020 included objectives to improve health of LGBT persons.In recent decades, public health awareness of health disparities among lesbian, gay, bisexual, and transgender (LGBT) populations has increased ( BRFSS is an annual state-based, random-digit\u2013dialed telephone survey of noninstitutionalized U.S. adults aged \u226518 years, which collects information on health-related topics.The prevalence and 95% confidence intervals of demographic characteristics and of engaging in the five health-related behaviors was estimated by sexual orientation status for men and women separately, and by transgender status. The health-related behaviorsIn 2016, among 86,185 men who answered the sexual orientation question, 92.7% reported being heterosexual, 2.2% reported being gay, and 1.5% reported being bisexual; among 114,842 women, 91.7% reported being heterosexual, 1.3% reported being lesbian, and 2.3% reported being bisexual . OverallCompared with heterosexual men, gay men had a lower prevalence of not currently smoking cigarettes (77.0% versus 81.4%) and moderate or no drinking (51.8% versus 60.8%), but had a higher prevalence of performing any leisure-time exercise (82.0% versus 77.9%); gay men also had a higher prevalence of having a normal body weight (40.3%) than did bisexual (29.8%) and heterosexual men (25.0%). The prevalence of not currently smoking cigarettes, moderate or no alcohol consumption, and getting \u22657 hours\u2019 sleep during a 24-hour period was higher among heterosexual women than among lesbian and bisexual women . Engaging in any leisure-time exercise was more prevalent among lesbian (80.6%) and bisexual women (77.6%) than among heterosexual women (73.8%); however, having a normal body weight was less prevalent among lesbian women (30.4%) than among heterosexual women (37.0%); the difference in prevalence between heterosexual women and bisexual women (35.8%) was not statistically significant. In addition, the prevalence of reporting zero or one health-related behavior was higher among lesbian (10.0%) and bisexual (10.7%) women than among heterosexual women (4.9%), and the prevalence of reporting all five health-related behaviors was lower among lesbian (5.4%) and bisexual (6.9%) women than among heterosexual women (10.6%) .Among 200,874 adults from the 25 states and Guam who answered the gender identity question, 98.3% reported being cisgender, 0.2% reported being male-to-female transgender, and 0.1% each reported being female-to-male transgender and transgender nonconforming . Being aThe prevalence of performing any leisure-time exercise was higher among cisgender adults (75.5%) than among male-to-female transgender adults (56.7%). More than three quarters (77.4%) of male-to-female transgender adults reported sleeping \u22657 hours during a 24-hour period compared with cisgender adults (65.0%), female-to-male transgender adults (58.9%), and transgender nonconforming adults (52.9%). In addition, male-to-female transgender adults had a lower prevalence of engaging in any two of five health-related behaviors (12.3%) than did cisgender adults (18.6%), but had a higher prevalence of engaging in any three of five health-related behaviors (47.2%) than did female-to-male transgender adults (28.2%) .The findings from this study support those of other studies showing that disparities in sociodemographic characteristics and health-related behaviors exist among the LGBT populations , the prevalence of not currently smoking cigarettes, moderate or no drinking, maintaining a normal body weight, performing any leisure-time physical activity, and sleeping \u22657 hours per day was lower among lesbian (5.4%) and bisexual women (6.9%). Male-to-female transgender adults had a lower prevalence of engaging in any two of five health-related behaviors (12.3%) than did cisgender adults (18.6%), but had a higher prevalence of engaging in any three of five health-related behaviors (47.2%) than did female-to-male transgender adults (28.2%).Implementation of targeted strategies to increase community-based health intervention programs and mass media campaigns to improve health-related behaviors of lesbian, gay, bisexual, and transgender adults are needed."} +{"text": "Lavandula species, which continues to increase in a variety of industries. Lavandula pubescens might be a good alternative, as it exhibits strong antibacterial activity. In this study, the chemical composition of the essential oils from different organs of L. pubescens was identified using gas chromatography-mass spectrometry. Furthermore, the antimicrobial activities of different solvent extracts and different organ extracts of L. pubescens were evaluated. Only the ethyl acetate extracts of L. pubescens exhibited antibacterial activity against all bacterial strains tested, including Staphylococcus haemolyticus, Escherichia coli (KF 918342), Aeromonas hydrophila (KCTC 12487), E. coli (ATCC 35150), Cronobacter sakazakii (ATCC 29544), and Aeromonas salmonicida (KACC 15136). In particular, the extracts exhibited significant activity against S. haemolyticus. Ethyl acetate extract of the leaf exhibited the best activity against all bacterial strains. This study provides valuable information on the chemical compositions in essential oils and antimicrobial properties of L. pubescens.The discovery of a new species exhibiting more effective antibacterial properties is necessary because of the demand on Lavandula pubescens, also known as downy lavender, is an aromatic flowering plant belonging to the Lamiaceae family. Lavandula, consisting of approximately 39 known species, has been largely cultivated as ornamental plants for gardens and scenery use. This perennial plant is widely distributed in the Mediterranean, North Africa, Southwest Asia, western Iran, and eastern India [Lavandula angustifolia, Lavandula officinalis, Lavandula latifolia, and Lavandula vera. Lavandula pubescens is a newly discovered species of lavender, which occurs in the Mediterranean. In recent years, the plants have been extensively studied as resources for medicine and aromatic products and used largely for their medicinal potentials, because these plants contain a number of bioactive compounds that act against human and plant pathogens [rn India . The widathogens , as wellLavandula is widely studied because of its commercial use in the fragrance industry [Lavandula species is presently used in food manufacturing industries for flavoring. Lavandula essential oil contains monoterpenes and is used in soaps, shampoos, mouthwashes, and household cleaners [Lavandula essential oil has been used in the food industry [Presently, industry ,5. The pindustry . The esscleaners . Previoucleaners as well cleaners ,10. Furtindustry ,12.Essential oils, also called volatile or ethereal oils, are defined as an aromatic hydrophobic liquid, including a broad diversity of volatile compounds, and are derived from plant materials, such as the roots, stem, flowers, leaves, buds, seeds, and fruits . LavendeLavandula has been widely studied [Lavandula essential oil have been reported [L. pubescens using gas chromatography-mass spectrometry (GC-MS) and the antibacterial activities of different plant parts of L. pubescens.The antimicrobial activity of studied ,19,20. L studied ,22. Antireported ,24,25. TEthanol (EtOH), methanol (MeOH), hexane, and ethyl acetate (EA) were purchased from Samchun Pure Chemical, Pyeongtaek, Korea. Diethyl ether (DE) and dimethyl sulfoxide (DMSO) were purchased from Sigma-Aldrich, Yongin, Korea. Luria-Bertani (LB) broth and streptomycin sulfate was purchased from MB cell, Seoul, Korea.L. pubescens were collected from the green house of Chungnam National University , Staphylococcus haemolyticus (KCTC 3341), Aeromonas hydrophila (KCTC 12487), Escherichia coli (ATCC 35150), Cronobacter sakazakii (ATCC 29544), and Aeromonas salmonicida (KACC 15136). These strains were collected from the medicine department of Chungnam National University. The bacterial strains (Escherichia coli (KF 918342), Staphylococcus haemolyticus (KCTC 3341), Escherichia coli (ATCC 35150), Cronobacter sakazakii (ATCC 29544), and Aeromonas salmonicida (KACC 15136)) were cultured at 37 \u00b0C and the strain (Aeromonas hydrophila (KCTC 12487)) was cultured at 30 \u00b0C for 18\u201324 h in a 50 mL sample of LB broth prepared in a 250 mL conical flask medium placed on an orbital shaker. Optical density (OD) measurement was performed at 600 nm using a UV-1800 spectrophotometer . The culture flask was inoculated at 0.1 OD600 with freshly prepared LB medium under the same culture conditions. The mid log phase bacterial cultures were used for the antibacterial studies. Staphylococcus haemolyticus (KCTC 3341) was the only gram-positive bacteria used in this study; all others were gram-negative bacteria.Six bacterial strains were used in this study: Volatile compounds were extracted and analyzed using a previously reported GC-MS method . GC-MS a600 of the different overnight bacterial cultures was swabbed on a 25 mL LB agar plate. Whatman disk was then placed on the plates. A 30 \u00b5L sample of different solvent extracts of L. pubescens was added to the sterilized disk and incubated overnight at 37 \u00b0C. For screening of the different plant organs, the powdered samples were dissolved in ethyl acetate, and the resulting extract was added to the Whatman disk. Streptomycin (250 \u00b5g/mL) was used as the standard antibacterial agent. The experiment was performed in triplicate.A 0.1 ODL. pubescens extracts was established according to the method of Abdullah Al-Dhabi et al. [8 CFU/mL of each of the six bacterial strains was added to the 96-well plate and incubated at 37 \u00b0C for 17 h. After the incubation time, the minimum inhibitor concentration was determined by the lowest visible growth in LB broth. The experiment was performed in triplicate.The minimum inhibitory concentration (MIC) of the i et al. by usingL. pubescens, such as the roots, stems, leaves, and flowers, were identified by GC-MS analysis. Most of the essential oils from different organs were characterized by the dominant presence of terpenes, including monoterpenes, diterpenes, and sesquiterpenes (p-cymenene (18.15%), terpinolene (3.31%), isothymol methyl ether (2.8%), m-cymene (2.1%), \u03b3-terpinene (1.64%), carvacrol (0.78%), 2,5,5-trimethyl-1,3,6-heptatriene (0.76%), and trans-3-caren-2-ol (0.76%); nine sesquiterpenes\u2014alloaromadendrene (2.45%), caryophyllene (2.45%), \u03b2-bisabolene (0.96%), \u03b1-muurolene (0.17%), (\u2212)-\u03b2-elemene (0.16%), \u03b2-ylangene (0.13%), \u03b2-guaiene (0.11%), \u03b1-calacorene (0.11%), and acoradien (0.07%); and one diterpene\u2014jolkinol D (0.16%), comprising 94.62% of the total leaf-derived essential oil.Chemical composition of the essential oils of different organs of terpenes . The oilp-cymenene (7.66%), m-cymene (2.89%), carvacrol (2.54%), trans-3-caren-2-ol (2.51%), 2,5,5-trimethyl-1,3,6-heptatriene (1.83%), and 4-terpinyl acetate (1.34%); and 10 sesquiterpenes\u2014caryophyllene (9.97%), \u03b2-bisabolene (3.52%), \u03b2-ylangene (1.46%), longifolene (1.04%), \u03b1-cubebene (0.65%), \u03b2-eudesmene (0.58%), \u03b1-ylangene (0.38%), caryophyllene oxide (0.33%), aromandendrene (0.11%), and acoradien (0.08%), comprising 99.47% of the total stem-derived essential oil.The essential oil from the stems contained 10 monoterpenes\u2014neo-allo-ocimene (15.68%), isothymol methyl ether (13.35%), \u03b3-terpinene (11.09%), terpinolene (10.17%), m-cymene (49%), \u03b1-terpinene (4.22%), 4-terpinyl acetate (3.73%), (\u2212)-4-terpineol (3.05%), p-xylene (2.46%), \u03b3-terpinene (2.28%), d-limonene (2.0%), p-cymenene (1.99%), terpinolene (1.90%), \u03b1-terpinene (1.57%), carvacrol (0.41%) neo-allo-ocimene (0.36%), trans-3-caren-2-ol (0.33%), and isothymol methyl ether (0.35%); and 21 sesquiterpenes\u2014(\u2212)-calamenene (6.33%), \u03b1-gurjunene (3.30%), \u03b1-copaene (1.54%), \u03b2-eudesmene (1.21%), \u03b1-bergamotene (1.00%), caryophyllene (0.91%), \u03b4-cadinene (0.88%), \u03b1-muurolene (0.86%), cyclosativene (0.81%), (\u2212)-\u03b2-elemene (0.66%), \u03b2-copaene (0.61%), \u03b3-cadinene (0.48%), \u03b1-calacorene (0.48%), \u03b1-cubebene (0.43%), \u03b2-guaiene (0.42%), \u03b1-ylangene (0.41%), acoradien (0.38%), caryophyllene oxide (0.19%), alloaromadendrene (0.16%), (+)-ledene (0.14%), and aromandendrene (0.07%), comprising 99.03% of the total root-derived essential oil.The essential oil from the roots contained 14 monoterpenes\u2014p-cymenene (11.66%), neo-allo-ocimene (8.55%), 1,3,5,5-tetramethyl-1,3-cyclohexadiene (2.95%), 2,5,5-trimethyl-1,3,6-heptatriene (2.75%), \u03b3-terpinene (2.39%), m-cymene (1.31%), trans-3-caren-2-ol (1.12%), \u03b1-terpinene (0.87%), carvacrol (0.27%), p-xylene (0.15%), and d-limonene (0.08%); and 5 sesquiterpenes\u2014longifolene (2.2%), \u03b2-bisabolene (0.72%), \u03b1-bergamotene (0.36%), caryophyllene (0.23%), and acoradien (0.07%), comprising 99.44% of the total flower-derived oil.The essential oil from flowers contained 13 monoterpenes\u20144-terpinyl acetate (16.99%), L. pubescens was performed using five different organic solvents. The ethyl acetate extract showed more antimicrobial activity against the six pathogenic bacteria because the disk diffusion method revealed that the ethyl acetate extract produced higher activity than that by the other organic solvents. In particular, L. pubescens possessed significant activity against S. haemolyticus, followed by E. coli (KF 918342), A. hydrophila (KCTC 12487), E. coli (ATCC 35150), C. sakazakii (ATCC 29544), and A. salmonicida (KACC 15136) . TherefoLavandula extract was studied by the micro broth dilution method and the results are shown in Lavandula ethyl acetate extract at different concentrations inhibited all the growth of all bacterial strain broths. The MIC for E. coli was 6.25 \u00b5L and for S. haemolyticus, A. hydrophila, and A. salmonicida was 12.5 \u00b5L. Cronobacter sakazakii inhibition was observed at 25 \u00b5L. Streptomycin showed better MIC values in comparison with those of the Lavandula ethyl acetate extracts. MIC values are shown in The MIC of crude L. pubescens through GC-MS analysis. The most abundant constituents were terpenes, including monoterpenes, diterpenes, and sesquiterpenes. Similarly, previous studies have shown that terpene metabolites were the major components of essential oils from a variety of Lavandula species: Barocelli et al. reported a total of 23 constituents in Lavandula hybrida Reverchon \u201cGrosso\u201d essential oil, with major constituents such as linalool (33.4%), linalyl acetate (36.2%), camphor (7.6%), and 1,8-cineole (5.8%) [Lavandula stoechas L. (Spanish lavender) [L. angustifolia essential oil were 1,8-cineole (44.9%), camphor (14.3%), \u03b2-phellandrene (5.0%), and \u03b1-pinene (4.7%) [Lavandula bipinnata essential oil had transcarveol (18.93%), pulegone (8.45%), camphor (7.09%), and menthol (5.89%) [L. latifolia Med.) and lavandin (Lavandula \u00d7 intermedia) essential oils contained camphor (32.70%), 1,8-cineole (26.9%), and caryophyllene (4.88%) and 1,8-cineol (40.5%), linalool (33.1%), and camphor (8.17%), respectively [L. pubescens, with main components including carvacrol (72.7%), carvacrol methyl ether (7.0%), and caryophyllene oxide (5.9%) [In this study, 71 volatile compounds were identified in the essential oils derived from the roots, stems, leaves, and flowers of e (5.8%) . Fenchonavender) . The maje (4.7%) . Shirugu (5.89%) . Spike llinalool .4%, linae (5.9%) .L. pubescens tested in the present study showed strong antibacterial activity against the six bacterial strains tested. However, antibacterial activities of the extracts dissolved in the other solvents were not observed. This could be caused by the difference in the chemical composition of these extracts. Often, variations in chemical composition may result from differences in the extraction solvents, season, and presence of secondary metabolites [Ethyl acetate extract of abolites . Previouabolites ,37,38.L. pubescens possessed strong antibacterial activity against the six pathogenic bacteria, and L. pubescens leaves had the most powerful antimicrobial capacity. Our results are supported by those of previous studies showing that the essential oil from Lavandula species had antibacterial properties [lavender essential oil showed anti-bacterial activities against E. coli and Staphylococcus aureus [L. angustifolia was effective against all tested turtle-borne pathogenic bacteria: A. hydrophila, Aeromonas caviae, and Aeromonas dhakensis [C. sakazakii [L. angustifolia showed anti-bacterial activity against S. aureus, E. coli, Citrobacter freundii, Enterobacter aerogenes, Propionibacterium acnes, Proteus vulgaris, Pseudomonas aeruginosa, Shigella sonnei, and Streptococcus pyogenes [Lavandula plants are expected to possess important antibacterial properties against various bacterial species.Ethyl acetate extracts of operties . Hui et s aureus . Hossainhakensis . Furtherakazakii . The esspyogenes . TherefoL. pubescens and the different antibacterial activity of ethyl acetate extracts of these plant parts. These properties could be successfully exploited to treat several diseases caused by bacterial infections. This may indicate that lavender species used in traditional remedies may possess beneficial biological activity. Thus, this study suggests the potential use of L. pubescens roots, stems, leaves, and flowers in traditional herbal medicine applications.According to the World Health Organization (WHO), approximately 80% of the world\u2019s population depends on herbal remedies for their primary healthcare ,45. ThisL. pubescens, and its extract possessed strong antibacterial activity against Escherichia coli (KF 918342), Staphylococcus haemolyticus (KCTC 3341), Aeromonas hydrophila (KCTC 12487), Escherichia coli (ATCC 35150), Cronobacter sakazakii (ATCC 29544), and Aeromonas salmonicida (KACC 15136). In particular, the leaves exhibited the strongest antimicrobial activity against these bacteria among the different plant parts tested. Therefore, this study suggests that L. pubescens could be considered a good source for human health.In this study, ethyl acetate was the most effective solvent for extracting a broad variety of compounds from"} +{"text": "Their structures were elucidated by extensive NMR spectroscopy studies. Compound 2 represents the first example of an R-configuration in the prenylated moiety. All these isolated compounds were examined for antimicrobial and cytotoxic activities. Compounds 1\u20139 exhibited antimicrobial activities against some human- and plant-pathogenic microbes with MIC values ranging from 2 to 64 \u03bcg/mL. Moreover, compound 9 displayed considerable inhibitory activity against the THP-1 cell line in vitro, with an IC50 value of 7.0 \u03bcg/mL.Considerable attention has been paid to marine derived endophytic fungi, owing to their capacity to produce novel secondary metabolites with potent bioactivities. In this study, two new compounds with a prenylated diphenyl ether structure\u2014diorcinol L ( Aspergillus sp. + and 351.12 [M + Na]+; HRESIMS at m/z 329.1377 [M + H]+ and 351.1199 [M + Na]+ .(R)-Diorcinol B (2): yellowish powder; c 0.1, MeOH); UV (MeOH) \u03bbmax (log \u03b5) 205 (4.44), 281 (3.30) nm; 1H and 13C-NMR data, see m/z 333.16 [M + H]+; HRESIMS m/z 333.1689 [M + H]+ .Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, Ralstonia solanacearum and plant pathogenic fungi Alternaria alternata, Cochliobolus heterostrophus, Gaeumannomyces graminis, Glomerella cingulata, Mucor hiemalis, and Thielaviopsis basicola were carried out using the well diffusion method [Antimicrobial assays against the human- and plant-pathogenic bacteria n method . ChloramThe cytotoxic activity of the isolated compounds against six tumor cell lines including A549 , Du145 (human prostate cancer cell line), HeLa (human cervix carcinoma cell line), MCF-7 (human breast adenocarcinoma cell line), MDA-MB-231 (human breast cancer cell line), and THP-1 (human monocytic cell line) were determined according to the previously reported the Cell Counting Kit-8 (CCK-8) colorimetric method .Aspergillus tennesseensis. Among them, compound 2 represents the first example of an R-configuration in the prenylated moiety. The antimicrobial and cytotoxic activities of the isolated compounds were evaluated, and some of the compounds showed promising activities. These results indicated that the algal-derived endophytic fungi are a prolific resource of novel bioactive natural products.In conclusion, nine prenylated diphenyl ethers, including two new ones, were isolated and identified from the marine algal-derived endophytic fungus"} +{"text": "We performed a meta-analysis to obtain the diagnostic and grading accuracy of 18F-FDOPA PET and PET/CT in patients with gliomas.Positron emission tomography (PET) and PET/computed tomography (PET/CT) imaging with 3,4-dihydroxy-6-[18F-FDOPA PET or PET/CT in glioma patients. Pooled sensitivity, specificity, and area under the summary receiver operating characteristic (SROC) curve were calculated from eligible studies on a per-lesion basis.PubMed, Embase, Cochrane Library and Web of Science were searched through 13 May 2019. We included studies reporting the diagnostic performance of 18F-FDOPA PET and PET/CT were 0.90 (95%CI: 0.86\u20130.93) and 0.75 (95%CI: 0.65\u20130.83). Across 7 studies (219 patients) for glioma grading, 18F-FDOPA PET and PET/CT showed a pooled sensitivity of 0.88 (95%CI: 0.81\u20130.93) and a pooled specificity of 0.73 (95%CI: 0.64\u20130.81).Eventually, 19 studies were included. Across 13 studies (370 patients) for glioma diagnosis, the pooled sensitivity and specificity of 18F-FDOPA PET and PET/CT demonstrated good performance for diagnosing gliomas and differentiating high-grade gliomas (HGGs) from low-grade gliomas (LGGs). Further studies implementing standardized PET protocols and investigating the grading parameters are needed. Glioma is the most common primary brain tumor, accounting for 81% of all malignant brain tumors with an annual incidence of 5.26 per 100,000 individuals , 4. Thus18F-FDG) has been the classic PET tracer used in tumor imaging, but it is not ideal in detecting gliomas due to the high physiologic uptake in normal brain tissue. Given the diagnostic limitations of 18F-FDG, amino acid tracers have been extensively investigated, such as 3,4-dihydroxy-6-[18F] fluoro-L-phenylalanine (18F-FDOPA). Unlike gadolinium, 18F-FDOPA is transported across the intact blood brain barrier (BBB) , indicating a moderately high overall diagnostic value of als Fig. c.p-value\u2009=\u20090.0006, I-square\u2009=\u200965.1%) through Chi-square, Cochran-Q, and I-squared tests , specificity of 0.76 (95% CI: 0.66\u20130.85), LR+ of 2.87 (95% CI: 2.01\u20134.11), LR- of 0.13 (95% CI: 0.07\u20130.23), DOR of 29.65 (95% CI: 13.09\u201367.15), and AUC of 0.90 (SE\u2009=\u20090.06). In the newly-diagnosed subgroup, only two studies were eligible for meta-analysis (in another three studies only sensitivity can be computed after stratification). In comparison with recurrent group, pooled data of newly-diagnosed group revealed a lower sensitivity of 0.71 (95% CI: 0.54\u20130.85) and a higher specificity of 0.86 (95% CI: 0.42\u20131.00). The LR+, LR- and DOR were 3.71 (0.87\u201315.81), 0.36 (0.19\u20130.68) and 10.88 (1.57\u201375.31) respectively.No threshold effect was detected in two subgroups. Pooled data and SROC curve manifested a high diagnostic value of 18F-FDOPA PET and PET/CT for Grading Gliomas.Aim 2: Investigating the Performance of 18F-FDOPA PET and PET/CT presented a pooled sensitivity of 0.88 (95% CI: 0.81\u20130.93), specificity of 0.73 (95% CI: 0.64\u20130.81), LR+ of 2.90 (95% CI: 2.19\u20133.85), LR- of 0.16 (95% CI: 0.08\u20130.36), DOR of 25.87 (95% CI: 10.53\u201363.54), and AUC of 0.89 (SE\u2009=\u20090.03) for differentiating HGGs from LGGs.As illustrated in the Fig. p-value\u2009=\u20090.0045), no significant heterogeneity was found among studies for specificity , LR+ , LR- and DOR .Other than sensitivity , and for HGGs and LGGs respectively. Besides the evidence presented above, our systematical analysis has also shown that 18F-FDOPA PET and PET/CT provide more reliable results in discriminating recurrent lesions from treatment related changes, with a pooled sensitivity and specificity of 0.92 and 0.76.Of increased interest is the value of patients . Howevera et al. reportedi et al. proved s18F-FDOPA PET and PET/CT is the utility in the detection of HGGs. Due to the differences between LGGs and HGGs in therapeutic regimen and prognosis evaluation, initial grading for gliomas through imaging approaches is of great significance. This meta-analysis proved the high overall value of 18F-FDOPA PET and PET/CT in evaluating tumor grade, with the AUC of 0.89. However, studies with respect to grading of recurrent gliomas demonstrated controversial results. In Fueger et al. -methyl-L-methionine (11C-MET). In the only study with direct comparison between 18F-FDOPA PET and 11C-MET, 18F-FDOPA performed equally well as 11C-MET in the imaging of brain tumors [11C-MET is being replaced by tracers labelled with fluorine-18 due to its short half-life (20\u2009min). The use of another amino acid tracer O-(2-[18F]-fluorethyl)-1-tyrosine (18F-FET) has rapidly grown in recent years. A previous meta-analysis of 5 studies including 180 patients reported a sensitivity and specificity of 0.82 and 0.76 of 18F-FET PET for the differential diagnosis of primary brain tumor [18F-DOPA and 18F-FET shared similar uptake pattern in primary and recurrent HGGs and had similar diagnostic accuracy in recurrent HGGs [18F-FET, the elevated physiological 18F-FDOPA uptake in striatum has been a concern which may limits its use to detect brain tumor with striatum involvement [18F-FET to examine patients with possible involvement of basal ganglia irrespective of tumor grade. Similarly, Morana et al. [18F-FDOPA PET/CT in dorsal striatum was concordant with its overall accuracy, while not in the ventral striatum, which required fused MRI to improve its performance.Evidence for comparisons of c tissue . 18F-FDO 18F-FDG , 10, 23.27\u20130.50) . The lon27\u20130.50) C-methyl-in tumor . In lateent HGGs , 41. Howolvement , 43. Thea et al. reported18F-FDOPA uptake with glioma molecular characteristics cannot be analyzed.Several study limitations also need to be addressed. Although 19 studies were included in this meta-analysis, the sample size of each study tended to be small, and the number of true negative cases was particularly limited, which might possibly yield less replicable results, especially the pooled specificity. Limited sample size also led to data loss in stratification of subgroups when true negative case was less than one . Besides, multiple specimens were obtained from one patient in three studies , 27, 30,18F-FDOPA PET and PET/CT have high diagnostic accuracy for the detection of gliomas, especially the discrimination between tumor recurrence and radiation-induced changes. 18F-FDOPA PET and PET/CT also demonstrate good grading performance for the distinction between HGGs and LGGs. However, the grading parameters needs further investigation with standardized imaging protocols in prospective studies.In conclusion, this meta-analysis provides evidence that"} +{"text": "Brassica napus) is preferred over black-seeded rapeseed for the desirable properties of the former. This study evaluated the metabolites and nutritive values of black-seeded rapeseed meal and yellow-seeded meal from the progeny of a B. napus\u2013Sinapis alba hybrid. Yellow-seed meal presented higher protein (35.46% vs. 30.29%), higher sucrose (7.85% vs. 7.29%), less dietary fiber (26.19% vs. 34.63%) and crude fiber (4.56% vs. 8.86%), and less glucosinolates (22.18 vs. 28.19 \u03bcmol/g) than black-seeded one. Amounts of ash (3.65% vs. 4.55%), phytic acid (4.98% vs. 5.60%), and total polyphenols (2.67% vs. 2.82%) were decreased slightly in yellow-seeded meal compared with black-seeded meal. Yellow-seeded meal contained more essential amino acids than black-seeded meal. Levels of the mineral elements Fe, Mn, and Zn in yellow-seeded meal were higher than black-seeded meal. By contrast, levels of P, Ca, and Mg were lower in yellow-seeded meal. Moreover, yellow-seeded meal showed lower flavonol content than black-seeded meal. Comparison of metabolites between yellow and black rapeseed confirmed the improved nutritional value of meal from yellow-seeded B. napus, and this would be helpful to the breeding and improvement of rapeseed for animal feeding.Breeding of yellow-seeded rapeseed ( Brassica napus) is the second most abundant oil crop worldwide next to soybean. Soybean meal is broadly used as an animal fodder for its abundant nutrients, but the supply of soybean meal is insufficient to meet current demands [B. napus [B. napus is an optimal perspective in breeding of rapeseed, and cultivars/lines with yellow seed coat have been selected from hybridization among Brassica species with yellow seed character [Sinapis alba) have been reported [B. napus has revealed different nutrient contents in the seed meals [et al., found higher protein , higher sucrose (10.2% vs. 8.8% DM), and less total dietary fiber (24.1% vs. 30.1% DM) in meal derived from yellow-seeded B. napus than black seed [et al., identified 31 polyphenols in canola meal, of which sinapine is the most abundant chemical, comprising 80% of the total phenolics [et al., reported that the unpleasant taste of meal with higher sinapine content affected the intake of pigs, which directly reduced their average daily feed intake and average daily weight gain [et al., reported significant differences in the PA contents of yellow- and black-seeded B. napus [Rapeseed . Introdureported . Comparied meals ,9,10. Beed meals . Slominsack seed . Antinuthenolics . Sinapinght gain ,15. Flavght gain . Jiang eB. napus .B. napus\u2013S. alba hybrids, and the oil content of this yellow-seeded rapeseed line (W82) was 6% higher than that of black-seeded rapeseed [B. napus cv. Yangyou 6) and yellow-seeded rapeseed . This comprehensive comparison will facilitate understanding of the differences in nutritional values between the two rapeseed lines and might contribute to the utilization and molecular dissection of yellow-seeded rapeseed.Rapeseed with yellow-seeded germplasm does not naturally exist. We obtained a novel yellow-seeded rapeseed from the progeny of rapeseed . In the B. napus were produced using a high-temperature press, degreasing with petroleum ether. The chemical compositions of seed meals from yellow- and black-seeded rapeseeds are listed in B. napus presented higher protein (35.46% vs. 30.29% DM) and higher sucrose (7.85% vs. 7.29% DM). Significant differences in protein and sucrose levels were identified between yellow- and black-seeded B. napus seed meals (p < 0.05). Proteins are the main nutrients in rapeseed meal, supplying energy for metabolism after animal absorption. Improved protein content in yellow-seeded rapeseed meal indicates higher nutritional value for animal feeding. Theodoridou et al., reported easier animal assimilation of yellow-seeded rapeseed meal from B. napus than that of black-seeded rapeseed meal [B. juncea and B. napus exhibited higher absorption efficiency of proteins in the rumen and intestines than when they were fed with meal from black-seeded B. napus. Higher intestinal digestibility of total metabolizable protein and lower degraded protein balance were reported when yellow-seeded rapeseed meal was consumed compared with black-seeded rapeseed meal. Thus, the increase in protein content of the novel yellow-seeded B. napus derived from somatic hybrids of B. napus\u2013S. alba indicates improved nutritional value for animal feeding, especially in the actual absorbed protein. High sucrose levels would improve the digestibility of rapeseed meal because sucrose is a carbohydrate that can be easily digested. Theander et al., reported the sucrose content in seed meal of Brassica to be approximately 6.2%\u20138.0% [Rapeseed meals from yellow- and black-seeded .2%\u20138.0% ,17.vs. 34.63% DM), crude fiber (4.56% vs. 8.86% DM), and glucosinolates (22.18 \u03bcmol/g DM vs. 28.19 \u03bcmol/g DM) were significantly higher in black-seeded rapeseed meal than in yellow-seeded rapeseed meal and total polyphenol (2.67% vs. 2.82% DM) contents were lower in yellow-seeded rapeseed meal than in black-seeded rapeseed meal , methionine and cysteine (1.36 mg/g vs. 0.21 mg/g), isoleucine (0.33 mg/g vs. 0.20 mg/g), glycine (0.62 mg/g vs. 0.39 mg/g), alanine (2.95 mg/g vs. 1.06 mg/g), phenylalanine (2.08 mg/g vs. 1.26 mg/g), histidine (0.98 mg/g vs. 0.50 mg/g), lysine (1.65 mg/g vs. 0.80 mg/g), and arginine (1.59 mg/g vs. 1.17 mg/g) (p < 0.05) (vs. 7.06 mg/g), lysine (9.52 mg/g vs. 9.02 mg/g), threonine (9.37 mg/g vs. 8.29 mg/g), isoleucine (13.39 mg/g vs. 11.97 mg/g), asparagine (12.91 mg/g vs. 11.71 mg/g), glutamic acid (23.75 mg/g vs. 21.18 mg/g), methionine and cysteine (32.15 mg/g vs. 29.01 mg/g), tyrosine (15.44 mg/g vs. 13.80 mg/g), glycine (2.28 mg/g vs. 1.83 mg/g), alanine (6.99 mg/g vs. 6.04 mg/g), histidine (6.73 mg/g vs. 5.88 mg/g), and arginine (12.13 mg/g vs. 10.44 mg/g) were significantly higher in yellow-seeded rapeseed meal than in black-seeded rapeseed meal directly affects the nutritional value of seed meal [et al., showed that the digestibility of total amino acids was higher in chickens fed with yellow-seeded rapeseed meal than in those fed with black-seeded rapeseed meal [Profiles of essential amino acids and total amino acids are listed in < 0.05) . In termeed meal . Methioneed meal .vs. 87.48 mg/kg), Mn (48.12 mg/kg vs. 37.63 mg/kg), Zn (74.89 mg/kg vs. 54.82 mg/kg), Cu (4.96 mg/kg vs. 4.67 mg/kg), and K , and the differences of Fe, Mn, and Zn contents between the two types of rapeseed meal were significant (p < 0.05). By contrast, the amounts of P , Ca (3990.40 mg/kg vs. 5645.36 mg/kg), and Mg (3767.20 vs. 3860.59 mg/kg) were lower in yellow-seeded rapeseed meal than in black-seeded rapeseed meal derived from the progeny of B. napus\u2013S. alba hybrids and black-seeded rapeseed (B. napus cv. \u201cYangyou 6\u201d) were used in this study [et al. [Seeds of yellow-seeded is study ,36. \u201cYan [et al. , seed meet al. [2SO4 (5 mL) in 30 g/L trichloroacetic acid (5 mL). After shaking for 2 h at room temperature, the suspension was collected after centrifugation at 13,000 g for 10 min. The pellet was re-extracted and all the suspension was combined. The phytic acid was precipitated with 0.3 g/L FeCl3 (2 mL), and its amount was calculated according to the difference of phosphorus value between the initial supernatant and the supernatant after precipitated with FeCl3. A conversion factor of 3.55 from phosphorus and phytic acid was used. Glucosinolates were determined via near-infrared spectroscopy, which developed a new calibration to measure major fraction, and no external standards were needed [et al. [et al. [For determination of protein contents, a nitrogen analyzer was used to obtain the content of N, and the content of crude protein was calculated by N \u00d7 6.25. Seed meal (0.5 g) was treated with 6 N HCl (20 mL) at 110 \u00b0C for 24 h, and total amino acid content was then determined using ninhydrin colorimetry and an Biochrom 30 amino acid analyzer . For free amino acid analysis, the seed meal (0.5 g) was extracted with picric acid (20 mL) then determined on the amino acid analyzer . Total det al. . Seed me [et al. . Inducti [et al. . Calibraet al. with some modifications, and the extracts were filtered through 0.45 \u03bcm Teflon membranes and then used for high-performance liquid chromatography (HPLC)-electrospray ionization (ESI)/tandem mass spectrometry (MS2) analysis [et al. [2CO3 (50 \u03bcL) was added. The total phenol content was reported as (\u2212)-epicatechin equivalents based on a calibration curve. Using (\u2212)-epicatechin as standard, the absorbance was measured at 725 nm after the incubation for 45 min to acknowledge the content of phenol content. The total phenol content was reported as (\u2212)-epicatechin equivalents based on a calibration curve. HPLC analysis of 10 \u03bcL extracts was performed on an Agilent 6460 instrument equipped with automatic injector, quaternary pump, thermostatted column compartment, and diode array detector (DAD). The Agilent Masshunter Qualitative Analysis software was used for data collection and analysis. LC/MS data of tentatively identified polyphenolics in meal of black- and yellow-seeded B. napus and their quantitative analysis using DAD at 280 and 330 nm. Samples were separated using XB-C18 column , with a flow rate of 0.3 mL/min, oven temperature of 30 \u00b0C, and a detection range of 190\u2013800 nm. The mobile phase consisted of a combination of solvent A and solvent B . The linear gradient was as follows: 10% B (v/v) for 5 min, 10%\u201390% B for 40 min, 90% B for 10 min, 90%\u201310% B for 1 min, and hold at 10% B for 10 min.Phenolics were extracted using the method previously described by Shao analysis . Seed me [et al. : extract2) pressure = 15 psi, sheath gas temperature 250 \u00b0C, sheath gas flow = 7 L/min, capillary voltage = 4000 V, and spraying voltage = 500 V. Full scan spectra of 500 ms and an m/z range of 90\u20132000 were selected. MS2 fragmentation patterns of phenolics were determined under 15\u201340 V, using the Agilent MassHunter Workstation Data Acquisition and Agilent MassHunter Qualitative Analysis software. Procyanidin B2, (\u2212)-epicatechin, sinapine, and quercetin-3-O-\u03b2-d-glucoside, which were purchased from Sigma , and isorhamnetin-3-O-glucoside, which was purchased from ChromaDex , were used as standards for phenolic quantification. Since not all the standards of the chemicals identified in the O-\u03b2-d-glucoside were adequate for quantification of all the chemicals, of which quercetin-3-O-\u03b2-d-glucoside was used as standard for quercetin, isorhamnetin and kaempferol. Statistical analyses of the contents were expressed as mean \u00b1 standard error of samples from three independent extractions. A significance level of p < 0.05 was considered.Tandem mass spectrometry was operated in positive and negative ESI modes. The mass spectrometer used in phenolic analysis was MS QQQ coupled in LC/MC system . The parameters were as follows: drying gas temperature = 300 \u00b0C, drying gas flow = 10 L/min, nebulizer gas (NB. napus improves the quality of rapeseed meal. In this study, a novel yellow-seeded line of B. napus derived from a somatic B. napus\u2013S. alba hybrid was shown to be of greater nutritional value compared with black-seeded rapeseed, that is, yellow-seeded rapeseed meal exhibited more nutrient substances and less antinutrients than black-seeded rapeseed meal. The chemical composition of rapeseed meal, in which proteins are the resources for animal feeding, but the antinutrients influence the actual digestibility and assimilation of the nutrients in rapeseed meal is rather complicated. Thus, further animal feeding experiments using seed meals from both yellow- and black-seeded rapeseeds are necessary to evaluate the actual value of yellow-seeded rapeseed meal.Rapeseed meal is abundant in protein compared with other seed meals, making it optimal for animal feeding. However, antinutrients in rapeseed meal limit its application. Breeding of yellow-seeded"} +{"text": "Correction to: BMC Cancer (2018) 18:325https://doi.org/10.1186/s12885-018-4261-5Following publication of the original article , the autAdditional file 1:Table S1. Sequences of the qPCR primers used in this study. Table S2. Cell numbers per well used in this study for cell proliferation, cell cycle and immunofluorescent assays. Table S3. KPNA7 silencing efficiencies of the cell lines used in Fig. 1 24\u2009h after siRNA treatment. (DOCX 17 kb)"} +{"text": "Correction to: BMC Genomics (2017) 18:693https://doi.org/10.1186/s12864-017-3951-8Following the publication of this article , the autFurthermore, in the \u2018Availability of data and materials\u2019 declaration the sentence \u201cSupplementary material can be found online at http://www.rna.uni-jena.de/en/supplements/nothobranchius-furzeri-mirnome/\u201c\u00a0should now read \u201cSupplementary material can be found online at https://osf.io/25mxb/ (DOI 10.17605/OSF.IO/25MXB).\u201d"} +{"text": "AbstractScolopsislacrimasp. nov. is described from a single specimen (213.6 mm standard length) collected from Grande-Terre Island, New Caledonia. The new species closely resembles S.meridiana, both species having the upper part of the pectoral-fin base with reddish blotch when fresh, two bands across the top of the snout, a dorsal scaled area on the head reaching anteriorly to between the anterior margin of the eye and anterior nostril, a similar number of lateral-line scales, and absence of a small antrorse spine below the eye. However, S.lacrimasp. nov. is distinguished from S.meridiana by having diagonal lines on the body absent , a dark longitudinal band below the lateral line , the caudal fin central area not patterned , a narrower body and shallower caudal peduncle.The new monocle bream Scolopsis Cuvier, 1814 is widespread throughout shallow Indo-West Pacific tropical and subtropical waters, some species being marketed in Southeast Asia recognised as a valid species by The monocle bream genus ast Asia , 2001. TScolopsis, a single specimen from New Caledonia, having a distinctively elongate body and unique colouration, was examined. It is described herein as a new species of Scolopsis.During a taxonomic study of DASMN). Examined specimens of S.meridiana and Scolopsistaenioptera are listed in Counts and proportional measurements followed Taxon classificationAnimaliaSpariformesNemipteridaehttp://zoobank.org/5AF65765-E484-41A9-ABB2-E88A93034AE5Scolopsistaeniopterus (non Cuvier): Scolopsistaenioptera (non Cuvier): MNHN 2002\u20132930, 213.6 mm SL, Noum\u00e9a, Grande-Terre Island, New Caledonia, 1 Aug 2002, purchased at market by P. B\u00e9arez.Scolopsis with the following combination of characters: pectoral-fin rays 17; lateral-line scales 47; no antrorse spine below eye; dorsal scaled area on head reaching anteriorly to between anterior margin of eye and anterior nostril; bony opercular ridge and lower limb of preopercle without scales; 3rd anal-fin spine longer than 2nd anal-fin spine; narrow body, its depth at dorsal, pelvic, and anal fin origins 29.2, 29.5 and 26.6% of SL, respectively; caudal-peduncle depth 10.4% of SL; head length 29.9% of SL; upper part of pectoral-fin base with reddish blotch when fresh; two dark bands across dorsum of snout; body below lateral line with a dark longitudinal band, without diagonal lines; no blotches or lines on central area of caudal fin.A species of st dorsal-fin spine length 6.2; 2nd dorsal-fin spine length 8.5; 3rd dorsal-fin spine length 10.4; 4th dorsal-fin spine length 10.8; 5th dorsal-fin spine length 11.0; 6th dorsal-fin spine length 11.0; 7th dorsal-fin spine length 10.9; 8th dorsal-fin spine length 11.0; 9th dorsal-fin spine length 10.7; 10th dorsal-fin spine length 10.4; longest dorsal-fin soft ray length 16.0; 1st anal-fin spine length 3.9; 2nd anal-fin spine length 7.4; 3rd anal-fin spine length 8.0; anal-fin base length 15.0; pectoral-fin length 21.3; pelvic-fin spine length (measured on right side because the left side damaged) 13.8; longest pelvic-fin soft ray length 24.0.Dorsal-fin rays X, 9; anal-fin rays III, 7; pectoral-fin rays (left / right) 17 / 17; pored lateral-line scales 47; pelvic-fin rays I, 5; scale rows above lateral line 5; scale rows below lateral line 10; gill rakers (upper / lower) 5 / 8; preopercle scale rows (behind eye) 3; preopercle scale rows (below eye) 4. The following morphometrics are expressed as percentages of SL: body depth at dorsal-fin origin 29.2; body depth at pelvic-fin origin 29.5; body depth at anal-fin origin 26.6; body depth at posterior margin of orbit 23.7; body depth at anterior margin of orbit 17.5; pre-dorsal-fin length 32.7; pre-pelvic-fin length 37.9; pectoral-pelvic length 15.4; pre-anus length 61.4; head length 29.9; snout length 11.4; posterior nostril 0.8; posterior nostril 0.8; upper-jaw length 10.7; orbit diameter 7.8; interorbital width 10.0; suborbital depth 5.7; caudal-peduncle length 22.8; caudal-peduncle depth 10.4; dorsal-fin base length 54.1; 1st to 10th dorsal-fin spines, thereafter more steeply to caudal peduncle. Ventral profile of body lowering from lower-jaw tip to anus, thereafter rising to caudal peduncle. Dorsal-fin origin just above posteriormost point of opercle, base extending posterior to posteriormost point of anal-fin base. First to 5th dorsal-fin spines gradually lengthening, 5th to 8th spine lengths similar, 8th to 10th spines gradually shortening. Seventh dorsal-fin soft ray longest. All dorsal-fin soft rays non-filamentous. Uppermost point of pectoral-fin base slightly posterior to posteriormost point of opercle. Lowermost point of pectoral-fin base anterior to pelvic-fin origin. Posterior tip of pectoral fin pointed, reaching to vertical through 7th dorsal-fin spine origin. Pelvic-fin origin posterior to dorsal-fin origin. Posterior tip of depressed pelvic fin reaching anus, not reaching anal-fin origin. Anal-fin origin below 1st dorsal-fin ray origin, ending below 6th dorsal-fin ray origin. First anal-fin spine shortest, 3rd spine longest. Caudal-fin forked, upper lobe longer than lower lobe. Posterior tip of both lobes of caudal fin pointed, non-filamentous. Anus oblong, anterior to anal-fin origin. Eye and pupil round. Lower margin of eye above a line from snout tip to uppermost part of pectoral-fin base. Nostrils round, paired, positioned close together anterior to orbit, anterior nostril with small dermal flap. Snout pointed. Posterior tip of maxilla not reaching to vertical through anterior margin of eye. Distinct suborbital spine posteriorly directed. Small antrorse spine below eye absent. Posterior margins of suborbital and preopercle serrated. Scales ctenoid; both lips, snout, area around eye, and bony opercular ridge and lower limb of preopercle scaleless. Lateral line complete, originating above opercle, extending to central part of caudal-fin base. Both jaws with small conical teeth, forming dense bands. Canine teeth absent. Gill rakers long, slender.Body oblong, rather compressed, deepest at pelvic-fin origin. Dorsal profile rising from snout tip to dorsal-fin origin, lowering slightly between origins of 1Based on colour photograph of holotype from New Caledonia. The latter two specimens have been reduced to bones and otoliths only. However, fresh colour photographs of both specimens prior to dissection (Fig. S.lacrima.ion Fig. support Scolopsismeridiana and S.taenioptera are restricted to northern Australia and Southeast Asia, respectively (Fig. Scolopsis with a reddish blotch on the upper part of the pectoral-fin base are allopatrically distributed in the Indo-West Pacific.ely Fig. , probabl"} +{"text": "Lactobacillus reuteri used prior to or concurrently with Staphylococcus aureus infection can increase epidermal keratinocyte survival, p < 0.01. Phenolics may not have been extensively studied for atopic dermatitis or skin burns. However, phenolics do have a role in photoprotection. The phenolic rutin increases ultraviolet B radiation filter reactive oxygen species scavenging at 75%, p < 0.002, and peak wavelength absorption, p < 0.001. While oral and topical probiotics have untapped potential for atopic dermatitis amelioration and skin infection prevention, phenolics will be increasingly used for photoprotection. With optimized bioavailability, dosage, and formulation, nutraceuticals will become crucial for healthy skin maintenance.Nutraceuticals are important for healthy skin maintenance. Probiotics, phenolics, and vitamins are just a few of the nutraceuticals meant to potentially prevent and assist medical management of dermatologic conditions. Among these, probiotics, vitamin E, and green tea catechins may offer the broadest array of skin protective mechanisms with probiotics having the greatest clinical range. Probiotics\u2019 amelioration of atopic dermatitis and opportunistic infections of skin burns has been targeted in recent research efforts. This includes the improvement of Scoring Atopic Dermatitis index scores, Nonmelanoma skin cancers (NMSC), which are comprised primarily of basal cell carcinomas (BCC) and squamous cell carcinomas (SCC), are one of the most common human cancers with an 18-fold to 20-fold higher incidence than melanoma . MeanwhiUltraviolet A radiation (UVA), which has a 320 nm to 400 nm spectrum range, is the deepest penetrating UVR at 1000 \u03bcm into the epidermis and dermis and comprises 90% to 95% of UVR . UVA actKeratinocytes are the major cells of the epidermis, which is the outermost skin layer . The mosStaphylococcus aureus in 42% of AD patients [Bifidiobacterium (Acintobacteria)-based intestinal microbiome [Increased outer horny skin layer thickness is associated with atopic dermatitis . About 1patients . Consistpatients ,13. In ccrobiome ,13.Although Hippocrates publicized foods\u2019 medicinal value, nutraceutical is a twentieth century term . Based oPropionibacterium and Corynebacterium, Firmicutes Staphylococcus, Proteobacteria and Bacteroidetes is achieved in childhood [S. aureus colonization with less than 106 cfu/cm2 of skin occurs in 20% of people and intermittent carriage occurs in 60% of people [S. aureus at greater than or equal to 106 cfu/cm2 of skin is considered an infection [S. aureus causes dose dependently severe opportunistic infections from 105 cfu/mL or greater [S. aureus infections with any skin barrier disruption, which occurs with burns, AD, and acne vulgaris [Long-term skin commensal microbiome stability dominated by the Actinobacteria hildhood . Skin cohildhood . Skin cohildhood . Stable f people ,18. NormLactobacillus plantarum have shown nonspecific immune system boosting and regulation [Probiotics are live, active, microbial cultures that are generally regarded as safe (GRAS) when consumed in quantities that achieve health benefits to the host ,9. Heat-gulation ,20. LactLactobacillus paracasei and Bifidobacterium longum reuter reportedly decreased leg dryness and facial roughness in 33 adult females over an eight-week trial [B. longum reuter lysate (disrupted bacteria) topically applied to reactive skin twice daily for two months achieved increased skin barrier resistance measured by reduced trans-epidermal water loss (TEWL) and reduced skin sensitivity and dryness in response to thermal and chemical physical changes [Historically, with oral formulations, probiotics had to survive gastric transport, adhere to, and colonize the gastrointestinal tract . These cek trial . Subsequ changes .2 = 61%, Absolute Risk Reduction 44 cases per 1000 children; 95% CI 20 to 64 [Lactobacillus rhamnosus Goldin and Gorbach (LGG), when not heat inactivated, significantly improves the Scoring Atopic Dermatitis index (SCORAD) scores in comparison to heat inactivated LGG or the placebo, p = 0.02 [p = 0.036 [9 cfu, oral Lactobacillus fermentum VRI-033 PCC, twice daily for 8-weeks achieved SCORAD improvements with sustained T-helper 1 IFN-\u03b3 responses, p = 0.046 for 2-months post-treatment, which were directly proportional to the SCORAD score improvement [L. fermentum VRI-003 use was not associated with reduced topical corticosteroid use [Based on a meta-analysis of 19 trials totaling 4076 intervention and 3700 control events, respectively, maternal probiotic consumption in late pregnancy and, during lactation, could reduce AD incidence in children younger than five years old, Risk Ratio 0.78, 95% Confidence Interval (CI) 0.68 to 0.90, I20 to 64 . A systeLactobacillus salivarius synbiotic (probiotic with prebiotics to increase probiotic delivery) was trialed against prebiotic only in sixty 2- to 14-year-old children with moderate to severe AD [L. salivarius synbiotic recipients had significantly lower SCORAD scores (27.4 \u00b1 12.7) than prebiotic recipients [L. salivarius LS01 has been shown to preserve Th1 cytokine production and Th1:Th2 ratios when compared to maltodextrin controls after four months of treatment [L. salivarius\u2019 reduction of AD severity via normalization of T-cell function is consistent with the hygiene hypothesis [A evere AD . At eigh= 0.022) ,24. In areatment . L. salipothesis .Bifidobacterium longum infantis and B. breve combination in fermented infant formula achieved greater IgA responses to the poliovirus vaccine challenge than standard formula [L. salivarius and B. breve BR03 combination led to improved SCORAD indices in adult AD patients [B. breve Bb99 synbiotic with three additional probiotics given to 459 women during the last two to four weeks of pregnancy and given to their newborns for six months after delivery reduced AD in comparison to 463 controls (Odds Ratio (OR) = 0.74; 95% CI, 0.55\u20130.98, p = 0.04) [L. rhamnosus LCS-742 and B. longum infantis M63 synbiotic administered to 39 term newborns for six months reduced AD in comparison with 45 formula-fed control newborns [p = 0.03, based on a SCORAD-weighted mean difference improvement of 7.32 for 80 treated participants from three studies [B. breve M-16V synbiotic versus placebo control in 90 infants less than seven months of age did not find differences in cytokine production or circulating regulator T-cell proportions [L. rhamnosus LC705, B. breve Bb99, and Propionibacterium freudenreichii spp. Shermanii JS, with 1223 subjects found that in cesarean delivered infants, IgE-associated allergic diseases at five years of age were significantly reduced [A formula . A L. sapatients . B. brev = 0.04) . Similar < 0.05) . Overall studies . Consistportions . However= 0.035) . It has L. plantarum K8 (KCTC 10887BP) lysates. The 2.1% L. plantarum K8 lysates increased forearm skin hydration by the fourth week (p = 0.03), but not after eight weeks of use (p = 0.068) [p = 0.00) and eight weeks (p = 0.007) of use [L. plantarum K8 lysates were associated with significantly decreased horny layer thickness of the forearm and face at four weeks and eight weeks with p = 0.002 and p = 0.000 for the face and p = 0.007 and p = 0.000 for the forearm [L. plantarum K8 lysates use was associated with statistically significant decreased TEWL of the forearm and face at eight weeks with p = 0.002 and p = 0.008, respectively [L. plantarum K8 lysates may be regarded as orally consumed skin moisturizers that reduce the need for topical corticosteroids and emollients for AD treatment [Lysates offer cost-savings over the use of selected single components. Lysates can be included in prepared foods. A randomized controlled trial (RCT) with 41 dry, dark-skinned 25- to 60-year-old patients tested orally consumed 2.1% Pseudomonas aeruginosa is known for opportunistic infections in burn patients through the use of a toll-like receptor-4 (TLR-4) associated lipopolysaccharide receptor complex to induce an inflammatory and adaptive immune response [L. plantarum, 105 cfu/mL injected into infected areas on days three, four, five, seven, and nine post infection inhibited P. aeruginosa PA100 colonization of an in vivo burned-murine model, which was measured by the lack of viable P. aeruginosa PA 100 cells, p < 0.001 [L. plantarum was tried against silver sulphadiazine in 80 patients with delayed, infected second-degree and third-degree burns, or early, non-infected third-degree burns [L. plantarum achieved a 2.72% lower bacterial load in second-degree burns and 1.07% less infection in early third-degree burns, but had 16.90% more infection in delayed, infected third-degree burns [response . L. plan < 0.001 . L. planee burns . Within ee burns . These ree burns . Lactobacillus reuteri ATCC 55730 at 105 to 108 cfu/mL and L. rhamnosus AC413 coinfections increase normal primary human epidermal keratinocytes (NHEK) survival in the presence of concurrent S. aureus infection from 8.8% in the absence of probiotics to 53.1% (p = 0.0012) and 42.7% (p < 0.0001), respectively [L. reuteri ATCC 55730 lysate also protects NHEK from S. aureus, p = 0.01. Heat-killed L. reuteri ATCC 55730 is ineffective against S. aureus infection [L. reuteri ATCC 55730 exposure after S. aureus infection is ineffective. L. reuteri ATCC 55730 introduction before or concurrently with S. aureus allows L. reuteri ATCC 55730 to competitively exclude S. aureus from NHEK binding sites, p = 0.026 and p = 0.0078, respectively [L. reuteri ATCC 55730, L. reuteri ATCC 55730 lysates are less effective staphylococcal adhesion inhibitors, p = 0.0002 versus p = 0.032 [L. salivarius UCC118 cannot be substituted for L. reuteri ATCC 55730 since L. salivarius UCC118 adheres less effectively to NHEK than does L. reuteri ATCC 55730, 5.6 \u00b1 0.1 log cfu versus 6.7 \u00b1 0.1 log cfu respectively, p = 0.005 [ectively . L. reutnfection . L. reutectively . Compare = 0.032 . L. saliS. aureus exposure with p = 0.006 and p = 0.01 after a 24-h incubation [S. aureus infection, p = 0.005 and p = 0.01, respectively [S. aureus from receptors [S. aureus from keratinocytes\u2019 receptors [S. aureus growth. However, spent culture did not inhibit S. aureus growth [In vitro studies show that LGG lysates and spent culture fluid can protect human keratinocytes from subsequent cubation . LGG andectively . Live LGeceptors . Live LGeceptors . Live LGs growth .Camellia sinensis derived tea is 20% green tea and is the second most common drink [Pigmented polyphenols absorb UVR primarily in the UVB spectrum with some UVA and UVC absorption, which facilitates sunscreen function . Globallon drink ,31. Topion drink . In murion drink .2) preceding UVR exposure also reduced photodamage [p = 0.02 [Anti-inflammatory, antioxidant, polyphenolic green tea catechins (GTC) inhibit cyclooxygenase-2 and lipoxygenases . Conjugatodamage . A 34-dap = 0.02 .2 to 28 mJ/cm2 in both intervention and placebo groups [+ T-lymphocyte counts were similar in each group, p = 0.85 and p = 0.62, respectively [Oral GTC metabolites are incorporated into the skin . Oral GTo groups . Post-UVectively .p < 0.05 versus 20.4 \u00b1 2.7%) [p < 0.05 [Topical green tea EGCG effects IL-12-dependent DNA repair . However \u00b1 2.7%) . \u03b1-Lipoi \u00b1 2.7%) . Interesp < 0.05 .p < 0.05, p < 0.01, and p < 0.001, respectively. Ferulic acid is least active with IC30 > 30 against melanin production and tyrosinase activity [p < 0.002) and peak wavelength absorption is increased (p < 0.001) [p \u2264 0.05) [p \u2264 0.05) [Aspalathus linearis (rooibos) tea. Caffeic acid and ferulic acid are constituents of Polypodium leucotomas, a tropical fern [P. leucotomas extract is commercially available in several products [P. leucotomas extract significantly reduced tumorigenesis and immunosuppression associated cyclobutane pyrimidine dimers formed by UVB action on DNA, p < 0.001 [P. leucotomas [Dietary phenolic acids are primarily UVA absorbing antioxidants with indirect regulatory effect on the nuclear factor E2-related factor 2-antioxidant responsive element (Nrf2-ARE) pathway . In primactivity . Nonetheactivity . Althoug< 0.001) . Rutin i \u2264 0.05) . UVA pho \u2264 0.05) . Of notecal fern . P. leucproducts . In a sm < 0.001 . This fiucotomas .Photoprotection and anti-photocarcinogenesis murine trials of resveratrol abound . In vivoSilymarin is up to 80% silibinin is GRAS . In addiVitamins C and E are normal skin components . UVR-indElaies guineensis , which was transported globally by the Portuguese in the 15th Century and the Dutch in the 19th Century [Elaeis oleifera has more oleic and linoleic acid and less palmitic and saturated acids than E. guineensis [E. guineensis tocotrienols are unusual since rice bran oil is the only other tocotrienol containing vegetable oil [p < 0.03, when compared to control cells [Vitamin E comprised 30% of mixed tocopherols and 70% of mixed tocotrienols and a water-soluble phenolic-flavonoid-rich antioxidant complex are minor components of Century . Elaeis ineensis . E. guinable oil . Palm oiable oil . Howeverable oil . Tocotriable oil . Consistable oil ,45. Nanoable oil . In vitrable oil . Cell viol cells .RRR-\u03b1-tocopherol daily for 12-weeks reduced dorsal skin erythema (p < 0.01) by week nine in comparison to 25 mg total carotenoids daily [Lactobacillus johnsonii 5.10 \u00d7 108 cfu was the intervention in a 12-week randomized, double-blinded, placebo-controlled trial with 60 patients who had polymorphic light eruptions [L. johnsonii 5.10 \u00d7 108 cfu was able to reduce the effect of a single exposure to longwave UV radiation (UVA1), p < 0.001, but that of multiple exposures [p < 0.001, and p = 0.022 in the placebo group [p = 0.03), increased procollagen deposition (p = 0.05), reduced UVR-induced matrix metalloproteinase-1 (p = 0.04), and reduced mitochondrial DNA 3895-base pair deletion after 3\u00d7 minimal erythema dose UV exposure (p = 0.01) [Based on 20 healthy adults, an oral combination of 25 mg total carotenoids and 335 mg ds daily . Combinads daily . This isds daily . A commeruptions . The comxposures . UVA1-inxposures ,49. Intr = 0.01) . Based o = 0.01) . The dos = 0.01) .2 \u00b1 0.04, 50 mg coenzyme Q10 MED was 0.72 J/cm2 \u00b1 0.06 and 150 mg coenzyme Q10 MED was 0.70 J/cm2 \u00b1 0.06, p = 0.49 [The antioxidant, coenzyme Q10 is essential for mitochondrial energy metabolism . In contp = 0.49 .2, p < 0.01, and reduced p53 UV-induced skin expression by 50%, p < 0.01 [A 3-month, 42-person, double-blind randomized trial of omega-3 polyunsaturated fatty acids 4 g daily, eicosapentaenoic acid (EPA), or monounsaturated oleic acid found that EPA was the most promising for photo-protection . EPA incp < 0.01 . This waL. salivarius symbiotic should be considered for AD treatment given reduced AD severity measured by SCORAD, p = 0.022 [B. breve may need additional trials as a combination probiotic in fermented foods before significant effects on AD was seen [L. rhamnosus LC705, B. breve Bb99, and Propionibacterium freudenreichii spp. Shermanii JS, reduced IgE-associated allergic diseases in cesarean-delivered infants (p = 0.035), but B. breve as a single administered probiotic did not affect cytokine production or circulating regulator T-cell proportion [The preceding sections and the synopsis of selected references in = 0.022 . Probiotwas seen . The comoportion ,27. Succoportion ,27.L. plantarum K8 lysates are skin moisturizers, which increase facial skin hydration through eight weeks of use (p = 0.007), decrease the horny layer thickness of the forearm and face through eight weeks of use (p = 0.000 for the face and forearm), and decrease TEWL of the forearm and face at eight weeks [L. plantarum K8 lysates should reduce the need for topical corticosteroids and emollients for AD treatment [L. plantarum is a candidate for further larger scale in vivo study as a topical burn treatment [Orally consumed 2.1% ctively) . Thereforeatment . Decreasreatment ,8. Givenreatment ,29. Ideareatment .L. reuteri ATCC 55730 for S. aureus opportunistic infection ensures the effectiveness of the non-denatured probiotic [Live or lysate probiotic preparations are biologically plausibly efficacious where heat-killed preparations are ineffective ,18. Liverobiotic ,18. Therrobiotic .Oral and topical polyphenols hold the photoprotection and anti-photocarginogenesis promise. Additional human trials on GTC and EGCG are needed. Formulations with improved GTC and EGCG bioavailability such as combinations with \u03b1-lipoic acid may allow anti-inflammatory photo protective effectiveness at doses equivalent to less than 10 cups of green tea daily ,30,32. H"} +{"text": "Escherichia coli (UPEC) are one of the main bacteria causing urinary tract infections (UTIs). The rates of UPEC with high resistance towards antibiotics and multidrug-resistant bacteria have increased dramatically in recent years and could difficult the treatment.Uropathogenic E. coli isolated from community (79 isolates) and hospital-acquired (31 isolates) urinary tract infections. The plasmid-mediated quinolone resistance genes presence was also investigated. A subset of 18 isolates with a quinolone-resistance phenotype was examined for common virulence genes encoded in diarrheagenic and extra-intestinal pathogenic E. coli by a specific E. coli microarray.The aim of the study was to determine multidrug-resistant bacteria, antibiotic resistance profile, virulence traits, and genetic background of 110 kpsMTII gene. Overall, fimH (71.8%) and fyuA (68.2%), had the highest prevalence as virulence genes among isolates. However, the profile of virulence genes displayed a great diversity, which included the presence of genes related to diarrheagenic E. coli. Out of 110 isolates, 25 isolates (22.7%) were positive to qnrA, 23 (20.9%) to qnrB, 7 (6.4%) to qnrS1, 7 (6.4%) to aac(6\u2032)lb-cr, 5 (4.5%) to qnrD, and 1 (0.9%) to qnrC genes. A total of 12.7% of the isolates harbored blaCTX-M genes, with blaCTX-M-15 being the most prevalent.Female children were the group most affected by UTIs, which were mainly community-acquired. Resistance to trimethoprim\u2013sulfamethoxazole, ampicillin, and ampicillin\u2013sulbactam was most prevalent. A frequent occurrence of resistance toward ciprofloxacin (47.3%), levofloxacin (43.6%) and cephalosporins (27.6%) was observed. In addition, 63% of the strains were multidrug-resistant (MDR). Almost all the fluoroquinolone (FQ)-resistant strains showed MDR-phenotype. Isolates from male patients were associated to FQ-resistant and MDR-phenotype. Moreover, hospital-acquired infections were correlated to third generation cephalosporin and nitrofurantoin resistance and the presence of E. coli may be difficult to treat empirically due to high resistance to commonly used antibiotics. Continuous surveillance of multidrug resistant organisms and patterns of drug resistance are needed in order to prevent treatment failure and reduce selective pressure. These findings may help choosing more suitable treatments of UTI patients in this region of Mexico.Urinary tract infection due to Escherichia coli is an important cause of extra-intestinal infections, enteric disease, and systemic infections in humans and animals. Uropathogenic Escherichia coli (UPEC), one of the members of the extra-intestinal pathogenic E. coli (ExPEC) is a predominant pathogen causing urinary tract infections (UTIs) . Trimethoprim\u2013sulfamethoxazole and cephalosporins [cefotaxime (p\u2009=\u20090.0232) and ceftazidime (p\u2009=\u20090.0001)] also showed a co-resistance.Co-resistance phenotype between cephalosporins and beta-lactams towards fluoroquinolones was frequently observed [(amoxicillin\u2013clavulanic acid (p\u2009=\u20090.0306), ceftriaxone (p\u2009=\u20090.0305), and nitrofurantoin (p\u2009=\u20090.0002) resistance phenotype (Table\u00a0p\u2009=\u20090.02329). MDR-phenotype (69.6%) as well as the FQ-resistant phenotype was also prevalent among older adults (>\u200960\u00a0years old).Overall, hospital-acquired isolates were slightly more resistant than community-acquired isolates . Both hospital and community-acquired isolates showed higher resistance towards ampicillin (77.4% vs 68.4%) and trimethoprim\u2013sulfamethoxazole (77.4% vs 70.9%). UPEC isolates from hospital-acquired infections were associated to ceftazidime (E. coli isolates. The phylo-groups D (23.6%) and A (19.1%) were the most commonly found, followed by B1 (15.5%), C (13.6%), B2 (11.8%), F (10%), cryptic clades (5.5%) and phylo-group E (0.9%). The different phylo-groups and cryptic clades were distributed in both hospital and community settings, except the phylo-group E which was only distributed in the hospital-acquired infections. MDR strains were distributed into all phylogenetic-groups: 26% (16/70) to A, 17.1% (12/70) to D, 15.7% (11/70) to B1, 12.9% (9/70) to C, 11.4% (8/70) to B2 and F, and 6.7% (5/70) to cryptic clades. Phylo-group D was significantly associated to MDR-phenotype (p\u2009=\u20090.0339) as well as FQ-resistant phenotype . Phylo-groups B2 and D were more common among community-acquired isolates than hospital-acquired isolates , as well as in females than in males but not significantly associations were found.All seven phylogenetic lineages and cryptic clades were found on the 110 urinary fimH (71.8%), fyuA (68.2%), and agn43 (54.5%) were the virulence genes with the highest distributions among isolates, while afa/dra (8.2%) and cnf1 (2.7%) had the lowest. Others virulence genes tested had the following distribution: chuA, 49.1%; papC, 42.7%; kpsMTII, 37.3%; vat, 20%; yfcV, 20%; sfaS 10%, and hlyA, 9.1% (Table\u00a0fyuA (71.0% vs 67.1%), papC (48.4% vs 40.5%), yfcV (25.8% vs 55.7%), hlyA (12.9% vs 7.6%), cnf1 (3.2% vs 2.5%), kpsMTII (58.1% vs 29.1%) and chuA (51.6% vs 48.1%) were higher among UPEC isolated from hospital-acquired than community-acquired infections. However, only the kpsMTII was significantly associated with hospital-acquired isolates . The presence of the chuA gene was associated to UPEC isolated from children (p\u2009=\u20090.0483). Furthermore, the presence of vat was associated to UPEC isolates from adults (p\u2009=\u20090.0153).Overall, nd agn43 4.5% werefimH (72.9%), fyuA (65.7%), agn43 (55.7%) and chuA , fyuA (67.3%) and chuA (57.7%) were highly distributed among FQ-resistant bacteria.Virulence genes ), fyuA 6.7%, agn4E. coli isolates belonging to the phylo-groups B2, D and F. Overall, 145 virulence and 40 antimicrobial resistance genes among the 315 and 82 genes and variants investigated were detected at least once in one or more of the isolates. The total number of virulence genes per isolate ranged from 18 to 63 genes. The median number of the virulence genes per isolate was 35. Microarray hybridizations demonstrated that all the E. coli isolates tested possessed virulence genes related to a pathotype including ExPEC and diarrheagenic E. coli (DEC). The total number of antimicrobial resistance genes per isolate ranged from 0 to 21 genes with a median number of 6.5 genes. Since the microarray carries a large set of virulence factors, numerous incomplete ExPEC that would normally be missed in a PCR-based assay were found. Thus, various unusual gene combinations were discovered, such as ExPEC pathogenic profiles with assorted EPEC genes coding for the type III secretion system 2 proteins ErpJ and SpaS . Moreover, detection of virulence (mean 39.0\u2009\u00b1\u200916.9) and antimicrobial resistance (mean 9.0\u2009\u00b1\u20091.9) genes were higher on hospital-acquired UTIs isolates compared to community-acquired infections , 20.9% (23 isolates) to qnrB, 6.4% (7 isolates) to qnrS1, 0.9% (1 isolates) to qnrC, 4.5% (5 isolates) to qnrD, and 6.4% (7 isolates) to aac(6\u2032)-Ib-cr , levofloxacin (LEV), and norfloxacin (NOR). The double mutations in Ser-83\u2009\u2192\u2009Leu and Asp-87\u2009\u2192\u2009Tyr or Asp-87\u2009\u2192\u2009Asn substitution in gyrA were present in 92% of the strain tested. Ser-80\u2009\u2192\u2009Ile substitution in parC were found in 92% of the isolates tested, which also were resistant to both ciprofloxacin and levofloxacin. The substitution Thr-66\u2009\u2192\u2009Ser , Thr-66\u2009\u2192\u2009Asn , and Thr-66\u2009\u2192\u2009Tyr were also found in parC. Other substitutions in parC as Glu-84\u2009\u2192\u2009Val and Glu-84\u2009\u2192\u2009Ala were also detected. Interestingly, one strain (isolated UEc 76) which was resistant to ciprofloxacin, levofloxacin and norfloxacin, belonging to B2 phylo-group and blaCTX-M-containing, also carried the double mutations in Ser-83\u2009\u2192\u2009Leu and Asp-87\u2009\u2192\u2009Asn substitution in gyrA and the triple mutation in parC Ser-80\u2009\u2192\u2009Ile, Thr-66\u2009\u2192\u2009Tyr and Glu-84\u2009\u2192\u2009Val.Overall, 22% of the isolates were positive for rB, 6.4% isolatesblaCTX-M (12.7%/14 isolates), blaTEM , blaPSE , and blaOXA (9.1%/10 isolates). Sequencing of the blaCTX-M amplicons identified the presence of blaCTX-M-15 in 7.2% of the strains (8 isolates), blaCTX-M-12 in 4.5% (5 isolates), blaCTX-M-3 in 1.8% (2 isolates), and blaCTX-M-14 in 1.8% (2 isolates). Furthermore, blaROB-1,blaSHV-37, and blaCMY-2 genes, were identified in one isolate (0.9%) through the microarray assay.ESBL genes were investigated through microarray and PCR assay. A total of 27 isolates (24.5%) suspected as cephalosporinase producers showed positive PCRs for blaCTX-M genes and PMQR genes as well as mutation in QRDR were found in both community- and hospital-acquired infections as well as in male and female genders. The PMQR qnrA (21.4%), and qnrB (18.6%), were highly distributed on MDR-phenotype (Table\u00a0aac(6\u2032)-Ib-cr gene compare to female isolates . Quinolone-resistance isolates also presented higher prevalence to blaCTX-M compared to quinolone-sensitive phenotype isolates .Overall pe Table\u00a0. IsolateIn accordance with global trends, our results reveal higher prevalence of urinary tract infections in female patients than in males , 34\u201336. Multidrug-resistant strain prevalence (63.3%) was higher in this work than in other study from Mexico, which reported only 16.4% of MDR strains . While wE. coli isolates from hospital-acquired UTIs are correlated to the presence of kpsMTII gene that has been associated to pyelonephritis, a more severe infection of the upper urinary tract [fyuA-encoding yersiniabactin receptor and, fimH encoding type 1 fimbrial adhesion.As detected by Ochoa et al. , phylo-gry tract . In agrery tract , 41, ourE. coli (EAEC and DAEC), including capU , deoK (deoxyribokinase), shf , virK and astA gene (EAEC heat-stable enterotoxin 1). This was also reported in previous works [E. coli reported in ExPEC strains. The deoK operon is frequently associated with strains isolated from infected urine and blood and is part of a large genetic island carrying genes contributing to the strain intrinsic virulence and/or adaptive properties [Detailed analysis of a strains subset using microarrays, revealed that some of them from both, hospital- and community-acquired infections carried virulence related genes of enteroaggregative and diffusely adherent us works \u201345, whicoperties . These soperties .E. coli (EPEC) related genes on five UPEC isolates. These genes included the eae , as well as virulence related genes such as espG , eprJ (E. coli type III secretion system 2 protein ErpJ), epaS (E. coli type III secretion system 2 protein EpaS), and eivG (E. coli type III secretion system 2 protein EivG) [Another finding was the presence of enteropathogenic in EivG) , 46. T3Sin EivG) , 48. Thein EivG) , 49, 50.qnrA, qnrB, qnrS, qnrC and qnrD as well as aac(6\u2032)-Ib-cr were detected. The most common PMQR-genes identified were qnrA and qnrB, which is in contrast to previous studies were aac(6\u2032)-Ib-cr gene detection was more frequent on ExPEC isolates [qnrA and qnrB were frequently found as a part of MDR-phenotype. qnrD gene was found in 4.5% of the isolates. Previous papers reported qnrD in bacteria isolated from rooks [Salmonella enterica serovar Kentucky, serovar Bovismorbificans, Proteus mirabilis and Morganella morganii [E. coli from dogs [qepA was not identified. Although PMQR genes provide a low level of FQ-resistance, they have been reported to favor the selection of additional chromosome-encoded resistance mechanism [gyrA and parC were prevalent in community-acquired infections (89% vs 11%). Overall, mutations in QRDR were equally present among isolates from males and females patients.In this study, UPEC strains carrying PMQR genes associated to quinolones resistance including isolates , 51. Morom rooks and humamorganii , 53, as rom dogs . In accorom dogs , 55, 56,echanism . In our blaCTX-M , blaTEM, blaPSE, and blaOXA were detected. For the isolates carrying resistance genes, ESBL genes such as TEM, SHV and CTX-M, are the most widespread and frequently detected in E. coli [In our study, ESBL genes E. coli . In addi E. coli , 59.E. coli UTI isolates from hospital and community in Mexico. Diverse genotypes and phenotypes including multidrug-resistance, fluoroquinolone resistance and carriage of virulence genes related to several enteropathogenic E. coli were found among UPEC isolates. Thus, continuous surveillance for antimicrobial resistance of UPEC is needed in order to prevent treatment failure and to improve the strategies to mitigate the occurrence of antibiotic resistance organisms and ensure the best treatment to UTI patients. This study highlights the importance of antimicrobial resistance of virulent E. coli from urinary tract infection in Mexico.Our study describes significant antimicrobial resistance in"} +{"text": "The impact of STAR-VA on psychotropic drug use among residents with behavioral symptoms of dementia was evaluated through a difference-in-differences framework. STAR-VA residents enrolled 2013-2017 were evaluated longitudinally pre-post intervention. The primary outcome was the number of as needed administrations with an indication of \u2018anxiety\u2019 or \u2018agitation\u2019. The analytical cohort included 214 training cases and 1,870 controls from untrained sites meeting eligibility criteria. STAR-VA cases were less white (48% vs. 54%), less black (11% vs. 14%), and had significantly longer median length of stay (830 vs. 261 days), respectively. STAR-VA cases had on average 3.5 as needed doses/month of psychotropic medication before the intervention and 1.7 after, controls averaged 1.8 doses/month. After adjustment for person-time-fixed effects, enrollment was associated with 55% reduction or an average 0.8 as needed psychotropic doses/month. Findings demonstrate effectiveness in decreasing as-needed psychotropic drug use among CLC residents, supporting continued implementation of STAR-VA."} +{"text": "Nature Communications 10.1038/s41467-017-02626-6; published online 15 Jan 2018Addendum\u00a0to: Nat. Commun. 7, 11369 (2016) and Phys. Rev. Mat. 1, 035604 (2017)), which report the spontaneous helix formation in a polar smectic liquid crystal phase made of achiral bent-core mesogens.We would like to make our readers aware of the related publications by S.P. Sreenilayam et al. ("} +{"text": "Scientific Reports 10.1038/s41598-019-46738-z, published online 12 August 2019Correction to: This Article contains an error in the Acknowledgements section.\u201cThis study also partly supported by Incheon National University (INU) Research Grant (2016) to H.W.K. and the INU Postdoctoral Fellowships to U.Y. and R.I.\u201dshould read:\u201cThis study also partly supported by Incheon National University (INU) Research Grant (2016) to H.W.K.\u201d"} +{"text": "Correction to: J ImmunoTher Cancer (2019) 7:288https://doi.org/10.1186/s40425-019-0778-7Following publication of the original article , the aut3)\u201d should change to black font;A: Red font \u201cMHC-I c reduces macrophage frequency and activates macrophages, cDC, B and NK cells. Figure S3. Poly(I:C)c triggers transcriptional reprogramming of MDSC. Figure S4. Significantly regulated genes in PMN- and M-MDSC upon poly(I:C)c therapy."} +{"text": "Scientific Reports 10.1038/s41598-017-10484-x, published online 31 August 2017Correction to: The Acknowledgements section in this Article is incomplete.\u201cWe thank D.M. Buss for his comments.\u201dshould read:\u201cWe thank D.M. Buss for his comments. Study was funded by National Science Centre-PL-2014/13/B/HS6/02644\u201d"} +{"text": "AbstractKSU). Included in this material, three species of Labiobaetis Novikova & Kluge, 1987 are recorded, two of them being new to science. Labiobaetispotamoticus Gattolliat & Al Dhafer, sp. n. is described from both larvae and adults, whereas Labiobaetisalahmadii Gattolliat & Al Dhafer, sp. n. is only known from the larval stage. The two species are compared morphologically with Palearctic and Afrotropical species of Labiobaetis. A third species, Labiobaetisglaucus is reported for the first time from the Arabian Peninsula. The species was originally described from South Africa and subsequently reported from the east and northeast of Africa. A molecular reconstruction including 18 Afrotropical and Palearctic species of Labiobaetis was performed using 658 bp of the mitochondrial gene CO1. The reconstruction highly supported the validity of the two new species and confirmed the occurrence of L.glaucus in KSU.Mayfly larvae and imagos were collected at approximately 50 localities of the Kingdom of Saudi Arabia ( Labiobaetis Novikova & Kluge, 1987 is a species-rich genus with an almost worldwide distribution ; it is mainly diversified in Afrotropical (28 species) and Oriental realms (23 species) . The staspecies) . Moleculphyletic . Larvae KSU) and Yemen despite potential suitable habitats present in Oman, Jordan and the United Arab Emirates were mentioned from KSU ; other paratypes are housed in the Museum of Zoology, Lausanne, Switzerland (MZL). Each GBIFCH code refers to a tube with group of specimens in or a slide with a single specimen (sequenced or not).The majority of the material was collected in November 2012 during a scientific expedition organised by King Saud University Museum of Arthropods, College of Food and Agriculture Sciences, Department of Plant Protection, CO1) gene. Specimens belonging to the different \u201cmorphospecies\u201d and collected in the same localities were selected for genetic analysis. The CO1 gene was sequenced using LCO1490 and HCO2198 primers ) as the maximal value for intraspecific divergence : Saudi Arabia (AR44); Wadi Shahadan; 17\u00b028'36\"/ 42\u00b042'50\"; Alt. 190m; 13.XI.2012; Coll. J-L Gattolliat.Paratypes: 4 larvae (GBIFCH00235716 + GBIFCH00235735 (Genetics)), 1 male imago (GBIFCH00235732 (Genetics)) + 3 larvae (KSU: GBIFCH00526192); same data as holotype.19\u00b055'32\"/ 41\u00b026'17\"; Alt. 752m; 13.X.2010; Coll. B. Kondratieff.42 larvae : Saudi Arabia (AR01); Al Jiwah, Thee Aine; 18\u00b047'29\"/ 41\u00b056'19\"; Alt. 490m; 13.III.2012; Coll. Al Dhafer, H. & Kondratieff, B.14 larvae (GBIFCH00235721): Saudi Arabia (AR20); Wadi Baqrah; 19\u00b055'46\"/ 41\u00b026'34\"; Alt. 760m; 3.VI.2012; Coll. Al Dhafer, H. & Kondratieff, B.5 larvae (GBIFCH00235722): Saudi Arabia (AR28); Thee Ain, Al-Baha; 19\u00b055'46\"/ 41\u00b026'34\"; Alt. 760m; 8.XI.2012; Coll. J-L Gattolliat.2 larvae (GBIFCH00235714): Saudi Arabia (AR31); Thee Ain, Al-Baha; KSU: GBIFCH00526173): Saudi Arabia (AR32); Wadi Elarj, near Adam; 20\u00b027'11\"/ 40\u00b048'56\"; Alt. 440m; 9.XI.2012; Coll. J-L Gattolliat.58 larvae , GBIFCH00517521 (Genetics)) + 11 larvae (KSU: GBIFCH00526224): Saudi Arabia (AR43a); Wadi Shahadan; 17\u00b028'36\"/ 42\u00b051'25\"; Alt. 460m; 12.XI.2012; Coll. J-L Gattolliat.23 larvae , GBIFCH00465155 (Genetics)) + 4 larvae (KSU: GBIFCH00526237): Saudi Arabia (AR43b); Wadi Shahadan; 17\u00b028'17\"/ 42\u00b051'14\"; Alt. 455m; 12.XI.2012; Coll. J-L Gattolliat.3 larvae .1 larva (on slide), Saudi Arabia, Wadi Buwah, 1340m, Larva: Tergites I-X medium brown with peculiar pattern formed of six ecru dots Fig. . Scape oLarva.Length: fully grown female: Body 5.1\u20137.7 mm, cerci 3.6\u20134.0 mm, terminal filament 2.5\u20132.6 mm. Fully grown male: Body 5.0\u20135.3 mm, cerci 3.4\u20133.6 mm, terminal filament 2.5 mm.Colouration : Saudi Arabia (AR43a); Wadi Shahadan; 17\u00b028'36\"/ 42\u00b051'25\"; Alt. 460m; 12.XI.2012; Coll. J-L Gattolliat.Paratypes: 151 larvae , GBIFCH00235737) + 8 larvae (KSU: GBIFCH00526208): same data as holotype.KSU: GBIFCH00526227): Saudi Arabia (AR43b); Wadi Shahadan; 17\u00b028'17\"/ 42\u00b051'14\"; Alt. 455m; 12.XI.2012; Coll. J-L Gattolliat.47 larvae (GBIFCH00235710) + 10 larvae (KSU: GBIFCH00526223): Saudi Arabia (AR39); Wadi Damad; 17\u00b012'21\"/ 43\u00b001'35\"; Alt. 260m; 11.XI.2012; Coll. J-L Gattolliat.29 larvae (GBIFCH00235727) + 6 larvae (KSU: GBIFCH00526179): Saudi Arabia (AR44); Wadi Shahadan; 17\u00b028'36\"/ 42\u00b042'50\"; Alt. 190m; 13.XI.2012; Coll. J-L Gattolliat.15 larvae , GBIFCH00465155 (Genetics) + GBIFCH00517526 (Genetics), GBIFCH00517527 (Genetics)) + 4 larvae Baetisglaucus Agnew, 1961: 14.Pseudocloeonglaucum , Labiobaetisglaucus , 19\u00b055'32\"/ 41\u00b026'17\"; Alt. 752m; 13.X.2010; Coll. B. Kondratieff.18 larvae (GBIFCH00235711 + 4 slides GBIFCH00235741 (Genetics), GBIFCH00235746, GBIFCH00235750 (Genetics), GBIFCH00235756: Saudi Arabia (AR01); Al Jiwah, Thee Aine; 19\u00b005'22\"/ 41\u00b058'16\"; Alt. 490m; 13.III.2012; Coll. Al Dhafer, H.3 larvae (GBIFCH00235708): Saudi Arabia (AR19); Wadi Khat; 19\u00b055'43\"/ 41\u00b026'34\"; Alt. 760m; 3.VI.2012; Coll. Al Dhafer, H. & Kondratieff, B.1 larva (GBIFCH00235712): Saudi Arabia (AR28); Thee Ain, Al-Baha; 19\u00b055'43\"/ 41\u00b026'34\"; Alt. 760m; 8.XI.2012; Coll. J-L Gattolliat.3 larvae (GBIFCH00235713): Saudi Arabia (AR31); Thee Ain, Al-Baha; 17\u00b028'36\"/ 42\u00b051'25\"; Alt. 460m; 12.XI.2012; Coll. J-L Gattolliat.1 larva (GBIFCH00235707): Saudi Arabia (AR43a); Wadi Shahadan; 17\u00b028'17\"/ 42\u00b051'14\"; Alt. 440m; 12.XI.2012; Coll. J-L Gattolliat.2 larvae GBIFCH00465151 (Genetics): Saudi Arabia (AR43b); Wadi Shahadan; 17\u00b028'36\"/ 42\u00b042'50\"; Alt. 190m; 13.XI.2012; Coll. J-L Gattolliat.7 larvae (GBIFCH00235723 + 1 slide GBIFCH00235738), 3 male imagos (GBIFCH00235724 + 1 slide GBIFCH00235731 (Genetics)): Saudi Arabia (AR44); Wadi Shahadan; Larva: abdominal pattern with moderate current. The substrate was a mix of sand, cobbles and rocks Figs , 52. ThiL.potamoticus and L.alahmadii as monophyletic clades (BS (Bootstrap support) of 83% and 100% respectively), with intraspecific K2P distances below 1% , with the three populations supported as monophyletic sister-clades . The sister group of Labiobaetispotamoticus is an undescribed species from South Africa; the distance between the two taxa is slightly higher than intraspecific distance (between 4.2 and 5.1%). Labiobaetispotamoticus possesses high distances to all the other species included in the study (16.2 to 25.5%). The relationships of L.alahmadii and L.glaucus with other species of Afrotropical and Palaearctic origins also are unclear and have no molecular support and L.balcanicus and the Afrotropical species L.boussoulius . The shape of the distolateral process of the second segment of the labial palp is of taxonomic importance to separate the different species: more elongated and curved in L.potamoticus , the shape of the apex of the segment II of the maxillary palp , distal margin of tergites , tarsal claw less curved and less stout in L.glaucus and the setation of the ventral margin of femora . Labiobaetispotamoticus and L.piscis show a peculiar pattern on the abdominal tergites . Labiobaetispotamoticus was initially identified as L.balcanicus and the shape of the distomedial projection of the segment II of the labial palp .Labiobaetis are generally similar. The presence or absence of the hindwings and the shape of the genital plates are the main characters to separate the species (Labiobaetispotamoticus cannot be separated from most other species of Labiobaetis with hindwings and broad, apically flat genital plates. Labiobaetisglaucus and L.boussoulius differ from most other species of the genus by the presence of a well-marked triangular expansion on the inner margin of the gonopods (Fig. L.tricolor Tshernova, 1928 (fig. 111a in The imagos of the different species of species . The malods Fig. . A similL.glaucus in KSU is rather unexpected despite that this species is widely distributed in Afrotropical Region (South Africa, Angola, Kenya, Lesotho, Namibia, and Zimbabwe (KSU. We found no clear morphological differences between them and they fully correspond to the original description and subsequent redescriptions (KSU form a highly supported monophyletic clade. Genetic distances between the three populations are clearly of intraspecific range especially if we consider that intermediate populations from East and North-East Africa are not included in the analysis.The discovery of Zimbabwe ; Comorosriptions . As alreriptions , segment"} +{"text": "Salmonella enterica serovar Typhimurium is a Gram-negative pathogen and a primary cause of foodborne illnesses worldwide. Here, we present the complete 47,393-bp genome sequence of the siphophage Skate, which was isolated against S. Typhimurium strain LT2. Salmonella enterica serovar Typhimurium is a Gram-negative pathogen and a primary cause of foodborne illnesses worldwide. Here, we present the complete 47,393-bp genome sequence of the siphophage Skate, which was isolated against S. Typhimurium strain LT2. Salmonella enterica serovar Typhimurium is a Gram-negative pathogen and a primary cause of foodborne illnesses worldwide was used for quality control of the reads. The reads were trimmed with FASTX-Toolkit 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/download.html) before being assembled into a single contig at 160.9-fold coverage using SPAdes 3.5.0 (http://transterm.cbcb.umd.edu/). Sequence similarity searches by BLASTp 2.2.28 (https://cpt.tamu.edu/).The phage Skate was isolated from soil in the cattle holding pen of a cattle harvesting facility in Michigan in August 2016 using rain LT2 . The pharain LT2 . Phage grain LT2 . Pooled es 3.5.0 . Contig es 3.5.0 and Metaes 3.5.0 were usees 3.5.0 . Rho-indp 2.2.28 were usep 2.2.28 interfacSalmonella phages, like phage IME207 (GenBank accession number KX523699) and E1 (GenBank accession number AM491472) , 19, shaMH321493. The associated BioProject, SRA, and BioSample accession numbers are PRJNA222858, SRR8787571, and SAMN11259649, respectively.The genome sequence of phage Skate was submitted to GenBank as accession number"} +{"text": "The generated UHPLC-MS data were analysed and dereplicated using the scientific databases Dictionary of Natural Products and SciFinder Scholar in order to potentially identify new dihydro-\u03b2-agarofurans from local Celastraceae plants. These investigations led to the large-scale extraction and isolation work on a prioritised fruit sample that belonged to the rainforest plant Denhamia celastroides. Chemical investigations resulted in the purification of four new natural products, denhaminols O\u2013R (1\u20134), along with the related and known compound, denhaminol G (5). The structures of all the new compounds were determined via detailed analysis of NMR and MS data.An analytical method using UHPLC-MS was developed and applied to 16 crude CH To confirm the presence of the new compounds and to unambiguously identify the structures, we conducted a large-scale extraction of the plant material and MS-directed purification to isolate the targeted compounds with the distinct molecular weights before NMR experiments were conducted.The scientific databases search indicateD. celastroides (10 g) were sequentially extracted with CH2Cl2. Subsequent purifications using silica gel column chromatography and RP-HPLC afforded five dihydro-\u03b2-agarofurans , respectively. During the isolation of the three targeted compounds, another new dihydro-\u03b2-agarofuran and a known congener, denhaminol G (5) +; (+)-HRESIMS m/z 637.2595 [M + Na]+ .Colourless gum; c 0.075, MeOH); ECD \u03bbext (MeOH) 217 (\u22124.79), 268 (\u22123.81) nm; UV (MeOH) \u03bbmax (log \u03b5) 282 (4.38) nm; IR (UATR) \u03bdmax 2952, 1739, 1705, 1373, 1197, 1162, 1076, 975, 769 cm\u22121; 1H-NMR see 13C-NMR see m/z 657 [M + H]+; (+)-HRESIMS m/z 679.2693 [M + Na]+ .Colourless gum; c 0.510, MeOH); ECD \u03bbext (MeOH) 216 (\u22124.60), 253 (\u22122.01), 301 (0.29) nm; UV (MeOH) \u03bbmax (log \u03b5) 630 (4.441) nm; IR (UATR) \u03bdmax 3419, 2971, 1747, 1710, 1391, 1278, 1120, 1163, 1078, 974, 713 cm\u22121; 1H-NMR see 13C-NMR see m/z 631 [M + H]+, 653 [M + Na]+; (+)-HRESIMS m/z 653.2531 [M + Na]+ .Colourless gum; c 0.110, MeOH); ECD \u03bbext (MeOH) 216 (\u22125.37), 235 (0.92), 279 (\u22121.31) nm; UV (MeOH) \u03bbmax (log \u03b5) 224 (4.42), 281 (4.39) nm; IR (UATR) \u03bdmax 3414, 2981, 1746, 1709, 1635, 1277, 1199, 1163, 1077, 973, 712 cm\u22121; 1H-NMR see 13C-NMR see m/z 653 [M + H]+; (+)-HRESIMS m/z 675.2400 [M + Na]+ .Colourless gum; 1\u20134) along with a known compound denhaminol G (5) were successfully isolated and characterised from one prioritised plant sample, namely the fruits of D. celastroides. Other Celastraceae samples that were prioritised for large-scale extraction and isolation studies will be investigated in the future. The pure compounds reported in this paper will be added to the Davis Open-Access Compound Library which is housed at Compounds Australia, Griffith University [A UHPLC-MS method and dereplication process was developed for the rapid identification of new dihydro-\u03b2-agarofurans from Celastraceae plants. This study further exemplifies how UHPLC-MS data and database mining can be used to extract molecular features related to characteristic secondary metabolites of a plant family and thus expedite new discoveries in natural products research. This approach was successfully applied to 16 Australian Celastraceae plant extracts. Consequently, four previously undescribed dihydro-\u03b2-agarofurans (denhaminols O\u2013R, iversity ,23,24,25"} +{"text": "Scientific Reports 10.1038/s41598-018-21753-8, published online 23 February 2018Correction to: In the original version of this Article, Jakub Wlodarczyk was incorrectly affiliated with \u201cCenter of New Technologies, University of Warsaw, Banacha 2c Street, Warsaw, 02-097, Poland\u201d. The correct affiliation is listed below.Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, Warsaw, 02-093, Poland.Additionally, the Acknowledgements section was incomplete.\u201cThis work was supported by the National Science Centre Grant - UMO-2015/17/B/NZ3/00557 and by an EMMA-West grant from the EU (S. B.). SB was also supported by a FASTTRACK grant (SR/FTP/ETA-04/2012) from DST and a UGC Research Award (F.30-31/2016 SA-II) from the Government of India. D.P. and S.B. were supported by the Polish National Science Centre (2014/15/B/ST6/05082) and D.P. by COST BM1405 and BM1408 EU actions.\u201dnow reads:\u201cThis work was supported by the National Science Centre Grant - UMO-2015/17/B/NZ3/00557 and by an EMMA-West grant from the EU (S.B.). S.B. was also supported by a FASTTRACK grant (SR/FTP/ETA-04/2012) from DST and a UGC Research Award (F.30-31/2016 SA-II) from the Government of India. M.M was also supported by the National Science Center Grant 2016/21/N/NZ3/03273. N.D. was supported by the PURSE-II project . D.P. and S.B. were supported by the Polish National Science Centre (2014/15/B/ST6/05082), and by Foundation for Polish Science (TEAM to D.P.). D.P. was also supported by grant 1U54DK107967-01 \u2018Nucleome Positioning System for Spatiotemporal Genome Organization and Regulation\u2019 within 4DNucleome NIH program (TEAM grant to D.P.) and COST BM1405 and BM1408 EU actions.\u201dThese errors have now been corrected in the PDF and HTML versions of the Article."} +{"text": "Salmonella enterica serovar Heidelberg phage Matapan. A myophage with a 157,408-kb genome, Matapan is most closely related to Vi01-like phages.Here, we describe the Salmonella enterica serovar Heidelberg phage Matapan. A myophage with a 157,408-kb genome, Matapan is most closely related to Vi01-like phages.Here, we describe the Salmonella enterica serovar Heidelberg is a member of Enterobacteriaceae and a zoonotic pathogen at 37\u00b0C with aeration, and phage isolation and propagation were done using the soft agar overlay method (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed with the FASTX-Toolkit 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). The genome was assembled to 26.9-fold coverage with SPAdes v3.5.0, with default parameters, and closed by PCR and Sanger sequencing (\u201314\u2013Matapan was collected from filtered (0.2-\u03bcm pore size) municipal wastewater in College Station, TX, via enrichment on y method . Phage my method . The geny method . Librarixy-pub/) , 9. Genexy-pub/) \u201312. The y-pub/) \u2013. Predictub/) \u201314\u2013. Whole-gub/) \u201314\u2013.Salmonella phage Vi01 (GenBank accession number FQ312032), Escherichia phage ECML-4 (GenBank accession number JX128257), Salmonella phage STML-13-1 (GenBank accession number JX181828), and Salmonella phage Marshall (GenBank accession number KF669653), respectively, and 196 similar proteins with phage Vi01. Similar to other Vi01-like phages, Matapan is predicted to use headful or pac-type packaging using PhageTerm (rIIA-like gene.Matapan is a Vi01-like myophage with a 157,408-kb genome with a G+C content of 44.9%, a 93.0% coding density, 214 protein-coding genes, and 3 tRNAs. As determined by progressiveMauve, Matapan shares nucleotide similarities of 91.3%, 89.5%, 88.2%, and 87.9% with MN066127, BioProject accession number PRJNA222858, SRA accession number SRR8869240, and BioSample accession number SAMN11360418.The genome sequence and associated data for phage Matapan were deposited under GenBank accession number"} +{"text": "T was isolated from the gut microbiota of a 28-year-old woman and exhibits a 2.23-Mb draft genome sequence containing 1,902 protein-coding genes, 49 tRNAs, and 3 rRNAs. The 16S rRNA sequencing and in silico DNA-DNA hybridization indicated that strain Marseille-P9525T represents a new species to be described.Strain Marseille-P9525 T was isolated from the gut microbiota of a 28-year-old woman and exhibits a 2.23-Mb draft genome sequence containing 1,902 protein-coding genes, 49 tRNAs, and 3 rRNAs. The 16S rRNA sequencing and in silico DNA-DNA hybridization indicated that strain Marseille-P9525T represents a new species to be described.Strain Marseille-P9525 Enorma massiliensis was the first species of the genus Enorma recently described within the family Coriobacteriaceae . Here, we report the genome sequence of strain Marseille-P9525T and describe its genomic content.eriaceae . The genmosphere \u20133. A culosphere \u2013 of the sT was subcultured on Colombia agar incorporating 5% sheep blood at 37\u00b0C under anaerobic conditions . DNA was extracted in 50 \u03bcl using the EZ1 BioRobot and EZ1 DNA tissue kit and was quantified using a Qubit assay with a high-sensitivity kit to 0.2\u2009ng/liter. DNA was then sequenced using MiSeq technology with paired-end applications. The DNA was fragmented and amplified by limited PCR (12 cycles), introducing dual-index barcodes and sequencing adapters. After purification on AMPure XP beads , libraries were normalized and pooled for MiSeq paired-end sequencing. An automated cluster generation of 12 runs with dual-indexed 2\u2009\u00d7\u2009251-bp reads was performed for 40 hours. A total of 7,810,996 paired-end reads with a 35 to 251-bp sequence length were quality checked using FastQC, trimmed using Trimmomatic version 0.36.6 , 96.76% identity with E. timonensis (NR_144707), 95.30% with E. massiliensis (NR_125606), 94.03% with Collinsella tanakaei (NR_112899), and 93.96% with Collinsella ihuae (LN881598).Strain Marseille-P9525T is smaller than those of E. phocaeensis, E. massiliensis, E. timonensis, C. tanakaei, and C. ihuae . Based on the 16S rRNA gene sequence proximity, genomes were selected and incorporated into an in silico genomic comparison. Genomic similarities estimated using OrthoANI version 0.93.1 (https://www.ezbiocloud.net/tools/orthoani) and in silico DNA-DNA hybridization (http://ggdc.dsmz.de/ggdc.php#) estimated using the GGDC version 2.0 online tool yielded 84.20% and 28.4% sequence similarity with E. phocaeensis, 80.77% and 25.3% with E. timonensis, 78.68% and 24.9% with E. massiliensis, 77.35% and 23.7% with C. ihuae, and 74.57% and 22.2% with C. tanakaei, respectively.The 2.23-Mb draft genome sequence of strain Marseille-P9525CABFVT000000000 and ERR3427549, respectively.The genome sequence reported here and the raw reads have been deposited at EMBL/GenBank under the accession numbers"} +{"text": "Vibrio parahaemolyticus is the lead causative agent for seafood-borne human gastroenteritis. While its occurrence has traditionally been uncommon in Europe and the United Kingdom, rising sea surface temperatures have resulted in an increased prevalence. Here, we present the complete genome sequences of four novel V. parahaemolyticus strains isolated in the United Kingdom. Vibrio parahaemolyticus is the lead causative agent for seafood-borne human gastroenteritis. While its occurrence has traditionally been uncommon in Europe and the United Kingdom, rising sea surface temperatures have resulted in an increased prevalence. Here, we present the complete genome sequences of four novel V. parahaemolyticus strains isolated in the United Kingdom. Vibrio parahaemolyticus is a ubiquitous marine bacterium and an important causative agent for human gastroenteritis EXE V18/004 from Ostrea edulis at Chichester Harbor (2018), (ii) V12/024 from Crassostrea gigas at Weymouth (2012), (iii) V05/313 from Eriocheir sinensis in the River Thames (2005), and (iv) V05/027 from an unknown shellfish source in Southampton (2005). Strains EXE V18/004 and EXE V13/004 were isolated at the University of Exeter, while strains V12/024 and V05/027 were isolated at Cefas Weymouth Laboratories. All four of these strains were isolated directly from shellfish following previously described methods V. parahaemolyticus was initially identified based on colony morphology on selective agar (marine agar and thiosulphate citrate bile sucrose agar) and by PCR targeting the toxR region (9 cells\u2009\u00b7\u2009ml\u22121) was added directly to a Qiagen DNeasy PowerWater kit (Germany) for DNA extraction, followed by library preparation for short-read and long-read sequencing. For short-read libraries, DNA was quantified in triplicate with the Quant-iT double-stranded DNA (dsDNA) high-sensitivity (HS) assay in an Ependorff AF2200 plate reader. Genomic DNA libraries were prepared using a Nextera XT library prep kit (Illumina) following the manufacturer\u2019s protocol with the following modifications: 2 ng of DNA instead of 1 ng was used as the input, and PCR elongation time was increased from 30\u2009s to 1\u2009min. DNA quantification and library preparation were carried out on a Hamilton Microlab Star automated liquid handling system. Pooled libraries were quantified using the Kapa Biosystems library quantification kit for Illumina on a Roche LightCycler 96 quantitative PCR (qPCR) machine. Libraries were sequenced on an Illumina HiSeq instrument. Long-read sequencing was performed in-house using a multiplexed SQK-LSK108 library preparation and sequenced on a FLO-MIN106 flow cell, following Oxford Nanopore Technologies protocol (https://github.com/rrwick/Porechop) with the following settings: -require_two_barcodes -discard_unassigned -discard_middle. Hybrid genome assembly was performed using Unicycler v0.4.7 (https://sourceforge.net/projects/bbmap/) with the following settings: idfilter=0.95 covstats=covstats.txt. Long-read coverage was calculated by first using minimap2 v.2.17 (https://github.com/lh3/minimap2) and SAMtools v.1.9 (http://samtools.sourceforge.net/) to create a bam file (minimap2 -t 16 -ax map-ont | samtools view -F 4 -buS | samtools sort -o long.sorted.bam) and then using BBMap\u2019s pileup.sh to calculate coverage (pileup.sh in=long.sorted.bam ref=ref.fa out=long.covstats.txt). Default parameters for all software were used unless otherwise noted.R region . IsolateR region at 37\u00b0C protocol . Short rprotocol with a sr v0.4.7 , and eacr v0.4.7 , developEach strain was found to have two chromosomes , one withttps://img.jgi.doe.gov/) using the following taxon identifiers (IDs): 2816332655 (V. parahaemolyticus EXE V18/004), 2816332656 (V. parahaemolyticus V12/024), 2816332657 (V. parahaemolyticus V05/313), and 2816332658 (V. parahaemolyticus V05/027). Read data are available from the European Nucleotide Archive under the following strain names and accession numbers: V. parahaemolyticus EXE V18/004, ERS3342146; V. parahaemolyticus V12/024, ERS3342147; V. parahaemolyticus V05/313, ERS3342148; and V. parahaemolyticus V05/027, ERS3342149.Assembled and annotated genomes are publicly available from JGI IMG/M ("} +{"text": "In sub-Saharan Africa, individuals infected with HIV who are severely immunocompromised have high mortality (about 10%) shortly after starting antiretroviral therapy (ART). This group also has the greatest risk of morbidity and mortality associated with immune reconstitution inflammatory syndrome (IRIS), a paradoxical response to successful ART. Integrase inhibitors lead to significantly more rapid declines in HIV viral load (VL) than all other ART classes. We hypothesised that intensifying standard triple-drug ART with the integrase inhibitor, raltegravir, would reduce HIV VL faster and hence reduce early mortality, although this strategy could also risk more IRIS events.3, from eight urban/peri-urban HIV clinics at regional hospitals in Kenya, Malawi, Uganda, and Zimbabwe were randomised 1:1 to initiate standard triple-drug ART, with or without 12-week raltegravir intensification, and followed for 48 weeks. The primary outcome was 24-week mortality, analysed by intention to treat. Of 2,356 individuals screened for eligibility, 1,805 were randomised between 18 June 2013 and 10 April 2015. Of the 1,805 participants, 961 (53.2%) were male, 72 (4.0%) were children/adolescents, median age was 36 years, CD4 count was 37 cells/mm3, and plasma viraemia was 249,770 copies/mL. Fifty-six participants (3.1%) were lost to follow-up at 48 weeks. By 24 weeks, 97/902 (10.9%) raltegravir-intensified ART versus 91/903 (10.2%) standard ART participants had died , with no evidence of interaction with other randomisations (pheterogeneity > 0.7) and despite significantly greater VL suppression with raltegravir-intensified ART at 4 weeks and 12 weeks . Through 48 weeks, there was no evidence of differences in mortality ; in serious , grade-4 , or ART-modifying adverse events ; in events judged compatible with IRIS or in hospitalisations . At 12 weeks, one and two raltegravir-intensified participants had predicted intermediate-level and high-level raltegravir resistance, respectively. At 48 weeks, the nucleoside reverse transcriptase inhibitor (NRTI) mutation K219E/Q (p = 0.004) and the non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations K101E/P (p = 0.03) and P225H (p = 0.007) were less common in virus from participants with raltegravir-intensified ART, with weak evidence of less intermediate- or high-level resistance to tenofovir (p = 0.06), abacavir (p = 0.08), and rilpivirine (p = 0.07). Limitations of the study include limited clinical, radiological, and/or microbiological information for some participants, reflecting available services at the centres, and lack of baseline genotypes.In a 2\u00d72\u00d72 factorial open-label parallel-group trial, treatment-naive adults, adolescents, and children >5 years old infected with HIV, with cluster of differentiation 4 (CD4) <100 cells/mmAlthough 12 weeks of raltegravir intensification was well tolerated and reduced HIV viraemia significantly faster than standard triple-drug ART during the time of greatest risk for early death, this strategy did not reduce mortality or clinical events in this group and is not warranted. There was no excess of IRIS-compatible events, suggesting that integrase inhibitors can be used safely as part of standard triple-drug first-line therapy in severely immunocompromised individuals.NCT01825031.ClinicalTrials.gov ISRCTN 43622374.International Standard Randomised Controlled Trials Number In the factorial randomised REALITY trial, Sarah Walker and colleagues document outcomes of intensified initial antiretroviral treatment for people with advanced HIV disease. 3) have high risks of dying shortly after starting treatment.Individuals in Africa who are HIV positive and initiating treatment with severe immunosuppression to standard triple-drug antiretroviral therapy for 12 weeks would reduce HIV viral load faster: we wanted to find out whether this would reduce high early mortality.We randomly allocated 1,805 adults, adolescents, and older children to receive standard antiretroviral therapy with or without 12 weeks of adjunctive raltegravir.We found that the group receiving 12 weeks of adjunctive raltegravir had significantly faster declines in HIV viral load.However, we found no significant difference in deaths within 24 weeks of starting treatment between those receiving adjunctive raltegravir (97/902 [10.9%]) or not (91/903 [10.2%]); nor were there differences in clinical disease progression, immune reconstitution, inflammatory syndrome, or adverse events.In this study, we found that intensifying the potency of initial antiretroviral therapy did not reduce early mortality on treatment, providing no support for its widespread use in individuals initiating treatment with severe immunosuppression.However, it also did not increase the rates of clinically important immune reconstitution inflammatory syndrome, suggesting that integrase inhibitors could replace other components of standard first-line antiretroviral therapy safely. Absolute 24-week mortality difference was +0.6% . By 48 weeks, 110 (12.4%) versus 115 (13.0%) participants, respectively, had died with no evidence of differences by cause (Table 2). There was no difference in longer-term (after week 48) mortality . Estimated mortality rates decreased sharply from day 19 through week 12 , with 71 (31.6%) of the 225 deaths occurring by 4 weeks, and 147 (65.3%) by 12 weeks. There was no evidence of early differences in mortality rates and no evidence of heterogeneity in the impact of raltegravir intensification over time on ART . Of nine preplanned and five exploratory subgroup analyses . Specifically, there was no evidence that mortality differences depended on pre-ART VL or pre-ART CD4 . No subgroup analyses suggested heterogeneity in the impact of raltegravir intensification on suppression <50 copies/mL at week 4 (pheterogeneity > 0.05) .By 24 weeks (primary endpoint), 97 (10.9%) raltegravir-intensified ART versus 91 (10.2%) standard ART participants died .There was no evidence of an impact of raltegravir intensification on any disease progression clinical outcome (S2 Text). One participant had predicted intermediate-level (mutations T97A+R263K) and two predicted high-level raltegravir resistance mutations . No patient had predicted intermediate- or high-level dolutegravir resistance.Integrase genotypes were obtained in 33 raltegravir-intensified ART participants with VL >1,000 copies/mL at 12 weeks (see p = 0.004) and the NNRTI mutations K101E/P (p = 0.03) and P225H (p = 0.007) were less common in raltegravir-intensified ART, with no evidence of differences for other mutations . There was marginal evidence suggesting less intermediate- or high-level resistance with raltegravir-intensified ART to tenofovir , abacavir , and rilpivirine copies/mL at 48 weeks. The NRTI mutation K219E/Q ; however, there was marginal evidence of a small difference at 48 weeks . There was similar weak evidence of slightly (2%\u20135%) greater percentages with CD4 \u2265 200 cells/mm3 at later time points . Changes in weight were also similar through week 24 , with small but significant differences appearing from 36\u201348 weeks. Similar late differences were observed for BMI in adolescents/adults (data not shown), fat mass , and muscle mass . There was no evidence of heterogeneity in these differences by age . Absolute CD8 count increases were similar in both groups through 48 weeks .Absolute CD4 count increases were similar in both groups through 24 weeks , grade-4 AEs (log-rank p = 0.29), grade-3/4 AEs (log-rank p = 0.72), grade-4 AEs definitely/probably/possibly related to ART (log-rank p = 0.52), grade-4 AEs definitely/probably related to ART (log-rank p = 0.07), AEs leading to ART modification (log-rank p = 0.51) or new hospitalisations (log-rank p = 0.59) (Table 2). Raltegravir was modified for AEs in 19 (2.1%) participants (S2 Table), including renal (n = 6) events, hepatic (n = 6) events, hypersensitivity reactions , and Stevens-Johnson syndrome in one participant . Only one participant experienced a grade-4 AE adjudicated as definitely/probably related to raltegravir (Table 2). There was no evidence of any difference in total hospitalisation-days or total hospitalisations .There was no evidence for differences in time to first SAEs (log-rank p = 0.79) (Table 2); 36 (4.0%) versus 31 (3.4%), respectively, experienced fatal IRIS events (p = 0.54). Tuberculosis IRIS events occurred in 53 (5.9%) participants with raltegravir-intensified ART versus 54 (6.0%) with standard ART (exact p = 1.00) and cryptococcal IRIS events in 15 (1.7%) versus 16 (1.8%) participants, respectively (exact p = 1.00) (S3 Table). IRIS events occurred a median 3.4 (IQR 2.0\u20136.3) weeks from randomisation, with rates declining from the third week on ART . IRIS was more common in participants initiating ART at older ages (p = 0.005), with lower CD4 counts (p < 0.001) or with pre-existing TB (p = 0.007); IRIS was less common in those initiating ART with enhanced prophylaxis against opportunistic infections (p = 0.001) (S4 Table). There was no evidence that raltegravir intensification was associated with IRIS after adjusting for these factors (p = 0.63).Fatal or nonfatal events judged compatible with IRIS occurred in 89 (9.9%) raltegravir-intensified ART versus 86 (9.5%) standard ART participants . However, the differential suppression occurred between weeks 4 and 12, with overall only 15.8% less time spent with VL <50 c/mL in the standard ART group through week 24 . Therefore, benefits at a population level would likely be modest at best. However, such a strategy might have particular value in swiftly reducing VL in women identified as HIV-infected during pregnancy to reduce mother-to-child transmission .S2B Fig). Association with twice-daily dosing, rather than pill burden, is supported by the lack of difference in self-reported ART adherence between participants randomised in this trial to enhanced-prophylaxis versus standard-of-care co-trimoxazole .The full trial protocol can be accessed at (PDF)Click here for additional data file.S1 Text(DOC)Click here for additional data file.S2 Text(DOC)Click here for additional data file.S1 TableSAE, serious adverse event.(DOC)Click here for additional data file.S2 TableAE, adverse event.(DOC)Click here for additional data file.S3 TableIRIS, immune reconstitution inflammatory syndrome.(DOC)Click here for additional data file.S4 TableIRIS, immune reconstitution inflammatory syndrome.(DOC)Click here for additional data file.S5 TableCD4, cluster of differentiation 4.(DOC)Click here for additional data file.S1 Fig(TIF)Click here for additional data file.S2 FigSelf-reported percentage reporting missing doses of any ART in the last 4 weeks (a) overall and (b) by backbone NRTI and NNRTI frequency. ART, antiretroviral therapy; NNRTI, non-nucleoside reverse transcriptase inhibitor; NRTI, nucleoside reverse transcriptase inhibitor.(TIF)Click here for additional data file.S3 FigVL suppression (a) <400 copies/mL and (b) <1,000 copies/mL. VL, viral load.(TIF)Click here for additional data file.S4 Fig(TIF)Click here for additional data file.S5 FigART, antiretroviral therapy.(TIF)Click here for additional data file.S6 Fig(TIF)Click here for additional data file.S7 FigVL, viral load.(TIF)Click here for additional data file.S8 FigNNRTI, non-nucleoside reverse transcriptase inhibitor; NRTI, nucleoside reverse transcriptase inhibitor; VL, viral load.(TIF)Click here for additional data file.S9 FigVL, viral load.(TIF)Click here for additional data file.S10 FigCD4, cluster of differentiation 4.(TIF)Click here for additional data file.S11 FigChanges in body composition, (a) fat mass and (b) muscle mass.(TIF)Click here for additional data file.S12 FigChanges in (a) CD4 cell count and (b) weight in children/adolescents (5\u201317 years) versus adults (18 years or older) at ART initiation. ART, antiretroviral therapy; CD4, cluster of differentiation 4.(TIF)Click here for additional data file.S13 FigCD8, cluster of differentiation 8.(TIF)Click here for additional data file.S14 FigIRIS, immune reconstitution inflammatory syndrome.(TIF)Click here for additional data file."} +{"text": "Diet plays a crucial role in sculpting microbial communities. Similar diets appear to drive convergence of gut microbial communities between host species. Captivity usually provides an identical diet and environment to different animal species that normally have similar diets. Whether different species\u2019 microbial gut communities can be homogenized by a uniform diet in captivity remains unclear.Rhinolophus ferrumequinum, Vespertilio sinensis, and Hipposideros armiger) in captivity and in the wild using 16S rDNA sequencing. In captivity, R. ferrumequinum and V. sinensis were fed yellow mealworms, while H. armiger was fed giant mealworms to rule out the impact of an identical environment on the species\u2019 gut microbial communities.In this study, we compared gut microbial communities of three insectivorous bat species (R. ferrumequinum and V. sinensis in captivity clustered together. All microbial functions found in captive V. sinensis were shared by R. ferrumequinum. Moreover, the relative abundances of all metabolism related KEGG pathways did not significantly differ between captive R. ferrumequinum and V. sinensis; however, the relative abundance of \u201cGlycan Biosynthesis and Metabolism\u201d differed significantly between wild R. ferrumequinum and V. sinensis.We found that the microbial communities of the bat species we studied clustered by species in the wild, while the microbial communities of Our results suggest that consuming identical diets while in captivity tends to homogenize the gut microbial communities among bat species. This study further highlights the importance of diet in shaping animal gut microbiotas. Trillions of microorganisms reside in animal guts, and these microorganisms constitute the animal\u2019s gut microbiota, which is important for animal health . Ley et Wild animals in captivity are usually housed under uniform conditions that include identical diets and environments . This reRhinolophus ferrumequinum), the Asian parti-colored bat (Vespertilio sinensis) and the great Himalayan leaf-nosed bat (Hipposideros armiger) in the wild and in captivity. We then compared the bacterial communities in both the wild and captive samples between these three species. We captured bats in the wild, brought them back to the laboratory and housed them in identical environments but provided different food. Rhinolophus ferrumequinum and V.\u00a0sinensis were fed the same food , while H.\u00a0armiger were provided giant mealworms, thus forming a comparison to eliminate the impact of environment on the gut microbiome. Given that diet strongly influences microbiome composition and similar diets appear to drive convergence of gut microbial communities between host species are the second largest mammalian group . Most ba species , we predosystems . Microbiosystems . Thus, mRhinolophus ferrumequinum feeds preferentially on lepidopterans, particularly the noctuid species, which constitute approximately 41% of the bat\u2019s diet (V.\u00a0sinensis mainly comprises Lepidoptera (mean relative percentage: 32.8%), Diptera (27.5%) and Coleoptera (22.6%), but the proportion of each order varies seasonally , while the great leaf-nosed bats were fed giant mealworms (Zophobas morio) for comparison. We kept the bats for 4\u20136 months, and collected their fecal pellets less than 15\u00a0min after defecationin the laboratory. Each bat\u2019s sex, age, weight, forearm length, and reproductive condition was recorded and the Forestry Bureau of Jilin Province, China approved all study protocols.\u00aeStool DNA Kit per the manufacturer\u2019s instructions and stored at \u221220\u00a0\u00b0C for further analysis. Extracted DNA was measured using a NanoDrop NC2000 spectrophotometer and agarose gel electrophoresis to estimate DNA quantity and quality, respectively.Fifty-three fecal samples were used, including 23 from the wild bats and 30 from the captive bats. DNA was extracted from all fecal samples using the E.Z.N.A.2O. The PCR conditions consisted of initial denaturation at 98\u00a0\u00b0C for 2 min, followed by 25 denaturation cycles at 98\u00a0\u00b0C for 15 s, annealing at 55 \u00a0\u00b0C for 30 s, extension at 72\u00a0\u00b0C for 30 s, and a final extension at 72\u00a0\u00b0C for 5 min. PCR products were purified with Agencourt AMPure Beads and quantified using the PicoGreen dsDNA Assay Kit . The individual PCR products were then pooled in equal amount, and sequenced using the paired-end 2\u00a0\u00d7300 bp method on the Illumina MiSeq platform with MiSeq Reagent Kit v3 at Shanghai Personal Biotechnology Co., Ltd. . All raw sequences were deposited into the NCBI Sequence Read Archive under accession numbers SRR8238420\u2013SRR8238472.The V3-V4 region of the bacterial 16S rRNA genes were amplified via PCR using the forward primer, 338F (5\u2032-ACTCCTACGGGAGGCAGCA-3\u2032), and the reverse primer, 806R (5\u2032-GGACTACHVGGGTWTCTAAT-3\u2032) . Sample-Sequencing data were processed using the Quantitative Insights Into Microbial Ecology . Brieflyt-test and the Monte Carlo permutation test with 1,000 permutations, then visualized using box-and-whiskers plots. For UniFrac distance-based pairwise comparisons among groups, we used a very conservative Bonferroni post-hoc correction method to perform the multiple corrections and evaluate the significance of the comparison. Permutational multivariate analysis of variance (PERMANOVA) and analRMANOVA) were conRMANOVA) to assesRMANOVA) based onRMANOVA) . MicrobiRMANOVA) in the KRMANOVA) based onRMANOVA) . ResultsA total of 768,990 and 1,466,150 16S rDNA sequences were obtained from the microbiomes of the 23 wild and 30 captive bats, respectively, and the average sequence numbers per sample were 33,434 and 48,872, respectively. Rarefaction analysis demonstrated that the sequencing depth was sufficient for each sample . A totalV. sinensis and R. ferrumequinum were shared, but only 18% were shared by these two species in the wild. The proportions of OTUs shared by V. sinensis and H. armiger were approximately 39% and 12% in captivity and the wild, respectively. Minimal difference was noted between the proportions of shared OTUs in the captive and wild R. ferrumequinum and H. armiger, of which, the proportions were nearly 36% and 29%, respectively.Venn diagrams were plotted to visualize the shared and unique OTUs among three species of wild and captive bats. The captive bats we sampled shared more OTUs than did the wild bats . A totalV.\u00a0sinensis and R. ferrumequinum fed yellow mealworms) clustered together, while the gut microbial communities of H. armiger, fed giant mealworms, clustered alone. A PCoA based on unweighted UniFrac distances also demonstrated similar clustering results using NMDS based on unweighted UniFrac distances. In the wild bats, PC1, PC2 and PC3 accounted for nearly 42% of the variation, and samples were separated roughly by bat species , Table 2 samples , Table 2H. armiger were shared by the other two species, and all microbial functions in captive V. sinensis were shared by R. ferrumequinum. Thus, in terms of presence/absence, the microbial functions appeared converged in the captive bats.Finally, we predicted the microbial functions of wild and captive bats using PICRUSt, which yielded 5,971 and 4,771 KEGG pathways, respectively. Venn diagrams showed that in total 5,495 KEGG pathways were shared among the wild bat samples, and 3,964 were shared among the captive bat samples . Unlike R. ferrumequinum and V. sinensis, while the relative abundance of \u201cGlycan Biosynthesis and Metabolism\u201d differed significantly between the wild R. ferrumequinum and V. sinensis fed the same food converged markedly, while they differed from those of H. armiger fed different food. This result highlighted the importance of diet on gut microbial communities. Diet shapes the gut microbiota by providing substrates that differentially support or enhance specific microbial growth than were R. ferrumequinum and V. sinensis, and the gut microbial communities of captive H. armiger did not converge with the other two bat species. This result eliminated the impact of environment on the gut microbial communities because the three bat species were housed in identical environments in the laboratory. Further, this suggested that identical diets contribute to microbial community convergence in various bat species. However, fecal samples usually include bacteria that are ingested with the food , and distinguishing these bacteria from the host-derived bacteria in the fecal microbiome is difficult. Thus, the gut microbiota in this study did not specifically refer to the host-derived bacteria. The microbial community compositions between species fed uniform diets may have converged due to changes in the compositions of the host-associated gut microbiome or a much larger shared component of the fecal microbiome based on a completely shared diet comprising mealworms and their commensal bacteria or both. Our results highlight the need for future studies to address this issue, for example, incorporating dietary classifications via metabarcoding and classifying the microbiomes of the invertebrate prey. In addition, our results differed from those obtained by Comparing the microbial communities in fecal samples from three captive bats species showed that the microbial compositions of two bat species Wild bats (B) Captive bats. Points are means \u00b1 SE, with the numbers of bats per group shown in Click here for additional data file.10.7717/peerj.6844/supp-2Figure S2Wild (A) and captive (B) bats\u2019 fecal bacterial communities clustered using principal coordinates analysis. Each point corresponds to a fecal sample colored according to bat species with different symbols corresponding to host family .Click here for additional data file.10.7717/peerj.6844/supp-3Figure S3X-axis, pairwise comparisons among groups. Y-axis, UniFrac distances. Box borders represent upper and lower interquartile ranges. Red lines, whiskers, and \u201c+\u201d represent the median values, 1.5 times the interquartile range beyond upper and lower quartiles, and outliers respectively. Significant differences in the UniFrac distances for pairwise comparisons among groups are shown in Click here for additional data file.10.7717/peerj.6844/supp-4Figure S4V. sinensis, R. ferrumequinum and H. armiger collected from the wild respectively.WFVs, WFRf and WFHa represent fecal samples from Click here for additional data file.10.7717/peerj.6844/supp-5Figure S4V. sinensis, R. ferrumequinum and H. armiger respectively.FVs, FRf and FHa represent fecal samples from captive Click here for additional data file.10.7717/peerj.6844/supp-6Data S1Sex, age, weight, forearm length, and sample site information of each bat.Click here for additional data file.10.7717/peerj.6844/supp-7Data S2raw data of FHa1.Click here for additional data file.10.7717/peerj.6844/supp-8Data S3raw data of FHa1.Click here for additional data file.10.7717/peerj.6844/supp-9Data S4raw data of FHa2.Click here for additional data file.10.7717/peerj.6844/supp-10Data S5raw data of FHa2.Click here for additional data file.10.7717/peerj.6844/supp-11Data S6raw data of FHa3.Click here for additional data file.10.7717/peerj.6844/supp-12Data S7raw data of FHa3.Click here for additional data file.10.7717/peerj.6844/supp-13Data S8raw data of FHa4.Click here for additional data file.10.7717/peerj.6844/supp-14Data S9raw data of FHa4.Click here for additional data file.10.7717/peerj.6844/supp-15Data S10raw data of FHa5.Click here for additional data file.10.7717/peerj.6844/supp-16Data S11raw data of FHa5.Click here for additional data file.10.7717/peerj.6844/supp-17Data S12raw data of FHa6.Click here for additional data file.10.7717/peerj.6844/supp-18Data S13raw data of FHa6.Click here for additional data file.10.7717/peerj.6844/supp-19Data S14raw data of FHa7.Click here for additional data file.10.7717/peerj.6844/supp-20Data S15raw data of FHa7.Click here for additional data file.10.7717/peerj.6844/supp-21Data S16raw data of FHa8.Click here for additional data file.10.7717/peerj.6844/supp-22Data S17raw data of FHa8.Click here for additional data file.10.7717/peerj.6844/supp-23Data 18raw data of FHa9.Click here for additional data file.10.7717/peerj.6844/supp-24Data S19raw data of FHa9.Click here for additional data file.10.7717/peerj.6844/supp-25Data S20Raw data of FHa10.Click here for additional data file.10.7717/peerj.6844/supp-26Data S21Raw data of FHa10.Click here for additional data file.10.7717/peerj.6844/supp-27Data S22Raw data of FRf1.Click here for additional data file.10.7717/peerj.6844/supp-28Data S23Raw data of FRf1.Click here for additional data file.10.7717/peerj.6844/supp-29Data S24Raw data of FRf2.Click here for additional data file.10.7717/peerj.6844/supp-30Data S25Raw data of FRf2.Click here for additional data file.10.7717/peerj.6844/supp-31Data S26Raw data of FRf3.Click here for additional data file.10.7717/peerj.6844/supp-32Data S27Raw data of FRf3.Click here for additional data file.10.7717/peerj.6844/supp-33Data S28Raw data of FRf4.Click here for additional data file.10.7717/peerj.6844/supp-34Data S29Raw data of FRf4.Click here for additional data file.10.7717/peerj.6844/supp-35Data S30Raw data of FRf5.Click here for additional data file.10.7717/peerj.6844/supp-36Data S31Raw data of FRf5.Click here for additional data file.10.7717/peerj.6844/supp-37Data S32Raw data of FRf6.Click here for additional data file.10.7717/peerj.6844/supp-38Data S33Raw data of FRf6.Click here for additional data file.10.7717/peerj.6844/supp-39Data S34Raw data of FRf7.Click here for additional data file.10.7717/peerj.6844/supp-40Data S35Raw data of FRf7.Click here for additional data file.10.7717/peerj.6844/supp-41Data S36Raw data of FRf8.Click here for additional data file.10.7717/peerj.6844/supp-42Data S37Raw data of FRf8.Click here for additional data file.10.7717/peerj.6844/supp-43Data S38Raw data of FRf9.Click here for additional data file.10.7717/peerj.6844/supp-44Data S39Raw data of FRf9.Click here for additional data file.10.7717/peerj.6844/supp-45Data S40Raw data of FRf10.Click here for additional data file.10.7717/peerj.6844/supp-46Data S41Raw data of FRf10.Click here for additional data file.10.7717/peerj.6844/supp-47Data S42Raw data of FVs1.Click here for additional data file.10.7717/peerj.6844/supp-48Data S43Raw data of FVs1.Click here for additional data file.10.7717/peerj.6844/supp-49Data S44Raw data of FVs2.Click here for additional data file.10.7717/peerj.6844/supp-50Data S45Raw data of FVs2.Click here for additional data file.10.7717/peerj.6844/supp-51Data S46Raw data of FVs3.Click here for additional data file.10.7717/peerj.6844/supp-52Data S47Raw data of FVs3.Click here for additional data file.10.7717/peerj.6844/supp-53Data S48Raw data of FVs4.Click here for additional data file.10.7717/peerj.6844/supp-54Data S49Raw data of FVs4.Click here for additional data file.10.7717/peerj.6844/supp-55Data S50Raw data of FVs5.Click here for additional data file.10.7717/peerj.6844/supp-56Data S51Raw data of FVs5.Click here for additional data file.10.7717/peerj.6844/supp-57Data S52Raw data of FVs6.Click here for additional data file.10.7717/peerj.6844/supp-58Data S53Raw data of FVs6.Click here for additional data file.10.7717/peerj.6844/supp-59Data S54Raw data of FVs7.Click here for additional data file.10.7717/peerj.6844/supp-60Data S55Raw data of FVs7.Click here for additional data file.10.7717/peerj.6844/supp-61Data S56Raw data of FVs8.Click here for additional data file.10.7717/peerj.6844/supp-62Data S57Raw data of FVs8.Click here for additional data file.10.7717/peerj.6844/supp-63Data S58Raw data of FVs9.Click here for additional data file.10.7717/peerj.6844/supp-64Data S59Raw data of FVs9.Click here for additional data file.10.7717/peerj.6844/supp-65Data S60Raw data of FVs10.Click here for additional data file.10.7717/peerj.6844/supp-66Data S61Raw data of FVs10.Click here for additional data file.10.7717/peerj.6844/supp-67Data S62Raw data of WFHa1.Click here for additional data file.10.7717/peerj.6844/supp-68Data S63Raw data of WFHa1.Click here for additional data file.10.7717/peerj.6844/supp-69Data S64Raw data of WFHa2.Click here for additional data file.10.7717/peerj.6844/supp-70Data S65Raw data of WFHa2.Click here for additional data file.10.7717/peerj.6844/supp-71Data S66Raw data of WFHa3.Click here for additional data file.10.7717/peerj.6844/supp-72Data S67Raw data of WFHa3.Click here for additional data file.10.7717/peerj.6844/supp-73Data S68Raw data of WFHa4.Click here for additional data file.10.7717/peerj.6844/supp-74Data S69Raw data of WFHa4.Click here for additional data file.10.7717/peerj.6844/supp-75Data S70Raw data of WFHa7.Click here for additional data file.10.7717/peerj.6844/supp-76Data S71Raw data of WFHa7.Click here for additional data file.10.7717/peerj.6844/supp-77Data S72Raw data of WFHa8.Click here for additional data file.10.7717/peerj.6844/supp-78Data S73Raw data of WFHa8.Click here for additional data file.10.7717/peerj.6844/supp-79Data S74Raw data of WFHa9.Click here for additional data file.10.7717/peerj.6844/supp-80Data S75Raw data of WFHa9.Click here for additional data file.10.7717/peerj.6844/supp-81Data S76Raw data of WFHa10.Click here for additional data file.10.7717/peerj.6844/supp-82Data S77Raw data of WFHa10.Click here for additional data file.10.7717/peerj.6844/supp-83Data S78Raw data of WFRf1.Click here for additional data file.10.7717/peerj.6844/supp-84Data S79Raw data of WFRf1.Click here for additional data file.10.7717/peerj.6844/supp-85Data S80Raw data of WFRf14.Click here for additional data file.10.7717/peerj.6844/supp-86Data S81Raw data of WFRf14.Click here for additional data file.10.7717/peerj.6844/supp-87Data S82Raw data of WFRf24.Click here for additional data file.10.7717/peerj.6844/supp-88Data S83Raw data of WFRf24.Click here for additional data file.10.7717/peerj.6844/supp-89Data S84Raw data of WFRf25.Click here for additional data file.10.7717/peerj.6844/supp-90Data S85Raw data of WFRf25.Click here for additional data file.10.7717/peerj.6844/supp-91Data S86Raw data of WFRf26.Click here for additional data file.10.7717/peerj.6844/supp-92Data S87Raw data of WFRf26.Click here for additional data file.10.7717/peerj.6844/supp-93Data S88Raw data of WFRf27.Click here for additional data file.10.7717/peerj.6844/supp-94Data S89Raw data of WFRf27.Click here for additional data file.10.7717/peerj.6844/supp-95Data S90Raw data of WFRf28.Click here for additional data file.10.7717/peerj.6844/supp-96Data S91Raw data of WFRf28.Click here for additional data file.10.7717/peerj.6844/supp-97Data S92Raw data of WFRf29.Click here for additional data file.10.7717/peerj.6844/supp-98Data S93Raw data of WFRf29.Click here for additional data file.10.7717/peerj.6844/supp-99Data S94Raw data of WFVs1.Click here for additional data file.10.7717/peerj.6844/supp-100Data S95Raw data of WFVs1.Click here for additional data file.10.7717/peerj.6844/supp-101Data S96Raw data of WFVs3.Click here for additional data file.10.7717/peerj.6844/supp-102Data S97Raw data of WFVs3.Click here for additional data file.10.7717/peerj.6844/supp-103Data S98Raw data of WFVs4.Click here for additional data file.10.7717/peerj.6844/supp-104Data S99Raw data of WFVs4.Click here for additional data file.10.7717/peerj.6844/supp-105Data S100Raw data of WFVs6.Click here for additional data file.10.7717/peerj.6844/supp-106Data S101Raw data of WFVs6.Click here for additional data file.10.7717/peerj.6844/supp-107Data S102Raw data of WFVs7.Click here for additional data file.10.7717/peerj.6844/supp-108Data S103Raw data of WFVs7.Click here for additional data file.10.7717/peerj.6844/supp-109Data S104Raw data of WFVs8.Click here for additional data file.10.7717/peerj.6844/supp-110Data S105Raw data of WFVs8.Click here for additional data file.10.7717/peerj.6844/supp-111Data S106Raw data of WFVs10.Click here for additional data file.10.7717/peerj.6844/supp-112Data 107Raw data of WFVs10.Click here for additional data file."} +{"text": "Scientific Reports6: Article number: 2291110.1038/srep22911; published online: 03182016; updated: 08092018This Article contains typographical errors in Table 2 in the Multivariate logistic regression analysis section. The OR values for Platelet count, Glucose level, WBC count and C-reactive protein level are duplicated from their partial regression coefficients (\u03b2).The correct values should read 2.85, 1.14, 1.13, and 1.23 respectively."} +{"text": "Correction to: Arthritis Res Therhttps://doi.org/10.1186/s13075-018-1790-xFollowing publication of the original article , the autn\u00a0=\u200925) and/or MRA .The sentence should read: Angiography was performed in all c-TA patients, including conventional angiography, CTA, and/or magnet resonance angiography (MRA) as the initial diagnostic modality in 36 (35.6%), 57 (56.4%), and 9 (8.9%), respectively, while 28 (27.7%) patients experienced additional catheter-based angiography for interventional therapy after TA diagnosis by CTA (24.7%,"} +{"text": "N-arylation of azole compounds utilizing selective aryl-transfer TMP-iodonium (III) reagents . For the title compound, phenyliodonium(III) acetate (Ph(TMP)IOAc), the single-crystal X-ray diffraction measurement together with NMR analysis, like also the method of synthesis and crystallization are presented. The X-ray structure analysis has revealed that the two types of geometries regarding the acetate anion attached to phenyl (TMP)iodonium (III) cation are found in the crystal states.The data in this article are related to research article \u2018\u2018Efficient The str22.1The solvents, starting materials, and reagents were purchased from Nacalai tesque and Tokyo Chemical Industry CO. Ltd.2.2Ph(TMP)IOAc was prepared according to our reported procedure 2.31H and 13C NMR spectra were recorded on an ECS 400 NMR spectrometer at 400 MHz and 100 MHz, respectively, using CDCl3 as the solvent. The chemical shifts (\u03b4) are expressed in ppm relative to tetramethylsilane (TMS) as an internal standard. Coupling constants (J) are expressed in Hz. Signal multiplicities are represented as singlet (s), doublet (d), and triplet (t). Assignments of the proton and carbon positions in the compound were performed by PFG-HMQC and PFG-HMBC analyses.The 2.43, TMS standard. Concentration: 13 mg in 0.75 mL : \u03b4 1.95 , 3.83 , 6.12 , 7.29 , 7.41 , 7.92 . 13C NMR : \u03b4 24.6 (CH3COO), 55.7 (p-OMe), 56.5 (o-OMe), 90.9 (m-TMP), 91.0 (ipso-TMP), 119.4 (ipso-Ph), 130.3 (p-Ph), 130.8 (m-Ph), 133.8 (o-Ph), 160.6 (o-TMP), 165.7 (p-TMP), 178.8 (CH3COO).JEOL ECS 400 NMR spectrometer, solvent CDCl 0.75 mL , Fig.\u00a04.2.5The crystals were obtained at room temperature from chloroform/hexane mixture under a shading condition. Ph(TMP)IOAc was dissolved in chloroform and the insoluble material was removed by filtration. Hexane was added to the filtrate in sample bottle to reach the chloroform/hexane ratio 2/5. After standing for 1 day, the several crystals suitable for the X-ray structural analysis were obtained.2.6The single-crystal X-ray diffraction experiment was performed on the HPC diffractometer (Rigaku XtaLAB P200)). The two types of geometries for Ph(TMP)IOAc in a crystal state are shown in"} +{"text": "Metarhizium anisopliae, chitindegradation is also used to breach the host cuticle during infection. In view ofthe putative role of NAGases as virulence factors, this study explored thetranscriptional profile and evolution of putative GH20 NAGases(MaNAG1 and MaNAG2) and GH3 NAGases(MaNAG3 and MaNAG4) identified inM. anisopliae. While MaNAG2 orthologs are conserved inseveral ascomycetes, MaNAG1 clusters only with Aspergilllus sp.and entomopathogenic fungal species. By contrast, MaNAG3 and MaNAG4 werephylogenetically related with bacterial GH3 NAGases. The transcriptionalprofiles of M. anisopliae NAGase genes were evaluated in sevenculture conditions showing no common regulatory patterns, suggesting that theseenzymes may have specific roles during the Metarhizium lifecycle. Moreover, the expression of MaNAG3 andMaNAG4 regulated by chitinous substrates is the firstevidence of the involvement of putative GH3 NAGases in physiological cellprocesses in entomopathogens, indicating their potential influence on celldifferentiation during the M. anisopliae life cycle.Cell walls are involved in manifold aspects of fungi maintenance. For severalfungi, chitin synthesis, degradation and recycling are essential processesrequired for cell wall biogenesis; notably, the activity of\u03b2-N-acetylglucosaminidases (NAGases) must be present for chitin utilization. Forentomopathogenic fungi, such as Chitin is the second most abundant polymer on Earth and its recycling from carapaces,cuticles and fungal cell walls impacts on carbon and nitrogen cycles. The chitinpolymer is composed of \u03b2-1,4-linked N-acetyl-D-glucosamine (GlcNAc) subunits and its NAGases are classified into three glycoside hydrolase (GH) families, 3, 20, and 84,on the basis of their amino acid sequence similarities 2-3 substrates. This report furthersupports the existence of GH3 NAGases in other fungal species, especially inascomycetes, considering their expansion of chitinolytic machinery genes . In these species, thechitinolytic system has, probably, two main biological functions: Firstly, as chitinis the major component of fungal cell walls, chitin-degrading enzymes act on thecell wall remodeling, which is necessary for hyphal vegetative growth , are processes that require chitin degradation (A.nidulans (XP_659106) (T.atroviride (EHK40646 and EHK46127) was used as a query in the tBLASTn search (R. miehei CAU-432(AGC24356), the only fungal GH3 family member with NAGase activity to date were cultured under seven different growth conditions prior to RNAextraction: i) Cove\u2019s Complete medium (MCc) containing(w/v) 1% glucose, 0.6% NaNO3, 0.15% casein hydrolisate, 0.05% yeastextract, 0.2% peptone, pH 7.0 plus 2% (v/v) salts solution and 0.04% (v/v) Trace Elements Solution (ii) 0.25% GlcNAc in minimum mediumcomposed of 0.6% NaNO3 (w/v) plus 0.25% GlcNAc) (w/v) as carbohydratesource, with salts and trace element solutions (iii) 1%Chitin in minimum medium composed of 0.6% NaNO3 (w/v)plus 1% crystalline chitin from crab shells as a carbohydrate source, with saltsand trace element solutions for 72 h at 28 \u00b0C, then washedwith sterile distilled water and filtered through Miracloth andfrozen in liquid nitrogen for total RNA extraction; iv)Autolysis: medium for mycelium autolysis induction (1% glucose(w/v) and 0.6% NaNO3 (w/v), sustained for 9 days) (v) Sporulation: on MCc agar plates for conidia RNAextraction; vi) Blastospores: Inoculation of5104 conidia/mL on ADAMEK medium for blastospore production , shaking for 64 h at28 \u00baC (vii)Appressoriuminduction medium: 5105 conidia/mL wasinoculated in 0.004% yeast extract solution on 500 glass coverslips for 16 h at28 \u00baC .at28 \u00baC ; vii)ApM. anisopliae cells harvested underall seven different growth conditions was performed in triplicate. Samples wereground using a mortar and pestle in liquid nitrogen, prior to standard RNAextraction using Trizol Reagent .Residual DNA was removed with DNase . Thereafter,extracted RNAs were passed through RNeasy Cleanup columns . RNA samples were quantified using a Qubit fluorometer , and stored at -80 \u00b0C. One microgram oftotal RNA was used for cDNA synthesis using MMLV-RT enzyme . All procedures were performed according to themanufacturer\u2019s instructions.Total RNA extraction from Polymerase chain reactions were carried out on ABI-7500 Real-Time PCR System. Platinum SYBR Green qPCRSuperMix-UDG was used to monitordsDNA synthesis. Each biological sample was analyzed in technical triplicates;no-template and no-reverse transcriptase controls were included.TableS1). Five housekeeping genes were evaluated:act (\u03b3-actin), gapdh , tef1-\u03b1 (translation elongationfactor 1-\u03b1), trp1 (tryptophan biosynthesis enzyme), andtub (\u03b1-tubulin). The efficiency of each reference geneacross samples was analyzed using geNorm version 3.5 .Primers for qPCR assays were designed using VECTOR NTI software (-DDCt method (p < 0.05) were performed to determine statisticaldifferences among 2-DDCt values of the seven experimentalconditions.Melting curves from each qPCR reaction were analyzed to confirm specificity ofthe synthesized products and absence of primer dimers. Relative transcriptexpressions were analyzed by Cq (quantification cycle) values, applying the2t method . ResultsM. anisopliae genome, usingNagA from A. nidulans and NAG1 and NAG2 from T.atroviride as queries, resulted in the identification of twoputative GH20 NAGases, named MaNAG1 and MaNAG2 . All otherfungal GH20 NAGase sequences and GH20 conserved domain sequences used as queriesresulted in alignments with the same two previously detected contigs. Therefore,MaNAG1 and MaNAG2 are most probably the only M. anisopliaeputative GH20 NAGases. The GH20 family domain (IPR015883) and the conservedmotif of GH20 proteins (H/N-x-G-A/C/G/M-D-E-A/I/L/V) were found in both MaNAG1and MaNAG2 sequences . Additionally, the putative GH20 NAGasesalso exhibited a chitobiase/beta-hexosaminidase N-terminal domain (IPR029018)(The survey of NAGase genes of the R029018).M. anisopliae genome allowed theidentification of seven positive matches. However, phylogenetic analysis clearlyrevealed that only two sequences, named MaNAG3 and MaNAG4 could be putative GH3 NAGases.Furthermore, these sequences exhibit higher similarity with bacterial GH3NAGases and the RmNag GH3 . MaNAG3 and MaNAG4 share a conserveddomain with GH3 family members (IPR001764) and exhibit the conserved sequencemotif of GH3 proteins (K-H-F/I-P-G-H/L-G-x-x-x-x-D-S/T-H). Furthermore, MaNAG3 and MaNAG4sequences present a conserved GH3 C-terminal domain (IPR002772) , raising the possibility of functionalequivalence.The GH3 domain screening of the R002772) . The othM. anisopliae putative NAGasesare listed in A.nidulans NagA (68 kDa) (T. atrovirideNag1 (73 kDa) (T. harzianum P1 Nag1 (72 kDa) , containingthe highest expected number of introns (4) and theoretical molecular mass (98.71kDa), with N-glycosylation translational modification signals on six sites. Incontrast, MaNAG4 ORF size is 2,057 bp, the theoretical molecular mass is 60.67kDa and the pI of predicted mature protein is 5.6. The predicted molecular massof MaNAG4 is similar to most known bacterial GH3 NAGases, as S.thermoviolaceus NagA (60 kDa) , were recognizedin all of GH20 orthologs .Twenty-six MaNAG1 and MaNAG2 orthologs were identified in 15 filamentous fungigenomes. Most of them are single copy of each putative GH20 NAGase of M. anisopliae and the other fifteen ascomycetes revealed anearly duplication event in GH20 NAGases, resulting in two distinct main clades. This cluster also formed a statistically supported cladewith species from the Aspergillus genus. In contrast, MaNAG2exhibits a more diverse evolutionary history, with orthologs present inTrichoderma sp., Fusariumsp, Neurospora sp., and Magnaporthe sp.Interestingly, the present evolutionary analysis revealed that both NAG1 andNAG2 from the mycoparasite T. atroviride, used in theM. anisopliae genome screening, are evolutionarily morerelated to MaNAG2 . All 15 filamentous fungi have MaNAG3orthologs. However, the M. acridum gene ortholog was notincluded in the phylogenetic analysis, since it was not properly annotated inthe M. acridum genome. In turn, onlyTrichoderma sp., Aspergillus sp., and theentomopathogens C. militaris and B. bassianahave MaNAG4 orthologs.Twenty-three MaNAG3 and MaNAG4 orthologs were identified on the filamentous fungigenomes examined. Conserved sequence motifs of GH3 proteins (K-H-F / I-P-G-H /L-G-x-x-x-x-D-S / T-H) were found in all of them, however, few amino acidresidues substitutions were observed . Additionally, geneduplication of MaNAG3 and MaNAG4 orthologs was not observed.The phylogenetic tree revealed that MaNAG3 and MaNAG4 orthologs formed twodistinct clusters . Both MaS. thermoviolaceus NagA, Clostridiumparaputrificum NagZ, Alteronomonas sp. HexA,V. furnissii NagZ, Thermotoga maritma NagAand T. neapolitana CbsA) grouped into distinct clades fromfungal NAGases. This is probably due to the fact that some bacterial NAGases donot necessarily have GlcNAc hydrolysis specificity over chitooligosaccharides.For example, E. coli NagZ cleaves GlcNAc from muropeptidespresent in the bacterial cell wall and GH3 family (MaNAG3 andMaNAG4) of M. anisopliae genome wereanalyzed.Virulence determinants are the main focus in the study of entomopathogenic fungi. As chitM. anisopliae by gel-filtration,with a pI of 6.4 and molecular mass of 110-120 kDa. We hypothesize that thisM. anisopliae purified enzyme could be the MaNAG1 presentedhere, based on the predicted pI (6.07) and molecular mass (66.98 kDa) of MaNAG1,likely forming a homodimer. In fact, some fungal GH20 NAGases clustered together with characterized \u03b2-glucosidases, again suggesting thepossibility of similar function would repressexpression of chitinolytic enzymes by their own activity products in M.anisopliae (catabolic repression) in T.reesei, the product of which, an MaNAG3 ortholog, holds suggestedNAGase activity. The phylogenetic analyses indicate that MaNAG3 and T.reesei NAG3 are phylogenetically related exhibits 63%identity with characterized GH84 from Penicillium chrysogenum(XP_002557703.1). The P. chrysogenum GH84 NAGase not only exhibitactivity against GlcNAc substrates, but also hydrolyzes substrates withgalacto-configuration and exhibits transglycosylation activity(Our results are in agreement to previous suggestions of the presence of GH3 NAGasesin fungi (RmNag) ( related . The exiM. anisopliae and entomopathogenic fungi. Thisanalysis will allow the selection of genes for further functional characterizationto elucidate the process and to identify redundancies and specificities. The viewthat chitinase diversity is merely redundant may not correct (M. anispoliae putative GH20 NAGase genesrevealed induced transcript production in the presence of chitin, potentially in theextracellular milieu. The detection of MaNAG3 andMaNAG4 putative genes is the first evidence for the presence ofa possible GH3 family of NAGases in entomopathogenic fungi. MaNAG3and MaNAG4 expression is responsive to chitinous substrates,suggesting their potential influence on cell differentiation during the M.anisopliae life cycle.In conclusion, this study explored relevant evolutionary aspects of putative GH3 andGH20 NAGase genes and the expression analysis highlighted possible functions forthese genes in"} +{"text": "Scientific Reports 10.1038/s41598-018-26198-7, published online 18 May 2018Correction to: The Acknowledgements section in this Article is incomplete.\u201cWe thank Sara Olenich, Kayley Abell-Hart and Thanh Von for technical assistance. This study was funded by the Osher Foundation, and in part by NCCIH RO1 AT009267.\u201dshould read:\u201cWe thank Sara Olenich, Kayley Abell-Hart and Thanh Von for technical assistance. This study was supported by the Osher Foundation (H.M.L.), NCCIH RO1 AT009267 (H.M.L.), Susan G. Komen Foundation PDF16376814 (J.B.), National Institutes of Health (NIH) R35 CA210057 (J.J.Z.) and Breast Cancer Research Foundation (J.J.Z.).\u201d"} +{"text": "Serratia marcescens is a ubiquitous Gram-negative opportunistic pathogen. This announcement describes the isolation and genome annotation of S. marcescens T5-like siphophage Slocum. Terminal repeats, 170 protein-coding genes, and 23 tRNAs were predicted in the 112,436-bp Slocum genome. Serratia marcescens is a ubiquitous Gram-negative opportunistic pathogen. This announcement describes the isolation and genome annotation of S. marcescens T5-like siphophage Slocum. Terminal repeats, 170 protein-coding genes, and 23 tRNAs were predicted in the 112,436-bp Slocum genome. Serratia marcescens is a Gram-negative bacillus that is ubiquitous throughout nature and is a member of the family Enterobacteriaceae , was cultured aerobically at 30\u00b0C and 37\u00b0C in LB (BD), and phages were propagated via the soft-agar overlay method (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). After trimming was performed using the FastX Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit), the raw Slocum contig was assembled using SPAdes v3.5.0, with default parameters, to 409.3-fold coverage (Bacteriophage Slocum originated from filtered (0.2-\u03bcm filter) municipal wastewater in Bryan, Texas. The host, y method . After py method . Phage gy method , and theoverage 810. Rho-ioverage 8. Functiooverage 8\u201315. Addiverage 8\u2013. Structuverage 8\u2013. The genverage 8\u2013. All lisaxy-pub) , 21. UnlEscherichia phage T5 (GenBank accession no. NC_005859) and T5-like Escherichia phage slur09 (GenBank accession no. LN887948), with 27 to 29% nucleotide identity to slur09 and several Salmonella phages, fragmented across the genome.The phage Slocum genome consists of 112,436 bp of double-stranded DNA, with a G+C content of 44.8%. With 170 predicted protein-coding genes and 23 predicted tRNA genes, the genome protein coding density is 88%. Additionally, 12,521-bp predicted direct terminal repeats were used as the boundary for genome reopening. At the amino acid level, phage Slocum shares 81 similar proteins with MN095770, BioProject accession no. PRJNA222858, SRA accession no. SRR8892204, and BioSample accession no. SAMN11411459.The genome sequence and associated data for phage Slocum were deposited under GenBank accession no."} +{"text": "Gemcitabine/nab-paclitaxel and FOLFIRINOX demonstrated significantly increased survival compared with gemcitabine in metastatic pancreatic ductal adenocarcinoma (PDAC): objective response rate (ORR) 23 and 31.6%, progression-free survival (PFS) 5.5 and 6.4 months, overall survival (OS) 8.7 and 11.1 months. Present phase II study evaluated recommended first-line triplet FIr/FOx schedule.010%, p130%, power 80%, \u03b15%, \u03b220%. Projected ORR: I step, 1/10; II 5/29. Schedule: 12h-timed-flat-infusion/5-fluorouracil 750-800-900 mg/m2 d1-2,8-9,15-16,22-23; irinotecan 120-140-160 mg/m2 d1,15; oxaliplatin 70-80 mg/m2 d8,22; every 4 weeks, according to clinical parameters , liver function). Activity and efficacy were evaluated, and compared using log-rank; limiting toxicity syndromes (LTS), using chi-square.Simon two-step design: pP 0.022).Twenty-nine consecutive patients were enrolled, according to primary/intermediate/secondary Cumulative Illness Rating Scale (CIRS). Median age 62; elderly 13 (44.7%); PS2 3 (10.4%), secondary CIRS 5 (17.2%). Primary endpoint was met: ORR 53% (7/13 patients) as-treated, 50% intent-to-treat. Cumulative G3-4 toxicities: diarrhea 17%, asthenia 14%, hypertransaminasemy 7%, mucositis 7%, vomiting 3%, anemia 3%, thrombocytopenia 3%. LTS were 27.5% overall, 38.4% in elderly. At 3 months median follow-up, PFS 4 months, OS 11 months. PS2 patients showed significantly worse OS (Intensive first-line triplet FIr/FOx is tolerable at modulated doses, and confirms high activity/efficacy in metastatic PDAC. Patients\u2019 careful selection, and exclusion of PS2, can maintain safety profile and efficient dose intensity. Fixed-dose rate gemcitabine (10 mg/m2/minute) maximized intracellular concentrations of the phosphorylated active forms of gemcitabine, and may substitute standard infusion over 30 minutes [Metastatic pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with approximately 6 months median overall survival (OS) \u20133. In th minutes , 5.BRCA 2 or PALB mutations).Even if phase III studies proposing gemcitabine-based associations failed to improve OS \u201316, exceThe association of nab-paclitaxel to gemcitabine reported highest clinical benefit in patients with PDAC, and significantly raised up OS 8.7 months, PFS 5.5 months, and ORR 23%, compared with gemcitabine alone , 23. IntThe most relevant issue limiting the feasibility of addition of more drugs in a chemotherapy combination is the proper design of the schedule assuring the balance between tolerability for individual patients and effective received dose intensity (DI) of each drug in order to obtain the expected efficacy of the combination. Intensive regimens based on triplet chemotherapy in MCRC, and FOLFIRINOX regimen in metastatic PDAC, frequently required proper clinical management of toxicity and treatment modulations due to moderate/severe toxicities , 25.PM to 10AM) timed-flat-infusion (TFI) 5-FU (TFI/5-FU), without leucovorin, associated to irinotecan (CPT-11) and OXP, according to a weekly alternating schedule, also added to bevacizumab [Over the last 10 years, we developed triplet chemotherapy regimen according to FIr/FOx schedule, characterized by 12-hour , lung 2 (6.8%), lymph nodes 22 (75.8%), local recurrence 2 (6.8%), cutaneous/subcutaneous tissue 1 (3.4%), peritoneal carcinomatosis 12 (41.3%), bone 2 (6.8%). Metastatic site was single in 2 patients (6.8%), multiple in 27 (93.1%). Single metastatic sites: lymph nodes 2 patients (6.8%). Liver metastases were single in 1 patient (3.4%), multiple in 17 (58.6%).Five patients underwent surgery of primary pancreatic tumor. One patient received adjuvant gemcitabine, 1 patient underwent radiotherapy associated with capecitabine.Baseline CA19.9 measurement was normal in 3 patients, elevated in 26.In the first step, according to two-steps Simon\u2019s design , assuminThe phase II study was performed among the projected 29 patients. In the intent-to-treat analysis, 14 patients were evaluable, 13 patients did not received at least 3 cycles of treatments, and 2 patients were on-treatment at data cut-off. OR were 7 out of 14 patients, ORR 50% ; PFS was not significantly different (P = 0.078) , even if OS was trendy worse in patients with other than head pancreatic tumor location , even if OS was trendy worse in patients with liver metastases , median OS 11 months (0-33); among 12 patients with other than head pancreatic tumor locations, median PFS was 2 months (0-21), median OS 3 months (0-25). PFS and OS were not significantly different (Ten patients (34.4%) received, at least, a second line treatment: FIr/FOx re-challenge in 1 patient (3.4%); gemcitabine/nab-paclitaxel association in 8 patients (27.5%); intra-arterial chemotherapy in 1 patient (3.4%). Two patients (6.8%) received a third line treatment: gemcitabine in 1 patient (3.4%); capecitabine in 1 patient (3.4%).All evaluable patients with an increased Ca19.9 baseline value had a >20% decrease: 58% \u226550% decrease, 42% \u226570% and 90% decrease. CA19-9 levels were not significantly correlated with PFS and OS.Median number of administered cycles was 2 (range 1-11).2/w, 70.4% of projected-DI (pDI); CPT-11 56 (30-80) mg/m2/w, 70%; OXP 29 (11-40) mg/m2/w, 72.5% mg/m2/w, 79%; OXP 33.5 (0-40) mg/m2/w, 83.75%. In yE patients, median rDIs per cycle were: 5-FU 1500 (375-1800) mg/m2/w, 83.3% of pDI; CPT-11 64 (30-80) mg/m2/w, 80%; OXP 34 (11-40) mg/m2/w, 85%.Median received dose intensities (rDI) per cycle were: 5-FU 1268.5 375-1800) mg/m75-1800 mTable Overall, LTS were observed in 8 patients 27.5%) , and OS 11 months , in the preliminary analysis of efficacy. Activity and clinical outcome of FIr/FOx exceeded that reported with gemcitabine: median OS 5.7 months, and 1-year OS rate 20%, median PFS 2.08 months, ORR 5.4% .P < 0.001) [Recently, phase III trials evaluating more intensive first-line chemotherapy regimen, such as gemcitabine plus nab-paclitaxel and triplet FOLFIRINOX, demonstrated to be much more, and equivalently effective, with significantly increased survival benefit over standard gemcitabine alone in metastatic PDAC patients : ORR 23%< 0.001) . OS rate< 0.001) , 27.Our present real life study on consecutive, unselected patients showed that 13 patients (44.8%) were not evaluable in the ITT analysis because they did not received at least 3 cycles of treatment, thus confiming that, even today, the primary challenge of clinical management of metastatic PDAC patients is to start and safely perform at least 3 cycles of intensive chemotherapy treatment, to evaluate activity contributing to increase clinical outcome.P = 0.022), thus confirming overall benefit in clinical outcome achieved by metastatic PDAC patients with PS 0-1, treated with gemcitabine-based combinations [Among patients treated with intensive triplet FIr/FOx regimen, PFS and OS were not significantly different among patients treated with modulated and standard drug dosage, due to clinical parameters requiring treatment modulations. PS 2 significantly affected worse OS , the safety profile was less favourable than that reported in the gemcitabine arm [Median rDIs were >80% of the projected dose for each drug, also in elderly patients. Cumulative G3-5 toxicities were prevalently represented by: diarrhea (17%), stomatitis/mucositis (6%), asthenia (14%), nausea (3%), vomiting (3%), hypoalbuminemia (3%), hypokalaemia (7%), hypertransaminasemia (7%), hyperbilirubinemia (3%), hypercreatininemia (3%), anemia (3%), neutropenia (17%), thrombocytopenia (3%). In the previously reported phase II trial proposing intensive first-line triplet chemotherapy plus bevacizumab according to FIr-B/FOx regimen, as first-line treatment in MCRC patients, cumulative G3-4 toxicities were similar: diarrhea (28%), stomatitis/mucositis (6%), asthenia (6%), hypertension (2%), hypertransaminasemy (4%), neutropenia (10%). Triplet FIr/FOx, even associated to bevacizumab, determined only 10% G3-4 neutropenia, while FOLFOXIRI schedule, added or not to bevacizumab , 27, prebine arm . More ad2 plus nab-paclitaxel 125 mg/m2 association, 3 out of 4 weeks [In the phase III trial, gemcitabine 1000 mg/m 4 weeks , prevale 4 weeks .In the present study, LTS were observed in 27.5% of individual patients and in 38.4% of elderly patients treated with FIr/FOx regimen. The innovative clinical evaluation of LTS, consisting of at least the LT associated or not to other G2 or LT, introduced to better evaluate, in the individual patient, the presence of LT alone, LTS-ss, or the association of major toxicities in different sites, LTS-ms, showed that: overall, they were 3.4% and 24.1%, respectively; among elderly patients, they were all LTS-ms 38.4%. LTS were not significantly represented by LTS-ms compared to LTS-ss, even if the small number of enrolled patients requires further analyses. LTS-ms were mostly represented by diarrhea, mucositis, asthenia, neurotoxicity, thrombocytopenia and/or anemia, associated to nausea, vomiting, anorexia and/or neutropenia, hypokaliemia, hypoalbuminemia, hypertransaminasemia. In the individual patient, limiting and moderate toxicities often characterized LTS, previously observed in 44% MCRC patients treated with FIr-B/FOx, and equally involving single or multiple sites .DPYD, UGT1A1, ABCB1, CYP3A4, specifically influencing fluoropyrimidines and CPT-11-related adverse events, justifying inter-patients variability in safety profile, may help selection of patients fit for triplet chemotherapy, and may predict the occurrence of individual LTS, prevalently gastrointestinal [Pharmacogenomic analysis evaluating 5-FU degradation rate (FUDR) and/or detection of a panel of DNA Single Nucleotide Polimorphisms (SNPs) involving different genes, such as testinal , 41, 42.Reported data confirmed that intensive regimens, such as FIr/FOx, frequently required proper clinical management of toxicity and treatment modulations due to moderate/severe toxicities. Careful selection of eligible patients, based on age, PS, comorbidity index, and monitoring of individual safety, also according to LTS in individual patients, are major parameters to optimize clinical management of metastatic PDAC. More, close monitoring of patients, expertise with a particular regimen, and toxicity management, remained the physician-related factors, that can guide personalized selection of first-line regimens in individual PDAC patients.Patients were eligible if they had clinical and/or histological/cytological confirmed diagnosis of measurable metastatic PDAC; age \u226518 years, specifically <65 years (non-elderly), \u226565 <75 years (yE), and \u226575 years (oE); WHO PS \u2264 2; adequate hematological, renal and hepatic functions; life expectancy more than 3 months.Ineligibility criteria: pregnancy and breast-feeding; uncontrolled severe diseases; cardiovascular disease ; thromboembolic disease, coagulopathy, pre-existing bleeding diatheses; sensory and/or motor polineuropathy; surgery within the previous 28 days; previous adjuvant chemotherapy or radiotherapy completed less than 6 months before. CIRS was used to evaluate the comorbidity status . Primaryin label for metastatic PDAC treatment in Italian public hospitals, and published in Gazzetta Ufficiale Repubblica Italiana . The study was approved by the Regional Review Board , and conducted in accordance with the Declaration of Helsinki. All patients provided written, informed consent.Treatment was approved by Agenzia Italiana del Farmaco (AIFA) for administration This was a single-arm phase II study evaluating safety and activity of weekly alternating 5-FU, CPT-11, and OXP (FIr/FOx) as first-line treatment of metastatic PDAC.2/die, over 12-hour (from 10:00 p.m to 10:00 a.m.), days 1-2, 8-9, 15-16 and 22-23; CPT-11 , 120-140-160 mg/m2, administered over 90 minutes as an intravenous infusion in 250 ml of NaCl 0.9%, days 1 and 15; OXP over 2-hours as an intravenous infusion in 250 ml of dextrose 5%, at the dose of 70-80 mg/m2, days 8 and 22. Cycles were repeated every 4 weeks. 5-FU was administered by a portable pump using a venous access device. According to patients\u2019 fitness, and particularly in patients with PS 2, and/or \u226575 years, secondary CIRS stage, and/or abnormal liver functional laboratory tests, such as \u2265 G2 hypertransaminasemia at baseline, drugs\u2019 doses were modulated in individual patients as reported, providing a received DI >75% for each drug, reported as active and efficacious in previous studies of triplet chemotherapy regimens [FIr/FOx association consisted of 5-FU associated to alternating CPT-11 or OXP according to the following weekly schedule: TFI/5-FU , 750-800-900 mg/mregimens , 26\u201331.Physical examination and routine laboratory studies were performed at baseline and every week on-treatment, including complete blood cell count, electrolytes, liver and renal function tests, urine examination and coagulation function; tumor markers every cycle; electrocardiogram every cycle, and echocardiogram at baseline, and every 3 cycles.Primary end-point was ORR; secondary end-points were toxicity, PFS, OS. ORR was evaluated according to RECIST criteria ; PFS andLTS, consisting of at least a LT associated or not to other limiting or G2 toxicities, were evaluated as previously reported , 32. TheCorrelations between maximum decrease from baseline in CA19.9 level and PFS and OS were analyzed, to assess possible relationships between CA19.9 and clinical outcomes.0 was considered as the estimated activity reported with gemcitabine alone (median ORR 10%), and confirmed with the association of gemcitabine plus erlotinib (ORR 8.6%) [1 as the projected ORR using the present intensive triplet combination, according to FIr/FOx schedule, increasing the activity \u2265 20% in metastatic PDAC patients, as reported with FOLFIRINOX (ORR 31.6%), and with the association of gemcitabine and nab-paclitaxel in the phase I/II trial [This phase II study was planned according to two-steps Simon\u2019s design : assuminRR 8.6%) , 16; p1 I trial) \u201324.FIr/FOx intensive triplet chemotherapy in metastatic PDAC patients preliminary showed high activity. Present schedule was feasible in non-elderly and elderly patients, with PS 0-1, with manageable toxicities, at proper CPT-11, OXP, and 5-FU doses. LTS were prevalently characterized by diarrhea, mucositis, asthenia, anemia, neurotoxicity and/or thrombocytopenia, associated to nausea, vomiting, anorexia and/or neutropenia. Elderly patients preliminary showed trendy, but not significantly worse OS. Adequate selection of suitable patients, based on clinical parameters, aimed to maintain safety profile at efficacious DIs, will verify if more intensive approaches, such as triplet chemotherapy regimen could increase OS, compared to historical gemcitabine control, in the clinical practice management of metastatic PDAC patients, and if it could be a treatment option in locally advanced/borderline resectable pancreatic cancer patients."} +{"text": "Also, the data include the bond lengths and angles of [Ln2(IMBA)6(dmp)2] .In this data article, we present the FT-IR and PXRD data of the lanthanide complexes constructed by 4-iodo-3-methylbenzoic acid (IMBA) and 4,7-dimethyl-1,10-phenanthroline (dmp). Detailed structure analysis, luminescence and sensing properties were discussed in our previous study, \u201cHighly Luminescent Lanthanide Complexes as Bifunctional Sensor for Et Specifications tableValue of the data\u2022This structure information would be valuable for FT-IR analysis of lanthanide complexes.\u2022This data would be worthy for further investigation of the PXRD properties.\u2022This data provide a new process to synthesize two ligands coordinated lanthanide complexes.1[Ln2(IMBA)6(dmp)2] , are isostructural. They crystallize in triclinic space group P-1 (no. 2). These complexes are dinuclear cluster structures which contain two lanthanide ions , six deprotonated IMBA and two dmp, forming an electroneutral unit (1a that incubation in aqueous solution for as long as the sensing time (1\u202fh) was in line with the as-synthesized sample and calculated data, confirming that the sensor 1a is a highly stable 6(dmp)2]\u00b7(1a). Yield: 37% based on Eu3+. Anal. Calcd (%): C, 39.92; H, 2.645. Found (%): C, 40.13; H, 2.633. FT-IR (\u22121): 3450 (m), 2947 (w), 1620 (s), 1584 (w), 1438 (s), 1403 (m), 1305 (m), 1193 (w), 1033 (m), 934 (w), 872 (m), 789 (s), 747 (w), 550 (w), 482 (w).[Eu3. FT-IR (KBr pel2(IMBA)6(dmp)2] (1b). Yield: 34% based on Gd3+. Anal. Calcd (%): C, 39.74; H, 2.633. Found (%): C, 39.61; H, 2.618. FT-IR (\u22121): 3435 (m), 2995 (w), 1648 (w), 1592 (s), 1542 (m), 1495 (w), 1438 (s), 1305 (m), 1152 (w), 1033 (s), 943 (m), 872 (s), 789 (s), 739 (m), 600 (w), 550 (w), 488 (m).[Gd8. FT-IR (KBr pel2(IMBA)6(dmp)2] (1c). Yield: 35% based on Tb3+. Anal. Calcd (%): C, 39.68; H, 2.629. Found (%): C, 39.79; H, 2.637. FT-IR (\u22121): 3443 (m), 2980 (w), 1627 (w), 1592 (s), 1542 (m), 1494 (w), 1430 (s), 1312 (w), 1152 (w), 1033 (s), 934 (w), 872 (m), 824 (m), 789 (s), 739 (w), 550 (w), 488(w).[Tb7. FT-IR 3\u00b76H2O , dmp and IMBA at a molar ratio of 1:1:1.5 at 333\u2009K for 120\u2009h. The colorless block single crystals of 1a\u20131c were collected by filtration, and mounted on a glass fiber Lanthanide complexes Single crystal X-ray diffraction data were obtained on an instrument of Bruker SMART 1000 CCD, at wavelength of 0.71073\u2009\u00c5 (Mo-Ka radiation) at 25\u2009\u00b0C. The structures were refined by full-matrix least-squares methods with SHELXL-97 module. Phase purity of bulk samples were tested by PXRD, on a DMAX2200VPC diffractometer"} +{"text": "Oribacterium sp. strain C9, isolated from the rumen of a steer grazing on Rhodes grass in Rockhampton, Queensland, Australia.We report the 3.7-Mb genome sequence of Oribacterium sp. strain C9, isolated from the rumen of a steer grazing on Rhodes grass in Rockhampton, Queensland, Australia. This draft genome consists of 3,720,024\u2009bp with a 42.8% G+C content, 3,130 predicted coding DNA sequences (CDSs), and 67 RNAs.We report the 3.7-Mb genome sequence of Oribacterium was first proposed by Jean-Philippe Carlier in Australia , using an anaerobic in vitro culture with 0.8% yeast extract. DNA sequencing was performed at Macrogen (South Korea) on a HiSeq 2500 instrument (2 \u00d7 100-bp paired-end sequencing) to produce 58,649,712 total reads with 15\u00d7 coverage. Raw reads were trimmed with Trimmomatic version 0.32 version 4 (https://www.ncbi.nlm.nih.gov/genome/annotation_prok) . The average nucleotide identity (ANI) was calculated using the algorithm described by Yoon et al. (Oribacterium sp. strains P6A1 (GenBank accession number JNKO00000000), WCC10 (FOPH00000000), NK2B42 (AUJX00000000), FC2011 (JNJM00000000), and KHPX15 (FNRG00000000) (from the Hungate1000 project [O. parvum strain ACB1T (AFZC00000000), and O. sinus F0268 (ACKX00000000), respectively.The 16S rRNA gene sequence was found to be 95% identical to that of in ACB1T and Oribn et al. with theOribacterium sp. strains P6A1, WCC10, NK2B42, FC2011, and KHPX15, O. sinus F0268, and O. parvum strain ACB1T are 28.4%, 24.9%, 24.4%, 24%, 24.1%, 21.1%, and 26.1%, respectively. Having both ANI values lower than 95% and dDDH values lower than 70% indicated that isolated strain C9 is a species distinct from the other isolates.The digital DNA-DNA hybridization (dDDH) was determined using the Genome-to-Genome Distance Calculator (GGDC) version 2.1 with default settings . The esthttp://www.cazy.org/) (http://csbl.bmb.uga.edu/dbCAN/) (zy.org/) and dbCA/dbCAN/) , we idenOribacterium sp. strain C9 has been deposited in DDBJ/EMBL/GenBank under the accession number MUHW00000000, BioProject number PRJNA362832, and BioSample number SAMN06249574. The genomic raw sequencing reads are available in the Sequence Read Archive (SRA) database under accession number SRR8449972.The draft genome sequence for"} +{"text": "Peptide nucleic acids (PNAs) are very useful tools for gene regulation at different levels, but in particular in the last years their use for targeting microRNA (anti-miR PNAs) has provided impressive advancements. In this respect, microRNAs related to the repression of cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is defective in cystic fibrosis, are of great importance in the development of new type of treatments. In this paper we propose the use of an anti-miR PNA for targeting miR-145, a microRNA reported to suppress CFTR expression. Octaarginine-anti-miR PNA conjugates were delivered to Calu-3 cells, exerting sequence dependent targeting of miR-145-5p. This allowed to enhance expression of the miR-145 regulated CFTR gene, analyzed at mRNA and CFTR protein (Western blotting) level. MicroRNAs are from 19 to 25 nucleotide-long noncoding RNAs that regulate gene expression by targeting mRNAs, leading to a translational repression or mRNA degradation ,4. SinceEpigenetic regulation of expression of cystic fibrosis transmembrane conductance regulator (CFTR) gene by miRNAs has been recently explored by different groups in cystic fibrosis (CF) primary bronchial epithelial cells in vitro or from bronchial brushings ex vivo. Expression of miR-145 and miR-494 was found anti-regulated with that of CFTR . The effPeptide nucleic acids (PNAs) are DNA analogues of outstanding properties ,13,14, sThe objective of this study was to design a PNA targeting miR-145, determine its activity in inhibiting miR-145, and verify whether it induces an increase of CFTR production. The PNA was conjugated to a poly-arginine tail, since this type of constructs was previously used by our group for the delivery of PNA into cell lines ,25,26. AIn Homo sapiens (H. sapiens), Pan troglodytes (Chimp), Macaca Mulatta (Rhesus), Saimiri sciureus (Squirrel), Mus musculus (Mouse), Rattus norvegicus (Rat), Oryctolagus cuniculus (Rabbit), Sus scrofa (Pig), Bos taurus (Cow), Felis catus (Cat), Canis lupus familiaris (Dog), Myotis lucifugus (Brown bat) and Loxodonta africana (Elephant). In red the differences with respect to the Homo sapiens sequence are underlined. The CFTR sequence complementary to miR-145-5p seed region is boxed. The region showing the highest level of homology (reaching 100% homology in some positions) belongs to the seed-complementary stretch, as also shown in 8) peptide was conjugated at N-terminus of the PNA chain since it induces an efficiency in the delivery which approaches 100% , as elsewhere published 4+, 1255.97 (1256.07) [MH5]5+, 1046.81 (1046.9) [MH6]6+, 897.41 (897.48) [MH7]7+, 785.36 (785.42) [MH8]8+, 698.21 (698.26) [MH9]9+.R8-PNA-a145-MUT: sequence H-R8-AGAGATGCCTTGGAGAAC-Gly-NH2; Rt = 10.23 min, HRMS: calculated MW: 6272.4698 g/mol; m/z found : 1569.70 (1569.84) [MH4]4+, 1255.97 (1256.07) [MH5]5+, 1046.81 (1046.9) [MH6]6+, 897.41 (897.48) [MH7]7+, 785.36 (785.42) [MH8]8+, 698.21 (698.26) [MH9]9+.R8-PNA-a509: sequence H-R8-CTACCCACAGACGTACCA-Gly-NH2; Rt = 11.17 min, HRMS: calculated MW: 6097.4456 g/mol; m/z found : 1525.95 (1526.07) [MH4]4+, 1220.96 (1221.06) [MH5]5+, 1017.64 (1017.71) [MH6]6+, 872.40 (872.47) [MH7]7+, 763.48 (763.54) [MH8]8+, 678.76 (678.81) [MH9]9+, 610.98 (611.03) [MH10]10+R8-PNA-a494: sequence H-R8-TTTCCCGTGTATGTTTCA-Gly-NH2; Rt = 12.30 min, HRMS: calculated MW: 6146.4044 g/mol; m/z found : 1538.19 (1538.32) [MH4]4+, 1230.75 (1230.86) [MH5]5+, 1025.80 (1025.88) [MH6]6+, 879.40 (879.47) [MH7]7+, 769.60 (769.66) [MH8]8+, 684.20 (684.25) [MH9]9+, 615.88 (615.93)[MH10]10+R8-PNA-a433: sequence H-R8-CGGGGAACCCTTCAAGAT-Gly-NH2; Rt = 10.47 min, HRMS: calculated MW: 6208.4525 g/mol; m/z found : 1036.14 (1036.22) [MH6]6+, 888.26 (888.33) [MH7]7+, 777.35 (777.41) [MH8]8+, 691.09 (691.15) [MH9]9+.2/air in DMEM/F12 medium supplemented with 10% fetal bovine serum , 100 units/mL penicillin and 100 \u03bcg/mL streptomycin and 1% NEEA (100\u00d7) . To determine the effect on proliferation, cell growth was monitored by determining the cell number/mL using a Z2 Coulter Counter .Calu-3 ,30 and NCultured cells were trypsinized and collected by centrifugation at 1500 rpm for 10 min at 4 \u00b0C, washed with PBS, lysed with Tri-Reagent , according to manufacturer\u2019s instructions. The isolated RNA was washed once with cold 75% ethanol, dried and dissolved in nuclease free pure water before use. RNA from human tissue sections was extracted and purified with miRNeasy FFPE Kit according to the manufacture's procedures. For miRNA quantification using real-time RT-qPCR reagents, the primers and probes were obtained from Applied Biosystems . Reverse transcriptase (RT) reactions were performed using the TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems); real-time PCR was performed according to the manufacturer\u2019s protocols . The quaGene expression analysis was performed by RT-qPCR. 300 ng of the total RNA was reverse transcribed by using random hexamers. Quantitative real-time PCR (qPCR) assays were carried out using gene-specific double fluorescently labeled probes. Primers and probes used to assay CFTR (Assay ID: Hs00357011_m1) gene expression were purchased from were from Applied Biosystems, (Applied Biosystems). The relative expression was calculated using the comparative cycle threshold method and, as reference genes, the human RPL13A (Assay ID: Hs03043885_g1) ,53. g for 10 min at 4 \u00b0C. Protein concentration was determined by the method of Lowry after precipitation with 5% Trichloroacetic acid (TCA), utilizing bovine serum albumin as a standard. For CFTR analysis 20 \u03bcg of total protein was heated in Laemmli buffer (Bio-Rad) at 37 \u00b0C for 10 min and loaded onto a 3 to 8% Tris-acetate gel (Bio-Rad). The gel proteins were transferred to PVDF membrane (Bio-Rad) by using Trans Blot Turbo (Bio-Rad) and processed for Western blotting by using mouse monoclonal antibody, clone 596, against NBD2 domain of CFTR at a dilution of 1:2500 by an overnight incubation at 4 \u00b0C. After washes, membranes were incubated with horseradish peroxidase-coupled anti-mouse immunoglobulin at room temperature for 1 h and after washes the signal was developed by enhanced chemiluminescence . After membranes stripping, \u03b2-Actin monoclonal antibody (Sigma-Aldrich) was used to confirm the equal loading of samples [Cell pellets were lysed in 1% Nonidet P40 (IGEPAL), 0.5% sodium deoxycholate, 200 mM NaCl, 10 mM Trizma base, pH 7.8, 1 mM EDTA plus protease inhibitor mixture and 1 mM PMSF for 30 min in ice. Lysates were cleared by centrifugation at 10,000\u00d7 samples . Annexin V and Dead Cell assay on Calu-3 cells, untreated and treated for 72 h with 2 \u03bcM PNA-a145, 5 \u03bcM Stattic together with 10% DMSO, were performed with \u201cMuse\u201d method, according to the instructions supplied by the manufacturer. This procedure utilizes Annexin V to detect PS (PhosphatidylSerine) on the external membrane of apoptotic cells. A dead cell marker is also used as an indicator of cell membrane structural integrity. It is excluded from live, healthy cells, as well as early apoptotic cells. Four populations of cells can be distinguished in this assay. Cells were washed with sterile PBS 1X, trypsinized, suspended and diluted (1:2) with the one step addition of the Muse Annexin V & Dead Cell reagent. After incubation of 10 min at room temperature in the dark, samples were put on ice, vortexed and analyzed. Data from prepared samples are acquired and recorded utilizing the Annexin V and Dead Cell Software Module (Millipore) .t test. Statistical significance was defined with p < 0.05 and p < 0.01 .Results are expressed as mean \u00b1 standard deviation (S.D.) Comparisons between groups were made by using paired Student\u2019s"} +{"text": "Brassica campestris L. ssp. chinensis var. rosularis Tsen). However, there is little information on the global gene expression of BRs under LT stress in wucai. In this study, the molecular roles of 24-epibrassinolide (EBR) after exogenously application, were explored by RNA sequencing under LT conditions.Brassinosteroids (BRs) have a positive effect on many processes during plant growth and development, and in response to various abiotic stressors. Low-temperature (LT) stress constricts the geographic distribution, growth, and development of wucai (According to the Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, photosynthesis was significantly enriched after spraying EBR under LT. The transcripts encoding the photosystem II (PSII) oxygen-evolving enhancer protein, photosystem I (PSI) subunit, light-harvesting chlorophyll protein complexes I and II, and ferredoxin were up-regulated after the application of EBR. Transcripts encoding several key enzymes involved in chlorophyll biosynthesis were also up-regulated, accompanied by significant differences in the contents of 5-aminolevulinic acid (ALA), porphobilinogen (PBG), protoporphyrin IX (Proto IX), Mg-protoporphyrin IX (Mg-proto IX), protochlorophyllide (Pchl), and photosynthetic pigments. Notably, transcriptional and physiological analyses revealed that under LT stress, plant responses to EBR involved a major reorientation of photosynthesis, as well as porphyrin and chlorophyll metabolism.This study explored the role of EBR as an LT stress tolerance mechanism in wucai. At the transcription level, LT tolerance manifests as an enhancement of photosynthesis, and the amelioration of porphyrin and chlorophyll metabolism. Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a variant of non-heading Chinese cabbage (Brassica campestris L.), a crucial species in the Brassicaceae family [\u03c8o / (1\u2013 \u03c8o)]. Maximum quantum yield of primary photochemistry was calculated as: \u03c6Po\u2009=\u2009Fv / Fm\u2009=\u2009(Fm - Fo) / Fm [In vivo chlorophyll formulae . The flumeasured . The folFo) / Fm . Other pp\u2009<\u20090.05. Analyses were conducted using SPSS v19.0 for Windows . Figures were plotted using GraphPad Prism v7.0 and Origin Pro v9.1 software .All of the data from the 4 treatments were subjected to an analysis of variance (ANOVA). The mean separation was performed using the Fisher\u2019s protected least significant difference (LSD) test with a significance level of Additional file 1: Figure S1. The quality control of six samples. A-F represent LT-1, LT-2, LT-3, LT\u2009+\u2009EBR-1, LT\u2009+\u2009EBR-2, and LT\u2009+\u2009EBR-3, respectively.Additional file 2: Figure S2. The reads mapping of six samples. A-F represent LT-1, LT-2, LT-3, LT\u2009+\u2009EBR-1, LT\u2009+\u2009EBR-2, and LT\u2009+\u2009EBR-3, respectively.Additional file 3: Figure S3. The 20 DEGs we randomly selected for qRT-PCR assay in EBR-mediated LT stress.Additional file 4: Figure S4. The results of identifying EBR concentration.Additional file 5: Table S1. Summary of sequence assembly after illumine sequencing.Additional file 6: Table S2. Number of reads sequenced and mapped to the Brassica rapa genome.Additional file 7: Table S3. The expression patterns of the cold acclimation and cold-induced genes.Additional file 8: Table S4. The expression patterns of the BR-responsive genes.Additional file 9: Table S5. Primers of verifying genes.Additional file 10: Table S6. Primers of photosynthesis genes.Additional file 11: Table S7. DEGs of photosynthesis\u2013antenna proteins and photosynthesis.Additional file 12: Table S8. Parameters derived from the OJIP transient for use in the current study."} +{"text": "An update of xanthones encountered in lichens is proposed as more than 20 new xanthones have been described since the publication of the compendium of lichen metabolites by Huneck and Yoshimura in 1996. The last decades witnessed major advances regarding the elucidation of biosynthetic schemes leading to these fascinating compounds, accounting for the unique substitution patterns of a very vast majority of lichen xanthones. Besides a comprehensive analysis of the structures of xanthones described in lichens, their bioactivities and the emerging analytical strategies used to pinpoint them within lichens are presented here together with physico-chemical properties (including NMR data) as reported since 1996. H-xanthen-9-one scaffold [Xanthones are ubiquitous polyphenolic compounds displaying a common 9scaffold . Bioactiscaffold likely tscaffold . Thus, mscaffold . Even thscaffold , variousAs with most lichen metabolites , the bioet al. [Most lichen xanthones arise through the folding of a polyketide intermediate as described by Cacho et al. , resultiPyrenochaeta terrestris [ortho carboxybenzophenone that might follow several metabolic fates. A first possibility is the 1,4-addition of a B-ring phenol to the A-ring dienone followed by dehydration and decarboxylation to access ravenelin-like xanthones after a final oxidation [Aspergillus variecolor, a skeleton thus far unknown from lichens.In contrast, a limited number of structures arise via a distinct biosynthetic pathway that leads to the ravenelin skeleton, with the methyl group in position 3. This biosynthetic scheme begins with the widespread anthraquinone emodin as a precursor Figure . To begirrestris ,10. The rrestris . Deeper rrestris , who proxidation . This reHypericum androsaemum) or 1,3,5-trihydroxyxanthone (Centaurium erythraea) [It is noteworthy that the xanthone nucleus of plants is of mixed biosynthetic origin with the A-ring being acetate-derived whereas shikimic acid pathway\u2013derived 3-hydroxybenzoic acid gives rise to the C-ring . Aromatiythraea) .Anthocleista djalonensis [Croton cuneatus [, Cupania cinerea [, Feroniella lucida [, Minquartia guianensis [Zanthoxylum microcarpum [Z. valens [Hypericum ascyron [Penicillium [Penicillium patulum [Ulocladium [Penicillium patulum [Given these different biosynthetic pathways, only few lichen xanthones are known from non-lichenized organisms. However, some can be produced by higher plants, such as lichexanthone , vineto ascyron ). Likewiicillium , norlich patulum and the ocladium ; 1,3,6-t patulum . Secalon patulum .Vismia parviflora [Weddelina squamulosa [Penicillium strain [Cassia obtusifolia [Astrocystis sp. BCC 22166 [Cassia occidentalis [Phomopsis sp. [Talaromyces bacillosporus [Engyodontium album [O-methyl-2-deprenylrheediaxanthone B ). It can therefore be stated that xanthones are highly unique to each realm, legitimating joint efforts on higher plants, non-lichenized fungi and lichens to widen the chemical diversity of these privileged structures.Likewise, very few xanthones are common to higher plants and fungi, with some such examples being 1,7-dihydroxyxanthone 1,8-dihusifolia and fungCC 22166 ), pinseldentalis and sevepsis sp. , Talaromlosporus and the um album ), 6-O-meillardii and fungpsis sp. ), as welca. 2000 occurrences of xanthones sensu lato . These considerable efforts might be explained by the discovery of promising leads such as the anti-angiogenic molecule Vadimezan (AS 404) which is currently undergoing phase III clinical trials as a tumor vascular-disrupting agent [Recent data regarding the number of naturally occurring xanthones are scarce, with the last numbered record of 278 xanthones listed by Vieira and Kijjoa more than 10 years ago . By Janung agent ,36, as wng agent ,38. ObviStructural diversity of lichen xanthones mostly stems from variations in the orientation and degree of chlorination of the norlichexanthone or ravenelin core, as well as from the position and extent of methylation of the phenolic groups. Elix and Crook tremendously advanced the understanding of chlorination and methylation processes affecting the xanthone core. Through the example of 40 different species of lichens, theoretical biosynthetic schemes mirroring the sequence of biogenetic events leading to the joint occurrence of xanthones among lichens were constructed . This reet al. in 2002 [Aspergillus nidulans, through the identification of prenyltransferase genes belonging to the fungal indole prenyltransferases, so far known for their involvement in the prenylation of amino acids [Further structural modifications might be taken into account to extend the chemodiversity of lichen xanthones. Important contributors to the chemical diversity of xanthones are prenyl groups which are most often incorporated as dimethylallyl moieties . General in 2002 . Underlyno acids . Glycosyno acids and hirtno acids . Blennoria sp. [ortho and para C positions [The diversity of lichen xanthones is also extended through some dimeric xanthones. Although the identification of key dimerization processes still warrants further investigation, xanthone dimers are most likely obtained after the biaryl linkage of monomers. This hypothesis is preferred to that of a tandem biosynthetic pathway which would involve a side-by-side cyclization of a double-length polyketide, especially since the discovery of the long-sought-after monomeric units of secalonic acids within the fungus oria sp. . Enzymatositions .Reductive dearomatizations are sometimes observed on xanthones to yield dihydro-, tetrahydro- or hexahydroxanthones. To date, in lichens, such reduced species were only observed from dimeric xanthones: secalonic acids, hirtusneanoside and eumitrin A1 (bis tetrahydroxanthones) and eumitrin A2, B and T . Overall, a vast majority of xanthones reported from lichens have a monomeric and fully aromatized structure.Lecanora dispersa [Lecanora rupicola. This lichen is known to produce metabolites of various polyketide classes: lecanoric acid (depsides), hematommic and orsellinic acids (monocyclic phenols), eugenitol and sordidone (chromones) and arthothelin (xanthone). The whole chemosyndrome could be produced from axenically grown mycobionts, with the notable exception of arthothelin [Physconia distorta but not by its isolated mycobiont [Pyrenula japonica and P. pseudobufonia revealed the biosynthesis of xanthones that cannot be evidenced from the lichen as a whole (see further), suggesting their significance in the pre-lichenized condition [Even though xanthones from free-living fungi are well known, a plant-fungus collaboration has been suggested for several lichen xanthones. As an example, the typical lichen xanthone 2,7-dichlorolichexanthone could be isolated from the lichen dispersa . Howeverhothelin , suggestycobiont . Adverseondition ,52.Dehalococcoides mccartyi that has gathered attention because of its ability to dechlorinate a large array of anthropogenic pollutants [p-dioxins (dioxins), such bacterial strains might be of paramount interest for bioremediation purposes [A total of 72 xanthones containing one to four chlorine atoms are currently known from lichens. Even though recent studies have shed light on chlorinated xanthone biosynthesis, no study has focused on their degradation. Dechlorination of organochlorines can be achieved by some bacterial strains, referred to as organohalide respirers. Such bacteria comprise the famous llutants ,54,55. Lllutants ,57,58. Tllutants , which illutants ,61,62. Hpurposes . Acting purposes ,63.Lecidella asema, without the need for matrix assistance [in situ [Lecidella asema shows an exhaustive chemical profile to perform separation and therefore to collect retention time and UV/Vis data as obtained with more traditional dereplication protocols [However, regarding the specific example of lichen xanthones, the lack of mutually supportive data such as chromatographic retention times and/or UV/Vis spectra precludes the differentiation of isomers and is a severe limitation of such methods. Possible ways to overcome such limitations while keeping an rotocols . Even throtocols . Such inrotocols ,83. Thisrotocols .\u00ae was dedicated to the identification of lichen metabolites from an original database of 550 compounds, including HPLC retention indices, TLC-Rf values, UV/visible colors of TLC spots and thalline reactions to guide their identification [Lichenized and non-lichenized Ascomycetes) [Together with analytical achievements, informatics tools were also developed to alleviate the dereplication holdup. A computer software named Wintabolitesfication . A most mycetes) , a databmycetes) .Lecanora schofieldii [O-methylnorlichexanthone , 2,4-dicalderae ), 2,5-diia fusca among otulescens and Phyldatinica ), 4,5,7-leprosum ) and 2,4rpallida ). Chlorirpallida . One migBesides these fully rationalized structures, a limited number of metabolites exhibit structural variations that are more or less difficult to explain. As an example, demethylchodatin displays a methoxy group in position 4 that might be introduced by a xanthone oxidase on this trichlorinated norlichexanthone derivative. Another unusual modification of the lichexanthone series is the occurrence of two acetyl groups in erythrommone. The chemical structures of xanthones with trivial names discussed in this manuscript are enlisted in Rinodina thiomela.However, 22 lichen xanthones display unusual structural features that make their biosynthetic intermediates tricky to unravel [Plasmodiumfalciparum and Trypanosoma brucei [Aedes aegypti [Very few lichen xanthones have been investigated to date for their bioactivities. Lichexanthone exerts a weak activity against rculosis and M. aM. aurum . DespiteM. aurum . Lichexa: 21 \u03bcM) . No antia brucei . Lichexaa brucei and indua brucei . Lichexaa brucei . At last aegypti .lck tyrosine kinase at 200 \u03bcg/mL [50 values ranging from 0.3 to 12 \u03bcM [Norlichexanthone was shown to display promising cytotoxic activities . Indeed,00 \u03bcg/mL and inhito 12 \u03bcM . Norlichto 12 \u03bcM . Dayan ato 12 \u03bcM . Alongsito 12 \u03bcM .Haematomma fluorescens as a response to a 365 nm UV light exposure, emphasizing its protective role as a light filter [As most structural classes of lichen metabolites, xanthones display strong UV-absorbing properties, predominantly in the wavelength range of UVA . Indeed,t filter . Depositt filter ,110. Suct filter . A Time-t filter .The past 20 years witnessed the isolation of 23 further lichen xanthones. It is noteworthy that those new xanthones displayed original substitution patterns and revealed original moieties compared to the previous state of the art.Pyrenula japonica and P. pseudobufonia afforded a series of five new ravenelin-type lichen xanthones, the first reports of such xanthones from aposymbiotically grown lichen mycobionts. A first report elucidated the structures of 1,5,8-trihydroxy-3-methylxanthone, 1,8-dihydroxy-5-methoxy-3-methylxanthone and 1,7-dihydroxy-3-methylxanthone [Cassia occidentalis [Cultures of the spore-derived mycobionts of xanthone while a xanthone . Notablydentalis ) and alsdentalis . Surprisdentalis . Besidesdentalis .Umbilicaria proboscidea [d-glucopyranose unit anchored at position O-7, whereas umbilicaxanthoside B stands for a C2,C8-diprenylxanthone with a disaccharide \u03b2-d-glucopyranose-(1\u21924)-\u03b2-d-glucopyranose moiety at O-7. These compounds were the first prenylated xanthones to be isolated from a lichen source and glycosides are not frequently encountered in lichens [O-glycosides corresponding to linolenoyl, lineoyl, palmitoleoyl, oleoyl, palmitoyl, eicosenoyl and stearoyl esters of both umbilicaxanthosides A and B [Two highly unusual glycosylated prenylxanthones were subsequently identified from the Ural lichen boscidea . Umbilic lichens . Besides A and B . FragmenCladonia incrassata [Sporormiella minimoides [Staphylococcus aureus even though the paucity of the compound precluded the determination of a minimal inhibitory concentration [The last monomeric xanthone isolated so far from a lichen source is cladoxanthone A , obtained from crassata . The occcrassata . It is nnimoides as well as antifungal (Microbotryum violaceum) and antialgal agent (Chlorella fusca) [Gliocladium sp. T 31 streamlined the isolation of secalonic acid D as the cytotoxic metabolite against four cell lines in a highly variable range of 0.03\u201315 \u03bcM, suggesting selective pharmacodynamic properties [50 of secalonic acid D on the carcinoma KB cells and an inhibition of human topoisomerase 1 with a promising IC50 of 0.16 \u03bcg/mL [++-dependent enzymes through competitive inhibition [Regarding dimeric xanthones, known metabolites of the secalonic acid series were first isolated from lichen sources in 2009, anescens . The joianescens . Secalonanescens . Secalonc acid D ,119, wara oryzae . Likewisa fusca) . Severala fusca) . Bioassaoperties . Further16 \u03bcg/mL . More re16 \u03bcg/mL . As a la16 \u03bcg/mL . Anotherhibition . Subsequhibition . As a cohibition ,128.Usnea hirta corresponding to a rhamnoside of an unsymmetrical dimeric tetrahydroxanthone [Staphylococcus aureus and Bacillus subtilis [l-rhamnose and the aglycone named hirtusneanin, the physico-chemical data of which were also reported by Rezanka and Sigler [Hirtusneanoside is a new xanthone dimer isolated from xanthone . If the subtilis . The enzd Sigler .Available physico-chemical properties regarding the newly described lichen compounds are listed below.Cladoxanthone A14H7O4Cl3 (343.94099)CYellow powdermax (MeOH)(log \u03b5): 381 (3.24), 323 (3.50), 259 (4.11) nmUV \u03bbmax (CHCl3): 3353, 3056, 1642, 1597, 1450, 800 cm\u22121IR \u03bdCladonia incrassata [Sources: crassata .1,8-Dihydroxy-3-hydroxymethyl-5-methoxyxanthone15H12O6 (288.06339)CYellow needles, mp 221\u2013222 \u00b0Cmax (MeOH)(log \u03b5): 387.5 (3.27), 341 (3.84), 271 (4.16), 263 (4.24), 255 (4.29), 236 (4.17)UV \u03bbmax (KBr): 3533, 1659, 1634, 1609, 1589, 1493 cm\u22121IR \u03bdPyrenula japonica [Sources: Mycobiont of japonica .1,2,8-Trihydroxy-5-methoxy-3-methylxanthone15H12O6 (288.06339)CYellow needles, mp 214\u2013215 \u00b0Cmax (MeOH) (log \u03b5): 421 (3.42), 352 (3.58), 280 (4.27), 263 (4.18), 243 (4.17), 206 (4.23)UV \u03bbmax (KBr): 3487, 1663, 1636, 1607, 1576, 1489 cm\u22121IR \u03bdPyrenula japonica [Sources: Mycobiont of japonica .1,7-Dihydroxy-3-methylxanthone14H10O4 (242.05791)CYellow needles, mp 259\u2013260 \u00b0Cmax (MeOH) (log \u03b5): 384 (3.84), 290 (3.98), 261 (4.58), 235 (4.45)UV \u03bbmax (KBr): 3285, 1653, 1607, 1585, 1483 cm\u22121IR \u03bdPyrenula japonica [Sources: Mycobiont of japonica .1,5,8-Trihydroxy-3-methylxanthone14H10O4 (258.05282)CYellow needles, mp 277\u2013278 \u00b0Cmax (MeOH) (log \u03b5): 403 (3.54), 341 (4.01), 272 (4.58), 263 (4.40), 255 (4.47), 236 (4.32)UV \u03bbmax (KBr): 3461, 1661, 1633, 1606, 1591, 1497 cm\u22121IR \u03bdPyrenula japonica and Pyrenula pseudobufonia [Sources: Mycobiont of obufonia .1,8-Dihydroxy-5-methoxy-3-methylxanthone15H12O5 (272.06847)CYellow needles, mp 214\u2013215 \u00b0Cmax (MeOH) (log \u03b5): 393 (3.54), 340 (4.00), 272 (4.30), 254 (4.49), 235 (4.36)UV \u03bbmax (KBr): 3445, 1661, 1631, 1609, 1585, 1489 cm\u22121IR \u03bdPyrenula japonica and Pyrenula pseudobufonia [Sources: Mycobiont of obufonia .Hirtusneanoside40H46O17 (798.27350)CFaint yellow crystals, mp 231\u2013232 \u00b0Cc = 0.02 in MeOH)max (MeOH)(log \u03b5): 340 (3.24), 275 (4.01), 230 (4.52) nmUV \u03bbmax (CHCl3): 3290, 1735, 1620, 1590, 870 cm\u22121IR \u03bdUsnea hirta [Sources: ea hirta .Hirtusneanine34H36O13 (652.21559)CPale yellow crystals, mp 251\u2013253 \u00b0Cc = 0.01 in MeOH)max (MeOH)(log \u03b5): 338 (3.97), 275 (4.04), 231 (4.43) nmUV \u03bbmax (CHCl3): 3290, 1734, 1608, 1590, 870 cm\u22121IR \u03bdUsnea hirta [Sources: ea hirta .Umbilicaxanthoside A25H28O11 (504.16316)CYellow needles, mp 114 \u00b0Cmax (MeOH) (log \u03b5): 345 (3.90), 310 (4.15), 270 (4.05), 245 (4.50).UV \u03bbmax (KBr): 3320, 2945, 2905, 1643 cm\u22121IR \u03bdUmbilicaria proboscidea [Sources: boscidea .Umbilicaxanthone A19H18O6 (342.11034)CUmbilicaria proboscidea [Sources: boscidea .Umbilicaxanthoside B36H46O16 (734.27859)CPale yellow needles, mp 133 \u00b0Cmax (MeOH) (log \u03b5): 355 (4.06), 319 (4.01), 271 (3.96), 244 (4.08)UV \u03bbmax (KBr): 3350, 2950, 2900, 1640 cm\u22121IR \u03bdUmbilicaria proboscidea [Sources: boscidea .Umbilicaxanthone B24H26O6 (410.17294)CUmbilicaria proboscidea [Sources: boscidea .Linolenoylumbilicaxanthoside B54H74O17 (994.49260)CPale yellow needles, mp 133 \u00b0Cmax (MeOH) (log \u03b5): 355 (4.06), 319 (4.01), 271 (3.96), 244 (4.08)UV \u03bbmax (KBr): 3350, 2950, 2900, 1640 cm\u22121IR \u03bdUmbilicaria proboscidea [Sources: boscidea .Secalonic acid A32H30O14 (638.16356)CFaint yellow crystals, mp 231\u2013232 \u00b0Cc = 0.1 in CHCl3)max (MeOH)(log \u03b5): 338 (4.52), 260 (4.12), 228 (4.32) nmUV \u03bbmax (CHCl3): 3464, 1726, 1610, 1585, 1566, 1436, 1233, 1067 cm\u22121IR \u03bdDiploicia canescens [Sources: anescens .Spectral data: .c = 0.14 in CHCl3)Enantiomeric secalonic acid D: similar physicochemical data except Secalonic acid B32H30O14 (638.16356)CFaint yellow crystals, mp 231\u2013232 \u00b0Cc = 0.38 in CHCl3)max (MeOH)(log \u0190): 338 (4.52), 260 (4.12), 228 (4.32) nmUV \u03bbmax (CHCl3): 3582, 3014, 1747, 1611, 1589, 1214, 1058, 796, 726 cm\u22121IR \u03bdDiploicia canescens [Sources: anescens .Spectral data: Even though lichens offer the widest diversity of compounds in the fungal realm, the bioactivities of their secondary metabolites remain under-investigated in regards to any other fungi , especia"} +{"text": "Cancer still is one of the leading causes of death and its death toll is predicted to rise further. We identified earlier the potential tumour suppressor zygote arrest 1 (ZAR1) to play a role in lung carcinogenesis through its epigenetic inactivation.ZAR1 is epigenetically inactivated not only in lung cancer but also across cancer types, and ZAR1 methylation occurs across its complete CpG island. ZAR1 hypermethylation significantly correlates with its expression reduction in cancers. We are also the first to report that ZAR1 methylation and expression reduction are of clinical importance as a prognostic marker for lung cancer and kidney cancer. We further established that the carboxy (C)-terminally present zinc-finger of ZAR1 is relevant for its tumour suppression function and its protein partner binding associated with the mRNA/ribosomal network. Global gene expression profiling supported ZAR1's role in cell cycle arrest and p53 signalling pathway, and we could show that ZAR1 growth suppression was in part p53 dependent. Using the CRISPR-dCas9 tools, we were able to prove that epigenetic editing and reactivation of ZAR1 is possible in cancer cell lines.We are the first to report that ZAR1 tumour suppressor in cancer.ZAR1 is a novel cancer biomarker for lung and kidney, which is epigenetically silenced in various cancers by DNA hypermethylation. ZAR1 exerts its tumour suppressive function in part through p53 and through its zinc-finger domain. Epigenetic therapy can reactivate the ZAR1 was reported to be expressed in porcine and bovine brain and testis -dCas9 (100087), DNMT3A-dCas9 (100090). Epigenetic editing of endogenous ZAR1 was performed in the ZAR1 partially methylated Hela, if not mentioned otherwise. ZAR1 RNA guides are #1 ACTTTCGCTCACTTAGCCAG, #2 TGGTTCCCTTACGGATCAGC, #3 GTAGGGAGAAGGACGAAGAG, #4 GTCGCCTATTTAGGGTGCGG, #5 CGCGGCCACCAAGGGCAAGG, and #6 CCGCGGTACAGTGCTCGCTG and are positioned relative to TSS at \u2212402 #1, \u2212230 #2, \u2212133 #3, \u22123 #4, +120 #5, and +386 #6.CRISPR-Cas9 vector px549 was obtained from Lienhard Schmitz and adapted for epigenetic editing by inactivation of Cas9 (dCas9 site-directed mutation). 2. I brief, beads were resuspended in two volumes urea buffer and incubated shaking for 30 min at room temperature. Cysteins were alcylated at 55 mM final concentration of iodoacetamide, shaking at room temperature and in the dark for another 30 min. Peptidolysis was then initiated with 0.5 \u03bcg Lys-C for 3 h shaking at room temperature, followed by dilution to 2 M urea/thiourea, addition of 0.5 \u03bcg trypsin (Serva) and an overnight shaking incubation at room temperature. Peptide-containing supernatants were brought to 1% NH3 and loaded onto three-layer SAX tips equilibrated previously with 30 \u03bcl of 0.1% NH3. After sequential washes with 30 \u03bcl 0.1% NH3 and 30 \u03bcl NH3 in 2-propanol, respectively, columns were syringe dried, peptides eluted using 30 \u03bcl 80% acetonitrile, 0.1% formic acid and vacuum dried. In-solution chemical labelling was performed as described [2 analysis used an in-house packed 70 \u03bcm ID, 15 cm reverse phase column emitter with a buffer system comprising solvent A and solvent B . Relevant instrumentation parameters are extracted using MARMoSET [ZAR1-EYFP, ZAR1delZF-EYFP vs. EYFP-empty were overexpressed in HEK293T cells (24 h), and pulldown was performed according to manufacturer's protocol by GFP Trap (ChromoTek). Triplicate sample pairs were processed by off-bead digest, strong anion exchange (SAX) extraction, and dimethyl-labelling, followed by LC-MSescribed , 72. PepMARMoSET and inclMARMoSET , 75 APS = 16.2 (407) Avg = 12.8, Source: GEO ID: gse36133 Dataset Date: 2012-03-20. Additional file ZAR1 expression in cancer cell lines vs. normal tissues, 1555775_a_at, log2, data Roth vs. Broad, Anova one way. ZAR1 methylation in normal to tumour tissues and cancer cell lines, cg22773661/cg1753764, data Lokk vs. Heyn vs. Esteller, Anova one way. ZAR1 methylation in normal to tumour tissues and cancer cell lines relative to CpG island/shores and for all ZAR1 (cg) reporters from array. T-SNE analysis on Broad and Roth, Transform: zscore, no gene filter, no sample filter, perplexity = 50, Colour mode: Colour by Gene (ZAR1), Transform log 2. Overview on R2 used datasets : Normal Various - Roth - 504 \u2013 MAS5.0 - u133p2, Source: GEO ID: gse7307 Dataset Date: 2007-04-09; Cellline CCLE Cancer Cell Line Encyclopedia - Broad - 917 - MAS5.0 - u133p2, Source: GEO ID: gse36133 Dataset Date: 2012-03-20; Normal Tissues - Lokk - 70 - custom - ilmnhm450, Source: GEO ID: gse50192 Dataset Date: 2014-02-26; Tumor Types (landscape) - Heyn - 493 - custom - ilmnhm450, Source: GEO ID: gse76269 Dataset Date: 2017-06-07; Cellline Cancer Pharmacogenomic - Esteller - 1028 - custom - ilmnhm450, Source: GEO ID: gse68379 Dataset Date: 2016-07-05. Figure Wanderer [ZAR1, dataset project: TCGA, data type: 450k Methylation Array, for LUAD lung adenocarcinoma and KIRC Kidney renal clear cell carcinoma. Pan-cancer mRNA RNA-seq using KM Plotter [MethSurv [PhyloP; UCSC genome browser [BioEdit [NCBI RefSeq [Swiss-Model [PhosphoSitePlus [cBioPortal [String v11 [Gene expression, promoter methylation correlation, and Kaplan\u2013Meier calculations were performed using Platform , WandereWanderer , KM Plot Plotter \u201381, and MethSurv . Gene serv [GSEA . The fol37, data . ZAR1 exZAR1 15555_a_at AP Plotter , Tumor tMethSurv on TCGA browser and BioE[BioEdit matrix: I RefSeq . Swiss-Mss-Model predictiioPortal , 90. FigZAR1 promoter (186 bp) were upper primer GGAGAAGGAYGAAGAGGGGTTTTT and lower primer TCCCCCAAAACCRCCATAAAC, and pyrosequencing primer was TGGTAGGAAGGGYGTGGAGG. Primers for RT-PCR were ZAR1 AGCTGGGCAAGGAGCGGCTG and GGTGGGGCCGTTTAGGGTCCA (264 bp), GAPDH TGGAGAAGGCTGGGGCTCAT and GACCTTGGCCAGGGGTGCTA (176 bp), ACTB CCTTCCTTCCTGGGCATGGAGTC and CGGAGTACTTGCGCTCAGGAGGA (226 bp), p21 CCTTGTGCCTCGGTCAGGGGAG and GGCCCTCGCGCTTCCAGGAC (183 bp), p27 GTGCGAGAGAGGCGGTCGTG and TCCACCGGGCCGAAGAGGTT (146 bp), WEE1 CACACGCCCAAGAGTTTGC and CACTTGAGGAGTCTGTCGCA (135 bp) and WEE1 3\u2032UTR primers are: pair 1 CTCCCCCTGAACACTGTGAC and ACTGACACCAATCGAGAAAGT (87 bp), pair 2 CACCAGCCTTTCCAGGGTTA and GGTCACTACAGGGAAAGACACC (92 bp), pair 3 AGCCTTCAATGTACCTGTGTGT and TGCCTACAAAGTGCTCCCAG (93 bp), pair 4 CTGGGAGCACTTTGTAGGCA and AGCAGCAAATTCACAAGGCA (77 bp), pair 5 AGTTTTGTCTTTGCTGTAAACTTGT and CATCAAAAGCAGCTATACATTTCAC (100 bp), pair 6 TGCACCCTTTCCCTCCTTTG and GTCCGGGAAGGACATTACCA (89 bp), pair 7 TGTTTTGCCCGGTTTTTCTCT and GTCAGAAGTCATTCTGGCATTTCA (95 bp), pair 8 TTTGCACTTGTCTTTGACTTGTGT and AGGTAAGCTCAGAGTGACTTTT (70 bp), pair 9 GCCATTTGACTAATAATACTGGCT and ACACAAGTCAAAGACAAGTGC (106 bp).Primers for CoBRA analysis of the Additional file 1: Figure S1. Overview ZAR1 genomic structure, expression pattern and GO-term correlation, Figure S2.ZAR1 promoter is hypermethylated across cancer cell lines. Figure S3.ZAR1 methylation in ovarian carcinoma. Figure S4. Epigenetic inactivation of ZAR1 across human cancers. Figure S5. ZAR1 is conserved across human, mouse, and xenopus with high C-terminal homology and structure prediction. Figure S6. Confirming human ZAR1 RNA binding ability. Figure S7. ZAR1 is cytosolic. Figure S8. Reexpression of ZAR1 alters the transcriptome and reveals association with mRNA 3\u2032end processing. Figure S9. ZAR1 function depends on its zinc-finger. Figure S10. ZAR1 binding partner GO-term association overview. Figure S11. ZAR1 binding partner GO-term association overview. Figure S12. Targeting the ZAR1 genomic region with CRISPR ZAR1 guide RNA oligos. Figure S13. Effective epigenetic editing of ZAR1 with distinct RNA guide combinations upstream the TSS."} +{"text": "Escherichia coli 4s is a Gram-negative bacterium found in the equine intestinal ecosystem alongside diverse other coliform bacteria and bacteriophages. This announcement describes the complete genome of the T7-like E. coli 4s podophage Penshu1. From its 39,263-bp genome, 54 protein-encoding genes and a 179-bp terminal repeat were predicted. Escherichia coli 4s is a Gram-negative bacterium found in the equine intestinal ecosystem alongside diverse other coliform bacteria and bacteriophages. This announcement describes the complete genome of the T7-like E. coli 4s podophage Penshu1. From its 39,263-bp genome, 54 protein-encoding genes and a 179-bp terminal repeat were predicted. Escherichia coli is a Gram-negative bacterium found living among the intestinal microbiome of all mammals. Due to multiple protective abilities, including extreme acid resistance, E. coli colonizes the intestine as a commensal . After trimming using FastX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/), they were assembled into a single contig at 376.4-fold coverage using SPAdes v3.5.0 wastewater treatment sample from Bryan, TX, using the host . Followithe host . The phathe host . The DNAs v3.5.0 . Contig xy-pub/) , 10. Proxy-pub/) , 12. No xy-pub/) . Protein-pub/) 1417. Rho-i-pub/) 14. Genome--pub/) 14.Escherichia phage ST31 (GenBank accession number KY962008) and 80.1% nucleotide sequence identity with Escherichia phage YZ1 (GenBank accession number MG845865). As for phage T7, Penshu1 has a slippery sequence in the major capsid protein (NCBI accession number QEG09806) that can lead to translation by frameshift of the minor capsid protein (NCBI accession number QEG09807).Penshu1 has a 39,263-bp genome, with a 93.4% coding density and 50.6% G+C content. Analysis predicted 54 protein-coding genes, with 30 being assigned a putative function. The Penshu1 genome was reopened at T7-like direct terminal repeats of 179 bp predicted by PhageTerm . Penshu1MK903281, BioProject accession number PRJNA222858, SRA accession number SRR8893626, and BioSample accession number SAMN11414580.The genome sequence and associated data for phage Penshu1 were deposited under GenBank accession number"} +{"text": "HERC1 and HERC2, are present in most metazoan taxa. They encode very large proteins that contain more than one RCC1-like domain as a structural characteristic. Accumulating evidences show that these unusually large proteins play key roles in a wide range of cellular functions which include neurodevelopment, DNA damage repair, and cell proliferation. To better understand the origin, evolution, and function of the Large HERC family, this minireview provides with an integrated overview of their structure and function and details their physiological implications. This study also highlights and discusses how dysregulation of these proteins is associated with severe human diseases such as neurological disorders and cancer.Homologous to the E6AP carboxyl terminus (HECT) and regulator of chromosome condensation 1 (RCC1)-like domain-containing proteins (HERCs) belong to the superfamily of ubiquitin ligases. HERC proteins are divided into two subfamilies, Large and Small HERCs. Despite their similarities in terms of both structure and domains, these subfamilies are evolutionarily very distant and result from a convergence phenomenon rather than from a common origin. Large HERC genes, Proteins containing a HECT domain are ubiquitin ligases (E3). These enzymes participate in the ubiquitylation process accepting ubiquitin from a ubiquitin-conjugating enzymes (E2) and catalysing its transfer to the protein to be ubiquitylated . In animAlthough traditionally classified together with the Small HERC proteins, Large and Small HERCs form two distant protein families . Large HMonosiga brevicollis and Salpingoeca rosetta, the emergence of HERC1 occurred in Metazoa. Both proteins are already present in the placozoan Trichoplax adhaerens and in most metazoan phyla, with the absence of HERC1 in certain insect clades . HERC2 induces BRCA1 degradation in breast cancer. This is inhibited either by binding of TUSC4 to HERC2 or by BAHERC1 deletions affect MSH2 protein levels and certain HERC2 SNPs can interfere OCA2\u2019s expression thus affecting eye, skin, and hair pigmentation , for HERC1: T. adhaerens (XP_002116356.1), Anoplophora glabripennis (Asian long-horned beetle) (XP_018567016.1), Callorhinchus milii (Elephant shark) (XP_007906088.1), Latimeria chalumnae (Coelacanth) (XP_005987767.1), Danio rerio (Zebrafish) (XP_021333511.1), Oreochromis niloticus (Tilapia) (XP_013121789.1), Xenopus tropicalis (Frog) (XP_004916026.1), Gekko japonicus (Gecko) (XP_015275623.1), Gallus gallus (Chicken) (XP_004943789.1), Ornithorhynchus anatinus (Platypus) (XP_028921613), Monodelphis domestica (Opossum) (XP_016284147.1), Sarcophilus harrisii (Tasmanian devil) (XP_023353554.1), Equus caballus (Horse) (XP_023471806.1), Rattus norvegicus (Rat) (XP_017451567.1), Mus musculus (Mouse) (NP_663592.3), Homo sapiens (Human) (NP_003913.3), Pan troglodytes (Chimpanzee) (XP_001174017.1), Canis lupus familiaris (Dog) (XP_544717.3), Felis catus (Cat) (XP_023110993.1), and Lepidosiren paradoxa (Lungfish) . For HERC2: M. brevicollis (XP_001743304.1), S. rosetta (XP_004996155.1), T. adhaerens (XP_002112421), Asian long-horned beetle (XP_018562376.1), Drosophila melanogaster (Fruit fly) (NP_608388.2), Apis mellifera (Honey bee) (XP_01677273), Coelacanth (XP_014343905.1), Zebrafish (XP_021332870.1), Tilapia (XP_013130527.1), Frog (XP_012813156.1), Gecko (XP_015266462.1), Chicken (XP_015133197.1), Platypus (XP_016083014.1), Opossum (XP_007501467.1), Tasmanian devil (XP_023356163.1), Horse (XP_023507879.1), Mouse (NP_001347009.1), Rat (XP_006229362.1), Human (NP_004658.3), Chimpanzee (XP_024204823.1), Dog (XP_022272508.1), Cat (XP_023110801.1), Elephant shark (XP_007889299.1), and Lungfish .Amino acid sequences were aligned using the Mafft FFT-NS-i algorithm . The phyHuman RCC1 (NCBI accession number P18754) and HECT domain from E6AP three-dimensional structures were modelled using Swiss-Model online software . RLDs anJG-C and JR conceived and designed the manuscript. JG-C, AM-M, and JR analysed the data and performed figures and tables. JG-C, AM-M, JS-G, LP, and JR wrote the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Staphylococcus aureus clones and genes encoding antimicrobial resistance and toxins were examined among 120 S. aureus strains from nosocomial infections in tehran, Iran.In the current research, the prevalence of mec, agr, spa, and MLST, the isolates were typed. Antimicrobial susceptibility was examined, based on disk diffusion and PCR method to identify resistance and toxin-encoding genes. Based on the polymorphisms in SCCS. aureus isolates, 85 (70.8%) were methicilin resistant S.aureus (MRSA), and 35 (29.2%) were methicilin sensetive S. aureus (MSSA). The tested isolates contained resistance genes, including ant(4\u0384)-Ia (90%), aac(6\u0384)-Ie/aph(2\u02dd) (80%), aph(3\u0384)-IIIa (30%), erm(A) (26.7%), erm(B) (10.8%), erm(C) (11.7%), msr(A) (40.8%), msr(B) (14.2%), tet(M) (45.8%), and mupA (8.3%). The MRSA strains were clustered into six different clones. The most common genotypes included ST239-SCCmec III/t037 (23.3%), ST239-SCCmec III/t388 (22.5%), ST22-SCCmec IV/t790 (8.3%), ST15-SCCmec IV/t084 (7.5%), ST585-SCCmec III/t713 (5%), and ST239-SCCmec III/t924 (4.2%), respectively. ST182/t196 (8.3%) and ST123/t171 (5%) belonged exclusively to MSSA strains. Overall, 10 (66.7%) and 5 (33.3%) out of 15 isolates with pvl genes were attributed to clones ST22-SCCmec IV/t790 and ST15-SCCmec IV/t084, respectively. ST22-SCCmec IV/t790, ST239-SCCmec III/t037, and ST15-SCCmec IV/t084, were related to high-level mupirocin-resistant phenotypes. Among 120 S. aureus was confirmed in our hospitals, and ST239-SCCmec III/t037 showed a relatively high prevalence in our study. It seems that assessment of resistance and virulence genes in different S. aureus molecular types is necessary for proper antibiotic consumption.The genetic diversity of Staphylococcus aureus, which is described as a common nosocomial pathogen, is responsible for various diseases, such as food poisoning, osteomyelitis, wound infections, and even fatal conditions, such as endocarditis (S. aureus (MRSA) occurred in the UK is recognized as a staphylococcal cassette chromosome mec (SCCmec). Generally, SCCmec is categorized into 11 types with respect to mec genes and ccr gene complexes infections. HA- and CA-MRSA strains can be distinguished with respect to some genotypic, phenotypic, and epidemiological characteristics, as well as virulence factors genes have significantly limited the availability of antibiotics over the past decades. In addition, the growing emergence of MDR-MRSA strains poses a major global health concern . Wide remupA and mupB genes are responsible for resistance to mupirocin which is used to treat various types of skin diseases caused by S. aureus including aminoglycoside nucleotidyltransferases, aminoglycoside phosphotransferases and aminoglycoside acetyltransferases . mupA an. aureus . Resistaing site . Thus, i spa, SCCmec and agr techniques in clinical samples taken from patients in Tehran, Iran.This study was conducted to identify antibiotic resistance patterns and the carriage of resistance and virulence genes as well as major MRSA clones by MLST,Sampling, MRSA isolation and antibacterial susceptibility testingThis cross-sectional study included 368 clinical samples from wound, blood, and urine specimens during April-December 2016. Ethics Committee of Shahid Beheshti University of Medical Sciences approved the implementation of this study (IR.SBMU.SM.REC.1395.157). All patients signed written informed consent forms.S. aureus identification was performed, based on the conventional biochemical tests. S. aureus identification was confirmed based on the PCR assay for nucA gene , clindamycin (CD 2 \u00b5g), ciprofloxacin (CIP 5 \u00b5g), trimethoprim- sulfamethoxazole (TS 2.5 \u00b5g), kanamycin (K 30 \u00b5g), ceftriaxon (CRO 30 \u00b5g), quinupristin-dalfopristin (SYN 15 \u00b5g), erythromycin (E 15 \u00b5g), amikacin (AK 30 \u00b5g), gentamicin (GM 10 \u00b5g), tobramycin (TN 10 \u00b5g), teicoplanin (TEC 30 \u00b5g), penicillin (PG 10 \u00b5g), and linezolid (LZD 30 \u00b5g) were determined, based on the CLSI criteria were considered as the reference strains for the quality control purposes.Using E-test strips (bioMe\u00b4rieux), the minimum inhibitory concentrations (MICs) were measured for mupirocin and vancomycin. Resistance to three antibiotic groups or more, besides beta-lactams, was defined as MDR. High mupirocin resistance was defined as antibiotic use \u2265 256 mg/l. Growth in a well containing clindamycin and erythromycin indicated inducible macrolide-lincosamide-streptogramin B and/or clindamycin resistance phenotypes; otherwise, constitutive MLSB and/or clindamycin resistance phenotype was confirmed . ATCC292Extraction of genomic DNAS. aureus cultures were used on 5% sheep blood agar , based on the protocols of InstaGene Matrix kit . For extracting genomic DNA, pure overnight Resistance and toxin genes profilingetb, tst, pvl, eta) and resistance (tet(M), aac (6\u0384)-Ie/aph (2\u02dd), mupA, erm(A), msr(A), msr(B), erm(B), erm(C), ant (4\u0384)-Ia, aph (3\u0384)-IIIa) genes, PCR assay was carried out. The details of the degenerated primers in this study are described in To identify toxin and reverse (agr1 to agr4) primers for the agr groups as previously recommended by Gilot et al . Chromas 1.45 was used to edit the sequences. To assign the sequences to specific spa types, the Ridom SpaServer database was searched.On the other hand, lleagues . After tMLST techniqueS. aureus isolates. The internal fragments of housekeeping genes were used to identify the allelic profiles; these genes included gmk, arcC, aroE, glpF, pta,yqiL, and tpi. The isolate was assigned a sequence type (ST) after comparing the sequences with the S. aureus MLST database.Via amplification and sequencing, MLST was carried out on Sampling and antibiotic susceptibility S. aureus. These isolates originated from wound (60%), blood (20.8%) and urinary tract infections (19.2%). Of the 120 S. aureus clinical isolates obtained from the hospitalized patients, 85 (70.8%) were MRSA and 35 (29.2%) were methicillin susceptible S. aureus (MSSA). In this study, out of 368 samples obtained from various clinical specimens, 120 isolates (83 (69.2%) obtained from men and 37 (30.8%) from women) were identified as in vitro antimicrobial susceptibility tests. All isolates were susceptible to vancomycin, among which 55 (45.8%), 48 (40%) and 17 (14.2%) isolates had a MIC of 0.5, 1 and 2 \u00b5g/ml, respectively. None of the isolates were susceptible to all of the antimicrobial agents tested regardingP= 0.145 and 0.128, respectively). The frequency of resistance for MRSA and MSSA isolates to different antibacterial agents are presented in Among the 35 MSSA isolates, no mupirocin resistance was detected, whereas 30 MRSA isolates (35.3%) were mupirocin resistant. Of these mupirocin resistant isolates, 14 (46.7%) and 16 (53.3%) had high and low resistance levels, respectively. All the high-level mupirocin-resistant (HLMUPR) isolates were collected from wound samples. Patients diagnosed with mupirocin-susceptible and -resistant MRSA infections were not significantly different in terms of age and gender were defined as MDR. The predominant multiple drug resistance profile among the MDR isolates were resistance to 9 and 7 antibiotics found in 75 (62.5%) and 12 (10%) isolates, respectively. Distribution of resistance profile and different clinical sample in S. aureus isolated from nosocomial infections are presented in Of the 120 The distribution of resistance genesant(4\u0384)-Ia (90%), aac(6\u0384)-Ie/aph(2\u02dd) (80%), aph(3\u0384)-IIIa (30%), erm(A) (26.7%), erm(B) (10.8%), erm(C) (11.7%), msr(A) (40.8%), msr(B) (14.2%), tet(M) (45.8%), and mupA (8.3%) (ant(4\u0384)-Ia, aac(6\u0384)-Ie/aph(2\u02dd), and mecA genes. Other detected antibiotic resistance genes included tet(M) (64.7%), msr(A) (57.6%), aph(3\u0384)-IIIa (42.3%), erm(A) (37.6%), msr(B) (20%), erm(C) (16.5%), erm(B) (15.3%), and mupA (11.8%), while 31.4% and 56.7% of MSSA strains were found to respectively carry aac(6\u0384)-Ie/aph(2\u02dd) and ant(4\u0384)-Ia. Particularly, the MRSA strains contained more resistance genes, compared to the MSSA isolates.In addition, the frequency of antibiotic resistance genes was measured. The genes included A (8.3%) . The MRSS. aureus isolates were identified as HLMUPR-MRSA, while mupA gene was confirmed in 10 isolates (71.4%). In addition, ant(4\u0384)-Ia , followed by aac(6\u0384)-Ie/aph(2\u02dd) , was recognized as the most common aminoglycoside resistance gene. A total of 75 (62.5%) isolates contained ant(4\u0384)-Ia, as well as aac(6\u0384)-Ie/aph(2\u02dd). On the other hand, 15 (12.5%) isolates harbored aph(3\u0384)-IIIa, besides ant(4\u0384)-Ia. Also, eleven (9.2%) isolates harbored ant(4\u0384)-Ia, aph(3\u0384)-IIIa, and aac(6\u0384)-Ie/aph(2\u02dd) genes, while 10 (8.3%) contained aac(6\u0384)-Ie/aph(2\u02dd), as well as aph(3\u0384)-IIIa; however, ant(4\u0384)-Ia alone was confirmed in 7 (5.8%) strains. Resistance to tetracycline was observed among 84 (70%) S. aureus isolates, 55 (45.8%) of which harbored tet(M) gene. Antibiotic resistance genes showed the highest prevalence among MRSA strains from wound infections.Fourteen (11.7%) out of 30 mupirocin-resistance Virulence gene profilingtst and etb genes, respectively . S. aureus isolates harbouring tst gene were isolated from wound , blood , and urinary tract infections while pvl positive isolates were detected in wound and blood samples. Eight isolates carrying pvl and tst genes, simultaneously, had mupA gene.Among toxin-encoding genes, the highest and lowest frequencies were attributed to ectively . In presDistribution of SCCmec typesAccording to SCCmec typing, 66 (77.6%) and 19 (22.4%) MRSA isolates contained SCCmec types III and IV, respectively. No isolate harbored SCCmec type V, II, or I. Based on the multiplex PCR, isolates positive for PVL were attributed to SCCmec type IV, while tst gene was found in MRSA isolates from SCCmec III and IV. The HA-MRSA origin was emphasized by the presence of SCCmec type III.Frequency of agr typesagr typing indicated that type I was the predominant agr type present in 91 isolates (75.8%), followed by type III which was present in 20 isolates (16.7%). agr type II was detected in 9 isolates (7.5%). Among 35 MSSA isolates, 20 and 15 harboured agr types I and III respectively .spa typingS. aureus isolates. spa typing discriminated eight different types: t037 (23.3%), t388 (22.5%), t713 (16.8%), t924 (8.3%), t790 (8.3%), t196 (8.3%) t084 (7.5%) and t171 (5%) . All theMLSTmec III/t037 was found to be the most prominent MRSA clone identified in this study. Distribution of MRSA clones isolated from nosocomial infections are presented in Apparently, 120 isolates belonged to six different STs including ST239 (65 strains), ST22 (10 strains), ST182 (10 strains), ST15 (9 strains), ST585 (20 strains) and ST123 (6 strains). ST239, ST585, ST182 and ST123 were found in MSSA strains. It should be noted that of these STs, ST182 and ST123 belonged exclusively to MSSA strains. In conclusion, MRSA strains are clustered into six different groups. ST239-SCCmec IV/t790 and ST15-SCCmec IV/t084 clones. Among the isolates under study, 58 (48.3%) isolates harboring tst-1 were distributed in ST239-SCCmec III/t037 , ST239-SCCmec III/t388 , ST15-SCCmec IV/t084 , ST585-SCCmec III/t713 , ST239-SCCmec III/t924 , and ST22-SCCmec IV/t790 clones. Among examined isolates, nine isolates (7.53%) were found to carry the eta gene. The eta positive isolates were distributed in ST15-SCCmec IV/t084 , ST22-SCCmec IV/t790 and ST239-SCCmec III/t037 clones. The etb gene was detected in ST585-SCCmec III/t713 and ST22-SCCmec IV/t790 clones. MRSA clones resistance profile varied. Resistance to mupirocin was detected in all the MRSA clones with the exception of ST585-SCCmec III/t713 clone. Interestingly, mupirocin resistant MSSA isolates belonged to ST182/spa type t196. HLMUPR-MRSA strains were detected in ST22-SCCmec IV/t790 , ST15-SCCmec IV/t084 and ST239-SCCmec III/t037 clones. Fifteen PVL-carrying strains in our study belonged to ST22-SCCB phenotype was detected in ST239-SCCmec III/t037 , ST239-SCCmec III/t388 , ST585-SCCmec III/t713 , ST15-SCCmec IV/t084 , ST239-SCCmec III/t924 and ST22-SCCmec IV/t790 while iMLSB phenotype distributed among 3 major clones ST239-SCCmec III/t388 , ST22-SCCmec IV/t790 and ST15-SCCmec IV/t084 . Of 12 MSSA isolates with cMLSB phenotype, 5 isolates belonged to ST182/t196, 4 isolates belonged to ST239/t924, 2 isolates belonged to ST585/t713 and 1 isolate belonged to ST123/t171. All the iMLSB phenotype among MSSA strains belonged to ST585/t713. Characteristics of MRSA clones are presented in cMLSet al. /aph(2\u2032\u2032) gene (40.3% ) in comparison with other AME genes, in the present study, ant(4\u0384)-Ia (90%) was the most frequent AME gene in S. aureus isolates. However, in this study, aph(3\u0384)-IIIa gene frequency rate was higher than the study reported by Ida et al. (8.9%) and Margtudy (aac\u2032/aph(2\u2032\u2032S. aureus strains (S. aureus isolates were found to be lower. We detected the resistance gene mupA in 10 isolates (8.3%) which is lower than 12.6% gene that may cause tetracycline resistance was detected in 55 (45.8%) isolates. In accordance with the results of our previous study a high tet al. (7%) reported low frequency of iMLSB phenotype among S. aureus isolates as well presented cMLSB phenotype while the frequency of iMLSB phenotype was 10% (12/120). In consistent with our findings, Schreckenberger as well . Accordiospitals . They fo. in USA reportedn survey , the fre ) or transposons (erm(A) and erm(B)) and msr genes expressing active efflux pumps mainly msr(A)) (msr(A), erm(A), msr(B),erm(C), and erm(B) genes to be 40.8%, 26.7%, 14.2%, 11.7%, and 10.8% respectively. In contrast to Rashidi Nezhad\u2019s study (erm(A) gene as the predominant gene among the isolates with inducible phenotype and erm(C) among the isolates with the constitutive phenotype, our finding revealed that the msr(A) gene was the most common gene among strains with the constitutive phenotype , followed by erm(A) , erm(C) , erm(B) , msr(B) while erm(A) , erm(B) , erm(C) , msr(A) and msr(B) were much more common among the isolates with inducible phenotype. It is worth mentioning that the frequency of erm and msr genes depends on the bacterial species as well as the geographic region in which the study is carried on. As previously mentioned, resistance to macrolides is encoded by genes often carried on plasmids ( msr(A)) . Our res\u2019s study who repomec (77.6%), according to the results of SCCmec typing, associated with an MDR pattern among MRSA isolates. This is in consistence with the results reported by Japoni and colleagues , type III (16.7%), and type II (7.5%), respectively. Goudarzi et al. . This spa type was reported from Saudi Arabia, China, Iran as well as among HA-MRSA isolates found in Europe, America and other regions of Asia . The review of the literature reveals that the multiresistant ST239 clone is responsible for at least 90% of HA-MRSA infections in Europe, United States, and some Asian countries, including Kuwait and Malaysia was the second most commonly detected MRSA clone. A similar result was reported by Ohadian Moghadam and ST30 .mec IV/t790 (8.3%). This clone was associated with high resistance to mupirocin, carrying resistance genes, including mecA, msr(A), ant(4\u0384)-Ia, msr(B), tet(M), and mupA. In our study, all ST22-SCCmec IV/t790 strains contained pvl genes. There are reports of S. aureus ST22 harboring pvl gene from Iran was the fourth most commonly detected clone. The low frequency of this clone has been previously reported in 16 European countries . The presence of eight different spa types, i.e., t037, t388, t713, t924, t790, t196, t084, and t171, was also confirmed. For the first time in Iran, STs 182 and 123, as well as spa types t196 and t171, were detected, which might be indicative of the emergence of new clones. Further studies on other neighboring regions, focusing on the emergence of new circulating clones, are necessary to reach an overall understanding of dynamic MRSA clones in Iran and the Middle East.To sum up, the present findings showed that MRSA isolates have various genetic backgrounds in our hospitals and involve six major clones. Certain molecular types were associated with some resistance and virulence genes (e.g.,"} +{"text": "Macrophages exposed to the Th2 cytokines interleukin (IL) IL-4 and IL-13 exhibit a distinct transcriptional response, commonly referred to as M2 polarization. Recently, IL-4-induced polarization of murine bone marrow-derived macrophages (BMDMs) has been linked to acetyl-CoA levels through the activity of the cytosolic acetyl-CoA-generating enzyme ATP-citrate lyase (ACLY). Here, we studied how ACLY regulated IL-4-stimulated gene expression in human monocyte-derived macrophages (MDMs). Although multiple ACLY inhibitors attenuated IL-4-induced target gene expression, this effect could not be recapitulated by silencing ACLY expression. Furthermore, ACLY inhibition failed to alter cellular acetyl-CoA levels and histone acetylation. We generated ACLY knockout human THP-1 macrophages using CRISPR/Cas9 technology. While these cells exhibited reduced histone acetylation levels, IL-4-induced gene expression remained intact. Strikingly, ACLY inhibitors still suppressed induction of target genes by IL-4 in ACLY knockout cells, suggesting off-target effects of these drugs. Our findings suggest that ACLY may not be the major regulator of nucleocytoplasmic acetyl-CoA and IL-4-induced polarization in human macrophages. Furthermore, caution should be warranted in interpreting the impact of pharmacological inhibition of ACLY on gene expression. Macrophages respond to changes in their environment, such as bacterial or viral infection, hormones, cytokines, or nutrients, with remodeling their transcriptome. Consequently, they alter their phenotype, a response known as macrophage polarization . Historide novo lipogenesis and thus, cell proliferation . IL-4 trSince we previously noticed considerable differences in metabolic requirements of human vs. murine macrophages toward IL-4-induced polarization , we quesHuman peripheral blood mononuclear cells were isolated from commercially obtained buffy coats using Ficoll density centrifugation. Monocytes were separated from lymphocytes by adherence to plastic after 1 h-incubation in serum-free medium, and differentiated into macrophages by culture in RPMI-1640 medium containing 3% heat-inactivated AB-positive human serum for 7\u201310 days. THP-1 cells were purchased from ATCC (cat. no. TIB-202) and maintained in RPMI-1640 medium containing 10% fetal bovine serum, penicillin and streptomycin. THP-1 cells were differentiated to macrophages by 24 h-treatment with 50 nM phorbol myristate acetate followed by overnight culture in serum-free medium. Unless indicated otherwise, cells were treated with 5 \u03bcM BMS-303141 (cat. no. 4609), 25 \u03bcM SB 204990 (cat. no. 4962) (both Tocris), 100 \u03bcM MEDICA 16 (cat. no. M5693), 20 mM hydroxycitrate (cat. no. 59847), 5 mM sodium acetate (cat. no. S2889), 5 mM sodium octanoate (cat. no. C5038), 1,2,3-benzene-tricarboxylic acid (cat. no. 51520), CTP inhibitor (cat. no. SML0068) , 5 \u03bcg/mL TOFA (cat. no. 10005263) (Cayman), 20 ng/mL IL-4 (cat. no. 200-04), or IL-13 (cat. no. 200-13) (Peprotech).\u2212(Ct(target)\u2212Ct(reference))] using expression of \u03b22-microglobulin or GAPDH as reference genes.Total RNA from macrophages was isolated using PeqGold RNAPure kit followed by reverse transcription using cDNA Synthesis kit . Quantitative real time PCR (Q-PCR) was carried out on a CFX96 system from Bio-Rad using iQ SYBR green . Primer sequences are listed in Supplementary Table Total cell lysates were prepared by scraping the cells into Laemmli buffer containing protease inhibitors followed by sonification. For histone extraction, cell pellets were lyzed in PBS containing 0.5% Triton X-100 , 5 mM sodium butyrate , and protease inhibitors for 10 min on ice. Lysates were centrifuged 0.5 min at 16,000 g, 4\u00b0C, and pellets containing nuclei were incubated with 0.2 M HCl overnight. After centrifugation of insoluble material for 10 min at 500 g, 4\u00b0C, supernatants were neutralized with NaOH , mixed with 5x Laemmli buffer and heated 5 min at 95\u00b0C.Protein lysates from macrophages were run on 7.5\u201315% polyacrylamide gels and blotted on nitrocellulose membranes. Following primary antibodies were used: pSTAT6 (Y641) (cat. no. #9361), STAT6 (clone D3H4) (cat. no. #5397), pSTAT3 (Y705) (cat. no. #9131), STAT3 (clone 124H6) (cat. no. #9139), pACLY (S454) (cat. no. #4331), histone H3 acK14 (clone D4B9) (cat. no. #7627), histone H3 acK23 (clone D6Y7M) (cat. no. #14932), DDK tag (clone 9A3) (cat. no. #8146) , ACLY , histone H3 acK9 (clone Y28) , histone H3 acK27 , histone H3 , nucleolin . Membranes were incubated with IRDye 700/800-coupled secondary antibodies, scanned and quantified using Odyssey imaging system (Licor).Silencing of ACLY was performed using siGENOME SMARTpool at 50 nM and Hyperfect transfection reagent . Cells were treated 96 h post-transfection.Human MDMs were transfected with 1 \u03bcg DDK-tagged ACLY or GFP-encoding plasmids using Viromer Red transfection reagent according to manufacturer's instructions. Twenty-four hours after transfection, cells were stimulated with 20 ng/mL IL-4 for 24 h.13C2-acetyl-CoA . Acetyl-CoA concentration was determined by reference to the standard. Analyst 1.6.2 and MultiQuant 3.0 (both Sciex), were used for data acquisition and analysis, respectively. Acetyl-CoA amounts in the sample were normalized to sample DNA concentration measured following incubation with H\u00f6chst 33342 fluorescent DNA dye on a Tecan fluorescence plate reader.Cells were rapidly washed with saline, and metabolism was quenched by putting the dishes into liquid nitrogen. Cells were scraped into methanol:water (5:3) mix on ice/dry ice followed by addition of cold chloroform , and vortexing for 10 min at 4\u00b0C. Aqueous phase was separated, evaporated, and re-suspended in 10% methanol . Acetyl-CoA concentration was determined with a Sciex QTrap5500 mass spectrometer operating in multiple reaction monitoring mode in positive electrospray ionization mode. Chromatographic separation was performed on an Agilent 1290 Infinity LC system (Agilent) using an Acquity HSS T3 column. The mobile phase consisted of (A) water, 10 mM ammonium formate , 0.01% ammonia, and (B) methanol, 10 mM ammonium formate, 0.01% ammonia. Elution of analytes was carried out under gradient conditions at a flow rate of 0.3 mL/min going from 2% B to 70% B in 5 min, increasing to 95% B in 1 min, hold 95% B for 0.5 min, and equilibrate at 2% B for 2.5 min. Calibration curve was performed with an authentic standard. All samples and dilutions of the standards were spiked with heavy isotope labeled internal standard containing pLentiCRISPRv2 (Addgene: cat. no. #52961) vectors harboring different sgRNAs designed using the benchling software package Table . Cell-frpost-hoc means comparison using GraphPad Prism. Differences were considered statistically significant at p < 0.05.Data are presented as means \u00b1 S.E. of at least three independent experiments. Data were analyzed by one-way analysis of variance (ANOVA) with Bonferroni Investigations were conducted in accordance with the ethical standards and according to the Declaration of Helsinki and to the national and international guidelines and have been approved by the authors' institutional review board. The ethics committee of Goethe-University waived the necessity of written informed consent when using the buffy coats from anonymized blood donors.To investigate the role of ACLY in IL-4-stimulated human macrophage polarization we initially analyzed mRNA expression of arachidonate 15-lipoxygenase (ALOX15) in MDMs in the presence of pharmacological ACLY inhibitors BMS 303141 , SB 2049A previous study showed that ACLY was necessary for IL-4-induced expression of a subset of IL-4 target genes in murine macrophages . To asseNext, we assessed the effect of silencing ACLY mRNA expression on IL-4-induced MDM polarization. For this, we treated MDMs for 96 h with control or ACLY siRNAs prior to 24 h-treatment with IL-4. Surprisingly, a knockdown of ACLY failed to reproduce the effect of ACLY inhibitors on IL-4-stimulated gene expression Figures , despiteConsidering these discrepancies, we decided to investigate the impact of ACLY inhibitors on human macrophage metabolism in more detail. Surprisingly, we did not find any differences in the levels of acetyl-CoA in cells treated with BMS 303141 or SB 204990 for 24 h Figure . AccordiWe then investigated the influence of ACLY inhibitors on initial steps of IL-4-induced signal transduction by pre-incubating MDMs with inhibitors for 1 h followed by 0.5 h-treatment with IL-4. ACLY inhibitors did not affect IL-4-triggered tyrosine phosphorylation of STAT6 with the exception of BMS 303141 and hydroxycitrate Figure . We notiMurine BMDMs responded to IL-4-stimulation with an Akt-dependent increase of ACLY phosphorylation at Ser454, which exhibited a delayed kinetics as compared with IL-4-induced Akt phosphorylation . We follde novo lipogenesis . Thus, the role of ACLY in metabolism and epigenetic regulation of terminally differentiated human macrophages remains unclear and warrants further research. Of note, ACLY may have greater impact during human macrophage differentiation, since this process is characterized by a temporary rise of de novo lipogenesis . ACSS2 contributes to histone acetylation in cancer cells, especially under hypoxia or glucose deprivation , 38, andOur results also highlight the notorious proneness of pharmacological inhibitors to off-target effects, which is in our case particularly remarkable, since we used structurally dissimilar substances . Off-target effects of ACLY inhibitors on IL-4-stimulated gene transcription could only be revealed using ACLY knockout cell line. Our findings also point to the limitation of studying human primary cells, since ACLY knockdown leaves substantial residual activity left whereas pharmacological inhibitors are unsuitable due to off-target activities. Whether induced pluripotent stem cell\u2014derived macrophages, where creation of knockout models is possible , will beDN designed the study, performed the experiments, and wrote the manuscript. SZ and IF contributed to acetyl-CoA measurements. FS, NK, and DF contributed to CRISPR/Cas9 THP-1 knockout cell line creation. BB contributed to study design and edited the final manuscript. All authors contributed to manuscript revision, read, and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Coastal regions experiencing declining dissolved oxygen are increasing in number and severity around the world. However, despite the importance of microbial metabolism in coastal hypoxia, few metagenomic surveys exist. Coastal regions experiencing declining dissolved oxygen are increasing in number and severity around the world. However, despite the importance of microbial metabolism in coastal hypoxia, few metagenomic surveys exist. Our data set from within the second largest human-caused hypoxic region provides opportunities to more deeply explore the microbiology of these systems. The northern Gulf of Mexico experiences seasonal bottom water hypoxia that can exceed 22,000\u2009km2 (http://www.noaa.gov/media-release/gulf-of-mexico-dead-zone-is-largest-ever-measured), impacting fisheries and other coastal industries (Marine systems suffering from declines in dissolved oxygen (DO) are becoming more numerous across the globe . Many codustries ; howeverActinobacteria (n = 12), Alphaproteobacteria (n = 5), Bacteroidetes (n = 6), Gammaproteobacteria (n = 3), Gemmatimonidetes (n = 1), Ignavibacteriae (n = 2), Nitrospina (n = 5), Planctomycetes (n = 7), Proteobacteria (n = 1), Synechococcus (n = 3), Verrucomicrobia (n = 3), and unclassified (n = 2). Twenty-four of the MAGs were estimated at >50% complete, with 16 estimated at >75% complete based on CheckM (https://doi.org/10.6084/m9.figshare.6911729.v1). All but 2 MAGs had estimated contamination of <9%, with 40 having estimated contamination of <3%. While several of our Actinobacteria MAGs grouped with sequences near the important OM1 clade of marine Actinobacteria (8https://doi.org/10.6084/m9.figshare.6911729.v1), but make useful references for future studies of the group.Site selection, marine chemistry metadata, and extraction, sequencing, and assembly methods were previously described , 4. Brieetes n = , Proteobacteria 810, theseeria n = , Gemmatihttps://doi.org/10.6084/m9.figshare.6911729.v1). Nitrospina MAGs were the only ones with predicted nitrite-oxidizing metabolism, matching observations from 2012 , including dissimilatory nitrate reduction to ammonium, and a few had predicted capacity for sulfur lithotrophy and possible autotrophy (see Table S1 at https://doi.org/10.6084/m9.figshare.6911729.v1). Future comparisons of these data with those from other low-DO systems will illuminate common functional features associated with hypoxia and also provide information about biogeographic distinctions among taxa associated with these regimes.Metabolic reconstruction and carbohydrate-active enzyme (CAZyme) prediction were also completed as described database under the accession numbers tandards . The ann"} +{"text": "Serratia marcescens strains cause serious nosocomial infections in humans. Here, we present the annotated genome sequence of S. marcescens podophage Pila. Similar to its closest relative, Enterobacteria phage T7, Pila has a 38,678-bp genome, predicted to encode 51 protein-coding genes, and contains 148-bp direct terminal repeats.Multidrug-resistant Serratia marcescens strains cause serious nosocomial infections in humans. Here, we present the annotated genome sequence of S. marcescens podophage Pila. Similar to its closest relative, Enterobacteria phage T7, Pila has a 38,678-bp genome, predicted to encode 51 protein-coding genes, and contains 148-bp direct terminal repeats.Multidrug-resistant Serratia marcescens, a facultative, Gram-negative bacterium of the family Enterobacteriaceae, causes nosocomial infections in severely immunocompromised or critically ill patients aerobically at 30\u00b0C and 37\u00b0C in LB broth and agar (BD). This phage was plaque purified, via the soft-agar overlay method (www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control of the 4,413 total reads in the phage-containing index, and reads were trimmed with the FastX Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit). SPAdes v3.5.0 was used with default parameters to assemble a single contig at 14.9-fold coverage , using default parameters unless otherwise stated . PhageTerm analysis predicted the genomic termini to be 148-bp direct terminal repeats, typical for T7-like phages .The 38,678-bp double-stranded DNA genome of podophage Pila has a G+C content of 48.8%. The 51 predicted protein-coding genes correspond to a coding density of 92.5%. Notably, Pila shares 83.7% nucleotide identity with e phages , which iMN098329, BioProject accession no. PRJNA222858, SRA accession no. SRR8892142, and BioSample accession no. SAMN11408657.The genome sequence and associated data for phage Pila were deposited under GenBank accession no."} +{"text": "Its\u2019 LOD is more than 74 times lower than the traditional Cu@Ni CSNPs modified working electrode. It also has higher sensitivity and wider linear range. This indicates the great potential of applying this kind of nano composites in electrode modification.In present work, a highly sensitive biosensor with high selectivity for glucose monitoring is developed based on novel nano-composites of nitrogen doped graphene quantum dots (N-GQDs) and a novel bimetallic Cu/Ni core-shell nanoparticles (CSNPs) (Cu@Ni CSNPs/N-GQDs NCs). With the tuned electronic properties, N-GQDs helped bimetallic core-shell structure nanomaterials from aggregation, and separate the charges generated at the interface. This novel nano-composites also have the good electrical conductivity of N-GQDs, catalyst property of Cu/Ni bimetallic nano composite, Cu@Ni core-shell structure and the synergistic effect of the interaction between bimetallic nano composite and N-GQDs. While modified the electrode with this novel nano-composites, the sensor\u2019 linear range is 0.09 ~ 1 mM, and the limit of detection (LOD) is 1.5 \u03bcM (S/N = 3) with a high sensitivity of 660 \u03bcA mM With the rapid development of nanotechnology, a lot of carbon materials have emerged in recent years, such as fullerenes, multi-wall carbon nanotubes, carbon nanofibers, graphene, graphenOwing to these properties, GQDs have gained wide attention for their enormous potential in varies applications. For instance they are widely applied in photovoltaics, organic light emitting diodes, fuel cells, photocatalysis, bioimaging, biosensing, biomedicine, environmental monitoring, thermal interface materials etc\u20138. Biose2 NTs[core-shellnanostructure of Ni/Cu bimetallic have attracted researchers\u2019 attention for glucose sensing[On the other hand, various nano-structured metals, alloys and metal oxides have been extensively applied in non-enzymatic electrode modification, due to their increased specific surface area, rapid mass transport, significant catalytic activity and so on\u201322. Amon2 NTs, Ni/Cu/M2 NTs are all 2 NTs\u201339. On te sensing.-1 cm-2. Comparing with the sensor based on Cu@Ni CSNPs modified working electrode, the electrode modified with Cu@Ni CSNPs/ N-GQDs NCs makes the sensor\u2019s LOD more than 74 times lower, higher sensitivity and wider linear range. These indicate that well designed N-GQDs\u2019 composites have great application prospects in improving electron migration rate and electrocatalytic performance of electrode surface.In this work, the novel bimetallic Cu/Ni and N-GQDs nano-composites (Cu@Ni CSNPs/N-GQDs NCs) have been synthesized by hydrothermal method and a one-pot solvothermal method. With our gentle synthesis method, the size of N-GQDs can be uniform with the nitrogen content about 12.93%. The size of Cu @ni CSNPs/N-GQDs NCs is 30\u201380 nm, and N-GQDs is uniformly coated on its surface, with bimetallic Cu/Ni co-catalytic performance and good electrical conductivity. A series of non-enzymatic glucose sensors are constructed with Cu@Ni CSNPs/N-GQDs NCs modified glassy carbon electrode (Cu@Ni CSNPs/N-GQDs/GCE), Cu@Ni CSNPs/GCE and Cu@Ni CSNPs/N-GQDs/GCE. Their electrochemical properties and electrocatalytic activities are compared. It is excited that Cu@Ni CSNPs/N-GQDs/GCE shows the best electrocatalytic performance for glucose oxidation, and displays the lowest detection limit(LOD) 1.5 \u03bcM (S/N = 3), a wider linear range from 0.09 mM to 1 mM and high sensitivity 660 \u03bcA mM2\u00b72H2O, 99.0%), Nickel (II) chloride hexahydrate , NaOH (96.0%), AA (\u226599.7%), sucrose, glucose and NaCl (\u226599.5%) were purchased from XiLong Scientific. Citric acid (99.5%) and DA (98%) were purchased from Aladdin. 5wt% of Nafion was purchased from Sigma Aldrich. Ethylene glycol , maltose, fructose, D-galactose and UA (99%) were purchased from Sinopharm Chemical Reagent Co., Ltd. Ultrapure water was used throughout the experiments, and all reagents which were not mentioned above were of analytical grade.Urea (\u226599.0%), N, N-dimethyl formamide , Copper (II) chloride dihydrate (CuCl2 20), ultraviolet-visible spectra , Fourier transform infrared spectra and X-ray diffraction measurement . All electrochemical experiments were performed on the electrochemical workstation . The working electrodes were modified glassy carbon electrode , the reference electrode was saturated calomel electrode (SCE), and a platinum wire electrode was usedas the auxiliary electrode.The samples were characterized by X-ray photoelectron spectra , transmission electron microscopy (TEM) and high resolution transmission electron microscope , Ipc = 6.1 \u00d710\u22123 v + 0.45125 (R2 = 0.99109), as shown in Ipa = -5.12 \u00d710\u22123 v\u20140.0932 (R2 = 0.99914), Ipc = 2.56 \u00d710\u22123 v + 0.06168 (R2 = 0.99952), as shown in 3+ and Ni2+ species[The modified Cu@Ni CSNPs/Nafion/GCE and Cu@Ni CSNPs/N-GQDs/Nafion/GCE electrodes were placed in cell containing 0.1 M NaOH solution to be tested at different scan rates. As shown in + species,42.-1. In Ipa = -0.00127 c\u20142.12802 (R2 = 0.95372), Ipc = 2.34641 \u00d710\u22125 c + 0.59356 (R2 = 0.63127). In Ipa = - 8.9 \u00d710\u22124 c\u20140.9307 (R2 = 0.99045), Ipc = -1.8 \u00d710\u22124 c + 0.3803 (R2 = 0.99435). Compared with the above two sets of experiments, Cu@Ni CSNPs/N-GQDs/Nafion/GCE has better linearity and better determination of glucose concentration.CVs was used to study the relationship between current and glucose concentration. The CVs was obtained by placing modified electrodes in solutions containing different glucose concentrations at scan rate of 100 mV si-t curve test.The CVs of modified Cu@Ni CSNPs/N-GQDs/Nafion/GCE electrode at different scan rates in 0.1 M NaOH containing 10 \u03bcM glucose is shown in i-t curve of Cu@Ni CSNPs/Nafion/GCE at different glucose concentrations. The linear relationship between current and glucose concentration is shown in i = 0.0853 c\u20140.00018, R = 0.99973). The detection limit of glucose using Cu@Ni CSNPs/Nafion/GCE is found to be 111.4 \u03bcM (S/N = 3) with the sensitivity of 85.3 \u03bcA mM-1 cm-2. As shown in i-t curve of Cu@Ni CSNPs/N-GQDs/Nafion/GCE at different glucose concentrations. The linear relationship between current and glucose concentration is shown in i = 0.66 c + 0.125, R = 0.99952). The detection limit of glucose using Cu@Ni CSNPs/N-GQDs/Nafion/GCE is found to be 1.5 \u03bcM (S/N = 3) with the sensitivity of 660 \u03bcA mM-1 cm-2. From this, it can be clearly concluded that Cu@Ni CSNPs/N-GQDs/Nafion/GCE is more sensitive to glucose determination. This is because GQDs itself is conductive, and N-GQDs has more hole electron pairs due to nitrogen atoms have been successfully doped, which greatly improve the electrical conductivity. Glucose is catalyzed by Cu and Ni in the composites, and N-GQDs are coated on the surface of Cu@Ni CSNPs, which improves the electron mobility between the electrode and the electrolyte, so that the working electrode to detect glucose within a very short time, which greatly improves the sensitivity of the electrode and reduces the detection limit, providing conditions for real-time, rapid and accurate determination of glucose concentration.Under the optimal conditions, +0.6 V is selected as the constant potential in the range of anodic potential of +0.5 ~ 0.7 V. In The anti-interference property and selectivity for glucose determination are crucial in the development of glucose biosensors. Chemical species such as uric acid (UA), dopamine (DA), ascorbic acid (AA), and NaCl that easily oxidize are always present with glucose in human blood. In this study, interference experiments were detected by adding 0.1 mM interference component to a 0.1 M NaOH solution containing 0.5 mM glucose. As shown in -1 cm-2, rapid response time (3 s). Comparing with the sensor based on Cu@Ni CSNPs modified working electrode, this novel nano-composite of Cu@Ni CSNPs/ N-GQDs NCs makes the sensor\u2019s LOD more than 74 times lower, also has higher sensitivity and wider linear range. Furthermore, the interference components show insignificant interference in determination of glucose, and Cu@Ni CSNPs/N-GQDs/Nafion/GCE has high selectivity for glucose determination. The results indicate that the biosensor based on Cu@Ni CSNPs/N-GQDs/Nafion/GCE has potential application prospect in the determination of glucose, the application of GQDs in biosensor has a great prospect. It also indicates the great potential to apply this kind of nano composites in electrode modification and high sensitivity biomolecule detection.In summary, Cu@Ni CSNPs and Cu@Ni CSNPs/N-GQDs NCs were successfully synthesized by one-pot solvothermal method. Our experiments show that the electrochemical response of Cu@Ni CSNPs/N-GQDs/Nafion/GCE to glucose determination was the highest. Cu@Ni CSNPs/N-GQDs/Nafion/GCE has the advantages of low cost, high sensitivity and good selectivity. One more advantage of Cu@Ni CSNPs/N-GQDs/Nafion/GCE is its\u2019 wide linear range is 0.09 ~ 1 mM. And the detection limit is 1.5 \u03bcM (S/N = 3), high sensitivity of 660 \u03bcA mMS1 Table(TIF)Click here for additional data file.S1 FigA) full spectrum, (B) C1s spectrum, (C) N1s spectrum, (D) O1s spectrum.((TIF)Click here for additional data file.S2 FigA) C1s spectrum, (B) Cu2p spectrum, (C) Ni2p spectrum.((TIF)Click here for additional data file.S3 FigMapping of Cu@Ni CSNPs/N-GQDs NCs (a), mapping-Cu (b), mapping-Ni (c).(TIF)Click here for additional data file.S4 FigA) and the histogram (B) of the Cu@Ni CSNPs/N-GQDs/GCE with successive addition of 0.5 mM glucose, 0.1 mM DA, 0.1 mM AA, 0.1 mM UA, 0.1 mM NaCl and 0.5 mM glucose in 0.1 M NaOH solution at +0.6 V, respectively.Amperometric response ((TIF)Click here for additional data file.S5 FigA) and the histogram (B) of the Cu@Ni CSNPs/N-GQDs/GCE with successive addition of 0.5 mM glucose, 0.1 mM maltose, 0.1 mM sucrose, 0.1 mM fructose, 0.1 mM D-galactose, 0.5 mM glucose in 0.1 M NaOH solution at +0.6 V, respectively.Amperometric response ((TIF)Click here for additional data file."} +{"text": "Testing sampling effort and relative abundance descriptors of belowground ectomycorrhizal fungi in a UK planted scots pine woodland. Mycology. Agerer R, Ammirati J, Blanz P, Courtecuisse R, Desjardin DE, Gams W, Hallenberg N, Halling R, Hawksworth DL, Horak E, Korf RP, Mueller GM, Oberwinkler F, Rambold, G, Summerbell RC, Tribel D and Watling R. 2000. Open letter to the scientific community of mycologists. Canadian Journal of Botany. 78:981\u2013983Agerer R. 1991. Characterization of ectomycorrhiza. In: Norris JR, Read DJ, Varma AK, editors. Techniques for the study of mycorrhiza. Methods in microbiology. 23:25\u201373.Palmer MW. 1991. Estimating species richness: the second order jackknife reconsidered. Ecology. 72:1512\u20131513.Erland S and Taylor AFS. 2002. Diversity of ecto-mycorrhizal fungal communities in relation to the abiotic environment. In: van der Heiden MGA and Sanders IR, editors. Mycorrhizal ecology. Ecological Studies. Berlin: Springer; p. 163\u2013200.When the above article was first published online, the following references were omitted by mistake:The caption for Figure 2 incorrectly read:\u201c(a) Illustration of transect line (blue dashed line) and replicated sampling points (red dots). (b) Field sampling procedure in stand 8. (1) transect line, (2) soil samples in a bucket, (3) soil corer. (c) Detail of soil sample (1) in the soil corer (2) (3) Ruler 15 cm.\u2019\u2019This has now been corrected to:\u201c(a) Illustration of transect line (dashed line) and replicated sampling points (dots). (b) Field sampling procedure in stand 8. (1) transect line, (2) soil samples in a bucket, (3) split soil core sampler. (c) Detail of soil sample (1) in the split soil core sampler (2) (3) Ruler 15 cm.\u2019\u2019The caption for figure 5 incorrectly read:\u201cResult of regression analysis: r2 = 0.676**, p < 0.01**.\u2019\u2019This has now been corrected to:\u201cResult of regression analysis: r2 = 0.676, p < 0.01.\u2019\u2019In Table 1 the reference to Agerer, mistakenly listed the year as 2006 in three places, this has now been corrected to Agerer 1987\u20132002.These items have now been corrected in both the print and online versions of the journal.Taylor and Francis apologises for these errors."} +{"text": "This article has been corrected: During the assembly of Figure 2B, the same image was inadvertently used for both H1299 (pEGFP-C3) and H1299 (pEGFP-4.1N) groups at 0h time point. The proper Figure 2 B specific for H1299 (pEGFP-C3) and H1299 (pEGFP-4.1N) groups are shown below. The authors declare that these corrections do not change the results or conclusions of this paper.509-523. https://doi.org/10.18632/oncotarget.6312Original article: Oncotarget. 2016; 7:509\u2013523."} +{"text": "Butia ordorata) and fishtail palm (Caryota uren), using liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF/MS) and assess their antioxidant potential. The total phenolic content (TPC), total tannins content (TTC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) antioxidant assay and 2,2\u2032-azinobis-(3-ethylbenzo-thiazoline-6-sulfonic acid) (ABTS) scavenging abilities and ferric reducing antioxidant power (FRAP) were higher in the jelly palm fruit while total flavonoid contents (TFC) were higher in the fishtail palm. The LC-ESI-QTOF/MS tentatively identified a total of 86 phenolic compounds in both jelly and fishtail palm fruits. Although both palm fruits exhibited different phenolic profiles, hydroxycinnamic acids and flavonols were the most common in both. In high performance liquid chromatography photodiode array (HPLC-PDA) quantification, 4-hydroxybenzoic acid (317.46 \u00b1 4.68 \u00b5g/g) and catechin (4724.00 \u00b1 32.39 \u00b5g/g) were the most abundant phenolic acid and flavonoid quantified in the jelly palm fruit, respectively. Quercetin (557.28 \u00b1 7.81 \u00b5g/g) and kaempferol 3-O-glucoside (220.99 \u00b1 2.06 \u00b5g/g) were the most abundant flavonoids quantified in the fishtail palm. Our study indicates that palm fruit is a good source of polyphenols and has strong antioxidant potential for health promotion. Furthermore, this study provides the scientific basis for an exploitation of jelly and fishtail palm fruits in the food, pharmaceutical and nutraceutical industries. Palm fruits have gained growing attention for their nutrition values and health promotion perspectives. They have a diverse range of bioactive compounds including carotenoids, vitamins, dietary fibres and especially polyphenolic compounds. These polyphenolic compounds contribute to the putative health benefits of palm fruits. Nevertheless, the detailed information about these polyphenols in palm fruits is limited. The present work was conducted to comprehensively characterize polyphenols in two palm fruits, jelly palm ( Palm fruits are mostly grown in tropical regions and are rich sources of bioactive compounds such as polyphenols, vitamin E, carotenoids and unsaturated fatty acids . BioactiButia ordorata) is a tropical palm species whose fruits and leaves can be processed into different food products +m/z 339.1081) and 3-O-methylrosmarinic acid ([M + H]+m/z 375.1069) were tentatively characterized in fishtail palm. Hoffman et al. [p-coumaroylquinic acid (p-coumaric acid) in the methanolic extract of jelly palm pulp and nectar.Compound 2 and 5 (retention time (RT) = 19.734 and 37.691 min) with [M \u2212 H]ectively , while c355.1017 . There wion mode , while flm fruit . Sinapinly palms . The ferly palms . The prely palms ,29,30. C+ at m/z 139.0394 and 4-hydroxybenzoic acid 4-O-glucoside with RT = 7.456 min and [M \u2212 H]\u2212 at m/z 299.0793 in extracts of jelly and fishtail palm, respectively (m/z 137.0242) and hydroxybenzoic hexose (m/z 299.0070) have already been characterized in jelly palm by Hoffmann, Carvalho, Barbieri, Rombaldi and Chaves + at m/z 167.0687 and 227.0916 were assigned as 3-hydroxyphenylpropionic acid and dihydrosinapic acid, while 3-hydroxy-3-(3-hydroxyphenyl) propionic acid was tentatively identified by a molecular ion at m/z 181.0513 in negative ionization mode. The hydroxyphenylpentanoic acid compounds conjugated with valerolactone were proposed for both palm fruits and 5--\u03b3-valerolactone ([M \u2212 H]\u2212m/z 207.0667) were detected and 23 detected in ethanolic extract of fishtail palm fruits were tentatively identified as kaempferol 3-O-glucosyl-rhamnosyl-galactoside and kaempferol 3-O-glucoside, respectively, in negative ionization mode (O-glucoside (14) tentatively identified by the parent ion at m/z 449.1072 in ESI+ mode , quercetin 3-O-rutinoside (16), and quercetin (17) exhibiting precursor ion at m/z 465.1008, 611.1579 and 303.0486 in positive ionization mode were proposed for jelly palm fruit (O-glucoside (RT = 37.133 min) giving precursor ion at m/z 463.0878 in ESI\u2212 mode . The detection of aglycone quercetin in the jelly palm was reported previously d Chaves also cha studies . Compounm/z 595.1634 and 595.163, respectively, was tentatively characterized in extracts of jelly and fishtail palm fruits. Compound 21 in the jelly palm and compound 32 in the fishtail palm were tentatively identified as apigenin 7-O-apiosyl-glucoside and apigenin 6-C-glucoside, respectively. The aglycone apigenin has been identified in different solvent extracts of jelly palm [\u2212 ion at m/z 461.1093 and [M + H]+ ion at m/z 549.1220, were proposed as chrysoeriol 7-O-glucoside and chrysoeriol 7-O-, respectively and fishtail palm fruit , respectively. The aglycone hesperetin displaying [M \u2212 H]\u2212 ion at m/z 301.0707 has been proposed for jelly palm fruits in the study of Hoffmann, Carvalho, Barbieri, Rombaldi and Chaves + ion at m/z 481.1340 was proposed as 3\u2019-O-methyl-(-)-epicatechin 7-O-glucuronide. Catechin has also been detected in ethanolic extracts of jelly palm in a study reported by Beskow, Hoffmann, Teixeira, Fachinello, Chaves and Rombaldi Rombaldi . ProcyanO-sambubioside-5-O-glucoside (RT = 25.648 min) and peonidin 3-O-diglucoside-5-O-glucoside (RT = 26.857 min) exhibiting precursor ions at m/z 756.2092 and 786.2195 were detected in jelly palm (O-sophoroside (RT = 44.148 min) with parent ions at m/z 624.1664 was tentatively characterized in fishtail palm (m/z 772.2033 and 564.1457 were assigned as cyanidin 3-O-diglucoside-5-O-glucoside (29) and pelargonidin 3-O-sambubioside (32), respectively. In fishtail palm fruit, compound 40 exhibiting precursor ion at m/z 520.1225 was proposed as petunidin 3-O-(6\u2019\u2019-acetyl-glucoside). Previously, two cyanidin derivative anthocyanins were characterized in jelly palm fruit + ion at m/z 151.1108 was detected in fishtail palm. Pyrogallol was the only compound belonging to other polyphenols subclass detected in both palm fruits in the positive mode of ionization (Compound 54 (RT = 33.745 min) and 55 RT = 79.779 min) tentatively characterized in the extract of fishtail palm fruit with [M \u2212 H]opoletin . 3-Methynization . Previou.779 min The screening and characterization of polyphenolic compounds showed that some of the polyphenols presented in two palm fruits have strong antioxidant potential. Hydroxycinnamic acid derivatives, hydroxybenzoic acids and their derivatives, protocatechuic acid, chlorogenic acid, catechin, matairesinol, hydroxytyrosol, quercetin and kaempferol derivatives are regarded as potential compounds showing considerable free radical scavenging capacity ,38,39. TO-glucoside, catechin, quercetin and kaempferol 3-O-glucoside) based on the LC-ESI-QTOF/MS characterization and previously reported antioxidant activities. The quantification of individual polyphenols was computed considering the UV\u2013Vis absorption and calibration curves of external standards.Seven polyphenols were targeted to quantify through HPLC-PDA including three phenolic acids and four flavonoids (quercetin 3-fw) was higher than fishtail palm fruit (140.23 \u00b1 1.78 \u00b5g/g fw). Boeing et al. [fw) was only detected in jelly palm fruit, while protocatechuic acid was only found in fishtail palm. Beskow, Hoffmann, Teixeira, Fachinello, Chaves and Rombaldi [The polyphenols quantified through HPLC-PDA in the jelly palm were higher than in fishtail palm. These HPLC results support our TPC values determined using the Folin\u2013Ciocalteu method. Among the three selected phenolic acids, chlorogenic acid was the only phenolic acid detected in both palm fruits . The cong et al. already fw in jelly palm and 557.28 \u00b1 7.81 \u00b5g/g fw in fishtail palm fruit. Beskow, Hoffmann, Teixeira, Fachinello, Chaves and Rombaldi [fw), which might be involved in higher antioxidant activity.Flavonols were found to be higher in fishtail palm fruit as compared to jelly palm fruits. Quercetin was the major compound in this group, with a concentration of 360.19 \u00b1 4.53 \u00b5g/g It has been established in this work that LC-ESI-QTOF/MS is an effective and powerful analytical tool to characterize most of the polyphenols present in jelly and fishtail palm fruits. The TPC, TTC, DPPH, FRAP and ABTS scavenging activity was higher in jelly palm compared to fishtail palm. LC-ESI-QTOF/MS characterizes a total of 42 and 60 phenolic compounds in jelly and fishtail palm fruits, respectively. Hydroxycinnamic acids and flavonols were the most common polyphenols reported in both palm fruits. The HPLC-PDA enabled the quantification of some targeted phenolic compounds and found that catechin and quercetin were the most abundant polyphenols in jelly and fishtail palm, respectively. In short, both palm fruits are a good source of polyphenols and could be utilized in food, feed and pharmaceutical industries."} +{"text": "P < 0.001, RFS; P < 0.001), cytoplasmic expression of FAM83H , nuclear expression of PANX2 , cytoplasmic expression of PANX2 , co-expression pattern of nuclear FAM83H and nuclear PANX2 . In multivariate analysis, nuclear expression of FAM83H and the co-expression pattern of nuclear FAM83H and PANX2 were independent indicators of shorter survival of CCRCC patients. Cytoplasmic expression of FAM83H was associated with shorter RFS (P = 0.030) in multivariate analysis. In Caki-1 and Caki-2 CCRCC cells, knock-down of FAM83H decreased PANX2 expression and cell proliferation, and overexpression of FAM83H increased PANX2 expression and cell proliferation. These results suggest that FAM83H and PANX2 might be involved in the progression of CCRCC in a co-operative manner, and their expression might be used as novel prognostic indicators for CCRCC patients.FAM83H is primarily known for its role in amelogenesis; however, recent reports suggest FAM83H might be involved in tumorigenesis. Although the studies of FAM83H in kidney cancer are limited, a search of the public database shows a significant association between FAM83H and pannexin-2 (PANX2) in clear cell renal cell carcinomas (CCRCCs). Therefore, we evaluated the clinicopathological significance of the immunohistochemical expression of FAM83H and PANX2 in 199 CCRCC patients. The expression of FAM83H and PANX2 were significantly associated with each other. In univariate analysis, individual, and co-expression pattern of FAM83H and PANX2 was significantly associated with shorter overall survival (OS) and relapse-free survival (RFS) of CCRCC patients: nuclear expression of FAM83H (OS; Family with sequence similarity 83 H (FAM83H) is one of the eight FAM83 family members, from FAM83A to FAM83H , 2. Accohttp://www.oncolnc.org). In addition, the cBioPortal database indicated pannexin-2 (PANX2) as the gene most significantly associated with FAM83H expression in CCRCCs is the most common type of kidney cancer . Most CCn CCRCCs , 12. Altst 2018) , 12. PANst 2018) . Howeverst 2018) . TherefoThis study evaluated CCRCC patients who underwent surgical resection between July 1998 and August 2011. Among them, 199 CCRCCs with complete medical records were available with original H&E slides, and paraffin-embedded tissue blocks. Clinical information was obtained by reviewing the medical records. The histopathologic information was retrospectively reviewed according to the 2016 World Health Organization classification of the renal tumors , and staIn this study, tissue microarrays were used for immunohistochemical staining. The tissue microarrays have 3.0 mm cores, and one core was arrayed per case from the areas composed mainly of tumor cells with no degenerative change or necrosis. The histologic sections from the tissue microarray tissue blocks were deparaffinized and boiled for 20 min in pH 6.0 antigen retrieval solution in a microwave oven. Primary antibodies for FAM83H and PANX2 was used. The slides were visualized with the enzyme substrate 3-amino-9-ethylcarbazole and counterstained with hematoxylin. The scoring for the immunohistochemical staining slides was performed without clinical information by two pathologists (KYJ and KMK) with consensus under a multi-viewing microscope. The immunohistochemical positivity for FAM83H and PANX2 was separately scored according to their expression patterns in the cytoplasm and nuclei. The immunohistochemical scores were obtained by adding their staining intensity score ranging from zero to three and staining area score ranging from zero to five , 19. The2 and 37\u00b0C.In this study, we used two human CCRCC cell lines. Caki-1 and Caki-2 cells were purchased from the Korean Cell Line Bank . The Caki-1 and Caki-2 cells were cultured in DMEM medium with 10% fetal bovine serum and streptomycin and penicillin (100 U/ml) in 5% COThe vector of shRNA for FAM83H was purchased from GenePharma . The sense and antisense sequences of the FAM83H shRNA were the 5\u2032-CAC CGC TCA TCT TCA GCA CGT CAC ATT CAA GAG ATG TGA CGT GCT GAA GAT GAG CTT TTT TG-3\u2032 and 5\u2032-GAT CCA AAA AAG CTC ATC TTC AGC ACG TCA CAT CTC TTG AAT GTG ACG TGC TGA AGA TGA GC-3\u2032, respectively. The vector for FAM83H overexpression was purchased from GeneCopoeia . JetPRIME transfection reagent was used for transfection.To isolate protein, the cells were lysed with PRO-PREP Protein Extraction Solution with 1x phosphatase inhibitor cocktails 2, 3 (Sigma-Aldrich). The primary antibodies for FAM83H , PANX2 , and actin (Sigma-Aldrich) were used for western blots.RNA was isolated with an RNeasy Mini Kit . The isolated RNA was reverse transcribed by probing 1.5 \u03bcg RNA with Reverse Transcription kits to generate cDNA that was used for quantitative polymerase chain reaction using Applied Biosystems Prism 7900HT sequence Detection System and SYBR Green Master PCR Mix (Applied Biosystems). The values were normalized to the expression of the glyceraldehyde-3-phosphate dehydrogenase reference housekeeping gene. All experiments were performed in triplicate. The sequences of the primers used in quantitative reverse-transcription polymerase chain reaction are listed in Table 5) and Caki-2 (2 \u00d7 105) cells were seeded in 24-well plates and the number of viable cells was counted by using hemocytometer. For the MTT assay, Caki-1 (3 \u00d7 103) and Caki-2 (3 \u00d7 103) cells were seeded in 96-well culture plates, and absorbance was measured at 560 nm using a microtiter plate reader .The proliferation of cells was evaluated by counting the number of cells and performing a 3--2,5-diphenyltetrazonium bromide (MTT) assay and a colony-forming assay. To compare the number of cells in control, FAM83H knock-down, and FAM83H overexpression groups, Caki-1 was used throughout, and P < 0.05 were considered statistically significant.The cut-off points of immunohistochemical staining scores for FAM83H and PANX2 were determined by receiver operating characteristic curve analysis , 19. SurP < 0.001), Cy-FAM83H (P < 0.001), Nu-PANX2 (P < 0.001), and Cy-PANX2 (P = 0.002) was significantly associated with death of patients from CCRCC and higher tumor stage (P = 0.001) (Table P = 0.004), larger tumor size (P < 0.001), higher tumor stage (P < 0.001), and higher histologic grade (P = 0.037) (Table P = 0.009), tumor size (P = 0.001), tumor stage (P < 0.001), and tumor necrosis (P = 0.003) (Table P = 0.032), tumor size (P < 0.001), tumor stage (P < 0.001), lymph node metastasis (P = 0.018), nuclear grade (P = 0.006), and tumor necrosis (P = 0.011) , tumor size (P < 0.001), tumor stage (P < 0.001), tumor necrosis (P = 0.006), Nu-FAM83H (P < 0.001), Cy-FAM83H (P < 0.001), Nu-PANX2 (P < 0.001), and Cy-PANX2 (P < 0.001) (Table P = 0.033), age (P = 0.022), tumor size (P < 0.001), tumor stage (P < 0.001), lymph node metastasis (P = 0.010), nuclear grade (P = 0.006), Nu-FAM83H (P < 0.001), Cy-FAM83H (P < 0.001), Nu-PANX2 (P < 0.001), and Cy-PANX2 (P < 0.001) , Nu-FAM83H , Cy-FAM83H , Nu-PANX2 , and Cy-PANX2 positivity are presented in Figure Nuclear positivity of FAM83H expression had a 6.205-fold greater risk of death and a 4.949-fold greater risk of relapse or death of CCRCC patients. Cy-FAM83H positivity showed a 4.617-fold greater risk of death and a 5.369-fold greater risk of relapse or death of CCRCC patients (Table P = 0.047), tumor stage (P = 0.018), tumor necrosis (P = 0.031), and Nu-FAM83H positivity (P < 0.001) (Table P < 0.001), Nu-FAM83H positivity (P = 0.003), and Cy-FAM83H positivity (P = 0.030) were the factors significantly associated with RFS of CCRCC patients in multivariate analysis , intermediate (Nu-FAM83H+/Nu-PANX2\u2212), and poor prognostic (Nu-FAM83H+/Nu-PANX2+) groups that were significantly associated with OS and RFS in univariate analysis greater risk of OS and 4.903-fold greater risk of RFS compared with the Nu-FAM83H\u2212/Nu-PANX2\u2212 and Nu-FAM83H\u2212/Nu-PANX2+ subgroups greater risk of lower OS and a 160% greater risk of lower RFS compared with the Nu-FAM83H\u2212/Nu-PANX2\u2212 and Nu-FAM83H\u2212/Nu-PANX2+ subgroups , higher expression of FAM83H RNA was associated with shorter OS of CCRCC predicted shorter survival of hepatocellular carcinoma patients . In a reConcerning the mechanism how FAM83H is involved in tumorigenesis, the role of FAM83H in the proliferation of cancer cells has been suggested in prostatic cancer cells . In addihttps://www.proteinatlas.org) also reported FAM83H expression to be in the cytoplasmic membrane and cytoplasm. In colorectal cancer cells, FAM83H expression was localized in the cytoplasm in association with keratin cytoskeleton structures , 12, theP = 0.004) and RFS (P = 0.015). The patients with Nu-PANX2-positive CCRCC had a 3.186-fold greater risk of cancer-related death and a 2.302-fold greater risk of relapse or cancer-related death compared with the patients with Nu-PANX2-negative CCRCC. Therefore, despite limited reports on the role of PANX2 in human cancers, our results suggest PANX2 as a potential biologic marker of CCRCC. In addition, when we searched the OncoLnc database (http://www.oncolnc.org), higher expression of PANX2 RNA was associated with shorter OS of CCRCC patients greater risk of death compared to CCRCC patients with low expression of PANX2 RNA. However, in contrast, PANX2 inhibited proliferation and tumor formation of C6 glioma cells in in vitro and in vivo , 12. Morn; 0.36) . In addiIn conclusion, this study presents the roles for FAM83H and PANX2 in CCRCCs and suggests that FAM83H and PANX2 are closely associated and involved in the progression of CCRCCs. Especially, the expression patterns of FAM83H and PANX2 were significantly associated with shorter survival of CCRCC patients. In addition, the co-expression patterns of FAM83H and PANX2 were also significantly associated with the survival of CCRCC patients. Therefore, individual and co-expression patterns of FAM83H and PANX2 might be useful prognostic indicators for CCRCC patients. Furthermore, understanding for the role of FAM83H in conjunction with PANX2 might be helpful in establishing a new therapeutic strategy for CCRCCs.KMK, UH, JB, S-HP, KSK, SH, HP, HL, MC, WM, MK, and KJ participated in the study design. KMK, UH, and JB performed the experiment. KMK, UH, JB, S-HP, KSK, SH, HP, HL, MC, WM, MK, and KJ were involved in data collection and data interpretation. KMK, UH, JB, S-HP, KSK, SH, HP, MC, WM, and KJ participated in the statistical analyses. KMK, UH, JB, S-HP, KSK, SH, HP, HL, MC, WM, MK, and KJ wrote the manuscript. All authors read and approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "The correct citation is: Bispo PC, Balzter H, Malhi Y, Slik JWF, Santos JR, Renn\u00f3 CD, et al. (2017) Drivers of metacommunity structure diverge for common and rare Amazonian tree species. PLoS ONE 12(11): e0188300. In the Funding section, the author Fernando D. Esp\u00edrito-Santo\u2019s initials are listed incorrectly. The sentence should read: FDES was supported by Natural Environment Research Council (NERC) grants (BIO-RED NE/N012542/1 and AFIRE NE/P004512/1) and Newton Fund (The UK Academies/FAPESP Proc. N\u00b0: 2015/50392-8 Fellowship and Research Mobility)."} +{"text": "The family environment is often overlooked in caregiver research and assessment, despite having implications for caregiver health and well-being . The purpose of the present study was to examine differences on two types of family conflict (beliefs and support) among a diverse sample of caregivers. The present sample consisted of help-seeking (n = 375) and non-help-seeking (n = 415) caregivers . Caregivers filled out the Caregiver Reaction Scale , a multidimensional assessment of the caregiver experience. Results of a 2 x 2 ANOVA indicated that help-seeking caregivers reported significantly more conflict over family beliefs than did non-help-seeking caregivers , F = 21.10 p < .001. Adult children caregivers reported significantly greater conflict over family beliefs (M = 1.91) than did spouse caregivers (M = 1.60), F = 10.66, p < .001. Adult children caregivers also reported significantly greater conflict over family support (M = 1.87) than did spouse caregivers (M = 1.57), F = 16.23, p < .001. Results highlight that certain caregiving contexts potentially increase family conflict, which has implications for caregiver burden. Family conflict over beliefs is also related to help-seeking in caregivers. Findings inform appropriate assessment and intervention regarding the family environment in caregiving."} diff --git a/PMC_clustering_728.jsonl b/PMC_clustering_728.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..668e8411042c5d6fb185c1936dfe7a312bcf2944 --- /dev/null +++ b/PMC_clustering_728.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:57b2c179db95daa7685e9c9079c7d3d26b3972434a6f978433649b36600f3e9e +size 29340198 diff --git a/PMC_clustering_729.jsonl b/PMC_clustering_729.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..20e84f5f5a61ee0f2a0e8996841018cd83ac04c8 --- /dev/null +++ b/PMC_clustering_729.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:239bea180ef90905c66c08650516ea4896e049522f7295644885f30d774f4337 +size 91020818 diff --git a/PMC_clustering_730.jsonl b/PMC_clustering_730.jsonl new file mode 100644 index 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For the first time, NSLTCP data will allow analyses at the services-user level. New policy-relevant topics about centers and ADSC participants include reasons for hospitalization, medication use, patient-centered and end-of-life care, staffing turnover, and unmet needs. Additionally, the presentation highlights latest findings from the 2016 survey. About 53% of centers were primarily medical model. Almost 79% of participants in medical model centers used Medicaid, compared to 51% in social model centers. About 4% of participants had at least one 90-day hospitalization. 40% of participants had difficulty bathing. The most prevalent chronic conditions were hypertension (50%), arthritis (38%), and diabetes (31%). Nearly 40% of participants had an advance directive. Findings are contextualized within the broader understanding of ADSCs."} +{"text": "Although medication for addiction treatment (MAT) is known to be the most effective treatment for opioid use disorder (OUD), these medications are widely underutilized, especially among older adults and racial/ethnic minorities. Of the three main MAT modalities, Medicare covered buprenorphine and naltrexone in 2017; methadone was not covered until 2020. We examined MAT prescribing among elderly compared with non-elderly Medicare beneficiaries. Our sample was drawn from a ~40% random sample of 2017 Medicare beneficiaries with Part D coverage and was comprised of elderly beneficiaries (age 65+) with OUD or who experienced opioid poisoning , and non-elderly Medicare beneficiaries with OUD or opioid poisoning . MAT was underutilized in both Medicare populations, but especially in the elderly population. Of elderly beneficiaries with OUD, 5.1% and 0.8% were prescribed buprenorphine and naltrexone, respectively, compared to 15.5% and 2.3% among non-elderly. Among elderly beneficiaries with opioid poisoning, 3.1% and 0.8% were prescribed buprenorphine and naltrexone, respectively, compared to 10.1% and 3.2% in the non-elderly population. Sharp racial/ethnic disparities were identified within each age group. These findings highlight the need to expand access to MAT for Medicare beneficiaries, particularly older adults among whom underutilization is pronounced. Several recent Medicare policy changes have sought to address this issue, but continuing efforts and close monitoring are warranted in an effort to dramatically increase rates of treatment for elderly with opioid use disorder."} +{"text": "Aims and Objectives. The study is undertaken to assess the types of bacterial infections in cancer patients undergoing anticancer treatment, the associated bacterial pathogens, and their antibiotic sensitivity patterns. Cancer patients being immunosuppressed are vulnerable to develop infections. Knowledge of the changing epidemiology of infections has a pivotal role in its management. A retrospective surveillance study was undertaken in our center. Positive culture reports and other clinical details of cancer patients diagnosed with infection during a stay in the tertiary care center from 1st January 2015 to 31st December 2016 were analysed by descriptive statistical methods chi-square test and odds ratio to study the association. Klebsiella spp. (18.30%), Pseudomonas spp. (17.65%), and Escherichia coli (14.71%) followed by Staphylococcus aureus (13.72%). Among the gram-negative organisms, the antibiotic resistance rates reported to fluoroquinolones, aminoglycosides, and third-generation cephalosporins were 45.13%, 39.20%, and 48.58%, respectively. 26.92% of the organisms are resistant to all three antibiotics. 50.4% of Klebsiella spp. and Escherichia coli were ESBL producers. Gram-negative organisms showed 11.63% resistance to \u03b2-lactam/\u03b2-lactamase inhibitor combination, and 22.22% of gram-negative organisms are resistant to carbapenems. 50% of the Staphylococcus spp. were methicillin resistant, but all were sensitive to vancomycin. Out of 638 cancer patients diagnosed with infections in the 2-year period, 140 patients had positive cultures, representing 272 specimens and 306 isolates. Common specimens sent for culture were blood sputum, urine, and pus. 214 isolates (69.9%) were gram-negative bacilli, and 92 (30.1%) were gram-positive cocci. The most common isolates were The surge in the number of gram-negative infections emphasizes the need for broad-spectrum empirical therapy targeting the same. Rate of resistance of the isolated gram-negative organisms to the routinely used empirical therapy is alarming. Prudent use of antibiotics, based on culture reports wherever possible, is of utmost importance to save the lives of infected patients and prevent further development of antibiotic resistance. It is unmistakable that patients in Oncology wards are more vulnerable to develop infections. Cancer and chemotherapy predispose these patients to infection . InfectiWhilst the mortality rates have fallen over the past years, infection remains a primary or associated cause of death, with bacteria most commonly accounting for infection-associated mortality, followed by fungi . The manTo successfully prevent, identify, and treat infections, sound knowledge of the ever-changing spectrum of infections is necessary. Management of infections is a major challenge . This prThe study was undertaken to monitor the types of the bacterial infections seen in cancer patients undergoing anticancer treatment, the associated bacterial pathogens with their antibiotic sensitivity patterns, types of infections associated with the type of cancers, and modes of treatment like chemotherapy and radiotherapy.A retrospective surveillance study was conducted in the Department of Oncology of Kasturba Medical College Hospital (KMCHA), Attavar, Mangalore, and the Department of Clinical Microbiology of Kasturba Medical College (KMC), Mangalore. Inclusion criteria were all the patients admitted to the hospital for the treatment of cancer and diagnosed with infection during the period from 1st January 2015 to 31st December 2016.Microbiological investigations: the clinical specimen received from suspected cases of infection were stained with Gram stain inoculated onto blood agar, chocolate agar, and MacConkey agar (HiMedia) and incubated aerobically at 35\u00b0C for 18 hours. Blood culture was done by BacT/ALERT system . Positive cultures were subcultured onto blood agar, chocolate agar, and MacConkey agar (HiMedia) and incubated aerobically at 35\u00b0C for 18 hours. The identification of the bacterial growth and antimicrobial susceptibility testing of the isolates was performed using the VITEK 2 system , and minimum inhibitory concentration (MIC) was interpreted as sensitive or resistant using the Clinical and Laboratory Standards Institute (CLSI) guidelines. The antibiotics tested in VITEK 2 system included amikacin, amoxyclav, ampicillin, cefixime, ceftazidime, ceftriaxone, ciprofloxacin, ertapenem, imipenem, meropenem, gentamicin, piperacillin tazobactam, and trimethoprim-sulfamethoxazole for gram-negative organisms. The antibiotics for gram-positive cocci were cefoxitin, cefalothin, cefoperazone, gentamicin, erythromycin, clindamycin, chloramphenicol, rifampicin, netillin, linezolid, teicoplanin, and vancomycin.The demographic and clinical data of the patients were collected from the case files including information on age, sex, type of cancer, type of treatment, type of infection, type of bacterial isolate, antibiotic sensitivity pattern, and details: anthropometry, comorbidities, haematological examination results, and any procedures .The collected data were entered into Microsoft Excel and analysed by descriptive statistical methods. The association was established by chi-square test and odds ratio. The results obtained are represented in the form of graphs and frequency tables.A total of 3784 patients were admitted to KMCHA for the treatment of cancer during the study period. 638 persons were diagnosed with infections. Out of these, 140 patients had documented infections with culture-positive isolates.The age and sex distribution are shown in Figures The most commonly encountered type of clinical infection was bloodstream infection (33.33%) in patients with haematological malignancies and respiratory tract infections (34.93%) in patients with solid organ tumours .Klebsiella spp. (18.30%). 214 isolates (69.93%) were gram-negative bacilli, and 92 (30.07%) were gram-positive cocci .The association of neutropenia with the outcome is shown in The infection sites in neutropenic and nonneutropenic patients are depicted in 80% and 27.9% of the 140 patients were on chemotherapy and radiotherapy, respectively, and 21.4% underwent surgical procedures. The overall mortality rate in cancer patients with documented infection was 60%.Infections are still a cause of substantial morbidity and mortality in cancer patients. In our settings, mortality was observed in 60% of the 140 cancer patients with microbiologically proven infections, and the rest caused significant morbidity and the increased expense of patient care. The important infections like bloodstream infections and pneumonia were major contributors to mortality in oncology patients. The previous studies have reported 36% mortality due to sepsis in cancer patients .In our study, out of the 306 isolated organisms, 214 were gram-negative and 92 were gram-positive bacteria. 69.9% of the infections were associated with gram-negative organisms. This is in contrast to the earlier reports from developed countries, where the incidence of infections caused by gram-positive bacteria is higher. In most of the studies from developed countries, around 70% of the infections are caused by gram-positive bacteria . On the Epidemiology of infections in cancer patients has changed across the globe overtime and is characterized by a shift from gram-negative bacteria (1960s and 1970s) to gram-positive ones (1980s). Gram-negative bacteria have predominated the scene as a major cause of infections in cancer patients in the last 20 years across the globe in many countries.Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii have been increasingly associated with cancer patients. However, the frequency of occurrence of such MDR-resistant organisms is variable depending on the reporting country and continent. At the same time, inadequate empirical/therapeutic therapy with antibiotics exposes these patients to increased risk of adverse outcome, especially in neutropenic bacteremic patients suffering from MDR infections [Among gram-negative bacteria, fections .The findings of a study conducted by Yadegarynia et al. in Texas showed that pneumonia was the most common infection seen in both the groups of patients with solid organ tumours (26%), as well as in patients with haematological malignancies (38%) BloodstrPseudomonas spp. (26.2%)\u2009>\u2009Enterococcus spp. (11.66%)\u2009>\u2009S. aureus (11.44%)\u2009>\u2009E. coli (11.34%)\u2009>\u2009Klebsiella spp. (10.59%)\u2009>\u2009Acinetobacter spp. (9.95%)\u2009>\u2009Coagulase-negative Staphylococcus (CoNS) (6.52%)\u2009>\u2009Streptococcus spp. (3.42%)\u2009>\u2009Enterobacter spp. (3.1%)\u2009>\u2009Burkholderia spp. (2.35%) [Klebsiella spp. (18.30%)\u2009>\u2009Pseudomonas spp. (17.65%)\u2009>\u2009Escherichia coli (14.71%)\u2009>\u2009Staphylococcus aureus (13.72%)\u2009>\u2009Coagulase-negative Staphylococcus (6.54%)\u2009>\u2009Acinetobacter spp. (6.21%)\u2009>\u2009Enterococcus spp. (3.92%)\u2009>\u2009Proteus spp. (2.61%)\u2009>\u2009Streptococcus spp. (2.94%)\u2009>\u2009Haemophilus spp. (1.96%). They found gram negative accounted for 66.96% of the isolates, which is similar to our findings of 69.9% [In a study conducted by Kumar et al. in Mumbai, the overall rank order of the most common pathogens was (2.35%) . This wahia coli .71%\u2009>\u2009StAcinetobacter spp, a nonlactose fermenting, multidrug-resistant organism, known to be a significant bug among neutropenic patients, accounted for 6.21% of the isolates. This is less than findings of Kumar et al. (9.95%) but greater than the findings of Siddaiahgari et al. in a study conducted in Hyderabad, among pediatric patients, who found only two out of 89 isolates (2.2%) were Acinetobacter spp. [ter spp. .Pseudomonas spp. was the most common causative organism of bloodstream infection, causing 36% of the bloodstream infections. E. coli accounted for 46.3% of the urinary tract infections [Klebsiella spp. was most common, causing 21.2% of the bloodstream infection. Similar to their study, E. coli was the predominant etiological agent of UTI in our study, causing 63.2% of the infections [In the study conducted by Siddaiahgari et al., fections . In our fections .S. aureus, whereas our study showed that 41% of S. aureus were methicillin resistant. They noted that 50% of Enterococcus were vancomycin resistant, whereas, in our study, only 8.3% of Enterococcus were vancomycin-resistant enterococci (VRE). This may be attributed to the fact that vancomycin is not used for empirical prophylactic therapy in our hospital settings [A study noted that 68.18% of the isolated from blood stream infections were gram negative, which is similar to the findings of our study. The same study also noted that there was low occurrence (18%) of methicillin-resistant settings .16Carbapenem resistance in our study was noted to be 15.4% among Klebsiella spp. and 17% among Pseudomonas spp. which is more promising than the results of a study, where 49% of Klebsiella spp. and 31% of Pseudomonas spp. were resistant. In contrast, E. coli in our study (15.6%) showed more carbapenem resistance than theirs (11%). Fluoroquinolone and aminoglycoside resistance in gram-negative isolates was noted to be 45.6% and 37.3%, respectively, in contrast to the higher resistance of about 70% and 64.7%, respectively, seen in the study done in Mumbai.Analysis of antibiotic resistance of gram-negative organisms revealed 50.4% of the isolates were ESBL producers, which is less than what is commonly seen in other studies. A study done in New Delhi by Batra et al. noted 80% ESBL production rates among the gram-negative bugs. In the study by Eleni Isidora et al., 14% of the study group had previous MDR colonization, which possibly contributes an increased risk of MDR infection. We have not studied the colonization of MDR bacteria in the cancer patients.A systematic review and meta-analysis revealed high colonization with extended beta-lactamase producing Enterobacteriaceae among patients with solid or haematological malignancy. This phenomenon increases the risk of bacteremia with the same pathogen and created important reservoirs for horizontal spread between oncological hospitalized patients .In our study, chemotherapy was the most common mode of treatment with 80% of patients undergoing chemotherapy.The risk of mortality was 1.22 times higher in neutropenic patients compared to nonneutropenic patients (odd's ratio 1.224). The results of a study among 7512 critically ill cancer patients confirmed neutropenia to be independently associated with mortality . FebrileA systematic review showed that neutropenia was associated with a 10% rise in overall mortality .Klebsiella pneumoniae and Acinetobacter baumannii. MDR bacterial infections were thus significantly associated with mortality in cancer patients [84 of the cancer patients succumbed to infections. Among the 84 patients, 71 (84%) cancer patients with documented bacterial infections had infections with MDR patients .Limitations of our study include its retrospective design and single institutional nature. Our study included only the positive cultures of those patients in whom infection was suspected and not of all cancer patients.Despite the improved management of cancer patients, infections remain a significant cause of mortality among cancer patients. Implementation of strict infection control practices would go a long way in improving this dreaded situation. In developing countries, the broad-spectrum empirical therapy provided must focus more on the treatment of gram-negative infections. However, not only does it increase the cost of patient care but also leads to the selection of multidrug-resistant organisms, as seen abundantly in this study, as well as many others. The prospective studies on the antibiotic sensitivity patterns in hospitals will help to formulate local guidelines and therapeutic strategies. The increasing development of resistance to existing antimicrobials necessitates a dire need to develop novel agents at a rate faster than the development of resistance. It is of utmost importance to restrict the use of antibiotics in all clinical practices, using narrow-spectrum antibiotics based on culture reports wherever possible. This may come a long way in improving the situation of patients with life-threatening infections, especially in those who are immunocompromised.The study included 140 cancer patients who were diagnosed clinically with infection and showed culture positivity. 182 infections were encountered in these patients, 272 specimens obtained from these patients were culture positive, and 306 organisms were isolated.The percentage of deaths in cancer patients with infections was found to be 60%. It was greater in those with solid organ tumours than in those with haematological malignancies.Bloodstream infections accounted for 36.3% of the total infections. Second most common were respiratory tract infections, accounting for 31.9%.Chemotherapy was the most common mode of treatment.Klebsiella spp. (18.30%).69.9% isolates were gram negative and 30.1% were gram positive. Most common isolate was Among the gram-negative organisms, 45.13% of the organisms tested showed resistance to fluoroquinolones, 39.20% show resistance to aminoglycosides, 48.58% show resistance to third-generation cephalosporins, and 26.92% of the organisms are resistant to all three antibiotics.Klebsiella spp. and 48.9% of the isolated Escherichia coli were ESBL producers.51.8% of the isolated \u03b2-lactam/\u03b2-lactamase inhibitor combination, and 22.22% of gram-negative organisms are resistant to carbapenems.Gram-negative organisms show 11.63% resistance to S. aureus were methicillin resistant. All the MRSA were susceptible to vancomycin.41% of Enterococcus spp. were resistant to vancomycin.8.3% of Implementing strict infection control practices, conducting frequent prospective studies on the antibiotic sensitivity patterns seen in hospitals to help formulate local guidelines, developing novel antimicrobial agents, and restricting the use of antibiotics in clinical practices is important to reduce the incidence and improve the prognosis of infections in cancer patients.Infections among cancer patients are a major challenge to deal with. They cause suboptimal delivery of chemotherapy which leads to poor treatment outcome, adds to cost of management, and contributes to increased morbidity. Resistant organisms have emerged owing to selective antimicrobial pressure, which further complicates the problem. To successfully prevent, identify, and treat infections, knowledge of the changing epidemiology of infections is essential. In this study, we examined the types of bacterial infections seen in cancer patients undergoing anticancer treatment, the associated bacterial pathogens, and their antibiotic sensitivity patterns:This study helps to achieve a precise knowledge of the common types of infections seen in cancer patients undergoing various forms of therapy, the associated bacterial isolates, and their antibiotic susceptibility. This understanding will aid in formulating a personalised and cost-effective treatment, improving prognosis, and ensuring the prudent use of antibiotics."} +{"text": "CDC\u2019s Division of Tuberculosis Elimination (DTBE) funds 61 state, local, and territorial tuberculosis programs in the United States through the TB Elimination and Laboratory cooperative agreement. Recipients report data to CDC on indicators that measure progress toward TB elimination and performance of essential TB program activities. After the first U.S. case of coronavirus disease 2019 (COVID-19) was reported on January 20, 2020 grantees to estimate the effect of COVID-19 deployments on essential TB activities. Eleven (18%) programs were not reached because of deployments among project officers and recipients. CDC project officers characterized the effect as 1) no impact (no changes in staffing assignments or TB program activities), 2) partial impact , or 3) high impact (50%\u2013100% of personnel time dedicated to COVID-19 response or major changes made to program activity or activity not being performed at the time of the program\u2019s response) .Among the 50 programs, 60%\u201372% were experiencing partial or high impact on staffing capacity for 1) cooperative agreement and fiscal management, 2) clinical consultation or clinic service delivery, 3) outreach and field services , 4) surveillance and case reporting, and 5) training and program evaluation.Changes in staffing capacity were assessed separately from changes in essential activities. For example, if staffing capacity had been reduced, nondeployed staff members could still have assumed additional, high-priority duties, such as ensuring patient care.Partial or high impact on indicators measuring essential TB control activities was reported by 52% of jurisdictions for diagnosis and treatment of persons with TB disease, 68% for diagnosis and treatment of persons with latent TB infection, 64% for contact investigations for infectious TB, 74% for targeted testing and treatment of latent TB infection among populations at risk, and 58% for case reporting and other surveillance activities . In addition, 74% of the TB programs reported reduced program evaluation, and 94% reported reduced education and training efforts.The National TB Controllers Association (NTCA), which represents all state, local, and territorial programs, observed similar effects. NTCA convenes monthly webinars for members to discuss emerging problems and share best practices. By March, webinar participation was declining because of deployments. To obtain moment-in-time impressions of how the response was affecting TB activities, NTCA queried participants using a series of real-time text questions and tallied responses to each question. In the March 18 and April 9, 2020, webinars, >90% of 43 (March) and 38 (April) responses indicated that TB programs had deployed personnel to their jurisdictions\u2019 COVID-19 response. TB program personnel possess skills that health departments needed for the response. For example, among 72 responses in April, 26% were providing expertise in contact tracing, 21% in infection control, 17% in clinical care and treatment, and 14% in monitoring patients in home isolation.Responses to polling questions indicated that capacity for essential TB activities declined between March and April. For example, during the April webinar, the percentage of responses regarding less time for interviewing patients doubled over responses to the same question in March , and 15% indicated challenges in obtaining TB medications, up from 7% in March. Transfer of TB resources for COVID-19 use was indicated by 12% of responses in April, up from 7% in March.These observations suggest that the COVID-19 response is diverting resources from essential TB elimination activities. Effects of reduced capacity on outcomes will become clearer after provisional surveillance data, including number of U.S. TB cases reported during 2020, are published in early 2021. CDC is monitoring state capacity for reporting TB cases and will document gaps in reporting associated with the COVID-19 response. However, signals of reduced capacity are concerning. Incomplete contact investigations and delays in diagnosis of TB disease are associated with outbreaks of TB disease (The COVID-19 response has affected multiple sectors of public health, recommended preventive screening, and clinical care. The United States will need to address the backlog of population health services that have been delayed or not done while public health resources are focused on COVID-19. The U.S. domestic TB elimination program is one example. If essential TB program activities are not sustained, gains made in reducing U.S. TB cases will be at risk. CDC has published guidance regarding non\u2013COVID-19 public health activities that require physical interaction with clients."} +{"text": "ObjectiveThe goal of this study was to evaluate foot-care practices by physicians throughout India who had participated in the Diabetic Foot Education Program (DFEP).MethodsA structured questionnaire was administered to physicians throughout India, and their responses were analyzed descriptively.ResultsA total of 377 doctors responded to the DFEP opinion survey, including 261 doctors who belonged to independent diabetic foot clinics. Of these doctors, 44.4% reported\u00a0managing fewer than five diabetic foot patients per week and 42.8% reported managing 5-10 patients per week. Most of these patients had non-ischemic foot, followed by those with ischemic and Charcot foot. About 58% of these physicians reported performing comprehensive clinical examinations and providing optimal preventive and therapeutic care in the treatment of diabetic foot, whereas only 25.7% reported performing only callus removal and changing dressings. Basic instruments to manage diabetic foot included the monofilament, tuning fork, biothesiometer, handheld Doppler, and pedometer, which were used by 76%, 75.5%, 59.5%, 27.7%, and 12.8% of doctors, respectively. The most common comorbidities were neuropathy, reported by 333 doctors, followed by peripheral vascular disease, reported by 297 doctors. Tools for diabetic foot education included posters in the clinic, used by 75% of doctors; pamphlets, used by 56.2%; videos, used by 45.2%; and diabetic foot applications, used by 36.7% of doctors.ConclusionsThere is a need to promote diabetic foot awareness and implement foot-care strategies to prevent diabetic foot and effectively manage this condition. Diabetic foot education programs will encourage clinicians to effectively use diagnostic tools for assessment and management of diabetic foot and to establish independent diabetic foot clinics. Globally, an estimated 463 million adults are living with diabetes; India, with\u00a077 million patients, has the second-highest number of patients\u00a0after China . DiabetiDiabetes foot management is based on comprehensive patient and wound assessment. Arterial inflow and infection control should be ensured, the degrees of sensory neuropathy and deformity evaluated, and trauma (footwear) and pressure (offloading) should be reduced . DiabetiThe DFEP India\u00a0was launched under the auspices of the International Working Group on the Diabetic Foot, the Southern Arizona Limb Salvage Alliance, and the Indian College of Physicians. The program focuses on early detection, identification of at-risk foot, and preventive care. A national opinion survey was undertaken to gather insights from doctors who participated in DFEP India\u00a0regarding their strategies to prevent and manage diabetic foot. The objective of this survey was to evaluate healthcare practices used by doctors in the diagnosis and initial management of diabetic foot disease in their routine clinical practice.The contents of the diabetic foot questionnaire survey Table were devA total of 377 doctors throughout India responded to the DFEP opinion survey, including 261 doctors who belonged to independent diabetic foot clinics.In-clinic diabetic foot managementAssessments of in-clinic management of diabetic foot found that approximately 79.4% of doctors performed comprehensive clinical examinations, 58% utilized optimal preventive and therapeutic care strategies along with comprehensive clinical examination, and only 25.7% performed comprehensive clinical examination, utilized optimal preventive and therapeutic care methods, removed calluses, and changed dressings Figure .Instruments used for the detection of diabetic foot and diabetic foot educationBasic instruments used for the detection and management of diabetic foot included the monofilament, used by 67% of doctors; the tuning fork, used by 75.5%; the biothesiometer, used by 59.5%; handheld Doppler, used by27.7%; and the pedometer, used by 12.8%. Tools for diabetic foot education included posters in the clinic, used by 75% of doctors; pamphlets, used by 56.2%; videos, used by 45.2%; and diabetic foot applications, used by 36.7% reported neuropathy, 297 (78.8%) reported peripheral vascular disease, 255 (67.6%) reported renal disease, and 233 (61.8%) reported diabetic retinopathy in their patients with diabetic foot . The diaThe present survey found that 261 (69.2%) of the 377 doctors who participated in the DFEP opinion survey practiced at independent diabetic foot clinics. The most common comorbid condition in diabetic foot patients was neuropathy, which puts patients at increased risk\u00a0of mechanical and thermal trauma without being aware of the injury . Non-iscEarly assessment of peripheral sensory neuropathy and peripheral circulation, using efficient, inexpensive, and non-invasive measurement tools, is important . The surApproach to diabetic foot management varies in primary and secondary healthcare. However, physicians are effectively using diagnostic tools to assess the nature and severity of diabetic foot. Physicians who were trained in the management of diabetic foot have reportedly been able to manage their patients\u00a0better initially, with a good success rate. A unified approach for foot-care management may be achieved by diabetes foot education programs and the provision of national foot-care guidelines. Diabetes foot education programs should be implemented nationwide throughout India to create awareness regarding the prevention of the condition and for improving the management of diabetic foot patients. This may reduce foot amputation rates and decrease the burden of diabetic foot throughout India."} +{"text": "Background: Although most thyroid nodules with indeterminate cytology are benign, in most of the world, surgery remains as the most frequent diagnostic approach. We have previously reported a 10-gene thyroid genetic classifier, which accurately predicts benign thyroid nodules. The assay is a prototype diagnostic kit suitable for reference laboratory testing and could potentially avoid unnecessary diagnostic surgery in patients with indeterminate thyroid cytology.Methods: Classifier performance was tested in two independent, ethnically diverse, prospective multicenter trials (TGCT-1/Chile and TGCT-2/USA). A total of 4061 fine-needle aspirations were collected from 15 institutions, of which 897 (22%) were called indeterminate. The clinical site was blind to the classifier score and the clinical laboratory blind to the pathology report. A matched surgical pathology and valid classifier score was available for 270 samples.Results: Cohorts showed significant differences, including (i) clinical site patient source ; (ii) ethnic diversity, with a greater proportion of the Hispanic population (40% vs. 3%) for TGCT-1 and a greater proportion of African American (11% vs. 0%) and Asian (10% vs. 1%) populations for TGCT-2; and (iii) tumor size . Overall, there were no differences in the histopathological profile between cohorts. Forty-one of 155 and 45 of 115 nodules were malignant . The classifier predicted 37 of 41 and 41 of 45 malignant nodules, yielding a sensitivity of 90% and 91% [95% CI 79\u201398] for TGCT-1 and -2, respectively. One hundred one of 114 and 61 of 70 nodules were correctly predicted as benign, yielding a specificity of 89% [95% CI 82\u201394] and 87% [95% CI 77\u201394], respectively. The negative predictive values for TGCT-1 and TGCT-2 were 96% and 94%, respectively, whereas the positive predictive values were 74% and 82%, respectively. The overall accuracy for both cohorts was 89%.Conclusions: Clinical validation of the classifier demonstrates equivalent performance in two independent and ethnically diverse cohorts, accurately predicting benign thyroid nodules that can undergo surveillance as an alternative to diagnostic surgery. The prevalence of thyroid nodules in the adult population reaches up to 65% . ExpandeCurrent guidelines suggest that molecular testing may be used to supplement malignancy risk assessment in lieu of proceeding directly with a strategy of either surveillance or diagnostic surgery . The emeCurrently, most of the molecular testing for indeterminate thyroid cytology is offered in the United States through centralized laboratories, which have in-house laboratory-developed tests. This significantly limits the access to molecular testing in the rest of the world where, in the absence of a diagnostic kit for local reference testing, surgery remains the most frequent choice for thyroid nodules with indeterminate cytology. We have recently reported the development of a 10-gene thyroid genetic classifier that accurately predicts benign thyroid nodules with an NPV of 96% and specificity of 87% and could potentially avoid more than 80% of unnecessary surgeries . The assClinicaltrials.gov. TGCT-1/Chile-NCT03061318 and TGCT-2/USA-NTC03309631). Protocols were approved by local institutional ethics committees and enrolled participants provided written informed consent. Eligible patients (>18 years old with a thyroid nodule size of 10\u2009mm or more) undergoing fine-needle aspiration were recruited from both community and academic centers. At the time of the procedure, two additional needle passes were collected and placed in RNAprotect Cell Reagent . Samples were transported to the laboratory in a temperature-controlled system. Indeterminate samples underwent RNA extraction, followed by cDNA synthesis, and were stored at \u221220\u00b0C are reported as two-sided 95%. All statistical analyses were performed using the SPSS, v15.0, software , and plotting was performed using GraphPad, v7.0 .Sensitivity, specificity, and area under the curve were estimated by receiver operating characteristic curves. PPVs and NPVs were estimated by Bayes' theorem. Multiple comparison tests were performed using Tukey's range test. Differences in proportions were evaluated using the The basic demographic and thyroid nodule characteristics are shown in After a maximum follow-up of 4 months, a total of 441 patients underwent surgical resection (189 Bethesda III and 252 Bethesda IV) . Of the A successful qPCR informative valid classifier score was achieved in 319 (204 cases in TGCT-1 and 115 cases in TGCT-2) of 340 (94%) samples that passed preanalytical quality control . Before CXCR3, CCR3, CXCL10, KRT19, TIMP1, CLDN1, CXADR, XMOX130, AFAP1L2, and CCR7) .To assess classifier performance, the surgical pathologic diagnoses were grouped to align with clinical management as nonsurgical (benign) or surgical entities based on the final pathologic diagnosis and central review . ClassifA summary of the classifier performance in the 270 matched samples is shown in This study reports the prospective clinical validation of a previously described thyroid genetic classifier . In two The diagnostic performance of the classifier showed high accuracy in a broad spectrum of cases that require surgical management, including papillary thyroid carcinomas , follicular carcinomas, H\u00fcrthle cell carcinomas, and NIFTP. Accurately predicting H\u00fcrthle cell lesions has been a challenge for molecular testing. The classifier predicted 7 of 8 (sensitivity of 88%) surgical H\u00fcrthle cell lesions and 8 of 10 (specificity of 80%) nonsurgical H\u00fcrthle cell lesions. Although the percent of H\u00fcrthle cell carcinomas in this study was relative low (8%), the performance in this tumor subtype is comparable with the Afirma genomic sequencing classifier and ThyroSeq v3 assays, which have reported a sensitivity of 89% and 100% for surgical lesions and a specificity of 59% and 62% for nonsurgical lesions, respectively . A limitFalse negative cases in this study did not have worrisome histopathological features, were pathologically low-risk tumors according to the American Thyroid Association, and followed a similar pattern of false negatives reported by the Afirma and ThyroSeq v3 tests ,12. TherThis study has several strengths. First, a meaningful proportion of samples were collected from both academic (66%) and community (34%) centers, reducing potential selection bias associated with tertiary academic centers. Second, 8 of 15 sites enrolled more than 10% of cases, where all, except 1, showed a disease prevalence ranging between 18% and 43%, indicating an appropriate representation of the intended use population . Third, Currently, outside of the United States, there is very limited access to molecular testing due to the difficulty of overseas sample shipping and high costs of available tests. Thus, diagnostic surgery continues to be the most frequent approach for indeterminate cytology. To the best of the authors' knowledge, no clinically useful diagnostic kit has been reported to be available for indeterminate cytology. As a multianalyte algorithm assay, validation of a kit can be a challenge given rigorous controls required to guarantee reproducibility of multiple analytes and the algorithm itself, which is considered a separate medical device. For breast cancer, EndoPredict, an eight-gene qPCR classifier in a diagnostic kit format, has successfully shown robust analytical and clinical performance in its respective validation studies ,20. In aThis study has some limitations. First, in the initial phase of patient enrollment, the sample RNA yield failure reached 14%, with failure occurring most frequently in clinical sites that did not have extensive previous experience in routine sample collection for both cytology and molecular testing. However, improved sample collection was achieved in the second half of both trials where sample RNA failure was reduced to 4% . Second,In conclusion, we have validated the clinical performance of a thyroid genetic classifier built into a diagnostic kit format in two independent and ethnically diverse multicenter cohorts. The technical simplicity and high accuracy of the test should provide accessible and valuable information for clinicians to identify patients who can safely undergo surveillance as an alternative to diagnostic surgery."} +{"text": "This study was designed to determine how feeding diets differing in crude protein (CP) and undegraded intake protein (UIP) levels affected productivity, blood metabolites, carcass characteristics, and the production economics of Hanwoo steers.Thirty-six Hanwoo steers were assigned at random to one of three treatments : i) a low-CP diet containing 12.1% CP with 35.1% UIP, 12.0% CP with 36.8% UIP, and 12.9% CP with 48.8% UIP, in the growing, fattening, and finishing periods, respectively; ii) a high-CP, low-UIP diet (HPLU) containing 15.0% CP with 33.7% UIP, 14.0% CP with 35.7% UIP, and 13.1% CP with 46.7% UIP, respectively; and iii) a high-CP, high-UIP diet (HPHU) containing 15.0% CP with 45.8% UIP, 14.0% CP with 44.6% UIP, and 13.0% CP with 51.1% UIP, respectively.longissimus muscle area, backfat thickness, yield index, and yield grade, plus quality traits including meat color, fat color, texture, and maturity. However, marbling score and frequency of carcass quality grade 1++ were greater in HPHU-fed steers.The treatments did not affect feed intake and growth performance, except for average daily gain during the fattening period that tended to be the lowest (p = 0.08) in the HPLU-fed steers. The feed CP conversion ratio over the entire feeding period was higher with high-CP diets. The treatments did not affect most blood metabolites; however, blood cholesterol and low-density lipoprotein concentrations during the fattening and finishing periods were the lowest in steers fed a HPLU diet. The treatments had negligible effects on cold carcass weight, yield traits including Feeding diets with higher CP and UIP levels did not affect growth performance but tended to improve the carcass quality of Hanwoo steers, resulting in greater economic return. Huuskonen et al found inAlthough increasing CP concentrations usually improves the performance in growing/finishing beef cattle, animal responses to increased CP content vary with respect to the CP source . This isThe effects of manipulating protein levels as well as the ratio of DIP to UIP on growth performance and carcass quality parameters of beef cattle are contradictory in literature. For example, Vasconcelos et al reportedin situ study was included in the model. When a significant effect was detected at a p-value less than 0.05, comparisons between means were made using the Tukey\u2019s multiple range test.No steer died or was removed from the experiment and over the entire experimental period all steers remained healthy without displaying any sign of illness. Treatment effects on the performance of Hanwoo steers according to the production phases are presented in Treatment effects on selected blood metabolites during the different production phases are presented in longissimus muscle (LM) area area . However+ were greatest with steers fed HPHU (83.3%), intermediate with LP (50.0%), and lowest with HPLU (41.6%). Treatments did not affect cold carcass weight, yield traits , and quality traits . Although non-significant, LM area increased an average of 6 cm2 for high CP-fed groups when compared to the control group. However, this numerical difference might be of practical importance in the beef cattle market.Treatment effects on carcass characteristics after slaughter are presented in Average feed costs calculated for each experimental diet according to the growing, fattening, and finishing periods, as well as the production economics of Hanwoo steers, are presented in Typically, the initial phase of growth period is when feed intake is relatively low and the rate of protein deposition is potentially high. Therefore, increasing CP concentration during this phase may increase the growth rate. However, as the animal matures, with the concurrent increase in DMI and a proportionally lower rate of protein deposition, an excessive supply of protein to the animal may negatively affect its growth performance ,8. ThereThe slight difference in growth performance agrees with a previous report on beef cattle, where a dietary CP reduction from 14.5% to 10.8% had a marginal effect on growth performance . LikewisGenerally, the shortage of N and an imbalance in the UIP:DIP ratio for ruminal microorganisms are associated with a reduction in total-tract nutrient digestibility, with subsequent depressions of DMI and growth performance ,17. BasiConcentrations of all blood metabolites fall within normal ranges previously reported for Hanwoo steers -22. SchiA negative correlation has been reported between protein intake and serum cholesterol concentration in ruminants . AlthougFeeding excessive amounts of DIP is associated with higher BUN concentrations, which is possibly caused by deamination of amino acids . Ruminan++ grade; however, at harvest the likelihood of an individual carcass qualifying as 1++ increased. Vasconcelos et al [longissimus dorsi muscle of steers. The authors associated this phenomenon to the increased availability of specific amino acids used for gluconeogenesis in the liver, which then increased the availability of glucose in the muscle. Contrary to the findings of this study that HPHU diet promoted marbling development, Wagner et al [Past studies with Hanwoo steers indicated that marbling scores reached an asymptotic level when cattle weighed about 570 kg, with an extended feeding beyond this weight only slightly benefiting carcass quality ,29. In tos et al also fouos et al compareder et al found ther et al and Koener et al ,29, whicer et al clarifieMarbling is the principal determinant of meat quality and price by meat distributors and consumers in the Korean beef cattle market, as increased marbling is associated with improved eating quality traits such as tenderness, flavor, and juiciness . This inOverall, the findings of this experiment indicate that despite of no meaningful effects on productivity, feeding a diet with higher CP and UIP levels improved the carcass quality of Hanwoo steers, which thus resulted in greater economic return."} +{"text": "Background: Due to the lack of a gold standard diagnostic test, reference centres with experienced personnel and costly procedures are needed for primary ciliary dyskinesia (PCD) diagnostics. Diagnostic flowcharts always start with clinical symptoms. Therefore, the aim of this work is to define differential clinical criteria so that only patients clinically compatible with PCD are referred to reference centres. Materials and methods: 18 variables from 476 Mediterranean patients with clinically suspicious PCD were collected. After analysing cilia function and ultrastructure, 89 individuals were diagnosed with PCD and 387 had a negative diagnosis. Simple logistic regression analysis, considering PCD as a dependent variable and the others as independent variables, was done. In order to define the variables that best explain PCD, a step-wise logistic regression model was defined. Aiming to classify individuals as PCD or PCD-like patients, based on variables included in the study, a classification and regression tree (CART) was designed. Results and conclusions: Simple logistic regression analysis shows statistically significant association between age at the beginning of their symptomatology, periodicity, fertility, situs inversus, recurrent otitis, atelectasis, bronchiectasis, chronic productive cough, rhinorrea, rhinusinusitis and recurrent pneumonias, and PCD. The step-wise logistic regression model selected situs inversus, atelectasis, rhinorrea, chronic productive cough, bronchiectasis, recurrent pneumonias, and otitis as PCD predictive variables ). A decision tree was designed in order to classify new individuals based on pansinusitis, situs inversus, periodicity, rhinorrea, bronchiectasis, and chronic wet cough. Primary ciliary dyskinesia (PCD) is a rare disease with an estimated prevalence of 1/20,000\u201340,000 births (Code Orphanet: ORPHA244). It is a genetically determined condition, characterized by abnormal or absent mobility of motile cilia and flagella. Consequently, PCD patients present a deficient clearance of secretions and detritus from upper and lower airways. Thus, these patients have infections and chronic inflammation of airways, as well as reduced fertility and situs inversus in 40\u201350% of cases (Kartagener syndrome) [At present, there is no \u201cgold standard\u201d diagnostic test. However, according to the European Respiratory Society Task Force guidelines , PCD patPCD testing is expensive and time-consuming and requires an experienced team of clinicians and scientists. It is, therefore, necessary to define specific and differential clinical criteria regarding other causes of chronic respiratory disease, so that only patients clinically compatible with PCD are referred to diagnostic centres ,2,9. In The definition of a specific clinical profile together with the decision tree based on clinical manifestations will help clinicians to know when do they have to refer a patient to a PCD diagnostic reference centre. Although there already exist other studies that aim to identify candidate patients for PCD diagnostic studies ,11, our 2. PCD patients were considered positive when having abnormal ciliary motility by HSVM and presented a TEM defect. Additionally, patients without the obvious TEM defect, who presented abnormal ciliary motility in three different HSVM analyses (when patients were free of infection), with strong clinical history, and low nNO in (those who had the measure), were also considered in the PCD group. In contrast, patients with normal HSVM and TEM tests were considered in PCD-like group.Samples of nasal epithelial cells for diagnostics and clinical data from patients were collected for the study after informed consent. The study protocol complied with the ethical guidelines of the 1975 Declaration of Helsinki . Before A total of 18 variables from 476 Mediterranean patients clinically suspicious of PCD were collected in the Valencian PCD Reference Centre from 2005 to 2018: gender, age at the beginning of their clinical symptomatology (younger or older than 2 years old), familiar history of respiratory diseases, periodicity, fertility problems, situs inversus, otitis, immunodeficiency, asthma, atelectasis, bronchiectasis, chronic productive cough, rhinorrhea, rhinosinusitis, pansinusitis, pneumonias, and nasal polyposis. Additionally, tobacco was included in the study as it is a standard variable included in the majority of respiratory disease studies. After studying ciliary motility frequencies and patterns and ciliary ultrastructure, 89 PCD cases were confirmed and 387 PCD-like cases were obtained.Male infertility was determined, only in adults, by a spermiogram after obtaining patients\u2019 informed consent. By contrast, females were considered infertile after 3 years of failure in their attempts to become pregnant . ImmunodStatistical analysis was carried out with R for windows software . A 5% prA multivariate logistic regression analysis was carried out. All variables were entered into the model individually, and a step-wise selection was made to identify and select the significant predictors of PCD. Moreover, the influence of each significant variable on PCD diagnosis was assessed. Finally, a receiver operating characteristic (ROC) curve showing sensitivity, specificity, and overall accuracy was used to interpret significant predictors . DiscrimAiming to classify individuals as PCD or PCD-like patients based on variables included in the study, a multivariate data analysis was carried out . A classFrom the initial population of 476 PCD clinically suspicious cases, 89 individuals were diagnosed with PCD (19%) and 387 (81%) had a negative diagnosis . The ageIn our PCD population, 18.6% had immotile cilia, 34.6% had stiff ciliary movement, and 46.8% had low frequency and uncoordinated movement when analysing using HSVM. Additionally, 20% of our PCD patients had normal ultrastructure, 14.1% undetermined defects , 18.6% combined Inner Dynein Arm (IDA) and Outer Dynein Arm (ODA) defects, 38.6% partial IDA, ODA, and short arms defects, and 9.2% presented other abnormalities (such as axoneme disorganization) when studying ciliary ultrastructure by TEM.p-value of 0.861, indicating that gender is not significantly related to PCD.A total of 53% of PCD-like individuals were males, while 47% were females. A total of 52% of PCD patients were males, whereas 48% were females. SLR has a p-value of 0.692, so was not significantly related to PCD.A total of 97% PCD-like patients were non-smokers, having the same percentages as the PCD patients group. As expected, SLR had a p-value of <0.001 in SLR shows that, in the great majority of PCD patients, symptoms started before they were 2 years old.Based on the age of the patients at the beginning of their clinical manifestations, two groups were made: younger than 2 years old and older than 2 years old. A tota, of 81% of PCD-like patients were under 2 years, whereas 19% were older than 2 years. A total of 98% of PCD patients were under 2 years and 2% of them were older than 2 years. A p-value of 0.076, indicating that familiar history is not significantly related to PCD.A total of 63% PCD-like individuals had no familiar history of respiratory diseases and 53% of PCD ones also had no familiar history of respiratory diseases. SLR had a p-value of <0.001 indicates that the variable periodicity is significantly related with PCD; the risk of having perennial symptoms being 11 times higher in PCD patients than in PCD-like patients.While 92% of PCD patients presented their clinical symptoms in a perennial manner, in PCD-like cases, 50% of them presented their symptoms perennially. A p-value of 0.029 indicated that fertility is significantly related with PCD, and the risk of having fertility problems in PCD patients was 67% higher than in PCD-like patiens.Out of 89 PCD patients, 60 did not proceed with any information about their fertility due to the fact that they were minors or they did not consent to spermiogram realization. Therefore, in our cohort, we had 66% with and 34% without fertility problems. On the other hand, 53% of PCD like-patients presented fertility problems and 47% of them had no problems related to fertility. A p-value of <0.001, indicating that the probability of having situs inversus is 11 times higher in PCD patients than in PCD-like patients. While 30% of PCD patients presented situs inversus, only 4% of PCD-like patients presented this characteristic. SLR had a p-value of <0.001, indicating that variable otitis is significantly related to PCD and the probability of having otitis in PCD patients is 4.38 times higher than in PCD-like patients. Results show that 33% of PCD-like patients suffered from chronic otits media during their life. In contrast, 68% of PCD patients presented chronic otitis media. SLR had a A total of 3% of PCD-like patients had immunodeficiency. However, as none of the PCD patients presented immunodeficiency, SLR analysis did not make sense.p-value of 0.785, indicating that asthma is not significantly related to PCD.A total of 28% of PCD-like patients had asthma. Similarly, 27% of PCD patients presented with asthma. SLR had a p-value of < 0.001, indicating that atelectasis is significantly related to PCD, and the risk of having atelectasis in PCD patients was 5.27 times higher than in PCD-like patients. Our results show that 7% of PCD-like patients presented atelectasis at any time. In contrast, 28% of PCD patients had atelectasis. SLR had a p-value of <0.001, indicating that the variable bronchiectasis is significantly related to PCD. The risk of suffering bronchiectasis is 5.37 times higher in PCD-diagnosed patients.A total of 29% of PCD-like patients presented bronchiectasis. In contrast, 68% of PCD patients had bronchiectasis. SLR analysis had a p-value of the t-test was <0.001, indicating that the mean age of PCD-patients with bronchiectasis was significantly higher than PCD-patients without bronchiectasis.Bronchiectasis are clinical manifestations that are not present from birth and appear with age . Our cohp-value of <0.001 indicates that a chronic productive cough is significantly related to PCD. The risk of presenting a chronic productive cough was 14.56 times higher in PCD patients than in PCD-like patients.Results show that 66% of PCD-like patients suffered a chronic productive cough. In contrast, 97% of PCD patients presented a chronic productive cough. SLR with a p-value of <0.001 in the SLR indicates that rhinorrhea is significantly related to PCD and is 17 times higher in PCD diagnosed patients.A total of 45% of PCD-like patients presented rhinorrhea. In contrast, 93% of PCD diagnosed patients presented this clinical manifestation. A p-value of <0.001, indicating that rhinosinusitis is significantly related with PCD, and the risk was 7.65 times higher in PCD patients than in PCD-like patients.A total of 17% of PCD-like patients had chronic rhinosinusitis. On the other hand, 62% of PCD patients had chronic rhinosinusitis. SLR analysis had a From 89 PCD patients, 68 patients had no information about pansinusitis . Of 21 patients with pansinusitis information, our cohort had 95% of PCD patients with pansinusitis. In contrast, none of the 89 analyzed PCD-like patients presented pansinusitis. In this case, SLR does not make sense because of the disequilibrium and low number of PCD patients.p-value of <0.001 indicates that recurrent pneumonias are significantly related to PCD. The risk of this clinical manifestation was 4.19 times higher in PCD patients than in PCD-like patients. Results show that 39% of PCD-like patients and 73% of PCD patients suffered recurrent pneumonias. SLR with a p-value of 0.497, indicating that nasal polyposis is not significantly related to PCD.Results show that only 4% of PCD-like patients and 2% of PCD patients presented nasal polyposis. SLR had a p-values indicate that all variables were statistically significant.Only individuals that started their symptomatology from infancy were considered for the step-wise logistic regression model, as there were not enough individuals that started in adulthood. From the 18 variables included in the program, 7 were selected for the best logistic regression model . These pp = 0.1182). The sensitivity (proportion of PCD patients correctly identified) and specificity (proportion of PCD-like patients correctly identified) of the model were 80% and 88%, respectively. The discriminant ability (AUC) of this model was 0.92, indicating a good discriminative capacity . Only individuals who started their symptomatology from infancy were considered for the CART design, as there were not enough individuals that started in adulthood. Based on these mentioned variables, an individual could be classified as a PCD patient or a PCD-like patient. As previously mentioned, pansinusitis only can be applied in patients older than 14 years old, as computed axial tomography findings could only be considered from this age. In each node , the probability of being PCD-like (p1) or PCD (p2) is specified . The numn = 20), with a 100% probability of being PCD and 0% probability of being PCD-like.An individual with pansinusitis will be classified in group 13 (n = 7) with a 100% probability of being PCD-like.An individual without pansinusitis that has situs inversus and intermittent periodicity will be classified in group 11 (n = 20), with a 10% probability of being PCD-like and a 90% probability of being PCD.An individual without pansinusitis that presents situs inversus and a perennial periodicity will be classified in group 12 (n = 154), with a 97.4% probability of being PCD-like and a 2.6% probability of being PCD.An individual without pansinusitis, situs inversus, and rhinorrhea will be classified in the fourth group (n = 62), with a 59.7% probability of being PCD-like and a 40.3% probability of being PCD.An individual without pansinusitis and situs inversus who presents rhinorrhea and bronchiectasis will be classified in the sixth group (n = 36), with a 100% probability of being PCD-like.An individual without pansinusitis, situs inversus, bronchiectasis, and chronic wet cough who presents rhinorrhea will be classified in group 8 (n = 90), with a 77.8% probability of being PCD-like and a 22.2% probability of being PCD.An individual without pansinusitis, situs inversus, and bronchiectasis who presents rhinorrhea and chronic wet cough will be classified in group 9 and theImmunodeficiency in some moments of its evolution could manifest with symptomatology similar to PCD, and thus we included it in our work to highlight it is an important criterion to discard before referring a patient to PCD diagnostics.Fertility problems are significantly greater in PCD patients than in PCD-like patients. However, as our cohort was majorly composed of children, these problems were unknown in a great number of patients, which gives us inconclusive results when comparing differences between sexes. Additionally, fertility was the variable with more missing data because many patients did not consent to spermiogram realization for personal reasons. Thus, this variable was not included in the logistic regression model and the CART diagram as it was a variable that introduced bias in our data.Bronchiectasis is also significantly more frequent in PCD patients than in PCD-like patients, being another PCD-clinical suggesting symptom. However, this clinical manifestation does not appear from birth, and our data demonstrated that this symptom became more frequent in adults than in children with PCD. Thus, bronchiectasis are helpful for PCD-suspicious adults, but it is a manifestation that is less informative in children.One critical aspect before starting the diagnostic flowchart in a PCD reference centre is to define which are the key clinical manifestations ,28. WithBehan et al. in the PICADAR (PrImary CiliARy DyskinesiA Rule) study used a similar statistical approach to decide seven variables significantly associated with PCD. They found associations between PCD and situs inversus, neonatal chest symptoms, and hearing problems . Our resComplementary to our work, Behan et al. in PICADSLR analysis shows a statistically significant association between some explicative variables and PCD: age at the beginning of their symptomatology, periodicity, fertility, situs inversus, recurrent otitis, atelectasis, bronchiectasis, chronic productive cough, rhinorrhea, rhinosinusitis, and recurrent pneumonias.Bronchiectasis is significantly more frequent in adults than in children with PCD.A step-wise logistic regression model selected situs inversus, atelectasis, rhinorrhea, chronic productive cough, bronchiectasis, recurrent pneumonias, and otitis as PCD predictive variables (from the most to the least important predicting factor), designing a model with 82% sensitivity, 88% specificity, and 0.92 AUC. Combination of all these clinical symptoms in the same patient determines a high probability of having PCD.A decision tree was designed in order to classify new individuals based on different clinical manifestations: pansinusitis, situs inversus, periodicity, rhinorrhea, bronchiectasis, and chronic wet cough."} +{"text": "The World Health Organization and national guidelines recommend HIV testing and counseling at tuberculosis (TB) clinics for all patients, regardless of TB diagnosis were used for all analyses. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policyThe number of participants in the PHIA survey was 19,652 in Malawi, 21,280 in Zambia, and 22,490 in Zimbabwe.Among participants who received positive HIV test results during PHIA and who also reported visiting a TB clinic, 47.7% to 64.4% (Zimbabwe) reported receiving? HIV testing at the TB clinic . Among pAmong participants who received positive HIV test results during PHIA and who reported not receiving an HIV test and not knowing their HIV status at the TB clinic visit, 10.6% , 20.4% (Zambia), and 18.5% (Zimbabwe) were unaware of their HIV-positive status before the PHIA survey. These percentages correspond to 5,008 of 47,383 in Malawi, 9,926 of 48,693 in Zambia, and 11,025 of 59,481 in Zimbabwe . In all In Malawi and Zimbabwe, awareness of HIV-positive status was significantly higher among TB clinic attendees with a confirmed TB diagnosis than among those with presumptive TB . Similarly, in Malawi and Zimbabwe, ART use was significantly higher among TB clinic attendees with a confirmed TB diagnosis than among those with presumptive TB . In Zambia, awareness of HIV-positive status or ART use did not significantly differ by TB diagnosis .Across these three countries, the percentage of TB clinic attendees who reported having been screened for HIV during a TB clinic visit ranged from 48.0% to 62.1%, highlighting a gap in screening, despite the World Health Organization and national recommendations for universal HIV testing at TB clinics . PreviouResults from the three PHIA surveys identified substantial gaps in HIV screening at TB clinics, with 16.2%\u201329.4% of participants who received positive HIV test results during PHIA reporting that they were not screened for HIV and did not know their HIV status at the time of their TB clinic visit . Of thesHIV-positive adults who reported having visited a TB clinic also had significantly higher levels of awareness of their HIV status, ART use, and viral load suppression than did those who never visited a TB clinic. HIV-positive patients with TB might be more likely to seek TB care than are HIV-negative patients with TB. However, an analysis using cross-sectional survey data from Kenya postulated that TB might serve as an indicator disease leading to HIV diagnosis and ART initiation for HIV-positive patients. Ensuring that all patients are screened for HIV at TB clinics can help identify HIV-positive persons and link them to care.The World Health Organization recommends HIV testing and counseling at tuberculosis (TB) clinics for all patients, regardless of their TB diagnosis.Population-based HIV Impact Assessment (PHIA) survey data from Malawi, Zambia, and Zimbabwe show that 16.2%\u201329.4% of HIV-positive persons were not screened for HIV during TB clinic visits; these visits represent missed opportunities for HIV diagnosis among persons who are not aware of their HIV-positive status.HIV screening of patients with presumptive or confirmed TB could be strengthened to leverage TB clinics as entry points into the HIV care and treatment cascade."} +{"text": "Hepatitis C virus (HCV) is among the highest priority diseases in custodial settings; however, the diagnosis remains suboptimal among people in custody. This study aimed to validate a short survey for identifying people with HCV infection in a provincial prison in Iran.Between July and December 2018, residents and newly admitted inmates of Gorgan central prison completed a questionnaire, including data on the history of HCV testing, drug use, injecting drug use, sharing injecting equipment, and imprisonment. Participants received rapid HCV antibody testing, followed by venipuncture for RNA testing (antibody-positive only). Each enrollment question (yes/no) was compared with the testing results (positive/negative).n = 130) and 4.8% (n = 90), respectively. The antibody prevalence was higher among people on OAT compared to those with no history of OAT (11.4% vs. 4.0%). History of drug use was the most accurate predictor of having a positive HCV antibody and RNA testing . The sensitivity of the drug use question was lowest among people with no OAT history and new inmates . Among all participants, sensitivity and negative predictive value of the other questions were low and ranged from 34 to 54% and 94 to 97%, respectively.Overall, 1892 people completed the questionnaire, including 621 (34%) who were currently on opioid agonist therapy (OAT); 30% of participants had been tested for HCV previously. About 71% had a history of drug use, of whom 13% had ever injected drugs; 52% had ever shared injecting equipment. The prevalence of HCV antibody and RNA was 6.9% (In resource-limited settings, HCV screening based on having a history of drug use could replace universal screening in prisons to reduce costs. Developing tailored screening strategies together with further cost studies are crucial to address the current HCV epidemic in low- to middle-income countries. Hepatitis C virus (HCV) infection is a global health concern with a rising disease burden\u00a0. The intIn Iran, the prevalence of HCV infection among the general population is estimated at 0.6% . HoweverIn high-income countries, risk-based surveys have been used to increase HCV diagnosis in custodial settings , 19. HowThis study was a non-randomized trial, evaluating the reliability of a self-reported questionnaire in predicting HCV antibody and RNA testing results. Enrollment occurred between July and December 2018. The study site was Gorgan central prison, located in Northern Iran. All residents and newly admitted inmates were eligible to participate in the study, given they were at least 18\u2009years old and had provided written consent. Participation was voluntary, and participants could withdraw their consent at any time. The Institutional Review Board of Tehran University of Medical Sciences approved the research protocol.Gorgan central prison is located in Gorgan city, Golestan province, Northern Iran. This prison has an approximate inmate population of 2000 and consists of eight wards: public, remands, serious crimes, female, juvenile, solitary confinement, and two wards for people receiving OAT. The prison had a general practitioner and two nurses providing healthcare services, including harm reduction activities and HIV testing. However, there was no HCV program available in this prison.Before enrollment, prison health officials invited all inmates to provide education on HCV disease and its complications, routes of transmission, and safe injection techniques. Further, an illustrated booklet was given to participants, containing useful information about HCV infection and liver health. Residents and newly admitted inmates completed a short questionnaire, including information on the history of HCV testing, drug use, injecting drug use, sharing injecting equipment, and imprisonment Table .Table 1All participants received on-site rapid HCV antibody testing, using a blood specimen from a fingerstick; post-test counseling was provided. Among participants with a positive HCV antibody test, the prison nurses were available to collect venipuncture blood samples weekly. These participants were\u00a0invited to attend the prison clinic once a week to provide a sample for HCV RNA testing and other routine clinical care, including HIV and hepatitis B virus serology, liver function tests, and complete blood count.Participants with positive HCV RNA received treatment with a locally manufactured combination of 400\u2009mg Sofosbuvir and 60\u2009mg Daclatasvir (Sovodak\u00ae). AST to Platelet Ratio Index (APRI) was used for liver disease assessment. The duration of antiviral therapy ranged from 12 to 24\u2009weeks for people without cirrhosis (APRI < 1) and those with cirrhosis (APRI > 1), respectively. We delivered all required education for treatment and monitoring to the prison physician. Patients released during the study were referred to the local health network for follow-up. All study activities were provided to participants free of charge.The primary outcome of this study was to investigate the role of a 1-min questionnaire as a risk-based strategy in HCV screening. The other outcome was to evaluate the prevalence of HCV antibody and HCV RNA among all participants and people with a positive antibody test, respectively.Data are presented as median (interquartile range (IQR)) or frequency and percentage, as appropriate. Each enrollment questionnaire (yes/no) was compared with the results of the HCV antibody testing (positive/negative) and RNA testing (positive/negative). The RNA testing results were evaluated among participants with available information. The enrollment question about previous HCV testing had multiple answers; for comparison, we combined the first three answers Table . Sensiti. The majority were male (96%), did not have higher education (89%), had a monthly income at minimum wage or below (77%), and 34% were currently receiving OAT services. Residents had lower education and monthly income, compared to newly admitted inmates. Similarly, people who were receiving OAT had lower education and monthly income than those who were not currently on OAT and 410 newly admitted inmatesn = 1341) had a history of drug use, of whom 13% (n = 174) had a history of injecting drug use; 52% (n = 91) of people with injecting drug use had ever shared injecting equipment. The history of drug use and injecting among residents was slightly higher than new inmates . People who were currently receiving OAT had a higher prevalence of drug use, injecting drug use, and sharing injecting equipment, compared to those who were not currently on OAT of participants had a history of HCV testing, including 36% 527/1478) and 8% (31/409) among residents and newly admitted inmates, respectively. Among people who had a history of HCV testing, only 41% (229/558) were aware of their test results. Having a history of testing was reported in 33% and 28% of participants on OAT and those who were not currently on OAT, respectively (Tables 7/1478 ann = 130) of all participants, including 7.5% (n = 111) of residents and 4.6% (n = 19) of newly admitted inmates. Among residents, the prevalence of HCV antibody was highest in OAT wards with 13.2% (80/607), followed by remands 3.5% (8/230) and public 3.5% (11/317). The prevalence of HCV RNA among residents was 5.7% (n = 84). Out of 19 newly admitted inmates with a positive antibody in the remand ward, 11 were released before the RNA testing; among those who received venipuncture, the HCV viremic rate was 75% (6 of 8). For participants who were currently on OAT and those who were not receiving OAT, the prevalence of antibody was 11.4% (71/621) and 4.6% (55/1190); HCV RNA was detected in 8.7% (54/619) and 2.9% (34/1182), respectively , with a higher sensitivity in residents compared to new inmates 96% vs. 89%). The sensitivity of the drug use question among participants who were currently receiving OAT and those with and without a history of OAT were 100%, 94%, and 87%, respectively , and people on OAT than those with no such history . The question about previous HCV testing did not find any new inmates with positive antibody but was 49% sensitive for case finding among residents. Among people on OAT, and those participants with and without a history of OAT, testing history was 45%, 25%, and 47% sensitive, respectively.The drug use question was the most accurate predictor of having a positive HCV RNA results as well . The sensitivity and negative predictive value of injection and sharing questions among all inmates ranged from 59 to 63%, and 97 to 73%, respectively. Only 9% (8/90) of people who had positive HCV RNA results truly answered that they currently have HCV disease. From participants who responded that they have HCV disease currently, only 33% (8/24) had positive RNA results, while among people who believed they do not have the disease, 3% (6/205) tested positive.This study validates a risk-based questionnaire for the identification of people with HCV infection in Gorgan central prison, Iran. Overall, 7.5% of residents and 4.6% of newly admitted inmates had a positive HCV antibody, which was a remarkably higher prevalence than the general population . ThThe history of drug use was the most sensitive question for predicting a positive HCV antibody test among all inmates (95%); this sensitivity was lower among newly admitted inmates compared to residents (89% vs. 96%), highlighting the fact that new inmates are more reluctant to disclose their drug use. Despite the high sensitivity of the drug use question, the other risk factors were low sensitive for case finding: among people with a positive HCV antibody test, 46% and 66% did not report any history of injecting drug use and sharing, respectively. Therefore, lifetime experience of injecting drug use and sharing needles is under-reported among people in prison. The unreliability of self-reported history of injecting drug use had been reported in other studies as well, which could be due to the existing reluctance of inmates to disclose their risk behaviors and face probable punishments in custody . It seemn = 19), 11 people were released before RNA testing. The venipuncture samples could not be collected daily, given limited capacity for RNA testing at the local laboratory and the lack of a fixed nurse in prison for obtaining blood samples. Participants were receiving HCV rapid testing upon admission daily, but those with a positive antibody were undergoing venipuncture after a few days, during which someone might be released. Aside from newly admitted inmates, all of the prison residents with positive antibody tests underwent venipuncture and had data available. Also, the small number of female participants limits the generalizability of this study.The main strength of this study was its novelty in developing a low-cost strategy for countries with limited resources in the battle against HCV. However, our study had some limitations like using self-reported data, which its reliability has been questioned , 23. TheScreening for HCV infection based on having a history of drug use could replace universal screening in correctional facilities to reduce costs. However, the history of drug injection and sharing injection equipment remain under-reported. History of HCV testing is sub-optimal among inmates in Iran; therefore, effective prison-based programs are needed to scale-up HCV diagnosis and linkage to care for the people who are rarely reached by healthcare systems. Moreover, drug interventions and co-morbid health assessments should be enhanced to reduce the harms from people who cycle through custody. In resource-limited settings, tailored HCV screening strategies are crucial for pursuing elimination targets, and further cost-effectiveness analysis is needed to confirm the optimal strategies."} +{"text": "Sogatella furcifera is one of the most harmful pests of rice in Southeast Asia. The fat body of WBPH harbors intracellular yeast-like symbionts (YLS). YLS are vertically transmitted to WBPH offspring by transovarial infection. YLS play an important role in the WBPH life cycle. YLS diversity and function have been extensively studied in the brown planthopper (BPH) and small brown planthopper but not in WBPH, even though a novel strategy for controlling the BPH based on suppressing YLS has been proposed. Here, using denaturing gradient gel electrophoresis, we identified 12 unique fungal sequences among YLS of WBPH, and five of them represented uncultured fungi. We then fed WBPH with rice plants treated with different fungicides and evaluated their effects on YLS abundance and WBPH survival rate. Both YLS abundance and adult WBPH survival rate were significantly decreased upon feeding fungicide-treated rice plants, and exposure to 50% IP resulted in the strongest reduction. The abundance of two Sf-YLS species (Ascomycetes symbiotes and Cla-like symbiotes) was significantly reduced upon exposure to 50% IP. The counts of Ascomycetes symbiotes, the most abundant YLS species, were also suppressed by the other fungicides tested. In conclusion, 50% IP was the most effective fungicide, reducing YLS abundance and WBPH survival rate under controlled conditions, suggesting its potential use to control WBPH.The white-backed planthopper (WBPH) Sogatella furcifera (Horv\u00e1th) is one of the most harmful pests in paddy fields in southeast Asia . Ea. Ea35]. p < 0.05 were considered to indicate statistical significance.The YLS counts in different WBPH treatment groups were compared by using SPSS 18.0 and single-factor analysis of variance (one-way ANOVA). Statistical mean separations were performed by Tukey\u2019s method; values of Alternaria alternata isolate Alt-C71, Periconia macrospinosa, Alternaria alternata strain PB-56, Fusarium sp., Cladosporium halotolerans, Naganishia albida, and S. furcifera YLS (Ascomycetes symbiotes)] and five uncultured fungi (S. furcifera YLS (Ascomycetes symbiotes), which was previously identified in BPH by Noda et al. [Using the nested PCR-DGGE approach, 12 DGGE bands were identified and selected for further analysis based on their position and abundance in the gel. The bands were sequenced using the first-round primers NS5\u2013ITS4 and second-round primers GCclampITS1\u2013ITS2 or GCclampITS3\u2013ITS4 . The sized fungi . With tha et al. , all othF = 120.158, df = 5,12, p < 0.0001), 15.92% , and 9.18% when compared to control group on days 1, 3, and 5, respectively. Furthermore, the survival rate of WBPH treated with IP declined from 93.33% to 42.22% at 5 days after female adult release.The five tested fungicides reduced YLS numbers and WBPH survival rate at 5 days after exposure, where the IP treatment exerted the strongest effect . The YLSp < 0.05). The ratio index represents that every treatment of YLS number is divided by the number of YLS in the control.Data were collected on days 1, 3, and 5 after the exposure of WBPH adults to rice plants treated with 70% propineb wettable powder (WP) (PR), 70% propamocarb hydrochloride aqueous solution (AS) (PH), 25% trifloxystrobin and 50% tebuconazole water-dispersible granules (WG) (TT), 40% pyrimethanil SC suspension concentrate (PY), and 50% iprodione suspension concentrate (SC) (IP). All the fungicides were dissolved in water according to the recommended concentration in the field . DiffereAscomycetes symbiotes and Cla-like symbiotes) in WBPH was determined by qPCR . Consistent with the observations for Ascomycetes symbiotes, IP treatment also resulted in the highest reduction in the abundance of Cla-like symbiotes. The inhibitory effect of IP on these two YLS species was the most significant, which was consistent with the results shown in Ascomycetes symbiotes were the dominant species in WBPH, and they exhibited the greatest drop in abundance in response to the fungicide.The effect of the five tested fungicides on the abundance of two YLS species were significantly suppressed by all the tested fungicides, and 50% IP showed the highest inhibition on these two Sf-YLS species. Taken together, our results suggest that fungicides could be used as an alternative additive to control WBPH.The current study explored the role of fungicides on suppressing YLS diversity and WBPH survival in white-back planthopper (WBPH). With a modified DGGE technique, we identified 12 unique fungal sequences in WBPH, and 11 of them were first reported. Five common fungicides were used to test their effects on survival rates of WBPH and YLS abundance, and 50% IP was the most effective fungicide to reduce the YLS abundance and adult WBPH survival. The abundance of two dominant"} +{"text": "The identification of prognostic factors of esophageal cancer has allowed topredict the evolution of patients. Assess different prognostic factors of long-term survival of esophagealcancer and evaluate a new prognostic factor of long-term survival calledlymphoparietal index (N+/T). Prospective study of the Universidad de Chile Clinical Hospital, betweenJanuary 2004 and December 2013. Included all esophageal cancer surgerieswith curative intent and cervical anastomosis. Exclusion criteria included:stage 4 cancers, R1 resections, palliative procedures and emergencysurgeries. Fifty-eight patients were included, 62.1% were men, the average age was 63.3years. A total of 48.3% were squamous, 88% were advanced cancers, theaverage lymph node harvest was 17.1. Post-operative surgical morbidity was75%, with a 17.2% of reoperations and 3.4% of mortality. The average overallsurvival was 41.3 months, the 3-year survival was 31%. Multivariate analysisof the prognostic factors showed that significant variables were anteriormediastinal ascent , anastomotic fistula, N classification , TNM stage , and lymphoparietalindex . The independent prognostic factors of long-term survival in esophageal cancerare anterior mediastinal ascent, anastomotic fistula, N classification, TNMstage and lymphoparietal index. In esophageal cancer the new lymphoparietalindex is stronger than TNM stage in long-term survival prognosis. Secondary objectives were: a) analyzepost-operative evolution; b) determine global overall survival greater than threeyears (OS3); and c) assess the value of a new prognostic factor of long-termsurvival called lymphoparietal index (N+/T), previously validated in gastriccancerThis study was a prospective analysis of the oncological database of a ChileanUniversity between January 2004 andDecember 2013.This article does not contain any experimental studies with human or animalsubjects performed by any of the authors.All patients with esophageal cancer in adult population, surgically treated witha curative intent, were identified, and only total esophagectomies with gastrictube ascent and cervical anastomosis where included. All patients were presentedto the hospital oncology committee and treated with neoadjuvant or adjuvanttherapy according to tumor stage. Exclusion criteria included were: proximaltumors, Siewert 3, stage 4 cancers, R1 resections, palliative procedures andemergency surgeriesThe surgeries were performed by surgeons with vast experience in oncologicalesophagectomies. All patients were subjected to minimally invasivethoraco-abdominal esophagectomy and cervical anastomosis. The thoracic time wasdone in the first years transhiatal and then by videothoracoscopy in leftlateral decubitus. The gastric tube was made in the first years open and thenlaparoscopic with linear staplers from the distal aspect of the lesser curvatureto the gastric fundus, 5 cm to the grater curve of the stomach preserving thegastro-omental arcade. The left gastro-omental vessels, right and left gastricvessels were cut. The gastric tube was pulled upwards to the cervicalcompartment through anterior or posterior mediastinal way according to surgeonpreference. The lymphadenectomy was standard in two fields. All patients had anintra-operative contemporary biopsy. ,A: 0-0.5 and N+/TB: >0.5;c) surgical mortality was defined as occurring from the moment of surgery up topostoperative day 90; d) global survival was defined as of when the patient wasdischarged from the hospital, eliminating surgical mortality; e) long termsurvival was defined as survival greater than three years postoperative; f) zerotime for determining prognostic association was the esophagectomy.The definitions used were: a )TNM classification was standarized using the AJCC7th editionThe present study had 100% follow up. The database was completed in a prospectivemanner: the survival update was carried out annually using the database of ourhospital and the Chilean Civil Registry. 25%-75%) ranges were used. The categorical variables weredescribed in percentages. The Fisher, xR 14 program was used and p< 0.05was considered statistically significant. Univariate and multivariate analyseswere performed calculating the odds ratio (OR) with a 95% confidence interval(CI). The Kaplan-Meier method was used to calculate the survival curves, and theROC curves to assess the prognosis accuracy of the variables14.The prognostics factors evaluated were demographic, clinical, surgical,anatomopathological and prognostic indexes, 31 variables in total. Thedistribution of variables was determined by the Shapiro-Wilk test. In accordancewith this test, the continuous variables with parametric distribution were expressed on average and standard deviation (SD), while for thenon-parametric distribution the median and inter-quartile ofwhich 62.1% were male, 74.1% of patients presented co-morbidities with tabacco, highblood pressure and pathological gastroesophageal reflux disease being the mostcommon with 48.3%, 44.83% and 43.1% respectively. According to the ASAclassification, 52.7% were ASA I, 47.3% were ASA II and III. With regards to the clinical manner, 81.8% presented epigastric pain, 50.9% weightloss and 21.8% pain. Anemia (hematocrit <35%) was observed in 16.4%, whileprotein malnutrition was present in 7.3%.25-75%: 11-35). In reference to the surgical technique, 61.8% of patients had anterior mediastinalpull-up of gastric tube. The median global lymph node harvest was 17.1 lymph nodes. Postoperative morbidity corresponded to75%, reoperations to 17.2%, while surgical mortality was 3.4% .The histopathological study revealed that 65.5% of the tumors were localized in thedistal esophagus, 52.7% of the sample was adenocarcinoma, 88% of the tumor wereadvanced and 72.7% of all had moderate to poor degree of differentiation. The TNMstage is specified in The mean global survival was 41.3 months . The rate of patients with an OS3 was 32.7%. The survival curve is detailed inA and N+/TB) p<0.009, In the lymphoparietal index Kaplan-Meier analysis, a statistically significantdifference was seen in the global long-term survival between subgroups the Chilean esophagealcancer is experimenting an epidemiological transition; 2) there are differentvariables that significantly predict the population susceptible to achievingpostoperative long-term survival; 3) the lymphoparietal index is as accurate as TNMsystem for predicting survival more than three years in patients who underwentsurgery for esophageal carcinoma with curative intent. ,,The esophageal cancer epidemiology has changed over the past 40 years. In ourcountry, comparing previous reports to the present results: the location of thetumor in the lower esophagus has increased from 26% to 65%, the adenocarcinomaincreased from 14% to 52%, and the surgical mortality dropped from 6% to 3%,,,,The SVg3 of the patients in this study was 32.7%, which is very similar to previousnational reportsThe prognostic effectiveness of the TNM classification to guide therapeutics is wellknownThe results of this publication suggest an independent association betweenfemales and long-term survival with p=0.03 (OR: 3.9). This finding has beenstudy by other groups, suggesting a possible estrogen protective effect,especially in adenocarcinoma,,The role of age in the prognosis of patients subjected to oncologic procedureshas been studied many foregut cancers, being gastricThe nutritional state has been studied by different authors in the preoperativeand postoperative stages. In a retrospective Brazilian study, MarinIn a recent retrospective Japan study, SchichinoheIn our study there was no independent correlation between BMI, weight loss,neither albumin level to OS3, which has been concluded by other as wellMeasurement of circulating tumor cells (CTC) and its prognosis, has been study indifferent solid tumors including esophageal cancerClassically, tumor localization and grade of differentiation are associated withlower long-term survival. The previous actualization of AJCC guideline foresophageal cancer, allowed to differentiate between different subtypes accordingto localization and tumor grade,23. Interestingly, in a retrospective Chinese analysis of 302 esophageal carcinomastaged T3N0M0, Situ et alth vs. 7th TNM staging,concluding that 7th edition is more accurate than 6th interms of prognosisOther publications have compared 6In our cohort neither the localization nor tumor grade affected long-termsurvival, while TNM staging was independent prognostic factors. The anterior (AP) or posterior mediastinal pull-up (PP) dilemma, has beenanalyzed in different series, there has been even combinations of thistechniques from posterior to anterior mediastinum after esophagectomy,Classically AP have had more leakages, lower Clavien-Dindo morbidity, and saferresults if post-operative radiotherapy is requiredRecent evidence with minimally invasive surgery supports no difference in lymphnode harvested, ICU and hospital stay, postoperative morbidity, and in-hospitalmortalityA previous experience of our group showed similar rate of leaks for AP and PP, but a worst post-operative morbidity concentrating all types CDIII-V and lower OS3 for PPSince CROSS studyA vs.N+/TB; p=0.009, Regarding the N+/T index, it has been validated in gastric cancer by ourgroupThe strengths of this investigation are the following: a) the analysis of thegreatest number of prognostic variables for long-term survival for esophagealcancer reported in the domestic literature, and b) the provision of a newsurvival prediction index. The weaknesses are as follows: a) it covers a periodof time in which there was a change in TNM classification, and treatmentstrategies, and b) it couldn`t include the adjuvant therapy used in theanalysis. The independent prognostic factors for more than three years survival in treatment ofesophageal cancer in a Latin American country are: gender, anterior mediastinalpull-up, anastomotic fistula, N classification, TNM stage, and lymphoparietal index.Concomitantly, it has been able to provide a new prognostic quotient in theevaluation of esophageal carcinoma patients who have been resected with curativeintent, the lymphoparietal index."} +{"text": "As facility-based deliveries increase globally, maternity registers offer a promising way of documenting pregnancy outcomes and understanding opportunities for perinatal mortality prevention. This study aims to contribute to global quality improvement efforts by characterizing facility-based pregnancy outcomes in Kenya and Uganda including maternal, neonatal, and fetal outcomes at the time of delivery and neonatal discharge outcomes using strengthened maternity registers.Cross sectional data were collected from strengthened maternity registers at 23 facilities over 18 months. Data strengthening efforts included provision of supplies, training on standard indicator definitions, and monthly feedback on completeness. Pregnancy outcomes were classified as live births, early stillbirths, late stillbirths, or spontaneous abortions according to birth weight or gestational age. Discharge outcomes were assessed for all live births. Outcomes were assessed by country and by infant, maternal, and facility characteristics. Maternal mortality was also examined.Among 50,981 deliveries, 91.3% were live born and, of those, 1.6% died before discharge. An additional 0.5% of deliveries were early stillbirths, 3.6% late stillbirths, and 4.7% spontaneous abortions. There were 64 documented maternal deaths (0.1%). Preterm and low birthweight infants represented a disproportionate number of stillbirths and pre-discharge deaths, yet very few were born at \u22641500g or <28w. More pre-discharge deaths and stillbirths occurred after maternal referral and with cesarean section. Half of maternal deaths occurred in women who had undergone cesarean section.Maternity registers are a valuable data source for understanding pregnancy outcomes including those mothers and infants at highest risk of perinatal mortality. Strengthened register data in Kenya and Uganda highlight the need for renewed focus on improving care of preterm and low birthweight infants and expanding access to emergency obstetric care. Registers also permit enumeration of pregnancy loss <28 weeks. Documenting these earlier losses is an important step towards further mortality reduction for the most vulnerable infants. While maternal mortality decreased 44% globally between 1990 and 2015, a considerable mortality burden persists in low-income regions , more thSub-Saharan Africa is an area of particular focus given the tremendous burden of mortality in the region. Maternal mortality estimates remain as high as 546 per 100,000 live births , and stiNevertheless, the magnitude of preventable death is large. The leading cause of neonatal mortality is preterm birth and nearThis study aims to contribute to the global quality improvement and mortality prevention efforts by using strengthened maternity register data from Kenya and Uganda to characterize facility-based pregnancy outcomes including maternal, neonatal, and fetal outcomes at the time of delivery as well as discharge outcomes for live born infants. A second objective of this study is to understand the relationship between pregnancy outcomes and infant, maternal and facility characteristics to inform opportunities for facility-based perinatal mortality prevention.st, 2016 and March 31st, 2018. Data were collected as part of the East Africa Preterm Birth Initiative (PTBi) [NCT03112018). The full study protocol is available elsewhere [This study is a descriptive, cross-sectional analysis of labor ward maternity registers in Kenya and Uganda between October 1e (PTBi) . This inlsewhere . This crMaternity register data were gathered from 23 health facilities including 17 in Migori county in western Kenya and six in Busoga region in eastern Uganda. In Migori county, facility births represent 53% of all births and in BWithin each country the level of care of included facilities varied. However, across both countries facilities ranging from level III through VI were represented [for facility level definitions see references In Uganda by contrast, all facilities were hospitals including five level V and one level VI facility. All Ugandan facilities were capable of performing cesarean sections and all had newborn special care units. Two hospitals had staff pediatricians and the remainder employed a general doctor .Anonymized patient level delivery data were extracted monthly from maternity registers. Pre-existing national maternity registers were used for this study. However, prior to the study period, data strengthening efforts were completed as part of the PTBi trial to improve the accuracy and completeness of these maternity registers. These efforts included provision of supplies with skill building sessions, monthly training and mentoring of labor and delivery staff on standard indicator definitions, and monthly feedback on the completeness of registers. Particular emphasis was placed on the accuracy of gestational age assessments, which were estimated by labor and delivery providers based on reported last menstrual period, fundal height, or antenatal records carried by the mother. Ultrasound was not universally available during antenatal care or at the time of delivery.The impact of data strengthening on register completeness has been evaluated and full results are available elsewhere . In brieInfant, maternal and facility characteristics abstracted from registers and their completeness in this study are as follows: infant sex 91%, multiple gestation 97%, gestational age 86%, birth weight 92%, maternal age 99%, incoming maternal referral status 59% (only available in Uganda), delivery mode 93%, and facility level 100%.Register entries were identified as deliveries if at least one of the following indices was documented: 1-minute Apgar score, birth weight, infant sex, birth outcome, or discharge status. Pregnancy outcomes were then classified as 1) live birth, 2) early stillbirth, 3) late stillbirth, or 4) spontaneous abortion.Live births were defined in this study as infants born with signs of life weighing \u2265500 grams or, if no birth weight was recorded, \u226524 weeks completed gestation. This differs from the WHO definition of live birth, which includes any infant born with signs of life regardless of gestational age or birth weight . The defStillbirths were classified as early or late. The WHO definition of stillbirth was used to define late stillbirths in this analysis\u2014infants born without signs of life weighing \u22651000 grams or, if no birth weight was recorded, \u226528 weeks completed gestation [Discharge outcomes were examined for all live born infants. In Kenya, registers included a field for discharge outcome distinct from birth outcome. In Uganda, there was only one field for infant status. In both countries, when delivery and discharge status could not be distinguished or there was conflicting information (i.e. non-zero 1-minute Apgar categorized as a stillbirth), Apgar scores were used to differentiate stillbirths from live births experiencing an immediate neonatal or pre-discharge death. Pre-discharge maternal mortality was also examined and was a unique field in registers in both countries.Entries excluded from this analysis included 1) births before arrival (n = 606), as the aim was to characterize facility-based outcomes and 2) births with no documented birth weight or gestational age (n = 36), as this prohibited outcome classification. Mothers were excluded if 1) they delivered before arrival (n = 562) or 2) were discharged pregnant (n = 9202). A unique maternal identification code was used to link maternal and neonatal data.Data are summarized using descriptive frequencies. Pearson chi square test was used to compare pregnancy outcomes by country as well as by maternal, infant, and facility-based co-variates. The Fisher\u2019s exact test was substituted for cases of small sample size (n<5) in instances where models converged. Early stillbirths and spontaneous abortions were excluded from the analyses by birth weight and gestational age as these outcomes were pre-defined by a narrow range of birth weights and gestational ages.A sub analysis was performed to compare fresh versus macerated late stillbirths. Other analyses available upon request include: country specific analyses and a sub analysis of multiple gestation vs singletons. All analyses except Fisher\u2019s exact tests were performed using SPSS 23 . Fisher\u2019This study was approved by Institutional Review Board at the University of California San Francisco (Study no: 16\u201319162), the Kenyan Medical Institute Scientific and Ethics Review Unit (SERU protocol no: KEMRI/SERU/CCR/0034/3251), the Makerere University Higher Degrees, Research, and Ethics Committee (Protocol ID: IRB00011353), and the Uganda National Council of Science and Technology. There was a waiver of consent to obtain line-item level data from maternity registers.De-identified data were collected from maternity registers, so there was no direct patient contact or time spent for this analysis. Results will be disseminated to health workers and health authorities from research areas.A total of 50,981 births to 48,675 mothers were included. Two thirds of deliveries were in Uganda and one third in Kenya .There were 64 documented pre-discharge maternal deaths over the study period , 20 in Kenya and 44 in Uganda. Half of the mothers who died had cesarean sections and the remainder had vaginal deliveries. Further, half of the mothers who died in childbirth had liveborn infants. Of the other half, 27 had late stillbirths, one had an early stillbirth, and three had spontaneous abortions. Another 11% of mothers who delivered in study facilities (n = 5344) left prior to discharge, were transferred, or had an undocumented discharge status .p<0.01).Of all registered deliveries, 91.3% were live births, 4.1% stillbirths (0.5% early and 3.6% late), and 4.7% spontaneous abortions. In Uganda, 88.7% were live births, 0.6% early stillbirths, 4.2% late stillbirths, and 6.5% spontaneous abortions. In Kenya, 96.4% were live births, 0.3% early stillbirths, 2.4% late stillbirths, and 0.9% spontaneous abortions , p<0.01.p<0.01). Over 85% of live births occurred at term. The preterm birth rate was 134 per 1000 live births (148/1000 in Kenya and 126/1000 in Uganda). Very few live births occurred at <28 weeks gestation (0.5%), with increasing numbers from 28 to 32 weeks (3.1%) and 33 to 36 weeks (9.8%). For late stillbirths, the percentages were 3.1%, 17.3%, and 16.5% by gestational age grouping respectively. Approximately 38% of late stillborn infants weighed \u22642500 grams (11% \u2264 1500g), whereas only 13% of live births were low birthweight. The prevalence of multiple gestation pregnancies were roughly equivalent in live births (4.1%), early stillbirths (5.1%), and late stillbirths (4.9%) but lower in spontaneous abortions (0.7%).Pregnancy outcomes varied by gestational age, gestation type , and birth weight as well as by maternal age, maternal referral status, delivery mode, and facility level . By comparison, only 11.9% of live births were following maternal referral, 10.2% of early stillbirths, and 6% of spontaneous abortions. Additionally, 30% of late stillborn infants were delivered by cesarean section compared to 20% of live born infants. Six early stillbirths and three spontaneous abortions were delivered via cesarean section . The percentage of deliveries via cesarean section after incoming maternal referral was 46.8% for live births, 44.7% for late stillbirths, and 0% for early stillbirths and spontaneous abortions.p = 0.02, all others p<0.01). Conversely, infant sex, single versus multiple gestation, and maternal age did not differ by stillbirth type. More fresh stillbirths were born after incoming maternal referral (31.8%) compared to macerated stillbirths (24.8%). Approximately 40% of fresh stillbirths were delivered by cesarean section compared to 21.8% of macerated stillbirths. Roughly 70% of fresh stillbirths were born at term compared to 58% of macerated stillbirths. A slightly higher percentage of macerated (3.5%) compared to fresh (2.7%) stillbirths occurred at \u226541 weeks. Finally, more macerate stillbirths were low birthweight (45.6%) compared to fresh stillbirths (31%).A sub-analysis of late stillbirth type revealed 46% of late stillbirths were categorized as fresh (n = 850), 33% as macerated (n = 612), and the remainder were undifferentiated (n = 372). Gestational age, birth weight, maternal referral status, delivery mode, and facility level differed by type of late stillbirth (p<0.01). The overall pre-discharge neonatal mortality rate was 16 per 1000 live births.Of live born infants, 1.6% (n = 653) died prior to discharge. The pre-discharge mortality rate was higher in Uganda (18/1000) than Kenya 11/1000, , p<0.01.p\u22640.01).Discharge status was unknown for 4,906 infants (10.5% of live births). This may include infants referred out to higher level facilities. Outgoing infant referral status was not recorded in registers. Of infants with no documented discharge status, 19.6% were preterm, 17.9% were low birthweight, 4.6% multiple gestations, 7.6% were born to mothers referred into study facilities prior to delivery, and 21.9% were born via cesarean section. For infants with known discharge status, outcomes varied by all infant, maternal, and facility characteristics analyzed (The majority of pre-discharge deaths occurred at level V facilities (59.6%) and very few occurred at level III facilities (4.1%). A higher percentage of infants who died prior to discharge were born to women \u226419 or \u226535 (33.5%) years old compared with infants discharged alive (28%). Just under a quarter (22.7%) of infants dying before discharge were born after maternal referral. By comparison, of infants surviving to discharge, only 12.1% were born after maternal referral. Over one third of infants (35.2%) who died before discharge were born via caesarean section compared to 19.5% of those discharged alive.More pre-discharge deaths were male (56.6%) than female (43.4%). Eleven percent of pre-discharge deaths were multiple gestation infants compared to only 3.9% of infants discharged alive. A higher percentage of infants deceased at discharge were preterm (45.1%) compared to those alive at discharge (12.4%). Of those infants that survived to discharge, 9.5% were born between 33 and 36 completed weeks of gestation, 2.5% between 28 and 32 weeks, and 0.4% <28 weeks. Approximately 12% of infants discharged alive were low birthweight, with nearly all of those infants falling in the 1501 to 2500-gram range. Half of pre-discharge deaths (50.3%) were low birthweight infants.This study used strengthened maternity register data to characterize pregnancy outcomes for nearly 51 thousand deliveries from 23 health care facilities in Kenya and Uganda over 18 months including pregnancy loss at <1000g or 28 weeks. Results highlight three priorities for further facility-based perinatal mortality reduction efforts: 1) continued attention to complete and accurate documentation of all pregnancy and discharge outcomes, 2) improvement in the care of low birth weight and preterm infants, and 3) expanded access to high quality emergency obstetric and neonatal care.Neonatal mortality and stillbirths occur within the same continuum of care, but are nevertheless often studied and reported separately leading to an underappreciation of the mortality burden associated with viable pregnancies. Further, pregnancy loss at <28 weeks is often excluded from international statistics with the current WHO definition of stillbirth [The pre-discharge, facility-based neonatal death rate in this study was 16 per 1000 live births, substantially lower than the published regional estimate for overall population-based 28-day neonatal mortality in sub-Saharan Africa (25.9 per 1000 live births) , and theAlthough with this adjustment rates in this study are comparable to current regional estimates, it is important to acknowledge that rates in this study are facility-based rates and the true population-based rates are likely higher. Additionally, some study characteristics suggest underreporting and emphasize the need for continued attention to both complete and accurate documentation of early neonatal deaths. First, discharge status was unknown for 4,906 infants (10.5%) in this study. Of these infants, nearly 20% were preterm and 18% low birthweight. Second, outgoing infant referral status was not known nor the ultimate discharge outcome for any infants referred to higher levels of care. Thus, ongoing efforts focused on documentation would likely only reveal more potentially preventable deaths.The late stillbirth rate in this study was 36 per 1000 total births. This is significantly higher than the previously published stillbirth estimate for sub-Saharan Africa of 29 per 1000 total births , which eThere is good reason to believe previously reported regional stillbirth rates may be significant underestimates. The first published global estimates of stillbirths emerged as recently as 2011 and the Of particular interest is improving accuracy of classification of fresh versus macerated stillbirths. While training was provided to labor and delivery providers as part of the data strengthening efforts in this study, about 20% of late stillbirths were not classified as fresh or macerated. Fetal heart rate assessment via doppler is one tool that has been successfully employed in Tanzania . RequiriOf all registered pregnancy outcomes, 0.5% were early stillbirths and 4.7% spontaneous abortions. Neither of these outcomes are routinely measured in LMIC settings and their documentation is a unique contribution of this study despite likely significant underestimation. Studies from high-income settings, suggest that approximately 17% of stillbirths occur between 24 and 28 weeks and thatUnderestimation stems from challenges associated with accurately measuring pregnancy loss including dating accuracy , 8 and lDespite the challenges, documentation of these pregnancy losses is important. In high income countries the decline in early stillbirth rates is similar to that of late stillbirths internationally . This suOf live births in this study, 13.4% were preterm births and 13.3% were low birthweight infants. This is comparable to regional estimates (12% and 13% respectively) , 33. DesIt has been suggested that preterm stillbirths should be included in reporting preterm birth rates to more accurately reflect international disparities, partially due to common misclassification of early neonatal deaths as stillbirths in preterm infants in low income settings . MaterniIntrapartum-related events are the second leading cause of early neonatal mortality globally and are Emergency obstetric care is critical for not only neonatal survival but also for maternal survival. Nearly 70% of maternal deaths occur prior to, during, or shortly after birth . The matThis study has many strengths including the large sample size, two country setting including a broad range of facility levels, data strengthening efforts, concurrent analysis of both delivery and discharge outcomes, and extension of gestational age limits to more comprehensively document spontaneous abortion and early stillbirth. However, this study also has important limitations.Uniformly, mortality rates were higher in Uganda compared to Kenya in this study. These differences are likely attributable to facility characteristics. All included Ugandan study facilities were level V and VI hospitals whereas Kenyan study facilities were level III or IV. Assuming complicated pregnancies are referred to higher levels of care, infants born at the study facilities in Kenya may have represented lower risk pregnancies, whereas in Ugandan facilities, where 12.2% of all births occurred after incoming maternal referral, there was likely a higher prevalence of high-risk pregnancies. More research is needed to rule out other possibilities such as differences in quality of care and other causes of morbidity that could be different in Uganda and Kenya. While direct comparison of countries is not possible due to these facility level differences, when taken in sum, the spread of facilities in this study fairly represents the various tiers of care in the region and improves the generalizability of the conclusions.Despite the benefits of using maternity register data highlighted throughout the paper, there are also important drawbacks. Data were recorded by frontline providers and were not 100% complete. Efforts to limit observer bias included explicit provider instruction on standard indicator definitions during data strengthening efforts. Data were also cleaned . Due to known issues with gestational age estimates in low income settings , 8, we cThis study seeks to characterize facility-based pregnancy outcomes and thus is not generalizable to the proportion of the population delivering outside of facilities, including at home. Additionally, some facilities included in this study were part of the PTBi trial. This study was not an evaluation of the PTBi trial and includes both intervention and control sites. However, mortality rates may be decreased as a result of the study. Nevertheless, overall concordance with regional estimates suggest the impact of this bias is likely limited.Other important limitations to discuss include lack of data on congenital anomalies. Anomalies are a significant cause of neonatal mortality and morbidity, yet were not systematically recorded in this sample. Additionally, prenatal care, while important, is not captured in registers. Further, spontaneous abortion and early pregnancy loss is likely underestimated given only obstetric registers are included in this analysis. Finally, this study is a cross-sectional analysis of pregnancy and discharge outcomes by infant, maternal, and facility characteristics. It does not adjust for confounding variables and does not attempt to make inferences on causes of perinatal or pre-discharge mortality.Translating strengthened registry data and the opportunities this descriptive data highlight for perinatal mortality reduction into concrete action is a crucial next step. At a national level, such data may inform funding priorities for government facilities or systems level improvements, such as referral systems. At a facility level, data may inform maternal and perinatal death surveillance and response (MPDSR) teams or qualiThere is a significant unsolved burden of fetal, neonatal, and maternal mortality amongst facility-based deliveries in Kenya and Uganda. Some of the most vulnerable lives include those of preterm and low birthweight infants as well as those pregnancies requiring emergency intrapartum care. Documenting all pregnancy outcomes, including pregnancy loss <28 weeks, to better understand when deaths occur is a critical first step towards highlighting the need for improved care for the most vulnerable infants and pregnancies. As facility-based deliveries increase, maternity registers are valuable data source, particularly with prior attention to data quality and efforts to ensure every pregnancy is counted."} +{"text": "Frailty is gaining importance as a predictor of disability and mortality in older people, and becoming frail poses a challenge for healthy aging. We investigated the prevalence and factors associated with pre-frail and frail status in a large study cohort of community-dwelling healthy older adults from Australia and the United States. A total of 19,114 individuals aged 65 years or older enrolled in a primary prevention clinical trial were evaluated. Frailty status was classified using the modified Fried phenotype criteria comprising of exhaustion, body mass index, grip strength, gait speed and physical activity. Prevalence and factors associated with frailty status (e.g. demographic characteristics and lifestyle factors) were reported using descriptive statistics along with a logistic regression model. At baseline, 2.3 % of older trial participants were frail and 39.2% were pre-frail, respectively. Women were more likely to be frail (65.1% vs 36.9%) and prefrail (58.0% vs 42.0%) than men. Lower levels of education (<12 years), living alone, ethnic minorities, current smoking and past alcohol use were some of the factors which were common among frail or prefrail. Despite being a relatively healthy cohort, more than one-third of the older trial participants were pre-frail, which was more prevalent among specific subgroups of individuals. This study emphasizes the high burden of the prefrailty status even among an apparently healthy cohort of community-dwelling older people."} +{"text": "Investigators from Denmark at Aarhus University studied the long-term risk of epilepsy, psychiatric disorders, and mortality among children with recurrent febrile seizures. Investigators from Denmark at Aarhus University studied the long-term risk of epilepsy, psychiatric disorders, and mortality among children with recurrent febrile seizures. This was a population-based cohort study that used data from the Danish civil registration system. Children born in Denmark between 1977 and 2011 were included. From a cohort of 2,103,232 children, 75,593 children (3.6%) diagnosed with febrile seizures were identified. The risk of febrile seizures peaked at age 16 months, and 90.9% had their first febrile seizure before age three years. History of recurrent febrile seizures appeared to be associated with a risk of epilepsy and psychiatric disorders, but only individuals who later developed epilepsy had an increased risk of mortality. The cumulative risk of recurrent febrile seizures was 22.7% after the first febrile seizure, 35.6% after the second, and 43.5% following the third. The 30-year cumulative incidence of epilepsy increased with the number of hospital admissions for febrile seizures, and it was 2.2% at birth, 6.4% after the first febrile seizure, 10.8% after the second, and 15.8% following the third. The 30-year risk of a psychiatric disorder was 17.2%. After the first febrile seizure, the risk increased to 21.4%, 25% after two or more admissions with febrile seizures, and 29.1% after three or more. Mortality increased with the number of hospital admissions associated with febrile seizures, which was likely explained by a subsequent diagnosis of epilepsy. [COMMENTARY. Febrile seizures are common, affecting 2-5% of children six months to 5 years of age. Several retrospective and prospective studies suggest that 2-7% of children with febrile seizures will later develop epilepsy . A prospAnother interesting finding is the association with recurrent febrile seizures and psychiatric disorders; reported previously by the same authors. While the initial analysis in this paper did not detail the types of psychiatric disorders, a subsequent letter to the editor showed the most common psychiatric diagnoses were anxiety, mood, attention-deficit/hyperactivity, and personality disorders .The increased risk of epilepsy in this study is supported by a recent, large retrospective study that found an 18-fold increased incidence of epilepsy in children with recurrent febrile seizure admissions in Taiwan . HoweverNevertheless, the current study adds important prognostic information regarding recurrent febrile seizures and the long-term risk of epilepsy, neuropsychiatric outcomes, and mortality.The authors have declared that no competing interests exist."} +{"text": "Inpatient data for COVID-19 (SARS-CoV-2) afflicted inpatients remain sparse. Data are needed to create accurate projections for resource consumption as the pandemic continues. Published reports of inpatient data have come from China, Italy, Singapore, and both the East and West coasts of the United States. Design, Setting, and Participants. This is a retrospective study of 681 patients with laboratory-confirmed COVID-19 from six hospitals in the Denver metropolitan area admitted between February 18 and April 30, 2020. Clinical outcomes of patients discharged or expired by April 30, 2020, were analyzed. Main Outcomes. We compiled patient demographics, length of stay, number of patients transferred to or admitted to the ICU, ICU length of stay, mechanical ventilation requirements, and mortality rates. The objective is to present our inpatient experience with COVID-19. n\u2009=\u20092), 97% survival of the 19\u201330 age group, 95% survival of the 31\u201364 age group, 79% survival of the 65\u201384 age group, and 75% survival of the 85 and older age group. Our total inpatient mortality was 13% (91 patients), rising to 29% (59 patients) for those requiring ICU care. Of the 890 patients with laboratory-confirmed COVID-19, 681 had discharged and were included in this analysis. We observed 100% survival of the 0\u201318 age group ( Compared to similar reports from other metropolitan areas, our analysis of discharged or expired COVID-19 patients from six major hospitals in the Denver metropolitan area revealed a lower mortality. This includes the subset of patients admitted to the ICU regardless of the need for intubation. A lower ICU length of stay was also observed. First identified in Wuhan, China, COVID-19 has spread worldwide with cases now in the millions in just six months [In December 2019, COVID-19 (SARS-CoV-2) began its spread across the globe, resulting in the 13x months . Studiesx months address x months . The stax months . This moIn order to compare our experience with other series from around the world, we evaluated inpatient data from 681 discharged patients from six hospitals in the Denver metropolitan area. This dataset includes inpatient and intensive care unit (ICU) length of stay, ICU admissions, mechanical ventilation days, total inpatient and ICU mortality, and readmissions. Our data show major differences from those collected by Zhou et al. , RichardThis retrospective cohort study was conducted with deidentified data from HCA's clinical database. Inpatient data abstracted from the HCA clinical data warehouse were aggregated for analysis and interpretation by the clinician authors.The study sample comprised patients admitted to any of the six HCA-HealthONE hospitals in the Denver metropolitan area between February 18 and April 30, 2020, and who had a laboratory-confirmed COVID-19 diagnosis. COVID-19 testing was performed using a variety of nasopharyngeal swab PCR tests during this period. Patients who remained admitted as of April 30, 2020, as well as those transferred to another acute care hospital, were excluded from the final sample so that only those patients with a known discharge disposition or who had expired were considered for analysis. For patients who were readmitted during the study period, only data from the initial admission during which they received treatment for COVID-19 were included.Patient demographic and clinical characteristics including age, sex, race, select baseline comorbidities, and smoking status were extracted. Comorbidities were categorized based on specific ICD-10 diagnosis codes documented in patient records. Primary clinical outcomes were discharge disposition, total length of stay, ICU admission, ICU length of stay, mechanical ventilation requirements, and mortality rates. Differences in these outcomes across age groups were also examined.Descriptive statistics were calculated using IBM SPSS Statistics Version 26 . Categorical variables were summarized as frequencies and percentages, while continuous variables were expressed as medians with interquartile ranges, due to the nonnormal distribution of the data. No imputation was made for missing data. Chi-square test and Cramer's V were used to analyze associations between different variables where appropriate.2\u2009=\u200920.75, p < 0.001). Since there were large sample size differences between the comorbidity subgroups, Cramer's V was used following the chi-square test to measure the effect size of any statistical difference and was determined to be \u201csmall\u201d .Of the 890 confirmed inpatient COVID-19 cases between February 18 and April 30, 2020, 209 were excluded. Excluded patients consisted of 197 who were still admitted at the time of data analysis and 12 who were transferred to an acute inpatient facility. We included 681 cases with definitive discharge data . Of thosAfter stratifying patients by age group, only 2 patients were of age 18 and under; both discharged alive. Of the 19\u201330 age group, 3% (1) died, while 97% (29) were discharged alive. Of the 31\u201364 age group, 5% (17) died, while 95% (301) were discharged alive. Of the 65\u201384 age group, 21% (48) died, while 79% (185) were discharged alive. Of the 85 and above age group, 26% (25) died, while 75% (73) were discharged alive .Total inpatient mortality was 13% (91). The median LOS was 5.00 days . Of those discharged alive, the median LOS was 4.75 days , while the median LOS for those expired was 6.96 . 30% (204) required ICU level of care. The total LOS for those requiring ICU was 6.82 days . ICU mortality was 29% (59). Total patients requiring invasive mechanical ventilation was 17% (118). Median days on mechanical ventilation was 9.00 . Mortality for those that received mechanical ventilation was 42% (49). Mortality of those that did not receive mechanical ventilation was 8% (42). Among the total patient population, there were 63% (430) discharged to home, 13% (91) expired, 8% (57) discharged to hospice, and 15% (103) discharged to either skilled nursing facility, inpatient rehabilitation facility, or a long-term care hospital. 13% (86) were readmitted . We combAs of May 3, 2020, the total cumulative case number in the world is 3,508,566. 1,158,041 are within the United States, 316,415 of which are in New York State, and 16,635 of which are in Colorado [Inpatient data are sparse, coming from just a few published sources. Of previously available inpatient data, the typical COVID-19 inpatient worldwide is male 54\u201373%) [% 3, 5\u20137, 12 and Compared to other available studies, we report decreased ICU LOS, mortality , and ventilator days. Our median length of stay is 5.00 days, which is similar to that reported by Richardson et al. but far less than reports from other metro areas with significant outbreaks . ICU lenBoth our admission rate to the ICU and ventilator requirement are similar to or higher than those in other studies. Our ICU admission rate (30%) is greater than that predicted for Colorado as well as that reported by Richardson et al. of 14% or Zhou et al. of 26% , 10. AmoThere can be a number of explanations for our experience in our six Denver area hospitals. First, and possibly most significant, our average COVID-19 patient has fewer comorbidities. 54% of patients have more than one comorbidity, compared to 88% reported by Richardson et al. from the New York City area, NY . 24% of Second, Colorado did not experience the resource constraints that were evident in Wuhan or New York City. We admitted a higher percentage of patients to the ICU (30%) than reported by Zhou et al. from Wuhan, China (26%) or RichaColorado lagged behind other states and countries in terms of number of cases, likely a result of geographic location and distance from coastlines. We therefore had the benefit of their experience. Experimental therapies were also available, but the extent of their use or efficacy is not known at this time. Other preparations such as a timely stay-at-home order, stopping all elective surgeries to preserve equipment, and upstaffing of hospitals could certainly have improved outcomes. Interestingly, Colorado ranks near the bottom of the United States in terms of hospital beds per 1,000 persons at 1.9. For comparison, New York State has 2.7 .COVID-19 is spread primarily by respiratory droplets . The NewCOVID-19 data on climate and transmissibility speak against decreased transmissibility in the Denver area. A study by Wang et al. investigated air temperature and relative humidity in 100 Chinese cities and 1,005 United States counties . This anWhile our data were obtained during peak incidence of COVID-19 in the United States, the clinical endpoint of inpatient mortality remains premature. A number of COVID-19 patients remain hospitalized at the time of data retrieval, and the pandemic is likely far from over. In this study, we excluded those that remained admitted to a hospital, while other studies did not \u20138, 12. AIn conclusion, we experienced a lower mortality , ICU length of stay, ventilator days, ICU patients requiring intubation, and mechanical ventilation mortality of COVID-19 in the Denver area compared to other reports. The reasons for this are unclear but may be best explained by geographic and population-based factors."} +{"text": "Rising care complexity in skilled nursing facilities (SNFs), coupled with growing shortages of geriatricians and other primary care physicians able to see SNF patients, have increased demand for nurse practitioners and physician assistants (NP/PAs). We used 2008-2016 Medicare Part A and B claims and nursing home assessment data to describe longitudinal trends in NP/PA practice in SNFs. We identified 8,877,094 SNF post-acute primary care visits for 1,494,113 Medicare beneficiaries. The total number of visits increased from 850,285 in 2008 to 1,189,553 in 2016. The share of visits by NP/PAs rose significantly over time, from 24% of visits in 2008 to 43% in 2016. 71% of SNFs used NP/PAs in 2016, up from 46% in 2008. The number of NP/PAs practicing in SNFs more than doubled, from 4,472 clinicians in 2008 to 10,000 in 2016. The number of physicians practicing in SNFs declined from 26,297 in 2008 to 19,745 in 2016. NP/PAs represented 14% of all SNF medical providers in 2008 and 34% of providers in 2016. In 2016, 48% of NP/PAs were SNFists (i.e. >90% of visits billed in SNF), vs. only 11% of physicians. SNFs with NP/PAs are on average larger, more likely urban, for profit, and care for larger populations of racial minorities, than SNFs without NP/PAs. SNFs with NP/PAs also have more short-stay Medicare residents, more admissions, higher nurse and rehab staffing levels, and higher case mix. These findings show that NP/PAs are taking on increasingly prominent roles as medical providers in SNFs."} +{"text": "Patients with systemic internal diseases present high risks for invasive fungal infections, which results in increased morbidity and mortality. Identification of high-risk departments and susceptibility systems could help to reduce the infective rate clinically. Correct selection of sensitive anti-fungal drugs not only could improve the cure rate but also could reduce the adverse reactions and complications caused by long-term antifungal drug treatment, which can be especially important in patients with serious systemic diseases. Therefore, the distribution changes of invasive fungal strains in patients with systemic internal diseases and the choice of antifungal drugs in clinical practice should be updated.This work aimed to investigate the incidence, strain distributions, and drug susceptibility of invasive fungal strains isolated from patients with systemic internal diseases.via the ATB Fungus-3 fungal susceptibility strip. Resistance was defined using the revised Clinical Laboratory Standardization Committee of United States breakpoints/epidemiological cutoff values to assign susceptibility or wild-type status to systemic antifungal agents.Samples were collected from 9,430 patients who were diagnosed with internal diseases in our hospital from January to December 2018. We then cultured and identified the fungal strains using API 20C AUX. We performed drug sensitivity analysis Candida (90.50%), Aspergillus (8.93%), and Cryptococcus neoformans (0.56%). The infective candida subgroups were Candida albicans (70.95%), Candida krusei (6.15%), Candida glabrata (5.59%), Candida parapsilosis (3.91%), and Candida tropicalis (3.91%). The susceptibility of non-Aspergillus fungi for amphotericin B was 100.0%. The susceptibility rates of 5-fluorocytocine (5-FC) and voriconazole were 72.73 and 81.82%, respectively, for C. krusei, 98.43 and 100% for C. albicans, and 100% for both drugs for C. glabrata, C. parapsilosis, and C. tropicalis. The susceptibility rates of fluconazole and itraconazole were 0 and 54.55%, respectively, for C. krusei, 20 and 20% for C. glabrata, and 57.14 and 57.14% for C. tropicalis. The resistance rate of C. tropicalis for both fluconazole and itraconazole was 41.43%.A total of 179 patients with fungal infection were included. The high-incidence departments were determined to be the respiratory department (34.64%), intensive care unit , and hepatology department (9.50%). The susceptible systems for infection were the respiratory tract , urinary tract , and gastrointestinal tract . The major pathogens were Candida, especially C. albicans, was the main pathogen. From the perspective of drug sensitivity, amphotericin B should be given priority in treating the non-Aspergillus fungi infection in patients with systemic internal diseases, while the susceptibility of invasive fungal strains to azoles was variant. These data might provide clinical evidence for the prevention and treatment of invasive fungal infection in patients with systemic internal diseases.Patients in the respiratory department, ICU, and hepatology department presented high rates of invasive fungal infections and should include special attention during clinical treatment. The respiratory tract, urinary tract, and gastrointestinal tract were the susceptible systems. Patients with systemic internal diseases present an increasing risk of invasive fungal infection. In recent years, the extensive use of broad-spectrum antibiotics, hormones, immunosuppressants, and other drugs used for the treatment of patients with internal diseases has given rise to an increase in the rate of invasive fungal infection. Furthermore, the development and extension of new technologies for organ transplantation and other procedures might also induce infections from conditional pathogens, especially fungal infections, as well as increase the likelihood to confer drug resistance changes . IdentifThe drug sensitivity and resistance of invasive fungi to the frequent use of fluconazole and itraconazole in clinical treatment are changing. Some of the mechanisms for antifungal drug resistance include drug absorption and drug accumulation, decreased affinity of the drug to its target, alteration of metabolic pathways to disturb cellular drug concentrations, and biofilm formation . FactorsFor the distribution of invasive fungi and drug sensitivity are varied, clinicians should select appropriate treatment schemes according to the patient\u2019s condition and the drug sensitivity results. Clinical awareness and knowledge of local epidemiology and pharmaceutical considerations could also help to achieve early diagnosis and treatment. Correct selection of sensitive anti-fungal drugs could not only improve the cure rate but also could reduce adverse reactions and complications caused by long-term antifungal drug treatment, especially in patients with serious systemic diseases. Therefore, knowledge of the susceptibility and resistance of invasive fungi strains to antifungal agents should be updated, especially in patients with systemic internal diseases who have received therapeutic drugs.In this study, we investigated the incidence, strain distributions, and drug susceptibility of invasive fungal strains isolated from patients with systemic internal diseases in the southern area of China.Both outpatient and inpatient samples, including sputum, urine, feces, blood, bile, cerebrospinal fluid, and secretion retained in the tracheal catheter, were collected from January to December 2018 at the Third Affiliated Hospital of Sun Yat-sen University\u2013Yuedong Hospital. The samples were collected from 9,430 patients who were diagnosed with internal diseases, and a total of 179 strains of invasive fungi were isolated.This work was an antifungal susceptibility surveillance study, and no human rights issues were involved. We obtained these strains in anonymized and de-identified forms.Candida chromogenic culture medium was purchased from Jiangmen Kailin Trading Co., Ltd. We used the API 20C AUX identification instrument and ATB Fungus-3 fungal susceptibility strip by the French biological company Merieux.The Candida chromogenic culture medium and identified with an API 20C-AUX system.The cultures were incubated in Sabouraud media and maintained at 35\u00b0C for 24\u201348 h in order to grow into a yeast-like colony. The single colony was then inoculated into Candida albicans, ATCC 90028.We carried out the susceptibility test using the ATB Fungus 3 fungal susceptibility strip. Testing of the drug sensitivity of the minimum inhibitory concentration was obtained by utilizing ATB instrument interpretation. The strains were classified as sensitive, intermediate, or drug-resistant according to the Clinical Laboratory Standardization Committee of United States standard and ATB Fungus 3 product specification. The instructions were observed in detail, and the results were read with the naked eye if necessary. The quality control strain used was P < 0.05 (two-sided).Data processing and statistical analysis were performed using SPSS software . Count data variables were expressed as frequencies and percentages. For all statistical analyses, statistical significance was accepted at n = 62) were in the respiratory department, 21.79% patients (n = 39) were in the intensive care unit (ICU), and 9.50% patients (n = 17) were in the hepatology department were included. Of those, 34.64% patients coming from sputum, 9.50% (17/179) from urine, and 9.50% (17/179) from feces .Candida, which accounted for 90.50%, with the remaining being Aspergillus, which accounted for 8.93%, and Cryptococcus neoformans, which accounted for 0.56%. Among the Candida species, Candida albicans accounted for 70.95%, Candida krusei accounted for 6.15%, Candida glabrata accounted for 5.59%, Candida parapsilosis accounted for 3.91%, and Candida tropicalis accounted for 3.91%.The invasive fungi isolated were primarily Aspergillus fungi to five kinds of antifungal drugs. The results showed that the drug susceptibility rate of the non-Aspergillus fungi for amphotericin B was 100.0%. The susceptibility rates for 5-FC and voriconazole were, respectively, 72.73 and 81.82% for C. krusei, 98.43 and 100% for C. albicans, and 100% for both drugs for C. glabrata, C. parapsilosis, and C. tropicalis. The susceptibility rates of fluconazole and itraconazole were, respectively, 0 and 54.55% for C. krusei, 20 and 20% for C. glabrata, and 57.14 and 57.14% for C. tropicalis. The resistance rate of C. tropicalis for both fluconazole and itraconazole was 41.43% . This suggested that amphotericin B and 5-FC should be considered more in clinical treatment of The Third Affiliated Hospital of Sun Yat-sen University\u2013Yuedong Hospital. Written informed consent to participate in this study was provided by the participants\u2019 legal guardian/next of kin.All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Many studies have shown that low health literacy (HL) is associated with several adverse outcomes. In this study, we systematically reviewed the prevalence of low HL in Europe.PubMed, Embase, and Scopus were searched. Cross-sectional studies conducted in the European Union (EU), published from 2000, investigating the prevalence of low HL in adults using a reliable tool, were included. Quality was assessed with the Newcastle-Ottawa Scale. Inverse-variance random effects methods were used to produce pooled prevalence estimates. A meta-regression analysis was performed to assess the association between low HL and the characteristics of the studies.\u03b2: 0.87, 95% CI: 0.40\u20131.35; \u03b2: 0.59, 95% CI: 0.25\u20130.93; and \u03b2: 0.72, 95% CI: 0.06\u20131.37, respectively). The assessment method significantly influenced the pooled estimate: compared to word recognition items, using self-reported comprehensions items , reading or numeracy comprehensions items , or a mixed method found higher rates of low HL. Refugees had the lowest HL . Finally, lower quality studies reported higher rates of low HL .The pooled prevalence of low HL ranged from of 27% (95% CI: 18\u201338%) to 48% (95% CI: 41\u201355%), depending on the literacy assessment method applied. Southern, Western, and Eastern EU countries had lower HL compared to northern Europe (We found that low HL is a public health challenge throughout Europe, where one in every three to almost one in every two Europeans may not be able to understand essential health-related material. Additional research is needed to investigate the underlying causes and to develop remedies.CRD42019133377The online version contains supplementary material available at 10.1007/s11606-020-06407-8. Low literacy is a worldwide phenomenon2: limited or non-adequate HL is associated with increased hospitalization4, higher rates of medication non-adherence5, lower uptake of preventive interventions3, poorer overall health status and increased mortality in the elderly5, as well as an increase in healthcare costs6. Furthermore, low literacy follows a social gradient and reinforces existing inequalities7.There is a growing interest among public health professionals and policy makers in health literacy (HL), which can be broadly defined as \u201c[people\u2019s ability] to make judgements and take decisions in everyday life concerning healthcare, disease prevention and health promotion to maintain or improve their quality of life\u201d8; in 2012, improving HL was included among the priorities of the Health 2020 strategy of the World Health Organization (WHO) Regional Office for Europe9; and in 2014, the first comparative survey on population literacy across eight EU countries was conducted10. At the international level, the WHO included HL as one of the key health promotion pillars needed for a successful 2030 Agenda for Sustainable Development 11.Given its health effects, several European Union (EU) initiatives address HL: in 2007, HL was identified as a policy priority in the European Commission\u2019s health strategy \u201cTogether for Health 2007-2013\u201d12; these studies have shown that most patient education material, including explanations of health services and their benefits, are often incomprehensible to a significant proportion of people13. However, small sample sizes, narrowly defined patient populations and heterogeneity in outcomes or study designs have limited the generalizability of the results14, limiting its usefulness for policymaking15. Within this context, we conducted a systematic review and meta-analysis of cross-sectional studies to quantify the prevalence of low HL in adult people living in EU countries, to provide a quantitative synthesis and estimation of its magnitude at national and European level, and to improve the\u00a0understanding of the underlying predictive factors.The number of studies on HL has escalated in recent yearsCochrane Handbook for Systematic Reviews and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement17. The review protocol was registered at PROSPERO (CRD42019133377).This study was performed according to the 18; therefore, all articles published between 1 January 2000 and 23 June 2019 were retrieved, without restrictions of language or paper type. The search was supplemented by scanning the reference lists of the relevant articles.Three reviewers searched the bibliographic databases PubMed, Embase, and Scopus using the following string: AND OR measure*[Title/Abstract]) OR assess*[Title/Abstract]). The string was adapted to fit the search criteria of each database cross-sectional design; (ii) conducted in one or more European Union countries (EU-28); (iii) quantified the prevalence of low HL using a valid and reliable tool; (iv) included people aged 18 years or over.We excluded articles that investigated only specific HL that assessed only specific HL domains without providing a general measurement or that did not report the prevalence of low HL in its target population(s).20. The target population was classified as general population , oncology patients, chronic disease patients, or refugees.For each record, three reviewers independently extracted the following information: first author, year of publication, tool used to quantify the prevalence of people with low HL, assessment method, number of items of the tool, proportion of people with low HL, sample size, country, EU geographic area, target population, mean or median age of the sample. Supplementary Table 21. Articles were considered of high quality when the total score was \u2265 7, fair quality if the score was \u2265 5 and < 7, and poor quality if the score was lower than 522.Three independent authors performed the quality assessment of the articles included in the systematic review using the Newcastle-Ottawa Scale for evaluating cross-sectional/survey studiesSince most articles provided two or more prevalence estimates , we considered each estimate to be a different estimate. They will hereafter be collectively referred to as \u201cstudies.\u201d23 and the restricted maximum likelihood method24. The I2 metric was used to test for heterogeneity25.As in a few reports the same target population was investigated using more than one HL tool, separate meta-analyses were conducted. Specifically, we performed an inverse-variance weighted meta-analysis using a logit transformation of the proportions for each HL assessment method. We pooled estimates using a random effects approach26. The robust variance estimation was used to take into account the correlation between studies27. We ran univariate and multivariable analyses including the covariates that could influence the prevalence estimate based on literature review. The final model consisted of the following variables: geographical area, study quality, assessment method, target population, and mean/median of the sample. The category with the highest number of studies was used as reference for geographic region, target population, and study quality; for the assessment method, we used the category yielding the lowest illiteracy pooled estimate; for the age groups, we followed the natural gradient, using the youngest as reference. For the breakdown of the age categories, we used the cut-off values reported in most studies. All analyses were performed using STATA (StataCorp), version 16.0.A random effects meta-regression analysis using logit-transformed prevalence was performed to explore the association between study characteristics and pooled low HL prevalence29 the same target population was investigated by different tools but applying the same HL assessment method, only the prevalence estimate coming from the most frequently used tool was included in the meta-analysis, for a total of 99 studies that were pooled.After removal of duplicates, 9120 records resulted from the systematic search Fig. . Since i53, South71, and West EU region85 86 and the Rapid Estimate of Adult Literacy in Medicine (n = 12)76. The European Health Literacy Survey Questionnaire with 47 items87 and its longer version with 86 items58 were used eleven and nine times each, respectively, followed by the Single Item Literacy Screener (n = 8)82 and the Medical Term Recognition Test (n = 7)65 (Table 86 (n = 38); 29 studies used reading or numeracy comprehension items84; 23 studies used word recognition items82; and nine studies used a mixed method58. Sixty-six studies quantified low HL in the general population84. Patients with chronic diseases were investigated in 25 studies85, whereas a smaller number of studies (n = 6) looked at oncology patients80. Only two studies88 investigated low HL in refugees. Among the 79 studies reporting it, the age of the sample varied, from 45 years or less in 17 studies78; between 46 and 64 years in 47 studies85; and over 64 years in 15 studies78. Lastly, the vast majority of studies (n = 81) were rated as high quality86. Eighteen studies were judged as being of fair or poor quality82; their main deficits were a lack of justification for the sample size and a lack of comparability between participants and non-participants (data not shown).A similar number of studies was available from countries of the NorthQ = 3451.2, I2 = 99.5%); reading or numeracy comprehension items was 42% ; word recognition items was 27% ; and mixed methods provided a pooled estimate of 48% ; Belgium, 41% (95% CI: 40\u201342%); Bulgaria, 62% (95% CI: 59\u201365%); Croatia, 58% (95% CI: 48\u201367%); Czech Republic, 44% (95% CI: 35\u201353%); Finland, 36% (95% CI: 31\u201342%), Hungary, 41% (95% CI: 35\u201346%); Lithuania, 33% (95% CI: 30\u201336%); and Poland, 45% (95% CI: 41\u201348%). Other EU countries had more than one study, often with different assessment tools. Denmark52 low HL was around 44%, in both the assessment methods used (Table 82 low HL was 51% (95% CI: 34\u201367%). Germany84 ranged from 44% to 46% (95% CI: 43\u201349%); Greece71 was 45% (95% CI: 42\u201348%) to 54% (95% CI: 45\u201363%). In Ireland49, the pooled estimates varied between 19% , 40% (95% CI: 37\u201343%), 41% , and 65% (95% CI: 46\u201381%). Italy low HL pooled estimates were by self-reported comprehension items66 42% ; by reading or numeracy comprehension items67, 38% ; by word recognition items65, 72% ; and by mixed method58, 54% (95% CI: 51\u201357%). As for Portugal70, the low HL prevalence estimates varied between 21% , 29% , and 50% (95% CI: 48\u201352%). In Spain89, the prevalence estimates of low HL were, in increasing order, 33% , 43% (95% CI: 34\u201352%), 58% (95% CI: 55\u201361%), and 71% (95% CI: 47\u201387%). In Sweden53, low HL ranged from 21% (95% CI: 14\u201330%) to 39% (95% CI: 36\u201343%). As for The Netherlands85, the highest pooled prevalence was 68% , followed by 29% (95% CI: 26\u201332%), 19% , and 14% . The UK90 had relatively low pooled estimates, varying between 16% , 21% , and 28% . Lastly, the refugees\u2019 population was investigated in two studies88 with a low HL pooled estimate of 65% .There was variation in the number of studies in each country as well as the assessment method used. AustriaMeta-regression analysis found that the geographic region, assessment method, target population, and study quality impacted the results Table . Western7. Although this proportion is slightly lower than that reported by a systematic review of studies on the US population91, where nearly one in two had low HL, and is lower than the mean prevalence of 55% reported in Southeast Asian countries92, our review confirms that low HL also represents a public health challenge in Europe12.We found that a third to nearly half of Europeans had low HL. This suggests that a significant percentage of people living in EU may have difficulties in getting access to prevention and healthcare services due to limitations in navigation, comprehension, and decision-making93. Countries with the lowest prevalence of low HL also have greater years of education94 and higher socio-economic status95, an important factor in HL96. However, specific future research is needed in order to better investigate the causes of such inequality and appropriately assess their impact on HL.While the prevalence varies considerably by country and the HL assessment method, it seemed to follow a geographic distribution, with the northern countries having lower prevalence than the other EU counterparts. It is possible that the intersection between culture, literacy, and HL may at least partially explain such a difference. Social and cultural context, which includes education, is inextricably linked to how citizens perceive and act on health information97; accordingly, when the researchers used different assessment methods to explore specific HL skills, the prevalence estimates varied significantly. Notably, apart from Italy, tools with word recognition items tended to provide lower illiteracy prevalence estimates, suggesting that investigating HL as medical vocabulary may underestimate the prevalence. Therefore, although the development and acceptance of a universal measure of HL is challenging, a common definition and a comprehensive instrument for its evaluation would enable a more precise estimation of the magnitude of the problem and a better comparison of evidence97.A widely accepted definition of HL is still under discussion91. While we found a slightly increasing, although not significant, trend of low HL prevalence across age groups, the combination of incomplete data and heterogeneity of the measures applied may have limited the reliability of this covariate. However, since older age is known to be associated with an increase in health needs and low HL could impair access to healthcare services99, the potential effect of aging on HL should not be overlooked.Older age is reported to be associated with a higher risk of low HL102. It was therefore not surprising that we found the strongest association with low HL in refugees, where the lack of knowledge of the healthcare services of the host country, different cultural conceptions, and the language barrier are probably the main drivers of the HL gap103. Since HL is most likely to improve when the messaging and delivery are tailored to the specific needs of individuals and populations97, it is imperative that healthcare systems become more culturally and linguistically competent, so that they are able to address the growing diversity among their target populations13.Differing cultural and educational backgrounds among patients and providers may result in different attitudes and beliefs, which might influence HL and impair access to healthcare services15, more high-quality studies are needed in order to properly understand the extent of the challenge and ensure the generalizability of the results. In particular, our study found that more attention should be paid to how the sample is selected, with regard to the justification of sample size and to demonstrating comparability between responders and non-responders.Lastly, the study quality was found to be a significant predictor of the prevalence of low HL. Therefore, as reported by WHO Action Network on Measuring Population and Organizational Health LiteracyTo the best of our knowledge, this is the first quantitative synthesis of data on prevalence of low HL in EU countries that enabled a comparison between member States. Nevertheless, it is important to acknowledge the limitations of our study. First, since our objective was to quantify the prevalence of low HL, we included only studies with a cross-sectional design. Second, we excluded articles that used an arbitrary cut-off to identify people with low HL, which provided only a mean measurement of HL, or which analyzed only specific sub-domains. Third, HL tools and target populations were consistently heterogeneous; however, separate analyses and a meta-regression were carried out.In conclusion, low HL is very common in the EU, where at least one in every three people may not be able to understand essential health-related material. Despite a few variations in the prevalence estimate due to the instrument applied, our results are consistent in showing that low HL represents a public health challenge throughout Europe. Additional efforts to increase the evidence on the underlying causes, to identify areas for intervention, and to implement health practices that effectively address a low level of HL are needed.ESM 1(DOCX 1146 kb)"} +{"text": "EGFR/ALK for non-small cell lung cancer (NSCLC) and extended-RAS for colorectal cancer). Results: 349 tests were sent for CGP from 333 patients and 95% had at least one actionable genomic alteration reported. According to the reported results, 23.2% had a Food and Drug Administration (FDA) approved therapy available, 61.3% had an off-label therapy available and 77.9% were potentially eligible for a clinical trial. Treatment recommendations were also reviewed within the OncoKB database and 47% of them were not clinically validated therapies. The CGP results led to treatment change in only 35 patients (10%), most commonly in NSCLC. Nineteen of these patients had documented clinical benefit with targeted therapy. Conclusion: we demonstrate that routine use of CGP in the community across all cancer types detects potentially actionable genomic alterations in a majority of patients, however has modest clinical impact enriched in the NSCLC subset. Purpose: next-generation sequencing based comprehensive genomic profiling (CGP) is becoming common practice. Although numerous studies have shown its feasibility to identify actionable genomic alterations in most patients, its clinical impact as part of routine management across all cancers in the community remains unknown. Methods: we conducted a retrospective study of all patients that underwent CGP as part of routine cancer management from January 2013 to June 2017 at an academic community-based NCI-designated cancer center. CGP was done in addition to established first tier reflex molecular testing as per national guidelines (e.g., BRAF, ERBB2 (HER2), MET, RET, NTRK, and ROS1, in addition to EGFR and ALK for metastatic non-small cell lung cancer (NSCLC) [Targeted therapy against driver genomic alterations has improved outcomes for patients with many different cancers, including lung cancer, melanoma, breast cancer, and others . Next-ge (NSCLC) ,5,6,7. S (NSCLC) ,9,10. Se (NSCLC) ,12. EGFR and ALK [EGFR and ALK testing and only 63 (8%) underwent testing for all eight NCCN recommended genomic alterations. The barriers cited for under-genotyping included sample handling issues, long turnaround times, confusion about test reimbursement, access to targeted therapies, and insufficient tissue. Despite guidelines, the uptake of CGP in the community has not been uniform, even in NSCLC patients and the general impact of CGP as to patient outcomes and cost effectiveness remains unclear ,14. A lan = 88) had at least one genetic alteration. CGP led to change in management in 31% of patients, including targeted therapy, change in diagnosis, and germline testing. However, some of the cases included in this subset were those treated with cytotoxic chemotherapy, due to lack of driver mutations, e.g., a pancreatic tumor with STK11 mutation treated with pemetrexed. Barriers to change in management were deteriorating patient clinical status and a lack of access to relevant clinical trials. Another prospective study assessed the feasibility of implementing CGP for all cancer patients at the institution and reported the results for the first 3727 patients who were successfully sequenced with their in-house gene panel [p = 0.024), as well as longer survival . A subsequent analysis of the same patient cohort found that patients on matched therapy had longer time on treatment (1.5 months), longer survival by 2.4 months, and higher drug treatment costs (by $38K) (p < 0.01) [Several studies, mostly from large academic centers, have reported successful implementation of CGP and have shown that most patients will have at least one potentially actionable genomic alteration on CGP. In a retrospective study of 125 patients who underwent CGP, clinically relevant genetic alterations were found in 111 (92%) patients . Only 15ne panel . Of thes < 0.01) . The altRecently, another study estimated that 8% of cancer patients in the United States were eligible for genome-targeted therapy and only 4.9% were estimated to actually derive benefit from this therapy . The MOSOur study aims to determine the real-world impact of routine incorporation of CGP in the community across all cancer types, regardless of stage or prior lines of therapy, while these studies have shed light on the feasibility as well as actionability in advanced cancers after standard treatments in the setting of clinical trials.RAS testing for colorectal cancer, HER2 for breast and esophagogastric cancer, and EGFR/ALK for lung adenocarcinoma. CGP constitutes the second tier and these tests are sent at the discretion of the treating oncologist. The assays used for NGS-based genomic profiling included the commercially available Foundation Medicine , Guardant Health , or Genoptix multi-gene panels. Testing facilities reported results defining potentially clinically actionable genetic alterations and listed treatment options available in three categories: FDA-approved on-label therapies, FDA-approved off-label therapies, and available clinical trials. Management change included patients in whom targeted therapy was initiated, continued, or withheld based on the results of CGP. Those who had clarification or confirmation of primary tumor or were enrolled on clinical trials based on CGP were also included. Patients already on targeted therapy based on previously known genetic alterations obtained by sequential or first-tier reflex testing were not included. Two independent physicians (A.S. and E.S.) reviewed all patient charts to obtain demographic as well as clinical data. We conducted a retrospective, observational study of all patients that underwent comprehensive genomic profiling from January 1, 2013 to June 30, 2017 at an academic community-based National Cancer Institute (NCI)-designated cancer center. The institution has a multidisciplinary molecular tumor board that was established in September 2015, where some of these cases were referred and reviewed. CGP was performed either on tumor or plasma samples. Our institution, like many others, has a two-tier algorithm for molecular testing. The first-tier included tests that are reflexively sent by the Pathology department based on histology according to established institutional guidelines following national recommendations. For example, this included during the study era extended Next, we utilized the publicly available precision oncology database, OncoKB to assesn = 107, 31.5%,), followed-by colorectal cancer , ovarian cancer , and carcinoma of unknown primary of tests were sent on tumor tissue samples and 20.1% (n = 70) were sent on plasma samples. The median number of therapies received for metastatic disease at the time of testing was 1 (range 0\u20135) and the median turnaround time for results was 12 days . In seven cases, the results were not reported due to failed sequencing. At least one clinically actionable genomic alteration was detected in 332 (95%) patients. According to result reports from testing platforms, 23.2% (n = 81) had an FDA approved targeted therapy available for their tumor, 61.3% (n = 214) had an off-label FDA approved targeted therapy available, and 77.9% (n = 272) were potentially eligible for a clinical trial. A total of 408 treatment recommendations were annotated as FDA-approved or off-label therapies and they were reviewed within the OncoKB database. Forty-seven percent of these did not have any level of evidence assigned. Of the 408 actionable alterations, 7.8% were assigned level 1, 9.8% were assigned level 2, 8.6% were assigned level 3, 17.6% as level 4, and 8.6% as level R1. See Three hundred and forty-nine tests were sent from 333 adult patients. The median age of patients was 63 years (range 19\u201398 years). One hundred and ninety-two (56%) of the patients were female. 112 (32%) patients were black and 71 (20.3%) identified as Hispanic. One hundred and twenty-four patients (63.4%) had Medicare or Medicaid and 26% had private insurance. The most common diagnosis for which CGP was sent was NSCLC (n = 35) of patients. In another seven patients, treatment change was planned, but the patient either declined treatment or died prior to its initiation. Of these 42 patients, the most common diagnosis was NSCLC (n = 28). CGP-driven management change was observed in 50% (n = 1/2) of thymoma, 40% of head and neck cancer (n = 4/10), 26.2% (n = 28/107) of NSCLC, 27.3% (n = 3/11) of esophagogastric, 25% (n = 1/4) sarcoma, 22.2% (n = 2/9) of breast cancer, 7.1% (n = 1/14) carcinoma of unknown primary, and 3.4% (n = 2/58) of CRC patients. p = 0.0002). The patients had a median follow-up of 1.3 years from the date of the reported CGP results. Despite the high number of listed actionable alterations, management was actually changed based on CGP in only 10% did not result in change in management. Twelve of these had previously known mutations in NSCLC/CRC/gastric/breast cancer as part of established first tier reflex testing. In 37 patients, the recommended targeted therapy was not standard of care, including high tumor mutational burden directed immunotherapy, four patients had early disease where targeted therapy was not indicated, in one patient therapy was reserved for future disease progression, and one patient died. Although 54 patients (15.5%) participated in clinical trials, only five were enrolled in clinical trials based on results from CGP (including two patients on NCI-MATCH).p = 0.0002). 28 of 107 (26.2%) NSCLC patients had change/potential change in management based on CGP. As a result of first tier Epidermal Growth Factor Receptor (EGFR)/Anaplastic Lymphoma Kinase (ALK) testing, the majority of EGFR/ALK mutated patients were identified outside of CGP testing. If such first-tier testing results were to be included, the impact of molecular testing would be much higher. In addition, recent studies, for example, with K-Ras G12C inhibitors offer the hope of further expansion of actionable targets [In our study, CGP identified at least one potentially clinically actionable genomic alteration in 95% of patients, which is similar to several other reports ,10,21. H targets . A recen targets . The stuHER2 in breast/upper GI and extended-RAS in colorectal cancer are included. The impact of CGP will likely also increase with the tissue/site agnostic approval of pembrolizumab in solid tumors with microsatellite instability and Tropomyosin Receptor Kinase (TRK) inhibitors for Neurotrophic Tropomyosin-Related Kinase (NTRK)-translocation positive malignancies; however, the frequency of these alterations admittedly is low [In other cancer types in our study, the impact was much less, soberingly with only 14 of 242 patients (5.8%) with change/potential change in management based on CGP results. Again, the impact would be higher if first-tier testing such as y is low ,24. Tumoy is low ,26. Despite the aforementioned emerging uses of CGP, at present, data to support therapeutic recommendations for many targeted drugs is not robust enough to warrant therapy off a clinical trial, e.g., trastuzumab in ERBB2 amplified lung cancer. Our review of treatment recommendations in the OncoKB database showed that 47% of them did not have strong clinical evidence to support their use. Only 17.6% of recommendations were based on level 1 or 2 evidence. Therefore, the actual actionability of these genomic alterations is currently significantly less than presented. Additionally, an increasing number of commercial as well as institutional multi-gene panels are now being utilized for CGP; however, there is no standardization of therapeutic recommendations based on results . MultidiOur study has certain limitations, particularly because of its retrospective nature. The timing and choice of CGP panel was not standardized and it was at the discretion of the treating oncologist; however, this indeed best captures a \u201creal-world\u201d scenario in the community as compared to other publishes studies. Another drawback is the short follow-up and the proportion of patients with change in management based on CGP would likely increase with time, due to disease progression or more targeted agents becoming standard of care. We did not include patients who benefited from targeted therapy based on first-tier testing. However, this study specifically assessed the impact of CGP in settings such as ours, where there might be a two-step process for genomic profiling, likely representing the majority of practice patterns both in and especially outside of the United States. Another issue is optimal timing for CGP. Whereas some patients with actionable genetic alterations had early stage disease and, hence, not initiated on targeted therapy, some deteriorated clinically prior to the initiation of treatment. This makes a case for obtaining CGP as soon as possible with metastatic disease or locally advanced disease with a high risk of recurrence. Serial liquid biopsies are now being utilized for the real-time assessment of tumor mutations and more studies are needed to inform the decision of ideal timing for CGP. The lack of available molecularly driven protocols was not a factor, with more than 200 open clinical trials, including the NCI-MATCH trial actively recruiting patients at our institution. Moreover, our enrolment rate of 15% was higher than the national average indicating the robustness of our clinical trials program . Our stuOverall, our study provides a real-world experience of the impact of CGP in a community-based academic NCI-designated cancer center serving a highly diverse patient population, where molecular testing is based on a two-tier testing algorithm. While recognizing that a 10% overall rate of management change that is based on CGP is very modest, its use in certain subsets, such as advanced NSCLC, where the impact currently is most significant appears to be justifiable and it has been found to be cost effective ,41,42. I"} +{"text": "Introduction and aimClinical indicators alone are insufficient for evaluating oral health. In addition to health and disease, oral health includes socio-dental indicators of physical, psychological, and social aspects of well-being. The adaptive capacity of an individual influences the perception of oral health-related quality of life (OHRQoL). Indices such as the Oral Health Impact Profile, Oral Impacts on Daily Performances, and the Geriatric Oral Health Assessment Index (GOHAI) have been used to measure OHRQoL. This study was designed to assess OHRQoL in older individuals using the GOHAI.MethodsSubjects aged older than 65 years who visited our institution from January to March 2016 were included. Subjects with cognitive behavior disorders were excluded. Subjects were assigned into three groups based on age: 65-69 years, 70-74 years, and 75 years or older. The participants were asked 12 questions, and their responses were assessed by age group. Our Institutional Ethics Committee approved the study protocol.ResultsThe 219 subjects recruited included 126 (57.5%) patients aged 65-69 years, 57 (26.0%) patients aged 70-74 years, and 36 (16.4%) patients aged 75 years or older. Several physical, physiological, and psychological aspects of the GOHAI differed significantly among these three groups, with overall OHRQoL decreasing with age.ConclusionAlthough oral healthcare problems were widespread in the geriatric population, they were not a primary concern. Attitudes toward dentistry require improvement. However, further studies in larger populations are required to assess geriatric oral health. Estimates indicate that, by 2050, 17% of the Indian population will be aged 65 years or older, compared with 7.4% in that age range in 2001 -4. This Geriatric oral health assessment indexThe GOHAI consists of 12 closed-ended questions (presented in Appendix I) evaluating self-perceived oral health, including pain, discomfort, and psychosocial impact . The resThe study was conducted in three stages. The first stage consisted of translating the questions on the GOHAI into Tamil, the local language, and the second stage consisted of its back translation into English. The third stage consisted of administering the GOHAI questionnaire to the study subjects. It was necessary to rephrase and shorten the questions on the GOHAI for more natural understanding. The administered form of the GOHAI questionnaire, modified to suit the target population, is shown in Appendix I.TranslationBefore administering the GOHAI to subjects with cultural and linguistic differences, it had to be translated and validated. Such translations pose two problems: 1) it may not be possible to translate some phrases or words directly\u00a0and 2) languages exist within unique cultural and social frameworks, changing the meaning of some questions or making them meaningless. The GOHAI questionnaire was translated from English into Tamil by two dental students, who were fluent in both languages . The TamParticipantsSubjects who visited the geriatric clinic of the Sri Ramachandra Institute of Higher Education and Research for three months were recruited. Subjects with cognitive and behavioral disorders and in-patients were excluded. The age, gender, and medical history of each participant were recorded, including whether subjects had diabetes mellitus or hypertension, whether they were smokers, and medicines taken. Dental histories were also recorded, such as denture usage, denture stomatitis, pigmentation of the tongue, and smokers\u2019 palate.Statistical analysisAll data were statistically analyzed using IBM SPSS Statistics for Windows, Version 24.0 . Chi-square test was performed for finding the significant differences between age groups.The University Ethics Committee approved the protocol of this study (Ref: CSP/17MAY/58/159), and all enrolled subjects provided written informed consent before participating.A total of 219 subjects aged 65 years or older were recruited. These included 126 (57.5%) subjects aged 65-69 years, 57 (26.0%) aged 70-74 years, and 36 (16.4%) aged 75 years or older. Table Responses to several GOHAI questions showed significant age-related differences. For example, 67.5% of subjects aged 65-69 years never experienced food limitations due to problems with teeth or dentures, whereas 63.9% of those aged \u226575 years always experienced these limitations; subjects aged 70-74 years showed intermediate responses (P = 0.00). Similarly, 82.5% of subjects aged 65-69 years never experienced difficulties biting firm foods, whereas about 50% of those aged \u226575 years always experienced difficulties (P = 0.00).Discomfort during swallowing was never experienced by 78.6% of subjects aged 65-69 years, compared with 47.2% of those aged \u226575 years. Only 4% of subjects aged 65-69 years always experienced problems with speech, compared with 25% of subjects aged \u226575 years. The percentage limiting contact with other people due to problems with teeth or dentures was significantly lower in subjects aged 65-69 years than those aged \u226575 years . The percentages reporting that they never worried about problems with teeth or dentures was higher in subjects aged 65-69 years than those aged \u226575 years (27% vs. 63.9%), whereas the proportion reporting that they always felt uncomfortable eating in front of others was significantly lower in those aged 65-69 years than \u226575 years .Responses to other questions on the GOHAI did not differ significantly among the three age groups.The results of this cross-sectional study showed that older geriatric subjects aged 75 years or older perceived physical problems associated with dentition more acutely than psychological problems. The higher percentages of subjects aged \u226575 years than those in the other age groups experiencing food limitations and having trouble biting firm foods may have been due to differences in the percentages who wore dentures. Although the oldest age group had the highest percentage of edentulous subjects, it had the lowest percentage of denture wearers, 11.1%, compared with the groups aged 65-69 years (12.7%) and 70-74 (26.3%) years. Edentulous subjects have greater difficulty eating foods like raw carrots, apples, and nuts. .Discomfort during swallowing was significantly more prevalent in subjects aged \u226575 years than in the other two groups. The prevalence of diabetes was higher in this group (30.6%) than in subjects aged 65-69 (29.4%) and 70-74 (28.1%) years. Diabetes has been associated with xerostomia, and xerostomia has been associated with swallowing difficulties -12.Despite the age-associated increase in problems with dentition, the percentage of subjects who never worried about problems associated with teeth or dentures was higher in those aged 75 years or older (63.9%) than in those aged 65-69 years (27.0%) and 70-74 years (31.6%). The use of dental services is a consequence of the patient-perceived need for treatment . AlthougSpeech problems due to problems with dentition were more acutely perceived by subjects aged 75 years or older than those aged 65-69 and 70-74 years. This difference may be due to the higher prevalence of edentulousness in the oldest age group . BecauseThe percentages of subjects experiencing discomfort while eating were similar in the three age groups. More than 50% of subjects in each of these groups report always experiencing discomfort while swallowing, suggesting that this may be a common geriatric complaint, not specific to any particular age group. The percentage of subjects always limiting contact with others was higher in those aged 75 years or older than those aged 65-69 and 70-74 years. Edentate non-denture wearing subjects aged 75 years or older experience more trouble with speech formation than dentate individuals . This diResponses to the other questions on the GOHAI did not differ significantly among the three age groups, suggesting that these problems may be perceived similarly across all geriatric age groups.LimitationsThe sample consisted mainly of women, preventing comparisons between men and women.This study revealed that perceptions of physical problems associated with oral health differed significantly among age groups in the geriatric population. The oldest group, those aged 75 years or older, reported physical problems more acutely than the other age groups. By contrast, problems related to appearance and attitude towards dental care were similar in the three age groups. Moreover, dental care was not regarded as a primary concern among geriatric subjects. Although these findings suggest that determination of the clinical and oral health of geriatric patients is required for optimum dental care, additional studies in larger populations are required to assess geriatric oral health."} +{"text": "The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires health care workers (HCWs) to be present at work, particularly in low- and middle-income countries (LMICs) where they are already in critically low supply. To inform whether and to what degree policymakers in Bangladesh, and LMICs more broadly, should expect a drop in HCW attendance as COVID-19 continues to spread, this study aims to determine how HCW attendance has changed during the early stages of the COVID-19 pandemic in Bangladesh.This study analyzed daily fingerprint-verified attendance data from all 527 public-sector secondary and tertiary care facilities in Bangladesh to describe HCW attendance from January 26, 2019 to March 22, 2020, by cadre, hospital type, and geographic division. We then regressed HCW attendance onto fixed effects for day-of-week, month, and hospital, as well as indicators for each of three pandemic periods: a China-focused period until January 29, 2020), international-spread period until March 6, 2020), and local-spread period until the end of the study period).On average between January 26, 2019 and March 22, 2020, 34.1% of doctors, 64.6% of nurses, and 70.6% of other health care staff were present for their scheduled shift. HCWs\u2019 attendance rate increased with time in 2019 among all cadres. Nurses\u2019 attendance level dropped by 2.5% points \u2009=\u2009-3.2% to -1.8%) and 3.5% points (95% CI\u2009=\u2009-4.5% to -2.5%) during the international-spread and the local-spread periods of the COVID-19 pandemic, relative to the China-focused period. Similarly, the attendance level of other health care staff declined by 0.3% points (95% CI\u2009=\u2009-0.8% to 0.2%) and 2.3% points (95% CI\u2009=\u2009-3.0% to -1.6%) during the international-spread and local-spread periods, respectively. Among doctors, however, the international-spread and local-spread periods were associated with a statistically significant increase in attendance by 3.7% points (95% CI\u2009=\u20092.5% to 4.8%) and 4.9% points (95% CI\u2009=\u20093.5% to 6.4%), respectively. The reduction in attendance levels across all HCWs during the local-spread period was much greater at large hospitals, where the majority of COVID-19 testing and treatment took place, than that at small hospitals.After a year of significant improvements, HCWs\u2019 attendance levels among nurses and other health care staff have declined during the early stages of the COVID-19 pandemic. This finding may portend an even greater decrease in attendance if COVID-19 continues to spread in Bangladesh. Policymakers in Bangladesh and similar LMICs should undertake major efforts to achieve high attendance levels among HCWs, particularly nurses, such as by providing sufficient personal protective equipment as well as monetary and non-monetary incentives. The novel coronavirus disease 2019 (COVID-19) was first reported in Wuhan, China in December 2019 . COVID-1For LMICs to respond as effectively as possible to the pandemic will require that the health system is able to fully utilize its existing resources. Arguably the most essential health system resource is health care workers (HCWs). In addition to a critically low density of HCWs in most LMICs, many of these health systems also struggle with alarmingly low HCW attendance rates. In prior studies, HCW attendance rates have ranged from 52%-60% in Bangladesh, India, Indonesia, and Uganda to 75% in Peru and Kenya .There is no empirical evidence so far on how HCW attendance rates at hospitals in LMICs will be affected by the COVID-19 pandemic. On the one hand, HCWs maybe more motivated to report to work because they feel compelled to contribute to the country\u2019s pandemic response. On the other hand, HCW attendance may decline due to workers\u2019 fear of infecting themselves and their families, especially given the lack of personal protective equipment (PPE) in many settings, or due to HCWs themselves falling ill with COVID-19. Previous studies suggested that HCWs were less likely to work during pandemics. The 2009 H1N1 influenza pandemic in Hong Kong was associated with an increase in the all-cause sickness absence rate by 57.7% for all health care cadres . SimilarUnderstanding whether and to what degree HCW attendance will change in LMICs during the COVID-19 epidemic could help policymakers take early action to increase attendance, such as ensuring a reliable and sufficient supply of PPE or providing monetary and non-monetary incentives to attend. This study leverages unique fingerprint-verified HCW attendance data collected daily at all public-sector secondary and tertiary care facilities in Bangladesh in 2019 and 2020 to i) describe the level of HCW attendance in Bangladesh and how this varies by health care cadres, hospital types, and geographic regions, and ii) to determine changes in HCW attendance during the early stages of the COVID-19 epidemic.Bangladesh is one of the world\u2019s most populous countries, with a population estimation of more than 167 million people . SimilarAs of May 4, 2020, the Institute of Epidemiology, Disease Control and Research (IEDCR) reported that the country had tested 87\u2009694 individuals, 10\u2009143 of whom were infected with the virus and 182 people died from infection [This study used attendance data from the Bangladesh\u2019s Ministry of Health and Family Welfare collected daily at all public-sector secondary and tertiary medical facilities from January 26, 2019 to March 22, 2020. Attendance was verified using fingerprints rather than self-reports. All HCWs must scan their fingerprint using a machine sensor on arrival and departure. The date and time of arrival and departure is recorded directly in the central system, and aggregated staff attendance data are available to the public . Data atOur analysis had three main steps. First, we calculated the daily percentage of workers present at work for each cadre as well as for all cadres at each facility. We eliminated administrative facilities and medical colleges that did not provide direct patient care (N\u2009=\u200946). The remaining 527 direct patient-care facilities comprised of all public-sector secondary and tertiary care facilities, which were categorized into hospitals/institutes \u2013 including medical college hospitals, hospitals with at least 100 beds, hospitals with fewer than 100 beds, general hospitals, district hospitals, and sub-district hospitals. Second, using locally weighted robust regression (LOWESS), we described smoothed unadjusted trends in attendance levels of all HCWs as well as attendance of doctors, nurses, and other staff from January 26, 2019 to March 22, 2020.Third, we investigated the association between the COVID-19 pandemic and HCW attendance from January 11, 2020 to March 22, 2020. We began with January 11, 2020, because this was the day on which the first COVID-19 death was confirmed in China. We ended the study on March 22, 2020, because the Bangladesh government ordered HCWs on this date to stop using fingerprint machines to record attendance due to fear that the practice of touching the fingerprint scanning device could spread SARS-CoV-2. The pandemic was divided into three periods based on the spread of COVID-19 internationally and within Bangladesh: the China-focused period , the international-spread period , and the local-spread period . We used a multivariable ordinary least squares regression model to estimate absolute changes in the attendance rate for all healthcare cadres during the international-spread and the local-spread periods relative to the China-focused period (the reference category). In these regressions, we controlled for secular trends and time-invariant hospital characteristics by including a series of day-of-week fixed-effects, month fixed-effects, and hospital fixed-effects. Standard errors were adjusted for clustering by hospitals to account for possible heteroskedasticity and correlation in the error terms over time. We repeated the regression analysis by healthcare cadre , hospital types , and geographic divisions.All analyses were conducted using Stata version 16.0 .Further investigation revealed different patterns across health care cadres. Among doctors, the attendance rate was significantly lower than those of nurses and other staff in 2019. Doctors\u2019 attendance rates increased significantly in December 2019 following the recruitment of 4607 doctors at sub-district hospitals in rural areas, from 31.1% (95% CI\u2009=\u200930.8% to 31.5%) in November 2019 to 42.2% (95% CI\u2009=\u200941.3% to 43.1%) during the first week of January 2020. Doctors\u2019 attendance further increased to 57.1% (95% CI\u2009=\u200956.6% to 57.6%) during the China-focused period, and then continued growing to 65.7% (95% CI\u2009=\u200965.3% to 66.0%) and 70.4% (95% CI\u2009=\u200969.9% to 70.9%) during the international-spread and the local-spread periods, respectively. The attendance levels of nurses and other staff followed a different pattern. In 2019, the attendance levels of nurses and other staff were much higher than that of doctors (62.0% (95% CI\u2009=\u200961.9 to 62.1%) and 68.2%% (95% CI\u2009=\u200968.1% to 68.3%) for nurses and other staff, respectively, vs 26.5% (95% CI\u2009=\u200926.4% to 26.6%) for doctors). Attendance levels of nurses and other staff increased during the China-focused period and then started to decline after the occurrence of the first COVID-19 case in Bangladesh.Panel A). In addition, the reduction in attendance levels across all HCWs during the local-spread period was much greater at large hospitals than that at small sub-district hospitals.Trend analyses for each of the eight geographic divisions , our results pertain to those HCWs who are most heavily involved in the COVID-19 response. Third, the data did not allow us to differentiate between voluntary absence and absence due to sickness. Finally, we lacked data on attendance across units within hospitals. Since HCWs in certain units \u2013 particularly emergency departments and intensive care units \u2013 are more heavily involved in caring for COVID-19 patients, analyses stratified by units may provide additional insights to attendance associated with occupational exposures and help inform resource allocation within hospitals.Low work attendance by HCWs could become a major obstacle to LMICs\u2019 efforts to combat the COVID-19 pandemic. Using Bangladesh as a case study, we show that HCW attendance has been worryingly low in 2019 and 2020 but, encouragingly, has been increasing steadily over time. We also provide evidence that while doctors were more likely to report to duty during the early stages of the COVID-19 pandemic, work attendance by nurses and other staff has dropped since the WHO declared COVID-19 a global emergency. Given that nurses and other staff account for the largest share of the health care workforce in LMICs, policymakers should undertake major efforts to boost their attendance levels during the rapidly spreading COVID-19 pandemic."} +{"text": "Background: Variation in breast cancer surgical practice patterns can lead to poor clinical outcomes. It is important to measure and reduce variation to ensure all women diagnosed with breast cancer receive equitable, high-quality care. A population-based assessment of the variation in breast cancer surgery treatment and quality has never been conducted in Manitoba. The objective of this study was to assess the variation in surgical treatment patterns, quality of care, and post-operative outcomes for women diagnosed with invasive breast cancer. Methods: This descriptive study used data from the Manitoba Cancer Registry, Hospital Discharge Abstracts Database, Medical Claims, Manitoba Health Insurance Registry, and Statistics Canada. The study included women in Manitoba aged 20+ and diagnosed with invasive breast cancer between 1 January 2010 and 31 December 2014. Results: Axillary lymph node dissection (ALND) for node-negative disease ranged from 11.8% to 33.3%, timeliness (surgery within 30 days of consult) ranged from 33.3% to 60.2%, and re-excision ranged from 14.7% to 24.6% between health authorities. Women who underwent breast-conserving surgery had the shortest median length of stay and women who underwent mastectomy with immediate reconstruction had the longest median length of stay. In-hospital post-operative complications were higher among women who received mastectomy with immediate reconstruction (9.9%). Conclusion: Variation in surgical treatment, quality, and outcomes exist in Manitoba. The findings from this study can be used to inform cancer service delivery planning, quality improvement efforts, and policy development. Influencing data-driven change at the health system level is paramount to ensuring Manitobans receive the highest quality of care. Health care quality measurement has evolved into a routine part of health care planning and delivery. Quality is defined as \u201cthe degree to which health services for individuals and populations increase the likelihood of desired health outcomes and are consistent with current professional knowledge\u201d . High-quVariations in healthcare practice patterns have been studied for decades among multiple specialties ,7. StudiA descriptive study design was used to address the objective stated above. The following data sources were used: Manitoba Cancer Registry (MCR), Hospital Discharge Abstracts Database, Medical Claims Database, Manitoba Health Insurance Registry, and Statistics Canada 2006 Census. The MCR is a population-based registry that is legally mandated to collect, classify, and maintain accurate, comprehensive information about cancer cases including diagnosis date, tumor type and location, stage, and treatment in the province of Manitoba. The MCR was used to identify women diagnosed with invasive breast cancer and to identify surgical procedures. The Medical Claims Database, maintained by Manitoba Health, Seniors and Active Living (MHSAL), is generated by claims filed by health care providers for reimbursement of services and includes services provided, diagnosis, provider, and service date and was used to identify surgical consult dates. The Hospital Discharge Abstracts Database includes all hospital admissions for Manitoba residents and was used to identify surgical procedures, in-hospital complications, and length of stay. The Manitoba Health Insurance Registry contains individual and family-level information including demographic, vital status, and migration information. The Manitoba Health Insurance Registry was used to refine the cohort by ensuring all individuals were eligible for health care coverage and lived in the province during the study period. The 2006 Census data contains information about area-level average household income based on each individual\u2019s area of residence and was used to stratify results by income quintile. All Manitoba residents have been assigned a personal health identification number which was used to link the provincial health information databases. The study included women in Manitoba aged 20 years or older who were diagnosed with invasive breast cancer C50.0\u201350.9 between 1 January 2010 and 31 December 2014. Atypical and rare morphologies including lymphomas and sarcomas of the breast, phyllodes tumors, Paget\u2019s disease, and benign breast lesions were excluded. Manitoba is a Canadian province with publicly funded health care and five regional health authorities . 2 and the northern town of Churchill (16.7 per km2) = 53\u201373). Among the women who underwent surgery, the majority were under age 70 (69.8%) . In bothn = 3658) underwent surgical resection. Breast-conserving surgery was the most common procedure (66.7%) followed by mastectomy without immediate reconstruction (22.8%) and mastectomy with immediate reconstruction (10.5%). The youngest age group (20\u201339) underwent the highest percentage of mastectomy with immediate reconstruction . This percentage decreased with increasing age. Women in the lowest income quintiles had a lower percentage of mastectomy with immediate reconstruction compared to women in the highest income quintile . Surgical treatment patterns in Manitoba are described in Procedures differed by RHA of residence at diagnosis . MastectThe quality indicators measured are summarized in Fifty percent of women in Manitoba received surgery within 30 days of the first surgical consult. This indicator ranged from 33.3% (95% CI: 20.8 to 45.9) to 60.2% (95% CI: 54.3 to 66.0) depending on the RHA of residence. Among women who underwent breast-conserving surgery, 18.5% underwent a re-excision. Among women who underwent treatment in the urban RHA, 17.5% (95% CI: 15.9 to 19.1) underwent re-excision and this ranged from 23.0% (95% CI: 17.7 to 28.2) to 46.8% (95% CI: 29.6 to 64.2) in rural RHAs. The percentage of women who underwent re-excision after breast-conserving surgery also increased with stage from 15.5% (95% CI: 13.6 to 17.4) for women diagnosed with stage I breast cancer to 32.7% (95% CI: 25.7 to 39.8) for women diagnosed with stage III cancer. The post-operative outcome measures are summarized in We found that surgical treatment patterns, quality of care, and post-operative outcomes for women diagnosed with invasive breast cancer from 2010 to 2014 in Manitoba varied by age, income quintile, regional health authority, and stage. The differences that are the most clinically significant are disparities in access to immediate reconstruction and variations in ALND for node-negative disease. With a high five-year survival rate of 88% , survivo2 = 4.29, p > 0.05 RHAs. Due to the remote nature of the northern RHA, women most often travel to the urban RHA for treatment. Since patients have to travel to the only facility offering immediate reconstruction for their primary treatment, they are more likely to also opt-in to receive immediate reconstruction. In contrast to this, rural RHA 1 is the only other region (besides urban RHA) to offer surgery, systemic, and radiation therapy locally to their patients. As a result, women living in this region could potentially be choosing non-reconstructive surgery in their home center, where they can also receive the remainder of their care. It may also be possible that providers are more reticent to refer patients to another site, for a variety of reasons. Thus, patient and provider preferences may play a role in the variation shown in the data. However, as per the pan-Canadian standards for breast cancer surgery . all patp > 0.05 . In orde2 = 9.56, p > 0.05 is the standard of care in breast cancer patients who are clinically node-negative . The latStrengths of this study include the use of population-based data which permitted geographic comparisons, limited missing data, the use of administrative databases that have been evaluated for completeness, reliability, and validity, and the development of indicators based on a comprehensive review of the literature. However, several limitations should be noted. Income is an area-level measure that was used as a proxy for individual-level income. This may result in some misclassification of an individual\u2019s actual income. However, several studies have shown a substantial correlation between area-level and self-reported individual-level income ,39. PostIn conclusion, we have identified variations in practice patterns, quality of care, and post-operative outcomes for breast cancer surgery in Manitoba. Further research is needed to determine the reasons for the identified variations. Quality improvement initiatives, such as further training and audit and feedback reports, can be implemented to reduce variation and improve the quality of care and are being actively pursued by team members."} +{"text": "High lamb mortality rates following birth reduce on-farm profitability and contribute to perceived lower animal welfare standards of the sheep industry. The aim of this study was to understand producer knowledge of lamb mortality rates, causes of lamb mortality, and to investigate practices and perceptions of producers that may contribute to lamb deaths. Approximately 50% of producers estimated less than 10% lamb mortality between birth and marking, compared to published data in Australia reporting around 20\u201325% mortality rate. Clostridial vaccination of lambs was undertaken by 96% of producers; however, 17% of Merino and 23% of crossbred lamb producers indicated only one vaccination was administered, instead of the recommended initial vaccination plus booster. This lower estimated mortality rate and misuse of vaccination may lead to producers underestimating the perceived benefits of management strategies, as the number of lambs lost is of less concern. It is important producers are aware of the actual on-farm lamb losses to allow accurate determination of the benefits of management strategies, such as pre-lambing supplementation and vaccination.High lamb mortality rates reduce profitability and reduce the perceived animal welfare standards of the industry. This study aimed to understand producer knowledge of lamb mortality rates and causes of lamb mortality, and to investigate various practices and perceptions of producers that may contribute to lamb deaths. Postal and online surveys gathered data on Australian sheep producer\u2019s knowledge and practices around lambing and management practices. Based on results, approximately 50% of producers estimated less than 10% mortality of lambs between birth and marking, compared to published data estimates of 20\u201325% mortality. Pre-lambing vaccination of ewes was not undertaken by 10\u201320% of producers. Ninety-six percent of producers vaccinated lambs; however, 17% of Merino and 23% of crossbred lamb producers only gave a single vaccination instead of the recommended initial vaccine and booster. The lower estimated mortality impacts producer\u2019s perceived benefits of management strategies being undertaken. Research undertaken needs to be more effectively distributed to producers via extension services to ensure producers understand the causes of mortality. Important messages to convey to producers include the limited impact of predation in most cases and the total costs of lamb mortality on-farm. Mortality rates of lambs from birth to weaning continue to be a major source of lost production reducing profitability in sheep production systems . AverageAs more than 10 million lambs die before weaning in Australia , the cauPre-lambing supplementation of ewes with cereal grains, such as maize has increased colostrum production , which wAs animal welfare issues continue to be of great concern in the industry, and there are known practices that improve survival, it is important to understand producer knowledge and uptake of these practices. Published data are not available on the extent to which NSW producers are using existing options to reduce the mortality rates on-farm, and if farmers are aware of the number of lambs lost from birth to marking. Therefore, the objectives of this study were to understand producer perceptions on lamb mortality and the various practices producers implement to reduce post-natal lamb mortality rates on-farm.A 30-question survey on management practices of ewes and lambs and mortality around lambing was distributed to sheep producers across the state of NSW between May and October 2019. Initially, a pilot survey was distributed to three producers, with their feedback used to revise the survey prior to wider circulation. These responses were not included in the final dataset as the questions were revised. The survey was made available online via SurveyMonkey, and paper copies were offered to producers at a producer meeting. As a result of the online distribution method the percentage of respondents is unknown. To assist with distribution a variety of organizations/businesses within the sheep industry circulated the online link to members or readers. The sample size required was estimated using the Epitools calculator (epitools.ausvet.com.au), to estimate a simple proportion assuming an estimated 40\u201350% proportion of producers conducting a specific practice, 10% desired precision of the estimate, a 95% confidence level and infinite population (>1000). According to these assumptions, the required sample size was just under 100 (93 to 97).To participate in the survey producers must have been either farm owners or managers, had ewes lambing on the property in 2019 and had more than 50 sheep on the property. The survey was kept short to maximize the number of respondents. Survey questions focused on practices and perceptions of sheep producers around scanning, supplementation at lambing, and vaccination practices and producers identified risk factors associated with lamb mortality. Twenty-three close-ended questions and seven open-ended questions were asked. Close-ended questions were used to identify postcode, age, years farming, generations farming, causes of lamb mortality, and reasoning for supplementary feeding. Close-ended questions were also asked to identify gender, farming system, number of ewe breeds, lambing time, vaccination, scanning, marking percentages, when supplementary feed was provided, amount of supplement, and reasoning for not providing a cost-effective supplement. For further details, the survey is available in the Marking of lambs in Australian flocks is generally undertaken at 2\u20138 weeks of age, following the end of the lambing period. At marking, husbandry procedures likely to be undertaken include tail docking, ear tagging, ear marking, vaccination, and castration of male lambs. Weaning in Australia is recommended around 14 weeks following the start of the lambing period (lambs aged 8\u201314 weeks at weaning) . At weanp-value < 0.05.Responses were entered into Microsoft Excel and expoA total of 178 producers participated in the survey, although 33 responses were unable to be used due to producers either not being located in NSW, duplicate response, having less than 50 sheep, or only answering on population demographics. Usable survey respondents included 145 NSW-based sheep producers. Of these producers, 23% were sheep-only producers, 24% produced sheep and cattle, 25% were sheep, cattle, and cropping farmers, while 28% were sheep and cropping farmers. Producers varied in age from 18 to 78 years with a median of 44 years (Interquartile Range (IQR) 31\u201355 years). These producers had been farming for between 1 and 65 years with a median of 25 years (IQR 10\u201337 years). Participating producers were from 1st to 7th generation farmers, with a median of 4 generations. The location of producers completing the survey is shown in n = 107) of producers, with median ewe numbers of 1250, ranging from 75 to 20,000. Meat breed ewes were owned by 14% (n = 21) of participating producers with a median mob size of 270 ranging from 36 to 3000 breeding ewes. Purebred meat breeds included Australian Whites, Border Leicester, Dohne, Dorper, Poll Dorset, South African Meat Merino, Suffolk, White Suffolk, and Wiltipoll. Crossbred ewes were owned by 35% (n = 51) of participating producers with a median mob size of 850 ranging from 20 to 10,000 breeding ewes. Lamb breed was also identified with 65% (n = 89) of producers breeding purebred Merino lambs and 72% (n = 97) breeding purebred meat or crossbred lambs.Producers participating identified all ewe breeds on-farm with some producers having several breeds of ewe. Purebred Merino ewes were owned by 75% (n = 78) of Merino ewe owners, 71% (n = 14) of purebred meat ewe owners and 76% (n = 38) of crossbred ewe owners. The distribution and type of scanning practice identified by those producers scanning ewes are identified in In Australia, there are two main lambing periods, autumn lambing from February to May and winter/spring lambing from June to September, with some producers using a continuous breeding cycle where rams remain with ewes year-round. Few producers use the three-lambings-every-two-years management practice, usually in meat operations to maximize ewe production. Lambing times indicated by producers are summarized in n = 84) vaccinated Merino ewes, 90% (n = 19) vaccinated meat breed ewes and 80% (n = 41) vaccinated crossbred ewes. The types of vaccinations administered to ewes are detailed in Vaccination of ewes pre-lambing was reported by most producers. Among participating producers, 79% (n = 88) of producers vaccinated to increase immunity transfer to lambs, while 74% (n = 82) vaccinated to increase lamb survival rates. Fifty-five percent (n = 61) of producers chose to vaccinate because they had always vaccinated. Producers who vaccinated also sought advice about vaccination from veterinarians 13% (n = 14), animal nutritionists 10% (n = 11), family members 8% (n = 9) and rural stores 8% (n = 9). Fewer producers (n =5) chose to vaccinate ewes due to education course participation, understanding technical data identifying benefits, keeping the ewe healthy, increasing ewe survival, and participating in trial protocols.Producers were also asked about the reasons they vaccinate ewes. Seventy-nine percent (n = 17), cost , and the thought that the vaccination was ineffective . Other reasons identified (n = 3 producers) included having never vaccinated, never previously had issues with disease and the belief there is a lack of research around vaccine effectiveness.Among producers who chose not to vaccinate, reasoning included time constraints ; crossbred n = 72 (77%)), with some producers vaccinating at marking only (Merino n = 12 (15%); crossbred n = 21 (23%)) or at weaning only (Merino n = 1 (2%)). Producers who did not vaccinate did so as they either identified as organic farmers, thought vaccination was not cost-effective, too costly, time constraints, or did not identify a reason.Vaccination of lambs was undertaken by most producers (96%) with four Merino lamb and four crossbred lamb producers not vaccinating. n = 59) vaccinated to increase immunity levels, 65% (n = 58) to increase lamb survival and 47% (n = 42) vaccinated because they have always vaccinated. Producers who vaccinated also sought guidance from veterinarians 12% (n = 11), rural stores 7% (n = 6), animal nutritionists 7% (n = 6), and family members 3% (n = 3). Additional explanations identified by three producers for vaccination included for carcass characteristics, previous pulpy kidney issues, and adherence to trial protocols.Among producers vaccinating Merino lambs, 69% (n = 67) vaccinated to increase immunity levels, 62% (n = 60) to increase lamb survival, and 62% (n = 60) vaccinated because they have always vaccinated. Producers who vaccinated crossbred lambs also sought advice from veterinarians 13% (n = 13), rural stores 10% (n = 10), animal nutritionists 6% (n = 7) and from family members 4% (n = 4). A single producer indicated previously having Ovine Johne\u2019s Disease as the reason for vaccination.Among the respondents vaccinating crossbred lambs, 69% using dead lambs observed, 48% (n = 61) using scanning to marking figures, and 22% (n = 28) using their overall general impression. Among producers, 33% (n = 42) identified to use more than one method to estimate lamb mortality between birth and marking. Producers also estimated birth to marking losses by live lamb counts at shearing or weighing lambs at birth. Producers also indicated how losses between marking and weaning were estimated, with 68% (n = 88) of respondents using marking to weaning rates, 42% (n = 55) used observed dead lambs, and 15% (n = 19) using their general impression. Twenty-two percent (n = 29) of producers identified to use more than one method to estimate lamb mortality rates from marking to weaning.Forty-nine percent of producers estimated mortality of lambs between birth and marking to be 9% or less, as shown in p = 0.049), and energy supplementation during mid-pregnancy (p = 0.021). Farming system affected estimated mortality rate with sheep-only producers estimating lower marking to weaning mortality than sheep and cropping producers = 6.135, p = 0.013). The odds ratio of producers who supplement ewes during mid-pregnancy with energy and protein of estimating lower marking to weaning mortality was 0.424 times that of producers who do not supplement with energy and protein mid-pregnancy (\u03c72 (1) = 5.207, p = 0.022). All other farm practices had no significant association with marking to weaning rates.Through ordinal logistic regression, no significant associations among farm practices or characteristics and birth to marking rates were found. Marking to weaning rates were significantly related to the farm system (n = 125). Producers also advised on when these energy and protein supplements were given to reproducing ewes supplementing barley, 37% (n = 45) supplementing oats and 37% (n = 45) supplementing cereal hay. Other less common supplements used by less than 30% of producers included lupins, wheat, Lucerne hay, pre-purchased pellets, and corn. The supplementation amount given per day varied, with 16% (n = 18) of producers supplementing less than 200g, 35% (n = 40) supplementing 200\u2013399 g, 22% and (n = 25) supplementing 400\u2013599 g. Less common supplementation amounts by producers included those supplementing more than 600 g.Producers who gave energy and protein supplements identified the supplement provided, with 63% (n = 113) of respondents. Supplementation of minerals around lambing was provided by 55% (n = 72) of producers every year. Supplementation was also provided by less than 15% of producers when ewe body condition score was below target, on certain pasture types, and in poor seasons only. Sixty-two of the 72 producers who supplemented every year identified their reasoning with, 27% (n = 17) doing so due to poor pasture quality or deficiencies in pasture, 21% (n = 13) for ewe health and 12% (n = 8) to provide calcium for lambing ewes. Other less common practices by fewer producers (<10%) for supplementing every year included always offering minerals year-round, providing essential minerals in diet, reducing incidence of metabolic disorders, increasing lamb survival, and milking ability of ewes.Mineral supplementation was used by 86% (n = 69) using pre-purchased licks or blocks, 60% (n = 68) supplementing salt, and 58% (n = 66) supplementing lime. Other less common supplements used by producers included magnesium, copper sulphate, and selenium. The most common times for producers to supplement ewes was a month before lambing, with 77% of producers (n = 87) and during lambing by 66% of producers. Less common times for supplementation included two weeks prior to lambing, after lambing, and during mid-pregnancy.Supplementation type was identified by producers, with 61% (n = 26) noting that nothing would prevent them from using the supplement. The main reasons producers would not use the supplement were identified by 40% (n = 42) of producers to be due to time constraints, 31% (n = 33) as too wet (paddocks), and 26% (n = 28) due to disturbing ewes. Other less common reasons identified by producers for not using the supplement included costs, not bothered to provide a supplement, and not listening to advice.Producers were asked about the reasons which would prevent them from using a cost-effective supplement to increase lamb survival, with 25% (This survey investigated the practices and perceptions of NSW sheep producers on lamb mortality and supplementation practices around lambing. In recent years, significant research has been undertaken in order to improve lamb mortality rates via supplementation of ewes with various feedstuffs, as perinatal lamb mortality is known to be a major cause of reproductive wastage in sheep breeding enterprises . PreviouMortality rates on-farm may be largely underestimated. Nearly half of producers surveyed estimated less than 10% mortality of lambs between birth and marking. Of the producers surveyed, 73% estimated mortality between marking and weaning to be less than 5%, in agreement with previous experimental research that most lamb losses occur within days of birth . AlthougFrom the data by Fowler , 16.5% oUnderstanding of the causes of mortality helps to direct producers on improvements to reduce mortality. Causes of mortality can vary due to breed type with somPredation deaths were estimated by producers to be 18% for merinos, 19% for crossbred, and 21% for meat breeds, which are considerably higher than published data at 7\u20138% ,30,34. RInfection deaths were estimated by producers to cause 5\u20136% of all lamb deaths, similar to previous reports of 1\u20137.6% lamb mortality associated with infection in Australia ,36. AlthA limitation of the survey design resulted was not knowing whether producers are undertaking practices such as post-mortem examinations to determine cause of lamb mortality. This would have been beneficial to understand in greater detail how producers are determining mortality. It is a necessity that producers are undertaking accurate post-mortem exams on dead lambs to determine the cause of lamb mortality. If producers are not undertaking post-mortem exams their estimations on the cause of lamb mortality may be inaccurate which may affect strategies undertaken to reduce mortalities.Clostridial vaccination of ewes and lambs is important as these diseases are largely not treatable, with vaccines aiding in their control . ClostriErysipelas vaccine controls bacterial arthritis in lambs, and the scabby mouth vaccination is used to control the viral infection causing pustules on the mouth which is most commonly seen in lambs and may reduce production. Vaccination rates for Erysipelas and scabby mouth are low with between 14\u201323 % of producers using these vaccines indicating there may be large numbers of flocks with lost production associated with scabby mouth and Erysipelas. Therefore, further extension activities are required to give producers knowledge of cost-effective and appropriate vaccines, vaccination timelines, and to ensure complete vaccination of lambs.The Ovine Johne\u2019s vaccination was the second most common vaccination administered to lambs by 48% of Merino lamb producers and 17% of crossbred lamb producers. Ovine Johne\u2019s Disease is a bacterial infection affecting sheep causing wasting, leading to reproductive wastage and death. With less than 50% of surveyed producers vaccinating, this disease may be having a greater impact on production in some flocks where vaccines are not administered. The Management choices throughout pregnancy and lactation can affect the mortality rates of lambs, allowing producers to make decisions to improve the survival of lambs. Supplementation of energy and protein to ewes during pregnancy and lactation is a significant factor that can have major implications on marking rates. Supplementation of ewes has been widely studied over recent decades. Undernutrition can have major impacts on the growth of the lamb and its birth weight. In the first 90 days of gestation nutrition affects placental growth allowing lambs to grow to their potential in the last 60 days of gestation . ProduceMinerals such as calcium and magnesium are required for fetal and neonatal development and normal physiological functioning of adult sheep. As a result, the demands of the ewe for calcium and magnesium during pregnancy and lactation are high. Eighty-six percent of producers surveyed supplemented minerals around pregnancy and/or lactation with calcium and magnesium being the major supplements provided mainly in the form of loose licks and blocks. Calcium and magnesium supplementation has been shown to improve the energy balance of ewes and improve lamb immune responses . TherefoErysipelas vaccination may reduce lamb mortalities. Therefore, extension services need to be further developed to enable producers to increase on-farm productivity and to reduce lamb mortality.This survey has identified the current practices and perceptions of sheep producers in NSW around lamb mortalities and management practices during pregnancy and lactation. It was identified that producers have estimated lower mortality rates of lambs between marking and weaning compared to published literature. This may have follow-on impacts, as if mortalities are not well understood by producers, economic losses associated with mortality are also unknown. Consequently, producers may not be able to determine the effectiveness of practices such as supplementation to increase lamb survival. Ensuring producers are aware of the recommended booster clostridial vaccination, pre-lambing ewe vaccinations, and the lamb"} +{"text": "Practice patterns and bleeding complications of percutaneous native kidney biopsy (PNKB) have not recently been investigated and the Japanese Society of Nephrology performed a nationwide questionnaire survey in 2018.The survey consisted of nine sections about PNKB: (1) general indications; (2) indications for high-risk patients; (3) informed consent; (4) pre-biopsy evaluation; (5) procedures; (6) sedation; (7) post-biopsy hemostasis, bed rest, and examinations; (8) bleeding complications; and (9) specimen processing. A supplementary survey examined bleeding requiring transcatheter arterial embolization (TAE).Overall, 220 directors of facilities completed the survey. Indications, procedures, and monitoring protocols varied across facilities. Median lengths of hospital stay were 5 days in NFs and 6 days in PFs. Gauge 14, 16, 18 needles were used in 5%, 56%, 33% in NFs and 0%, 63%, 64% in PFs. Mean limits of needle passes were 5 in NFs and 4 in PFs. The bed rest period was 16\u201324 h in 60% of NFs and 65% of PFs. Based on 17,342 PNKBs, incidence rates of macroscopic hematuria, erythrocyte transfusion, and TAE were 3.1% , 0.7% , and 0.2% , respectively. Forty-six percent of facilities processed specimens all for light microscopy, immunofluorescence, and electron microscopy, and 21% processed for light microscopy only. Timing of bleeding requiring TAE varied among PNKB cases.Wide variations in practice patterns of PNKB existed among facilities, while PNKBs were performed as safely as previously reported.The online version of this article (10.1007/s10157-020-01869-w) contains supplementary material, which is available to authorized users. Kidney biopsy (KB) is an essential tool for the diagnosis and treatment of patients with numerous kidney diseases. However, its invasive nature results in bleeding complications, leading to increased patient morbidity, longer hospital stay, and higher medical costs. Advancements have been made in biopsy techniques to improve diagnostic yield and to minimize complications, but there remain no global guidelines available to the nephrology community on indications and procedures of KB to improve diagnosis and prognosis.The Japanese Society of Nephrology (JSN) originally published the \u201cGuidebook of the renal biopsy\u201d in 2004 to develop best strategies for KB and to minimize the risk of complications . Over 10This study aimed to obtain information on the current clinical practice patterns and bleeding complications of PNKB in Japan. The survey could be helpful in providing a reliable consensus and developing better guidelines for PNKB.The JSN designed a nationwide questionnaire survey of medical directors of nephrology and pediatric nephrology in Japanese hospitals in 2017. The questionnaire was developed through an iterative review process with the Committee members of the Practical Guide for Kidney Biopsy 2019 of the JSN, to clarify clinical practice patterns and bleeding complications of KB in Japan.The survey consisted of 70 questions about PNKB, with the exception of transplanted graft biopsy, in nine sections: (1) general indications; (2) indications for high-risk patients; (3) informed consent; (4) pre-biopsy evaluation; (5) biopsy procedures; (6) sedation; (7) post-biopsy hemostasis, bed rest, and examinations; (8) incidence rate of bleeding complications; and (9) specimen processing. The complete survey is described in the supplementary material (Supplement 1).The JSN distributed the anonymous online survey to nephology teaching hospitals designated by the JSN in February 2018. Respondents were limited to only one director of each facility. Pediatric nephrologists were not asked questions regarding kidney size, since kidney sizes among children vary by age. Conversely, only pediatric nephrologists were asked questions on sedation, since sedation is not routinely performed during PNKB in adult patients. The incidence rates of bleeding complications were investigated over a 3-year period (from January 2015 to December 2017).The JSN also conducted an anonymous online survey in September 2018 on serious bleeding cases with transcatheter arterial embolization (TAE) after PNKB, which had emerged during the original survey in February 2018. The supplementary questionnaire survey was designed separately from the original to clarify clinical background of hemorrhage events requiring TAE over a period of 5 years (from January 2013 to December 2017). The complete survey is described in the Supplement 2.These surveys were approved by the ethics committee of the JSN . Multiple approaches to improving participation were implemented, including outreach to the directors through email and verbal contact, reminders through the JSN website, and extending the participation deadline of the surveys.Standard descriptive statistics were used to describe the practice patterns and incidence rates of complications of PNKB. Percentages, medians (interquartile ranges [IQRs]), and means (standard deviations [SDs]) were reported as appropriate. Data regarding nephrology facilities (NFs) for adult patients and pediatric nephrology facilities (PFs) for child and adolescent patients were analyzed separately, except for the section on specimen processing. In the analyses of incidence rates of bleeding complications, facilities with missing data on minor or major complications were excluded. Only facilities having complete data for both minor and major complications over the 3 years of the survey period were included in the analyses to adequately compare incidence rates of the complications. All statistical analyses were performed using Stata version 14.2 .Overall, 224 of 667 directors of Japanese nephrology teaching hospitals responded and of these 220 directors completed the survey (33% response rate). The annual number of PNKBs performed varied depending on the facilities (range 0\u2013193) and the number of PNKBs in all facilities totaled 24,238 for the 3-year period (average: 8079 per year).Twenty-six percent and 60% of respondents in NFs and PFs, respectively, did not regard isolated hematuria (IH) as an indication for PNKB. Conversely, patients with IH with macroscopic/gross hematuria, suspected of having IgA nephropathy (IgAN) or hereditary nephritis were considered a specific indication . Sixty-two percent of NFs, but only 4% of PFs, recommended a biopsy with IH in the presence of dysmorphic urinary red blood cells of glomerular origin.Seventy percent of respondents from NFs and 50% in PFs did not regard isolated proteinuria (IP) less than 0.5 g/day as an indication for PNKB, while IP of 0.5 g/day or more in chronic kidney disease (CKD) stage G1, G2, and G3 was considered an indication , such as antineutrophil cytoplasmic antibody (ANCA)-associated nephritis and anti-glomerular basement membrane (GBM) nephritis, and acute renal failure (ARF), including drug-induced nephropathy, were recommended or performed in most facilities . However, the indication for PNKB for RPGN or ARF varied according to kidney function. The proportion of positive responses for RPGN or ARF with estimated glomerular filtration rate (eGFR) less than 60, 30, and 15 mL/min/1.73 mN-acetyl-\u03b2-d glucosaminidase.High proportions of all respondents gave positive answers for PNKB indications involving urinary abnormalities with systemic diseases, such as systemic lupus erythematosus and vasculitis . Interestingly, SLE and VA with no urinary abnormalities also presented indications for PNKB in a number of facilities . Other diseases or conditions not associated with urinary abnormalities were also indications for PNKB, including enlarged kidney or kidney dysfunction of unknown cause; IgG4-related diseases; hypocomplementemia; hereditary diseases, such as Fabry disease; and positive tubular injury markers, such as \u03b22 microglobulin (MG), \u03b11 MG, and Diabetes mellitus (DM) with urinary abnormalities was an indication for PNKB in 88% of respondents in NFs and 11% in PFs. Surprisingly, only 2% of NFs, but 38% of PFs had no experience with PNKB in cases with diabetic kidney disease (DKD). Indications for PNKB of DKD varied according to CKD G stage and proteinuria .A number of respondents in both NFs and PFs regarded hereditary diseases as an indication for PNKB or experienced a PNKB of hereditary diseases, such as Alport syndrome , mitochondrial disease (22%), nephronophthisis (27%), and autosomal dominant tubulointerstitial kidney disease (12%).Table PNKB was commonly performed in inpatient settings and only one NF performed PNKB in the outpatient setting. Informed consent (IC) was obtained for PNKB in an outpatient consultation room , at bedside after hospitalization (55%), or in a patient interview room (31%). IC for blood transfusion was routinely obtained in advance of PNKB only in 26% of NFs and 35% of PFs. Clinical paths were utilized for hospitalization of PNKB in 88% of NFs and 77% of PFs. The lengths of hospital stay were 4\u20136 days in 79% of NFs and 6 days or more in 71% of PFs. PNKB was performed the next day after admission in 77% of all facilities.Pre-biopsy evaluations included assessments of bleeding diathesis, kidney function, kidney size, blood pressure, and anemia. The cutoff values of contraindications for PNKB are described in Table KB was usually performed percutaneously under ultrasonic guidance with local anesthesia in all facilities, but open biopsy (17% of NFs and 56% of PFs) and laparoscopic biopsy (5% of NFs and 0% of PFs) were performed for high-risk patients. Automatic biopsy needles (biopsy gun) were utilized for KB in 98% of NFs and 96% of PFs, while Tru-Cut needles and Silverman needles were used in only a few facilities . Gauge 14, 16, and 18 needles were usually used for KB in 5%, 56%, and 33% of NFs and in 0%, 63%, and 37% of PFs, respectively. The maximum number of sampled specimens for KB varied across facilities. Two specimens were sampled in 17% of NFs and 56% of PFs and three specimens in 38% of NFs and 23% of PFs. There was also variation in the limit of needle passes for sampling specimens. Three, 4, and 5 passes at a maximum were allowed in 11%, 15%, and 26% of NFs, and 17%, 25%, and 17% of PFs, respectively. Thirty-three percent of NFs and 27% of PFs had no limit of needle passes for sampling specimens.Maximal barrier precautions for KB included the use of a cap , a mask , sterile body gown (68% of PFs and 54% of PFs), sterile gloves , and sterile drape (67% of NFs and 60% of PFs). The proportion of facilities using all equipment and instruments described above was 38% of NFs and 35% of PFs.Antibiotics and atropine were regularly used before PNKB in 62% and 21% of NFs, and 58% and 15% of PFs. An indwelling urethral catheter was routinely used in 56% of NFs and 15% of PFs.Sixty-five percent of NFs and 39% of PFs had a target for BP during the PNKB. The target varied among facilities, but the most common target for systolic BP was less than 160 mmHg in NFs (62%) and less than 130 or 140 mmHg in PFs (53%). The most common target for diastolic BP was less than 100 mmHg in both in NFs (49%) and PFs (62%). For adult patients with high BP during KB, antihypertensive agents were administered orally in 28%, sublingually in 4%, and intravenously in 50%, and were not used in 27% of NFs. For pediatric patients, antihypertensive drugs were administered orally in 12%, sublingually in 6%, intravenously in 25%, and were not used in 61% of NFs.Intravenous anesthesia (IVA) in a hospital ward was performed during the PNKB in 78% of PFs and the age of indication for IVA varied vastly across facilities. IVA was indicated for all pediatric cases, or patients aged 15 years or younger, in 42% of facilities. Hydroxyzine was used for induction in 49%. For intravenous anesthetics, midazolam, pentazocine, ketamine, and thiopental or thiamylal were administered in 59%, 56%, 49%, and 34% of PFs, respectively. A wide variation was also found in the age of indication for general anesthesia (GA) in the operating room setting during the PNKB. GA was indicated for patients younger than 3 years in 81% and was indicated for all pediatric cases, or patients aged 15 years or younger, in 12% of PFs. Open biopsy was indicated for patients aged less than 1 year in 86% of PFs.Manual compression on the biopsy site was performed soon after PNKB in 95% of NFs and 100% of PFs. The median manual compression periods were 10 (IQR 10\u201315) min in NFs and 15 (IQR 10\u201315) min in PFs. Sandbags were used for compression on the biopsy site in 62% of NFs and 63% of PFs. The median compression periods using sandbags were 4 (IQR 2\u20136) h in NFs and 6 (IQR 3\u201312) h in PFs. Abdominal taping or bandage was used over the biopsy sites in 78% of NFs and 85% of PFs. The median duration of abdominal taping or bandaging was 16 (IQR 6\u201320) h in NFs and 20 (IQR 14\u201324) h in PFs. It depended largely on facilities when discontinued anticoagulant or antiplatelet drugs before PNKB could be restarted after biopsy. The mean duration of drug discontinuation was 2 (IQR 1\u20137) days in NFs and 7 (IQR 2\u20137) days in PFs. Hemostatic agents were routinely used after PNKB in 66% of NFs and 60% of PFs. Carbazochrome sodium sulfonate hydrate and tranexamic acid were regularly used in 96% and 100% of NFs and in 83% and 63% of PFs, respectively.The prescribed period of strict bed rest in a supine position after PNKB varied among facilities. Strict bed rest for 4\u20138 h was prescribed in 44% of NFs and in 33% of PFs. Total bed rest for 16\u201324 h overall was prescribed in 60% of NFs and in 65% of PFs. The median period of subsequent exercise restriction was 14 (IQR 7\u201328) days in NFs and 14 (IQR 14\u201328) days in PFs.Blood tests were routinely performed for monitoring patients after the PNKB in 95% of NFs and in 84% of PFs. The examinations were conducted the day after the PNKB in 68% of NFs and 51% of PFs. Ultrasound examinations were routinely performed to confirm hemostasis after KB in 84% of NFs and 82% of PFs and were performed immediately after the KB in 70% of the NFs and in 60% of the PFs. When severe bleeding occurred after the PNKB, surgical procedures could be adopted in their own hospitals in 84% of NFs and 80% of PFs. Transcatheter arterial embolization could also be adopted in their own hospitals in 66% of NFs and 39% of PFs.One hundred and eighty-one of the 220 facilities and 17,342 of 24,238 PNKBs were included in the analyses of incidence rates of bleeding complications. Tables Biopsy specimens were fixed and processed in each facility\u2019s laboratory for light microscopy (LM), immunofluorescence (IF), and electron microscopy (EM), in 98%, 78%, and 46% of facilities. Forty-six percent fixed and processed specimens comprehensively for all LM, IF, and EM, and 21% only for LM.Assistant operators (39%) or biopsy operators (31%) mainly divided biopsy specimens and put them in the fixatives. The specimens were routinely assessed with a microscope before dividing in 60% of facilities (34% with a dissecting microscope and 26% with a light microscope), but were not assessed in 31%. Biopsy specimens were kept from drying before fixation in 84% of facilities. The specimens were wrapped with saline-soaked gauze in 52% and placed directly in normal saline in 24% of the facilities. Each facility determined how biopsy specimens were to be divided for LM, IF, and EM. Either end of the specimen core was taken for IF and EM, with the remainder divided for LM in 40% of facilities, and both ends from all cores were taken for IF and EM, with the remainder divided for LM in 21%. Samples were randomly taken from all cores for IF, EM, and LM in 39% of facilities.The fixative used was 10% formalin in 61% of facilities, while neutral buffered formalin was used in 22%. Formalin alone was used as a fixative in 68% of the facilities, while both formalin and another fixative, such as picric acid, were used in 16%. Liquid nitrogen, dry ice, dry ice with acetone, hexane bottle in dry ice with acetone, and a deep freezer were used for freezing specimens for processing in 24%, 23%, 17%, 12%, and 9% of biopsy samples, respectively.In the supplementary questionnaire survey, 40 patients from 29 NFs were identified who underwent TAEs after PNKB over the previous 5 years. No patients requiring TAEs were reported from PFs.2; hemoglobin, 11.0 (9.6\u201313.2) g/dL; platelet count, 21.5 (15.5\u201329.9)\u2009\u00d7\u2009104/\u03bcL; PT-INR, 1.0 (1.0\u20131.2); APTT, 29 (27\u201333) s; and BT, 2.5 (2.0\u20134.0) min. Mean systolic and diastolic BP at the PNKB were 137 (IQR 119\u2013158) and 80 (IQR 72\u201390) mmHg, respectively. Median kidney size (major axis) was 100 (IQR 96\u2013109) mm.The median age was 56 (IQR 39\u201369) years and 53% of the patients were male. The median BMI was 22 (IQR 19\u201325) and 89% of the patients carried out normal activities of daily living (ADL) without being bedridden or confined to a wheelchair. Approximately 20% had DM and 63% had no high-risk background, such as unilateral/hypoplastic/atrophic kidney, cystic kidney diseases, malignant hypertension, or pregnancy. The PNKBs were all performed in inpatient settings, where anticoagulant and antiplatelet agents were used at biopsy in 7.5% and 5.0% of the cases, respectively. More common among the patients with TAE were chronic glomerulonephritis (31%) and RPGN (28%) in the clinical diagnoses and IgAN (18%) and crescentic glomerulonephritis (15%) in the histological diagnosis. Laboratory values before the PNKB (median [IQR]) were as follows: eGFR, 35 (10\u201370) mL/min/1.73 mTable This nationwide survey describes the clinical practice patterns and bleeding complications of PNKB in Japanese nephrology facilities. This is the first comprehensive report showing the wide variations in clinical practice across facilities and the low rate of bleeding complications observed in Japan when PNKBs are performed using current techniques and devices.First, the survey extensively investigated indications for PNKB. Previous studies did not recommend performing a biopsy for patients with IH, since many patients with IH might manifest no abnormality or slight changes in histology, requiring no specific therapy with excellent prognosis , 5. The RPGN, ARF, and systematic diseases such as SLE and VA presented good indications for PNKB. Interestingly, systemic diseases without urinary abnormalities also presented an indication for PNKB for many nephrologists, since active pathological lesions are often found in patients with systemic diseases without urinary abnormalities (known as \u201csilent lupus nephritis\u201d) , 9.Policies on performing PNKB for patients with DM and elderly patients have been changing. DM is now the leading cause of end-stage kidney disease in the world, and the previously established opinion among nephrologists was that KB for DKD would provide little diagnostic, prognostic, or therapeutic value . HoweverHigh-risk patients may be contraindicated for PNKB. Potential contraindications include unilateral kidney, bilateral atrophic or hypoplastic kidney, horseshoe kidney, multiple bilateral cysts, hydronephrosis, malignant hypertension, uncorrectable bleeding diathesis, pregnancy, and severe obesity. In the previous Japanese Guidebook , most ofThe survey found common practices before performing PNKB included assessment of bleeding diathesis, kidney function, kidney size, blood pressure, and anemia, but cutoff values for these parameters contraindicating PNKB and transfusion policies varied enormously across facilities. A previous study reported that bleeding complications were associated with APTT, PT-INR, BT, and platelet count . AdditioPNKB was most commonly performed by nephrologists in inpatient settings, and clinical paths were utilized for hospitalization in many Japanese facilities. IC for PNKB was obtained in outpatient settings or after admission, while IC for blood transfusion was not routinely obtained in advance of biopsy in most facilities. The length of hospital stay was usually 4\u20136 days in NFs and 6 days or more in PFs. The duration of hospitalization was likely based on recommendations from the previous Japanese guidebook indicating that patients should be discharged 4\u20137 days after PNKB to allow better monitoring of bleeding complications after hemostasis . PreviouPNKB was most commonly performed with automatic biopsy needles under local anesthesia, while IVA or GA was often performed during pediatric PNKB. Gauge 16 needles were used in many facilities, but a wide variation was found among facilities in the maximum number of sampled specimens and needle passes. A previous systematic review suggested that the use of 14-gauge needles was associated with higher transfusion rates compared with 16- and 18-gauge needles, and that the number of passes did not affect the rate of complications . AdditioConcerning the prevention of infections, only a minority of facilities used all the equipment and instruments for maximal barrier precautions, while many facilities routinely administered antibiotics regularly for prevention of infections. Although infections during PNKB rarely occurred using sterile techniques, infectious complications have been described in some case series , and prePolicies on hemostasis, bed rest, and examination after PNKB varied enormously among facilities. Manual compression on the biopsy site was performed soon after the PNKB in almost all facilities, while it depended on the facilities whether sandbags and abdominal taping/bandage were used for compression. As manual compression and abdominal bandaging may increase the frequency of reflex syncope during PNKB , it may The present survey showed that the incidence rates of MH 3.1%), ET (0.7%), TAE (0.2%), and death attributed to biopsy (0.006%) were as low as those reported in a previous systematic review in 2013 and in a.1%, ET over a 3-year period and was sufficiently large to describe the current approach of the Japanese nephrology community towards PNKB. Despite being only descriptive analyses, the results of the survey are still impressive and informative. The reported practice patterns and estimates of complications provided helpful information in the decision-making process involved for PNKB procedures.Despite its strengths, the limitations of our survey should be recognized. First, the study was based on a cross-sectional descriptive design, and the reported practice patterns were mostly determined by personal experience and the confidence of the physician with the procedure and were not necessarily based on clinical evidence. It is underlined that the application of the results from this study to clinical practice for PNKB should be done carefully. Next, this was the online questionnaire survey of facility directors, and the response rate was 33% (220 of 667 facilities). The survey presented a lower response rate than the previous questionnaire surveys among nephrology directors (60\u201380%) , 41, 42,In conclusion, the present survey showed wide variations of clinical practice patterns of PNKB according to facilities, while PNKBs were performed as safely as previously reported in Japan. These findings may help provide a reliable consensus among nephrologists and develop better guidelines for PNKB.Supplementary file1 (DOCX 53 kb)Supplementary file2 (DOCX 27 kb)Below is the link to the electronic supplementary material."} +{"text": "To the Editor:Western Journal of Emergency Medicine.We are honored to have our systematic review of remdesivir for the treatment of COVID-19 published in the Grein et al analyzed open-label data from 61 patients who were treated with remdesivir between January\u2013March 2020. Patients were administered a loading dose of 200 milligrams (mg) on the first day followed by nine days of 100 mg infusions. Clinical improvement was based on a six-point scale: 1 = not hospitalized; 2 = hospitalized but not requiring supplemental oxygen; 3 = hospitalized and requiring supplemental oxygen; 4 = hospitalized and requiring nasal high-flow oxygen therapy, noninvasive mechanical ventilation or both; 5 = hospitalized requiring mechanical ventilation, extracorporeal membrane oxygen, or both. Most patients (68%) exhibited clinical improvement and 84% were discharged or showed a decrease of two points or more at follow-up. In total, 13% died and 60% exhibited adverse events, most commonly hepatic and renal dysfunction. Although these findings are encouraging, the small sample size, lack of a comparison group, case-by-case variation in supportive care, and missing data make it difficult to draw robust conclusions.The Lancet on April 29. This study analyzed treatment of 237 patients (158 given remdesivir and 79 given placebo). Although the remdesivir group showed a reduced time to clinical improvement (18 vs 23 days), this was statistically insignificant. Neither mortality (14% vs 13%) nor adverse events (66% vs 64%) were commonly associated with remdesivir. The most common complications included constipation, hypoalbuminemia, hypokalemia, and anemia. However, there are several limitations to these results. Firstly, patients in the remdesivir and placebo groups received interferon alfa (29% vs 38%), lopinavir-ritonavir (28% vs 29%), antibiotics (90% vs 94%), and corticosteroids (65% vs 68%) before and after enrollment. These additional drugs make it difficult to differentiate between the effects of remdesivir and other treatments. Moreover, the placebo group received a higher percentage of these drugs. Secondly, 36 patients discontinued treatment due to adverse events, reducing the sample size. Since the trial was terminated early on March 29, the statistical power was reduced from 80% to 58%. Though these findings do not support remdesivir to treat COVID-19, the methodological limitations, missing data, and early termination moderate the results.The first randomized, controlled clinical trial of remdesivir for treatment of COVID-19 was published in The ACTT is an ongoing randomized, double-blinded controlled trial of remdesivir that began enrolling on February 21."} +{"text": "Studying health and mortality among centenarian Veterans is critical to understanding the limit of the male human life span and Veterans\u2019 extraordinary model of successful aging. The majority of VA users are male, but little is known about social characteristics and health among male centenarians in general. We investigated the annual mortality rate of male centenarian Veterans seeking care from the VA and identified social characteristics and health conditions that influenced the risk of mortality. This longitudinal study used VA Electronic Health Record (EHR) data from 1997 \u2013 2012 (n=1858). Dates of death were obtained from the EHR, aggregated by the Corporate Data Warehouse from multiple sources. Independent variables included age, race, marital status, and periods of military service. Health conditions consisted of cancer, congestive heart failure (CHF), diabetes, chronic renal disease, chronic pulmonary disease, peripheral vascular disease, dementia, myocardial infarction, liver diseases. The mean age was 100.4 (range: 100-115), 76% were white and 49% married. The average annual mortality rate was 32 per 100 person-years. The annual mortality rate was stable and not affected by race, but did differ by marital status. Divorced or separated centenarians had a 21% higher rate of death than married centenarians . A diagnosis of dementia increased the mortality risk by 37% and CHF by 37% . Providers should consider prevalent health conditions, as well as marital status, in managing care of centenarian veterans."} +{"text": "Background: Prescription opioid use during pregnancy has been associated with poor outcomes for mothers and infants. Studies using administrative data have estimated that 14%\u201322% of women filled a prescription for opioids during pregnancy; however, data on self-reported prescription opioid use during pregnancy are limited.Methods: CDC analyzed 2019 data from the Pregnancy Risk Assessment Monitoring System (PRAMS) survey in 32 jurisdictions and maternal and infant health surveys in two additional jurisdictions not participating in PRAMS to estimate self-reported prescription opioid pain reliever (prescription opioid) use during pregnancy overall and by maternal characteristics among women with a recent live birth. This study describes source of prescription opioids, reasons for use, want or need to cut down or stop use, and receipt of health care provider counseling on how use during pregnancy can affect an infant.Results: An estimated 6.6% of respondents reported prescription opioid use during pregnancy. Among these women, 21.2% reported misuse , 27.1% indicated wanting or needing to cut down or stop using, and 68.1% received counseling from a provider on how prescription opioid use during pregnancy could affect an infant.Conclusions and Implications for Public Health Practice: Among respondents reporting opioid use during pregnancy, most indicated receiving prescription opioids from a health care provider and using for pain reasons; however, answers from one in five women indicated misuse. Improved screening for opioid misuse and treatment of opioid use disorder in pregnant patients might prevent adverse outcomes. Implementation of public health strategies can support delivery of evidence-based care for pregnant women.During 2017\u20132018, 42.5% of opioid-related overdose deaths among women in the United States involved a prescription opioid during pregnancy was indicated by selection of any of the following: hydrocodone, codeine, oxycodone, tramadol, hydromorphone or meperidine, oxymorphone, morphine, or fentanyl.Prevalence of prescription opioid use during pregnancy was estimated overall and by maternal characteristics. Maternal age, race/ethnicity, education, trimester of entry into prenatal care, health insurance at delivery, and number of previous live births were derived from birth certificate data. Self-reported cigarette use during the last 3 months of pregnancy and depression during pregnancy were obtained from the surveys. Among women reporting prescription opioid use during pregnancy, estimates were generated for source, reasons for use, want or need to cut down or stop use, and receipt of health care provider counseling on how use during pregnancy could affect an infant. Prevalence of receipt of health care provider counseling was estimated by maternal characteristics. In addition, the percentage of women who wanted or needed to cut down or stop using was estimated among those who reported misuse as defined in this study and those who did not. Chi-squared tests were used to assess the differential distribution of prescription opioid use during pregnancy and receipt of health care provider counseling by maternal characteristics, as well as the want or need to cut down or stop use by misuse classification. Weighted prevalence estimates and 95% confidence intervals (CIs) were calculated using SUDAAN .In 2019, among 21,488 respondents, 20,643 (96.1%) provided information regarding prescription opioid use during their most recent pregnancy. Among these women, 1,405 (6.6%) reported prescription opioid use during pregnancy . The preAmong women who used prescription opioids, 91.3% reported receiving the opioids from a health care provider, 8.9% from a source other than a health care provider , and 4.3% from other/undetermined sources . SpecifiAmong women who used prescription opioids, 88.8% reported using the opioids for pain reasons, 14.4% for reasons other than pain, and 4.9% for other/undetermined reasons. In particular, prescription opioids were used to relieve pain from an injury, condition, or surgery that occurred before (22.2%) or during (63.8%) pregnancy or during an unstated time frame (11.7%). Commonly reported reasons for use other than pain were to help sleep (7.9%) and relieve tension or stress (7.7%).Overall, 21.2% of women who used prescription opioids during pregnancy reported misuse; 4.0% reported both a non\u2013health care provider source and use for reasons other than pain. Among women who used prescription opioids during pregnancy, 27.1% indicated wanting or needing to cut down or stop using . Among wAmong women with prescription opioid use during pregnancy, 68.1% reported that a health care provider counseled them about the effect of use on an infant . The preIn this population-based sample of women with recent live births in 34 jurisdictions, one in 15 (6.6%) respondents self-reported using prescription opioid pain relievers during pregnancy. This observed prevalence of use during pregnancy in 2019 is lower than estimates of prescription opioid fills from administrative data in previous years women with prescription opioid use indicated wanting or needing to reduce or stop their use, potentially because of concerns about the effect of medication on their infant, possible opioid dependence, or opioid use disorder. Among women reporting prescription opioid use, nearly one in three (31.9%) reported not receiving provider counseling on the effects of prescription opioid use on an infant.Clinical guidance addresses opioid prescribing and tapering during pregnancy, the risks to the mother and infant, and screening and treatment for opioid dependence and opioid use disorder , 27.1% wanted or needed to cut down or stop using, and 31.9% reported not receiving provider counseling about how use could affect an infant.Obstetric providers should discuss risks and benefits of opioid therapy for chronic pain during pregnancy, screen all pregnant women for substance use, misuse, and use disorders, including those involving prescription opioids, and provide referral and treatment, as indicated."} +{"text": "People undergoing mass home- and community-based quarantine are vulnerable to mental health disorders during outbreaks of coronavirus disease (COVID-19), but few studies have evaluated the associated psychosocial factors.This study aimed to estimate the prevalence of anxiety and depressive symptoms and identify associated demographic and psychosocial factors in the general Chinese population during the COVID-19 pandemic quarantine period.Participants aged 18 years or above were recruited in a cross-sectional online survey using snowball sampling from February 26-29, 2020. The survey included questions on demographics, family relationships, chronic diseases, quarantine conditions, lifestyle, COVID-19 infection, and anxiety and depressive symptoms. Logistic regression analyses were conducted to identify factors associated with elevated anxiety or depressive symptoms.Out of 2331 participants, 762 (32.7%) experienced elevated anxiety or depressive symptoms. Nine risk factors associated with anxiety or depressive symptoms included younger age, reduced income, having cancer or other chronic diseases, having family members living with cancer, concerns related to COVID-19 infection for themselves or family members, living alone, having family conflicts, having <3 or >8 hours of sedentary time per day, and worsened sleep quality.The findings highlight an urgent need for psychological support for populations at high risk for elevated anxiety or depressive symptoms during the COVID-19 pandemic. Pandemics and other public health crises such as severe acute respiratory syndrome (SARS), Ebola, and the current coronavirus disease COVID-19) pandemic often result in elevated rates of mental health problems 9 pandemi. AnxietyAlthough several studies have reported on factors associated with mental health disorders during the COVID-19 pandemic, some factors particularly characteristic of the pandemic and corresponding quarantine strategy remain understudied. In the existing literature, factors such as demographic characteristics, lifestyle, and concerns about COVID-19 infection have been examined during the pandemic ,9,10. SpIn addition, previous studies have shown mixed findings about the effects of some factors such as age on anxiety or depressive symptoms during the COVID-19 pandemic. One study reported that individuals between 18 and 30 years or above 60 years had the highest rates of psychological distress during the COVID-19 outbreaks , while aSome populations such as people living with cancer or other chronic diseases may be at increased risk for developing mental health problems during a pandemic due to their tenuous physical health, barriers to accessing medical treatment, higher risks of COVID-19 infection, and higher probability of severe illness if infected -19. DuriTo fill these gaps in the literature, the current study aimed to estimate the prevalence of anxiety or depressive symptoms and identify associated demographic and psychosocial factors in the general Chinese population during the COVID-19 pandemic quarantine in China in February 2020. Specifically, we examined the effects of associated factors including demographics, family relationships, chronic disease status, quarantine conditions, lifestyle, and COVID-19 infection. Special attention was paid to characteristics particularly relevant to the COVID-19 pandemic quarantine such as household composition, family conflict, and chronic disease status.Participants aged 18 years or above were recruited through a snowball sampling process via WeChat from February 26-29, 2020 during the community- or home-based quarantine in China. WeChat is the most widely used social media platform in China with over 1 billion active users . We deveData on demographics , family relationships , chronic diseases , quarantine conditions , lifestyle , COVID-19 infection , and anxiety and depressive symptoms were collected.Anxiety and depressive symptoms were assessed by the 14-item Hospital Anxiety and Depression Scale (HADS) that comprises two 7-item subscales; participants with an Anxiety subscale (HADS-A) score \u22658 or a Depression subscale (HADS-D) score \u22658 were classified as having elevated anxiety or depressive symptoms . We chosThe sample size was calculated based on the estimated rate of anxiety or depressive symptoms in the general population. A pre\u2013COVID-19 epidemiological study reported the lifetime prevalence of anxiety and depressive symptoms in the Chinese population as 7.6% and 6.8%, respectively [P<.10 in univariate analysis were included in the multivariate logistic regression model and those with P<.05 were retained in the final model. R software version 3.5.1 was used for data analyses.Logistic regression models were employed to identify factors associated with elevated anxiety or depressive symptoms. All variables were categorized and described by frequencies and percentages. Univariate logistic regression models were used to analyze the distribution of anxiety or depressive symptoms among different categories for each variable and select risk factors for multivariate analysis. For example, to identify whether chronic disease status was a potential risk factor for anxiety or depressive symptoms, we compared the rate of anxiety or depressive symptoms among participants with chronic diseases to that of participants without. Variables with This study was approved by the institutional review board of the School of Public Health, Sun Yat-sen University, and all participants provided informed consent.Out of 2441 questionnaires collected, 2331 (95.5%) were deemed valid using a quality-control question, which stated that its purpose was to screen out invalid questionnaires and requested participants to check a specific option. Questionnaires that checked the correct option were considered valid. The mean age of participants was 34.4 (SD 11.1) years, 56.1% (n=1307) were female, 60.0% (n=1398) were married, 73.7% (n=1718) had a bachelor\u2019s degree or above, 11.5% (n=269) had a chronic disease, 41.6%(n=970) had family members with a chronic disease, 44.7% (n=1041) had been quarantined for over 3 weeks, and 54.5% (n=1271) went out no more than once a week. In total, 32.7% (n=762) of participants experienced elevated anxiety or depressive symptoms. Specifically, 25.4% (n=592) experienced anxiety, 21.3% (n=496) experienced depressive symptoms, and 13.9% (n=326) experienced both anxiety and depressive symptoms.Rates of elevated anxiety or depressive symptoms among people without chronic diseases, with cancer, and with other chronic diseases were 31.5% (n=649), 34.8% (n=32), and 45.8% (n=81), respectively. Rates of elevated anxiety or depressive symptoms among people whose family members had no chronic diseases, cancer, and other chronic diseases were 31.7% (n=431), 45.0% (n=36), and 33.1% (n=295), respectively.As shown in China\u2019s large-scale quarantine was implemented in late January 2020, resulting in weeks of social isolation. In our sampled population, 32.7% experienced elevated anxiety or depressive symptoms during the quarantine, with 25.4% and 21.3% experiencing anxiety and depressive symptoms, respectively. This is more than triple the rates of lifetime anxiety and depressive symptoms previously reported for the Chinese population [Consistent with the existing literature, this study also found that financial loss, infection concerns, sedentary behavior, poor sleep quality, living with cancer or other chronic diseases, or having family members with cancer were associated with elevated anxiety or depressive symptoms ,25-27. PThis study found some unique risk factors associated with elevated anxiety or depressive symptoms in the Chinese population during the COVID-19 outbreak. We found that people who lived alone had an increased risk of anxiety or depressive symptoms, which might be due to diminished social interactions during the quarantine. Conversely, we also found that family conflict related to COVID-19 might be a source of stress contributing to mental health problems. In our survey, the rate of family conflict during the COVID-19 quarantine was found to be 36%, and most family conflict was related to COVID-19, such as disagreements over how family members should protect themselves from the pandemic and different opinions about information related to COVID-19. These results provide important empirical evidence for policy making; tailored strategies are advisable for different populations at high risk of increased psychological distress and problems. Social connectedness and support should be promoted and provided, especially to those who live alone as an effort to protect them from social isolation. Information on COVID-19 and health promotion could be delivered more effectively through multiple channels to minimize family conflict and cultivate better mental health.There are some limitations in this study. Our sample was more educated than the general Chinese adult population and may not be representative due to limitations of the sampling method used. However, since random sampling is difficult to achieve in a situation like the COVID-19 pandemic, social media\u2013based sampling is a preferred alternative . Though The results of this study highlight an urgent need for psychological support and counseling for populations at high risk for elevated anxiety or depressive symptoms during the current pandemic or any quarantine implementation. The WHO needs to urge the global medical community to provide screening for mental health problems and psychological services to vulnerable populations such as patients with cancer or other chronic diseases."} +{"text": "In a large-scale survey of 9,526 parents in China, we investigated antimicrobial drug use for common childhood infections. Of children with self-limiting conditions, formal care was sought for 69.2%; of those, 53.4% received drug prescriptions, including 11.2% from parental demands. Where drugs were taken without prescriptions, 70% were from community pharmacies. China accounts for half of global consumption of antimicrobial drugs . For data quality control, we used measures (including trap questions and IP address control) to detect random responses or duplications, resulting in 70% of the completed surveys verified as valid. We classified missing data (<11%) as missing-completely-at-random and excluded from the final analysis.+ 3.6 years) were ill sought care for the child. Before seeing a doctor, 16.5% of children had already been medicated with antibiotics at home; moreover, among them, 15.4% (63/410) of parents admitted to having then asked for more antibiotics at the facility. Among those for whom care was sought after parents medicated with antibiotics, 83.9% (344/410) were prescribed antibiotics, 17.2% (59/344) of them because of parental demand. Data showed the success rate of obtaining antibiotic prescriptions for children was 79.6% (148/186); parental demand for antibiotics was more likely to occur in lower-level hospitals than tertiary hospitals and was associated with \u22484-fold increase in prescribed antibiotics Table.Overall, 53.4% of children for whom care was sought were prescribed antibiotics. The most commonly prescribed antibiotic classes were penicillins, macrolides, and cephalosporins, either alone or in combination. Differences emerged in prescription rates by type of healthcare facility, ranging from 47.4% (174/367) in tertiary hospitals to 56.0% in county hospitals. More than 33% of children were administered intravenous antibiotics; about half of those infusions were combined with oral antibiotics.Our data showed that, among the 3,579 children who had common minor childhood illnesses (mostly self-limiting) in the previous month, 621 were administered nonprescription antibiotics by their parents and 1,323 obtained a prescription, with 148 of those deemed inappropriate due to parental demand. We estimated that demand from parents contributed to 40% of antibiotic use on children for self-limiting illnesses. Although some doctors\u2019 prescriptions (supply-side) might be considered appropriate, all antibiotic demands and nonprescription uses from parents were inappropriate.Overuse of medical care for self-limiting illnesses combined with a high prescription rate and a large population size drive high antibiotic consumption in China. We found that, of children for whom care was sought, 53.4% received prescriptions for antibiotics; this proportion is at least twice as high as the official cap of outpatient prescriptions enforced in 2012 (Enforcing existing stewardship policies is an important step to reduce inappropriate antibiotic use in the community (This study is limited by its cross-sectional design; it cannot be used to establish causal conclusions and is subject to recall bias. We limited questions about healthcare-seeking behaviors to the month before the survey and recruited a large sample to reduce the risk for bias. Because we estimated antibiotic consumption by a snapshot survey and not by prescriptions or use, the true magnitude of misuse in children may be underestimated. Common childhood illness cases reported in this study were diagnosed by parents; such diagnoses may or may not reflect true prevalence of the diseases, yet were a key determinant of parents\u2019 childcare behaviors that dictated healthcare decisions parents made for their children.Additional information about parental use of antimicrobial drugs for common childhood illnesses, China."} +{"text": "This study describes the relationships between the number of selected chronic conditions among residents and the number and provision methods of services provided by residential care communities (RCCs). Estimates are from the 2016 wave of the National Study of Long-Term Care Providers conducted by the National Center for Health Statistics. Chronic conditions were measured by whether the RCC reported having at least one resident with any of the most common chronic conditions: dementia, diabetes, depression, or heart disease. Services included were mental health, social work, therapeutic, dietary, and skilled nursing. Each service type was categorized by provision method . Among RCCs, 63% had all four conditions among residents, 23% had three, 12% had one to two, and 1% had none. About 66% of RCCs provided all five services, 16% provided four, 15% provided 1-3, and 3% provided none. Of the 63% of RCCs that had all four conditions among residents, 69% provided all five services, 29% provided 1-4, and 2% provided none. In these RCCs, a greater percentage provided dietary (69%) and skilled nursing services (33%) with employees compared to the other methods; a greater percentage provided therapeutic (85%) and mental health services (83%) solely through arrangement or referral compared to the other methods. This study found that, in 2016, RCCs with multiple selected conditions among their residents tended to provide a greater number of services for managing chronic conditions. How these RCCs provide services varied based on service type."} +{"text": "Early diagnosis of pancreatic ductal adenocarcinoma (PDAC) is challenging but essential for improving its poor prognosis. We established a multicenter study to clarify the clinicopathological features, and to propose new algorithm for early diagnosis of PDAC. Ninety-six patients with stage 0 and IA PDAC were enrolled from 13 high-volume centers. Overall, 70% of the patients were asymptomatic. The serum pancreatic enzyme levels were abnormal in half of the patients. The sensitivity of endoscopic ultrasonography (EUS) for detecting small PDAC was superior to computed tomography and magnetic resonance imaging (MRI) . Indirect imaging findings were useful to detect early-stage PDAC; especially, main pancreatic duct stenosis on MRI had the highest positive rate of 86% in stage 0 patients. For preoperative pathological diagnosis, the sensitivity of endoscopic retrograde cholangiopancreatography (ERCP)-associated pancreatic juice cytology was 84%. Among the stage IA patients, EUS-guided fine-needle aspiration revealed adenocarcinoma in 93% patients. For early diagnosis of PDAC, it is essential to identify asymptomatic patients and ensure close examinations of indirect imaging findings and standardization of preoperative pathological diagnosis. Therefore, a new diagnostic algorithm based on tumor size and imaging findings should be developed. Patients with pancreatic ductal adenocarcinoma (PDAC) are generally diagnosed at the advanced stage and generally have a very poor prognosis. The American Cancer Society estimated that in 2019, approximately 56,770 patients were diagnosed with PDAC in the USA and 45,750 would be dead due to the disease . In contRecently, several reports on imaging features of early-stage PDAC have been published ,7,8,9. IThese previous observations prompted us to establish this multicenter study to clarify the clinicopathological features of early-stage PDAC and to propose an effective diagnostic algorithm for detecting early-stage PDAC based on the data from this study.This study was a retrospective, multicenter, observational study. From January 2000 to September 2020, patients with early-stage PDAC from Hiroshima University Hospital and 12 affiliated high-volume centers were enrolled. Early-stage PDAC was defined as patients with stage 0 ) and stage IA based on post-operative pathological classification according to the seventh edition of the Japanese Classification of Pancreatic Carcinoma . PatientWe retrospectively reviewed data on the following items: (1) patient characteristics, (2) reasons for medical examination, (3) blood tests and imaging findings, and (4) preoperative pathological examination. Depending on the facilities available at each institution, CT (computed tomography) was performed using a multidetector row (from 64 to 320 slices). CT included unenhanced and contrast material-enhanced biphasic imaging, the latter of which comprised arterial and portal phases. Magnetic resonance imaging (MRI) was performed using 1.5 or 3 T. For endoscopic ultrasonography (EUS), we used a radial echoendoscope , which was superior for observing the MPD in the long axis, equipped with processors . If the pancreatic tail was poorly observed, linear echoendoscope was also used as needed. According to the previous reports ,9, indirTM; Boston Scientific, Marlborough, MA, USA) into the MPD. We chose patients with localized stenosis or distal dilatation of the MPD among those undergoing ERCP, and an endoscopic nasopancreatic drainage (ENPD) catheter was placed into the MPD for serial pancreatic juice aspiration cytologic examination (SPACE) [For preoperative pathological examinations, we performed endoscopic retrograde cholangiopancreatography (ERCP) using a video duodenoscope . After pancreatography, we inserted a 0.025 inch guidewire . We usedTM and AcquireTM; Boston Scientific, EZ Shot 3 Plus; Olympus Medical System, EchoTipTM; COOK Medical, Bloomington, IN, USA). These examinations were performed under the supervision of specialists who had experienced more than 100 EUS-FNA and 500 ERCP procedures for a period of more than ten years, according to the standard imaging procedures of Hiroshima University Hospital.When obvious lesions were observed, or when ERCP-associated pancreatic juice cytology (PJC) results were negative, EUS-guided fine-needle aspiration (EUS-FNA) was performed using a linear echoendoscope with a 22 or 25 gage needle . The Kaplan\u2013Meier method was used to estimate cumulative survival. With respect to two-tailed tests, Pearson\u2019s \u03c72), 6.5% for a history of acute pancreatitis, 7.4% for chronic pancreatitis, and 2.4% for a family history of pancreatic cancer (at least one PDAC patient among the first-degree relatives). Seventy-one percent of the patients had one or more of the above risk factors, with a mean of 1.3.Twenty-seven patients (28%) came to the first medical examination with some symptoms, whereas 67 patients (70%) were asymptomatic. The asymptomatic patients comprised those with abnormalities detected during medical health check-ups (39%), those with abnormalities incidentally detected during screening or surveillance for other diseases (52%), and those with changes found during the follow-up of pancreatic diseases (9%).Of the 26 patients with abnormalities detected during the medical health check-ups, 18 (69%) were detected by US (ultrasonography), two (7.7%) were detected by CT, and three patients (11%) exhibited elevated serum pancreatic enzyme levels. The abnormal findings detected by US included tumors in four patients and indirect imaging findings in 14 patients. The abnormal findings detected by CT included a pancreatic tumor in one patient and indirect imaging finding in one patient.Among the 35 patients in whom any abnormalities were incidentally detected during examination or follow-up for other diseases, two (5.7%) were detected by US, 19 (54%) were detected by CT, two (5.7%) exhibited elevated serum pancreatic enzyme levels, and one patient (2.9%) exhibited elevated serum tumor marker level. All of the abnormal findings detected by US were indirect imaging findings. The abnormal findings detected by CT included tumors in four patients and indirect imaging findings in 15 patients. Of the other four patients, three patients had pancreatic abnormalities noted on imaging examination other than US or CT, and one patient was diagnosed with PCIS in the post-operative specimen performed for extrahepatic cholangiocarcinoma.Six patients were detected pancreatic abnormalities during follow-up for pancreatic disease, including pancreatic cysts, and acute and chronic pancreatitis. All patients had been followed up every six months with either CT, EUS, or MRI and measurement of serum tumor markers including carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9) .The serum pancreatic enzyme levels were abnormal in 49% patients. Increased lipase levels were observed in 48% patients, increased pancreatic amylase levels secreted from pancreas in 30% patients, and increased elastase 1 levels were observed in 29% patients. As for serum tumor markers, the levels of carcinoembryonic antigen, carbohydrate antigen 19-9, duke pancreatic monoclonal antigen type 2, and s-pancreas-1 antigen were elevated in 6.9%, 27%, 17%, and 19% patients, respectively. The positive rate of all tumor markers in patients with stage IA was higher than that of patients with stage 0 .p < 0.01).Imaging diagnostic data are shown in For the stage 0 patients, the vast majority of abnormal findings reflected MPD abnormalities, such as stenosis and dilatation. US, CT, and MRI including magnetic resonance cholangiography (MRCP), and EUS showed MPD dilatation in 62% (8/13), 72% (28/39), 78% (28/36), and 78% (31/40) patients, respectively. MRI including MRCP and EUS showed MPD stenosis in 86% (31/36) patients and 73% (29/40) patients, respectively. The detection rate of MPD abnormalities by MRCP was similar to that by ERCP. In addition, localized pancreatic tissue atrophy was observed in 31% (12/39) patients on CT and 10% (4/40) patients on EUS.Preoperative pathological diagnostic data are shown in p = 0.021 and 0.013, respectively) rate was 87% for stage 0 and 71% for stage IA, while the 10-year OS rate was 57% for stage 0 and 41% for stage IA. The 5-year disease-specific survival (DSS) rate was 94% and 82% for stage 0 and stage IA, respectively, and the 10-year DSS rate was 81% and 51% for stage 0 and stage IA, respectively. The 5-year recurrence-free survival (RFS) rate was 92% and 68% for stage 0 and stage IA, respectively, and the 10-year RFS rate was 83% and 49% for stage 0 and stage IA, respectively. The DDS and RFS rates of stage 0 patients were significantly superior to stage IA patients (ctively) . Twenty In this study, we investigated the process from identifying patients with early-stage PDAC to scrutinizing the pancreas by imaging examination and pathological diagnosis.First, this study indicates that efficient identification of asymptomatic PDAC patients is important for early diagnosis. The Clinical Practice Guidelines for Pancreatic Cancer (CGL) issued by Japan Pancreas Society (JPS) in 2019 have identified risk factors for PDAC listed in In asymptomatic patients, 38% were identified at medical health check-ups, and abnormalities noted on US were the most common. Of these, 78% of patients were detected with indirect imaging findings. Hanada et al. established a social diagnostic project on early-stage PDAC ,16. DoctRegarding blood tests, the levels of tumor markers may generally be low in the early-stage PDAC in this study . HoweverBefore forming a tumor, small PDACs may increase the intraductal pressure of the pancreatic ducts and could lead to the dilatation of the caudal or branched pancreatic ducts, resulting in the formation of cystic lesions ,20. TherFurthermore, we would like to recommend EUS as the third imaging modality. In this study, EUS enabled a significantly higher rate of tumor detection in stage IA patients than CT or MRI, and more than half of the patients in which a mass was not detected by CT or MRI had a tumor detected by EUS. It has been reported that EUS has a diagnostic sensitivity of 94.4% for detecting small PDAC (<20 mm) . Yasuda In this study, patients with PDAC were frequently diagnosed during the screening or surveillance for other diseases by CT and indirect imaging findings were observed in 43%. In recent years, it has been reported that patients with chronic liver disease who underwent surveillance for hepatocellular carcinoma may be diagnosed with PDAC at an early stage . In addiFor preoperative pathological diagnosis of early-stage PDAC, the utility of ERCP-associated PJC has been reported, especially SPACE using an ENPD catheter ,27. In tThe sensitivity of EUS-FNA in stage IA was 93%, which was comparable to the sensitivity of EUS-FNA for PDAC including advanced patients (89\u201392%) ,33. We cRecently, concerns were raised regarding needle tract seeding by EUS-FNA. Yane et al. reported that out of 176 patients with pancreatic body and tail cancer undergoing preoperative EUS-FNA, 3.4% were diagnosed as having needle tract seeding . A summaThis study has several limitations. First, a retrospective study design was used. Although this study was a multicenter report, the number of patients was small. Second, regarding EUS and ERCP, no standardized training course is available in Japan. Therefore, these methods are not necessarily used, and effective training courses for young endoscopists should be implemented in the future. Third, although there have been no severe patients, there is still a concern about the problem of PEP.Meanwhile, the ongoing development of biomarkers using microRNA of pancreatic juice and studEarly diagnosis is essential for improving the prognosis of PDAC. The algorithms in the current CGL issued by JPS in 2019 may have some limitations regarding the early diagnosis of PDAC, and new diagnostic algorithms for early diagnosis of PDAC should be developed.In the future, increased awareness on imaging findings associated with early-stage PDAC and the value of EUS and ERCP in early diagnosis combined with the development of a new diagnostic algorithm for small PDAC should lead to an increased number of diagnosis of early-stage PDAC patients and finally contribute to improving prognosis in patients with PDAC."} +{"text": "Oregon legislation requires assisted living (AL) communities to report selected quality measures to the state licensing agency. The Quality Measurement Program (QMP) includes five metrics that assess different areas of resident safety and wellbeing: falls, antipsychotic medication use, staff training, staff retention, and resident satisfaction. This paper describes findings based on our 2019 survey of AL communities and offers suggestions for stakeholders interested in public reporting and quality metrics. Assisted living providers reported 28% of AL residents and 38% of memory care (MC) residents fell at least once in the prior 90 days, with 39% and 45% reporting an injury, respectively. Antipsychotic medication use was 20% among AL and 44% among MC residents. These findings and the survey methods used to collect them, combined with stakeholder and state agency staff participation, informed the current QMP approach. We describe how to collect meaningful quality metrics within the AL context."} +{"text": "Nutritional status is important for health and competitive achievement. This area remains understudied among elite-level female athletes and is appropriate for research. We examined nutritional status and cardiovascular health markers of two groups of female athletes of the same age and competition period, involved in weight-bearing and a non-weight-bearing sport: gymnasts D), calcium, magnesium, phosphorus, potassium, and iron), blood lipids, and blood pressure (BP) were measured. Setting and Participants. A cross-sectional study of 31 athletes from Slovenia. Body composition and dietary intake were assessed by bioelectrical impedance and Food Frequency Questionnaire. The concentrations of serum micronutrients and lower fat free mass than swimmers and comparable body fat percentage (22.5 vs. 22.8%). Both groups had low intake of carbohydrates, fibre, polyunsaturated fats, protein (only gymnasts), and micronutrients (11/13 micronutrients gymnasts and 4/13 swimmers) and high intake of free sugars and saturated fats. Both groups also had significantly lower-than-recommended serum levels of 25 (OH) D. All cardiovascular risk factors were within recommended ranges. Gymnasts had higher LDL cholesterol , and swimmers had higher systolic BP . Gymnasts had higher body mass index (21.5 vs. 20.1\u2009kg/m Dietary intake especially in gymnasts was suboptimal, which may reflect in anthropometric and cardiovascular marker differences between gymnasts and swimmers. Body mass management of elite athletes is pivotal for sport participation and competitive achievement, especially in sports where the athlete's body mass is an important determinant of success, such as artistic gymnastics or swimming , 2. ApprD (25 (OH) D) [Artistic gymnasts may be especially at risk because of specific dietary patterns and needs , 10 due (OH) D) , 15, whi (OH) D) .Dietary requirements for swimmers are dependent on swimming style , competitive distances , training requirements, and competition phase , 18. A sA healthy diet has been the cornerstone of cardiovascular diseases (CVDs) prevention and treatment for decades . SpecifiAthletes may have an increased risk of CVD later in life, although data on the association between elite sports participation and cardiovascular health remains largely inconclusive. Studies in endurance runners and team sport athletes, for instance, have demonstrated a relatively high incidence of CVD later in life , 8. Howe12 status remain pivotal [In terms of possible cardiometabolic dysfunction, several humoral markers have been associated with increased morbidity and mortality in the general population and in athletes. Blood lipid levels and triglycerides) and blood pressure (BP) represent important determinants of cardiovascular health , 27. The pivotal .There is a lack of studies examining a nutritional and health status in elite-level female athletes. The present study is a component of a larger cross-sectional study on various aspects of elite-level female indoor athletes, who were gymnasts and swimmers matched according to age and competition period. The study examined athletes involved in a weight-bearing and a non-weight-bearing sport. Both groups of athletes are faced with the problem of a predominantly indoor institutionalized lifestyle and have special dietary requirements , 18. In In the present study, we aimed to investigate the anthropometric measures, dietary intake, serum micronutrient concentrations, and cardiovascular health status of two elite-level indoor female athlete groups.th to 6th 2018) to mitigate possible seasonal effects and training status. Blood samples were collected and measurements performed after an overnight fast. For complete biochemical assays , a single sample of 15\u2009mL of blood was taken. The gymnasts were tested at Ljubljana Medical Centre , whereas the swimmers were tested at Maribor Medical Centre .The study was conducted during the competition period and within three days and registered at https://clinicaltrials.gov (NCT03584256). All participants and/or their parents/legal guardians (for participants below the age of 18) signed an informed consent at inclusion. The study was conducted in accordance with the Declaration of Helsinki. Participants were not remunerated financially for participation in the study.We included 31 elite-level female indoor athletes: 17 gymnasts (aged 17.4\u2009\u00b1\u20094.1 years) and 14 swimmers (aged 16.6\u2009\u00b1\u20093.1 years). All participants were from the same ethnic group (Caucasian), resided in Slovenia, and many of them (58%) were performing at the highest international competitive level . The participants were invited through personal contact with the National team coach and other gymnastic and swimming coaches working in clubs in Slovenia. The criteria for inclusion in the study were competing internationally and nationally, currently fully actively involved in a training program, and no use of any prescribed medications that affect bone metabolism. All invited athletes who met the inclusion criteria responded to the invitation, and we did not exclude anyone's data from the final analysis. All measurements that were part of the study were paid for by the Slovenian Research Agency.The outcome variables included basic characteristics , basic anthropometric measures, dietary intake, serum micronutrient concentrations, and CVD risk and safety factors.The amount of training and menarche data were evaluated by a questionnaire developed by the authors that included questions about hours of training each day of the week, year of first menstrual period, regular/irregular menstrual cycle, and type of menstrual period .Basic anthropometrics included body height, body mass, and body mass index (BMI), body fat percentage (BF%), and fat free mass (FFM). Heights (cm) were measured by the body height gauge . Fat free mass (FFM) and BF% was assessed by an 8-electrode medically approved and calibrated bioelectrical impedance body composition monitor , which provides an valid tool to measure total BF% in healthy young males and females regardless of their level of habitual physical activity . AccuracTo assess dietary habits in the past year, we used a manual monitoring technique, a 52-item qualitative Food Frequency Questionnaire (FFQ), that was based on a validated 50-item FFQ . The FFQ\u03bcg of macro- and micronutrients/kg BM/day (unit of nutrient/kg BM/day).We calculated data for dietary intake of gymnasts and swimmers expressed as kcal/day (energy), g/day (macronutrients), except for dietary cholesterol (mg/day) and water intake (L/day), % of daily energy intake (macronutrients), kcal/kg FFM/day (energy intake), and g, mg, or The energy availability (EA) and several macronutrients intakes were compared with the joint position of the Academy of Nutrition and Dietetics, Dietitians of Canada, and the American College of Sports Medicine for nutrition and athletic performance , whereas12 (S-vit B12) and D (measured as the 25 (OH) D, calcium (S\u2013Ca), magnesium (S\u2013Mg), phosphorus (S\u2013P), and potassium (S\u2013K), and trace element iron (S\u2013Fe). For serum micronutrients, both laboratories (for gymnasts and swimmers) used the same manufacturer and methodology.Serum micronutrients that are frequently of concern were assessed in a certified biomedical laboratory in Ljubljana (gymnasts) and Maribor (swimmers) and included analysis of vitamins B12 levels of all the participants were measured using a competitive-binding immunoenzymatic assay, the Elecsys Vitamin B12 II assay (ECLIA), according to the manufacturer's instructions (Roche Elecsys 2010). The assay has a linearity range of 36.9\u20131.476\u2009pmol/L. For the S-vit B12, level, there is no clear, accepted cutoff value to define deficiency, but for additional comparison of athlete micronutrient status and recommended values, the S-vit B12 was compared with 258\u2009pmol/L as suggested by German researchers to prevent neurocognitive disorders late in life [The S\u2013B in life .The 25 (OH)D levels were measured using a commercially available Elecsys\u00ae Vitamin D total assay with a Cobas e601 analyser , which uses a competitive electrochemiluminescence binding technique. The method was standardized according to internationally accepted procedures. For the purpose of interpreting 25 (OH) D levels, which is a known challenge for indoor athletes , we used2+ in the sample and Arsenazo III results in a purple complex, the absorbance is measured bichromatically at 660/700\u2009nm, and the increase in absorbance is directly proportional to the total calcium concentration in the sample.The S\u2013Ca concentrations were determined on an automated clinical chemistry analyser device using colorimetric photometric methods based on the Arsenazo III complex. For total Ca, the reaction between CaThe S\u2013Mg concentrations were determined on an automated clinical chemistry analyser by a photometric colour test for the quantitative determination of magnesium in human serum. The magnesium reagent utilises a direct method in which magnesium ions form a coloured complex with xylidyl blue in a strongly basic solution. The colour produced is measured bichromatically at 520/800\u2009nm and is proportional to the magnesium concentration in the serum.The S\u2013P concentrations were determined on an automated clinical chemistry analyser that uses System Calibrator for serum application. Inorganic phosphorous reacts with molybdate to form a heteropolyacid complex. The use of a surfactant eliminates the need to prepare a protein-free filtrate. The absorbance at 340/380\u2009nm is directly proportional to the inorganic phosphorous concentration in the sample.The S\u2013K concentrations were determined on an automated clinical chemistry analyser using a precise volume of sample (40 microliters) that was mixed with a buffered solution (ISE Electrolyte Reference reagent). The ratio used was one-part sample to 33 parts buffer. The high molar strength buffer is used to establish a constant activity coefficient for potassium ions, calibrating the electrode to concentrations.The S-Fe concentration was determined using a Vitros 950 analyser . S-Ca concentrations were determined using a Beckman Coulter AU 640 , and S-P concentrations were determined on an automated clinical chemistry analyser .Serum mineral concentrations of gymnasts and swimmers were compared with the reference values of the University Medical Centre Ljubljana, Slovenia, which is the national core laboratory .Appraised CVD risk factors were total cholesterol (S-cholesterol), high-density lipoprotein (HDL cholesterol) and LDL cholesterol measured directly, and blood pressure (BP). The safety markers that we included in the blood analysis were S-UA, fasting glucose (S-glucose), and haemoglobin.For biochemical analyses of lipids, S-glucose, and S-UA, a Beckman Coulter AU 640 was used at one laboratory (for gymnasts), whereas a Becton Dickinson Vacutainer\u00ae SSTII Advance analyser was used at another laboratory (for swimmers). For serum haemoglobin concentrations, both laboratories used an Advia 2120i haematology analyser. Blood pressure (BP) was assessed using an oscillometric technique in the supine position after five minutes of rest and before taking the blood sample. The average of two measurements three minutes apart was used for analysis. LDL cholesterol and BP were our primary CVD risk factors.To assess the proportion of participants reaching the recommended targets for LDL cholesterol (<3.4\u2009mmol/L) and triglycerides (<1.7\u2009mmol/L), we used the values from the European Atherosclerosis Society (EAS) . Further\u03bcmol/L seems to identify true healthy subjects for all subjects [There is no clear consensus for normal S-UA. However, a threshold value\u2009<\u2009360\u2009subjects . For S-gsubjects . For haesubjects .U test for independent samples, and for comparing intakes against recommendations, we used one-sample Wilcoxon signed-rank test exclusively. We chose the nonparametric tests because the sample size was quite small, and the skewness coefficient indicated that all variables, except from three, were not normally distributed. Further exploration of remaining three variables showed the differences between the \u201cnormality\u201d in groups. Importantly, where the dietary intake recommendations were specified as a range , we took the average of the range. The threshold for statistical significance was less than 0.05. No missing data were present. No sensitivity analysis was performed. Data are presented as the means (standard deviation).Statistical analysis was performed with R 3.5.2 with the dplyr , ggplot2Characteristics of gymnasts and swimmers are presented in 53% of gymnasts and 86% of swimmers reported consuming an omnivorous diet, whereas others characterized their diet as vegetarian or occasionally vegetarian. Important, 18% of gymnasts and 21% of swimmers reported to have irregular menstrual cycle.Comparisons between daily energy and nutrient intakes of gymnasts and swimmers and comparisons with recommendations are presented in p < 0.001). The mean proportions of ingested energy among the main macronutrients for gymnasts were 47% from carbohydrates, 40% from fat, and 14% from protein, whereas in swimmers, it was 54% from carbohydrates, 38% from fat, and 13% from protein. Water intake from beverages and solid foods was higher in swimmers than in gymnasts . Between the studied groups, there were no significant differences in intake of macronutrients . Furthermore, there were no significant differences in intakes of several micronutrients .The reported absolute energy intake was significantly lower in gymnasts than in swimmers (mean\u2009\u00b1\u2009SD) (p < 0.001 in gymnasts and p < 0.05 in swimmers). Gymnasts and swimmers consumed the daily recommended intake (% of daily energy intake) of fat and MUFA, and swimmers also consumed the daily recommended intake of protein, whereas both groups consumed significantly below reference intakes of carbohydrate , fibre (g/day), and PUFA (% of daily energy intake). Both groups consumed high amounts of free sugars and SFA but acceptable amounts of dietary cholesterol (the recommended\u2009<\u2009300\u2009mg/day). Concerning the intake of micronutrients, gymnasts met the recommended intake for only two (2/13) (vitamin B12 and zinc), whereas swimmers met recommendations for nine micronutrients (9/13).The EA was significantly lower than recommended in both groups, but more in gymnasts than in swimmers and vegetables (in cooked or fresh) were not consumed by all gymnasts or swimmers, whereas no one in either group reported regular daily consumption of legumes, potatoes, plant-based meat alternatives , or fish.Specifically, 29% of gymnasts and 21% of swimmers consumed fruits at least once per day, whereas 47% of gymnasts and 50% of swimmers consumed fruits 2-3 times per day. Twenty-four percent of gymnasts and 29% of swimmers did not consume fruits on a regular basis. Twenty-nine percent of gymnasts and 14% of swimmers consumed vegetables (cooked or fresh) at least once per day, whereas no gymnasts and 7% of swimmers consumed vegetables 2\u20133 times per day. Whole grains were consumed at least once per day by 41% of gymnasts and 64% of swimmers, whereas 12% of gymnasts and 36% of swimmers consumed whole grains 2\u20133 times per day. Forty percent of gymnasts and 36% of swimmers reported consuming whole grain foods 2\u20134 times weekly. Only 8% of gymnasts and none of the swimmers consumed nuts and seeds daily, whereas 30% of gymnasts and 43% of swimmers did not consume any nuts or seeds.Dairy and meat products were consumed daily by 41% and 12% of gymnasts and 29% and 50% of swimmers, respectively, whereas eggs were consumed daily by 6% of gymnasts and 7% of swimmers. Only 23% of gymnasts and 21% of swimmers consumed fish at least once weekly.Processed plant-based food products were reportedly consumed daily by 65% of gymnasts and 79% of swimmers, whereas processed meat or ultraprocessed foods were reportedly consumed very rarely by gymnasts (18% of them 2\u20134 times weekly) and more frequently by swimmers (43% of them 2\u20134 times weekly).A total of 88% of gymnasts and 86% of swimmers drank water more than 3 times/day, whereas other drinks that were reported to be consumed for both groups were coffee or tea. Sport drinks were consumed by the majority of swimmers (71%) but only a minority of gymnasts (6%). Fifty-seven percent of swimmers consumed sport drinks two or three times per day (during training). Gymnasts and swimmers reported not consuming any alcohol on a daily or weekly basis.D supplements. Eighteen percent of gymnasts and 7% of swimmers consumed dietary supplements of omega-3 long-chain PUFA (eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)). Twelve percent of gymnasts consumed calcium, and 12% of gymnasts consumed iron supplements, whereas no swimmers consumed calcium and 7% of swimmers consumed iron supplements. Among swimmers, 14% consumed dairy protein shakes (whey protein) compared to 6% of gymnasts.Dietary supplements or sport drinks were not consumed by 41% of gymnasts and 14% of swimmers. The most frequently consumed dietary supplement among gymnasts was magnesium (35%), whereas swimmers consumed multivitamins (21%). Eighteen percent of gymnasts and no swimmers consumed vitamin Most gymnasts and swimmers (59 and 64%) regularly consumed all three main meals: breakfast, lunch, and dinner. Six percent of gymnasts and 7% of swimmers reported never eating breakfast, whereas 29% of gymnasts and 14% of swimmers reported not consuming breakfast every day. Twenty-three percent of gymnasts and 29% of swimmers did not eat lunch every day, and 18% of gymnasts and 36% of swimmers skipped dinner one-two times per week.Serum micronutrients are presented in All mean serum micronutrients for both athlete groups were within the recommended range, except for 25 (OH) D for both groups and S\u2013P for gymnasts. The mean 25 (OH) D levels were sufficient (>75\u2009nmol/L) in 23% of gymnasts and in 43% of swimmers, insufficient (50\u201374\u2009nmol/L) in 35% of gymnasts and 36% of swimmers, and deficient (<50\u2009nmol/L) in 42% of gymnasts and 21% of swimmers.12 was found to be, on average, above the reference values for gymnasts and swimmers. However, only 53% of gymnasts and 79% of swimmers had S-vit B12 above the reference value of 258\u2009pmol/L.Other minerals that were also not within reference ranges for all gymnasts were S\u2013Fe and S\u2013P, whereas for swimmers, S-P and S-Mg were not in reference ranges. S-Fe was found not to be within the reference range for 23% of gymnasts, whereas S-P was found to be higher than the upper threshold of the reference range for 35% of the gymnasts and 21% of swimmers. S-Mg was found to be within the reference range for all gymnasts and swimmers. The mean value of S-vit BCardiovascular health (CV) status is shown in All blood variables and BP were, on average for both groups, within recommended target ranges. However, there are some important insights within groups that help interpret the athletes' CV status. Ninety-four percent of the gymnasts and 93% of the swimmers had S-cholesterol values within the reference range, whereas 71% of gymnasts and 93% of swimmers had LDL cholesterol within recommendations. Furthermore, 59% of the gymnasts had LDL cholesterol above 2.6\u2009mmol/L, and 41.2% had LDL cholesterol above 3\u2009mmol/L, whereas these numbers among swimmers were lower (21% swimmers had above 2.6\u2009mmol/L and 7% above 3\u2009mmol/L). HDL cholesterol values were within recommendations in 82% of gymnasts and 100% of swimmers. Furthermore, 35% of gymnasts and 29% of swimmers had triglycerides \u22640.6\u2009mmol/L. None of the athletes had triglycerides above the reference value. BP was below the recommended target (\u2264129/84\u2009mmHg) for all gymnasts, whereas systolic BP and diastolic BP were higher than recommended in 36% and 7% of swimmers, respectively.\u03bcmol/L). One gymnast and no swimmers had haemoglobin values below the recommended cutoff (\u2265120\u2009g/L).Importantly, none of the gymnasts and swimmers had S-glucose outside the recommended level (<5.8\u2009mmol/L). Furthermore, all gymnasts and swimmers had S-UA values below the threshold value , SFA, protein (% of energy), and several micronutrients .The dietary intake of gymnasts and swimmers, when compared to current recommendations and duly acknowledging the limitations of our methodology , may be regarded as suboptimal. In particular, free sugars and SFA exceeded the upper limit of acceptable intakes and showed ample room for improvement.12 represent the most challenging micronutrients.Third, gymnasts had significantly higher S\u2013K and S\u2013P status compared with swimmers. Furthermore, serum micronutrients were on average within recommended ranges for both groups, except for 25 (OH) D for both groups and S\u2013P for gymnasts. Further analysis, however, suggests that 25 (OH) D and S-vit BFinally, markers of cardiovascular health were within guidelines/recommended ranges. However, gymnasts had significantly higher LDL cholesterol compared to swimmers, whereas swimmers had significantly higher systolic BP than gymnasts. In terms of safety factors, average S-glucose, S-UA, and haemoglobin values were in line with recommendations.2 vs. 20.3\u2009kg/m2, for Slovenian and US gymnasts, respectively) [Our results indicate that gymnasts, compared to swimmers, were shorter and lighter but had higher BMI, lower FFM, and comparable BF%. By comparison, a recent anthropometric study suggested a mean body height of 153\u2009cm and mean body mass of 44\u2009kg in elite-level female artistic gymnasts with a mean age of 15.8 years . Previouctively) . Furtherctively) . Importactively) .2) and BF% (18.2%) compared to our results [For female swimmers, previous studies yielded even more inconclusive information. One US cross-sectional study on 43 female competitive sprint swimmers (aged 19.7 years) showed much lower mean body height (168.3\u2009cm), higher body mass (63.8\u2009kg), and higher BF% (25%) compared to our results. Moreover, the same study suggested that BF% is a predictor of swimming performance in women . Convers results . These a results . Hence, 12 and zinc), whereas swimmers had below recommended intakes of vitamin D, calcium, potassium, and selenium [In our study, gymnasts had lower intake of energy and all macro- and micronutrients compared to swimmers. More importantly, dietary patterns of both indoor athlete groups had ample room for improvement. Gymnasts had below recommended energy intake , whereasselenium , 42. Conselenium and ESPGselenium upper lip=0.002). Furthermore, fibre intake was markedly low for gymnasts and swimmers . This va30\u2009g/day ). Water 30\u2009g/day and cannApart from being an important determinant of health status and anthropometry measures, dietary intake was found to be directly associated with effectiveness of training, performance, and recovery status among athletes , 71. TheFurthermore, we measured vitamin D intake from diet and supplements. It is well-known that it is hard to reach acceptable serum levels of vitamin D through diet alone , and supIt is also important to note that the frequency of daily consumption of food groups of vegetable origin were very limited, whereas the consumption of very important and healthy food groups was alarmingly low in both groups of athletes. Together, an increase in these factors may greatly contribute to sufficient consumption of protein (in gymnasts), fibre, omega-3 PUFA, and numerous micronutrients .2), and the authors suggested that their study results represented evidence of malnutrition [n\u2009=\u20091, age\u2009=\u200918.5 years) and one rhythmic gymnast who were both members of the Greek National Team [6, and zinc exceeded daily recommended amounts, whereas calcium intake was insufficient and had the highest deviation from the recommended daily amount. Despite the fact that our results are hardly comparable to values reported in this case study, we can clearly see a similar trend. In brief, in both investigations, there was evident low energy intake and very low dietary fibre intake (14.7 vs. 11\u2009g in Greek and our study). Conversely, the Greek study revealed much better micronutrient intake, which is probably a result of significantly higher energy intake resulting in increased intake of some micronutrients.The issue of inadequate dietary intake in artistic gymnasts is not novel. Several previous studies suggested inadequate intake of energy and micronutrients in artistic gymnasts on national teams , 71. Ourutrition . In a ranal Team . Using aAccording to the available literature, dietary intake among swimmers is generally less problematic. However, a study with 85 US female collegiate swimmers suggests that the mean proportion of macronutrients was 25\u201330% energy from fat, 55\u201365% energy from carbohydrate, and 11\u201315% of energy from protein , which i12 above the reference value of 258\u2009pmol/L [All serum micronutrients, both in gymnasts and swimmers, were within reference ranges, except for 25 (OH) D for both groups and S\u2013P for gymnasts. Insufficient or deficient levels of 25 (OH) D were found in 77% of gymnasts and 57% of swimmers, with 42% of gymnasts and 21% of swimmers being outright deficient. However, this study was intentionally conducted just after the winter season, when serum levels of 25 (OH) D are expected to be naturally lowest in that specific period and at that geographic latitude . Of note8\u2009pmol/L .Our results suggest relatively favourable cardiovascular health status of included athletes both in terms of CVD risk profile , 50, 53 Gymnasts had a less favourable lipid profile, higher LDL cholesterol, and lower HDL cholesterol levels, whereas swimmers had, on average, higher systolic BP. Almost two-thirds of gymnasts had LDL cholesterol levels above 2.6\u2009mmol/L (41% above 3.0\u2009mmol/L), which is higher than the currently recommended levels for long-term preservation of cardiovascular health , 52. AllThere are several possible explanations for these observed differences. Higher LDL cholesterol in gymnasts could be associated with dietary patterns, including lower energy intake, higher overall total fat, SFA, and free sugar intake and lower fibre intake. SFA and refined carbohydrates are associated with increased risk of CVD , 22, wheHigher systolic BP in swimmers can also be explained by dietary patterns. Swimmers' relative intake (per kg BM/day) analysis showed that they consumed more energy, carbohydrates, sugar, and total fat than gymnasts. Importantly, four times more swimmers consumed meat daily. In comparison, 47% of gymnasts consumed a vegetarian or sometimes vegetarian diet, while 86% of swimmers characterized their diet as omnivorous. Vegetarian diets, if properly designed, have significantly favourable CVD risk . ImportaA rare, older cross-sectional study on Portuguese gymnasts and a cr\u03bcmol/L (our gymnasts and swimmers had S-UA 265 and 282\u2009\u03bcmol/L) were shown to be associated with the lowest mortality [In terms of safety factors, all athletes had S-glucose, S-UA, and haemoglobin within recommendations \u201356, exceortality .We included all female members of the Slovenian gymnast and swimming teams, representing two comprehensive age-matched, elite-level indoor sports populations rather than samples. In fact, none of the invited gymnasts and swimmers declined to participate, and none were excluded from the study. No missing data for study outcome were presented. Furthermore, the study design was comprehensive with data acquisition completed within three days, thus minimising seasonal confounders.The study has some limitations inherent to the sample size. The sample size was relatively small, and therefore, the results should be interpreted with caution and should ideally be replicated in larger samples. In addition, we acknowledge the limitations of collecting data using an FFQ. Initially, we planned to evaluate the dietary intake also by a three-day weighted dietary protocol, which is a golden standard for evaluating the dietary intake. However, the coaches of the participating elite-level artistic gymnasts and swimmers advised us against it, as it would be too time-consuming for the participants. However, the FFQ allowed us to distinguish between different dietary patterns in subpopulations , 86. TheGymnasts in our study were shorter and lighter and had higher BMI, lower FFM, and comparable BF% to swimmers. Energy availability, especially in gymnasts, was too low. Both groups consumed too much of free sugars, total fat, and SFA and low intake of proteins (gymnasts only), polyunsaturated fatty acids, fibre, and several micronutrients (11/13 in gymnasts and 4/13 in swimmers). Both groups, especially gymnasts, have room for dietary optimisation, which would include increasing the intake of whole plant-based foods, especially whole grains, legumes, fresh fruits, and vegetables as well as small sea fish , while decreasing the intake of processed, ultraprocessed, and fried foods. Dietary optimisation would also benefit their training and athletic performance.12 levels. As 25 (OH) D and S-vit B12 were low (25 (OH) D: for 77% of gymnasts and 57% of swimmers; S-vit B12: for 47% of gymnasts and 21% of swimmers), it should be regularly tested and supplemented in those with suboptimal levels. CVD risk and safety factors were mostly within guideline-recommended ranges. However, gymnasts had more unfavourable lipid profiles (increased LDL cholesterol), whereas swimmers had more unfavourable BP profiles (increased systolic BP).In gymnasts and swimmers, the most challenging serum micronutrient shortcomings were 25 (OH) D and S-vit BDespite the novelty of our results, single assessment does not allow for a definitive conclusion concerning anthropometry or dietary and cardiovascular health. For more conclusive data, frequent comprehensive analysis of same female gymnasts is warranted."} +{"text": "Haemophilus influenzae type b vaccine (Hib), hepatitis B vaccine (HepB), and human papillomavirus vaccine (HPV). Achieving universal coverage with all recommended vaccines will require tailored, context-specific strategies to reach communities with substantial proportions of zero-dose and incompletely vaccinated children, particularly those in remote rural, urban poor, and conflict-affected communities established the Expanded Programme on Immunization to ensure that all infants have access to four recommended vaccines to protect against six diseases . Since then, additional vaccines and doses have been introduced in the first year of life and beyond (MCV2 and HPV) and DTP3 (84%\u201385%) remained stable. The only region with a decline in DTP3 coverage during 2000\u20132019 was the Americas (from 91% to 84%). In 2019, DTP1 coverage ranged from 81% in the African region to 97% in the European region . DTP3 coThe number of zero-dose children varied by region and economic classificationIn 2000, low-income countries accounted for the highest percentage of zero-dose children ; by 2019, however, middle-income countries accounted for the highest percentage of zero-dose children . This shift occurred largely because 36 countries advanced from low- to middle-income classification from 2000 to 2019 and because the number of zero-dose children increased in 32 (51%) of the 63 countries classified as middle-income in both 2000 and 2019. In 2019, 10.6 million (77%) zero-dose children lived in countries eligible for support from Gavi, the Vaccine AllianceDuring 2010\u20132019, global coverage with MCV1 remained stable at 84%\u201385%, and in 2019 ranged from 69% in the African region to 96% in the European region. MCV2 coverage increased from 42% to 71% . Among aSince establishment of the Expanded Programme on Immunization in 1974, substantial progress in vaccination coverage has been made worldwide. In 2019, 90% of children received at least 1 DTP dose and 85% received 3 DTP doses and at least 1 MCV dose. However, challenges to achieving higher routine immunization coverage remain. Despite large gains in vaccination coverage during 2000\u20132010, coverage with established vaccines has increased little since 2010 and progress is uneven: coverage in the African region lags that in other regions, and progress in the Americas has reversed.Extending immunization services to regularly reach zero-dose and underimmunized children and communities is one of the objectives of the Immunization Agenda 2030 pandemic. Although countries have attempted to maintain their immunization programs, reduced availability of health workers and personal protective equipment, vaccine distribution system delays, and reduced demand for immunization have contributed to fewer children being vaccinated in 2020 , third dose of polio vaccine, and first dose of measles-containing vaccine has remained between 84% and 86% since 2010.In 2019, 13.8 million children worldwide did not receive the first dose of DTP (zero-dose children). During 2010\u20132019, the number of zero-dose children increased in the African, Americas, and Western Pacific regions.Increasing vaccination coverage beyond levels achieved in the past decade will require targeted, context-specific strategies to identify zero-dose and underimmunized children, introduce interventions to minimize missed vaccinations, monitor vaccination coverage, and respond to immunization program setbacks."} +{"text": "This study intends to describe a HIV intake screening strategy in recentlyincarcerated adults in Distrito Federal, Brasilia, Brazil. We tested 455 recently incarcerated adults in Distrito Federal in 2016 usingrapid tests (RT) applied to oral samples (OS). The estimated frequency of positive tests was 0.88% . The present findings reveal the potential significance of detecting new HIVinfection cases in a vulnerable population using point-of-care rapiddiagnostic tests. According to 2014 data, the Brazilian prison population was 607,731, and it has increasedby 161% since 2000 - 10 times higher than the general population. If the same rate ofincarceration is maintained in 2022, Brazil\u2019s prison population will surpass the 1million people mark. There are no official data regarding the number of people detainedyearly, even brieflyThe majority of prisoners are young uneducated males, mostly between 18 and 29 years ofage, arrested for robbery, burglary, drug dealing, and homicideThis population, mostly derived from disfavored communities, is usually affected by poorhealth and sanitary conditions even before incarceration. Unfavorable hygieneconditions, poorly ventilated prison cells, and overcrowding contribute to the worseningof their health statusIn a perverse manner, the justice system confines society members with higher risk ofgetting sick and who frequently do not seek health services. This provides anopportunity to improve public health efforts. For some detainees, this becomes the firstcontact with the health system,Regarding infectious diseases, intake screening should be an integral part of the prisonsystem, because of transmission rates and high prevalence of diseases, such as HIVRapid tests are simple immunoassays that can be performed within 30 minutes. As theybecome more available, HIV diagnoses can be made away from labs, improving access. Theyhave more than 99.5% sensitivity and 99% specificity for the detection of HIVConsidering that rapid HIV tests are approved in Brazil and recommended by the Ministryof Health for use in vulnerable populations, such as prison inmatesCandidates who were eligible to participate in this cross-sectional descriptive studywere adult males recently arrested in the Federal District, Brasilia, Brazil, in 2016.Exclusion criteria were absence of cognitive capacity for making an autonomous decision to signthe written consent. Potential candidates\u2019 cognitive capacity was subjectively evaluatedby the researcher. In the Federal District, individuals are taken to a centralized intake unit, \"Carceragemdo Departamento de Pol\u00edcia Especializada (DPE)\" after being arrested. An average of 40people are admitted daily. The subjects were recruited at this unit, in a sequentialmanner, during weekdays, between July and August 2016.Subjects were approached in a collective holding cell, where they were allocatedimmediately after arrival while waiting police identification procedures. They wereinformed that everyone would be tested but individuals were allowed to refuse (opt-outstrategy). Those who refused were instructed to go to the back of the cell. A consentexplanation ensued. Those willing to have the exam formed a queue for signing thewritten informed consent and receiving the oral swab. The sample collection instructionswere provided collectively, but each individual collected his own sample. Subjects were informed of their results after 30 minutes, and those testing negative orindeterminate were instructed on how to proceed. The oral sample rapid test was \u201cTR DPP HIV \u00bd - FO/BIO-MANGUINHOS,\u201d lots 159RO047Z (goodthrough 08/16) and 155RO045Z, (good through 09/16). The test was applied following themanufacturer\u2019s instructions. ).This study followed ethical principles involving research with human beings in accordancewith the National Health Council and was approved by the of the Department of Medicineof the University of Brasilia Ethics Committee (CAAE:51813615.2.0000.55582p(1-p)]/e2, where: z =1,96; p = 1%; e = 0,9%. Data were analyzed using thesoftware Statistical Package for Social Sciences (SPSS version 22). We estimated a sample size of 455 individuals, considering a total population of arrestedadult males of 15,000 in 2016, with 0.9% precision, 95% confidence level, and 1%expected HIV infection prevalence, using the formula n=[ZBetween 07/06/2016 and 08/18/2016, within 28 weekdays, HIV oral fluid rapid tests wereoffered to 618 recently incarcerated adult men, from which 455 consented (73.6%). Nosubjects were excluded. On average, 12.7 people were tested daily, with a minimum ofnine and maximum of 25. Of the 455 individuals tested, 34.5% (n=157) remained only 1 day after being arrested andwere released after presentation before a judge on the subsequent day of the arrest.Within 30 days, 59.6% (n=271) remained imprisoned, and 41.4% had been released .Age data were made available by the criminal authority for only 366 subjects (80.4%) whowere not released by the judge or were previously convicted . Mean agAmong the 455 subjects, four tested positive for HIV corresponding to an estimatedfrequency of 0.88% (95% CI 0.34% to 2.24%). Three were new cases. All cases that testedpositive were still detained one month after incarceration, were later confirmed as HIVcases, and initiated treatment while detained.As this was the first Brazilian study in a recently arrested population, there are nosimilar data for comparison. Considering other surveys among prisoners, a recent studyin the Brazilian State Mato Grosso do Sul found an HIV prevalence of 1.54%Regarding the Brazilian general population, the estimated HIV prevalence was 0.4% in2014There was a considerable testing rate (73.3%) even though the opt-out strategy wasadopted. Compared to the opt-in strategy, in which the test is performed only afterdirectly asking the person if he or she wants to be tested, in the opt-out method theexaminer declares that the test will be given, providing the option to decline toparticipate. The opt-out method often yields a higher test rateThe choice of rapid test proved to be reasonable considering approximately 30% of thesubjects were released the next day, which would have caused difficulty in deliveringthe results, considering the test options currently availableThere is controversy regarding whether the oral fluid rapid test sensitivity andspecificity are similar to tests using finger or venous blood samples. A meta-analysisrevealed as much as a 2% lower sensitivity in the oral sample testsIn regard to the immunoassays (ELISA) in venous samples, the new fourth generation tests,which also include antigen direct testing, have higher sensitivity for acute infections,which is of special interest for higher risk populationsRapid tests using finger blood samples and the conventional immunoassays still allow formultiple testing of other bloodborne diseases, such as syphilis and hepatitis B and C,and are also important in the imprisoned populationThere are reports of North American emergency services where venous sample ELISA resultswere available within three hoursThus, considering the transitory nature of this population, the chosen opt-out strategywith the oral fluid rapid tests and dissociated individual pre-counseling, can beconsidered appropriate. Challenges remain regarding resources and more appropriatetechnologies.Concerns about free consent and potential interference of a coercive environmentPotential discrimination of those testing positive is also a concernDetainees need access to screening and treatment of infectious diseases, such as HIV,upon entering the prison system. This is important not only for their own benefit butalso for the community to which they will eventually return.Research in the prison environment is always challenging. These challenges may includebureaucracy and the necessary cooperation of several stakeholders, including justice,security, and health personnel. Logistic issues include movement of the researcherwithin the facilities, lack of appropriate rooms for interviews, and unavailability ofthe prisoner due to justice appointments, meal time, cell transfers, courtyard time,lockdowns, and other security procedures.Therefore, despite the need for additional studies on HIV prevalence, screening,prevention, and treatment in imprisoned populations, the present evidence demonstratesthe usefulness of rapid tests using oral fluid as an accessible alternative forapproaching this high-risk population."} +{"text": "Objectives: To evaluate and compare practices regarding the diagnosis, isolation measures, and treatment of tuberculosis (TB) in high-income countries and mainly in Europe.Materials and Methods: A survey was conducted from November 2018 to April 2019 within the European Society of Clinical Microbiology and Infectious Diseases Study Group for Mycobacterial Infections (ESGMYC). The practices observed were compared to the main international guidelines.Results: Among 136 ESGMYC members, 64 (17 countries) responded to the questionnaire. In their practice, two (20.7%) or three sputum samples (79.3%) were collected for the diagnosis of pulmonary TB, alternatively induced sputum , bronchoscopy , and gastric aspirates . Nucleic acid amplification tests (NAATs) were performed by 41 (64%) respondents whatever the smear result and by 47 (73%) in case of smear-positive specimens. NAAT and adenosine deaminase measurement were used for extrapulmonary TB diagnosis in 83.6 and 40.4% of cases, respectively. For isolation duration, 21 respondents (42.9%) were keeping isolation until smear negativity. An initial treatment without ethambutol was offered by 14% (n = 9) of respondents. Corticosteroid therapy, cerebrospinal fluid opening pressure testing, and repeated lumbar puncture were carried out for central nervous system TB by 79.6, 51.9, and 46.3% of the respondents, respectively. For patients with human immunodeficiency virus\u2013TB coinfection, the preferred antiretroviral therapy included dolutegravir 50 mg twice a day (56.8%). Comparing with the recommendations of the main guidelines, the practices are not totally consistent.Conclusion: This study shows heterogeneous practices, particularly for diagnosis, and isolation, although rapid molecular testing is implemented in most centers. More standardization might be needed. In 2017, 10 million people were diagnosed with tuberculosis (TB) in the world , TB remaAn evaluation of TB case management in the EU/EEA countries, with special focus on MDR and XDR-TB, was conducted in 2010, using a standardized survey tool in five European centers. Deviations from international standards of TB care were observed in the following areas: surveillance (no information available on patient outcomes); infection control (lack of respiratory isolation rooms/procedures and negative-pressure ventilation rooms); clinical management of TB, MDR-TB, and HIV coinfection ; laboratory support; and diagnostic/treatment algorithms .A response to this need of harmonization has already been initiated through the development of European Union Standards for TB Care (ESTC) in 2012 with an update in 2017. They identified key standards for the diagnosis, management, prevention, and control of TB, MDR-TB, and XDR-TB. These standards aim to support health care workers in optimizing TB case management and thus at contributing to improved TB control in the EU/EEA . In factA survey was conducted from November 2018 to April 2019 among members of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), an offshoot of the ESCMID. The questionnaire was initially sent out on November 8, 2018, with subsequent reminders, the last being sent on March 15, 2019. The online questions comprised 63 items and focused on three topics: . DescripIn a second step, in order to understand the differences in the management of TB in high-income countries, we compared the participants' responses to the main principles of TB management according to the following international recommendations: Infectious Disease Society of America/Centers for Disease Control/American Thoracic Society (IDSA/CDC/ATS) guidelines , 13, Natn = 43/64) or clinical microbiology department. Sources of medical information for their practice were national guidelines alone for 8% (n = 5/64) of them, international guidelines only for 11% (n = 7/64), and an association of both for 64% (n = 41/64). TB specialist opinion was consulted, alone or together with other sources, by 50% (n = 32/64) of respondents. Among international recommendations, the main source was the WHO guidelines for 34% of respondents (n = 15/44).Among 136 ESGMYC members, 64 (47.1%) responded to the questionnaire representing 14 European countries , with 1\u201313 per country, and 3 non-European countries of respondents used to collect at least one sputum in the early morning on an empty stomach, with 19% (n = 12/64) and 81% collecting two or three samples, respectively. The two remaining responders collected induced or spontaneous sputum at admission or randomly timed sputum sample. Multiple samples are usually taken during 3 consecutive days , or 2 or within the same day . If the patient could not produce sputum, the alternatives were induced sputum , bronchoscopy aspirate , and gastric aspiration .For the microbiological diagnosis of pulmonary TB, 97% (n = 14/45) or multiple respiratory specimens . In case of strong suspicion of pulmonary TB with negative sputum smears, 16/64 (25%) respondents would start treatment, 11/64 (17%) would wait for the culture result before starting, and 44/64 (78.6%) would perform additional diagnostic tests, namely, rapid molecular tests (66%), or bronchoscopy aspirate testing (61.3%). In case of positive sputum smear, a rapid molecular test was performed to detect mutations conferring resistance to rifampicin by 84% (n = 52/64), to isoniazid by 29% (n = 18/62), and to other drugs by 7% (n = 4/62), whereas 10 (16%) did not perform any rapid molecular test. Regarding the type of mutation sought for isoniazid resistance, among the 26 microbiologists who gave an answer, 17 (65%) perform rapid molecular tests to detect mutations in both katG gene and the inhA promoter, and four only in the katG gene (15%). Eight respondents (31%) were looking for genotypic resistance to other drugs besides rifampicin and isoniazid, with five of them performing whole-genome sequencing.A rapid molecular test was performed systematically by 41/64 (64%) respondents, on one were asking for molecular detection of rifampicin resistance mutation, 24 (39%) for an isoniazid resistance mutation, and 9 (15%) for resistance mutations to other drugs, whereas 23 (38%) were not looking for genotypic resistance.n = 52/61 responses) and 40% (n = 25/62 responses) of cases, respectively. ADA was performed mainly for the diagnosis of pleural effusion , but also on the cerebrospinal fluid (CSF) in case of suspicion of TB meningitis and on peritoneal fluid . Sputum smear was repeated after 2 and 6 months of treatment by 53/63 (83%) and 37/63 (58%) participants, respectively. Overall, interferon-\u03b3 release assays (IGRAs) and tuberculin skin testing (TST) were performed by 31% (n = 20/64) and 23% (n = 15/64) of respondents, respectively, even for the diagnosis of active TB.For the diagnosis of extrapulmonary TB, nucleic acid amplification test (NAAT), and measurement of adenosine deaminase (ADA) were performed in 85% (n = 15/63) of respondents used a conventional single room to isolate pulmonary TB patients, whereas 77% (n = 50/63) reported using a negative-pressure room whatever the drug susceptibility profile of the strain. Regarding the duration of isolation for pulmonary TB with smear-positive sputum, 23/64 (36%) respondents adopted a standardized duration of 2 to 3 weeks, whereas 23/64 (36%) reported waiting for the sputum smear-negative conversion. In case of patients hospitalized with a suspicion of pulmonary TB but negative sputum smears and pending culture results, 18/64 (28%) of the respondents did not isolate the patient. Patients with a positive sputum smear were allowed to leave the hospital by 75% (n = 48/64) of respondents, in the following cases: if they agreed to wear a mask , if there were no other people at home , and in the absence of children or of immunocompromised individuals at home.Overall, 23% (n = 52/64) used the standard first-line treatment with isoniazid, rifampicin, pyrazinamide, and ethambutol for 2 months, followed by 4 months of treatment with isoniazid and rifampicin; but 14% (n = 9/64) of respondents offered an initial treatment without ethambutol. Fluoroquinolones were never prescribed as part of first-line treatment by 29/61 (45%) of respondents; conversely, 5/61 (8%) and 26/61 (41%), respectively, used them under certain conditions such as bone TB or suspicion of resistance to isoniazid. Overall, 30% (n = 19/63) of respondents reported to discontinue ethambutol treatment in the absence of mutations conferring resistance to isoniazid. Among respondents, 89% (n = 57/63) systematically gave B6 vitamin therapy. With regard to treatment monitoring, 50% (n = 32/62) of respondents performed an ophthalmology assessment during the first 2 months of ethambutol treatment. Overall, 50% (n = 32/64) of respondents never performed therapeutic drug monitoring for rifampicin and isoniazid, 17% (n = 11/64) routinely performed it, and 23% (n = 15/64) performed it only in specific cases . For neuromeningeal TB cases, 80% (43/54) of respondents added corticosteroids to the TB treatment for a variable duration, from 2 to 12 weeks . The measurement of CSF pressure and repeated lumbar punctures were performed by 51% and 46% of the 59 respondents, respectively. In case of HIV coinfection, the most frequently used antiretroviral drugs were dolutegravir 50 mg twice a day (BID) , efavirenz 600 mg daily , a protease inhibitor with rifabutin , raltegravir 800 mg BID , raltegravir 400 mg BID , and efavirenz 800 mg daily . All respondents offered preventive treatment to HIV-positive patients with latent TB infection, using the following: isoniazid for 6 months , isoniazid and rifampicin for 3 months , rifampicin for 3\u20134 months , or isoniazid plus rifapentine for 3 months . To optimize adherence and treatment support, clinicians used an interpreter , a nurse specialized in therapeutic education , systematic Directly Observed Therapy (DOT) , or hospitalization for the full duration of treatment . As an alternative to hospitalization, 39/64 (61%) offered a DOT at home with a nurse.A majority of respondents . The role of rapid molecular tests for resistance to isoniazid in guiding the withdrawal of ethambutol from the intensive phase treatment is yet unclear. The role of fluoroquinolones in first-line treatment, pyridoxine prophylaxis, CSF pressure measurement, and therapeutic drug monitoring should be better defined with additional studies. Similarly, monthly ophthalmologic monitoring of ethambutol patients is recommended only by the North American ATS/IDSA/CDC guidelines . On the It is difficult to analyze the variability of practices observed between the different respondents. There may be variability between countries due to different local recommendations but also a disparity of human or economic resources. The availability of medications, funding of TB programs, laboratory practice, staff availability, and TB epidemiology can differ between countries, but this phenomenon is probably lower in high-resource European countries than on other continents. Furthermore, in our survey, 7% of respondents used only local recommendations for TB care management, whereas 78% also relied on international recommendations, which should also limit the variability between countries. It must also be emphasized that interindividual variability within the same country is possible. Although the respondents are among the TB experts for each country, their management practice cannot be fully representative of their respective countries. For instance, the practice survey conducted in France in 2013 with specialists in infectious diseases, pneumology, and internal medicine showed that different doctors often had very different habits concerning the treatment of TB or the isolation of active TB . FinallyThe ISTC defined the essential level of care for managing patients who have or are presumed to have TB or are at increased risk of developing the disease. In a high-resource setting, such as the EU/EEA, higher standards of care can be attained with regard to TB diagnosis, prevention, and treatment. On this basis, the ESTC was published in 2012 as standards specifically tailored to the European setting. Since the publication of the ESTC, new scientific evidence has become available, and therefore, the standards were reviewed and updated in 2017. Despite these new standards tailored to the EU setting, the harmonization of practices needs to be further improved. This is conditioned by a better standardization of national and international recommendations, a wider communication with people in charge of TB, and complementary studies to increase the level of evidence on controversial aspects of TB care. If we take the example of the joint ERS and ESCMID guidelines on the management of infections due to nontuberculous mycobacteria, which are being updated, collaboration between the various European academic societies would probably be beneficial.Our study has several limitations. First, our sample is too small to be representative. Second, the responders were selected within the ESGMYC group, with mainly microbiologists and infectious disease specialists. Therefore, this sample does not include a lot of pulmonary physicians, although they are also very involved in TB care. Third, as mentioned above, the management practice of the responders could not be fully representative of their respective countries. Nevertheless, we think that this survey gives an interesting overview of different practices in Europe and highlights a heterogeneity in the management of TB that should be confirmed by a study with larger sample. In conclusion, WHO's international recommendations for TB management are focused on countries with high incidence. Recommendations that are more adapted to the European socioeconomic and epidemiological context have also been developed under the auspices of the ERS and the ECDC. This study shows that the management of TB is probably still heterogeneous within high-income countries, in particular for the prevention of transmission and the treatment. Concerning microbiological diagnosis, the practices seem to be better standardized, as rapid molecular testing takes an important role across most European centers. With the main objective of control and eventual elimination of TB, it seems necessary to better harmonize and disseminate the recommendations for the management of TB in Europe. European scholarly societies, and in particular ESCMID, should play a prominent role.The datasets analyzed in this article are not publicly available. Requests to access the datasets should be directed to frederic.mechai@aphp.fr.All authors participated in the writing and editing of the article, the analysis of the data as well as the dissemination that the investigation at the origin of this work.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "In poultry production, consuming diets with low or excessive methionine levels leads to negative effects on growth performance. The requirements of methionine may differ among the fast and slow-growing breeds; therefore, the optimal dietary methionine level should be estimated for each. In this study, six dietary methionine levels were evaluated to estimate the optimal level for fast and slow-growing yellow feathered chicken breeds. The quadratic polynomial and exponential asymptotic regression showed that the optimal methionine requirements for maximal growth performance were 0.50% and 0.53% in the fast-growing breed, and 0.48% and 0.52% in the slow growing breed.Two experiments were carried out to investigate the dietary methionine requirement for fast and slow-growing Chinese yellow-feathered breeds during the starter phase, based on growth variables and regression models. In Experiment 1, a total of 2880 one-day-old Lingnan chicks (fast growing breed) were used to test the methionine requirement from 1 to 21 days of age for males and females separately. Of each gender, 1440 birds were allocated into 6 dietary methionine levels , each with 6 pen replicates of 40 chicks. Experiment 2 had the same design with Guangxi chicks (slow growing breed) from 1 to 30 d of age. Results indicated that significant nonlinear or quadratic responses to increasing dietary methionine levels were observed in body weight, daily gain, feed intake and feed conversion ratio of both breeds. In summary, the quadratic polynomial regression showed that the optimal methionine requirements for maximal growth performance of Lingnan chickens were 0.52\u20130.58% in males, 0.51% in females, and 0.53% in mixed genders. The corresponding values for Guangxi breed were 0.53% in males by quadratic polynomial regression and 0.43% in females, and 0.48% to 0.49% in mixed sexes by exponential asymptotic models. With the rapid development of economy in China, the second largest worldwide producer of chicken meat, market demands for nutrient-rich and tasty meat have been in continuous increase, which is boosting the industry of Chinese yellow-feathered chickens. The contribution of such chicken type in production has been growing; 3.7 billion birds annually with more than 30% of whole chicken meat shares in recent years . The indSome essential amino acids are often added as pure to poultry diets to ensure the optimal balance required for poultry in order to maximize the production efficiency. Globally, methionine (Met) is considered to be the first limiting amino acid for poultry fed on typical corn\u2013soybean meal-based diets . Met is Chinese yellow-feathered chicken is a general name, which consists of quite a few breeds, mainly referring to Chinese local breeds and the improved breeds. Chinese yellow-feathered chickens grow slowly and are reared for a longer time compared with white-feathered broilers. The Lingnan yellow-feathered chicken breed is classified according to its growth rate to fast , medium , and slow growing ,16. The The Met requirement of feeding standard of chicken (CNY/T33-2004) is mainly for medium-growing yellow-feathered broilers . As the Two experiments were carried out to estimate the Met requirement for Lingnan (Exp1) and Guangxi (Exp2) yellow-feathered chicken breeds following the same experimental design. Before trial, the Met content of the basal diet ingredients used in both experiments was determined by ion-exchange chromatography on an automatic amino acid analyzer , according to the procedures described by Xi et al. . In eachPelleted feed and drinking water were freely available to chicks. The different diets were prepared three weeks prior to the trial to allow time for checking content homogeneity, in terms of dry matter, ash, crude protein, ether extract, crude fiber, and amino acid concentrations.Birds were weighed at the beginning (day 1) and end of each experiment to record the initial and final body weights (FBW), which were used to calculate the average daily gain (ADG). Average daily feed intake (ADFI) was measured on a per pen basis for the entire experimental period, and the feed conversion ratio (FCR) was calculated. Mortality was checked daily and dead birds were weighed in order to adjust the feed intake calculations.p < 0.05. All data were expressed as means and SEM, derived from ANOVA error mean square. When the main effect was significant (p < 0.05), linear and quadratic effects of Met content were determined. For key performance variables, the dietary methionine requirement of the birds was estimated using quadratic polynomial (QP) or exponential asymptotic (EA) models by the NLIN procedure of SAS .Data were subjected to one-way ANOVA using the GLM procedure of SAS . Tukey\u2013Kramer test was used for means comparison, and pairwise comparisons among the means were assessed by Duncan\u2019s multiple-range tests at QP model:2), Akaike information criteria (AIC) and mean square error values (MSE).EA model:ic point ,19,20. Tp < 0.01; quadratic, p < 0.01) of males; and final BW, ADG and FCR of females; and final BW, ADG and ADFI of mixed genders. According to the EA and QP regression, the optimal dietary Met level for the highest body weight were 0.54% and 0.55% in males, 0.47% and 0.51% in females, and 0.50% and 0.53% in mixed genders. The corresponding EA and QP values for the highest ADG were 0.54% and 0.55% in males, 0.47% and 0.51% in females, 0.50% and 0.53% in mixed genders. With regard to these results, it is worth mentioning that obtaining the same optimum Met requirement value for maximal final BW and ADG is logically expected; certainly, because these two variables are linearly correlated, where the ADG is calculated as the /days. This, therefore, led to the same values of R2 and the same calculated Met requirements for these two variables , ADG and ADFI of males; final BW, ADG, and ADG of females; and final BW , ADG , and ADFI of mixed genders. According to the EA and QP regression models, the optimal Met for the highest final BW were 0.51% and 0.53 in males, 0.43% and 0.51% in females, and 0.48% and 0.52% in the mixed males and females. The EA and QP indicated that the optimal Met for the maximal ADG were 0.51 and 0.53% in males, 0.43% and 0.51% in females, and 0.48% and 0.52% in mixed genders. Additionally, the QP model showed that 0.49% was optimal for the best FCR in mixed genders. Fitness of the two growth performance models are shown in 2, lower AIC and MSE values, in estimating the optimal Met requirement , but the EA function was better fitting for females and mixed sexes. The QP models predicted the requirement of Met for males as 0.53%, and the EA models predicted the requirements of Met for females and mixed genders as 0.43% and 0.48% to 0.49%, respectively.The growth performance results of male, female and mixed genders of Guangxi yellow-feathered chickens as affected by dietary Met levels between 1 and 30 days of age are shown in uirement a,b for gDiets having low or excessive Met levels could engender important influences on poultry performance . An optiThe Met requirement of Chinese yellowed-feathered chicks (unsexed) was 0.46% at the starter phase, according to the old estimations of . AccordiSupplementation of graded Met levels in basal diets of yellow feathered broilers during the starter period showed beneficial influences on their growth performance indices. The results indicated that the optimal Met requirement differed between the fast (up to 21 d of age) and slow-growing (up to 30 days of age) yellow-feathered chicken breeds as well as between males and females of each breed. The QP regression model was more appropriate for estimating the optimal Met requirements for the best body weight, average daily gain, feed intake and FCR indices of Lingnan (fast-growing) males (0.52% to 0.58%), females (0.51%), and mixed genders (0.53%), as well as for Guangxi (slow-growing) males (0.53%), whereas the EA model was found to be better for estimating the optimal Met requirement of Guangxi females (0.43%) and mixed genders (0.48% to 0.49%)."} +{"text": "Ensuring health literacy among underserved populations is essential amid an aging population. Accessible and appropriate information is important when considering digital media education for older Chinese Americans.This study aims to investigate how social media fare over time in disseminating health information and how we may most effectively educate this population.For this study, 5 geriatric-themed educational videos about Parkinson disease, fall prevention, gastrointestinal health, oral health, and pulmonary disease were uploaded to YouTube. Data were collected over a 40-month period. Descriptive statistics and chi-square analysis were used to compare results from the first and second 20-month periods.In 40 months, the 5 videos in aggregate accrued 1171.1 hours of watch time, 7299 views, and an average view duration of 9.6 minutes. Comparing the first and second 20-month periods, there was a significant increase in mobile device usage, from 79.4% (3541/4458) to 83.3% (2367/2841). There was no significant difference in the usage of various external traffic sources and methods of sharing, with WhatsApp accounting for the majority of sharing in both 20-month periods.Our study provides insight into where to focus future strategies to optimize digital media content, and how to best recruit, direct, and disseminate health education to an older adult Chinese American population. Combining the success of YouTube, social media, and messaging platforms such as WhatsApp can help to transcend cultural and linguistic barriers to promote healthy aging. By the year 2060, there will be roughly 98 million Americans aged over 65 years, roughly 1 in 5 people, in large part due to the aging baby boom generation . ChallenThe older adult population is not only growing, but also becoming more racially and ethnically diverse, making inequities in health and access to resources more apparent . NationaAmid an aging population, distribution of health education over the internet and social media can contribute to healthy aging. Today, more and more Americans turn to the internet for health information. Social media has transformed into a platform for health communication among the general public, patients, and health professionals . Among tPrevious studies have shown that YouTube is effective in delivering dementia knowledge to older Chinese Americans -14. AnotA board-certified psychiatrist delivered 5 geriatric-themed educational talk shows in Cantonese at the radio station KMRB AM1430 in Los Angeles. Real-time recordings were then individually uploaded to YouTube. Average video length was 36.4 minutes. Topics addressed include Parkinson disease, fall prevention, gastrointestinal health, oral health, and pulmonary disease.The sample of this study included YouTube video viewers over a 40-month period (November 2016 to March 2020).Data were extrapolated from YouTube Analytics. Parameters recorded included number of views, watch time, average view duration, devices used to view, traffic sources, and modes and means of sharing via various social media platforms. The first and second 20-month intervals were dichotomized . Descriptive statistics and chi square test were used to compare data collected between the first and second 40-month intervals.This study used anonymous data exclusively collected by YouTube. A waiver for Institutional Review Board exemption was obtained through the Human Subjects Protection Committee of University of California, Los Angeles.In 40 months, the 5 videos in aggregate accrued a total of 1171.1 hours of watch time and 7299 views, and an average view duration of 9.6 minutes. A breakdown of each of the 5 video topics is shown in \u03c721=17.0, P<.001; Average view duration on computers increased 13.0% from 8.4 to 9.5 minutes between the first and second 20-month periods. In comparison, average view duration on mobile devices (mobile phones and tablets) decreased 6.9% from 10.9 to 10.2 minutes. Despite an overall decrease in views in the second 20-month period, the relative usage of computers decreased from 20.6% (917/4458) to 16.7% (474/2841), while relative mobile usage increased from 79.4% (3541/4458) to 83.3% (2367/2841). The increase in relative mobile device usage compared to computer usage from the first to the second 20-month period is statistically significant or WhatsApp between the two 20-month periods and 6.9% (198/2841) of views, respectively. Of external sources, the top platforms were Facebook, Google search, and WhatsApp. Over 40 months, traffic generated from Facebook drastically decreased from 1.8% to 0% of total views (82/4458 versus 0/2841), Google search increased from 0.9% to 1.4% of total views (41/4458 versus 39/2841), and WhatsApp decreased from 0.8% to 0.5% of total views (34/4458 versus 15/2841). Despite the significant drop in Facebook-generated traffic, there was no significant difference in traffic generated through Google search to 83.3% 2367/2841) over the 40 months, while computer usage decreased from 20.6% (917/4458) to 16.7% (474/2841). As there is a continued shift from computer to mobile device usage, ensuring mobile device compatibility in future digital health communication should be a priority. Furthermore, it becomes important to examine and understand any barriers and challenges that this population faces to better shape the design of future platforms and systems of health-related communication via mobile device. Barriers and challenges may include functional limitations such as visual or motor impairment, having low technology literacy, or being adverse to new methods. Work can be done to develop more user-friendly interfaces to maximize potential use among older adults. The development of user-friendly interfaces is not limited to only mobile device but extends to the development of future technologies such as voice-activated speaker devices, and the growing number of products on e-commerce platforms tailored for an aging population ,23.67/2841 oWith regards to external traffic sources, while there was a significant decrease in Facebook-generated traffic, there was no significant change in Google search and WhatsApp traffic. Our study reveals an increase in Google search from 0.9% to 1.4% of total views (41/4458 versus 39/2841) and a decrease in WhatsApp from 0.8% to 0.5% of total views (34/4458 versus 15/2841). Although WhatsApp remains the top sharing service, there was no significant change in the amount of sharing that occurred between the two periods. Taken together, this study entertains questions of how to increase visibility via Google search amid a saturating field, and how to promote viewer sharing via WhatsApp. For example, future studies can investigate whether using long tail keywords (more specific keyword phrases) increase visibility via Google search.It has previously been shown that digital recruitment via Facebook and, more recently, Instagram, is promising in directing individuals to health education materials ,17,24. HFinally, previous studies have shown that WhatsApp has become the preferred means of sharing dementia knowledge and is used more for its sharing capability than for its viewing function ,19. AlthThere are several limitations in this study. As the videos used in this study were filmed in Cantonese, the audience was limited to those in the Chinese American population who are fluent in Cantonese. Furthermore, each video retained a rather short average viewing duration of 9.9 to 9.1 minutes, which is a fraction of the average video length of 36.4 minutes. Future studies should consider shortening video lengths and incorporating more interactive elements to increase audience engagement time with the goal of improved audience experience and greater retention of educational information. As a retrospective longitudinal analysis, data collected were limited to that collected by YouTube Analytics. Being able to design a prospective study would enable us to focus on WhatsApp as a sharing service, or the effectiveness of various recruitment methods.The internet and usage of social media are continually evolving and changing the way in which we communicate health information among individuals and the medical community. YouTube is a promising and valuable tool to deliver culturally and linguistically appropriate health education to isolated populations. More studies need to be done to harness technologies now available on mobile devices with meaningful improvement in the health of older adults. In addition, future studies could investigate how WhatsApp can achieve its full potential as a top platform for health information dissemination. As such, further studies looking at both short- and long-term strategies and outcomes are necessary to learn how different populations of interest search for and disseminate information to best be able to serve and deliver pertinent health education, ensure healthy aging, and promote healthy outcomes."} +{"text": "During March 2018\u2013May 2019, an outbreak of 4,115 measles cases occurred in Israel, following international importations, mainly from Ukraine. Approximately one half of the cases occurred in residents of Jerusalem District, primarily in unvaccinated children in orthodox Jewish communities. The district\u2019s population is 70% Jewish, approximately one third of whom are orthodox Jews. Children in those orthodox communities have lower rates of routine vaccination coverage; for measles vaccine, first dose coverge is 78.4%, compared with 90.1% among children in all other communities. Measles outbreak control in communities with long-standing inadequate vaccination coverage is challenging . Cases were confirmed by reverse transcription\u2013polymerase chain reaction testing or detection of measles-specific immunoglobulin M in 708 (32%) patients and by epidemiologic linkage in 1,494 (68%). Approximately 8% of patients (176) were hospitalized .Jerusalem District Health Office teams conducted case finding and confirmation and contact tracing and distributed updates to health care providers. Measles patients and their parents were instructed to self-isolate; however, epidemiologic investigations revealed inadequate adherence. Infectious patients participated in crowded social events, attended child-care facilities, and used public transportation. Because of the large number of close contacts, tracing proved challenging. Outbreak response measures involved providing postexposure prophylaxisThe emergence of a large number of measles cases and the very high incidence among young children in the orthodox communities engendered parental and societal anxiety and concern. Rabbinic leaders supported the vaccination campaign by issuing positive written statements, resulting in high levels of acceptance and compliance with control activities at the peak of the epidemic. Following the campaign, first-dose measles vaccination coverage in all maternal-child health clinics in orthodox neighborhoods increased from 76.3% in June 2018 to 96.1% in November. Since December 2018, the number of cases has decreased considerably. During October\u2013December 2018, Jerusalem District accounted for 66% of all measles cases in Israel; that percentage declined to 25% (248 of 969) during January\u2013April 2019. As measles outbreaks continue to spread globally ("} +{"text": "According to USA organic standards, farmers can apply a certified allowable insecticide when all non-chemical practices fail to control pests. However, there exists a lack of control efficacy information to enable decision-making about which organic product works best for a given target pest. In this study, we conducted 153 field trials on different host crops to evaluate the control efficacy of common active ingredients in organic insecticides against insect pest groups considered difficult to control in organic production. The performance of organic products Entrust (spinosad), Azera (pyrethrin and azadirachtin), PyGanic (pyrethrin) and Neemix (azadirachtin) varied widely among pest groups, as well as among pest species within a group, providing an overall reduction in pest infestations by 73.9%, 61.7%, 48.6% and 46.1%, respectively. Those insect pests that were particularly difficult to control included thrips, stinkbugs, cucumber beetles and fruitworms. Several caveats pertaining to the application of the results are discussed.There exists a lack of control efficacy information to enable decision-making about which organic insecticide product works best for a given insect pest. Here, we summarize results of 153 field trials on the control efficacy of common active ingredients in organic insecticides against 12 groups of the most difficult to control insect pests. These trials evaluated primarily the organic products Entrust (spinosad), Azera (pyrethrin and azadirachtin), PyGanic (pyrethrin) and Neemix (azadirachtin), which reduced pest infestations by an overall 73.9%, 61.7%, 48.6% and 46.1% respectively, averaged across all trials. Entrust was the most effective control option for many insect pests, particularly providing >75% control of flea beetles, Colorado potato beetle, cabbageworms and alfalfa weevil, but was relatively ineffective against true bugs and aphids. Azera provided >75% control of green peach aphid, flea beetles, Japanese beetle, Mexican bean beetle, potato leafhopper and cabbageworms. PyGanic was less effective than Entrust and Azera but still provided >75% control of green peach aphid, flea beetles and potato leafhopper. The growth inhibition effects of azadirachtin in Neemix were particularly effective against larvae of Mexican bean beetle and Colorado potato beetle but was generally less effective in trials with insect infestations consisting mainly of adult stages. Those insect pests that were particularly difficult to control included thrips, stinkbugs, cucumber beetles and fruitworms. Several caveats pertaining to the application of the results are discussed. Organic production in the U.S. has experienced phenomenal growth since the 1990s, with double-digit increases in the number of certified farms during most years and current production accounting for 5.8% of total food sales in 2019 providesSaccharopolyspora spinosa . We then pooled the percent control means of all trials for each pest/crop group to represent the overall control efficacy of the insecticide. This pooled dataset only included data from trials with consistent pest densities high enough to rigorously test for treatment effects. The pooled results for each insecticide were visualized with box-whisker plots to display the percent control data of individual trials, the 25% and 75% percentile range of the trial data and the overall mean control efficacy. We calculated the 95% confidence limits (95% CL) around the mean using a Student\u2019s t distribution to indicate significant differences in overall control efficacy among insecticides tested for each pest/crop group.We analyzed data from each trial as a randomized block analysis of variance (ANOVA) using SAS Proc Mixed to test Thrips are major pests causing direct and indirect damage to many field and greenhouse-grown crops worldwide . In orgaResults of thrips control are summarized in We measured onion yield in four trials but only one showed a significant yield increase in the Entrust plots. Moreover, there was no significant relationship in any trial between thrips numbers and yield; thus, the level of control was apparently not high enough for treatments to show a yield response or the onion plants compensated for the injury. Variation in control among trials, particularly for Azera, Neemix and PyGanic, was noticeably greater for flower thrips. In several trials, densities in treated plots averaged higher than levels in untreated plots. The variable results were most likely due to differences in species composition, ratio of adults to larvae and disproportionate levels of insecticide coverage on flower heads. Several studies reported that the direct contact and systemic activity of neem-based formulations resulted in high mortality of early larvae but had no effect on older larvae and adult thrips ,27. In cOur results agree with other studies reporting 42% to 62% control of onion and flower thrips with Entrust, and generally ineffective control <30%) with products containing pyrethrin, azadirachtin or combinations of both % with pr,37,38,39Aphids are common pests of most major families of organic crops . Their pBrevicoryne brassicae) were also present in several trials but densities were not high enough to discern treatment effects. GPA infestations averaged 23.3 per plant and ranged up to 58 per plant in untreated plots. Each insecticide was applied weekly either two or three times depending on the trial. Overall, control efficacy averaged 78.3%, 52.6% and 75.1% for Azera, Neemix and PyGanic respectively, but overlapping 95% CL indicated no significant differences. Three trials in 2006 showed a small but consistent increase in control efficacy with treatments of PyGanic applied with different adjuvants . A weekly treatment schedule of Entrust at the standard rate was also tested against GPA in two collard trials and gave <40% control.For PA, we applied a single application of each insecticide in seven alfalfa trials. Untreated infestations ranged from 3.5 to 11.5 aphids per sweep, which was below the reported economic threshold of 30 aphids per sweep ; howeverAphis glycines) by 47%, but control was significantly less than the PyGanic treatment.We evaluated other organic products and treatment combinations for aphid control in several trials. A greenhouse trial in 2008 tested several soap and oil products against a heavy infestation of GPA on pansy bedding plants. Compared to the control, Ultra-Pure oil at 2% v/v, M-Pede at 2% v/v, Trilogy at 2% v/v and Oroboost at 4% v/v provided 62.5%, 42%, 34% and 28% control, respectively. No signs of phytotoxicity were evident with any of these treatments. Oroboost at 4% v/v and Ecotec at 1.17 L/h, when each were applied alone in two alfalfa trials, provided no control of PA. In a 2015 soybean trial, two weekly applications of Des-X at 2% v/v reduced a high infestation of soybean aphid per plant, starting when crown fruit reached marketable size. After five days to allow nymphs to acclimate, we applied two treatments three days apart of each insecticide alone and in combination with other products. Treatments that significantly reduced nymphal densities included Azera at 2.34 L/h (79.2%), PyGanic at 4.68 L/h (73.3%) and Entrust at 71.2 g a.i./h (84.5%). Treatments that were less effective included M-Pede 2% v/v (46.8%) and PFR 97 at 1.68 kg/h (22.7%). We also did not observe any significant gain in nymphal control with Entrust or Azera in combination with M-Pede.Other studies have reported variable control efficacy of STB with organic insecticides, which are consistent with our findings on Azera, PyGanic and Entrust. Laboratory bioassays have shown that pyrethrin, pyrethrin combined with azadirachtin, spinosad, azadirachtin, and insecticidal soaps have activity against STB ,69,70. HFlea beetles are common pests of many cruciferous and solanaceous crops. They are difficult to control with organic insecticides because they feed on more protected parts of the plants and can quickly recolonize fields after treatment . FeedingThe standard rates of Azera, PyGanic and Entrust significantly reduced flea beetle populations by an overall 73.6%, 76.6% and 77.4%, respectively . AlthougOur findings align closely with other field studies testing organic materials against different species of flea beetles. Taken together, most studies show consistently high levels of flea beetle suppression with Entrust and PyGanic, but limited efficacy with azadirachtin products ,77,78,79Erwinia tracheiphila, which is transmitted to susceptible cucurbits as beetles feed on young plants. These beetles are particularly difficult to manage with short-residual organic insecticides because they quickly re-invade after treatment and are often sheltered from insecticide sprays during the day in soil cracks or under the straw or plastic mulch.Cucumber beetles colonize fields shortly after seedlings emerge or are transplanted and feed on the cotyledons and young leaves, which either kills plants or greatly retards their growth . More imWe evaluated organic insecticides in four cucumber trials and two zucchini trials that were direct-seeded in fields that had a history of cucumber beetle activity the previous year. Trials received two or three weekly applications, starting a few days after plant emergence when beetles were active. In all trials, moderate to high populations of striped cucumber beetles caused significant leaf and cotyledon injury, with several trials showing bacterial wilt symptoms during later plant growth. Infestation densities in untreated plots ranged from 1.6 to 3.1 beetles per seedling. Pooled over trials, the overall reduction of beetles relative to the control averaged 48.7% for Azera, 46.1% for Neemix, 39.4% for PyGanic and 56.2% for Entrust . All treLaboratory bioassays have documented that permethrin can cause high mortality of striped cucumber beetles and extracts of neem have antifeedant effects on adults ,82. HoweJapanese beetles (JB) cause defoliation injury to over 300 plant species and can significantly reduce the marketable quality or aesthetic value of many horticultural crops . We evalTrial results of percent control at two and four days post-treatment in Other studies have reported evidence of residual repellency and feeding deterrent activity on JB with foliar applications of azadirachtin ,88,89,90The Mexican bean beetle (MBB) ranked ninth in importance out of 29 problem insects identified by organic farmers . OverwinWe conducted nine trials in different years on late plantings of snap beans. To attract a high infestation, we established an earlier untreated plot at each trial location to serve as a nursery for MBB population buildup. In all trials, adult beetles invaded plots during the early vegetative stages and larval infestations reached damaging levels prior to bloom. Percent defoliation in untreated plots ranged from 28% to 73%, and late larval densities ranged from 5 to 17 per plant. Each treatment was applied weekly either 4 or 5 times depending on the trial, starting as soon as the first egg masses hatched.The knockdown and direct toxicity effects of PyGanic resulted in significantly less control against larvae (52.2%) but still reduced defoliation by an overall average of 73.5%. In several trials, treatments of PyGanic with different adjuvants showed a slight gain in control but not significantly different from PyGanic alone. Entrust was tested in only four trials and showed similar but more variable levels of control efficacy (53.4%). We also pooled data on adults recorded in seven trials, which showed mean control efficacy ranging from 12% to 83% for Azera, 10% to 82% for Neemix and 10% to 68% for PyGanic. Effects on adults were more variable due to inter-plot movement during the treatment period of each trial. Other tested organic products included Surround WP applied in combination with 1% v/v Trilogy, which reduced late larvae densities by 24.8% and defoliation by 39.3%. Similarly, combining Surround with Azera provided very little additional control compared to Azera alone. Aza-Direct, another azadirachtin product, applied at 2.34 L/h, reduced levels of late larvae and defoliation that were similar to those provided by Neemix.There is considerable research published on controlling MBB with conventional insecticides and nonchemical approaches ; howeverPotato leafhopper (PLH) is major pest of potatoes and legumes, such as snap beans, dry beans and alfalfa, but also infests other horticultural and field crops . Nymphs We evaluated Azera, Neemix and PyGanic for PLH control in four trials of snap beans, five trials of alfalfa and six trials of potato. Treatments were applied weekly for an average of 1.6, 2.7 and 2.5 applications on alfalfa, potato and green beans, respectively. Since Entrust is not labeled for PLH and previous trials have indicated poor control, we tested the standard rate in only three trials. Treatments commenced when adults began to invade plots or when adult densities exceeded one per sweep, depending on the crop. PLH infestations reached moderate to high levels in most trials, causing noticeable yellowing and leaf curl injury by the end of the treatment period. Average densities in untreated plots ranged from 1.1 to 6.2 adults per sweep or 1.3 to 6.4 nymphs per leaf, depending on the trial.\u22121 averaging 87.6% control compared to 76.9% control at the standard 2.34 L/h rate. The addition of the adjuvant Oroboost with Azera resulted in no improvement in control. In several trials, PyGanic with different adjuvants also showed only slight gains in control and not significantly different from PyGanic alone. Control efficacy of Azera and PyGanic was mainly due to the knockdown and direct mortality effects of pyrethrin on adults and nymphs, while the repellency and antifeedant effects of Neemix provided poor control of adults and only moderate but highly variable efficacy against nymphs. Neemix performed better in trials with earlier infestations of developing nymphs that allowed more time for the IGR effect to work during the treatment period.Trial results for adults and nymphs are given separately in Of the three trials testing Entrust, control was consistently less than 10%; however, control efficacy increased to 75.2% when Entrust was applied in combination with 1% v/v M-Pede in one trial. PyGanic formulations alone or in combination with Neemix have provided satisfactory control of adults and nymphs in other trials, while Neemix alone has been ineffective ,103,104.Other types of organic products evaluated for PLH control were only moderately effective. In several trials, M-Pede at 2% v/v, Oroboost at 4% v/v, Ecotec at 1.17 L/h and Des-X at 2% v/v applied alone reduced PLH numbers by 18.1%, 32.4%, 30.8% and 38.6%, respectively. These findings are in general agreement with published results on leafhopper control but provide a quantitative assessment of the range in control efficacy of these insecticides.Colorado potato beetle (CPB) can cause complete loss of a potato crop if not controlled and inflicts economic damage to eggplant when infestations are high. Control is very challenging, even for conventional farmers, owing to the insect\u2019s ability to develop resistance to insecticides. Seaman et al. recommenWe conducted 14 potato trials to evaluate different organic insecticides and treatment combinations against CPB. Treatments were initiated when the first-generation population exceeded 40 small larvae per 10 plant hills, and either 2 or 3 weekly applications of each insecticide were applied depending on the trial. Populations of CPB were consistently high in all trials, causing 36.6% to 73.3% defoliation and up to 53% tuber yield loss in untreated plots. Although all stages were sampled, densities of adults, egg masses and early instars (1st and 2nd instars) were highly variable and did not show any significant treatment effect in most trials. Older larvae (3rd and 4th instars) caused the majority of feeding injury, and thus reductions in their density and resulting defoliation provided better indicators of the control effectiveness of each insecticide. Numbers of older larvae in untreated plots ranged up to 22.2 per plant hill.In comparison, Azera (71.4% control) and Neemix (63.3% control) were less effective but still gave relatively good control of late larvae at the standard rate. The feeding deterrent and IGR effects of azadirachtin had a greater impact on larval development than was evident by the observed reductions in larval numbers, because both insecticides reduced defoliation by about 86%. Such reduction in leaf damage would be acceptable economic control in organic potato production because plants can normally withstand up to 30% defoliation without yield loss. Neem extract products inhibited feeding of adult and larval CPB in laboratory studies ,106,107 PyGanic was the least effective treatment and more variable across trials, reducing larval densities and defoliation by only 14.7% and 34.3%, respectively. CPB is known to exhibit resistance to pyrethroid insecticides , which iTrichoplusia ni) and diamondback moth (DBM) are common insect pests of cole crops. Mixed infestations of these caterpillars can cause extensive feeding injury on the leaves and head of cabbage, broccoli, cauliflower and other crucifers, resulting in contaminated and unmarketable produce [Imported cabbageworm (ICW), cabbage looper , collards and broccoli . ICW was the predominant cabbageworm, comprising 70% of the infestations with densities ranging from 0.6 to 23.3 larvae per plant in untreated plots. Lower DBM densities ranged from 0.7 to 3.6 larvae per plant but were still consistently high enough to discern treatment differences. Feeding injury caused significant reductions in head development and subsequent >50% losses in marketable yield in untreated plots. Because ICW was the predominant pest, we applied the first application when adult butterflies were active and eggs were hatching. Each insecticide was then repeated weekly either 3 or 4 times depending on the trial. Control efficacy was indicated by the percent reduction in cabbageworm density and the percent of marketable plants at the end of the treatment period. Broccoli heads were marketable if no caterpillars and feeding injury were present, while cabbage heads and collard plants were marketable if only the outer leaves had minor damage. Since treatment differences were relatively the same for the three crops, we combined the efficacy data on each insecticide across all trials.Control effectiveness of Neemix and PyGanic was more variable and significantly lower compared to Azera and Entrust. Moreover, both insecticides were less effective against DBM compared to ICW . Percent of marketable plants in Neemix and PyGanic-treated plots ranged from 59% to 83% compared to less than 20% in untreated plots. DBM has a long history of developing resistance to many insecticide classes, including pyrethroids ; thus, rWe also evaluated other organic products in a number of trials. Agree WG (841g/h) and Javelin WG (1.7 kg and 3.4 kg/h) provided similar levels of control in four trials, averaging 78% and 82% reduction of DBM and ICW respectively, and resulting in 71% to 84% marketable cabbage and broccoli heads. Bt insecticides have been widely used to control lepidopteran larvae but are relatively short-lived and more effective on early instars. Nevertheless, the control efficacy of the Bt treatments was about the same as Azera. Treatments of Surround WP plus 1% Trilogy reduced cabbageworm densities by an average of 51.3% across three trials. Our results corroborate the findings on cabbageworm control by other field studies that reported 85% to 99% control with spinosad-based insecticides ,119,120,Several curculionid species are major pests causing feeding injury to fruiting structures, leaves and roots of organic crops. However, information on the control efficacy of organic insecticides against these pests is very limited. Given the increased demand for organic dairy feed , we evalEntrust at the 71.2 g a.i./h rate reduced larval populations by an overall 86.8% compared to the other insecticides that provided <30% control . DoublinThe higher rates of Azera and PyGanic showed some additional suppression but still not enough to be effective control options. Neemix was also relatively ineffective, yet laboratory studies have shown high mortality, repellency and IGR effects of azadirachtin extracts against AW and other curculionids ,130,131.Several types of lepidopteran larvae are major pests of fruit and vegetable crops in organic production. The predominant species is the corn earworm (CEW) (or tomato fruitworm) that feeds internally near the stem end of the tomato and pepper, creating a messy, watery cavity contaminated with excrement and cast skins . The damWe evaluated the control efficacy of different organic insecticides against fruitworms in nine trials on trellised tomato plantings and six trials on sweet corn. All trials were planted later in the growing season to increase the chance of higher infestations. On tomato, mixed infestations consisted of CEW, yellow-striped armyworm and variegated cutworm, together causing an average 18.6% of the fruit damage in untreated plots across all trials. Insecticide treatments were initiated at the beginning of fruit set and repeated weekly five times to cover the fruiting period in each trial. At 6 days following each treatment, we harvested all ripe fruit to record the number of damaged fruits.In two trials, four weekly applications of Deliver at 1.1 kg/h resulted in 92.8% reduction in fruit damage, and five weekly applications of Gemstar at 731 ml/h significantly reduced CEW-damaged fruit by 89.5%. However, fruitworm infestations were well below economic levels in both trials. In general, our results agree with other field studies that report reductions in fruitworm damage ranging from 35% to 78% for Entrust, 65% to 78% for Bt products and 42% to 68% for Gemstar ,141,142.In sweet corn trials, treatments were applied at 25% to 50% silking and repeated on a 2-, 3- or 4-day schedule depending on the trial and moth activity. The number of applications per trial ranged from five to nine treatments. We sampled 50 ears per plot at fresh market maturity to determine the percentage of ears damaged. In all trials, heavy CEW infestations caused significant kernel injury to 50% to 95% of the ears in control plots. Due to differences in spray schedules, treatments tested and CEW population pressure, we did not combine control efficacy data across trials.Overall, Entrust, applied at the standard 71.2 g a.i./h rate, provided the most effective control of CEW compared to the other treatments. Since Entrust was approved for organic use in 2003, other studies have reported effective control with Entrust ,148,149,Of other products tested, Azera, Neemix and PyGanic were relatively ineffective compared to Entrust. The Bt product, Deliver, applied alone and mixed with vegetable oil injections in the silk tube, also gave unsatisfactory control in a 2002 trial , which aOur results compiled over multiple trials during different years provide the first quantitative assessment of the range of control efficacy by Entrust, Azera, PyGanic and Neemix against the most difficult to control insect pests in organic production. The performance of these insecticides varied widely among pest groups, as well as among pest species within a group. Weighted for the number of trials and averaged across all pest groups, Entrust, Azera, PyGanic and Neemix reduced pest infestations by an overall 73.9%, 61.7%, 48.6% and 46.1%, respectively. Entrust applied at the 71.2 g a.i./h rate of spinosad provided >75 % control of flea beetles, Colorado potato beetle, cabbageworms and alfalfa weevil. Nearly as effective against CPB larvae were lower rates of Entrust compared to the standard rate. Entrust also provided better control than the other insecticides against thrips, cucumber beetles, fruitworms and corn earworm in sweet corn, reducing infestations by >50%. As expected, Entrust was relatively ineffective against sucking insects, particularly true bugs and aphids. Although trial results showed that Entrust was the most effective control option for many insect pests, field-evolved resistance to spinosad has occurred in a number of insect pests, especially diamondback moth, several thrips species and Colorado potato beetle . For exaThe combination of azadirachtin and pyrethrin in Azera at the rate of 2.34 L/h ranked second in overall performance, providing >75% control of green peach aphid, flea beetles, Japanese beetle, Mexican bean beetle, potato leafhopper and cabbageworms. Azera tested at higher rates or at shorter spray intervals provided 10% to 20% additional control of true bugs, flea beetles, Japanese beetle and potato leafhoppers. Azera was generally more effective against pest infestations comprised of both adult and immature stages, which allowed for the combined direct toxicity, behavioral and physiological effects of both active ingredients. Pyrethrin in PyGanic at the 2.34 L/h rate was less effective but still provided overall >75% control of green peach aphid, flea beetles and potato leafhopper. In general, higher rates of PyGanic or the addition of adjuvants did not consistently increase control of most pest groups. The repellency, antifeedant and growth inhibition effects of azadirachtin in Neemix provided >75% control against Mexican bean beetle and >60% control against Colorado potato beetle larvae, even at the lower rate. Arguably, Neemix would be more effective against pest groups in infestations consisting mainly of developing immature stages. However, adults were the predominate stage in most trials and thus subject only to the repellent and antifeedant effects of azadirachtin.There are some noteworthy caveats when applying these findings. First, organic farmers use insecticides only as a last resort after all nonchemical methods have been explored. This management scenario frequently involves higher infestations of older insect stages compared to the younger age structure of infestations that triggered treatments in our trials. Thus, control efficacy of insecticides applied as a rescue treatment against older infestations may be lower than the levels reported here. Secondly, the spatial scale of our trials was conducive to movement of adults among small plots during the treatment period, which was an issue with highly mobile pests, such as thrips, flea beetles, cucumber beetles and potato leafhoppers. Possibly, the control efficacy of the insecticides could be higher when applied to whole fields, where there is less chance of insects re-invading the treated area from outside or from untreated control plots. Thirdly, we arbitrarily implied above that >75% reduction in the pest population provided acceptable control by the organic insecticide. Caldwell et al. also def"} +{"text": "To explore the current situation faced by Latin American urology departments during the COVID-19 Outbreak in terms of knowledge, actions, prioritization of urology practices, and implementation of internal clinical management protocols for inpatients and outpatients.A non-validated, structured, self-administered, electronic survey with 35 closed multiple choice questions was conducted in Spanish, Portuguese, Italian, and English and Deutsch versions from April 1st to April 30th, 2020. The survey was distributed through social networks and the official American Confederation of Urology (CAU) website. It was anonymous, mainly addressed to Latin American urologists and urology residents. It included 35 questions exploring different aspects: 1) Personal Protective Equipment (PPE) and internal management protocols for healthcare providers; 2) Priority surgeries and urological urgencies and 3) Inpatient and outpatient care.Of 864 surveys received, 846 had at least 70% valid responses and were included in the statistical analyses. Surveys corresponded to South America in 62% of the cases, Central America and North America in 29.7%. 12.7% were residents. Regarding to PPE and internal management protocols, 88% confirmed the implementation of specific protocols and 45.4% have not received training to perform a safe clinical practice; only 2.3% reported being infected with COVID-19. 60.9% attended urgent surgeries. The following major uro-oncologic surgeries were reported as high priority: Radical Nephrectomy (RN) 58.4%, and Radical Cystectomy (RC) 57.3%. When we associate the capacity of hospitalization (urologic beds available) and percentage of high-priority surgery performed, we observed that centers with fewer urological beds (10-20) compared to centers with more urological beds (31-40) performed more frequently major urologic cancer surgeries: RN 54.5% vs 60.8% (p=0.0003), RC 53.1% vs 64.9% (p=0.005) respectively.At the time of writing (May 13th 2020) our data represents a snapshot of COVID-19 outbreak in Latin American urological practices. Our findings have practical implications and should be contextualized considering many factors related to patients and urological care: The variability of health care scenarios, institutional capacity, heterogeneity and burden of urologic disease, impact of surgical indications and decision making when prioritizing and scheduling surgeries in times of COVID-19 pandemic. Coronavirus disease 2019 (COVID-19) is an emerging, highly infectious respiratory disease, that is caused by a novel coronavirus, now designated as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) that was first reported on 31st December 2019 in Wuhan, China and is considered responsible for a cluster of new cases of interstitial pneumonia (At the time of writing (13th May 2020) 4,262,799 cases were confirmed, 291,981 deaths reported with 187 countries around the world facing this health emergency which involves 24 urological societies in 22, conveys different scenarios in professional development and heterogeneous public health care infrastructures and policies influencing the way of facing the pandemic.To explore the current situation faced by Latin American urology departments during the COVID-19 emergency in terms of knowledge, actions, prioritization of practices, and implementation of internal clinical management protocols for inpatients and outpatients.http://www.caunet.org/en/urology>, and anonymous mainly for from Latin American urologists and urology residents. The 35 queries explored different issues: 1) Personal Protective Equipment (PPE) availability and design of internal managment protocols for healthcare staff; 2) Prioritization of surgeries and urological urgencies. The level of priority groups for procedures was categorizing into: a) High priority; b) Low Priority and c) No priority and 3) Inpatient and outpatient care activity.This was an electronic survey based on a non-validated, structured, self-administrated questionnaire consisting of 35 closed multiple choice queries. It was conducted in Spanish, Portuguese, Italian and English versions. The survey was opened on April 1st and closed in April 30th 2020. The survey was distributed on-line through social networks, the official CAU website and CAU Categorical responses were expressed as its absolute values and percentages (%). In each issue analyzed we included if responses were categorized as excluded answers. Descriptive analyses were carried out. All variables were compared using chi-square test and multiple comparisons adjusted by Bonferroni's method. In all cases a p value less than 0.05 was considered as statistically significant. Data analysis was performed using SPSS .Of 864 surveys received, 846 had at least 70% valid responses and were included in the statistical analyses. Surveys corresponded to South America in 62% of the cases , Central America and North America in 29.7% and Europe and other countries the remaining 8.3% .Participants' age distribution was: less than 40 years in 36.3%, between 40 and 55 years in 39.5% and older than 55 years in 23.3%. In terms of gender 17% were female. Of 841 surveys which specifing educational level, 12.7% were residents in training; 362 (41.9%) trained urologists reported not having residents under their charge. In terms of urological clinical practice: 70% practiced general urology, 25% uro-oncology and 26% endourology. In terms of practice setting: 363 (43.2%) were in university hospitals and 249 (39.7%) in public and non-academic hospitals. Overall characteristics of the study population are shown in .Regarding PPE and internal management protocols for healthcare provides, of 833 valid responses, 733 (88%) confirmed the implementation of specific protocols. Strikingly, only 455 (54.6%) professionals, received training on COVID-19 self-care protection protocols and 45.4% did not receive training to perform a safe clinical practice. Only 2.3% reported being infected with SARS-CoV-2; in contrast, the remaining 87.6% of non-infected urologists reported working in health care centers with proper internal management protocols. Lastly, 91.7% of urologists kept themselves updated about the latest news published publications regarding management protocols.Analyzing surgical activity, 60.9% performed urgent procedures as ureter stentings or nephrostomy tube placement due to infection, obstructive lithiasis or both; in 50% of these cases, there was not any COVID-19 protocol available for urological urgencies; in 37.4% of the cases the patient was assumed to be COVID-19 positive without prior testing; and only 13% of patients received COVID-19 testing before hand.Uro-oncologic surgeries were reported by 43.9% of participants, followed by endourologic procedures in 18.5% . Of 777 In terms of urologic cancer care, 76.2% reported that their centers continued to provide oncological treatments, including intravesical instillations or chemotherapy, and 25.4% of internal radio-oncology departments continued with a regular treatment schedulea.Regarding to urologic outpatient's follow-up, many hospitals or healthcare systems have reported the implementating technologic resources into the provision of urologic consultations in order to supply recommendations and prescriptions. Of these, 32.2% used telephone calls and 16% adopted telemedicine thus connecting to platforms as facetime, skype and zoom.The World Health Organization declared COVID-19 as a \u201cGlobal pandemic\u201d and public health emergency on March 11th, 2020, calling for collaborative efforts from all countries to prevent the rapid spread of the disease .Many hospitals and healthcare urologic centers around the world have adapted resources, limited surgeries as well as diagnostic procedures and have postponed major elective surgeries. Internal management protocols and recommendations for inpatient and outpatient care, have been provided by different international societies of urology to optimize patients' management, including decreasing the general inflow of patients to hospitals and reducing the number of medical and surgical procedures, therefore ensuring that only urgent and non-deferrable oncological surgeries are performed \u20136.On February 28th, the president of the Robert-Koch-Institute (RKI) in Berlin, Germany suggested to defer all non-urgent surgeries \u20136.Our study provides data from 22 Latin American countries that may contextualize the ongoing recommendations on selection of high-priority major uro-oncologic surgeries as RN 58.4% and RC 57.3% which are more frequently performed in Latin American urologic centers with less capacity of hospitalization (10-20 urologic beds available) compared tocenters with more capacity (31-40 urologic beds available). Our findings have practical implications and should be analysed considering many factors related to patients and urologic care: the variability of health care scenarios, the volume capacity at each center, the volume and variability of urologic disease, the impact of surgical indications and decision making when prioritizing and scheduling surgeries in times of the COVID-19 pandemic. Oderda et al. , the volume and variability of urologic disease, the health situation of each Latin American country with respect to the pandemic at the time of the survey analysis, the impact of surgical indications and decision making when prioritizing as well as scheduling surgeries in times of COVID-19 pandemic.At the time of writing, our data represents a snapshot of COVID-19 outbreak in the Latin American urological practice. Our findings have practical implications and should be contextualized considering many factors related to patients and urological care: the variability of health care scenarios, the volume capacity at each center, the volume and variability of urological disease, the impact of surgical indications and decision making when prioritizing as well as scheduling surgeries in times of COVID-19 pandemic.The COVID-19 era represents one of the biggest challenges is modern health care history. Urological practice has been severely impaired beyond the tragic effects of this emergency. However, several opportunities for improving urological research, clinical and surgical care of outpatient and inpatient settings have been rapidly developed, creating an excellent feedback of knowledge among the urological community around the world."} +{"text": "Preventing unintended pregnancies among HIV positive women has a vital role to prevent mother to child transmission. Besides, increasing access to contraceptives has a number of economical importance and reducing the costs for mitigating the unintended pregnancy consequences. Therefore, this study is aimed at assessing the contraceptive use and method of preference among HIV positive women in Ethiopia. Q test and I2 test statistics. Egger's test was used to check the evidence of publication bias within the studies. Subgroup analysis and sensitivity analysis was computed with the evidence of heterogeneity. A systematic review and meta-analysis reporting guideline was applied. Articles searched from the Scopus, Pubmed/MEDLINE, EMBASE, AJOL, Hinari, and Google scholar were included in this review. The Stata 11 software was used to compute the analysis. Heterogeneity of the studies was detected using the Cochran Ten thousand one hundred twenty one (10121) women living with HIV/AIDS were recruited in this study. The national estimated prevalence of contraceptive use among HIV positive women in Ethiopia was 57.78% (95% CI: 48.53-67.03). Injectables and male condom were the most preferred contraceptives accounted for 36.00% (95% CI: 6.64-45.35) and 32.74% (95% CI: 21.08-44.40), respectively. Discussion with husband/partner , disclosure of HIV status to spouse/partner , ever counseled for modern contraceptives , attending secondary and above education , and having more than one live child were increasing the likelihood of contraceptive use whereas not currently married women was decreases the odds of contraceptive use. In Ethiopia, more than half of the women living with HIV/AIDS were using contraceptives. Discussion with husband/partner, disclosure of HIV status to spouse/partner, ever counseled for modern contraceptives, attending secondary and above education, and having more than one live child were increasing the uptake of contraceptives among HIV positive women. Partner discussion, having adequate information towards contraceptive use, and having desired number of child could increase the utilization; as a result, obstetric complication with HIV positive women due to unintended pregnancy is significantly decreasing. Human immunodeficiency virus (HIV) is the most common public health issue and destructive epidemics that the world has ever faced. According to UNAIDS 2019 report, globally 37.9 million people were living with HIV and 1.7 million people became newly infected with HIV as well as around 770000 people died from AIDS-related illnesses. Around 6000 young women among age group of 15-24 years become infected with HIV every week. However, in sub-Saharan Africa, four in five new infections among adolescents aged 15\u201319 years are in girls. Worldwide, the epidemiology of new HIV infections is 54% varied across the countries in the range of 25%-95% in Eastern Europe and Central Asia, Middle East and North Africa, Western and Central Europe and North America, Asia and the Pacific, and Eastern and Southern Africa [Different literatures showed that unintended pregnancy has emergency obstetric complications for women living with HIV/AIDS; furthermore, the magnitude of unintended pregnancy is 96%, 71%, and 43% in Thailand, South Africa, and Uganda \u20134. AccorA study conducted in sub-Saharan African population showed that contraceptive strategy averts 28.6% more HIV positive births than Neverapine for PMTCT, furthermore increasing access to contraception and preventing unintended pregnancies, integration reduces new and opportunistic pediatric HIV infections, and the number of children needing HIV treatment, care, and support , 8.According to the 2016 Ethiopia demographic and health survey report, one in every three currently married women used modern contraceptive. Besides, injectable contraceptive method, long acting or permanent methods, and condom constituted 23%, 8%, and 4%, respectively .In Ethiopia, different studies have been showed variation in the magnitude of contraceptive use among women living with HIV accounted for 30.3% in Amhara region, 39% Addis Ababa, 46% Tigray region, 64.1% southern Ethiopia, and 50% in Gondar University specialized hospital \u201314, wherUptake of contraception helps women avoid unplanned or unwanted pregnancies and prevent unsafe abortions. A systematic review and meta-analysis study showed that HIV positive women have eight times the risk of a pregnancy-related death compared to women without HIV infection. Besides, contraceptive use helps the women to space and limit the births, which benefit the health of the mother and her baby .Various factors such as sociocultural norms and traditions, lack of comprehensive knowledge on contraceptive methods, lack of advice from health professionals, not start ART, fear of side effects, illiteracy, and inaccessibility of preferred contraceptives limit women living with HIV to seek and use modern contraceptive service and information , 17.Even though there are different single studies reported the prevalence of contraceptive use among HIV positive women and its associated factors, there are no national studies which show the nationwide magnitude of contraceptive use among women living with HIV/AIDS in Ethiopia. Therefore, this systematic review and meta-analysis is aimed at estimating the pooled prevalence of contraceptive use and method of preferences among women living with HIV/AIDS in Ethiopia.Articles accessed in the Scopus, Pubmed/MEDLINE, Hinari, EMBASE, Google scholar, African journals, and online university repositories were considered in this systematic review and meta-analysis . Differe(1) Study Design. Cross-sectional studies reported the prevalence or widely used contraceptives and risk factors for contraceptive use among HIV positive women were included.(2) Language. Only English language literature and research articles were included.(3) Publication. Both published and unpublished research articles were used.(4) Searching Date. Articles searched from April 1-30, 2020 were included.(5) Study Population. Women living with HIV/AIDS were included in this study.Articles without full text and abstract, duplicated studies, anonymous reports, and editorial reports were excluded.The Standard Microsoft Excel spread sheet was used to export data from online databases. Two authors (GG and AD) were independently extracted and reviewed all the articles included in this study. Any disagreement was handled by the third reviewer (AW). After all, a consensus was reached through discussion between authors. The Newcastle-Ottawa Quality Assessment Scale (NOS) for cross-sectional studies was used to assess the methodological quality of each study , comparability, and measurement of outcomes . Each stThis systematic review and meta-analysis had two main outcome measurements. Contraceptive use was the first outcome of the study whereas method of preference and predictors of contraceptive use among HIV positive women were the second outcome of this review. The pooled prevalence and adjusted odds ratio were calculated for risk factors reported in the study.(1) Contraceptive Use. Contraceptive use is the current use of any modern method by women to delay or avoid unintended pregnancy for the last one month.(2) Modern Methods. The modern methods are oral pills, intrauterine device, injectable, implants, male condom, female condom, and female and male sterilization.Q test and I2 with its corresponding p value were used to assess the heterogeneity of the study [p value < 0.05 was considered statistically significant. The odds ratio was calculated to measure the association between the outcome variable and the determinants.The Microsoft Excel 2016) and STATA version 11 software were used for the data entry and analysis, respectively. The funnel plot and Egger's regression test were conducted to check potential publication bias , 20. The16 and SThe study , 22. HenWe retrieved 577 studies from the PubMed/MEDLINE, HINARI, EMBASE, Scopus, Google Scholar and African Journals, and online university repository research articles. After duplicates were expunged, 234 studies remained.Out of the remaining 234 articles, 193 articles were excluded after review of their titles and abstracts. Therefore, 41 full-text articles were accessed and assessed for inclusion criteria, which resulted in the further exclusion of 22 articles. Out of these, 20 studies were excluded due to the outcome of interest is not reported, and 2 of them were excluded due to inaccessibility of the full text. As a result, 19 studies were met the inclusion criteria to undergo the final systematic review and meta-analysis .Studies were conducted from different regions of Ethiopia , Addis Ababa (AA), and Tigray). Totally, ten thousand one hundred twenty one women living with HIV/AIDS were included in this systematic review and meta-analysis. In this review, four studies were from Addis Ababa , 23\u201325, In this study, the national estimated prevalence of contraceptive use in Ethiopia was 57.78% (95% CI 48.53-67.03) .In this systematic review and meta-analysis, the commonest preferred contraceptive use among women living with HIV/AIDS was injectable 36.00% (95% CI: 26.64-45.35), male condom 32.74% (95% CI: 21.08-44.40), and implants 13.10% (95% CI: 8.82-17.38) .I2 = 99.1%, p < 0.001). We also assessed the presence of publication bias by using Egger's test, which suggests the presence of publication bias (p = 0.012). As a result, trim and fill analysis was conducted to overcome the publication bias. After one study was filled, twenty studies were enrolled and computed through the trim and fill analysis with a pooled prevalence of 59.26% (95% CI: 58.44-60.08) using a random effect model and 59.33% (50.59-68.07%) after deletion of a single study .We conducted a subgroup analysis based on the region where the study was conducted and year and sample size. With regard to sample size, the highest prevalence was observed among those studies with sample size of less than 500, 59.07% (95% CI: 46.88-71.25). Regarding the region of study conducted, the highest prevalence was observed in studies done in Oromia region with 61.65% (95% CI: 52.10-71.19), and the lowest was in Tigray with 44.83% (95% CI: 42.03-47.63) .In this systematic review and meta-analysis, a total of nineteen primary studies with datIn this meta-analysis, mothers who have discussed with their husband/parent were 4.7 times more likely to use contraceptives as compared with mothers who have not discussed with their husband/parent with odds ratio .HIV status disclosure was also another determinant factor associated with contraceptive use. Mothers who disclose their HIV status to their spouse/parent were 2.18 times more likely to utilize contraceptives as compared with mothers who did not disclose their HIV status to their spouse/parent .Those mothers who ever counseled about modern contraceptives were 2.79 times more likely to use contraceptives as compared with their counter parts . SimilarModern contraceptive utilization among HIV positive mothers added the benefit of preventing unintended pregnancies, reducing the need for unsafe abortions, and HIV positive births and can have a major impact on improving the overall maternal and infant health. Therefore, this systematic review and meta-analysis is aimed at estimating the pooled prevalence of contraceptive use among HIV positive mothers and its associated factors in Ethiopia. In this meta-analysis, the pooled prevalence of contraceptive use among HIV positive mothers in Ethiopia was 57.78% (95% CI: 48.53-67.03). Even though there was no analogous meta-analysis study conducted on this specific research question within the area, the pooled prevalence of contraceptive use among HIV positive mothers is comparable with a survey done in Nairobi, Kenya (55.5%) , NortherIn this meta-analysis concerning method of contraceptive preference, the most widely preferred contraceptive method was injectable for 36.00% (95% CI: 26.64-45.35) and male condom for 32.74% (95% CI: 21.08-44.40). This is supported with a study conducted in Northern Tanzania . This miThis meta-analysis showed that women who attended secondary and above education were more likely to utilize contraceptive as compared with their counter parts. This is supported with a study done in Northern Uganda and LusaThose mothers who ever counseled about modern contraceptives were more likely to use contraceptives as compared with their counter parts. This is consistent with a study conducted in Northern Tanzania . This miContraceptive use was higher among mothers who have more than one living child as compared with mothers who have one child. This finding is supported with a study conducted in Nairobi, Kenya . This miThe study designs for all primary studies included in this systematic review and meta-analysis were cross-sectional; as the result, the confounding variables most of the time might affect the outcome variable. Despite, generalizability is possible since the study is at national level; however, establishing temporal cause and effect relationship is impossible due to the natural design limitation of cross-sectional studies.In this study, nearly three-fifth of HIV positive women used contraceptive methods. HIV status disclosure, attending secondary and above education, women discussed with their spouse/parent, having more than one living child, and ever counselled about contraceptive methods were factors that increase the likelihood of contraceptive use among HIV positive women. Therefore, based on the study findings, husband involvement and providing counselling about contraceptive methods for HIV positive women should be encouraged, and there is a need for an intensified effort to improve reproductive health service utilization. Health care providers in charge of HIV care giving must also integrate family planning services in HIV care during follow-up visits."} +{"text": "Models of successful aging underscore the critical role of external social resources in older adults\u2019 health and well-being. Neighborhood socioeconomic position is known to influence health, but little is known about the linkages between neighborhood conditions, social relationships and health among older adults. We identified a cohort of 12,434 adults (aged 65+) who attended a Medicare Annual Wellness Visit from the NEOCARE Learning Health Registry. NEOCARE includes electronic health record (EHR) and neighborhood data from 1999-2017 on over 3 million unique Northeast Ohio individuals. The study population was 60% White, 32% Black or African American, 64% female, and 90% non-Hispanic. Over 60% were ages 65-74, 29% 75-84, and 10% 85 years or older (range from 65 to 101). We used ANOVA and chi square tests to examine variation in social support by quintile of the census tract area deprivation index. Compared to those in less disadvantaged neighborhoods, older adults in more disadvantaged neighborhoods were more likely to report needing help with care needs but were less likely to report having help at home . Similarly, adults in more disadvantaged neighborhoods reported less help available to them compared to those in more advantaged communities . Furthermore, older adults living in more disadvantaged neighborhoods experienced significantly less functional independence . Our results suggest that the pathway from neighborhood socioeconomic conditions to successful aging includes perceived social needs and social support."} +{"text": "For reasons including the opioid epidemic and more widespread substance use across all ages, the prevalence of individuals meeting preadmission criteria for skilled nursing facility (SNF)-level care and who have substance use disorders (SUDs) is growing. However, little is known about this population. We characterized a sample of residents with SUDs in two SNFs that target admission of difficult-to-place individuals in Hartford, Connecticut. Residents admitted between June 1, 2018 and May 31, 2019 and had an SUD per Pre-Admission Screening and Resident Review (PASRR) were included. Using retrospective chart review, we collected data including demographics, physical and mental health conditions, psychiatric medications, and participation in SNF-provided SUD counseling. Of 163 residents admitted with an SUD, all were admitted following an acute hospitalization. Residents\u2019 average age was 49.9(SD=11.7) years (range 21-79). They were 61% male and racially diverse; 56% Caucasian, 27% Hispanic, 16% Black. SUDs on admission included opioid use disorder (48%), alcohol use disorder (33%), unspecified psychoactive SUD (26%), cocaine use disorder (25%), and Other (20%). Of these, 18% and 16% were taking methadone or suboxone, respectively and 25% were taking an antipsychotic medication. Comorbidities such as bipolar disorder (15%) and viral hepatitis (26%) were prevalent. A total of 40 (25%) residents participated in SUD counseling; none of the aforementioned factors was associated with participation. This is the first study to characterize a sample of residents from SNFs that target individuals with SUDs. Improved understanding of this unique and growing subset of the SNF population may help optimize their treatment."} +{"text": "Background: to compare the extent of the detached retina and retinal tears location in rhegmatogenous retinal detachment (RRD) among non-mydriatic ultra-wide field (UWF) imaging, dilated fundus exam (DFE), and intraoperative evaluation. Methods: this retrospective chart review comprised 123 patients undergoing surgery for RRD. A masked retina specialist analyzed the UWF fundus images for RRD area, status of the macula, and presence and location of retinal breaks. The same variables were collected from a database including DFE and intraoperative recordings. Evaluation methods were compared. Results: mean age was 59.8 \u00b1 14.9 years. Best-corrected visual acuity improved from 0.25 \u00b1 0.3 (Snellen) to 0.67 \u00b1 0.3 at 12 months (p = 0.009). The RRD description and assessment of macula status (34.5% macula-on) did not differ between UWF, DFE, and intraoperative examination. The inferior quadrant was involved most frequently (41.5%), followed by the superior (38.9%), temporal (27.8%) and nasal quadrant (14.8%). Intraoperative exam detected 96.7% of retinal tears compared with DFE and UWF imaging . UWF imaging and DFE did not differ significantly. Conclusion: RRD extent on DFE and UWF images was consistent with intraoperative findings. UWF and DFE detection of peripheral retinal tears was similar, but 25% of retinal breaks were missed until intraoperative evaluation. The ophthalmoscope, developed by Hermann von Helmholtz in 1850, allows for visualization of the structures of the eye fundus and detailed studies of the vitreous, retina, and optic nerve head .For many years, most digital instruments for fundus photography captured images with only a 30 or 45\u00b0 field of view. To obtain an image beyond the vascular arcades, photographs were obtained of the eyes during fixation at different points. For a wider vision of the retina, the photos were joined to create a composition or collage covering approximately 75\u00b0 [Retinography of the anterior retina is difficult. Recent technologic advances, however, allow for imaging of the entire retina. Ultra-wide field (UWF) imaging is a rapidly evolving diagnostic modality that can image the peripheral retina to a greater extent than traditional fundus photography. The Optos 200Tx imaging system is a confocal laser scanning ophthalmoscope with a parabolic mirror designed to obtain UWF images of the retina, up to 200\u00b0 . A single shot, acquired with or without mydriasis, provides a retinogram of more than 80% of the retinal surface ,5. Thus,The gold standard for evaluating the peripheral retina is the dilated fundus examination (DFE) with scleral depression performed by a retina specialist. Documentation of retinal pathology, such as rhegmatogenous retinal detachment (RRD) or retinal tears, frequently relies on drawings. This method is time-consuming, requires an experienced retina specialist, active patient collaboration, and is uncomfortable for the patient. The purpose of this study was to compare the location and extent of RRD and retinal tears position evaluated by a non-mydriatic UWF fundus imaging, DFE, and intraoperative examination.This was an observational retrospective chart review of patients operated on for primary RRD during 14 months in a vitreoretinal clinic at FISABIO Medical Ophthalmology Center . The Research Ethics Committee (CEI of FISABIO) approved the study design and all methods adhered to the tenets of the Declaration of Helsinki.Adult patients who presented with acute RRD during those dates and underwent surgical repair were reviewed. Only those who underwent UWF imaging were included. Participants without a detailed DFE (prior to surgery) or intraoperative examination by a retinal specialist, or with poor image quality were excluded from the study.An Optos 200Tx UWF 200\u00ba retinal camera using green (532 nm) and red (633 nm) lasers was used to obtain fundus images in the primary position of gaze (PPG) by a single photographer without pupil dilation prior to surgery.All patients underwent pre- and postoperative best-corrected visual acuity (BCVA) testing , slit lamp biomicroscopy, and DFE. All patients also underwent spectral-domain optical coherence tomography (SD-OCT) using the Spectralis HRA + OCT .A trained retina specialist masked to the clinical data independently analyzed the UWF fundus images for RRD quadrant location , macula on/off, and the presence and location of retinal breaks (anterior or posterior to equator). Then, a different retina specialist reviewed the medical records of patients looking for the same variables obtained during DFE and intraoperatively. Other data collected included demographics, presence of macular involvement based on SD-OCT, type of surgical repair, and the re-detachment rate. RRD surgeries were performed within 48 h after DFE and UWF imaging acquisition.Comparison between UWF imaging, and clinical and intraoperative examination findings were made using the chi-square test. The association of UWF imaging with Lincoff\u2019s rules for RRD was also analyzed. A p value of less than 0.05 was considered statistically significant.One hundred and twenty-three patients (123 eyes) with primary RRD were included in the final analysis. Their demographics and clinical features are summarized in p = 0.009, paired t-test).Regarding the type of surgical repair, 18.7% underwent pars plana vitrectomy, 62.6% additionally underwent a scleral buckle, and 17.9% underwent an extrascleral procedure. The vitreous substitutions used for exchange were 54.6% sulfur hexafluoride (SF6) gas, 25.2% perfluoropropane (C3F8) gas, 17.6% air, and 2.5% silicon oil, depending on the RRD characteristics. The rate of re-detachment was 13.8%. The BCVA increased from 0.25 \u00b1 0.3 decimal (20/80 Snellen) before surgery to 0.67 \u00b1 0.3 decimal (20/30 Snellen) at 12 months (p < 0.001) and 65% as assessed by UWF fundus imaging (p < 0.001). No significant differences were detected between UWF imaging and DFE. Anterior retinal breaks were identified in 74% of the patients based on intraoperative examination, compared with 45.5% when assessed by DFE (p < 0.001) and 39% when assessed by UWF fundus imaging (p < 0.001). Assuming that intraoperative examination detected all the retinal breaks, UWF imaging in PPG missed 47.3% and DFE missed 38.5% of anterior retinal breaks. UWF imaging did not differ significantly from DFE. Posterior retinal breaks were detected in 28.5% of the patients during the intraoperative exam, 29.3% when assessed by DFE, and 30.9% when assessed by UWF fundus imaging. Detection of posterior retinal tears was equivalent among the three techniques with no significant difference between them. Retinal breaks observed in the intraoperative exam and not detected using UWF .Evaluation of the macula with OCT was not possible in 29.3% of the cases. Among those that were evaluated, 34.5% of the patients had macula-on retinal detachment, whereas 57.5% had macula-off retinal detachment, and 8% were not evaluable. Assessment of macular status by UWF imaging was possible in 121 patients (98.4%); 31.4% were estimated to have macula-on retinal detachment, 51.2% had macula-off retinal detachment, and 17.4% were not evaluable. No significant differences were detected between the two methods (macula-on, RRD is a medical emergency. Proliferative vitreoretinopathy and blindness may result if left untreated or if surgery is delayed. Therefore, early diagnosis and treatment are essential for preserving visual function. DFE with scleral depression remains the gold standard for diagnosis and documentation of peripheral retinal lesions and RRD . Many clThe results of this study confirmed that DFE and UWF imaging identify the extent of RRD consistently with intraoperative findings. UWF fundus imaging, however, has several advantages over other techniques: detailed 200\u00ba high-resolution images can be obtained in less than half a second and in a single shot, mydriasis is not required, and findings can be easily documented for clinical, teaching, or legal purposes. This makes it an ideal technique for areas where retina specialists are not readily available.Kornberg et al. comparedEarly detection of anterior retinal breaks is crucial because missed retinal breaks are responsible for up to 64% of the cases of failed RRD surgery . KornberThis work has several limitations. The retrospective nature of the study and perhaps a more complete RRD classification system could have been used. UWF imaging was performed in PPG. If eye steering was used to obtain the images, the percentage of retinal breaks detected would likely have been higher. Nevertheless, no significant differences were detected between DFE and UWF imaging. Regarding posterior retinal breaks, there were no differences among the three examinations. Mackenzie et al. found thLincoff provided the essential guidelines, four rules, to find the primary break in RRD . LocalizConsistent with previous studies , our resThe status of the macula is a significant factor for the final visual outcome in RRD and must be evaluated at the time of surgical repair. SD-OCT is an excellent tool for macular evaluation, but clear preoperative OCT measurements could not be obtained in up to 29% of the patients in the present study due to a bullous RRD or vitreous opacity. UWF imaging allows for simultaneous evaluation of the peripheral and central retina, and 98.4% of the patients were satisfactorily evaluated.Another limitation of the study is that we only included patients with good-quality UWF images. Media opacity, pupil size, retinal pigment epithelium status, and centering of the eye, assessed clinically, are factors that may affect the image quality and lead to underestimating the location of RRD and number of retinal breaks. Moreover, according to our RRD protocol, all participants were instructed to keep a relative rest and to maintain the most appropriate head position to minimize the risk of increasing the area of the detached retina prior to surgery. Most of them were operated within 24 h after DFE and, exceptionally, within 48 h. Consequently, we assumed that RRD extent did not change between clinical examinations and intraoperative evaluation.UWF imaging precisely documented the RRD extent, consistent with DFE and intraoperative findings. The detection of anterior retinal breaks in PPG, however, is suboptimal compared with intraoperative findings. The UWF technology is still expensive, but may have an important clinical role for diagnosis, surgical planning, and follow-up of RRD. Further studies are warranted to determine the utility of UWF imaging in the management of RRD and other retinal diseases."} +{"text": "Stray cats are a reservoir for various zoonotic diseases relevant to public health in Thailand. The vector-borne infection, hemoplasmosis, also known as infectious anemia, is one such disease carried by domestic and wild felids. This study focuses on molecular characterization and phylogenetic analysis of hemoplasma in semi-domesticated cats in Bangkok, Thailand.In total, 473 blood samples were collected from 53 temple communities in 34 metropolitan districts and assayed using polymerase chain reaction (PCR) to amplify partial 16S rRNA genes for hemoplasma detection. Risk factors for hemoplasma infection were analyzed using Chi-square tests, logistic regression, and odds ratios (OR) with 95% confidence intervals (95% CI) using R software (version 3.6.1). A phylogenetic tree was established from genetic characterization of hemoplasmas.Candidatus Mycoplasma haemominutum (CMhm), 13.33% with Mycoplasma haemofelis (Mhf), and 3.33% with Candidatus Mycoplasma turicensis (CMt). Cats over 5 years old were more likely to be infected than younger cats . Cats were diagnosed as positive based on PCR assays in 97% (33/34) of districts surveyed. The phylogenetic tree showed two majority clusters with three clades of feline hemotropic mycoplasma.In total, 180 samples (38.05%) were positive for hemoplasma. Of half of the positive sequenced samples, 83.33% were infected with Overall, the survey shows the prevalence (38.05%) and distribution of feline hemoplasma in semi-domesticated cats. This information will contribute to effective prevention and control strategies to minimize infections by feline vector-borne pathogens in Thailand. Mycoplasma haemofelis (Mhf), Candidatus Mycoplasma haemominutum (CMhm), and Candidatus Mycoplasma turicensis (CMt) ). This difference was statistically significant (\u03c7% to 42% .CMhm16S rRNA sequences (approximately 557 \u2013 595 bp in length) were 99.29-99.47%, which is identical to published sequences . CMt (approximately 557 \u2013 595 bp in length) showed high sequence identity (99.12%) with published sequences in GenBank . Similarly, Mhf sequences (approximately 557 \u2013 595 bp in length) shared 99.29% identity with submitted sequences . From this study, 30 sequences of hemoplasma obtained and previously published reports were used to establish a phylogenetic tree. Phylogenetic analysis showed three clades of feline hemoplasma: CMhm (Clade 1), CMt (Clade 2), and Mhf (Clade 3) .CMhm was the most prevalent species (83.33%). Semi-domesticated cats showed higher rates of infections than owned cats in Bangkok, displaying 22.9% positive incidence by PCR analysis [et al. [All three species of feline hemoplasmas were detected in semi-domesticated cats. analysis . The higanalysis ,17,25. F [et al. found a The prevalence of hemoplasmas in the survey (38.05%) was higher than prevalence reported in other studies on stray cats worldwide, where incidence ranged from 9% to 16% -17,18. TCMhm infection in semi-domesticated cats was higher than other feline hemoplasmas species (CMt and Mhf), which is consistent with other investigations worldwide [et al. [CMhm that allows it to efficiently infect and survive for extended periods in asymptomatic animals. Furthermore, hemoplasmas-infected cats were significantly older than uninfected cats, which are concordant with the previous reports that adult animals are more frequently exposed to bloodsucking arthropods and also have more aggressive interactions, both of which could enhance transmission through infected blood [In the current study, the prevalence of orldwide ,25,26. T [et al. reporteded blood ,17,27.Mhf and CMt species and a hemominutum group with CMhm [Mhf and CMt belong to the same clades as Mhf and CMt strains from Brazil, Italy, Taiwan, and Australia. Sequences of CMhm from semi-domesticated cats show more variation from strains isolated in Italy, Taiwan, China, and Brazil; however, they all belong to the same clade, CMhm. Interestingly, based on phylogenetic analysis, CMhm in cats in the current study was 99.29-99.47% identical to CMhm in stray dogs in Thailand (GenBank accession no. KU765207). This observation may be due to stray cats and dogs residing in the same location and also being exposed to the same pathogens through transmission modes discussed above. Control of hemotropic mycoplasmas in semi-domesticated cats, along with control of other pathogens in stray animals, should be considered by Thai veterinarians, the Thai government, and Thai authorities.Phylogenetic 16S rRNA gene-based analysis shows that our sequences separate into three distinct clades, one for each hemoplasmas species. A previous report identified two major groups of hemoplasmas, including a group encompassing ith CMhm . PhylogeThis survey demonstrates the prevalence and distribution of feline hemoplasmas in semi-domesticated cats. Such information can contribute to developing effective prevention and control strategies to minimize infections by feline vector-borne pathogens. However, further investigation involving sampling of domesticated house cats and the prevalence of hemoplasmas infection in ectoparasites is needed to clarify routes of pathogen transmission and to fully elucidate the prevalence of feline hemoplasmas infections in Thailand.TI planed and designed the experiment and data analysis and revised the manuscript. TD conducted the experiment, interpreted the results, and drafted the manuscript. KK collected the samples and revised the manuscript and LKB revised the manuscript. All authors have read and approved the final manuscript."} +{"text": "The institution of social distancing and punitive measures to contain the spread of COVID-19 through human-to-human transmission has environmental, health and economic impact. While the global pandemic has led to the enhancement of the health system and decline of emissions, economic development appears deteriorating. Here, we present the global environmental, health and economic dimension of the effect of COVID-19 using qualitative and empirical assessments. We report the health system policies, environmental sustainability issues, and fiscal, monetary and exchange rate measures introduced during lockdown across countries. While air pollution is reported to have declined, municipal and medical waste is increasing. The COVID-19 global pandemic uncertainty ranks the UK as the country with the highest uncertainty level among 143 countries. The USA has introduced 100% of pre-COVID-19 crisis level GDP, the highest policy cut-rate among 162 countries. Science, innovation, research and development underpin COVID-19 containment measures implemented across countries. Our study demonstrates the need for future research to focus on environment-health-economic nexus\u2014a trilemma that has a potential trade-off. Hence, the outbreak of COVID-19 pandemic is a public health concern with dire health, environmental and economic consequences , Avian flu (2003\u20132009), Swine flu 2009\u20132010) and Ebola (2014\u20132016) since 1996 , corresponding to a 6% reduction in global emissions and forest reserve. The reduction in road and railway transportation, and shutdown of commercial, power plants and manufacturing activities are likely to reduce ambient noise levels has affected global economic development, resulting in several fiscal measures, monetary policies and private sector economic burden-sharing across countries. The average estimate of economic policy response comprises of monetary stimulus package (% of GDP), fiscal policy package (% of GDP), monetary intervention to control the balance of payment (BOP) and exchange rate (% of GDP), policy rate cut (as a % of pre-crisis level) and total economic stimulus (% of GDP) across 162 countries, followed by Malta (25.61% of GDP), Austria (25.11% of GDP), Luxembourg (22.91% of GDP), France (22.59% of GDP), Oman (22.59% of GDP), Belgium (19.61% of GDP), Sweden (18.65% of GDP), Germany (17.29% of GDP) and Malaysia 16.42% of GDP) [see Fig. 2% of GDPThe highest reported policy rate cut occurs in the USA (100% of pre-COVID-19 crisis level), the UK (86.67% of pre-crisis level), Norway (83.33%), Croatia (75% of pre-crisis level), New Zealand (75% of pre-crisis level), Sweden (73.33% of pre-crisis level), Saudi Arabia (63.49% of pre-crisis level), the UAE (62.50% of pre-crisis level), Oman (60% of pre-crisis level) and Canada (57.14% of pre-crisis level) across 162 countries, followed by Oman (25.09% of GDP), China (14.14% of GDP), Malta (13.31% of GDP), Germany (12.49% of GDP), Sweden (9.45% of GDP), the UK 9.09% of GDP), New Zealand (8.86% of GDP), Bulgaria (8.60% of GDP) and Cyprus (7.77% of GDP) (see Fig. % of GDP The global distribution of economic policy response to COVID-19 across 166 countries is presented in Fig. In OECD countries, economic policy responses to COVID-19 amidst containment measures include 100% financial support to affected local firms,\u2009~\u200994% income support to self-employed people and residents with loss of job or income,\u2009~\u200980% financial assistance to pay rent, mortgages or utilities and\u2009~\u200947 to 67% income support to quarantined and sick workers OECD . In AustIt is reported that the choice of a government to undertake strong fiscal stimulus depends mainly on sovereign credit ratings and economic stringency to salvage the deteriorating economic effect of social distancing policies to reduce the spread of COVID-19 (Balajee et al. The critical assessment presented in this study reveals a trade-off between environment, health and economic development. Though the study is limited in terms of data due to the progressive nature of the COVID-19 pandemic. However, the global pandemic has demonstrated the need to empirically assess the trilemma of environment-health-economic nexus. While environmental pollution is reported to have declined due to shutdown in vital economic sectors such as transportation, aviation and industries, the health systems have been improved significantly to save lives at the expense of economic deterioration. Nevertheless, a rebound effect is projected to occur across countries via rebooting of primary economic sectors to salvage economic loss. Based on both qualitative and quantitative assessment, the post-COVID-19 is expected to rekindle and intensify environmental degradation while improving and sustaining the health system to recover and sustain economic productivity. On the contrary, the aftermath of the COVID-19 pandemic will have a long-lasting societal effect on workplaces, public places and social events, which will directly affect the economic transition. Thus, governmental effort across countries is required to strike a balance between environmental sustainability, health outcomes and sustained economic development due to the potential trade-off effects."} +{"text": "Dorea, Oscillibacter, and Alisitpes were decreased, while Lactobacillus, Parasutterella, Akkermansia, Bifidobacterium, and Barnesiella increased. Bifidobacterium spp. and Akkermansia spp. were significantly increased in mice consuming the highest melanoidin amounts, suggesting remarkable prebiotic potential. Melanoidins are the final Maillard reaction products (protein\u2013carbohydrate complexes) produced in food by prolonged and intense heating. We assessed the impact of the consumption of melanoidins from barley malts on gut microbiota. Seventy-five mice were assigned into five groups, where the control group consumed a non-melanoidin malt diet, and other groups received melanoidin-rich malts in increments of 25% up to 100% melanoidin malts. Feces were sampled at days 0, 1, 2, 3, 7, 14, and 21 and the microbiota was determined using V4 bacterial 16S rRNA amplicon sequencing and short-chain fatty acids (SCFA) by gas chromatography. Increased melanoidins was found to result in significantly divergent gut microbiota profiles and supported sustained SCFA production. The relative abundance of The Maillard reaction (MR) generates several low-weight molecules by reducing sugars and amino acids during food thermal processing and storage, such as Amadori rearrangement products, furfural, reductones, and other dicarbonyl compounds. These low-weight compounds are often recombined through a range of advanced MR to form melanoidins , which aIn contrast with other Maillard reaction products (MRP), melanoidins are generally considered to be harmless, and even potentially beneficial to human health . Though Helicobacter pylori infection [Escherichia coli by causing irreversible changes to both the inner and outer membranes [Bifidobacteria strains were shown to use bread melanoidins as a carbon source in batch cultures [Bacteroides and Prevotella during fermentation in an in vitro study [It was actually suggested that dietary melanoidins possess prebiotic properties due to tnfection . Moreoveembranes . While kembranes ,25, gut embranes , with evembranes . In an iembranes . Bifidobcultures , while cro study . Anotherro study ; this soThe animal study was conducted at the Animal House Facility of the University of Arkansas after receiving approval from the Institutional Animal Care and Use Committee (IACUC). Seventy-five male mice (Mus musculus strain C57BL/6J) aged 8 weeks (20 g) were purchased from Jackson Laboratory . Mice were housed in stainless steel cages under a controlled temperature (70 \u00b0F) and a 12 h light\u2013dark cycle, with free access to water and food. Before dietary intervention, mice were provided with Teklad (standard) 40 g of chow pellets .\u00ae Melanoidin), resulting in grain-browning and specific organoleptic properties [n = 5 for each group). Cages were randomized in the rack to limit potential block effects.Melanoidin-free and melanoidin-rich barley malts were purchased from Weyermann Company . Melanoidin-free malts were considered to be normal barley grains pre-germinated to release saccharolytic and amylolytic enzymes for beer-brewing purposes and contained low amounts of LMW melanoidins . Melanoidin-rich malts were considered to be enriched in HMW melanoidins due to intense toasting : Melanoidin-free malts (0% melanoidins) only.Group (2): 75% of melanoidin-free malts and 25% of melanoidin-rich malts.Group (3): 50% of melanoidin-free malts and 50% of melanoidin-rich maltsGroup (4): 25% of melanoidin-free malts and 75% of melanoidin-rich maltsGroup (5): Melanoidin-rich malts (100% melanoidins) only.Malts were added to the stainless cages twice a week, and the unconsumed amounts were measured before adding new malts. Body weight was measured at 7, 18, and 25 days. The mice were transferred from stainless steel cages to metabolic cages for 6 h/day in order to collect feces at day 0, 1, 2, 3, 7, 14, and 21. Day 0 samples represented the baseline, with all groups previously fed chow pellets. After that, each group was provided with their specific amounts of melanoidin malts over the 21 days.Short chain fatty acids (SCFAs), specifically, acetate, propionate, and butyrate, were measured by gas chromatography (GC) for the 0% and 100% groups. Briefly, 1 g of fecal sample was transferred into centrifuge tubes, and 9 mL of distilled water was added. After vortexing and centrifugation, 900 \u03bcL of the supernatant was transferred into 2 mL tubes containing 100 \u03bcL of buffer consisting of the internal standard 4-methyl-valeric acid (50 mM), meta-phosphoric acid (50%), and copper sulfate (1.56 mg/mL). After vortexing and centrifugation, 1 \u03bcL of sample was loaded to the GC. SCFA concentrations were estimated by the integration of peak areas in relation to acetate, propionate, and butyrate standards .Genomic DNA was extracted from mice fecal samples using commercial QIAamp DNA stool Mini Kit following the manufacturer\u2019s protocol, with the addition of bead-beating at 5 m/s for 60 s, which was performed twice . PCR ampIllumina MiSeq sequencing was used to study the composition of gut microbiota by targeting the V4 region of the bacterial 16S ribosome RNA gene of each group following the dual-indexed strategy . Normali2) and quality scores .The libraries were pooled, denatured with NaOH, and diluted to 0.75 nM, following recommended Illumina protocols. The pooled denatured libraries were diluted to 6 pm as a final concentration, with the addition of 20 pm of Phix V3. The diluted denatured libraries were loaded onto an Illumina MiSeq sequencing cartridge V3-600 cycles, with the addition of 3 sequencing primers due to the use of different indices, as described by Kozich et al. . The runn = 9) were discarded; the remaining samples analyzed had an average of 502,020 \u00b1 37,097 reads per sample. All reads were analyzed together using the MOTHUR1.39.5 pipeline.From 175 samples, a total of 10,123,928 raw sequences were obtained, of which 9,290,708 high-quality reads were used for further analysis. Samples yielding less than 3000 high-quality reads (https://www.mothur.org/wiki/MiSeq_SOP). Briefly, sequences were screened and aligned to the Silva database (Release 128) for the 16S RNA gene sequences. Subsequently, operational taxonomic units (OTUs) were picked and assigned to taxonomic groups. The resulting OTUs and taxonomic tables were exported to Excel sheets for basic analysis.FASTQ files were readily demultiplexed by the built-in BaseSpace Sequence Hub program and downloaded from the BaseSpace website. The 16S amplicon reads were analyzed by using the MOTHUR software package 1.39.5 following the Illumina Standard Operating Procedures (SOP) based on count-distance metrics : p < 0.05) considered to show significant similarities between groups using Past3 software [The results of feed intake, average daily gain, and short-chain fatty acids were analyzed by analysis of variance (ANOVA) followed by Tukey\u2019s post hoc test, with Norway) .Feed intake varied considerably during the study for all mice. A significant increase was observed between 4 and 7 day, followed by a return to the baseline feed intake afterwards. Intriguingly, feed intake decreased significantly after day 18 . Dietaryp < 0.05; Average daily weight gain (ADG) varied during the study , while they were not distinguishable on day 0 (p < 0.05). On day 7, the groups that consumed melanoidin malts were all significantly different from the group that consumed 0% melanoidin malts (p < 0.05). On day 14, the 75% and 100% groups clustered significantly and separately from the 0% and 25% groups (p < 0.05). Long-term (day 21) consumption of melanoidins resulted in significant clustering, separating the 50%, 75%, and 100% groups from the 0% and 25% groups (p < 0.05).The NMDS plots for days 0, 3, 7, 14, and 21 showed that the gut microbiota profiles of the five groups became distinctly different at days 3, 7, 14, and 21 at days 7, and 21. Barnesiella abundance was significantly higher in low percentage melanoidin malts , as well as Bifidobacterium (Akkermansia (p < 0.005). Significant increases in Parasutterella were present in the mice that were fed 0%, 25%, and 50% melanoidin malts during the study, but the relative abundance of Parasutterella was lower in groups that received 75% and 100% melanoidin malts throughout the study from day 0 to day 2, and there were no or only slight differences among the days Dorea .The relative abundance of several Firmicutes genera (acterium and Akkeermansia were incThe purpose of this study was to investigate the impact of melanoidin-rich malts, which may represent a major source of specific dietary melanoidins for humans, on the composition of the gut microbiota and their potential prebiotic effects. It was reported that a large proportion of HMW melanoidins are excreted in feces and urine . We noteThe consumption of coffee melanoidins had no effect on the weight gain of rats that were fed a high-fat diet . HoweverThe quantification of SCFAs in feces is a useful index of the fermentative potential of the gut microbiota. In this study, the proportion of acetate was stable throughout, but the quantities of propionic and butyrate decreased. The concentrations of butyrate, acetate, and propionate were higher in the mice that consumed 100% melanoidin malts compared to 0% melanoidin malts at days 14 and 21, respectively. The total SCFA concentrations were stable in mice that consumed 100% of melanoidin malts, while a significant decrease was observed in the control group, which was consistent with the higher SCFA concentration observed in rats that were fed bread crusts compared to the controls . ImportaAkkermansia spp. and Ruminococcus spp., while Roseburia spp. and Lactobacillus spp. were more abundant in the cecum of rats fed barley malt, compared to the control group that was enriched in Oscillospira spp. and Dorea spp. [Ruminococcus spp. and Lactobacillus spp. had higher abundances in mice fed 0% melanoidin malts. However, there were significant decreases in Dorea and Oscillibacter throughout the study, which may be in line with a previous study showing the reduction of some genera belonging to Firmicutes, such as Dorea, after oral supplementation of glutamine [Roseburia spp. was observed during the study, which may be in line with a study on Roseburia growth in healthy humans who consumed whole-grain barley for 60 days [Clostridium cluster XIVb compared to the pure cellulose diet of suckling piglets [Clostridium cluster XIVb during this study, with slight differences between the groups.In this study, the relative abundance of Firmicutes decreased, but Bacteroidetes, Verrucomicrobia Acinobacteria, and Proteobacteria increased during the study, which was consistent with a previous study that included higher abundances of Verrucomicrobia and Acinobacteria and a lower abundance of Firmicutes in rats fed barley malt . Zhong erea spp. . We obselutamine . A signi 60 days . The eff piglets . We indeBacteroides spp. in mice that were fed fewer melanoidin malts, especially 25% melanoidin malts, which may be in line with the previous in vitro report of an increase in the proportion of Bacteroides spp. in light- and medium-roasted coffee compared to dark-roasted coffee [Bacteroides spp. are known for their ability to ferment different mucin polysaccharides because they possess a wide range of carbohydrate-depolymerizing enzymes [Bacteroides spp. Relative abundances of Barnesiella spp. were found at low levels, which made up less than 1% of an individual\u2019s total gut bacteria; they, in particular, are known for their ability to control the spread of highly antibiotic-resistant bacteria [Barnesiella were detected in a guinea pig model fed a Western diet associated with metabolic syndrome [Barnesiella, Ruminococcus, and Bifidobacterium in a rodent colitis-associated colorectal cancer model, which suggested resistant starch might have a beneficial effect on patients with ulcerative colitis [Barnesiella were observed, especially in the mice fed 0% and 25% at 21 days. A decreased abundance of Alistipes was also shown in the present study. Wang et al. similarly showed that oligosaccharide treatment decreased the levels of Alistipes in mice with constipation [In this study, we observed a significant increase in d coffee . Bactero enzymes . Moreovebacteria ,47. Signsyndrome . However colitis . In the tipation .Akkermansia spp. are known as mucin-degrading bacteria that use glycated proteins as an energy source [Akkermansia muciniphila are known for their ability of anti-inflammatory effects in the intestine. A significant decrease in A. muciniphila was found in colitic mice [Akkermansia spp. in mice that were fed melanoidin-rich malts. Bifidobacterium spp. were also found in high abundances in the melanoidin-rich malt group. Dietary fiber enhances the growth of Bifidobacterium spp. [Bifidobacterium spp. in vitro compared to other anaerobic bacteria [Bifidobacterium spp. was also shown after coffee consumption in humans [Bifidobacterium spp. using a static batch culture [Bifidobacterium spp. Coffee melanoidins are characterized by considerable carbohydrates, but bread crust melanoidins demonstrate a prevalence of amino acids. Thus, the coffee melanoidins increased the growth of Bifidobacterium spp. compared to bread crust melanoidins [Parasutterella, known as the saccharolytic strain, were detected during the study, which might be in line with previous reports of the proportion of Parasutterella that were elevated by carbohydrate consumption in rodent models [y source . Akkermatic mice . We deteium spp. . Coffee ium spp. . The roabacteria . An incrn humans . In addi culture . The typanoidins . The strt models .Bifidobacterium, Akkermansia, and Lactobacillus, although there were no significant differences in the population of Lactobacillus between the groups that consumed 0% and 100% melanoidin malts. These results confirm that the gut microbiota responds differently to different melanoidin-rich foods, and that melanoidin-rich malts appear to exert potentially beneficial changes, a property that could potentially lead to the development of novel prebiotic foods.We conclude that the long-term consumption of melanoidin malts increased microorganisms often considered beneficial, such as"} +{"text": "Wisconsin was the first state to hold an election with in-person voting after stay-at-home orders were issued to limit transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). The statewide primary election, held on April 7, 2020, occurred fewer than 2 weeks after the statewide \u201cSafer at Home\u201d orderhttps://stacks.cdc.gov/view/cdc/90768). In addition to the nearly 500 poll workers, election inspectors, and chief inspectors, Milwaukee city health department personnel and the Wisconsin National Guard were assigned to support mitigation efforts at each of five Milwaukee polling sites and the central count location. Mitigation measures implemented at the direction of the city health department complemented public messaging campaigns to encourage absentee voting. According to the Milwaukee Election Commission, comparing the number of persons voting in the spring of 2016 with those voting in the spring of 2020, the percentage of persons who voted by absentee mail-in ballots increased approximately fifteenfold, from 4.1% to 68.0% of voters; those who voted early increased by 160%, from 4.7% to 12.2% . Although the proportion of those who voted in person on election day decreased 78%, from 91.2% to 19.8% ,On March 3, 2020, CDC published interim guidance to prevent spread of SARS-CoV-2 at polling locations were obtained from the Wisconsin Electronic Disease Surveillance System (WEDSS).An estimated 95% of persons with COVID-19 develop symptoms within 2\u201314 days after exposure , compareThese data provide an initial assessment of potential impacts of public health efforts to mitigate COVID-19 transmission during an election. No clear increase in cases, hospitalizations, or deaths was observed after the election, suggesting possible benefit of the mitigation strategies, which limited in-person voting and aimed to ensure safety of the polling sites open on election day. Epidemiologic trends were likely also influenced by a relatively lower turnout of voters overall compared to spring 2016.These data provide preliminary evidence that CDC\u2019s interim guidance for ensuring various voting options, encouraging physical distancing, personal prevention practices, and employing environmental cleaning and disinfection lower COVID-19 transmission risk during elections ("} +{"text": "It remains unknown how the COVID-19 pandemic has changed neuro-oncology clinical practice, training, and research efforts.We performed an international survey of practitioners, scientists, and trainees from 21 neuro-oncology organizations across 6 continents, April 24\u2013May 17, 2020. We assessed clinical practice and research environments, institutional preparedness and support, and perceived impact on patients.Of 582 respondents, 258 (45%) were US-based and 314 (55%) international. Ninety-four percent of participants reported changes in their clinical practice. Ninety-five percent of respondents converted at least some practice to telemedicine. Ten percent of practitioners felt the need to see patients in person, specifically because of billing concerns and pressure from their institutions. Sixty-seven percent of practitioners suspended enrollment for at least one clinical trial, including 62% suspending phase III trial enrollments. More than 50% believed neuro-oncology patients were at increased risk for COVID-19. Seventy-one percent of clinicians feared for their own personal safety or that of their families, specifically because of their clinical duties; 20% had inadequate personal protective equipment. While 69% reported increased stress, 44% received no psychosocial support from their institutions. Thirty-seven percent had salary reductions and 63% of researchers temporarily closed their laboratories. However, the pandemic created positive changes in perceived patient satisfaction, communication quality, and technology use to deliver care and mediate interactions with other practitioners.The pandemic has changed treatment schedules and limited investigational treatment options. Institutional lack of support created clinician and researcher anxiety. Communication with patients was satisfactory. We make recommendations to guide clinical and scientific infrastructure moving forward and address the personal challenges of providers and researchers. Clinical trial suspension, including phase III trials, was a hallmark of the pandemic.Practitioners and researchers perceive significant personal risk in doing their jobs.No consensus exists about risks for SARS-CoV-2 infection in neuro-oncology patients.This is the first international study of the impact of the COVID-19 pandemic on the field of neuro-oncology. We observed changes in treatment options for patients with brain and spine tumors, as well as burdens on clinicians and researchers. We highlight major challenges in the field, including suspension of clinical trials, financial pressures for practitioners to see patients in person, and unmet safety concerns and high anxiety of practitioners and scientists. We also identified positive outcomes in perceived quality of communication with colleagues, patients and families, and reduced travel and expenses for patients. This work serves as a benchmark assessment of the field during the early days of the pandemic.1 Neuro-oncology, which focuses on treating patients with primary and metastatic brain and central nervous system (CNS) tumors and neurologic complications of cancer, has faced challenges, particularly in maintaining quality patient care and conducting clinical trials and laboratory research.The COVID-19 pandemic has created many challenges for healthcare.2 There are significant differences in incidence by world region, with the highest incidence of malignant brain tumors in Northern Europe and Canada and the lowest in Southeast Asia.The provider pool in neuro-oncology is relatively small. In 2018, there were 2600 members in the Society for Neuro-Oncology (SNO) database, of which 1040 (40%) were clinical members, including physicians, nurses, and nurse practitioners. Equally small numbers of neuro-oncologists practice in Europe, Asia, and the rest of the developed world. In the United States, approximately 25 000 malignant primary brain tumors are diagnosed annually.4 Immunotherapy is not approved for primary brain tumors; it remains under investigation and is sometimes used as an off-label treatment at the time of tumor recurrence.Gliomas are the most aggressive primary brain tumor, and they make up the majority of diagnoses in neuro-oncology. Standard treatment for high-grade gliomas includes surgical resection, followed by radiation and temozolomide, an alkylating chemotherapy, and more recently, adjuvant use of tumor-treating fields. Often during the course of care, patients receive dexamethasone, which reduces edema; bevacizumab, a monoclonal antibody that reduces angiogenesis and edema; and/or lomustine, an alkylating chemotherapy. Radiation, temozolomide, and lomustine all commonly cause myelosuppression and lymphopenia.5 Patient management guidelines6\u20138 have emerged, and discussions have centered on how to approach brain tumor patient treatment in resource-limited settings and when significant exposure risk to patients and health care providers exists.9 These recommendations notwithstanding, it remains unknown as to what practically changed during the pandemic. The pandemic has also affected medical teams. While physicians and allied professionals are accustomed to dealing with stress and dying patients, the burden of these new challenges has been unprecedented on professional and personal lives. Clinicians need support during the COVID-19 pandemic,10 and guidelines exist for managing psychological stress and maintaining healthy physical and mental states.11 However, we lack basic measurements of what clinicians and researchers are experiencing.The pandemic has required re-organization of clinic visits, treatment and diagnostic testing schedules, and the development of new processes managing therapy-related complications.13 Many programs are facing financial challenges that jeopardize the continuity of their training mission and the ability to accept new trainees.Medical education was restructured so medical students, residents, and fellows may continue learning to take care of patients and advance through their training programs.Finally, scientists in neuro-oncology, attempting to understand the mechanisms underlying brain tumor development or identify new treatments, have had to stop or postpone costly experiments and are now at risk of losing funding to continue supporting these effortsHere, we sought to address these issues and evaluate the perceived effects of these changes on neuro-oncology patient care. We asked the international community of healthcare providers, scientists, and trainees in the field to share their experiences during the pandemic. This survey tool is not a method to identify the root causes of the problems we identify. This framework will guide further studies and recommendations on how to best take care of CNS cancer patients, support clinical caregivers, and identify opportunities for institutions to continue to advance their research mission. These findings and principles will be broadly applicable to other oncology specialties and those caring for patients with chronic disease.www.surveymonkey.com) from April 24 to May 17, 2020 and contained 134 questions, presented in a modular format with smart logic. We used R 4.0.0 software to generate summary statistics and perform statistical analyses. Categorical variables were compared using chi-square tests, and continuous variables were compared using t-tests (when only 2 comparison groups) or ANOVA (when more than 2 comparison groups). Data on sex, age, and ethnicity of the respondents were not collected for this survey.The survey was deveA total of 582 responses were received. Respondents were located in the United States and internationally ; 48.9% believed that steroids increase susceptibility to SARS-CoV-2 infection (173/487), but 43.8% reported they were unsure and needed more evidence (155/487). Twenty-eight percent believed that radiotherapy increases infection risk (100/487). Forty-six percent believed that temozolomide use increases susceptibility (165/487), and 21.6% believed that immunotherapy increases the risk (77/487).The pandemic required changes to clinical practice and clinical trial opportunities, and in some cases, clinicians reported pressures related to billing. While practitioners voiced concerns about the emotional well-being of their patients, there were perceived positive benefits to patients in terms of communication of treatment plans and other aspects of care.P = .003). Regarding survival, 44.5% thought practice changes due to the pandemic would reduce survival, outside of any direct effect of SARS-CoV-2 infection in their patients (151/339). This perception was highest in Asia compared to Europe and the United States , but not statistically significant (P = .101). Almost all respondents transitioned to the use of video or telephone visits for some aspects of clinical care . A majority reported this transition was at least somewhat difficult; however, 80.1% received adequate information technology support (285/351).Ninety-four percent of participants reported changes in clinical practice due to the pandemic (361/386). The proportion reporting changes was highest in the United States , compared to Europe and Asia .While practitioners greatly used telemedicine, 85.9% (322/375) canceled what they deemed nonessential patient visits, and 16.2% moved patient visits at least 2 months into the future (61/376). Of these, 55% of scheduling changes were requested by patients or caregivers (206/371). Regarding chemotherapy scheduling, 12.3% (35/285) of practitioners moved inpatient chemotherapy by up to 2 weeks and another 6.7% moved it out by up to a month (19/285). Regarding referrals, 27.2% (101/372) practitioners referred patients to other institutions as a result of pandemic pressures, and 65.4% (233/356) changed MRI schedules for their patients. Referrals to other providers were most frequently reported in Asia , as compared to Europe or the United States . About 59.5% (275/462) of practitioners also agreed or strongly agreed that the quality of care exchange would be positively affected by the change in norms during the pandemic. This was highest in Asia , compared to the United States (62.2%) or Europe .When asked whether there may be any positive aspects of the pandemic, 88% agreed or strongly agreed (415/471) that new technologies applied toward patient care were a positive outcome. In fact, 84% (403/474) agreed or strongly agreed that virtual meetings, including tumor boards, were very helpful. Remarkably, 74.3% (347/ 467) of respondents agreed or strongly agreed there was increased satisfaction of patients and families, due to decreased burdens of spending time and money traveling to appointments. This was highest in Asia , compared to Europe and the United States . Overall, 29.4% (94/320) of respondents had not received effective support in billing for these types of visits. Among those who reported billing for telephone and video visits, 82.8% (193/233) reported receiving effective support as compared to only 35.5% (27/76) of those who did not bill for telephone and video visits (P < .001). Additionally, nearly 10% (28/322) of respondents felt pressured by their institution to do in-person visits, because of billing needs and not because patient care necessitated an in-person visit; this pressure was greatest in Asia , followed by the United States and then Europe .In terms of reimbursement, 25.9% (83/321) of respondents stated they were not billing for technology-assisted visits. This was highest in Asia and Europe , compared to the United States , with 50% for phase I trials (99/198), 52% for phase I/II trials (102/193), 53% for phase II trials (106/197), and 62% for phase III trials 124/202; . The effTwenty-eight percent of respondents believed that radiotherapy increases susceptibility to SARS-CoV-2 (100/363). Radiation oncology plans for high-grade glioma were unchanged in 77.1% (37/48); 16.7% of cases were delayed by 2\u20134 weeks (8/48). For other indications, less than 40% of radiation oncology plans remained unchanged (18/48); approximately 58.3% (28/48) were delayed by at least 2 weeks. In cases of modified radiation plans, 68% (17/25) were changed to shorter courses with higher daily doses or shorter courses with a lower total dose of cases that were planned with an endonasal approach were converted to craniotomy because of guidelines from respective institutions and surgical organizations. Notably, in cases where there was inadequate personal protective equipment (PPE), approximately 19.5% (16/82) of respondents reported already scheduled surgical procedures proceeding at times or very often.Neuro-oncology laboratory-based research significantly slowed during the early months of the pandemic. Overall, 63% of respondents closed their laboratories (34/54), with the number being 78.6% in the United States (22/28); 72.7% of respondents stopped long-term experiments (32/44). Respondents were not asked how long these laboratories were closed. Regarding funding prospects, 47.1% (24/51) were \u201cvery concerned\u201d about their own research funding because of the economic strains associated with the pandemic. For 34.9% (22/63), grant submission deadlines had been postponed, while 48.7% (19/39) believed that pandemic-related changes gave them more time to write scientific manuscripts. Nearly 30% of respondents (17/57) reported their academic careers would be altered. For the US-based respondents, only 13.3% (2/15) reported that a visa status was at risk because of pandemic-related pressures or policies; of note, the survey was conducted prior to the June 22, 2020 presidential executive order suspending H1B and other foreign worker visas.P = .0016). Of those with salary reductions, 53.6% (74/138) had salaries reduced by at least 20%. Four percent (16/434) of respondents had been furloughed or fired. The majority of respondents in Asia reported salary reduction, as compared to 33.2% US respondents (68/205) and 21.6% European respondents . This was higher in private practice as compared to academic institutions and was highest in the United States , compared to Europe or Asia .While approximately 30% (125/433) of respondents reported increased work hours since the pandemic started, 37% (160/436) had their salary temporarily reduced. This was higher for respondents who primarily treated adults as compared to children . Regarding personal fears, 81.4% (188/231) of practitioners had moderate or severe fear for the health of their own families, specifically because of their clinical duties; 71.4% (5/7) of researchers reported that they were fearful for their health, specifically because of their research duties. Of all respondents, 53.8% (161/299) had a moderate or severe concern about transmitting SARS-CoV-2 to their family, and 37.4% (111/297) had moderate or severe concerns about transmitting to other health care workers. \u201cSevere concern\u201d about one\u2019s own health and survival was reported in approximately 10% (27/298) of all respondents. While a majority faced increased stress, only 56% (242/432) had psychosocial support offered by their institution. Institutional psychosocial support availability varied significantly by region, with 72% of US respondents (147/203) reporting they were offered support, compared to 49.5% in Europe (48/97) and 22.4% in Asia .The majority of respondents reported increased stress during the early months of the pandemic. This was higher in the United States , compared to Asia and Europe , and 40% (14/35) reported concerns they would not be able to completely fill neuro-oncology fellowship slots for 2021.14 and analyses of the caregiver, not-for-profit and brain tumor charity experiences.16 Our international survey provides data that reveal the impact of the pandemic on the practice of neuro-oncology care, its effects on clinical caregivers and patients, and research and other insurance reimbursement policies for telemedicine use should be improved. Ten percent of respondents felt pressured by their institution to continue to see patients in person because of billing considerations. While there may be more nuanced reasons for this that our survey did not capture, this compounds stress without improving patient care, and clinical societies should advocate toward the end of this practice. Beyond the perceived health risks of clinical practitioners and researchers, the degree of reported professional caregiver anxiety and depression should be addressed by institutions.18\u201323 this is not certain and there remain open questions for further research, specifically in the care of patients with brain tumors. There are strongly divergent opinions on whether or not having a brain tumor increases the risk of contracting the virus and whether or not temozolomide and standard steroid dosing affect susceptibility. Retrospective and laboratory-based studies may yield insights. Additionally, comorbidities in the brain tumor population, such as venous thrombosis and pulmonary embolism, or pulmonary disease in those with Pneumocystis jirovecii, may have ramifications for the susceptibility of this patient population to infection with SARS-CoV-2.While there are early observations that cancer patients in general may be more vulnerable to developing COVID-19,24 Our study did not address aspects of discriminatory behavior as a result of the COVID-19 pandemic, nor were we able to assess the impact of stressors faced by women providers and single parents responsible for the care and education of their children.A study of this kind is not without limitations given the fluid nature of the pandemic and varied institutional, national, and international responses. Due to the way that the survey was advertised, it is not possible to calculate a response rate. The number of total responses represents a small proportion of membership in professional organizations that were contacted about participation, suggesting that only a small proportion of the neuro-oncology community was captured by this survey. The survey was offered only in English, which limited participation from non-English speakers. These factors introduce the possibility of selection bias. While we were able to capture the burden providers felt related to the angst over uncertainty and the well-being of their patients, staff, families, and themselves, we recognize that women and people of diverse backgrounds may have been impacted in ways we did not capture due to the lack of inclusion of these demographic variables. The xenophobia that emerged resulting in bias faced by Asian colleagues and patients reported elsewhere is unprecedented.Our work serves as a baseline appraisal of neuro-oncology during the early months of the pandemic. Evidence suggests practitioners are at risk for burnout. Clinical trial and off-label options are being reduced. Standard treatment options are being modified. New research efforts have been slowed. On the other hand, our assessment provides institutions and advocacy groups with a framework to intervene. As we all learn more, our hope is that such interventions will make oncologic care more efficient and improved on the other side of the pandemic.This work was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health (NIH) under award numbers R01 NS107833 and R01 NS117149 (to M.G.C.), grant 2015215 from the Doris Duke Charitable Foundation (M.G.C.), and the generosity of the friends and families of Larry Stark and Brett Pickle (M.G.C.). Q.T.O. is supported by a Research Training Grant from the Cancer Prevention and Research Institute of Texas (RP160097T). The funding sources had no role in any decisions regarding the survey questions, analysis, or writing of the manuscript.vdab035_suppl_Supplementary_MaterialsClick here for additional data file."} +{"text": "When available, SARS-CoV-2 vaccines will be deployed to countries with limited immunization systems.We conducted an immunization capacity assessment of a simulated WHO African Region country using region-specific data on immunization, population, healthcare workers (HCWs), vaccine cold storage capacity , and characteristics of influenza vaccines to represent future SARS-CoV-2 vaccines. We calculated monthly increases in vaccine doses, doses per vaccinator, and cold storage volumes for four-month SARS-CoV-2 vaccination campaigns targeting risk groups compared to routine immunization baselines.Administering SARS-CoV-2 vaccines to risk groups would increase total monthly doses by 27.0% for \u226565 years, 91.7% for chronic diseases patients, and 1.1% for HCWs. Assuming median nurse density estimates adjusted for absenteeism and proportion providing immunization services, SARS-CoV-2 vaccination campaigns would increase total monthly doses per vaccinator by 29.3% for \u226565 years, 99.6% for chronic diseases patients, and 1.2% for HCWs. When we applied quartiles of actual African Region country vaccine storage capacity, routine immunization vaccine volumes exceeded national-level storage capacity for at least 75% of countries, but subnational levels had sufficient storage capacity for SARS-CoV-2 vaccines for at least 75% of countries.In the WHO African Region, SARS-CoV-2 vaccination campaigns would substantially increase doses per vaccinator and cold chain capacity requirements over routine immunization baselines. Pandemic vaccination campaigns would add volume to national-level stores already at their limits, but sufficient capacity exists at subnational levels. Immediate attention to strengthening immunization systems is essential to support pandemic responses.None There is a robust pipeline of SARS-CoV-2 vaccine candidates in various stages of preclinical and clinical development , 2. WhilThe SARS-CoV-2 pandemic has already caused more severe health impact than the 2009 H1N1 pandemic , and natSince 2014, a concerted global effort has improved cold chain infrastructure in developing countries , 10, whiThis analysis is similar to cold chain capacity assessments that are performed routinely by countries in preparation for new vaccine introductions . We aimeWe used a standard routine immunization schedule for the simulated country based on current WHO policy recommendations 13]. We. We13]. We identified WHO prequalified routine vaccine products , and we th percentile, 50th percentile, 75th percentile, and upper range values of total country storage capacities, as well as the median proportion of national-level stores and health facility-level stores to total country capacity. For comparisons, capacity data were standardized by dividing the total cold storage capacity by the population of children aged < 2 years in each country.We estimated vaccine storage volumes using WHO tools and guidance , 20, 22.th percentile, 50th percentile, 75th percentile, and upper range nurse density for African Region countries, and we determined median values for other WHO Regions. To assess the range of immunization program workloads that would be experienced across the African Region, we applied the different nurse density estimates to the simulated country. We multiplied each nurse density estimate by 46%, the proportion of nurses estimated to provide immunization services [We calculated the monthly doses and cold storage volumes required for routine immunization programs and SARS-CoV-2 vaccination campaigns to reach 90% of target populations . We deveservices , 25. We services , 27. To services . The WHOThis work had no specific funding support.We simulated a country of 20 million people in the African Region . The perAs in most developing countries, all routine vaccination services in the simulated country would be received by children aged <5 years and 9 through 14 years. Assuming systems would also be in place to provide immunization services to HCWs, established routine immunization platforms would reach 31.0% of the national population. A total of 1,020,931 routine vaccine doses would be given each month. Each month during the SARS-CoV-2 vaccination campaign, 275,313 doses would be delivered targeting persons \u226565 years, 935,878 targeting persons with chronic diseases, 11,511 targeting HCWs, and 1,058,536 targeting all risk groups combined . TargetiUsing the median value of nurse density from countries in the African Region , we estimated 13,840 nurses in the simulated country, of which an estimated 6,366 (46%) would provide vaccination services. Accounting for baseline and pandemic absenteeism, one vaccinator would administer 165.3 routine doses per month at baseline and 179.7 routine doses per month during the pandemic .During the SARS-CoV-2 vaccination campaign, the number of persons vaccinated monthly per vaccinator would be 48.5 targeting persons \u226565 years, 164.7 targeting persons with chronic diseases, 2.0 targeting HCWs, and 186.3 targeting all risk groups combined. Compared to routine vaccines given at baseline, SARS-CoV-2 vaccination of risk groups would increase the immunization program workload for vaccinators by 29.3% for persons \u226565 years, 99.6% for persons with chronic diseases, 1.2% for HCWs, and 112.7% for all risk groups combined. Due to nursing personnel shortages in the African Region, the immunization program workload would be substantially lower if nurse density were similar to other WHO Regions. Repeating the analysis using nurse density estimates from other WHO Regions , the immunization program workload would increase by 26.9% using estimates from the Americas, 36.6% using estimates from the Eastern Mediterranean, 10.4% using estimates from Europe, 42.2% using estimates from South-East Asia, 19.8% using estimates from the Western Pacific, and 24.3% using global estimates (with the relative proportion changes being the same regardless of risk group) .th percentile: 4,177; 50th percentile: 6,366; 75th percentile: 12,654; and upper range value: 62,957 was still lower than all other WHO Region nurse density estimates . The upper range value exceeded the nurse density estimate for all other WHO Regions . Additional monthly doses per vaccinator for SARS-CoV-2 risk groups ranged from 4.9\u201373.9 targeting persons \u226565 years, 16.7\u2013251.1 targeting persons with chronic diseases, 0.2\u20133.1 targeting HCWs, and 18.8\u2013284.0 targeting all risk groups combined.We repeated the workload analysis using quartiles and upper range estimates for nurse density from countries in the African Region . For each nurse density value, we estimated the following number of vaccinators: 25: 62,957 . The 75tWe applied standardized African Region vaccine cold storage capacity range and quartiles to the simulated country. The total storage capacity would range from 38,403 L to 1,605,826 L, and national-level storage capacity would range from 12,535 L to 524,141 L . We asseWe estimated the volume required to store SARS-CoV-2 vaccines in tertiary packaging at the national level and in secondary packaging at subnational levels and 3. AWe used WHO tools and guidelines to estimate the operational impact of a SARS-CoV-2 vaccination campaign in the African Region , 22. WhiOur analysis revealed that the national-level storage capacity would be insufficient to accommodate additional SARS-CoV-2 vaccines for a vaccination campaign targeting risk groups as large as persons \u226565 years (3.1% of the population) in at least 75% of African Region countries. However, all African Region countries likely have sufficient subnational-levels storage capacity to accommodate SARS-CoV-2 vaccines for mass vaccination campaigns. This means that there is insufficient excess cold storage capacity at the national level, whereas once vaccines are distributed to subnational levels in the health system there should be adequate storage capacity. This bottleneck in the vaccine cold chain at the national level can be addressed in advance by decreasing reserve stocks, shortening supply intervals, removing products from tertiary packaging earlier in the chain, distributing vaccines to the subnational levels, and/or installing or leasing more refrigeration capacity. However, implementation of SARS-CoV-2 vaccination campaigns will also require increases in accompanying dry goods, such as syringes, safety boxes, cotton, alcohol, and personal protective equipment, necessitating additional planning and budget for operations and waste management. More in-country vaccine shipments will be required to distribute routine and SARS-CoV-2 vaccines if transportation capacities are not increased, adding costs and logistical challenges. Care should be taken not to disrupt routine vaccine supply and distribution, as stockouts of routine vaccines will exacerbate national immunization programs already impacted by the pandemic.While we found that the aggregate subnational-level storage capacities are adequate for SARS-CoV-2 vaccines, with very large margins expected for a majority of countries, it should be noted that it is not possible nor practical to fill all available subnational-level storage capacity. For example, at the health facility level, standard vaccine refrigerators may have multiple times the capacity needed for vaccines used at that facility, but that excess capacity cannot be easily used to store vaccines for other facilities.The complicated logistics of fully utilizing the available storage capacity at the lower levels of the cold chain makes it impractical. Nevertheless, our findings show that there is ample vaccine storage capacity available at subnational levels, and creative management of both routine and campaign vaccines could leverage some of that excess capacity during the SARS-CoV-2 vaccination campaign period.Another major obstacle for SARS-CoV-2 vaccine delivery in the African Region will be the availability of qualified vaccinators. The African Region has the smallest health workforce of any WHO Region , and theThere is reason for optimism that the African Region SARS-CoV-2 vaccination response will be much improved from the 2009 H1N1 pandemic experience. Over the last ten years, a concerted global effort has greatly improved cold chain infrastructures and increased storage capacity . FurtherA SARS-CoV-2 vaccination campaign would be greatly facilitated if vaccine delivery were simplified . While aWHO has advised that certain products would be challenging to include in national immunization schedules if they do not meet specific Programmatic Suitability Criteria . VaccineOur study should be interpreted in light of its strengths and limitations. Our use of real-world data inputs and WHO tools and guidance strengthen the generalizability of the results and comparability to other cold chain capacity assessments. Since there is no currently licensed SARS-CoV-2 vaccine, we used the characteristics of influenza vaccines as proxies. If a SARS-CoV-2 vaccine requiring only one dose for protection is eventually licensed, the estimated doses and storage volumes required could substantially decrease. Conversely, if only products requiring ultra-low temperature cold chain or extra effort and training to administer are licensed, the operational feasibility of mass vaccination campaigns for developing countries would be very limited. We applied WHO recommended routine vaccination schedules and product characteristics , 37, howThe development of candidate SARS-CoV-2 vaccines must take into account operational realities and programmatic suitability in developing countries. While we believe that African Region countries currently have sufficient overall cold chain capacity to accommodate SARS-CoV-2 mass vaccination campaigns, our study highlights the limitations in cold storage capacity at national levels and in workforce availability to administer these vaccines. Vaccination of risk groups with SARS-CoV-2 vaccines is possible with sufficient planning and infrastructure strengthening, but we anticipate risks to routine immunization and significant logistical challenges. Further, the development of products that are not programmatically suitable for use in developing country contexts will result in massive inequities, and concerted global efforts are urgently required to ensure that appropriate preventive interventions are made available to all who need them globally. Resources must be mobilized urgently to ensure that infrastructures and training are in place to maximize the impact of future SARS-CoV-2 vaccines in the African Region and other developing country settings.Supplement 1Supplement 2020"} +{"text": "ToRCH is the acronym for several pathogens associated with pregnancy complications and sequelae in the unborn or newborn child. Particularly primary infections during pregnancy are associated with increased risk. Seroprevalence data of ToRCH infections are important, especially in countries with weak disease surveillance systems, to estimate immunity and vaccination levels, as well as exposure rates and thus the risk of infection during pregnancy. A systematic literature search spanning a 30-year time period was conducted to identify serosurveys on ToRCH pathogens in Southeast Asia. The 96 identified studies showed that some pathogens were well studied, while only limited data were available for others. Studies from the better-developed countries of the region were more abundant. Moreover, seroprevalence data were often limited to a certain geographical region within the country or to certain cohorts, there was an evident lack of recent serosurveys, and the study quality was often not adequate. Well-designed and area-wide serosurveys of ToRCH pathogens are clearly warranted. If combined with risk factor analysis, these studies may guide the development and implementation of effective measures for infection prevention, especially during pregnancy. In addition, educational programs for health care workers and for pregnant women during antenatal care are urgently needed. Toxoplasma gondii (T. gondii), others (such as Varicella zoster virus\u2014VZV and Primate erythroparvovirus 1\u2014B19V), Rubella virus (RV), Cytomegalovirus (CMV), and Herpes simplex virus (HSV) [ToRCH is the acronym for several pathogens associated with pregnancy complications. ToRCH pathogens include us (HSV) (Table 1us (HSV) ,4,5. Usuus (HSV) .The global impact of congenital infections remains largely unknown. In developing countries, the burden is thought to be higher than in industrialized countries, because of coinfections of the mother or mother and child malnutrition . In addiIn several Southeast Asian countries, the neonatal mortality rates (NMR) still rank among the highest worldwide. The upper-middle-income countries Malaysia and Thailand had NMR of 4.3 and 5.0, the lower-middle-income countries Cambodia and Laos reported NMR of 14.4 and 22.7 and only the high-income country Singapore reported a very low NMR of 1.1 per 1000 live births in 2018 . It is lPresence of immunoglobulin (Ig) G antibodies against a specific pathogen indicates past infection or vaccination. Consequently, IgG serosurveys represent an efficient approach to estimate immunity and vaccination levels, as well as exposure rates. When combined with socio-demographic and behavioral data, such studies allow the identification of risk factors (RFs) for infection and of vulnerable population groups, as well as the need for introducing new vaccines . HoweverTo get an overview over the current situation in Southeast Asia, a systematic review of ToRCH serosurveys was conducted. Focus was put on Cambodia, Laos, Myanmar, Malaysia, Singapore, Thailand, and Vietnam, because of their geographic proximity and their social and economic disparities. Based on the available seroprevalence data, we assessed the risk of pregnant women to become infected and identified RFs for past infection.A systematic literature review was conducted. The database PubMed was searched in January 2019 for studies published between 1 January 1989 and 31 December 2018. The search terms included Name of the pathogen (abbreviation as well as full name), Name of the country (different spellings if applicable) and the Year range (1 January 1989 to 31 December 2018) a. After https://www.surveysystem.com/sscalc.htm, 11 January 2019) using the given sample size and overall seroprevalence. If studies included more than one study cohort, the seroprevalence of each cohort was considered separately if it met the inclusion criteria were extracted from the studies. If not available, a free online sample size calculator was applcriteria b. If onlcriteria b, the IgThe quality of the studies was evaluated by applying criteria of a recent review after slIn total, 96 studies were eligible . The criteria \u201cOverall result given\u201d was fulfilled most often (n = 92), while only 14 studies provided the least fulfilled criteria \u201cSample size calculation done\u201d . Five of these studies reported seroprevalence rates in more than one study population and aduFor Laos, the only available study dated back to the early 1990s and the seroprevalence was relatively low (15.3%) in the general healthy population .n = 17) of the 21 seroprevalence rates mentioned in the 19 studies exceeded 30.0%. The seroprevalence among pregnant women ranged between 33.5% [Nearly half of the studies (19/42) were from Malaysia and the seroprevalence ranged from 10.6% to 59.7%en 33.5% and 39.7en 33.5% with an en 33.5% . Most stThe two regionally limited studies from Myanmar targeted pregnant women and the seroprevalence ranged from 30.2% to 31.7%The two studies from Singapore showed a higher rate in the HIV-infected cohort (23.7%) than in Many studies were from Thailand (14/42) covering diverse study cohorts with a wide range of reported seroprevalence rates . The hige: 4.2% . Most stge: 4.2% .T. gondii seroprevalence included different populations with the majority focusing on healthy pregnant women (15/42) or HIV-infected individuals (8/42), with the seroprevalence mostly being higher among HIV-infected people. While the large majority (28/42) of the studies used a commercial ELISA kit, other detection methods were used especially in studies published before 2000. Similar seroprevalence rates were found using the different test methods in the respective countries and study populations.For 15 of the reported seroprevalences, no study year was available. The remaining studies were conducted between 1992 and 2015T. gondii antibodies.Only 21 studies included an assessment of RFs for seropositivity to T. gondii seropositivity. This RF did not seem to be restricted to a specific study population. Identified RFs were often indirectly linked to age such as parity [Nine studies conducted in Laos, Malaysia or Thailand reported that higher age already in the 15- to 24-year-olds . The only study from Malaysia reported a seroprevalence of 86.6% among HIV-infected patients in Kuala Lumpur . LikewisIn the three studies from Singapore, the seroprevalence ranged from 55.3% to 91.7%Nearly half of the studies were from Thailand (5/11) and all except one were conducted in Bangkok. The seroprevalence ranged from 52.8% to 92% . High seAll studies in the region reported VZV IgG seroprevalence rates exceeding 50% . The earRegardless of the study year, all identified studies used enzyme immunoassays (EIA) for detection of VZV IgG antibodies.Several studies suggested that VZV IgG seroprevalence increases with age. In fact, the lowest seroprevalence was found among children aged less than 4 years and 1- to 6-year-olds were from Thailand, where B19V IgG seroprevalence rates ranged between 10.9% and 20.2In the two studies from Singapore, seroprevalence rates of 16.2% and 30.0% were reported in a healthy study population and in pRecent studies were missing. Before 2000, B19V IgG seroprevalence did not exceed 40% . Due to Due to differing study designs and the limited number of studies, it was difficult to extract trends or identify RFs. In Singapore, highest rates were found in pregnant women and lowest rates in healthy individuals. Whether there is a statistically significant difference in seroprevalence between different age groups remains unknown. In one study, seropositivity increased with age, but remained below 70% even in older participants .Eighteen studies covered anti-RV IgG seroprevalence . Four ofAll studied countries currently use rubella-containing vaccine (RCV) for infants . The only study from Cambodia was conducted before the introduction of RCV in the country ,99 and rIn the three studies from Laos, anti-RV IgG seroprevalence ranged from 43.6% to 86.2%The three studies from Malaysia were conducted after introduction of RCV ,87,88,99In the four studies from Singapore, seroprevalence rates ranged from 71.7% ,90 to 88The six studies from Thailand were also conducted after introduction of RCV ,94,95,96The only study from Vietnam was done before introduction of RCV ,99 and fWhile RV IgG seroprevalence was generally high in all locations, the situation in certain countries is less clear due to the limited number of studies. All studies, except one including only unvaccinated children , reporteThe studies used various types of immunoassays, but seroprevalence results did not seem to vary greatly between these assays.In contrast to the other pathogens, most studies reported RFs for susceptibility to RV rather than for seropositivity. As expected, several studies conducted before introduction of RCV found that younger age groups ,84,97 weSingaporean studies identified Malay ethnicity or permanent residency in Singapore as RF for susceptibility to RV ,92. One Overall, 14 studies on CMV seroprevalence were identified .No studies were found for Cambodia, Laos, or Myanmar. The seroprevalence reported in the three studies from Malaysia ranged between 84.0% to 97.6%In the two studies from Singapore, the seroprevalence values were 87.0% and 96.8Eight studies were identified for Thailand, where the seroprevalence ranged between 52.4% and 100%One study from Vietnam conducted in 1996 included HIV-infected drug users in Ho Chi Minh City and showed an overall seroprevalence of 100% . Seroprevalence was high in all countries and except for one study investigating Thai blood donors , rates wFew RFs for seropositivity to CMV were identified. Although some studies noted an increase of seropositivity with age, this difference was not statistically significant ,102. OneSimilar to studies of other pathogens from Singapore, ethnicity was identified as RF for seropositivity (Non-Singaporean ethnicity) .In total, 19 studies were identified for HSV. The studies included seven seroprevalence rates for HSV-1, 16 for HSV-2 and one for unclassified HSV .No studies on either HSV-1 or HSV-2 seroprevalence were identified for Cambodia, Laos, or Myanmar and only one study from Kuala Lumpur, Malaysia, reporting seroprevalence rates of 70.7% and 53.9% for HSV-1 and HSV-2, respectively, in adult HIV-infected individuals . Two studies were identified for Singapore with seroprevalence rates of 55.8% and 76.7Seven studies were identified for Thailand and the seroprevalence for HSV-1 and HSV-2 was between 56.5% to 91.0%Nine studies were identified for Vietnam and the only reported HSV-1 seroprevalence was 98.0% while HSOverall, HSV-1 seroprevalence seemed to be similarly high in all countries, generally above 55%, irrespective of the study population. When comparing HSV-1 to HSV-2 seroprevalence in similar study populations, HSV-1 seroprevalence seemed to be generally higher than HSV-2 seroprevalence. Most studies (11/19) focused on high-risk groups such as sex workers and HIV-infected individuals. For HSV-1 IgG seroprevalence, there was only one study focusing on the general population . For HSVOne study did not report the method used . Most stMost studies did not identify RFs for HSV-1 seropositivity, except for one where participants of higher age were statistically significant more likely to be seropositive . For anti-HSV-2 IgG seropositivity, higher age was identified as statistically significant RF in Thailand, Singapore, and Vietnam in different study populations ,116,117.As mentioned, study populations of sex workers showed high HSV seroprevalence rates, regardless of the subtype ,109. StuT. gondii), only limited data were available for others, such as VZV and B19V. The majority of the studies was conducted in the better-developed countries of the region, namely Malaysia, Singapore, and Thailand. In contrast, there was a general paucity of studies from Cambodia, Laos, Myanmar and Vietnam. Moreover, seroprevalence data were often limited to a certain geographical region within the country or to certain cohorts. There was an evident lack of recent serosurveys: many studies date back to the early 2000\u2019s or late 1990\u2019s. Finally, the study quality (This review provides an overview about serosurveys of ToRCH pathogens conducted in Southeast Asia during a 30-year time period. While some pathogens were well studied (e.g., quality was ofteT. gondii studies demonstrated a wide disparity in seroprevalence rates ranging from 2.6% in healthy Thai women [T. gondii was limited among pregnant women from the Philippines, Malaysia, and Thailand [T. gondii serostatus during antenatal care is widely discussed in the literature [The ai women to 59.7%ai women . This diai women ,124 wereai women ,59,61,64ai women ,47,61,64ai women . The serai women , their iai women ,128. IndThailand . While sterature . In low VZV seroprevalence was rather high in all studied countries and ranged between 52.8% in young Thai adults and 99.0B19V was the least studied ToRCH-pathogen in the region. The lack of recent data makes it difficult to make well-founded statements about the infection risk during pregnancy. However, the low seroprevalence ranging between 10.9% in Thai undergraduate students and 37.6% in the general Malay population suggestsIn contrast to B19V, many studies covered the vaccine-preventable RV infections. The main goal of rubella vaccination is the prevention of CRS . HoweverDespite the vaccination, local outbreaks of rubella have been described in recent years, which were most likely due to above mentioned immunity gaps ,9. NeverHigh levels of CMV circulation have been reported in Africa, South America, and Asia . Also inHSV-1 is another virus for which the global burden is high . SeropreInterestingly, for most countries, especially Thailand and Vietnam, more studies on HSV-2 than on HSV-1 were available, probably due to the strong influence of sex tourism in these countries. Seroprevalence of anti-HSV-2 IgG among individuals with risky sexual behavior ranged between 24.9% and 79.0Although the present review provides a comprehensive overview of current knowledge of ToRCH pathogens in the region, there are some limitations. Geographical restrictions, different study cohorts and test methods hampered result comparability and the suboptimal quality of many studies raises concerns related to data reliability. However, despite these constraints, the review provides insights into pathogen distribution, identifies immunity gaps and susceptible populations in the region, allows a risk-estimation of primary infections during pregnancy and provides guidance for future research.Women of childbearing age in Southeast Asia are susceptible to many ToRCH pathogens. The paucity of reliable information for several pathogens and the often low quality of the studies warrant comprehensive nationwide serosurveys including pregnant women but also the general population. The data could serve as a basis to evaluate and improve current prevention measures. To raise knowledge and awareness of the risks posed by ToRCH pathogens both in HCW and in pregnant women, is an important first step to prevent fetal loss and congenital malformations."} +{"text": "Culex genus. We retrospectively analyzed sera from domestic and wild birds sampled in 2008 in two wetlands, namely the Inner Niger Delta, Mali, and the Lake Alaotra area, Madagascar. Sera were first tested using a commercial ID Screen West Nile Competition Multi-species ELISA kit. Then, positive sera and sera with insufficient volume for testing with ELISA were tested with a Microneutralization Test. In Mali, the observed seroprevalence in domestic birds was 28.5% 95%CI, 3.1 % 95%CI, 6.2% 95%CI and 9.8 % 95%CI, for West Nile virus (WNV), Usutu virus (USUV), undetermined flavivirus, and WNV/USUV respectively. Regarding domestic birds of Madagascar, the observed seroprevalence was 4.4 % 95%CI for WNV, 0.9% 95%CI for USUV, 1.3% 95%CI for undetermined flavivirus, and null for WNV/USUV. Among the 150 wild birds sampled in Madagascar, two fulvous whistling-ducks (Dendrocygna bicolor) were positive for WNV and two for an undetermined flavivirus. One white-faced whistling-duck (Dendrocygna viduata) and one Hottentot teal (Spatula hottentota) were tested positive for USUV. African and European wetlands are linked by wild bird migrations. This first detection of USUV\u2014as well as the confirmed circulation of WNV in domestic birds of two wetlands of Mali and Madagascar\u2014emphasizes the need to improve the surveillance, knowledge of epidemiological patterns, and phylogenetic characteristics of flavivirus in Africa, particularly in areas prone to sustained, intense flavivirus transmission such as wetlands.The geographical distribution and impact on animal and human health of both West Nile and Usutu viruses, two flaviviruses of the Japanese encephalitis complex, have been increasing during the past two decades. Both viruses circulate in Europe and Africa within a natural cycle between wild birds and mosquitoes, mainly from the Culex genus. WNV has the most widespread geographic distribution ever described for flaviviruses: it is present in Africa, Europe, Asia, the Middle East, Australia, and Americas 95%CI, 6.2% 95%CI and 9.8 % 95%CI, for West Nile virus (WNV), Usutu virus (USUV), undetermined flavivirus, and WNV/USUV respectively. Regarding domestic birds of Madagascar, the observed seroprevalence was 4.4 % 95%CI for WNV, 0.9% 95%CI for USUV, 1.3% 95%CI for undetermined flavivirus, and null for WNV/USUV. Among the 150 wild birds sampled in Madagascar, two fulvous whistling-ducks (Dendrocygna bicolor) were positive for WNV and two for an undetermined flavivirus. One white-faced whistling-duck (Dendrocygna viduata) and one Hottentot teal (Spatula hottentota) were tested positive for USUV. African and European wetlands are linked by wild bird migrations. This first detection of USUV\u2014as well as the confirmed circulation of WNV in domestic birds of two wetlands of Mali and Madagascar\u2014emphasizes the need to improve the surveillance, knowledge of epidemiological patterns, and phylogenetic characteristics of flavivirus in Africa, particularly in areas prone to sustained, intense flavivirus transmission such as wetlands.We retrospectively analyzed sera from domestic and wild birds sampled in 2008 in two wetlands, namely the Inner Niger Delta, Mali, and the Lake Alaotra area, Madagascar. In Mali, the observed seroprevalence in domestic birds was 28.5%"} +{"text": "Background: The consequences of fall-related injuries are becoming more significant due to ageing societies worldwide. This study aims to provide information on medications prescribed to older adults within one year before they experienced fall-related injury in Ontario, Canada. Methods: A population-based descriptive study of older adults (66 years and older) who experienced fall-related injury was conducted using administrative secondary health care data of Ontario. The percentages of patients prescribed each Anatomical Therapeutic Chemical 4th level medication class and fall-risk increasing drugs one year before their fall-related injuries was summarized. Results: From 2010 to 2014, 288,251 older adults were admitted to Emergency Department due to fall-related injury, 39.9% were fall-related fractures, 12.6% were head injuries. One year prior to their injury, 48.46% of older adults were prescribed with statins; 35.23% were prescribed with diuretics; 26.84% were prescribed with antidepressants; 25.90% were prescribed with opioids and 16.61% were prescribed with anxiolytics. A higher percentage of females were prescribed with diuretics, antidepressants, and anxiolytics than males. 85 years and older people had higher percentage of prescription of diuretics, antidepressants and antipsychotics than other age group. Discussion: In general, older adults diagnosed with fall-related injuries were prescribed with more opioids, benzodiazepines and antidepressants than other general older adults. There were distinct patterns of prescription medication within each sex and age group . Further association between medications and fall-related injuries need to be established using well-defined cohort studies."} +{"text": "Mycobacterium tuberculosis complex is the leading cause of death and diseases from a single infectious agent and continues to be a major global public health problem [Tuberculosis (TB) caused by problem . However problem ,2.In the last few decades, there has been a renewed interest in the study of the long-term outcomes of patients previously treated for TB ,4. In a Pulmonary TB (PTB), the most common form of TB, causes extensive structural lung changes in more than two-thirds of the patients that persists after treatment despite microbiological cure of the active disease \u201310. ThesAspergillus species following inhalation of infectious spores from the environment. This leads to expansion of the existing or creation of new cavities with associated parenchymal and pleural damage [Aspergillus hyphae, tissue debris, inflammatory cells, and mucin known as a fungal ball (aspergilloma) may form in these cavities [CPA is a progressive respiratory syndrome that largely occur in immunocompetent or subtly immunocompromised individuals with underlying structural lung diseases, most commonly treated TB . Residual damage . A complcavities .M. tuberculosis bacilli in their sputum for at least a year were studied. About 25% of the patients had positive Aspergillus precipitins in their serum, 14% had aspergillomas, and 10% had precipitins without evidence of an aspergilloma. Three years later, 34% had positive Aspergillus precipitins, 22% had aspergillomas, and 14% had precipitins alone. In more recent studies among patients previously or currently being treated for TB, up to 39% of whom had residual cavities, the prevalence of CPA ranged between 6.3% and 13.7% [The significance of treated PTB in the pathogenesis of CPA was established by a large cohort study across over 50 clinics in Great Britain in the mid- to late 1960s . In thisnd 13.7% ,16. Amonnd 13.7% ,17.In high-burden TB countries, the proportion of CPA with TB as underlying condition is higher than low\u2013TB-burden countries ,17,18. HIt is important to note that most patients with CPA have multiple underlying lung conditions . Other iCPA presents with chronic productive cough, systemic symptoms , haemoptysis, and chest pain . These sAspergillus-specific IgG is particularly sensitive and is positive in over 90% of patients with CPA [Aspergillus infection (microscopy or culture from biopsy) or an immunological response to Aspergillus spp., and exclusion of alternative diagnoses, all present for at least 3 months [Aspergillus spp. is time consuming, has low sensitivity, and may represent colonization or contamination. Therefore, Aspergillus serology is the cornerstone for CPA diagnosis. Introduction of a cheap and rapid point-of-care Aspergillus IgG/IgM lateral flow assay with a sensitivity and specificity of 91.6% (86%\u201395.4%) and 98.0% (94.2%\u201399.6%), respectively, has made the diagnosis of CPA possible even in resource-constrained settings [M. tuberculosis GeneXpert. NTM is a cause of smear-positive/M. tuberculosis GeneXpert-negative mycobacterial infection with a very high risk of concurrent or precedent CPA development [Given the striking similarities in the clinical and radiological manifestations of these diseases, more specific microbiological and serological tests are required to make a definitive diagnosis ,26. Aspewith CPA ,27\u201329. T3 months ,26. Isolsettings ,27. PTB settings ,31. Howeelopment . CPA patelopment . There iAspergillus spp. and M. tuberculosis, respectively [Aspergillus co-infection rate of 15.4% (95% CI: 11.4\u201320.5) among patients with PTB [Both CPA and PTB are caused by the opportunistic respiratory pathogens, ectively ,11. Howeectively . A systewith PTB .Aspergillus in respiratory samples of patients with confirmed M. tuberculosis was achieved in 50 out of 140 (35.7%) patients, of whom 92% had underlying lung conditions, 35 (70%) had positive Aspergillus IgG, and 3 (6%) were confirmed to have CPA [Aspergillus IgG at the end of their TB treatment [Klebsiella pneumoniae triple co-infection has also been described in a patient with poorly controlled diabetes mellitus [In one study, co-isolation of have CPA . Among Ht of 140 .7% patiemellitus . Two climellitus and 8.7%mellitus .Concurrent treatment of CPA and TB is very challenging due to the significant drug-drug interactions between anti-TB agents and the triazoles. Rifampicin markedly reduces exposures to itraconazole to sub-therapeutic levels, and hence co-administration should be avoided.Aspergillus nodule may not necessitate therapy; a simple aspergilloma occurring in a well-circumscribed cavity without extensive destruction of surrounding lung tissue is best managed surgically. Meanwhile chronic cavitary pulmonary aspergillosis (CCPA) and chronic fibrosing pulmonary aspergillosis (CFPA)\u2014characterised by multiple enlargement of existent or creation of new cavities and extensive destructive fibrotic pleuro-parenchymal changes\u2014respectively are the most common forms of aspergillosis and always require antifungal management [The management of post-TB CPA is the same as that for any underlying lung disease such as COPD or sarcoidosis and depends on the radiological phenotype of CPA . An incinagement ,37.Aspergillus spp. isolates resistant to the first-line agents [Long-term oral antifungals with itraconazole at a dose of 400 mg/day or voriconazole at a dose of 400 mg/day administered for at least 6 months is the recommended first-line therapy for CPA associated with improvement in quality of life, relief of symptoms, and retardation of disease progression ,39. Newee agents . Azole re agents . In casee agents .Antifungal treatment improves survival. However, survival rates vary significantly among published studies. Reported survival rates are 58%\u201393% at 1 year of follow-up, 17.5%\u201385% at 5 years of follow-up, and 30%\u201350% at 10 years of follow-up \u201349. In aIn addition to conventional antifungal treatment, pulmonary rehabilitation has been shown to improve symptoms and quality of life of patients with PTBLD, including those with post-TB CPA . At the The relationship between CPA and TB is well established. CPA complicates previously treated TB due to the residual structural lesions. About one-third of patients previously treated for PTB will have residual lung cavities. Specific serological and microbiological tests are mandatory to differentiate CPA from active PTB disease, recurrent PTB, and PTBLD."} +{"text": "The use of substances such as cigarettes, khat, alcohol, and other illicit drugs like hashish, heroine, cannabis, and cocaine is a global major public threat, which affects young adult people particularly in developing countries. This study aims to assess the risk factors associated with substance use and exposure to sexually explicit materials among high-school adolescents in north Shewa zone, Oromia region. A cross-sectional study was conducted to assess substance use and exposure to sexually explicit materials among high-school adolescents in North Shewa zone, Oromiya, Ethiopia, using a structured self-administered questionnaire adapted from the 2008 \u201cCommunity That Care Youth Survey\u201d for adolescent substance use and problem behaviors. The study used descriptive statistics and logistic regression analysis to identify the significant factors associated with substance use and exposure to sexually explicit materials among high school adolescents in the study area. The prevalence of lifetime and current substance use was 47.7% and 30.4% , respectively. 17.8% use khat in their life and 16.6% used khat in the past 30 days; 42.2% ever used alcohol and 26.1% currently uses alcohol; 4.8% and 4.5% used cigarette in lifetime and in the past 30 days, while 16.4% use other illicit drugs in lifetime and 8.4% use illicit drugs in the past 30\u2009days, respectively. Distributions of substance use by sex indicate that male adolescents are more like likely 61.1% use substances than females. While, the prevalence of exposure to sexually explicit materials among high school adolescents was 35.8% . Factors positively associated with increased substance use were being male , living through high level of family conflict , poor family management OR\u2009=\u200927.084, 95% CI: 1.624, 45.56), peer pressure , poor academic performance , and low school commitment . While, being male , age 14\u201316 , friends watch/read sexually explicit materials , and khat chewing were factors significantly associated with high-school adolescents exposure to sexually explicit materials. The magnitude of prevalence for substance uses and exposure to sexually explicit materials in the study area was still higher. Therefore, interventions that focus on family management, peer pressure, and school commitment are required to decrease the prevalence of substance uses and exposure to sexually explicit materials among high-school adolescents. The use of substances such as cigarettes, khat, alcohol, and other illicit drugs like hashish, heroine, cannabis, and cocaine is a global major public threat, which affects young adult people particularly in developing countries \u20133. Drug The United Nations in 2014 indicated globally, alcohol consumption accounts for about 5.9% or nearly 3.3 million deaths of the global deaths, and 5.1% of the global burden of disease and injury were attributable to alcohol consumption in 2012 . Early sThe most locally produced and highly consumed alcohols in Ethiopia are tella, areque , shamita, tej, and borde. Aside from locally fermented alcohols beers, gin, wine, and other alcoholic liquors are widely used alcohols products . The EthPrevious studies showed that peer pressure, accessibility, cultural accessibility, parental involvement, and low self esteem are the major reasons for starting using substances in Ethiopia, while some adolescents use substances to relax, and to avoid or forget their problems and anxieties, like problems arising from economic stress .A cross-sectional study conducted on substance uses and associated factors among Haramaya university students indicated that more than 62% of students use at least one substance, 50.2% use alcohol, 41% chewed khat in their lifetime, 23.6% currently use khat, while 22% were using cigarettes at least once in their lifetime, 10.8% currently smoke cigarette and 7.4% used illicit drug like hashish . A systeWakgari and Aklilu studied substance use and its predictors among undergraduate medical students of Addis Ababa University in Ethiopia, the study reported 22% of students used alcohol, 7% used khat, and 9% of students use cigarette . A similA study conducted in Nepal reported, 6% prevalence of substance use among high-school adolescents . A similAnother study conducted in Gondar University showed 62.9% prevalence of drug uses and the major contributing factors of substance uses are relations, increase performance, and peer pressure . While GIn Harar, eastern Ethiopia, Reda found a Exposure to sexually explicit materials (SEM) means a picture, photograph, drawing, sculpture, motion picture film, or similar visual representation which is obscene for children. Pornography and SEM will be used interchangeably. Webster's dictionary defines pornography as \u201cthe depiction of erotic behavior intended to cause sexual excitement.\u201d Exposure to sexually explicit materials stands viewing sexually explicit material through media such as the Internet, videos, and magazines that may be directly linked with the sexual behavior of adolescents and young adults. Globally, adolescents spend more time with the media than they do in school or with their parents [ parents . Much of parents . These l parents .Risk and protective factors for youth substance abuse should be assessed as a prevention program as they help decrease unhealthy behavior , 30. IndUses of substance and its consequence is one of the recent problems aggravate adolescents. The sustainable development goal (SDG) indicator, 3.5 targeted to strengthen the prevention and treatment of substance abuse, including narcotic drug abuse and harmful use of alcohol by the year 2030 .Despite the fact that a number of researches have been done on substance uses, nowadays in Ethiopia many adolescent students and young adults migrate from rural to urban areas to attend secondary and higher educations or in search of job. This will in turn relate to risky sexual behavior. The prevalence of substance uses and exposure to risky sexual behavior is still high, and more effort is needed to minimize the rate of substance use and exposure to sexually risky materials. The finding of this study will help for the development of preventive policies, effective intervention priorities, and any cost benefit analysis-related substance abuse and exposure to SEM. It will contribute to the literature by highlighting the influential characteristics of substance abuse and exposure to SEM by various social, economic, cultural, and demographic factors. It could also be part of baseline information for policy makers. Therefore, the main objective of this study is to assess the prevalence and associated factors of substance use and exposure to sexually explicit materials among high-school adolescents in North Shewa zone of Oromia regional state, Ethiopia Figures and 2.The study was conducted from March\u2013May, 2019 in North Shewa zone of Oromia regional state, which is located around 114\u2009km northwest of the capital Addis Ababa, with an elevation between 2515 and 2547 metres above sea level. Based on the 2007 census conducted by the Central Statistical Agency of Ethiopia (CSA), this zone has a total population of 1,431,305, of whom 717,552 are men and 713,753 women; with a population density of 138.66. Only 10.25% are urban inhabitants. The largest ethnic group of CSA reported on this area was Oromo (84.33%) and followed by Amhara (14.99%); all other ethnic groups made up 0.68% of the population.A cross-sectional study was conducted to assess substance abuse and exposure to sexually explicit materials (SEM) among high-school adolescents in North Shewa zone, Oromiya, Ethiopia. A structured self-administered questionnaire will be adapted from the 2008 \u201cCommunity That Care (CTC) Youth Survey\u201d for adolescent substance uses and problem behaviors. Relevant modifications were made to incorporate information specific to this study and its local context. The data will be collected by trained data collectors and supervisors.The target population comprised all high-school adolescences aged 14\u201319 years. There were more than 10,000 high-school students in the north Shewa zone, Oromia region.All high-school adolescences were randomly selected from the target population.n\u2009=\u2009sample size, z\u03b1/2\u2009=\u2009critical value to obtained from standard normal distribution, \u03b1\u2009=\u2009level of significance, p\u2009=\u2009proportion of street children, and d\u2009=\u2009margin of errors:The sample size was determined using the formula of sample size determination for single population proportion considering 50% prevalence of substance use from prior similar study , assuminn0+0.1\u2217n0)=424\u2009.Then considering 10% nonresponse rate, the total sample size was =(k\u2009=\u200912).The survey used a two-stage simple random sampling technique. The first stage involved selecting schools in the study areas and the second stage, number of students per school was selected with a probability proportional to size. There were 14 districts in the North Shewa zone. The sampling frame was obtained from North Shewa zone education bureau. In the first stage, eight districts and one high school was selected within each district using simple random sampling technique. Accordingly the selected districts (schools) are Abichu (Mendida secondary school), Dera (Gundo meskel secondary school), Kuyu (Gebregurracha secondary school), Fiche (Abdissa Aga secondary school), Kimbibit (Sheno secondary school), Wechale (Mukaturi secondary school), Wara jarso (Tullu milki secondary school), and Debre Libanos (Derbretsige secondary school). In the second stage, a fixed number of students were selected using systematic random sampling technique. Sample size has been allocated for every grade based on proportional allocation to their size. Lastly, students from every class had been selected by systematic random sampling , religiosity, friends' use of drugs/substances, poor family management , family history of alcohol and substance use, poor academic performance/academic failure, low commitment to school, and perceived availability of substances.Descriptive statistics such as frequency distribution and cross tabulation and bar charts were used to summarize the distribution of selected characteristics of high school adolescents, while logistic regression analysis was employed to identify the statically significant factors of substance uses and exposure to sexually explicit materials among high-school adolescents.The study was undertaken after the approval of the research proposal by research and community service directorate of Salale University before the data collection started. A formal letter was written from Salale University to all the concerned authorities. For confidentiality, the name of the participants and ID number were not typed on the questionnaire. All responses were anonymous and kept confidential.All regular high-school students in the North Shewa zone, Oromia regionAdolescents ages between 14 and 19 yearsAll students less than 14 years old and adolescents greater than 19 years oldAdolescence. The period from age 14\u201319 years.\u2009Substance. The three commonly used psychoactive drugs alcohol, cigarette, and khat that produce changes in mood, thinking, feeling, and/or behavior that can cause dependence.\u2009Substance Use. Taking any of the three commonly used psychoactive substances: alcohol, cigarette, and/or khat in the past 30 days.\u2009Risk Factors. Characteristics or conditions within the individual or in the family, school, or community that increase the likelihood that someone will engage in the use of alcohol, cigarette, and khat or discourage positive behavior that might prevent them [\u2009ent them .Lifetime/Ever-Use. Adolescents' use of the particular substance at least once in their lifetime.\u2009Current Use/30-Day Uses. Adolescents' use of the substance at least once in the 30\u2009days prior to data collection and is a more sensitive indicator of the level of current use of the substance.\u2009The total sample 424 identified 386 high school students fill the questionnaire with a response rate of 91%. About 61% of the students included were male. Slightly more than half 56.5% of the respondents were grade 10 students. The vast majorities (87.4%) of respondents were Coptic orthodox Christian and 39.2% were attending religious programs daily. About two-thirds (66%) were reported they had academic rank of 1\u201310 in the recent semester. 71.1% were living with their biological parents and 16.9% were living oneself. 53.7% and 62.1% of respondents were from father and mother with no formal education respectively. The age distribution of respondents showed that majority of the respondents 71.1% were in the age group 17\u201319\u2009years old. The economic level of respondents' parents also varied, 64.3% of the respondents were from moderate income families, 20.5% were from poor families, and 15.2% were from families with high income status.Overall, 47.7% of the respondents reported ever used any substance and 30.4% uses any substances in the past 30 days. 17.8% use khat in their life and 16.6% uses khat in the past 30 days, 42.2% ever used alcohol and 26.1% currently uses alcohol, 4.8% and 4.5% uses cigarette in lifetime and in the past 30 days, while 16.4% use other illicit drugs in lifetime and 8.4% use illicit drugs in the past 30 days, respectively. Distributions of substance use by sex indicate that male adolescents more likely (61.1%) use substances than females.Students are also asked to respond for how long they used substances. Accordingly, 35.5% used substance for shorter than six months, 26.8% uses substance for six months to one year, 21.4% of respondents used substances for one to three years and 16.1% used substances for at least three years. Regarding the question where was the first place you consumed the drugs, 71% respond at home, 8.3% reported at khat or shisha store, 4.1% in school ground, 2.4% at party, and 14.3% were started using substance at bar or restaurant and others. Additionally, respondents were asked to rate the problem of drug uses in their school; 31.8% reported the problem is very high/very serious, 9.3% said it is somewhat serious, while 7.7% reported substance use is not too serious problem in school.The students were also asked to respond what motivates them to use substances. Accordingly, about 9.1% use substance due to peer pressure, 13.4% due to academic failure, 15.1% to cope up with various life challenges, 18.8% to experience pleasure, and 22.5% of respondents motivated to use substance to be sociable. 30.8% of students reported they use khat to spend the leisure time, 16.9% being addicted, and 13.8% uses khat to be sociable. Similarly, 27.2% of adolescents use alcohol to pass the time, 6.4% use alcohol to leave depression, 10.4% to forget their problems, 13.6% report they use alcohol to be sociable, and 8% of the adolescents reported that they use alcohol being they are addicted.This study has found that substance use has various consequences. Concerning the behavioral consequences 12.5%, 15%, 16.7%, and 6.7% of respondents were experienced lateness from school, violence (disciplinary problems), absenteeism from school, and loss of interest in daily activities as a result of using substances, respectively. On other hand, regarding the social aspects, 22.6% were experienced losing friends, 39.3% experienced problems with parents/guardians and 7.1% being arrested due to substance use. Similarly, for heath related problems, 35.8% reported physically ill-health, 11.1% reported sleep disorder, and 16% experienced mental illness. From a total substance users 54.1% reported psychological distress and 11.2% were reported suicide attainment as psychological consequences of substance use. Generally, 26.9%, 21.8%, 10.3%, and 9% of respondents experienced health-related problems, social problems, psychological problems, and behavioral problems consequences of substance use in their lifetime for both models. Additionally, the Hosmer\u2013Lemeshow test revealed that there was a significance difference between the model with no covariate and the model with explanatory variables. A model with a covariate is a good fit to the data onto both models.We start first by checking the overall goodness of fit using the likelihood ratio test and Hosmer\u2013Lemeshow goodness of fit test. We then proceed to test the significance of each predictor variable included in the model using the Wald test. Accordingly, the results are summarized in In the multivariable logistic regression analysis, the variables sex, high level of family conflict, poor family management, age, low academic performance, substance use by friends, low level of school commitment, and mothers' education level showed a statistically significant association with adolescents' substance use.Male adolescents were 2.334 times more likely to use any substances than females. The odds of substance use were 27.084 times higher among students with poor family management. Similarly, living through high levels of family conflict was positively associated with substance use among adolescents keeping other variables constant. Adolescents whose friends use substance were more likely to use of substance than those who have friends who did not use substance . As adolescents' age is, concerned adolescents aged 14\u201316 were at a lower risk of substance use compared to 17\u201319 years old adolescents . Those adolescents who had poor academic performance were more likely to use substance than those who performed well. The odds of substance uses were higher among adolescents who have reported low school commitment . Further peer pressure from friends was another variable that significantly associated with substance use. The odds of substance use were 12.882 times more likely for those with peer pressure from friends than that of no peer pressure.From the total adolescents included in the study, about 35.8% were exposed to sexually explicit materials. The major sources of sexually explicit materials were mobile phone (38.3%), video discs (14%), Internet access/search (14.5%), video houses (7%), games (5.4%), and magazines (2.8%). The mean age of adolescents at the start of watching sexually explicit materials was 15.08 with \u00b13.307 standard deviation (SD). Regarding frequency of watching sexually explicit materials 18.6% reported they were watching SEM daily, 26.1% watch three to four times per week while 55.3% of respondents watch such materials one to four times a month.Concerning to the question on sexually explicit materials consumed by most adolescents, 27.3% reported child pornography, 25.3% adult pornography, and 22% romantic pornography. 24.8% of respondents were watching/read pornographic materials alone, while 43.3% and 17.7% were watching such materials with friends and families, respectively.Regarding access to sexually explicit materials, the vast majority 61.5% of adolescents download sexually explicit materials from their mobile phone while 17.3% get from Internet cafes. As practice of SEM is concerned, 19.3% of adolescents had practiced what they had seen/read from sexually explicit materials. Concerning exposure to sexually explicit materials by sex, 71.1% adolescents exposed to sexually explicit materials were male adolescents. Among adolescents who drink alcohol, 51.4% were exposed to SEM while 33.3% and 31.9% of adolescents chewing khat and using other illicit drugs, were reported they were exposed to SEM, respectively.The multivariate logistic regression analysis presented in As family educational status is concerned, those adolescents whose father had secondary education level were 7.996 times less exposed than those whose father had attained a diploma or higher education. Adolescents whose mother did not work and self-employed had less exposed to SEM and , respectively. Similarly, regressing family economic status, the odds of exposure to sexually explicit materials among adolescents that belongs to a household with poor and moderate income levels was less than that of rich income.The lifetime prevalence of substance uses was 47.75% and the prevalence of current substance use is 30.4%. The finding of this study is lower than studies conducted in Haramaya university that repIn the current study, the prevalence of a lifetime and current alcohol use was 42.16% and 26.1%, which is congruent with a study in Uganda that repThe magnitude of the prevalence lifetime and current cigarettes smoking were almost similar 4.8% and 4.5%, respectively. This finding is lower than a study in Woldia Town 23.5% and a stIn the multivariable logistic regression analysis, the study found significant associations between substance and sex, living through high levels of family conflict, poor family management, age, friends' use of substance, poor academic performance, low school commitment, and illiterate education level of mother. Similarly, exposure to sexually explicit materials was strongly associated with sex, age, friends watching SEM, father education level, mother occupation, family's economic status, and chewing khat. Substance use was highly probable among male students compared to females. Male students were more likely to use substances than females. This finding agrees with earlier researches , 20, 38 This study shows that substance use is associated with poor family management and living through high level of conflict. Students who are living through high level of conflicts are more likely to use substances. Findings from previous research suggest Poor academic performance was another variable identified as a significant predictor of substance uses among adolescents in the multivariate analysis. The findings show that adolescents with poor academic performance have a significantly higher odds of substance compared to those with good academic performance. This finding was consistent with the result of , 42 thatThis study also found that friends' use of sexually explicit material has increased rates of exposure to sexually explicit materials among adolescents, which was congruent with previous studies . This evKhat chewing was also an important factor that significantly related to adolescents exposure to sexually explicit materials. It is vital that use of khat and other illicit drugs initiate adolescents to read/watch pornographic materials. The findings of this study showed that adolescents who chew khat were probably highly exposed to SEM than those who had not chewing khat. Existing literature also indicates that khat chewing and using drug had a higher access to get exposure to SEM , 50, 53.The study did not find a significant association between grade levels, access of substance near school, family history of substance use, family economic status and substance use, which was inconsistent with prior studies on determinants of substance use , 18, 22.The study has examined the prevalence and factors associated with high-school adolescents' substance use and exposure to sexually explicit materials in North Shewa zone Oromia region using logistic regression analysis. The finding of this study supports that the prevalence of substance use and exposure to sexually explicit materials among high school adolescents is still high and is an important public health issue in the study area. In the results of multivariable logistic regression analysis, it was found that being male sex, living through high levels of family conflict, poor family management, friends' use of substance, poor academic performance, adolescents age 17\u201319 years, and low school commitment were factor significantly increase the risk of substance uses. On the other hand, being male sex, adolescents age 17\u201319 years, having friends watching sexually explicit materials, father's education level, family's economic status, and chewing khat were factors strongly positively correlated with high school adolescents exposure to sexually explicit materials.To achieve the sustainable development goal indicator, 3.5 targeted to strengthen the prevention and treatment of substance abuse, interventions that focus on family management, peer pressure, and school commitment are required to decrease the prevalence of substance uses and exposure to sexually explicit materials among high-school adolescents.This study used a questionnaire adapted from the standard the 2008 \u201cCommunity That Care Youth Survey\u201d for adolescent substance use and problem behaviors. The major limitation was that misreporting or underreporting of illicit drugs uses. Also the study included only students studying in school. The other limitation was that interaction effects were not used included in the analysis due to large number of variables to compute."} +{"text": "We investigated the effects of paternal characteristics, including age, body mass index (BMI), and semen parameters on chromosomal aberration-related miscarriages in couples that underwent treatment with assisted reproductive technology (ART). Single nucleotide polymorphism (SNP) array analysis showed chromosomal aberrations in 60.2% (557/925) of miscarried fetuses, including trisomy in 73.1% (407/557) of cases. There were higher chromosomal aberration rates in fetuses for men aged 20-24 years and \u226530 years compared with controls. After adjusting for age and BMI of the female partners, and the BMI and semen parameters of the males, there was no statistically significant effect of paternal age \u226530 years on the risk of chromosomal aberrations-related miscarriages. However, the odds of chromosomal abnormality-related miscarriage were 148% higher for the youngest fathers (age: 20-24 years) than fathers aged 25-29 years . Furthermore, high male BMI and low semen volume were associated with increased risk of chromosomal aberration-related miscarriages. These findings demonstrate that very young paternal age, high BMI, and low semen volume are associated with increased risk of chromosomal aberration-related miscarriages in couples undergoing ART treatment. Infertility affects 10-15% of couples globally . AssisteIn terms of research that focuses on the effects of paternal age on their offspring, studies have often found conflicting results. Most analyses show that advanced age of the male partners is associated with lower pregnancy rate and a higher risk of early spontaneous pregnancy loss , 7. ConfThe World Health Organization (WHO) published a global trend towards a decline in different sperm parameters in the last decades . Sperms Recent estimates from the WHO suggest that more than 1.9 billion adults aged 18 years and older, were overweight worldwide . High BMExpression of paternal genes in the chorionic villus samples (CVS) significantly correlate with fetal growth parameters during pregnancy . Genome-2, which is considered overweight.The mean age of female partners increased with advancing age of their male partners. In different paternal age groups, there were no significant differences in the female partner-related parameters such as BMI, TSH levels, fertilization method, gestational age at miscarriage (irrespective of the type of fertilization method), and the number of embryos transferred. The older couples showed higher percentage of prior births and prior miscarriages compared to the younger group. The median ovum pick-up numbers were higher in the younger group compared to the older group . The proportion of day 5 blastocysts transferred were higher for the younger group when compared with the older group .Monosomy was found in 5.7% of samples (32/557), of which, 81.3% (26/32) were on the X-chromosome and 18.8% (6/32) were on autosomal chromosomes. Chromosomal structural abnormalities were found in 9.0% of the samples (50/557), of which, 88.0% (44/50) were duplications or deletions, and 12.0% (6/50) were complex abnormalities. Triploidy was found in 5.9% of samples (33/557) and mosaicism was found in 6.3% of samples (35/557). Representative examples of SNP results are shown in 2 and semen volume <1.5 ml . However, the percentage of chromosomal abnormalities in abortuses were slightly higher for the youngest male partner group aged 20-24 years compared to male partners aged 25-29 years (53.3% vs. 45.4%). In addition, there were higher chromosomal aberration rates in miscarried fetuses for male partners BMI \u226525 kg/m <1.5 ml . Univari <1.5 ml . Univari2) were at greater risk for chromosomal abnormality-related miscarriages compared to male partners with a lower BMI . Furthermore, the risk of chromosomal abnormality-related miscarriages was higher for male partners with low semen volume (less than 1.5 ml) compared to those with higher semen volume , whereas the other sperm parameters assessed, including sperm concentration, motility, and morphology were not significantly correlated with chromosomally abnormal abortus (P>.05). Moreover, our study was in agreement with the previous findings that advanced maternal age was a risk factor for chromosomal abnormality-related miscarriages .Multivariate analyses showed that the effect of male partner aged \u226530 was no longer statistically significant when they were adjusted for the age and BMI of female partners, and the BMI and semen parameters of the male partners. Interestingly, after adjustment, the youngest group in our study (fathers aged 20-24 years) showed a 148% higher risk of having a chromosomal abnormality-related miscarriage compared to the control group . Furthermore, multivariate analyses showed that male partners with a high BMI to identify any chromosomal abnormalities that may indicate a risk of miscarriage. Further large-scale multicenter clinical studies are necessary to confirm our findings.We conducted this retrospective analysis using data from the Clinical Reproductive Medicine Management System/Electronic Medical Record Cohort Database (CCRM/EMRCD), obtained from the Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, and Henan Province Key Laboratory for Reproduction and Genetics. This study was approved by our Hospital Ethics Committee. We obtained written informed consent from all patients during the first consultation.The database included clinical information regarding 1103 patients who experienced involuntary miscarriage between January 2013 and December 2018 in our fertility clinic after ART. The patients sent their miscarried fetuses to our pre-implantation genetic diagnosis center for analysis. As shown in in vitro fertilization (IVF), and 203 received intracytoplasmic sperm injections (ICSI) as described previously [Among the study participants, 80 underwent intrauterine insemination (IUI), 642 received eviously . The serhttp://dgv.tcag.ca/dgv/app/faq) to identify the candidate pathogenic CNVs. All the steps were analyzed independently by at least two expert technicians.The chorionic villi were thoroughly separated from the maternal deciduas as previously published to avoid maternal genome contamination . Total DWe reported the characteristics of all study couples and the ART variables. Continuous variables with normal distribution were represented as means and 95% confidence interval, and the differences between groups were analyzed using Student\u2019s t-tests or one-way ANOVA. Continuous variables with skewed distribution were represented as median and interquartile range, and the differences between groups were analyzed using the Wilcoxon two-sample test. Categorical data were expressed as frequencies and percentages, and the differences between groups were analyzed using the Chi-square test. The numbers and percentages of abnormal chromosomal karyotypes for each paternal age group were compared using the chi-square test for trends to confirm if chromosomal aberration rate changed with paternal age.2 group, according to the World Health Organization definition of normal body weight [Logistic regression analysis was performed to identify risk factors for chromosomal aberrations-related miscarriage. The variables analyzed include male partner age, BMI, sperm concentration, motility, morphology, semen volume, female recipient age, and BMI. Embryo transfer information was not included in the multivariable analysis because some study participants were treated with IUI. Multivariable analysis was carried out to determine the role of male partner age, BMI, and semen parameters on miscarriage due to chromosomal abnormalities. We categorized 925 patients into 6 age groups based on paternal age, namely, 20-24, 25-29, 30-34, 35-39, 40-44, and 45-60 years. The control group for the logistic regression models was 25 to 29 years male partner\u2019s age group. The control group for BMI was the male BMI <25 kg/my weight . The cony weight . Althougy weight . Thus, wSupplementary Tables"} +{"text": "Information on microbiological and susceptibility profiles of clinical isolates in Mongolia is scarce, hampering infection control and clinical care.Species and resistance profiles of 6334 clinical gram negative isolates, collected at Mongolia's National Center for Maternal and Child Health between 2014 and 2017 were analyzed.E. coli and Enterobacter isolates increased from 2.8% to 16.6% and 3.5% to 22.6% respectively; Klebsiella isolates exhibiting susceptibilities suggestive of extended spectrum beta-lactamase (ESBL) production from 73% to 94%. By 2017, 60.6% of Klebsiella isolates were multidrug-resistant, most originated from intensive care wards. Enterobacteriaceae exhibiting susceptibility patterns suggestive of ESBL production and multidrug-resistant organisms were common and their incidence increased rapidly.Annual proportion of multidrug-resistance among These findings will serve to build strategies to strengthen microbiological surveillance, diagnostics and infection control; and to develop empiric therapy and stewardship recommendations for Mongolia's largest Children's and Maternity hospital. Approximately half of the 3 million inhabitants reside in the capital Ulaanbaatar, the remainder in provincial capitals, many of which follow a traditional nomadic lifestyle. The country's economy is growing rapidly, mainly as a result of an expanding mining industryThe National Center for Maternal and Child Health (NCMCH) is the largest government-run pediatric and maternity hospital and only tertiary referral center. The pediatric hospital has 270 medical and 150 surgical beds accommodating 19 subspecialties and treats approximately 40.000 inpatients and over 175.000 outpatients each year. The adjacent 250-bedded maternity hospital provides gynecological and obstetric care, and manages approximately 12.000 deliveries per annumThe aim of this study is to provide pathogen and susceptibility data for gram negative organisms (GNOs) among in- and outpatients of different ages in Ulaanbaatar; allowing the development of evidence-based empirical antimicrobial treatment and infection control policies.All gram negative isolates of cultured specimens submitted to the microbiology laboratory at NCMCH between 01/2014 and 08/2017 were included. Data was collected via the WHONET database (version 5), retrospectively (2014-2016) and prospectively (2017), including demographic data, specimen type, in- /outpatient status, hospital ward, species identification and antimicrobial susceptibility testing (AST) profile, and adequacy of microbiological work-up. The study was approved by the NCMCH ethics committee (NCMCH-AS2014).At times, test panels differ from the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines due to limitations of AST available. Additions or omissions to standard test panels are specified in the text. Organisms identified by means other than culture and stool samples are processed at another facility and were excluded. Molecular detection of organisms and/or determination of susceptibility status was not available during the study period.,,\u2013Of identical organisms isolated from a patient within 30 days, only the first isolate was included. Only species with a minimum of 30 isolates per year, per specimen category and antimicrobial agent tested, were used for guiding empirical antimicrobial recommendations. Susceptibility is interpreted as per CLSI 2016 and CESAR guidelines,Carbapenem susceptibility testing became available in July 2016. Classification of carbapenem susceptibility used the most conservative estimate: if tested for one carbapenem only or if the test result was concordant, the report was analyzed as the final result. Discordant carbapenem susceptibilities, with resistant or intermediate susceptibility for at least one, were reported as carbapenem resistant (CR)Quantitative variables were reported as absolute numbers and percentages. For continuous variables comparisons between groups to test equality were performed using the t-test when appropriate, or Mann-Whitney test when skewed. Tests of association between categorical variables were based on Chi-square and Fisher-Exact Tests. All P values reported are two-sided and considered statistically significant if < .05. Statistical computations were performed using SPSS 22.0 .Epidemiology and origin of isolates: In total, 6334 (53.3%) GNOs were included. E. coli and Enterobacter spp. were most common, accounting for 90% of isolates and blood stream isolates (37.1%) (BSI); pediatric samples by wound (28.8%) and urinary (42.3%), isolates from adults by genital (63.5%) and urinary (30.8%) samples. Predominant GNOs differed considerably depending on age group . Sample Enterobacter spp.: Frequency of Enterobacter spp. isolates increased over time. Most were inpatient isolates , almost half from neonates and children. The annual increase of Enterobacter spp. among neonatal BSIs was significant (P<0.001), contributing to a third of gram negative BSIs in 2017.Enterobacter susceptibility to quinolones and aminoglycosides was reliable, resistance increased sharply from 2016 , especially among inpatients and BSIs. From 2017, virtually all Enterobacter spp. blood isolates were aminoglycoside resistant . In the first half of 2017 alone, 57/277 (20.6%) of Enterobacter isolates tested were carbapenem resistant (CR), particularly blood and urinary isolates . CR Enterobacter isolates originated mainly from NICU and PICU .Whilst in 2014/15 E. coli: Among E. coli, adult samples accounted for 75.1% (n=2459/3274), predominantly from urine or genital tract . The number of E. coli isolates fulfilling criteria for ESBL confirmatory testing doubled over the study period from 27.0% to 60.3%; attributable to inpatient and NICU isolates (E. coli isolates underwent Carbapenem susceptibility testing. The proportion of CR isolates increased from 12.8% (2016) to 28.2% (2017), almost all were inpatient samples (29/32), 72% (n=23/32) from ICUs . MDR increased between 2016 and 2017 among E. coli from 2.8% to 16.6% originated from inpatients, most from NICU, 66.3% of which were BSIs (138/208); the remainder wound (9.2%) and urine isolates (6.7%). In nine instances, Klebsiella was isolated from neonatal CSF. The majority showed susceptibility patterns suggestive of ESBL production, most frequently among isolates from neonates , but increasing across all age groups from 73% in 2014 to 94% in 2017. Most were gentamicin resistant by 2017 , as opposed to only 25% (6/24) in 2014. Again, this was most pronounced among neonates, where aminoglycoside resistance increased from 26% to 95.7% . Quinolone resistance increased from 5.5% to 60.6% . Only 135/282 (48%) underwent carbapenem susceptibility testing, 24.7% and 28.1% were identified as CR and originated mainly from NICU, where CR rates increased from 13.8% to 32.5% .Pseudomonas spp., Raoultella spp., Serratia spp., Acinetobacter spp.Remaining GNOs, including : Documentation of specimen origin was only available for 42/66 (63.6%) of P. aeruginosa isolates, urines and wound swabs predominated. Reduced susceptibility to ceftazidime , gentamicin and quinolones occurred, however isolate numbers with susceptibility data available for all antimicrobials of interest were lower than 30 per year. All multidrug resistant isolates originated from NICU (n=3) and PICU (n=2), carbapenem susceptibility was not documented.Pseudomonas spp. group increased significantly (p<0.001) with PICU (n=42) and NICU (n=42) contributing most isolates. The majority did not undergo susceptibility testing.Samples yielding isolates of the non-aeruginosa Raoultella spp. were mainly isolated in 2015/16, when 16/24 isolates, mainly R. terrigenica of identical susceptibility pattern, were isolated from specimens of multiple wards. Most Serratia isolates were identified in 2015 (10/13), mainly on neonatal wound swabs and BSIs, and genital samples from maternity wards. Quinolone susceptibility was universal , a quarter were aminoglycoside resistant. Infections with Chryseomonas luteola occurred exclusively in November/December 2015; isolated from urine (n=3), pleural (n=2) and peritoneal (n=2) fluid; and confined to NICU (n=5) and the pediatric nephrology ward (n=4).Acinetobacter baumannii was isolated in six patients: four from neonatal BSIs and one from neonatal CSF and a joint aspirate of a young child - all in November 2016. All were quinolone, aminoglycoside and carbapenem susceptible.ESBL production and Multidrug resistance across species over time: Rates of ESBL phenotype diverged when comparing in- and outpatients in ESBL producers (P<0.001).roducers . In 2014P<0.001, Klebsiella and Enterobacter isolates could be included, as the choice of antimicrobials tested for were not agents recommended for treatment, or susceptibilities for too few antimicrobials were documented, however adequate microbiological work up was achieved for almost all isolates by 2017. MDR among E. coli tested increased from 2.8% in 2014 to 17.2% by 2017; among Enterobacter from 3.5% to 22.6%. The increase in MDR was most pronounced among Klebsiella spp. where no multidrug-resistance was identified in 2014/15, affected a third in 2016 and doubled within a year to 60.6% of isolates by 2017.MDR increased significantly more among inpatients, too P<0.001, . In earlThis data represents the largest published dataset on pathogen and resistance profile of clinical GNOs from Mongolian patients. Mongolia's health care system has evolved to apply novel therapeutic options, that are associated with an increasing use of antimicrobials for nosocomial infections in intensive care settings and hence accompanied by new challenges in governance and stewardship.Klebsiella isolates will undergo AST for quinolones and aminoglycosides.With ESBL confirmation testing indicated for the majority of inpatient isolates, this study identified an urgent need for implementation of improved microbiological diagnostics enabling accurate identification of drug-resistant GNOs; and steps are being taken to address it,\u2013It must be acknowledged that the present study has important limitations. First, a more detailed molecular and genotypic characterization of the organisms would have been of interest, at both local level - impacting infection control and treatment options - and on a transnational level, putting Mongolian isolates into context within Asia. Financial restraints and the need for prioritization within the healthcare sector have hampered molecular diagnostics at NCMCH to date, and diagnostic possibilities for AST remains limited. We found that the microbiological work up was not always in keeping with recommendations made by professional agencies The results of the available testing presented here however are concerning and serve as an opportunity to put AMR in Mongolia at the forefront of public health policies in the months and years to come. It is of utmost importance that data is made accessible to clinicians and to serve as an indicator for stakeholders that AMR poses a clinical risk at NCMCH, and in the Mongolian capital at large.E. coli and Enterobacter spp. isolates underwent Carbapenem susceptibility testing, the data may not reflect true susceptibility rates. A sizeable proportion of isolates underwent testing for less than three antimicrobials, disqualifying them from MDR analysis, particularly impacting Enterobacter and Klebsiella spp. isolates.Only a minority of E. coli in Mongolia from 2016E. coli isolates were multidrug resistant. While in this cohort, MDR rates among E. coli were lower, proportion of CR isolates was much higher. Testing to more antimicrobial classes, including Co-trimoxazole and NitrofurantoinE coli isolates from MDR analysis, as they underwent testing for fewer than three antimicrobials. However, our data encompasses a larger sample; and results did not change upon subanalysis of urine isolates (n=1201): 13.4% were multidrug resistant, relying on gentamicin, quinolone, beta-lactams and, since 2016, carbapenem testing.Whilst the representation of phenotypical ESBL status may overestimate the true rate of ESBL producers by 5-30%E. coli isolates were ESBL producers, mediated by TEM1 and associated with fluoroquinolone resistance. Our data shows rising rates the following year, identifying 27% of E. coli inpatient- and 19% of outpatient isolates as ESBL producers. The diagnostics available at NCMCH may influence ESBL rates, underlining the need for rapid introduction of ESBL confirmatory testing, not only to ensure accurate surveillance but also to avoid unnecessary use of carbapenems. Given that ESBL rates in our cohort doubled between 2014 and 2017 from 27% to 60%, the difference between the two studies may reflect the true increase in ESBL rates over time.Kao et alIn summary, the here presented data is in keeping with studies reporting susceptibilities that included the confirmation of ESBL. As no significant changes to the diagnostic work up occurred during the study period it has to be assumed that the significant increase in multidrug resistance, ESBL production and Carbapenem resistance may well reflect an approximation of the true development of AMR, which was mainly driven by inpatient isolates. This information may represent a chance to effectively impact spread of MDR and ESBL positive GNOs in Mongolia by intensifying infection control in health care facilities.Klebsiella BSIs on NICU, steeply rising since 2016. CR affected one third of Klebsiella isolates on NICUs by 2017. In keeping with reports from ICUs globally, Carbapenemase-positive Klebsiella has been included in the WHO global priority pathogen listProportion of ESBL phenotype and carbapenem resistance was extraordinarily high among nosocomially acquired Klebsiella, and despite empiric treatment of neonatal BSIs with imipenem, neonatal demise due to Klebsiella BSIs whilst on imipenem therapy was reportedly common, though no mortality data was available. Neonatal PICC lines were not routinely used, and staff did not feel competent in sterile line insertion. Nursing staff were unfamiliar with line care, hub sterilization before flushing and connecting, fixation of lines etc. Newborns requiring antibiotic treatment or total parenteral nutrition underwent frequent peripheral re-cannulations, performed routinely every three days.Given the level of concern due to these results, a detailed assessment of clinical and infection control practices on NICUs was performed. NICU staff were aware of the high prevalence of In the interim, guidelines addressing infection control procedures, central venous access insertion and line care have been provided to staff. Sterile line insertion was supervised and training provided. The introduction of medium-term, silver or heparin coated long lines for neonates has been discussedOur study emphasizes the preeminent role BSIs have played in the overall increase of MDR at NCMCH, especially affecting intensive care units. With a use of ICU beds in Mongolia equivalent to that of Western European or North American countries at 11.7 per 1.000.000 inhabitants,The largest published record of clinical GNOs in Mongolia to date emphasizes the importance of consequent surveillance and raises attention to multidrug-resistance in Central Asia, and highlights the intensive care environment as important source of AMR emergence"} +{"text": "South Asian countries report the highest prevalence of common mental disorders (CMDs) globally. This systematic review and meta-analysis report the pooled prevalence of CMDs among the South Asian countries. Database searches were conducted in eight electronic databases. Titles, abstracts, full-text screening, and extraction of data on the event rate of 17 indicators of CMDs were performed by two independent reviewers. A total of 160 studies were included and data analysis was done using the Comprehensive Meta-analysis Software (v.3). A prevalence of depressive symptoms was 26.4% among 173,449 participants, alcohol abuse was 12.9% ; anxiety 25.8% ; tobacco smoking 18.6% ; PTSD 17.2% ; mixed anxiety and depression 28.4% ; suicidal behaviors 6.4% ; misuse of opiates 0.8% ; tobacco chewing 21.0% ; use of cannabis 3.4% ; GAD 2.9% ; bipolar disorder 0.6% ; IV drug abuse 2.5% ; panic disorder 0.01% ; stimulant use 0.9% ; OCD 1.6% and phobic disorders 1.8% . This study reported a high prevalence of CMDs in South Asian countries; necessitating further research on psychiatric epidemiology in those contexts. It informs the need for effective policymaking and implementation of culturally appropriate multilevel interventions. Mental disorders are highly prevalent across the globe, especially in low- and middle-income countries (LMICs) . The WorSouth Asian countries comprise one-quarter of the world\u2019s population and include countries like India, Pakistan, Nepal, Sri Lanka, Bhutan, Bangladesh, Afghanistan, and the Maldives, comprise one-quarter of the world\u2019s population , 6. MarrSouth Asia has a diverse and rapidly growing population of people from different cultures, religions, and socioeconomic backgrounds . HoweverThis systematic review was conducted as per the updated PRISMA guidelines and the [ AND (\u201cMood disorder\u201d OR \u201cDepression\u201d OR \u201cSubstance abuse\u201d OR \u201csubstance use\u201d OR \u201cPosttraumatic stress disorder\u201d OR PTSD OR \u201cobsessive-compulsive disorder\u201d OR \u201cOCD\u201d OR\u201dbipolar disorder\u201d OR \u201cAnxiety\u201d OR \u201cPanic disorder\u201d OR \u201cschizophrenia\u201d OR \u201cGAD\u201d OR \u201cAcute stress disorders\u201d) AND ].We only included studies that were published in the last 10 years, i.e., from 2009 to 2019. No restriction of language was applied. Three independent reviewers screened the databases for eligible studies based on their titles and abstracts, followed by the screening of full texts. All discrepancies among reviewers were resolved through discussion between reviewers and guidance from a senior author (SN).All studies reporting the prevalence of common psychiatric disorders among adults (\u226518 years of age) including major depressive disorder, substance abuse, and related disorder, post-traumatic stress disorder, obsessive-compulsive disorder, bipolar disorder, panic disorder, schizophrenia, and generalized anxiety disorder were considered. Only those studies were considered that reported from any country within South Asia . To obtain precise estimates of prevalence considered sufficiently powered studies with a minimum sample size of 250. Data regarding any specialized population was not included in this study. Only those studies were selected that were published between 2009 and 2019 to inform our review with the latest evidence base published from the South Asian region. Only original cross-sectional investigations or baseline data of longitudinal cohort studies were considered; which applied census or either probabilistic or non-probabilistic epidemiological procedures to ascertain prevalence CMDs. Essentially, we used cross-sectional data to extract point prevalence estimates. While from prospective studies, we extracted point or period prevalence estimates and lifetime prevalence estimates from most recent publications from the cohort.All the data were extracted independently by three teams of reviewers using manual data extraction forms, and any disagreement among the reviewers was resolved through discussion with a senior author (SN). The last name of the first author, year of publication, study design, setting, geographical scope, educational and income level, country of study, percentage of male participants, and characteristics of study participants were extracted. Moreover, the data regarding the psychiatric disorder studied, mode and type of diagnostic interview, screening instruments, cut-off scores of the screening instruments, sampling techniques, sample size, response rates, and the number of participants with psychiatric and comorbid medical disorders was also tabulated.Three teams of reviewers assessed the quality of the studies independently without blinding to authorship or journal. At this stage, discrepancies in decision-making were resolved by discussion in conjunction with the senior author (SN). The risk of bias across studies was evaluated by using a modified version of the Newcastle Ottawa Scale , across Descriptive statistics on the characteristics of the study and populations were reported. Comprehensive meta-analysis software was used to run a series of meta-analyses to pool prevalence of specific mental disorders, using random-effects analysis . Due to The initial literature search revealed 1,827 unique citations, among which 160 studies met the inclusion criteria of our meta-analytical studies. I2 = 99.53%) yielding a prevalence of 26.4% among 173,449 participants. Alcohol abuse was reported in 43 studies yielding a prevalence of 12.9% ; anxiety 25.8% ; tobacco smoking 18.6% ; PTSD 17.2% ; mixed anxiety and depression 28.4% ; suicidal behaviors 6.4% ; misuse of opiates 0.8% ; tobacco chewing 21.0% ; use of cannabis 3.4% ; GAD 2.9% ; bipolar disorder 0.6% ; IV drug abuse 2.5% ; Panic disorder 0.01% ; stimulant use 0.9% ; OCD 1.6% and phobic disorders 1.8% . We assessed the pooled prevalence for 17 different mental disorders over a period of 10 years. All the outcomes presented significant heterogeneity ranging from 0% to 99.79% for stimulant use and alcohol abuse, respectively. The prevalence of depressive symptoms was reported in 135 studies . A total of 373 studies reported the percentage of males or female participants. Meta-regression analysis revealed that the percentage of males in the study explained 3% of the variation in heterogeneity . These meta-regression plots are presented as A meta-regression was conducted which revealed a significant geographical variation in the prevalence of CMDs, explaining 15% of the variation in total between-study variance. Taking Bangladesh as a reference point, the highest burden of mental illnesses was reported in Pakistan (B = 1.96). Nepal and Sri Lanka also reported a higher prevalence than Bangladesh. Moreover, no significant differences in the prevalence of CMDs were reported between Bangladesh and India. Subgroup analyses were conducted for several factors, showing large variations in prevalence estimates across different subgroups Table 3.In the risk of bias assessment, most studies scored eight and above, which informs a low risk of bias across the recruited studies. Furthermore, a funnel plot of the standard error by logit event rate among studies showed publication bias in the literature, with a significant Egger\u2019s regression statistic . The quality of the studies was measured across nine matrices: representativeness of the population, adequacy of sample size, reporting of characteristics of non-respondents, use of a commonly employed tool to ascertain psychiatric disorder, reporting of reliability measure and valid measure of scales, reporting of descriptive statistics, reporting of the method of informed consent and ethical approval. According to it, only 111 of the studies surveyed among populations that were representative of their setting, 122 reported ethical approval status, 126 characteristics of respondents, use of commonly employed methods for the ascertainment of mental disorder (n = 132), use of reliable (n = 136) and valid tool (n = 136), reporting informed consent procedures (n = 145), descriptive statistics (n = 146), and adequate sample size (n = 158). Overall, a small proportion of studies (n = 16) reported < 5 of these matrices, 6\u20138 (n = 90), and 56 scored positively on all of these criteria.South Asian countries have a high disease burden of psychiatric illnesses. Our study showed a prevalence of 14.2% (12.9% to 15.7%) for CMDs. This is higher compared to the worldwide-pooled prevalence of mental disorders was 13.4% . Our finThe total prevalence of depressive symptoms in South Asian countries was reported in 135 studies, yielding a prevalence of 26.4% (23.6% to 29.4%) among 173,449 participants which is significantly higher than a previous study presenting data from 30 countries , 16. MorIn Southeast Asia, a high prevalence of tobacco (smoking and smokeless) use in the general population has been observed . This meAmong the illicit use of substances, alcohol dependence is the most prevalent substance use disorder in South Asia, with a prevalence of 13%, which is consistent with previously conducted studies . While tThe variation in the prevalence of mental disorders in different South Asian countries is speculated to be due to varying levels of psychosocial, cultural, and political stressors. Increasing inflation levels leading to economic stress, transitioning urban communities, inter-religious, sectarian, and ethnic violence, and war hysteria in countries such as India and Pakistan are recent examples of these stressors \u201328. In aIt is essential to improve the mental health services in South Asia, which will require further well-designed epidemiological and clinical research examining psychopathology of diverse population groups in this region. Moreover, public education and awareness campaigns on mental health conditions should be undertaken to ameliorate the substantial public health burden in South Asian countries. There should also be public awareness programs to convey the adverse long-term effects of tobacco, alcohol, and other illegal drugs. Also, treatment centers at the community level for drug addictions should be set up. In these discourses, evidence-based multipronged interventions found to be effective in other contexts \u201335 may iLegislations and mental health laws have significant shortcomings such as the lack of emphasis on human rights and community-based mental health care approaches. Moreover, there are major flaws in the implementation of these legislations. Therefore, mentally ill people continue to be vulnerable to various types of abuse and violation of their rights in the region . AdditioThis meta-analysis has several limitations; therefore, its results should be interpreted with caution. Most of the included studies used screening instruments rather than diagnostic tools. Moreover, it was difficult to compare data from the selected studies due to differences in settings (clinic vs. community-based), different assessment tools, and the different scales used to determine the psychiatric disorders. Also, our review may have been subject to selection and publication bias as we were unable to contact the experts and collect unpublished materials or access any grey literature that may have met the criteria for this review.Detailed analyses in our report primarily show that a high proportion of studies had poor study design, for instance, employing non-probabilistic sampling procedures, the use of screening instruments rather than diagnostic tools, and limited to a smaller study site. Although the present pooled analyses show high prevalence rates of different CMDs, we recommend future research employing diagnostic interviews to diagnose mental disorders and recruiting participants in multiple community settings with appropriate sample size calculation, to yield precise prevalence estimates.This systematic review and meta-analysis found a high prevalence of CMDs in South Asian countries. Among the eight nations in this region, Pakistan had the highest prevalence of CMDs. Also, the epidemiological burden of different diseases affects diverse population groups at varying levels, which need further research on how different risk factors contribute to such a high prevalence of mental disorders in South Asia. This study provides cumulative baseline evidence on the prevalence of CMDs and informs an urgent need for effective policymaking and multipronged interventions that are culturally appropriate in the context of South Asia.All datasets presented in this study are included in the article/SN and AW conceived the idea of this review article. SN, AW, AC, SK, NA, RA, NJ, and SS extracted and analyzed data, prepared tables, and wrote the manuscript. SN was responsible for the supervision of this project. SN and AC equally contributed to this work.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Ejection fraction (EF) is a measurement of heart function that reflects the portion of pumped out blood from the filled left ventricle per each heartbeat. The current study aimed to investigate the prevalence of left ventricular thrombus in patients with EF lower than 35% by using Transthoracic Echocardiography (TTE).st to December 31st 2017 at the Military Cardiac Centre in Sana\u2019a, Yemen.In this prospective study, 82 cardiac patients underwent TTE procedure in order to assess the presence of left ventricular thrombus (LVT) from January 1Out of 82 patients enrolled in this study, the mean age was 49.13 \u00b1 14.8 years and 87.8% were male. The mean of EF was 31.16% and LVT was found in 6.1%. The spontaneous contrast was seen in 25.6% of patients indicating strong relationship with low EF (p < 0.001). Among patients with low EF, ischemic heart disease (IHD) was identified in 50%, hypertension in 30.5%, diabetes mellitus (DM) type 2 in 23.2%, and hyperlipidemia 12.2%. Exactly 80% of LVT were detected in IHD patients with dilated cardiomyopathy (DCMP) and 80% of detected LVT were apical in site.Cardiac patients with low ejection fraction developed left ventricular thrombosis, and most of the affected patients were ischemic heart disease with dilated cardiomyopathy. Interestingly, spontaneous contrast was found high significantly in these patients, which may reflect the continuous process of thrombus formation. Ejection fraction (EF) is the portion of pumped out oxygen-rich blood from a filled left ventricle to the aorta per each heartbeat. It measures the pumping ability and function of the heart. The cutoff of normal EF value is poorly-defined, however 50% of volume of blood in the left ventricle (LV) is considered as the lower boundary of normal.11This study is intended firstly to assess the incidence of LV thrombus in patients with low EF, and secondary to assess the relationship between common habits in Yemeni population such as khat chewing, smoking, shamma using with reduced EF of the heart. Khat is a plant that is chewed for its stimulant action which is popular in Yemen.12Shammah is a snuff of smokeless tobacco that is used in the middle east especially Saudi arabia, Sudan and Yemen.st to December 31st 2017 and met the inclusion criteria of this study were collected. The inclusion criteria were:This cross-sectional, prospective study was conducted at Military Cardiac Center in Sana\u2019a, Yemen. Data of 82 patients who underwent echocardiography in the outpatient clinic from January 1Patients with EF less than 35% and more than 12 years old age.The Exclusion criteria were:Patients with rheumatic heart disease (RHD) who were under anticoagulant drugs.Patients with atrial fibrillation (AF).This study was approved by the Cardiac Center Research ethics committee. Full institutional ethical approval was obtained before beginning the study. Verbal consent from each patient was also obtained before examination. Confidentiality of all patient information was assured.A pre-tested questionnaire was prepared to include all relevant information. Researcher through direct interview filled the questionnaire with the patients. Explanation of the study purpose was explained to each patient, and consent was obtained. The following variables are included: sociodemographic, clinical history for cardiac disorders causes, risk factors such as hypertension (HTN), diabetes mellitus (DM), smoking, hyperlipidemia, drug in-use and disease duration, severity and complications.Physical examination was performed for each patient looking for signs of congestive heart failure (CHF) as increase jugular venous pressure (JVP), hepatomegaly, lower limb edema. Investigations were done included complete blood count (CBC), cardiac enzymes, liver function tests (LFT), renal function test (RFT), electrocardiogram (ECG), and chest x-ray (CXR). Patients with EF less than 35% underwent another TTE to assess the presence of left ventricular thrombus (LVT).The ECHO procedure was performed with the same ultrasound imaging machine using a standard protocol. All selected patients were examined by the same cardiologist with 25 years\u2019 experience in echocardiography.LVT was defined as a hyperechoic mass with definite margins adjacent to the myocardium on multiple plane views through the cardiac cycle. Regional wall motion abnormalities were considered present whether hypokinesia, akinesia or dyskinesia were observed in at least two segments of the left ventricular wall. Left ventricular function was assessed by echocardiographic examination. LV end diastolic and end-systolic volumes and ejection fraction were determined from apical 2 and 4 chamber views using Simpson`s biplane formula according to recommendation of the American Society of echocardiography: EF=(EDV-ESV)/EDV.2EF: Ejection fractionEDV: End Diastolic Volume (ml)ESV: End Systolic Volume (ml)Data analysis was performed using SPSS version 21 (IBM). Data are presented as frequency and percentage for continuous variables and mean \u00b1 Standard Deviation (SD) for descriptive variables. Quantitative data were analysed using One sample student t-test, and qualitative data were compared using Chi square test. P-value was assumed to be significant when P < 0.05.In total, 82 patients who had EF <35% included in this study. The mean age at diagnosis was 49.13 \u00b1 14.8 years; 87.8% were male and 12.2% were female. Echocardiographic findings showed the mean of EF was 31.16% and LVT was present in 6.1%, which is statistically not significant (p = 0.61). The spontaneous contrast picture was seen in 25.6% of patients (p < 0.001) -. Among pKhat chewer and smokers were the most common popular habits in the patients of low EF then Khat chewing only but no significant relationship (p=0.96) . ExactlyLV thrombus is a serious complication of heart failure. In this study, we assessed the prevalence of LV thrombus in patients with heart failure with low EF. Disertori et al., reported that patients with LVEF less than 35% have a high risk of death due to evolution of HF.22It was a single-center study and the sample size was limited by 82 patients.Cardiac patients with low ejection fraction developed left ventricular thrombosis and most of the affected patients were of dilated cardiomyopathy. Interestingly, spontaneous contrast was significantly high in patients with low ejection fraction which is a continuous process of thrombus formation. This make starting anticoagulant therapy in this group of cardiac patients is an individual decision based on patient and physician discussion.NMA: Conceptualization, and data collection.ZAM: data analysis.SAA: writing the original draft and is responsible for integrity of research.FHA: manuscript review & editing.EF:ejection fraction,ASE:American society of echocardiography,EACVI:European association of cardiovascular imaging,LV:left ventricle,LVEF:left ventricular ejection fraction,HFpEF:heart failure with preserved ejection fraction,HFrEF:heart failure with reduced ejection fraction,MI:myocardial infarction,DCMP:dilated cardiomyopathy,AF:atrial fibrillation,TTE:Transthoracic echocardiography,TEE:trans-esophageal echocardiography,RHD:rheumatic heart disease,HTN:hypertension,DM:diabetes mellitus,CHF:congestive heart failure,JVP:jugular venous pressure,CBC:complete blood count,LFT:liver function tests,RFT:renal function test,LVT:left ventricular thrombus,ECG:electrocardiography,LVT:left ventricular thrombus,EDV:end diastolic volume,ESV:end systolic volume,SPSS:statistical package for the social sciences,IBM:international business machines,SD:standard deviation."} +{"text": "Chinese children are facing health challenges brought by chronic non-communicable diseases, such as physical problems and psychological related health problems. Childhood represents a critical life period when the long-term dietary and lifestyle behaviors are formed. It is necessary to survey the prevalence of suboptimal health status (SHS) among Chinese children and to research the relationship between SHS and lifestyles. This study aimed to examine the prevalence of SHS among Chinese children using a large-scale population survey sample covering school students and nonstudent children, and clarified the relationships between SHS and lifestyle factors using multi-level models controlled for the cluster effect of location and the confounding effect of demographics. Multi-level generalized estimating equation models were used to examine the relationships between SHS and lifestyle factors. Prevalence ratios (PR) and 95% confidence intervals (CI) were used to assess the strength of these relationships. Of the 29,560 children, 14,393 reported one or more SHS symptoms, giving a SHS prevalence of 48.69%. The prevalence of SHS for boys (46.07%) was lower than that for girls (51.05%). After controlling for the cluster effect of living areas and confounding effect of demographic characteristics, lifestyle factors associated with SHS were: less sleep duration, current smokers , current drinkers , children\u2019 parents suffering from chronic diseases , poor sleep quality , stress , negative life events , hypertension , unhealthy diet choice and irregular meal time . Children who could exercise regularly and those with regular medical checkup were associated with lower prevalence probability of SHS. SHS has become a serious public health challenge for Chinese children. Unhealthy lifestyles were closely associated with SHS. Implementation of preventative strategies are needed to reduce the potential SHS burden associated with these widespread high-risk unhealthy lifestyle behaviors. With further understanding of health in its broader sense, the definition of health has sensed as not only the absence of disease or infirmity, but also a state of complete physical, mental, and social well-being. Accordingly, suboptimal health status (SHS) are catching more attention among medical professionals as a physical state between health and disease, characterized by declines in vitality, physiological function, and the capacity for adaptation, and including medically undiagnosed or functional somatic syndromes ,2. In thWith the transformation of the disease spectrum from predominantly infectious diseases to chronic non-communicable diseases (NCDs), Chinese children are facing health challenges brought by chronic NCDs, such as physical problems and psyFurthermore, in multi-stage sampling, survey data have a hierarchical structure in which individuals were nested within higher level sampling units. Individual SHS was determined by not merely individual characteristics , but features of the social environments in which individuals live too . Children living in the same areas or studying in the same schools were likely to suffer from the effects of similar living circumstances, developing into a similar health status. Traditional analytical methods such as least square regression and logistic regression assumed that observations were independently but identically distributed. Analyzing multi-level data with traditional analytical methods would result in incorrect inferences in statistical analyses because of violation of these assumptions. Multi-level models provided an appropriate analytical framework to deal with observation dependence in multi-level data . More imThe data was from a large-scale population survey conducted from 2007 to 2011. In brief, this survey was conducted in six provinces or autonomous regions of China to cover a variety of municipal regions and include sufficient minority subjects: Hunan Province, Yunnan Province, Heilongjiang Province, Inner Mongolia Autonomous Region, Sichuan Province, and Ningxia Hui Autonomous Region. In each selected province or autonomous region, a two-stage sampling method was used to recruit eligible subjects. First, two or three cities were selected based on their population and economic conditions using a simple random sampling method. Then, considering that some teenagers might have quit from school, dozens of communities were also selected within each city. All subjects of the selected schools or communities were considered eligible for this study if they were aged 10\u201317 years, were not suffering from serious chronic diseases, and were not running a high fever in the past 15 days. In each province or autonomous region, about 5000 subjects were chosen, who were of dozens of ethnicities, including Han, Yi, Miao, Mongolian, Tibetan, Korean, Hui, Tujia, and others.The study was approved by the ethics review board of the Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (No. 005-2008). Both selected children and their parents signed written informed consent forms. Children carried the informed consent forms to their parents, and then submitted the signed written informed consent forms to medical professionals before the survey. The interview and physical exams were performed by the medical professionals. Both their teachers and adult parents were not present in the interview. This study adhered to strict quality control standards. Trained medical professionals conducted the survey and interviews.A Delphi self-rating SHS scale was used to assess the SHS of children ,23. The Education was classified into three groups: primary school, junior middle school, and senior middle school. Parents\u2019 diseases indicated whether or not children\u2019 father and/or mother were suffering chronic diseases, such as cardiovascular diseases, cerebrovascular diseases, diabetes, cancer, kidney diseases, etc. According to the fourth report on the diagnosis, evaluation, and treatment of high blood pressure in adolescents , hyperteSleep duration and sleep quality were self-reported by children. Sleep duration was their average sleep time per day in the last year, which was classified into >8 h, 6\u20138 h and <6 h. And sleep quality was dichotomized into good sleep quality and poor sleep quality.Stress was defined as self-perceived economic, life, or study stress in the past year. Negative life event was defined by whether the child had experienced loss of job, retirement, loss of crops/business failure, burglary, marital separation/divorce, other major intra-family conflict, major personal injury or illness, violence, death of a spouse, death/major illness of another close family member, and other major stressors in the past year. Diet choice was defined as whether the child had unhealthy diet choice preferences, such as food that was highly salty, sweet, spicy, or greasy. Meal time was used to indicate whether the child regularly had breakfast, lunch, and dinner at fixed times or not in the past year. p-value < 0.05 was defined as statistically significant. Continuous data were described using mean and standard deviation. Categorical data were described with number and percentage. Categorical data were compared using chi-square tests. Children living in the same area and studying in the same school were likely to suffer the effects of similar living circumstances and educational culture. Accordingly, multi-level log-binomial GEE models were conducted to examine the relationships between SHS and lifestyle factors to control for the cluster effect of location and the confounding effect of demographic characteristics. Prevalence ratios (PR) and 95% confidence intervals (CI) were used to assess the strength of these relationships.All case report forms and database were double-checked to guarantee the authenticity and accuracy of raw data. Statistical analysis was performed with SAS9.4 software . A two-tailed In total, 30,071 children signed written informed consent forms and were willing to participate in this survey. Of these, 29,560 children completed all survey scales, giving a completion rate of 98.3%.The average age of all subjects was 13.8 \u00b1 2.3 years, and 52.61% of subjects were girls. The majority of all subjects (73.28%) were of Han nationality. The percentages of current smokers and drinkers were 3.95% and 3.22%, respectively. The percentages of obese and hypertensive children were 4.50% and 4.13%, respectively. In addition, 567 children reported feeling high levels of study, home, or economic stress, and 1513 children had recently experienced negative life events. Just under half (45.00%) of the children took part in medical checkup regularly and 63.80% of the children exercised regularly. Just half (50.19%) of the children slept for >8 h per days and only one-third of children (35.37%) reported good sleep quality. The majority of children (60.41%) had unhealthy dietary choices and 11.10% of children did not have meals at fixed hours regularly. Further, about one-eighth of all children reported that their father and/or mother were suffering from chronic diseases.Of the 29,560 children, 14,393 reported one or more SHS symptoms, giving a SHS prevalence of 48.69%. The most common SHS symptoms were inattention (26.38%), forgetfulness (19.24%), and upset (18.13%). p < 0.0001). The prevalence of SHS was significantly different between ethnicities: children from Tujia had the lowest prevalence of SHS (38.65%) and those from Yi had the highest prevalence (69.83%). The prevalence of SHS increased as educational level increased (p < 0.0001). The average age of children with SHS was 14.6 \u00b1 2.1 years and that of children without SHS was 13.1 \u00b1 2.3 years. The prevalence of SHS was 22.59% for subjects aged 10\u201311 years, 43.39% for those aged 12\u201313 years, 59.35% for those aged 14\u201315 years and 67.32% for those aged 16\u201317 years. The prevalence of SHS for boys (46.07%) was lower than that for girls (51.05%) . Compared with children with normal blood pressure, hypertensive children had a higher prevalence of SHS (54.95% vs. 48.42%). Current smokers (65.12% vs. 48.02%) or alcohol consumers (69.40% vs. 48.00%) had a higher prevalence of SHS than their counterparts. We observed higher prevalence rates of SHS among children with poor sleep quality compared with their counterparts (54.27% vs. 38.50%). The prevalence rate of SHS was 38.60%, 56.46% and 79.92% for subjects with >8 h of sleep, 6\u20138 h of sleep and <6 h of sleep per day respectively. Children who reported experiencing stress had a higher prevalence of SHS than their counterparts (88.89% vs. 47.90%), as did those who had experienced negative life events (78.39% vs. 47.09%). Children who had unhealthy diet choices had a higher prevalence of SHS than their counterparts (52.05% vs. 43.57%). Children who exercised regularly had a lower prevalence of SHS than their counterparts (44.82% vs. 55.50%), as did those who had regular medical checkup (38.75% vs. 56.82%), and those who had regular meals at fixed hours (47.06% vs. 61.75%). The prevalence of SHS by different demographic characteristics and lifestyle factors are detailed in Compared to children sleeping more than 8 h per day, children sleeping 6\u20138 h per day or those sleeping less than 6 h per day had higher prevalence probability of SHS. Current smokers , current drinkers , children whose parents were suffering from chronic diseases , children with poor sleep quality , children who felt about some stress or negative life events , hypertensive children , children who had unhealthy diet choice and children who could not have breakfast, lunch and dinner at fixed hours regularly had higher prevalence probability of SHS. Children who could exercise regularly and those who could take part in medical checkup regularly were associated with lower prevalence probability of SHS. We excluded those who suffered from serious chronic diseases and retained those with mild hypertension (1211 children) in our study. A sensitivity analysis where those with hypertension were excluded was conducted and the findings of multivariate analysis are shown in Previous studies ever reported the prevalence of SHS among college students aged above 18 years old ,28,29,30Lifestyle was one of the most important factors affecting diseases and unhealthy lifestyles were closely related with many chronic diseases ,32,33,34Tobacco smoking and drinking alcohol have been confirmed as associated with many chronic diseases ,37,38,39If their parents were suffering from chronic diseases, children were more anxious and in worse economic conditions which could in turn make them more susceptible to SHS. Economic, life, or study stress and negative life events were important factors for depression and anxiety ,52, and A systematic review reported ever that there was a relationship between unhealthy diet, consumption of low-quality diet and depression or poor mental health . In our This study had several limitations that should be mentioned. First, because of the cross-sectional design, it was not possible to confirm causal relationships between SHS and lifestyle factors. There was a possibility that both some lifestyle factors and SHS resulted from some other predictors simultaneously. Further, even children with SHS may not have enough energy to engage in physical activity, thus leading to inadequate physical activity. Therefore, we could conclude that unhealthy lifestyles were closely associated with SHS, but not confirm the independent prediction effect of unhealthy lifestyle on SHS. Second, considering that low-aged children had difficulty understanding the question items of the SHS scale, we didn\u2019t enroll children aged less than ten years old. Third, since the basic data of this study were obtained 10 years ago and the health problems and factors of Chinese children are changing, the study findings reflected the situation at that time, and may not reflect current situation. Finally, some data were self-reported, such as smoking, alcohol drinking, sleep, diet in this study, and such self-reported knowledge reduced the precision of lifestyle measurement.Despite these limitations, our findings showed that SHS has become a serious public health challenge for Chinese children. Unhealthy lifestyles were closely associated with SHS, with key factors being smoking, drinking alcohol, short sleep duration, poor sleep quality, lack of regular checkup, inadequate physical activity, stress, negative life events, parents suffering from chronic diseases, unhealthy diet choices, and irregular meal times. Implementation of preventative strategies are needed to reduce the potential SHS burden associated with these widespread high-risk unhealthy lifestyle behaviors."} +{"text": "There is a growing young and active patient subgroup with high return to sports (RTS) expectations after TKA. The current lack of evidence regarding RTS capacity in this patient cohort, requires the consolidation of experts\u2019 opinions and experiences to address the special needs among these patients. The aim of this study was to assess current expert opinions in regard to preoperative patient assessment, surgical technique and decision-making and patient counseling for these patients. (2) Methods: We performed a survey among surgeons specialized in arthroplasty with a questionnaire designed to assess current recommendations, surgical techniques, and implant preferences as well as patient counseling in patients with high expectations for RTS after TKA. (3) Results: The majority of surgeons are in favor of return to low-impact sports after TKA within 3 to 6 months. Some even recommend return to high-impact sports. Despite improvement of surgical techniques and implants, we observed no clear preference for a single surgical technique or implant specification in active patients. (4) Conclusions: Current evidence for sports-associated complications after TKA is scarce. Despite a growing array of surgical techniques and implants, the available literature is still controversial with no single surgical technique or TKA design distinguishing itself clearly from others. Surgeons\u2019 recommendations are mostly based on their experience and training. Nonetheless, we observed growing faith in modern implants with some surgeons even recommending high-impact sports after TKA. The benefits of an active lifestyle to prevent chronic diseases, such as cardiovascular disease, obesity, type 2 diabetes mellitus, hypertension, osteoporosis, and even depression have been demonstrated and emphasized extensively in the current literature ,2. MeanwAlongside these developments, knee arthroplasty surgical techniques and implant designs have improved tremendously since the first vitallium prostheses attempts began in 1940s by Campbell, Walldius, Rocher, Kraft, Levinthal, and others . Knee arStudies have shown that patient satisfaction is strongly dependent on the return to physical activity after surgical intervention. The identified main drivers for patient satisfaction include pain, physical health, and mental health ,16,17,18We conducted a survey among German arthroplasty experts to assess their patient-assessment, surgical decisions in regard to surgical approach, choice of implant design and materials as well as patient counseling in patients with high RTS expectations. These patients are likely a growing subgroup among TKA patients. The questionnaire was designed for surgeons specialized in joint arthroplasty. The aim was to identify, whether surgeons make specific decisions to address the heightened expectations in this specific subgroup. We developed a questionnaire in close dialogue with the leadership of the German Arthroplasty Society (AE\u2014Arbeitsgemeinschaft f\u00fcr Endoprothetik)\u2014Germany\u2019s largest and leading society of hip and knee arthroplasty surgeons. For the development of the questionnaire a committee was formed that developed a first draft, which was then shared for feedback and comments with leading surgeons in the field. The feedback was then incorporated for the final version of the questionnaire. The questions were designed to evaluate current recommendations regarding return to sports after total knee arthroplasty (TKA). We assessed what surgeons currently recommend, what implant specifications and surgical techniques they prefer in patients with high RTS expectations and what factors may influence some of their decision-making. We distributed 300 questionnaires among surgeons specialized in hip and knee arthroplasty and members of the AE, who attended the 21st Annual AE Conference in December 2019. In total, 344 participants were registered for the meeting. Membership approval in the AE society requires a completed residency in orthopedic and trauma surgery with sub-specialization in arthroplasty and an endorsement by an AE member. AE members must perform at least 50 arthroplasty surgeries per annum to maintain status. Of the 300 distributed questionnaires, 101 were returned, equaling a 34% response rate.The original questionnaire was designed in German. The original, as well as an English translation of the questionnaire, are provided in the Previous surveys performed among American surgeons used the Clifford and Mallon classification to distinguish between low- and high-impact sports . These cFor data analysis, each returned questionnaire received a unique identity (UID) and answers given were coded into an R data frame for statistical analysis. The data frame is provided in the Our survey was conducted among surgeons specialized in knee and hip arthroplasty. Of 300 distributed questionnaires 101 were returned, corresponding with a response rate of 34%. In total, 86.13% of survey participants had more than ten years of surgical experience, and 55.44% more than twenty years of surgical experience; 54.46% stated a high and 38.61% a medium level of personal physical activity.Preoperative patient assessment: In total 78% of surgeons included assessment of the patient\u2019s physical activity level in their standard preoperative patient work-up. According to the surgeons\u2019 estimation, the most significant factors that influenced postoperative RTS capacity included coordination (94 counts), body mass index (BMI) (66 counts), and age (64 counts), less often neurological preconditions (50 counts) and muscle mass (40 counts) A.Estimated risks associated with sports after arthroplasty: We asked surgeons to estimate the risks associated with sports after arthroplasty of the lower limb in general, among which \u201cperiprosthetic fractures\u201d (60 counts) ranked first, while polyethylene wear (37 counts) and implant loosening (37 counts) ranked only third B.There were 54.5% of surgeons who considered physical activity as important, 29.7% as very important\u2014totaling 84.2% in favor of physical activity after knee arthroplasty. Only 8.9% considered it unimportant, 2% stated it did not matter, 5% NA. A total of 49% of surgeons did not think that RTS had a negative impact on the longevity of the knee implant, even so, 33% did . Conversely, 72.3% expected a positive impact of sports on the longevity of knee implant, only 14.9% did not, 8.9% did not know, 4% NA. A total of 42% of surgeons considered their patients\u2019 weight bearing on the implant was \u201ctoo low\u201d, 1% \u201cmuch too low\u201d, while 35% considered it \u201cjust right\u201d. A total of 16% stated that patient-induced weight bearing was \u201ca little too high\u201d, 1% \u201cmuch too high\u201d (6% NA) A. The daSurgical approach: 91% of surgeons stated high RTS expectations had no influence on the surgical approach, 3% stated they preferred \u201cmedial parapatellar\u201d, 3% a \u201csubvastus\u201d approach 0% chose a \u201cmidvastus\u201d approach, and 3% NA. TKA alignment: 71% said high RTS expectations in patients had no influence on their targeted TKA alignment, 9% preferred anatomical-, 8% kinematic-, 6% mechanical alignment, and 6% NA A. The maPain catheters: were applied by only 9.9% of surgeons. 62.4% did not opt for the application of any pain catheters, 22.8% stated it had no influence, 5% NA A. PostopA total of 53.5% of surgeons recommended high-impact sports after TKA with adequate training of the patient, 36.6% did not recommend it at all. A total of 5.9% recommended high-impact sports without limitations. A. Most lThe results of this study showed that sports including basketball, boxing, gymnastics, handball, hockey, ski slope, soccer, squash, volleyball were recommended with greater restrictions compared to lower-impact sports, such as ballroom dancing, biking (both level and cross), dancing, golf, hiking, swimming, and walking. The lower-impact activity types were recommended without limitations .With 223 knee replacement surgeries per 100,000 capita, Germany ranks fourth after Austria, Luxembourg, and Finland in knee arthroplasties performed per annum ,25, wherThe Clifford and Mallon classification was used to distinguish high-, intermediate-, and low-impact sports in previous surveys ,31,32. DThe majority of surgeons who participated in this study responded that a return to low-impact sports was recommended after 3 months or 6 months (latest). Regarding high impact sports the responses were more controversial. Although available studies suggest that physical activity may negatively impact the longevity of the implant ,33,34, oThe question of return to high-impact sports after total joint replacement has been investigated previously ,39,40 anWhen we compared our results with previously published recommendations for RTS after total hip arthroplasty (THA), we observed no striking differences between activity recommendations after THA vs. TKA . Knee arSurgical approach: Surgical approaches in TKA include the traditional medial parapatellar , the subTKA alignment: The vast majority of surgeons (71%) opted for \u201cno influence\u201d of high RTS expectations on the targeted alignment. Early propositions claiming that clinical outcomes were dependent on good TKA alignment ,51 have By increasing the postoperative range of motion (ROM) and mimicking the physiological motions of the native knee, present-day TKA designs aim to provide higher patient satisfaction and outcomes especially in younger and more active patients with high RTS expectations . TKA desPostoperative training and rehabilitation are likely essential to acquire good ROM, function and RTS level. However, few studies demonstrate these effects in a systematic approach. Application of pain catheters: Most surgeons opted for \u201cno application\u201d of pain catheters after TKA in patients with high RTS expectations or no influence. There are various types of pain catheters available including intraarticular, continuous femoral nerve analgesia, epidural, and local infiltration analgesia (LIA) ,79,80,81In order to increase patient satisfaction and physical activity as well as improving long-term knee arthroplasty outcomes, new approaches for implant designs as well as surgical techniques have been developed over the years. These various alterations have led to a wide spectrum of available techniques and improved implant materials that are hypothesized to increase implant longevity and weight-bearing capacities ,53,84. HThis study has several limitations. It was designed to assess expert opinions of arthroplasty experts for patients with high RTS expectations and an active lifestyle after TKA. This study does not provide in vivo tested evidence and the results may be subjected to the surgeons\u2019 observer-bias as well as recall-bias: Patients often return to low-impact sports after TKA . A partiKnee arthroplasty surgery in young and active patients with high RTS expectations make up a growing subgroup of patients with TKA. Evidence regarding the best standard-of-care for patients receiving knee arthroplasty with high RTS expectations is scarce and available findings are often controversial . Biomech"} +{"text": "Health risk behaviours during adolescence can have long-term negative consequences. Little is known, however, about the recent health risk behaviour trends in adolescents in Lebanon. This investigation aimed to report the trends in the prevalence of various health risk behaviours, such as alcohol use, dietary behaviour, interpersonal violence, mental health, oral and hand hygiene, among adolescents in Lebanon. Cross-sectional nationally representative data were analysed from 13,109 adolescents (14 years median age) that participated in three waves of the \u201cLebanon Global School-Based Student Health Survey (GSHS)\u201d. Results indicate that significant improvements were found among both boys and girls in the decline in interpersonal violence , poor washing of hands after using the toilet, and suicide planning, and among girls only loneliness, worry-induced sleep disturbance and suicidal ideation. Significant increases were found among both boys and girls in the prevalence of inadequate fruit consumption, and among boys only unintentional injury and not always washing hands before eating. In conclusion, several decreases but also increases in health risk behaviours were found over three assessment points during a period of 12 years calling for continued health enhancing activities in this adolescent population. Lebanon, an upper middle-income country in the Arab region, has a population of 5.5 million (2.4 million in Beirut) , includiIn Lebanon, 91% of all deaths are attributed to non-communicable diseases (NCDs), including 47% cardiovascular diseases, 16% cancers, 6% injuries, 5% diabetes, 4% chronic respiratory diseases, and 19% other NCDs . The burAs stated by the World Health Organization (WHO), \u201calcohol use, dietary behaviours, drug use, hygiene, mental health, physical activity, protective factors, sexual behaviours, tobacco use, violence and unintentional injury\u201d are the leading causes of morbidity/mortality among children and adults globally . The gloPrevious cross-sectional studies among adolescents in Lebanon found a high prevalence of various health risk behaviours. In terms of interpersonal violence, a high prevalence of involvement in physical fight almost 42%) were found among school adolescents in Beirut, Lebanon . In a na% were foAssessing behavioural risk factors, such as injury and violence, poor mental health, substance use, unhealthy diet and sedentary lifestyle, over time may aid in improving strategies to prevent or ameliorate reducing health risk behaviours in the adolescent population ,20,21. HStudies investigating trends in health risk behaviours among adolescents showed different results ,21,25, rCross-sectional nationally representative data from the 2005, 2011 and 2017 Lebanon GSHS were analysed . More deThe questionnaire used is shown in p < 0.05 was considered significant. Missing values were excluded from the analysis.Statistical analyses were done with \u201cSTATA software version 15.0 \u201d. Data from the 2005, 2011 and 2017 Lebanon GSHS were merged and were weighted for non-response and probability selection . Descrip2 = 1083.26, p \u2264 0.001) . The proportion older adolescents increased across the three different surveys X001) see .p for trend 0.006) and 54.4% among girls (p for trend 0.007) in 2017. Inadequate vegetable consumption (81.4% among boys and 85.7% among girls in 2005) did not significantly change over time among both boys and girls. The prevalence of students who reported frequently experiencing hunger (3.4% among boys and 2.6% among girls in 2005) did not significantly change from 2005 to 2017 in both males and females.Among students, 42.2% of males and 47.2% of females ate less than two fruit servings daily in 2005, and the proportion of inadequate fruit intake significantly increased to 50.3% among boys , ever drunk (21.2% among boys and 7.1% among girls in 2005) and trouble from drinking alcohol (23.7% among boys and 11.1% among girls in 2005) did not significantly change over time among both boys and girls.p for trend 0.004) but not in girls (28.4% in 2005 and 31.5% in 2017). Being bullied (38.7% among boys and 29.4% among girls in 2005), a victim of physical assault (50.0% among boys and 33.4% among girls in 2005) and involved in physical fighting (64.6% among boys and 29.0% among girls in 2005) significantly decreased in both sexes (p for trend <0.001).The prevalence of annual injury increased significantly from 37% to 44% in boys (p for trend 0.012), while not always washing hands after using the toilet decreased both among boys (p for trend 0.002) and girls (p for trend <0.001), and \u201cnot always washing hands with soap\u201d did not change over time.The prevalence of inadequate tooth brushing was 38.4% among male and 30.4% among female students in 2005, which remained high over time. Not always washing hands prior to eating significantly increased among boys (p for trend <0.001), and loneliness (p for trend 0.004), worry-induced sleep disturbance (p for trend 0.022), suicidal ideation (p for trend <0.001) and suicide planning (p for trend <0.001) significantly decreased among girls.Among all five poor mental health indications , suicide planning decreased among boys (School truancy (20.9% among boys and 10.3% among girls in 2005), peer support (64.5% among boys and 73.3% among girls in 2005) and the three parental support indicators did not change over time among both boys and girls see .The study found, across three GSHS in 2005, 2011 and 2017 in Lebanon, significant decreases among both boys and girls in interpersonal violence , inadequate hand hygiene (after toilet use), and suicide planning, and among girls only suicidal ideation, loneliness and worry-induced sleep disturbance. Significant increases were found among both boys and girls in the prevalence of inadequate fruit consumption, and among boys only unintentional injury and inadequate hand hygiene (before eating). Several studies investigating the implementation of health education in schools in Lebanon showed poor or mixed results. For example, in a survey of 50 different schools, 80% of the school principals reported that their schools do not offer any health educations to their students , and in Violence-related behaviour decreased in this study, which concurs with four other studies ,28,29,30The prevalence of inadequate fruit and vegetable intake was high in the 2005 GSHS and increased for fruit intake over the study period, which was also shown in a trend study in Oman and otheThe prevalence of sub-optimal oral hygiene (tooth brushing 0.05). The mean (SD) total cost for those with TB/HIV co-infection reached $188 ($33). Similarly, the total cost of care significantly varies by type of TB, it was $104 ($107) for pulmonary, $140 ($138) for extra-pulmonary and $446 ($732) for DR-TB .HIV and TB care results in adverse financial consequences for households. Nearly 24% of HIV and 68% of TB study participants have adopted coping mechanisms. Nine per cent of HIV and 4% of TB patients have borrowed money; while, 2% of HIV and 19% of TB patients sold their household assets. Furthermore, 12% of HIV patients relied on family assistance and 16% of TB patients used their savings to cope with the costs. Only 2% of HIV and 6% of TB participants are covered by health insurance.As shown in As shown in 2 for trend \u221210.58, p<0.001). The incidence is 33% for individuals with inpatient HIV care. The corresponding level of TB was 40% (291 households); with 58% and 20% of the poorest and richest income quintile experienced CHE, respectively ; with 43% of the poorest and 4% of the richest household experiencing CHE (\u03c7p<0.001) . The incp<0.001) (online sp<0.001) .In our study, for example, the mean overshoot of TB-related CHE was 6.3% (range: 1.9% to 15.3%). On average, households spent 6.3% beyond the 10% threshold for TB care. However, the average positive overshoot among households that experienced CHE was 15.8% (range: 9.2% to 26.6%). Thus, on average, households that experienced CHE spent 25.8% (10% threshold+mean positive overshoot) of their total annual consumption for TB care online s.In addition, as shown in In the multivariate analysis , three vSeven variables were significantly associated with TB-related CHE : privateIn this study, we tried to estimate the OOP, total cost, incidence and determinants of CHE among individuals seeking HIV and TB care. This could provide valuable insight into the level of financial risk protection that a health system offers to its population.In Ethiopia, where ART is given free-of-charge, PLHIV had to pay a total of $78 per year for HIV care ($19.5 per visit). The total HIV patient cost was equivalent to 7% of their annual income. As HIV requires lifelong care, such costs have a devastating impact on affected households. Our estimate was lower than the level and rate found in Cameroon 17%,42In our study, the average direct OOP expenditure for HIV care was $54 and comparable with that of the previous studies from Lao, Ethiopia and Nepal.43In our study, about a fifth (20%) of patients seeking HIV care experienced CHE. A study from India also depicts similar findings.19 42In our study, patients with TB incurred a total cost of $115 per episode and represents 21% of the annual household income, comparable to a study in South Africa 22%).%.22 onlyIn this study, one-half of the mean TB cost was incurred prior to initiation of treatment, which was consistent with many previous studies.47The direct patient costs incurred constitute 46% of the total, comparable with findings from elsewhere (36%)A higher percentage of households incurs CHE for TB care (40%), which was comparable with studies from Fiji (40%), Ghana (47.6%), China (53%), Philippines (35%) and lower than reported rates from Ethiopia (63%), Nigeria (65%) and Benin (72%).56The mean overshoot for TB was 6.3% and the mean positive overshoot was 15.3%, both were similar with finding from Benin (7.8% and 14.8%) and Nigeria (6.0% and 9.3%).This study has some limitations. First, the cost measurements relied on patient\u2019s ability to remember, which increases risk of recall bias. However, we reduced the recall bias by interviewing participants who sought HIV and TB care within the past 1 month, when patients have a better recollection of their pathway to care.Despite OOP exemption of HIV and TB services in Ethiopia, we found that there is a large gap between the actual level of financial protection provided and the ideal goal. Our findings highlight important policy implications. First, more patient-centred care with effective diagnostics, appointment spacing for stable patients and community-based treatment are required to improve the delivery of HIV and TB services. Second, strategies are required to ensure social and financial risk protection for the households affected by HIV and TB. This requires effective integration of HIV and TB services with social and financial protection schemes, including the provision of travel vouchers, nutritional support and paid sick leaves through multisectoral collaboration.HIV and TB affected individuals and their households in Ethiopia face substantial costs in seeking care despite \u2018free medical services\u2019. The incidence of CHE related to HIV and TB care was high in all income quintiles, though more so in the poorest households. Policymakers should introduce patient-centred care; expand social and financial risk protection measures to minimise the high patient cost of HIV and TB care, particularly among vulnerable populations."} +{"text": "This cross-sectional study uses 2015-2017 data from the Pregnancy Risk Surveillance and Monitoring System to examine the association between health insurance coverage and use of perinatal health care among low-income women in the US. We limited the sample to women with complete insurance information and household incomes less than 138% of the federal poverty level, the minimum required by federal statute to qualify for pregnancy-related Medicaid.5 The University of Michigan institutional review board deemed the study exempt from the need for institutional review board approval and informed consent because it used publicly available, deidentified data. This study followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guideline.This cross-sectional study used pooled 2015-2017 data from the Pregnancy Risk Surveillance and Monitoring System (PRAMS),P < .05 was considered statistically significant. Statistical analyses were conducted from December 27, 2019, to November 19, 2020, using Stata, version 14.2 (StataCorp LLC).We hierarchically characterized insurance at each time point into 3 categories: Medicaid, private, or uninsured. We then generated 4 insurance patterns across these time points: continuous insurance, shifts between private and Medicaid coverage, shifts between insurance and uninsurance, and continuous uninsurance. We examined 3 health care use outcomes: prenatal care in the first trimester, in-hospital birth, and postpartum visit attendance. For each insurance pattern, we estimated the probability of each outcome using weighted logistic regression with margins at observed sample values. We weighted all models using PRAMS sample weights and adjusted for age, race/ethnicity, educational level, marital status, and parity. All statistical tests were 2-sided, and P\u2009<\u2009.001 for each comparison) (P\u2009<\u2009.001).The study sample consisted of 39\u2009378 women with a mean (SD) age of 27.4 (5.9) years. Of these, 43.6% were continuously insured, 21.3% experienced shifts between private coverage and Medicaid, 32.8% experienced shifts between insurance and uninsurance, and 2.4% were continuously uninsured. Spanish-speaking Hispanic women composed 60.1% of the continuously uninsured category . Women wparison) . Almost 3 National efforts to extend Medicaid through the first year post partum are supported by the American Medical Association and are another possible mechanism for improving health care access among postpartum women.6Continuous uninsurance or shifts between insurance and uninsurance from preconception to postpartum were associated with a lower likelihood that women received early prenatal care or recommended postpartum care compared with women with continuous insurance. Hispanic, Spanish-speaking women composed nearly two-thirds of the women with continuous uninsurance, suggesting particularly high barriers to enrollment among this population potentially associated with immigration status. Study limitations include the use of self-reported insurance status, exclusion of 10 states that did not participate in PRAMS, and the inability to discern citizenship, which may affect insurance eligibility. Improving receipt of recommended maternity care among women who experience uninsurance in the perinatal period is a clinical and policy priority. Adoption of the Patient Protection and Affordable Care Act\u2019s Medicaid expansion has improved perinatal insurance continuity for low-income women."} +{"text": "Worldwide, tuberculosis (TB) is the leading cause of death from a single infectious disease agent has been demonstrated to prevent TB disease among persons who might be infected with TB and are at risk for TB disease , a 2% decline from 2017 . IncidenThe WHO region of South-East Asia accounted for the highest percentage of TB cases in 2018 . TB inciIn 2018, 65 countries reported data on TPT use among eligible persons living with HIV and 109 countries among children aged <5 years. Among these countries, 1.8 million persons living with HIV received TPT in 2018 . Less progress was observed among eligible children aged <5 years: 350,000 children received TPT in 2018, a 20% increase compared with 292,000 in 2017.WHO\u2019s initiative, The End TB Strategy have been set in a World Health Organization (WHO) initiative, The End TB Strategy. Achieving these targets will require substantial annual reductions in the incidence of TB and the number of TB deaths.In 2018, an estimated 10 million incident TB cases and 1.5 million TB deaths occurred, reductions of 2% and 5%, respectively, from 2017. TB epidemiology varied by WHO region.Innovative approaches to case finding, scale-up of TB preventive treatment, use of newer TB treatment regimens, and prevention and control of HIV will contribute to decreasing TB incidence."} +{"text": "Compared to tamoxifen users, AI users had a higher risk of any arthritis and carpal tunnel syndrome . No significant difference was observed in the risks of any arthritis and carpal tunnel syndrome across different AIs. Taxane use was not associated with any arthritis or carpal tunnel syndrome compared to other chemotherapies. Taiwanese women with breast cancer-initiating AIs had an increased risk of arthritis and carpal tunnel syndrome compared to those who initiated tamoxifen.Tamoxifen or aromatase inhibitor (AI) therapy may prevent breast cancer recurrence, however, adverse effects may lead to treatment discontinuation. Evidence regarding the occurrence of AI-associated musculoskeletal problems among Asians is scarce. We identified women with breast cancer-initiating tamoxifen or AIs from the Taiwan National Health Insurance Research Database (2007\u20132012). Using multivariable cause-specific hazard models, we examined the association between endocrine therapy and the risk of any arthritis and carpal tunnel syndrome, adjusting for age, prior cancer treatment, and other health status factors. Among 32,055 eligible women with breast cancer (mean age = 52.6 \u00b1 11.5 years), 87.4% initiated tamoxifen, 3.9% initiated anastrozole, 8.0% initiated letrozole, and 0.7% initiated exemestane. AI users had a higher 1-year cumulative incidence for any arthritis (13.0% vs. 8.2%, Breast cancer is the most common newly diagnosed and prevalent female cancer, with 1.7 million new and 6.3 million prevalent cases worldwide in 2012 [Musculoskeletal problems occur commonly among AI users ,4, with n < 400) from Japan found that 35% to 72% of AI users reported joint pain [Approximately 40% of women with newly diagnosed breast cancer are Asians but the int pain ,11,12. Cint pain , responsint pain . The Firint pain found thOur data sources were the Taiwan National Health Insurance Research (NHIRD) and Catastrophic Illness Patient Databases (CIPD) from 2004 to 2013. NHIRD is the administrative claims data of the Taiwan National Health Insurance (NHI) Program that has covered >99% of the Taiwanese population (>23 million unique people) since 1997. NHIRD datasets include enrollment information, medical claims including inpatient, outpatient and emergency department visits, and prescription claims reimbursed by the NHI Program. The CIPD registry covers more than 30 major chronic diseases and requires histological and/or clinical validations for CIPD eligibility.In this retrospective cohort study with new user design, we identified women with breast cancer-initiating endocrine therapy from 2007 to 2012. We identified endocrine therapy including tamoxifen and AIs using the Anatomical Therapeutic Chemical (ATC) Classification System codes Table S. ConsideTwo separate outcomes were examined in the 12 months after initiation of endocrine therapy: time to the first episode of (1) any arthritis including osteoarthritis, rheumatoid arthritis, and other arthritis and (2) carpal tunnel syndrome. Any arthritis and carpal tunnel syndrome were identified by at least one inpatient claim or two outpatient claims that were more than 30 days apart . Based on the prior literature on breast cancer treatment, we adjusted for a series of covariates to address potential confounding ,6. Covarp < 0.05).Patient characteristics were summarized by endocrine therapy groups with appropriate descriptive statistics . We used multivariable cause-specific hazard models to estimate the risk of any arthritis and carpal tunnel syndrome within a year across different AIs compared to tamoxifen, adjusting for the covariates mentioned above such as age and history of chemotherapy within a year prior to initiation of endocrine therapy. Both unadjusted and adjusted hazard ratios (aHRs) and 95% confidence intervals (CI) were presented. Statistical significance was determined based on 2-tailed tests .Given that patients initiating different endocrine therapies or chemotherapy regimens may have different disease severity and characteristics, we conducted two additional sensitivity analyses for each outcome using propensity score (PS) matched cohorts to ensure comparability. We then estimated the risk of outcomes of interest using multivariable cause-specific hazard models. We matched the cohorts using the optimal caliper widths method with widths of 0.2 standard deviations of PS . Detailsp < 0.0001), more likely to have more taxane-based chemotherapy (14.8\u201337.8% vs. 10.8%), a higher NCI index \u22652 (12.1\u201313.7% vs. 5.9%), more non-cancer comorbidities such as hypertension (45.5\u201348.4% vs. 30.5%), and more opioid use (8.0\u201311.2% vs. 4.4%), as shown in p < 0.0001).Among 32,055 eligible Taiwanese women with breast cancer (mean age: 52.6 \u00b1 11.5 year), 87.4% initiated with tamoxifen, 3.9% with anastrozole, 8.0% with letrozole, and 0.7% with exemestane. Compared with tamoxifen users, AI users were older . Overall, AI users were associated with a 21% higher risk of any arthritis in the year after treatment initiation compared to tamoxifen users. Among AIs, only letrozole users were associated with a statistically significant increased risk of any arthritis compared to tamoxifen users . Other factors significantly associated with an increased risk of any arthritis included older age , previously receiving radiation therapy , hypertension , dyslipidemia , affective disorders , opioid use , and NSAIDs/acetaminophen use (As shown in 19\u20131.47) . Prior ep = 0.008). Overall, AI users were associated with a 68% higher risk of carpal tunnel syndrome in the year after treatment initiation compared to tamoxifen users. Among AIs, anastrozole and letrozole users were associated with a statistically significant increased risk of carpal tunnel syndrome compared to tamoxifen users. Other factors significantly associated with an increased risk of carpal tunnel syndrome included age of 45 to 54 years and having a history of affective disorders ( \u2212 1.70) . Prior eAs shown in Our study using nationwide claims data in Taiwan yielded three key findings regarding the association between type of endocrine therapy use and the occurrence of musculoskeletal problems within a year after treatment initiation. Overall, over one-tenth of Taiwanese women with breast cancer-initiating endocrine therapy experienced any arthritis within the first year of treatment, whereas the occurrence of carpal tunnel syndrome was less than 2%. Secondly, women who used AIs were associated with a 21% and 68% increased risk of any arthritis and carpal tunnel syndrome, respectively, compared to those who used tamoxifen after adjustment for relevant confounders such as age, prior cancer treatment, and other comorbidities. Thirdly, there are no significant differences in the risk of any arthritis or carpal tunnel syndrome for women initiating letrozole versus anastrozole in the sensitivity analyses using PS-matched cohorts. Notably, prior exposure to taxane was not a risk factor for either outcome of interest in the main and sensitivity analyses.To our knowledge, this is the first study to assess the effect of different endocrine therapies on the subsequent risk of musculoskeletal problems using a real-world, population-based claims dataset of Asian women with breast cancer. Our incidence rate of any arthritis (8% to 14%) after initiation of endocrine therapy was lower than the rates reported from the previous studies 20% to 74%) , while o% to 74% Consistent with prior studies ,20,21 ouMoreover, relationships between any arthritis and carpal tunnel syndrome and other factors including age, taxane use, affective disorders, and analgesic use observed in our study have noteworthy implications for future research and patient care. AI use may increase arthritis risk or worsen arthritis symptoms, especially among older adults. Prior exposure to taxane use has been considered a risk factor of musculoskeletal problems based on one small cross-sectional study , but thiStrengths of the current study include use of a nationwide claims database that covers nearly all Taiwanese women with breast cancer, the ability to capture complete information on comorbidities, treatments, procedures, and medications reimbursed by the NHI, and use of sophisticated PS matching approaches to balance numerous confounding factors that may influence the risk estimates. Furthermore, we recognized death as a competing risk in our analysis . We applied cause-specific Cox models and included the National Cancer Institute Index as a facOur study has several limitations. First, our study relied on administrative claims data that lacked information on cancer stage, laboratory results, and socio-behavioral information . However, we excluded women who had a history of bone metastasis and included prior cancer treatments, procedures and image work-ups as surrogates for cancer staging in our analyses. Second, due to the inherent limitations of an observational retrospective study using claims data, it is unknown whether the dispensed drugs were actually taken by the patients. Potential unmeasured confounders cannot be ruled out from our observational study. Third, we grouped women based on their initial endocrine therapy, but they might switch to different therapies. A previous study using NHIRD data has shown that 16% of the tamoxifen users switched to AIs, 6% of the AI users switched to tamoxifen, and less than 4% of women had multiple switches . If a hiIn conclusion, in this population-based study using nationwide claims data, Taiwanese women with breast cancer-initiating AIs had an increased risk of any arthritis and carpal tunnel syndrome compared to those who initiated tamoxifen. Prior exposure to taxane was not a risk factor of any arthritis and carpal tunnel syndrome. Our findings provide real-world evidence for clinicians to consider the possibility of AI-associated musculoskeletal problems when women initiate endocrine therapy and provide timely and proper management to avoid discontinuation of AI therapy."} +{"text": "The Medicare Annual Wellness Visit (MWV) includes an assessment of health risks for older adults in the United States. Research suggests that neighborhood-level social inequality influences multiple health outcomes. We sought to examine the association between neighborhood socioeconomic position and older adults\u2019 cognition, health management self-efficacy, and other health risks. We identified a cohort of 12,434 adults aged 65 and over from the NEOCARE Learning Health Registry who attended a routine MWV between 2011 and 2019. NEOCARE includes electronic health record and neighborhood data from 1999-2017 on over 3 million unique Northeast Ohio individuals. The study population was 60% White, 32% Black or African American, 64% female, and 90% non-Hispanic. Over 60% were ages 65-74, 29% 75-84, and 10% 85 years or older (range from 65 to 101). We used ANOVA and chi square tests to examine variation in health risks by quintile of census tract area deprivation index. Cognitive functioning differed across quintiles of area deprivation and Bonferroni-corrected tests indicated that adults in the most socioeconomically disadvantaged neighborhoods had lower average cognitive screening scores as compared to older adults in less disadvantaged areas . The proportion of adults feeling efficacious in managing their health differed according to area deprivation, with adults in more disadvantaged neighborhoods having slightly lower self-efficacy, . Better understanding of the relationship between cognitive functioning and health self-efficacy and neighborhood environment is critical for designing programmatic and policy interventions aimed at supporting proactive aging in older adulthood."} +{"text": "Men who have sex with men (MSM) attending university are a high-risk population for human papillomavirus (HPV) infection and are a neglected population of HPV vaccination programs in China. To provide evidence for HPV vaccination policies, we conducted this study to examine the prevalence and factors associated with anal HPV infection among MSM attending university in China. A self-administered online questionnaire was conducted to collect information on social demographics and sexual behaviors. A self-collected rectal swab specimen was collected to test for 37 HPV types. A total of 426 participants were tested for HPV. The median age was 20 years. HPV prevalence was 37.5% for any type, 29.8% for nine-valent vaccine types, 24.6% for four-valent vaccine types, 11.5% for HPV-16/18, and 15.7% for HPV-6/11. Men enrolled in a technical diploma, living in Northern China, having more than two sex partners, being bottom or versatile in anal sex, and having a human immunodeficiency virus (HIV) testing history were more likely to have positive anal HPV of any type. Our study found a high prevalence of anal HPV infection among MSM attending university in China, with HPV vaccine-preventable types being the most popular types in this group. Thus, our findings highlight the urgency of promoting HPV vaccination among teenage MSM. Human papillomavirus (HPV) has been identified as one of the most common sexually transmitted infections (STIs) worldwide . Most HPAlthough there is an abundance of literature on HPV among men who have sex with men (MSM), data on HPV among very young MSM are still lacking. A systematic review that only included 698 MSM \u2264 25 years of age, all of whom were from North America and Europe, found that the rate of anal HPV-16 infection was up to 16% among MSM aged \u2264 20 years and up to 18% among those aged 21\u201325 years . It was MSM are a neglected population in HPV prevention programs around the world. Three prophylactic HPV vaccines, directed against certain HPV types, are currently available for the prevention of HPV-related disease: the bivalent vaccine is recommended to females, and the quadrivalent and the nine-valent vaccines are recommended to both males and females . HoweverThe methodology of the University Student HIV Test Intervention Study (the UniTest Study) has previously been published elsewhere . BrieflyParticipants were required to finish a self-administrated online questionnaire to collect information regarding sociodemographics, sexual behavioral, HIV testing history, and alcohol and recreational drug use.Participants conducted a self-collected anal swab sample for HPV testing. The polymerase chain reaction (PCR) HPV genotyping test was used to determine the HPV-type distribution in specimens. The PCR test amplified the target HPV DNA for 37 anogenital HPV types, which included HPV-6, 11, 16, 18, 26, 31, 33, 34, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59 61, 66, 67, 68, 69, 70, 71, 72, 73, 81, 82, 83, and 84.\u00ae Determine HIV-1/2, Alere Medical Co., Ltd., Matsudo, Japan). Participants that tested positive for HIV were referred to local centers for disease control and prevention (CDC) for confirmation testing and subsequent services.HIV testing was conducted by trained doctors with rapid HIV testing ), dwelling location, sexual orientation, and the gender of sex partners. Sexual behaviors included age of first anal intercourse, number of sexual partners in the past 3 months, commercial sex history, compulsive sex history, engaging in group sex in the past 3 months, role of anal sex in the past 3 months, unprotected anal sex in the past 3 months, and condom use during last anal sex encounter.The HPV detection variables consisted of type-specific HPV prevalence, any HPV type, high-risk HPV types, low-risk HPV types, single infection types, multiple infection types , and vacp < 0.10 in the univariate analyses were included in the multiple logistic regression model to determine factors associated with HPV infections. The chi-square test with trends was used to demonstrate the significance of the trends in HPV prevalence with the time since first anal sex. Analyses were conducted using STATA MP 16 .Descriptive statistics included summary measures of the mean or median and interquartile range (IQR) for continuous variables and frequency tables for categorical variables . HPV prevalence was given as a percentage and corresponding 95% confidence intervals (CIs) for binomial proportions. Adjusted odds ratios (AORs) and 95% CIs of HPV infections were calculated according to characteristics using multivariate logistic regression models. Predictors with A total of 447 MSM attending university were enrolled in the study from January to April 2019. The demographic characteristics of the participants are shown in p = 0.018) and having > 2 sex partners . Participants with a positive HPV diagnosis practiced significantly more receptive anal sex . Compared to HPV-negative participants, HPV-positive participants had a greater history of HIV testing . About one in five of all participants had sex after drinking alcohol. Approximately one-third of all participants reported recreational drug use.A total of 431 anal swabs were collected and tested for HPV types\u2014Of which, five failed to test, with unsatisfactory samplings. p < 0.05).We found positive trends between positive anal HPV infections and time since first anal sex . The proWe found a high HPV prevalence among MSM attending university in China. The great majority of infected HPV types could have been prevented by HPV vaccination. To our knowledge, this is the first study to characterize the prevalence and types of anal HPV infections in this young population in China.Our study found that the prevalence of any anal HPV infection among MSM attending university was 37.5%, which was lower than the overall prevalence of 52\u201366% among MSM with HIV-negative status in the general population in China ,19. The According to our results, the majority of participants were infected with HPV vaccine-preventable types, indicating that promoting HPV vaccinations could potentially be an effective way to prevent HPV infections among this young population. In our study, HPV-16 and 18 were the most prevalent high-risk HPV types. Studies have found that the persistence of high-risk HPV types, specifically HPV-16/18, is an important risk factor for the development of anal cancer . FortunaOur study also found some risk factors associated with anal HPV infections. The proportion of anal HPV infections increased with time since the first anal intercourse among MSM attending university. With the increase of sexual activity, they are more likely to be exposed to HPV, which correspondingly increases the risk of HPV infection. Similar to the results in the general MSM population, playing a receptive role in anal sex and having multiple sex partners are also risk factors of anal HPV infections among MSM attending university ,26. FurtWe found that participants enrolled in technical diploma programs were more likely to be infected with HPV than undergraduates. In the Chinese education system, the admission scores and learning tasks of technical diploma programs are lower than those of undergraduates . StudentOur study had limitations. Firstly, this study was cross-sectional, thus limiting our ability to differentiate between transient HPV infections and persistent HPV infections. HPV detection at a single time cannot represent persistent HPV infections. A prospective study found that 66% and 90% of HPV infections would be cleared within 12 and 24 months, respectively, in men . ConsecuOur study found a high prevalence of anal HPV infections among MSM attending university, especially for HPV vaccine-preventable types, suggesting that this population are a potential target group for HPV vaccinations. Prospective studies are needed to understand the natural history and influencing factors of HPV infections in this young population and to evaluate the effectiveness of HPV vaccinations in young males in China."} +{"text": "Utilizing the traditional centers of excellence approach to conduct clinical trials involving rare diseases remains challenging. Patient-based registries have been shown to be both feasible and valid in several other diseases.This report outlines the clinical characteristics of a large internet registry cohort of participants with a self-reported diagnosis of granulomatosis with polyangiitis or microscopic polyangiitis.Patients with a self-reported diagnosis of granulomatosis with polyangiitis or microscopic polyangiitis in an internet-based prospective longitudinal cohort (from the Vasculitis Patient-Powered Research Network) were included. Data on symptoms, diagnostic testing, and treatment were collected using standardized questionnaires.z=10.42, P<.001), fevers , joint involvement , and pulmonary involvement . Compared to microscopic polyangiitis, patients with granulomatosis with polyangiitis reported significantly less renal involvement and renal transplantation . Antineutrophil cytoplasmic antibody positivity was reported in 94.2% (652/692) of patients with granulomatosis with polyangiitis and 96.1% (147/153) of patients with microscopic polyangiitis. A biopsy showing vasculitis was reported in 77.0% (562/730) of patients with granulomatosis with polyangiitis and 81.9% (131/160) of patients with microscopic polyangiitis.The study compared patients with granulomatosis with polyangiitis (n=762) and patients with microscopic polyangiitis (n=164). Of the cohort, 97.7% (904/925) reported the diagnosis had been confirmed by a physician. Compared to microscopic polyangiitis, patients with granulomatosis with polyangiitis reported significantly more ear, nose, and throat manifestations (granulomatosis with polyangiitis: 641/723, 88.7%; microscopic polyangiitis: 89/164, 54.3%; In this large, internet-based cohort of patients with a self-reported diagnosis of granulomatosis with polyangiitis or microscopic polyangiitis, disease manifestations were consistent with expectations for each type of vasculitis. Given the rarity of these and other vasculitides, conducting some types of research through internet-based registries may provide an efficient alternative to inperson, center-of-excellence clinical trials. Granulomatosis with polyangiitis and microscopic polyangiitis are forms of antineutrophil cytoplasmic antibody\u2013associated vasculitis that primarily target small arteries. These are rare diseases, with annual prevalence of granulomatosis with polyangiitis estimated from 24 to 160 per 1,000,000 and annual prevalence of microscopic polyangiitis estimated from 39 to 94 per 1,000,000 [Established in 2014, the Vasculitis Patient-Powered Research Network is an international, internet-based prospective longitudinal registry of patient- or caregiver-reported information. The Vasculitis Patient-Powered Research Network was established as a partnership between the Vasculitis Clinical Research Network (a vasculitis research network) and the Vasculitis Foundation (the largest patient advocacy group for vasculitis). The network represents a collaboration among a variety of vasculitis stakeholders including patients, patient advocacy organizations, academic clinical investigators, expert clinicians, biomedical informaticians, methodologists, and funding organizations. Patient-partners are an integral part of team and are involved in strategically planning, developing, reviewing, and approving research studies. Patient-partners receive training in patient participation in research.The Vasculitis Patient-Powered Research Network is the largest patient-based registry for primary systemic vasculitis with over 3000 patients enrolled to date; patients (or caregivers) consent to participate in studies and provide self-reported information longitudinally using the internet-based platform . For thiyes, no, or I don\u2019t know and were able to review or change previously answered questions. Responses that were left blank or where the answer was not known were excluded from the analysis. Patient participation was encouraged by sending email reminders to participants; however, no incentives were offered for completion of the questionnaires. Multiple entries by the same individual were prevented through the use of password-protected user log-ins.Only patients with a self-reported diagnosis of granulomatosis with polyangiitis and microscopic polyangiitis were included in this study. Patients provided consent online and were enrolled between November 2014 and May 2019. The data were obtained via convenience (or opportunity) sampling methods. Using the internet-based patient portal, participants filled out standardized questionnaires were female and 244 (32.0%) were male. The median age of patients at the onset of symptoms was 45 (IQR 31-57) for 619 respondents, and the median age at diagnosis was 48 (IQR 35-57) for 683 respondents. Out of 761 respondents, 248 (32.6%) reported their disease as active, 465 (61.1%) reported their disease as being in remission, and 48 (6.3%) reported they were unsure. Respondents reported seeing one or more of the following specialists: rheumatologist , nephrologist , pulmonologist , otolaryngologist , neurologist , immunologist , dermatologist . Respondents reported their country of origin as the United States , Canada , United Kingdom , Australia , or other .A total of 164 participants reported a diagnosis of microscopic polyangiitis; 133 (81.1%) were female and 31 (18.9%) were male. The median age of patients at the onset of symptoms was 52 (IQR 36-61) for 129 respondents, and the median age at diagnosis was 53 (IQR 41-62) for 158 respondents. Out of 160 respondents, 55 (34.4%) reported their disease as active, 96 (60.0%) reported their disease as being in remission, and 13 (8.1%) reported they were unsure. Respondents reported seeing one or more of the following specialists: rheumatologist , nephrologist , pulmonologist , neurologist , immunologist , dermatologist and otolaryngologist . Respondents reported their country of origin as the United States , Canada , United Kingdom , Australia , or other In patients with granulomatosis with polyangiitis, the most common self-reported manifestations were nasal or sinus in 82.9% (600/723), joint pain in 79.8% (549/688), pulmonary in 71.3% (523/734), peripheral nerve in 62.8% (411/654), and renal in 61.5% (457/743) of respondents. Pulmonary\u2013renal syndrome was reported by 26.9% (184/684) of participants. Venous thromboembolisms were reported by 13.7% (96/701) of respondents.In patients with microscopic polyangiitis, the most common self-reported manifestations were renal in 82.8% (135/163), joint pain in 68.8% (106/154), peripheral nerve in 64.6% (95/147), nasal or sinus in 61.0% (89/146), rash in 59.6% (93/156), and pulmonary in 58% (90/154) of respondents. Pulmonary\u2013renal syndrome was reported by 29% (47/161). Venous thromboembolism was reported in 13.6% (21/154) of respondents. Patients also reported isolated renal manifestations without other organ manifestations , although constitutional symptoms such as myalgia , fever , and weight loss were reported.Confirmation of diagnosis by a physician was reported by 97.5% (742/761) of respondents with granulomatosis with polyangiitis. Patients with granulomatosis with polyangiitis underwent antineutrophil cytoplasmic antibody testing , laboratory testing , biopsy , and imaging for diagnosis; symptom-based diagnosis was also reported . Out of 730 respondents, 562 (77.0%) reported having a biopsy showing vasculitis at some point, of which the biopsy sites included kidney , lung , nasal or sinus , skin , nerve , artery , and other sites .Confirmation of diagnosis by a physician was reported by 98.8% (162/164) of respondents with microscopic polyangiitis. Patients with microscopic polyangiitis underwent antineutrophil cytoplasmic antibody testing , laboratory testing , biopsy , and imaging for diagnosis; symptom-based diagnosis was also reported . Of 160 respondents, 131 (81.9%) reported having a biopsy showing vasculitis at some point, of which the biopsy sites included kidney , lung , skin , nerve , nasal or sinus , artery , and other sites . Additional diagnostic testing information can be found in For respondents with granulomatosis, the most commonly used medications included glucocorticoids , cyclophosphamide , sulfamethoxazole and trimethoprim , rituximab , methotrexate , azathioprine , mycophenolate , and intravenous immunoglobulin ; 8.4% (64/762) reported receiving plasma exchange at some point. For respondents with microscopic granulomatosis, the most commonly used medications included glucocorticoids , rituximab , cyclophosphamide , azathioprine in , sulfamethoxazole and trimethoprim , mycophenolate , methotrexate , and intravenous immunoglobulin ; 9.9% (16/161) reported receiving plasma exchange at some point. Additional data on the medications used by patients with granulomatosis with polyangiitis and by patients with microscopic polyangiitis to treat their vasculitis can be found in 746=\u20132.46, P=.01) and diagnosis . Patients with granulomatosis with polyangiitis reported more sinonasal disease , hearing loss , tracheal involvement , pulmonary involvement , eye involvement , joint involvement and fevers than patients with microscopic polyangiitis; whereas, those with microscopic polyangiitis reported more renal involvement and were more likely to have undergone a renal transplant than patients with granulomatosis with polyangiitis , no difference in the percentage of patients reporting a positive antineutrophil cytoplasmic antibody test , and no difference in the percentage of patients reporting a diagnosis based on biopsy . There were more diagnoses from lung and nasal or sinus biopsies in participants with granulomatosis with polyangiitis than those in participants with microscopic polyangiitis. Conversely, there were more diagnoses from kidney biopsy in participants with microscopic polyangiitis than those in participants with granulomatosis with polyangiitis. A biopsy was more likely to have been performed in participants with microscopic polyangiitis than in those with granulomatosis with polyangiitis . Oral cyclophosphamide , methotrexate , and sulfamethoxazole and trimethoprim were more commonly used by patients with granulomatosis with polyangiitis than by those with microscopic polyangiitis closely reflected what was emphasized by the 1990 American College of Rheumatology classification criteria for granulomatosis with polyangiitis and the Chapel Hill Consensus Conference definition of microscopic polyangiitis. Only 1% of participants were not sure of the means of their diagnosis, reflecting good insight and recall of participants regarding the basis for their original diagnosis.There were also important differences between this cohort and center-based cohorts. First, there was a higher than expected prevalence of skin (57.4% and 59.6%) and peripheral nerve involvement (62.8% and 64.6%). This could reflect the nonspecificity of the queries where patients were asked to attribute manifestations to vasculitis. Patients may have had difficulty adjudicating whether their symptoms were caused by vasculitis or as a result of complications of therapy.z=10.42, P<.001) prevalence of these manifestations in granulomatosis with polyangiitis as expected, but there was also a higher than expected prevalence in microscopic polyangiitis with nasal-sinus manifestations being reported in 54.3% of patients. This may represent the nonspecificity of queries which included asking patients to attribute manifestations to vasculitis. Alternatively, it may in part also reflect misclassification in the medical community in which patients who test positive for myeloperoxidase antineutrophil cytoplasmic antibodies are classified as having microscopic polyangiitis; and only patients who test positive for proteinase 3 antineutrophil cytoplasmic antibodies are classified as having granulomatosis with polyangiitis.Ear, nose, and throat manifestations are a hallmark manifestation for granulomatosis with polyangiitis distinguishing it from microscopic polyangiitis. In a study comparinz=\u20135.18, P<.001) to have had renal involvement than patients with granulomatosis with polyangiitis. In the microscopic polyangiitis group, 8.5% patients had isolated renal manifestations . Overall, the proportion of renal involvement was similar to that reported in the literature [As expected, patients with microscopic polyangiitis were significantly more likely , which makes clinical research for these disorders difficult and requires the use of multiple centers which can be financially and logistically challenging. Patient registries offer an alternative to the centers of excellence approach to conducting clinical research. The data reported herein for an internet-based cohort demonstrated the feasibility of such registries across broad geographic regions and the high level of comparability between an internet-based and traditional academic center-based participant populations. These data provide investigators and patients with confidence that internet-based patient-reported data are reliable and can be used to conduct novel, cost-efficient medical research. Such internet-based registries offer an advantage in capturing participant data from those who would not otherwise be able to participate in studies."} +{"text": "To estimate the proportion of patients hospitalized with COVID-19 who undergo dialysis, tracheostomy, and extracorporeal membrane oxygenation (ECMO).A network cohort study.Seven databases from the United States containing routinely-collected patient data: HealthVerity, Premier, IQVIA Hospital CDM, IQVIA Open Claims, Optum EHR, Optum SES, and VA-OMOP.Patients hospitalized with a clinical diagnosis or a positive test result for COVID-19.Dialysis, tracheostomy, and ECMO.842,928 patients hospitalized with COVID-19 were included . Across the six databases, 35,192 (4.17% [95% CI: 4.13% to 4.22%]) patients received dialysis, 6,950 (0.82% [0.81% to 0.84%]) had a tracheostomy, and 1,568 (0.19% [95% CI: 0.18% to 0.20%]) patients underwent ECMO over the 30 days following hospitalization. Use of ECMO was more common among patients who were younger, male, and with fewer comorbidities. Tracheostomy was broadly used for a similar proportion of patients regardless of age, sex, or comorbidity. While dialysis was generally used for a similar proportion among younger and older patients, it was more frequent among male patients and among those with chronic kidney disease.Use of dialysis among those hospitalized with COVID-19 is high at around 4%. Although less than one percent of patients undergo tracheostomy and ECMO, the absolute numbers of patients who have undergone these interventions is substantial. For those patients who do undergo them, the use of these interventions can be taken to indicate severe disease and, for survivors, will likely be associated with long-term morbidity.7Treatment of patients hospitalized with coronavirus disease 2019 (COVID-19) may involve a range of medical interventions. Three distinct invasive interventions that can be readily identified in routinely collected health data and have been used in the treatment of severe COVID-19 are extracorporeal membrane oxygenation (ECMO), tracheostomy, and dialysis. For those patients with refractory hypoxemia, ECMO provides an advanced organ support alternative.Evidence on the extent of the use of invasive interventions among individuals hospitalized with COVID-19 can help improve our understanding of patient outcomes, inform healthcare resource planning, and provide an indication of some of the long-term consequences of the disease. Our objective in this study was therefore to describe the use of ECMO, tracheostomy, and dialysis among patients hospitalized with COVID-19.\u00ae de-identified COVID-19 Electronic Health Record dataset (Optum EHR) Dataset represents Optum\u2019s EHR data, while Optum\u00ae De-Identified Clinformatics\u00ae Data Mart Database \u2013 Socio-Economic Status Database (Optum SES) is an adjudicated administrative health claims database. The Department of Veterans Affairs OMOP (VA-OMOP) database reflects the national Department of Veterans Affairs health care system. This study is part of the ongoing Observational Health Data Sciences and Informatics (OHDSI) Characterizing Health Associated Risks, and Your Baseline Disease In SARS-COV-2 (CHARYBDIS) project, with the findings presented here based on data submitted as of 1st October 2020.Seven large databases containing routinely-collected health care data from the United States (US) provided the basis for the analysis, with each mapped to the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM). The HealthVerity database contains information on individuals with a test for COVID-19 with linkage to medical claims and pharmacy data. The Premier Healthcare Database (Premier) includes clinical coding, hospital cost, and patient billing data. The IQVIA Hospital charge data masters (CDM) includes data from resource management software within short-term, acute-care and non-federal hospitals, while IQVIA Open Claims captures open, pre-adjudicated medical claims. Optum8 COVID-19 hospitalizations ran up to March 2020 in OPTUM SES, June 2020 in HEALTHVERITY and VA-OMOP, July 2020 in IQVIA Hospital CDM, September in Premier, and October 2020 in IQVIA Open Claims and OPTUM EHR. The characteristics of study participants up to and including each individuals\u2019 date of hospitalization (index date) were extracted, including age, sex and comorbidities .Patients hospitalized with COVID-19 were identified in the same way as in a previous study using the OMOP CDM.Instances of ECMO, tracheostomy, and dialysis were identified between the index date and up to 30 days following the date. Instances of dialysis were also identified in the interval from 30 days to 1 day prior to index date. The proportion of patients who underwent the interventions was calculated for each database, and stratified by age , sex, and comorbidities of interest.https://github.com/ohdsi-studies/Covid19CharacterizationCharybdis/blob/master/documents/CharybdisPhenotypeLibrary.csv.The entire list of definitions used to identify patients with a COVID-19 hospitalization, their comorbidities, and interventions of interest can be explored at A total of 842,928 patients hospitalized with COVID-19 were included. Their baseline characteristics are described in Across the seven databases, 1,568 (0.19% [95% CI: 0.18% to 0.20%)] patients underwent ECMO. The proportion of patients who underwent ECMO ranged from 0.10% (0.06% to 0.15%) in HealthVerity to as high as 0.26% (0.20% to 0.31%) in OPTUM EHR. ECMO was more often seen among patients under 65 and males, In total, 6950 (0.82% [0.81% to 0.84%]) had a tracheostomy, with this proportion ranging from 0.28% (0.12% to 0.43%) in OPTUM SES to 1.05% (1.00% to 1.10%) in Premier. Use of tracheostomy was broadly similar by age and sex, A total of 35,192 (4.17% [4.13% to 4.22%]) patients received dialysis over the 30 days following hospitalization across the six databases, ranging from 2.61% (2.13% to 3.08%) in OPTUM SES to 6.93% (6.80% to 7.06%) in Premier. In comparison, in the 30 days prior to hospitalization, 0.6% of patients in VA-OMOP, 0.5% in OPTUM EHR, and 1.5% in IQVIA Open Claims were seen to have undergone dialysis. Use of dialysis was similar by age but was more common among men, 7 While continued follow-up is required to observe the long-term outcomes of the patients hospitalized with COVID-19 and underwent such interventions, it can be expected that those individuals that survived their hospitalization will face long-term morbidity and require ongoing care.Prior to COVID-19, ECMO, tracheostomy, and dialysis for acute renal failure have each been associated with poor long-term health outcomes.9 Higher use has though been seen for the Mount Sinai hospital system in New York City, where 9% of 3,993 hospitalized patients underwent dialysis,10 and among the first 1,000 patients hospitalized in the NewYork-Presbyterian/Columbia University Irving Medical Center, where 14% received dialysis.11 These higher rates might reflect differences in patient populations, if those admitted in these centers had particularly severe disease, or differences in treatment protocols. Given their rare occurrence, relatively few studies have reported on the use of tracheostomy and ECMO among COVID-19 patients. One of the aforementioned studies showed the use of ECMO to be 0.6%,11 which is slightly higher than seen in this study, which likely reflects both the setting and the severity of the patients seen at this center.Around 4% of patients hospitalized with COVID-19 identified in this study were seen to have undergone dialysis between the day of their admission and 30 days later. This is broadly in line with the findings of a multi-center study across 12 hospitals in New York City, where around 4% of 5,700 patients hospitalized with COVID-19 received kidney replacement therapy.In this study we have focused on three invasive interventions which could be readily identified in each of the databases. The consistency of our results across databases is reassuring. However, it is possible that use of interventions may be underestimated if not all interventions used are unambiguously reported. This, for example, may be the concern for dialysis which when performed in intensive care may not have been recorded with a specific code, but rather billed as part of overall intensive care stay. In addition, among the databases with limited prior observation time, comorbidities can also be expected to be underreported, as can be seen with obesity in particular in HEALTHVERITY and Premier. Further interventions are of interest but were beyond the scope of this study. In particular, while we also assessed the feasibility of summarizing the use of mechanical ventilation, this was seen to have heterogeneous reporting across databases.The findings from this study underline the severity of disease among hospitalized individuals with COVID-19. The long-term consequences for individuals who underwent the interventions and were discharged alive are likely to be substantial, both in terms of morbidity for the patients and economic burden for both patients and the health system, with individuals likely to have long-term health care needs."} +{"text": "Hearing and vision impairment have been independently linked to accelerated cognitive decline in older adults, however there is limited evidence on the effect of dual sensory impairment (DSI) (both hearing and vision impairment) on cognition. Additionally, the impact of social isolation and loneliness, both correlates of DSI and independent risk factors for cognitive decline, on the DSI-cognition relationship has yet to be studied. Using data from the National Social Life, Health, and Aging Project , multivariable linear regression models were used to describe the cross-sectional relationship between self-reported functional sensory impairment and cognitive function, measured by the survey adapted Montreal Cognitive Assessment. We also included an interaction term in the model to investigate whether cognition is worse among older adults with sensory impairment who also are socially isolated or lonely. Participants in this sample are between 62-91 years with 15% reporting hearing impairment, 11% reporting vision impairment, and 7% reporting DSI. DSI was associated with significantly lower global cognitive function compared to no sensory impairment (-0.31 standard deviations (SD), 95% CI:-0.44 to-0.18), hearing impairment alone , and vision impairment alone . Furthermore, cognitive function was significantly worse among older adults with both DSI and smaller social networks (p-interaction <0.05). No differences in the DSI-cognition relationship were observed by level of loneliness. These findings add to the limited research on the relationship between DSI, social isolation and loneliness, and cognition."} +{"text": "Progress towards the World Health Organization\u2019s End TB Strategy is monitored by assessing tuberculosis (TB) incidence, often derived from TB notification, assuming complete case detection and reporting. This assumption is unlikely to hold in many settings, including European Union (EU) countries.We aimed to assess observed and estimated completeness of TB notification through inventory studies and capture\u2013recapture (CRC) methodology in six EU countries: Croatia, Denmark, Finland, the Netherlands, Portugal Slovenia.We performed record linkage, case ascertainment and CRC analyses of data collected retrospectively from at least three national TB-related registers in each country between 2014 and 2016.Observed completeness of TB notification by inventory studies was 73.9% in Croatia, 98.7% in Denmark, 83.6% in Finland, 81.6% in the Netherlands, 85.8% in Portugal and 100% in Slovenia. Subsequent CRC analysis estimated completeness of TB notification to be 98.4% in Denmark, 76.5% in Finland and 77.0% in Portugal. In Croatia, CRC analyses produced implausible results while in the Netherlands and Slovenia, it was methodologically considered not meaningful.Inventory studies and CRC methodology suggest a TB notification completeness between 73.9% and 100% in the six EU countries. Mandatory reporting by clinicians and laboratories, and cross-checking of registers, strongly contributes to accurate notification rates, but hospital episode registers likely contain a considerable proportion of false-positive TB records and are thus less useful. Further strengthening routine surveillance to count TB cases, i.e. incidence, accurately by employing record-linkage of high-quality TB registers should make CRC studies obsolete in EU countries. In 2014, the World Health Organization (WHO) published the Action Framework towards TB elimination in low-incidence countries, and in 2016, the WHO Regional Office for Europe (WHO/Europe) published the Roadmap to implement the tuberculosis action plan for the WHO European Region 2016-2020: Towards ending TB and multidrug-resistant tuberculosis. They outline blueprints to carry out the WHO\u2019s global End TB Strategy in Europe and to reach the sustainable development goal (SDG) target for tuberculosis (TB) . Key strInventory studies (IS) are a widely accepted methodology to study the level of under-reporting of TB cases . To deteAt the time of the study and writing this article, the United Kingdom (UK) was still part of the EU and only two EU countries, the Netherlands and the UK, had assessed the level of TB under-reporting using IS/CRC studies on a national basis ,12. In 2The objective of this study was to assess observed and estimated TB notification completeness in EU countries, selected after an eligibility and feasibility appraisal, and determine whether data collected at national level reflect the real TB situation in these countries.This study used inventory studies and capture-recapture analyses as per the methodology outlined by Van Hest and the WHO ,8.To select the six most appropriate and representative EU and European Economic Area (EEA) countries for the study, we followed a predefined selection procedure that was developed by the consortium commissioned to perform this work and agreed upon with ECDC during the project kick-off meeting in June 2016. First, eligibility and feasibility for IS and more specifically CRC studies was assessed by an 11-item tick-box questionnaire that was distributed to the TB operational contact points for epidemiology at ECDC and WHO/Europe TB surveillance network meeting in Bratislava in June 2016 . Non-resTo obtain detailed information regarding TB-related registers, data availability, data access and data quality, the 14 countries identified in this rapid eligibility and feasibility assessment were contacted by 1 hr telephone or Skype calls, with a follow-up call or email for some countries. Subsequently, a simple scoring system was applied to ensure a consistent and systematic selection of countries . A matriMycobacterium tuberculosis complex (gold standard), (ii) bacteriologically confirmed by a positive auramine or Ziehl-Neelsen stained respiratory or non-respiratory sample and/or a positive PCR for M. tuberculosis complex, or (iii) based on clinical, radiological, histopathological or epidemiological findings with an intention to treat. Hospital episode records were included when coded with International Code of Disease (ICD)-9 code 010\u2013018 or ICD-10 code A15-A19 [This study included all cases recorded as active pulmonary or extrapulmonary TB, new as well as previously treated or diagnosed cases, in the various registers of the six EU countries in the selected study year. Double entries in each of the registers, cases caused by non-TB mycobacteria (NTM) or cases later diagnosed as not having TB were excluded. TB diagnosis was either: (i) bacteriologically confirmed by a positive culture for A15-A19 ,14.TB cases with a date of notification, mycobacteriological confirmation, first day of hospital admission or death between 1 January and 31 December of the same study year were included. Study years varied in the countries between 2014 and 2016 . To alloThe national electronic databases with case-based records of registered TB cases used in the IS in the six EU countries are listed in Two different approaches were used to link records of the same individual in different databases . DetermiObserved TB notification completeness was calculated as the proportion of TB cases notified among the total number of TB cases observed after record linkage through the retrospective ISs. Estimated TB notification completeness were obtained through CRC analysis. The preferred CRC method entails log-linear modelling of at least three possibly incomplete, partially overlapping and preferably, but not necessarily, independent registers. Three-source log-linear modelling is less compromised by violation of the underlying modelling assumptions ,8,15-19.National medical-ethical authority permission was obtained , the Netherlands (Data Protection Committee of the Netherlands Tuberculosis Register Number: 04-2017) and Portugal Processo no: 11543/2017)) or not required .In Croatia, record linkage of three national registers (notifications (489 cases), reference laboratory (334 cases), and hospital episodes (476 cases)) resulted in a total of 662 registered TB cases, translating into an observed completeness of notification of 73.9% (489/662). Of the 173 TB cases not notified, 140 (81%) were only known to the hospital episode register . In CRC In Denmark, record linkage of three national registers (notifications (379 cases), reference laboratory (283 cases), and hospital episodes (188 cases)) resulted in a total of 384 registered TB cases, translating into an observed completeness of notification of 98.7% (379/384). Of the five TB cases not notified, two were only known to the hospital episode register, two to the laboratory register only and one to both registers. CRC analysis selected a model with one interaction , estimating one unobserved TB case, and resulting in an estimated completeness of notification of 98.4% (379/385) (95% CI: 97.9\u201398.7).In Finland, complete overlap between the reference laboratory and the notification registers was expected due to automatic registration of the laboratory results. Record linkage of the notification register (260 cases) with the hospital episode (402 cases) and primary care episode (246 cases) registers resulted in a total of 569 registered TB cases, translating into an observed completeness of notification of 45.7% (260/569). After record linkage with a fourth register, the mortality register (20 cases), 573 TB cases were observed, translating into an observed completeness of notification of 45.4% (260/573). A large part of the TB cases not notified (573\u2013260\u2009=\u2009313) appeared either only in the hospital register (52% (163/313) or in the primary care register (40% (125/313). Unpublished findings from a Finnish pilot study, brought to our attention during implementation of our research, in which hospital records of TB patients with ICD-10 codes A15-A19 were reviewed in detail, found that only 10% were true, notifiable, TB cases . Since it was not in the scope of our study to review clinical records, we assumed 90% of the hospital or primary care only cases to be false-positive. After adjusting for these suspected false-positive TB cases, the observed completeness of notification was 83.6% (260/311). CRC analysis on the unadjusted data preferred the saturated model, which estimated an implausibly high number of unobserved TB cases in Finland in 2014, more than 15 times the number of observed TB cases. Several other models were considered, as described in detail elsewhere (country report for Finland available upon request from ECDC). The four-source CRC was the preferred analysis because it provided a very similar estimate to the three-source CRC which included the mortality register, and it corroborated the assumption that many of the Hilmo-only or Avohilmo-only cases are false positive TB cases. The preferred four-source CRC analysis on the data adjusted for the 90% suspected false-positive TB cases estimated 29 unknown TB cases, translating into an estimated completeness of notification of 76.5% (95% CI: 63.7\u201381.3%) (260 notified cases/340 estimated true TB cases).In the Netherlands, record linkage of three national registers (notifications (814 cases), reference laboratory (526 cases), and hospital episodes (489 cases)) resulted in a total of 998 registered TB cases in 2014, translating into an observed completeness of notification of 81.6% (814/998). All culture-confirmed laboratory TB cases were notified (observed completeness of notification of 100%). Because of this complete overlap two linked registers remained, with all TB cases not notified and latent TB infections (4 cases)) only known to the hospital episode register, indicating that 49.0% (489/998) of the TB cases in the Netherlands in 2014 were hospitalised. Scrutinising the individual patient records of the cases only available in the hospital episode registry to assess whether they had signs, symptoms or diagnostic test results suggestive for TB, or whether treatment was initiated and completed, was not possible for confidentiality, logistical and financial reasons. A CRC analysis was methodologically not considered meaningful due to the complete overlap of the notification this would be a two-source CRC (see Discussion) [In Portugal, three TB registers were identified in 2015: the national TB programme register , the public health register and the hospital episode register . Case ascertainment was 3,561 ; 2,914 ; 2,786 ; and 2,328 TB cases ; with an observed completeness of notification of 60.2% , 64.6% , 80.0% , and 85.8% , respectively. For all datasets, a parsimonious CRC model with two (positive) pairwise interactions was selected. The preferred model estimated completeness of notification at 77.0% (95% CI: 74.3%\u201379.1%), after probabilistic record linkage and excluding the \u2018possible\u2019 TB cases ).M. tuberculosis starting treatment abroad and assumed notified there, 118 TB cases were registered in Slovenia in 2016, translating into a completeness of notification of 100%. Due to the almost complete overlap of the registers used, CRC analysis was methodologically considered not meaningful.In Slovenia, a strong positive interaction between the notification (118 cases), reference laboratory (111 cases) and hospital episode (115 TB cases) registers was expected, as all these services are mainly concentrated in one university hospital. Record linkage of these registers with the mortality (19 cases) register resulted in a case ascertainment of 119 TB cases. Excluding one person with a positive culture of Observed completeness of TB notification was calculated to be 73.9% in Croatia, 98.7% in Denmark, 83.6% in Finland, 81.6% in the Netherlands, 85.8% in Portugal, and 100% in Slovenia. Subsequent CRC analyses estimated completeness of TB notification to be 98.4% in Denmark, 76.5% in Finland and 77.0% in Portugal. In the other three countries, CRC analysis gave implausibly high estimates of unobserved TB cases (Croatia) or was not performed because it was methodologically not considered meaningful . In the Netherlands and Slovenia only two databases could be used and using two-source capture\u2013recapture models for epidemiological data often violates the underlying capture\u2013recapture assumptions, resulting in biased estimates and is thus not preferred . AccordiIn monitoring progress in TB control, the ultimate aim is to count TB cases (incidence) accurately through routine surveillance. When routine surveillance is not robust, alternative methods can be used to assess completeness of notification, as described elsewhere . One sucSurveillance by notification may result in inaccurate incidence rates because of under-ascertainment of the true number of cases or over-ascertainment due to false-positive cases . StandarPrevious regional and national IS and CRC studies in EU countries often used the notification, reference laboratory and hospital episode registers, assuming absence of major interdependencies ,12,25,26The two previous national IS and CRC studies in EU countries suggested a considerable proportion of false-positive TB cases in hospital episode registers, possibly coding a differential diagnosis upon admission or a presumptive diagnosis upon discharge ,12. The Alternative registers that could be used in some EU countries are mortality registers, when not nested in other registers. Other registers include health insurance registers and prescription registers for anti-TB medication, most specifically pyrazinamide, since other first-line drugs are also prescribed for different conditions, such as latent TB infection and treatment of NTM. Possible problems with these registers could be collection of only aggregate data, unsuitable for record linkage, or unavailability of data due to privacy regulations, such as the EU General Data Protection Regulation (GDPR) , which cIn some studies, the saturated CRC model, i.e. the model incorporating all pairwise interdependencies but also the highest order interdependency between all registers which cannot be controlled, was preferred based on the lowest AIC . The litGiven the intrinsically complex nature of TB epidemiology, variations in diagnoses , socioeconomic background and disease severity, the assumption of homogenous probabilities of observations is unlikely to hold. Log-linear models may partially incorporate population heterogeneity, especially if relevant covariate information explaining variation is available, but the problem is likely persistent to some extent and a limitation of CRC . The limAnother limitation of this study is that the six countries were selected after an eligibility and feasibility appraisal, with likely selection bias, limiting extrapolation of the results to other EU countries. The six countries selected were predominantly countries with a small population, a limited number of TB cases and a well-organised TB notification and control system.Our analysis suggests that only in Denmark and Slovenia the assumption that TB notification reflects TB incidence is likely to be true. In these countries, the estimated number of unobserved TB cases was minimal (Denmark) or expected to be minimal because of complete overlap of TB cases between registers (Slovenia). In the other countries, observations and estimates were more difficult to interpret.Mandatory reporting by both clinicians and laboratories, and cross-checking of registers, strongly contributes to accurate notification rates but hospital episode registers likely contain a considerable proportion of false-positive TB records and more scrutiny is needed. Further strengthening routine (computerised) infectious disease surveillance systems to count TB cases (incidence) accurately, by structurally employing electronic record linkage of high-quality TB registers, should make CRC studies obsolete in EU countries."} +{"text": "The mental health needs of older adults are largely unmet, a finding even more prevalent within culturally diverse older adult populations. Added to this is the high rate of social isolation. Research has indicated increased connection to mental health services when services are embedded within physical health care settings. For those attending community centers, 85% indicate that they are socially isolated, 68% indicate they are lonely, and 53% have a mental health need . The need for innovative programming is evident. When examining the needs of diverse older adults, it is increasingly important that new and innovative approaches address social isolation, loneliness, and mental health problems experienced by this cohort. Utilizing this knowledge an innovative model of embedding and integrating mental health services, provided by bilingual and bicultural clinicians, into congregate sites (older adult centers) was implemented. Those that participated were mainly female (72.1%), 68.5% English-speaking, 14.5% Spanish-speaking, 13.6% Chinese-speaking and 3.4% other. Spanish-speakers had more depression than English-speakers and both had more depression than Chinese-speakers. English and Spanish-speakers reported more social isolation and Chinese-speakers compared were more likely to participate in engagement. Chinese-speakers were less likely to be in clinical services with a positive screen compared to English-speakers. Overall, 75% engaged in treatment; 37.3% and 41% showed a 3-month improvement of depression and anxiety, respectively. This presentation focuses on the innovative components of this model, how to engage diverse older adults to utilize treatment, steps needed for replication, and policy implications around integrated mental health treatment."} +{"text": "Prevalence of dementia among American Indian/Alaska Natives (AI/AN) is higher than in white populations, and AI/AN communities experience dementia care service gaps. This study explored perspectives within AI/AN communities regarding dementia, the family caregiver role, and home and community-based service use. Using tenets of Community-Based Participatory Research, qualitative interviews and a brief survey were conducted with 22 members of the Oneida Nation of Wisconsin . Of the sample, 63.6% identified as a past or current family caregiver for a loved one with dementia. Awareness of services varied; 82% were aware of memory cafes, 75% knew of the caregiver support group, and 43% were familiar with dementia care specialist services. Thematic analysis revealed shared values of involving the family and community in dementia care, and offer guidance to support greater engagement in services. Implications for culturally-tailored service provision within AI/AN communities are discussed."} +{"text": "JAK1/2 inhibitor (JAKi) ruxolitinib as therapy for hyperinflammation. By JAK1 inhibition, ruxolitinib had demonstrated to exert a broad anti-inflammatory activity against the myeloproliferative neoplasms (MPNs) cytokine storm and has been used in the setting of COVID-19 infection with positive results [We read with interest the perspective by von Lilinfeld-Toal et al. that provides recommendations for the management of cancer patients during the coronavirus disease 2019 (COVID-19) pandemic, caused by the spreading of the coronavirus SARS-CoV-2 [ results .Philadelphia-negative MPNs include polycythemia vera (PV), essential thrombocythemia (ET), and myelofibrosis (MF) and are To understand how the behavior of Italian hematologists towards MPN has changed during the COVID-19 pandemic, and how ruxolitinib was managed, the GIMEMA MPN Working Party e\u2010mailed to 239 hematologists, belonging to 102 Italian hematology institutions, an anonymous online questionnaire of 28 muJAK2, MPL, or CALR genotyping according to standard indications. During the pandemic, marrow biopsy was performed by 73.9% of respondents normally, by 10.9% only in the suspect of MF, and never by 14.1%.For MPN diagnosis, 93.5% of physicians continued to routinely assess In PV patients, 65.2% of respondents prescribed phlebotomies with a hematocrit (HCT) target at \u226445%, while 32.6% accepted the target HCT to >48%, and 2.2% did not suggest phlebotomies at all during the pandemic.Hydroxyurea (HU) was started in all ET and PV patients at high thrombotic risk by 82.6% of hematologists; however, 13% started HU only if cardiovascular risk factors were concomitant to high-risk features. Conversely, >50% of the hematologists declared to postpone interferon (IFN) after the resolution of the pandemic Fig.\u00a0. InsteadThe start of ruxolitinib was postponed in 17.4% and 28.6% of MF and PV patients, respectively. Fig.\u00a0. Before In MF patients with an allogeneic transplant already scheduled, only 8.8% of hematologists proceeded without delay, while 15.4% postponed the transplant to pandemic resolution.Regarding the use of phone contacts in place of in-person hematological visits, 12% of the hematologists believed that MF patients always require a full medical visit; this percentage decreases to 1.1% and to 0% when PV and ET were considered, respectively. Accordingly, 19.8%, 38%, and 50% of respondents converted >80% medical visits into phone follow-up in MF, PV, and ET patients, respectively. After the resolution of the pandemic, 67.3% of hematologists will implement the use of telemedicine .Notably, we documented no substantial difference in practice in colleagues with more (>10) years of experience, or who followed COVID-19-positive patients, or who work in the northern Italian regions most affected by the pandemic. This remarkable uniformity is probably owed to homogeneous recommendations from the central government and from Italian Societies of Hematology and Transplantation.Diagnostic procedures remained consistent to standard criteria, with most patients receiving molecular and histology evaluations during the pandemic, as already described in Italy , 5, 7, 8Concerning ruxolitinib, the ASH panel of MPN experts suggests not starting ruxolitinib during the pandemic, but, maintaining the drug if beneficial, with a slow tapering in case of discontinuation . We convThe evaluation of each allogeneic transplant case individually well reflects the indications of the European Society for Blood and Marrow Transplantation to postpone transplant in low-risk patients, assessing on individual basis the risk-benefit ratio of transplant deferral .Finally, telemedicine was perceived as an appropriate, though exceptional, follow-up strategy. While its future implementation in routine practice may possibly offer some benefits, some fundamental concerns need to be addressed regarding the challenges for proper patient management, mutual patient\u2013doctor satisfaction, and legal protection.Despite significant reduction of in-person visits, the clinical approach to MPN was only mildly modified during the pandemic. However, we acknowledge that clinical choices, particularly regarding the use of JAKi, may be based on multiple factors. Also, many clinicians were not directly involved in the treatment of COVID-19 MPN patients. Future epidemiological studies may clarify whether this is an underestimation or the result of appropriate patient management.Supplemental TableSupplemental Figure"} +{"text": "In 2010, the World Health Assembly (WHA) set the following three milestones for measles control to be achieved by 2015: 1) increase routine coverage with the first dose of measles-containing vaccine (MCV1) among children aged 1 year to \u226590% at the national level and to \u226580% in every district, 2) reduce global annual measles incidence to <5 cases per 1 million population, and 3) reduce global measles mortality by 95% from the 2000 estimateWHO and the United Nations Children\u2019s Fund (UNICEF) determine vaccination coverage using data from administrative records and vaccination coverage surveys, to estimate MCV1 and second dose measles-containing vaccine (MCV2) coverage through routine immunization services.Among 194 WHO member states, 122 (63% of member states) achieved \u226590% MCV1 coverage in 2019, a 42% increase from 86 (45%) countries in 2000, but a 4% decrease from a peak of 127 (65%) countries in 2012. In 2019, 42 (22%) countries achieved MCV1 coverage \u226590% nationally and \u226580% in all districtsEstimated global MCV2 coverage nearly quadrupled from 18% in 2000 to 71% in 2019, largely because of an 86% increase in the number of countries providing MCV2, from 95 (50%) countries in 2000 to 177 (91%) in 2019 . Six couApproximately 204 million persons received MCV during supplementary immunization activities (SIAs)In 2019, all 194 countries conducted measles surveillance, and 193Countries report the number of incident measles casesThe number of measles cases increased 556% from 132,490 in 2016 to 869,770 in 2019, the most reported cases since 1996. Since 2016, the number of reported measles cases increased 1,606% in WHO\u2019s African Region (AFR), 19,739% in the Region of the Americas (AMR), 194% in the Eastern Mediterranean Region (EMR), 2,282% in the European Region (EUR), 6% in the South-East Asia Region (SEAR), and 36% in the Western Pacific Region (WPR). In 2019, nine (5%) of 184 reporting countries experienced large outbreaks, and in each of these countries, reported measles incidence exceeded 500 per 1 million population; these nine countries accounted for 631,847 (73%) of all reported cases worldwide during 2019.Genotypes of viruses isolated from persons with measles were reported by 88 (62%) of 141 countries reporting at least one measles case in 2019. From 2005 to 2019, 20 of 24 recognized measles genotypes were eliminated by immunization activities. The number of genotypes detected decreased from 11 during 2005\u20132008, to eight during 2009\u20132014, six in 2016, five in 2017, and four during 2018\u20132019 individual countries had been verified by independent regional commissions as having achieved or maintained measles elimination. The two countries verified in 2019 to have achieved elimination were Iran and Sri Lanka. No AFR country has yet been verified as having eliminated measles. The AMR had achieved verification of measles elimination in 2016; however, endemic measles transmission was reestablished in Venezuela in 2018 and in Brazil in 2019.Despite substantial decreasing global measles incidence and measles-associated mortality during 2000\u20132016, the global measles resurgence that commenced during 2017\u20132018 continued in 2019 and marked a significant step backward in progress toward global measles elimination. Compared with the historic low in reported cases in 2016, reported measles cases increased 556% in 2019, with increases in numbers of reported cases and incidence in all WHO regions. Estimated global measles mortality increased nearly 50% since 2016. In all WHO regions, the fundamental cause of the resurgence was a failure to vaccinate, both in recent and past years, causing immunity gaps in both younger and some older age groups. Lessons can be learned from outbreaks in various countries, as well as from notable successes in countries such as China, Colombia, and India regions have a measles elimination goal.During 2000\u20132016, annual reported measles incidence decreased globally; however, measles incidence increased in all regions during 2017\u20132019. Since 2000, estimated measles deaths decreased 62% and measles vaccination has prevented an estimated 25.5 million deaths worldwide. No WHO region has achieved and maintained measles elimination.To achieve regional measles elimination goals, additional strategies are needed to help countries strengthen routine immunization systems, identify and close immunity gaps, and improve case-based surveillance."} +{"text": "Objective. The objective of this study was to assess newborn care practice and associated factors among mothers with babies of one-month-old in Hossana town, Southern Nations, Nationalities, and Peoples' Region, Ethiopia, 2018. Methods. A community-based cross-sectional study was conducted among randomly selected 422 mothers with babies of one-month-old in Hossana town, southwest Ethiopia. The data were entered to EpiData 3.1 and exported to Statistical Package for the Social Sciences (SPSS) version 22. Bivariate and multivariate analyses were applied, and frequencies and odds ratios were calculated to determine the prevalence and associated factors, respectively. Results. In this study, 31% of participants had good newborn care practice based on three composite variables such as 84% who have done early breastfeeding initiation, 32.9% who have done safe cord care, and 30.6% who have done thermal care. Educational status of the mother's, primary , secondary , and college and above ; mothers who practiced handwashing (hygiene) before touching a newborn ; and mothers who had good knowledge on newborn care practice were significantly associated with newborn care practice. Conclusion and Recommendation. The present study indicated that the level of comprehensive newborn care practice was unsatisfactory; all responsible bodies were giving attention and intervene on the predictors to improve newborn care practice and provide health education regarding newborn care practice. Education level, health education (counseling) on hygiene, and knowledge of mother on newborn care practice were independent predictors of newborn care practice.Newborn care refers to the care that is provided to the baby from birth to one-month-old by a caregiver or by the mothers including thermal care, hygienic care, cord care, eye care, breastfeeding, immunization, and identification of newborn danger signs. According to Ethiopian Demographic and Health Survey (EDHS) 2016, the neonatal mortality rate was 29 deaths per 1000 live births, and the postneonatal mortality rate was 19 deaths per 1000 live births with neonates contributing 48 deaths per 1000 of the infant mortality. Neonatal mortality accounts for approximately two-thirds of all infant mortality worldwide. Essential newborn care is the basic care required for every baby and comprises thermal care , infection prevention , feeding support (early and exclusive breastfeeding), and postnatal care, including monitoring of newborns for danger signs of serious infections and identifying babies requiring additional care . Deaths There is a global underfive mortality rate of 42.5 per 1000 live births; of those deaths, 45% were newborns, with a neonatal mortality rate of 19 per 1000 live births .In Ethiopia, neonatal morbidity and mortality rates were among the highest in the world and neonEven only 26% of births occur in a health facility, there is an increase in neonatal death . To reduThe objective of this study was to assess newborn care practice and associated factors among mothers of one-month-old infants in Hossana town, Hadiya zone, southern Ethiopia, 2018.To assess newborn care practice among mothers with babies aged one monthTo identify factors associated with newborn care practice among mothers with babies aged one monthHossana town is the capital city of Hadiya zone, Southern Nations, Nationalities, and Peoples' Region (SNNPR), which was located 194\u2009km from Hawassa, the capital city of the region, and 230\u2009km from Addis Ababa, the capital city of the country.Hossana town is a purely woinedega agroeconomic zone, situated at an altitude of 1800-2950 meters above sea level, and has an average temperature ranging from 10 to 24 degree centigrade. The annual rainfall is 1250\u2009mm per year.Based on the 2007 Ethiopian national population and housing census, the population of the town was 78,432: male 38,800 and female 39,632; the number of childbearing age women (15-49 years) was 18,275 (Hossana town administrative office report 2007).A community-based cross-sectional study was conducted from January 20 to February 19, 2018, in Hossana town, southwest Ethiopia.A community-based cross-sectional study design was conducted.The source population is all women in the reproductive age group, who had one-month age infants in Hossana town.Study populations were all sampled mothers who had one-month age infants during the data collection period in Hossana town.Mothers resident in the area for six or more months before this study was conducted were included in the study.Mothers who were unable to feed breast milk and too sick or critically ill during the data collection period were excluded in the study.The sample size was determined by using a single population proportion formula:n is the minimum sample, p is the 52.1% prevalence level for early breastfeeding on four regions of Ethiopia \u2009=\u2009correct response and 0\u2009=\u2009incorrect response ; any mother who did not know the answer is considered to have an incorrect response.Good knowledge of mothers on newborn care: those mothers who respond correctly above 50% of knowledge-related questions.Poor knowledge of mothers on newborn care: those mothers who respond correctly less than or equal to 50% of knowledge-related questions.Newborn care practice: good newborn care practice: those mothers who mentioned three newborn care practices; poor newborn care practice: those who reported two or less newborn care practices.Kebele: it is the smallest administrative unit, similar to a ward, a neighborhood, or a localized and delimited group of people and a part of woreda (district).Data quality was assured by using a pretested data collection tool, and training was given for data collectors and supervisors before actual data collection. Supervisors were engaged in continuous supervision and monitoring during data collection. Completeness and consistency of data were checked by supervisors, data clerks, and investigators before and during data entry.p value < 0.05, at 95% confidence interval. Finally, the results were presented in the form of tables, figures, and charts as appropriate.Collected data was checked for its completeness and then coded and entered into EpiData version 3.1, and entered data was exported to SPSS version 20 for analysis. Binary and multivariate logistic regressions were employed. Frequencies and proportions were computed. A significant association was determined by odds ratios with A total of 422 mothers who had one-month infants were involved in the study, yielding a 100% response rate. The majority of respondents, 289 (68.5%), were between 25 and 34 years of age, 213 (50.5%) were housewives, 418 (99.1%) were married, 258 (61.1%) were protestant religion, 279 (66.1%) were Hadiya ethnicity, 378 (89.6%) had a formal education, and 46 (10.9%) had a high income .From the participants, 303 (71.8%) had a home visit in the last one month and had health educations; 369 (87.4%) had knowledge on handwashing with soap and clean water before handling their neonate, 347 (82.2%) on keeping neonate dry and wrapping after delivery, 402 (95.3%) on breastfeeding immediately after birth within an hour, 383 (90.8%) on danger sign, 373 (88.4%) on immunization, and 361 (85.5%) on how to care for low-birth-weight baby by HEW.The majority of participants, 351 (83.2%), had no history of neonatal death before this delivery, 411 (97.4%) had ANC follow-up when they were pregnant, and 405 (96.0%) had given birth at health facilities .From the total participants, 409 (96.9%) gave the first breast milk for their baby, 352 (85.4%) initiated breast milk within an hour after birth, 336 (79.6%) did not apply anything on the cord of the newborn baby, 214 (50.7%) took care of bleeding to keep the cord clean and safe, 144 (34.1%) kept the cord dry and clean to keep the cord clean and safe, and 64 (15.2%) took the newborn baby to a health facility in order to keep umbilical cord clean and safe.More than half of the respondents, 215 (50.9%), had given the first bath for newborn baby within the first 24 hours of delivery, and 293 (69.4%) placed the newborn baby to skin-to-skin contact always until the baby becomes stable .Among the 422 study participants, 406 (96.2%) had known about care for their newborn, 331 (78.4%) applied nothing to the cord immediately after cutting up to 7 days except ordered medication, 294 (69.7%) handled umbilical cord after cutting without dressing, 327 (77.5%) bathed her newborn baby after 24 hours after delivery, 372 (88.2%) breastfed their baby within 1 hour after delivery, 368 (87.2%) believed feeding breast milk as the first food for a newborn baby after delivery, and 367 (87.0%) had knowledge about newborn danger sign .From the total of 422 participants, the mentioned danger signs of a newborn baby are as follows: 84.8% were poor sucking, 77% were fast breathing, 64% had hypothermia, 64.7% had fever, 46% had drowsiness (unconscious), and 66.1% had cord bleeding and infection .In this study, the proportion of newborn care practices was 130 (30.8%) of the respondents in terms of the three composite practices, namely, 354 (83.9%) were early breastfeeding initiation, 139 (32.9%) were safe cord care, and 129 (30.6%) were thermal care (delay bathing) .In this study, education of the mothers, mothers who had practice handwashing, and knowledge of mothers on newborn care practice were significantly associated with newborn care practice.Hence, those who had primary, secondary, and college and above educational status had three times , three times , and four times more likely to practice newborn care than mothers who had no formal education, respectively, mothers who had practice handwashing were three times more likely to practice newborn care than mothers who had not practice handwashing , and mothers who had good knowledge on newborn care practice were sixteen times more likely to practice newborn care than those who had poor knowledge .In this study, one-third of the participants had good newborn care practice based on three composite variables such as early breastfeeding initiation 83.9%, safe cord care 32.9%, and thermal care 30.6%.Good newborn care practice was almost nearly similar to study done in Aksum Town, North Ethiopia 26.7%) , but thi% , but tBreastfeeding 83.9% which was higher than study done in Hoima District, western Uganda 31% dry cord care 60.5% [15], Mandura District, Northwest Ethiopia (48.1%) , tamale Safe cord care was 32.9% and similar to the study done in Hoima District, western Uganda (31%) , but lowThermal care was 30.6% in this study and nearly similar to the study done in Aksum Town, North Ethiopia (32.6%) , but lowKnowledge of the mother on newborn care practice had a significant association with newborn care practice and similar to the study in Hoima District, western Uganda, Gulomekada District, Eastern Tigray, and Mekelle City, North Ethiopia , 13, 15.Education of the mothers also has a significant association with newborn care practice and was similar to the study done in Mandura District, Northwest Ethiopia, and Mekelle City, North Ethiopia , 13.Mothers who had health education on hygiene (hand) had a significant association with newborn care practice in this study, but no study was similar to this result.In this study, almost one-third of the mothers had good newborn care practice and it was very low when compared with other studies done in the country. Mothers' educational status, mothers who had health education on hygiene, and knowledge of mothers on newborn care practice were independent predictors of newborn care practice.Hadiya Zone Health Bureau: to work hard on the promotion of health facility delivery system and to increase the level of newborn care practice and involve health extension workers to apply home-to-home visit program to convince all childbearing women on the positive outcome of health facility delivery service to have good newborn care practiceHealth care providers: to provide ongoing education and counseling to mothers to give birth at a health facility to have good newborn care practice during ANC follow-upHealth care planners: to provide health education during ANC and PNC regarding these predictorsFuture researcher: we suggest researchers to undertake repeatable studies in this area, and as this study lacks qualitative information that can underpin the quantitative study results, we recommend that the researcher have to do qualitative study design and other methodsBased on the findings of this study, we recommend the following:The cross-sectional nature of the study is impossible to establish a temporal relationship between newborn care practice and identified risk factors."} +{"text": "Obstructed labor is a preventable obstetric complication. However, it is an important cause of maternal mortality and morbidity and of adverse outcomes for newborns in resource-limited countries in which undernutrition is common resulting in a small pelvis in which there is no easy access to functioning health facilities with a capacity to carry out operative deliveries. Therefore, this systematic review and meta-analysis aimed to estimate the incidence, causes, and maternofetal outcomes of obstructed labor among mothers who gave birth in Ethiopia.for this review, we used the standard PRISMA checklist guideline. Different online databases were used for the review: PubMed, Google Scholar, EMBASE, Cochrane Library, HINARI, AFRO Library Databases, and African Online Journals. Based on the adapted PICO principles, different search terms were applied to achieve and access the essential articles. The search included all published and unpublished observational studies written only in the English language and conducted in Ethiopia. Microsoft Excel 16 was used for data entrance, and Stata version 11.0 was used for data analysis.2\u2009=\u200998.0%, p\u2009<\u20090.001). Out of these, 67.3% (95% CI: 33.32\u2013101.28) did not have antenatal care follow-up, 77.86% (95% CI: 63.07\u201392.66) were from the rural area, and 58.52% (95% CI: 35.73\u2013 82.31) were referred from health centers and visited hospitals after 12\u00a0h of labor. The major causes of obstructed labor were cephalo-pelvic disproportion 64.65% (95% CI: 57.15\u2013 72.14), and malpresentation and malposition in 27.24% (95% CI: 22.05\u201332.42) of the cases. The commonest complications were sepsis in 38.59% (95% CI: 25.49\u201351.68), stillbirth in 38.08% (95% CI: 29.55\u201346.61), postpartum hemorrhage in 33.54% (95% CI:12.06\u2013 55.02), uterine rupture in 29.84% (95% CI: 21.09\u201338.58), and maternal death in 17.27% (95% CI: 13.47\u201348.02) of mothers who gave birth in Ethiopia.I included sixteen (16) primary studies with twenty-eight thousand five hundred ninety-one mothers who gave birth in Ethiopia. The pooled incidence of obstructed labor in Ethiopia was 12.93% (95% CI: 10.44\u201315.42, IThis systematic review and meta-analysis showed that the incidence of obstructed labor was high in Ethiopia. Not having antenatal care follow-up, rural residency, and visiting hospitals after 12\u00a0h of labor increased the incidence of obstructed labor. The major causes of obstructed labor were cephalo-pelvic disproportion, and malpresentation and malpresentation. Additionally, the commonest complications were sepsis, stillbirth, postpartum hemorrhage, uterine rupture, and maternal death. Thus, promoting antenatal care service utilization, a good referral system, and availing comprehensive obstetric care in nearby health institutions are recommended to prevent the incidence of obstructed labor and its complications.The online version contains supplementary material available at 10.1186/s12978-021-01103-0. Labor is considered obstructed when the presenting part of the fetus cannot progress into the birth canal, despite strong uterine contractions. The most frequent cause of obstructed labor is cephalo- pelvic disproportion, a mismatch between the fetal head and the mother's pelvic brim. The fetus may be large to the maternal pelvic brim, such as the fetus of a diabetic woman, or the pelvis may be contracted, which is more common when malnutrition is prevalent. Some other causes of obstructed labor may be malpresentation and malposition of the fetus . In rare cases, locked twins or pelvic tumors can cause obstruction. To the best of my knowledge, no systematic review was conducted to estimate the national prevalence of obstructed labor. Therefore, this systematic review and meta-analysis aimed to estimate the incidence, causes, and maternofetal outcomes of obstructed labor among mothers who gave birth in Ethiopia. Sixteen (16) primary studies with twenty-eight thousand five hundred ninety-one mothers who gave birth in Ethiopia were included. The pooled incidence of obstructed labor) mothers who gave birth in Ethiopia was 12.93%. Out of these, 67.3% did not have antenatal care follow-up, 77.86% were from the rural range, and 58.52% were referred from health centers and visited hospitals after at least 12\u00a0h of labor. The major causes of obstructed labor were cephalo-pelvic disproportion 64.65%, and malpresentation and malposition in 27.24% of the cases. The commonest complications were sepsis in 38.59%, stillbirth in 38.08%, postpartum hemorrhage in 33.54%, uterine rupture in 29.84%, and maternal death in 17.27% of mothers who gave birth in Ethiopia. Thus, promoting antenatal care service utilization, a good referral system, and availing comprehensive obstetric care in nearby health institutions are recommended to prevent the incidence of obstructed labor and its complications.Obstructed labor is defined as a failure of the fetal presenting part to descent in the birth canal due to mechanical reasons, despite having adequate uterine contraction , 2. It iGlobally, at least 585,000 women die each year from complications of pregnancy and childbirth. More than 70% of all maternal death is due to five major complications: hemorrhage, infection, unsafe abortion, hypertensive disorders of pregnancy, and obstructed labor .It is an indicator of inadequacy and poor quality of obstetric care, and immediate cause of maternal and prenatal morbidity and mortality due to uterine rupture, complications of cesarean delivery, postpartum hemorrhage, anesthesia complications, puerperal sepsis, asphyxia, and brain damage. Moreover, neglected obstructed labor resulted from poverty and prohibiting high cost of maternal care in hospitals, ignorance, illiteracy, obstructed transportation, socio-cultural belief to achieve vaginal delivery at all cost, late referrals, and aversion to caesarean delivery and hospital delivery especially after a previous caesarean operation .The fetus dies first, followed by the death of the mother that puts the lives of other children in the family in jeopardy. Many parturient women die undelivered and delivered by postmortem cesarean delivery . The fewOther complications of abdominal delivery include sepsis and septic shock, anemia, blood transfusion, wound infection, and burst abdomen, prolonged hospital stay, high cost of care, infertility, aversion to hospital delivery, and caesarean delivery in a subsequent pregnancy, obstetric fistulas, abandonment, and even divorce. Complications that have been attributed directly to fetal destructive vaginal operations include uterine rupture in 2.6\u20139.1% of cases, postpartum hemorrhage in 4.5%, and cervical and vaginal lacerations in 1.3% .Maternal mortality arising from destructive operations in the management of neglected obstructed labor ranged from 0 to 2.7% when compared to 7.5% for abdominal delivery , 12. CerMaternal and perinatal mortality and morbidity associated with obstructed labor are almost totally prevented in developed countries because of improved nutritional status, wide health coverage, adequate transportation and communication system, availability of trained health personnel, optimal antenatal and intrapartum care, and other related factors .In most sub-Saharan countries including Ethiopia, women are traditionally expected to give birth at home and consequently delay their health care seeking in childbirth, even if complications arise. Moreover, women are often marginalized in decision making regarding where and when to seek care . UnofficObstructed labor has different magnitudes in different developing countries ranging from 2 to 8%. When we come to Africa some research finding showed that the magnitude of obstructed labor was more than the above determined once; In Uganda and Ethiopia, the magnitude of obstructed labor was described as 10.5% and 12.2% respectively . In EthiApart from maternal deaths, obstructed labor had different maternal outcomes such as uterine rupture, postpartum hemorrhage, puerperal sepsis, bladder injury, Vesico-Vaginal fistula (VVF), recto-vaginal fistula (RVF), and fetal outcomes including birth asphyxia, stillbirth, neonatal jaundice, and umbilical sepsis , 19, 20.This systematic review and meta-analysis were conducted to estimate incidence, causes, and maternofetal\u00a0outcomes of obstructed labor among mothers who gave birth in Ethiopia. We used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist guideline Additio.http://www.library.UCSF.edu) were searched to check whether published or ongoing projects exist related to the topic. The literature search strategy, selection of studies, data extraction, and result reporting were done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines .A total of five articles were included to identify the association between rural residency and obstructed labor. Mother\u2019s residency was significantly associated with obstructed labor. Mother\u2019s from rural areas were more likely to have obstructed labor than those (women) from urban areas, 77.86% (95% CI: 63.07\u201392.66).Moreover, four studies showed a significant association between not having antenatal care follow-up and obstructed labor. Mother\u2019s who did not have antenatal care follow-up were 67.3% more likely to develop obstructed labor compared to mothers who had antenatal care follow-up , and malpresentation and malposition in 27.24% (95% CI: 22.05\u201332.42) of the cases .Following obstructed labor, different adverse maternal and neonatal complications were reported. Sepsis, stillbirth, postpartum hemorrhage, uterine rupture, and maternal death were the most common complications following obstructed labor Table\u00a0.Table 3MObstructed labor is a life-threatening obstetrical complication associated with significant maternal as well as fetal morbidity and mortality. Early recognition and immediate intervention are important to prevent associated complications and to improve maternal and fetal outcomes . SeveralThe purpose of this review was to assess the incidence, mernofetal outcome, and associated factors of obstructed labor by reviewing the findings of available primary studies. The pooled incidence of obstructed labor in Ethiopia was 12.93%. The result higher than the studies conducted in India 1.9%, PaThis study also elucidated that, 67% of the obstructed labor cases did not have ANC follow-up during pregnancy. The result is supported by studies conducted in Pakistan , and NigAmong mothers who had obstructed labor, 77.86% were from rural areas. The result is in line with studies conducted in Uganda and BangAdditionally, 58.52% of mothers who had obstructed labor were referred from health centers and visited hospitals after at least 12\u00a0h of labor. The result is supported by studies conducted In Ghana . This coThe main obstetric causes of obstructed labor in this review were cephalopelvic disproportion accounted for 64.65%. The result is supported by studies in Uganda , NigeriaSepsis was the commonest maternal complication of obstructed labor accounted for 38.08% of cases. The result is in line with studies conducted in Uganda , India , EasternUterine rupture resulted in 29.84% of obstructed cases. The result is supported by the study conducted in Uganda , Dar es This review revealed that obstructed labor results stillbirth 38.59% of cases. The result is in line with studies in Boston,\u00a0Massachusetts, United States , and PakMaternal death has also resulted in 17.27% obstructed labor cases in Ethiopia. The result is supported by a systematic review in Sub-Saharan Africa , Uganda Since it is the first systematic review and meta-analysis, it is taken as a strength. The included articles were restricted to the English language only; this is a limitation of the study as it missed studies published in local languages. Additionally, one of the limitations of this systematic review is the credibility of the unpublished and non-peer-reviewed publications included in this review.This study revealed the high incidence of obstructed labor and its complications in Ethiopia. Not having antenatal care follow-up, rural residency, and referred from health centers and visited hospitals after at least 12\u00a0h of labor were contributing factors for the incidence of obstructed labor. Additionally, the major causes of obstructed labor were cephalo-pelvic disproportion and malpresentation and malposition. Sepsis, stillbirth, postpartum hemorrhage, uterine rupture, and maternal death were the commonest complications of obstructed labor among mothers who gave birth in Ethiopia. Therefore, to prevent the incidence of obstructed labor; promoting ANC service utilization during pregnancy, improving the referral system, and infrastructure to reach health faculty that had a capacity to manage obstructed labor is recommended. Moreover, it is better to promote institutional service utilization for the prevention and early management of obstructed labor and its complications.Additional file 1. Prisma checklist.Additional file 2. NOS quality assessment score for the included studies."} +{"text": "Coronavirus disease 2019 (COVID-19) pandemic has had a significant impact on public mental health. Our objective was to assess prevalence of depression, anxiety, and stress among the general population in Saudi Arabia during this pandemic. A descriptive cross-sectional approach was used targeting all accessible populations in Saudi Arabia. Data were collected from participants using an electronic pre-structured questionnaire. Psychological impact was assessed using the Arabic version of Depression, Anxiety, and Stress Scale (DASS-21). A total of 1597 participants completed the survey. In total, 17.1% reported moderate to severe depressive symptoms; 10% reported moderate to severe anxiety symptoms; and 12% reported moderate to severe stress levels. Depression, anxiety, and stress were significantly higher among females, younger respondents, and health care providers. Depression was higher among smokers, singles, and non-working respondents. Anxiety was higher among those reporting contacts with COVID-19 positive cases, previously quarantined and those with chronic health problems. Our findings reaffirm the importance of providing appropriate knowledge and specialized interventions to promote the mental well-being of the Saudi population, paying particular attention to high-risk groups. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of coronavirus that causes coronavirus disease 2019 (COVID-19), the highly infectious illness responsible for the COVID-19 pandemic . More thIn Saudi Arabia, the first case was detected on 2 March 2020, after which there has been a rapid rise in cases . As of 1Even though COVID-19 has emerged very recently, due to the unusual nature of this pandemic, several studies have already been accomplished to examine its psychological consequences, primarily in China and Europe ,11. StudIn Spain, another study administered the Spanish version of the Impact of Event Scale-Revised, an instrument examining psychological distress caused by a traumatic life event in terms of three symptomatic responses . Results from 3055 participants showed that 36.6% experienced psychological distress because of the COVID-19 pandemic. Avoidance was the most commonly cited symptom, with the psychological impact consistently higher for young people and women compared to men . The DepGiven the paucity of research addressing the mental health impacts of COVID-19 in Saudi Arabia, the present study intends to assess the psychological impact of the national restrictive measures through a public cross-sectional survey that estimates the prevalence of depressive symptoms, anxiety symptoms, and stress during the last weeks of lockdown. Our objective was to describe the mental health implications of COVID-19 among our sample, and to identify potentially vulnerable groups or possible contributing factors targeting strategies to reduce the burden of mental health issues during the COVID-19 pandemic.A descriptive cross-sectional approach was used targeting men and women aged 18 and over in Saudi Arabia. After obtaining permission from the Institutional ethics committee, data were collected from participants using an electronic pre-structured questionnaire. The questionnaire was uploaded online using social media platforms by the researchers and their relatives and friends between May 10 and 16 May 2020. The researchers constructed the survey tool after an intensive literature review and expert consultation. The tool was reviewed using a panel of 5 experts for content validity. Tool reliability was assessed using the study entire population with a reliability coefficient (\u03b1-Cronbach\u2019s) of 0.89. The tool covered the following data: participants\u2032 socio-demographic data like age, gender, residence, education, participants\u2019 medical history, and participants hazardous practice regarding COVID-19 pandemic such as traveling abroad, contact with COVID-19 cases, and being quarantined. Psychological impact was assessed using the Arabic version of Depression, Anxiety, and Stress Scale (DASS-21), a reliable and valid measure in assessing mental health status in Arabic speakers . Once muAfter data were extracted, it was revised, coded, and fed to statistical software IBM SPSS version 22 . All statistical analysis was completed using two-tailed tests. A p-value of less than 0.05 was statistically significant. Descriptive analysis based on frequency and percent distribution was done for all variables, including participants personal data, medical health condition, and high risk for COVID-19 practice. Scores for depression, anxiety, and stress subscales were calculated by summing up all items discrete scores. The total score for each subscale was categorized reference to the cut off points mentioned in the methodology section. Cross tabulation was used to assess the distribution of participants depression, anxiety, and stress levels by their personal and other related data. The significance of relations in cross-tabulation was tested using the Pearson chi-square test.The study was conducted in accordance with the Declaration of Helsinki, and the Ethics and Research Committee of the College of Medicine of King Khalid University approved the protocol. Approval number (ECM#2020-237)\u2014(HAPO-06-B-001)54.5 % of the sample (n = 871). More than 96.1% of respondents were Saudi (n = 1535), and they were overwhelmingly university graduates . Almost half worked in the governmental sector, while only 12% (n = 188) worked in the private sector. Among all respondents, 34% (n = 542) worked in the health care sector, and over half (54.5%) had monthly incomes that exceeded 10,000 SR. More than two thirds (69.1%) of the sample were married, and almost half had 3\u20135 children, while only 9.6% of those married had no children. Thirty-four (6.7%) female respondents were pregnant. Almost 18% (n = 283) of the sample were current smokers had recently travelled, 35 (2.2%) had been exposed to a COVID-19 positive cases, and 38 (2.4%) were previously quarantined. Considering chronic health problems, most of the participants were healthy. The most-reported health conditions were autoimmune diseases, including asthma followed by diabetes , hypertension with treatment , and immunosuppressive disorders .n = 462) reported experiencing any depression, with 11.8% reporting mild symptoms, 10.1% reporting moderate symptoms and 7% reporting severe symptoms. The most-reported depressive item was feeling downhearted and blue (50.1%), followed by not experiencing any positive feelings at all (41.55%), and lack of motivation (35.1%). More than 16% of respondents experiencing anxiety (n = 262), with more than 10% reporting moderate to severe symptoms. The most reported anxiety factors were concerns about panic and making fool of oneself (43.5%) followed by awareness of dryness of mouth (27.5%) and unexplained fear (22.5%). Almost 18% of sample respondents reported experiencing stress, with the majority (12%) reporting moderate and severe stress symptoms. The most-reported stress items were difficulty winding down (62.6%), followed by getting agitated (49.2%) and difficulty relaxing (44%).Participants\u2019 psychological health status during COVID-19 pandemic illustrap < 0.05). Moreover, younger respondents (<35 years) were significantly more depressed, anxious, and stressed than older respondents (>35 years) . Non-working respondents (34.5%) were more likely to report experiencing depression than those who were working, and health care practitioner, in particular, disproportionately experienced depression, anxiety, and stress . Single participants were significantly more depressed and anxious than others . More current smokers reported experiencing depression and stress than others . Almost a quarter (24.6%) of those who had travelled abroad were experiencing stress compared to 17.3% of non-travelers (p = 0.047). Anxiety was significantly higher among those reporting contacts with a COVID-19 positive cases , and those who were previously quarantined were more anxious than others . Of those suffering from chronic health problems, 21.6% were anxious compared to 14.5% of healthy persons (p = 0.001). Stress was also detected among 21.4% of high-risk participants compared to 16.6% of the healthy group (p = 0.025).This study aimed to assess the psychological impact of COVID-19 pandemic on the general population of Saudi Arabia. Our survey of 1597 respondents a cross Saudi Arabia showed that 28.9% of respondents reported depressive symptoms, 16.4% reported anxiety symptoms and 17.8% reported stress symptoms. Moderate to severe features of depression, anxiety, and stress were experienced by 17.1%, 10.5%, and 12.3%, respectively. Our respondents were less likely to report experiencing anxiety and stress compared to other international studies, such as those from Iran, where the prevalence of severe anxiety was 19.1% , and ChiOur results suggested that being female was associated with increased depression, anxiety, and stress, which is similar to finding reported in previous studies ,19, and In the present research, young age was found to be associated with increased depression, anxiety, and stress. To date, the literature reports mixed results for this variable concerning the mental health of different age groups during the COVID-19 crisis ,22,23,24Being married was a protective factor against psychological suffering, as has usually been found in the literature ,30,31. SIn contrast to Wang C. et al., study results , educatiThe present study found an association between a history of chronic medical problems and increased anxiety and stress. These finding echoes previous studies indicating that chronic illness or a self-evaluation of poor health is associated with increased psychological distress ,35. A poSmoking was associated with a higher degree of depression and stress, which could be attributed to the awareness of smokers that they have a high chance of developing more medical complications if they were infected with COVID-19 because of smoking habits .The results showed that health care workers were associated with increased stress anxiety, and depression. Such workers tend to have a high degree of contact with the public, and hence are at a higher likelihood of being infected; this may increase their stress levels. Moreover, this is in agreement with previous studies published recently and during the Middle East respiratory syndrome (MERS) outbreak in Saudi Arabia and studies conducted during the current COVID-19 pandemic in Singapore and India ,39,40,41This study had some limitations that should be considered when interpreting the data. The first one we do not have a DASS-21 baseline of pre-pandemic data and detailed pre-post analyses could not be done; hence, we cannot be sure of any increase in distress levels or if any increase was COVID-19 related. The survey provides only a snapshot of psychological responses at a particular point in time, and a longitudinal study is required to provide information on whether the observed impact will last for more extended periods. Another limitation, the quality of cohabitation was not included in this study, while it was shown to be a key variable in the psychological impact of the participants, since its poorer quality was related to higher scores of stresses . The psyDepression, anxiety, and stress are prevalent among the general population during the COVID-19 pandemic lockdown in Saudi Arabia. We identified the specific subgroups of the general population at higher risk: females, those living alone during the COVID-19 pandemic lockdown, people with a history of smoking or chronic medical problems, and healthcare providers. Medical Authorities should focus on providing appropriate knowledge about the disease using appropriate methods, and specialized interventions to promote the mental well-being of the Saudi population, paying particular attention to high-risk groups. For instance, healthcare workers are known to be at a higher level of risk and thus should be prioritized when such interventions are implemented. Moreover, community mental health care should be made accessible to people who are at increased risk."} +{"text": "BRAF wild-type metastatic melanomas, localized exclusively to the pelvic region, un-eligible for immunotherapy and treated with melphalan hypoxic pelvic perfusion (HPP), is both feasible and useful in predicting response to therapy. Viable MM CTCs , enriched by transient culture, were characterised in flow cytometry-based Annexin V-PE assays for chemosensitivity to several drugs.Circulating tumour cells (CTCs) from liquid biopsies provide an exceptional opportunity to obtain real-time tumour information and are under current investigation in several cancers, including cutaneous melanoma, but face significant drawbacks in terms of non-standardised methodology, low viable cell numbers and accuracy of CTC identification. In this pilot study, we report that chemosensitivity assays using liquid biopsy-derived metastatic melanoma (MM) CTCs, from 7 patients with stage IIIC, Using melphalan as a standard, chemosensitivity cut-off values of\u2009>\u200960% cell death, were predictive of patient RECIST 1.1 response to melphalan HPP therapy, associated with calculated 100% sensitivity, 66.67% specificity, 33.33% positive predictive, 100% negative predictive, and 71.43% accuracy values. We propose that the methodology in this study is both feasible and has potential value in predicting response to therapy, setting the stage for a larger study.Trial registration Clinical Trials.gov Identifier NCT01920516; date of trial registration: August 6, 2013 BRAF/MEK inhibitors have resulted in 3-year overall survival (OS) rates of 44%, pembrolizumab, a monoclonal anti-PD-1 antibody, has resulted in 4-year OS rates of 44% and the combination of ipilimumab anti-CLTA-4 and nivolumab anti-PD-1 antibodies has resulted in three-year OS rates of 58%. However, in these studies, published over the past 5\u00a0years, unresectable stage III melanomas represent only 3% of cases, making the extrapolation of these data to patients with unresectable stage III melanoma localized to the pelvic region, challenging [V600E mutated patients [BRAF wild-type patients [Approximately 10% of cutaneous melanomas (CMs) recur as locoregional metastases following treatment , with onllenging . Furtherpatients , 18 and patients \u201321. Finapatients .This apparent plethora of therapeutic options not only reflects the fact that not all treatments are available in each institution but also that no single strategy is suitable for every patient, with treatment choice dependent upon lesion number, size, anatomic location, the presence of regional lymph node or distant metastases and also biomolecular aspects, concomitant disease and previous therapy. For these reasons, we believe that treatment strategies for pelvic locoregional metastases should be multidisciplinary and could benefit greatly from the detailed characterisation of biomolecular characteristics and relative chemosensitivity of metastatic melanoma cells, a possibility that is offered by liquid biopsies, using purified circulating tumour cells (CTCs) obtained from individual patients. This method has been approved for prognosis by USA Food and Drug Administration and despBRAF wild-type metastases located exclusively to pelvic region, who were not eligible for immune checkpoint inhibitor therapy and were submitted for melphalan HPP therapy. The aim of this study was to confirm both the feasibility and utility of assessing the chemosensitivity of CTCs purified from liquid biopsies, as a predictive test for selecting therapeutic strategy.Here, we report a pilot study of CTCs purified from a homogeneous group of stage IIIC melanoma patients with locoregional, BRAF wild-type status, stage IIIC, not eligible for immunotherapy, submitted to melphalan HPP . Written informed consent was obtained from each patient. From a prospective trial of melanoma patients undergoing melphalan perfusion/hypoxic infusion , a subset of 41 were selected with stage III and IV patients with locoregional metastases located in the pelvis and/or inguinal region and/or upper third of the thighs. From this 41-patient cohort, 7 patients were selected with CTC purification and chemosensitivity assays are detailed in Additional file More than 5 viable metastatic melanoma cells/ml were isolated in liquid biopsies of all 7 patients Table\u00a0B, medianPFS Table\u00a0A ranged BRAF wild-type status and locoregional metastases located exclusively to the pelvic region, all of whom were un-eligible for novel immunotherapy and were treated with melphalan HPP, in accordance with percentage MGMT promoter methylation levels in tissue-specimen, as a relevant index of melphalan efficacy [This pilot study was initiated to assess the feasibility of using purified CTCs, in terms of reproducibility, sampling, storage, transport, purification and enrichment methodologies, and the utility and suitability of subsequent CTC chemosensitivity assays in selecting therapeutic strategies and predicting response. For this purpose, we selected a homogeneous group of 7 stage IIIC melanoma patients with efficacy .The numbers of metastatic melanoma CTCs from all liquid biopsies were greater that the cut-off value of 5 CTCs/ml, required for chemosensitivity assays. The interval between blood sampling and qRT-PCR analysis did not exceed 80\u00a0h, which has previously been reported to minimise gene and protein expression alterations . We alsoMGMT promoter methylation, which was assessed in tissue biopsies from all 7 patients and was also predictive for melphalan efficacy [In order to evaluate the predictive potential of in vitro CTC chemosensitivity assays in prognosis and therapeutic strategy, melphalan was employed as the principle drug, with patient RECIST responses to melphalan HPP used to evaluate sensitivity, specificity, accuracy and predictive potential. This resulted in values of 100% for sensitivity, 66.67% for specificity, 33.33% for PPV, 100% for PNV and 71.43% for accuracy, which were better overall values than those of 85.7% for sensitivity, 18.2% for specificity, 40% for PPV, 66.7% for PNV and 44.44% for accuracy, reported for in vitro tissue-validated chemosensitivity assays in ovarian cancers, applying a cut-off value of 30% . Our obsefficacy .This pilot study supports the feasibility of a methodology for liquid biopsy sampling, storage, transport, CTC purification, transient in vitro CTC culture and subsequent use of CTCs in chemosensitivity assays. We demonstrated: (i) the numbers of CTCs purified from liquid biopsies obtained from melanoma patients with locoregional metastases, is sufficient for Annexin V-PE flow cytometry-based chemosensitivity tests; (ii) in vitro CTC chemosensitivity assays are feasible to predict RECIST 1.1 responses to locoregional melphalan chemotherapy with an accuracy value of 71.43%.The scope of this pilot study was to provide preliminary evaluation of the feasibility of this CTC-based methodological approach, as a forerunner to a larger cohort study, depending upon results, and was not designed to evaluate treatment safety, efficacy or effectiveness , justifyAdditional file 1.Methodology for liquid biopsies, CTCs chemosensitivity assays, and molecular evaluation."} +{"text": "Background: Despite the high rate of HIV infections, there is still high rate of early unprotected sex, unintended pregnancy, and unsafe abortions especially among unmarried adolescent girls and young women (AGYW) 10-24 years of age in sub Saharan Africa. AGYW face challenges in accessing health care, contraception needs, and power to negotiate safer sex. This study aimed to estimate the rate of pregnancy among AGYW aged 10-24, 10-19 and 15-19 years in the Southern African Development Community (SADC) economic region. Methods: A systematic review and meta-analysis was used to describe the prevalence of pregnancy among AGYW in 15 SADC member countries between January 2007 and December2017. The articles were extracted from PubMed/MEDLINE, African Index Medicus, and other reports. They were screened and reviewed according to PRISMA methodology to fulfil study eligibility criteria. Results: The overall regional weighted pregnancy prevalence among AGYW 10-24 years of age was 25% (95% CI: 21% to 29%). Furthermore, sub-population 10-19 years was 22% (95% CI:19% to 26%) while 15-19 years was 24% (18% to 30%). There was a significant heterogeneity detected between the studies , even within individual countries. Conclusion: The findings revealed a high pregnancy rate among AGYW in the SADC region. This prompts the need to explore innovative research and programs expanding and improving sexual and reproductive health communication to reduce risk and exposure of adolescents to early planned, unplanned and unwanted pregnancies, SRHR challenges, access to care, HIV/STIs, as well as other risk strategies. In South Africa alone, approximately 113 000 new HIV infections occur annually among AGYW: four times higher than their male counterparts.36 Pregnant AGYW are less likely to access early antenatal care (ANC) and test for HIV which complicates the prevention of mother to child transmission of HIV (PMTCT).12 Identifying and scaling up access to SRHR services aligns with universal access to health among adolescents. Hence, exploring the SRH affecting AGYW is essential for implementing interventions that can be integrated into public health policies and practices. This is particularly true for AGYW aged 10-24 who are at higher risk of HIV acquisition.25 Furthermore, data indicates that by the age 18 years, more than 30% of AGYW would have given birth at least once25due to high birth rates, early marriages, lack of access to health services.31 These behaviours are likely to be underpinned by unsafe sexual practices30 resulting in higher pregnancy rates.23According to UNAIDS2336 The availability and accessibility of the pooled data will indicate the impact of AGYW pregnancy rate that can be used to address emerging public health challenges, both nationally and regionally within the economic region. The outcome of the study seeks to enhance cost effective interventions that link AGYW early into healthcare, empowering them to negotiate safe sex, uptake of contraception and adherence.38 This systematic review will therefore provide a reflection of the true pooled index pregnancy rate in the economic region which can be used as a measure in HIV and comprehensive sexuality education interventions and policy development.The purpose of this review is to estimate the pooled pregnancy among AGYW in the SADC economic region.40 and used the PRISMA checklist41 to ensure that we applied the relevant methods. The study objectives were framed to assess the rate of pregnancy among AGYW in the 15 SADC countries: Angola, Botswana, Democratic Republic of Congo (DRC), Lesotho, Madagascar, Malawi, Mauritius, Mozambique, Namibia, Seychelles, South Africa, Swaziland, United Republic of Tanzania, Zambia and Zimbabwe. This included clear criteria for probing the literature, the search techniques/ search wordings and language, appraisal and retrieval of evidence data. The abstracts, the published articles and the data quality were reviewed according to the study eligibility criteria.We conducted a systematic review according to the Cochrane methodologyTypes of studies and participantsThis study focused only on AGYW pregnancy, looking for studies reporting \u201cever pregnant\u201d using a collection of search terms including \u201cadolescent pregnancy, youth pregnancy, young women pregnancy, teen pregnancy\u201d in SADC region.The type of studies included in this systematic review were cross sectional, baseline data from cohort or randomized controlled trial (RCT) study designs, and from national Demographic and Health Survey (DHS) studies published as full papers, conference proceedings/abstracts, policy or reports. The eligibility screening criteria for the studies were: (1) population: all \u201cever pregnant\u201d studies describing AGYW, aged between 10-24 years; (2) setting: AGYW studies from the 15 SADC economic hub countries; (3) Studies having the number of ever pregnant AGYW (n) or ever pregnant proportion (%) and 95% confidence interval (CI) of ever pregnant in addition to the total AGYW population (N). The time frame for the review was restricted from 2007 to 2017. Studies describing general population rate of pregnancy were ineligible for the study as well as studies without clear pregnancy rate among AGYW.Search methods for identification of studiesElectronic searches41 We limited studies to those published in English/French dating from 1 January 2007 to December 2017. We searched the following electronic databases: PubMed/MEDLINE, African Index Medicus and other African Journal online, EMBASE, Web of Science, Google Scholar, and Cochrane, using the following keywords: \u201cadolescent pregnancy\u201d, \u201cyouth pregnancy\u201d, and \u201cyoung women pregnancy\u201d \u201cteen pregnancy\u201d. The PubMed advanced mesh search features used for example was: ((adolescent) OR adolescent pregnancy [MeSH]) AND ((pregnancy) OR (pregnancy adolescents) OR youth [MeSH] OR youth pregnancy [MeSH]) AND (((teen) OR teen pregnancy[MeSH] ) OR ((young women ) OR young women pregnancy A[MeSH])). Similarly, we searched using the following French key words: \u201cgrossesse et adolescents\u201d, \u201cgrossesse et jeunes\u2019\u2019, \u201cgrossesse et jeunes femmes\u201d. For example the Pubmed search English strategy used was \u201c AND (\u201cwomen\u201d[MeSH Terms] OR \u201cwomen\u201d[All Fields]) AND (\u201cpregnancy\u201d[MeSH Terms] OR \u201cpregnancy\u201d[All ])\u201d Fields]) OR \u201ccountry specific\u201d (tw))\u201d. The search strategy was modified to include other online electronic databases such as BMC, Science Direct and PLoS One. Some of these studies were published as abstracts, conference posters and conference proceedings. Other data sources were national surveillance systems reporting on the rate of pregnancy among AGYW in some SADC countries. We embraced these sources as there were no specific pooled factor ratio describing the rate of pregnancy among AGYW between the ages of 10-24; 10-19 and 15-19 years in the 15 member states of the SADC Economic hub - a region with the highest unabated HIV reduction when compared to other region of the world.18We carried out a comprehensive literature search of quantitative published studies reporting on pregnancy rate among AGYW according to Moher et al.Selection of studiesTwo independent review authors TM and SN extracted, screened the title and abstract results from the search online databases and applied pre-piloted checklist eligibility criteria to identify eligible studies. The articles were screened for duplicates, multiple publications, and other irrelevant studies under guidance of CY.77 The included age sub-groupings were: 10-24 years (25 studies),10-19 years (22 studies)and 15-19 years (12 studies). Only Somba et al42 had restricted data on subgrouping 19-23 years age (youth group). This was further reviewed by CY and AM for consistency. The rate of pregnancy from each study was extracted, together with the total number of participants enrolled, and the total number ever pregnant.Using Microsoft Excel designed data extraction spreadsheet, TM and SN reviewed the extracted \u201cever pregnant\u201d data among AGYW aged between 10-24 years on adolescent pregnancy\u201d, \u201cyouth pregnancy\u201d, and \u201cyoung women pregnancy\u201d \u201cteen pregnancy\u201d. The major data fields extracted were: country, age group and years, study design and recruitment methods, sample size, number pregnant, sample populationas shown in78The AGYW pregnancy was defined as \u201cever been pregnant within the ages 10-24 years\u2019\u2019. We used the prevalence of pregnancy to measure the rate of pregnancy. We calculated prevalence for each included study by dividing the number of AGYW ever pregnant (n) by the total number of AGYW in the study sample and expressed it as percent.78 Using STATA 13.1 , the prevalence of pregnancy from the different studies were pooled in a random effects meta-analysis since we anticipated heterogeneity owing to the studies in different countries and settings. We applied the I2 test statistic which estimates the percentage of variation that is due to heterogeneity rather than the chance occurrences, where values exceeding 50% indicate significant heterogeneity. We also applied the chi-square test to infer the extent of heterogeneity.39 In addition, the Egger\u2019s regression test was used to estimate the study publication bias using metabias command.79 Results were displayed using forest plots. We investigated sources of heterogeneity through subgroup analysis with respect to the country from which the study was done and with respect to whether the study was from DHS.The sampling distribution for the prevalence statistic was assumed to have a normal distribution since the sample sizes were large enough to assume Central Limit Theorem.74 the majority from cross-sectional studies.69 Exploratory studies and DHS that reported only point prevalence without denominators or confidence intervals were also excluded. Qualitative studies were also excluded. Similarly, the non-experimental study from Zimbabwe had no denominator and was excluded.75 The following studies had no specific sample sizes: reporting pregnancy among adolescent in Botswana76 the Angola MIHS (2015-2016),43 and data from Zambia.61 The Mauritius teenage pregnancies of approximately 2000 cases per year arising from unsafe abortions77 was also excluded for the same reason. All the case control studies were ineligible and were excluded from the study.61 The female sex workers data from DRC was included because it met the inclusion criteria, having a sample size, prevalence and the population was 12-21 years of age45 reporting AGYW pregnancy from 2007 to 2017. We removed 7444 citations which were either not relevant or from non-SADC countries or had not reported quantitative data for the number of ever-pregnant AGYW. From the remaining 184 citations, 144 were out of the study age range (study age eligibility), duplicates and irrelevant articles. The remaining 40 articles were further subjected to review and 14 articles were non eligible due to study design (case control) or not reporting on study denominator (sample size) . Of the of age45 despite Of the 15 countries in SADC economic hub: 13 countries had 25 eligible studies of pregnancy among AYGW aged 10-24 years freely available online-internet. The described 25 eligible studies were used to pool the national and regional pregnancy rate among AGYW. Of the 25 studies, 81 692 AGYW were enrolled, and of those 14 089 reported ever pregnant translating to a crude prevalence of 17.3% .P = 0.900), indicating that there is no evidence of publication bias in the included studies of this systematic review. From the random effects meta-analysis, the overall regional weighted pregnancy rate (10-24 years)was estimated at 25% (95% CI: 21% to 28%). With regards to country specific weighted pregnancy rate, from highest to lowest, the overall meta-analysis results yielded pregnancy prevalence estimates as follows: DRC 62% (95% CI 57% to 68%), Madagascar 54% (95% CI: 51% to 58%), Mozambique 38% (95% CI: 36% to 39%), Malawi 30% (95% CI: 28% to 31%), Zambia 28% (95% CI 27% to 30%), Namibia 25% (95% CI: 12% to 39%), Swaziland 23% (95% CI: 20% to 25%), Zimbabwe 22% (95% CI: 20% to 23%), South Africa 19% (95% CI: 16% to 22%), Angola 19% (95% CI: 15% to 23%), Lesotho 19% (95% CI: 17% to 21%), Tanzania 17% (95% CI: 9% to 25%), Seychelles 6% (95% CI: 5% to 7%) as shown in 74 The chi-square test was estimated at 1775.66, degrees of freedom (df) at 12 (P < 0.001) and the I-square statistic (I2) at 99.40% (P < 0.001) indicating significant heterogeneity between the country subgroups.A test of small study effects using metabias stata command found no significant small study effect (74Those within the age range of 10-19 years (N = 80 287 vs n = 13 400) ever pregnant had a crude AGYW pregnancy rate of 16.7% ( 95% CI 16% to 17%) ) while the meta-analysis overall regional weighted ever pregnancy rate was estimated at 22% (95% CI: 19% to 26%) and nationally: Mozambique 38% (95% CI 36% to 39%), Malawi 30% (95% CI: 28% to 31%), Zambia 28% (95% CI 27% to 30%), Namibia 25% ( 95% CI: 12% to 39%), Swaziland 23% (95% CI: 20% to 25%), Zimbabwe 22% (95% CI: 20% to 23%), South Africa 19% (95% CI: 16% to 22%), Angola 19% (95% CI: 15% to 23%), Lesotho 19% (95% CI: 17% to 21%), Tanzania 17% (95%CI: 7% to 28%), Seychelles 6% (95% CI: 5% to 7%) as shown in 74 The following countries (Botswana and Mauritius) were not included in Figure 477 because of no age range data knew their HIV status and 179 (11%) were without documented viral load records at PMTCT.83 Also, mental health is one of the factors limiting AGYW attending PMTCT.84 According to a study by Nyamukoho et al,84 HIV positive AGYW attending PMTCT were 3.2 times more likely to suffer from depression, compared to older women.Therefore, detailed age appropriate epidemiological data is needed to provide an accurate estimate of pregnancy rate among AGYW which can be used to enhance interventions towards mental health interventions.High AGYW pregnancy and HIV/STIs new infections is of concern in the SADC region. This study was conducted to estimate the prevalence of pregnancy among AGYW aged 10-24, 10-19 and 15-19 years in the SADC region. The pregnancy evaluation was to enhance interventions that could enable the early linkage of AGYW to SRHR, contraceptive needs, and increase power to negotiate safer protected sex, proper use of contraceptives and reduction of HIV/STIs acquisition. Similarly, intensifying advocacy interventions that strengthen SRHR, family planning education and PMTCT for AGYW.37 The same report37 documents measures to reduce AGYW pregnancy, such as joint regional commitment task force, sub regional and national action plans targeted age appropriate disaggregation by engaging and empowering youth to contribute and drive the design, implementation, and monitoring of interventions. Our results show the pooled pregnancy rate for AGYW aged 15-19 years at 24% and national variation from 11% in South Africa to 38% in Zambia. The national variation for Latin America and the Caribbean was between 11.6% in Uruguay to 30.7% in Panama.37 To reduce AGYW pregnancy by 20%, UNFPA85 has instigated the leveraging of proven and effective interventions such as access to effective contraceptives, comprehensive sexual education (CSE), age-appropriate counselling, access to available, equitable and acceptable information, building and creating gender equality, adolescent SRHR education at targeted settings. In addition, reports by Yakubu et al13 and UNICEF80 also highlight awareness and knowledge regarding sexual education, health and family planning, and parenting skill development that include, contraception methods, and SRH misconceptions. Although, contraception misconceptions are likely to differ in some settings due to differences between modern and traditional attitudes towards contraceptive methods.89Our results showed a varied national pregnancy rate among AGYW in SADC countries. This result was similar to other low-income countries such as Latin America and the Caribbean where adolescent fertility remains high.80 For example, in settings such as India, IIPS90 conducted a household survey in 2008 among AGYW aged 15-24 years and found that more than half of the AGYW population had never received any formal education about sex or family planning. In the same study 77% of the girls had no formal contraception education.90 Sexual and gender-based violence (SGBV) and gender inequalities are some of the root causes of the high pregnancy rate in the region.34 Based on these limitations, the SADC Maputo Protocol of 2016 was held to harmonize national abortion and pregnancy laws and policies in Southern and Eastern Africa.91 The meeting proceedings advocated for more research and interventions by expanding women comprehensive sexual and reproductive education and health services.In some settings, the majority of AGYW do not make use of contraception methods.92 However, AGYW are still confronted with negative and stigmatizing attitudes of health care providers when seeking health care.93 Due to these challenges and according to report by Panday,94 AGYW delay access to health care services during pregnancy95 resulting in five times SRH consequences among adolescents girls less than 15 years of age when compared to older women96With respect to AGYW accessing health care for contraceptives and SRHR information, many SADC countries have rolled-out adolescent friendly youth services including SRHR information.97 and Willan et al98 among AGYW who had \u2018ever been pregnant\u2019. This number decreased but still high.98 According to reports by Lillian et al,99 high AGYW pregnancy in Namibia is influenced by educational background, socio-economic status, and cultural beliefs. In response to these challenges the Namibian government has geared intervention programs and policy towards youth CSE regardless of the socio-economic and/or cultural contexts and status. In Mozambique, Decree 39/GM/2003 has been initiated where pregnant schoolgirls are initiated on extra mural studies in order to complete their education.100The pooled estimate of pregnancy rate among AGYW in South Africa and Zimbabwe was estimated at 16% and 22%. This was slightly less than the 30% reported by Flanagan et al101This review showed that DRC has the highest pregnancy rate, estimated at 62%: this correlates with the country\u2019s high birth rate. DRC is the highest populated country in SADC region and the 3rd populated country in sub Saharan Africa with an estimated population of over 80 million people and a fertility rate of 6.1% per woman.102 and the pregnancy rate was estimated at 22% among adolescents aged 10-19 years.Swaziland has the highest rate of HIV among women of 15-49 (35.1%) and adolescents (16.7%) globally103 Furthermore, according to reports by Neal et al,104 approximately 2.5 million AGYW give birth before the age of 16 each year in low resource settings and around 50%\u201365% of them before the age of 15 especially in Chad, Guinea, Mali, and Mozambique. Due to the increased risks of engaging in unsafe sexual intercourse among unmarried AGYW: identifying and scaling up evidence-based programs for sexually active AGYW is critical. Positive cost-effective ways of addressing and reshaping AGYW CSE, access to SRHR, and use of pre exposure prophylaxis (PrEP). Pregnancy itself does not increase the risk of HIV/STI acquisition, however unprotected sex, a singular incident of pregnancy acquisition plays a significant role of HIV/STI transmission. It should be noted that AGYW pregnancy has been a neglected research area despite the risks associated with HIV/AIDS, sexual abuse, infant and maternal mortality, school drop-out, and loss of self-esteem. The study suggests the strengthening of SRHR and CSE programs among AGYW as part of the care package during clinical and ANC visits.AGYW who desire to be pregnant are less likely to practice safer sex. This was highlighted by findings from the Mozambique DHS showing AGYW who want to get pregnant were less likely to use condoms and other prevention methods with non-marital partners than those who want to delay childbearing.40 there is always potential biases in study reviews, including agreements and disagreements, applicability of evidence and quality of the evidence.105 Only English and French were used as the language of study search. There was no relevant data from Botswana and Mauritius and the sex worker data from DRC skewed the outcome of 10-24 years of age. The studies were not also aggregated as urban and rural areas limiting setting generalizability. Due to publication bias, findings with favourable outcomes may not have been available especially those of Population Council, Guttmacher and WHO. Despite these limitations, the search generated real time generalizable effect size estimates. The majority of the cross-sectional studies included had adjusted key variables. In addition, adolescent pregnancy data between those aged 15-19 years were mostly from DHS our intern student who helped in the the data extraction and Dr. Alfred Musekiwa (AM) who opted and carefully reviewed the meta-statistics. The study had no funding support.None declared.Since all data used in this systematic review have already been published or available in the public domain, there was no ethical clearance required for this review.CSY conceptualized, designed, reviewed the data, analysed and wrote the initial draft of the article. TM, SN extracted and reviewed the eligibility criteria. Differences or disagreements between the reviewing authors were resolved through a discussion meeting by a third party (CSY). CSY conducted and performed the meta-analysis statistics which was further reviewed by AM and advised on the general methods and structure. CSY, SN, NN, TM, AK and SM gave further interpretation and critical appraisal.The findings, interpretations, and conclusions expressed in this publication do not necessarily reflect the views of any regional or national governments but represent those of the researchers."} +{"text": "Social support has a rich foundation in family gerontology benefiting older adults, such as bolstering mental health, decreasing social isolation, and connecting them in families and communities. This study draws from a decade review of 995 empirical articles focusing on family gerontology from 13 of the top journals in gerontology, family, and relationships. Of the 995 articles, 86 were coded as social support or social network. Of these 86 articles, less than 3% included dyadic analyses, 95% were quantitative with just over 30% longitudinal. Over 30 different theories were identified with many building their work off multiple theories. Two key theories appear in over 30% of the articles, social support and socioemotional selectivity. Only 4% did not cite any theoretical framework. Overall, this presentation will review the methods, theories, and key findings of the social network/social support subtheme of a decade review of family gerontology and identify related gaps."} +{"text": "The updated Physical Activity Guidelines for Americans (2nd edition) removes the requirement that physical activity should occur in bouts lasting 10 minutes or more to count toward the minimum aerobic guideline. Using self-reported data from the 2017 Behavioral Risk Factor Surveillance System , we examined differences in national physical activity estimates with and without this requirement. Overall, 1.9% of adults reported activities in short bouts (<10 minutes). When excluding short bouts, 29.9% were inactive, 20.7% were insufficiently active, and 49.4% were active. When including short bouts, 29.1% were inactive, 21.4% were insufficiently active, and 49.5% were active. Eliminating the 10-minute-bout requirement had little effect on physical activity estimates. Our findings suggest the change in surveillance measures to accommodate the elimination of the 10-minute-bout requirement is unlikely to markedly influence national prevalence estimates obtained from the Behavioral Risk Factor Surveillance System or similar surveys.The Physical Activity Guidelines for Americans, 2nd edition, states that adults should perform at least 150 minutes per week of moderate-intensity aerobic physical activity or 75 minutes per week of vigorous-intensity physical activity, or an equivalent combination of both for substantial health benefits , race/ethnicity , educational attainment , and US Census region , and 2) 2 tests, with the significance level at .05. We also estimated the prevalence of each physical activity level by using both measures of volume overall and by respondent characteristics. Respondents with missing demographics or physical activity were excluded . Analyses were conducted in Stata 13.1 (StataCorp LP) by using weights and SVY procedures to account for the complex sampling design of BRFSS.We estimated the prevalence of reporting at least 1 physical activity occurring in short bouts overall and by respondent characteristics . Differences in prevalence across characteristics were tested by using corrected Pearson \u03c7P < .05). Overall, 29.9% of adults were classified as physically inactive and 20.7% as insufficiently active when excluding short bouts, compared with 29.1% and 21.4% when including all bouts , respondents report physical activity performed for at least 10 minutes continuously . SimilarThis study has limitations. First, BRFSS data are self-reported and could be subject to social desirability or recall biases. Second, respondents report only their top 2 nonoccupational physical activities. Thus, total physical activity, particularly activities occurring in short bouts, might be underestimated. Third, the median response rate was 45.9%; lower response rates could result in response bias, although BRFSS weighting and survey methodology are designed to adjust for nonresponse, noncoverage, and undercoverage issues . The stuAccurate public health monitoring of behaviors relies on consistent definitions and measures over time; however, new guidelines can necessitate changes to how outcomes are defined and measured. Our findings suggest that removal of the 10-minute bout requirement to align with updated physical activity guidelines is unlikely to markedly influence national estimates of physical activity obtained from BRFSS or similar surveys."} +{"text": "Factors associated with seroprevalence were analysed with multiple logistic regression. We found seroprotective titers in 29% for diphtheria (\u22650.1 IU/mL), in 83% for tetanus (\u22650.1 IU/mL) and 22% had antibodies against pertussis (\u22655 IU/mL). Seroprotection rates were higher (p < 0.001) when vaccinated within the last ten years. Furthermore, diphtheria seroprotection decreased with age (p < 0.001). Tetanus seroprotection was less reached in women (p < 0.001) and older age groups (p < 0.001). For pertussis, women had more often a titer suggestive of a recent infection or vaccination . We conclude that except for tetanus, the vast majority of at-risk patients remains susceptible to vaccine-preventable diseases such as diphtheria and pertussis.Patients with chronic diseases are at increased risk of complications following infection. It remains, however, unknown to what extend they are protected against vaccine-preventable diseases. We assessed seroprevalence of antibodies against diphtheria, tetanus and pertussis to evaluate whether current vaccination programs in Belgium are adequate. Antibody titers were assessed with a bead-based multiplex assay in serum of 1052 adults with chronic diseases. We included patients with diabetes mellitus type 1 (DM1) ( Patients with a chronic condition are often at increased risk for complications after exposure to infectious diseases. Although the exact contribution of underlying conditions to infectious disease outcome is not completely elucidated, it is known that patients hospitalised with, for example, severe pertussis often have co-morbidities . As a paThe present study is a monocentric cross-sectional serosurvey in adult at-risk patients attending the University Hospitals of Leuven. This is a tertiary referral hospital in Belgium, which has about 1800 beds and covers approximately 700,000 outpatient consultations annually ,18. All A magnetic bead-based Luminex multiplex assay was used for determination of IgG antibodies against diphtheria toxin (DT), tetanus toxin (TT), pertussis toxin (PT), filamentous hemagglutinin (FHA) and pertactin (Prn) at the Belgian scientific institute of public health (Sciensano) . Anti-DTAntibody titers below the lower limit of quantification (LLOQ) were replaced by LLOQ divided by two for the calculation of GMTs and confidence intervals. The prevalence rates of seroprotection against tetanus and diphtheria and seroprevalence of pertussis antibodies are reported with exact binomial 95% confidence intervals (95% CI). Determinants of seroprotection against diphtheria and tetanus and anti-PT seropositivity were analysed with multiple logistic regression. Time since vaccination controlled for age and sex was analysed separately within the group of vaccinated patients. A test probability of 5% was considered statistically significant. All data were analysed with R version 3.0.2 .2 and 45.4% were men who have sex with men (MSM). Of the 230 SOT patients, 128 patients had received a lung transplantation and 127 a heart transplantation. Overall, less than one third of the patients was vaccinated against diphtheria-tetanus.A total of 1331 patients participated in the vaccination coverage study, of whom 1052 (85.5%) gave additional consent for blood sample collection. The present analysis is limited to these patients , whose characteristics are shown in The GMTs and the percentage of seroprotective, seropositive, equivocal and seronegative titers are shown in Among the vaccinated patients, 36.6% were protected against diphtheria, 89.9% against tetanus, 67.3% were seropositive for anti-PT, 16.3% had titers indicative of pertussis infection or vaccination in the past few years and 5.1% titers indicative of infection or vaccination in the past few months. Among the incorrectly vaccinated patients, 25.7% were protected against diphtheria, 79.8% against tetanus, 43.7% had an anti-PT titer \u2265 5 IU/mL, 6.6% had titers indicative of infection in the past few years and 1.7% titers indicative of infection in the past few months.p = 0.06). Women were also more likely to have a titer indicative of recent infection or vaccination . These analyses further revealed that a European origin other than Belgian was associated with better protection against diphtheria . For tetanus, a net family income of more than 3000 euros was associated with better protection , and a non-European origin with less protection . For pertussis, past smoking was associated with a seropositive titer (anti-PT \u2265 5 IU/mL) and with a titer indicative for previous infection or vaccination (anti-PT \u2265 50 IU/mL) and active smoking was associated with titers indicative for a recent infection or vaccination (anti-PT \u2265 100IU/mL) .The inclusion of smoking, family income, education and origin in the analyses had a negligible effect on these results (data not shown), except for the effect of vaccination on titers indicative for recent pertussis exposure or vaccination or diphtheria . For pertussis, the number of years since vaccination was significantly associated with decreased odds for a seropositive anti-PT titer (\u22655 IU/mL) , past infection or vaccination (anti-PT \u2265 50 IU/mL) .Within the subgroup of patients who were vaccinated less than 10 years before the study, we did not observe an effect of time since vaccination on protective titers for tetanus (OR: 0.96; 0.84\u20131.1; This study demonstrates that a large group of at-risk patients remain susceptible to vaccine-preventable diseases. It provides a comprehensive insight into the seroprotective status of clinical risk groups because of the diversity of clinical conditions and number of patients that were included.We found a seroprotective status for tetanus in 83% of patients, but only 29% reached protective titers for diphtheria and 46% were anti-PT seropositive. Overall, less than 15% of the patients were protected against tetanus and diphtheria and anti-PT seropositive. These numbers are considerably lower than corresponding data from the general Belgian population ,12. In aTime since last vaccination can also influence the level of immunity against vaccine-preventable disease. Evidence exist that antibody titers wane even faster in high-risk groups. Studies in transplant and CKD patients show an accelerated decline, particularly in diphtheria antibodies compared to tetanus antibodies ,27. In aIn addition to the influence of vaccination, it is also likely that antibodies were evoked or boosted by natural infection since pertussis has been increasing in Belgium since 2011 ,30. SincIt remains striking, however, that only 38% of the vaccinated patients had protective titers against diphtheria. The exact impact of chronic disease on vaccine immunology is complex, incompletely studied and influenced by many factors, such as the characteristically older age of at-risk patients, comorbidities, disease severity and treatment.Consistent with previous seroprevalence studies, we found age to be a negative predictor for the seroprevalence of antibodies against diphtheria and tetanus ,15. IncrFinally, we also observed some gender differences. Firstly, men were significantly better protected against tetanus than women. This difference has been reported in other seroprevalence studies and has been linked to vaccination practice during the military service and to vaccination after manual work-related injuries ,12,13,14We also looked at titers suggestive of recent pertussis infection or vaccination. In total, 8% had a PT-IgG titer suggestive of an infection or vaccination in the past few years and 2% of a more recent infection or vaccination. Patients with COPD were more likely to have had a recent infection or vaccination compared to DM type 1 patients. This is consistent with another study where the seroprevalence of anti-PT was higher in COPD patients compared to healthy controls . In addiGiven the high susceptibility of at-risk patients, we advocate for a close follow-up of their vaccination status. Vaccination is the best available tool to prevent infectious diseases, even when vaccine immunity is reduced due to age, disease or treatment. It still has the benefit of reducing the likelihood of acquiring severe disease, such as pertussis infection requiring hospitalization or resulting in post-tussive vomiting ,36,37,38Some limitations of our study should be mentioned. The study was performed in a single, albeit large, tertiary care hospital, which may limit extrapolation of the results to all at-risk patients. A general limitation inherent to all seroprevalence studies is the unknown origin of anti-pertussis antibodies, i.e., from vaccination or from natural infection. However, the vaccination coverage was below 10%. We believe that lack of documentation plays a limited role since adult booster vaccination were only recommended since 2013 and cocoon vaccination since 2009, but compliance with these strategies was rather low before and during the recruitment of patients . UnfortuIn conclusion, our data show that patients with chronic diseases are at increased risk for vaccine preventable diseases. Noticeably, 17% of patients remain susceptible to tetanus, 71% to diphtheria and 54% have low titers to pertussis. This might be explained by the low vaccination coverage, age or the influence of disease and therapy on vaccine immunity. We recommend close follow-up of the vaccination status in patients with chronic diseases and advocate additionally indirect protection through universal vaccination programs and vaccination of their direct contacts."} +{"text": "Staphylococcus and Streptococcus; the most frequent Gram-negative organism is Pseudomonas, and yeasts, probably Candida, usually cause fungal infections. In all-cause EE, prognostic factors of better visual outcomes are initial VA better than counting fingers, performing a pars plana vitrectomy (PPV), performing an intravitreal injection within the first 24 hours after clinical diagnosis, and the presence of a focal type of EE. In endogenous fungal endophthalmitis, more than 1/4 of patients have bilateral involvement. Blood samples have a low rate of positivity. Yeasts remain the most prevalent cause. Many authors report using azoles and echinocandins for systemic therapy . Although PPV was performed in small proportions of eyes, the anatomical success rate is quite high. Klebsiella pneumoniae is an important cause of EE in Southeast Asia (and probably an emergent etiology in other regions), which is frequently associated with diabetes. There is a robust association with pyogenic liver abscess (PLA) . Blood cultures have a high diagnostic yield, while vitreous samples have a low yield. K. pneumoniae may carry antibiotic resistance. Anatomical and functional success rates are small, but they may be improved with PPV.This is a literature review of 31 case series of endogenous endophthalmitis (EE) published in the last ten years, identified from a literature search of several databases . While diabetes mellitus and malignancies remain the most frequently associated medical conditions, intravenous drug use is a significant risk factor . Ophthalmologic screening is recommended for candidaemia, but not in patients with sepsis of other aetiologies . The most frequent Gram-positive microorganisms that cause EE are Endogenous endophthalmitis (EE) is an intraocular infection caused by hematogenous spread from distant foci. It is an uncommon but visual severe loss cause that may have devastating ocular and systemic complications . Most auOcular inflammation may be the first patient complaint, or EE may complicate an already-diagnosed (and treated) systemic infection.Since EE is relatively rare, there are no guidelines for its treatment. In many cases, collaboration with a medical team is mandatory. In some cases, it is associated with septicemia and, unlike most ocular inflammations, may have a significant mortality rate. Therefore, it remains a challenge for the ophthalmologist.Several systematic reviews have been published on this subject 3\u20135 years ago. We have attempted to study the last decade's literature, focusing on case series, hoping to bring together significant information about the evolution of diagnosis, management, and EE prognosis. Our rationale was that case reports tend to be published if they are unusual, but case series provide valuable insight into ophthalmology departments' real-life experience.\u2009 Articles on endogenous fungal endophthalmitis (EFE) are summarized in Klebsiella endophthalmitis (EKE) are presented in \u2009 Articles on endogenous A literature search of several databases was performed using the keyword \u201cendogenous endophthalmitis\u201d and a publication date between 2011 and 2020; articles published in English, French, and German were included. Of the 547 results, we have selected the papers reporting case series of more than 10 eyes and presented the gathered information in tables. Thirty-one series have been found in the literature published between 2011 and 2020, from different aetiologies. The list of known risk factors includes the presence of long-term indwelling catheters, intravenous drug abuse (IVDA), chronic immunosuppression , debilitating diseases , endocarditis, or urinary tract infections , 5\u20137. TyDiabetes mellitus was a predisposing medical condition in 19 of the 21 papers reporting EE of various aetiologies (in 9.3% to 85.7% of patients) . MalignaIn a case series of 53 pediatric cases (we have excluded the parasitic causes) reported by Maitray et al., only 13% of patients presented with fever, 3.3% had bronchopneumonia, and 3.3% had diarrhea. The authors attributed the lack of systemic features to the subjects' immunocompromised state .Candida EE) [Malignancies were present in 21.4% to 69.7% of cases, while IVDA was the predisposing condition in 15.4% to 28.6% of patients \u201324.In a 22-year retrospective study, patients with EE caused by mold species were significantly more likely to be receiving iatrogenic immunosuppression (including chemotherapy) and have a history of whole-organ transplantation. Also, mold infections were significantly associated with having an indwelling venous line or catheter .In hospitalized patients without a history of IVDA, risk factors for EFE include prolonged hospitalization and parenteral therapy , 26.Diabetes mellitus was present in all EKE case series, in large proportions of patients (50% to 70%) .The presence of endocarditis has been reported in 5.8% to 31% of patients. Seven Asian authors have reported an association with hepatobiliary infections in 10% to 39.5%. Others reported that the foci were urinary tract infections (10% to 36% of patients) and indwelling catheters or dialysis vascular access (9.5% to 16%).Hepatobiliary infections were the extraocular foci in 77.7% to 100% of patients .K. pneumoniae endophthalmitis appears to be a particularly frequent etiology in East Asia [Klebsiella's prevalence causing exogenous or endogenous endophthalmitis in non-Asian countries ranges from 3.1% to 5% [Endogenous atients) , 27\u201329. atients) . Klebsie1% to 5% .Klebsiella's virulent strain with hypermucoviscous properties [K. pneumoniae EE) [K. pneumoniae liver abscesses were associated with a 3% to 11% incidence of EE [EKE is part of an invasive syndrome characterized by multifocal metastatic infection , 32, 33.operties . There ice of EE . In a lace of EE .Klebsiella infection, increasing liver abscesses in patients with the underlying hepatobiliary disease [Klebsiella serotypes K1 and K2 to avoid phagocytosis has been demonstrated to be enhanced in diabetes mellitus patients with poor glycaemic control [Diabetes mellitus is a recognized risk factor for disease . In pati disease , 38. The control .The presenting symptoms of EE are variable, from mild discomfort and visual loss to severe pain and visual acuity (VA) of light perception or worse . The antDelayed diagnosis or initial misdiagnosis is a common occurrence, reported in 16% to 63% of cases . A largeThe prevalence of positive blood cultures varied widely from 0 to 100% of cases. Three studies reporting very low rates of positive blood cultures (0 to 3.4%) were conducted in India , 8, 20, The rate of positive vitreous cultures ranged from 18% to 100%. Regan et al. found 28.6% positive results, but when patients with prior antibiotic treatment were excluded, the percentage grew to 41.7% . Ratra eModjtahedi et al. reported 69% of vitrectomies with positive cultures . In a seK. pneumoniae was the most frequent microorganism (26.8% to 53% of patients) [Staphylococcus was the most frequent cause [Staphylococcus (57%) and Candida (30%) [In 7 of 8 studies conducted in Southeast Asia, Gram-negative infections predominated (43.9% to 83.3% of patients) and atients) , 41\u201344. nt cause . In two da (30%) .Staphylococcus (4.6% to 62%), Streptococcus (0 to 31%), Pseudomonas (3.7% to 38.8%), and Candida (2% to 32.8%). Klebsiella was a rare occurrence (1.5% to 6.2%). One study from Turkey reported 71.2% of Candida infections [In case series from India, Australia, USA, and Europe, the distribution of the most frequent aetiologies was variable: fections .In six studies reporting only EFEs, the rate of positive blood cultures ranged from 9.2% to 25.6% (one study reported 90.1%). Only two authors reported the positive vitreous culture rates: 70.7% and 30%, respectively.Candida preferentially sequesters within inflammatory nodules, limiting the yield of culturing techniques; therefore, negative cultures should be interpreted with caution [Lingappan et al. suggested PPV as the primary diagnostic method (instead of tap) because EE generally begins with seeding the choroid and progresses to the anterior pole . Histopa caution .Candida sp. In our study, the predominant microorganisms were yeasts (71.4% to 76.1%), with Candida the most frequently found (50% to 65%). The most common mold was Aspergillus (11.7% to 16.4%).While many exogenous endophthalmitis cases are caused by molds , most EFAll 4 papers on EKE found high rates of positive blood cultures, from 66.6% to 92.9%. Positive vitreous cultures were reported in 25% to 50% of patients.There are no specific treatment guidelines for EE , 49. ConInitial systemic therapy is empirical, and the recommendations differ significantly: oral ciprofloxacin (750\u2009mg twice a day) , systemiIntravitreal antibiotic/antifungal injections (IVIs) were recommended by all authors in 48% to 100% of eyes (10 papers reported that more than 80% of eyes received IVI). The injections were repeated in 36.7% to 100% of the eyes. In one study, intravitreal injections were repeated, on average, 3.2 times in bacterial infections and 2.5 times in fungal infections . For EFEFew authors have reported the use of intravitreal corticosteroids. There is likely insufficient support in the current literature to recommend intravitreal corticosteroids as a standard of care .Intravenous therapy was used in all patients . The mosCandida endophthalmitis, intravitreal voriconazole was associated with a favourable clinical outcome [Candida resistant to azoles [Intravitreal antifungals were administered in 54% to 100% of eyes and were repeated in 33% to 50%. In a small case series of outcome . Newer eo azoles .K. pneumoniae isolates are susceptible to ampicillin-sulbactam, third-generation cephalosporin, aztreonam, quinolones, and amikacin [Klebsiella EE) [All patients received intravenous antibiotics. Intravitreal antibiotics were administered in a large proportion of eyes (84.5% to 100%). Most of the amikacin , 36. Angella EE) . Howeverella EE) .In a retrospective study from Taiwan, most patients received intravitreal injections with a combination of teicoplanin and ceftazidime .Most authors reported that vitrectomy was performed in a small percentage of eyes (6.5% to 66%) and repeated (as vitreous lavage) in 3.7% to 36.7%. Only 3 papers reported vitrectomies in over 70% of eyes , 19, 46.Primary vitrectomies were performed in 24.2% to 56.9% of eyes. One author stated that vitrectomy was indicated only in complications . The lowVitrectomy rates were very low in 8.1% to 26.8% of cases. There was one exception, a small case series that reported vitrectomies performed in 100% of eyes .Anatomical success was defined in most papers as retention of the globe, without intractable retinal detachment or phthisis bulbi. Most authors reported anatomical success rates ranging from 64.3% to 100%. The lowest percentages were recorded in a pediatric case series (47%) and in a series where most patients were young and immunocompetent (43.9%) , 20.All authors reported high anatomical success rates, from 75% to 100%. In one study, the enucleation rate was significantly higher in EE caused by molds (25%) than yeasts (0%) .Anatomical success was achieved in 40% to 83.3% of the eyes. Connell et al. have reported a 25% anatomical success in eyes with EKE .Functional success was usually defined as visual acuity (VA)\u2009\u2265\u200920/400, and it was reported in 4.5% to 64% of cases. One case series of IVDA-related EE reported 75% functional success. Connell et al. reported VA\u2009\u2265\u200920/400 in 35.4% of bacterial cases and 74% of fungal cases .Three studies reported only the percentage of eyes that achieved VA\u2009>\u2009counting fingers: 32% to 73% \u201344.Only three authors reported the functional success: from 33% (in mold infections) to 56% of eyes (in yeast infections) , 22, 47.Functional success was achieved in 16.6% to 50% of the eyes. The best success (50%) was in a small series where all eyes were subject to vitrectomy .Eleven authors have reported mortality rates . The mortality rate was 52.2% in a Korean study of fungal endophthalmitis and 38% in a small USA series in which 92% of the identified microorganisms were Gram-positive organisms , 58.While EE may be the first manifestation of bacteremia/fungemia, ocular involvement is diagnosed in patients already under treatment for a systemic infection. Therefore, the question has been raised if patients with sepsis should routinely receive an ophthalmological examination.Vaziri et al., in a large retrospective cross-sectional study on 258092 patients with hematogenous infections and 3704 with fungemia, found an EE incidence rate of 0.05% (the risk was higher in patients with fungemia: 0.4%) . They haSimilar results were reported by Wang et al. .Routine ophthalmological screening is not warranted in all sepsis patients.K. pneumoniae infection) [K. pneumoniae sepsis [In a large retrospective cohort study from Taiwan, 0.84% of PLA patients developed EE . In anotfection) . A screee sepsis .In patients with candidaemia, several authors have reported the advent of ocular candidiasis (OC) in 16% to 26.5% of cases \u201365. 50% Paediatric EE accounts for 0.1% to 4% of all cases, the highest incidence being reported from India and the lowest from the USA , 74. We The published case reports tend to present an unusual presentation of a disease. In contrast, the case series offers a typical array of aetiologies, courses of the disease, and outcomes . As Jackson et al. noted, an example is EKE: as its importance has been well established in the literature, cases may be less likely to be reported .When assessing the predisposing medical conditions, we have found that diabetes mellitus was present in 9.3% to 85.7% and malignancies in 11.7% to 33% of patients. Diabetes was especially prevalent in EKE (50% to 70% of patients).In the case series published in the past 3 years in Western countries, IVDA was an important risk factor, present in 8.3% to 43.3% of patients \u201314. In aThe most frequent extraocular foci of infection were endocarditis (5.8% to 31%), urinary tract infections, indwelling catheters, or dialysis vascular access infections. However, in many cases, an extraocular focus was not found. Authors from Asian countries reported a high prevalence of associated hepatobiliary infections linked to EKE.When a diagnosis of EE is suspected, the clinician should always request blood cultures sampling, which may be positive in 20% to 100%. This is especially helpful when vitreous cultures return negative . Blood cultures have a low yield in EFE (9.2% to 25.6%) and a very high yield in EKE (66.6% to 92.9%). To maximize the rate of positive results, the blood sampling should be performed during fever spikes, before systemic treatment (and three consecutive blood samples should be taken) , 18.The yield of vitreous cultures was highly variable (18% to 100% positive). This rate is higher when no prior antibiotic treatment was administered; thus, ocular fluid sampling should be a high priority for the clinician suspecting an EE diagnosis. In young and immunocompetent patients, the rate of positive vitreous samples was very high (93%).Staphylococci are Gram-positive organisms that grow in pairs, chains, or clusters. Coagulase-negative staphylococci include 11 subspecies, but only Staph. epidermidis is consistently pathogenic for humans. Being a prevalent species, that is, colonizing human skin and mucous membranes, it is an increasing aetiology of infections associated with implanted catheters [Staphylococcus aureus is identified by positive reactions to catalase, coagulase, deoxyribonuclease test, and mannitol fermentation.almitis) . StaphylStreptococci are Gram-positive, catalase-negative, and coagulase-negative cocci that occur in pairs or chains. They are divided into three groups by the type of hemolysis on blood agar: beta-hemolytic (complete lysis of red cells), alpha-hemolytic (green hemolysis), and gamma-hemolytic (no hemolysis). Beta-hemolytic streptococci are characterized as Group A streptococci (Streptococcus pyogenes) and Group B streptococci [lactiae) .Pseudomonas are Gram-negative, catalase-positive, nonfastidious organisms (thus having a wide distribution in nature) and are predominantly isolated due to nosocomial, opportunistic infections. They are the most common cause of Gram-negative endophthalmitis [Haemophilus influenzae and Enterobacteriaceae such as Escherichia coli and Klebsiella.solated) . Other GStaphylococcus and Streptococcus; the most frequent Gram-negative organism is Pseudomonas, while yeasts, most probably Candida, are the usual etiology of fungal infections.Systemic treatment was recommended by all authors given the specific pathogeny of EE, and in some cases, it was the only therapy administered , 45. It Staph. epidermidis is often resistant to multiple antibiotics, particularly methicillin , but almost all strains are sensible to vancomycin and rifampin [Staph. aureus usually produces beta-lactamases [The initial antibiotic treatment should consider general knowledge about the resistance manifested by different species and then modified according to laboratory tests results for antibiotic sensibility . rifampin . Staph. istance) .Penicillin is universally active against Group A, B, C, and G streptococci. Amoxicillin and cephalosporins are also effective against different streptococcal infections. In allergic patients, the first options are macrolides (clarithromycin) and/or lincosamides (lincomycin and clindamycin) , 77.Pseudomonas is usually sensible to aminoglycosides and ceftazidime. Most K. pneumoniae isolates are susceptible to ampicillin-sulbactam, third-generation cephalosporin, aztreonam, quinolones, and amikacin [amikacin , 36.P. aeruginosa were sensitive to ciprofloxacin, all staphylococci were sensitive to vancomycin, and all E.coli isolates were sensitive to amikacin [In a 10-year retrospective study, Ratra et al. found that all isolates of amikacin . Jacksonamikacin . Recent amikacin , 79.Candida strains are generally responsive to amphotericin and triazoles [riazoles , 75, butK. pneumoniae etiology was suspected, most patients received intravitreal injections with a combination of teicoplanin and ceftazidime [Intravitreal antibiotics are also recommended by all authors, usually respecting the indications and dosage for postoperative endophthalmitis (many authors have repeated the injections). If administered within 24 hours to supplement immediate systemic antibiotics, they may provide a relatively favorable visual prognosis . The typtazidime .Intravitreal antifungals were administered in 54% to 100% of eyes . The intPPV was performed in a small proportion of eyes (6.5% to 66%). This may be linked to the fact that EE patients have a systemic infection, which is sometimes severe, and patients may not withstand surgery. When PPV is performed, vitreous samples should be sent for microbiological examination, even if previous ocular fluid samples were negative.The prognosis of EE is worse than in other types of endophthalmitis. In a retrospective study on all-cause endophthalmitis, EE was an independent risk factor for evisceration or enucleation .Globe retention without a phthisis bulbi was reported in 64.3% to 100% of the case series of EE of multiple causes. In EFE, the anatomical success was even higher, from 75% to 100%. The enucleation rate was significantly higher in EE caused by molds (25%) than yeasts (0%) .K. pneumoniae endophthalmitis), intravitreal dexamethasone has significantly reduced the need for enucleation (odds ratio\u2009=\u20094) [EKE's prognosis is particularly poor: anatomical success was achieved in 40% to 83.3% of eyes. In a large review (120 eyes with endogenous tio\u2009=\u20094) .Streptococcus, Yoshida et al. reported that visual prognosis is poor, 60% of eyes losing all vision [In a review of eyes with EE caused by Group B l vision .Functional success was achieved in 4.5% to 64% of the case series with multiple aetiologies. Lim et al. found that EE caused by Gram-negative bacteria had worse visual outcomes than Gram-positive bacteria or fungus EE .In EFE, functional success was reported in 33% to 56% of eyes. Patients with EE caused by molds had worse VA on presentation and final follow-up.In EE of various aetiologies, factors associated with better visual prognosis were initial VA better than counting fingers (3 studies), PPV (2 studies), focal-type EE (1 study), and intravitreal injection within the first 24 hours after diagnosis (1 study). Ratra et al. found a significantly improved chance for anatomical and functional success with vitrectomy . In a raK. pneumoniae endophthalmitis in 50% of eyes, the vision was counting fingers or better [Functional success in EKE was achieved in only 16.6% to 50% of the eyes. Ang et al. found that the risk factors for poor visual outcomes were the presence of hypopyon, unilateral involvement, a longer interval from sepsis onset to ocular symptoms, and the advent of panophtalmia . Chen etr better . The samr better .Eleven authors have reported mortality rates associated with EE, ranging from 3.7% to 52.2%.While diabetes mellitus and malignancies remain the most frequently associated medical conditions, intravenous drug use is a significant risk factor .Ophthalmological screening is recommended for candidaemia, but not for patients with sepsis of other causes .In all-cause EE, factors of better visual prognosis were as follows: initial VA better than counting fingers, performing a PPV, performing an intravitreal injection in the first 24 \u2009hours after clinical diagnosis, and the presence of a focal type of EE.In endogenous fungal endophthalmitis, more than 1/4 of patients have bilateral involvement. Blood samples have a low rate of positivity. Yeasts remain the most common cause. Many authors report using azoles and echinocandins for systemic therapy . Although PPV was performed in low proportions, anatomical success was quite high. EE caused by molds has worse functional outcomes.Klebsiella pneumoniae is an important cause of EE in Southeast Asia (and probably an emergent etiology in other regions), frequently associated with diabetes. There is an influential association with pyogenic liver abscess (PLA) . Blood cultures have a high diagnostic yield, while vitreous samples have a low yield. Hypervirulent K. pneumoniae may carry antibiotic resistance. Anatomical and functional success rates are small, but they may be improved with PPV."} +{"text": "Staphylococcusaureus was the predominant pathogen overall (41%), and 3% of the isolates were the methicillin-resistant Staphylococcus aureus. Escherichia coli and Klebsiella pneumoniae were the most frequently isolated gram-negative pathogens, of which 14% and 26% were extended-spectrum \u03b2-lactamase-producing, respectively. Our results suggest there is a need for other Pacific Island Countries and Territories to conduct similar studies. There are gaps in knowledge about antimicrobial resistance in Pacific Island Countries and Territories. Antibiograms based on reliable data will define and inform local and national actions for containing antimicrobial resistance. There is also a need to establish a regional surveillance network to strengthen national efforts and to link surveillance data for collaborative action against antimicrobial resistance.The World Health Organization has identified surveillance as a key objective in the containment of antimicrobial resistance. Local antimicrobial resistance surveillance data are used to generate antibiograms to monitor resistance patterns and inform clinicians in the selection of the appropriate empiric treatment when culture results are pending, or if laboratory diagnosis is unavailable. However, producing robust bacteriology data is challenging for Pacific Island Countries and Territories with limited microbiology laboratory capacity. The aim of this study is to describe pathogen occurrence and antibiotic resistance in specimens cultured at the main referral hospital in Vanuatu. We reviewed specimen culture results for the period from January 1, 2017 to December 31, 2019. Demographic and clinical data were extracted from printed and electronic registers and described and analysed. A total of 5816 specimens were cultured, of which 21% were culture positive. Addressing and containing antimicrobial resistance (AMR) is a global priority and all countries have committed to developing action plans for this purpose . It is pVanuatu and other Pacific Island Countries and Territories (PICTs) face challenges when it comes to combatting AMR. PICTs are in the southwest Pacific Ocean, a region prone to natural disasters and disease outbreaks, both increasingly being worsened by the effects of global environmental and climate change . PICTs hGood surveillance data at the local, national, and international levels are essential for understanding the global spread of AMR, and for developing policies and interventions to contain AMR . In highNonetheless, laboratories which function at the local level can play a crucial role in monitoring the occurrence of clinically significant organisms, assessing the prevalence of the pathogen, and determining antimicrobial susceptibility. Antibiograms, a collation of antimicrobial susceptibility results, can be used to inform health workers in selecting the most appropriate empiric treatment (whilst awaiting microbiology culture results), or when laboratory diagnosis is unavailable. Local data can contribute towards building a representative picture of national trends, and planning and measuring the impact of interventions, such as hygiene campaigns and clinical practice guidelines . Staphylococcus aureus was reported as being the predominant gram-positive pathogen in the region, mainly in association with community-acquired infection. Methicillin-resistant S. aureus is >50% in Papua New Guinea and <20% in other PICTs [Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumonia, and Escherichia coli, to name a few. All were reported in association with HCAIs [Whilst no research has been conducted on AMR in Vanuatu so far, there have been a small number of studies in other PICTs . Staphyler PICTs . Severalth HCAIs . In otheth HCAIs ,11,12,13th HCAIs ,15,16,17th HCAIs , AMR is th HCAIs ,20,21. Rth HCAIs .A. baumannii, carbapenem-resistant Enterobacteracales, extended-spectrum \u03b2-lactamase producing (ESBL) Enterobacteracales, carbapenem-resistant Pseudomonas aeruginosa (CRPA), and MRSA. The ESCAPPM group of Enterobacteracales are inducible AmpC \u03b2-lactamase producing, resulting in resistance to the cephalosporins, and include the following: Enterobacter spp., Serratia spp., Citrobacter freundi, Hafnia alvei, Acinetobacter/Aeromonas spp., Providencia spp., Proteus spp. (not mirabilis), and Morganella morganii [In 2017, to highlight the urgent need for new treatments to be developed, WHO published a list of globally important antibiotic-resistant pathogens, for which therapeutic options are limited . This limorganii . The aim of this study was to describe pathogen occurrence and antibiotic resistance in specimens cultured at Vila Central Hospital (VCH), the main referral hospital in Port Vila, the capital of Vanuatu, between 1 January 2017 and 31 December 2019. The results may guide selection of empiric therapy, provide data for continued guideline development, and contribute to a better understanding of AMR at the local level.A total of 5,816 specimens were cultured in the microbiology laboratory between January 2017 and December 2019. This included 3084 (53%) blood specimens; 855 (15%) urine; 1216 (21%) wound/pus; 178 (3%) respiratory tract; 105 (2%) cerebrospinal fluid (CSF); 169 (3%) stool; 138 (2%) body fluids; and 71 (1%) eye, ear, and genital tract specimens .Culture-positive pathogens were isolated from 21% (1238/5816) of the specimens and 49% (607/1238) were gram-negative. Whilst 61% (761) of the culture-positive pathogens were from pus and wound specimens, 17% (210) and 16% (194) were from blood and urine specimens, respectively. Pathogens isolated from respiratory tract, CSF, stool, body fluids, ear and eye, and genital tract specimens made up 6% (73).The proportion of culture-positive pathogens was highest in the surgical ward with 36% (451), and this was followed by the outpatient department (OPD) with 18% (217), and the paediatric ward with 17% (213) .Overall, slightly more than 50% (625) of the pathogens were from male patients. Neonates accounted for 10% (92), child and adult patients accounted for 33% (414) and 57% (710), respectively . Details about the distribution of pathogens by type of specimen and patient age can be found in S. aureus was the most frequently isolated pathogen, accounting for 41% (502/1238) of all pathogens, followed by E. coli, K. pneumoniae, P. aeruginosa, and then P. mirabilis, with 15% (187), 8% (96), 6% (73), and 4% (55), respectively. The proportion of ESCAPPM pathogens cultured from all specimens was 10% (126).S. aureus 23% (45), followed by E. coli 15% (30), K. pneumoniae 8% (16), and then Streptococcus pyogenes 7% (13). Whilst the total number of pathogens isolated from blood cultures was 194, half were gram-negative. The percentage of true positives and contaminants was 6.2% (194/3084) and 11.9% (368/3084), respectively. The predominant blood pathogen was Overall, 24% (47) of the blood pathogens were cultured from samples taken from neonates, 34% (65) from children, and 39% (76) from adult patients (6 isolates missing age data) .S. aureus was by far the most predominant overall. The most frequently isolated gram-negative pathogen was P. aeruginosa , followed by K. pneumonia , E. coli , and then Proteus mirabilis . Most pathogens cultured from wound and pus specimens were gram-positive and Just 5% (41) of the pathogens were cultured from samples taken from neonates, whilst 35% (270) and 58% (444) were taken from children and adults, respectively. Thirteen pathogens were missing age data.E. coli comprised 53% (112) and K. pneumoniae . Slightly more than half of the bacteria were isolated from specimens taken from female patients.Ninety-four percent of pathogens cultured from urine specimens were gram-negative. Antibiotic susceptibility of the pathogens is profiled in a cumulative antibiogram: gram-positive a and graS. aureus, with a total of 502 isolates. There were 489 methicillin-susceptible S. aureus (MSSA) isolates and 13 MRSA. Eighty-six percent (86%) of the MSSA (423) were cultured from wound and pus specimens. Rates of susceptibility across all MSSA isolates to locally used antibiotics were >90% to cefoxitin , doxycycline , trimethoprim-sulfamethoxazole , and Rifampicin . The isolates had reduced susceptibility to chloramphenicol and erythromycin . The most frequently isolated gram-positive organism was The MRSA isolates all displayed resistance to cefoxitin. Twelve of the MRSA isolates were cultured from pus specimens and one was from blood. Neonates accounted for two of the MRSA isolates, four were from children, six were collected from adults, and the patient\u2019s age was not recorded for one isolate. Enterococcus species (16 isolates) was the only other pathogen tested for antibiotic susceptibility, but the number tested was <12 and therefore not reported. Whilst there were other gram-positive pathogens, E. coli was the predominant gram-negative pathogen and accounted for 31% (187/607) of all gram-negative organisms. The rates of susceptibility to locally used antibiotics were 12% for ampicillin (20/172), 42% for amoxicillin (62/147), 61% for cefaclor (47/77), 84% for ceftriaxone (143/171), 83% for gentamicin (141/170), 80% for ciprofloxacin (138/172), 42% for trimethoprim-sulfamethoxazole (53/127), and 90% for chloramphenicol (106/118). The susceptibility rates for nitrofurantoin and nalidixic acid (urinary isolates only) were 94% (92/98) and 68% (15/22), respectively. K. pneumoniae followed E. coli in frequency with 96 isolates, and these made up 16% of gram-negative organisms. The levels of susceptibility to locally used antibiotics when calculated across all specimens were: amoxicillin 43% (25/57), ceftriaxone 76% (68/90), gentamicin 76% (65/86), ciprofloxacin 72% (63/87), trimethoprim-sulfamethoxazole 61% (55/90), and chloramphenicol 76% (42/55). For urinary isolates, susceptibility to nitrofurantoin was 74% (18/24). All organisms in the ESCAPPM group were isolated in Vanuatu. They comprised 21% (126) of the gram-negative organisms. Levels of susceptibility to locally used antibiotics for the group were as follows: chloramphenicol 82% (45/55), ciprofloxacin 83% (90/108), ceftriaxone 77% (77/109), gentamicin 84% (88/105), trimethoprim-sulfamethoxazole 57% (50/87). More information about this group can be found in E. coli isolates and 26% (25/96) of all Klebsiella spp. isolates were susceptible to ceftriaxone, indicating moderate levels of ESBL. The ESBL-producing Klebsiella spp. was also non-susceptible to ciprofloxacin and gentamicin. Findings indicate that, whilst the total number of ESBL-producing isolates (51) identified from these two pathogens decreased from 32 in 2017 to 10 in 2018 and 9 in 2019, there was no significant difference in the proportions being produced . At VCH, 14% (26/187) of all Fifty-seven percent of the ESBL-producing isolates were taken from adult patients, 25% from children (13), 16% (8) from neonates, and the age of 1 patient was not recorded. P. aeruginosa isolates were identified in 2019 (2/10) to be CRPA: one cultured from a urine specimen from an adult patient, and the other from a pus specimen from a child patient. Ten inducible AmpC \u03b2-lactamase producing isolates, including Enterobacter Cloacae (5), Citrobacter Freundii (2), Enterobacter spp. (2), and Serratia marcescens (1) were also reported in 2019. Six were cultured from urine specimens, three from pus, and one from a blood specimen. All but two were taken from adult patients.Two This is the first study to report on pathogen occurrence and antibiotic resistance in Vanuatu. The total number of specimens cultured was 5816. Twenty-two percent (22%) of the tests yielded a positive culture, and slightly more than 50% of these were gram-positive organisms. Male patients accounted for half of the culture positive results.S. aureus was the most predominant pathogen overall and was isolated from all specimen types. The proportion of MRSA was 3% (13/502). Rates of MRSA across the PICTs are highly variable [S. aureus isolates collected from Papua New Guinean children (70), with hematogenous osteomyelitis in 2012 and 2017 [variable . MRSA waand 2017 and 40% and 2017 . Recent and 2017 ,29. Thesand 2017 and it iTo date, there has been no research about MRSA, either hospital-associated MRSA (HA-MRSA) or community-associated MRSA (CA-MRSA) in Vanuatu, and there is scarce data about HA-MRSA in other PICTs . Given tE. coli, 25 (26%) K. pneumoniae isolates and two CRPA (3%) isolates. Vanuatu has lower rates of resistance to third generation cephalosporins in E. coli and K. pneumoniae compared with other PICTs, according to previously published WHO data [Apart from the MRSA isolates, several gram-negative pathogens identified on the WHO list of priority pathogens were isolated in Vanuatu. Whilst the clinical significance of these pathogens is yet to be determined, they include 26 (14%) ESBL-producing WHO data . E. coli, K. pneumoniae, A. baumannii, and P. aeruginosa have been reported in hospital settings in Fiji and the French Territories in the Pacific. During 2011 and 2012, in Fiji\u2019s main referral hospital, 17% (114/663) of intensive care patients developed culture-confirmed sepsis. Twenty-two percent of isolates cultured were ESBL-producing K. pneumoniae, whilst 21% (92/437) and 17% (73/437) were A. baumannii and P. aeruginosa [A. baumannii were detected in 2004 in the Central Hospital (CH) in Noumea, , and accounted for a quarter of all multi-drug resistant bacteria isolated [A. baumannii affecting 24 patients (19 colonised and 5 infected) occurred in the CH in Papeete, French Polynesia in the same year [E. coli and K. pneumoniae have also been increasing in recent years in New Zealand, although rates remain low [Multi-drug resistant pathogens associated with HCAIs, including gram-negative ruginosa , respectisolated . Over 40ame year ,34. ESBLHealthcare associated infections are recognised as a problem in hospitals worldwide, resulting in increased morbidity and mortality for patients and in increased costs for the healthcare system . There iInternational travel has been identified as a risk factor in the dissemination of AMR . During We found the rate of contaminated blood cultures was high at 12%, suggesting blood (and other) specimen collecting skills may need improvement. False-positive blood cultures (contaminated samples) lead to longer hospital stays, increased use of broad-spectrum antibiotics, exacerbating the incidence of antibiotic resistance and patient mortality, and increasing the workload for laboratory staff . FindingTherapeutic guidelines are evidence-informed recommendations intended to optimise patient care for use by health care providers . An antiWhilst there is a small laboratory in the NPH, the laboratory has less capacity than the one at VCH, uses a paper-based record system, and has had limited internet connectivity. These factors hamper communication and data sharing. Therefore, this study describes the bacteriology and ABR in pathogens collected at Vanuatu\u2019s referral laboratory, and it is unknown how representative this data is for the whole of Vanuatu. However, this is not uncommon in LICs, as microbiology laboratories are generally located in dense urban areas.The data cover the years 2017 to the end of 2019. For several pathogens, there were <30 isolates identified. CLSI guidelines specify reporting only species with testing data for \u2265 30 isolates. If <30 isolates are used, CLSI recommends caution in interpreting the data, as small numbers may result in biased results. . Slightly more than 75% of positive cultures were attributed to hospital wards. Therefore, the data is more representative of a hospital antibiogram than a community antibiogram. It is likely there is a collection bias, as specimens will be collected in patients with more severe infections, those who received prior antibiotic therapy, those whose first line treatment has failed, and those with HCAIs. Therefore, milder infections in those that responded to first line treatment, and community-acquired infections, are likely to be under-reported. This means that the profiles of pathogens and antimicrobial susceptibility are likely to bias toward a higher rate of hospital pathogens and resistance. Vanuatu, a small island nation in the southwest Pacific Ocean is made up of an archipelago of 80 islands, and 12 of these have significant populations and economy . VanuatuVCH has 230 beds across several wards: medical, surgical, obstetrics and gynaecology (O&G), paediatrics, maternity, tuberculosis and psychiatry. There is an emergency department (ED), outpatient department (adult and children) (OPD), a radiology department, and several specialist outpatient clinics, including dental; antenatal; eye; ear, nose and throat (ENT); physiotherapy; and the diabetic foot clinic. Whilst there is a small laboratory attached to the NPH, the diagnostic laboratory in VCH is the national referral laboratory.Currently, the microbiology laboratory documentation system is paper based, but information is transcribed into Excel spreadsheets to produce monthly statistics and annual antibiograms. An information system to support laboratory surveillance is under consideration. The VCH laboratory includes the following specialist areas: clinical biochemistry, microbiology, haematology, anatomical pathology and cytology, serology, blood bank, and tuberculosis diagnostics. The laboratory is enrolled in the External Quality Assessment Programme coordinated by the Pacific Pathology Training Centre in New Zealand. Assessments are conducted annually, and the External Quality Assessment Programme performance assessments for the microbiology laboratory in 2017, 2018, and 2019 were 90%, 95%, and 94%, respectively. We conducted a descriptive study involving the review, collection and analysis of laboratory specimen results from January 1, 2017 to December 31, 2019. Throughout this period, the microbiology laboratory was staffed by the same qualified microbiologist, ensuring consistency in testing procedures. The following data were extracted from printed microbiology registers and Excel spreadsheets: patient number; age, gender, month, and year the specimen was received; department from which the request originated; specimen type; reasons for request; culture; and susceptibility test results. The analysis included the following specimen types: blood, urine, pus and wound, respiratory tract, cerebrospinal fluid (CSF), stool, body fluids, urogenital tract, ear and eye. The pus and wound specimens included wound discharge and pus samples. The upper and lower respiratory tract specimens included throat and nasopharyngeal swabs, sputum and, tracheal, and lung aspirate samples. Body fluid specimens included abdominal ascites, synovial, and pleural. Eye and ear samples included discharge swabs, whilst sample types from the urogenital tract included urethral and virginal swabs. Pathogen occurrence and antibiotic susceptibility are presented respectiEnterobacteracales and other gram-negative bacteria. Identification and testing were performed according to the 2016-9 Clinical and Laboratory M100 Standards and interpretive criteria (CLSI -M100) [Specimens were set up on human blood agar plates and other routine plates appropriate for the specimen type. Identification of the microorganisms was conducted using conventional culture-based techniques\u2014basic phenotypic and biochemical identification. The API 20E test kit was also used to identify and differentiate I -M100) . SusceptI -M100) . The antI -M100) .Escherichia coli ATCC 52922, Staphylococcus aureus ATCC 25923, and Pseudomonas aeruginosa ATCC 27853 were used as negative and positive controls, respectively, to quality control the susceptibility testing procedures in line with CLSI guidelines [idelines .E. coli and Klebsiella spp. were confirmed by double disk diffusion method. The growth-inhibitory zones were measured around cefotaxime (CTX) (30 \u00b5g) and ceftazidime (CAZ) (30 \u00b5g) disks with and without clavulanic acid (CA) (10 \u00b5g). An increase of \u22655mm in the diameter of the zone of inhibition around each pair of antibiotics compared with CTX or CAZ alone, respectively, confirmed the presence of an ESBL-producing organism. MRSA were detected using a cefoxitin (30ug) disk and the isolate zone of \u2264 21 mm was confirmed phenotypically to be MRSA [Extended-spectrum beta-lactamase-producing (ESBL) be MRSA .For the purposes of analysis, patients were categorised as neonate (<1 month), paediatric (\u22651 month to <18 years), and adult (\u226518 years). The hospital wards and departments that requested the laboratory tests included: surgical, medical, O&G, paediatric, nursery, maternity, OPD, ED, dental, eye, and ENT.Bacillus spp., and mixed bacteria were excluded from analyses. The data were entered in an Excel spreadsheet and analysed using Stata version 15 . Data were described and analysed as proportions. The two-sample test of proportions was used to test for difference in population proportions. A P-value of \u2265 0.05 was considered statistically significant.Demographic and clinical data were described and analysed. For each patient, only the first isolate of a given species identified during the study period was considered, irrespective of body site (first isolate strategy) . If an iEthical approval was obtained from Vanuatu\u2019s National Cultural Council, the Vanuatu Ministry of Health, and the Research Ethics Committee of the Australian National University (Protocol number 2017/056).Our study characterises current pathogens and antibiotic resistance patterns in Vanuatu. There are gaps in knowledge of pathogen occurrence and AMR across PICTs. Therefore, it is important for other PICTs to conduct similar studies, so that a representative picture of pathogen occurrence and ABR can be mapped for the region. However, this will require participation in a regional surveillance network. A regional network may be facilitated by utilising the existing Pacific Pathology Training Centre network expanded to include bacterial pathogens and AMR. At least 21 laboratories across PICTs currently participate .Advance laboratory capacity, including the training of staff, the creation of infrastructure to improve access to microbiology services, adopting international standards, and establishing a continuing laboratory education program;Implement antimicrobial stewardship programmes in healthcare settings, including AMR awareness raising, improving prescribing practices, and education for infection prevention and control; andDevelop a regional AMR surveillance network to support national containment efforts and link surveillance data to enable collaborative efforts against AMR.Vanuatu and other PICTs are currently working with WHO WPRO to develop action plans to address AMR following health principles. Once ratified, these plans may lead to more formal commitments to:"} +{"text": "Solanum tuberosum) is a major food source in the whole world including Bangladesh. Viral diseases are the key constraint for sustainable potato production by reducing both quality and quantity. To determine the present status of eight important potato viruses in Bangladesh, tuber samples were collected from three major potato growing regions in January\u2013February 2017 and February 2018. Reverse transcription polymerase chain reaction (RT-PCR) with coat protein (CP)-specific primers were used to amplify CP sequences of the respective viruses, and confirmed by sequencing, which were deposited in the GenBank. Results indicated that the tuber samples were subjected to Potato leafroll virus (PLRV), Potato virus X (PVX), Potato virus Y (PVY), Potato virus S (PVS), Potato virus H (PVH), Potato aucuba mosaic virus (PAMV) and Potato virus M (PVM) infection, whereas mixed infections were very common. Phylogenetic analysis revealed that the PLRV from this study was closely related to a Canadian and a Chinese isolate, respectively; PVX was closely related to a Canadian and a Chinese isolate, respectively; PVY was closely related to a Chinese isolate; PVS was closely related to a Chinese and an Iranian isolate, respectively; PAMV was closely related to a Canadian isolate; PVH was closely related to a Huhhot isolate of China; and PVM was closely related to an Indian and an Iranian isolate, respectively. As far as we know, PAMV in this study is the first report in Bangladesh. These findings will provide a great scope for appropriate virus control strategies to virus free potato production in Bangladesh.Potato ( Potato leafroll virus , Potato virus X , Potato virus Y , Potato virus S , Potato virus H , Potato virus M and Potato virus A have been reported so far [Potato aucuba mosaic virus is an emerging potato virus worldwide, especially in Southeast Asia [2 to 105 times more sensitive in comparison to traditional ELISA technique for potato virus detection [Potato, the power house of energy, is the principal vegetable crop in Bangladesh . In 2018d so far ,10,11,12d so far ,14,15. Bast Asia ,16,17. Aast Asia . Accuracast Asia ,22. In aetection . Althougetection ,25,26. Netection ,28,29. Hetection .>In the present study, RT-PCR based detection followed by subsequent sequencing was performed to identify and characterize eight important potato viruses in three key potato growing regions of Bangladesh and also accomplish their relative incidence. Additionally, phylogenetic association with formerly reported virus isolates from the National Center for Biotechnology Information (NCBI) database was also analyzed. Findings from this study will provide an excellent scope for future research on the biological features of these viruses, including the effects on yield and quality, host range and distribution, and also for virus free potato production.Rapid and exact detection of viruses are pre-requisite for virus-free seed potato production, and planting of these virus-free potato seed is an important approach to control potato viruses in field to enhance the commercial potato production . RT-PCR Sequence analysis from this study with the BLASTn server of NCBI confirmed the presence of PLRV, PVX, PVY, PVS, PVH, PAMV and PVM . All theComparison of viral sequences found in Bangladesh showed that PLRV isolates shared a maximum 95.69% nucleotide (nt) identity with each other; PVX shared a maximum 96.36%, 97.06% and 99.30% nt identity with each other; PVS shared a maximum 93.79% nt identity with each other; PVM shared a maximum 80.59% nt identity with each other; and PAMV shared a maximum 96.93%, 97.47% and 97.60% nt identity with each other. Comparison of viral sequences from the present study with the respective viral sequences from the GenBank database further exhibited that PLRV from this study shared a maximum 95.52% and 100% nt identity with a Chinese isolate (GenBank accession no. MF062487) and a Canadian isolate (GenBank accession no. D13954), respectively; PVX shared a maximum 98.31%, 99.72% and 98.59% nt identity with a Scottish isolate (GenBank accession no. GU144353), a Shandong isolate (GenBank accession no. AF528555) and a Heilongjiang isolate of China (GenBank accession no. GU373815), respectively; PVY shared a maximum 99.38% nt identity with a Chinese isolate (GenBank accession no. KC296825); PVS shared a maximum 98.87% and 95.14% nt identity with a Chinese isolate (GenBank accession no. AY512653) and an Iranian isolate (GenBank accession no. MH159208), respectively; PVH shared a maximum 100% nt identity with a Huhhot isolate of China (GenBank accession no. HM584819); PAMV shared a maximum 97.07\u201397.60% nt identity with a Canadian isolate (GenBank accession no. S73580); and PVM shared a maximum 93.68% and 82.24% nt identity with an Indian isolate (GenBank accession no. KJ473993) and an Iranian isolate (GenBank accession no. KC129092), respectively. As PVH-CP sequence exhibited 100% nt similarity with a Huhhot isolate of China, we executed an additional RT-PCR with a primer pair encoding the triplegene block-1 region, whereas the sequence (GenBank accession no. MH932394) shared a maximum 99.86% nt identity with the same isolate.To assess the evolutionary relationship, nucleotide sequences from this study and existing sequences in NCBI database of respective viruses were aligned by ClustalW . Here, iViruses are the principal threat for potato production all over the world, including Bangladesh ,10,34. APhylogenetic analysis denotes various important information including the degree of relationship among genera, species and strains, diversity of geographical isolates, and the origin and evolution of plant viruses ,43. An aGlobally, a number of researchers used identical potato virus identification techniques to our study ,47,48,49Potato tuber samples from the three major potato growing regions of Bangladesh, Munshiganj , Jessore and Bogra districts were collected at harvesting stage in January\u2013February 2017 and February 2018. Altogether, a total of 220 tuber samples were picked randomly from 44 small fields taking five tubers from each field for further RT-PCR detection.The occurrence of eight economically important potato viruses in three major potato growing regions of Bangladesh were determined by RT-PCR and confirmed by successive sequencing. Total RNAs from all the five tubers of 44 sample lots were extracted using the method described formerly by Han et al. . BrieflyThe cDNAs were synthesized using Moloney murine leukemia virus (M-MLV) reverse transcriptase as described by Khine et al. . These cEscherichia coli strain MC1022 as described earlier by Sambrook et al. [AxyPrepTM DNA gel extraction kit was used to purify amplified products from the agarose gel. The purified PCR harvests were ligated to pMD19-T (Simple) vector following the manufactures instruction and subsequently transformed into the competent cell of k et al. . RecombiSequences from this study were aligned with related available sequences from the NCBI database by ClustalW . PhylogeViruses are major constraint for global potato production, including Bangladesh. Along with the expanding global trade, chance to migrate potato viruses is mounting day-by-day. Consequently, rapid and reliable potato virus detection techniques are mandatory to stop these migration as well as for virus free seed potato production. This study confirmed the presence of PLRV, PVX, PVY, PVS, PVH, PAMV and PVM in the three major potato growing regions of Bangladesh. In addition, virus incidence and their evolutionary relationship were also demonstrated here. As far as we know, this is the first report of PAMV in Bangladesh. Our findings will provide a base for further research on the biological features of the above-mentioned viruses, including the effects on yield and quality, host range, distribution, and also to develop appropriate management strategies for virus free potato production."} +{"text": "Prostate cancer (PCa) is the most common cancer in males and affects 16% of men during their lifetime . Despitep < 0.001], and the obtaining of more positive nodes without increasing risk of any complications and of lymphocele . Furthermore, we must consider that approximately 40% of high-risk patients present a specimen-confined disease, hence they harbor a completely removable and more favorable disease and could mainly benefit from a surgical approach. Moreover, at least 30% of the patients do not need any adjuvant therapy [Several studies have shown excellent oncological outcomes after RP: 10-year cancer-specific and overall survival ranges from 70% to 90% and from 58% to 83%, respectively. This wide range of prognosis depends on several factors, including biological heterogeneity, different definitions of high-risk group and number of removed nodes [ therapy . Use of therapy ,14. As m therapy . Althoug therapy . Evaluat therapy . These fRegarding primary radiotherapy treatment, European Association of Urology guidelines recommend external beam radiation therapy plus ADT with or without brachytherapy boost . Some asTherefore, in consideration of all this evidence, we advocate an urgent requirement for head-to-head comparison of surgery versus radiotherapy option, to improve our knowledge and to better counsel patients selecting personally preferred treatment. Results from randomized trials comparing RP versus EBRT + ADT are expected soon . HoweverAlthough RP and RT are considered both equally valid options in the treatment of high-risk PCa, recently the surgery option has considerably increased, equaling radiotherapy rates ,43. In t"} +{"text": "This is the first systematic review and meta-analysis to ascertain incidences of post-vasectomy pain following traditional scalpel, or non-scalpel vasectomy. Electronic databases PubMed, Embase and PsycINFO were searched up to 1 July 2019 for peer-reviewed articles recording post-vasectomy pain. We identified 733 publications, screened 559 after removal of duplicates and excluded 533. Of the remaining 26 full-text articles, 8 were excluded with reasons, leaving 18 for detailed analyses. Meta-analysis was performed on 25 separate datasets . Study follow-up ranged from 2 weeks to 37 years and sample sizes from 12 to 723 patients. The overall incidence of post-vasectomy pain was 15% (95% CI 9% to 25%). The incidences of post-vasectomy pain following scalpel and non-scalpel techniques were 24% (95% CI 15% to 36%) and 7% (95% CI 4% to 13%), respectively. Post-vasectomy pain syndrome occurred in 5% (95% CI 3% to 8%) of subjects, with similar estimates for both techniques. We conclude that the overall incidence of post-vasectomy pain is greater than previously reported, with three-fold higher rates of pain following traditional scalpel, compared to non-scalpel vasectomy, whereas the incidence of post-vasectomy pain syndrome is similar. Vasectomy is a form of permanent contraception which is increasingly considered as men age beyond mid-life. The procedure involves sealing a part of the vas deferens, preventing the transport of spermatozoa out of the testis. Vasectomy is achieved in two parts: exposing the vas deferens out of the scrotum (isolation) and blocking the vas (occlusion). Isolation can be done conventionally using a scalpel to make an incision through the scrotum or by a non-scalpel vasectomy (NSV). This involves clamping the vas and overlying skin by an extracutaneous ring and piercing the skin using pointed dissection forceps to gain access. The NSV technique is less invasive, with reduced damage to microvasculature, lymphatics and nerves, unlike the scalpel technique where these microscopic structures are more likely to be severed. Therefore, NSV may result in less trauma and post-procedure pain. As for occlusion, different methods were developed in order to reduce complications. These include excision and ligation, surgical clips, thermal or electrocautery, intraluminal mucosal cautery or chemical occlusion. However, excision and ligation are still the most widely used methods .Complications of vasectomy can be classified as early or late. Early complications include acute pain, haematoma, bleeding, infection and trauma. Late complications are vasectomy failure, fistula formation and chronic pain . Sperm gChronic pain following vasectomy is very challenging to diagnose and treat. Being a diagnosis of exclusion, it exposes the patient to a series of investigations and treatment regimens over months. Once a diagnosis is made, the treatment starts with non-invasive behavioural or pharmacological options. If these fail, patients might require invasive surgical interventions, such as repeating the vasectomy with wide excision of the severed ends, microdenervation of the spermatic cord, epididymectomy, vasectomy reversal or orchiectomy . The lasAlthough chronic post-vasectomy pain is a recognized complication, current literature shows lack of consensus regarding its frequency. Recent narrative reviews report the incidence of post-vasectomy pain to be between 1% and 6% . Howeverhttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=87244.This review protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO) on 29 January 2018 in accordance with Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) (registration number: CRD42018087244); The primary outcome measure was the incidence of post-vasectomy pain, presenting two weeks or later after the procedure, thus ensuring that pain was not related to any post-surgical complication such as infection, haematoma, bleeding or incisional pain. Pain could be assessed using validated pain scales, VAS or patient report. Studies where measurements of complications including pain were reported in men aged 18 years or older, who underwent scalpel or non-scalpel vasectomies, were included in the review and meta-analysis. The secondary outcome measure was the incidence of PVPS.Electronic databases PubMed, Embase and PsycINFO were searched from inception up to 1 July 2019. Peer-reviewed publications reporting observational studies; cohort, cross-sectional, case control and randomized control trials were eligible for review. Case series, case reports, conference abstracts and articles not published in English were excluded.The PubMed search strategy used is as follows: (((\u201cVasectomy\u201d[Mesh]) OR ((((vasectomy[Title/Abstract]) OR vasectomies[Title/Abstract]) OR post-vasectomy[Title/Abstract]) OR post-vasectomies[Title/Abstract]))) AND ((\u201cPain\u201d[Mesh]) OR pain[Title/Abstract]). No limits, expansions, explosions were applied to the search. The full search histories are provided in All references were imported into ENDNOTE X8 in preparation for the screening process, and duplicates were identified and removed. All titles and abstracts generated were double screened by two independent reviewers. Any differences after the initial search in terms of inclusion/exclusion, or subsequent data extraction, were settled after discussion between the two reviewers and when necessary, a third reviewer.Data from included studies were also independently extracted by two reviewers and discrepancies were discussed with a third reviewer if necessary. Extracted information included: author, country, study design, sample size, mean age, inclusion criteria, exclusion criteria, type of procedure, follow-up duration, definition of PVPS, incidence of pain, incidence of PVPS and comments (any aspect of the study that required further commentary/explanation).metaprop_one command in Stata 15.1, to ensure results that were always within the 1%\u2013100% range [2 test assessed heterogeneity, with >50% indicating \"substantial\" heterogeneity. Egger\u2019s test was used to determine the potential effects of small study and publication bias.For statistical analysis, overall meta-analytic incidence was estimated using the user-written 0% range . A randoAll studies included for review were assessed using the Cochrane Risk of Bias Tool .All included studies were assessed using Cochrane\u2019s Risk of Bias Tool . Since tThe primary outcome measured was the incidence of post-vasectomy pain, presenting two weeks or later after the procedure. Pain was measured by patient-reported or investigator-administered questionnaires at the time of follow-up, with the majority utilising some form of graded pain scale. The follow-up durations were widely variable among the studies and ranged from 2 weeks to 10 years (median 1 year) for the scalpel and non-scalpel studies, and up to 37 years for one of the other/combined studies. Sample sizes ranged from 12 to 649 patients.p > 95% for overall estimates and for each subgroup) and there was significant evidence of small study effects or publication bias .The overall incidence of post-vasectomy pain across all studies was 15% (95% CI 9% to 25%), with a higher incidence of 24% (95% CI 15% to 36%) for traditional scalpel vasectomy compared to 7% (95% CI 4% to 13%) for NSV . Heterogp > 95% for overall estimates and for each subgroup). In contrast, scalpel vasectomy studies were not heterogeneous. There was significant evidence of small study effects or publication bias for the PVPS estimates .The range of PVPS across all studies was 0.4 to 20% . The incLiterature reports have estimated the incidence of post-vasectomy pain to range between 1% to 6% ,15,18,29Across studies, the incidences of pain following conventional incisional scalpel vasectomy and NSV ranged between 5% to 79% and 0.6% to 26%, respectively. When scalpel, NSV and other/combined studies were included, the overall range of post-vasectomy pain was 0.6% to 79%. These were wide ranges, which resulted in significant heterogeneity, and may have been attributable to the different measures and follow-up durations of the studies. However, there may have been other unmeasured factors that also contributed to these differences. It is noteworthy that the majority of the studies in the NSV group were prospective studies investigating non-scalpel vasectomy techniques, whereas many of the traditional scalpel studies were retrospective, with a focus on chronic pain and complications of vasectomy.This is the first meta-analysis of the incidence of post-vasectomy pain. We found that the incidence of pain was more than double that reported in previous narrative reviews ,7. We alThere is controversy in the literature regarding the definition of PVPS and subsequently, its reported incidence . DiffereApplication of the Cochrane Bias tool revealedThis review has several strengths and limitations. Particular strengths are that the literature was reviewed systematically, risk of bias assessment was used and we followed PRISMA guidelines. We also included all reports of pain, not just PVPS, increasing generalisability. We did not include studies that were not written in English, which may lead to bias. The reporting criteria for pain, and specifically PVPS were not uniformly applied across studies ,15,20,28The results of our systematic review and meta-analysis indicate that the incidence of post-vasectomy pain is higher than previously reported estimates. Following traditional scalpel vasectomy, the incidence of post-vasectomy pain is more than three-fold higher than after NSV. However, the incidence of PVPS is similar between the two techniques. Therefore, less invasive NSV should be considered as the preferred procedural method compared to the incisional scalpel approach to mitigate the complication of post-vasectomy pain."} +{"text": "COVID-19 is now impacting every country in Africa and healthcare workers (HCWs) across the continent remain susceptible to professional burnout. We designed a 43-question survey addressing multiple aspects of the COVID-19 pandemic. The survey was anonymous, distributed via email and phone messaging to 13 countries in Africa. We obtained 489 analyzable responses. 49% off HCWs reported a decrease in income, with the majority experiencing between 1\u201325% salary reduction. Sixty-six percent reported some access to personal protective equipment (PPE), 20% had no access to PPE and only 14% reported proper access. Strikingly, the percentage reporting never feeling depressed changed from 61% before the pandemic to 31% during the pandemic, with an increase in daily depression from 2% to 20%. We found no association between depression and change in income, household size, availability of PPE or lockdown. Safety concerns related to stigma from being HCWs affected 56% of respondents. To the Editor,africanhepbnetwork.org) from April to May 2020. We used risk ratio analysis to quantify the relationship between binary variables and Chi-square testing to quantify the statistical significance of these relationships. Tables (2 \u00d7 2) were constructed for survey questions of interest and the proportion (\u201crisk\u201d) of a particular survey response was calculated using these tables. Chi-square tests using a standard p-value of 0.05 were run using SAS. The study was approved by the ethics committee of Hennepin Healthcare. We obtained 489 analyzable responses out of a total of 535. Participants from six countries represented over 90% of our survey data, which limits generalizability across the continent. Remaining data included Kenya, Sierra Leone, Somalia, The Gambia, Rwanda, South Sudan, and Malawi. The median age of respondents was 30 years (IQR 26\u201336) and 73% identified as male. Most HCWs included in survey data were physicians (62%), followed by medical/clinical officers (8%), nurses (7%), students (6%) and pharmacists (6%). Seventy-two percent reported living under stay-at-home orders with some intercountry variation. Questions to address depression utilized the framework from the Patient Health Questionnaire (PHQ-2) asking survey respondents to answer questions about depressive symptoms currently and prior to the pandemic, which had a risk of availability bias. Strikingly, the percentage of HCWs reporting never feeling depressed was 61% prior to the pandemic on retrospective questioning as compared to 31% during the pandemic at the time of survey completion. Similarly, a higher percentage of respondents asserted daily depression symptoms during the pandemic (20%) in comparison to prior to the pandemic (2%). We found no association between self-reported depressive symptoms during the pandemic and change in income, household size, availability of PPE or lockdown as noted in Table COVID-19 is now impacting every country in Africa . Despite3"} +{"text": "Canine leishmaniosis (CanL) is a parasitic zoonotic disease, endemic in the Mediterranean basin including Spain. While knowledge about CanL, its management, treatment, prevention and control mounts, it remains unclear whether all clinical veterinarians follow the same international recommendations, such as those of the LeishVet group. This study was thus designed to assess recent trends in the clinical management of CanL in veterinary clinics across Spain through a questionnaire-based survey. Results were compared with those of a prior national multicenter questionnaire administered by our research team in 2005.A questionnaire consisting of 28 questions about CanL was developed using Google Forms and distributed by email to 1428 veterinary clinics in Spain. Questions were designed to obtain data on common clinical signs, techniques and complementary exams used to diagnose the disease, and on its monitoring, treatment and control measures. Data were collected in a database for statistical analysis.Completed questionnaires were returned by 295 clinics. Compared to the situation in 2005, responses indicate that clinical signs of CanL have not changed significantly, cutaneous lesions being still the most prevalent sign observed by practitioners. Quantitative serological techniques are considered an adequate approach to diagnosis, provided their results are supported by the findings of a thorough physical exam, as well as complementary tests . Treatment protocols and check-ups follow international recommendations. Finally, a multimodal approach is being endorsed to adequately control CanL including preventive measures such as annual serological check-ups and the combination of repellents and vaccines. Additionally, owners are being better informed about CanL by veterinarians, which translates to the improved control of this zoonosis.The clinical management of CanL has recently undergone significant changes owing to improvements in clinical knowledge of the disease, more unified international criteria, improved diagnostic techniques and their adequate interpretation, as well as a greater awareness of the disease transmitted to owners. Leishmania infantum, endemic in the Mediterranean basin including Spain. The disease is transmitted by female blood-feeding phlebotomine sand flies, and dogs (Canis familiaris) are both its natural host and the major reservoir of infection for humans and other animals . Further, 58.4\u201366.4% also reported they did not carry out PCR techniques on bone marrow or lymph node aspirates, while a blood sample was used by Among the serological techniques used, quantitative methods such as IFAT and ELISA were used always or frequently by 66.7% and 61.8%, respectively. However, responses indicated that qualitative methods such as a rapid test were used as the first diagnostic tool by 70.5%.c.94% of veterinarians, as well as serum electrophoretogram (89%). This was followed by urinalysis (58.9%) and UPC (61.2%) used frequently or always, although 9.4% and 11.7% had never used UPC and urianalysis, respectively, to assess CanL infection status. Additional proof such as an abdominal ultrasound was frequently used by 21% of veterinarians. Besides, 63.9% of veterinarians diagnosed CanL while conducting tests for other CVBDs described they used meglumine antimoniate as treatment for CanL. However, 31.9% and 23.6% stated they had never used the doses recommended by LeishVet of 50 mg/kg/BID/28 d and 100 mg/kg/SID/28 d. Miltefosine was used by around 80% of veterinarians , and usually at the dose recommended by the manufacturer. Allopurinol was used systemically practically by 100% of participants, the most common dose being 10 mg/kg BID. Immunomodulators such as domperidone were often or sometimes added by 30.6% and 34.3% of veterinarians, respectively; and systematically used by 20.9%. Regarding the use of Impromune\u00ae , 50.6% reported they had never used it compared to 4.2% and 13.6% who did so systematically or often, respectively. Finally, 95% of the survey respondents indicated they had never used autovaccine for the treatment of CanL ; (iv) use of mosquito nets (32%); (v) use of domperidone (47.1%); and (vi) vaccination against L. infantum (87.6%). Repellents most frequently recommended were: Seresto\u00ae , Advantix\u00ae and Scalibor\u00ae annual serological analysis (80.4%); (ii) use of repellents against the vector 96.7%); (iii) avoiding going outdoors during hours of greater %; (iii) When asked about vaccines, 87.6% recommended this practice. However, when we asked about the type of vaccine, 22.1% and 69.4% said they frequently or systematically used CanLeL. infantum before vaccination, 96.9% of the veterinarians said they obtained serology proof before primary vaccination (85.2% undertook rapid tests while 11.7% conducted a quantitative test (IFAT or ELISA), whereas this figure was 66.3% before re-vaccination .When we asked about the detection of antibodies against Veterinarians considered that vaccination was safe, as associated clinical signs were not usually observed. The most common clinical signs reported were pain and erythema at the point of inoculation.One of the last questions was whether the veterinarians explained to owners the zoonotic impacts of CanL. Replies were 73.4% always, 12.7% often, 8.7% sometimes and 5.2% rarely.Veterinarians surveyed mentioned they knew about the LeishVet research group (64.9%) compared to 35.1% who have never heard about LeishVet.via a veterinary laboratory, 8.9% via a veterinary journal, 7.1% via an internet search, 6.5% via their University and 5.9% via a colleague.Of those who were aware of LeishVet, 53.6% had heard of LeishVet in a conference about CanL, 17.8% \u03c72=\u200913.643, df\u2009=\u20094, P\u2009=\u20090.009).When comparing which veterinarians followed LeishVet guideline recommendations on diagnostic tools, treatment and monitoring of sick dogs, preventative measures, and vaccination, significant differences were only detected in the use of abdominal ultrasound as a recommendation (n\u2009=\u20091428), we consider that the number of veterinarians who answered was low. However, these results are more representative than those of our initial study in 2005 in which data were obtained from only 106 veterinarians across five Spanish provinces [In this survey, we collected information about the clinical management of CanL from 295 practitioners working in 43 Spanish provinces. Despite the large number of surveys sent (rovinces . Moreoverovinces and Le Rrovinces .Leishmania-endemic areas (e.g. taken there by their owners on holiday); (iii) other non-vector routes of transmission such as vertical, venereal, blood transfusion or dog-to-dog [Before asking about CanL, a question was included about other CVBD, and many of the veterinarians indicated they mainly detected CanL and ehrlichiosis. Nevertheless, other CVBD (e.g. dirofilariosis and piroplasmosis) were also reported. According to previous epidemiological studies, the presence of some vector-borne diseases is associated with geographical distribution \u201333. Indeg-to-dog \u201343 whichThe clinical manifestations of CanL vary from subclinical to severe disease. In the present study, weight loss, lymphadenomegaly and exfoliative dermatitis were frequently observed in agreement with the findings of other studies and surveys , 44\u201347. Regarding the diagnosis questions, the present survey differentiated between an etiological diagnosis (microscopy observation and/or PCR), serology and complementary tests. It should be noted that more than 35% of the practitioners surveyed mentioned they had never performed an etiological diagnosis, and if this was done, the most common method used was PCR on blood samples or cytology on lymph node aspirates. Cytology (5.3%) or PCR (3.9%) on bone marrow aspirates were infrequently used for an etiological diagnosis.Similar results have been obtained in questionnaire surveys by other authors , 46. HowQuantitative serological diagnosis is essential in the diagnosis and monitoring of CanL, and although many veterinarians used the IFAT technique (66.7%) and quantitative ELISA (51.8%) frequently or systematically, there were also many clinics that used rapid tests (70.5%) as the first diagnostic approach, in agreement with the results of similar surveys , 26, 63.c.80% also used electrophoretograms. These rates are significantly higher than those of our previous survey [via the LeishVet guidelines, IRIS guidelines and specialized conferences [According to the responses, almost all veterinarians used CBC and biochemical profiles to monitor infected dogs, and s survey , and inds survey , 21. Regs survey , 69. Anoferences .The LeishVet guidelines suggest that CanL therapy should be based on clinical staging , and recommended regimens are the combination of allopurinol and meglumine antimoniate or miltefosine in dogs with disease stage II or III , 21. TheWhen veterinarians were asked about regimens of n-methylglucamine antimoniate, they indicated the 100 mg/kg/SID/28 d dose was more used than 50 mg/kg/BID/28 d, although differences were not significant. This could be related to the fact that some owners prefer to inject their dogs once a day rather than twice.Most veterinarians stated they used allopurinol in combination with leishmanicide drugs, as allopurinol has been shown to prevent recurrence . LikewisL. infantum infection [Avoiding sand fly bites is one of the best ways to stop the spread of nfection , 81. Resnfection , 62, 82.nfection . Sixty-sc.70% [Lastly, another preventative measure recommended was vaccination. In the 2005 survey, 100% of veterinarians asked about vaccination answered that if there were a vaccine available, they would use it. In this survey, 87.6% replied they recommended vaccination as a preventative measure. Further, it is remarkable that the most common vaccine used by veterinarians surveyed is LetiFend\u00ae and not Canileish\u00ae. This lower use than initially expected could be because its percentage effectiveness is c.70% . In addic.70% \u201386.When asked about adverse reactions associated with vaccination, while most veterinarians consider them safe enough, adverse reactions to vaccination are mentioned in the vaccine\u02bcs Summary of Product Characteristics (SPC). In experimental trials by Oliva et al. and LemeVaccine manufacturers recommend performing a serological test before vaccination. In this survey almost all veterinarians mentioned they undertook a pre-primovaccination test. However, a high percentage of veterinarians stated they never performed any test before revaccination so it cannot be known if a dog has been infected during the inter-vaccination period. This test is strictly necessary since vaccines do not protect 100% . On the Current treatments and follow-up have allowed for a greater survival of dogs with CanL compared to the results of the 2005 survey , over 50L. infantum. Several studies have shown that Leishmania-competent vectors feed on cats naturally infected with L. infantum and through xenodiagnosis have confirmed that infected cats can transmit the infection to P. perniciosus and L. longipalpis [Another aspect to consider is that the dog is not the only reservoir capable of transmitting gipalpis \u201395. Howegipalpis , 96, 97.The LeishVet group is a scientific association focusing on offering a consensus statement on the clinical management of CanL and standardizing criteria for its diagnosis and treatment. The results of the present survey indicate that around 65% of the surveyed practitioners knew about LeishVet. This contradicts the data collected in the questionnaire of Le Rutte et al. , in whicDespite significant changes in the clinical management of CanL, its incidence has not decreased in recent years, due to factors such as improved clinical knowledge of the disease on the part of veterinarians, better available diagnostic techniques and their adequate interpretation, as well as a greater awareness of owners of control measures available (repellents and vaccines). We should thus continue to well inform practitioners so that they can improve health education among dog owners.Additional file 1: Text S1. Questionnaire that was distributed to veterinarians."} +{"text": "In December 2020, two COVID-19 vaccines (Pfizer-BioNTech and Moderna) were authorized for emergency use in the United States for the prevention of coronavirus disease 2019 (COVID-19).Data on COVID-19 vaccine doses administered in the United States are collected by vaccination providers and reported to CDC through multiple sources, including jurisdictions, pharmacies, and federal entities, who use various reporting methods including immunization information systems,During the first month of the U.S. COVID-19 vaccination program, 12,928,749 persons received at least 1 dose of COVID-19 vaccine . VaccinaDuring the first month of the U.S. COVID-19 vaccination program, 12,928,749 persons received \u22651 dose of COVID-19 vaccine, representing approximately 4% of the total U.S. population and 5% of the U.S. population aged \u226516 years.Among persons who received the first vaccine dose and had available data for the respective demographic characteristic variable, 63.0% were women, 55.0% were aged \u226550 years, and 60.4% were White, which likely reflects the demographic characteristics of the persons recommended to be vaccinated in the Phase 1a priority group among early vaccine recipients. Differences in how race and ethnicity data are collected and categorized, for example 14.4% of persons initiating vaccination reported as multiple or other race/ethnicity, also make comparisons difficult. The percentage of persons initiating vaccination who were Black appears lower relative to the percentage of persons who are Black among health care personnel and LTCF residents. Overall, 39.6% of persons who were vaccinated represented racial and ethnic minorities. Because persons who are Black, AI/AN, or Hispanic have been found to have more severe outcomes from COVID-19 than persons who are White, careful monitoring of vaccination by race/ethnicity is critical (The findings in this report are subject to at least three limitations. First, race/ethnicity was unknown for approximately one half of the population who initiated vaccination during the first month of the COVID-19 vaccination program in the United States. In addition, the proportion of persons with unknown race/ethnicity varied across jurisdictions, including six jurisdictions that reported no race/ethnicity data.Although these data reflect characteristics of persons initiating vaccination during the initial phase of the U.S. COVID-19 vaccination program and have several limitations, the findings underscore the need for more complete reporting of race and ethnicity data at the provider and jurisdictional levels to ensure rapid detection of and response to potential disparities in COVID-19 vaccine administration. Jurisdictions should monitor the demographic characteristics of vaccinated persons to identify emerging disparities. In addition, as vaccination expands to include additional groups, monitoring coverage by the Social Vulnerability Index, which uses U.S. Census Bureau variables to identify communities that might need support, will be useful to ensure equity and to identify communities where focused immunization efforts might be required.In December 2020, two COVID-19 vaccines were authorized for emergency use in the United States. The first groups prioritized for vaccination included health care personnel and long-term care facility residents.During the first month of the U.S. COVID-19 vaccination program, approximately 13,000,000 persons received \u22651 dose of vaccine. Among persons with demographic data, 63.0% were women, 55.0% were aged \u226550 years, and 60.4% were non-Hispanic White.As the vaccination program expands, it is critical to ensure efficient and equitable administration to persons in each successive vaccine priority category, especially those at highest risk for infection and severe health outcomes."} +{"text": "Limited research exists on the coronavirus disease 2019 (COVID-19) pandemic pertaining to otolaryngology\u2013head and neck surgery (OHNS). The present study seeks to understand the response of OHNS workflows in the context of policy changes and to contribute to developing preparatory guidelines for perioperative management in OHNS.Retrospective cohort study.Pediatric and general adult academic medical centers and a Comprehensive Cancer Center (CCC).OHNS cases from March 18 to April 8, 2020\u2014the 3 weeks immediately following the Ohio state-mandated suspension of all elective surgery on March 18, 2020\u2014were compared with a 2019 control data set.During this time, OHNS at the general adult and pediatric medical centers and CCC experienced 87.8%, 77.1%, and 32% decreases in surgical procedures as compared with 2019, respectively. Aerosol-generating procedures accounted for 86.8% of general adult cases, 92.4% of pediatric cases, and 62.0% of CCC cases. Preoperative COVID-19 testing occurred in 7.1% of general adult, 9% of pediatric, and 6.9% of CCC cases. The majority of procedures were tiers 3a and 3b per the Centers for Medicare & Medicaid Services. Aerosol-protective personal protective equipment (PPE) was worn in 28.6% of general adult, 90% of pediatric, and 15.5% of CCC cases.For OHNS, the majority of essential surgical cases remained high-risk aerosol-generating procedures. Preoperative COVID-19 testing and intraoperative PPE usage were initially inconsistent; systemwide guidelines were developed rapidly but lagged behind recommendations of the OHNS department and its academy. OHNS best practice standards are needed for preoperative COVID-19 status screening and PPE usage as we begin national reopening. In these cases, the virus can spread via inhalation or mucosal contact with infected respiratory secretions.5Coronavirus disease 2019 (COVID-19) is an acute infectious respiratory disease caused by the novel \u03b2-coronavirus SARS-CoV-2, or 2019 novel coronavirus (2019-nCoV). COVID-19 was recognized by the World Health Organization as a global pandemic on March 11, 2020.6 In the early stages of the pandemic, many health care workers, specifically non\u2013primary care or consulting service providers such as otolaryngologists, were getting infected at higher rates as compared with other specialties.8 As nearly half the patients with COVID-19 present as afebrile and asymptomatic or with generalizable symptoms of nasal congestion, sore throat, and hyposmia, screening for clinical signs of COVID-19 infection is not effective to guide perioperative precautions.10 The possibility for occult positivity among children and adults who raise low clinical suspicion puts health care workers at risk of infection. For these reasons, otolaryngology examinations and aerosol-generating procedures (AGPs) are considered high risk for exposure from aerosol and droplet contamination by asymptomatic carriers of disease.11 Any procedure involving the mucosa of the aerodigestive tract is considered an AGP.12 Researchers posit that following manipulation of any of these areas, viral particles may be airborne for \u22653 hours.13Otolaryngologists have been identified as a particularly vulnerable population among health care workers, as the majority of otolaryngologic procedures involve instrumentation of the upper aerodigestive tract.11 A high-risk procedure is defined as surgery involving the nasal mucosa or contact with oral, pharyngeal, and pulmonary secretions.11 Researchers assert that the risk of transmission is highest during intubation, tracheostomy, and open airway procedures, which most often involve positive-pressure ventilation.5 Regarding surgical management of otolaryngologic cases, it is recommended that patient COVID-19 status be determined ahead of surgery, that high-risk operations be performed in negative-pressure operating rooms with appropriate personal protective equipment (PPE) worn by all staff, and that only essential staff be in the operating room for intubation and extubation.11 The American Academy of Otolaryngology\u2013Head and Neck Surgery (AAO-HNS) released COVID-19-related resources, including patient screening algorithms and postexposure risk classifications.5 On March 18, 2020, the Centers for Medicare & Medicaid Services (CMS) released recommendations to delay all adult elective surgery and nonessential medical, surgical, and dental procedures during the COVID-19 response.14 CMS organized procedures into a series of tiers (1a-3b) meant to provide a framework for hospitals and clinicians to implement immediately during the COVID-19 response. The tier system takes into account patient risk factors; the availability of beds, staff, and PPE; and the urgency of the procedure.14Recent safety guidelines on the recommended management of otolaryngologic cases suggest that examinations and procedures be limited to patients with clear indication and need, performed by the most experienced personnel available, and deferred if nonessential .16 Additionally, the availability of timely COVID-19 testing has been limited due to regulatory processes and the time required to validate clinical tests, the initial lack of certified laboratories with polymerase chain reaction capabilities, and the shortage of chemicals and supplies.1719 These limitations have restricted feasibility of consistent COVID-19 testing in the preoperative setting. Moreover, false-negative rates for these tests have been reported up to 21.4%.2022 As national and local policies affecting the health care workforce change rapidly without consistent perioperative guidelines and adequate supplies, otolaryngologists are increasingly left to develop their own policies and practices to ensure surgeon and patient safety.While guidelines on the perioperative management of otolaryngology\u2013head and neck surgery (OHNS) cases are developing, there are several challenges to the implementation of such recommendations. One obstacle confronting otolaryngologists is the nationwide shortage of PPE necessary to perform surgical procedures.Limited research exists on the COVID-19 pandemic as it pertains to OHNS experiences, and urgent studies are required to characterize specialty response to the disease and streamline perioperative management. The purpose of the present study is to understand the impact of COVID-19 on perioperative workflows for OHNS at 2 tertiary academic medical centers in the context of national and state policy changes. The study focuses on the period since the Ohio state-mandated suspension of all elective surgery on March 18, 2020. This date was selected to capture the earliest phase of COVID-19 preparation in our state, prior to a peak in COVID-19 cases. This study examines institutional recommendations, department recommendations, society recommendations, and surgeon practices during this time. We seek to contribute to anticipatory efforts and preparatory guidelines for surgical planning and perioperative management in OHNS moving forward.The objectives of the present study are 2-fold. First, we seek to examine the change in OHNS case volume and nature during the COVID-19 pandemic in the context of policy changes. We compare COVID-19 pandemic case numbers and types directly with 2019 control data from the same date range, to understand the impact of the OHNS department response to policy changes. Second, we explore the spectrum of essential care that otolaryngologists are providing during COVID-19 in the adult and pediatric settings. We hypothesize that the majority of essential OHNS procedures performed remain high-risk despite efforts to minimize surgical volume. We also examine the prevalence of perioperative COVID-19 testing and aerosol-protective PPE selection among otolaryngologists in response to the pandemic and national policy changes.This was a retrospective cohort study of all OHNS cases performed from March 18 through April 8, 2020, at a pediatric academic medical center and an adult academic medical center, inclusive of a Comprehensive Cancer Center (CCC). The study was approved by the Institutional Review Board of the Ohio State University Wexner Medical Center. Data were extracted from the electronic medical record through chart review.International Classification of Disease, Tenth Revision code, and Current Procedural Terminology code), case airway management , and PPE utilized. A case was determined to be mucosal or an AGP if it involved the mucosa of the head and neck, specifically within the nose, sinuses, nasopharynx, oral cavity, oropharynx, larynx, trachea, mastoid or middle ear, and esophagus.11 Rationale for including the esophagus is that instrumentation of the upper airway is required to access.The following data points were extracted from electronic medical record chart review: COVID-19 history and symptoms, comorbid conditions , whether COVID-19 testing was performed, surgical procedure details , 142 pediatric cases (225 procedures), and 58 CCC adult cases (221 procedures). Canceled cases during this time frame included 258 general adult, 418 pediatric, and 46 CCC adult. Of the general adult procedures, 86.8% were AGPs; of pediatric procedures, 92.4%; of CCC adult procedures, 62.0% Table 1.Preoperative COVID-19 testing was performed in 7.1% of general adult cases, 9% of pediatric cases, and 6.9% of CCC cases. No tested patients were COVID-19 positive at any of the 3 sites. General adult procedures included 71.4% CMS tier 3a, 7.1% CMS tier 3b, 7.1% CMS tier 2, and 14.3% CMS tier 1. Pediatric procedures included 71.1% CMS tier 3a, 28.2% CMS tier 3b, 0.7% CMS tier 2, and no CMS tier 1. Procedures performed at the CCC included 81% CMS tier 3a, 15.5% CMS tier 3b, 1.7% CMS tier 2, and 1.7% CMS tier 1. All data are summarized in Of the general adult patients, 35.7% were female, and their mean age was 46.4 years. Of general adult patients included in this study, 50% had no comorbidities; 42.9% had heart disease; 35.7% were \u226559 years old; 28.6% were immunocompromised secondary to malignancy; 14.3% had pulmonary disease; and 7.1% had other comorbidities.Among pediatric patients, 52.5% were female, and their mean age was 3.4 years. Of the pediatric patients included in this study, 69.6% had no comorbidities; 34.1% were <1 year old; 8.9% had pulmonary disease; 5.9% had other comorbidities; 4.4% had heart disease; and 0.7% were immunocompromised.At the CCC, the patient population was 50% female and averaged 59.4 years of age. Of CCC patients included in this study, 87.0% were immunocompromised secondary to malignancy; 57.4% were \u226559 years old; 40.7% had heart disease; 20.3% had pulmonary disease; 13.0% had other comorbidities; and 13.0% had no comorbidities.All data are summarized in Of the general adult patients, 92.9% were intubated for procedures; 7.1% underwent jet ventilation; and no patients underwent ventilation via tracheostomy or bag mask ventilation as the sole form of perioperative ventilation. Of the pediatric patients, 47.2% were intubated for procedures; 35.2% underwent bag mask ventilation; 16.2% underwent spontaneous ventilation; and 1.4% were ventilated via tracheostomy. At the CCC, 96.6% of patients were intubated for procedures; 3.4% were ventilated via tracheostomy; and no patients underwent bag mask ventilation, spontaneous ventilation, or jet ventilation. Data on bag mask ventilation on emergence or during transportation were not available. Laryngeal mask airway was not used at any of the 3 sites. All data are summarized in In this study, \u201caerosol-protective PPE\u201d means N95 mask and full eye protection, as opposed to regular surgical mask and loupes, for instance. PPE data were collected from direct questioning of surgeons at all 3 sites or from standardized templates in brief operative notes. At the general adult medical center, surgeon response rates were 100%. At the pediatric medical center, there was an overall surgeon response rate of 70.4% (100 of 142) regarding PPE. At the CCC, surgeon response rates were 100%. PPE was worn by surgeons in 28.6% of general adult cases (33.3% of AGP cases), 90% of pediatric cases (89.4% of AGP cases), and 15.5% of CCC cases (15.8% of AGP cases). At the general adult medical center, PPE usage increased from 25% during week 1 (March 18-24) to 33.3% during week 2 (March 25-31); no cases were performed at the general adult medical center during week 3. PPE was used in 94.5% of pediatric cases (63.2% response rate) during week 1, 88.8% (94.7% response rate) during week 2, and 66.6% (52.9% response rate) during week 3. At the CCC, PPE usage increased from 14.8% during week 1 (March 18-24) to 23.1% during week 3 (April 1-8).Procedure volume and type were collected for March 18 to April 8, 2019, across all 3 sites. During this period, 313 general adult procedures were performed, of which 307 were AGPs (98.1%). A total of 983 pediatric procedures were performed, of which 925 were AGPs (94.1%), and 325 CCC adult procedures were completed, of which 236 were AGPs (72.6%). Comparison of 2019 and 2020 surgical volume by week across all 3 sites is summarized in Proper preparation and health system response in the setting of a pandemic involve the implementation of social precautions, medical resource conservation and reallocation, and development of standardized best practices responsive to the situation at hand. Also of importance is the protection of all members of the perioperative ecosystem from potential infection. As a result, many states have mandated the suspension of elective procedures for staff safety as well as resource preservation. Despite dramatic de-escalation of overall surgical volume, we identified that otolaryngologists remain at high risk when providing essential care during the COVID-19 pandemic due to the overwhelming proportion of AGPs forming their case load. The goal of the present study is to describe the responses of a health care system and OHNS departments to inform future preparedness efforts.During the COVID-19 pandemic, OHNS departments proactively responded to institutional, national, and state mandates by adjusting operative case volumes and types. In the 3 weeks immediately following the Ohio state-mandated suspension of all nonelective surgery on March 18, 2020, general adult, pediatric, and CCC medical centers experienced 87.8%, 77.1%, and 32% decreases in surgical volume as compared with 2019, respectively. As seen in 4 In this study, we defined AGP as any procedure involving mucosal surfaces of the nose, sinuses, nasopharynx, oral cavity, oropharynx, larynx, trachea, esophagus, and middle ear/mastoid. During March 18 to April 8, 2019, AGPs made up 98.1% of all general adult procedures, 94.1% of all pediatric procedures, and 72.6% of all CCC procedures. Although the number of overall OHNS procedures decreased during this time, the proportion of AGPs did not change significantly across these 3 medical centers. Of the general adult, pediatric, and CCC procedures performed during the COVID-19 pandemic and response, 86.8%, 92.4%, and 62.0% were AGPs, respectively , with the increasing availability of efficient COVID-19 tests, all 3 medical centers developed systemwide standardized protocols for universal preoperative COVID-19 testing of all scheduled essential cases.While AGPs continued, changes in perioperative management occurred in the immediate COVID-19 response period of March 18 to April 8, 2020. Preoperative COVID-19 testing took place in 7.1% (n = 1) of general adult cases, 9% (n = 13) of pediatric cases, and 6.9% (n = 4) of CCC cases Table 1.23 The AAO-HNS stated that, based on the experiences of OHNS departments during the SARS-1 pandemic in 2003, N95 masks are necessary for patients who are undergoing airway surgery and have suspected or confirmed COVID-19 positivity.24 While OHNS societal recommendations call for appropriate PPE for all staff during any potential AGP, independent of patient COVID-19 status,11 the operationalization of this recommendation was hindered in the earliest stages of the COVID-19 response period by a shortage of available supplies. Among cases for which PPE data were available at our institutions, aerosol-protective PPE was worn by surgeons in 28.6% of general adult cases, 90% of pediatric cases, and 15.5% of CCC cases. The low aerosol-protective PPE utilization numbers reflect significant nationwide concerns during the immediate COVID-19 response period regarding PPE availability resulting from the national shortage.16 Additionally, the establishment of recommendations regarding the use of aerosol-protective PPE selection is a multifactorial process. Differences among institutional N95 utilization reflect many contributing variables, including availability of aerosol-protective PPE, procedure type, hospital policy, and surgeon preference. The present study findings reaffirm the need for standardization of perioperative risk management protocols, including aerosol-protective PPE usage, among OHNS providers during the pandemic response period. Immediately following the present study period of data collection , with the increasing availability of PPE, OHNS departments across all 3 centers developed standardized protocols for universal use of aerosol-protective PPE for all AGPs, regardless of the patient\u2019s COVID-19 status. Data from this phase of the COVID-19 response are currently being analyzed and will be reported in a separate publication.Aerosol-protective PPE use during this time also reflects developing perioperative risk mitigation strategies during the immediate COVID-19 response period. We defined PPE as eye protection and an N95 mask. On March 23, 2020, the AAO-HNS recommended that otolaryngologists limit their practice to only urgent or emergent care, treat any patient with unknown COVID-19 status as COVID-19 positive, and have necessary PPE for all procedures.11 Jet ventilation airway management also poses a high risk of viral transmission, as the patients\u2019 airways are unobstructed without an endotracheal tube and aerosolized particles have fewer barriers to their spread in a positive pressure\u2013ventilated open airway. In the present study, 50 pediatric cases (35.2%) involved bag mask ventilation. This form of airway management also exposes surgeon and staff to aerosolized particles through the intermittent covering and uncovering of patient\u2019s upper aerodigestive tract throughout a procedure. Guidelines for preferred airway management for OHNS recommend closing circuits, minimizing bag mask ventilation, and avoiding awake intubation.5 Additionally, researchers discourage THRIVE, jet ventilation, or positive-pressure ventilation without a cuffed tracheal tube.5 Such guidelines on best practices for airway management must be made abundantly clear to OHNS and anesthesia departments early on during pandemic response efforts.Definitive airway management data during this time demonstrate a delay in the development of aerosolization risk-minimization strategies in the immediate COVID-19 response period. Across all 3 sites, intubation was performed in the majority of cases. One general adult case (7.1%) involved jet ventilation, and 23 pediatric cases (16.2%) involved spontaneous ventilation Table 1.Several barriers exist to the operationalization of standardized protocols for aerosol-protective PPE and COVID-19 testing in the setting of OHNS. From the experience of OHNS departments at pediatric and adult academic medical centers, we identified availability of rapid COVID-19 testing and adequate aerosol-protective PPE to be significant limitations to operationalizing society recommendations. Large tertiary academic medical centers specifically face a host of challenges to the rapid integration of standardized testing and equipment requirements. The larger the care center, the more that levels of leadership and policy changes are necessary for the operationalization of new initiatives. The integration of preoperative COVID-19 testing into perioperative workflows is therefore a complex issue with multiple contributing limiting factors. Standardized protocols recommended by OHNS societies should reflect the various stages of pandemic response. For example, as fast COVID-19 testing and PPE become more readily available through enhanced production and sterilization processes, preoperative COVID-19 testing and aerosol-protective PPE for all otolaryngologic procedures should become standards of practice. The present academic medical centers adopted these practices starting April 9, 2020, when testing and PPE were more readily available. Preoperative COVID-19 testing became a universal requirement for all OHNS cases, and recycling policies with check-in/check-out rules for N95 masks were instituted. The present study represents an opportunity for international OHNS leadership to better define barriers to operationalization of pandemic response measures and to improve the design of emergency preparedness and response planning.There are several limitations to the present study. PPE information that was not readily available in the electronic medical record was collected retrospectively by asking attending surgeons to recall their PPE usage for each case. Additionally, detailed intubation information across all 3 sites was not available to researchers . The academic centers studied herein also present unique geographic considerations. The centers are located directly across from the Batelle N95 sterilization processes. We are aware that ready access to these resources has afforded our institutions opportunities.The present study represents an analysis of OHNS experiences during the COVID-19 pandemic across pediatric and adult academic medical centers. In the present study, we examine perioperative management in the COVID-19 pandemic response immediately following the national mandate to suspend all elective cases. The pandemic response led to decreased case volume and a shift in the nature of surgery performed, from elective to nonelective/urgent cases. In the field of OHNS, the majority of essential surgical cases remained high-risk AGPs. During this initial response period, preoperative COVID-19 testing was performed and PPE worn by surgeons for a limited number of cases. These practices reflect a misalignment between OHNS society recommendations and the reality of hospital operations during a time of international COVID-19 testing and PPE shortages. OHNS departments responded by creating standardized protocols for universal COVID-19 testing and PPE usage. The findings of the present study highlight the need to create gold standards of preoperative screening for COVID-19 status, perioperative PPE usage, and airway management for OHNS procedures during pandemic response periods. Additionally, further definition is needed for essential versus nonessential cases as well as staffing requirements in the field of OHNS as the country transitions toward national reopening."} +{"text": "Several types of complications including constipation, fecal soiling,perianal excoriation, were reported among different types of surgery forHirschsprung\u2019s disease. To compare circular and oblique anastomoses following Soave\u2019s procedure forthe treatment of Hirschsprung\u2019s disease. Children who underwent Saove\u2019s pull through procedure with oblique andcircular anastomoses were included. Duration of the follow up was two yearsafter surgery. Postoperative complications, such as wound infection, wounddehiscence, peritonitis, fecal soiling, perianal excoriation, were recordedfor each patient. Thirty-eight children underwent oblique anastomoses. Circular ones were donefor 32 children. Perianal excoriation was seen in 57.89% and 46.87% ofchildren in oblique and circular group, respectively. Enterocolitis was morefrequent in circular (40.62%) than oblique (28.94%) group. Anastomoticstricture was more frequent in circular (15.62%) than oblique (7.89%). Perianal excoriation was the most common complication among patient in bothgroups. Oblique anastomoses had fewer complications than circular, and maybe appropriate option for patient who underwent Soave\u2019s procedure. Several type of procedures weredeveloped for the treatment of Hirschsprung\u2019s disease such as Duhamel, Soave\u2019s andposterior neurectomyThe aim of this study was to compare complications and outcome of patients whounderwent circular vs. oblique type of anastomoses for the patients withtransabdominal Soave\u2019s procedure.This retrospective analysis was carried out on the children who underwenttransabdominal Soave\u2019s procedure using circular or oblique anastomoses starting from2013 for five years. Duration of post-surgery follow up was two year. This study wasdone in Imam Khomeini Hospital of Ahvaz Jundishapur University of Medical Scienceswhich is the referral center for pediatric and neonatal surgery. This study wasapproved by research affair of Ahvaz Jundishapur University of Medical Sciences(Registration number=U-98011) and ethical committee of the Ahvaz JundishapurUniversity of Medical Sciences (IR-AJUMS-1398-059). Patient consent form was signedby parents.Patients with other perineal or gastrointestinal abnormality, total colonicaganglionosis, with poor follow up, and the ones who underwent laparotomy due toacute abdomen were excluded. Patients with body weight >=10 kg at time ofpull-through were included.Circular anastomosis was done routinely in Soave\u2019s procedure. In oblique typeanastomosis there was 1.5 cm distance between anterior aspects of anastomosis fromdentate line while 0.5 cm distance between posterior aspects of anastomosis anddentate line . In the Patients were categorized into circular and oblique type anastomosis. They werestudied in terms of complications such as enterocolitis, constipation, anastomoticstricture, wound infection, fecal incontinency, postoperative fistula, postoperativefever, urologic complication, pelvic infection, wound dehiscence, perianalexcoriation, postoperative leukocytosis and mortality.Duration of postoperative follow up was two years. In the current study 38 children underwent oblique anastomosis and 32 circularanastomoses. Duration of follow up was two years after surgery. Complications of twoanastomoses are shown in Perianal excoriation was the most common complication in both groups, although it wasmore frequent among cases in oblique group than in circular, but this difference wasnot statistically significant.There was no significant difference between two groups in terms of wound infection,length of hospital admission, bleeding during operation, and length of surgery. There wEarly complications of Soave\u2019s procedure include anastomotic leak, peritonitis,pelvic infection, septicemia, and late complications include strictures,enterocolitis, mucosal prolapse, incontinence and perianal excoriationPerianal excoriation was seen in 57.89% and 46.87% of patients with oblique andcircular anastomoses. In the study by Pratap et al.5 showed 12% single episode of enterocolitis afterpull-through for Hirschsprung. In the study by Langer11 four of 27 children showed enterocolitis followingSoave procedure. The rate of Hirschsprung associated enterocolitis after Soavepull-through was 10% in Prahita et alEnterocolitis was one of the most frequent complications after Soave\u2019s procedureregardless the type of anastomosis, which is similar to our previous studyPeritonitis was seen 3.12% and 2.63% of children in circular and oblique anastomosisrespectively. In the study by Matiolli et alConstipation was seen in 13.15% and 9.37% of the children in oblique and circulargroup respectively. Constipation was reported as a common complication followingpull-through in different studies. WidyasariFecal soiling was seen in 5.26% and 6.26% of children who underwent oblique andcircular anastomosis respectively. In the study by Onishi et alThree of 38 cases (7.89%) in oblique group developed anastomotic stricture. Paul etal,,Anastomotic leakage is one of the most serious complication following pull-throughsurgery. Rate of anastomotic leakage was reported between 1.3% and 8% in differentstudiesIn our study, urologic complication following pull-through was not seen in obliqueand circular type anastomoses, as well as mortality. In another study mortality wasseen in 5%As seen above, oblique anastomosis may reduce complication rates following Soave\u2019s.Similar findings were reported by Paul et alThe main limitations of this paper are it was done in a single center and withlimited sample size. Another multicentric study including a bigger number ofpatients is recommendedOblique anastomosis can reduce postoperative complications in contrast to circularanastomosis."} +{"text": "People with HIV (PWH) require lifelong treatment to achieve and maintain viral suppression. The modality and frequency of dosing for chronic medications may impact adherence, quality of life, and effectiveness. Preference data reported by potential users can inform which products in development may be preferred among people with various characteristics and social determinants of health, and can inform development for which product may have the largest health impact if it were available on the market. This study used the preference results from a latent class analysis to model uptake by product of a potential future market of HIV treatment options.Data from an online discrete choice survey among 829 US adult PWH about treatment modality , or yearly implants) were used in a latent class model to estimate partworth utility of each product in the 4 identified classes of participants. Probabilities of product uptake were estimated based on partworth utility-predicted product use among study participants and weighted for the US population of PWH. Characteristics considered for weighting were those previously reported to be associated with HIV care and treatment outcomes; they were included in weighting if available data from representative national data sources were found through a targeted literature search.Preference data weighted for the US population of PWH predicts that if all 5 products were available, they would be used in following proportions: 23.8% yearly implants, 23.7% weekly oral pills, 23.6% 6-month HCP-injections, 18.4% daily oral pills, and 10.5% 3-month HCP-injections. Despite oversampling PWH who were < 40 years old, people with a history of food insecurity, and transgender men (Table 1), the weighted model including the characteristics in Table 1 did not alter predicted uptake by more than 2% for any product compared with the unweighted data.Based on stated preference survey results, if 5 product delivery options for HIV treatment were available, product use would be broadly distributed, with weekly oral pills, yearly implant, and 6-month HCP-injections used in a similar proportion.Elizabeth S. Russell, PhD, Merck & Co. Inc: Employee Yan Song, PhD, Merck & Co., Inc.: Grant/Research Support Yipeng Gao, PhD, Merck and Co.: Grant/Research Support James Signorovitch, PhD, Merck & Co., Inc.: Grant/Research Support"} +{"text": "At a median (IQR) follow-up of 60 (24\u201384) months, no intraoperative urethral injury and only one noniatrogenic erosion occurred. The actuarial 12 mo and 5 yr overall erosion-free rates were 95.74% (95% CI: 84.04\u201398.92) and 91.76% (95% CI: 75.23\u201397.43), respectively. In preoperatively potent patients, the IIEF-5 score remained unchanged. The social continence (0\u20131 pads per day) rate was 82.98% (CI 95%: 68.83\u201391.10) at 12 mos and 76.81% (CI 95%: 60.56\u201387.04) at 5 yrs follow-up. Our technically refined approach to AUS implantation may help to avoid intraoperative urethral lesions and lower the risk of subsequent erosion without compromising sexual function in potent patients. Prospective and adequately powered studies are necessary to achieve more compelling evidence.The artificial urinary sphincter (AUS) implantation is an effective treatment of post-prostatectomy urinary incontinence (PPI). Still, it may result in troublesome complications such as intraoperative urethral lesion and postoperative erosion. Based on the multilayered structure of the tunica albuginea of the corpora cavernosa, we evaluated an alternative transalbugineal surgical technique of AUS cuff placement with the aim to decrease perioperative morbidity while preserving the integrity of the corpora cavernosa. A retrospective study was conducted in a tertiary referral center from September 2012 to October 2021, including 47 consecutive patients undergoing AUS (AMS800 Urinary incontinence is a common complication of prostatic surgery for benign and malignant prostatic disease , affecti\u00ae , which currently is the device with the longest follow-up and the largest amount of supporting literature ..25].Perioperative outcomes are summarized in At a median (IQR) follow-up of 60 (24\u201384) months, urethral erosion occurred in three patients who underwent device explantation and concomitant urethroplasty. An 82-year-old man suffering from post-radical prostatectomy incontinence, hypertension, and chronic heart ischemic disease, without previous irradiation, experienced a noniatrogenic urethral erosion at 24 mos follow-up. Another patient had urethral erosion five months after implantation due to catheterization in the emergency department because of a stroke episode. The third urethral erosion occurred in a 76-year-old man five years after AUS implantation and four weeks after a second radiotherapy treatment for local tumor recurrence. Overall, six patients (12.7%) presented with Clavien\u2013Dindo grade \u2265 2 late postoperative complications: specifically, three urethral erosions, one patient underwent cuff relocation eight years after AUS implantation, and two patients with initial failure that were surgically rescued with the addition of a second cuff seven and four years after AUS implantation, respectively. Consequently, only one event occurred according to our primary outcome definition, with a 12 mo and 5 yr event-free survival rate of 100% and 97.2% (95% CI: 81.87\u201399.61), respectively . All eroFunctional outcomes are summarized in The actuarial cure rate was 46.81% (95% CI: 32.17\u201360.16) at 12 mos and 44.21% (95% CI: 29.67\u201357.79) at 5 yrs follow-up .The social continence rate was 82.98% (95% CI: 68.83\u201391.10) at 12 mos and 76.81% (95% CI: 60.56\u201387.04) at 5 yrs follow-up . Most , may weaken the posterior urethral wall and also potentially lead to further urethral devascularization, predisposing to intraoperative urethral lesions and future erosions. Thus, we hypothesized that leaving an extra layer of tunica albuginea of the corpora cavernosa attached to the posterior bulbar urethral wall may be beneficial, also increasing the surgeon\u2019s awareness during the procedure. Furthermore, we implemented a standardized protocol of asepsis to avoid infection, including dual single-shot antibiotic prophylaxis, minimum air exposure time of the device components, limitation of the operating room traffic, use of double gloves by the members of the surgical team with frequent gloves changes, as well as rinsing of the perineal field and device components with antibiotic solution, use of medicated drapes to isolate the skin, meticulous hemostasis, and minimization of tissue dissection. All our erosions occurred in the ventrolateral position, in compliance with a previous report also evaluating the transcorporal approach . Even thThe overall reintervention rate of 19.1% also compares favorably with the literature: in a pooled analysis of 549 patients (10 studies) , the meaOver the past decade, different surgical approaches have been described for AUS implantation. Transcorporal AUS implantation has been described as a salvage surgical technique in patients with a damaged or frail urethra, with the aim to mitigate the risk of urethral erosion . The traThe data regarding sexual function in AUS patients are scarce in the literature, probably because of the high prevalence of erectile dysfunction secondary to prostatic surgery or radiation therapy. Few studies on transcorporal AUS cuff placement analyzed erectile function outcomes. Theoretically, the incision of the corpora cavernosa performed during the transcorporal approach may cause loss of erectile rigidity, although a few authors consider the transcorporal AUS implantation as a sexually safe procedure. Indeed, Brant and Martins argue that closure of the corporal body may prevent postoperative bleeding as well as loss of erectile rigidity . HoweverSerra et al. , in 2016Our refined implantation technique demonstrated to be an effective, safe, and reproducible procedure, with continence rates similar to those achieved when using a conventional approach ,38,39,40Urethral atrophy is a late complication, usually presumed when incontinence recurrence occurs during follow-up with a functioning sphincter . The comOur study has several strengths: the prospectively maintained database of consecutive patients, single-surgeon experience using a standardized technique, long-term follow-up, and use of multiple outcomes including pad weight that are recognized as the most accurate metrics for UI assessment . NeverthOur study is the first to describe the AUS transalbugineal placement, showing that it is a technically feasible, safe, and effective procedure. Our modified approach may lower the occurrence of urethral erosions and prosthetic infection by avoiding shallow urethral dissection and increasing surgeon awareness of often unrecognized urethral injuries. However, prospective and adequately powered, possibly multicenter, studies are necessary to achieve more compelling evidence."} +{"text": "Pharmacological secondary prevention in patients after an acute coronary syndrome (ACS) has contributed substantially to reductions in cardiovascular morbidity and mortality and, overall, has undergone important improvements in recent years. Nevertheless, there is still a considerable adherence gap and opportunity for improvement.To assess, in a cohort of patients who survived an ACS, adherence to commonly prescribed secondary prevention drugs, factors associated to adherence, and variations among health care delivery areas.We combined the medical and pharmacy databases from a regional public health service in Valencia, Spain, to construct a population-based cohort of patients discharged alive after an emergency admission for an ACS to any hospital of the Valencia Health Agency in 2008. We evaluated medication adherence by determining the proportion of days covered (PDC) for each therapeutic group in the 9 months following hospital discharge. Fully adherent patients were defined as those having enough treatment to cover 75% (PDC75) of the follow-up period.The study cohort consisted of 7,462 patients. PDC75 was reached by 69.9% of patients taking antiplatelet agents, 43.3% taking beta-blockers, 45.4% taking angiotensin antagonists, and 58.8% taking statins. Approximately 18% of patients did not reach PDC75 with any treatment, while 47.6% did so for 3 or more therapeutic groups. Lower adherence was found in diagnoses other than myocardial infarction. Other factors associated with nonadherence were older age, women, having copayment, foreign born, and most comorbidities . Health care delivery areas showed certain variability in their performance on these adherence measures that remained after the adjustment for covariates, although confidence intervals overlapped except between areas at the extremes.The proportion of fully adherent patients remains suboptimal, and important improvements are still possible in secondary prevention of ischemic heart disease. The combination of electronic health information systems may be very useful for monitoring adherence and evaluating the effectiveness of adherence and other quality improvement interventions."} +{"text": "Malassezia furfur (M. furfur) is a lipophilic, conditionally pathogenic yeast that mainly causes skin infections, but the reports of related invasive infections are increasing. The aim of this study is to provide clinical data to assist physicians in the management of patients with invasive infections caused by M. furfur.M. furfur in a hematopoietic stem cell transplant patient for aplastic anemia was reported. In addition, the literature on invasive infection by M. furfur published in PubMed and Web of Science in English until 31 July 2022 was reviewed.A case of pulmonary infection caused by M. furfur fungemia occurred in 79.1% of the 86 patients, and 45 of them were clearly obtained from catheter blood. Other patients developed catheter-related infections, pneumonia, peripheral thromboembolism, endocarditis, meningitis, peritonitis and disseminated infections. Thirty-eight preterm infants had underlying diseases such as very low birth weight and/or multiple organ hypoplasia. The remaining patients had compromised immunity or severe gastrointestinal diseases. 97.7% of patients underwent invasive procedures and 80.2% received total parenteral nutrition (TPN). Fever, thrombocytopenia and leukocytosis accounted for 55.8%, 38.4% and 24.4% of patients with M. furfur invasive infections, respectively. 69.8% of the patients received antifungal therapy, mainly amphotericin B (AmB) or azoles. Of 84 patients with indwelling catheters, 58.3% underwent the removal of catheters. TPN were discontinued in 30 of 69 patients. The all-cause mortality of 86 patients was 27.9%.Clinical data analysis of 86 patients (from 37 studies and our case) revealed that most of them were preterm (44.2%), followed by adults (31.4%). M. furfur can cause a variety of invasive infections. These patients mostly occur in premature infants, low immunity and severe gastrointestinal diseases. Indwelling catheters and TPN infusion are major risk factors. AmB, l-AmB and azoles are the most commonly used agents, and simultaneous removal of the catheter and termination of TPN infusion are important for the treatment of M. furfur invasive infections. Malassezia are yeast species belonging to Basidiomycota, Ustilaginomycotina, and class Malasseziomycetes, which are commonly found on the skin surfaces of human body and other warm-blooded animals is the most encountered species from bloodstream infections in the Malassezia genus, followed by M. pachydermatis and M. sympodialis, especially in premature neonates and immunocompromised hosts for aplastic anemia (AA). As the largest tertiary medical center in the region, M. furfur is isolated from respiratory specimen for the first time in our hospital, which arises our great interest. In order to improve the understanding of M. furfur among clinicians and laboratory personnel, this article reviews the cases of invasive infections caused by it. In addition, the latest advances in the pathogenesis, diagnosis and treatment of M. furfur invasive infections were summarized and discussed.Here, we describe a case of pulmonary infection caused by 9/L) and low hemoglobin (105 g/L). His C-reactive protein (CRP) was markedly elevated (52.1 mg/L), and the level of galactomannan was normal. Multi-row CT chest scan showed multiple patchy ground-glass shadows in the lower lobe of both lungs, considering the possibility of infectious lesions.A 17-year-old male underwent HSCT in our hematology department 7 months ago for AA. Immunosuppressant and hormone therapy were routinely administered after transplantation. The patient developed fever 3 days before admission, and a chest computed tomography (CT) examination at the local hospital indicated severe infection of both lungs. At admission, laboratory tests revealed a normal white blood cell count (WBC) but with a markedly reduced platelet count and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) with a 99.9% confidence level. Furthermore, the second-generation sequencing results of BALF showed that the number of sequences of M. furfur was as high as 5830.Blood cultures drawn from peripheral vein and central venous catheter (CVC) were negative. No abnormality was observed in sputum culture. Due to the aggravation of infection, bronchoscopy with bronchoalveolar lavage was performed. After centrifugation of bronchoalveolar lavage fluid (BALF), gram staining and Gomori methenamine silver (GMS) staining revealed some bottle-shaped and budding yeast cells for antifungal treatment. After 14 days of treatment, the patient had no fever, and the symptoms of chest distress and asthma were improved. The results of chest CT reexamination showed that the infection was better than before. The patient was transferred from the intensive care unit to the hematology department and continued oral VOR (200mg twice daily) for 14 days. At follow-up 3 months later, the patient continued to show clinical improvement with no signs of infection.Originally, Malassezia furfur\u2019, and article type choosed \u2018Case report\u2019. All relevant, available full texts published in English were extracted and the details of clinical data were retrieved.We conducted literature searches in PubMed and Web of Science, and the literature was published until 31 July 2022. The query was \u2018M. furfur invasive infections were shown in A total of 37 articles including 85 patients were obtained through retrieval Figure\u00a03M. furfur were reported.The majority of 86 patients in this study were reported from USA with 68 patients (80%), 6 from Belgium, 3 each from China and Portugal, 2 in Australia, and 1 each from France, UK, Italy and Japan. 79.1% of the patients were isolated from the blood culture, of which 45 were definitely drawn from catheter blood. In addition, mycotic thrombosis around the indwelling catheter tip or leading to catheter occlusion, peripheral thromboembolism, pneumonia, endocardial neoplasms, meningitis, peritonitis, pulmonary vasculitis, inflammation of alveolar, bronchial and bronchiolitis, and disseminated infections caused by 62.0% were male in 79 patients with known gender. The majority of 86 patients were premature neonates (44.2%), followed by adults older than 18 years (31.4%) and infants younger than 1 year (12.8%). Among 38 premature infants, 78.9% were less than 32 weeks of gestational age and all had very low birth weight . These premature infants were born with multiple organ hypoplasia. In addition, 12 patients had hematological malignancy and half of which underwent stem cell transplantation (SCT), and 11 patients had solid malignant tumor. Other patients reported in the literature presented with a variety of underlying diseases such as Crohn\u2019s disease, Hirschsprung disease, short bowel syndrome, bowel surgery, and HIV infection.97.7% of patients underwent invasive procedures, and predominantly with central venous access devices (CVADs). All 38 premature infants had CVADs and received total parenteral nutrition (TPN). Among the 48 patients of non-premature infants, 31 patients (64.6%) received intralipid emulsions, and 20 of them were statistically found to be caused by feeding intolerance, gastrointestinal disease and/or intestinal resection. The most common presentations were fever (55.8%), bradycardia (15.1%), apnea (14.0%), and respiratory distress (8.1%). Laboratory examination showed thrombocytopenia in 38.4% patients and leukocytosis in 24.4% patients. Leukopenia was found in 15 patients, and further analysis revealed that 6 of them were premature, and the other 9 had immunodeficiency disease or had received chemoradiotherapy or SCT for malignancy.M. furfur. All deaths had CVADs, and 20 patients received TPN infusion. There were 22 deaths that were treated with antifungal therapy, 17 of which were treated with AmB or l-AmB. Only 6 of these 22 patients had the catheter removed.69.8% of the patients received anti-microbial therapy. Of 84 patients with indwelling catheters, 58.3% underwent the removal of catheters. Parenteral lipid emulsions were discontinued in 30 of 69 patients. Amphotericin B (AmB) or liposomal-AmB (l-AmB) was the most commonly used antifungal agent, accounting for 76.7% (46/60). 17 patients were treated with azole drugs, most of which were combined with AmB or sequential therapy. Of the 26 patients who did not receive antifungal therapy, 80.8% had catheters removed and 34.6% terminated TPN. The all-cause mortality of 86 patients was 27.9%. Among the 24 patients who died, 15 cases of bacteremia, 5 of pneumonia and 4 of disseminated infection were caused by Candida and Aspergillus were generally considered to be the most common pathogens of invasive fungal disease (IFD). However, increasingly emerging opportunistic fungal infections were being recognized and might play an important role in IFD than candida spp. (1.4%) in patients with very complex underlying diseases or premature infants was approximately 6 cases per 100 000 persons per year, with a mortality of 27.6% . Recent e in IFD . The maj infants . The sevth death . Due to M. furfur infection in premature infants. M. furfur colonization has been reported to occur in rates of 36.8% to 64% of infants hospitalized in NICU . MALDI-TOF MS was increasingly used and provided faster and more reliable identification at the Malassezia species level and European Committee on Antimicrobial Susceptibility Testing (EUCAST) was not suitable for clusters . A varieclusters . HoweverMalassezia-related infections in humans and animals. Topical antifungal agents (mainly azoles) were adequate for the treatment of localized skin lesions, while systemic fluconazole (FLZ) or itraconazole (ITZ) for severe skin diseases. Intravenous AmB or its formulations was recommended for the treatment of systemic infections caused by M. furfur . All deaths had CVADs, and 20 patients received TPN infusion. As risk factors for M. furfur, demonstrating the epidemiology, risk factors, pathogenesis, diagnosis and treatment. M. furfur invasive infections generally present with nonspecific symptoms and occur in preterm infants or patients with immunocompromised or underlying gastrointestinal diseases. Indwelling catheter and TPN infusion are the main risk factors and involved in the pathogenesis of infection. Pathogenic diagnosis requires special attention to the lipophilic characteristics of M. furfur. Standard procedures for in vitro antimicrobial susceptibility testing of M. furfur needed to be further established. Currently, the most commonly used anti-M. furfur drugs in clinical practice are azoles and polyenes, especially AmB or l-AMB. Removal of the catheter and termination of TPN infusion are effective in the treatment of M. furfur invasive infections.In summary, we provide a case report and literature review on invasive infections caused by The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding authors.The studies involving human participants were reviewed and approved by Ethics Committee of Jiangsu Province Hospital. Written informed consent to participate in this study was provided by the participants\u2019 legal guardian/next of kin. Written informed consent was obtained from the minor(s)\u2019 legal guardian/next of kin for the publication of any potentially identifiable images or data included in this article.XZ designed the study, collected the data, and wrote the manuscript. FJ and FN contributed to the fungal identification and manuscript writing. FJ, YX, YL contributed to extract data from literature and drawing of figures and tables in the manuscript. WX and YL contributed to manuscript revisions. All authors contributed to the article and approved the submitted version."} +{"text": "We examined age, residence, education and wealth inequalities and their combinations on cervical precancer screening probabilities for women. We hypothesised that inequalities in screening favoured women who were older, lived in urban areas, were more educated and wealthier.Cross-sectional study using Population-Based HIV Impact Assessment data.Ethiopia, Malawi, Rwanda, Tanzania, Zambia and Zimbabwe. Differences in screening rates were analysed using multivariable logistic regressions, controlling for age, residence, education and wealth. Inequalities in screening probability were estimated using marginal effects models.Women aged 25\u201349 years, reporting screening.Self-reported screening rates, and their inequalities in percentage points, with differences of 20%+ defined\u2009as high inequality, 5%\u201320% as medium, 0%\u20135% as low.The sample size of participants ranged from 5882 in Ethiopia to 9186 in Tanzania. The screening rates were low in the surveyed countries, ranging from 3.5% (95% CI 3.1% to 4.0%) in Rwanda to 17.1% (95% CI 15.8% to 18.5%) and 17.4% (95% CI 16.1% to 18.8%) in Zambia and Zimbabwe. Inequalities in screening rates were low based on covariates. Combining the inequalities led to significant inequalities in screening probabilities between women living in rural areas aged 25\u201334 years, with a primary education level, from the lowest wealth quintile, and women living in urban areas aged 35\u201349 years, with the highest education level, from the highest wealth quintile, ranging from 4.4% in Rwanda to 44.6% in Zimbabwe.Cervical precancer screening rates were inequitable and low. No country surveyed achieved one-third of the WHO\u2019s target of screening 70% of eligible women by 2030. Combining inequalities led to high inequalities, preventing women who were younger, lived in rural areas, were uneducated, and from the lowest wealth quintile from screening. Governments should include and monitor equity in their cervical precancer screening programmes. Collinearity was present, especially between the wealth and residence variables which tend to correlate with each other, consistent with how the wealth variable is constructed.Recall bias was present as cervical precancer screening is self-reported.We did not control for the type of cervical precancer screening because we did not have information on the types of screening women received.Although all countries are affected by cervical cancer, its incidence and mortality are more than twice and three times as high in low-income and middle-income countries as in high-income countries.Cervical cancer is a disease of inequality. Its burden reflects inequalities in society, including those related to socioeconomic status. Inequality in health and healthcare is defined as the unequal distribution of health goods, services and outcomes across income or other measures of wealth. In contrast, equity is the lack of avoidable and remedial differences in the distribution of health goods and services or outcomes due to people\u2019s socioeconomic status in society.This is cross-sectional study of a secondary data analysis of available Population-Based HIV Impact Assessment (PHIA) data for countries that included cervical precancer screening variables. The countries and the years in which the PHIA surveys were conducted include Ethiopia (2017\u20132018),We restricted our analysis to women aged 25\u201349 years who responded to the cervical precancer questions. This is the group WHO recommends for cervical precancer screening\u2014ages 30\u201349 years for the general population and 25\u201349 years for women living with HIV\u2014including all gender diverse people at risk of cervical cancer.No patient involved.We assessed inequalities related to age, residence, education and wealth in cervical precancer screening according to women\u2019s self-reports. These dimensions of inequalities are familiar sources of disadvantage or discrimination.10.1136/bmjopen-2022-067948.supp1Supplementary dataWe assessed inequalities in self-reported cervical precancer screening in three steps. For each country, we first presented sample characteristics descriptively. Second, we determined the associations between screening for cervical precancer and each dimension of inequality, and analysed the differences using multivariable logistics regression, controlling for covariates. We corrected the p values of odds ratios (OR) for multiple hypothesis testing with sharpened q\u2019s. In step 3, we used marginal effects models to estimate the probabilities of reporting cervical precancer screening for each inequality alone and combined with other inequalities, holding the other inequalities constant at their mean values. We applied survey weights to account for complex survey design. Using jack-knife replicate weights, 95% CIs were estimated.The sample size of females aged 25\u201349 years ranged from 5882 in Ethiopia to 9186 in Tanzania. The median age and Interquartile ranges (IQRs) were 32 yearsMore urban residents than rural residents reported screening for cervical precancer in Ethiopia, Tanzania, Zambia and Zimbabwe before adjusting for covariates . In thesRespondents in Malawi, Rwanda, Zambia and Zimbabwe had education-related inequalities . EducatiThis study examined cervical precancer screening inequalities related to age, residence, education and wealth in six sub-Saharan African countries\u2014Ethiopia, Malawi, Rwanda, Tanzania, Zambia and Zimbabwe. We found that self-reported cervical precancer screening was low and inequitable. None of the countries reached one-third of 70% WHO cervical precancer screening target, 8\u2009years away from the 2030 deadline. Self-reported cervical precancer screening rates ranged from 3.5% (95% CI 3.1% to 4.0%) in Rwanda to 17.1% (95% CI 15.8% to 18.5%) in Zambia and Zimbabwe (17.4% (95% CI 16.1% to 18.8%). However, women who were older, residing in urban areas, who were more educated and in the highest wealth quintile reported a higher uptake of cervical precancer screening than women who were younger, living in rural areas, who were uneducated and in the lowest wealth quintile. Age-related inequalities were the most common\u2014observed in all six surveyed countries. Rural\u2013urban, education and wealth-related inequalities were each observed in four countries, ranging from low to moderate in magnitude. We also observed high inequalities from combinations of inequalities in age group, residence , education level and wealth in a few countries. These results have policy implications for the rapid scale-up of equitable life-saving cervical precancer screening.In this study, self-reported cervical precancer screening was lower than one-third of the WHO target of screening 70% of eligible women for cervical precancer by 2030, consistent with other studies conducted in the surveyed countries. Studies found that cervical precancer screening uptake ranged from 11% in Tanzania to 26.5% in Malawi, despite differences in methodologies used to estimate cervical precancer screening.Evidence supports the finding that inequalities in these underserved cervical precancer screening countries favoured women who were older, resided in urban areas, were more educated and in the highest wealth quintile than women who were younger, who lived in rural areas, were uneducated and in the lowest wealth quintile.This study also determined the magnitude of the socioeconomic inequalities in reported cervical precancer screening to aid policy-making in the prioritisation of inequalities to eliminate in the scale-up of cervical precancer screening. We found low to moderate age, rural\u2013urban, education and wealth-related inequalities in cervical precancer screening in the surveyed countries. Age-related inequalities were reported in all the surveyed countries and residence, education and wealth-related inequalities in four of the six surveyed countries. Although the inequalities were low to moderate, our study found that their combined effects on cervical precancer screening probabilities were substantial, especially in countries with higher rates of self-reported cervical precancer screening. The inequalities in cervical precancer screening rates between rural residents aged 25-34, with no education in the lowest wealth quintile, and their urban resident peers, with highest education in the highest wealth quintile, ranged from low inequalities in Rwanda, to moderate inequalities in Ethiopia and Tanzania to high inequalities in Malawi, Zambia and Zimbabwe. Comparing primary educated rural residents aged 25-35 years old, in the lowest wealth quintile with the highest educated urban residents aged 35\u201349 years old, in the highest wealth quintile showed substantial differences. Inequalities did not disappear between the 25\u201334 years old most affluent, highest educated, urban residents, and 35\u201349 years old, most affluent, highest educated, urban residents. These results suggest that inequalities persist. Minor or moderate inequalities compound into high inequalities, further leaving women behind in cervical precancer screening. Starting with age-related inequalities, eliminating socioeconomic inequalities should be prioritised in the urgent scale-up of cervical precancer screening interventions.Comparing the proportion of HIV-positive women in the sample and their reported cervical precancer screening showed cervical precancer screening gaps among HIV-positive women. In our study, the proportion of HIV-positive 25\u201349\u2009years old women ranged from 4.7% (95% CI 4.1% to 5.4%) in Rwanda to 22.6% (95% CI 21.6% to 23.7%) in Zimbabwe. By contrast, self-reported cervical precancer screening among this population ranged from 0.4% (95% CI 0.3% to 0.5%) in Rwanda to 5.4% (95% CI 4.7% to 6.1%) in Zambia. Not all HIV-positive women were screened for cervical precancer for several reasons. One reason may be the perception that linking women testing HIV-positive to HIV treatment eliminates the risk of cervical precancer for such women. A study in Zimbabwe found that many women living with HIV on ART screened positive for cervical precancer, despite the country attaining HIV treatment targets.Besides intensifying cervical precancer screening in HIV programmes, governments should fulfil their obligations to the right to sexual and reproductive health by increasing the accessibility of their health systems.This study has several limitations. Collinearity was present, especially between the wealth and residence variables which tend to correlate with each other, consistent with how the wealth variable is constructed. Recall bias was present as cervical precancer screening is self-reported. We did not control for the type of cervical precancer screening because we did not have information on the types of screening women received. Cervical precancer screening uptake may have worsened because of the COVID-19 pandemic. We did not determine if women had received two screenings by age 45 years as recommended by WHO, which could change our results. However, we used high-quality population-based data providing useful study findings to countries in sub-Saharan Africa.Cervical precancer screening in the surveyed countries was inequitable and low\u2014less than one-third of the WHO target to screen 70% of eligible women by 2030 for cervical precancerous lesions. Women who were younger, lived in rural areas, had no education and were from poor backgrounds were left behind in cervical precancer screening. Age-related inequalities were the most common type of inequalities observed. In combination, inequalities related to age, residence, education and wealth left further behind women who were younger, resided in rural areas, were uneducated, and poor. Focused and inclusive national cervical precancer interventions are required to scale-up equitable cervical precancer screening. Governments should include and monitor equity in their cervical precancer screening programmes. Research is needed to understand how to scale-up equitable cervical precancer screening in sub-Saharan Africa countries."} +{"text": "Despite being preventable, cervical cancer remains a lead killer among women in low\u2013middle income countries. The reasons are clear. Global inequity is reflected in limited health resources, such as limited access to HPV-vaccination, screening, and treatment, which are the key pillars for the elimination of cervical cancer. The high burden of HPV-coinfections in women living with HIV/AIDS challenges the use of sensitive HPV-testing, leading to massive over-treatment. As advised by the WHO, a \u201ctest-and-treat\u201d strategy could be optimal. In this study, 710 under-screened South African women, about half of them living with HIV, were tested for mRNA expression restricted to the predominant HPV types of cervical cancer. The effectiveness of a test-and-treat strategy to detect and manage severe cervical abnormalities (CIN3+) by increasing the number of HPV types included in the test was modeled. A combination of 6 types resulted in 25% positive tests requiring treatment, with the potential to prevent up to 85% of all cervical cancers.p < 0.01). The 6-type combination showed the best balance of sensitivity, specificity and treatment group size, and effectiveness to prevent cervical cancer. A 4-type combination could potentially prevent 77.6% (95% CI: 71.2\u201384.0) of cervical cancer burden by treating 20% and detecting 41.1% of CIN3 cases in the study group. Similarly, a 6-type combination , treating 25% and including 62% of CIN3 cases, might prevent 85% of cervical cancer cases (95% CI: 79.6\u201390.6) among HIV-positive and negative women. Conclusion: Employing mRNA HPV tests within a test-and-treat approach holds huge promise for targeted cervical cancer prevention in under-screened populations. Testing for mRNA of the 6 highest-risk HPV types in this population and treating them all is projected to effectively prevent progression from CIN3 to invasive cervical cancer while reducing overtreatment in resource-constrained settings.Background: Cervical cancer prevention in regions with limited access to screening and HPV vaccination necessitates innovative approaches. This study explored the potential of a test-and-treat strategy using mRNA HPV tests to impact cervical cancer prevention in a high-prevalence HIV population. Methods: A cervical screening study was conducted at three South African hospitals involving 710 under-screened, non-pregnant women (25 to 65 years) without known cervical diseases. Cytology, HPV testing, colposcopy, and biopsies were performed concurrently. Histopathologists determined final histological diagnoses based on biopsy and LLETZ histology. mRNA-HPV-genotyping for 3 to 8 high-risk types was performed on leftover liquid-based cytology material. The preventive potential of the test-and-treat approach was estimated based on published data, reporting the causative HPV types in cervical cancer tissue from South African women. Treatment was provided as needed. Results: The HPV positivity rate more than doubled from 3-type to 8-type mRNA combinations, significantly higher among HIV-positive women. CIN3+ prevalence among HIV-positive women (26.4%) was double that of HIV-negative women (12.9%) ( Today\u2019s extensive knowledge and applied scientific advancements regarding human papillomavirus (HPV) as the pivotal causative agent of cervical cancer offer profound opportunities for enhancing cervical cancer prevention strategies. Cervical cancer screening programs have evolved significantly since the 1960s, progressing from opportunistic to interval screening, and more recently adopting molecular tests targeting oncogenic HPV types. However, these advancements pose new challenges, including limited healthcare resources, how to manage screen positives and structural impediments best, selecting the appropriate test systems, determining HPV types to include, establishing screening intervals, devising follow-up and treatment algorithms, and defining target populations ,3,4.The World Health Organization (WHO) envisions cervical cancer as a preventable ailment. Their elimination strategy entails 90% vaccine uptake, and screening coverage of 70% using a high-performance HPV test followed by treating 90% of screen-positive women, to achieve the ambitious goal of an incidence rate of less than 4 per 100,000 women in all countries . ObviousThe South African Guidelines for Cervical Cancer Screening were introduced to provide asymptomatic women aged 30 years and older with three free Pap smears at 10-year intervals throughout their lifetime. However, the ambitious goal of screening at least 70% of women nationally within a decade of its initiation in 1999 has faced significant challenges, and a suboptimal coverage below 50% is reported ,9. The sThe school-based HPV vaccination initiative using a two-dose schedule (targeting HPV types 16 and 18) commenced in 2014, is focusing on girls aged nine and above and reporting first dose coverage of 69% in 2019 ,12,13. STo formulate an optimal screening and vaccination strategy to reduce the burden of cervical cancer in South Africa, accurate data on HPV prevalence and types, stratified by HIV status, are essential. The understanding that type-specific HPV prevalence varies by geography and cervical abnormalities, underscores the importance of determining which HPV types to include in primary and secondary prevention ,18,19. MThis study aimed to evaluate the efficacy of HPV mRNA tests in primary cervical cancer screening, assessing various combinations of mRNA HPV types to predict histologically proven CIN3+ lesions in women based on their HIV status. Additionally, the study modeled the effectiveness of a test-and-treat approach in detecting and managing CIN3+ lesions, with a focus on optimizing the selection of HPV types for screening. The analysis included an assessment of the number mRNA positive cases that needed to be treated in order to address one CIN3+ case as a measure of screening effectiveness. The choice of HPV types for the screening algorithm was informed by the HPV types identified in invasive cancer cases from the region. This approach aims to prevent the progression of CIN3 to invasive cervical cancer, particularly in resource-constrained settings where access to colposcopy, biopsy, and pathologists may be limited.Between December 2016 and March 2020, the multicentric DIAgnosis in Vaccine and Cervical Cancer Screen (DiaVACCS) screening trial, enrolled a total of 1104 women aged 25 to 65 years from general and anti-retroviral outpatient clinics at two hospitals in Pretoria and one hospital in Cape Town, South Africa . ParticiThe study protocol dictated that any woman presenting with abnormalities detected during visual inspection, HPV testing, or cytology tests would be scheduled for a follow-up colposcopy and biopsy. If a lesion was observed, targeted biopsies were taken, and in those without, at the 6 o\u2019clock and 12 o\u2019clock positions. All women with positive screening tests and a cohort of screen negatives were recalled for treatment or biopsy. In response to low attendance rates for this subsequent visit, the protocol was adjusted early in the study to conduct a colposcopy and biopsy during the initial visit. Treatment, when necessary, involved large loop excision of the transformation zone (LLETZ) and was performed as an outpatient procedure. Histology was eventually available for 91.7% (555/605) of screen-positive participants (605/1104) and 42.7% (213/499) of screen-negatives (499/1104) .The Bethesda system served as the framework for reporting and classifying cervical cytology. All cervical biopsies underwent routine microscopic examination and processing. An experienced pathologist following the World Health Organization\u2019s Cervical Intraepithelial Neoplasia (CIN) classification evaluateFor participants with undisclosed or unknown HIV status, a rapid HIV test Test, InTec PRODUCTS, INC., Xiamen, China) was administered. HIV-positive participants provided information on their antiretroviral (ARV) therapy usage. Age was categorized into two groups (25\u201339 years and 40\u201365 years), while HIV status, ARV therapy, and HPV mRNA types were classified into three categories . ARV status is only reported in Phase 1 baseline results, and not stratified within the data reported here.HPV mRNA E6/E7 expression was assessed using two commercially available tests: PreTect SEE-SA and PreTect HPV-Proofer\u20197 . These tests enabled the detection and direct genotyping of high-risk HPV genotypes, including four and seven genotypes. The qualitative assays employed real-time nucleic acid sequence-based amplification (NASBA) technology, targeting full-length E6/E7 transcripts and incorporating an intrinsic sample control for sample adequacy. The assay results were validated using positive and negative controls, which corresponded to viral mRNA targets for all specified types. Total nucleic acids were extracted from 1 mL of the residual frozen liquid-based cytology (LBC) material preserved in ThinPrep, using PreTect X, and subsequently analyzed for mRNA expression following the manufacturer\u2019s instructions.The results from the two mRNA assays were utilized to evaluate test performance for detecting CIN3 disease and cervical cancer. Various combinations of HPV types, ranging from three to eight , were assessed, and the subsequent impact on cervical cancer prevention was estimated based on the reported types detected in cervical cancer cases from the same hospitals . The prep-values < 0.05. Confidence intervals for percentages and proportions, such as test performance outcomes and the estimated number of prevented cervical cancers, were calculated as the value of the percentage or proportion plus or minus the standard error, multiplied by 1.96.The data were analyzed using Statistical Package for Social Sciences version 29.0. Armonk, NY, USA: IBM Corp. The significance of associations was assessed using the Chi-square test and the Chi-square test for trend, with a significance level set at ClinicalTrials.gov identification number NCT02956031). All study participants provided written informed consent prior to their inclusion in the study.The study protocol received approval from the Faculties of Health Sciences Research Ethics Committee at the University of Pretoria, Pretoria, under reference number 196/2014 and Stellenbosch University, reciprocal approval 2015, and was registered as a clinical trial (p < 0.01) , where the most common types were found to be HPV 16, 45, 58, and 18 in decrescent order . The HPV < 0.01) .Across all histological diagnoses, the prevalence of HPV on various mRNA combinations was higher among HIV-positive women compared to HIV-negative women but not statistically significant . Three op < 0.001). The sensitivity rates were 31.3% (95% CI: 26.6\u201336.0) and 66.6% (95% CI: 61.8\u201371.4) among HIV-negative women, and 46.1% (95% CI: 10.8\u201351.4) and 84.3% (95% CI: 80.4\u201388.2) among HIV-positive women, for three and eight mRNA types, respectively (Chi-square trend p < 0.001) (p < 0.001) compared to HIV-positive women .Sensitivity for CIN3+ disease showed a significant increase from screening with three mRNA types to eight mRNA types (Chi-square trend < 0.001) . Similarp = 0.92) to slightly above 50% for HIV-positive women (Chi-square trend p = 0.45), with no substantial difference across HIV status. The negative predictive value increased as the number of included mRNA types rose in the exposure categories, more for HIV-positive women compared to HIV-negative women of various mRNA combinations for CIN3+ varied from less than 50% in HIV-negative women (Chi-square trend < 0.01) .In a prior investigation by Rad et al., the distribution of HPV types was examined in 159 women with confirmed cervical cancer and known HIV status. This cohort was drawn from the same hospitals involved in our present study . LeveragIn elucidating the potential impact of mRNA HPV screening, it is crucial to acknowledge the nuanced distribution of HPV types in cervical intraepithelial neoplasia grade 3 (CIN3) as opposed to invasive cervical cancer. CIN3 may exhibit a diverse range of HPV types, reflecting the heterogeneity in precancerous lesions. In contrast, our analysis of cervical cancer cases in South Africa revealed a substantial concentration, with 85% attributed to HPV types 16, 18, 45, 31, 33, and 35. While CIN3 may manifest with various HPV types, our focus on the high-risk types prevalent in invasive cervical cancer underscores the targeted approach of our screening strategies. Detecting and treating these specific HPV types, as identified in local cervical cancer cases , are shoUsing a 4-type mRNA test for screening in a population with a high prevalence of CIN3 cases required treating 30% of HIV-positive and 10.7% of HIV-negative individuals . This approach identified 41.1% of prevalent CIN3 cases and had the potential to prevent 77.6% (95% CI: 71.2\u201384.0) of the associated cervical cancer burden.Similarly, a 6-type mRNA primary screening test necessitated treating nearly 25% of the study population, detecting 62% of all prevalent CIN3 cases, and exhibited the potential to prevent 85% of cervical cancers (95% CI: 79.6\u201390.6), with an even distribution among HIV-positive and HIV-negative women.The transition from conventional to liquid-based cytology and the introduction of HPV testing in South Africa\u2019s laboratories marks a significant step forward. Nevertheless, the prevalence of HPV in the general female population varies markedly, ranging from 76.1% overall to 37.1% for the types included in the Gardasil-9 vaccine . From thIn contrast to HPV DNA tests, which detect both transient and persistent infections, HPV mRNA tests primarily detect persistent infections where viral DNA may not be integrated into the host cell\u2019s DNA . The mRNOur study\u2019s findings demonstrated an expected increase in the HPV mRNA positivity rate by increasing number of types involved, with more than a two-fold rise observed from the 3-type (8.8%) to the 8-type (19.0%) mRNA test combination. This increase was consistently observed among HIV-positive women, who exhibited a positivity rate 2\u20133 times higher than that of HIV-negative women, in line with previous reports ,43,44. FThe sensitivity of HPV mRNA test combinations in detecting CIN3+ disease displayed a significant increase with the inclusion of additional HPV types, ranging from 46.1% (3 types) to 84.3% (8 types) among HIV-positive women. Interestingly, Snyman et al. reported CIN3+ sensitivity at 77.1% for the HPV DNA test including 13 types (Hybrid capture 2 (HC2), Qiagen, Germantown, MD, USA) among HIV-positive women, who also were recruited within the larger Diagnostic Vaccine and Cervical Cancer Screen (DiaVACCS) initiative . The senBased on the 12 cases in this study, the sensitivity for invasive carcinoma was 91.7% for tests including the top 5, 6, 7, and 8 types, emphasizing the robust performance of mRNA testing even using a limited number of types.The study findings accentuate the significant potential for cervical cancer prevention through targeted screening approaches using HPV mRNA tests. Both the 4-type and 6-type mRNA combinations demonstrated the capacity to prevent approximately 78% and 85% of cervical cancer cases, respectively, by identifying a substantial portion of CIN3 disease cases by treating 20% to 25% of the study population. These results highlight the effectiveness of such strategies, offering the potential for a substantial reduction in cervical cancer burden, particularly in high-risk populations. It is important to note that the composition of our study population, with a higher proportion of HIV-positive women, may impact the generalizability of these findings to the broader South African population.Our study population consisted of relatively unscreened women (without previous screening or with a lapse of five years since their last screen) but was enriched for cervical disease. Moreover, the proportion of HIV-positive women (47.5%) in our study was twice that of the general female population reported in 2020 (42). Despite these discrepancies, the positivity rate for any mRNA combination remained relatively low in this high-risk population, indicating the potential utility of mRNA tests in such settings.Demonstrably, HIV-positive women are diagnosed with ICC approximately 15 years earlier in life than HIV-negative women . Due to It is important to recognize that while treating CIN3 lesions is crucial for preventing cervical cancer, not all CIN3 lesions progress to invasive cancer ,48,49. CThis study demonstrated that by treating 25% of the study population screened with the 6-type mRNA test, the potential to prevent 85% of ICC cases is possible. The compelling results from our study underscore the critical importance of further research, including extensive controlled studies, to validate and refine the proposed \u201cscreen and treat\u201d strategy. Continued investigation and optimization of such approaches hold the potential to revolutionize cervical cancer prevention, particularly in regions grappling with limited resources.Our study benefited from a robust design, ensuring material representative for the South African general population . Most scThe most important limitation of the current study is that the study population does not totally reflect the South African screening population and should therefore not be extrapolated to the general population. Firstly, the HIV prevalence and ARV status do not represent that of the South African screening population, in that HIV-positive women are intentionally overrepresented to have a sufficiently large HIV population for accurate sub-group analysis. Secondly, the study group was enriched for cervical disease when all women without histology were excluded from the calculation of test performance to ensure accuracy.Among the 1001 women mRNA tested, 291 women were excluded because of a lack of histology, unknown HIV status, or having invalid test results. Among the 251 participants who were excluded due to the absence of histology, 96% were mRNA-negative and 97% had normal cytology, indicating the missed disease burden to be relatively low. Whilst the first publications from this cohort presented data for all women and used multiple imputations to estimate verification bias-adjusted histology values, in this analysis we elected to calculate test performance purely on known histology-proven disease status, to ensure robust test performance outcomes.In conclusion, the test-and-treat approach emerges as a promising strategy for cervical cancer prevention in resource-constrained settings. Our study sheds light on the effectiveness of this approach, particularly in the context of a population characterized by a high prevalence of HIV, HPV, and CIN3+. Utilizing either a 4-type or 6-type mRNA test in unscreened or under-screened women presents a compelling opportunity to detect the vast majority of women at high risk to prevent progression to invasive cervical cancer. We consider the calculated number of women needed to treat in order to detect and treat a single case of CIN3+ in this study as very acceptable. Treatment capacity should probably be used to determine the treatment threshold and in this case the number of HPV types in the test. Ultimately, through strategic implementation and continuous advancement, we can aspire to mitigate the impact of cervical cancer and improve the well-being of countless women in vulnerable populations."} +{"text": "BackgroundFalls are common among older adults, and they constitute a major public health\u00a0issue with high morbidity and mortality.AimThis study aimed to estimate the prevalence of falls and investigate the contributing risk factors among the elderly population in Tabuk City, Saudi Arabia.MethodsThis cross-sectional study recruited a random representative sample of the elderly aged \u2265 60 years. We collected data by interviewing the participants using a structured, Arabic-language questionnaire. It included personal information, a history of falls in the past three and 12 months, comorbidities, and environmental factors. The main outcome was a history of falls in the preceding year. Multivariable logistic regression was used to evaluate the association between potential risk factors and falls.ResultsThe study included 296 participants. Most participants were female (66.9%), aged 60-69 years (68.2%), and married (68.9%). The self-reported prevalence of falls over the preceding 12 months was 25.3% : 20.6-30.5). Older people with depressive symptoms had significantly increased vulnerability to falls (adjusted odds ratio (AOR): 0.452, 95% CI: 0.239-0.854). Environmental factors were associated with a 1.799 times (95% CI: 1.041-3.109) increased likelihood of fall, and gait impairment was the strongest risk factor .ConclusionsFalls are common among the elderly population in Tabuk City, Saudi Arabia. Gait impairment, the presence of depressive symptoms, and environmental hazards were substantially associated with falls, suggesting that most falls are preventable. The World Health Organization (WHO) identified a fall as an event enforcing a person to rest inadvertently on the ground, floor, or other lower level . Falls aAn increasing interest has recently been noticed regarding the problem of elderly falls and their consequences because of the increasing life expectancy and, subsequently, the proportion of the elderly population .Several studies from developed countries have explored the burden of falls among the elderly -12. NeveOlder individuals with a lack of physical activity and the presence of comorbidities such as hypertension and diabetes mellitus are more vulnerable to falls . PolyphaThe reported burden and risk factors of falls among the elderly exhibit a wide variation, which is attributed to the differences in environmental factors and population-based characteristics . UnfortuFalls and their consequent complications pose a major burden for the elderly, their caregivers, and the healthcare system . DetermiTherefore, this study aimed to estimate the prevalence of self-reported falls and explore the related risk factors among the elderly population in Tabuk City, Saudi Arabia.Study design, setting, and durationThis is a cross-sectional study conducted at ten primary healthcare centers in Tabuk City, Saudi Arabia, from the start of June 2023 to the end of August 2023.Ethical considerationsThis study obtained ethical approval from the Tabuk Institutional Review Board . We asked the willing subjects to sign an informed written consent form before participating in the study. We informed the participants about the study objectives and methodology and that we would use their anonymized data only for research purposes while maintaining their confidentiality.Sample size calculation and sampling techniquehttp://www.raosoft.com/samplesize.html) using a margin of error of 5%, a confidence interval of 95%, and an average expected prevalence of nearly 26.5% [The sample size was estimated with an online sample size calculator \". The last part is the 10-item Missouri Alliance for Home Care (MAHC-10) tool. It is a standardized, validated tool that explores 10 variables of fall risk. These include advanced age (>65 years), comorbidities of more than three medical diagnoses, history of falls within the last three months, incontinence, impaired vision, impaired functional mobility, polypharmacy, which refers to using four or more concurrent medications, cognitive impairment, chronic pain affecting the level of function , and environmental hazards such as poor illumination, equipment tubing, inappropriate footwear, pets, hard-to-reach items, uneven or cluttered floor surfaces, and outdoor entry and exit points. Each item in this tool received a score of one if present and zero if absent. A total score of \u22654 indicated an increased risk of falling ,24. We pStatistical analysisAll data were tabulated and analyzed by the statistical package for the social sciences software program, IBM\u00a0SPSSStatistics for Windows, Version 26.0 . We presented categorical data as frequencies and percentages. We performed a univariate regression analysis to determine the risk factors significantly associated with falls in the preceding 12 months. This was followed by a multivariable regression analysis to determine a model of risk factors associated with falls in the preceding 12 months. Each variable that showed a p-value of 0.1 or less in the univariate analysis was included as an independent variable. Crude and adjusted odds ratios (OR) with 95% confidence intervals (CI) were presented. A p-value <0.05 was considered statistically significant.The study included 296 participants. Approximately two-thirds were females (66.9%), aged 60-69 years old (68.2%), and married (68.9%). Most (93.9%) of them were Saudi. More than half (58.8%) were uneducated, and 40.2% were educated to the pre-university level. The monthly income varied between less than 5000 (68.9%) and more than 10000 (7.4%) Saudi Arabian Riyal (SAR) , visual impairment (73.3%), memory loss (53.0%), urinary incontinence (57.8%), hypertension (67.2%), diabetes mellitus (DM) (66.6%), hyperlipidemia (50.7%), arthritis (70.6%), and transient ischemic attacks (31.4%). Furthermore, nearly one-third (30.7%) showed depressive symptoms, 37.2% of them reported using four or more concurrent drugs (polypharmacy), and 11.5% reported using sleeping pills. The commonly described environmental factors related to falls were inappropriate footwear (95.6%) and high door sills (71.3%), followed by uneven floor surfaces (45.9%) while the prevalence over the preceding 12 months was 25.3% (95% CI: 20.6-30.5%). Most falls over the last 12 months occurred indoors (73.3%), with the washroom (47.3%) being the most reported place. Regarding outdoor falls, streets (35.0%) followed by mosques (30.0%) were the most frequent locations of falls. Furthermore, the calculated risk score of falls revealed that a high percentage (72.3%) of the participants are at risk of falling , polypharmacy , memory loss , the presence of environmental factors , and having risk of fall . Environmental factors were associated with 1.799 times (95% CI: 1.041-3.109) increased likelihood of fall. Gait impairment was the strongest risk factor . The recorded prevalence rate is comparable to the reported WHO frequencies of falls among people aged 65 and older each year . PreviouThe observed disparity in the prevalence rates reported from different regions in Saudi Arabia might be attributed to differences in lifestyle or environmental conditions . DiffereFalls among older adults result from complex individual factors and environmental circumstances. Generally, the prevalence of falls increases with the number of risk factors. The prevalence surges up to 78% among people with numerous risk factors .In the current study, elderly individuals with gait impairment showed a significantly higher risk of falls . This finding agrees with Osoba et al. , who repThe present study also revealed that older people with depressive symptoms had significantly increased vulnerability to falls . In this context, several studies have reported that depressive symptoms characterized by sadness, loss of interest in activities, and reduced energy are consistently associated with the risk of falls and injuries among the elderly . Hence, Home settings and neighborhood environments have an impact on the individual health and well-being of older adults. In this study, the falls were significantly linked to a variety of environmental hazards, such as inappropriate footwear, poor lighting, clutter, uneven floors, and obstacles. This agrees with earlier reports ,37 showiBased on the calculated MAHC-10 fall risk assessment score, this study showed that participants at risk of falls had higher odds of falls in comparison to those who were not at risk. However, this relationship was not statistically significant in the multivariable regression model. Identification of older adults at risk of first or subsequent falls by family physicians or aged care providers certainly helps prevent such adverse events and the associated negative effects on health and quality of life .Strengths and limitationsThis study simultaneously investigated many intrinsic and extrinsic risk factors for falls, which may direct fall prevention programs. However, the cross-sectional survey design has an inherent recall bias and cannot establish causal relationships or analyze the impact of the identified risk factors on falls over time.The findings of the present study indicated that the prevalence of falls among the elderly residents of Tabuk City in the preceding year was 25.3%. The elderly at increased risk of falls include those with gait impairment, depressive symptoms, or who live in an inappropriate environmental condition, such as unfitting footwear, poor lighting, clutter, and uneven floors. Based on the identified risk factors, tailored interventions, including exercise, management of depression, and environmental monitoring, can effectively reduce the frequency of falls in high-risk communities. Primary healthcare providers play an important role in the prevention of falls among the elderly. Caregivers, along with the elderly, should be given more detailed health education related to fall prevention."} +{"text": "As upper tract urothelial carcinoma is a relatively rare disease, much of clinical practice has been extrapolated from urothelial carcinoma data. Here we summarize data, current guidelines, and future directions in the management of upper tract urothelial carcinoma with a particular focus on systemic therapy.Upper tract urothelial carcinoma comprises 5\u201310% of all urothelial carcinoma cases. This disease tends to have a more aggressive course than its lower urinary tract counterpart, with 60% of patients presenting with invasive disease and 30% of patients presenting with metastatic disease at diagnosis. The diagnostic workup of UTUC involves imaging with CT urogram, urine cytology, and direct visualization and biopsy of suspected lesions via ureteroscopy. Standard treatment of high-grade UTUC involves radical nephroureterectomy (RNU) and excision of the ipsilateral bladder cuff. Both the NCCN and EAU Guidelines include neoadjuvant chemotherapy as a treatment option for select patients with UTUC; however, there are no strict guidelines. Much of the rationale for neoadjuvant chemotherapy is based on extrapolation from data from muscle-invasive bladder cancer, which has demonstrated a 5-year OS benefit of 5\u20138%. Retrospective studies evaluating the use of NACT in urothelial carcinoma have yielded pathologic objective response rates of 48% in UTUC cohorts. The randomized Phase III POUT study noted a DFS advantage with adjuvant platinum-based chemotherapy, compared with surveillance in UTUC, of 70% vs. 51% at 2 years. Though not the standard of care, multiple studies have explored the use of perioperative immunotherapy or chemoimmunotherapy in the management of invasive urothelial carcinoma. The PURE-02 study explored the use of neoadjuvant pembrolizumab in patients with high-risk UTUC. A small study of 10 patients, it showed no significant signals of activity with neoadjuvant pembrolizumab. Another Phase II study of neoadjuvant ipilimumab and nivolumab in cisplatin-ineligible UTUC yielded more promising findings, with 3/9 patients attaining a pathologic CR and the remaining six pathologically downstaged. The ABACUS trial found a 31% pathologic complete response rate amongst cisplatin-ineligible MIBC patients treated with neoadjuvant atezolizumab. The use of adjuvant immunotherapy has been explored over three phase III trials. The CheckMate-274 trial found a DFS benefit with the addition of one year of adjuvant nivolumab in patients with high-risk urothelial carcinoma. The IMvigor-010 study of adjuvant atezolizumab was a negative study. The AMBASSADOR trial of adjuvant pembrolizumab is pending results. With the FDA approval of erdafitinib in metastatic urothelial carcinoma, similar targets have been explored for use in perioperative use in invasive urothelial carcinoma, as with adjuvant infigratinib in the PROOF-302 trial. As the treatment paradigm for urothelial carcinoma evolves, further prospective studies are needed to expand the perioperative treatment landscape of UTUC. Urothelial cell carcinoma (UCC), also known as transitional cell carcinoma, is the predominant histological subtype of urinary tract cancer. It is the sixth most common tumor entity in developed countries . The majAlthough UTUC constitutes a minority of urothelial carcinomas, it is of particular interest due to its relatively aggressive biological behavior and higher mortality rate compared to other genitourinary tract malignancies. UTUC has a tendency to present at an advanced stage; at the time of diagnosis, around 60% of patients have invasive disease, and 30% present with metastatic disease . This isGlobal incidence of UTUC exhibits geographic variation. Western countries report a rate of 1\u20132 cases per 100,000 individuals annually, whereas in certain regions, such as Taiwan, UTUC comprises nearly a quarter of all urothelial carcinomas due to specific endemic factors . SeveralDespite advancements in diagnostic methodologies and therapeutic strategies, there has been limited improvement in the 5-year survival rate of UTUC over the preceding decades, underscoring the critical necessity for ongoing research. The advent of genomic sequencing techniques has facilitated the identification of a significant amount of genetic and epigenetic alterations within UTUC, thus providing a richer understanding of its pathogenesis and revealing novel potential therapeutic targets. The following sections will delve deeper into the intricacies of urothelial carcinoma of the upper urinary tract, shedding light on its diagnostic modalities, therapeutic approaches, and future directions in research. By doing so, we hope to provide a comprehensive understanding that may guide healthcare providers in delivering optimal care and contribute to the ongoing quest to improve outcomes for patients afflicted with UTUC.Upper tract urothelial carcinoma (UTUC) often elicits diagnostic consideration upon the manifestation of clinical symptoms such as hematuria and flank pain. Hematuria is particularly notable, present in an estimated 75% of UTUC cases . Other cParallel to imaging, urine cytology adds another dimension to the diagnostic paradigm. Despite its high specificity of 94\u201398%, the sensitivity of cytology is quite variable, particularly for low-grade tumors, with sensitivity rates of 20\u201350%, increasing to 60\u201380% for high-grade tumors . In an aThe diagnostic paradigm for UTUC also incorporates the direct visualization and biopsy of suspected lesions via ureteroscopy. Biopsies in UTUC can be challenging due to difficulties accessing the upper urinary tract anatomy. Reported rates of nondiagnostic biopsies range from 10\u201320% . SamplinThe diagnosis of UTUC constitutes a complex, multifaceted process, encompassing aspects of clinical symptomatology, imaging, urine cytology, and endoscopic biopsy. Nonetheless, inherent limitations within each of these modalities underscore the imperative for continued advancement in diagnostic technologies and strategies. As research progresses, the future may see enhancements in imaging techniques, the introduction of novel biomarkers, and potentially novel diagnostic methodologies, all culminating in earlier and more accurate diagnoses of UTUC.Treatment of high-grade upper tract urothelial carcinoma (UTUC) with radical nephroureterectomy (RNU) and excision of the ipsilateral bladder cuff is standard for tumors of the renal pelvis. Endoscopic ablation and segmental ureterectomy can be considered for low-risk tumors, as is further discussed in subsequent chapters of this manuscript ,16. Natin = 811 patients) demonstrated an 11% pathologic complete response rate (defined as \u2264ypT0N0M0) and 43% partial response rate (defined as \u2264ypT1N0M0). Pathologic downstaging from the clinical tumor stage occurred in 33% across six studies. In comparative studies, NAC was associated with improved overall survival (OS) and cancer-specific survival (CSS) versus radical nephroureterectomy (RNU) alone. For AC, pooled analysis of 14 studies (n = 7983 patients) revealed an OS benefit , while 18 studies (n = 5659 patients) showed improved CSS and 4 studies (n = 602 patients) demonstrated superior disease-free survival with AC compared to RNU alone [Unfortunately, the accurate staging of UTUC is much more challenging than in bladder cancer given the limitations and feasibility of biopsies ,22,23. CNU alone . OverallNU alone ,30,31,32Neoadjuvant cisplatin-based therapy is the clinicians\u2019 preference, rather than adjuvant platinum-based therapy, given the possible decline in renal function post-RNU which may render a patient ineligible for cisplatin-based therapy. One prospective study of neoadjuvant split-dose gemcitabine and cisplatin of 53 patients showed a CR of 19%, downstaging to ypT1 or less in 60% of patients, 2-year PFS of 76% . AdjuvanAdibi et al. conducted a retrospective study between 2004\u20132017 of 126 patients with high-risk UTUC who were treated with NAC prior to RNU. NAC regimens did differ, as 62 received ddMVAC , 28 received cisplatin with or without gemcitabine, and 19 were treated with gemcitabine, paclitaxel, and doxorubicin. Seventeen patients received multiple different regimens or non-platinum-based therapy due to decreased renal function. Median OS was 107 months (95% CI 86\u2013125), 14.3% achieved a pathologic complete response, while 60% were downstaged to ypT0-1N0. Estimated 5- and 10-year DSS rates were 89.8% (95% CI 0.836\u20130.965) and 80.6% (95% CI 0.691\u20130.94), respectively. Five- and 10-year metastasis free survival rates were 81% (95% CI 74\u201388.6) and 75.4% (95% CI 65.3\u201387), respectively, and 5- and 10-year OS were 73.7% (95% CI 65.3\u201383.1) and 35.9% (95% CI 23.9\u201354). Median time to recurrence was 15.5 months, with 24 metastatic recurrences documented, 50% to retroperitoneal, pelvic, of supraclavicular lymph nodes and 25% in the lung. This study supported the benefit of NAC prior to RNU with a durable 5-and 10-year OS and DSS . This stThere is limited data on the use of perioperative immunotherapy in the management of UTUC. The PURE-02 study was a feasibility study evaluating the use of three cycles of neoadjuvant pembrolizumab in patients with high-risk UTUC . DespiteGao et al. further evaluated the efficacy of PD-L1 plus CTLA-4 blockade in the neo-adjuvant setting. In this open-label, single-arm pilot study, 28 cisplatin-ineligible patients with high-risk muscle-invasive urothelial carcinoma received neoadjuvant durvalumab plus tremelimumab every 4 weeks for two doses. The pathologic complete response (pCR) rate was 38% among those completing cystectomy. In 12 patients with T3/T4 disease, the pCR rate was 42% (5/12 patients). The overall downstaging rate to \u2264pT1N0 was 58% . At a median follow-up of 19 months, the 1-year overall survival rate was 89% (95% CI 70\u201396%) and 1-year relapse-free survival rate was 83% (95% CI 61\u201393%). Grade \u2265 3 treatment-related adverse events occurred in 21% (6/28 patients) of patients. High baseline tertiary lymphoid structure density was significantly associated with improved survival. In summap= 0.24) [Several Phase III studies have explored the use of adjuvant immunotherapy in patients with high-risk muscle-invasive urothelial carcinoma. The CheckMate-274 trial, which randomized patients to receive one-year of adjuvant nivolumab or placebo, found a disease-free survival benefit with the addition of adjuvant nivolumab; overall survival results are not mature. Of the 709 patients in the intention-to-treat population, 149 had upper tract disease . On subgp= 0.24) . On the p= 0.24) .In recent years, advancements in the genomic understanding of UTUC have delineated the potential therapeutic promise of the Fibroblast Growth Factor Receptor (FGFR) pathway. Comprising a group of receptor tyrosine kinases, FGFR is instrumental in the regulation of critical cellular processes, including proliferation, differentiation, and survival. The dysregulation of FGFR signaling pathways, predominantly due to gene mutations or fusions, is implicated in the tumorigenesis of a wide range of cancers, UTUC included. The prevalence of FGFR mutations or fusions in UTUC is relatively high, with genetic alterations involving FGFR reported in an estimated 20% of patients with advanced urothelial cell cancer . This reErdafitinib, an FGFR1-4 inhibitor, has been tested in the clinical setting for patients with UTUC and other urothelial carcinomas. It was granted accelerated approval by the FDA based primarily on the results of a multicenter, open-label, single-arm study conducted by Loriot et al. In this open-label phase 2 trial, 99 patients with metastatic or unresectable urothelial carcinoma harboring FGFR alterations received the pan-FGFR inhibitor erdafitinib continuously at 8 mg or 9 mg daily doses. The confirmed objective response rate was 40% (95% CI 31\u201350%). Among FGFR mutation patients, the response rate was 49%. Median progression-free survival was 5.5 months and median overall survival was 13.8 months. The 12-month overall survival rate was 55%. Grade \u2265 3 treatment-related adverse events occurred in 46% of patients, most commonly hyponatremia, stomatitis and asthenia [Infigratinib, a selective FGFR1-3 inhibitor, has also shown promise in FGFR-altered urothelial cancer, including UTUC. Lyou et al. conducted an open-label multicenter phase 1b study, where 13 patients received the FGFR1-3 inhibitor infigratinib early-line before platinum chemotherapy for metastatic urothelial carcinoma, while 54 received it after \u22651 prior therapies. The confirmed objective response rate was 31% with early-line and 24% with later-line infigratinib. Disease control rates were 46% and 69% in the early-line and salvage settings, respectively. Median progression-free survival was 12.0 months versus 5.6 months, and median overall survival was 13.8 months versus 12.9 months in the early-line compared to later-line groups . InfigraNotwithstanding the encouraging preliminary results of FGFR-targeted therapies, multiple challenges endure. These include the emergence of resistance to FGFR inhibitors, the management of therapy-associated side effects, and the necessity for reliable biomarkers to guide patient selection. Moreover, the definitive impact of FGFR inhibitors on overall survival remains under investigation. These studies represent important strides in the treatment of UTUC and other urothelial carcinomas. They underscore the importance of genomic profiling in urothelial cancer to identify patients who might benefit from these targeted treatments. As further studies are conducted, the role of FGFR inhibitors in the treatment paradigm of UTUC is likely to become better defined.In addition to immunotherapy and chemotherapy, there is significant interest in the role of radiation therapy in the adjuvant space. A systematic review by Iwata et al. evaluated the role of adjuvant radiotherapy (ART) after surgery for bladder cancer and UTUC. For bladder cancer, the review included three randomized controlled trials comprising 456 patients and 11 retrospective studies comprising 7571 patients . Some stFurther prospective, randomized clinical trials of peri-operative chemo- and immunotherapy in the treatment of UTUC are needed to answer efficacy questions and establish a new standard of care."} +{"text": "Infectious complications of substance use are rising nationally among people who use drugs (PWUD), highlighting the need to integrate Infectious Diseases (ID) practice with addiction care. Training experiences among ID fellows, whose practice patterns are likely to be impacted by this syndemic, remain unknown. We conducted a national survey to understand U.S. ID fellows\u2019 training, practices, and perspectives regarding care of PWUD.An 18-item survey was developed to assess program characteristics, clinical practices, and perspectives regarding knowledge, comfort, and scope of practice. Recruitment was conducted via emails to fellowship programs, social media , and IDSA platforms. Responses were collected over three weeks. Statistical analyses were conducted by chi square test. The study was deemed exempt from institutional review.196 U.S. ID fellows completed the survey (\u224524% response rate), with representation from 9 of 9 geographic regions. All respondents cared for PWUD during their training. 49% had formal curriculum in their programs and 64% reported faculty advocates. 50% typically counseled on harm reduction; 37% referred to outpatient resources and 33% recommended medications for opioid use disorders (MOUD) and naloxone. Respondents were unsure of community resources . 69% rated harm reduction counseling as extremely within scope of ID practice, versus 20% for the practice of recommending MOUD; 25% and 11%, respectively, reported feeling extremely comfortable with these skills. Engagement in discussions of harm reduction, MOUD, naloxone, and outpatient resources was significantly associated with presence of a faculty advocate .Self-reported engagement in clinical practices among Infectious Diseases fellowsPerspectives on comfort level and scope of practice among Infectious Diseases fellowsAvailability and knowledge of resources at Infectious Diseases training sitesU.S. ID fellows frequently care for PWUD but infrequently engage in integrated care practices. Harm reduction counseling is seen as highly within ID scope of practice, however, comfort and knowledge are low. Both comfort and perception of scope are low for discussing MOUD, though this appears to be impacted by faculty modeling. Our findings highlight an opportunity to formalize training in ID fellowship to better address the need for integrated ID/addiction care nationally.All Authors: No reported disclosures"} +{"text": "Growing concerns over health and welfare impacts from extreme phenotypes in dogs have created an urgent need for reliable demographic information on the national breed structures of dogs.This study included all dogs under primary veterinary care in the UK during 2019 at practices participating in VetCompass. Demographic data on these dogs were analysed to report on the frequency of common breeds and also to report on conformation, bodyweight, sex and neuter associations with these breeds.n = 1,551,462) were classified as purebred, 6.7% as designer-crossbred and 24.0% as nondesigner-crossbred. Across 800 unique breed names, the most frequent breeds at any age were nondesigner-crossbred , Labrador Retriever and Jack Russell Terrier . Among 229,624 (10.3%) dogs aged under one year, the most frequent breeds were nondesigner-crossbred , French Bulldog and Cockapoo . Overall, based on breed characteristics, 17.6% were classified as brachycephalic, 43.1% as mesaticephalic and 8.3% as dolichocephalic. Of 1,551,336 dogs that were classifiable based on breed, 52.6% were chondrodystrophic. Of 1,462,925 dogs that were classifiable, there were 54.6% short haired, 32.6% medium haired and 12.8% long haired. Of 1,547,653 dogs that were classifiable for ear carriage, 24.5% were erect, 28.1% were semi-erect, 19.7% were v-shaped drop and 27.7% were pendulous. Overall, there was a 1.09:1.00 ratio of male to female dogs .The study included 2,237,105 dogs under UK veterinary care in 2019. Overall, 69.4% (Health and welfare issues linked to popular breeds with extreme phenotypes suggest that there is much work to do to help owners to make more welfare-friendly decisions when choosing which type of dog to own. Population ecology examines how and why populations change over time and space , 2. It sDogs and man have a long joint history, with dogs being the first species domesticated by man and the only species known to share a domestic relationship with humans during the Pleistocene . It is wth century, the advent of breed clubs and the concept of breed standards provided structure for reproductive isolation of canine sub-populations, with the aim of ensuring breed differentiation and standardisation [During the mid-19disation , 24. Thidisation \u201327. As adisation , 24. Whidisation .A description of present-day UK-based dog demographics that includes information on important attributes such as sex, neuter status, age, breed and phenotype would offer analytical and inferential benefits to welfare, veterinary, educational, epidemiological and business stakeholders, amongst others. For example, national demographic structures are key determinants of inter-animal contact patterns and hence are critical for understanding infectious disease spread. As such, demographic insights would support the design and implementation of improved disease transmission control measures \u201333. DemoUntil recently, despite the recognised importance of having a good understanding of canine demography, it has been challenging to accurately describe the demography of the UK dog population. This was mainly due to a lack of representative and accessible data on UK dogs. Previous UK-based statistics on dog demography, such as those published by the Kennel Club and the In an effort to address some of these limitations, the current study aimed to report the demography of dogs under primary veterinary care in 2019 across the UK using anonymised veterinary clinical data from the VetCompass Programme . VetCompThis study placed particular focus on reporting breed and conformational attributes of dogs in the UK. Detailed methodological data are provided showing the VetCompass system of using breed type information to classify dogs by a range of morphological criteria. The results of the current study could assist welfare scientists, breeders, veterinary practitioners and owners with a deeper understanding of the demographic structure of the wider UK dog population and can also support future work by other research groups that could apply these VetCompass breed classification systems and data on common breeds.The study population included all available dogs under primary veterinary care at clinics participating in the VetCompass Programme during 2019 . Dogs unA cross-sectional study design was used to explore and report on demography and conformation in this population. Power calculations estimated that a sample of at least 366,193 dogs was needed to estimate the frequency of a breed that includes 0.1% of all dogs in a wider national UK population of 8 million dogs to a precision of 0.01% acceptable margin of error at 95% confidence level , 47. AllPurebred status variable categorised the individual breeds as purebred, designer-crossbred or nondesigner-crossbred. A Kennel Club breed group variable classified breeds recognised by the UK Kennel Club into their relevant breed groups and all remaining types were classified as non-Kennel Club recognised [Descriptive information on breed entered by the participating practices was cleaned and mapped to a VetCompass breed list derived and extended from the VeNom Coding breed list . The brecognised . Note thcognised \u201353. The cognised . The median is reported rather than the mean to avoid assumptions of normality for continuous variables . ProportThe study included an overall population of 2,250,417 dogs at any age under veterinary care in 2019 within six veterinary groups participating in VetCompass across the UK. There were 13,312 (0.59%) dogs without any breed information recorded that were excluded from further analysis, leaving 2,237,105 dogs in the final analysis. The overall dataset included 800 unique dog breed names. The most frequent breeds at any age were nondesigner-crossbred , Labrador Retriever , Jack Russell Terrier , English Cocker Spaniel , Staffordshire Bull Terrier and Chihuahua . The 10 most common breeds represented 59.56% of all dogs while the 20 most common breeds represented 75.93% of all dogs .n = 45,995, 20.03%), French Bulldog , Cockapoo , Labrador Retriever , English Cocker Spaniel and Chihuahua . The 10 most common breeds represented 58.79% of all dogs aged under one year while the 20 most common breeds represented 75.89% of all dogs aged under one year , Jack Russell Terrier , Labrador Retriever , Staffordshire Bull Terrier , English Cocker Spaniel and Border Collie . The 10 most common breeds represented 67.93% of all dogs aged over 10 years while the 20 most common breeds represented 81.55% of all dogs aged over 10 years of dogs were classified as purebred with 6.7% classified as designer-crossbred and 24.0% as nondesigner-crossbred. Designer-crossbred dogs were statistically significantly younger than nondesigner-crossbred dogs (P < 0.001) and purebred dogs (P < 0.001). Designer-crossbred dogs were statistically significantly heavier than nondesigner-crossbred dogs (P < 0.001) and lighter than purebred dogs (P < 0.001) . Proport< 0.001) .Of 2,237,105 dogs with breed (including crossbreds) information available, 67.54% were of a breed recognised by the UK Kennel Club and 32.46% were of a breed not recognised by The Kennel Club. It should be noted that it was not possible to ascertain which individual dogs within the breeds regcognised by The Kennel Club were actually registered with The Kennel Club. Among the breeds recognised by The Kennel Club, the most common breed groups were Gundog , Terrier and Toy . Kennel n = 202,015) were purebred Spaniel types, 5.80% were Spaniel-designer crosses and 82.32% were non-Spaniel types. There were 1.24% purebred Poodle, 6.70% Poodle designer crosses and 92.06% non-Poodle types. There were 2.59% purebred Dachshund types, < 0.01% (36) Dachshund-designer crosses and 97.40% non-Dachshund types.There were 1,700,770 (76.03) dogs that were recorded as either a purebred or a designer breed. Of these, 11.88% of dogs were classified by breed as brachycephalic, 43.08% as mesaticephalic and 8.28% as dolichocephalic (P < 0.001) and dolichocephalic dogs (P < 0.001). Brachycephalic dogs were statistically significantly lighter than mesaticephalic dogs (P < 0.001) and dolichocephalic dogs (P < 0.001). Proportional skull shape varied widely between the young and older dogs (P < 0.001), with mesaticephalic dogs comprising 51.2% of dogs aged under one year compared with 75.9% of dogs aged over 10 years while conversely, brachycephalic dogs comprised 34.3% of dogs aged under one year compared with 13.9% of dogs aged over 10 years were chondrodystrophic and 47.42% were non-chondrodystrophic. Of 1,462,925 dogs that could be classified according to their haircoat, 54.58% were short haired, 32.60% were medium haired, 12.78% were long haired and 0.05% (682) were hairless. Of 1,547,653 dogs that could be classified by the ear carriage conformation, 24.53% were erect, 28.06% were semi-erect, 19.74% were v-shaped drop and 27.68% were pendulous . The median adult bodyweight of females was lighter than for males (P < 0.001) to female dogs , and one animal recorded as hermaphrodite. The median age of females was statistically older than for males (< 0.001) .P < 0.001) (P < 0.001).Of the 2,231,064 dogs with neuter status recorded, there were 975,966 (43.74%) animals recorded as neutered on their final available clinical record. Across all ages, female dogs were statistically significantly more likely to be neutered than males (P < 0.001). Among dogs aged under one-year, female dogs were statistically significantly less likely to be neutered than males (P < 0.001). Among dogs aged over 10 years, female dogs were statistically significantly more likely to be neutered than males (P < 0.001). Across all ages, proportional neutering differed between non-designer crossbred , designer crossbred and purebred dogs (P < 0.001). In non-designer crossbred dogs across all ages, female dogs were statistically significantly more likely to be neutered than males (P < 0.001). In designer crossbred dogs across all ages, female dogs were statistically significantly more likely to be neutered than males (P < 0.001). In purebred dogs across all ages, female dogs were statistically significantly more likely to be neutered than males (P < 0.001). Neutered animals were statistically significantly older than entire animals (< 0.001) . The medPopulation dynamics within the UK dog population are inherently tied to human ecology and behaviour. As such, the demographic landscape of dogs described here has been moulded, in part, by social , culturaThe modern companion dog has become the most phenotypically diverse domestic species on the planet, featuring hundreds of recognisable breeds that each represents a unique collage of morphological, behavioural, and physiological traits , 66, 67.Selection pressures towards exaggerated and extreme physical traits that are associated with high levels of conformation-related and hereditary pathology has led to major discussion and rethinking, especially over the past 15 years, around the ethics and welfare implications of breed as a concept for dogs , 70\u201375. Reliable data on population dynamics and health are a key component of effective canine health and welfare surveillance , 80 and An additional new phenomenon in breed distributions identified in the current work is the substantial increase in designer-crossbred breed types . DesigneThe population sex ratio in the current study was skewed towards males in line with many previous reports , 86, 87.The influence of demographic change in dogs upon the spread of zoonotic infection should not be under-estimated. Demographic characteristics of dog populations have been shown to greatly affect the transmission and maintenance of a range of zoonotic pathogenic agents , 32, 33.In addition to providing information directly on the demography of dogs in the UK, the current study also provides a demographic resource that can be used by other researchers and research groups to ground their own research. Many research projects collect information on numerator cases, e.g., dogs recorded with a clinical condition such as Alabama rot, but do not have ready access to a denominator sampling frame for the underlying population of dogs from which these affected dogs (i.e. cases) was drawn. The consequence of this is that such studies with only cases are limited to reporting descriptive information on these cases or to reporting risk factor analysis just within the cases themselves but are unable to report demographic risk factor results that help to explain why cases became cases in the first place. However, the detailed breed demography of UK dogs provided by the current study can enable other researchers and research groups to extend their own analyses to report on risk factors relative to the wider UK dog population. This concept of using a VetCompass denominator demographic population to underpin research on cases identified from other datasets has already been validated on disorders including Alabama rot and leptThis study had some limitations. Although a high proportion of owned companion animals tend to receive veterinary care in countries with developed pet industries, it is estimated that just 77% of owned dogs in the UK are formally registered with a veterinary practice . TherefoThis paper aimed primarily to report on breed and conformational factors in UK dogs. Although information on neuter status was provided, this was not a primary focus of the paper. Breed and conformation status are fixed over time in individual dogs and therefore a cross-sectional analysis such as the current study is appropriate. However, neuter status is a time-varying parameter and therefore a study with a primary focus on exploring neuter status would require a cohort design with animals followed over time to identify the age at neutering. Unfortunately, information on the dates of neutering were not available for the current analysis and so the results on neutering given here should be interpreted with caution.The current study relied on the breed status information recorded in the veterinary clinical records. Although these breed terms reflected the sum of the insights of the owners and the relevant veterinary teams and could be updated over time in the clinical records to improve accuracy, it is still possible that some misclassification on the precise breed existed. The breed status of each dog was not individually validated using genetic ancestry tests, cross-referencing to kennel club registries or using photographs. The current study did not aim to link the VetCompass and Kennel Club datasets and therefore was unable to identify the subset of VetCompass dogs that were registered with The Kennel Club. The classifications within breeds for phenotypic characteristics such as ear carriage, hair coat and skull shape were derived based on typically expected values for the breed but it is possible that these values did not apply equally to each individual dog within each breed. The growing phenomenon of designer-crossbred dog breeds in the UK means that many of the breeds listed in the current study may not be classically considered as formal breeds according to definitions developed over the past century by kennel clubs . Breed dIn conclusion, this analysis of over 2 million dogs under primary veterinary care in the UK during 2019 has identified that the most common breeds overall were the nondesigner-crossbred, Labrador Retriever and Jack Russell Terrier. However, changing preferences for extreme breeds and the emergence of new designer-crossbred breeds are reflected by differing breed profiles in dogs aged under one year where the most common breeds were nondesigner-crossbred, French Bulldog and Cockapoo. Brachycephaly was shown to be a highly popular phenotype among UK dog owners, with 17.6% of UK dogs representing a breed with brachycephaly, raising substantial questions about the canine welfare impact from our collective breed selection choices.S1 Filehttps://rvc-repository.worktribe.com/output/1596183.(TXT)Click here for additional data file.S2 Filen = 2,237,105. https://rvc-repository.worktribe.com/output/1596183.(TXT)Click here for additional data file."} +{"text": "The success of diabetes prevention based on early treatment depends on high-quality screening. This study compared the diagnostic properties of currently recommended screening strategies against alternative score-based rules to identify those at high risk of developing diabetes.The study used data from ELSA-Brasil, a contemporary cohort followed up for a mean (standard deviation) of 7.4 (0.54) years, to develop risk functions with logistic regression to predict incident diabetes based on socioeconomic, lifestyle, clinical, and laboratory variables. We compared the predictive capacity of these functions against traditional pre-diabetes cutoffs of fasting plasma glucose (FPG), 2-h plasma glucose (2hPG), and glycated hemoglobin (HbA1c) alone or combined with recommended screening questionnaires.Presenting FPG > 100 mg/dl predicted 76.6% of future cases of diabetes in the cohort at the cost of labeling 40.6% of the sample as high risk. If FPG testing was performed only in those with a positive American Diabetes Association (ADA) questionnaire, labeling was reduced to 12.2%, but only 33% of future cases were identified. Scores using continuously expressed clinical and laboratory variables produced a better balance between detecting more cases and labeling fewer false positives. They consistently outperformed strategies based on categorical cutoffs. For example, a score composed of both clinical and laboratory data, calibrated to detect a risk of future diabetes \u226520%, predicted 54% of future diabetes cases, labeled only 15.3% as high risk, and, compared to the FPG \u2265 100 mg/dl strategy, nearly doubled the probability of future diabetes among screen positives.Currently recommended screening strategies are inferior to alternatives based on continuous clinical and laboratory variables. We considered a prevalent case at baseline when any of these criteria were present. To be consistent with clinical recommendations, we required confirmation of our incident diabetes cases. We thus ascertained incident diabetes only if at least one of these five criteria were present at both follow-up visits or at least two were found at a single visit. Research staff ascertaining diabetes at follow-up were unaware of baseline laboratory values. We considered those who met two criteria at the first follow-up but none at the second follow-up as not having developed diabetes. We excluded those without data for incident diabetes due to death, who lack follow-up, or with incomplete data from analyses.2.2We first assessed screening strategies based on traditional laboratory cutoffs for pre-diabetes (intermediate hyperglycemia) , 8, 21. 2.3http://elsabrasil.org/funcoes-de-risco/risco-diabetes-10-anos/) for risk calculation based on scores composed of different combinations of variables to predict the 10-year risk of developing diabetes to be made available to the public.We randomly divided our sample equally into training and validation datasets. We described our sample characteristics calculating either the mean (standard deviation) or mean for continuous variables and the absolute frequency for discrete variables. We used logistic regression on the training dataset to develop risk functions to predict incident diabetes. We initially produced models only with clinical variables, keeping those that significantly improved the area under the receiver operating characteristic (AUC) curve. We considered age, sex, self-reported ethnicity, educational attainment, parental history of diabetes, daily consumption of fruits or vegetables, leisure-time physical activity , smoking, hypertension or self-reported use of hypertension medication, body mass index (BMI), and waist circumference. We then selected the best of these derived risk functions to calculate the probability of developing diabetes for each participant in our validation dataset. Using this same approach, we next evaluated risk scores composed of laboratory results and their combination with the clinical data. We provide risk function formulas in the Supplementary Material. Additionally, we built an online tool using R Shiny , selecting ones where being positive reflected 20% and alternatively 15% probabilities of developing diabetes over our sample\u2019s follow-up. These were close to the probabilities of developing the disease among those labeled by current ADA laboratory testing strategies.These risk scores, different from categorical rule approaches, for which cutoff points have already been defined , 12, 22,Using the same ELSA database, we also constructed the clinical scores recommended by national strategies. As we lacked information for one of the FINDRISC questions\u2014a previous finding of pre-diabetes\u2014we randomly attributed the presence of prior pre-diabetes to 90% of those with baseline hyperglycemia by WHO criteria.Finally, in our validation sample, we calculated diagnostic properties for the rules assessed: the percentage deemed at high risk, sensitivity, specificity, and positive and negative (1 \u2212 PPV) predictive values. We also report the AUC and the net reclassification index . We esti3Our study used data from the 15,105 participants of the ELSA-Brasil cohort. We excluded those with diabetes at baseline , missing information to ascertain diabetes (n = 5), or missing values for variables we considered in the construction of risk scores (n = 20). We additionally excluded those not returning to follow-up visits , missing data to ascertain incident diabetes (n = 351), or using oral antidiabetic medication but not reporting to have diabetes (n = 212). Finally, due to our requirement of confirmation of incident cases, we excluded those with no finding of diabetes at the first follow-up and only one criterion present at the second follow-up visit (n = 592). Our final sample thus consisted of 9,525 participants Figure\u00a01Over a mean (standard deviation) of 7.4 (0.54) years of follow-up, 864 participants developed diabetes. We considered 24 participants who met two criteria for diabetes at the first follow-up but none at the second follow-up as not having developed diabetes. vs. 76.6%) while labeling marginally fewer (39.8% vs. 40.6%) as high risk with a slightly lower false-positive rate (82.7% vs. 82.9%). Testing all with the WHO fasting glucose cutoff of \u2265110 mg/dl labeled considerably fewer participants (11.0%) as high risk and produced fewer false positives but identified a lower percentage of future cases (40.1%).In the lower portion of Next, we evaluated the clinical scores that we had developed. The best score is based only on readily available clinical variables of modeled risk as a function of age, sex, self-declared ethnicity, BMI, waist circumference, hypertension, and parental history of diabetes . Further adjustment with other diabetes risk factors did not improve this score.We additionally evaluated similarly derived prediction rules composed of laboratory tests, alone or combined with clinical variables, expressing these laboratory variables continuously rather than categorically based on recommended cutoffs. For these analyses, we initially defined high risk as a 20% probability of developing diabetes over our 7.4-year average follow-up. vs. testing all) identified 43.8% and 48.0% (vs. 49.7%) of future cases, respectively, while labeling as positive slightly smaller percentages (13.1% and 14.1% vs. 14.7%). Adding HbA1c and lipids improved future case detection slightly (48.7% and 53.1%).vs. 64.0%) of future cases, with marginally fewer labeled as positive (17.6% and 19.5% vs. 20.3%). Additionally adding HbA1c and lipids in these two-step approaches improved future case identification to 58.1% and 63.1%, respectively.When we lowered the score positivity cutoff to a 15% probability of future diabetes, rules identified considerably more future cases at the cost of labeling more of the sample as high risk. The clinical score alone performed better at this lower cutoff, labeling 20.1% at high risk and identifying 45.9% of those developing future diabetes. Adding FPG to this screening approach labeled 20.3% at high risk and identified 64.0% of future cases, and adding HbA1c and lipids labeled 15.3% at high risk and identified 65.0% of future cases. Testing FPG in only the 50% or 67% at highest clinical risk using the 15% cutoff identified slightly lower percentages of participants being labeled high risk, detected considerably fewer future cases (35.0% to 45.2%).vs. 47.2% for the ADA FPG and HbA1c lab-only strategy) and doubled the probability of developing diabetes among those at high risk (PPV = 32.8% vs. 15.7%) while detecting 53.1% of future cases. This strategy also compared favorably with the ADA two-step categorical approach, identifying more future cases (53.1% vs. 34.0%) while labeling only a slightly higher percentage as high risk (14.7% vs. 13.1%). Those labeled were more likely to develop diabetes (32.8% vs. 24.9%). Adding the 2hPG of an OGTT instead of an HbA1c as the additional laboratory test produced little benefit in strategies that included clinical variables and lipids (data not shown).Compared with recommended one- or two-step categorical approaches presented in Of note, all of these continuous variable strategies presented PPVs, though higher than almost all of the categorical approaches, well below 50%, indicating the presence of many false positives. High false positivity was especially notable using a 15% cutoff or only the clinical score. False-positive rates (1 \u2212 PPVs) were usually ~5%\u201310% lower with the 20% probability cutoff.4We compared different screening strategies for diabetes in adults \u2265 35 years using easily obtainable clinical variables and laboratory results. Our findings showed that risk scores combining clinical variables and glycemic measures expressed continuously outperformed traditional laboratory-based categorical approaches and the two-step categorical approaches frequently recommended in national screening programs. Combining a continuously expressed FPG with clinical variables resulted in the largest gain in accuracy. Including additional laboratory results produced some further improvement. While all strategies identified considerably more false than true positives, those based on continuously expressed variables had a more balanced mix between greater future case detection and less false-positive labeling. Finally, using two-step strategies, with the first step evaluating only clinical variables to identify those initially at the highest risk and the second step adding laboratory testing only for those identified, considerably reduced the need for laboratory testing.Three major national programs of diabetes prevention have defined specific rules to label high risk and initiate preventive intervention. In the United States, the CDC recommends lifestyle counseling for overweight individuals at high risk based on the ADA questionnaire, an ADA lab cutoff, or having a previous pregnancy complicated by gestational diabetes . The UniOur findings indicate that the UK/NICE and especially the CDC/ADA approaches label a relatively high percentage of the sample as high risk, producing many referrals, a significant fraction of whom will not develop diabetes in the subsequent decade. Additionally, as shown in a priori probability of participants developing diabetes can markedly reduce the gains of screening. Lifestyle intervention in community settings, primarily in North America, has been estimated to prevent diabetes in only 3% of those enrolled (As has been noted , almost enrolled . Improveenrolled and otheThe use of continuous variable screening strategies, here documented to be superior, as additionally found by another recent study , combineA potential limitation to our study is that our rules using HbA1c performed relatively poorly, suggesting that greater laboratory error in HbA1c determination, although not reflected in our evaluation of its reliability coefficient , could hOur study presents several strengths. Its outcome of future incident diabetes and its focus on the most relevant screening metrics permit clinically relevant, head-to-head comparisons of different strategies. Our ascertainment of diabetes required confirmation, approximating it to the clinical definition, giving our findings greater generalizability. Standardized collection of data and centralized laboratory measurement add quality and precision to our results. Our relatively large sample size allows for more precise estimates of diagnostic properties. Rates of obesity and central obesity and other diabetes risk factors in ELSA-Brasil, being a contemporary cohort, are more in line with their current prevalence, permitting more easily generalizable clinical scores. Finally, our provision of an online calculator permits immediate use of findings.5All evaluated screening strategies to predict future diabetes are far from perfect. However, risk scores combining clinical variables with glycemic measures expressed in a continuous form are superior to traditional screening strategies and currently recommended two-step categorical strategies. National programs and those making recommendations should favor continuous variable scores in their recommended screening strategies to maximize the potential benefit for those invited to screening programs while guaranteeing an adequate balance between benefits and costs. They should also make explicit the impact of their screening strategy recommendations in terms of the percentage labeled as high risk and the probability that those so labeled, without intervention, will develop diabetes in the foreseeable future.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The studies involving human participants were reviewed and approved by Comit\u00ea de \u00c9tica em Pesquisa do Hospital de Cl\u00ednicas de Porto Alegre. The patients/participants provided their written informed consent to participate in this study.Concept and design: PB, MS, and BD. Acquisition, analysis, or interpretation of data: PB, MS, AV, JM, PV, SB, and BD. Drafting of the manuscript: PB and BD. All authors made critical revisions to the manuscript for important intellectual content. All authors contributed to the article and approved the submitted version."} +{"text": "Tumors located at the skull base constitute a particular challenge for medical teams. This is linked to the complex anatomy and the presence of functionally important structures, including the cochlea, vestibulum, cranial nerves, blood vessels, and brainstem. Typical skull base tumors are cholesteatoma, chordoma, chondrosarcoma, meningioma, paraganglioma, schwannoma, and cholesterol granuloma. The surgical treatment of such tumors is often located in the territory of both the ENT surgeon and neurosurgeon. Therefore, in most skull base teams, ENT surgeons and neurosurgeons work and operate together. A multi-disciplinary approach is necessary in order to be able to provide a high level of care and includes the presence of a radiologist, pathologist, and radiotherapist specialized in skull base pathology. Historically, skull base tumor surgery was aggressive, mainly striving for complete resection. However, the modern treatment goal has shifted towards the preservation of neurological function, often resulting in less aggressive tumor removal. With the arrival of new radiotherapy options, such as proton beam therapy, tumor control may be achieved without placing the patient at risk of severe surgical complications. In this Special Issue; six original articles and one systematic review provide an overview of recent developments in the field ranging from experimental to clinical studies.Meningioma are the most common intracranial tumors . In geneIntraoperative neuronavigation and, more recently, augmented reality (AR) are tools that may aid in achieving the aforementioned surgical goals. Pojskic et al. demonstrate the feasibility of AR in guiding safe skull base meningioma resection . FurtherThe meningioma recurrence rate is strongly related to the level of resection and WHO grading ,3. ThereVestibular schwannoma (VS) is the most common benign tumor of the cerebellopontine angle . Its groCholesterol granuloma comprises benign cystic lesions that may occur in the temporal bone . It is aWe stay at the lateral skull base and move onto jugular foramen schwannoma (JFS): rare tumors originating from the lower cranial nerves that are often associated with severe neurological symptoms . There iYildiz et al. advocates opposing treatment strategies in the management of temporal bone paraganglioma (TBP) . In theiThe final paper in this Special Issue is a systematic review on skull base chondrosarcoma (SBC) . A totalCerebrospinal fluid leaks requiring revision surgery were observed in 6.5% of post-surgical patients. In total, 10.6% suffered from permanent post-operative complications and 15.8% suffered from transient complications; in both groups, mainly new cranial nerve deficits were observed. Regarding radiotherapy complications, a total of 30.7% experienced severe adverse events, predominantly hypopituitarism (15.4%), hearing loss (7.1%), and cerebral necrosis (3.7%).At follow-up, symptom improvement was recorded in 46.7% after treatment with no differences between radiotherapy types. Over half of the lesions (58.3%) showed a stable tumor volume, 27.1% demonstrated shrinkage, and 14.6% recurred after a median follow-up time of 67 months (range of 0.1\u2013376). Finally, 5-year and 10-year overall survival rates were 94% and 84%, respectively.In conclusion, these studies portray the ongoing challenges skull base teams face in treating their patients. A paradigm shift started a few decades back with the field turning from debilitating complete surgical resections towards patient-tailored multimodal treatment strategies. We believe that the future management of skull base tumors will become increasingly based on molecular tumor characteristics, guiding treatment choices and not solely relying on anatomical and surgical parameters."} +{"text": "Vibrio cholerae serogroup O1 among adults was 12.4% in Cerca-la-Source and 9.54% in Mirebalais, suggesting a high recent prevalence of infection. Improved surveillance programs to monitor cholera and guide public health interventions in Haiti are necessary.In Haiti in 2017, the prevalence of serum vibriocidal antibody titers against Vibrio cholerae, was introduced into Haiti, resulting in >800,000 cases and >10,000 deaths instead of the cards used in that study. We used target V. cholerae strains 19479 El Tor Inaba and X25049 El Tor Ogawa.We obtained dried blood spots from consenting adults V. cholerae for each community. We defined seropositivity as a vibriocidal antibody response titer threshold of >320 on the basis of the best available evidence, a recent study in Bangladesh that estimated that a vibriocidal modal titer of 320 had a sensitivity of 80.6% and specificity of 83.0% for infections within the preceding year (https://cran.r-project.org) of vibriocidal antibody responses against The study was approved by the Partners Healthcare Institutional Review Board (protocol 2016P002781) and the Zanmi Lasante Institutional Review Board (protocol ZL IRB ID AK). All study participants provided written informed consent.Overall, we enrolled 265 (27.6%) of 960 invited households in the study. Samples from 48 households were lost during tumultuous sociopolitical events, resulting in samples from 217 households available for analysis: 99 households with 156 persons in Cerca-la-Source and 118 households with 121 persons in Mirebalais.V. cholerae was 12.4% (95% CI 6.76%\u201320.0%) in Cerca-la-Source and 9.54% (95% CI 4.91%\u201316.0%) in Mirebalais (We analyzed unweighted demographic characteristics for the census population and for serosurvey participants . Serosurrebalais . We analrebalais . Only 4 We calculated seroprevalence estimates for potential risk factors for cholera Appendix . SeroposV. cholerae and is the best characterized immunologic marker of recent exposure to cholera. However, there is no widely agreed-upon threshold to quantify exposure over a given period, and our understanding of the relationship between symptom severity and antibody kinetics is limited. In the study from Bangladesh, a vibriocidal titer of >320 was the best marker of infection in the preceding year (The vibriocidal antibody is a complement-dependent, bactericidal antibody directed against the lipopolysaccharide O-antigen of V. cholerae are available from Haiti. One prior serosurvey, conducted during March\u2013April 2011, within the first 6 months of the onset of the epidemic in the Artibonite Department of Haiti, estimated that 39% of persons had a vibriocidal titer >320, whereas 64% had titers >80, which suggested extensive infection and was consistent with high early case counts (Limited serologic data on >18 years of age in 1 department of Haiti participated, so the data cannot be directly extrapolated to younger age groups and other regions; however; during 2017\u20132018, that department was the most affected according to case counts (The findings from this study should be interpreted considering several limitations. Only adults V. cholerae vibriocidal antibodies was 12.4% in Cerca-la-Source and 9.54% in Mirebalais in Haiti, suggesting a high rate of recent infection even at a time when case incidence was declining. Although commune-level incidence data were not available for direct comparison, in 2017, the reported annual incidence for the Centre Department, where Cerca-la-Source and Mirebalais are located, was 4.3 cases/1,000 inhabitants, which offers a general frame of reference (In summary, in 2017, the seroprevalence of Vibrio cholerae in adults, Haiti, 2017.Additional information about seroprevalence of"} +{"text": "Unfortunately, instruction on optimal program staffing structure is lacking. Furthermore, existing data are dichotomized into large (>40 transplants/y) or small (<40 transplant/y) programs, limiting program-specific interpretation for process improvement. Moreover, there are few details on procedure volumes, inpatient census, and planning for anticipated growth. Consequently, many lung transplant programs look to data in other solid organ fields for staffing guidance.5 However, such models may not be generalizable to the lung transplant community because lung allograft recipients have greater mortality, acute rejection, and comorbidities.7 To address this knowledge gap, we performed a prospective, multicenter, survey assessment of staffing in lung transplant programs across the United States and Canada. Program leadership was surveyed about clinical volumes, staffing adequacy, anticipated growth, and accommodations for coordinator workplace flexibility. These results provide a critical overview of staffing and identify key opportunities for improving logistics.Approximately 2500 lung transplants are performed in the United States annually, yet there remains a significant shortage of suitable donor organs, resulting in lung transplant waitlist mortality of 15%.Table S1, SDC, http://links.lww.com/TP/C658) was administered via Research Electronic Data Capture to medical directors of active adult lung transplant programs in the United States and Canada identified through the Organ Procurement and Transplantation Network.8 Only 1 response was allowed per program. Weekly reminders were sent for 1 mo if there was no response.A 29-item survey .Results were stratified into thirds by program size based on transplant procedures performed in 2021 with <30, 30\u201365, and >65 transplants/y defining small, medium, and large programs, respectively. Results were adjusted to 2021 transplant rates or total living cohort size, to facilitate comparisons between programs. Workload was calculated by dividing the metric of interest by number of full-time equivalents for the respective role; full-time equivalent equals scheduled hours divided by number of full-time workweek hours. Kruskal-Wallis testing was used to compare continuous variables across program sizes. Pairwise comparisons were performed using Mann-Whitney Table S2, SDC, http://links.lww.com/TP/C658, summarizes the volume at each program, pretransplant metrics , and posttransplant metrics . Across all programs, 15% of referred patients were added to the transplant waitlist, whereas 40% of patients who completed evaluation were waitlisted . There was no difference in progression from referral through evaluation and waitlisting by program size. Daily inpatient census was 33% of the annual transplant volume and was significantly higher for smaller programs . The ratio of inpatient volume relative to the census of alive patients was 5% and did not vary by program size (P = 0.56). Ambulatory weekly volume was 103% of the annual transplant volume and did not vary by program size. Weekly bronchoscopy volume was 18% of annual transplant volume, with small programs performing more bronchoscopies than large programs . Program metrics normalized to annual transplant volumes are in Figures S1, S2, SDC, http://links.lww.com/TP/C658.The survey was distributed to 63 active adult lung transplant programs, with 39 (62%) responding. Responses were received by 11 of 27 (41%), 13 of 19 (68%), and 15 of 17 (88%) of small, medium, and large programs, respectively. Medical directors (85%), other physicians (13%), or administrators (3%) provided responses. The median number of new transplants performed in 2021 was 46 (interquartile range 28\u201370). There was a significant difference in the number of transplants performed between small, medium, and large programs. Table S3, SDC, http://links.lww.com/TP/C658. There were significant differences in the number of surgeons, pulmonologists, inpatient advanced practice providers, coordinators, social workers, administrative assistants, and nutritionists by program size. There were no significant differences in the number of outpatient advanced practice providers, pharmacists, psychiatrists, or physical therapists by program size. There were significant differences in the number of pulmonologists and posttransplant coordinators between medium and large programs . There were significant differences in the number of pulmonologists, pretransplant coordinators, and posttransplant coordinators between small and medium programs.Professional staffing by each position is in Figure and Table S4, SDC, http://links.lww.com/TP/C658. Across all programs, there was 1 surgeon per 16 new lung transplants and 1 pulmonologist per 13 new transplants. Each posttransplant nurse coordinator provided care for a median of 77 patients, with 15% being within the first-year posttransplant. There were significant relative workload differences for pretransplant coordinators, posttransplant coordinators, pharmacists, and social workers between medium and large programs. The only role with a difference in workload between medium and small programs was nutritionists. When referenced to total cohort size, there was a relative workload difference between medium and large programs for postcoordinators and between small and large programs for pharmacists .Relative workloads for each staff position are described in Table S5, SDC, http://links.lww.com/TP/C658). The most understaffed positions reported were pulmonologist (36%), surgeon (23%), and posttransplant coordinator (10%). There were no differences in perceived sufficiency by program size. Despite perceptions of insufficient staffing, most programs (77%) planned to increase program volume within 5 y by a median of 37% .Only 23% of programs perceived that current staffing resources were sufficient; most of these were large . Although remote work options for nurse coordinators were numerically greater in large versus small programs (60% versus 20%), this difference was not statistically significant. Nursing and medical leadership had differing perspectives as to the ideal remote work schedule, with nursing suggesting that 2\u2009d/wk (40%) was adequate, whereas medical leadership felt that 1\u2009d/wk (20%) was sufficient (P = 0.04).The COVID-19 pandemic provided an impetus to improve workplace flexibility for transplant staff. Regardless of program size, most programs polled (59%) instituted remote capabilities for nurse coordinators. Most programs allowed for 40% of the work week to be spent working remotely of the week. Further assessment is necessary to determine the ideal balance between staff flexibility and patient outcomes.4 High participation was achieved because of the concise design, use of proactive weekly reminders to facilitate responses, and recognition among program leadership about the need for granular staffing data. Another strength is the breadth of representation of programs of different sizes. We also included workload assessments for a wide variety of clinical and nonclinical transplant team roles. Our study also has some limitations. Response rate of small programs was lower than large programs. In addition, we were unable to account for program-specific variation in staff role responsibilities; for example, pharmacists might have an outpatient presence in some programs, but only work with inpatient teams at others. It is also possible that staffing needs vary by patient demographics, geographic region, urban versus rural environment, patient travel distance, or involvement of medical housestaff. Notably, this work does not directly assess the influence of staffing ratios on patient outcomes, which would be an important natural extension in future studies.Our study has multiple strengths. The 62% response rate shows that our data represent most North American transplant programs and exceeds the survey response rate of 30%\u201340% seen in similar studies.In conclusion, our study provides a detailed description of staffing resources for lung transplant programs across North America, highlighting current staff workloads and providing critical data to provide logistical support for program optimization."} +{"text": "As of March 31, 2023, more than 30,000 monkeypox (mpox) cases had been reported in the United States in an outbreak that has disproportionately affected gay, bisexual, and other men who have sex with men (MSM) and transgender persons met the minimum data element requirementsAmong the 917 participants included in the VE analysis, 206 (22.5%) were fully vaccinated, 295 (32.2%) were partially vaccinated, and 416 (45.4%) were unvaccinated. Unadjusted VE was 75.7% for partial vaccination and 87.4% for full vaccination . After aIn this real-world assessment of JYNNEOS VE in 12 U.S. jurisdictions during the 2022 mpox outbreak, adjusted VE against mpox was 75.2% for partial vaccination and 85.9% for full vaccination. The results from this study are consistent with those from previous studies evaluating vaccine performance or effectiveness , adjusted VE estimates were 51.0% for partial vaccination and 70.2% for full vaccination among immunocompromised participants, and 72.1% for partial and 87.8% for full vaccination among immunocompetent participants. Overlapping CIs for these VE estimates suggest no difference by immunocompromise status, although the lower VE point estimates in participants who are immunocompromised might suggest a less robust response to the vaccine. Persons with immunocompromising conditions might mount a less effective immune response after vaccinationThe findings in this report are subject to at least seven limitations. First, selection bias was likely present because participation was voluntary and recruitment for controls took place in sexual health, HIV care, or HIV PrEP clinics. Second, survey data were self-reported and might be subject to social desirability or recall bias, particularly because the time between index event and survey completion varied. Third, vaccination status could have been misclassified if participants were vaccinated outside of their jurisdiction or if a participant\u2019s vaccination dates were incorrectly reported. Fourth, immunocompromise status was based on self-report; these persons might not be considered immunocompromised by clinical standards. In addition, because of limited data on HIV status, some participants with well-controlled HIV might have been incorrectly classified as immunocompromised. Fifth, some jurisdictions had challenges recruiting controls. As a result, 35 case-patients were not matched and were excluded from the analysis. Sixth, because of small sample sizes, VE for PEP could not be estimated. Finally, although the 12 U.S. jurisdictions included in this study covered a broad geographic area, data might not be generalizable to the entire U.S. population.Vaccination is an important tool for preventing mpox,Real-world vaccine effectiveness (VE) estimates for JYNNEOS vaccine against monkeypox (mpox) are limited. To date, no VE estimates by route of administration or for immunocompromised persons have been published.In this study, adjusted VE was 75% for 1 dose and 86% for 2 doses of JYNNEOS vaccine, indicating substantial protection against mpox, irrespective of route of administration or immunocompromise status.Persons at high risk for mpox exposure should be vaccinated with the recommended 2-dose JYNNEOS series."} +{"text": "Cases of syphilis have been increasing in the US for several years. We assessed the epidemiology of syphilis in MN.Syphilis cases are reported to MN Dept of Health through electronic laboratory reporting and are interviewed by disease intervention specialists. We reviewed early syphilis case data and evaluated demographics, geographic region, HIV infection and substance use.From 2018-2022 there was a 108% increase in early syphilis with a total of 4,306 cases; 76% males, 65% of whom identified as men who have sex with men (MSM). Median age was 33 (IQR 27-42) years. The average 5-year rates of early syphilis in those who identify as American Indian (AI) and Black, Non-Hispanic were 22.2-fold and 9.2-fold higher respectively, compared to White . 25% of early syphilis cases occurred in persons with HIV (PWH), a 68% increase from 2018-2022 (165 cases in 2018 to 276 in 2022). Substance use was reported in 23% of cases. Cases in females rose 267% (97 in 2018 to 344 in 2022) and in males 81% (478 in 2018 to 866 in 2022). Among early syphilis female cases, 30% were AI and 19% were Black. Congenital syphilis cases also increased from 10 cases in 2018 to 20 in 2022 .Across 3 impacted MN regions over the 2018-2022 timeframe, case characteristics varied. In the Twin Cities Region 81% were male, of whom 73% identified as MSM. In the Duluth Region , 71% were male of whom 54% identified as MSM. In TCR, 31% cases were PWH and in DR, 13% of cases were PWH. In the Northwest Region , 45% were male, of whom 6% identified as MSM. In NWR, 51% cases reported substance use, compared with 20% in TCR and 11% in DR.Similar to other US areas, syphilis is increasing in MN and is disproportionately impacting AI and Black populations. These trends and the rise in female and congenital cases warrant accelerated public health action. Rather than one statewide syphilis approach, regional differences in epidemiology highlight the need for understanding root challenges, engaging effectively with communities to develop locally specific interventions, access to testing and prenatal screening, and access to care.All Authors: No reported disclosures"} +{"text": "Organ motion compromises accurate particle therapy delivery. This study reports on the practice patterns for real-time intrafractional motion-management in particle therapy to evaluate current clinical practice and wishes and barriers to implementation.An institutional questionnaire was distributed to particle therapy centres worldwide (7/2020\u20136/2021) asking which type(s) of real-time respiratory motion management (RRMM) methods were used, for which treatment sites, and what were the wishes and barriers to implementation. This was followed by a three-round DELPHI consensus analysis (10/2022) to define recommendations on required actions and future vision. With 70 responses from 17 countries, response rate was 100% for Europe (23/23 centres), 96% for Japan (22/23) and 53% for USA (20/38).Of the 68 clinically operational centres, 85% used RRMM, with 41% using both rescanning and active methods. Sixty-four percent used active-RRMM for at least one treatment site, mostly with gating guided by an external marker. Forty-eight percent of active-RRMM users wished to expand or change their RRMM technique. The main barriers were technical limitations and limited resources. From the DELPHI analysis, optimisation of rescanning parameters, improvement of motion models, and pre-treatment 4D evaluation were unanimously considered clinically important future focus. 4D dose calculation was identified as the top requirement for future commercial treatment planning software.\u00a0A majority of particle therapy centres have implemented RRMM. Still, further development and clinical integration were desired by most centres. Joint industry, clinical and research efforts are needed to translate innovation into efficient workflows for broad-scale implementation. Simulations and experiments have shown that rescanning RRMM effectiveness is patient-, equipment- and facility-specific, depending on clinical criteria and commercial or in-house-developed approaches In this study, we aim to determine the current status of the clinical use of RRMM for PT and to identify the barriers to clinical implementation through a global institutional survey. The survey was followed by a DELPHI consensus analysis among the authors to reach recommendations on the next steps from research, development and clinical implementation aspects.2The Patterns Of Practice for Adaptive and Real-Time motion management in Particle Therapy (POP-ART PT) questionnaire was adapted from a survey to EBRT centres This paper focuses on RRMM for intrafractional respiratory motion management. Plan adaptation to mitigate interfractional anatomical changes (APT) is addressed in a parallel paper The questionnaire was completed by 70 PT centres from 17 countries worldwide, resulting in a response rate of 100% for Europe (23/23), 96% for Japan (22/23) and 53% for USA (20/38). Four centres from China and one centre from Thailand participated. Forty-three percent (30/70) of responders were academic clinical centre, and over 50% of responders have been in clinical operation for more than 5\u00a0years. Details on the responders can be found in A three-round DELPHI consensus analysis 3Out of all clinically operational responders , 85% (58/68) had implemented at least one RRMM modality (either rescanning or active RRMM) a. Here aGlobally, 65% of clinical responders (44/68) used active RRMM to treat at least one mobile treatment site (\u201cactive RRMM users\u201d hereafter). Between 14 and 55% of clinical responders were applying active RRMM by default, depending on the treatment site . The mosThe most common RRMM techniques were voluntary deep inspiration breath-hold (29%) and free-breathing expiration gating (28%) . Except The three most commonly used motion monitoring signals to guide RRMM were external marker (20%), surface monitoring (18%) and breathing volume (17%) a. MotionA dedicated coaching session was used by 55% of active RRMM users for at least one mobile tumour indication. For lung and liver, 55% (24/44) and 52% (23/44) of active RRMM users implemented coaching, mostly for 30\u00a0min. Moreover, 25% of active RRMM users had either audio or visual feedback during treatment delivery, with 18% (8/44) using both simultaneously . For lunGlobally, 48% (21/44) of active RRMM users planned to expand the use of RRMM or change their technique for a treatment site already treated with active RRMM in the next two years . Priority was given to lung, liver and pancreas. All of them ranked the barriers with the top three challenges being technical limitations, limited equipment/financial resources and limited human resources a. ReimbuIn total, 46% (32/70) of responders wished to implement active RRMM for a new treatment site. Of the current 44 active RRMM users, 30% (13/44) wished to implement RRMM for a new indication, with priority given to liver, lung and breast. For non-RRMM user (26/70), 73% (19/26) stated their wish to implement active RRMM, of which 42% (11/26) already had concrete plans for implementation in the next two years; 19% (5/26) had no wish to implement active RRMM for a new indication. The barrier for implementation of active RRMM for a new treatment site, were ranked by 63% (44/70) responders. The top three barriers were the same as for expanding/changing technique for currently treated indications b. The reThe most important outcomes with full consensus (FC) from the DELPHI analysis were summarized in 4This study provides a comprehensive picture of the clinical implementation of RRMM in 70 PT centers across 17 countries worldwide, including current status and future plans. While a majority of centers have adopted RRMM, many seek further improvements for better clinical integration. The study also outlines a 10-year vision for RRMM implementation, emphasizing the need for collaboration across industry, clinic, and research to translate innovation into clinical practice.Globally, 85% of clinical responders used rescanning or active RRMM, with 41% using both, emphasizing the importance of motion management. Within two years, 78% of responders are expected to use rescanning, indicating that all centers capable of treating mobile tumors with rescanning will use it. However, the current heterogeneity of rescanning parameters necessitates consensus guidelines for effective implementation Sixty-four percent of clinical responders were active RRMM users, which is comparable to rescanning users (62%). More than 90% of the active RRMM users treated lung and liver tumours, with over 50% using it as default . In JapaBesides compensating for motion , reducing motion , the rest had no wish to extend due to limitations from both technical and human resource aspects. However, as automatic techniques are emerging The 64% of active RRMM users in the present study is similar to the 68% in the 200 EBRT centres The higher percentage of active RRMM users for lung and liver in PT centres compared to EBRT centres may be due to patient selection, where PT centres treat moving indications only when a suitable motion mitigation strategy is in place The PT community is well aware of the importance of RRMM, which has been addressed in recent clinical guidelines In conclusion, RRMM with rescanning, active methods or both has been implemented by the majority of PT centres. Substantial interests were shown to implement more active RRMM, requiring joint efforts to address technical limitations and lack of resources. More research and development to translate 4D functions integrated in efficient workflows are needed to extend the use of RRMM clinically. This will require synergistic action from the industry, users and future users to translate ongoing research into clinical applications.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "IntroductionThe way pancreatoduodenectomy (PD) is performed can vary a lot around the world, and there is no agreed-upon standard approach. To learn more about how PD is practised in India, a survey was conducted among Indian surgeons to gather information about their current practices.MethodsA survey was created and shared with surgeons in India who practice\u00a0pancreatic surgery. It had 33 questions that aimed to capture information about different aspects of PD practice. These questions covered topics such as the surgeons' education and experience, how they evaluated patients before surgery, what they considered during the operation, and how they managed patients after surgery.ResultsA total of 129 surgeons were sent the survey, and 110 of them completed it. The results showed that 40.9% of the surgeons had less than five years of experience, and 36.4% of them performed more than 15 PDs in a year. When deciding whether to perform preoperative biliary drainage, 60% of surgeons based their decision on the level of bilirubin in the patient's blood, while the rest considered other specific indications. The majority of surgeons (72.7%) looked at the trend of albumin levels to assess the patient's nutritional status before surgery. Venous infiltration was seen as a reason for neoadjuvant therapy by 76.4% of the participants, whereas 95.5% considered upfront surgery in cases of venous abutment. When it came to the type of PD, 40% preferred classical PD, 40.9% preferred pylorus-resecting PD (PRPD), and the rest chose pylorus-preserving PD (PPPD). Pancreatojejunostomy (PJ) was the preferred method for 77.3% of surgeons, while 6.3% preferred pancreatogastrostomy (PG). About 65.5% of surgeons used octreotide selectively during the operation when the duct diameter was small. Nearly all surgeons (94.5%) preferred to secure feeding access during PD, and all of them placed intraperitoneal drains. As for postoperative care, 37.3% of surgeons attempted early oral feeding within 48 hours, while 28.2% preferred to wait at least 48 hours before initiating oral feeds.ConclusionsThe survey revealed significant differences in how PD is practised among surgeons in India, highlighting the heterogeneity in their approaches and preferences. According to the GLOBOCAN 2018 estimates, pancreatic cancer is the 11th most common cancer worldwide, accounting for approximately 4.5% of all cancer-related deaths [There is significant variation in the way PD is practiced worldwide and an ongoing debate about the best techniques for resection and reconstruction -5. WhileConsidering this premise, a survey was conducted among Indian surgeons to acquire comprehensive data pertaining to the current practice of PD. This survey serves as a pivotal preliminary measure in the endeavor to establish a standardized practice\u00a0in this part of the world.A web-based survey was created and administered to surgeons who specialize in pancreatic surgery in January-March, 2021. The survey was distributed through e-mail by the investigators to potential participants identified through professional associations such as the Indian Association of Surgical Gastroenterology, the Indian Association of Surgical Oncology, and the International Hepato-Pancreato-Biliary Association-Indian Chapter. However, while participants were invited from most of the states of the country, there is no exact data on which region each participant belonged to. To ensure a representative sample from various regions of India, a snowball sampling method was employed, where participants were asked to recommend potential future participants. If potential participants failed to complete the questionnaire, two follow-up attempts were made to elicit participation through electronic correspondence. The survey was administered exclusively in English.The survey instrument (see Appendix) consisted of 33 objective items, which were designed to capture information on various aspects of PD practice, including the educational qualifications and experience of surgeons, preoperative evaluation of patients requiring PD, operative considerations, and postoperative management. By assessing these four domains, the study aimed to provide a comprehensive understanding of the practice of PD in India.In the domain of training and experience, the survey sought to elicit information on the highest level of education attained by the surgeon, the number of years of experience in surgical practice, and the average annual volume of PDs performed. This information was used to characterize the respondent's current clinical practice. In the domain of preoperative evaluation, the survey enquired about the surgeon's philosophy regarding preoperative biliary drainage, the assessment of preoperative nutritional status, and the decision-making process for upfront surgery. In the domain of operative aspects, the survey sought information on the surgical approach used , the level of transection of the proximal gastrointestinal tract, the method for pancreas parenchymal transection, the technique for pancreatic-luminal anastomosis, the methods used to prevent postoperative pancreatic fistula (POPF), and the use of drains and feeding access. In the domain of postoperative management, the survey enquired about the timing of initiation of feeding, the timing of removal of the nasogastric tube (NG), and the timing of removal of the drain, with a specific focus on POPF. All questions were objective in nature, with four or five options provided for each question.Demographic and experience detailsA total of 129 participants were sent the questionnaire, of which 110 completed it. The respondents' ages ranged from 31 to 70 years, with a median age of 40. All participants were male. Regarding the training received, 90 participants (81.8%) had subspecialty training in the form of MCh (Master of Chirurgiae (surgery))/DNB , which is three-year higher specialty training in India, in Gastrointestinal Surgery or Surgical Oncology, while 20 (18.2%) had General Surgery training along with fellowship training in Hepato-Pancreato-Biliary Surgery, Organ Transplant Surgery, etc. Most participants were in the early phase of their surgical practice, with 40.9% having less than five years of experience after obtaining their highest degree, 29.1% having 6-10 years of experience, and 20.9% having 11-20 years of experience. Only 9.1% of the participants had more than 20 years of experience respondents preferred to use a specific target value of serum albumin to assess fitness for surgery. Only four (3.7%) surgeons believed that preoperative albumin infusion could be used to address poor preoperative status Figure .Upfront SurgeryRegarding upfront surgery, 95.5% of the surgeons preferred to proceed with an upfront surgery in cases of venous abutment of the tumor. However, 76.4% (84) of the surgeons tended to offer neoadjuvant therapy before surgery in cases of venous infiltration. Interestingly, 5.5% (six) of the participants considered upfront surgery even in cases of suspected arterial involvement performed open PD, while 13.6% selectively performed minimally invasive PD (<10% of surgeries). A small percentage (8.2%) performed more than 10% of PDs minimally invasive, and only 2.8% performed more than 50% of PDs in this way where the stomach is transected 1-2 cm proximal to the pylorus. Only 19.1% of the participants prefer to perform pylorus-preserving PD (PPPD) Figure . RegardiLymphadenectomyRegarding lymphadenectomy, 70.9% of the surgeons removed common hepatic artery station nodes, and 68.2% did hepatoduodenal lymphadenectomy along with the nodes that are removed with the specimen preferred to construct a pancreatojejunostomy (PJ) routinely to drain the remnant pancreas, while 6.3% preferred a pancreaticogastrostomy (PG) and 15.5% a tailor-made approach. Only one surgeon used an isolated Roux-en-Y jejunal limb for PJ construction Figure . RegardiTrans-anastomotic StentsOf the surgeons, 34.5% used trans-anastomotic stents in all pancreatic-digestive anastomosis, while another third used them selectively, and 28.2% did not use stents. Among the surgeons who used a stent, 86.1% drained it internally Figure .Perioperative OctreotidePerioperative octreotide was used by 14.5% of surgeons to prevent POPF, while 19.1% did not use it at all. The majority (65.5%) preferred to use it selectively in the case of a soft pancreas or small diameter duct Figure .Biliary-enteric AnastomosisRegarding biliary enteric anastomosis, 53.6% of surgeons used interrupted sutures, 10.9% used continuous sutures irrespective of bile duct diameter, and 27.3% used a tailor-made approach based on bile duct diameter Figure .Feeding AccessNearly all surgeons (94.5%) preferred to secure feeding access when performing a PD, with 64.5% preferring a feeding jejunostomy (FJ) and 12.7% using a nasojejunal tube (NJ). In comparison, 17.3% used an FJ or NJ, depending on the risk of developing a POPF Figure .Peritoneal DrainsAll surgeons preferred to place intraperitoneal drains; 36.4% of surgeons used two drains, one near the PJ site and another in the subhepatic space, 31.8% used two drains selectively, and 29.1% preferred to use a single drain.Duration of SurgeryThe duration of the surgery varied, with 30% of surgeons claiming to complete a standard resection and reconstruction (no vascular resection and standard lymphadenectomy) in less than five hours, while 65.5% took five to eight hours.Postoperative considerationsStart of Oral FeedsOf the surgeons,\u00a037.3% initiated early oral feeding within 48 hours, while 28.2% preferred to maintain fasting for at least 48 hours; 16.4% of surgeons based their decision on the return of bowel sounds, while 14.5% waited for the patient to pass flatus or stool before starting oral feeds or dextrose normal saline (DNS); 15.5% of the surgeons used albumin infusion, and 6.4% used colloids.Monitoring for POPFRegarding monitoring for POPF, 40% of the surgeons checked drain fluid amylase levels on postoperative day three and before drain removal, 24.5% checked them on alternate days starting from postoperative day three until drain removal, 23.6% checked them only on postoperative day three, 10% checked them only when clinically indicated, and 1.9% did not rely on this method at all Figure .Removal of DrainMore than 40% of the surgeons (42.7%) considered the character of the effluent as the most critical factor determining drain removal; meanwhile, 29% considered the most critical factor to be drain amylase levels and 28.3% believed it to be the volume of the effluent Figure .Duration of Hospital StayThe majority of the surgeons (62.7%) advised a stay of 8-10 days. 26.5% of the surgeons suggested a stay of five to seven days, while a small percentage (9.1%) advised a stay of 11-15 days during preoperative counseling.This survey demonstrated the considerable heterogeneity in the practice of PD among surgeons in India. Considering the complex nature of this procedure with numerous preoperative, intraoperative, and postoperative implications, evident from the questionnaire we used, one can expect considerable heterogeneity in its practice.One notable demographic finding in the survey was that all respondents were male, concurrent with the poor female representation in general surgery, especially hepatobiliary pancreatic surgery, globally . Women'sPreoperative biliary drainage in pancreatic cancer in the absence of cholangitis or any other factors precluding a timely surgery is generally not recommended, as evident from current literature . But draVarious professional bodies have attempted to categorize pancreatic cancer into resectable, borderline resectable, and unresectable/locally advanced pancreatic cancer with slight variations and recommended management strategies for each -14. It iEven though early attempts for minimally invasive pancreas surgery kickstarted in the 1990s, the adoption of the same was very slow owing to apparent factors such as the complexity of the procedure, lengthy learning curve, etc. The adoption is still very low when it comes to PD, with a 2019 American registry-based study showing that just more than 15% of the PDs were performed minimally invasive [Classical PD and PPPD were equivalent in morbidity and oncological terms, the same as PPPD and\u00a0PRPD, based on meta-analyses of randomized controlled trials (RCTs), the highest level of evidence ,17. PancAs per the International Study Group on Pancreatic Surgery (ISGPS) consensus statement, standard lymphadenectomy for pancreatoduodenectomy should strive to resect lymph node stations 5, 6, 8a, 12b1, 12b2, 12c, 13a, 13b, 14a, 14b, 17a, and 17b . From ouPJ and PG do not differ in the rate of POPF and overall complication rates, as evident from multiple well-conducted RCTs and meta-analyses of RCTs . Still, Invagination and duct-to-mucosa techniques do not differ in terms of POPF rates as per the latest literature ,23.\u00a0StilThe use of prophylactic octreotide is generally found to be not helpful in preventing POPF . In our Currently, there is no high-quality evidence comparing biliary-enteric anastomosis techniques. Comparative data on the different methods of hepaticojejunostomy is available only in the context of liver transplants and few retrospective studies. These studies suggest that an interruptedly sutured hepaticojejunostomy is associated with a higher leakage rate . Our surThe usage of a drain in PD was a controversial subject till 2014, when an RCT published data favoring the usage of drains, stating that avoiding drains increases morbidity and mortality . In our Even though many studies bring the complications of feeding access to light , nearly ISGPS defines POPF as a drain output of any measurable fluid volume with an amylase level greater than three times the upper limit of institutional normal serum amylase activity on or after postoperative day three, associated with a clinically relevant development/condition related directly to the postoperative pancreatic fistula . It has In the literature review, we identified three surveys assessing PD practice -5. Two sThe survey from the UK had 57 participants . SimilarThe Brazilian survey had 51 participants [Despite the valuable insights gained through questionnaire surveys, it is crucial to recognize their potential for bias. Incomplete responses, idealized answers from clinicians, preferential responses from participants, and limited statistical power can all skew the results. This is particularly true in a sprawling country like India when the pool of surveyed surgeons is limited in size, leading to additional limitations in the study.As far as we are aware, this survey marks a pioneering effort to explore the practices surrounding PD in India, a country home to one-fifth of the world's population. A deeper understanding of the practice of complex surgical procedures like PD will be instrumental in standardizing surgical procedures, a pressing need in today's world.The survey results provide valuable insights into the significant disparities observed in the surgical practices of PD among surgeons in India. This heterogeneity is not limited to a particular aspect of the procedure but is apparent across all stages, including evaluation, surgical technique, and postoperative management. The wide range of approaches and preferences among surgeons highlights the urgent need for standardization in order to optimize patient outcomes. Standardization can facilitate a more consistent favorable patient outcomes."} +{"text": "In December 2021, the oral antivirals (OAVs) nirmatrelvir/ritonavir and molnupiravir were authorized for the treatment of COVID-19 in high-risk patients. Initial supplies were limited and states designated pharmacies to receive OAVs from a weekly federal allocation. New York City (NYC) has nearly 3,000 pharmacies serving a diverse population across a large urban area. To ensure fair access to OAVs, the NYC Health Department partnered with an online pharmacy to provide rapid delivery to any NYC address. Here we describe characteristics of patients served and metrics used to evaluate the program as the pandemic and OAV access evolved in 2022.The NYC partner pharmacy provided data on OAV prescriptions including patient age, sex, delivery zip code, and dates of prescription and delivery. These data were matched with the NYC Health Department\u2019s COVID-19 surveillance data including positive lab reported cases, Citywide Immunization Registry, deaths, all-cause emergency department (ED) visits and hospital admissions. Descriptive statistics were calculated using R Statistical Software.A total of 48,947 OAV prescriptions were delivered in 2022, reaching 99.5% of residential zip codes, accounting for 17.5% of the OAVs dispensed in NYC. The median time from prescription receipt to delivery was 17 hours (IQR 6-24) with half (49%) of deliveries going to high social vulnerability zip codes. Of OAV recipients, most (58%) were female, with a median age of 56 years with 32% aged 65 years or older; 78% had received at least a primary vaccination series; 36% matched with a lab reported COVID-19 case; 5.5% had an ED visit and 0.8% were hospitalized in NYC for any cause within 30 days of prescription date.The NYC antiviral delivery program provided broad and timely access to COVID OAVs, serving a significant proportion of patients in high social vulnerability neighborhoods and older adults at higher risk for severe outcomes. Of note, an increasing proportion of people receiving OAVs were not reported as cases to public health, which likely reflects the increasing use of home tests in 2022. Limitations include the lack of data on race/ethnicity, underlying medical conditions and for patients receiving OAVs through other pharmacies.All Authors: No reported disclosures"} +{"text": "Background: Hand-hygiene technology (HHT) intends to monitor and promote hand washing by healthcare workers, a critical measure of infection control. Healthcare worker noncompliance with HHT is a major limitation to its implementation and utility in clinical settings. We assessed perspectives on HHT in an academic hospital system. Methods: Hand-hygiene team members created an anonymous, 37-question, Likert-scale survey to assess healthcare worker attitudes toward HHT. Surveys targeted nursing staff, advanced practice providers, care partners, and internal medicine physicians. Clinical coordinators from 5 distinct nursing units and 1 physician department emailed surveys to eligible employees. Research coordinators and clinical coordinators also posted a QR code for survey fliers at nursing stations. Results: Overall, 120 surveys were completed. Most surveys were completed by nurses and physicians (66.4% and 14.0%). Most respondents (67.5%) do not find HHT useful. Additionally, 78.3% of respondents believe that HHT does not accurately record hand-washing events. Most (78.3%) do not like using HHT, and 75.8% find it annoying. Only 10.8% believe that patient care suffers because of HHT. Conclusions: Most healthcare workers dislike the HHT badges, primarily due to perceived inaccuracies, lack of utility, burden of use, and pressure to comply. Distrust and effect on patient care do not appear to be substantial factors contributing to negative perceptions of HHT. Weaknesses of the study include overrepresentation of nursing staff and potential bias because respondents may have provided exceptionally negative responses believing it could lead to the removal of HHT.Disclosures: None"} +{"text": "Anemia and Diabetes Mellitus (DM) are amongst major clinical and public health challenges in South Asia that influence the progression of chronic health problems in this population. Despite a growing body of research on these problems, there is a lack synthesized evidence on the burden of anemia among people with DM in this region. This meta-analytic review was conducted to estimate the prevalence of anemia among people with DM in South Asia.A systematic search of the literature was conducted in five primary databases and additional sources up to July 29, 2022, that reported the prevalence of anemia among DM patients in any of the eight South Asian countries. Observational studies that met pre-determined eligibility criteria according to the protocol registered in PROSPERO (CRD42022348433) were included in this meta-analysis. Random effect models were used to estimate pooled prevalence.I2 = 99.28%, p = 0.00) among diabetic people in South Asia. In sub-group analysis, the pooled prevalence of anemia was higher in females compared to males . Diabetic patients with older age (\u2265 50 years) reported higher pooled estimates of anemia than younger age group (< 50 years) . In addition, we found variation in pooled prevalence estimates of anemia considering the type of DM, such as type 1 reported 2% (95% CI: 0.00\u20134.00), type-2 reported 48% , and Gestational diabetes mellitus (GDM) reported 6% (95% CI: 3.00\u201312.0).Of the 40 eligible studies, 38 underwent meta-analysis representing 14,194 participants with DM. The pooled prevalence of anemia was 45% (95% CI: 37.0\u201354.0, High pooled estimates of anemia among diabetic patients in South Asia, including publication bias, warrants further clinical and public health research following standard research methods to understand the more context-specific epidemiological insights and evidence. Diabetes is a chronic metabolic syndrome manifested by hyperglycemia, which eventually can cause serious macro and microvascular complications . It is hAnemia is a hematological condition with a global prevalence of 22.8%, while Africa and South Asia were identified as the regions with the highest anemia burden . The conThe dual burden of anemia and DM are challenging from the public health perspective. Evidence suggests that people with DM may have a high anemia prevalence, and chronic anemia can be associated with DM-related complications , 12, 14.This meta-analysis was conducted adhering to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) 15]. Th. Th15]. Anemia is a condition characterized by reduced number of red blood cells or low levels of hemoglobin, leading to diminished ability of the blood to transport oxygen to the body\u2019s tissues . Type-1 We systematically searched five electronically databases\u2013Medline, American Psychological Association (APA) PsycInfo, Academic Search Ultimate, Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Web of Sciences for scholarly articles. The search query was organized using MeSH terms (where applicable), and appropriate set of keywords applied with Boolean operators and retrieved articles from respective databases . The detWe included articles that met the following criteria:observational studies i.e., cross-sectional, case-control, and cohort studies by design.reported prevalence/incidence of anemia (any kind of anemia) amongst persons with Diabetes Mellitus studies conducted in any of eight countries in South Asia.articles published in peer-reviewed journals in selected databases by English language.We excluded articles that did not comply with any of these primary criteria. Case reports, case series, letters to editor, commentaries, protocols, conference proceeding or abstract, and review papers were excluded from this review. Moreover, preprints were excluded since they did not go through the peer-review process.We used a cloud-based systematic review management portal (rayaan.ai) to evaluate all retrieved citations. Two authors independently screened the title and abstract of retrieved articles following removal of duplicates. At the end of primary screening, a third author resolved any conflicts in terms of eligibility of citation through discussion. Then, articles appeared to be eligible and underwent full-text review, data extraction, and subsequent analyses.We have created a template in Microsoft Excel to capture data from the finally recruited articles. Data on the following variables were extracted: author information, year of publication, study design and settings, sample size, study population characteristics, diagnostic cut-off value of hemoglobin and prevalence of anemia in the respective study. Two authors independently extracted data from each of the included articles. Then, these two separate datasets were evaluated by a third author to resolve potential inconsistencies at the end of the data extraction.In this review, we used JBI critical appraisal checklist for prevalence using 9 criteria , which hI2 value. Hence, I2 statistic is categorized as low (25%-50%), moderate (51%-75%), or high (>75%) [Statistical analyses were performed to estimate the pooled prevalence of anemia in diabetes mellitus using a random-effect model with DerSimonian and Laird transformed inverse variance method in STATA SE 17.0 software , 23. Heth (>75%) .Subgroup meta-analyses were conducted for studies reporting anemia by age (<50 years vs \u2265 50 years), gender , duration of having DM (less than 5 years vs 5 years and over), type of DM, population with diabetic complications, study design, country, publication year, sample size, study settings, and risk of bias to identify between-group variations including the possible sources of heterogeneity.Sensitivity analyses were performed to quantify the impact of individual study on the overall pooled estimates and calculated pooled prevalence for rest of the studies after excluding each one.Meta-regression was performed to investigate the association between the potential covariates in studies and pooled prevalence of anemia among Diabetic population. We used mean age, country, sample size, study settings, type of DM, and risk of bias in meta-regression analyses to assess their association with pooled estimates.The visual inspection of forest plot and performing Egger\u2019s regression test were undertaken to evaluate publication bias which may affect the generalizability of the study results. A p-value < 0.05 in Egger\u2019s test was considered as evidence that publication bias exists .A total of 813 articles were retrieved from selected electronic databases, from which 428 duplicates were removed. We found 23 citations that underwent full-text evaluation following preliminary title and abstract screening using pre-determined eligibility criteria. From additional sources, another 26 citations went through full-text evaluation. A PRISMA flowchart illustrating the detailed literature search process is shown in . FinallyThe summary overview of the included articles is provided in \u201cFollowing quality assessment using JBI critical appraisal checklist, we identified 7 studies with low, 11 with moderate, and 22 with a high risk of bias . In addiI2 statistics, which was found statistically significant .Since there was high heterogeneity in the meta-analysis, we conducted sub-group analysis and meta-regression to evaluate the potential source of heterogeneity and correlations between the study-level explanatory variables and pooled estimate. The prevalence of anemia among people with DM was not significantly associated with country context (p = 0.156), study design (p = 0.970), sample size (p = 0.439), type of DM (p = 0.281), study settings (p = 0.720), and risk of bias (p = 0.332) . Only thI2 = 98.94%, n = 34), 2% among Type-1 DM and 6% among gestational DM patients. Female participants showed a higher prevalence of anemia compared to male participants . Considering the mean age or age range of greater proportion of the sample population, we categorized study populations into two groups- less than 50 years and 50 years or more. Hence, diabetic patients aged 50 years or more reported pooled prevalence of anemia of 48% , whereas patients aged less than 50 years reported pooled anemia prevalence of 34% . Since 37% (n = 14) studies specifically reported duration of having DM among study participants, those having DM 5 years or more showed higher prevalence than those of having DM less than 5 years . Few studies explored anemia among patients with diabetic complications and reported prevalence of 68% in diabetic neuropathy, 49% in diabetic nephropathy and 43% in diabetic retinopathy patients.In sub-group analysis, we showed variations in the pooled estimates considering different groups of the study characteristics . We straI2 = 97.67%, n = 5) had the highest prevalence of anemia in DM, followed by Bangladesh and India . Studies with case-control design had pooled prevalence of anemia 47% whereas Cross-sectional studies had 45% and cohort study had 40% anemia prevalence. Studies having smaller sample sizes reported a higher pooled prevalence of anemia compared to larger sample sizes . Moreover, a huge variation in pooled estimates of anemia was observed in different study settings. Hospital-based studies demonstrated pooled prevalence of anemia of 46% , whereas community-based studies reported 16% . We found a lower prevalence of anemia in studies having a high risk of bias and showed an ascending trend with moderate and low risk of bias. Furthermore, studies published in 2020 and afterwards showed a little higher prevalence of anemia than studies published before 2020 .At the country level, Pakistan compared to type-1 and gestational DM (6% (95% CI: 3.00\u201312.0). Female diabetic patients reported a prevalence of anemia of 48% (95% CI: 37.0\u201360.0), whereas males reported 39% (95% CI: 29.0\u201348.0). In addition, we found a higher anemia burden among diabetic patients aged 50 years or over than their younger aged counterparts . Since the majority of studies recruited sample population from the hospital, pooled estimates of anemia in the community and hospital-based settings showed substantial variation in sub-group analysis. Studies with low risk of bias reported a higher anemia prevalence, followed by studies with moderate and high risk of bias .The overall pooled prevalence of anemia was 45% (95% CI: 37.0\u201354.0) with 14194 DM patients in South Asia- which was higher than the prevalence of anemia among DM patients in Africa [12 deficiency, and systemic inflammation [In this study, female diabetic patients in South Asia reported a higher prevalence of anemia compared to their male counterparts 39% (95% CI: 29.0\u201348.0). However, this finding contradicts other evidence from the USA and African countries , 67, 68.ammation \u201375. A diammation .Understandably, most of the studies included in this review reported the prevalence of anemia among type-2 diabetic patients due to its growing burden in South Asia. Patients with type-2 DM were two-fold more likely to develop anemia than patients without DM . The preOnly one study reported anemia prevalence in patients with gestational DM (GDM), which was 6% (95% CI: 3.00\u201312.0). Although there is limited evidence, it implies that GDM may be associated with iron disorder, providing a basis for further investigation. The relationship of anemia and GDM is yet to conclusive, however suggested an inverse association. A retrospective case-control study found that pregnant women with iron deficiency anemia had lower risk of developing GDM . Some stThe risk of microvascular complications can be accelerated among diabetic patients in the presence of anemia , 86. We In patients with DM, anemia is identified as an independent risk factor for the progression of diabetic microvascular complications , 90, 95.I2 statistics. Studies conducted in hospital settings showed a higher pooled prevalence of anemia compared to studies based on community . Of the hospital-based studies, a small variation in the pooled prevalence of anemia was observed considering the location of recruitment such as In-patient department (IPD) , Both OPD & IPD/unspecified , and out-patient department (OPD) . The huge variation in the pooled estimation of anemia in study settings may occur since the tendency of diabetic patients visiting the hospital are more likely to be in poor health status than patients recruited from the community. Moreover, substantial changes in socioeconomic, lifestyle, and dietary behavior due to rapid urbanization, industrialization, and technological advancements resulting a high burden of metabolic risk factors among south Asians [Sub-group analysis revealed the highest prevalence of anemia in Pakistan , followed by Bangladesh and India . However, these interpretations should be used cautiously due to the high heterogeneity marked by h Asians , which mConsidering study quality, studies with a low risk of bias reported the prevalence of anemia at 50% (95% CI: 26.0\u201374.0) and descended in moderate and high risk of bias . Studies with case-control and cross-sectional design showed somewhat similar prevalence of anemia among diabetic patients while cohort study reported a lower prevalence. However, most studies had serious methodological limitations regarding study design, sampling, and recruitment strategy. Studies with case-control and cohort design did not elaborate on details of recruiting case and control groups in method sections, leaving their studies seriously inconsistent. Furthermore, heterogeneity and variability of pooled estimates as indicated in sub-group analysis may result due to methodological and other population-level differences across the studies. High publication bias in this review emphasizes the lack of overall research evidence that reflects a research gap in the related field. Additionally, inadequate information on the sociodemographic, household, and other modifiable/non-modifiable risk factors limits our ability to assess further potential sources of variances in population groups. Diverse study settings, including a greater number of hospital studies and a few community-based studies, may affect the true burden of anemia within the study population. Since a major proportion of the recruited studies had low quality, it compromised the generalizability of synthesized findings. Despite such limitations, this quantitative synthesis of epidemiological evidence may provide a broader and contextual understanding that can be useful for evaluating the current burden of anemia in diabetic patients and its contributing factors.The summarized evidence can facilitate establishing country-specific or regional priorities in developing and implementing pragmatic, cost-effective, scalable, evidence-based policies in reducing diabetes mellitus and related complications. Hence, need to focus on the following areas: increasing community awareness, screening of high-risk groups, prioritizing vulnerable groups of people , strengthening primary or community health centers for regular hematological screening, early diagnosis, and timely management, and effective referral system by connecting health centers across different tiers. Finally, intervention studies are required by addressing all modifiable determinants to establish context-specific, cost-effective strategic plans for preventing and managing anemia in diabetes among the South Asian population.This review implies that anemia is a critical public health burden among patients with DM in South Asia. These suggest the inclusion of anemia screening into the routine assessment for early diagnosis and management that may deter the progression of diabetes-related complications. However, limited research, high heterogeneity, and low-quality studies necessitate more clinical and epidemiological research following a high scientific protocol to investigate the pathophysiology of anemia among DM patients in South Asia.S1 Checklist(PDF)Click here for additional data file.S1 Fig(TIF)Click here for additional data file.S2 Fig(TIF)Click here for additional data file.S1 Table(PDF)Click here for additional data file.S2 Table(PDF)Click here for additional data file.S1 File(PDF)Click here for additional data file."} +{"text": "Recent trends in prostate cancer incidence suggest that widening cancer disparities mean a greater number of prostate cancers in Black men . Black mThe distribution of prostate cancer across Florida remains uneven, with Black men bearing the greatest burden . AlthougThis study focuses on prostate cancer screening among all reported Black respondents between 2012 and 2020. The geographic unit of analysis was state-level data to identify trends over time in prostate cancer screening. Additionally, we incorporated complete county-level data to show patterns of screening distribution.Sample survey data were obtained from the Florida BRFSS, an annual survey distributed to civilian, noninstitutionalized Florida adults aged 18 years or older, using random-digit\u2013dialed landline and cellular telephone numbers. Florida BRFSS collects information on sociodemographic characteristics, health behaviors, health care access, and preventive health practices, including cancer screening. Prostate cancer screening questions are included on the Florida BRFSS during even-numbered years as part of the rotating core questionnaire in 2012 to 36.4% in 2020, representing 503,443 fewer Floridians screened for prostate cancer. Relative to differences in prostate cancer screening prevalence between individual years within the period, the percentage of Florida male residents who received a PSA test in the past 2 years declined from 51.2% in 2012 to 49.7% in 2014, a 2.9% decrease; and from 49.7% in 2014 to 46.2% in 2016, a 7.0% decrease. A 14.5% reduction occurred between 2016 and 2018, from 46.2% to 39.5% , and another 7.8% between 2018 and 2020, from 39.5% to 36.4% .The investigation of these PSA testing trends by race and ethnicity resulted in substantial differences. In 2012, the highest screening prevalence was for non-Hispanic Black men and non-Hispanic White men , followed by Hispanic men . The greatest decline in prostate cancer screening between 2012 and 2020 was for non-Hispanic Black men (37.8%), while the screening rate for non-Hispanic White men decreased to 30.4%.The continuous increase in prostate cancer incidence from 2014 to 2019 urges imA strength of our study was the use of a large, state-level health surveillance system generalizable to the Florida population to examine trends in PSA screening over time and across racial and ethnic groups. Another strength was our in-depth exploration of disparities in PSA screening frequency at the county level to better understand geographic heterogeneity in screening. Our study also has limitations. First, because BRFSS data are self-reported, the prevalence of prostate cancer screening may have been underestimated or overestimated, leading to measurement error, especially during the COVID-19 pandemic. Second, not all respondents eligible for the BRFSS prostate cancer screening module answered all the questions, resulting in missing data."} +{"text": "Background: The burden of hospital-associated infections (HAIs) and antimicrobial resistance (AMR) in Latin America is high. Improving engagement by healthcare workers (HCWs) in infection prevention and control (IPC) may lead to better patient outcomes; however, little is known about HCW perceptions of IPC in the region. We sought to understand HCW perceptions of IPC processes and practices. Methods: During August\u2013September 2022, HCWs from 30 hospitals with IPC programs in 4 Latin American countries were invited to participate in an electronic, voluntary, anonymous survey about their perceptions of IPC at their hospitals. Physicians, nurses, and environmental care (EVC) personnel were prioritized for recruitment. All respondents were asked 18 questions; IPC team members were asked 5 additional questions about specific activities implemented by IPC programs, how data are used, and how IPC could be improved. Answers with 5-point Likert scale responses were categorized into 2 groups for analysis. Results: Of 1,252 HCWs who completed the survey, 181 (14%) were IPC team members, 1,095 (87%) had direct patient contact, and 1,156 (92%) worked >20 hours per week. Figure 1 shows participant characteristics. Most participants (56%) rated their IPC program as very good, 38% rated it as good, and 6% rated it as bad. Physicians were less likely to give a favorable rating. Compliance with prevention bundles and hand hygiene (HH) by colleagues was rated as poor by 28% and 22% of HCWs, respectively; however, only 11% and 5% indicated that their own compliance was poor, respectively. Also, 25% of participants reported not receiving or only occasionally receiving HH compliance data. Similarly, 41% of participants reported not receiving HAI data on a regular basis, and 19% of IPC nurses reported not receiving data despite being responsible for conducting surveillance. Furthermore, 41% of respondents indicated not receiving or only occasionally receiving IPC training or education relevant to their role. When asked about the safety climate, 16% of participants reported not feeling appreciated. In addition, 22% of IPC nurses and 37% of individuals in the \u201cother\u201d category were more likely to report this. When IPC team members were asked how frequently specific activities were conducted , several opportunities for improvement were identified, including improving HCW access to HH data and development of strategic plans. Conclusions: Improving HCW access to training on IPC and to data on HAI burden and compliance with HH and prevention bundles should be emphasized in Latin American hospitals.Disclosures: None"} +{"text": "Central catheters expose ICU patients at risk of catheter-related bloodstream infections. A mechanism by which these infections occur is the contamination of the catheter during its insertion if aseptic techniques are not strictly applied. Recent studies suggest that the use of ultrasound guidance (USG) may increase the risk of catheter contamination during insertion. We assessed current practices regarding the use of USG during catheter insertion, with a focus on identifying breaches of the surgical asepsis required for this invasive procedure.In 26 intensive care units, we evaluated the use of USG during catheter insertion, using a questionnaire addressed to intensivists and direct observation of their practices.We analyzed 111 questionnaires and 36 observations of intensivists placing catheters. The questionnaires revealed that 88% of intensivists used USG for catheter insertion. Among those using USG, 56% had received specific training, 17% benefited from specific recommendations, 76% marked the insertion site before skin antisepsis, and during catheter insertion, 96% used sterile gel and 100% used a sterile sheath and sterile gloves. We identified potential deviations from strict aseptic technique, including contact between the sheath and the needle (19.4%), handling of the US system during catheter insertion (2.8%), and use of sterile devices, where they were not yet necessary (during the marking site or skin antisepsis), resulting in their contamination at the time of catheter insertion.Interventions aimed at ensuring compliance with measures to prevent CRBs should be organized to prevent an increase in infections associated with US-guided catheter insertion.The online version contains supplementary material available at 10.1186/s40001-023-01518-4. Critical care patients often require the use of intravascular catheters for their treatment, but these devices also increase the risk of catheter-related bloodstream infections (CRBs) . One of Between January 1st and July 31st, 2022, we conducted a two-part study among French intensivists. In the first part, we asked intensivists to describe their use of USG during the insertion of CVCs, dialysis catheters (DCs), arterial catheters (ACs), peripheral intravenous central catheters (PICClines) and MIDlines in ICU patients. The questionnaire collected information on the types of catheters inserted with USG, insertion sites, frequency of USG use, training, and the use of a procedure , frequently (n\u2009=\u20092), sometimes (n\u2009=\u200910), or rarely (n\u2009=\u20095).111 intensivists, including 26 residents (23.4%), completed the questionnaire , were observed inserting catheters . Of the intensivists, 44.4% had received training on USG, mostly during their initial/continuing education (68.7%). Before skin antisepsis, 58.3% marked the insertion site using USG, with 28.6% using a sterile sheath and 23.8% using sterile gel. Compliance with skin antisepsis recommendations was satisfactory , except for the use of a 2% chlorhexidine alcoholic solution (36.1%) and hand hygiene compliance (63.0%). For catheter insertion, a sterile sheath covering the probe and cable was used in 88.9% of cases, and single-dose sterile gel was applied in all cases. However, only 33.3% of intensivists complied with surgical hand disinfection and/or wearing sterile gloves. In 19.4% of cases, the tip of the needle came into contact with the sheath, and one intensivist handled the US system without changing their gloves after the incident (2.8%) by 111 intensivists for catheter insertion, according to catheter type. Table S2. Use of gel and sheath (%) by 105 HCWs for site marking and catheter insertion."} +{"text": "State-of-the-art research highlights that borderline personality disorder have high rates of comorbid Axis I disorders, which imply uncertainty in establishing an accurate diagnosis and can be some of the most challenging patients for clinicians and researchers.This study seeks to observe the diagnostic stability in borderline personality disorder patients, in order to increase empirical knowledge through a retrospective look at the historical line of diagnoses.th Revision (WHO ICD9). A 346 patients\u2019 sample was identified aged between 18 and 83 years ; excluding organic cerebral syndrome and no comorbidity besides drug abuse, or no comorbidity at all.A twenty-year retrospective study at a psychiatric hospital, searching at the electronic clinical records for all patients with borderline personality disorder diagnosis, under the code 301.83 from World Health Organization\u2019s International Classification of Diseases, 9As a general observation, the following diagnoses are indicated: 44.09% major depressive disorder, 33.16% affective disorder, 13.05% schizophrenia, and 9.70% mania. As a spectrums disorders analysis , differential percentage occurrences are identified in patients with borderline personality disorder.Image:Based on clinical diagnoses records of borderline personality disorder patients, some spectrums disorders are highlighted, to be reported in descending order of incidence: depressive, affective, schizoaffective and schizophrenia spectrums.None Declared"} +{"text": "IntroductionHereditary bleeding disorders, such as hemophilia and von Willebrand disease (VWD), result from specific deficiencies or malformations in the coagulation cascade proteins. These disorders can significantly impact both physical and psychological health. Complications such as depression, anxiety, and stress (DAS) can further exacerbate these impacts. Despite their significance, detailed prevalence data remain limited, especially for regions such as Madinah province in Saudi Arabia. This study aimed to determine the prevalence of DAS and their associated risk factors among patients with hereditary bleeding disorders in Madinah province, Saudi Arabia.MethodsWe conducted a cross-sectional study using telephonic interviews involving patients diagnosed with severe hemophilia A or B or VWD attending a hematology clinic in Madinah. Patients over 10 were included, and the study excluded those with central nervous system insults and platelet count concerns. The validated and reliable Depression Anxiety Stress Scale-21-item questionnaire and Statistical Product and Service Solutions (SPSS), version 26.0 , facilitated data collection and analysis, respectively.ResultsOf the 44 patients studied, 25% exhibited symptoms of depression, 45.5% showed signs of anxiety, and 29.5% had stress symptoms. Regarding symptom severity, 9.1% of patients experienced extremely severe depression, 15.9% had moderate anxiety, and 13.6% reported moderate stress. The prevalence of these psychological issues varied with patients' age and economic status. Notably, a significantly higher rate of depression was observed in patients over 15 years . Additionally, while not statistically significant, patients with a high economic status reported increased rates of DAS.ConclusionsPatients with inherited bleeding disorders, particularly those older than 15, manifest significant psychological distress. There is a pressing need for enhanced awareness, specialized screenings, and tailored counseling services to improve treatment adherence and overall quality of life. Given the findings, a comprehensive national study in Saudi Arabia is highly recommended, alongside the integration of specialized psychological services. Hereditary bleeding disorders arise due to a decrease or absence of specific clotting proteins in the coagulation cascade. The three most common inherited bleeding disorders are factor VIII deficiency (hemophilia A), factor IX deficiency (hemophilia B), and von Willebrand disease (VWD) . HemophiThe signs and symptoms of hemophilia vary based on disease severity, which correlates with factor levels. Patients with mild hemophilia often present symptoms later in childhood. In contrast, severe cases might manifest as early as the neonatal period, with most diagnoses occurring within the first year of life. Factor levels can be influenced by both age and the patient's blood group. Thus, it is crucial to account for physiological variations in factor levels when diagnosing factor deficiency. If not appropriately managed, hemophiliac patients can develop severe complications, including joint deformities that limit movement, contractures, chronic pain, muscle atrophy, and significant neurological issues .von Willebrand factor, a glycoprotein, plays a crucial role in both primary hemostasis and the intrinsic pathway of secondary hemostasis. It is the most prevalent congenital bleeding disorder globally, impacting both sexes since it follows an autosomal inheritance pattern. Depending on the disease type, patients might exhibit a total absence, partial absence, or functional anomaly of the von Willebrand factor ,4.All hereditary bleeding disorders can inflict considerable psychological strain on both patients and their families. Symptoms such as depression, anxiety, and stress often stem from the disease's chronic nature and its associated physical complications. The ensuing financial hardships, potential unemployment, and frequent school absences or failures can further deteriorate their psychological health . This stWe conducted a cross-sectional study using questionnaires via individual telephonic interviews with patients and their families. Interviews were initiated after securing approval from the Taibah University Research Ethics Board Committee .We included patients older than 10, diagnosed with severe hemophilia A or B or VWD, who were registered with the Madinah Hereditary Blood Disorders Charity Society in the year 2022, resided in Madinah Province, and spoke Arabic. Patients were only included after providing informed consent. We excluded patients with a central nervous system insult, either from a prior bleed or another disease, and patients with platelet count issues or functional disorders. The questionnaire captured demographic information, such as age, sex, nationality, family residence, and economic status.Post-data extraction, we rigorously reviewed and coded the information, ensuring the highest standards of patient confidentiality. Statistical analysis was performed using Statistical Product and Service Solutions (SPSS), version 26.0 . Numerical data were described as mean (\u00b1SD), while frequencies (number of cases) and valid percentages represented categorical variables. We employed the chi-square and Fisher's exact tests to ascertain the association between depression, anxiety, stress, and demographic factors. A p-value less than 0.05 signified statistical significance.The Depression, Anxiety, and Stress Scale-21-item questionnaire (DASS-21) was used to determine emotional states. The DASS-21 comprises 21 questions, with every seven questions assessing one emotional state: depression, anxiety, or stress. The depression subscale encompasses questions 3, 5, 10, 13, 16, 17, and 21. The anxiety subscale features questions 2, 4, 7, 9, 15, 19, and 20. The stress subscale includes questions 1, 6, 8, 11, 12, 14, and 18. For each subscale, the total score of the seven questions (multiplied by two) categorizes the severity, from normal to extremely severe, of depression, anxiety, or stress.The study included 44 participants diagnosed with one of the inherited bleeding disorders: hemophilia A or B or VWD. The mean age of the participants was 17.5 (\u00b17.4). A substantial majority, 95.5%, hailed from Saudi Arabia, and 88.6% resided in Al-Madinah City. Over half of the participants, 52.3%, were classified within a high economic status level. Table When assessing the prevalence of depression, anxiety, and stress among the participants, it was determined by aggregating the scores across the mild, moderate, severe, and extremely severe degrees. Our findings indicate that 25% of the participants exhibited symptoms of depression, 45.5% showed signs of anxiety, and 29.5% demonstrated symptoms of stress, as illustrated in Figure Regarding the severity of emotional states, 9.1% of the participants reported experiencing extremely severe depression. In contrast, 15.9% were found to have a moderate level of anxiety, and 13.6% indicated a moderate stress level. Figure On further examining the factors linked to the prevalence of depression, we observed that depression was significantly more common in participants over 15 years (p=0.009), as highlighted in Table Our analysis also explored the correlation between participant characteristics and degrees of depression. Age emerged as a significant determinant influencing depression levels, with a p-value of 0.009 Table .Conversely, the participant characteristics exhibited no significant impact on the degrees of anxiety or stress, as delineated in Tables Depression affects approximately 350 million people globally and is projected to become the second leading cause of debilitating illness by 2030 . PatientRecent research corroborates these high prevalence rates. A cross-sectional study noted that 33% of patients with congenital bleeding disorders experienced anxiety, 64% depression, and 60% other minor psychological complications ,8. An anMost prior studies employed the Patient Health Questionnaire-9 and Generalized Anxiety Disorder 7-item scale to diagnose depression and anxiety. We opted for the DASS-21 due to its validation in Arab populations. Our region's emphasis has often been on assessing the health-related quality of life (HRQoL) among these patients to understand the impacts on various life aspects, guiding subsequent decisions. A study at King Khalid University Hospital in Riyadh found that a significant portion (89.7%) of hemophilia patients experienced knee joint issues. While treatment concerns were a prominent challenge, dimensions such as work/school, family, and social life were less affected .The prevalence rates we observed varied based on patient characteristics. We noted a significantly higher depression rate in patients over age 15 . This aligns with previous findings: a similar 33% rate of depression in adult hemophilia patients . Hence, Interestingly, our findings of lower DAS rates in patients aged 15 or younger contrast with some previous studies. One study, for instance, found that VWD patients aged 12-17 years had a higher depression rate than adults aged 18 years or older . The same study also found a higher anxiety rate in the 12-17-year group , although the difference was not statistically significant . This paAdolescents with inherited bleeding disorders are navigating the transition to adulthood, assuming greater self-care responsibilities. Our data showed that being unmarried was significantly associated with anxiety, underlining the value of robust social support networks for individuals with VWD. However, in the general population, earlier studies from the USA report a lower prevalence rate for depression and anxiety, ranging between 6% and 9% in younger demographics -17.Though not statistically significant, we observed a variation in the prevalence of depression by patients' economic levels. Notably, rates of DAS were higher among those reporting a higher economic status. The influence of socioeconomic status (SES) on depression is well-documented, with a significant association between depression and income observed across many countries . Our resRegarding the high prevalence rate of severe DAS among patients aged 15 years or older, especially those with higher income levels, a different retrospective case-control study on hemophilia patients showed that younger patients exhibited milder depression symptoms compared to a healthy control group without hemophilia (2%) . AnotherThis study's strengths lie in its unique contribution to the limited current research on this crucial medical topic. To our knowledge, this is the first study from Madinah Province examining the extent of psychological burdens, especially concerning patients' age and economic status. Moreover, the employment of DASS-21 for psychological disturbance screening, previously validated for the Arab population, strengthens our research methodology. DASS-21, developed by Antony et al. in 1998,However, we must also acknowledge the study's limitations. Its cross-sectional nature precludes causal inferences. Cultural sensitivities in the study area might have made certain depression-related factors challenging to measure. Furthermore, since our sample comprises only hemophilia and VWD patients from Madinah Province, generalizing our findings to the entire inherited bleeding disorder patient population in the Kingdom or region becomes challenging. Nevertheless, our primary objective was to determine psychological burden prevalence, thereby enhancing regional literature on the topic.This study underscores the high prevalence of psychological burden in patients with inherited bleeding disorders, especially those over age 15. Acknowledging these findings in hemophilia treatment centers may elevate awareness among patients and healthcare providers. This awareness can propel the adoption of specialized screening tools, especially for high-risk patients.Proactively screening for psychological burdens can enhance patient adherence to treatment, potentially reducing bleeding episodes and improving their quality of life. These insights should motivate hematologists and psychiatrists to design a comprehensive national multicenter study involving multiple hemophilia centers in the Kingdom. Such initiatives aim to establish robust psychological counseling services and possibly culminate in national guidelines addressing these concerns."} +{"text": "The effect of psychotropic drugs on sexuality is difficult to evaluate because psychiatric disorders are frequently accompanied by sexual dysfunction, independently of any drug intake. However, the iatrogenic aspects of psychotropic drugs linked to their side effects should not be underestimated since they are an important cause of treatment discontinuation.The aim is to show the type of sexual impairment observed according to the different psychotropic drugs used and the means to remedy it. Psychiatric disorders are accompanied by sexual dysfunctions which can be aggravated by psychotropic drugs, and the associated risk factors can be sought or aggravate this undesirable effect.This is a cross-sectional study, concerning patients followed at ArRazi hospital under antipsychotic treatment. We used the \u201cInternational Index of Erectile Dysfunction\u201d scale, and the data were analyzed by SPSS software.68% are men, Age: 71% are between 20 and 50 years old.Marital status: 43% are single, 24% are married, 34% are divorced.83% have a low socioeconomic level, 45% have a family history of a psychiatric disorder.58% of patients have a substance use disorder.38% of patients consulted for a psychotic syndrome, 23% for a depressive syndrome, 17% for a manic syndrome, 11% for a behavioral disorder, 6% for a suicide attempt.46% of the medications are antipsychotics, 18% are antidepressants, 15% are mood regulators.83% of the sexual disorder appeared in the first 5 years.72% of the patients did not receive information by their doctor about this side effect.64% of the patients informed their doctor.32% stopped the treatment, 47% asked to change the treatment.Careful assessment of sexual function at the initial visit followed by monitoring at subsequent visits is essential. Treatment of adverse sexual effects may be pharmacological, behavioral, complementary and integrative, or a combination of these modalitiesNone Declared"} +{"text": "Antibiotic prophylaxis before dental procedures (DP) in patients with prosthetic joints has not been shown to decrease the risk of prosthetic joint infections (PJI). Current American Academy of Orthopedic Surgeons (AAOS) guidelines do not recommend DP in low-risk patients, and no longer mention clindamycin for penicillin allergic patients. The CDC recently prioritized antimicrobial stewardship (AS) for dental procedures. Orthopedic provider compliance with AAOS guidelines is unknown.This was a single-center, retrospective study of patients who underwent primary hip or knee replacement (TJR) from January to October 2019, and received DP prescribed by an orthopedic provider from the time of TJR through August 2021. DP was determined by chart review. Appropriateness was assessed according to 2016 AAOS guidelines. Further data was recorded, including demographics, pertinent orthopedic history, risk factors for PJI, and possible adverse effects from DP.Of 1800 patients that were evaluated, 250 patients (13.9% of TJR) were given 258 prescriptions for DP. 64.8% were prescribed by advanced practice providers. Of the patients who received DP, 66.8% were female, and 22.5% were obese. There were slightly more hip replacements than knee replacements. 2.7% of patients were immunocompromised per AAOS definitions. Of the 33 diabetic patients, 87.9% were well-controlled, and thus considered low- risk. 240/258 prescriptions for DP (93%) were inappropriate, with the great majority of those in low-risk patients. Five patients inappropriately received clindamycin. Two patients received the incorrect dosage of antibiotic. Within 6 months of DP, C. difficile was diagnosed in 0.4% of patients, and resistant organisms from any source were cultured in 0.4% of patients. One patient developed PJI within one year of TJR, despite receiving DP.Though only a minority of patients undergoing TJR received DP, most were low-risk patients and thus considered inappropriate per 2016 AAOS guidelines. Further study is warranted, including analysis of dentists and other providers\u2019 prescribing of DP, use of targeted educational materials, and utility of electronic health record order sets.All Authors: No reported disclosures"} +{"text": "Objectives: As no data are available regarding the influenza vaccination status of Swiss healthcare workers (HCW) in the ambulatory setting, this study aims to investigate their influenza vaccination behaviours.Methods: We conducted an online survey using a four-item, semi-structured questionnaire to assess HCWs influenza vaccination coverage and behaviour. Associations between influenza vaccination status, age and language as well as recommendation behaviour and reasons for vaccination were assessed using descriptive statistics and logistic regression analyses.Results: Of the 1057 completed questionnaires, 425 (40.2%) HCW were vaccinated and 632 (59.8%) not. 78.1% of the physicians and 47.3% pharmacists were vaccinated, compared to only 29.1% of the nurses, 24.3% pharmacy technicians and 13.0% medical practice assistants (MPA). There was a significant association between influenza vaccination status and HCW profession, age, language and how often an influenza vaccination recommendation was made.Conclusion: Demographic factors seem to influence HCWs\u2019 attitudes towards influenza vaccination, which in turn affects the prospect of them recommending the influenza vaccination. Diverse strategies might be necessary to encourage HCW to get vaccinated and hence, promote influenza vaccination. Vaccinations are one of the most effective public health measures to prevent the spread of infectious diseases, which is considered a human right .Orthomyxoviridae family are also recommended to get vaccinated in order to protect the vulnerable populations in their care . A surveStudies on the benefit of HCW being vaccinated as well as their vaccination coverage against influenza are diverse, small or of low quality and show mixed evidence. Nevertheless, the importance of HCW being vaccinated against influenza is indisputable \u201314. WorlSwitzerland\u2019s population was approximately 8.4 million people in 2016 . With 26This cross-sectional study was conducted in autumn 2016, concerning the influenza season 2015/16. Data was collected anonymized at the individual level using a semi-structured online-questionnaire in three of the four official Swiss languages - German, French and Italian.Assuming an influenza vaccination coverage of 30% among HCW and a population size of approximately 77,800 HCW \u201325, we cvia participating national professional societies, healthcare leagues and medical networks (HMOs) who sent a short descriptive text about the survey and the links to the online questionnaires in a single newsletter or direct electronic mailing to their members. To ensure absolute anonymity of the data, the online platform Survey Monkey was set up for the responses to not be traceable to the source of input. Participation was voluntary and the mailing was done only once. By responding to the survey, the participants consented to the fully anonymized use of the submitted data for analysis. The questionnaire was available online during the month of November 2016.The target population consisted of HCW in an ambulatory setting, namely physicians, pharmacists, nurses, medical practice assistants (MPA) and pharmacy technicians as well as other HCW in diverse functions. Participants were recruited An enquiry to the Ethics Committee confirmed that the study did not fall within the scope of the Human Research Act (HRA) and authorization was not required (BASEC Nr. Req-2023-00101).The questionnaire contained a demographic section and four items regarding the study objective. The demographics age, sex and healthcare profession/function were collected. The four items included: 1) influenza vaccination status during the preceding winter 2015-16, 2) reasons for getting/not getting an influenza vaccination, 3) how often they recommended the influenza vaccination to their patients and 4) reasons for and not recommending the influenza vaccination HCW completed the questionnaire. 3 cases did not indicate their influenza vaccination status and sex was missing in 3 cases, leaving 1057 cases for further analysis. Among these were 11 different HCW professions, with highest participation seen in pharmacists (41.0%), physicians (14.3%), pharmacy technicians (13.2%), nurses (10.4%) and MPA (9.5%) . The geop = 0.000): 78.1% of physicians, 47.3% of pharmacists, 29.1% of nurses, 25.0% of psychosocial counsellors, 24.3% of pharmacy technicians, 20.8% of other health professions, 20% of management/administration, 13% of MPA, 7.7% of prevention/public health officers and 17.9% of Others being vaccinated against influenza. Two participants identified as Other Medical Professions were not vaccinated.There was a significant difference in the vaccination coverage across the 11 HCW professions , where 37.3% of German-speaking participants reported receiving the influenza vaccination. With the French-speaking participants, this figure was 48.1% and with Italian-speaking participants 36.4%. In p = 0.000) and physicians: Chi-square = 10.04, p = 0.007; in contrast, there was no significant association between language and likelihood of vaccination among pharmacists and nurses .We further examined the relationship between profession, language and vaccination status. Based on the number of participants, this analysis was only conducted for physicians, nurses, pharmacists and pharmacy technicians . There wp = 0.000) between age and vaccination status .In the questionnaire, five reasons to be vaccinated against the influenza were listed: self-protection, patient protection, to protect family members, role model function, good experience with earlier vaccination, or another specific reason . Of the Fourteen reasons not to be vaccinated against the influenza were also listed on the questionnaire . Of thesp = 0.000). Physicians, pharmacists, nurses and MPAs most likely either always recommended vaccination to their patients or only in certain cases . Of these four HCW, 67.3% of physicians, 61.8% of pharmacists and 57.4% of nurses always recommended vaccination to their patients compared to only 43.3% of MPA.p = 0.000). Of the 616 HCWs who were not vaccinated, 8.9% never recommended vaccination to their patients, 54.4% did so only in certain cases and 36.7% always recommended vaccination. When looking at the 424 HCWs who were vaccinated, 0.9% never recommended vaccination to their patients, 23.3% did so only in certain cases and 75.7% always recommended vaccination . Among 698 German-speaking HCWs 47.9% always recommended vaccination to patients, 6.0% never recommended vaccination, and 46.1% recommended vaccination only in certain cases. Out of 288 French-speaking HCWs, 63.2% always recommended vaccination to patients, 5.9% never recommended vaccination, and 30.9% recommended vaccination only in certain cases. With the 54 Italian speaking HCWs, 57.4% always recommended vaccination to patients, 0% never recommended vaccination, and 42.6% recommended vaccination only in certain cases were most likely to be vaccinated, followed by pharmacists (47%), nurses (29%), pharmacy technicians (24%) and MPAs (13%), who appeared to be more critical of vaccinations. Various international studies have confirmed this trend, with a closer examination in the following case studies: A study in Italy confirmed a significant global vaccination hesitancy in nurses, finding far lower than optimal vaccine rates among nurse practitioners , and a sCompared to German- and Italian-speaking HCW, French-speaking HCW in Switzerland were more likely to be vaccinated. French-speaking pharmacy technicians and physicians had a higher prospect of being vaccinated compared to their German- and Italian-speaking counterparts. This observation corresponded with the findings of a previous study that concluded that the HCWs in French speaking-regions of Switzerland had the highest influenza vaccination coverage . It is hThe average age of HCW was a notable factor in vaccination rates, with distinct vaccination behaviour discrepancies among the various age ranges. Younger HCW were less likely to get the yearly influenza due to feeling stronger and healthier, an attitude corroborated by a study carried out in Turkey after the H1N1 influenza pandemic in 2009 . A majorAs confirmed in previous studies , 36, selHCW who were vaccinated were more likely to recommend vaccination for their patients, which was supported by another study on immunization attitudes of vaccinated physicians . 75.8% oOne limitation of this study is the unknown response rate due to the recruiting method, as the participating organisations sent out the link to all their members but the exact number of recipients and people who read the newsletter or direct mailing could not be assessed. Therefore, we could not determine the representativeness of the results. As we also relied on the distribution of the questionnaire-links on professional societies and other organisations to recruit participants, we cannot guarantee that only HCWs from the ambulatory sectors participated in the study. However, the participating professional societies and the other participating organisations comprise of mainly HCW from the ambulatory setting or work exclusively in the ambulatory setting, respectively. Additionally, selection bias was highly possible, as participants who were more likely to have a positive attitude towards vaccinations or were more interested in the topic would respond. For example, as the participating organizations were members of the non-profit association QualiCCare and therefore known for their investment in quality of care, their members might have also shown a higher affinity to the investigated topic. Additionally, the high participation of female HCW in this study could have biased the results as female HCW have a higher tendency to provide or recommend vaccinations to their patients . HoweverAlthough the questionnaire was not pre-tested for reliability and validity prior to its distribution, the evaluation of the responses showed no misleading questions. Our survey could serve as a pilot study which could be used to develop further research with a larger sample size overall to gather more data on HCW attitudes towards the influenza vaccination, its effect on the general population, and their vaccination uptake.As this study occurred prior to the COVID-19 pandemic, it would be beneficial to examine how attitudes and behaviours towards vaccinations have changed in Switzerland with the new global pandemic , 44. HCWOur study analysed different factors that could affect the vaccination behaviours of HCW, which can be ultimately used to positively affect the populations\u2019 attitudes toward influenza vaccination. Demographic factors seem to influence the HCWs\u2019 attitudes towards influenza vaccination, which in turn affects the prospect of them recommending the influenza vaccination. Diverse strategies might be necessary to encourage HCW to get vaccinated and hence, promote influenza vaccination."} +{"text": "BackgroundSarcopenia is highly prevalent among elderly patients with hip fracture. Studies reported a significant association between sarcopenia and clinical outcomes in patients with hip fractures. The current study aimed to determine the prevalence of sarcopenia among elderly patients with hip fracture and its effect on short-term functional outcomes, highlighting predictors of postoperative functional decline.\u00a0Methods;\u00a0sarcopenia\u00a0using the SARC-F questionnaire assessing strength, ambulation, rising from a chair, climbing stairs, and fall history. Perioperative risk assessment and post-discharge care were obtained through medical records and by questioning patients or families. Preoperative sarcopenia was confirmed using the Ishii equation which is an equation that includes .This is a cross-sectional study followed by a prospective cohort. Elderly patients (60 years and above) with hip fractures\u00a0were recruited from the orthopedic department. Patients were followed by the ortho-geriatric team in the perioperative period and for three postoperative months. Patients were subjected to comprehensive geriatric assessment including a full history and physical examination. In the preoperative state and after three months of follow-up the following were assessed:\u00a0functional independence using the Barthel index (BI); nutritional state using a checklist named DETERMINE Your Nutritional HealthResultsPreoperative sarcopenia screening showed that 29.3% of patients suffered sarcopenia by SARC-F questionnaire and 28.6% by Ishii equation score. At the end of the follow-up, 57.9% of patients suffered sarcopenia by SARC-F questionnaire. There was a marked post-fracture decline in independence level; 52.1% had slight dependence in function, 27.1% had moderate dependence in function, and 20.7% had total dependence in function.ConclusionThis study gives us the chance for a greater understanding of the negative effects of sarcopenia on the outcomes following hip fracture surgery in the geriatric population. It shows a prevalence of sarcopenia among the elderly with hip fractures at 29.3%. The elderly experience a marked post-fracture decline in their level of independence concerning basic activities of daily living. Those with older age, higher comorbidities, cognitive\u00a0impairment, and functional dependence with poor nutritional state are more vulnerable to functional decline. Other perioperative risks include\u00a0delayed surgery, surgery type, postoperative complications, longer hospital stays, lack of planned rehabilitative and nutritional plans, and postoperative depression. Early detection of sarcopenia helps\u00a0establish early interventional plans to reverse such poor outcomes. Sarcopenia is a common clinical condition among the elderly. It\u2019s one of the geriatric syndromes with a multifactorial character and different biological mechanisms. It is characterized by progressive and generalized loss of skeletal muscle mass, strength, and function . The EurSarcopenia overlaps with frailty, which is characterized by fatigue, weight loss, impaired movement, and weakness and thus increases the risk for future fractures. Low muscle mass is positively related to lower bone mineral density (BMD) resulting in osteosarcopenia, which is a predictor of fracture. This is due to several chemokines, interleukins, and growth factors mediating the communication between bone and muscle .Sarcopenia is highly prevalent among the elderly with hip fractures. The overall prevalence (for both sexes) of sarcopenia ranges from 11% to 76.4% depending on diagnostic tools . Hip fraMultiple factors may precipitate postoperative sarcopenia, such as the impact of surgery, the overall physical and mental stress, reduced caloric intake during hospitalization, inflammation, medication, type of anesthesia, and medical comorbidities. Cumulative periods of disuse not only impact muscle loss during hospitalization but also contribute to impaired recovery and physical functioning after discharge .Hospital-associated deconditioning contributes to the overall functional decline during and following periods of hospitalization, affecting long-term clinical outcomes, quality of life, the need for readmission, and permanent institutionalization. Greater attention to muscle weakness may promote better recovery after a hip fracture .This study aimed to determine the prevalence of sarcopenia among the elderly with hip fractures who were admitted to a university hospital and its effect on short-term functional outcomes, highlighting predictors of postoperative functional decline.This is a cross-sectional study followed by a prospective cohort. A total of 140 elderly (60 years and older) patients with proximal femur fractures were recruited from the orthopedic department. They were followed by the orthogeriatric team in the perioperative period and for three months after surgery. Ethical approval was obtained from the Research Ethics Committee of Ain Shams University Hospitals, Cairo, Egypt . Written, informed consent was obtained from participants.Exclusion criteria included refusal to participate in the study, previously non-ambulant patients, patients with dementia, patients with neuromuscular diseases, patients who were not surgically managed, patients with multiple fractures , and patients with hand problems impeding hand grip strength testing.Patients were subjected to full history taking (from patients or relatives) and clinical assessment. Height was estimated through demi-span measurements . Weight Sarcopenia was screened preoperatively through the SARC-F questionnaire. The SARC-F is a recommended screening tool for sarcopenia by the EWGSOP2 . SarcopePerioperative risk assessment was done through medical records, including the Charlson comorbidity index, the American Society of Anesthesiology (ASA) score, information about the type of fracture, time to surgery, type of surgery, type of anesthesia, postoperative complications, and length of hospital stay. Postdischarge care was assessed based on the presence or absence of involvement in formal rehabilitation and nutrition plans.At the end of the follow-up, participants were classified according to postoperative functional decline as either stable or deteriorating in function using the BI score. Both groups were compared to detect predictors of such a decline.Statistical analysisThe analysis of data was performed using SPSS Statistics version 16 . A description of all data in the form of the mean (M) and standard deviation (SD) for all quantitative variables was done. Frequency and percentage were calculated for all qualitative variables. Comparison between quantitative variables was done using the t-test to compare two groups. A comparison of qualitative variables was done using the chi-square test or Fisher\u2019s exact test when appropriate. A significant level was measured at p\u22640.05, and highly significant at p\u22640.01.For this study, 140 patients were recruited from the orthopedic surgery department from March 2021 to September 2021. The studied population involved 67 males and 73 females. Age ranged from 61.33 years to 75.29 years, with a mean of 6.98 years. Around 83.6% lived in urban regions, and 59.3% were educated. About 29.3% of them were current smokers. Body mass index (BMI) ranged from 22.98 Kg/m2 to 32.62 Kg/m2 with a mean of 4.82 Kg/m2. The number of comorbidities ranged from 1.13 to 3.45 with a mean of 1.16, while the Charlson comorbidity index ranged from 1.03 to 3.53 with a mean of 1.25 . Slippage resulted in 42.1% of the fractures, followed by high-energy trauma in 31.4%, while 26.4% had simple falls. Intertrochanteric fractures and the neck of the femur were the most common fractures seen in 44.3% and 43.6%, respectively. The rest were subtrochanteric fractures. The median of the past year's falls was 1 (0-2) , 25.7% had bipolar arthroplasty, 15% had dynamic hip screws (DHS), 7.1% had total hip arthroplasty (THA), and 4.3% had cannulated screws. About 86.4% underwent spinal anesthesia; 22.9% of patients had postoperative delirium; 7.9% had postoperative infections (mainly chest infections); and 5.7% had postoperative comorbidity-related complications. Hospital stay was one week on average (6.90 \u00b1 2.07 days) , early surgery, use of bipolar arthroplasty, postoperative complications (delirium and infections), postoperative nutritional plans, postoperative depression, and postoperative sarcopenia. Multivariate logistic regression analysis showed that the most significant factors were age and postoperative depression Table .Sarcopenia is an important and highly prevalent health problem in the elderly that has a high rate of negative health-related outcomes, including falls and functional decline. Fractures result in significant impairment of independence for all basic and instrumental activities of daily living compared to baseline status. Functional outcomes following hip fractures are often unsatisfactory, and limited data about contributing factors exists .Sarcopenia prevalence varies among studies according to diagnostic criteria, measurement tools, racial characteristics, the studied population, age groups, gender, dietary regimens, and quality of life. In this study, the prevalence of preoperative sarcopenia among participants was 29.3% when assessed by the SARC-F questionnaire and 28.6% by the Ishii equation. This is consistent with a systematic review, where the prevalence of sarcopenia ranged between 1% and 29% in community-dwelling populations . In anotWe found preoperative sarcopenia to be statistically significant, with functional decline post-fracture. Around 97% of those who remained stable were non-sarcopenic in their pre-fracture state. While almost 60% of those who deteriorated were sarcopenic in their pre-fracture state. About 95.5% of those who deteriorated were sarcopenic in the third month of follow-up. In the literature, sarcopenia was found to be an important factor in poor functional outcomes following hip fracture surgery .Some studies postulated that a poor recovery in sarcopenia status over time might be indicative of the weak effect of standard rehabilitation in the year following the fracture. It may also be the inability of such programs to overcome aging-related loss of muscle and strength as they focus more on eliminating disability in basic and instrumental activities of daily living than increasing muscle mass and strength . More stDuring our follow-up period, a marked post-fracture decline in independence level in basic activities of daily living occurred. Around 85% of participants were fully independent or had a slight dependence pre-fracture. At the end of follow-up, almost 50% of participants suffered from moderate to severe dependence. Around 20.7% were not walking at all.This finding goes with other studies, where walking recovery following hip fracture surgery was very poor at three to six months. Around 25% of participants failed to walk as well. Reasons behind this were pre-fracture walking abilities, the number of comorbidities, a longer hospital stay, and the lack of availability of rehabilitation .Other studies state that recovery from a femoral fracture takes a long time. Patients were followed up for six months, and around 50% of patients recovered the pre-fracture level of activity of daily living, and only 25% recovered their instrumental activity of daily living .According to our results, preoperative predictors of postoperative functional decline were related to preoperative sarcopenia, older age, a higher number of comorbidities, preoperative functional dependence, and a poor preoperative nutritional state. Multivariate logistic regression analysis showed that the most significant preoperative factor was age >67 years). Higher age and comorbidities were associated with more decline in function at the end of the follow-up, which was similar to previous studies years. H.During our follow-up period, 98.6% of functionally stable participants had good nutritional status, while 53.1% of deteriorated participants had a moderate to high risk of malnutrition. Such results are similar to those found in other studies where pre-fracture nutritional status determined functional status at discharge. Participants who were malnourished or at risk of malnutrition before fracture had a lower functional status than those who were well-nourished ,24. AnotAccording to our results, perioperative predictors of postoperative functional decline were related to delayed surgery, type of surgery, postoperative complications, a longer hospital stay, and a lack of planned rehabilitative and nutritional plans. Early surgery was found to promote stability of function. Around 77% of those who remained stable in function had early surgery. Studies have reported that early surgical intervention is associated with better restoration of baseline function .During our surgery, 48% had CMN, 25.7% had bipolar arthroplasty, 15% had DHS, 7% had THA, and 4.3% had cannulated screws. Choosing the implant depends on the type of fracture, pre-fracture activity level, joint congruence, presence of osteoarthritis, and available resources. The discrepancy in fracture type and stability guides the choice of surgery and implant, and accordingly, heterogeneity in rehabilitation programs may be the reason behind different functional outcomes within the follow-up period. We cannot recommend for or against a specific surgical intervention or implant choice from this study, and further patient stratification is needed. This can be one of the limitations of our study, although it is not one of the parameters for the primary outcome of the study.The length of hospital stay was statistically correlated with functional deterioration. This goes with other studies where longer hospitalization without rehabilitation was found to extend bed rest and worsen walking status . TherefoUndergoing postoperative rehabilitative and nutritional plans affected functional outcomes. All participants who stayed stable in function were attached to formal rehabilitative plans. While 74% of those who deteriorated in function didn\u2019t do the rehabilitation. Similarly, nutritional plans affected functional outcomes. Around 79% of those who deteriorated in function didn\u2019t engage in nutritional interventions. While 47% of those who remained stable in function had undergone nutritional modifications.Former studies state that interventions such as exercise and nutrition are effective in preventing and treating sarcopenia by preserving or even increasing muscle mass, strength, and physical performance. It is recommended to perform resistance training or multicomponent combined training for at least three months to have a significant impact on function ,27. OtheDespite having no evidence suggesting that high protein intake during short-term hospitalization decreases muscle loss, studies proved that lowering protein intake below habitual levels aggravates muscle loss during the immobilization period . StudiesAccording to our results, cognitive abilities and mood directly affected functional outcomes. Participants with baseline moderate cognitive impairment and postoperative depression were associated with worsening BI\u00a0scores through follow-up. Multivariate logistic regression analysis showed that the most significant postoperative factor was postoperative depression. Some other studies also related cognitive impairment and depression to postoperative functional recovery .We experienced a complication rate of 36.5%. About 22.9% had postoperative delirium, 7.9% had postoperative chest or soft tissue infections, and 5.7% had comorbidity-related complications. Postoperative complications are one of the modifiable risks of postoperative functional decline . ComplicLimitations and strengthsThis study is limited by its small sample size, and being a single-center study, it may not be representative of all geriatric populations with hip fractures in Egypt. There may be other modifiable factors that need further assessment. Details about socioeconomic factors, availability, and type of rehabilitation should have influenced our results. It would be even better to study each significant predictor on its own to avoid heterogeneity in the studied population and to create a better regression model of predictors of postoperative functional decline. Physical frailty is also an important predictor that affects the response of the geriatric population to acute stressors; therefore, it is essential to be assessed in future research. Nevertheless, our study opens the gate to further studies using such simple screening tools as the SARC-F and BI score for the assessment of sarcopenia and functional status, which can be done at outpatient clinics or using telemedicine.This study highlights the magnitude of sarcopenia and associated predictors of functional decline following hip fracture surgery in the geriatric population. The prevalence of sarcopenia among the elderly with hip fractures was 29.3% and reached 49.4% in the third month of postoperative follow-up.Preoperative predictors include older age, higher comorbidities, cognitive impairment, functional dependence, and a poor nutritional state. Other perioperative predictors include delayed surgery, surgery type, postoperative complications, longer hospital stays, a lack of planned rehabilitative and nutritional plans, and postoperative depression. The early detection of such predictors helps establish early interventional plans to reverse such poor outcomes."} +{"text": "The treatment of invasive fungal infections (IFI) is often complicated by drug-drug interactions, toxicities, and host comorbidities. Isavuconazole (ISA) has a favorable side effect profile and has FDA approval for invasive aspergillosis and mucormycosis, but there are fewer data on its efficacy for other microbes and non-pulmonary infections. We report our experience of ISA in IFI treatment, with a particular focus on non-pulmonary sites and other microbial etiologies.We identified patients who received ISA as part of IFI treatment from 1/1/2015\u20134/1/2020 at Mayo Clinic. We categorized them by organ involvement and by pathogens, and identified patterns of ISA use and clinical outcomes.A total of 131 patients were identified. Similar to the existing literature, the majority were pulmonary infections (60%), with 12% invasive sinus infection, 12% central nervous system (CNS) infection, and 7% fungemia. Aspergillus was the most common pathogen (39%), yeast comprised 19%, dimorphic fungi 15%, Mucormycosis 12%, phaeohyphomycosis 5%, and other molds 3%.ISA was used as secondary/salvage therapy in 89% of cases. The response rate varied by organ involvement and pathogen. ISA had complete/partial resolution or achieved stability in 57% of fungemia cases, 63% of invasive sinus infections, 64% of pulmonary infections, and 73% of CNS infections. Aspergillus species had a 67% response rate, with 72% response in yeast infections, 65% rate in dimorphic fungi, 53% for mucormycosis, and 86% in dematiaceous molds.Although limited by a small sample size, the subgroup review based on organ site and microbial etiology did seem to show roughly similar results to approved uses. The CNS infections treated with ISA were particularly of interest, given the limited options available with reliable CNS penetration.The current available literature has little to say on the efficacy of ISA in these off-label uses, with the majority being similar case series. This report highlights the importance of prospective trials comparing ISA to other antifungals in a greater variety of indications to better identify when this better-tolerated agent can be safely used.Courtney E. Harris, MD, Dynamed: Advisor/Consultant"} +{"text": "Allium sativum L.) leaf powder. The experiment was carried out by varying the ultrasound amplitude (30\u201360%), treatment time (5\u201315 min), and ethanol concentration (40\u201360%) required to obtain the maximum extraction yield of total phenol content (TPC), total flavonoid content (TFC), and antioxidant activity. Rotatable central composite design (RCCD) provided experimental parameter combinations in the ultrasound-assisted extraction (UAE) of garlic leaf powder. The values of extraction yield, TPC, TFC, and antioxidant activity for the optimized condition of RSM were obtained at 53% amplitude, 13 min of treatment time, and 50% ethanol concentration. The values of the target compounds predicted at this optimized condition from RSM were 32.2% extraction yield, 9.9 mg GAE/g TPC, 6.8 mg QE/g TFC, and 58% antioxidant activity. The ANN-GA optimized condition for the leaf extracts was obtained at 60% amplitude, 13 min treatment time, and 53% ethanol concentration. The predicted values of optimized condition obtained by ANN-GA were recorded as 32.1738% extraction yield and 9.8661 mg GAE/g, 6.8398 mg QE/g, and 58.5527% for TPC, TFC, and antioxidant activity, respectively. The matured leaves of garlic, if not harvested during its cultivation, often go waste despite being rich in antioxidants and phenolic compounds. With the increased demand for the production of value-added products, the extraction of the bioactive compounds from garlic leaves can resolve waste management and potential health issues without affecting the crop yield through the process for high-end use in value addition.This study explains the effect of ultrasound on the extraction of the bioactive compounds from garlic ( Allium species. Allium is one of the most produced and consumed vegetative products worldwide, with a world production of 32.4 MMT in the year 2020, with China being the highest producer, followed by India . Th. Th\u22121 restretch) . The regretching . The peac groups . The speal group .Twelve phenolic compounds were identified in the HPLC chromatogram against the used known phenolic compound standard . The retUltrasound-assisted garlic leaf powder bioactive component extraction was optimized using response surface methodology and an artificial neural network coupled with genetic algorithm (ANN\u2013GA) approach. Analysis of variance data for assessing the impact of different independent parameters on the EY, TPC, TFC, and antioxidant content were analyzed, and the developed models were assessed for predicting the responses in accordance with the experimental results. The artificial neural network coupled with genetic algorithm approach was much more efficient in prediction and estimation capabilities even with fewer datasets as compared to RSM, making it a more reliable tool. The optimum values of the independent variables obtained using ANN-GA were 60% ultrasound amplitude, 13 min treatment time, and 53% ethanol concentration, having applied energy of 26,150 J and calorimetric energy of 161.37 J. The expected values for this optimized condition were obtained as 32.1738%, 9.8661 mg GAE/g, 6.8398 mg QE/g, and 58.5527% for EY, TPC, TFC, and antioxidant activity, respectively. The results also showed the potential of garlic leaf powder in the extraction of free radical scavenging characteristics. FTIR and FE-SEM further revealed the positive effect of applied high-power ultrasound in releasing active components, specifically polyphenols and sulfur-containing compounds. This paves the way for the high-end applications of developed garlic leaf powder and extract. Scaling up the developed process thus may have the potential to unlock a multitude of benefits in the exploration of bioactive compounds derived from garlic leaves, preferably at the industrial level."} +{"text": "Legionella bacteria transmitted by inhalation of contaminated water droplets found in poorly maintained water systems. During 2012\u20132020, 53% of California LD patients were white and 14% were black; however, these groups account for only 39% and 6% of the population, respectively. Healthy Places Index (HPI) measures census tract health, which can affect risk for LD, by combining 23 indicators of social and environmental conditions. We assessed associations between race/ethnicity and neighborhood health, with LD case exposure classifications to establish priorities for decreasing LD disparities in California.Legionnaires\u2019 disease (LD) is a severe pneumonia caused by Using all California LD cases reported during 2011\u20132021 and six, individual modified Poisson regression models, we estimated incidence rate ratios (IRRs) and 95% confidence intervals (CIs) for associations between race/ethnicity and neighborhood health (using HPI quartile) with three LD case exposure classifications . The most advantaged HPI quartile and non-Hispanic white race/ethnicity were the referent groups. All models controlled for birth sex, age, and year.Among 4,373 people with LD, 47% were white, 22% were Hispanic, 12% were black, and 22%\u201328% fell in each HPI quartile. Among cases, 78% were sporadic, 16% were travel-associated, and 5% were healthcare-associated. Black and Hispanic race/ethnicity were associated with decreased rates of travel-associated LD. Black and Hispanic race/ethnicity, and living in the least advantaged quartile were associated with increased rates of sporadic LD. Healthcare-associated LD was not associated with race/ethnicity or HPI.We found evidence of racial and neighborhood disparities in sporadic LD, racial disparities in travel-associated LD, and no evidence of disparities in healthcare-associated LD. Efforts to increase uptake of water management programs in buildings in disadvantaged neighborhoods and travel accommodations might lessen LD burden and disparities in California.All Authors: No reported disclosures"} +{"text": "Candida auris (CA) is an emerging pathogen of concern, and surveillance studies have shown an increase in the number of BSI caused by CA over the last 3 years. In this study, the in vitro antimicrobial activity of TAU was evaluated against a set of CA strains/isolates using reference methods.Taurolidine (TAU) exhibits broad antimicrobial activity and is under development as a component of a new catheter lock solution with the goal of reducing catheter-related bloodstream infections (CRBSI). The Centers for Disease Control and Prevention (CDC) have recently warned that the fungus 41 CA strains/isolates were obtained from the CDC Antimicrobial Resistance Isolate Bank, the Westerdijk Fungal Biodiversity Institute, and JMI Laboratories\u2019 SENTRY Antimicrobial Surveillance Program. Most CA isolates were from BSI. The CA set was tested for antifungal susceptibility using Clinical and Laboratory Standards Institute (CLSI) broth microdilution guidelines and supplemented Roswell Park Memorial Institute 1640 broth. JMI Laboratories produced the minimal inhibitory concentration (MIC) panels. CLSI-recommended quality control strains were also tested. MIC values were read after 24 hours. TAU MIC values were read at 50% and 100% growth inhibition. Tentative CDC breakpoints for amphotericin B and fluconazole were applied.50/90 values, 256/512 mg/L using the 50% inhibition reading criterion and 512/512 mg/L using the 100% inhibition reading criterion). The TAU MIC range was 128\u2013512 mg/L and 256\u20131,024 mg/L using the 50% and 100% inhibition reading criteria, respectively. Additional CA isolates are being tested.The full set of CA isolates was 53.7% resistant to amphotericin B and 85.4% resistant to fluconazole. TAU exhibited antimicrobial activity against all CA strains and isolates regardless of source, clade, or known resistance mechanisms . There was no evidence that TAU activity was affected by isolate source or clade. Based on these data, catheter lock solutions containing the broad-spectrum antimicrobial TAU at 13,500 mg/L have the potential to prevent CRBSI caused by CA.TAU activity was similar for all CA subsets tested Phoebe Mounts, JD, CorMedix: Slary|CorMedix: Stocks/Bonds"} +{"text": "The objectives of our study were to describe quarter-level prevalence of intrammamary infection (IMI), to evaluate the performance of commonly used somatic cell count (SCC) thresholds for the diagnosis of quarter-level IMI, and to determine those with maximized sensitivity (Se) and specificity (Sp) for identifying quarter-level IMI as defined by positive aerobic culture in late-lactation grazing dairy cows. In this observational study, quarter milk samples were collected from all cows in 21 commercial spring-calving, pasture-based Irish dairy herds. Total SCC determination and aerobic bacterial culture were performed in 8,177 quarter milk samples obtained between 238 and 268 d in milk from 465 primiparous and 1,609 multiparous cows. The Se and Sp of SCC thresholds used for diagnosis of IMI were evaluated against the gold standard aerobic culture separately for all, primiparous, and multiparous cows. The overall prevalence of bacteriologically infected quarters was 6.3%, and it was higher among primiparous (11.3%) than multiparous cows (5.5%). However, considering all samples, quarter-level SCC was higher for multiparous than for primiparous cows . Associated Se and Sp for the 200,000 cells/mL threshold were 59.2% and 88.0% for all, 52.7% and 95.4% for primiparous, and 62.9% and 85.9% for multiparous cows, respectively. Receiver operating characteristic curve analyses determined the thresholds that optimized the Se and Sp of a positive bacterial culture: 101,000 cells/mL for all cows , 61,000 cells/mL for primiparous , and 101,000 cells/mL for multiparous . The results indicate that the 200,000 cells/mL threshold was inefficient in identifying late-lactation quarter-level IMI (low Se) in the studied herds where the main etiological agent was Staphylococcus aureus. Suggested quarter-level SCC thresholds have the potential of serving as a supporting tool for dry cow therapy decisions and warrant further study in late-lactation cows from spring-calving, pasture-based herds with S. aureus as the main pathogen causing IMI. SDCT). Increased SCC is commonly associated with IMI, defined as a positive bacterial culture and specificity associated with different SCC thresholds are generally higher for SCC determinations performed at the quarter level, compared with those performed in composite samples to identify quarter-level IMI, and to determine the threshold with maximized Se and Sp for identifying quarter-level IMI in a cohort of late-lactation cows in spring-calving, pasture-based Irish herds.To the best of the authors' knowledge, no study has evaluated the association between quarter-level SCC and IMI in Ireland or herds where the majority of infections are caused by IQR) for enrolled herds' size was 66 to 122 cows . All-herd quarter milk samples were collected from a convenient sample of 21 commercial spring-calving grazing herds in Ireland in late lactation . Irish spring-calving, pasture-based herds are characterized by a compact calving season that coincides with the onset of the grass growing season. In this system, cows are generally out to pasture for the majority of the year and housed during the winter and dry period. The interquartile range , and negative predictive (NPV) values were determined for identification of quarter-level IMI based on SCC for a 200,000 cells/mL and a 100,000 cells/mL threshold; for all, primiparous, and multiparous cows; for a 120,000 cells/mL threshold for primiparous cows; and for a 150,000 cells/mL threshold for multiparous cows. The SCC threshold that optimized Se and Sp for identification of quarter-level IMI was determined by receiver operating characteristic curve analyses and maximized area under the curve (AUC), weighing false-positive and false-negative results equally, and separately for all, primiparous, and multiparous cows using MedCalc .Data summarization and analyses were conducted with SAS unless otherwise stated. Linear and logistic models were used to evaluate the effect of parity (primiparous vs. multiparous) on quarter-level SCC and prevalence of infection . Random effects were added at the herd level to account for clustering of cows within herds and at the cow level to account for clustering of quarters within cows. To comply with assumptions of the analysis and facilitate results interpretation, Among the 2,074 cows sampled , 92 cows had a missing sample from 1 quarter and 1 cow had a missing sample from 2 quarters. Culture was not performed from 1 quarter sample, and insufficient milk volume for SCC determination was collected from 24 quarters. Consequently, the total number of samples available for analyses with quarter SCC and bacterial culture results was 8,177 .P < 0.001). However, the proportion of multiparous cows' quarter-level samples with SCC \u2265200,000 cells/mL was higher than that for primiparous cows . The prevalence of cows with at least one quarter infected was 19.0% for all , 29.3% for primiparous (n = 136/465), and 16.0% for multiparous cows . Isolated microorganisms in this study included Staphylococcus aureus , Streptococcus uberis , Streptococcus dysgalactiae , NAS , and non-hemolytic Escherichia coli .Of all the sampled quarters, 6.3% were infected . Cows had 1 , 2 , 3 , or 4 infected quarters. A higher quarter-level prevalence of IMI was observed among primiparous compared with multiparous cows , and for quarters with IMI than for uninfected quarters . Quarter-level SCC in infected quarters was higher for multiparous than for primiparous cows (P < 0.001). Within parity groups, quarter-level SCC was also higher for quarters with IMI compared with the uninfected quarters .Descriptive statistics showed that median quarter-level SCC was 30,000 cells/mL for infected and uninfected quarters from all cows , 18,000 cells/mL for primiparous cows , and 40,000 cells/mL for multiparous cows . Considering all samples, statistical analyses showed that quarter-level SCC was higher for multiparous than for primiparous cows for all cows (primiparous and multiparous combined) and primiparous and multiparous cows are presented in S. aureus (5.5%) for both, primiparous, and multiparous cows. The definition of infection in our study should be considered when interpreting the etiology of IMI. A standard definition of IMI for all pathogens could result in different Se of the milk culture and multiparous cows (4%)]. Different etiological pathogens have been reported as cause for first clinical mastitis case among parities, whereas a similar profile has been described for succeeding cases under confined production systems based on the 200,000 cells/mL cow-level SCC threshold had no effect on udder health . However"} +{"text": "PFTs before and after treatment did not significantly differ. The mean FVC% difference was +0.9 (sd = 7.6) and the mean DLco% difference was +3.4 (sd = 12.6), suggesting numerical improvement of PFTs. The average percentage change was \u22120.3% and +7.6% for FVC% and DLco%, respectively, indicating stabilization of lung function. Our real-world data across a broad spectrum of CTD-ILD suggest that nintedanib could be beneficial in combination with immunosuppressives in slowing the rate of lung function decline.Connective Tissue Disease-Interstitial Lung Disease (CTD-ILD) is a severe and fatal manifestation of systemic autoimmune disorders. Therapies rely on immunomodulators but their efficacy in ILD progression remains uncertain. Nintedanib, an antifibrotic agent that slows pulmonary function decline, has been approved for CTD-ILD treatment. The aim of this study was to assess the effectiveness and safety of nintedanib in CTD-ILD patients in a real-world data setting. A single-center, retrospective, and descriptive analysis of CTD-ILD patients treated with nintedanib from June 2019 to November 2022 was performed. The assessment of nintedanib treatment\u2019s efficacy was judged solely on the evolution of pulmonary function tests (PFTs), which were evaluated before and after treatment. Twenty-one patients with CTD-ILD (systemic sclerosis Interstitial Lung Diseases (ILDs) are a large group of several relatively different pulmonary pathologies. Many ILDs are characterized by fibrosis and lung parenchyma damage, especially of the interstitium, as well as various degrees of inflammation . The fibThe most prevalent connective tissue diseases that develop CTD-ILD are rheumatoid arthritis (RA) and systemic sclerosis (SSc). RA conveys high rates of inflammation and affects several organs. RA-ILD affects almost 7.7% of RA patients, 25% of whom present with serious pulmonary decline already from diagnosis, whereas 25% of RA individuals will develop severe lung impairment in the first 5 years after diagnosis . Major rLung involvement is a significant prognostic factor of CTD as it is associated with an unfavorable outcome, thus great emphasis on an early diagnosis is given. The diagnosis of CTD-ILD is based on imaging investigations, lung function tests, and patient-reported dyspnea. The imaging of CTD-ILD is mainly conducted by high-resolution computed tomographic scan (HRCT) that focuses on usual interstitial pneumonia (UIP) and fibrosing nonspecific interstitial pneumonia (fNSIP) patterns . The UIPDue to their common clinical phenotype and refractory nature, CTD-ILDs are generally grouped together, mainly in view of common treatment strategies including steroids, immunosuppressive and antifibrotic agents ,17,18. CNintedanib is a potent oral tyrosine kinase inhibitor that suppresses different processes of lung fibrosis . The TOMThe aim of the current study was to evaluate, via the evolution of lung function parameters, the efficacy and safety profile of nintedanib in CTD-ILD patients with progressive fibrotic phenotype requiring treatment with antifibrotic agents in a real-world data setting.We retrospectively reviewed the medical files of all CTD-ILD patients on nintedanib being followed up in outpatient clinics of the Rheumatology Department of the Fourth Department of Internal Medicine, Hippokration General Hospital of Thessaloniki, Greece, from June 2019 to November 2022. All patients were receiving nintedanib for CTD-ILD according to the recommendation of the treating physician. Due to the anonymized and non-interventional nature of the study, ethics approval was not required. CTD-ILD was identified using high-resolution computed tomographic scans, reduced values of FVC and diffusion capacity of the lungs for DLco , and via clinical manifestations of worsening dyspnea. Nintedanib was started on patients with progressive fibrosing ILD as previously defined ,30,32. PData that was collected from the outpatient clinic\u2019s record included demographic information , smoking status , duration of CTD-ILD, type of autoimmune disease, serological profile, and presence of other systemic manifestations. The FVC , the DLco and FEV1 before and after treatment with nintedanib, the FVC% difference and DLco% difference after treatment, and the percentage change of the % predicted value of FVC and Dlco for every patient were also recorded. The initial measurements of FVC and FEV1 were in L, and the initial measurements of DLco were in mL/min/mmHg. Additionally, we recorded FVC%/DLco% ratio measurements before and after nintedanib treatment, as a result >1.5 might be a predictor of pulmonary arterial hypertension . Other dp-value < 0.2 were also analyzed in multivariate models. The level of statistical significance was set at p-value < 0.05 unless otherwise noted. The statistical analysis was performed using the SPSS statistical package version v27.Data were handled anonymously. Normally distributed variables are presented as mean and standard deviation (sd). Non-normally distributed variables are presented as the median and interquartile range (IQR). The normality of the variables\u2019 distribution was checked with the Shapiro\u2013Wilk test. Differences in baseline variables were tested with t-tests for continuous variables. The homogeneity of variances was tested via Levene\u2019s test. Wilcoxon\u2019s test was used for categorical variables that were normally distributed and the Mann\u2013Whitney U test was used for categorical variables that were not normally distributed. The comparisons between two continuous variables were conducted via univariate linear regression models. The effect of one or more independent variables on the values of a continuous dependent variable was also examined via linear regression models. The individual variables from the univariate analyses that met the criterion of n = 9), rheumatoid arthritis (RA) 23% (n = 5), dermatomyositis (DM) 19% (n = 4), juvenile rheumatoid Arthritis (JRA) 5% (n = 1), undifferentiated connective tissue disease (UCTD) 5% (n = 1), and interstitial pneumonia with autoimmune features (IPAF) 5% (n = 1). The marker autoantibodies of the patients were by order of prevalence: Scl-70 42% (n = 9), rheumatoid factor (RF) 19% (n = 4), Jo1+ 19% (n = 4), ro+ 10% (n = 2), anti-CCP 5% (n = 1), and anti-ENA screening 5% (n = 1). The majority of patients, 57% (n = 12), also had other systemic manifestations, which were: 14% (n = 3) gastrointestinal disorders such as gastroesophageal reflux disease, 14% (n = 3) cardiac disorders such as arrythmias, 14% (n = 3) pulmonary arterial hypertension, 1% (n = 5) digital ulcers, 1% (n = 5) skin disease, and 1% (n = 5) SICCA symptoms . Eighty-six percent (n = 18) of the patients were receiving other concomitant treatments besides nintedanib due to the underlying connective tissue disease which were: prednisolone 67% (n = 14), mycophenolate mofetil 48% (n = 10), calcium channel blockers 19% (n = 4), endothelin receptor inhibitors 19% (n = 4), methotrexate 14% (n = 3), tocilizumab 14% (n = 3), hydroxychloroqine 10% (n = 2), sildenafil 10% (n = 2), abatacept 5% (n = 1), azathioprine 5% (n = 1), and rituximab 5% (n = 1). The clinical and serological characteristics of the participants as well as concomitant medications are presented in A total of 21 CTD-ILD patients were included in the study. Of these, 14 were female, all were nonsmokers, and the median age was 64 years . The mean duration of CTD-ILD was 4.8 years . The CTDs of the patients were by order of prevalence: systemic sclerosis (SSc) 43% . During the follow-up period, two (10%) patients discontinued treatment due to gastrointestinal (GI) side effects, predominantly severe nausea and stomachache, two (10%) patients died due to severe CTD, three (14%) patients discontinued for unknown reasons, and one (5%) has not been followed-up yet for unknown reasons. Some patients included in the analysis could not perform a before-treatment DLco measurement due to COVID-19 restrictions, although the spirometry examination was conducted as usual. As expected, no statistical difference was demonstrated in FVC%, DLco%. FEV1% and FVC%/DLco% values before and after nintedanib treatment for the remaining 13 patients included in the analysis. However, the results indicate the stability and deceleration of deterioration of PFTs. In particular, PFTs are consistent, the mean FVC% difference is mildly increased by +0.9 (sd = 7.6), whereas the mean DLco% difference is increased by +3.4 (sd = 12.6) and the mean FEV1% presented a numerical improvement of +3.4%. The percentage change of FVC% is \u22120.3% (sd = 13.9) and the percentage change of DLco (% Pred) is +7.6% (sd = 27.1), suggesting stabilization of pulmonary function . The meaRegarding patients\u2019 inflammatory markers, no statistical difference was demonstrated in the CRP and ESR values before and after nintedanib treatment, which is as expected because nintedanib is not considered as an anti-inflammatory regimen. The median CRP and ESR after treatment presented numerical improvements of 0.1 mg/dL and 16.5 mm/h, correspondingly. The inflammatory markers\u2019 values before and after treatment are presented in Regarding adverse effects, two (10%) patients developed serious, intolerable nausea and discontinued nintedanib treatment, and one (5%) patient developed diarrhea that was managed with dietary changes and antidiarrheal drugs.p-value = 0.015). As expected, a significantly important increase in the mean duration of CTD-ILD of 2.5 years was observed in patients with extrapulmonary involvement, highlighting the cumulative effect of inflammation on various organs in patients with CTD. The relationship between CTD-ILD duration and other systemic manifestations is presented in t-test was conducted in order to evaluate the FVC% difference (before and after nintedanib treatment) and DLco% difference (before and after nintedanib treatment) between patients that received prednisolone or not and between patients that received MMF or not. A significant mild improvement in DLco% measurements was noticed in the group that received MMF , enhancing the importance of the coadministration of nintedanib with immunosuppressive drugs. Additionally, we added univariate linear regressions for all the concomitant treatments and multivariate linear regressions for the concomitant treatments that met the criterion of p-value < 0.2. The results of the univariate analyses confirmed the result of the subgroup analysis regarding MMF. The results of the multivariate analysis were not significantly important.Supplemental exploratory objectives included correlations between FVC% (before and after treatment), DLco% (before and after treatment), FVC%/DLco% difference, CTD-ILD duration, and the recorded data via statistical tests or univariate and multivariate linear regression when the criteria were met. Statistical significance was found between CTD-ILD duration and other systemic manifestations were also under immunosuppressive treatment. As expected, the most common concomitant medications were corticosteroids (prednisolone < 7.5 mg/day) and MMF. Fewer patients were treated with biologic drugs such as tocilizumab, abatacept, and rituximab, as indicated by recent studies ,52,53,54The adverse effect profile in our study was characterized by gastrointestinal manifestations, mainly severe and resistant nausea, which led two older patients to discontinue treatment. In contrast, diarrhea presented in about 5% of the patients and was manageable with practical recommendations , enabling patients to maintain the use of nintedanib. The two deaths recorded in our population were attributed to critical CTD, and the remaining missing follow-up was irrelevant to side effects. In summary, the safety profile of nintedanib in our cohort was consistent across different subgroups of CTD-ILD and with what has been reported in randomized trials . Of noteThis study has some limitations. Since it is an observational and descriptive study, it cannot draw many conclusions on causality and effect. Moreover, the small patient group may lead to temporal and unsafe associations. There was no control group as it was not ethical to include a placebo parallel group once a therapy has been approved as the standard of care. Additionally, the evolution of symptoms and imaging progression were not considered in this study. Furthermore, there were no fixed follow-up appointments or standardization of the follow-up process, as it was regulated by the individual patient\u2019s visit schedule. Many patients delayed their follow-up due to restrictions associated with the COVID-19 pandemic, and the lockdown disruption may have led to missing or delayed data. However, this study includes CTD-ILD patients across the whole spectrum of autoimmune disorders in concomitant treatment with other immunosuppressives in a real-life setting.ILD remains a severe and difficult-to-treat complication of systemic autoimmune disorders with an unfavorable impact on patients\u2019 quality of life and prognosis. The results of the current study provide real-world evidence of the beneficial effect of nintedanib in slowing the rate of fibrosis progression across the whole spectrum of patients with CTD-ILD that were parallelly treated with other anti-inflammatory and immunosuppressive drugs. The adverse effect profile consisted mostly of gastrointestinal manifestations, especially nausea in elderly patients with a low drop-out rate related to this symptom, consistent with relevant studies. Further targeted randomized controlled trials are needed to assess the efficacy of nintedanib in CTD-ILD."} +{"text": "Assessing the validity and clinical utility of axillary ultrasonography (AUS)-guided fine needle aspiration biopsy (FNAB) in detection of nodal metastasis during preoperative axillary investigation in comparison to the histopathologic diagnosis in early-stage breast cancer.A total of 279 operated primary breast cancer patients were included. Data on AUS findings at the time of initial diagnosis (first look AUS), second-look AUS findings performed by the breast radiologist during breast biopsy procedure and the AUS-guided FNAB findings were evaluated with respect to the final histopathology report obtained through axillary surgery via sentinel lymph node biopsy (SLNB) and/or axillary lymph node dissection (ALND). The diagnostic performance of each method in detecting metastatic ALNs were compared in terms of sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV).The sensitivity, specificity, and accuracy of the first look AUS in detecting nodal metastasis were 64.56%, 86.78%, and 74.19% while the PPV and NPV were 86.44% and 65.22%, respectively. The sensitivity, specificity, and accuracy of the second-look AUS were 70.25%, 87.60%, and 77.78%, while PPV and NPV were 88.10% and 69.28%, respectively. The sensitivity, specificity, and accuracy of the second-look AUS guided FNAB were 89.19%, 73.33%, and 87.30%, while the PPV and NPV were 96.12% and 47.83%, respectively. The consideration of second-look AUS and finding of nodal metastasis in FNAB was associated with significantly higher likelihood of ALND and lower likelihood of SLNB compared to consideration of nonmetastatic ALN status. In 23 (22.3%) patients with positive findings on AUS-guided FNAB, SLNB was applied; 21 had positive results after surgical dissection, indicating that nearly 20% of patients had unnecessary SLNB.US-guided FNAB of suspicious ALNs is a simple, minimally invasive, and highly effective method for preoperative axillary staging in patients with invasive breast cancer avoiding the more invasive method SLNB and it enables the surgeon to proceed directly to ALND in positive cases. Axillary ultrasonography (AUS) is the primary imaging modality for evaluating axillary lymph nodes (ALNs) and its ability to identify the nodal metastases is considered critical for staging, prognosis, and treatment of patients with invasive breast cancer ,2. PreopIn the clinical practice, while these \u201cclinically node-positive\u201d patients undergo ALND without undergoing SLNB, \u201cclinically node-negative\u201d patients undergo SLNB and those with negative results on SLNB has no further axillary dissection since there is no survival benefit for performing ALND in this setting ,7. SLNB Hence, the main goal of the radiologist is to determine the presence of metastatic disease in nonpalpable ALNs to reveal clinically node-positive patients before surgery by means of imaging with a positive predictive value that is high enough to be useful to the surgeon in selecting patients for upfront ALND or neo-adjuvant chemotherapy without undergoing SLNB ,10,16,17In the context of alternative methods to replace SLNB with a decreasing role for axillary node dissection, US-guided FNAB has become a promising minimally invasive method in the accurate staging of the axilla with the preoperative detection of nodal metastasis, while a need for larger-scale and longer\u2013follow-up comparative studies has been emphasized ,18,19.This study aimed to assess the validity and clinical utility of AUS- and US-guided FNAB in detection of nodal metastasis during preoperative axillary investigation in comparison to the final histopathologic results in early-stage breast cancer patients and to determine its impact on the selection of ALND and/or SLNB by the surgeon.A total of 279 operated primary breast cancer patients were included in this retrospective study conducted between September 2014 and December 2018. Patients who received preoperative neoadjuvant chemotherapy and those without axillary histopathology report were excluded from the study.The study was conducted in accordance with the ethical principles stated in the \u201cDeclaration of Helsinki\u201d and approved by the institutional ethics committee along with the permission for the use of patient data for publication purposes.Second-look AUS was performed during histopathological examination of the primary breast tumor and FNAB was performed to all patients with suspected lymph nodes. In our study; lymph nodes with a short diameter greater than 1 cm, a round shape, an indistinct fatty hilum, and more than 3 mm of concentric or focal cortical thickening were considered suspicious. Afterwards, all patients were gone through axillary surgery for the final histopathologic report. The patients with malignant FNAB underwent SLNB and/or ALND at the time of definitive surgery, while those with benign, suspicious, or insufficient FNABs underwent SLNB using blue-dye and/or radio-colloid injection.Data on AUS findings at the time of initial diagnosis, second-look AUS findings performed by the breast radiologist to consider the need for axillary biopsy during the primary breast tumor biopsy procedure, and the FNAB findings were evaluated with respect to the final operative histopathologic results. The diagnostic performance of each method in detecting metastatic axillary lymph nodes were compared in terms of sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV). By comparing the FNAB with final histopathologic result, the rate of unnecessary SLNB was estimated.Statistical analysis was made using IBM SPSS Statistics for Windows, version 23.0 . Pearson\u2019s chi-squared test and Fisher\u2019s exact test were used for the comparison of categorical data. Data were expressed as percent (%) and 95% confidence interval (CI) where appropriate. p < 0.05 was considered statistically significant.Invasive ductal carcinoma was the most common tumor subtype, while the rates of luminal A and luminal B molecular subtypes were 41.6% each. Nonbreast-conserving surgery was applied in 67.0% of patients, while axillary lymph node dissection and sentinel lymph node dissection were applied in 48.4% and 27.6% of patients, respectively .The nodal metastasis was considered in 42.3% of patients by the first-look axillary US, in 45.1% of patients by second-look AUS. Metastatic LAP was detected in 36.9% of patients who underwent FNAB. After axillary SLNB and/or ALND, the presence of metastatic LAP was histopathologically proven in 56.6% of patients .Final histopathologic report revealed the number of benign and metastatic lymph node yield to be mean 8.84 \u00b1 6.15 (ranged 1 to 31) and 3.68 \u00b1 2.69 (ranged 1 to 13), respectively. Mean size of metastatic lymph nodes was 16.76 \u00b1 7.81 (ranged 3\u201345) mm.In 103 of 118 ALNs suspected of metastatic involvement in the first-look AUS, the second-look AUS was required with decision of FNAB. In 23 of 161 patients with ALNs considered to be normal in the first-look AUS, second-look AUS was required with decision of FNAB .The sensitivity, specificity and accuracy of the first-look AUS in detecting the nodal metastasis were 81.75%, 90.20%, and 86.38%, while the PPV and NPV were 87.29% and 85.71%, respectively .Of 126 patients who underwent FNAB after second-look AUS, FNAB findings revealed nodal metastasis in 56.5% of cases considered to be nonmetastatic in the second-look AUS, while in 87.4% of cases considered to be metastatic in the second-look AUS .The sensitivity, specificity and accuracy of the second-look AUS in detecting nodal metastasis were 87.38%, 43.48%, and 79.37%, while the PPV and NPV were 87.38% and 43.48%, respectively .The definite operative histology confirmed nodal metastasis in 86.4% of 118 patients with suspicious ALNs on initial AUS, in 88.1% of 126 patients with suspicious ALNs in second-look AUS, and in 96.1% of 103 patients with positive findings on FNAB .The definite operative histology confirmed nodal metastasis in 34.8% of 161 cases considered to be not metastatic in the first-look AUS, in 30.7% of 153 cases considered not necessary to be evaluated via FNAB in second-look AUS, and in 52.2% of 23 cases considered to be not metastatic in FNAB .When compared to negative findings, the likelihood of positive findings suggestive of metastasis in the first-look AUS, second-look AUS, and FNAB was significantly higher to reveal a nodal metastasis on definite operative histology, overall (p < 0.001 for each) as well as in luminal A (p < 0.001), luminal B (p < 0.001), triple negative (p = 0.009) subcategories .When compared to definite operative histology; the sensitivity, specificity, and accuracy of the first-look AUS in detecting nodal metastasis were 64.56%, 86.78%, and 74.19%, while the PPV and NPV were 86.44% and 65.22%, respectively. The sensitivity, specificity, and accuracy of the second-look AUS were 70.25%, 87.60%, and 77.78%, while the PPV and NPV were 88.10% and 69.28%, respectively. The sensitivity, specificity and accuracy of the second-look AUS guided FNAB were 89.19%, 73.33%, and 87.30%, while the PPV and NPV were 96.12% and 47.83%, respectively .Nonbreast-conserving surgery was significantly more commonly selected for cases considered vs. not considered to be metastatic during first-look AUS . The sensitivity, specificity, and accuracy of first-look AUS in selecting the surgery type were 44.06%, 67.39%, and 53.76%, respectively .The consideration of nodal metastasis during first-look AUS was associated with significantly higher likelihood of ALND and lower likelihood of SLNB compared to consideration of nonmetastatic ALN status .The consideration of second-look AUS and finding of nodal metastasis in FNAB was associated with significantly higher likelihood of ALND and lower likelihood of SLNB compared to consideration of nonmetastatic ALN status .In 23 (22.3%) of 103 patients with positive findings on US guided FNAB, SLNB was applied. Of 23 patients with SLNB, 21 (91.03%) had positive results after surgical dissection, indicating that nearly 20% of patients had unnecessary SLNB.The nodal metastasis rates obtained via first-look AUS (42.3%), second-look AUS-guided FNAB (36.9%) and the definite operative histology (56.6%) in our study were consistent with the definite histopathology report in 86.4%, 88.1%, and 96.1% of initial predictions, respectively; while US-guided FNAB was positive in 70.3% of cases with definite pathology.Similarly, in the study of Leenders et al., it was reported that AUS showed suspicious lymph nodes in 28.4% cases, FNAB showed axillary metastases in 32.7% of these LNs, and the final histological analysis confirmed metastatic disease in 37.3% of these suspected LNs . Other sThe sensitivity and specificity of second-look AUS (70.25% and 87.60%) and FNAB (89.19% and 73.33%) in the current study are in line with the reported ranges of moderate sensitivity (25% to 87%) and a higher specificity (77%\u2013100%) for AUS-FNAB in the literature, supporting that both sensitivity and specificity of AUS increases when combined with FNAB and with selection of only the ALNs deemed to be suspicious on AUS for aspiration ,25,26.However, considering the definite operative histology as a reference, the second-look AUS and FNAB revealed false-negative results in 30.7% and 52.2% of our cases, respectively. Hence, AUS-guided FNAB was associated a PPV of 96.12% but an NPV of 47.83%, supporting the previously reported low NPV (ranged 59.3% to 73.0%) and high false negativity (ranged 19.4% to 31.8%) of this method in detecting ALN metastases ,20,27,28The sampling error, micrometastasis, and errors in radiologic and pathologic assessment are considered to be the possible causes of false-negative results ,22,29,30Notably, in a past study with 27 early-stage breast cancer patients, FNAB in comparison with SLNB was reported to have a sensitivity, specificity, PPV and NPV of 45%, 100%, 100%, and 73%, respectively . The autIn contrary, for patients with preoperative identification of positive AUS and AUS-guided FNAB, the need for SLNB is considered likely to be eliminated; thus, AUS-guided positive FNAB is suggested to allow patients to be triaged to ALND, bypassing the potentially unnecessary SLNB ,11,35.Likewise, our findings indicated the increased likelihood of ALND rather than SNLB to be considered for a ALN found metastatic on a second-look USG guided FNAB, while in nearly 20% of patients who had been initially positive for AUS-FNAB, the SLNB revealed positive findings. Hence, indicating the primary role of radiologist by providing accurate AUS guidance for FNAB, our findings emphasize that the unnecessary SNLBs can be avoided in at least one fifth of node-positive patients with primary breast cancer via preoperative AUS-FNAB-based axillary investigation. This supports the consideration of node positive group to benefit most from axillary FNAB with consequent reduction of SLNB ,17,20,36In a past study, the authors reported US-guided FNAB positivity in 821 of 1152 patients which resulted in avoiding 11.7% of patients to undergo needless SLNB . LikewisIn a prospective study including 100 female patients with breast cancer, the overall AUS-FNAB sensitivity was reported to be 79.4% with PPV and NPV of 100% and 69.5%, respectively, while the AUS-FNAB sensitivity was 0% for lymph nodes with normal sonographic features, 80% for indeterminate lymph nodes and 90.5% for suspicious lymph nodes . The autThe increased likelihood of ALND rather than SNLB in cases with second-look AUS-guided FNAB positivity compared to those with negative FNAB findings in the current study seems notable given the consideration of an abnormal AUS and positive FNAB to correlate with patients eligible for ALND as well as with a higher nodal burden on final pathology compared with patients with metastasis identified on SLNB . Indeed,Given its association with lower false-negative rate than the AUS-FNAB, the AUS-guided core needle biopsy (CNB) has also become an increasingly more popular approach of axillary staging in breast cancer patients which avoids SLNB and a second trip to the operating room . NonetheThe FNAB positivity in 56.5% of AUS negative cases in the current study seems also notable given that AUS-FNAB is performed for only patients with suspicious ALN on AUS and the use of US-FNAB for nonsuspicious ALNs is considered to be associated with classification of these cases as true negatives . Hence, Notably, in a study among 101 patients including those with positive AUS-FNAB and corresponding ALND (n = 65) and those with negative US-FNA with corresponding ALND/SLNB (n = 36), 43% of patients in the positive US-FNA group were reported to have two or fewer positive lymph nodes upon ALND pathologic examination (indicating the risk of overtreatment) . The autThe retrospective single-center design of the present study seems to be the major limitation that prevents the establishing temporality between the cause and effect as well as generalizing our findings to overall breast cancer population.In conclusion, US-guided FNAB of suspicious ALNs is a simple, minimally invasive and highly effective method for preoperative axillary staging in patients with invasive breast cancer that can identify those patients with high metastatic nodal burden and thus potentially avoid SLNB and enable the surgeon to proceed directly to ALND in positive cases."} +{"text": "Depressed patients who initially fail to achieve remission when placed on a selective serotonin reuptake inhibitor (SSRI) may require a second treatment.The purpose of this study was to evaluate the effectiveness, cost, cost-effectiveness, and budget impact of second-line pharmacologic treatment for major depressive disorder (MDD).A cost-effectiveness analysis was conducted to evaluate second line therapies for the treatment of depression. Effectiveness data were obtained from published clinical studies. The primary outcome was remission defined as a score of 7 or less on the Hamilton Rating Scale for Depression (HAM-D) or a score of 10 or less on the Montgomery-Asberg Depression Rating Scale (MADRS) depression rating scales. The wholesale acquisition cost (WAC) for medications and medical treatment costs for depression were included. The perspective was derived from a managed care organization (MCO) with 500,000 members, a 1.9% annual incidence of depression, and treatment duration of 6 months. Assumptions included: second-line treatment is not as effective as first-line treatment, WAC price reflects MCO costs, and side effects were identical. Sensitivity analyses were conducted to determine variables that influenced the results.Second-line remission rates were 20.4% for venlafaxine XR, 16.9% for sertraline, 16.4% for escitalopram, 15.1% for generic SSRIs (weighted average), and 13.6% for paroxetine CR. Pharmacy costs ranged from $163 for generic SSRIs to $319 for venlafaxine XR. Total cost per patient achieving remission was $14,275 for venlafaxine XR, followed by $16,100 for escitalopram. The incremental cost-effectiveness ratio (ICER) for venlafaxine XR compared with generic SSRIs was $2,073 per patient achieving remission, followed by escitalopram with an ICER of $3,566. The model was most sensitive to nonpharmacy costs.This analysis suggests that second-line treatment of depression with venlafaxine XR may result in more patients achieving remission, with an ICER that is favorable to other therapies."} +{"text": "More than half of US adults over the age of 40 have already been infected by CMV. Despite high prevalence, patient awareness and understanding of CMV is low. This study assessed the impact of online patient education on knowledge, confidence and intent to act regarding CMV.The educational intervention consisted of 4 activities hosted on a dedicated learning center on WebMD Education from February-June, 2022. The activities were comprised of text, integrated visuals, and either a patient or healthcare professional (HCP) video commentary. Demographic questions were asked prior to each activity. Knowledge questions were asked both before and after to assess learning gains. Intent to change and confidence questions were asked at the end of each activity. Absolute improvements were calculated for pre/post questions.What is Cytomegalovirus (CMV)?Activity 1: 63,476 learners; 9,239 completers of all questions72% female; 57% white, non-Hispanic; 18% 35-44 years of age24% improvement in knowledge regarding complications of CMV infection; 50% intend to talk to HCP about CMV; 52% confident in talking to HCP about what CMV means for familyCMV: What You Can Do to Help Stop the SpreadActivity 2: 61,818 learners; 3,583 completers of all questions56% female; 40% black/African American; 22% 25-34 years of age18% improvement in knowledge regarding the spread of CMV; 75% intend to talk to HCP about CMV; 90% confident in preventing spread of CMVPregnant, Thinking About Pregnancy, or Have a New Baby? What to Know About CMVActivity 3: 66,918 learners; 4,504 completers of all questions91% female; 21% black/African American; 44% 25-34 years of age38% improvement in knowledge regarding CMV in pregnancy and babies; 69% intend to talk to HCP about CMV; 76% confident in understanding how CMV effects pregnancy and babiesAre You at Risk for CMV?Activity 4: 2,802 learners; 368 completers of all questions62% female; 51% white, non-Hispanic; 25% 35-44 years of age17% improvement in knowledge regarding who is at risk for CMV infection; 61% intend to talk to HCP about CMV; 75% confident in understanding CMVThe outcomes gathered in this assessment are a strong indicator that online patient activities on WebMD Education improved knowledge and confidence and prompted intent to act related to CMV.All Authors: No reported disclosures"} +{"text": "Prostaglandin analogs are the most effective treatment for glaucoma, a common condition among older adults. Despite the availability of generic drugs, the costs associated with these prescription drugs are rising.To characterize Medicare prescription drug plan (PDP) formulary coverage and beneficiary out-of-pocket cost for prostaglandin analogs from 2009 to 2017 and Medicare spending on prostaglandin analogs from 2013 to 2017.This study was a retrospective analysis. We used 2009, 2013, and 2017 Medicare PDP formulary, beneficiary cost, and pricing files to determine beneficiary first-prescription out-of-pocket costs and plan coverage of branded latanoprost 0.005%, travoprost 0.004%, bimatoprost 0.03% and 0.01%, and tafluprost 0.0015% and of generic latanoprost 0.005% and generic bimatoprost 0.03%. We also used Medicare Part D spending data to determine aggregate spend in 2013 and 2017.In 2009, 92% of plans covered branded latanoprost, 83% covered branded bimatoprost; and 49% covered branded travoprost, whereas in 2017, 6% of plans covered branded latanoprost; 95% covered branded bimatoprost; and 96% covered branded travoprost. Although generic latanoprost was universally covered, generic bimatoprost was only covered by 35% of plans in 2017. Median out-of-pocket cost of branded prostaglandins without generic equivalents was $35 (IQR = $29-$40) in 2009, $45 (IQR = $42-$101) in 2013, and $90 (IQR = $45-$159) in 2017. Median out-of-pocket cost of all available generic prostaglandins was $10 (IQR = $5-$33) in 2013 and $10 (IQR = $4-$15) in 2017. In 2013, Medicare spent $733 million on prostaglandin analogs; in 2017, this increased to $1.09 billion, with $943 million (86%) spent on branded prostaglandins and $148 million (14%) spent on generics.Medicare PDP coverage of branded prostaglandins remained stable from 2009 to 2017. While median beneficiary out-of-pocket costs associated with generic prostaglandins remained stable, those associated with branded prostaglandins increased nearly 3-fold. What is already known about this subjectProstaglandin analogs are the most effective treatment for glaucoma.Adherence to prostaglandin analogs is suboptimal, which may partly be attributable to their high cost.Previous studies have been limited to characterizing the costs of branded prostaglandin analogs in aggregate or in specific subpopulations of patients.What this study addsThis study uses Medicare Part D formulary coverage data from all stand-alone and Medicare Advantage prescription drug plans in 2009, 2013, and 2017 to offer a comprehensive view of Medicare beneficiary access to glaucoma drugs over 8 years.We determined that while generic latanoprost was universally covered, generic bimatoprost was not, and coverage of branded bimatoprost and travoprost increased, while coverage of branded latanoprost declined.Median out-of-pocket cost of branded prostaglandins increased from $35 in 2009 to $90 in 2017 but was unchanged at $10 for generic prostaglandins.1 Lower intraocular pressure is correlated with slower progression of visual field deficits and optic disc deterioration, so the mainstays of therapy are aimed at decreasing intraocular pressure.2 Prostaglandin analogs are the most effective first-line treatment for lowering intraocular pressure in glaucoma.4Glaucoma is the second leading cause of irreversible blindness in the United States and is most common among older adults; approximately 12% of Medicare beneficiaries have been diagnosed with glaucoma.5 High prescription cost is an important factor that increases the likelihood of nonadherence to topical ocular hypotensive medications in Medicare beneficiaries.6Adherence is suboptimal for prostaglandin analogs\u2014studies of prescription records for ocular hypotensive agents in patients with glaucoma and ocular hypertension found that only 56% of days could have been dosed with the medication supply dispensed over the first year of therapy.7 Further, no study has examined both coverage and beneficiary out-of-pocket costs of prostaglandin analogs at an individual drug level.8 Such an analysis may offer insight into how plans use formulary design to incentivize the use of certain prostaglandin analogs over another and may elucidate areas of opportunity for future cost savings.Although some previous studies have characterized the high cost of branded prostaglandin analogs, they have focused on limited subsets of the affected population, such as beneficiaries of a single Medicare Advantage plan or a single pharmaceutical benefits manager.Accordingly, our research objective was to use Medicare prescription drug plan (PDP) and spending data to characterize the coverage of, beneficiary out-of-pocket cost associated with, and total Medicare Part D spending on prostaglandins between 2009 and 2017. By using data from all Medicare PDPs, including stand-alone Part D plans and Medicare Advantage plans, we aimed to characterize how the coverage and pricing of prostaglandins throughout this period may have contributed to difficult patient access to these drugs. We combined this with an analysis of total Medicare spending on prostaglandin analogs, which may help identify areas of potential cost savings through incentivizing the use of generics over branded products.We conducted a retrospective analysis of quarter (Q) 2 2009, Q2 2013, and Q2 2017 Medicare PDP formulary, beneficiary cost, and pricing files, which are available from Centers for Medicare & Medicaid Services (CMS). These files provide information on all PDPs that submitted complete and accurate information to CMS, including stand-alone Part D and Medicare Advantage plans operating in the United States. We excluded special needs PDPs and plans outside of the United States .We characterized beneficiary coverage (including utilization management restrictions) and out-of-pocket costs for each prostaglandin analog used for glaucoma treatment: Xalatan (latanoprost) 0.005%, Travatan (travoprost) 0.004%, Lumigan (bimatoprost) 0.03% and 0.01% , Zioptan (tafluprost) 0.0015%, generic latanoprost 0.005%, and generic bimatoprost 0.03%. By examining data from 2009, 2013, and 2017, our study includes points in time after which generic versions of certain prostaglandin analogs first became available, including latanoprost in 2011 and bimatoprost in 2015, in order to examine the effect that these launches may have had on coverage and cost of other prostaglandin analogs.9For each drug, we determined the number and median proportion of plans that did not provide coverage; provided coverage with utilization management restrictions ; and provided coverage without restrictions. We also determined the number of branded prostaglandins that each plan covered (with or without restrictions); determined the tier of coverage for each drug in each plan; and using this information, determined how many plans had fewer restrictions for a branded drug compared with its generic and how many covered a branded drug under the same cost-sharing tier or under a lower (more favorable) cost-sharing tier than its generic.Next, we determined the median out-of-pocket cost for a first-prescription, 30-day supply of each drug across all plans. While some Medicare beneficiaries obtain 90-day drug supplies, these are not offered by all Medicare PDPs. For consistency of comparisons, our analyses considered only the out-of-pocket costs associated with 30-day supplies. Because we focused on first-prescription cost, we assumed that the deductible, where applicable, had not been met when calculating out-of-pocket cost.10 All analyses were performed using Stata, version 15.1 , and Excel, version 14.1.3 .We also used Medicare Part D drug spending data (available from CMS) to look at aggregate Medicare Part D spending for each prostaglandin analog for 2013 and 2017 (these data are not available for 2009). These costs are based on the gross drug cost, which represents total spending for the prescription claim, including Medicare, plan, and beneficiary payments. The Part D spending metrics do not reflect any manufacturers\u2019 rebates or other price concessions, so we performed a sensitivity analysis to estimate the effect of rebates on spending using a previously described method.Data were available on 3,607 Medicare PDPs in 2009, 2,609 in 2013, and 2,668 in 2017. In 2009, 92% of plans covered branded latanoprost; 83% covered branded bimatoprost; and 49% covered branded travoprost . In 2013In 2009, 12% of plans covered only 1 branded prostaglandin; 52% of plans covered 2 branded prostaglandins; and 35% of plans covered 3 branded prostaglandins. In 2013, 6% of plans covered only 1 branded prostaglandin; 73% of plans covered 2 branded prostaglandins; 10% of plans covered 3 branded prostaglandins; and 11% of plans covered 4 branded prostaglandins. In 2017, 2% of plans covered no branded prostaglandins; 6% of plans covered 1 branded prostaglandin; 72% of plans covered 2 branded prostaglandins; 15% of plans covered 3 branded prostaglandins; and 5% covered 4 branded prostaglandins. Notably, of the 2,531 plans that covered branded bimatoprost in 2017, 1,648 (65%) did not also cover generic bimatoprost.The median Medicare beneficiary out-of-pocket cost of branded prostaglandins without generic equivalents was $35 (interquartile range [IQR] = $29-$40) in 2009, $45 (IQR = $42-$101) in 2013, and $90 (IQR = $45-$159) in 2017. Median out-of-pocket costs in each year of branded latanoprost, bimatoprost, travoprost, and tafluprost were broadly similar. In contrast, the median out-of-pocket cost of generic latanoprost was $10 (IQR = $5-$33) in 2013 and $7 (IQR = $2-$12) in 2017, whereas generic bimatoprost was $30 (IQR = $12-$154) in 2017 . AlthougIn 2013, Medicare spent $733 million on all prostaglandins\u2014$122 million on generic prostaglandins and $611 million on branded prostaglandins. Generic latanoprost, the generic glaucoma drug for which Medicare had the highest spend, accounted for $120 million (16%) of all spending on prostaglandins. Branded bimatoprost, the branded glaucoma drug for which Medicare had the highest spend, accounted for $313 million (43%) of all spending on prostaglandins. Assuming 17.5% manufacturer rebates (the average rebate reported by Medicare in 2014), total spending would have been $626 million; branded spending would have been $504 million ; and branded bimatoprost spending would have been $259 million . Assuming 26.3% manufacturer rebates (the highest reported rebate by Medicare in 2014), total spending would have been $572 million; branded spending would have been $451 million ; and branded bimatoprost spending would have been $231 million .In 2017, Medicare spent $1.09 billion on prostaglandins, a 49% increase over the 2013 spend\u2014$148 million was spent on generics, while $943 million was spent on branded drugs. Branded latanoprost accounted for $145 million , while branded bimatoprost accounted for $517 million (47%) of all spending on prostaglandin analogs ($517 million). Only $3.6 million, or 0.33% of total spending, was for generic bimatoprost. Assuming 17.5% manufacturer rebates, total spending would have been $926 million; branded spending would have been $778 million ; and branded bimatoprost spending would have been $427 million . Assuming 26.3% manufacturer rebates, total spending would have been $843 million, branded spending would have been $695 million , and branded bimatoprost spending would have been $381 million .In our study of Medicare prescription drug coverage of prostaglandins used for the treatment and management of glaucoma, we found that the number of branded prostaglandins covered by plans did not increase from 2009 to 2017, but the patterns of formulary coverage shifted from predominantly covering branded latanoprost to branded travoprost, with consistent coverage of branded bimatoprost. However, during this time frame, median beneficiary out-of-pocket costs associated with branded prostaglandins increased nearly 3-fold, to $90 for a 30-day supply.11 Third, Allergan\u2019s rebate contracts may have explicitly stipulated the exclusion of generic bimatoprost from the formularies of the pharmacy benefit managers in exchange for manufacturer rebates. Finally, plans may have offered more limited coverage because the results of an Allergan-funded trial demonstrated better safety and equivalent efficacy for the 0.01% compared with the 0.03% dosage.12 However, the clinical importance of the safety differences is less clear and may not fully explain the large differences in coverage between branded bimatoprost and generic bimatoprost because at the end of the 12-month study period, 80% of bimatoprost 0.01% users and 77% of 0.03% users reported being very or extremely willing to continue using the study medication.12After 2009, generic versions of 2 prostaglandin analogs became available: latanoprost in 2011, which is now universally covered, and bimatoprost in 2015, which has limited coverage. Moreover, 65% of plans covering branded bimatoprost did not also cover generic bimatoprost in 2017. Of the plans that did cover both, only 58% incentivized use of generic bimatoprost over the branded version by placing generic bimatoprost in a lower (more favorable) cost-sharing tier than branded bimatoprost. There are 4 possible reasons that may account for this more limited coverage. First, bimatoprost is priced higher, perhaps making latanoprost a more competitive selection for plans. Second, the branded product\u2019s manufacturer, Allergan, may have dampened coverage through a \u201cforced switch\u201d strategy, whereby branded bimatoprost was reformulated from a 0.03% to a 0.01% dosage in 2010 in anticipation of generic competition, a strategy previously employed by pharmaceutical manufacturers.We are also likely observing the effects of pharmaceutical manufacturer marketing and promotion strategies in the Medicare Part D spending trends from 2013 to 2017. Despite the entry of generic bimatoprost as a new drug between the 2 years, the percentage of total spend that branded drugs accounted for increased from 83% to 86%. Also, in both years, more was spent on branded bimatoprost than on any other prostaglandin analog, and the percentage of total prostaglandin analog spend it accounted for increased from 43% to 47%. At the same time, after market entry of generic bimatoprost in 2015, as of 2017 it only accounted for 0.33% of total spend on prostaglandin analogs. Even assuming maximum manufacturer rebates of 26.3%, the percentages of total spend accounted for by branded bimatoprost individually, and branded drugs as a whole, increased. Further, branded bimatoprost was still the prostaglandin analog with the highest spend in both years.This large amount of spending suggests that there remains huge potential for cost savings to Medicare and its beneficiaries through increased coverage and use of generic bimatoprost and generic latanoprost. This conversation becomes even more important as new branded prostaglandin analogs are released, for example, Vyzulta (latanoprostene) in 2018, since trends from 2009 to 2017 show that increased medication options do not necessarily lead to improved coverage or lower prices for Medicare beneficiaries.Our research highlights that Medicare PDPs overall are not adequately incentivizing the use of lower-cost generic prostaglandin analogs through utilization management strategies. Inadequate PDP coverage enables branded drugs that already have generic competition, such as branded bimatoprost, to continue to secure large amounts of revenue simply through a dosage reformulation, while leaving unrealized the potential cost savings for Medicare and its beneficiaries through generic drug use. Despite the launch of several new drugs in the past decade, this lack of coverage by Medicare PDP formularies and the tripling of out-of-pocket costs associated with branded prostaglandins increasingly puts patients at risk for cost-related nonadherence. Since these drugs are used chronically, the financial burden on patients is multiplied over time, increasing the risk of nonadherence that can lead to significant morbidity.There are important limitations to our study that deserve consideration. First, because we looked at first-prescription cost, our analysis may not be generalizable to all beneficiaries\u2019 prescriptions throughout a coverage year, since our calculations assumed that a plan\u2019s deductible had not yet been met, which may not be representative of cumulative annual prescription costs. For instance, our estimates did not take into account prescription costs during the coverage gap phase, which often require larger out-of-pocket costs than during the initial coverage phase.Second, our analysis focused on median beneficiary out-of-pocket prescription costs and did not take into account insurance plan premiums, which may have changed over the study period. Third, Medicare PDP data do not include the number of beneficiaries enrolled in each plan, nor the volume of prescriptions filled, so our coverage and out-of-pocket cost estimates do not weight more heavily plans with more enrollees nor those that filled greater numbers of prescriptions for prostaglandin analogs.Fourth, by focusing our analyses on the out-of-pocket costs associated with 30-day prescriptions, we may have slightly overestimated costs, since 90-day prescriptions may be available for lower prorated amounts.Finally, although our analysis accounts for the potential effect of manufacturer rebates on the overall amount Medicare spent on these drugs, our data do not include rebates on an individual drug and plan level.Medicare PDPs provided coverage for similar numbers of branded prostaglandin analogs in 2009 as in 2017, but beneficiary out-of-pocket costs were almost 3 times higher, despite the introduction of 2 generic versions over this time. All Medicare PDPs provided coverage of generic latanoprost, but not of generic bimatoprost, and median beneficiary out-of-pocket costs for generic prostaglandin analogs remained stable. Because the entry of generic bimatoprost has neither lowered the cost of nor diverted spend away from the more expensive branded version of the drug, our findings suggest that there are opportunities for Medicare PDPs to increase generic prostaglandin analog use, which may improve patient access to therapy by reducing out-of-pocket prescription drug costs and thereby decreasing glaucoma-associated disease morbidity."} +{"text": "Candidemia can lead to ocular complications, including endophthalmitis and chorioretinitis. Prompt management of such ocular diseases is paramount due to the risk of blindness. Management of candidemia usually includes a dilated ophthalmic exam; however, there are concerns regarding the utility of performing ophthalmic exams in all patients due to a low rate of ocular complications and lack of changes in medical management. Thus, there is a need for prognostic factors suggestive of ocular involvement that warrant a thorough ophthalmic examination. We sought to evaluate if positive repeat blood cultures are associated with ocular involvement in candidemia.A single-center, retrospective chart review was conducted at an academic medical center. All candidemia cases from 2017 to 2022 were analyzed for demographics, culture results, treatment, inpatient ophthalmic exam findings, and mortality at discharge, at 30 days, and at 90 days. Descriptive statistics and Chi-Square tests were performed on the collected data.104 episodes of candidemia among 84 patients were included: the mean age was 54 years, 55% were male, 74% were Black, and 13.1% were Latino. The most common Candida species isolated was C. albicans (37%) and most patients were treated with micafungin (51%). 12% had visual symptoms and 84% underwent ophthalmic exams. 15% of the exams were concerning for ocular involvement: 5% endophthalmitis, 5% chorioretinitis, and 5% other infectious findings . There was no significant association between repeat positive blood culture results and development of endophthalmitis (p = 1.00), chorioretinitis (p = 0.93), or any ocular involvement (p = 0.97). Furthermore, no significant associations were found between repeat blood culture and death at discharge, 30 days, or 90 days.No significant associations were found between repeat positive blood culture and ocular involvement in the setting of candidemia. Other indicators of ocular involvement in candidemia are needed to assess patients who would benefit from ophthalmic exam.All Authors: No reported disclosures"} +{"text": "Cefpodoxime is increasingly being explored as an option for intravenous-to-oral step-down therapy in Enterobacterales infections, but it is rarely included in routine susceptibility testing. The Clinical and Laboratory Standards Institute (CLSI) states that cefpodoxime susceptibility among urinary isolates can be inferred from the result for cefazolin. However, cefazolin resistance may overcall resistance to cefpodoxime. Studies directly comparing ceftriaxone, cefazolin, and cefpodoxine susceptibilities are lacking. The purpose of this study was to determine correlation of ceftriaxone or cefazolin susceptibilities as a surrogate marker for cefpodoxime susceptibility in Enterobacterales.E. coli, Klebsiella spp., and Proteus spp. from urine, blood, respiratory, surgical, or wound cultures. Susceptibility testing was conducted by manual Kirby Bauer disk diffusion for cefpodoxime, ceftriaxone, and cefazolin (in duplicate) following standard procedures. The VITEK 2 automated system was used to adjudicate discrepancies between duplicates. Breakpoints from the current CLSI M100 were used to assign categories for the different methods of susceptibility testing. Categorical agreement, very major, major, and minor error rates between ceftriaxone or cefazolin and cefpodoxime were calculated.The study was conducted on clinical isolates of P =0.0001). The major error rate was 15% (11/74) for cefazolin and 0% for ceftriaxone. The very major error rate was 7% (1/14) for cefazolin and 21% (3/14) for ceftriaxone. The minor error rate was 22% (19/88) for cefazolin and 0% for ceftriaxone.A total of 88 clinical isolates were evaluated. The categorical agreement rate was 64% for cefazolin and 97% for ceftriaxone (Isolate CharacteristicsCeftriaxone appears to be a better surrogate marker for predicting cefpodoxime susceptibility, when compared to cefazolin. In addition, ceftriaxone demonstrated lower major and minor error rates.All Authors: No reported disclosures"} +{"text": "Background and Objective: Cisplatin is a chemotherapy drug used to treat several types of malignancies. It is a platinum-based compound that interferes with cell division and DNA replication. Cisplatin has been associated with renal damage. This study evaluates the early detection of nephrotoxicity through routine laboratory tests. Materials and Methods: This is a retrospective chart review based on the Saudi Ministry of National Guard Hospital (MNGHA). We evaluated deferential laboratory tests for cancer patients treated with cisplatin between April 2015 and July 2019. The evaluation included age, sex, WBC, platelets, electrolytes, co-morbidities and interaction with radiology. Results: The review qualified 254 patients for evaluation. Around 29 patients (11.5%) had developed kidney function abnormality. These patients presented with abnormally low magnesium 9 (31%), potassium 6 (20.7%), sodium 19 (65.5%) and calcium 20 (69%). Interestingly, the whole sample size had abnormal electrolytes presenting magnesium 78 (30.8%), potassium 30 (11.9%), sodium 147 (58.1%) and calcium 106 (41.9%). Some pathological features were detected, such as hypomagnesemia, hypocalcemia and hypokalemia. In addition, infections that needed antibiotics were dominant in patients treated with cisplatin alone, representing 50% of this group. Conclusions: We report that an average of 15% of patients with electrolyte abnormalities develop renal toxicity and reduced function. Moreover, electrolytes may serve as an early indicator for renal damage as part of chemotherapy complication. This indication represents 15% of renal toxicity cases. Changes in electrolyte levels have been reported with cisplatin. Specifically, it has been linked to hypomagnesemia, hypocalcemia and hypokalemia. This study will help reduce the risk of dialysis or the need for kidney transplant. It is also important to manage any underlying conditions and control patients\u2019 intake of electrolytes. Cisplatin, which also called cis-diamminedichloridoplatinum(II), is a chemotherapy agent based on platinum . It is u\u22122 body surface area) was also reported to increase side effects, especially nephrotoxicity [Cisplatin is associated with dose-dependent complications, including nausea, vomiting, hypomagnesemia, peripheral neuropathy, bone marrow suppression and hearing loss. Two of the most common cisplatin side effects are ototoxicity and nephrotoxicity. The ototoxicity (toxicity or damage to the ear) shows bilateral and irreversible symptoms of tinnitus and hearing loss . The neptoxicity . Additiotoxicity . Cisplattoxicity ,10. Cispp < 0.05) and this was the criterion to consider the results statistically significant.Analysis included descriptive statistical frequency, data presentation, mean and standard deviation. Significance was assessed using the chi-square test and parametric or non-parametric binomial tests where appropriate. The level of significance was set at 0.05 for all tests , a tertiary hospital in Riyadh. All medical records of patients diagnosed with cancer who received cisplatin treatment between April 2015 and July 2019 were included. Inclusion criteria were patients receiving cisplatin alone or in combination with chemotherapy or radiation. We used a non-probability consecutive sampling technique. The patients were followed up for at least two months based on physicians\u2019 recommendation. The evaluation included age, sex, WBC, platelets, electrolytes, co-morbidities, tumor size and interaction with radiology. Exclusion criteria were patients with no clinical treatment information or patients who had undergone cancer treatment prior to admission to MNGHA. p = 0.631). The median score for BMI was 23. In addition, the median age for the study was 46 years old. The patients\u2019 marital status was recorded, with 150 (59.3%) married, 75 (29.6%) single and 28 (11.1%) other patients. The patient cohort included 19.7% treated with cisplatin alone while 80.3% were treated with cisplatin in combination with other chemotherapies. The cohort included pediatric patients, who represented 13.4% of the total. The patients\u2019 demographic characteristics are detailed in Overall, 260 Saudi patients found for the period between 2015 and 2019. The number of qualifying patients based on the criteria was 254. Gender was found to be an insignificant controller for the cisplatin data. In this study, the number of males was 124, while there were 130 females. The BMIs were calculated to represent normal (56.7%) and overweight (43.3%) scores, which were insignificant for developing nephrotoxicity , breast cancer (9.8%), nasopharyngeal cancer (7.5%), stomach cancer (6.3%), neuroblastoma (5.8%), medulloblastoma (5%), testicular cancer (5%), lung cancer (4.7%), Hodgkin lymphoma (4.3%), and others (<4%); see ll cases . The resThere are 24 different chemotherapies used in the MNGHA center in combination with cisplatin. Any medication used in more than 10% of cases was listed as frequent therapy, such as gemcitabine, etoposide and cytarabine; see Kidney toxicity was reported in 11.5% of all cases. Among the affected patients, 69% had low calcium abnormality, while only 20% had low potassium abnormality, representing the upper and lower limit, respectively. Total abnormalities which are above or below the normal range were documented as follows: calcium 41.9%, sodium 58.1%, magnesium 30.8% and potassium 11.9% .p = 0.5), (Co-morbidities consider = 0.5), .In total, 36.6% of patients in the cohort suffered from large tumors >5 cm, while 64.8% had tumors smaller than 5 cm. Abnormal ranges of platelets represented 15.6% (excess) and 26% (deficiency) of the whole cohort. White blood cell (WBC) distribution was measured as 17% above normal and 44% below normal range .We evaluated renal damage in 254 patients who had received cisplatin as part of their cancer therapy between 2015 and 2019. We observed an overall incidence of kidney toxicity of 11.5%. p = 0.631).Looking at the study demographic characteristics, we found no significant predictor relevant to gender or nationality. Moreover, kidney toxicity was not detected in any of the pediatric cases, even though they represent 13.4% of the cohort treated with cisplatin. This suggests that pediatric patients have more tolerance to the chemotherapy treatments than adults. Nonetheless, it is important to consider that this is a relatively small sample size to draw solid conclusions for pediatric patients. Other studies have observed ototoxicity (severe hearing loss), which was not investigated in this study ,12. FurtThis study extracted cancer cases that were associated with cisplatin treatment. These cases represented 27 different cancers, of which lymphoma represented 20% of the cohort. The other cancers were present in the cohort at levels from 10 to 4%. This study did not intend to study a particular cancer, but rather trace the complications arising from cisplatin therapy. Furthermore, as part of the treatment protocols, we documented 24 different chemotherapies used in combination with cisplatin. These treatments were used by physicians relevant to particular malignancies and standards. It is worth noting that some of these drugs, such as etoposide, rituximab and capecitabine, were reported to contribute to kidney toxicity ,14,15. HCisplatin affects the tubulointerstitial components of the kidney with relative sparing of glomeruli. Therefore, glomerular filtration rate and creatinine level may not be the best indicators of nephrotoxicity. As electrolytes are mostly reabsorbed in the tubular system, cisplatin-induced tubular atrophy would result in electrolyte disturbance ,20. MagnThe mechanisms of the underlying renal injury are mainly secondary to cisplatin accumulation in the kidney . The renCancer stem cells (CSCs) were reported to be resistant to conventional chemotherapy and radiation . CisplatIn this study, we reviewed electrolytes such as sodium, calcium, magnesium and potassium as early indicators for kidney dysfunction. We found that in the kidney failure group, abnormally low levels of calcium 69%, sodium 65.5%, magnesium 31% and potassium 20% were present before severe kidney dysfunction. The data suggest that calcium and sodium level abnormalities may work as the best indicators in this context. Deficiency in both the electrolytes shown predicted 65% of the nephrotoxicity cases. However, conventional diagnostic and clinical methods will still be in place for confirmation and proper medical response. Looking at the whole data, we see an exaggeration of calcium and sodium abnormality, representing 41.9% and 58.1% of cases, respectively. While kidney toxicity cases represent only 11.5% of all cases, better indicators are needed. Therefore, we suggest using all electrolytes, calcium 69%, sodium 65.5%, magnesium 31% and potassium 20%, as indicators that give a narrow window for kidney dysfunction prediction. Even though cisplatin treatment alone represents 20% of all cases, infection in patients treated with cisplatin alone was documented in around 10% of all cases. This means that 50% of patients treated with cisplatin alone developed infection. Similarly, cisplatin is reported in the literature to lead to infection, anemia, feeling sick, loss of appetite, changes in tongue, kidney problems, hearing disorders, bruising and bleeding ,10.Hydration was suggested to postpone or decrease the nephrotoxic effect of cisplatin. However, its efficacy is still limited . HydratiAmifostine and sodium thiosulfate also protect against platinum-induced hearing loss ,41. AmifEven though this study reports an association between electrolyte abnormality and renal failure, other chemotherapies used in this study need to be considered. This study reports that only 20% of patients were exposed to cisplatin alone, while 80% of patients had combination therapy including cisplatin. This affects the reliability of the data as some of the nephrotoxicities may be caused by combination therapy rather than cisplatin alone. The cause-and-effect relationship cannot be considered in this case. However, 17% of the kidney failure group were from the cisplatin-alone cohort, which is a significant number. Additionally, this study is a retrospective review, which adds another layer to the limitation.We reported herein a possibility of using electrolyte deficiency as an early indicator for renal failure. We encountered limited early and late nephrotoxicity. Importantly, nephrotoxicity was not the main dose-limiting toxicity. This study will help reduce the risk of dialysis or the need for kidney transplant when better patient management and patient\u2019 awareness are practiced. Our results emphasize the importance of close monitoring and additional replacement of water and electrolytes as needed. Patients should be advised to increase electrolyte intake or prescribed electrolytes as a precaution. On the other hand, patients who suffer from abnormally high electrolytes should take a prescribed drug to reduce electrolyte imbalance. More effort needs to be made to generate a consistent method of measuring and reporting chemotherapy-induced nephrotoxicity, which would be a valuable contribution to the literature."} +{"text": "To determine the factors important in approving prescription reimbursement under prior authorization (PA) in a Medicaid managed care organization (MCO).A cross-sectional statistical analysis was performed using administrative data for one month of PA requests to an MCO with more than 250,000 Medicaid recipients in the northeast United States.More than 95% of PA reviews resulted in payment for the originally prescribed products. The most common treatments involved were atypical antipsychotics, antacids, antidepressants, antihypertensives, anticonvulsants, and Cox-2 inhibitors. The rejection rate for nonformulary products was 7.1% while that for formulary products was 3.7%. Nevertheless, most drugs requiring PA were formulary-listed, with protocols to reinforce prescription guidelines. Rejection of reimbursement was inversely related to patient age. Most likely to be authorized were drugs for smoking cessation, pain, and nausea, while those least likely to be approved were multivitamins, sleep aids, and high-cost antidepressants.Although nonformulary products are more frequently subject to PA, 78.6% of PA procedures are performed in response to requests for formulary-listed products. The PA rejection rate for this Medicaid MCO was small; 4.4% overall and 7.1% for nonformulary versus 3.7% for formulary drugs."} +{"text": "This study focused on providing a report about the current situation of AMR in Yastebsheron Hospital in Khartoum, Sudan, monitoring and identifying the resistant trends in clinical isolates, highlighting the gaps in the IPC and ASP through antibiogram analysis, and implementing its data to improve antibiogram-guided empirical antibiotic therapy selection.A retrospective longitudinal study. The study retrieved data from microbiology laboratory records from 1 January 2022 to 31 December 2022, at Yastebsheron Hospital. A total of 1182 clinical specimens were processed in 2022.Staphylococcus aureus accounted for 98%; out of the total specimens, MRSA accounted for 48.6%, and MSSA accounted for 11.8%. The total Gram-negative isolates were 48.3%, of which Escherichia coli Enterobacter, Proteus mirabilis, Pseudomonas aeruginosa and Klebsiella pneumoniae represented 25.4%, 21.8%, 9.8%, 9.4% and 3.8%, respectively. MSSA were highly susceptible to meropenem (97%) and vancomycin (95%), and luckily, MRSA isolates were susceptible to levofloxacin and colistin at 86% and to meropenem (84%), with minimal susceptibility to clindamycin (37%) and nalidixic acid (12%). Meropenem, colistin and nitrofurantoin were the most effective antibiotics against E. coli with more than 80% susceptibility rates, while cephalosporins and nalidixic acid showed minimal efficacy. Meropenem and levofloxacin were highly effective against Enterobacter, P. mirabilis, while the susceptibility rates for second-, third- and fourth-generation cephalosporins were less than 50% for both of them, and less than 30% for P. aeruginosa, P. aeruginosa was 100% susceptible to colistin.The most frequent samples were urine, with a prevalence rate of 59.3%, of which 69.8% were female and 30.2% were male. The total Gram-positives were 52.6%, with S. aureus, then came Enterobacteriaceae, particularly E. coli, and then P. aeruginosa. Contrary to ciprofloxacin and norfloxacin, meropenem showed high efficacy against G-positive and G-negative isolates, while levofloxacin displayed moderately high results. Except for MSSA, the effectiveness of second-, third- and fourth-generation cephalosporins against G-positive and G-negative organisms was compromised. In order to stop the deterioration of the AMR status, it is crucial to implement the ASP strategies and tools effectively, as the emergence of MDR strains is alarming. Antibiogram\u2019s formulation is essential for directing empirical antibiotic therapy and tracking the emergence of resistance.Among infections, UTIs had the highest incidence rates. The majority of the isolates were"} +{"text": "We sought to evaluate the contribution of Global TravEpiNet (GTEN) sites in providing influenza and pneumococcal vaccinations during pretravel visits.1. We conducted descriptive analyses on vaccinations and reasons for non-administration .We analyzed prospectively-collected data from 31 GTEN sites between 07/01/2012 -06/31/2022 and included demographics, travel-related characteristics and vaccines administered at the visit. Vaccine eligibility was based on CDC recommendations. Influenza seasonality at the destination was determined based on WHO dataThe 10-year study period included 116,865 pretravel visits during which clinics administered 1,732 pneumococcal and 15,658 influenza vaccines (Table 1) and referred an additional 3,588 patients to their PCPs for pneumococcal and 6,955 for influenza vaccination.Of travelers eligible for pneumococcal vaccination, 49.9% were not recognized as having indications for vaccination. In the case of influenza, the vaccine was not offered to 14.3% of eligible travelers due to unavailability (6.9%) or because the provider did not consider it to be indicated based on the itinerary (7.4%).Among 66,056 travelers with an itinerary falling within an area with active influenza transmission, the vaccine was unavailable for 10% and not considered indicated in 9.5% . These issues occurred mostly during the summer months in the USA. Specifically, 89.8% of travelers for whom there was no available vaccine, and 83.4% of travelers not recognized as eligible for the vaccine, were traveling between April and September.GTEN clinics provide routine vaccinations against respiratory pathogens, but some missed opportunities are identified. GTEN providers often referred patients to their PCPs for pneumococcal vaccination, perhaps reflecting issues of insurance coverage. The influenza vaccine expiration dates lead to lack of the vaccine for almost 3 months, during summer in the USA. Finally, persons traveling between April and September or to areas with year round transmission may not be recognized to have potential influenza exposure, despite traveling to destinations with active influenza transmission.References:https://www.who.int/tools/flunet1. WHO Global Influenza Programme. Lin H. Chen, MD, Merck: Honoraria|Sanofi: Honoraria|Shoreland Inc: Advisor/Consultant|Valneva: Advisor/Consultant"} +{"text": "We reviewed the available studies assessing salvage surgery after recurrent prostate cancer with primary non-surgical treatment. While the studies used had the potential for bias, due to their retrospective type, we looked at treatment outcomes and toxicity for men treated with a number of salvage radical prostatectomies for recurrent prostate cancer. We demonstrated that SRP can be considered a suitable treatment option for selected patients.n = 3240, 84%). Other first-line treatments included HIFU , electroporation , proton beam therapy , cryotherapy , focal vascular targeted photodynamic therapy , and transurethral ultrasound ablation . Median preoperative PSA, at the time of recurrence, ranged from 1.5 to 14.4 ng/mL. The surgical approach was open in 2300 (60%) cases, robotic in 1465 (38%) cases, and laparoscopic in 71 (2%) cases. Since 2019, there has been a clear increase in robotic versus conventional surgery . The median operative time and blood loss ranged from 80 to 297 min and 75 to 914 mL, respectively. Concomitant lymph node dissection was performed in 2587 cases (79%). The overall complication rate was 34%, with a majority of Clavien grade I or II complications. Clavien \u2265 3 complications ranged from 0 to 64%. Positive surgical margins were noted in 792 cases (32%). The median follow-up ranged from 4.6 to 94 months. Biochemical recurrence after sRP ranged from 8% to 51.5% at 12 months, from 0% to 66% at 22 months, and from 48% to 59% at 60 months. The specific and overall survival rates ranged from 13.4 to 98% and 62 to 100% at 5 years, respectively. Urinary continence was maintained in 52.1% of cases. sRP demonstrated acceptable oncological outcomes. These results, after sRP, are influenced by several factors, and above all by pre-treatment assessment, including imaging, with the development of mpMRI and metabolic imaging. Our results demonstrated that SRP can be considered a suitable treatment option for selected patients, but the level of evidence remains low.The aim of this study was to systematically review the current evidence regarding the oncological and functional outcomes of salvage radical prostatectomy (sRP) for recurrent prostate cancer. A systematic review was conducted throughout September 2022 using the PubMed, Science Direct, Scopus, and Embase databases. Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines were followed to identify eligible studies. A total of 55 studies (3836 patients) met our eligibility criteria. The vast majority of men included had radiation therapy (including brachytherapy) as their first-line treatment ( Prostate cancer (PCa) is the most commonly diagnosed cancer in men, with an estimated 1.4 million diagnoses recorded worldwide in 2020 . While tSalvage radical prostatectomy (sRP) is a challenging procedure that is rarely performed, although it represents a guidelines-validated option for BCR after primary nonsurgical treatment. The historical series of sRP with frequent major complications, such as rectal injury and poor functional outcomes , have plIn this study, we aimed to systematically review the current evidence regarding the oncological and functional outcomes of sRP for recurrent PCa after primary nonsurgical treatment.We conducted a systematic review in line with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines .prostatectomy, Prostate Cancer, Neoplasm Recurrences, treatment, Local, Radiation Therapy, Cryotherapies, Salvage Treatment, Robot-Assisted Surgery, and Surgical Procedure. Initial screening was independently performed by two investigators (A.S. and G.P.) based on the titles and abstracts of the articles to identify ineligible reports. Reasons for exclusions were noted. Potentially relevant reports were subjected to a full-text review, and the relevance of the reports was confirmed after the data extraction process. Disagreements were resolved by consultation with a third co-author (M.B.).This protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) database (Registration Number: CRD42022378227). We conducted a literature search in PubMed/Medline, Embase, and Science Direct databases, to identify reports published through September 2022, which addressed the oncological and functional outcomes of sRP. The search strategy included the following MeSH terms: Studies were deemed eligible if they included men with recurrent PCa after primary nonsurgical treatment (patients), managed with sRP (intervention), and if they assessed oncological and/or functional outcomes (outcome) in randomized controlled trials, nonrandomized prospective studies, and retrospective studies (study design). In case of duplicate publications, either the higher-quality or the most recent publication was selected. Reviews, meta-analyses, editorials, commentaries, authors\u2019 replies, meeting abstracts of unpublished studies, and case reports were excluded, but the reference section was checked for relevant articles. No restriction on the publication language was applied. We searched reports published between January 2008 to September 2022 . We extracted the following variables from the included studies: first author\u2019s name, publication year, sample size, age, pre-sRP PSA, pre- and post-sRP TNM stage, International Society of Urological Pathology (ISUP) score at pre-sRP biopsy, surgical approach, operative time, estimated blood loss, rate and severity of postoperative complications according to the Clavien-Dindo classification, rate of urinary continence, follow-up data, BCR rates, cancer-specific survival, and overall survival.Two authors (A.S. and G.P.) independently assessed the quality of the studies and the risk of bias. The risk of bias was assessed according to EAU recommendations for performing systematic reviews and meta-analysis . The QuaThe study selection process is outlined in the PRISMA flow diagram . A totalThe baseline characteristics of the included studies are summarized in The perioperative data are presented in A total of 45 studies reported data on concomitant lymph node dissection. The median number of nodes yielded was reported in 14 studies and ranged from 6 to 17, including 593 (20.5%) patients which were staged pN+ at final pathology.Regarding pathological features, stage \u2265pT3, positive surgical margins, and pN+ status ranged from 5 to 75%, 25 to 82%, and 3 to 60%, respectively. The pathological Gleason score was \u22658 in 6 to 67% of cases. These data were missing in nine studies.The reported postoperative complications are summarized in The urinary continence rate in the primary non-radiation-treatment group was 67% versus 55% in patients formerly treated by RT.The median follow-up ranged from 4.6 to 94 months . Biochemical recurrence ranged from 8% to 51.5% at 12 months, from 0% to 66% at 22 months, and from 48% to 59% at 60 months. Specific and overall survival rates ranged from 13.4 to 98% and 62 to 100% at 5 years, respectively .The rates of BCR were 20%, 27%, and 47%, respectively, in laparoscopic, robotic, and open approaches. Overall survival was 100% and 98% in the laparoscopic and robotic groups, respectively, and 74% in the open surgery group. The rates of BCR were 36% and 21% in the group of patients treated by non-radiation therapy and RT, respectively. Overall survival was 98% in the group of other primary treatments and 85% for patients treated by RT.sRP for recurrent PCa after primary non-surgical treatment failure is challenging for urologists due to its aggressive features and technical demands. The majority of PCa patients who present recurrent disease after RT are therefore treated with palliative ADT while a salvage treatment initiated early may change the disease course. As a result, only 1% of the patients recurring after RT indeed undergo salvage surgery .In the present systematic review, we found that sRP may represent a good alternative that can be provided to carefully selected patients. It may lead to a durable response if initiated early and may delay progression and use for systemic therapies.The introduction of minimally invasive approaches regarding sRP could be associated with many advantages, such as decreasing the rates of overall and high-grade complications . The robotic approach has been also associated with lower rates of blood loss, rectal injury, anastomotic stricture, and postoperative incontinence . RecentlOne of the major limitations attributed to sRP is the poor functional outcomes regarding the urinary continence associated with this option. Thus, we found an overall complication rate of 34%, including rectal wounds, ureteral complications, rectourethral fistula, lymphoceles, anastomotic leakage, and urinary tract infections, which is in line with a previous report from Matei et al., who reported a Clavien > 2 complication rate of 0\u201333% .However, the functional results widely differed between the studies included in this systematic review. Continence rates reported after sRP ranged from 10 to 100%. This heterogeneity could be explained, once again, by the surgical approach used. Robotic-assisted sRP appeared to improve the early return to continence, compared to open surgery series. This is thought to be due to the support of the surrounding ligaments to the anterior urethra, which helps to maintain sphincteric integrity after SRS ,68. MasoOncological outcomes after sRP are influenced by several factors and may vary depending on the patient/tumor characteristics, type of initial treatment, surgical approach used, length of follow-up, and, above all, pre-treatment assessment . At the mid-term follow-up, we found that the oncological outcomes were acceptable, as a significant proportion of men were disease-free after five years . In addition, cancer-specific survival and overall survival rates ranged from 13.4 to 98% and 62 to 100% at 5 years, respectively. However, long-term data remain poorly reported in the literature. Two series showed a 10-year BCR-free survival of 31% and 37%, respectively ,36. We tOur study has several strengths, including the important number of studies/patients included, with a variety of nonsurgical primary treatments with a clear distinction between them, the inclusion of most updated data, and their careful review for study inclusion.Some limitations must be acknowledged. The main limitation is the significant risk of bias, as all included studies were retrospective, which prevented us from reaching a high level of evidence and from providing clear recommendations. Finally, the heterogeneity regarding the surgical approach used, the type of initial local, and the functional erectile results, which are not reported in our review, are important limitations to notice. Of note, although we performed a systematic review, a meta-analysis was not possible given the heterogeneity of the studies in terms of the initial treatment proposed and the surgical approach.sRP appears to be feasible with acceptable morbidity in well-selected PCa patients who recur after primary non-operative surgical treatment. The development of a minimally invasive approach and the improvement of surgical techniques are considered to be two key factors in improving perioperative outcomes. However, the level of evidence remains low as comparative and long-term data are lacking."} +{"text": "Raising backyard chickens is a common practice in Morocco, mainly in rural or periurban areas. Constraints due to devastating avian diseases have been recognized as a major limiting factor in backyard poultry production. Consequently, these flocks could potentially be implicated as reservoirs for poultry diseases. However, there is a considerable lack of information on disease prevalence in this production system, and the risk represented by these small flocks remains under debate. This study aimed to estimate the seroprevalence and identify related risk factors of a range of bacterial and viral pathogens of outstanding importance for the economy and public health in backyard poultry in Morocco.Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) using a rapid serum agglutination test. Swab samples were compiled into 86 pools and submitted for molecular detection using real-time reverse-transcription\u2013polymerase chain reaction (RT-PCR).A total of 712 sera samples and 258 cloacal swabs were collected from 712 backyard chickens from 15 rural markets in the Khemisset and Skhirat-Temara provinces. None of the sampled chickens received any vaccination. Sera samples were screened for antibodies against Newcastle disease virus (NDV) and low pathogenic avian influenza H9N2 subtype (LPAI H9N2) using a hemagglutination-inhibition test, against bursal infectious disease virus (IBDV) and infectious bronchitis virus (IBV) using enzyme-linked immunosorbent assay, and against The seroprevalences in backyard chickens for NDV, LPAI H9N2, IBDV, IBV, MG, and MS were 52.1% (371/712), 63.5% (452/712), 84.7% (603/712), 82.2% (585/712), 58% (413/712), and 74.8% (533/712), respectively. Based on the RT-PCR results, 2.3% (2/86), 62.8% (54/86), 2.3% (2/86), 63.9% (55/86), 40.7% (35/86), and 29.1% (25/86) of the pools were positive for NDV, H9N2 LPAI, IBDV, IBV, MG, and MS, respectively. Multiple coinfections (H9N2-IBV-MG), (H9N2-IBV-MS), or (IBV-MG-MS) were observed in 15.1%, 8.5%, and 8.5% of the tested samples, respectively.The results show that backyard chicken flocks and rural markets have the potential to serve as reservoirs or amplifiers for poultry pathogens and could pose a risk to the commercial poultry sector. This highlights the need for a comprehensive and adapted vaccination plan for backyard chickens, and extension of efforts to increase flock owners\u2019 awareness of avian diseases and incite the implementation of biosecurity measures at the farm level. In recent decades, the Moroccan poultry sector has undergone remarkable expansion, with the country currently being a significant contributor to the production of chicken meat and eggs on the African continent. According to the Interprofessional Federation of the Poultry Sector , this inDespite the above, backyard poultry farming in Morocco still occupies an important and promising position as, it can contribute to food security, income improvement, women\u2019s empowerment, and alleviation of poverty as well This study aimed to estimate the prevalence of a selected group of avian pathogens among backyard chickens at rural markets in Khemisset and Temara provinces to obtain more information on the spread of these pathogens and explore the potential transmission risk for the industrial sector.This study does not require the approval of the Institutional Ethics Committee as live animals were not used in the study.The study was conducted from February 2021 to June 2022. We selected the weekly rural markets of Khemisset and Temara provinces as sampling sites. A weekly rural market is held once a week, during which backyard poultry flock owners and traders market weekly live or slaughtered poultry, among other farm products. Khemisset and Skhirate-Temara provinces have 36 weekly rural markets. Most of the rural markets are generally poorly structured and unhygienic, and poultry of different species are kept together due to space constraints. We targeted 15 major rural markets in the area (10 in Khemisset and 5 in Temara). The global positioning system coordinate data of each rural market were collected using Google Maps\u2122 (https://www.google.com/maps) and entered into a digitalized map of the Rabat-Sale-Kenitra region. We used a geographic information system program to prepare a map showing the spatial distribution of the sampled rural markets .Using a convenience sampling technique, we collected blood samples and cloacal swabs at slaughter from 712 apparently healthy local chickens >2 months of age. Approximately 5 mL of blood was collected aseptically from each chicken using a clot activator vacutainer and allowed to clot under normal atmospheric conditions. Cloacal swabs were obtained using Dacron swabs. A total of 712 blood samples and 258 swabs were obtained. Samples were labeled and transported in a cool box to the Avian Pathology Unit at Institut Agronomique et V\u00e9t\u00e9rinaire Hassan II in Rabat. Sera were harvested into properly labeled 2-mL Eppendorf tubes and stored with the cloacal swabs at \u221220\u00b0C until analysis. In addition to collecting samples, we also conducted interviews with chicken owners to gather information about the health status of their chickens over the past 6 months. We conducted the interviews using a structured questionnaire administered in face-to-face meetings, with questions focused on symptoms related to the respiratory, digestive, and nervous systems; incidents of mass mortality; and the vaccination history of their flocks. The chicken owners were informed of the purpose and context of the study, and their consent was obtained before conducting the interviews.Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) antibodies.Serum samples were analyzed using the hemagglutination-inhibition (HI) test for the presence of antibodies against Newcastle disease virus (NDV) and low pathogenic avian influenza H9N2 subtype (LPAI H9N2). In addition, we used enzyme-linked immunosorbent assay (ELISA) to screen for the presence of infectious bronchitis virus (IBV) and bursal infectious disease virus (IBDV) antibodies and the rapid serum agglutination (RSA) test to determine the presence of We conducted the HI tests on serum samples using the \u03b2 procedure (constant antigen and varying serum dilutions) according to the terrestrial manual of the World Organization for Animal Health (WOAH) . We used\u00ae IBV Indirect ELISA kit and PROFLOK\u00ae Plus IBD Ab test kit according to the manufacturer\u2019s protocols. The results were read using an ELx800 spectrophotometer at 450 nm using the provided software .We used the commercially available ID ScreenWe conducted the RSA test in accordance with the WOAH\u2019s terrestrial manual recommendations . A drop \u00ae RNA/DNA Purification kit following the manufacturer\u2019s instructions. One-step reverse-transcription\u2013polymerase chain reaction (RT-PCR) was performed to detect viruses using the Brilliant III Ultra-Fast qRT-PCR master mix . \u00ae MGS Triplex real-time . Any sample with a Ct value of \u00a342 was considered positive.Cloacal swabs were grouped into 86 pools by grouping three swabs from the same rural market in a common tube containing 5 mL of sterile phosphate-buffered saline. The mixture was then vortexed for a few seconds. We extracted combined RNA/DNA from each pool using the KyltData from the laboratory analyses were stored in a spreadsheet, and seroprevalence and molecular prevalence were computed. We calculated the prevalence of each disease with 95% confidence intervals (Cls). The prevalence was compared between provinces and rural markets using a chi-square test. A significance level of 5% was used. Analyses were performed using Statistical Package for the Social Sciences 24 . In addition, we summarized responses from the survey regarding the health status and vaccination history of backyard chickens using descriptive statistical analysis.According to the interviews with backyard poultry keepers and traders, vaccination against avian diseases was never administered. However, 98.6% of the surveyed persons asserted that they had experienced diseases among their poultry flocks during the previous 6 months, with chickens showing various signs, including depression, inappetence, diarrhea, respiratory distress, and torticollis in some cases.2, respectively. The province of Skhirat-Temara showed the highest rate of H9N2 seroprevalence of 71.7% against 61.8% noted in the province of Khemisset. Chi-square test showed a statistically significant difference between the two areas (p \u2264 0.05). The lower prevalence value observed in the rural markets was 25%, whereas the upper prevalence was almost 96%.The seroprevalence of LPAI H9N2 and the mean IHA titer of anti-H9N2 antibodies recorded in the present study were 63.5% (95% CI: 53%\u201372%) and 7.4 LogOf the 712 serum samples collected, 603 tested positive for IBDV, resulting in an overall prevalence of 84.7% (95% CI: 79%\u201392%) in the study area. In the Khemisset and Skhirat-Temara provinces, the prevalences were 82.6% and 95%, respectively, with statistically significant differences (p \u2264 0.05). The seroprevalence of Gumboro disease in the Skhirat-Temara region varied from 80% to 100%, whereas slightly lower seroprevalences were observed in the Khemisset province. Values ranged from 62.5% to 100%. In addition, most titer values (69%) were between 3000 and 18,500.Mycoplasmas, Of the 712 serum samples tested by RSA test, 413 and 533 were found to be positive for MG and MS, respectively, showing an overall prevalence of 58% (95% CI: 52%\u201365%) and 74.8% (95% CI: 74%\u201386%).Of the 712 chickens sampled, 82.2% (95% CI: 77.4%\u201386.4%) were positive for IBV antibodies, 82.6% (489/592) and 80% (96/120) in Khemisset and Skhirat-Temara, respectively . For MycOf the 86 pooled swab samples tested by real-time RT-PCR and PCR, we identified 2.3% (2/86) of the samples as positive for NDV in the study area. H9N2 was detected in 62.8% (54/86) of the pooled swabs sampled from backyard chickens in rural markets. Regional variations were observed in H9N2 detection. Khemisset province had significantly higher H9N2 detection (p < 0.05) than Skhirat-Temara province . OverallInvestigations of the health status of backyard chickens during periods without epidemics provide important information on the circulation of low-noise diseases for backyard flock owners, industry poultry farms, and state animal health decision-makers. The positive serological results prove that the unvaccinated birds had been exposed to the infectious agents under inquiry. In this study, the chicken owners confirmed that they had never vaccinated their birds against any poultry disease. Therefore, antibodies against ND, H9N2, IBD, IBV, MG, and MS were viewed as proof of natural exposure to infection.Our study revealed that the prevalence of NDV in backyard chickens was slightly high by HI test at 52.1% and low by RT-PCR at approximately 4%. A study published in 1988 reported the exposure of backyard chickens to NDV in Morocco, with an estimated overall ND seroprevalence of 35.2% in six different regions . In addiFurthermore, the very low prevalence of NDV detected by RT-PCR in the tested samples demonstrates the absence of recent or current virus infection in most of the sampled chickens. Various studies have reported positive serology and negative RT-PCR results for NDV. In Oman, 2,350 domestic birds were tested, and RT-PCR detected no cases of NDV . In BrazThe serological and molecular results indicated that the LPAI H9N2 virus was present in backyard chickens with high prevalence of 63.5% and 62.8% using the HI test and RT-PCR, respectively. These high prevalence levels confirm the endemic nature of this disease in backyard poultry flocks in Morocco. Since its first detection in broiler poultry farms in 2016 , LPAI H9et al. [et al. [The IBV prevalence observed in this study averaged 82.2% and 63.9% by ELISA and RT-PCR, respectively. Little information is available on the IBV prevalence in backyard poultry flocks in Morocco. Investigations on IBV are predominantly focused on the commercial poultry sector. Since the first isolation and characterization of the virus in Morocco in 1985 , severalet al. and Tesf [et al. in Ivory [et al. , 35.The results of the present study revealed a very high seroprevalence (84.7%) of IBD in unvaccinated backyard chickens, indicating evidence of virus circulation and subsequent field exposure of chickens. Indeed, Gumboro disease has been endemic in Morocco since it was first detected in commercial poultry flocks in 1978. Recently, the highly virulent strain very virulent IBDV has been isolated and characterized in many regions of the country, demonstrating that this strain, which is distinct from classic and vaccine strains, is widespread . Our obsSeveral pathogenic mycoplasmas cause avian mycoplasmosis, the most important of which are MG and MS. Both MG and MS can cause respiratory diseases and synovitis in poultry, resulting in severe economic losses. Antibodies against MG and MS were found in 58% and 74.8% of the chickens by RSA and in 40.7% and 29.1% of the pools tested by RT-PCR, respectively Tables-. SeveralDespite the great importance of backyard poultry farming to a large proportion of the rural population in Morocco, as in many other developing countries, and its potential implication as a serious threat to the industrial sector, to the best of our knowledge, very few studies have been performed on the presence of poultry diseases among the backyard chicken population in Morocco. Within this context of a lack of information, our finding constitutes the first investigation on the disease prevalence within the backyard chicken population in this country. The results of our study provide evidence of a high prevalence of avian diseases in backyard chickens, which has the potential to serve as a reservoir or amplifier of avian diseases that might affect commercial poultry , 54. TheThis study provided evidence that the most feared pathogens in commercial poultry farms are circulating among backyard chicken populations. The epidemiological figures in this study highlight the need for an effective and adapted avian disease prevention and control strategy for backyard chickens in Morocco. In addition, great efforts should be made in terms of awareness, extension, and education of flock owners about avian diseases. Implementation of biosecurity measures in farms should improve the epidemiological situation, productivity, and income of small farmers. On the other hand, backyard poultry flocks have proven to be good sentinels of avian pathogens in a given environment. Therefore, it is imperative to consider their relevance for any avian disease surveillance system. Most importantly, exhaustive studies should be conducted to isolate and identify pathogen strains and investigate their molecular profiles to better understand the potential epidemiological role of strains circulating among backyard chicken populations.AF, MB, and SF: Designed the study. AF, OA, and OK: Collected the samples. AF, OA, OK, and FZE: Conducted the analysis. AF, MB, SF: Interpreted results. AF: Wrote the manuscript. MB, FK, and SF: Reviewed the manuscript. All authors have read and agreed to the published version of the manuscript."} +{"text": "BackgroundThe global burden of chronic kidney disease (CKD) has been on an alarming increase in the last two decades. The morbidity and mortality associated with CKD are even worse in Nigeria, like other developing countries, due to multiple socioeconomic and demographic factors in the country. CKD contributes to the increasing need for hospital admission. Hypertension and chronic glomerulonephritis have been the leading causes of CKD in Nigeria. However, diabetic nephropathy has recently gained more significance as a cause of CKD in developing countries.Aim and methodsThis study aimed to describe the current trend in the burden and population characteristics of CKD in Southern Nigeria. This is a cross-sectional, hospital-based study. The study recruited adult patients with prehemodialysis CKD seen in renal clinics over a two-year period (November 2014 to October 2016). Data were obtained using a questionnaire and from the clinic register. All participants were clinically assessed, including history, anthropometric measurements, and urinary albumin-creatinine ratio.ResultsA total of 1,549 patients were seen at the Medical Outpatient Clinic over the study period. CKD accounted for 9.7% of medical outpatient clinic attendance. The mean age of participants was 49\u00b113 years. The leading causes of CKD were diabetes mellitus (32%), chronic glomerulonephritis (30%), and hypertension (22%). Among the participants, CKD stages 3, 4, and 5 were prevalent in 26.7%, 43.3%, and 14.7%, respectively.Conclusion and recommendationCKD is very prevalent among medical clinic patients. Diabetic nephropathy seems to be a more significant cause of CKD than was previously reported. Late presentation of patients to nephrologists remains an obstacle to improving CKD outcome in Nigeria. There is need for more intensive preventive measures and early intervention. The global burden of chronic kidney disease (CKD) has been on an alarming increase in the last two decades . The morA South-South Nigerian community study among rural adults reported a prevalence of CKD of 27.2% . Thus, CConsequently, the economic burden of the disease is worse in SSA due to a higher indirect cost in the form of man hour loss at workplace. Several studies have reported a male predominance in the CKD population in Nigeria ,17. HoweThe cost of renal replacement therapy in Nigeria is highly prohibitive, leading to a more than 70% drop-out rate within one month of hemodialysis . The catThe study was conducted at the renal unit of the Department of Medicine, Delta State University Teaching Hospital (DELSUTH), Oghara, South-South Nigeria, from November 2014 to October 2016 (spanning a period of two years). DELSUTH is a state-owned teaching hospital established by the Delta State Government in 2010. The health facility has 230 beds and it serves as the major tertiary health institution in the state and also a referral center for a large catchment area in the Southern part of Nigeria, including Edo, Bayelsa, Ondo, and Anambra states.This is a hospital-based descriptive cross-sectional study. Ethical clearance was obtained from the Ethics Committee of DELSUTH. Consenting CKD patients attending the two renal clinics were recruited consecutively. However, patients in KDIGO CKD stage 1, those with acute-on-chronic kidney disease, and those already on dialysis were excluded to avoid classification bias. Estimated glomerular filtration rate was calculated using the Modification of Diet in Renal Disease (MDRD) equation. A structured interviewer-administered questionnaire (close-ended) was used to obtain information on demographic data and the health status of participants. All participants were subjected to a thorough clinical assessment with emphasis on past medical history, social history, drug history, anthropometric measurements, blood pressure measurement, fundoscopy, urinalysis, fasting blood glucose, serum creatinine, urinary albumin-creatinine ratio (UACR), hepatitis B virus, hepatitis C virus, HIV screening, and renal ultrasonography.2 [CKD was defined and classified according to the 2012 KDIGO guidelines . Diabeti2 .Statistical analysisThe Statistical Package for Social Sciences (SPSS) computing program version 22 was used for data management and analysis. Frequency of parameters is presented in tables, graphs, and pie charts. All continuous variables are presented as mean\u00b1 SD, whereas categorical variables are presented as percentages and proportions. Mean of continuous variables was compared using Student's t-test, whereas categorical variables were compared using the chi-square test.Prevalence of CKD in the medical outpatient clinicDuring the study period, 1,549 patients attended the Medical Outpatient Clinic. Predialysis CKD patients constituted 9.7% of the total number of medical outpatient clinic patients. This is represented in Table Sociodemographic characteristics and health status of participantsThe mean age of participants was 49\u00b113 years. The mean age of males was 47\u00b112 years, which was significantly lower than that of females . Of the patients, 89% were less than 65 years of age, and 46.7% were in the age group of 45-64 years. There were 92 males and 58 females, making a male-to-female ratio of 3:2. Of the participants, 45%, 12%, 20%, and 23% were traders, farmers, civil servants, and others , respectively. Majority (60%) of respondents earned between 10,000 and 100,000 nairas (US$28- US$280) per month. Only 25 (16.7%) earned more than 100,000 nairas (US$280) per month, and 32 (23.3%) were either unemployed or earned less than 10,000 nairas (US$28) per month. This is shown in Table CKD risk factors among participants2 and 46 30.7%) had a history of hypertension and diabetes, respectively. Based on urinary albumin excretion (UAE) rates, only 20 (13.3%) were normoalbuminuric, whereas 41.3% and 45.3% of participants had microalbuminuria and overt albuminuria, respectively. Of the study group, 107 (71%) had no history of smoking, 31 (21%) had a previous history of smoking, and 12 (8%) had a current history of smoking. Also, 32 (21.3%) had a significant history of nephrotoxic agent use, 12 (8%) had a family history of kidney disease, and 28.7% had BMI equal to or greater than 30 kg/m0.7% had Etiology and stages of CKD among participantsDiabetic nephropathy, chronic glomerulonephritis, and hypertensive nephrosclerosis were the leading causes of CKD in this population, accounting for 32%, 30%, and 22.6%, respectively. A total of 13 (8.6%) cases could not be attributed to a particular etiology, and 87 (58%) of the participants presented in either CKD stage 4 or 5. Only 23 (15.3%) cases presented in stage 2, as shown in Table This study showed that CKD accounts for a high proportion of clinic patients seen in our medical outpatient clinic. The 9.7% prevalence of CKD among medical outpatient clinic patients is comparable with an earlier South-West Nigerian study, which reported CKD to account for 8-10% of medical admission . The preThe observation of the mean age of male CKD patients being lower than that of their female counterparts is similar to an earlier report by Ulasi and Ijoma in a South-East Nigerian study . The reaThe predominant occupation of participants was trading. While this could be a coincidence, the sedentary lifestyle associated with trading may contribute to CKD risk factors such as hypertension, diabetes mellitus, and obesity. Most participants in this study earned between 10,000 and 100,000 nairas ($28 and $280) per month. The catastrophic health spending in the developing countries wherein individuals mostly pay for Medicare out of pocket will undoubtedly further impoverish this CKD population with incomes already below the poverty line . It is tThe prevalence of hypertension in this study of 42.7% falls within the overall prevalence in Nigeria of 8.0% to 46.4% . The disThe leading causes of CKD in this study were diabetes nephropathy, chronic glomerulonephritis, and hypertensive nephrosclerosis, accounting for 32%, 30%, and 22.6%, respectively. Of those with diabetic nephropathy, 11% had no prior history of diabetes before presentation. This observation is both surprising and concerning as most earlier reports in Nigeria have observed much less significance of diabetes as an etiology of CKD ,12. HoweThis study, despite its strength of using the highly sensitive UACR in detecting UAE, had limitations, which included a one-time UACR, which did not differentiate between reversible and persistent proteinuria as well as being a single-center study, which will not allow generalization of findings. However, the findings in this study will stimulate future prospective studies on the subject.CKD is a major cause of medical outpatient consultation. Diabetic nephropathy seems a more significant etiology of CKD than was previously reported. Late presentation of CKD patients to nephrologists continues to be a norm in the developing countries. This calls for a concerted effort to raise awareness and implement programs for early screening and diagnosis of diabetes and CKD, especially in the high-risk populations."} +{"text": "Objectives: The present study was carried out to investigate COVID-19 vaccination coverage among populations of internally displaced persons (IDPs), refugees, and host communities in northern Iraq and the related underlying factors.Methods: Through a cross-sectional study conducted in five governorates in April\u2013May 2022, 4,564 individuals were surveyed. Data were collected through an adapted questionnaire designed to gather data on participants.Results: 4,564 subjects were included . 50.48% of the participants had been vaccinated with at least one dose of COVID-19 vaccine. 40.84% of participants had been vaccinated by two doses, and 1.56% were vaccinated with three doses.Conclusion: Sociodemographic factors including age, gender, education, occupation, and nationality could affect vaccination coverage. Moreover, higher acceptance rate of vaccination is associated with belief in vaccine safety and effectiveness and trust in the ability of the vaccine to prevent complications. As a worldwide pandemic, coronavirus disease 2019 (COVID-19) is referred to as a public health emergency of international concern .So far, over 2,460,844 cases and 25,356 deaths due to COVID-19 have been reported in Iraq till 20 October 2022 [As of 11 October 2022, Iraqis have received 19.3 million doses of COVID-19 vaccine, and 18.8% of the population (7.57 million people) are fully vaccinated , while sIt is important to understand socio-demographic factors that affect vaccine decision-making . MoreoveWe conducted a cross-sectional study over 4\u00a0weeks in April\u2013May 2022 in five districts of Sulaimaniyah, Erbil, Dahuk, Kirkuk, and Ninawa.The study sample comprised different sub-populations in each governorate. To select the sample, every household in the selected communities was identified on a sketch map and the household list of each area under study. From these lists a small number of households were randomly selected to participate using a household form 550 households were chosen following the recommendations by WHO and finaThe target population in the present study included Iraqi population who were able to read or understand Arabic and/or Kurdish . All people aged 12\u00a0years and older and living in the five governorates were considered eligible. COVID-19 vaccination coverage was estimated overall, and in each governorate, stratified by subpopulation. This estimation involved conducting essentially five separate surveys, and then combining the results in a weighted fashion to estimate regional vaccination coverage. Data were collected using Kobo Toolbox. Required data were gathered using a 16-item questionnaire originally developed in Malaysia . The quep-value less than 0.1 in univariate analyses were entered into a multivariate ordinal logistic regression to identify independent factors affecting vaccine coverage. Additional analyses were performed to assess the influential factors of COVID-19 vaccination in each sub-population . A p-value of below 0.05 and a confidence interval of 95% were considered statistically significant.The collected data were analyzed using STATA 17.0. For this purpose, descriptive analysis was employed for sociodemographic and categorical data, and analytical statistics were used for the variables associated with COVID-19 vaccine coverage. We assessed the influential factors of COVID-19 vaccination using univariate ordinal logistic regression. Then, all the factors that had a The research was approved by the General Directorate of Health\u2019s ethical committee under reference number HR022,27, and informed consents were obtained from the participants. All participants provided informed consent and no identifying data was used in the data analysis.Data of 4,564 subjects were included in this study consisting of 3,519 subjects from host communities, 428 IDPs and 617 refugees. Of all the participants, 59.55% were 19\u201345\u00a0years old and 54.51% were male; 28.59% lived in Ninawa, 27.39% in Erbil, and 24.45% in Sulaymaniyah. Most of participants (77.1%) lived as permanent residents. Kurds (59.79%) were the largest ethnical group, followed by Arabs (33.57%) and Turkman (5.26%). Most (95.46%) were Muslims, and 69.89% were married. Occupation varied widely; 14.77% were students. The results revealed that 50.48% of all the participants had been vaccinated by at least one dose of COVID-19 vaccine, while 49.5% had not vaccinated . 40.84% Univariate ordinal logistic regression showed that COVID-19 vaccination coverage was significantly associated with age, gender, place of residence, nationality, religion, marital status, education, occupation and health status . The posMultivariate ordinal logistic regression showed that receiving at least one dose of COVID-19 vaccination is higher in age groups of 19\u201345\u00a0years , 46\u201365\u00a0years and 65\u201398\u00a0years than age less than 19\u00a0years of age. Women are less willing to prescribe the COVID-19 vaccine and the Arab nationality have less tendency in receiving the COVID-19 vaccine . The analysis shows that less Sulaimani and Ninawa residents than other governates have gotten COVID-19 vaccines. It seems that there is an increasing trend in receiving the COVID-19 vaccine with increasing the level of education .The results also indicated that there was an independent association between COVID-19 vaccination coverage and the possible attitudinal barriers of COVID-19 vaccination coverage. Fear of being unsafe , not being effective , COVID-19 is not dangerous , fear of infection following vaccination , inappropriate attitude against the principle of vaccination in general , religious reasons , believing on traditional and local medicine and other reasons were the important personal barriers against COVID-19 vaccination .Our results revealed that 51.49% of the participants of host communities had received at least one dose of COVID-19 vaccination. 42.28% of host communities subjects were vaccinated by two doses and 1.65% had received three doses of vaccination. Multivariate ordinal logistic regression showed that in host communities subjects, vaccination is higher in age groups of 19\u201345\u00a0years , 46\u201365\u00a0years and 65\u201398\u00a0years than age less than 19\u00a0years of age. Christians and educated subjects had more tendency in receiving COVID-19 vaccination. Beliefs of vaccination being unsafe , not effective , corona disease not being dangerous , fear of infection , being against the principle of vaccination in general and religious reasons were the personal attitude barriers against COVID-19 vaccination in host communities. Our results show that 48.83% of the IDPs had received at least one dose of vaccination, with 35.75% receiving two doses and 0.93% receiving three doses of COVID-19 vaccination. In multivariate analysis, IDPs were shown to have higher tendency for vaccination in age groups of 19\u201345\u00a0years , 46\u201365\u00a0years and 65\u201398\u00a0years than age less than 19\u00a0years of age and educated subjects were also shown to have higher tendency for vaccination. However, females and Arab and Turkman nationality subjects had lower tendency for vaccination. Believing that vaccination is unsafe , not effective and being against principle of vaccination were the personal attitude barriers against COVID-19 vaccination in IDPs. Our results demonstrate that 45.87% of the refugee subjects received at least one dose of COVID-19 vaccination. 36.14% of refugee subjects received two doses and 1.46% received three doses of vaccination. Multivariate ordinal logistic regression revealed that not married (single) subjects had lower tendency for vaccination . As for the personal attitudinal barriers against COVID-19 vaccination in refugee subjects, belief in vaccination being unsafe , not being effective , fear of infection and being against the principle of vaccination were the most important factors against vaccination. Infectious diseases can be successfully controlled through vaccination; therefore, vaccination can be labeled as one of the most remarkable achievements of science. However, vaccination success can be negatively affected by people\u2019s hesitation to get vaccinated. Therefore, there has always been the challenge of encouraging people\u2019s desire to be vaccinated . Iraq haThe results of the current study revealed that nearly half of the participants had not been vaccinated at all. In a study conducted on Iraqi population, Alatrany et al. reported that 68% of the study population had received atleast one vaccine dose; which is close to the results of our study , while iIn their review Troiano and Nardi report that vaccination rate varies between the studies with a maximum of 77.6% of general population declaring that they will accept the COVID-19 vaccine . Over 40The results of the current study showed that the participants\u2019 place of residence, age group, gender, nationality, level of education, and occupation had a significant effect on COVID-19 vaccination coverage. Similarly, other studies indicated that willingness to receive COVID-19 vaccine varies in different communities and countries and is significantly influenced by factors like urban residence, being a physician or health professional, having children, previous interaction with someone infected by COVID-19, access to the media, and good practice of COVID-19 preventive measures , 23. As Regarding the reasons for avoiding vaccination in the present study, nearly 17% of the participants believed that the COVID-19 vaccine was not safe, 11.94% feared infection, and 10.79% feared its possible side effects. About 9.77% of them were generally against the principle of vaccination, and 6.46% said that vaccination could not be an effective option against COVID-19. In a study on the Iraqi population, Alatrany et al. reportedStudies have reported varying degrees of COVID-19 vaccine hesitancy among refugees/migrants and asylum seekers, ranging between 10 and 40 percent . Our resSeveral interventions have been conducted in studies to increase the public\u2019s willingness to receive the vaccine. A systematic review of 39 studies shows that communicating about vaccine concerns on social media does not reduce willingness to get vaccinated, but making vaccination mandatory has negative impact on vaccine uptake . GovernmOur study is limited by no reports on the rate of refusal to participate in the study, which might lead to selection bias, not assessing the effect of the available vaccine type on participants vaccine hesitancy, and not investigating the accessibility of vaccination facilities, which might hinder vaccination in rural, deprived, or underprivileged districts. Future studies could address these issues in order to better investigate the contributing factors to vaccine hesitancy.Vaccination is one of the main acceptable options for preventing and controlling COVID-19; however, people\u2019s refusal to accept the vaccine remains as a global challenge. It seems that due to such refusal, a very small portion of the participants in the present study received their third dose. Sociodemographic factors including age, gender, level of education, occupation, and nationality could significantly affect vaccination coverage. Moreover, higher acceptance rate of vaccination is associated with belief in vaccine safety and effectiveness and trust in the ability of the vaccine to prevent the complication. Hesitancy, uncertainty, and rumors regarding the vaccine should be minimized through the social media and appropriate health programs, resulting in controlling the pandemic through increasing the acceptance of COVID-19 vaccination."} +{"text": "To investigate whether artificial intelligence (AI) can differentiate septic from non-septic total hip arthroplasty (THA) failure based on preoperative MRI features.We included 173 patients subjected to first-time THA revision surgery after preoperative pelvis MRI. We divided the patients into a training/validation/internal testing cohort (n\u2009=\u2009117) and a temporally independent external-testing cohort (n\u2009=\u200956). MRI features were used to train, validate and test a machine learning algorithm based on support vector machine (SVM) to predict THA infection on the training-internal validation cohort with a nested fivefold validation approach. Machine learning performance was evaluated on independent data from the external-testing cohort.P\u2009<\u20090.001), except bone destruction, periarticular soft-tissue mass, and fibrous membrane (P\u2009>\u20090.005). Considering all MRI features in the training/validation/internal-testing cohort, SVM classifier reached 92% sensitivity, 62% specificity, 79% PPV, 83% NPV, 82% accuracy, and 81% AUC in predicting THA infection, with bone edema, extracapsular edema, and synovitis having been the best predictors. After being tested on the external-testing cohort, the classifier showed 92% sensitivity, 79% specificity, 89% PPV, 83% NPV, 88% accuracy, and 89% AUC in predicting THA infection. SVM classifier showed 81% sensitivity, 76% specificity, 66% PPV, 88% NPV, 80% accuracy, and 74% AUC in predicting THA infection in the training/validation/internal-testing cohort based on the only presence of periprosthetic bone marrow edema on MRI, while it showed 68% sensitivity, 89% specificity, 93% PPV, 60% NPV, 75% accuracy, and 79% AUC in the external-testing cohort.MRI features were significantly more frequently observed in THA infection (AI using SVM classifier showed promising results in predicting THA infection based on MRI features. This model might support radiologists in identifying THA infection. Hip osteoarthritis is a frequent cause of hip pain and total hip arthroplasty (THA), which, to date, is one of the most common surgical procedures in orthopedic surgery, with the number of implants growing over time due to population aging. THA failure may occur due to prosthetic joint infection and non-septic reasons, such as aseptic loosening, dislocation, adverse reaction to metal debris (ARMD), bone fracture, or implant rupture . SeveralInstitutional Review Board of Ospedale San Raffaele, Milano, Italy, approved this retrospective study and waived the need for informed consent (Protocol RETRORAD). After matching imaging, laboratory, and surgical data, our database was completely anonymized to delete any connections between data and patients\u2019 identity according to the General Data Protection Regulation for Research Hospitals.This study was concerned with the assessment of MRI examinations performed by a consecutive series of patients managed at IRCCS Istituto Ortopedico Galeazzi, Milan, Italy, from January 2015 to January 2022. These patients were affected by painful THA requiring revision surgery and were all subjected to preoperative pelvis MRI. We gathered all imaging, surgical, and clinical data of these patients cross-referencing the database of our Radiology Department with that of our Hip Department and Laboratory of Clinical Chemistry and Microbiology. The following inclusion criteria were considered: (i) patients subjected to first-time revision procedures for monolateral failed THA; (ii) availability of intraoperative microbiological tests; and (iii) preoperative unenhanced pelvis MRI performed up to 1\u00a0month before revision surgery with the same imaging protocol. The exclusion criteria were: (i) nondiagnostic MRI due to prosthesis-related artifacts; (ii) inflammatory arthritis, tumors, bowel inflammatory disease, or autoimmune disease. Overall, a total of 173 patients were included in this study . They were divided into training/validation/internal-testing and external-testing cohorts as detailed below in the machine learning section.Intraoperative samples from periprosthetic material collected during revision surgery were sent to our laboratory for culture analysis. Agar plates and enrichment broths were incubated for 48\u00a0h and 15\u00a0days, respectively, and daily checked for microbial growth. In case of broth turbidity, an aliquot was plated onto blood agar. Colonies grown from agar plates were identified by biochemical testing performed on a Vitek 2 analyzer . The final diagnosis of THA infection was obtained according to the International Consensus Meeting Criteria , which iAll MRI scans were done at in the same1.5\u00a0T unit at our institution. A combination of the table-integrated coil and abdominal coil was used. Our metal artifact reduction sequence (MARS) protocol included coronal T1-weighted, coronal STIR, axial T1-weighted, axial T2-weighted, and sagittal T2-weighted images : coronalThe machine learning analysis was performed using the TRACE4\u00a9 platform .Our popuP\u2009<\u20090.003. SPSS software was used for statistical analysis. AUC, accuracy, sensitivity, specificity, PPV, and NPV of the machine learning classifier were calculated in the training-internal validation and test cohorts, respectively.Chi-square statistics were used to compare each MRI feature between patients with infected and non-infected THA. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy, area under the curve (AUC), and odds ratios (OR) were calculated for each MRI feature. We also assessed the diagnostic performance of a combination of conventional MRI features with the highest OR. Continuous variables were reported as mean\u2009\u00b1\u2009standard deviation. Discrete variables were summarized as median and interquartile range. Bonferroni correction for multiple comparisons was applied and statistical significance was set at P\u2009<\u20090.001), except bone destruction (P\u2009=\u20090.155), periarticular soft-tissue mass (P\u2009=\u20090.005), and fibrous membrane (P\u2009=\u20090.081). The values of sensitivity for detecting THA infection ranged from 5.4% (periarticular soft-tissue mass) to 80.7% (bone edema), specificity from 51.7% (bone destruction) to 97.4% (lamellated synovitis), PPV from 10.3% (periarticular soft-tissue mass) to 87.9% (synovitis), NPV from 62.5% (periarticular soft-tissue mass) to 89% (bone edema), accuracy from 46.8% (bone destruction) to 81.5% (synovitis), and OR from 0.198 (periarticular soft tissue mass) to 29 (synovitis). Data on diagnostic performance of all MRI features are reported in Table Conventional MRI features were significantly more frequently observed in patients with THA infection compared to patients without infection (all with When all MRI features were considered in the training/validation/internal-testing cohort, SVM classifier reached 92% sensitivity, 62% specificity, 79% PPV, 83% NPV, 82% accuracy, and 81% AUC in predicting THA infection, with bone edema, extracapsular edema, and synovitis resulting the best predictors ranked by descending importance. After being tested on the external-testing cohort, the classifier showed 92% sensitivity, 79% specificity, 89% PPV, 83% NPV, 88% accuracy, and 89% AUC in predicting THA infection.SVM classifier showed 81% sensitivity, 76% specificity, 66% PPV, 88% NPV, 80% accuracy, and 74% AUC in predicting THA infection in the training/validation/internal-testing cohort based on the only presence of periprosthetic bone marrow edema on MRI, while it showed 68% sensitivity, 89% specificity, 93% PPV, 60% NPV, 75% accuracy, and 79% AUC in the external-testing cohort.The main finding of our study is the validation of a diagnostic machine learning classifier to support physicians in the interpretation of imaging findings when dealing with preoperative MRI of patients with failed THA.Few papers have investigated the diagnostic performance of preoperative MRI in predicting infection in patients with THA infection of the hip \u201310, 19 aSome limitations of our study must be pointed out. First, the relatively limited number of patients included in our series. It is well known that a huge amount of data is essential to build robust machine learning classifiers \u201326; thusIn conclusion, AI using SVM classifier showed promising results in predicting THA infection based on MRI features assessed preoperatively. This model might represent an adjunctive tool to support radiologists in identifying THA infection and could form the basis for further trials in this little explored field. Future studies are warranted to build AI-based models that combine imaging, clinical, and laboratory data to improve the accuracy of preoperative evaluation of patients undergoing revision surgery for failed arthroplasty."} +{"text": "Optimizing dietary intake during pregnancy and lactation is crucial to the growth and development of children and their lifelong health. We performed a systematic review and meta-analysis to describe the nutrient intakes of pregnant and lactating women in Indonesia and Malaysia, countries that are experiencing rapid nutrition transition in Southeast Asia.We screened 2,258 studies published between January 1980 and March 2021. The nutrient intakes of pregnant and lactating women were quantitatively analyzed to calculate the percentage of adequacy using national recommended daily allowances or nutrient intakes (RDA/RNI) and estimated average requirements (EAR) for micronutrients. Standardized mean differences (SMD) between dietary intake and RDA/RNI were determined for selected nutrients.Fifty-three studies were included and showed that energy and macronutrient intakes among pregnant and lactating women in both countries were below the RDA/RNI. In addition, most studies reported that women failed to meet the EAR for vitamin D (<70% EAR), vitamin E (<50% EAR), and water-soluble vitamins (<80% EAR) except for vitamin C and A among Malaysians. Moreover, calcium, potassium, and iron intakes of pregnant women were <60% EAR in Indonesia and <80% EAR in Malaysia. Phosphorus intake among pregnant women in both countries and sodium intake among Malaysian pregnant women exceeded 100% EAR. Indonesian lactating women had <60% EAR for calcium and potassium intakes, while Malaysian women had more than 100% EAR. For 21 studies reporting overall protein intakes, the standard mean difference (SMD) was \u22122.26 below the RDA/RNI for pregnant women and \u22120.67 SMD for lactating women. When the four studies from Malaysia were analyzed separately, protein intakes of pregnant women were above the RNI. Moreover, low intakes of vitamin D, vitamin C, calcium, and iron, but sufficient intakes in vitamin A, zinc, and phosphorus were observed in pregnant women in both countries.Dietary intakes of energy, macronutrients, and micronutrients of pregnant and lactating women in Indonesia and Malaysia were below the recommendations. Important heterogeneities were observed even between these two countries for specific essential nutrient intakes. Innovative research and targeted programs to address specific deficiencies should be prioritized.https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021252204, identifier: CRD42021252204. The first 1,000 days of life, spanning from conception to the age of two, is pivotal to the offspring's neurodevelopment and lifelong health. Adequate nutrient intake during pregnancy and lactation has been associated with maternal and child health outcomes and will ensure healthy growth and development of the children .Chronic energy deficiency (CED) commonly occurs among pregnant women and women of reproductive age in developing countries due to multiple factors, such as low socioeconomic status, living in rural areas, family size, inadequate meal frequency, and low dietary quality , 4. CED Meanwhile, micronutrient supplement consumption was not a popular practice among pregnant women in Indonesia and Malaysia, particularly for certain nutrients such as vitamin D , 12. MorAsia is a continent of diverse cultures, represented by various traditional foods and culinary practices. Various traditional dishes are healthy and promote fruits and vegetable consumptions. People residing in developing countries of Southeast Asia region inevitably experienced diet transition that shifted food consumption to more practical and modernized yet heavily processed foods, neglecting traditional foods that are healthy and rich in bio-active compounds . MoreoveA balanced diet with appropriate nutrient intake is recommended during pregnancy and lactation. However, previous studies highlighted that poor diet quality was predominant among healthy and pregThe literature on nutrient intake in Indonesia and Malaysia was systematically searched through four electronic databases: PubMed, Scopus, ProQuest, and Cochrane. A manual search was conducted when certain nutrient intakes were not found in the directories. The search strategy was designed to find published studies in English or Indonesian language. The search terms used are shown in the Nutrient intake and supplement consumption were determined as the outcomes during the selection of studies. Inclusion criteria of the study were published papers between the period of January 1980 and March 2021 that involved healthy and unhealthy pregnant and lactating women (mothers who breastfed children up to 2 years of age), assessed the quantity of dietary intake using nutritional assessment methods that can quantify actual and habitual nutrient intake . The exclusion criteria were applied to studies that had no abstract, were not in English or Indonesian language, had irrelevant topic, and were not human studies. Moreover, intervention studies were included if the baseline data were provided.The titles and abstracts were screened by two reviewers (FS and RM). Any disagreements over the included studies were resolved through discussions. The full text was assessed based on the exclusion criteria after the duplicate studies were removed. The flow diagram of studies using PRISMA guidelines is provided in Extracted information of the eligible studies was summarized in Studies of selected nutrients that provided mean and standard deviation without data transformation (e.g. logarithm transformation) were included in the meta-analysis. Standardized mean differences were calculated with the following criteria; (1) larger sample size was chosen if the study divided the subject into several groups; (2) data conversion to mean and standard deviation was made if the study only provided median, quartile, and interquartile range, according to a study by Wan et al. . Meta-anThe risk of bias assessment was modified from Shahar et al. that wasIn total, 2,258 articles were screened. After removing 655 duplicates, 1,603 articles were selected for the title and abstract review. Finally, 57 articles were assessed for full-text review. Four papers were excluded because the full texts were not found. Of 53 articles selected and presented in tables, 36 articles identified pregnant women and 17 mentioned lactating women as the subjects. Among these, 20 studies were carried out in Malaysia and 33 in Indonesia . Most stStudies in Indonesia and Malaysia reported various energy intake profiles among pregnant and lactating women. Assessments of energy intake among pregnant women in Malaysia were mainly conducted in the second and the third trimesters. Daily energy intakes in the second and the third trimesters ranged from 1,376 to 2,310 kcal (64.9\u2013109% RNI), and from 2,021 to 2,042 kcal (87.5\u201387.9% RNI), respectively. In contrast, energy intake among pregnant women in Indonesia barely achieved 80% RDA. The first trimester of pregnancy had the lowest daily energy intake compared to other trimesters, ranging from 1,166 to 1,608 kcal (45.7\u201366.2% RDA). The energy intake range of the second trimester of Indonesian pregnant women was 1,269 to 2,096 kcal (49.8\u201382.2% RDA). Only one out of seven studies found the energy intake of the second trimester to be >80% RDA . LikewisOf three studies among Malaysian lactating women, Khor et al. indicateAll four studies conducted among the second and third trimesters of Malaysian pregnant women \u20137 showedIn Malaysia, protein intake among lactating women exceeded 80% of RNI . Only one study in 1985 found a low protein intake in this population . MoreoveCarbohydrate intake in Malaysian pregnant women did not meet the recommendation with a range of 245.6 to 306.4 g (63.8\u201381.9% RNI) , 49. FivOverall, the carbohydrate intake of lactating women in Indonesia and Malaysia failed to meet 100% of the recommendation. Malaysia's studies reported a wide range of carbohydrate intake among lactating women , 45, 46.Fat intake among pregnant women in Indonesia and Malaysia barely achieved 100% of the recommendation. In Malaysia, the fat intake among pregnant women failed to meet at least 80% RNI with a range of 69\u201372.4% RNI, while in Indonesia, the range of fat intake was wider, from 26.7 to 162.8% of RDA with two , 64 out Studies in Malaysia indicated that a fat intake among lactating women ranged from 32.7 to 77.1 g (41.4\u201397.6% RNI). Saturated fat intake data was only found among Malaysian lactating women showing the intakes were consistently below the recommendation . However, the fat intake among lactating women in Indonesia was higher than in Malaysia with a range of 57.8\u201373 g (86\u2013108.6% RDA) and most intakes exceeded 80% RDA and reached 100% RDA , 64. A sVitamin A intake among pregnant and lactating women was the most studied fat-soluble vitamin. Ten studies assessing vitamin A intake among Indonesian pregnant women were mainly conducted in rural areas of Java Island with an overall range of 0.3\u2013176.2% RDA (0.4\u2013246.7% EAR). The lowest intake of vitamin A was 2 \u03bcg/day and the highest was 505.5\u20131,585.7 \u03bcg/day , 66. SomFour Indonesian studies , 57, 70 Four studies reported vitamin E intake among Indonesian pregnant women to be between 0\u201342.7% RDA (0\u201351.2% EAR). These studies were conducted among the second trimester of anemic pregnant women , 59, durVitamin C was the most common nutrient intake assessed among pregnant and lactating women in Indonesia and Malaysia, while studies on niacin, pyridoxine, folate, and cobalamin intakes were lacking. Data on water-soluble vitamin intake including thiamine, riboflavin, niacin, pyridoxine, folate, cobalamin, and vitamin C were scarce among lactating women in Malaysia.Thiamine intake among Indonesian pregnant women as reported in five studies was predominantly < 60% RDA , 74, 75 The range of riboflavin intake among second- and third-trimester Indonesian pregnant women in West Java was 38.5\u2013123.1% RDA 46.2\u2013147.7% EAR). Only one study by Suprapto et al. found th7.7% EAR.Studies on niacin, pyridoxine, folate, and cobalamin intakes were fewer than studies of other vitamins. A case-control study among Indonesian pre-eclampsia and normotensive pregnant women reported that niacin intake achieved only 23.9\u201332.2% RDA (28.7\u201338.7% EAR) . Niacin The range of vitamin C intake among Indonesian pregnant women stretched from 1.9 to 309.9% RDA 2.3\u2013371.9% EAR). Four studies in hospitals or health facilities reported the mean vitamin C intake among Malaysian pregnant women. One study in second-trimester pregnant women demonstrated an intake of 156.3% RNI (187.5% EAR) 1.9% EAR., 69 showAmong studies reporting the macro-mineral intake, calcium was the most studied in both Indonesian and Malaysian pregnant women , which were commonly performed in the second and the third trimesters of pregnancy , 72\u201374. Two studies assessed the magnesium intake among Indonesian pregnant women in all trimesters, while no study was found in Malaysia. Magnesium intake among Indonesian pregnant women were below RDA (63.6\u201383.1% RDA), and not meeting the EAR (72.4\u201397.4% EAR) , 74. A sPhosphorus intake among Indonesian pregnant women ranged from 92 to 165% RDA and exceeded the EAR (123\u2013199% EAR) . LikewisPotassium intakes among pregnant women were below the EAR for Indonesian (15.6\u201342%) and Malaysian (33\u201353.1%) . The IndIron intake is the most commonly studied trace element intake in both Indonesia and Malaysia [five studies in Malaysian , 49, 69 Iodine intake among pregnant women in Indonesia was insufficient, with the highest intake being 32.5% RDA (44% EAR) . In contStudies about zinc intake among pregnant women were only found in Indonesia, which were conducted in all trimesters throughout pregnancy. Four of seven studies showed inadequate zinc intake among pregnant women in Indonesia ranging from 21.3 to 72.4% RDA (25.5\u201386.9% EAR) , 70, 74,Data for chromium, manganese, molybdenum, selenium, boron, and chloride intakes for pregnant women were unavailable in both countries. However, we found a study that assessed intakes of chromium, manganese, molybdenum, and selenium for Malaysian lactating women, reporting 71.1%, 73.1%, 97.2%, and 91.7% of RNI for these nutrients, respectively . A studySeven studies from both countries among lactating women were analyzed . OverallAs shown in Nine studies assessing vitamin D intake (mcg/day) among pregnant women in Indonesia and Malaysia were included in the meta-analysis . The vitA meta-analysis of 13 studies showed iOn the contrary, six studies among Indonesian and Malaysian lactating women indicated a tendency for higher iron intake than 100% EAR with an n = 5 studies) that exceeded the optimal EAR levels with average excess of 2.55 mg/day .A low to high risk of bias was found in this study. The total score of the bias assessment are shown in The present review discovered that the energy and macro-nutrient intakes among Indonesian and Malaysian pregnant and lactating women (53 studies) were below RDA/RNI. Water- and fat-soluble vitamin intakes failed to meet the recommendation and were mainly lower than 80% EAR, except for vitamin C and A in Malaysian pregnant women. Macro-minerals and trace element intakes tended to be insufficient. Moreover, zinc intake was adequate among pregnant women in Indonesia, but no zinc intake study was found in Malaysia. Dietary intakes of these nutrients exceeded 100% EAR . To the best of our knowledge, this study is the first systematic review and meta-analysis of nutrient intake among pregnant and lactating women in Indonesia and Malaysia. A thorough review with a double-screening approach was performed to assure the quality of the data in the systematic review.The energy intake of Indonesian and Malaysian pregnant women exhibited a similar pattern of not meeting the national recommendation. A comparable finding was also observed in a study conducted among pregnant women in Thailand . On the Despite the need to increase energy requirements among lactating women to produce sufficient breast milk , our preOur review and meta-analysis also found that the protein intakes among Malaysian pregnant and lactating women were adequate. Yong et al. reported that Malaysian lactating women had perceived belief that protein rich foods such as meat, cheese, and milk products benefit the infant growth and development . The exiThis present review discovered that studies of omega-3 and omega-6 fatty acids intakes among pregnant and lactating women in both countries were limited. One study in Indonesian pregnant women indicated inadequate intake of these nutrients. This result was not aligned with a study conducted in China showing the omega-3 fatty acid intake among pregnant women was higher than the recommendation . Many stMost studies reported low carbohydrate intakes among pregnant and lactating women in Indonesia and Malaysia (only met 60\u201380% of RDA/RNI). Lower carbohydrate intake among obese pregnant women had been associated with lower fat mass in the offspring . In the We discovered the vitamin intakes among pregnant and lactating women were different between Indonesia and Malaysia. Most studies suggested adequate intakes of vitamin A based on the EAR, except for Indonesian lactating women. Study in Indonesia suggested that although vitamin A intake of the women was adequate (predominantly from vegetables consumption), the serum retinol in this population was low . RahmannAlmost all vitamin B intakes were inadequate and could not meet the expected EAR among pregnant and lactating women, particularly in Indonesia. While in Malaysia, our findings suggested that vitamin B intake exceeded the recommendation. Some studies recorded inadequate vitamin B intakes among adults and pre-The mean vitamin C intake among Malaysian pregnant women exceeded the RNI and was greater than the intake of Indonesian pregnant women who had lower intake of this nutrient than the expected vitamin C EAR. A review done by Caut et al. reported that pregnant women in Malaysia frequently adhered to the recommendations for fruits consumption as a source of vitamin C . HoweverVitamin D intake was inadequate among Malaysian and Indonesian pregnant and lactating women. Woon stated tDietary supplements consumption was not a common practice among pregnant and lactating women in Indonesia and Malaysia , 19, 20,The data from Indonesia Health Survey showed an increased prevalence of anemia among pregnant women from 37.1% in 2013 to 48.9% in 2018 , 114. MeOur meta-analysis from five studies available only in Indonesia, not in Malaysia, showed that the zinc intake among pregnant women was above the recommendation, in contrast with their iron intake profile. This finding is not in line with the previous study by Lim et al., in which inadequacy of iron intake was often associated with low zinc intake as both nutrients were rich in similar animal protein food sources .Our present study found inadequate calcium intake among pregnant women, which was below the recommended intake based on the National Dietary Guidelines of Indonesia and Malaysia. Similarly, a study on the global trend of micronutrient intake by Beal et al. showed tAssessments of iodine intake were only available in one study among Indonesian pregnant women and one study among Malaysian lactating women, which demonstrated inadequate intake of this nutrient. Iodine intake in Indonesian study was estimated based on the result from the National Health Survey and National Total Diet Study covering urban and rural women , whereasFew limitations were addressed in this study. As mentioned above, the macro and micronutrient dietary intake data were limited among pregnant and lactating women in Indonesia and Malaysia. Therefore, this review summarized all eligible studies including those with moderate to high risk of bias. Since the recommended intake of pregnant women was different in each trimester, it was challenging to draw the average percentage of excessive or deficit intake in terms of RNI/RDA/EAR in meta-analysis. Thus, we only provided the percentage of certain nutrients which had a similar recommendation. The various nutritional assessment methods applied in the available studies may cause discrepancy in estimating and providing significant range of the dietary intake.Our result also demonstrated that studies on pregnant women in the first trimester and lactating women were lacking. Thus, future research should consider focusing on these populations, along with more exploration to nutrient of interest with limited data, such as vitamin E, vitamin K, vitamin B, macro-minerals, and trace elements.In summary, the overall findings of this comprehensive review of dietary intake indicated that Indonesian and Malaysian pregnant and lactating women had insufficient intake of essential nutrients. Dietary intakes of energy, macronutrients, and micronutrients of pregnant and lactating women in Indonesia and Malaysia were below the recommendations. Important heterogeneities were observed even between these two countries for specific essential nutrient intakes. Innovative research and targeted programs to address specific deficiencies should be prioritized. Promotive and preventive national programs to improve maternal nutrient intake can be implemented such as promoting maternal diet rich in nutrients even before conception, reevaluating the required supplementation during pregnancy and lactation for specific nutrient deficiencies, enhancing compliance of the current dietary supplementation and initiating the implementation of multi-micro-nutrient supplementation for pregnant women. Fortified and functional food formulations targeted these populations could be explored as the alternative mode in ensuring the nutrient content of specific food products. The utilization of digital technology to educate proper nutrition and promote healthy diet practice for pregnant and lactating women should be enhanced and financed.The original contributions presented in the study are included in the article/Conceptualization: RA, DR, VS, and WL. Methodology and validation: RA, DR, and WL. Software, visualization, and project administration: DR. Formal analysis: WL, FB, and RM. Writing\u2014original draft preparation: RA, WL, FB, and RM. Writing\u2014review and editing, supervision, and funding acquisition: RA. All authors have read and agreed to the published version of the manuscript."} +{"text": "We examined national estimates of breast, cervical, and colorectal cancer (CRC) screening test use and compared them with Healthy People 2030 national targets. Test use in 2021 was compared with prepandemic estimates.In 2022, we used 2021 National Health Interview Survey (NHIS) data to estimate proportions of adults up to date with US Preventive Services Task Force recommendations for breast (women aged 50\u201374 y), cervical (women aged 21\u201365 y), and CRC screening (adults aged 50\u201375 y) across sociodemographic and health care access variables. We compared age-standardized estimates from the 2021 and 2019 NHIS.P < .001).Percentages of adults up to date in 2021 were 75.7% , 75.2% , and 72.2% for breast, cervical, and CRC screening, respectively. Estimates were below 50% among those without a wellness check in 3 years , among those without a usual source of care or insurance (aged <65 y) (breast and CRC screening), and among those residing in the US for less than 10 years (CRC screening). Percentages of adults who were up to date with breast and cervical cancer screening and colonoscopy were similar in 2019 and 2021. Fecal occult blood/fecal immunochemical test (FOBT/FIT) use was modestly higher in 2021 (In 2021, approximately 1 in 4 adults of screening age were not up to date with breast, cervical, and CRC screening recommendations, and Healthy People 2030 national targets were not met. Disparities existed across several characteristics, particularly those related to health care access. Breast, cervical, and colonoscopy test use within recommended screening intervals approximated prepandemic levels. FOBT/FIT estimates were modestly higher in 2021. Breast, cervical, and colorectal cancer screening has been below the national 2020 Healthy People targets.We used 2021 National Health Interview Survey data to examine the most recent national estimates of screening test use, disparities, and comparisons with 2030 Healthy People targets. Estimates were compared with 2019 estimates to examine differences during the COVID-19 pandemic.Approximately 1 in 4 adults of screening age were not up to date with breast, cervical, and colorectal cancer screening in 2021. Estimates were below current national targets and disparities existed. Test use within recommended intervals may approximate prepandemic levels; fecal occult blood test and fecal immunochemical test use may have increased modestly.The US Preventive Services Task Force (USPSTF) recommends breast, cervical, and colorectal cancer (CRC) screening to reduce cancer mortality rates . Use of We used data from the 2021 and 2019 NHIS, an in-person survey of nationally representative samples of the civilian, noninstitutionalized US population . One samWe included women aged 50 to 74 years n = 6,851), women aged 21 to 65 years , and adults aged 50 to 75 years in breast, cervical, and CRC screening analyses, respectively. Exclusions (in order) included prior or unknown hysterectomy , personal or unknown history of the cancer screened for , and insufficient information to determine screening status . USPSTF updated CRC screening recommendations to include adults aged 45 to 49 years (B recommendation) in May 2021 , NHIS has included a set of cancer control questions sponsored by the Centers for Disease Control and Prevention and the National Cancer Institute. The content of these questions varies from year to year on a rotating basis. In 2019 and 2021, this content included additional questions about breast, cervical, and CRC screening tests to complement rotating core questions in those years about whether respondents ever received these tests and the time since the most recent test. These screening tests included mammography (breast cancer); Papanicolaou (Pap) and human papillomavirus (HPV) tests ; and colonoscopy, sigmoidoscopy, computed tomography (CT) colonography, home fecal occult blood test (FOBT) or fecal immunochemical (FIT) test, and FIT-DNA test (CRC). For blood stool tests, separate questions were not asked about FIT and guaiac tests. Rather, they were asked about in combination . In 2019, questions about nonendoscopic CRC screening tests were asked of respondents who answered yes when asked if they had received a CRC test other than colonoscopy or sigmoidoscopy. In 2021, questions about nonendoscopic tests were asked of all respondents aged 40 years or older. NHIS responses regarding time since FIT-DNA test were not released in 2019 but were available for 2021. Because of this, CRC screening comparisons between years do not examine FIT-DNA use or overall CRC estimates (which include FIT-DNA).We defined being up to date with screening as reporting having received a USPSTF-recommended test for any reason within recommended screening intervals 1). Eac. Eac1). P < .05). Overall estimates were also age-standardized to the projected 2000 US standard population of US women were up to date with breast cancer screening, 75.2% 95% CI, 73.9%\u201376.4%) were up to date with cervical cancer screening, and 72.2% of US adults were up to date with CRC screening and 3. C.9%\u201376.4%Estimates were below 50% among those without a wellness check in 3 years across all screening types, among those without a usual source of care or insurance (aged <65 years) for breast and CRC screening, and among those residing in the US for less than 10 years for CRC screening. American Indian or Alaska Native (AIAN) and Asian adults tended to have lower estimates by race across screening types. Hispanic adults were less likely than non-Hispanic adults to be up to date with cervical and CRC screening. Significant differences existed across all screening types by urbanization level, education, and income and 3.P = .51 for breast cancer screening and 75.5% vs 76.8% , P = .09 for cervical cancer screening). Colonoscopy estimates were also similar . Estimated FOBT/FIT use was somewhat higher in 2021 .Age-standardized estimates of being up to date with breast and cervical cancer screening were similar in 2021 and 2019 . Limited evidence exists about self-reported HPV test accuracy ,24. AssuApproximately 1 in 4 adults of screening age were not up to date with breast, cervical, and CRC screening recommendations in 2021. Estimates were below current national targets and disparities persisted across sociodemographic and health care access groups, with particularly low use among those with less health care access. Use of these tests within recommended screening intervals may approximate prepandemic levels. FOBT/FIT use may have increased modestly. Survey changes could have affected estimates although findings are consistent with previous evidence ("} +{"text": "Tick-borne encephalitis (TBE) represents a potential health threat for tourists in high-risk areas, including the Dolomite Mountains in northeastern Italy. The present questionnaire-based survey was, therefore, designed in order to assess knowledge, attitudes, and preventive practices (KAP) in a convenience sample of Italian tourists visiting the Dolomite Mountains, who were recruited through online discussion groups. A total of 942 participants filled in the anonymous survey from 28 March 2023 to 20 June 2023. Overall, 24.1% of participants were vaccinated against TBE; 13.8% claimed to have previously had tick bites, but no cases of TBE were reported. The general understanding of TBE was relatively low; while 79.9% of participants acknowledged TBE as a potentially severe disease, its occurrence was acknowledged as high/rather high or very high in the Dolomites area by only 51.6% of respondents. Factors associated with the TBE vaccine were assessed by the calculation of adjusted odds ratios (aOR) and 95% confidence intervals through a logistic regression analysis model. Living in areas considered at high risk for TBE , better knowledge on tick-borne disorders , high risk perception regarding tick-borne infections , a favorable attitude toward vaccinations , and a tick bite(s) in a previous season were characterized as being positively associated with TBE vaccination uptake. Conversely, being <50 years old and with a higher risk perception regarding the TBE vaccine were identified as the main barriers to vaccination. In summary, tourists to the high-risk area of the Dolomites largely underestimate the potential occurrence of TBE. Even though the uptake of the TBE vaccine in this research was in line with European data, public health communication on TBE is required in order to improve acceptance of this effective preventive option. Flaviviridae, genus Flavivirus .,39.38,39p-value of \u2265 0.100 were considered normally distributed and were compared using Student\u2019s t-test for unpaired data or an ANOVA where appropriate, while their correlation was assessed by means of Pearson\u2019s correlation coefficient. A K2 test p-value of <0.100 identified those variables not normally distributed, which were analyzed using a Mann\u2013Whitney or Kruskal\u2013Wallis test, while their correlation was analyzed by means of Spearman\u2019s rank test. Continuous variables were initially reported as mean \u00b1 standard deviation (SD), and their distribution was assessed through the D\u2019Agostino-Pearson K2 test. Variables with a K2 test inf, RPSvac, GKS, SKS) were initially normalized to a percentage value and then dichotomized by the median value as \u201chigh\u201d vs. \u201clow\u201d estimates, these being managed as categorical variables. The distribution of the categorical variables was assessed through the chi-squared test with respect to the dichotomous outcome variable of having been or not been vaccinated against TBE. All variables that, in univariate analysis, were associated with an outcome variable with a p-value of < 0.05 were included in stepwise binary logistic regression analysis, along with the calculation of the corresponding adjusted odds ratio (aOR) and their 95% confidence intervals (95%CI).Categorical variables were initially reported as percentage values. Cumulative scores , R (version 4.3.1) , and RstAs shown in As shown in p < 0.001 for both summary scores) (As shown in scores) . Cronbac scores) .inf estimate of 52.20% \u00b1 24.28. Conversely, only 5.7% of respondents acknowledged as being somewhat high both the frequency and severity of the side effects associated with the TBE vaccine (vac of 11.63% \u00b1 15.42 (p < 0.001).The frequency of TBEV infection was perceived as high/very high by 51.6% of respondents, while the severity of the clinical syndrome was acknowledged as high/very high by 79.9% of respondents, with a corresponding RPS vaccine , with a \u00b1 15.42 b,c. In bThe large majority of respondents were somewhat in favor of vaccination practice (74.3%), and a total of 267 participants (28.3%) had reportedly been vaccinated against TBEV . As shown in A fairly large proportion of respondents (30.9%) had been recommended TBE vaccination by healthcare professionals, including personnel from the competent Local Health Unit (10.8%) and other medical professionals . Personal reasons for being or not being vaccinated against TBEV are reported in When dealing with perceived barriers, 18.6% of non-vaccinated individuals (N = 675) did not know that an effective vaccine against TBE exists. Nonetheless, the most frequently reported reason for avoiding or delaying TBE vaccination was identified as not perceiving the individual risk of getting TBEV infection (24.1%), followed by not having had enough time (16.2%), the unavailability of the TBE vaccine from vaccination services (10.6%), while the fear of side effects and the lack of trust in vaccines were reported by only 3.2% and 1.3% of participants, respectively. Interestingly, only 2.4% of the non-vaccinated respondents complained about the high cost of TBE vaccination.As shown in Overall, 67.3% of participants reported taking at least one preventive measure against tick bites, while 25.0% reported taking up to 2 preventive measures, and 7.7% of participants reported taking 3 or more preventive measures. The single most frequently reported intervention was tucking pants into socks or boots (42.3%), followed by the use of repellent (25.0%), wearing long sleeves and pants (13.5%), wearing a hat (11.5%), avoiding typical tick habitats (11.5%), and wearing light-colored clothing (7.7%). Interestingly, checking the body was never reported. Focusing on participants not reporting any preventive measure against tick bites, their proportion decreased from 55.56% in the 30\u201339 age group, to 43.75% in the 40\u201349 age group, 27.27% in the 50\u201359 age group, and 10.00% in the 60\u201369 age group, but the proportion was 20.00% in \u226570-year-old respondents . p < 0.001). Conversely, a negative correlation was found between RPSvac and RPSinf . Moreover, both GKS and SKS were positively correlated with RPSinf and were negatively correlated with RPSvac . In othep < 0.001), SKS , and RPSinf were significantly higher among those participants who had previously been vaccinated against TBEV than among those who had not. Conversely, RPSvac scores were higher among participants not reporting the previous uptake of the TBE vaccine than among vaccinated participants . Estimates for GKS , scoring better GKS and SKS , reporting a higher risk perception for natural TBEV infection , exhibiting a better attitude toward vaccines , and reporting a tick bite in the previous holiday season . Conversely, TBE vaccination was less frequently reported among individuals aged under 50 and in those having higher RPSvac scores .The association between the descriptive variables and TBE vaccination status is detailed in vac, and RPSinf scores, reporting a favorable attitude toward vaccination, and reporting any tick bite during 2022. The results of the multivariable analysis are reported in inf scores, reporting a better attitude toward vaccines , and reporting a tick bite during 2022 were all collectively characterized as positive predictive variables. Conversely, being under 50 and having higher RPSvac scores were characterized as negative predictive variables.In fact, being resident in high-risk areas , higher GKS or RPSinf scores; reporting a favorable attitude toward vaccines; and reporting a tick bite in the previous holiday season. Conversely, belonging to younger age groups and higher RPSvac scores were identified as negative explanatory variables. The occurrence of tick bites (16.6% of participants) and preventive interventions allegedly being put in place were heterogeneously distributed across the age groups, with a large share of participants reporting a low proportion of protective strategies, particularly among younger individuals regarding TBE and TBE vaccination, a total of 942 questionnaires were ultimately collected. The self-reported TBE vaccination rate was 28.3% (38.5% in people living in high-risk areas). No cases of TBE were reported, but 5.1% of respondents with a previous tick bite did allegedly receive a diagnosis of Lyme disease. TBE was acknowledged as a serious disorder by 79.9% of participants, while the likelihood of its occurrence was considered high/very high by 51.6% of them. Overall knowledge status was substantially unsatisfactory, although the inclusion criteria may reasonably have led to the oversampling of individuals with a better understanding of TBE ,30. Indiividuals . As the Although avoiding tick bites remains the most effective strategy for preventing the entirety of tick-borne diseases ,43,44, tTo the best of our knowledge, here, we report on the first Italian study regarding TBE vaccine acceptance in people who may potentially be exposed to tick bites, not only within the domain of travel medicine but also among the general population living in high-risk areas ,50,51, aInterestingly, the reported barriers and positive effectors regarding TBE vaccination uptake were also consistent with the available reports ,53, whicA notable feature of our study was the very low proportion of respondents identifying the cost of the vaccine as a limitation, as the direct and indirect costs of TBE vaccines usually represent a potential barrier to achieving high vaccination rates ,22,30,55Our study is affected by several limitations. First, the cross-sectional design cannot support conclusions on the causal relationships between the assessed risk factors and the targeted outcomes ; potentiSecond, our sample was collected by convenience sampling, and we cannot rule out some degree of self-selection bias, a substantial shortcoming shared by web-based cross-sectional studies that ult\u00ae, with the third dose still being required for achieving long-term protection. Hence, future iterations of the present study should more carefully retrieve information on the timeframe of the vaccination in order to provide more accurate estimates of actual protection against TBE.Third, the working definition of vaccination status has reasonably impaired the eventual reliability of our estimates. Compared to other immunization programs, the classical schedule of TBE vaccination is quite complicated, requiring a priming series of three doses, followed by a booster dose and several periodic shots ,27; the Fourth, since the collected data were not externally validated, we cannot rule out a certain degree of declarative bias. It is plausible that some of the respondents did not truly adhere to the study requirements, having preferentially reported \u201csocially desirable\u201d status and attitudes instead of their actual ones. Not coincidentally, 18.0% of vaccinated responders acknowledged the aim of avoiding the spread of the disease as a key motivation for having been vaccinated against TBE, with 12.7% allegedly aiming to protect those who cannot be vaccinated. TBEV has shown no inter-human spreading , and eveFifth, even though our sample largely fulfilled the minimum sample-size requirements, around 1000 respondents are relatively few when compared to the whole of the population from Italian regions as characterized by TBEV circulation, with millions of tourists each year traveling to the Dolomite Mountains; they may also be drawn from a potentially targeted population . In factSixth, due to its design, our survey does not provide any substantial insight into pediatric age groups . Although there is some evidence that the incidence of TBE is higher in older vs. younger children, and in adults vs. children , with yoinf, RPSvac, and their components. In other words, risk perception on TBE, TBEV infections, and tick-borne diseases among the study participants was seemingly not influenced by new media coverage.Last but not least, previous studies have stressed the importance of media coverage of TBEV infections . By raisOur study suggests that tourists to the Dolomite Mountains, a high-risk area for TBE and TBEV virus infection, collectively exhibit an extensive lack of knowledge of this pathogen, with inappropriate risk awareness. Moreover, actual uptake of the TBE vaccine, while still in line with European data, was largely unsatisfactory. As TBEV infection may be effectively countered through a combination of effective behavioral practices and TBE vaccination for people either living or performing outdoor activities in high-risk areas, 69 improving overall awareness of these preventive options could, therefore, be instrumental in reducing the eventual burden of TBEV infections see ."} +{"text": "In this study, after conducting a comprehensive review of 1356 papers that evaluated the diagnostic performance of deep learning (DL) methods based on medical images for hepatocellular carcinoma (HCC), the findings showed a pooled sensitivity of 89% (95% CI: 87\u201391), a specificity of 90% (95% CI: 87\u201392), and an AUC of 0.95 (95% CI: 0.93\u20130.97). In addition, both the DL methods and human clinicians demonstrated similar levels of performance in HCC detection, with receiver operating characteristic curve (ROC) values of 0.97 (95% CI: 0.95\u20130.98) for both groups, indicating no discernible difference. Although the heterogeneity was obvious, the utilization of DL methods for diagnosing HCC through medical images has shown promising outcomes.(1) Background: The aim of our research was to systematically review papers specifically focused on the hepatocellular carcinoma (HCC) diagnostic performance of DL methods based on medical images. (2) Materials: To identify related studies, a comprehensive search was conducted in prominent databases, including Embase, IEEE, PubMed, Web of Science, and the Cochrane Library. The search was limited to studies published before 3 July 2023. The inclusion criteria consisted of studies that either developed or utilized DL methods to diagnose HCC using medical images. To extract data, binary information on diagnostic accuracy was collected to determine the outcomes of interest, namely, the sensitivity, specificity, and area under the curve (AUC). (3) Results: Among the forty-eight initially identified eligible studies, thirty studies were included in the meta-analysis. The pooled sensitivity was 89% (95% CI: 87\u201391), the specificity was 90% (95% CI: 87\u201392), and the AUC was 0.95 (95% CI: 0.93\u20130.97). Analyses of subgroups based on medical image methods (contrast-enhanced and non-contrast-enhanced images), imaging modalities , and comparisons between DL methods and clinicians consistently showed the acceptable diagnostic performance of DL models. The publication bias and high heterogeneity observed between studies and subgroups can potentially result in an overestimation of the diagnostic accuracy of DL methods in medical imaging. (4) Conclusions: To improve future studies, it would be advantageous to establish more rigorous reporting standards that specifically address the challenges associated with DL research in this particular field. Liver cancer, also known as HCC, is a prevalent and deadly form of cancer, ranking as the sixth most common type worldwide and the third leading cause of mortality . Early-sMedical imaging is essential in clinical practice for diagnosis, staging, and treatment planning. Modalities such as ultrasound (US), magnetic resonance imaging (MRI), and computed tomography (CT) are noninvasive and offer valuable tumor images, reducing patient discomfort and risks compared to invasive procedures like biopsies ,6,7. TheDL is a machine learning technique that includes multiple model architectures and can solve various types of machine learning problems. Common DL methods are based on convolutional neural networks, recurrent neural networks, long short-term memory networks, generative adversarial networks, etc. DL methods have shown promising results in the automatic detection of medical images, enabling automatic diagnosis and classification of diseases by analyzing and identifying features and lesions ,11. CompWe registered our study protocol in PROSPERO with the number CRD42023442527. The study followed the guidelines outlined in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) to ensure comprehensive and transparent reporting and AsseA systematic search was conducted with several databases, including Embase, IEEE, PubMed, Web of Science, and the Cochrane Library. The search aimed to identify studies published from the inception of the database to July 3, 2023 that focused on the development of DL methods for diagnosing HCC based on medical images. Two investigators assessed eligibility by screening titles, abstracts, and relevant citations. Discrepancies were resolved through discussion with an additional contributor. Inclusion criteria consisted of studies reporting DL models\u2019 diagnostic performance in early HCC detection using medical images. Studies that reported diagnostic results such as sensitivity and specificity or detailed information on 2 \u00d7 2 contingency tables were considered eligible for inclusion. The use of DL models was not limited by participant characteristics, imaging modality, or intended setting.The study characteristics and diagnostic yield data were independently extracted by two investigators using a standardized data extraction sheet. Uncertainties were resolved through discussions with a third researcher. With a meticulous approach, we diligently extracted the diagnostic accuracy data and precisely organized it into contingency tables, including the number of true positives (TPs), false positives (FPs), true negatives (TNs), and false negatives (FNs). Three researchers utilized the QUADAS-2 tool to assess both the risk of bias and concerns about the suitability of the included studies . This to2I statistic, exploring potential sources through subgroup meta-analyses and regression analyses. The random-effects model accounted for the substantial heterogeneity. Publication bias was assessed visually with funnel plots.Hierarchical SROC curves assessed the DL methods\u2019 diagnostic performance, presenting averaged estimates of sensitivity, specificity, AUC, and 95% CI with prediction regions. A meta-analysis using contingency tables identified the most accurate DL methods across studies with multiple methods. Heterogeneity was evaluated with the p < 0.05, and we employed a robust two-sided approach to determine statistical significance for all tests. In the process of collating the data, we found that DL methods combined with contrast-enhanced images had higher diagnostic accuracy than non-contrast-enhanced images. The following subanalyses were further conducted: (a) Based on the medical image method, the DL methods were divided into two categories: contrast-enhanced and non-contrast-enhanced images. Image enhancement methods used contrast media, and non-contrast-enhanced images did not use contrast media. (b) The DL methods were categorized by their respective imaging modalities, including CT, US, and MRI. (c) The DL methods were classified as internal or external methods depending on the type of validation. Internal validation was conducted using internal data for validation. External validation was conducted using external data for validation. (d) The DL methods were assessed and compared with human clinicians based on aggregated performance measures using the same datasets. Meta-analyses were conducted if at least three original studies were available. We harnessed the mighty STATA (version 17.0) to dissect our data with precision. Our threshold for significance was set at n = 10), US (n = 7), and CT (n = 13). As shown in Out of the 48 studies included, 30 offered enough data for creating contingency tables and calculating diagnostic yields, making them eligible for the meta-analysis. The meta-analysis included 102 contingency tables, as shown in Since most studies investigated multiple DL methods and reported their diagnostic performance, we chose to report the highest accuracy achieved by various DL methods across the included studies, which resulted in 30 contingency tables. As we combined their findings, we discovered a pooled sensitivity of 93% (95% CI: 91\u201395) and a specificity of 95% (95% CI: 92\u201397). The AUC was calculated to be 0.98 (95% CI: 0.96\u20130.99). More detailed information was shown in Among the studies included in the analyses, 23 studies focused on contrast-enhanced images, resulting in a total of 65 contingency tables. The pooled sensitivity for these studies was 92% (95% CI: 89\u201393), while the pooled specificity was 94% (95% CI: 92\u201396). Additionally, the AUC was 0.97 (95% CI: 0.96\u20130.99). More detailed information is shown in Among the studies included in the analyses, 10 studies investigated MRI data, which resulted in a total of 29 contingency tables. The pooled sensitivity of these studies was 92% (95% CI: 88\u201394), and the pooled specificity was 94% (95% CI: 87\u201397). Furthermore, the AUC was 0.97 (95% CI: 0.95\u20130.98). More detailed information about these studies is shown in The meta-analysis included 29 studies that used within-sample datasets, comprising a total of 92 contingency tables. For these studies, the pooled sensitivity and specificity were 89% (95% CI: 87\u201391) and 90% (95% CI: 88\u201392), respectively. The AUC was determined to be 0.95 (95% CI: 0.93\u20130.97), as illustrated in Among the 30 included studies, 6 directly compared the diagnostic performance of the DL methods with human clinicians using the same dataset. These studies consisted of 20 contingency tables for the DL methods and 10 contingency tables for the human clinicians. The pooled sensitivity for the DL methods was 91% (95% CI: 88\u201393), while the human clinicians had a pooled sensitivity of 88% (95% CI: 80\u201393). The pooled specificity for the DL methods was 92% (95% CI: 89\u201395), compared to 95% (95% CI: 89\u201397) for the human clinicians. Both the DL methods and the human clinicians exhibited an AUC value of 0.97 (95% CI: 0.95\u20130.98), as depicted in 2I value of 99.83% (p < 0.01) and the specificity had an 2I value of 99.84% (p < 0.05), indicating high heterogeneity. p < 0.05). More detailed information was presented in The meta-analysis of 30 studies indicated that the DL methods were beneficial in diagnosing HCC from medical imaging based on the random-effects model. However, the sensitivity showed an n = 30) and reference standards (n = 22), over half of the studies demonstrated a high or unclear risk of bias. This was mainly due to a lack of clarity in describing the included patients, such as previous testing, presentation, setting, intended use of the index test, and insufficient external evaluation.QUADAS-2 was used to assess the quality of the included studies, and the results were summarized in Through this study, we assessed the diagnostic effectiveness of DL methods for HCC detection based on medical images. When averaging the results across the studies, the pooled sensitivity, specificity, and AUC were found to be 89%, 90%, and 0.95, respectively. When determining the highest accuracy of each DL method among the included studies, we found that the DL methods demonstrated superior performance in terms of sensitivity (93%), specificity (95%), and AUC (0.98). In subgroup analysis, to begin with, we found that DL methods combined with contrast-enhanced images had higher diagnostic accuracy than non-contrast-enhanced images. The reason may be that the image enhancements have a higher resolution ratio so that tiny lesions are displayed more clearly, which is more conducive to the diagnosis of cancer. Furthermore, MRI, US, and CT are the main imaging techniques for the diagnosis of HCC. The selection of imaging techniques for HCC diagnosis depends on several factors, including the patient\u2019s condition, availability of medical resources, and specific circumstances. Typically, doctors choose the most suitable imaging examination based on each patient\u2019s needs and the characteristics of their condition. Moreover, using an internal dataset may overstate diagnostic value since homogeneity is produced, but external validation through out-of-sample data can offer insights into subgroups and variations among different ethnic groups. However, the presence of high heterogeneity and variance between studies results in considerable uncertainty surrounding the estimates of diagnostic accuracy in this meta-analysis.A systematic search for relevant articles resulted in the identification of four systematic reviews or meta-analyses that explored the significant role of artificial intelligence (AI) and medical images in HCC diagnosis. However, these reviews considered diverse domains, making direct comparisons with this research challenging. Chou et al. discovered that image-based diagnosis of HCC had a sensitivity of 84% and specificity of 99%, highlighting its importance. However, they did not explore AI methods . In our Our research showed that DL methods are a powerful tool in diagnosing HCC, and we summarize our results as follows. First, the DL methods can extract intricate patterns and features based on medical images, enabling accurate identification of early-stage liver tumors that may be challenging for human experts to detect . This eaOur study had some limitations. First, there was evident heterogeneity in our study. Despite subgroup and meta-regression analyses being carried out, the heterogeneity could not be completely eliminated. Second, due to limited data, we could not perform subgroup analysis based on tumor size and location. Third, the included studies were almost entirely retrospective, and potential confounding variables and confounding bias may limit the internal validity of retrospective studies. Research on DL methods based on medical images for HCC diagnosis should be improved in terms of study design.In conclusion, the DL methods based on medical images for detecting HCC were found to be highly accurate, although the heterogeneity is obvious. Furthermore, the sensitivity of the DL methods significantly improved when utilizing contrast-enhanced imaging techniques."} +{"text": "Lung cancer incidence patterns and clinical characteristics across the heterogeneous non-Hispanic Black and Hispanic racial\u2013ethnic populations of the United States (US) are understudied. This characterization of lung cancer rates across US minority populations is important for targeting clinical and public health measures in high-risk populations. The aim of our population-based study is to assess lung cancer heterogeneity among these populations by detailed race\u2013ethnicity or nativity using all lung cancer cases from the Florida state cancer registry, 2012\u20132018, and computing, for the first time, age-adjusted incidence rates (AAIR) for each population. AAIRs among Blacks and Hispanics vary approximately 3-fold between detailed groups and highlight the need to look beyond aggregate groups for tailored approaches in the fight against lung cancer. The implications of these findings are significant for public health surveillance and for clinical professionals working with diverse US populations.Lung cancer (LC) incidence rates and tumor characteristics among (non-Hispanic) Black and Hispanic detailed groups, normally characterized in aggregate, have been overlooked in the US. We used LC data from the Florida state cancer registry, 2012\u20132018, to compute LC age-adjusted incidence rates (AAIR) for US-born Black, Caribbean-born Black, Mexican, Puerto Rican, Cuban, Dominican, and Central and South American populations. We analyzed 120,550 total LC cases. Among Hispanics, Cuban males had the highest AAIR , only 8% lower than Whites, but 2.7 (IRR 95%CI: 2.31-3.19) times higher than Central Americans. Among Blacks, the AAIR for US-born Black males was over three times that of those Caribbean-born and 14% higher than White males . Among women, US-born Blacks and foreign-born Mexicans had the highest and lowest rates. Aggregation of non-Hispanic Blacks or Hispanics obscures inherent disparities within groups. Understanding the distinct LC rates in US populations is crucial for targeting public health measures for LC diagnosis, prevention, and treatment. Further LC research exploring detailed race\u2013ethnicity regarding LC in never-smokers is necessary, particularly among females and considering pertinent environmental factors. Lung cancer in the United States of America (US) has the highest overall mortality rate and is the second in overall incidence, compared to other cancers ,2. DespiIn existing population-based studies, there is little recognition of the diversity within the US Black population because US cancer surveillance program, the North American Association of Central Cancer Registries (NAACCR), standards do not collect information on heterogeneity among this racial group. As a result, most studies categorize Blacks based on nativity and are majority mortality studies ,9, becauTo further the discourse regarding granular analysis of US Black and Hispanic populations and to address the lack of specific lung cancer incidence rates and characteristics by detailed racial\u2013ethnic group, we conducted a population-based analysis of lung cancer incidence among major racial\u2013ethnic groups and specific Black and Hispanic groups in the diverse state of Florida, the third US state in population and the second US state in number of cancer cases, with over 150,000 newly diagnosed cancers in 2022 .Individual level data from all lung cancer cases : ICD-O-3 codes C34.X and histology codes 8000\u20139540) diagnosed during 2012\u20132018 were obtained from the Florida Cancer Data System (FCDS), including demographic, tumor, and socioeconomic characteristics. FCDS is the legislatively mandated, population-based central cancer registry for Florida, which has been collecting incidence data from hospitals, radiation centers, surgery centers, and physician offices since 1981. FCDS has met or exceeded the NAACCR standards of quality, timeliness, and completeness (>95%) for every year since 1995.Data were aggregated on race and ethnicity and were reported in four major, mutually exclusive, racial\u2013ethnic groups and 11 detailed racial\u2013ethnic groups: among Blacks, US-born and Caribbean-born; among Hispanics, Mexican, with two divisions , Puerto Rican, Cuban, Dominican, Central American, South American, and combined Central and South American.Gathered FCDS characteristics comprise sex, age at diagnosis, histology, microscopic verification, stage at diagnosis, socio-economic status, and insurance type. Sex as female include n = 41 identified as non-binary . Histology is classified according to previous research into theDemographic and tumor characteristics were compared among the four major racial\u2013ethnic groups , among Blacks (US-born and Caribbean-born), among Hispanics , and among Mexicans (US-born and foreign-born) by Chi-square tests of differences: 5-year age group, histology, microscopic verification, SEER stage at diagnosis, census tract poverty level, and insurance status.Missingness among detailed racial\u2013ethnic group was 20.1% of Hispanic cases and 13.9% of non-Hispanic Black cases (n = 1346 of 9710). To avoid underestimating rates by racial\u2013ethnic group status and obtain comparable numerators for our population-based rates, we conducted multiple imputations of specific ethnic (for Hispanics) and nativity group (for Blacks), with 20 iterations based on a multivariate imputation by fully specification method ,20 for eLung cancer incidence rates by detailed race\u2013ethnicity and sex were calculated per 100,000 people and age-adjusted by the direct method to the 2000 US standard population. Tiwari incidence rate ratios (IRR) with 95% confidence intervals (CI) were comSAS v9.4 software was used for data management and statistical analysis. Exempt status was granted by the Florida Department of Health\u2019s Institutional Review Board.Of 120,550 lung cancer cases diagnosed in Florida during 2012\u20132018, the majority identified as White , with 51.0% males and 49.0% females ; following were Hispanics at 10.0% with 58.3% (n = 7038) and 41.7% (n = 5024) males and females, respectively; Blacks at 8.1% (n = 9710) with 57.2% (n = 5553) and 42.8% (n = 4157) males and females, respectively; and API at 0.9% (n = 1030) with 49.7% (n = 512) and 50.3% (n = 518) males and females, respectively . Cubans Compared to other Hispanic groups, Cuban and foreign-born Mexican patients disproportionately reside in areas of high poverty . There are also significant differences in Hispanic lung cancer patients by insurance status, with Mexicans and Cubans having lower proportions of private insurance , compared to other Hispanic lung cancer groups. Foreign-born Mexicans have the lowest proportions of private insurance , compared to other Hispanic lung cancer groups. Lung cancer patients with microscopic verification were lowest among Hispanic females at 90.1%, comprising detailed groups with proportions varying from 83.3% for foreign-born Mexican females and 91.5% for Puerto Rican females.The distribution of lung cancer cases by SEER stage at diagnosis show higher proportions of late-stage lung cancer among Black and API populations ; however, a larger distant stage percentage for APIs is partially explained by the lower proportion of unknown stage. Among Hispanic lung cancer patients, higher proportions of distant stage at diagnosis were observed among Mexicans and Central Americans (55.8% and 52.1%).Histologically, lung cancer cases show larger proportions of adenocarcinomas to be among APIs , Caribbean-born Blacks (50.0% and 58.8%), Dominicans (49.9% and 58.0%), Central Americans (53.2% and 58.9%), and US-born Mexican women (58.1%). Among Black females with lung cancer, those who are US-born have larger proportions for squamous cell carcinoma (18.5%) and small cell carcinoma (10.2%) compared to those who are Caribbean-born .Significant disparities across lung cancer cases by racial\u2013ethnic group in census tract poverty level show the highest overall proportions of high poverty for Blacks . Proportions of high poverty among Blacks by detailed racial\u2013ethnic group reveal US-born Black males and females at 59.6% and 57.4%, respectively, and Caribbean-born Black males at 47.1% and females at 37.6%. The lowest proportions of high poverty among lung cancer cases are for API , White , and South American populations.Overall, age-adjusted lung cancer incidence rates (AAIR) per 100,000 people were higThis novel analysis of lung cancer incidence rates during 2012\u20132018 in Florida by detailed race\u2013ethnicity provides significant insight into this important disease in US Hispanic and Black minority populations. In these thus far unstudied detailed populations, we demonstrate remarkable variation in lung cancer risk within each racial\u2013ethnic group, most apparently Cubans versus Central Americans, US-born Black persons versus Caribbean-born Black persons, and US-born Mexicans versus foreign-born Mexicans. Such marked heterogeneity is important, as it supports recommendations to limit consideration of race\u2013ethnicity as strictly blocked groups , in an effort to reduce inequities in scientific literature . In juriOur analyses show higher overall lung cancer rates in males than females, which reflects secular trends in the prevalence of smoking by sex ,24. MoreAlthough lung cancer incidence rates are overwhelmingly driven by prevalence of current or past smoking, it is important to consider that lung cancer also occurs among never-smokers. The characterization of lung cancer among never-smokers displays distinct patterns with higher proportions of adenocarcinomas, and for lung cancer patients with no smoking history, there is the potential for improved prognosis due to the availability of targeted therapies . In a prThe US is becoming increasingly diverse, due largely to immigration and lower birth rates, with US youth and children at the leading edge of the nation\u2019s growing heterogeneity as the population of racial\u2013ethnic minority children increased by 11.8% over the last decade to 38.5 million in 2020, when 52.7% of U.S. population under age 18 belonged to a minority group ,35. ThisWhen aggregated, the Florida Black population shows a lower risk of lung cancer, compared to national rates for Blacks , exposinWithin Hispanics, we found a higher proportions of late-stage lung cancer diagnoses among Mexican and Central American populations. Such notable differences in the distribution of stage at diagnosis are highly suggestive of disparities within Hispanics that are critical for understanding cancer patterns in this population. US immigrants from Mexico and Central America tend to be highly vulnerable populations, with lower socio-economic status and lower levels of education and English language proficiency compared to other foreign-born groups, all considerably lower than their US-born counterparts . TailoreA thorough literature review returns few published studies evaluating lung cancer incidence across detailed race\u2013ethnicity, and existing studies primarily focus on non-Hispanic API racial groups ,45, exclThe primary strength of this study is its utilization of all-inclusive, population-based data in the calculation of lung cancer incidence rates and rate ratios which, compared to a cohort study, minimizes error and produces more accurate comparisons across populations, given selection factors in current cohorts ,47. SignThe disparities in lung cancer incidence in Hispanic and non-Hispanic Black populations, presented here, highlight the heterogeneity of lung cancer in rapidly expanding, racial\u2013ethnic populations that is often hidden by aggregation of groups. AAIRs among Blacks and Hispanics vary approximately 3-fold in their more detailed groups, as opposed to the monotonous aggregate groups, requiring more refined approaches in the fight against lung cancer. The implications of these findings are significant for public health surveillance and for clinical professionals working with diverse US populations. The characterization of disparate lung cancer rates between groups helps to identify local populations that may benefit from targeted prevention programming and education and from enhanced lung cancer screening. Areas for future research include the calculation of specific rates of lung cancer in never-smokers by detailed racial\u2013ethnic population, especially among females; further research into the effects of environmental factors on lung cancer risk in diverse populations; and the replication of this study in other states with varied racial\u2013ethnic populations."} +{"text": "BackgroundChronic liver diseases account for approximately 1.9 million deaths globally every year and negatively\u00a0affect health-related quality of life. Early detection of liver disease may enable timely treatment, potentially improving patient outcomes. This study aimed to determine the prevalence and determinants of liver steatosis and fibrosis in US adults with no previously diagnosed liver condition.MethodsWe conducted an observational, nationally representative, cross-sectional study using data from the National Health and Nutrition Examination Survey (NHANES) conducted from January 2017 to March 2020. Study participants were 7,391 adults aged 21 and older with no history of diagnosed liver disorders who underwent vibration-controlled transient elastography (VCTE) to determine liver steatosis and fibrosis. Controlled attenuation parameter (CAP) values between 248 and 267 dB/m were classified as mild steatosis, and those over 267 dB/m as advanced steatosis. Liver stiffness measurement (LSM) values between 7.65 and 13 kPa were classified as moderate/severe fibrosis, and those over 13 kPa as cirrhosis. Covariates included age, sex, race, body mass index (BMI), diabetes mellitus, kidney disease, smoking history, alcohol intake, alanine aminotransferase (ALT), aspartate aminotransferase (AST), physical activity, sedentary time, and sleep time. The associations of subject characteristics with liver CAP and LSM were evaluated using survey multivariable linear regression. Shapley Additive Explanations values determined the relative importance of each attribute in the model. The discriminative performance of classification models was assessed using the area under the receiver operating characteristic (AUROC) curve.Results2.The population prevalence of liver steatosis was 57.2% . The relative importance of covariates in predicting liver CAP was 63.1% for BMI, 10.7% for ALT, and less than 10% for the other covariates. The prevalence of significant fibrosis was 11.4% . The relative importance of covariates in predicting LSM was 67.3% for BMI and less than 10% for the other covariates. BMI alone demonstrated acceptable discriminative performance in classifying varying severities of steatosis and fibrosis (AUROC range 72%-78%) at cutoffs between 28 and 33 kg/mConclusionsUndiagnosed chronic liver disease based on VCTE findings is highly prevalent among US adults, particularly in obese individuals. Efforts to increase\u00a0awareness about liver disease and to reconsider existing BMI thresholds for liver disease screening may be warranted. Chronic liver diseases account for approximately 1.9 million deaths globally every year . NonalcoWhile liver biopsy is commonly used to qualitatively diagnose and stage liver fibrosis, procedural morbidity and risk of disease misclassification have prompted the development of non-invasive modalities for staging liver disease. Vibration-controlled transient elastography (VCTE) is an ultrasound-based test that generates a shear wave across the liver using a transducer probe. A controlled attenuation parameter (CAP) measurement is obtained from ultrasonic attenuation of the echo wave due to fat accumulation, an indicator of liver steatosis. The shear wave propagation velocity is measured and converted to a liver stiffness measurement (LSM), an indicator of fibrosis or cirrhosis. Due to the noninvasive nature of the test, VCTE is preferred over liver biopsy by 95% of patients ,11. ThusSource populationThis cross-sectional observational study utilized data from NHANES, a continuous sample survey conducted every two years by the National Center for Health Statistics. The NHANES project is a complex, stratified, multi-stage probabilistic health survey representative of the noninstitutionalized civilian US population. The NHANES data are obtained from interviews, laboratory tests, and physical examinations conducted by trained staff. For this study, we used NHANES data from January 2017 to March 2020. The NHANES program suspended field operations in March 2020 due to COVID-19. Thus, the 2019 to March 2020 data were combined with the 2017-2018 data to create a nationally representative pre-pandemic sample.\u00a0Eligible subjects for this study were US adults aged 21 years and older without a history of liver disease who underwent VCTE. The data utilized in this study were publicly available from the National Center for Health Statistics . ParticiVibration-controlled transient elastography measurementTrained technicians obtained a minimum of 10 VCTE measurements from fasted participants, generating median CAP (measured in decibels per meter) and LSM values for each participant. The CAP and LSM data were extracted from the Liver ultrasound files available from the NHANES database . Higher CovariatesCovariates in this study were included based on their known clinical associations with liver disease and their feasibility of use during routine healthcare screening. Covariate data were extracted from the Alcohol use, Biochemistry, Body measures, Cigarette use, Demographic, Diabetes, Kidney conditions, Medical conditions, Physical activity, and Sleep files available from the NHANES database .2). Diabetes mellitus was defined as a self-reported physician diagnosis or current use of diabetes medication. Smoking history was categorized as current (smoked >100 cigarettes ever and currently smoke on some days or every day), former (smoked >100 cigarettes ever and do not currently smoke), or never (smoked <100 cigarettes ever). Alcohol intake was calculated from self-reported drinking frequency and the number of drinks consumed when drinking over the past 12 months. Heavy alcohol intake was defined as at least 15 drinks per week for men and at least eight drinks per week for women. Kidney disease was defined as a self-reported physician diagnosis of weak or failing kidneys. The serum concentration of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were included, both measured in U/L.Demographic variables included age, sex, and race. Analyses were restricted to individuals aged 21 years and older to minimize possible reporting bias related to alcohol consumption in younger individuals. Body mass index (BMI) was calculated as weight(kg) divided by height -minutes per week. One MET indicates the amount of oxygen consumed while sitting at rest, equivalent to 3.5 ml Or minute . Vigorour minute . SedentaStatistical analysesStatistical analyses utilized complex sample methodologies incorporating sampling weights, sample strata, and clusters. The sample weight for each respondent indicated the number of individuals in the target population they represent. The sampling weights were calculated as the inverse of the selection probability, with adjustments for nonresponse patterns. Variance estimation utilized Taylor series linearization to accommodate the stratified cluster sampling design.We compared participant characteristics across liver steatosis and liver fibrosis classifications using analysis of variance for continuous variables and chi-square\u00a0tests for categorical variables. We developed multivariable linear regression models to identify determinants of liver CAP and LSM, respectively. Since identifying trivial statistically significant associations is common in population-based studies, statistical machine learning has been increasingly utilized to improve liver disease prediction models . Therefo2, diabetes mellitus was reported in 9.2%, and heavy alcohol intake was reported in 6.6% of participants.A total of 15,560 participants were recruited into the study during the combined January 2017 to March 2020 NHANES cycle. After sequentially excluding 6,450 participants under 21 years, 480 with a history of a liver disorder , and 1,239 without VCTE data, 7,391 individuals remained in the analysis sample. These results represented approximately 211.3 million US adults aged 21 and older without a history of diagnosed liver conditions. The mean age was 48.4 years, 47.7% were male, most (63.0%) self-identified as White, mean BMI was 30.4 kg/mNormative population-based CAP and LSM values by age group and sex are provided in Figure Overall, the prevalence of liver steatosis and/or significant fibrosis was 59.0%. The inter-relationships between VCTE-determined liver steatosis and fibrosis are displayed in Table The population prevalence of liver steatosis was 57.2% . Comparing individuals with no, mild, or advanced liver steatosis, statistically significant differences were noted among all measured covariates , followed by ALT (10.7%), diabetes mellitus (7.1%), age (5.7%), and race (5.4%). The relative importance of each remaining covariate in the model was less than 5% Figure .The population prevalence of significant fibrosis was 11.4% . Comparing individuals with no/mild fibrosis, moderate/severe fibrosis, or cirrhosis, statistically significant differences were noted among all measured covariates except sleep quantity and alcohol consumption (Table The highest relative importance in predicting LSM was given to BMI 67.3%), followed by AST (9.8%), diabetes mellitus (7.9%), ALT (7.5%), and the remaining variables (<5%) and a 28.7 kg/m2 cutoff. The AUROC for classification of significant fibrosis (moderate/severe fibrosis or cirrhosis) using BMI was 71.8% , with a cutoff of 31.7 kg/m2, and the AUROC for classification of cirrhosis only was 75.3% , with a cutoff of 33.0 kg/m2.Using BMI alone to identify liver steatosis (mild or advanced) resulted in an AUROC was 78.4% with maximum discriminatory power at a cutoff of 28.2 kg/mOur study revealed that among US adults aged 21 and older without a history of liver disease, VCTE identified liver steatosis and/or significant fibrosis in 59.0% of individuals, with liver steatosis prevalence of 57.2% and significant fibrosis prevalence of 11.4%. BMI emerged as the primary determinant of both measures, with a limited independent contribution from the other covariates such as diabetes mellitus, liver enzymes, age, and alcohol consumption. Although previous studies have reported associations between higher BMI and higher liver steatosis and fibrosis scores , our stuObesity disrupts hepatic adipokine and hormone release, promoting steatosis, inflammation, and fibrosis. Triglyceride accumulation in hepatocytes comprising at least 5% of liver parenchyma leads to NAFLD. Other proposed mechanisms include alterations in the gut microbiota and dysregulation of intestinal hormones associated with obesity and NAFLD ,25. Rece2, or BMI >35 kg/m2 with obesity-related complications) [2 in the current study, and 73% of obese adults (BMI >30 kg/m2) had advanced steatosis. This suggests that routine liver disease screening based on lower BMI thresholds may be warranted and could help to identify the approximately 100 million US adults with advanced liver steatosis or cirrhosis. Since approximately 40% of individuals with NAFLD progress to cirrhosis within eight years, and eight-year mortality rates are 13% with NAFLD and 31% with NAFLD cirrhosis [The finding that 59.0% of US adults with no prior history of liver disease have liver steatosis or significant fibrosis carries significant public health implications given the strong association of liver steatosis and fibrcations) , the meaThis population-based study has several important strengths. First, the results are generalizable to the US population of adults without a previous diagnosis of liver disease, contrasting with much prior work on correlates of VCTE measures that included individuals with prior liver disease ,22 or smDespite these strengths, this study had several limitations. First, the cross-sectional study design prevents determining causal relationships between the observed associations and VCTE parameters. Second, the self-reported components of the NHANES data may introduce inaccuracies due to recall and response bias. Third, model accuracy was higher for detecting liver steatosis than fibrosis. Factors such as medication use, long-term exposure to environmental toxins, and social determinants, which were not measured in this study, may influence liver fibrosis detection. Fourth, the reliability of VCTE measures may be compromised in morbidly obese individuals due to increased skin-to-liver capsule distance, although using a larger probe can largely mitigate this issue. Fifth, while we utilized results of previous meta-analyses to define liver steatosis and fibrosis categories ,15, no uUndiagnosed chronic liver disease\u00a0based on VCTE findings is highly prevalent among US adults, particularly in individuals with obesity. Demographics, diabetes mellitus, liver enzyme concentrations, and lifestyle factors provided little additional predictive value. The high prevalence of undiagnosed liver disease revealed in this nationally representative study indicates that current practices to detect chronic liver disease early may be inadequate. Efforts to increase awareness about liver disease\u00a0among patients and providers and to reconsider existing BMI thresholds for liver disease screening may be warranted. Integration of liver disease screening into routine primary care, particularly for overweight and obese adults, could promote earlier diagnosis and treatment to reduce population morbidity and mortality."} +{"text": "Diagnostic strategies rapidly evolved during the COVID-19 pandemic in response to the unprecedented worldwide testing demand. The public\u2019s perception in regards to testing has also evolved. Testing remains essential for understanding the current state of the pandemic and directing efforts and resources. The purpose of this study was to better understand the public view regarding clinical sample types to inform future diagnostics development and surveillance planning.To assess SARS-CoV-2 testing preferences, we distributed a Qualtrics survey via social media and email to connections in > 100 countries. The questionnaire covered testing preferences and key demographic information. Python was used to analyze the raw data.From 03/30-11/30/2022, a total of 2,094 responses were received from Africa (22%), Asia (8%), Europe (22%), North America (27%), Latin America and the Caribbean (9%), the Middle East (7%), and Oceania (6%). Participants were 55% female, 44% male, and 1% non-binary and ranged in ages . Education level and employment was skewed with 52% holding a graduate degree and 26% holding a bachelor\u2019s degree; 27% were scientists/researchers and 29% were healthcare workers. Assuming equal accuracy between COVID-19 test types, respondents most preferred oral sample collection and least preferred methods involving coughing. The most preferred sample collection method varied by region . In the majority of regions, saliva based testing was the most preferred method by parents and guardians for their children.This study identified a preference for oral sample types for the detection of SARS-CoV-2, with saliva collection from children preferred by parents. Large-scale, easily accessible diagnostic testing is vital for detecting, monitoring, and containing outbreaks of respiratory pathogens; utilization of oral sample types supports the feasibility of this, if individuals are then more likely to test. Results from this study should be considered when new testing practices are designed to encourage maximum participation from individuals and improve community health.Anne L. Wyllie, PhD, Co-Diagnostics: Board Member|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Pfizer: Grant/Research Support"} +{"text": "Urinary tract infections (UTIs) are one of the most common healthcare-associated infections (HAIs). Trauma patients acquire UTIs almost exclusively due to hospital or treatment-related causes. Healthcare-associated UTIs (HA-UTIs) have increased morbidity, antimicrobial treatment cost and length of stay. Temporal evaluation of HA-UTIs will help in assessing the actual magnitude of the problem and the variation in antibiograms. In this study, we have evaluated the prevalence of uropathogens and their antimicrobial resistance (AMR) pattern over 10 years from patients admitted to a level-1 trauma centre in India.The study reports the pathogen profile and their antibiograms from the period 2012 to 2022. Antibiotic susceptibility was done in our laboratory using Vitek 2. In cases where the CLSI guidelines do not recommend Vitek 2, disc diffusion testing was done. The most prevalent organisms with their antimicrobial susceptibility testing were analysed using appropriate statistical measures.Escherichia coli (1074), Klebsiella pneumoniae (643) and Pseudomonas aeruginosa (638). Amongst Gram-positives, Enterococcus faecium (171) was the most significant. The AMR pattern of the Gram-negative organisms showed that the majority were MDR. Amikacin resistance was consistently in the range of 20%\u201325% for all E. coli isolates except in 2021 and 2022, where it was 8.47% and 17.82%. K. pneumoniae isolates (>60%) were consistently resistant to amikacin, cefepime, ciprofloxacin and piperacillin/tazobactam. However, there was a slight dip in resistance to amikacin in 2017, which was 52.38%. Imipenem showed consistent resistance in the 30%\u201360% range, but there has been a spike in resistance (>60%) after the pandemic. Resistance to ceftazidime, cefepime, ciprofloxacin and amikacin was >80% for Pseudomonas isolates except in 2019 and 2020, where their resistance pattern was within 60%\u201380%. Imipenem resistance was >60% throughout the period except for 2021, where resistance was 53.3% (8/15).From a total of 3432 isolates, the most common uropathogens were E. coli. In conclusion, AMR trends are very important, and antibiograms should be revised on a timely basis.All the antibiotics showed an upward trend in resistance post the pandemic except amikacin in isolates of"} +{"text": "Appropriate patient selection for coronary angiography (CAG) is essential to minimize the unnecessary risk of morbidities and exposure to radiation and iodinated contrast. This becomes even more relevant in low-to-middle-income settings where most health expenditures are out-of-pocket due to lack of medical insurance. We determined predictors of non-obstructive coronaries (NOC) in patients undergoing elective CAG.CathPCI Registry\u00ae, single-center data was extracted for 25,472 patients who had CAG over an eight year period. After excluding patients for compelling conditions or known CAD, 2,984 (11.7%) patients were included in this study. Non-Obstructive Coronaries was defined as <50% left main coronary artery and major epicardial vessel stenosis. Multiple Cox proportional algorithm was employed to report prevalence ratios (PR) of predictors of NOC along with 95% confidence interval.Mean age of patients was 57.9 \u00b1 9.7 years, 23.5% were women. Preprocedural non-invasive testing (NIT) was performed in 46% of the patients; of which 95.5% reported to be positive but only 67.3% were stratified as high risk. Of 2,984 patients undergoing elective CAG, 711 (24%) had NOC. Predictors of NOC included younger age <50 years , Women , low and intermediate risk stratification on Modified Framingham Risk Score and inappropriate and uncertain classification of CAG on Appropriate Use Criteria. Patients with heart failure as an indication of CAG and No NIT or positive low risk NIT were more likely to have NOC.Approximately one out of four patients undergoing elective CAG had NOC. Yield of diagnostic catheterization can be improved by adjudicating NIT especially in younger patients, women, patients with heart failure as an indication of CAG, patients classified as inappropriate on Appropriate Use Criteria and patients categorized as low or intermediate risk on MFRS. Coronary angiography (CAG) is a key diagnostic test to identify patients with obstructive coronary artery disease (CAD) and deci56Although definitions vary, angiographically normal or NOC finding has been reported in 21% to 58.4% of patients undergoing CAG for the diagnosis of CAD in a non-emergency setting 78910. Pr7897In Western world data, the number of NOC findings has raised concerns. The implication of this becomes even more relevant in a LMICsetup with an enormous aggregate global burden of CAD and a self-pay environment due to lack of medical insurance or national health care systems. Due to cost constraints, NIT may be under-utilized by the physicians, and additionally, the AUC for CAG, at best, remains unused in these setups. Moreover, unnecessary risk of morbidities and exposure to radiations and contrasts might also be avoided if predictors of NOC are identified and considered during patient selection. The rationale for this study is to explore patterns and predict factors associated with NOC in resource-limited settings in order to develop an evidence base to aid clinicians in deciding when to employ CAG. Thus this study determines the frequency and predictors of NOC in patients undergoing elective CAG.\u00ae data associated with National Cardiovascular Data Registry (NCDR)\u00ae was extracted for 24,472 patients. We excluded patients with compelling indications for CAG, including acute coronary syndrome (ACS), cardiogenic shock, pulmonary edema, known CAD , and prerequisite elective CAG for valve replacement surgery.A cross-sectional study design based on a retrospective record review was employed to determine the frequency and predictors of NOC in patients who underwent elective CAG in a tertiary care setup of Tabba Heart Institute (THI), Karachi, Pakistan, during the span of June 2012 to July 2020. CathPCI RegistryPatients\u2019 baseline demographic data, such as age and gender, cardiovascular risk factors history, clinical presentation, medications history, other relevant cardiac test findings, and angiographic findings, were extracted from the electronic medical records. Patients presenting symptoms were categorized as: typical, angina without change in frequency or pattern for the past six weeks and is controlled by rest or oral or transcutaneous nitroglycerine; atypical/unlikely ischemia, pain or discomfort in chest, neck, or arms, not necessarily or exertion and not consistent with the pain of myocardial ischemia, likely due to non-cardiac conditions; and asymptomatic, no angina symptoms .Non-invasive testing included exercise electrocardiogram stress test (ETT), stress echocardiogram (SE), myocardial perfusion imaging (MPI), and Coronary CT angiogram (CCTA). Non-invasive testing results were taken as positive, negative, or indeterminate. In addition, risk stratification of positive NIT into high, intermediate, and low risk was done. In patients with a positive stress test, a Duke Treadmill score of \u22655 was taken as low risk, a score between \u201310 and +4 as intermediate risk, and a score \u2264\u201311 as high risk. In patients who underwent SE, normal stress echocardiographic wall motion or no change of limiting wall motion abnormalities was taken as low risk, peak segmental wall motion index (peak WMSI) of 1.1 to <1.7 as intermediate, and peak 1.7 or more as high risk. In patients who underwent MPI, summed stress score (SSS) of 4 to 7 was taken as low risk, SSS of 8 to 12 as intermediate risk, and SSS of 13 or higher as high risk.MFRS was computed using parameters of age, sex, smoking status, dyslipidemia, hypertension, and diabetes. As the data was unavailable for parameters, like total cholesterol and high density lipoprotein, the score was imputed as 2 points if the patient had dyslipidemia or was taking statins. Likewise, for unavailability of parameters like systolic blood pressure and the number of medications for hypertension, the score was imputed as 2 points for a man with a history of hypertension or was taking anti-hypertensives and 3 points for a woman with a history of hypertension or was taking anti-hypertensives. The computed score was categorized as low risk (<10%), intermediate-risk (10\u201319%), and high risk (>20%) 13.Appropriate use criteria for diagnostic catheterization was calculated based on the severity of angina, use of anti-ischemic therapy, and NIT findings. Based on the above parameters, each cardiac catheterization procedure was assigned an appropriateness score from 1 to 9. A score of 7 to 9 denoted the patient as an appropriate indication for CAG, a score of 4 to 6 denoted uncertain indication, whereas a score of 1 to 3 denoted inappropriate indication .Non-obstructive coronaries was defined as <50% in the left main (LM) coronary artery and major epicardial vessels 16. StenoMean and standard deviations were reported for quantitative variables and frequency and percentages for categorical variables as a part of descriptive analysis. In addition, the frequency and percentages of NOC were reported. Baseline and procedural characteristics were compared between NOC and MoSOC. The cox-proportional algorithm was employed for univariate and multivariable modeling. Adjusted prevalence ratios (PR) (significance level <0.05) of predictors of NOC, along with 95% confidence intervals (CI), were reported. All statistical analyses were performed using STATA version 16.Approval was taken from THI Institutionalized Review Board (IRB) (THI/IRB/SQ/11-12-2020/082). THI IRB granted a waiver of informed consent and exemption for this study.Out of 25,472 patients who underwent CAG at the THI cath lab over eight years, 2,984 (11.7 %) were analyzed in our study after applying the exclusion criteria .Overall of 2,984 patients undergoing elective CAG, 24% (n = 711) had NOC. Out of patients with MoSOC \u2265 50% stenosis) , 31.6% had a single vessel, 28.8% had two vessels coronary artery disease (2 VCAD) and 39.6% had three vessels coronary artery disease (3 VCAD). Significant LM disease was present in 7% of patients.In the NOC group, patients were more likely to be younger <50 years (28.4% vs. 16.1%) (55.2 \u00b1 10.2 vs. 58.8 \u00b1 9.4 years) compared to the MoSOC group. Also, more women were likely to have NOC (39.9% vs. 18.3%). Diabetes was less common in patients with NOC (42.3% vs. 55.8%) compared to MoSOC patients. A lower proportion of patients underwent CAG due to positive stress tests (25.8% vs. 53.3%) and the presence of chest pain (without positive NIT) (23.4% vs. 26.8%) in the NOC group compared to the No MoSOC group . Also, patients with NOC were more likely to present with atypical/unlikely angina (20.4% vs. 7.4%) or were asymptomatic at presentation (38.7% vs. 21.9%). More patients were categorized as low (48.4% vs. 28.6%) or intermediate risk (36.3% vs. 44.4%) on MFRS in the NOC group compared to the no MoSOC group .NIT was performed in 49% of the patients prior to CAG. Of patients who didn\u2019t undergo any NIT, 32.7% had NOC. Abnormal or positive NIT result was reported in 95.5% of patients who underwent NIT. The majority of patients with positive NIT results had MoSOC (86.8%). Most patients with positive high-risk NIT findings had MoSOC (91.7%) , Table 2In almost 80.5% (n = 2403) of the patients, CAG was classified as appropriate, followed by 17.6% (n = 525) of patients in whom CAG was categorized as uncertain. Patients classified as appropriate on AUC were less likely to have NOC (21% vs. 79%) .The multivariable Cox proportional algorithm results indicated younger age <50, women, heart failure as an indication of CAG, inappropriate stratification on AUC, low and intermediate MFRS, and no NIT or positive low-risk NIT as significant predictors of NOC In this single-center registry from an LMIC spanning an eight year period, among the entire group of patients undergoing CAG, in a large majority (>75%) of patients, the procedure was performed for urgent or emergent indications. Elective CAG in patients without known CAD comprised only 11.7% of the overall diagnostic CAG volumes; of these 2,984 patients, 24% had NOC. Significant predictors of NOC were younger age, female, heart failure indication for the procedure, low and intermediate-risk MFRS, no NIT or positive low-risk NIT findings, and being categorized as inappropriate on AUC for CAG.Coronary angiography is an essential diagnostic test, the role of which in patients with suspected stable ischemic heart disease is to define the presence and pattern of obstructive CAD and help select patients who may benefit from coronary revascularization in addition to background optimal medical therapy. In our study, the proportion of patients without known CAD who underwent non-emergency CAG is much smaller than in other reports. Our study had an 11.7% inclusion rate compared to approximately 21% in the NCDR registry and data from Ontario and VA-CART, with an inclusion rate of 31% and 25%, respectively 89. Addit8617We found obstructive CAD (>70% stenosis) in over 70% of patients without known coronary disease undergoing elective CAG. The frequency of obstructive CAD has ranged from 30% to 52% in the different North American registries, including the overall 38% from the large NCDR data 7. This maWe also found an overall increase in the frequency of NOC findings over the study duration which was accompanied by more patients undergoing CAG with indication of heart failure due to left ventricular systolic dysfunction. This subset makes up nearly half of all the patients enrolled. This finding further endorses one of our previously published data on patients that, with unexplained left ventricular systolic dysfunction as the indication for CAG, 58.8% had any MoSOC, very similar to the 56.5% in the current larger data set . AlthougNon-invasive testing was performed in 49% of our study patients with a decreasing trend over the study duration, comparatively lower than NIT performed in the North American registries 59%\u201384%) 789. This74% 789. T826Our study findings indicated that women, younger age, absence of symptoms, or atypical angina were predictors of NOC. Moreover, low and intermediate risk on MFRS and inappropriate for CAG on AUC were also factors associated with NOC. Additionally, NOC was also associated with positive low-risk NIT findings or no NIT. These predictors are consistent with the published literature 89. Altho8Overall, as compared to US results, our study patients are younger, less likely to be a woman, smoker, having dyslipidemia, obesity, or family history of premature CAD, and twice likely to have diabetes. These findings are very consistent with prior published reports where patients of South Asian origin tend to get the coronary disease at a younger age with two-fold higher diabetes prevalence and are less likely to have other traditional risk factors for CAD 29. CurreTo the best of our knowledge, this is the first study reporting frequency and predictors of NOC in a LMIC setting. The sample is also one of the study\u2019s strengths as it represents the population reporting to tertiary care hospitals for elective CAG.Our study has limitations. First, it is a retrospective single-center study, where interpretation of NIT is done by a cardiologist certified in nuclear cardiology or stress echocardiography with an active peer-review process. Second, analysis of CAG findings is limited to subjective individual physician interpretation. Moreover, due to our database format, percentage of stenosis is reported only for those patients with more than 50% stenosis, hence there is an inability to differentiate between near normal and non-obstructive findings. Third, MFRS might have underestimated the risk of CAD in our study because we imputed values for blood pressure and lipid levels. This was evident from our results as MFRS classified 25.7% of the study population as high risk whereas the 76% had CAD, out of which 28.8% and 39.6% had 2 VCAD and 3 VCAD. It is one of the limitations of our study that the data is just from a single center, therefore the geographical variations of Pakistani population couldn\u2019t be assessed. Lastly, NIT risk stratification couldn\u2019t be assessed for half of the patients included in this study, and we only have the outcome of patients who underwent CAG after abnormal stress test. There is also a lack of data on patients who did not undergo CAG after normal or abnormal NIT results.In our current clinical practice, one in four patients undergoing elective CAG had NOCAD. The number of NOC have increased over an eight year period. Despite the guideline, only 49% of the patients underwent NIT. Preprocedural NIT performed well in risk stratification with a very high yield of obstructive CAD. Yield of CAG can be vastly improved by adjudicating alternate modalities like NIT especially in younger patients, women, patients with heart failure as an indication of CAG, and patients classified as low or intermediate risk on MFRS. Additionally, utility of coronary calcium score and CCTA can also be explored to improve patient selection and preprocedure assessment of disease likelihood."} +{"text": "The Israeli Prison Services implemented a hepatitis C virus (HCV) elimination program in 2020. Inmates considered high risk for HCV were offered serology; HCV-seropositive participants were offered HCV RNA testing. Among participants, 7.0% had detectable HCV RNA and were offered antiviral drug therapy. This program reduced HCV burden among incarcerated persons. In 2019, the Israeli Ministry of Health joined the World Health Organization initiative to eliminate hepatitis C virus (HCV) , which operates 33 prisons and houses \u224814,500 prisoners across the country .We compared HCV-seropositive and seronegative participants. We used the Student Serologic screening was offered to all 2,824 inmates in the IPS who were at high risk for HCV infection; 1,751 (62.0%) opted to be tested and 1,021 (36.2%) declined . Of the Altogether, 80/119 (67.2%) inmates completed antiviral drug treatment during incarceration. Of those followed up after 12 weeks, 97.8% (46/47) had confirmed sustained viral response; the other 33 refused follow-up testing or were discharged from prison.Compared with nonparticipants, the participant group comprised more female inmates, married persons, nonsmokers, IVDUs, and HIV- or HBV-infected persons; participants were also older and had fewer previous incarcerations . InmatesHCV seroprevalence among study participants was 21.6% and detectable HCV RNA was 7.0%. Those prevalences are higher than the estimates of 1.9% seroprevalence and 0.7% HCV RNA-positive in the general population of Israel (The rates of HCV infection among inmates vary widely in different prison populations worldwide. A previous meta-analysis (Older age, being single, having a greater number of previous incarcerations, being born in the former Soviet Union or Romania, and being HBV-positive were risk factors associated with HCV-positive serology among participants in our study. Inmates who had used intravenous drugs had higher rates of HCV-positive serology, as previously published (A total of 67.2% of infected inmates completed antiviral drug treatment during their sentences. That completion rate helped lower the overall HCV burden in IPS and highlights the contribution of the screening program to decrease HCV in prison settings among persons at high-risk for HCV. The IPS plays a critical role in the national efforts to achieve HCV elimination in Israel. In line with the high turnover of inmates who revolve between the community and prisons, the success in reducing HCV burden during incarceration also positively affects the community (The first limitation of this study is that the data were collected from IPS medical files, and we had limited access to community medical records of inmates who were discharged from prison. Thus, antiviral drug treatment outcomes in those cases could not be determined. Second, not all eligible inmates were willing to be screened, which might lead to selection bias. To assess the bias, we compared the characteristics of those refusing to those who were tested and found lower proportions of all individual high-risk criteria among those who declined screening . Thus, tIn conclusion, HCV seroprevalence among inmates at high risk was 21.6% and HCV RNA was detectable in 7.0%. The risk factors associated with HCV-positive serology among inmates included older age, being single, and having more previous incarcerations, as well as other HCV risk criteria, such as IV drug use, being born in former Soviet Union or Romania, and being co-infected with HBV. The IPS-led HCV elimination program achieved a decrease in HCV burden among inmates at high risk for HCV. To achieve national HCV elimination, Israel should strengthen cooperation between IPS and medical insurers in the community."} +{"text": "Healthcare associated infections impose serious challenges to safe and high-quality healthcare delivery, and have been closely associated with poor infection prevention practices. Infection prevention practices are poorly studied in Bangladesh, and no previous studies have examined these practices among healthcare providers of community clinics. The study aimed to assess infection prevention practices and associated factors among healthcare providers of community clinics in the rural area of Bangladesh. A cross-sectional study was conducted among 128 community healthcare providers in the Kurigram district of Bangladesh who were identified from 128 community clinics using a stratified random sampling technique. Data were collected between November and December, 2019 via face-to-face survey using a pre-tested semi-structured questionnaire. Only 37.5% community healthcare providers had adequate knowledge on infection prevention measures, and 39.1% had good infection prevention practices. Community healthcare providers with higher education were significantly more likely to have good infection prevention practices, and good infection prevention practices were associated with availability of hand washing facilities, and of soap in community clinic, and adequate knowledge of infection prevention. Implementation of an effective training program regarding infection prevention, along with adequate supply of infection prevention basic resources, and continuous monitoring and supervision are required to improve the currently faltering infection prevention knowledge and practices among community healthcare providers in Bangladesh. Healthcare associated infections (HAIs) are the most frequent adverse events in healthcare facilities worldwide, and impose major detrimental effects on the quality of clinical services for hundreds of millions hospitalized patients every year affecting approximately 10% in developed countries and 25% in developing countries . In BangThe absence of adequate IP and patient safety practices increases the risk of acquiring HAIs in both healthcare providers and patients , 8\u201310. HThe Centers for Disease Control and Prevention (CDC) and the Healthcare Infection Control Practices Advisory Committee (HICPAC) demonstrated a significant shift in healthcare delivery from the acute, inpatient hospital setting to a variety of outpatient and community-based settings over the past several decades . CompareA cross-sectional study was conducted among CHCPs working at 128 community clinics within five Upazilas (Sub-districts) including Kurigram Sadar, Nageshwari, Bhurungamari, Phulbari and Ulipur in the Kurigram district of Bangladesh. According to the Household Income and Expenditure Survey, Bangladesh Bureau of Statistics (BBS), and World Food Programme (WFP), the Kurigram district is the poorest district in Bangladesh with a recorded 70.8% poverty rate , 24. DatIn the study area, a total of 192 CCs were functionally active during the study period. The sample size was 128, which was calculated using the following sample size determination formula, sampling , 26.Data were collected via face-to-face survey using a pre-tested semi-structured questionnaire. Approximately fifteen minutes spent for each survey. The study was formulated based on the previous studies , 27\u201331 aTo assure the data quality, data collection instruments were pre-tested on 13 CHCPs (10% of the intended sample size) who were drawn from the study area but not included in the actual study. The results and experiences from the pre-test were evaluated for clarity, reliability, accuracy and relevance and changes were made to the instrument by three experts who were knowledgeable in this field. The reliability coefficient for IP knowledge and practice items had a Cronbach\u2019s Alpha value of 0.768 and 0.753 respectively. Data were examined by the principal investigators for completeness and consistency during data collection on a daily basis.The dependent variables evaluated were CHCP\u2019s self-reported IP practices, whereas independent variables included socio-demographic characteristics and existing factors regarding respondent\u2019s community clinics , and knowledge of IP.Respondents\u2019 knowledge regarding IP and self-reported IP practices, findings were categorized using a scoring system in which, the respondent\u2019s correct or incorrect responses to the questions were allocated \u201c1\u201d or \u201c0\u201d points respectively. The total score of knowledge questions was classified into two categories: adequate (> mean) and inadequate (\u2264 mean). Similarly, healthcare providers\u2019 self-reported IP practices were classified into two categories: good (> mean) and poor (\u2264 mean) , 31, 32.p-value of less than 0.2 in the binary analysis were then entered into a multiple logistic regression to control for the effect of potential confounders. The statistical significance was declared as a p-value < 0.05 with a 95% of confidence interval (CI).Statistical analysis relied on the Statistical Package for Social Sciences (SPSS) version 22.0. Descriptive statistics were used to calculate the frequencies, percentages, means and standard deviations of relevant variables. Chi-square tests and Fisher\u2019s exact tests were applied to assess associations between the dependent and independent variables. In addition, binary logistic regressions were employed between dependent and independent variables and those variables with a This study was approved by the Biosafety, Biosecurity and Ethical Committee of the Jahangirnagar University, Savar, Dhaka-1342, Bangladesh and all procedures were performed in accordance with the ethical standards of Institutional research ethics and Helsinki declaration. The objectives of the research were explained to the participants prior to participate in the study and written informed consent was obtained from all participants. Strict confidentiality of information and anonymity to the participants were ensured.In this study, a total of 128 CHCPs were surveyed. The average age of participants was 32.6 \u00b1 3.7 years [SD] and half of the respondents were in the age group between 31 and 35 years old. The majority were male (57.8%) and most were Muslim (96.1%). Among the respondents, 43.8%, 33.6% and 22.7% had bachelors, masters, and higher secondary levels of education, respectively. The vast majority of the respondents\u2019 community clinics had no IP guideline/recommendations/evidence. Only 85.9% reported that soap was always available in their community clinics. Availability of gloves and masks at all times was reported by only 13.3% and 7%, respectively .In this study, only 37.5% of the respondents had adequate IP knowledge. The average knowledge score was 5.17\u00b11.38 [SD], with scores ranging from 2\u20139. Furthermore, only 42.2% of the respondents were knowledgeable that gloves cannot provide complete protection against transmission of infections and only 47.7% recognized that wearing of gloves does not replace the need for hand washing. Among the respondents, 55.5% believed that use of an alcohol-based antiseptic for hand hygiene is as effective as soap and water when hands are not visibly dirty. Furthermore, only 21.9% respondents knew how to prepare 0.5% chlorine solution, while 50% were knowledgeable that safety box should be closed/sealed when three quarters filled .Of those interviewed, 39.1% reported good IP practices. Moreover, only 57.9% CHCPs wash hands with soap/antiseptic before each patient care, and 86.7% wash hands with soap after patient care or contact with body fluids. The frequency of respondents who always used aprons, gloves and masks when splashes and spills of any body fluids were likely was 57.8%, 25% and 7%, respectively. In addition, 7.8% of CHCPs used IP guidelines/ evidence and 55.5% recapped needles before disposing them or preferably placing then in a safety box.Further, 28.9% of the respondents had a preceding history of contact with blood, body fluids or needle stick injury, and among them only 24.3% underwent post-exposure prophylaxis (PEP). The majority of the CHCPs (86.7%) provided health education to healthcare recipients concerning HAIs, but only 25.8% were vaccinated against common viral pathogens. Furthermore, the majority of the CHCPs (96.1%) placed needles or sharps in safety/sharp boxes, and 55.5% disposed of the safety/sharp boxes when they were three-quarters full .2 = 8.541, df = 2, p = 0.014), presence of a hand washing facility , availability of soap in clinic setting and IP knowledge (The IP practices were significantly associated with respondents\u2019 education (\u03c7= 0.002) .p = 0.032 and COR = 5.03, 95% CI 1.62\u201315.63, p = 0.005, respectively) (p = 0.045). Moreover, permanent availability of soap in CCs was 3.7 times more likely to result in more frequent IP practices . Furthermore, CHCPs who had more adequate knowledge about IP, were three times more likely to have more frequent IP practices (p = 0.013) and adequate IP knowledge emerged as significant independent factors associated with more frequent IP practices . The una51\u20136.73) . In the ractices .(i) differences in education: most of the healthcare providers in the aforementioned studies had Diploma/Bachelor/Masters level education in Medicine or Nursing but government of Bangladesh had recruited CHCPs who had at least Higher secondary level of education in science/arts/commerce. These jobs were most suitable for individuals with Diploma of Medical Faculty (DMF), and Diploma in Nursing Sciences and Midwifery degree who studied several courss related to primary healthcare services including community medicine, public health, microbiology, etc. . However, during the recruitment of such prospective CHCPs, the government authorities were not concerned about these issue. Therefore, the lack of academic knowledge generated a significant knowledge gap on several issues of healthcare including IP; (ii) the type of healthcare staff (CHCPs vs. others [Doctor or Nurse]); (iii) difference in the availability and implementation of IP training; (iii) difference in the instrument to categorize IP knowledge. However, lower knowledge rates have also been reported among primary health workers in Nepal (22%) [This study assessed the IP knowledge and practices, and their associated factors among CHCPs in Bangladesh. The findings of the present study show that the majority of the CHCPs scored low on the IP knowledge questions (62.5%), and only 37.5% of the CHCPs had adequate knowledge about IP. The frequency of adequate knowledge is comparatively lower than several previous studies conducted among healthcare professionals in northwest Ethiopia (81.6%) , healthcal (22%) .Our study found that 39.1% of CHCPs had good IP practices, a finding that is commensurate with the findings of a study conducted in Southeast Ethiopia . ComparaNot unexpectedly, IP practices were significantly associated with the level of CHCPs education, availability of hand washing facilities and soap, as well as IP knowledge. In comparison, a conducted among healthcare workers in Northwest Ethiopia found that IP practices were significantly associated with age, sex, marital status, educational status, working experience, availability of personal protective equipment and training on IP methods . SimilarAlthough some previous studies assessed healthcare provider IP knowledge and practice, and showed associations with different factors including socio-demographic factors and IP basic resources and facilities , 18, 36,The study is not without limitations. Indeed, it is limited by the use of self-reported data, which might have influenced the findings through well-known biases . In addiWe herein report important baseline information and related factors concerning several IP practices among CHCPs in Bangladesh. The majority of the respondents had limited IP knowledge and implemented IP practices less frequently. Only 39.1% CHCPs had good IP practices. Indeed, knowledge of IP, education levels, access to hand washing facilities, and availability of soap in CCs were associated with higher engagement in IP practices. Therefore, our findings suggest that healthcare authorities need to pay close attention to IP measures in CCs in order to enhance the quality of healthcare services. Implementation of an effective training program regarding IP, and fulfillment of the necessary IP resources in CCs appears to be a highly desirable, and a relatively not onerous approach that should improve IP practices among CHCPs and consequent outcomes. In addition, government and non-government stakeholders will need to ensure continuous training, monitoring and supervision to improve IP practices among CHCPs.S1 Data(XLS)Click here for additional data file."} +{"text": "Background: Acute appendicitis is a common surgical emergency worldwide, yet data specific to Central America, including Honduras, are limited. This study aimed to investigate the epidemiological, clinical, surgical, and post-surgical characteristics of acute appendicitis in a Honduran general hospital.Methods: A descriptive, quantitative, non-experimental, cross-sectional study was conducted at the Mario Catarino Rivas Hospital in San Pedro Sula, Honduras. The study sample consisted of 100 patients admitted with acute appendicitis from January to April 2022. Data on demographic factors, surgical interventions, appendicitis phases, appendix location, and laboratory findings were collected and analyzed.Results: The mean age of the participants was 28.5 years, with a slight male predominance (52%). Timely surgical intervention was performed in 95% of cases within the first 12 hours. The gangrenous phase was observed in 30% of patients, followed by the perforated (24%), edematous (24%), and suppurative (22%). Retrocecal appendicitis accounted for the majority of cases (66%). Moderate leucocytosis (46%) and severe leucocytosis (39%) were associated with acute appendicitis severity. A higher neutrophil percentage was indicative of complicated appendicitis. Computed tomography was underutilized, with only one patient undergoing the examination.Conclusion: This study provides valuable insights into Honduras' epidemiological, clinical, and surgical characteristics of acute appendicitis. Early surgical intervention and laboratory findings, such as leukocyte count and neutrophil percentage, can aid in assessing disease severity. Further research is warranted to understand the unique aspects of acute appendicitis in Central America and optimize patient management. This study highlights the need for multi-centre studies and long-term follow-up to enhance our understanding of appendicitis in similar populations. Acute appendicitis is the most common surgical emergency globally, with the highest incidence occurring between the second and third decades of life . It invoAccording to the Global Appendicitis Score Initiative, appendicitis incidence has significantly increased in countries undergoing industrial development, while Western hemisphere countries exhibit a decrease in cases. Some countries were excluded from the initiative due to insufficient studies to generalize statistics. Unevaluated regions include Central and South America. Specifically, Honduras was excluded from this global study due to a lack of data .Although acute appendicitis is the most common indication for abdominal surgery worldwide, population data for Central and Latin America are scarce. Consequently, generalizing global data to national realities is necessary. The global annual incidence is 139.54 per 100,000 inhabitants, with a risk of 16.33% in men and 16.34% in women ), obesity (10% [n=10]), T2 diabetes mellitus (6% [n=6]), and hypertension (3% [n=3]). Regarding the acute appendicitis phase, 30% (n=30) were in the gangrenous phase, 24% (n=24) in the perforated phase, 24% (n=24) in the oedematous phase, and 22% (n=22) in the suppurative phase involved open surgery with a McBurney incision , followed by a mid-line infra-umbilical incision . The most common complication was localized peritonitis . Concerning appendix location, 66% (n=66) were retro-cecal, 9% (n=9) were pelvic, 25% (n=25) were in other positions, and 1% (n=1) were para-ileal.3), 39% (n=39) had severe leukocytosis , and 15% (n=15) had a normal leukocyte count . Regarding neutrophil percentage, 58% (n=58) had a percentage of 83% to 96% (indicating complicated appendicitis), 25% (n=25) had a value of 76% to 82% (uncomplicated appendicitis), and 17% (n=17) had a normal percentage (56% to 75%). In total, 43% (n=43) presented a neutrophil-lymphocyte index of 9 to 89 associated with complicated appendicitis, 42% (n=42) presented a range of 4-8 associated with uncomplicated appendicitis, and 15% (n=15) of patients showed a normal range with values of 2 and 3 had a moderate leukocyte count of patients did not undergo an examination. Among those examined, 20% (n=20) showed no alterations, 11% (n=11) displayed leukocytosis, and 1% (n=1) tested positive for leukocytes and nitrites. Regarding abdominal ultrasounds, 65% (n=65) did not undergo this examination. Of those examined, 17% (n=17) presented a non-compressible appendix with double wall thickness and a diameter greater than 6 mm, 5% (n=5) presented fluid in the right lower quadrant, and 3% (n=3) presented pain upon compression. As for computed tomography use, only one patient (1%) underwent this examination, which revealed peri-appendicular fat deformation and/or appendicular wall enhancement.In our study, the mean age of participants was 28.5 years, aligning with the global trend of acute appendicitis being more prevalent among young adults . The ageRegarding gender distribution, our study found a slightly higher proportion of male patients (52%), compared to female patients (48%). This finding is in line with previous studies reporting a slightly higher incidence of acute appendicitis in males . HoweverThe majority of patients in our study 95%) underwent timely surgical intervention within the first 12 hours. This is a crucial factor in reducing the risk of complications, such as perforation, which can lead to more severe consequences like intra-abdominal abscesses or generalized peritonitis 5% underw and the In terms of the phases of acute appendicitis, our study found that 30% of patients were in the gangrenous phase, 24% in the perforated phase, 24% in the edematous phase, and 22% in the suppurative phase. The distribution of appendicitis phases in our study is similar to results reported in other regional studies . This unRegarding appendix location, our study found that 66% of cases were retro-cecal, which aligns with previous research reporting a higher prevalence of retro-cecal appendicitis . This inOur study also showed that 46% of patients had a moderate leukocyte count and 39% had severe leukocytosis, indicating an association between leukocyte count and the severity of acute appendicitis. This finding is consistent with other studies that have reported a correlation between leukocyte count and appendicitis severity . The neuIn conclusion, this study highlights valuable insights into acute appendicitis's clinical characteristics and management, emphasizing the importance of early surgical intervention to prevent complications. The high neutrophil percentage can serve as an indicator of complicated appendicitis. By understanding the specific characteristics of acute appendicitis in this population, healthcare professionals can better identify high-risk individuals, optimize treatment strategies, and ultimately improve patient outcomes. The study's limitations should be considered, such as its single-centre design, limited sample size, confounding factors, and lack of follow-up data. Future multi-centre studies and longer-term patient follow-up could provide additional insights into appendicitis in Honduras and similar demographic settings."} +{"text": "Unhealthy habits and poor diet patterns are significant concerns among adolescents, impacting their overall quality of life. This study aimed to assess and improve these habits in adolescents.This is a cross-sectional study conducted in 2017\u20132018 in Karachi. The research participants, aged 11\u201317 years, were drawn from lower-middle-income secondary schools using multistage random selection. Sociodemographics, the Physical Activity Questionnaire for Adolescents (PAQ-A), and breakfast consumption were determined through questionnaire and a food frequency survey.A study of 334 school-going adolescents in Karachi, Pakistan, found that 82% consumed breakfast daily, with chapatti being the preferred choice (72.2%). Physical activity levels varied, but 56.6% engaged in regular activity. No significant differences were found in breakfast consumption by age or parental education.Understanding South Asian adolescents\u2019 breakfast habits is crucial. Promoting healthier breakfast options and increased physical activity are recommended for long-term well-being, with further research needed for targeted interventions. Breakfast is considered the most important meal of the day; it plays an integral role in a balanced diet for an individual. Skipping breakfast among adolescents may lead to nutritional deficiencies and poor nutritional status. Information regarding breakfast patterns may help in improving unhealthy breakfast habits and enhance the overall diet patterns of adolescents, thereby improving their quality of life .During the growth and development of an individual from childhood to adulthood, an intermediate period of drastic changes occurs, which is defined as adolescence. It is the most critical period of time that requires intensive mental and physical care for an individual. More specifically, physical growth, mental development, and physiological and psychological changes occur at their peak between the shifts from childhood to adulthood. Ultimately affecting the nutritional demands, while at the same time environmental influences, changes in behaviour, and emotional distress also influence the dietary habits .Nutritional demands are primarily dependent on eating preferences and meals . AnthropMany studies have identified the role of breakfast in enhancing cognition and academic achievements. Regular breakfast is associated with optimal nutritional demand and ultimately satiates the energy demands for mental and physical problem solving, thus improving the level of cognition in those adults . At thisPhysical activity is closely linked to breakfast consumption, as it provides the body with the energy and nutrients needed for sustained activity. Skipping breakfast can lead to decreased energy levels, fatigue, and difficulty concentrating, making it more challenging to be physically active . StudiesMost of the studies suggest a strong correlation between missing breakfast and increased body weight, increased junk food intake, and a high-fat diet at inappropriate times in the day . UnhealtStudies reported that adolescents like \u201cready-to-eat\u201d foods that are already prepared by someone else at home and are usually influenced by choices among peers and other family members. Regarding the food choices of adolescents, other views suggest that cultural trends, socio-economic status, and family influence are major determinants of choice rather than personal perceptions or taste .The discussion focuses on Karachi, the largest city in Pakistan and the sixth-largest in the world by population. Despite its economic and cultural importance, the city faces challenges such as poverty, crime, pollution, and traffic congestion. The Economist Intelligence Unit (EIU) ranked Karachi as the 10th least liveable city globally, affecting stability, healthcare, education, infrastructure, and access to basic services. Access to healthy food is a significant concern for many adolescents in Karachi, compounded by factors like poverty, lack of education, and cultural norms. Nutrition and diet patterns are crucial for health and well-being, and Pakistan's economic situation, health outcomes, and food security influence these patterns .This study investigates breakfast patterns among school adolescents in Karachi, Pakistan, focusing on their relationship with physical activity. It analyses daily consumption, food preferences, and potential links to physical activity, considering sociodemographic factors. The findings can inform targeted interventions to promote healthier habits and physical activity, benefiting the overall well-being of adolescents in the region. Limited research on breakfast consumption patterns among Pakistani adolescents is needed to improve unhealthy habits and enhance overall diet patterns, ultimately improving adolescents' quality of life.In order to account for predicted dropouts and cases with missing data, the sample was inflated by over 30%. Study population was selected using multistage random sampling from six districts of Karachi. One town from each district and a random selection of two schools were made from each of the six randomly chosen union councils (UC). The participants, aged 11\u201317 years, grades 6\u201310th, were enrolled based on probability proportional to the enrolment size of each class and school after getting permission from the school administration. Before the sample was finalized, parental written approval was acquired. Strict confidentiality was maintained before the data collection. The study was conducted from November 2017 to November 2018. The sample size of 334 adolescents was determined with a 95% confidence interval, calculated using the OpenEpi calculator.This study involved students aged 11\u201317 years, both boys and girls, with signed parent consent. To maintain the integrity of the study\u2019s findings and ensure participant safety, specific selection criteria were applied, participants were expected to be in good general health and not have clinically significant medical abnormalities. Exclusion criteria excluded individuals with a history of serious, chronic, or unstable illnesses or medical disorders deemed unsuitable for study participation. This included conditions that could potentially confound the study's outcomes or pose a risk to the participant\u2019s well-being.A pretested questionnaire that was translated into the local language and used to gather the data asked participants for personal information, sociodemographic data, tobacco and betel nut use, and information about their parent\u2019s education were also noted.The participants' dietary data, anthropometric measures, and food preference data were collected using the 80-item Food Frequency Questionnaire (FFQ) . To assiThe Physical Activity Questionnaire for Adolescents (PAQ-A) were used which consists of a series of questions related to their participation in physical activities. Prior to each anthropometric measurement, the scale was reset to zero. Belts, bulky outerwear, and shoes were taken off. Height was measured with a portable stadiometer Seca 213). Participants positioned their arms alongside them, aligned their heels, buttocks, and upper back with the scale, and kept their heads in the Frankfort plane while standing on the stadiometer. A portable bioelectric impedance analysis (BIA) device (Omron BF508) was used to assess weight (to the nearest 0.1 kg) and BF% [. ParticiAccording to the World Health Organization (WHO) standards, the body mass index (BMI) was utilized to assess children\u2019s weight status. Those falling below the fifth percentile were categorized as 'underweight', while a BMI greater than or equal to \u2212\u20091 standard deviation (SD) for the same age and gender was considered 'normal weight'. 'Overweight' encompassed BMI greater than or equal to\u2009+\u20091 SD but less than the 85th percentile, and \"obese\" included BMI exceeding\u2009+\u20092 SD or surpassing the 95th percentile for children of the same age and gender, providing distinct weight status classifications based on BMI measurements .After this, participants were asked to choose their choices from the list of five food groups that are dairy group, grain group, fat group, fruits/vegetable and fruit juices group, and meat and poultry group. The FFQ will also include a specific question to assess breakfast consumption patterns. Breakfast will be defined as any food or drinks consumed before the first school break .p-value\u2009\u2264\u20090.05.Data analysis was performed using SPSS version 24. Descriptive statistics were calculated for demographic information about children like age, gender, parent\u2019s educational status, physical activities, substance abuse, and BMI. For quantitative study variables, the mean and standard deviation were calculated, and for qualitative study variables, frequency and percentages were computed. The study outcome 'Breakfast consumption' was presented in a bar diagram with frequency and percentages, and the frequency of food item preference was also presented in frequency and percentages. A Chi-square test was applied to observe the statistical significance between breakfast consumption and other study variables, with the statistical significance set at a The study adhered to ethical guidelines, ensuring the confidentiality and privacy of participants\u2019 data. Ethical review board approval from Dow University of Health Sciences was obtained before the commencement of the study.A total of 334 participants were included in the study, out of which 29.6% (99) were younger adolescents, and 70.4% (235) were older adolescents, and the gender distribution was 42.5% 142) males and 57.5% (192) females. The demographic characteristics of the study are presented in Table 42 males While the educational status of the mothers of the study participants showed 17.4% (58) had no formal education, 9% (30) had completed primary education, 7.8% (26) had done secondary schooling, 21.9% (73) were matriculated, 15.3% (51) had done intermediate, and similar numbers had completed graduate studies.Using PAQ-A, a straightforward question regarding engaging in regular physical activity, participants were asked to rate their physical exercise behaviour. 56.6% (189) of the participants said they engaged in regular physical activity, 17.4% (58) reported they did sometimes, and 26% (87) stated they did not.BMI categories for participants were determined using BMI values calculated from weight and height measurements. These categories were based on age- and gender-specific BMI percentiles recommended by health organizations like the WHO. Underweight participants fell below the 5th percentile, normal weight individuals were between the 5th and 85th percentiles, and overweight or obese participants were at or above the 85th percentile. Consequently, 20.7% were underweight, 69.8% had a normal BMI, and 9.6% were overweight or obese.The frequency of daily breakfast consumption was reported by 82% (274) participants, and the remaining did not consume breakfast on a daily basis Fig.\u00a0. We haveThe majority of children (72.2%) considered chapatti a primary and main meal for breakfast. 75.7% use baked bread for breakfast. Rusk was a popular choice for breakfast among 60.8% (203) participants. Whole wheat and refined flour were also used by 38.3% (128) and 74.3% (248) children. Puri was consumed by 72.8% (243), porridge by 29.6% (99), cereal by 16.2% (54), beans by 76.3% (255), and lentils by 87.7% (293) were considered a good source of breakfast. In addition to this, tandoori naan was also preferred by 83.2% (278) of participants. The pattern of preference also depended on the socio-economic status of the participant.In dairy products, whole milk consumption was preferred by 36.2% (121), milk without cream 35.6% (119), milk powder 21% (70), only cream 43.7% (146), yoghurt 80.8% (270), sweet lassi 59.3% (198), and saltish lassi 34.7% (116) of the participant in the study. The most preferred dairy products were yoghurt, milk, and lassi in this study. While in fat, margarine or butter was the only choice, which was preferred by 68.6% (229) participants.Assessment of preference for consuming fruits and vegetables among the students showed that 69.2% (231 participants) preferred consuming mixed vegetables, 80.5% (269) preferred potato bhujiya, and more than 80% of the students preferred to have fruits in breakfast, the same as for fruit drinks like juices/shakes, etc.In meat/poultry and seafood, participants who preferred to have red meat in the breakfast, 88% 294), chicken meat was 92.2% (308), fish/seafood was 76.3% (255), and 83.2% (278) of them preferred to keep eggs in their breakfast routine. In other foods, 83.5% (279) participants took bakery items, 86.5% (289) participants consumed tea (brewed), and 60.5% (202) participants preferred using honey/jam or jelly in the breakfast . Out of the total, 13.4% male participants and 21.4% female participants skipped breakfast, which also showed the non-significant effect of gender on skipping breakfast . A comparison between breakfast consumption and a parent\u2019s education status showed no significant association , respectively. 15.9% of participants who were physically active skipped breakfast, whereas 27.6% of those who were sometimes physically active skipped breakfast and 16.1% of those who were physically inactive skipped breakfast in their routine life. Substance abuse also showed an insignificant association . Body mass index and breakfast consumption status showed that 11.6% of underweight participants skipped breakfast, 79.8% with normal BMI, and 84.4% of overweight participants consumed breakfast daily with an insignificant effect . Further, it was observed that skipping breakfast was nearly always associated with being younger, a girl, having low educational status, and having an occasional physical activity pattern showed some non-significant trends, with physically active and overweight participants more likely to consume breakfast regularly.Our study also sought to explore the relationship between breakfast consumption and physical activity among adolescents. We observed that the majority of participants (56.6%) reported engaging in regular physical activity, while 17.4% were occasional participants, and 26% had no physical activity routine. While the study did not find a statistically significant association between physical activity and breakfast consumption, trends suggest that physically active individuals were more likely to consume breakfast regularly. This observation underscores the potential benefits of promoting both physical activity and healthy breakfast habits among adolescents.In line with the results of the study, numerous studies around the world also showed breakfast consumption has increased, which might be due to a variety of factors like the availability of different foods for breakfast and awareness from social media, which may have played an important role in having breakfast . On the Moreover, a survey conducted in Canada also reported that school children skipped breakfast due to a lack of parental education . SimilarIn the current study, more boys consumed breakfast as compared to girls. The results are analogous to a study conducted in Punjab, where more boys tend to eat breakfast as compared to girls . Boys feThe study reveals that school children in Pakistan prefer lentils with tandoori naan for breakfast, as they differ from western culture's preference for cereals and whole bread. Additionally, 86% of school children had tea with milk, indicating that tea is more common in the east, while western children prefer semi-skimmed milk. This highlights the cultural differences in food choices among children .Furthermore, the results also showed that sociodemographic factors did not have any effect on breakfast consumption. It can be said that breakfast consumption by school children is entirely an individual\u2019s choice. Hence, the present study did not show any significance .The study on breakfast consumption and physical activity among Pakistani adolescents has limitations, as it did not explore the broader aspects of quality of life. Future research should focus on assessing breakfast habits and physical activity patterns. The study highlights the need for more research on Pakistani adolescents, as breakfast is the most important meal of the day and contributes to a healthy lifestyle. The findings have significant implications for public health policy and interventions, emphasizing increasing awareness of breakfast's importance, providing access to healthy options, and addressing underlying factors like poverty, gender inequality, and food insecurity.Although there are various studies in Pakistan regarding breakfast patterns, the current study showed basic food choices among school children, and there is no significant association with any of the demographic characteristics. School children should be counselled to adopt healthy food choices for breakfast. There should be measures to prevent unhealthy eating during breakfast, and parents should be targeted for this health promotion \u201324.More focus should be given to breakfast intake among older students in secondary schools, though, as rates of breakfast consumption decline throughout childhood and adolescence. The number of kids skipping breakfast can be greatly reduced through school meal programmes. Families should also be the focus of the campaign because family mealtimes are crucial for developing good eating habits in adolescents. Interventions should emphasize the inclusion of fruit, vegetables, and drinks while encouraging a high-quality breakfast.The study on breakfast consumption patterns among adolescents has limitations, including a small sample size of 334 participants, self-reported data collection, potential recall bias, and cross-sectional design. It also lacks information on overall dietary intake beyond breakfast, potential confounding factors, and self-selection bias in participation. Despite these limitations, the study provides valuable insights into breakfast consumption among adolescents, but further research with larger, more diverse samples and longitudinal designs is needed to gain a more robust understanding of this important health behaviour. Therefore, we recommend conducting more studies on this crucial topic and promoting health for the benefit of our young population.The study provides valuable insights into the breakfast habits of adolescents in this region. The findings indicate that a significant percentage of participants consumed breakfast daily, with chapatti, baked bread, and yoghourt being popular choices. The study did not find significant differences in breakfast consumption based on age or gender, but physical activity and BMI showed some non-significant trends, suggesting a potential relationship between regular breakfast consumption and healthier lifestyle habits. Overall, this study focused on food choices that were not previously studied in Pakistan. However, it is important to acknowledge the study's limitations, such as a small sample size, self-reported data, and cross-sectional design, which may impact the generalizability and causality of the results. Nonetheless, this research serves as a foundational step in understanding the relationship between breakfast patterns and physical activity among school adolescents in Karachi, Pakistan, and underscores the need for further exploration in larger, more diverse samples using longitudinal designs to establish robust conclusions and inform effective interventions promoting healthy behaviours in this population."} +{"text": "Discharging against medical advice (AMA) can have significant, detrimental effects on burn patient outcomes. Prior studies in non-burn injured patients have found that patients who leave AMA have a higher risk for adverse 30-day and 12-month outcomes, as well as higher hospital readmission rates and healthcare expenditures, in comparison to patients who are discharged to home in a conventional manner. The goal of this study is to identify risk factors for burn patients who left AMA and suggest solutions to mitigate these factors.Data was collected at a Level 1 Trauma Center over a 15 year period (2007-2022). Patients who left AMA from the burn center were identified using discharge patient codes. Demographic information was collected, including: age, sex, past medical and substance use history, insurance status, and language barriers. Additional information was recorded, including: time to presentation, mechanism of injury, total body surface area (TBSA) burned, burn depth, number of ICU days, length of stay, treatment, consultant teams, readmission and/or known complications after leaving the hospital. Descriptive statistics were used to determine potential trends within this patient population.Over 2007-2022, 37 patients were identified as having left AMA from the burn unit. The average patient age was 37-years-old. Of those who left AMA, 64.9% were male and 70.2% were identified as having a substance abuse history. The majority (51.4%) had Medicaid or State health insurance, 29.7% had no insurance, and 18.9% had private insurance. In regards to the type of injury, 43.2% presented due to a frostbite injury, with the majority of AMA patients sustaining a < 1% TBSA burn. Most (83.7%) had social work and/or case management involved during their admission and all (100%) had their involvement if the length of admission was greater than one day. Almost half (48.6%) returned to the ED within 2 weeks with complications relating to pain, need for dressing change, or infection.Leaving AMA is associated with greater patient morbidity, including higher rates of hospital readmission and subsequently, higher healthcare expenditures. This study found that burn patients leaving AMA were more likely to suffer from small (< 1% TBSA) burns, often related to frostbite injuries. These patients were more likely to have substance abuse, a psychiatric history, and the majority had Medicaid or state health insurance. Recruiting interdisciplinary care members, including social work, psychiatry, and addiction medicine, early may help these patients by encouraging completion of their hospital care and setting up crucial follow-up care.Recruiting interdisciplinary team members to meet with patients at higher risk for leaving AMA, including those with small burns, substance use history, or psychiatric diagnoses may be useful to help lower the incidence of AMA discharges within the burn unit."} +{"text": "Tracheal aspirates (TAs) are collected on mechanically ventilated patients to aid in diagnosis of tracheitis or ventilator associated pneumonia. Accuracy of TA cultures to diagnose lower respiratory tract infections is low, limited by normal respiratory flora contamination, making interpretation difficult. To aid diagnostic stewardship efforts, we analyzed TA order indications to better understand why TA cultures were ordered and which indications were associated with a clinically significant culture result.Order indications for TA specimens were implemented in Sept. 2021 at Children\u2019s Hospital Colorado. At least one indication was required at the time of order placement, Table 1. We extracted all TA orders from Sept. 2021 to Aug. 2022, as well as demographics, collection department, and Gram stain/culture results.1,439 tracheal aspirate specimens were ordered for 496 unique patients. 34% were collected in the Emergency Department (ED), 22% in the Neonatal Intensive Care Unit (NICU), and 20% in the Pediatric Intensive Care Unit . The two most common order indications were increase in secretions (37%) and increase in ventilator support (36%). 296 (22%) cultures grew 1 or 2 predominant organisms, with the most common indication being increased secretions; 57% of these cultures grew respiratory pathogens. Overall, 42% of cultures grew normal respiratory flora and 12% had no growth. For cultures with no growth and those with no organisms on Gram stain, the most common indication was increase in ventilator support. For all order indications, 50% or more grew normal respiratory flora with abnormal chest imaging and fever having the most cultures with 1 or 2 predominant organisms.The majority of TAs are collected in the ED, NICU or PICU. The most common order indications were increase in secretions or increase in ventilator support. The most common order indication that was noted in actionable cultures (1 or 2 predominant organisms) was increased secretions, though order indication was not predictive. These results have informed potential Gram stain rejection criteria to improve diagnostic yield for clinically relevant pathogen detection.Sarah A. Jung, PhD, Abbott Molecular Inc: Research support|DiaSorin Molecular: Research|Karius: Advisor/Consultant|Karius: Industry talks at two conferences Samuel R. Dominguez, MD, PhD, Biofire Diagnostics: Advisor/Consultant|Biofire Diagnostics: Grant/Research Support|Cobio Diagnostics: Board Member|Karius: Advisor/Consultant|Pfizer: Grant/Research Support"} +{"text": "Obesity is a major public health problem and some developed countries have declared it \u2018the modern day epidemic\u2019. One of the major eating disorders that leads to obesity is BED, which involves consuming large quantities of high carbohydrate food. Studying the factors that cause and contribute to BED can help tackle this major health hazard and alleviate a huge burden on the nationalized health service.To determine the frequency of Binge Eating Disorder (BED) among obese adults, and to study its relationship to depression, anxiety, life stressors, personality and self esteem.The sample was a randomised sample of clinically obese individuals, body mass index (BMI) of 30 and above. The sample was collected from two sites; Nutrition Clinic in Student\u2019s Hospital, Cairo University and a Private Nutrition Centre. 250 cases were recruited over one year. All patients were subjected to a clinical interview derived from Kasr El Aini sheet , and measurement of Waist- Hip Ratio. Assessment of depression and anxiety was through Beck Depression Inventory , Hamilton Depression Rating Scale and Taylor Manifest Anxiety Scale(TMAS). Other tools used were the Eysenck\u2019s Personality Inventory, Eating Disorder Inventory -2.BED among obese adults was 48%; 83 % of them had drive for thinness, 25% were bulimics, 45 % had ineffectiveness feeling. Also 83 % had body dissatisfaction, 8% were perfectionism seeking, 43 % showed interpersonal distrust and 25% presented maturity fears. Impulsivity was scored high in 25% , 66.6%had social insecurity and 77% had severe Extraversion. All were statistically significant. On the other hand there were no statistical significant difference between obese adults with BED and those without on TMAS. Half percent of participants with BED and 34.6 percent of participant without BED had moderate level of anxiety. In addition , there were no significant difference between obese participants with BED and those without BED according to BDI. However, 83.3% of obese cases with BED while 60 % for those without BED had manifest depression ranging from mild to severe depression.Obese adults with BED have more drive for thinness, body dissatisfaction, feeling of ineffectiveness, perfectionism seeking, interpersonal distrust, maturity fears and social insecurity than non BED. Extraversion and Neuroticism are also more among BED. There were no significance different between both group in relation to Anxiety and Depression.None Declared"} +{"text": "Recent randomized clinical trials have shown that risedronate reduces the risk of nonvertebral fractures and clinical vertebral fractures within 6 months of initiating treatment. The objective of the current study was to determine whether this early antifracture effect could be demonstrated in nonvertebral fractures for risedronate and other osteoporosis therapies in an observational administrative claims database.A proprietary administrative claims database was used to identify managed care members who received a new prescription for risedronate, alendronate, or nasal calcitonin from July 1, 2000, to December 31, 2001. Patient records were analyzed for the incidence of nonvertebral fractures in the first 6 and 12 months following initiation of treatment. A Cox proportional hazards regression model was used to estimate relative risk (RR) of fracture at 6 and 12 months.In the 6-month analysis, 774 patients (11%) received calcitonin, 5,307 (75%) received alendronate, and 1,000 (14%) received risedronate. Twelve-month data were available for a subset (71%) of patients . Most were women (93%); mean age was similar for alendronate and risedronate, and nasal calcitonin patients were about 3 years older, on average. Risedronate and alendronate patients were more likely to have used estrogen, while nasal calcitonin patients were more likely to have been hospitalized and had higher use of concomitant medications and more physician visits. Relative risks were adjusted for these differences. Risedronate and alendronate patients were similar with respect to these indicators of general health status. In the 6-month analysis, nonvertebral fractures were observed in 2.2% of patients receiving nasal calcitonin, 1.4% of patients receiving alendronate, and 0.6% of patients receiving risedronate. The adjusted RR reduction was 69% for risedronate versus calcitonin , 54% for risedronate versus alendronate , and 26% for alendronate versus calcitonin . In the 12-month analysis, nonvertebral fracture rates were 2.9% for nasal calcitonin, 2.4% for alendronate, and 0.9% for risedronate patients. The adjusted RR reduction was 75% for risedronate versus calcitonin , 59% for risedronate versus alendronate , and 25% for alendronate versus calcitonin .This analysis of medical and pharmacy claims contained in an administrative database confirms the early fracture reduction with risedronate that was shown in randomized clinical trials. Risedronate was more effective than calcitonin in reducing the risk of nonvertebral fractures within the first 6 months of treatment. Risedronate was more effective than either calcitonin or alendronate in reducing the risk of nonvertebral fractures within 12 months of treatment."} +{"text": "Free sugars are a major source of calories in diets and contribute to the burden of many non-communicable diseases (NCDs). The World Health Organization (WHO) recommends reducing free sugars intake to less than 10% of total energy. This study aimed to estimate the number of diet-related NCD deaths which could be averted or delayed if Canadian adults were to reduce their calorie intake due to a systematic 20% reduction in the free sugars content in foods and beverages in Canada. We used the Preventable Risk Integrated ModEl (PRIME) to estimate the potential health impact. An estimated 6770 (95% UI 6184\u20137333) deaths due to diet-related NCDs could be averted or delayed, mostly from cardiovascular diseases (66.3%). This estimation would represent 7.5% of diet-related NCD deaths observed in 2019 in Canada. A 20% reduction in the free sugars content in foods and beverages would lead to a 3.2% reduction in calorie intake, yet an important number of diet-related NCD deaths could be averted or delayed through this strategy. Our findings can inform future policy decisions to support Canadians\u2019 free sugars intake reduction, such as proposing target levels for the free sugars content in key food categories. Similarly to global trends, 88% of all deaths in Canada are due to non-communicable diseases (NCDs), with cardiovascular diseases (CVDs), cancer, and diabetes responsible for 59% of all deaths . The preAn unhealthy diet is one of the major preventable risk factors for a range of NCDs . A healtmonosaccharides and disaccharides added to foods and beverages by the manufacturer, cook or consumer, and sugars naturally present in honey, syrups, fruit juices and fruit juice concentrates\u201d .,35.30,35Canadian free sugars and calorie intakes, stratified by DRI age\u2013sex groups, under the actual (baseline) and counterfactual (reformulation) scenario were estimated using both available days of 24 h recalls from CCHS Nutrition 2015. Usual nutrient intake distributions were determined using the National Cancer Institute (NCI) method . BalanceIn the present study, population demographics and the most recent available data (2019) on mortality associated with CVDs , cancers , diabetes, chronic renal failure, and liver disease\u2014stratified by sex and five-year age bands\u2014were obtained from the publicly available Statistics Canada CANSIM tables ,52,53,54p-value < 0.05 was considered statistically significant. For this study, mean height and BMI were calculated for the same sample included in both the baseline and counterfactual scenario (CCHS Nutrition 2015). Previous research on both the 2004 and the 2015 cycles of CCHS Nutrition has shown that adult women tend to underreport their weight, and adult men tend to overreport their height. To mitigate the introduction of these systematic biases into the analyses, BMI correction factors provided by Statistics Canada were used in this manuscript to generate respondents\u2019 BMI and height from self-reported values, if measured values were not available . The finAll required data were inputted into PRIME. The model estimated changes in the annual number of deaths attributable to the diet-related NCDs under study between the baseline and the counterfactual scenario. Monte Carlo analysis, built into PRIME, was performed at 10,000 iterations to estimate 95% uncertainty intervals (UIs) around the results (based on the 2.5th and 97.5th percentiles). This allowed the epidemiological parameters to vary randomly according to the distributions reported in the literature . The PRIME estimated that overall, 6770 (95% UI 6184\u20137333) diet-related NCD deaths could be averted or delayed by reducing Canadian adults\u2019 calorie intake as a result of a systematic 20% reduction in the free sugars content in packaged foods and beverages . From total deaths that could be prevented or delayed, 66.3% (4491 [95% UI 3999\u20134953]) are related to CVDs, followed by diabetes 14.1% (954 [95% UI 734\u20131083]), cancers 11.5% (781 [95% UI 609\u2013958]), liver disease 5.2% (351 [95% UI 188\u2013471]), and chronic renal failure 3.2% (218 [95% UI 85\u2013307]) .When looking individually at each disease, we observed the greatest sex differences for ischemic heart disease, where the difference between men (1593 [95% UI 1401\u20131774]) and women (806 [95% UI 534\u20131047]) almost doubles. Furthermore, 33.9% of potential deaths averted or delayed would be in people under 75 years old, affecting significantly more men (1545 [95% UI 1415\u20131661]) than women (752 [95% UI 659\u2013834]) .The model estimated that the changes in calorie intakes between the baseline and counterfactual scenario would impact 13 of the 23 diet-related NCDs included in this analysis. To put our results in context, in 2019, there were a total of 90,035 deaths due to these 13 diet-related NCDs in Canada ,52,53,54The current study, to the best of our knowledge, is the first modeling study to estimate the potential health impact of reducing calorie intakes through a systematic 20% reduction in the free sugars content in food and beverages in the Canadian food supply. As a result of this simulated food reformulation scenario, Canadians\u2019 overall mean intake of free sugars would fall from 56.2 g/day (12.1%TE) to 44.9 g/day (10.0%TE), resulting in a reduction in overall calorie intake of 60 calories (\u22123.2%) . If suchThe current literature demonstrates that most of the adverse health effects associated with an excess intake of free sugars are mediated to some extent by their energy contribution ,16,17,58In Canada, a previous modeling study estimated that, over 25 years, 7874 95% UI 6630, 9118) deaths could be postponed by implementing a 20% SSB tax . The sim0, 9118 dIn Canada, evidence demonstrates that, although there has been little effort to reduce overall sugars content through food reformulation between 2013 and 2017, some foods still presented significant reformulation of their free sugars content (with a median decrease of 19%) . BeveragThe present study has strengths and limitations. Estimated intakes in the counterfactual scenario were calculated using nutrient data derived from a reformulation scenario that wasThe baseline and counterfactual intake scenarios were estimated from a nationally representative sample of the Canadian population (CCHS Nutrition 2015) . Given tFurthermore, our counterfactual scenario takes into account substitution effects at the food composition level . HoweverTo estimate the number of diet-related NCD deaths that could be averted or delayed in Canada, we used PRIME, which uses relative risks from robust meta-analyses, and which has been widely used in different countries , includiFinally, implementing target levels for the free sugars content in key food categories in addition to other proposed initiatives in Canada that aim to improve the food environment, such as FOPL and restrictions on food marketing to children ,68, coulThis study provides evidence of the potential health gains from reducing intakes of calories from free sugars as a result of reducing the free sugars content in foods and beverages in Canada. Our results show that a 20% reduction in the free sugars content in foods and beverages could lead to a 3.2% reduction in calorie intake, and 7.5% of diet-related NCD deaths could be averted or delayed in Canada. Our findings can inform future policy decisions to support Canadians\u2019 free sugars intake reduction, such as proposing target levels for the free sugars content in key food categories."} +{"text": "Improving children\u2019s motor competence through school-based physical activity interventions may be a mechanism for promoting positive mental health through psychosocial factors. Move Well, Feel Good (MWFG) is a such an intervention that was co-designed with children, class teachers, physical education (PE) teachers, and school leaders. This presentation describes the feasibility evaluation of MWFG.Five primary schools were recruited from a low socioeconomic status community in northwest England. A 10-week intervention was co-designed which aimed to enhance children\u2019s mental health through motor competence and psychosocial development. The core delivery of the programme involved one PE lesson per week devoted to development of locomotor, object control, and stability skills. This was supplemented by optional recess and home activities, and by non-PE curricular activities. Teachers were asked to record details of each MWFG session taught, and feasibility was evaluated against pre-defined criteria using surveys, interviews (teachers), and participatory focus groups (children). Pre- and post-intervention assessments of motor competence, mental health, wellbeing, psychosocial factors, and 24-hour movement behaviours were also completed.The 5 schools represented 83% of the target number of schools and 108 children consented (43% of target). PE and class teachers were recruited in all schools (100% of target). Intervention dose was reflected by 76% of scheduled PE lessons being delivered. Adherence was strong with >85% of children attending \u226575% of lessons. Positive indicators of acceptability were provided by 86% of children, 83% of PE teachers, and 90% of class teachers. Teachers commented on the children\u2019s positive engagement irrespective of ability, the quality of resources provided, and the challenges of competing demands for curriculum time and spaces to deliver MWFG. The data collection methods were deemed acceptable by 91% of children and 80% of class teachers, and children spoke positively about participating in the data collection. Secondary outcome data collection was completed by 87%-100% of children, with a 0%-6% attrition rate at post-intervention. Descriptive analysis revealed favourable changes in motor competence and mental health.MWFG was deemed to be feasible to develop further into a pilot trial, with improved school and child recruitment strategies warranted."} +{"text": "Nearly one million patients undergo hip or knee replacements in the United States every year This number is expected to double by 2030. The rate of prosthetic joint infection (PJI) ranges from 0.5 to 2% which translates to between 50,000 to 200,000 PJIs annually. Prosthetic joint infections have high rates of morbidity and mortality. These complex patients are best managed in a multidisciplinary clinic. In 2018, we implemented a specialized Ortho ID clinic where PJI patients are seen by their joint surgeon and ID physician in a single coordinated visit. In this study, we compared no-show rate, miles traveled to clinic, C diff rates, and other complication rates for PJI patients before and after the implementation of our Ortho ID clinic.We performed a chart review of PJI patients treated at our institution, comparing a group of patients who were treated prior 2018 in the General ID clinic to a group of patients who were treated after 2018 in the Ortho ID clinic. We assessed no-show rates, cumulative distance driven and time spent driving , C. diff rate, and rates of side effects between the 2 groups.The combination clinic improved ID follow-up. Prior to the clinic, only 70% of PJI patients were followed by ID after hospital discharge compared to 100% after the clinic was founded. The no-show rate for PJI patients decreased from 18.2% pre-clinic to 6.9% post-clinic. The mean distance traveled pre-clinic was 226 miles compared to 192 miles post-clinic. The C diff rate decreased from 9.09% pre-clinic to 5.22% post-clinic. Rate of acute kidney injury decreased from 11.1% pre-clinic to 3.45% post-clinic.Our Ortho ID Clinic\u2019s biggest impact was improving ID follow-up for these complicated patients. Prior to the Clinic\u2019s implementation, approximately 30% of PJI patients never followed up with ID after being discharged from the hospital. We saw positive outcomes with regards to reducing C diff rates and rates of acute kidney injury.All Authors: No reported disclosures"} +{"text": "Congenital Syphilis (CS) has increased markedly in the Houston-TX metropolitan region; the rate per 100,000 live births was 138.6 in 2018. Therefore, we reviewed CS exposures presented to our network of institutions to identify possible changes in practice having the potential to improve CS management.2 test was used, and significance was set to P \u2264 0.05. The institutional IRB approved the study.Retrospective record review. From June 2015 through July 2022, 754 RPR+ at-delivery mothers were identified. A random sample of 25% was selected for an ongoing investigation. Eighty-seven mothers and their 89 newborns have had their medical records extracted and analyzed for the presented analysis. Prenatal care was defined as \u2265 3 visits to an obstetrics provider. Maternal treatment of syphilis was categorized as complete when the CDC criteria were met. The \u03c7Notable characteristics of the 87 mothers were 68% African American, 81% not Hispanic, 79% single parents with median gestation of 3 (1-11) and age of 26 (\u00b16).Of the 89 newborns, 54% were female, 57% were full-term, and 51% were delivered by C-section. In addition, 53% were RPR-reactive at birth, and 57% were treated for CS.Analyses targeting interventions doable within our institutional circumstances revealed that 36% of mothers who received prenatal care and delivered newborns who were RPR-reactive at birth had no record of receiving recommended treatment for syphilis, Table1.Our population has a well-established pattern of risk factors for CS, including the use of illicit drugs. In addition, our medical record review identified a possible failure to provide or record treatment for syphilis for women who received prenatal care and delivered RPR-reactive infants. Therefore, an effort is being directed to improve these outcomes.All Authors: No reported disclosures"} +{"text": "Vaccination against COVID-19 is one of the most important measures to reduce the spread, morbidity, and mortality of the disease.We conducted a cross-sectional study to evaluate knowledge, attitudes, and practices regarding vaccination against COVID-19 in medical students at Universidad Peruana Cayetano Heredia (UPCH), for which an online survey was administered through e-mail and WhatsApp in July 2022. The following independent variables were evaluated: To be in the clinical phase of medical school (last four years), having more online classes ( >= 4 semesters with non-face-to-face classes), having received >= 3 doses of COVID-19 vaccine, and having reliable sources of information . Through linear regression multivariate analysis, we assessed the factors associated with the number of correct answers (knowledge), the standardized attitude index (attitudes), and the number of vaccine doses received (practice).A total of 352 medical students completed the survey. 96.6% of participants knew that vaccines improved immunity, and 91.2% believed they were effective in reducing hospitalizations, severe illness, and death. 98% of students agreed that the benefits of vaccination outweighed the risks, 90.9% would recommend the population to get vaccinated, and 59.1% agreed that vaccines were safe. 99.7% of respondents have received at least one dose of vaccine, of which 100% received at least two doses, 88% three, and 4.8% four or more. In the multivariate analysis, we found that being in the clinical phase of medical school was associated with a higher knowledge and a higher standardized attitude index. Having received >=3 doses was associated with a higher standardized attitude index. Lastly, having a higher standardized attitude index was associated with having received more vaccine doses. (Table. 1)Table 1Regarding vaccination against COVID-19, medical students at UPCH have a high level of knowledge, a positive attitude, and good practices. Our study suggests that educational strategies in the pre-clinical phase may be needed to improve knowledge and attitudes regarding vaccination. Also, a higher standardized attitude index may predict a higher number of vaccine doses.All Authors: No reported disclosures"} +{"text": "Orofacial injuries constitute the medico-legal cases reported, especially, in cases associated with road traffic accidents, assaults, and violence makingit an emerging healthcare problem. Therefore, it is of interest to document data on the maxillofacial trauma and fractures among Indians. 150 subjects withinthe age of 15 to 60 years with maxillofacial fractures, detailed medical history including demographics, radiographs, medical history, associated injuries,and etiology of fractures were used for this study. Sites for both maxillary and mandibular fractures were noted. The type of intubation used and post-operative complications were also recorded. Lefort I, II, and III fractures were seen in 4%, 12%, 6% subjectsrespectively, whereas, ZMC fracture was seen in 66% study subjects. Mandibular fractures were most commonly seen in the para-symphysis region with 30% subjectsfollowed by condylar region with 28.66% subjects. Data shows that maxillofacial trauma has a high incidence in India with RTA (road traffic accidents beingthe most common reason for the trauma seen in young males with significant concomitant injuries. Most common fracture is seen in mandible region. However,they can be managed well with very few postoperative complications. Maxillofacial trauma is increasing in incidence and is commonly seen in assaults, emergency, and accident cases reported to hospitals. OrofaciThe retrospective clinical study was aimed to assess the pattern, etiology, intubation mode, associated complications, and outcomes following the managementof maxillofacial trauma in subjects reporting to a tertiary care hospital in India. The study also aimed to obtain a clear picture of demographics,epidemiology, and etiology of maxillofacial injuries. The study was preceded after the ethical clearance from Rama Medical College and Hospital Kanpur.The study subjects were recruited from the patients admitted to Department of Emergency and Trauma, Rama Medical College and Hospital, Kanpur and were diagnosedwith maxillofacial fracture post-surgery. The study assessed 150 subjects, both males and females in the age of 15-60 years. The mean age of the participantswas 32.43\u00b16.28 years.The inclusion criteria for the study were subjects with a confirmatory diagnosis of maxillofacial both clinically as well The data collected were analyzed statistically to formulate the results. The data were expressed as percentage and number, and mean and standard deviation.As shown in It was noted that in maxillary and mid face fractures, Lefort I, Lefort II, and Lefort III fractures were seen in 4% (n=6), 12% (n=18), 6% (n=9) subjectsrespectively, whereas, ZMC fracture was seen in 66% (n=99) study subjects. Mandibular fractures were most commonly seen in the para-symphysis region with 30%(n=45) subjects followed by the condylar region with 28.66% (n=43) subjects. Angle fracture was seen in 20.66% (n=31) subjects followed by body fracture in 12%(n=18) subjects, symphysis fracture in 4% (n=6) subjects, and ramus fracture in 0.66% (n=1) study subject. Pan facial fracture was seen in 2.66% (n=4) ofstudy subjects .Data shows that nasotracheal intubation was done in 86.66% (n=130) study subjects, whereas, sub mental intubation was done in 13.33% (n=20) study subjects. Sub menet al. [et al. [et al. [et al. [The present clinical retrospective study was conducted to assess the pattern, etiology, intubation mode, associated complications, and outcomes followingthe management of maxillofacial trauma in subjects reporting to a tertiary care hospital in India. The etiology of maxillofacial injuries is known to varyfrom one geographical region to another. In developing countries, road traffic accident is generally believed to be the most common cause of facial trauma and thiset al. In 2006 et al. in 2008 [et al. in 2003 [et al. in 2010 [et al. in 2009 Data shows that maxillofacial trauma has a high incidence in India with road traffic accidents being the most common reason for trauma seen among youngmales with significant concomitant injuries. Most common fracture seen is in mandible region. However, they can be managed well with very few postoperativecomplications. Ensuring proper traffic rules following and setting dedicated maxillofacial trauma centres can help in reducing the incidence and ensureeffective management."} +{"text": "It is generally accepted that children with large total body surface area (TBSA) flame burns have worse outcomes as compared to those with scald injury. Anecdotally, we have observed the opposite. We sought to compare outcomes of patients using data from the Pediatric Injury Quality Improvement Collaborative (PIQIC).This multicenter, retrospective cohort study collected data from 4 pediatric hospitals participating in PIQIC over a 10 year period. Exclusion criteria were TBSA <15% and mechanism not scald or flame. Patients were categorized by age in years: 0 to <3, toddler; 3 to <10, child; and age \u2265 10. Demographics, clinical features, and adverse events were collected. Models were controlled for percent full thickness burn.Due to small sample size of age >10, this group was excluded. 164 patients were identified: 96 (59%) with scald and 68 (41%) were flame. Patients in the toddler group were mainly scalds while the child group was mostly flame . Only 28% of scald patients had full-thickness burns compared to 67% of flames.In the scald group, toddlers experienced significantly longer PICU LOS and mechanical ventilator (MV) days than the child group . Hospital LOS was significantly higher in the child group compared to toddlers. There was trend of higher incidence of sepsis, nosocomial infection, and abdominal catastrophe in toddlers. All mortalities were observed in the child group.In flame patients, toddlers had no mortalities, cases of sepsis or abdominal catastrophe. Toddlers had significantly shorter hospital LOS , PICU LOS , and MV days . Older patients with flame burns had higher %TBSA and full-thickness burns.Odds of mortality in both mechanisms was significantly increased for higher TBSA. Each 1% increase in TBSA related to an average 3% increase mortality , P=0.04). Separating mechanisms, the model determined mortality was affected by age. While scalds had significantly reduced mortality , P=0.02), each additional year of age increased mortality by 42% , P=0.02). Each additional year of age resulted in an 18% reduction in nosocomial infection , P=0.01).Given the differences in hospital and PICU LOS, MV days, and complication rates, this study confirms that not all burns carry the same risks across age groups and mechanisms. Despite lower rates of full thickness burns, younger patients with scalds may have a longer PICU course, more time on the ventilator, and increased risk of sepsis, nosocomial infection, and abdominal catastrophe than similarly aged patients with flame burns or older patients with scalds.Burn mechanism and patient age should be considered in addition to TBSA and burn thickness when caring for a critically ill patient."} +{"text": "Background: Healthcare workers (HCWs) are at increased risk of influenza exposure and represent a potential transmission source. The Department of Health and Human Services (HHS) set a goal for 2020 to have 90% of all HCWs in acute-care hospitals (ACHs) vaccinated. Vaccination against influenza decreases symptomatic illness and absenteeism and protects HCWs and their contacts. We assessed characteristics of facility intervention programs based on their success in meeting this benchmark. Methods: Data from the NHSN were utilized, including answers to the Annual Flu Survey for 2014\u20132022 and the rate of vaccine compliance by facility. Flu surveys detail facility-specific programs implemented for each influenza season, from October to March. We used SAS version 9.4 software for univariate analyses to determine factors significantly associated with meeting the HHS benchmark target of \u226590% vaccination among all HCWs, split into categories for employees, students or volunteers, and licensed independent practitioners. Facilities were excluded if they were not ACHs or Critical Access Hospitals (CAH), did not complete the Annual Flu Survey for at least 1 year, or required vaccination as a condition of employment. Results: From 2014 to 2022, 745 surveys were completed. Overall, 48.58% of respondents succeeded in meeting the HHS benchmark. Also, 306 surveys completed noted that their facility did not require influenza vaccination. Among those, only 19.93% respondents succeeded. Moreover, 80.33% of successful respondents for all HCWs required personal protective equipment (PPE) upon vaccination refusal compared to 34.29% of unsuccessful respondents (P < .0001). Furthermore, 98.36% successful respondents required documentation of offsite vaccination, compared to 89.39% of unsuccessful respondents (P = .027). For employees, 64.56% of successful respondents tracked vaccination rates in some or all units compared to 45.81% of unsuccessful respondents (P = .004). Also, 63.29% successful respondents had visible vaccination of leadership, compared to 43.61% of unsuccessful respondents (P = .003). Furthermore, 86.08% of successful respondents had mobile vaccination carts, compared to 73.57% unsuccessful respondents (P = .023). For the student- or volunteer-specific benchmark, 24.59% of successful respondents provided vaccination incentives compared to 14.63% of unsuccessful respondents (P = .035). Conclusions: Facilities with \u226590% vaccination among HCWs were more likely to require PPE after vaccination refusal and documentation for offsite vaccination. Other strategies for vaccination were differentially associated by employee type for Tennessee facilities. For future outreach, a multipronged approach is more likely to be successful in addressing vaccine uptake among employees with lagging rates. Strategies for influenza vaccine uptake could also improve other occupational vaccinations. More research is needed on the barriers to vaccination among HCWs specifically.Disclosures: None"} +{"text": "The burden of antimicrobial resistance (AMR) in Latin America is high. Little is known about healthcare workers\u2019 (HCWs) perceptions of antimicrobial stewardship (AS) and antibiotic use (AU) in the region.HCWs from 42 hospitals in Panama, Guatemala, Colombia, Ecuador, and Argentina were invited to participate in an electronic, voluntary, anonymous survey regarding perceptions of AS and AU from March-April 2023. All participants were asked 21 questions; prescribers were asked additional questions about antibiotic prescribing. Answers with 5-point Likert scale were categorized into two groups, strongly agree/agree and neutral/disagree/strongly disagree.P< 0.01).Of 475 HCWs that completed the survey, 52% were physicians (29% in training), 28% nurses, 13% pharmacists, 3% microbiologists, and 3% \u201cother.\u201d Median years of experience was 12 . Although 93% indicated optimizing AU was a priority at their healthcare facility (HCF), only 69% said the importance of AS was communicated at their HCF. Nurses and those in \u201cother\u201d roles were more likely to report lack of familiarity with the term AS than physicians . Of prescribers, 99% reported to modify antibiotics based on culture results, 55% do not consult non-physician staff to make antibiotic decisions, 20% do not use local guidelines or do not receive training on how to interpret culture results to make antibiotic decisions . Prescribers felt pressure from colleagues (38%) and patients or their families (63%) to make antibiotic decisions.Most (99%) respondents acknowledged that appropriate AU can reduce AMR and that inappropriate AU could harm patients. However, fewer thought antibiotics were overused (30%) or AMR was a problem (52%) in their HCF. Thirty-eight percent of HCWs did not have access to guidelines and 24% did not value recommendations by the AS team (Although most HCWs perceived improving AU as a priority, they did not perceive AU or AMR to be a problem in their HCF. Opportunities to optimize AU include improved access and adherence to guidelines, access to AMR data, teamwork, and education on AS for HCW.Sara E. Cosgrove, MD, MS, Debiopharm: Advisor/Consultant|Duke Clinical Research Institute: Advisor/Consultant Payal K. Patel, MD MPH, qiagen: Honoraria"} +{"text": "Universal congenital cytomegalovirus (cCMV) screening is controversial. In 2023, we completed a study evaluating analytical and clinical sensitivity of dried blood spots (DBS) for detection of cCMV infection and disease. Analytical sensitivity is the ability of an assay to detect infection, while clinical sensitivity is an assay's ability to identify individuals with disease. The completion of this study coincided with implementation of new legislation making Minnesota the first state in the USA to mandate universal cCMV testing.In six newborn nurseries in Minnesota, consented newborns were screened for cCMV, comparing PCR of saliva with PCR of the DBS obtained for routine newborn screening. Screen-positive infants had a confirmatory urine PCR, and a diagnostic clinical evaluation. Using international consensus criteria, we categorized cCMV cases as: moderate-to-severe; mildly symptomatic; asymptomatic with isolated sensorineural hearing loss (SNHL); or asymptomatic.From February 2016 - January 2023, among 23,644 newborns screened, 87 were identified with cCMV. Analytical sensitivity of saliva was 93.1% (81); for DBS, it was 73.6% (64) by the UMN lab, and 77.0% (67) by the CDC lab. At birth, 67 (77%) infants were asymptomatic; 6 moderately-to-severely symptomatic (2 with SNHL); 10 mildly symptomatic; and 4 asymptomatic with isolated SNHL. 4 infants had delayed-onset SNHL . Among 20 infants with symptomatic cCMV at birth and/or SNHL, clinical sensitivity of saliva was 95% (19), and for DBS was 75% (15) in the UMN lab, and 85% (17) in the CDC lab.This unselected screening study demonstrated a prevalence of 3.7/1000 of cCMV in Minnesota newborns. The enhancement in clinical sensitivity of DBS to identify children with symptoms or sequelae suggests their usefulness for cCMV screening, though most identified infants will be asymptomatic. In parallel with this work, in the spring of 2023, Minnesota became the first state to screen all newborns for cCMV, using the newborn DBS. Continued evaluation of CMV DBS testing methods for reproducibility, efficiency, high-throughput capability and clinical correlation will be important as other states consider universal cCMV screening.All Authors: No reported disclosures"} +{"text": "Background: Palliative care in Saudi Arabia has witnessed significant recent progress through the establishment of the Saudi Society for Palliative Care and the National Palliative Care Program. The objective of this study was to assess knowledge and attitudes regarding palliative care and end-of-life decision-making in Saudi Arabia's Eastern and Central provinces among individuals residing in these regions.Methods: Utilizing a cross-sectional survey-based research design, we assessed knowledge and attitudes regarding palliative care and end-of-life decision-making in Saudi Arabia's Eastern and Central provinces. Participants were recruited through purposive sampling via social media. Data collection included demographic information, palliative care knowledge, attitudes toward palliative care, and cultural influences on end-of-life decisions.Results: A total of 710 participants completed the survey, resulting in a response rate of 85%, with a balanced gender distribution, predominantly aged 25-54. Over half were healthcare providers, many possessing more than 15 years of healthcare experience. A substantial proportion had received formal palliative care training and had personal involvement in end-of-life decisions. While most participants demonstrated a good understanding of palliative care, knowledge gaps, especially regarding its timing, persisted. Generally, participants felt at ease discussing end-of-life care and believed in palliative care's effectiveness. Cultural influences on end-of-life decisions were perceived both positively and negatively, with some facing cultural challenges in palliative care.Conclusions: This study underscores a promising understanding of palliative care in Saudi Arabia alongside persistent misconceptions. It highlights the necessity for targeted education to rectify misperceptions, particularly concerning the initiation timing of palliative care. Cultural factors strongly impact end-of-life decisions, emphasizing the need for culturally sensitive healthcare discussions and provider training. Palliative care in Saudi Arabia has witnessed substantial growth and development in recent years, signifying a progressive shift in healthcare priorities. The establishment of the Saudi Society for Palliative Care in 2010 and the initiation of the National Palliative Care Program by the Ministry of Health in 2016 have played pivotal roles in elevating the quality of palliative care services within the country [The provision of palliative care services has diversified and expanded across Saudi Arabia, encompassing various healthcare settings, including hospitals, primary healthcare centers, and home care ,3. PrivaThe intricate interplay of cultural and religious beliefs, particularly within the framework of Islam, strongly influences attitudes toward palliative care and end-of-life decisions in Saudi Arabia . IslamicDespite the increasing acceptance and development of palliative care in Saudi Arabia, significant knowledge gaps persist, necessitating further exploration. These gaps include limited research and the influence of cultural variations, which encompass a diverse range of cultural and regional differences within the country ,7. AddreStudy designThis study employed a survey-based cross-sectional research design to assess knowledge and attitudes toward palliative care and end-of-life decision-making among participants in Saudi Arabia.ParticipantsThe target population for this study comprised individuals residing in the Eastern and Central provinces of Saudi Arabia, representing a diverse cross-section of the Saudi Arabian population. Inclusion criteria encompassed individuals aged 18 and above who were residents of the specified provinces, while there were no specific exclusion criteria.Participants were recruited through a combination of purposive sampling and open online recruitment, utilizing social media platforms, including Facebook, Twitter, and WhatsApp groups, to ensure representation from a diverse cross section of the population. Recruitment messages included invitations to participate in the online survey, accompanied by links to the survey instrument.Data collection instrumentParticipant Information section aimed to gather demographic data, including age, gender, profession, years in healthcare, formal palliative care training, personal involvement in end-of-life decisions, exposure to palliative care, and cultural background. In the Knowledge section, participants' knowledge of palliative care was assessed using close-ended questions. These questions included inquiries about the definition of palliative care, its aims, timing of introduction, and compatibility with curative treatments. The Attitudes Toward Palliative Care section utilized close-ended questions to explore participants' comfort levels in discussing end-of-life care, their beliefs in the effectiveness of palliative care\u00a0and their perceptions of the importance of palliative care training for healthcare providers. In the Cultural Influence on End-of-Life Decisions section, participants' beliefs about the cultural impact on end-of-life decision-making and their personal experiences with cultural challenges in palliative care were assessed using close-ended questions.The survey questionnaire was developed through an extensive review of relevant literature, existing validated scales, and expert consultation. The questionnaire consisted of four main sections: The Data collection procedureThe survey was administered online using a secure and user-friendly platform, specifically Google Forms, to facilitate participant responses. The survey link was widely disseminated across selected social media groups, with a particular focus on reaching participants in the Eastern and Central provinces of Saudi Arabia.Data collection occurred over a predefined period, spanning from January 15, 2023\u00a0to February 28, 2023, to ensure the recruitment of a representative sample. The participants had the flexibility to complete the survey at their convenience during this timeframe.Prior to initiating the survey, the participants were presented with an informed consent statement. This statement outlined the study's purpose, voluntary participation, and data usage. The participants provided informed consent by proceeding with the survey.Data analysisThe data were analyzed using statistical software, specifically IBM SPSS Statistics for Windows version 26 . Descriptive statistics, including frequencies and percentages, were utilized to summarize demographic characteristics, knowledge, attitudes, and perceptions of the participants.Ethical considerationsThis study adhered to ethical guidelines by obtaining informed consent from all participants. Participant identities remained confidential, and data were anonymized during analysis. Ethical approval for this study was obtained from the Ministry of Health, ensuring compliance with ethical standards and participant protection. The Institutional Review Board of Al-Ahsa Health Cluster issued approval .Participant informationA total of 710 participants from Saudi Arabia completed the survey, resulting in a response rate of 85%, offering insights into their knowledge and attitudes toward palliative care and end-of-life decision-making. The demographics of the respondents are as follows: The age distribution revealed that the majority of participants fell within the 25-54 age range, accounting for 63.5% of the total respondents. Specifically, 11.5% were aged 18-24, 24.5% were 25-34, 20.0% were 35-44, and 19.9% were 45-54. Moreover, 23.9% were aged 55 or older, with 11.9% in the 55-64 age group and 12.1% aged 65 or older.In terms of gender distribution, the responses were relatively balanced, with 50.7% identifying as male and 49.3% as female. The professional backgrounds of the participants encompassed a wide range, with 35.2% being healthcare providers, 8.5% educators or researchers, 14.1% patient or family members, and 42.3% indicating other professions.In addition, 39.6% of the respondents reported personal involvement in end-of-life decisions, while 60.4% did not. Exposure to palliative care varied among the participants, with 45.4% reporting high to very high exposure, 47.7% reporting moderate to low exposure, and 6.9% reporting very low exposure Table .Palliative care knowledgeWhen asked about the definition of palliative care, the majority of the respondents (70.3%) correctly identified it as care focused on relieving suffering and improving the quality of life. However, some participants held misconceptions, with 7.9% associating it exclusively with hospice care, 11.1% believing it is provided at the beginning of a serious illness, and 10.7% thinking it only includes pain management.Concerning the aims of palliative care, the majority understood them correctly, with 88.2% recognizing that it aims to provide emotional support, relieve physical and emotional suffering, and improve the patient's overall quality of life.The participants' perceptions of when palliative care should be introduced varied, with 61.1% believing it should be introduced as soon as the diagnosis is made. However, some participants had misconceptions, with 10.0% suggesting it should only be introduced in the final weeks of life and 16.3% when the patient requests it. Furthermore, the majority 88.2%) correctly understood that palliative care can be provided alongside curative treatments reported feeling very comfortable, while 36.0% felt somewhat comfortable. Only 13.8% expressed some degree of discomfort in discussing end-of-life care.In terms of belief in the effectiveness of palliative care, 83.5% either strongly agreed or agreed that palliative care can significantly improve the quality of life of patients. Moreover, 88.3% considered palliative care training for healthcare providers to be very important or important exhibited a comprehensive understanding of palliative care, correctly identifying it as a form of care that focuses on relieving suffering and enhancing the quality of life. However, it is concerning that some misconceptions persist, with 7.9% associating palliative care exclusively with hospice care and 11.3% believing it should be initiated at the onset of a serious illness.Despite a generally positive understanding of palliative care, we observed knowledge gaps. For instance, 16.2% of participants believed that palliative care should only be introduced when the patient requests it. This misperception highlights an opportunity for educational interventions that emphasize the importance of early integration of palliative care alongside curative treatments -10.Cultural factors, including the influence of cultural beliefs and values on end-of-life decision-making, were explored in the study. While we did not specifically measure cultural diversity among the survey population, the study aimed to understand participants' beliefs and experiences related to cultural factors as they pertain to palliative care and end-of-life decision-making within the broader Saudi Arabian context.\u00a0Over half of the participants (52.1%) believed that culture had a positive or somewhat positive influence on these decisions, while 41.6% perceived no significant influence or a somewhat negative influence. These findings highlight the complex interplay between culture, religion, and healthcare decisions. Therefore, it is imperative for healthcare providers to acknowledge these influences and engage in culturally sensitive discussions with patients and their families ,12.Understanding participants' comfort levels in discussing end-of-life care is of paramount importance. Nearly 75% expressed some degree of comfort, with 38.7% indicating that they were very comfortable\u00a0and 36.0% stating that they were somewhat comfortable. However, approximately 18.0% reported varying degrees of discomfort. These findings underscore the critical need for fostering open and empathetic communication in healthcare settings .Approximately 35.2% of the participants reported encountering cultural challenges in palliative care, with 13.4% facing frequent challenges and 21.8% experiencing occasional obstacles. These challenges may encompass differences in treatment preferences, disclosure of diagnoses, and decision-making dynamics within families . AddressThe results of this study hold several significant implications for healthcare practice in Saudi Arabia. First, there should be directed efforts to enhance public awareness and understanding of palliative care, emphasizing its holistic approach and advocating for early integration. Second, healthcare providers, particularly those without formal palliative care training, should receive ongoing education to enhance their knowledge and communication skills. Lastly, healthcare institutions should develop policies and practices that respect cultural and religious diversity while ensuring the delivery of high-quality palliative care services.However, it is important to acknowledge the limitations of this study. Response bias may have influenced the survey-based nature of the research, and the sample may not be entirely representative of the Saudi population due to the reliance on online surveys. In addition, while the study assessed knowledge and attitudes, it did not measure actual behaviors in clinical settings. Future research could explore these aspects in greater depth to provide a more comprehensive understanding of the subject matter.This study sheds light on the current landscape of palliative care knowledge and attitudes in Saudi Arabia, revealing both promising understandings and persistent misconceptions. While a significant proportion of participants exhibited a comprehensive grasp of palliative care's essence and benefits, there remains a need for targeted educational initiatives to rectify misperceptions, particularly concerning the timing of palliative care initiation. The study underscores the complex interplay of cultural influences on end-of-life decisions, emphasizing the importance of culturally sensitive healthcare discussions and training for providers. As Saudi Arabia continues to advance its palliative care services, addressing these knowledge gaps and cultural factors will be pivotal in ensuring that palliative care aligns with the unique cultural and religious context of the nation, ultimately enhancing the quality of end-of-life care for individuals and their families."} +{"text": "Provider-patient communication (PPC) about goals of care (GOC) facilitates goal-concordant care (GCC) delivery. Hospital resource limitations imposed during the pandemic made it vital to deliver GCC to a patient cohort with COVID-19 and cancer. Our aim was to understand the population and adoption of GOC-PPC along with structured documentation in the form of an Advance Care Planning (ACP) note.A multidisciplinary GOC task force developed processes for ease of conducting GOC-PPC and implemented structured documentation. Data were obtained from multiple electronic medical record elements, with each source identified, data integrated and analyzed. We looked at PPC and ACP documentation pre and post implementation alongside demographics, length of stay (LOS), 30-day readmission rate and mortality.494 unique patients were identified, 52% male, 63% Caucasian, 28% Hispanic, 16% African American and 3% Asian. Active cancer was identified in 81% patients, of which 64% were solid tumors and 36% hematologic malignancies. LOS was 9 days with a 30-day readmission rate of 15% and inpatient mortality of 14%. Inpatient ACP note documentation was significantly higher post-implementation as compared to pre-implementation . We saw sustained ACP documentation throughout the pandemic suggesting effective processes.The implementation of institutional structured processes for GOC-PPC resulted in rapid sustainable adoption of ACP documentation for COVID-19 positive cancer patients. This was highly beneficial for this population during the pandemic, as it demonstrated the role of agile processes in care delivery models, which will be beneficial in the future when rapid implementation is needed. The Covid-19 pandemic has stressed healthcare systems across the globe, with hospitals facing resource challenges such as low bed capacity, ventilator shortages, staffing inadequacies and scarcity of personal protective equipment (PPE), to name a few. It has been found that there is futility in cardiopulmonary resuscitation in the Covid-19 patient population, with one retrospective multi-hospital study showing that patients with Covid-19 who suffered from in-hospital cardiac arrest had 100% mortality regardless of their baseline comorbidities, illness severity, and location of arrest, with 81% of these patients being on a mechanical ventilator prior to arrest and a majority of the cardiac arrests (84.1%) occurring in the ICU setting., however only 29% of clinicians report having such conversations. It is also worthwhile to note that only roughly 11% of patients report having GOC conversations with their providers, though 92% of Americans indicated they would be comfortable having GOC and End-of-Life (EoL) discussions with their provider. Inconsistencies with care preferences has been associated with higher medical costs and lower quality of care for the patient., 5 Literature indicates that timely GOC contributes to better care experience by the patient,, 7 longer survival, better quality of life,, 9, 10 and fewer depressive symptoms by patients., 11 Now, more than ever, prioritizing timely GOC conversations and ensuring delivery of goal-concordant care is important, as we strive to respect the wishes of patients who do not prefer higher levels of care at EoL, while efficiently navigating potential shortages in resources and effectively steering resource allocation. Our primary aim is thus to give a global overview of our experience in delivering goal concordant care to the Covid-19 patient population within a cancer institution.While it has always been of paramount importance to prioritize timely goals of care (GOC) conversations, the gravity of the pandemic and the known futility of resuscitation in this setting, placed further urgency on timely delivery of goal concordant care for our unique population of patients with cancer plus Covid-Effective and empathetic communication about disease prognosis, patient values and preferences, and treatment options is vital in delivering goal-concordant care (GCC). While appropriate discussions about advance care planning (ACP) are best initiated in the outpatient setting by primary oncologists, an admission to the hospital presents an important opportunity to re-evaluate and continue GOC discussions, as it signals a change in the trajectory of the patient\u2019s illness, giving increased relevance to these conversations. It is recorded that 99% of clinicians believe that GCC discussions are importantAt the direction of institutional leadership, a multidisciplinary GOC task force was created to accelerate the ongoing work of engaging patients with timely GOC conversations on March 17, 2020. This taskforce included medical oncologists, intensivists, ethicists, palliative care physicians, internal medicine hospitalists, nursing, case managers, and social workers. The task force convened daily to create appropriate criteria and workflow for the inpatient cancer population, to develop virtual training and allocating resources to support primary oncologists in initiating these sensitive yet essential conversations. Additionally, the task force was responsible for creation of standardized ACP note templates, to capture essential information related to goal-concordant care. A day later, March 18, 2020, a national emergency was announced due to the rapid spread of Covid-19. The institution set up a designated Covid-19 unit and our first Covid-positive patient was admitted on March 24, 2020. This unique turn of global events prompted the initiation of a separate work stream for GOC on the Covid-19 unit.Following initial review, the Covid-19 GOC team assessed challenges in the current process, strategized and proposed an updated workflow to tailor delivery of GCC to our distinctive population of Covid-19 patients with cancer. This new workflow included daily multidisciplinary virtual rounds/discussions with team members including nursing, oncologists, hospitalists, ethicist, physical therapy/occupational therapy, social worker and case management. This multidisciplinary method was taken to ensure that a holistic approach was utilized in determining each patient\u2019s clinical condition, performance status, and severity of cancer and Covid-19 illness, and urgency for GOC conversation. A workflow process included a 3-tiered model for GOC conversations in the Covid-19 unit , which iOn April 24, 2020 the GOC team for the Covid-19 unit was formalized. All patients admitted to the Covid-19 unit were required to have a GOC conversation documented at some point during hospital admission, with preference given to documentation within first 24 hours of admission to the Covid-19 unit. After the initial GOC conversation, any acute change in condition would appropriately necessitate a follow-up GOC conversation with either the patient or family members . We instituted this workflow during a pilot period from April 24, 2020 through May 24, 2020 and continued the efforts from May 25, 2020 onwards to present day, making efforts to measure sustainability of this care model through January 24, 2021 ., 13 REDCap (Research Electronic Data Capture) is a secure, web-based software platform designed to support data capture for research studies, providing 1) an intuitive interface for validated data capture; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for data integration and interoperability with external sources.This research was performed as part of the institutional Data-Driven Determinants for COVID-19 Oncology Discovery Effort (D3CODE), IRB-approved protocol 2020\u20130348. Data were obtained from structured and unstructured electronic medical record elements, clinical note text, and ACP note documentation. Each source was identified, data integrated and analyzed using the Palantir Foundry platform (Syntropy), part of the Context Engine Data Management System at the MD Anderson Cancer Center (MDACC). Additionally, for some areas of our research, which required manual data analysis, we utilized data that were collected and managed using REDCap electronic data capture tools hosted at MDACC.In our cancer institution, 494 unique patients who required hospitalization to the Covid-19 unit were identified from March 24, 2020 through January 24, 2021. 81% of patients admitted had an active cancer diagnosis, while the other 19% either had non-active cancer or cancer of indeterminate/unspecified origin. Of the 81% active cancers, 36% of patients had underlying active hematologic malignancies, and 64% had active solid tumor malignancies. 4.5% of total admitted patients were identified as having a cancer involving the respiratory tract.Other high-risk comorbidities identified included hypertension (72%), chronic kidney disease/end-stage renal disease (45%), diabetes mellitus (44%), chronic obstructive pulmonary disease (17%), congestive heart failure (16%), asthma (13%), venous thromboembolism (12%) and obesity (12%). Mean patient age was 59, with median being 61. Gender distribution showed 52% of patients being male and 48% of patients being female. Race and ethnicity demographics showed 63% of patients identified as Caucasian, 28.6% as Hispanic/Latino, 16.2% as African American and 2.7% as Asian.Inpatient average length of stay (LOS) was 9 days, and 30-day readmission rate was 15%. Inpatient Covid-19 mortality during this time was 14%. Of the patients that expired during their hospitalization for Covid-19 in this timeframe, 90.4% were Do Not Resuscitate (DNR), 82.2% opted for comfort care, and 9.6% remained full code status, expiring after a terminal code blue event . ReferraDuring the timeframe of our study, a mean of 90% of patient encounters had ACP note documentation, with 6 out of 11 of the study period months having greater than 90% ACP note documentation . We note This is further highlighted by our analysis showing 90.4% of those patients (or caregivers of patients) who expired opted for DNR status leading up to EoL, along with 82.2% of those patients electing to go the comfort care route.It is challenging to make conclusive statements regarding pre- and post-GOC algorithm implementation outcomes for the Covid-19 patients, given that pre-implementation patient cohort consisted of patients (n = 29) admitted from March 24, 2020 through April 23, 2020 and post-implementation cohort included patients admitted from April 24, 2020 through January 24, 2021 (n = 465). However, our experience showed that with implementation of a daily multidisciplinary goal-concordant approach on the Covid-19 unit, a significant proportion of physicians had routine GOC conversations with patients and/or caregivers and documented their outcomes in the format of a templated ACP note (90%), which identified goals of cancer care as well as goals of Covid-19 care specifically. Our benchmark goal for ACP note documentation during this study period was 70%. Our benchmark goal as well as achieved ACP documentation rate of 90% substantially exceeds the 11% of patients reported as having GOC conversations with their providers in literature.\u201317 that our inpatient mortality rate of 14% was amongst the lowest published hospitalized Covid-19 patient mortality rate, during a time when Covid-19 vaccination was not yet widely available or robustly implemented. We were able to extract data on illness severity for our Covid-19 cancer patient population during the study time period and found that 67.4% of patients required some degree of supplemental oxygen support, while 19.8% of patients required higher levels of non-invasive oxygen support , and 8.3% of patients ultimately required mechanical ventilation (Additionally, we found through literature search tilation . Additiotilation . MaintaiThese figures demonstrate that early initiation of conversations regarding goal concordant care between patients, caregivers and providers have significant impact on EoL outcomes. The more traditional model of care in cancer medicine previously has been dichotomous, with curative or disease-modifying treatment offered primarily and palliative options only being discussed later in disease course. Including a selected team of experts in having these discussions, not only lowers the burden of responsibility of the primary treating physician, but also increases the support system for the patient/family/caregiver. Within our Covid-19 patient cohort for the study period, we found that 53.4% of patients were referred to social work for either medical power of attorney identification, living will documentation, hospice education, out-of-hospital DNR documentation, or other social/financial issues. 15.4% of patients were referred to our supportive/palliative care consultants for either pain/symptom management, assistance with GOC, or psychologic services. 12.6% of patients were referred to spiritual services.This type of multidisciplinary approach affords patients/family/caregivers the opportunity to look at their current situation from more than just the medical perspective. Palliative care specialists are skilled in EoL issues and questions, while ethicists are skilled in the methodology of facilitated conversations. Ethicists also ensure that different value systems are respected and integrated into the conversation. Thus, integrating these specialists into GOC conversations, along with the primary inpatient teams and oncologists, provides greater value for patients/caregivers, whose decision-making is optimized when they are presented with a global view of their treatment options and overall prognosis.Our model suggests more compassionate outcomes when utilizing a goal-concordant approach to those patients with cancer plus multiple comorbidities including Covid-19, so that they are educated early in the disease process on the option of a palliative approach and thus, may receive timely and high-quality palliative care when appropriate. Accordingly, we conclude that there is notable utility in implementing a multidisciplinary approach to goal concordant care in the hospitalized cancer population with Covid-19 illness. This concept likely has broader benefit in fundamental application to all hospitalized cancer patients. Covid-19 will likely continue its significant impact on our vulnerable immunocompromised community of patients, thus as clinicians, it is our ethical responsibility to provide patients and caregivers with the tools and education to make informed decisions regarding end-of-life care."} +{"text": "Purpose: Iron deficiency (ID) is a complication of gastrointestinal (GI) cancers that may manifest as iron deficiency anemia (IDA). Serum ferritin monitoring and oral iron supplementation have the limitations of being falsely elevated and poorly absorbed, respectively. This study aims to assess the discordance in surveillance, treatment practices, and awareness of ID/IDA in GI cancer patients by Canadian physicians treating these patients. Methods: From February 2020 to September 2021, a 22-question electronic survey was sent to medical oncologists (MOs), surgical oncologists (SOs), and gastroenterologists (GEs). The survey collected information about four domains: physician demographics, surveillance practices, treatment practices, and awareness of ID/IDA in GI cancer patients and ASCO/ASH guidelines. Results: A total of 108 of the 872 (12.4%) invited physicians completed the survey. Of these, 26.5% of MOs, 36.8% of SOs, and 70.9% of GEs measured baseline iron parameters, with few continuing surveillance throughout treatment. Ferritin was widely measured by MOs (88.9%), SOs (100%), and GEs (91.4%). Iron was supplemented if ID/IDA was identified pre-treatment by 66.7% of MOs, 85.7% of SOs, and 94.2% of GEs. Parenteral iron was prescribed by SOs (100%), while oral iron was prescribed by MOs (83.3%) and GEs (87.9%). Only 18.6% of physicians were aware of the ASCO/ASH guidelines regarding erythropoiesis-stimulating agents with parenteral iron for treating chemotherapy-induced anemia. Conclusion: Results illustrate variations in practice patterns for IDA management across the different physician specialties. Moreover, there appeared to be gaps in the knowledge and care surrounding evidence-based IDA management principles which may contribute to poor clinical outcomes. Gastrointestinal (GI) cancer refers to malignancies affecting the GI tract, including the stomach, colon, and rectum. In 2022, colorectal cancer (CRC) was estimated to be the second highest cause of cancer mortality, with 24,300 individuals diagnosed and 9400 deaths in the Canadian population . That saCommon lab tests for ID surveillance include ferritin, serum iron, total iron binding capacity (TIBC), and transferrin saturation (TSAT). Cancer patients with FID can be identified with TSAT < 20% and serum ferritin \u2265 100 ng/mL . RecogniMethods of ID treatment include parenteral iron, oral iron, and RBC transfusion. Parenteral iron is an intravenous (IV) supplementation that is a safe and effective treatment option for the management of ID/IDA ,17,18. TWe proposed a Canada-wide electronic survey sent to medical oncologists (MOs), surgical oncologists (SOs), and gastroenterologists (GEs) who treat luminal GI malignancies. The purpose of this study was to better understand the practices in ID/IDA management throughout treatment, the beliefs and attitudes toward iron monitoring and supplementation, and Canadian physicians\u2019 awareness concerning iron surveillance and supplementation methods, as it relates to clinical outcomes in this patient population. We hypothesize a wide disparity in the surveillance, treatment practices, and awareness of ID/IDA for this patient population. This Mount Sinai Hospital Research Ethics Board approved, cross-sectional study involved a 22-question electronic survey disseminated to 872 eligible physicians across Canada). The eligible physicians were conveniently sampled and classified into one of three subgroups: MOs, SOs, and GEs. An invitation to complete the survey was emailed to all eligible physicians, and the email contained a link to an online survey developed using the software Survey Monkey. The data collection period occurred from 20 February 2020 until 19 September 2021. General reminder emails were sent on two occasions to maximize response rate. Participation in the survey was completely voluntary. Responding to the questions would imply consent. The four main domains of questions in the survey included demographics, surveillance practices, treatment practices, and physician awareness. The demographic variables collected about the participants were specialty, experience, location, and gender. Iron surveillance practices analyzed measurements of ferritin, serum iron, TIBC, and iron saturation . A mean percentage of patients that presented with ID/IDA was determined by a subjective estimate of the average number of GI oncology patients presenting with ID/IDA as reported by the physicians divided by the sum of physicians that responded. The counts, percentages, means, and SD values were calculated using the application Excel.n = 71, 65.7%) and practicing in academic/teaching institutions with a wide range of years in practice.A total of 108 of the 872 invited physicians completed the survey, resulting in a 12.4% response rate. The majority of physicians were from Ontario with 24 (70.6%) MOs, 15 (78.9%) SOs, and 32 (59.3%) GEs . There wn = 108) responded to the question assessing whether they measured baseline iron parameters for their GI oncology patients. The total physician population was nearly evenly split with 50.9% (n = 55) measuring baseline iron parameters compared to SOs , and MOs measured baseline iron parameters. Of the 55 physicians who measured baseline iron parameters, 51 physicians consistently answered the subsequent iron surveillance questions in n = 4, 44.4%), SOs , and GEs , with few continuing surveillance throughout treatment course , serum iron , TIBC , and iron saturation c. When a, 88.9%) d. There n = 45) supplemented iron if ID/IDA was identified prior to systemic/surgical oncologic treatment, including 66.7% (n = 6) of MOs, 85.7% (n = 6) of SOs, and 94.3% (n = 33) of GEs , while oral iron was preferred among GEs and MOs of GEs a. When a, 83.3%) b. Out of, 83.3%) c. n = 16) of MOs, 38.9% (n = 7) SOs, and 44% (n = 22) of GEs (n = 19) of MOs, 94.4% (n = 17) of SOs, and 72% (n = 36) of GEs (n = 25) of MOs, 66.7% (n = 12) of SOs, and 92% (n = 46) of GEs were unaware of these guidelines of GEs b. Most p) of GEs c. When aidelines d. This cross-sectional study is the first and largest study evaluating multispecialty clinician practices relating to absolute and functional iron deficiency anemia management in patients with GI cancer. This study is important as IDA is entirely correctable and associated with improvements in both health related QoL and patient performance which ultimately affects survival. In this cross-sectional study, the national survey results presented evidence suggesting the existence of inconsistencies in practice patterns between different specialties regarding ID/IDA surveillance and treatment in GI oncology patients. Management of ID/IDA is clinically relevant to all GI cancer patients, and should be incorporated into routine care for each patient. To create the most comprehensive and standardized care for all GI cancer patients, learning from survey results such as this one can aid in pointing healthcare practitioners and educators in the correct direction, even if these results are only reflective of a certain subset of clinicians.Our study had some weaknesses that should be considered. We recognize that each physician specialty type and institution of practice were not represented in equal proportion in this study. Additionally, not having physicians represented from each province and territory in the study means our results may not be reflective of practices on a national scale. Furthermore, the low response rate (12.4%) to the survey may also reflect the significant need to educate and improve awareness of ID/IDA and treatment guidelines in oncology. These survey results of 12.4% of physicians involved in GI cancer patient management, may also have been a self-selection-biased cohort as these physicians were interested in and aware of testing for ID. Additionally, not all 12.4% of physicians responded to every question in the survey. For instance, approximately only half of the 12.4% of physicians provided a subjective estimate of the average number of GI oncology patients presenting with ID/IDA in Our data shows that the majority of MOs 73.5%) and SOs (63.2%) did not measure baseline iron parameters. We observed that these physicians also did not respond to questions regarding the time points and frequency of iron surveillance, suggesting that most respondents do not include iron surveillance in their routine practice. Results revealed that even when iron parameters were measured, it was not always continued during the course of treatment. Repeated testing of iron parameters during treatment is crucial to ensure adequate iron repletion in patients with persistent anemia, or who have undergone surgeries\u2013such as a gastrectomy\u2013causing chronic ID due to malabsorption 3.5% and . The mosOf the physicians who measured baseline ID/IDA a, most pThe clinicians who participated in this study are likely more invested in the management of IDA, representing self-selection bias. Thus, it is likely that these findings are attenuated which suggest an even larger knowledge gap amongst other practicing clinicians managing this patient population. Given this low response rate, drawing concrete conclusions about the prevalence of management of ID/IDA in gastric cancer patients is not possible. However, taking the population that provided responses to the survey under consideration, it is evident that there is lack of physician awareness in at least this subset of physicians. Thus, extrapolating this data to reach the broader physician population can yield the assumption that there is a general lack of ID/IDA management amongst Canadian physicians. We found that about half of physicians who did not measure baseline iron parameters were unaware of the extent of ID/IDA in the GI oncology patient population. This lack of awareness could be a possible explanation for the absence of screening practices a,b. ArouThe overall results of our survey can be compared to a recent cross-sectional study analyzing the practices around patient blood management (PBM) of Dutch coloproctological surgeons in 2017 . The stu"} +{"text": "Streptococcus (iGAS), defined as infections beyond simple skin and soft tissue infection or pharyngitis, are rising nationally. We report an increase in incidence of iGAS at two urban, quaternary care health systems that contain 6 hospitals in the city of Philadelphia.Invasive infections involving Group A Streptococcus pyogenes were identified using the laboratory information systems at the Temple University Health System and the University of Pennsylvania Health System. Two cohorts were compared: cases diagnosed between January 1, 2019 and December 31, 2019, and between January 1, 2021 to December 31, 2021. We excluded 2020 data to avoid analysis of disease incidence when hospital admission patterns may have been highly biased due to COVID-19 pandemic. Electronic health records were reviewed and data pertaining to demographics, month of infection, culture site, HIV status, HCV status, housing status, and injection drug use were abstracted. Descriptive statistics were used to summarize findings.All blood, sterile fluid, and tissue cultures that yielded In 2021, there were 301 unique cases of iGAS (148 involving bacteremia) compared to 169 in 2019 (with 70 cases of bacteremia). This represented an overall increase in iGAS of 178% and a 211% increase in cases involving bacteremia. Of the cases in 2021, 210 (69.8%) were PWID compared to only 54 (32%) in 2019, a 388% increase. In 2021, 7.5% of patients had a diagnosis of HIV compared to 8.9% in 2019, but a large percentage did not have an HIV test (37% in 2019 and 19% in 2021). HCV Antibody positivity was 52.3% in 2021 versus 26.6% in 2019. Housing instability was recorded in 151 cases (50.2%) in 2021 and 31 (18.3%) in 2019, a 487% increase.Table 1Demographic and clinical characteristics of iGAS cases in 2019 and 2021Table 2Age and Sex data in PWIDFrom 2019 to 2021, there was an increase in iGAS infections among an adult population in a large metropolitan city. We noted a 178% total increase in iGAS during our study period, with a 388% increase among PWID and 487% increase among those unstably housed. As the overdose crisis continues, public health practitioners and medical providers should be aware of the increase in iGAS when providing empiric treatment for PWID with infections and utilize local and national resources to report and manage cases.Sara K. Schultz, MD FACP FIDSA, AbbVie: Advisor/Consultant"} +{"text": "Background: Across the globe, obesity stands as a prominent public health concern, linked to a heightened susceptibility to a range of metabolic and cardiovascular disorders. This study reveals a disproportionate impact of obesity on African American (AA) communities, irrespective of socioeconomic status. Structural racism plays a critical role in perpetuating healthcare disparities between AA and other racial/ethnic groups in the United States. These disparities are reflected in limited access to nutritious food, safe exercise spaces, health insurance, and medical care, all of which significantly influence healthcare outcomes and obesity prevalence. Additionally, both conscious and unconscious interpersonal racism adversely affect obesity care, outcomes, and patient-healthcare provider interactions among Blacks.Study objective: This study aims to analyze and compare obesity-related mortality rates among AAs, Whites, and other racial groups.Methodology: We queried the CDC WONDER dataset, incorporating all US death certificates. During data extraction, various ICD 10 codes were used to denote different obesity categories: E66.1 (drug-induced obesity), E66.2 , E66.3 (overweight), E66.8 (other forms of obesity), E66.9 (unspecified obesity), E66.0 , E66.01 , and E66.09 . Our study encompassed decedents aged \u226515 years, with obesity-related diseases as the underlying cause of death from 2018 to 2021. Sex- and race-specific obesity-related mortality rates were examined for AAs, Whites, and other races. Resultant mortality trends were computed and presented as ratios comparing AA and White populations.Results: This study reveals lower obesity-related mortality rates in AAs compared to Whites. Furthermore, women exhibited higher rates than men. In the 15 to 24 age bracket, males comprised 60.11% of the 361 deaths, whereas females made up 39.89%. In this demographic, 35.46% of deaths were among Blacks, with 64.54% among Whites. Within the 25 to 34 age group, females constituted 37.26% of the 1943 deaths, and males 62.74%. Whites made up 62.94% of the fatalities, Blacks 33.40%, with other racial groups accounting for the remainder. These trends extended through the 35-44, 45-54, 55-64, 65-74, and 75+ age categories, with variations in death proportions among genders and races. Whites consistently accounted for the highest death percentages across all age groups, followed by Blacks. Our data indicate\u00a0that obesity-related mortality tends to occur earlier in life.Conclusion: Our results corroborate previous studies linking elevated mortality risk to obesity and overweight conditions. The uniformity of our findings across age groups, as well as genders, supports the proposal for applying a single range of body weight throughout life. Given the ongoing rise in obesity and overweight conditions across the United States, excess mortality rates are projected to accelerate, potentially leading to decreased life expectancy. This highlights the urgency for developing and implementing effective strategies to control and prevent obesity nationwide. Significant disparities in the prevalence, complications, and treatment outcomes of obesity among Blacks and other racial or ethnic groups in the United States have been well-documented over time. Much of the disproportionate impact of obesity on African Americans (AAs) has been linked to structural racism -3. A nuaNevertheless, in relation to sex and gender, a marked disparity in obesity prevalence rates has been observed among different racial and ethnic groups. Specifically, higher rates of obesity are found in the Black female population compared to other groups, a phenomenon not paralleled in men. Interestingly, AA men show a comparatively lower obesity prevalence rate of 41.1%, as opposed to their non-Hispanic White counterparts who have a prevalence rate of 44.7% . In factNonetheless, racial disparities in obesity prevalence rates among women predominantly occur within highly educated, affluent groups, suggesting an independent correlation between race and individual weight status. Black women consistently display higher BMI values than their White counterparts at every level of educational attainment, with the most significant disparity seen in those with post-high school education . MoreoveObesity significantly increases the risk of various health complications, including non-alcoholic fatty liver disease, type 2 diabetes, and cardiovascular disease . AAs expPathophysiology of obesityObesity is an escalating health concern of increasing complexity, characterized by alterations in adipose tissue quantity, function, and distribution. It arises from the confluence of various factors including physiological, environmental, behavioral, sociocultural, and genetic elements . PathogeIn our study, we utilized the CDC WONDER (Wide-Ranging Online Data for Epidemiologic Research) dataset, which incorporates all US death certificates, to investigate mortality trends related to obesity. To identify different obesity categories, we employed various ICD-10 codes during the data extraction process. These codes included E66.1 (drug-induced obesity), E66.2 , E66.3 (overweight), E66.8 (other forms of obesity), E66.9 (unspecified obesity), E66.0 , E66.01 , and E66.09 . The selection of these codes was based on the fact that diseases in the CDC WONDER database are codified using ICD classifications. Our study focused on data from decedents aged \u226515 years, with obesity-related diseases as the underlying cause of death, during the period from 2018 to 2021. The choice of a minimum age of 15 years was made to account for potential deaths occurring in the younger age group. To examine sex- and race-specific obesity-related mortality rates, we categorized the deceased individuals into AAs, Whites, and other races, utilizing the information provided in the database. Age brackets were created by grouping individuals into 10-year ranges.Ethical approvalCDC WONDER is a user-friendly system that provides both public health professionals and the general public with easy access to the extensive information resources of the Centers for Disease Control and Prevention (CDC). Serving as a valuable tool, it offers a wide range of public health information. Developed and operated by the CDC, CDC WONDER is a public service provided by the US federal government agency. The public website , which fData managementFor data management and basic analysis tasks, we employed Microsoft Excel , leveraging its functionalities for this purpose. It is worth noting that while Excel provided us with adequate capabilities for our analysis, it does have limitations compared to specialized statistical software. To present our findings, we calculated the resulting mortality trends and organized them into tables and ratios, allowing for a clear and concise presentation of the results.\u00a0We performed a chi-squared test to examine the association between racial groups , Asians, and American Indian or Alaskan Natives (AIAN)) and obesity-related mortality in each age group. The p-values indicated whether there are statistically significant differences among racial groups in each age group.The study utilized data extracted from the CDC WONDER dataset acquired from 2018 to 2021. Specifically, CDC WONDER is a user-friendly Internet platform that grants public health professionals and the general public access to CDC's abundant information resources. This comprehensive tool serves as a gateway to a diverse range of valuable public health data and knowledge.\u00a0The participants were grouped based on their ages ( >15 years) and racial groups, with the groups being 10-year age groups, gender, and single/multi-race groups. They were further grouped based on their gender and coded as either single or multi-race. The findings indicated that in the age group of 15 to 24 years, 361 deaths were reported, out of which the males had the highest percentage of deaths at 60.11% (217 deaths) and females had 39.89% (144 deaths). Further, Blacks accounted for 128 deaths (35.46%) in the age group, while Whites accounted for 233 deaths (64.54%).\u00a0AA females had comparable mortality rates to AA males at 17.73%, respectively.\u00a0In comparison to other racial groups, AA women had a higher rate of obesity-related mortality at 17.73% compared to White females at 3.05%. However, among males, White males had a higher obesity-related mortality rate at 39.34% compared to AA males at 17.73%.Further, within the age group 25 to 34 years, a total of 1943 deaths related to obesity complications were reported. Out of the deaths, females accounted for 724 deaths (37.26%), while males accounted for 1219 deaths (62.74%). Further, with regard to racial disparities in the obesity prevalence and mortality rates between the various racial groups, it can be noted that Whites accounted for 1223 deaths (62.94%), Blacks accounted for 649 deaths (33.40%), NHOPI accounted for 12 deaths (0.66%), Asians accounted for 15 deaths (0.77%), and AIAN accounted for 44 deaths (2.26%). Consequently, within the age group, AA males had a higher mortality rate (18.27%) than AA females (12.82%). Further, in comparison to Whites, AA females had lower obesity mortality rates at 12.82% compared to White females\u00a0at 21.41%, while AA females had lower mortality rates at 18.27% compared to White males at 41.53%.\u00a0See Table For the 35-44 years age group, a total of 4368 obesity complication-related deaths were reported. Of the total number of deaths reported, 1736 were females, while 2632 were males. Consequently, with regard to racial disparities in the obesity prevalence and mortality rates between the various racial groups, it can be noted that Whites accounted for 68.34% of deaths, Blacks accounted for 28.46% of the deaths, NHOPI accounted for 0.004% of the deaths, Asians accounted for 0.008% of the deaths, and AIAN accounted for 0.02% of the deaths. Still, for the age group of 45-54 years, a total of 7103 obesity complication-related deaths were reported. Of the total number of deaths reported, 2958 were females, while 4145 were males. Further, regarding racial disparities in the obesity prevalence and mortality rates between the various racial groups, it can be noted that Whites accounted for 5190 deaths, Blacks accounted for 1760 deaths, NHOPI accounted for 37 deaths, Asians accounted for 40 deaths, and AIAN accounted for 76 deaths.Further, regarding the age group of 55-64 years, a total of 9962 obesity complication-related deaths were reported. Of the total number of deaths reported, 44.76% were females, while 55.24% were males. Further, regarding racial disparities in the obesity prevalence and mortality rates between the various racial groups, it can be noted that Whites accounted for 80.37% of the deaths, Blacks accounted for 17.97% of the deaths, NHOPI accounted for 0.002% of the deaths, Asians accounted for 0.002% of the deaths, and AIAN accounted for 0.009% of the deaths, and AIAN and Whites accounted for 0.002% of the deaths. Further, regarding the age group of 65-74 years, a total of 8608 obesity complication-related deaths were reported. Of the total number of deaths reported, 50.70% were females, while 49.30% were males. Further, regarding racial disparities in the obesity prevalence and mortality rates between the various racial groups, it can be noted that Whites accounted for 85.99% of deaths, Blacks accounted for 12.89% of the deaths, Asians accounted for 0.0009% of deaths, and AIAN accounted for 0.0066% of the deaths.Additionally, regarding the age group of 75-84 years, a total of 4077 obesity complication-related deaths were reported. Of the total number of deaths reported, 58.72% were females, while 41.28% were males. Further, regarding racial disparities in the obesity prevalence and mortality rates between the various racial groups, it can be noted that Whites accounted for 87.29% of the deaths, Blacks accounted for 11.45% of the deaths, Asians accounted for 0.59% of deaths, and AIAN accounted for 0.66% of the deaths. Lastly, regarding the age group of 85+ years, a total of 1049 obesity complication-related deaths were reported. Of the total number of deaths reported, 67.68% were females, while 32.32% were males. Further, regarding racial disparities in the obesity prevalence and mortality rates between the various racial groups, it can be noted that Whites accounted for 89.13% of the deaths and Blacks accounted for 10.87% of the deaths. See Table Persistent disparities in obesity care and health outcomes for Black individuals have been documented, with systemic racism identified as a fundamental cause -6. SysteIn this regard, our study reveals discernable patterns of obesity mortality rates among AAs and Whites, contingent on age. Specifically, for the 15-24 years age bracket, the prevalence of obesity and resultant mortality is higher among Whites than AAs. Our data demonstrate that, within this age group, Whites are twice as likely to be obese and succumb to obesity-related complications as compared to their Black counterparts. Further examination of gender disparities within this age group shows that males exhibit higher obesity prevalence rates than females, with a consequential increase in obesity-related mortality. To quantify, the obesity-related mortality rate among males stands at 60.11%, surpassing the female rate of 39.89%. Remarkably, within the 15-24 years demographic, AA males and females share similar probabilities of developing obesity and enduring obesity-related complications. This aligns with Anene's study which identified around 35.9% of AA youths as overweight or obese . MoreoveThe relationship between obesity, gender, and mortality is complex and can be influenced by various factors, leading to variations across different populations and time periods. In our research, we found that among individuals aged 25-34, there was a higher prevalence of obesity-related mortality among males (62.74%) compared to females (37.26%) in the studied period. In terms of racial disparities, White individuals within the same age bracket exhibited almost double the mortality rate from obesity-related complications compared to Black individuals. Furthermore, males within this age group, regardless of their race, were more prone to obesity-related deaths than females. In comparing AA men and women within this age cohort, AA men demonstrated a higher likelihood of suffering and succumbing to obesity-related complications. However, in contrast, White males (41.53%) were more susceptible to obesity-related mortality than White females (18.27%). Interestingly, the data suggest a lower obesity-related mortality rate in AAs (33.40%) compared to Whites (62.94%). This is counterintuitive considering previous studies' findings that showed a higher prevalence of obesity among Black individuals aged 20 years and above. These studies also indicated Blacks were over twice as likely to be diagnosed with obesity-related complications, including diabetes and cardiovascular disease, and were more likely to be hospitalized than Whites . NotablyThus, based on our findings, there is a notable gender disparity among the 35-44 age group, where male individuals (n = 2632) demonstrated a higher prevalence of obesity-related complications compared to females (n = 1736). Furthermore, an exploration of racial disparities reveals a pronounced impact of obesity on mortality rates within the White population (n\u00a0=\u00a02985) of the same age group, presenting more than double the likelihood of experiencing obesity-related complications compared to the Black population (n = 1243). The study further uncovers a higher susceptibility among AA men (n = 649) to succumb to obesity-related complications than AA women (n = 594). Additionally, among the White population, male individuals (n = 1886) were found to have a greater likelihood of mortality due to obesity than their female counterparts (n = 1099). A direct comparison within the 35-44 age group between AA males and White males, as well as between AA females and White females, elucidates a higher propensity for both male groups to succumb to obesity-related complications. Similarly, our study reiterates that, within the 35-44 age group, Whites display a higher likelihood of mortality due to obesity-related complications than Blacks.The observations presented above align with findings from prior research, such as recent pooled cohort assessments demonstrating J-shaped associations between BMI and all-cause mortality. Among White individuals classified as extremely obese, the risk of mortality more than doubled, while in other racial groups, the correlation was consistent but less pronounced . NeverthIn the 45-54 age group, the data reveals a higher number of males (4145) than females (2958) succumbing to complications related to obesity. Furthermore, when addressing racial disparities in obesity mortality rates, White individuals (5190) in the same age group were nearly three times more likely to suffer fatal outcomes from obesity than their Black counterparts (1760). Among AA populations, men (885) exhibited a higher risk of mortality due to obesity than women (875). Within the White demographic, male individuals (3165) were more likely to fall victim to obesity than females (2025). Moving to the 55-64 age group, the trend continues with more males (5503) than females (4459) facing fatal obesity-related complications. Analyzing racial disparities in obesity mortality rates within this age group, Whites (8006) were again almost three times more prone to obesity-related fatalities than Blacks (1790). Interestingly, in this age group, AA women (956) were observed to have a higher susceptibility to fatal obesity-related complications than their male counterparts (832). Similarly, among Whites, men (4588) displayed a higher likelihood of succumbing to obesity than women\u00a0(3418).Our findings contrast with previous studies indicating that being female is associated with a doubled risk of obesity and overweight and suggest a greater propensity for women to develop physical and psychological comorbidities linked to obesity. These studies also found women to have a twofold higher risk of mortality compared to obese and overweight men. However, our results align with those of Elo et al., who found that men generally had higher cardiovascular disease mortality rates than women across various anthropometric obesity measure categories, even after adjusting for age, leisure time physical activity, and smoking status . NotablyIn our study, we noted a higher mortality rate due to obesity-related complications within the 65-74 age group for females (4364) than males (4244). When examining racial disparities, we observed that White individuals (7402) had nearly sevenfold higher obesity mortality rates compared to Black individuals (1110). Additionally, AA women were more susceptible to obesity complications (698) than their male counterparts (412). Among the White population, the data demonstrated that males (3787) had a greater risk of obesity mortality than females (3615). In the 75-84 age bracket, again more females (2394) were observed to die from obesity-related complications than males (1683). Pertaining to racial disparities, Whites (3559) were more susceptible to obesity-related mortality than Blacks (467). Further delineating these results by gender, AA women had higher obesity mortality rates (341) compared to AA men (126). Within the White population, a higher likelihood of succumbing to obesity was seen among females (2019) compared to males (1540). Moreover, when comparing across racial lines within the same age bracket, White women (2019) had a higher rate of obesity-related mortality than their AA counterparts (341). A similar pattern was also seen in males, with more White men (1540) than AA men (126) exhibiting higher mortality rates due to obesity complications. In the age group of 85 years and older, our findings highlight a significantly higher number of females\u00a0(710) succumbing to obesity-related complications than males (339). A further examination of racial disparities, in relation to obesity-related mortality rates, shows a higher susceptibility among Whites (935) compared to Blacks (114). Specifically, AA women displayed a higher likelihood of experiencing and succumbing to obesity-related complications (90) than AA men (24). Furthermore, within the White demographic, the study showed a higher likelihood of female individuals (620) succumbing to obesity than their male counterparts (315). Interestingly, when comparing across racial lines, White women (710) demonstrated a higher mortality rate from obesity-related complications than AA women (90). Similarly, White men (315) also had a higher mortality rate from obesity-related complications compared to their AA counterparts.In elucidating the noted disparity in obesity-related mortality rates between AA and White individuals, prior research has suggested a stronger association between obesity and increased all-cause mortality risk in Whites relative to AA . SpecifiOur study underscores that the association between obesity and mortality is notably diverse among different racial groups and genders and is significantly influenced by the age at which obesity onset occurs. We found a strong link between obesity at younger ages (below 75 years) and an increased mortality risk for both genders, in contrast to those who become obese at more advanced ages. Specifically, our findings reveal that for individuals below 65 years, each obesity and overweight category correlates with a heightened mortality risk. However, the correlation between obesity and mortality becomes progressively diminished when obesity onset occurs at the age of 70 and above. Notwithstanding, for women across all age categories analyzed, the statistical significance of the relationship between obesity and mortality persisted. Prior studies have well documented the association between obesity and mortality in Whites -34. HoweStudy limitationsThis study acknowledges two primary limitations. First, current ICD codes (E66 and E67) that explicitly attribute obesity as a primary cause of death tend to underestimate the total count of obesity-associated fatalities . It is eIn conclusion, the results from our current investigation reinforce the well-documented correlation between obesity and an elevated risk of mortality. Our data illustrate an age-dependent increase in mortality rates, with a peak observed in those aged 85 and above. Across all age categories, males exhibit a consistently higher mortality rate than females, indicating a pressing need for interventions that cater to specific male health issues. The distribution of mortality rates also reveals disparities across racial and ethnic groups. Whites appear to be predominantly represented in older age groups, whereas Blacks are over-represented in younger age categories. Addressing the underlying causes of these discrepancies, such as healthcare accessibility and socioeconomic determinants, is imperative. Furthermore, our study highlights distinct mortality rates among different racial and ethnic groups within the same age cohort, underscoring the importance of incorporating diversity in the development of healthcare strategies and policies aimed at achieving equitable health outcomes."} +{"text": "With advances in antiretroviral therapy, life-expectancy for people living with HIV (PLWH) has increased. Many HIV specialists function as primary care providers for PLWH and are often the front-line of defense when it comes to preventative healthcare. The Infectious Disease Practice (IDP) at University Hospital in Newark, NJ serves as a medical home and primary care site for many PLWH. The clinic incorporates preventative healthcare measures into providing whole patient care as well as focusing on HIV specific care. Here, we present data from multiple quality assessment projects at our clinic assessing preventative health measures in PLWH.Following IRB NHS determination, data was collected from an EPIC database of PLWH seen at IDP. Guidelines for Primary Care by Infectious Disease Society of America, the Advisory Committee on Immunization Practices, JNC8, and the US Department of Health and Human Services were reviewed.Bone mineral density (BMD) screening was ordered for 59% and completed in 39% of PLWH who met guideline criteria compared to national average of 7.4%Among PLWH with Diabetes mellitus (DM), 62% achieved A1C goals, 65% achieved blood pressure goals and 67% achieved LDL-c goals. National averages for achieving A1C, blood pressure, and LDL-C goals in people with DM were 51%, 70%, and 66% respectively in 2018.Hypertension pharmacologic therapy was initiated, and blood pressure controlled to systolic blood pressure < 150 diastolic blood pressure < 90 in 72% of PLWH compared to national average of 65%Among PLWH, 64% received at least one dose of PCV13, 60% received at least one dose of PPSV23, and 38% were fully up to date compared with national average 23% in PLWH in 2018 receiving at least one dose of either vaccine.Clinicians practicing in HIV clinics should be up to date on age-appropriate screenings and vaccinations. The IDP has matched or outperformed national standards in several aspects of preventative healthcare for PLWH including DM, hypertension, vaccinations, and BMD screening. Infectious disease specialists who provide care for PLWH are in a unique, trusted position to deliver preventative healthcare and should have expertise in primary care to optimize patient centered care.Eli S. Goshorn, MD, Genmark Diagnostics Inc: Advisor/Consultant"} +{"text": "MIBI was unambiguously positive in 74% of patients. Among patients with negative or inconclusive MIBI, 90% had a positive PTHw result. Among patients with negative PTHw, two out of three had a positive MIBI result. The PTHw of lesions <10 mm in their largest diameter yielded positive results in 95%, compared to 75% for MIBI. For lesions \u226510 mm in largest diameter, 88% were visualised using MIBI. In conclusion, PTHw is a highly effective, easy, quick, safe, and relatively cheap procedure which might be considered for PA localisation, especially in patients with lesions presenting typical ultrasound features and a size below 10 mm. MIBI remains a useful procedure in specialized centres, particularly for patients in whom PTHw failed, larger lesions, and in cases of the ectopic location of PA.The purpose of the study was to assess the clinical, biochemical, and sonographic factors influencing the performance of parathormone washout measurement (PTHw) vs. MIBI in the preoperative localization of parathyroid adenoma (PA). The studied group consisted of 39 patients with primary or tertiary hyperparathyroidism. The measurement of PTH concentrations was performed using an electro-chemiluminescence immunoassay. Scintigraphic localization of PA was carried out using dual-tracer planar neck scintigraphy, using 74 MBq Unforlization . The senlization . The comlization .The aim of the study was to assess the clinical, biochemical, and sonographic factors influencing the performance of PTHw vs. MIBI in the preoperative localization of PA.The studied group consisted of 39 patients . Mean age of subjects was 57.4 years; min\u2013max was 32\u201374 years. Patients were diagnosed with primary (36 subjects) and tertiary (3 subjects) HPT and were referred to the department of endocrinology for localization diagnostics before qualifying for parathyroidectomy from January 2018 to December 2020.The PTHw procedure was performed with a fine needle (lumen diameter 0.5 mm), under ultrasound guidance. The aspirate was dissolved in 1 mL of 0.9% NaCl. PTHw and PTH serum (PTHs) concentration measurements were performed using the electro-chemiluminescence third-generation immunoassay, Elecsys PTH 1\u201384, using a cobas e 801 analyzer . Results above the upper limit of detection were assumed as equal to the upper limit of detection.Ultrasound examination was performed with the AIXPLORER system . PTHw was considered positive if PTHw was \u22651.0 of PTHs.99mTc-pertechnetate to visualise tracer distribution in the thyroid gland. Subsequently, patients were injected with 740 MBq of 99mTc-MIBI , and anterior images of the neck were registered twice: 15 min and 120 min after injection. Any focus of increased 99mTc-MIBI accumulation that did not show any 99mTc-pertechnetate uptake was regarded a positive for PA.Scintigraphic localization of PA was carried out using dual-tracer planar neck scintigraphy and a Nucline gamma camera . First, planar images of the neck area were acquired 15 min after an injection of 74 MBq of p < 0.05. The study was retrospective, based on the analysis of medical documentation. Thus, the requirement of approval was waived by our institutional Bioethical Review Board.Statistical analysis was performed with the use of Statistica 13 and Microsoft Excel software. Results were presented as median with a Q1\u2013Q3 interval. In addition to the descriptive statistics, non-parametric tests were used for comparison (Mann\u2013Whitney U test) and correlation (Spearman test). The level of statistical significance was set at The surgery was effective in 97% of patients (38/39). Biochemical characteristics of the studied group are presented in p = 0.005).PTHw was positive in 92% (36/39) of subjects. In 21 cases (54%), the PTHw concentration exceeded the ULD. The median PTHw concentration was significantly different between PTHw-positive and -negative subgroups of cases. MIBI was unambiguously positive in 74% (29/39) of cases. Among patients with negative or inconclusive MIBI , 90% (9/10) had a positive PTHw result. In MIBI-positive patients, PTHw confirmed the presence of the PA location in 93% of cases (27/29). Within the group with positive PTHw, in 25% (9/36) of subjects, MIBI was inconclusive . Among patients with negative PTHw, two out of three had positive MIBI and underwent successful surgery .The most common PA was located in the left lower parathyroid gland (44%), followed by the right lower parathyroid gland (41%). In 85% of lesions (33/39), the ultrasound image was considered typical of PA . Among lesions presenting typical ultrasound features of PA, PTHw was positive in 97% and MIBI was positive in 73% .The median diameter of the lesion suspected of PA and selected for PTHw was 9 mm . The PTHw of the lesions < 10 mm in their largest diameter yielded positive results in 95%, compared to 75% for MIBI. On the other hand, in the group of MIBI-negative results, 80% of them had a largest diameter < 10 mm. In lesions \u226510 mm in largest diameter, 88% were visualised on MIBI, while 87% of them had positive PTHw. In the group with negative PTHw, 66% of lesions were \u226510 mm.Upon ultrasound examination, 59% of patients had at least one concomitant thyroid focal lesion, and 38% demonstrated features of autoimmune thyroid disease (AITD), namely, decreased echogenicity and inhomogeneous structure of the gland parenchyma. All three subjects with negative PTHw had nodular goitre. Among patients with negative PTHw, one out of three cases had AITD. Seventy percent of patients (7/10) with negative or inconclusive MIBI had concomitant thyroid focal lesions. In the ultrasound results, among cases with negative or inconclusive MIBI, AITD features were present in half of the cases (5/10).p = 0.01) and PTHw/PTHs concentration ratio correlated with the maximum diameter of the lesion on ultrasound. Additionally, eGFR was significantly higher in the group with positive PTHw than those with a negative result . In the ROC curve analysis, serum calcium level \u2264 11.2 mg/dL predicted PTHw confirmation with a sensitivity of 58.8% and specificity of 100% .The PTHs . Of note, MIBI exposes a patient to radiation ; therefore, it requires access to a nuclear medicine laboratory and may provide falsely negative or inconclusive results, particularly in cases of small lesions ,15. On tThe suboptimal results of PA detection achieved using MIBI in this study may be attributed to the fact that only planar images were analysed. With technical progress, SPECT-CT, as an additional modality, has also been introduced in our centre. Moreover, it has highly improved the PA detection rate ,18. Unfo18F-choline, even for small Pas [18F-choline PET was equal to 95%, with a very high PPV of 97%. The procedure is simple, involves only one tracer injection, and the image acquisition is restricted to several minutes. Its disadvantages involve the high cost and relatively low availability of the radiopharmaceutical in comparison to 99mTc-MIBI. However, radionuclide imaging continues to play a pivotal role in the diagnostics of HPT. A particular advantage is its ability to detect ectopic PA [Interestingly, even higher values of diagnostic accuracy have been obtained with PET-CT using mall Pas ,19. In atopic PA ,19.A limitation of our study was the relatively low number of patients; however, only patients who could be surgically and histopathologically verified were included in the analysis.In conclusion, PTHw is a highly effective, easy, quick, safe, and relatively cheap procedure which can be considered for PA localisation, especially in patients with lesions presenting typical ultrasound features and that are below 10 mm and are accessible for ultrasound-guided biopsy. MIBI remains a useful procedure in specialized centres, particularly for patients for whom PTHw failed to identify a source of PTH overproduction, larger lesions (>10 mm), and in cases where there is a suspicion of the ectopic location of PA. Therefore, an adequate patient profile needs to be considered for each method. In order to obtain the best diagnostic results, PTHw and MIBI scintigraphy should be applied as complementary techniques. Further studies are required to increase the evidence."} +{"text": "In Mexico, the Hospital Epidemiological Surveillance Network previously the COVID-19 pandemic, reported a total of 61,969 health care associated infections with an incidence rate of 4.7 per 100 discharges, 20.7% of which were categorized as ventilator associated pneumonia.Biofire Filmarray pneumonia panel has been accepted as a tool for early and rapid diagnostic of pneumonia with recognition of several hospital acquired pathogens including resistant genes. However, there are some mismatch in the multiplex PCR detection and the culture isolation.An observational, comparative, retrospective, non-randomized, cross-sectional, open study was performed using files from patients diagnosed with ventilator associated pneumonia who underwent diagnostic testing on culture and PCR multiplex FilmArray pneumonia panel to determine diagnostic accuracy.Intensive care unit files from August 2021 to February 2022 with ventilator associated pneumonia with airway samples for Filmarray pneumonia panel and cultures. Evaluation of the used diagnostic tests was carried out using: sensitivity, specificity, positive predictive value and negative predictive value.55 patients were included, each of them with both test. 72% of the study population were males, with a mean age of 61 years. 76% of the population had severe COVID-19.E.Coli had 100% sentitivity and 96% specificity , P. aeruginosa 100% sentitivity and 88% specificity, E.Cloacae 100% sentitivity and 91% specificity, and S. aureus had 100% sentitivity and 89% specificity on Biofire Filmarray pneumonia panel. While K. pneumoniae had 50% sensitivity and 89% specificity. NPV was 98% for K. pneumoniae, and 100% for E. coli, P. aeruginosa, E. cloacae, and S. aureus.S.maltophilia was isolated in 3 culture samples and the Filmarray pneumonia panel was reported negative because lacking of testing this microorganism, as well as 1 A. fumigatus isolation.Samples for cultures and Biofire FilmArray pneumonia panelThe different samples that were included from 55 patients in this study correlated with pneumonia panel and conventional cultures.PCR Biofire FilmArray pneumonia panel diagnostic study evaluationEach of the microorganism that had correlation between Filmarray pneumonia panel compared with conventional culturesBiofire Filmarray pneumonia panel provides early and accurate information on pathogens causing ventilator associated pneumonia. However it cannot replace conventional culture because of lacking of some microorganism detection. It provides a useful tool for early decision-making in treatment.All Authors: No reported disclosures"} +{"text": "In the sub-section Intervention and procedures, within the Methods section, the fifth sentence contains an error. The correct sentence is as follows: A daily dose of the BEP (72 g) provided an energy top up of 393 kcal and consisted of 36% lipids, 20% protein, and 32% carbohydrates [34]. The supplement covered at least the EARs of pregnant women for 11 micronutrients, except calcium, phosphorous, and magnesium."} +{"text": "Single tablet regimens (STRs) are widely utilized in HIV treatment in the Western world largely because they improve convenience of oral regimens and eliminate differential adherence. US Blacks are disproportionately impacted by HIV, and are also disproportionately affected by chronic kidney disease (CKD) for a variety of reasons, especially in their later years. For PWH and CKD, STR options are limited due to pharmacokinetic considerations. We evaluate the impact on viral suppression, adherence, treatment satisfaction and quality of life (QOL) of switching to DTG/RPV STR for a largely Black aging US cohort with HIV and CKD.2, an HIV RNA < 50 copies/mL and no known prior resistance to DTG or RPV were switched to DTG/RPV STR. HIV RNA and CD4 were monitored per standard national clinical guidance following switch. Standardized tools for medication adherence, treatment satisfaction and QOL were administered at baseline, 24 weeks and 48 weeks. We present final 48-week data.In this 48-week open label single arm switch study conducted in a community health center setting, adults with HIV, a GFR< 60 mL/min/1.73m2 per race-based calculation . At 48 weeks, 97% of participants maintained viral suppression with an HIV RNA < 50 copies/mL in a per protocol analysis . One participant with an HIV RNA of 62 copies/mL at 48 weeks subsequently re-suppressed on DTG/RPV. 69% reported an improvement in adherence, 77% noted an improvement in treatment satisfaction and 66% reported an improvement in QOL. The only adverse event reported in >5% of participants was nausea (5.7%). There were no serious adverse events.Between August 2019 and December 2021, 35 participants were enrolled. One dropped out after 19 weeks and one after 22 weeks due to drug-drug interaction concerns following renal transplantation. 94% of participants were Black, 57% were female and 43% were 65 years and older. At baseline, 20% had a GFR < 30 mL/min/1.73mFor this diverse aging cohort with HIV and CKD in a real-life community health center setting, DTG/RPV STR was efficacious, well-tolerated and associated with improvements in adherence, treatment satisfaction and QOL, sustained over 48 weeks. DTG/RPV is a feasible oral ARV option for PWH and CKD.Helena Kwakwa, MD, MPH, ViiV Healthcare: Grant/Research Support"} +{"text": "The predominant mode of transmission in the 2022 mpox outbreak was sexually associated. Best practices for mpox evaluation include a sexual history, an anal and/or genital exam and STI testing. We hypothesized that the quality of clinical evaluation (QoC) for mpox varied by clinical setting.A retrospective chart review was conducted on all patients in the Johns Hopkins Health System (JHHS) who tested for mpox from June 15 through December 15, 2022. Outcome measures included three QoC metrics . Fisher\u2019s exact test was used to compare the frequency of QoC indicators by location of mpox testing .Of 269 patients tested for mpox, median age was 37 years, 48% were Black, 8% Latino, 71% assigned male sex at birth, 2% transgender women and 25% living with HIV (Table 1). Location of mpox testing was ED/UC (n=165), HIV/SH (n=50), or non-HIV/SH (n=54). Rates of mpox diagnosis and documentation of a sexual history, anal and/or genital exam and concomitant STI testing varied by site and were statistically significantly different (Table 2). HIV/SH had the highest rate of mpox test positivity (58%) and were most likely to meet these QoC indicators followed by ED/UC and HIV/SH clinics .In a high-volume tertiary care health system, only 50% of individuals tested for mpox had a documented anal and/or genital exam and 57% had concomitant STI testing. QoC indicators for mpox evaluation were highest in clinics where sexual health assessments are routine , intermediate in ED/urgent care settings and lowest in non-HIV/sexual health settings. These findings support other studies that demonstrate a lack of consistent sexual health evaluation among individuals at risk for STIs. Strategies that decrease barriers to completed sexual history, exam and STI testing should be explored including audio-computer assisted patient report of sexual history, patient self-collection of STI testing and provider training.Matthew M. Hamill, MBChB, PhD, Roche diagnostics: Honoraria Kelly Gebo, MD, MPH, Pfizer: Advisor/Consultant|Spark HealthCare: Advisor/Consultant"} +{"text": "Background: Irrational antibiotic use among hospitalized patients can lead to antibiotic resistance. For rational use, the WHO introduced the Access, Watch, and Reserve (AWaRe) classification of antibiotics. We explored antibiotic use according to the AWaRe classification among patients hospitalized with severe acute respiratory infection (SARI) between the prepandemic and COVID-19 pandemic periods in Bangladesh. Methods: From June 2017 to November 2022, we analyzed SARI inpatient data from the hospital-based influenza surveillance platform at 9 tertiary-level hospitals in Bangladesh. We defined June 2017\u2013February 2020 as the prepandemic period and March 2020\u2013November 2022 as the pandemic period. Physicians identified inpatients meeting the WHO SARI case definition and recorded patient demographics, clinical characteristics, and antibiotics received during hospitalization. We used descriptive statistics to summarize the data. Results: We enrolled 20,640 SARI patients ; and among them, 18,197 (88%) received antibiotics (26% of those received >1 different course of antibiotics). Compared to the prepandemic period, the proportion of antibiotic use among SARI patients was higher during the pandemic: 93% versus 83% (P < .001). According to AWaRe classification, Access, Watch, and Reserve groups accounted for 32% , 86% , and 0.05% (n = 4), respectively, before the pandemic and 32% , 90% , and 0.08% (n = 8), respectively, during the pandemic . The most common antibiotic prescribed for children aged <5 years during the prepandemic was ceftriaxone , followed by amikacin and flucloxacillin ; similarly, during the pandemic, most common antibiotic prescribed was ceftriaxone , followed by amikacin and flucloxacillin . The most common antibiotic prescribed for patients aged \u22655 years during the prepandemic period was ceftriaxone , followed by amoxicillin-clavulanic acid and azithromycin . During the pandemic, the most common antibiotic prescribed for patients aged \u22655 years was ceftriaxone , followed by amoxicillin-clavulanic acid and clarithromycin . Among children aged <5 years, use of the Watch group of antibiotics during the prepandemic and pandemic periods was similar: 94% versus 95% (P = .099). However, among patients aged \u22655 years, the use of Watch antibiotics was higher during the pandemic compared to the prepandemic period: 87% versus 82% (P < .001). Conclusions: Use of antibiotics in the Watch group was predominant among SARI patients both before and during the COVID-19 pandemic, and it increased among SARI patients aged \u22655 years during the pandemic period in Bangladesh. Promoting antibiotic stewardship programs for physicians, including in-service training on antibiotic use, could reduce irrational antibiotic use, which might contribute to mitigating antibiotic resistance in the country.Financial support: This study was funded by the CDC.Disclosures: None"} +{"text": "IntroductionDiabetic foot ulcer (DFU) is a prevalent complication of diabetes mellitus (DM), affecting approximately 15% of all diabetic patients. This condition poses significant challenges due to its association with major morbidity, mortality, high costs, and diminished quality of life. The incidence of diabetic foot complications among diagnosed diabetes cases is alarming, making it a primary concern in diabetes management. Diabetes mellitus, a chronic metabolic disorder, impacts nearly every system in the body.MethodsIn this study, a cross-sectional design was employed to assess the level of knowledge, attitude, and practices related to foot care among 432 diabetic patients in Tabuk City, Saudi Arabia.ResultsThe participants' ages ranged from 18 to above 60 years, with being male and female. Type 2 diabetes was prevalent, constituting of cases, whereas had type 1 diabetes. Approximately of patients had been diagnosed with diabetes for less than 10 years. A significant portion of patients did not report any foot complaints. However, had a history of healed ulcers, and had undergone amputation due to diabetes. The majority of patients were under oral agent treatment.ConclusionThe study population demonstrated adequate knowledge about diabetes management and exhibited positive attitudes toward diabetes and its related complications, particularly concerning foot care. While most patients displayed appropriate practices related to diabetic foot care, some participants showed inadequate adherence to essential procedures. Addressing these gaps in knowledge and practices is crucial for enhancing the overall management of diabetic foot complications among patients. Diabetes mellitus (DM) is a chronically debilitating medical condition that is spreading around the globe. According to the International Diabetes Federation Atlas, the prevalence of diabetes worldwide was predicted to be 9.3% (463 million people) in 2019, 10.2% (578.4 million) by 2030, and 10.9% (700.2 million) by 2045 [A crippling consequence of diabetes mellitus, diabetic foot disease eventually affects up to 50% of individuals with type 1 and type 2 diabetes. The affected patient's years of life and quality of life are still being significantly reduced as a result of this condition. Moreover, it accounts for at least 12-15% of the total expenses related to diabetes, and as much as 40% in underdeveloped nations. Furthermore, the diabetic foot disease treatments that are currently offered are typically not as successful as they should be .Diabetic foot\u00a0significantly increases health care expenses, and improper foot care among diabetics is a primary cause of indisposition and early death. Overall, 3.3% of diabetic patients experienced foot problems; these included 2.05% foot ulcers, 0.19% gangrene, and 1.06% amputations . On the The Saudi Ministry of Health is facing a major dilemma because, according to its 2018 statistical yearbook, there were 1280 cases of amputation as a result of diabetes mellitus in males and 765 cases in females . The fooThe incidence of diabetic foot ulcers and amputations can be effectively decreased by raising patient awareness, encouraging regular foot care routines, and helping diabetes patients maintain appropriate glycemic control . Many scThe current study aimed to assess patients' knowledge and practices concerning diabetic foot care in Tabuk City, Saudi Arabia. As no similar study has been conducted in this area before, our research was designed to evaluate the level of knowledge and adherence to foot care practices among individuals diagnosed with diabetes mellitus. Implementing patient education strategies can significantly contribute to minimizing diabetic foot ulcers and amputations within the healthcare system.Study design and areaIn this cross-sectional study, our objective was to assess the knowledge, attitudes, and practices concerning foot care among diabetic patients in Tabuk City, Saudi Arabia. Data collection took place between July 10 and October 10, 2023, in diabetic clinics located within both civil and military hospitals. The selection of these clinics was done using a random sampling technique to ensure a representative sample for the study.\u00a0Tabuk City is situated in the northwestern region of Saudi Arabia and is home to an estimated population of around 534,893 individuals, as per the latest data provided by the General Authority for Statistics in Saudi Arabia.Study population and eligibility criteriaThe study focused on diabetic patients aged 18 years and older, receiving care at diabetic centers in both civil and military hospitals in Tabuk City. Patients who were unable to provide the necessary information were excluded from the study.\u00a0Sample size\u00a0The sample size for this study was calculated using the following formula:n = (Z^2 * P * Q) / d^2Where: n = sample size;\u00a0Z = z-score corresponding to the level of confidence desired ; P = expected prevalence of adequate knowledge and positive attitudes towards GDM management (assumed to be 50%); Q = 1 minus P; d = margin of error (assumed to be 5%). Assuming a 10% non-response rate, the final sample size was 432 diabetic patientSampling techniqueParticipants were chosen randomly utilizing a systematic random sampling method. In particular, every second individual receiving care at the diabetic centers during the study period was included. This method was employed to ensure the sample's representativeness, ensuring it closely mirrored the population, and to ensure a substantial number of participants for the study.Data collection toolsA structured questionnaire with closed-ended questions was utilized for this study, adapted from a similar research conducted in Alkharj . The queData analysis planFor our analysis, we employed the Statistical Package for Social Sciences (SPSS) version 28 . Descriptive statistics were used to compile and summarize the data. To explore the relationship between knowledge, attitudes, and practices concerning foot care among diabetic patients\u00a0and demographic characteristics, we utilized the Chi-square test and logistic regression analysis. Statistical significance was determined by a p-value less than 0.05; any result below this threshold was regarded as statistically significant.Ethical considerationEthical clearance for this study was obtained from the Institutional Review Board (IRB) of King Salman Armed Forces Hospital, as evidenced by approval number KSAFH-REC-2023-516. Before participating in the trial, all individuals gave oral informed consent. Stringent measures were implemented to guarantee the confidentiality and privacy of the participants.Table Table Table Table Table In analyzing the association between participants' knowledge, attitudes, and practices as presented in Table Diabetic foot disease stands out as a prevalent and potentially fatal complication of diabetes mellitus (DM). Its persistence often leads to significant morbidity and premature mortality. The American Diabetes Association underscores the importance of an annual comprehensive foot examination for individuals with diabetes. Diligent foot care can effectively prevent the majority of foot-related complications. Although cultivating meticulous foot care practices demands dedication and time, self-care remains pivotal in averting potential problems.This study enrolled 432 diabetic patients, with 64.2% (n = 277) diagnosed with type 2 diabetes, and the remaining 35.88% (n = 155) diagnosed with type 1 diabetes. The age range of the participants spanned from 18 to above 60 years. Among them, 52.31% (n = 226) were female, and 47.69% (n = 206) were male. The majority of the participants were of Saudi nationality, accounting for 94.21% (n = 407), while 5.79% (n = 25) were non-Saudi patients.The majority of patients did not report foot complaints . A total of 21 patients (4.6%) had undergone amputation, while 29 patients (6.71%) had renal diseases. Heart diseases were present in 74 patients (17.13%), dyslipidemia was observed in 191 patients (44.21%), and retinopathy was found in 119 patients (27.55%). Among the participants, 224 individuals (51.85%) had diabetes for 10 years or less. Uncontrolled HbA1c levels were predominant, with 187 patients (43.29%), and the majority of participants were undergoing oral agent treatment .This study demonstrated that diabetic patients possessed a high level of knowledge concerning diabetes, its complications, and appropriate foot care practices, with over 70% of participants providing accurate responses to all questions. These findings contrast with studies conducted by Taksande et al., where patients displayed poor knowledge about diabetes and its complications , and anoOur study found that the primary source of information for the participants was physicians and healthcare providers . This percentage was notably higher than the 22% reported by Alshammari et al. and signParticipants exhibited more positive attitudes toward managing their diabetes than anticipated. Responses indicating regular exercise and dietary modifications to prevent further complications from diabetes were satisfactory , as were those related to regular foot care and the examination of feet and footwear . Moreover, participants displayed positive attitudes, with more than 75% endorsing the advice of specialist consultants regarding foot care in diabetes. These results align with a similar study conducted in the Aseer Region of Saudi Arabia .Our study revealed inadequate practices among the participants, notably in the daily examination of their feet, with 227 participants (52.55%) failing to inspect their feet daily. Additionally, participants exhibited insufficient adherence to regular physician foot check-ups, as 260 patients 60.19%) did not visit physicians for regular foot examinations. Similar findings were reported by Vighnesh et al. and supp% did notRegarding the association between the knowledge, attitude, and practices of the participants and their responses, we observed varied associations, with approximately 47% exhibiting an association and nearly 53% lacking association. Female participants demonstrated higher knowledge levels than males on several aspects: understanding that diabetics can experience reduced blood flow , recognizing that diabetics may have reduced sensations , understanding the importance of inspecting the feet , recognizing the significance of foot care due to the increased likelihood of flat feet , acknowledging that regular medication intake reduces diabetes complications , and understanding that exercise aids in preventing diabetic foot problems . No significant gender differences were noted in other knowledge variables, consistent with findings from previous studies -22.Our findings align with prior research, particularly concerning attitudes where women demonstrated higher associations than men. In terms of engaging in regular exercise to prevent further diabetes complications, women exhibited associations of 74.3%, compared to 64.6% in men (p = 0.018). Similarly, concerning wearing footwear indoors as recommended by foot care specialists, women's associations were 81%, while men's associations were 73.3% (p = 0.037). Additionally, regarding the ability to lead a normal life with appropriate diabetes measures, women's responses were 89.4%, surpassing men's responses at 77.7% (p = 0.001) ,23. ThesIn terms of practices, similar patterns were observed, with female associations significantly higher than males. Regarding daily foot examination, 56.6% of females responded affirmatively compared to 37.4% of males (p=0.001). When it came to checking shoes before wearing them, 69.5% of females practiced this habit, while only 51% of males did so (p=0.001). Changing socks daily was more prevalent among females, with 74.8% following this practice compared to 63.6% of males (p=0.008). Inspecting feet for marks resulting from shoes or socks was more common among females, with a response rate of 78.8%, while only 61.2% of males reported this practice (p=0.001). Additionally, the application of daily moisturizer on feet exhibited a significant gender difference, with 65% of females adhering to this practice, contrasting with 38.3% of males (p=0.001). These findings corroborate with studies by Navarro-Peternella et al. and CiarLimitations of the studyThe study's questionnaire design had limitations as it only allowed for yes or no responses to questions about knowledge, attitude, and practices, which can be considered a drawback. While closed-ended questions simplify participant responses, they might have led to affirmative answers when participants were unsure, potentially inflating the perceived knowledge and attitude levels. To mitigate this bias, incorporating a \"how often they should do it\" would give more precise insight into their attitude and practices. Additionally, the study lacked information about participants' family history of diabetes, a factor important in understanding the genetic predisposition to type 2 diabetes. Genetic factors, including various gene mutations, have been associated with diabetes development. Addressing these limitations in future research can enhance the comprehensiveness of the study and provide a more nuanced understanding of the factors influencing participants' knowledge, attitudes, and practices related to diabetes management.The study's findings highlight the need for targeted foot care interventions for patients with diabetes mellitus. In summary, our research revealed that nearly two-thirds of the diabetic patients studied possessed a strong understanding of diabetic foot issues. Furthermore, patients exhibited positive attitudes regarding the management of diabetic feet and the implications of diabetes on foot health. However, both the practice of daily foot checks and participants' willingness to consult a doctor for regular check-ups were insufficiently addressed. Despite these gaps, the Tabuk community demonstrates a commendable level of awareness, attitude, and practice concerning diabetes."} +{"text": "Burn management is complex and outcomes depend on injury severity, timing of presentation, and specialized multidisciplinary care. Burn injuries among the homeless are an increasing problem in the United States (US) as record numbers of people are unsheltered and using unsafe heating practices. This study aims to characterize mechanism, demographic, and social factors related to burn injuries in homeless persons.Burn encounters were extracted from the 2019 Nationwide Emergency Department Sample (NEDS) database. Two cohorts were created comparing homeless and non-homeless encounters. Burn characteristics , comorbidities, demographics, and ED treatments were compared with univariate testing. Multivariable regression evaluated the likelihood of admission. Discharge weights were used to yield national estimates.Of 316,334 ED visits meeting criteria for burn injuries in 2019, 1,919 (0.6%) had a diagnosis code for homelessness. Homelessness burn encounters were significantly older (mean age 32.4 vs. 44.8), were more often male (71% vs. 52%), were more often White (59% vs. 54%) or Black (24% vs. 21%), were more often presenting to EDs in the Western region of the US (43% vs. 19%), and more often had Medicaid as primary payer (51% vs 33%). Burns in homeless encounters more commonly resulted from flame injury and more commonly involved the lower extremity (p< 0.001). Among homeless encounters, burn injuries were more often due to self-harm (12% vs. 2%) or assault (5% vs. 1%)(p< 0.001). In addition, homeless encounters had significantly greater mental illness related to substance abuse and had greater comorbidity burden . Homeless encounters experienced higher rates of third degree burns and concomitant injuries (p\u22640.003). 49% vs 7% of homeless and non-homeless encounters, respectively, required admission, and homelessness was associated with higher odds of admission .Burn injuries in the homeless affect a vulnerable population who is older, has more comorbidities, and has deeper burns. Mental illness is over 4 times more likely in this population who is also at increased risk of getting burned through assault.Burn injuries presenting to the ED should be screened for homelessness given the associated risk factors. Legal, medical, and mental health resources can then be appropriately targeted."} +{"text": "Women get hospitalized for various serious mental disorders that are gender specific, half of them married with children, the other half single\\divorced women stigmatized and marginalized in our society.The aim of this study is to describe mentally ill women admitted into the psychiatric hospital, socio demographically and clinically, highlighting differences, specificities and multiple roles distress deviate with the course of disorder.This is a prospective cross-sectional study involving 50 patients admitted to Ar-razi Psychiatric HospitalThe average age is 39years, 41% of them are single, with a low educational level (primary school). 77% of our women are from the urban region, 59% are jobless. 19% of patients in our study have positive family history, 65% of them suffered from schizophrenia. 65% of patients are admitted for schizophrenia, followed by bipolar I disorder 22%, MDD is only represented by 10%. 25% of inpatients deal with a toxic habit, 18,5% abuse nicotine and only one woman have tried quitting. Suicide attempts are closely linked to major depressive episodes of MDD and BID, in patients were already under a combination of antidepressants and anxiolytics for at least 3 months. Psychotic features are observed in most of admitted disorders, 80% in BIP and 64% in MDD. According to HAMILTON-DEPRESSION 62,9% of women are admitted for a severe depressive episode, 30% present anxiety comorbidity and a history of CBT sessions months prior hospitalization.Shading the light into admitted women in psychiatry and deciphering specific demographic, clinical and therapeutic features may improve the global care system and women\u2019s adherence to treatment and follow up.None Declared"} +{"text": "Emerging data suggest an increasing prevalence of persistent symptoms in individuals affected by coronavirus disease-19 (COVID-19). The objective of this study was to determine the relative frequency of altered taste and smell in COVID reinfection (multiple COVID positive tests) and long COVID (one COVID positive test). We sent an electronic survey to patients in the Indiana University Health COVID registry with positive COVID test results, querying if they were experiencing symptoms consistent with long COVID including altered chemosensory perceptions. Among the 225 respondents, a greater long COVID burden and COVID reinfection was observed in women. Joint pain was reported as the most common symptom experienced by 18% of individuals in the long COVID cohort. In the COVID reinfection cohort >20% of individuals reported headache, joint pain, and cough. Taste perception worse than pre-COVID was reported by 29% and 42% of individuals in the long COVID and COVID reinfection cohorts, respectively. Smell perception worse than pre-COVID was reported by 37% and 46% of individuals in long COVID and COVID reinfection cohorts, respectively. Further, Chi-square test suggested significant association between pre-COVID severity of taste/smell perception and headache in both cohorts. Our findings highlight the prevalence of persistent chemosensory dysfunction for two years and longer in long COVID and COVID reinfection. Globally as of April 2023, there have been 762,201,169 confirmed cases of coronavirus disease-2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (CoV-2) . VariablIntense disturbances of taste, smell, and chemesthesis were widely reported in acute COVID-19 infection with a prevalence of over 30% in most studies ,11,12,13An electronic survey was sent to individuals aged 18 years and older, who had previously agreed to be notified about COVID-19 studies registered at IU School of Medicine\u2019s COVID-19 Research Registry. The questionnaire was designed in consultation with the Indiana Clinical and Translational Sciences Clinical Research Core and included demographics, COVID-19 test results and questions on commonly reported long COVID symptoms. Only individuals who self-identified as testing positive for COVID completed the survey. The survey was divided into two parts: the first part included 9 items on sociodemographic characteristics and the second part consisted of 30 items that measure the following eight dimensions: general health ; physical activities (PA: limitations in performing everyday work and other daily activities); emotional/mental health ; specific general health symptoms previously reported in long COVID ; social function ; chemosensory perception (CP: effects on taste and smell sensations); and oral health . For positive COVID tests, the responders reported the date of initial positive testing and the number of times they tested positive subsequently. Specific questions on physical/emotional health and limitation in activities recorded binary responses as yes/no. Response to symptom specific items were recorded on a five-point scale for long COVID symptoms . Response to taste- and smell-specific questions were recorded on a four-point scale . Study data were collected and managed using REDCap (Research Electronic Data Capture) tools hosted at Indiana clinical and translational sciences institute .p value.Data from surveys completed between August and September 2022 were analyzed in this study. Descriptive statistics were used to express categorical data (frequency and percentage) of long COVID symptoms and changes in chemosensory perceptions. Age was summarized using means and standard deviations. Chi-square test was used to study the association between the parameters of duration, number reporting specific symptoms, and the intensity of the symptoms. Data are provided as mean \u00b1 SD or as Chi-square score and The survey was distributed to 13,561 volunteers. Two hundred and twenty-five responders self-reported the date and the number of times they had COVID-19 positive test results. Of the 225 responders, 57 were males and 157 were females, and the rest chose not to identify themselves. The mean age was 45.8 years (range: 19\u201384 years). One hundred and ninety-four identified as white, 18 as African American, 7 as Asian, 3 as Hispanic and rest chose not to report their race. One hundred and seventy-two individuals reported a single COVID-19 positive test. The duration since testing positive ranged between 6 and 906 days with a median of 222 days A. Only dFifty-two individuals self-reported testing positive for COVID-19 two times or more. Of these, 78.8% (41) tested positive twice, 17.3% (9) tested positive three times, and two individuals (3.8%) reported four positive COVID-19 tests A. The duAll individuals in this study were vaccinated, with 57% in the long COVID cohort and 55% in the COVID reinfection cohort receiving two boosters. In the COVID reinfection cohort, 11% received four boosters and in the long COVID cohort, 2% received five boosters .Common symptoms that comprise the post-COVID conditions include tiredness or fatigue that interferes with daily life activities that get worse after physical or mental effort , joint pain, muscle pain, respiratory symptoms such as cough and chest pain, neurological symptoms such as headache, depression, anxiety and changes in taste or smell ,3,5,23. In the COVID reinfection cohort the symptoms of joint pain, muscle pain, cough, and headache were reported to be experienced often or always by 23%, 23%, 21% and 17% of individuals, respectively. The frequency of symptoms that was experienced sometimes was higher for chest pain and headache (35%), followed by cough (20%), joint pain (19%), and muscle pain (19%) B. In thip < 0.003 reported worse taste perception A with du < 0.003 A. p < 0.36 reported worse taste perception than pre COVID with duration ranging between 79 and 875 days C. Furthep < 0.36 A. p < 0.012 reported worse smell perception worse than pre COVID for durations between two and thirty months A. Furthe < 0.012 B. p < 0.25 reported worse smell perception than pre COVID for durations ranging between 79 days and 875 days C. Furthep < 0.25 B. p < 0.3.In both the long COVID and the COVID reinfection cohorts, a higher percentage of individuals that received two boosters experienced worse taste or smell perception A,B. Intep < 0.024. The Chi-square test statistic for the comparison of long COVID and COVID reinfection groups for persistent smell dysfunction across the three discrete time periods of less than one year, one to two years, and over two years was 8.7, p < 0.045 and headache was 17.2, ectively .In this single survey study, we assessed non-hospitalized individuals with long COVID (one positive COVID test) and with COVID reinfection (two or more positive COVID tests) for persistent symptoms and chemosensory dysfunction. Our data show that 29% and 42% reported worse taste and 37% and 46% reported worse smell perception than pre COVID in the long COVID and COVID reinfection cohorts, respectively. This is consistent with the previous reports of persistent dysgeusia and anosmia in long COVID studies . Viral infections such as influenza have been associated with altered smell and taste ,26,27. TA recent observational study showed that repeat CoV-2 infections increases risk for cardiac, pulmonary, or neurological problems . We obseThe available literature suggests that the severity of smell and taste alterations is reduced in CoV-2-infected individuals during the periods of Omicron variant dominance ,34. HoweThe interest in elucidating the pathogenesis of altered taste and smell has escalated since COVID-19, with several hypothesis projected including viral infection-induced changes in tongue biofilm, local inflammatory responses, and neurological disturbances ,36. InteLimitations: While our study provides significant new knowledge with respect to COVID reinfection and chemosensory dysfunction, multiple limitations are recognized. 1) Our data does not specify the time period between the COVID-19 positive tests in the reinfection cohort, and hence could potentially include repeat positive tests in relation to the first infection. However, since we analyzed only data from responders reporting symptoms that lasted longer than two months, and >60% of individuals experienced symptoms for longer than one year and 10% for longer than two years, it is likely that the responses are symptoms that persisted after first positive COVID-19 test in the COVID re-infection cohort. A second limitation is that the retrospective questions about pre-COVID health status may be biased by the current health status. While we report age, sex, and race distribution, we did not perform symptom analyses by subgroup. Further, while the relative prevalence of altered chemosensation in our study is concomitant with previous studies ,17, comoIn summary, our data are consistent with the observations that the long COVID characterized by persistent multi-organ symptoms affects a proportion of COVID-19 infected individuals despite vaccination. Repeat infections are more likely associated with altered chemosensory perception for extended periods. Since chemosensory dysfunction has been strongly associated with neurological pathologies, depression, and inadequate quality of life, protective measures to prevent reinfection with SARS-CoV-2 are warranted. Future longitudinal follow-up studies or in-depth electronic health data mining studies are needed to better elucidate these relationships."} +{"text": "The aim of this study was to analyze real-world practice patterns and graft survival after corneal transplantation for infectious keratitis in the Netherlands.All consecutive keratoplasties for infectious keratitis registered in the Netherlands Organ Transplant Registry were included. Graft survival was analyzed using Kaplan\u2013Meier survival curves with Cox regression to compare the 3 most common pathogens with subgroup analysis for type and reason of transplantation, sex, and graft size. Multivariable analysis was performed using the same explanatory factors.Acanthamoeba (n = 121). Human leukocyte antigen (HLA) matching did not provide a significant survival benefit, whereas emergency procedures showed worse graft survival . Graft size >8.5 mm was significantly worse than graft size 8.5 mm . In therapeutic keratoplasty, graft survival was significantly worse for Acanthamoeba than viral keratitis . In the multivariable model, adjusting for graft size, type, and reason for transplantation, viral and bacterial keratitis did not differ significantly in graft survival, and Acanthamoeba showed a significantly worse prognosis .Between 2007 and 2017, 1111 keratoplasties for infectious keratitis were registered in the Netherlands Organ Transplant Registry. The most common pathogens were viruses (n = 437), bacteria (n = 271), and Acanthamoeba keratitis. HLA matching did not offer protection over elective non-HLA\u2013matched procedures, whereas emergency procedures and grafts sized >8.5 mm showed poor survival. In optical keratoplasty, survival is high for all pathogens, whereas in therapeutic keratoplasty Acanthamoeba shows poor outcome.Viral keratitis was the most common indication for transplantation, followed by bacterial and Donor corneas are centrally allocated and registered in the NOTR in the Netherlands. Using the NOTR, the NTS prospectively captures data related to the recipient, donor, eye bank processing, and surgical procedure of all corneal transplantation performed in the Netherlands. Corneal surgeons completed relevant follow-up data at predefined time points using a standardized electronic data capture system. Data collection was continued until graft failure or loss to follow-up. For this study, the NOTR Steering Group provided institutional review board approval for data extraction and analysis. Informed consent was obtained from all patients to participate in the registry and to use the data for research. The study adhered to the tenets of the Declaration of Helsinki and Dutch legislation.Data for this multicenter prospective registry study were obtained from the NOTR, a prospective national database founded by the Netherlands Transplantation Foundation , type of surgery , reason for surgery , and graft size . Cox regression analysis was performed over 5 years or 2 years postoperatively, depending on the number of patients still in the study at that time. The proportional hazard assumption was verified using a log(-log) survival function plot. Two-sided P values \u22640.05 were considered statistically significant.Statistical analyses were performed using the IBM SPSS Statistics for Windows . To avoid dependency between the 2 eyes, repeat transplants were excluded, and for patients who underwent corneal transplantation in both eyes, only the first eye was included in the graft survival analysis. Baseline characteristics are reported as frequencies with percentages or mean \u00b1 SD. The number of transplants over time was tested using the \u03c7nd, 2007, and December 24th, 2017. Although the volume of corneal transplant procedures has increased in the last decade, the overall number of transplants for infectious keratitis has not changed significantly over time (P = 0.070) . In this cohort of primary transplants, patients were on average 61 (\u00b118) years, 51% (n = 420) were male, 74% (n = 613) were phakic, and 13% (n = 105) were pseudophakic at the time of surgery . Of the surgeries, 65% (n = 540) were optical keratoplasties, 28% (n = 235) were therapeutic keratoplasties, and 7% (n = 54) was missing. HLA matching was performed in 6% (n = 53) of all cases, 15% of all cases (n = 126) were emergency (non-HLA matched) procedures, and 78% (n = 650) were elective non-HLA\u2013matched procedures. The mean graft size was 8.3 mm, 16% of the grafts was 8.5 mm (n = 131), 58% was smaller than 8.5 mm (n = 481), 21% was larger than 8.5 mm, and 5% (n = 44) was missing. For viral, bacterial, and Acanthamoeba keratitis, 9% (n = 38), 3% (n = 9), and 5% (n = 6) were HLA-matched; 9% (n = 41), 23% (n = 62), and 15% (n = 18) were emergency (non-HLA matched) procedures; and 77% (n = 335), 69% (n = 184), and 76% (n = 92) were elective non-HLA\u2013matched procedures, respectively. A total of 46 repeated transplants were identified. The causative pathogens included viruses , bacteria , Acanthamoeba , and fungi . Compared with the incidence of the causative agents of the first transplant, fungal keratitis had the highest risk of repeat transplantation (15%), followed by Acanthamoeba keratitis (8%), viral keratitis (5%), and bacterial keratitis (2%), P < 0.001. Of repeated transplants, 50% (n = 23) were therapeutic keratoplasties and 50% (n = 23) optical keratoplasties. HLA matching was performed in 11% (n = 5) of repeated transplants, 15% of repeated transplants (n = 7) were emergency procedures, and 74% (n = 34) were elective non-HLA\u2013matched procedures.In total, 1111 corneal transplant procedures for infectious keratitis were registered in the NOTR between January 2Acanthamoeba keratitis was 93%, 94%, and 76% at 1 year; 89%, 89%, and 67% at 2 years; 86%, 85%, and 56% at 3 years; and 83%, 79%, and 55% at 5 years, respectively. The outcomes of corneal transplantation for fungal keratitis were analyzed separately due to the low number of cases in our cohort (n = 47) and the high censoring rate (45% of cases available at 1 year). The graft survival for fungal keratitis was 90% (n = 26) at 1 year, 83% (n = 18) at 2 years, 83% (n = 13) at 3 years, and 71% (n = 4) at 5 years.A total of 784 procedures were available for graft survival analysis. Loss to follow-up was registered in 45 cases (5%). The overall graft survival rates for primary transplantation and retransplantation were 97% and 88% at 3 months, 95% and 88% at 6 months, 91% and 84% at 1 year, 86% and 75% at 2 years, and 82% and 70% at 3 years, respectively . Emergency procedures showed significantly worse 5-year graft survival compared with elective non-HLA\u2013matched procedures . The graft survival rates for optical (n = 511) and therapeutic keratoplasty (n = 224) were 96% and 78% at 1 year; 92% and 72% at 2 years; 82% and 65% at 3 years; and 88% and 59% at 5 years, respectively , emergency procedures (n = 121), and elective non-HLA\u2013matched procedures (n = 611) was 100%, 79%, and 92% at 1 year; 98%, 70%, and 88% at 2 years; 91%, 62%, and 85% at 3 years; and 90%, 59%, and 81% at 5 years, respectively and donor sex . Graft survival rates for sex-matched (n = 381) and sex-mismatched (n = 403) cases were 90% and 91% at 1 year; 88% and 86% at 2 years; 83% and 84% at 3 years; and 82% and 83% at 5 years, respectively .No significant differences in 5-year graft survival were observed for both recipient sex . However, grafts sized >8.5 mm showed significantly worse 5-year graft survival compared with grafts sized 8.5 mm . In 44 cases, the graft size was missing.Graft survival for transplants with a graft size of 8.5 mm n = 123), <8.5 mm (n = 450), and >8.5 mm (n = 167) was 90%, 94%, and 81% at 1 year; 87%, 90%, and 75% at 2 years; 84%, 88%, and 69% at 3 years; and 83%, 87%, and 65% at 5 years, respectively and bacterial keratitis and bacterial keratitis and bacterial keratitis Fig. C. For thAcanthamoeba keratitis were the most common indications. Most transplants were performed for visual rehabilitation , and a minority for debulking and preserving globe integrity (therapeutic keratoplasty). Two-year graft survival was 72% for therapeutic keratoplasty and was comparable between viral and bacterial keratitis but substantially lower in Acanthamoeba keratitis, even after correction for type, reason for surgery, and graft size.This registry study demonstrated the practice patterns and outcomes of corneal transplantation for infectious keratitis in the Netherlands. Although the volume of corneal transplantation has increased substantially in the last decade due to endothelial keratoplasty, the number of corneal transplants for infectious keratitis has remained stable. Viral, bacterial, and 8 However, we do not know what the outcomes would have been, should these high-risk patients have received non-HLA\u2013matched grafts. Nonetheless, it is unlikely that a randomized controlled trial would be conducted in high-risk patients with infectious keratitis, and the registry data may be as close as possible to answer this question. HLA matching in the Netherlands is performed at the discretion of the physician, taking into consideration the characteristics of the recipient and the delay associated with finding a matching donor. Because the use of HLA matching has become rare (<3% according to the EEBA 2008 report), our national registry provides a unique opportunity to explore this topic. A comparison of causative agents within emergency procedures revealed that viral and bacterial keratitis showed promising results, even in so-called high-risk procedures, whereas Acanthamoeba showed significantly worse outcomes.Infectious keratitis may rapidly deteriorate, necessitating corneal transplantation in an emergency setting, making it a high-risk therapeutic procedure. In our cohort, emergency procedures resulted in significantly worse graft survival rates. Although information on donor parameters for emergency transplantation is available in the registry, because of the relatively small number of cases compared with nonemergent cases, a comparison can be misleading and was therefore not included. The value of matching HLA subtypes for corneal transplantation remains controversial, and there are little data in the context of infectious keratitis. In the current study, HLA-matched grafts did not provide a significant survival benefit compared with elective non-HLA\u2013matched procedures. Similarly, a recent randomized controlled trial on penetrating keratoplasty for any indication did not find a survival benefit of HLA matching.Acanthamoeba keratitis carried a higher risk of repeat transplantation than viral and bacterial keratitis. Half of the cases involved therapeutic procedures, indicating that the primary graft was insufficient for disease management or did not yield the desired outcome. The Australian Graft Registry reported that a consecutive graft has a lower survival rate than the previous graft.9 This trend is confirmed in this study for infectious keratitis and shows the burden on patients and health care.Fungal and 13 Against the background of penetrating keratoplasty for infectious keratitis, we failed to detect a significant effect for donor\u2013recipient matching.A much-debated question is the impact of donor\u2013recipient sex matching on graft survival. Previous studies reporting on sex matching in the context of both endothelial keratoplasty and penetrating keratoplasty have shown inconsistent results.16 but not all studies found a significant association.17 Lower graft survival of larger grafts in our cohort may be related to a higher antigenic load in the proximity of the limbus increasing the risk of rejection and a more severe infection requiring debulking.Large-diameter corneal grafts have been previously described as a risk factor for graft failure,18 in particular herpes simplex keratitis which affects 1.5 million people globally.20 In our study, 2-year graft survival for therapeutic viral keratitis measured 77% which is high compared with studies reporting 55%\u201375% at 2 years.23 The cause of failure is manifold, for instance, in herpes simplex keratitis, stromal keratitis is associated with deep vascularization which increases rejection risk,24 and disease recurrence is common after nerves regenerate in the graft. Moreover, herpes keratitis is accompanied by hypoesthesia, which facilitates recurrent trauma and exposure keratopathy.25 The relatively high graft survival in our cohort may be related to standard use of oral prophylaxis to prevent herpes recurrence in the Netherlands.26In most parts of the developed world, viral keratitis is the most common cause of unilateral infectious corneal blindness,27 Although promising, the US Center for Disease Control estimated that annually 2.8 million people are infected with drug-resistant microbes and resistance is increasing.28 In our cohort, the number of keratoplasties varies over time but does not follow a directional trend. Two-year graft survival of therapeutic keratoplasty for bacterial keratitis was 81%, slightly lower than that reported in previous studies (over 90%).30In bacterial keratitis, the introduction of newer and more potent antibacterial agents led to a decrease in the number of therapeutic keratoplasties in some centers.Acanthamoeba keratitis accounted for 14% of all indications and increased from a handful of cases before 2009 to double digits since 2015. This increase may be due to the use of silicone hydrogel contact lenses,31 multipurpose solutions,32 or local environmental factors.33 In line with the literature, corneal grafting for Acanthamoeba keratitis showed poor survival outcomes.36 Importantly, Acanthamoeba keratitis showed the worst outcomes of all causative agents even when outcomes were adjusted for type of procedure , reason for grafting , and graft size. Age was omitted from the multivariable analysis because Acanthamoeba predominantly affects younger individuals. Since the introduction of biguanides for medical therapy, most cases are treated medically and therapeutic keratoplasty is traditionally reserved for cases of insufficient response to medical therapy or severe complications.37 A much debated question is the value of early therapeutic deep anterior lamellar keratoplasty in Acanthamoeba keratitis.38 However, at the moment, this is not standard of care in the Netherlands, as a result of which there were too few cases available for separate analyses.In our cohort, the volume of corneal transplantation for 39 The disease accounts for a significant burden of blindness,39 causing nearly 5 times as many corneal perforations as bacterial keratitis.40 In our cohort, graft survival for fungal keratitis was 83% 2 years postoperatively, mirroring the outcomes of transplants performed for viral and bacterial keratitis, and comparable to reports in the literature.41Fungal keratitis has a global incidence of more than 1 million cases each year.Central graft allocation by the NTS ensured the robustness of our primary outcome measure: graft survival. Nonetheless, our study has the following limitations. The NOTR database is not designed to specifically capture differences in virulence, predisposing factors, extensiveness of keratitis, and ocular surface inflammation. Moreover, to reduce the registration burden, not all parameters are mandatory, for example, corneal neovascularization, sutures, and use of topical and systemic immunosuppressive therapy. The time between disease onset and transplantation is also an interesting factor that was unavailable in this study. However, therapeutic and emergency procedures may be used as surrogates.Acanthamoeba. Viral keratitis was the most common indication, followed by bacterial and Acanthamoeba keratitis. Graft survival was promising, except in Acanthamoeba keratitis and grafts larger than 8.5 mm. The benefit of HLA matching is unclear, but our data suggest that it may not provide additional survival benefits. Timely therapeutic keratoplasty should be considered as needed given the relatively successful outcomes in our study, especially for viral and bacterial keratitis.In conclusion, this prospective Dutch registry study shows that the volume of corneal transplantation for infectious keratitis has remained stable over the last decade, with the exception of The Netherlands Corneal Transplantation Network (excluding writing committee): Lies Remeijer, MD, PhD; Jeroen van Rooij, MD; Robert H.J. Wijdh, MD; Annette J.M. Geerards, MD; Cathrien A. Eggink, MD, PhD; Michel J.W. Zaal, MD, PhD; Carla P. Nieuwendaal, MD; Remco Stoutenbeek, MD, PhD; Tom A. van Goor, MD; Marjolijn C. Bartels, MD, PhD; Bart T.H. van Dooren, MD, PhD; Ype P. Henry, MD; Siamak Nobacht, MD; Mei L. Tang, MD; Robert P.L. Wisse, MD, PhD; Ivanka J. van der Meulen, MD, PhD; Ruth Lapid-Gortzak, MD, PhD; Chantal M. van Luijk, MD; Nathalie T.Y. Santana, MD, PhD; Isabelle Saelens, MD, PhD; Yanny Y. Cheng, MD, PhD; Sacha Gast, MD; Annemiek Rijneveld, MD, PhD; Allegonda van der Lelij, MD, PhD; Michel Zaal, MD, PhD; Nayyirih de Koning Tahzib, MD, PhD; Cesar Sterk, MD; Martine Jager, MD, PhD; Gabriel van Rij, MD, PhD; Mario Dhooge, MD; Hugo van Cleynenbreugel, MD, PhD; Isabel Bleyen, MD, PhD; and Benedicte Putting MD, PhD."} +{"text": "Background: Most antibiotic use occurs in ambulatory settings. Antibiotic prescribing for children living in the United States in medically underserved areas or in populations is not well understood.Objective: To characterize antibiotic prescribing for children in a practice-based research network (PBRN).Design and Methods: In this retrospective cohort study, we characterized oral antibiotic prescribing in a large PBRN. Patients aged 0\u201317 years with at least 1 in-person visit between January 1, 2014, and December 31, 2018, at 1 of 25 primary-care clinics located within the WWAMI region of the Practice and Research Network (WPRN) were included. Data were extracted from DataQUEST, a centralized data repository from included primary-care clinics. Encounters for wellness visits or those lacking a diagnosis code and patients with complex chronic conditions were excluded. Diagnoses were categorized using International Classification of Disease, Ninth Revision (ICD-9) and ICD-10 codes. Oral antibiotics prescribed within 3 days of an encounter were associated with that encounter. Demographic data included age, sex, race, and ethnicity. Antibiotic appropriateness was determined using a previously published 3-tiered classification system using diagnosis codes as always, sometimes, or never appropriate. Patient-level data (ZIP codes) were used to designate medically underserved areas (MUAs) and medically underserved populations (MUPs). Antibiotic prescribing was then analyzed within these groups. Results: In total, 37,314 patients across 206,845 encounters were included, of which 34,601 encounters (17%) resulted in antibiotic prescription (Table 1). Of those, appropriateness data were available for 34,286 (99%). Of the antibiotics prescribed, 14% were always appropriate, 57% were sometimes appropriate, and 27% were never appropriate (1% missing). In total, 64% and 35% of encounters occurred with patients from an MUA and MUP, respectively. Conclusions: Targets to improve oral antibiotic prescribing for children in a large PBRN include antibiotic prescribing for diagnoses that never require an antibiotic. Larger comparative studies may focus on the role (if any) that MUA/MUP has on antibiotic prescribing.Disclosures: None"} +{"text": "Objectives: Influenza vaccination is encouraged for all healthcare workers (HCWs) to reduce the risk of acquiring the infection and onward transmission to colleagues and patients during the influenza season. Thus, vaccination was introduced at Singapore General Hospital (SGH) in 2007 and has been offered to all HCWs at no cost. The HCW influenza vaccination program is conducted annually in October and biannually during years with vaccine mismatch.\u00a0However, influenza vaccine uptake remained low among HCWs. We sought to determine the impact of the coronavirus disease 2019 (COVID-19) pandemic on influenza vaccine uptake among HCWs. Methods: At SGH, 2 methods of vaccine delivery are offered: centralized (1-month drop-in system during office hours) and decentralized (administered by vaccination teams in offices or ward staff in inpatient locations). In the 4-year study period between 2018 and 2021, 6 influenza vaccination exercise campaigns were conducted during 8 influenza seasons. During each exercise, ~9,000 HCWs were eligible for vaccination. Results: Prior to the COVID-19 pandemic, vaccine uptake in the Southern Hemisphere was 77.6% in 2018 and 84.2% in 2019. During the COVID-19 pandemic in 2020, vaccine uptake in the Southern Hemisphere increased by 10% to 94.1% . In the Northern Hemisphere, vaccine uptake was 79.2% in 2018, and this increased by 17.9% to 97.1% during the COVID-19 pandemic in 2020. During the 2021 Southern Hemisphere influenza season, no vaccination program was conducted because the risk of influenza was considered low due to the closure of international borders and the implementation of public health measures. In addition, priority was given to COVID-19 vaccination efforts. Conclusions: Increased uptake of the influenza vaccination was observed during the COVID-19 pandemic. Anxiety created by the respiratory disease pandemic and debate surrounding vaccines likely contributed to increased awareness and uptake in influenza vaccine among HCWs."} +{"text": "Congenital syphilis (CS) rates have increased in the United States since 2013. Management of infants exposed to syphilis during pregnancy entails a detailed clinical evaluation, followed by stratified work-up and treatment.During 2016\u25002021, 9,827 surveillance cases of CS were notified to the National Notifiable Diseases Surveillance System. Using the clinical framework described in the 2015 CDC Sexually Transmitted Diseases Treatment Guidelines, we assigned a clinical scenario to 8,280 liveborn cases which had sufficient data for case classification . Based on data documented in the case report, we described the elements of evaluation and therapy provided to neonates, assessing whether they met, were in excess of, or were less extensive than recommendations, and stratified these findings by race, ethnicity, and geography.Of the 8,280 surveillance cases which were assigned a clinical scenario, the majority (80.9%) were classified as Possible CS, of whom 60.7% received an appropriate evaluation, while 68.4% received appropriate treatment. Of those assigned to Proven or Highly Probable CS, 46.0% received an appropriate evaluation, while 82.3% received appropriate treatment.By U.S. census region, infants born in the Northeast were most likely to receive evaluation (75.7%) and treatment (87.3%) at or above recommendations for their case scenario, while infants born in the South were least likely to receive at or above recommended evaluation (49.5%) and treatment (59.3%). Infants born to a birth parent reporting non-Hispanic Native Hawaiian/Pacific Islander race were most likely to report less than recommended evaluation (36.7%), while infants of a non-Hispanic Black birth parent were most likely to experience less than recommended treatment (32.2%).This analysis of CS clinical scenarios underscores disparities in evaluation and therapy across geographic, racial, and ethnic lines. Further research is needed to understand factors involved in the evaluation and treatment of infants affected by CS, particularly for those born in the South and to birthing parents reporting minority racial and ethnic backgrounds.All Authors: No reported disclosures"} +{"text": "Butyrivibrio fibrisolvens and Streptococcus gallolyticus; and reduced protozoa and methanogens. Our results suggest that neem leaf could be an interesting substitute supplement for goat feed. We believe that neem leaf has the potential to help the goat meat industry meet the demands of health-conscious consumers.Neem leaves are a rich source of tannin, may prevent protein degradation in the rumen, and may increase growth performance because they are natural substances; thus, they are appealing as rumen modifiers. Animal nutritionists must manipulate ruminal ecology and fermentation to improve feed intake in ruminants. Therefore, the purpose of this study was to evaluate the effect of neem leaf supplementation on digestibility, growth performance, rumen fermentation, and ruminal microbial population in goats. The findings indicated that goats fed 6% neem leaf (NL) + 15% (polyethylene glycol (PEG)) in the concentrate had the highest values of feed intake, nutrient digestion, and nitrogen utilization increased growth performance; the highest values of p < 0.05) feed intake gDM/d, % BW, g/kgBW0.75, nutrient intake, nutrient digestion, weight change, and ADG than did the goats that were fed with 0% NL + 0% PEG, 0% NL + 15% PEG, and 6% NL + 0% PEG in concentrate, respectively. The feeding with 6% NL + 15% PEG had a higher (p < 0.05) level of propionic acid at 2 and 4 h post feeding compared to the other treatments. Supplementation with 6% NL + 15% PEG in the concentrate had the lowest (p < 0.05) methanogen, protozoa, blood urea nitrogen, ammonia nitrogen, acetic acid, and butyric acid, as well as a lower ratio of acetic acid to propionic acid at 2 and 4 h post feeding than the other treatments. However, supplementation with 6% NL + 15% PEG in concentrate had the highest values of Butyrivibrio fibrisolvens and Streptococcus gallolyticus at 2 and 4 h post feeding compared to the other treatments (p < 0.05). Collectively, this study indicates that neem leaf supplements can increase growth performance and propionic acid and can modulate the abundance of Butyrivibrio fibrisolvens and Streptococcus gallolyticus. Thus, neem leaf could potentially be a good supplement for goat feed.This study aims to investigate the effect of neem leaf supplementation on the feed intake, digestibility, performance, fermentation characteristics, and ruminal microbes in goats. We included 24 Anglo-Nubian Thai native male goats with a body weight of 20 \u00b1 2.0 kg, using 2 \u00d7 2 factorial in a completely randomized design for the following four treatments: (1) control, (2) control + 15% PEG in the concentrate, (3) 6% NL in concentrate, and (4) 6% NL + 15% PEG in concentrate. The results show that supplementation with 6% NL + 15% PEG in the concentrate had a higher ( Animal nutritionists are interested in improving ruminant feed efficiency by modifying rumen fermentation. Feed additives that influence rumen fermentation improve feed utilization . Goat prAzadirachta indica) is a tropical tree that grows in Thailand and India. The leaf extract is used as an antibacterial and bacteriostatic compound. It promotes digestibility and metabolism of proteins in ruminants. Neem leaves have been found to be a rich sources of secondary plant compounds, including alkaloids, flavonoids, polyphenolic components, and condensed tannins (CT). Moreover, they might have antimicrobial properties, particularly toward protozoal and methanogen populations. Neem leaf may prevent protein breakdown in the rumen and increase amino acid absorption in the small intestine. Animal feed containing protein\u2013tannin compounds can increase protein production by microorganisms in goats. Tannins can decrease the bacterial population in the rumen, resulting in a decrease in the protozoa population, which could be caused by a decrease in cell membrane permeability. The effect of tannin supplementation on the methanogen population to help minimize methane permeability has been researched 3-N levelstudy in stated tSupplementation with 6% NL + 15% PEG resulted in high values of propionic acid at 2 and 4 h and a decrease in total VFA, but with values within the normal range for goats. Because of its high molecular weight, neem leaf has a strong effect on total VFAs and acetic acid production, unlike low molecular weight substances . Since tButyrivibrio fibrisolvens and Streptococcus gallolyticus at 2 and 4 h. It was also discovered that Streptococcus gallolyticus can assist animal health by helping improve goat growth and reducing the occurrence of mastitis. Neem leaf supplementation can reduce the quantity of Streptococcus gallolyticus, [Streptococcus gallolyticus, which improves the digestibility of nitrogen in sheep, may be reduced due to supplementation with tannins. The rumen bacterium Butyrivibrio fibrisolvens has been identified as undertaking biohydrogenation of fatty acids and forming conjugated linoleic acid (CLA), which is an intermediate isomer of C18:2, in the process.Supplementation with 6% NL + 15% PEG is reported to have antibacterial properties, helping to reduce gastrointestinal tract fermentation. In this study, the use of neem leaf in the concentrate led to the highest amount of tannins, which were found to increase lyticus, , increaslyticus, found th4 production [In this study, supplementation with 6% NL + 15% PEG reduced methane production because neem leaf contains tannins, compounds with good anti-protozoa properties. Adding condensed tannins with a higher molecular weight has been found to reduce acetic acid formation and CHoduction ,37. Tannoduction , which iButyrivibrio fibrisolvens at 2 and 4 h, which increased the amount of protein-producing microorganisms. Nevertheless, depending on the tannin and microbial levels in the rumen, roughage is one of the factors that affects the rumen microbe population. In [In this experiment, supplementation with 6% NL + 15% PEG increased tion. In , it was Butyrivibrio fibrisolvens, and Streptococcus gallolyticus, as well as decreased protozoa and methanogens. Further studies are warranted to investigate the effect of neem leaf on meat products and antioxidant activity in meat.In our study, supplementation with 6% NL + 15% PEG in the concentrate increased the feed intake, nutrient intake, nutrient digestion, nitrogen utilization, and growth performance of goats. Moreover, supplementation with 6% NL + 15% PEG in the concentrate had the highest propionic acid,"} +{"text": "Lower limb amputation (LLA) is a major surgical procedure with a significant impact on quality of life and mortality rates as well. Previous studies have shown that mortality rates following LLA can range from 9-17% within 30 days in the UK. This study systematically evaluates and reviews the published literature on life expectancy, mortality, and survival rates following lower extremity amputation (LEA). We have conducted a comprehensive search on Medline, CINAHL, and Cochrane Central databases resulting in 87 full-text articles. After a thorough review, only 45 (52.9%) articles met the minimum inclusion criteria for the study. Our analysis indicated 30-day mortality rates following LEA ranged from 7.1% to 51.4%, with an average mortality rate of 16.45% (SD 14.35) per study. Furthermore, 30-day mortality rates following below-knee amputation (BKA) and above-knee amputation (AKA) were found to be between 6.2% to 51.4%, X= 17.16% \u00b1 19.46 SD and 12.7 to 21.7%, X= 16.15% \u00b1 4.17 SD, respectively. Our review provides a comprehensive insight into the life expectancy, mortality, and survival rates following LEA. These findings highlight the importance of considering various factors, including patient age, presence of comorbidities such as diabetes, heart failure, and renal failure, and lifestyle factors such as smoking, in determining prognosis following LLA. Further research is necessary to determine strategies for improving outcomes and reducing mortality in this patient population. The earliest documented use of lower-limb amputation (LLA) dates back to the Hammurabi era in Babylon, where it was utilized as a form of punishment . SubsequThe primary determinants for the selection of amputation include surgeon preference, physician supply, geographical factors, healthcare delivery systems, and socioeconomic factors ,6. The rThe only absolute indication for this is irreversible ischemia, which can be due to traumatic or non-traumatic etiologies. This ischemia can manifest as gangrene, wet gangrene, spreading cellulitis, arteriovenous fistula, malignancy, severe rest pain with irreversible critical leg ischemia, and paralysis . FactorsPeripheral vascular disease (PVD) and diabetes mellitus (DM) have been identified as primary risk factors for lower limb amputations . AmputatDespite the development and wider availability of novel diagnostic procedures and peripheral vascular interventions, the rates of amputation and subsequent survival have remained relatively unchanged over the past few decades . UltimatMaterials & methodsTo achieve a rigorous search for studies relating to Life Expectancy Score in LEA (Lower Extremity Amputation), In February 2021, we searched Medline using OVID, CINAHL, and the Cochrane Central database using a search strategy built on terms that include: \"lower limb amputation (LEA), life expectancy, above knee amputation (AKA), below knee amputation (BKA), survival, mortality\".Searching for the used keywords and MeSH terms has been done through Boolean combinations of keywords based on our inclusion and exclusion criteria.For the identification phase, extensive title and abstract screening were done to detect their relevance. Abstracts that didn't have either mortality or survival rate data of amputees were excluded. Papers that were cited by or used as references in the search set studies were collected and included in our review; after acquiring full-text versions of included studies, deep and extensive reviewing was done. Studies were excluded if they did not present quantitative data on mortality. Moreover, papers were evaluated to determine which outcomes could be meaningfully extracted.ResultsAfter a comprehensive database search was conducted, PRISMA guidelines for reporting the systematic reviews were followed. Search results led to the identification of 87 full-text articles and 729 (7.5%), respectively. The 30-day mortality rates among the 8 studies that did not differentiate the type of amputation ranged from 7.1% to 51.4%, with an average mortality rate of 16.45% (SD 14.35) per study. The studies that investigated the mortality rates following BKA reported a range of 6.2% to 51.4%, with an average mortality rate of 17.16% (SD 19.46). Meanwhile, the studies investigating the mortality rates following AKA reported a range of 12.7% to 21.7%, with an average mortality rate of 16.15% (SD 4.17) per study. One study reported a 12% mortality rate following a combination of BKA and AKA. In the three studies, the mortality rates following toe, Transtibial (TTA), and Transfemoral (TFA) amputations were reported as 1.7%, 7%, and 11.1%, respectively. Four studies reported the mortality rates following trans-metatarsal amputation (TMA) as 1.98%, 2.7%, 4%, and 7%, with an average mortality rate of 3.92% (SD 2.22) per study.One-year MortalityThe studies that investigated the one-year mortality rates among individuals who underwent LEA with a specified operation reported a range of 9.2% to 64.3%, with an average mortality rate of 33.49% (SD 16.38) per study. Two studies each reported the mortality rates following BKA (range 23-33%) and AKA (range 41-58%) with average mortality rates of 28% (SD 7.07) and 49.5% (SD 12.02), respectively. One study reported a 40% mortality rate following TTA, and another reported a 15.8% mortality rate following both BKA/AKA.Overall MortalityEight studies reported the overall mortality rates among individuals who underwent LEA with a range of 10.6% to 80% and an average mortality rate of 34.24% (SD 26.08) per study.DiscussionIn this systematic review, we have screened the extensive research yield of 85 full-text articles and selected 45 articles that contained representative information about survival and mortality rates in patients who underwent LEA. Very few numbers of published articles explicitly explored the life expectancy of patients after amputation, and it was often only a very small part of every article. Furthermore, only a few studies classify outcomes of patients who underwent amputation depending on the surgical procedures and levels specifically, making it difficult to focus on survival outcomes after either operation. Consequently, we had to include studies where mortality or survival rates are mentioned disregarding than study design.First, it showed that 30-day mortality has a very wide range of rates with highly variable SD; mortality rates reached up to half of the cohort included. In their retrospective cohort study, the cause of early mortality and low survival rates in the first month and first 1-year after amputation was investigated by Peter Gebuhr et al. , where tPotential causes of 30-day mortality after amputation include cardiovascular disease, especially in case of declined mobility after AKA, postoperative wound infection, which includes bacterial and fungal infection, and thromboembolic events such as DVT and pulmonary embolism -19.This highlights the importance of considering pre-and postoperative confounding factors that affect short-term survival, which was concluded by P.U. Dijkstra et al., they demonstrated that factors significantly associated with 30-day mortality were age, location admission from the previous peripheral vascular procedure and cerebrovascular disease . It is cSeveral factors contribute to 1-year mortality after amputation, including medical comorbidities, surgical factors, and rehabilitation outcomes . The autAlthough both BKAs and AKAs result in improved quality of life and survival outcomes compared to limb-saving procedures, it was documented in the literature that there is a difference in postoperative functional outcomes of mobility between the two surgical procedures . Our revOur review has some limitations. Firstly, the inclusion of studies from different years of publication generalizes our results harder and is not fair because of the variability of healthcare availability, improvement in surgical methodology, and advancement of postoperative follow-up through the years as well as increased incidence of metabolic burden and atherosclerotic changes which not only control the type of operation but also affect post-amputation outcomes.Secondly, due to the lack of homogeneity of the included cohort, extensive analysis of extracted data had not been done; therefore, we can't conclude solid results of the mortality score of all involved patients.Our review summarizes the last hundred-year literature involving mortality data for almost half a million amputees in approximately 17 countries worldwide. This gives a comprehensive overview of the life expectancy of amputation survivors and encourages researchers, internal physicians, and surgeons to collaborate to prevent amputation at first and eventually improve pre and postoperative comorbidities of amputees."} +{"text": "The dental surgeon may be the cause of a psychological trauma - without necessarily knowing it - as well as being confronted with patients who have undergone a trauma as a result of dental care or with patients who have undergone some kind of trauma and that the dental practice exacerbates their anxieties. In this case, the treatment becomes difficult or even inaccessible or a cause of treatment failure.Study the events that can cause trauma and the different approaches to psychological trauma in dental care.How to explore the traumatic event in a patient and propose its erasure?Study the events that can cause trauma and the different approaches to psychological trauma in dental care. How to explore the traumatic event in a patient and propose its erasure?This is a descriptive and analytical cross-sectional study based on a hetero questionnaire filled in by patients who consulted a dental surgeon.41% are men, 76% are aged between 30 and 50 years, for the marital status: 43% are single, 38% are married, 72% have an average socioeconomic level, 36% of patients have a personal history of a psychiatric disorder, 21% personal history of a medical disease, 32% have a disorder related to the use of psychoactive substances,For the reason of consultation: 28%: dental square, 42%: oral malformations, 17%: gingival problem, 8% dental extraction. Medication used: 65% of patients used anti-inflammatory drugs, 77% used antibiotics, 13% used paracetamol. Duration of treatment: 86% one year41% are men, 76% are aged between 30 and 50 years, for the marital status: 43% are single, 38% are married, 72% have an average socioeconomic level, 36% of patients have a personal history of a psychiatric disorder, 21% personal history of a medical disease, 32% have a disorder related to the use of psychoactive substances, For the reason of consultation: 28%: dental square, 42%: oral malformations, 17%: gingival problem, 8% dental extraction. Medication used: 65% of patients used anti-inflammatory drugs, 77% used antibiotics, 13% used paracetamol. Duration of treatment: 86% one year .He should be careful, attentive and open to the principles of the psychology of communication in his psychological approach, in order to adapt the level of difficulties of care to the capacity of comprehension, so as to take care of the patient in his globality and avoid any traumatic act. He should not hesitate to send his patient to a psychiatrist if necessary.None Declared"} +{"text": "P. aeruginosa active antibiotics are recommended for people residing in subtropical and tropical climates with moderate and severe DFIs. However, there is limited data supporting this recommendation. Our systematic review and meta-analysis aimed to understand the prevalence of gram-negative and P. aeruginosa DFIs across solar climate zones .Diabetic foot infections (DFIs) are the leading cause of preventable limb loss globally. The International Working Group on Diabetic Foot Infection guidelines advise an empiric antibiotic regimen choice for DFI partly based on climate: gram-negative and P. aeruginosa\u00ad in foot soft tissue and/or bone cultures. We reported common and random effects models.We searched PubMed, Embase, AIM, IMSEAR, IMEMR, LILACS, and WPRIM for studies published in any language between 2010-2020 reporting \u22655 unique patients with a DFI . Two reviewers independently assessed studies for eligibility, and we used double data entry. The senior author resolved disagreements. We assigned climate zone based on study center location and built Forest plots to depict the proportion of patients with (1) \u22651 gram-negative bacteria and (2) with P. aeruginosa. A random effects model found the proportion of patients with gram negative infection varied by climate zone: 40% in temperate regions; 58% (95% CI 51% \u2013 65%) in sub-tropical regions; and 67% (95% CI 49% \u2013 61%) in tropical regions . The proportion of DFI with P. aeruginosa was 14% (95% CI 12% - 17%) in temperate areas; 15% (95% CI 13% - 17%) in subtropical regions; and 16% (95% CI 14 \u2013 17%) in tropical regions .293 studies out of 4101 studies met our inclusion criteria. Of these, 53 studies representing 4,970 patients reported the proportion of patients with gram negative infections, and 270 studies representing 36,026 patients reported the proportion with P. aeruginosa DFIs and climate.Our meta-analysis suggests that gram-negative infections occur at higher proportions in tropical and sub-tropical areas compared to temperate regions. Future studies should aim to elucidate the interactions between other risk factors for gram-negative and/or All Authors: No reported disclosures"} +{"text": "Candida and Aspergillus species. Additionally, incidences of Candida auris infections have increased in Lebanese hospitals during the COVID-19 pandemic, with a uniform resistance to fluconazole and amphotericin-B. Taken together, a One Health approach, reliable diagnostics, and prudent antifungal use are required to control the spread of resistant fungal pathogens in healthcare and agricultural settings.Antimicrobial resistance is a serious threat, particularly in low- and middle-income countries (LMICs). Antifungal resistance is often underestimated in both healthcare and non-clinical settings. In LMICs, it is believed that the inappropriate use of antifungals, limited surveillance systems, and low diagnostic capacities are significant drivers of resistance. Like other LMICs, Lebanon lacks antifungal use and resistance surveillance programs, and the impact of antifungal resistance in the country remains unclear, especially during the unfolding economic crisis that has severely affected medical care and access to safe food and water. Interestingly, the widespread use of antifungals in medicine and agriculture has raised concerns about the development of antifungal resistance in Lebanon. In this light, we aimed to survey available antifungal drugs in the country and evaluate susceptibility patterns of prevalent fungal species to guide empiric treatments and develop antifungal stewardship programs in Lebanon. We noted that the economic crisis resulted in significant increases in antifungal drug prices. Additionally, a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar databases identified 15 studies on fungal infections and antifungal resistance conducted from 1998 to 2023 in Lebanon. While data on antifungal resistance are limited, 87% of available studies in Lebanon focused on candidiasis, while the remaining 13% were on aspergillosis. Overall, we observed a marked antimicrobial resistance among Antimicrobial resistance has become a significant global public health threat, especially in low- and middle-income countries (LMICs) that are challenged with different medical, environmental, and socioeconomic problems ,2,3. AltPichia kudriavzevii (formerly known as Candida krusei) towards fluconazole [Aspergillus terreus towards amphotericin-B [Fungal diseases represent a growing concern in human and veterinary medicine, with a significant impact on morbidity and mortality, particularly among predisposed patients, and substantial healthcare costs ,5,6,7. Aconazole and the ericin-B . In addiericin-B . For exaericin-B ,14.It is known that the inappropriate use of antifungals poses a selective pressure that is a key driver for the emergence and dissemination of antifungal resistance in the human\u2013animal\u2013environment continuum ,16,17,18In 2017, Lebanon joined the World Health Organization\u2019s (WHO) Global Antimicrobial Resistance Surveillance System (GLASS) ,24. HoweCandida spp. and Aspergillus spp. prevalent in Lebanon in order to facilitate effective treatment of fungal infections and reduce the morbidity and mortality associated with these diseases. The results of this study provide valuable bases for developing antifungal stewardship programs and mitigating the emergence of antifungal resistance in the region and beyond.The pervasive use of antifungal agents in healthcare and agriculture has raised concerns regarding the emergence of antifungal resistance in Lebanon. To address this issue, we conducted a survey to identify the antifungal drugs available in both pharmaceutical and agricultural markets. Additionally, we evaluated the current trends of antifungal susceptibility patterns of We identified a total of 18 antifungal drugs belonging to four different classes. The drugs were classified as follows: (1) azoles , (2) allylamines (terbinafine), and (3) echinocandins , and (4) polyenes (amphotericin-B liposome and nystatin) . These dIn human medicine, antifungal drugs are either locally manufactured in Lebanon or imported from various European countries and Japan, and they can be administered topically, orally, or intravenously. Most of the drugs are available in both topical and oral forms and can be easily obtained from pharmacies without prescriptions. However, drugs administered intravenously, such as caspofungin, anidulafungin, micafungin, and amphotericin-B liposome, are strictly reserved for hospital use and are not available in pharmacies.In response to the economic crisis in Lebanon, the Ministry of Public Health initially subsidized a range of essential medications, including antifungal drugs, to ensure patients had access to affordable drugs. However, as the crisis persisted, the government was forced to remove or drastically reduce these subsidies, resulting in a significant increase in drug prices across the country. To assess the impact of these changes on the availability and affordability of antifungal drugs in Lebanon, we evaluated the market prices of antifungal medications that are important in human medicine. We observed that the prices of the most used antifungal drugs significantly increased, by 3 to 12 times in comparison to the pre-crisis cost in some instances, from October 2019 to February 2023 .We found that six fungicides are currently available in agricultural drug stores and used in Lebanon. Specifically, the highest number of antifungals present in the Lebanese agricultural drug stores belonged to triazoles , followed by pyrimidine derivatives , thioureas (thiophanate methyl), and copper (copper oxychloride). In addition, three drugs that are widely used in animals without the requirement of a veterinarians\u2019 prescription were found. These drugs belong to different classes of antifungals, including pyrimidine derivatives (diazinon), polyenes (nystatin), inorganic sulfurs , and carboxylic acid amides. . The druMost of the antifungals used to prevent fungal infections in plants and animals are systemic fungicides. Our data revealed six systemic fungicides. For example, difenoconazole, penconazole, pyrimethanil, nystatin, and calcium polysulfide are among the systemic fungicides detected . PreventCandida, and the remaining two (13%) were on Aspergillus. These investigations primarily adopted a cross-sectional approach, complemented by two case reports, one prospective and two retrospective studies. Overall, our analysis revealed a limited number of well-designed national studies , the non-use of reference susceptibility testing methods in most clinical laboratories, and the absence of epidemiological tracking and national reports.We screened all available studies (n = 15): 13 (87%) focused on Candida and Aspergillus isolates exhibited a notable resistance to almost all antifungal agents , ketoconazole (6% to 19%), itraconazole (12.1% to 44%), posaconazole (20.7%), voriconazole (2.5% to 13.8%), micafungin (13.8%), anidulafungin (41.4%), amphotericin-B (0% to 13.8%), and flucytosine (6%). We also found moderately significant resistance rates to antifungal drugs in Candida glabrata and Candida tropicalis. Specifically, fluconazole resistance ranged from 22.2% to 100% in C. glabrata and 16.4% to 95.7% in C. tropicalis, while ketoconazole resistance affected 0% of C. glabrata isolates and 67% of C. tropicalis isolates. Itraconazole resistance was identified in 16.7% to 70.5% of C. glabrata isolates and 40% to 67% of C. tropicalis isolates, while 11% of C. glabrata and 50% to 96.1% of C. tropicalis were posaconazole-resistant. Voriconazole resistance was found in 25% to 33% of C. glabrata and 0% to 10.5% of C. tropicalis isolates. Additionally, C. glabrata showed resistance to micafungin (1.5% to 16.7%) and anidulafungin (0% to 61.1%), while 0% to 10% of C. tropicalis were resistant to amphotericin-B. Flucytosine resistance was not noted in C. glabrata or C. tropicalis isolates. Moreover, an important antifungal drug resistance was identified in Candida parapsilosis and P. kudriavzevii, where 0% to 93.2% and 68% to 100% were resistant to fluconazole, 0% to 75% and 0% to 20% were resistant to itraconazole, 8.3% to 100% and 0% were resistant to posaconazole, 0% to 41.7% and 20% were resistant to micafungin, 0% to 33.3% and 20% were resistant to anidulafungin, and 0% to 8.3% and 0% to 60% were resistant to amphotericin-B, respectively. It is worth mentioning that all tested isolates were susceptible to voriconazole.Assessing the available data, our findings highlighted that l agents . We founKluyveromyces marxianus (formerly known as Candida kefyr), 41.6% of the isolates were resistant to fluconazole, 33.3% were resistant to itraconazole, 50% were resistant to miconazole, and 33.3% were resistant to micafungin; all isolates were susceptible to voriconazole, posaconazole, anidulafungin, and amphotericin-B. The emergent Candida auris was frequently reported in different hospitals during the COVID-19 pandemic. C. auris circulating in Lebanon consistently demonstrated resistance to fluconazole (100%) and amphotericin-B (100%) and susceptibility to echinocandins (0%). Resistance to voriconazole was observed in 3% of the C. auris isolates.Regarding Aspergillus isolates in Lebanon. Specifically, 32.5% of Aspergillus niger isolates were resistant to itraconazole, followed by 25% to posaconazole, 12.5% to voriconazole, and 20% to amphotericin-B. Furthermore, 20% of Aspergillus flavus isolates were resistant to itraconazole, along with 30% to posaconazole, 40% to voriconazole, and 70% to amphotericin-B. However, lower resistance rates were observed in Aspergillus fumigatus isolated from both clinical [Our analysis showed also a concerning increase in multidrug-resistant clinical and enviclinical settingsThe inappropriate and unsupervised use of antifungals in Lebanon appears to be a growing public health concern with significant implications associated with the emergence of multidrug-resistant fungal pathogens, patient outcomes, and healthcare and agricultural systems. Our findings showed an increasing trend in antifungal resistance, emphasizing an urgent need to address this critical issue promptly and effectively at the human\u2013animal\u2013environment continuum. Addressing this burden requires a comprehensive approach that combines various aspects of the One Health ethos, from surveillance to outreach, targeting the proper use of antifungals, appropriate diagnostics, infection control, and patient management.Antifungal use in the community in Lebanon increased by 88% from 2004 to 2018, as measured by the number of defined daily doses, with the highest consumption level noted in 2017 . Triazolalbicans species that inherently possess higher resistance to these treatments [C. auris infections in critically ill patients in healthcare settings has been steadily increasing across hospitals in Lebanon [C. auris occurred during the pandemic (October\u2013December 2020) at the American University of Beirut Medical Center [C. albicans toward less susceptible non-albicans Candida over the last two decades [Intravenous antifungals are often appropriately used because they are typically reserved for in-hospital use. However, the COVID-19 pandemic has brought about a concerning surge in fungal infections within intensive care units of healthcare facilities, resulting in an increased reliance on broad-spectrum antifungals . This waeatments . Notably Lebanon ,29,30. T decades ,44, whicCandida and Aspergillus isolates exhibited a notable level of resistance to almost all antifungal drugs compared to neighboring countries. In Lebanon, fluconazole resistance ranged from 2% to 33% in C. albicans, 22.2% to 100% in C. glabrata, and 16.4% to 95.7% in C. tropicalis. In Tunisia, resistance to fluconazole was observed in 63\u2009% and 16% of C. albicans and C. glabrata isolates from vaginal swab samples of pregnant women, respectively [C. auris have been recently reported in the MENA region, including Lebanon [Aspergillus showed differing frequency of azole resistance as follows: 31.5% were resistant in Lebanon [Little information is available in the literature about antifungal susceptibility in the Middle Eastern and North African (MENA) countries, but a few previous studies reported varied rates of resistance to antifungals. Overall, the data from Lebanon showed that ectively . Moreove Lebanon ,46,47,48 Lebanon , 30.6% w Lebanon , 3.3\u201325% Lebanon ,51,52, 4 Lebanon , 2.9% we Lebanon , and 0% Lebanon .The majority of antifungals used in agriculture are classified as preventive fungicides . This haCandida and Aspergillus; thus, the epidemiological significance of the existing findings remains to be confirmed. Furthermore, the lack of reliable identification tools in most of the available studies hindered attempts to explore genetic profiles of isolates and identify underlying resistance mechanisms. To better understand the dissemination of these fungi and the risk factors associated with the spread of antifungal resistance, it is necessary to conduct further prospective multicentric studies involving a substantial number of clinical and non-clinical isolates.The study presented here had a few limitations. Our approach did not encompass the consideration of non-official antifungals that might have been illicitly introduced into Lebanon or brought in by the diaspora to support local communities. Additionally, the available data obtained previously in Lebanon addressed only the epidemiology of clinical strains of This study was conducted between January and February 2023 to identify antifungal drugs that are used in human and animal medicine in Lebanon. The Lebanese Ministry of Public Health, as well as major pharmacies, veterinary clinics, and agriculture markets located in Tripoli and Beirut, provided the primary data sources. The study collected comprehensive data on the available antifungals, including their antifungal class, brand name, active molecules, administration routes, availability in pharmacies, veterinary and agricultural stores, and healthcare settings. The study also recorded the usual recommended treatment regimens, treatment indications, and manufacturing country of origin. In addition, the current price of the antifungal drugs of clinical interest was compared to the price before the economic collapse (October 2019) in Lebanon.Candida\u201d, \u201caspergillosis\u201d, \u201cazole\u201d, and \u201cOne Health\u201d. We reviewed all relevant publications. Original publications in English or French that were indexable and of any epidemiologic methodology, sampling technique, or type were included. All research that published original data on antifungal resistance in Lebanon was considered for inclusion in the study.Moreover, we searched PubMed, Science Direct, and Google Scholar databases for studies on fungal and antifungal resistance between 1998 and 2023. We selected a word combination that included \u201cyeast\u201d, \u201cfungal\u201d, \u201cfungal infection\u201d, \u201cfungi\u201d, \u201cantifungal\u201d, \u201cantimicrobial resistance\u201d, \u201cCandida and Aspergillus species continue to challenge healthcare settings, implementing robust One Health programs that rely on reliable diagnostic tools is essential to monitor the prevalence of these species and assess their susceptibility patterns. Indeed, using the micro-broth dilution technique following the international guidelines has become crucial in patient management and resistance surveillance. Additionally, enhancing awareness and strengthening infection control measures, such as strict adherence to hand hygiene protocols and proper disinfection practices, are required to limit the spread of these resilient pathogens. Lastly, we recommend the establishment of national reference centers for invasive mycoses and antifungal resistance and new regulations to prevent the inappropriate use of antifungal drugs in humans and agriculture.As"} +{"text": "Accurate malaria diagnosis and timely treatment are requirements for effective management of the disease. However, treatment efficacy may be significantly reduced in resource-constrained healthcare facilities with poorly equipped laboratories and frequent drug and rapid diagnostic test kit (RDT) stock-outs. Furthermore, patient may avoid seeking treatment from such facilities. The study\u2019s goal was to determine treatment-seeking behavior, malaria diagnosis and treatment quality, and likely treatment-seeking determinants in the local population. Passive case detection, which targeted all patients with suspected malaria cases, was conducted in ten public healthcare facilities over a three-month period. Monthly malaria cases, methods of diagnosis and antimalarial drug availability were assessed. A household-based survey was also carried out. Structured questionnaires were used to collect knowledge, attitude and practice (KAP) data from household heads. Malaria knowledge, treatment seeking behavior, and predictors of malaria treatment-seeking were all determined. Three of the seven dispensaries lacked a laboratory to conduct microscopy- diagnosis. These three dispensaries also experienced frequent RDT stock-outs, which resulted in depending on clinical signs as diagnosis for malaria. The majority of local residents with fever (50.3%) purchased antimalarial drugs from a chemist. About 37% of fever patients sought treatment at healthcare facility while the remaining 12.7% did not treat their fevers. In irrigated areas, 45.5% (46/64) of fever patients sought treatment at healthcare facilities, compared to 25% (18/64) in non-irrigated areas (p = 0.009). Most children aged below 5 who had fever (77.7%) were taken to healthcare facility for treatment compared to 31.4% of children aged 5\u201314 years or 20.9% of adults (0.0001). Predictors of treatment seeking included access to healthcare facility , and ability to pay hospital bills . Other factors that influenced health-seeking behavior included the severity of symptoms, the age of the patient and knowledge of malaria symptoms. Malaria is still a major public health challenge in sub-Saharan Africa, with young children suffering the highest morbidity and mortality rates \u20133. The dIn an effort to streamline with WHO recommendation, the Kenyan ministry of health endorsed the test and treat policy in all patients presenting with fever . This enSignificant reductions in parasite prevalence have been reported in Homa Bay county, where malaria infections were previously above 20% \u201324. The 0S and 0.520 S and between longitude 340 E and 350 E. The government of Kenya initiated an irrigation scheme in parts of Homa Bay county to boost food production and household incomes [The study was conducted in two sub-counties (Rachuonyo south and Rangwe) of Homa Bay county, Kenya. The county is situated in the southern part of former Nyanza Province and lies between latitude 0.15 incomes . The stuThe major economic activity is subsistence farming where crops such as rice, maize, beans, vegetables and variety of fruits are grown. Other economic activities practiced in the area include small scale businesses, fishing, while some are government employees. Malaria transmission within the county is perennial with a parasite prevalence of 27% . Vector Plasmodium infections in Kenya [This was a cross-sectional household and healthcare facility-based survey. Healthcare facility survey was conducted between October and December 2019, during the short rainy season. Healthcare facilities with a minimum catchment population of 3000 people were selected. As a result, ten government healthcare facilities were identified and included in the study due to low cost of services. Children under the age of five, for example, are eligible for free malaria testing and treatment. However, for older children and adults, a malaria laboratory test costs KSH. 100 (USD 1), but antimalarial drugs are free. in Kenya .Household-based survey was conducted in the month of July 2020, at the end of long rains, when malaria transmission typically was at its peak. Households were the study units in the selected villages. A total of 240 households were considered sufficient to answer study objectives and were randomly selected using a two-stage cluster sampling design as previously described . First, Trained interviewers administered the structured questionnaires to the household heads. All 240 household heads responded to questions regarding knowledge, attitude and practice towards malaria. However, to determine the treatment seeking behavior, only households that had reported cases of fever (increase in body temperature) accompanied by headache or joint pains or both in the two weeks preceding data collection, were interviewed. Information on the age, gender, severity of fever, treatment-seeking behavior, bed net ownership, and use was collected. The integrity of nets was physically examined. Health-seeking behavior was the primary outcome of the study. The operational definition of treatment-seeking behavior was considered to be seeking treatment at health facility or self-medication using antimalarial drugs bought from a chemist. The proportion of participants who did not treat their fever was also recorded. We also enquired whether antimalarial drugs were available in healthcare facilities for fever patients seeking treatment, or if they were referred to a chemist. Most chemists in the study area were not run by a pharmacist. The cost of AL at the chemist is KSH. 100 but the cost of other antimalarial drugs varies depending on the dosage.Potential covariates to treatment seeking behavior such as easy access to hospital, ability to pay hospital bills, the nature of symptoms (severe or mild), age group, whether the house was sprayed (IRS), knowledge of malaria symptoms, region of residence (irrigated or non-irrigated), household head level of education and use of a bed net were considered and included in a predictive model. Assessment of knowledge of malaria symptoms was based on the ability of the household head to link fever or headache to malaria.The data were coded, entered in Excel sheet, and analyzed using GMP Pro 16. Demographic characteristic of participants, knowledge, attitude and practice towards malaria were summarized using descriptive statistics. Differences in proportions were compared using either Fisher\u2019s exact test or Chi-square test. To assess treatment-seeking behavior, we first used descriptive analysis to determine the difference among those who sought treatment at health facility versus those who used antimalarial drugs bought from the chemist or those who did not seek treatment to manage the fever. We then used multiple logistic regression to identify the factors that influence treatment-seeking behavior.Plasmodium falciparum and P. vivax malaria\u201d whose ethical review and approval (MSU/DRPI/MUERC/00456/17) was obtained from Maseno University (Kenya) Ethics and Research Committees and University of California, USA. Written informed consent was obtained from the parent/guardian of each participant under 18 years of age.The current study was part of a larger project on \u201cEnvironmental Modifications in sub-Saharan Africa: Changing Epidemiology, Transmission and Pathogenesis of We visited 240 households with a total population of 1,142 people (574 from irrigated and 568 from non-irrigated areas). Children under the age of 5 constituted 20.2% (231/1142), followed by children aged 5 to 14 years , and those aged 15 years and older constituted 46.8 (535/1142). The mean household size was 4.8persons, with a range of 1-11individuals per household. The majority of the respondents were females as indicated in 2 = 5.0, df = 1, p = 0.03). Bed net usage survey indicated that in most households (83.3% in irrigated and 73.7% in non-irrigated area), all family members used bed net. Although bed net ownership and usage was above average in the study area. The majority of the households (59.2% in irrigated and 57.5% in non-irrigated areas) had nets which were torn. Indoor residual spray coverage was at 66.7% (80/120) in irrigated and 69.2% (83/120) in non-irrigated areas.The overall bed net ownership by study participants was 93.3% (224/240). The irrigated area had significantly higher bed net ownership of 98.3% compared to that of non-irrigated area (88.3%) (Fisher\u2019s exact test = 0.003). The proportion of households having 1 LLIN for two people was 37.5% (45/120) in irrigated compared to 24.2% (29/120) in non-irrigated area in the study area are dispensaries which are headed by clinical officers and provide only outpatient services. Health centers and a hospital which are headed by at least one doctor provide inpatient services for 20% (2/10) and 10% (1/10) respectively. A total of 1264 suspected malaria cases in the 10 healthcare facilities were recorded during a period of 3 months. Out of the 1264 cases, 76.7% (972/1264) were diagnosed by microscopy, 4.2% (53/1264) by RDT kits while 18.9% (239/1264) were clinically diagnosed. The overall clinical malaria cases were 19.7% (65/330), 18.2% (109/600), and 21% (70/334) during October, November and December respectively as illustrated in During the three months of the study, three dispensaries , did not have RDT kits and thus relied on clinical symptoms to presume suspected malaria infections. The number of cases presumed by clinical diagnosis was always greater than 30% during the 3 months of the study. Microscopy confirmed cases, however, accounted for less than 20% of all cases during the same period. For example, during the month of October 2019, the proportion of suspected malaria which were confirmed by microscopy was 16.2% (39/241) compared 38% (23/62) clinically diagnosed cases (p = 0.0005). During the month of November 2019, the proportion of microscopy confirmed cases was 15% (70/466) compared to 30.1% (34/113) cases confirmed clinically (p = 0.0003). Similarly, during the month of December 2019, cases confirmed by microscopy were 17.7% (47/265) while those diagnosed clinically were 35.6% (23/64) (p = 0.0025) .Attitude towards malaria indicted that 95.4% (229/240) of the participants regarded malaria as a serious disease while 4.6% (11/240) mentioned that malaria is a mild disease. Approximately 93.8% (225/240) indicated that it was very important to follow malaria treatment prescription given by the doctor, while 6.2% (15/240) indicated that it was not important.2 = 5.0, df = 1, p = 0.03). Among these 173 individuals, 37.0% (n = 64) sought treatment at the health facility, 50.3% (n = 87) used antimalarial drugs bought from the chemist while 12.7% (n = 22) did treat the fever. The proportion of individuals seeking treatment at a health facility for fever cases were more common in irrigated than in non-irrigated areas as shown in 2 = 3.8, df = 1, p = 0.05). Similarly, the proportion of those who did not treat the fever or waited to get better when they experienced fever, was 10.9% in irrigated and 15.3% in non-irrigated areas .Treatment-seeking behavior among fever patients is described in 2 = 37.07, df = 2, p < 0.0001). However, use of antimalarial drugs purchased from a chemist for fever-related cases was highest among adults (59.7%), followed by 58.6% of children aged 5\u201314, and lowest among children under the age of 5 (16.7%) . Approximately 5.6%, 10% and 19.4% of children under the age of 5, children aged 5\u201314 and those aged \u226515 years old, respectively, did not receive any form of treatment and instead their caregivers just waited for the fever to subside .Treatment seeking behavior differed significantly among age groups. The majority of children aged < 5 years (77.7%) were taken to a health facility for treatment compared to 31.4% and 20.9% of children aged 5\u201314 years old and those aged \u226515 years respectively than those who had a challenge accessing the health facility . MoreoveWith regard to use of antimalarial drugs bought at the chemist, family members from houses which were not sprayed (IRS), were more likely to buy antimalarial drugs from the chemist than those from sprayed households. Study participants who experienced mild fever or headache, were more likely to buy antimalarial drugs from the chemist than those who experienced severe fever or headache. Knowledge of malaria symptoms also played key role towards buying of antimalarial. Those who believed that fever or headache was due to malaria, were more likely to buy drugs at the chemist than to go to hospital for treatment. Caregivers of older children or adults were 4 times more likely to buy antimalarial drugs at the chemist than seeking treatment at the hospital.This study assessed the rural population\u2019s knowledge, attitude, and practice regarding malaria, as well as treatment-seeking behavior and predictors of treatment-seeking in malaria endemic zone. Malaria knowledge and appropriate treatment seeking behavior are critical components of malaria clinical management . Our finDespite widespread knowledge of malaria control methods, study\u2019s findings revealed that only a small percentage of households met the requirement of \u201cone LLIN for every two people\u201d. A minimum coverage of 60% is required for LLINs to provide optimal protection . The preThe findings further indicated that the majority of participants consider malaria to be a serious disease, acknowledge stagnant water as the suitable breeding place for mosquitoes, and are aware of the groups of people who are most vulnerable to malaria. This high level of knowledge in malaria disease may be attributed to the community\u2019s location in a malaria endemic region where the disease is common, and also the fact that the majority of the respondents (90%) had at least a primary education. The good knowledge about malaria from the current study is comparable to other studies conducted in southeastern Iran , in MozaPlasmodium infections. As a result, many participants who were familiar with malaria symptoms, were more likely to delay or fail to seek treatment at a health facility when fever developed. Similarly, some studies conducted in Ethiopia [According to the study findings, 44% of the total households surveyed had at least one fever patient. More than a half of these fever cases were treated with antimalarial drugs obtained from a local chemist. This is similar to studies in in Indonesia , Ghana , India , MyanmarEthiopia , 41 repoEthiopia , 43. TheEthiopia . TherefoEthiopia . This grEthiopia .Access to healthcare facilities, ability to pay hospital bills, severity of symptoms, and age of fever patients were factors that predicted treatment-seeking at healthcare facilities. The ease of access to healthcare facilities has been reported in previous studies to encourage treatment-seeking at healthcare facilities , 49\u201351. The study\u2019s findings also demonstrated that young children with fevers, were more likely to be taken to the healthcare facility by their caregivers than older children or adults. This could be due to the majority of respondents being aware that children under the age of five are more vulnerable to malaria than older children or adults, as previously reported , 54. In et al [According to survey findings, some dispensaries were resource constrained. Chronic challenges that plagued the day-to-day operations of most of these dispensaries included a lack of well-equipped laboratories, RDT kits stock-outs, and antimalarial drug shortages. These challenges if not addressed, may have an impact on treatment seeking behavior. For example, patients who are referred to some distant healthcare facilities for proper checkups may resort to buying drugs at local chemists due to a lack of funds for transportation. Similarly, drug shortages in healthcare facilities are likely to hamper effective treatment seeking as reported in previous studies . For inset al in the sThe World Health Organization recommends that all suspected malaria cases be confirmed through microscopy or the use of rapid diagnostic test kits before antimalarial drugs are administered . ParticuThe study findings indicate that most people from this region have good knowledge about malaria. However, the majority of fever patients self-treat with drugs purchased from local chemists. Access to healthcare facilities, knowledge of malaria symptoms, age of febrile patients, severity of symptoms, and income were all likely factors influencing treatment seeking behavior. Antimalarial drugs and RDT kits stock outs were common challenges to some dispensaries. The Ministry of Health should consider launching a community-based awareness campaign to educate local population about the importance of seeking medical attention at a healthcare facility. The ministry of health should also consider improving access to healthcare facilities as well as quality services in terms of diagnosis and drug availability.S1 Data(XLSX)Click here for additional data file.S2 Data(XLSX)Click here for additional data file.S3 Data(XLSX)Click here for additional data file."} +{"text": "Embryonic chromosomal abnormalities represent a major causative factor in early pregnancy loss, highlighting the importance of understanding their role in spontaneous abortion. This study investigates the potential correlation between chromosomal abnormalities and spontaneous abortion using copy number variation sequencing (CNV-seq), a Next-Generation Sequencing (NGS) technology.We analyzed Copy Number Variations (CNVs) in 395 aborted fetal specimens from spontaneous abortion patients by CNV-seq. And collected correlated data, including maternal age, gestational week, and Body Mass Index (BMI), and analyzed their relationship with the CNVs.Out of the 395 cases, 67.09% of the fetuses had chromosomal abnormalities, including numerical abnormalities, structural abnormalities, and mosaicisms. Maternal age was found to be an important risk factor for fetal chromosomal abnormalities, with the proportion of autosomal trisomy in abnormal karyotypes increasing with maternal age, while polyploidy decreased. The proportion of abnormal karyotypes with mosaic decreased as gestational age increased, while the frequency of polyploidy and sex chromosome monosomy increased. Gene enrichment analysis identified potential miscarriage candidate genes and functions, as well as pathogenic genes and pathways associated with unexplained miscarriage among women aged below or over 35 years old. Based on our study, it can be inferred that there is an association between BMI values and the risk of recurrent miscarriage caused by chromosomal abnormalities.Overall, these findings provide important insights into the understanding of spontaneous abortion and have implications for the development of personalized interventions for patients with abnormal karyotypes. Fetal cde novo and inherited variants. De novo CNVs refer to genomic alterations that arise spontaneously during embryonic or fetal development. These variations are not inherited from the parental genomes and occur as novel changes in the DNA sequence. On the other hand, inherited CNVs are genetic changes passed down from one or both parents to the offspring. These variants can be present in the parental genomes and transmitted through generations.In addition, CNVs can be further categorized into Though the exact mechanism of how chromosomal abnormalities lead to miscarriage is not yet fully understood, but it is believed to occur due to embryo implant or development failure. In certain scenarios, chromosome abnormalities cause miscarriage by disrupting normal embryonic development or leading to abnormal implantation in the uterus , 21. Altin situ hybridization (FISH) has solved the problem of cell culture and shortened the operation time, but it cannot fully reflect the chromosome situation of abortion tissues limited by the number of specific fluorescent probes to assess potential correlations with chromosomal abnormality patterns. Furthermore, by conducting gene enrichment analysis, we aimed to uncover potential candidate genes and pathways associated with miscarriage in different age groups. This study enhanced our understanding of the genetic landscape of chromosomal abnormalities and their impact on adverse pregnancy outcomes.22.1We collected a total of 395 specimens from pregnant women who had experienced spontaneous abortions during the period between March 2018 and June 2022 and were admitted to the Wenzhou Hospital of Traditional Chinese Medicine Affiliated Zhejiang University of Traditional Chinese Medicine. All participants had experienced either sporadic or recurrent miscarriages, and voluntarily underwent CNV-seq testing following the loss of their pregnancies. Additionally, they provided signed informed consent before participating in the study. The age range of the participants was between 21 and 45 years. We divided the pregnant women into two groups: those under 35 years old who were in the non-advanced age group, and those who were aged 35 years or older, in the advanced age group. Their gestational age ranged from 3 to 23 weeks.2.2p-value < 0.05 was considered statistically significant. Furthermore, we performed the Cochran-Armitage trend test using R software to test for any trends in proportion across different groups. A p-value < 0.05 was also considered statistically significant. Additionally, we conducted the Wilcoxon rank sum test using R software to compare the differences in BMI values between groups, with a p-value < 0.05 being deemed statistically significant.We used the statistical software SPSS 26.0 to conduct chi-square tests and Fisher\u2019s exact tests on count data. A 2.3Under sterile conditions, approximately 50 mg of villous tissue from miscarriages or muscle tissue from formed fetuses was collected. The collected tissue samples were then washed thoroughly with sterile physiological saline. The tissue samples can be stored in sterile physiological saline. It is important to ensure that the tissue samples are fully submerged in the preserving solution. Additionally, peripheral blood samples were obtained from the mothers of these fetuses. The samples should then be refrigerated at temperatures between 2 to 8\u00b0C during transportation, making sure that the transportation period does not exceed three days. DNA extraction from the tissue and blood samples was performed using the QIAGEN DNeasy Blood & Tissue Kit following the manufacturer\u2019s instructions. The concentration of the extracted DNA was diluted to a range of 20-50 ng/\u03bcl for further experimental procedures.2.4We amplified 17 autosomal Short Tandem Repeat (STR) loci using fluorescently labeled multiplex PCR technique, then employed capillary electrophoresis on an ABI 3500 xL sequencer to detect the alleles of each locus, and imported the resultant electropherogram data into GeneMapper 6.0 software for data analysis and interpretation of the results. Based on the analysis outcomes generated by the GeneMapper 6.0 software, we calculated the peak area ratios of each locus to determine whether the chromosomal ploidy was normal or abnormal . Additionally, we evaluated maternal contamination by confirming if all of the mother\u2019s polymorphic loci were detected in the fetal sample. Detecting all polymorphic loci indicated the presence of maternal blood contamination.2.5http://dgv.tcag.ca/dgv/app/home), DECIPHER database (http://decipher.sanger.ac.uk), OMIM database (http://www.omim.org), and following American College of Medical Genetics and Genomics (ACMG) guidelines. We classified CNVs into five categories: pathogenic, likely pathogenic, uncertain significance, likely benign, and benign.We fragmented genomic DNA by random enzymatic digestion and constructed DNA libraries using DNA Library Construction Kit produced by BioelectronSeq Biotechnology Co., Ltd. Subsequently, performed sequencing using the BioelectronSeq 4000 platform at an approximate 1\u00d7 depth. To determine whether there were any CNVs in the samples, we aligned raw data to the reference genome GRCh37/hg19 and analyzed them for CNVs at a resolution of 100 kb using a Bayesian . The res2.6p-value was < 0.05.We used bedtools software to extract genes from the chromosomal structural abnormality regions detected in abortion tissues based on chromosomal positions. However, considering the detection precision of CNV-seq is 100kb, we excluded genes that were located within 100kb of the edges of the detected regions. Enrichment analysis was performed for functional categories defined in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). In the current study, we considered the enrichment to be statistically significant when the 33.1This study involved the collection of a total of 395 fetal samples to undergo CNV-seq testing. Maternal age ranged from 21 to 45 years, with a median of 31 years. Gestational weeks ranged from 4 to 23 weeks, with a median of 10 weeks. Of the pregnant women, 145 (36.71%) were below 29 years, 138 (34.94%) were between 30 and 34 years, 80 (20.25%) were between 35 and 39 years, and 32 (8.1%) were above 40 years in age. The study discovered chromosomal abnormalities in 265 cases (67.09%), while normal karyotypes were observed in the remaining 130 cases (32.91%). Chromosomal abnormalities were composed of 187 cases (47.34%) of numerical abnormalities, 31 cases (7.85%) of structural abnormalities, and 5 (1.27%) cases of both numerical and structural abnormalities (excluding 42 cases of mosaicism). The study detected 138 cases (34.94%) of autosomal trisomy, accounting for 52.08% of the abnormal karyotypes. Among the cases with chromosomal trisomy, chromosome 16 was found to be the most common site, the trisomy of chromosome 16 was observed in 36 cases, accounting for 19.25% (36/187) of all numerical abnormalities, this result is consistent with previous research Figure\u00a013.2p-value = 0.01921.To investigate the association between maternal age and chromosomal abnormalities in cases of spontaneous abortion, participants were categorized into four groups based on maternal age: \u226429 years old, 30-34 years old, 35-39 years old, and \u226540 years old, comprising of 145, 138, 80, and 32 cases, respectively. The samples were subjected to CNV-seq analysis for karyotyping. The detection rates of normal karyotypes for each group were 37.93% (55/145), 33.33% (46/138), 30% (24/80), and 15.63% (5/32), respectively , 14.13% (13/92), and 7.14% (4/56) of all chromosomal abnormalities in the other three groups, respectively , 50% (46/92), 64.29% (36/56), and 85.19% (23/27) of all chromosomal abnormalities in each group . Moreover, pregnant women were categorized into three groups based on their gestational age: less than 8 weeks (78 cases), no less than 8 weeks, but less than 10 weeks (151 cases), and no less than 10 weeks (103 cases), to examine the association of gestational age with various chromosomal abnormalities in cases of spontaneous abortion. The detection rates of normal karyotypes were 44.87% (35/78), 29.80% (45/151), and 32.04% (33/103), respectively, with no significant difference observed .We investigated the detection rates of fetuses with normal karyotypes in early pregnancy (less than 12 weeks) and mid-pregnancy (12 weeks or more) in this study. The rates were found to be 33.33% (103/309) and 43.48% (10/23), respectively, with no significant difference , 12.26% (13/106), and 17.14% (12/70) for the three groups, respectively , 3.77% (4/106), and 14.29% (10/70) for the three groups, respectively , 13.21% (14/106), and 8.57% (6/70) for the three groups, respectively and a non-advanced age group (<35 years old). The advanced age group had a significantly higher BMI compared to the non-advanced age group. Within the normal karyotype group, there was no significant difference in BMI between the two groups. However, in the abnormal karyotype group, the advanced age group had a significantly higher BMI compared to the non-advanced age group. Among different types of abnormal karyotypes, the advanced age group had significantly higher BMI values compared to the non-advanced age group in patients with numerical abnormalities. However, there were no significant differences in BMI between advanced and non-advanced patients in the other two groups, mosaicism and structural abnormalities and advanced age group (<35 years old). We then performed KEGG enrichment analysis , which may be attributed to the fact that the autosomal trisomy accounts for a higher proportion of abnormal karyotypes as maternal age increases, but not all chromosomal abnormalities account for a higher proportion of abnormal karyotypes as age increases. In our study results, polyploidy accounts for a lower proportion of abnormal karyotypes as maternal age increases. Therefore, our study suggests that maternal age is an important risk factor for fetal chromosomal abnormalities, especially for autosomal trisomy. However, various chromosomal abnormalities, such as polyploidy, may have different associations with maternal age , while normal karyotypes were relatively rare (32.91%). The chromosomal trisomy was most often detected in chromosome 16, this is consistent with prior studies . Chromosrnal age . Previournal age , 40, yetIn this study, we also explore the correlation between gestational weeks and fetal chromosomal abnormalities. Previous research has suggested that the incidence of chromosomal abnormalities in fetuses is higher during early pregnancy than in the mid-pregnancy phase , and triThe association between BMI and recurrent miscarriage in patients with chromosomal anomalies was a significant finding in our study. There was a significant difference in BMI values between the recurrent miscarriage group and the sporadic miscarriage group in patients with chromosomal anomalies, indicating a potential link between higher BMI values and chromosomal anomalies causing recurrent miscarriage. This finding supports previous research that obesity can negatively affect pregnancy outcomes and result in adverse fetal outcomes , 43. HowIt is generally believed that BMI is influenced by age, with an increase in age resulting in a natural increase in body fat and a decrease in muscle mass . Our finAdditionally, age is a significant risk factor for the malignant tumors occurrence. While the association between HPV infection and miscarriage risk is debated, HPV infection has been confirmed as a major cause of cervical cancer and other malignancies , 49, andIn contrast, the pathogenic mechanisms of miscarriage in non-advanced age pregnant women are more complex and diverse. We observed enriched pathways related to organ development, neural transmission, and immune function. For example, the olfactory transduction pathway may be related to neural system development. homophilic cell adhesion via plasma membrane adhesion molecules and cell-cell adhesion via plasma-membrane adhesion molecule are involved in cell adhesion. cell adhesion is the process of adjacent cells adhering to each other through specific adhesion molecules on the cell membrane. This adhesion maintains the integrity of tissue architecture, facilitates interactions and communication between cells, and participates in various biological processes such as development, tissue repair, and immune response , 53. AddIt is important to note that these findings are preliminary and further research is needed to validate and explore these issues in more depth. The genetic and molecular aspects are just part of the complex causes of miscarriage, and other factors such as environmental factors, lifestyle, and genetic backgrounds may also play important roles.Nevertheless, our study results provide valuable clues for understanding the genetic causes of miscarriage in different age groups. These findings can guide improvements in the quality of care for older pregnant women and other pregnant women. We recommend individualized interventions and enhanced monitoring of metabolic dysregulation, cancer risk, and immune function issues for pregnant women of different age groups in clinical practice. Moreover, our study provides a foundation and direction for future in-depth exploration and comprehensive research in related fields.In conclusion, our study provides valuable insights into the prevalence and distribution of fetal chromosomal abnormalities using CNV-seq. It also demonstrates the association of maternal age, gestational weeks, and BMI with fetal karyotype abnormalities. These findings have implications for the genetic etiology and risk evaluation of miscarriage.However, our study also has some limitations. It is crucial to expand our analysis to larger cohorts to obtain a more comprehensive understanding of these associations. Additionally, conducting fundamental experiments will be essential to delve deeper into the underlying molecular mechanisms involved in this phenomenon.The data presented in the study are deposited in the CNGB Sequence Archive (CNSA) of the China National GeneBank Database (CNGBdb) repository, accession number CNP0004438.The studies involving humans were approved by Wenzhou Hospital of Traditional Chinese Medicine Ethics Committee. The studies were conducted in accordance with the local legislation and institutional requirements. The participants provided their written informed consent to participate in this study.Conception and design: WC, QZ. Study development and methods: WB, ZL. Medical and technical support: WC, WB, ZL. Collection and assembly of data: XS, LZ. Data analysis and interpretation: WB, QZ. Manuscript writing: WB, QZ. All authors contributed to the article and approved the submitted version."} +{"text": "Staphylococcus aureus bacteremia (SAB) has increased in Alberta over the past two decades. It is unclear whether this trend reflects the expansion of a single strain or multiple strains and how much it has been influenced by changes in antibiotic use and resistance.The incidence of S. aureus isolates representative of all SAB episodes from patients in the greater Calgary region from 2006-2019. Bacteremia episodes were defined as all positive isolates collected from a patient within a 30-day period. Each episode was categorized as community-onset (within 48 hours after admission) or hospital-onset (after 48 hours post admission). Isolates for which sequencing was successful (97.8%) were assigned strain and clonal complex (CC) designations. We computed the incidence of strains and antimicrobial susceptibility to cloxacillin, clindamycin, erythromycin, and ciprofloxacin. Antibiotic prescribing rates for the region were obtained from Alberta Health Services.We used data from 5,881 S. aureus antibiotic susceptibility was driven primarily by an increased incidence of susceptible sub-lineages within several strains mainly causing community-onset SAB. The incidence of SAB resistant to all four antibiotics decreased over the study period due to a decline in community and hospital-onset infections by one resistant sub-lineage of CC5; from 4.1 to 0.3 per 100,000 population, and was associated with a decline in community antibiotic prescribing for beta-lactamase resistant penicillins, lincosamides, macrolides, and fluoroquinolones .SAB incidence increased from 30 to 40 per 100,000 population. The prevalence of resistance to cloxacillin, clindamycin, erythromycin, and ciprofloxacin fluctuated and decreased from a maximum of 31.8% to 15.6%, 28.2% to 19.2%, 39.1% to 27.5%, and 37.4% to 15%, respectively, by the end of the study period. An overall increase in Incidence rate of Staphylococcus aureus bacteremia per 100,000 Calgary residents stratified by community- and hospital-acquired infections.Bacteremia episodes were defined as all isolates collected from a patient within a 30-day period, and the incident isolate represents the first isolate from each episode.Prevalence of resistance to cloxacillin, clindamycin, erythromycin, and ciprofloxacin between 2006 and 2019.Points represent the proportion of incident isolates resistant to the respective antibiotic. Solid lines are smoothing curves using the loess method. Grey bands represent 95% confidence intervals.Incidence rate of Staphylococcus aureus bacteremia per 100,000 Calgary residents stratified by onset of infection.Points represent the incidence rate, dashed lines are linear interpolations between points, solid lines represent smoothing curves using the loess method. Grey bands represent 95% confidence intervals. Clonal complex designations in brackets represent the clonal complex assigned to the majority of the isolates for the respective strain.From 2006-2019, Calgary observed a decline in community antibiotic use, a reduction in the incidence of a resistant strain, and a greater increase in the incidence of community-onset SAB caused by several antibiotic susceptible strains.Dan Gregson, MD, BioMerieux Canada: Advisor/Consultant Yonatan H. Grad, MD, PhD, Day Zero Diagnostics: Board Member|GSK: Advisor/Consultant"} +{"text": "Since the COVID-19 pandemic\u2019s beginning, psychiatrists and searchers have been worried about mental health degradation, especially for caregivers and students. Health students are still students and yet caregivers.th to May 11th 2021 . Second only on medical students from May 27th and June 27th 2021. Both used online surveysTwo national studies were done in 2021. First on all health students from April 4In the first, 16,937 health students answered, including 54% of nurse students. Regarding Kessler- 6 scale for psychological distress, 14% had moderate (8\u201312), and 83% had high (\u226513) levels of psychological distress. In multivariate analysis, being unable to isolate themselves and having financial difficulties were associated with an increased risk ofpsychological distress. On the opposite, being a man and not living alone were associated with a reduced risk of psychological distress.In the second, 11,754 participants (response rate: 15.3%) were included. Prevalence of 7-day anxiety symptoms, 7-day depressive symptoms assessed by Hospitalization Anxiety and Depression Scale (HADS), 12-month MDE , and 12-month suicidal thoughts were 52%, 18%, 25%, and 19%, respectively. Burnout syndrome concerned 64% of clinical students and residents and 30% of preclinical students.These 2 studies highlighted the elevated level of mental distress in health students, especially medical students in France. Preventive and curative actions are needed to help them.None Declared"} +{"text": "From the beginning of the pandemic in Georgia, Covid clinics and Covid hotels were not ready to receive and manage people confirmed Covid 19 with pre-existing mental disorders, because of stigma. As a result of this, the Ministry of Health created special Covid-Psychiatric clinics.Study the impact of stigma on people with pre-existing mental disorders during Covid 19 pandemic. Also clinical, and dynamic characteristics of Covid 19 infection in people with severe mental illness.A retrospective statistical analysis of medical records of all hospitalized patients at the specialized Rustavi Covid \u2013Psychiatric clinic from November 23, 2020, to March 15, 2022, according to the following parameters: age, gender, mental disorder diagnosis, comorbid chronic illness, vaccination rates, degree of covid infections ongoing, and outcome.57% of patients were men. Average age-44 years. 67% were asymptomatic or mild with covid symptoms, 25% with moderate severity and 8% were referred to the intensive care unit. 56% of referred patients were hospitalized already in serious conditions. 46% of patients had schizophrenia spectrum disorders. Among referred patients, 60% were women, and 25% had comorbid diabetes mellitus. 44% of patients transferred to the intensive care unit died. Most of the hospitalized patients with pre-existing mental disorders were in remission, and only 7% were referred to other psychiatric clinics for continuing their inpatient treatment.The study showed that only due to the lack of readiness of the relevant structures, individuals with Covid 19 infection were hospitalized in psychiatric clinics because of their past mental history. Vaccination rates were extremely low than in the general population. The aforementioned indicates a high degree of stigma in the country that makes obstacles for people with mental disorders from receiving adequate and timely medical care. Comorbidities played a big role in degree of COVID infections ongoing, especially diabetes. Statistics also showed that the majority of hospitalized patients did not require inpatient treatment and covid infection did not aggravate the course of most severe mental disorders.None Declared"} +{"text": "Burn Behavioral Health (BBH) program, a burn center-based technology-enhanced stepped-care model of delivering mental health services for burn survivors, spanning the inpatient to outpatient continuum. This model was adapted from the Trauma Resilience and Recovery Program which has been successful in meeting the needs of traumatic injury patients.Annually, nearly half a million people in the U.S. receive medical treatment for burns, 40,000 of whom are hospitalized. Burn patients experience significant psychological burden during acute burn treatment. Long-term psychiatric problems are highly prevalent compared to patients with other injuries. Undetected or untreated psychiatric symptoms can complicate recovery, increase length of stay, and cause long-term problems and readmission. Burn centers are ideally suited to provide these services to burn patients on an inpatient and outpatient basis; however, few burn centers in the U.S. have mental health programs to address patients\u2019 needs. This presentation will describe the BBH includes 4 main steps: (1) initial screening, education, and early intervention; (2) symptom self-monitoring and self-help resources; (3) follow-up screening 30 days post-injury; and (4) provision of best-practice mental health treatment for patients who need it, using both in-person and telehealth modalities, including individual and skill-based group therapy.Data were collected as part of clinical care. BBH services. Of these, 342 (90%) were enrolled in BBH and completed initial screening. 50% of patients screened positive for depression/PTSD risk or symptoms and were offered brief intervention. 54% of enrolled survivors received brief intervention, 21% of whom completed more than one session. We reached 84% of patients for the 30-day follow-up, 20% of whom screened positive for depression/PTSD and 29% were connected to mental health services.Between February 2021 and September 2022, 384 patients were identified as eligible for BBH is sustainable and capable of reaching and engaging a large proportion of burn patients across the inpatient to outpatient continuum. In the U.S., only 25% of burn centers have structured screening in place for inpatient and 11% for outpatient burn survivors. Data from the traumatic injury population (which includes burns) suggest only 10% of patients received intervention after a positive screen and 42% did not know how or where to get help. Psychological recovery is an essential component of a comprehensive burn program and availability of psychological screening and intervention is a requirement for the ABA verification.This study provides preliminary support demonstrating that BBH shows promise in increasing access and quality of mental health care to address the unique needs of burn survivors."} +{"text": "An updated overview of ultrasound (US) for diagnosis of acute cholecystitis (AC) remains lacking. This systematic review was conducted to evaluate the diagnostic performance of US for AC.A systematic review was conducted following PRISMA guidelines. We meticulously screened articles from MEDLINE, Embase, and the Cochrane Library, spanning from inception to August 2023. We employed the search strategy combining the keywords \"bedside US\", \"emergency US\" or \"point-of-care US\" with \"AC\". Two reviewers independently screened the titles and abstracts of the retrieved articles to identify suitable studies. The inclusion criteria encompassed articles investigating the diagnostic performance of US for AC. Data regarding diagnostic performance, sonographers, and sonographic findings including the presence of gallstone, gallbladder (GB) wall thickness, peri-GB fluid, or sonographic Murphy sign were extracted, and a meta-analysis was executed. Case reports, editorials, and review articles were excluded, as well as studies focused on acalculous cholecystitis. The study quality was assessed with the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool.Forty studies with 8,652 patients were included. The majority of studies had a low risk of bias and applicability concerns. US had a pooled sensitivity of 71% , a specificity of 85% , and an accuracy of 0.83 for the diagnosis of AC. The pooled sensitivity and specificity were 71% and 92% performed by emergency physicians (EPs), 79% and 76% performed by surgeons, and 68% (95% CI 66\u201371%) and 87% performed by radiologists, respectively. There were no statistically significant differences among the three groups.US is a good imaging modality for the diagnosis of AC. EP-performed US has a similar diagnostic performance to radiologist-performed US. Further investigations would be needed to investigate the impact of US on expediting the management process and improving patient-centered outcomes.The online version contains supplementary material available at 10.1186/s13017-023-00524-5. Acute cholecystitis (AC) is one of the most common diseases in emergency departments (EDs), occurring in 3\u201310% of patients with acute abdominal pain .Diagnostic imaging modalities for AC include ultrasound (US), computed tomography (CT), or hepatobiliary iminodiacetic acid (HIDA) scan . A 2012 Hence, we aim to perform a meta-analysis to investigate the diagnostic performance of US for AC.This meta-analysis adhered to the Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies (PRISMA-DTA) Statement . The metTo identify relevant articles for our study, we conducted a comprehensive search in three databases: MEDLINE, Embase, and Cochrane Library. The search included articles published before August 2023, without any language restrictions. We employed the search strategy combining the keywords \"bedside US\", \"emergency US\" or \"point-of-care US\" with \"AC\". Two reviewers (SSH and KWL) independently screened the titles and abstracts of the retrieved articles to identify suitable studies. The inclusion criteria encompassed articles investigating the diagnostic performance of US for AC. We excluded case reports, case series, editorials, and review articles from our search strategy, as well as studies focused on acalculous cholecystitis. The complete literature search strategy is available in Additional file The quality of the included studies was evaluated by two independent reviewers (SSH and KWL) using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool . Any disWe extracted and summarized data from each study into 2\u2009\u00d7\u20092 contingency tables to perform sensitivity and specificity analysis. To mitigate bias in the presence of zero observations in false-positive or false-negative results, we applied a continuity correction of 0.5. Summary estimates of sensitivity, specificity, predictive values, likelihood ratios, and accuracy along with their 95% confidence intervals (CIs) were calculated using a bivariate random-effects model with restricted maximum likelihood estimation for diagnostic meta-analysis . The forAdditionally, we performed a subgroup analysis to assess the diagnostic performance of US among different sonographers, namely EPs, surgeons, and radiologists. Furthermore, we conducted a separate subgroup analysis to investigate the diagnostic accuracy of various sonographic findings in diagnosing AC.I2. Additionally, we assessed publication bias using Deek\u2019s test [p value\u2009<\u20090.05. All analyses were conducted using R software version 4.3.0 .To measure heterogeneity between the included studies, we utilized the inconsistency index k\u2019s test . StatistFigure\u00a0Figure\u00a0I2\u2009=\u200989.7%; 95% CI, 87\u201392%), which could be due to varying patient enrollment criteria and the presence of potential confounders due to non-randomized assignment in the included studies. No significant publication bias was detected through Deek\u2019s test .Across all 40 studies, a total of 8652 patients were included, with an average age of 45.9\u00a0years and a male gender composition of 34%. Detailed information about the included studies can be found in Table The subgroup analysis included 14 studies involving EPs, 3 studies involving surgeons, and 18 studies involving radiologists. Two studies compared the performance between EPs and radiologists, and one compared EPs with surgeons, while 8 did not provide detailed information on the sonographers.The pooled sensitivity and specificity of US were 71% and 92% performed by EPs, 79% and 76% performed by surgeons, and 68% (95% CI 66\u201371%) and 87% performed by radiologists, respectively curve of the included studies.Additional file 2: Fig. S2 The forest plot of diagnostic performance of ultrasound performed by emergency physicians.Additional file 3: Fig. S3 The forest plot of diagnostic performance of ultrasound by surgeons.Additional file 4: Fig. S4 The forest plot of diagnostic performance of ultrasound by radiologists.Additional file 5: Table S1 The complete literature search strategy."} +{"text": "Inappropriate antibiotic prescribing for acute respiratory infections is a common source of low-value care in the emergency department. Racial disparities have been noted in episodes of low-value care, particularly in children, but the intersection between race and socioeconomics in inappropriate prescribing has received less attention. Decisions to prescribe antibiotics outside of guideline recommendations may result from underlying bias. We evaluated inappropriate prescribing by race and socioeconomic status in five emergency departments of a large hospital system.We conducted an observational analysis of antibiotic prescribing in adult and pediatric EDs at five hospitals between October 2015 and March 2023. We calculated the rate of inappropriate prescribing for ED encounters that had an ICD-10 for an acute respiratory tract infection (ARTI) that did not require antibiotics and that had no secondary ICD-10 code on the record for which antibiotics may be indicated. Multivariable regression analysis controlling for comorbidities and patient-level factors was used to estimate the odds ratio of prescribing.A total of 147,402 ED encounters were included, of which \u223c50% identified as Black, 23% as White, and 15% as Hispanic. Inappropriate prescribing rates were 8.5% overall, 13.6% for White patients, 7% for Black patients and 6% for Hispanic patients. After adjusting for patient-level factors, including socioeconomic status,White patients had 1.39 higher odds of receiving an inappropriate prescription compared to Black patients. Patients residing in areas of greater socioeconomic deprivation, regardless of race, had 0.70 lower odds of receiving a prescription.Inappropriate Prescribing Rate by Year and RaceThe overall rate of inappropriate prescribing did fall over the years, both overall (black line) and by race, but differences in prescribing by race persisted.Odds ratios of a patient being prescribed an inappropriate antibioticOur results suggest that after controlling for patient-level factors, White patients and patients from wealthier areas are more likely to receive inappropriate antibiotic treatment. While likely multifactorial in origin, it is possible that these disparities are driven by clinicians\u2019 implicit biases that lead to overtreatment of White and wealthier patients. Further qualitative and quantitive approaches are needed to elucidate mechanisms and solutions to these disparities in care.Oluwakemi Badaki-Makun, MD, PhD, Beckman Coulter: Grant/Research Support Sara E. Cosgrove, MD, MS, Debiopharm: Advisor/Consultant|Duke Clinical Research Institute: Advisor/Consultant Jeremiah S. Hinson, MD, PhD, Beckman Coulter: Advisor/Consultant|Beckman Coulter: Grant/Research Support|Beckman Coulter: TriageGO"} +{"text": "Rt to just below 1. At higher transmission increase, a threshold of at most 40% was required with mitigation that reduced Rt below 0.75 within the first two weeks after mitigation. Our analysis demonstrates a quantitative approach for the selection of ICU occupancy thresholds that considers parameter uncertainty and compares relevant mitigation and transmission scenarios. An appropriate threshold will depend on the location, number of ICU beds available for COVID-19, available mitigation options, feasible mitigation strengths, and tolerated durations of intensified mitigation.In non-pharmaceutical management of COVID-19, occupancy of intensive care units (ICU) is often used as an indicator to inform when to intensify mitigation and thus reduce SARS-CoV-2 transmission, strain on ICUs, and deaths. However, ICU occupancy thresholds at which action should be taken are often selected arbitrarily. We propose a quantitative approach using mathematical modeling to identify ICU occupancy thresholds at which mitigation should be triggered to avoid exceeding the ICU capacity available for COVID-19 patients and demonstrate this approach for the United States city of Chicago. We used a stochastic compartmental model to simulate SARS-CoV-2 transmission and disease progression, including critical cases that would require intensive care. We calibrated the model using daily COVID-19 ICU and hospital census data between March and August 2020. We projected various possible ICU occupancy trajectories from September 2020 to May 2021 with two possible levels of transmission increase and uncertainty in core model parameters. The effect of combined mitigation measures was modeled as a decrease in the transmission rate that took effect when projected ICU occupancy reached a specified threshold. We found that mitigation did not immediately eliminate the risk of exceeding ICU capacity. Delaying action by 7 days increased the probability of exceeding ICU capacity by 10\u201360% and this increase could not be counteracted by stronger mitigation. Even under modest transmission increase, a threshold occupancy no higher than 60% was required when mitigation reduced the reproductive number In the first half of 2020, the global spread of SARS-CoV-2 left many countries with no option other than to shut down their economies and encourage people to isolate by staying home. In the United States (US), stay-at-home policies implemented in late March and April of 2020 reduced the number of new infections and deaths . In mid-Intensive care resources, particularly staffed beds and ventilators, are limited , 5 especIn response to fluctuations in SARS-CoV-2 transmission, states formulated COVID-19 response strategies to guide transitions between mitigation and relaxation policies . The selThresholds for action should not be arbitrarily selected but rather be designed to meet COVID-19-related public health targets. Several modeling studies explored short-term forecasting of ICU occupancies \u201325 and mThis study investigates how ICU occupancy can be used as an indicator to drive mitigation decisions to avoid exceeding ICU capacity using Chicago, Illinois as a case study. We modeled COVID-19 transmission and disease progression under various levels of transmission increase, mitigation effectiveness, and mitigation timeliness, corresponding to the situation in Chicago in late 2020. The results of this analysis provide a quantitative approach for selecting robust thresholds in Chicago that can be applied in similar areas.Chicago is an urban area of 2.7 million people in the US state of Illinois, and around 12% of the population is aged 65 years or older . 17.4 inThe first SARS-CoV-2 infection was reported in Chicago in mid-January 2020 . On MarcWe used a stochastic Susceptible, Exposed, Infectious, and Recovered (SEIR) compartmental model, with additional compartments for the symptomatic subgroups , hospitalizations, critical cases that require treatment in ICUs, and deaths . The symTime-varying detection rates for severe and mild cases were taken from an analysis of Illinois case and death data Figs B,. All Illd) compartment (COVID-19 ICU occupancy) and the transmission rate parameter, such that Cd triggers mitigation at specified occupancy thresholds . We set a feedback loop between the population in the critical detected , initial transmission rate, and transmission rate under mitigation for March 2020. We then fitted twice-monthly adjustments to the transmission rate between April and August 2020. Other parameters were set to their mean value according to local data or epidemiological studies will be referred to as ICU capacity in this work. We assumed the capacity of 516 ICU beds to stay constant capacity during the simulation period, whereas in practice the capacity ranged between 407 to 744 beds on a seven-day rolling average .We imposed a gradual increase in the transmission rate beginning on September 1, 2020, and leveling off on September 30 to allow reduction in transmission starting from October due to mitigation if occupancy thresholds were reached . The levBetween October 2020 and May 2021, mitigation (immediate reduction in transmission rate) was triggered either one or seven days after the COVID-19 ICU occupancy threshold was reached. An extended simulation period until May 2021 was selected to capture a wide range of trajectories that reach the ICU occupancy threshold to trigger mitigation and to include at least four weeks follow-up time post-trigger. Hence the time after October 2020 was treated as time relative to predicted ICU occupancies reaching the threshold. Mitigation was simulated to reduce the transmission rate by 20, 40, 60, or 80% to sample a wide range of possible actions. Once applied, changes in transmission rate due to mitigation were never reversed. A table comparing the assumed transmission increase and reduction values to other studies is included in the Supplement (Table E in We explored scenarios in which we varied the increase in transmission (two levels), mitigation effectiveness (four levels), and mitigation delay (two levels), and ICU occupancy threshold that triggered mitigation (eleven levels), resulting in a total of 176 unique scenarios . Each scDaily COVID-19 ICU occupancy was the primary outcome in the analysis. The probability of exceeding ICU capacity (for COVID-19 patients) was calculated by dividing the number of trajectories that exceeded COVID-19 ICU capacity by the total number of trajectories that reached the COVID-19 ICU occupancy threshold to trigger mitigation. To account for different numbers of trajectories reaching the ICU trigger 4.57\u20135.41). After the stay-at-home order starting on March 22, 2020, we estimated a 92.5% reduction in the transmission rate (Rt) to 0.74 (90% PI 0.72\u20130.77) . The model captured trends in ICU occupancies reasonably well with an average MAE of 44 ICU beds occupied (range across trajectories 27\u201366) between March to August 2020.We fit a compartmental model of SARS-CoV-2 transmission to hospiion rate , reducin72\u20130.77) . At the Rt of 1.14 (90% PI 1.12 to 1.16) for the lower level of increase and a Rt of 1.28 (90% PI 1.25 to 1.30) for the higher level of transmission increase on October 1, 2020. ICU occupancy increased until peaking in mid-December at the earliest and mid-February 2021 at the latest, depending on the level of transmission increase and parameter sample. The mean peak ICU occupancy reached 663 beds (90% PI 421\u2013948) at the lower transmission increase and 1656 beds (90% PI 1096\u20132236) at the higher transmission increase, compared with ICU capacity of 516 beds. Across both levels of transmission increase, the projected peak ICU demand was 1.2\u20133.2 times more ICU beds needed than available.To test the success of using ICU occupancy to trigger mitigations, we implemented two levels of an increase in transmission rate in September 2020. Without mitigation, the transmission increase led to a Rt reached a minimum after around two weeks, before increasing again and leveling off below 1. The estimated Rt varied slightly across the simulated scenarios, and at the high transmission increase scenario, the Rt two weeks prior to mitigation was estimated at of 1.23 (90% PI: 1.18\u20131.29) and was reduced to 1.03 (90% PI: 0.99\u20131.07) at weak, to 0.92 (90% PI: 0.88\u20130.96) at moderate, to 0.75 (90% PI: 0.71\u20130.79) at strong, and to 0.47 (90% PI: 0.40\u20130.54) at very strong mitigations under weak mitigation, by 59.7% (90% PI: 43.6\u201371.4%) under moderate mitigation, by 65.6% (90% PI: 50.3\u201375.2%) under strong mitigation, and 68.5% (90% PI: 54.4\u201377.4%) under very strong mitigation .ICU occupancy continued to grow for a short time after mitigation was imposed . At the Rt was not reduced below 1, had a substantially higher probability of overflow than the other mitigation levels, and differences were greater for the higher level of transmission increase.We calculated the probability of exceeding ICU capacity under different possible ICU occupancy thresholds at which mitigation was dynamically triggered . We compAt the lower level of transmission increase, the probability of ICU overflow was almost identical for moderate, strong, and very strong mitigation, whereas at the higher transmission increase the difference between the mitigation levels was more pronounced with consistently high probability of overflow for weak mitigation. At the lower level of transmission increase, the probability of ICU overflow increased at thresholds above 30% occupancy when mitigation was weak, whereas when mitigation was moderate or stronger, the probability remained near zero until an ICU occupancy threshold of 60\u201370% after which the probability increased sharply. The incremental difference in the overflow probability between weak and moderate mitigation was 10% and less than 3% for the other mitigation strengths at the low increase level. In comparison, at the high increase level, the probability of exceeding capacity increased at thresholds above 40\u201350% occupancy and reached 100% for occupancy thresholds above 60\u201370% at strong and very strong mitigation. The difference in the overflow probability was 42% between weak and moderate mitigation, 16% between moderate and very strong mitigation, and negligible between strong to very strong mitigation (<1%) .A delay of seven days shifted the probability curves to the left, with higher probability of overflow at each of the ICU occupancy thresholds. For instance, at an 80% ICU occupancy threshold and very strong mitigation, the probability of overflow increased from 41.8% to 89.6% under the lower level of transmission increase when mitigation was delayed by seven days. At the higher level of transmission increase, a 60% occupancy threshold and very strong mitigation had 37% probability of overflow if mitigation was immediate but 97.4% probability of overflow if mitigation was delayed. When assessing mitigation strengths against delay, the probability of overflow was higher for strong mitigation that was delayed by seven days compared to moderate mitigation with immediate action. For a hypothetical risk tolerance of 25% probability of ICU overflow, the required ICU occupancy thresholds for action were 40 to 60% across the tested scenarios.A policy of 80% ICU occupancy to trigger mitigation did not prevent exceeding capacity, as mean peak ICU occupancy was at or above ICU capacity for all mitigation strengths and both levels of transmission increase. A 60% ICU occupancy threshold for mitigation was barely sufficient for preventing ICU overflow: mean peak ICU occupancy remained below capacity for the lower transmission increase at all mitigation strengths but remained below capacity for the higher transmission increase only under very strong mitigation. Under the higher level of transmission increase, weak mitigation (20% reduction in transmission) could not contain mean peak ICU occupancy to below ICU capacity regardless of the ICU occupancy that triggered mitigation . Above mFor simulation trajectories where ICU capacity was exceeded, we measured the number of days in each trajectory where ICU occupancy exceeded capacity . WithoutRt to below 1, and occupancy thresholds for action are conservatively low.We developed a quantitative approach to explore how ICU occupancy can be used as an indicator for triggering new mitigations in response to increasing transmission. The approach considers parameter uncertainty using a SARS-CoV-2 transmission model for comparing relevant mitigation and transmission scenarios, applied to the city of Chicago, US. ICU occupancy is a late indicator for SARS-CoV-2 transmission since ICU admission lags symptom onset by 10 days , which lIn an initially expanding epidemic, ICU occupancy of COVID-19 patients will continue to increase for around two weeks after imposing mitigations. Higher ICU occupancy thresholds for action thus increase the probability of overshooting ICU capacity during those two weeks. Furthermore, mitigation measures could be delayed to give individuals and businesses warning in advance of changing policies. Scaling up of hospital beds and staff might require even longer notice times of three to four weeks , 45. TheThis study models mitigation as an abstracted decrease in transmission rate. In current practice, mitigation is achieved through a mix of social distancing, masking, diagnostic testing, isolation, and contact tracing . The strRt, anticipated population behavior, ICU flexing capacity, and overall risk tolerance for exceeding ICU capacities. The Illinois Department of Public Health defined an 80% threshold on total ICU occupancy, translating to an occupancy threshold of around 50% for COVID-19 patients when assuming a maximum 60% occupancy by non-COVID-19 patients. In our analysis, a 40% occupancy threshold is associated with relative low probabilities of overflow. In practice, using region-specific thresholds risks an uncoordinated response [Rt had already begin to decrease prior to implementation of official mitigation measures as individual action preceded government policy , corresponding to around 40% occupancy of beds available for COVID-19 patients . In theoresponse , and mitresponse when theFig R in .A threshold of 60% is suggested for Chicago, since probability of overflow rapidly increases after an ICU occupancy of 60% when assuming strong mitigation and a risk tolerance of 20\u201325%. Our suggested threshold of 60% for Chicago aligns with thresholds used in a modeling study that simulated multiple on-off cycles based on a fixed 50% ICU occupancy threshold . AnotherWe defined ICU capacity as the number of staffed, supplied beds available to treat critically ill COVID-19 patients, and we assumed COVID-19 ICU capacity stayed constant. Historical trends, however, showed fluctuations in ICU capacity, reflecting both non-COVID-19 use and hospitals following COVID-19 ICU response strategies to scale up or ramp down beds in response to trends , 14, 15.At the state level, COVID-19 ICU management also includes patient transfers across hospitals and regions. Transfers are more common from smaller hospitals in more rural areas to larger specialized hospitals in urban areas than the reverse . In urbaThe model used a well-mixed homogeneous population without age structure or vaccinations, and we assumed 34% of hospitalized COVID-19 patients will require ICU care . Age-speVaccination, changing demographics, and changing virulence may mean that ICU occupancy is no longer a good indicator of transmission and hence should not be used to make mitigation decisions. Whether and when to implement mitigation will need to increasingly depend on more direct measures of transmission. Nevertheless, it remains crucial to monitor COVID-19 hospitalizations and ICU occupancies and to have fail-safe thresholds in place to allow timely action to prevent severe illness and deaths.The presented framework with probabilities of overflow for different mitigation and transmission scenarios can be applied to other locations to inform selection of thresholds under the consideration of local contexts. Since determinants of overflow probability also change over time, continuous reapplication of the model to provide overflow probabilities would be required.We used a SARS-CoV-2 and COVID-19 disease transmission model to evaluate how ICU occupancy can be used as an indicator for triggering new mitigations in response to increasing transmission in Chicago, USA. The model suggests that a threshold of at most 60% ICU occupancy can reliably prevent exceeding capacity, and amount of transmission increase, mitigation strength, and anticipated delays in mitigation effects are important factors when selecting thresholds. In each area, the appropriate threshold will further depend on the options available for mitigation, feasible mitigation compliance levels, and tolerable durations of intensified mitigation.S1 Text(DOCX)Click here for additional data file."} +{"text": "As written by Warsan Shire, \u201cno one leaves home until the home is the mouth of a shark\u201d. UNHCR defines forced displacement as \u201cdisplaced because of persecution, conflict, generalized violence or human rights violations\"to study the prevalence of common Mental health disorders among forcibly displaced people and comparing with the common mental health disorders among host community members.The OPD of BIPBS in SPH and BMCH of Quetta attends 800+ patients per month the data of the OPD of both hospitals was collected for Jan-May 2022 and was analyzed to numerate both the host community and refugees. out of 4120 for 354 refugee patients identified using their POR card and for 3776 of host community using their CNIC, data was analyzed for the prevalence of mental health disorders among them.This study states that Afghan Refugees presented to OPD services of BIPBS, 47% were diagnosed as MDD with/without psychosis, 19% with GAD, 5% diagnosed as BAD, 5% With schizophrenia, 4% as PTSD, 3% as migraine, 3% conversion disorder, 2% OCD, 1% somatoform disorder and 10% of them presented with other psychiatric disorders, while in host community 21% were diagnosed as MDD with/without psychosis, 24% as GAD, 12% as somatoform disorder, 10% as OCD, 8% as migraine, 7% as conversion disorder, 4% as BAD, 3% as Schizophrenia, 3% as MBD due to substance misuse and rest of 7% presented with other psychiatric disorders.The conclusion of this study states that mental health disorders are more common among refugees than in other populations, the result of this study shows that there is a big difference in the prevalence of mental health disorders among displaced people and the rest of the population, some of the Mental health disorders are present in higher percentage among displaced people rather than among host community, while some other disorders are present in lower percentage among displaced people rather than among host community, this study also highlights that further studies are needed to determine, risk and protective factors within the host community.None Declared"} +{"text": "Prescriptions that are ordered by physicians but not picked up by patients represent a potential quality improvement opportunity in health systems. Previous research has demonstrated that anywhere from as little as 0.28% to as much as 30.0% of prescriptions are unclaimed, and that 0.45% to 22.0% of patients fail to claim prescriptions. In the Military Health System (MHS), prescriptions filled at military pharmacies are dispensed with no copayment, providing an opportunity to examine the factors that contribute to unclaimed prescriptions other than out-of-pocket cost.To estimate the prevalence of unclaimed prescriptions in the MHS, investigate reasons for unclaimed prescriptions, and compare self-reported noncompliance, defined as the failure to pick up at least 1 prescription in a 12-month period, with evidence from an administrative database of prescription orders and dispensings.Research methods included pharmacy staff interviews at 6 military pharmacies, a telephone survey of beneficiaries who filled prescriptions at these pharmacies, descriptive analysis of survey data, and comparison of administrative pharmacy data with self-reported survey data. Beneficiary interviews, conducted from May through July 2004, covered background characteristics, medical conditions, and unclaimed prescriptions, relying on 12 months of recall regarding noncompliance. Interviews with pharmacy staff covered day-to-day operations, factors that alleviate or exacerbate noncompliance, and the burden that noncompliance places on pharmacies. Administrative data from the Pharmacy Data Transaction Service (pharmacy claims) and Composite Health Care System (CHCS) prescription orders and dispensings) databases were used to select a random sample for the beneficiary survey. Survey respondents' CHCS data were matched to their responses to determine the degree of agreement between self-reports and administrative data.Pharmacy interviews were completed with 30 staff members at 6 military pharmacies, and telephone interviews were completed with 1,214 beneficiaries (60.6% response rate). Beneficiary respondents filled an average of 7 prescriptions in the 5 months approximately surrounding the survey administration time frame (from March to July 2004). More than half (56.8%) of respondents were female, and nearly 60.6% were retired military or their dependents. Among all respondents at all study pharmacies, 8.0% reported failing to claim at least 1 prescription during the prior 12 months. Among survey respondents deemed compliant by CHCS data, 93.8% correctly identified themselves as compliant. However, among patients identified as noncompliant using CHCS data, only 16.0% selfidentified as noncompliant. The administrative data were not concordant with self-report data: of 105 survey respondents identifying themselves as noncompliant in the prior year and matched to administrative data (CHCS), only 58.1% were noncompliant per administrative data, and of 1,065 selfidentifying as compliant, only 61.1% were compliant per administrative data. The most common reasons cited by respondents for not picking up their prescriptions were: no perceived need for the prescription (18.5% of the noncompliant), forgot to pick it up (17.3%), the prescription was not in stock (14.8%), long wait time (11.1%), the prescription was not yet available (10.5%), was out of town (9.9%), and was too busy to pick up the prescription (6.2%). Factors associated with unclaimed prescriptions were: younger age, active duty military status, lower educational levels, and the absence of certain chronic medical conditions .The present study's survey findings of an 8.0% self-reported noncompliance rate fall in the midrange of noncompliance rates reported in previous literature: between 0.45% and 22.0% in nonmilitary populations. Although reported reasons for noncompliance were generally consistent with those identified in previously published studies, they were only partially consistent with previous military pharmacy literature, which also found that patients did not know they had a prescription waiting or had some of the prescribed medicine at home. Concordance between measures of noncompliance, comparing administrative data with patient self-report based on 12-month recall, was poor."} +{"text": "Non-Hispanic Asian (Asian) and non-Hispanic Native Hawaiian and Pacific Islander (NHPI) persons represent growing segments of the U.S. population . Cases were stratified by race, sex, and age for all cancers combined and then categorized into the 10 most common cancer types among all Asian and NHPI persons. A subset of cancer types detectable by screeningCentral cancer registries collect race and ethnicity information from different sources, including self-reported intake questionnaires, abstracted patient records, electronic health records, linkages to administrative databases, and algorithms to impute missing data .Breast cancer accounted for the highest proportion of new cancer diagnoses among 18 (72.0%) of the 25 Asian and NHPI subgroups. Lung cancer was the most common cancer among Chamoru, Micronesian race NOS, and Vietnamese persons; colorectal cancer was the most common cancer among Cambodian, Hmong, Laotian, and Papua New Guinean persons to 40.2% (Other Southeast Asian) and 40.3% (Pacific Islander) for breast cancer; from 38.1% (Other Asian) to 61.1% (Korean) for cervical cancer; from 52.4% (Other Asian) to 64.7% (Other Southeast Asian) for colorectal cancer; and from 70.0% (Other Asian) to 78.5% (Other Southeast Asian) for lung cancer .Persons of Asian and NHPI origin are often aggregated into one racial group persons represent a growing segment of the U.S. population, and are often aggregated in analyses.Cancer incidence among 25 Asian and NHPI subgroups differed by sex, age, cancer type, and stage at diagnosis. For example, lung cancer was the most common cancer among Chamoru, Micronesian, and Vietnamese persons; colorectal cancer was the most common cancer among Cambodian, Hmong, Laotian, and Papua New Guinean persons. Understanding cancer distribution among Asian and NHPI subgroups might help guide development and implementation of culturally and linguistically relevant programs addressing health disparities and social determinants of health."} +{"text": "Migraine is a common neurological disease affecting 12% of Americans and millions worldwide. Medication adherence has been studied extensively in many chronic conditions, with poor adherence adversely affecting treatment outcomes. However, little is known about adherence to oral prophylaxis for migraine.To examine the literature on assessing oral prophylaxis medication adherence and persistence among migraine patients.A systematic search of the PubMed (1966 to present) and EMBASE (1974 to present) databases was conducted to locate prospective and retrospective observational studies and randomized controlled trials (RCTs) of propranolol, amitriptyline, and topiramate. RCTs were pooled, weighted by sample size, and stratified by drug and length of study. Average persistence rates and reasons for discontinuation cited in RCTs were examined for each medication.A total of 788 unique articles were identified using the search criteria, 33 of which were included in the final review. Observational studies (n\u2009=\u200914) showed adherence ranges of 41% to 95% at 2 months, 21% to 80% at 6 months, and 35% to 56% at 12 months and persistence ranges of 41% to 88% at 2 months, 19% to 79% at 6 months, and 7% to 55% at 12 months. Pooled persistence from RCTs on propranolol, amitriptyline, and topiramate (n\u2009=\u200919) showed rates of 77%, 55%, and 57%, respectively, at 16-26 weeks. Adverse events were the most common reason for discontinuation cited (24% for topiramate and 17% for amitriptyline).Observational studies and pooled data from RCTs demonstrate poor adherence and persistence to oral migraine prophylaxis."} +{"text": "The first biosimilar product filgrastim-sndz was approved by the FDA in 2015, but real-world evaluations of its uptake and cost in nationally representative populations are limited.To evaluate the uptake and cost of filgrastim-sndz, relative to its originator filgrastim and alternative biologic tbofilgrastim, among Medicare and Medicaid populations.Using the annually aggregated, product-level utilization and cost data of biologic and biosimilar filgrastim products in 2015-2018 from CMS drug spending data, total number of claims and costs for all 3 filgrastim products were identified and extracted for Medicare Part B, Part D, and Medicaid reimbursement. Annual average cost per claim and per beneficiary of individual filgrastim products were also extracted, and their annual growth rates were calculated.Three years after entering the US market, use of filgrastim-sndz increased to 49.1% and 46.0% of all filgrastim claims paid by Medicare Parts B and D, respectively, and to 38.7% of filgrastim Medicaid claims in 2018. Total cost for filgrastim-sndz also reached 42.8%, 41.8%, and 26.9% of all filgrastim products paid by Medicare Parts B and D and Medicaid, respectively. Significant reductions in average cost per claim for filgrastim-sndz in 2017 and 2018 were observed in Medicare Part B and Medicaid.Significant uptake of biosimilar filgrastim in Medicare and Medicaid programs occurred during the first 3 years of marketing. Policymakers may use the evidence to evaluate existing barriers and policies regarding biosimilar adoption. What is already known about this subjectA number of studies using clinical trial and real-world evidence data has demonstrated the similar efficacy, effectiveness, and safety between biosimilar and reference filgrastim.Initial uptake of biosimilar filgrastim appeared among commercially insured, Medicare fee-for-service, and Medicare Advantage populations.What this study addsSignificant uptake of biosimilar filgrastim in Medicare and Medicaid programs occurred during the first 3 years of marketing.Significant reductions in average cost per claim for filgrastim-sndz in 2017 and 2018 were observed in Medicare Part B and Medicaid.After the marketing of biosimilar filgrastim, the annual total spending paid for all biologic and biosimilar filgrastim products, as well as the alternative biologic tbo-filgrastim, decreased by 28.1% for Medicare Part B, 5.1% for Part D, and 22.1% for Medicaid in 2018 compared with 2015.2 Biologics are used to prevent, treat, or cure a variety of diseases, such as cancer, chronic kidney disease, diabetes, cystic fibrosis, and autoimmune disorders.1 Biologics are expensive, which leads to significant financial burdens for payers and patients. Spending on biologics in the United States totaled $125.5 billion in 2018, a 9.5% increase over 2017.3 Through the Biologics Price Competition and Innovation Act of 2009, the US Food and Drug Administration (FDA) started to approve biosimilars through an abbreviated licensure pathway for biological product that is highly similar to and has no clinically meaningful differences in terms of safety, purity, and potency (safety and effectiveness) from an existing FDA-approved reference product.4 As of December 17, 2020, the FDA has approved 29 biosimilar products.5Biologics, often referred to as specialty drugs, are medicines made from living organisms through highly complex manufacturing processes, including a wide range of products such as vaccines, blood and blood components, allergenics, and gene therapy.6 Biologic filgrastim has been approved by the FDA since February 1991 and had $839 million in US sales in 2014.7 Filgrastimsndz is the biosimilar product of the originator filgrastim and also the first biosimilar product approved by the FDA.5 It was approved for the same 5 indications as originator filgrastim in March 2015 and marketed in September 2015.8 In addition, a stand-alone alternative biologic tbo-filgrastim was approved in August 2012 for the single indication of severe neutropenia in patients with nonmyeloid malignancies.9 Both tbofilgrastim and filgrastim-sndz are direct competitors for biologic filgrastim and are priced with at least 15% or higher discounts.10Biologic filgrastim is a human granulocyte-colony stimulating factor and is used to stimulate the production of granulocytes in patients undergoing therapy that causes low white blood cell counts.14 In addition, Grewal et al and McBride et al developed theoretical frameworks and showed potential cost savings for filgrastim products in the US market.16 But real-world evaluations in the uptake and cost savings of biosimilar filgrastim-sndz in nationally representative populations remain limited. An earlier study using the Medicare Part B claims data from 2014 to 2016 found that initial uptake of filgrastim-sndz increased to 32% of all filgrastim use.17 A recent study using the FDA Sentinel Distributed Database found that filgrastim-sndz\u2019s use had increased to 49.3% by August 2018.18 Similarly, Karaca-Mandic et al also confirmed similar uptake among the commercially insured and Medicare Advantage populations.19 In addition, Socal et al used the 2015-2017 Medicare Part B claims data and found an improved uptake of biosimilar filgrastim in the Medicare Part B program.20A number of studies using clinical trial and real-world evidence data have demonstrated the similar efficacy, effectiveness, and safety between biosimilar and reference filgrastim.This study used the most recently available Medicare and Medicaid drug spending data to evaluate the uptake and cost of filgrastim-sndz, relative to its originator filgrastim and alternative biologic tbo-filgrastim, among Medicare and Medicaid populations in 2015-2018.18 no findings in cost or spending of the product were reported.Findings from the current study could fill the important knowledge gap in the uptake and spending of biosimilar filgrastim in national populations, especially Medicare fee-for-service beneficiaries with Part D prescription coverage and Medicaid beneficiaries. Although the Dutcher et al study described the use of biosimilar filgrastim-sndz at the national level, using the FDA\u2019s Sentinel Distributed Database,21 Medicare Part B drugs include drugs administered in doctors\u2019 offices and other outpatient settings and paid through the Medicare Part B program, which includes all Part B fee-for-service Medicare beneficiaries but excludes any beneficiaries in the Medicare Advantage program (which represents approximately 30% of the Medicare population).21 Medicare Part D drugs include drugs that patients generally administer themselves and that are paid through the Medicare Part D program (approximately 70% of Medicare beneficiaries).21 Finally, the Medicaid drug data represent national-level drug utilization data for covered outpatient drugs paid for by state Medicaid agencies.21 The CMS drug spending data represent drug payments reimbursed for about 70% of Medicare beneficiaries and nationwide Medicaid population. Data files are publicly available and can be directly downloaded from https://www.cms.gov/Research-Statistics-Data-and-Systems/Statistics-Trends-and-Reports/Information-on-Prescription-Drugs.This analysis used the new, publicly available Centers for Medicare & Medicaid Services (CMS) drug spending data, which include annually aggregated, product-level Medicare Part B, Part D, and Medicaid drug spending data for individual drugs in 2014-2018.21); average cost per claim; and average cost per beneficiary (Medicare only) for each of the 3 filgrastim products were extracted in each year for the Medicare Part B and D programs, as well as for Medicaid.Annually aggregated, product-level claims and costs for all 3 filgrastim products were identified using Healthcare Common Procedure Coding System (HCPCS) billing codes from Medicare Part B and their generic/brand drug names from Medicare Part D and Medicaid drug spending data. Annual total number of claims; total spending .Supplementary Figure 1, available in online article). Medicare Part B was the dominate payment source for filgrastim claims, compared with Medicare Part D and Medicaid. The percentage of Medicare Part D and Medicaid claims for filgrastim products was about 11.2% and 27.6% of Part B claims in 2018, respectively.From 2015 to 2018, annual total numbers of Medicare Part B and Medicaid claims of all filgrastim products decreased by 4.2% and 9.2% , respectively, while annual Medicare Part D claims of filgrastim products increased by 4.3% . Overall, $59 million spending was saved for all filgrastim products reimbursed from the Medicare Part B, Medicare Part D, and Medicaid programs in 2018 compared with 2015.Annual total Medicare Part B spending for all filgrastim products decreased from $128 million in 2015 to $92 million in 2018, which represented a 28.1% reduction in 3 years of marketing. Similarly, annual total Part D and Medicaid spending for all filgrastim products reduced from $78 million to $74 million (5.1% reduction), and from $86 million to $67 million (22.1% reduction) during the same period, respectively . In 2018, the average cost per claim in Medicare Part B for filgrastim-sndz and tbo-filgrastim was 68.8% and 64.9% of filgrastim, respectively. The average cost per claim in Medicare Part D for filgrastim-sndz and tbo-filgrastim was 83.2% and 89.7% of filgrastim, respectively. The average cost per claim in Medicaid for filgrastim-sndz and tbo-filgrastim was 49.6% and 46.4% of filgrastim, respectively.The average cost per claim for filgrastim products varied significantly across Medicare and Medicaid programs . In 2018, the average cost per beneficiary in Medicare Part B for filgrastim-sndz and tbo-filgrastim was $2,037 and $1,479, respectively, which was 74.9% and 54.4% of the cost of filgrastim . The average cost per beneficiary in Medicare Part D for filgrastim-sndz and tbo-filgrastim in 2018 was $6,551 and $6,416, respectively, which was 79.9% and 78.2% of the cost of filgrastim .The average cost per Medicare beneficiary for filgrastim-sndz and tbo-filgrastim was lower than filgrastim .In Medicare Part B, the average costs per claim for filgrastim-sndz and tbo-filgrastim reduced by 11.3% and 20.9% in 2018 compared with 2017, respectively, which exceeded the cost reduction for filgrastim (5.6%) in the same time period. Similarly, the average costs per beneficiary for filgrastim-sndz and tbo-filgrastim claims reduced by 11.6% and 19.5% in 2018 compared with 2017, respectively, while the cost per beneficiary for filgrastim claims decreased by 9.0% in 2018 compared with 2017. Although the average cost per claim for tbo-filgrastim reduced by 1.5% in 2018, its average cost per beneficiary increased by 9.0%.In Medicaid, the average costs per claim for the 3 filgrastim products varied across years. Specifically, cost per claim for filgrastim-sndz had a 29.1% reduction in 2017 (vs 2016), but cost per claim for the other 2 products increased by 10.1% (filgrastim) and 8.0% (tbo-filgrastim) during the same time. In 2018, average costs per claim for the 3 filgrastim products decreased by 8.6% (filgrastim-sndz), 2.0% (filgrastim), and 4.7% (tbo-filgrastim) when compared with 2017.22 Indeed, the adoption of filgrastim-sndz was slower in Medicaid compared with Medicare Part B and Part D, which was likely driven by the progressive state laws and legislation related to biologic medications and substitution of biosimilars.23 From 2013 to 2018, 45 states and Puerto Rico signed their biosimilar substitution laws.23 Larger price discounts relative to reference product and state biosimilar substitution laws could support further improvement of the uptake of filgrastim-sndz in the US market and increase in cost savings.Significant uptake in use of biosimilar filgrastim in Medicare and Medicaid populations was observed with its introduction since 2015. Specifically, after 3 years of entering the US market, the use of filgrastim-sndz increased to almost half of all filgrastim claims paid by Medicare Parts B and D and to over one third of filgrastim products in Medicaid. The significant uptake of filgrastim-sndz, especially in Medicare, is encouraging, which was mainly led by the increased discount per claim compared with the originator product filgrastim from 16% in 2016 to 31% in 2018 in Medicare Part B and from 17% in 2016 to 50% in 2018 in Medicaid. It has been reported that use of biosimilar filgrastim is about 60% in European countries, where it is marketed at a 30%-40% discount.Similar to the significant uptake in use, notable savings in total spending for the 3 filgrastim products were reached during the same time in Medicare Parts B and D, as well as Medicaid. Compared with 2015, the annual total spending paid for all filgrastim products decreased by 28.1% for Medicare Part B, 5.1% for Part D, and 22.1% for Medicaid in 2018, which reflected an annual total saving of $59 million for these 3 programs.15 who predicted a savings of $123 million in 5 years for Medicare alone and $256 million nationwide. Indeed, a variety of factors could have influenced the uptake and cost savings of biosimilar products in the United States, including but not limited to patient and health care provider acceptance,26 limited distribution channel,27 state biosimilar substitution laws,28 and pharmaceutical company incentives .29 On May 10, 2019, the FDA issued the final guidance on the pathway for interchangeable biologics.30 Once the approved biosimilars are designated as interchangeable, state biosimilar substitution laws can begin to take affect across the nation.However, the actual cost savings appeared smaller than the predictions by Grewal et al,5 and more assessment on its market impact is warranted when newer, national-level utilization and cost data become available. Findings on nationwide uptake and cost savings of filgrastim products are warranted and can inform the approval and uptake of future biosimilar products.The significant reductions in average cost per claim for filgrastim-sndz in 2017 and 2018 were observed in Medicare Part B and Medicaid, which directly led to reduced average cost per beneficiary for the biosimilar product . However, the increased market competition due to biosimilar entry has not impacted the unit price of originator product filgrastim yet. Only a 5.6% reduction in average cost per claim for filgrastim in Medicare Part B was observed in 2018. The second biosimilar filgrastim product, filgrastim-aafi , was approved in July 2018 and marketed in October 2018,Study limitations included annually aggregated product-level instead of patient-level data used for this study, which could only support descriptive analysis instead of covariate controlled, multivariable analysis. In addition, there were missing data in number of claims and spending for tbo-filgrastim in Medicare Part B in 2015, as well as the average cost per beneficiary for all 3 filgrastim products in Medicaid.The average cost per claim and per beneficiary was aggregated to the total cost of the product and associated services, which prevented us from looking at beneficiary-level out-of-pocket costs for these products. In addition, the Medicare Parts B and D drug use spending data were not adjusted for the Consumer Price Index, and the data do not include beneficiaries enrolled in the Medicare Advantage program. However, our findings provided new, national-level evidence of use and cost of biosimilar filgrastim and competitor products in Medicare and Medicaid programs.Although the uptake and cost savings due to the biosimilar entry in the case of filgrastim was smaller than previous predicted, the significant uptake in the first 3 years of new biosimilar marketing is encouraging and promising. Policymakers may use the evidence to evaluate existing barriers and policies regarding biosimilar approval and adoption. Additional consideration and efforts regarding biosimilar approval and marketing are warranted for further improving policy pathway, reducing barrier to entry, and regulating marketing manipulation to increase market competition and patient accessibility and achieve cost savings."} +{"text": "This study investigated HPV vaccination rates and associated factors among 265,554 patients aged 18\u201326 within a large healthcare system. Alarmingly, only 30% had completed the vaccine series, far below national averages and targets. Significant disparities were found, with males less likely to be vaccinated than females and Black Americans less likely to complete vaccination despite higher initiation rates. Many patients remained unvaccinated despite recent primary care visits, highlighting missed opportunities. Low uptake, particularly among males, and disparities emphasize the urgent need for targeted interventions to improve provider communication and community education around HPV risks and vaccine benefits to increase vaccination coverage in this population.Human papillomavirus (HPV) is a common sexually transmitted infection, with over 40% prevalence in the US. Oropharyngeal cancers (OPCs) driven by high-risk HPV are increasing (up to 90%), with HPV vaccination being the only prevention available. The aim of this study was to investigate HPV vaccination among patients aged between 18 and 26 years old with at least one encounter at a large healthcare system and identify sociodemographic factors associated with vaccine initiation and completion. A cross-sectional retrospective study was conducted between 2018 and 2021, including 265,554 patients identified from the Clinical Data Warehouse. HPV vaccination status by age, sex, race/ethnicity, insurance type, primary care (PCP) visits in the past year, alcohol, tobacco, illicit drug use, and age at vaccination was examined. Overall, 33.6% of females and 25.4% of males have completed the HPV vaccine. Black Americans were 35% more likely to initiate the vaccine than White Americans but were less likely to complete the entire course. Overall, HPV vaccination prevalence was far below the Health People 2030 goal of 80%, especially in young males. This low rate is troubling, since many patients had a PCP visit and remained unvaccinated, which serves as a missed opportunity for vaccination. Human papillomavirus (HPV) is the most common sexually transmitted infection in the United States (US), with over 40% of people infected . The symHPV vaccination is highly effective and recommended for boys and girls between 11 and 12 years old and can be started at nine years old, with catch-up vaccines at the age of 26. Vaccination is the only primary prevention available for oropharyngeal cancer. While HPV vaccination is not recommended after 26 years of age, some patients between 27 and 45 years old could benefit depending on whether they were vaccinated adequately when younger after discussing it with their physician . In 2020In this study, an estimate is provided of HPV vaccination uptake among eligible adults aged between 18 and 26 years old within the University of Pittsburgh Medical Center (UPMC) hospital system, which is a large private healthcare system operating multiple hospitals. The aim was to identify which sociodemographic factors are associated with low vaccination initiation and completion in this population to reduce the burden of diseases related to HPV in vulnerable populations.Data were collected from Clinical Data Warehouse, an extensive database that stores healthcare data from the University of Pittsburgh Medical Center.A cross-sectional retrospective study was conducted between 2018 and 2021, including 265,554 patients aged between 18 and 26, who received the vaccine either from their primary care physician, pediatrician, or upon direct request to pharmacies. Patients with inconsistent reporting of gender were excluded in order to ensure data integrity and analytical accuracy. The University of Pittsburgh Medical Center Review Board reviewed and approved this study.The primary outcome of this study was HPV vaccination status, classified as none, initiated, and completed (3 doses). Several factors were investigated, including age, gender, race/ethnicity, type of insurance , number of primary care (PCP) visits in the past year, and alcohol and tobacco use. The Area Deprivation Index (ADI) 2020, which measures the level of deprivation in the census block group geographic area with a ranking of 1, indicating the lowest level of \u201cdisadvantage\u201d within the nation, and an ADI with a ranking of 100, indicating the highest level of \u201cdisadvantage\u201d, was also included. Race/ethnicity was classified as Hispanic/Latino , Non-Hispanic (NH) White, NH Black, NH Asian, NH Native American, other, and refused. Additionally, age was classified at first vaccination with the following categories: a recommended age between 11 and 12 years old; early vaccination, 9 years old; early adherent, 9 to 10 years; catch-up, 13\u201318 years old; and a catch-up between 18 and 26 years old.p < 0.05.The median (interquartile range (IQR)) for continuous variables and counts, and percentages for categorical variables were calculated. The prevalence of HPV vaccination was assessed in the study population and was stratified using the chi-square test for descriptive statistics. A Poisson regression with robust standard errors was performed to calculate prevalence ratios and examine risk factors associated with vaccine initiation and completion. The statistical analysis was conducted using R software for statistical computing (R version 4.3.1). Statistical significance was defined as A total of 104,426 patients, with a mean age of 21.89 \u00b1 2.63 years old, received at least one vaccination dose .Overall, 42.2% of all the females in the study population received a dose of the HPV vaccine. Females were 37% more likely (PR: 1.37 (95% CI 1.35\u20131.38)) to initiate the vaccine than males were. When examining vaccination by race, NH Black Americans were 35% more likely (PR: 1.35 (95% CI 1.33\u20131.37)) to initiate the vaccine compared to NH White Americans. No difference was found regarding insurance, where 40.7% and 40.4% of patients covered by private insurance and Medicaid initiated the vaccine, respectively. However, in the adjusted model, patients with Medicaid coverage were 8% less likely (PR: 0.92 (95% CI 0.91\u20130.94)) to initiate the vaccine than those with private insurance coverage. A PCP visit was important for vaccination, where 49.2% of patients who visited a PCP in the past year had received at least one dose of the vaccine, compared to 33.1% who received a vaccine dose with no PCP visit. When stratified by gender , 53.9% . Females were 10% more likely (PR: 1.10 (95% CI 1.09\u20131.11)) to complete the vaccination than males were. Among NH Black Americans, 68.5% (n = 9551) completed the entire vaccine course, while NH White Americans had a completion percentage of 78.8% . NH Black Americans were 11% less likely (PR: 0.89 (95% CI 0.88\u20130.9)) to complete the entire vaccination course when compared to NH White Americans. Patients with private insurance were more likely to complete the HPV vaccine course than patients with Medicaid or another type of insurance . When adjusted, patients with Medicaid coverage were less likely (PR: 0.96 (95% CI 0.95\u20130.98)) to complete the vaccine than those with private insurance coverage. Out of the patients who did not have a PCP visit in the past year, 75.5% completed the entire vaccine course. Conversely, among patients who visited a PCP, 78.7% completed the vaccine. Gender stratification is shown in Completion rates were lower among NH Black individuals compared to those of NH White individuals. Specifically, 71.4% (6670) of NH Black females and 62.7% (2881) of NH Black males completed the HPV vaccine, whereas 81.4% of NH White females and 74.3% of White males completed the vaccine. NH Black females and males had similar prevalence ratios of 0.89 (95% CI 0.88\u20130.91) and 0.87 (95% CI 0.85\u20130.90), respectively, indicating that they were less likely than their White counterparts to complete the HPV vaccine.A total of 25.1% of the females received their vaccine dose during the routine age range of 11\u201312 years old, compared to 15.4% (5004) of the males .Among females, 55.5% received their first vaccine dose between the ages of 13 and 17 years (in the catch-up group), while among males, the prevalence was 67.9% in this category. When considering races, NH Black Americans had the highest rate of vaccine initiation at early routine age (5.9% (671)) and routine age (25.5% (2916)). NH White Americans had the highest prevalence ) of vaccination during the catch-up phase (13\u201317 years old). Of the patients who did not visit a PCP, 25.3% received the first vaccine dose in the routine age, while 17.6% (7648) of the patients who visited a PCP were in the routine group. Among patients who received the first dose during the routine group, 27.7% (3211) of patients were covered by Medicaid, the highest insurance type rate in this group. In comparison, private insurance had a prevalence of 20.5% in the routine group.The present study aimed to investigate HPV vaccination among patients aged between 18 and 26 years old with at least one encounter at a large healthcare system and identify sociodemographic factors associated with vaccine initiation and completion. In the current sample of 265,554 patients, only 30.3% of participants reported having completed the HPV vaccine, while 9.0% reported having initiated the HPV vaccine. These rates are substantially lower than the Healthy People 2030 goal of 80%. Moreover, it was found that males were 37% less likely than females to initiate and 10% less likely to complete the vaccination schedule. Although the Advisory Committee on Immunization Practices (ACIP) recommended routine vaccination for males in 2011, vaccination rates for males remain well below those for females. This highlights the importance of further implementing policies to increase male vaccination rates.In the United States (US), HPV vaccination coverage has been below the recommended optimal levels. Moreover, HPV coverage rates may differ by region and US state. Southern and Midwestern states have exhibited lower rates of HPV vaccination than other states ,12. The Several studies have demonstrated that racial and ethnic minority populations are less likely to receive vaccine recommendations from healthcare providers ,22,23,24Vaccine hesitancy is a crucial barrier to HPV vaccination. In a recent study conducted by Szilagyi et al. , it was Socioeconomic status and health insurance coverage play an important role in vaccination rates. The cost of vaccination is widely recognized as a significant obstacle to initiating and completing the HPV vaccination series in the US . Indeed,According to a study by Berdnarczyk et al. , approxiFinally, it has been demonstrated that access to a primary care provider is a crucial factor associated with improved HPV vaccination rates , which wDespite its strengths and significant research findings, this study has some limitations. First, as this is a cross-sectional descriptive study, causality cannot be inferred from the observed associations. Second, the study focuses on patients aged 18\u201326 years with at least one encounter at a large healthcare system. Thus, the observed trends may not be generalizable and fully represent the wider population. Finally, HPV status was abstracted from the clinical intake forms, which is subject to potential misclassification by recall and may have introduced bias that can impact validity accuracy. However, the subjects were also randomly sampled for clinical chart review, and high concurrence was found.In conclusion, HPV vaccination rates among patients aged 18\u201326 years within a large healthcare system were significantly below national rates and far from the Healthy People 2030 goal. Implementing targeted education and training programs becomes imperative, aiming to provide individuals, particularly males, with the necessary knowledge to make informed decisions regarding vaccination. Furthermore, enhancing healthcare providers\u2019 communication skills by effectively conveying the benefits and safety of vaccines can effectively alleviate concerns and uncertainties surrounding vaccination. Moreover, efforts should be made to ensure that education and training programs are accessible, inclusive, and tailored to the diverse needs of different communities. Engaging with individuals and communities, gaining insights into their specific concerns, and adapting communication strategies, accordingly, will help build a more trusting and supportive environment that promotes vaccine acceptance. Therefore, empowering individuals through knowledge, dispelling myths, and nurturing trust can significantly increase vaccination rates."} +{"text": "Stevens-Johnson Syndrome(SJS),toxic epidermal necrolysis(TEN), and SJS/TEN Overlap Syndrome are on the same spectrum of severe blistering skin diseases affecting mucosal surfaces of the body.They have an immunological etiology and are caused by toxins, drugs, or infectious agents. The mortality rate for patients with these conditions ishigh, but there is limited research on the outcomes for those patients with additional comorbidities.This study investigates the association of inflammatory conditions such as diabetes mellitus, obesity, and tobacco usage have on the outcomes of patients with SJS or related disease. It was predicted that each of these comorbidities would be associated with higher rates of mortality and disease complications.This study is a retrospective observational cohort study using the TriNetX Research Network, which provides deidentified electronic medical data from health care organizations all over the world. TriNetX was used to perform a search and analysis for patients with SJS, SJS-TEN Overlap Syndrome, and TEN as well diabetes mellitus(DM), tobacco usage(TU), or overweight/obesity status.A fourth, control cohort of patients without any comorbidities was also included. In total, 8,962 patients were included in the study: 6,348patientsin the control group;426 patients in the TU group; 1,186 patients in the DMgroup, and 1,002 patients in the Obesity group. Outcomes measured were rate and incidence of pneumonia, sepsis, and endotracheal intubation. Outcome variables from each of the four cohorts were analyzed with a total of six unique comparisons. Statistical analyses used included measure of association, Kaplan-Meyer Survival Curve, and measure of incidence.Compared to the control group, the DM group had a mortality rate14.3% higher, pneumonia rate7.6% higher , sepsis rate 4.7% higher , and endotracheal intubation rate of 1.9% higher . Furthermore,compared to the Obesity group, the DM group had a mortality rate 11.6% higher and sepsis rate 4.7% higher . Compared to the TU group, the DM group had a mortality rate 12.4%higherand sepsis rate 8.1% higher (CI 95% 4.7%-11.6%). Besides this data on the DM group, the Obesity group showed statistically significant worse outcomes as well. Compared to the control group, the Obesity group showed a mortality rate 2.7% higher , pneumonia rate 5% higher , sepsis rate 4.5% higher , and intubation rate of 2.1% higher .Diabetes mellitus is associated with worse outcomes for patients with SJS, SJS-TEN overlaps, or TEN compared to obesity and tobacco usage.This data argues the importance of examining a patient\u2019s past medical history when evaluating their prognosis for SJS, SJS-TEN overlaps or TEN."} +{"text": "Patients suffering from moderate-to-severe burns are known to experience significant metabolic perturbations, such as hyperglycemia, as the result of a systemic hypermetabolic response. Hyperglycemia in these patients is in part due to the development of peripheral insulin resistance. Glycemic control is important, as hyperglycemia in patients with moderate-to-severe burns is associated with increased morbidity and mortality. Insulin and metformin are the first lines of treatment, with previous studies showing metformin to be superior to insulin in reducing burn-induced hyperglycemia. We queried a large multi-institutional national database to investigate whether the use of metformin in burn patients is associated with improved glycemic control and morbidity/mortality outcomes compared to insulin therapy.We accessed TriNetX, a global health research network, and queried ICD-10 codes for burn injuries across 54 participating health care organizations. We then identified cohorts of patients who were administered either metformin or insulin, but not both, within 1 week of burn. These cohorts were balanced using propensity score matching for age, gender, ethnicity, race, and type 2 diabetes mellitus and subsequently compared for the following outcomes: hyperglycemia (R73), hypoglycemia , lactic acidosis (E87.2), sepsis (A41), and death.A total of 16,569 patients were given insulin within 1 week of burn. This patient cohort had a mean age of 54 years, with 60% being male, 67% White, and 19% Black or African American. In contrast, 7,308 patients received metformin within 1 week of burn, with a mean age of 56 years, 55% female, 70% White, and 16% Black or African American. Burn patients who received insulin within 1 week of burn showed a comparative increased risk of 3.009% (p < 0.0001) for the development of hyperglycemia compared to those who were given metformin within 1 week of burn . Additionally, burn patients given insulin displayed an increased risk of 2.452% for development of hypoglycemia , 3.078% for development of lactic acidosis , 3.67% for development of sepsis , and 7.422% for death .Patients receiving insulin within 1 week of burn showed increased risk of poor glycemic control than those receiving metformin. Morbidity and mortality are also higher in those receiving insulin than those receiving metformin. Additional research is necessary to further understand these findings.These findings should encourage clinicians to appreciate the importance of glycemic control in burn patients, as well as recognize the importance of choosing the most appropriate pharmacologic agent for glycemic control."} +{"text": "Poor adherence to malaria treatment guidelines among healthcare workers (HCWs) is a major contribution to diagnostic challenges, treatment failure, and non-rational use of antimalarial medicines. However, there is limited information about adherence to malaria treatment guidelines among HCWs in private health facilities in informal settlements in Uganda. This study therefore assessed the level of adherence to malaria treatment guidelines and associated factors among HCWs in private health facilities in Kampala\u2019s informal settlements. A cross-sectional study was conducted among 339 HCWs from private health facilities in slums of 4 selected divisions in Kampala, Uganda. Quantitative data was collected using a semi-structured questionnaire, cleaned in MS Excel 2016 and analyzed using STATA 15.0 statistical software. Bivariate and multivariate analysis were conducted using a generalized linear model of modified Poisson regression to obtain factors associated with adherence to malaria treatment guidelines. The study revealed that majority of respondents 71.1%(241/339) were aged 30 years and below, and 50.1%(170/339) of the were female. Almost all of the respondents 98.8%(335/339) reported that they had malaria diagnostic equipment (microscopy or rapid diagnostic tests) at their facilities, 47.5%(161/339) had non-recommended anti-malarial drugs present in stock and 36.0% reported that they did not refer severely ill patients to higher health facilities in the previous 3 months. Although 92.6%(314/339) of the respondents had heard about the national malaria treatment guidelines, 63.1%(214/339) of them adhered to these guidelines. Having a bachelors degree P 0.006), and having high levels of knowledge P 0.001) were positively associated with high adherence to malaria treatment guidelines. In conclusion, adherence to malaria treatment guidelines was suboptimal and less than the national target of 90%. Enforcement, supervision, trainings, and continuous medical education should be enhanced in private healthcare facilities to improve adherence to malaria treatment guidelines in informal settlements. The global prevalence of malaria increased by 13 million cases from 2020 to 2022 , over haThe World Health Organization (WHO) introduced a global malaria strategy targeted to reduce malaria incidence and mortality rates by at least 90% by 2030 . GuideliMalaria, however, remains a major public health problem at both public and private health facilities in Uganda. The disease accounts for 30\u201350% of outpatient visits, 15\u201320% of all hospital admissions, and up to 20% of all hospital deaths . The 202The majority of slums dwellers in Uganda obtain malaria treatment from private health facilities, which largely rely on using fever as a major symptom to diagnose malaria . This coThis was a cross-sectional study using quantitative data collection methods. The study was conducted in Kampala city, Uganda\u2019s capital. Kampala has a population of over 3.6 million people, constituting 25% of the country\u2019s total urban population , 41. AdmThe study was conducted among HCWs in private health facilities in Kampala\u2019s informal settlements. The sample size was determined using the formula by Kish Leslie considering a prevalence of 27.3% adherence to malarial treatment guidelines . A samplth April\u2013 20th June 2022. Quantitative data were collected by trained research assistants, with a bachelors degree in any health related course, using a semi-structured questionnaire uploaded on the Kobo collect mobile application. The research assistants were trained on the study and use of data collection questionnaire. The questionnaire was designed and adopted from similar studies [Recruitment of participants and data collection was conducted from 26 studies \u201344 and t studies . It was A set of 13 questions was designed to assess adherence to malaria treatment guidelines among respondents . These qKnowledge of malaria treatment guidelines was assessed using 9 questions . QuestioThe data was collected using Android-enabled mobile phones loaded with the Kobo collect application software. The data was synchronized onto the server daily and only the principal investigator and data manager had access to it. The collected data was cleaned in MS Excel 2016 and analyzed using STATA 15.0 statistical software. Descriptive analyses such as frequencies, proportions, and means (where appropriate) were performed for demographic characteristics, knowledge of antimalarial resistance, adherence to guidelines, and associated factors. To assess the association between the outcome variables (level of adherence) and explanatory variables, generalized linear model of modified Poisson regression was conducted providing Crude Prevalence Risk ratios (CPRs) and their corresponding 95% confidence intervals (CIs). Variables with p<0.05 were added to the multivariate analysis to ascertain significant variables for each outcome. The statistical significance levels were two-sided at p<0.05.Ethical approval was obtained from the Makerere University School of Public Health Research and Ethics Committee (MakSPH-REC) (REC No: SPH-2021-207). The study was also registered by Uganda National Council for Science and Technology (REG No. HS2161ES). Administrative clearance was obtained from the Department of Public Health and Environment at Kampala City Council Authority. Study participants provided written informed consent at the initiation of data collection. The data collected was stored on drives that were only accessed by the principal investigator and data manager.Out of the 339 respondents, 50.1% (170/339) were females, more than two-thirds, 71.1% (241/339) were aged 30 years and below, and 51.9% (176/339) were enrolled nurses / midwives. In terms of education, 50.7% (172/339) of respondents were national certificate holders, The majority of respondents 68.4% (232/339) had five or fewer years of experience in the management and treatment of malaria cases, 74.3% (252/339) had an average monthly expenditure of 150 USD and below, and 57.8% (196/339) had not been supervised by authorities in the previous 6 months.Considering the previous 3 months, almost all respondents reported having had malaria diagnostic equipment (microscopy or RDTs) (98.8% (335/339)) had recommended anti-malarial drugs 99.7% (338/339) at their health facility. Nearly half, 47.5% (161/339) respondents reported availability of non-recommended anti-malarial drugs in the previous 3 months .Regarding factors influencing the type of anti-malarial drugs prescribed, more than three quarters of the respondents 80.2% (272/339) agreed to anti-malarial drug availability, 94.1% (319/339) agreed to anti-malarial drug effectiveness, 85.8% (291/339) agreed to existing national malaria treatment guidelines, 48.1% (163/339) agreed to drug promotion by manufacturers, 64.0% (217/339) agreed to patient preferences, and 57.8% (196/339) agreed to the need to make profits.Most respondents 92.6% (314/339) reported that they had heard about the national malaria treatment guidelines mostly through training and continuous medical education (70.2%). Almost all of the respondents 95.6% (324/339) agreed that malaria was clinically suspected mostly based on fever or a history of fever. More than three quarters of the respondents 78.8% (267/339) agreed that treatment solely based on clinical suspicion was only considered when a parasitological diagnosis was not accessible in a severely ill patient, and 86.1% (292/339) agreed that ACTs were the recommended treatments for uncomplicated falciparum malaria. The majority of respondents 95.9% (325/339) agreed that the first-line treatment for uncomplicated malaria was an ACT (Artemether/Lumefantrine\u2014AL), 85.8% (291/339) agreed that the second-line treatment for uncomplicated malaria was an ACT (Dihydroartemisinin Piperaquine\u2014DHA-PPQ), and 95.9% (325/339) agreed that Artesunate (given intravenously) was recommended for the treatment of severe malaria .Regarding diagnosis of malaria, over 95% of respondents reported always asking about symptoms of the illnesses 98.5% (334/339), presence or history of fever 96.5% (327/339), and signs of severe illness 93.5% (317/339). Most respondents 93.8% (318/339) always took both medical history and physical examinations appropriately, and 85.5% (290/339) always recommended/offered a blood test (RDT and microscopy) for malaria (even if the patient refused to test). Regarding treatment, more than three quarters of the respondents 86.7% (294/339) reported that they used Artesunate Quinine (given intravenously) to treat severe malaria, 73.7% (250/339) used Quinine treatment when ACTs were contraindicated, and 64.0% (217/339) referred severely ill patients .Less than two-thirds of the respondents 63.1% (214/339) had a high level of adherence to malaria treatment guidelines. At bivariate analysis, sex, age, highest level of education, cadre of health worker, level of knowledge were associated with adherence to malaria treatment guidelines. After adjusting for potential confounders having a bachelors degree as the highest level of education, being an enrolled nurse/midwife, and having high knowledge on malaria treatment guidelines were significantly associated with having good adherence to malaria treatment guidelines. Respondents who were female were 24% less likely to have a high adherence to malaria treatment guidelines as compared to males . Respondents who had a bachelors degree were 1.54 times more likely to have good adherence to malaria treatment guidelines as compared to those with certificates . Respondents who were enrolled nurses/midwives had a 51% higher likelihood of having good adherence to malaria treatment guidelines as compared to nursing assistants . Respondents who had high level of knowledge on malaria treatment guidelines were 1.35 times more likely to have good adherence to malaria treatment guidelines as compared to those who had low knowledge .This study assessed the level of adherence to malaria treatment guidelines and associated factors among health care workers in private health facilities in Kampala\u2019s informal settlements. The knowledge of healthcare workers on malaria treatment guidelines was also investigated. Many health workers adhered to malaria treatment guidelines. High adherence was associated to having a bachelors degree as the highest level of education, being an enrolled nurse/midwife, and having high knowledge on malaria treatment guidelines. In addition, females were less likely to adhere to malaria treatment guidelines compared to their male counterparts. Nonetheless, some HCWs also had non recommended drugs in stock, did not refer patient to higher level facilities. These findings could be used by public health policymakers, administrators of private health facilities, local authorities, and other stakeholders to strengthen policies aimed at improving adherence to malaria treatment guidelines in private health facilities.Although many health workers (63.1%) in this study adhered to malaria treatment guidelines, adherence levels were below the national malaria strategic plan target of 90% by 2020 . The proOur study revealed that healthcare workers with higher knowledge and education levels (bachelors degree and above) had high adherence to malaria treatment guidelines. This could be that their advanced training comes with better attention and improved clinical performance. Furthermore, in our study, HCWs who obtained information from training/ continuous medical education (70%) and seminars (32.4%) could have improved their knowledge levels. In addition, studies conducted in Uganda revealed that training health workers increased their adherence to treatment related to parasitological diagnosis with microscopy and RDTs from 24% in 2009 to 59% in 2013 . TherefoAlmost half of the health facilities had non-recommended antimalarial drugs in the previous three months. Using non recommended anti-malarial increases the risk that patients will not receive the necessary dosage, which will lead to treatment failure, poor efficacy, and antimalarial drug resistance . This alIn comparison to their male counterparts, this study revealed that female HCWs were less likely , to adhere to malaria treatment guidelines. This could be attributed to many family work balance challenges, gender inequalities , 48, uneThis study revealed that a significant proportion (48.1%) of healthcare workers reported the demand from patients and manufacturers\u2019 marketing influence as factors that influenced the types of drugs to be prescribed. Yet, evidence shows that drug promotion by manufacturers to providers is an important element that affects the drugs that HCWs prescription practices in private settings. This is concerning because it could lead to supplier-induced demand and superfluous prescriptions, aggravating the financial burden of the disease on the patients and also increasing the likelihood of antimalarial drug resistance. Furthermore, studies conducted in rural areas have revealed that non recommended antimalarial drugs pose an economic burden of US$2.6 million to the Ugandan government, and US$26.1 million in direct and indirect costs to patients due to loss of productivity and death . These hA significant proportion of health workers in our study did not prescribe antimalarial drugs to malaria positive patients, and more than a third 36% of health facilities did not refer severely ill patients to higher health facilities in the previous 3 months. Non-referral to higher level health facilities could likely be attributed to HCWs perceptions that referral leads to loss of prestige, profit, as well as poor quality of care at private facilities . In addiOur study had some limitations such as being prone to recall bias due to some questions asking for information of many months in the past. Furthermore, participants may have over-reported adherence as part of social desirability bias, because it was measured using self-reports. Despite these limitations, the study results are very important because they give a current assessment of the state of the adherence to malaria treatment guidelines in informal settlements in Kampala city.Adherence to malaria treatment guidelines was suboptimal and less than the national target of 90% adherence. Adherence was associated to having a bachelors degree as the highest level of education, being an enrolled nurse/midwife, and having high knowledge on malaria treatment guidelines. However, many health workers did not refer patients to higher facilities, and had in stock non-recommended antimalarial drugs. Therefore, routine supervision, training on malaria treatment guidelines, and continuous medical education should be conducted among healthcare workers to improve adherence to malaria treatment guidelines. In addition, the effectiveness of these interventions should also be studied further to establish their impact on the level of adherence to malaria treatment guidelines.S1 Text(PDF)Click here for additional data file.S2 Text(PDF)Click here for additional data file."} +{"text": "Cytomegalovirus retinitis (CMVR) is the most common and sight-threatening opportunistic retinal infection in patients with acquired immunodeficiency syndrome (AIDS) and several controversies remain to be settled. We aimed to summarize the current evidence and clarify the clinical features and prognosis of CMVR in AIDS patients.The databases PubMed, EMBASE, and Ovid from inception to April 2022 were searched to identify the relevant studies. R software version 3.6.3 was used to perform the statistical analyses. Results in proportion with 95% confidence interval (CI) were calculated using the Freeman-Tukey variant of arcsine square transformation.We finally included 236 studies comprising 20,214 patients. CMVR in AIDS was male-dominated , with 57% (95%CI 55%-60%) aged <41 years and 44% (95%CI 41%-47%) being bilaterally involved. CMVR was preponderant in AIDS patients with the following characteristics: white and non-Hispanic, homosexual, HIV RNA load \u2265 400 copies/mL, and CD4+ T-cells <50 cells/\u03bcL. The positivity of CMV-DNA in blood, aqueous humor, and vitreous humor was 66% (95%CI 52%-79%), 87% (95%CI 76%-96%), and 95% (95%CI 85%-100%), respectively. The most common symptoms were blurred vision , followed by asymptomatic, visual field defect, and floaters. CMVR was first diagnosed and regarded as the clue to AIDS diagnosis in 9% (95%CI 6%-13%) of CMVR patients. Approximately 85% (95%CI 76%-93%) of the CMVR patients have received cART. CMVR remission was observed in 72%-92% of patients depending on the specific category of anti-CMV therapy. The general incidence of CMVR-related RD in the entire course was 24% (95%CI 18%-29%), of which most patients received PPV with SO or gas tamponade and the rate of anatomic success was 89% (95%CI 85%-93%).CMVR is a common opportunistic infection with diverse clinical features in AIDS patients, preponderant in those who are male, homosexual, or with CD4+ T-cells <50 cells/\u03bcL. Current therapies for CMVR and CMVR-related RD were shown to be effective. Early detection and routine ophthalmic screening should be promoted in AIDS patients.PROSPERO, identifier CRD42022363105. CMVR paHowever, numerous controversies still need to be addressed. Firstly, identifying CMVR as the clue to AIDS diagnosis may help to initiate cART as early as possible , but verHowever, no such meta-analysis has been conducted yet, and a comprehensive analysis is urgently needed. Our aim in this meta-analysis is to summarize information and help addressing existing controversies on the demographics, clinical features, treatment, and prognosis of CMVR. The results may be used to inform clinical practice by providing ophthalmologists with a comprehensive overview of the current state of knowledge on this condition.2This study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement and was 2.1PubMed, EMBASE, and Ovid were searched to identify relevant studies published from inception to April 2022. The language was restricted to English with no restriction on publication date. The following keywords and MeSH terms were searched: cytomegalovirus retinitis, human immunodeficiency virus, acquired immunodeficiency syndrome, and multiple synonyms. A detailed search strategy for the PubMed database was developed and then adapted for searching studies in other databases (see 2.2The eligibility criteria were as follows: 1) research data on CMVR in AIDS patients; and 2) full-text available. Exclusion criteria included: 1) studies with a sample size <5; and 2) literature reviews, systematic reviews, meta-analysis, editorial, conference abstract, or technical notes; and 3) studies on animal or cadaver subjects.2.31) Study characteristics: the first author, publication year, study design, group size (patients and eyes), and duration of follow-up. 2) Patient characteristics: age, gender, ethnicity, HIV transmission route, HIV RNA load, CMV load, CMV positivity, extraocular CMV infection, and other systemic co-morbidities. 3) CMVR characteristics: laterality, CMVR as a clue to AIDS diagnosis, symptoms, signs, retina area involved, location, baseline and final VA, therapy, prognosis, and ocular complications. \u201cRetina area involved\u201d was categorized into \u201c0\u201325%\u201d, \u201c25\u201350%\u201d, and \u201c50%-100%\u201d. \u201cLocation\u201d was grouped as \u201ccentral type\u201d or \u201cperipheral type\u201d. The \u201ccentral type\u201d was defined as CMVR involving the region of one optic disc diameter (1500 \u03bcm) from the edge of the optic disc or two optic disc diameters (3000 \u03bcm) from the fovea; the \u201cperipheral type\u201d was defined as CMVR involving regions other than those categorized in the central type independently screened the titles and abstracts of the retrievals to identify eligible studies. Full texts of all potentially eligible studies were then read for further discrimination. The following data were extracted: ral type . The basCochrane Handbook for Systematic Reviews of Interventions. Two researchers (QZ and XYZ) independently scored each study, and any disagreements were resolved through discussion or by consulting a third researcher (YXC).For quality assessment, we used the Newcastle-Ottawa Scale to assess the non-randomized studies. Studies with a score of 6 or higher were considered moderate to high quality. The randomized studies were assessed using the criteria outlined in Chapter 8 of the 2.42 statistics. If heterogeneity was low , the fixed-effect model would be chosen. When heterogeneity was significant , sensitivity analysis and subgroup analysis would be performed to identify its source, and a random-effect model would be applied when encountering clinical homogeneity. We will perform descriptive analysis if clinical heterogeneity was found in the result of the meta-analysis. The publication bias was evaluated using the funnel plot of the Egger test. P<0.05 was considered statistically significant.We employed R version 3.6.3 for statistical analyses. The Freeman-Tukey variant of arcsine square transformation was applied to calculate proportions with 95% confidence interval (CI) and to build forest plots. The heterogeneity across studies was evaluated using the chi-square test and I33.1Initially, we identified 4,659 studies. After removing duplicates and screening titles and abstracts, we ultimately reviewed the full texts of 3,180 articles. Of these, 236 studies comprising 20,214 patients were eligible for this study. The screening process was presented using the PRISMA flow chart see Figure\u00a013.22 = 86%), with 57% aged <41 years and 44% bilaterally involved. CMVR was more prevalent in AIDS patients with the following characteristics: white and non-Hispanic , homosexual , HIV RNA load \u2265 400 copies/mL , or CD4+ T-cells <50 cells/\u03bcL .CMVR was male-dominated and 48% of the included CMVR patients, respectively (see 2 = 91%), 87% , and 95% , respectively (see 2 = 85%). The pooled incidence of other systemic co-morbidities in CMVR patients was summarized in Positive urine or blood CMV culture was found in 67% , followed by asymptomatic, visual field defect, floaters, photophobia, watering, and pain. The pooled incidence of these symptoms was summarized in 2 = 0%). The pooled results of the retina area involved, retinitis location, and baseline VA were also shown in The most common symptoms of CMVR were blurred vision of 8,724 CMVR patients in 72 studies have ever received cART either at CMVR diagnosis or at enrollment. The pooled incidence of systemic, local or combinational anti-CMV therapy was 45% , 35% , and 20% , respectively. Detailed therapy in the induction and maintenance stage was shown in 2 = 78%) after achieving immune recovery and discontinuing maintenance anti-CMV therapy. The all-cause mortality rate of CMVR patients was 36% . Immune recovery uveitis (IRU) was observed in 26% of 3748 CMVR patients in 28 studies after cART initiation and immune recovery. The specific postoperative complications after intraocular ganciclovir implants were summarized in A total of 85% of 2,064 CMVR eyes in 10 studies (see 2 = 97%), followed by no therapy, laser, and scleral buckle (see 2 = 40%). SO-dependent eyes were observed in 26% of patients receiving PPV with SO.General RD during the entire course was observed in 24% was found using Egger\u2019s test.4The present study summarizes information on the demographics, clinical features, treatment, and prognosis of CMVR in AIDS patients. Based on all the currently available evidence, the study found that CMVR is male-dominated, with a high proportion of patients aged <41 years, and is commonly bilateral. CMVR was preponderant in white and non-Hispanic, homosexual AIDS individuals with high HIV RNA load or low CD4+ T-cell count. Blurred vision is the most common symptom, and CMVR may be the initial manifestation leading to AIDS diagnosis. The CMV-DNA positivity rate varied remarkably, being 66%, 87%, and 95% in blood, aqueous humor, and vitreous humor, respectively. The CMVR remission rate can achieve 72%-92% depending on the specific category of anti-CMV therapy. RD is a common complication of CMVR with a general incidence of 24% in the entire course, but PPV with SO or gas tamponade can provide a good anatomical outcome (89%).4.1+ T-cells of most (78%) CMVR patients in this study count <50 cells/\u03bcL. Previous studies have also indicated that CD4+ counts <50 cells/\u03bcL are significant risk factors for the development of CMVR in AIDS patients and men who have sex with men (54%) . The CD4patients . These f% to 91% ; the pooVitreous CMV-DNA is a highly sensitive marker for CMVR diagnosis, with a pooled positivity of 95% in our study. However, it is only reserved for unusual CMVR cases considering the risk of hemorrhage, infection, and vision loss associated with the sampling procedure. The previously reported aqueous CMV-DNA positivity was inconsistent, ranging from 20% to 100% ; the pooTherefore, blood CMV-DNA is still important for CMVR diagnosis despite its relatively lower sensitivity (66%). Studies have further explored the cut-off value of blood CMV-DNA for diagnosing CMVR, hopefully enhancing its diagnostic efficacy . Additio4.2In our study, the main symptoms of CMVR included blurred vision, floaters, and visual field defects. We also observed several common symptoms of ocular inflammation in these CMVR patients, including photophobia, watering, and pain, which are easily ignored. Additionally, 29% of the included CMVR patients were asymptomatic, revealing the difficulty in the early diagnosis of CMVR in AIDS patients since patients without ocular symptoms may not seek ophthalmic examinations. A delay in CMVR diagnosis, potentially leading to irreversible vision loss, as well as a delay in identifying and managing life-threatening extraocular CMV infection , is detrimental for CMVR patients. All these findings highlight the importance of routine ophthalmic screening for AIDS patients, even for those with only slight or no ocular discomfort. However, due to the lack of trained ophthalmologists and the enormous burden of AIDS, routine ocular examination is rarely performed in clinical practice, especially in resource-limited developing countries . A comprThe incidence of CMVR as the initial AIDS-defining clinical manifestation remains largely unknown. In this study, CMVR was the clue to AIDS diagnosis in 9% of CMVR patients, indicating a potentially important role of ophthalmologists in identifying HIV infection. Additionally, we found that CMVR was distributed slightly more distributed as \u201cperipheral type\u201d than \u201ccentral type\u201d (51% versus 49%). Based on this finding, we assumed that an imaging system capturing a wider field might facilitate the identification of peripheral lesions and the diagnosis of CMVR. Recently, 4.3+ T-cells, thus restoring immunity to CMV and enabling the discontinuation of anti-CMV therapy without CMVR recurrence , fundus autofluorescence (FAF), or UWF retinal imaging has recently been applied in the diagnosis and evaluation of CMVR . However4.6CMVR is a common opportunistic infection with diverse clinical features in AIDS patients. Current therapies for CMVR and CMVR-related RD were shown to be effective. Early detection and routine ophthalmic screening should be promoted in AIDS patients.The original contributions presented in the study are included in the article/QZ devised this study, carried out the literature search and data extraction, and drafted the manuscript. X-YZ helped in the data extraction, contributed to statistical analysis and revision of the manuscript. N-NL and Y-XC coordinated and participated in the entire process of drafting and revised the manuscript. All authors contributed to the article and approved the submitted version."} +{"text": "Children < 6 months of age are not eligible for influenza vaccine but are at high risk of influenza and its complications. Maternal influenza immunization (MII) in pregnancy or during lactation are two ways to provide infants vaccine specific influenza antibodies that could confer protection. Limited data delineate the individual and combined protective effects of MII and breastfeeding on influenza in infants. We aimed to evaluate the independent and combined protective effects of MII during pregnancy and breastfeeding against influenza during the first 6 months of life.We utilized a retrospective cohort of mother-infant pairs, including infants born between January 1, 2012, to December 31, 2019 with longitudinal care within a single health system. Maternal influenza vaccine, breastfeeding and important covariates (Table 1) were obtained from electronic health records. We evaluated the odds of laboratory-confirmed influenza among infants < 6 months of age based on MII in pregnancy and breastfeeding status at 3 months of age using unadjusted and adjusted logistic regression following stepwise regression for covariates with p-value < 0.15.Of the 44,132 mother-infant pairs included, 0.3% (N=141) of infants had laboratory-confirmed influenza between birth and 6 months of age. 54% of infants received some/exclusive breastmilk at 3 months of age; 51% of mothers had MII during pregnancy. Breastfeeding alone did not significantly protect against influenza compared to infants who received no breastmilk and no MII. In contrast, exposure to MII trended toward decreased risk of influenza by 37% , and the combination of MII in pregnancy and breastfeeding significantly decreased odds of infant influenza by 60% (Table 1).MII in pregnancy can effectively reduce the risk of influenza between 40-60% in children < 6 months. Breastfeeding significantly enhances that protection, either through its broad immune properties and/or the vaccine-specific antibodies in milk. Increasing the administration and acceptance of MII in pregnancy and improving sustained breastfeeding rates may help reduce the burden of infant influenza.John V. Williams, MD, Merck: Grant/Research Support|Quidel: Board Member Judith M. Martin, MD, Merck, Sharp and Dhome: Grant/Research Support"} +{"text": "Publication bias was assessed using funnel plot and Egger's test. We estimated the pooled LTBI prevalence in CKD patients along with 95%CI.This study was conducted following the PRISMA guidelines. We identified, 3694 studies from the whole search, and 59 studies were included. Each study's quality was assessed using JBI checklist. We employed STATA version 17 for statistical analysis. We assessed heterogeneity using IThe pooled prevalence of LTBI among CKD patients using data collected from 53 studies having 12,772 patients was 30.2% . The pooled prevalence among pre-dialysis, hemodialysis, peritoneal dialysis, and renal transplanted patients was 17.8% , 34.8% , 25% , and 16% , respectively. The pooled prevalence of LTBI stratified by the laboratory screening methods was 25.3% (95%CI: 20.3\u201330.3) using TST, 28.0% using QFT, and 32.6%, (95%CI: 23.7\u201341.5) using T-SPOT.There is high prevalence of LTBI among CKD patients mainly in patients on dialysis. Thus, early diagnosis and treatment of LTBI in CKD patients should be performed to prevent active TB in CKD patients.PROSPERO registration number: CRD42022372441. It is the second leading cause of mortality among infectious diseases next to COVID-19 . HoweverMycobacterium tuberculosis [Early detection and treatment of latent tuberculosis infection (LTBI) among groups of people with weakened immune systems, such as CKD patients, is critical for preventing the development of active TB. In addition, dialysis patients frequently travel to health facilities for medical care, which may increase the risk of infection with rculosis . When corculosis . The WHOrculosis . There hrculosis . The prerculosis ,25 to 82rculosis . The sysrculosis . However22.1The protocol for this systematic review and meta-analysis study is registered on the International Prospective Register of Systematic Reviews (PROSPERO) with a registration number CRD42022372441.2.2This systematic review and meta-analysis study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines . Two ind2.3Participants: Patients with chronic kidney disease.Intervention: Not applicable.Comparator: Not applicable.Outcome: Latent TB infection.Study design: Observational studies.Study setting: Any setting in any country across the globe.2.4Studies that assessed prevalence of LTBI among different categories of CKD patients were included in the study. Review studies, incomplete studies and articles with different outcomes were excluded.2.5.We extracted data from all studies included in the current systematic review and meta-analysis using the 2016 Microsoft Excel Spreadsheet. Two investigators extracted data independently, and the inconsistencies were resolved through discussion and consensus was reached with the guidance of the third author (AA). The extracted data included; first author name, publication year, country, data collection period, study design, age group, type of CKD patients included, laboratory screening method, sample size, and number of patients who had LTBI. In addition to the above variables, the studies were categorized based on continent, WHO regional classification, and country TB burden category .Table 1C2.6The primary outcome of this study was detection of LTBI among CKD patients with any category including pre-dialysis, hemodialysis, peritoneal dialysis, and renal transplant. The included studies used different laboratory screening methods alone or in combination for screening of LTBI in CDK patients; Tuberculin Skin Test (TST), QFT (QuantiFERON\u00ae-TB Gold), T-SPOT, and ELISPOT (enzyme-linked immunospot). The TST result was considered positive when the cut-off induration was \u226510\u00a0mm. From studies that employed a two-step TST, only the baseline results were taken to avoid a boosting phenomenon.2.7Two independent investigators assessed the quality and validity of individual studies included in this study using the Joanna Brigg's Institute critical appraisal tool . The inc2.82 heterogeneity test where I2 >50% was considered as the presence of substantial heterogeneity [The data that were summarized in the 2016 Microsoft Excel Spreadsheet were exported to STATA version 17 for statistical analysis. The pooled prevalence of LTBI among CKD patients was estimated along with 95%CI. Sub-group analysis was performed based on CKD categories, LTBI laboratory screening methods, WHO regional classification, continent, country's income level, publication year, and TB burden category. We have presented the pooled estimates using forest plot. The presence of heterogeneity among studies was assessed using Iogeneity ,32. We hogeneity ,34. A trogeneity .33.1From the whole search, 5316 studies were identified and 854 duplicates were removed. Title and abstract screening was conducted for the 4462 studies and 4388 were excluded. Then, the remaining 74 studies were assessed for full text and 59 studies were included in the final analysis. While the remaining 15 studies were excluded due to different reasons (AppendiThe studies were conducted in 18 countries from four continents. The highest number of studies were from Asia (39 studies) followed by North America (8 studies), South America (6 studies), and Europe (5 studies). The least number of study was from Africa with only one study conducted in Egypt. Based on the WHO regional classifications, the highest number of studies were from the West Pacific Region (WPR) with 16 studies followed by the European Region (EUR) (15 studies), the Region of Americans (AMR) (14 studies), Eastern Mediterranean Region (EMR) (9 studies), and South East Asian Region (SEAR) (5 studies). No study was reported from the WHO African Region (AFR). Specifically, the most frequent studies were from Turkeye (10 studies) followed by Taiwan (9 studies), South Korea (5 studies), Canada (5 studies), and Brazil (5 studies). The other studies were reported from Saudi Arabia, United States, India, Iran, Indonesia, Japan, Switzerland, Belgium, Egypt, Germany, Iraq, Mexico, and United Kingdom. Based on the World Bank income classification, 6, 20, and 27 studies were reported from lower middle income, upper middle income and high income countries, respectively..Based on publication year, 22, 17, and 20 studies were published from 1998 to 2010, from 2011 to 2015 and from 2016 to 2022. Based on the 2021 global TB report, 10 studies were reported from high TB burden countries while the remaining 49 studies were reported from countries that were not included in the high TB burden country list. The majority of the studies (43 studies) were conducted using a cross-sectional study design ..Different laboratory diagnostic methods such as TST and IGRA were used to detect LTBI in CKD patients. The IGRA method was used in 36 studies where QFT, T-SPOT, and ELISPOT were used in 29, 11 and 1 studies, respectively. However, the type of IGRA methods were not specified in three studies. Tuberculin skin test was used in 47 studies. These diagnostic methods were used alone or in different combinations .3.22; 97.82%) . There w 97.82%) and Egge 97.82%) Table 22; 97.82%2; 82.78%) followed by Asia , South America , and North America . Since there is only one study from Africa conducted in Egypt with a prevalence of 38% , we were unable to estimate the pooled prevalence. Per the WHO regional classification, the highest pooled estimate was found in EUR followed by EMR , SEAR , WPR , and AMR , 34% , and 24% , respectively. Besides, we performed a sub-group analysis considering classification of countries with TB burden category. Thus, the pooled prevalence of LTBI among CKD patients residing in high TB burden countries was 25% , while the pooled LTBI prevalence among CKD patients residing in the countries not included in the list of high TB burden countries was 31% . Furthermore, we have conducted a sub-group analysis based on the World Bank Group classification of countries by their income level. Accordingly, the pooled prevalence of LTBI was 24% , 33% , and 37% in CKD patients living in high income, lower middle income and upper middle income countries, respectively (Appendix).Per continent, the highest pooled prevalence of LTBI among CKD patients was found in Europe . In addiectively ((Appendix). However, there is no change in the pooled prevalence after the trim and fill analysis. The QFT test was used in 29 studies where the largest and the smallest LTBI prevalence among CKD patients detected by QFT were 54% [2; 90.83%) ((Appendix). After the trim and fill analysis, the pooled estimate became 25.4% . The other laboratory method used to detect LTBI in CKD patients was T-SPOT that is used by 13 studies. Based on this method, the smallest and the highest LTBI prevalence was found to be 4% [2; 97.53%) ((Appendix). Since there is only one study that used ELISPOT, it was difficult to estimate the pooled prevalence .We have performed a sub-group analysis, using the laboratory diagnostic method used to detect LTBI in CKD patients. Accordingly, TST, QFT, T-SPOT, ELISPOT, and unspecified IGRA were used. Tuberculin skin test was used by 47 studies, where the highest prevalence was 82% and the 97.71%) . The Eggwere 54% , and 6% were 54% , respect 90.83%) . The preto be 4% , respect 97.53%) . Based oevalence .Fig. 4Fo3.42; 90.61%) . In hemo 96.87%) . The Egg 83.48%) . The las 94.26%) Table 22; 90.61%.We conducted a meta-regression analysis to assess the effect of sample size and publication year on the heterogeneity among studies. The multivariate meta-regression model revealed that sample size (P\u00a0=\u00a00.064) and publication year (0.553) did not significantly predicted heterogeneity among studies. However, this model only explains 4.58% of the heterogeneity .Table 3M4In this study, we estimated the pooled prevalence of latent tuberculosis among patients with chronic kidney disease based on data collected from 53 studies that included 12,772 CKD patients. The study findings indicated that nearly one-third of CKD patients had LTBI with regional disparities. In addition, we conducted a sub-group analysis to estimate the pooled prevalence of LTBI based on the type of CKD, the laboratory diagnostic methods, continent, WHO regional classification, country's income level, publication year, and TB burden classification.This study revealed that, 30% of CKD patients had LTBI, which is higher compared to the prevalence in the general population, where one-fourth of the global population is infected with TB . In addiWe also conducted a sub-group analysis based on publication year, and the study findings revealed that the pooled estimate is lower in studies published after 2016 (24%) compared to studies published between 1998 and 2010 (34%), and between 2011 and 2015 (34%). A global study similarlMycobacterium tuberculosis through person-to-person transmission since they travel frequently and spend lengthy periods in health facilities.The current study found that dialysis patients in general and hemodialysis patients in particular, had higher LTBI prevalence as compared to pre-dialysis and post-renal transplanted patients. Dialysis patients, particularly those on hemodialysis, are at increased risk of contracting Besides, we have performed a sub-group analysis based on the laboratory diagnostic method used to diagnose LTBI in CKD patients. We found a relatively a higher pooled estimate in CKD patients diagnosed with IGRAs compared with TST. One possible reason might be the use of 10\u00a0mm cut-off in the TST. Likewise, this was reported by a previous global pooled estimate conducted in the general population .In general, CKD patients suffer from multitude complications ranging from anemia, psychiatric diseases, cardiovascular complications, endocrine and metabolic abnormalities that needs to be given a focus to decrease high morbidity, mortality and poor quality of life .Finally, the findings of this study should be interpreted by considering the following limitations. Primarily, under representation of CDKs from Africa in this review may have affected the global prevalence of LTBI in CDK patients. Second, the high heterogeneity among studies and the presence of publication bias may affect the true estimates. Lastly, since most of the original studies did not use specific cutoffs based on age and immunosuppression status of CKD patients, we did not perform analysis based on the specific cutoffs. However, we have performed stratified analysis that validated the current study findings.5This study identified higher prevalence of LTBI among CKD patients that needs attention of all concerned bodies to early detect and treat LTBI in this group of individual. There is disparities in the prevalence of LTBI per WHO regional classification, where CKD patients residing in the EUR, EMR and SEAR had relatively higher LTBI prevalence. In addition, dialysis patients mainly hemodialysis patients had higher LTBI prevalence compared to pre-dialysis and post-renal transplanted CKD patients. Besides, the prevalence of LTBI is higher in patients diagnosed with IGRA compared with those CKD patients diagnosed with TST. The findings in this study indicate the need to give attention for the early diagnosis and treatment of LTBI in CKD patients. We recommended more studies from the African Region where TB is endemic and the prevalence of CKD is increasing.Ayinalem Alemu: Conceived and designed the experiments; Performed the experiments; Analyzed and interpreted the data; Wrote the paper.Zebenay Workneh Bitew: Performed the experiments; Analyzed and interpreted the data; Contributed reagents, materials, analysis tools or data.Getu Diriba; Getachew Seid; Emebet Gashu: Performed the experiments.Shewki Moga; Saro Abdella; Kirubel Eshetu; Getachew Tollera; Mesay Hailu Dangisso; Balako Gumi: Analyzed and interpreted the data; Wrote the paper.Data included in article/supp. material/referenced in article.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "The rising economic burden of cancer on patients is an important determinant of access to treatment initiation and adherence in India. Several publicly financed health insurance (PFHI) schemes have been launched in India, with treatment for cancer as an explicit inclusion in the health benefit packages (HBPs). Although, financial toxicity is widely acknowledged to be a potential consequence of costly cancer treatment, little is known about its prevalence and determinants among the Indian population. There is a need to determine the optimal strategy for clinicians and cancer care centers to address the issue of high costs of care in order to minimize the financial toxicity, promote access to high value care and reduce health disparities.A total of 12,148 cancer patients were recruited at seven purposively selected cancer centres in India, to assess the out-of-pocket expenditure (OOPE) and financial toxicity among cancer patients. Mean OOPE incurred for outpatient treatment and hospitalization, was estimated by cancer site, stage, type of treatment and socio-demographic characteristics. Economic impact of cancer care on household financial risk protection was assessed using standard indicators of catastrophic health expenditures (CHE) and impoverishment, along with the determinants using logistic regression.p <\u20090.001). The extent of CHE and impoverishment due to direct costs incurred on outpatient treatment increased from 83% to 99.7% and, 63.9% to 97.1% after considering both direct and indirect costs borne by the patient and caregivers, respectively. In case of hospitalization, the extent of CHE increased from 23.6% (direct cost) to 59.4% (direct+ indirect costs) and impoverishment increased from 14.1% (direct cost) to 27% due to both direct and indirect cost of cancer treatment.Mean direct OOPE per outpatient consultation and per episode of hospitalization was estimated as \u20b98,053 (US$ 101) and \u20b939,085 (US$ 492) respectively. Per patient annual direct OOPE incurred on cancer treatment was estimated as \u20b9331,177 . Diagnostics (36.4%) and medicines (45%) are major contributors of OOPE for outpatient treatment and hospitalization, respectively. The overall prevalence of CHE and impoverishment was higher among patients seeking outpatient treatment than hospitalization . The odds of incurring CHE was 7.4 times higher among poorer patients [Adjusted Odds Ratio (AOR): 7.414] than richest. Enrolment in PM-JAY or a state sponsored scheme (CHE AOR\u2009=\u20090.304 and impoverishment AOR\u2009=\u20090.371) resulted in a significant reduction in CHE and impoverishment for an episode of hospitalization. The prevalence of CHE and impoverishment was significantly higher with hospitalization in private hospitals and longer duration of hospital stay (There is high economic burden on patients and their families due to cancer treatment. The increase in population and cancer services coverage of PFHI schemes, creating prepayment mechanisms like E-RUPI for outpatient diagnostic and staging services, and strengthening public hospitals can potentially reduce the financial burden among cancer patients in India. The disaggregated OOPE estimates could be useful input for future health technology analyses to determine cost-effective treatment strategies. Cancer accounted for nearly 10 million deaths in the year 2020, or nearly one in six deaths . The GLOThe rising prevalence of cancer further increases the stress on already burdened healthcare system, and also imposes physical, psychosocial, and financial strain on the patients and their families . The cosIn view of this, it is important to reduce socioeconomic inequalities in access to cancer care by increasing the provision of quality, affordable, and accessible healthcare services . In 2018Several studies have attempted to estimate the economic burden of cancer in the past . HoweverCertain inconsistencies were also observed in the range of medical services for which OOPE was recorded , type of cost included , cancer categories , and type of healthcare setting . Although the 75th round of National Sample Survey on Social Consumption on Health in India reports the economic burden of different ailment categories including cancer, the sample barely includes 1,751 cancer patients . This saN =\u200912,148) drawn from different regions of India. We report estimates on direct out-of-pocket expenditure incurred on outpatient and hospitalized treatment at overall level, and by site, stage, response, and type of treatment. In a subsample of 3,251 patients, we have also assessed indirect costs borne by the patient due to outpatient treatment and hospitalization. We also measured financial toxicity in terms of extent of CHE and impoverishment among patients seeking cancer care in India using the standardised methodology, as well as assessed the determinants of financial toxicity due to only direct costs and total societal costs (direct plus indirect costs).We undertook the present study to provide comprehensive evidence on the economic burden of cancer by collecting primary data on direct out-of-pocket expenditure (OOPE) from a large representative sample of cancer patients using the ratio of disability adjusted life years (DALYs) lost as a result of communicable, maternal, neonatal and nutritional diseases, to the DALYs lost due to non-communicable diseases (including cancer and injuries) . Among hAt the second stage, seven health-care facilities that catered to largest volume of oncology patients in these sites were purposively selected. Two of these cancer centres contribute to the highest volume of patients treated under India\u2019s largest national insurance programme, AB PM-JAY. At the third stage, the total desired sample of patients to be recruited at each facility was achieved using systematic random sampling technique .The patients were recruited prospectively between October 2020 to March 2022 at outpatient and inpatient departments of the selected health care facilities. For facilities with common clinics for all types of cancer, systematic random sampling was used to recruit patients with a sampling interval based on mean daily number of patients. For centres with cancer clinics representing different disease management groups (DMGs), PPS method was used to determine the sample size of patients to be recruited at each DMG.Considering the mean OOPE of \u20b9 57,232 with standard deviation of \u20b9 86,871 at 95% CI and 5% margin of error, a sample size of 1,536 was estimated for each of the seven healthcare facilities . Taking Patients of all age groups and gender with an established cancer diagnosis who sought outpatient and hospitalized treatment at selected health care facilities for any cancer type or stage were eligible to be included in the study. Case definitions used for recruiting patients are described in A written informed consent was obtained and data on OOPE were collected from all study participants above 18\u2009years of age and from parents/guardians/proxy respondents for minors. A pretested structured interview schedule was used to collect information on socio-demographic characteristics, household consumption expenditure, clinical data, and OOPE .Newly diagnosed and on-treatment patients who sought outpatient care within last 30\u2009days were recruited and interviewed on the same day for recording direct medical and non-medical OOPE incurred since last visit. However, for cases who sought care more than 30\u2009days ago, telephonic interviews were conducted on the 15th day following recruitment to elicit the data. For ensuring high response rate on telephonic interviews, a minimum of 2\u20133 contact numbers were recorded . DetailsIn a subsample of 3,251 patients drawn from five states data of India using systematic random sampling technique, we have also assessed the indirect costs due to loss of productivity in addition to direct costs incurred on cancer treatment. We have used the human capital approach for estimation of indirect costs . The morper capita consumption expenditure. Total household consumption expenditure was divided by equivalent household size to compute per capita consumption expenditure.We have considered average time duration of work as 8\u2009h based on International Labor Organization 2017 report . The tot\u03b2 has been estimated from previous studies based on 59 countries\u2019 household survey data which is equal to 0.56 (where to 0.56 . For carThe mean OOPE and standard error (SE) were computed for both per episode of hospitalization and outpatient treatment. In addition, total annual OOPE per patient was also estimated by using the following equation:where h) is the minimum requirement to maintain basic life in a society. We have used a food share based poverty line for estimating household subsistence. This poverty line is defined as the mean food expenditure of the household whose food expenditure share of total household expenditure (Exph) is within 45th to 55th percentile of the total sample but lower than subsistence spending net of out of pocket health payments (SEh >\u2009Exph-OOPEh) . DetailsThis was followed by logistic regression model for estimation of parameters. The logistic regression is used to analyse the association between the catastrophic and impoverishment while controlling for potential confounders. Logistic regression is actually an extension of linear regression rather than modelling a linear relationship between the independent variables (Xi) and the probability of the outcome. The logistic regression equation is assumed to bewhere, t is the log-odds, X_i is the value of the ith predictor, \u03b2_i represent parameters of model, i\u2009=\u20091, 2, \u2026k.Independent variables comprised of socio-demographic variables including age, gender, area of residence, level of education, income status, type of financial benefit scheme and, clinical characteristics namely type of cancer, type of treatment, cancer stage, type of response, line of treatment and adverse effects.where exp. represents consumption expenditure, SE is subsistence expenditure, OOP is out of pocket expenditure and CTP represents household capacity to pay. In addition, bivariate analysis was done to assess the associations between OOPE and socio-demographic as well as clinical characteristics . The facThe study complies with the Declaration of Helsinki and an ethical approval to undertake the study was obtained from Institute Ethics Committee of the Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh with reference number IEC-03/20202-1565. Informed written consent was obtained from all the study participants.A total of 9,897 patients were recruited in the outpatient setting. Out of these, 2,736 patients reported at least one episode of hospitalization during last 1 year. In addition, a total of 2,361 patients were recruited while being hospitalized in study centres. The expenditures incurred on all episodes of hospitalization during 1 year time period was used to compute indicators of financial risk protection.Majority of the patients seeking cancer treatment, were in the age group of 45\u201360\u2009years , belonged to rural area and were females . Approximately 60% of the patients seeking outpatient treatment and 62.8% hospitalised patients were found to be covered under some health insurance schemes. Nearly, 10.3% outpatient cases and 13.3% hospitalized cases were enrolled under AB PM-JAY; 33% were covered under state-sponsored health insurance schemes . The sociodemographic profile of cancer patients is summarised in Per visit mean OOPE on outpatient cancer treatment was computed as \u20b9 8,053 . Taking into account the average number of visits per month for outpatient treatment as 2.76 , mean monthly direct OOPE incurred on outpatient treatment was estimated as \u20b9 22,227 . The estimated OOPE per episode of hospitalization was \u20b9 39,085 . The total annual direct OOPE on cancer treatment was estimated as \u20b9 331,177 . The diaThe overall prevalence of CHE was found to be 80.4% due to outpatient treatment and 29.8% as a result of cancer-related hospitalization. The overall prevalence of impoverishment was 67% due to outpatient cancer treatment and 17.2% due to hospitalization.p <\u20090.001). Similarly, CHE was significantly higher for those admitted in private hospitals (36.7%), compared to public hospitals (18.6%). The prevalence of CHE among different subgroups of cancer patients seeking outpatient and hospitalized treatment has been summarized in For both outpatient treatment and hospitalisation, the prevalence of CHE showed a declining trend from poorest to the richest income quintiles as shown in ospitals 6.7%, comp value <0.001] as compared to chemotherapy. The odds of CHE were significantly higher for stage IV cancer [AOR: 1.806 (95%CI: 1.235\u20132.639)] as compared to stage I. Patients with ongoing response to treatment had a 46.2% higher likelihood of experiencing CHE than those in the progression-free survival stage. Variables such as age, gender, level of education, marital status, type of cancer, cancer stage, type of treatment (except hormone therapy), line of treatment, and adverse effects of treatment did not significantly impact the odds of experiencing CHE due to outpatient cancer treatment (The odds of incurring CHE were 10.9 times higher among poorest patients [AOR: 10.959 (95% CI: 7.636\u201315.728)] as compared to richest patients. Lower odds of CHE were observed among patients supported by philanthropist/charitable trusts [AOR: 0.258 (95%CI: 0.17\u20130.391)] and enrolled under state sponsored schemes [AOR: 0.5 (95%CI: 0.393\u20130.635)] and AB-PMJAY [AOR: 0.631 (95%CI: 0.429\u20130.93)]. There was lesser odds of incurring CHE among patients on hormone therapy as compared to richest income groups. The odds of incurring CHE were lower among patients covered under publically financed health insurance schemes namely AB PM-JAY [AOR: 0.426 (95%CI: 0.33\u20130.548)], state government sponsored schemes [AOR: 0.304 (95%CI: 0.253\u20130.365)], social insurance scheme [AOR: 0.69 (95%CI: 0.534\u20130.892)], and those supported by philanthropists/NGOs/trusts [AOR: 0.157 (95%CI: 0.113\u20130.217)] respectively. However, the odds of CHE were found to be approximately 15.7% higher for patients enrolled under private health insurance . Hospitalization in private facilities [AOR: 2.188 (95%CI: 1.816\u20132.636)] and a longer duration of hospital stay [AOR: 1.037 (95%CI: 1.031\u20131.044)] were significantly associated with higher odds of CHE , s of CHE .The prevalence of impoverishment declined with increase in the level of income, from poorest to richest income groups for both hospitalisation (51% among poor versus 6% among rich) and outpatient treatment (86.9% among poor versus 44.6% among rich). Higher impoverishment rates were found among patients who sought hospitalization in private facilities (25.9%). Lowest impoverishment rates (8.1%) were observed among hospitalized patients enrolled under AB PM-JAY . The prep <\u20090.05). The odds of impoverishment were lower among patients who received hormone therapy [AOR: 0.412 (95%CI: 0.239\u20130.709)] as compared to those on chemotherapy. Variables such as age, gender, marital status, level of education, type of cancer, stage of cancer, type of treatment (other than hormone therapy), line of treatment, and adverse effects of treatment had no significant effect on the odds of impoverishment (The risk of incurring impoverished expenditures for outpatient treatment was 46.7 times higher among poorest income groups [AOR: 46.78 (95%CI: 21.101\u2013103.71)] as compared to richest income groups. As compared to patients with no health insurance coverage, the likelihood of impoverishment was 40.3%, 49.7%, 60% and 56.6% lower among those covered under AB PM-JAY, state government sponsored, social insurance scheme, and patient support groups (philanthropists/NGOs) respectively (rishment .p =\u20090.892) higher for patients having private health insurance. The patients hospitalised in private health facilities were nearly 3 times more likely to experience impoverishment than those admitted in public hospitals. Similarly, likelihood of impoverishment was found to increase with every one unit increase in duration of hospital stay ] as compared to the richest income groups. The odds of impoverishment for patients covered under health insurance schemes were lower among patients covered under AB PM-JAY [AOR: 0.395 (95%CI: 0.277\u20130.565)], state government sponsored schemes[AOR: 0.371 (95%CI: 0.29\u20130.474)], social insurance scheme [AOR: 0.676 (95%CI: 0.481\u20130.95)], and those supported by philanthropists/NGOs/trusts [AOR: 0.129 (95%CI: 0.074\u20130.226)] respectively. However, the odds of impoverishment were found to be approximately 2.4% .The total estimated indirect cost borne by a patient and caregiver per month due to outpatient treatment was INR 46,868 . Indirect cost borne by a patient and a caregiver per episode of hospitalization was computed as INR 25,173 .The extent of CHE and impoverishment due to outpatient treatment increased from 83% (direct costs) to 99.7% (direct+ indirect costs) and, 63.9% (direct costs) to 97.1% after considering both direct and indirect costs borne by the patient and caregivers, respectively. In case of hospitalization, the extent of CHE increased from 23.6% (direct cost) to 59.4% (direct+ indirect costs) and impoverishment increased from 14.1% (direct cost) to 27% on considering both direct and indirect cost of cancer treatment.p <\u20090.001), as compared to those who were not covered by any health insurance (34.4%). Similarly, lower impoverishment rates (8.1%) were observed among hospitalized patients enrolled under AB PM-JAY.The prevalence of CHE due to hospitalization was lower among those covered under AB PM-JAY (16.1%) which was statistically significant ], state government sponsored schemes [AOR: 0.304 (95%CI: 0.253\u20130.365)], social insurance scheme [AOR: 0.69 (95%CI: 0.534\u20130.892)], and those supported by philanthropists/NGOs/trusts [AOR: 0.157 (95%CI: 0.113\u20130.217)] respectively. However, the odds of CHE were found to be approximately 15.7% higher for patients enrolled under private health insurance , state government sponsored schemes[AOR: 0.371 (95%CI: 0.29\u20130.474)], social insurance scheme [AOR: 0.676 (95%CI: 0.481\u20130.95)], and those supported by philanthropists/NGOs/trusts [AOR: 0.129 (95%CI: 0.074\u20130.226)] respectively. However, the odds of impoverishment were found to be approximately 2.4% , as compared to patients with no health insurance coverage.In case of outpatient treatment, lower odds of CHE were observed among patients supported by philanthropist/charitable trusts [AOR: 0.258 (95%CI: 0.17\u20130.391)] and enrolled under state sponsored schemes [AOR: 0.5 (95%CI: 0.393\u20130.635)] and AB-PMJAY [AOR: 0.631 (95%CI: 0.429\u20130.93)] as compared to those who were not covered under any financial benefit scheme. The likelihood of impoverishment due to outpatient treatment was 40.3%, 49.7%, 60% and 56.6% lower among those covered under AB PM-JAY, state government sponsored, social insurance scheme, and patient support groups (philanthropists/NGOs) respectively . Digital technological solutions may have an important role to play here. The Government of India recently launched a digital voucher to provide social assistance on subsidy. This digital voucher-E-RUPI , can be Globally, several studies have attempted to estimate the economic burden of cancer. However, a recent systematic review from India found only 22 studies reporting financial hardship among cancer patients , 43, 44.The review also reported that the proportion of cancer patients facing CHE ranged from 34% to 84% , 19, 21.Moreover, given the kind of informal economy that prevails in India, there is under reporting of income. Hence, the true impact of economic burden cannot be assessed without reliable income data. In addition to this, poverty line is also arbitrarily defined and there are a lot of ongoing debates on defining the poverty line. Literature on deprivation and economic hardship is also now pointing towards multidimensional criteria for defining poverty rather than a single cut-off value. Further, there are practical difficulties in collecting a reliable income data which is widely acknowledged , 50. HenThe determinants of CHE observed in our study are in line with those reported in previous studies , 19, 21.Furthermore, patients without any health insurance had higher odds of experiencing CHE as compared to those covered under some health insurance scheme . A systep <\u20090.01, highly statistically significant) in the year 2018, in contrast to inpatient cases wherein it got decreased by 7.5% (p <\u20090.01) .Secondly, majority of the publicly financed health insurance schemes include only inpatient care in its health benefits package, leaving outpatient care out of the ambit. Thirdly, even for the inpatient care which is covered, the financial protection starts to tick in once the diagnosis is established, which implies that the initial diagnostics and staging in case of probable cancer cases is paid out-of-pocket by the patients. Our study findings also suggests that diagnostics account for 36.4% of total OOPE incurred on non-hospitalized cancer treatment followed by medicines having a share of 27.8%.The study findings provide important policy implications. Firstly, the health benefits package of Ayushman Bharat PM-JAY should prioritise the expansion of cancer packages, by including the cost-effective treatments which may be delivered in outpatient care. Secondly, the digital payment systems should be used to finance the cost of diagnostic services availed for staging of cancer patients before the treatment begins.We would like to mention several methodological strengths of our study. Firstly, this is the first study to have estimated OOPE, catastrophic health expenditure and impoverishment due to both outpatient and hospitalized cancer treatment on such a large sample of 12,148 cancer patients. Secondly, the data were collected from patients recruited at seven health care facilities across six states of the country. Two of the selected hospitals in our sample, are among the top 10 hospitals in terms of cancer treatment claims as part of the largest insurance scheme in India-AB PM-JAY . ThirdlyFurthermore, our study is the first study which estimates the extent of OOP expenditure in the post-PMJAY, and measuring the impact of the PM-JAY on reducing financial hardship. In a way, our study is the first of its kind which shows a positive effect of a government funded health insurance scheme on the OOP expenditure and catastrophic spending for healthcare in India.Our study also has certain limitations. Firstly, the OOPE estimates for outpatient treatment are applicable to public and semi-private hospitals in India. Although, three out of seven selected health care facilities cater services to four categories of patients . Therefore, inpatients charges for private category represents private sector. Secondly, some part of the data collection occurred during the Covid-19 pandemic, which could have negatively impacted the non-food consumption expenditure among cancer patients and their families due to loss of earnings, further increasing the financial risk due to cancer treatment.There is high economic burden on patients and their families for cancer treatment. Our findings emphasize the need for urgent strategies to mitigate financial toxicity among cancer patients in India, especially in the most deprived sections of society. There is also a need to have a broader consultation group including multiple stakeholders such as healthcare providers, government agencies, insurance companies, and patient advocacy groups so as to make comprehensive strategies to address the issue of financial toxicity in cancer patients in India. The increase in coverage of PFHI schemes, rationalization of HBP\u2019s, strengthening public health care facilities, creating prepayment mechanism like E-RUPI in the form of social insurance can potentially reduce the financial distress among cancer patients in India . The disFuture research should aim at undertaking a more longitudinal follow-up study to determine the non-health consequences of cancer. This should include the social consequences of health care expenditures on cancer, such as leading to drop out of children from school, lack of ability to carry out other social responsibilities, need to curtail other important spending etc. In addition, such a study could also lead to intergenerational impact of cancer expenditures. Secondly, the future research should also more rigorously examine the effectiveness of different measures of reducing the OOP spending on cancer. Thirdly, a more detailed examination of the distributional impact of OOP expenditures for cancer, as well as strategies to improve the access for the most needy and vulnerable needs to be undertaken. This is also in line with the global call for the cancer day .The original contributions presented in the study are included in the article/The study was reviewed and approved by the Institutional Ethics Committee of Post Graduate Institute of Medical Education and Research, India with reference number IEC-03/20202-1565 as it involved human participants. A written informed consent was obtained from all study participants.SP: conceptualization, funding acquisition, resources, and supervision. SP, JD, and AD: data curation and writing \u2013 original draft. SP, JD, and AG: formal analysis. SP and JD: investigation, methodology, project administration, and software. SP, JD, NG, AD, AK, PR, NM, LK, AS, PM, AG, KR, MK, and SG: validation, visualization, and writing \u2013 review and editing. All authors contributed to the article and approved the submitted version.The study was funded by the Department of Health Research, Ministry of Health and Family Welfare, Government of India vide grant number F.No.T.11011/02/2017-HR/3100291. However, the funder did not play a role in the design of the study; the collection, analysis, and interpretation of the data; the writing of the manuscript; and the decision to submit the manuscript for publication. We did not receive any funds for paying open access publication fees from our institutions, library or any other source.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.https://www.frontiersin.org/articles/10.3389/fpubh.2023.1065737/full#supplementary-materialThe Supplementary material for this article can be found online at: Click here for additional data file."} +{"text": "Whole genome sequencing (WGS) of bacterial pathogens directly from clinical samples or cultured isolates is a promising technique for diagnosing infections, yet challenges remain in using WGS to guide antimicrobial therapy. The standard approach predicts antimicrobial susceptibility test (AST) profiles using the presence/absence of known resistance markers. Here we measure the performance of resistance markers compared to a machine learning method for predicting AST.gAST, a machine learning method we developed that predicts AST from WGS data using the entirety of the bacterial genome without limiting to known resistance markers. Performance was assessed on >36,000 bacterial strains from MicrohmDB\u00ae, a large-scale database containing WGS data and phenotypic AST results for tens of thousands of clinical bacterial isolates.We assessed ResFinder, a publicly available bioinformatics tool that detects a curated set of resistance genes and point mutations, to test the utility of resistance marker presence or absence for predicting resistance/susceptibility on 107 species/drug combinations relevant for bloodstream infections. We also tested the performance of Keynome gAST had a median balanced accuracy of 92% , and was superior to ResFinder in 69% and equivalent to ResFinder in 28% of species/drug combinations.ResFinder performance varied widely across species/drug combinations, with a median balanced accuracy of 80% . ResFinder detected a resistance marker in only 72.3% of resistant and 50.3% of intermediate sample-drug combinations, indicating that many phenotypically nonsusceptible organisms may be mischaracterized by relying on resistance marker presence. Conversely resistance markers were present in 14.2% of susceptible sample-drug combinations. In contrast, across the same species/drug combinations Keynome Resistance marker presence/absence is often discordant with antimicrobial resistance phenotypePanels A, B, and C show the proportion of samples with or without relevant resistance markers in resistant (R), intermediate (I), and susceptible (S) samples respectively. Resistance markers relevant to each drug were detected using ResFinder. We evaluated species/drug combinations relevant to bloodstream infections. Overall, ResFinder detected a resistance marker in 72.3% of resistant, 50.3% of intermediate, and 14.2% of susceptible sample-drug combinations.Comparison of balanced accuracy between Keynome gAST and ResFinderBoxplots compare balanced accuracy across bloodstream relevant species/drug combinations between Keynome gAST and ResFinder. Each box covers the 1st through 3rd quartile, and the horizontal line within the box represents the median. ResFinder performance varied widely across species/drug combinations, with a median balanced accuracy of 80% . Keynome gAST had a median balanced accuracy of 92% , and was superior to ResFinder in 69% and equivalent to ResFinder in 28% of species/drug combinations.The lack of robust correlation between resistance markers and true phenotype highlights the limitations of predicting resistance/susceptibility based on the use of curated resistance markers. A more flexible machine learning approach that accesses the entire bacterial genome allows for complex combinations of genomic regions to inform AST prediction.Arolyn Conwill, PhD, Day Zero Diagnostics: salary|Day Zero Diagnostics: Ownership Interest Mohamad Sater, PhD, Day Zero Diagnostics: Employee|Day Zero Diagnostics: Stocks/Bonds Nicholas Worley, PhD, Day Zero Diagnostics: Salary|Day Zero Diagnostics: Ownership Interest Jason Wittenbach, PhD, Day Zero Diagnostics: Salary|Day Zero Diagnostics: Ownership Interest Miriam H. Huntley, PhD, Day Zero Diagnostics: Salary|Day Zero Diagnostics: Ownership Interest"} +{"text": "BackgroundThe effect of geriatric events (GEs) on outcomes of acute coronary syndrome (ACS) admissions is poorly understood.\u00a0We evaluated the prevalence and impact of GEs on clinical outcomes and resource utilization of older patients admitted with ACS.MethodsUsing the 2018 National (Nationwide) Inpatient Sample, we analyzed all elective hospitalizations for\u00a0ACS in older adults (age \u2265 65 years) and a younger reference group (age 55-64). Nationally-weighted descriptive statistics were generated for GEs based on ACS subtypes. Multivariate logistic regression models controlling for comorbidities, frailty, patient procedure, and hospital-level variables were used to estimate the association of age with GEs and GEs with outcomes.ResultsOut of 403,760 admissions analyzed, 71.9% occurred in older adults (\u226565 years). The overall rate of any GE in older adults with ACS was 3.4%. With advancing age, the number of GEs was found to significantly increase (p<0.001). After adjustments, having any GE was found to have a significant impact on mortality (adjusted OR (AOR): 1.32; 95%CI: 1.15-1.54; p < 0.001), post-myocardial infarction (MI) complications , prolonged hospital stays , and non-home (acute care and skilled nursing home) discharge . The occurrence of GEs was also associated with a substantial increase in total hospitalization costs with a mean increase of $48,325.22 \u00b1 $5,539 (p < 0.001). A dose-response relationship was established between GEs and all outcomes. Limitations of the study included the use of retrospective data and an administrative database.ConclusionGeriatric events were found to significantly worsen outcomes for older adults with ACS. There is, therefore, a need for increased awareness and effective management of GEs in older adults to improve their health outcomes and reduce the burden on the healthcare system. The aging population \u2265 65 years) in the United States is projected to increase by 50% by 2050 . With ag years inApproximately 60% of hospital admissions for acute coronary syndrome (ACS) are for individuals over 65 years of age, and about 85% of ACS-related deaths occur in this population [Data sourceThe 2018 National (Nationwide) Inpatient Sample (NIS) was queried for all elective hospitalizations related to ACS. For comparison, the study population included elderly persons (65 years) and a younger age group (55-64 years). Although the descriptive analysis focused on older people, a younger reference group was included to investigate the relationship between age and GEs.Outcome variablesPatient variables included age category , race or ethnicity, sex, median income in the patient\u2019s Zone Improvement Plan (ZIP) code, and the Charlson comorbidity index (CCI). Procedures and diagnoses variables were defined using the International Classification of Diseases, 10th revision, Clinical Modification, and Procedure Coding System (ICD-10-CM/PCS). Hospital variables included hospital bed size , location and teaching status , and the expected primary payer , and self-pay). Geriatric events were defined using a combination of the relevant ICD-10-CM/PCS codes and statistical commands. Clinical outcomes of interest included sudden cardiac death, all-cause mortality, post-myocardial infarction (MI) complications , prolonged length of stay (LOS), and non-home discharge and acute care hospitals). Prolonged LOS was defined as a diagnosis-specific LOS in the top decile.Statistical analysisStatistical analysis was performed using Stata\u00ae version 17 . The p-value was determined using two-tailed tests with a significance level of 0.05. The analyses were based on weighted samples to provide national estimates. The relationship between age and GEs and the impact of GEs on clinical outcomes and LOS were examined using multivariate logistic regression models. The models were adjusted for patient characteristics , Charlson comorbidity index, frailty , procedures, time to revascularization, and hospital factors . The research also explored the potential linear relationship between the number of GEs and clinical outcomes. The national-level descriptive statistics were generated for GEs based on age group and diagnosis. Using chi-squared statistical tests, the prevalence of GEs was compared across age groups and diagnoses. Categorical and continuous variables are reported as proportions or mean with standard deviation. Regression outcomes are reported as adjusted odds ratios (AORs) with 95% confidence intervals (CIs).Ethical considerationsThis research endeavor did not require institutional review board approval\u00a0owing to the fact that it relied exclusively on publicly accessible retrospective data procured from the NIS database. Since 2012, this database has been purged of any\u00a0patient- and hospital-level identification information.Within the total study population of individuals aged 55 years or older, the total number of hospitalizations due to ACS was 403,760, of which a nationally-weighted 71.9% occurred in older adults aged 65 or older. When considering solely admissions for older adults, the vast majority, 94.6% , were admitted with non-ST-elevation myocardial infarction (NSTEMI), while STEMI represented 3.2% , unstable angina 2% , and repeat MI 0.2% (520). A total of 0.62% of patients underwent revascularization procedures, either by means of coronary artery bypass grafting (CABG) or percutaneous coronary intervention (PCI).Analysis of the overall clinical outcomes among the older adult population revealed the following results: a mortality rate of 5.1% , post-MI complications in 10.4% , a prolonged LOS in 27.5% , and a non-home discharge rate of 25.9% . The incidence of sudden cardiac death was 1.5% while the mean time to revascularization was 1.2 \u00b1 0.1 days.The overall incidence of any GE among the entire study cohort was found to be 3.4% , and this rate was observed to increase with increasing age categories, with the highest rate of 4.8% observed among individuals aged 75 years or older . A similar trend was observed for each individual GE, with the incidence increasing with age (p < 0.001). Among older adults, a minimum of 4.2% experienced at least one GE. The majority of these patients experienced one GE (90.4%), while 4.3% experienced two GEs, and 5.3% had three or more GEs. The prevalence of GEs varied depending on the diagnosis, with the lowest incidence (0.9%) observed for unstable angina, and the highest incidence (4.2%) observed for repeat MI (p < 0.001) , post-MI complications , prolonged LOS , and non-home (acute care and skilled nursing home) discharges . The occurrence of GEs was also associated with higher total hospitalization costs . A dose-response relationship was identified between GEs and all outcomes, such that with each additional GE, the predicted probability of unfavorable outcomes increased in a linear manner Chronic health conditions: Chronic conditions commonly associated with aging, such as heart disease, diabetes, and lung disease, can increase the risk of geriatric events; (ii) Cognitive impairment:\u00a0Dementia and other forms of cognitive decline can increase the risk of events such as falls, failure to thrive, and dehydration by impairing the ability to make decisions, follow instructions, and perform daily activities , (iii) MStrategies for preventing GEs and mitigating their risk factors have been the focus of numerous research studies. Preventive home visits have been found to be effective in reducing falls among community-dwelling older adults . In the This study had some limitations. First, the NIS, as an administrative database, is susceptible to variations in local coding practices. This could result in an underestimation of the occurrence of GEs, and thus, the actual prevalence of GEs may be higher than reported in this study. Furthermore, the NIS has limitations in providing comprehensive clinical data, including the type of admission, the LOS in a skilled nursing facility, medications administered, readmission rates, and intensity of care. Lastly, the use of retrospective data may not reflect current prevalence rates and does not provide information on patient outcomes beyond the year of the claim. Despite these limitations, the findings of the index study offer crucial insight into the impact of GEs on patient outcomes and provide a compelling rationale for the implementation of more robust GE prevention initiatives in geriatric cardiology.The study found that independent of comorbidities and frailty, geriatric events are important predictors of morbidity and mortality in older patients with ACS. The findings of this study highlight the need for healthcare providers to be aware of and proactive in preventing GEs in the care of older adults with ACS to improve outcomes and reduce admission costs. Further research is needed to explore the best strategies for identifying and managing GEs in this patient population."} +{"text": "From May 2022 through the end of January 2023, approximately 30,000 cases of monkeypox (mpox) have been reported in the United States and >86,000 cases reported internationally.Monkeypox virus infections during the current outbreak have been transmitted through close, intimate contact with symptomatic persons , recipient .JYNNEOS vaccination coverage (the estimated proportion of the population recommended for vaccination that has been vaccinated) was calculated by jurisdiction.During May 22, 2022\u2013January 31, 2023, 57 jurisdictions administered a total of 1,189,651 doses of JYNNEOS vaccine, 734,510 (61.7%) of which were first doses, 452,884 (38.1%) of which were second doses, and 2,257 (0.2%) of which were reported as dose 3 or higher . The majThe distribution of administration routes differed between the first and second doses. Overall, 45.9% of first doses were administered intradermally, 50.6% were administered subcutaneously, and 3.5% were administered by other routes. Among the second doses, 85.7% were administered intradermally, 11.7% subcutaneously, and 2.6% by other routes. The change from predominantly subcutaneous to predominantly intradermal administration occurred after the week of August 20, 2022 .National first and second dose JYNNEOS coverage among persons at increased risk for mpox were estimated to be 36.7% and 22.7%, respectively. Coverage estimates varied by jurisdiction, ranging from 7.4% (West Virginia) to 94.8% (DC) for first dose coverage and 4.6% (West Virginia) to 66.2% (DC) for second dose coverage. Jurisdictions estimated to have achieved \u226550% coverage for first dose were DC (94.8%), New York City (88.8%), California (61.4%), Rhode Island (58.9%), Massachusetts (53.9%), and New York (excluding New York City) (50.1%) .The national public health response strategy for mpox has resulted in administration of >1 million JYNNEOS vaccine doses. Although approximately one in eight first dose recipients were reported to be Black, this group accounts for approximately one in three mpox casesMonkeypox virus and for areas with higher case counts, making more doses available in highly affected jurisdictions during the period of peak vaccine demand.Estimating vaccination coverage among persons at risk is useful for implementing and assessing public health action. Mpox vaccination coverage varied widely by jurisdiction. Three of the six jurisdictions estimated to have 1-dose coverage rates of \u226550% were also among the jurisdictions with the highest case counts .The findings in this report are subject to at least four limitations. First, coverage estimates include assumptions based on national data applied to subnational jurisdictions. For example, the increase by 25% of the vaccine-eligible population might not be appropriate for each jurisdiction. Consequently, coverage estimates for some jurisdictions might be biased. Second, residence information was self-reported and might be incomplete; in cases for which residence was not provided to the vaccination site, the site\u2019s location might have been used. Overall, among vaccinations reported to CDC, residence data were missing for 8%. Third, some vaccination-related data elements are not available for all jurisdictions; therefore, national estimates for some characteristics might not include all jurisdictions. For example, some jurisdictions do not report recipients\u2019 sex or race and ethnicity. Finally, information on sexual orientation and gender identity are not routinely collected during vaccine administration, and existing IIS systems do not include those variables; therefore, it is not possible to assess how vaccine recipients identify.Although the number of mpox cases has decreased sharply, much is unknown about the risk for potential reintroduction of the virus and resurgence of disease in the United States. Thus, the need to improve vaccination coverage among populations at risk, increase vaccine equity, and increase the number of persons fully vaccinated (JYNNEOS vaccine is effective in preventing monkeypox (mpox) among persons at risk.During the current multinational outbreak, U.S. 1- and 2-dose vaccination coverage reached an estimated 37% and 23%, respectively, among persons at risk, with wide variation among jurisdictions. The predominant administration route switched from subcutaneous to intradermal after the week of August 20, 2022, in accordance with Food and Drug Administration recommendations.Despite administration of >1 million vaccine doses, only 23% of the at-risk population has been fully vaccinated. Targeted outreach and continued access to and availability of mpox vaccines to persons at risk is important to help prevent and minimize the impact of a resurgence of mpox."} +{"text": "Acinetobacter baumannii infection in intensive care unit (ICU) patients in a large general hospital. Bacterial infections such as Acinetobacter baumannii contribute to significant mortality and complications of treatment in ICU patients. We aimed to describe bacterial pathogens and their resistance profile among ICU patients to inform infection prevention and control programs.Between January and April 2022, an audit of surveillance data revealed five cases of bloodstream We conducted a cross-sectional study of patients admitted to the ICU of a large general hospital in Kazakhstan from January to April 2022. The study included all patients \u2265 18 years old diagnosed with a bacterial infection as detected in blood, urine or sputum samples. Demographic, clinical, and laboratory data were abstracted from medical records.Acinetobacter baumannii 63% (n=41). Of which, 15% was detected in blood, 41% in urine, and 44% in sputum. The hospital only tests for drug-resistance for the prescribed antibiotic, and 63% (26/41) of strains tested were resistant to their prescribed medicines. Klebsiella pneumoniae was detected in 22% (n=15) patients. Of which, 60% was detected in sputum, 20% in urine and 20% in blood. Also, 60% were drug-resistant. Staphylococcus aureus was detected in 11% of patients. Of which, 57% was drug-resistant in sputum. Overall 60% (39/64) of pathogens tested had resistance for the antibiotic prescribed, but there was no evidence that prescribed antibiotics changed based on resistance results.Among 65 patients identified, 54% were male, mean age 64 years (range 20-93). Majority (35%) were admitted directly to the ICU, 15% had been transferred to the ICU from the infectious surgery department, 14% from the stroke department, and 5% from the gynecology department. Sixty-eight percent (44/65) of patients had surgery prior to transfer to the ICU. The most frequent pathogen in the study patients was Antimicrobial resitance and antibiotics prescribed to patients in an ICU of a large general hospital (n=65), Kazakhstan, 2022Map of bacterial infection in ICU patients admitted from different wards in a large general hospital, Kazakhstan, 2022The identification of infectious pathogens with demonstrated drug resistance reinforces the need for improved basic infection control practices and the need for improved antimicrobial stewardship. Increased surveillance and reporting of hospital-acquired infections is needed.All Authors: No reported disclosures"} +{"text": "Considering the high reoperation rate in degenerative lumbar spondylolisthesis (DLS) patients undergoing lumbar surgeries and controversial results on the risk factors for the reoperation, we performed a systematic review and meta-analysis to explore the reoperation rate and risk factors for the reoperation in DLS patients undergoing lumbar surgeries.Literature search was conducted from inception to October 28, 2022 in Pubmed, Embase, Cochrane Library, and Web of Science. Odds ratio (OR) was used as the effect index for the categorical data, and effect size was expressed as 95% confidence interval (CI). Heterogeneity test was performed for each outcome effect size, and subgroup analysis was performed based on study design, patients, surgery types, follow-up time, and quality of studies to explore the source of heterogeneity. Results of all outcomes were examined by sensitivity analysis. Publication bias was assessed using Begg test, and adjusted using trim-and-fill analysis.A total of 39 cohort studies (27 retrospective cohort studies and 12 prospective cohort studies) were finally included in this systematic review and meta-analysis. The overall results showed a 10% (95%CI: 8%-12%) of reoperation rate in DLS patients undergoing lumbar surgeries. In surgery types subgroup, the reoperation rate was 11% (95%CI: 9%-13%) for decompression, 10% (95%CI: 7%-12%) for fusion, and 9% (95%CI: 5%-13%) for decompression and fusion. An increased risk of reoperation was found in patients with obesity , diabetes , and smoking .We found a 10% of reoperation rate in DLS patients after lumbar surgeries. Obesity, diabetes, and smoking were risk factors for the reoperation.The online version contains supplementary material available at 10.1186/s12893-023-02082-8. Degenerative lumbar spondylolisthesis (DLS) refers to anterolisthesis of one vertebral body over another vertebral body secondary to osteoarthritic degeneration, leading to spinal canal stenosis . DLS is Surgeries have been regarded as the standard treatment modality for intractable cases . The proConsidering the controversial results, we aimed to perform a systematic review and meta-analysis to evaluate the incidence and risk factors of reoperation in DLS patients for the purpose of improving surgical outcomes and prognosis.This study was performed based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) . Two resStudies meeting the following inclusion criteria were selected: (1) population: DLS patients; (2) patients undergoing lumbar surgeries, including decompression surgeries and fusion surgeries; (3) outcome: reoperation rate and risk factors; and (4) studies: cohort studies. The population included DLS patients and DLS patients with lumbar spinal stenosis (LSS). Fusion surgeries included posterolateral lumbar fusion (PLF) and lumbar interbody fusion (LIF). Reoperation was defined as the secondary lumbar surgeries due to progression of lumbar degenerative changes or postoperative instability . Risk faStudies were excluded by meeting one of the following criteria: (1) animal studies; (2) other degenerative spinal diseases including lumbar spine stenosis, degenerative disc disease, and degenerative cervical spondylosis; (3) not English articles; (4) unable to extract data; (5) case reports, conference abstracts, letters, reviews, and meta-analysis.The following data were extracted: the first author, year of publication, country, study design, patients, definition of spondylolisthesis, sample size, age, sex, BMI, disease duration, surgery types, follow-up time, number of reoperations, reasons for reoperation, reoperation methods, and risk factors of reoperation. The Newcastle\u2013Ottawa Scale (NOS) was applied to evaluate the quality of cohort studies . This sc2). Random-effect model was used for analysis if I2\u2009\u2265\u200950%, and fixed-effect model was used if I2\u2009<\u200950%. For the high heterogeneity (I2\u2009\u2265\u200950%), subgroup analysis was conducted based on study design, patients, surgery types, follow-up time, and quality of studies to explore the source of heterogeneity. Sensitivity analysis was carried out for all outcomes. Begg test was used to assess publication bias for the outcome included more than 10 articles. Trim-and-fill analysis was used to adjust the publication bias. P\u2009<\u20090.05 was considered statistically significant.All statistical analyses were performed using Stata15.1 software . Rate was used as the effect index in the analysis of reoperation rate. Odds ratio (OR) was used as the effect index for categorical data, and effect size was represented as 95% confidence interval (CI). Heterogeneity test was performed for each outcome effect size, and results were quantified as I-squared (In\u2009=\u20091026), Embase (n\u2009=\u20091349), Web of Science (n\u2009=\u20094441), and Cochrane Library (n\u2009=\u2009846). After removing the duplicates, 5,251 articles remained. Further, 5,150 articles were excluded due to publishing as reviews or meta-analyses (n\u2009=\u2009929), conference abstracts (n\u2009=\u2009310), animal trials (n\u2009=\u200922), case reports (n\u2009=\u2009226), and letters (n\u2009=\u20099), not English articles (n\u2009=\u2009112), and topic not meeting the requirements (n\u2009=\u20093542). In the remaining 101 articles, we further excluded 3 articles unable to extract data, 29 articles reporting other degenerative spinal diseases, and 30 articles with topic not meeting the requirements. Finally, 39 cohort studies were retained in this meta-analysis [A total of 7,662 articles were searched from Pubmed . To explore the source of heterogeneity, subgroup analyses were performed. In study design subgroup, 10% of reoperation rate was found in both prospective cohort study (95%CI: 7%-13%) and retrospective cohort study (95%CI: 8%-13%). In patients subgroup, DLS patients showed 11% of reoperation rate (95%CI: 8%-13%) and DLS patients with LSS showed 10% of reoperation rate (95%CI: 6%-13%). In surgery types subgroup, the reoperation rate was 11% (95%CI: 9%-13%) in patients undergoing decompression, 10% (95%CI: 7%-12%) in patients undergoing fusion, 9% (95%CI: 5%-13%) in patients undergoing decompression and fusion, and 7% (95%CI: 3%-11%) in patients undergoing other surgeries. In follow-up time subgroup, the reoperation rate was 9% (95%CI: 6%-12%), 12% (95%CI: 9%-14%), and 10% (95%CI: 6%-15%) at follow-up time\u2009<\u20095\u00a0years, between 5 to 10\u00a0years, and\u2009\u2265\u200910\u00a0years, respectively. In study quality subgroup, there was 11% (95%CI: 9%-13%) of reoperation rate in studies with fair quality and 7% (95%CI: 5%-10%) of reoperation rate in studies with high quality. The overall and subgroup analysis results were shown in Table This meta-analysis showed a 10% (95%CI: 8%-12%) of reoperation rate in DLS patients , diabetes , and smoking were associated with an increased risk of reoperation. Age , sex , and more bleeding were not associated with the reoperation. The overall results were demonstrated in Table The meta-analysis showed that obesity Table A. TherefThe reoperation rate of DLS patients undergoing lumbar surgeries remains high in spite of improved surgical skills and techniques; therefore, exploring risk factors of reoperation is important , 8. ConsSeveral previous studies have reported the reoperation rate after lumbar surgeries in DLS patients , 49\u201352. Identifying risk factors of reoperation for patients after lumbar surgeries is of clinical interest. In this study, obesity, diabetes, and smoking were found to be associated with higher risk of reoperation. Rabah et al. and Chan et al. have confirmed that smoking status was associated with greater risk of reoperation , 23. AlsAnimal studies have long recognized the close association between diabetes and lumbar spine disorders \u201357. DiabThis meta-analysis explores the reoperation rate and risk factors for the reoperation. Results show that there is 10% of reoperation after lumbar surgeries, and obesity, diabetes, and smoking are found to increase the risk of reoperation. Our findings suggest that DLS patients should control glycemic level and weight, and reduce smoking to decrease the risk of reoperation. There are some limitations in this study. First, all fusion techniques (PLF and LIF) were put together. Due to the limitations of the included studies, it is unable to further analyze the reoperation rate in DLS patients undergoing the single fusion technique. Second, the number of studies reporting the risk factors of reoperation is relatively small, and some outcomes can only be qualitatively described, which may affect the stability of the results. Third, the risk of reoperation may be different according to the severity of lumbar spondylolisthesis and the first surgical methods; however, data provided in the currently available studies are insufficient to further analyze. Future meta-analysis including more relevant studies are needed to verify our findings and to explore the effect of lumbar spondylolisthesis severity and the first surgical methods on the risk of reoperation.Our meta-analysis found 10% of reoperation rate in DLS patients undergoing lumbar surgeries, and identified obesity, diabetes, and smoking as risk factors for the reoperation. Our findings suggested that patients should improve glycemic level and weight, and quit smoking to reduce the reoperation after lumbar surgery.Additional file 1: Supplementary figure 1. Funnel plot for publication bias before\u00a0and after trim-and-fillanalysis."} +{"text": "There is no consensus on the prevalence of salivary gland tumors (SGTs) in Iran. Thus, we systematically reviewed the literature about the prevalence of SGTs in Iran and applied the last world health organization (WHO) classification. The systematic literature search was performed in EMBASE, Scopus, PubMed MEDLINE, Google Scholar, Scientific Information Database (SID), and Magiran; we searched for \"salivary gland,\" \"tumor,\" \"prevalence,\" and \"Iran\" until 1 March 2021. The studies included were written in the English and Farsi languages. The weighted mean prevalence of SGTs was calculated as prevalence (%) * . We used the unpaired Two-sample T-test to compare the weighted means.P=0.01). Pleomorphic adenoma (PA), followed by Warthin's tumor (WT), was the most prevalent benign tumor. Moreover, the most common malignant tumors were mucoepidermoid carcinoma (MEC) and adenoid cystic carcinoma (AdCC). A total of 17 studies, including 2870 patients, were selected for the data synthesis. The weighted mean prevalence of benign and malignant tumors was 66% (95% CI: 59-73) and 34% (95% CI: 27-41), respectively. The patients' mean age was reported in 10 out of the 17 studies. The weighted mean age of the patients was 40 (95% CI: 37-42) and 49 (95% CI: 43-55) years for benign and malignant tumors, respectively (More than one-third of SGTs in Iran were malignant, which is higher than the reports from Middle Eastern countries. Information about risk factors and the burden of SGTs in Iran is insufficient. Thus, further well-designed longitudinal studies are warranted. Salivary gland tumors (SGTs) are uncommon lesions that account for three to six percent of head and neck cancers \u20134. With The most common tumor of salivary glands is pleomorphic adenoma (PA), a benign, slow-growing, and painless tumor usually found in the parotid glands . In 2017The epidemiology of SGTs is a function of genetics and environmental factors that vary according to the geographic region. It has been reported that SGTs are not common in Iran, and Iranian patients with malignant SGTs are younger with a different pattern of involvement than in other countries . There iProtocol, Registration, and Eligibility CriteriaThis systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) . We desiWe included observational studies, randomized controlled trials, and non-randomized studies that investigated histopathologically confirmed cases of SGTs. Studies in the English or Farsi languages were included, with no limitation on age and gender. Reviews, case reports, book chapters, letters, conference abstracts, personal opinions, and studies without access to the full text were excluded. Information Sources and Search Strategy\u00a0We searched Google Scholar, Scientific Information Database (SID), and Magiran to find articles published in Persian. All the scientific articles in Farsi have an English abstract and English keywords. Therefore, it is possible to identify such papers using an English keyword combination in local databases/repositories such as SID and Magiran. We identified the English literature through EMBASE, Scopus, and PubMed MEDLINE. All the databases were searched until 1 March 2021. As a complementary search, we reviewed the reference list of the relevant studies. The following combination of the free-text terms was used on PubMed MEDLINE:\" AND (tumor OR cancer) AND AND (Iran).\" Although the combination rules could vary, we used the same terms in other databases/repositories (Appendix).Study Selection, Data Collection Process, and Measurements(2). Due to the risk of selective bias, three studies that only included malignant SGTs critical appraisal checklist (version 2017) for prevalence studies was usedP=0.01) (Supplementary Table 1). The weighted mean prevalence by gender for patients with benign tumors was 47% (95% CI: 40-55) and 53% (95% CI: 46-61) in males and females, respectively (P=0.214); also, for patients with malignant tumors, it was 45% (95% CI: 39-51) and 55% (95% CI: 49-61) in males and females, respectively (P=0.01). Seventeen of the 323 records were suitable for data extraction , which rThe reported prevalence of benign tumors ranged from 56- 81% . The weiNew WHO ClassificationBased on the new classification, eleven cases of metastasizing PA were moved from the malignant category to the benign PA. Furthermore, inverted ductal and intraductal papilloma were merged as the ductal papilloma group. Two single cases of cystadenocarcinoma and papillary cystadeno-carcinoma were assumed as adenocarcinoma, not specific otherwise (NOS). Moreover, polymorphous low-grade adenocarcinoma was renamed to Poly-morphous adenocarcinoma. Location of the SGTsTumor location was reported in 2166 out of 2870 SGTs. Most tumors were identified in the parotid (n=1455), followed by minor salivary glands (n=476), ,submandibular (n=199), and sublingual (n=36) glands.. The weighted mean prevalence of malignant tumors was 33% (95% CI: 19-47) and 32% (95% CI: 16-49) in the parotid and submandibular glands, respectively, while the weighted mean prevalence of malignant tumors was 80% (95% CI: -5.9-166) and 62% (95% CI: 48-76) in the sublingual and minor salivary glands, respectively . The preTumor Types. The weighted mean prevalence in female patients with PA and WT was 56% (95% CI: 50-62) and 17% (95% CI: -15-49), respectively, whereas the weighted mean prevalence was 50% (95% CI: 43-58) and 57% (95% CI: 48-66) in female patients with MEC and AdCC, respectively.PA followed by Warthin's tumor (WT) with a weighted mean age of 36 (95% CI: 32-41) and 54 (95% CI: 41-67) years were the most prevalent benign tumors, respectively. Furthermore, mucoepidermoid carcinoma (MEC) and adenoid cystic carcinoma (AdCC) with a weighted mean age of 44 (95% CI: 38-50) and 50 (95% CI: 47-53) years were the most frequent malignant tumors, respectively . The weiRisk of Bias Within StudiesFifteen (88.2%) studies had a low risk of bias, mainly due to non-valid methods that were used for the identification or measurement of the condition in an unreliable way for all the included participants . This systematic review aimed to investigate the prevalence of SGTs in Iran. About two-thirds of SGTs were benign, and the majority of the included patients were middle-aged women. Furthermore, the patients with malignant tumors were significantly older than those with benign tumors. The benign tumors accounted for 66% of SGTs, with the ratio of benign to malignant tumors being 1.9:1. In reports from other Middle Eastern countries such as Iraq (4.7:1), United Arab Emirates (2.8:1), Jordan (2.3:1), and Turkey (2.2:1), the prevalence of malignant tumors was lower than Iran (33\u201336), while in Nigeria 1: 2.5), Brazil (1.4:1), and China (1.8:1) this ratio is higher , Brazil ,38. AmonIn our study, the most frequent benign tumors were PA and WT, and the most frequent malignant tumors were MEC and AdCC, respectively. This finding contrasts previous studies ,26,29,32In line with some other reports, we found a high prevalence of adenocarcinoma (NOS) ,40,42. IIn this study, the mean age of the patients with benign and malignant tumors was 40 and 49 years, respectively. Consistent with this result, previous studies ,37,43 shIn our study, SGTs were more common in females. Reports from Iraq, China, Poland, and Brazil are consistent with this result ,6,33,37;Most SGTs were identified in major salivary glands, with parotid as the most prevalent location. Most of the tumors in the parotid and submandibular glands were benign, whereas in sublingual and minor salivary glands, malignant tumors were more common. These findings are in agreement with previous studies ,6,41,43.This systematic review had some limitations; the new WHO classification introduced some new tumors that could only be identified if the tumor morphology was re-evaluated and molecular diagnostic methods were considered. We could reclassify the tumors only based on the previous diagnoses; however, researchers in Japan and Mexico ,41 couldThis systematic review was carried out on the prevalence of SGTs in Iran. More than one-third of SGTs were malignant, which is higher than those reported from Middle Eastern countries. Most of the patients were in the fifth decade of life. The majority of the tumors in minor salivary glands were malignant, with an equal prevalence of AdCC and MEC. Our findings could be used by healthcare authorities and decision-makers to improve preventive strategies. Information about the risk factors and burden of SGTs in Iran is insufficient. Thus, further, well-designed longitudinal studies are warranted.There are no conflicting interests.This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors."} +{"text": "Background: Healthcare systems in many low- and middle-income countries (LMICs) are not yet designed to tackle the high and increasing burden of non-communicable diseases (NCDs), including hypertension. As a result, a large proportion of people with disease or risk factors are undiagnosed. Policymakers need to understand the disparity better to act. However, previous analyses on the disparity in undiagnosed hypertension, especially from LMICs, are lacking. Our study assessed the geographic and socioeconomic disparity in undiagnosed hypertension and compared it with diagnosed hypertension. Methods: We used the Basic Health Survey (Riskesdas) 2018 and performed geospatial and quantitative analyses across 514 districts in Indonesia. Dependent variables included diagnosed and undiagnosed hypertension among adults (18+ years) and by gender. Results: A high prevalence of undiagnosed hypertension at 76.3% was found, with different patterns of disparity observed between diagnosed and undiagnosed hypertension. Diagnosed hypertension was 1.87 times higher in females compared with males, while undiagnosed hypertension rates were similar between genders. Urban areas had up to 22.6% higher rates of diagnosed hypertension, while undiagnosed hypertension was 11.4% more prevalent among females in rural areas. Districts with higher education rates had up to 25% higher diagnosed hypertension rates, while districts with lower education rates had 6% higher rates of undiagnosed hypertension among females. The most developed regions had up to 76% and 40% higher prevalence of both diagnosed and undiagnosed hypertension compared with the least developed regions. Conclusion: The disparity patterning differs between diagnosed and undiagnosed hypertension among adults in Indonesia. This highlights the need for effective measures, including healthcare system reforms to tackle NCDs in LMICs. Hypertension, or high blood pressure, is linked with increased heart, brain, and kidney disease risks . GloballThe current literature provides some evidence of social determinants of cardiovascular diseases and risk factors including hypertension . A comprTo achieve the SDG target 3.4.1 to reduce premature mortality from NCDs by one-third by 2030, efforts need to aim at reducing the disparity in diagnosed and undiagnosed hypertension ,7,8,9,10This is a cross-sectional study comparing the disparity in diagnosed and undiagnosed hypertension among adults. We analyzed geographic and socioeconomic disparities across 514 districts within 34 provinces in Indonesia. We took advantage of the 2018 Basic Health Survey (Riskesdas) data that were representative at the district level for diagnosed and undiagnosed hypertension. The survey conducted interviews and physical examinations of about 300,000 households from a two-stage sampling procedure. The sampling first randomly selected 30,000 census blocks . Within each block, 10 households were systematically selected, which resulted in 624.563 adults (18+ years). The mean ages (standard deviation) were 41.0 (15.5) years, 40.8 (15.3) years, and 41.3 (15.7) years for all adults, males, and females, respectively [The main independent variables included geographic and socioeconomic indicators at the district level. The variables used in our analyses were region, urbanicity, income level, and education level. This information was taken from the World Bank. The regional variable includes five regions: Sumatera, Java , Kalimantan, Sulawesi, and Papua . Generally, the eastern parts of the country are the least developed ,20,21. AThere were six dependent variables used in our analysis, including diagnosed adults, diagnosed males, diagnosed females, undiagnosed adults, undiagnosed males, and undiagnosed females. Diagnosed hypertension was a binary variable with a value of 1 if one reported ever being told by a doctor that they have high blood pressure and 0 if otherwise. We defined undiagnosed hypertension as not diagnosed but meeting the criteria for hypertension based on the blood pressure measurement .We performed both geospatial analyses and multivariable regression analyses in this paper. In conducting the geospatial analyses, we grouped each dependent variable for 34 provinces and 514 districts by quintile. In conducting the regressions, we employed ordinary least squares and examined the relationship between independent and dependent variables. We compared the regional variations between the western and eastern parts of the country, and the income/education variations between the poorest/least educated and wealthiest/most educated. The geospatial analyses were conducted in ArcMap 10 and the statistical analyses were performed in STATA 15, using 5% as statistically significant.Moreover, For socioeconomic disparity analysis at the district level, Using nationally representative survey data of adults, we found the prevalence of overall hypertension was 33.3%, of which 76.3% were undiagnosed . Global estimates showed similar hypertension prevalence in adults 30\u201379 years of age at 32% and 34% among women and men in 2019 . In termBy sex, diagnosed hypertension among females was 1.87 times higher compared with males , while undiagnosed hypertension was similar between both sexes . This finding aligns with evidence from other LMICs, such as Nepal, Bangladesh, and Peru, showing a significantly lower prevalence of undiagnosed hypertension among women ,29.We found significant disparities (geographic and socioeconomic) between the prevalence of diagnosed and undiagnosed hypertension across 514 districts. Diagnosed hypertension was higher by up to 22.6% in urban areas, while undiagnosed hypertension among females was higher by 11.4% in rural areas. Previous studies showed a higher prevalence of diagnosed hypertension in urban areas but a higher prevalence of undiagnosed hypertension in rural areas ,8,9,10. By region, the patterning is similar for diagnosed and undiagnosed hypertension. Districts in the most developed areas had up to a 76% and 40% higher prevalence of diagnosed and undiagnosed hypertension compared with the least developed areas . This is likely due to a higher burden of hypertension (diagnosed and undiagnosed) among higher socioeconomic levels of the population in more developed regions. By income, the richest districts had a higher prevalence of diagnosed and undiagnosed hypertension among all adults, males, and females than that of the poorest districts . By education, districts with the most education had up to a 25% higher prevalence of diagnosed hypertension, while those with the least had a 6% higher undiagnosed prevalence among females.While evidence from LMICs are limited in the literature, our findings align with previous studies. Studies using provincial-level data in China showed a higher prevalence of hypertension in the least disadvantaged areas than that in the most disadvantaged ones ,16. SimiEffective efforts are needed to reduce undiagnosed hypertension (and other NCD risk factors such as high cholesterol and diabetes) by sex, urbanicity, region, and socioeconomic status ,35. EffoOur study is the first analysis from LMICs to compare the disparity (geographic and socioeconomic) in the prevalence of diagnosed and undiagnosed hypertension across over 500 localities. However, our study also has limitations. Because of the lack of information, our analysis could not conduct sub-group analysis by ethnicity . AdditioIn Indonesia, a high prevalence of undiagnosed hypertension at 76.3% was found with different patterns of disparity observed between diagnosed and undiagnosed hypertension. Diagnosed hypertension was 1.87 times higher in females compared with males, while undiagnosed hypertension rates were similar between genders. Urban areas had up to 22.6% higher rates of diagnosed hypertension, while undiagnosed hypertension was 11.4% more prevalent among females in rural areas. Districts with higher education rates had 25% higher diagnosed hypertension rates, while districts with lower education rates had 6% higher rates of undiagnosed hypertension among females. The most developed regions had up to a 76% and 40% higher prevalence of both diagnosed and undiagnosed hypertension compared with the least developed regions. This study highlights the need for effective measures, including healthcare system reforms, to tackle NCDs in LMICs."} +{"text": "Little is known about HIV risk perception, or PrEP awareness, and acceptability in rural populations.The We analyzed baseline survey data from 69 residents as part of a larger study aiming to increase PrEP utilization in rural Colorado with virtual PrEP visits (TelePrEP) and mailed lab kits. The baseline survey on HIV risk, PrEP awareness, and access was conducted in 3 low-income rural Colorado counties from March 2022-February 2023. Residents were recruited from rural community settings, including a syringe service program, a substance treatment program, a migrant housing complex, a Native American Pow Wow, a college campus, and a public health clinic. All survey respondents were given the opportunity to enroll in TelePrEP services if eligible. Respondent demographics, HIV risk factors, risk perception, PrEP awareness, and access were examined. Descriptive statistics were used to characterize the cohort.Seventy-five % of the rural cohort identified as female; 23.2% as male; and 1.5% as other gender. Thirty-three % of the cohort were White; 34.8% were Hispanic; 26.1% were Native American; and 2.9% were Black. Seventy-eight % self-identified as heterosexual; 13% as bisexual; 8.7% as homosexual. Sixty-seven % self\u2013rated personal HIV risk as low, though almost a third of the cohort reported 2 or more sexual partners, 58% reported condomless sex, and 59% reported heavy alcohol or drug use, in the prior six months. Almost 40% of the cohort reported that they or a partner had a history of incarceration. Sixty-three % reported seeing a regular health care provider (HCP). Forty-two % had heard of PrEP previously, but only 5 respondents had heard of PrEP from an HCP. Seventy-two % of the cohort felt that taking PrEP was a good way to protect themselves from HIV; however, none of the respondents chose to enroll in PrEP services.Despite elevated risk for HIV acquisition and the majority having regular access to a health care provider, PrEP awareness and utilization was low in this cohort of rural residents. A gap in perceived versus objective HIV risk exists.Lorna Allen, FNP-C, MERCK: Grant/Research Support Donna V. McGregor, MSN, ANP-BC, Gilead Sciences: Grant/Research Support"} +{"text": "Primary central nervous system (CNS) tumours are heterogeneous, with different treatment pathways and prognoses depending on their histological and molecular classification. Due to their anatomical location, all CNS tumours, regardless of malignancy, can be debilitating. We used vital statistics linked to Canadian Cancer Registry data to estimate the age-standardized incidence rates (ASIR), Kaplan\u2013Meier survival rates (SR), and limited-duration prevalence proportions (PP) of 25 histology-specific CNS tumour groups that were classified based on site and histology. During 2010\u20132017, 45,115 patients were diagnosed with 47,085 primary CNS tumours, of which 19.0% were unclassified. The average annual ASIR was 21.48/100,000 person-years and did not vary by sex. The ASIR increased with age, particularly for meningioma, unclassified tumours, and glioblastoma. The eight-year PP was 102.1/100,000 persons (index date 1 January 2018). The most common histology was meningioma . The overall five-year SR among 51,310 patients diagnosed during 2008\u20132017 was 57.2% (95% CI: 56.8\u201357.7%). SRs varied by tumour behaviour, histology, and patient age, with the lowest SR among glioblastoma patients (5-year SRs ranged from 1.3\u201325.7%). For non-malignant tumours, the 5-year SRs ranged from 37.4\u2013100%. We provide the most up-to-date histology-specific surveillance estimates for primary CNS tumours in Canada. Primary central nervous system (CNS) tumours are those originating in tissues encased by the skull and spinal column, including the brain, cranial nerves, spinal cord, cauda equina, meninges, pineal, and pituitary glands, as well as the craniopharyngeal duct ,2. Althohttps://braintumourregistry.ca/ accessed on 19 December 2022) [The Brain Tumour Surveillance Research Collaborative of Canada (BTSRC) was established in 2016 to enhance primary CNS tumour surveillance in Canada and periodically provide high-quality surveillance estimates (er 2022) ,8. At ther 2022) .We present the most up-to-date surveillance statistics on primary CNS tumours diagnosed in Canada between 2008 and 2017 for incidence and prevalence and between 2008 and 2018 for survival. Estimates are stratified by tumour (histology and behaviour) and/or demographic characteristics.Each Canadian provincial/territorial cancer registry collects data on new cancer diagnoses in their respective jurisdictions, and reports them to Statistics Canada for compilation in the CCR, including diagnosis based on pathology, radiology, or clinical, among other methods . The colCNS tumours can be classified according to a combination of their site, histology, behaviour, and molecular features. At present, data on the molecular features of primary CNS tumours are not routinely available in the CCR. The classification system used by cancer registries in Canada is the International Classification of 2nd and 3rd edition for Topography and the 3rd edition for histology and behaviour . PrimaryThe demographic variables included in this article are sex and age group . Patients with missing birth and/or death dates were removed from the incidence, prevalence, and survival cohorts. In cases where dates had missing months and/or days, but not years, the missing data was imputed using an average of days. Patients diagnosed solely through death certificate or autopsy were excluded from survival analyses. For patients with the same date of diagnosis and death, the date of diagnosis was changed to one day prior to the date of death to prevent these records from being excluded from survival analysis.The most recent death-linked CCR data available was up to 31 December 2017. Ontario did not report primary non-malignant CNS tumours to CCR prior to 2010. We thus limited the incidence and prevalence cohort in our analysis to all primary CNS tumours diagnosed from 1 January 2010. We created a 10-year survival cohort by extending the primary CNS tumour diagnosis date back to 1 January 2008.We used direct standardization to account for differences in the age distribution across geographic regions and over time, with the 2011 Canadian standard population as the reference when calculating incidence rates and prevalence proportions. In this article, person-based eight-year limited-duration prevalent cases are the number of patients diagnosed with primary CNS tumours between 1 January 2010 and 31 December 2017, and who were still alive as of the index date (1 January 2018). Number of prevalent cases and prevalence proportions were estimated for the age at the index date. A popular metric for reporting cancer patients\u2019 survival is net survival, which measures the probability of surviving cancer in the absence of other causes of death ,16. We hAll primary CNS tumours are defined according to the National Cancer Institute Surveillance, Epidemiology, and End Results (SEER) Program. Individuals may be diagnosed with more than one primary CNS tumour, which may or may not be of the same type or subtype. SEER multiple primary rules ,17 were Several measures were taken to protect the confidentiality of individuals underlying the data. All frequency counts reported were randomly rounded using an unbiased random rounding scheme with a base of five. Incidence and prevalence estimates were suppressed if the category contained <5 but >0 patients. We combined categories or suppressed estimates as appropriate if stratification by specific histology groups disclosed additional categories with fewer than 5 patients. Survival estimates were suppressed if the standard error was \u22650.10, or if less than 10 patients contributed to the estimate. The study was approved by the Research Ethics Board of Alberta Cancer Committee.A total of 47,085 primary CNS tumours were diagnosed in 45,115 Canadians between 2010 and 2017 , correspThere was no noticeable difference in overall incidence by sex: the ASIR for females was slightly higher than that of males ; males: ASIR: 21.11/100,000 PY (95% CI: 20.83\u201321.39)). However, there were differences in the frequencies of some major and specific histology groups between the sexes. The most common major histology group among males was tumours of the neuroepithelial tissue , whereas, for females, it was tumours of the meninges . The most common specific histology group among males was glioblastoma , whereas, for females, it was meningioma . Conversely, females and males had similar ASIRs for the following histological subtypes: choroid plexus tumours, tumours of the pineal region, tumours of the cranial and spinal nerves, mesenchymal tumours, primary melanocytic lesions, and other hematopoietic neoplasms. Males had a higher percentage of malignant tumours compared to females (43.7% vs. 28.8%).Overall, the ASIRs for primary CNS tumours increased with age. The ASIRs in children, AYA, adults, and older adults were 5.30 (95% CI: 5.06\u20135.54), 9.00 (95% CI: 8.78\u20139.22), 25.88 (95% CI: 25.52\u201326.25), and 58.16 (95% CI: 57.33\u201358.99) per 100,000 PY, respectively . The mosThere were 50,670 primary CNS tumour patients diagnosed between 2008 and 2017 that were included in the survival analyses . Figure Among those with non-malignant tumours, patients with unclassified tumours had the poorest long-term survival, with a pronounced decrease in survival rate within the first year after diagnosis . PatientEstimated 5-year SRs and MSTs for patients with primary malignant CNS tumours stratified by age group and histology are presented in Estimated 5-year SRs and MSTs for patients with primary non-malignant CNS tumours stratified by age group and histology are presented in There were 28,530 Canadians who were diagnosed with a primary CNS tumour between 2010 and 2017 and who were alive as of 1 January 2018 . Among tAlthough Ontario had the highest proportion of unclassified primary malignant CNS tumours in Canada from 2008 to 2016 (17.4% to 8.0%), this proportion decreased over time and is presented in We presented population-based surveillance of CNS tumours in Canada from 2010\u20132017 (excluding Quebec). The average annual age-standardized incidence rate (ASIR) per 100,000 for all primary CNS tumours in Canada (excluding Quebec) was 21.48 (95% CI: 21.28\u201321.67). Although the ASIR for all CNS tumours combined was similar for males and females , differences existed by histology. Men had higher rates for glioblastoma, while females had higher rates for meningioma. The ASIR for all CNS tumours combined significantly increased with age from 5.30 per 100,000 (95% CI: 5.06\u20135.54) in children (age 0 to 14 years), to 9.00 (95% CI: 8.78\u20139.22) in adolescents and young adults (age 15\u201339 years), to 25.88 (95% CI: 25.52\u201326.25) in adults (age 40\u201364 years), to 58.16 per 100,000 (95% CI: 57.33\u201358.99) in older adults (65+). Interestingly, the proportion of incident tumour diagnoses that were malignant was consistent across all adolescent and adult age groups at ~34%, but approximately double among those aged 0\u201314 years (67%). Of classifiable histological subtypes, 8 were associated with a median survival time of more than 8 years. The shortest median survival was among patients with glioblastoma (8 months) or lymphoma (12 months). Younger age was associated with longer survival time. However, the AYA age category had the longest survival time for glioblastoma and anaplastic astrocytoma. At the index date of 1 January 2018, there were an estimated 28,530 patients living with a primary CNS tumour in Canada for an eight-year limited-duration prevalence proportion (PP) of 102.1 per 100,000 persons. Of these, 80.3% were non-malignant, which is consistent with the longer survival time among those diagnosed with non-malignant tumours.Patients with unclassified tumours consistently had poor survival outcomes, which were second only to glioblastoma patients for malignant behaviours. It is difficult to interpret the meaning of this finding, given the potential heterogeneity in tumours included in these unclassified categories. Within Canada, the highest proportion of unclassified tumours was in Ontario, which was predominantly driven by non-malignant unclassified tumours with an incidence proportion approximately 7.6 times that of other provinces included in the analysis . ConversOverall, the findings are consistent with other regions. The overall rate of CNS tumours in Canada is lower than that of the United States . In addiEuropean 5-year relative survival estimates for primary malignant neuroepithelial tumours from the EUROCARE-5 study showed survival estimates of 24.6% for Norway, 17.9% for Ireland and UK, 25.1% for Germany, 18.5% for France, and 20.3% for Europe as a whole . GlioblaThe estimates presented in this paper represent broader categories of histological subtypes than may be relevant clinically. This is because primary CNS tumours are rare, and the number of diagnoses is often too low to permit reporting on smaller categories of tumours while adhering to reporting guidelines set by Statistics Canada to ensure the privacy of those represented by these numbers. Additionally, data on molecular markers are not currently available through the CCR. Therefore, tumour classifications do not strictly include molecular subtypes, although this information may have been included in the initial diagnosis and used to inform treatment decisions. There is incomplete correspondence between the ICD-O-3 diagnoses used in our analysis and the 2021 World Health Organization classification of tumours of the CNS . This liOverall, the findings were consistent with the expected frequency and distribution of primary CNS tumours in Canada and comparable to those reported in US and some European countries. These findings reflect the improvements made by provinces in collaboration with the BTRC in capturing non-malignant CNS tumours in their respective registries. However, there remains evidence of incomplete capture to varying degrees across provinces. Further, the high frequency of unclassified tumours indicates the need for further efforts to improve the consistency and completeness of information across provinces. The BTRC continues to collaborate with provincial cancer registries to identify strategies for addressing the issues highlighted in this manuscript. Currently these are the most up-to-date histology-specific brain tumour surveillance estimates available in Canada."} +{"text": "To characterize routine non-pharmacological care for youth with ADHD.76 audio-recorded work-samples were collected from community mental health therapists in a large metropolitan area in the United States and were analyzed for operationally defined practice elements commonly included in evidence-based non-pharmacological treatment for ADHD. Analyses characterized community provider practices and examined predictors of using evidence-based practices.Individually delivered social skills training was the most commonly detected practice element (31.6% of practice samples). Parent involvement in routine care was uncommon . Core elements of evidence-based practices were rarely delivered ; when evidence-based content was introduced, it was typically implemented at a very low intensity. Patient and provider characteristics did not predict use of evidence-based practices.Routine non-pharmacological care for adolescent ADHD primarily consisted of low value practices such as youth-directed treatment and social skills training with low parent involvement and only occasional therapy homework. To improve quality of care, efforts to de-implement low value practices should be coupled with efforts to implement evidence-based practices . Adolescence is a critical period for ADHD treatment given close relationships between adolescent functioning and adult outcomes \u20133. The tWhile psychosocial treatments for children with ADHD typically are limited to training parents to apply operant behavioral strategies , adolescThe present study analyzes 76 work samples submitted by 26 community therapists at four mental health clinics who delivered behavior therapy to 74 adolescents with a primary diagnosis of ADHD. Work samples were collected as part of a routine care condition in a randomized community-based effectiveness trial of an ADHD behavior therapy . Herein,Full study design and CONSORT diagram are described elsewhere . Herein SD = 1.50). The sample 62.6% male, 90.8% Latinx, 6.8% Black or African-American, and represented a broad socio-economic distribution. Approximately 20% of the sample received naturalistic adjunctive stimulant medication for ADHD during psychosocial treatment.The 74 adolescents (ages 11\u201317) received routine mental health therapy for ADHD at one of four community mental health clinics in a large U.S. city. Participants were required to meet DSM-5 ADHD criteria according to a systematic evaluation conducted by the research team that integrated parent and teacher ratings of symptoms and impairment. Autism spectrum disorder and intellectual disability (IQ < 70) were exclusionary. Full characteristics of the subsample can be found in p < 0.001) and were slightly older (p = 0.032) than those not represented on work samples. They also attended significantly more sessions than those without a work sample .Two adolescent participants transferred therapists during the course of treatment and, therefore, were represented on two separate work samples submitted by separate therapists. Usual care participants represented on work samples were more likely to have a parent with limited English proficiency (N = 26) were mental health professionals employed at four community agencies. Therapists self-identified as 15.4% non-Hispanic White, 15.4% Black or African-American, and 65.4% Hispanic. They were 80.8% female therapists, with 65.4% offering treatment in both Spanish and English. 19.2% of therapists were licensed and 84.6% held a master's degree (7.7% held a doctorate and 7.7% were bachelor's level). On average, clinicians reported 6.73 years of experience delivering therapy (range: 1\u201331).Therapists (n = 26) and those who were not (n = 14). Reasons for missing work samples included therapist refusal, inaudible recordings, parents who did not consent to this aspect of the research, participants who dropped out of treatment before work samples could be collected, and human error.There were no demographic differences between usual care therapists who were represented on work samples ; in 62.9% (22 of 35) of these, the parent attended at least 75% of the session. Thus, 28.9% of sessions were considered joint parent-teen sessions, 17.1% were adolescent-directed with some parent involvement, and 53.9% were adolescent-only sessions. Four sessions (5.3%) included another family member such as a second parent or sibling. 30.3% of sessions were conducted in Spanish.The adolescent was present for the full session in 100% of samples. A parent was present in 46.1% of the sample sessions (SD = 1.65). 81.6% of work samples included at least one practice element. On average, sessions integrated 2.14 practice elements per session .Routine care for adolescent ADHD tended to take adolescent-directed, rather than parent-teen collaborative or parent-directed approaches, and only seldom engaged additional stakeholders in session. Clinicians tended to integrate EBPs into most sessions (81.6% of work samples), but with very low extensiveness. The most frequently implemented practice elements were social skills training, skill application therapy homework, and time management skills training. Extensiveness of EBP implementation was not related to any predictors.Evidence-based psychosocial treatments for adolescent ADHD typically employ a hybrid format that requires involvement of both parent and teen. Less than 30% of sessions utilized the parent-teen model and most delivered treatment to the adolescent alone (53.9%). Failure to engage the parent, or other stakeholders, in care may undermine the effectiveness of adolescent treatment , 11. ThuWhen EBPs were implemented, it was typically at a very low intensity see . This fiThe most common focus of adolescent ADHD treatment in community contexts was social skills training (31.6% of sessions). However, meta-analysis demonstrates no effects for social skills training on adolescent ADHD , 10, 32.We were unable to detect associations between EBP implementation and adolescent or provider characteristics. There was modest variability in extensiveness of EBP implementation, which may have prevented patterns from emerging. In addition, an inevitable limitation of community-based research is lower control and data collection rates than university trials. Thus, we were only able to collect usable work samples for about 2/3rds of the treated sample. Work samples were collected from four agencies in a single geographic region who primarily serve minority youth; it is unclear whether findings generalize to other contexts, such as non-Latinx families in other locations. It is also unclear if these findings would generalize to samples with higher medication utilization or higher rates of hyperactivity/impulsivity symptoms. It is unclear whether work samples adequately represent non-recorded sessions, which could introduce a selection bias.Offering psychosocial treatment for adolescent ADHD (in addition to or instead of medication) is an opportunity to increase engagement in routine care services. However, to ensure effectiveness, care must reflect evidence-based practices. Based on this study, strategic directions for routine care include improving parent engagement in adolescent ADHD treatment, increasing the integrity with which EBPs are delivered, reducing low value practices , and appropriately incorporating common elements of adolescent ADHD psychosocial treatment \u201311, 32. https://nda.nih.gov.The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: The studies involving human participants were reviewed and approved by Florida International University Institutional Review Board. Written informed consent to participate in this study was provided by the participants' legal guardian/next of kin.MS contributed to the trial administration, conceptualization, data analysis, and primary manuscript writing. JR contributed to data coding and manuscript editing. AR-D contributed to conceptualization, data coding, and manuscript editing. PG contributed to trial administration, conceptualization, and manuscript editing. All authors contributed to the article and approved the submitted version.This project was funded by grant R01 MH106587 from the National Institute of Mental Health (USA).MS receives book royalties from Guilford Press for a book on treating ADHD in adolescence using non-pharmacological approaches. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "People with HIV (PWH) face many challenges in obtaining HIV care. Long-acting (LA)-injectable antiretroviral therapies (ART) can address some of these barriers. This project aimed to determine the percentage of patients who could receive the LA-injectable ART cabotegravir/rilpivirine (CAB/RPV) as an alternative to an oral daily pill regimen based on clinical indications.We retrospectively reviewed medical records of adult PWH seen at the University of Missouri Health Care (MUHC) HIV outpatient clinic in Columbia, MO. We collected demographics, CD4 counts, hepatitis B status, HIV viral load, and HIV genotype resistance data. The primary endpoint was the percentage of PWH who would qualify to receive the LA-injectable ART CAB/RPV based on an undetectable HIV viral load, no documented chronic hepatitis B status, and no resistance to either CAB or RPV based on the Stanford University HIV Drug Resistance Database.Six hundred and twenty-five unique PWH were receiving care at MUHC with a median age of 49 years old, 20% female, 27.5% Black/African American, 4.8% Hispanic and/or Latino, and 9.1% with AIDS (CD4 count < 200 cells/uL). 17.9% of PWH were not eligible for the LA-injectable ART CAB/RPV due to a detectable HIV viral load . An additional 7.2% did not qualify due to having a genotype resistance to CAB or RPV and 1.8% did not qualify due to having chronic hepatitis B. Altogether, 151 PWH (24.2%) had one or more clinical contraindications for the LA-injectable ART CAB/RPV based on current guidelines. Genotype resistance testing was not available for 59.6% of PWH. However, out of the 474 PWH who are eligible to receive the LA-injectable ART CAB/RPV, only 76 (16.1%) are currently in care and on this regimen.In this study, we identified a high percentage of patients with no available genotype and a low uptake of the new LA-injectable ART CAB/RPV. To optimize the use of the the LA-injectable ART CAB/RPV and to make it accessible to PWH who could benefit from it, further research needs to be done using both quantitative and qualitative measures to identify barriers and facilitators at the patient, provider, and system level and to develop effective implementation strategies.Dima Dandachi, MD, MPH, ContraFect Corporation: Grant/Research Support|Missouri Foundation for Health: Grant/Research Support|ViiV healthcare: Grant/Research Support|ViiV healthcare: Honoraria"} +{"text": "Background: In-hospital mortality rates following all types of pancreatic resections (PRs) have decreased over recent decades. Our aim was to identify predictors of in-hospital mortality following pancreatic resection.Methods: All patients undergoing pancreatic resection were sampled from the National Inpatient Sample (NIS) in the years 2007-2012. Predictors of in-hospital mortality were identified and incorporated into a binary logistic regression model.Results: A total of 111,568 patients underwent pancreatectomy. Annual mortality rates decreased from 4.3% in 2007 to 3.5% in 2012. Independent predictors of in-hospital mortality included age \u226575 years , nonelective procedure status , resection other than distal pancreatic resection , lower hospital volume , indication for pancreatic resection other than benign diseases , pulmonary complications , infectious complications , noninfectious wound complications and pancreatic leak , and acute myocardial infarction .Discussion: Our findings identify predictors of inpatient mortality following pancreatectomy, with pulmonary complications representing the single most significant factor for increased mortality. These findings complement and expand on previously published data and, if applied to perioperative care, may enhance survival following pancreatectomy. The first reports of pancreatic resection (PR) date back to the late 19th century , postopeA combination of disease processes and patient-specific and hospital-level factors have been previously linked with increased morbidity and mortality following pancreatectomy -6,8-9,11Study populationThe National Inpatient Sample (NIS) database, from 2007 to 2012, was queried for all admissions with ICD-9-CM procedural codes for PR. These included proximal pancreatectomy, distal pancreatectomy, radical subtotal pancreatectomy, other partial pancreatectomy, total pancreatectomy, and radical pancreaticoduodenectomy . With the intention of covering the entire cohort of patients undergoing PR, neither age cut-offs nor any other exclusion criteria were used. Our data captured patient demographics, PR type and indication, elective procedure status, hospital size, location, surgical volume, and teaching status. Weighting (provided in NIS for each record) was used to calculate nationwide estimates.Statistical considerationsPotential predictors of in-hospital mortality were determined by the standard bivariate tests: the Chi-squared test, the independent-samples t-test, and the Mann-Whitney U test. We used an augmented list of codes for intra- and postoperative complications published by Simons et al. . AccidenCharacteristics of the study populationA total of 111,568 patients underwent PR between 2007 and 2012. The study population consisted of an even ratio of male to female patients. Age was characterized by an unimodal distribution (60.3 \u00b1 15.4), with individuals 55-74 years old constituting 51.8% of the entire study population. Patients \u226575 years old accounted for 17.6% of the study population.Overall, 79.3% of the patients underwent an elective pancreatic resection. Malignant indications accounted for 51.8% of all pancreatic resections . Of all pancreatic resections, PD accounted for 55.3% . PR most commonly took place in teaching hospitals (83.1%), in an urban location (97.2%), and in hospitals with the highest pancreatic surgery volume . The structure of the study population is provided in Figure In-hospital mortality trend and predictorsAnnual in-hospital mortality rates following pancreatic resection decreased from 4.3% in 2007 to 3.5% in 2012. This follows a decreasing mortality trend between the years 2000 and 2006, with respective mortality rates of 7.39% and 4.92%. In-hospital mortality by pancreatic resection type is displayed in Figure Predictors of in-hospital mortality following pancreatectomy are highlighted in Table Previous studies have reported mortality following PR ranging between 1% and 8% -10. Our Preoperative assessment of candidates for PR has been paramount in optimizing survival following surgery, but there is no one assessment tool universally standardized or accepted as the best. The Eastern Cooperative Oncology Group (ECOG) performance status scale has long been utilized to assess readiness to undergo major surgery . AdditioGiven the importance of technique and the inherent risk of injury in pancreatic surgery, we examined accidental intraoperative injuries, showing that such injuries were associated with doubled in-hospital mortality. These data do not reveal if such injuries were due to challenging dissection attributable to locally advanced disease leading to unavoidable violation of adjacent viscera or requiring vascular reconstructions, due to other patient-related disease, or to other factors. Surgeons attributed technical errors or poor intraoperative judgment to poor outcomes in 21% of the cases, as per the root-cause analysis of >10,000 pancreatectomies . BesidesThe overall decrease in mortality following PR has been attributed in part to the implementation of a multidisciplinary approach to postoperative patient care, including the utilization of interventional radiology and intensive care unit optimization in high-volume hospitals. Complications such as postpancreatectomy hemorrhage and frequently coinciding pancreatic fistulas have been implicated in mortality following pancreatectomy . AdditioIn this study, we demonstrate that the presence of pulmonary complications is by far one of the most significant predictors of mortality following pancreatectomy. Pulmonary complications encompass aspiration pneumonitis, respiratory failure, and the need for mechanical ventilation. Prior studies have reported on this correlation with pneumonia and respiratory distress, which was shown to be more prevalent in those patients who experienced mortality following pancreatectomy . PneumonOur study has limitations that are inherent in administrative databases, including the difficulty of assessing the severity of comorbid diseases and distinguishing pre-existing comorbidities from postoperative ones. Within the limitations of this kind of study, we highlight predictors of in-hospital mortality following pancreatectomy using a large, national database. Additionally, although our query of the NIS database is limited to the years 2007 and 2012 and thus utilizes exclusively ICD-9 codes, our results remain relevant to present-day practice. Our literature review was maintained current and reveals that our results add to and strengthen the wealth of data highlighting risk factors for in-hospital mortality after PR.In summary, our findings identify predictors of inpatient mortality following PR, with pulmonary complications representing the single most significant factor for increased mortality, followed by other modifiable and non-modifiable factors including increasing age, malignant disease, type of pancreatic resection, intraoperative injury, postoperative infection, and myocardial infarction. This complements and expands on previously published data. Although mortality continues to decline following PR, our study suggests an important avenue for further improving outcomes following pancreatic surgery, namely respiratory prehabilitation. Ongoing focus on preoperative patient selection and optimization, operative decision-making, and postoperative care can further enhance survival following PR."} +{"text": "Sepsis is a leading cause of pediatric mortality, with nearly 5,000 children dying annually. Clinical advances in care bundles to improve sepsis recognition and timely treatment have demonstrated improved outcomes. Recently, literature suggests an association between pediatric sepsis mortality and various social determinants of health, including race and socioeconomic status. It is unclear what may contribute to these disparities; therefore, we chose to evaluate if race, ethnicity or other factors resulted in delayed antibiotic administration.This retrospective cohort review of a single center quality improvement pediatric sepsis dataset included admitted patients with a blood culture and intravenous antibiotics within 4 hours and a hospital diagnosis of sepsis. Patients admitted to the neonatal intensive care unit were excluded. The primary outcome was antibiotic administration > 60 minutes. Exposures of interest included age, gender, race, ethnicity, language, sepsis severity level, ICU admission and mortality. Analysis included descriptive statistics and Chi-Square testing.From 2016 \u2013 2023 there were 322 patients , with 61% identified as non-Hispanic and 39% Hispanic. English was the primary language (83%) and there were 52% females, and 48% males. Overall, 58% of patients required intensive level care and 6.8% died. The mean time to antibiotics was 75 minutes. There was no statistical significance when evaluating if race, ethnicity, language, or sepsis severity contributed to antibiotic delays of > 60 minutes. Factor associated with a statistically significant delay in antibiotic administration were: mortality and female gender ; regardless of sepsis severity and infants < 1 year .Inequities exist in the timely delivery of antibiotics for younger infants and female patients with an admitting diagnosis of sepsis. Further investigation is warranted to identify drivers for these inequities.All Authors: No reported disclosures"} +{"text": "Given the physiological changes during pregnancy, pregnant women are likely to develop recurrent urinary tract infections (UTIs) and pyelonephritis, which may result in adverse obstetric outcomes, including prematurity and low birth weight preeclampsia. However, data on UTI prevalence and bacterial profile in Latin American pregnant women remain scarce, necessitating the present systematic review to address this issue.To identify eligible observational studies published up to September 2022, keywords were systematically searched in Medline/PubMed, Cochrane Library, Embase, Web of Science, and Bireme/Lilacs electronic databases and Google Scholar. The systematic review with meta-analysis followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, and the quality of studies was classified according to the Strengthening the Reporting of Observational Studies in Epidemiology guidelines. The meta-analysis employed a random-effects method with double-arcsine transformation in the R software.Escherichia coli (70%) was identified as the most frequently isolated bacterial species, followed by Klebsiella sp. (6.8%).Database and manual searches identified 253,550 citations published until September 2022. Among the identified citations, 67 met the inclusion criteria and were included in the systematic review, corresponding to a sample of 111,249 pregnant women from nine Latin American countries. Among Latin American pregnant women, the prevalence rates of asymptomatic bacteriuria, lower UTI, and pyelonephritis were estimated at 18.45% , 7.54% (95% CI: 4.76\u201310.87), and 2.34% (95% CI: 0.68\u20134.85), respectively. Some regional differences were also detected. Among the included studies, Pregnant women in Latin America exhibit a higher prevalence of bacteriuria, UTI, and pyelonephritis than pregnant women globally. This scenario reinforces the importance of universal screening with urine culture during early prenatal care to ensure improved outcomes. Future investigations should assess the microbial susceptibility profiles of uropathogens isolated from pregnant women in Latin America.This research was registered at PROSPERO (No. CRD42020212601).The online version contains supplementary material available at 10.1186/s12884-023-06060-z. Bacteriuria reportedly affects 1.78\u201348.3% of pregnant women . Its preUTIs are classified into three subgroups: (a) asymptomatic bacteriuria (ASB); (b) lower UTI, characterized by vaginal mucosa inflammation and irritative urinary tract symptoms; and (c) acute pyelonephritis or upper UTI, a systemic condition. In addition, UTIs can be classified as simple or complicated, depending on the presence of kidney and ureter involvement .Urinary tract dilation and ureteral smooth muscle relaxation during pregnancy increase the susceptibility of the urinary tract to microorganisms. The implementation of universal screening for bacteriuria during pregnancy has substantially reduced the incidence of pyelonephritis; thus, urine culture should be routinely requested for all pregnant women at their first prenatal visit \u20137.Bacterial colonization of the urinary tract during pregnancy may also be associated with adverse perinatal outcomes such as prematurity , 9, low Notably, there are substantial discrepancies in data regarding the prevalence of bacteriuria during pregnancy. In 2019, Latin America recorded the highest regional UTI incidence globally , the highest mortality from UTI , and the highest number of disability-adjusted life years (DALYs) secondary to UTI . HoweverThe present systematic review would help plan public policies and the implementation of measures to optimize perinatal outcomes related to urinary tract infections during pregnancy.This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. The studies were selected independently by two reviewers (MAKG and HD). Disagreements regarding study inclusion or exclusion were resolved through discussions until a consensus was reached. This systematic review is registered at PROSPERO (No. CRD42020212601).The researchers systematically searched Medline/PubMed, Cochrane Library, Embase, Web of Science, and Bireme/Lilacs electronic databases, as well as the Google Scholar search engine. Studies published up to September 2022 were deemed eligible. The studies were searched using the following keywords alone or in combination: bacteriuria OR urinary tract infection OR pyelonephritis OR cystitis OR asymptomatic bacteriuria OR bacteriuria in pregnancy OR urinary tract infection in pregnancy OR pyelonephritis in pregnancy OR cystitis in pregnancy.5\u00a0CFU/ml in a midstream urine sample or of 1\u2009\u00d7\u2009102\u00a0CFU/ml in a sample obtained by urinary catheterization; published in English, Spanish, or Portuguese; and reported relative risks (RRs) or odds ratios (ORs) or presented original datasets that allowed the calculation of these association measures. This systematic review only included studies conducted in the 20 most populous countries in Latin America, according to the 2020 United Nations Statistical Division: Brazil, Mexico, Colombia, Argentina, Peru, Venezuela, Chile, Guatemala, Ecuador, Bolivia, Haiti, Cuba, Dominican Republic, Honduras, Paraguay, Nicaragua, El Salvador, Costa Rica, Panama, and Uruguay [Inclusion criteria were as follows: observational studies regarding the prevalence of bacterial urinary tract colonization in pregnant women from Latin American countries; objective diagnostic criteria for UTI, including urine culture reports with minimum bacterial growth of 1\u2009\u00d7\u200910 Uruguay . ExclusiTwo investigators (MAKG and HD) independently extracted relevant data from the studies using a standardized form. The retrieved data included first author details, year of publication, study demographic coverage area, study design, sample size, the prevalence of bacteriuria, the prevalence of UTI, diagnostic criteria for bacteriuria, and association measures such as RRs or ORs. In addition, information on the frequency of microorganism isolation in urine cultures of pregnant women was extracted.Considering the quality, the studies were classified according to the Strengthening the Reporting of Observational Studies in Epidemiology guidelines, analyzing five dimensions: sample population, sample size, percentage of participation among those eligible, result evaluation, and analysis of statistical methods employed. Each of these dimensions received a score ranging from 0 to 2 points. The final total score ranged from 0\u201310 points, with 10 representing the lowest overall risk of study bias and 0 representing the highest overall risk of study bias , 17.I2 index. Publication bias was measured by reviewing the funnel plots and using Begg\u2019s and Egger\u2019s tests. The random-effects model was used to combine highly heterogeneous data. The adjusted ORs and 95%CI of included studies were used for data analysis. Study results were combined to produce a pooled OR-95%CI. Statistical analyses were performed using the R statistical software. Statistical significance was set as p\u2009<\u20090.05.Study-specific synthesized estimates were pooled using the random-effects meta-regression model to estimate the overall prevalence across studies after stabilizing the variance of individual studies using the Freeman-Tukey double-arcsine transformation . Heterogn\u2009=\u200963); non-Latin American pregnant women (n\u2009=\u200930); incomplete information (n\u2009=\u200924); qualitative studies, review articles, or case reports (n\u2009=\u200924). Overall, 67 citations published until September 2022 met the established inclusion criteria and were included in the present systematic review . Studies were selected by title and abstract, resulting in the exclusion of 253,315 irrelevant studies. Of the remaining 235 citations, 27 were removed as duplicates. Thus, 208 full-text citations were evaluated for eligibility, with 141 excluded owing to unclear assessment methods or uncertain bacteriuria definitions . The prevalence of ASB in Latin American pregnant women was 18.39% (95% CI: 15.45\u201321.53) . The prevalence of lower UTI in Latin American pregnant women was 7.54% (95%CI: 4.76\u201310.87) in 10 studies comprising 5,781 participants [p\u2009=\u20090.038) . The prevalence of pyelonephritis in Latin American pregnant women was 2.34% (95% CI: 0.68\u20134.85) in five studies comprising a sample size of 4,349 participants . The prevalence of ASB in Latin American pregnant women was 13.11% (95% CI: 8.42\u201318.65) in 15 studies comprising 23,782 participants, which was lower than the previous global rate , i.e., persistent publication bias . The prevalence of ASB in Latin American pregnant women was 14.97% (95% CI: 11.10\u201319.28) in 26 studies comprising 20,896 participants .The heterogeneity rate for the prevalence of ASB in the Latin American articles, except the Brazilian articles, was high . The prevalence of ASB in Latin American pregnant women, except Brazilian women, was 12.62% (95% CI: 9.26\u201316.40) . The prevalence of ASB in Brazilian pregnant women was 23.62% (95% CI: 18.0\u201329.74) . The prevalence of ASB in Brazilian pregnant women was 19.05% (95% CI: 13.18\u201325.70) in 10 studies comprising 18,137 participants , the heterogeneity rate for the prevalence of ASB was high ; Klebsiella sp. ; Staphylococcus sp., excluding Staphylococcus aureus, ; Proteus mirabilis ; and Enterobacter sp. . This prevalence is higher than frequencies reported in international meta-analyses, including those from Ethiopia (15.37%), Africa (11.1%), and Iran (8.7%) \u2013127.Despite the current propensity to prevent unnecessary antibiotic use, screening and treatment for asymptomatic bacteriuria have become routine in almost all prenatal care guidelines. This occurs because, when the incidence of bacteriuria reaches values \u200b\u200bgreater than 2%, the cost-effectiveness of universal screening appears to be adequate to prevent the occurrence of pyelonephritis during pregnancy , 129. OuIn a broad worldwide study in 2019, Tropical Latin America had the highest worldwide UTI incidence standardized by age, with approximately 13,852.9 cases per 100,000 population. Notably, Ecuador presented the highest incidence of UTI globally, with approximately 15,511.3 cases per 100,000 population. In 2019, a global analysis of UTI revealed that the highest mortality rate was recorded in southern Latin America , and the highest number of DALYs lost was recorded in Tropical Latin America . EvaluatBetween 1990 and 2019, the global UTI incidence rate adjusted for age increased from 4,715 to 5,229 per 100,000 population, with the global death rate due to UTI increasing from 1.8 to 3.1 per 100,000 population. A comparison between three-decade-old and current data revealed an absolute increase of approximately 130,000 UTI-related deaths. Over the past three decades, the largest estimated annual percentage changes in UTI incidence rates were observed in Central Latin America and Andean Latin America , and the highest estimated annual percentage changes in UTI mortality rates were documented in southern Latin America and Tropical Latin America . Given the impact of bacterial urinary tract colonization on public health outcomes and the highest global percentage of bacteriuria prevalence documented in Latin America, it is crucial to further explore this topic [Bacteriuria is associated with some adverse perinatal outcomes. Antimicrobial treatment of bacteriuria can reduce the incidence of pyelonephritis in pregnant women , premature birth and low birth weight . There iE. coli was the most frequently isolated uropathogen in the urine cultures of Latin American pregnant women. The results of this meta-analysis corroborate documented findings in the literature, with up to a 95% frequency of E. coli noted among the total number of bacteria isolated from the urinary tract [Based on the present study, ry tract .Klebsiella sp. or Proteus sp.) [Klebsiella sp. was the second most frequently isolated bacterial species among Latin American pregnant women , followed by Proteus mirabilis as the fourth most frequently identified species in urine cultures and Enterobacter sp. as the fifth .Considering the total number of uropathogens, the second most isolated bacterial species belonged to the Enterobacteriaceae family (eus sp.) . The preStreptococcus agalactiae among the total number of uropathogens. Collin et al. have analyzed the prevalence of Lancefield group B Streptococcus in non-invasive bacterial infections worldwide. The authors identified UTI prevalence rates of 1.61% among bacterial isolates collected from the community and 0.72% among UTI bacterial isolates collected from a hospital environment [This meta-analysis supports previously reported findings regarding the frequency of ironment .Although the present systematic review with meta-analysis presents up-to-date evidence on the prevalence of bacteriuria in Latin American pregnant women, the limitations should be addressed. First, the lack of studies in southern Latin America and Central America may hinder generalization, warranting further investigation of UTIs in these regions. Second, there was significant heterogeneity in the overall pooled prevalence analysis of bacteriuria in Latin American pregnant women, a characteristic maintained in almost all subgroup analyses. Third, we noted a significant publication bias in the general assessment of the prevalence of bacteriuria among pregnant women, both in funnel plots and Egger\u2019s test, reinforcing the need for careful data interpretation. The inclusion of non-published studies in the sub-analyses helped reduce this bias.Our systematic review with meta-analysis included a total of 67 studies. Of this total research, more than a third had not been published. Of the articles published, only a few were selected in journals indexed in the main international databases. Although bacteriuria is a common topic in obstetric clinical practice, available data on Latin American pregnant women were scarce or difficult to obtain and, according to our review, at rates much higher than those from other regions and indicated by other previous studies, strengthening the value of our current research.In our study we also examined the profile of microorganisms isolated in positive urine cultures from pregnant women living in the 20 most populous countries in Latin America. This information can help in the construction of care protocols guided by the local bacterial profile, favoring treatments with lower-cost antimicrobials. There are still limitations to Latin American pregnant women's access to health services. In the most populous country in the region, Brazil, in 2021, only two thirds (76.55%) of women had access to adequate prenatal care, that is, starting in the first trimester of pregnancy and with at least six outpatient consultations . TherefoE.coli. Another frequently isolated uropathogen was S. agalactiae, with a higher prevalence than that reported in other international studies. This information is highly relevant, as maternal colonization with Lancefield group B streptococci has been associated with adverse perinatal outcomes, such as neonatal sepsis. Given the higher frequency of UTI among Latin American pregnant women, additional studies are needed to assess the effectiveness of screening protocols and better identify the different microbial sensitivity profiles of uropathogens isolated from these women.UTI and asymptomatic bacteriuria are markedly common among Latin American pregnant women. The prevalence of bacteriuria among Brazilian pregnant women tends to be higher than the mean of Latin America or other regions worldwide. These results reinforce the need for universal screening with urine culture during early prenatal care. Evidence supporting repeated screening for bacteriuria during different trimesters or gestational ages is lacking. Among Latin American pregnant women, the most common microorganism in the etiology of bacteriuria was Additional file 1:\u00a0Supp 1. Funnel plot to test the publication bias in 67 studies with 95% Confidence limits. Suppl 2. Funnel plot to test the publication bias in 10 studies with 95% Confidence limits. Supp 3. Funnel plot to test the publication bias in 5 studies with 95% Confidence limits. Supp 4. Prevalence of bacteriuria in pregnant women in Latin America, considering only articles published with samples greater than 500 individuals. Supp 5. Funnel plot to test the publication bias in 15 studies with 95% Confidence limits. Supp 6. Prevalence of bacteriuria in pregnant women in Latin America, with the exception of Brazilian articles. Supp 7. Prevalence of bacteriuria in pregnant women in Latin America, with the exception of Brazilian articles, in studies with samples greater than 200 individuals. Supp 8. Funnel plot to test the publication bias in 28 studies with 95% Confidence limits. Supp 9. Funnel plot to test the publication bias in 20 studies with 95% Confidence limits. Supp 10. Prevalence of bacteriuria in Brazilian pregnant women, considering published or unpublished studies, in studies with samples greater than 200 individuals. Supp 11 Funnel plot to test the publication bias in 10 studies with 95% Confidence limits. Supp 12. Prevalence of Escherichia coli among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 13. Prevalence of Klebsiella sp. among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 14. Prevalence of Staphilococcus sp. (exceptStaphilococcus aureus) among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 15. Prevalence of Proteus mirabilis among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 16. Prevalence of Enterobacter sp. among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 17. Prevalence of Enterococcus sp. among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 18. Prevalence of Streptococcus agalactiae among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 19. Prevalence of Staphilococcus aureus among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 20 Prevalence of Citrobacter sp. among the total number of uropathogens isolated from urine cultures of Latin American pregnant women. Supp 21. Prevalence of Pseudomonas aeruginosa among the total number of uropathogens isolated from urine cultures of Latin American pregnant women."} +{"text": "ETOAs had the lowest GTR rates , while combined ETOA and EEA had the highest CSF leak rates . ETOAs were associated with better proptosis improvement , while anatomical class I lesions were associated with better visual acuity and proptosis recovery. No significant differences were found in PFS rates between surgical approaches. Conclusion: Surgical treatment of SOMs aims to preserve visual function and improve proptosis. Different surgical approaches offer varying rates of GTR, complications, and functional outcomes. A multidisciplinary approach involving a skull base team is crucial for optimizing patient outcomes.Background: Spheno-orbital meningiomas (SOMs) are rare tumors arising from the meninges surrounding the sphenoid bone and orbital structures. Surgical resection is the primary treatment approach for SOMs. Several surgical approaches have been described during the decades, including microsurgical transcranial (MTAs), endoscopic endonasal (EEAs), endoscopic transorbital (ETOAs), and combined approaches, and the choice of surgical approach remains a topic of debate. Purpose: This systematic review and meta-analysis aim to compare the clinical and surgical outcomes of different surgical approaches used for the treatment of SOMs, discussing surgical techniques, outcomes, and factors influencing surgical decision making. Methods: A comprehensive literature review of the databases PubMed, Ovid MEDLINE, and Ovid EMBASE was conducted for articles published on the role of surgery for the treatment of SOMs until 2023. The systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. Meta-analysis was performed to estimate pooled event rates and assess heterogeneity. Fixed- and random-effects were used to assess 95% confidential intervals (CIs) of presenting symptoms, outcomes, and complications. Results: A total of 59 studies comprising 1903 patients were included in the systematic review and meta-analysis. Gross total resection (GTR) rates ranged from 23.5% for ETOAs to 59.8% for MTAs. Overall recurrence rate after surgery was 20.7%. Progression-free survival (PFS) rates at 5 and 10 years were 75.5% and 49.1%, respectively. Visual acuity and proptosis improvement rates were 57.5% and 79.3%, respectively. Postoperative cranial nerve (CN) focal deficits were observed in 20.6% of cases. The overall cerebro-spinal fluid (CSF) leak rate was 3.9%, and other complications occurred in 13.9% of cases. MTAs showed the highest GTR rates (59.8%, 95%CI = 49.5\u201370.2%; Spheno-orbital meningiomas (SOMs) are rare tumors, accounting for 0.2% and 9% of all meningiomas, arising from the meninges surrounding the sphenoid bone and orbital structures ,2. TheseSurgical resection is the primary goal in the treatment of SOMs, aiming for gross total resection (GTR) to achieve optimal oncological control. However, the choice of surgical approach can have a significant impact on the extent of resection and postoperative outcomes. Additionally, postoperative complications and progression-free survival (PFS) are important outcome measures to assess the overall success of the surgical intervention ,6.The objective of this systematic literature review and meta-analysis is to compare the clinical and surgical outcomes among patients undergoing MTAs, EEAs, ETOAs, and combined approaches for the surgical treatment of SOMs. By examining the existing evidence, this study aims to provide clinicians with valuable insights into the advantages and limitations of each approach, and facilitate evidence-based decision making in the management of these challenging tumors.The systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines . A comprFor each study, we abstracted the following baseline information: author, country, journal, title, and year of publication; design and period in which the population was collected; sample size, mean and range of age, percentage of female; histology and grade of the lesion (according to WHO classification 2021); clinical presentations, including visual acuity decrease, proptosis, cranial nerves (CNs) deficits, and other signs and symptoms; number and percentages of patient who received gross total resections, adjuvant radiotherapy (RT), other adjuvant therapies; follow-up period.Outcomes were meta-analyzed based on the type of surgical approach . The outcomes were also tested to evaluate any statistically significant differences according to the anatomical site and extension of the SOM and according to the WHO grade . Based on site, SOMs were divided into four categories, specifically, superior or superolateral, inferior or inferomedial, apex, and diffuse.Our primary outcomes were GTR, progression-free survival at 5 years (PFS 5-y) and at 10 years (PFS 10-y), and recurrences rate. Secondary outcomes were improvement of visual acuity, improvement of proptosis, postoperative CNs deficits, postoperative cerebrospinal fluid (CSF) leak, and other complications.We modified the Newcastle\u2013Ottawa scale (NOS) to assess the methodologic quality of the studies included in our meta-analysis. This tool is designed for use in comparative studies. However, as there was no control group in our studies, we assessed their methodologic quality based on selected items from the scale, focusing on the following questions: (1) Did the study include all patients or consecutive patients vs. a selected sample? (2) Was the study retrospective or prospective? (3) Was clinical follow-up satisfactory, thus allowing ascertainment of all outcomes? (4) Were outcomes reported? (5) Were there clearly defined inclusion and exclusion criteria? .p values. The level of statistical significance was set to p < 0.05. Meta-regression was not used in this study. Statistical analyses were performed using OpenMeta Analyst http://www.cebm.brown.edu/openmeta accessed on 20 June 2023) and the R statistical package v3.4.1 http://www.r-project.org (accessed on 20 June 2023).Descriptive statistics were reported, including ranges and percentages. For the purpose of the meta-analysis, we estimated from each cohort the cumulative prevalence and 95% confidence interval for each outcome. Event rates were pooled across studies with a random-effects meta-analysis. Heterogeneity across studies was evaluated using the I2 statistic. An I2 value of >50% suggests substantial heterogeneity. For formal statistical comparisons and subgroup analysis, we also extracted a chi-square contingency table to calculate A total of 157 papers were identified after duplicate removal. After title and abstract analysis, 94 articles were identified for full-text analysis. Eligibility was ascertained for 82 articles. The remaining 23 articles were excluded for the following reasons: (1) not relevant to the research topic (16 articles), (2) not in English (1 article), lack of method details (3 articles), systematic literature review or meta-analysis (3 articles). All studies included in the analysis had at least one or more outcome measures available for one or more of the patient groups analyzed. A summary of the included studies is provided in p = 0.001) and 78.6% , while lesions treated through ETOA combined with EEA and WHO grade I lesions had the lowest GTR rate at 23.5% and 43.1% . Overall recurrence rates were reported in 1409 patients. The overall rate of recurrence following SOMs resection through any surgical approach was 20.7% (95%CI = 16.6\u201324.8%). p = 0.014). The overall rates of PFS 5-y and PFS 10-y were reported in 230 and 159 patients, and were 75.5% (95%CI = 70\u201381.1%) and 49.1% (95%CI = 41.3\u201356.8%), respectively. The overall rates of visual acuity and proptosis improvement were reported in 910 and 1132 patients and were 57.5% (95%CI = 51.7\u201363.3%) and 79.3% (95%CI = 73.7\u201384.8%), respectively. p = 0.003). Lesions treated through the ETOA and anatomical class I lesions had the highest proptosis improvement rates at and 79.4% , respectively.Overall GTR rates were reported in 1542 patients. The overall rate of GTR following SOMs resection through any surgical approach was 57.3% (95%CI = 47.5\u201367.1%). Lesions treated through the MTA and anatomical class I lesions had the highest GTR rate at 59.8% and was the lowest for lesions treated through the MTA . Other complication rates were reported in 1181 patients. The overall rate was 13.9% (95%CI = 10.1\u201317.7%). The rate of other complications was the lowest for WHO grade I and II lesions . The efficacy and safety outcomes are summarized in Overall CN focal deficits and CSF leak rates were reported in 763 and 517 patients, respectively. The overall rate of CN focal deficits was 20.6% (95%CI = 14.9\u201326.3%). The lowest rate was reported for lesions treated through the ETOA and the highest rate was reported for lesions treated through the MTA . The overall rate of CSF leak was 3.9% (95%CI = 2.3\u20135.5%). The CSF leak rate was highest for lesions treated through the combined ETOA and EEA (20.3%; 95%CI = 0\u201346.7%; The I2 values were >50%, indicating substantial heterogeneity for the following outcomes: GTR, recurrence, visual acuity improvement, proptosis improvement, CN focal deficits, and other complications. The I2 values were <50%, indicating a lack of substantial heterogeneity for the following outcomes: PFS 5-y, PFS 10-y, and CSF leak.As far as we know, this is the largest systematic literature review and meta-analysis available in the literature. Clinical and surgical outcomes of SOMs surgically treated have been analyzed. According to our findings, SOMs treated through the MTAs and anatomical class I lesions had the highest GTR rate, while ETOAs either as single or combined approach with EEAs offered the lowest GTR rate. On the other hand, MTAs presented the higher recurrence rates, and no statistically significant differences were detected between the different approaches regarding the PFS 5-y and PFS 10-y. Anatomical class I SOMs and SOMs treated with ETOA showed better rates of postoperative vision acuity and proptosis improvement. MTAs are more prone to postoperative CNs deficits, while combined ETOA and EEA have the highest rate of postoperative CSF leaks.MTAs are commonly utilized for the surgical treatment of SOMs, with the pterional approach being the most frequently employed . MTAs ofSOMs manifest as the expansion of the sphenoid bone, extending into the orbit and causing hyperostosis . These tAccording to the literature, proptosis is the most frequently observed preoperative finding and indication for surgery, with a reported occurrence rate of 45\u2013100%. Postoperatively, proptosis improvement has been documented in 52\u2013100% of patients ,34,43,64The patient\u2019s prognosis and quality of life heavily depend on visual acuity, rendering it a crucial clinical outcome for SOM patients . To imprComplications following surgery for SOMs commonly include deficits in extraocular movements and trigeminal hypoesthesia . PreviouOver the past three decades, the surgical management of SOMs has undergone signif icant evolution, resulting in improved outcomes and reduced morbidity for patients. In the early 1990s, surgical approaches often involved extensive craniotomies and aggressive tumor resections, aiming to achieve complete tumor removal . While t75 Preliminary evidence suggests that RT may contribute to prolonged PFS, but the decision to administer RT should be carefully evaluated, considering factors such as age, tumor size, and pathology of the residual tumor [Both recent studies and those conducted over 20 years ago provide evidence supporting the utilization of RT for subtotally resected meningiomas, demonstrating improved overall survival and PFS compared to surgery alone ,68,69,70al tumor ,20.There are several limitations to the study. This meta-analysis was based primarily on single-center case series and, thus, has limitations inherent to single-center retrospective studies. While we were able to perform subgroup, analyses based on the surgical approach used, we were unable to perform more granular analyses stratifying outcomes by each WHO grade and anatomical class. Nonetheless, our study provides helpful information for providers who are considering surgery for the treatment of SOMs and provides guidance for future areas of investigation.The limitations of this review stem from a dearth of high-quality studies and significant heterogeneity among those included, which may have constrained our ability to derive definitive conclusions. Moreover, we cannot disregard the possibility of publication bias, as studies reporting positive outcomes or statistically significant results tend to be more readily published. Such bias may have influenced the overall summary effect estimate, potentially leading to an overestimation of the treatment effect. Furthermore, our search strategy may have introduced limitations despite our comprehensive efforts; it is conceivable that some pertinent studies were inadvertently overlooked. Language restrictions and the exclusion of unpublished research may have also contributed to potential bias. Lastly, it is essential to consider the generalizability of our findings. The included studies may pertain to specific populations, interventions, or settings, thus potentially limiting the applicability of our results to other populations or clinical contexts.Performing surgery for SOMs is intricate and challenging due to the tumor\u2019s diffuse nature and its proximity to critical structures. The goals of surgical treatment for SOMs have undergone an evolution. Presently, the primary objective of surgical intervention is to safeguard visual function and ameliorate proptosis, rather than pursuing complete tumor resection. When visual compromise is evident, surgery has the potential to enhance and stabilize visual function.To optimize patient outcomes, a multidisciplinary approach involving a skull base team is essential. This team comprises neurosurgeons, ophthalmologists, otorhinolaryngologists, maxillofacial surgeons, and radiologists. Their collaborative efforts yield several advantages, including early detection of optic nerve compromise, preoperative and postoperative evidence-based management, and improved surgical resection and clinical outcomes facilitated by the combined expertise of the team members."} +{"text": "Cancer is a major cause of mortality and a major contributor to health care costs in the United States. An increasing number of cancer patients are treated with oral cancer therapy. Older patients are more likely to have cancer and to be at risk for adherence problems with oral cancer drugs. As a result of substantial cost sharing required for oral cancer drugs and the possibility of early entry into the Medicare Part D coverage gap, high out-of-pocket (OOP) drug costs could put elderly beneficiaries at great risk for delaying or discontinuing their cancer therapies.To (a) determine the OOP costs of oral cancer treatment and the numbers of patients that delay or discontinue oral cancer therapy and (b) examine the relationship between OOP costs and medication discontinuation or delay among older Medicare beneficiaries.A cross-sectional study was conducted using a 5% sample of Medicare beneficiaries who filled a prescription for imatinib, erlotinib, anastrozole, letrozole, or thalidomide during 2008. Patients included in the analysis sample did not receive drug subsidies, were aged 65 years or older, and were enrolled in Medicare Part D for all 12 months of 2008. Logistic regression was used to determine the association between OOP costs and medication discontinuation or delay.Mean OOP costs per day were $2.96 for anastrozole, $3.10 for letrozole, $22.90 for imatinib, $28.35 for erlotinib, and $37.47 for thalidomide. The percentages of patients who discontinued or delayed oral cancer therapy were 58% for anastrozole, 64% for letrozole, 35% for imatinib, 61% for erlotinib, and 70% for thalidomide. For each $10 increase in OOP spending per month, the likelihood of discontinuation or delay increased 13%, 14%, and 20% for imatinib, erlotinib, and thalidomide users, respectively, but decreased 26% for anastrozole and letrozole users.Beneficiaries with higher OOP costs for the more expensive oral cancer drugs were more likely to discontinue or delay drug therapy."} +{"text": "Primary total knee arthroplasty (TKA) is a preferred treatment for end-stage knee osteoarthritis. In the setting of a failed TKA, revision total knee arthroplasty (rTKA) acts as a salvage procedure and carries a higher risk compared to primary TKA. Given increased interest in postoperative outcomes from these procedures, a thorough understanding of the demographics, comorbidities, and inpatient outcomes is warranted. This study aimed to report the epidemiological data of demographics, comorbidity profiles and outcomes of patients undergoing TKA and rTKA.A retrospective review of NIS registry discharge data from 2006 to 2015 third quarter was performed. This study included adults aged 40 and older who underwent TKA or rTKA. A total of 5,901,057 TKA patients and 465,968 rTKA patients were included in this study. Simple descriptive statistics were used to present variables on demographics, medical comorbidities, and postoperative complications.vs. 25.05%).A total of 5,901,057 TKA and 465,968 rTKA discharges were included in this study, with an average age of 66.30 and 66.56\u00a0years, and the major payor being Medicare, accounting for 55.34% and 59.88% of TKA and rTKA cases, respectively. Infection (24.62%) was the most frequent reason for rTKA, and was followed by mechanical complications (18.62%) and dislocation (7.67%). The most common medical comorbidities for both groups were hypertension, obesity, and diabetes. All types of inpatient complications were reported in 22.21% TKA and 28.78% of rTKA cases. Postoperative anemia was the most common complication in both groups (20.34% Our data demonstrated a 41.9% increase in patients receiving TKA and 28.8% increase in rTKA from the years 2006 to 2014. The data showed a 22.21% and a 28.78% \u201ccomplication\u201d rate with TKA and rTKA, with postoperative anemia being the most common complication. The top 3 medical comorbidities were hypertension, obesity, and diabetes for both groups and with increased focus on perioperative optimization, future analyses into preoperative medical optimization, and improved primary arthroplasty protocol may result in improved postoperative outcomes. Primary total knee arthroplasty (TKA) is an effective procedure to improve function and provide pain relief in patients with advanced osteoarthritis . ArthritTKA ranked as the second most common procedure performed in the US in 2018, with a 134% increase from 2005 . RevisioHealthcare systems shifted focus towards minimizing cost while improving quality of delivered care as a continued trend throughout the last decade towards the conceptualization of value-based care. The implementation of systematic perioperative care pathways, such as the Enhanced Recovery After Surgery Society's protocols, demonstrated reduced LOS and increasing home discharge . DespiteThe aim of this study was to provide a thorough understanding of the comorbidity profile, demographics, and in-hospital outcomes of TKA and rTKA recipients. Furthermore, the indications for rTKA and type of revision performed during the study duration in the United States were reported. Through this report, the authors aimed to provide an in-depth understanding of medical comorbidities and demographics of patients undergoing TKA and rTKA, which could form a critical starting point to design effective optimization protocols for this population.A retrospective analysis of data collected from the National Inpatient Sample (NIS) was performed using discharge data from the years 2006 through the third quarter of 2015. The NIS database comprises a stratified 20% sample of inpatient stays within the United States and contains demographic information, comorbidity profiles, and in-hospital outcomes. Specifically, to rTKA, it also includes types and reasons for revision surgery. The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) was used to search for procedure and diagnosis codes within the NIS. We elected to exclude patients from the fourth quarter of 2015 as an effort to maintain integrity of the methodology and homogeneity of the database, as the NIS had transitioned to the ICD-10 coding system starting in that quarter. Patients were identified with ICD code 81.54 or 81.55 . Reasons for revision were also included with the use of ICD codes: 996.42 (dislocation/instability), 996.41 , 996.66 (infection), 996.43 (implant failure), 996.45 (periprosthetic osteolysis), 996.44 (periprosthetic fracture), 996.46 (bearing surface wear), 996.47 and 996.49 . We chose to combine \"other mechanical problems\" and \"other mechanical complications\" into one category in the results. The type of revision was also included with ICD codes: 00.80 , 80.06 , 00.84 , 00.81 , 00.83 (patellar), 00.82 , and 81.55 . All patients aged 40\u00a0years or older were included in this study to provide a representative national sample of typical patients undergoing the procedures.vs. non-elective admission, as well as region and bed size of hospital. In-hospital outcome data harvested included average cost, LOS, and complications during the inpatient stay as reported in the database. This dataset includes cardiac complications, respiratory complications, peripheral vascular disease (PVD) complications, hematoma/seroma, wound dehiscence, postoperative infection, gastrointestinal complication, genitourinary complication, deep vein thrombosis, pulmonary embolism or postoperative anemia, which collectively are referred to as \"any complications\". A comorbidity profile using the Elixhauser comorbidity index, which is frequently used in database studies to evaluate patient comorbidities, is presented to highlight the common medical comorbidities with potential impact on postoperative outcomes [Demographic data collected included calendar year, age, race, sex, primary payor, elective outcomes .A total of 5,901,057 TKA and 465,968 rTKA discharges were included in this study. The average age in the TKA and rTKA groups was 66.30 and 66.56\u00a0years, respectively. The major payor was Medicare at 55.34% and 59.88% of TKA and rTKA cases, respectively. Non-Hispanic whites were the majority race receiving TKA and rTKA discharges at 71.25% and 70.96% of discharges, respectively.Overall, there was an increase of 41.81% and 28.79% in TKA and rTKA procedures from the year 2006 to 2014. The decrease in 2015 can be attributed to our methodology, which did not include the 4th quarter data. Figure\u00a0Hypertension was the most common comorbidity in both TKA and rTKA groups, accounting for 67.74% and 65.04%. The five most prevalent comorbidities in the TKA group were hypertension (67.74%), obesity 21.73%), uncomplicated diabetes (19.83%), hypothyroidism (15.57%) and chronic pulmonary disease (14.79%). The five most prevalent comorbidities in the rTKA group included hypertension (65.04%), obesity (22.98%), uncomplicated diabetes (19.82%), chronic pulmonary disease (16.54%) and deficiency anemia (15.67%). The full Elixhauser comorbidity profile for both TKA and rTKA is summarized in Table 1.73%, unAny complication occurred after TKA in 22.21% of cases and after rTKA in 28.78%. The most common complication for both TKA and rTKA was postoperative anemia, making up 20.34% and 25.05% respectively. In terms of cost, TKA had a total cost of $49,789 with an average LOS of 3.22\u00a0days while rTKA incurred a total cost of $71,872, with an average LOS of 4.44\u00a0days. Table Total joint infection 24.62%) was the most common reason for rTKA. This was followed by mechanical loosening (19.74%), and other mechanical complications (18.62%). With regard to type of revision, the majority of patients underwent revision of all components (37.23%). The tibial component (20.75%) was revised more often than the insert or femoral component . The reason and type of rTKA are summarized in Tables .62% was TKA volume in the US is projected to increase 153% from 2012 to 2050 . As prim. between 2005\u20132006, which identified infection as the most common cause of revision, accounting for 25.2% of all revisions [Despite the widespread success of TKA in treating end-stage osteoarthritis, failed TKA and the need for subsequent revisions present a significant burden to the healthcare system and patients' quality of life. This study demonstrated a 28.79% increase between 2006 to 2014 in rTKA incidence, with infection remaining the most common reason for rTKA and accounting for 24.62% of all revisions. This was similar to an epidemiological study from Bozic et alevisions . Their sevisions . As to mDemographic variables of this study were similar to previously reported age, gender distribution, hospital size, and location/teaching status of hospital . Our stuThis study reported on the comorbidities that constitute the Elixhauser comorbidity index, which has been proven to be a superior tool for outcome prediction at population level through extensive utilization in epidemiologic studies , 18, 19.. demonstrated morbid obesity was associated with higher complication rates, lower implant survivorship, and lower postoperative function scores, suggesting a BMI of 40 as a cutoff to guide perioperative optimization [Obesity has been extensively studied as a comorbidity in TKA . In thismization . Future . demonstrated a significantly higher readmission risk with uncontrolled diabetes in Medicare recipients. The authors suggested diabetes and associated systemic complications should be included in reimbursement models [. found that optimization of medical comorbidities by screening demonstrated patients had shorter average LOS and lower costs following total joint arthroplasty [Diabetes, as a preoperative comorbidity, has been shown to affect post-TKA outcomes. Na et alt models . The efft models . Optimizroplasty .. utilized an artificial neural network trained with NIS patient variables to predict LOS, total cost, and discharge disposition [Recently, machine learning algorithms have been gaining popularity in the prediction of postoperative outcomes after TKA , 25. ComSimilar to other large registry cross-sectional studies, this study has several limitations. While the NIS supplies vast data on healthcare resource utilization at a population derived level, there are errors inherent to suboptimal coding and manual entry of data . AlthougDespite the inherent database limitations, this study presented the largest available population level report stratifying medical comorbidities of TKA and rTKA patients. The duration of the study and volume of data provided an in-depth inquiry of demographics, medical comorbidities, postoperative clinical and economic outcomes following TKA and rTKA. The comprehensive information provided allows for a generalizable understanding of perioperative comorbidities to facilitate future studies to further understand the demographics and medical comorbidities among TKA and rTKA recipients. This study aimed to achieve a baseline understanding of common perioperative conditions that have a potential impact on postoperative outcomes.In conclusion, this study analyzed the epidemiological and demographic characteristics of TKA and rTKA recipients between 2006\u20132015. There was an increase of 41.9% and 28.8% in TKA and rTKA procedures, respectively. This study demonstrated anemia had a 22.21% and a 28.78% in-patient rate of occurrence with TKA and rTKA, and was the most commonly reported complication. As focus is increasingly placed on value-based care with optimization of care delivery and minimization of medical waste, a thorough understanding of patient comorbidities is critical to developing care protocol pathways to systematically improve outcomes. This study highlights important areas for future studies on targeted interventions for various patients undergoing TKA or rTKA."} +{"text": "The U.S. President\u2019s Emergency Plan for AIDS Relief (PEPFAR) prioritizes infection prevention and control (IPC) activities in its 40,000 supported facilities in over 50 countries. PEPFAR\u2019s 2015 quality assurance tool included four IPC indicators . In 2022, four new IPC indicators were added . As of October 2022, PEPFAR programs are required to assess IPC indicators in 10% of facilities over the course of one year. We report quarter one data results.Indicator data from October 1 - December 31, 2022 were analyzed. Scores were calculated based on compliance with 2-4 criteria each: green, yellow, and red represented good, fair, and poor compliance, respectively. Percentages of yellow and red scores were combined, to represent the percent of facilities requiring improvement.A total of 272 sites were assessed across 15 countries; each PEPFAR program selects the indicators to assess in each site. For existing indicators , 16%, 34%, 22%, and 57% of sites assessed scored red or yellow, respectively; for indicators added in 2022 , 74%, 67%, 64%, and 61% scored red or yellow, respectively . Specific gaps include: 63% of facilities lack adequate IPC leadership; \u223c50% lack adequate environmental cleaning staff, protocols, and methods; 41% lack respirators; 30% lack device reprocessing protocols.Unknown IPC weaknesses were identified in PEPFAR supported facilities. PEPFAR requires that facilities with fair or poor compliance be reassessed within six months to monitor improvements. Strengthening IPC leadership is a priority. Improvement activities will require collaboration between facilities, implementing partners, and Ministries of Health (MOH). Future plans include increasing compliance with conducting required IPC indicator assessments; timely, data driven identification of gaps and advancements towards IPC standards; and developing guidance and resources to facilitate improvements. MOHs can leverage data to inform priorities and design context-specific interventions.All Authors: No reported disclosures"} +{"text": "Introduction: Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder, mainly in children. The signs and symptoms of ADHD include inattention, impulsivity, and hyperactivity. Consequently, Childhood Absence Epilepsy (CAE) tends to present in children with sudden and recurrent episodes of loss of awareness alongside symptoms that occasionally include clonic, atonic, and simple automatisms. The present study evaluates parents' knowledge in Makkah regarding the difference between ADHD and CAE.Methodology: The study was conducted among Saudi Arabian parents living in Makkah. Data were collected in April 2022 through the use of an online survey that was distributed electronically via social media platforms. The inclusion criteria entailed parents from different socio-economic backgrounds. In contrast, the exclusion criteria entailed parents who had not been involved in raising their children and those with children with intellectual disabilities. A group of consultants was tasked with validating all data collected through an original questionnaire. To effectively calculate the study sample size, OpenEpi Version 3.01 was used. Lastly, all statistical analyses were conducted with Stata Social Sciences (SPSS\u00ae) software for Mac, version 26 .Results: A total of 633 participants completed the survey. Of the total respondents, approximately 1% indicated having a good knowledge level, 15.17% indicated having moderate knowledge, and the remaining 84% indicated poor knowledge of the subject under study. Approximately 46% of the participants reported that social media was the primary source of information. One significant issue regards the observation that the parent's level of education was statistically associated with the level of knowledge.Conclusion: There is limited awareness of the difference between (ADHD) and (CAE) among parents in the pediatric population. These findings highlight an opportunity to raise awareness using well-organized education programs in Makkah City. Attention deficit hyperactivity disorder (ADHD) is a common neurodevelopmental disorder that affects children and often continues into adulthood. The symptoms of ADHD include patients experiencing difficulties paying attention and the inability to control impulsive behaviors by acting without thinking about the consequences or hyperactivity . The preConsequently, CAE refers to the sudden and recurrent episodes of loss of awareness infrequently accompanied by clonic, atonic, or simple automatisms or autonomic components. Two types of CAE exist, namely, typical and atypical. Approximately 10% of children with epilepsy tend to have typical CAE. The prevalence rate of CAE in the general population is 5 to 50/per 100,000. Comparable figures have been disclosed by studies conducted in the US (Connecticut) and Europe-based .As previously mentioned, CAE and ADHD are two completely different disorders. For instance, the observed differences include the view that in the CAE, the episodes are always accompanied by eyelid fluttering and jerky muscle movement . In ADHDThis article was previously posted to the 18th PAN Arab & 13th GCC & 26th SNS conferences on January 12-14, 2023.Study population and sampling methodologyThe present study is a\u00a0community-based cross-sectional descriptive research conducted in Makkah City, Saudi Arabia, among parents living there. Parents from different socioeconomic statuses, both males and females, who agreed to partake in the study were included. Further, participants who were not involved in raising their children and parents with children suffering from intellectual disabilities were excluded. Data were collected in April 2022 using an original online questionnaire that a selected group of consultants validated. The survey was formulated in Arabic and English and completed using Google Forms. The survey was also distributed electronically through various social media platforms. A total of 632 participants completed and delivered the study.The questionnaire was organized into sections that included the participants' sociodemographic data, the assessment of the participant's knowledge of ADHD and CAE, and the participants' source of information about both conditions. The responses from the participants were collected as either yes or no, multiple choice, and written answers. Still, the knowledge levels were categorized as a poor level of knowledge (0-60%), moderate knowledge level (60 - 79%), and good knowledge level (80 - 100%). The original questionnaire used in this study is provided in the appendix section.Data analysisFor the present study, data were analyzed using the Statistical Package for Social Sciences (SPSS\u00ae) software for Mac, version 26 . To analyze the numerical variables, the authors used the t-test and chi-square test in analyzing the categorical data. The 95% confidence intervals and P-values were reported for every variable included. Moreover, the present study's P-value was < 0.05 for statistical significance.\u00a0Ethical considerationsFor the present study, ethical approval was provided by the Institutional Review Board (IRB) of UQU (No. HAPO-02-K-012-2022-04-1049). Further, consent was obtained electronically from all participants following an explanation of the study's aims and objectives.DemographicsA total of 632 study participants completed and returned their questionnaires. Females formed the most significant proportion of the participants at 68.2%. Most of the study participants, 33.86%, were aged between 18 and 28. Concerning the participants' place of residence, 82.75% reported that they were residing in Makkah. Still, 85.13% of the participants reported being married, even as 67.25% noted they held a bachelor's degree. A more significant proportion of the participants, 42.25%, were employed even as 31.06% reported having incomes ranging between 5000 and 10000SR. Table\u00a0Awareness levelsThe awareness levels of CAE and ADHD were divided into three categories: good, moderate, and poor.Gender\u00a0The study's findings indicated that, of the female participants, 82.59% had poor awareness levels, 16.47% showed moderate awareness levels, and 0.92% portrayed good awareness levels. None of the male participants' groups showed an excellent awareness level, even as 12.43% showed a moderate awareness level and 87.56% showed poor awareness.Social statusRegarding marital status, of the divorced participants, 0.55% indicated good knowledge and awareness levels, 16.35% indicated moderate knowledge and awareness, and 83.08% indicated poor knowledge and awareness levels. Consequently, among the married participants, none indicated good familiarity and awareness levels, 9.3% indicated having moderate knowledge and awareness levels, and 90.69% indicated poor knowledge and awareness levels. Further, 1.96% of the widows' participants had good knowledge and awareness levels, 7.84% had moderate knowledge, and 90.19% had poor knowledge and awareness. The P value was 0.237. Nevertheless, the overall results showed that 0.79% presented good familiarity and awareness levels even as 15.17% had moderate knowledge and awareness levels, and 84.4% had poor knowledge and awareness levels.\u00a0Age category\u00a0The number of participants who displayed a poor level of awareness was highest among participants aged between 18 and 28 years at 85.51%. Consequently, 13.55% and 0.93% of the participants showed moderate and reasonable levels of awareness, respectively. Similar results regarding participants aged 29 to 39 were observed, given that 0.62% indicated good awareness levels, 15.62% showed moderate awareness, and 83.75% displayed poor awareness. A more significant proportion of participants aged between 40 and 50 indicated an insufficient level of awareness at 84.02%. In comparison, a small proportion portrayed a moderate level of understanding at 15.38%, and 0.59% portrayed an excellent level of awareness. None of the participants aged between 51 and 61 indicated a good level of understanding, even as 17.72% of them portrayed moderate awareness levels and 82.27% indicated poor awareness levels. Additionally, none of the participants above 62 years of age had a good level of awareness, even as 20% showed moderate awareness levels, and the remaining 80% indicated poor awareness levels.Home residenceRegarding residency awareness among individuals residing in Makkah, the results indicated no participant had good awareness levels. In contrast, 11.92% of the participants portrayed moderate knowledge levels, and 88.07% had poor knowledge levels. However, among the participants residing outside Makkah, 0.76% had good knowledge levels, 15.86% had moderate knowledge levels, and 83.36% had poor knowledge levels. The p-value was 0.369.Educational levelThe highest proportion of participants who displayed a poor awareness level included those with general high school/middle school education at 85.17%, followed by those bachelor's degree education level at 85.91%, those with master's degree and above education level at 72.41%, and lastly the illiterate at 85.71%. Also, the highest proportion of participants who displayed a moderate awareness level was general high school/middle school level of education at 14.58%, followed by bachelor's degree level of education at 13.38%, master's degree and above level of education at 24.13%, and the illiterate at 14.28%. However, participants with master's degrees education level presented the highest rate of a good level of awareness at 3.44%, which was followed by bachelor's degree holders at 0.73%, general high school/middle school level of education at 0.23%, and the illiterate at 0%. The above result was analyzed and found to be statistically significant (P < 0.045)\u00a0Income and employment statusRegarding the existing correlation between income and awareness levels, it was noted that 0.85% of participants who were employed with incomes that ranged from 10000 to15000 SR presented good knowledge and awareness levels, 9.4% of them presented moderate knowledge and awareness levels, and 89.74% presented poor knowledge and awareness levels. Consequently, regarding the employed participants with incomes ranging from 5000 to 10000 SR, it was noted that 0.51% presented good knowledge and awareness level, 15.81% showed moderate knowledge and awareness level, and 83.67% showed poor knowledge and awareness level. Nevertheless, regarding participants whose earnings were below 5000 SR, it was noted that 1.22% presented good familiarity and awareness levels, 17.17% showed moderate knowledge and awareness level, and 81.59% showed poor knowledge and awareness level. Although none of the participants earning incomes above 15,000 SR presented good familiarity and awareness levels, 16.77% portrayed moderate knowledge and awareness level, while 83.22% showed poor knowledge and awareness level. The p-value was 0.433.Still, regarding the participants' employment status, it was noted that no unemployed participant portrayed good knowledge and awareness level, even though 13.33% of the unemployed participants presented moderate knowledge and awareness level, and 86.66% portrayed poor knowledge and awareness level. Consequently, 0.74% of the employed participants showed good knowledge and awareness level, 15.73 presented moderate knowledge and awareness level, and 83.52% portrayed poor knowledge and awareness level. Regarding the students, it was observed that 0.78% showed good knowledge and awareness levels, 14.17% had moderate awareness levels, and 85.03% had poor awareness levels. Lastly, 2.32% of the retired participants presented a good awareness level, 23.25% had a moderate awareness level, and 74.41% portrayed a poor one. The p-value was 0.384 , doctors (2.69%), television and newspapers 3.64%), and personal experience (0.63%). Nevertheless, 20.73% of the participants needed information regarding these topics between educational level and the awareness level of ADHD and CAE. For instance, master's degree holders were observed to have the highest rate of good awareness level status (n=2). In contrast, individuals with general high school/middle school education had the highest rate of moderate awareness level (n=62). They were followed immediately by participants with a bachelor's degree education level who portrayed a moderate level of 19 out of 142. In this regard, it can be noted that master's degree holders have solid academic backgrounds and knowledge acquired through their careers, including various scientific research methods and academic appraisal of various research papers and sources. Such academic accomplishments and career experiences have been acknowledged to generate increasingly knowledgeable individuals capable of effectively applying such skills in various situations. This is also a strong indicator of the reason underlying higher ratings regarding good ADHD and CAE awareness levels.A larger proportion of the younger age participants fell into the general high school/middle school education level category, which clarifies why they were highly rated in the moderate awareness level status category, as previously observed. On the contrary, the bachelor's degree holders were rated second in the moderate awareness level category despite making up the biggest proportion of the study sample, at 67%. The underlying rationale for the rating includes the divergent learning approaches between the two groups, even as the younger generation is increasingly open to accessing and acquiring information outside their fields. Generally, poor awareness level rates were observed in every group, corroborating previous studies' findings -10. For Owing to the observation that the target group was mainly individuals/parents residing in Makkah City, for the present study, a four-fold increment in the responses from Makkah was observed compared to responses received from participants living outside Makkah. The researchers discovered no considerable correlations between ADHD and CAE awareness levels and the other demographic data, including age, sex, residence, income, employment status, and marital status. As indicated by the study findings, 84% of parents residing in Makkah City presented poor awareness and knowledge levels, despite the observation that social awareness is a vital aspect impacting early diagnosis of ADHD and CAE in children, leading to improved education performance and general well-being. Such low awareness levels may be improved with future awareness campaigns alongside health awareness programs. Further, the study findings have disclosed that a larger proportion of the participants utilized social media as the main source of information that could be used to spread knowledge regarding ADHD and CAE awareness.LimitationsThe notable limitations of the present study include the observation that it was conducted using an original online questionnaire, which might affect the validity of the responses. Also, there needs to be more previous research and literature regarding these two topics, especially CAE, which carted a need for comparison data. Finally, the study sample size is small compared to the general Saudi population, so the results can only be generalized to some Saudi populations.From the outcomes of the present study, one may conclude that the awareness and knowledge about ADHD and CAE among parents residing in Makkah City remain suboptimal. Such poor awareness and knowledge of the two conditions are likely to have a negative effect on children suffering from the condition, their communities and families, and the education and healthcare systems. As such, there is an urgent need to increase and regulate awareness campaigns on ADHD and CAE through mass media and various educational programs. This will enable filling gaps within the community knowledge regarding ADHD and CAE.The researchers recommend a country-wide study to attain more valid and generalizable results. Further, it is recommended that prospective studies should include larger sample sizes and populations drawn from different parts of Saudi to increase the validity and generalizability of the findings."} +{"text": "Staphylococcus aureus bacteremia (SAB) source is often unclear. One of the most common origins of SAB is cutaneous wounds and intravascular catheter-related bloodstream infection (CRBSI). Moreover, as our study group previously described, abscess formation and SAB following intramuscular injections are rare but possible complications from vaccines/inoculations. After an initial period of heightened SAB due to COVID-19 vaccines, we noticed a reversal of this circumstance.In this case series, we present a cohort of 100 patients with SAB from January 1, 2021 through April 24, 2023, attended in our Institution . We identified the SAB association with previous events, and the change in the recent paradigm of its genesis.During the study period, 100 SAB were identified. 85/100 patients were COVID-19 vaccinated. 64% were male and the rest were female. We identified the source of SAB in 90% of cases: in 12% (12/100) it clearly was a previously recent intramuscular vaccine . All-inclusive, the emergence of SAB was represented as follows: 24% from CRBSI, 23% from skin and soft tissue infections (SSTI), 11% - urinary tract infections (UTI), 10% - respiratory tract infections (RTI), 5% - endovascular reservoirs, 3% from postoperative complications in trauma surgery; septic mouth and bacterial parotiditis were responsible for one case (1% each). Finally, we were not able to identify 10% of the bacteremic fount. Overall, 54 patients died - 54% (46 deaths directly related to the SAB \u2013 85.2%).SAB always implies an outstanding risk due to its potential complications. Although we previously found an increased incidence of SAB related to COVID-19 vaccines, common causes such as CRBSI and SSTI, are now restored as usual sources. Nevertheless, mortality remains still high amongst our patients.All Authors: No reported disclosures"} +{"text": "From the 2019\u201320 to the 2021\u201322 school year, national coverage with state-required vaccines among kindergartners declined from 95% to approximately 93%, ranging from 92.7% for diphtheria, tetanus, and acellular pertussis vaccine (DTaP) to 93.1% for polio.During the 2022\u201323 school year, coverage remained near 93% for all reported vaccines, ranging from 92.7% for DTaP to 93.1% for measles, mumps, and rubella and polio. The exemption rate increased 0.4 percentage points to 3.0%. Exemptions increased in 41 states, exceeding 5% in 10 states. Exemptions >5% limit the level of achievable vaccination coverage, which increases the risk for outbreaks of vaccine-preventable diseases. Vaccination before school entry or during provisional enrollment periods could reduce exemptions resulting from barriers to vaccination during the COVID-19 pandemic.U.S. states and local jurisdictions set vaccination requirements for school attendance and conditions and procedures for exemptions from these requirements. States annually report data to CDC on the number of children in kindergarten who meet, are exempt from, or are in the process of meeting requirements. National- and state-level estimates for complete vaccination with measles, mumps, and rubella vaccine (MMR); diphtheria, tetanus, and acellular pertussis vaccine (DTaP); poliovirus vaccine (polio); and varicella vaccine (VAR); exemptions from vaccination; and legally allowed kindergarten attendance while meeting requirements were based on data reported by 49 states and the District of Columbia (DC) for the 2022\u201323 school year. This kindergarten class became age-eligible to complete most state-required vaccinations during the COVID-19 pandemic. National coverage remained near 93% for all vaccines; exemptions were low but increased to 3%, compared with those during the 2021\u201322 school year (2.6%). At the state level, coverage with MMR, DTaP, polio, and VAR decreased in 29, 31, 28, and 25 states, respectively, compared with coverage during the 2021\u201322 school year. Exemptions increased in 40 states and DC, with 10 states reporting an exemption from at least one vaccine for >5% of kindergartners. Schools and providers should work to ensure that students are vaccinated before school entry, such as during the enrollment process, which is often several months before school starts. State and local provisional enrollment periods that allow students to attend school while on a catch-up schedule also provide the opportunity to fully vaccinate students and to prevent nonmedical exemptions resulting from lingering undervaccination due to COVID-19 pandemic\u2013related barriers to vaccination, such as reduced access to vaccination appointments.State and local school vaccination requirements promote vaccination to protect students, schools, and communities against vaccine-preventable diseases . Kindergartners were considered up to date with a given vaccine if they received all doses for that vaccine required for school entry, except in nine statesNational estimates, medians, and summary measures include only U.S. states and DC. Vaccination coverage and exemption estimates were adjusted on the basis of survey type and response rate.https://stacks.cdc.gov/view/cdc/134740).Nationally, 2-dose MMR coverage was 93.1% (range\u00a0=\u00a081.3% [Idaho] to \u226598.4% [Mississippi]), with coverage of \u226595% reported by 13 states and <90% by 12 states and DC . DTaP cohttps://stacks.cdc.gov/view/cdc/134739). Exemptions from receipt of one or more vaccines increased in 40 states and DC and increased by at least 1 percentage point in seven states . Third, vaccination coverage, exemption rates, grace period, or provisional enrollment might be under- or overestimated because of inaccurate or absent documentation. Finally, national coverage estimates for the 2022\u201323 school year include only 49 of 50 states and DC, and nine states use lower bound estimates; exemption estimates include 49 states and DC, and five states use lower bound estimates.Nationwide vaccination coverage among kindergarten students remains below prepandemic levels, and exemptions have increased. Because clusters of undervaccinated children can lead to outbreaks ("} +{"text": "Introduction: There are prevalent financial relationships between physicians and the pharmaceutical industry in medical specialties, including otorhinolaryngology. Although these relationships might cause conflicts of interest, no studies have assessed the size and contents of the financial relationships between otorhinolaryngologists and pharmaceutical companies in Japan. This study aims to\u00a0evaluate the magnitude, prevalence, and trend of the financial relationship between Japanese otolaryngologists and pharmaceutical companies.Methods:\u00a0Using payment data publicly disclosed by 92 pharmaceutical companies, we examined the size, prevalence, and trend in personal payments made to the otorhinolaryngologist\u00a0board certified by the Japanese Society of Otorhinolaryngology-Head and Neck Surgery (JSO-HNS) between 2016 and 2019 in Japan. Furthermore, differences in payments were evaluated by whether otolaryngologists were clinical practice guideline authors, society board members, and academic journal editors or not. Trends in payments were evaluated by generalized estimating equations.Results:\u00a0Of 8,190 otorhinolaryngologists, 3,667 (44.8%) were paid a total of $13,873,562, in payments for lecturing, consulting, and writing by 72 pharmaceutical companies between 2016 and 2019. The median four-year combined payment\u00a0per physician was $1,022 . Top 1%, 5%, and 10% of otorhinolaryngologists received 42.3% : 37.2%-47.4%), 69.3% (95% CI: 65.9%-72.8%), and 80.6% (95% CI: 78.3%-82.9%) of overall payments, respectively. The median payments per physician\u00a0were significantly higher among otorhinolaryngologists authoring clinical practice guidelines , society board members , and journal editors than those without. The payments and number of otorhinolaryngologists receiving payments remained stable between 2016 and 2019.Conclusion:\u00a0This study demonstrates that a minority but a large number of otorhinolaryngologists received personal payments from pharmaceutical companies for the reimbursement of lecturing, consulting, and writing in Japan. Large amounts of these personal payments were significantly concentrated on a small number of leading otorhinolaryngologists. Although collaborations between industry and healthcare professionals can bring breakthroughs in medicine, several medical scandals and limited transparency in the financial relationships between healthcare professionals and pharmaceutical companies led to concern for the undue influence of financial relationships on patient care. Since 2013, the Japan Pharmaceutical Manufacturers Association (JPMA), the largest pharmaceutical trade organization in Japan, has required all pharmaceutical companies belonging to the JPMA, whose share account for more than 80% of total sales for pharmaceutical products in Japan -12.As shown in previous studies in the United States, there are large and prevalent financial transfers from pharmaceutical industries to otorhinolaryngologists for various purposes -17, as wStudy design and study participantsAuris Nasus Larynx). This study defined leading otorhinolaryngologists as board-certified otorhinolaryngologists authoring clinical practice guidelines, board members of the JSO-HNS, and editorial members of Auris Nasus Larynx.This retrospective study examined the magnitude and trends in financial relationships between pharmaceutical companies and all otorhinolaryngologists board-certified by the Japanese Society of Otorhinolaryngology-Head and Neck Surgery (JSO-HNS). As the JSO-HNS did not disclose the name list of board-certified otorhinolaryngologists for the previous years, we considered all board-certified otorhinolaryngologists in 2021. The JSO-HNS, established in 1893, is the sole and most authoritative professional medical society certifying otorhinolaryngologists in the field of otorhinolaryngology and head and neck surgery in Japan. The JSO-HNS has contributed to training otorhinolaryngologists, funded clinical trials and basic research, published many clinical practice guidelines for otorhinolaryngological diseases, and issued the English-language academic journal , the JSO-HNS board members in 2018-2019 and 2020-2021, and editorial members of 020-2021 . As the The payments concerning lecturing, consulting, and writing paid to the board-certified otorhinolaryngologists were extracted from a total of 92 pharmaceutical companies belonging to the JPMA between 2016 and 2019. The period of payment data collection was determined by our availability of data collection. The companies have published and updated the payment data each year on their company websites. The payment data for all companies belonging to the JPMA were collected from 2016 and May 2022, and the payment data from 2019 are the latest analyzable data in Japan. Payment categories were described in our previous study and the JPMA transparency guideline ,35. The AnalysisFirst, the payment data were descriptively analyzed. Payments per physician were also calculated only for physicians receiving payments each year, as in other previous studies ,18,36-38Furthermore, the linear log-linked Poisson regression model was used to assess the association between the relative risk of payment receipt and the otorhinolaryngologist characteristics. To account for the highly\u00a0skewed distribution of payment values, a negative binomial regression model was employed to evaluate the association between the relative monetary value of payments per physician and the otorhinolaryngologist characteristics, including practicing prefecture, participation in clinical guideline development, JSO-HNS board membership, and editorial membership of the society journal, as in previous studies ,35,37,38Ethical approvalThe Ethics Committee of the Medical Governance Research Institute approved this study . As this retrospective analysis only included publicly available information, informed consent was waived by the ethics committee.Patient and public involvementNo patient was involved in this study.Overall and per-otorhinolaryngologist paymentsAt the time of this study, we identified 8,190 otorhinolaryngologists board-certified by the JSO-HNS. Of the 8,190 otorhinolaryngologists, 3,667 (44.8%) were paid a total of $13,873,562, entailing 22,076 contracts in payments for lecturing, consulting, and writing by 72 pharmaceutical companies between 2016 and 2019\u00a0 and 84.8% of overall payment contracts between 2016 and 2019. Of\u00a08,190 eligible otorhinolaryngologists, 3,373 (41.2%), 1,112 (13.6%), and 494 (6.0%) received one or more compensation payments for lecturing, consulting, and writing from the pharmaceutical companies over the four years, respectively.While majority of otorhinolaryngologists did not receive any payments from the pharmaceutical companies over the four years, top 1%, 5%, 10%, and 25% of otorhinolaryngologists received 42.3% (95% CI: 37.2%-47.4%), 69.3% (95% CI: 65.9%-72.8%), 80.6% (95% CI: 78.3%-82.9%), and 94.8% (95% CI: 94.1%-95.5%) of overall payments, respectively. The Gini coefficient for the four-year combined payments per physician was 0.889, indicating that the payments disproportionately concentrated on small numbers of otorhinolaryngologists.Payments to leading otorhinolaryngologists: clinical practice guideline authors, society board members, and academic journal editorsWe identified a total of 139 individual authors from eight clinical practice guidelines accredited or authorized by the JHO-HNS between 2015 and 2020\u00a0 received a total of $1,234,715 and a median payment of $22,261 per physician\u00a0 board-certified otorhinolaryngologists who are editors of Auris Nasus Larynx received payments of $774,171 in total and $35,143 in median per-physician payments from pharmaceutical companies\u00a0 times, 1.47 (95% CI: 1.10-1.79) times, and 1.21 (95% CI: 1.11-1.33) times higher likelihood to accept personal payments from pharmaceutical companies than those without authorships or memberships\u00a0 with the industry, and the authors disclosed their FCOIs in the guidelines. Meanwhile, there was no FCOI disclosure among the JSO-HNS board members and the academic journal editors.Trends in personal payments between 2016 and 2019The total annual payments from the pharmaceutical companies ranged from $3,356,647 in 2016 to $3,615,634 in 2017. A total of 1,988 (24.3%) otorhinolaryngologists in 2019 to 2,129 (26.0%) otorhinolaryngologists in 2018 received more than one personal payment from the companies in a single year\u00a0(Table Payments by companyTotal payments by company are described in Figure This study demonstrates that a minority but a large number of otorhinolaryngologists received personal payments from pharmaceutical companies for the reimbursement of lecturing, consulting, and writing in Japan. Large amounts of these personal payments were significantly concentrated on a small number of otorhinolaryngologists with leading positions, such as clinical practice guideline authors, society board members, and academic journal editors in the field of otorhinolaryngology. We observed that the personal financial relationships between the otorhinolaryngologists and pharmaceutical companies had remained stable over the four years in Japan. Our findings show significant similarities and differences compared to previous studies assessing this issue in Japan and other developed countries.First, this large sample-sized longitudinal observational study elucidated that 44.8% of all board-certified otorhinolaryngologists received a median personal payment of $1,022 from pharmaceutical companies. Previous studies in Japan reported that there was an increasing trend in physicians receiving payments from pharmaceutical companies in terms of the number of physicians with payments and payments per physician ,35,42,43Second, the personal financial relationships between the otorhinolaryngologists and pharmaceutical companies remained stable over the four years at both low monetary payment values and number of otorhinolaryngologists with payments. In contrast to our findings, Morse et al. previously observed that there was an increasing trend in personal payments among the US otorhinolaryngologists between 2014 and 2016 , prescriAnnals of Emergency Medicine, the official journal of the American College of Emergency Physicians, and the Journal of Urology, the official journal of the American Urological Association, disclose the editors\u2019 FCOIs on journal webpages [In addition, our study directly demonstrated that large amounts of personal payments significantly concentrated on only a small number of otorhinolaryngologists positioned in authoritative and public roles, such as clinical practice guideline authors, society board members, and academic journal editors. A high concentration of payments on leading physicians, namely, key opinion leaders, is pervading in medicine worldwide ,37,66-69webpages . TranspaLimitationsThis study included several limitations: First, there would be underestimated payments made by non-member companies of the JPMA to the otorhinolaryngologists. However, as the member companies accounted for 80.8% of the total pharmaceutical sales in Japan in 2018 . This coAlthough a minority of otorhinolaryngologists board-certified by the JSO-HNS\u00a0stably received personal payments from pharmaceutical companies for the reimbursement of lecturing, consulting, and writing between 2016 and 2019, large amounts of payments significantly concentrated on a relatively small number of otorhinolaryngologists. Leading otorhinolaryngologists, such as clinical practice guideline authors, society board members, and academic journal editors, significantly accepted far larger personal payments than those who were not."} +{"text": "In Mississippi, USA, infant hospitalization with congenital syphilis (CS) spiked by 1,000%, from 10 in 2016 to 110 in 2022. To determine the causes of this alarming development, we analyzed Mississippi hospital discharge data to evaluate trends, demographics, outcomes, and risk factors for infants diagnosed with CS hospitalized during 2016\u20132022. Of the 367 infants hospitalized with a CS diagnosis, 97.6% were newborn, 92.6% were covered by Medicaid, 71.1% were African American, and 58.0% were nonurban residents. Newborns with CS had higher odds of being affected by maternal illicit drug use, being born prematurely (<37 weeks), and having very low birthweight than those without CS. Mean length of hospital stay (14.5 days vs. 3.8 days) and mean charges were also higher for infants with CS than for those without. To address escalation of CS, Mississippi should invest in comprehensive prenatal care and early treatment of vulnerable populations. Treponema pallidum, is a severe disease with potential for immediate and long-term health complications. Infection in pregnant mothers can lead to serious neonatal conditions, such as deformities, hepatosplenomegaly, anemia, jaundice, and failure to thrive , caused by infection with the bacterium According to Centers for Disease Control and Prevention surveillance data, the nationwide rate of CS increased by 30.5% in 1 year, from 59.7/100,000 live births in 2020 to 77.9/100,000 live births in 2021 . We used data from this more inclusive group to study prevalence, trends, and demographics among infants hospitalized with CS. The second group (delivery subcohort) included only infants either delivered in the hospital or delivered outside of the hospital but admitted with a delivery code from the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM). We needed data from the delivery subcohort because we were interested in pregnancy outcomes associated with syphilis, including preterm and low-birthweight deliveries. To identify the delivery subcohort, we developed an algorithm that incorporated infant age and ICD-10-CM code Z38, the neonatal diagnostic code for birth. In hospital discharge data, neonatal patient age was based on date of admission. In our delivery subcohort, we included all infants whose ages were recorded as 0\u20133 days with day 0 being the day of birth. <27 completed weeks of gestation) and P0.73 for premature births (<36 completed weeks of gestation). We referenced ICD-10-CM code P22 to screen the data for newborn respiratory distress, which were of special interest for this study because this condition is a major cause of neonatal illness and death , amphetamines (P04.16), cocaine (P04.41), hallucinogens (P04.42), cannabis (P04.81), unspecified drugs of addiction , and neonatal abstinence syndrome . For preterm deliveries, we referenced codes P0.72 for extreme newborn immaturity . We categorized data on race into 3 groups: African American, White, and others (because few infants with CS in the study were not either African American or White). The following racial categories are included in the hospital discharge dataset: White, African American/Black, American Indian/Alaska Native, Asian, Native Hawaiian/other Pacific Islander, multiracial, declined, and race unavailable/unknown. We were unable to examine ethnicity because few infants of Hispanic origin were included in the CS cohort. We used Medicaid insurance coverage as a proxy for low socioeconomic status. For our research, we collected key demographic characteristics, such as urbanicity, race, and socioeconomic status, for each individual CS patient. We defined urban versus nonurban status on the basis of the CDC National Centers for Health Statistics urban\u2013rural classification scheme , 92.6% covered by Medicaid, 71.1% African American, and 58.0% residents of nonurban counties; 50.7% were male and 49.3% female. Most infants with CS were identified as delivery hospitalizations and included in the delivery subcohort. The remaining 27 infants were postdelivery admissions. Among the postdelivery admissions, 18 were newborn and 9 were >28 days of age, meaning \u22487% of the infants with CS received the diagnosis during postdelivery hospitalization.During the 2016\u20132022 study period, 367 infants were hospitalized in Mississippi with diagnosed CS. Of those infants, 97.6% were newborn , covered by Medicaid , and >3 days of age . After adjusting for covariates, Medicaid insurance coverage was the strongest independent demographic risk factor; however, infants >3 days of age and African American race also retained associations with congenital syphilis risk .We compared findings on clinical characteristics from this analysis between infants with and without CS . In the In the multivariable analysis of clinical characteristics, the variable with the strongest association with CS was maternal substance use. Even after controlling for demographic risk factors, the CS cohort had almost 10 times higher odds of being affected by maternal illicit drug use than the cohort without CS . Aside from minor variations, the proportion of maternal illicit drug use among the CS cohort remained high throughout the study period. In 2016, the year with the highest proportion of substance-exposed infants, 25% of all newborns with CS also had a diagnostic code indicating maternal use of illicit drugs. During the last 3 years of the study period, there was a gradual but steady increase in the proportion of newborns hospitalized with CS and exposed to illicit substances in utero: 17.7% in 2020, 22.7% in 2021, and 23.8% in 2022 . Infants in the CS cohort were also more likely to suffer from severe complications, including prematurity and low birthweight, than infants in the cohort without CS. Among newborns with CS, 92 (27.1%) were premature, compared with 43 (12.7%) for newborns without CS. Among premature infants with CS, 8/92 were extremely premature . Newborns with CS had >2 times higher odds of being born prematurely than did newborns without CS after controlling for demographic risk factors. Among 87 newborns with CS who had birthweights <2,500 g, 59 had low birthweight (LBW) of 1,500\u20132,499 g and 28 had very low birthweight (VLBW) of <1,500 g. Compared with the cohort without CS, infants in the CS cohort were more likely to be LBW and VLBW . Alarmingly, odds for newborns with CS to be LBW were nearly 2 times higher and to be VLBW >4 times higher than for newborns without CS. On average, newborns with CS weighed 349 g less than newborns without CS . NewbornIn terms of resource use, infants with CS had a longer mean hospital stay and mean hospital charges than did infants without CS. During 2016\u20132022, hospital charges for the CS cohort totaled $20,846,196; Medicaid-insured infants accounted for $19,444,608 (93.3%) of those charges.During the last 4 years of the study period (2019\u20132022), 6 infants with CS died in hospital, half of those during the last year of the study period (2022). Among the infants with CS who died, 83.3% had extremely low birthweight , and 66.7% were extremely premature. Among our study population, no records indicated both stillbirth and CS. From 2016 through 2022, CS hospitalization rates in Mississippi increased more than 10-fold. Although the upward trend was consistent with national-level surveillance data for CS, the upturn in Mississippi was even steeper was >2 times higher than for the cohort without CS (12.7%). Likewise, the CS cohort had a higher proportion of newborns with VLBW. We acknowledge that other associated risk factors more commonly seen in the CS cohort, such as maternal substance abuse, might also have contributed to this difference. Still, those differences require urgent action because preterm birth and VLBW are leading causes of infant death in Mississippi, a state that already has the highest preterm birth and infant mortality rates in the nation (Our study provides evidence that the spike in CS is already elevating the high number of infant deaths in the state. Our research identified 6 infant deaths associated with a CS diagnosis during the study period. Half those deaths occurred in 2022, underlying the current nature of this rapidly escalating reemergent public health menace and urgent need for public health interventions. Infant deaths associated with CS are preventable; Mississippi could reduce infant illness and death by promptly diagnosing and treating pregnant patients with syphilis (In addition to harmful health sequalae, CS was associated with significant healthcare expenditure as measured by the mean length of stay and hospital charges. The mean length of stay was nearly 4 times higher among the CS cohort than for the cohort without CS. Furthermore, total charges for this preventable condition reached >$20 million during the 7-year study period. This result further underlines the pressing need to prevent CS to reduce its physical and economic toll in Mississippi. To combat this emerging crisis, however, it is critical to understand the different behavioral, social, and economic factors driving up maternal syphilis rates (We further uncovered substantial economic and racial disparities among families of infants diagnosed with CS, consistent with previous research (In addition to behavioral and socioeconomic risk factors, insufficient prenatal screening has been implicated in rapidly rising CS rates (To address the evolving CS crisis in Mississippi effectively, comprehensive public health and health policy approaches must be implemented. State agencies and political leaders should be encouraged to adopt all available tools to support early comprehensive prenatal care. At the front line of this battle, public health structures should receive adequate resources to diagnose and treat the most vulnerable populations, including underserved and uninsured/underinsured infected mothers, in a timely and effective manner. In addition, healthcare providers and systems should align their processes to prioritize and ensure early diagnosis and treatment of syphilis in pregnancy. Enhancing sexual health literacy, including providing comprehensive sex education for youth, would further empower Mississippi residents to prevent or seek treatment for reemerging syphilis infection. Our investigation shows that the rapid rise of CS hospitalizations in Mississippi is a serious public health concern because of its grave social and health-related consequences. By analyzing hospital discharge records from Mississippi, we performed an in-depth epidemiologic evaluation of infants hospitalized with CS. Although limited by lack of data on prenatal care, perinatal syphilis treatment, and laboratory diagnostic tests, the database provided population-level data that enabled us to explore statewide trends, study comorbidities and costs, and make robust inferences specific to the population of Mississippi. Study findings suggest the benefits of obtaining more granular data, improving public health surveillance, and enhancing education for physicians and providers to diagnose and treat syphilis. Congenital syphilis is a disease with dire health, social, and financial consequences that can be prevented. Providing comprehensive prenatal care, effective screening, and early treatment for pregnant women in Mississippi constitute not only sound public health policy in general but also smart strategies to improve pregnancy outcomes, reduce infant illness and death, curtail medical costs, and promote greater health equity."} +{"text": "Listeria monocytogenes may cause serious, life-threatening disease in susceptible persons. We combined data from Finnish national listeriosis surveillance, patient interview responses, and laboratory data of patient samples and compared them to listeria findings from food and food production plants collected as part of outbreak investigations during 2011\u20132021. The incidence of invasive listeriosis in Finland (1.3/100000 in 2021) is higher than the EU average (0.5/100000 in 2021), and most cases are observed in the elderly with a predisposing condition. Many cases reported consuming high-risk foods as well as improper food storage. Since ongoing patient interviews and whole genome sequencing were introduced, several listeriosis outbreaks were detected and food sources identified. Recommendations about high-risk foods for listeriosis and proper food storage should be better communicated to susceptible people. In Finland, patient interviews and typing and comparing listeria isolates in foods and patient samples are crucial in solving outbreaks and determining measures to control invasive listeriosis.Foodborne pathogen Listeria monocytogenes. It mostly affects people with a predisposing condition, such as immunocompromised persons, the elderly, pregnant women, and neonates, causing sepsis, infections in the central nervous system, stillbirth, and foetal death [Invasive listeriosis is caused by the foodborne pathogen al death , 2. The al death .L. monocytogenes is ubiquitous in nature and can withstand variable environmental conditions, such as temperatures from 2 to 45 degrees Celsius, low pH, and high salinity [In 2021, listeriosis was the fifth most reported zoonotic disease in the EU and, along with West Nile virus infections, had the highest mortality rate . In thatECDC has envisioned whole genome sequencing (WGS) to be the method of choice for typing of microbial pathogens to improve disease surveillance, outbreak investigation, and the evaluation of prevention policies . In FinlL. monocytogenes isolates to THL [Since 1995 in Finland, clinicians and clinical microbiology laboratories report data on culture-confirmed invasive listeriosis cases to the FIDR and submit ) to THL , 8. We fDepending on the isolation site, the cases notified in 2011\u20132021 were classified as septic, meningitis, or materno-foetal. Materno-foetal cases include pregnancy-associated listeriosis or listeriosis in a newborn (infection in both the mother and the newborn was counted as a single case with the mother being included in the data set). For cases notified in 2016\u20132021, data on underlying conditions, medications, and the consumption of risk-associated food products were collected by local healthcare staff or THL from patients or their family members using an online questionnaire. The questionnaire focused on the consumption of ready-to-eat meat products and cold cuts; cold- or hot-smoked, cured, and raw fish products; unpasteurized milk and dairy products; frozen vegetables; and convenience food consumed within two weeks prior to the onset of symptoms. In addition, the questionnaire asked about travelling in Finland or abroad and eating in a restaurant two weeks prior to the onset of symptoms, as well as knowledge of risk foods, the habit of checking the fridge temperature, and the best-before dates of the food products. Mortality data were obtained from the Finnish Population Registry. To estimate the case fatality rate, deaths within 30\u00a0days of sampling were considered listeriosis related.L. monocytogenes isolates from food samples to the Finnish Food Authority (before 1 January 2019 Finnish Food Safety Authority Evira) strain collection and, when needed, for further characterization and typing [The local official food control laboratories send d typing . The samL. monocytogenes isolates sent by the local official food control laboratories to the Finnish Food Authority were further typed using the same methods as in THL. In 2011\u20132017, the strains were typed using PFGE, and after 2018, using WGS. The WGS typing was done using the same method and the same schemas as in THL.The L. monocytogenes, especially in vacuum-packed smoked or cured fish products and ready-to-eat products, have been performed within the national monitoring of zoonoses [L. monocytogenes. Samples were taken from retail randomly. All L. monocytogenes isolates detected in these surveys are stored at the national reference laboratory in the Finnish Food Authority.National surveys to estimate the presence and levels of zoonoses . In 2012L. monocytogenes from patient samples were performed in clinical microbiology laboratories. The isolates were sent to the reference laboratory (THL) for confirmation and further typing. In 2011\u20132014, the species confirmation and serogroup determination were performed using PCR and molecular typing using PFGE as previously described [The detection and isolation of escribed , 13. In DNA isolation, library preparation, and sequencing on MiSeq (Illumina Inc.) were performed as earlier described . Ridom SL. monocytogenes Finland 1998 strain, which was chosen as a reference (Genbank accession no. NC_01747.1.) [For creating a core genome MLST (cgMLST) protocol, the Target Definer function of Ridom SeqSphere+ was used to identify 1503 target loci shared by the 1747.1.) , and 45 In 2011\u20132021, a total of 722 invasive listeriosis cases were notified in Finland . Cases wInterview data were obtained for 68% (304/449) of the cases in 2016\u20132021. For 38% (115/304) of the interviewed cases, the person who answered the questionnaire was the patient\u2019s spouse or other relative. Twelve cases (4%) did not have any underlying illness, and of them, four were pregnant women. Of the cases with underlying disease(s), 51% (154/301) had heart disease, 29% (87/301) diabetes, 21% (62/301) other cancer than leukaemia, 20% (60/301) lung disease, 15% (44/301) chronic kidney disease, 13% (40/301) rheumatics, 11% (34/301) gastrointestinal disease, 7% (21/301) chronic liver disease, 7% (20/301) immunological illness, 6% (18/301) leukaemia, 4% (12/301) alcohol addiction, and 1% (4/301) had undergone a tissue transplant. In the last three months prior to listeria infection, immunosuppressive medication had been used by 40% (118/296) of the interviewed cases and medication to prevent acidity of the stomach by 50% (148/298).Two weeks prior to start of symptoms, 24% (71/297) of the cases had been in inpatient treatment, 29% (84/294) had eaten in a restaurant, 13% (38/285) had travelled in Finland, and 5% (14/283) had travelled abroad. Ready-to-eat meat cold cuts as well as cured and cold- or hot-smoked fish were the most consumed risk foods reported .Figure 2Of the cases, 34% (96/286) reported a habit of checking their fridge\u2019s temperature once a week, 9% (25/286) once a month, and 26% (73/286) less frequently, and for 32% (92/286) the information was not available. Furthermore, 63% (179/286) reported throwing out outdated products once a week, 10% (29/286) once a month, and 9% (25/286) less frequently, and for 19% (53/286) the information was not available. Of the cases, 57% (94/166) did not have knowledge of risk foods for listeriosis prior to infection.Since starting the listeriosis case interviews in 2016, eight listeriosis outbreaks could be solved with both epidemiological and microbiological evidence.In 2015, both PFGE and WGS were used for typing 45 isolates. Eighteen MLST types and 30 PFGE types were identified . Each MLSupplementary\u00a0Table\u00a01).In 2011\u20132015, 282 strains were typed and a total of 89 different Ascl profiles were detected in PFGE, the most common being 225, 62, and 96 . In 2015L. monocytogenes isolates from foods and food production plants from 23 local official food control laboratories. Isolated strains represented 3353 food or food production plant samples . In 2011\u20132021, 3.1% (104/3353) of food samples (3\u201318 samples per year) contained more than 100 colony-forming units (CFU)/g of L. monocytogenes.In 2011\u20132021, the Finnish Food Authority received 4939\u00a0L. monocytogenes isolates from foods or food production plants were genotyped in 2011\u20132021. During 2011\u20132017, 105 different PFGE AscI profiles were detected, type 96 being the most common . In 2017\u20132021, when WGS was used as the typing method, 36 different 7-gene MLST types were identified among the strains typed.In total, 626 (13%) L. monocytogenes was detected in 10 (1.3%) samples. In nine of those samples, the count of L. monocytogenes was 10\u00a0CFU/g or below. One bacterial count result was missing.In 2012\u20132014, the Finnish Food Authority received results of 793 sliced, heat-treated, or cold-smoked ready-to-eat meat product samples from local official food control laboratories as part of an official survey. Of the products, 94% were manufactured in Finland, and 47% of the food samples contained only domestic meat. Of the analysed food samples, 82% (652/793) were stored in packaging gas and 16% (126/793) were vacuum-packed. In 11% of the samples, the temperature of the product in retail was above the statutory limit of 6.0 degrees Celsius. At the end of shelf-life, L. monocytogenes was not found.In 2015\u20132016, the Finnish Food Authority received results of 398 sliced cheese samples from local official food control laboratories. The samples were from domestic and foreign, packed, sliced cheeses in retail. There were 16 mutual PFGE AscI profiles in patient samples in 2011\u20132015 and in food and food production plant samples in 2011\u20132016 . Of all L. monocytogenes were sequenced. These originated from patients (490), food items (184), and samples from food production environments (13). The MLST type of seven patient samples and two food samples could not be determined. The strains showed 49 MLST types, 16 of which contained nine or more patient isolates than the EU average (14% in 2021 ). HoweveL. monocytogenes is capable of growth in refrigeration temperatures and growth is faster in higher temperatures [Despite being immunocompromised, the cases had often consumed high-risk foods, such as ready-to-eat meat products, cured and cold- or hot-smoked fish, and salami or other sliced sausages. Over half of the cases did not have knowledge of high-risk foods for listeriosis prior to infection. In addition, one third of cases checked their fridge\u2019s temperature monthly or less often; one fifth reported throwing out outdated products monthly or less often. This suggests that recommendations about high-risk foods and proper food storage should be highlighted also to other risk groups than pregnant women. THL and the Finnish Food Authority have produced a leaflet on listeriosis for doctors to distribute to patients . Howevereratures , it is ieratures ) should Salmonella and Campylobacter [Half of the cases in our study had used medication to treat gastric acidity. Use of proton pump inhibitors (PPI) and other medications that neutralize or inhibit gastric acid are considered to increase the risk of listeriosis, possibly because a low gastric pH is a natural defence against listeria , 32. Thelobacter , 34, whoIn over one third of the cases, the patient\u2019s spouse or other relative answered the questionnaire due to the frail condition or forgetfulness of the patient. The incubation period of listeriosis varies by clinical manifestation, but the median is estimated to be 11\u00a0days with most cases occurring within four weeks . Old ageThe serogroup IIa accounted for most of the listeriosis cases followed by IVb. According to the literature, these serotypes account for most human infections . In 2011In the eight listeriosis outbreaks that could be solved with both epidemiological and microbiological evidence since starting the listeriosis case interviews, 133 people fell ill. The causative food items belonged to fish products , fresh or frozen vegetables , and meat products . The outbreaks were long-lasting, with the duration varying from three to seven years. In 2016\u20132018, a widespread outbreak affecting five European countries was caused by frozen corn . This ouL. monocytogenes. In 2010, the Finnish Food Authority received 323 food L. monocytogenes isolates of which the majority were genotyped [L. monocytogenes [The overall occurrence of listeria in food products in Finland is currently unknown. A small proportion of food samples investigated have contained more than the regulatory limit of 100\u00a0CFU/g of enotyped . Since 2ytogenes . Since 2In Finland, the notification rate for listeriosis is higher than the EU average, and the trend is slightly increasing (from 0.8/100000 in 2011 to 1.3/100000 in 2021), probably due to the ageing population and age-related illnesses affecting the immune system. Pregnancy-related listeriosis is rare, due to effective maternity clinic counselling. Recommendations about high-risk foods for listeriosis should be better communicated to other risk groups, as well as to relatives and people taking care of the elderly. Several listeriosis outbreaks have been detected and food sources identified since ongoing patient interviews and WGS were introduced. Patient interviews and testing and typing listeria isolates in foods and comparing them to patient isolates are crucial for solving outbreaks and determining measures to control invasive listeriosis in Finland."} +{"text": "Healthcare workers (HCWs) are at risk of contracting TB, particularly when in high tuberculosis (TB) burden settings. Routine surveillance data and evidence are limited on the burden of TB amongst HCWs in Indonesia. We aimed to measure the prevalence of TB infection (TBI) and disease among HCWs in four healthcare facilities in Yogyakarta province in Indonesia, and explore risk factors for TBI. A cross-sectional TB screening study targeted all HCWs from four pre-selected facilities in Yogyakarta, Indonesia. Voluntary screening included symptom assessment, Chest X-ray (CXR), Xpert MTB/RIF (if indicated) and tuberculin skin test (TST). Analyses were descriptive and included multivariable logistic regression. Of 792 HCWs, 681 consented (86%) to the screening; 59% (n = 401) were female, 62% were medical staff (n = 421), 77% worked in the one participating hospital (n = 524), and the median time working in the health sector was 13 years (IQR: 6\u201325 years). Nearly half had provided services for people with TB and 9% reported ever having TB (n = 60). Among participants with presumptive TB , none were diagnosed microbiologically or clinically with active TB disease. TBI was detected in 25% of eligible HCWs with a TST result. A significant association was found between TB infection and being male (adjusted Odds Ratio (aOR) 2.02 (95%CI: 1.29\u20133.17)), currently working in the participating hospital compared to primary care (aOR 3.15 (95%CI: 1.75\u20135.66)), and older age (1.05 OR increase per year of life between 19\u201373 years (95%CI: 1.02\u20131.06)). This study supports prioritisation of HCWs as a high-risk group for TB infection and disease, and the need for comprehensive prevention and control programs in Indonesia. Further, it identifies characteristics of HCWs in Yogyakarta at higher risk of TBI, who could be prioritised in screening programs if universal coverage of prevention and control measures cannot be achieved. Tuberculosis (TB) remains one of the most burdensome and deadliest infectious diseases worldwide, causing an estimated 10.6 million cases and 1.6 million deaths in 2021 [Healthcare workers (HCWs) are at an increased risk of contracting TB compared to the general population \u20134. The bMeeting ambitious End TB strategy targets by 2035 requires a well-resourced, skilled and healthy healthcare workforce . The burIndonesia has the third highest TB caseload internationally and an annual disease incidence of 301 per 100,000 . SurveilYogyakarta province, located in central southern Java, has an estimated TB disease incidence rate between 250\u2013300 per 100,000 population and an estimated case detection rate of 34.2% . The YogThe study selected all healthcare facilities delivering TB care within two sub-districts of two districts of Yogyakarta province. Selection of healthcare facilities in this study was targeted, based on the respective sub-district\u2019s involvement in a TB Reach funded active case finding program . Health The target population for this cross-sectional study was all healthcare facility staff from the four pre-selected facilities aged \u226517 years , including non-medical and medical staff. There were 792 HCWs across the four facilities; 613 at the private hospital and 179 staff across the PHCs. No sampling methodology was used in this study as we invited the entire target population to participate.Information about the screening, including its purpose, date, and location were disseminated through advertisements in staff break rooms, online notification through the facility\u2019s human resource network, and awareness-raising sessions for staff before the period of screening. The sessions were conducted by the study team and included information on TB, TB burden in HCWs, the value of screening, the screening process, dates and location of the screening, the consent process and participant confidentiality. The study was voluntary, free of charge, and participants did not receive incentives for participating.Screening of health workers was conducted for one week at each PHC and two weeks at the private hospital between December 2020 to May 2021. HCWs were invited to join the study at a time that was convenient to them, which could be prior to, during or after work hours. Trained research staff screened and interviewed the participants.TB infection and disease screening included symptom assessment, Chest X-ray (CXR), one spot sputum sample for Xpert MTB/RIF testing (if indicated) and TST. Culture was used when there were indeterminate or positive Xpert MTB/RIF results. TBI was classified as TST positivity (>10mm induration or >5mm in immunosuppressed participants) with no evidence of clinically manifest active TB , 16. TheFinal TB diagnoses were made by the study team doctor, based on Indonesian and WHO definitions/criteria. Diagnostic results and information on treatment options were disseminated by formal letter if the participant screening outcome was negative, or through a doctor consultation if TBI was diagnosed. Pending consent, participant eligibility to take TB preventive treatment (TPT) was assessed, and when relevant, participants were supported to attend their chosen healthcare facility to initiate TPT according to the National guidelines.Interview and examination data were entered electronically at the point of care using REDCap . The stuRe-identifiable study data were exported into Stata v15 .Descriptive analyses were utilised to measure TBI prevalence and examine cohort characteristics. Categorical variables were reported as numbers and proportions. Continuous variables were assessed for normality and reported as median and interquartile range (IQR).Risk factors associated with TBI were investigated by examining demographic, occupational, and clinical factors using univariable and multivariable logistic regression. The effect was expressed as an unadjusted and adjusted odds ratio (OR) with 95% confidence intervals (95% CI). Variables were added to the multivariable model if p < 0.2 in the univariable analyses. Those recorded only for sub-sets of the sample or demonstrating collinearity were excluded. Backward selection was employed, and selection stopped when the multivariable model Likelihood Ratio test showed only a statistically non-significant improvement in modelling. Levels of significance in the multivariable model and statistical tests were set at 5%.Ethical approval was obtained from the Institutional Ethical Review Board of the Faculty of Medicine, Public Health and Nursing, University of Gadjah Mada, Indonesia (number KE/FK/0323/EC) and the Alfred Hospital Human Research Ethics Committee, Australia (number 639\u201320). All participants provided informed written consent.Participation in the study was high with 86% (n = 681/792) of registered HCWs at the facilities participating, ranging from 73\u201394% by facility. Of the 681 participants the median age was 40 years (IQR:30\u201348), 59% (n = 401) were female, 71% (n = 486) reported completing a university degree, and participant\u2019s median household size was 4 people (IQR:2\u20135 people) . Nearly Among the 681 participants, 67% (n = 450) were overweight or obese, 29% currently or previously smoked, self-reported diabetes mellitus (DM) prevalence was 4% (n = 24), self-reported HIV status was known or disclosed among 28% (n = 190) of participants and all were negative Table 1Table 1. During screening, 1% (n = 5/681) of participants reported cough for more than two weeks or haemoptysis. Of those CXR screened , 36% had a lung or pleural abnormality (n = 239/662), and 15% (n = 97/662) of findings were consistent with possible active TB disease requiring further investigation and assessment . Of the TST was offered to all participants who had not reported previously receiving TB treatment (n = 621). It was administered to 78% (n = 489/621) of those eligible and read in 90% (n = 441/489) of them . TBI wasOf the 112 participants diagnosed with TBI, 8% (n = 9) were underweight, 35% currently or previously smoked, 5% (n = 6) reported having DM and 80% (n = 90) were unsure of or unwilling to disclose their HIV status . A signiIn this study among HCWs in four healthcare facilities in Yogyakarta, no HCWs were diagnosed microbiologically or clinically with active TB disease, although 9% reported previous or current TB disease. TBI was diagnosed in 25% of those eligible for TST and who had the TST read; this was highest in staff from the hospital . A significant association was found between TBI and being male, currently working in the participating hospital and older age.Annual incidence of active TB disease among HCWs has been reported to range from 69\u20135,780 per 100,000 population, and has consistently been documented to be higher than the general population .Prevalence of TBI (using TST) among HCWs in LMICs has been reported to range from 14\u201398% (mean 49%), and is higher among HCWs in high burden settings , 11. OurBeing male and increasing age as non-occupational risk factors for TBI among HCWs are consistent with several international studies , 20\u201326. The evidence is varied surrounding occupational factors as risk factors for TBI, such as years of work in the healthcare sector, contact with a TB patient, occupation type or work location , 23, 29.Control measures, such as adoption of N95 respirators, engineering controls, staff screening, and FAST infection control strategies, may decrease annual TB incidence among HCWs by as much as 81% in high incidence settings . Even adThis study has some limitations. Primarily, the cross-sectional design and target population of all staff at pre-selected study sites meant that while all facilities in the sub-districts participated, the prevalence of TB among HCWs and characteristics associated with TBI may not be generalisable to the district, provincial or sub-national level. Ascertaining the acquisition source for infection was not possible, with community sources possible in addition to healthcare facility sources. Secondly, 14% of HCW registered at the facilities did not participate, close to 20% of eligible participants did not have a TST administered, and 10% were loss to follow up for TST reading. Attrition at each stage may have introduced bias and potentially over or under-estimated the prevalence and association estimates. The main reason for not having a TST administered was due to the recommendation to delay TST for 4-weeks post COVID-19 vaccination . The scrIndonesia is a high incidence setting for TB, and nosocomial and occupational TB hinder TB elimination efforts. This study supports prioritisation of HCWs as a high-risk group for TB infection and disease, and the need for comprehensive prevention and control programs in Indonesia. These include annual staff TB screening, ensuring implementation of IPC procedures in facilities, TB infection and disease surveillance, access to preventive therapy and clear national guidelines. Further, it identifies characteristics of HCWs in Yogyakarta at higher risk, identifying certain groups who could be prioritised in screening programs if universal coverage of prevention and control measures cannot be achieved."} +{"text": "Chronic pain is a debilitating condition that affects daily work and life activities for many adults in the United States and has been linked with depression .Using data from the 2019\u20132021 NHIS, the prevalence of chronic pain and high-impact chronic pain were estimated for the adult U.S. population overall and within population groups defined by demographic, geographic, socioeconomic, and health status characteristics. Age-adjusted rates were calculated because the prevalence of pain is reported to vary by age and adults with a family income <100% of the federal poverty level (FPL) (14.4%) was approximately two and four times as high, respectively, as among those residing in large central metro areas (5.5%) and those with family income \u2265400% FPL (3.5%). Adults reporting poor general health and adults with a disability experienced an exceptionally high prevalence of chronic pain and high-impact chronic pain . Among all chronic medical conditions reported, the age-adjusted prevalence of chronic pain and high-impact chronic pain was highest among adults with a history of myalgic encephalomyelitis/chronic fatigue syndrome and dementia .Chronic pain is a debilitating condition that affects the lives of millions of adults in the United States. During 2021, an estimated 20.9% of U.S. adults experienced chronic pain, similar to the reported estimate of 20.4% in 2016 in 2016, resulting in substantial health care costs and lost productivity.During 2021, an estimated 20.9% of U.S. adults (51.6 million persons) experienced chronic pain, and 6.9% (17.1 million persons) experienced high-impact chronic pain with a higher prevalence among non-Hispanic American Indian or Alaska Native adults, adults identifying as bisexual, and adults who were divorced or separated.Clinicians, practices, health systems, and payers should vigilantly attend to health inequities and ensure access to appropriate, affordable, diversified, coordinated, and effective pain management care for all persons."} +{"text": "Knowing local risk factors for tuberculosis (TB) facilitates identification of individuals with latent or active TB. The purpose of this study is to describe the epidemiology of TB among patients seen in the Detroit Health Department. We will refer to our study population as Detroit TB cases.A retrospective descriptive study was conducted in collaboration with the Michigan Department of Health and Human Services. TB data submitted to MDHHS from Detroit between January 2017 and December 2022 was evaluated. Information on demographics, genotype clusters, and clinical / lifestyle risk factors was collectedOne-hundred forty-one TB cases were verified in Detroit during the study period and will be referred to as the study population. See Table 1 for baseline demographics. Sixty percent (85) of cases were males. Fifty-eight % (81) were Black / African American (B/AA). Sixty-two % (87) of cases were born in the U.S. Of persons with positive cultures for TB, 45% (37) were in a genotype cluster. Please see figure 1 for example of genotype cluster. The major clinical risk factors were diabetes mellitus in 31% (43) of cases, followed by incomplete treatment of latent TB infection (LTBI) in 11% (16). Major life-style risk factors included any substance use in 24% (34), non-injecting drug use in 18% (26), and excess alcohol use in 13% (18) of cases.This study highlights epidemiologic differences between individuals with TB in Detroit and the US. Almost 60% of the 141 Detroit TB cases were B/AA. Nationally, 10% of non-US-born individuals and 30% of US-born ones were B/AA in 2022. More than 60% of the Detroit cases were US-born. This is in stark contrast to the U.S., where 37% of cases in 2022 were US-born. A significant number of Detroiters belonged to a genotype cluster, indicating continued transmission of TB. Alcohol and drug use were major lifestyle risk factors, suggesting increased contact in shared venues contributing to transmission of TB. Knowing these local risk factors for TB should lead to earlier detection and treatment of TB and LTBI and eliminate opportunities for transmission.All Authors: No reported disclosures"} +{"text": "The increase in dental healthcare facilities and the use of single-use equipment have increased the production of healthcare waste. Their mismanagement exposes healthcare workers, waste managers, and the population to an infectious risk and negatively impacts the environment. Therefore, a correct management procedure has to be adopted from separation through storage to disposal. This study aimed to investigate dentists' knowledge, attitudes, and practices regarding managing infectious healthcare waste in private dental offices. A descriptive and analytical cross-sectional survey was conducted between December 2020 and March 2021 among private dentists registered at the Moroccan National Council of Dentists in the Rabat-Sal\u00e9-K\u00e9nitra region. A questionnaire was developed to assess waste management in dental offices. Of the 500 questionnaires distributed, 190 completed and exploitable questionnaires were collected. Only 27.3% of healthcare waste managers in dental practices received training, 21,5% of practitioners assimilated the used gloves into household waste, 71.5% disposed of the waste generated by their offices directly into public bins, and 86.4% were unaware of Moroccan law 28-00 on waste management and disposal. This study highlights dentists' apparent lack of knowledge regarding healthcare waste management, and significant gaps were identified between actual practices and recommended regulations. To address these issues, developing a comprehensive medical waste management plan is crucial to encourage the practical cooperation of all stakeholders in this sector. Nowadays, healthcare waste (HCW) is continuously increasing due to population growth, the development of healthcare facilities, and the increasing use of disposable medical products . SimilarAccording to the World Health Organization (WHO), 75% to 90% of waste is comparable to household waste and is not hazardous. The remaining 10-25% are considered dangerous, resulting in public health risks and catastrophic environmental impacts due to poor management .Among the waste generated annually in Morocco, a significant portion consists of healthcare waste (HCW) or medical and pharmaceutical waste (MPW) from hospitals. It is estimated that hospitals in Morocco produce approximately 21,000 tons of HCW each year, with hazardous medical waste accounting for about 28% or 5,979 tons . HoweverRecognizing the need for ecological and rational management of medical waste, the Moroccan government has implemented a range of strategies and legal frameworks to govern this sector, including Law No. 28-00 2006) and Decree No. 2-09-139 (2009), on the management of MPW. According to articles 3 and 6 of this decree, MPW is classified into four categories based on their nature and characteristics, outlining specific procedures for sorting, packaging, storage, collection, transportation, treatment, and disposal 5, 6]., 6.5, 6] and DecrHowever, most healthcare facilities dispose of their HCWs in an uncontrolled manner . FurtherTherefore, the present study aimed to investigate the knowledge, attitudes, and practices (KAP) concerning managing HCWs at risk of infection among private dentists. This study excluded liquid, amalgam, chemical, and toxic radiological waste, subject to specific regulations.This cross-sectional survey was carried out for descriptive and analytical purposes between December 2020 and March 2021.The study included practitioners registered with the Moroccan National Council of Dentists and worked in private dental offices or clinics in the Rabat-Sal\u00e9-K\u00e9nitra region. Dentists who did not practice in the private sector, replacement dentists, or those who declined to participate were excluded from the study.A questionnaire was developed to assess the management of healthcare waste (HCW) generated by dental practices. The questionnaire was based on previous studies , 19\u201321 aThe questionnaire aimed to explore private practitioners' knowledge, attitudes, and practices related to HCW management. It included closed and open-ended questions divided into eight parts, covering socio-demographic characteristics, training in waste management, quantity and composition of waste generated, conditions of waste management from production to disposal, management of health risks, and general questions.Specifically, items were used in the questionnaire to assess participants\u2019 knowledge of household waste identification, compliance of waste conditioning equipment with international standards, treatment and disposal mode of contaminated waste, and healthcare risks inherent to HCW. Additional items were formulated to evaluate participants\u2019 attitudes towards HCW management, such as reasons for not using a specific waste management disposal, awareness about Moroccan law 28.00 relating to waste management, satisfaction with their waste management system, and suggestions for improvement. The other items were designed to assess their practices regarding HCW management, from production to disposal and prevention of related healthcare risks. All questionnaire respondents were included in the study, and efforts were made to avoid duplicate or repeated responses to ensure data accuracy and reliability.Cronbach's alpha coefficient was calculated to assess the reliability of the practice items in the questionnaire. An alpha coefficient >0.6 was considered acceptable for internal consistency. The internal consistency measurement in this study estimated Cronbach's alpha coefficient at 0.651.The sample size was calculated based on the percentage of practitioners performing sharps waste separation in special containers. This percentage was estimated at 89.9% in the study by Brunot and Thompson . The samQuantitative variables were reported as mean and standard deviation for symmetric distribution and median and quartiles for asymmetric distribution. Categorical variables were expressed as counts and percentages. An analysis was conducted to determine a possible association between different variables with waste management attitudes. The Chi-square or Fisher's Exact test was used to compare categorical variables. Statistical significance was set at a p-value of 5%. Data analysis and graphical representation were performed using Jamovi and Microsoft Excel (version 16.0).A total of 190 private dentists completed the questionnaire, resulting in a response rate of 38%. The participating dentists were evenly distributed between men and women and represented three cities in the Rabat-Sal\u00e9-K\u00e9nitra region. Most dentists (67.4%) practiced in Rabat, and most (96.2%) practiced in dental offices rather than clinics. Additionally, 38.4% of the participants had more than 15 years of clinical experience .About half of the dentists (52.6%) had basic training in waste management, and the majority (92.1%) had assigned dental assistants to manage office waste. Only 27.3% of the waste managers were trained on this topic .Dentists reported generating various types of HCW, but approximately half of the respondents (49.7%) indicated that they did not know the quantity of waste generated in their offices .Regarding the sorting and packaging of HCW, most dentists considered glove packaging, sterilization packaging, and used printer paper similar to household waste, with percentages of 86.2%, 81.8%, and 76.8%, respectively .For sharp wastes, 93.5% of dentists sorted them in bottles filled with plaster (53.2%) or specific rigid containers (39.8%) . MoreoveMost participants (77.6%) had adequate waste containers for collection, and most (90.9%) disinfected them regularly. Approximately three-quarters (73.5%) reported having a specific storage area in their office, and a minority (7%) used the sterilization area as a storage place.Only 25.1% of participants used a specific waste disposal route, with the majority (82.4%) collecting their waste from a service provider . ConversThe annual cost of the services was estimated at less than 1000 MAD (Moroccan dirhams) per year for 40.8% of the practitioners. In addition, 13.3% were informed about the waste treatment method, of which 90.9% is incineration .The dentists who did not use a specific disposal method for their waste mentioned several reasons, the most important of which was the lack of knowledge about waste collection companies (52.3%) and the cost of services (41.4%) .In this study, 55.5% of dentists reported no history of injuries or cuts from sharp wastes. Nearly all participants used protective equipment such as gloves, masks, and gowns, while 46.9% used safety glasses. Most staff (95.1%) were aware of the health risks associated with HCW, but only 24.6% reported being fully vaccinated.A small proportion of dentists (13.6%) stated they were sufficiently informed about Law 28-00 on waste management and disposal. Additionally, most dentists indicated that they had never been inspected by the Ministry of Health (97.5%) or the Municipal Hygiene Office (96.4%).When asked about suggestions for improving HCW management in their practices, dentists prioritized the need for information on waste collection in their geographical area (73.6%), training (63.2%), or contracting with a specialized company for biomedical waste treatment (61.5%). Other proposals included assigning responsibility to qualified personnel (36.8%), improving selective sorting at the office level (28.0%), and reducing waste at the source (13.7%).Among dentists with more than 15 years of practice, 56.7% had not received basic training in HCW management, compared to 22% who had received training (p<0.001).A statistically significant difference was observed between dentists who received basic training and those who did not, in terms of sorting non-sharp HCW (p<0.025), methods of sorting, use of a specific waste disposal route (p<0.001), and knowledge of law 28-00 (p=0.014) .Less than a third of dentists (30.2%) who sorted their HCWs used a specific waste disposal system compared to 2.9% who did not (p<0.001). A statistically significant difference in the percentage of the annual cost of services was also noted between dentists who sorted their HCWs and those who did not (p=0.017) and betwMoreover, 34.4% were aware of law 28-00 among those who used a specific waste disposal route, compared to 7.5% who did not use it (p<0.001). Similarly, 97.7% who used a specific waste disposal route were satisfied with their current management of HCW, compared to 48.1% who did not use it (p<0.001).The findings of this study provide an overview of the knowledge, attitudes, and practices of HCW management in private dental practices in the Rabat-Sal\u00e9-K\u00e9nitra region. The results highlight insufficient knowledge among dentists and non-compliance with Moroccan and international regulations regarding the various stages of HCW management.Almost half of the participants stated that they did not quantify their HCW. This percentage is significantly higher than reported in a French study of liberal health professionals in the Dordogne region, where only 14% of respondents were unaware of the quantity of HCW waste produced in their offices . Estimatet al. in Lebanon, where only 41% of participants received training programs on medical waste management , which explains the need for appropriate vaccination protection of personnel handling HCWs, including hepatitis A and B, as well as tetanus . Howeveret al. study, where only 50 completed and usable questionnaires were retrieved . Indy (29%) , 22. Thi. Indy (2HCW management practices in private dental practices in the Rabat-Sal\u00e9-K\u00e9nitra region should be improved. Several actions must be implemented to ensure their improvement and compliance with recognized standards. All dental health professionals, including those in private practices, must be integrated into awareness programs, continuing education, and assessment processes to manage HCW. National guidelines should be widely disseminated to all healthcare facilities along with all regulatory documents defining roles, responsibilities, obligations, and penalties related to the improper management of HCW. Adequate monitoring teams with warning and sanctions powers must be organized to compel all generators of HCW to comply with the regulations in force. The ultimate goal is a medical waste management system that is harmonious with sustainable development and protects the environment and human health."} +{"text": "ObjectiveThe purpose of this study is to evaluate the antibiotic prescription patterns of endodontists, general dentists, and other dental specialists for endodontic procedures in India by using the knowledge, attitude, and practices (KAP) survey method.MethodsThis cross-sectional study was carried out from February 2022 to May 2022 and involved dentists across India. A self-made questionnaire survey was created to judge the knowledge of various dental practitioners, which includes general dentists, endodontists, other dental specialists, and post-graduates with regard to antibiotic usage guidelines for endodontic purposes. A total of about 310 dental practitioners were surveyed across India. The questionnaire was circulated via social platforms such as WhatsApp, Instagram, and Facebook Messenger.Statistical analysisData for KAP regarding antibiotic prescription patterns among general dentists, endodontists, other dental specialists, and postgraduates were entered into Microsoft Excel and analyzed using IBM SPSS Statistics for Windows, Version 20 . Descriptive statistics of the study population were examined. The level of statistical significance was determined at p<0.05.ResultsFor the percentage of patients who were prescribed systemic antibiotics every day for endodontic reasons, about 38.6% (119) responded 0-10% and 27.3% (84) responded 10-30%. For the order of antibiotics that they prefer from most to least, about 85.4% (263) responded amoxicillin > metronidazole > doxycycline > azithromycin > clindamycin > ciprofloxacin. For the question of whether they use local antibiotics, about 35% answered yes of which 25% were endodontists, 2% were general dentists, 5% were other dental specialists, and 3% were post-graduates. About 77.3% of the total participants were unaware of the antimicrobial stewardship concept and AwaRe classification from WHO. About 53.2% (164) attended CDE programs with regard to antibiotic usage.ConclusionIt is evident from the results of the present study that there is over-prescription of antibiotics by practitioners especially by general dentists without following proper guidelines for endodontic treatments. More emphasis should be made on the proper prescription pattern of antibiotics, proper understanding of endodontic diagnosis, and the need for antibiotics at the undergraduate level. In addition, proper awareness, as well as proper prescription of antibiotics, should be made for existing dental professionals. Antibiotics were introduced in the late 1920s. These life-saving medicines should be used appropriately, or they would result in the development of resistance. Unfortunately, antibiotic over-prescription has resulted in the development of newer strains of bacteria that are resistant to these antibiotics. A large number of antibiotics that were effective in the past are not prescribed nowadays because of the development of resistance [Agnihotry et al. 2019) stated that the prescription of systemic antibiotics has become a common part of dental practice and has increased to a greater extent in the last two decades. Dental antibiotic prescription accounts for about 7-10% of the total antibiotic that has been prescribed worldwide for other medical reasons 019 state. The oveClinical situations that require antibiotic therapy include oral infections in medically compromised patients and those with systemic involvement such as malaise, elevated body temperature, trismus, lymphadenopathy, and progressive and persistent infections. Endodontic conditions, such as symptomatic reversible and irreversible pulpitis, pulpal necrosis, acute apical periodontitis, acute apical abscess with no systemic involvement, and chronic apical abscess, do not require antibiotic coverage .The primary cause of pulpal and periapical pathosis is micro-organisms . SystemiAbuse and irrational prescription are the main contributing factors to the emergence of antimicrobial resistance (AMR). Hence, the primary goal of this knowledge, attitude, and practices (KAP) survey is to assess the antibiotic prescription pattern among general dentists, endodontists, other dental specialty persons, and post-graduates in India for endodontic procedures.The null hypothesis is that there is no difference in the KAP regarding antibiotic prescription patterns among endodontists and other dentists.The research hypothesis is that there is a difference in the KAP regarding antibiotic prescription patterns among endodontists and other dentists.This cross-sectional study was carried out from\u00a0February 2022 to May 2022 and involved dentists across India. Ethical approval was obtained from the Institutional Human Ethics Committee registered with the\u00a0Central Drugs Standard Control Organisation (reg. no.: ECR/212/Inst/TN/2013/RR-19) of Chettinad Academy of Research and Education . The purpose of this study is to evaluate dental professionals' KAP\u00a0about the usage of antibiotics for endodontic reasons. The current study's inclusion criteria include general dentists, endodontists, other dental specialists, and post-graduates of all dental specialties in India. In addition, dental professionals who perform endodontic procedures in their day-to-day practice were only included in the survey. Practitioners who refused to take part in the study and those who do not perform endodontic procedures were excluded.A self-made questionnaire survey was created to judge the knowledge of various dental practitioners with regard to antibiotic usage guidelines for endodontic purposes. The questionnaire consisted of two parts: Part A contained demographic details and Part B contained the questionnaire proper with 16 questions regarding endodontic practice. They were presented as follows: six multiple-choice questions, one open-ended question, and nine yes/ no questions.The sample size of the current study was estimated using statistical power analysis G*Power software (version 3.1.9.2) and considering \u03c7\u00b2 tests, goodness-of-fit tests, contingency tables, and other input parameters:1. \u03b1 error as 0.05 at 95% CI2. \u03b2 error as 0.203. Power of the test (1-\u03b2 error) as 80%4. Degrees of freedom as 45. Effect size (Cohen\u2019s w statistic) as 0.1880 )The required total sample size for the current study was 338 participants with an output actual power of 80.04%. The questionnaire was circulated based on 338 participants, but only 310 participants responded to\u00a0the questionnaire, thereby having a non-response rate of 8.87%. The questionnaire was circulated via social platforms like WhatsApp, Instagram, and Facebook Messenger.Data regarding KAP regarding antibiotic prescription patterns among general dentists, endodontists, other dental specialists, and postgraduates were entered into Microsoft Excel and analyzed using IBM SPSS Statistics for Windows, Version 20. The descriptive statistics of the study population were examined. The relationship between the designation and years of experience and KAP regarding antibiotic usage was analyzed using the Chi-square test. The level of statistical significance was determined at p<0.05.In this study, among 308 dentists who answered the questionnaire survey, 32.5% 100) were general dentists, 24.4% were from other specialty PGs, 20.8% were endodontic PGs, 13% were endodontists, and only 9.4% were other dental specialists of which 2% were pedodontists, 2% were prosthodontists, 1.2% were orthodontists, 1.2% were oral surgeons, 1% were oral pathologists, 1% were periodontists, and the remaining 1% were public health dentists. In addition, 77.6% (239) had less than five years of clinical experience, 14.6% had 5-15 years of clinical experience, and only 7.8% had more than 15 years of clinical experience responded 0-5, and 35.7% (110) responded 6-10. For the percentage of patients who were prescribed systemic antibiotics every day for endodontic reasons, about 38.6% (119) responded 0-10%, and 27.3% (84) responded 10-30%. For the question conditions for which antibiotics were being prescribed, about 15.9% (49) responded dentoalveolar abscess, replantation after avulsion, and 84.1% (259) responded pain relief, reversible pulpitis, irreversible pulpitis, and endodontic flareups. For the most commonly prescribed antibiotics, about 87%(268) responded amoxicillin, and 11% (34) responded metronidazole. In the clinical situation for which they prescribe antibiotics, about 41.9% (129) responded based on radiological findings like periapical lesions\u00a0and 25%(77) responded that they would prescribe in the presence of systemic disorders like diabetes mellitus, hypertension, and cardiac conditions. For the order of antibiotics they would prefer from most to least, about 85.4% (263) responded amoxicillin > metronidazole > doxycycline > azithromycin > clindamycin > ciprofloxacin. For the question of whether they use local antibiotics, about 35% answered yes of which 25% were endodontists, 2% were general dentists, 5% were other dental specialists, and 3% were post-graduates.Regarding the prophylactic prescription of antibiotics prior to apical surgery, 76.6% (236) responded \"yes,\" and 84.7% (261) responded \"no.\" For the question of whether they advise antibiotic culture tests for their patients, 61.4% (189) responded that their patients had self-prescribed antibiotics, and 50% responded that their patients haven\u2019t responded to the prescribed antibiotics. With regard to the use of a combination of antibiotics for synergistic effects, 70.1% (216) responded \"yes,\" 67.5% (208) prescribed drugs based on drug dosage formula, half-life, and weight of the patient, and 71.8% (221) upgraded themselves with the new guidelines and updates regarding antibiotics prescription patterns. About 77.3% of the total participants were unaware of the AMS concept and AwaRe classification from WHO. About 53.2% (164) have attended CDE programs with regard to antibiotic usage.A recent study by the American Association of Endodontists (AAE) states that general dentists perform the majority of root canal treatments when compared with endodontists. Studies have reported that about 10 million deaths would occur per year globally by 2050, which makes drug resistance a curse of the medical profession unless sustained actions are not taken .Various contributing factors for AMR include inappropriate antibiotic prescription by medical or dental practitioners . Once reThe British Society for Antimicrobial Chemotherapy states that improper antibacterial drug prescription by dental practitioners is a major contributing factor in the development of drug-resistant strains. Factors such as inappropriate dosing, duration, and prophylaxis may contribute to the development of resistant strains. Therefore, it is essential to evaluate the prescription pattern in India to know whether there is a need for continuous education on antibiotic prescription patterns for dentists .AMR has been acknowledged as a global danger to public health by the World Health Assembly's acceptance of the global action plan on AMR in May 2015 and the political statement of the high-level meeting of the general assembly on AMR in September 2017 .This study shows that though a large number of respondents 38.6% (119) found the requirement to prescribe antibiotics was only 0-10% of the endodontic patients who have been examined every day, there were also 27.3% (84) who prescribed antibiotics in the range of 10-30% and 19.5% (60) who prescribed antibiotics between 30% and 50%, which may contribute to over-prescription of antibiotic to some extent. In addition, the majority of general dentists prescribe antibiotics for 10-30% of endodontic cases they handle in their day-to-day practice. This may be due to anxiety about pain development, preventing endodontic flareups, improving patient comfort, and the lack of awareness of proper antibiotic prescription patterns.According to a systematic review by James et al., antibiotics were not essential for irreversible pulpitis and pain relief ,14. In lAbout 87% of participants chose Amoxicillin as the first line of drug, followed by metronidazole (11%). This is consistent with the study done by Maslamani et al. . AmoxiciThe 2017 AAE guidelines regarding antibiotic prophylaxis given recommend\u00a0prescribing antibiotics for diabetic patients with poor glycemic control . The ESEStudies conducted by Amisha et al. 2020 and Singh et al. found that <40% of dentists have advised antibiotic culture test, and in this study, only 15.3% of dentists have advised it ,22. FurtA combination of antibiotics is prescribed by more than 70% of dentists. Amoxicillin + clavulanic acid is one such combination that\u00a0may be used for serious oral infections and in cases where resistant species might be suspected, which is refractory to normal endodontic procedures .The antimicrobial stewardship (AMS) concept was introduced by WHO to take care of the health and well-being of the people and provide guidelines for health systems both nationally and globally. The three pillars that strengthen the health systems are AMS, medicine and patient safety, and infection prevention and control. AMR shall be controlled with the help of AMS, antibiotic surveillance, the AWaRe classification, and the essential medicine list (EMS) from WHO . In AWaRIn this study, about 77% of dentists were unaware of the AMS concept and AWaRe classification from WHO, and this clearly states the reason for the overuse or misuse of drugs. In addition, 53.2%\u00a0of dentists have not regularly attended CDE programs with regard to antibiotic resistance.The endodontic flareups shall be prevented by following the proper working length of the tooth being prepared, thereby preventing apical extrusion of debris. NiTi rotary instruments showed less debris extrusion when compared with the step-back technique using manual instruments . FurtherIt is evident from the results of the present study that there is an over-prescription of antibiotics by practitioners, especially by general dentists, without following proper guidelines for endodontic treatments. More emphasis should be made on the proper prescription pattern of antibiotics at the undergraduate level. In addition, dental practitioners must be updated on recent guidelines for antibiotic prescription, the WHO\u2019s EML, and the AWaRe classification with the help of CDE programs and by following proper endodontic\u00a0diagnosis and treatment protocols to prevent endodontic flareups, thereby reducing the need for antibiotics. Patients should be warned about the adverse effects of self-prescribing antibiotics."} +{"text": "To assess the efficacy and effectiveness of seasonal influenza vaccines in healthy children up to the age of 18 years.MedLine, EMBASE, CENTRAL, CINAHL, WHOLIS, LILACS, and Global Health were searched for randomized controlled trials and cohort and case-control studies investigating the efficacy or effectiveness of influenza vaccines in healthy children up to the age of 18 years. The studies were assessed for their quality and data on the outcomes of influenza-like illness, laboratory-confirmed influenza, and hospitalizations were extracted. Seven meta-analyses were performed for different vaccines and different study outcomes.Vaccine efficacy for live vaccines, using random effects model, was as follows: (i) for similar antigen, using per-protocol analysis: 83.4% (78.3%-88.8%); (ii) for similar antigen, using intention to treat analysis: 82.5 (76.7%-88.6%); (iii) for any antigen, using per protocol analysis: 76.4% (68.7%-85.0%); (iv) for any antigen, using intention to treat analysis: 76.7% (68.8%-85.6%). Vaccine efficacy for inactivated vaccines, for similar antigen, using random effects model, was 67.3% (58.2%-77.9%). Vaccine effectiveness against influenza-like illness for live vaccines, using random effects model, was 31.4% (24.8%-39.6%) and using fixed-effect model 44.3% (42.6%-45.9%). Vaccine effectiveness against influenza-like illness for inactivated vaccines, using random effects model, was 32.5% (20.0%-52.9%) and using fixed-effect model 42.6% (38.3%-47.5%).Influenza vaccines showed high efficacy in children, particularly live vaccines. Effectiveness was lower and the data on hospitalizations were very limited. Influenza virus causes an acute respiratory tract infection, which results in considerable morbidity and mortality worldwide ,2. InfluThere are two types of vaccine available \u2013 live and inactivated, both of which can be used in children. They contain three different virus strains: two influenza A (H1N1-like and H3N2-like) and one influenza B, which have to be administered annually. Live vaccines are administered via an intranasal spray, whereas inactivated vaccines are injected, either intramuscularly or intradermally. Inactivated influenza vaccines contain killed virus, which makes them safer for use in pregnant women and those with underlying medical conditions; they cannot induce mild signs and symptoms of influenza like live vaccines. Vaccines can be adjuvanted to improve their immunogenicity . InactivWe aimed to identify all randomized control trials (RCTs) and cohort or case-control studies investigating the effectiveness or efficacy of influenza vaccines in reducing the incidence of influenza-like illness (ILI) or laboratory-confirmed influenza in children. In order to achieve this we searched Ovid MEDLINE (In-Process & Other Non-Indexed Citations and Ovid MEDLINE 1946 to Present), Embase + Embase Classic (1947 to present), the Cochrane Central Register of Controlled Trials (CENTRAL), Cumulative Index of Nursing and Allied Health Literature (CINAHL), World Health Organisation Library Information System (WHOLIS), Latin American and Caribbean Health Sciences Literature (LILACS), and Global Health Library (1910 to December 2011) using different combinations including the following search terms: influenza vaccines, attenuated vaccines, live vaccines, vaccination, human influenza, child, preschool-child, infant, influenza-like illness, hospitalization.After elimination of duplicates, results of searches from all databases combined identified 2105 potentially relevant articles. The titles and abstracts were screened and studies measuring only the safety or immunogenicity of vaccines were excluded, and so were the studies on pandemic influenza vaccines, studies assessing efficacy or effectiveness of vaccines in adults and children with asthma, and review articles. This process left 122 articles that required a more detailed evaluation, 92 of which did not fulfill the inclusion criteria. The number of studies that met all of the inclusion criteria was 30 .This review included RCTs, cohort studies, and case-control studies carried out in any country until the end of December 2011. Studies eligible for inclusion were those assessing any preparation of seasonal influenza vaccine, administered via any route to healthy participants up to and including the age of 18 years. For inclusion, studies had to have a comparison to a control group that received either an alternative vaccine, placebo, or no intervention. Outcome measures considered for inclusion were cases of influenza or ILI confirmed either clinically or by laboratory techniques, hospitalizations due to influenza, and preventive efficacy or effectiveness of vaccines. For the purposes of this review, efficacy was defined as the ability of the vaccine to reduce the number of laboratory-confirmed cases of illness caused by influenza infection. Effectiveness was defined as the ability of the vaccine to reduce clinical cases of symptomatic influenza-like illnesses.We excluded the studies that assessed vaccines in children with chronic illnesses, such as asthma. Searches also produced a considerable number of studies that did not record clinical outcomes, but rather defined the presence of infection using serological data, such as antibody titers. Those studies were also excluded from the assessment of effectiveness.We extracted information on the main characteristics of the studies on live vaccines and inacVE\u2009=\u2009100% - odds ratio (OR); or VE\u2009=\u2009100% - risk ratio (RR),with 95% confidence intervals (CIs) provided, results were entered directly into the data extraction table. Wherever studies had reported OR or RR, the overall VE and CIs were calculated. In the studies that only reported the number of ILIs (or laboratory-confirmed influenza cases) in vaccinated individuals and controls, the OR was calculated and overall VE and CIs recorded. Studies were then classified by outcomes, to allow separate assessment of efficacy and effectiveness. Tables were created to compare the efficacy or effectiveness of live and inactivated vaccines -6. From The retained 30 studies comprised 19 RCTs -28, 9 coTo assess the quality of studies we used the GRADE criteria supplem. In termVaccine efficacy for live vaccines, using random effects model, was as follows: (i) for similar antigen, using per-protocol analysis: 83.4% (78.3%-88.8%); (ii) for similar antigen, using intention to treat analysis: 82.5 (76.7%-88.6%); (iii) for any antigen, using per protocol analysis: 76.4% (68.7%-85.0%); (iv) for any antigen, using intention to treat analysis: 76.7% (68.8%-85.6%). Vaccine efficacy for inactivated vaccines, for similar antigen, using random effects model, was 67.3% (58.2%-77.9%). The results of fixed-effects model consistently showed slightly greater efficacy than the results of random-effects model and using fixed-effect model 44.3% (42.6%-45.9%). Vaccine effectiveness against influenza-like illness for inactivated vaccines, using random effects model, was 32.5% (20.0%-52.9%) and 42.6% (38.3%-47.5%) using fixed-effect model , antigen used (similar or any), and analysis used (per protocol or intention to treat). Still, studies that were grouped together varied in study designs, case definitions, and age ranges applied (Supplementary materialIn many studies, there was a lack of information on the composition of the vaccine used and its matching to the circulating strains of influenza viruses for that season. This is vital as it inevitably will have a significant effect on the efficacy of vaccines. Influenza vaccines will not have effect against antigenically dissimilar viruses. There are also some limitations imposed by the nature of research available in the area of influenza vaccines. There were no studies that directly compared live and inactivated vaccines, although such studies would allow an analysis of the efficacy and effectiveness of the vaccines in a comparable context. There was a considerable heterogeneity in the outcome definitions used in the studies, particularly with reference to ILI definitions. Studies also differed according to methods of collecting data on ILIs; in some studies cases were diagnosed by general practitioners or pediatricians on visits to a clinic and in others according to parental reports of symptoms.The main strength of this review, compared to other relevant literature, is that it summarized the available information on this issue and provided an evidence base from which further research could be conducted. It exposed differences in the quality and methodological approaches to studies, such as the definition of outcomes and study designs and gaps in information provided for certain age groups. It strengthened the existing knowledge, providing a summary of the data on the effect of live and inactivated vaccines in preventing influenza in children, in whom it showed comparable results to healthy adults. Areas for future research have also been highlighted, such as the direct comparison of the efficacy of live and inactivated vaccines, more systematic research into benefits of each type of vaccine for different age groups, and the need for a wider evidence base supporting potentially promising adjuvanted inactivated influenza vaccines ."} +{"text": "To the Editor: West Nile virus (WNV), spread by infected mosquitoes, is a serious public health threat throughout the United States and can cause life-altering and even fatal disease regarding WNV among Hispanics in San Diego County. According to the US Census Bureau, the county is home to >900,000 Hispanics, of whom \u224841% are foreign born from which the interviewee indicated yes or no. Multiple responses were allowed. Questions were based on those used in previous studies and in border-region focus groups and were modified according to input from local experts and pilot testing. Spanish translation and back translation were conducted separately by 2 translators.Interviewers completed 226 surveys, which represented 53.8% of all houses approached and 69.5% of 325 households in which a person answered the door. Respondents\u2019 mean age was 41 years (range 18\u201387 years), 79.2% were foreign born, 85.8% completed the survey in Spanish, and 65.9% were women. Overall, 149 (66.2%) of the 226 respondents were aware of WNV; key demographic covariates differed, including greater awareness among English speakers, respondents living in the United States >5 years, and respondents completing >12 years of education . News meAmong the 149 respondents who were aware of WNV, 62 (41.6%) adopted PPBs to protect themselves or their families; more women than men adopted PPBs . The mos\u2013We found lower awareness of WNV among San Diego County Hispanics (66.2%) than previously reported for predominantly non-Hispanic populations (range 77.2%\u201399.0%) (The finding of low awareness, concern, and PPB adoption may have 2 possible explanations. First, the observations may be appropriate given the low incidence of WNV in San Diego County and Mexico. At the time the survey was conducted, only 1 locally acquired case of WNV infection among humans had been reported in San Diego County; through 2006, WNV was rarely reported among humans in Mexico (Differences in awareness, concern, and practices among Hispanics by age, education, gender, language, years living in United States, and region of San Diego County indicate that varied educational tactics are needed to inform this population. Most educational efforts for Hispanics are simple translations of material into Spanish, which are likely not sufficient to reach this heterogeneous population."} +{"text": "We aimed to examine the prevalence of botanical dietary supplement (BDS) use among Hispanics in the United States (US) through a systematic review of the literature.We performed a systematic review of BDS use among adult Hispanics living in the US. Our strategy included electronic database searches with keywords: herbal, herb, medicinal plant, botanical and Hispanic or Latino along with a manual search of retrieved references. We included only studies with at least 1% Hispanics, prevalence estimates for Hispanics, and publication dates 1998-2011. We extracted information on study and sample characteristics, and rates of disclosures to clinicians.Of the 35 studies reporting prevalence of BDS use among Hispanics, estimates ranged from 5% to 94% with a slightly narrower range restricting to use over the past 12 months (7-75%). Eighty-one percent (n=27) of studies included non-Hispanics and 54% reported <500 subjects. Smaller study size, regional location, convenience sampling, and longer recall periods were associated with greater prevalence of BDS use among Hispanics . Studies with predominantly Hispanic samples also reported higher prevalence (p = 0.02). Of the predominantly Hispanic studies (n=11), 64% were conducted in states bordering Mexico, all in both English and Spanish. Rates of use and disclosure to clinicians ranged from 7 to 65% and did not depend on the presence of underlying health conditions. Health conditions included breast cancer, HIV, diabetes, heart disease, menopause, and pregnancy.Variability in reported prevalence of herb use among Hispanics depends, in part, on sample composition, possibly related to the use of Hispanic-specific instruments. Disclosure rates also varied widely, even in high risk illness. Because of marked variability in estimates, more research is needed to understand patterns of BDS use and disclosure among Hispanic populations in the US."} +{"text": "Dear Editor,Since the world came into existence, humanity has striven relentlessly to be happy. The prevModification of cardiovascular risk factors can reduce the incidence of ischemic heart disease, effectively extend survival, decrease the need for interventional procedures, and improve quality of life in persons with known cardiovascular diseases. AlthoughTobacco in any form, chewable or non-chewable and passive smoking are equally injurious, and are major predisposing factors for a premature heart attack and sudden death. Coronary artery disease has been seen in 80 percent of smokers. Public eFrom 8.10.2008 to 8.2.2009, a quasi-experimental study was conducted among 200 unstable angina patients selected by simple randomized sampling method who were admitted at Ruby Hall, Jehangir and NM Wadia Hospital in Pune city, India. The research method adopted for the study was quasiexperimental with one group pre-test and post-test design. The instrument used for data collection was the Modified Life Style Assessment Questionnaire. The collected data were organized and analyzed according to objectives of the study using distribution of demographic variables in frequency and percentage.In demographic variables, most of the participants were in the age group 45-54 years (66%), 78% were male, 87% were married, 26.5% were university graduates and 22% were employed. Sixty four percent of those employed had 8000 Rs or more monthly incomes, 58% were couples and 37.5% had more than 5 family members. Fifty one percent had mixed dietary habits and 90% patients had a family history of heart disease.Fifteen percent of patients smoked cigarette in the pre-test while in the post-test 10% of patients were smokers. Eighty eight percent did not smoke cigarette before the age of 20. Fifty two percent in pre-test and 67% in post-test smoked 5-10 cigarettes per day. Fifty five percent smoked cigarette for more than 15 years. The majority of smokers (40%) were less than 1 hour in the pre-test.Knowledge about quitting of smoking . Self ex"} +{"text": "Hepatitis delta virus (HDV) leads to the most severe form of chronic viral hepatitis.To determine the prevalence of HDV and create pooled estimations of possible risk factors, a systematic review was conducted to collect all epidemiological studies on HDV among chronic hepatitis B patients in Iran.In this systematic review, databases such as PubMed, Embase, ISI, Google scholar, and Iranian databases were searched.Studies that clearly stated information about the number of HBsAg positive patients infected with HDV were selected.The name of the city, the author's name, year of study, HDV detection method, sample size, HBsAg positive frequency, mean age, total prevalence of HDV, and risk factors were extracted.The pooled HDV prevalence was 7.8% (95% CI: 5.89 - 9.71). In the survey-data analysis, HDV prevalence was 6.61%. HDV prevalence was 30.47% (95% CI: 9.76 to 51.19), 14.4% (95% CI: 7.72 to 21.07), and 4.94% (95% CI: 3.73 to 6.15) in cirrhotic, chronic-hepatitis, and inactive-carrier patients, respectively. Pooled ORs were calculated for several factors common to Iranian HBsAg-positive patients, including history of blood transfusion [OR: 1.1 (95% CI: 0.40 to 2.98)], intravenous drug abuse [OR: 1.6 (95% CI: 0.78 to 3.21)], previous hemodialysis [OR: 1.72 (95% CI: 0.79 to 3.76)], and HBeAg-positive status [OR: 1.26 (95% CI: 0.66 to 2.4)].The prevalence of HDV is less common in Iran than in endemic regions such as Italy and Turkey; however, it is a severe form of hepatitis in HBsAg-positive patients. The most probable route of HDV transmission is hematologic, which suggests the importance of blood screening for HDV, especially in groups with numerous blood transfusions. Delta hepatitis infection leads to the most threatening form of chronic viral hepatitis, which can cause cirrhosis, fibrosis, and hepatocellular carcinoma (HCC) 2]3]. M[3]. M2][. M[3]. MTo provide a clear estimate of HDV prevalence in Iran and address a gap in the field's knowledge, we designed a systematic review to collect all respective epidemiological studies conducted in Iran about HDV in chronic hepatitis B patients. The prevalence of HDV was analyzed separately in the setting of chronic hepatitis, liver cirrhosis, HCC, and inactive carriers to show the effects of HDV on hepatitis progression. We investigated regional differences as well as potential chronological changes to analyze epidemiological changes of hepatitis D in various parts of Iran. Pooled estimations for each possible risk factor, especially in high-risk groups, were calculated to identify the most important routes of HDV transmission.The authors reviewed studies and evaluated the prevalence of HDV infection in HBsAg positive cases. The outcomes considered in this review were the prevalence and risk factors of HDV infection.One author (N.A.) conducted an electronic literature search through Scopus, ISI, Google scholar, and three Medline database engines-PubMed, Embase, and Ovid-using different combinations of the word Iran and the key words \"hepatitis D, Delta antigen, HDV, and hepatitis delta virus\". Iranian databases, including MagIran, IranMedex, and SID, were also searched with relevant English and Persian key words. At the time when these searches were conducted, the databases were limited to published and unpublished information up to and including December 2010. Search sensitivity was checked by considering duplicated papers. If the full text of articles were not accessible, an e-mail was sent to the author. If no response was received after one month, the abstract was used to extract data .Only studies that clearly stated information about the numbers of HBsAg-positive patients infected with HDV were selected. Studies in which all patients had acute hepatitis B 14]15] [15] 14][ [15] 14]A critical appraisal (CA) was conducted using the Epible checklist by threeData extraction was completed by three investigators and rechecked by one of them (NA). Information was entered into Microsoft Office Excel 2007. The name of the city the author's name, year of study, HDV-detection method, sample size, HBsAg-positive frequency, mean age, and total prevalence of HDV were extracted. Moreover, standard errors (SE) were calculated as SE = \u221a (P \u00d7 [1-P] / N), where P = prevalence and N = sample size. HDV prevalence was extracted in different subgroups consisting of cirrhotic patients, inactive carriers, chronic hepatitis patients, and male and female participants.A 95% CI of the seroprevalence of anti-HDV antibody was computed for each of the included studies using the approximate normal distribution model. The summary estimate of HDV prevalence was calculated as an average of the individual study results weighted by the inverse of their variances using fix/random models (DerSimonian and Laird) based on the heterogeneity test result using Q, I-squared and Tau-squared statistics. Due to the low power of this test, a minimum cut-off P value of 0.1 was established as a threshold of heterogeneity. I-squared lies between 0% and 100% and heterogeneity increases with increasing of I-squared value. Because few articles were available on some subgroups, Tau-squared is more suitable because it is not influenced by the number of studies. The results were expressed in geographic maps using Arc View 3.2 software . For provinces with more than one study, the pooled estimation of anti-HDV prevalence was computed using the meta command, and then a survey-data analysis was used to estimate more accurate HDV-infection prevalence considering the weight of each city , which wSubgroup analyses were designed according to disease patterns and quality assessment scores (good and moderate). An overall meta-analysis was performed for each risk factor to determine whether the factor increased HDV prevalence. The available data were used to calculate or confirm the unadjusted odds ratio (OR). Risk factors, without complete data to calculate their OR, were omitted. To make pooled estimates, the authors used the \"metan\" command to compute point-estimation ORs with a 95% CI for each risk factor. The analysis was performed with STATA 11 software (STATA Corp. LP).Ninety-six articles were found in the literature review, 40 of which 11]12][[12][11][[[12][11]Reported HDV prevalence varied widely, from 0% in Sari to 20% iOne source of heterogeneity was the different target populations in the studies. Therefore, the point estimations were broken into three subgroups: cirrhotic, chronic-hepatitis, and inactive-carrier patients. There were 198 patients in the cirrhotic and HCC groups , and the pooled estimation in this group was 30.47% (95% CI: 9.76 - 51.19). In chronic hepatitis group among 1,114 patients, the HDV prevalence in the random model was 14.4% .In 4,372 inactive carrier patients, the HDV prevalence was 4.94 % among 2,644 men and 5.34% (95% CI: 5.26 - 5.44) among 1,390 women.Ten articles 21]22][[22][21][[[22][21]According to our results, the overall estimation of HDV seropositivity in Iran is about 6.61% in HBsAg positive patients. The estimates were also run for asymptomatic and symptomatic HBsAg-positive patients. In our findings, the overall estimation in the asymptomatic group was about 5%, and the time trend did not follow a recognizable pattern. Without considering outliers, the HDV prevalence moved closer to 5%. The HDV prevalence among symptomatic HBsAg-positive patients was about 14.5%, and it has been increasing over the years. The increase in HDV prevalence among symptomatic HBsAg-positive is different from the reports of declining cases in Italy , Spain , Taiwan HDV is more common in the south of Iran than in the north. However, HBV prevalence is higher in the north . The difOur findings show that HDV is more common among cirrhotic and HCC patients. In a retrospective study in European patients with HBV-related cirrhosis, Fattovich et al. found thIn our study, the prevalence of HDV was higher in males 8.63%) than in females (5.34%). Blood transfusion was generally more common in women, but we could not detect this factor's impact on HDV prevalence. However, other factors, such as a greater possibility of multiple partners, intravenous drug abuse, war injury, and a higher rate of HBV infection in men , can be 3% than iThis review has some limitations, such as the lack of library and thesis searches. Additionally, data were available from 43% of provinces, and most of the data came from urban areas. The common method used for HDV detection was ELISA. Confirmation of ongoing HDV infection by PCR testing of HDV RNA was missing. The impact of this lack of information was that patients with and without active delta infection could be differentiated. The strongest part of this study was the use of a survey-data analysis in addition to the usual meta commands to generalize the results to the whole population. Moreover, a critical appraisal allows for more accurate estimates. A quality subgroup analysis showed that the low-quality papers underestimated HDV prevalence.In conclusion, the prevalence of HDV is less common in Iran than in endemic regions; however, this is a severe form of hepatitis in Iranian patients. The most probable route of HDV transmission is hematologic, which shows the importance of blood screening for HDV, especially in groups with numerous blood transfusions. Information is lacking from some provinces, and ongoing research is required to understand the effects of HDV infection on HBsAg-positive patients and its risk factors. More research should be conducted on HDV to develop innovate strategies to control and diagnose this most severe form of viral hepatitis."} +{"text": "The Alcohol Needs Assessment Project estimated that 20% of people aged \u226555 years consume alcohol at levels hazardous to their health, which is associated with a wide range of physical, psychological, and social problems, including coronary heart disease, hypertension, stroke, liver disease, and increased risk of a range of cancers. The Alcohol\u2014Evaluating Stepped Care for Older Populations (AESOPS) research study is a randomized controlled trial looking at the effectiveness and cost-effectiveness of an opportunistic screening, brief intervention, and stepped care framework for older hazardous alcohol users in primary care compared with minimal intervention. Opportunistic screening of patients aged \u226555 years was conducted in 53 primary health care practices from eight areas across England. Patients who screened positive for an alcohol use disorder (AUD) were randomly allocated to one of two intervention conditions: brief structured advice or stepped care. Approximately 78,260 screening questionnaires were distributed, and 21,524 (27.5%) were returned. Seven-and-a-half percent of respondents screened positive for AUD. Of eligible patients, 51.3% were randomized to stepped care, most (99.6%) of whom received step one (brief lifestyle intervention); 55.1% received step two , and 10.2% were referred to step three . Results to date are discussed."} +{"text": "Folic acid (FA) added to foods during fortification is 70-85% bioavailable compared to 50% of folate occurring naturally in foods. Thus, if FA supplements also are taken during pregnancy, both mother and fetus can be exposed to FA exceeding the Institute of Medicine's recommended tolerable upper limit (TUL) of 1,000 micrograms per day (\u03bcg/d) for adult pregnant women. The primary objective is to estimate the proportion of women taking folic acid (FA) doses exceeding the TUL before and during pregnancy, and to identify correlates of high FA use.During 2005-2008, pre-pregnancy and pregnancy-related data on dietary supplementation were obtained by interviewing 539 pregnant women enrolled at two obstetrics-care facilities in Durham County, North Carolina.Before pregnancy, 51% of women reported FA supplementation and 66% reported this supplementation during pregnancy. Before pregnancy, 11.9% (95% CI = 9.2%-14.6%) of women reported supplementation with FA doses above the TUL of 1,000 \u03bcg/day, and a similar proportion reported this intake prenatally. Before pregnancy, Caucasian women were more likely to take FA doses above the TUL , compared to African American women, while women with chronic conditions were less likely to take FA doses above the TUL . Compared to African American women, Caucasian women were also more likely to report FA intake in doses exceeding the TUL during pregnancy .Fifty-one percent of women reported some FA intake before and 66% during pregnancy, respectively, and more than one in ten women took FA supplements in doses that exceeded the TUL. Caucasian women were more likely to report high FA intake. A study is ongoing to identify possible genetic and non-genotoxic effects of these high doses. Previous studies have demonstrated that daily folic acid (FA) supplementation during preconception lowers the risk of neural tube defects -4 and otFolic acid added to foods during fortification is 70-85% bioavailable compared to 50% of folate occurring naturally in foods ,13. Thusin utero exposure to cigarette smoke is associated with poor birth outcomes and may predict high FA use ?\". To obtain folic acid intake during pregnancy, women were asked to respond to the question \"Since you found out you were pregnant, did you take [dietary supplement]?\" Supplement users were asked the brand name, the frequency of intake and trimester when intake started, if intake started during pregnancy. Study participants were unaware of the study hypothesis. The frequency and dose of FA intake before and during pregnancy was converted into daily \u03bcg/day FA intake using dosage information provided on the packet. Where specific brands were not recalled, a conservative value of 400 \u03bcg was assigned.Women were categorized as non-users (no supplementation), users within recommended range , and users exceeding the TUL for adults . A dose of \u22641,000 \u03bcg/d was assigned to women reporting \"over-the-counter daily multivitamin\" as these supplements provide ~400 \u03bcg/d of FA. Women taking \"additional FA\" providing ~800 \u03bcg/d of FA, and those reporting intake of \"prenatal vitamins only\" which provide ~600-1,000 \u03bcg/d of FA, were also included in the category of users within the recommended range. Doses exceeding 1,000 \u03bcg/d were assigned to women who reported intake of a combination of \"prenatal vitamins\" including those prescribed and \"over-the-counter multivitamins\" (~400 \u03bcg/d) of FA, and/or multivitamins with \"additional FA\" (~400 \u03bcg/d). Total FA intake ranged from 0 to >1,600 \u03bcg/d.any FA use including ethnicity . During pregnancy, some FA use was reported by 66% (95%CI = 62%-70%) of women. FA intake within recommended doses of \u22641,000 \u03bcg/d was reported by 295/539 or 55% (95%CI = 51-59%), and intake of doses exceeding the TUL for adults of >1,000 \u03bcg/d was reported by 11% (95%CI = 8%-14%) of women. Because we targeted smokers, we also evaluated whether FA use exceeding the TUL varied by smoking status. We found no statistically significant differences in FA use by smoking status as 6% (95%CI = 2%-11%) of smokers and 13% (95%CI = 10%-17%) of non-smokers reported FA intake \u22651,000 \u03bcg/d before pregnancy (data not shown). During pregnancy, the proportion of women reporting FA use exceeding TUL for adults was also similar in smokers 12% (95%CI = 6%-17%) and non-smokers 11% (95%CI = 8%-14%) .Overall, 51% (95%CI = 47-55%) of women reported some FA use before pregnancy. Recommended FA doses taken either as a multivitamin or a single dietary supplement were reported by 209/539 or 39% (95%CI = 35%-43%), and intake of doses exceeding the TUL for adults was reported by 12% (95%CI = 9%-15%) of women before pregnancy [Table 2]. The direction and magnitude of these associations was similar among FA users exceeding the TUL and those whose intake was within recommended doses, and among smokers.Compared to non-users, FA intake exceeding 1,000 \u03bcg/d before pregnancy was reported more frequently by women who were aged >35 years , married or living with partner , privately insured , Caucasian , and women with a college or higher education . Smokers , those exposed to second hand smoke and those reporting any chronic disease , were less likely to report FA intake exceeding the TUL. Mutual adjustment of these factors revealed some attenuation of these effects as FA intake exceeding the TUL remained significantly more likely to be reported by Caucasian women , and less likely by women reporting at least one chronic condition during pregnancy . The direction of the association between high FA intake and advanced maternal age , being married or living with a partner , and having a college or higher education were maintained in multivariate analyses, although the magnitude of associations was attenuated Table Five percent of women reported FA supplementation \u22651,000 \u03bcg/d both before pregnancy and during pregnancy, and 75% were Caucasians with a college or higher education.Our key findings were that overall, 51% of women reported some FA intake before pregnancy and 66% reported the same during pregnancy. In addition, more than 10% of women reported daily FA supplementation exceeding the TUL before or during pregnancy. Notably, 5% of the women reported taking FA exceeding the TUL, both before and during pregnancy. FA intake exceeding TUL was most frequently reported by Caucasian women, and least frequently by those reporting at least one morbid condition. Borderline associations were also found with advanced maternal age and having a college or higher education. Recently, data from the National Health and Nutrition Examination Survey estimated that in women of childbearing age, ~1% of women are exposed to FA doses exceeding 1,000 \u03bcg/d from fortified food alone, and 26% report FA intake in doses exceeding the recommended 400 \u03bcg/d .methylenetetrahydrofolate reductase (MTHFR) 677T-allele in the fetus [insulin-like growth factor (IGF2) differentially methylated region (DMR) that regulates IGF2 imprinting in children [IGF2 DMR has been associated with a higher risk of overgrowth disorders in childhood [Median folate intake among women of child-bearing age in the US is 450 \u03bcg/d and approximately 75% is contributed by FA ,23. Becahe fetus ,31. Carrhe fetus -35. Convchildren . Loss ofhildhood and colohildhood . Our finany FA supplementation was evaluated [The estimate of 66% FA use during pregnancy in our study is consistent with previous reports among pregnant women in the US ,40 and ovaluated ,45, and While the design is hospital-based, the distribution of demographic characteristics in this population is similar to that of the three-county region from which study participants largely arose ,46 and aIn summary, while the FDA goal of consuming at least 400 \u03bcg/d of FA pre-conceptionally has been achieved by 50% of women of childbearing age, more than one-tenth of pregnant women consume daily doses that exceed the TUL with unknown effects to humans. The use of FA exceeding the TUL was associated with Caucasian race/ethnicity, advanced maternal age and a college or higher education. This study is part of a larger effort to characterize the role of early exposures on genetic and epigenetic perturbations in humans.The authors declare that they have no competing interests.CH conceived of the study, designed the study directed the data collection, analysis and interpretation of the data, and drafted the manuscript. APM oversaw participant recruitment in the clinic, contributed to interpretation of the results and drafting the manuscript. JMS contributed to the study design, analysis, interpretation of the data and drafting the manuscript. MRF contributed to analysis and interpretation of the data. BC performed the statistical analysis. WDW contributed to the inception of the research hypothesis and aims. JK contributed to the logistics of data collection and interpretation of results. RLJ contributed to analysis and interpretation of the data. SKM helped conceive the study, contributed to the data interpretation and drafting the manuscript.All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2458/11/46/prepub"} +{"text": "An increased lung cancer risk in SLE has been suggested in the literature . Our objData from an SLE sample of 15,980 SLE patients from 28 centers were analyzed . Information on date of birth, sex and race was available, along with the date of SLE diagnosis. Cancer occurrence was ascertained through linkages with regional tumor registries. We assessed the demographic characteristics for all lung cancer cases in the SLE patients, and information on histology types was analyzed from the centers where this information was available.n = 54, 53.5%) followed by nine African-American, one Asian, one Pacific-Islander and one of unknown racial/ethnic origin. Histological lung cancer type was only provided by 12 centers (59 cases). The most common histological type reported within these 59 cases was squamous cell carcinoma followed by adenocarcinoma and nonsmall-cell carcinoma . The remaining 44% were composed of carcinomas not otherwise specified and a variety of uncommon tumors: large cell, clear cell, solid, bronchoalveolar, adenosquamous, epithelial hemangioendothelioma, oat cell, carcinoid, small cell and mucinous histological types.In the current analyses, 101 lung cancer cases that had occurred after SLE diagnosis were studied. The lung cancer cases were distributed across 21 centers. The average age of the SLE patients at lung cancer diagnosis was 60 years 10.9). The average SLE duration at the time of lung cancer diagnosis was 13 years . Race/ethnicity was not provided by six centers (35 cases). Of the remaining 66 cases, the majority were Caucasian (In the general population, about 30 to 40% of lung cancer cases are adenocarcinoma, with 20 to 30% squamous cell carcinoma, and 10% large cell carcinoma ["} +{"text": "Triple-negative breast cancer (TNBC) accounts for 10 to 15% of diagnosed breast cancers worldwide. TNBC is negative for oestrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 expression, and is associated with a poor prognosis. Our study aims to systematically review the possible link between various minority ethnic groups and development of TNBC.A systematic review of carefully selected studies was carried out with search of relevant articles in Medline, Science Direct and PubMed from 2005 up to 2013 with studies specifically aimed at TNBC. In the UK, receptor data have not been consistently recorded and involve smaller sample sizes. Hence, the relevant articles include ethnic groups from Asia Pacific and USA. Keywords were: triple negative, TNBC, ethnicity, incidence, prevalence. The data from all relevant articles were combined to give a sufficiently large sample size.n = 50,797), Black , Asian , Hispanic and other (n = 190). Overall there were 9,887 TNBC cases in the sample group with Caucasian , Black , Asian (n = 842), Hispanic and other (n = 16). Hence, overall 13.59% of all diagnosed breast cancers were TNBC with 11.73% in Caucasian, 26.99% in Black, 12.19% in Asian, 17.5% in Hispanic and 8.42% in other women.Complete receptor data were available for 72,763 cases, which constitute the sample group. On the available ethnicity data these were divided into five groups: Caucasian (Overall minority ethnic women have higher incidence of TNBC than Caucasian women with resultant poor prognosis. With rising minority ethnic population in the UK the overall number of TNBC will rise. Further research is required into the reasons for this."} +{"text": "Temporomandibular joint (TMJ) involvement occurs up to 80% of patients with juvenile idiopathic arthritis (JIA). Currently they are no standardized procedures regarding diagnosis and treatment of this common presentation of JIA.To assess the current clinical practices regarding diagnosis and treatment of TMJ involvement in JIA.Paediatric rheumatology colleagues were asked to fill out a survey with 8 items regarding diagnosis and treatment of TMJ involvement. The survey was distributed over the worldwide Paediatric Rheumatology electronic list-serve.87 centres responded to the survey by Oktober 2010. Fortythree of the centres followed more than 300 patients with JIA. All responding centres were actively screening for TMJ involvement, 85 by history, all by physical exam and 2 by imaging. Seventy-seven (88%) were screening at first visit and 76 (87%) at each follow-up visit. If imaging was requested, 77% asked for MRI, 10% for ultrasound, 9% for CT and 33% for Xray. The centres reported the following prevalence of TMJ involvement: over 50% - 3 % of the centres, between 25 and 50% -10% of the centres; between 10% and 25% - 50% of the centres, less than 10% - 32% of the centres. The first line treatment of the TMJ involvement was a DMARD in 47%, an NSAID in 43%, an intraarticular corticosteroid injection in 34% and an anti-TNF agent in 6%. Overall, 57 of the centres (65%) were using intraarticular corticosteroid injections as treatment; of these centres 32 (56%) were using imaging. 20 centres gave details about imaging. MRI were used in 10% , CT in 30%, ultrasound in 45% and fluoroscopy in 15% as imaging for guidance during injections.TMJ arthritis is common among children with JIA, but a wide array of diagnostic and therapeutic approaches are being employed. An expert opinion/consensus statement regarding TMJ arthritis in JIA will likely benefit patients worldwide."} +{"text": "In the United States, AIDS was first reported in women in 1981 in men and 29,865 (29.3%) in women. Among women, 71.9% were non-Hispanic blacks, 18.2% were non-Hispanic whites, 8.4% were Hispanics, 0.6% were American Indian/Alaska Natives, and 0.4% were Asian/Pacific Islanders. The two principal modes of HIV exposure for women were heterosexual contact and injection drug use, accounting for 77.7% and 20.5% of diagnoses among women, respectively. Women were diagnosed with HIV at younger ages than men. For the 4-year period, 31.3% of women with HIV were in the 13- to 29-year age group compared with 19.9% of men in the same age group. HIV diagnosis rates were consistently higher among non-Hispanic black women compared with women from other racial and ethnic groups for all 4 years.In 2003, the Centers for Disease Control and Prevention (CDC) introduced the Advancing HIV Prevention (AHP) initiative (HIV-infected women may be at increased risk for medical problems and metabolic changes. Studies have shown that HIV-positive women were more likely to develop genital warts and cervical intraepithelial neoplasia (Determining when to initiate antiretroviral therapy for HIV-infected women is based on CD4+ T cell count (For many reasons, women with HIV may avoid HIV testing and care. Often, women may be stigmatized and endure discrimination because of their HIV status. Women are often the primary caregivers for other family members, which may lead to avoiding or delaying testing and care. Economic dependence on a spouse or significant other may also play a role in whether a woman seeks testing and care. Mistrust of the healthcare system may also exist. Depression or domestic violence may also affect a woman\u2019s ability to seek needed care for HIV infection.In 2003, CDC, the Health Resources and Services Administration, National Institutes of Health, and the HIV Medicine Association of the Infectious Diseases Society of America issued recommendations to assist clinicians in integrating HIV prevention into primary care for HIV-infected persons. Providers are encouraged to deliver brief prevention messages during primary care visits, screen for HIV risk behaviors and sexually transmitted disease, provide HIV behavioral risk-reduction messages, and facilitate partner notification and counseling ("} +{"text": "Despite consistent evidence supporting physical activity (PA) in prevention of chronic diseases, many individuals of Mexican-origin, including children, fail to meet PA recommendations. Environmental influences on PA, founded in ecological and social cognitive perspectives, have not been examined among children living in colonias. The purpose of this study was to identify and better understand (1) household and neighborhood environmental PA resources/supports, (2) perceived barriers to engaging in PA, and (3) PA offerings, locations, and transportation characteristics for Mexican-origin children living in colonias.The increasing numbers of promotora-researchers using face-to-face interviews conducted in Spanish. The sample consists of 94 mother-child dyads from Texas border colonias in Hidalgo County. Interviews included questionnaire items addressing PA barriers, household and neighborhood environmental support assessments conducted with each dyad, and open-ended questions that were coded to identify availability and locations of PA opportunities and transportation options. Descriptive statistics were calculated and differences between genders, birth countries, and BMI categories of children were determined using chi-square tests.Data for this study were collected by colonias. Differences in PA barriers, options, and environmental resources for genders, birth countries, and BMI categories were detected.All children were of Mexican-origin. The most frequently reported barriers were unleashed dogs in the street, heat, bad weather, traffic, no streetlights, and no place like a park to exercise. Prominent locations for current PA included schools, home, and parks. Common PA options for children were exercise equipment, running, playing, and sports. Environmental assessments identified exercise equipment , paved/good streets, yard/patio space, and social norms as the most frequent household or neighborhood resources within these colonias children are similar to previous studies and distinctively unique. As expected, built resources in these communities are limited and barriers exist; however, knowledge of PA opportunities and available PA resources within colonias households and neighborhoods offers insight to help guide future research, policy, and PA initiatives.This study suggests that PA environmental resources, barriers, and opportunities for Potential differences in barriers for boys and girls, countries of birth, and BMI categories, (1) under to normal weight and (2) overweight or obese, were examined using chi-square tests or fisher\u2019s exact test when estimated cell sizes were less than 5.[Descriptive statistics, including frequencies, means, and standard deviations were calculated to describe the demographic and health characteristics of the sample. Frequencies were also calculated to determine the most commonly reported environmental resources using data collected via the environmental assessments and barriers for childhood physical activity as perceived by s than 5. Analysespromotora-researchers and an initial review of interview responses to ensure saturation of themes. All data were coded independently by two primary coders. When a discrepancy in coding occurred, a third coder was incorporated and consensus was reached. Potential differences in opportunities and locations were examined for gender, birth country, and BMI category as described above.Analysis of open-ended questions followed a deductive approach tailored to identify physical activity opportunities and locations, and available transportation methods. A coding tree was developed based on previous literature within the areas of physical activity barriers, environmental support, rural settings, and Hispanic communities.,58,61,62th percentile) and 30 of the children were obese (\u226595th percentile). Mean BMI percentile for the children was the 68th (SD=32.8) and 12% were either underweight or at risk for being underweight . Mean BMI percentile for children born in Mexico was 62nd (SD=31.6), 70th (SD=33.3) for children born in the U.S., 65th for female children, and 71st for male children. T-tests revealed no significant differences when comparing either set of groups, although greater proportions of male children (53.8%) and children born in the U.S. (52.2%) were overweight or obese as compared to female children (43.6%) and children born in Mexico (36.0%). Eighty-four percent of mothers (n=79) were either overweight or obese (BMI\u226525), where 12 were normal weight, 21% (n=20) were overweight, 32% (n=30) were obese class I (BMI = 30.0-34.99), 18% (n=17) were obese class II (BMI = 35.0-39.99), and 13% (n=12) were obese class III (BMI \u2265 40.0).[The average age of the children was 8.9\u2009years (SD=1.5) and just over half were female . All children and mothers were of Mexican-origin (100%), where 73.4% of the children were born in the U.S. (n=69). Eighty-seven percent of mothers were born in Mexico (n=82). Just under half of the children were either overweight or obese using BMI percentiles . NineteenEnvironmental support assessments were completed by each mother pertaining to her household and neighborhood . Children with overweight or obese BMI classification were more likely to have blocks for walking , volleyball nets , and pools within their neighborhoods than children with normal BMI classifications . No other significant differences in household or neighborhood resources or supports were detected between BMI classifications.Chi-square analyses examining differences in household and neighborhood resources and supports for normal weight versus overweight-obese children revealed significant differences for the following neighborhood resources: blocks available for walking, soccer fields, volleyball nets, and pools. Children with a normal BMI classification were more likely to have soccer fields within their neighborhood (63.3%) than overweight or obese children , where more girls (81.8%) perceived dogs in the street to be a barrier to physical activity as compared to boys (64.1%). The only significantly different barrier to physical activity, exercise, or sport for boys and girls as reported by their mothers was time , where mothers more frequently reported time as a barrier to physical activity for boys (38.4%) than girls (16.4%). Barriers for boys and girls as reported by children and their mothers are presented in Table\u2009Barriers to children\u2019s physical activity, exercise, or sport reported by children and their mothers were assessed and transportation . More children born in the U.S. reported \u201cnot having energy\u201d as a barrier to being active (42.0%) as compared to children born in Mexico (12.0%), and more children born in Mexico reported transportation as a barrier to being active (40.0%) as compared to children born in the U.S. (20.3%). Perceived barriers to being active reported by mothers significantly differed by birth country for two barriers: immigration status and kidnappings . Mothers of children with normal BMI classification were more likely (40.8%) to report transportation as a barrier to physical activity than mothers with children who had an overweight or obese BMI classification . Children with normal BMI classification were also more likely to report traffic and crime as barriers than children with overweight or obese BMI classifications . No other significant differences between BMI classifications were detected.Chi-square analyses examining differences in barriers to physical activity for normal weight versus overweight-obese children revealed significant differences for transportation, traffic, and crime as reported by children, and transportation as reported by mothers. Children with a normal BMI classification were more likely (38.8%) to report transportation as a barrier to physical activity than children with an overweight or obese BMI classification and mothers (73.4%), which included school grounds, physical education, and school gyms. Physical education at schools was specifically reported by 12.8% of the children and 11.7% of mothers. The home-area was the second most prominent location for current physical activity and involved any physical activities occurring within the home, yard, or patio space, and included yard work and recreational activities. Of the children, 18.1% reported parks, 9.6% neighborhood, 5.3% activities with others, and 3.2% reported open fields/lots, sports, walking, and no physical activity. Of the mothers, 25.5% reported parks, 11.7% neighborhood, 8.5% playing, 4.3% exercise equipment, and 3.2% biking. Location codes with a frequency of \u2264 2 for both children and mothers included other homes, running, church, strength activities, cardio activities, and community facilities. No significant differences for locations of current physical activities were detected between genders or birth countries. However, mothers of children with an overweight or obese BMI classification were more likely to report exercise equipment (8.9%) than mothers of children with a normal BMI classification .Salient themes were identified from open-ended responses describing where Salient themes identified from the open-ended question inquiring about available physical activity options and opportunities for these children as reported by the children and their mothers were examined. The most frequently reported physical activity opportunities for children were using exercise equipment , which included balls, bikes, trampolines, monkey bars, etc. When a ball was mentioned in relation to a sport itself, the response was double-coded to capture the equipment and the sport. When biking was mentioned, it was double-coded to capture both biking and the equipment. Running , playing , sports , and biking were the next most commonly reported opportunities reported by both the children and their mothers. Of the children, 17.0% reported cardiovascular activities, 12.8% walking, 8.5% activities at home, 5.3% activities at a park, 5.3% strength activities, 4.3% activities at school, and 3.2% activities with pets and activities at a community facility. Of the mothers, 18.1% reported walking, 14.9% cardiovascular activities, 10.6% activities at a park, 8.5% activities at school, 6.4% none, 4.3% activities at home and activities with music, and 3.2% activities in neighborhood. Opportunity codes with a frequency of \u2264 2 for both children and mothers were activities with others, activities at church, in an open field or lot, and swimming.2=4.807, df=1, p=.028). Similarly, more mothers of boy children (41.0%) reported \u201csports\u201d as a physical activity opportunity as compared to mothers of girls . More children born in Mexico (32%) reported biking as a physical activity opportunity as compared to children born in the U.S. . Overweight or obese children (20.0%) and mothers of these children (28.9%) were more likely to report walking as an opportunity as compared to children with a normal BMI classification and their mothers . Normal weight children (10.2%) were more likely to report strength training activities as opportunities as compared to overweight or obese children . No other significant differences between groups were detected for children or mothers\u2019 responses.Significant differences for birth country, gender, and BMI classification for physical activity opportunities were detected. More boys (38.5%) than girls (18.2%) reported \u201csports\u201d (\u03c7colonia or neighborhood). Forty-four percent said these were located within their same town, 7% said a neighboring town within 5 miles, 12% said a neighboring town 5\u201310 miles away, and only one person said a town 10\u201315 miles away. When asked how they get to and from the physical activity opportunities, 47% of the children stated they use the school bus for transportation to physical activity options, 45% are driven in a car, and 20% said they walk. No children mentioned using any type of public transportation or cycling. Three-fourths of these children\u2019s mothers owned a car and 60% of them reported having a car available to them during the day. Alternative forms of transportation included relatives (41%) and family friends (20%); although, 54% of mothers said they are charged to use these alternative forms of transportation.When the children were asked where physical activity opportunities were located, 31% said they were at a school, 25% said their home , 14% said a park (various city parks were mentioned), and 8% said in their neighborhood household and neighborhood infrastructure for physical activity, (2) perceived barriers to physical activity for these children, taking into account potential gender and birth country differences, and (3) physical activity opportunities and locations. Specifically, environmental support was assessed using items derived from current literature and previously developed environmental audits for rural and urban settings.[colonia areas as compared to both urban and rural areas, it was imperative to tailor environmental support items to be culturally relevant and specific. In these assessments, several environmental factors consistently supportive of physical activity and health in previous research were reported. These included paved streets, streets deemed good for walking or running,[colonias,[colonias households and neighborhoods that are consistent with previous research and often more salient for low-income children. These included few recreation buildings[This study furthers our understanding of the physical activity environment for high-risk, underserved Mexican-origin mothers and children living in Texas border settings.,58-60 Gi running, playgroucolonias,,70 and scolonias, These asbuildings,73 and tbuildings,75 limitbuildings and highbuildings and grafbuildings,77colonias were also identified in this study, including a high occurrence of yard and/or patio space and exercise equipment . Although relationships between yard presence and/or yard size and exercise equipment with physical activity are not always supported in the literature,[colonia houses are on relatively generous lots, often fenced or walled-in, the houses themselves are usually built piece-by-piece as the family can afford to do so , usually providing limited space for active recreational endeavors indoors.[colonias children, as relatively few driveways were paved (15%). While paved driveways are not usually included as physical activity resources in the literature, given the context of colonia housing and neighborhood barriers, paved driveways could provide an additional home-based physical activity resource for children. Future research should investigate benefits and safety issues around paved driveways as a potential physical activity resource among less developed and unincorporated areas.Environmental characteristics unique to terature,,78,79 th indoors.,24 In adcolonia streets was the predominant barrier to children being physically active for the sample as reported by both children and their mothers, regardless of gender or birth country. While the intensity of this finding is somewhat distinct to the colonias population as compared with other literature, unleashed dogs have been reported as relevant barriers to physical activity for other populations living in communities with potentially less infrastructure and development, such as rural U.S. areas, and for some international adolescents.[colonias children, especially girls, should address this barrier with children themselves and their mothers.Items representing perceived barriers, both environmental and individual-level, were also derived from current literature and tailored for cultural relevance. As with the environmental assessment, interview responses highlighted barriers that are both unique to this population and similar to those within other samples. Unleashed dogs in the lescents.,80,81 Thcolonias are not within local governance, but rather within county-level governance. Advocacy efforts should occur at the local, county, and state-level, and communication across all levels is essential.Traffic, lack of street lights, and bad weather/heat are other environmental barriers prominent in this study previously identified for children and other underserved communities.,80,82,83colonias children. Time was reported by mothers as a significantly more prominent barrier to physical activity for boys in comparison (39%) to girls (16%). While time is not the predominant barrier for boys in this study, this difference is worth examining and is consistent with previous research reporting time and other priorities as barriers to physical activity for Hispanic adolescent boys.[Several group differences detected in this study highlight unique considerations when encouraging physical activity among ent boys. Because ent boys. boys\u2019 peent boys. Boys parent boys. thus linent boys. This difcolonias should take this into account, as up to 1/3 of colonias residents are born in Mexico.[Four differences in barriers were also detected when comparing children born in different countries. Children born in Mexico were more likely to report lack of transportation as a barrier to physical activity (42%) than children born in the U.S. (20%), even with no significant differences between car ownership or availability during the day and mother\u2019s employment (part/full-time versus not working or full-time versus part-time/not working) for mothers of children born in Mexico as compared to the U.S. . Physical activity initiatives targeting children residing in n Mexico.colonias families are at greater risk for food insecurity.[Children born in the U.S. were more likely to report a lack of energy as a barrier as compared to children born in Mexico . Although the subsample of children born in Mexico is modest, this difference is notable. While lack of energy, feeling tired, or fatigue has been inversely related with physical activity and positively related with sedentary time among adult populations,,83,87 itsecurity.,89 AlthoDifferences seen between normal weight children and those who were overweight-to-obese suggest cultural preferences and support metabolic understandings.,90 Givencolonia in which they reside), only 20% of these children reported walking as a form of transportation to these locations. In addition, this supports both the need for school-based physical activity opportunities that incorporate transportation and the importance of home-based physical activity options. These findings substantiate previous studies that suggest the greatest opportunity for lower income children to engage in physical activity is within the school setting, as school-based physical activity has demonstrated an equalizing effect for socio-economic status differences associated with physical activity.[Locations of current physical activities and available physical activity opportunities emphasize the importance of school and home environments and supportive physical activity resources and modes including exercise equipment, running, playing, sports, and biking. Although most physical activity opportunities reported are located within a relatively short distance from the areas that the children live , as these items were both based on previously used measures and culturally tailored for relevance and specificity to this distinct population. However, given this approach, validity and reliability of these measures is not established. Additionally, although these results provide a rich description of the physical activity environment for children residing in south Texas colonias, causality was not examined. While future studies should seek to validate these measures in similar colonias within the Texas-Mexico border region, these findings should be used to inform future research, policy, and public health initiatives for other colonias communities along the U.S.-Mexico border and rapidly growing new-immigrant destination communities seen throughout America. While immigrants in the past century have primarily settled in one of a few gate-way urban cores, more recent trends evidence an increase of new-immigrant destinations throughout rural and less-settled urban-periphery counties found across the U.S., including the Midwest and Southeast among others.[colonias residents regardless of geographical location, including severe poverty, educational disadvantages, escalated risk for chronic diseases, underemployment, and residences within ethnic enclaves,[colonias can serve as an archetypal example for researchers, public health practitioners, and policy makers in understanding these new-immigrant destinations scattered across the nation.While this study focuses on children residing in g others.,101 Receg others. Given moenclaves,colonias colonias, in addition to school and church-based policies, programming, and infrastructure as they relate to physical activity support. Future physical activity initiatives targeting colonias children should incorporate a community-based participatory research (CBPR) approach working with community promotoras and consider programs incorporating currently available exercise equipment, while developing physical activity initiatives within schools, homes, and parks that incorporate transportation for children. Policy makers should use these findings to help guide decisions about resource allocation within colonias and new-destination immigrant communities to increase parks, playgrounds, and access to school grounds. This study suggests that environmental resources and barriers for colonias children are both similar to previous studies and distinctively unique. As expected, built resources for these communities are limited; however, knowledge of barriers and available physical activity resources within colonia households and neighborhoods offers insight and can help guide policy and physical activity initiatives. Future work should also focus on facilitating neighborhood groups and linkages with non-governmental organizations to increase advocacy for community change.Future research should aim to understand the social environment of children residing in The authors declare that they have no competing interests.MRUM contributed to the conception of this study, analysis and interpretation of the data, and drafted the manuscript. JRS contributed to the conception and design of the study, acquisition of data, and critically revised the manuscript. MSP contributed to the analysis and interpretation of data and critically revised the manuscript. WRD contributed to the design of the study and critically revised the manuscript. All authors have given final approval of the manuscript for publication.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2458/13/14/prepub"} +{"text": "The majority of pancreatic cysts are detected incidentally when abdominal imaging is performed during unrelated procedures. The aim of the present study was to assess the diagnostic utility and clinical value of carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA 19-9) and amylase analysis in pancreatic cyst fluid. The study included 52 patients with pancreatic cystic lesions, who underwent fine-needle aspiration biopsy to collect cystic fluid for cytological and biochemical analysis. Cysts were classified as benign in 36 patients or premalignant/malignant in 16 patients. CEA and CA 19-9 were elevated in patients with malignant cysts compared with benign lesions . Based on these results, the sensitivity and specificity of CEA were 91.8 and 63.9% and of CA 19-9 were 81.3 and 69.4%, respectively. Mean amylase levels in benign lesions (27825.7\u00b191.9 U/l) were higher compared with malignant pancreatic cysts . Cyst fluid analysis may prove a safe and useful adjunct for the differential diagnosis of pancreatic cystic lesions. In the present study, promising results for CEA and CA 19-9 have been demonstrated, however, the clinical value of these molecules must be confirmed. Pancreatic cysts are commonly detected incidentally in patients undergoing abdominal imaging for unrelated procedures. Simple (retention) cysts, pseudocysts and serous cystadenomas lack malignant potential. However, mucinous cystic neoplasms and intraductal papillary mucinous neoplasm (IPMN) have a malignant potential and require surgical treatment \u20134. Due tAnalysis of cystic fluid may be useful for distinguishing between benign and malignant pancreatic lesions. To date, several tests using cyst fluid to diagnose premalignant cyst are in use. These include cytology, tumor markers , biochemical markers and cyst fluid viscosity. Among these tests, CEA has the highest diagnostic accuracy for discriminating premalignant mucinous from nonmucinous cysts ,6. HowevCA 19-9 is the most popular serum-based marker for pancreatic cancer diagnosis and is important for the detection of recurrent disease and surveillance of patients following surgery. Previous studies have demonstrated that CA 19-9 cyst fluid analysis may also be useful for differential diagnosis of pancreatic cysts, particularly in pancreatic cystadenocarcinoma detection . CurrentThe third analyzed parameter, pancreatic cyst fluid amylase, may be particularly useful for the identification of pseudocysts. Distinguishing pseudocysts from malignant cystic tumors is essential during selection of appropriate surgical procedures. Pseudocysts may be managed by observation or, in specific cases with endoscopic or surgical drainage. The amylase content of pseudocysts is almost always high, whereas the level in neoplastic cysts is generally low. However, cystic tumors of all types may exhibit elevated amylase levels. Consequently, the efficacy of amylase measurements in pancreatic cyst fluids is limited, although low values indicate a neoplastic tumor ,8,12,13.The aim of the present study was to assess the diagnostic utility and clinical value of CEA, CA 19-9 and amylase analysis in pancreatic cyst fluid.The present study included 52 patients with pancreatic cystic lesions. Patients underwent fine-needle aspiration biopsy to collect cystic fluid for cytological and biochemical analysis. Informed consent was obtained from all patients. The study was approved by the ethical committee of Lodz Medical University. Based on surgical histopathology, cytology results and/or imaging follow-up (>18 months), cysts were classified as benign or premalignant/malignant in 36 and 16 patients, respectively.The following characteristics were analyzed: maximum pancreatic cyst diameter, cyst number and location, wall thickness, mural nodules, pancreatic duct communication and/or dilation and presence of septations or calcifications. Following cyst fluid aspiration, a portion of the specimen was sent to the chemistry laboratory of the Department of Digestive Tract Diseases for CEA, CA 19-9 and amylase analysis. The fluid was also examined by a cytopathologist.Age and gender of patients, presenting symptoms and medical history of acute or chronic pancreatitis were also assessed. Criteria for resection included premalignant/malignant lesions identified by cytology or fluid analysis and suspicious radiographical observations, including cyst size >3 cm and intramural nodules, pancreatic duct dilation, peripheral calcifications or associated mass. Resection was also advised for symptomatic benign pancreatic cysts. All patients with premalignant/malignant lesions underwent surgical treatment. Fifteen patients with a final diagnosis of benign lesions also underwent surgical resection due to symptoms or suspicious features of imaging and/or cyst fluid analysis.Statistical analysis comprised arithmetical mean, median and standard deviation. Mann-Whitney or Fisher\u2019s exact tests were performed to determine differences between groups. P<0.05 was considered to indicate a statistically significant difference. A receiver operating characteristic (ROC) curve depicting the ability to discriminate between benign and premalignant/malignant cysts was plotted for CEA, CA 19-9 and amylase and optimal cut-off points were estimated.The mean age of patients included in the present study was 55\u00b13.2 years; there were 28 male (53.8%) and 24 female (46.2%) subjects. A total of 36 cysts were classified as benign and 16 patients had premalignant/malignant cysts . The majority of patients were asymptomatic, whereas 23 patients presented abdominal pain, weight loss and/or jaundice. Nine patients had a previous history of acute pancreatitis, whereas chronic pancreatitis was confirmed in 11 patients.The mean diameter of pancreatic cyst was 3.3 cm . No statistically significant difference was identified between benign and malignant cyst size . Cyst localization was identified in the pancreatic head and body or tail of pancreas in 29 (55.8%) and 23 (44.2%) patients, respectively. Cytology was assessed in all patients and was reported as acellular, benign or atypical in 49 patients and positive for malignant cells in 3 patients.CEA and CA 19-9 were higher in patients with malignant cysts compared with benign lesions was identified as significantly higher compared with malignant pancreatic cysts . Sensitivity for CEA and CA 19-9 was 91.8 and 81.3%, respectively, for mucinous lesions. Previously, the combination of CEA fluid assessment and K-ras mutation analysis levels was confirmed to maximize the diagnostic yield of pancreatic cyst biopsy and improve sensitivity and specificity of cyst classification . Howeveret al identified that CA 19-9 fluid assessment had higher sensitivity and specificity compared with CEA for detection of pancreatic cystadenocarcinomas suggest benign lesions ,17. The et al reported that CEA and amylase fluid levels less than 30 ng/ml and more than 8500 U/l, respectively, were observed in 91% of pseudocysts , however, this difference was identified to be at the limit of statistical significance (P=0.05). The authors reported a high sensitivity (100%) and specificity (63.6%) of cyst fluid amylase at a cut-off of 5,000 U/l for differentiating pseudocysts from all other pancreatic cysts (In the present study, sensitivity of the third analyzed parameter, amylase, was 62.5% and the specificity was 69.4%, which was lower than those of CEA and CA 19-9. Previous studies on the clinical efficacy of amylase for differential diagnosis of pancreatic cysts are inconsistent. However, the parameter may be useful for confirmation of pseudocyst diagnosis, particularly in patients with a medical history of pancreatitis. Snozek udocysts . In addiet al, following surgical resection of 398 pancreatic cystic tumors, observed that 6% of mucinous cystadenomas and 10% of cyst-adenocarcinomas were associated with pancreatic ducts (et al identified that 54% of noninflammatory cysts, including mucinous cystic neoplasms had an increased level of amylase. However, lower amylase levels were identified in malignant mucinous cysts than benign mucinous cysts (Increased amylase fluid levels are not specific for pseudocysts and has been observed in additional cysts, including mucinous cystadenomas and IPMN ,18,19. LAt present, the efficacy of amylase level analysis for the differentiation of benign from premalignant/malignant cysts has not been determined. However analysis of amylase may be useful for patients with a medical history of pancreatitis where there is a greater probability of a pseudocyst. Further evaluation of this efficacy, based on long-term prospective studies in patients with pancreatic cysts, must be performed.In conclusion, the present study indicates that analysis of pancreatic cyst fluid may be a safe and useful adjunct for the differential diagnosis of pancreatic cystic lesions. This analysis may distinguish inflammatory and benign neoplastic cysts from premalignant/malignant pancreatic lesions. Results appear promising, not only for CEA, but also for CA 19-9, however, the clinical value of these markers must be confirmed."} +{"text": "To the Editor: Typhoid fever (TF) remains a problem of concern in many low-income countries. Salmonella enterica serovar Typhi causes \u224822,000,000 symptomatic infections and 220,000 fatalities worldwide annually with access to the study hospital was assessed in a healthcare utilization survey. A proportional-to-size number of children were randomly selected in each village, and a standardized interview was conducted. TF incidences were calculated for September 2007\u2013November 2008 . A bacteThe study included 1,456 children <15 years of age who were admitted to the pediatric ward of Agogo Presbyterian Hospital over the 23-month study period. Overall, 52.1% were male; mean age of children was 32.2 months . Blood was cultured by using a BACTEC 9050 blood culture system (Becton Dickinson), and positive samples were examined by standard methods. Antimicrobial drug susceptibility testing was performed on all serovar Typhi isolates by using the Kirby-Bauer disk-diffusion method for ampicillin, chloramphenicol, tetracycline, trimethoprim/sulfamethoxazole, amoxicillin/clavulanic acid, gentamicin, ciprofloxacin, and ceftriaxone.Candida spp., 37 (12.4%) isolates were positive for S. enterica ser. Typhi. The frequency of TF was low among children <2 years of age , increased among those 2 to <11 years of age , and decreased among children \u226511 years of age , trimethoprim/sulfamethoxazole (71%), ampicillin/amoxicillin (70%), tetracycline (64%), gentamicin (46%), and amoxicillin/clavulanic acid (24%) but susceptible to ciprofloxacin and ceftriaxone.Children <2 years of age had the highest proportion of positive blood cultures . One and 5\u20138 years of age . In chilS. enterica ser. Typhi drug resistance. A study from Nigeria showed that, among serovar Typhi strains isolated from hospitalized patients in Lagos during 1997\u20132004, resistance rates reached 87% for ampicillin and were 0.7% for ciprofloxacin, compared with 70% and 0%, respectively, in the present study. Resistance to trimethoprim/sulfamethoxazole was 59% in Nigeria, compared with 71% in Ghana. In Togo, proportions of serovar Typhi strains resistant to chloramphenicol and trimethoprim/sulfamethoxazole were 33% and 46%, respectively, before 2002 and 73% and 79% in 2003\u20132004 was observed in 63% of children in our study, compared with 7% in India, 22% in Vietnam, and 65% in Pakistan (Salmonella infections and to sustain TF surveillance and drug sensitivity surveys. Moreover, introduction of a vaccination program should be discussed after more data are obtained from other areas in Ghana and West Africa. Such data currently are collected in an extensive standardized surveillance program across the continent performed by our group and others. In parallel, trials should be conducted to assess the effectiveness and cost-effectiveness of currently available and newly developed TF vaccines.More effort is needed in Africa to enable reliable and standardized laboratory diagnoses of"} +{"text": "Inappropriate antibiotic use is an important factor associated with antibiotic resistance and related medical costs. These outcomes impede the effectiveness of infection prevention control programmes. Our study is to determine the prevalence of antibiotic prescription and rationale for prescribed antibiotics to hospital inpatients in Vietnam.A one-day prevalence survey in 2008 was conducted in 36 hospitals representing three different hospital levels across Vietnam. Medical records of all inpatients were reviewed to collect demographics, number and antibiotic class, and indications for antibiotic prescription. Based on the guidelines of the Association for Professionals in Infection Control and Epidemiology, USA, reasons for antibiotic use were classified into (1) identified pathogen directed, (2) empirical, or (3) prophylactic.The crude antibiotic use was 67.4% (3811/5654). Broad-spectrum antibiotics such as cephalosporins (70.3%), penicillins (21.6%), and aminoglycosides (18.9%) were most commonly used. Of antibiotic used patients, 54.7% were prescribed empirically and 30.8% were unclearly indicated. Risk factors independently associated with unclear antibiotic prescription were as follows: National level hospitals , provincial/regional hospitals , obstetrics ward , and surgical ward .Suboptimal antibiotic prescription practices are common in our participating hospitals and emphasise the necessity for evidence-based guideline to be developed and implemented in Vietnamese hospitals.None declared."} +{"text": "Dementia increases the risk of death in older patients hospitalized for acute illnesses. However, the effect of dementia on the risks of developing acute organ dysfunction and severe sepsis as well as on the risk of hospital mortality in hospitalized older patients remains unknown, especially when treatments for these life-threatening situations are considered.In this population-based cohort study, we analyzed 41,672 older (\u226565 years) patients, including 3,487 (8.4%) with dementia, from the first-time admission claim data between 2005 and 2007 for a nationally representative sample of one million beneficiaries enrolled in the Taiwan National Health Insurance Research Database. Outcomes included acute organ dysfunction, severe sepsis, and hospital mortality. The effect of dementia on outcomes was assessed using multivariable logistic regression.Dementia was associated with a 32% higher risk of acute organ dysfunction , a 50% higher risk of severe sepsis and a 28% higher risk of hospital mortality after controlling age, sex, surgical condition, comorbidity, principal diagnosis, infection status, hospital level, and length of hospital stay. However, the significant adverse effect of dementia on hospital mortality disappeared when life-support treatments, including vasopressor use, hemodialysis, mechanical ventilation, and intensive care, were also controlled.In hospitalized older patients, the presence of dementia increased the risks of acute organ dysfunction, severe sepsis and hospital mortality. However, after intervention using life-support treatments, dementia only exhibited a minor role on short-term mortality. Dementia increases the risk of death in older patients hospitalized for acute illnesses Patients with dementia are at increased risk of infection-related hospitalization We hypothesize that hospitalized older patients with dementia are at increased risk of acute organ dysfunction, severe sepsis, and death. The levels or processes of care, especially during life-threatening situations, may be affected by the presence of dementia. Hence, we also hypothesize that the effect of this disease on death still persists after interventions using life-support treatments. In this retrospective population-based cohort study, we tested these hypotheses by characterizing hospitalized older patients with dementia and comparing their risks of acute organ dysfunction, severe sepsis, and hospital mortality with the risks for hospitalized individuals without such disease.This study was approved by the review board of the Medical Research Committee in Chi Mei Medical Center (grant No. CMFHR9855). The review board waived the need for formal ethical approval and written informed consent from the participants because we used a reimbursement database, that is, the National Health Insurance Research Database (NHIRD) International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnosis (up to five) and procedure (up to five) codes, outcome at hospital discharge , and hospital charges.In Taiwan, a compulsory and universal National Health Insurance program has been implemented by the government since 1995 One million beneficiaries enrolled in 2005 were randomly selected from the NHIRD by the NHRI and included in the Longitudinal Health Insurance Database of 2005, which contained all claim data of the cohort from 1997 to 2007 Dementia was defined by the diagnostic codes for senile or presenile organic psychotic condition (ICD-9-CM code 290) or Alzheimer's disease (311.0) The definitions of acute organ dysfunction , severe Baseline characteristics of the study subjects were examined, including age, sex, surgical condition, Charlson comorbidity index Continuous variables were presented as median (inter-quartile range) because of a skewed distribution, whereas discrete ones as count and percentage. The effects of dementia on outcomes, including acute organ dysfunction, severe sepsis, and hospital mortality, were assessed using multivariable logistic regression adjusting for all the baseline characteristics as aforementioned. In addition, we used another model for hospital mortality by enrolling life-support measures as additional covariates to account for the effect of different levels or processes of care on mortality. Potential interaction between dementia and infection status on the development of organ dysfunction was assessed by adding a cross-product term into the model. As we simultaneously included a number of covariates in the multivariable regression models, a potential numerical problem concerned collinearity between covariates, rendering estimated regression coefficients invalid. We assessed such potential problem by examining the estimated slope coefficients and standard errors of the mean, and found no indication of collinearity.p<0.05 (two-tailed).Finally, we performed sensitivity analyses for all the estimates using a broader definition of dementia by including patients with dementia coded only in positions other than the principal diagnosis Among the 41,672 patients identified during the study period, 3,487 (8.4%) patients with dementia were included in the analyses . CharactWith the exception of hemodialysis, patients with dementia used more life-sustaining resources including vasopressors, mechanical ventilation, and intensive care as well as stayed longer in the hospital .p<0.001). After controlling the baseline covariates, the risk remained 32% higher in patients with dementia. When individual organ systems were examined, dementia was associated with a 30% higher risk of respiratory dysfunction, a 37% higher risk of cardiovascular dysfunction, and a 102% higher risk of neurological dysfunction (The incidence of acute organ dysfunction (\u22651 system) was approximately twice higher in patients with dementia than in control subjects . The profunction . Renal, The incidence of severe sepsis was also higher in patients with dementia . After cn\u200a=\u200a2,026) were younger (median 79 vs. 80 years) and predominantly male (54.2% vs. 48.1%), had more cerebrovascular (28.4% vs. 19.9%) and diabetic (25.8% vs. 23.1%) comorbidities, and had more cardiovascular (23.0% vs. 15.1%) but fewer respiratory (17.5% vs. 21.7%) diagnoses and fewer infections (38.8% vs. 46.3%). After including all these patients and adjusting the baseline covariates, the effects of dementia on the risks of acute organ dysfunction , severe sepsis and hospital mortality were slightly attenuated but remained significant.Compared with patients with dementia coded in the principal diagnosis, those coded elsewhere Click here for additional data file."} +{"text": "To compare clinical status, mother-to-child transmission (MTCT) rates, use of prevention of (PMTCT) interventions and pregnancy outcomes between HIV-infected injecting drug users (IDUs) and non-IDUs.Prospective cohort study conducted in seven human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) Centres in Ukraine, 2000\u201310.n = 6200); 1028 women followed post-partum.Pregnant HIV-infected women, identified before/during pregnancy or intrapartum, and their live-born infants and low birth weight (LBW).P < 0.01). Among women with undiagnosed HIV at conception, 20% of IDUs were diagnosed intrapartum versus 4% of non-IDUs (P < 0.01). At enrolment, 14% of IDUs had severe/advanced HIV symptoms versus 6% of non-IDUs (P < 0.001). IDUs had higher rates of PTD and LBW infants than non-IDUs, respectively, 16% versus 7% and 22% versus 10% (P < 0.001). IDUs were more likely to receive no neonatal or intrapartum PMTCT prophylaxis compared with non-IDUs . MTCT rates were 10.8% in IDUs versus 5.9% in non-IDUs; IDUs had increased MTCT risk . Fewer IDUs with treatment indications received HAART compared with non-IDUs .Of 6200 women, 1111 (18%) reported current/previous IDU. The proportion of IDUs diagnosed with HIV before conception increased from 31% in 2000/01 to 60% in 2008/09 (Pregnant human immunodeficiency virus-infected injecting drug users in Ukraine have worse clinical status, poorer access to prevention of mother-to-child transmission prophylaxis and highly active antiretroviral therapy, more adverse pregnancy outcomes and higher risk of mother-to-child transmission than non-injecting drug user women. Injecting drug use (IDU) accounts for one in three new human immunodeficiency virus (HIV) infections outside subSaharan Africa , and driLow uptake of health services, including antenatal care (ANC), is a well-recognized problem among female IDUs ,18, inclOur aim was to compare clinical status, MTCT rates and risks, use of PMTCT interventions and pregnancy outcomes between HIV-infected IDUs and non-IDUs participating in a prospective cohort study of pregnant HIV-infected women and their children in Ukraine.http://www.eurocoord.net).The European Collaborative Study (ECS) is an ongoing prospective cohort study established in 1985 in western Europe, with centres from Ukraine joining in 2000 . The ECSWomen identified as HIV-infected before or during pregnancy, or through intrapartum testing, and delivering a live-born infant, are eligible to enrol with informed consent. Seven HIV/AIDS centres in Ukraine participate: Odessa, Mykolaiv and Simferopol (since January 2000), Kyiv, Donetsk and Mariupol (since September 2006) and KrivA nested substudy of the ECS was established in December 2007, with the aim of obtaining longitudinal information on childbearing HIV-infected women after delivery in order to investigate the impact of treatment, coinfection and exposure to abbreviated antenatal PMTCT prophylaxis on prognostic markers of HIV disease progression. Five sites of the ECS participate , collectn = 32) were treated as separate mother\u2013child pairs. By June 2010, 1028 women were being followed in the postnatal cohort.The study population for this analysis was 6200 mother\u2013child pairs in the Ukraine ECS (enrolled up to February 2010); 447 women with two infants were included, 45 with three infants and five with four or more infants. Multiple births deliveries were defined as CS deliveries occurring pre-labour and before rupture of membranes. Time period was classified as follows: 2000\u201301, 2002\u201303, 2004\u201305, 2006\u201307 and 2008\u201310. Infants with persistence of antibody beyond 18 months of age and/or a positive virological marker of infection regardless of age were included as HIV-infected. If a child was HIV antibody-negative and no virus had been detected (s)he was classified as uninfected, regardless of age.IDU history (current or past) was assigned according to maternal self-report and/or clinical report; six women without self- or clinical report of IDU delivered infants with NAS and were included in the IDU group. Women were defined as \u2018current IDUs\u2019 if IDU was reported during the current pregnancy and/or if their infant had NAS, but we considered all women with an IDU history to be IDUs in recognition that IDU can be a chronic and relapsing condition . In some2 test for categorical variables. Logistic regression was used to obtain unadjusted odd ratios (OR), adjusted odds ratios (AOR) and 95% confidence intervals (CI) in separate analyses identifying factors associated with non-receipt of PMTCT prophylaxis, adverse pregnancy outcomes and MTCT. For the MTCT analysis, available variables known to be associated with MTCT risk were included a priori and 34 cm ; the AOR for past versus current IDU was 0.70 .Overall, 25% (275 of 1110) IDUs had a PTD and/or a LBW infant (\u2018adverse pregnancy outcome\u2019). IDU was associated significantly with adverse pregnancy outcomes in univariable logistic regression analyses, together with late HIV diagnosis (used as a proxy for no or inadequate ANC), having a cohabiting partner/spouse and PMTCT prophylaxis (n = 61) women breastfed their infants, eight of whom were IDUs. Unadjusted MTCT rates were 5.9% for non-IDUs and 10.8% for IDUs: 10.0% for past IDUs , 13.1% for current IDUs and 21.8% for IDUs with intrapartum HIV diagnosis. MTCT rates declined over calendar time among IDUs, from 17.6% in 2000\u201301 to 3.8% in 2008\u201309 and among non-IDUs from 11.6% to 2.8% in the same years. In unadjusted logistic regression, IDU was associated with a nearly twofold increased risk of MTCT (P < 0.001) (n = 4328), IDUs had a 32% increased risk of transmitting infection to their infants compared with non-IDU (aOR 1.32) (P = 0.08).Overall, <1% (< 0.001) . ClassifOR 1.32) . RepeatiIn this Ukrainian cohort, spanning more than 10 years, just under one-fifth of women were current or past-IDUs. IDUs had higher prevalence of coinfections, advanced HIV disease and severe immunosuppression compared with other women. One in 10 IDUs did not access PMTCT prophylaxis, mainly because they were diagnosed too late. Adverse pregnancy outcomes, including PTD and LBW as well as MTCT, were more frequent in IDUs and IDU history was associated independently with a 30% increased MTCT risk.IDUs are frequently socially marginalized and socio-economically deprived, and can be hard to reach with services, including HIV testing. Coverage of IDUs with HIV testing (in previous 12 months) is an estimated 30% in Ukraine . More IDIn unadjusted analyses, IDU was associated with a twofold increased MTCT risk and IDUs contributed 31% of all vertical transmissions. The main mechanisms behind the elevated MTCT risk associated with IDUs were most probably their lower coverage with PMTCT interventions and higher rate of PTD. Infants of current IDUs were at greatest risk of MTCT, with a rate of 13.1%. Such infants were significantly more likely to be delivered preterm than other infants and had a nearly threefold increased probability of non-receipt of PMTCT prophylaxis, resulting in a nearly 2.5-times increased transmission risk versus never IDUs in unadjusted analyses. The finding that current IDUs were at greatest risk of MTCT underscores the need to strengthen harm reduction in Ukraine as a key component of the broad PMTCT strategy. IDUs remained associated significantly with a 30% increased MTCT risk in adjusted analysis; this might be explained by factors including poorer adherence to prophylaxis/treatment and higher rates of some coinfections, including HCV \u201343, but The trend of declining MTCT rates over time applied to IDUs as well as other women, with both groups having rates <4% by 2008\u201309. This is above the target for \u2018virtual elimination\u2019 of HIV among infants , but is in utero to opiates [NAS, which occurs in approximately 60% of all newborns exposed opiates , was ide opiates ,31,46,47 opiates . Materna opiates \u201351, and opiates .Problems faced by IDUs in accessing addiction, HIV, reproductive and other services ,31,53 reA comprehensive package of care for IDUs should include HIV testing, treatment and care, tuberculosis (TB) and STI services and harm reduction, including needle/syringe exchange programmes (NSP) and opioid agonist maintenance treatment . For femImplementation of opioid agonist maintenance treatment for IDUs has also been slow, with methadone maintenance not available until mid-2008 ; no womeOne of the most effective ways of preventing HIV infection in infants is to prevent their mothers from becoming infected in the first place. Recent models suggest that HIV prevalence in Odessa could be reduced by 41% over the next 5 years if there were a 60% reduction in unmet need for services, including NSP, opioid agonist maintenance treatment and antiretroviral therapy started promptly when indicated .This study is limited by its observational nature and the potential for confounding. Social desirability bias may have prevented some women from reporting IDU. Although our classification also used clinical observation and NAS, up to 40% of infants with fetal exposure to opiates do not develop NAS. We therefore cannot exclude the possibility that some IDUs may have been included in the non-IDU group, underscored by the 22% prevalence of HCV in the non-IDU group. Our study population lives in cities with the highest antenatal HIV prevalence in Ukraine, including Odessa, Kyiv and Mykolaiv , and we Some important successes documented here include the increasing proportion of IDUs knowing their HIV status before pregnancy, the declining proportion receiving no PMTCT prophylaxis and substantially lower MTCT risk in recent years, regardless of IDU status. However, important challenges remain, such as provision of comprehensive care to female IDUs, including harm reduction, family planning and HIV treatment as well as provision of ANC and PMTCT, with an emphasis on improving timely access.Claire Thorne holds a Wellcome Trust Research Career Development Fellowship, which supports the Ukraine Cohort Study of HIV-positive Childbearing Women. The ECS has previously received funding from the European Union Sixth Framework Programme (grant agreement PENTA/ECS 018865) and the research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007\u201313) under EuroCoord grant agreement no. 260694. Some of this work was undertaken at GOSH/UCL Institute of Child Health which received a proportion of funding from the UK Department of Health's NIHR Biomedical Research Centres funding scheme. The Centre for Paediatric Epidemiology and Biostatistics also benefits from funding support from the Medical Research Council in its capacity as the MRC Centre of Epidemiology for Child Health. Claire Thorne has previously carried out consultancy work for pharmaceutical industry (Roche)."} +{"text": "Current treatments for chronic pain have limited effectiveness. Although major life stressors are elevated in those with chronic pain, emotional awareness, expression, and processing have not been utilized. We evaluated treatment outcomes and predictors of outcomes of a novel emotion-oriented intervention for chronic pain.An initial individual session was conducted by one of the authors (HS) to assess medical conditions and review life stressors and symptom progression in order to identify linkages between stressors and symptoms. The treatment program consisted of 4 weekly small group 2-hour sessions. Components included readings, writing about emotions, mindfulness and emotional awareness exercises (on CD), and other techniques to help people identify and process emotions related to stress and pain. Homework was assigned daily. Patients were assessed at baseline by a research team and at post-treatment and 6-month follow-up. Included instruments were the Brief Pain Inventory (BPI) and the McGill Pain Questionnaire (MPQ).Fifty-nine adults with chronic musculoskeletal pain, primarily headaches, neck, back, and widespread pain , were included. Individuals with significant structural disease processes were excluded. Baseline demographics and characteristics were 76% women (mean age 51 years). 91% Caucasian, mean duration of pain 8.8 years, and baseline pain level 5.03 (0-10). Percent improvement was calculated for pain (% change from baseline BPI score). At post-treatment 64% had \u2265 30% improvement and 43% had \u2265 50% improvement; at 6-months 67% had \u2265 30% improvement and 53% had \u2265 50% improvement. Mean BPI scores were 5.38, 3.04, and 3.03 , respectively. The MPQ showed similar reductions.This high rate of improvement may surpass that of cognitive-behavioral interventions for chronic pain. An approach focusing on confronting emotional contributions to pain appears beneficial. Studies with control groups are underway to determine if targeting unresolved stress and emotions offers an advance in the treatment of chronic non-structural pain."} +{"text": "There are substantial morbidity and mortality associated with vascular catheter use among crictically ill patients. The attributable mortality is 10% to 25% which is associated with bacteremia among those who are hospitalized. This study was undertaken to identify catheter related blood stream infections, to isolate pathogenic microorganisms present in intravascular catheter related local infections, exit site infections, and to determine the predisposing factors for the development of such infections and antibiotic sensitivity pattern of the isolated organisms in tertiary care hospital. Intravascular catheters are indispensable in modern-day medical practice, particularly in intensive care units (ICUs). Although such catheters provide necessary vascular access, their use puts patients at risk for local and systemic infectious complications, including local site infection, catheter related blood stream infections (CRBSIs), septic thrombophlebitis, endocarditis, and other metastatic infections .The incidence of CRBSI varies considerably by type of catheter, frequency of catheter manipulation, and patient-related factors . Peripheral venous catheters are the devices most frequently used for vascular access. Although the incidence of local or bloodstream infections (BSIs) associated with peripheral venous catheters is usually low, serious infectious complications produce considerable annual morbidity because of the frequency with which such catheters are used. However, the majority of serious catheter-related infections are associated with central venous catheters (CVCs), especially those that are placed in patients in ICUs. In the ICU setting, the incidence of infection is often higher than in the less acute in-patient or ambulatory setting. In the ICU, central venous access might be needed for extended periods of time; patients can be colonized with hospital-acquired organisms; and the catheter can be manipulated multiple times per day for the administration of fluids, drugs, and blood products. Moreover, some catheters can be inserted in urgent situations, during which optimal attention to aseptic technique might not be feasible. Certain catheters can be accessed multiple times per day for hemodynamic measurements or to obtain samples for laboratory analysis, augmenting the potential for contamination and subsequent clinical infection.Bloodstream infections may be either primary or secondary. Secondary infections are related to infections at other sites, such as the urinary tract, lung, postoperative wounds, and skin. Primary BSIs comprise the majority (64%) of nosocomial BSIs reported to the CDC's National Nosocomial Infection Surveillance (NNIS) system, and most are due to infected intravascular, mostly central venous catheters. The remaining patients with primary BSIs have bacteremia with no identifiable source. More than 250,000 vascular catheter-related bacteremia and fungemia occur annually in the USA with an attributable mortality ranging from 12% to 25% in critically ill patients [CRBSI. Bacteremia/fungemia in a patient with an intravascular catheter with at least one positive blood culture obtained from a peripheral vein, clinical manifestations of infections , and no apparent source for the BSI except the catheter. One of the following should be present: a positive semiquantitative (>15 CFU/catheter segment) or quantitative (>102 CFU/catheter segment catheter) culture whereby the same organism (species and antibiogram) is isolated from the catheter segment and peripheral blood.CABSI. Vascular access device terminates at or close to the heart or one of the great vessels. An umbilical artery or vein catheter is considered a central line. BSI is considered to be associated with a central line if the line was in use during the 48-hour period before development of the BSI. If the time interval between onset of infection and device use is >48 hours, there should be compelling evidence that the infection is related to the central line.It was case-control study done in tertiary care hospital. The number of participants in this study was 50 cases and 50 controls. Patients aged >18\u2009yrs, admitted in intensive care units with intravascular catheters, were included. Patients with fever prior to catheter placement and proven source for sepsis other than the intravascular catheter of interest were excluded from this study. The following definitions were used to describe cases and controls.Case. Any patient with proven localized catheter colonization, exit site infection, or bloodstream infection (as per CDC guidelines).Control. Any patient in whom intravascular catheter grows no organism on semiquantitative cultures.Skin was cleaned with 70% alcohol prior to catheter removal. The proximal end of catheter was held and carefully removed from the patient with a sterile instrument, taking care to avoid contact with the skin. The distal end was held over a sterile tube, and tip was cut with a sterile scissors and the terminal 2 to 3 inches dropped into the tube. Drying was avoided by sealing the tube and transporting the same to the laboratory as soon as possible. Catheter tip processing was done by Maki's Roll over plate method and catheter flush culture , 5. In b\u03bcg) disk in Mueller Hinton agar plate for MRSA detection and double disc approximation or double disk synergy using Amoxicillin-Clavulanic acid (20/10\u2009\u03bcg) and Ceftriaxone (30\u2009\u03bcg) at a distance of 30\u2009mm between centers of the two disks. American type culture collections (ATCC) were used as control strains. Statistical analyses were done using SPSS 16.0 for windows and strength of association is expressed as odds ratio which was derived using logistic regression analysis.Antibiotic sensitivity pattern was done by Kirby-Bauer disk diffusion method as recommended by Clinical Laboratory Standard Institute (CLSI). Screening method for the detection of MDR organism was done by using Oxacillin while that among the patients with local catheter infections was diabetes (28.2%) and the commonest purpose of cannulation was for administration of IV fluids and parenteral antibiotics as shown in Candida species and only 2.77% were polymicrobial.86.12% of the isolates were bacteria, while 11.11% of the pathogens were 64% of the pathogens of CRBSI were Gram positive and 36% were Gram negative while 57.84% of the pathogens causing CRLI were due to Gram-negative organisms and 42.16% were Gram-positive.Staphylococcus aureus (40%) and the least common was Acinetobacter baumannii (4%). Candida spp. and Pseudomonas aeruginosa both accounted for about 16% of the infections while about 8% infections were caused each by E. coli, K. pneumonia, and coagulase-negative Staphylococcus spp.The commonest pathogen of CRBSI was Pseudomonas and Acinetobacter showed growth in 16.87% of the cases followed by Staphylococcus aureus (13.25%) and E. coli (10.84%). Klebsiella pneumoniae and Candida spp. each showed growth in 9.64% cases.The commonest pathogen of CRLI was CONS (19.28%) and the least common were polymicrobials (3.61%). Both Staphylococcus (MRSA and MRCONS) isolated from local catheter infections were 100% sensitive to vancomycin, teicoplanin, and linezolid and all sensitive Staphylococcus were 100% resistant to ciprofloxacin.All resistant Pseudomonas aeruginosa strains isolated in CRLI was piperacillin (85.7% sensitive) and the most sensitive reserved antibiotics were cefoperazone-salbactum, piperacillin-tazobactum, ticarcillin-clavulanic acid (85.7% each), and meropenem (78.6%).The most sensitive routine antibiotic for E. coli isolated in CRLI was cefuroxime (88.9% sensitive) and the most sensitive reserved antibiotic was meropenem (88.9% sensitive) while the most sensitive routine antibiotic for K. pneumoniae isolated in CRLI was amikacin (12.5% sensitive) and the most sensitive reserved antibiotic was meropenem (50% sensitive). In case of A. baumannii isolated in CRLI, the most sensitive routine antibiotic used was amikacin (35.7% sensitive) and cefoperazone-salbactum in reserved antibiotic (35.7% sensitive).The most sensitive routine antibiotic for Staphylococcus (MRSA) isolated from CRBSI were 100% sensitive to cotrimoxazole and chloramphenicol among routine antibiotic and 100% sensitive to vancomycin, teicoplanin, and linezolid among reserved antibiotics. All sensitive Staphylococcus (MSSA and MSCONS) were 100% resistant to ciprofloxacin.All resistant P. aeruginosa isolated from CRBSI were piperacillin and ciprofloxacin (100% sensitive each). Among the reserved antibiotics the most sensitive were cefepime, cefoperazone-salbactum, piperacillin-tazobactum, ticarcillin-clavulanic acid, and meropenem (100% sensitive each).The most sensitive routine antibiotics for E. coli isolated from CRBSI and both were ESBL producers and among reserved antibiotics meropenem was most sensitive (100%). For K. pneumoniae isolated from CRBSI, the most sensitive routine antibiotics were gentamicin, netilmicin, amikacin , and meropenem among reserved antibiotics (100% sensitive). Only one strain of A. baumannii isolated from CRBSI was resistant to all routine and reserved drugs (multidrug resistant). As shown in Tables There were no routine antibiotics sensitive for There is no role for empirical antibiotics as the majority of patients (81.5%) developed infections despite being under antibiotic cover.P = 0.04) for the development of catheter-related infections. The mean duration of catheter in situ (in days) was higher among cases than controls (14.1 versus 10.9).Duration of catheter in situ is a predisposing risk factor (As shown in S. aureus was the commonest pathogen isolated accounting to 19.44% followed by CONS (16.67%), P. aeruginosa (16.67%), A. baumannii (13.88%), Candida species (11.1%), E. coli (10.18%), K. pneumoniae (9.26%), and polymicrobial (2.77%). Overall multidrug resistant organisms accounted for 31.48% of the infections. Candida species were isolated from 11.1% of the patients. Although this is lower than available Indian statistics [Our study investigated the incidence, microbiological profile, clinical profile, and the risk factors for the development of catheter-related infections in a tertiary care hospital. The commonest isolates among the patients with CRLI were Gram-negative organisms (59.0%) while Gram-positive organisms 64.0%) caused the majority of the CRBSI. Overall, in the entire study 4.0% causCONS 16.6%, P. aerStaphylococcus (MRSA and MRCONS) isolated from CRLI were 100% sensitive to vancomycin, teicoplanin, and linezolid and all sensitive Staphylococcus were 100% resistant to ciprofloxacin. All resistant Staphylococcus (MRSA) isolated from CRBSI were 100% sensitive to cotrimoxazole and chloramphenicol among routine antibiotics and 100% sensitive to vancomycin, teicoplanin, and linezolid among reserved antibiotics. All sensitive Staphylococcus (MSSA and MSCONS) were 100% resistant to ciprofloxacin. The most sensitive routine antibiotic for P. aeruginosa strains isolated in CRLI was piperacillin (85.7% sensitive) and the most sensitive reserved antibiotics were cefoperazone-salbactum, piperacillin-tazobactum, ticarcillin-clavulanic acid (85.7% each), and meropenem (78.6%). The most sensitive routine antibiotics for P. aeruginosa isolated from CRBSI were piperacillin and ciprofloxacin (100% sensitive each). Among the reserved antibiotics the most sensitive were cefepime, cefoperazone-salbactum, piperacillin-tazobactum, ticarcillin-clavulanic acid, and meropenem (100% sensitive each).All resistant E. coli isolated in CRLI was cefuroxime (88.9% sensitive) and the most sensitive reserved antibiotic was meropenem (88.9% sensitive). There was no routine antibiotic sensitive for E. coli isolated from CRBSI and both were ESBL producers and among reserved antibiotic meropenem was the most sensitive (100%). The most sensitive routine antibiotics for K. pneumoniae isolated in CRLI was amikacin (12.5% sensitive) and the most sensitive reserved antibiotic was meropenem (50% sensitive). The most sensitive routine antibiotics for K. pneumoniae isolated from CRBSI were gentamicin, netilmicin, amikacin , and meropenem among reserved antibiotics (100% sensitive).The most sensitive routine antibiotic for A. baumannii isolated in CRLI was amikacin (35.7% sensitive) and cefoperazone-salbactum in reserved antibiotic (35.7% sensitive). The only one strain of A. baumannii isolated from CRBSI was resistant to all routine and reserved drugs (multidrug resistant).The CRBSI incidence density at our hospital is 8.75 per 1000 catheter days. This is similar to observations from meta-analyses by the National Nosocomial Infections Surveillance System in the United States which reported an incidence density ranging between 2 and 11.3 per 1000 catheter days, as shown in P = 0.000).The most sensitive routine antibiotic for P = 0.002). The duration of catheterization was a significant factor that determined the development of catheter-related infections. Although previous studies have confirmed that central venous catheterization longer than 5 to 7 days was associated with a higher risk of catheter-related infection [P = 0.016).In our study the incidence of catheter-related infection was highest with triple lumen catheters when compared with double and single lumen catheters (39.8% versus 37% versus 23.1%). By logistic regression analysis we were able to derive an odds ratio of 35.9 for triple lumen catheters were ESBL producers. Overall 31.48% were multidrug resistant strains.As shown in There are few limitations on this study. False positive culture may result if skin contacts with catheter. If portion of the catheters not inside the patient is submitted, both false positive and false negative cultures are possible. Potential pathogens may die if the removed catheter is not transported to the laboratory promptly. Different insertion sites were not randomly assigned. No randomized trials, however, have compared infection rates for CVCs placed in the three different sites. Only in the study of Merrer et al. patientsThe increasing rate of CRBSI is a matter of concern to our hospital setup. This work will highlight the common microorganisms responsible for CRBSI, their antibiotic susceptibility pattern and also will correlate the clinical significance. This work will help both the clinicians as well as microbiologists in better management of patients as well as in prevention of nosocomial bloodstream infection, especially due to multidrug resistant organisms."} +{"text": "Delirium is an acute temporary and fluctuating mental-organic syndrome, characterized by a global impairment of cognitive function, reduced level of consciousness, attentional deficits and altered sleep-wake cycle, and changes in arousal . The Confusion Assessment Method (CAM and CAM ICU) is a diaTrained and capacitated physiotherapists applied the CAM ICU in patients admitted to Albert Einstein Jewish Hospital ICU, older than 18 years old and with 24 hours physiotherapy assistance per day. The content and level of consciousness investigation was performed daily in all physiotherapy sessions, which allowed characterizing the need to apply the CAM ICU. These data were evaluated twice a week during a 30-day period through medical charts.n = 16), of these patients 25% were under mechanical ventilation and 25% were spontaneously breathing. In regards to the clinical admission diagnosis, delirium was present in 20% vascular patients, 16% neurologic patients, 14% liver patients, 8% respiratory patients and 2% cardiac patients. We found no correlation of delirium with clinical admission diagnosis .During the study period, 226 patients were evaluated by physiotherapists, median age 70 years old (range 21 to 92), and 60% were male. The clinical admission diagnoses were: 36% sepsis, 20% cardiac, 19% neurologic, 11% respiratory, 4% orthopedic, 3% liver and gastric patients, and 2% vascular. The mean Simplified Acute Physiology Score (SAPS 3) was 45 points. We found a delirium incidence of 7% (There was a low incidence of delirium in ICU patients followed by physiotherapists. This may be due to physiotherapy and multi-professional team interventions performed earlier."} +{"text": "Giardia/Cryptosporidium antigens in human stool specimens. Initially, Giardia/Cryptosporidium Chek kit (TechLab), an enzyme-linked immunosorbent assay (ELISA), was adopted for screening. The ELISA-positive reactions were subsequently characterised by RIDA Quick Giardia and RIDA Quick Cryptosporidium immunochromatographic kits (R-Biopharm). A gold standard test comprising PCR and microscopy was used for preparing control samples. Performance of individual kits was tested against these samples which included 50 Giardia-positive, 40 Cryptosporidium-positive, and 70 Cryptosporidium/Giardia-negative. For Cryptosporidium, specificities of the ELISA and RIDA Quick Cryptosporidium kits were 95.71% and 100%, respectively. Both kits demonstrated sensitivity of 95%. For Giardia, the ELISA and RIDA Quick Giardia kits showed sensitivities of 100% and 97.5%, respectively. Specificities obtained by the ELISA and RIDA Quick Giardia were 95.7% and 100%, respectively. Based on the results of two reference PCRs, on 250 random samples, the algorithm exhibited sensitivity, specificity, positive predictive value, and negative predictive value of 97.06%, 100.00%, 100.00%, and 98.91%, respectively. In conclusion, this immunoassay-based algorithm can be used as routine test in diagnostic laboratories for screening and identification of a large number of samples.An immunoassay-based algorithm, involving three commercial kits, was introduced and evaluated for screening and identification of Cryptosporidium and Giardia are two common intestinal protozoa causing gastroenteritis in humans [Giardia, and oocyst stage of Cryptosporidium in faecal specimens. In developing countries, this is routinely done through classical microscopic-based techniques, namely, the iodine-saline mount for Giardia and the modified Ziehl-Neelsen (mZN) staining for Cryptosporidium [Cryptosporidium and Giardia antigens in stool samples. These lateral flow immunoassays can be accomplished within 10 minutes with a sensitivity more than 97% and specificity of 100% [n humans , 2. Manyn humans . Infectin humans , 5. Defiporidium , 7. Howeporidium . Accordiporidium . The dirporidium , 10. Theporidium \u201313. In tporidium , 11, 13.poridium , 15. In of 100% .Giardia and Cryptosporidium in human faecal specimens [Giardia and Cryptosporidium in human stool samples from Taif, Saudi Arabia. This algorithm is based on three commercial coproantigen kits, namely, TechLab, Inc., Giardia/Cryptosporidium Chek ELISA kit for Giardia and/or Cryptosporidium screening in a large number of samples [Giardia, and RIDA Quick Cryptosporidium cassettes (R-Biopharm) to identify the ELISA-positive samples.In Saudi Arabia, few studies have used these immunoassay-based tests for detection of pecimens , 18. In pecimens \u201322. In t samples , RIDA QuGiardia/Cryptosporidium positive and negative control samples. Samples were collected from those submitted to the Microbiology Laboratory at King Faisal Public Hospital in Taif, Saudi Arabia, for routine parasitological examination. Additionally, 250 faecal specimens were randomly collected between January and August 2013 for further evaluation and validation of the combined immunoassay-based algorithm. Faecal samples, without any preservatives, were properly labelled and transmitted to the Medical Laboratory at College of Applied Medical sciences, Taif University, within 2-3 hours of collection. Upon arrival to the laboratory, samples were stored at 4\u00b0C for microscopic and immunoassays testing. An aliquot of each specimen was prepared, marked, and stored at \u201320\u00b0C for PCR examination.One hundred sixty diarrhoeal and nondiarrhoeal fresh stool samples were used for preparation of Giardia and Cryptosporidium. According to this gold standard test's results, positive and negative samples were classified into control groups.The aforementioned 160 samples were subjected to a combined gold standard test comprising microscopic as well as PCR testing for Giardia trophozoite or cyst stages [Cryptosporidium oocysts identification [Unpreserved faecal specimens without prior concentration procedure were subjected to microscopic examination within 2-3 hours after collection. Wet mount preparations, one with saline and the other with iodine, were prepared and each coverslip area was scanned for t stages . A thirdfication . The staCryptosporidium and the protocol of Hopkins et al. for Giardia [2O for stock preparation (100\u2009pmol/\u03bcL) and stored at \u221220\u00b0C until use. Reactions were carried out in Techne TC-4000 thermal cycler. GoTaq Hot Start Polymerase (Promega) and other PCR reagents were used in amplification reactions with final concentrations closely similar to the published protocols.Aliquots, stored at \u221220\u00b0C, were subjected to DNA extraction within one to two weeks after arrival to the laboratory using QIAmp Stool Mini Kit (Qiagen) following the manufacturer's protocol. DNA extracts were subsequently subjected to amplification by two published PCR assays. PCR assays were conducted following the protocol of Xiao et al. for Giardia , 25. PriGiardia and/or Cryptosporidium coproantigens using TechLab, Inc., Giardia/Cryptosporidium Chek ELISA kit. Subsequently, the ELISA-positive specimens were tested for the presence of Giardia coproantigen by the RIDA Quick Giardia and for Cryptosporidium oocysts surface antigen by RIDA Quick Cryptosporidium kits. All immunoassays were performed according to the corresponding manufacturers' directions. The rapid tests' results were interpreted visually by the naked eye, while the ELISA test's results were analysed on a multiwell scanning spectrophotometer (ELISA reader) with \u22650.150 being the cutoff for the positive sample at an optical density (OD) of 450\u2009nm.Unpreserved specimens, stored at 4\u00b0C, were subjected to examination by the three coproantigen detection kits, under evaluation. Samples were initially screened for Results obtained from examination of the clinical stool samples were stored and analysed through Microsoft Excel TM 2007. The diagnostic sensitivity, specificity, positive predictive value, and negative predictive value of various diagnostic assays were determined by standard formulae .Based on the combined gold standard test-results on the preceding 160 stool samples, three positive control groups were assigned. Samples were diagnosed as positives by microscopy see and the Cryptosporidium- and 30 Giardia-positive stool samples. Samples diagnosed as negative by microscopy but positive by the PCR tests diagnosed as Cryptosporidium- and Giardia-negative by both microscopy and PCR tests were selected as a negative control group (group-3).This group included 25 ests see were selCryptosporidium- and Giardia-positive control faecal samples apart from two . Interestingly, these three false-positive samples gave no reactions when individually tested by the two subsequent discriminatory rapid kits. Based on these results, the TechLab ELISA test exhibited different diagnostic performance rates for Cryptosporidium and Giardia as shown in The screening kit successfully detected the target antigens of all two see . These tGiardia-positive control faecal samples apart from one . Importantly, this sample was Giardia PCR positive but negative by the microscope. No coproantigen for Giardia was detected for all negative control samples (n = 70). Equally important, no coproantigen for Giardia was detected when Cryptosporidium-positive control samples (n = 40) were examined by the kit. As seen in Giardia kit showed SE, SP, PPV, and NPV of 97.5% (95% CI: from 0.86 to 0.99), 100% (95% CI: from 0.9 to 1.0), 100% (95% CI: from 0.9 to 1.0), and 98.5% (95% CI: from 0.9 to 1. 0), respectively.The kit successfully identified the target antigens of all Cryptosporidium-positive control faecal samples apart from two . Interestingly, these two samples were those diagnosed as false negatives by the ELISA screening kit. No coproantigen for Cryptosporidium was detected for all negative control samples (n = 70). Equally important, no coproantigen for Cryptosporidium was detected when Giardia-positive control samples (n = 50) were examined by the kit. As shown in Cryptosporidium kit showed SE, SP, PPV, and NPV of 95% (95% CI: from 0.8 to 0.9), 100% (95% CI: from 0.9 to 1.0), 100% (95% CI: from 0.9 to 1.0), and 97% (95% CI: from 0.9 to 1. 0), respectively.The kit successfully identified the target antigens of all Giardia and/or Cryptosporidium coproantigens in 76 samples. By the second discriminatory kits, Cryptosporidium was identified in 24 samples and Giardia was identified in 42 samples . Neither Cryptosporidium nor Giardia coproantigen was identified in the remaining ten samples (4%). Neither Cryptosporidium nor Giardia copro-DNA was detected when these samples were subjected to diagnosis by the two reference PCR tests. By reviewing the hospital laboratory records regarding these 250 randomly collected samples, Cryptosporidium oocysts were identified in 13 samples by microscopic examination of mZN stained wet mounts prepared from fresh unconcentrated specimens. Giardia trophozoite and/or cyst stages were detected in 33 samples using microscopic examination of iodine-stained wet mounts prepared directly from fresh faecal specimens. On the other hand, the reference PCR assays accurately detected Cryptosporidium DNA in 26 faecal samples and Giardia DNA in 42 samples . The Cryptosporidium oocysts surface antigens being present in these two specimens below the detection limit of the assay may be an explanation to this reduced sensitivity, especially when we know that Cryptosporidium oocysts could not be seen microscopically in the mZN stained smears. Chalmers and her colleagues reported sensitivity of 93.4% of the same kit towards Cryptosporidium control samples from United Kingdom [Giardia/Cryptosporidium and IVD Research Giardia/Cryptosporidium ELISA kits offered sensitivities of 91.4% and 92.8%, respectively. In many previous studies the kit proved to be 100% specific; however, in this study, it exhibited a slightly lower specificity of 95.71% [To address the performance characteristics of the algorithm, an assembled reference standard test comprising PCR and microscopy was assembled. Samples were subjected to the combined gold standard test and the results were interpreted as follows. First, stool sample that tested as positive with microscopy was assumed to contain high parasite loads. Second, samples that were negative by microscopy but diagnosed as positive by a reference PCR test were likely to have low to moderate parasite loads. This assumption was taken relying on the previously reported sensitivities of the two diagnostic methods , 14, 27. Kingdom . In the f 95.71% , 29. ThiGiardia rapid test demonstrated sensitivity and specificity of 97.5% and 100%, a performance which is much better than it has achieved in previous study. Authors at the Institute of Tropical Medicine in Berlin, Germany, in 2006, have reported sensitivity and specificity figures of 80% and 99.4%, respectively [Cryptosporidium lateral flow test, used in the study, showed higher performance than it offered previously. Equally important, the RIDA Quick Cryptosporidium did not cross-react with stool samples containing Giardia and RIDA Quick Giardia kit did not cross-react with Cryptosporidium-positive stool samples. Previous studies have reported false-positive Cryptosporidium infections with other rapid tests [On the other hand, the RIDA Quick ectively . Similarid tests , 32. Othid tests , 34.Giardia/Cryptosporidium diagnosis. This performance rates achieved by the algorithm were higher than those reported for the individual kits, under evaluation, [Cryptosporidium coproantigen was confirmed in 24 samples (9.6%) and Giardia coproantigen was confirmed in 42 (16.8%). These prevalence rates of infections do not reflect the true prevalence of these two protozoa in Taif city because samples were collected within a short period. Ten samples were positive by the ELISA kit but were negative for Giardia or Cryptosporidium coproantigens by the two rapid tests. None of these samples was positive for Giardia or Cryptosporidium by the reference PCR assays and microscopy. It is clear that the high specificities offered by the two rapid tests counterbalanced the unwanted false-positive results of the ELISA kit and, as a result, the overall algorithm test results were not affected.Further evaluation of the algorithm was carried with a fairly large number of random stool samples with blinded microscopic test results as generated by routine testing procedures at the Clinical Microbiology Laboratory. Based on tests' results on randomly collected samples, the immunoassay-based algorithm performance was comparable to two PCR tests' results and much better than the two traditional staining methods used for luation, , 30 and luation, , 14, 27.The immunoassay-based algorithm performed well with the collected stool samples. It was proved to be a very useful screening tool for the target specific protozoan antigens in stool specimen. The algorithm showed diagnostic performance higher than those achieved by the classical staining methods. Its results were comparable to those given by the reference PCR assays used in the study. Bearing in mind the large number of samples that can be screened, the ease of use, the less hands-on time, and its amenability for future semiautomation, the introduced algorithm has a real potential to be adopted in diagnostic laboratories, especially those having a large number of specimens likely to be tested."} +{"text": "To study the Impact of educational activities on the rates and frequencies of Percutaneous Injuries at a tertiary care hospital in Saudi Arabia.PIs Surveillance is a routine activity in King Abdulaziz Medical City in Riyadh using the Exposure Prevention Information Network (EPINet) data collection tool. On 2001 through 2003, we started educational activities of HCWs aiming at preventing PIs. This education included lectures and inservice training about the risk factors and unsafe practices contributing to PIs and how to avoid it. Data before the intervention (1997-2000) and after the intervention (2004 - 2008) were imported from our surveillance system and statistically analyzed., the overall rate of PIs during the post intervention period has dropped significantly (14% vs. 32.8% per 1000 HCWs). The rates among nurses and housekeepers showed a significant drop (15% vs. 37.6% for nurses and 10% vs. 34.5% for housekeepers). PIs frequencies in Emergency Department (ED) and Intensive Care Units (ICU) showed significant decrease (3.4% for both vs. 12.4 % & 13.7% respectively). Devices as needle on IV line, IV catheters, lancets and suture needles showed significant decrease in frequency. PIs frequencies occurring during device disassembly and devices left inappropriately showed significant decrease.Compared to the pre-interventional periodThe educational program appeared to have positive impact on reducing some categories of PIs including the overall rate, nurses and housekeepers job categories, ED and ICU, Needle on IV line, IV catheters, lancets and suture needles. However, other PIs categories did not change significantly.None declared."} +{"text": "The SPV is used to compare tissue perfusion with average whole-body perfusion at enhanced MDCT; the SPV is conceptually similar in its derivation of the SUV used to quantify FDG uptake at PET. The aim of this study was to characterize solitary pulmonary nodule (SPN) comparing SPV and SUV value.Twenty nine patients, age range 52-74, with SPN diagnosed with a chest radiography, underwent MDCT and PET and, if necessary, nodule biopsy. The SPV and SUV value were compared with histological features.Of the twenty nine patients, 21 underwent CT-guided FNAB with histological analysis and for 8 \u201cwait and watch strategy\u201dwas adopted. Seventeen patients showed malignant SPN and four patients had benignant SPN at CT-guided FNAB. In patients with definite histology the specificity of SPV was 75% compared to 83% of SUV; the sensitivity (88%), the accuracy (85%) and the positive predictive value (94%) were equal for both. The negative predictive value of SPV and SUV was 60% and 67% respectively. The comparison of specificity, sensitivity and accuracy, between SPV and SUV was 90% (r=0.9), 100% (r=1) and 100% (r=1), respectively.The similarities between SPV and SUV suggest that the CT-derived SPV may be useful, not only for distinction of benign and malignant lesions, but also for acquisition of prognostic information and assessment of treatment response, with less exposure of ionizing radiations."} +{"text": "Background & Objective: Although the magnitude of HIV in Pakistan has been well documented, but no record of HIV prevalence in Faisalabad region exists. A retrospective study was carried out at Sexually Transmitted Infections (STIs) clinic, District Headquarter (DHQ) hospital, Faisalabad, Pakistan to find out the prevalence of HIV and related risk factors.Methods: Between March, 2010 and December, 2012, a total of 31040 subjects were either interviewed or their medical records were reviewed. From those recruited by convenient sampling method, written informed consent was obtained and informed about the study protocol. Blood serum was tested for antibodies to HIV-1 and HIV-2 .Results: On the whole, Anti-HIV was demonstrated in 173 (0.557%) of the respondents. This gives an overall HIV prevalence of 557 per 100,000.Averaged age of the patients was 49.5 years (range: 30-45) with 85.55% male. Majority of the patients were urban dwellers (87.28%), divorced or widowed (46.82%) and uneducated (50.28%). A large proportion (78%) of the patients was injection drug users. Compared to blood donation/transfusion and sexual interactions, injection drug use was the major potential risk factor for HIV infection.Conclusion: Most important finding was higher HIV prevalence in Faisalabad region as compared to the previous assessments at the national level. This reflects an alarming situation necessitating contextual preventive interventions. Precarious practices such as injection drug abuse, blood donation/transfusion needs to be amended and extramarital sexual contacts should be avoided. This epidemic has resulted in 25 million deaths worldwide.2,3,5,6 Another factor that poses serious intimidation to Pakistani population is the limited knowledge about HIV/AIDS. In view of the current scenario, a comprehensive study to characterize HIV in the local populations is suggested.1,7 A common misconception in Pakistani society is that being Muslim, HIV cannot be contracted. Such foresight demands continuous monitoring and preventive intrusions to control the spread of HIV.2Although, Pakistan currently portrays a low HIV prevalence, however, the concerns of a widespread HIV epidemic are primarily due to unsafe high-risk practices. More Pakistani men are infected with HIV than women and modes of HIV transmission include sexual relations, infectious blood and drug addiction.There are no reports on HIV prevalence among residents of Faisalabad, Pakistan. We aimed to determine prevalence of HIV and related risk factors in Faisalabad, Pakistan.Population and Sampling: This retrospective report covered about two and a half year period from March, 2010 to December, 2012 and included 31040 individuals visiting Sexually Transmitted Infections (STIs) clinic, DHQ hospital, Faisalabad, Pakistan. Participants were either recruited or their medical records were reviewed. From those recruited by convenient sampling method, written informed consent was obtained and they were informed about the protocol.Questionnaire: The following data were collected for each patient: age, gender, residential and marital status, occupation, education, history of sexually transmitted diseases (STD) and high risk behaviours . Trained investigators pre-tested the validity of the form and some queries regarding sexual behaviours were modified. Sexual orientation was determined. The study was anonymous.Biological Tests: From Clinical Pathology Laboratory, District Headquarter hospital, Faisalabad, Pakistan, patients\u2019 records were procured. For new enrolments, blood samples were centrifuged and the sera were tested for the presence of antibodies to HIV-1 and HIV-2 .Statistical Analysis: All data were expressed as number (n) or mean (standard error).Potential risk factors were assessed by multivariate analysis of variance (MANOVA). The p value of less than 0.05 was considered to be significant. Statistical analysis was performed by Statistical Package for the Social Sciences software (version 15.0).Patients (n=31040) were either examined or their medical records were reviewed for HIV-1 and HIV-2.Data pertaining to demographic characteristics and risk factors is summarized in Average age of the HIV infected population was about 50 years and majority (85.55%) were male. The age group for HIV incidence was 30-45 years, as it accounted for the 51% of the infected sample.HIV positivity was more prominent (p=.001) in male as compared to the female sample (6:1 ratio).It was observed that 87.28% HIV positive patients were urban dwellers (p = .035).The burden of HIV in the divorced/widowed was more as compared to the unmarried and married . Almost half (50.28%) of the infected subjects were illiterate and 35% had primary education.HIV was significantly (p = .001) higher in uneducated and those having primary education (p = .041).Employment category was insignificant in diseased individuals, as 31.79% were self-employed (p = 0.116), 42.19% were employees (p = 0.074). Percentage of unemployed persons was 26% (p = 0.310).A large proportion (78%) of the participants was injection drug users (IDU). Whereas, minor fractions (15.6% and 6.35%) were involved in unprotected blood donation and transfusion respectively. In statistical analysis, IDU was a constant causative factor (p = .001) for HIV infection. Blood donation and transfusion were not sensitive markers for the risk of HIV infections.Multiple partners and extramarital relationships were apparently uncommon among local population. About 97% were heterosexual (P = 0.039) and were reluctant in disclosing the details of partners, if any. Self-reported history of sexually transmitted diseases (STDs) was 22.54% (p = 0.341). However, 53.75% (p = 0.115) had no knowledge of former STDs occurrence.HIV) is a global health challenge that has both social and economic implications. Since 1987, when the first case of HIV was identified, slow but steady HIV incidence is documented in Pakistan. Given the lack of initial prevalence magnitude, and causative factors, indigenous HIV positivity and subsequently AIDS cases will rise. It is important to measure HIV prevalence, associated factors and institute preventive measures at early stages.4The explosive spread of the human immunodeficiency virus reported 0.052% and 0.064% HIV prevalence data for the years 1992 and 1995 respectively.9 For the year 2007, 0.00542% HIV magnitude was stated.10 Most important finding of the study was higher HIV prevalence than the previous assessments. This reflects alarming situation that needs preventive interventions. Several regional studies from Lahore, Karachi, Peshawar and Northern areas are available. Khanani et al.11 and Mujeeb & Hashmi12 observed 0.73% and 0.147% HIV seroprevalence among general populations in Karachi. Reports from Lahore, Peshawar and Northern Pakistan cited 0.06%, 0.1% and 0.05% prevalence rates respectively.13-15Later on, 0.1% HIV prevalence was estimated by NACP in 2001.4 Present study identified 6:1 gender wise ratio in HIV subjects. Previously, Male to female ratio of 5:1 16 and 2:1 15 were described.As regards age and gender distribution, our results were partially in compliance with the other studies, as an age range of 20-50 years, with median age of 35 is established for infection.4,17 Most of the HIV diagnosed subjects were urban residents. So, it can be concluded that rural populations are vulnerable to HIV to lesser extent. In addition, HIV prevention strategies should be more focused in urban Faisalabad. Contrary to current finding, Solomon et al.18 identified negligible difference in HIV prevalence in urban and rural Indian population.Residential area, marital status, education and occupation are socio-economic determinants of HIV serostatus. Urban residence was positively significantly related to HIV status.19, married people have less HIV occurrence than unmarried.Review of literature revealed that no research in Pakistan has examined the relation between the risk of HIV infection and marital status. In present research, married people had lower HIV infection. The matrimonial role in hindering HIV spread needs to be highlighted, as indicated by Shisana et al20 It was determined by Kirunga and Ntozi17 that level of education affects HIV status. Religious and socio-economical contexts hinder new educational syllabi, especially those concerned with sex education in Pakistan.21The proportion of individuals with infection was found to be inversely related to the literacy levels in the present study. The prevalence decreased as the educational level increased. Low literacy rate is key factor for HIV in the developing countries.17 described insignificance of occupation in HIV development.All the infected subjects in recent investigation were almost equally disseminated in three occupational categories. Hence, the livelihoods opted by subjects was not significant in acquisition of HIV. Similar to our inferences, Kirunga and Ntoziviz.blood donation/transfusion, Injecting drug use, sexual conducts and history of STD were analysed by MANOVA. Drug use via injections was the main source of HIV transmission. Current nationwide estimations of HIV are based on large screening programs on high and low risk populations. Such information cannot portray accurate picture of IDU in the general population. The data indicated excessive HIV prevalence among IDU, suggesting an urgent need to educate public about hazardous reuse of syringes.21,22Four potential risk factors 21-23Blood donation and transfusion activities were not potential risks for HIV in our study. Although a low prevalence of HIV is cited for Pakistan, the concerns of HIV epidemic in future are due to specific risky behaviours prevailing in Pakistani society, especially habitual blood donation and transfusion practices. Poor facilities and negligence in blood screening at public and private health care centers are common.22,24 Neither sexual preference nor absence of past STD had significant role in developing HIV. These inferences should be accepted with caution, as religious and social values not only minimize such tendencies but also impede the disclosure.STD may contribute to the spread of HIV. History of STD in study subjects was not a significant aspect for HIV. According to WHO, 0.3% HIV prevalence is present among Pakistani STD patients.Limitations of the study: This is the first study of HIV prevalence in Faisalabad and it provides insight on certain factors that may be contributing to the HIV epidemic. However, it had several limitations. First, high-risk groups (sex workers) were not included. Secondly, the study sample may be biased in that only those who visited STI clinic were involved. Thirdly, drug abuse and sexual behaviours are sensitive issues. The odds of their miscommunication must not be ignored.HIV is widely prevalent in Faisalabad region, Pakistan and this study provides an opportunity to restrict its further spread. High risk practices such as injection drug abuse, blood donation/transfusion needs to be amended and extramarital sexual contacts should be avoided.MAM: Conceived and designed the study, data collection, FH: Conceived and designed the study, did manuscript writing, editing and review of final manuscript, MJ: Did biological testing, data collection."} +{"text": "Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities.Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs and taxonomic dominance perturbations favoring the Anthropogenic activities such as mining and smelting trigger profound damage to aquatic ecosystems is universally reported as the major mechanism to facilitate rapid adaptation in microbial communities . AMD severely impacted sites are extreme environments as very acidic, very low in organic matter and rich in heavy metals or metalloids. When in excess in living cells, trace metals can bind to physiologically sensitive intracellular molecules or organelles, leading to deleterious effect and then flash frozen into liquid nitrogen until DNA extraction.These procedures were described in Laplante and Derome . Brieflym NaCl , mixed and centrifuged 20 min at 17 000 g. The supernatant was transferred again into a clean microcentrifuge tube containing 1 volume of ice-cold isopropanol, mixed gently and stored 30 min at \u221220\u00b0C. The mixture was centrifuged 20 min at 16 162 g and the supernatant was thrown away. The pellet was washed with ice-cold 70% ethanol, air-dried and finally resuspended in 25 \u03bcL of sterile MilliQ H2O. Subsequently, DNA purity (260/280 ratio) and quantity were measured using a Nanodrop instrument .Genomic DNA was extracted using a modified protocol of salt-extraction from Aljanabi and Martinez . During m of each primer and sterile MilliQ H2O to up to 50 \u03bcL. To achieve the PCR amplifications, a general reverse primer (R519) combined with B primer (Roche) was used in combination with a unique tagged forward primer (F63-targeted) combined with A primer (Roche) . All PCR reactions were performed in a final volume of 50 \u03bcL containing 25 \u03bcL of Premix Taq, 1 \u03bcche) see . PCR conhttp://www.mothur.org) were undertaken using the R commands \u2018model = lm(tableau$X\u223ctableau$Y)\u2019 and \u2018anova(model)\u2019 to assess the factors explaining the variance of the models. Effects for the anova tests were deemed significant at P < 0.05 and marginally significant at P = 0.05\u22120.10. In addition, for each linear regression, the coefficient of determination (R2) was calculated to assess the validity of the model. The statistical analyses were performed using R statistical software (http:/http://www.r-project.org/).All data were first tested for normality and equality of variances Zar . Linear P-value <0.01) values measured in the five lakes, bacterial networks were built using Rcmdr, a platform-independent menu interface running with R software. The correlation coefficients were calculated by applying the Spearman algorithm. This previous filtering step removed poorly represented OTUs and reduced network complexity. We considered a valid co-occurrence event to be a robust correlation if the Spearman's correlation coefficient was both >0.6 and statistically significant , major cations , DOC, pH, and temperature for the studied lakes are summarized in H' = 4.564), followed by Das (H' = 3.834), Tur (H' = 2.924), and Lar (H' = 2.161), while the lowest Shannon value was calculated for Bar (H' = 0.728). The estimated species richness, as seen with the Chao values, was the highest in Das (SChao = 2674.010), followed by Lar (SChao = 1794.754), Opa (SChao = 1308.438), and Tur (SChao = 1204.238), while the lowest richness was observed in Bar (SChao = 836.324).After trimming the primer sequences, barcodes and adapter tags, the average sequence length was 425 nt and the total dataset comprised 47 124 high quality sequences with a minimum length of 300 nt. Then, after removing the chimeras and retrieving the unique sequences, the analyses using Mothur generated multiple outputs, which are summarized in Venn diagrams of the percentages of species shared between communities see reveal tThe membership and structural similarities between the studied communities are illustrated by the distinct dendrograms provided using Mothur see . FirstlyPrincipal coordinate analyses (PCoA) of the unweighted (diversity) and weighted (structure) UniFrac distance matrix are showed in Proteobacteria were prevalent among the disturbed communities. Deeper analysis at the class level among the Proteobacteria exerts the high relative proportion of OTUs belonging to the Alphaproteobacteria (Lar = 64.30% > Tur = 56.93% > Bar = 33.58% > Opa = 30.66% > Das = 15.43%), followed by the Betaproteobacteria (Bar = 34.34% > Das = 25.76% > Opa =16.25% >Lar = 16.17% > Tur = 13.20%). The second most dominant phylum based on the relative OTUs abundance was represented by the Bacteroidetes, which are found primarily in the undisturbed sites and mainly encompassed the classes Flavobacteria (Das = 18.35% > Opa = 8.47% > Tur = 0.65% > Bar = 0.38% > Lar = undetected) and Sphingobacteria (Das = 9.48% > Opa = 7.78% > Tur = 5.41% > Bar = 3.02% > Lar = 0.59%). The third phylum that showed high degree of OTU diversity was Actinobacteria which, as for the Bacteroidetes, exhibited higher OTU diversity within the noncontaminated sites. Among the Actinobacteria, most representatives were regrouped in the class of the Actinomycetales (Das = 16.04% > Opa = 10.30% > Bar = 3.40% > Lar = 1.18% > Tur = 0.43%) followed by the class Acidimicrobiales (Das = 1.58% > Lar = 0.79% > Bar = 0.75% > Tur = 0.43% > Opa = 0.23%). Several other phyla were identified within the studied system such as the Acidobacteria, Firmicutes, TM7, Chloroflexi, OP10 and Verrucomicrobia, but they showed very weak relative OTU abundances (less than 2.29% in at least one site).Based on each phylum's relative OTUs abundance, the taxonomical survey at the diversity level see revealedPolynucleobacter (class Betaproteobacteria) showed greatest relative abundance (Bar =28.30% > Lar = 11.83% > Das = 8.87% > Tur = 6.06% > Opa = 5.26%). The second best represented genus was Kozakia from the class Alphaproteobacteria (Lar = 19.33% > Bar = 0.38% > Das = 0.24% > Tur-Opa = undetected), followed by the Acidisphaera (Lar = 13.21% > Bar = 1.89% > Tur = 0.87% > Das = 0.12% > Opa = undetected), the genus Flavobacterium from the Bacteroidetes phylum (Opa = 8.47% > Das = 6.93% > Bar = 0.38% > Tur-Lar = undetected), and the genus Citreimonas from the class Alphaproteobacteria (Tur = 14.07% > Opa = 0.23% > Das-Bar-Lar = undetected).The relative OTUs abundance survey permitted establishing the ten most dominant genera at the diversity level within each community see . The genProteobacteria are dominant among disturbed communities (Lar = 97.94% > Bar = 98.21% > Tur =92.53% > Opa = 70.86% > Das = 61.16%). Deeper analysis within the Proteobacteria phylum revealed the high relative proportion of sequences belonging to the Betaproteobacteria (Bar = 94.82% > Tur = 36.13% > Das = 35.06% > Opa = 27.45% > Lar = 19.79%), followed by the Alphaproteobacteria (Lar = 77.51% > Tur = 54.68% > Opa = 38.99% > Das = 24.02% > Bar = 2.94%). The second most dominant phylum based on the relative sequences abundance was represented by the Actinobacteria, which contained higher OTU diversity within the noncontaminated sites (Das = 20.66% > Opa = 16.90% > Lar = 1.65% > Bar = 1.37% > Tur = 0.20%). Among the Actinobacteria, most representatives were regrouped in the class of the Actinomycetales (Das = 19.60% > Opa = 2.06% >Lar = 1.61% > Bar = 1.33% > Tur = 0.17%).Based on each phylum's relative sequences abundance, the taxonomical survey at the structure level see revealedBacteroidetes, which were found mostly in the undisturbed sites (Das = 17.78% > Opa = 9.44% > Tur = 3.74% > Bar = 0.16% > Lar = 0.15%) and mainly regrouped two classes: Flavobacteria (Das = 12.22% > Opa = 4.08% > Tur = 0.05% > Bar = 0.02% > Lar = undetected) and Sphingobacteria (Das = 4.85% > Opa = 2.97% > Tur = 3.64% > Lar = 0.14% > Bar = 0.13%).The third phylum exposing the broader structural complexity was the Polynucleobacter (class Betaproteobacteria) prevailed within all the communities (Bar = 94.55% > Tur = 34.34% > Das = 28.74% > Lar = 19.55% > Opa = 16.61%). The second genus with the highest representatives was Kozakia from the class Alphaproteobacteria (Lar = 47.66% > Das = 3.53% > Bar = 1.02% > Tur-Opa = undetected), followed by the genus Pelagibacter (Opa = 22.09% > Das = 18.57% > Bar = 5.09% > Das-Tur = undetected) and the genus Fodinicurvata (Tur = 33.37% > Bar = 1.02% > Das-Bar-Lar = undetected).The survey of the relative sequences abundance allowed establishing the ten most structurally dominant genera within each community see . The genanova analyses between the diversity data collected and the physicochemical parameters measured at each site are summarized in R2 = 0.90; P = 0.01379).All the correlation results gained from Actinobacteria was negatively influenced by the cadmium gradient while favored by near neutral pH measures . Interestingly, the most diverse order within the class Actinobacteria, namely the Actinomycetales, mainly explained such a negative correlation with cadmium . On the reciprocal, the diversity of the phylum Proteobacteria was significantly correlated with cadmium concentrations and negatively influenced by alkaline pH environments . Deeper analysis among the Proteobacteria revealed that the Alphaproteobacteria was the sole class showing significant correlations with cadmium measures . Moreover, the phylum OP10 exhibited a significant negative correlation with calcium concentrations and the phylum TM7 was negatively correlated with DOC values .At the phylum level, statistical analyses also revealed that the relative abundance of OTUs belonging to the Acidisphaera and Acidocella. Furthermore, the community of Lar showed additional significant correlations as revealed by the genera Acidiphilium, Acidobacteria_GP1 Unclassified, Kozakia and the genus Rhodovarius. Interestingly, the Lar bacterial consortium hosted the genus Tanticharoenia which was also found in Tur, the reference community for contamination.At the genus level, trends indicated that the interconnected and disturbed communities of Lar and Bar shared two genera with similar co-tolerances to various metalloids: anova analyses at the structure level by assessing the correlations between the relative sequences abundance and the physicochemical parameters are summarized in Actinobacteria was negatively influenced by the cadmium gradient, while favored by higher dissolved organic carbon content and neutral pH . Within the class Actinobacteria, the Actinomycetales still mainly explained such a negative correlation with cadmium . As found at the diversity level, the structure of the phylum Proteobacteria significantly correlated with cadmium concentrations, and negatively correlated with alkaline pH environments and high DOC values . Interestingly, the class Alphaproteobacteria did not support the correlation found between the structure of the phylum Proteobacteria and the cadmium gradient as observed at the diversity level.The results recovered from Acidisphaera and the Acidocella. Moreover, Lar community still showed significant correlations considering the genera Kozakia and Rhodovarius. However, no more correlation with cadmium was found for the disturbed communities of Lar and Tur. In contrast, the undisturbed community of Opa still showed a negative correlation with cadmium considering the genus Pelagibacter, a genus also shared with the undisturbed community of Das. Moreover, an additional negative correlation between cadmium and the relative sequences abundance of the genus Beijerinckia was found for Opa, and shared with Das and Bar communities. The genus Zunongwangia, newly retrieved from the community of Opa, also exposed such a negative influence induced by the cadmium content.At the genus level, Lar and Bar still shared the two same genera correlated with multiple metalloids, namely the Proteobacteria and Bacteroidetes was negatively correlated , as for the Proteobacteria and the Actinobacteria , while a significant positive correlation was detected between the OTUs diversity of the Bacteroidetes and the Actinobacteria . Considering the communities' structure as assessed by the relative sequence abundance for each OTU, similar interphylum correlations were observed. In this respect, the structure of the phyla Proteobacteria and Bacteroidetes were negatively correlated , as for the Proteobacteria and the Actinobacteria , while a significant positive correlation was detected between the structure of the Bacteroidetes and the Actinobacteria .Interphylum correlation analyses using the relative OTUs abundances revealed that the species diversity between the phyla Swaminathania, while negatively correlated with the abundance of the species Fodinibacter, Thiorhodospira, Phenylobacterium and Pelagibacter, Flavobacterium, and Arcicella. The second parameter-associated network identifies the DOC parameter positively correlated with the relative abundance of Ferrimicrobium. Ferrimicrobium was found to be negatively correlated with the Simiduia abundance, which in turn was positively correlated with the TM7_unclassified OTU. The third abiotic parameter-associated network put in evidence the negative correlation between the pH parameter and the abundance of Acidisphaera. Besides these particular abiotic parameter-associated networks, networks based exclusively on correlations found between bacterial species were also identified. The first bacteria-exclusive network regrouped OTUs of the Actinobacteria , few members of the Proteobacteria and a sole representative of the Bacteroidetes (Zunongwagia). The second bacteria-exclusive network regrouped species from the Actinobacteria and members of the Bacteroidetes (Fulvivirga and Persicobacter). The third bacteria-exclusive network involved only Actinobacteria member interactions, namely with OTUs Methylovorus, Beijerinckia, Ideonella, and Derxia. The three last bacteria-exclusive networks consisted in single correlations between two species: Seinonella - Roseomonas, OP10_unclassified - Roseomonas, and Parasegetibacter - Catellibacterium.Among the 50 dominant species, only 31 exhibited strong and significant correlations. Based on these significant correlations, three abiotic parameter-associated networks and six bacteria-exclusive networks were built see . The firThrough the identification of taxonomic interactions impacted by similar selective pressures, our study aimed to shed light on the importance of analyzing communities from a phylogenetic perspective. However, we also demonstrated that the inclusion of a quantitative approach provides even deeper insight into the evolutionary forces that shape the dynamics of key taxonomic interaction networks in bacterial communities. Our first objective was to assess whether natural selection drove parallel adaptation at the community taxonomical diversity and structure levels on two geographically isolated bacterial communities under similar selective pressure. The second objective was to test whether a polymetallic gradient exposure in three interconnected lacustrine bacterial communities triggered significant taxonomical membership and abundance shifts. Finally, the third objective was to identify the related environmental factor driving community changes in the studied system.Despite recent progress in characterizing the diversity of freshwater microorganisms, drivers of changes in community composition have not yet been well characterized. Anthropogenic environmental disturbance may have a great impact on the functional diversity of bacterial processes. Given such disturbances are increasingly common, there is a need for accurate predictive models regarding their impact on bacterial community ecology and taxomonic diversity Konopka . More spAmong the collected data, geochemical analysis of lake water samples indicated that the heavy metal content in Opa was similar to the one found in Das, while the heavy metal concentrations in Tur were similar to those measured in Bar. Consistent with the geochemical data, PCoA, Venn and phylogenetic analyses at the microbial diversity level supported the clustering of undisturbed communities on one side and disturbed communities on the other. In this respect, the clustering of the geographically isolated community of Tur with the interconnected communities of Bar and Lar revealed that parallel adaptation can occur at the taxonomic level between independent communities if impacted by a similar selective pressure. Such a parallel change of interacting taxonomical networks suggests that community adaptation is the net effect of individual members' successful and unsuccessful acclimation/adaptation to environmental perturbation, as proposed by DeAngelis et al. . TherefoAt the structure level (i.e. OTU relative abundance), PCoA, Venn and phylogenetic analyses supported the clustering of the communities into three groups according to the cadmium gradient, thus exerting the fact that cadmium was the most lethal heavy metal measured in this study. As such, in relation to relative taxon abundance, weighted structural analyses grouped communities Tur and Bar into an intermediate metallic contaminated communities cluster and further demonstrated that higher cadmium concentrations thoroughly disturbed Lar community structure B. This roriginal core microbiome due to selection of a heavy metal resistant core OTUs combined to the loss of most sensitive bacterial species. Consequently, all the OTUs shared across the five lakes may be considered as part of the original core microbiome. Then, the OTUs shared between Opa and Das may be identified as the healthy core microbiome mirroring the absence of contamination while the persistent species shared between the polluted sites make up the heavy metal resistant core microbiome selected from the original core microbiome. A comparable bacterial community adaptation pattern was observed for copper contamination, where membership shifts translated by an increase of Proteobacteria in Lar. Alphaproteobacterial genera encompassed Acidiphilium, Acidimicrobium, Acidisphaera, Acidocella, Kozakia, and Rhodovarius, which were found to be favored at both the diversity and structure levels in Lar. Interestingly, the Alphaproteobacteria are known to be highly successful aquatic lineages. Competitive at low nutrient levels and resistant to grazing by organisms of higher trophic levels . We can therefore conclude that there were strong patterns of co-variation between phyla, suggesting that interphylum interactions are affected in parallel across communities when impacted by a similar perturbation. This result suggests in turn that taxonomic interphylum interactions are likely conserved.Interphylum correlation analyses revealed that the anova analyses between environmental parameters and the phylogenic survey strongly suggest that both cadmium and pH exert the widest influence over the diversity and structure of bacterial communities. Furthermore, network analyses highlight that the pH parameter was negatively correlated with the Acidisphaera, meaning that acidic waters favor this particular genus, consistent with its extensive isolation from acidic environments (Hiraishi et al. Ferrimocrobium, although commonly found in acid mine drainages due to its capacity for ferrous iron oxidation, showed a lower abundance in the highly impacted sites where the lowest DOC values would result from weaken bacterial activities. This particular genus may therefore regroup sensitive bacterial species with great potential for assessing the intensity of a disturbance over the bacterial activities sustaining ecosystem services such as the organic matter decomposition.The significant correlations found with the Overall, our study brought evidence confirming the hypothesis that following a strong perturbation, sensitive bacterial lineages are eliminated, thus allowing opportunistic species to dominate the emptied niches. The disappearance of sensitive species gradually drives the ecosystem to an overall decrease in biodiversity, which in turn favors biotic homogenization (McKinney and Lockwood In conclusion, our results demonstrate that heavy metal contamination caused significant shifts within lacustrine bacterial communities both at the membership and structure levels, and drove parallel adaptation of two independent bacterial communities impacted by a similar selective pressure. Determining the extent to which ecologically relevant traits are phylogenetically conserved in such a parallel way is critical to understand the parameters that control the community phylogenetic structure, and their evolutionary consequences. In this respect, the parallel changes of interacting taxonomical networks would suggest that HGT of heavy metal resistance genes were limited to closely related species, as argued by Andam and Gogarten . OtherwiAlphaproteobacteria, which were observed to have a functional repertory enriched in detoxifying genes (Debroas et al. Finally, cadmium and acidic pH were identified as the physicochemical parameters that exerted the strongest influence on the whole community taxonomic network. These two physicochemical parameters favored the Such insights therefore clearly demonstrate the need to study bacterial community diversity and structural changes triggered by abiotic contaminant exposure from an ecological and evolutionary point of view. Heavy metals affect the bacterial communities that occupy different ecological niches and participate in a variety of biogeochemical processes and ecosystem functions. As the world's freshwater resources are under severe stress, next-generation sequencing and bioinformatics are promising avenues to explore the functional interacting network adaptability of bacterial communities, and in turn, predict their capacity to maintain ecosystem homeostasis when facing rapid environmental changes."} +{"text": "Advances in drug therapy have dramatically extended the life of people living with HIV/AIDS (PLWHA). Empirical evidence shows that as the HIV disease progresses, quality of life deteriorates. PLWHA face physiological, physical, psychological and socio-cultural problems that are caused by these factors affect quality of life. The purpose of this study was to study the clinico-epidemiological profile and assess quality of life of PLWHA.Study involved cross sectional assessment of 754 PLWHA above 18 years of age and having treatment duration \u2265 6 months. Socio-demographic characteristics and clinical profile which included associated morbidities, WHO clinical staging and CD4 counts of the patients were studied. Quality of life was assessed with WHO QOL BREF instrument. Chisquare test, Z-test, Pearson\u2019s correlation coefficient, ANOVA with Bonferroni post-hoc test and Multiple Logistic Regression were used for analysis.Out of 754 study subjects, 61.01% were males, 67.24% were married and 20.56% were widowed, 71.75% patients belonged to lower class, 58.22% patients were symptomatic and 22.2% patients suffered from peripheral neuropathy. Scores in the independence domain were highest and those in the physical domain were the lowest. Inter-domain consistency was found to be good (p=0.001). Age \u2265 50 years , female sex , illiteracy , no spouse support and higher WHO clinical staging were found to be the major risk factors for poor quality of life.Though anti-retroviral therapy has prolonged life of PLWHA, their quality of life remains poor."} +{"text": "The problems Parkinson's disease (PD) patients encounter when admitted to a hospital, are known to be numerous and serious. These problems have been inventoried through a systematic review of literature on reasons for emergency and hospital admissions in PD patients, problems encountered during hospitalization, and possible solutions for the encountered problems using the Pubmed database. PD patients are hospitalized in frequencies ranging from 7 to 28% per year. PD/parkinsonism patients are approximately one and a half times more frequently and generally 2 to 14 days longer hospitalized than non-PD patients. Acute events occurring during hospitalization were mainly urinary infection, confusion, and pressure ulcers. Medication errors were also frequent adverse events. During and after surgery PD patients had an increased incidence of infections, confusion, falls, and decubitus, and 31% of patients was dissatisfied in the way their PD was managed. There are only two studies on medication continuation during surgery and one analyzing the effect of an early postoperative neurologic consultation, and numerous case reports, and opinionated views and reviews including other substitutes for dopaminergic medication intraoperatively. In conclusion, most studies were retrospective on small numbers of patients. The major clinical problems are injuries, infections, poor control of PD, and complications of PD treatment. There are many (un-researched) proposals for improvement. A substantial number of PD patients' admissions might be prevented. There should be guidelines concerning the hospitalized PD patients, with accent on early neurological consultation and team work between different specialities, and incorporating nonoral dopaminergic replacement therapy when necessary. \u00a9 2011 Movement Disorder Society Parkinson's disease (PD) is the second most common neurodegenerative disorder with a life-time risk of 2 percent in men and 1.3 percent in women.We recently surveyed the majority of movement disorder specialist neurologists in the Netherlands and found that no specific guidelines or protocols exist to guide caregivers and PD patients in the hospital environment (manuscript in preparation). Before such guidelines can be formulated, one needs to know the prevalence and spectrum of the problems PD patients may experience during their hospital stay. To this end, we systemically reviewed all the existing literature on the problems encountered by the hospitalized PD patients.We systematically reviewed the literature on reasons for emergency room (ER) and hospital admissions in patients with PD, problems encountered during hospitalization of this patient population, and possible solutions for the encountered problems, using the Pubmed database. Last research date was 17 June 2010.To identify articles, we included (combinations of) keywords: See Analysis of prevalence and reasons for ER visits and subsequent admission.Clinical problems during hospital stay.Peri- and postoperative problems.Suggestions for improvement of care for the hospitalized PD patient.We also searched the reference list of each relevant article for other applicable articles.In our search, there were no language limitations. We excluded articles concerning brain surgery.P = 0.05).14Patients with PD often need emergency treatment. There are four studies analyzing the reasons for ER admission,We found 12 studies on hospital admissions : 11 stud20PD/parkinsonism patients are hospitalized approximately one and a half times more frequently30Reasons for emergency and hospital admission can be divided in:Direct disease related morbidity: motor complications, psychiatric symptoms, autonomic dysfunction, sensory symptoms, sleep disorders, and side effects of anti-parkinsonian drugs.Indirect disease related morbidity: traumas and pneumonia.Non-PD related causes.As most studies vary greatly in selection of patients, exact relative proportions of these 3 groups cannot be assessed and 3. S21We found one prospective study on acute events occurring during hospitalization.4Another retrospective study shows that in 74% of 35 emergency hospital admissions of PD patients, their medication was stopped, omitted or prescribed inappropriately with 61% of this group suffering significant sequelae. Nonadherence to medication schedules was a large problem and in 11% of cases antidopaminergic medication (metaclopramide) was prescribed.31In a study analyzing inpatient falls, the use of anti-Parkinson's medication was an evident risk factor (OR 5.04).32Apart from the studies above, we found several opinionated views and reviews on problems during hospitalization of PD patients. These authors point to disease fluctuations, stress,39We found 15 retrospective studies on problems during and after surgery in patients with PD, with an emphasis on the postoperative period. Of these 15, two retrospective studies included a control group of non-PD patients.50The first study compared 234 PD patients with a control group of 40,979, undergoing elective bowel resection, cholecystectomy, or radical prostatectomy, during a 6-year period. PD patients had a significantly increased incidence of aspiration pneumonia, urinary-tract infection, bacterial infections, with odds ratios of 3.8, 2.0, 1.7, respectively. Odds ratios for postoperative delirium and hypotension in PD patients were 2.6 and 2.5, with lesser significance. PD patients had a mortality rate of 7.3%, compared with a 3.8% in the control group.25In the second study with a non-PD control group, 51 PD patients, treated on different surgical departments, were compared using matched-pair analysis. There were significantly more postoperative falls in the PD group (18% vs. 4%), and a higher although not significantly increased number of urinary tract infections (33% vs. 24%), pneumonia (10% vs. 4%), and also wound infection, urinary retention, respiratory insufficiency, and postoperative confusion. PD patients were hospitalized for more days and stayed on the intensive care unit longer.27Another retrospective study showed that 60% of 25 PD patients with no pre-existent mental status abnormalities suffered postoperative confusion, some with hallucinations. The onset of the delirium was often delayed, 70% after 36 hours. In this study, there was no relationship between delirium and type of anti-Parkinson medication or anaesthetic procedure.33In a retrospective study on pharmacological management during 51 surgical admissions of PD patients or patients with parkinsonian syndromes treated with PD medication, 71% had missed doses of their medication. Overall, antidopaminergic medication was prescribed in 41% and administrated in 22% although not allowed. 47% (69% for non-day-cases admissions) had complications: neuropsyciatric 41%, falls 8%, and worsening of motor symptoms 5%.41In the smallest study (n = 10), all patients had complications. This paper identified the same problems as mentioned above, and additionally found pressure sores as an important problem.42Next to the above studies, there are nine retrospective research articles on orthopaedic surgery and its complications. These studies and less patients were confused: 15 to 48%.29In a retrospective study, the postoperative period was analyzed in PD patients undergoing total knee arthroplasty receiving a preoperative or immediate postoperative neurologic consultation (n = 13) compared with patients receiving a delayed or no visit (n = 21). Only in the first group, there was a significant improvement in total Unified Parkinson's Disease Rating Scale with most improvement in activities of daily living but also an improvement of mood, mentation and behavior, and motor examination. In this group, there was also a shorter length of stay mobilization, recognition of unique physical limitations and medication combinations, physiotherapy, turning regimens, maintenance of volume status, antiparkinsonian therapy adjustments, analyzing urine for urinary tract infections, and deep venous thrombosis prophylaxis may prevent complications like pulmonary emboli, infections, deep vein thrombosis and decubitus.98There are few studies analyzing the problems a PD patient encounters during hospitalization, and there are even less studies analyzing possible solutions. Most studies are retrospective and have small numbers of patients. In some studies, PD patients were diagnosed according to clear diagnostic criteria ,82Overall PD patients are more frequentlyThere are more studies on complications in PD patients hospitalized for surgery, particularly in the postoperative period. (Aspiration) pneumonia, UTI, bacterial infections, postoperative falls, postoperative delirium/confusion proposals for improvement during hospitalization in PD patients. A substantial number of PD patients' admissions might be prevented. There should be guidelines concerning the hospitalized PD patients, with accent on early neurological consultation or consultation of another specialist like a geriatrician with a special interest in PD and team work between different specialities, and on sufficient training of all people involved in the treatment and recovery of this patient group. This protocol should include dopaminergic replacement therapy in case PD patients are not allowed or able to take their oral medication. Preferably this therapy should not be laborious and not invasive so that it is easily applicable."} +{"text": "The present study was designed to compare ulcer protective effect of proton pump inhibitors viz. omeprazole, rabeprazole and lansoprazole against dexamethasone plus pylorus ligation induced ulcer model. Dexamethasone (5 mg/kg) was used as an ulcerogen. Dexamethasone suspended in 1% CMC in water was given orally to all the rats 15 min after the pylorus ligation. Omeprazole (20 mg/kg), rabeprazole (20 mg/kg), and lansoprazole (20 mg/kg) were administered by oral route 30 min prior to ligation was used for ulcer protective studies, gastric secretion and mucosal studies. Effects of proton pump inhibitors were determined by the evaluation of various biochemical parameters such as ulcer index, free and total acidity, gastric pH, mucin, pepsin and total proteins. Oral administration of proton pump inhibitors showed significant reduction in gastric acid secretion and ulcer protective activity against dexamethasone plus pylorus ligation induced ulcer model. The % protection of omeprazole, rabeprazole and lansoprazole was 84.04, 89.36 and 79.78, respectively. Rabeprazole significantly inhibited the acid-pepsin secretion and increased the gastric mucin secretion. The observations made in the present study suggest that rabeprazole is the most effective gastric antisecretory and ulcer healing agent as compared to omeprazole and lansoprazole. Helicobacter pylori infection, reduced generation of nitric oxide and increased generation of free radicals[Acute gastric ulcers occur due to erosion in the mucosal membrane, generally in gastric and duodenum regions and occur as a result of alteration in the balance between mucosal damaging agents and mucosal defense mechanisms. Peptic ulcer is one of the most frequent disorders of the alimentary tract and in various countries its prevalence is estimated as 5-10% of the adult population[ radicals\u20135. Ulcer radicals. Frequen radicals. Cortico radicals, inhibit radicals leading +/K+ATPase pump. Omeprazole shows an ulcer healing effect by inhibiting neutrophil chemotaxis, superoxide production and release of active oxygen metabolites[Proton pump inhibitors (PPIs) inhibit release of hydrogen ion from parietal cells. It inhibits gastric acid secretion by blocking Htabolites leading Helicobacter pylori and exerts its antioxidant effect[While lansoprazole prevents gastric mucosal damage by gastric prostaglandin production, expression of cyclo-oxygenase (COX) isoforms and release of stable nitric oxide metabolites into gastric juice and blocks the oxygen derived free radical output from neutrophils activated by nt effect12.Rabeprazole causes perhaps the fastest acid suppression and so aid gastric mucin synthesis. This is necessary for the maintenance of mucosal integrity. Although these PPIs being similar in pharmacological actions they differ in clinical pharmacology. TherefoOmeprazole was obtained from Cipla Ltd, Goa, India. Rabeprazole, lansoprazole and dexamethasone were obtained from Cadila health care, Ahmedabad, India. The chemicals and solvents used were sodium hydroxide, Topfer\u2019s reagent, copper sulphate, phenolphthalein, sodium carbonate, phenol reagent, bovine albumin, sucrose, alcian blue, sodium acetate, ethanol, methanol, dil. HCl and chloroform. All were of analytical grade.ad. libitum. The study was conducted after obtaining institutional animal ethical committee clearance.Healthy Wistar rats of either sex weighing between 150-200 g were used. Animals were housed individually in polypropylene cages, maintained under standard conditions, the animals were fed with standard rat pellet diet, and water Dexamethasone (5 mg/kg) suspended in 1% w/v carboxy methyl cellulose (CMC) in water was given orally to all the rats 15 min after the pylorus ligation. Omeprazole (20 mg/kg), rabeprazole (20 mg/kg), and lansoprazole (20 mg/kg) were administered by oral route, 30 min prior to ligation was used for ulcer protective studies, gastric secretion and mucosal studies.Wistar rats of either sex were divided into four groups of 6 animals each. In this method rats were fasted in individual cages for 24 h. Care was taken to avoid coprophagy. Control vehicle, omeprazole (20 mg/kg), rabeprazole (20 mg/kg) and lansoprazole (20 mg/kg) were administered by oral route 30 min prior to ligation. Dexamethasone suspended in 1% w/v CMC was given orally to all the rats 15 min after pylorus ligation. Under ether anesthesia, the abdomen was opened and the pylorus was ligated. The abdThe PPIs significantly reduced the gastric volume, total and free acidity, and increased the pH of the gastric fluid, proving its antisecretory activity. Animals in the omeprazole, rabeprazole and lansoprazole groups showed decrease in volume of gastric juice by 41.17, 48.46 and 34.31 %, respectively, free acidity was found to be 51.13, 63.44 and 30.60 %, respectively and total acidity was found to be 47.65, 55.16 and 35.07 %, respectively. pH was found to increase by 148.87, 166.85 and 134.83 %, respectively. It is evident from the results that rabeprazole is more effective than omeprazole and lansoprazole .Percent protection in ulcer index offered by omeprazole, rabeprazole and lansoprazole was 83.92, 89.28, and 79.45, respectively . Rabepra+/K+ ATPase pump inhibition and a greater effect on intragastric pH as compared to omeprazole and lansoprazole. The present findings agree with earlier reports.In the present study gastric ulcer was induced by dexamethasone plus pylorus ligation model. Pylorus ligation induced ulcers are due to autodigestion of the gastric mucosa and break down of the gastric mucosal barrier. Reactive oxygen species are involved in the pathogenesis of pylorus ligation induced mucosal injury. Gastric+/K+ ATPase pump. Cytoprotective effect of omeprazole is due to increased expression of COX-2 protein and elevating the levels of PGE2. It also showed increased gastric pH and reduction in gastric acid secretion, which may be due to inhibition of gastric mucosa enzymes, carbonic anhydrase II (CA) and CA IV, which are located in abundance in the gastric parietal cells and in the secretory canaliculi walls. This inhibition potentiates the inhibitory effect on the proton pump[Omeprazole, rabeprazole and lansoprazole have shown increased gastric pH and decrease in the protein content of gastric juice. Gastric acid is an important factor for the genesis of ulceration of pylorus ligation ulcer in rats. Gastric acid secretion is influenced by many factors including anxietic effect in the CNS, vagal activity, cholinergic, histaminergic and gastrinergic transmissions. The antoton pump. Similaroton pump.Amount of gastric mucus secretion in gastric mucosa was found to be increased in rabeprazole treated group. This muThus, the ulcer healing effect of rabeprazole may be due to its effect on both offensive and defensive factors. Further work on other mucosal factors like nitric oxide, prostaglandins, cAMP etc would provide more insight into the activity of rabeprazole."} +{"text": "In BC, pediatric patients with spina bifida are followed by a multidisciplinary clinic at BC Children\u2019s Hospital. Upon graduation, patients transition into the adult healthcare system where they must coordinate their own care. The purpose of this study is to determine the functional and health outcome of graduates transitioning from the spina bifida clinic at BC Children\u2019s Hospital.Graduates of up to 10 years (1999-2008) from the pediatric spina bifida clinic were mailed a questionnaire. It consisted of 11 sections, including two standardized questionnaires on quality of life (QOL), the Medical Outcomes Study 36-item short-form (SF-36) and Spina Bifida-specific Health Related QOL (SBHRQOL).113 graduates were identified; 19 were lost to follow-up. 27 (29%) questionnaires were returned. 96% graduated from high school; 63% went on to post-secondary education. 30% had never been employed. 85% lived with parents. 48% had never been in a relationship. 81% were satisfied with their present bowel care; 38% were always clean and 15% had no bowel control. 85% were satisfied with their present bladder care; 22% were always dry and 11% had no bladder control. 19% voided independently and 78% self-catheterized. The wheelchair (58%) was most commonly used for community ambulation. 74% drove or utilized public transit. 93% were satisfied with life in general. The SF-36 physical function domain had the lowest average score (56/100). SBHRQOL mean score was 191. Overall, 89% were satisfied with their ambulation. 96% were satisfied with the care from the pediatric clinic; 52% were satisfied with their adult care. 96% of patients had a family physician; of these, 61% felt that their physician understood spina bifida.Health and functional outcomes may indicate the level of independence of adults living with spina bifida. Physical and financial dependence may limit these graduates from full independence. Most patients completed high school; fewer pursued higher education. Many patients demonstrated independence in the community by driving or using transit. Although largely satisfied with their bladder and bowel function, patients continued to have episodes of incontinence. Bladder function was mostly managed by self-catheterization.Overall, the majority of patients were satisfied with life in general, however, our results suggest that more physical support is required for adult graduates. Our results show that fewer adults were satisfied with adult care than in the pediatric clinic; this may result from a perception that their adult healthcare providers inadequately understood spina bifida."} +{"text": "Although the prevalence of cigarette smoking has declined in the United States, little documentation exists to ascertain which health care providers (HCPs) promote smoking cessation. We used data from the 2000, 2005, and 2010 Cancer Control Supplement of the National Health Interview Survey to examine changes in the number of adults who received smoking cessation advice from their HCP. The percentage of smokers who received cessation advice was 53.3% in 2000, 58.9% in 2005, and 50.7% in 2010. To affect noticeably declining rates, HCPs should increase their efforts to advise smokers to quit. Medscape, LLC is pleased to provide online continuing medical education (CME) for this journal article, allowing clinicians the opportunity to earn CME credit.This activity has been planned and implemented in accordance with the Essential Areas and policies of the Accreditation Council for Continuing Medical Education through the joint sponsorship of Medscape, LLC and Preventing Chronic Disease. Medscape, LLC is accredited by the ACCME to provide continuing medical education for physicians. AMA PRA Category 1 Credit(s)\u2122. Physicians should claim only the credit commensurate with the extent of their participation in the activity.Medscape, LLC designates this Journal-based CME activity for a maximum of 1 www.medscape.org/journal/pcd (4) view/print certificate.All other clinicians completing this activity will be issued a certificate of participation. To participate in this journal CME activity: (1) review the learning objectives and author disclosures; (2) study the education content; (3) take the post-test with a 70% minimum passing score and complete the evaluation at Release date: August 01, 2012; Expiration date: August 01, 2013Upon completion of this activity, participants will be able to:Describe changes in the number of adults who received smoking cessation advice from their HCPs, based on data from the 2000, 2005, and 2010 Cancer Control Supplement of the National Health Interview SurveyDescribe the association between respondents\u2019 reported desire to quit smoking and receipt of smoking cessation advice from their HCPsDescribe other factors associated with receipt of smoking cessation advice from HCPsCME EDITORPreventing Chronic Disease. Disclosure: Camille Martin has disclosed no relevant financial relationships.Camille Martin, Editor, CME AUTHORLaurie Barclay, MD. Freelance writer and reviewer, Medscape, LLC. Disclosure: Laurie Barclay, MD, has disclosed no relevant financial relationshipsAUTHORS AND CREDENTIALSDisclosures: Judy Kruger, PhD, MS; Lauren Shaw, MS; Jennifer Kahende, PhD; and Erica Frank, MD, MPH have disclosed no relevant financial relationships.Judy Kruger, PhD, MS, Epidemiology Branch, Office on Smoking and Health, Atlanta, Georgia; Lauren Shaw, MS, Jennifer Kahende, PhD, Centers for Disease Control and Prevention, Atlanta, Georgia; Erica Frank, MD, MPH, University of British Columbia, Vancouver, British Columbia, Canada.Tobacco use can lead to multiple serious health conditions , and thehttp://www.cdc.gov/nchs/nhis/methods.htm. The NHIS survey response rate was 72.1% in 2000, 69.0% in 2005, and 60.8% in 2010.We obtained data on respondents\u2019 demographic characteristics and smoking status from the entire NHIS sample for each year. The survey queried whether respondents had ever smoked 100 or more cigarettes and currently smoked every day or some days. Those responding yes to both questions were identified as current smokers. A random selection of NHIS respondents were asked to engage in a Cancer Control Supplement in 2000, 2005, and 2010. We limited these samples to current smokers who had seen an HCP in the past 12 months. Smokers were asked, \u201cIn the past 12 months, has a medical doctor or other health professional advised you to quit smoking or quit using other kinds of tobacco?\u201d Respondents\u2019 desire to quit was measured by asking, \u201cWould you like to completely quit smoking cigarettes?\u201dWe used 3 years of cross-sectional data from the annual National Health Interview Survey (NHIS), a continuing survey of approximately 40,000 households of civilian noninstitutionalized adults aged 18 years or older in the United States. Information about NHIS methods is available at P < .001) for linear trends was determined using orthogonal polynomial contrasts. Logistic regression reporting odds ratios (ORs) and 95% confidence intervals (CIs) were computed using 2010 data to determine characteristics associated with receiving advice to quit from an HCP.Analyses were conducted using SAS version 9.1 and SUDAAN version 9.0 to account for the complex sample design. Data were age-adjusted based on the 2000 US Census and weighted using NHIS methods . DescripP < .001). Among women, 53.6% received cessation advice in 2010, 62.8% in 2005, and 56.0% in 2000 .In 2000, 53.3% of smokers received cessation advice in the past year; in 2005, 58.9% received advice; and in 2010, 50.7% received advice . Among mIn 2010, women were more likely than men to receive advice from their HCP, and the likelihood of this advice increased with age . HispaniIn 2010, 67.7% of smokers wanted to quit. A positive correlation was found between respondents who wanted to quit smoking and those who received smoking cessation advice from their HCP. Among smokers who wanted to quit, 68.8% received cessation advice from their provider. Respondents who received advice to stop smoking from an HCP were more likely to want to quit smoking than those who did not receive such advice .In the United States, the number of patients reporting smoking cessation advice from HCPs initially increased from 2000 to 2005 then decreased from 2005 to 2010 to pre-2000 levels. Between 1974 and 1990, Malarcher et al found a positive trend in HCP advice to quit among both people with and without diabetes . ApproxiWe found that receiving cessation advice was strongly related to the desire to stop smoking: smokers advised by HCPs to quit were nearly twice as likely as those who did not receive such advice to want to stop smoking. Other researchers have shown a positive relationship between physician advice and patient action that encLimitations of our study include the use of self-reported data; however, NHIS uses standard questions that are well-accepted . Also, dWith only half of HCPs encouraging smokers to quit and declining rates of cessation advice overall, increased efforts are essential to motivate HCPs to provide cessation advice that ultimately will yield more quit attempts and higher cessation rates."} +{"text": "N = 95,677) was used to estimate prevalence of parent-reported mental health problems in children. Prevalence of mental disorders was 22.9% among children born prematurely, 28.7% among very-low-birth-weight (<1500\u2009g) children, and 18.9% among moderately low-birth-weight (1500\u20132499\u2009g) children, compared with 15.5% in the general child population. Compared to those born full term, children born prematurely had 61% higher adjusted odds of serious emotional/behavioral problems, 33% higher odds of depression, and 58% higher odds of anxiety. Children born prematurely had 2.3 times higher odds of autism/ASD, 2.9 times higher odds of development delay, and 2.7 times higher odds of intellectual disability than term children. Very-low-birth-weight children had 3.2 times higher odds of autism/ASD, 1.7 times higher odds of ADD/ADHD, 5.4 times higher odds of development delay, and 4.4 times higher odds of intellectual disability than normal-birth-weight children. Social factors were significant predictors of mental disorders in both premature/low-birth-weight and term/normal-birth-weight children. Neurodevelopmental conditions accounted for the relationship between prematurity and depression/anxiety/conduct problems. Prematurity and low birthweight are significant risk factors for mental health problems among children.We examined the effects of prematurity (<37 weeks of gestation) and low birthweight (<2500\u2009g) on mental health outcomes among US children aged 2\u201317 years. The 2011-2012 National Survey of Children's Health ( Perinatal factors such as preterm birth and low birthweight (LBW) have significant impacts on the health and well-being of children and adolescents, which have been shown to persist well into adulthood and, indeed, throughout the life course \u20134. PremaNearly a quarter of all infants born with very low birthweight <1500 grams) die during the first year of life 00 grams . DespiteMost of the studies that have examined mental health problems among children born preterm or with LBW are small case-control studies, the findings of which may not be generalizable to the population at large or the US population , 7\u201323. MThe 2011-2012 National Survey of Children's Health (NSCH), which is a large nationally representative sample of US children aged 0\u201317 years, allows us to explore the association between perinatal conditions and mental health outcomes in both childhood and adolescence, while controlling for current household socioeconomic status (SES), family environments, and other demographic variables. In this study, we examine (1) the prevalence of overall and specific mental health outcomes among US children by prematurity and LBW before and after controlling for household SES and sociodemographic characteristics, (2) whether mental health outcomes associated with prematurity and LBW vary by child's sex and age, (3) whether social factors are significant predictors of mental health problems in both preterm/LBW and general child populations, and (4) the extent to which neurodevelopmental conditions such as autism/ASD, ADHD, and developmental delay might account for the relationship between perinatal conditions and common emotional/behavioral disorders of depression, anxiety, and conduct problems.Data for the present study came from the 2011-2012 NSCH , 23. TheThe 2011-2012 NSCH was a cross-sectional telephone survey conducted between February 2011 and June 2012 , 25. TheThe sample size for the present analysis was 85,535 children aged 2\u201317 years. Each of the 10 mental health outcomes studied is defined in Using a life-course/social-determinants-of-health framework and past research as a guide, we considered, in addition to prematurity and birthweight, the following covariates of childhood mental disorders: child's age, sex, race/ethnicity, household composition, metropolitan/nonmetropolitan residence, household/parental education level, and household poverty status measured as a ratio of family income to the poverty threshold , 29\u201335. Income was imputed for 9% of the observations by using a multiple imputation technique , 27. Les\u03c72 statistic was used to test the overall association between covariates and mental disorders. The t-statistic was used to test the difference in prevalence between any two groups. Logistic regression was used to examine the association between perinatal factors and mental health problems, after adjusting for the above covariates. To account for the complex sample design of the NSCH, SUDAAN software was used to conduct all statistical analyses [The analyses .Descriptive characteristics of the study sample are shown in The prevalence of mental health problems was higher in premature/LBW children than in term/normal-birth-weight children . The preTables Adjustment for socioeconomic and demographic covariate did not attenuate the effects of prematurity and LBW on specific mental disorders. Compared to term children, children born prematurely had 61% higher adjusted odds of serious emotional/behavioral problems, 33% higher odds of depression, and 58% higher odds of anxiety . ChildreSES, race/ethnicity, and household structure were significant predictors of mental health problems in the general population as well as among premature/LBW and term/normal-birth-weight children. Children living in poverty had 2.0\u20133.6 times higher odds of depression, anxiety, and conduct disorders than their most-affluent counterparts. Children in stepfamilies and single-mother households had 1.7\u20133.4 times higher odds of depression, anxiety, and conduct disorders than children from two-parent biological families. Black and Hispanic children had 46\u201350% lower adjusted odds of emotional/behavioral problems than non-Hispanic white children . AlthougSocial inequalities in mental health problems were smaller among premature/LBW children than among term/normal-birth-weight children (data not shown). For example, among premature/LBW children, 27.1% of children in stepfamilies and 20.2% of children in single-mother households had mental health problems, compared with 17.2% of children in two-parent biological families. Among term/normal-birth-weight children, the respective prevalence rates were 21.8%, 20.2%, and 11.3%. Among premature/LBW children, 25.0% of poor children had mental health problems compared with 17.3% of affluent children , whereas among term/normal-birth-weight children, 19.2% of poor children had mental health problems compared with 11.9% of affluent children .We estimated regression models of both the overall emotional/behavioral problem variable and specific conditions of depression, anxiety, and conduct disorder that included sociodemographic characteristics and prematurity, along with comorbid conditions of ASD, ADD/ADHD, development delay, learning disability, and intellectual disability. The increased risks of mental health problems associated with prematurity were accounted for by these neurodevelopmental conditions, whose effects on emotional/behavioral problems were quite marked (data not shown for brevity). Children diagnosed with autism, ADHD, developmental delay, and learning disability, respectively, had 4.4, 8.4, 3.0, and 2.4 times higher adjusted odds of emotional/behavioral problems than children without such neurodevelopmental conditions. Children diagnosed with autism had 2.1, 4.7, and 3.3 times higher adjusted odds of depression, anxiety, and conduct disorders than children without autism, respectively. Children with ADD/ADHD had 5.8, 4.9, and 14.0 times higher adjusted odds of depression, anxiety, and conduct disorders than children without ADD/ADHD, respectively. In each of the comorbidity models, SES, family structure, and race/ethnicity remained strong risk factors for mental health problems.The prevalence of mental health problems increased with child's age. Approximately 19.6% of adolescents aged 12\u201317 had mental health problems, compared with 15.9% of children aged 6\u201311 and 6.7% of children aged 3\u20135 years. Given that the prevalence of overall mental health problems and of depression, anxiety, ADHD, learning disability, and intellectual disability were mostly concentrated among older children and adolescents, we explored age interactions by estimating prematurity and LBW models stratified by child's age. However, the age interactions were not statistically significant, and the effects of the prematurity and LBW on mental health problems were similar for younger and older children and adolescents (data not shown).Although the rates of preterm birth and LBW in the USA have declined slightly in recent years, the current rates remain fairly high and represent a 10\u201316% increase compared to the rates in 1990 , 38. GroTo our knowledge, ours is the first large-scale population-based US study to examine the prevalence of several mental health problems among preterm and LBW children using a nationally representative sample of preschool and school-aged children and adolescents. The analysis of the large NSCH sample allowed us to study in detail age- and sex-specific variations in the prevalence of some of the rarer mental health conditions such as depression, ASD, and intellectual disability among premature and LBW children. The overall prevalence of mental health problems among premature, VLBW, and MLBW children in our study generally varied from 20% to 30%, which is consistent with the prevalence estimates from other smaller-scale studies using diagnostic evaluations despite their use of extremely low-birth-weight and gestational-age categories [While our study adds to the current US and international research on mental disorders associated with perinatal conditions, additional research is needed to explain the substantial effects of social factors on mental health outcomes among both premature/LBW and term/normal-birth-weight children. Consideration of additional factors such as adverse neighborhood social conditions, built environments, parental health status, parental stress, family conflict, family cohesiveness, social support, child's exposure to environmental tobacco smoke, alcohol and substance use, excess television viewing or recreational computer use, and physical inactivity may further explain the role of social factors in mental health problems , 31\u201335.Mental health effects of prematurity and LBW reported here are generally consistent with previous research that shows higher risks of mental disorders in children associated with these perinatal outcomes , 7\u201323. CIn our study, the association between prematurity/LBW and mental health problems was largely explained by the consideration of neurodevelopmental conditions of ASD, ADHD, and developmental delay. This appears to provide evidence in support of biological pathways through which prematurity and LBW might lead to increased risks of mental health problems , 2. BraiA major strength of our study includes estimating the effects of prematurity and LBW on a variety of mental health conditions across the entire age range of childhood and adolescence. Another important contribution of this study is the estimation of overall prevalence of mental disorders in the preterm/LBW and the general child populations. The other strengths of our study include the large sample size, the generalizability of our findings, and examination of whether the effects of prematurity/LBW and socioeconomic factors vary by sex, age, and mental health outcome.Our study has limitations. Children's mental health conditions in the NSCH were based on parental reports and may not accurately reflect the true prevalence, particularly among older adolescents , 33. HowIn conclusion, the evidence presented here suggests that premature birth and LBW are significant risk factors for mental health problems among children and adolescents. The most prevalent disorders among premature/LBW children are ADHD, learning disability, developmental delay, and anxiety. Increased mental health surveillance and screening are recommended for children born prematurely and/or with LBW, providing the opportunity for early diagnosis and intervention . Given t"} +{"text": "Rapid and accurate detection of MRSA carriage is a key element for therapy and for implementation of measures to prevent onward transmission. Nose is the anatomical site universally recommended for screening. However, other sites are also recommended, especially in countries with low MRSA incidence. Due to the high price of rapid PCR testing, it is important to know the value of testing each additional site.To evaluate the value of each anatomical site for the screening of MRSA by culture and by a rapid PCR test.Screening samples included at least swabs of nose, throat, and groin. If applicable, others samples included swabs of wounds, catheterized urines, sputum, or others. Samples for culture were inoculated into an enrichment broth, which were plated after incubation onto chromogenic MRSA agar. Rapid PCR test were performed with GeneXpert MRSA.12456 MRSA screening were performed by culture, among which 3137 (25.2%) had at least one MRSA-positive sample. The cumulative percentages of MRSA detection by culture increased from 48.1% for nose only, to 78.9 by adding groin, to 95.7 % by adding throat, and to 100% by adding other sites. These values were similar if the analysis was performed according to major MRSA genotypes, except a higher percentage of positive groin samples for the ST228-SCCmec-I clone.2876 MRSA screening were performed by rapid PCR test, among which 312 (10.8%) had at least one positive sample. The cumulative percentages of MRSA detection increased from 61.9% for nose only, to 92.3 by adding groin, to 99.0 % by adding throat, and to 100% by adding other sites.Neither by culture nor by rapid PCR test is nose sampling sufficient for MRSA detection. Additional anatomical sites should include at least swabs from groin and throat.None declared."} +{"text": "Our paper is a study about metabolism syndrome (MS) incidence situations of different nationalities, including Uighur, Kazak and Han nationality in Xinjiang by means of a cross-sectional survey and compare differences and adaptabilities of applications of the diagnostic criteria for MS recommended by Adult Treatment Protocol III of National Cholesterol Education Program of America (ATP III), International Diabetes Federation (IDF) and Chinese Diabetes Society (CDS) in three groups of populations. Conclusion tell us, for Uighur population and Kazak population, IDF criterion and ATPIII criterion had a better consistence, and CDS criterion was worst. For Han population, CDS criterion and IDF criterion had a better consistence, and ATPIII criterion was worst. For the screening of MS incidence rate of Uighur and Kazak adult populations in Xinjiang region, ATPIII criterion was optimal, while CDS criterion was optimal for Han population. However, as for screening of clustering of multiple risk factors of MS, IDF criterion was better than other criteria for the three nationalities. Metabolism syndrome (MS) mainly manifests the clustering of hypertension (HP), obesity, lipid abnormality, hyperglycemia, and insulin resistance (IR) in individuals and rapid increase of its incidence rate has become a global public health focus. However, the adaptabilities of different diagnostic criteria in different populations are always debatable . AccordiAt present, there are at least 8 diagnostic criteria of MS in the world . As variThis study respectively adopted the diagnostic criteria of MS recommended by International Diabetes Federation (IDF), Adult Treatment Protocol III National Cholesterol Education Program of America (ATP III), and Chinese Diabetes Society (CDS) to analyze MS of Uighur, Kazak and Han populations in Xinjiang and incidence situations of various components and compare the consistence of 3 criteria diagnosing MS of 3 groups of populations in order to further understand the epidemiological situations of MS of Uighur, Kazak and Han populations in Xinjiang, investigate screening consistence and population suitability of currently used 3 diagnostic criteria and provide a basis for further conducting targeted health education and clinical intervention and provide the necessary based evidence for subsequently revising or preparing diagnostic criteria of MS for different nationalities. A cluster-sampling survey was carried out for Uighur, Kazak, and Han residents from 12 units in Urumqi city, Xinjiang, a multistage-cluster sampling survey was carried out for in Uighur, Kazak and Han residents in Aletai city and Kashgar city and their surrounding countries and towns. There were a total of 6928 persons aged 30 to 80 years old. Although 7140 persons should have been surveyed, 6928 persons were investigated in fact. The response rate was 97.03%. Among them, there were 2053 Uighur persons , 2219 Kazak persons and 2656 Han persons . This study was conducted in accordance with the declaration of Helsinki. This study was conducted with approval from the Ethics Committee of the First Affiliated Hospital of Xinjiang Medical University. Written informed consent was obtained from all participants.Demographic indicators and health questionnaire included age, gender, diabetes mellitus history, hypertension history, and so forth. The questions were asked by professionally trained investigators. According to the methods, blood pressure, height, body weight and waist circumference (WC) were measured, and body mass index (BMI) was calculated. Laboratory test indicators included fasting blood glucose (FPG), total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and blood glucose at 2\u2009h of OGTT test (PPG). 2); (2) hyperglycaemia: FPG \u22656.1\u2009mmol/L and PPG \u22657.8\u2009mmol/L, and (or) the cases with diagnosed diabetes mellitus receiving treatment; (3) hypertension: SBP/DBP \u2265140/90\u2009mmHg, and (or) the cases with diagnosed hypertension receiving treatment; (4) lipids disorder: TG \u22651.7\u2009mmol/L, and (or) HDL-C <0.9\u2009mmol/L or <1.0\u2009mmol/L . ATP III reversion criterion compliesMeasurement data were expressed as For Uighur population, central obesity ratios of diagnosed MS cases according to ATP III, IDF, and CDS criteria were, respectively, 91.43%, 100%, and 91.58%, the hypertension ratios were, respectively, 40.95%, 50.06%, and 59.75%, high TG albumosemia ratios were respectively 86.67%, 81.58%, and 85.63%, low HDL-C albumosemia ratios were, respectively, 72.79%, 62.67% and 50.51%, and the ratios of cases with blood glucose increase were respectively 62.72%, 55.01%, and 72.69%. For cases with MS diagnosed by 3 criteria, the ratios of cases with multiple (\u22653 factors) risk factors clustering were respectively 98.64%, 97.9% and 92.81%. For Kazak population, central obesity ratios of diagnosed MS cases according to ATP III, IDF and CDS criteria were respectively 98.83%, 100% and 92.57%, hypertension ratios were respectively 93.79%, 90.94% and 91.34%, high TG albumosemia ratios were respectively 29.32%, 28.30% and 33.66%, low HDL-C albumosemia ratios were respectively 50.68%, 56.79% and 32.67%, and the ratios of cases with blood glucose increase were respectively 46.80%, 45.66% and 69.80%. For cases with MS diagnosed by 3 criteria, the ratios of cases with multiple (\u22653 factors) risk factors clustering were respectively 100.00%, 96.23% and 91.34%. For Han population, central obesity ratios of diagnosed MS cases according to ATP III, IDF and CDS criteria were respectively nationality 81.20%, 100% and 72.77%, the hypertension ratios were respectively 66.30%, 62.86% and 36.15%, high TG albumosemia ratios were respectively 67.41%, 61.85% and 76.06%, low HDL-C albumosemia ratios were respectively 52.79%, 50.25% and 41.78%, the ratios of cases with blood glucose increase were respectively 78.13%, 74.79% and 88.73%. In addition, the ratios of cases with multiple (\u22653 factors) risk factors clustering were respectively 100%, 98.49% and 89.91% . For Uighur population, incidence rates (standardized incidence rates) of cases with MS respectively diagnosed according to ATP III, IDF and CDS criteria were respectively 35.80% (29.64%), 39.41% (35.88%) and 23.72% (19.17%). The detection rate for IDF criterion was highest, and detection rate of MS for CDS criterion was lowest. For Kazak population, incidence rates (Standardized incidence rate) of cases with MS respectively diagnosed according to ATP III, IDF and CDS criteria were respectively 23.21% (21.29%), 23.88% (21.96%) and 18.21% (16.65%). The detection rate of MS for IDF criterion was highest, and the detection rate of MS for CDS criterion was lowest. For Han population, incidence rates (standardized incidence rate) of cases with MS respectively diagnosed according to ATP III, IDF and CDS criteria were respectively 27.03% (27.18%), 22.40% (20.39%) and 16.04% (16.02%). The detection rate of MS for ATP III criterion was highest, and the detection rate for MS for CDS criterion was lowest. See For Uighur population, diagnosis consistence rate, Youden's index and Kappa value between ATPIII criterion and IDF criterion were highest . For Kazak population, diagnosis consistence rate, Youden's index and Kappa value between ATP III criterion and IDF criterion were highest . For Han population, diagnosis consistence rate, Youden's index and Kappa value between CDS criterion and IDF criterion were highest . MS is the clustering status of a group of risk factors closely related to cardiovascular disease, and obesity or overweight, blood glucose increase, lipids disorder and HP are its main components. Its incidence rate rapidly increases in recent 20 years, and it has become a hot issue of common concern at home and abroad in recent years , 10. AlsThe study respectively used three common diagnostic criteria of MS, namely ATP III, IDF and CDS to carry out screening for the same population among Uighur, Kazak and Han populations. As a result, it was found that for Uighur nationality and Han nationality, MS incidence rates (standardized incidence rate) for ATP III criterion were highest, respectively 35.80% (29.64%) and 27.03% (27.18%), and both MS detection rates for CDS criterion were lowest; For Kazak population, the detection rate for IDF criterion was highest 23.88% (21.96%), and MS detection rate of CDS criterion was lowest. As for single-risk factor, detection rates for three criteria had great differences, which was related to different emphases of various criteria; For screening of MS risk factor clustering, ATP III criterion was most sensitive for Uighur, Kazak, and Han populations , and the detection rate for CDS criterion was lowest , indicating that as MS-related studies and prevent and treatment were carried out for Uighur, Kazak, and Han residents in Xinjiang region, the detection rate for ATP III criterion was highest for Uighur nationality and Han nationality, and the detection rate for IDF criterion was highest for Kazak nationality. However, for screening of risk-factor clustering, ATP III criterion was better than the other criteria for the three populations. Comparisons of consistence of MS incidence rate of Uighur, Kazak, and Han populations diagnosed by the three criteria showed that for Uighur nationality and Kazak nationality, consistence rate, Youden's index and Kappa value between ATP III criterion and IDF criterion were highest, indicating that for Uighur and Kazak populations, ATP III criterion and IDF criterion had a better consistence, and the consistence rate between CDS criterion and the other two criteria (ATP III and IDF) wasn't high. For Han population, consistence rate, Kappa value, and Youden's index between CDS criterion and IDF criterion were highest, while consistence rate, Kappa value, and Youden's index between ATP III and IDF criterion were lowest. It is suggested that ATP III criterion and IDF criterion are relatively more suitable for Uighur and Kazak populations, rather than Han population. For Han population in Xinjiang region, CDS criterion adaptability was best, IDF criterion is second, and ATP III is the most unsuitable. According to the analysis of this study, it is found that MS definition itself has some defects. For the judgment and treatment of risk factors of high-risk population, it is necessary to select the most suitable criterion for this population on the base of comprehensive consideration of existent generally-accepted diagnostic criteria and treatment principle. For Uighur, Kazak, and Han populations in Xinjiang region, diagnostic criteria of MS shall be different due to their different genetic factors and life styles and differences for physical characteristics, and body metabolism. The study suggests that ATP III criterion is preferred for screening of MS incidence rate of adult Uighur and Kazak populations, while CDS criterion ispreferred for Han population. For screening of clustering of MS multiple-risk factors, IDF criterion is better than the other criteria for the three nationalities."} +{"text": "To examine the remission rates and functional outcomes in an inception cohort of patients with juvenile idiopathic arthritis (JIA).The Research in Arthritis in Canadian Children, emphasizing Outcomes (ReACCh-Out) cohort is a 16-centre inception cohort of patients with JIA enrolled within 1 year of diagnosis. All patients who completed 5 six-monthly study visits from baseline to 24 months were included in this analysis. Disease activity and functional measures were collected at each visit. Criteria for disease remission status in this study were defined by Wallace et al (2006) modified by omission of ESR or CRP due to incomplete data. Inactive disease (ID) was defined as no active joints, physician global assessment 0, and no active extra-articular disease; clinical remission on medications (CRM) is ID for \u2265 6 months on medications; and clinical remission (CR) is ID for \u2265 12 months off medications. Health status was measured using the Juvenile Arthritis Quality of Life Questionnaire (JAQQ), and functional status using the Child Health Assessment Questionnaire (CHAQ).Data for 347 of 1574 patients enrolled in the ReACCh-Out cohort was available for analysis. Median age of disease onset was 7.5 yr , with 35% oligoarticular, 22% polyarticular RF negative, 13% enthesitis related arthritis, 8% systemic, 8% undifferentiated, and 7% for each polyarticular RF positive and psoriatic subtypes. The percentage of patients with ID was 33% at 6 months, 39% at 12 months and 49% at 24 months; CRM increased from 4% at 6 months to 18% at 12 months and 26% at 24 months, while CR at 24 months was 7%. Differences in remission rates were evident amongst the JIA subtypes by 12 months, with the highest remission rates in oligoarthritis and lowest in the RF positive polyarthritis (CRM of 29% and 4% respectively). Even when ID was not reached, a decrease in active joint count was noted in all JIA subtypes. CHAQ and JAQQ scores improved in all patients as early as 6 months. Differences were also evident amongst the JIA subtypes with the best 24 month median scores in oligoarthritis patients compared with the worse scores in RF+ polyarthritis patients .While active joint counts and functional outcomes improved within the first 24 months, disease remission rates differed amongst JIA subtypes, and CRs are rare. The remission rates derived from our inception cohort of JIA patients will assist in family counseling, pinpoint subgroups requiring aggressive therapy and inform the design of clinical trials.Shirley M.L. Tse: None; Lori B. Tucker: None; Gaelle Ch\u00e9deville: None; Janet E. Ellsworth: None; Jaime Guzman: None; Kim Morishita: None; Rosie Scuccimarri: None; Natalie J. Shiff: None; Ciaran M. Duffy: None; Rae S.M. Yeung: None; Kiem G. Oen: None."} +{"text": "In 2006, the Norwegian Medicines Agency mandated a switch from desloratadine, ebastine, or fexofenadine to cetirizine or loratadine in patients with allergic rhinitis (AR) or chronic urticaria (CU). In an online survey, patients whose medication was switched assessed the impact on efficacy, fatigue, and work productivity/attendance.Allergy patients in Norway completed a 25-item online survey. Patients aged \u2265 18 years with AR or CU who were switched to cetirizine or loratadine from desloratadine, ebastine, or fexofenadine were included. Participants rated post-switch efficacy, fatigue, and effect on work productivity/attendance compared with their pre-switch medication. Patients also reported post-switch change in number of doctor visits required, total treatment cost, and whether they had switched or wanted to switch back to their previous medications.Of 1920 patients invited, 493 responded and 409 of these were eligible. Previous antihistamines were desloratadine (78.4% of respondents), ebastine (16.0%), and fexofenadine (5.6%). Post-switch, 64.7% received cetirizine and 35.3% loratadine. Compared with previous therapy, cetirizine and loratadine were rated less effective by 46.3% of respondents; 28.7% reported increased fatigue; and 31.6% reported decreased work productivity with the generic agents. At the time of the survey, 26% of respondents had switched back to their previous medication.This is the first survey to assess the impact on patient-reported outcomes of a mandated switch from prescription to generic antihistamines in Norway. The findings suggest that patient response to different antihistamines will vary and that treatment decisions should be individualized for optimal results. Allergic rhinitis (AR) and chronic urticaria (CU) are common diseases that disturb sleep and reduce work/school productivity ,2. TreatAlthough data on comparative efficacy of second-generation antihistamines are limited, clinical studies demonstrate that patients with AR or CU who fail to respond to one antihistamine may benefit from a switch to another -6. In 20An online survey conducted in 2007 in Norwegian general practice settings evaluated patient experiences regarding efficacy, fatigue, and impact on work productivity and attendance after a mandatory switch from desloratadine, ebastine, or fexofenadine to cetirizine or loratadine.Between January and April 2007, general practice centers across Norway each invited up to 15 patients to participate in an online survey. Patients were identified through a data software program run on the physicians' computers. If the practice had more than 15 eligible patients, the total number was randomly reduced to a maximum of 15.These patients were sent a letter, signed by their physician, inviting them to answer an Internet-based questionnaire. The letter contained a unique username and password that permitted the patients to answer the questionnaire only once. Internet service was provided by Questback AS , an independent IT services group.Participants aged 18 to 65 years treated with desloratadine, ebastine, or fexofenadine, and switched to cetirizine or loratadine after May 1, 2006, completed the 25-question survey on demographics, antihistamine therapy, physician visits, and treatment cost. Anonymity was maintained by Questback AS using a method approved by the Norwegian Data Inspectorate.Participants rated post-switch efficacy, fatigue, and effect on work productivity and attendance compared with their pre-switch medication using the following descriptors: \"much less,\" \"slightly less,\" \"similar,\" \"slightly more,\" or \"much more.\" Instances of no response were included in \"similar.\" Patients also reported post-switch change in number of doctor visits required , total treatment cost , and whether they had switched back or wanted to switch back to their previous medications.Descriptive analyses were performed on main findings, and responses by patients are given as proportion of patients (%) in Table A total of 343 physicians invited 1920 patients to participate. Of 493 patients (25.7%) responding to the invitation, 421 were eligible . Twelve patients who failed to specify pre-switch or post-switch antihistamine were excluded. The number of participants included in the final assessment totaled 409 and skin allergy (6.9%); other allergies comprised the remaining 14.3%. Most patients (78.4%) were taking desloratadine prior to the mandatory switch, followed by ebastine (16.0%) and fexofenadine (5.6%); post-switch, 64.7% of patients received cetirizine and 35.3% loratadine.Respondents (46.3%) rated cetirizine or loratadine as less efficacious than desloratadine, ebastine, or fexofenadine; 21.1% of respondents reported much less efficacy than with their previous treatment; and 25.2% reported slightly less efficacy (Figure In reporting impact on work productivity, 31.6% of respondents reported decreased work capacity; 63.1% said post-switch work productivity was similar to that of previous treatment, while 3.3% reported greater work productivity after switch. Post-switch, 6.0% reported reduced work attendance, and 2.0% stated that work attendance had increased.Respondents reported increased contact with their physician post-switch compared with pre-switch: 13% visited their physician more often, compared with 4% who reported fewer visits. Total costs post-switch increased for 16% of respondents and decreased for 10%. Due to limited data, the actual number of consultations and total costs were not possible to measure.Subgroup analyses stratified by diagnosis, pre-switch antihistamine, or post-switch antihistamine found no significant difference in ratings for efficacy, fatigue, or work productivity and attendance irrespective of type of allergy. This confirmed that the above-mentioned factors had no impact on the outcomes assessed.At the time of the survey, 26% of all participants had already switched back to their pre-switch antihistamine, and 25% reported dissatisfaction with cetirizine or loratadine and wanted to switch back to their original agent; 38% remained on their post-switch agent (Figure This online survey provided the first patient assessment of the impact of a mandatory switch from one antihistamine to another. Although the Norwegian Health Agency claimed that all second-generation antihistamines were equally efficacious and safe , 46.3% oPatients with AR and CU report varying degrees of symptom relief with different second-generation antihistamines, raising the issue of whether a mandated switch in treatment is ethically acceptable in patients well controlled by or satisfied with their treatment. Clinical management guidelines for urticaria recommend changing to another second-generation antihistamine in patients whose symptoms do not respond to first-choice treatment at standard or higher-than-indicated doses after a defined period .Moreover, clinical studies and patient surveys indicate that switching patients dissatisfied with their current treatment to another second-generation antihistamine may provide symptom relief. In a post hoc analysis of data from 4 post-marketing studies in patients with AR or CU who had failed previous therapy with cetirizine, fexofenadine, or loratadine, 90.3% of patients rated efficacy with desloratadine as excellent or good . Those pThe Norwegian Health Agency conducted no patient-impact assessment or health-economic analysis prior to mandating use of generic antihistamines to maintain governmental reimbursement. Instead, it based its decision solely on the cost of the 6 antihistamines. Post-switch, respondents reported a trend toward more consultations with their physicians, increased total costs for medication, and decreased work productivity and attendance, suggesting that the mandate may not be as cost-effective as assumed.Some limitations of this survey should be noted. There was no control group; responses were sought only from patients for whom a switch from desloratadine, ebastine, or fexofenadine to loratadine or cetirizine was mandated. In addition, differences in efficacy and tolerability among agents can only be determined through head-to-head, controlled clinical trials. The results of this survey cannot be extrapolated to other groups of allergy patients, and any drug comparisons should be made with great caution.A mandatory switch to the generic second-generation antihistamines cetirizine or loratadine to continue reimbursement in patients well controlled on desloratadine, ebastine, or fexofenadine decreased symptom control and work productivity and attendance. Taken together, the results from this survey and from clinical trials and other surveys indicate that treatment decisions should be made only after a thorough patient evaluation and then individualized for each patient. Further, periodic follow-up should be made to assess patient response post-switch.Medical writing and editorial assistance was provided by Carol Sibley and Patricia C. Abramo of AdelphiEden Health Communications, New York, New York. This assistance was funded by Merck, Sharpe and Dohme & Co. and MSD Norway AS.HC, TO and EH conceived the survey and participated in its design and coordination; they also participated in the preparation of the manuscript. FT participated in the design and coordination and had patients who answered the survey. RM performed the statistical analysis and participated in the preparation of the manuscript. All authors read and approved the final manuscript."} +{"text": "Primary care plays a key role in the prevention and management of cardiovascular disease (CVD). We examined primary care practice adherence to recommended care guidelines associated with the prevention and management of CVD for high risk patients.We conducted a secondary analysis of cross-sectional baseline data collected from 84 primary care practices participating in a large quality improvement initiative in Eastern Ontario from 2008 to 2010. We collected medical chart data from 4,931 patients who either had, or were at high risk of developing CVD to study adherence rates to recommended guidelines for CVD care and to examine the proportion of patients at target for clinical markers such as blood pressure, lipid levels and hemoglobin A1c.Adherence to preventive care recommendations was poor. Less than 10% of high risk patients received a waistline measurement, half of the smokers received cessation advice, and 7.7% were referred to a smoking cessation program. Gaps in care exist for diabetes and kidney disease as 54.9% of patients with diabetes received recommended hemoglobin-A1c screenings, and only 55.8% received an albumin excretion test. Adherence rates to recommended guidelines for coronary artery disease, hypertension, and dyslipidemia were high (>75%); however <50% of patients were at target for blood pressure or LDL-cholesterol levels (37.1% and 49.7% respectively), and only 59.3% of patients with diabetes were at target for hemoglobin-A1c.There remain significant opportunities for primary care providers to engage high risk patients in prevention activities such as weight management and smoking cessation. Despite high adherence rates for hypertension, dyslipidemia, and coronary artery disease, a significant proportion of patients failed to meet treatment targets, highlighting the complexity of caring for people with multiple chronic conditions.NCT00574808 Cardiovascular disease (CVD) is the leading cause of death and disability in Canada,2, with Primary care providers are well placed to play a central role in preventing and managing CVD and other chronic diseases, as 95% of Canadian adults with chronic conditions in Canada report having a regular family physician. The freAs part of a large quality improvement initiative based in 84 primary care practices in Eastern Ontario, Canada, we studied practice-level adherence to recommended guidelines, in nine areas of care including coronary artery disease, peripheral vascular disease, stroke/transient ischemic attack, chronic kidney disease, diabetes, dyslipidemia, hypertension, smoking cessation care, and weight management. To the best of our knowledge, this is the most comprehensive evaluation of CVD care to ever be conducted in primary care practices in Canada.http://www.idocc.ca)) of these high risk patients, while few were referred for dietary advice . The highest level of adherence for waist circumference measurement and referral for dietary advice was seen for patients with diabetes (14.3% [9.4-19.2%] and 25% [20.1-29.9%] respectively), however, levels were still quite low. Similarly, less than half of the smokers had documented evidence of receiving smoking cessation advice , 7.7% (95% CI [5.1-10.6%]) were referred to a smoking cessation program, and less than a quarter were recommended or prescribed any pharmacotherapy to assist with quitting.Less than half of all high risk patients who had a lipid profile or blood pressure measure were within the recommended target range , we did not explore the presence of any trends in quality over time, because trends would have likely been confounded with observed differences among the groups of practices allocated to the different steps in the stepped wedge design. Lastly,There remain significant opportunities for primary care providers to engage high risk CVD patients in prevention activities such as weight management and smoking cessation. In addition, despite high adherence rates for hypertension, dyslipidemia, and coronary artery disease, a significant proportion of patients failed to meet treatment targets highlighting the complexity of caring for people with multiple chronic conditions.CVD: Cardiovascular Disease; FBG: Fasting Blood Glucose; HbA1c: Hemoglobin A1c; ICES: Institute for Clinical Evaluative Sciences; IDOCC: Improved Delivery of Cardiovascular Care; LDL: Low Density Lipoprotein; LHIN: Local Health Integration Network.The authors have no competing interests to declare.CL and WH originally conceived and designed the study protocol. CDA and GR also contributed to the conception of this study. JS, MT and GW contributed to the analysis plan. All authors have contributed substantially to the ongoing project implementation and have participated in the preparation and review of this article. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2261/12/74/prepub"} +{"text": "There is limited data about the epidemiology of SSIs in developing countries.To investigate incidence rates of SSIs, risk factors, etiological agents and antimicrobial resistance rates of pathogens in a developing country.Prospective surveillance of SSIs was performed during May 2005 and April 2009 in neurosurgery (NS) and general surgery (GS) unit. All patients who had gallbladder (CHOL), colon (COLO), gastric (GAST), small bowel (SB) and bile duct, liver or pancreatic surgery (BILI) in GS and craniotomy (CRAN), ventricular shunt (VSHN) and spinal fusion (FUSN) surgery in NS were included.Escherichia coli in GS and Acinetobacter baumannii in NS.Isolated pathogens were multiresistant, with 58% quinolone resistance in E.coli and 67% imipenem resistance in A.baumannii.SSI was determined in 415 (10.8%) patients in GS and 146 (4%) of patients in NS.SSI rates were 4%,16.8%,6%,16.4% and 14% in CHOL,COLO,GAST,SB and BILI, respectively in GS.In NS, SSI rates were 4%, 4.8% and 4.5% in CRAN,VSHN and FUSN.Cefazolin was used in 780 (49%) operations in GS, 1266 (95%) of operations in NS for antimicrobial prophylaxis.Broad spectrum antibiotics were administered in the rest of the patients.Antimicrobial prophylaxis (AMP) were administered for >24 h in 69% and 64% of patients in GS and NS, respectively.The most significant risk factors for SSIs were total parenteral nutrition, transfusion and presence of drain in GS, and total parenteral nutrition, transfusion, stress ulcer prophylaxis, presence of drain and foreign material in NS.The most common pathogen was Surveillance of surgical site infections is one of the most important infection control issue. Prolonged use of AMP and use of broad spectrum antibiotics are associated with emergence of resistant bacterial strains.None declared."} +{"text": "With the advent of target therapies, imatinib became the mainstay for treatment of chronic myeloid leukemia. However, despite the brilliant results obtained with this drug, more than 30% of patients discontinue therapy in long-term due to several reasons, including failure and/or intolerance. Second-generation tyrosine kinase inhibitors (TKIs) are more potent drugs and have expanded inhibition against a broad spectrum of mutations resistant to imatinib. Both nilotinib and dasatinib have demonstrated in vitro and in vivo clinical activity against different types of mutations and various forms of resistance. However, patients with T315I mutation do not obtain an advantage from these drugs and a third generation inhibitor ponatinib, a pan-BCR drug, was tested with significant results. In this review, we report the results of second-and third-generation TKIs tested as second or third line therapy in patients resistant and/or intolerant to previous inhibitors. Although the use of standard dose imatinib as first therapeutic strategy has dramatically changed the outcome of chronic myeloid leukemia patients in chronic phase, one third of patients does not achieve an optimal outcome and requires alternative therapies due to the emergence of drug resistance. Eight-year follow-up of the international IRIS study showed 85% overall survival (OS) rate, but 30% of patients had unfavourable outcome, mostly due to primary 17%) or acquired resistance (15%).7% or acqIn 2006, the European LeukemiaNet (ELN) group published recommendations and identified at 3, 6, 12 and 18 months different categories of patients defined as optimal or suboptimal response or failure to imatinib given as first line therapy.In the present paper, we analyse the different options for patients resistant or intolerant to TKIs through a review of second-generation drugs trials performed in this category of subjects.Dasatinib is a second-generation BCR-ABL inhibitor that has 325-fold higher potency in vivo with inhibitory activity against the majority of imatinib-resistant BCR-ABL mutants. Several studies tested the efficacy and safety of dasatinib as a second line therapy7The START-R trial included imatinib-resistant patients that were randomized, with a ratio of 2:1, to dasatinib 70 mg twice daily or high-dose imatinib (800 mg daily).START-A trial recruited 174 accelerated phase (AP) CML patients, with the majority of them being resistant to imatinib. At a minimum follow-up of 14 months, major hematologic response (MaHR) and CHR were achieved in 64% and 45% of patients treated with dasatinib 70 mg twice daily. MCyR and CCyR were obtained in 39% and 32% of patients, respectively. No significant differences in terms of rate of responses were observed among resistant or intolerant patients, previous stem cell transplant or presence of baseline mutations. At a median follow-up of 1 year, PFS and OS were 66% and 82%. Grade 3/4 neutropenia and thrombocytopenia occurred in 76% and 82% of patients, respectively. Diarrhoea occurred in 52% of patients with 8% being of grade 3/4, whereas pleural effusion occurred in 27% of patients (5% as grade 3/4).9Dasatinib was tested also in CML blast phase (BP) and Ph+ acute lymphoblastic leukemia (ALL) ; the former enrolled 74 myeloid blast phase (MBP) and 42 lymphoid blast phase (LBP) patients.50) > 3 nM obtained a CCyR rate of 32% and MMR rate of 23% compared to CCyR rate of 53% and MMR of 38% of patients with IC50 < 3 nM, with also different PFS, that was 67% in IC50 > 3 nM group and 80% in IC50 < 3 nM group.14CA180-034 study was an international, open-label, four-arm randomized phase III study, which enrolled 662 patients resistant or intolerant to prior imatinib therapy. Patients received 140 mg or 100 mg of dasatinib, both administered in one (QD) or two daily (BID) doses.A subsequent phase 3 study assessed safety and efficacy of two different schedules (140 mg QD or 70 mg BID) of dasatinib in patients in blast phase. A two-year follow-up showed that MaHRs were similar in MBP treated with the two different schedules (28%), whereas for LBP the response rate was 42% for 140 mg QD and 32% for 70 mg BID. MCyR rate was 25% for 140 mg QD and 28% for 70 mg BID in MBP patients and respective rates were 50% and 40% for LBP. Two-year OS rate with 140 mg QD and with 70 mg BID was 24% and 28% in MBP patients, respectively and 21% and 16% in LBP, respectively. In this trial a trend of better tolerability was reported among patients treated with 140 mg QD.15Nilotinib (Tasigna) was rationally designed to have enhanced selectivity and potency toward BCR-ABL, with clinical activity against the majority of resistant mutations to imatinib and was recommended as second line therapy for CP and AP patients resistant or intolerant to a previous imatinib.16Nilotinib was tested in a phase II trial enrolling 321 CP patients with resistance or intolerance to imatinib that received nilotinib at 400 BID. Results were reported at a median follow-up of 48 months: 94% of patients reached CHR in a median time of 1 month and 59% of patients achieved MCyR in a median time of 1.4 months, with 45% of these being CCyR; 78% of patients achieving MCyR, maintained this response. MMR rate was 28%, PFS was 57% and OS was 78%.18An expanded access characterized safety of nilotinib in a large series of patients . In CP subjects, the CHR and CCyR rates were 43% and 34%, respectively. Faster responses were detected in particular in patients with sub-optimal response to imatinib, who reached 50% of CCyR. The 18-month PFS was 80%. Non-hematologic side effects reported were mild to moderate and included rash, headache, nausea and elevations in serum bilirubin and lipase that occurred in 45 and 7% of patients, respectively.20Nilotinib at the dose of 400 mg BID was tested in 105 MBP patients and 31 LBP: at 2-year follow-up, 60% of MBP and 59% of LBP had achieved a MaHR and 38% and 52% had obtained an MCyR, respectively. CCyR rate was 30% and 32%, respectively. Two-year OS was 32% for MBP and 10% for LBP patients. Fourteen patients underwent allogeneic stem cell transplant. Hematological toxicity was frequent with grade 3/4 neutropenia, thrombocytopenia and anemia occurring in 68%, 63% and 47%, respectively. Laboratory abnormalities were common, with grade 3/4 hypophosphatemia being detected in 15%, hyperbilirubinemia in 11% and lipase elevation in 11% of patients.21Bosutinib (or SKI-606) is an oral once-daily dual Src/ABL inhibitor approved by FDA for the treatment of adult patients with CP, AP or BP Ph+CML, resistant or intolerant to imatinib or second-generation TKIs. It was tested in a phase I/II study, which enrolled 288 patients (200 resistant and 88 intolerant to imatinib) and the final dose of 500 mg QD was found. After a median follow-up of 24 months, 86% of patients achieved a CHR, 53% an MCyR (of them 41% had a CCyR). Among patients with CCyR, 64% of imatinib-resistant and 65% of imatinib-intolerant patients achieved MMR with CMR being obtained in 49% of imatinib-resistant and 61% of imatinib-intolerant patients. Two-year OS was 92%. Responses were seen across all types of mutants, with the exception of T315I. Most frequent side effects reported were diarrhea, rash and vomiting.22Bosutinib was tested also in third line after imatinib and dasatinib and/or nilotinib failure . The study included 118 patients that, after a median follow-up of 28 months, achieved CHR with a rate of 73% and CCyR with a rate of 24%. An MCyR was reported for 31% and 30% of dasatinib resistant and intolerant patients, with 14% and 28% achieving a CCyR, respectively. An MCyR and CCyR were observed in 35% and 27% of patients resistant to nilotinib. After 2 years, PFS was 73% with a median OS estimated to be 83%. Also in third line, bosutinib was able to overcome all types of mutations , except T315I.23A recent sub-analysis of 119 patients aged over 65 years treated with bosutinib was reported in comparison with 451 younger patients.Bosutinib was evaluated also in 63 patients with AP, in 48 with BP and in 23 with Ph+ALL. After a median follow-up of 8 months, 61% of AP patients and 32% of BP achieved a CHR. MCyR and CCyR rates were 48% and 33% in AP patients and 52% and 29% in BP patients, respectively. MMR and CMR rates were 15% and 4% in AP patients and 28% and 12% in BP patients, respectively. Also in advanced phase of disease, bosutinib was found to be active in mutated patients.25A third generation inhibitor was recently tested in resistant/intolerant CML patients: ponatinib is a potent, synthetic, oral multi-target pan-BCR/ABL inhibitor able to block native and mutated BCR/ABL, including T315I mutation, resistant to dasatinib and nilotinib. The results of a phase 1 dose-escalation study, which enrolled 81 patients (60 with CML), showed dose-limiting side effects, which included elevated lipase and amylase and pancreatitis. Of 43 chronic phase CML patients, 72% achieved an MCyR and 44% a MMR. Similar responses were obtained in patients without mutations and with T315I.28Nilotinib and dasatinib tested as a second line after imatinib failure and/or intolerance have been proven to be effective and safe drugs, with the possibility of rescuing about 50% of patients with different forms of resistance. Bosutinib was proven effective not only in the second line, but also in patients resistant to previous therapy with imatinib and nilotinib and/or dasatinib. All these drugs are less or completely ineffective in patients carrying the T315I mutation. In this latter subset a third-generation inhibitor, ponatinib, was tested with brilliant results, and recently approved for patients with resistance to previous TKIs lines. This agent allowed the rescue of the majority of patients with T315I mutation with most of responses being maintained. In the last edition of 2013 ELN recommendations, allogeneic bone marrow transplant should be considered at the time of starting second line after failure of any type of TKIs, whereas it is recommended for patients after failure of two previous TKIs."} +{"text": "Antibodies against bluetongue virus were detected in cattle, sheep, goats, and camels in Algeria in 2008. Antibodies against epizootic hemorrhagic disease virus were detected in cattle, but antibodies against African horse sickness virus were not detected in horses and mules. Epizootic hemorrhagic disease in northern Africa poses a major risk for the European Union. Orbivirus contains several viruses such as bluetongue virus , epizootic hemorrhagic disease virus , and African horse sickness virus . These viruses cause serious diseases in domestic and wild animals. Several orbiviruses have been reported in Algeria. Bluetongue disease caused by BTV serotype 2 (BTV-2) was detected in 2000 . For reasons of animal health, transportation of animals is not allowed between southern and northern Algeria. Vaccination against bluetongue disease, EHD, and African horse sickness in Algeria is forbidden by law because vaccinated animals cannot be differentiated from naturally infected animals.Sampling was conducted during August\u2013September 2008. Cattle, sheep, goats, and camels were sampled in the BTV survey, cattle were sampled in the EHDV survey, and horses and mules were sampled in the AHSV survey. To avoid detection of antibodies from previous outbreaks, only livestock 6\u201312 months of age were sampled. For detection of EHDV and BTV, the epidemiologic unit was the herd.>2% of infected cattle farms at a 95% confidence level (149 herds) and a within-herd prevalence >30% . In addition to cattle for detection of BTV, 359 samples were obtained from 65 sheep flocks, 71 samples from 27 goat herds, and 92 samples from 26 camel herds. For detection of AHSV, the epidemiologic unit was the animal, and sample size was calculated for detection of >2% of infected horses and mules at a 95% confidence level .Sample size was calculated to enable detection of IgG against BTV was detected by using a competitive ELISA . To detect BTV genotypes, a real-time reverse transcription PCR (RT-PCR) was performed. Positive samples were tested by using RT-PCR kits for BTV-1, 2, 4, 6, 9, 11, and 16 . A competitive ELISA provided by the Institute of Animal Health was performed to detect IgG against EHDV according to the protocol of Thevasagayam et al. obtained in 20 wilayas throughout Algeria were tested by BTV RT-PCR. BTV RNA, which indicates recent infection, was detected in 37 of samples (34 from cattle and 3 from sheep), most of which had been obtained in northeastern Algeria. The serotype identified was BTV-1.Antibodies against EHDV were detected in 9% of the cattle tested. EHDV seroprevalence was detected in 15 of 21 wilayas sampled , althougCulicoides imicola midges are abundant in northern and central Algeria , plus several suspected vectors (EHDV in northern Africa poses a major risk for the European Union because of likely wind-borne dispersal of infected vectors ("} +{"text": "Objective. The aim of this study was correlation of skin adnexal tumors with age, sex, and location and determining its incidence in the Department of Pathology at Dr. D. Y. Patil Medical College and Hospital, Kolhapur, Maharashtra. Material and Methods. 56 cases were included in this study from Jan 2004 to June 2010 with respect to incidence of adnexal tumors, age, and sex distribution. All slides were stained with haematoxylin and eosin and then findings were corroborated with special stains like PAS and reticulin wherever required. Results. 80.36% (45/56) were benign and 19.64% (11/56) were malignant adnexal tumors. The sweat gland tumors constituted the largest group (42.86% 24/56) cases followed by the hair follicle tumors of cases and sebaceous gland tumors cases. Overall male\u2009:\u2009female ratio was 1.07\u2009:\u20091. The commonest age group was 51\u201360 years and the commonest affected body part was head and neck region followed by trunk . Clear cell hidradenoma and pilomatricoma were commonest benign tumors and sebaceous carcinoma was the only malignant tumor seen. Conclusion. The incidence of benign skin adnexal tumors was more as compared to the malignant tumors. Malignant tumors were seen in older age group, usually over 50 years of age. Skin adnexal tumors (SATs) are those neoplasms that differentiate toward or arise from pilosebaceous unit, eccrine sweat glands or apocrine sweat glands, and these tumors are classified into four groups that exhibit histologic features analogous to hair follicles, sebaceous glands, and eccrine glands . These tMost of the benign SATs present as asymptomatic papules or nodules and often difficult to diagnose clinically however anatomic location, number and distribution of lesions provide important clue, No change required . They arThe present study includes the cases from Jan 2004 to June 2010. 56 cases were included in this study, which were reported by the Histopathology Sections of the Department of pathology at Dr. D. Y. Patil Medical College and Hospital, Kolhapur, Maharashtra. The clinicopathological data was taken from the record office for the given period. The histopathological examination was done on formalin fixed tissues and paraffin embedded blocks were made. Haematoxylin and Eosin stained sections were examined and few special stains like PAS and reticulin were performed wherever required. However in our laboratory setup, the facility for histochemical staining for enzymes like alkaline phosphatase, phosphorylase, succinic dehydrogenase, indoxyl esterase, and acid phosphatase was not available; they were not performed.In the present study, benign adnexal tumors constituted 80.36% (45/56) cases and malignant adnexal tumors constituted 19.64% (11/56) cases. The sweat gland tumors constituted the largest group involving 42.86% (24/56) cases followed by the hair follicle tumors 37.71% (20/56) cases followed by sebaceous gland tumors 21.43% (12/56) cases . The malThe sweat glands tumors are comprised of chondroid syringoma, eccrine poroma, nodular clear cell hidradenoma, apocrine hidrocystoma, and syringocystadenoma papilliferum . SebaceoIncidence of benign tumors is more as compared to malignant cases. In present study 80.36% 45/56) tumors were benign and 19.64% (11/56) tumors were malignant which was also seen in studies of Radhika et al. 5/56 tumo observedIn Indian population, an overall incidence of skin adnexal tumors is very low. The incidence of benign skin adnexal tumors is more as compared to the malignant ones. Most of the malignant tumors occur in older age group usually over 50 years of age. However benign tumors show a wide age variation. Skin adnexal tumors can occur anywhere in the body; however head and neck region constitutes the most common site. Majority of the tumors can be classified into different subgroups on the basis of light microscopy alone. Skin adnexal tumors showing sweat gland differentiation are seen more frequently. In our institutional study, clear cell hidradenoma is the commonest tumor with sweat gland differentiation, while pilomatricoma is the most common type of hair follicle tumor. Amongst the tumors with sebaceous differentiation, sebaceous carcinoma (meibomian carcinoma) is commonest."} +{"text": "To the Editor: The directly observed treatment strategy (DOTS) for tuberculosis (TB) treatment has been implemented in Ghana since 1994. Before then, TB was treated without adherence to any concerted guidelines. The 2003 report of the Ghanaian National Tuberculosis Programme (NTP) stated a TB incidence of 281/100,000 and centrifugation, sediments were transferred onto Lowenstein-Jensen (LJ) media, incubated (37\u00b0C), and read weekly for 10 weeks for mycobacterial growth. Subsequently, cultures were sent to the German National Reference Centre for Mycobacteria in Borstel, Germany, a reference laboratory of the World Health Organization, for drug sensitivity testing . Sensitivity to isoniazid, rifampin, pyrazinamide, ethambutol, and streptomycin was determined for 2,064 isolates and to thiacetazone for 1,288 isolates. For ambiguous results and DST of thiacetazone, the modified proportion method was performed. Data were analyzed with EpiInfo and Fourth Dimension software programs.A total of 2,064 Of the isolates, 32.8% were from female patients, and 67.8% were from male patients. The mean age of participants did not differ by sex. HIV prevalence was 14.3% .A total of 1,578 (76.5%) isolates were susceptible to all drugs tested, whereas 304 (14.7%) were monodrug resistant, and 177 (8.7%) were multi- or polydrug resistant to combinations (multidrug resistance meant resistance to at least isoniazid and rifampin (2.2%); polydrug resistance meant resistance to several drugs, excluding combined resistance to isoniazid and rifampin (6.5%). The overall prevalence of any drug resistance was 23.5% (486 isolates) . No diffIn all, 6.5% of isolates were polydrug resistant and virtually always included resistance to isoniazid. Among isolates with double- and triple drug resistance, combinations of resistance to isoniazid and streptomycin and to isoniazid-thiacetazone-streptomycin occurred most frequently. Other combinations were relatively rare.In 1989, an initial drug resistance rate of 54.5% in pulmonary TB was observed in Ghana (The overall primary drug resistance rate of 23.5% in Ghanaian TB patients ranks Ghana among those African countries with a high prevalence of drug-resistant TB. The high degree of mono-, multi- and polyresistance to streptomycin may be the result of selective pressure exerted by treatment of other infections with streptomycin and to incomplete treatment courses. Drug resistance to streptomycin and isoniazid are of concern, since these drugs are core components of the NTP. The relative ineffectiveness of streptomycin and the low level of resistance to ethambutol justify the most recent replacement of streptomycin by ethambutol by the Ghanaian NTP.Low rates of initial drug resistance have been reported in countries in which the DOTS strategy has been successfully implemented. Adequate use of standardized treatment regimens under DOTS will limit further emergence of drug resistance but not substantially reduce the current degree of resistance ("} +{"text": "Introduction. Cutaneous foot melanoma is rare, challenging to manage, and not adequately examined in the literature. This study evaluated the prognostic variables and surgical management of foot melanoma. Materials and Methods. Foot melanoma cases managed at an academic center from 1985 to 2010 were retrospectively reviewed. Results. 46 patients were identified with a broad range of demographic characteristics. Overall recurrence was 32.6%: 19% acral lentiginous, 57% nodular, 66% superficial spreading, 30% melanoma unspecified, 50% severely atypical; 53% ulcerated, 23% nonulcerated; 29% on the dorsum of the foot, 17% heel, 60% ankle, 22% toe, 50% plantar; 0%\u2009<1\u2009mm thick, 47%\u20091\u20134\u2009mm, 33% >4\u2009mm. 13 had positive nodes, 4 (31%) of whom recurred. Prognostic factors and recurrence did not correlate, and survival was 96% with a median followup of 91 months. Conclusions. Aggressive management of foot melanoma may result in excellent long-term survival even following disease recurrence. Malignant melanoma represents a major public health concern worldwide and the annual incidence has been steadily rising since 1935 . When maHistorically, clinicians have focused on clinical factors, histology, anatomic location, and the presence or absence of metastatic disease to determine the prognosis of patients with melanoma , 6. PathThe literature does not adequately analyze the prognostic variables, management, and outcomes of foot melanoma. Because foot melanoma is so rare, many publications combine melanoma of the foot with the hand, leg, or thigh for statistical purposes. Even papers that focus solely on the foot are often confounding in their conclusions because they combine cutaneous melanoma with subungual melanoma. In addition, there has been great variability in the factors that the literature has analyzed, even in regard to such clinically significant considerations as pathology, thickness, lymph node status, metastasis, recurrence, and survival. This retrospective study was performed to review the prognostic variables, management, and outcomes of foot melanoma to try to arrive at surgical guidelines.Patients treated for cutaneous melanoma of the foot from 1985 to 2010 at the Virginia Commonwealth University Health System were retrospectively reviewed for demographic data, histology, anatomic location, Breslow thickness, mitotic index, ulceration, operation, surgical margin, lymph node status, location of recurrence, disease-free survival, and overall survival. The Virginia Commonwealth University Institutional Review Board granted approval for this study, and this study complied with all guidelines for ethical research. Recurrence analysis was performed by calculating and plotting the median cumulative function using JMP8 software. Statistical analysis utilized logistic regression to evaluate for significance.46 patients were treated for foot melanoma from 1985 to 2010. Patient followup was a median of 91 months, a mean of 101 months, and ranged from 4 to 300 months. Patients were followed for 3 months for the first 2 years, then for 6 months until the 5th year, followed by yearly thereafter. No patients were lost to follow up. Patients were treated with wide local excision with primary closure or skin grafting; amputation was performed when a lesser procedure was unable to obtain an adequate margin and leave a functioning foot. Lymphadenectomy was performed when lymph node metastasis was detected clinically or by sentinel node biopsy. Palliative debulking of wound, regional, and distant recurrences was performed when appropriate. No patients received adjuvant therapy. The patient demographics, pathology, site of origin, and surgical treatment were examined. Of the 46 patients, 15 were men and 31 were women. Age at diagnosis ranged from 16 to 99 years of age, with a median of 62 years (mean 59) . Ethnic The correlations between site of origin, pathologic subtype, thickness, and mitotic index were examined. Acral lentiginous, nodular, superficial spreading, unspecified, severely atypical, desmoplastic, and ulcerated melanomas were well distributed across the sites of origin . SimilarThe correlations between recurrence rate and site of origin, pathologic subtype, mitotic index, average thickness, surgical treatment, and lymph node status were examined. The rate of recurrence by histologic subtype of melanoma is shown . There dIn order to compare the recurrence rates among the different prognostic variables, the mean cumulative function (MCF) of each population was calculated. MCF assigns a cost to a population each time a recurrence occurs in that population \u20139. The MMCF analysis was used to compare the risk of recurrence by histologic subtype, site of origin, and thickness. The MCFs for each histologic subtype are shown . The risFoot melanoma is a rare disease which has not been adequately examined in the literature. From 1957 to 2010 only one publication examined cutaneous foot melanoma alone without confounding results by combining with subungual, hand or other lower extremity primary sites 2, 3, 66, 10\u201324.This study reviewed 46 cutaneous foot melanoma patients with a broad distribution of demographic characteristics, histology, thicknesses, mitotic indexes, and sites of origin. Although there were more cases of acral lentiginous melanoma, it was not the predominant subtype as had been historically thought of the acral sites . There wP = 0.0946). There was no significant correlation between recurrence rate or prognostic factor and site of recurrence, but wound recurrences had the highest mitotic index and lymph node recurrences the greatest thickness , 68% for intermediate thickness (1\u20134\u2009mm), and 42% for thick lesions (>4\u2009mm) \u2009mm, 68% \u201324. Our In conclusion, foot melanoma remains a challenge to clinicians who must balance oncologic resection against preserving limb function. A review of the literature since 1957 reveals that there has not been an adequate analysis of prognostic factors to guide management. This study focused exclusively on patients with cutaneous foot melanoma treated over a 25-year period to comprehensively examine the prognosis and management of this rare disease. Although there were no statistically significant correlations between disease free survival and prognostic variables, only trends, survival was 96% at a median followup of 91 months. Therefore, patients with foot melanoma appear to have an excellent long-term survival even if they develop recurrent disease.The authors have no financial interests or any conflict of interests to disclose."} +{"text": "Prior longitudinal studies have shown high cumulative dating violence exposure rates among U.S adolescents, with 36 percent of males and 44 percent to 88 percent of females experiencing victimization across adolescence/young adulthood. Despite promising information characterizing adolescents\u2019 dating violence experiences longitudinally, prior studies tended to concentrate on physical and sexual types of violence only, and did not report information on the number of times dating violence was experienced across multiple abusive partners. We used a method similar to the timeline follow-back interview to query adolescents about dating violence victimization from age 13 to 19\u2014including dating violence types , frequency, age at first occurrence, and number of abusive partners.A total of 730 subjects were randomly sampled from university registrar records and invited to complete an online survey, which utilized methods similar to the timeline follow-back interview, to retrospectively assess relationship histories and dating violence victimization from age 13 to 19 . Then, for each dating violence type, we asked about the number of occurrences, number of abusive partners, and age at first occurrence. Of 341 subjects who completed the survey, we included 297 who had a dating partner from age 13 to 19.Fully 64.7 percent of females and 61.7 percent of males reported dating violence victimization between age 13 and 19, with most experiencing multiple occurrences. More than one-third of abused females had two or more abusive partners: controlling behavior (35.6 percent); put downs/name calling (37.0); pressured sex (42.9); insults (44.3); slapped/hit (50.0); and threats (62.5). Males also had two or more abusive partners, as follows: controlling behavior (42.1 percent); insults (51.2); put downs (53.3); threats (55.6); and unwanted calls/texts/visits (60.7). Among abused females, 44.7 percent first experienced controlling behavior between age 13 and 15, whereas the majority (62.5 percent) first experienced pressured sex between age 16 and 17. Among males, for most abuse types, 16 percent to 30 percent of victimization began before age 15.Our study adds information to a substantial, but still growing, body of literature about dating violence frequency, age of occurrence, and number of abusive partners among adolescents. Dating violence is widespread among adolescents in the United States, with cross-sectional studies showing that between 9% and 38% of adolescents have been victimized in the past year and/or within any dating relationship -13. Thesphysical and/or sexual violence beginning in adolescence through young adulthood [Studies have also captured adolescents\u2019 longitudinal experience of dulthood -20. Halpdulthood . Smith\u2019sdulthood . Other ldulthood -20. In adulthood . In sum,In addition to the high prevalence of dating violence among adolescents shown in U.S. studies and the tendency for re-victimization, as a public health concern, dating violence victimization has been shown to be associated with adverse mental and physical health problems, including depression, anxiety, suicide attempts, injuries, problem alcohol use and drug use, disordered eating, and risky sexual behavior -11,20. TDespite the large body of extant literature documenting prevalence of dating violence victimization and health correlates, including longitudinal studies that have characterized adolescents\u2019 experience of dating violence at multiple points in time -20, prioPreventing Mental, Emotional, and Behavioral Disorders Among Young People \u2013 called for a critical focus on the prevention of mental, emotional and behavioral disorders in young people [The 2009 Institute of Medicine report \u2013 g people . Given tData for the study were collected as part of a feasibility study for testing the study questionnaire. The feasibility study was to serve as a platform for a larger longitudinal study that tracked dating violence experiences and health outcomes across subjects\u2019 college/university career.Study procedures were approved by the institutional review board of The Ohio State University . A random sample of 730 female and male students ages 18 to 21 enrolled at The Ohio State University on January 1, 2011 were identified through the registrar\u2019s office to participate in a one-time only internet survey to assess dating violence experiences from age 13 to 19 and health. Subjects were credited $20 to their university student account for their participation in the study. During the first week of the academic spring quarter, using students\u2019 university email account, we sent a recruitment email to all 730 students along with the study information sheet and link to the online survey. Two follow-up reminders were sent by email, three and seven days after the initial email, reminding students to complete the survey. The overall response rate at each recruitment email was as follows: initial email ; second email ; final email \u2014 rates similar to prior studies of adolescents recruited using random sampling ,28. The Of the 341 subjects who completed the online questionnaire, 44 were excluded because they were older than age 21 (n\u2009=\u20097) or because they reported never having a dating, romantic or sexual partner between age 13 and 19 (n\u2009=\u200937). After these exclusions, the final analytic sample comprised 271 subjects .We used a method similar to the timeline follow-back interview to retrospectively assess subjects\u2019 dating violence victimization histories from age 13 to 19 -24; we hAfter information about subjects\u2019 relationship history was gathered, dating violence victimization was assessed retrospectively using eight modified questions covering the three core conceptual areas of teen dating violence as recognized by the Centers for Disease Control and Prevention . Table Our eight questions were adapted from the Centers for Disease Control and Prevention\u2019s Youth Risk Behavior Survey Surveillance System , Foshee For each question in Table In gender-stratified analyses, we estimated overall dating violence prevalence ; 27.4% ; 30.5% ; and 42.6% (insults/yelling/swearing). Nearly 25% of females experienced sexual pressure due to a partner\u2019s persistent begging or threats and 5% due to physical force, 9% experienced threats of physical force, and 3.7% had been hit, slapped or otherwise physically hurt by a partner.Among males, psychological dating violence rates were: 15.0% ; 18.7% (controlling behavior); 27.1% ; and 43.9% (insults/yelling/swearing). A total of 11% of males experienced sexual pressure due to partner\u2019s persistent begging or threats, and 1% due to physical force, 9.3% experienced threats of physical force and 13.1% had been hit, slapped or otherwise physically hurt by a partner.Tables In contrast to our studies on adults where most women and men indicated they had only one abusive partner ,38, teenAmong female and males reporting violence, dating violence was rarely reported as an isolated incident. Dating violence was commonly experienced as 2 to 5 occurrences of each dating violence type. However, of note, roughly 15% of females and males reported 20 or more occurrences of some dating violence types. Namely, for females, 16.0% experienced 20 or more occurrences of unwanted calls/texts/visits, 17.7% experienced threats, 16.7% were hit, and 25.0% were pressured sexually using physical force. For males, 15.0% experienced 20 or more occurrences of controlling behavior and 14.3% experienced unwanted calls/texts/visits.Some dating violence types tended to occur at earlier ages than other dating violence types. For example, among females reporting dating violence, 44.7% reported that they first experienced controlling behavior between the ages of 13 and 15, whereas the majority of females (62.5%) reporting being pressured into sex due to threats or physical force first experienced this type of dating violence between the ages of 16-17. Among males, age 13 to 15 was the most common age at earliest occurrence of put downs/name calling (60.0%). For most other dating violence types, between 16% and 30% of victimization began before age 15.Our study used an assessment approach similar to the timeline-follow back method -24 to esOur study was not powered to statistically compare prevalence rates between males and females. This said, our study generally showed that females and males tended to experience comparable rates of threats (9%), unwanted calls/texts/visits 27%), and being yelled/sworn at 43%), but females experienced higher rates of being put down and called names (30.5% versus 15.0%) and sexual pressure due to persistent begging or threats (23.8% versus 11.2%). Our findings corroborate results from prior studies showing higher rates of sexual violence victimization in females compared to males and similar rates of psychological abuse among adolescent females and males in dating relationships [3%, but f%, and beOur findings on the age at first dating violence occurrence, number of occurrences, and number of abusive partners add to our understanding of how dating violence unfolds during the teen years. Females and males rarely reported an isolated incident of dating violence. While teens most commonly experienced 2 to 5 occurrences of dating violence, of note, roughly 15% of both females and males reported 20+ occurrences of some dating violence types . The age at first occurrence tended to be similar for males and females, with a few exceptions. Females tended to report controlling behavior earlier than males, and males tended to report put down and name calling earlier than females. In general, the first occurrence of pressure to have sex, and threats and physical harm tended to occur later than first occurrences of psychological dating violence such as controlling behavior, or name calling.Our study results must be considered within the context of its limitations. First, generalizability is compromised due to our sample of young adults\u2014predominantly White 83%)\u2014enrolled at a large Midwestern university. While the racial/ethnic breakdown of our sample mirrors that of the university, our sample is less diverse than that of the U.S. population generally . Studies3%\u2014enrollWe used a query approach similar to the timeline follow-back interview method to facilitate recall of dating violence victimization experiences in a sample of males and females. Our study documented dating violence victimization experiences across the teen years, from age 13 to 19, including dating violence types, frequency, number of abusive partners, and age at first occurrence\u2014providing important information for health professionals and others to respond to a very common problem among teens, even those at higher socioeconomic levels who go on to college. Our results point to the need to amplify primary and secondary prevention efforts; school-based programs have been effective in reducing dating violence occurrence in adolescents ,42-49. AThe authors declare they have no competing financial or non-financial interests.AEB conceptualized the study and survey, oversaw data collection and analysis, and wrote the manuscript with co-authors\u2019 input. MA helped design the survey, conducted the data analysis and critically reviewed the manuscript. JMN helped conceptualize the study and survey, added to the statistical analysis, and critically reviewed the manuscript. SBH, CB, and DS helped conceptualize the study and survey, and critically reviewed the manuscript. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2458/12/637/prepub"} +{"text": "The incidence of tonsil cancers has increased in several countries. French data on HPV prevalence in tonsil cancers are scarce. The objective of this study was thus to assess the overall and type specific HPV prevalence in tonsil histological samples.This French retrospective multicenter study involved 12 centres located throughout the country. Were included 185 histological samples collected from year 2000 to 2009 with a validated diagnosis of tonsil invasive carcinomas. HPV prevalence was studied according to gender, age and histological type of cancer.Overall HPV prevalence was 57% in tonsil cancers. Mean age of diagnosis was comparable in HPV positive tonsils cases (60 \u00b1 11.2) and HPV negative tonsil cases (59 \u00b1 9.6). HPV prevalence was significantly higher in female than in male cases . About 53% of tonsil cases were infected by a single HPV type. Only eight (4%) samples were infected by more than one HPV type. Among HPV positive samples, HPV 16 was found in 89% of tonsil cases. All other HPV types had prevalence below 5%.Our results indicate that HPV is common in tonsil carcinomas and emphasize the predominant role of HPV 16. Head and neck cancers (HNC) are the fifth most common cancer worldwide with more than 600,000 cases diagnosed each year . France The overall incidence of HNC has fallen in recent years. This seems to be consistent with the decrease in tobacco and alcohol consumption. By contrast, the incidence of cancers in particular anatomical sites has increased . The incWell known main risk factors for developing oropharyngeal cancer are tobacco usage and alcohol consumption . Socio-eFrench data on HPV prevalence in tonsil cancers are scarce. The objective of this study was thus to assess the overall and type specific HPV prevalence in tonsil histological samples.The overall study which involved oropharyngeal and oral cavity invasive cancers is described elsewhere. We present here results of a substudy focused on tonsil cancers. This French retrospective multicenter study involved 12 centres located throughout the country. Selection of the centres was mainly based on their willingness to participate trying to get most French geographical areas represented. To be included, histological samples had to be collected after year 2000. Each sample with a validated diagnosis of tonsil cancers and fixed in 4% buffered formalin before paraffin embedding were retrospectively included. Cases with diagnosis other than SCC were excluded. Each centre decided whether its own cases could be included. Patient data such as age at diagnosis, gender, area of residence, year of sample collection were collected for each case when available.According to the French legislation and since this study only involved data extracted from medical records and stored histological specimens, no informed consent from the patients was necessary. Data collected from participating pathology centres were strictly anonymous.HPV genotyping was centrally performed using the INNO-LiPA HPV Genotyping extra test . This kit allows the detection of 28 HPV types, 15 high-risk (HR) and 13 low-risk (LR) . In ordeThe HPV genotype-specific prevalence was expressed as the proportion of HPV-positive samples among all carcinoma cases and among HPV positive cases. HPV prevalence was studied according to gender, age and histological type of cancer. Prevalence of HR and LR HPV was also calculated. Categorical variables were studied using 2-sided Chi-square or Fisher exact test when necessary. All statistical analyses were performed using SPSS v.11.5 for Windows. A p-value below 0.05 was considered as statistically significant.A total of 220 of histological samples of tonsil invasive SCC were retrospectively collected from 12 French pathology centres scattered throughout the country. Patients were recruited throughout France: 28% in Paris area, 8% in the West area, 35% in the North and North East, and 28% in the South of France. 84% (185/220) were included in the study while 16% (35/220) were excluded from the analysis because neither HPV nor cellular DNA could have been amplified. Mean age at diagnosis was 60 \u00b1 10.5 years. There were 81% (150/185) of males.We found an overall HPV prevalence of 57% 106/185). Mean age of diagnosis was comparable in HPV positive tonsil cancer cases (60 \u00b1 11.2) and HPV negative tonsil cancer cases (59 \u00b1 9.6). HPV prevalence was higher in female than in male cases (80% (28/35) versus 52% (78/150) respectively, p = 0.003). About 53% (98/185) of tonsil cancer cases were infected by a single HPV type. Only 4% (8/185) of tonsil samples were infected by more than one HPV type, with at least one HPV HR. HPV 16 was found in 89% (94/106) of HPV positive tonsil cases. All other HPV types had prevalence below 5%. HPV 16 and/or 18 was found in 91% (96/106) of HPV-positive tonsil cases. in the 1970s, 29% (12/42) in the 1980s, 57% (48/84) in the 1990s and 68% (32/47) in 2000-2002 /30 in th. We did HPV 16 was the genotype the most identified in the literature, 93% (77/83) of HPV-positive cases in the series of Nasman et al 2003-2007 .In our series, HPV prevalence was higher in female than in male cases (80% versus 52%) even if men accounted for the majority (81%) of the total tonsil cancers, which was concordant with some studies. Nasman et al found that HPV was present in 95% 21/22) of women cases of tonsil cancers and in 82% 62/76) of men cases of tonsil cancers 2/76 of m. Chien e of womenDifferent authors found that HPV positive carcinoma was associated with younger patients. Nasman et al observed that patients with HPV positive tonsillar cancer were younger than patients with HPV negative cases (59 years versus 68 years) [Our study has limitations. First since the recruitment was rather heterogeneous between centres and centres were not evenly scattered on French territory despite patients were recruited throughout France, the study sample can not be considered as fully representative of the French tonsil cancer population. Secondly, we used DNA detection only; in this retrospective study it was not possible to determine the presence of transcripts. However, Nasman et al found that HPV 16 E6 or E7 RNA were expressed in the majority of the analysed HPV 16 positive tumors [a posteriori to clarify the possible causal association between tonsil cancers and HPV.Our results indicate that HPV has a high prevalence in tonsillar SCC. We emphasize the predominant role of HPV 16 since 89% HPV-positive tumors were linked with HPV 16; moreover 91% were associated with HPV 16 and/or 18. Unlike for cervical cancer, the association of HPV and oncogenic mechanisms remain to be clarified. These results are an indicator of the HPV distribution in tonsil cancers before HPV vaccine implementation among women. The HPV vaccination of young women will be able to contribute - Jean Lacau Saint Guily, MD: Member of the scientific EDiTH VI advisory board- Claire Oka\u00efs, PharmD, is an employee of Sanofi Pasteur MSD- Anne-Carole Jacquard, PhD is an employee of Sanofi Pasteur MSD- Jean-Luc Pr\u00e9tet, PhD: occasional speaker for SPMSD- Agn\u00e8s Beby-Defaux, MD, PhD: The author declares that he has no competing interest- Christine Clavel, PharMD, PhD, belongs to the steering committee of MERCK about vaccines- G\u00e9rard Agius: The author declares that he has no competing interest- Philippe Birembaut, MD: The author declares that he has no competing interest- Yann Leocmach, MD, is an employee of Sanofi Pasteur MSD- Beno\u00eet Soubeyrand, MD, is an employee of Sanofi Pasteur MSD- Didier Riethmuller, MD, PhD: expert for SPMSD- Christiane Mougin, MD: Travel support- Fran\u00e7ois Denis, MD, PhD: The author declares that he has no competing interestJLSG participated to the study design, data analysis and interpretation and manuscript preparation and review. CC participated to the study design, data analysis and interpretation and manuscript preparation and review. CO participated to the data analysis and interpretation and manuscript preparation and review. JLP participated to the study design, data analysis and interpretation and manuscript preparation and review. ABD participated to the study design, data analysis and interpretation and manuscript preparation and review. GA participated to the study design, data analysis and interpretation and manuscript preparation and review. PB participated to the study design, data analysis and interpretation and manuscript preparation and review. ACJ participated to the study design, data analysis and interpretation. YL participated to the study design, data analysis and interpretation and manuscript preparation and review. BS participated to the study design, data analysis and interpretation and manuscript preparation and review. DR participated to the study design, data analysis and interpretation and manuscript preparation and review. FD participated to the study design, data analysis and interpretation and manuscript preparation and review. CM participated to the study design, data analysis and interpretation and manuscript preparation and review. All the authors have given approval of the version to be published."} +{"text": "To the Editor: Community-based epidemiologic studies have shown beneficial effects of hand sanitizers. Hand sanitizers were effective in reducing gastrointestinal illnesses in households . In addition to failing to decrease CFU, colonies were more evenly distributed on postwash plates after use of 40% gel. The even postwash colony distribution may be caused by dispersion of aggregates of microbes without sufficient killing.Tap water, 40% ethanol, and 40% ethanol gel yielded no significant reductions in CFU . The 40%Staphylococcus aureus.Qualitative colony assessment suggested 40% gel and 40% ethanol were as effective as 62% gel against fungi; in contrast, bacterial CFU tended to show little change or increases. The most prevalent bacteria were staphylococci, including those with characteristics of After conducting experiments, a survey of 6 local retail chains found no substandard products. In the fall of 2005, a more extensive survey of 18 retail chains uncovered a substandard product at all 3 stores of 1 deep-discount chain. The marketing profile of deep-discount chains suggests that poorer segments of the population may be more at risk of purchasing inadequate antiseptic gels. Moreover, 40% ethanol products may be stockpiled in homes and offices. An extensive Internet survey identified no additional substandard commercial products. However, the alcohol content of less-common brands was not always available online, and several Internet sites provide recipes for a bubble gum\u2013scented children's hand sanitizer that contains 33% isopropanol as the sole active ingredient. Educational efforts should emphasize that effective sanitizers must be of a sufficient alcohol concentration.The efficacy experiments reported here reinforce what has been known for >50 years: 40% ethanol is a less effective bacterial antiseptic than 60% ethanol ("} +{"text": "In the past 20 years, research has shown that brief interventions are effective in reducing health risk behaviors. Now we are in the second generation of brief intervention trials, investigating how to improve efficacy, including the investigation of cost-saving communication channels. Our aim was to investigate whether motivationally tailored interventions are more effective in reducing unhealthy alcohol use when delivered by computer or in person. Proactively recruited general hospital inpatients with unhealthy alcohol use (n=975) participated in a randomized controlled trial, and were allocated to one of three groups: 1) individualized theory-based computer generated feedback letters, 2) motivational interviewing based counselling, and 3) assessment only (controls). Both intervention groups received up to three interventions. All groups are followed up at 6, 12, 18 and 24 months. Between February 2011 and December 2012, recruitment and interventions have been completed. We have assessed 10,591 inpatients aged 18-64 years for eligibility. We have screened 6,236 inpatients regarding unhealthy alcohol use, corresponding to 91.1% of those eligible. Of all inpatients with unhealthy alcohol use, 80.6% gave informed consent to participate in the trial. So far, 71.3% to 81.5% of these have participated in the follow-ups. A large study has been successfully implemented at a general hospital. Satisfactory participation rates provide a solid basis to investigate the comparative efficacy of brief alcohol interventions delivered by computer versus in person. The follow-up period of up to 24 months provides an excellent opportunity to investigate gradually increasing effects."} +{"text": "Escherichia coli isolates of serotypes O26, O103, O111, O128, and O145. Strains of these serotypes may cause urinary tract and enteric infections in humans and have been implicated in infections with Shiga toxin\u2013producing E. coli (STEC). Approximately 50% of the 137 isolates from humans were resistant to ampicillin, sulfamethoxazole, cephalothin, tetracycline, or streptomycin, and approximately 25% were resistant to chloramphenicol, trimethoprim-sulfamethoxazole, or amoxicillin-clavulanic acid. Approximately 50% of the 534 isolates from food animals were resistant to sulfamethoxazole, tetracycline, or streptomycin. Of 195 isolates with STEC-related virulence genes, approximately 40% were resistant to sulfamethoxazole, tetracycline, or streptomycin. Findings from this study suggest antimicrobial resistance is widespread among E. coli O26, O103, O111, O128, and O145 inhabiting humans and food animals.Susceptibilities to fourteen antimicrobial agents important in clinical medicine and agriculture were determined for 752 The emergence and dissemination of antimicrobial resistance in bacteria has been well documented as a serious problem worldwide . SelectiEscherichia coli are facultative anaerobes in the normal intestinal flora of humans and animals ,3; howevRecent reports have suggested the use of tetracyclines, sulfa drugs, cephalosporins, and penicillins to be a major factor in the emergence and dissemination of antimicrobial-resistant E. coli \u201314. HoweWe included 752 E. coli isolates from the collection of The Pennsylvania State University\u2019s E. coli Reference Center in the study ; this ceAntimicrobial susceptibility testing of all isolates was done with broth microdilution using the PASCO MIC/ID system . Testing was done according to manufacturer\u2019s instructions and according to guidelines developed by the National Committee for Clinical Laboratory Standards (NCCLS) . Tested Isolates were grown at 37\u00b0C overnight on veal infusion agar . A loopful of culture was resuspended in 200 \u00b5L of distilled water, incubated at 99\u00b0C for 15 min, and centrifuged at 12,000 x g for 2 min. The supernatant was used as a template for amplification of Shiga toxin genes (stx1 and stx2), the intimin gene (eae), and the enterohemolysin A gene (hlyA) through multiplex polymerase chain reaction (PCR) . PrimersOf the isolates in this study, the highest frequencies of antimicrobial-resistant phenotypes were observed for E. coli isolates from humans and turkeys . Fifty-nResistance profiles among isolates from cattle, chicken, and swine were largely similar to each other . Fifty pResistance frequencies were lowest for isolates from nonfood animals ; howeverOf 174 isolates resistant to ampicillin, 73% were resistant to streptomycin and tetracycline. Of 23 isolates resistant to cefoxitin, 91% were resistant to amoxicillin-clavulanic acid. Each of the five ceftiofur-resistant isolates was resistant to cefoxitin and amoxicillin-clavulanic acid. Based on NCCLS interpretive criteria for confirmatory ESBL testing , none ofBased on the presence of stx1 and stx2, 26% of the isolates were characterized as STEC. Of these, 89% contained stx1 only, 2% contained stx2 only, and 9% contained both. Eighty-one percent of STEC possessed eae and hlyA, 7% eae only, and 7% hlyA only. Of isolates that were not characterized as STEC, 34% possessed eae and hlyA, 2% eae only, and 24% hlyA only (data not shown).The highest frequency of STEC was among isolates from cattle, in which 34% were characterized as STEC, followed by 27% of isolates from humans, 14% of isolates from nonfood animals, 12% of isolates from swine, and 6% of isolates from turkeys. None of the isolates from chickens were characterized as STEC.Of E. coli isolates from cattle, resistance frequencies were generally similar between STEC and other E. coli, respectively, with the exception of ampicillin (26% vs. 8%), chloramphenicol (14% vs. 4%), cephalothin (14% vs. 3%), and trimethoprim-sulfamethoxazole (11% vs. 2%), in which resistance frequencies were noticeably higher . In contOf the 752 E. coli isolates characterized in this study, approximately half displayed resistance to one or more antimicrobials, including penicillins, sulfonamides, cephalosporins, tetracyclines, and aminoglycosides. These data are in accord with multiple previous studies suggesting use of these drugs has been a key factor in the emergence of antimicrobial-resistant E. coli -13,27,28Approximately 40% of E. coli from humans was resistant to trimethoprim-sulfamethoxazole. Because this drug combination is recommended for treating a range of human infections, including complicated urinary tract infections, acute uncomplicated cystitis, and pyelonephritis , E. coliCeftiofur is the sole extended-spectrum cephalosporin approved for use in food animals in the United States, and it is not approved for use in human clinical medicine . The obsThe observation that 20% of E. coli isolates from turkeys were resistant to nalidixic acid (concomitant with increased MICs for ciprofloxacin) is important considering fluoroquinolones are used to treat a range of E. coli infections in humans . This fiVirtually all E. coli isolates from nonfood animals were susceptible to each of the antimicrobials tested. Notable exceptions, however, were isolates from dogs, cats, and rabbits. While these data yield preliminary evidence suggesting companion animals may be an important reservoir of antimicrobial-resistant E. coli of these serotypes, additional studies are required to more clearly define the impact of antimicrobial use in companion animal medicine on the emergence of antimicrobial-resistant E. coli.STEC-associated virulence genes, including stx1, stx2, eae, and hlyA, were detected primarily in isolates from humans and cattle. Differences in pathogenicity of STEC for these two hosts may explain why STEC from humans had a higher frequency of antimicrobial resistance compared to STEC from cattle. Specifically, because in human clinical medicine antimicrobials are likely used less often to treat STEC infections compared with other E. coli infections ,8, frequThe multiple antimicrobial-resistant phenotypes observed in this study may have resulted from the spread of mobile genetic elements. For example, the observation that nearly 75% of ampicillin-resistant E. coli isolates were also resistant to streptomycin and tetracycline suggests resistance genes for these drugs are linked on plasmids. Moreover, the widespread resistance to sulfamethoxazole implies the presence of class I integrons, which are also important in conferring resistance to multiple antimicrobials . ResearcBecause the isolates from this study were to a large extent unevenly distributed as to source of isolation versus year of isolation, analyzing resistance trends over time was not possible. Likewise, meaningful analysis of antimicrobial resistance in relation to geographic origin or to serotype was not possible. Long-term prospective studies examining isolates from defined geographic locales are required to more precisely detect temporal and spatial differences in antimicrobial resistance in strains of E. coli.Emergence and dissemination of antimicrobial resistance in E. coli strains of serotypes O26, O103, O111, O128, and O145 may complicate treatment of certain urinary tract and enteric infections in humans and animals. Data from this study did not demonstrate a steadfast link between antimicrobial use in any particular venue and development of antimicrobial resistance among these E. coli isolates. The data did, however, suggest that antimicrobial use in clinical medicine and in agriculture was important in the selection of antimicrobial-resistant phenotypes. Continued surveillance of E. coli collected from agricultural and clinical settings, including the food production continuum, is merited to identify emerging antimicrobial-resistant phenotypes."} +{"text": "Objective: Early studies of plastic surgery patient triage using telemedicine are descriptive and deal with feasibility rather than accuracy. The inpatient study arm compares on-site wound-evaluation accuracy with remotely viewed digital images. The outpatient arm prospectively compares on-site and remote diagnosis, management, and outcomes in a busy, urban, reconstructive-surgery clinic. The concurrent 6 patient case studies illustrate significant systems improvement by using remote consultation. Methods: A total of 43 inpatients and 100 consecutive outpatients were evaluated by on-site and remote surgeons as performed in previous arms with digital-camera and store and forward technology. Consent was obtained from all patients participating. Agreements regarding diagnosis and management were calculated. Results: In the first study arm, on-site and remote agreement (46%-86% for wound description and 65%-81% for management) generally matched agreement among on-site surgeons (68%-100% and 84%-89%). Moreover, when on-site agreement was low (68% for edema), agreement between on-site and remote surgeons was also low (57%). Remote evaluation was least sensitive detecting wound drainage (46%). On-site surgeons opted for more treatment, often prescribing antibiotics and admitting the patient. The second teleconsult arm provides further evidence of accuracy, overall agreement of 32%, sensitivity 48.55%, specificity 96.92%, positive predictive value 49.26%, negative predictive value 96.83%, and P < .001 regarding diagnosis . Patient transfer, postoperative monitoring, and outcomes via electronic image transfer, as well as cost-benefit analysis of this clinic-based study, are presented. Conclusions: eConsultation renders similar outcomes to standard, on-site examination in a selected group of plastic surgery patients. Remote evaluation may assist triage decisions, thereby decreasing emergency room throughput time and office-visit frequency, supplementing satellite facility consultation by plastic surgeons, and providing real-time postoperative assessments, thereby improving quality and reducing costs. Telemedicine is in broad use in radiology and cardiology, where the electronic transmission and initial evaluation of radiographs and electrocardiographic tracings improve the efficiency of clinical care.In 1998, Stoloff et alGiven the reliance on photography for surgical outcome evaluation and achieving reproducible and valid results in research, Galdino et alWe seek to develop an understanding of the accuracy of remote temporal and physical digital interpretation. It is our observation that the feasibility of patient triage for most plastic and reconstructive surgery consultations is less dependent on the quality of photographs than it is on the ability to process and remotely interpret such images. Standardization in the emergency room (ER) is less practical when triaging surgical patients. Because of the scarcity of studies examining nonstandardized photography with low-quality digital imaging, we set out to determine the validity in plastic surgery e-consultation and ER triage. For the purpose of this manuscript, eConsultation refers to remote interpretation and management utilizing store and forward digital images.In the initial study arm, 43 wounds in 37 inpatients were photographed with a Canon A80 camera (resolution 4.0 megapixels). On-site evaluation consisted of bedside examination by 2 physicians at the time of digital imaging and transmission. Remote evaluation consisted of 2 physicians examining digital images remotely at the time of transmission and 2 physicians examining digital images remotely at later time. A questionnaire was recorded by all physicians, and agreements regarding wound description and wound management were calculated among on-site surgeons and remote surgeons and between on-site and remote surgeons.In the second arm, 100 patients were photographed at an urban outpatient plastic surgery clinic with a Fujifilm FinePix A330 digital camera (resolution 2.0 megapixels) without standardized photography. A medical student, untrained in medical photography, took the pictures. On-site evaluation consisted of bedside examination by a surgeon at the time of digital image capture and transmission and remote evaluation consisted of digital image consultation via store and forward technology at a later date. The remote surgeon was given no information in addition to the picture. An injury questionnaire was recorded and agreements regarding diagnosis were calculated between on-site and remote surgeons with SAS statistical software program version 9.2. A series of 5 clinical cases is presented in which patient transfer decisions, home-based postoperative monitoring, and overall outcomes were improved and costs reduced via electronic image transfer. These studies were approved by the institutional review board.P < .001, regarding diagnosis .Inpatient examination by on-site surgeons agreed 68% to 100% for wound description and 84% to 89% for wound management , showed 68% to 100% agreement among on-site surgeons for wound description and 84% to 89% agreement for wound management. A similar study in vascular surgery revealed comparable results among on-site surgeons (64%-85% for wound description and 63%-91% for wound management).,17A review of the trauma and burn literature reveals wound evaluation studies using high-quality digital images. Galdino et al14P < .001 with an overall sensitivity 48.55%, specificity 96.92%, PPV 49.26%, and NPV 96.83% and nonstandardization of photographs showed an overall agreement of 32% with Therefore, the original hypothesis that digital image quality and standardization of photos do not affect diagnosis and management cannot be rejected. Table P < .001, overall sensitivity 48.55%, specificity 96.92%, PPV 49.26%, NPV 96.83%; category analysis: P < .001, agreement 26.67% to 41.18%, sensitivity 36.36% to 50%, specificity 92.22% to 96.92%, PPV 41.46% to 63.64%, NPV 90.86% to 99.49%; and 24 choice analyses: P value, sensitivity, specificity, NPV, and PPV (Table ER physicians treating surgical patients who require plastic surgery consultation can use store and forward technology. Halstead et alForty-three inpatients and 10 consecutive outpatients were examined on site.Medium- and low-quality digital images were obtained without standardization and evaluated using store and forward technology. Accuracy and concordance rates were high. Variations in concordance were comparable to on-site variability. Five cases demonstrate systems improvement using eConsultation. The authors conclude that eConsultation is an accurate, cost-saving, time-saving technique in the evaluation and management of select plastic surgery patients."} +{"text": "Regular transfusion in thalassemia major patients increases life expectancy and improves quality of life, but results in iron overload, which had toxic effects to organs including endocrine glands. The introduction of iron chelation therapy has reduced its toxicity, but complications may still occur. In Indonesia, most of our patients did not receive optimal iron chelation therapy, which might result in higher prevalence of endocrine complications.To find out the endocrinopathies profile in thalassemia major patients in Thalassemia Center Jakarta.This was a retrospective study based on the registry database in Thalassemia Center, Jakarta. We included patients who diagnosed as thalassemia major with complete data on glucose metabolism, thyroid function, pituitary-gonadal axis, bone profile, bone age, and serum ferritin level. We analyzed the association between ferritin level, chelation therapy and type of thalassemia with endocrine profile using chi-square with the significant value of 0.05.Complete data on endocrine profile were found in 67 subjects , 23 (34%) were diagnosed as \u03b2-thalassemia homozygote and the rest as \u03b2-thalassemia/HbE. The mean age was 16.7\u00b15.8 years. Most of the patients (63%) received iron chelation therapy with desferrioxamine followed by deferiprone (20%) and only two patients have not taken any iron chelation therapy yet. Short stature was found in 65% of subjects, while 20% of subjects suffered from delayed puberty, 41% had hypothyroidism, and 29% had retarded bone age. None of them was diagnosed as DM or IGT, but one diagnosed as IFG. Hypocalcemia was found in 27% subjects. Subjects with serum ferritin level \u2265 2,500 ng/mL had increased risk to develop hypothyroidism, hypocalcemia and hyperphosphatemia, even though not statistically significant . Serum ferritin level also not associated with short stature and delayed puberty. Subjects with thalassemia beta-major had increased risk to develop hypothyroidism (p=0.036), but no differences found in the prevalence of short stature, delayed puberty, hypocalcemia, and hypophosphatemia . The frequency of transfusion per year and type of chelation therapy did not influence the endocrine profiles.This study showed that the prevalence of short stature among thalassemia patients is higher in Thalassemia Center Jakarta, while the risk to develop impaired glucose metabolism is lower, despite of poor compliance in iron chelation therapy. The risk to develop hypothyroidism, delayed puberty, and hypoparathyroidism were comparable to other studies."} +{"text": "Adherence to guidelines is associated with improved outcomes of patients with acute coronary syndrome (ACS). Clinical registries developed to assess quality of care at discharge often do not collect the reasons for non-prescription for proven efficacious preventive medication in Continental Europe. In a prospective cohort of patients hospitalized for an ACS, we aimed at measuring the rate of recommended treatment at discharge, using pre-specified quality indicators recommended in cardiologic guidelines and including systematic collection of reasons for non-prescription for preventive medications.In a prospective cohort with 1260 patients hospitalized for ACS, we measured the rate of recommended treatment at discharge in 4 academic centers in Switzerland. Performance measures for medication at discharge were pre-specified according to guidelines, systematically collected for all patients and included in a centralized database.Six hundred and eighty eight patients(54.6%) were discharged with a main diagnosis of STEMI, 491(39%) of NSTEMI and 81(6.4%) of unstable angina. Mean age was 64 years and 21.3% were women. 94.6% were prescribed angiotensin converting enzyme inhibitors/angiotensin II receptor blockers at discharge when only considering raw prescription rates, but increased to 99.5% when including reasons non-prescription. For statins, rates increased from 98% to 98.6% when including reasons for non-prescription and for beta-blockers, from 82% to 93%. For aspirin, rates further increased from 99.4% to 100% and from to 99.8% to 100% for P2Y12 inhibitors.We found a very high adherence to ACS guidelines for drug prescriptions at discharge when including reasons for non-prescription to drug therapy. For beta-blockers, prescription rates were suboptimal, even after taking into account reason for non-prescription. In an era of improving quality of care to achieve 100% prescription rates at discharge unless contra-indicated, pre-specification of reasons for non-prescription for cardiovascular preventive medication permits to identify remaining gaps in quality of care at discharge.NCT01000701ClinicalTrials.gov Cardiovascular disease remains the leading cause of death in adults in the United States (US) and in Europe. Acute coronary syndrome (ACS) is the most frequent cause leading to myocardial infarction, heart failure, and sudden death Systematic monitoring of performance and annual report cards on quality of care, such as the US Healthcare Effectiveness Data and Information Set (HEDIS) We aimed at measuring the rate of recommended treatment at discharge for patients hospitalized for an ACS in 4 university hospitals in Switzerland, using pre-specified quality indicator recommended in cardiologic guidelines in a centralized database, and including systematic collection of reason for non-prescription for preventive medication.The SPUM-ACS research network was established in 2008 and collects data since 2009 on a prospective cohort of patients hospitalized for an ACS in 4 university medical centers in Switzerland , Geneva (GE), Lausanne (LA) and Z\u00fcrich (ZH)) The study protocol was approved by the institutional review board of all participating centers; namely, the Ethics Committee on Clinical Research of the University of Lausanne, the Ethics Committee of the Department for Internal Medicine and Community Medicine of the University Hospital of Geneva, the Cantonal Ethics Committee (KEK) of the Canton of Bern, and the Cantonal Ethics Committee (KEK) of the Canton of Zurich. All patients provided written, informed consent.Clinical data for the patients included in the SPUM-ACS study were collected by trained nurses and medical doctors on standardized, web-based case report forms and stored in a central database . Data abstracted were (1) demographic characteristics such as age, sex, race, education and (2) medical history, such as previous coronary heart disease (CHD), stroke, renal failure requiring dialysis, valvular heart disease, congestive heart failure (CHF) as well as hypercholesterolemia, hypertension and diabetes. We further collected administrative data of the hospital stay and prescription of recommended medication at discharge such as aspirin, P2Y12 inhibitors , beta-blockers, angiotensin converting enzyme inhibitors/angiotensin II receptor blockers (ACEI/ATII) and statins.Performance measures for medication at discharge were pre-specified, systematically collected for all patients and included in the centralized database. They were based on the ACC/AHA 2008 performance measures for adults with STEMI and NSTEMI and included the following pre-specified reasons for non-prescription Frequencies, means with standard deviations (SDs), medians with interquartile ranges (IQR) were used when appropriate, as were chi2 tests, Fisher's exact test, Wilcoxon rank sum test and ANOVA for bivariate analyses. Statistical significance was set at 0.05. All analyses were performed using STATA version 12 .A total of 1260 patients with a main diagnosis of ACS were discharged from 4 university hospitals from September 2009 to October 2010 . 688 patFor patients with a left ventricular ejection fraction (LVEF) of \u226440%, the rate of patients hospitalized for ACS who were prescribed ACEI/ATII at discharge was 94.6%. However, when including reasons non-prescription, 99.6% were prescribed ACEI/ATII or had a documented reason for non-prescription at discharge. The rate of patients hospitalized for ACS who were discharged on statins increased from 98% to 98.6% when including reasons for non-prescription. For beta-blockers, rates increased from 82% to 93% and for aspirin, from 99.4% to 100%. For patients that had had a PCI-stent treatment, rates further increase from 99.8% to 100% for P2Y12 inhibitor or had a documented reason for non-prescription and 99.9% on dual antiplatelet therapy .147 pati33% of smoking participants were offered a specialized smoking cessation intervention in 2 university hospitals .We found high adherence to ACS guidelines for drug prescriptions when including reasons for non-prescription to drug therapy. For beta-blockers, prescription rates were suboptimal, even after taking into account reason for non-prescription. In addition, bradycardia was often reported as a reason for non-prescription despite its absence from recommended reasons for non-prescription in guidelines. The prescription rate of recommended treatments were between 100% and 99% for antiplatelet therapy, statin therapy and ACEI/ATII for patients with LVEF\u226440% after taking into account pre-specified and documented reason for non-prescription, suggesting that the optimal threshold has been achieved for these medications. Despite the proven benefits of dedicated smoking cessation interventions, only 33% of smokers received such an intervention.In countries with systematic performance monitoring such as the US, an improvement of the recommended discharge medication has been reported Comparative data on quality of care at discharge taking into account reasons for non-prescription to medication is limited in Switzerland. The only study which considered reasons for non-prescription published so far was a retrospective chart review by trained medical doctors which selected patients hospitalized for a main diagnosis of acute myocardial infarction (AMI) (NSTEMI and STEMI) in three out of the four academic medical centers included in our study Data from a registry in Switzerland (AMIS Plus) on patients with STEMI suggested that 84.2% were discharged on a P2Y12 inhibitor, 96% on aspirin, 89% on an ACEI/ATII, 91.7% on statins and 79.2% on beta-blockers in 2011, but report on quality data was on a voluntary basis and reasons for non-prescription were not reported ESC and AHA Guidelines recommend the adoption of dedicated smoking cessation program in each hospital These data are derived from university hospitals and might not represent patients hospitalized for an ACS in other hospital in Switzerland. Compared to the AMIS+, a national registry in academic and non-academic centers accounting for 78 out of 106 hospitals treating ACS in Switzerland, the mean age of participants with STEMI was similar in both men and women, but was lower than in other registries in Europe, and rates of revascularization were higher We found a found high adherence to ACS guidelines for drug prescriptions when including reasons for non-prescription to drug therapy. Achieved rates of prescribed medication at discharge were above 99% for Aspirin, P2Y12 inhibitors, ACEI/ATII and statins. Prescription rates for beta-blockers taking into account reasons for non-prescription were lower at 94%. In an era of improving quality of care to achieve 100% prescription rates at discharge unless contra-indicated, pre-specification of reasons for non-prescription for cardiovascular preventive medication within clinical registries permits to identify remaining gaps in quality of care at discharge."} +{"text": "Despite the heavy burden and impact of the polycystic ovary syndrome (PCOS) in reproduction and public health, estimates regarding its prevalence at community levels are limited. We aimed to ascertain prevalence of PCOS in a community based sample using the National Institute of Health (NIH), the Rotterdam consensus (Rott.) and the Androgen Excess Society (AES) criteria.Using the stratified, multistage probability cluster sampling method, 1126 women were randomly selected from among reproductive aged women of different geographic regions of Iran. PCOS were diagnosed using universal assessment of ultrasonographic parameters, hormonal profiles and clinical histories.The mean +/- SD of age of study population was 34.4 +/- 7.6 years. Estimated prevalence of idiopathic hirsutism was 10.9% (95% CI: 8.9-12.9%); 8.3% of women had only oligo/anovulation and 8.0% had only polycystic ovaries. The prevalence of PCOS was 7.1% (95% CI: 5.4-8.8%) using the NIH definition, 11.7% (95% CI: 9.5-13.7%) by AES criteria and 14.6% (95% CI: 12.3-16.9%) using the Rott definition.At community level, widespread screening of Rotterdam criteria will increase the estimated prevalence of PCOS over twofold. Establishing an explicit and contemporaneous method for definition and screening of each PCOS criteria has important investigational implications and increase the comparability of published research. Polycystic ovary syndrome (PCOS) is the most common gynecological endocrinopathy ,2. WomenDespite the heavy burden and impact of the polycystic ovary syndrome (PCOS) in reproduction and public health, estimates regarding its prevalence are limited; considering the controversy regarding its diagnostic criteria and difficulties in conducting prevalence studies at community levels, data on its current prevalence are questionable . The repTo the best of our knowledge there is no population based study that estimates the prevalence and clinical characteristics of PCOS in the Eastern Mediterranean Region. The objective of the present study was to determine the prevalence of PCOS under the NIH, Rott. and the AES criteria, in a well-defined, non-selected population of Iranian reproductive aged women, using universal assessment of ultrasonographic parameters, hormonal profiles and clinical histories.Sample size was calculated based on these parameters: P = 0.085 [A total of 1126 women, aged 18-45 years, were recruited from among reproductive aged women living in urban areas of four randomly selected provinces of different geographic regions i.e. Ghazvin , Kermanshah (East), Golestan (North) and Hormozgan (South). The age and sex distribution of the population of these provinces is representative of national general population based on 2006 national population and housing census of Iran. Menopausal women, those who had undergone hysterectomy or bilateral oophorectomy and pregnant women were excluded (n = 90). To minimize the effect of treatment bias, all other women, regardless of hormonal therapy including insulin sensitizers and oral contraceptive pills were included, but their hormonal and biochemical parameters were not considered for statistical analysis.Pairs of trained staff members of local medical universities/schools (midwives) served as interviewers, and a trained supervisor monitored the process in each district. The interviewers, thoroughly explained the purpose and procedure of the study to subjects and obtained their consent and a checklist questionnaire, based on the inclusion and exclusion criteria, was completed at subjects' homes (n = 1126). Women who met the inclusion criteria (n = 1036) were invited to a referral clinic in each province for a comprehensive interview and physical exam. Ninety seven eligible women who signed the inform consent did not came to the clinics, as a result the response rate of our study was 91%. For those eligible women who referred to clinics (n = 939) a standard questionnaire including demographic and reproductive variables, with emphasis on regularity of menstrual cycle, gynecological history, hyperandrogenic symptoms, family history of irregular menstrual cycle and hirsutism was completed, during face-to-face interviews by trained midwives under supervision of a gynecologist. The hirsutism scores were assessed using the modified Ferriman-Gallwey (mFG) scoring method . Acne wa2).All participants underwent clinical examinations, where body weight, height, waist (WC), hip circumferences (HC) and blood pressure were measured. Body mass index was calculated as weight in kilograms divided by the height in meters squared . All sera were stored at -80\u00b0C until the time of measurements.All of the study subjects were invited for transvaginal (n = 760) or transabdominal (n = 169) ultrasound scans of the ovaries, which were performed using the 3.5-MHz transabdominal and 5-MHz transvaginal transducer by an experienced sonographer in each province and all scans were assessed by a single sonographer. Ultrasound was performed as the same day as the blood samples were collected.Dehydroepiandrosterone sulfate (DHEAS), 17-hydroxyprogesterone (17OH-P), Total testosterone (TT) and Androstendion(A4) were measured by enzyme immunoassay (EIA), . Sex Hormone Binding Globulin (SHBG) was measured by immunoenzymometric assay (IEMA), . All ELISA tests were performed using Sunrise ELISA reader .Luteinizing hormone (LH), Follicle stimulating hormone (FSH), Prolactin (PRL), and Thyroid stimulating hormone (TSH) was measured by immunoradimetric assay (IRMA), using gamma counter Wallac Wizard, Turku, Finland).It has been shown that in women the free androgen index (FAI) has a good correlation with free testosterone measured by physical separation method; therefoWe defined PCOS in our study using the NIH, Rott.3 and AES ANOVU was considered as vaginal bleeding episodes at no less than 35-day intervals ,37. HA wPCO was diagnosed by the presence of 12 or more follicles in each ovary, measuring 2-9 mm in diameter and/or increased ovarian volume (10 cm3) ,39.Idiopathic hirsutism(IH) was defined as hirsutism without ANOVU and/or PCO. BH plusPrimary infertility was defined as the having the history of trying to conceive for at least one year without success despite of regular sexual intercourse, no use of contraception and no previous pregnancy.2 test. Data analysis was performed using the SPSS 15.0 PC package .Continuous variables were checked for normality using the one-sample Kolmogorov-Smirnoff test; they are expressed as mean \u00b1 standard deviation and/or median and interquartile ranges, as appropriate. The categorical variables are expressed as percentages. Distributions between groups are compared using the Kruskal-Wallis test, followed with Mann-Whitney test with Bonferroni correction for pair wise comparison. The categorical variables are compared using the Pearson's \u03c7The ethical review board of the Research Institute for Endocrine Sciences has approved the study proposal and informed consent was obtained from all subjects.The ethical review board of the Research Institute for Endocrine Sciences has approved the study proposal (approved number: 47854 Date: 15/12/2007) and informed consent was obtained from all subjects.A study checklist was completed for 1126 women, aged 18-45 years. Figure Of a total of 929 women, 423(45.5%) subjects were eumenorrheic and did not have HA and or PCO , 205 22.1%) women had only HA and overall, 3.5% of all women had acne. Seventy-seven (8.3%) women had only ANOVU and 74 (8.0%) women had only PCO in ultrasonography; the estimated prevalence of IH was 10.9% (95% CI: 8.9-12.9%) . Of these 37, 8 women would possibly have remained undiagnosed, had we not assessed the serum concentrations of androgens in women without oligo/anovulation.From among 314 (33.8%) women who had HA in our study, 109 had PCOS using Rott. definition using the NIH definition, 11.7% (95% CI: 9.5- 13.7%) by AES criteria and 14.6% (95% CI: 12.3- 16.9%) using the Rott. criteria in our sample of an Iranian population. To the best of our knowledge there is no study in the Eastern Mediterranean Region that estimates the prevalence and clinical characteristics of PCOS among an unselected population.The reported prevalence of PCOS in various geographic regions ranges between 2.2% to 26% ,11-21. I, [The PCOS prevalence depends on the recruitment process of the study population and criteria used for its definition; in the present study considering the Rott. versus NIH criteria increased its prevalence by 2 times, as reported before ,22, [42-, . Further, ,11,16. T, ; e.g. th, . We did , ,25,45. T, . HoweverThe reported prevalence of idiopathic hirsutism varies from 5-29% ,47. In tThe main strength of the present study is its methodology, as it is a community based prevalence study carried out on an ethnically homogenous population and had an appropriate response rate of 91%. The majority of previous studies on PCOS have relied upon a convenience sample of applicants for university employment , blood dOur study does have some limitations; we did not use the menstrual diary to identify menstrual intervals and we did not measure progesterone to identify eumenorrheic women, who had subclinical menstrual dysfunction; our results may therefore be underestimates; for some cases, socio-cultural constraints precluded a vaginal approach for ultrasonography and as a result a specific and sensitive tool was not used for determining the polycystic ovaries. We did not have any information about those few women who refuse to participate in our study, which may also have affected our estimates.This study shows that widespread screening of Rotterdam criteria, at the community level, will increase the estimated prevalence of PCOS over twofold. Establishing a clear and contemporaneous method for screening and recognition of PCOS criteria is essential for improving the comparability and potentially the value of published research.The authors declare that they have no competing interests.FRT contributes in study design, execution, analysis, manuscript drafting and critical discussion.MS contributes in study design, manuscript drafting and critical discussion. MT contributes in study design, laboratory testing and manuscript drafting. FH contributes in analysis, manuscript drafting and critical discussion. FA contributes in study design, execution and manuscript drafting. All authors read and approved the final manuscript."} +{"text": "The EuroCMR registry determined indications, image quality, safety and impact on patient management of clinical routine CMR in a multi-national European setting.Furthermore, interim analyses of two specific protocols evaluating the prognostic potential of CMR in patients with coronary artery disease (CAD) and hypertrophic cardiomyopathy (HCM) are presented.Multi-center registry with consecutive enrollment of patients in 57 centers in 15 countries [27,781 patients were enrolled. The most frequent indications were risk stratification in CAD/ischemia (34.2%), workup of cardiomyopathies (32.2%) and assessment of viability (14.6%). Image quality was diagnostic in 98%. Severe complications were rare (0.03%).In 61.8% CMR findings had an impact on patient management. In 8.7% the final diagnosis changed based on CMR findings , and in HCM without delayed enhancement (2.7% per year).The most important CMR indications in Europe are risk stratification in suspected CAD/ischemia, work-up of cardiomyopathies and assessment of viability. CMR is a safe procedure, has diagnostic image quality in more than 98% of cases, and its results have a strong impact on patient management. Interim analyses underscore the prognostic value of clinical routine CMR in patients with CAD and HCM.Medtronic Inc., Minneapolis MN, USA.Novartis International AG, Basel, Switzerland.Siemens Health Care, Erlangen, Germany."} +{"text": "Blood transfusion is one of the most common transmission pathways of hepatitis C virus (HCV). This paper aims to provide a comprehensive and reliable tabulation of available data on the epidemiological characteristics and risk factors for HCV infection among blood donors in Chinese mainland, so as to help make prevention strategies and guide further research.A systematic review was constructed based on the computerized literature database. Infection rates and 95% confidence intervals (95% CI) were calculated using the approximate normal distribution model. Odds ratios and 95% CI were calculated by fixed or random effects models. Data manipulation and statistical analyses were performed using STATA 10.0 and ArcGIS 9.3 was used for map construction.vs 7.9%).Two hundred and sixty-five studies met our inclusion criteria. The pooled prevalence of HCV infection among blood donors in Chinese mainland was 8.68% (95% CI: 8.01%-9.39%), and the epidemic was severer in North and Central China, especially in Henan and Hebei. While a significant lower rate was found in Yunnan. Notably, before 1998 the pooled prevalence of HCV infection was 12.87% (95%CI: 11.25%-14.56%) among blood donors, but decreased to 1.71% (95%CI: 1.43%-1.99%) after 1998. No significant difference was found in HCV infection rates between male and female blood donors, or among different blood type donors. The prevalence of HCV infection was found to increase with age. During 1994-1995, the prevalence rate reached the highest with a percentage of 15.78% (95%CI: 12.21%-19.75%), and showed a decreasing trend in the following years. A significant difference was found among groups with different blood donation types, Plasma donors had a relatively higher prevalence than whole blood donors of HCV infection (33.95% The prevalence of HCV infection has rapidly decreased since 1998 and kept a low level in recent years, but some provinces showed relatively higher prevalence than the general population. It is urgent to make efficient measures to prevent HCV secondary transmission and control chronic progress, and the key to reduce the HCV incidence among blood donors is to encourage true voluntary blood donors, strictly implement blood donation law, and avoid cross-infection. Chronic infection with hepatitis C virus (HCV) is a major and growing public health problem, which could easily lead to chronic liver disease, cirrhosis and even hepatocellular carcinoma . The preThe rapid global spread of HCV is believed to have occurred primarily because of efficient transmission through blood transfusion and parenteral exposures with contaminated equipment . Blood dA large amount of studies have been done in the last decade on HCV infection and its associated risk factors among blood donors. However, many of them drew incompatible or even contradictory conclusion and the utilization of these statistics are therefore limited. This paper reviews on the available studies so as to provide comprehensive and reliable epidemiological characteristics of HCV infection among blood donors in China, which is speculated to help make prevention strategies and guide further research.Literatures on the HCV prevalence among blood donors in China were acquired through searching PubMed, Embase, China National Knowledge Infrastructure (CNKI), and Wanfang Database from 1990 to 2010. In order to search and include related studies as many as possible, we used combinations of various key words, including hepatitis C virus or HCV, blood donors, and China or Chinese Mainland.All the potentially relevant papers were reviewed independently by two investigators through assessing the eligibility of each article and abstracting data with standardized data-abstraction forms. Disagreements were resolved through discussion. The following information, though some studies did not contain all of them, were extracted from the literatures: first author's name, publication date, study period, province of sample, blood donor recruitment methods , type of blood donation (categorized as plasma donors and whole blood donors), sampling size, the number of subjects infected with HCV, HBV, and HIV or co-infected with two or three of these viruses, gender, age (18-30 years and 31-60 years), and blood type, etc.The inclusion criteria were: (1) studies in the mentioned four databases with full text, despite the language of original text; (2) studies reporting anti-HCV positive rates among blood donors in Chinese Mainland; (3) studies using anti-HCV as a detection index of HCV. The exclusion criteria were: (1) studies without specific sample origins; (2) studies with overlapping time intervals of sample collection from the same origin; (3) studies with a sample size less than 50; (4) studies that failed to present data clearly enough or with obviously paradoxical data.P < 0.10 was considered indicative of statistically significant heterogeneity) and the 2Istatistic . Freeman-Tukey arcsin transform to stabilize variances, and after the meta-analysis, investigators can transform the summary estimate and the CI boundaries back to proportions using sin function, the specific conversion details can be seen in reference [2 test was used to assess the differences among the subgroups. Data manipulation and statistical analyses were undertaken using the Statistical Software Package (STATA) 10.0 , and ArcGIS 9.3 was used for map construction.In our review, random effect models were used for meta-analysis, considering the possibility of significant heterogeneity between studies which was tested with the Q test were identified, but 461 studies were excluded based on the inclusion and exclusion criteria longer than 15 years. The majority of blood donors were men, approximately 57.72% (101319/175540), while women accounted for 42.28% (74221/175540). The occupation of blood donors was widely distributed. Voluntary blood donors mainly came from college students, health care providers, officials, and military from Chinese People's Liberation Army (PLA), while paid blood donors were mostly from peasants, low-wage workers, and unemployed individuals.The blood samples mainly came from blood banks, hospitals, and Centers for Disease Control and Prevention (CDC). The studies of our review involved in the following regions of 29 provinces and cities: Central China , North China , South China, Northwest China, Northeast China , Southwest China , East China .As seen in Table P = 0.54).A total of 79 studies have investigated the association between the prevalence rate of HCV infection and gender among blood donors. HCV infection rate of male blood donors was 9.87% (95%CI: 8.26%-11.63%), while female blood donors had a rate of 9.78% (95%CI: 7.88%-11.89%). There was no significant statistical difference between males and females .There were 30 studies indicating the association between the prevalence rate of HCV infection and age among blood donors. In most studies blood donors were divided into two groups by the age of 30 years old. HCV infection rate of individuals aged 18-30 was 4.91% (95% CI: 3.89%-6.05%), while the prevalence rate of individuals aged 31-60 was 8.99% (95% CI: 6.86%-11.37%), and there was significant statistical difference between two groups .As displayed in Table P < 0.01). The prevalence of HCV infection differed significantly among plasma donors and whole blood donors, which was 7.90% (95%CI: 6.44%-9.51%) and 33.95% (95%CI: 29.80%-38.17%), respectively.As seen in Table As a blood-borne pathogen, HCV virus was frequently detected among paid blood donors in China in the early 1990s . This trOur results showed significant geographic difference of the prevalence of anti-HCV. Compared with other regions, North and Central China had relatively higher anti-HCV positive rates among blood donors, accounting for 13.45% and 14.74%. Meanwhile, the lowest epidemic rate was found in South China with a percentage of 2.88%. Notably, during the period through 1990 and 1998, the prevalence rates were commonly at high level among different regions of China. Especially in Henan and Hebei, the rates even reached 35.04% and 29.26% respectively. After 1998, the general epidemic rates have rapidly decreased, benefited from the government's prohibition of using paid blood donors. However, the reduction of HCV prevalence was not that obvious in North and Central China. Possible reasons for this lack of reduction may include larger population migration, poor economic conditions, higher HCV infection rates in the general populations, or limited sampling.According to the national epidemiological survey of viral hepatitis from 1992 to 1995, HCV infection rate among the general population increased gradually with age, but the prevalence rate had no significant difference between male and female , which iBy and large, the prevalence rate of HCV infection showed a rising trend among blood donors from 1990 to 1995, but significantly decreased from 1996 to 2010 Figure . Our resOur study showed that among blood type A, B, AB, and O donors, the prevalence of HCV infection were 8.18%, 7.58%, 8.15%, and 7.85%, respectively. No significant difference was found between blood types and the epidemic rate of HCV, indicating that blood type is not associated with susceptibility to HCV infection. This finding was consistent with the studies of Lu KQ , Zhou ZDvs 0.97%). Those paid donors who were attracted by high compensation and chose to donate blood in illegal blood stations, also risked a greater risk of cross-contamination. The prevalence rate among plasma donors was significantly higher than among whole blood donors (33.95% vs 7.90%), possibly due to cross-contamination of blood collection equipment by HCV positive plasma donors [Numerous research has showed that paid blood donors are more likely to be infected with HCV than both employer-organized donors or true voluntary donors. Our results confirmed that HCV infection rate in paid blood donors was significantly higher than in voluntary blood donors (15.53% a donors . The eliSeveral limitations in our study need to be addressed. First of all, the studies were observational and blood donors were not randomly chosen. Therefore selection bias and confounding seems inevitable. Secondly, many of our data were extracted from studies written in Chinese, which makes it difficult for non-Chinese reviewers, editors, and readers to trace back to the original materials. Thirdly, our ability to assess study quality was limited by the fact that many studies failed to offer detailed information of selected subjects or valid data on important factors. Besides, as with all meta-analyses, this study has potential limitation of publication bias. Negative trials are sometimes less likely to be published. However, we have confidence on our results since the included literatures were mostly from multi-resources and had large sample size, which should reduce publication bias to some extent.This meta-analysis provides a comprehensive and reliable data on the prevalence and trend of HCV infection among blood donors. The pooled epidemic rate of HCV infection has rapidly decreased after 1998, though some provinces still showed relatively high prevalence. Achievements and lessons in previous work indicated that long-term, comprehensive and effective interventions and preventions are urgently needed. In particular, implementing and enforcing the \"Blood Donation Law\" and promoting HCV screening, diagnosis, and treatment among blood donors are very important measures to control the transmission of HCV infection. In addition, the key to reduce the incidence of HCV infection among blood donors is to encourage true voluntary blood donation, pay more attention to exclude those high-risk persons from the volunteers, and eliminate cross-infection completely when collecting single plasma.The authors declare that they have no competing interests.XFG, QC, XS, JS and RBY were involved in the design, literature searching, assessment of study quality, and drafted the manuscript. JS and RBY revised critically the manuscript. XFG, QC and ZHP performed statistical analysis and critically revised the manuscript. KQD, NL and XC constructed the maps. LW and NW critically revised original study design and the manuscript. All the authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2334/11/88/prepub"} +{"text": "MRSA carriers admitted to surgical wards may pose both clinical and epidemiological problems. We performed a prospective, observational cohort study of patients screened for MRSA on admission to 13 surgical wards in 4 European hospitals, to identify risk factors of previously unknown MRSA carriage and to define a common predictive rule.Multivariate logistic regression models were used to predict probabilities of MRSA colonization on admission based on patient characteristics. A scoring system was defined based on odds ratio results. The c-statistic was calculated to evaluate several models.We enrolled 2901 patients, of whom 111 (3.8%) were unknown MRSA carriers on admission. We identified 7 independent risk factors associated for newly identified MRSA carriage on admission: urinary catheter, nursing home residency, chronic skin disease, wounds, recent hospitalization, diabetes, and age \u226570 years. No risk factor was common to all 4 centres. The overall prediction rule with a lower cut-off had 87% sensitivity and 32% specificity, while values for a higher cut-off were 40% and 89%, respectively. Local predictive rules performed slightly better: 56% sensitivity and 96% specificity for Barcelona. The c-statistic for the model including all centres was 0.64, indicating limited predictive power of the common model.Risk factors for unknown MRSA carriage vary substantially between surgical wards across Europe. A common predictive rule is of limited clinical value.None declared."} +{"text": "Feminization of HIV epidemic, and increasing in HIV infection among house wives is seen in most of the world. Yet, community prevalence data on RTI are sparse in Sri Lanka, and little is known about rates among community women. The objective was to describe the prevalence and risk factors of RTI in women aged 22\u201349years, living in highly populated poor urban settlements of Sri Lanka.A community-based cross-sectional study was conducted among 770 married women living in 116 urban slums of Colombo city, Sri Lanka. Participants were interviewed on sociodemographic data, sexual history, knowledge on STI/HIV, and condom use. Laboratory specimens were collected for thediagnosis of RTI.Prevalence was calculated with corresponding 95% confidence intervals (CI). Analyses of risk factors were carried outseparately for the outcomes of sexually transmitted infections: chlamydia, gonorrhoea, trichomoniasis; and endogenous infections:bacterial vaginosis (BV) and candida.Ninety three percent of women had single life time partner, only 9% was previously screened for STI/HIV. Condom use was mainly decided by the male partner and none of them used condom for prevention of STI/HIV.Endogenous infections were relatively common [BV 8.6% (95% CI: 6.6.-10.6)candida 6.8 % ( 95%CI: 5.0-8.6)], and sexually transmitted infections (STI) were infrequent (1.1%-95% CI: 0.34-1.86).Of the risk factors investigated none of the factors were associated with RTI on multivariate analysis.Married women in this community had a low prevalence of RTI and risky sexual behavoiurs were infrequent. Most of the population burden of RTI is attributedto endogenous infections. However, education and outreach screening facilities are needed to reduce the stigma, embarrassment and lack of knowledge related to STI/HIV in order to facilitate screening and condom use."} +{"text": "Praziquantel has been used as first-line drug for chemotherapy of schistosomiasis since 1984. Besides praziquantel, artemether and artesunate have also been used for the control of this infectious disease since late 1990s. In this article, we conducted a systematic review and meta-analysis to evaluate the antischistosomal efficacy of different medication strategies including monotherapy or combination therapies of these drugs.S. haematobium, S. japonicum or S. mansoni. Protection rates were higher when praziquantel doses were elevated, as concluded from the nRCTs results: the protection rate of praziquantel at 40 mg/kg was 52% (95% CI: 49%-55%), and it increased to 91% (95% CI: 88%-92%) when the dosages were elevated to 60/80/100 mg/kg divided two or more doses. Multiple doses of artemether or artesunate over 1- or 2-week intervals resulted in protection rates of 65% to 97% for preventing schistosomiasis, and increased doses and shorter medication intervals improved their efficacies. Praziquantel and artemisinin derivatives (artemether or artesunate) in combination resulted in a higher protection rate of 84% (95% CI: 64%-91%) than praziquantel monotherapy for treatment. praziquantel and artesunate in combination had a great protection rate of 96% (95% CI: 78%-99%) for preventing schistosomes infection.A number of 52 trials from 38 articles published in peer-reviewed journals before July 2011 were selected for analysis after searching the following literature databases: the Cochrane Library, PubMed/Medline, ISI Web of Science, Chinese Biomedicine Literature Database, and China National Knowledge Infrastructure. Our meta-analyses showed that a dosage of 30-60 mg/kg praziquantel compared with placebo produced a protection rate of about 76% (95% CI: 67%-83%) for treating human schistosomiasis, which varied from 70% to 76% with no significant differences among the subspecies According to the results, praziquantel remains effective in schistosomiasis treatment, and multiple doses would improve its efficacy; meanwhile, praziquantel is also a good drug for preventing acute schistosomiasis morbidity. It's better to use multiple doses of artemether or artesunate with 1- or 2-week intervals for prevention against schistosome infection. Praziquantel and artemether or artesunate in combination perform better in treatment than praziquantel monotherapy, and they are especially suitable for treating the patients with repeated exposure to infected water. Schistosomiasis, an infectious disease caused by parasitic trematodes (schistosomes) dwelling in the host's mesenteric portal system, is a great public health problem in tropical and subtropical regions. The disease causes health and labor loss, and finally a significant reduction in socioeconomic benefits. Approximately 207 million people (more than 97% in Africa) are infected, and 779 million (85% in Africa) are at risk of being infected in 76 endemic countries worldwide, leading to the loss of about 4.5 million disability-adjusted life years (DALYs) -4. Thus Schistosoma japonicum, S. mansoni, S. haematobium, S. mekongi, and S. intercalatum. S. japonicum is transmitted by the amphibian snail Oncomelania and causes intestinal and hepatosplenic schistosomiasis in the People's Republic of China, Philippines, and Indonesia; S. mansoni, transmitted by Biomphalaria snails, causes intestinal and hepatic schistosomiasis in Africa, the Arabian peninsula, and South America; S. haematobium, transmitted by Bulinus snails, causes urinary schistosomiasis in Africa and the Arabian peninsula. S. mekongi and S. intercalatum are only of local importance or schistosomiasis mansoni [70% (95% CI: 25%-88%)]. But, the differences of protection rates among the three species are of no statistical significance with regard to their 95% CIs, and their overall pooled protection rate is 73% (95% CI: 67%-78%); meanwhile, the increasing dosage within 30-60 mg/kg gives no significant improvement in efficacy. Compared to this, 20 mg/kg PZQ seems to be less effective resulting in a protection rate of just 16% (95% CI: -81%-61%). For PZQ's efficacy during nRCTs, dosages of 60-100 mg/kg (i.e. 60/(40 \u00d7 2 doses)/(30 \u00d7 2 doses + 40) mg/kg) provide better efficacies than a single dose at 40 mg/kg, their protection rates were 91% (95% CI: 88%-92%) vs. 52% (95% CI: 49%-55%), respectively. In addition, several doses of PZQ at 40 mg/kg of both two RCTs and one nRCT produced great effects on preventing schistosomiasis morbidity, their protection rates were 98% (95% CI: 93%-99%) and 100%, respectively. Multiple (6-7) doses of 6 mg/kg AM applied in 1-month intervals resulted in protection rates of 24% (95% CI: 8%-37%) with respect to preventing S. japonicum infection. The P value of Egger's test was 0.01, which indicated that a publication bias may exist. In addition, sensitivity analyses indicated there were no significant changes in the results of RRs' estimation and their 95% CIs between the restricted data sets and their combined overall values in each subgroup when the PZQ dosage decreased to a single dose of 20 mg/kg. Similarly, 60-100 mg/kg PZQ during nRCTs revealed protection rates of 91% (95% CI: 88%-92%). The protective effect declined significantly to 52% (95% CI: 49%-55%) when the dosage was reduced to a single dose of 40 mg/kg. Thus it can be concluded that multiple doses of 40/60 mg/kg PZQ provide an enhanced efficacy in treating schistosomiasis compared to a single dose. Additionally, when PZQ was applied during the 3rd-4th week after the first exposure of a patient to infected water harboring schistosome cercariae, is turned out to be also effective in preventing acute schistosomiasis morbidity with a protections rate of 98% (95% CI: 93%-99%) in two RCTs, and 100% of one nRCT ) than PZQ alone (73% [95% CI: 67%-78%]), respectively. Thus PZQ-ARTs combinations are useful for schistosomiasis patients repeatedly exposed to infected water. It's well known that ARTs are used in large-scale programmes for malaria treatment (mostly epidemic in Africa). However, ARTs-resistant malarial parasites have been identified and confirmed in some areas -108. ThuOne limitation of this meta-analysis is that the diagnostic approaches used to determine parasites were different among the included trials. There were differences between Kato-Katz technique and urine filtration, the number of specimens, and the number of examinations between trials. The former cannot be changed because it is determined by the two kinds of different clinical pathogenesis. The latter can be improved through using a standardized, quality-controlled diagnostic criterion within and between trials. As discussed by Bergquist et al. and DansP values <0.05, which indicates that the studies included in these three subgroups were heterogeneous. We presume that some factors such as e.g. regional variances, participants' differences, or drug dosage differences among these studies, may have contributed to this heterogeneity [S. haematobium, S. japonicum and S. mansoni were studied have ogeneity . RCTs ar Figures , 3 and 5P value of Egger's publication bias test was 0.01, implying the existence of publication bias.Publication bias is usually cited as a reason for the lack of validity in meta-analyses . PublicaS. mansoni. Thus our meta-analysis represents a good complementary data set adding to the results obtained in these studies.Additionally, we had found two Cochrane reviews discussing drugs for human schistosomiasis treatment ,114, oneFacing the fact that an integrated strategy, which emphasizes health education, access to clean water and adequate sanitation, mechanization of agriculture, and fencing of water buffaloes (mainly for schistosomiasis japonica endemic areas), along with mass chemotherapy for both human and livestock, have been suggested to be carried out in parallel to control the infection sources and to stop schistosome transmission -118, we Sh: Schistosoma haematobium; Sj: Schistosoma japonicum; T: treatment; yr: years old; 95% CI(s): 95 percent confidence interval(s).AM: artemether; ARTs: artemisinin derivatives; AS: artesunate; CBM: Chinese Biomedicine Literature Database; CNKI: China National Knowledge Infrastructure; DALYs: disability-adjusted life years; nRCT(s): non-randomized controlled trial(s); PZQ: praziquantel; P: prevention; RCT(s): randomized controlled trial(s); RR(s): relative risk(s); The authors declare that they have no competing interests.RL, HFD and MSJ designed this work. RL and YG searched databases, selected studies and abstracted information. RL entered and analyzed data, drafted the manuscript. RL, HFD and YG contributed to the interpretation of results. RL, HFD, MSJ and QPZ contributed to the refinement of the manuscript. RL, HFD and MSJ revised the manuscript. All of authors have read and approved the final version of the manuscript.Table S1 Summary of the characteristics of the included trials in our meta-analyses evaluating antischistosomal drugs , used alone or in combination, for human schistosomiasis treatment or prevention. This table describes the extracted characteristics of the included studies: Author, Year; Test sites; Time; Participants; Species; Interventions; Diagnostic approach; Follow-up time; Treated (n/N); Controlled (n/N); Relative Risk; (95%CI); Design Type; Usage.Click here for file"} +{"text": "The advent of the Global Positioning System (GPS) has transformed our ability to track livestock on rangelands. However, GPS data use would be greatly enhanced if we could also infer the activity timeline of an animal. We tested how well animal activity could be inferred from data provided by Lotek GPS collars, alone or in conjunction with IceRobotics IceTag pedometers. The collars provide motion and head position data, as well as location. The pedometers count steps, measure activity levels, and differentiate between standing and lying positions. We gathered synchronized data at 5-min resolution, from GPS collars, pedometers, and human observers, for free-grazing cattle (n = 9) at the Hatal Research Station in northern Israel. Equations for inferring activity during 5-min intervals , classified as Graze, Rest (or Lie and Stand separately), and Travel were derived by discriminant and partition (classification tree) analysis of data from each device separately and from both together. When activity was classified as Graze, Rest and Travel, the lowest overall misclassification rate (10%) was obtained when data from both devices together were subjected to partition analysis; separate misclassification rates were 8, 12, and 3% for Graze, Rest and Travel, respectively. When Rest was subdivided into Lie and Stand, the lowest overall misclassification rate (10%) was again obtained when data from both devices together were subjected to partition analysis; misclassification rates were 6, 1, 26, and 17% for Graze, Lie, Stand, and Travel, respectively. The primary problem was confusion between Rest (or Stand) and Graze. Overall, the combination of Lotek GPS collars with IceRobotics IceTag pedometers was found superior to either device alone in inferring animal activity. This Historically it has been very difficult to study the spatial component of landscape use by animals, but application of the Global Positioning System (GPS) to the study of grazing systems has led to a quantum leap in our ability to track many species of livestock and wildlife . The GPSThe inference of behavior from data provided by sensors mounted in the head region, such as a tri-axial accelerometer for goats and a piWe hypothesized that leg movements might correspond to activity more directly and mechanistically than head and neck movements. Combining data from a pedometer with those from a GPS collar might, therefore, enable reduction in the rates of misclassification of animal activity. This would, however, require a pedometer of exceptional temporal resolution. In recent years, such a pedometer has become available in the form of the IceTag . This device provides a step count and a time allocation between three states for any time resolution down to 1 s. The distinction between lying and standing is an added benefit in the context of studies that integrate the spatial dimension of landscape use with calculations of energy expenditure ,23.The purpose of the present study was to examine whether the addition of this sophisticated pedometer would enable us to reduce the rates of misclassification of animal activity. The overall approach was to gather synchronized GPS collar, pedometer and observer data for free-grazing cattle, to derive calibration equations for prediction of activity on the basis of data from each device separately and from both together, and to compare the prediction accuracy of these equations.2.2.1.Quercus calliprinos), interspersed with batha vegetation comprising shrubs and dwarf shrubs, mainly Calicotome villosa and Sarcopoterium spinosum IceTagctiveA \u2265 3% and IceTagctiveA < 37% and IceTagtepsS < 2.4 and IceTagtandingS < 89%: Rest (97% probability)IceTagctiveA \u2265 3% and IceTagctiveA < 37% and IceTagtepsS < 2.4 and IceTagtandingS \u2265 89%: Graze (57% probability)IceTagctiveA \u2265 3% and IceTagctiveA < 37% and IceTagtepsS \u2265 2.4: Graze (85% probability)IAfter five splits the overall misclassification rate was 15%, and the misclassification rates separated for Graze, Rest, and Travel were 12, 18, and 3%, respectively . The par3.6.P < 0.001). Misclassification rates separated according to activity were fairly evenly balanced, at 11, 11, and 6% for Graze, Rest, and Travel, respectively. Partition analysis with two splits yielded an overall misclassification rate of 17% and separate rates of 11, 22, and 3% for Graze, Rest, and Travel, respectively (ceTagctiveA < 3%: Rest (94% probability)IceTagctiveA \u2265 3% and LotekistanceD \u2265 96 m: Travel (91% probability)IceTagctiveA \u2265 3% and LotekistanceD < 96 m: Graze (68% probability)IInference of GRT activity by discriminant analysis of both Lotek collar and IceRobotics pedometer outputs yielded an overall misclassification rate of 11% resulted in an overall misclassification rate of 10% and separate rates of 8, 12, and 3% for Graze, Rest, and Travel, respectively (ceTagctiveA < 3% and LotekeftRightL < 52: Rest (99% probability)IceTagctiveA < 3% and LotekeftRightL > 52 and LotekeadDownH \u2265 85%: Rest (96% probability)IceTagctiveA < 3% and LotekeftRightL > 52 and LotekeadDownH < 85%: Graze (82% probability)IceTagctiveA \u2265 3% and LotekistanceD \u2265 96 m: Travel (91% probability)IceTagctiveA \u2265 3% and LotekistanceD < 96 m and LotekeftRightL < 48 and IceTagctiveA < 7%: Rest (81% probability)IceTagctiveA \u2265 3% and LotekistanceD < 96 m and LotekeftRightL < 48 and IceTagctiveA \u2265 7%: Graze (66% probability)IceTagctiveA \u2265 3% and LotekistanceD < 96 m and IceTagctiveA \u2265 48%: Graze (84% probability)IIncreasing the number of splits to six (involving Iectively . The par3.7.P < 0.001). The misclassification rate of Graze as Lie was relatively low (9%), but that as Stand was relatively high (22%). Lie and Stand were frequently confused: 26% of Lie intervals were misclassified as Stand, and 41% of Stand intervals were misclassified as Lie. The overall misclassification rate for Stand reached 54%. Partition analysis failed to classify any intervals as Stand within the first four splits. In contrast, the misclassification rates for Graze were 15% (split 1) and 16% (splits 2\u20134), those for Lie were 11% (splits 1 and 2) and 12% (splits 3 and 4), and those for Travel were 100% (split 1), 32% (split 2), and 3% (splits 3 and 4). By the sixth split, the misclassification rate for Stand fell to 56%, but this was at the expense of a large increase in the misclassification rate for Lie (from 12% to 35%). At the sixth split, the overall misclassification rate was 32%, and those for Graze and Travel were 16 and 3%, respectively (otekeftRightL < 39 and LotekistanceD \u2265 96 m: Travel (81% probability)LotekeftRightL < 39 and LotekistanceD < 96 m and LotekorAftF < 9 and LotekeadDownH < 1%: Stand (80% probability)LotekeftRightL < 39 and LotekistanceD < 96 m and LotekorAftF < 9 and LotekeadDownH \u2265 1%: Lie (74% probability)LotekeftRightL < 39 and LotekistanceD < 96 m and LotekorAftF \u2265 9: Stand (44% probability)LotekeftRightL \u2265 39 and LotekistanceD \u2265 100 m: Travel (91% probability)LotekeftRightL \u2265 39 and LotekistanceD < 100 m and LotekeadDownH \u2265 77%: Graze (39% probability)LotekeftRightL \u2265 39 and LotekistanceD < 100 m and LotekeadDownH < 77%: Graze (90% probability)LThe inference of GLST activity by discriminant analysis of Lotek collar outputs yielded an overall misclassification rate of 36% (ectively . The par3.8.P < 0.001). Misclassification rates according to activity were 45, 1, 19, and 7% for Graze, Lie, Stand, and Travel, respectively. The percentage of Stand intervals that were misclassified as Graze was 16%, but 43% of Graze intervals were misclassified as Stand. After three splits partition analysis yielded an overall misclassification rate of 19%, and rates separated according to activity were 37, 1, 20, and 17% for Graze, Lie, Stand, and Travel, respectively (ceTagtandingS < 55% and IceTagctiveA < 48%: Lie (97% probability)IceTagtandingS < 55% and IceTagctiveA \u2265 48%: Travel (97% probability)IceTagtandingS \u2265 55% and IceTagctiveA < 6%: Stand (63% probability)IceTagtandingS \u2265 55% and IceTagctiveA \u2265 48%: Graze (80% probability)IInference of GLST activity from discriminant analysis of IceRobotics pedometer outputs yielded an overall misclassification rate of 21% (ectively . The parceTagtandingS < 55% and IceTagctiveA < 48%: Lie (97% probability)IceTagtandingS < 55% and IceTagctiveA \u2265 48%: Travel (97% probability)IceTagtandingS \u2265 55% and IceTagctiveA < 6% and IceTagtandingS \u2265 97%: Stand (81% probability) [reduces to IceTagtandingS \u2265 97% and IceTagctiveA < 6%]IceTagtandingS \u2265 55% and IceTagctiveA < 6% and IceTagtandingS < 97%: Graze (54% probability)IceTagtandingS \u2265 55% and IceTagctiveA \u2265 6%: Graze (80% probability)IAt the fourth split, the overall misclassification rate went down to 17% and ther3.9.Inference of GLST activity by discriminant analysis of both Lotek collar and IceRobotics pedometer outputs yielded an overall misclassification rate of 14% (ceTagtandingS < 55% and LotekistanceD < 96 m: Lie (97% probability)IceTagtandingS < 55% and LotekistanceD \u2265 96 m: Travel (92% probability)IceTagtandingS \u2265 55% and LotekeftRightL < 41: Stand (77% probability)IceTagtandingS \u2265 55% and LotekeftRightL \u2265 41: Graze (79% probability)IPartition analysis with three splits yielded an overall misclassification rate of 15% and separated rates of 16, 1, 30, and 17% for Graze, Lie, Stand, and Travel, respectively . MisclasceTagtandingS, LotekistanceD, LotekeftRightL, LotekeadDownH and IceTagctiveA) resulted in an overall misclassification rate of 10%, and separated rates of 6, 1, 26, and 17% for Graze, Lie, Stand, and Travel, respectively (ceTagtandingS < 55% and LotekistanceD < 96 m: Lie (97% probability)IceTagtandingS < 55% and LotekistanceD \u2265 96 m: Travel (92% probability)IceTagtandingS \u2265 55% and LotekeftRightL < 41 and IceTagctiveA < 6%: Stand (92% probability)IceTagtandingS \u2265 55% and LotekeftRightL < 41 and IceTagctiveA \u2265 6%: Graze (60% probability)IceTagtandingS \u2265 55% and LotekeftRightL \u2265 41 and LotekeadDownH \u2265 84% and IceTagctiveA < 6%: Stand (84% probability)IceTagtandingS \u2265 55% and LotekeftRightL \u2265 41 and LotekeadDownH \u2265 84% and IceTagctiveA \u2265 6%: Graze (74% probability)IceTagtandingS \u2265 55% and LotekeftRightL \u2265 41 and LotekeadDownH < 84%: Graze (89% probability)IIncreasing the number of splits to six of 30%. Likewise, the misclassification rates for GRT activity based on each of LotekorAftF, LotekeadDownH and LotekistanceD alone would be 38, 39, and 31%, respectively. We would, therefore, advise strongly against inferring GRT activity from any single GPS collar output, even though the means of that output may differ significantly according to activity. The misclassification rate fell to approximately 16% when all collar outputs were included in the analysis, although partition analysis could achieve a misclassification rate of 17% on the basis of only two variables: LotekeftRightL and LotekistanceD.Examined individually, each of the four Lotek GPS collar outputs responded clearly to GRT and GLST activities, and the effect of activity was highly significant in the non-parametric analysis of each variable. However, for our purposes, although statistical significance may be a necessary condition, it is far from being a sufficient one. For GRT activity, LFor GLST activity, the case against inference on the basis of just one GPS collar output is even stronger: discriminant analysis would yield a misclassification rate of at least 50%. In the present study, even when all collar outputs were included in the analysis, the separation between Lie and Stand, by either discriminant or partition analysis, was highly problematic. In discriminant analysis the misclassification rate of Graze was greater for GLST than for GRT activity. Partition analysis avoided this problem and gave somewhat better results overall for the inference of GLST activity on the basis of GPS collar outputs. Nevertheless, GPS collar outputs were not found to be an effective basis for inference of GLST activity.ceTagtandingS and IceTagyingL would yield misclassification rates of 63 and 58%, respectively; in contrast, each of IceTagctiveA and IceTagtepsS (which are highly correlated) would yield a relatively low misclassification rate of 18%, although the misclassification rate for Graze would be greater than 40%. If partition analysis were used, IceTagctiveA alone (two splits) would yield a similar overall misclassification rate, but a much more balanced error profile across the three activities. A quite highly branched partition model with five splits, involving IceTagctiveA, IceTagtandingS and IceTagtepsS, was required to reduce the misclassification rate by just a few percentage points. The main problem with both the two-split and five-split models was misclassification of Rest as Graze.As was found for the GPS collar variables, each of the four IceRobotics IceTag pedometer outputs responded clearly to GRT and GLST activities, and the effect of activity was highly significant in the non-parametric analysis of each output. However, when considered alone, two of the outputs were very poor predictors of GRT activity, whereas the other two performed much better: IceTagtandingS, 33% for IceTagctiveA, 59% for IceTagyingL, and 36% for IceTagtepsS. Inclusion of all the outputs in the analysis yielded a substantial reduction in the misclassification rate, though each analytical method had a major weakness. Discriminant analysis misclassified 43% of Graze events as Stand, and although this problem was largely avoided by use of the four-split partition model, in this model 45% of Stand events were misclassified as Graze. Overall, pedometer outputs proved a more effective basis than GPS collar outputs for inference of GLST activity, but significant errors remained.For GLST activity, the misclassification rates obtained by discriminant analysis of the four respective pedometer outputs separately were 27% for IceTagctiveA.The finding that GRT activity could be inferred from pedometer data alone might prove useful, even when GPS data are available. Lotek collars are often operated at GPS-fix intervals much longer than 5 min, in which case a single activity cannot be assumed to continue throughout the entire interval. This requires a different analytic approach was achieved by means of a six-split partition model. However, Graze and Rest were confused in this model, with a greater proportion of Rest events misclassified as Graze than The level of generality is an important issue with regard to any calibration study. Some indication of this can be gleaned by comparison of the present results with those of an earlier study , in whict-test assuming equal variances were not significant (P > 0.2). The median distances travelled during 5-min Graze events were 13 m (previous study) and 11 m (present study), and these values did not differ significantly . However, differences in motion sensor responsiveness between the two models of Lotek GPS collar used cannot be ruled out.It is possible that the presence of woody vegetation at the Hatal site (present study) may have made it more difficult to distinguish between Graze and Rest, because consumption from the shrub and tree layers slows down animal movement and may also lead to a less distinct Graze signature in terms of the motion sensor counts. We compared the rates of animal movement in the two studies, according to the distance travelled during 5-min Graze events. Means in the previous and the present studies were 24 m (n = 95) and 20 m (n = 489), respectively. Results of tests for unequal variances of the means were not significant, and those of the The possible role of GPS error in the confusion between Graze and Rest was discussed in the previous study. The test that was performed then, with stationary collars, yielded relatively short distances between successive GPS location readings, even without differential correction: the 97.5 percentile, median and mean values were 9.3, 2.1 and 2.7 m, respectively. However, a similar test conducted in September 2010 with collars of the same model as that used in the present study yielded larger values: the 97.5 percentile, median and mean values were 33.6, 6.5 and 9.4 m, respectively . In another test, with a stationary Lotek GPS collar , followiThe equations generated by discriminant and partition analyses are dependent on the relative proportions of the various activities in the dataset. This raises the question as to whether, ideally, this balance in the calibration dataset should reflect the balance obtained in the field, as was the case, approximately, in the present study, or whether each activity should be covered by the same number of observations. We do not have a rigorous proof as to which is preferable. In a preliminary analysis, the GRT activity with the fewest records was used to determine the number of records that should be sampled randomly from each of the other two activity types. Partition analysis of GRT activity, based on GPS collar and pedometer outputs was then applied to the resulting dataset (n = 264). By the third split in the classification tree, the same variables were selected as in the original analysis of the complete dataset, and almost identical split thresholds were used, although the order of splitting differed. Thereafter, the two analyses diverged, but this may have been influenced by minimum cell count constraints. A more thorough investigation of this issue is warranted, but it would require a much larger dataset. This analysis does seem to indicate that more parsimonious models are more robust.ceTagyingL). Travel can be separated well from other activities on the basis of LotekistanceD or IceTagtepsS, but some threshold needs to be assumed. Given that calibration equations are required, the question is how widely they can be applied. The list of factors that could conceivably influence them is long, and only a well-coordinated multi-site study can shed light on this important issue. Similarly, questions related to within- and between-animal variability and sample size await larger-scale studies.In more general terms, how easy is it to infer activity from the sensors deployed in this study? It does not seem possible to classify activity well from direct inspection of the data; calibration equations are required. The only activity that can be identified with complete confidence directly from the data is lying (from I5.In general, partition analysis performed better than discriminant analysis for inferring animal activity from outputs provided by Lotek GPS collars and/or IceRobotics IceTag pedometers. For classification of GRT activity, if partition models with only two or three splits are sought, either device alone can yield a misclassification rate of approximately 18%, and no benefit is accrued from their combined use. However, a misclassification rate of 10% can be achieved by their combined use if a more highly branched classification tree is acceptable. The primary problem in GRT classification is confusion between Graze and Rest, and if it is required to divide Rest into Lie and Stand, the use of GPS collars alone is inadequate. However, the pedometer enabled Lie activity to be inferred with high accuracy. The combination of GPS collars and pedometers yielded a misclassification rate of 10% in a six-split partition model, and misclassification of both Stand and Travel as Graze was the main source of error. If short-interval GPS fixes are not feasible, the IceRobotics IceTag pedometer alone can yield a reasonable estimation of the activity timeline of cattle on rangeland."} +{"text": "The objective of this study was to investigate immediate postoperative lung function changes after resection for primary lung cancer in patients without and with postoperative complications.Sixty patients undergoing surgical resection for non-small cell lung cancer were included in a prospective, single institution study. Sex, age, stage and type of lung cancer, comorbidities, preoperative values of lung function tests including DLCO and exercise test were analyzed. Postoperative complications were classified as surgical, respiratory and cardiovascular. FEV1 and FVC were measured on postoperative days 1, 3 and 7, regardless of postoperative complications.Study encompassed 60 patients . Mild degree of COPD was noted in 20% and moderate in 35% of patients, according to GOLD classification. All postoperative adverse events, not only major complications were recorded. Respiratory complications occurred in 20%, surgical in 41.7% and cardiac in 19% of patients. Measured postoperative values of FVC% and FEV1% on days 1, 3 and 7 after surgery shoved continuous improvement, with significant difference between the days of measurement, specially days 3 and 7. Values recorded on day 7 did not differ from ppo FEV1%. No difference in early postoperative trend of lung function recovery was noted between patients without and with postoperative complications. However, patients that developed respiratory complications showed significantly lower values of FEV1 and FVC on postoperative day 1.Early lung function after resection for lung cancer shows significant improvement despite of postoperative complications."} +{"text": "Staphylococcus aureus(MRSA) colonization status among newly admitted newborn in neonatal intensive care unit and risk factors for MRSA colonization.To determine the prevalence of methicillin-resistant All patients admitted to the neonatal intensive care unit(NICU) at a university hospital in Seoul, Korea from January 1 to December 31, 2008. Data were collected by electronic medical record and retrospectively reviewed. Prevalence was assessed and risk factors for MRSA colonization were compared.A total of 599 patients were admitted to the NICU during the study period. Surveillance culture for MRSA was done within 48 hours after admission. MRSA was isolated from 139(23.3%) of the patients. Among the 361 inborns, Fifty-three percents of the patients were admitted via emergency room, and then 36.1% via outpatient department, 19.3% via nursery room, 0.8% via operating room, and 0% via delivery room. Among the 238 outborns, the prevalence of MRSA was vary from 0% to 80% based on the birth place. In multivariate analysis comparing MRSA colonized patients, over 2,500g of admission weight, over 1day of admission age, admission via outpatient department and admission via other hospital were independent predictors of MRSA colonization.These results showed that MRSA colonization is typically considered to be associated with the neonatal care process than the neonatal status. National support and community participation is necessary to prevent MRSA transmission more effectively.None declared."} +{"text": "We analyzed HIV testing rates, prevalence of undiagnosed HIV, and predictors of testing in the Kenya AIDS Indicator Survey (KAIS) 2007.KAIS was a nationally representative sero-survey that included demographic and behavioral indicators and testing for HIV, HSV-2, syphilis, and CD4 cell counts in the population aged 15\u201364 years. We used gender-specific multivariable regression models to identify factors independently associated with HIV testing in sexually active persons.Of 19,840 eligible persons, 80% consented to interviews and blood specimen collection. National HIV prevalence was 7.1% (95% CI 6.5\u20137.7). Among ever sexually active persons, 27.4% (95% CI 25.6\u201329.2) of men and 44.2% (95% CI 42.5\u201346.0) of women reported previous HIV testing. Among HIV-infected persons, 83.6% (95% CI 76.2\u201391.0) were unaware of their HIV infection. Among sexually active women aged 15\u201349 years, 48.7% (95% CI 46.8\u201350.6) had their last HIV test during antenatal care (ANC). In multivariable analyses, the adjusted odds ratio (AOR) for ever HIV testing in women \u226535 versus 15\u201319 years was 0.2 . Other independent associations with ever HIV testing included urban residence , highest wealth index versus the four lower quintiles combined , and an increasing testing trend with higher levels of education. Missed opportunities for testing were identified during general or pregnancy-specific contacts with health facilities; 89% of adults said they would participate in home-based HIV testing.The vast majority of HIV-infected persons in Kenya are unaware of their HIV status, posing a major barrier to HIV prevention, care and treatment efforts. New approaches to HIV testing provision and education, including home-based testing, may increase coverage. Targeted interventions should involve sexually active men, sexually active women without access to ANC, and rural and disadvantaged populations. HIV testing and counseling (HTC) is the cornerstone of HIV prevention, care, and treatment. Knowledge of HIV status among HIV-infected persons is associated with a 60% reduction in transmission risk behavior In spite of HTC's central role in HIV programming, HIV testing coverage remains low in sub-Saharan Africa. Testing coverage documented in population-based surveys in sub-Saharan Africa 2007\u20132008 ranged from 3.2% in women and 4.9% in men in Liberia to 56.7% in women and 43.0% in men in South Africa Kenya has scaled up HTC capacity significantly since 2003, including traditional voluntary counseling and testing sites, mobile, provider-initiated KAIS was a nationally representative, cross-sectional, household sero-survey of persons aged 15 to 64 years conducted from August to December 2007. The survey used a two-stage, stratified sampling design to provide national estimates and separate estimates for urban and rural areas and for each of the eight provinces. The design was comparable with the design of the 2003 Kenya Demographic and Health Survey (DHS), which also included basic questions on HTC. The first stage involved selecting clusters from the same sampling frame that was used for the 2003 DHS, based on the 1999 national census, and the second stage involved the selection of households per cluster with equal probability of selection in the rural-urban strata within each district. Fieldwork was conducted by 29 field teams, each consisting of six data collectors (four interviewers and two laboratory technicians), one supervisor and one driver. Interviewers and laboratory technicians were provided by the Kenya National Bureau of Statistics and the National AIDS/STI Control Programme, respectively. In addition to questionnaires in Kiswahili and English, teams administered questionnaires in local languages where necessary to accommodate respondents that were not conversant in vernacular languages. All questionnaires were back translated into English. Survey personnel participated in intensive two-week training in KAIS procedures, including finger stick, specimen collection for HIV testing and HIV education and counseling. All participants had the option to receive their results individually or as a couple at a nearby referral site Treponema pallidum particle agglutination (TPPA) assay was used as a screening test and rapid plasma reagin (RPR) for confirmation.Blood specimens obtained in households were tested at Kenya's national reference laboratory in Nairobi for HIV, HSV-2, syphilis and CD4 count for HIV-infected persons. HIV testing was performed in a serial testing algorithm by using Vironostika HIV Uni-Form II antigen/antibody and Murex HIV antigen/antibody tests for HIV screening and confirmation, respectively. HIV discrepant specimens were retested with the two assays and polymerase chain reaction (PCR) (Roche HIV DNA v 1.5) tests were conducted on all samples with two sets of discrepant results. For quality control, all positive specimens and a random sample of 5% of negative specimens were retested in a different laboratory using the same testing algorithm. The Kalon HSV Type 2- specific IgG EIA was used for HSV-2 testing. This was a recombinant type-2 antigen (gG2) modified to eliminate reactivity arising from HSV type 1 infection and at the same time retaining the natural antigenic characteristics of HSV-2. For syphilis testing, the Correct knowledge of HIV status was defined as reported HIV status validated by laboratory testing during the survey. Ever testing was defined as self-report of one or more HIV tests prior to the survey. We developed gender-specific models to assess factors associated with ever having been tested for HIV in ever sexually active persons. Predictor variables included socio-demographic characteristics, pregnancy history and status, HSV-2 infection, syphilis infection, perception of HIV risk, lifetime sexual partners, condom use at last sex, number of outpatient visits in the last 12 months, number of hospitalizations in the last 12 months , and male circumcision status. We reported predictors for men and women separately because of differences in testing rates. Wealth was defined using a DHS standard composite index of the living standard of a household, calculated using data on a household's ownership of selected assets, materials used for housing construction, water access and sanitation facilities We performed all analyses in SAS version 9.2 using the sample survey procedures to take into account the sampling structure , and with appropriate domain analysis for each subpopulation of interest. Statistical significance in cross-tabulations was assessed based on Rao-Scott chi-square p-values. The p-value for the difference between CD4 cell counts was calculated using linear regression (PROC SURVEYREG) on log-transformed CD4 counts. Using multivariable logistic regression (PROC SURVEYLOGISTIC), we calculated adjusted odds ratios (AOR) and 95% confidence intervals (CI) to identify variables independently associated with the outcome. Analyses accounted for the stratified cluster design of the survey. Each response was weighted to account for its sampling probability and to adjust for non-response rates. Variables with a p-value <0.1 in bivariate analyses were selected for final multivariable models and backwards elimination was used if they did not remain significant at a 0.05 p-value level. The category with the strongest association was defined as the maximum negative or positive difference from the reference 1. Two-way interactions between variables were considered. Population estimates were calculated based on the 2007 projected Kenyan population Oral informed consent was obtained from all eligible persons in a three-stage-process: 1) to be interviewed, 2) to have a blood specimen drawn, and 3) to have their blood stored without identifiers for possible future tests. For each of the components, the interviewer signed the consent form to indicate whether or not consent was given. For participants aged 15\u201317 years, parental or guardian permission was obtained. Eligible persons aged 15\u201317 years were then asked for their assent. Mature minors, operationalized in KAIS as persons who were married, pregnant or parents, or who were guardians of children aged 0\u20134 years whose mother died or was HIV infected, did not need parental consent A total of 15,853 of 19,840 eligible persons aged 15\u201364 years participated in interviews and blood specimen collection, representing a response rate of 80% . Among those, 1104 or 7.1% (95% CI 6.5\u20137.7) were HIV infected . HIV prevalence ranged between 0.8% (95% CI 0\u20131.6) in North-Eastern to 8.8% (95% CI 6.3\u201311.4) in Nairobi and 14.9% (95% CI 13.1\u201316.6) in Nyanza province. Among participants in interviews and blood draws, 87.8% (95% CI 87.1\u201388.5) reported that they had ever been sexually active . Among those ever sexually active, 27.4% (95% CI 25.6\u201329.2) of men and 44.2% (95% CI 42.5\u201346.0) of women reported that they had ever tested for HIV. The gap between Kenya's national testing target and testing coverage documented in KAIS in 2007 was an estimated 4,366,000 men aged 15\u201364 years old and 3,295,000 women.There were no significant differences between HIV-infected and HIV-uninfected persons regarding HIV testing history. Highest ever HIV testing rates in men were found for age 30\u201334 years, urban residence, Nairobi province, secondary or higher education, highest wealth index quintile and contact with health facilities. Women who had had an HIV test had similar characteristics as men, but had a highest testing rate at age 20\u201324 . HIV tesAmong ever sexually active adults aged 15\u201364 years who had never been tested for HIV, 39.6% (95% CI 37.2\u201341.9) of women and 48.9% (95% CI 46.7\u201351.1) of men reported they had not been tested because they perceived themselves to be at low risk for HIV infection; 26.7% (95% CI 24.2\u201329.2) of women and 20.7% (95% CI 18.8\u201322.5) of men provided no reason for never having been tested. Less than 10% of ever sexually active respondents reported lack of access to testing, fear of others knowing about the test result, not knowing where to go to get tested or lack of access to treatment as reasons for not getting tested.Among all laboratory-confirmed HIV-infected persons in KAIS 2007, 56.0% (95% CI 51.9\u201360.0) had never been tested, 27.6% (95% CI 24.3\u201331.0) of HIV-infected persons reported not to be infected based on their last HIV test, and 16.4% (95% CI 13.2\u201319.6) reported being infected based on the results of their last HIV test. HIV-infected women were significantly more likely than men to self-report negative based on their last test result. In total, 83.6% (95% CI 76.2\u201391.0) of HIV-infected adults aged 15\u201364 years were unaware of their HIV infection . Based oAmong laboratory-confirmed HIV-infected persons who reported that they had received a negative HIV test before KAIS 2007, 56.8% (95% CI 50.3\u201363.3) reported that their last HIV test was performed over 12 months prior to the survey, suggesting that these persons may have been exposed and infected since their last negative test. In addition, the median CD4 cell count was significantly higher in this group (595.0 cells/\u00b5L) suggesting possible recent infection, as compared to HIV-infected respondents who also reported that they were positive .HIV-infected, undiagnosed women who had never been tested for HIV had the highest proportion of missed testing opportunities during an ANC visit in the 12 months before the survey . In 2007KAIS showed that only one-quarter of ever sexually active men and less than half of ever sexually active women aged 15\u201364 years in Kenya in 2007 had been tested for HIV. Furthermore, more than 80% of HIV-infected adults aged 15\u201364 years were unaware of their HIV infection, and among those, one-third reported being uninfected but had a laboratory-confirmed positive HIV test. Time since last HIV test and higher CD4 counts suggests that many of these had sero-converted since their last HIV test.Considering that in 2003, only 15% of all Kenyans aged 15\u201349 years had ever been tested (compared to 37% of that age group in KAIS), Kenya made substantial progress in expanding testing Testing rates for both men and women were higher in urban areas , in better-educated and wealthier persons, and in persons who had contact with health facilities. In multivariable analyses, variables that were independently associated with ever HIV testing for both men and women included age, province, education and contact to health services . In men only, wealth index and condom use at last sex were independently associated with ever HIV testing. In women only, marital status, ever having been pregnant, and perceived HIV risk were independently associated with ever HIV testing. The considerably lower odds for ever testing in women aged 35 years and older compared to men of that age confirmed that women are testing at younger age, most likely driven by ANC services during pregnancy. All provinces with significant AOR were negatively associated with ever HIV testing when compared to Nairobi. This included North-Eastern, the province with limited need for HIV testing, given a HIV prevalence of <1%, and Nyanza with a 40% lower odds for ever HIV testing in women yet an HIV prevalence in women of 17% compared to 10% in Nairobi. Nyanza is a mostly rural province on the shore of Lake Victoria with the highest rates for HIV in the country, at least partially due to a low prevalence of male circumcision, while North Eastern province is less populated and ethnic groups in this area traditionally circumcise. Independent associations with ever HIV testing of both education and wealth (men only) in our study highlight linkages between HIV infection, access to services, and socio-economic status We found that considerable opportunities for testing were missed during general or pregnancy-specific contacts with health facilities. Our study suggests that more than 90% of all persons in Kenya with undiagnosed HIV infection who had never been tested could potentially be identified through a combination of provider-initiated testing and door-to-door testing in high prevalence provinces. However, coverage of door-to-door testing can decrease when family members cannot be reached at home The 2008 National Guidelines for HIV Testing and Counselling in Kenya promote a diversified approach to reduce the number of missed opportunities for providing HTC including client-initiated, provider-initiated, self-testing, home-based testing and mass HIV testing campaigns In times of increasing restrictions of funding, national strategies need to consider the most cost-efficient interventions. Menzies and colleagues estimated costs and effectiveness of four HTC strategies in Uganda in 2003\u20132005 Program and survey data in Kenya suggest that testing coverage has continued to increase since KAIS. In 2008\u20139 Our study had several limitations. Cross-sectional surveys do not allow for determination of the sequence of events in time. KAIS was not designed to assess HIV testing among high-risk populations, such as sex workers, men who have sex with men, or intravenous drug users (Kenya has increased surveillance efforts for these populations since 2010). Some data were not available from the study, e.g., whether respondents had not tested for HIV because no transport was available to reach a testing site or they were not able to pay for the transport, or whether they had tested as a couple. There is no generally accepted definition of a high HIV prevalence area; therefore, missed opportunities were reported across Kenya without excluding provinces with relatively low prevalence such as North-Eastern. High rates of undiagnosed infection suggest limited coverage of testing services and relatively high incidence; however, they may also partially reflect reporting bias due to misunderstanding of prior results, denial, misreporting, or false-negative test results. Finally, Kenya's population structure with over 40 ethnic groups of considerable cultural differences may have resulted in some differences in self-reporting. The example of reporting bias of HIV results was discussed above. In general, the direction and magnitude of any potential reporting bias is unknown.In spite of these limitations, by including for the first time questions on HIV status and CD4 count testing among HIV-infected persons, Kenya's nationally representative HIV survey helped inform HIV program planning with unprecedented detail. Our findings illuminated both the high rates of undiagnosed infection throughout Kenya and the clear opportunities for expanding testing coverage to meet the national and 2008 United Nations goals of universal access to HIV prevention, treatment, care and support"} +{"text": "Although bystander cardiopulmonary resuscitation (CPR) can improve survival from cardiac arrest, the reported prevalence of bystander CPR remains low in most countries. This study was performed to investigate factors affecting laypersons' willingness in performing CPR.Questionnaires including 10 questions regarding personnel backgrounds, knowledge regarding the use of AED, CPR training, willingness in performing CPR, and EMS dispatcher's advice were distributed to citizens who gathered at a ball park stadium, a typical public place in Hiroshima, Japan.P < 0.0001; 91% vs. 58%, P < 0.0001, respectively) and doing rescue breathing . Fifty-two percent of the respondents did not know the service of dispatcher-assisted CPR.Ten thousand questionnaires were distributed and a total of 5,956 were collected for analysis. Age distributions of the respondents were: <20 years old: 13%, 20 to 49 years old: 67%, 50 to 69 years old: 16%, >70 years old: 3%. Fifty-seven percent were male. Ninety-one percent had heard of AED; however, only 45% knew how to use it. Forty-nine percent took CPR training before. As for the willingness to perform CPR, 38% answered they would start CPR, 34% would do it if any advice was available. On the other hand, 23% said they were not capable of performing CPR, and 4% were not willing to do it. Of those who were not capable of performing CPR, the reasons included lack of knowledge and/or skills to perform CPR (50%), no previous CPR training (27%), concern over harm to the victims (25%), and lack of confidence to determine cardiac arrest (19%). Of those who were willing to perform CPR, 61% answered they would prioritize rescue breathing over chest compression. In comparison of those with and without previous CPR training or knowledge of the use of AED, significant differences were found in the willingness in performing CPR (88% vs. 58%, Our study indicated that proper knowledge of CPR, prior CPR training, and onsite bystander CPR assistance may enhance laypersons' willingness in performing CPR. More emphasis should be exerted on the roles of chest compression and the EMS dispatcher assistance in CPR education."} +{"text": "We describe universal screening in a large urban hospital-based primary care practice. Trained staff aimed to screen all adult patients presenting for primary care visits between July 2010 and February 2011. Screening included three items about past three-month drug use: frequency of heavy drinking (>3 standard drinks in a day for women and >4 for men); any use of prescription sedatives, opioids, or amphetamines without a prescription or in greater amounts than prescribed; and any use of illicit drugs. A convenience sample of those who screened positive for drug use was evaluated for eligibility to be in a study of brief counseling efficacy; enrollment resulted in further research assessment. During six months, 15,818 patients arrived for primary care appointments. Of these, 5549 (35%) were screened, 539 (10%) of whom reported heavy drinking (5.9% of those screened) or drug use (6.2% of those screened). Of the 539, 41% reported drug use only, 38% heavy drinking only, and 21% reported both. Of patients meeting eligibility criteria for the brief counseling study for drug use , 14% had lower risk scores (2 or 3) on the Alcohol, Smoking, and Substance Involvement Screening Test (ASSIST). Of those with scores of 4 or more (moderate risk), marijuana was the drug of most concern for 61%, cocaine for 19%, and opioids for 18%. Twenty-one percent reported prescription drug misuse, 31% used more than one drug, 20% had high-risk ASSIST scores (27+), and 48% met criteria for drug dependence. In-person universal screening in busy urban primary care settings reaches some but misses many. Drug use prevalence was 6.2%, most of which was marijuana, and many of those screened had drug dependence. Most drug use would have been missed if drug screening had been done only for those who screened positive for heavy drinking."} +{"text": "The most common treatment modality for epileptic patients is antiepileptic drug (AED) therapy. However, more than 30% of epileptic patient suffers from drug-resistant epilepsy despite the use of appropriate AEDs. Surgery is a common option for these patients. Epilepsy surgery requires sophisticated medical technologies, many of them not available in Iran. The authors of the present study aim to report the clinical and technical issues of establishing an epilepsy surgery protocol in Iran and the limitations and recommendations for further development. Medically-refractory epileptic patients underwent common imaging techniques as well as continuous video EEG monitoring. A specialized committee consisting of epileptologists, neurologists, neurosurgeons and radiologists discussed the eligibility of each patient, and defining treatment plans for the surgery.A total of 22 committee sessions were hold to discuss 140 cases with medically-refractory seizures during March 2009 to May 2012. Eighty-eight patients (62%) underwent the surgery, 35 patients (25%) were considered not appropriate for surgery, and 17 patients (12%) refused to undergo surgery. The most common cause of intractable seizures was mesial temporal sclerosis (36%), brain tumors (21%), cortical malformations (6%), and encephalomalacia (4%). Among 81 operated patients, 39.5% had anterior temporal lobectomy, 34.5% corpus callosotomy, and 30% underwent lesionectomy.The success of epilepsy surgery depends on the accurate identification of good surgical candidates based on available resources and technologies without jeopardizing safety. The key step in establishing a successful plan is having access to trained epileptologist and neurosurgeon.Epileptology, Epilepsy surgery, Antiepileptic drug, Surgery portocol"} +{"text": "Skin prick tests (SPT) are the gold standard for determining atopy. In epidemiological studies of childhood allergy, questionnaire responses are often used to define atopy and predict sample size. Questionnaire-reported hayfever symptoms have shown 28-76% sensitivity and 21-94% specificity compared to SPT. We evaluated how questionnaire definitions of atopy affect sensitivity, specificity and sample size calculations in a population of Canadian children.We used questionnaire data from 5619 Toronto schoolchildren participating in the 2006 T-CHEQ study to determine 3 possible questionnaire definitions of atopy, including having any 1, any 2 or all 3 parent-reported physician diagnoses of hayfever, eczema or food allergy. In a nested case-control sample of 208 of these children, atopy was evaluated by SPT to14 common aeroallergens. Using SPT as the gold standard for atopy, we calculated sensitivity, specificity and sample size for a nested cohort study of particulate exposure and atopy outcome.Compared with SPT, sensitivity, specificity and Youden\u2019s index were 54.3%, 65.8% and 20.1% for 1 reported atopic condition and 24.4%, 98.7% and 23.1% for 2 reported atopic conditions, respectively (Table Questionnaire definitions of atopy in Canadian children have moderate sensitivity and specificity. More specific definitions decrease sensitivity and increase sample size requirement. Depending on the purpose of the proposed study, either definition of atopy may lead to an adequately-powered study."} +{"text": "While the diagnostic accuracy of stress cardiac magnetic resonance imaging (CMR) for detecting obstructive coronary artery disease (CAD) has been established, the prognostic value of stress CMR is less well described in the literature. Thus, we performed meta-analysis to study the role of stress CMR in assessing cardiovascular prognosis.CENTRAL, mRCT, and PubMed were searched for eligible studies that provided greater than 6 months of prognostic data on patients that underwent stress CMR. The primary end-points evaluated were cardiovascular mortality, myocardial infarction, and the combined endpoint of cardiovascular mortality or myocardial infarction. Pooling was performed using a random-effect model with summary effect estimates and annualized event rates were assessed. Values presented as mean \u00b1 standard error of the mean.Data was included from 19 studies with a total of 10,573 patients and an average follow-up of 27 months. Patients had a mean age of 61 years, 58% were male, 19% had a prior MI, 65% had hypertension, 58% had hyperlipidemia, and 24% had diabetes mellitus. CMR demonstrated a mean LV ejection fraction of 60% and stress testing demonstrated ischemia in 27% of patients. Studies demonstrated that patients with positive stress CMR had significantly increased combined outcome is associated with very low risk of cardiovascular mortality or myocardial infarction. Thus, stress CMR has excellent prognostic characteristics comparable to stress echocardiography or stress nuclear imaging and may help guide risk stratification of patients presenting with known or suspected CAD.AHA 10SDG2650038, NIH K23 HL112910-01"} +{"text": "Multiresistant-bacteria infection control measures in hospitals may include screening of patients at high risk of colonization, patients who are admitted to high-risk wards, patients submitted to high-risk procedures, roommates of patients with colonized or infected patients and screening during outbreaks.To study the rate of multiresistant bacteria colonization in roommates of patients infected or colonized by multiresistant microorganisms.Retrospective observational study of smears collected from roommates of multiresistant-bacteria positive patients between 2010 and 2012. Percentages and 95% confidence intervals (CI95%) were calculated.Acinetobacter baumanii multiresistant 4,48% , Carbapenemase-producing bacteria 1,85% . Rates along the study period were: 2010, 4,56% , 2011 and 2012 3,82% .Altogether, 3306 roommates samples were collected, out of which 172 were positive ). Rates for MRSA were 6,50% , extended-spectrum beta-lactamase-producing bacteria 4,33%, and The percentage of positive samples in roommates of patients colonized or infected by multiresistant bacteria was relatively low during the studied period. However, further studies are needed to compare colonization rates between these roommates and other hospitalised patients to study if colonization can be due to sharing room in hospitals or not.None declared."} +{"text": "Staphylococcus aureus has been endemic in Hong Kong, and accounts for approximately 40-45% of all Staphylococcus aureus isolates. A territory-wide admission screening of 7387 patients from Department of Medicine of acute care hospitals in 2011 revealed that 14.2% carried MRSA. Efforts to enhance infection control from all parties, including the patients, are keys to prevention of transmission.Methicillin-resistant To assess the patients\u2019 level of understanding, prevention and control of MRSA, identify improvement measures from patients\u2019 perspective, and explore the public education in relation to MRSA.A cross-sectional study was conducted in the out-patient clinics of the medical department of an acute regional hospital in Hong Kong in 2012. Face-to-face interview using a structured questionnaire was used.A total of 429 patients completed the interview. There were 203 male and 226 female; 65% aged over 40 years old. 253 (59%) have heard of MRSA, mainly from the media (85.8%). Around 50% correctly recognized it as bacteria and 18.2% knew about asymptomatic carriage. 30-40% associated MRSA with pneumonia and soft tissue infection, whereas 40% had no idea of disease association. 63.6% considered antibiotics for treatment and 28.5% had no idea at all. Droplets (37.5%) and direct contact (30.4%) were considered as common routes of MRSA transmission, 39.7% showed no idea. Around 65% perceived that crowded hospital environment and having MRSA patients at neighborhood increase the risk of acquisition. 15-20% regarded surgery, line insertion and total dependency as risk factors. 20% expressed moderate worry about MRSA acquisition. Two-third did not consider visitor and family member's role are extremely important in MRSA control.This study showed that patients\u2019 general knowledge on MRSA was low. The main source of information was from the media, and role of patient's visitor or family member in MRSA control is not considered essential. Patients are interested to get further information about MRSA, in particular for transmission and prevention. Enhancement of public knowledge and responsibility on MRSA control via multi-disciplines and multimedia could be helpful in reducing the spread of MRSA.None declared"} +{"text": "The Xpert MTB/RIF assay was introduced for timely and accurate detection of tuberculosis (TB). The aim of this study was to determine the diagnostic accuracy and turnaround time (TAT) of Xpert MTB/RIF assay in clinical practice in South Korea. We retrospectively reviewed the medical records of patients in whom Xpert MTB/RIF assay using sputum were requested. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for the diagnosis of pulmonary tuberculosis (PTB) and detection of rifampicin resistance were calculated. In addition, TAT of Xpert MTB/RIF assay was compared with those of other tests. Total 681 patients in whom Xpert MTB/RIF assay was requested were included in the analysis. The sensitivity, specificity, PPV and NPV of Xpert MTB/RIF assay for diagnosis of PTB were 79.5% (124/156), 100.0% (505/505), 100.0% (124/124) and 94.0% (505/537), respectively. Those for the detection of rifampicin resistance were 57.1% (8/14), 100.0% (113/113), 100.0% (8/8) and 94.9% (113/119), respectively. The median TAT of Xpert MTB/RIF assay to the report of results and results confirmed by physicians in outpatient settings were 0 (0\u20131) and 6 (3\u20137) days, respectively. Median time to treatment after initial evaluation was 7 (4\u20139) days in patients with Xpert MTB/RIF assay, but was 21 (7\u201333.5) days in patients without Xpert MTB/RIF assay. Xpert MTB/RIF assay showed acceptable sensitivity and excellent specificity for the diagnosis of PTB and detection of rifampicin resistance in areas with intermediate TB burden. Additionally, the assay decreased time to the initiation of anti-TB drugs through shorter TAT. Early and accurate detection of tuberculosis (TB) is important for the timely initiation of treatment and prevention of TB transmission. In addition, early detection of drug resistance is crucial for early treatment of multi-drug resistant (MDR) TB. Conventional methods for the diagnosis of TB have limitations in terms of early and accurate detection. Acid-fast bacilli (AFB) smears show short turnaround times (TAT) and high specificity rpoB gene, was validated for simple and rapid diagnosis of TB rpoB gene is known to be specific for TB diagnosis, and mutation of the rpoB gene is associated with resistance to rifampicin (RIF). Using probes complementary to the rpoB gene, the Xpert MTB/RIF assay can identify M. TB and RIF resistance simultaneously in 2 h. In South Korea, the Xpert MTB/RIF assay was adopted for the diagnosis of TB since 2011.The Xpert MTB/RIF assay, using RT-PCR for the TB specific Previous studies showed the high sensitivity and speed of the Xpert MTB/RIF assay for detection of TB and RIF resistance. When performed more than 3 times, the sensitivity of the Xpert MTB/RIF assay for detection of TB and RIF resistance was greater than 98% and 97%, respectively The design of this study was approved by the Institutional Review Board of Seoul National University Hospital. We retrospectively reviewed the medical records of patients in whom the Xpert MTB/RIF assay using sputum were requested due to suspicion of pulmonary TB between January 1 2011 and May 31 2013 at Seoul National University Hospital. Using data from these patients, we evaluated the accuracy of the Xpert MTB/RIF assay and compared the TAT of the assay with those of other TB tests. Obtaining consents from individual patients was waived by the Institutional Review Board.We calculated the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the Xpert MTB/RIF assay using sputum for the diagnosis of pulmonary TB. Diagnosis of pulmonary TB was confirmed by culturing M. TB from sputum for primary analysis. In this analysis, patients in whom M.TB was detected using the Xpert MTB/RIF assay, but M.TB isolation by mycobacterial culture failed, were excluded although all were treated with anti-TB drugs. We also calculated the sensitivity, specificity, PPV, and NPV of the Xpert MTB/RIF assay regarding the patients with positive Xpert MTB/RIF assay as having pulmonary TB.We calculated the sensitivity, specificity, PPV, and NPV of the Xpert MTB/RIF assay using sputum to detect RIF resistance. Drug susceptibility tests (DST) using the absolute concentration method was used as a gold standard for detection of RIF resistance. Resistance to RIF was defined as \u22651% bacterial growth in L\u00f6wenstein\u2013Jensen medium at a concentration of 40.0 \u00b5g/ml.The TAT of the Xpert MTB/RIF assay was compared with those of acid-fast bacilli (AFB) smears, cultures on liquid media or solid media, and conventional DST against anti-TB drugs. In addition, we compared the intervals from the request of diagnostic tests for TB to the initiation of anti-TB drugs between patient diagnosed as pulmonary TB using the Xpert MTB/RIF assay and pulmonary TB patients diagnosed without using the Xpert MTB/RIF assay. To perform this comparison, we matched twice as many TB patients diagnosed without using the Xpert MTB/RIF assay to patients diagnosed with Xpert MTB/RIF assay.g for 20 min. AFB smears were performed using Auramine-Rhodamine fluorescent staining and confirmed by Ziehl\u2013Neelsen staining. Sediment was cultivated on Ogawa medium for 9 weeks in 5\u201310% CO2 incubators, as well as in BACTEC\u2122 MGIT\u2122 for 6 weeks. Once cultured, the isolation of M.TB was confirmed using the Gen-Probe\u00ae method Patients were asked to submit one spot and one or two subsequent morning sputa for AFB smear. One additional sputum was submitted for Xpert MTB/RIF assay. All sputum specimens were pretreated with equal volumes of 4% sodium hydroxide and centrifuged at 3000\u00d7The Xpert MTB/RIF assay was performed and interpreted according to the manufacturer\u2019s instructions. Sputum specimens were lodged in the Xpert MTB/RIF assay cartridges, and tests were performed within 24 h after sputum submission.t-tests, Mann-Whitney tests and Kruskal-Wallis tests were used to compare continuous variables. All analyses were performed using the SPSS software, version 19.0 .The sensitivity, specificity, PPV and NPV of the Xpert MTB/RIF assay were calculated and 95% confidence intervals were estimated. Clinical data of included patients were described with the medians and ranges. Chi-square tests and Fisher\u2019s exact tests were used for comparison of categorical variables, and independent Between Jan 1 2011 and May 31 2013, the Xpert MTB/RIF assay using sputum was requested in 681 patients with suspicion of pulmonary TB. The median age of these patients was 61 years and 426 (62.5%) were male. Median number of submitted samples for each patients was 2 for AFB smear and mycobacterial culture. A total of 84 patients (12.3%) had diabetes. Among 681 pulmonary TB suspects, culture-proven pulmonary TB was diagnosed in 156 patients (22.9%). In addition, 59 patients were diagnosed with pulmonary TB based on their symptoms and radiographic findings, although M. TB was not cultured from their sputum .p\u200a=\u200a0.017) and PPV (p<0.001) were higher than in the negative sputum AFB smear group. (The sensitivity of the Xpert MTB/RIF assay for diagnosis of pulmonary TB was 79.5% (124/156) and specificity was 100.0% (505/505), while PPV was 100.0% (124/124) and NPV was 94.0% (505/537). Among patients with positive sputum AFB smears, sensitivity, specificity, PPV and NPV of the Xpert MTB/RIF assay was 88.9% (56/63), 100.0% (16/16), 100.0% (56/56), and 69.6% (16/23), respectively. Meanwhile, the sensitivity, specificity, PPV and NPV of the Xpert MTB/RIF assay were 73.1% (68/93), 100.0% (489/489), 100.0% (68/68), and 95.1% (489/514) among patients with negative sputum AFB smears. In the positive sputum AFB smear group, the sensitivity (r group. .The sensitivity of the Xpert MTB/RIF assay was 81.8% (144/176) for diagnosis of pulmonary TB if we classified not only patients with culture-proven TB but also patients with positive Xpert MTB/RIF assay as having pulmonary TB. .Among 79 patients with positive sputum AFB smears, the results of the Xpert MTB/RIF assay were negative in 23 patients. In 7 of these 23 patients, pulmonary TB was confirmed by culturing M.TB from their sputum. Nontuberculous mycobacteria (NTM) instead of M.TB were cultured from the sputum of the other 16 patients and these patients were excluded from the analysis .Conventional DST failed in 29 of 156 patients with culture-confirmed pulmonary TB. These 29 patients were excluded from the accuracy analysis using the Xpert MTB/RIF assay for the detection of RIF resistance. Using conventional DST, RIF resistance was identified in 14 of 127 patients with available DST results. The Xpert MTB/RIF assay correctly detected RIF resistance in 8 of 14 patients. Subsequently, the sensitivity of the Xpert MTB/RIF assay was 57.1%. False-positive RIF resistance using the Xpert MTB/RIF was not detected. Consequently, the specificity (113/113) and PPV(8/8) of the assay were 100%.In five of six patients in whom the Xpert MTB/RIF assay failed to detect RIF resistance, the assay also failed to detect the presence of M.TB. If these five patients were excluded from the analysis, the sensitivity was 88.9% (8/9) and the specificity to 100% (90/90). In addition, PPV was 100% (8/8) and NPV was 98.9% (90/91) .The median TAT from requested Xpert MTB/RIF assays to reported laboratory results was 0 days (0\u20131 days). This was significantly shorter than those of AFB smears , culture on liquid or solid media, and drug susceptibility tests based on solid media . Median Among pulmonary TB patients diagnosed using the Xpert MTB/RIF assay, anti-TB treatment was initiated median 7 days (4\u20139 days) after the evaluation for TB. However, among pulmonary TB patients in whom the Xpert MTB/RIF assay was not performed, the median time to initiation of anti-TB treatment was 21 days (7\u201333.5 days) .As an initial diagnostic method of M.TB, the accuracy and speed of the Xpert MTB/RIF assay have been demonstrated in previous studies. However, many of these were performed in low-income countries with limited medical resources In our study, the sensitivity, specificity, PPV and NPV of the Xpert MTB/RIF assay for diagnosis of pulmonary TB were 79.5%, 100.0%, 100.0% and 94.0% respectively. The sensitivity in our study was lower than 90.4%, which was also reported in a recent meta-analysis The threshold of M.TB detection using the Xpert MTB/RIF assay is affected by the number of colonies in the sample In our study, of 681 TB suspects, 156 patients were diagnosed with pulmonary TB with confirmation by mycobacterial culture. However, mycobacterial culture failed to identify M.TB in 59 patients who were concluded to have pulmonary TB based on the symptoms and radiographic findings. The fact that approximately one third of pulmonary TB cases could not be identified by mycobacterial culture suggests that more sensitive diagnostic methods are required. In fact, the Xpert MTB/RIF assay yielded positive results in 20 of these 59 TB suspects without bacteriological confirmation. This observation suggested that the Xpert MTB/RIF assay could be a complimentary test for the diagnosis of TB, including in the regions in which mycobacterial cultures are readily available.In our study, the specificity and PPV of the Xpert MTB/RIF assay were each 100%. The high specificity and PPV of the assay are useful in countries such as South Korea, where the incidence of NTM is increasing rapidly The detection of MDR-TB is important because a prolonged treatment duration is required, but treatment success rates are low. Because RIF resistance serves as a surrogate of multidrug resistance Mathematically, the PPV of the Xpert MTB/RIF assay for RIF resistance varies according to the prevalence of MDR-TB. PPV for RIF-resistance is expected to be less than 70% based on the prevalence of MDR-TB in South Korea As expected, the TAT of the Xpert MTB/RIF assay in an outpatient setting was shorter than those of AFB smears, liquid culture, solid culture and DST in terms of interval to the report of results from the laboratory, as well as interval to the confirmation of results by physicians, in our study. In particular, the Xpert MTB/RIF assay shortened the time to initiation of anti-TB drugs by 14 days. However, the 5.5-day delay from the report of the Xpert MTB/RIF assays to confirmation by physicians suggested that the follow-up system requires improvement when the Xpert MTB/RIF assay is used in routine practice.In conclusion, the Xpert MTB/RIF assay has acceptable sensitivity and excellent specificity for the diagnosis of pulmonary TB, as well as for the detection of RIF resistance in intermediate TB burden countries. In addition, the assay significantly shortened the time to anti-TB treatment."} +{"text": "In Luxembourg, viral hepatitis and HIV infection data in problem drug users (PDUs) are primarily based on self-reporting. Our study aimed to determine the prevalence of HAV, HBV, HCV and HIV infections in ever injecting (IDUs) and non-injecting drug users (nIDUs) including inherent risk factors analysis for IDUs. Secondary objectives were immunisation against HAV and HBV, referral to care and treatment facilities as well as reduction in risk behaviour.A nationwide, cross-sectional multi-site survey, involving 5 in-, 8 out-treatment and 2 prison centres, included both an assisted questionnaire (n = 368) and serological detection of HIV and Hepatitis A, B, C (n = 334). A response rate of 31% resulted in the participation of 310 IDUs and 58 nIDUs.Risk factors such as drug use, sexual behaviour, imprisonment, protection and health knowledge , piercing/tattoo and use of social and medical services were studied by means of chi2 and logistic models.Seroprevalence results for IDUs were 81.3% for HCV, 29.1% for HBV (acute/chronic infection or past cured infection), 2.5% for HIV-1 and 57.1% for HAV (cured infections or past vaccinations). Seroprevalence results for nIDUs were 19.1% for HCV, 8.9% for HBV (acute/chronic infection or past cured infection), 4.8% for HIV-1 and 65.9% for HAV. Prisoners showed the highest rates for all infections. Age, imprisonment and setting of recruitment were statistically associated with HCV seropositivity. Age, speedball career and nationality were significantly associated with HBV seropositivity. Only 56% of the participants in outpatient centres collected their serology results and 43 doses of vaccine against HAV and/or HBV were administered.Despite the existing national risk-reduction strategies implemented since 1993, high prevalence of HCV and HBV infections in injecting drug users is observed. Our study showed that implementing risk-prevention strategies, including immunisation remains difficult with PDUs. Improvement should be looked for by the provision of field healthcare structures providing tests with immediate results, advice, immunisation or treatment if appropriate. The prevalence of hepatitis C virus (HCV) infection in injecting drug users varies between regions in Europe from 40 to 90% . Before Prevalence of HCV among nIDUs varies in Europe between 10 and 20% and remaEpidemiological follow-up of problem drug use in Luxembourg relies on a nation-wide multi-sector surveillance system called \"RELIS\". RELIS was established in 1995 and conceived on the methodological assumption that data exclusively collected from drug treatment settings may not provide an accurate picture of the problem drug-using population as it notably excludes out-of-treatment drug users who for instance have had conflicts with law enforcement bodies due to the problematic aspect of their drug use. The RELIS network includes in- and out-patient treatment centres (100% coverage), including hospitals providing detoxification treatment, national prisons and law enforcement agencies. Data collection is performed via a series of contextual protocols , self-reported data and setting-related data . The yearly output of RELIS largely contributes to the publication of the national annual drugs report. According to RELIS data a weak uOur study pursued three goals: i) defining the prevalence of viral hepatitis B, C and HIV in IDUs and nIDUs in Luxembourg, ii) analysing risk factors of viral infections in IDUs and iii) assessing the need and feasibility of HAV and HBV immunisations in PDUs.To approach the genuine heterogeneity of the drug misuse phenomenon, RELIS routinely compiles data from law enforcement agencies, the 2 prisons, inpatient or outpatient centres providing counselling, assistance and drug treatment to PDUs throughout the country. Also, the national drug surveillance system relies on the concept of the 'institutional contact indicator', as an alternative to the better-known treatment demand indicator . FurtherAccording to the RELIS case definition, a problem user of illicitly acquired drugs (referred to as PDU) is defined as a person who shows a) current and regular use of opiates, cocaine, and/or amphetamines, and b) current contact with a health or law enforcement institution due to the use of listed drugs. Route of administration is not considered as a selection criteria. The use of other licit or illicit substances whether prescribed or not, is not an exclusion criteria as long as it is associated with the described drug use pattern.The latest PDU prevalence study prior to the present research reported an absolute prevalence of 2530 PDUs among the national population aged 15 to 64 years . To reacAmong the 16 eligible sites and leaving aside law enforcement agencies and one outpatient centre for minors only, the study sites included all the RELIS network centres with the exception of one hospital. This allowed reaching remarkable national service representativeness.PDUs in contact with participating institutions were eligible for inclusion in the study when reporting use of opiates, cocaine, amphetamines or being under medical substitution irrespective of the route of administration and duration of use. IDUs are defined as having injected at least once in lifetime.The study was designed as a \"research-action\", offering participants free medical counselling, risk-reduction material and immunisation against HAV and HBV. The study was performed according to the Declaration of Helsinki and approved by the National Research Ethics Committee and the National Commission for Data Protection (NCDP).The trained field investigator informed each participant on the study before proceeding to an assisted questionnaire and a prevention message with handover of risk reduction material. A personal identification code (RELIS code) approved by the NCDP, was computed from gender, date and country of birth variables.Written informed consent was obtained for all interviews, blood sampling or medical file consultation. Each stage of participation gave right to a free meal voucher for the participants. Multiple strategies were used to facilitate recruitment such as flyer distribution and direct approaching of PDUs by street workers.Consensus questionnaire for Young Problematic Drug Users. Lisbon EMCDDA meeting 2000 jun 15-16. Unpublished reports.) focusing on socio-demographic information, drug use, injecting behaviour, sexual behaviour, imprisonment, protection and health knowledge , piercing/tattoo and use of social and medical services. This questionnaire was made available in French, German and Portuguese after a validated translation procedure. On average, it took 30 minutes to be completed.The questionnaire was based on a \"Scottish questionnaire\" and the In ITCs and PCs, serology results and immunisation follow-ups were gathered from medical files. In OTCs, PDUs were offered blood sampling for HIV and hepatitis serology. During the 8-month recruitment period and for an additional 6 months after the inclusion of the last respondent, results and, if needed, immunisations were given at the same location by a physician. Blood samples collected on site were transported to the laboratory on the same day. Serum specimens were aliquoted and stored at -20\u00b0C until the ELISA serology tests were performed on an automated Abbott AXSYM System . The following tests were performed: for HAV, IgG (HAVAB 2.0 Reagents) and IgM antibodies (HAVAB.M 2.0 Reagents), for HBV, HBs antigen, anti-HBs antibodies (AUSAB reagents), anti-HBc antibodies (CORE reagents), for HCV, anti-HCV antibodies (HCV 3.0 reagents), and for HIV-1 and 2 (HIV Ag/Ab Combo Reagents). In case of a positive ELISA test for HCV or HIV, confirmation tests were manually performed and for HIV, HIV BLOT 2.2 and Vironostika HIV-1 Antigen ).When appropriate, immunisations against HAV and HBV with Havrix 1440, Engerix B20, or Twinrix Adult were offered free of charge in OTC. Immunisations were provided routinely - independently of the present study - in ITC and PC.The use of the RELIS code coupled with a single field investigator allowed avoiding duplicates in the process of data management. Student T-tests compared continuous variables, Chi-square or Fisher's exact tests where appropriate compared categorical variables. Odds ratio and their Confidence Intervals (95%CI) were calculated when possible. For both HCV and HBV, logistic regression was applied by using a stepwise manual backward approach to select probable risk factors where a non-significant likelihood ratio test was found. The final model was also adjusted for known covariates (age).A p-value below 0.05 was considered statistically significant. All tests were two-tailed. Analyses were carried out with SPSS Statistical software version 13 and SAS System version 9.2 .From January 1 to August 31, 2005, 1,169 contacts were made with PDUs than in ITCs and PCs but no difference in the distribution of IDUs and nIDUs (non-IDUs) between the 3 settings was observed. 84% of respondents were IDUs and 16% nIDUs, constituting the studied population whose main characteristics are displayed in Table Among IDUs the average number of years elapsed since the first use of injectable drug was 10.0 years (SD: 7.5). From the IDUs having injected in the last 6 months, 75% of the sterile syringes were obtained through syringe exchange programs and 12% from pharmacies. Sixty-five percent gave back their used syringes at a syringe exchange program point, although 15% of these syringes were separated from their needle and 8% of the needles were discarded in an inappropriate location (e.g. dustbin or street).In prisons, 75 in 122 IDUs (55%) injected drugs during their detainment. Forty of them (53%) reused their own syringes and needles which had never been shared with another person. Among the 60 IDUs who reused their syringes whether shared or not, 43 (71%) cleaned them with water only.HBV serology was considered positive (HBVab) - either acute or chronic active or past cured infection in 29.1% (95%CI: 25.5-34.7) of IDUs and 8.9% (95%CI: 0.5-17.2) in nIDUs -including 18 anti-HBc antibodies-only cases and HBV non- vaccinated status (p = 0.0001). There is no statistical difference between IDUs and nIDUs for HBV vaccinated status (p = 0.30), HAVab (p = 0.31) nor HIVab (p = 0.43), but HCVab is higher in IDUs .Among participants with HCVab, HBVab or HIVab, 96% (218/227), respectively 95% (74/78), and 71% (5/7) were IDUs.Among HCV positives, 61.0% were protected against HBV either by vaccination or past infection . All 7 respondents with active HBV infection and all 7 HIV-1 positives were co-infected with HCV.In IDUs, HCV Table and HBV HCV infection was associated with type of setting (ITC and PC), substitution treatment history and multiple stays in prison or drug use in prison. None of the disinfection procedures in prison correlated significantly with HCV. The duration of drug use for cannabis and a distant date and amphetamine career in IDUs.In order to assess the risk factors of the different infections, we entered in the multivariate models variables with a p-value lower than 0.20 in the univariate analysis.For HBV infection in IDUs, multivariate logistic modeling discarded cocaine, heroin and amphetamine careers. The final model included age , speedball career and nationality as the only significant factors. Age did not appear as a factor of interaction for speedball career (p = 0.66) and the model was adjusted to avoid any confusion between HBV infection and speedball career.Regarding HCV, the multivariate modeling discarded cocaine, heroin, speedball and cannabis careers, last heroin and amphetamine consumption, substitution treatment, sex partners, imprisonment and drug use in prison. The final logistic model for HCV infection in IDUs included age and the settings of recruitment as the only significant factors. Age appeared as a confounding factor for drug use careers (p = 0.0001).Comparability and validity of self-reported study results and respective RELIS data, including sensitivity, sensibility and agreement analysis have been specifically addressed in a former research paper .As far as the infection status awareness of PDUs is concerned, respectively 81 and 59 PDUs out of 360 did not know about their past 10 years acquired HAV or HBV immunisation. Respectively 131 and 120 PDUs self-declared not having been vaccinated against HAV or HBV.Of 148 and 181 respondents recalling previous HAV and HBV vaccination respectively, 22% (33/148) and 20% (36/181) reported one single dose of vaccine, 20% (29/148) and 16% (29/181) two doses, 47% (69/148) and 55% (99/181) three doses of vaccine; 17 PDUs did not know the number of administrated boosters.\u00ae dose, 32% (14/43) one Havrix\u00ae dose and 28% (12/43) one Engerix\u00ae dose. Of the 123 interpretable blood samples, respectively 28 (23%), 30 (24%), 20 (16%) PDUs were potential candidates for vaccination against hepatitis A, hepatitis A and B and hepatitis B. Fifty-seven percent of PDUs requiring HAV and HBV immunisation received one Twinrix\u00ae dose, 50% requiring HAV immunisation received one Havrix\u00ae dose and 60% requiring HBV immunisation received one Engerix\u00ae dose. In OTC, 78 (52%) respondents needed immunisation (HBV and/or HAV) and 43 (55%) received a first dose of vaccine. No second dose of vaccine was administered, as none of the PDUs showed up for a booster.Protection against HBV was either acquired by past infection , or by vaccination and higher ones in inpatients (100%) and prisons (99%). A cross-sectional study conducted in Luxembourg in 1999 also showed a 33.9% response rate . Other lOverall, HCV prevalence was 81.3% in IDUs and 19.1% in non IDUs. Those rates put Luxembourg in the upper range of HCV prevalence among IDUs in Europe ,6, but rCompared to PCs , the prevalence of HCV was lower in ITCs and OTCs . There may be a selection bias in recruitment as outpatients showed less motivation to participate in the study by postponing their participation. Also, in prison the access to sterile material brings IDUs to be more at stake when it comes to infection risks.Alike, Belgium reportedSince no viral load assays were performed in our study, we were unable to distinguish chronic active from past resolved HCV infections. Based on literature, we can estimate however that about 55-85% of seropositive had indeed an ongoing chronic infection . In addiIn IDUs, HBVab prevalence was 29.1%. Again we found significantly higher HBVab prevalence in prisons compared to other settings. In IDUs, national prevalence rates for HBcAb, HBsAg and HBsAb are scarce in Europe, ranging respectively from 0.7%-64%, 2.3%-6.1% and 25%-37% . BelgiumThe results of the multivariate analysis with increasing age, more than 6 years' speedball career and non-Luxembourg nationality favouring HBV transmission are consistent with those of other studies ,22. TheyVaccinations for PDUs are recommended in all the settings wherever feasible and although no difference in HBV vaccination rates according to different settings has been observed, awareness should be further raised among physicians regarding the importance and usefulness of HBV vaccination in PDUs.We found no case of acute HAV infection; however, 41% of PDUs were unprotected against HAV and would have benefited from immunisation.The prevalence of HIV among IDUs was 2.5%. Again the highest prevalence was found in prison (7.7%). In the European Union, HIV prevalence in IDUs varies from 1% in the UK to 30% in Spain ; NeighboOur data shows that co-infections are common. The univariate analysis in the IDU population associates gender with HBV, age with HBV and HCV, and nationality with HCV infection. Likewise findings from other studies ,21 showeDrug injectors are particularly exposed to infection risks ,28 as thIn conclusion, our findings confirm that the prevalence of chronic viral infections and especially HCV is high among IDUs in Luxembourg. Also, the prevalence among nIDUs is noticeable for HBV. Therefore low- threshold opportunities for immediate testing, information on prevention, access to prevention material, immunisation and treatment if appropriate should be improved among PDUs. A syringe distribution programme for IDUs in prisons is highly suggested and has been in force in Luxembourg since the summer of 2005. Awareness should be further raised among physicians regarding the importance and usefulness of HBV/HAV vaccination in PDUs at the earliest stage of PDU. Tackling the problem of chronic viral infections in PDU is difficult, especially when it comes to gaining adherence to screening and immunisation schemes as shown in our study. In order to evaluate future trends in viral infections and effects of prevention programmes, the implementation of a continuous surveillance system for chronic viral infections in the PDU population should be considered ,31.PDUs: Problematic Drug Users; IDUs: Injecting Drug Users; nIDUs: non Injecting Drug Users; HAV: Hepatitis A Virus; HBV: Hepatitis B Virus; HCV: Hepatitis C Virus, HIV: Human Immunodeficiency Virus; OR: Odds Ratio; OTC: Out Treatment Centre; ITC: In Treatment Centre; PC: Prison Centre; IgG: Immunoglobulin G, IgM: Immunoglobulin M, NCDP: National Commission for Data Protection.The authors declare that they have no competing interests.All authors read and approved the final manuscript. AO developed the concept and tendered for funding. NR and AO developed the protocol and reported the study. NR supervised the fieldwork, the data collection and the data entry. NR, AO, SC contributed to the analysis plan. NR carried out the analysis. MV supervised the statistical analysis. MLL and AO supervised the implementation of the study. JCS supervised the development of laboratory methods and laboratory analysis and was a reference physician on the fieldwork. JCS, MV, AO, MLL and SC reviewed different versions of the manuscript. NR wrote the first draft and amended subsequent versions.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2458/11/351/prepub"} +{"text": "The role of plant hormone abscisic acid (ABA) in plants under drought stress (DS) is crucial in modulating physiological responses that eventually lead to adaptation to an unfavorable environment; however, the role of this hormone in modulation of glycinebetaine (GB) metabolism in maize particularly at the seedling stage is still poorly understood. Some hydroponic experiments were conducted to investigate the modulation role of ABA on plant growth, water relations and GB metabolism in the leaves of two maize cultivars, Zhengdan 958 , and Jundan 20 , subjected to integrated root-zone drought stress (IR-DS) simulated by the addition of polyethylene glycol . The IR-DS substantially resulted in increased betaine aldehyde dehydrogenase (BADH) activity and choline content which act as the key enzyme and initial substrate, respectively, in GB biosynthesis. Drought stress also induced accumulation of GB, whereas it caused reduction in leaf relative water content (RWC) and dry matter (DM) in both cultivars. The contents of ABA and GB increased in drought-stressed maize seedlings, but ABA accumulated prior to GB accumulation under the drought treatment. These responses were more predominant in ZD958 than those in JD20. Addition of exogenous ABA and fluridone (Flu) (ABA synthesis inhibitor) applied separately increased and decreased BADH activity, respectively. Abscisic acid application enhanced GB accumulation, leaf RWC and shoot DM production in both cultivars. However, of both maize cultivars, the drought sensitive maize cultivar (JD20) performed relatively better than the other maize cultivar ZD958 under both ABA and Flu application in view of all parameters appraised. It is, therefore, concluded that increase in both BADH activity and choline content possibly resulted in enhancement of GB accumulation under DS. The endogenous ABA was probably involved in the regulation of GB metabolism by regulating BADH activity, and resulting in modulation of water relations and plant growth under drought, especially in the drought sensitive maize cultivar JD20. Drought drought ,3. Under drought .Plants sense and adapt to different stresses by altering their physiological metabolism, and growth pattern, and mobilizing various defense mechanisms . Therefo2 uptake [Abscisic acid (ABA) plays an important role in physiological adaptation of plants to drought stress \u201314. It h2 uptake ,15,16,182 uptake ,19,20. A2 uptake ,22, it r2 uptake ,24.i.e., Zhengdan 958 and Jundan 20 by employing up-regulation of constitutive GB metabolism to mediate plant adaptation to DS. Previously, the former cultivar showed relatively higher drought index as well as dry matter production and grain yield under drought. Thus, Zhengdan 958 was ranked as drought tolerant and Jundan 20 as drought sensitive [Keeping in view the above facts, we hypothesized that plant hormone ABA can compensate for drought-induced retardation in the growth of two maize cultivars ensitive \u201326. WithTwelve days of integrated root-zone DS (IR-DS) induced by PEG significantly caused a decline in the growth of seedlings of both maize cultivars. The shoot dry weights (SDW) of Zhengdan 958 (ZD958) and Jundan 20 (JD20) under IR-DS were only 74% and 61% of those of the same two cultivars, respectively, under the controls in the absence of both exogenous ABA and fluridone (Flu), 89% and 73%, respectively, in the presence of ABA, and 67% and 65%, respectively, in the presence of Flu. The leaf relative content (RWC) of ZD958 and JD20 treated with PEG alone had 90% and 87% of the controls, 96% and 91% with both PEG and Flu, and 87% and 82% with both PEG and ABA. Regardless of ABA or Flu treatment, ZD958 showed higher values of SDW and leaf RWC than those of JD20 under IR-DS .Exogenous ABA increased but Flu decreased the SDW of ZD958 and JD20 by 16% and 20%, and 17% and 14%, respectively under IR-DS treatments. As for leaf RWC, application of ABA caused increase while Flu induced decrease in ZD958 and JD20 by 4.8% and 5.1%, and 4.4% and 3.8%, respectively. However, under the controls, ABA or Flu application had no obvious impact on SDW and leaf RWC .Endogenous ABA and GB in both cultivars accumulated with prolonged period of IR-DS treatment. These responses were more predominant in ZD958 than that in JD20. The ABA contents in ZD958 and JD20 reached their maximum after 24 and 36 h of the start of DS treatment, respectively, being 540% and 480% of those of the control plants. In contrast, GB contents in ZD958 and JD20 were maximum after 48 and 60 h of DS treatment, being 250% and 180% of those of the control plants, respectively. The maximum accumulation of ABA took place earlier than that of GB in the leaves of both drought-stressed maize cultivars .The accumulation of endogenous ABA and GB was affected by the exogenous application of ABA or Flu in maize plants subjected to IR-DS. In the absence of ABA or Flu, endogenous ABA and GB levels increased 210% and 140% in ZD958 and 190% and 90% in JD20, respectively under IR-DS. The corresponding values in the presence of ABA and Flu were 230% and 160% in ZD958 and 210% and 130% in JD20 for ABA level as well as 200% and 70% in ZD958 and 140% and 50% in JD20 for GB level, respectively .Addition of ABA and Flu caused increases and decreases, respectively, in endogenous ABA level of drought-stressed plants by 26% and 34% in ZD958, and 29% and 31% in JD20 as well as in GB level by 23% and 25% in ZD958, and 28% and 21% in JD20, respectively, as compared with those in plants without ABA or Flu application. As for the controlled plants, application of ABA and Flu also increased and decreased the endogenous ABA level of both cultivars. However, the increase/decrease rates became less than those in drought-stresses plants. Additionally, ABA and Flu treatments had no significant impacts on GB level in the controlled plants .Glycinebetaine metabolism determination can be done by assessing the amount of its precursor choline and the activity of the key enzyme BADH. The choline content and BADH activity in the leaves are shown in Exogenous ABA increased but Flu decreased BADH activity in both cultivars under IR-DS. The beneficial effects of ABA/negative effects of Flu on BADH activity were greater/less in JD20 than those in ZD958. However, these responses were not recorded under control conditions. As for choline content, there were no significant impacts of added ABA/Flu under both IR-DS and control treatments. However, choline content in plants treated with ABA was greater than that in plants treated with Flu under IR-DS.Correlation coefficients among all traits evaluated were significantly higher under DS than those under control. Importantly, correlations among DM, RWC and content of ABA and choline as well as BADH activity were evident under DS but not for those under control treatment .F values across the above parameters were in the order: water regime > exogenous ABA (Flu) > cultivars except choline content. The interaction effects among the above treatments were also mostly significant for all response variables except Cv \u00d7 A and W \u00d7 Cv \u00d7 A as well as W \u00d7 Cv \u00d7 Flu for choline content and BADH activity.Water regimes and exogenous ABA or Flu treatments had significant effects on all parameters . The magDrought stress (DS) is one of the most important abiotic stresses which severely affect crop growth and productivity . Relativ+ dependent enzyme [Hordeum vulgare L.) during prolonged water stress and in sugar beet (Beta vulgaris L.) under salinity. Considerable genetic variation in betaine-accumulating potential in them was also reported [It is well known that glycinebetaine (GB) accumulates in many drought-stressed plants including maize . Glycinet enzyme . Some rereported ,28. Howereported . The curA widely reported adaptation in plants to counteract abiotic stress is high accumulation of stress hormones and compatible organic solutes ,29,30. AAdditionally, exogenous ABA imposed greater positive impacts of ABA and GB accumulation in the drought-sensitive cultivar, and the abscisic acid synthesis inhibitor Flu had negative effects on the drought resistant cultivar .Pyrus pyrifolia) under drought stress [Sorghum bicolor) under salinity treatment [Avena sterilis) and periwinkle (Vinca major) [Plant growth inhibition and relative adaptive physiological processes such as osmotic regulation caused by environmental stress might be regulated by the application of plant hormones ,24,29,30t stress and sorgreatment . Howevera major) ,35. The a major) . Up to nZea mays L.) cultivars Zhengdan 958 and Jundan 20 were supplied for the present experiments by the Agronomy College of the same University. According to the previous hydroponic experiment and a field experiment carried out in the farm belonging to the same university, dry matter production and grain yield of the Zhengdan 958 cultivar were relatively little affected by drought [Hydroponic experiments were performed in a controlled growth chamber at the College of Life Sciences of Northwest A & F University, Yangling, China. The seeds of two maize containing treatment solutions. The experimental units were placed in the growth chamber under the following environmental conditions: average day/night temperature 25/18 \u00b0C, relative humidity 60\u201370%, light intensity 350 \u03bcmol/msolution , respectWhen seedlings were at the stage of three-leaf, drought stress (DS) treatment started by adding 120 g/kg (w/w) polyethylene glycol (PEG-6000) to achieve drought (osmotic) stress level of approximately \u22120.23 MPa, dissolved in full strength nutrient solution . The nutTo explore the relationship between ABA and drought stress (DS) in promoting glycinebetaine (GB) accumulation in maize plants, a second experiment was carried out using both maize cultivars Zhengdan 958 and Jundan 20 under the two treatments, control and 12% (w/v) PEG-6000 in nutrient solution.Plants were grown in a growth chamber in 3.4 L plastic pots, which were sealed carefully to avoid evaporation, with a sponge wrapped around the interface of the roots and the shoots. All treatment units were replicated four times, with a completely randomized design. The treatment solutions were aerated twelve hours a day.n = 8).All experiments were repeated twice. Data presented here are means of four replicates of the two experiments was determined using fresh weight (FW), dry weight (DW) and the turgid weight (TW). RWC was calculated from the equation described by Gao : RWC (%)2SO4. Aliquots of 0.5 mL were put in test tubes and cooled in ice water for 1 h, before a cold KI-I2 reagent (200 \u03bcL) was added. The tubes were stored at 0\u20134 \u00b0C for 16 h and then centrifuged at 12,000\u00d7 g for 15 min at 4 \u00b0C. The supernatant was aspirated. The periodite crystals were dissolved in 5 mL of 1, 2-dichloroethane. After 2\u20132.5 h, the absorbance was read at 365 nm with a UV\u2013visible spectrophotometer. Reference standards of GB (50\u2013200 g/mL) were used for calibration and estimation of GB concentration in unknown samples. The GB content was expressed as nmol/g DW.Glycinebetaine (GB) content was determined following Grieve and Grattan with somet al. [BADH activity was assayed as described by Daniell et al. with somet al. using boCholine content was determined following Feng and Ren and RichThe content of ABA was assayed in plant leaves by ELISA (enzyme-linked immunosorbent assay) using a monoclonal antibody (MAB) raised against ABA. The polyclonal antibody (RAMIG) was raised against the mouse immunoglobulins and ABA labeled with alkaline phosphatase, according to Weiler . The ABAThe data for all attributes were analyzed statistically to work out analysis of variance using the SAS software package . The anaThe results presented in this paper provide evidence that both BADH activity and choline content were involved for enhanced accumulation of GB in maize plants under drought stress. The endogenous ABA seemed to be involved in modulating GB accumulation by enhancing BADH activity, thereby improving leaf RWC and enhancing shoot DM in drought-stressed maize plants, especially in the drought sensitive cultivar (JD20). The peak of ABA content reached earlier than that of GB in the leaves of drought-stressed maize plants. Such, endogenous ABA probably played a positive role as a signal in the regulation of GB metabolism, water relations and plant growth by regulating BADH activity, but not choline content. The above results have proved that the drought-induced GB accumulation in maize may be involved probably in ABA-dependent pathway. The exogenous ABA provided some protection against the DS effects on maize plants by regulating endogenous ABA level and GB metabolism."} +{"text": "The literature indicates that outbreaks of viral hepatitis B may occur with the contaminated materials from manicure and pedicure. In Brazil, there is an important concern due to the habit of removing the nail cuticles that causes bleeding.This study aimed to identify the occurrence of accidents involving exposure to biological material, immediate actions after accidents and vaccination coverage in these professionals.A Survey was run with a random sample of 200 professionals, older than 18, covering 200 beauty salons in Belo Horizonte, Brazil. A questionnaire was used (Jul/12-Jan/13) to obtain information of demographics, accidents involving exposure to biological material, immediate actions after accidents and vaccination coverage of these professionals. The results were analyzed by the software SPSS. The Ethics Committee of the Federal University approved the study.All professionals interviewed were women, the average age was 30, have 10 years of experience (11%), work an average of 8 hours per day (57%), employed less than a year in that salon (34%). About education 55% had completed high school, 54% had done some training course in the field, yet 38% became manicure/pedicure by their own initiative. Moreover 76% hadn\u2019t got instruction about biosafety. Among the 200 participants, 66% reported having experienced accidents with needlestick material working. There was no statistical association (p>0.05) between demographic profile and accidents, except for education level. Those with complete high school qualification have injured the most (38%/p=0.02). In 65% of the cases, pliers to remove cuticle were the agent of the accident. Some professionals (57%) take care of their own nails using the material that was used in their customers and 52% mentioned have been injured while removing their own cuticle. Only 33% washed the local with water after accidents. Regarding immunization status, 54% had received the hepatitis B vaccine and 68% tetanus.The results of this research reinforce the biological risk the professionals are exposed to, especially due to needlestick accidents, lack of vaccination and prophylactic actions after the exposure, which minimize the transmission of pathogens.Fapemig PPM n\u00ba 00340-11None declared"} +{"text": "The evidence for therapy in autoinflammatory diseases is limited. There are few randomized controlled trials or disease registries.To evaluate the response to treatment of autoinflammatory diseases based on data of an international registry.A web-based registry collecting baseline and clinical information of autoinflammatory diseases was located at the member area of the PRINTO website (www.printo.it). Participating hospitals included pediatric rheumatology centers of the PRINTO network and adult centers with a specific interest in autoinflammatory diseases. Data was collected on Blau\u2019s syndrome, Beh\u00e7et\u2019s disease, CAPS, CRMO, DIRA, FMF, MKD, NLRP12-mediated periodic fever, PAPA, PFAPA TRAPS and undefined periodic fevers. In total, 704 patients were included in this retrospective study on therapy.NSAIDs and steroids were beneficial in most diseases. Anakinra induced a complete response in 70% of 40 treated CAPS patients, 82% of 28 TRAPS patients and in both DIRA patients. Furthermore, it was beneficial in 80% of 10 MKD patients. Etanercept was completely effective in all 6 Beh\u00e7et patients, 34% of 32 TRAPS patients and 13% of 8 MKD patients and partially effective in 53% of TRAPS and 38% of MKD patients. Colchicine was beneficial in approximately 95% of 131 FMF and 18 Beh\u00e7et patients, although the complete response rate was just 56% and 22%, respectively. For PFAPA syndrome, corticosteroids aborted the attacks in 78% of 113 patients.The results were compared to the literature. These combined findings could serve as a base for therapeutic guidelines and identify candidate drugs for future therapeutic trials."} +{"text": "Visceral fat (VF) increases cardiometabolic risk more than fat stored subcutaneously. Here, we investigated how well routine clinical measures of adiposity, namely body mass index (BMI) and waist circumference (waist), predict VF and subcutaneous fat (SF) in a large population-based sample of adolescents. As body-fat distribution differs between males and females, we performed these analyses separately in each sex.VF and SF were measured by magnetic resonance imaging in 1,002 adolescents . Relationships of BMI and waist with VF and SF were tested in multivariable analyses, which adjusted for potentially confounding effects of age and height.In both males and females, BMI and waist were highly correlated with VF and SF, and explained 55\u201376% of their total variance. When VF was adjusted for SF, however, BMI and waist explained, respectively, only 0% and 4% of VF variance in males, and 4% and 11% of VF variance in females. In contrast, when SF was adjusted for VF, BMI and waist explained, respectively, 36% and 21% of SF variance in males, and 48% and 23% of SF variance in females. These relationships were similar during early and late puberty.During adolescence, routine clinical measures of adiposity predict well SF but not VF. This holds for both sexes and throughout puberty. Further longitudinal studies are required to assess how well these measures predict changes of VF and SF over time. Given the clinical importance of VF, development of cost-effective imaging techniques and/or robust biomarkers of VF accumulation that would be suitable in everyday clinical practice is warranted. Obesity is a major public health problem ,2. Due t2), which is an imprecise, and possibly misleading vs. late [stages 4-5] puberty) with each of the tested main independent variables . Again, these analyses were carried out in each sex separately.In preliminary analyses, distributions of all continuous variables were assessed for the normality assumption on which the statistical inference about the linear model estimates relies. The values of variables for which the empirical distribution showed substantial positive skeweness , namely BMI, waist, suprailiac skinfold, waist/hip, VF and SF were all log transformed, using logarithm with base 10, which improved the fit of the multivariable models in the main analyses (data not shown). All statistical analyses were performed using JMP software .higher waist (p<0.0001) and waist/hip (p<0.0001), and lower suprailiac skinfold (p<0.0001) and SF and females (n=520) differed by only 1 month, but, as expected , males wAs expected, SF was closely associated with VF; the two measures shared 77% (p<0.0001) and 64% (p<0.0001) of variance in males and females, respectively . The slo BMI was closely associated with VF and SF (p<0.0001) in both sexes; it explained 58% and 55% of variance of VF and 72% and 76% of variance of SF in males and females of the same age and height, respectively. Relationships of waist with VF and SF were equally strong (p<0.0001); it explained 61% (p<0.0001) and 56% (p<0.0001) of variance of VF and 67% (p<0.0001) and 62% (p<0.0001) of variance of SF in males and females of the same age and height, respectively and 4% (p<0.0001) of VF variance ; similarly in females, BMI and waist explained, respectively, just 4% (p<0.0001) and 11% (p<0.0001) of VF variance . In cont Major changes in body size and composition happen during puberty, with accelerated weight gain occurring in most boys and girls at stages 4 and 5 of pubertal development . Therefo In addition to BMI and waist, we investigated two other anthropometric measures of adiposity that could be used in clinics as predictors of VF and SF, namely suprailiac skinfold and waist/hip. Suprailiac skinfold showed strong relationships with VF and SF in both sexes, explaining 62% (p<0.0001) and 52% (p<0.0001) of VF variance and 72% (p<0.0001) and 64% (p<0.0001) of SF variance in males and females, respectively \u2013 it explained only 22% (p<0.0001) and 20% (p<0.0001) of VF variance and 12% (p<0.0001) and 6% (p<0.0001) of SF variance in males and females, respectively with VF and SF did not differ between early and late puberty groups . The results of the present study demonstrate that, during adolescence, routine clinical measures of adiposity, namely BMI and waist, predict SF but not VF. These relationships are similar in both sexes and exist throughout puberty. The current study is a large-scale investigation of adolescents testing BMI and waist as predictors of VF and SF measured directly with MRI. A few such investigations have been conducted in adults \u201343 but n In the present study, we examined two additional anthropometric measures of adiposity that could be used in clinics as predictors of VF and SF \u2013 these were suprailiac skinfold and waist/hip. Both measures performed either similarly or even worse that BMI and waist medicine, as youth at risk for obesity-related CMD cannot be easily identified using these clinical measures . Further Given the clear limitation of currently used clinical measures of adiposity (BMI and waist circumference) to predict VF, development of cost-effective imaging techniques to quantify VF that would be suitable for everyday clinical practice and/or identification of robust circulating biomarkers of VF accumulation are warranted. File S1Supporting table and figures.Table S1, Basic characteristics and adiposity measures for early and late puberty males and females. Figure S1, BMI and waist circumference as predictors of VF and SF quantities (VF and SF not adjusted for each other). Figure S2, suprailiac skinfold thickness and waist\u2013to-hip ratio as predictors of VF and SF quantities (VF and SF not adjusted for each other). Figure S3, suprailiac skinfold thickness and waist-to-hip ratio as predictors of VF and SF quantities (VF and SF adjusted for each other).(DOC)Click here for additional data file."} +{"text": "No data have been available on severe allergic reactions in Finland.We summarize the data accumulated from 2000 to 2007 in the national register established at the Skin and Allergy Hospital of the Helsinki University Central Hospital, where physicians voluntarily report on patients with severe allergic reactions.During the period, the 530 reported cases of severe allergic reactions represented an annual frequency of 0.001%. Of the patients, 66% were adults and 56% were female, with a median age of 27 years. Food was the causative agent in 53% of the cases, drugs in 26%, allergen preparations in 12%, and insects in 8%. Dermatologic symptoms were reported in 85%, respiratory in 76%, cardiovascular in 50%, gastrointestinal in 33%, and eye/nose symptoms in 18%. The reaction was a life-threatening anaphylactic shock in 26% of the cases, with no deaths reported. Patients were treated with intramuscular adrenaline in 75% of the cases. Not only nuts and seeds, but also fruit and vegetables were the most important allergens for the adults. Nuts were also important allergens for children, along with milk, egg, and wheat. In addition, many \"exotic\" allergens were identified: patent blue, carmine dye, yeast, buckwheat, and macrogol.Severe allergic reactions are underreported, but a register reflects the real-life situation and helps to identify new causative agents. It also contributes to improvements in first aid treatment practice. Anaphylaxis is an immunoglobulin E (IgE)-or non- IgE-mediated, severe, life-threatening systemic allergic reaction, with a rapid onset and multiple organ system involvement ,2. IndepTo our knowledge, nationwide anaphylaxis registers or similar organizations exist at least in Denmark, France-Belgium, Germany-Austria-Switzerland, Italy, the Netherlands, Norway, Sweden, the United Kingdom and Ireland, and also in the United States Table 3-7]. M-7. M3-7]No data reveal actual frequency of severe allergic reactions in Finland. The literature has reported incidence figures of 7.9 to 21 anaphylaxis cases per 100,000 person-years,-10 alongIn 2000, the Finnish register of severe allergic reactions was established at the Skin and Allergy Hospital of the Helsinki University Central Hospital, where physicians--mostly allergologists--voluntarily report patients with severe allergic reactions independently of the causative agent. A 1-page questionnaire form is available on the Internet.We summarize the first 530 cases reported to the register between 2000 and 2007. Our results are based on the anonymous patient data provided by the physicians in the questionnaire form evaluated by an allergy specialist.Any adverse reactions from vaccines that were reported to the National Public Health Institute are absent from the present article.A total of 530 cases of severe allergic reactions were reported between 2000 and 2007 throughout the country, mostly (65%) from the Helsinki capital area, which represents 25% of the entire population of 5.2 million. This represents an annual incidence of 0.001%.Of the 530 cases, 348 (66%) were adults and 182 (34%) were children younger than 16 years. Females accounted for 295 (56%). Median age was 27 years; range was from 2 months to 92 years. Two peaks in age distribution were for children younger than 5 years and young adults aged 25 to 35 years.A previously diagnosed allergy occurred in 91%; skin disorders were present in 43%, allergic rhinoconjunctivitis in 43%, asthma in 33%, and gastrointestinal disorders in 6%. A previous anaphylaxis affected 23%.The reactions were regarded as severe anaphylactic shock reactions in 26% of the cases, with a systolic blood pressure in adults less than 90 mm Hg or with severe respiratory symptoms such as bronchospasm and upper airway angioedema . Other sIn 74% of the cases, the first symptoms predicting severe allergic reaction appeared less than 30 minutes after contact with the inciting allergen.Skin symptoms were most commonly reported, in 85%, followed by respiratory (76%), cardiovascular (50%), and gastrointestinal (33%) symptoms.Most frequently, corticosteroids were used for treatment, in 84%, followed by adrenaline in 75%, and antihistamine in 67%. Of the adrenaline-treated patients, 10% used a ready-to-use adrenaline autoinjector.Foods were the causative agent in 279 53%) cases, drugs and medical interventions in 136 (26%), allergen preparations for diagnostic work and immunotherapy in 64 (12%), and insects in 40 (8%) , followed by the home (30%), hobbies (14%), restaurants (7%), day care/schools (7%), and work places (6%).Food (n = 279) was the most common cause of severe allergic reaction (53%). Of these patients, 53% were adults, 64% of whom were females, but most (60%) of the children were boys. The home was the most common place for food reaction (36%).Food was responsible for 72% of the reactions in children, but for only 43% in adults. An association with exercise was documented in 8% with food-related reactions. Food caused 46% of the most severe shock reactions, including peanut/tree nuts/seeds (n = 17), grains (n = 11), milk (n = 10), fruit/vegetable (n = 8), egg (n = 6), fish/shellfish (n = 2), soy, and yeast among others.An allergen-containing food was accidentally given to 53 patients, 60% of whom were children. These included milk, wheat, egg, fish, nuts, and seeds. Most episodes (77%) took place outside the home.Most food-related reactions were from peanuts, tree nuts, and seeds (21%), 36% of which occurred in children .casein and whey were unknown. The patient had an adrenaline autoinjector, but she did not dare use it. One adult experienced anaphylaxis from cow's milk feta cheese, but she tolerated goat's milk feta, whereas another adult experienced anaphylaxis from goat cheese without a cow's milk allergy . Five reports were toxic reactions from tuna fish in which a high histamine content was suspected as the causative agent because no fish allergy was evident. Eight cases were from shrimp and one from roe in the absence of fish allergy [Fish or seafood was reported in 8% of the cases. Fish nuggets were given to a child instead of chicken nuggets . In otheYeast used as a flavoring agent in a spaghetti sauce repeatedly caused severe anaphylactic reactions in a mould-sensitive patient .Drinks were reported in 11 cases (4%), mostly (73%) in adults. Reported drinks included red and white wine, beer, long drink, cider, juice, and gl\u00fchwein. One patient repeatedly experienced anaphylaxis when dancing the tango after drinking a beer.Drugs n = 136), allergen preparations (n = 64), and other medical interventions such as food provocation tests (n = 22) were reported in 222 cases (42%), mostly (75%) in adults and ibuprofen accounted for 45% of painkillers. In 4 cases, ASA in a combination product was not recognized by the patient as such.In 68% of the operation-related reactions, a neuromuscular blocking agent (rocuronium) was suspected as the causative agent either alone or with other anesthetic agents. Three cases were caused by the patent blue dye (E 131) used to locate sentinel lymph nodes. One reaction was caused by chlorhexidine used as skin disinfectant . Local aIn a drug, the active ingredient is not always the agent causing harm. One case of penicillin anaphylaxis was caused by macrogol (polyethylene glycol) used as an excipient in the tablet vehicle .Allergen preparations were the causative agent in 64 cases (12%), 18 of which occurred in children. Ten reports with mild reactions were from skin prick testing with fish, egg, penicillin, moulds, pollens, animals, chironomid, or carmine dye (E120). Carmine IgE was positive in in-house immunospot test but remained negative in the commercial IgE test, which, however, was improved in collaboration with our laboratory.Of all reports, 54 (10%) concerned specific immunotherapy (SIT). In 83% of the reactions, timothy grass was the causative allergen, either alone or with other pollen allergens. Nine patients were on a maintenance dose; some for several years.\u03b2-lactams (n = 11), timothy SIT (n = 5), x-ray contrast media (n = 5), infliximab, sodium aurothiomalate, and a natural remedy (pollen) among others.Of the severe anaphylactic shock reactions, 45% were caused by drugs, allergen preparations, and other interventions, such as operations (n = 16), painkillers , Insects were reported in 8% of the cases, 63% of which were in adults. Wasps (92%) were by far the most commonly reported. Insects caused 9% of the severe shock reactions.Based on our study, during the 8 years, 530 severe allergic reactions were reported to the Finnish register for an annual incidence of 0.001%. Reactions are undoubtedly underreported, with higher figures per population reported elsewhere .From the reactions, 26% were life-threatening circulatory or respiratory shock reactions. Adrenaline was the first aid treatment for 75%, but corticosteroids were more frequent: 84% of all cases. In a Swiss study, 48% of the anaphylaxis patients with circulatory symptoms received adrenaline, whereas In 5% of our cases, a late-phase reaction occurred compared with late reactions reported in 2% to 20% of cases elsewhere ,25.Food, drugs, and insects alternate globally as the most common causes of anaphylaxis ,13,18,26Diagnostics and other interventions are not without risks ,15,28,29Severe allergic reactions from allergy diagnostics and allergy treatment (SIT) comprised 18% of the cases, and a high frequency of SIT anaphylaxis has been reported only by Mehl et al. Timothy Insects are important anaphylactic allergens in Switzerland and in the United Kingdom but account for only 8% of the reports in Finland, wasps being the most frequently reported . BecauseWe found only 1 report on severe reaction from latex, an important allergen in France and the United States ,25,27,30To avoid is to identify. Our register has been proven to be valuable for identifying causes for severe allergic reactions in Finland. Thus far, poorly recognized allergens and allergen sources have been detected, such as patent blue, carmine, yeast, buckwheat, soy drink, and macrogol. In addition, hidden allergens have been demonstrated in food and drugs. In France, hidden allergens have accounted for 13% of severe anaphylactic reactions .Our register has also contributed to first aid treatment practice by highlighting the importance of intramuscular adrenaline as first-line treatment.All patients experiencing a severe allergic reaction should be sent to an allergologist who will evaluate the causative agent, provide guidance for avoidance and prevention, and also consider SIT. The patient, family members, and caregivers must be instructed on how to use an adrenaline autoinjector."} +{"text": "The aim of this study was to determine the microorganisms prevalent in the necrotic dental pulp and root canals of unsuccessfully treated teeth.The present study was conducted on 150 single-rooted teeth of patients referring to a dental clinic. Sampling was performed by placing a sterile paper point in the canal for 60 s. Bacterial samples were evaluated by a microbiological technique specific for anaerobic species, used for isolation and identification of sampled strains.From the 150 samples taken, 101 were from necrotic pulps (primary infection) and 49 were from the teeth with an unsuccessful endodontic treatment (secondary infection). Enterococcus faecalis was a prevalent species in the failed root canals evaluated. Colonizing microorgan-isms result in pulpal and periapical diseases.3treatment involves the treatment of both primary and secondary infections in the root canal system. Primary infected root canals are untreated canals, into which the microorganisms have gained access to colonize the pul-pal tissue, resulting in dysfunction.4Secondary infection in the root canal occurs due to the failure of endodontic treatment and presence of bacterial infection in the root canal system.6Several studies have investigated the microflora of root canal system infections. In primary root canal infections, necrotic pulpal tissue has revealed polymicrobial flora with an average of 4-7 intra-canal species, which are often Gram-negative anaerobics.12 Several studies have shown obligatory anaerobic bacte-ria in root canal infections, which comprise 90% of all bacterial species.13It has been established that bacteria initiate pulpal and periapical infections.12 Studies have also demonstrated the presence of facultative aerobic bacteria in the oral cavity, but obligatory anaerobics have not been isolated.12Studies have reported various species in the pulp of necrotic teeth and, therefore, one or multiple species of bacterial pathogens can be isolated from an infected root canal.13 The purpose of the present study was to evaluate the presence of bacteria and spores in the untreated and unsuccessfully-treated root canals of human teeth using culture techniques.Recent studies investigating bacteria in teeth with an unsuccessful restoration have revealed a certain group of microorganisms including Gram-positive facultative aerobics, especially Enterococcus faecalis.This study was conducted on 150 single-rooted teeth of patients referring to the Dental Clinic of Tabriz University of Medical Sciences between October 2007 and September 2008. Medical and dental histories were taken as part of the routine at the clinic. Patients with a systemic disease or those who had taken antibiotics in the last three months were excluded from the study. Bacterial samples were evaluated by means of an advanced microbiological technique specific for anaerobic species, which was used for isolation and identification of sampled strains.1 The teeth were isolated with rubber dam. Two-step access cavity preparation was accomplished using sterile burs under water spray. Sterile saline was used where rinsing was necessary. All coronal restorations, posts, and carious lesions were removed. The teeth were rinsed using 30% hydrogen peroxide and 2.5% sodium hypochlorite for 30 s, and 5% sodium thiosulfate was used as the deactivating solution. All the instruments used during access cavity preparation and afterwards were sterile. In the case of a treated canal, canal filling material was removed with the use of Gates Glidden drills and endodontic files without the use of any chemicals. Canals were rinsed with sterile saline to remove the remnants of filling material and debris, and to moisten the canals before sampling. Working length of the canal was determined radiographically using a #20 K-file. The root canal was prepared with a #20 K-file 0.5 mm short of the radiographic working length without any rinsing. Sampling was performed by placing a sterile paper point in the canal for 60 s. During the sampling procedure, nitrogen gas was pumped into the canal orifice. Following removal from the canal, the paper point was immediately put into an intermediate medium containing 3 mL of sterile reduced transport liquid and sent to the microbiology laboratory within 15 min. The maximum time between collecting the samples and starting laboratory procedures was 4 h.Sampling was carried out according to the asepsis instructions described previously.2, 10% CO2, and 80% N2 for 2, 5, and 14 days, respectively. Colombia agar plate was incubated at 37\u00b0C for 2 days under aerobic conditions. Sabouraud\u2019s agar plate was kept at room temperature for 5 days. Following incubation, the plates were tested and the colonies were cultured unspecifically on FAA-blood plate to obtain pure cultures. Colonies were selected based on appearance for further evaluation. On the obtained pure culture, Gram staining and catalase production tests were performed and their gaseous need was provided through a 2-day aerobic and anaerobic incubation period. Bacterial colonies were cultured to be identified and purified. Anaerobics were identified using phase contrast microscopy, morphotyping, Gram staining, and biochemical tests with enzymes-based kits . Facultative anaerobics and aerobics were identified using Gram staining, micromorphology, colony morphology, growth in specific media, and enzyme-based biochemical kits . Additional tests including fluorescence under ultraviolet light at 366 nm, 3% bovine erythrocyte hemagglutination, lactose fermentation using 4-methyl-\u03b2-galactosidease fluorogenic substrate, and determining trypsin-like activity using synthetic fluorogenic peptide were performed for Gram-negative black-pigmented anaerobes.In an anaerobic setting in the laboratory, tubes containing transport medium were shaken for 60 s in the mixer. Ten series of 1:104 dilutions of anaerobic unreduced broth were prepared and 50 \u00b5L of each was added to the following media: 5% fibrin FAA bovine blood, 0.001% w/v nalidixic acid, 0.025% w/v nalidixic acid and vancomycin, 0.075% w/v neomycin for anaerobics, 5% Colombia agar and fibrin bovine blood for aerobics and 100 \u00b5g/mL of Sabouraud\u2019s agar with chloramphenicol for spores. To culture anaerobics, plates were incubated at 37\u00b0C under the pressure of 10% HOut of 150 samples, 101 were taken from necrotic pulps (primary infection) and 49 had an unsuccessful endodontic treatment (secondary infection). Clinical and radiographic evaluation of the teeth revealed conditions including previous history of pain (40 cases), acute pain (28 cases), sensitivity to percussion (32 cases), tooth mobility (6 cases), swelling (26 cases), bloody canal (36 cases), pus formation (21 cases), hemorrhage (8 cases), clear drainage (7 cases) , and periapical radiolucency (26 cases). Vitality tests showed non-vital pulps in all teeth. In teeth that had been treated endodontically, weak obturation and radiographic signs of apical periodontitis in 19 cases and recurrent caries in 34 cases were present. In 8 secondary infection cases, coronal restorations were not present, and from the 41 cases with coronal restorations, 11 teeth showed microleakage.In the cultured plates, 35 teeth had only one species, 44 teeth had two species, and 46 teeth showed multimicrobial infection involving three or more species from each root canal. With regard to primary endodontic infection, 17 teeth had only one species, 40 teeth had two species and 34 teeth had multimicrobial infection, involving three or more species. No species was detected in the 10 remaining teeth. Each canal had five species at most.A total of 197 isolated culturable species were identified from root canals evaluated. Of these, 85 species (43.1%) were obligatory anaerobes and 104 species (52.8%) were facultative anaerobes. Eight species (4.1%) were identified as fungi. 68.9% of isolated species were Gram positive and 27% were Gram negative. 62.4% of species collected from primary necrotic pulps were Gram positive and 31.2% were Gram negative. 77% of species collected from failed endodontically-treated teeth were Gram positive and 23% Gram negative.Peptostreptococcus was the most prevalent species followed by Streptococcus, Porphyromonas, and Enterococcus faecalis. Strains of P. provetti, S. sanguis, S. salivarius, P. endodontalis, and especially E. faecalis were prevalent in the unsuccessfully-treated root canals. C. albicans, Veillonella spp., E. coli, Actinomyces meteri, Fusobacterium, Eubacterium lertum, and S. oralis were only found in samples from untreated canals. S. salivarius, P. endodontalis, A. odontolyticus, and Peptostreptococcus provetti were almost equally found in both primarily and secondarily infected root canals. The prevalence of bacteria from the root canals evaluated is presented in4The present study evaluated the microorganisms collected from primary and secondary infection of root canals. Microorganisms were found in 140 of all the canals evaluated in this study. In 6.7% of the evaluated samples, no microorganisms were found. Other studies using culture methods for endodontic samples have also shown canals without any microorganisms.13 It has been shown that improper restorations, carious lesions, and enamel cracks produced during access cavity preparation provide access routes to large dentinal tissues in many cases, leading to pulpal infection. In the present study, 61 teeth had a necrotic pulp, 10 of which revealed radiographic signs of periapical lesions. The results of this study showed that among the samples, Gram positive bacteria (67.8%) are more prevalent in primary root canal infections. This is consistent with the results of previous studies indicating 69% facultative anaerobics and 70% Gram positive bacteria in the infected root canals.11 The two most prevalent species among the collected samples were Peptostreptococcus and Streptococcus spp. Black-pigmented bacteria including Prevotella and Porphyromonas spp. were also seen in primary pulpal infections. These results coincide with the findings of previous studies.11Primary infection of root canals is the result of colonization of microorganisms in a necrotic pulpal tissue leading to a dysfunction of the pulp. Propagation of pulpal infection depends on factors such as number of bacteria, caries, trauma, and iatrogenic variables.7Secondary infections are produced by microorganisms resistant to chemico-mechanical procedures or as a result of bacterial invasion from microleakage of coronal restorations.10 Other isolated species included A. odontolyticus, L. aerophilus, S. salivarius, S. sanguis, P. corporis, P. gingivalis, and P. odontoma.Of the 49 teeth treated endodontically in the present study, 19 had a weak obturation for more than two years with radiographic signs of apical periodontitis. The most prevalent microorganisms among the samples of secondary infection were Gram positive bacteria. E. faecalis isolates were the most prevalent species, which is consistent with the results of previous studies.The results of the present study indicate that root canal infection occurs as a result of multiple microorganism activity, dominated by Gram positive bacteria. Polymicrobial anaerobic infections were also found in the root canal. Regarding the secondary infection, E. faecalis was found to be the most prevalent species."} +{"text": "Preterm birth (PTB) is a major cause of infant morbidity and mortality, but the relationship between comorbidity and PTB by clinical subtype and severity of gestational age remains poorly understood. We evaluated associations between maternal comorbidities and PTB by clinical subtype and gestational age.We conducted a retrospective cohort study of 1,329,737 singleton births delivered in hospitals in the province of Qu\u00e9bec, Canada, 1989-2006. PTB was classified by clinical subtype , spontaneous preterm labour) and gestational age . Odds ratios (OR) of PTB by clinical subtype for systemic and localized maternal comorbidities were estimated using polytomous logistic regression, adjusting for maternal age, grand multiparity, and period. Attributable fractions were calculated.PTB rates were higher among mothers with comorbidity (10.9%) compared to those without comorbidity (4.7%). Several comorbidities were associated with greater odds of medically indicated PTB compared with no comorbidity, but only comorbidities localized to the reproductive system were associated with spontaneous PTB. Drug dependence and mental disorders were strongly associated with PPROM and spontaneous PTBs across all gestational ages (OR > 2.0). At the population level, several major comorbidities were key contributors to all clinical subtypes of PTB, especially at < 32 weeks. Major systemic comorbidities were key contributors to PPROM and medically indicated PTBs.The relationship between comorbidity and clinical subtypes of PTB depends on gestational age. Prevention of PPROM and spontaneous PTB may benefit from greater attention to preeclampsia, anemia and comorbidities localized to the reproductive system. Preterm birth (PTB) is a major cause of mortality and morbidity throughout life and rates are increasing in many countries -3. The dFewer studies have examined the relationships between comorbidity and PTB clinical subtype at different gestational ages, despite evidence suggesting that factors triggering PTB may differ depending on gestational age ,13. ReseThis gap in the literature needs to be addressed to better understand which maternal comorbidities to target for prevention of PTB at different gestational ages, especially PPROM and spontaneous preterm labour which are difficult to prevent ,8. This This study was based on a retrospective cohort of all births in Qu\u00e9bec hospitals from 1989 to 2006 . Nearly 100% of infants in Qu\u00e9bec are delivered in hospitals . MaternaBirths at < 37 completed weeks of gestation were defined as PTBs . GestatiMaternal comorbidities based on the ICD-9 were claCovariates included maternal age , grand multiparity , and perDescriptive statistics were computed. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for comorbidity indicators and overall preterm birth in models that were unadjusted and adjusted for maternal age, grand multiparity and period. Polytomous logistic regression ,23 was uOverall, 6.2% of births were preterm, of which 28.7% were medically indicated, 30.7% PPROM, and 40.6% spontaneous. Over 5% of PTBs occurred at < 28 weeks, 7.3% at 28-31 weeks, and 87.2% at 32-36 weeks. The majority of PTBs at < 28 weeks were spontaneous (44.2%), followed by PPROM (29.3%) and medically indicated (26.5%). A similar pattern was observed for PTBs at 32-36 weeks, among which 41.5% were spontaneous, 30.7% PPROM, and 27.8% medically indicated. In contrast, PTBs at 28-31 weeks were more frequently medically indicated (40.6%) than PPROM (31.8%) or spontaneous (27.6%). The proportion of PTB was greater for mothers with localized (10.9%) and systemic comorbidities (8.7%), compared to those without comorbidity , drug dependence (21.4%), and edema/renal disease (17.0%) , fetal anomalies 43.2%), placenta previa (35.2%) and placental abruption (31.9%) than systemic comorbidities . For systemic comorbidities, associations with overall PTB were highest for preeclampsia/eclampsia , drug dependence , and edema/renal disease . For localized comorbidities, odds of overall PTB were highest for cervical incompetence , fetal anomalies , placenta previa , and placental abruption .Associations between comorbidities and clinical subtype of PTB depended on gestational age Table . For sysLocalized comorbidities were generally associated with medically indicated PTB and PPROM at most gestational ages, while the associations with spontaneous PTB tended to be stronger at < 32 weeks of gestation. Previous cesarean delivery was associated with greater odds of medically indicated PTB after 28 weeks, but lower odds of PPROM at 32-36 weeks and spontaneous PTB at all gestational ages.Attributable fractions suggested that preeclampsia/eclampsia, anemia, placental abruption, structural abnormalities, and chorioamnionitis were important contributors to medically indicated PTB at the population level, though the contribution varied by gestational age Table . Anemia To our knowledge, this study is the first to evaluate relations between systemic and localized maternal comorbidities with PTB by clinical subtype and gestational age. In a large population-based cohort, we demonstrated that comorbidities overall were associated with higher likelihoods of medically indicated PTB, while only comorbidities localized to the reproductive tract were associated with spontaneous PTB. At the population level, several major localized comorbidities were key contributors to all three clinical subtypes of PTB, especially at < 32 weeks of gestation. In contrast, major systemic comorbidities were the key contributors to medically indicated PTBs, but not spontaneous PTBs. This study is the first to identify anemia as the most important maternal systemic comorbidity contributing to PPROM at the population level.Hypertension is a major pregnancy complication . We founThe influence of diabetes, another common pregnancy complication, also depended on clinical subtype of PTB and gestational age. We confirmed that compared to gestational diabetes, pre-existing diabetes was more strongly associated with medically indicated PTB ,33. DiabDrug dependence and mental disorders are increasingly recognized as drivers of PTB -37. We oRemaining causes of systemic comorbidity including cardiovascular disease, edema/renal disease, thyroid disease, and anemia were mainly associated with medically indicated PTB at all gestational ages, as observed elsewhere ,18,30. TLocalized comorbidities in general were associated with PTB, especially medically indicated PTB and PPROM at most gestational ages. Several studies have found that overall PTB was associated with cervical incompetence, fetal anomalies, placenta previa, placental abruption, and oligohydramnios ,4,5,17, This study was subject to limitations. Some comorbidities could not be examined in finer categories due to limited ICD code availability or sample size , and underreporting of certain comorbidities is probable. Though hospital data are routinely used for surveillance in Qu\u00e9bec , validatThis study demonstrated that the associations between maternal comorbidities and PTB may differ by clinical subtype and gestational age. Preventive strategies to reduce PTB should target major systemic and localized co-morbidities that account for large proportions of PTBs, especially maternal hypertension, anemia, placental abruption, and structural abnormalities. Better clinical management of these maternal comorbidities may be helpful, but such measures should take into account variation in associations by clinical subtype and gestational age.The authors declare that they have no competing interests.NA and TUNL conceived the study, with contributions from ZCL. NA prepared the data. TUNL/ALP performed the statistical analyses. NA and TUNL interpreted the results with contributions from ALP and ZCL. NA and TUNL reviewed the literature and wrote the manuscript. ALP and ZCL critically revised the manuscript for scientific quality and content. All authors approved the final version for publication.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2393/11/67/prepubDefinition of systemic and localized maternal comorbidity based on International Classification of Diseases (ICD)-9 codes. International Classification of Disease codes (ninth revision) for the causes of maternal comorbidity analyzed in the current study.Click here for file"} +{"text": "Objectives. Determine outcome of the 2005 appropriateness use criteria (AUC) for SPECT in a diverse population of patients and physicians. Background. AUC for SPECT were the first cardiology document to identify 52 clinical indications for imaging, 49 of them for stress SPECT. AUC have been proposed as cornerstone of responsible use of perfusion imaging. Methods. 585 consecutive patients undergoing SPECT were evaluated prospectively. Appropriateness was examined for demographic variables, clinical variables, and for physician and patient subgroups. Combined end-point of total mortality, cardiac revascularization, and cardiac admissions at 1 year post SPECT was evaluated. Results. SPECT indications were: appropriate, 63%; uncertain, 20%; inappropriate, 14%; not assigned, 3%. Most appropriate SPECT were observed in patients with known coronary disease (72%), chest pain syndrome (89%), high pre-test likelihood of disease (100%), men (70%), inpatients (72%), and cardiovascular physicians' referrals (69%). End-point was reached in 53 patients (97.4% follow up). Unadjusted event rates were: appropriate (12%), uncertain (7.1%), inappropriate (2.4%) SPECT (P = .01). Conclusion. Appropriateness of SPECT differs in subgroups of patients and physicians. Clinically significant outcomes occur more frequently in the appropriate stress SPECT group. Focused efforts are need for outpatients, asymptomatic patients, women, and non-cardiovascular physicians. There has been an explosive growth in cardiovascular imaging with stress testing demonstrating 6.1% annual increase versus 2% for cardiac catheterization, 0.8% for percutaneous intervention, and 0.1% for acute myocardial infarctions in population-based study of the United States Medicare patients from 1993 to 2001 [http://www.cms.gov/DemoProjectsEvalRpts/downloads/Medicare_Imaging_Demonstration.pdf). To encourage the best use of AUC and decrease inappropriate imaging, the ACC national quality initiative Imaging in \u201cFocus\u201d contains multiple resources pertaining to the AUC, including a decision algorithm has been developed by the ACC in partnership with Skyscape [http://www.astellasapps.com/).In response to these developments, the American College of Cardiology pioneered appropriateness criteria for single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) in 2005. The criteria were developed to account for evidence-based clinical relevance of stress perfusion imaging and were the first cardiology-specific document to address appropriateness. The criteria relied on the modified RAND/UCLA methodology to identify 52 common clinical scenarios that were divided by level of appropriateness into appropriate, uncertain, and inappropriate indications . 49 indiSkyscape . A free Despite these developments, the clinical use of the appropriateness criteria has not become standard of practice for physicians. Gibbons et al. have investigated performance of appropriateness criteria for stress SPECT and stress echocardiography in 284 and 298 patients, respectively . OverallThe objectives of the current study were to identify clinical value of 2005 AUC in various patient and physician groups and to focus on downstream use of resources as defined by patient outcomes in relation to appropriateness. We have prospectively applied appropriateness criteria to a diverse population of patients and physicians to evaluate:impact of demographic (gender) and clinical , and admission status) factors,impact of referring physician specialty and practice type,outcomes at 1 year after SPECT .Over 3,000 patients undergo SPECT at our institution annually. From March 2007 thorough April 2008, consecutive patients older than 18\u2009yrs of age were enrolled if they were English speaking, had a capacity for primary decision making, had no chronic illnesses or malignancy with estimated life expectancy of less than 1 year, and were willing to provide informed consent for access to their medical record, phone call followup and/or social security number. The final cohort consisted of 585 patients. Admission status was ascertained at the time of SPECT as inpatient or outpatient based on registration record. Reason for stress, type of stress, known cardiac history , risk factor profile, and name of the referring physician were obtained and recorded. Followup was complete in 554 patients (94.7%).Referring physician name for each patient was cross-referenced with the hospital roster of credentialed physicians for both voluntary and full-time faculty. All cardiology and cardiac surgery physicians were designated as cardiovascular (CV MD). All other physicians were designated as noncardiovascular (non-CV MD). There were 258 patients referred by CV MDs, and 327 referred by non-CV MDs.Appropriateness criteria tables were included in each patient's file upon recruitment into the study , 13. AppLipid values were often not available for calculation of FRS. Total cholesterol and HDL cholesterol were assigned 0 points if no dyslipidemia or treatment with statins were reported, and 1 point if reported.Any chest pain syndrome or anginal equivalent were recognized as symptoms.If more than one indication was identified, the most appropriate for SPECT was chosen by consensus opinion of investigators. Chi-square was used, and Fisher exact test was substituted for chi-square as indicated by frequencies of observations. SAS 9.1 was used for analysis.Patient characteristics are presented in Two site-specific patterns of care are important to mention. Our emergency room policy expedites admission to the in-house hospitalist service for any patient with a \u201csoft rule out MI\u201d, thus many of them were inpatients at the time of SPECT MPI. Additionally, despite a rather high number of patients with symptoms (53%), only 6% of patients were in the high pre-test category reflecting a bias toward invasive coronary angiography.570 (97%) patients were classified by clinical indications with 15 (3%) not assigned . Most coappropriate with the most common indications as follows: Of all stress SPECT studies, 63% were detection of CAD, symptomatic: 37%intermediate pre-test probability, ECG interpretable and able to exercise: 21%; ECG uninterpretable or unable to exercise: 12%,high pre-test probability, ECG interpretable and able to exercise: 3%; ECG uninterpretable or unable to exercise: 2%,Risk assessment: 23%after revascularization (PCI or CABG): 12%symptomatic, evaluation of chest pain: 7%,asymptomatic prior to CABG, \u2265 5\u2009yrs after CABG: 3%; symptomatic prior to CABG, \u22655\u2009yrs, 3%,preoperative evaluation for noncardiac surgery intermediate risk predictor or poor exercise tolerance (<4\u2009METS): 4%,with prior test results: 4%asymptomatic or stable symptoms, abnormal catheterization or prior SPECT \u22652\u2009yrs to evaluate worsening disease: 2%,high FRS, asymptomatic: 3%,Uncertain indications for SPECT were observed in 20%. The most common uncertain indications were.detection of CAD: asymptomatic, moderate FRS: 15%,risk assessment: 5% after revascularization, symptomatic prior to revascularization \u22652\u2009yrs after PCI: 4%; asymptomatic, \u22652\u2009yrs after PCI: 1%.Inappropriate indications were observed in 14%detection of CAD: 13%asymptomatic, low FRS: 7%,symptomatic, ECG interpretable and able to exercise: 6%,risk assessment: 1% Preoperative evaluation prior to non-cardiac surgery, minor to intermediate risk predictor, normal exercise tolerance (>4\u2009METS): 1%.There were 15 3%) unclassifiable patients. The observed indications were: syncope , asympto% unclassWhile most of the appropriate, uncertain, and inappropriate indications observed in our patients were similar for 2005 and 2009 AUC, most of the unassigned patients were categorized as uncertain by 2009 AUC as shown in , symptoms , and at a higher pre-test likelihood risk but did not differ by gender, known CAD, or FRS. Most inpatients (66%) were referred by non-CV MDs , and less known CAD but did not differ in pre-test likelihood categories as compared with men. FRS were different for asymptomatic women as compared to men with more women in the low, and fewer women in the high risk groups: low, 41% versus 24; intermediate, 54% versus 61%; high, and 5% versus 15%, P = .01. Most women were referred by non-CV MDs (66%) with more even distribution among specialty of physicians for men . More men (39%) than women (15%) had known CAD (P < .0001). 72% of all known CAD patients were referred by CV MDs. Patients with known CAD had more appropriate SPECT (74% versus 61%), and the least of inappropriate SPECT .Compared to patients without known CAD, patients with CAD had fewer symptoms . Among CV MDs, private practitioners had a trend for more appropriate SPECT than full-time faculty cardiologists (74% versus 63%) although this difference was not significant. As described above, more women and inpatients were referred by non-CV MDs while more men, outpatients, and patients with known CAD were referred by CV MDs.There were differences in admission status, gender, and known CAD by referring physician specialty . Most inP = .01).Follow up was completed in 554 patients: 359 with appropriate, 113 with uncertain, and 82 with inappropriate SPECT. Combined end-point of total mortality, revascularization and hospital admission for a cardiac reason other than revascularization was reached in 53 patients. There were 20 death (17 in appropriate SPECT patients), 14 revascularizations (13 in appropriate SPECT patients), and 28 admissions (21 in appropriate SPECT patients). Unadjusted events rates were 12% (43 of 359 patients) for appropriate, 7.1% (8 of 113 patients) for uncertain, and 2.4% (2 out of 82 patients) for inappropriate SPECT and inappropriate (14%) SPECT was similar to those reported by previous studies . The patSeveral important conclusions emerge from this study. First, appropriateness of SPECT was strongly influenced by presence of symptoms , pre-tesSecondly, findings emerged in patient subgroups that are interesting and require further investigation. As may be expected, inpatients were more symptomatic and at a higher clinical probability of coronary artery disease. Thus, it is not surprising that more appropriate SPECT studies were observed in inpatients. Appropriateness criteria appeared more favorable toward patients with established CAD. Women were more symptomatic than men but did not differ in pre-test likelihood of disease and had a lower prevalence of known CAD. Among asymptomatic patients, more women were at a lower FRS. While less of appropriate SPECT was observed for women , the most notable difference was in the occurrence of the inappropriate studies (22% in women versus 9% in men). It is likely that such a difference cannot be attributed solely to less prevalent CAD or lower FRS. These findings suggest a gender-related referral bias and indicate that it may be important to include gender-specific recommendations in the appropriateness criteria. http://asnc.org/imageuploads/Asymptomatic.pdf.Another challenging group were asymptomatic patients in an intermediate FRS group . Most ofThere were notable differences by referring physician specialty. Cardiovascular physicians outperformed their noncardiovascular colleagues with more appropriate SPECT referred, although that difference was small (69% versus 62%). Importantly, significantly fewer inappropriate studies were referred by cardiovascular MDs , lower for those with uncertain SPECT (7.1%), and lowest for the inappropriate SPECT patients (2.4%). A 7.1% event rate in the uncertain group suggests that it is prudent to perform these studies until factors or scenarios are identified that would allow to further risk stratify this group.Notable limitations exist in this study. First, this represented a single medical center experience. As such, selection bias, referral bias, and practice preference bias were all present. Second, we have made assumptions in calculating FRS that may have affected appropriateness designations. Third, not all appropriateness indications were equally prevalent in our cohort, and some were observed in less than 1% of the patients. Fourth, we have not been able to evaluate cardiac mortality but rather a combined end point that included total mortality, revascularization, and cardiac admissions. Fifth, 15 of our patients remained unclassified. Most of them would have been assigned as uncertain if 2009 AUC were used, and not likely to affect appropriate and inappropriate groups.We have established that appropriateness criteria are effective in identifying appropriateness of SPECT in a diverse patient population. More appropriate studies were observed in patients with symptoms and at higher pre-test likelihood and Framingham risk. Most of the inappropriate studies were observed in asymptomatic and low risk patients. Patients without known CAD, women, and those with an intermediate Framingham risk emerged as subgroups where further investigation is warranted. Physician specialty was an important factor determining appropriateness with cardiovascular physicians outperforming their noncardiovascular colleagues. Unadjusted event rates were highest in the appropriate SPECT group, intermediate in the uncertain group, and lowest for the inappropriate SPECT patients."} +{"text": "Campylobacter, Salmonella, and Shigella. The weighted mean incidence of reactive arthritis was 9, 12, and 12 cases per 1,000 cases of Campylobacter, Salmonella and Shigella infections respectively. To our knowledge, this is the first systematic review of worldwide data that use well-defined criteria to characterize diarrhoea-associated ReA. This information will aid in determining the burden of disease and act as a planning tool for public-health programmes.Reactive arthritis (ReA) is a spondyloarthropathic disorder characterized by inflammation of the joints and tissues occurring after gastrointestinal or genitourinary infections. Diagnostic criteria for ReA do not exist and, therefore, it is subject to clinical opinion resulting in cases with a wide range of symptoms and definitions. Using standardized diagnostic criteria, we conducted a systematic literature review to establish the global incidence of ReA for each of the three most commonly-associated enteric pathogens: Salmonella, Shigella, and Campylobacter (Reactive arthritis (ReA), also known as post-infectious arthritisis, is a spondyloarthropathic disorder characterized by inflammation of the joints and tissues occurring after gastrointestinal or genitourinary infections -3. The mlobacter .There is no diagnostic test for ReA; it is based entirely on clinical characteristics and, thus, is subject to clinical opinion . In addiSince there is considerable inconsistency in the diagnosis of ReA, it is important to determine the burden of reactive arthritis due to enteric infections, using standard criteria. To our knowledge, this is the first systematic review of worldwide data that use well-defined criteria to establish the global incidence of ReA for each of the three most commonly-associated pathogens.Campylobacter, Salmonella, and Shigella . This is an incidence of 12 reactive arthritis cases per 1,000 cases of Salmonella infection.We identified 34 articles for a full manuscript review. Out of these, 16 cohort studies ,21,24-34rthritis . These cShigella-induced reactive arthritis . This is an incidence of 12 reactive arthritis cases per 1,000 cases of Shigella infection.We identified 15 articles for full manuscript review. Out of these, 7 cohort studies ,21,35,36rthritis . These sCampylobacter, Salmonella, and Shigella, using well-established criteria. Among the studies analyzed, ReA incidence ranged from 0-16%, 0.1-29%, and 0-12% among Campylobacter, Salmonella and Shigella infections respectively. The weighted mean incidence was 9, 12, and 12 ReA cases per 1,000 Campylobacter, Salmonella and Shigella infections respectively.We sought to characterize the incidence of ReA among cases of Campylobacter-associated ReA ranged from 8% to 16% with a median of 8% among adults compared to 0% to 6% with a median of 3% among children. Salmonella-associated ReA ranged from 1% to 24% with a median of 11% among adults compared to 0% to 12% with a median of 5% among children. Shigella-associated ReA ranged from 7% to 12% with a median of 9.5% among adults compared to 0% to 7% with a median of 3.5% among children. Although the burden of enteric infections is higher among children aged <5 years for Salmonella, and 0.012 (95% CI 0.009-0.016) for Shigella.Our incidence estimates are comparable to previous estimates ,32,35,38Additionally, ReA is known to be a sequela of asymptomatic enteric infections ,40. In tCampylobacter-associated ReA and found an incidence of 1-5%. However, this review did not establish any inclusion or exclusion criteria, and a distinction was made between acute and chronic ReA. The authors noted that cases of ReA varied considerably due to limitations in case assessment and diagnostics for ReA. This review suggested that young adults were more commonly affected by ReA. Genetics, specifically the presence of human leukocyte antigen (HLA)-B27, was found to have a mixed association with ReA. There is considerable discussion regarding HLA-B27 and its role in ReA for her assistance in statistical analysis."} +{"text": "Objective. To study the correlation of cytomorphological features in fine needle aspiration smears from patients suspected of having tuberculous lymphadenitis with Ziehl-Neelsen staining (ZN), auramine-rhodamine staining (ARS), and autofluorescence (AF). Methods. A total of 145 lymph nodes were aspirated, 3 air-dried smears were stained with Giemsa, Ziehl-Neelsen, and auramine-rhodamine stains, and 1 smear was wet fixed for Papanicolaou staining. Needle washes were incubated in Lowenstein-Jensen medium for culture. Papanicolaou and auramine-rhodamine stained smears were examined under fluorescent microscope using a blue excitation filter (450\u2013480\u2009nm). Results. Ninety aspirates were reported on cytomorphology as suggestive of tuberculous lymphadenitis. Smear positivity for Mycobacteria by Ziehl-Neelsen method was 26.67% (24/90), while positivity increased to 34.44% (31/90) by auramine-rhodamine and 42.22% (38/90) on autofluorescence. Culture was positive in 27.78% (25/90) aspirates. Using culture as the reference method, the statistical values of ZN, ARS, and AF were as follows: sensitivity 80.0%, 88.0%, 96.0%; specificity 93.85%, 86.15%, 78.46%; positive predictive values 83.33%, 70.97%, 63.16%; and negative predictive values 92.42%, 94.92%, 98.08%, respectively. Conclusion. There is a definite advantage of autofluorescence over Ziehl-Neelsen and auramine-rhodamine which is to detect Mycobacteria, being more sensitive as well as an inexpensive technique. Autofluorescence can be a useful addition to routine cytology for early diagnosis and effective treatment. Tuberculosis (TB) is a major health problem in developing countries. Lymphadenopathy is the most common presentation of extrapulmonary tuberculosis , 2. The The cytological criteria for the diagnosis of possible tubercular lymphadenitis have been clearly defined as epithelioid cell granulomas with or without multinucleated giant cells and caseation necrosis . CultureMycobacteria because lower magnifications are used as well as less time is required to examine smears. Fluorescence microscopy using auramine-rhodamine (AR) or Papanicolaou (PAP) staining has been considered to be superior to ZN staining [Fluorescent microscopy plays an important role for detection of staining , 9. The Mycobacterium and to compare it with conventional ZN method on lymph node aspirates in cytology.Basically, the study was an attempt to find out cost-effective, rapid, and sensitive technique which can be used routinely in developing countries for early diagnosis and effective treatment of tuberculous lymphadenitis. The study demonstrated the correlation of the cytomorphological features with various techniques in FNA smears from patients who are suspected of having tuberculous lymphadenitis. We tried to use fluorescent microscopy (auramine-rhodamine staining (ARS) and autofluorescence (AF)) to detect A total of 145 patients suspected clinically of having tuberculosis with peripheral lymphadenopathy were referred for FNAC to the cytology unit of the Department of Pathology, from August, 2010 to July, 2011. A pretested proforma was used for collection of demographic information, relevant clinical history, and physical examination findings of each patient. Routine investigations including hemogram, mantoux test, and chest radiogram were performed. Both males and females (>1\u2009yr) with well palpable and enlarged peripheral lymph node were included. Patients with multiple enlarged lymph nodes were enrolled, but a separate study form was not used for each lymph node. Exclusion criteria were age <1 year, very small or nonpalpable lymph nodes, or known cases of malignant, allergic, or skin disorders.Mycobacteria appear as greenish yellow, slender, and slightly curved rod-shaped (400X). ZN stained smears were examined for AFB under oil immersion (1000X) using light microscopy which appeared as pinkish, thin curved rod-shaped bacterium measuring 0.5 to 3 micrometer and sometimes as beaded.Four smears were made from each aspirate: three air-dried smears were stained with Giemsa, ZN, and AR stains and one was wet fixed for PAP stain for autofluorescence. Needle washes were incubated for culture over Lowenstein-Jensen medium at the same time. If aspirate was found to be inadequate, FNA was repeated at the same time for better retrieval of aspirate. Culture over Lowenstein-Jensen medium was taken as a reference method. PAP and AR stained slides were examined under fluorescent microscope using the blue excitation filter (450\u2013480\u2009nm). Out of the 145 cases, 90 (62.1%) aspirates were reported as cytomorphology suggestive of tuberculous lymphadenitis. Rest of the aspirates showed either blood or a reactive population of lymphoid cells only. Culture was also negative for these aspirates. Mantoux test was positive in 64.4% (58/90) cases, but significantly positivity (more than 10\u2009mm.) was in 38.8% of the cases. Chest radiograms showed features of pulmonary tuberculosis in 32.2% (29/90) cases. Depending upon cytomorphological features, three patterns were found in tuberculous lymphadenitis: (1) granulomatous lymphadenitis, (2) caseating necrotising lymphadenitis, and (3) acute inflammation with granulomas. The cytomorphological features observed were granulomatous lymphadenitis in 57.8% (52/90), caseating necrotising lymphadenitis in , while positivity increased to 34.4% (31/90) by ARS and to 42.2% (38/90) on AF of the cases with suggestive cytomorphology of tubercular lymphadenitis were in the range of 10\u201330 years of age. Male preponderance was noted accounting for 61.1% (55/90) of cases. In this study, the most common site of involved lymph nodes was of the cervical region in 83.3% (75/90) of the cases. On the basis of appearance of aspirate, blood mixed aspirates were found more commonly in 51.1% cases (46/90), followed by pus in 31.1% (28/90), cheesy white material in 15.6% (14/90), and clear fluid in 2.2% (2/90). Smear positivity for Figures . ComparaMycobacterium Tubercular adenitis does. Laboratory tests may be essential to establish the cause of such adenopathy correctly, because treatment and prognosis may differ. Demonstration of Mycobacterium tuberculosis in fine needle aspirates becomes necessary for an early and accurate treatment. Directed treatment may decrease morbidity and prolong life expectancy.FNAC is an easy, reliable outpatient procedure for the diagnosis of tubercular lymphadenitis in palpable superficial lymph nodes, and it is ideally suited for use in resource limited settings, especially in developing countries where tuberculosis is a major cause of morbidity and mortality . SeveralMycobacteria using fluorescent microscope. Mycobacteria AF, also known as primary fluorescence, is seen as brilliant yellowish green bacilli, thin, and slightly curved with polar enhancement and sometimes even beaded appearance.Auramine-rhodamine involves the use of toxic and carcinogenic substances, but it requires less time, low power examination and shows superiority to ZN staining as auramine combined more readily with mycolic acid than the conventional carbol-fuchsin acid-fast stain. In comparison to both, AF on PAP stained smears provides a safe, inexpensive, and exposure-free diagnostic procedure along with more positive results. Even this technique does not require any addition to the standard PAP stain. Single PAP stained smear can be used for routine light microscopy to determine cytological diagnosis and for demonstrating Previous studies for detection of AFB from various clinical specimens, comprising sputum, CSF, fine needle aspirate, pus, and miscellaneous body fluids which were examined by ZN and AR staining techniques, showed that AR was 86.6% sensitive as compared to ZN 67.3% sensitive with more marked difference in extrapulmonary samples , 12, butMycobacterium and to compare it with conventional ZN method on lymph node aspirates in cytology. During the present study by using culture as the reference method, true statistical values of these techniques were given in The present study was an attempt to use fluorescent microscopy (ARS and AF) to detect A comparison between AF and ARS was also done in the present study. It was found that autofluorescence was more sensitive for identifying the bacilli. There was only one case (1.1%) which showed ARS positivity on smear but was negative by AF. However, 8 cases (8.89%) were AF positive, but they were found to be ARS negative. No comparative study between autofluorescence and auramine-rhodamine staining on FNAC smears could be found in literature searched.Mycobacteria. These organisms such as spore-forminglike Bacillus subtilis, nonspore-forming bacteria like Staphylococcus aureus, Nocardia, budding yeast may produce fluorescence [Mycobacteria by fluorescent microscopy. There is also increased frequency of false positivity of AF due to subjective biased errors and interobserver's variability.However, some organisms exhibiting spontaneous emission spectra following excitation at specific wavelengths may pose problem in the detection of rescence . Even aiFNAC as a primary diagnostic procedure in tubercular lymphadenitis has demonstrated the adaptability of autofluorescence on Papanicolaou stain which is the most frequently utilized stain for cytologic specimens and autofluorescence on the Pap smear is a rapid and relatively simple method. This study explores the utility of autofluorescence as an adjunct to routine cytology as it is simple, rapid, and cost-effective screening technique especially in developing countries where tuberculosis is widely prevalent and shows continued presence of infection in the community. However, limited and cautious use of AF is necessary because of its increased false-positivity rate and subjective-biased errors. AF should be used in addition to other ancillary techniques."} +{"text": "In order to understand the extent of serum vitamin D deficiency we measured vitamin D levels in an unselected multi-ethnic population of pregnant women. We report the prevalence of insufficiency and deficiency, explore risk factors and discuss the public health implications. This report may be the first of its kind.Sample women with sufficient stored serum were randomly selected from among all women who had delivered in year 2008/09. Serum vitamin D levels were determined using liquid chromatography coupled to tandem mass spectrometry). Vitamin D levels were analyzed with respect to ethnicity (as marker for skin tone), calendar quartile, body mass index trimester and parity. Deficiency was defined as < 25 nmol/L, insufficiency 25 - 75 nmol/L, and adequacy > 75 nmol/L.Three hundred and forty six women were included and represented the total population in terms of skin tone, quartile, BMI, gestation, and parity. Overall, 18% (95% CI: 15% to 23%) of sample women had adequate vitamin D levels; 36% were deficient, 45% insufficient. Among women with dark skin, only 8% (95% CI: 5% to 12%) had adequate levels compared to 43% (95% CI: 33% to 53%) of those with light skin. Obese women were found have significantly lower Vitamin D levels than non-obese women.Vitamin D deficiency and insufficiency are prevalent year round among pregnant women in northwest London, especially those with darker skin. Existing supplementation guidelines should be supported however; other measures are required to improve status among all women."} +{"text": "Advance directives (AD) are intended to ensure patient autonomy in the event of loss of decision-making capacity. According to German law, ADs are now legally binding. It is unclear whether they are helpful in the ICU . The aimapplicable if they described the potentially applicable clinical situation as 'final stage of a fatal disease' or 'inevitable immediate dying process'. In contrast, AD were defined as not applicable if they described other situations, including 'mental deterioration', 'breakdown of vital organs' or '(in)direct brain damage'.The setting was surgical, neurological and cardiological ICUs of one German university hospital with a total of 72 beds. All patients with AD who died on the ICU between December 2010 and December 2011 were included. ADs were collected from patients' files, and their exact specifications, wishes and preferences were extracted and tabulated. Patient demographics and medical treatment was extracted from an Electronic Patient Data Management System. The time period was 48 hours preceding death. AD were defined as 2 >21%, 30% on vasopressors. Of these 43 patients, 21 were surgical and 22 nonsurgical patients. Fourteen out of 43 applicable AD were pre-printed forms, 29 were written individually. No trend was noticeable regarding compliance with single patients' wishes in these subgroups.Sixty-four ICU patients were included. AD were written a median 109 weeks before the ICU stay. Forty-four AD were applicable according to the definition. Of 44 patients with applicable ADs, 50% were surgical patients, 41% patients had severe sepsis. Within 48 hours prior to death, 27% received a DNR/I (do-not-resuscitate/intubate) order or DND order. Eighteen per cent received a decision to withhold, 43% a decision to withdraw therapy. Twenty-two patients (50%) refused intensive care, 98% (43/44) specifically refused life-sustaining measures and, in addition, many specifically named measures to be avoided. Patients who refused life-sustaining measures received the following treatments: within 48 hours prior to death, 12% received CPR and 23% underwent surgery. Within 24 hours, 77% were mechanically ventilated and on vasopressors. At the time of death, 72% were intubated, 74% with FiOAD do not seem to direct end-of-life care in the ICU. Our findings strengthen concerns that AD in their current form may not be suitable for this patient population. Moreover, inability to comply with patients' wishes may add to the emotional burden of ICU staff."} +{"text": "Systemic lupus erythematosus (SLE) is characterized by a wide spectrum of manifestations and severity, frequently affecting women and ethnic minorities. Health disparities among ethnic groups adversely impact medical care access, treatment choices and long-term outcomes. Over the past 30 years our lupus cohort has changed to include many patients of Afro-Caribbean ethnicity. Understanding ethnic and sociodemographic characteristics is critical to designing strategies to decrease health disparities and improve patient care.A demographic questionnaire was distributed to lupus patients from June 2009 to May 2012. All patients met \u22654 1982 ACR SLE criteria. Questions concerned date of diagnosis, place of birth, ethnicity, religion, main language, marital status, housing, education, employment, financial support, disability and medical insurance. Descriptive statistics were compared with similar demographic studies done in 1980 and 1994, including 164 and 169 patients respectively.One hundred and fifty patients participated in the survey; 90% were women with average disease duration of 15 (0.4 to 52) years. Forty-seven percent were born in North America, 37% in the Caribbean and 15% in other regions, with a similar distribution in 1994 (47% North America and 45% Caribbean), but a notable change from 1980s demographics, with 74% born in North America and 22% in the Caribbean. The most common ethnicities were Black non-Hispanic (68%) followed by Black-Hispanic (17%) and White-Hispanic (5%). Currently the main spoken language is English (93.3%). Only 21.3% are married, with 54% never married. Eighty percent completed a high-school education, and 26.2% have full-time jobs while 51% are unemployed. The most common occupations are childcare, healthcare, and clerical. Average adjusted gross income is below New York State income . A total of 47.3% of patients receive disability with 40% reporting disability as the main source of financial support, an increase in disability status compared with 1980 (38.4%) and 1994 (46.1%). Access to healthcare and insurance plans increased compared with 1980 . Drug plan coverage is available for 85% of the current cohort.Although genetic variations highly influence disease patterns, adverse sociodemographic factors negatively influence disease course. Most of our patients come from Caribbean communities with limited education, high unemployment rate, low income and high disability rates. Despite improved access to healthcare, sociocultural barriers may limit access to optimal medical therapies, necessitating interventions to decrease health disparities. Studies comparing clinical characteristics and their influence on outcome of Afro-Caribbean populations and other ethnicities will help to improve medical care for this population."} +{"text": "Physical activity helps diabetic older adults who have physical impairments or comorbid conditions to control their disease. To enable state planners to select physical activity programs for these adults, we calculated synthetic state-specific estimates of inactive older adults with diabetes, categorized by defined health status groups.Using data from the 2000 through 2009 National Health Interview Survey (NHIS) and the Behavioral Risk Factor Surveillance System (BRFSS), we calculated synthetic state-specific estimates of inactive adults with diabetes who were aged 50 years or older for 5 mutually exclusive health status groups: 1) homebound, 2) frail , 3) functionally impaired (difficulty in 1 to 3 of these functions), 4) having 1 or more comorbid conditions , and 5) healthy (no impairments or comorbid conditions). We combined NHIS regional proportions for the health status groups of inactive, older diabetic adults with BRFSS data of older diabetic adults to estimate state-specific proportions and totals.State-specific estimates of health status groups among all older adults ranged from 2.2% to 3.0% for homebound, 5.8% to 8.8% for frail, 20.1% to 26.1% for impaired, 34.9% to 43.7% for having comorbid conditions, and 4.0% to 6.9% for healthy; the remainder were older active diabetic adults. Except for the homebound, the percentages in these health status groups varied significantly by region and state.These state-specific estimates correspond to existing physical activity programs to match certain health status characteristics of groups and may be useful to program planners to meet the needs of inactive, older diabetic adults. Type 2 diabetes is a major cause of illness and death in the United States, especially among older adults, resulting in human and economic costs . In 2010Adults with diabetes are at 1.8 to 2.4 times greater risk of various forms of disability than their nondiabetic counterparts . Older aReference Guide of Physical Activity for Older Adults (PARG) identifies and promotes physical activity programs for older adults , we identified health status categories to correspond to the health status groups defined by the PARG Box). H. HBox). www.cdc.gov/nchs/nhis/about nhis.htm). The response rates for its sample adult questionnaire were 72.1% in 2000 and 65.4% in 2009.NHIS and BRFSS conduct annual nationally representative surveys of the health of the civilian, noninstitutionalized US population. NHIS incorporates a household interview in which trained staff annually visit approximately 35,000 households containing approximately 87,500 people (www.cdc.gov/brfss/index.htm#content_area). In 2000, overall response rates ranged from 28.8% to 71.8% and cooperation rates from 35.5% to 77.7% . In 2009, 53.2%) .From the NHIS data, we identified inactive older diabetic adults as those aged 50 or older who had been told they had diabetes and indicated they had never engaged or were unable to engage in leisure-time moderate or vigorous activities and categorized them by US census region . We grouped respondents by their difficulty in performing the following 6 functions: walking one-fourth mile; climbing up 10 steps; standing for 2 hours; stooping, bending, or kneeling; reaching above their head; and lifting or carrying 10 pounds. Because few respondents had difficulty with reaching, lifting, or carrying, we defined 2 of our health status groups on the basis of the respondents' reported difficulty with only the remaining 4 functions. Using the most restrictive health status group (homebound) as a starting point, we assigned each respondent to only 1 of the 5 health status groups .We calculated synthetic state-specific estimates of older, physically inactive diabetic adults in each health status group by multiplying the region-specific proportion of each health status group (2000-2009 NHIS) by the state-specific proportion of older diabetic adults (2000-2009 BRFSS).To estimate the standard error of these state-specific synthetic proportions, we applied a simple exact formula for the variance of each proportion . The finWe conducted all analyses using SAS-callable SUDAAN version 9.1 and accounted for the complex survey design, nonresponse, and weighting to represent the US population. National proportions and 95% confidence intervals (CIs) for the 5 health status groups were stratified by the 4 census regions. We calculated nonoverlapping 95% confidence intervals to determine whether proportion estimates among regions and states differed .BRFSS percentage distributions by age and sex resembled those of NHIS for similar years but differed by education and race (Table). In the 2000 through 2009 NHIS, the overall percentage of inactive older diabetic adults who were homebound was approximately 3% ; frail, 9.6% ; impaired, 29.8% ; having a comorbid condition, 50.5% ; and healthy, 6.7% .The NHIS regional percentages in the health status groups varied significantly for the frail, people with comorbid conditions, and the healthy . SpecifiNone of the state-specific percentages of the homebound differed significantly among the states . State-sThe estimated total of adults in each health status group tended to be lowest in the least populous state, Alaska, and highest in the most populous state, California (Appendices This study provides the first set of state-specific estimates of the percentages and the number of inactive, older, diabetic adults in 5 health status groups who may benefit from physical activity programs. These estimates may facilitate planning of physical activity programs for diabetic older adults with varying functional health status .The highest percentage of the homebound and the frail corresponds with higher diagnosed diabetes rates in Southern states , and thePhysical activity programs can help older diabetic adults by improving glycemic control ,25, whicOur state-specific synthetic estimates for the 5 health status groups are, to our knowledge, the first to correspond with the interventions in the PARG . PlannerOur study had several limitations. We used the statistically conservative method of nonoverlapping confidence intervals to determine significance and assumed, within region, that states did not vary in their proportions of inactive, older, diabetic adults by specific health status group. This conservative approach has the advantage of partially controlling for multiple comparisons. We used self-report items of impairment and disability from NHIS rather than a detailed geriatric assessment protocol that migIn summary, among older, physically inactive, diabetic adults, the homebound, the frail, and the otherwise healthy were less common than those who were impaired or who had comorbid conditions. Tailored physical activity programs have much to offer older, physically inactive, diabetic adults. State program planners may use these estimates to select physical activity programs for each kind of health status group to enhance diabetes control and to prevent adverse health outcomes that lead to progressively worse impairment. Making such programs available may help to control the preventable burden of diabetes that is otherwise expected to grow unabated with the anticipated expansion of the older adult diabetic population. Because of this expansion, we anticipate that these state-level numbers may also change; therefore, future studies may investigate changes in these estimates as well as urban-rural and racial differences that may exist in health status groups among the states."} +{"text": "Sustaining research subject recruitment in biomedical HIV prevention trials requires continual innovation. Since June 2009, the University of Pennsylvania HIV Vaccine Trials Unit (UPenn HVTU) has employed multiple strategies to recruit men who have sex with men (MSM) for a phase IIb HIV vaccine trial, HVTN 505.Between 12/1/2011 and 1/3/2012, the HVTU contracted with a consumer marketing company to recruit potential trial participants. For $3000, the company emailed MSM a scripted message inviting them to participate in a clinical HIV vaccine trial, and the company provided the trial site with contact information for those who responded. Site staff emailed and phoned each respondent to provide study information and conduct a phone-screen interview for the trial. Those eligible were scheduled for in-office screening appointments.266 MSM were emailed; 118 viewed the message, and 109 responded that they were interested in participating. 83% of responders were White, and 71% earned >$50,000/year. Staff successfully contacted 64 individuals, and 58 completed phone-screens. Of these, 17 were eligible for, and 9 completed, screening visits. Five enrolled in HVTN 505 during January-February, 2012. Of 41 phone-screened ineligible, primary reasons for ineligibility were: being HIV-positive , not meeting protocol-specified sexual risk criteria , out of age range , and/or being uncircumcised . Ineligible participants were referred to phase I or future prevention trials as appropriate.This strategy reached MSM not engaged by previous efforts, and doubled site HVTN 505 enrollment over two months. Respondents included a higher proportion of White MSM than the population screened for HVTN 505 at the HVTU. This approach has wider potential use for recruitment in biomedical HIV prevention trials. To understand the true utility of this approach, respondent HIV risk data and financial costs associated with this strategy must be carefully examined."} +{"text": "Identifying women in the US with sufficient risk of HIV infection for inclusion in HIV vaccine efficacy trials has been challenging. Using geography and sexual network characteristics to inform new recruitment strategies, HVTN 906 determined the feasibility of recruiting and retaining women at high risk and assessed HIV incidence.HIV uninfected women were enrolled in Chicago, New York City and Philadelphia if they were 18-45 years, not pregnant or intending to become pregnant for 18 months and reported unprotected vaginal/anal sex in the prior six months and either i) resided or engaged in risk behavior in local geographical HIV risk pockets; and/or ii) had a male partner who had either been incarcerated or injected drugs in the last year or had concurrent sex with another partner in the last six months. Behavioral risk assessment, risk reduction counseling, HIV and pregnancy testing were done at baseline, 6, 12 and 18 months.Among 799 women, 71% were from local high-risk pockets and had high-risk male partners, 18% were from local high-risk pockets only and 10% had high-risk male partners only. Median age was 37 years; 79% were Black and 15% Latina. At baseline, the median number of male partners was 3 , 76% had unprotected sex while intoxicated , and 52% exchanged sex for money or drugs. Retention at 18-months was 80%. Pregnancy incidence was 11% with 48% of pregnancies occurring during the first 6 months of follow-up. HIV incidence was 0.31% . Risk behaviors decreased between screening and 6 months with little change thereafter.Women recruited using new strategies based on geography and sexual network characteristics did not have a substantial HIV incidence, despite baseline levels of risk behaviors. New strategies to identify women at high risk in the US are needed."} +{"text": "The American College of Surgeons Committee on Trauma (ACS/COT) has mandated alcohol screening and brief intervention (SBI) for all level-I trauma centers. Few investigations have assessed alcohol and drug comorbidity among patients receiving mandated alcohol SBI at trauma centers. In this study, 878 randomly selected level-I trauma center inpatients were systematically screened for alcohol and drug use problems with blood and urine toxicology laboratory results and self-report questionnaire items. Patients were systematically screened for alcohol use by blood alcohol concentration (BAC) testing and administration of the Alcohol Use Disorders Identification Test-Consumption (AUDIT-C). Screening for stimulant use included urine toxicology testing and single-item self-report. Screening for marijuana use included urine testing and single-item self-report. Screening for prescription and nonprescription opioid use included single-item self-report only. Fifty percent of patients (435/878) screened positive for problem alcohol use. Approximately 20% screened positive for cocaine use, 7.7% for amphetamine use, 7.5% for opioid use, and 37% for marijuana use. Among the 50% of patients who screened positive for problem alcohol use, 61.1% had one or more drug comorbidities. Of all 878 patients in the sample, 166 were seen by the trauma center\u2019s addiction intervention service for mandated alcohol SBI. Of these, 33% were positive for problem alcohol use only, 44% were positive for alcohol and other drug use, 12% were positive for marijuana, stimulants, or opioid use only, and 11% screened negative for both alcohol and drugs. The majority of patients receiving mandated alcohol SBI at a level-I trauma center screened positive for comorbid use of one or more drugs. Clinical SBI research protocols that realistically account for alcohol and drug comorbidity are needed to inform the development of ACS/COT SBI guidelines."} +{"text": "HIV-infected persons are at increased risk for cardiovascular disease and cancers due to various reasons. Smoking is the most prevalent modifiable risk factor for these diseases.We studied the prevalence of smoking, cessation rates, relapse rates, and predictors of these events.The Swiss HIV Cohort Study (SHCS) is a prospective observational database which semi-annually collects demographic, clinical and laboratory data, including on self-reported smoking status. Smoking cessation was defined by 2 consecutive visits without smoking (after 2 visits with smoking). We used Kaplan-Meier analyses to assess the probability of smoking cessation and relapse in different patient groups; and uni-/multivariable Cox models to study associations between such events and patient characteristics.Between 2000-2009, we followed 10,511 patients at 107,220 visits. Prevalence of smoking decreased from 60% (2000) to 44 % (2009). Prevalence of smoking was 84% in IDU, 42% in MSM, 50% in heterosexual men, and 47% in heterosexual women. Smoking prevalence differed in geographic/language regions of Switzerland , and in different care settings , private practice (46%)). The incidence of smoking cessation was 4.0/100 ys of smoking without appreciable time-trends. The probability of smoking cessation was 31% after 10 ys. Hazard ratios for smoking cessation in multivariable models differed significantly: IDU less likely stopped smoking , whereas MSM and patients in care of private physicians more likely stopped . No significant differences of cessation rates were found in different age groups, heterosexual women, or language regions. The probability of relapse 6 years after smoking cessation was 44%; half of relapses occurring within first 2 ys. HR for relapses in Cox models differed significantly in IDU and in private practice but not in MSM, age groups, heterosexual women, or in different language regions.Smoking is highly prevalent in HIV-infected participants of the cohort, but decreased during the recent years. Relapse rates after smoking cessation were high. Counselling for smoking cessation, and prevention of relapse are important aspects of care for HIV-infected persons."} +{"text": "Most of the HTLV-1 carriers remain asymptomatic through life, and genetic and immunological factors may be responsible for the appearance of associated diseases. Objective: To describe the nutritional status and some behavioral factors of individuals with HTLV-1 patients with tropical spastic paraparesis (HAM / TSP).A retrospective, cross-sectional observational study in adults with HAM / TSP patients, both genders attended the Institute of Infectious Diseases Emilio Ribas (IIER) in 2013. The variables studied were age, gender, weight, height, alcoholism, smoking, total cholesterol, glucose, triglycerides, Revised Scale of Motor Osame and Beck Depression Inventory (BDI), Body Mass Index .This study evaluated 30 patients, 80% female, mean age 51 years, mean BMI of 24.6, and 40% were overweight and 6.7% obese. With respect to metabolic aspects 6.7% had increased triglycerides, blood glucose and 13.3% presented increased total cholesterol. Importantly, as the behavioral aspects 46.7% had moderate depression and 23.3% needed support of both hands to walk. Regarding the social factors were absent consumption of tobacco and alcohol.The assessment of functional capacity changes were identified and commitment gait and balance. Overall, the data showed that patients with moderate depression also had metabolic alterations and overweight. Although it was observed prevalence of normal weight, the excess rate of over weight and metabolic disorders may require monitoring and nutritional interventions. In conclusion, the data suggest that the particular conditions as overweight, metabolic changes impact the daily quality of life of patients with HAM / TSP."} +{"text": "Cellular Rhinitis represent a form of vasomotor rhinitis, they are studied by means of the nasal cytology which allows through the taking of a minimum amount of mucus in the nasal mucosa of studying with an optical microscope such cells. The cells are stained with May Grunwald Giemsa methods, such methods allows to highlight the major cellular components at the level of the surface layer of the nasal mucosa.The forms of rhinitis cell are represented by non-allergic eosinophilic rhinitis (NAres), nonallergic rhinitis by mast cell eosinophilic (NARESMA), neutrophilic from non-allergic rhinitis (NARNE), nonallergic rhinitis by mast cell (Narma).An epidemiological study in Italy, done by members dell\u2019AICNA, Italian Academy of Nasal Citology) have highlighted these results on a population of 3872 people seen during a ENT visit: NARES 2.69%, 1.47% Naresma, 1.47% Narma, 16,50% allergic, 1.26% of narne, 2.38 overlapping, 70.53% normal, 1.47% yeast, 2.24 % bacterial.Therefore represent a significant percentage of the vasomotor rhinitis.The therapy today is not defined so many type of therapy are used by the clinician so the academy try to establish a rule to treat this rhinitis so actually are in study the treatment of such rhinitis with an association between a topical steroid, fluticasone propionate with a topical antihistamine azelastine hydrochloride. the primary results are satisfactory in the treatment of NARES."} +{"text": "Juvenile idiopathic arthritis (JIA) is a heterogenous disease, classified according to the International League of Associations for Rheumatology (ILAR). Initial treatment is based largely on disease severity; intra-articular injections for oligoarthritis, methotrexate (MTX) for polyarthritis and systemic presentations. The recent licensing of biologic therapies for use in JIA has revolutionised treatment of the disease. It is not currently known what proportion of children who present with polyarthritis will require biologic therapy. Although not studied formally, it is recognised a proportion of children with oligoarthritis will also require systemic therapy to control symptoms.To describe prescribing patterns in JIA over the first 3 years on presentation to rheumatology.Children with at least 3 years of follow-up within the Childhood Arthritis Prospective Study (CAPS), a prospective observational inception study of inflammatory arthritis, were included.For analysis, children were placed into one of 4 groups based on physician-assigned ILAR category and number of active joints at first presentation (baseline): oligoarthritis, polyarthritis, systemic (sJIA) and enthesitis-related arthritis (ERA). All treatment exposures were categorised into NSAID, intra-articular steroids, disease modifying anti-rheumatic drug (DMARD) including MTX and sulphasalazine (SSZ) and biologics including adalimumab (ADA), etanercept (ETN), infliximab (INF), and tocilizumab (TCZ).790 children were included originally . Of these, 78 had missing ILAR and were excluded, leaving 712 children. Over a 3 year period, almost 100% of children with polyarticular presentation and 50% with oligoarthritis went on to receive a DMARD. 44% with polyarthritis and 17% with oligoarticular presentation also received a biologic (Table). The most recent ILAR category among children with oligoarticular onset who received a biologic comprised 39% extended, 19% polyarthritis, 4% ERA, 11% other subtypes; 27% had persistent oligoarthritis. All sJIA patients were treated with DMARDs with 36% having biologics . 63% of ERA patients receive a DMARD with 26% going on to receive a biologic. Table Over a three year period almost all patients with polyarthritis received treatment with MTX and almost 50% also received a biologic therapy. A high proportion of children presenting with oligoarthritis also went on to receive DMARDs and biologics, many children for persistent oligoarthritis. This is despite the lack of clinical trial evidence for effectiveness in this subtype. Further studies on the efficacy/effectiveness in this subtype should be undertaken to ensure appropriate use of advanced therapies in this population.None declared."} +{"text": "Plasma samples from 157 patients with advanced cancers who progressed on systemic therapy were tested for 21 mutations in BRAF, EGFR, KRAS, and PIK3CA using the BEAMing method and results were compared to mutation analysis of archival tumor tissue from a CLIA-certified laboratory obtained as standard of care from diagnostic or therapeutic procedures. Results were concordant for archival tissue and plasma cfDNA in 91% cases for BRAF mutations , in 99% cases for EGFR mutations , in 83% cases for KRAS mutations and in 91% cases for PIK3CA mutations . Patients (n = 41) with > 1% of KRAS mutant cfDNA had a shorter median survival compared to 20 patients with 1% of mutant cfDNA had a shorter median survival compared to 33 patients with 1% of KRAS mutant cfDNA had a shorter median survival compared to 20 patients with 1% of mutant cfDNA had a shorter median survival compared to 33 patients with 5 u/ml, abnormal FSH, LH and testosterone results.Psychiatric disorders were assessed according to DSM-IV criteria by psychiatrist. .New post-HSCT malignancies that are related to primary therapy for cancer are rare but devastating complications. All results were recorded in checklists. Data were analyzed using the SPSS software version 15.0 A total of 122 patients with acute leukemia were enrolled in the study, 72 (59%) had AML and 50 (41%) had ALL. There were 65 (53%) males and 57 (47%) females. In this series, 97.5% of patients received allogeneic transplantation, while 2.5% underwent autologous transplantation. DLI was not given to 96% of patients, while 3% received DLI once and 1% twice during treatment. Stem cells were derived from bone marrow (1%) and peripheral blood (99%) in this study.83.5% of patients were transplanted in first complete remission (CR1), 14% in CR2 and 1% in CR3. 1.5% of transplantations were also performed in patients with primary induction failure.Patients underwent transplantation from HLA-identical siblings (89.5%), other related (6.5%) and unrelated donors (1.5%). As mentioned above 2.5% received autologous transplantation. 95% of patients had HLA-matched donor and 2.5% had one-locus mismatched donor.Late ComplicationsOphthalmic problems: Sicca syndrome (dry eye) was the most frequent late ophthalmic complication after HSCT, which occurred in 34% ) n=41) of patients in this study. 15 (12.5%) patients developed cataract.Endocrine: 8% (n=10) of patients developed primary hypothyroidism. None of the HSCT survivors had already experienced fertility and gonadal dysfunction. 17 of 57 female patients did not take LH and FSH tests and 4 patients were over 50 years. According to LH and FSH levels, 15% and 9% of patients had ovarian failure, respectively. 7 of 65 male transplant patients did not do hormonal tests. Testosterone level was less than normal in 49 (84%) men and according to their FSH and LH levels, 20 (41%) had secondary hypogonadism and 29 (59%) had primary gonadal dysfunction.Pulmonary complications: Obstructive and restrictive pulmonary diseases were detected in 15% and 6% of HSCT recipients, respectively. BOOP was identified in 6 (5%) patients.Cardiac: Mitral and tricuspid regurgitation (MR/TR) were the most common cardiac complications among patients . Pericardial effusion occurred in 1 (1%) patient and right bundle branch block (RBBB) was observed in 1 (1%) patient.Psychological disorders: Transplant-related psychological distress is very common among recipients. The present study has documented psychological disorders in 39% of HSCT survivors, of whom 87% were diagnosed with depression and 13% with anxiety disorders and insomnia. One patient presented with convulsion.Secondary solid tumors: One patient was affected by astrocytoma. Also, 37 (30%) patients experienced chronic and non-pulmonary GvHD, including skin and liver GvHD.19 Hartsell et al.20 retrospectively compared pulmonary complications in patients conditioned with cyclophosphamide and TBI (CY/TBI) and busulfan and cyclophosphamide (BU/CY). Late pulmonary events (occurring >45 days after transplant) were significantly higher in the CY/TBI, compared to BU/CY . In a meta-analysis done by Gupta et al. CY/TBI was associated with a moderate though non-significant increase in the risk of clinically significant pulmonary complications, compared to BU/CY.21 In our study, 21% of patients developed spirometric abnormalities. BOOP was identified in 6 (5%) patients. Pulmonary symptoms were found in 13 (10.6%) patients. It may be due to busulfan toxicity on lung or subsequent GvHD. The 2-year cumulative incidence of late pulmonary complications was 10% among 438 patients surviving more than 3 months in the retrospective study conducted by Patriarca et al.22,23 Several studies have shown cataract formation in more than 80% in the single-dose TBI group and <20% in the no TBI group.11 In our study, cataract formation was only found in 12.5% of patients. This finding may be due to short period of follow-up, but it still seems to be much less than TBI-based conditioning post-HSCT cataract formation. In prospective studies of the incidence of cataracts, patients who treated with Cy/TBI had a higher incidence of cataract formation than those received Bu/Cy.24The probability of developing cataract after fractionated TBI is about 30% at 3 years. This incidence may be more than 80% 6 to 10 years after HSCT.25 The majority of HSCT survivors become infertile although HSCT without total body irradiation can spare fertility in nearly one-third of men and women. Semen analysis was not done in our study and we just assessed fertility in our patients following HSCT. No pregnancy happened in HSCT recipients.In one study, 85% of the patients receiving TBI developed azoospermia versus 51% in the no TBI group.24 90% of patients who have received single-dose TBI need levothyroxine as hormone replacement therapy, while 14\u201315% of patients treated by fractionated TBI and a small number of patients conditioned with Bu/Cy need that remedy.24 In our study, 8% of patients developed primary hypothyroidism. Like other studies, our findings favor the use of non-TBI-based conditioning regimen.Studies show that 7% to 15.5% of patients will demonstrate subclinical hypothyroidism during the first year post HSCT.16 The cumulative incidence of invasive solid tumors is about 8% at 20 years.24 We found just one patient with solid tumor in our study that may be due to short follow-up period and small number of patients evaluated.The median time from HSCT to presentation of solid tumors is between 5 to 6 years. They account for 5% to 10% of deaths among HSCT recipients who survive two years or longer. In order to improve the quality of life and overall survival in HSCT recipients, careful assessment of treatment-related complications should be part of regular follow-up of HSCT survivors. Diagnostic and therapeutic interventions must also be taken into account to prevent, early diagnosis and treatment of late effects of \u00a0HSCT. Survivors should be screened for evidence of hypothyroidism at the periodic health examination. There also should be regular periodic examination of the ocular, cardiovascular, pulmonary and mental status. Due to high risk of infertility in survivors of HSCT, it is recommended to store male\u2019s sperm and female\u2019s ovule prior to HSCT to preserve fertility in adult patients with leukemia. In addition, our results imply that non-TBI based conditioning regimen has fewer late complications at least in acute leukemia patients who have undergone HSCT. These results should be confirmed by studies involving larger sample sizes."} +{"text": "We aimed to audit the prescribing practice on a busy 14-bedd general ICU, and develop standardised practices and tools to improve safety. Prescribing errors occur as commonly as in 10% of UK hospital admissions, costing 8.5 extra bed days per admission, and costing the National Health Service an estimated \u00a31 billion per annum .We audited the daily infusion charts of all patients in three separate spot checks, over 1 week. We assessed all aspects of prescriptions that make them legal and valid, in accordance with national guidance . New proWe assessed 129 prescriptions in the first round, and 111 after intervention, demonstrating a 70% improvement in safe prescribing. Only 24% of prescriptions initially fulfilled best practice criteria, improving to 94% afterwards. We also reduced the number of infusions running without prescription, 7 (6%) versus 24 (19%). See Figures Our audit supports the need for standardised prescribing practices within critical care, especially when dealing with potentially harmful vasoactive/sedative drugs. With a small, cost-effective intervention , we improved prescribing accuracy, and thus patient safety in intensive care."} +{"text": "Here, we present the full-length genome sequencing of severe fever with thrombocytopenia syndrome (SFTS) virus, isolated from South Korea in 2014. The five Korean strains were compared by phylogenetic analysis with full SFTS genome sequences of two neighboring nations, China and Japan. Haemaphysalis longicornis ticks, a major vector of SFTSV, was at least 0.46% in South Korea (Severe fever with thrombocytopenia syndrome (SFTS) virus (SFTSV) is an emerging novel phlebovirus that causes SFTS, which is associated with a high mortality rate. SFTSV was first isolated in China and moreth Korea .Phlebovirus, family Bunyaviridae) consists of three segmented negative-sense RNAs. These L, M, and S segments encode a viral RNA polymerase, glycoproteins (Gn and Gc), a nucleoprotein (NP), and a nonstructural S segment (NS) protein, respectively , and MEGA 6 was employed for the genomic sequence alignment and phylogenetic analysis using the maximum-likelihood method.The 5\u2032- and 3\u2032-terminal regions were determined by rapid amplification of cDNA ends (RACE) technology. The genome sequences covering all three segments were generated using The genomes of each of the five Korean SFTSV strains possessed 6,368 nucleotides in segment L, 3,378 nucleotides in segment M, and 1,746 nucleotides in segment S. Full-length genome sequences within these five Korean SFTSV strains shared high similarity ranging from 96% to 99%, 93% to 99%, and 95% to 99% at the nucleotide level for segments L, M, and S, respectively.Phylogenetic analysis was performed with the full-genome sequences of SFTSV from two neighboring Asian countries, China and Japan; seven Chinese strains and eight Japanese strains were used. Phylogenetic analysis based on S segment sequences demonstrated that all Korean strains clustered with the Chinese strains. The four Korean sequences, excluding that of strain KASJH, grouped with those of all Japanese strains, with nucleotide identities ranging from 95.8% to 99.6% and 96.3% to 99.7% for the M and L segment sequences, respectively. We may assume that these four Korean SFTSV genome sequences possibly underwent recombination.KP663731 to KP663733; KAGWH3, KP663734 to KP663736; KAGBH5, KP663737 to KP663739; KAGBH6, KP663740 to KP663742; and KACNH3, KP663743 to KP663745.The full-genome sequences were deposited in GenBank as follows: strain KASJH, accession numbers"} +{"text": "Ventilator-associated pneumonia (VAP) is associated with increased length of ventilation, ICU stay, mortality, cost and antibiotic burden . There iA retrospective review of all adult patients admitted to the ICU at The Royal London Hospital over a 6-month period (February to August 2014). The diagnosis of VAP was based on the Clinical Pulmonary Infection Score. Patients were identified with VAP if they were started on antibiotics for chest sepsis 48 hours after start of mechanical ventilation. Demographic, clinical, microbiological and radiological data were collected to identify risk factors, and compare VAP and non-VAP groups. Chi-squared and ANOVA tests were performed using the SOFA statistics package.P < 0.001), and had longer ICU and hospital LOS . However, APACHE II scores and hospital mortality were unaffected . Despite rising inflammatory markers and secretion load, many patients did not exhibit oxygenation deficits. Sputum microbiology showed S. aureus, H. Influenza, Klebsiella and Enterobacter as predominant pathogens with low rates of Pseudomonas, Acinectobacter and other resistant organisms. Average length of antibiotic use was 6 (3 to 18) days.A total of 535 mechanically ventilated patients were admitted in the study period, with 281 ventilated for more than 48 hours. The incidence of VAP was 11% in all ventilated patients and 19.6% in those ventilated more than 48 hours. VAP rates were 31% in polytrauma, 25% in neurotrauma and 18% in the neuromedical/surgical cohort. Early and late onset VAP were equal in number. Patients with VAP spent longer on mechanical ventilation (9 \u00b1 9 in no VAP vs. 18 \u00b1 18 days in VAP patients; Chest sepsis after 48 hours of mechanical ventilation commonly complicates neurocritical illness and polytrauma requiring significant ICU resources and antibiotic burden. However, it does not affect mortality. Further research should focus on pathophysiology and new preventative measures to reduce VAP in the at-risk population."} +{"text": "Male-to-male sex and illicit injection drug use are important transmission routes for human immunodeficiency virus (HIV) infection. Of all new HIV infections in 2010, 80% were among men, of which 78% were among men who have sex with men (MSM), 6% among male injection drug users (IDU), and 4% among men who have sex with men and inject drugs (MSM/IDU) by accouFour national surveillance systems collect data on both male-to-male sex and injecting drug behaviors, though in differing ways . NHANES Of the 7,011 men, representing an estimated 71,111,352 men in the adult male population (NHANES), a weighted estimate of 0.35% ever had sex with a man and ever injected drugs, and thus were classified as MSM/IDU, corresponding to 248,890 MSM/IDU. MSM comprised 5% of all men, corresponding to approximately 3,555,568 MSM. MSM/IDU comprised 7% of MSM. Similarly, IDU comprised 3% of all men, corresponding to approximately 2,133,341 IDU. MSM/IDU comprised 11% of male IDU . Data weIn 2008, of 9,903 MSM interviewed for the NHBS MSM cycle, 681 (7%) were MSM/IDU . OverallFor 2011, NHSS data indicate there were an estimated 1,416 men diagnosed with HIV whose infections were attributed to male-to-male sex and injection drug use; these men comprised 4% of all men diagnosed with HIV infection in 2011. MSM comprised 78% of all men aged \u226518 years diagnosed with HIV infection and MSM/IDU were 4% of all MSM. IDU comprised 6% of all men diagnosed with HIV infection aged \u226518 years in 2011, and MSM/IDU comprised 38% of male IDU . Among MAmong 6,635 HIV-infected men in medical care for HIV infection who participated in MMP during 2007\u20132009, 596 (9%) were MSM/IDU. MSM comprised 66% of all men, and MSM/IDU comprised 12% of MSM; similarly, IDU comprised 14% of all men, and MSM/IDU comprised 39% of male IDU . Among MFor each data source, compared with men who were not MSM/IDU, a higher proportion of MSM/IDU were white and a lower proportion were black/African American . MSM/IDUMSM/IDU constitute an estimated 0.35% of the general male population , based on data from NHANES, a general population survey of a probability sample of U.S. households. Other methods for estimating the size of HIV risk behavior populations include meta-analysis of multiple national surveys . Fourth, some participants might not have accurately reported their behaviors, which might result in underestimates of proportions of MSM/IDU. Finally, the NHSS data were adjusted statistically to account for diagnosed cases with a missing transmission category. The degree of uncertainty introduced by this imputation is unknown.What is already known on this topic?Men who have sex with men (MSM) and are injecting drug users (IDU) (MSM/IDU) comprise a small proportion of persons with human immunodeficiency virus (HIV) infections, but they are at increased risk for acquiring and transmitting HIV.What is added by this report?Using data from four national surveillance systems, the proportion of MSM/IDU was estimated to better describe the prevalence of persons engaging in both behaviors. MSM/IDU comprised an estimated 0.35% of adult males in the general household population of the United States, 7%\u201320% of males at high risk for HIV infection because of behaviors such as male-to-male sex or injecting drugs, 4% of males diagnosed with HIV, 8% of males living with a diagnosis of HIV infection, and 9% of males diagnosed with and in medical care for HIV infection. Across surveillance systems, MSM/IDU accounted for 4%\u201312% of MSM and 11%\u201339% of male IDU.What are the implications for public health practice?Risk reduction programs and interventions targeted toward male IDU populations might be more effective if they incorporate messages about male-to-male sex because 11%\u201339% of male IDU were also MSM in this analysis. A combination of effective, scalable, and evidence-based approaches that address male-to-male sex and injection drug use behaviors might help reduce HIV infections among MSM/IDU.Because MSM/IDU engage in both of the HIV risk behaviors considered in this analysis, they are particularly vulnerable to infection and can transmit HIV through sexual behavior or by sharing syringes. This analysis demonstrates that the population proportion of MSM/IDU is small, but it comprises a considerable proportion of both MSM and IDU populations at risk for or infected with HIV. For persons at increased risk, such as MSM or IDU, HIV testing at least once a year is recommended . An inte"} +{"text": "Migraine equivalents are clinical conditions which often involve children who do not complain of headache. They include abdominal migraine, motion sickness, limb pain, cyclical vomiting, benign paroxysmal vertigo, and benign paroxysmal torticollis (BPT). The aim of our study was to investigate whether children referred to us for BPT have developed migraine at a distance from our first observation.Forty-one children were included in the study. Only 36 families could be contacted by phone, but 2 of them refused to answer our questionnaire. Therefore, the present results were obtained from 34 children (22 girls and 12 boys).Migraine could be diagnosed in 14 children (41%), while the remaining 20 patients (59%) did not complain of headache. At the moment of our interview, children who had developed migraine had a mean age of 5 years, while the mean age of non-migrainous children was 3.5 years. Among migraine children, 43% developed it when they were 4 years, 21% at the age of 3, and 14% when they were 7 years old. The last three migraineurs developed migraine at the age of 5 years, 13 years and 18 months, respectively. Moreover, 55% of patients had developed other migraine equivalents. In particular, 73% children had abdominal migraine, 55% vertigo, 45% limb pain, 27% motion sickness, 27% cyclical vomiting. As for the paroxysmal torticollis time course, two children have had only one event, one child had been still presenting episodes of torticollis, while in the remaining patients the torticollis events had not occurred for some years.Our findings suggest that migraine follows BPT in approximately half of the children within the age of 13 years. Moreover, BPT is often associated to other migraine equivalents. Considered all together, all these periodic syndromes increase the risk of developing migraine.Written informed consent to publish was obtained from the patient(s)."} +{"text": "Critical Care. We invited 39 ARDS centers in Germany to participate in a survey about respiratory and adjuvant ARDS therapy. The questionnaire was completed by 25 centers, 22 of which applied ECMO therapy at the specific time point of the survey (2011 to 2012).Lung protective ventilation is the mainstay of treatment in acute respiratory distress syndrome (ARDS). However, in patients who have severe ARDS and who are receiving extracorporeal membrane oxygenation (ECMO), the ventilation strategy might be modified. This was the subject of the review by Schmidt and colleagues in a recThe majority of the ARDS/ECMO centers preferred controlled mechanical ventilation during ECMO therapy, and only 14% favored assisted or spontaneous breathing. During ECMO, peak/plateau pressures and tidal volumes were lowered by 96% and 91% of the centers, respectively. The specified minimal and maximal tidal volumes were 2 (1.8 to 3) and 6 (4 to 6) mL/kg ideal body weight (median and interquartile range), respectively. Positive end-expiratory pressure (PEEP) was determined by using a \u2018Best-PEEP-Trial\u2019 in 50%, empirical means in 46%, or the ARDS-Network table in 36%. Pressure volume curves, computed tomography, and electrical impedance tomography, on the other hand, were rarely consulted to determine the optimal PEEP. However, a reduction in PEEP was done by only two institutions. Respiratory rates during ECMO were nearly equally distributed between fewer than 4, 4 to 12, 13 to 19, and 20 to 29 breaths per minute. The inspiratory-to-expiratory time ratios were 1:1 in seven and 1:2 in three centers. Inversed ratio (2:1 to 4:1) ventilation was conducted by 14%; only three applied recruitment maneuvers. Sixty-eight percent used 135\u00b0 prone positioning, 36% full prone positioning, and 27% continuous axial rotation during ECMO therapy. Other strategies, such as the daily interruption of sedation and spontaneous breathing trials, were conducted in 72% and 86% of the centers, respectively. Eighteen used specific protocols for the weaning from ECMO. Early tracheostomy was aimed for in 64% and actually performed within the first 4\u00a0days of ECMO therapy in 41% of the centers.The current survey shows that mechanical ventilation is frequently altered toward a protective, or even \u2018ultraprotective\u2019, strategy during ECMO. Adjuvant strategies were not limited by the presence of the extracorporeal circuit and remained integral elements of care. Notably, assisted or spontaneous breathing was seldom accomplished, despite daily interruption of sedation, the use of specific weaning protocols, and early tracheostomy. All in all, most centers relied on proven ARDS standards of care, assuming the physiologically most favorable response while randomized controlled trials during ECMO are missing.ARDS: Acute respiratory distress syndrome; ECMO: Extracorporeal membrane oxygenation; PEEP: Positive end-expiratory pressure.The authors declare that they have no competing interests."} +{"text": "P < 0.001) and multivariate Cox regression (P < 0.001). Thus, the neoadjuvant RT and surgery may be the optimal treatment pattern in elderly patients, especially for patients who are medically fit for the operation.Patients were excluded if they were older than 75 years of age in most clinical trials. Thus, the optimal treatment strategies in elderly patients with locally advanced rectal cancer (LARC) are still controversial. We designed our study to specifically evaluate the cancer specific survival of four subgroups of patients according to four different treatment modalities: surgery only, radiation (RT) only, neoadjuvant RT and adjuvant RT by analyzing the Surveillance, Epidemiology, and End Results (SEER)-registered database. The results showed that the 5-year cancer specific survival (CSS) was 52.1% in surgery only, 27.7% in RT only, 70.4% in neoadjuvant RT and 60.4% in adjuvant RT, which had significant difference in univariate log-rank test ( Neoadjuvant chemoradiotherapy (CRT) followed by total mesorectal excision (TME) is a standard treatment in patients aged 75 years and younger with locally advanced rectal cancer (LARC) \u20135. PatieWe designed our study to specifically evaluate the cancer specific survival of four subgroups of patients according to four different treatment modalities: surgery only, radiation (RT) only, neoadjuvant RT and adjuvant RT by analyzing the Surveillance, Epidemiology, and End Results (SEER)-registered database.We identified 4,121 eligible elderly patients with LARC in SEER database during the 8-year study period (between 2004 and 2011), which included 1460 patients in surgery only, 577 patients in RT only, 1498 patients in neoadjuvant RT and 586 patients in adjuvant RT. There were 2077 (50.4%) males and 2044 (49.6%) females. Patient demographics and pathological features are summarized in Table P < 0.001) was identified as a significant risk factor for poor survival on univariate analysis -Medicare study of patients more than 65 years of age who were receiving postoperative therapy for rectal cancer showed that 96.6% of Stage III rectal cancer patients completed radiation therapy, only 68.2% and 67.5% completed chemotherapy and both modalities. Among Stage II cancer patients, 91.5% completed radiation therapy but only 49.8% and 47.6% completed chemotherapy both modalities [Aparicio et al. found a standard cancer treatment according to recommendations was performed in 53 (48%) colorectal cancer patients: adjuvant chemotherapy in 6/23 patients with stage III tumour, palliative chemotherapy in 3/18 patients with stage IV tumour and adjuvant radiotherapy in 4/14 patients who had a rectal tumour resection . MargaliIn contrast, Tougeron et al. found in selected elderly patients, chemoradiotherapy is well-tolerated, without any significant increase in adverse events, and the results are similar to those recorded in younger patients . Cai et p = 0.001). However, overall survival at 5 years, distant metastases free survival and cancer-free survivalIn the Dutch TME-study, patients aged 75 years and older showed a better response in the study arm when compared to younger patients. Younger patients have a significantly lower local recurrence rate of 5.2% after preoperative radiotherapy versus 11% for patients without preoperative radiotherapy (p = 0.02), also distant metastases free survival and cancer-free survival were improved. Thus, the biological behavior of rectal cancer in the elderly in response to radiotherapy is better than in younger patients [were not improved. Whereas in the elderly, apart from local recurrence rate . As for patients who are older than 75 years of age, they may receive less chemotherapy. Finally, the current analysis of the nonrandomized patient population could not exclude the possibility of selection bias. One of the treatment patterns was chose for patients may according to their performance status and comorbidities. However, if patients are medically fit for surgery, they may benefit from neoadjuvant radiation.In conclusion, multimodal therapy is underused in elderly patients. It appears that standard treatment established in young patients is not applied to every elderly patient. However, the neoadjuvant RT and surgery may be the optimal treatment pattern in elderly patients, especially for patients who are medically fit for the operation.The SEER, a population-based reporting system, was surveyed for the retrospective collection of data used in the analysis. The SEER program collects and publishes cancer incidence and survival data from 18 population-based cancer registries, covering >25% of the US population. Because no personal identifying information was used in the analysis, this study was granted an exemption from the Institutional Review Board of the study institution on March 30, 2012.Cases of rectal cancer from 2004 to 2011 were extracted from the SEER database (SEER*Stat 8.1.5) according to the Site Recode classifications with limitation to radiation prior to surgery and radiation preoperatively and post-surgery. Histological type were limited to adenocarcinoma , mucinous adenocarcinoma , and signet ring cell carcinoma . We selected this range because American Joint Committee on Cancer (AJCC) TMN stage was available since 2004. Other exclusion criteria were as follows: synchronous distance metastases and patients with unknown TNM stage.P < 0.05 was considered statistically significant. PASW Statistics 13 was used for the statistical analysis.Age, sex, race, histological grade, histotype and cancer specific survival (CSS) were extracted from SEER database. CSS was calculated from the date of diagnosis to the date of cancer specific death. Deaths attributed to the rectal cancer were treated as events and deaths from other causes were treated as censored observations. The Kaplan-Meier method was used to estimate the CSS . The ass"} +{"text": "Non-communicable diseases (NCDs) result in more deaths globally than other causes. Monitoring systems require strengthening to attribute the NCD burden and deaths in low and middle-income countries (LMICs). Data from health and demographic surveillance systems (HDSS) can contribute towards this goal.2 linear trend 93.4; p<0.001). While overall annual mortality rates (MRs) for NCDs fell, cancer-specific MRs rose from 200 to 262 per 100,000 population, mainly due to increasing deaths in adults aged 65y and older, and to respiratory neoplasms in all age groups. The substantial fall in CD MRs resulted in similar MRs for CDs and NCDs among all adult females by 2010. NCD MRs for adults aged 15y to <65y fell from 409 to 183 per 100,000 among females and from 517 to 283 per 100,000 population among males. NCD MRs were higher among males than females aged both below, and at or above, 65y.Between 2003 and 2010, 15,228 deaths in adults aged 15 years (y) and older were identified retrospectively using the HDSS census and verbal autopsy in rural western Kenya, attributed into broad categories using InterVA-4 computer algorithms; 37% were ascribed to NCDs, 60% to communicable diseases (CDs), 3% to injuries, and <1% maternal causes. Median age at death for NCDs was 66y and 71y for females and males, respectively, with 43% of NCD deaths occurring prematurely among adults aged below 65y. NCD deaths were mainly attributed to cancers (35%) and cardio-vascular diseases . The proportionate mortality from NCDs rose from 35% in 2003 to 45% in 2010 (\u03c7NCDs constitute a significant proportion of deaths in rural western Kenya. Evidence of the increasing contribution of NCDs to overall mortality supports international recommendations to introduce or enhance prevention, screening, diagnosis and treatment programmes in LMICs. Non-communicable diseases (NCDs) are reported to be responsible for two out of every three deaths worldwide Areas in sub-Saharan Africa (SSA) with potential to monitor changing trends in causes of death over time can contribute towards global knowledge on disease burdens of LMICs 2 area along the shores of Lake Victoria, with a population in 2010 of 224,500 adults in aged 15 years (y) and above. The population, mainly subsistence farmers, are almost exclusively members of the Luo ethnic group and traditionally polygynous, have been described in detail elsewhere The HDSS study site is located in a rural part of Siaya County, in western Kenya The HDSS is a population-based system with GPS locational data, that longitudinally records demographic information Verbal autopsy is conducted in subpopulations covered by HDSS. All deaths in residents, defined as having resided in the area for at least four consecutive months, are identified by local village reporters through ongoing local monitoring, and are validated during the tri-annual census. At least one month following death, and within four months to reduce recall bias, an interviewer returns to the home and records events surrounding the death, using standardized WHO verbal autopsy (VA) questionnaires endorsed by the INDEPTH Network The HDSS protocol and consent procedures, including surveillance and VA, are approved by the Ethical Review Committee of the Kenyan Medical Research Institute (#1801) and by the Centers for Disease Control and Prevention Institutional Review Board (#3308). Following cultural customs, compound heads provide written informed consent for all compound members to participate in HDSS activities. Individuals can refuse to participate at any time. All HDSS census and VA data are maintained on a secure server accessed by authorized researchers only. Named data are securely stored in a MS-SQL database and only authorized data personnel have access rights. Datasets analysed by scientists are stripped of names to protect identity.For this evaluation, adults were defined as persons aged 15 years and older. Data were extracted from the HDSS database for all adult deaths in residents, generated from the adult VA questionnaire, between January 2003 and December 2010. Primary cause was derived from aggregated ICD-10 codes generated by the InterVA-4 algorithms Key social and demographic characteristics generated from questioning the compound head during HDSS census surveys were examined, to compare differences among deaths from NCD and CD, and by sex. This included marital status , education , and socio-economic status (SES). SES quintiles were based on multiple correspondence analysis (MCA) generated from biennial surveys on wealth indicators, reported elsewhere 2) test for linear trend (LT) determined the significance of changing rates by sex and age over time (2003 to 2010). Pearson's \u03c72 test was used to determine differences between groups. Mantel Haenszel Relative Risks (RR), with Taylor Series 95% confidence intervals (CI), were used to compare annual mortality rates between sexes. We stratified RR analyses for mortality rates by age groups, sex, and year generating a summary \u03c72, with a Mantel Haenszel weighted RR (MHRR) and Greenlands-Robins 95% CI. Significance was set at 5% or less.Analyses were conducted using SPSS for Windows , and EpiInfo Stat Calc . Chi-squared had a defined primary cause of death, and 1,935 were of indeterminate or unknown cause. Of the 12,808 adult NCD and CD deaths, two-thirds were 15y to <65y of age, among both female and male deaths. The median age at death among females was significantly lower than males for CD causes, and significantly higher for NCD causes .2 LT 93.4; p<0.001) of all deaths. This trend was consistent for both sexes , evident in both sexes recorded between 2003 and 2010, the overall number of deaths fell by 35% from 1,550 in 2003 to 1,003 in 2010 . While tth sexes . Distribth sexes . Among dth sexes .Among the 12,808 deaths, there was no difference in marital status between NCD and CD with nearly all (93%) ever married, and half married at the time of death; however, divorce (separation) was almost twice among CD compared with NCD deaths . Half of persons who had died were in the poorer socio-economic status (SES) two quintiles, with NCD marginally higher (50%) compared with CD (46%). A significantly higher proportion of deaths of persons from CD completed primary school compared with NCD . Less than 1% of NCD and CD deaths completed secondary schooling. Differences by sex were noted for the proportion in the lowest two SES quintiles with females significantly poorer among NCD compared with CD , but not among males . Differences between NCD and CD for schooling held for both sexes. Married at time of death reversed for males and females; thus while 70% of male NCD deaths were married (compared with 64% of CD), among females 31% of NCD were married and 36% of CD, illustrating the high proportion of female deaths, particularly from NCDs, occurring in widowhood.Among the 4,847 NCD-attributed deaths, two-thirds were ascribed to cancers and CVDs . For mal2 13.7, p<0.001).Digestive, respiratory/intrathoracic, reproductive, female breast, oral, and other/unspecified . Deaths attributed to neoplasms were distributed equally between males and females. The median age of death for all cancers was 66y . This was due to a sharp rise in deaths attributed to neoplasms among persons \u226565y rising nearly 3-fold, and more than doubling the overall contribution of cancers to NCD deaths among older adults by 2010 . Among deaths in adults aged <65y, the number of cancer deaths ascribed fell slightly over time, but due to steep reductions in other NCD deaths in adults aged <65y, the relative proportion of cancers against all NCDs increased in this younger age group, most notably among females <65y. The interVA-4 computer algorithm allocated cancers into five broad neoplasms: digestive, respiratory, male and female reproductive, oral, female breast, and other or unspecified.Among 1,410 cancer deaths assessed for trends over time (excluding Karemo), the annual number of cancer deaths rose 41% from 150 to 212 deaths between 2003 and 2010 . This inDigestive neoplasms (501 deaths): This included carcinomas of the oesophagus, gut, and liver and constituted 29% of all attributed cancers. The median age at death for digestive neoplasms was 62y (IQR 49-75), with 55% of deaths occurring among adults <65y of age. While the overall number and proportion of deaths from neoplasms classified as digestive did not change over time, there was a decrease in deaths in adults <65y dying from digestive neoplasms, with a concomitant increase among persons who died aged \u226565y.2 LT: males 57.1, p<0.001; females 42.8, p<0.001). Significant linear trends were also observed among both sexes for such deaths in persons aged \u226565y.Respiratory/intrathoracic neoplasms (460 deaths): This includes carcinomas of the trachea, bronchus and lung; thymus; heart, mediastinum and pleura, and other/ill-defined respiratory and intrathoracic sites. These represented 27% of all fatal cancers. The median age at death for respiratory/intrathoracic neoplasms was 70y (IQR 53-79), with 39% of deaths occurring in persons <65y of age. The annual number of deaths ascribed to respiratory cancers rose from 5% to 50% of all attributed cancers. In adults aged <65y, both the proportion and the absolute number of deaths from respiratory/intrathoracic neoplasms rose significantly (\u03c7Reproductive neoplasms (97 deaths): In females, these include vulva, vagina, cervix uteri, corpus uteri, uterus, ovary, and other/unspecified genital sites. In males this category includes penis, prostate, testis, and other/unspecified genital sites. These neoplasms contributed 6% of all fatal cancers, 2% of male cancer deaths and 10% of female deaths. The median age at death for reproductive neoplasms was 65y (IQR 44-76), with 50% <65y of age.Female breast neoplasm (20 deaths): This was recorded as the cause of 2% of female cancer deaths with no reported deaths among males. The median age at death for female breast cancer was young - 41y (IQR 31-47); 85% of female breast cancer deaths were reported among females <65y of age.Oral neoplasms (33 deaths): This category includes neoplasms of the tongue, gum, floor of the mouth, palate and other/unspecified sites of the mouth. These contributed 2% of all cancers, 2% for each sex. The median age at death for oral neoplasms was 47y (IQR 34-71) with 67% of deaths occurring among persons <65y of age.Other or unspecified neoplasms (591 deaths): This large group aggregates a broad range of sub-categories including Kaposi sarcomas, neoplasms of the urinary tract, brain, thyroid and other endocrine glands. These were reported in 35% of all cancers. The median age at death for other/unspecified neoplasms was 67y (IQR 48-78), with 46% below 65y of age. Males died at a younger age than females with a median age of 57y (IQR 39-74), compared with 73y (IQR 60-81), respectively. The proportion and absolute number of deaths attributed to these neoplasms reduced over time, for both sexes, and among adults who died above and below 65y of age.2 9.4, p\u200a=\u200a0.002).Ischemic heart disease, stroke, and other, unspecified cardiac and vascular disease . The median age of death for CVDs was 73y , deaths fell marginally from 141 to 127 between 2003 and 2010 apart from a spike in deaths in 2008 . This waIschemic heart disease (100 deaths): This category is limited to angina pectoris, myocardial infarction and, acute and chronic ischemic heart disease. These constituted 7% of all CVD deaths, 9% of all male and 6% of all female CVD deaths. The median age at death for was 69y (IQR 55-78) with 36% aged <65y old. The number of deaths attributed to these diseases did not increase over time.Stroke (327 deaths): This includes cerebral haemorrhage, occlusions, infarctions and other cerebrovascular disease and sequelae. These represented 24% of all CVD deaths, 24% for male and for female CVD deaths. The median age at death for stroke was 70y (IQR 56-79) with 42% of deaths in adults aged <65y. The number of deaths attributed to stroke did not increase over time.2 LT: males 16.2, p<0.001; females 14.7, p<0.001).Other/unspecified cardiac and vascular diseases (957 deaths): This category comprises a broad range of circulatory and hypertensive disorders. These represent 69% of all CVD deaths. The median age at death for other/unspecified cardiac and vascular disease was 74y (IQR 61-81) with 32% of deaths occurring among adults <65y. Overall, the absolute number of deaths from these diseases varied over time, with a spike in 2008. There was a significant increase in adults \u226565y . The median age of death for abdominal disease was 61y .Among 680 deaths attributed to abdominal disease assessed for trends over time (excluding Karemo), deaths fell 4-fold over time; from 113 reported in 2003, to 32 deaths in 2010 . This deAcute abdomen (635 deaths): This was recorded in 84% of deaths from abdominal disease, equally for males and females. The median age at death for abdominal disease was 58y (IQR 35-75), with 59% occurring among adults aged <65y. The absolute number of deaths ascribed to acute abdomen decreased among younger aged adults over time, particularly among females.Liver cirrhosis (125 deaths): This includes alcoholic liver disease, toxic liver disease, hepatic failure and chronic hepatitis, not elsewhere classified, liver fibrosis/cirrhosis, inflammatory or other liver diseases. These represented 16% of deaths from abdominal disease, with a similar proportion in both sexes. The median age at death for liver cirrhosis was 71y (IQR 56-81) with 37% of adults <65y of age. The number of deaths attributed to liver cirrhosis also fell over time.Asthma, chronic or obstructive pulmonary disease . The median age of death for pulmonary disease was 75y .Among 167 deaths attributed to pulmonary disease assessed for trends over time (excluding Karemo), deaths rose from 4 in 2003 to 36 in 2010 . The conAsthma was contributed 39% of pulmonary disease deaths, with a median age at death of 64y (IQR 42-78) and half of deaths occurring among adults aged <65y.Other chronic or obstructive pulmonary disease included bronchitis, emphysema, and other chronic obstructive pulmonary disease contributing 61% of the pulmonary disease deaths, with a similar proportion in both sexes. The median age at death was 78y (IQR 70-85) with 18% occurring in adults aged <65y. Significantly fewer males were <65y (10%) compared with females .Includes diabetes mellitus, severe anaemia, and severe malnutrition . The median age of death for diseases of the metabolism was 70y , deaths fell from 6% to 2% of NCD deaths between 2003 and 2010 .Diabetes mellitus (136 deaths): This contributed 63% of deaths attributed to metabolic causes; 74% of metabolic deaths among males and 48% among females. The median age at death for diabetes mellitus was 72y (IQR 61-79), with 33% of deaths among adults aged below 65y. The number of deaths attributed to diabetes was sporadic over time.Severe malnutrition (39 deaths): This contributed 18% of deaths attributed to metabolic causes. The median age at death for severe malnutrition was 63y (IQR 43-79). While 93% of male malnutrition deaths died <65y of age, among females this was distributed across the age range.Severe anaemia (41 deaths): 19% of deaths attributed to metabolic causes were ascribed to severe anaemia. The median age at death for severe anaemia was 68y (IQR 51-79), with 39% <65y of age.Acute kidney failure, chronic kidney disease, unspecified kidney failure . The median age of death for renal disease was 72y , deaths fell from 4% to 2% of NCD deaths . The median age of death attributed to epilepsy was 24y . The median age of death for all other/unspecified NCDs was 70y .Among 345 deaths attributed to all other and unspecified NCDs assessed for trends over time threshold, and against CD mortality rates. Trends in mortality rates ascribed to the main NCD causes of death; cancers, CVDs, and abdominal diseases were examined in greater detail.2 LT 4.2, p\u200a=\u200a0.04; 2 LT 5.8, p\u200a=\u200a0.02), the fall from 644 to 536 per 100,000 among females was not significant (p\u200a=\u200a0.32). These trends comprise a significant rise in NCD MRs among both males and females in persons aged \u226565y, in tandem with very significant reductions in NCD MRs in both males and females aged <65y varied by year, with a modest overall reduction between 2003 and 2010 of all NCD deaths; the 41% rise between 2003 and 2010 was, as noted above, due to a sharp rise in persons aged>65y. The proportion of cancers appears to be considerably higher than that reported nationally in Kenya Until relatively recently, cancer was poorly recognised as a public health priority in African countries, particularly in areas with a high burden of CDs such as HIV, TB and malaria. Concern has now been raised that cancers are an emerging public health problem in Africa, with 715,000 new cases and 542,000 deaths estimated in 2008 The fall in cancers among adults aged <65y reflected the halving of \u2018other neoplasms\u2019 (for both sexes) and a fall in digestive cancers among males. The category \u2018other neoplasms\u2019 includes Kaposi's sarcoma, which prior to the use of interVA-4, ascribed HIV as the cause of death and was therefore classified as a CD In addition to poverty and poor access to care, and continued exposure to infectious diseases, the rising cancer burden in SSA is considered to be a consequence of increasingly westernised lifestyles Many barriers to diagnosis and treatment remain, however, including a lack of population awareness of symptoms leading to early diagnosis, lack of knowledge by health workers, lack of chemotherapy and radiotherapy services, and a lack of suitable pain relief and palliative care Globally, deaths from CVDs are expected to rise from 16.7 m to 23.3 m between 2002 and 2030 The HDSS infrastructures could be utilized to facilitate intervention studies; for example, by providing anti-hypertensives and follow-up monitoring to persons identified to be hypertensive during mass screening at census. Such sentinel sites also provide opportunities for longitudinal surveillance of key risks such as diet, smoking and alcohol consumption.The international community is justly striving for concerted global action with leadership, prevention, treatment, international cooperation, and monitoring and accountability proposed as the five overarching priority actions needed to respond to the global crisis of NCDs We acknowledge a number of caveats when interpreting these data. First, misclassification between CDs and NCDs, and co-morbidity between diseases may contribute to the higher proportion of NCD deaths than the 28% estimated countrywide Second, we note ascription of cause of death through verbal autopsy depends on the symptoms reported; symptoms of a chronic disease might have been reported but for some cases, an underlying disease such as HIV may be undiagnosed and contribute to cause of death. This is a recognised limitation of verbal autopsy Fourth, the significant rise in cancer mortality rates may also reflect improvement in diagnostic test availability, public perception, or of increased reporting. We have not identified any obvious systematic bias as a cause for this rise although capacity in hospitals may be improving, as we have occasional case reports documenting a confirmatory pathology diagnosis, such as squamous cell carcinoma in a person who died in the community. Thus, for example, past respiratory cancers presumptively labeled as TB may now be better detected. Despite these limitations we believe our data will contribute towards an understanding of NCDs in LMICs, and will provide a platform for studies exploring the prevalence, risk factors, and potential interventions to control the NCD burden in the years ahead.Data generated from the HDSS in rural western Kenya illustrate the important contribution of NCDs to adult deaths among rural African communities. Our data suggest mortality from NCDs are proportionately increasing compared with CD deaths, with evidence of a rise in the absolute number of deaths from cancer, and rising mortality rates. Findings presented highlight the need for improvements in prevention, screening, diagnosis, treatment and effectively delivered care of NCDs and their risk factors Figure S1Distribution of absolute number of deaths ascribed to non-communicable diseases by type, sex, age threshold, and year of death.(TIF)Click here for additional data file.Figure S2Distribution of absolute number of deaths ascribed to neoplasms by type, age threshold, sex and year of death.(TIF)Click here for additional data file.Figure S3Distribution of absolute number of deaths ascribed to cardio-vascular diseases by type, age threshold, sex and year of death.(TIF)Click here for additional data file.Figure S4Distribution of absolute number of deaths ascribed to abdominal diseases by type, age threshold, sex and year of death.(TIF)Click here for additional data file.Figure S5Distribution of absolute number of deaths ascribed to metabolic diseases by type, age threshold, sex and year of death.(TIF)Click here for additional data file.Figure S6Distribution of absolute number of deaths ascribed to pulmonary diseases by type, age threshold, sex and year of death.(TIF)Click here for additional data file.Figure S7Distribution of absolute number of deaths ascribed to renal diseases by type, age threshold, sex and year of death.(TIF)Click here for additional data file.Figure S8Distribution of absolute number of deaths ascribed to epilepsy by type, age threshold, sex and year of death.(TIF)Click here for additional data file.Figure S9Distribution of absolute number of deaths ascribed to other and unspecified non-communicable diseases by type, age threshold, sex and year of death.(TIF)Click here for additional data file.Table S1WHO Verbal Autopsy (VA) cause of death ICD equivalent codes for Non-Communicable Diseases (NCD).(DOCX)Click here for additional data file.Table S2Breakdown of Non-Communicable Disease Deaths by Age Threshold, Year of Death, and Sex: All NCDs, Cancers, and CVD: absolute number of deaths in study site, excluding Karemo.* * Time trends on absolute number of deaths 2003\u20132010 exclude deaths from villages added to the study site (Karemo) 2008\u20132010.(DOCX)Click here for additional data file.Table S3Breakdown of Non-Communicable Disease Deaths by Age Threshold, Year of Death, and Sex: Abdominal, Other, and Metabolic diseases: absolute number of deaths in study site, excluding Karemo.* * Time trends on absolute number of deaths 2003\u20132010 exclude deaths from villages added to the study site (Karemo) 2008\u20132010.(DOCX)Click here for additional data file.Table S4Breakdown of Non-Communicable Disease Deaths by Age Threshold, Year of Death, and Sex: Pulmonary, Renal Diseases and Epilepsy: absolute number of deaths in study site, excluding Karemo.* * Time trends on absolute number of deaths 2003\u20132010 exclude deaths from villages added to the study site (Karemo) 2008\u20132010.(DOCX)Click here for additional data file."} +{"text": "Three years after beginning employment at a bakery, a 32-year-old Japanese man began experiencing acute asthma exacerbations after exposure to rye flour. Antigen-specific serum IgE antibodies were detected to the albumin and globulin, gliadin, prolamin, and glutenin protein fractions of rye flour purified from the crude antigen, but only to the albumin and globulin fraction of wheat flour. The histamine concentration producing one-half maximal effect was lower for all four rye flour fractions than for the wheat flour fractions. After inhalation of the albumin and globulin fraction of rye flour, forced expiratory volume in 1 sec decreased to 77.7% of that pre-provocation. To our knowledge, this is the first report of baker\u2019s asthma due to rye flour in Japan. Baker\u2019s asthma is caused by inhalation of cereal flours and is a common occupational allergic disease in Europe and the United States, where bread is a staple food , 2]. Wh. Wh2]. WA 32-year-old Japanese male ex-smoker (Brinkman index: 390) presented with a history of allergic seasonal rhinoconjunctivitis since the age of 20, but with no history of asthma, although his younger brother did have bronchial asthma. The patient had worked as a baker since the age of 25. Since the age of 27, he had experienced rhinoconjunctivitis exacerbations while handling rye flour but not wheat flour. At the age of 28, he experienced the first episode of chest tightness, cough, and wheezing while handling rye flour; the episode persisted until the next day. At age 32, 30 min after eating 200 g of bread that included 50% rye flour, the patient experienced anaphylactic symptoms, including upper body urticaria, facial swelling, angioedema of the eyelids, and dyspnea, due to narrowing of the respiratory tract.We purified crude antigen extracted from wheat or rye flour into four protein fractions \u2013 albumin and globulin, gliadin, prolamin, and glutenin \u2013 as described . We perfThere were no abnormal chest radiograph findings. The patient had airway obstruction. His spirometry parameters when not experiencing acute asthma exacerbation were: forced vital capacity (FVC), 4.76 L; percent-predicted FVC, 115.0%; forced expiratory volume in 1 sec, 3.87 L; percent forced expiratory volume in 1 sec, 100.3%; maximum expiratory flow rate at 50% FVC, 3.86 L/sec; percent maximum expiratory flow rate at 50% FVC, 66.0%; maximum expiratory flow rate at 25% FVC, 1.48 L/sec; and percent maximum expiratory flow rate at 25% FVC, 47.9% (Table The incidence of cereal-induced occupational asthma is 0.081/1000 person-years in the UK and 3.4/1000 person-years in Norway [Recently, the demand for bread made with rye flour has increased in Japan because of the diversification of eating habits and greater concern for a healthy lifestyle. This is the first report of baker\u2019s asthma caused by exposure to rye flour in a Japanese patient. This report will contribute to progress in the diagnosis and management of occupational asthma."} +{"text": "Knowledge and avoidance of allergies can lead to better allergy symptom control. The AIRS study assessed approaches to diagnosis of nasal and eye allergies or allergic rhinoconjunctivitis in the US.A national sample of 34,030 households using a dual frame approach of random digit dialing and cell phone sample were targeted. Patients aged =5 years with a health care professional diagnosis of hay fever, allergic rhinitis, rhino-conjunctivitis, nasal or eye allergies and symptoms or medication for condition in past 12 months were surveyed. Data on specific diagnosis and allergy testing were collected.Based on screening land-line sample of 20,835 households, 18% of individuals were diagnosed with one of conditions of interest. Of the 2765 surveyed patients, 86% were diagnosed with nasal allergies, 59%, hay fever, 54% eye allergies, 30%, allergic rhinitis and 13%, rhinoconjunctivitis. Four percent of respondents reported they were given an allergy test by doctor or health professional in past four months, 3% in past year, 7%, 1-2 years ago, and 37%, 3 or more years ago. Of those, 71% reported that they had a skin prick test, 13% had blood test and 12% had both blood and skin prick test. 47% report they never received an allergy test.The AIRS survey demonstrated that 18% of individuals > 5 years were diagnosed with an above allergic condition. Although these respondents had been diagnosed by a health care professional with \u201callergies\u201d, almost half never had any allergy testing to determine the triggers of their condition."} +{"text": "Age is the only independent predictor of poor bowel preparation amongst hospitalized patients.We examine the impact of key variables on the likelihood of inpatient poor bowel preparation for colonoscopy. Records of inpatients that underwent colonoscopy at our institution between January 2010 and December 2011 were retrospectively extracted. Univariable and multivariable logistic regression models were fitted to assess the effect of clinical variables on the odds of poor preparation. Tested predictors included age; gender; use of narcotics; heavy medication burden; comorbidities; history of previous abdominal surgery; neurological disorder; product used for bowel preparation, whether or not the bowel regimen was given as split or standard dose; and time of endoscopy. Overall, 244 patients were assessed including 83 with poor bowel preparation. Cecal intubation was achieved in 81.1% of patients (95% CI: 76.2\u201386.0%). When stratified by quality of bowel preparation, cecal intubation was achieved in only 65.9% (95% CI: 60.0\u201371.9%) of patients with poor bowel preparation and 89.9% (95% CI: 86.1\u201393.7%) of patient with good bowel preparation. In multivariate logistic regression analysis, only advancing age was an independent predictor of poor bowel preparation (OR = 1.026, CI: 1.006 to 1.045, and The Multisociety Task Force on Colorectal Cancer recommends a target of 90% colonoscopy completion rate , 2, whicOn the matter of bowel preparation, investigators have also examined characteristics associated with an adequate bowel preparation. These include admission status, gender, age, obesity, socioeconomic status, comorbidities, insurance status, number and type of medications, and time of endoscopy, as well as time between preparation and endoscopy \u201312. Few The records of inpatients who underwent colonoscopy at our institution between January 1, 2010, and December 31, 2011, were retrospectively extracted from EndoWorks . Endoscopists at our institution have a mean annual caseload of 533 colonoscopies between 2013 and 2015. Fellows and residents participated in 59% of cases, all of which were supervised. Six individuals reviewed hospital charts, and 10% of cases were audited for validation. All data collection and analyses were undertaken following the approval and institutional oversight of the Institutional Review Board for the Protection of Human Subjects.The primary endpoint examined was poor bowel preparation. Patient and demographic information collected included age, gender, race, body mass index, comorbidities , indication for colonoscopy, number of previous colonoscopies, previous abdominal surgery, and time between bowel preparation and start of colonoscopy, as well as time of the day and context of endoscopy. Baseline comorbidities were determined using the Charlson Comorbidity Index (CCI) and stratified according to four levels: 0, 1, 2, and \u22653 , 15.Bowel preparation was categorized according to four groups: poor, fair, good, and excellent preparation by the endoscopist. Poor bowel preparation was defined as poor or fair bowel preparation.The sample size of 500 was chosen to reflect the estimated number of events for the least frequently reported outcome of interest, for example, 23% incomplete bowel preparation, and the number of variables to be tested .p value approach, as described by Mazumdar and Glassman [The incidence of poor bowel preparation was assessed. In univariate analyses, quantitative variables were examined as both continuous and categorized variables. The minimum Glassman , was useTo assess multicollinearity between variables and CCI, we assessed the variance inflation factor (VIF) collinearity statistic and the tolerance . Analysep < 0.001). Incomplete colonoscopy due to poor bowel preparation added a total of 64 extra days of admission before performing repeat colonoscopy or CT-colonography, in 21 patients, representing a mean additional hospitalization duration of 3 days.Overall, 244 charts of patients undergoing colonoscopy during hospitalization were assessed. Of those, 83 patients had poor bowel preparation. During endoscopic examination, the cecum was reached in 198 patients . The mean age of the patients was 66 years; 133 were men (54.5%). The rate of complete colonoscopy in patients with poor bowel preparation was 65.9% (95% CI: 60.0\u201371.9%) compared to 89.9% (95% CI: 86.1\u201393.7%) in patients with good bowel preparation . Certain factors such as diabetes (p = 0.06), limited mobility (p = 0.075), and elevated comorbid score trended towards significance . The model obtained a VIF of 2.52 and a tolerance of 0.40. Based on this, we calculated that, for every 10-year increase in age, the likelihood of poor bowel preparation increased by 1.29 , which is similar to previously published data where rates range from 17 to 38% .1\u201339.9%,, 22\u201324. We identified that age was a key factor predicting poor bowel preparation in hospitalized patients. In uni- and multivariable analysis, age was the only significant predictor of poor preparation. Furthermore, for every 10-year increase in age, the odds of having poor bowel preparation increased by 1.29. Age has been previously described as a predictor of poor bowel preparation , 8, 11, The high rate of poor bowel preparation and subsequent lower cecal intubation rate may have been impacted by our cohort's comorbid status. Moreover, increasing comorbidities has been identified previously as causally related to inadequate bowel preparation in primary outpatient populations , 9, 11. Inpatient status has been identified as a predictor of poor bowel preparation , 23. EvePatients with poor bowel preparation stayed an average of 3 additional days in hospital. This raises concern of increased costs to the health care system. A study from 2002 documented that incomplete examinations were associated with a 12% and 22% increase in costs in private and public hospitals, respectively . This hiThe limitations of our study include its retrospective design, which can lead to bias, as well as being underpowered. It is possible that we did not observe any significant differences because of the inability to achieve the desired sample size. The lack of power may explain why other patient-centered factors, particularly comorbid status, were not significant in our data set. Preparation-based factors such as split-dose preparation and runway time could also have been affected by the lack of power thus leading to a type 2 error. Other possible reasons for not duplicating findings from other studies would include variations in patient characteristics, including language barriers, as well as nursing and medical practices. Moreover, bowel preparation was not standardized at our institution, which may represent an important confounder. On that matter, there are potentially other unmeasured confounders that may ascertain for our findings. For example, sicker patients were potentially unable to take the prep and had a longer hospital stay due to their multimorbidity.In conclusion, 34.0% of inpatients had poor bowel preparation and the rate of complete colonoscopy in this group was 65.9% (95% CI: 60.0\u201371.9%). In uni- and multivariable analysis, age was the only independent significant predictor of poor bowel preparation. An age-specific approach should be implemented to minimize this factor in relation to poor bowel preparation. The broader use of split-dosing preparations may result in increased bowel cleanliness in this patient population, although high quality evidence in this difficult group is lacking at present.At the authors' tertiary care referral center, poor bowel preparation is frequently reported (34.0%) in the hospitalized settings. In the hospitalized patients, age is the only independent predictor of poor bowel preparation."} +{"text": "Central venous catheterization is commonly used in critically ill patients and may cause different complications, including infection. This type of infection contributes to morbidity, mortality and, as a consequence, to the increase in health care costs.Evaluation of the incidence and adherence of the ICU team to an implemented protocol for prevention of central venous catheter- related bloodstream infection (CVCRBI).Exploratory-descriptive research based in auditing an implemented protocol through the use of checklists. After CVC- related bloodstream infection prevention protocol implementation, auditing was made during the period of 26 of November of 2014 to 3 of March of 2015. Population study: 17 doctors and 36 nurses were under observation. Auditing was made in random labor time of the investigators. Auditing checklists:1- evaluation during insertion of CVC;2- evaluation during maintenance and removing of CVC.From all the 185 in-patients in the ICU, 141 had CVC. Mean age was 61 years old, 54% were males, mean length of ICU stay was 7 days. Type of admission: 49% medical; 18% elective surgery; 23% urgent surgery; 7% trauma; 3% potential organ donors. Mean SAPS II was 48; mean SOFA was 7. Overall catheter day's was 1196 that corresponds to 1,7% of CVCRBI. A total of 119 auditings were made .Audit results: compliance with protocol during insertion of CVC - 87%; compliance with protocol during maintenance was 83%.During the audit period we had a low incidence of CVCRBI. Compliance with implemented protocol was very high. During the same period the ICU mortality rate decreased. Although direct correlation can't be made, we might speculate, that the incidence of CVCRBI's could aid, in same way, to this decrease in mortality."} +{"text": "During last decades C. difficile infection (CDI) has emerged as a most frequent health-care associated cause of morbidity and mortality in developed world. In Europe about 40,000 patients die each year of CDI, in Poland rapid increase of CDI rates has been observed, reaching appr. 11,500 hospitalized cases in 2013.In mild cases metronidazole is the first-line therapy, with effectiveness of 66%. In severe cases vancomycin is used with cure rate about 78%. Novel therapy with fidaxomicin shows similar clinical cure rates to vancomycin with lower recurrence rates. Alternative method, fecal microbiota transplantation (FMT) for CDI treatment has been reported since 1958 with worldwide response rates of 83-94% as claimed by reviews.We perform the first prospective, non-randomized, multicenter, observational study to estimate the effectiveness of FMT in the treatment of recurrent CDI, including 2 hospitals and one ambulatory center in Poland. The procedure has been proposed for patients with recurrent C. difficile infection that have failed to respond to antimicrobial therapy. All donors, related or unrelated, after obtaining informed consent, have been screened for enteric bacterial pathogens, viruses and parasites according to published guidelines.Donor stool after dilution with 0,9% saline has been filtered and resulting suspension has been infused via a nasogastric tube. All patients have signed informed consent according to the written procedure. From 2013 to 2014, in total, 62 patients aged 24-90 years received FMT with resolution of clinical symptoms of 88,7%. Among 55 successfully treated patients, in 76,5% cases recovery has been observed after first FMT procedure, in 14,5% after the second, and in 9% after the third one. There were no statistically significant differences between the cure rates of related and unrelated donor or fresh and frozen samples. There were no severe adverse events observed. Mild diarrhoea, temporary constipation, nausea, flatulence and abdominal pain were most frequently reported side effects.Although majority of physicians currently consider FMT as an experimental therapy, we showed that FMT is safe, well tolerated, and highly effective therapy for recurrent CDI.None declared."} +{"text": "Choline is an essential nutrient and betaine is an osmolyte and methyl donor. Both are important to maintain health including adequate lipid metabolism. Supplementation of dietary choline and betaine increase muscle mass and reduce body fat in animals. However, little data is available regarding the role of dietary choline and betaine on body composition in humans.To investigate the association between dietary choline and betaine intakes with body composition in a large population based cross-sectional study.A total of 3214 subjects from the CODING (Complex Disease in Newfoundland population: Environment and Genetics) study were assessed. Dietary choline and betaine intakes were computed from the Willett Food Frequency questionnaire. Body composition was measured using dual-energy X-ray absorptiometry following a 12-hour fast. Major confounding factors including age, sex, total calorie intake and physical activity level were controlled in all analyses.Significantly inverse correlations were found between dietary choline and betaine intakes, with all obesity measurements: total percent body fat (%BF), percent trunk fat (%TF), percent android fat (%AF), percent gynoid fat (%GF) and anthropometrics: weight, body mass index, waist circumference, waist-to-hip ratio in both women and men . Dietary choline intake had stronger association than betaine. Moreover, obese subjects had the lowest dietary choline and betaine intakes, with overweight subjects in the middle, and normal weight subjects consumed the highest dietary choline and betaine (p<0.001). Vice versa, when subjects were ranked according to dietary choline and betaine intakes, subjects with the highest intake of both had the lowest %TF, %AF, %GF, %BF and highest %LM among the groups in both sexes.Our findings indicate that high dietary choline and betaine intakes are significantly associated with favorable body composition in humans. Obesity is widely recognized as a chronic disease associated with many serious health problems including type 2 diabetes, cardiovascular disease, hypertension and at least a dozen of cancers , 2. In tCholine and betaine are quaternary ammonium compounds, which are obtained from diet or by de novo synthesis in tissues. Both of them are found in a wide variety of foods. Among the most concentrated sources of dietary choline are eggs, beef, pork, liver, seafood and milk, whereas betaine is mainly obtained from grains, cereal, beets and spinach \u201313. CholThe beneficial effect of choline and betaine on reducing body fat has been demonstrated in animals, including rats , pigs 2, 22, chiTo the best of our knowledge, there is no previous study examining the effects of dietary choline and betaine intakes on body composition in a large general population. Therefore, the current cross-sectional study was designed to investigate the association of dietary choline and betaine intakes with body composition in the general Newfoundland population after controlling for potential confounding factors such as age, sex, total calorie intake and physical activity level.All participants were from the CODING (Complex Diseases in the Newfoundland population: Environment and Genetics) study \u201335. Elig2) was calculated as weight in kilograms divided by height squared in meters. WC was defined as the midway point between the iliac crest and the lower rib, and hip by the maximum circumference over the buttocks below the iliac crest. Waist-to-hip ratio (WHR) was division of WC by hip circumference.Anthropometrics, body composition measurements were collected following a 12-hour fast. Trained personnel conducted the anthropometric measurements of each subject using standard procedures. Standing height was measured using a fixed stadiometer (to the nearest 0.1 cm). After urinating to empty their bladders, subjects wore standard hospital gowns for all weight measurements using a platform manual scale balance . BMI was used for the measurement of percent trunk fat (%TF), percent android fat (%AF), percent gynoid fat (%GF), total percent body fat (%BF) and total percent lean mass (%LM). The Lunar Prodigy software system determines automatically the regions. Trunk fat region is from the top of the shoulders to the top of the iliac crest, while the android fat region is the top of the second lumbar vertebra to the top of the iliac crest and the gynoid fat region extends down iliac crest twice the height of the android area. The enCORE software package was used for DXA data acquisition. Quality assurance was performed on the DXA scanner daily and the typical CV during the study period was 1.3% , 34.Information regarding lifestyles of participants was collected through a self-administered screening questionnaire. The questions were related to demographics (age and gender), disease status, smoking status, alcohol consumption, and medication use. A separate questionnaire was administered to women with relation to their menopausal status. Physical activity patterns were measured using the ARIC Baecke Questionnaire, which consists of a Work Index, Sports Index, and Leisure Time Activity Index .Dietary intake of each participant was assessed using a 124 item semi-quantitative Willett FFQ , 38. Thet test.All data are presented as mean \u00b1 standard deviation (SD). To perform effective statistical analysis, total calorie intake, dietary choline, betaine intakes per person per day, and dietary choline, and betaine intakes per kilogram body weight per day were log-transformed to normalize the data distributions. Differences in anthropometrics, body composition measurements and dietary choline and betaine intakes between females and males were assessed with independent Student\u2019s Statistical interaction between dietary choline, betaine intakes and gender on the main outcomes was tested by analysis of covariance (ANCOVA). Partial correlation analysis controlling for age, total calorie intake, and physical activity level was used to evaluate the correlations of dietary choline, betaine intakes with weight, BMI, WC, WHR, %TF, %AF, %GF, %BF and %LM within female and male groups. To overcome the possible influence of smoking, medication use, drinking and menopausal status, participants were also divided into subgroups according to smoking status (yes or no), medication use (yes or no) and alcohol consumption (yes or no). Women were further divided into pre- or post-menopausal groups according to their menopausal status.2), overweight (25.0\u201329.9 kg/m2) and obese groups (\u226530.0 kg/m2). As the number of underweight subjects (BMI<18.5 kg/m2) was too small to perform any effective statistical analysis, they were excluded from analyses. Obesity status was also categorized by percent body fat according to age and gender specific criteria recommended by Bray [According to the criteria recommended by World Health Organization (WHO) , obesity by Bray . SubjectAll statistical analyses were performed using SPSS 20.0 . All tests were two sided and a p<0.05 was considered to be statistically significant.Demographic, physical and dietary characteristics of the entire population and different gender groups are presented in Significant interactions between dietary choline, betaine intakes and gender on weight, BMI, WC, WHR, %TF, %AF, %GF, %BF and LM% were found . The correlations between dietary choline, betaine intakes and weight, BMI, WC, WHR, %TF, %AF, %GF, %BF and %LM in different gender groups are presented in Subjects were divided into three adiposity groups by gender: normal weight, overweight and obese groups according to BMI recommended by WHO and according to %BF by Bray criteria.According to BMI, as shown in When subjects were divided by %BF, as shown in 2, -11.79 cm, -0.02), and %TF, %AF, %GF, %BF but higher %LM (6.30%). Male subjects of high dietary choline intake group had significantly lower weight (-11.19 kg), BMI (-3.87 kg/m2), WC (-12.82 cm), WHR (-0.03), %TF (-10.56%), %AF (-12.66%), %GF (-5.94%), %BF (-8.35%), but higher %LM (8.25%) compared with low choline intake group. While, the average differences of obesity measures between high and low dietary betaine intake (mg/kg/day) groups were -7.42 kg (weight), -2.77 kg/m2 (BMI), -7.31 cm (WC), -0.02 (WHR), -6.19% (%TF), -6.24% (%AF), -3.13 (%GF), -4.55% (%BF), 4.00% (%LM) in females, and -8.60 kg (weight), -3.01 kg/m2 (BMI), -8.81 cm (WC), -0.03 (WHR), -7.77% (%TF), -8.92% (%AF), -4.19% (%GF), -6.19% (%BF), 6.19 (%LM) in males.Subjects were divided into tertiles according to dietary choline and betaine intakes (mg/kg/day). As shown in Tables To the best of our knowledge, this is the first large cross-sectional study specifically designed to investigate the association between dietary choline, betaine intakes and DXA-derived body composition. We found significant associations of higher dietary choline and betaine intakes with better body composition profile . Furthermore, the inverse correlation of dietary choline intake with obesity measures was stronger than that of betaine.Association study is relatively easy to do but hard to do well, especially in large population based study. The first challenge is the accurate measurement of physiological and biological markers because sophisticated equipment is required, and long period of time is needed to recruit large number of subjects. In the present study, body composition in all subjects was measured using the same DXA system by certified technicians over 12 years. DXA produces accurate measurement of adipose tissue in the body with a low margin of error and is considered to be one of the most reliable measurements of adiposity . The secet al found a negative association between serum choline and body weight and BMI [We used the unit of mg/kg/day to express choline and betaine intakes in all analyses because dietary intake of both is highly correlated with body weight. It would be physiologically inappropriate not to account for body mass when comparing dietary intake among subjects with large difference of body weight. Physiological dynamics of nutritive intake is in many ways similar to that of pharmacodynamics where in the case of choline and betaine, the same dose may be adequate for a person with 60 kg body weight, but insufficient for a person with a body weight of 100 kg or more. The use of mg/kg/day in the present study eliminates the bias of body weight variation in the population and reveals the true relationship between dietary choline, betaine intakes and body composition. Otherwise, we also analyzed the data for mg/day and the negative associations were also significant but not strong . Further and BMI . The rel and BMI . It is r and BMI , 27, 53.et al found that a choline-deficient diet decreased fat mass in mice with high fat diet or genetic defect induced obesity [To date, a few small interventional studies have examined the effect of betaine supplementation on body fat but no study is available on the effect of choline supplementation in humans. A significant decrease in fat mass and percent body fat was observed among 11 male participants received a periodical training program . However obesity , 55. Ano obesity . HoweverThe exact mechanisms by which choline and betaine improve body composition are unclear, while several mechanisms have been suggested. It has been postulated that choline and betaine supplementation could promote fatty acid \u03b2-oxidation in pigs and humans by enhancing muscle carnitine accretion and thereby increase carnitine palmitoyl transferase I-mediated free fat acid translocation into the mitochondria \u201361. CholAlthough our study provides clear evidence on association of increased dietary choline and betaine intakes with favorable body composition, a number of limitations of the work should be considered. Our use of FFQ to evaluate patterns of dietary intake raises the possibility of recall bias by subjects . HoweverIn conclusion, the present study provides solid evidence for the first time, in the large Newfoundland population, that higher dietary choline and betaine intakes were associated with a more favorable body composition (lower body fat and higher lean body mass) in both women and men. In addition, this favorable association was independent of age, gender, total calorie intake, physical activity level, menopausal status, smoking status, medication use, and alcohol consumption. The beneficial correlation for choline seems better than betaine.S1 FigA. variations of dietary choline intake (mg/kg/day) in different obesity status grouped based on BMI criteria; B. variations of dietary betaine intake (mg/kg/day) in different obesity status grouped based on BMI criteria; C. variations of dietary choline intake (mg/kg/day) in different obesity status grouped based on %BF recommended by Bray; D. variations of dietary betaine intake (mg/kg/day) in different obesity status grouped based on %BF recommended by Bray; **p<0.01 compared with normal weight group, ##p<0.01 compared with overweight group.(TIF)Click here for additional data file.S2 FigA. variations of total body fat according to dietary choline intake; B. variations of total lean mass according to dietary choline intake; C. variations of total body fat according to dietary betaine intake; D. variations of total lean mass according to dietary betaine intake. **p<0.01 compared with low dietary choline or betaine intakes; ##p< 0.01 compared with medium dietary choline or betaine intakes.(TIF)Click here for additional data file.S1 Table(DOC)Click here for additional data file.S2 Table(DOC)Click here for additional data file.S3 Table(DOC)Click here for additional data file.S4 Table(DOC)Click here for additional data file.S5 Table(DOC)Click here for additional data file."} +{"text": "Staphylococcus aureus (MRSA) thaneither targeted decolonization or screening and isolation. Since regional health-carefacilities are highly interconnected through patient-sharing, focusing on individualICUs may miss the broader impact of decolonization. Using our Regional HealthcareEcosystem Analyst simulation model of all health-care facilities in Orange County,California, we evaluated the impact of chlorhexidine baths and mupirocin on all ICUadmissions when universal decolonization was implemented for 25%, 50%,75%, and 100% of ICU beds countywide (compared with screening andcontact precautions). Direct benefits were substantial in ICUs implementingdecolonization . When100% of countywide ICU beds were decolonized, there were spillover effects ingeneral wards, long-term acute-care facilities, and nursing homes resulting in median8.0%, 3.0%, and 1.9% relative MRSA reductions at 1 year,respectively. MRSA prevalence decreased by a relative 3.2% countywide, withsimilar effects for methicillin-susceptible S. aureus. We showedthat a large proportion of decolonization's benefits are missed whenaccounting only for ICU impact. Approximately 70% of the countywide cases ofMRSA carriage averted after 1 year of universal ICU decolonization were outside theICU.A recent trial showed that universal decolonization in adult intensive care units(ICUs) resulted in greater reductions in all bloodstream infections and clinicalisolates of methicillin-resistant Staphylococcus aureus (MRSA) is considered aserious public health threat by the Centers for Disease Control and Prevention showed that universal decolonization of allpatients without MRSA screening in adult ICUs resulted in a significantly greaterreduction in MRSA clinical isolates than either targeted decolonization or screening andisolation . UniversS. aureus (MSSA) prevalence andnumbers of carriers, we utilized a computational simulation model of all inpatienthealth-care facilities and the community in Orange County.Since health-care facilities in a region are highly interconnected throughpatient-sharing, focusing on individual facilities may miss the potential broader impactof decolonization. Previous work in Orange County, California, has demonstrated theextent to which patients move among health-care facilities via both direct transfers and readmissions afterdischarge , 12. PatUsing our custom-designed software, the Regional Healthcare Ecosystem Analyst (RHEA), 16, we The model used 2011\u20132012 patient-level data for all adult inpatient admissionsfrom the 102 facilities and inclS. aureus carriers or noncarriers,with carriers harboring either MRSA or MSSA. In each health-care facility, the totalprevalence of S. aureus colonization was set to 30% . We assumed acertain influx of MRSA from the community . Forhospitals, this influx was optimized such that the model targeted thefacility-specific point prevalence data; for nursing homes, it was set to 10%, which represented 23%,51%, 74%, and 100% of ICU beds countywide, respectively . Additional experiments varied contact precaution effectiveness(50%\u201370%) and decolonization efficacy(75%\u201390%) when decolonization was implemented for 100% ofICU beds.Our baseline scenario consisted of active surveillance cultures in ICUs and contactprecautions for patients identified as harboring MRSA in any ward. This baseline wascompared against ICU decolonization scenarios. To evaluate potential synergisticeffects, we analyzed countywide impacts on MRSA and MSSA prevalence when 25%,50%, 75%, and 100% of ICU beds had a universal decolonizationprotocol in place. Universal decolonization was implemented by hospital size measuredin number of ICU beds, starting with the largest. We thus implemented universaldecolonization in the ICUs of 2, 7, 13, and all hospitals . The model proceeded in 1-day time steps and simulated 9years after a run-in equilibration period. The impact of decolonization was thedifference between scenarios with decolonization and the baseline scenario. Outcomesof interest included the relative changes in MRSA and MSSA prevalence and the numberof carriers. By comparing the numbers of carriers across various scenarios, wedetermined the number of cases of MRSA carriage averted , or those cases of MRSA carriage that would haveoccurred had decolonization not been performed.Table Results were similar for decolonization efficacy of 75%. Trends were similarover time, with median relative reductions in MRSA and MSSA prevalence of47.5% and 47.9% , respectively, in ICUs with decolonizationprocedures when decolonizing all ICU patients. Decolonization resulted in largergains with lower contact precaution effectiveness (50%), with median relativereductions in MRSA and MSSA prevalence of 60% and 57%, respectively,when decolonizing all ICUs.After 1 year, when decolonization was implemented for all countywide ICU beds,general wards in hospitals that implemented ICU decolonization saw a median8.0% relative reduction in MRSA prevalence ; 3 of 28 hospitals had a relative decrease of\u226510%. These benefits increased slightly over time . When allOrange County ICU beds were decolonized, 47% of the countywide cases of MRSAcarriage were averted after 1 year of decolonization in hospitals with decolonizationprocedures, with 19% of the total reduction occurring in non-ICU wards. After6 years, 31% and 15% of countywide MRSA carriers averted were inhospitals with decolonization procedures and non-ICU wards, respectively. Resultswere similar with a lower decolonization efficacy (75%); general wards inhospitals with decolonization procedures achieved a median 5.9% relativereduction for a 13.6% relative reduction hospitalwide after 1 year whendecolonizing all ICU patients. Decolonization resulted in larger reductions whenreducing the effectiveness of contact precautions relative reduction hospitalwide when decolonizingall ICU patients).Figure Table Figure As more countywide ICUs implemented decolonization, the number of MRSA carriers inhospitals not implementing ICU decolonization, LTACs, and nursing homes decreased.After 1 year, approximately 53% of countywide cases of MRSA carriage avertedwere outside of hospitals with decolonized ICU beds (regardless of the number ofOrange County ICU beds decolonized). These benefits in other facilities accrued overtime; the proportion of averted cases in other hospitals and facilities increased toapproximately 70%, regardless of the number of ICU beds decolonized, with amajority of the benefits accruing in nursing homes. When 100% of ICUs weredecolonized, 53% of countywide MRSA carriers averted after 1 year were innon\u2013acute-care facilities (1.5% in LTACs and 51.5% in nursinghomes); this figure increased to 69% after 6 years.Decreasing decolonization efficacy (75%) had little impact on the relativereduction in LTACs (2.2%) and nursing homes (1.5%). Countywide, a2.5% relative reduction was achieved after 1 year of decolonizing all ICUpatients. Decreasing the effectiveness of contact precautions increased the benefitsof decolonization. LTACs and nursing homes garnered median 3.3% and2.1% relative reductions, respectively, and countywide a median 3.5%relative reduction in MRSA prevalence was achieved after 1 year of decolonizing allICU patients.For MSSA Figure , the effS. aureus carriage, universal decolonization in ICUsproduced direct and rapid reductions in MRSA and MSSA prevalence, halving overall ICUlevels of both within a year. Clinical trial findings suggest that this strategysignificantly reduces transmission and health-care-associated infection risk in averted MRSA carriers was seen downstreamin non-ICU settings . Nevertheless, while the total numbers of averted carriers countywidewere high over time, the facility-specific indirect effects on MRSA prevalence weremodest. Our findings suggest that universal ICU decolonization will have somespillover effect and synergy but will not substantially contribute to a countywideMRSA eradication program, thereby warranting the broader use of decolonization beyondthe ICU or other control measures. ICU decolonization should be coordinated acrosshospitals in a region, but coordinated ICU efforts alone are not enough to eradicateMRSA in a region."} +{"text": "The pre-marital sex and live-in relationship among young people are increasing at an alarming rate. Remote consequences of such high risk behaviors are increase in the incidence of STDs (including HIV), unsafe and illegal abortion, adolescent pregnancy and motherhood, single mother child/abandoned child, juvenile delinquency and many more.The aim of this study was to investigate the high-risk sexual behaviors in depth, influenced by various factors including age at sexual debut, type of partners, consistent condom usage, hostel stay, socioeconomic class, etc. among college-going male youth.The study was conducted in Jamnagar among undergraduate (18-24 years) male college students. A total of 450 students were randomly selected from three colleges of Jamnagar.Out of all 450 participants, 49.11% were in the age group of 18-20 years. Among study subjects, 13.78% had one or more pre-marital sexual exposures. In students with positive pre-marital sexual history, the various sex partners were girlfriends (95.16%), commercial sex workers (14.5%), homosexuals (6.45%), and multiple sex partners (33.88%). Among students, 62.9% were using condom consistently. Three-fifth of the ones indulged in premarital sex, were in the age group of 16-20 at the time of sexual debut.Most of the students were quite young (16-18 years) at the time of first pre-marital sexual exposure. Consistent condom usage was not uniform. The students staying at hostels, indulged in premarital sex, were found to have multiple sex partners. The present young generation of India is following life-style of their counterparts in the western culture. There is a competitive behavior among young college-going youth to prove themselves as more modern, impressive and so-called high-cultured people.Young people mature earlier but marry later. So many of them start sex at a younger age and may have multiple partners including sex workers. The repercussion of pre-marital sex in terms of health-related or psychosocial problems is hardly affecting the young people who are the potential growth engine of the country.Pre-marital sex and live-in relationship among young people are increasing at an alarming rate. The young generation is becoming a prey of this social evil and facing the remote consequences of such high risk behaviors which are increase in the incidence of sexually transmitted diseases (STDs) (including HIV), unsafe and illegal abortion, adolescent pregnancy and motherhood, single mother child/abandoned child, juvenile delinquency and many more.At present, the Government and various non-governmental organizations (NGOs) working in the field of health are concentrating towards particular communicable and non-communicable (life-style) diseases; but the ongoing psycho-social problems in the country due to the increasing trend of experimentation\u2013\u201ctaking a chance\u201d behavior are undermined, especially among male youth. In such relationships, males are considered to possess the decision-making and dominating roles, as far as this situation is concerned. The reported rate of students engaging in pre-marital sex in different region of India varies from 8% to 15% college going male students from January to June 2009. Sample size was calculated according to the given guideline in surveillance of HIV risk behaviors, participant manual module 5 were in the age-group of 18-20, 38% in 20-22, and 12.89% \u2265 22 years; 82.22% of participants came from an urban background and 30.22% belonged to higher socioeconomic classes, while 49.11% and 20.67% were from middle and lower socioeconomic classes, respectively. At the time of survey, 437 (97.11%) students were un-married and 101 (22.44%) had hostel stay history of any duration within the past 5 years , 69.30% Out of 450 total studied cases, 62 (13.78%) had one or more pre-marital sexual exposures . Among tMajority (about 60%) of students indulged in premarital sexual activities, were in the age group of 16-20 at the time of their sexual life initiation, while 24.18% were > 20, 16.13% were below 16, and unfortunately, four students were only 12-14 years . Out of 62 total participants with positive premarital sexual exposure, 39 (62.90%) used condom during their first premarital coitus while 23 (37.10%) did not, meaning that they were taking the risk of STDs including HIV in their very first sexual exposure. Among students who indulged in premarital sexual relations, 39 (62.9%) regularly, 27.4% sometimes, and 9.68% never used condom . Out of 62 total participants, 4 (6.45%) had history of STD after sexual exposure, 50% of which did not take any kind of treatment. Considering association between ages of premarital sexual debut and use of condom, it was found that the condom usage increased with the growth of students\u2019 ages. The result was statistically significant (P = 0.0257). Out of five total students in the age group of < 15, none of them used condom at their first sexual experience, but in the age group of 15-17, almost 2/3 of them used it . Surveys on the association between two high-risk behavioral characteristics including multiple sex partners and regular use of condom, revealed that only 42.85% of participants with multiple sex partners were using condom at each exposure; meaning that young people taking the risk of multiple sex partners, were also ignorant of consistent condom usage. Among students with single sex partners, 73.17% used condom consistently; meaning that they are quite protective by having single partners as well as regularly using condom . Among the upper-class students with history of premarital sex, 78.26% used condom at their first sexual exposure, while it was 64% for the middle class and only 35.71% for the low socio-economic class. It was observed that use of condom at first sexual exposure was on a decreasing trend from the upper to the lower class. The result was statistically significant . Analyzing the association between residence region and involvement in premarital sex, it was observed that 11.89% were from urban backgrounds while 22.5% belonged to rural residencies. The association was statistically significant with P value = 0.0205.The association between hostel stay and tendency for multiple partners was also analyzed. Among the students staying at hostels who indulged in premarital sex, 57.90% had multiple partners while among others, it was 23.26%. The result was also statistically significant with P value = 0.0180.The national pre-marital sex ratio among maIn the similar study by the national AIDS research institute (NARI) among undergraduates from six colleges of Pune , 37% of According to the national family health survey-3 (NFHS-3) , at the In a behavioral surveillance survey performed in Maharashtra in 2001, among 15-24 years unmarried youth of Slums, the findings were: 71% of respondents always used condoms for CSWs, but only 33% consistentlyused it for noncommercial partners. Among youth aging 20-24 years, 66% reported consistent condom usage during commercial sexes, but only 30% for noncommercial partners.Adhikari and Tamang in theirJeejibhoy and Sebastien found grIn the information era, young generations are getting early puberty, but without psychological maturity. The age of sexual debut is also decreasing as low as 12-14 years. Socio-economic class plays its own role; upper class students have more prevalence of premarital sex and consistent condom usage, while lower socio-economic class students have more prevalence of multiple sex partner and occasional condom usage. The prevalence of indulgence in premarital sex was more in students staying at hostels compared to the ones not staying at hostels. Even among hostel-staying students, the incidence increased with longer hostel accommodation, which might be due to the fact that they still hesitate to follow such high risk behaviors when they are in custody of parents, despite living in mixed cultures. Under the effects of western acculturation in our country, the rate of premarital sex indulgence by young people is on an increasing trend. So the actions such as easy and continuous condom availability development, especially around colleges, hostels and campuses, repeated generation awareness programs at colleges and hostels, availability of youth counselors at colleges, and promoting diagnostic and treatment facilities for sexually transmitted infections (STIs) should be strongly considered."} +{"text": "P < .001), visit frequency , and days between appointments . Further study of MCCs among pediatric patients is needed given their increasing prevalence and their associated health care cost and use.Studies investigating the prevalence of multiple chronic conditions (MCCs) and their associated health care cost and use among pediatric populations have been limited. Among 14,404 pediatric patients receiving outpatient care in southeastern Michigan from 2008 through 2013, 82.1% had 0 chronic conditions, 16.2% had 1 chronic condition, and 1.6% had 2 or more chronic conditions. Greater numbers of chronic conditions significantly predicted outpatient cost (\u03b2 = 581.7, Recent research concerning the epidemiology and cost implications of multiple chronic conditions (MCCs) has primarily centered on adult patients ,2. The sWe analyzed outpatient evaluation and management claims for patients under age 18 years and insured by the Beaumont Employee Health Plan (BEHP) to study MCC prevalence, cost, and use from 2008 through 2013. The BEHP is a regional health insurance provider serving Beaumont Health System employees and their families (spouses and children) in Southeastern Michigan. Beaumont Health System comprises 3 primary health care campuses and several satellite clinics and facilities in metropolitan Detroit. The BEHP provides health insurance coverage to approximately 30,000 people annually of whom about 7,000 are pediatric patients. The Beaumont Health System Research Institute for Human Investigation Committee (HIC) granted approval for this study (HIC no. 2014\u2013051).International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes assigned to patients\u2019 primary and secondary diagnoses on outpatient claims only: attention deficit disorder (ADD), asthma, autism, cancer, depression, diabetes, hyperlipidemia, hypertension, obesity, and substance abuse. Chronic conditions selected for this analysis represent a subset of prevalent and potentially preventable diseases specified by the Office of the Assistant Secretary for Health of the US Department of Health and Human Services for the purpose of standardizing MCC research initiatives were dropped from the analysis because of missing demographic or outcomes information.P < .001), outpatient visit frequency , and days between appointments . Asthma (9%), ADD (5.4%), the combination of asthma and ADD (1%), depression (0.6%), and diabetes (0.4%) were the most prevalent chronic conditions in this population . Among these patients, 82.1% had 0 chronic conditions, 16.2% had 1 chronic condition, and 1.6% (n = 230) had 2 or more chronic conditions . Outpatipulation . These cFrom 2008 through 2013, the proportion of pediatric patients with chronic conditions rose from 9.8% to 13.8% in this population. Compared with 2008, the adjusted odds of having a chronic condition in 2013 were 1.5 . Despite rising chronic condition prevalence, average outpatient cost, visit frequency, and days between appointments did not grow significantly over time. However, total outpatient cost and visits increased for chronic condition patients during the study period, and total days between appointments decreased. Throughout the study period asthma was consistently a highly prevalent chronic condition, affecting approximately 6% of the population each year. The most growth in prevalence occurred among patients with diagnosed ADD (3.2% to 6.8%) and depression (0.3% to 1.0%). By 2013 ADD was the most prevalent chronic condition among pediatric patients.Our study demonstrates that prevalence of MCCs among pediatric patients is increasing along with associated health care costs and office visits, whereas time between outpatient appointments is decreasing. We found that the top 5 most prevalent chronic conditions accounted for over 30% of outpatient costs attributable to pediatric patients.An inpatient study by Zhong and colleagues found that more than 40% of pediatric patients had 1 chronic condition, whereas 17% had MCCs . AlthougChronic conditions can affect a child\u2019s emotional, physical, and social development and often have lasting health and health care consequences ,10. UnliAn important limitation of this study is that our results may not be applicable to children whose parents are unemployed. Our analysis captures data on pediatric patients whose parents have diverse occupations in terms of salary . However, it would be inappropriate to apply our results to uninsured, unemployed, or Medicaid populations. We know that people at the greatest risk for acquiring chronic conditions are those from low social and economic classes , who werOur investigation helps to demonstrate the importance of studying MCCs among pediatric patients, because MCCs are growing in prevalence and are associated with increased health care use and cost. Asthma, ADD, depression, and diabetes are prevalent and costly chronic conditions among children and are appropriate targets for intervention."} +{"text": "Allergen exposure in sensitized patients has been associated to asthma and allergic rhinitis exacerbations, to severe symptoms and to medication need. Indoor allergens control is important in the management of atopic diseases in children, as they spend a large proportion of their time at home.A cross-sectional study design was adopted in order to access the adherence to environmental control recommendation in the management of asthma and allergic rhinitis. We selected patients aged between 5 and 18 years, who had the diagnosis of allergic asthma and/or allergic rhinitis and who were in regular follow-up for more than 6 months.96 patients were recruited. The median age was 10.3 years, and 66% (64) were male. All patients had a diagnosis of allergic rhinitis and 84 patients (87.5%) had a diagnosis of asthma. The responder was the child\u2019s mother in 87% of cases. 56% of responders had secondary or tertiary education and 45% of them were atopic. 76% of responders recognized that their children\u2019s doctors had instructed them about environmental control measures. In order to reduce house dust, 91% of houses had hard flooring and 97% were cleaned by moping the floor daily (52%) or weekly (45%). Moreover, 92% of housekeepers used to wash bedding every week, 72% minimized dust-accumulating objects, 90% removed soft toys, 83% removed rugs and 51% removed curtains. However, only 33% encased mattresses and pillows in impermeable covers. Other practices included ventilating the house by opening the windows every day in 96%, carefully cleaning the house to avoid cockroaches in 95% and chemical controlling cockroaches in 26% of cases. For pet allergen avoidance, 54% of families chose not to have pets. Among the families who had them, 52% kept the pet out of the main living areas and 27% used to wash the pet every week. Finally, 33% of families had at least one member who smoked, but only 3% of caregivers quit smoking. Among non-smoking caregivers, 29% reduced their child\u2019s exposure to sources of passive smoke outside the family.Caregivers understood and applied general allergen-avoidance measures in their homes. Despite of that, the majority of caregivers did not implement some specific measures with proven benefit in reducing allergen levels, such as encasing mattresses and pillows in impermeable covers, chemical controlling cockroaches and quitting tobacco smoke."} +{"text": "To evaluate the completeness of intervention descriptions in test-treatment RCTs.Reports of published RCTs of diagnostic tests evaluating patient outcomes published 2004-2007 were identified in CENTRAL. Two raters assessed trial reports for the presence of care pathway diagrams and for the completeness of written descriptions. Test-treat interventions descriptions were considered in their four components: 1) the test, 2) diagnosis decision-making, 3) management decision-making, and 4) interventions.103 trials evaluating 105 control and 119 experimental interventions were included from cardiovascular medicine , obstetrics and gynaecology , gastroenterology or orthopaedics . Trials evaluated imaging , biochemical assays and clinical assessment .Only 3 (3%) trials mentioned all four components in descriptions of the interventions, only one of which also provided a complete care pathway diagram. Descriptions were missing or incomplete for: 42% of experimental and 71% of control tests, 57% of experimental and 71% of control diagnostic decision-making, 74% of experimental and 73% of control management planning, and 80% and 86% interventions.Reporting of test-treat interventions is very poor and worse than for other complex interventions. Current descriptions are inadequate for implementing results of these trials into clinical practice. Reporting needs to improve, with greater emphasis on describing the decision-making components of the care pathways in pragmatic as well as explanatory trials. Expansion of the TiDIER checklist for test-treat trials is required."} +{"text": "Diabetes mellitus (DM) has been cited as the most challenging health problem in the 21st century. Successful management of this disease requires that we understand the lifestyle, attitudes, family and social networks of the patients being treated.To assess the sociodemographic, dietary practices and current food consumption among males and females with type 1 diabetes mellitus.A case-control, descriptive study was conducted in the city of Fortaleza, Brazil, applying a survey on sociodemographic, lifestyle, feeding behavior and food consumption in people treated as diabetic outpatients at the Federal University Hospital. The food consumption was collected through recall 24 h.15 individuals were interviewed . Mean of age was 31.3 yrs. Among educational levels was observed that 40% had finished high school and 27% had uncompleted primary education. Analyzing the occupation 40% are students or housewives and 33% are retired or self-employed. Evaluating the lifestyle, 80% do not smoke and drink alcohol. However, 73% of individuals are sedentary. Dietary aspects revealed that 73% follow a food plan, which were oriented: 73% by Nutritionist, 20% for Medical and 7% follow their own guidelines. In addition, 33% performs specific diet for diabetes prescribed by a nutritionist, another 20% follow carbohydrate counting diet, 13% just do not eat sugars and food sugars and 27% do not follow a specific diet for diabetes. Most of patients, 73% answered \u201crespect the amount of food in the diet\u201d when questioned about the difficulties of adhering to diet.\u201d The food consumption of the group was characterized by a deficit in energy intake, adequate carbohydrate percentage energy contribution, excessive in protein, cholesterol and saturated fat. While, polyunsaturated and monounsaturated fat had presented a very low consumption. Fibers consumption proved to be suitable, however it was found deficiency of vitamin D, E and folato.Sociodemographic studies like this are fundamental to improve the understanding of lifestyles and dietary practices of individuals with diabetes mellitus 1, being useful in proposing a better treatment strategy for these patients. Preliminary results in general show that the group requires actions of nutritional intervention to correct the dietary inadequacies, because the eating pattern indicates risk to health."} +{"text": "Clinical features comparison between adut and pediatric SLE patients.to describe clinical and serological features of juvenile Systemic Lupus Erythematosus (jSLE) patients; to compare the main differences between jSLE characteristics and adult SLE (aSLE).we detected all our jSLE patients from our database. We collected sociodemographic data and both clinical and serological variables from our jSLE patients' charts at Hospital Sant Joan de D\u00e9u, Esplugues . We defined the following variables: cutaneous disease , joint disease (arthritis), hematological disease , renal disease , neurolupus (psychosis and/or convulsions). We collected the following data: age at onset, time disease evolution, and gender. In regarding to serological markers: DNAds positivity through follow-up was recorded. We also collected information from a well-recognised aSLE cohort of 124 patients in the same Mediterranean urban area. We analysed all data in order to depict the type of clinical and serological features for each group of patients.we assessed charts from 42 jSLE (n = 42), and compared to aSLE (n = 124). 90% of the jSLE patients were female, compared to a 95% of the aSLE cohort. Age at onset was 12.1 years in jSLE. In the jSLE group of patients: 81% had had cutaneous disease, 62% haematological disorder, 44% arthritis, 40% nephropathy , and 14% convulsions. In the aSLE cohort: 80% had cutaneous disease, 54% haematological disorder, 29% arthritis, 14% nephropathy and 3.2% neuro-lupus. DNAds positivity was 68% in jSLE and 54.8% in aSLE.jSLE and aSLE are slightly different in our Mediterranean region. Most of cases were women and main features were similar in both groups. Pediatric patients had more frequently nephropathy (most of them class IV-WHO), and DNAds positivity. Further follow-up, in which are already involved, is needed to assess the outcome of our jSLE.None declared."} +{"text": "We aimed to investigate the clinical and para clinical manifestations of neuro metabolic disorders, in patients who presented by neuro developmental delay in their neuro developmental milestones.The patients diagnosed as neuro developmental delay and regression with or without seizure at the Neurology Department of Mofid Children Hospital in Tehran, Iran between 2004 and 2014 were included in our study. These patients diagnosed as neuro developmental delay by pediatric neurologists in view of diagnostic /screening neuro developmental assessment tests. The patients who completed our inclusion criteria as neuro metabolic disorders were evaluated in terms of metabolic and genetic study in referral lab.Overall, 213 patients with neurometabolic disorders were diagnosed. 54.3% of patients were male. The average age of patients was 41 +-46.1 months. 71.4% of parent\u2019s patients had consanguinity of marriages. Eighty seven percent of patients had developmental delay (or/and) regression. 55.5% of them had different type of seizures. Overall, 213 patients with 34 different neurometabolic disorders were diagnosed and classified in the 7 sub classes, consisting of: 1- organic acidemia and aminoacidopathy (122 patients), 2-storage disease (37 patients) 3- eukodystrophy (27 patients), other classes consisted: lipid oxidation disorders, urea cycle disorders, progressive myoclonic epilepsy; and peroxizomal disorders (27 patients).In patients with developmental delay or regression, with or without seizure, abnormal neurologic exam along with positive family history of similar disorder or relative parents, abnormal brain imaging with specific patterns, neurometabolic disorders should be considered as one of the important treatable diseases The incidence of autosomal recessive neurometabolic disorders is relatively high in Iran, probably due to the frequency of consanguineous marriages. Reevaluation of patients with delayed neurodevelopmental milestones in a referral neurometaboliccenter is very important. Early detection and early intervention of patients with neuro developmental delay/ regression as treatable neuro metabolic disorder can cause prevention of more brain insults during early infants and childhood. There are few beneficial clinical criteria for differentiating neuro metabolic disorders , 3. MostThis diagnostic study was performed on patients referred to the Neurology Department of Mofid Children\u2019s Hospital in Tehran, Iran with neuro developmental delay and regression with or without seizure or other items that predisposed them to metabolic disease. The diagnosis was done based on clinical manifestation, laboratory assessment and neuro imaging findings. The demographic data of patients were gathered as age, gender, developmental status, past medical history, and clinical and neuro imaging findings. We applied practical criteria for our patients in view of elementary diagnosis and then evaluated them by metabolic /genetic study for confirming of our diagnosis. The neuro metabolic disorders diagnosis was confirmed based on the type of disorder including acylcarnitine profile assessment in lipid oxidation disorders; enzyme assessment in Sandhoff and Tay\u2013Sachs disease; biotinidase deficiency (BD); metachromatic leukodystrophy (MLD) and galactosemia; very long chain fatty acid (VLCFA) assessment in peroxisomal disorders; serum acyl carnitine profile assessment and urine organic acid in organic acidemia; and genetic assessment in plezeousmerzbacher disease (PMD), PMD-like and for confirmation of other neurometabolic disorders. In the radiological assessment, location and pattern of white matter involvement , brain edema, brain atrophy , hemorrhage , basal ganglia involvement , thalamus, cyst, subdural effusion, axial hydrocephaly, heterotopia, cortical malformation, MRS involvement, and corpus callosum agenesia were assessed. Institutional ethical approval was obtained from the Pediatric Neurology Research Center of ShahidBeheshti University of Medical Sciences, Tehran, Iran. All parents signed a written consent for participation in this study. The data were analyzed using SPSS .Overall, 213 patients with 34 different neurometabolic disorders were diagnosed. A total of 54.3% were male. The median age of patients at detection time was 41 +- 46.1 months . A totalTotally, in developmental assessment 87% of patients showed neuro developmental delay/regression and only 13% of patients had normal development. Normal developmental status was seen in girls more than boys =1.57). Normal developmental status was seen more on MCAD (8 patients) and homocystinuria (7 patients) disorders. Abnormal EEG was seen in 10.7% patients with normal development and 22.3% of patients with abnormal development =2.38 with confidence interval 95%. MRI showed normal pattern in 10.7% of patients with normal development and 30% of patients with abnormal developmental status. Behavioral disorder was detected in 16.9% of patients. On examination, positive points in order of frequency consisted of: Abnormal muscular tonicity in 49.8% of patients, and ophthalmological problems in 32.9% of patients. Decreased level of consciousness episodes was seen in 5.2% etc. . A total of 16% of patients were microcephaly and 12.7% were macrocephaly. Atotal of 55.5% of patients had seizures, of which the most common type was tonic and then GTC. Auditory problems were seen in 6.6% of patients. Positive points in paraclinical assessments in patients in order of frequency consisted of: increased ammonia and lactate increased liver enzymes, etc. .Brain imaging in 36% of patients was normal; 20.4% of patients had brain atrophy; 25.1% had white matter involvement; 4.3% had basal ganglia involvement; 2.8% had basal ganglia and white matter involvement; 2.4% had basal ganglia involvement and brain atrophy. Brain atrophy with white matter involvement was seen in 5.7% of patients. In patients with organic acidemia and aminoacidopathy ; in 33% of patients, brain imaging was normal; 28.9% of patients had brain atrophy; 24.5% of patients had white matter involvement; the rest of patients had basal ganglia along with other area involvement. For example, among 22 patients with glutaricaciduria, 20 patients had brain atrophy especially in fronto temporal regions with sylvian groove widening ; 6 patieFor example, all the patients with Canavan disease (17 patients) had extensive white matter and u-fiber involvement, one patient had subdural effusion. From 4 patients with MLD, all of patients had white matter involvement as leukodystrophy with bilateral periventricular involvement without u-fiber involvement. Thirty six percent of patients with progressive myoclonic epilepsy , had normal imaging; 20.4% of patients had brain atrophy; 25.1% had white matter involvement, and the rest of patients had involvement in different regions. MRS was done in some of these patients, consisting of 17 patients with canavan disorder (that showed elevated level of N-acetyl aspartic acid), 3 patients with mitochondrial disorder (that showed elevated level of lactate), 4 patients with leukodystrophy in Brain MRI (that showed elevated level of choline/NAA ratio).Finally, patients who were fulfilled a number of our practical criteria items consisting : Consang71.4% of parents of our patients were relative (71.4%) and 23.5% of patients had positive family history of similar metabolic disordes. that in the other articles, the same results were noted. For example total of patients with MLC had history of consanguinity of marriage . SeizureIn conclusions, we suggest that patients, who have our criteria, are highly suspected to neurometabolic disorders, and should be assessed for these disorders."} +{"text": "Tragelaphus strepsiceros) rumen digesta, revealing a diverse community of microbes and some novel hydrolytic enzymes.Ruminant herbivores utilize a symbiotic relationship with microorganisms in their rumen to exploit fibrous foods for nutrition. We report the metagenome sequences of the greater kudu ( Tragelaphus strepsiceros), utilize dry plant material, which is high in cellulose content , Veillonellaceae, (14%), and Ruminococcaceae (10%). The observed taxonomic distribution is consistent with the current understanding of rumen microbiota composition showed that 95.8% of the sequences were of bacterial origin, 3.8% were unassigned, and 0.3% were archaea. At the phylum level, 39.2% of the reads were assigned to Functional analysis was done on 930,067 reads with predicted coding sequences. Of these only 396,910 had InterPro matches. Of interest were notable carbohydrate metabolic processes and general hydrolase activities, which were found to be 6.2% of biological processes and 13.1% molecular functions, respectively. The data generated from this kudu rumen metagenome add valuable information for future studies, particularly to those relating to isolation of novel enzymes such as cellulases, which can be used in the production of biofuels.ERR688806.This whole-genome shotgun metagenomic project has been deposited in the European Nucleotide Archive at EMBL-EBI under the accession number"} +{"text": "Tuberculosis and HIV are major global health problems. Tuberculosis is the most common opportunistic infection, leading to the mortality among HIV patients. This study aims to determine and compare the knowledge, attitude, and compliance regarding tuberculosis amongst HIV seropositive and HIV seronegative TB patients.This study was conducted at Raichur district hospital. Data regarding socio demographic profile, knowledge, attitude, and compliance was collected from the subjects with the help of pretested semi structured questionnaire. Data was analyzed using Microsoft Excel and SPSS 15.0 and Chi square test was applied.A total of 240 subjects aged 19-67 years were enrolled in the study. Out of them, 120 were HIV seropositive, 53% were male, and 68% had primary education. About 55.4% had average knowledge of TB but in depth knowledge about symptoms and the spread was not adequate among HIV seropositive patients. Regarding knowledge on the symptoms and spread of TB, only 35% knew about chest pain and 23% knew about hemoptysis. There were few misconceptions regarding the spread; majority (77%) believed that TB spreads by unprotected sex and 53.5% believed that it occurs through infected blood transfusion. We noticed positive attitude and positive compliance with TB treatment among majority of the respondents, however the compliance was better (92%) among HIV seropositive patients.Our study revealed that the knowledge regarding Tuberculosis among HIV seropositive patients is inadequate when compared to HIV seronegative patients. This calls for an awareness program targeting the HIV/AIDS infected individuals through advocacy, communication, and social mobilization."} +{"text": "Chronic pain is common among patients with drug use disorders. The prevalence of chronic pain and its consequences in primary care patients who use drugs is unknown and deserves further study.The objectives are to determine the prevalence of chronic pain and pain-related dysfunction among primary care patients who screen positive for drug use. To examine the prevalence of substance use to self-medicate chronic pain in this population.Cross-sectional analysis of adult patients who screened positive for any illicit drug use or prescription drug misuse, recruited from an urban, hospital-based primary care practice. Both pain and pain-related dysfunction were assessed by numeric rating scales, and grouped as: (0) None, (1-3) mild, (4-6) moderate, (7-10) severe. Questions were asked about the use of substances to treat pain.Among 589 participants, chronic pain was reported by 87%, with 13% mild, 25% moderate and 50% severe. Pain-related dysfunction was reported by 74% of participants, with 15% mild, 23% moderate, and 36% severe. Among those who used marijuana, cocaine, and/or heroin, 51% (283/576) reported using to treat pain. Of the 121 with prescription drug misuse, 81% used to treat their pain. Of the 265 participants who reported drinking any alcohol, 38% did so to treat pain compared to 61% of the 114 with heavy alcohol use.Chronic pain and pain-related dysfunction were the norm for primary care patients who screened positive for drug use. Almost half of these patients reported severe pain and approximately a third reported both severe pain and severe pain-related dysfunction. Many patients using illicit drugs, misusing prescription drugs and using alcohol reported doing so in order to self-medicate their pain. Pain needs to be addressed when patients are counseled about their substance use."} +{"text": "Adequate reprocessing of reusable medical devices is vital to protecting patient safety. Therefore, inadequate or improper cleaning of reusable medical devices puts patients at risk for healthcare-associated infections (HAIs). There are few studies carried out in the field of decontamination and sterilization of reusable medical devices in Africa, thus the current situation of sterile services in Africa remains unknown.This survey will help to establish needs in Africa for sterile services and education programmes.This survey was conducted during March and September 2014. The questionnaire developed and emailed to all ICAN Board members and PDIC students. The questionnaire composed by 6 components: hospital general information, CSSD design, reprocessing equipment, autoclaves, testing sterilizers, Sterile storage and CSSD environmental cleaning. 53 completed forms from 11 countries returned to the investigator. Data entered into access database, and then analysed with MS Excel.62% of CSSD is managed by Nurse, and only 17% managed by CSSD qualified manager. 68% of CSSD fall under operating theatre. Only 4% of CSSD staff are SSD qualified. 38% of surgical devices cleaned only in CSSD. 60% surgical devices are cleaned manually 47% 62% sterilizers reported as good functioning. 43% perform Leak test daily, 56% Bowie Dick test, 60% chemical indicator is placed in each pack daily, 90% autoclave tape is placed on each pack daily, 60% biological indicator is performed daily.Ineffective surgical devices reprocessing, inappropriate CSSD design, lack of adequate training for CSSD staff, lack of appropriate and sufficient equipment, materials and supplies are the major obstacles to the effective CSSD service delivery in Africa. Adequate training of SSD staff should be taken as the first priority and provision of necessary equipment, supplies to be considered for better service delivery.None declared."} +{"text": "Blastocystis spp. were the most predominant parasite (16% in cases versus 8% in controls), followed by Giardia duodenalis (10% in cases versus 12% in controls) and Cryptosporidium spp. (10% in cases versus 6% in controls). Cyclospora cayetanensis was identified in two cases, while Entamoeba histolytica was described in one case and one control. Intestinal parasitism was positively associated with the male gender, urban residence, and travel history. Clinical symptoms of nausea/vomiting and abdominal pain were significantly varied between the parasitized cases and controls . Given the results, we recommend screening all diarrheal feces for intestinal protozoa in the study's population, particularly those with CRF.It has been hypothesized that chronic renal failure (CRF) predisposes patients to infection with intestinal protozoa. We tested this hypothesis with a matched case-control study to determine the prevalence of these protozoa and their diarrhea associated symptoms among 50 patients with CRF (cases) from Taif, western Saudi Arabia. Fifty diarrheal patients without CRF were recruited in the study as controls. Participants were interviewed by a structured questionnaire and stool samples were collected. Samples were thoroughly examined with microscopy and three coproantigens detection kits. Enteric protozoa were detected in 21 cases and 14 controls. Giardia duodenalis, Entamoeba histolytica, Cryptosporidium spp., Cyclospora cayetanensis, Cystoisospora belli, and Microsporidia spp. have been certainly recognized to cause diarrhea in humans [ Entamoeba coli and Entamoeba dispar almost certainly have not [ Blastocystis spp. and Dientamoeba fragilis have been recently identified in patients with diarrhea, but their causal role is still uncertain [Enteric protozoa are a diverse group of unicellular microparasites inhabiting the intestinal tract of high vertebrate hosts including humans . Infectin humans , others have not . In addincertain . Regardlncertain .By definition, patient with chronic renal failure (CRF) is a patient with end stage kidney disease causing marked decline in the glomerular filtration rate as well as uremia and requires kidney replacement or scheduled dialysis to survive . It has Two hundred and four patients comprising 139 with CRF and 64 without CRF from those patients attending the outpatient clinics at King Abdulaziz Specialized Hospital, Taif, Saudi Arabia, seeking treatment of their diarrheal episodes, were invited to participate in the study.An episode of diarrhea was defined as \u22653 loose bowel movements over a day prior to interviewing. Individuals with history of diabetes mellitus, malignancy, autoimmune disease, or any other chronic diseases were excluded from the study. Patients with history of taking antiparasitic, antidiarrheal, or immunosuppressive medications, 2 weeks prior to meeting, were also excluded from participation in the study. Following these exclusion criteria, 50 patients with CRF, described as cases, and 50 patients without CRF, named as controls, were allocated in the current study.All participants were informed of the purpose of our study and signed consent forms authorizing their voluntary participation. The regional ethics committee approved data collection, clinical samples collection, and analysis of the study.On enrollments, face-to-face interviews were conducted using a structured questionnaire for the basic demographic data in terms of age, sex, and residence. Questions about drinking water resources, history of travel to foreign countries, and/or exposure to animals during the three-week period preceding diarrhea were also included. Moreover, some clinical data concerning the number of bowels/day, duration of diarrhea, accompanying nausea/vomiting, mucous or blood in feces, abdominal pain, bloating/flatulence, general fatigue, and loss of weight were also sought for in the questionnaire.A total of 100 fecal samples, one sample from each participant, were collected between June and December 2014. Fresh samples were obtained in clean screw-capped cups. Feces were transported to the Microbiology Laboratory at College of Applied Medical Sciences, Taif University, within 2-3 hours after collection. Samples were appropriately coded and immediately stored at 4\u00b0C till the time of parasitological examination. Blastocystis spp., Microsporidium spp., and intestinal coccidian protozoa, respectively. Staining and examination techniques were carried out according to Garcia, 2009 [Fresh feces were examined for consistency and presence of mucous or blood. Direct wet mount smears were microscopically examined for parasites ova, cysts, oocysts, and/or larvae, as previously described . Formol-ia, 2009 . G. duodenalis with RIDA Quick Giardia , Cryptosporidium spp. with RIDA Quick Cryptosporidium , and for E. histolytica with E. histolytica II Test commercial kits. Immunoassays were performed following the corresponding manufacturer's protocol.Fresh fecal specimens were also examined forP value \u2264 0.05 was considered significant.Statistical package for social science (SPSS) program, version 16 for windows, was used for data entry and data analysis. Summaries with descriptive statistics were generated and the data was further statistically analyzed according to the objectives of the study. Appropriate statistical tests (parametric or nonparametric tests) were used according to the type of data whether qualitative or quantitative. Among 100 participants, 67 were males (mean age of 54.4 \u00b1 12.8) and 33 were females (mean age of 51.9 \u00b1 14.3). Eighty-three participants were urban, while the remaining 13 participants were from remote rural areas. Forty-seven patients had travel history to one tropical country 1\u20133 months before their diarrheal episodes. Twenty-six participants had contact with one or more domestic animal 3-4 weeks prior to their diarrheal episodes. Treated bottled water was the main drinking water resource for 56 participants, followed by desalted sea water for 31 participants and the underground well water for 13 participants.P = 0.14). Blastocystis spp. were the most frequently identified parasite followed by G. duodenalis and Cryptosporidium spp. . Blastocystis spp., Cryptosporidium spp., G. duodenalis, C. cayetanensis, and E. histolytica were identified in cases at infection rates of 16% (8/50), 10% (5/50), 10% (5/50), 4% (2/50), and 2% (1/50), respectively. In the control group, Blastocystis spp., Cryptosporidium spp., G. duodenalis, and E. histolytica were diagnosed with prevalence rates of 8% (4/50), 6% (3/50), 12% (6/50), and 2% (1/50), respectively cases and 14 (28%) controls, with an overall prevalence rate of 35%. No significant differences were statistically observed between both groups and were absent in the control group.ts feces was confn = 21), 14 (66.7%) were males and 7 (33.3%) were females. Infections were more frequent in cases from urban areas than those residing rural areas . Eleven cases had travel history and 10 cases had not. Among the parasitized controls (n = 14), intestinal protozoa were identified more in males than in females , in persons from urban areas than those residing rural areas , and in participants with travel history than those without . No significant differences were statistically observed for any of these variables between the parasitized cases and controls (Concerning the parasitized cases (controls .P = 0.06) between both groups. Diarrhea continued for a duration of more than 2 weeks only in 28.6% (6/21) of protozoa-positive cases. Persistent diarrhea was reported in two G. duodenalis positive cases, two Cryptosporidium spp. positive cases, one Blastocystis spp. positive case, and one C. cayetanensis positive case. Mucous and blood were seen in feces of two cases and one control . One of these two cases was positive for E. histolytica and Blastocystis spp., while the other was positive for Blastocystis spp., as a sole infection. The only patient in the control group who reported mucous and blood in his feces was E. histolytica positive. Bloating/flatulence, abdominal pain, general fatigue, and nausea/vomiting were the common symptoms found associated with the diarrhea (Acute and transient diarrhea was reported in 71% (15/21) of the parasitized cases and by all parasitized controls , with no significant differences observed (diarrhea .n = 14), diarrhea accompanied with symptoms of abdominal pain, nausea/vomiting, bloating/flatulence sensation, feeling fatigued, and losing weight was practiced by \u224879% (11/14), 93% (13/14), \u224871% (10/14), and 100% (14/14) of patients, respectively. Significant differences were found between parasitized cases and parasitized controls regarding the association of their diarrhea with abdominal pain (P = 0.05) and with nausea/vomiting (P = 0.02). No significant difference between the parasitized cases and controls was observed for other symptoms.Diarrhea associated with abdominal pain and fatigue sensation was reported by all the parasitized cases. Diarrhea associated with nausea/vomiting, bloating/flatulence sensation, and losing some weight was reported by \u224857% (12/21), \u224876% (16/21), and 9.5% (2/21) of the parasitized cases, respectively. Among the parasitized controls (Diarrhea was often mild (87.5% of cases versus 100% of controls) and nondysenteric (87.5% of cases versus 100% of controls). The commonly associated symptoms were abdominal pain, fatigue (100% of cases and controls), nausea/vomiting (87.5% of cases versus 100% of controls), flatulence/bloating (75% of cases versus 25% of controls), and losing weight (12.5% of cases versus 0% of controls). No significant difference was found between the parasitized cases and controls .Cryptosporidium species associated diarrhea was often mild (60% of cases versus 100% of controls) and nondysenteric in all parasitized patients. The commonly reported associated symptoms were fatigue (100% of cases and controls), abdominal pain (100% of cases versus 33.3% of controls), nausea/vomiting (60% of cases versus 100% of controls), flatulence/bloating (80% of cases versus 100% of controls), and losing weight (12.5% of cases and controls). Statistically, no significant difference was described for any of these symptoms between the parasitized patients in both groups and nondysenteric (100% of cases and 83.3% of controls). The common associated symptoms were fatigue (100% of cases and controls), abdominal pain (100% of cases versus 83.3% of controls), nausea/vomiting (80% of cases versus 83.3% of controls), flatulence/bloating complaints (100% of cases versus 83.3% of controls), and losing weight (00% of cases versus 9% of controls). None of these symptoms showed significant statistical differences between the parasitized cases and controls.As described in In the study's population, protozoan infections associated with diarrhea were common (35%). Infections were identified in considerable number of patients in the diarrheal control group. This is not surprising for this population where several protozoan infections predominate . IntestiIt has been argued that CRF predispose patients to helminths but thisBlastocystis spp. were the most frequently isolated protozoa in the present study. These protozoa were detected more in cases than in controls, consistent with earlier studies [ Blastocystis spp. infections have been described in the Turkish study [ Blastocystis spp. have been identified more in controls than in cases , according to Gil et al. [ Blastocystis spp., with prevalence rate of 13.6% (12/88), have been reported in dialysis patients [ studies , 17. Higsh study . In the l et al. . In a crpatients . Lower ppatients \u201325. C. belli nor Microsporidia spp. were identified in our study. Except for a recently published case report for C. belli infection overwhelming a patient with eosinophilic gastroenteritis [ Microsporidium spp. infections has been reported in Turkish patients with CRF [ Cryptosporidium spp. was revealed in the present study. While higher rates (11\u201335%) have been described in earlier studies [ Cryptosporidium spp. infection has been stated with prevalence rate of 2.7\u20138.1% in Saudi general populations [ C. cayetanensis in two patients with CRF was interesting. To the best of our knowledge, this protozoan has never been reported in patients with CRF. In Saudi Arabia, C. cayetanensis has been rarely detected even in immunocompromised patients [Considering the opportunistic enteric protozoa, neithernteritis , little with CRF . High pr studies \u201329, lowe studies , 30. Cryulations , 25. Idepatients .Giardia duodenalis was detected in considerable number of the study's participants. Infections were identified more in the control group, compatible with an earlier study [ Giardia duodenalis has been commonly detected in Saudi communities. Infection rates of 3\u201318% have been reported [ E. histolytica, the tissue-invasive intestinal protozoan, was rarely determined among cases in this study, consistent with a previous study [ E. histolytica infection has been recognized as a public health threat in Saudi Arabia. Prevalence rates of 6\u201335% have been described in Saudi Arabia [er study and incoer study . Giardiareported , 22\u201326. us study and incous study . E. histi Arabia , 21\u201324. i Arabia . In the E. histolytica. Acute dysenteric diarrhea was described in six cases, two of them were found parasitized with Blastocystis spp. concomitantly with G. duodenalis in one patient and with E. histolytica in the other. In addition, acute dysenteric diarrhea was observed in three controls, one of them was found parasitized with E. histolytica. In the presence of coinfection, it is very challenging to attribute patients' symptoms to one protozoan and neglect the other [ E. histolytica being a well-known tissue-invasive parasite [ Blastocystis infection relying on a previous research [Diarrhea was often acute and transient in most of the parasitized patients. Persistent diarrhea was reported by few parasitized cases, consistent with previous report . Persisthe other . Perhapsparasite . One elsresearch , 35. Any E. histolytica. Nevertheless, our study was not free from the limitations. Low number of cases was enrolled in this study due to the strict selection criteria adopted. We could not rely on the recent immune status of participants based on doing laboratory tests because many participants were reluctant to give blood samples. Lastly, we did not include tests for intestinal bacteria and viruses that could be concomitantly present with protozoan infection(s), due to time and cost limits of our study. All these limitations plus performing longitudinal study have to be considered in the near future research.This is the first study comparing the frequency of intestinal protozoa-associated diarrhea in CRF patients and nonrenal controls from Taif, Saudi Arabia. In this study, special considerations were given to avoid well-known potential confounders while enrolling patients and subsequent selection bias. Another strength of our study was the inclusion of a number of immunoassays in the study's methodology to avoid the low sensitivity of microscopy-based methods in diagnosis of certain parasites such asIn conclusion, high frequency of intestinal protozoan infections was described in the study's population. Protozoa were detected more in patients with CRF than in diarrheal controls. Further studies are required before attributing diarrhea in patients with CRF to a protozoan detected in patients' feces. Until these studies, we advise screening all diarrheal patients for intestinal protozoa in the study's population, with greater concern that should be given to patients with CRF."} +{"text": "Objective: A neurogenic bladder is one which functions abnormally due to disorders of sacral nerves that control the bladder's ability to fill, store and empty urine. Abnormal bladder function can cause the bladder to be underactive or overactive. This study was planned to evaluate the treatment outcome of our patients with neurogenic bladder dysfunction (NGBD).Methods: Thirty three patients who have been treated for NGBD were evaluated. Diagnosis was confirmed by voiding-cysto-urethrography (VCUG) and urodynamic study. The patients were treated medically and all had clean intermittent catheterization (CIC). Data regarding age, sex, clinical and paraclinical findings, sonography, imagings, renal scan, associated anomalies, treatment and outcomes were collected and entered in SPSS software version18 and analyzed by descriptive statistical.Findings: Totally 33 patients aged three days to four years (mean 6.8 months) were included in this study. There were 20 (61%) males and 13 (39%) females. Mean follow-up period was 3.4\u00b11.2 years (1.5 months to 5 years). Eighty two precent cases had bilatral and 18% unilatral hydronephrosis and bilatral vesicouretral reflux (VUR) existed in 67% and unilatral in 33% of the patients. Treatment consisted of antibiotherapy and CIC in all patients, which was only in 33% of the cases succesful. The most common associated anomaly was meningomyelocle in 8 patients. Vesicostomy was performed in 22 (67%) cases. Kidney scan showed scar in 10 patients at follow-up study. Complete continence on follow-up was achieved in 24 (71% ) patients, and it was improved in 6 (18% ) cases. Mortality rate was 9% (3 cases). Cure rate was 85% in urinary tract infection, 82.7% in hydronephrosis, 80% in VUR and 86.5% in kidney function.Conclusion: Anticholinergic medications was not effective in all our patients. We believe that permanent vesicostomy is an effective and acceptable surgical intervention for protection of upper urinary tract decompression, especially in those who do not respond to medical treatment and have high risk position. Children with NGB have a higher risk of urinary tract infection (UTI) and kidney damage. Neurogenic lower urinary tract dysfunction (NLUTD) may be caused by various diseases and events affecting the nervous system controlling the lower urinary tract. NLUTD depends grossly on the location and the extent of the neurologic lesion. Both in congenital and acquired NLUTD, early diagnosis and treatment is essential as irreversible changes may occur in paticular in children with myelomeningocle (MMC), but also in patients with traumatic spinal cord injury, even if the related neuropathologic signs were normal. Diagnosis is based on history, physical examination, urodynamics, and typical manifestation of NLUTD. Treatment is based on non-invasive conservative measures such as catheterization, intravesical drug application . Surgical treatment can consist of urethral and bladder neck procedures, detrusor myectomy (auto-augmentation), denervation, covering bladder by striated muscle, bladder augmentation or substitution, and urinary diversion.Neurogenic bladder results from neurological lesions that end in a lower urinary tract dysfunctionIn a retrospective and descriptive study, 33 patients who have been treated for NGBD were evaluated in Mofid Children\u2019s Hospital from January 2007 to December 2012. Detailed history was taken and paraclinical examinations were performed and diagnosis was confirmed by ultrasonography (US), voiding-cysto-urethrography (VCUG), urodynamic study and lumbo-sacral MRI in myelodysplastic cases. We performed urodynamic evaluation without uroflowmetry in neonates after 3 months. The patients were treated medically with anticholinergic and antibiotics and all had clean intermittent catheterization (CIC). Urine culture and sonography were checked every three months and diethylene triamine pentaacetic acid and dimercaptosuccinic acid renal scan every six months to one year, if necessary, during follow-up. Reduction in grade of hydronephrosis or vesicouretral reflux (VUR) was considered as improvement, and absence of disorders on evaluation was considered as cure. All records were evaluated and patients followed by personal visits in clinic or per phone call. Data regarding age, sex, clinical and paraclinical findings, sonography, imaging, renal scan, associated anomalies, treatment and outcomes were collected, entered in SPSS software version18 and analyzed by descriptive statistica.FindingsTotally 33 patients aged three days to four years (mean 6.8 months) were included in this study . There w The most common associated anomaly was meningomyelocle in 8 patients (24.2%). Kidney anomaly, bladder anomaly, club foot and ureteropelvic junction obstruction were seen each one in 1 patient and 21 cases (63.6%) didn\u2019t have any anomaly. Urodynamic study was performed in 20 cases (61%), and after three months in neonates without uroflowmetry, which confirmed NGB.All patients received antibiotherapy and CIC, the treatment was succesful in 11 (33.3%) cases and 9 (27.3%) patients improved, but CIC was not successful in 13 cases (39.4%). Diversion was performed in 22 (67%) cases who did not respond to medical treatment and were in high risk position for diversion. High levels of creatinine and BUN decreased to normal in 90% of patients after medical treatment, CIC and vesicostomy during follow-up. Kidney scan showed scar in 10 patients (30.3%) at follow-up study, 7 patients in left, 2 patients in right kinney and 1 patient bilatral. Complete continence on follow-up was achieved in 24 (71%) patients, and improved in 6 (18%) of cases. 9% (3 cases) died. Mean follow-up period was 3.4\u00b11.2 years (1.5 months to 5 years). Cure rate was 85% in UTI (based on negative u/c), 82.7% in hydronephrosis (based on AP pelvic diameter), 80% in VUR (from grade V and IV to II and I), and 86.5% in kidney function (based on GFR/creatinine).[4]. After brief physical examination, urodynamic tests, uroflowmetry and ultrasound assessment are needed to clarify fine pathologic causes[5]. In cases with high detrusor pressure, the principal aim of treatment is conversion of high pressure bladder into a low-pressure reservoir. Alpha-blockers have been successful in decreasing bladder-outlet resistance, residual urine and automatic dysfunction. Neurogenic bladder pathologies that commonly occur in patients with MMC include an elevated detrusor leak point pressure, VUR, and detrusor-external sphincter dyssynergia[8-10]. McGuire and colleagues[11] first showed increased risk for upper tract dilatation in children with MMC. Shapiro and colleagues[12] published outcomes of a 10-year therapy on 90 children with MMC treated with ileal loop diversion, and showed stable renal units in 69% of the patients. Kasabian and colleagues[13] demonstrated normal renal function in 92% of children with MMC with voiding dysfunction treated with Oxybutynin and CIC. We peformed vicicostomy as a diversion In those patients who did not respond to medical treatment, were in risk position and had severe VUR and hydronephrosis., So we achieved a cure rate of 85% in UTI, 82.7% in hydronephrosis, 80% in VUR, and 86.5% in kidney function. After failure of conservative treatment in patients with NGB urinary diversion represents a safe long-term compromise. In Stein et al[16] study, upper urinary tract improved or remained stable in 97% of the renal units in patients with diversion, We performed too vesicostomy protection for urinary tract in some of our patients. Rawashdeh and colleagues[17] in a retrospective study in children younger than 16 years old with NGB who had undergone detrusor myotomy showed a safe and effective alternative for the management of pharmacologically intratable NGBD in children. Murphy and colleagues[18] reported obtaining total continency or major improvement with conservative care in 91% of 214 cerebral palsy patients with neurogenic bladder. Nue and colleagues[19] evaluated the management of acquired NGB in children using intradetrusor botulinum toxin type A injection and achieved five (62.5%) patients completely dry. Complete continence on follow-up was achieved in 24 (71%) patients, and it was improved in 6 (18%) of cases in our study, but in Rawashdeh et al[17] study it was reported in 8 (73%) patients, and improved only in one case. Stein et al[16] reported 98% complete continence in those with a continent stoma. Murphy et al[18] reported 91% total continence or major improvement with conservative care.The diagnosis and treatment of NLUTD, which is a complex field, needs experience and requires up-to-date knowledge. The aims of treatment in NGB/NLUTD are the preservation of the upper urinary tract, bladder and bowel continence, independence, autonomy, and facilitation of self-estreamAlthough anticholinergic medications and CIC have proved an effective treatment method for many children with NGB dysfunction, it was not effective in all our patients. We believe that permanent vesicostomy is an effective and acceptable surgical intervention for protection of upper urinary tract decompression, especially in those who do not respond to medical treatment and have high risk position.F. Roshanzamir: Acquisition of data, manuscript prepation and surgery.M. Rouzrokh: Concept, design, data analysis and surgery.A. Mirshemirani: Design, data analysis and surgery.A. Khaleghnejad: Critical revision of manuscript, surgery and funds collection.L. Mohajerzadeh: Data collection and analysisR. Dalirani: Data collection, analysis and medical management.All authors approved the final version of the manuscript."} +{"text": "Patients with decompensated cirrhosis admitted to the ICU have historically had a very high mortality rate . It has A retrospective analysis was performed of all adult patients with decompensated chronic liver disease admitted to a general (nontransplant) critical care unit between January 2012 and December 2013. Data were collected regarding demographics, ICU mortality, hospital mortality, aetiology of chronic liver disease, severity scores, acute diagnoses, and organ support requirements.Thirty-seven patients were identified, with a median age of 57 years, predominantly male (62%). Seventy-six per cent had alcohol-related cirrhosis. Overall ICU mortality was 29.7% and hospital mortality was 48.6% - these values were higher in the alcoholic group (39.3% and 57.1% respectively). All ICU deaths were in those with alcoholic liver disease. Median scores were: APACHE III 93, SOFA (day 1) 9, Child-Pugh 11, MELD 21. Seventy per cent were treated for sepsis, 22% had a GI bleed, 57% had encephalopathy, 24% had suspected/ confirmed spontaneous bacterial peritonitis, and 70% had an acute kidney injury. Organ support requirements were: 35% respiratory (non-invasive or invasive ventilation), 38% vasoactive agent support, 24% renal replacement therapy (RRT). Alcoholic liver disease patients requiring respiratory or cardiovascular support had an ICU mortality of 64%, and those requiring RRT had a mortality of 75%. Alcoholic liver disease patients requiring combined respiratory, cardiovascular, and RRT support had 100% mortality.Those with decompensated chronic liver disease admitted to the ICU have a significant ICU/hospital mortality, which is increased in alcoholic liver disease. Sepsis and AKI were the most common acute diagnoses in this cohort. Alcoholic liver disease patients requiring organ support have a very high mortality, and the outlook for multiorgan failure requiring RRT in this group is dismal."} +{"text": "To grade clinical practice variation within pediatricians of the north region of Spain society (SCCALP), and the adherence to current evidenced-based clinical guidelines.To test significant differences depending on the grade of experience and work environment.An anonymous survey was emailed to the pediatrician members of SCCALP using the online platform provided by Google Drive. The test consisted in multiple clinical scenarios, and multiple answers were available.A total of ninety-nine surveys were submitted. Distribution of the pediatricians who answered was as follow: 15% ER, 14% inpatient ward, 10% subspecialties, 6% neonatology, 41% general pediatrics, and 13% were residents.On a clinical scenario of an asthma exacerbation, 71,8% pediatricians correctly identified the severity of the exacerbation as moderate using the pulmonary score, and 86,2% would start an oral glucocorticosteroids treatment plus inhaled rapid-acting b2 agonists at adequate doses. Moreover, up to 48,9% would start a controller treatment. However, only 89,2% of them would use an adequate inhaled glucocorticosteroids dose and for an adequate period of time.There were no significant differences in the population surveyed answers, although their experience and working environment were not homogeneous.Severity scores are not widespread in our region, although this fact does not affect the assessment and correct treatment of exacerbations.There is a positive trend towards starting a controller treatment from the ER consultation.The adherence to the current asthma evidence-based clinical guidelines is insufficient.It is important to perform periodical revisions of the adherence to the guidelines in order to detect our flaws and to improve our clinical performance."} +{"text": "The measurement of total serum IgE is made in some cases to investigate if there is the occurrence of allergic processes. However, does not identify specific antibodies. When it is high may indicate an allergic process, or the ability to initiate some. However, increased IgE levels may also indicate other problems such as parasitic diseases, IgE myeloma, hyper-IgE syndrome and some stages of HIV infection. Therefore, to make a diagnosis of allergy is interesting to use other allergy tests, such as specific IgE (RAST) or prick-test. We surveyed data from patients who underwent the examination of serum total IgE to know which allergic diseases that most affect the examination, which gender and age group most affected, and also calculated an average of IgE in each pathology or group of pathologies.A retrospective observational study of the period 2010 to 2013 was conducted, we analyzed the key data from patient files of an Allergy and Immunology\u2019s public ambulatory service in the city of Campina Grande, who had undergone the examination of serum total IgE.Among the 100% investigated (n = 100), 52% were male and 48% female. 61% of range 0-10 years, 10% of 10-20 years old, 13% of 20-30 years old, 9% of 30-40 years old, 3% of 40-50 years old, 4% of 50-60 year old. As pathologies, 27% had allergic rhinitis averaging 379.33 kU / L of total IgE, 18% had Bronchial Asthma averaging 223.89 kU / L of IgE, 11% had the association Allergic Rhinitis and Bronchial Asthma averaging 453.85 KU / L of total IgE, 8% had Atopic Dermatitis with an average of 931.6 KU / L of IgE, 9% had Food Allergy averaging 199.89 KU / L of IgE, and 27% other diseases or associations.We conclude that in this service there is an equivalence between the number of men and women who have changes in examination of IgE. We have also seen that children and adolescents are the most feature changes and perform the test. Furthermore, we showed that the majority of patients with high IgE levels has allergic rhinitis, although the values are higher in patients with atopic dermatitis."} +{"text": "Mosquito-borne Rift Valley fever virus (RVFV) causes acute, often severe, disease in livestock and humans. To determine the exposure factors and range of symptoms associated with human RVF, we performed a population-based cross-sectional survey in six villages across a 40 km transect in northeastern Kenya.A systematic survey of the total populations of six Northeastern Kenyan villages was performed. Among 1082 residents tested via anti-RVFV IgG ELISA, seroprevalence was 15% . Prevalence did not vary significantly among villages. Subject age was a significant factor, with 31% (154/498) of adults seropositive vs. only 2% of children \u226415 years (12/583). Seroprevalence was higher among men (18%) than women (13%). Factors associated with seropositivity included a history of animal exposure, non-focal fever symptoms, symptoms related to meningoencephalitis, and eye symptoms. Using cluster analysis in RVFV positive participants, a more severe symptom phenotype was empirically defined as having somatic symptoms of acute fever plus eye symptoms, and possibly one or more meningoencephalitic or hemorrhagic symptoms. Associated with this more severe disease phenotype were older age, village, recent illness, and loss of a family member during the last outbreak. In multivariate analysis, sheltering livestock , disposing of livestock abortus , and village location (P = 0.009) were independently associated with the severe disease phenotype.Our results demonstrate that a significant proportion of the population in northeastern Kenya has been infected with RVFV. Village and certain animal husbandry activities were associated with more severe disease. Older age, male gender, herder occupation, killing and butchering livestock, and poor visual acuity were useful markers for increased RVFV infection. Formal vision testing may therefore prove to be a helpful, low-technology tool for RVF screening during epidemics in high-risk rural settings. Rift Valley fever virus (RVFV) causes serious disease in both animals and humans. Large-scale outbreaks result in devastating economic losses and create many urgent public health concerns. Among humans, the symptoms of RVF are variable, having a broad spectrum of disease that ranges from mild to severe fever symptoms, and can include ocular complications, encephalitis, and sometimes hemorrhagic disease. In this study, 1082 at-risk Kenyan subjects were serum antibody-tested for evidence of prior RVFV infection and their demographic, health, and exposure data were collated. Seroprevalence was moderately high across the study area (15%) but did not differ significantly among villages across the study region. Age, gender, and herding occupation were all significantly associated with being RVFV seropositive. Older age, village and certain animal husbandry activities were associated with more severe disease. Poor visual acuity was more likely in the seropositive group. This better definition of risk factors and associated symptom complexes should prove helpful for RVF screening during future outbreaks in high-risk rural settings. Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic disease that poses a significant risk to human health in endemic regions of Africa and the Middle East . EpizootClinically, most often RVFV causes no symptoms or a mild illness manifesting with fever and liver abnormalities . More raAll participants provided written consent under a protocol approved by the Human Investigations Review Board of University Hospitals Case Medical Center (No. 11\u201309\u201301) and the Ethical Review Committee of the Kenya Medical Research Institute, Nairobi, Kenya (Non-SSC Protocol No. 195). Before participation, written informed consent was obtained from adult study subjects, and parents provided written informed consent for their participating children. Children over 7 years of age also provided individual assent.This study was performed in the semi-arid Sangailu Location of Ijara constituency, Kenya. Six villages were sampled for demographic, epidemiological, and health information during area-wide household surveys performed from August through November of 2011, five years after the last known RVF epidemic in the area (2006\u20132007). The villages are located off a main road across a span of approximately 40 Km, in a transect running southwest to northeast centeredStudy recruitment began after consultation and approval by local leaders and administrators. After an initial demographic census was performed to determine the current local population and its distribution, a systematic survey of the total populations of six Northeastern Kenyan villages was performed. The villages were systematically surveyed in sequence to reach the desired sample size of >1000 enrolled individuals. All residents were eligible for inclusion, except that those residing in the area for <2 years, and children less than 1 year of age were excluded. The study sample was representative of the local ethnic mix of 99% Kenyan Somali and < 1% Bantu, Indian, or other Asian.Participants had formal interviews to detail their demographics, occupation, mosquito exposure, and animal exposure within the last 6 months, and any previous nonspecific symptoms related to RVF in the last 30 days, or severe symptoms at any time .Statistical analysis examined the association of subject demographic and exposure factors with two primary outcomes: i) odds of seropositivity and ii) odds of having had the more severe symptoms of RVF. Initial chi-square tests were performed to identify the association of categorical factors with RVFV seropositivity and t-tests were used for continuous variables. A series of nested multivariable logistic regression models were next developed that initially included predictors significant in bivariate comparisons, as well as those considered of biological relevance prior to conduct of the study. Bivariate results and stepwise regression models were used to aid in the selection of variables to be included in the final models. Non-significant variables (p > = 0.10) were removed in stepwise fashion to help identify the variables with the greatest multiply adjusted links to RVFV seropositivity or symptom score. For this analysis, statistical significance was set at the 0.05 level. Following analysis of individual symptoms, a relative RVF severity score was developed using the two-step cluster algorithm in SPSS v. 21 to empirically define significant constellations of milder, moderate, and more severe symptom states among RVFV seropositive subjects . The sevStatistical analysis of spatial patterns of seropositivity among the participating households was performed with the use of Point Pattern Analysis software and Clus95% 13\u201317%). Males were more likely to be RVFV infected: 18% (79/433) were seropositive compared to 13% (85/646) of females . The average age of seropositive people was 42 \u00b1 19.5 years (range 6\u201385 years) vs. 17 \u00b1 17 for seronegatives (range 1\u201384 years). No significant differences in seropositivity were seen among the six villages studied in the Sangailu region: Golabele , Korahindi ; Sabenale ; Matarba ; Gedilun , and Tumtish . This was not surprising given the uniformity of landscape and environmental features, and the socioeconomic homogeneity within pastoralist communities of this region.Of the 1134 participants enrolled in the study, 1082 completed all phases of the examination and were tested for RVFV infection. Of these, 164 were RVFV seropositive , male gender (adjusted Odds Ratio (aOR) = 1.8, CI95% 1.2\u20132.7, P < 0.01), poor measured visual acuity , a history of malaise , and a history of killing livestock were each independently associated with seropositivity . Sixteen percent (111/710) of tested subjects had poor measured visual acuity. Those who were anti-RVFV positive were more likely to have poor measured visual acuity, 36% (57/159) compared to 9.8% (54/551) of seronegatives (P < 0.0001). Fundoscopic exams were performed on 118 study participants. Here, objective eye disease was defined as having uveitis, retinitis, retinal scar or retinal hemorrhage. Overall, 26% (30/118) were found to have eye disease defined as retinitis or retinal hemorrhage. Of those serologically tested for RVFV seropositivity, 21% (6/28) were RVFV seropositive.Ten percent (112/1081) of people surveyed self-reported poor vision. Those who were RVFV-infected were more likely to report poor vision: 26% (43/164), as compared to 7.5% (69/917) among uninfected of sign95% 0.93\u201313.61, P = 0.064). Disposing of livestock abortus put one at four times risk of having a severe disease phenotype .One hundred sixty-four people were RVFV exposed and included in this analysis. Ninety-three percent (152/164) were adults and 52% (85/164) were female. Thirty percent (49/164) were from Korahindi, 20% (33/164) from Matarba, 20% (32/164) from Gedilun, 15% (25/164) from Tumtish, 9% (15/164) from Golalbele, and 6% (10/164) from Sabenale. Those in the moderate/severe group (N = 111) were more likely to be older than those in the mild group (N = 53). In bivariate analysis, the most severe of the RVF symptom-cluster phenotypes was associated with older age, village, recent illness, and death of a family member . In a muA significant proportion of the population in the semi-arid areas of northeastern Kenya have been infected with RVFV. Other than older age, most of the factors significantly associated with anti-RVFV seropositivity and RVF disease severity were related to pastoralist lifestyles and animal exposures. These included the common practices of livestock shelter at home and livestock fetus disposal, as typically observed in this region. During epizootics, RVFV-infected herds will experience abortion storms and affected virus-contaminated abortus is often handled by herders, significantly increasing their risk for RVFV infection by aerosol and direct contact, and possibly, their risk for more severe RVF disease . SimilarAs noted in other studies, RVFV seropositivity rates were much lower among children ,6,12. AlOf the subject symptoms we elicited, backache was the most strongly associated with RVFV seropositivity. Among confirmed, hospitalized RVF patients, an initial syndrome consisting of severe headache, fever, arthralgias, and general malaise has been described that occurs prior to the onset of delirium and mental confusion and/or hemorrhagic manifestations . Among eSelf-reported visual impairment and reduced measured visual acuity were both correlated with RVFV seropositivity. Uveitis and/or retinitis are two of the most common sequelae of human RVF . In our The analysis of RVF disease severity Tables and 4 suThis study was limited by the self-reported nature of the exposures and symptom data, which are subject to recall bias. Other prevalent infections, such as malaria, may have accounted for the reported fever-related symptoms. In particular, other arbovirus infections, such as West Nile virus, chikungunya virus, and dengue, might have accounted for reported ocular symptoms, as they, too, are known to cause uveitis and retinitis \u201323. BecaIn conclusion, RVFV infection in northeastern Kenya is significantly associated with older age, male gender, livestock harvesting, and poor vision. Spatial analysis suggests that very high-risk households exist within at-risk communities, which appear to harbor most of the RVFV infection burden. Animal exposure factors were linked to severity of human RVF disease symptoms, as suggested in previous studies . FinallyS1 Checklist(DOC)Click here for additional data file.S1 Text(PDF)Click here for additional data file.S1 Figsevere RVF had multiple eye-related symptoms plus systemic symptoms of acute febrile illness. Those with moderate RVF reported systemic symptoms, but not eye complaints. Subjects with mild disease had seropositivity but reported no symptoms. Ten additional symptoms were scored and entered into the analysis, but did not differ among the three groups.The relative weights for presence or absence of a given symptom used in the classification are indicated in the left-hand panel. As indicated the right side columns, subjects classified as (TIFF)Click here for additional data file.S1 Dataset(XLS)Click here for additional data file."} +{"text": "The increasing burden of sexually transmitted infections (STIs) including HIV and syphilis among male sex workers (MSWs) is a major global concern. The aim of our study was to evaluate the difference between MSWs and non-commercial MSMs in China.During 2008-09, in a cross-sectional study, 2618 adult MSM were recruited through respondent-driven and snowball sampling from seven cities of China. Information regarding socio-demographics, risk behaviors, HIV-related knowledge and STI-related symptoms were collected and participants were tested for HIV and syphilis.Among 2618 participating MSM, 9.97% sold sex to males. HIV prevalence was 7.45% (6.13% among MSWs and 7.59% among non-MSW MSM) and syphilis prevalence was 14.32% (10.73% for MSWs and 14.72% for non-MSW MSM). Compared to non-MSW MSM, MSWs were more likely to be younger , never married , less educated, heterosexual , less knowledgeable regarding HIV , experiencing symptoms of STI , engaging in condomless vaginal intercourse and less likely to engage in condomless anal intercourse .High HIV and syphilis prevalence warranted urgent intervention targeting MSWs as a separate sentinel group for efficient surveillance owing to their different distribution from non-MSW MSM. Although male sex workers and non-commercial homosexuals have similar rates of HIV and syphilis, MSWs have different characteristics which should be considered in designing intervention programs targeting them. The high burden of HIV and syphilis among men who have sex with men (MSM) are major public health concerns worldwide and China is no exception \u20133. GlobaRisk of acquisition of HIV and other STIs were found to be driven by a spectrum of biological and behavioral factors. Higher burden of these factors cumulatively resulted in a very high prevalence of HIV and other STIs among MSWs in different parts of the globe . StudiesOne prior investigation involving MSWs in two cities in China raised similar concern regarding the burden of risky sexual practices in this largely hidden and thus understudied population. Only 53.1% and 70.7% MSWs were found to use condom while engaging in receptive and insertive anal intercourse with clients . Based oThe dearth of information regarding comparative evaluation of the burden and correlates of HIV and syphilis between MSWs and non-MSW MSM called for a detailed investigation involving a multisite, representative sample of MSWs. Thus to answer the public health question\u2014whether MSWs are different from non-MSW MSM, in terms of the risk and determinants of acquisition of HIV and syphilis- we analyzed data from a comprehensive, cross-sectional study conducted among MSM from seven metropolitan cities in China during 2008\u201309.Respondent-driven sampling (RDS) was usedAfter the collection of inform consents and biological samples, a structured questionnaire was administered by a trained interviewer to collect information through a face-to-face interview regarding socio-demographics, sexual behaviors and services received regarding prevention/management of HIV and other STIs.Socio-demographic information included age (continuous and categorized into < 20/ 20-29/30-39/\u226540 years), educational level (primary school and below/junior or senior high school/ college and above), marital status (never married/ever married), residence , race (Han/others), annual income (\u22642000/2001-6000/\u22656000 USD), social network size and usual venues for finding male partners . Self-identified sexual orientation of the participants was also requested.Information on sexual behaviors of the participants, condom use during last anal sex (yes/no), consistent condom use during last six months, number (continuous) of different male partners in past six months and history of selling anal sex to men during last six months (yes/no) was gathered. Condom-less anal intercourse (CAI) was defined as inconsistent condom use during anal intercourse in previous six months with all male partners, CAI during last anal intercourse was defined as non-use of condoms during last anal intercourse with a male partner and condom-less vaginal intercourse (CVI) was defined as inconsistent condom use during vaginal intercourse in the previous six months with all female partners. Male commercial sex workers were defined as the participants who sold anal sex to men in the past six months, either for money, goods or other benefits (like getting shelter).Each of the participants was also interviewed to collect information regarding history of experiencing any symptom of STI during the last year, knowledge regarding HIV (correct answer for at least six questions out of eight was defined as correct knowledge) and history of receiving any kind of HIV related service in the last year.Before the interview, five ml of venous blood was collected from each participant for HIV and syphilis testing. HIV antibodies were screened using a rapid test . Screened positive samples were further confirmed by Western blot . Syphilis antibodies were screened using Rapid Plasma Reagin test and those individuals with a positive RPR titer received the Treponema Pallidum Particle Agglutination assay . Syphilis positivity was deemed \u201ccurrent\u201d when both TPPA and RPR assays were positive.Data were douSigned informed consent was obtained from each of the participants prior to interview, blood collection and intervention. Each of the participants had the ability to withdraw from this survey at any time after recruitment. The questionnaires and written consent document were separately kept in locked cupboards at the study sites, and unauthorized persons were unable to access them. The study protocol, procedures and content were reviewed and approved by the Ethics Committee of the China CDC in Beijing .Altogether 2618 participants were recruited in this comprehensive survey involving MSM from seven urban cities in China between 2008 and 2009. About 59.13% were aged between 20 and 29 years, 74.60% were never married, 50.19% resided in the city from which they were recruited, 97.67% had Han ethnicity, 49.24% attended junior or senior high school and 56.19% self-identified themselves as homosexuals.Participants identified their male sexual partners most commonly through internet (55.84%) followed by pubs/clubs (14.40%). Social network size was only one for 12.18% subjects, while 48.93% had network sizes larger than 10. During the last year, 69.10% of participants used some kind of STI related services. HIV related knowledge was correct for 79.37% and 19.81% experienced some STI related symptoms during last year.A total of 261 (9.97%) participants reported that they sold sex to other males in past six months, 33.94% did not use a condom during their last anal sex with a male partner , 55.04% reported that they had CAI during the last six months and 18.68% engaged in CVI in the last six months.P = 0.39]. Among participating subjects, 375 were currently sero-positive for syphilis, with a prevalence of 14.32% .In this study, 195 HIV positive MSM were identified through lab testing, with an overall prevalence of 7.45% . They also had relatively less education, as evidenced from the unadjusted ORs of 5.84 (95% CI: 4.12\u20138.27) and 9.79 (95% CI: 5.06\u201318.96), respectively for junior/senior high school and elementary school or less education compared to those who were at least educated up to college level.Odds of finding male partners on the internet, in pubs/disco, spa/bathhouse and park/public restrooms were also higher for MSWs (relative to the non-MSW MSM), with unadjusted ORs of 5.53 (95% CI: 4.01\u20137.61), 1.84 (95% CI: 1.19\u20132.84) and 2.60 (95% CI: 1.74\u20133.89), respectively. MSWs were also more likely to be self-identifying heterosexuals, with unadjusted OR of 14.61 (95% CI 7.15\u201329.85).With reference to their non-MSW counterparts, MSWs had a lower HIV prevalence, although the result was not significant. MSWs were also less likely to be syphilis positive but more likely to have symptoms suggestive of STIs during the last year, unadjusted OR of 1.87 (95% CI: 1.28\u20132.71).After adjustment for recruitment site, monthly income, social network size and race, using multiple logistic regression models, the results did not change much, except for residence, which was no longer associated with commercial sexual behaviors in our study. In the adjusted model, compared to non-MSWs, MSWs were more likely to be younger , never married and less educated . They also had higher odds of being heterosexual , less knowledgeable regarding HIV , seeking male sexual partners usually in pub/disco/tearoom/club and park/public restroom , experiencing symptoms of STI . With reference to the non-MSW MSM, MSWs engaged more commonly in unprotected vaginal intercourse but less often in unprotected anal intercourse .The burden of HIV among MSWs across the globe warranted a comparative evaluation of the burden and correlates of HIV and syphilis between MSWs and their non-MSW counterparts in China where such comparisons were conducted rarely . The finIn this survey involving a multicentre population of urban MSM of China the prevalence of HIV and syphilis were found to be slightly lower among MSWs compared to their non-MSW counterparts although the difference was not statistically significant for HIV. Our study further confirmed the results of one meta-analysis that focused on Chinese MSM. SimilarThe non-consistent results between CAI in the last six months and CAI during last anal intercourse might have indicated that CAI during last anal intercourse could be a more sensitive way to measure the behavior regarding getting engaged in CAI among MSM.Although MSWs had a slightly lower syphilis prevalence compared to non-MSW MSM, relatively higher proportion of them experienced STI related symptoms in the last year. This finding emphasized the potentially higher risk of recurrent STIs among MSWs.MSWs were typically younger, less likely to be married, received less education and were more often migrants. These characteristics probably indicated that the SES of MSWs in China was poor in general. These findings were likely to explain the relative lack of knowledge regarding HIV among MSWs. All of these factors were found in previous studies to enhance the spread of HIV, syphilis and other STIs in different high risk population including MSM and MSWs seemed to be no exception. They were probably more vulnerable owing to poorer self-esteem and resultant self-neglect . The strDespite these limitations, this comprehensive multicenter study suggests that HIV and syphilis prevalence among MSWs and non-MSWs MSM is high in urban China. MSWs differed from non-MSWs in terms of SES, sexual orientation, usual venues for finding sexual partners, high risk behaviors, syphilis prevalence and STI related symptoms. Further studies should be conducted to explore these differences in details. Although male sex workers and non-commercial homosexuals have similar rates of HIV and syphilis, MSWs have different characteristics which should be considered in designing intervention programs targeting them.S1 Dataset(XLS)Click here for additional data file."} +{"text": "A dengue fever surveillance study was conducted at three medical facilities located in the low-income district of San Javier in Medellin, Colombia. During March 2008 to 2009, 781 patients with fever regardless of chief complaint were recruited for acute dengue virus infection testing. Of the 781 tested, 73 (9.3%) were positive for dengue infection. Serotypes DENV-2 (77%) and -3 (23%) were detected by PCR. One patient met the diagnostic criteria for dengue hemorrhagic fever. Only 3 out of 73 (4.1%) febrile subjects testing positive for dengue infection were diagnosed with dengue fever by the treating physician. This study confirms dengue virus as an important cause of acute febrile illness in Medellin, Colombia, but it is difficult to diagnose without dengue diagnostic testing. Aedes aegypti, prefers breeding in artificial containers commonly found in peridomestic areas; the burden of DF will continue to increase with the population of tropical cities. Currently, dengue causes about 100 million symptomatic cases and 25,000 deaths annually ), asthenia (72.6% [n = 53]), and cough (67.1% [n = 49]) followed by headache (75.6% [n = 34]), vomiting (52.1% [n = 38]), rhinorrhea (49.3% [n = 36]), and nasal congestion (49.3% [n = 36]). Myalgias (53.3% [n = 24]), arthralgias (48.9% [n = 22]), and retro-orbital pain (44.4% [n = 20]) were less frequently observed. Rash was noted in 9.6% of patients (n = 7) with laboratory-confirmed dengue virus infections. Compared to patients with OFI, only neck pain was statistically significantly more common among patients with laboratory-confirmed dengue virus infections .The most frequently observed symptoms in patients with laboratory-confirmed dengue virus infections were anorexia . In addition, the median pulse was statistically significantly higher , and median diastolic blood pressure was statistically significantly lower in patients with laboratory-confirmed dengue virus infections than OFI patients , tonsillitis/pharyngitis (17.9% [n = 14]), and acute diarrheal disease (8.9% [n = 5]) in ambulatory and pneumonia (35.3% [n = 6]) in hospitalized patients patients with laboratory-confirmed dengue virus infections were diagnosed with dengue fever by the treating physician. One patient was ambulatory; the other two were hospitalized. The most common clinical diagnoses among patients with laboratory-confirmed dengue virus infections were viral syndrome , targeted population (pediatric versus adults), and the presence of an outbreak. The most comparable study was conducted by Ramos et al. in Patillas, Puerto Rico, in which all patients presenting to the only health center in the municipality with fever who met the WHO clinical DF case definition were tested regardless of the treating physician's diagnosis. In that study 11% were laboratory-positive . In a coDengue cases were diagnosed every month of the year with higher frequency in May and October consistent with the typical nonoutbreak pattern in Colombia. This biphasic pattern corresponds to periods of increased rainfall. The same pattern is seen in Brazil but occurs during different months, February through May, indicating the importance of local weather patterns . In addiThe results of our study suggest that routine clinical laboratory tests could not differentiate patients with laboratory-confirmed dengue virus infection from those with OFI. The frequency of \u201ctypical\u201d symptoms and clinical signs such as myalgias, arthralgias, retro-orbital pain, rash, and hemorrhages, including positive tourniquet test, was not significantly different; only neck pain, crepitus, and rhonchi, which are not typical DF symptoms, were more frequently observed in patients with laboratory-confirmed dengue virus infections. However, the clinical usefulness of this difference is questionable. Similarly, low counts of platelets, white blood cells, and neutrophils were not statistically associated with DF in these patients. Respiratory symptoms such as nasal congestion, rhinorrhea, and cough were frequently observed in both laboratory-confirmed dengue virus infections and OFI cases with no significant differences. This is different than findings in other studies and demonstrates the difficulty of clinical diagnosis \u201319.A systematic review showed that the frequency of rash, myalgia, arthralgia, lethargy/prostration, and hemorrhagic signs was higher in patients with laboratory-confirmed dengue virus infections than patients with OFI, but adult patients accounted for most of these differences and only petechiae or positive tourniquet test was consistently higher in children with dengue . A previThis study may have been limited by the inability to distinguish through diagnostic tests true symptomatic dengue virus infections from coincidental asymptomatic infections. Several studies have confirmed that the rate of asymptomatic infection is at least the same or higher than the rate of symptomatic infection in the general population , 24. HowIn conclusion, dengue, predominantly in its nonsevere form, proves to be an important cause of febrile illness in the Medellin area. The burden of disease is much larger than national surveillance data would suggest with roughly 10% of fevers regardless of the presenting symptoms are potentially caused by dengue infection. That said the clinical picture of the more mild infection we identified was nonspecific making it difficult to recognize but again accounting for the greatest burden of disease. Rapid, reliable, and inexpensive dengue diagnostics for use at point of care would greatly improve the accuracy of the medical diagnosis of the infection of dengue virus in the primary health care setting. However, a dengue vaccine would be more practical to prevent the disease and perhaps eliminate the diagnostic dilemma of this important cause of fever in endemic countries."} +{"text": "One of many challenges for Emergency Departments is having access to clinical guidance when and where it is needed. In this abstract we provide a first experience from a pilot study involving the use of Google Glass in the Emergency Department among nurses. The involved nurses were asked to evaluate the experience of using Google Glass as a communication device instead of traditional mobile phones.Each participant responded to a two-part survey with two descriptive and four Likert scaled questions. Responses were analyzed in Excel through descriptive analysis of the survey responses. The descriptive section asked for clinical role, number of usage attempts, and number of patients attended to. The Likert questions where: 1) Experience of call quality, 2) Experience of sound quality, 3) Total usage experience, and 4) Patient interaction experience. Each of these questions where scaled in five steps from poor, below average, average, above average, good, and grouped into below, average, and above in the analysis.11 of 12 involved nurses responded to the survey, with a role distribution of 1 triage shift, 4 receiving ward shifts, 2 coordinating nurse shifts, 3 shifts treating fast track injuries, and one who covered several of these roles. The average nurse attended to 9.9 patients, and on average attempted to use the equipment 5.5 times during each shift. 55% experienced call quality as below average, 36% as average, and 9% as above average. 73% experienced sound quality as below average, 18% as average, and 9% above average. 64% marked total usage experience as below average, 27% as average, and 9% above average. 64% said patient interaction experience was below average, 27% as average, and 9% above average.The main obstacle of using Google Glass was issues with the quality of sound. Usability measures such as total usage and patient interaction experience may have scored higher had experience with sound quality been better. Thus, given the ubiquitous and individual nature of wearable technology, further studies should be made."} +{"text": "The aim of this audit was to assess the clinical impact of out-of-hours (OOH) discharge from the adult critical care unit (ACCU) in a tertiary care hospital. Discharging patients from critical care OOH has been associated with both higher mortality and increased rate of readmissions ,2. As a A retrospective snapshot analysis of patients was conducted at least 48 hours after discharge from the ACCU in October 2014. Patients discharged OOH (20:00 to 07:59) were compared with those discharged in hours . Analysis included: patient demographics, APACHE II score, handover procedure prior to discharge, follow-up by the receiving team, appropriate and timely drug prescribing, recognising and acting upon clinical deterioration and readmission rates.A total of 161 patients were discharged from the ACCU in October 2014. Of these, 46% of the patients were discharged OOH. Forty-one (of 74) OOH and 19 (of 87) IH discharges were sampled for further analysis. The baseline demographics and APACHE II score were similar between both groups. The majority of discharges were delayed . More patients had nursing handover completed if discharged IH (88% IH vs. 61% OOH) and doctors' summaries were less frequently completed OOH (83% OOH vs. 94.4% IH). A management plan for the ward was outlined in 94% of IH versus 65.% of OOH discharges. Seventy-eight per cent OOH versus 95% IH patients discharged were reviewed by a doctor within 24 hours. Twenty-nine per cent OOH versus 67% IH patients discharged were reviewed by a consultant within 24 hours. Following discharge a management plan was followed in 94% of IH patients versus 44% OOH, patients had drug charts correctly charted in 100% of IH cases versus 66% OOH and missed/delayed doses were documented in 11.1% of IH cases versus 61% OOH. There was no difference between the groups in incidence of clinical deterioration and recognition and follow-up of clinical deterioration. Two patients were readmitted within 48 hours from the OOH group.This audit compares with current evidence suggesting harm from OOH discharge despite most discharges being delayed. Discharging patients is a complex hospital process, but focus needs to be on discharging patients IH. Therefore, areas for improvement include targeting forward flow of patients throughout the hospital, completion of handover documents IH and publication of guidance for receiving teams."} +{"text": "This study aimed to investigate the occurrence of and determine the risk factors for steatorrhea in chronic pancreatitis (CP). It was based on analysis of both retrospectively and prospectively acquired database for CP patients admitted to our center from January 2000 to December 2013. Demographic data, course of disease, medical history, and follow-up evaluations of patients were documented in detail. Cumulative rate of steatorrhea was calculated by using the Kaplan\u2013Meier method. For risk factor analysis, multivariate analysis by Cox proportional hazards regression model was performed. A total of 2,153 CP patients were included with a mean follow-up duration of 9.3 years. Approximately 14% of CP patients presented with steatorrhea at diagnosis of CP. Cumulative rates of steatorrhea at 1, 5, 10, and 20 years after diagnosis of CP were 4.27% (95% CI: 3.42%\u20135.34%), 12.53% (95% CI: 10.74%\u201314.59%), 20.44% (95% CI: 17.37%\u201323.98%) and 30.82% (95% CI: 20.20%\u201345.21%), respectively. Male gender , diabetes , alcohol abuse and pancreaticoduodenectomy were independent risk factors for steatorrhea while CP in adolescents was a protective factor. In conclusion, male gender, adult, diabetes, alcohol abuse and pancreaticoduodenectomy lead to increased risk of steatorrhea in CP patients. Chronic pancreatitis (CP) is a progressive condition characterized by pancreatic acinar atrophy and fibrosis, which leads to irreversible damage of pancreatic endocrine and exocrine function. CP patients with pancreatic exocrine insufficiency (PEI) usually present with nutrition malabsorption which leads to vitamin and micronutrient deficiency and weight loss134It has been reported that 42%\u201399% of CP patients may develop PEI67891113Factors concerning disease duration and etiology might be associated with increased/decreased risk of developing steatorrhea. For example, steatorrhea is more common during the second decade after the onset of CP681617This study was based on a retrospective-prospective cohort of 2,153 CP patients with a long duration of follow-up after the onset of CP. We aimed to determine the prevalence of steatorrhea in CP patients and identify the risk factors, which might help to improve the outcome of CP patients with PEI.From January 2000 to December 2013, a total of 2,287 CP patients were enrolled in Changhai CP Database. A total of 134 patients, which consisted of 16 patients diagnosed with pancreatic cancer within two years after the diagnosis of CP, 108 AIP patients, and 10\u2009GP patients, were excluded from this study . The genAs Changhai Hospital is a tertiary medical center, almost 30% of the patients admitted to our center had received interventional procedures in primary medical centers. Minimally invasive interventions were used as principle methods prior to surgery in our center, and the overall treatment strategy was classified as endotherapy (including ESWL) alone , surgery alone , both endotherapy and surgery , and no interventions due to lack of clinical symptoms . A total of 70 patients died during the follow-up period, and the causes of death were pancreatic cancer , complications of CP , non-pancreatic diseases , and accidental death .Steatorrhea patients differed from non-steatorrhea patients in the following aspects: more male patients, fewer adolescent patients, higher prevalence of diabetes mellitus (DM), more ACP, more patients with initial manifestations of DM or steatorrhea, and different types of abdominal pain. No significant differences between these two groups were detected in terms of age at the onset or diagnosis of CP, common bile duct (CBD) stricture, pancreatic pseudocyst, stone, development of cancer, interventional treatment strategy, and death .Steatorrhea developed in 22.90% (493/2153) of the 2,153 eligible patients after the onset of CP; the rates were 24.83% in male patients (369/1486) and 19.19% in female patients (128/667). Steatorrhea developed in 200, 298, 381 and 466 patients at 1, 5, 10 and 20 years after the onset of CP, with the cumulative rates being 9.34% (95% CI: 8.18%\u201310.66%), 14.76% (95% CI: 13.27%\u201316.40%), 21.87% (95% CI: 19.89%\u201324.03%) and 41.14% (95% CI: 36.94%\u201345.62%), respectively. Moreover, a significant difference in the rate of steatorrhea was observed between male and female patients of patients manifested with steatorrhea at the diagnosis of CP. After excluding these patients, the remaining 1,862 patients were included to calculate the cumulative rate of steatorrhea after the diagnosis of CP. Steatorrhea developed in 74, 165, 198 and 201 patients 1, 5, 10, and 20 years after the diagnosis of CP, with the cumulative rates being 4.27% (95% CI: 3.42%\u20135.34%), 12.53% (95% CI: 10.74%\u201314.59%), 20.44% (95% CI: 17.37%\u201323.98%) and 30.82% (95% CI: 20.20%\u201345.21%), respectively. Male patients had a significantly higher rate of steatorrhea compared with female patients , 10.86% (95% CI: 8.93%\u201313.17%) and 15.09% (95% CI: 12.34%\u201318.39%), respectively . Among tp value less than 0.10. These eight variables were selected as candidates for multivariate analysis by the Cox proportional hazards regression model. The results showed that five factors were independent predictors of newly onset steatorrhea. The risk factors were male gender (hazard ratio (HR)\u2009=\u20091.771, p\u2009=\u20090.004), DM , alcohol abuse , and pancreaticoduodenectomy and the protective factor was CP in adolescents .All 20 variables in et al. and is a direct and decisive evidence of PEI for CP in clinical practice. We detected the prevalence of steatorrhea in CP and its predictors with a relatively large sample size For 2,153 CP patients, the overall incidence rate of steatorrhea was 22.9% over a median follow-up period of 7.8 years after the onset of CP. The cumulative rate of steatorrhea after the diagnosis of CP was 12.5% at 5 years, whereas Sandhu We identified several predictors for steatorrhea. Possible explanations for decreased risk of steatorrhea for CP in adolescents were: (1) compared to adult CP patients, adolescent CP patients have better preservation of pancreatic function and also better repair capacity after injury; (2) most of adolescent CP cases were followed up in less than 20 years, and we expect similar cumulative risk of steatorrhea with a long-term follow-up. A previous study also showed that exocrine and endocrine insufficiency developed more slowly in early-onset CP than in late-onset CPPancreaticoduodenectomy was identified as an independent risk factor for steatorrhea, while drainage of pancreatic duct (by ESWL/ERCP or LPJ) or partial resection of pancreas (head resection or tail resection) seemed not to increase the risk of steatorrhea. This indicates that steatorrhea as a sign of pancreatic exocrine function failure is due to diffuse and severe loss of pancreatic parenchyma. CP being a progressive disease with loss of pancreatic acinar tissue, minimally invasive method rather than resectional procedures may be a better choice given the advantage of preservation of pancreatic parenchymaIn the current study, ACP was considered when alcohol intake exceeded 80\u2009g/d for male and 60\u2009g/d for female for at least 2 years for CP patients in the absence of other causes, respectively. ACP patients showed a higher risk of steatorrhea, but the risk might be underestimated. There might be a proportion of patients considered as ICP who might probably have ACP. The Oriental population might be more sensitive to alcohol-related injuries than the Caucasian population because they tend to have a less-active aldehyde dehydrogenase, which is a key detoxifying enzyme for alcohol20Patients with DM showed higher risk for steatorrhea. Considerable evidence suggests important functional interactions between the exocrine and endocrine pancreas. The interactions occur at several regulatory levels, and the true dimension is still unknownet al.Pancreatic stone was analyzed as one of the potential predictors of steatorrhea, which was indicated in several studies723The Changhai CP Database established in 2005 has been collecting clinical data of CP patients since January 2000, and data have been collected retrospectively before January 2005 and prospectively ever since. Statistical analysis showed that there was no significant difference between the clinical characteristics of patients who were first admitted before January 2005 and those admitted after that date. Therefore, the recall bias minimally influenced the results of the study.Our study has some limitations. First, clinical steatorrhea was used as a sign of severe PEI; dietary habits and celiac disease-related steatorrhea were not considered. Second, the retrospectively acquired data collected between 2000 and 2004 might introduce recall bias. Prospective data collection since January 2005 minimized the chance of incomplete or inaccurate data collection. Third, risk factor analysis did not include all potential factors related to the development of steatorrhea. Fourth, 603 CP patients were followed up for less than 2 years after the diagnosis of CP; among these patients, several pancreatic cancer patients may have been misdiagnosed as CPIn conclusion, CP patients showed increased risk of steatorrhea for those of male gender, adults, DM, alcohol abuse and pancreaticoduodenectomy. The evaluation of risk factors in CP patients before the occurrence of steatorrhea might help determine the replacement therapy of pancreatic enzyme earlier, which ensures that severe complications related to PEI can be avoided. Prospectively conducted studies are expected to confirm the benefit of early treatment of PEI on CP patients.This study was based on analysis of both retrospectively and prospectively acquired database.et al.), course of CP, medical history, history of other diseases, smoking history/status, alcohol history/status, family history of pancreatic diseases and DM, laboratory and imaging findings, and treatment strategy.Since the 1990s, an electronic medical record system has been used in Changhai Hospital , which has facilitated several studies on CP262728The database system was also set a reminder for investigators to call patients for clinical checkups. Aside from visits due to complaints of discomfort related to CP, all patients were periodically (at least once a year) recalled for clinical checkup and investigations. Ultrasound, MRI, or CT was selected as an evaluation modality during each follow-up visit. An evaluation of each revisit, or an evaluation via telephone inquiries for patients who did not have follow-up visits to Changhai Hospital, was added to the CP database.In December 2013, we contacted all the patients in our database for a final evaluation, except those who were lost to follow-up or died. The duration of follow-up is defined as the duration from the onset of CP to the date of the last personal contact, death, or December 2013, whichever came first.The study was approved by the Ethics Committee of Changhai Hospital, The Second Military Medical University, Shanghai, China according to the Helsinki Declaration. Written informed consent was obtained from all participating patients. All of the diagnostic and therapeutic modalities were carried out in accordance to the approved guidelines.CP was diagnosed according to the Asia-Pacific consensus of CP27Patients who were diagnosed with pancreatic cancer less than two years after the diagnosis of CP were excluded from this study26Diagnosis of steatorrhea was established when either of the following conditions was met: (1) chronic diarrhea with foul-smelling, oily bowel movementset al.; DM or steatorrhea was not an indication for invasive treatment of CPAs a tertiary medical center, Changhai Hospital admitted patients with previous pancreas-related surgical, endoscopic, or other invasive procedures from primary medical centers. In our center, minimally invasive interventions were taken as principle methods prior to surgery: extracorporeal shock wave lithotripsy (ESWL)/endoscopic retrograde cholangiopancreatography (ERCP) for stone removal and main pancreatic duct (MPD) drainage, insertion of stents to treat dominant MPD stricture and biliary duct stricture, and endoscopic drainage for uncomplicated pseudocyst with endoscopic reach283538394041424344Continuous and categorical variables were presented as mean\u2009\u00b1\u2009SD and counts (percentages), respectively. Student\u2019s t-test or Mann\u2013Whitney U test and \u03c7-square test or Fisher\u2019s exact test were used as indicated. Cumulative rates of steatorrhea were calculated by using the Kaplan\u2013Meier method after the onset of CP , after the diagnosis of CP (patients with steatorrhea at the diagnosis of CP were excluded), and after the first successful drainage of MPD (only patients who without steatorrhea at the time of the first successful drainage of MPD were included). Log-rank test was used to further analyze the difference of cumulative rates of steatorrhea between two groups . For risk factor analysis, multivariate analysis by Cox proportional hazards regression model was performed to identify the independent predictors based on the results of univariable analyses . Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated. Statistical analyses were conducted at a significance level of 0.05 for all analyses. Data were analyzed by using SPSS 18.0 .How to cite this article: Li, B.-R. et al. Risk Factors for Steatorrhea in Chronic Pancreatitis: A Cohort of 2,153 Patients. Sci. Rep.6, 21381; doi: 10.1038/srep21381 (2016)."} +{"text": "Private practitioners are frequently the first point of healthcare contact for patients with tuberculosis (TB) in India. Inappropriate TB management practices among private practitioners may contribute to delayed TB diagnosis and generate drug resistance. However, these practices are not well understood. We evaluated diagnostic and treatment practices for active TB and benchmarked practices against International Standards for TB Care (ISTC) among private medical practitioners in Chennai.A cross-sectional survey of 228 practitioners practicing in the private sector from January 2014 to February 2015 in Chennai city who saw at least one TB patient in the previous year. Practitioners were randomly selected from both the general community and a list of practitioners who referred patients to a public-private mix program for TB treatment in Chennai. Practitioners were interviewed using standardized questionnaires.Among 228 private practitioners, a median of 12 (IQR 4\u201328) patients with TB were seen per year. Of 10 ISTC standards evaluated, the median of standards adhered to was 4.0 (IQR 3.0\u20136.0). Chest physicians reported greater median ISTC adherence than other MD and MS practitioners , or MBBS practitioners . Only 52% of all practitioners sent >5% of patients with cough for TB testing, 83% used smear microscopy for diagnosis, 33% monitored treatment response, and 22% notified TB cases to authorities. Of 228 practitioners, 68 reported referring all patients with new pulmonary TB for treatment, while 160 listed 27 different regimens; 78% (125/160) prescribed a regimen classified as consistent with ISTC. Appropriate treatment practices differed significantly between chest physicians and other MD and MS practitioners .TB management practices in India\u2019s urban private sector are heterogeneous and often suboptimal. Private providers must be better engaged to improve diagnostic capacity and decrease TB transmission in the community. India accounts for approximately one-quarter of the world\u2019s 9 million incident tuberculosis (TB) cases every year . The TB Based on the International Standards for TB Care (ISTC) , India hCurrently, there are several ongoing efforts to engage and improve the quality of TB care in the private sector. These include NGO-led models and PrivChennai is the sixth largest city in India with a population of 4.6 million . There aWe recruited qualified, allopathic medical practitioners of all specialties working in the urban private sector. From January 2014 through February 2015, we enrolled consenting PPs from the ten 2011 census tract zones in Chennai and conducted interviews using a structured questionnaire. To identify PPs for recruitment, we used a listing of all city streets in Chennai to randomly select up to 50 street corners per zone. REACH staff started at each selected corner and used a structured movement algorithm until an eligible PP was located to recruit a maximum of five PPs per health facility and minimum of five PPs per zone. Additionally, we randomly selected PPs from REACH\u2019s database of PPM-referring PPs. All qualified PPs with formal medical training who diagnosed at least one patient with pulmonary TB (PTB) in the year prior to recruitment were eligible. After a PP agreed to be interviewed for the study, up to three attempts were made to complete the interview. Trained study staff performed the interviews privately in the PPs\u2019 offices. Structured interviews lasted approximately 15\u201320 minutes and collected data on PPs\u2019 self-reported socio-demographic information , patient volume, TB disease knowledge, diagnostic and treatment practices, intervals between patient presentation, diagnosis, and treatment, and patient referral practices. PPs were asked about the drug regimen that they prescribed for their new adult patients of 60 kilograms with PTB using an open-ended format. PPs were subsequently asked to give the average total duration of treatment for PTB from a set of standardized responses. PP-reported education was used to assess level of training by comparing those with higher levels of training or master of surgery degree (MS)), to those with undergraduate bachelor of medicine and bachelor of surgery degrees (MBBS). We also compared chest specialists against those without such specialty training.The ISTC include 21 standards of diagnosis, treatment, and other practices that describe a widely accepted level of TB care ,10. We eOur primary comparisons were of PPs seeing >12 TB patients per year (versus \u226412), and of MD and MS specialty physicians versus MBBS practitioners. We estimated estimate univariate and multivariable associations of self-reported volume of TB patients with provider specialty, usage of diagnostic tests, and adherence to ISTC using Poisson regression with robust standard errors, as the outcome was not rare and log-binomial models failed to converge . These mThis study protocol was approved by the Johns Hopkins Bloomberg School of Public Health Institutional Review Board, McGill University Health Center Biomedical Research Ethics Review Board, and REACH Independent Ethics Committee. Written informed consent was obtained from all practitioners prior to being interviewed for the study.Of the 249 eligible private practitioners approached to participate, 228 were interviewed (92% participation rate). Among these, 161 (71%) were randomly selected within Chennai city and 67 (29%) from REACH\u2019s PPM database. The majority of PPs were men (70%) and median practice experience was 20 years (IQR 15\u201330) . Over haThe mean annual patient volume in our sample was 6,387 and 30 patients with TB (median 12 [IQR 4\u201328]). Chest physicians saw a mean of 92 (95%CI: 59\u2013125) TB patients per year, versus 20 (95%CI: 15\u201325) among other MD/MS physicians, and 14 (95%CI: 8\u201320) among MBBS practitioners . Chest pIn univariate analysis, providers who saw more than 12 patients with TB per year were more likely to be specialists, have more years of practice experience, work in a private hospital, initiate TB treatment without referral to the public sector, know about Indian TB policies, and obtain knowledge about TB from such sources as medical journals . In adjuSputum smear microscopy was commonly used by all providers for diagnosis of active TB , as was chest X-ray . Practitioners frequently relied on non-microbiological tests not generally recommended for active TB diagnosis as part of their diagnostic process including erythrocyte sedimentation rate (ESR) and tuberculin skin testing . Over onChest physicians and other MD/MS practitioners were more likely to report using smear microscopy and Xpert MTB/RIF for TB diagnosis than MBBS practitioners. In adjusted analyses, chest physicians and other MD/MS providers were significantly more likely to use smear, Xpert, and DST in the TB diagnostic process or at the first patient visit than MBBS providers . In a coAmong those practitioners that reported using smear, Xpert, and culture for TB diagnosis, 57% (107/228), 83% (29/35), and 55% (18/33) of practitioners, respectively, reported sending patients to private labs for diagnostic testing. The majority of practitioners reported sending patients to private labs for other diagnostic tests including: 65% (144/222) for chest X-ray, 70% (85/122) for ESR, 73% (75/103) for TST, and 93% (13/14) for IGRAs. The main reason given by all PPs for using smear and chest X-ray were test accuracy (34% and 51%), while the main problem with existing diagnostic tests reported was the necessity of sputum samples (30%).Adherence to the ISTC was generally inadequate with an Median ISTC scores were significantly higher among chest physicians than other MD/MS practitioners , or MBBS practitioners , reflecting greater reported adherence . ProvideOf 228 responding PPs, 160 listed 27 different treatment regimens for PTB, while the other 68 referred all patients for TB treatment. Prescriptions inconsistent with ISTC included incorrect treatment durations (16/160), drug regimens lacking pyrazinamide and/or ethambutol (10/160) or including quinolones or injectable second-line agents (10/160). Of 160 PP\u2019s, only 78% prescribed a regimen consisting of (a) 6 to 8 months of isoniazid and rifampin, (b) at least one of pyrazinamide or ethambutol, and (c) no second-line agents for a hypothetical patient with new PTB. Appropriate prescription practices were significantly lower among chest physicians compared to MD/MS practitioners (54% (20/37) vs. 87% (67/77), P<0.001) and MBBS providers (54% (20/37) vs. 83% (38/46), P<0.01), but not among providers that saw over 12 TB patients per year versus those who saw less (80% vs. 77%). Inappropriate prescriptions among chest physicians included 27% prescribing incorrect treatment durations exceeding six to eight months (vs. 7% other MD/MS and 2% MBBS), 11% prescribing regimens including quinolones or injectable second-line agents (vs. 5% other MD/MS and 4% MBBS), and 8% prescribing regimens lacking pyrazinamide and/or ethambutol (vs. 1% other MD/MS and 11% MBBS).Only 40% of all PPs utilized DOTS-based approaches to ensure treatment adherence, including referral to RNTCP DOTS (55/228), REACH PPM (30/228), or both (7/228). In adjusted analyses, use of these approaches was significantly among lower chest physicians and other MD/MS practitioners compared to MBBS providers . One-thiDiagnostic and treatment practices were variable in this study of qualified private practitioners who diagnosed at least one patient with TB in the past year in the urban Indian private sector. As examples, less than half of surveyed practitioners tested patients with long-lasting cough for TB, nearly half used TST as part of their suite of diagnostic tests for diagnosis of active TB, less than one-quarter notified patients treated for TB to public health authorities, and over one-fifth used treatment regimens that were either too short, lacked critical drugs, or included second-line agents for patients with new pulmonary TB. NGO-led efforts to engage PPs in PPM partnerships in Chennai have empPrior studies of practitioners in India have consistently documented variable quality of TB care in the private sector ,13,19. IOur study is among the first to assess PP practices by patient volume, practitioner specialty, and type of practice facility . We founMismanagement of TB diagnosis and treatment negatively affects the patient and the Indian public health system. The lack of testing for TB among patients with long-lasting cough and the use of inappropriate diagnostic tests for active TB by private practitioners in this study may be due to modified practices to make medical visits more convenient to avoid losing patients who may seek fast results or no tests to reduce costs . The useAs a cross-sectional study of PP practices, this study has several important limitations. We included only formally trained qualified practitioners and providers referring to a public-private mix organization. While we were thereby able to attain a high response rate, our results are not representative of all urban private practitioners providing TB care and likely overestimate the quality of care provided in Chennai as a whole. We restricted interviews to PPs who had diagnosed at least one patient with TB in the past year to reduce recall bias. Further, we used structured questionnaires for data collection, which allowed us to collect a larger volume of data in the short times available to interview PPs; however, for describing actual practices, vignette-based questions may be preferred . Lastly,Our findings emphasize the TB burden and management challenges to practitioners in the urban private sector with several implications for policy. First, TB diagnosis and treatment patterns were variable, and while chest physicians and high-volume providers reported greater ISTC adherence in some aspects , they reported lower adherence in others . This widespread variability in practices highlights the need for broad-based education and involvement at all levels of the private sector. Practices in the informal sector and among lower-volume providers are expected to be substantially worse . Second,In conclusion, our study shows variability in TB diagnostic and treatment practices in India\u2019s urban private sector, including among qualified providers, high-volume providers, chest physicians, and those referring to public-private mix organizations for TB treatment. In particular, screening of individuals with persistent cough, use of TB-specific tests at the initial encounter, expanded use of molecular tests and treatment monitoring, and prescription of appropriate first-line regimens for PTB should be emphasized. Innovative approaches to TB control in India must include broad-based engagement of the private sector if TB elimination in India is to become a reality in the foreseeable future."} +{"text": "The use of aortic counterpulsation therapy in advanced heart failure iscontroversial.To evaluate the hemodynamic and metabolic effects of intra-aorticballoon pump (IABP) and its impact on 30-day mortality in patientswith heart failure.2), arterial lactate, and use of vasoactive drugsat 48 hours after IABP insertion. The 30-day mortality was estimatedby the Kaplan-Meier method and diferences in subgroups were evaluatedby the Log-rank test.Historical prospective, unicentric study to evaluate all patientstreated with IABP betwen August/2008 and July/2013, included in aninstitutional registry named TBRIDGE . We analyzed changes in oxygen central venous saturation and use of nitroprusside , and adecrease in lactate levels and useof vasopressors after IABP insertion.Thirty-day survival was 69%, with lower mortality in Chagas diseasepatients compared without the disease (p = 0.008).A total of 223 patients (mean age 49 \u00b1 14 years) were included.Mean left ventricle ejection fraction was 24 \u00b1 10%, and 30% ofpatients had Chagas disease. Compared with pre-IABP insertion, weobserved an increase in ScvOAfter 48 hours of use, IABP promoted changes in the use of vasoactivedrugs, improved tissue perfusion. Chagas etiology was associated withlower 30-day mortality. Aortic counterpulsation therapy is aneffective method of circulatory support for patients waiting for hearttransplantation. Despite pharmacological therapy including diuretics,vasodilators and inotropic agents, many of these patients persists in shock,demanding support until recovery or heart transplantation.Cardiogenic shock is a clinical condition with a high mortality rate.4 Its effectiveness for the management of these patientsis based on the positive hemodynamic effects on cardiac output, coronaryperfusion and left ventricular afterload, in addition to its suitability to theintensive care setting.6Introduced in the 1960s, the intra-aortic balloon pump (IABP) remains the mostwidely used circulatory assist device in cardiogenic shock.9 Its indication in advanced cardiomyopathy also lacksevidence, although is related to clinical stabilization and maintenance oftissue perfusion during advanced stages of the disease. The aims of this studywere to evaluate hemodynamic and metabolic effects of IABP and 30-day mortalityin patients with advanced cardiomyopathy.Although there are no randomized controlled trials showing a reduction inmortality, the IABP has been indicated to patients with acute coronary syndromesand hemodynamic instability until recovery of stunned myocardium.2), pH,bicarbonate, base excess, arterial lactate, hemoglobin, white blood cell count,platelet count, urea, creatinine, sodium, brain natriuretic peptide (BNP),C-reactive protein (CRP), and echocardiographic data - left ventricular ejectionfraction (LVEF), left ventricle end-diastolic diameter, left ventricleend-systolic diameter, pulmonary artery systolic pressure, presence and degreeof right ventricular dysfunction, presence and degree of mitral regurgitation.We also investigated the percentage of patients using vasoactive drugs and vasopressors (norepinephrineand dopamine). Patients were classified according to the level of respiratorysupport and severity of renal dysfunction.Renal failure was defined as need for hemodialysis or estimated creatinineclearance < 60 mL/min, calculated by the Cockroft-Gault formula. Clinical andlaboratory data immediately before (pre-IABP) and 48 hours after the insertionof IABP (post-IABP) were compared.Historical prospective, unicentric study, performed to evaluate all patientstreated with IABP between August/2008 and July/2013, in a cardiac ICU dedicatedto heart failure patients. Data were obtained from an institutional registrynamed TBRIDGE , created to evaluate the IABPperformance on circulatory assistance in patients with advanced cardiomyopathybased on information collected from patients' electronic medical records. Weassessed the central venous oxygen saturation , and the rate ofanticoagulant use.Quantitative variables were expressed as mean and standard deviation and medianand interquartile range (IQR), as appropriate. Qualitative variables wereexpressed as absolute frequencies and percentages. Pre- and post-IABPquantitative data were compared by paired Student's t-test or by the Wilcoxon test , and qualitative data were compared by the McNemartest.Survival curve was calculated by the Kaplan-Meier method and diferences insubgroups were evaluated by the Log-rank test. Clinical assessment of patientsin the late follow-up was based on the last outpatient visit data contained intheir medical records. A p-value < 0.05 was considered to be statisticallysignificant. Analysis of data was performed using the SPSS software, version17.0 . The study was approved by the local ethicscommittee.A total of 2,892 patients were admitted to the cardiac ICU, and 223 (7.7%)received 302 IABPs, during the five-year period of the study. Clinical featuresare described in The median time of hemodynamic support with IABP was 10 days (IQR: 4-22.5). Thelongest time on IABP was 263 days. Fifty-two patients (23.3%) used two or moreIABP devices during hospitalization.The mean LVEF assessed by echocardiogram was 24 \u00b1 10%, with leftventricular diastolic diameter of 69 mm. Moderate or severe mitral regurgitationwas observed in 62% of patients, and moderate or severe right ventriculardysfunction was found in 70.8% of patients .vs. 17.1 mg/dL, p < 0.01), and an increase inScvO2 , pH , serum bicarbonate and base excess . Although creatinine levels didnot significantly change after the IABP, a significant decrease in the levels ofurea was observed.Laboratory data before and 48 hours after the insertion of IABP are presented invs 47.5%, p = 0.0002) and reduceduse of norepinephrine and dopamine .No significant differences in the rate of dobutamine or milrinone use were found patients were on room air, 84 (38%) received high flownasal cannula oxygen, 23 (10%) were on non-invasive positive pressureventilation and 65 (29%) on mechanical ventilation.vs. 62.33%, p = 0.001).Before IABP, 172 (77.1%) patients had renal failure, and 20 (8%) of them receivedhemodialysis. A significant decrease in the number of patients with renalfailure, on or not on hemodialysis, was observed after IABP as compared withpre-IABP .The median duration of hospitalization was 37 days. Thirty-day survival was 63.9%. Heart t3 occurred in 39% of patients, and absolutethrombocytopenia in only 15% of them. A decrease in hemoglobin > 3 g/dL wasobserved in 8% of patients, and only one patient was diagnosed withretroperitoneal hematoma. Arterial and venous thromboembolic events occurred in6% of patients, including stroke, peripheral arterial and venousthromboembolism.With respect to the safety of IABP, a platelet count fall greater than50,000/mmMost patients (50.6%) did not receive full anticoagulation; 2,7% of patientsreceived anticoagulation due to the presence of the IABP and 46.6% for otherreasons .11our population was composed predominantly of patients with advanced chronicheart failure, refractory to pharmacological therapies. The advanced stage ofcardiomyopathy in our study population was characterized by severe leftventricular dysfunction, which was frequently associated with right ventriculardysfunction, hyponatremia, pulmonary arterial hypertension, and increased BNPlevels.This study evaluated clinical data of patients with advanced cardiomyopathyadmitted to a cardiac ICU. Differently from previous studies on cardiogenicshock, wich focus on acute myocardial infarction,The use of IABP reduced the use of vasopressors, which are known to increase theafterload in left ventricular dysfunction. There was also a significant increasein the use of sodium nitroprusside, a potent arterial vasodilator, beneficial toheart failure patients. Laboratorial data markedly improved after the IABPinsertion, with reduction of lactate and urea levels, and increase of ScvO2, pH,bicarbonate and base excess, which may be explained by the effects of IABP onthe hemodynamic profile and on the use of vasoactive drugs.There was a high prevalence of renal failure in our study population. Although themean creatinine levels did not change, both the percentage of patients withrenal failure and urea serum concentrations significantly decreased after 48hours of aortic counterpulsation. Further studies are needed to evaluate therole of IABP on the maintenance and recovery of renal function in patients withcardiogenic shock.13 In our study, however,chances of early survival were higher in Chagas disease patients using the IABPcompared with patients with other etiologies of heart failure. Data from theliterature show that transplant patients with Chagas disease had betterprognosis than those without the disease, with survival rates of 83%, 71%, 57%and 46% at 1 month, 1 year, 4 years and 10 years of follow-up,respectively.14 Theparadox of greater survival of Chagas disease patients after hearttransplantation was also demonstrated in a Brazilian muti-centric studyinvolving 720 patients.15Heart failure caused by Chagas disease has been associated with unfavorableprognosis.Despite an initial clinical improvement following IABP insertion, more than 80% ofnon-transplant patients died during hospitalization, which emphasizes the needfor therapies to improve prognosis. This was highlighted by the difference inmortality between transplant and non-transplant patients.11Another important consideration was the number of patients (50.6%) not receivingtherapeutic anticoagulation and the low incidence of thromboembolic events. Theuse of IABP in this population reinforces its role as prolonged circulatorysupport in patients with advanced cardiomyopathy, candidates fortransplantation. One patient used the IABP for 217 days until receiving asuccessful transplant. In agreement with the largest randomized study on thesubject, the IABP-SHOCK II trial which involved 600 patients, the use of IABPwas considered safe, as it did not increase the risk of complications, such asperipheral ischemia, infection or bleeding.Finally, this is the largest registry of circulatory support in advancedcardiomyopathy patients in Brazil. Nevertheless, due to its observational andunicentric design, this study aimed to generate hypotheses that may contributeto the management of these high mortality risk patients.IABP showed beneficial effects in the first 48 hours, promoting changes in thevasoactive drugs regimen and improving tissue perfusion. Chagas etiology wasassociated with lower 30-day mortality. Aortic counterpulsation therapy is aneffective alternative method of circulatory support for patients waiting forheart transplantation."} +{"text": "It is important to understand the local burden of non-communicable diseases including within-country heterogeneity. The aim of this study was to characterise hypertension and type-2 diabetes profiles across different Peruvian geographical settings emphasising the assessment of modifiable risk factors.Analysis of the CRONICAS Cohort Study baseline assessment was conducted. Cardiometabolic outcomes were blood pressure categories and glucose metabolism disorder status . Exposures were study setting and six modifiable factors . Poisson regression models were used to report prevalence ratios (PR). Population attributable risks (PAR) were also estimated.Data from 3238 participants, 48.3% male, mean age 45.3\u2005years, were analysed. Age-standardised (WHO population) prevalence of prehypertension and hypertension was 24% and 16%, whereas for prediabetes and type-2 diabetes it was 18% and 6%, respectively. Outcomes varied according to study setting (p<0.001). In multivariable model, hypertension was higher among daily smokers (PR 1.76), heavy alcohol drinkers (PR 1.61) and the obese (PR 2.06); whereas only obesity (PR 2.26) increased the prevalence of diabetes. PAR showed that obesity was an important determinant for hypertension (15.7%) and type-2 diabetes (23.9%).There is an evident heterogeneity in the prevalence of and risk factors for hypertension and diabetes within Peru. Prehypertension and prediabetes are highly prevalent across settings. Our results emphasise the need of understanding the epidemiology of cardiometabolic conditions to appropriately implement interventions to tackle the burden of non-communicable diseases. Worldwide, non-communicable diseases (NCDs) cause 36 million deaths annually,1A modelling study reported that reducing the prevalence of six risk factors, including smoking and alcohol consumption, among others, would contribute to reducing NCD mortality due to cardiovascular disease and diabetes, with most of these benefits in low and middle-income countries (LMICs).5Health research and development efforts for NCDs in LMICs are limited, despite repeated calls for action.The aims of this study were to characterise the profile of two leading cardiometabolic conditions, hypertension and type-2 diabetes, across distinct Peruvian geographical settings. In addition, emphasis was placed on the magnitude of the associations between these cardiometabolic conditions and modifiable risk factors in these settings, their respective population attributable risks (PAR) and the pattern of aggregation of common risk factors.A cross-sectional, baseline assessment of the CRONICAS cohort study8Individuals aged \u226535\u2005years, full-time residents in the area, who provided informed consent, were invited to participate in the study. We identified a sex- and age-stratified random sample of potentially eligible subjects. Single stage random sampling was conducted using the most updated census available (year 2010) in each of the sites. Only one participant per household was enrolled.Main outcomes were two: blood pressure status and glucose metabolism disorder status. Blood pressure status was categorised based on hypertension and prehypertension definitions. Hypertension was defined as any of the following conditions: systolic blood pressure (SBP) \u2265140\u2005mm\u2005Hg or diastolic blood pressure (DBP) \u226590\u2005mm\u2005Hg; or self-report of physician diagnosis and current use of antihypertensive drugs10The main exposures were study site , and six well-established modifiable factors associated with hypertension and diabetes: daily smoking , heavy alcohol drinking , leisure time and transport-related physical activity based on the International Physical Activity Questionnaire domains as recommended for Latin American populationsOther variables of interest included in the analysis were self-reported parental history of hypertension and/or diabetes, and metabolic syndrome defined by using the 2009 harmonised definition that incorporates region-specific cut-off points.http://www.biorad.com). Plasma glucose was measured using an enzymatic colourimetric method . Detailed information on evaluation and measurement techniques is reported elsewhere.8Participants responded to a detailed questionnaire. Fieldworkers in rural areas were fluent in Spanish, Aymara or Quechua and they administered the survey to those with poor literacy. Fieldworkers measured weight, height and blood pressure in triplicate using standardised techniques.2 test for categorical variables. age-standardised prevalence of our outcomes of interest was calculated using WHO standard population distribution.15Statistical analyses were conducted in STATA V.13 in 2014. Characteristics of the population were tabulated according to study site and comparisons were performed using one-way analysis of variance or Kruskal-Wallis test for numerical variables, and \u03c7Poisson regression with robust SEspunaf command in STATAIn addition, population attributable risk (PAR) was calculated using the All participants provided verbal informed consent due to high-illiteracy rates, especially in rural areas. The study was approved by the Institutional Review Boards at Universidad Peruana Cayetano Heredia and AB PRISMA, in Lima, Peru, and at the Bloomberg School of Public Health, Johns Hopkins University, in Baltimore, USA.Overall response rate after enrolment was 62.9% (4325/6872) and, of these, 83.3% (3601/4325) completed all questionnaires. Among those with completed questionnaires, 89.8% (3232/3601) and 87.1% (3135/3601) had all clinical and blood laboratory evaluations completed, respectively (see online supplementary E-figure S1).A total of 3238 participants, 48.3% male, mean age 45.3\u2005years (IQR: 45.3\u201365.2), were included in the analysis. Of them, 21.3% had \u226512\u2005years of education and 90.3% had a family income of 10. Overall, 62.5% had weaned and 50% had survived at the time of this report. They should have both recognition and equity of access to NHS (England) resource. There is nowhere else to turn.1. King's College Hospital meets the caseload criteria, ELSO guidelines and quality assurance data for a centre undertaking all modes of ECLS2. In a young moribund group of patients who were unsuitable for VV ECMO in the national centres, our VV ECMO cohort did excellently with 50% surviving even though such patients would normally be denied this critical care rescue technique - particularly in the UK3. NHSE should work with hospitals outside of the commissioned centres to ensure equity of access and effective outcomes for patients with complex multi-system disease4. ECMO should form part of the armamentarium of tertiary critical care services, especially for super-specialist populations that are not represented in the commissioned centres - and there are disadvantages - in terms of equity of access - to overly restricting this service"} +{"text": "In addition to standard precautions, transmission-based precautions (TBP) aim to prevent cross transmission of micro-organisms from patient to patient or to healthcare workers (HCW). In France, guidelines were updated in 2009 for contact precautions and in 2013 for droplet and airborne precautions.The objective was to assess TBP implementation in healthcare settings (HCS).st and December 31st 2014. Inclusion criteria were voluntary public and private hospitals in France. Self-assessment questionnaires were administered at two levels: institutional and HCW. At ward level, an external auditor observed how TBP were applied for each patient requiring them . Data were computed online by each HCS. Results were given as a percentage of objectives attained at institutional and ward levels, and as percentages of correct answers attained at HCW level. Pooled scores were calculated by criteria.The study consisted in a mixed audit of procedures, resources and knowledge. It was conducted between January 1A total of 547 hospitals participated, including 6,148 patients requiring TBP, 129,514 HCW and 5,114 physicians. At institutional level, the alert system score was 81.5%. In particular, 99.1% of HCS had a procedure to follow concerning internal information in case of multidrug resistant bacteria (MDRB), 60.3% had an information system in case of re-admission of a MDRB patient. Moreover, 84.6% of HCS had a procedure to check whether TBP were implemented in case of MDRB, 91.6% of whom traced it. At ward level, 95.0% of the implemented TBP belonged to the appropriate category. The overall score was 84.2%, going from 68.6% for prescription traceability to 92.2% for room organisation. Further analyses are ongoing and these results will be available in June 2015 .Such a large participation will serve as a national reference leading to TBP promotion actions for security improvement at local and national levels, as announced in the French national programme on healthcare-associated infections prevention.None declared."} +{"text": "Studies suggest individuals of low socioeconomic status (SES), immigrants, and Aboriginal peoples, may have fewer food allergies than the general population. However, given the difficulty in recruiting such populations using conventional survey methodologies, the prevalence of food allergy among these populations in Canada has not been estimated.To compare the prevalence of food allergies among children from low-income, immigrant and Aboriginal populations to children from the general Canadian population.Using 2006 Canadian Census data, postal codes with high proportions of low-income, immigrant, and Aboriginal populations were extracted and households randomly selected to participate in a telephone survey. Information on food allergies and demographic data was collected for all children (defined as below 18 years of age). Food allergy was defined according to self-report. Prevalence estimates were weighted using Census data to account for our targeted sampling.Between September 2010 and September 2011, 12,747 households were contacted to complete the survey, of which 6,403 responded (50.2% response rate), representing 3,271 children. Among all children, the prevalence of allergy to any food was 7.49% , 5.93, 9.05). Children born in Canada had considerably more food allergies than those born elsewhere [7.96% versus 3.26% ]. The prevalence was higher for children residing in households above the low income cut-off (LICO) than below the LICO [7.81% versus 6.24% ], and for children with versus without Aboriginal ancestry [7.62% versus 6.03% ]; however, these differences were not statistically significant due to overlapping confidence intervals.Our study found that immigrant children experience fewer food allergies than Canadian-born children. Although the data suggest a trend towards a lower prevalence of food allergy among low-income and Aboriginal children, wide confidence intervals preclude definitive conclusions."} +{"text": "Wound infection is common in diabetic foot ulcers with potentially life changing sequelae. Targeted treatment of infective organisms requires accurate identification of pathogens to enable refinement of antibiotic protocols to improve outcomes and reduce antibiotic resistance. Wound sampling is routinely conducted using swabs although some guidelines recommend use of tissue samples. To date there is a lack of robust evidence to inform clinical practice regarding sampling technique.This study aimed to evaluate the extent to which results from wound swab and tissue samples taken from the same patient agree with each other; one might report pathogens more than the other, they might both report the same pathogens consistently, or they might disagree with a more complex pattern of disagreement. Here we report agreement and disagreement between the techniques based upon reported presence of likely pathogens.In this multi-centre, cross-sectional study, 401 patients with a suspected infected diabetic foot ulcer were recruited from 25 sites across England. All patients had both a swab and tissue sample taken from same ulcer for plating and culture. Agreement between techniques in the reported presence of likely pathogens was assessed by overall prevalence and bias adjusted Kappa (PABAK). McNemar\u2019s test was used to investigate patterns of disagreement.401 patients were recruited between 2011 and 2013 with a median age of 63 years; 79% were male; 85.5% had type 2 diabetes; 27.5% presented with a recurrent ulcer; and 45.5% had a neuro-ischaemic ulcer, 50.5% neuropathic, and 3.5% ischaemic.Both swab and tissue reports were available for 395 patients, and at least one pathogen was reported in 70.1% of swab samples and 86.1% of tissue samples. In 58% of patients the two samples resulted in a difference in the reported pathogens, with: 13.2% both reporting different pathogens; 36.7% reporting additional pathogens in the tissue sample; and 8.1% reporting additional pathogens in the swab sample.In the most prevalent pathogens (those present in >8%), there were significantly higher rates of reporting of the following pathogens from tissue samples than swabs : Gram Positive Cocci, Gram Negative Bacilli, Enterobacteriacea, Anaerobes, Streptococcus, Enterococcus, Coagulase-Negative Staphylococcus, Gram Positive Bacilli, Corynebacterium; with differences ranging between 3.3% (Streptococcus) and 13.7% (Gram Positive Cocci). There was no evidence of a difference in reporting for Methicillin-resistant S. Aureus (MRSA) (p=0.22); Staphylococcus Aureus and Pseudomonas (the latter two both had p=1.00). In terms of agreement, the PABAK ranged from 0.58 (Gram Positive Cocci) to 0.97 (MRSA).Investigation of the influence of baseline factors on agreement of the number of reported pathogens found, despite large centre variation, significant evidence (p=0.02) of an association with ulcer duration, such that older ulcers ( \u226556 days old) had a reduced odds ) of the tissue sample reporting more pathogens than the swab.Overall, there were significant differences in the pathogens reported from swab and tissue samples in patients with suspected infected diabetic foot ulcers. This has potential implications for choice of sampling technique in clinical practice."} +{"text": "Pulmonary hypertension (PH) has traditionally been associated with a poor prognosis. However, recent advances in the understanding of its pathophysiology have opened new avenues for treatment . Of noteTo assess critical care outcomes in patients with pre-existing pulmonary hypertension and evaluate potential predictors of survival.We conducted a retrospective observational study of patients with PH admitted to the critical care department (CCD) in a UK national pulmonary hypertension referral centre between April 2000 and July 2014. Critical care data on demographics, admission details, physiological and biochemical parameters as well as treatment modalities in the CCD were collected from our electronic patient record system (Metavision). These were amalgamated with data on WHO functional state, right heart catheter examinations and shuttle walk distance from the PH unit clinical database. Predictors of critical care and hospital survival were assessed using uni- and multivariate logistic regression analysis. Results are expressed as mean \u00b1 SD and odds ratios (OR) with 95% confidence intervals (CI).One hundred and forty seven patients were included in the study, accounting for 169 individual admission episodes to critical care. Baseline demographics and PH data are shown in Table Medical, surgical and obstetric categories accounted for 79%, 14% and 8% of admissions. Hospital survival in these subgroups was 65, 91 and 85%, respectively. Thirty percent of patients received CPAP, 9% bilevel NIV, 5% invasive ventilation, 23% vasopressors, 19% inotropes and 12% CVVH. These therapeutic modalities were associated with a hospital survival of 51, 47, 11, 41, 34 and 57%, respectively. Overall, 76% of patients survived to discharge from critical care and 70% left hospital alive. Several parameters at admission to the CCD were identified as predictors of hospital discharge at univariate and multivariate logistic regression analysis, most notably Sp02/Fi02 ratio, serum lactate and serum sodium concentration (see Table Overall, more than two thirds of patients with pre-existing PH admitted to critical care survived to hospital discharge. Medical reasons for admission were associated with a worse outcome compared with surgical and obstetric indications. Independent predictors of hospital mortality were low serum sodium, high lactate and low Sp02/Fi02 ratio, reflecting heart failure, poor cardiac output and poor oxygenation."} +{"text": "This study aimed to determine the diagnostic accuracy of computed tomography imaging for the diagnosis of chronic thromboembolic pulmonary hypertension (CTEPH). Additionally, the effect of test and study characteristics was explored. Studies published between 1990 and 2015 identified by PubMed, OVID search and citation tracking were examined. Of the 613 citations, 11 articles (n=712) met the inclusion criteria. The patient-based analysis demonstrated a pooled sensitivity of 76% , and a pooled specificity of 96% (95%CI: 93% to 98%). This resulted in a pooled diagnostic odds ratio (DOR) of 191 (95%CI: 75 to 486). The vessel-based analyses were divided into 3 levels: total arteries\u3001main+ lobar arteries and segmental arteries. The pooled sensitivity were 88% (95%CI: 87% to 90%)\u300195% (95%CI: 92% to 97%) and 88% (95%CI: 87% to 90%), respectively, with a pooled specificity of 90% (95%CI: 88% to 91%)\u300196% (95%CI: 94% to 97%) and 89% (95% CI: 87% to 91%). This resulted in a pooled diagnostic odds ratio of 76 (95%CI: 23 to 254),751 (95%CI: 57 to 9905) and 189 (95%CI: 21 to 1072), respectively. In conclusion, CT is a favorable method to rule in CTEPH and to rule out pulmonary endarterectomy (PEA) patients for proximal branches. Furthermore, dual-energy and 320-slices CT can increase the sensitivity for subsegmental arterials, which are promising imaging techniques for balloon pulmonary angioplasty (BPA) approach. In the near future, CT could position itself as the key for screening consideration and for surgical and interventional operability. Chronic thromboembolic pulmonary hypertension (CTEPH) is a life threatening complication and carries poor diagnosis. It is cThis meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guideline . We searQUADAS-2 tool was used to assess the quality of studies included. We assumed that only V/Q scanning or DSA could correctly rule in or rule out CTEPH.First, identifying information about the study such as first author, journal, and year of publication was extracted . Further2 index was used to test for the heterogeneity between study results, which described the significance of total variation across studies rather than chance[2 statistic value of >50%. Differences in study characteristics between articles can be a cause of considerable heterogeneity . Therefore, the study characteristics were compared using the meta-regression to test for the sources of heterogeneity. Additionally, pooled estimates were calculated for subgroups of studies that were defined according to specific study characteristics on vessel-based analysis. Furthermore, sensitivity analysis were also performed to assess the reliability and stability of the meta-analysis results. Meta-Disc 1.4 was used for data analysis. Publication bias was examined using Deeks' test[Based on the results from the derived contingency tables, pooled sensitivity, specificity and DOR were calculated. The generated output of sensitivity and 1-specificity were used for the construction of summary receiver operating characteristic (SROC) curves. Also, the area under the curve (AUC) with 95%CIs was computed. SROC curves would generate a composite statistic which can demonstrate the diagnostic ability of CT. The I2 an chance. Statisteks' test.Bayes's theorem was used to calculate the post-test probability of CT on patient-based analysis. We presThe search process and results were shown in the flow chart in Methodological quality of the studies according to the QUADAS-2 tool was summarized in Baseline characteristics of patients included in the studies were summarized in 2 = 93.8%, p<0.01) and a high specificity of 96% . The vessel-based analyses were divided into three levels: total arteries\u3001main+ lobar arteries and segmental arteries. The more peripheral areas the emboli located, the lower the sensitivity and specificity were. The pooled sensitivity were 88% (95%CI: 87% to 90%)\u300195% (95%CI: 92% to 97%) and 88% (95%CI: 87% to 90%), respectively. And the pooled specificity were 90% (95%CI: 88% to 91%)\u300196% (95%CI: 94% to 97%) and 89% (95% CI: 87% to 91%), correspondently. SOC curves of CT on both patient and vessel basis were in Forest plots of sensitivity and specificity were shown in Figs The effective sample size funnel plot and associated regression test of asymmetry (Deeks 2005) were used to detect publication bias. The resThere are three challenges in imaging of patients with suspected CTEPH: an accurate diagnostic performance of the imaging modality is essential for the presence of CTEPH. It should enable detection of a patient with confirmed CTEPH suitable for PEA with great certainty, and finally, allow the adequate quantification of PH by measuring pulmonary hemodynamics. SeveralOur results indicated a moderate sensitivity and a high specificity of CT for the assessment of CTEPH on patient basis. However, in vessel-based analysis, our meta-analysis revealed both a satisfactory sensitivity and specificity, especially at the main+ lobar artery level. In addition, study quality was identified as a significant source of heterogeneity among studies on vessel-based analysis. And high-quality studies showed a much higher pooled sensitivity of 99% and specificity of 97%, which was considered adequate to confirm and rule out the presence of pulmonary embolism. Whereas patients with acute emboli are practically treated with anticoagulant therapy, regardless of burden of emboli, knowledge of the location and extent of disease in CTEPH helps in the selection of candidates for thromboendarterectomy. Based oA higher but non-significant diagnostic performance was observed for promising CT in comparison with routine CT in overall arterials level. Dual-energy CT has two promising advantages. First, it may be used to provide a \u201cone-stop\u201d diagnostic assessment of CTEPH in anatomy and perfusion without any additional radiation exposure. Small occlusive clots sometimes have a greater influence on oxygenation changes than larger non-occlusive emboli. Lung perfusion imaging can increase the diagnostic performance of CTEPH by identifying those clots in the small vessels, which are difficult to visualize in CTPA. Functional information derived from perfusion imaging can offer a better representation of haemodynamic significance than CTPA alone. CompareThe sensitivity of the study by Tunariu et al. was much lower than that of the other studies . The reaOur meta-analysis has following potential limitations. First, the number of included studies was insufficient. This might reduce the statistical power of meta-analysis. Second, our meta-analysis combined results from trials with different CT techniques, which may lead to bias. Third, patients referred for suspected or confirmed CTEPH may lead to bias although subgroup analysis revealed no significant effect of patient selection. Fourth, the reference standards of included studies referred as DSA or V/Q scanning influence the reliability of the pooled data. Fifth, although subgroup analyses were conducted in overall arterials, some potential factors might be missed such as the contrast agent and the prevalence. Meta-regression wasn't conducted in patient-basis, main+ lobar arterials and segmental arterials because of insufficient trials. Sixth, diagnostic value of CTEPH in subsegmental arterials wasn't evaluated due to lack of data.In conclusion, CT is a favorable method to rule in CTEPH and to rule out pulmonary endarterectomy (PEA) patients for proximal branches. Furthermore, dual-energy and 320-slices CT can increase the sensitivity for subsegmental arterials, which are promising imaging techniques for balloon pulmonary angioplasty (BPA) approach. In the near future, CT could position itself as the key for screening consideration and for surgical and interventional operability.S1 Table(PDF)Click here for additional data file."} +{"text": "As a means to contribute to the response to the Ebola virus disease (EVD) epidemic and support health system strengthening, Jhpiego, with funding from USAID, committed to strengthening health service capacity in IPC.Determine IPC performance level in selected health facilities.Identify gaps in IPC performance.The assessment was conducted in December 2014 and January 2015 in three teaching hospitals, comprising 66 services, and six communal medical centers (CMC). The main assessment tool was based on SBM-R performance standards for IPC. Data collection consisted of observation, interview and document review by a team of two evaluators per facility, for 2-3 days per facility.In the three national teaching hospitals, among 66 services, one service achieved 75% of performance standards, and eight achieved none. 33 of the services achieved below 30% of standards, while 17 scored between 31 and 49% and seven were performing at 50-74% of standards. In the 6 CMC, four were performing between 16 and 20% of standards, and two were performing at 35% and 37% respectively. Key reasons for poor performance included: 1) Insufficient knowledge in IPC, 2) lack of IPC materials and equipment, 2) non-observance of IPC procedures and norms, 3) poor management of IPC activities.Key interventions included training of healthcare workers, provision of an initial stock of IPC materials, onsite follow-up. These actions will contribute to the improvement of healthcare services, and help to restore community confidence in the public health services.None declared."} +{"text": "Endotoxin is a lipopolysaccharide in the membrane of gram negative bacilli, and is known to be one of the most potent activators of the inflammatory response in humans. In patients subjected to cardiac surgery, transient endotoxemia has been shown in many occasions, which seems to be closely related to extracorporeal circulation. The magnitude of endotoxemia, the high risk criteria and correlation with clinical evolution vary widely between studies.To examine the prevalence of endotoxemia related to cardiopulmonary bypass (CPB) in a cohort of patients undergoing cardiac surgery, using the Endotoxin Activity Assay (EAA). High risk criteria of endotoxemia were also investigated.EAA assay was performed within two hours of ICU admission in a prospective observational study. An EAA of < 0.40 units was judged as \"low\u201d, and \u22650.40 units as \"high\". Data collected included patient's demographics, cardiac history, EuroSCORE and intra-operative data collected included bypass time and the aortic cross clamp time, drugs and transfusions.A total of 107 patients were enrolled. The median age was 66 years (36-87), most were males (69%), 38% had diabetes, 71% hypertension, 12% peripheral vascular disease, 11% chronic renal failure and 21% were active smokers. Median EuroSCORE I was 6 (0-16). Out of 107, 99 were elective, 5 urgent and 3 emergent cardiac surgeries. 73 were valve replacement, 38 coronary vascular diseases, 12 aortic disease and 21 combined surgery. The median CPB time was 95 (24-300) and cross clamp time 68 (17-175) minutes. 37% required blood transfusion. 88% required norepinephrine, 49% dobutamine and 17% epinephrine. Only 24 patients had EAA\u22650.4 EA. We found a significant relation between peripheral vascular disease , p = 0,0070) and more red blood packs transfusion with higher EAA levels , p = 0,06). On the other hand the rest of variables were similar in both groups.The results of the study indicate that in postoperative cardiac surgery there is endotoxemia at least in moderate degree. As risk factors, we found that patients with peripheral vascular disease and those who had been transfused with more red blood packs during surgery were at increased risk of endotoxemia."} +{"text": "Trichosurus vulpecula), stoats (Mustela ermine), and ship rats (Rattus rattus) are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha), 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several single-capture traps rather than investing in fewer, but more expense, multiple-capture traps.Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums ( Trichosurus vulpecula), stoats (Mustela erminea), and ship rats (Rattus rattus) among other species have become significant invasive species, and have had (and continue to have) significant impacts on indigenous plants and animals [http://goodnature.co.nz/). Because current and future multiple-capture traps are, or are likely to be, more expensive ($US125\u2013140) than single capture traps ($US7-$25 depending on target species), it is important to understand the relative cost efficiencies of the different trap types in various situations. That is, knowing how many individual captures a trap might have at a single site over a fixed time period will enable prediction of how many potential captures a multiple-capture trap might require to obtain the same result, or alternatively if single capture traps are used, how many need to be set at a single site.Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production, infrastructure, and animal and human health , and a w animals . All thr animals ). Possum animals . Ship ra animals . Control animals ,7 and gr animals . Recentl animals , and the animals . AlthougEffective management of possums, stoats and rats in New Zealand usually involves an initial knockdown of the target population to below some threshold density level at which that population no longer causes unacceptable impacts , followeOur aim in this study was therefore to determine, for a given density of target pest animals and checking period, what would be the maximum number of captures that any one trap might achieve. Such information would enable pest controllers to make choices between the need for expensive multiple-capture traps and the possible alternative of using multiple cheaper single-capture traps. Additionally, such information will enable the developers of multiple-capture traps to consider what an optimal number of captures the traps should be designed to deliver, in order to avoid designing redundant capture capacity that might make the trap more expensive than required.Field-based comparisons of trap efficiency at low animal densities are expensive because a large number of trap-nights are required to capture sufficient animals to obtain acceptable statistical power, so we chose to initially model the different trap options using an individual-based spatially explicit modelling approach .dij between the centre of its home-range and the trap [An individual-based simulation model, based on the spatially explicit possum model of Ramsey and Efford , was devthe trap . Thus:Pits time ).Traps for possums, stoats and rats were located in a grid across a simulated area with the spacing between trap-lines and between traps along lines following current best practice . At the 0 and \u03c3) were, foThe size of the simulated trapped area varied between species : for posEach simulation was run for 30 days using 100 replicates to generate the number of traps that caught 0,1,2\u2026N captures. To compare the costs of multiple- versus single-capture traps we used the price per trap as well an estimate of time for setting up and checking the traps . The timhttp://dx.doi.org/10.7931/J28G8HMC or alternatively can be accessed via doi: 10.7931/J28G8HMC.Output data from the modelling simulations, as well as the R code used to generate the model, are publicly accessible at: The trap layout for modelling possum captures resulted in 2106 trap sites being allocated across the 1000 ha simulated area . At the When possum densities were higher (i.e. 3 possums/ha), there were 3420 animals available to be captured and captured. At these higher densities, 98% of single-capture traps captured a possum . MultiplAt low possum densities, increasing the trap capture capacity had little effect on the proportion of animals captured , with >9For modelling stoat trapping, the layout of traps resulted in 84 traps being distributed across the simulated area. At the lowest density simulated of 0.02 stoats/ha , 29% of single capture traps captured a stoat . For mulWhen stoat densities were higher (0.12 stoats/ha), there were 177 animals available to be captured. At these higher densities, 99.9% of single-capture traps captured a stoat indicating almost total trap saturation. Increasing the capacity to two captures resulted in 74% of traps capturing two stoats and18% capturing one. For the multiple-capture traps with 12 potential captures per trap, 10% of such traps caught four or more stoats, with most catching either one (30%), two (26%) or three (14%) stoats .At low simulated stoat densities, increasing the trap capacity had little effect on the proportion of animals captured , with c.For modelling the trapping of rats, the trap layout resulted in 4200 traps being allocated across the simulated area.Rats were modelled with the highest densities of the three species simulated, ranging from 1 to 11 rats/ha, . At the lowest density simulated (1 rat/ha), 22% of single-capture traps captured a rat. For multiple-capture traps with a capacity of two, 80% of traps caught no rats, 18% caught one rat and 2% caught two. When the capacity was increased to 12 captures per trap, only 0.2% caught 2 or more rats with 79%, 18% and 2% of traps capturing zero, one or two rats respectively.At the highest simulated rat densities (11 rats/ha), 98.2% of single-capture traps captured a rat indicating almost total trap saturation. Increasing the potential capture capacity per trap to two captures resulted in 82% of traps capturing two rats and 13% capturing one. For the multiple-capture traps with 12 potential captures per trap, 20% captured 1 rat, 25% 2rats, 22% 3 rats and 25% caught four or more rats . At the At low simulated rat densities, increasing the trap capture capacity had little effect on the proportion of animals captured , with 77When immigration was included as a confounding variable, a higher proportion of single capture traps captured a rat than without immigration. At the lowest density simulated (1 rat/ha), 32% of single-capture traps captured a rat. For multiple-capture traps with a capture capacity of two, 25% caught one rat and 5% caught two. When the capacity was increased to 12 potential captures per trap, 0.5% caught 3 or more rats with 25% and 4.5% of traps capturing one or two rats, respectively.The higher proportion of traps with captures was also apparent at higher densities of rats. At the highest simulated rat densities (11 rats/ha), there were 12,628 animals available to be captured. At these higher densities, 99.7% of single-capture traps captured a rat indicating almost total trap saturation. Increasing the capture capacity to two captures per trap resulted in 96% of traps capturing two rats and 3.5% capturing one. For the multiple-capture traps with 12 captures per trap, 9% captured 1 rat, 16% 2 rats, 20% 3 rats and 52% caught four or more rats .At the highest rat densities, 80% of multiple capture traps had captures of five rats or fewer . At mainThe choice of whether to invest in relatively expensive multiple-capture traps or several cheaper single-capture traps depends on the price of the traps and, if using single-capture traps, how many are placed at each site. For possums we compared the Sentinel (a single-capture trap) and the Goodnature A12 (a multiple-capture trap). For stoats we compared the Goodnature A24 (capacity to kill 24 stoats or rats), and the DOC 150, and the Victor snap-back trap (both single-capture traps). The simulations showed that only two traps need to be used at a site to catch 99% of stoats even at the highest densities simulated , and thiFor ship rats we compared the same traps as for stoats, but because of the higher densities of rats and the higher density of traps used, the costs per hectare were considerably higher than for trapping stoats . In the in situ population, but would place any potential immigrants at risk of capture. For possums and stoats, however, the number of immigrants over such a time-frame is likely to be low [The individual-based simulation models provided an efficient method for determining the distribution of the number of captures likely to be obtained at any one trap site and therefore the likely maximum numbers of captures expected. This information could then be used to assist in designing optimal trapping strategies or informing the design of multiple-capture traps. For possums, that are generally maintained at densities less than one per hectare as a result of active population control , and foro be low althougho be low ,24, checRattus rattus) occur in similar densities to possums, but because of their high rates of reproduction, population increase and reinvasion potential they are more difficult to maintain at reduced densities [Rats, predominantly ship rats compared to using 12 potential captures per site (68.6% of the population) would significantly affect the rate that the residual fast-breeding rat population could recover, and would therefore justify additional control effort. However, if rat densities were indeed high (10/ha and above) it would imply that either the control strategy being used had failed or, if an initial knockdown is required, that alternative control methods (e.g. poisons) should be used to achieve this.In our simulations we had assumed that the capture probability (i.e. g(0)) for possible single- and multiple-capture traps was equivalent, even though in practise most traps differ in their capture efficiency ,27. In oMaking choices between multiple-capture and single-capture traps will depend on their component cost as well as their relative capture efficiency as discussed above. The current price of the multiple-capture traps are $US140 compared to $US18.90 to $US114, if three single-capture traps are required per site. This cost difference provides the users with savings they could potentially invest in controlling pests over a greater area. Using single-capture traps also provides the user with greater flexibility\u2014for example, if the control area requires 100 trap sites, then when using multiple-capture traps 100 would be required. However, if using three single-capture traps at each site, 300 traps would be required, but as these do not have to be deployed in sets of three at each site they provide greater flexibility in locating traps throughout the control area and relocating some of them elsewhere if pest population densities are reduced to very low levels.Multiple-capture traps such as the Goodnature A12 and A24 might provide a cost-effective option for perimeter protection during a pest control operation, by reducing the rate that immigrants establish in a control area and at which these can contribute to the acceleration of population recovery . HoweverThe simulations used here for determining optimal trap use could also be applied to optimising toxin delivery in static bait-stations, and for testing trapping and bait-station strategies for other pest species, including those with an environmental impact within and beyond New Zealand . For example, if an acute toxin such as Feratox (potassium cyanide) is used in bait-stations , the sim"} +{"text": "Oral food challenge (OFC) is the most reliable method to diagnose food allergy in suspected children. The aim of this study was to describe the profile of patients undergone to OFC in the Division of Allergy and Clinical Immunology, Federal University of S\u00e3o Paulo, especially for cow\u00b4s milk (CM).A retrospective study of chart analysis of 171 patients undergone to 220 OFC, between June/2007 and Feb/2014. Food tests comprised CM, egg, soy, peanuts, nuts, seafood, meat, chicken, tartrazine, chocolate, wheat and coconut. Patients were evaluated according to the type of CM\u2019s challenge (open or double-blind placebo-controlled), aim of the procedure (diagnosis or follow up tolerance), symptoms, body mass index, time of breastfeeding, age at first reaction, family history of food allergy, presence of other atopic diseases and skin prick test.65% of patients were male (n=111) with median age of 3 years and 2 months. The most common tested foods were CM (n=148), egg (n=22) and soy (n=19). CM\u2019s challenges were: negative in 109 (74%), inconclusive in 4 (3%) and positive in 34 (23%) tests . From patients who had a positive OFC, 52% had referred cutaneous symptoms, 22% gastrointestinal symptoms, 19% respiratory symptoms and 7% claimed to have had anaphylaxis. When they undergone to OFC, cutaneous symptoms were observed in 68% and 5% had an anaphylaxis episode. 35% of children elicited symptoms after less than 1ml ingestion of CM. 67% of all reactions were classified as mild (skin and/or upper respiratory tract) and 18% as severe reaction (skin and lower respiratory tract). Among the group that passed OFC, 17% (n=18/109) were in a CM free diet just because of wheezing or recurrent respiratory tract infection.Although there are some difficulties in performing OFC in the routine, there are multiple discrepancies between referred symptoms and diagnosis of food allergies. CM responds for the great majority of food allergy in this population."} +{"text": "Oral food challenge (OFC) is the most reliable method to diagnose food allergy in suspected children. The aim of this study was to describe the profile of patients undergone to OFC in the Division of Allergy and Clinical Immunology, Federal University of Sao Paulo, especially for cow/s milk (CM).A retrospective study of chart analysis of 171 patients undergone to 220 OFC, between June/2007 and Feb/2014. Food tests comprised CM, egg, soy,peanuts, nuts, seafood, meat, chicken, tartrazine, chocolate, wheat and coconut. Patients were evaluated according to the type of CM's challenge (open or double-blind placebo-controlled), aim of the procedure (diagnosis or follow up tolerance), symptoms, body mass index, time of breastfeeding, age at first reaction, family history of food allergy, presence of other atopic diseases and skin prick test.65% of patients were male (n=111) with median age of 3 years and 2 months. The most common tested foods were CM (n=148), egg (n=22) and soy (n=19). CM's challenges were: negative in 109 (74%), inconclusive in 4 (3%) and positive in 34 (23%) tests . From patients who had a positive OFC, 52% had referred cutaneous symptoms, 22% gastrointestinal symptoms, 19% respiratory symptoms and 7% claimed to have had anaphylaxis. When they undergone to OFC, cutaneous symptoms were observed in 68% and 5% had an anaphylaxis episode. 35% of children elicited symptoms after less than 1ml ingestion of CM. 67% of all reactions were classified as mild (skin and/or upper respiratory tract) and 18% as severe reaction (skin and lower respiratory tract). Among the group that passed OFC, 17% (n=18/109) were in a CM free diet just because of wheezing or recurrent respiratory tract infection.Although there are some difficulties in performing OFC in the routine, there are multiple discrepancies between referred symptoms and diagnosis of food allergies. CM responds for the great majority of food allergy in this population."} +{"text": "In this study, we aimed to estimate one- to five-year survival rates in Iranian patients with gastric cancer (GC). In addition, we preformed subgroup analyses and meta-regression to explore possible sources of heterogeneity between studies.According to literatures, there has been increasing attention to the long-term survival rate in patients with GC in Iran. However, results have been inconsistent and remain controversial in overall survival rates. Literature searches were conducted using PubMed, Scopus, and ISI, as well as Magiran, Medlib, SID, and Iran Medex databases. Studies were pooled and summary one to five survival rates were calculated. Univariate and multivariate regression analyses were used to explore possible sources of heterogeneity among studies. Subgroup analyses were also conducted. Analyses were conducted using the STATA statistical software package.Final analysis of 29361 patients from 26 eligible studies was performed. The overall survival rate (one to five years) in all studies, by meta-analysis of 24, 14, 23, 12 and 22 studies were 52%, 31%, 24%, 22%, and 15%, respectively. Meta-regression analysis showed an increase in one- and five-year survival rate over the time and , respectively. Positive heterogeneity was observed between quality of papers and data sources (P<0.001). More than half of GC deaths happened in the first year at diagnosis, and another 30% plus they occurred during the second year after confirmed diagnosis. Our results admit lower survival rates in Iran, similar to other developing countries. Every year, 7 million lives are lost due to preventable and treatable cancers . IncidenMisdiagnosis is the greatest obstacle facing treatment of GC in Iran -10. In mIt is difficult to conduct population-based cancer studies in Iran, due to incomplete hospital records, careless registration processes, insufficient training, haphazard patient follow-up policies, and a lack of regional and provincial cancer centers. Inconsistent GC survival rates are also a prevalent feature in Iranian medicine, the lowest and highest of which were 81% and 21% According to our research, no recent systematic review has focused on GC survival in Iran. The present study intends to contribute to the extant literature by providing a systematic review and meta-analysis of one- and five-year survival rates in Iranian GC patients, and performing subgroup analyses and meta-regression to explore possible sources of heterogeneity among included studies. Through an electronic and manual search, 102 papers were identified . After e2= 98.5%, 95% CI 97.4\u201399.8) . Twenty-four eligible papers including 28949 patients were included in meta-analysis to estimate of one-year survival rate. The overall one year survival rate in patients with GC in Iran was 0.52 (95% CI: 0.52 to 0.53). A significant heterogeneity among these studies was observed .2 = 91.8% (95% CI: 90.1\u201393.5) . Subgrou.1\u201393.5) . AccordiUsing electronic searches, 102 papers were identified. After exclusion of reviews and duplicate articles and title screen, 43 separate publications remained for further appraisal. Remained articles, subsequent to abstract and full text review, we removed 17 publications according to the exclusion criteria and in the final data set consisted of 26 publications . InterprThe pooled participants in study were 29361 patients with GC . 2 = 98.5%, 95% CI 97.4\u201399.8) . Twenty-four eligible papers, including 28949 patients were included in meta-analysis to estimate one-year survival rate. The overall one-year survival rate in patients with GC in Iran was 0.52 (95% CI: 0.52 to 0.53). There was a significant heterogeneity among these studies . A significant heterogeneity among these studies was observed . Subgrou.1\u201393.5) . AccordiIn the present meta-analysis, we employed a large sample size to generate a reliable estimation of GC patient survival rates. We found a significant heterogeneity in our results, sources of which we explored using meta-regression and stratified subgroup analysis according to characteristics of the included studies. Our results showed that sample size and publication year were significant contributing factors to heterogeneity, where larger sample size and later year of publication were associated with a lower recorded rate of survival. In the present study, heterogeneity might result from different characteristics of patients, differing stages of disease progression, adjuvant treatment, duration of patient follow-up, or histological type. Due to limited resources in previous studies, we were unable to specify the role of these features that might contribute to disparate survival rates.Ultimately, 26 studies were incorporated into our meta-analysis. Estimation of overall survival rate, and the one- through five-year rates of 24, 14, 23, 12, and 22 were 52%, 31%, 24%, 22%, and 15%, respectively. These numbers indicate that more than half of GC deaths occurred within the first year following diagnosis, and another 30% took place during the second year. It is the greatest difficulty about patients with GC in Iran versus worthwhile clinical finding to correct rational strategies to address these problems. Various histological and demographic factors such as age, gender, surgery and treatment type, cancer site, grade of tumor, as well as metastasis have been found to impact the rate of GC survival in Iran. An investigation into risk factors associated with GC may help to reduce the probability of death in patients. Other strategies include a comprehensive follow-up plan for patients with premature signs of the disease, as well as the study and application of suitable treatments is lower than the survival rate in countries such as China (29.6%), the United States (37%), Switzerland (22%), France (30%), and Japan (40-60%)5% is low, 41. We As mentioned, a nationwide lack of cancer registry centers presents an additional obstacle to investigating GC in Iran, and the results of this study demonstrate this limitation. Although 64.4% of sources were derived from cancer registry data, the overall survival rates were lower than the results obtained from hospital records. Hospital records in developing countries are generally limited because data are missing, riddled with errors, or not deliberately gathered for the purpose of later scrutiny. Additionally, eligible patients for the present study were from one distinct hospital and could not represent all coverage patients in a population.The present meta-analysis expanded the number of participants to produce reliable and generalizable results regarding the GC survival rate in Iran. Limitations of this study were heterogeneity among 26 included studies, a scarcity of abstracts, and the inclusion of only 11 studies out of 102 gathered due to lack of available survival statistics. These limitations could impact the findings of this analysis. According to our research, more than half of GC deaths occurred in the first year after diagnosis, and another 30% took place during the second year. These findings support previous reports that suggest a poor diagnosis is the greatest challenge to GC patients in Iran."} +{"text": "The goal of this analysis was to determine the agreement between body mass index-based and cholesterol-based ten-year Framingham general cardiovascular disease risk scores among a convenience sample of 773 South Asian Canadian adults attending community-based screening clinics. Scores were calculated using age, systolic blood pressure, antihypertensive use, current smoking, diabetes, and total cholesterol and high density lipoprotein (for cholesterol-based risk) or height and weight (for body mass index-based risk). Mean risk score differences (body mass index-based risk minus cholesterol-based risk) were estimated using paired t-tests. Bland-Altman plots were used to assess agreement between scores. Finally, agreement across risk categories was examined using the kappa statistic. Average agreement between the two risk scores was quite good overall (mean differences of 0.6% for men and 0.5% for women), but increased to about 3% among participants 60\u201374 years of age. However, Bland-Altman plots revealed that the differences between the two scores and the variability of the differences increased with increasing average 10-year risk. In terms of clinical importance, the limits of agreement were reasonable for women < 60 years , but of concern for women 60-74 years , men < 60 years and men 6-074 years . Agreement across categories was moderate for most sex and age groups examined , except for men 60-74 years, where agreement was only fair (kappa = 0.26). In light of these disagreements, evaluation of a participant\u2019s change in cardiovascular disease risk over time will necessitate use of the same risk score at all screening sessions. Heart disease and stroke are the second and third leading causes of death in Canada, responsible for 21% and 6% of all deaths, respectively . InternaThe CVD burden in these high-risk populations has prompted the development of targeted strategies to identify and manage at-risk individuals. Participating in available programs can be challenging for SAs, however, because of language barriers, cultural differences, limited health literacy, lack of knowledge about or mistrust of available service, and circumstantial challenges such as lack of transportation or financial limitations \u20137. CommuAt baseline, Framingham general CVD risk scores were determined. The risk scores, developed by D\u2019Agostino et al , are calThis study received ethical approval from the University of Calgary Conjoint Health Research Ethics Board (Protocol Number E-24224) and the Health Canada and Public Health Agency of Canada Research Ethics Board (Protocol Number 2011\u20130034). All participants provided written informed consent.The University of Calgary research team was approached by SA community leaders to implement a national program similar to three local projects that addressed CVD risk reduction ,12,13. TFrom February through August 2012, 792 predominantly SA participants , 30\u201374 years of age with no prior history of CVD, underwent cholesterol-based screening at community-based clinics. Ethnicity was not directly assessed in the study but we estimate that 98% of the participants were of SA origin .Participants completed a brief health history questionnaire which assessed basic demographic data and self-report of: a prior history of heart disease or stroke; a physician diagnosis of, or prescription for, hypertension, high cholesterol, and/or diabetes; current use of any medication(s) for blood pressure, cholesterol and/or blood sugar; and current smoking status. They then underwent measurement of height, weight, blood pressure (BP) and random capillary total cholesterol (TC) and high density lipoprotein (HDL). Height and weight were measured using rigid tape measures and simple bathroom scales, purchased locally by each team. BP was measured using the BPTru , an automated device that yields a more reliable and accurate assessment of resting BP (when compared with 24-hour ambulatory measurement) than a manual measurement taken with a stethoscope and mercury sphygmomanometer ,16. To rQuestionnaire and measured health data were summarized using counts and percentages , means and standard deviations and medians, ranges and interquartile ranges . While the clinic volunteers calculated CVD risk using the paper-based charts published by D\u2019Agostino et al , for theFor each participant, the difference between the BMI-based risk estimate and the cholesterol-based risk estimate was determined (BMI-based risk minus cholesterol-based risk). Mean risk score differences and 95% confidence intervals (CIs) were estimated separately for men and women, and by the Framingham age categories used in the risk calculations, using paired t-tests.The differences were then examined using Bland-Altman plots . In a BlFinally, both sets of scores were categorized as low (<10%), moderate (10% to <20%) or high (> = 20%) risk. Agreement between BMI-based risk and cholesterol-based risk across categories was examined using the kappa statistic .Given that the Framingham risk functions that we used do not account for use of cholesterol medications, we repeated the analysis after excluding the 91 participants who reported hypercholesterolemia treatment. All analyses were conducted using Stata/IC 12.0 .Of the 792 participants who underwent cholesterol-based risk assessment, 773 (98%) had their height and weight measured, permitting comparison of cholesterol-based CVD risk with BMI-based CVD risk. Four hundred one women (52%) and 372 men (48%) 30\u201374 years of age (mean: 48.9 years) were included in this analysis. The majority of participants were not born in Canada, but of those, about half had lived in Canada for longer than 20 years . Ninety The average differences between BMI-based and cholesterol-based scores for women and men were 0.6% (95% CI: 0.3% to 0.8%) and 0.5% (95% CI: 0.0% to 1.0%), respectively. When examined by the age categories used in the Framingham calculations, the average differences were larger for both women and men in the three youngest age groups compared with those in the two older age groups (60\u201369 years and 70\u201374 years). Accordingly, the average difference was calculated for two age groups: < 60 years and 60\u201374 years. For women, the mean difference between the scores for those < 60 years was-0.1% (95% CI: -0.3% to 0.1%) compared with 3.1% (2.1% to 4.2%) for those 60\u201374 years. For men, the same pattern was observed. Mean differences were 0.1% (95% CI: -0.3% to 0.5%) among those < 60 years and 2.5% (95% CI: 0.4% to 4.5%) among those 60\u201374 years.While these differences suggest that BMI-based and cholesterol-based scores agree well on average, they offer no insight into our primary goal of determining whether or not the two forms of the general CVD risk score yield similar estimates of overall risk for a given individual. Bland-Altman plots showing the agreement between the two risk scores for men and women by age group are shown in Categorical agreement between the two risk scores is shown in Overall agreement in risk category classification was 80% for men . As with women, there was a tendency for BMI-based risk to be higher than cholesterol-based risk classifications. BMI-based risk categories were higher than cholesterol-based risk categories for 50 men (13%) and lower for only 26 (7%). Agreement across risk categories was 79% for men < 60 years . Among the younger men, 39 (13%) had higher and 25 (8%) had lower BMI-based risk classifications relative to their cholesterol-based classifications. None of the men 60\u201374 years were classified as low risk by either scoring system. Overall agreement among the moderate and high risk categories was 81% . Eleven (17%) classified as moderate risk according to their cholesterol-based measures were considered high risk based on their BMI-based scores, while 1 (2%) classified as high risk according to his cholesterol-based score was considered moderate risk based on his BMI-based score.As expected, when the 91 participants on cholesterol-lowering medication(s) were excluded from the analysis, the mean differences between BMI-based and cholesterol-based risk scores decreased slightly, most noticeably among older participants who were more likely to be on treatment. For women, the mean differences were 0.2% (95% CI: 0.0% to 0.5%) overall, -0.2% (95% CI: -0.3% to 0.0%) for those < 60 years, and 2.1% (95% CI: 1.1% to 3.1%) for those 60\u201374 years. For men, the mean differences were-0.1% (-0.6% to 0.4%) overall, -0.2% (95% CI: -0.6% to 0.2%) for those < 60 years, and 0.5% (95% CI: -2.0% to 3.1%) for those 60\u201374 years. For both men and women across both age groups, however, the limits of agreement on the Bland-Altman plots were essentially unchanged . Again, In our convenience sample of largely SA participants in a national screening program, average agreement between BMI-based and cholesterol-based 10-year general Framingham CVD risk scores at the group level was quite good overall, with average differences of 0.6% for women and 0.5% for men. These increased to about 3% among participants 60\u201374 years of age. Bland-Altman plots illustrating agreement between scores for individuals, however, revealed that both the differences between the two scores and the variability of the differences increased as the average of the two scores increased. In terms of clinical importance, the limits of agreement were reasonable for women < 60 years (-3.2% to 3.1%), but of concern for women 60\u201374 years (-6.0% to 12.3%), men < 60 years (-7.1% to 7.3%) and men 60\u201374 years (-13.8% to 18.8%). Considered from the perspective of low (<10%), moderate (10% to <20%) and high (> = 20%) risk, which is what our participants were counseled on, agreement as assessed by the kappa statistic was moderate to good among all sex and age groups examined, except for men 60\u201374 years, where agreement was only fair . LimitinIn our study, practical and budget considerations prevented us from standardizing the measurement of height and weight. Volunteers purchased bathroom scales and tape measures locally, and it was not possible to calibrate the scales or use the same models across the country. Accordingly, both BMI measures and BMI-based risk scores for some individuals may have been under- or overestimated. This, in turn, may have increased or decreased the observed differences between their BMI-based and cholesterol-based risk scores. However, BMI measurement errors were likely randomly distributed across the country and were not likely related to the measurement of any other variables used in the risk score calculations. Therefore, while the specific impact of BMI measurement error on the agreement between the two scores is unknown, it is unlikely that it contributed to any systematic differences between the BMI-based and the cholesterol-based CVD risk scores.Practical considerations also led us to measure BP only once among participants for whom the first reading was considered normal, whereas we took the average of the final five BPTru readings for all others. While we may have overestimated BP among participants with a single reading , this oFew publications have compared laboratory and non-laboratory based CVD risk scores, and to the best of our knowledge, none report on agreement among South Asians. D\u2019Agostino et al did not We selected the Framingham 10-year general CVD risk score because Perhaps most importantly, no published CVD risk prediction tool has been developed, validated or calibrated for any Canadian SA population. To do so would require population-based, longitudinal data on both risk factors and CVD events specific to SAs, data that are currently unavailable in Canada. We selected the two Framingham-based scores recognizing that they would provide general estimates of CVD risk, and we were careful to explain to participants that the extent to which the scores over- or underestimate risk for SAs in Canada is not known.An important component of our screening program will be the evaluation of change in CVD risk scores from baseline to follow-up. Accordingly, we needed to ascertain whether or not the two scoring tools we used similarly classified participants. While differences between scores were acceptable at the aggregate level, our Bland-Altman plots and comparison of categorical agreement show that the two risk scores cannot be used interchangeably in our study population.Further, in this analysis, we computed the two Framingham risk scores using the formulae as published . In pracIn light of the observed differences between the two risk scores as calculated, combined with the implications of adapting our scores, evaluation of a participant\u2019s change in CVD risk over time will necessitate use of the same risk score at all screening sessions. It will be important for both participants and volunteer counselors to understand that the CVD risk score is an estimate, and only and estimate, useful as part of a comprehensive risk factor assessment and risk reduction plan. As our SA community-based research partners consider the continuance of a simple and sustainable program, they will need to adopt a protocol that ensures consistent risk appraisal within individuals.Despite acceptable average differences in BMI-based vs. cholesterol-based Framingham ten-year general CVD risk scores in our SA convenience sample, only moderate agreement between the scores was found when risk was categorized as low, moderate or high. While disagreements occurred in both directions, BMI-based risk was assessed as higher than cholesterol-based risk more often than it was found to be lower. Accordingly, the two risk scores cannot be used interchangeably in our national, community-based screening program. Valid assessment of change in participants\u2019 CVD risk over time will require that one or the other be used consistently within participants who attend repeated screening sessions. Evaluation of the accuracy of either risk score in our population will require population-based longitudinal cohort studies among SAs in Canada."} +{"text": "Escherichia coli strains isolated from healthy Portuguese Gallus gallus was evaluated. Resistance profiles were determined against 33 antimicrobials by microbroth dilution. Resistance was prevalent for tetracycline (70%) and ampicillin (63%). Extended-spectrum beta-lactamase (ESBL) phenotype was observed in 18% of the isolates. Multidrug resistance was found in 56% of isolates. A subset of 74 isolates were screened by DNA microarrays for the carriage of 88 antibiotic resistance genes and 62 virulence genes. Overall, 37 different resistance genes were detected. The most common were tet(A) (72%), blaTEM (68%), and sul1 (47%), while 21% isolates harbored an ESBL gene . Of these, 96% carried the increased serum survival (iss) virulence gene, while 89% presented the enterobactin siderophore receptor protein (iroN), 70% the temperature-sensitive hemagglutinin (tsh), and 68% the long polar fimbriae (lpfA) virulence genes associated with extraintestinal pathogenic E. coli. In conclusion, prevalence of antibiotic resistant E. coli from the microbiota of Portuguese chickens was high, including to extended spectrum cephalosporins. The majority of isolates seems to have the potential to trigger extraintestinal human infection due to the presence of some virulence genes. However, the absence of genes specific for enteropathogenic E. coli reduces the risk for human intestinal infection.The presence of antimicrobial resistance and virulence factors of 174 The use of antibiotics as growth promoters in animal production has led to the development of major reservoirs of antibiotic resistance genes among bacterial strains that could enter the food-chain, leading to an increased risk for human health. In 2006, the European Union limited these types of drugs to prophylactic and therapeutic use .Gallus gallus represents the major section. However, a recent report revealed alarming rates of antibiotic resistance among Escherichia coli isolated from all types of fowl production [E. coli resistance to ampicillin reached 44.1%, 40.5% to ciprofloxacin, 50.8% to sulfonamides, and 45.2% to tetracyclines [According to the Eurostat, the overall production of poultry meat for human consumption in Europe in 2012 passed 11,000 tons, among which cyclines .E. coli, 57.4% of the strains were resistant to aminopenicillins, while 22.3% were resistant to fluoroquinolones [E. coli (APEC) strains, the virulence genotyping was similar to human uropathogenic E. coli (UPEC), suggesting a food-borne link between APEC and UPEC [According to the report of the European Centre for Disease Prevention and Control (ECDC), under the EARS-Net surveillance program, among human clinical and UPEC ,7.E. coli collected from poultry. Therefore, in this study we have examined the burden of antibiotic resistance and virulence factors harbored by E. coli isolates recovered from healthy Portuguese chickens. Isolates (n = 174) were examined for susceptibility to 33 antimicrobials of therapeutic relevance in humans and poultry infections. Subsequently, a subset of isolates (n = 74) demonstrating resistance to at least one antibiotic was screened for the presence of 88 antimicrobial resistance genes and 62 virulence genes by using a DNA microarray.To our knowledge, no data have been reported from Portugal regarding the resistance and virulence of n = 121, 70%), ampicillin , mezlocillin , moxifloxacine , and piperacillin .The susceptibilities of the 174 isolates were tested by Microscan, and 150 (86%) had resistance to at least one antibiotic in the panel and 24 (14%) were susceptible to all antibiotics tested. The number of isolates resistant to each antibiotic tested is presented in et al. [A lower frequency of resistance was detected against other antibiotics used in human therapeutics, such as trimethoprim-sulfamethoxazole (33%), gentamycin (17%), and amoxicillin plus clavulanic acid (17%). Resistance to cefotaxime was present among 21% of strains and associated with the production of ESBL. All isolates were susceptible to meropenem, ertapenem, imipenem, amikacin, and tigecycline. Multidrug resistance, defined as non-susceptibility to at least one agent in three or more antimicrobial classes , was detet al. .E. coli collection, a subset of 74 isolates presenting resistance to at least one antibiotic was selected for microarray analysis. Selected isolates were distributed over the study time and according to the proportions of the different production types. A total of 37 different resistance genes were detected in these isolates by microarray and each isolate harboured between two to fifteen genes. The most commonly detected genes were tet(A), blaTEM, and sul1 (tet(A) and tet(B) gene, respectively. Ten isolates were positive for a blaCTX-M group 1, one for a blaCTX-M group 2, and four for blaCTX-M group 9 genes. The integrase genes intI1 (43 isolates) and intI2 (two isolates) were also detected, which are associated with class 1 and 2 integrons, respectively.From the total and sul1 . In factiss, involved in the increased serum survival (96% of isolates); iroN, encoding a siderophore receptor (89% of isolates); the bacteriocin gene mchF (72% of isolates); the temperature-sensitive hemagglutinin gene tsh (70% of isolates); the fimbriae encoding gene lpfA (68% of isolates); and the polypeptide toxin gene cofA (46% of isolates). The gene gad, encoding glutamate decarboxylase, is a housekeeping gene used as a control.Virulence genes were detected by microarray in 73/74 isolates . Many isblaTEM, aadA1, sul1, tet(A), and intI1 and 8% presented blaTEM, aac6IbcatA1, sul1, tet(B), and intI1, all from intensive production.Overall, 50% of the multidrug resistance strains, for which the genotype was evaluated by microarray, presented between five to eight virulence factors and three to six antibiotic resistance encoding genes. E. coli from healthy poultry and their carriage of virulence determinants. The main objective of this study was to evaluate the concomitant presence of antimicrobial resistance genes and some virulence factors among E. coli strains isolated from Gallus gallus from Portuguese farms. We detected higher resistance frequencies to several antibiotics from different classes when compared to other European countries. Resistance to ampicillin (63% vs. 44%), cefotaxime (21% vs. 6%), gentamicin (17% vs. 4%), and tetracycline (70% vs. 37%) were higher than the average resistance among the ten members states that reported to EFSA. However, these Portuguese isolates presented a similar resistance profile to that described in Spain [E. coli infections. Again, this value was higher than those reported in most European countries, with the exception of Spain where 20.8% of isolates showed this co-resistance [E. coli strains [E. coli can colonize the human gut and constitute a reservoir for subsequent infection [E. coli collected from retail meat, especially poultry, to extraintestinal human disease. Many of these zoonotic isolates belonged to B2 and D phylogenetic groups, the most commonly found in human urinary tract infections. Thus, it was suggested that poultry could be considered one of the reservoirs of antimicrobial resistant E. coli causing human UTIs [To our knowledge, in Portugal there is a lack of reports on antibiotic resistance among fotaxime 1% vs. 6%in Spain . More thfotaxime 1% vs. 6% 63% vs. 4%, cefottamicin 1% vs. 4%,man UTIs . In thistet(A), blaTEM, and sul1 genes, which are common in clinical and non-clinical isolates [Prevalent antimicrobial resistance genes included isolates ,12,13. MThe use of antibiotics in poultry production, either prophylactically or for treatment, has been considered as a major contributor to the increased resistance frequencies detected among bacteria isolated from this type of samples. Among Portuguese poultry farms, fluoroquinolones have been detected at higher levels than the maximum residue level allowed , which cAntimicrobial resistance determinants detection by microarray supported the high resistance observed to beta-lactams and tetracyclines. Similar frequencies were observed in another study on poultry in China , while aE. coli in Portugal was 13% [et al. described a high incidence of blaCTX-M from group 1 among human UTI isolates [Gallus gallus strains is worrisome. Resistance to fosfomycin (in one isolate) associated with beta-lactam resistance mechanism blaCTX-M group 2, and aminoglycoside resistance mechanism aadB, could potentiate co-resistance in case of co-selection [ESBLs production was detected in 21% of samples. In 2012, ECDC reported that the frequency of ESBL among clinical was 13% , which helection . Despiteiss), a distinguishing trait of avian extraintestinal pathogenic E. coli (ExPEC) [iroN), the temperature-sensitive hemagglutinin (tsh), and the long polar fimbriae (lpfA) normally associated with ExPECs, including uropathogenic E. coli (UPEC) [iroN has been directly associated with human UTI, by allowing bacterial growth even under iron-limiting conditions which are found during the infection process [E. coli from UTI than commensal E. coli [lpfA has been described as an adherence determinant among E. coli O157:H7 [The virulence traits detected in this study revealed an almost total presence of the increased serum survival ( (ExPEC) . Other ii (UPEC) ,18. iroN process , while t E. coli . Finally O157:H7 .E. coli strains were found, such as eae (intimin gene), stx1 and stx2 (shiga toxins), or sta1 and sta2 . The gene astA coding for the heat-stable enterotoxin 1 was found in 13 isolates, but was the only gene of the enterotoxigenic E. coli (ETEC) pathogroup. These findings reduce the public health concern on acquisition intestinal pathogenic E. coli strains. For extraintestinal pathogenic E. coli (ExPEC), iroN was common but most isolates had no other gene from this pathogroup. Only one strain showed three of the five ExPEC genes represented in the array [None of the genes characteristic of human intestinal pathogenic fB/papB) .E. coli (APEC). It has been difficult to identify genes that define APEC strains. They cause different types of systemic extraintestinal infections probably derived from the combinations of virulence genes acquired by the causative bacterial pathogen, and host characteristics such as age and immune status. Johnson et al. tried to define a set of five genes to characterize highly pathogenic APEC [lpfA and tsh genes were very common but only one isolate had the hlyE gene and seven the iha. Three isolates carried three of the four APEC genes represented in the array. So, considering the current limitations of this microarray in representation of APEC genes, and the complexity in defining clearly which virulence genes characterize APECs as a pathogroup we have limited ability to predict the health risk for the chickens in this study; although this could be resolved by expanding the microarray in the future.Colibacillosis is a disease in poultry caused by avian pathogenic nic APEC . Neverthnic APEC . More renic APEC . In the iha) and bacteriocins (mchB and mchC) (r = 1.000), present in 9% of strains. In these strains, the presence of genes encoding resistance to at least two antibiotics combined with an adherence factor [E. coli for colonization and establishment of its niche in the urinary tract [Nevertheless, a strong statistical relationship was detected for the iron-regulated gene homologue adhesin (n = 174) originating from intensive meat production farms , intensive layers farms , intensive breeding farms , and extensive meat production farms were collected in central Portugal between November 2010 and November 2012. E. coli isolates were recovered from the carcasses (58%) or internal organs (42%) of the birds at the ControlVet laboratory using standard protocols, as defined in ISO 7251:2005 [Healthy chickens according to the Clinical and Laboratory Standards Institute guidelines (CLSI) . The antE. coli isolates were cultured overnight on Luria Bertani agar plates at 37 \u00b0C and DNA extracted by lysis as described previously [et al. [The eviously ,28. A mieviously and 60 geviously . Represeeviously ,28,29, aPearson\u2019s correlation was used to analyze the possible relationships among or between antimicrobial resistance phenotype, genotype, and virulence factors encoding genes. Statistical analysis was performed by the use of the statistical software SPSS .E. coli from the microbiota of healthy Portuguese chickens might have the potential to trigger human extraintestinal infection, although the risk of acquisition of specific enteropathogenic E. coli strains from poultry appears to be low. The high level of resistance to some antibiotics, including extended spectrum cephalosporins, and the frequency of multidrug resistance found compared to data from other European countries is worrisome and a more effective control on the prophylactic and therapeutic use of antibiotics in avian production is recommended.In conclusion,"} +{"text": "The serial founder model of modern human origins predicts that the phylogeny of ancestries exhibits bifurcating, tree-like behavior. Here, we tested this prediction using three methods designed to investigate gene flow in autosome-wide genotype data from 3,528 unrelated individuals from 163 global samples. Specifically, we investigated whether Cushitic ancestry has an East African or Middle Eastern origin. We found evidence for non-tree-like behavior in the form of four migration events. First, we found that Cushitic ancestry is a mixture of ancestries closely related to Arabian ancestry and Nilo-Saharan or Omotic ancestry. We found evidence for additional migration events in the histories of: 1) Indian and Arabian ancestries, 2) Kalash ancestry, and 3) Native American and Northern European ancestries. These findings, based on analysis of ancestry of present-day humans, reveal migration in the distant past and provide new insights into human history. Genetic data provide insight into the migratory history and geographic structuring of modern human populations. The recent origin of modern humans reflects migration from sub-Saharan Africa, with the oldest divergence event at approximately 140,000 years ago evident from analysis of Y DNA haplogroups13i.e., some ancestries may have formed due to a mixture process rather than a splitting process. Here, we investigate this possibility using three different approaches: analysis of the distance matrix using split decomposition analysisf3 and f4 statisticsAlthough most ancestries showed topological consistency in phylogenetic relationships assuming a strictly bifurcating or tree-like process, Cushitic ancestry showed unstable placement between East African and Middle Eastern ancestries34FST estimates between ancestries. This analysis revealed network-like behavior, with Cushitic ancestry appearing the most non-tree-like and misspecification of the topology . To further investigate network-like behavior in our data set, we used two approaches based on ancestry-specific allele frequencies. First, we estimated all 2,907 possible combinations of the f3 statisticf3 statistic is consistent with admixture, as well as isolation by distance. Of the 2,907 combinations, 273 were significantly negative after Bonferroni correction and , we estimated a median mixture proportion of 0.490 (IQR 1.604), indicating that Kalash ancestry is a mixture of 49.0% Northern European and 51.0% Indian ancestries. Similarly, we estimated mixtures of 37.1% Arabian and 62.9% Indian ancestries or 49.4% Levantine-Caucasian and 50.6% Indian ancestries. It is possible that Arabian, Levantine-Caucasian, Northern European, and Southern European ancestries are proxies for one ancestry. However, the distribution of Y DNA haplogroups in the Kalash people consists of 20.5% H and 25.0% L, common in India and South Asia, respectively, mixed with 18.2% G, 9.1% J, and 18.2% R1a, common in the Levant and the Caucasus, the Middle East, and Northern Europe, respectivelyConditional on one migration event, we observed the tree containing the subtree 71% of the time and the admixed . Using tf4 statistics and , we estimated a median mixture proportion of 0.412 (IQR 1.024), indicating 41.2% Nilo-Saharan and 58.8% Arabian ancestry. The f4 statistics and yielded 41.7% Omotic ancestry and 58.3% Arabian ancestry, suggesting that Nilo-Saharan and Omotic ancestries are nearly equally good proxies for one parent of Cushitic ancestry.Conditional on two migration events, we observed the tree containing the subtree 69% of the time . The secLevantine-Caucasian, Khoisan; Northern European, Native American) and , we estimated a median mixture proportion of 0.776 (IQR 0.916), indicating 22.4% Native American ancestry. Four f3 statistics supported Northern European ancestry as significantly admixed subtree 71% of the time . The thi admixed . The remSouthern European, Khoisan; Arabian, Indian) and , we estimated a median mixture proportion of 0.728 (IQR 1.582), indicating 27.2% Indian ancestry. It is possible that the second and fourth migration events are part of the same global-scale event, connecting India and East Africa. The migration event involving Kalash ancestry was also redefined to indicate specifically a mixture involving Northern European ancestry.Conditional on four migration events, we observed the tree containing the subtree 79% of the time . The fouStarting with five migration events, we observed positive log-likelihoods and the range of residuals stopped decreasing . DespiteAnalyses of ancestries of modern humans typically assume a divergence under isolation model. Here, we performed analyses of human ancestry explicitly allowing for gene flow. We found evidence for four migration events, including one that reconciles the origin of Cushitic ancestry that has been the subject of debate in the literature.Topologically, the distributions of graphs found by TreeMix were not unimodal. In the primary mode, Northern and Southern European ancestries were siblings, consistent with the distribution and genealogical relationship of Y DNA haplogroups R1a and R1b, respectivelyet al.The first migration event we detected is consistent with the distribution of Y DNA haplogroups in the Kalash people: H and L, common in India and South Asia, respectively, mixed with G, J, and R1a, common in the Levant and the Caucasus, the Middle East, and Northern Europe, respectivelyThe second migration event indicates that Cushitic ancestry is a mixture of ancestries closely related to Nilo-Saharan/Omotic and Arabian ancestries. This migration event resolves the observed unstable placement between East African and Middle Eastern ancestries341314To interpret the third migration event, we note that the main Y DNA haplogroups consistent with Native American ancestry pC\u2009=\u2009pX .Using We converted ADMIXTURE output for TreeMixThis project was determined to be excluded from IRB Review by the National Institutes of Health Office of Human Subjects Research Protections, Protocol #12183.How to cite this article: Shriner, D. et al. Ancient Human Migration after Out-of-Africa. Sci. Rep. 6, 26565; doi: 10.1038/srep26565 (2016)."} +{"text": "As the number of cyclists in Britain continues to grow , interesst 2011 and December 31st 2013 were identified from Intensive Care admissions, Emergency Department records, the Trauma Audit and Research Network and patient lists for the Trauma Ward.Cyclists with any head injury requiring admission to hospital between January 1After identification of the patient group, data was collected from emergency department and pre-hospital documentation, imaging, toxicology and Intensive Care documentation where relevant.93 patients were identified with an average age of 37. 89% were male. 54% were not wearing helmets, 20% were wearing helmets and helmet use was not recorded for 26%. The most common mechanisms of injury were cyclists vs car (41%) and falls (38%).There was no pattern of laterality in terms of intracranial or extracranial injuries. In those with intracranial injury 53% sustained contusions, 49% Subarachnoid haemorrhage, 38% subdural haematoma (SDH) and 23% extradural haematoma (EDH). Where helmet use was recorded no patients wearing a helmet sustained an EDH and only 1 had a SDH.25% of patients had a significant alcohol history or positive alcohol level where 27% had negative alcohol levels, the remainder had no levels sent.62% of those not wearing a helmet suffered intracranial injuries compared to 32% of those who were.Although numbers in this study are small these results suggest that helmet use is protective against intracranial injury.Additionally 25% of those admitted to hospital with head injury were intoxicated, suggesting that this a risk factor in serious cycling accidents."} +{"text": "Pulmonary involvement in juvenile dermatomyositis (JDM) is frequent and associated with poor outcome. However, a systematic assessment of pulmonary function and high-resolution computed tomography (HRCT) was rarely reported in this population.To assess pulmonary function and HRCT in JDM patients and to evaluate possible associations between pulmonary abnormalities and disease activity, cumulative damage and health-related quality of life (HRQL) scores.A cross-sectional study was performed in 20 JDM patients. Pulmonary function test included spirometry, body plethysmography and diffusion capacity for carbon monoxide (DLCO). They were also carried out six-minute walk test (6MWT) and HRCT scan. Disease activity score (DAS), childhood myositis assessment scale (CMAS), myositis damage index (MDI) and HRQL data were also assessedThe mean age was 11.6 years (6-18). Subclinical mild/moderate obstruction according to American Thoracic Society criteria was observed in 35% and DLCO was reduced in 20% of JDM patients. Spirometric and/or DLCO abnormalities were observed in 45% of patients. In plethysmography, reduced total lung capacity (TLC) and conductance were observed in 25% and 50% of JDM patients, respectively. In contrast, increased resistance and residual volume (RV)/TLC were evidenced in 10% and 35% of JDM patients, respectively. Thirteen patients underwent HRCT and 8 had alterations: interstitial lung disease in 6 and a mixed pattern in two. A positive correlation was observed between DAS and ratio between forced expiratory volume in one second and vital capacity (VEF1/CV) , conductance and HRCT score . A positive correlation was observed between CMAS and VEF1/CV , DLCO and 6MWT , and negative correlation between DAS and HRCT score . Correlations were identified between MDI and conductance , DLCO and HRCT score ; and between PedsQL and VEF1/CV , conductance and HRCT score . Correlations were also observed between HRCT score and VEF1/CV , forced expiratory flow between 25 and 75% of vital capacity (FEF25%>75 %) and conductance .Subclinical pulmonary abnormalities were frequent in this rare idiopathic inflammatory myopathy. Importantly, these findings may be related to disease severity and activity, and may influence HRQL of these patients.None declared."} +{"text": "Lyme borreliosis is the most common vector-borne disease in Europe and North America. The objective of this study is to estimate the incidence of tick bites and Lyme borreliosis, representative of our entire country, including erythema migrans, disseminated Lyme borreliosis and persisting symptoms attributed to Lyme borreliosis.A questionnaire on clinical diagnoses of Lyme borreliosis was sent to all GPs, company physicians, and medical specialists. To adjust for possible misclassification and telescoping bias, we sent additional questionnaires to categorize reported cases according to likelihood of the diagnosis and to exclude cases diagnosed outside the target period.Adjusted annual incidence rate for disseminated Lyme borreliosis was 7.7 GP reports per 100,000 inhabitants, and for persisting symptoms attributed to Lyme borreliosis was 5.5 GP reports per 100,000 inhabitants, i.e. approximately 1,300 and 900 cases respectively. GP consultations for tick bites and erythema migrans diagnoses were 495 and 132 per 100,000 inhabitants, respectively, i.e. 82,000 and 22,000 cases in 2010.This is the first reported nationwide physician survey on the incidence of tick bites and the whole range of manifestations of Lyme borreliosis, including persisting symptoms attributed to Lyme borreliosis. This is crucial for complete assessment of the public health impact of Lyme borreliosis.The online version of this article (doi:10.1186/s13071-015-0777-6) contains supplementary material, which is available to authorized users. Borrelia burgdorferi sensu lato species, and transmitted through tick bites. The disease most commonly manifests as erythema migrans, a slowly expanding skin lesion indicating early localized infection. If the infection spreads to other tissues and organs, it can cause disseminated Lyme borreliosis such as Lyme neuroborreliosis, Lyme arthritis, borrelial lymphocytoma, acrodermatitis chronica atrophicans, Lyme carditis or ocular manifestations. Occasionally, symptoms persist after treatment [Lyme borreliosis is an infectious disease caused by reatment . Marked reatment -4 and inreatment ,6. Assesreatment -4,7.Underreporting and misclassification are common to all surveillance systems, and if only high-risk regions are studied, data collections are not representative for whole countries. Particularly with Lyme borreliosis, surveillance is complicated due to the non-specific nature of some disease expressions and the pitfalls of laboratory diagnostics -4. The mIn the Netherlands, periodic nationwide cross-sectional retrospective studies among general practitioners (GPs) have revealed a continuing and strong increase in GP consultations for tick bites and erythema migrans between 1994 and 2009. The incidence of tick bite consultations increased linearly from 191 per 100,000 in 1994 to 564 per 100,000 inhabitants in 2009, and concurrently the incidence of erythema migrans diagnoses increased from 39 to 134 per 100,000 inhabitants -18. AparThe objective of the current study is to estimate the incidence of tick bites and the whole range of disease expressions of Lyme borreliosis, including erythema migrans, disseminated Lyme borreliosis and persisting symptoms attributed to Lyme borreliosis. To achieve this, we repeated our earlier nationwide GP surveys, this time including all manifestations of Lyme borreliosis, surveying all GPs, company physicians, and medical specialists who might be involved in the diagnosis of Lyme borreliosis.To rapidly assess a nationwide representative incidence rate for Lyme borreliosis, we performed a two-step approach. Firstly, a broad inquiry was required to also detect the less common disease manifestations. We sent a two-page retrospective questionnaire to all physicians possibly involved in the diagnosis and treatment of Lyme borreliosis in our country: 9178 GPs, 1321 company physicians , and 5374 medical specialists in hospitals including neurologists, dermatologists, cardiologists, pediatricians, rheumatologists, internists and ophthalmologists. Questionnaires were sent and returned by the postal service. A reminder was sent to non-responding physicians. The questionnaire inquired about consultations for tick bites and diagnosed erythema migrans in 2010. For the less common manifestations of disseminated Lyme borreliosis and persisting symptoms attributed to Lyme borreliosis, we requested clinical diagnoses for the two-year period of 2009\u20132010. The inquired manifestations of disseminated Lyme borreliosis included borrelial lymphocytoma, acrodermatitis chronica atrophicans, Lyme neuroborreliosis, Lyme arthritis, Lyme carditis and ocular manifestations, and diagnoses of persisting symptoms attributed to Lyme borreliosis, including Lyme encephalopathy and persisting symptoms after treatment for Lyme borreliosis.As every person in the Netherlands is registered with only one GP, we used the practice populations of reporting GPs to calculate incidence rates and national estimates of total numbers among the population of the Netherlands. As company physicians and medical specialists do not have a clearly defined patient population at risk, their questionnaires were only used for proportional comparison of reported numbers of tick bites and Lyme borreliosis. Physician responses to the questions on consultations for tick bites, erythema migrans diagnoses, and size of practice population were pre-coded in categories to which values were assigned based on the best fit of an assumed underlying negative binomial distribution. Incidence rates for the three categories of Lyme borreliosis were estimated per 100,000 GP practice population in 2010, and bootstrap 95% confidence intervals (95%CI) for the incidence rates were calculated by resampling of the GP reports 10,000 times. Bootstrap resampling was required, as the 95%CI for incidence rates should reflect the number of reporting GPs and each GP practice population combined, instead of the size of the practice populations over all reporting GPs. We screened questionnaires of physicians that reported the top 10% highest incidence of Lyme borreliosis, and excluded questionnaires with clearly deviating answers or unsatisfactory internal consistency .et al. [To establish case definitions, we adapted the clinical case definitions proposed by Stanek et al. with inpConsidering the complexities in the diagnosis of Lyme borreliosis, we categorized the cases of disseminated Lyme borreliosis according to the likelihood of diagnosis into \u2018very likely\u2019, \u2018likely\u2019, and \u2018possible\u2019 , representing a total practice population of 8.7 million persons, which is 53% of the 16.6 million inhabitants of the Netherlands. Among company physicians, the response rate was 30% (391/1321) representing one million employees, which is 14% of our country\u2019s labor force. Among medical specialists, the response was 35% . Table\u00a0The response rate to our validation questionnaire among GPs was 47% 855/1832) for the short questionnaire, and 20% (276/1399) for the long questionnaire. As shown in Table\u00a0 for the We estimated the adjusted annual incidence for a very likely diagnosis of disseminated Lyme borreliosis at 7.7 95% CI 7.2-8.2) per 100,000 inhabitants in 2009 and 2010. For persisting symptoms attributed to Lyme borreliosis, we estimated the adjusted annual incidence at 5.5 (95% CI 5.1-5.8) per 100,000 inhabitants. Consequently, the national number of patients annually seen by all GPs in 2009 and 2010 was estimated at approximately 1300 patients with disseminated Lyme borreliosis and 900 patients with persisting symptoms attributed to Lyme borreliosis , although the proportion of hospital diagnoses of erythema migrans from Northeastern France (60%) , and in Considering all GP-reported Lyme borreliosis, 4.7% of the diagnoses concerned disseminated Lyme borreliosis, and 3.4% concerned persisting symptoms attributed to Lyme borreliosis (see Figure\u00a0The current study demonstrates that nationwide representative incidence rates for GP reported tick bites and all manifestations of Lyme borreliosis can be obtained rapidly through a two-step approach of a cross-sectional retrospective questionnaire among physicians, followed by a validation questionnaire to adjust for possible misclassification and telescoping bias. We report the first estimations for the occurrence in the Netherlands of disseminated Lyme borreliosis and of persisting symptoms attributed to Lyme borreliosis, respectively 7.7 and 5.5 GP diagnoses per 100,000 inhabitants. These estimates are crucial for assessment of the public health impact of Lyme borreliosis."} +{"text": "Previous studies have reported an association between sun exposure and improved cutaneous melanoma (CM) survival. We analysed the association of UV exposure with prognostic factors and outcome in the National Clinical Melanoma Registry.Clinical and socio-demographic features were collected melanoma patients at diagnosis, together with information on sunbed exposure and sunny holidays. Analyses were carried out to investigate the associations between UV exposure and melanoma prognostic factors.From December 2010, we retrieved information from 3299 melanoma patients from 39 IMI sites geographically representative. 40% of the patients are over 60 years old, 52% are men, 49% live in the north of Italy and 56% are at high educational level (at least high school). 8% of the patients have melanoma familiarity and 55% have fair phenotype (Fitzpatrick skintype I or II). 2% have metastases and 11% lymph-node involvement. 8% have very thick melanoma (Breslow>4 mm) and 21% ulcerated melanoma.Holidays in the sun five years before CM diagnosis, among non-metastatic patients, were significantly associated with lower Breslow thickness (p=0.003), after multiple adjustment including socio-demographic status, degree of doctor making the diagnosis and residence. Sunbed exposure is not significantly associated with Breslow thickness.Holidays in the sun were associated with thinner melanomas. However, these results do not prove a direct causal effect of sun exposure on survival since other confounding factors, such as Vitamin D serum levels, may play a role."} +{"text": "Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. Patients in the study included retrospectively consenting adults who attended the emergency department of Lausanne University Hospital between February 2019 and August 2020 for a community-acquired LRTI, with available NP swab and a high-quality LRT sample. These samples were tested with the FilmArray PP (cutoff of \u2265104 copies/mL). Positive (PPA) and negative percent agreement (NPA) of FilmArray PP in NP swab were calculated, using (i) FilmArray PP in LRT sample and (ii) standard microbiological tests as reference standards. To assess the performance of a lower detection cutoff, NP samples were also tested with an in-house PCR (cutoff of \u226510 copies/mL) for S. pneumoniae and H. influenzae. Overall, 118 patients were included. FilmArray PP in LRT sample and standard microbiology tests detected S. pneumoniae in 19/118 and 12/118, H. influenzae in 44/118 and 19/118, and M. catarrhalis in 14/118 and 0/118, respectively. Using LRT FilmArray PP as reference, PPA and NPA of FilmArray PP on NP were 58% and 100% for S. pneumoniae, 61% and 100% for H. influenzae, and 57% and 99% for M. catarrhalis. Using standard diagnostic tests as reference, PPA and NPA were 58% and 96% for S. pneumoniae, 74% and 87% for H. influenzae, and indefinite and 92% for M. catarrhalis. Using a lower cutoff on NP (\u2265102 copies/mL), PPA was 68% for S. pneumoniae and 77% for H. influenzae with LRT FilmArray PP as reference. FilmArray PP in NP swabs has a limited PPA for identifying the most common etiologies of community-acquired LRTI irrespective of the reference standard, preventing its use for withholding antibiotics. The PCR detection cutoff does not explain the low PPA. The excellent NPA suggests the use of NP PCR results for rapidly targeted antimicrobial therapy.Timely identification of a pathogen in lower respiratory tract infections (LRTI) can support appropriate antibiotics use. The difficulty of obtaining lower respiratory tract (LRT) samples limits the utility of point-of-care syndromic molecular assays. We assessed the performance of the FilmArray Pneumonia plus panel (FilmArray PP) in nasopharyngeal (NP) swab for detection of IMPORTANCE Timely identification of a pathogen in patients with lower respiratory tract infections is of paramount importance to avoid inappropriate antibiotic prescription. We aimed to evaluate the performance of a rapid syndromic molecular assay in nasopharyngeal swabs for identifying the most common bacterial causes of lower respiratory tract infections in adults . Our data show that nasopharyngeal molecular assay has a good concordance with lower respiratory tract sample when positive but not when negative. A positive result is therefore concordant with a lower respiratory tract infection and can be used to target antibiotics. Nevertheless, a negative result does not have a good concordance, so it cannot be used to withhold antibiotics. Our findings illustrate the potential utility of these easily collected samples for the management of patients with lower respiratory tract infections. Lower respiratory tract infections (LRTIs) are one of the most common motives to attend emergency departments (ED) and the main reason for inappropriate antibiotic prescription . Timely Mycoplasma pneumoniae and Chlamydia pneumoniae in NP specimen of patients with community-acquired pneumonia (CAP) with negative percent agreements (NPA) of >90% but with wide differences in positive percent agreement using standard microbiological tests as gold standard in adults using (i) FilmArray PP in LRT sample and (ii) standard microbiological tests as reference standards. Our study also aims to test the performance of different PCR threshold cutoffs on NP swabs.Our study aims to define the performance of the FilmArray Pneumonia plus panel (FilmArray PP) in NP swabs for identifying the most common bacterial causes of LRTIs eligible with NP swab and LRT samples available, 1,708 (92%) were excluded . After excluding 22 patients because we did not find their samples, our study population consisted of 118 patients (27 from phase 1 and 91 from phase 2) .Median age was 71\u2009years , 43 (36%) patients were female, and 34 (29%) had chronic obstructive pulmonary disease (COPD) . OverallH. influenzae (16%), S. pneumoniae (10%), and influenza virus (10%) .Based on the standard composite microbiology diagnostic tests, 56% (66/118) of patients had a documented infection, while 44% (52/118) did not have any detected pathogen. A total of 39% (46/118) had a bacterium detected, 24% (28/118) a virus, and 6.8% (8/118) a virus and a bacterium. The most frequent pathogens were H. influenzae (37%), S. aureus (25%), S. pneumoniae (16%), M. catarrhalis (12%), enterovirus (25%), and influenza virus (14%) (Table S1).Based on the FilmArray PP in the LRT samples , 88% (104/118) of patients had a documented pathogen, while 12% (14/118) did not. A total of 76% (90/118) patients had a bacterium detected, 57% (67/118) a virus, and 45% (53/118) a virus and a bacterium. The most frequent pathogens were Based on the FilmArray PP in the NP swab, 82% (97/118) of patients had a documented pathogen, while 18% (21/118) did not. A total of 62% (73/118) of patients had a bacterium detected, 48% (57/118) a virus, and 13% (15/118) a virus and a bacterium. The most frequent pathogens are similar to those identified by FilmArray PP in the LRT samples (Table S1).Compared to standard microbiology, the FilmArray PP increased the diagnostic yield of bacteria by 95% (from 39% using standard microbiology to 76% using FilmArray PP in LRT samples).S. pneumoniae in 12 (10%), 19 (16%), and 11 (9.3%), H. influenzae in 19 (16%), 44 (37%), and 27 (23%), and M. catarrhalis in none, 14 (12%), and 9 (7.6%) patients, respectively. S. pneumoniae, H. influenzae, and M. catarrhalis. Using FilmArray PP in LRT sample, the performance for detecting the three bacteria was similar using a positive cutoff of >104 or >105 copies/mL. Concordance between standard and molecular diagnostic tests in LRT samples was high for S. pneumoniae and lower for H. influenzae (79%) and M. catarrhalis (88%).Standard microbiology and FilmArray PP in LRT samples and in NP swabs identified S. pneumoniae, H. influenzae, and M. catarrhalis in patients with community-acquired LRTI. We calculated the performance according to two reference standards. Using FilmArray PP on LRT sample as the reference standard, the PPA, NPA, positive predictive values (PPV), and negative predictive values (NPV) were, respectively, 58%, 100%, 100%, and 93% for S. pneumoniae, 61%, 100%, 100%, and 81% for H. influenzae, and 57%, 99%, 89%, and 94% for M. catarrhalis. Using the standard microbiology results as reference standard, the PPA, NPA, PPV, and NPV were, respectively, 58%, 96%, 64%, and 95% for S. pneumoniae, 74%, 87%, 52%, and 95% for H. influenzae, and undefinable, 92%, 0%, and 100% for M. catarrhalis.n\u2009=\u200955), the NPA of FilmArray PP on NP sample compared to the standard microbiology results as reference standard was not different .Considering only patients with a respiratory sample taken before antibiotics administration . The performance was similar to that with standard microbiology as the reference standard but also to that of in-house PCR on LRT samples.Hypothesizing that the performance of the PCR could be better with a lower positive cutoff, we performed an in-house PCR for The difficulty in obtaining high-quality sputum and the long time-to-result of standard \u201cculture-based\u201d microbiological analyses are major limitations for timely identification of a pathogen in patients with LRTI and tailored use of antibiotics. Our data show that molecular analyses in NP swabs for identifying the most common bacterial causes of pneumonia have a high NPA and a limited PPA, suggesting their utility to promptly use targeted antibiotics in case of positive results but not their utility to withhold antibiotics in case of negative results. Lowering the detection cutoff of the molecular analysis in NP swab only slightly improves the PPA.Few studies assessed the performance of molecular diagnostic tests on URT samples to identify the most common causes of bacterial community-acquired pneumonia. Comparison between studies is difficult, as they use different URT samples , different PCR targets, and different reference standards .S. pneumoniae, H. influenzae, and M. catarrhalis on a combination of URT samples (NP and OP) using the same molecular assay on high-quality sputum as reference standard in hospitalized patients with CAP: the first one, performed in the United States, found a PPA between 50 and 80% for arrhalis , and thearrhalis . Three s and 72% , 18. How and 72% . This malytA RT-PCR in NP specimens for S. pneumoniae diagnosis and standard microbiology as reference standard in patients with CAP, three studies confirmed the excellent NPA: two studies of patients in Western Europe with an NPA between 92 and 99% on a URT sample and high-quality sputum in hospitalized patients with CAP, a study performed in the United States and a study conducted in Kenya confirmed the high NPA , 20. Usi and 99% , 18 and and 99% .lytA in NP aspirate of patients admitted for CAP in Sweden found an increased PPA of the NP aspirate from 53% to 81% and a decreased NPA from 93% to 80% when lowering the detection cutoff value of the PCR (105 to 102 copies/mL) . Howeverigh NPA. \u201317. To oSurprisingly, considering only the respiratory sample taken before antibiotics administration as the reference standard, we did not find a better NPA of FilmArray PP on NP. This can be explained by a good performance of standard microbiology, as only 12 (10%) patients received antibiotics more than 48\u2009h before lower respiratory tract samples were collected.S. pneumoniae, H. influenzae, or M. catarrhalis in the NP swab of 38% of patients (45/118) who could have benefited from targeted antibiotics. However, because the first-line empirical antibiotic in patients with CAP is amoxicillin clavulanate, which is the treatment of choice of H. influenzae and M. catarrhalis, we expect an added value of a molecular test on the use of targeted antibiotics only in patients with S. pneumoniae (amoxicillin being the antibiotic of choice). However, only 9% (11/118) of patients had S. pneumoniae detected in the NP swab, limiting the potential impact of molecular tests in this CAP population.Various retrospective studies suggested the utility of molecular diagnostic tests on LRT samples to deescalate or discontinue antibiotics \u201311. The \u2013Our study has several limitations. The first one, which is shared by all similar studies, is the absence of a gold standard for microbiological diagnostic in LRTIs, limiting the evaluation of new diagnostic tests. For this reason, we evaluated the performance of an NP swab molecular test using two reference standards, (i) standard microbiological tests , which are validated diagnostics tests , and ii, 22, 23.Staphylococcus aureus isolates and Gram-negative enteric bacilli in patients with CAP who attended the University Hospital of Lausanne, a tertiary care center in Switzerland, and who had available NP swab and LRT sample during two periods: February to May 2019 (phase 1) and November 2019 to August 2020 (phase 2). We chose these periods because of the systematic use of NP swab in patients with respiratory symptoms during the flu season and the COVID-19 pandemic.Exclusion criteria were absence of LRTI , presencPatients\u2019 demographics, comorbidities, symptoms, vital signs, radiology reports (chest X-rays or CT scans), and laboratory test results performed at admission were retrospectively recorded using a standardized electronic case report form in Research Electronic Data Capture (REDCap software). A radiologist reviewed chest X-rays that had no report available.All respiratory samples were collected during routine care. Nurses performed the NP swabs (COPAN UTM with 3\u2009mL of medium) according to standard institutional guidelines. If a patient had several LRT samples available, we chose first the bronchoalveolar lavage, then the lung aspirate, and finally the sputum. All respiratory samples were kept at \u221280\u00b0C within 24\u2009h of collection. LRT samples were liquefied using a solution containing dithiothreitol to homogenize the specimens and improve the reliability of molecular tests, as described previously \u201331.\u20133.5: negative; 104, 105, 106, or \u2265107: positive) in DNA copies per mL for bacteria and as qualitative results (presence/absence) for atypical bacteria and viruses. We also tested all specimens with in-house real-time PCR on the automated molecular diagnostic platform of the Institute of Microbiology for (i) S. pneumoniae and (ii) H. influenzae using, respectively, lytA and rdB as targeted genes using two reference standards: (i) FilmArray PP in lower respiratory tract sample and (ii) a composite of standard microbiological tests .We calculated the PPA, NPA, overall percent agreement (OPA) , positivWe also calculated the performance of the FilmArray PP in NP swabs in a subgroup analysis: patients without prior use of antibiotics .Data were analyzed using RStudio software, version 1.3.1056 .All included patients signed a general consent form for research or provided written informed consent retrospectively. The study was accepted by the ethical commission of Canton de Vaud (Project-ID 2019-00961)."} +{"text": "Considering the early inequity in global COVID-19 vaccine distribution, we compared the level of population immunity to SARS-CoV-2 with vaccine uptake and refusal between rural and urban Kenya two years after the pandemic onset. A population-based seroprevalence study was conducted in the city of Nairobi (n = 781) and a rural western county (n = 810) between January and February 2022. The overall SARS-CoV-2 seroprevalence was 90.2% , including 96.7% among urban and 83.6% among rural populations. A comparison of immunity profiles showed that >50% of the rural population were strongly immunoreactive compared to <20% of the urban population, suggesting more recent infections or vaccinations in the rural population. More than 45% of the vaccine-eligible (\u226518 years old) persons had not taken a single dose of the vaccine (hesitancy), including 47.6% and 46.9% of urban and rural participants, respectively. Vaccine refusal was reported in 19.6% of urban and 15.6% of rural participants, attributed to concern about vaccine safety (>75%), inadequate information (26%), and concern about vaccine effectiveness (9%). Less than 2% of vaccine refusers cited religious or cultural beliefs. These findings indicate that despite vaccine inequity, hesitancy, and refusal, herd immunity had been achieved in Kenya and likely other African countries by early 2022, with natural infections likely contributing to most of this immunity. However, vaccine campaigns should be sustained due to the need for repeat boosters associated with waning of SARS-CoV-2 immunity and emergence of immune-evading virus variants. The COVID-19 vaccine has replaced the earlier mitigation measures as the most effective measure for controlling the spread of the SARS-CoV-2 virus and ending the public health and economic devastations brought about by the most severe pandemic since the 1918 influenza pandemic . For AfrWith vaccine availability addressed, Africa embarked on vaccinating at least 36 million eligible persons weekly from January 2022 to achieve the 70% coverage global target by June 2022 . Lack ofIn March 2021, one year after reporting its first COVID-19 case, Kenya rolled out the COVID-19 vaccination program, initially limiting it to frontline health workers, other essential services providers, and security personnel . While tWe conducted a cross-sectional survey among residents of urban (Nairobi city) and rural (Kakamega) counties of Kenya between The sample size was estimated at 768 persons per site as determined using the Fleiss formula with an Criteria for replacing selected households included households without a suitable respondent to grant consent, households whose head declined to grant consent, and if there was no household at the expected geocoordinates. Households without a competent adult or household head were revisited twice before being declared non-respondent. Replacement was carried out using randomly selected replacement households. Participants who were not home during the study visit were revisited within seven days during a time they were likely to be available.Data were collected from consenting participants using a structured questionnaire , programVenous blood samples for antibody assays were collected from each participant. The blood samples were collected using a sterile technique and shipped at 2\u20138 \u00b0C to the Center for Virus Research at the Kenya Medical Research Institute (CVR/KEMRI) in Nairobi, Kenya, for serum separation, testing, and storage. To detect both infection- and vaccine-induced SARS-CoV-2 spike protein antibodies, the Wantai SARS-CoV-2 total antibodies ELISA kit was used, while including extra validation steps previously described . Data were cleaned and analyzed using R Statistical Software, version 4.2.0 . Descripp < 0.05 and the 95% confidence level and calculated as previously described [Calculating seroprevalence of SARS-CoV-2, the unweighted SARS-CoV-2 seroprevalence was the proportion of the individuals positive for anti-SARS-CoV-2 antibodies, whereas the weighted prevalence was adjusted for age and sex to the population of the study county based on the Kenya National Census of 2019 . Seropreescribed . p-values with the outcome were determined. Explanatory variables that had a p-value < 0.2 were moved into the multivariable model. For factors associated with vaccine uptake and refusal, separate multivariable Poisson regression for two outcome measures were fitted to assess the independent associations with explanatory variables. In the univariable analysis, explanatory variables that were selected a priori were evaluated and the crude prevalence ratio and corresponding p-value < 0.05. Model goodness of fit was assessed by the Hosmer\u2013Lemeshow test. Multivariable regression was then applied to identify independent explanatory factors associated with the outcome variables and estimate the magnitude of the adjusted prevalence ratios (aPR) for the assessed factors. Model selection was conducted using the stepwise backward elimination method with the Akaike information criterion values used for model selection. The 95% confidence intervals (CIs) were computed for the aPR with statistical significance set at a This study was reviewed and approved by the Kenya Medical Research Institute Scientific and Ethical Review Committee (number SSC 4098) and the National Commission for Science, Technology, and Innovation (License number NACOSTI/P/21/13539). Additional ethical approval was provided by the University of Nairobi Institutional Review Board . Administrative approvals were provided by the Nairobi and Kakamega County health departments. All study participants provided written assents (for those aged 12\u201317 years) or consents (for those aged \u2265 18 years) before enrolment.We enrolled 1591 participants, 781 (49.1%) from the urban site with a median age of 29 years (IQR 20), and 810 (50.9%) from the rural site with a median age of 26 years (IQR 36). Overall, 29.9% (n = 476) of the participants were <18 years old, while 10.0% (n = 159) were \u226560 years, as shown in p < 0.001) when compared to <20% of the seropositive urban participants (p = <0.001). Serum samples from 1565 participants were tested for SARS-CoV-2 antibodies, 769 (49.1%) from urban and 796 (50.9%) from rural counties. The untested samples did not meet the quality control thresholds. Conclusive test results were obtained for 1537 (98.2%) participants, while the rest (1.8%) were indeterminate. The overall unweighted SARS-CoV-2 seroprevalence was 91.0% , while the weighted prevalence was 90.2% . In the urban county, the unweighted seroprevalence was 97.3% , while the weighted prevalence was 96.7% . In the rural county, the unweighted seroprevalence was 84.7% , while the weighted prevalence was 83.6% . The comparison of immunoreactivity against SARS-CoV-2 between participants from the two groups showed that 52.3% of seropositive rural participants were significantly more immunoreactive who were \u226512 years old, including 670 (53.4%) from the urban and 584 (46.6%) from the rural counties, participated in the assessment of COVID-19 vaccine knowledge, attitude, and uptake. Almost all participants were aware of the availability of the COVID-19 vaccines. Among those aware, 70.0% of urban and 74.2% of rural participants knew that it protected those vaccinated, however, only 39.2% of urban and 40.4% of rural participants knew that community vaccination might also protect people who did not receive the vaccine . Mass media was the most common source of vaccine information , and the most trusted . Other less used and trusted sources of information included government workers, healthcare workers, and churches, as shown in Over 90% of the participants agreed that vaccines were necessary, and that the government should make them available for everyone eligible .Of 1115 enrolled participants that were \u226518 years old and therefore vaccine-eligible, 52.4% (n = 326) of urban and 53.1% (n = 262) of rural participants had received at least one dose of the vaccine, despite widespread availability and public education of the vaccine at least 3 months before the study was conducted. Among vaccinated participants, 40.7% had received AstraZeneca, 35.3% received Johnson and Johnson, 12.6% received Pfizer, and 11.4% received Moderna. Reasons given for uptake of the vaccine included perceived high-risk health status , belief in vaccine effectiveness , and government directive on mandatory vaccination for certain groups , as shown in The vaccination rate among those previously diagnosed with COVID-19 was 81.8%, and 53.6% among those with chronic medical conditions. Although age, occupation, previous COVID-19 diagnosis, vaccine knowledge and attitudes were significantly associated with vaccine uptake on univariable analysis , only agAmong the 1115 vaccine-eligible participants, 47.9% (298/622) of urban and 46.9% (231/493) of rural participants had not been vaccinated. Among the eligible participants, 19.6% (122/622) of urban and 15.6% (77/493) of rural participants indicated that they would never take the vaccine. Key reasons for vaccine refusal included concern about its safety, side effects, and a lack of information . Although occupation, history of chronic breathing problems, source of COVID-19 vaccine information, vaccine knowledge and attitudes were significantly associated with vaccine refusal on univariable analysis , only paTwo years after the first case of COVID-19 was confirmed and six months after the widespread availability of vaccines, we found high levels (84\u201397%) of population immunity against the SARS-CoV-2 virus among both rural and urban populations of Kenya. This herd immunity was observed despite low levels (<55%) of vaccine uptake and high levels (16\u201320%) of vaccine refusal among the two populations. Widespread SARS-CoV-2 transmission across all communities in the country is the most plausible explanation for this herd immunity, an argument supported by the findings of significantly higher seroprevalence in urban (97.8%) than rural (85.9%) populations. Throughout the pandemic, Nairobi City, densely populated (>4 million people) with >65% of residents living in informal settlements, served as a hotspot of the pandemic . In contThe population immunity to SAR-CoV-2 reported in this study, which was higher than in studies conducted in Kenya during the early phases of the pandemic , reflectThe COVID-19 vaccination efforts faced considerable hesitancy, with <50% of the population having started receiving doses by February 2022, almost a year after the introduction of vaccines . Our stuOur study found up to 20% of the eligible population refusing to take the COVID-19 vaccine. While this proportion may not be large enough to prevent the achievement of herd immunity, it may create pockets of SARS-CoV-2 transmission and associated morbidities and mortalities in the future. The COVID-19 vaccine refusal levels reported in other African countries ranged from 6% to 61%; however, these studies often failed to segregate hesitancy from refusal . Among tThe study had some limitations. First, we did not verify the vaccination status of all participants who reported being vaccinated, possibly indicating that the vaccine uptake may have been lower that reported. Second, our serological test did not differentiate between infection- and vaccination-induced SARS-CoV-2 antibodies, which would have more clearly defined the levels of population immunity induced by the two pathways. However, given the introduction of multiple types of vaccines, the commonly suggested comparative ELISA between SARS-CoV-2 anti-spike protein and anti-nucleoprotein would not have provided a conclusive answer. Despite considerable COVID-19 vaccine hesitancy and refusal, Kenya and likely other African countries had achieved herd immunity by early 2022, with natural infections contributing almost 50% of this immunity. However, due to the rapidly waning SARS-CoV-2 immunity and emergence of immune-evading virus variants, vaccine campaigns with upgraded vaccines should be sustained globally. There is considerable vaccine hesitancy and refusal; however, its impact on controlling the pandemic appears minimal, with almost all participants having attained antibodies against SARS-CoV-2."} +{"text": "Thoracic radiotherapy (TRT) with concurrent chemotherapy is the standard treatment of limited-stage small-cell lung cancer (LS-SCLC). However, there is still a controversy surrounding the treatment strategy especially optimal dosing and fractionation schedule. Current practice patterns among Chinese oncologists are unknown.We surveyed 212 Chinese oncologists using a questionnaire including 50 questions designed by experienced oncologists. Questions covered demographic data, treatment recommendations, and self-assessed knowledge of guidelines or key clinical trials for SCLC. The chi-square test and Fisher\u2019s exact test were utilized to describe the result of the study.The response rate was 97% (207/212). Of all the respondents, 69% preferred TRT QD, 29% preferred BID, and 2% chose HFRT. For those who prefer TRT QD, 72% preferred a total dose of 60 Gy, followed by 15% opting for 66 Gy, 12% for <60 Gy, and 1% for 70 Gy. Of those who prefer BID, 79% preferred a total dose of 45 Gy, with 4% choosing 30 Gy, 8% choosing 50 Gy, 7% choosing 54 Gy, and 2% choosing >54 Gy. Regarding PCI, 82% of participants believed that PCI should be performed when treatment is completed and 13% believed that PCI should begin immediately after concurrent chemoradiotherapy. As for other therapies, 26% of participants choose concurrent anti-angiogenic therapy during SCLC treatment, and 49% recommended small-molecule TKI as the main anti-angiogenic therapy.Substantial variation exists in how Chinese oncologists approach TRT dosing and fractionation for LS-SCLC. Almost 70% of respondents reported administering TRT QD more often in daily work. The most common doses were 60 Gy QD and 45 Gy BID. Small-cell lung cancer (SCLC) is a highly malignant neuroendocrine tumor with strong invasiveness and rapid progression and accounts for about 15% of all lung cancers, and the incidence of limited-stage small-cell lung cancer (LS-SCLC) is about 33,000 people per year . ThoraciIn 1999, a survey from ECOG INT 0096) showed that while twice-daily TRT of 1.5 Gy in 30 treatments improved survival compared with conventional TRT, it still had a higher rate of local failure, as well as hematological and pulmonary side effects . However showed tMore recent assessments have been presented in response to the controversy. A multicenter retrospective review reported in the 2020 ASTRO annual meeting showed that a total of 804 patients with LS-SCLC was followed from 2000 to 2016 and divided randomly into 3 groups by different treatment strategies, including hypofractionated RT using 40 Gy in 15 fractions with once-daily treatment, standard RT using 50 Gy in 25 fractions with once-daily treatment, and hyperfractionated RT using 45 Gy in 30 fractions with twice-daily treatment. The analysis revealed no differences in OS across three commonly used RT regimens, while the use of hyperfractionated RT appeared to have a tendency of survival advantage . AnotherGiven the ongoing debates and progress of studies, we designed an online survey including the time and fractionation schedule of TRT for LS-SCLC, choices of prophylactic cranial irradiation (PCI), and angiogenesis inhibitors to learn how Chinese oncologists treat patients with LS-SCLC.Relying on the Chinese Anti-Cancer Association, we surveyed 212 Chinese oncologists using an online questionnaire including 50 questions designed by experienced oncologists. The questions covered demographic data, treatment recommendations including the timing of TRT, dose fractionation schedule, PCI, and angiogenesis inhibitor use. The questions also covered self-assessed knowledge of key clinical trials or guidelines of LS-SCLC, including NCCN guidelines, INT 0096study, CONVERT trial, and RTOG 0538 trial. The duration since residency training related to SCLC treatment is also included in the self-evaluation. All the participants were asked to provide their answers for each question and choose the reasons prepared. An \u201cother\u201d option was also provided for the participants to type their reasons.https://www.wjx.cn). The questionnaire link was sent to oncologists across the country to participate in this project using email. Invitations were sent in August 2021 and closed in October 2021.The data were collected through an online questionnaire developed by Wenjuanxing software . The chi-square test was used to identify differences between groups for categorical variables. Fisher\u2019s exact test was utilized to compare the correlation between two categorical variables. We sent 3,495 email addresses and received 548 undeliverable/failed automatic replies, 207 completed responses, and 5 inapplicable ones. Among the 207 participants, 206 are clinical oncologists from various levels of hospitals in China, and one is a student majoring in radiation oncology. Considering the rigor and credibility of the research, only the responses from 206 oncologists were analyzed. Among the 206 participants, there are 174 radiation oncologists, 31 are engaged in medical oncology, and one is an oncological surgeon. Of all the participants who completed the questionnaire, 5.8% of oncologists were from grade II hospitals while 94.2% were from grade III hospitals of which 86% oncologists were from grade III level A hospitals. The classification of all hospitals is based on the Chinese 3-tier classification system that recognizes a hospital\u2019s ability to provide medical care and medical education and conduct medical research. Of all the 206 oncologists, 76% were practicing for over 10 years after completing residency training, while 13% practiced for 5\u201310 years and 11% for 5 years. The characteristics of 206 oncologists who completed the survey are summarized in P = 0.002), the number of SCLC patients treated in the department (Fisher\u2019s exact P = 0.001), and the number of SCLC patients treated by their own (Fisher\u2019s exact P = 0.007). There were no statistically significant correlations between the preferred start time of TRT and other demographic characteristics of respondents, including geographic location (Fisher\u2019s exact P = 0.9) and years since residency training (Fisher\u2019s exact P = 0.5). However, the preferred start time was not strongly correlated with the actual start time of the TRT . For nearly a half of respondents (43%), the actual start time of TRT differed from their preferred time, in which 47% of oncologists started TRT later than they preferred to, while 53% started earlier. Oncologists in high-level hospitals are more likely to start TRT after two cycles of chemotherapy and have more stable choices in actual practice.In our questionnaire, 100% of participants recommended TRT in LS-SCLC patients. More than half of participants (65.5%) preferred to begin TRT after two cycles of chemotherapy, 26.7% preferred one cycle, and 7.8% preferred to start 3 cycles or later. When asked at what time most of their patients with LS-SCLC started TRT in actual practice, 66.5% of participants answered 2 cycles, 26.2% answered 1 cycle, and 7.3% said in 3 cycles or later. There was a statistical significance between the preferred start time of TRT and some of the demographic characteristics of participants, including practice setting , geographic location (Fisher\u2019s exact P = 0.51), and years since residency training (Fisher\u2019s exact P = 0.72). There was a statistical significance between the preferred fractionation schedule and the number of SCLC patients treated in the department (Fisher\u2019s exact P = 0.02) and by their own (Fisher\u2019s exact P = 0.03). Moreover, the preferred fractionation schedule was highly correlated with the actual fractionation schedule of TRT , meaning that actual practice frequently aligned with preference.Our questionnaire provided three options for the radiotherapy fractionation schedule: QD, BID, and HFRT. Approximately 69% of all the respondents preferred TRT QD compared with 29% who preferred BID fractionation and only 2% who chose HFRT recommended QD TRT, 1% supported BID TRT, and only one participant recommended HFRT, while 74.7% of radiation oncologists and 83.9% of medical oncologists utilize QD TRT more frequently in practice, with 23.6% vs. 9.7% who use BID TRT more frequently. There were no statistically significant correlations between the preferred fractionation schedule and demographic characteristics of respondents in either the radiation oncologist or medical oncologist groups, including practice setting , geographic location , years since residency training , the number of SCLC patients treated in the department , and by their own (Fisher\u2019s exact P=1.00).The results are summarized in For those who preferred BID TRT, 23 out of 60 (38%) reported that BID TRT coincided with the characteristics of SCLC proliferation, 35 (59%) chose BID therapy for the reason that BID TRT has been proved to be efficient by INT 0096 and CONVERT trial, and only 2 respondents (3%) noted that BID TRT may shorten the time of treatment for patients who can tolerate radiotherapy. Regarding the reasons for choosing the BID TRT, 44.8% of radiation oncologists and 22.6% of medical oncologists believed that it had proven efficacy, 39.7% of radiation oncologists and 64.5% of medical oncologists believed that it was more compatible with the proliferative properties of SCLC, and 15.5% of radiation oncologists believed that it was more effective for tolerating shorter treatment cycles for patients.Two of those who preferred HFRT said that HFRT met the recommendation of clinical practice, only 1 of them chose \u201cother.\u201dWhen administering QD TRT, more than two-thirds (72%) of the respondents preferred a total dose of 60 Gy, followed by 13% opting for 61\u201366 Gy, 13% for <60 Gy, and 2% for 70 Gy (P = 0.22), geographic location (Fisher\u2019s exact P = 0.71), the number of SCLC patients treated in the department (Fisher\u2019s exact P = 0.87), and the number of SCLC patients treated by their own (Fisher\u2019s exact P = 0.79) were not correlated with the choice of dose, while the preferred TRT dose was highly correlated with the years since residency training (Fisher\u2019s exact P = 0.009). Those experienced oncologists with over 10 years of experience after residency training were more likely to recommend doses of 45 Gy. For QD TRT, physicians with >10 years of experience after residency training and those who work in higher-level hospitals were more likely to recommend doses of 60 Gy . There were no statistically significant correlations between preferred TRT dose and demographic characteristics of respondents in either the radiation oncologist or medical oncologist groups, and P values were all higher than 0.05.For BID TRT, demographic characteristics including practice setting recommended PCI, 8 (3.8%) recommended that PCI is not necessary, while 16 (7.8%) chose \u201cnot sure.\u201d Almost all of the respondents (99%) required patients to have a routine head MRI before PCI, and only 54 (26%) recommended administrating memantine. For those who recommended PCI, 142 (79%) chose 25 Gy as the total dose, 37 (20%) recommended 30 Gy, and only 2 (1%) chose the \u201cother\u201d option.As for the timing of PCI, nearly 82% of participants thought that it should be performed when treatment is completed, 13% believed that PCI should begin immediately after concurrent chemo-radiotherapy, and 5% chose the \u201cother\u201d option.Respondents were more likely (78%) to recommend PCI in patients who achieve complete clinical response (CR) after chemotherapy, 20% recommended partial response, and only 2% recommended stable disease.P = 0.037, P = 0.005).In our study, 52 out of 206 (26%) participants recommended concurrent anti-angiogenic therapy, while 154 (74%) did not. For those who recommended angiogenesis inhibitors, 49% preferred small-molecule TKI as the main treatment, followed by VEGFR antibodies (35%) and ENDOSTAR (16%). Those who work in higher-level hospitals and have over 10 years of experience after residency training were more likely not to recommend concurrent anti-angiogenic therapy said they were \u201cunsure,\u201d 32 (16%) said they were \u201cnot recommended,\u201d and 84 (41%) said they would suggest immunotherapy with concurrent chemo-radiotherapy. When it came to those who preferred concurrent immunotherapy, 48 out of 84 (57%) said the target volume should be narrowed, 20 (24%) said the immunotherapy program should be altered with the radiotherapy and chemotherapy, 7 (8%) said PD-L1 only, and 9 (11%) chose \u201cother\u201d were enthusiastic about new developments in SCLC treatments. The last question is the proportion of patients with LS-SCLC treated according to the guidelines in China, and the results are summarized in In this study, 90% of participants recommended concurrent chemo-radiotherapy, and 92.2% chose to proceed TRT in cycle 1 or 2, which is consistent with NCCN guidelines, which require TRT to be administered concurrently with chemotherapy in cycle 1 or 2 . This reIn our study, 69% of respondents preferred TRT QD, 29% preferred BID fractionation, and 2% preferred HFRT. In actual practice, 76% chose QD TRT, 22 chose BID TRT, and 2% recommended HFRT, indicating that they were more inclined to choose QD TRT regardless of expert recommendations or in the actual practice process. This conclusion is consistent with the findings of a survey of US radiation oncologists on practice patterns of radiation dose and fractionation for LS-SCLC and conventional segmentation (CFRT), with HFRT and CFRT (60 Gy/30 or 66 Gy/33 fractions). The findings reveal that there is no difference in survival or toxicity between HFRT and CFRT, implying that HFRT might be used in place of CFRT . In the In this study, for high-level hospitals, such as grade III level A hospitals , oncologists who treat more LS-SCLC patients in their daily work are more likely to prefer QD TRT over BID and HFRT. This not only implies that QD TRT is a more popular fractionation strategy in China, but it also indicates that, as the number of patients requiring TRT grows, QD TRT is a way to maximize medical resources. This study investigated the selection among different specialties. Although the proportion of radiation oncologists who picked QD TRT was only 66.7%, with that of medical oncologists being 87%, the differences may relate to the small number of medical oncologists (only 31). Nonetheless, there was no statistical association between the choice of different fractionation schedules and the participants\u2019 fundamental information , and more data are still needed to draw accurate conclusions.The NCCN recommends 2.0-Gy fractions over 6 to 7 weeks for a total dose of 60\u201370 Gy for QD TRT and 1.5-Gy fractions over 3 weeks for a total dose of 45 Gy for BID . In AmerIn this study, almost all responding oncologists advised PCI and pre-PCI brain MRI for LS-SCLC patients for whom the disease was responding to initial therapy which met the recommendation of NCCN guidelines in which PCI should be performed especially for those who show complete or partial response to initial therapy . A randoAngiogenesis inhibition has been demonstrated to be an effective strategy in the treatment of a variety of tumors . CompareIn our study, two-thirds of respondents did not recommend concurrent anti-angiogenetic therapy for LS-SCLC patients. For those who recommended, small-molecule TKI was the most popular choice. Moreover, it may be due to the approval of anlotinib as third-line treatment for ES-SCLC in China. Further study is still needed to determine the survival advantage of angiogenesis inhibitors combined with concurrent chemotherapy or radiotherapy in SCLC patients.https://clinicaltrials.gov/ct2/show/NCT03811002).There was no evidence to suggest that radiotherapy with concurrent immunotherapy has benefits for SCLC patients. Randomized phase III trials, such as IMpower133 and CASPIAN, found that atezolizumab or durvalumab in combination with platinum-etoposide treatment enhanced overall survival in patients with advanced disease , 28, whiA large sample of radiation oncologists in the United States was investigated to better understand their decisions on the timing of radiation treatment beginning and fractionation schedule of LS-SCLC patients. Both US and Chinese data show that more oncologists actually recommend early concurrent radiotherapy with cycle 1 or 2 for patients with LS-SCLC, possibly due to NCCN guideline recommendation or data from clinical trials , meta-analyses, or systematic reviews supporting that early TRT can significantly improve patient survival . AccordiThis study has some limitations as well, such as a low response rate of just 216 valid replies. Furthermore, because the participants\u2019 replies to the questions may be subjective, they may be vulnerable to some mistake owing to participant bias. As a result, our findings should be interpreted with caution. Although this study investigated and examined the choice of oncologists in various specialties, it was not able to assess the choice of the surgeon since only one answer was obtained. Furthermore, due to the gap in the number of medical oncologists vs. radiation oncologists, follow-up studies are still required to extend the data and reach more accurate findings. Our team will continue to update the data in order to obtain more accurate and thorough results.The goal of this survey was to broadly sample oncologists in China on their management of LS-SCLC. Despite differences in LS-SCLC treatment plans, our survey found that most Chinese oncologists still follow the NCCN guidelines in practice, namely, early timing of (QD) TRT in 2.0-Gy fractions over 6 to 7 weeks for a total dose of 60 Gy with a universal endorsement of PCI and pre-PCI brain MRI practices recommended. This study created a practice pattern baseline for future clinical trials for patients with LS-SCLC, provided Chinese oncologists with an agreement on management, and was of reference significance for radiation oncologists worldwide in the treatment of small-cell lung cancer.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.CX: conceptualization, formal analysis, writing\u2014original draft. ML: methodology, writing\u2014original draft. XC, SY, and JC: data collection and curation, project administration. SZ, MC, NB, and XH: data collection and curation. JL, WZ, and PW: data collection. LZ and NL: supervision, validation, writing\u2014review and editing. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "According to the Legal Services Corporation, each year, 56% of older adults have at least one civil legal problem yet 87% receive inadequate or no professional legal help for their civil legal problems. Unmet legal needs can have cascading catastrophic effects on the health and well-being of older adults. To address this, we took the innovative approach of creating a Medical-Legal Partnership (MLP) within a community based social service agency on aging. MLPs have been successful by addressing the social determinates of health. However, previous studies have not investigated MLPs aimed at older adults. We used a single arm, pretest-posttest design to investigate the effects and feasibility of providing legal services to community dwelling older adults. The MLP served over 88 clients referred both internally from the agency as well as external partners. The participants had a mean age of 73, , were 60% female. African Americans represent 9% of the clients, 7% are Hispanic/Latino and 74% Caucasian. Additionally, 5% were veterans. 52% of clients were at or below the Federal Poverty line at baseline. 50% of clients reported greater financial stability as a result of legal services. 75% reported improved health of between 1 and 3 points on a 5 point likert scale . This pilot project demonstrates a successful intervention to work across professional silos coordinating lawyers, medical providers and social workers to better meet the legal needs of older adults by creating MLPs in social service agencies to support their well-being."} +{"text": "Although COVID-19 is a viral infection, it is known that antibiotics are often prescribed due to concerns about combined bacterial infection. Therefore, we aimed to analyze how many patients with COVID-19 received the antibiotic prescription as well as what kinds of factors contributed to it using the National Health Insurance database.We retrospectively reviewed claims data for adults 19 years of age and older hospitalized for COVID-19 from December 1, 2019 to December 31, 2020. According to severity classification of the National Institutes of Health guidelines, we calculated not only the proportion of patients receiving antibiotics but also days of treatment per 1000 patient days. In addition, we investigated the factors contributing to antibiotic use by linear regression analysis.Of the 55,228 patients, 47% were male, 55% were older than 50 years of age, and most patients (89%) had no underlying diseases. The majority were classified as having mild to moderate illness, with 11% and 5% having severe and critical, respectively. Antibiotics were prescribed in a total of 27% . While 74% of patients with severe illness and 88% of those with critical illness received antibiotic treatment, even 18% of mild to moderate cases were prescribed antibiotics. Fluoroquinolones were the most commonly prescribed antibiotics , followed by third generation cephalosporins and beta-lactam/beta-lactamase inhibitors as shown in Figure\u00a01. Older age, severity of disease and underlying medical conditions contributed to overall prescription rates as well as days of antibiotic use significantly (Table\u00a01).Although most of COVID-19 patients had mild to moderate illness, more than a quarter were prescribed antibiotics. Judicious use of broad-spectrum antibiotics is necessary for COVID-19 patients, considering the severity of disease and the risk of bacterial co-infection.All Authors: No reported disclosures."} +{"text": "We know little about differences between hospice enrollees with dementia co-existing with another terminal illness (like cancer), those dying from dementia , and those dying with no dementia. We used the National Health Aging and Trends Study linked to Medicare claims to compare characteristics, hospice use patterns, and care quality ratings. Among 1,105 decedent hospice-enrollees age 70+, we found 39% were dying with coexisting dementia, 17% from dementia, and 44% without dementia. In adjusted analyses, those dying with dementia had similarly high rates of functional impairment, higher rates of clinical needs, and worse measures of care quality compared to elders dying from dementia. Hospice use patterns were different for elders dying with dementia compared to elders without dementia. In summary, 56% of older hospice enrollees have dementia, mostly in addition to another terminal illness. Their differing hospice experience implies changes are needed to hospice care and policy."} +{"text": "Wound infection or so-called surgical-site infection (SSI) is a common occurrence after surgery. For some breast cancer patients, these infections can lead to delays in starting their onward systemic treatments such as chemotherapy and/or radiotherapy after surgery. More importantly, treatment delays in patients can lead to worsened overall survival. SSIs also have considerable negative impacts on financial and staffing resources in healthcare. The World Health Organization has recommended the usage of a surgical care bundle (SCB), which is a group of preventative measures that are effective in reducing SSIs. However, the impact of care bundles on SSIs has not been well documented in the context of breast cancer surgery. Therefore, we aimed to investigate the outcomes of SSI following the implementation of a surgical care bundle protocol for non-reconstructive breast cancer surgery.p = 0.15). The largest SSI rate reduction was seen in the subgroup that underwent breast conservation and sentinel lymph node biopsy (SLNB), from 18.8% to 9.8% (p = 0.01). In this multivariable analysis adjusting for patient and treatment factors, the implementation of SCB resulted in a statistically significant reduction in SSI risk . Conclusions: The implementation of a SCB could reduce the incidence of SSI in breast cancer surgery.Background: Surgical-site infections (SSIs) are the commonest cause of healthcare-related infections. Although a surgical care bundle (SCB), defined as a group of preventative measures, is effective in reducing SSIs, it has not been well documented in breast cancer surgery. We aimed to investigate the impact of SCB on SSI. Methods: A single-centre retrospective comparative cohort study between 2016 and 2020 was carried out. An SCB including eight different measures was implemented in October 2018 at Sahlgrenska University Hospital, Sweden. Patients who underwent non-reconstructive breast cancer surgery were included for analysis. The primary endpoint was SSI within 30 days after surgery. Results: Overall, 10.4% of patients (100/958) developed SSI. After SCB implementation, the overall SSI rate reduced from 11.8% to 8.9% ( Breast cancer is one of the most common cancers and the leading cause of death amongst females. Surgery is an important and effective treatment, either alone or together with endocrine treatment, chemotherapy, targeted treatments and radiotherapy. However, surgical site infection (SSI) is also a common complication in the immediate postoperative period, which can have negative impacts on patient safety, hospital resources and aesthetic surgical outcome of the breast. Postoperative SSI can also lead to delays in adjuvant treatments, which is associated with an increased risk of breast cancer recurrence ,2.Between 2013 and 2018, 34% of healthcare-related patient injuries in Sweden were due to infections, of which up to a third were classified as SSI. The reported overall SSI rate was 1% to 3% but there were no specific data relating to breast surgery ,6. Due tThere are multiple factors associated with increased risk of wound healing problems and SSI after breast surgery, including smoking, body mass index, diabetes and hypothermia ,8,9. RecA surgical care bundle (SCB) is defined as a group of strategies that can be implemented as part of pre-, intra-, or perioperative care routines to minimize SSI amongst patients undergoing surgery . The WorHowever, the impact of the care bundle has not been well determined in non-reconstructive breast cancer surgery. Therefore, in this study, the primary aim was to describe SSI and investigate the impact of implementing SCB on SSI amongst patients who had non-reconstructive breast conservation surgery (BCS) and mastectomy. Secondary aims included the adherence rate of SCB after implementation and potential adverse effects of SCB with reference to rates of thromboembolic events (pulmonary emboli and deep vein thrombosis), seroma aspiration, day surgery, re-operation and delayed start of adjuvant chemoradiotherapy treatment.In 2018, the WHO introduced thirty recommendations for preventing SSI, consisting of ten preoperative, fifteen intraoperative and five postoperative measures . In thisTM hospital database using infection International Classification of Diseases (ICD) code T81.4. The primary aim was to investigate the impact of SCB in reducing SSI using a multivariate analysis, adjusting for patient and tumour characteristics. This was a retrospective cohort study of patients who underwent non-reconstructive-related breast cancer surgery between January 2016 and December 2020 at Sahlgrenska University Hospital, Sweden. The SCB was implemented in October 2018. The period between November 2018 and January 2019 was considered an early SCB introductory phase and therefore excluded from the study. Patients with SSIs were identified through investigation of the electronic medical records (Melior) as well as by searching the Cognos AnalyticsThe primary outcome measurement was 30-day postoperative SSI adjusted for age, BMI, smoking, diabetes, types of surgery, NACT and seroma aspirations. Surgical site infection was diagnosed according to the Centre for Disease Control and Prevention criteria that include presence of erythema, localized swelling, pain, purulent discharge with or without fever, or positive bacterial culture, as well as diagnosis being made by a qualified physician . AdequatTM). The following operative ICD breast surgery codes HAB00, HAB40, HAC10, HAC15, HAC20, HAC22, HAC30, HAD30, HAF00, HAC99 and ZZR70, in combination with axillary surgery codes PJA10, PJD42 and PJD52, were used for searching the hospital database system , types of surgery, surgical care bundle measures, SSI, microbiological cultures, chemo-radiotherapy, tumour biology, reoperations, postoperative thromboembolic events, seroma aspirations, length of stay and time to start of adjuvant treatments, were registered retrospectively. p < 0.05 was used. Sample size calculation was not performed in this retrospective observational study.The study cohort was divided into two groups depending on time periods: before and after SCB implementation. The impact of SCB on SSI was analysed using SPSS version 28.0.1.0. Descriptive data for the variables were presented in absolute numbers and their percentages. Comparisons of proportions were calculated using the chi-squared analytical function. Risk factors for SSI were analysed using binary logistic regression using the Enter method including SCB implementation, age, BMI, smoking, diabetes, types of surgery, NACT and seroma aspirations. A statistical significance of Out of all 3232 patients operated with non-reconstructive breast surgery, a total of 1132 patients were identified from the hospital registry following the inclusion criteria. Of those, 174 were excluded: 133 patients from the first 3 months of SCB introduction (introduction phase), 17 patients who underwent implant-based reconstructions, and 44 patients who underwent complex partial oncoplastic reconstructive surgery. In total, 958 patients were included in the study analyses . p < 0.001), more mastectomies and fewer patients receiving NACT . Patient characteristics were not statistically significant different before and after SCB implementations based on age, menopausal status or smoking status. All patients with diabetes had well-treated and stable disease with no differences between both groups. However, in the pre-SCB implementation period, there were statistically significant fewer BCSs and HER2-luminal breast cancer subtypes of all included patients developed SSI. Microbiological cultures from wound or seroma aspirate were carried out in 53% (53/100) of patients with SSI but only 49.1% (26/53) showed clinically significant bacterial growth. Of these positive cultures with confirmed SSI, 84.6% (22/26) contained either staphylococcus or streptococcus bacteria.p = 0.15). When comparing SSI rates following different types of surgery, there was a statistically significant absolute reduction of 9.0% amongst patients who underwent BCS combined with SLNB, but a non-statistically significant reduction of 5.7% in SSI rate amongst patients who had BCS combined with axillary lymph nodal dissection (ALND). In comparisons of SSI rates amongst patients who underwent mastectomy, SCB implementation led to a non-statistically significant increase of 4.1% in those who had SLNB, and a decrease of 3.3% in those who underwent ALND. In further subgroup analyses of SSI rates in the NACT and non-NACT group, there were a non-statistically significant 4.4% reduction in SSI and 2.1% , respectively, after SCB implementation in both sites. These proportions were not statistically significantly different before or after SCB implementation (p = 0.32). Of all SSI cases, 7.7% (74/958) occurred in the breast, 0.5% (5/958) in the axilla and 2.2% (p < 0.001). Amongst the subgroups, there was decrease in SCB adherence of 10.1% (p = 0.09) for NACT and an increase of 42.4% (p < 0.001) for non-NACT. The changes in SCB adherence rates for individual preventative measures are also summarized in p = 0.87, respectively).An overall 22.0% of patients were already receiving SSI preventive measures on an ad hoc basis before the formal SCB implementation, with larger proportions in the NACT group (89.1%) compared with the non-NACT subgroup (12.4%) . Followip = 0.04) . Factorsp = 0.20). Likewise, there was a small but non-statistically significant increase in seroma aspirations after SCB implementation . Day surgery rates increased significantly . In contrast, there were non-statistically significant decreases both in re-operation rate due to bleeding and in the proportion of patients who started their adjuvant chemoradiotherapy within 30 days , respectively , while the overall absolute reduction in SSI rate did not reach statistical significance, which could be explained by various factors. Firstly, the fact that only 60% adhered to the SCB protocol despite formal implementation may have limited the care bundle\u2019s impact in reducing SSI. Secondly, we found an unexpected proportion of both NACT and non-NACT patients already receiving SSI preventative measures sporadically before the formal SCB implementation. These pre-existing measures amongst patients could have limited the overall impact of SCB on SSI when implemented. It could also partially explain the paradoxical effect of NACT being associated with decreased SSI risks. Alternately, there was suggestion that NACT has an unexplained protective effect against SSI [The primary endpoint with an adjusted analysis showed a decrease in the risk of SSI Gallagher et al. showed that preoperative antibiotics probably reduce the risk of SSI in breast surgery with a moderate grade of certainty . In contThis study showed that mastectomy was associated with an increased SSI risk when compared with BCS procedures, which was in line with some recent studies . HoweverOverall, there were no statistically significant adverse events in patient care following SCB implementation. Nevertheless, the reported small increase in seroma aspirations could potentially account for the low impact of SCB in reducing SSI as reported in our study. In addition, it was surprising to note that more patients had a delayed start of their adjuvant treatments following SCB implementation. The explanations for these treatment delays could be multifactorial, including patient and hospital resource factors. As this study was not aimed to investigate factors associated with treatment delays, we were therefore unable to accurately account for the potentially paradoxical relationship between SCB implementation and treatment delays.In summary, our study demonstrated that implementation of an SCB could lead to a reduction in risk of SSI in non-reconstructive breast cancer surgery when adjusted for BMI, diabetes, types of surgery, NACT and seroma aspirations. Further prospective studies with an optimally constructed SCB protocol could be beneficial to further investigate the true effectiveness of SCB in improving patient safety."} +{"text": "The current study was conducted to examine the percentages of cognitive skills deficits among Chinese children with developmental dyslexia. Via a systematic review, we collated twenty-two available studies on the proportion of cognitive skills deficits, including phonological awareness, rapid automatized naming, morphological awareness, orthographic knowledge, short-term memory and working memory, and visual and motor skills deficits, among Chinese children with developmental dyslexia. The results of a meta-analysis showed that the rapid automatized naming deficits are the core deficit of developmental dyslexia among Chinese children, with a pooled percentage of 44%. This is followed by orthographic knowledge deficits (43%), phonological awareness deficits (41%), morphological awareness deficits (40%), visual and motor skills deficits (33%), and short-term memory and working memory deficits (25%). At the same time, we compared the proportions of different locations, ages, standards and control groups. Developmental dyslexia, defined as a specific language-based disorder, is not attributable to a disorder of intellectual development, neurological disorder, lack of availability of education, lack of proficiency in the language of academic instruction, or psycho-social adversity. A percentage for developmental dyslexia has been reported as approximately 7% of the general population in western countries . In chinIn recent years, researchers have put forward various theories about cognitive deficits in Chinese dyslexia ,5. ExploA large number of studies in western countries show that phonological processing is the core deficit of developmental dyslexia. However, there are many differences between Chinese and pinyin characters, and researchers have different views on the core deficit of Chinese dyslexia. Ho examined patterns of cognitive deficits in dyslexia and found that 29% of children in the Chinese dyslexia group had phonological deficits, 57% had rapid automatized naming deficits, 42% had orthographic skills deficits and 27% had visual and motor skills deficits . TherefoIt can be observed from the above research that Chinese dyslexia has multiple language deficits, but the core deficit is still controversial among researchers. Understanding the core deficits of dyslexia can lead to targeted interventions and treatments. It is also important that clinicians have reliable prevalence estimates to gain an understanding of the proportion of individuals with developmental dyslexia who may meet the criteria for cognitive deficits at a given point in time, in order to appropriately assess and plan tailored treatment to maximize recovery outcomes. The study aim was to conduct a meta-analysis to estimate the percentage of cognitive deficits for developmental dyslexia in Chinese dyslexia. We reported the percentage for the different criteria. Furthermore, the study also wanted to identify which cognitive deficit is the core deficit in Chinese dyslexia.The articles for this meta-analysis were identified by searching the Web of Science (core collection) and CNKI. The combination of search terms applied included \u201creading dis* OR reading dif* OR poor read* OR developmental dyslexi*\u201d, \u201cindividual difference OR deficit OR subtype\u201d and \u201cChinese\u201d. The titles, abstracts, keywords and full texts were screened to determine whether the inclusion criteria were met. Databases including Web of Science and CNKI were searched to identify articles from inception to September 18th, 2021. The initial search yielded 2719 articles. The protocol for the systematic review was conceived based on the PRISMA 2020 Statement . It was The articles were included if (1) the type of study was experimental, including a group of native Chinese-speaking people with DD; (2) the percentage of cognitive deficits for Chinese developmental dyslexia were reported or can be calculated; (3) published in English or Chinese; (4) the studies are not duplicated in the existing literature; (5) different literatures came from the same sample, and the results with the most comprehensive reports and up-to-date data were selected. Articles were excluded if they were conference papers, review papers or qualitative studies. In addition, unpublished papers were not included, due to the difficulty of obtaining the full text and detailed information.The variables were discussed until a consensus was reached among all the authors. Then, two raters used the recorded variables to conduct the coding of all the articles. Across the total variable matrix, the mean inter-rater agreement coefficient (M.H. and H.L.) was 0.96. Any disagreements between raters were resolved by discussion with the third person (X.L.).For each study, the following variables were recorded: (1) the sample characteristics; (2) the definition criteria of cognitive deficits; (3) the type of cognitive deficits and percentages of different cognitive deficits. It is important to note that different cognitive skills may be measured using different tasks in different studies. In order to minimize the impact of the tasks, when a cognitive skill involved multiple tasks for evaluation, the average percentage in the various tasks was selected. p > 0.1, I2 \u2264 50%), the fixed effects model was selected for analysis. Otherwise, the random effects model was selected. A subgroup analysis was also performed to explore the possible sources of heterogeneity among studies. Publication bias was established based on the funnel plot and Egger test. For the meta-analysis results, p < 0.05 was considered as statistically significant.In the study, we used Stata Statistical 15.0 software, including summary estimation, forest mapping and publication bias assessment. If the heterogeneity was low .Publication bias was established based on the funnel plot and Egge2 to test the heterogeneity between studies. If the heterogeneity was low , the fixed-effect model was selected to estimate pooled percentage, otherwise, the random effect model was selected. We used IFor age, we divided the sample into two groups, with a cut-off age of 11. For the age group of children younger than 11 years old, 11 studies reported a pooled percentage of 41% (95% CI: 27\u201355%). The remaining six studies reported a pooled percentage of 38% (95% CI: 19\u201356%). For the type of areas, 12 studies reported ae pooled percentage of 49% (95% CI: 42\u201356%), with the sample from Mainland China. In addition, six studies reported a pooled percentage of 26% (95% CI: 5\u201347%), with the sample from Hong Kong, China. For the type of control group, fourteen studies used age-matched typically developing children as controls to confirm whether children with DD have phonological awareness deficits and reported a pooled percentage of 37% (95% CI: 26\u201347%). Two studies used reading-level-matched typically developing children as controls to confirm whether children with DD have phonological awareness deficits and reported a pooled percentage of 49% (95% CI: 38\u201359%). In addition, two studies used a cluster analysis and reported a pooled percentage of 64% (95% CI: 41\u201387%). For the criterion of deficits, ten studies used the cut-off criteria of 1.5 standard deviations below the mean on phonological awareness deficits screening and reported a pooled percentage of 36% (95% CI: 24\u201348%). Three studies used the cut-off criteria of 1 standard deviations below the mean and reported a pooled percentage of 31% (95% CI: 5\u201357%). Two studies used the cluster method and reported a pooled percentage of 64% (95% CI: 41\u201387%). A study used the criteria of 1.65 standard deviations below the mean and reported a pooled percentage of 47% (95% CI: 21\u201372%), a study used the criteria of 2 standard deviations below the mean and reported a pooled percentage of 40% (95% CI: 21\u201359%), and a study used the cut-off criteria of the mean and reported a pooled percentage of 73% (95% CI: 51\u201396%).In the age group of children younger than 11 years old, nine studies reported a pooled percentage of 46% (95% CI: 36\u201356%). The remaining seven studies reported a pooled percentage of 42% (95% CI: 32\u201353%). For the type of areas, nine studies reported a pooled percentage of 36% (95% CI: 29\u201343%), with the sample from Mainland China. In addition, seven studies reported a pooled percentage of 56% (95% CI: 51\u201361%), with the sample from Hong Kong, China. For the type of control group, 13 studies used age-matched typically developing children as controls to confirm whether children with DD have rapid automatized naming deficits and reported a pooled percentage of 48% (95% CI: 41\u201354%). Two studies used reading-level-matched typically developing children as controls to confirm whether children with DD have rapid automatized naming deficits and reported a pooled percentage of 28% (95% CI: 5\u201352%). In addition, one study used a cluster analysis and reported a pooled percentage of 37% (95% CI: 31\u201344%). For the criterion of deficits, eleven studies used the cut-off criteria of 1.5 standard deviations below the mean on rapid automatized naming deficits screening and reported a pooled percentage of 44% (95% CI: 34\u201354%). Four studies used the cut-off criteria of 1 standard deviations below the mean and reported a pooled percentage of48% (95% CI: 35\u201361%). A study used the cluster method and reported a pooled percentage of 37% (95% CI: 31\u201344%).In the age group of children younger than 11 years old, eight studies reported a pooled percentage of 40% (95% CI: 32\u201349%). The remaining three studies reported a pooled percentage of 51% (95% CI: 41\u201362%). For the type of areas, four studies reported a pooled percentage of 46% (95% CI: 29\u201364%), with the sample from Mainland China. In addition, seven studies reported a pooled percentage of 41% (95% CI: 34\u201349%), with the sample from Hong Kong, China. For the type of control group, eight studies used age-matched typically developing children as controls to confirm whether children with DD have orthographic knowledge deficits and reported a pooled percentage of 43 % (95% CI: 35\u201351%). Two studies used reading-level-matched typically developing children as controls to confirm whether children with DD have orthographic knowledge deficits and reported a pooled percentage of 31 % (95% CI: 22\u201341%). Furthermore, one study used a cluster analysis and reported a pooled percentage of 57 % (95% CI: 47\u201368%). For the criterion of deficits, seven studies used the cut-off criteria of 1.5 standard deviations below the mean on orthographic knowledge deficits screening and reported a pooled percentage of 43% (95% CI: 35\u201352%). Three studies used the cut-off criteria of 1 standard deviations below the mean and reported a pooled percentage of 33 % (95% CI: 24\u201342%). A study used the cluster method and reported a pooled percentage of 57 % (95% CI: 47\u201368%).In the age group of children younger than 11 years old, four studies reported a pooled percentage of 24% (95% CI: 0\u201348%). The remaining six studies reported a pooled percentage of 51% (95% CI: 35\u201367%). For the type of areas, the seven studies reported a pooled percentage of 37% (95% CI: 18\u201357%), with the sample from Mainland China. In addition, three studies reported a pooled percentage of 47% (95% CI: 23\u201371%), with the sample from Hong Kong, China. For the type of control group, seven studies used age-matched typically developing children as controls to confirm whether children with DD have morphological awareness deficits and reported a pooled percentage of 46% (95% CI: 28\u201364%). Two studies used reading-level-matched typically developing children as controls to confirm whether children with DD have morphological awareness deficits and reported a pooled percentage of 13% (95% CI: 6\u201320%). Furthermore, one study used a cluster analysis and reported a pooled percentage of 53% (95% CI: 47\u201360%). For the criterion of deficits, five studies used the cut-off criteria of 1.5 standard deviations below the mean on morphological awareness deficits screening and reported a pooled percentage of 44% (95% CI: 16\u201373%). Three studies used the cut-off criteria of 1 standard deviations below the mean and reported a pooled percentage of 35% (95% CI: 11\u201360%). A study used the cut-off criteria of 2 standard deviations below the mean and reported a pooled percentage of 16% (95% CI: 2\u201330%). A study used the cluster method and reported a pooled percentage of 53% (95% CI: 47\u201360%).In the age group of children younger than 11 years old, six studies reported a pooled percentage of 23% (95% CI: 13\u201333%). The remaining six studies reported a pooled percentage of 26% (95% CI: 17\u201336%). For the type of areas, five studies reported a pooled percentage of 28% (95% CI: 13\u201343%), with the sample from Mainland China. In addition, seven studies reported a pooled percentage of 23% (95% CI: 16\u201330%), with the sample from Hong Kong, China. For the type of control group, all twelve studies used age-matched typically developing children as controls to confirm whether children with DD have short-term memory and working memory deficits and reported a pooled percentage of 25% (95% CI: 18\u201331%). For the criterion of deficits, eight studies used the cut-off criteria of 1.5 standard deviations below the mean on short-term memory and working memory deficits screening and reported a pooled percentage of 26% (95% CI: 16\u201335%). Three studies used the cut-off criteria of 1 standard deviations below the mean and reported a pooled percentage of 25% (95% CI: 17\u201333%). A study used the cut-off criteria of 2 standard deviations below the mean and reported a pooled percentage of 16% (95% CI: 2\u201330%).In the age group of children younger than 11 years old, eight studies reported a pooled percentage of 31% (95% CI: 16\u201345%). The remaining one study reported a pooled percentage of 39% (95% CI: 16\u201361%). For the type of areas, five studies reported a pooled percentage of 35% (95% CI: 12\u201358%), with the sample from Mainland China. In addition, four studies reported a pooled percentage of 29% (95% CI: 23\u201335%), with the sample from Hong Kong, China. For the type of control group, eight studies used age-matched typically developing children as controls to confirm whether children with DD have deficits on visual and motor skills and reported a pooled percentage of 29% (95% CI: 18\u201340%). One study used reading-level-matched typically developing children as controls to confirm whether children with DD have visual and motor skills deficits and reported a pooled percentage of 24% (95% CI: 7\u201341%). In addition, one study used a cluster analysis and reported a pooled percentage of 65% (95% CI: 54\u201376%). For the criterion of deficits, five studies used the cut-off criteria of 1.5 standard deviations below the mean on visual and motor skills deficits screening and reported a pooled percentage of 31% (95% CI: 25\u201336%). Three studies used the cut-off criteria of 1.65 standard deviations below the mean and reported a pooled percentage of 15% (95% CI: \u22121\u201331%). A study used the cut-off criteria of the mean and reported a pooled percentage of 53 % (95% CI: 28\u201379%), and a study used the cluster method and reported a pooled percentage of 65 % (95% CI: 54\u201376%).After conducting a meta-analysis of all the available studies that adhered to our inclusion criteria (22 articles), we calculated the pooled percentages under different categories.We found that the rapid automatized naming deficits are the core deficit of Chinese developmental dyslexia, with a pooled percentage of 44% through meta-analysis. This is followed by orthographic knowledge deficits (43%), phonological awareness deficits (41%), morphological awareness deficits (40%), visual and motor skills deficit (33%), and short-term memory and working memory deficits (25%).It can be observed from the results that the incidence of rapid automatized naming deficits and orthographic knowledge deficits is relatively high in Chinese dyslexia. In a recent meta-analysis on the deficit profiles of Chinese children with reading difficulties, Peng et al. found that rapid automatized naming deficits and orthographic knowledge deficits may have a greater impact on developmental dyslexia than on any other skill deficits . This isCompared to the age-matched typically developing children, children with dyslexia have a higher percentage of rapid automatized naming deficit (48%). This is followed by morphological awareness deficits (46%), orthographic knowledge deficits (43%), phonological awareness deficits (37%), visual and motor skills deficits (29%), and short-term memory and working memory deficits (25%). However, compared to the reading-level-matched typically developing children, children with dyslexia have a higher percentage of phonological awareness deficits (49%). This is followed by orthographic knowledge deficits (31%), rapid automatized naming deficits (28%), visual and motor skills deficits (24%), and morphological awareness deficit (13%). According to the existing results, the percentage of rapid automatized naming deficits and orthographic knowledge deficits was relatively high, when the control group was age-matched typically developing children or reading-level-matched typically developing children. In addition, the percentage of visual and motor skills deficits and short-term memory and working memory deficits was relatively low. Since reading is a language activity, the deficits of dyslexia children were mainly related to reading language skills. So, researchers paid more attention to the linguistic cognitive deficits of dyslexia, such as phonological awareness deficits, orthographic knowledge deficits and rapid automatized naming deficits. However, in recent years, visual deficits have also been proposed as the core deficit of dyslexia. Bosse found in two studies of people in France and Britain that dyslexia did not seem to be due to phonological deficits and the visual attention deficit is likely to be the underlying cause of dyslexia . FrancesStudies have shown that age may influence the deficit profile of children with dyslexia . AccordiLocation may also be the reason for the difference in the incidence of cognitive deficits among dyslexic groups, as there are still many differences in spoken language, writing scripts and early reading instructions between Mainland China and Hong Kong . The perThe differences in the definition of a skill deficit may also lead to differences in incidence. Although most studies used standard deviation segmentation, some used 1 standard deviation lower than the control group, while others used 1.5 standard deviation or 2 standard deviation lower than the control group. However, this study did not find a trend of decreasing incidence with the stricter standards, which may be due to the fact that most of the existing studies were based on the cut-off score of 1.5 standard deviations, while the sample size of other standards was limited.Our findings are only based on the combined results of 22 articles, which is a small number of studies for a meta-analysis. This may be due to our poor search coverage and stringent screening criteria, which also reduce the reliability of the findings. In particular in the subgroup analysis, many groups involved only one study, which brings great challenges to the reliability of our research results. In addition, we paid more attention to language cognitive skills and general cognitive skills that affect developmental dyslexia, while higher-order cognitive skills, such as creativity, were not involved. However, some studies have found that dyslexia may be related to higher levels of creativity ,43. TherThe present study is the first meta-analysis to systematically investigate the core deficit among Chinese children with developmental dyslexia. Based on the above analysis, we found that the rapid automatized naming deficits are the core deficit of Chinese developmental dyslexia. In addition, the pooled percentages of orthographic knowledge deficits, phonological awareness deficits, and morphological awareness deficits among Chinese children with dyslexia are also relatively higher. The pooled percentages of short-term memory and visual and motor skills deficit are relatively lower. These findings could have important implications for the screening of developmental dyslexia. The accuracy of diagnosis could be improved through the measurement of cognitive skills of developmental dyslexia. Moreover, in the daily teaching of Chinese, we should emphasize rapid automatized naming, orthographic knowledge and phonological awareness and strengthen skills training to reduce the incidence of developmental dyslexia. Certainly, the findings support the multiple-deficit hypothesis in Chinese developmental dyslexia."} +{"text": "Mental disorders are a major public health concern. Genetic and environmental factors, both reflected in family health histories, jointly contribute to the onset of mental disorders. We examined the intergenerational transmission of mental disorders using objectively-measured family health histories from three generations.A population-based cohort study was conducted using administrative healthcare databases from Manitoba, Canada. The cohort included offspring who were 18 years or older between 1977 and 2020 with linkage to 1+ parent and 1+ grandparent. Mental disorders were identified using diagnosis codes from hospitalization and outpatient physician visit records and included mood and anxiety, psychotic, and substance use disorders. Logistic regression models were mutually adjusted for mental disorder history in grandparents, parents and/or siblings in addition to offspring demographics: sex, region, decade of birth and income quintile, and comorbidity. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were estimated.Out of 125,070 individuals, 59.1% were females and 57.8% were urban residents. 41,552 (33.2%) had a mental disorder during study period and 108,682 (86.9%) had a family member with a mental disorder history. Individuals were more likely to have a mental disorder if they had a family history: mother , father , sibling , grandparent . Compared with other mental disorders, psychotic disorders had the strongest association with family history: mother , father , sibling . However, there was no association between psychotic disorders and grandparent history .We observed a strong association between mental disorders family history across three generations and the risk of the mental disorders in offspring. This association was observed for all the investigated mental disorders. This work highlights the value of multigenerational data linkage in understanding the intergenerational transfer of mental disorders."} +{"text": "The Covid-19 pandemic disrupted service access and use for many older adults aging in place. This study focuses on understanding how a rural \u201cVillage\u201d, where services are primarily provided by volunteers to older adults, adjusted to Covid-19. The sample is drawn from service users of at least one or more services between January and October 2020 (N=233). Survey and qualitative data were gathered via telephone-interview (N=80). This study examined (1) the impact of Covid-19 on service use and ability to stay at home, 2) services offered, and 3) changes to day to day life. In the sample, 53.75% is 80+ in age, 70% female, and 43.75% lived alone. 15% of respondents reported reduction in service used, 10% an increase, 65% no change, and 6.25% used no services. Some services such as rides to medical care, and grocery delivery increased, other services were reduced. 26.24% respondents believed that the organization\u2019s services helped them stay at home during Covid-19. Other services were developed to better serve older adults such as phone reassurance and expansion of delivery of medication and food. Open ended responses identified how Covid-19 impacted day to day life. While many reported negative ways such as changing mental health perspectives and limiting medical care, others report life being more peaceful and providing time to enjoy nature. Findings provide an understanding that services while disrupted continued for one volunteer organization with some service users showing resilience in their day to day lives."} +{"text": "A longitudinal study to prevent self-neglect among at-risk, older (age 60+) or disabled (age 18+) healthcare patients was conducted collaboratively by a gerontological research institute, a health care system, and Texas Adult Protective Services (APS). Selected patients (n = 285) from 19 primary care clinics received targeted case management services for four months by a trained social worker. Their median age was 70, 72% were Hispanic/Latino, 79% had a high school education or less, and 73% had monthly income less than $1,361. A screening tool was used to identify adult maltreatment during baseline and posttest interviews. Consistent with national prevalence rates, 86% of participants at baseline, and 90% at posttest, reported they had not recently experienced abuse. In this sample, we found a significant decrease in mean scores on the screening tool from baseline to posttest ; t(241), p < 0.05. Six of the seven participants reported by project social workers to APS had at least one allegation of self-neglect. APS administrative data were also examined and included another 10 study participants reported to APS during the study. In total, 21 reports were made, with 26 allegations of maltreatment, of which 35% were validated, all for self-neglect; 70% of self-neglect allegations reported by project social workers were validated. Results suggest that targeted case management services could reduce the incidence of self-neglect. Similar targeted interventions may help to identify, report, and address other forms of adult maltreatment."} +{"text": "The COVID-19 pandemic has been causing relevant public health and psychosocial consequences.To assess the impact of the COVID-19 pandemic on mental health, lifestyle and personal relationships in the Italian general population.An online survey spread between May and June 2020 to collect socio-demographic, clinical, lifestyle, relationship, and mental health self-reported information. Mental disorder screening was performed by the Patient Health Questionnaire and PTSD Checklist for DSM-5.Participants were 2003, 1504 of which (75%) completed the entire questionnaire . Among the completers who have not had any mental disorder before , 263 (51.7%) met cut-off scores for psychiatric diagnoses on the self-report psychiatric screeners during the pandemic . In line with this, 39% of completers complained of insomnia, while 12% and 10% started using anxiolytics and antidepressants, respectively. Approximately 7-8 % of completers started/increased alcohol and/or nicotine consumption, 33% quitted/decreased physical activity, and 40% declared decreased sexual satisfaction. Approximately 21% and 38% declared worsening in relationship with partner and difficulty in child-caring, respectively.The COVID-19 pandemic appears to be a risk factor for new onset of mental disorders and worsening in lifestyle and familial relationships in the Italian population. These results should be confirmed by clinical interviews, and may represent a starting point for further monitoring of the medium and long-term consequences of the COVID-19 pandemic.No significant relationships."} +{"text": "The extent of the psychological impact of the pandemic is still unfolding. Despite existing literature, most studies lack rigor. We assessed the longitudinal rate of intra-individual change in maternal depression symptoms from before to after COVID-19 onset among US mothers enrolled in a home visiting program with robust adjustment for family contextual factors. We hypothesize that the rate of change in maternal depression symptoms increased after the pandemic onset.Eligibility included mothers with \u22651 depression assessment both prior to and after March 16, 2020; thresholds of \u2265 13 on the Edinburgh Postnatal Depression Scale and \u226510 on the Patient Health Questionnaire-9 identified probable depression. We used a generalized linear mixed effects longitudinal model with a random intercept and random slope for time (years) to analyze probable depression (event=\u2018Yes') pre- and post-COVID. Covariates for model estimation were based on the literature and theory.Our cohort of 3,431 mothers included 43% non-Hispanic White, 21% non-Hispanic Black, and 31% Hispanic races/ethnicities; 58% from rural/small towns, 18% Spanish-speaking, 63% with one child, median age of 29 and median 2 years follow-up. Households included: 82% low income, 24% low education, 10% insecure housing, 29% single parents, 21% mental illness, 10% substance abuse, and 8% domestic violence. Fourteen percent screened positive for depression pre-COVID, and 10% post-COVID. Depression was significantly higher pre- versus post-COVID, with no significant difference in the rate of change over time. Significant variables (p < 0.05) associated with depression included race/ethnicity, region of the country, number of home visits, mental illness, substance abuse, and domestic violence.After controlling for family contextual factors, we did not find a significant increase in maternal depression post-COVID-19. Additional research is needed to examine subgroups and the timing of events.\u2022\u2002The extent of the psychological impact from the pandemic is still unfolding.\u2022\u2002It is difficult to fully articulate its effects without rigorous, longitudinal research designs."} +{"text": "The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused the 2019 global Coronavirus disease (COVID-19) pandemic. A high disease burden, increasing hospitalization rates, and daily mortality numbers were reported in many countries during the initial waves of the pandemic. In the absence of specific prevention and therapy, non-pharmaceutical public health interventions targeted social distancing, contact reduction and universal masking to contain infections . FurtherPublicly available data on reported infections, deaths, and vaccinations were analyzed to study this question in the German population (eRef 1). Infections and vaccinations were recorded cumulatively as a proportion over time. Case fatality (CF) over time was calculated from the 7-day average data for infections and deaths. This was compared with the cumulative course for the first, second, or booster vaccination and infection rates.Ultimately, the German vaccination campaign was initiated focusing on vulnerable persons and healthcare workers (HCWs) on December 27, 2020. Within the following 8\u00a0months, 60% of the population received at least one vaccination, while a CF reduction from 4.5% to approximately 0.5% was observed. While from September to November 2021, an increase in CF to 1% was observed, from September 2021 onwards, a national booster campaign was carried out, focusing on vulnerable persons at risk of severe COVID-19 and the HCWs.Between mid and end of December 2021, the Omicron spread increased to 70%, while at the same time, CF decreased from 0.75% to 0.5%. With Omicron infections rising rapidly thereafter, CF dropped to 0.1% simultaneously Below is the link to the electronic supplementary material."} +{"text": "In 2019, Thailand legalized cannabidiol (CBD) for intractable epilepsy. The purpose of this study was to collect information regarding the experience and knowledge of CBD use in pediatric epilepsy. To the best of our knowledge, this is the first CBD survey in pediatric epilepsy in Southeast Asia.We performed a cross-sectional survey among all parents of pediatric epilepsy patients seen in the Pediatric Neurology Clinic at Phramongkutklao Hospital, Bangkok, Thailand between November 2018 and July 2020. The survey comprised 34 questions that assessed the demographics, knowledge, experiences, and opinions of parents/guardians regarding CBD use. The results were summarized using descriptive statistics. In addition, logistic regression was used to predict the factors for CBD use.Overall, 166 respondents (100%) participated in the study. Among the respondents, 9% have experienced using CBD; 56.25% of these reported reduced seizure frequency. CBD products were mostly obtained from folk healers (31.25%) and foreign products (25%). Common adverse effects included headache and nausea (31.5%). The number of anti-seizure medications , knowledge of CBD as treatment for epilepsy , and knowledge of CBD side effects were factors significantly associated with CBD use. Regarding CBD knowledge, our survey showed 80.72% of the respondents did not know the CBD compound for treating epilepsy, and 89.16% were not aware of CBD side effects. Interestingly, despite a lack of knowledge, 77.11% of the respondents expressed willingness to participate in future CBD trials.Our survey highlights that half of the parents of patients who previously used CBD reported reduced seizure frequency; however, none became seizure-free. Additionally, there were gaps in knowledge regarding the use of CBD. These findings suggest that the implementation of cannabidiol knowledge is crucial for both public and healthcare professionals. Survey limitations due to the retrospective nature of the self-report could have resulted in recall bias. Despite the development of new anti-seizure medications (ASMs), 30% of pediatric epilepsy patients remain refractory to treatment; these cases are considered as having drug-resistant or intractable epilepsy . Descriptive statistics, including means, standard deviations, confidence intervals, and simple percentages, were used to describe the demographic data, knowledge, experiences, and reasons for using CBD. Each independent variable was first entered into a univariate binary logistic regression analysis. Variables that predicted cannabis use with a degree of significance of There were 166 respondents (for 166 patients), and many of the respondents were from the central region (66.27%). The demographic information of the respondents is shown in Table The patients were mostly male (54.22%), and their ages ranged from 3 months to 18 years . The patients had received a median of two ASMs concomitantly.Among the patients, 9.64% (16/166) and 3.61% (6/166) previously used and are currently using CBD, respectively.Among those who previously used CBD, 56.25% (9/16) reported reduced seizure frequency and ASMs. The main reasons for CBD use were to manage treatment-resistant epilepsy and because it was recommended by an acquaintance . CBD products were obtained from folk healers and foreign products . Interestingly, 81.25% (13/16) of patients who previously used CBD were not aware of the composition of CBD products.The most common type of CBD product used in treating epilepsy was CBD oil followed by boiled fresh CBD . The dose of CBD used by patients varied from 1 drop per day to 4 drops twice a day; the milligrams of CBD per milliliter was unknown. The duration of usage was not more than 1 month in 56.25% (9/16) of the patients. Adverse effects of CBD, such as headache and nausea, were noted in 31.5% (5/16) of the patients. Meanwhile, lack of seizure improvement and inability to procure a CBD product were the reasons for discontinuing CBD in 43.75% (7/16) and 6.25% (1/16) of the patients, respectively.Most parents were aware that CBD was legally approved in Thailand; however, only 48.79% (81/166) were aware of CBD as treatment for epilepsy in children. Furthermore, 80.72% (134/166) did not know the composition of CBD required for treating epilepsy, and 89.16% (148/166) were not aware of any side effects of CBD. Regarding knowledge on CBD, 89.76% (149/166) answered that cannabis is a plant that does not absorb heavy metals, pesticides, and toxins from the soil, 39.16% (65/166) answered that CBD could cure cancer, and 56.02% (93/166) answered that CBD could be used in women during pregnancy and breast-feeding replied with the pediatric neurologist trained by the Department of Medical service. Additionally, some respondents answered that folk healers and those practicing Thai traditional medicine could prescribe CBD for pediatric epilepsy management.Regarding factors for CBD use, the number of ASMs , knowledge of CBD as a treatment for epilepsy , and knowledge of CBD side effects were factors significantly associated with CBD use as shown by multivariate analyses were reported to have used CBD products due to treatment-resistant epilepsy, and 37.5% (6/16) used CBD as it was recommended by an acquaintance. Meanwhile, 56% 84/150) of children with no history of using CBD products for epilepsy reported the lack of medical advice and support from medical doctors as the leading cause for not trying CBD products, while 18.67% (28/150) were concerned regarding their safety. The reasons for using CBD products to manage epilepsy in children are summarized in Table /150 of cAmong the parents/guardians of epilepsy patients, 77.11% (128/166) expressed a willingness to participate in future CBD clinical trials, with the most common reason being the desire to cure epilepsy. Additionally, 72.89% (121/166) were uncertain whether CBD was a cure for epilepsy, while 25.9% (43/166) believed it could improve seizures. Lastly, the acceptable costs for CBD in treating pediatric epilepsy were <1000 baht (32.42 US dollars)/month in 42.77% (71/166), and 30.12% (50/166) were inconvenienced by the cost of the treatment.This study aimed to obtain information on the experience in treating epilepsy in children using CBD as well as knowledge and understanding of CBD. To our knowledge, this is the first CBD survey on pediatric epilepsy in Southeast Asia.In a previous Australian survey (Suraev et al. Regarding the efficacy of CBD in epilepsy, Porter et al. (Porter and Jacobson The side effects in patients were then analyzed. Porter et al. reported improved cognition, mood, and sleep after CBD administration (Porter and Jacobson In terms of knowledge, an Australian nationwide survey indicated that both parents/guardians of children and adults who have used cannabis extracts for epilepsy reported a high level of perceived efficacy with cannabis products (Suraev et al. A previous systematic review of healthcare professionals\u2019 beliefs, knowledge, and concerns regarding CBD use reported that healthcare professionals lacked confidence and self-reporting competence as well as harbored concerns regarding the associated risks of CBD (Gardiner et al. We recognize that our study has multiple limitations, including the retrospective nature of the parents/guardians\u2019 self-report, which could have resulted in poor recollection and recall bias. Additionally, this study was conducted in a single clinical setting; thus, a prospective multicenter study is necessary. Moreover,the patients in whom seizure frequency was reduced used CBD without medical advice from a physician, resulting in the varied doses, chemical ingredients, and duration of CBD use. Hence, we cannot compare the dose and duration of CBD use in this study with other previous clinical trial studies. Despite the limitations of our study, we believe that the data we have reported here are relevant given the paucity of prospective clinical trial studies in this population of pediatric patients with epilepsy.Our survey revealed that half of the parents of patients who previously used CBD reported reduced seizure frequency; however, no patient became seizure-free. In addition, although Thailand legalized CBD in 2019, we found significant gaps in the knowledge of parents and guardians regarding CBD use in Thailand. These findings suggest that imparting knowledge and disseminating information regarding CBD is crucial before initiating CBD use. Moreover, further evidence-based studies on CBD are warranted."} +{"text": "Increase in very old individuals is observed in all developed countries around the world. The number of centenarians has also been rising, requiring the investigation of the characteristics of these exceptionally long-lived individuals as well as their experience of life at age 100. In the present study, we present findings from the first nation-wide Swiss centenarian study SWISS100. Given the ongoing COVID-19 pandemic, we conducted a telephone study with centenarians and a family member as proxy informant, using a mixed-methods approach to investigate specific characteristics, their life circumstances and their experience during the pandemic. Recruitment was conducted with the help of the national address registry. A total of 64 centenarians and 62 family members participated, leading to data for 119 centenarians. Centenarians were on average 102 years old, with a range of 100 to 108 years. In line with higher survival rates in females, 76% were women and 24% were men. Most centenarians had received basic education and had completed an apprenticeship. Concerning their residence, 43% lived in private homes and 57% lived in institutions. Of those living in private, half lived alone, one fourth lived with their spouse and one fourth lived with a child. The majority was widowed. Over 80% had children. Although over 70% of the centenarians reported health restrictions, 60% reported good to excellent subjective health. Over 90% of the sample were aware of COVID-19. Despite substantial COVID-19-related restrictions, life-satisfaction was high. Overall, Swiss centenarians show health-related vulnerability but also psychological resilience."} +{"text": "Oral antifungals are typically preferred over topicals for moderate to severe onychomycosis due to efficacy and shorter treatment courses. However, systemics are contraindicated or cautioned in patients with liver dysfunction and with some autoimmune diseases, and in those taking interacting medications. Efinaconazole 10% solution is a topical antifungal therapy, but application for fingernail onychomycosis has not been adequately studied.We present a case of a 78-year-old female with scleroderma and moderate onychomycosis of the right 4th fingernail successfully treated with topical efinaconazole 10% solution.We review the literature on contraindications to oral antifungals for onychomycosis, precautions with terbinafine in patients with some autoimmune diseases, and topical onychomycosis therapies. Topical efinaconazole may represent an effective alternative for patients with fingernail onychomycosis who have contraindications to oral medications. Topical efinaconazole 10% solution is an effective treatment for toenail onychomycosis but has not been well studied for fingernail onychomycosis.Alternative therapies are needed for patients with onychomycosis who have contraindications or precautions to taking oral antifungals.We demonstrate effective treatment of fingernail onychomycosis with efinaconazole 10% solution in a 78-year-old patient with scleroderma.Treatment with efinaconazole 10% solution should be considered for treatment of fingernail onychomycosis in older patients and those with contraindications to oral antifungals.Trichophyton rubrum and T. mentagrophytes. Treatment of fingernail onychomycosis with efinaconazole 10% solution has not been well studied.Efinaconazole 10% solution is a topical triazole antifungal that is approved by the United States Food and Drug Administration (FDA) for treatment of toenail onychomycosis due to For moderate to severe onychomycosis, treatment with oral antifungals is preferred due to generally better efficacy and shorter courses compared to topical therapy. However, treatment with oral antifungals may not be advised in onychomycosis patients with hepatic dysfunction, with some autoimmune diseases, or those taking interacting medications .A 78-year-old female presented with yellow discoloration and lifting of the right 4th fingernail for the previous 3 months. Medical history was significant for scleroderma, hypertension, osteoarthritis, osteoporosis, iron-deficiency anemia, and gastroesophageal reflux. Medications included mycophenolate mofetil, atorvastatin, duloxetine, famotidine, olmesartan, omeprazole, raloxifene, iron, and calcium.Clinical examination of the fingernails was significant for sclerodactyly, digital ulceration, and severe onycholysis of the right 4th fingernail Fig. . ToenailHistopathology of fingernail clippings showed extensive infiltrating large septated hyphal forms, highlighted by PAS and GMS stains, and rare spores. Toenail clippings were negative for fungal and yeast elements. X-ray of the right hand was significant for diffuse osseous demineralization, degenerative changes at the wrist and triscaphe joints, and flexion deformity at the 2nd\u20135th proximal interphalangeal joints, related to known history of osteoporosis, osteoarthritis, and scleroderma, respectively.Pseudomonas aeruginosa colonization , with 50% of patients exhibiting complete clinical cure, 20% with marked improvement, 10% with improvement, and 20% with slight improvement (average treatment duration of 8.9 months) [For patients who cannot take or prefer not to take oral onychomycosis therapies, effective and safe topical treatments are needed. FDA-approved topical therapies include efinaconazole 10% solution, tavaborole 5% solution, and ciclopirox 8% lacquer. While clinical trials were not head-to-head and had different study designs and endpoints, efinaconazole appears to have the greatest efficacy with mycologic cure rates of 53.4\u201355.2% , compare months) .In this case, the patient had clinical cure with 6 months of efinaconazole treatment and no side effects. Topical efinaconazole is prescribed for 12 months for toenail onychomycosis. However, based on average fingernail growth rate of 2\u20133 mm/month, fingernail cure would be expected at 6 months, as was seen in this patient.P. aeruginosa colonization during efinaconazole treatment was likely unrelated to the drug. More likely the patient's onycholysis and immunosuppression, coupled with hand washing, predisposed her to P. aeruginosa colonization [Green nail syndrome has not been reported in case reports, clinical trials, or product labeling for efinaconazole 10% solution. The concomitant nization , 14. TheAdditionally, in the phase III clinical trials of efinaconazole 10% solution for onychomycosis treatment, patients ages 75 and older were excluded. Our patient was 78-years-old with a favorable clinical outcome and no adverse events, demonstrating that efinaconazole treatment may be considered in older adults with onychomycosis. Older patients are more likely to have comorbidities or take medications that prevent them from taking oral therapy, so effective topicals are particularly necessary for this population.Topical efinaconazole 10% solution should be considered in the treatment of moderate fingernail onychomycosis in patients who have contraindications or precautions to taking oral antifungals.Since this study was a case report, ethics approval was not required by the Weill Cornell Medicine Institutional Review Board. Written informed consent was obtained from the patient for publication of this case report and any accompanying images.Rhiannon Miller has no conflicts of interest. Dr. Lipner has served as a consultant for Ortho-dermatologics, Verrica, Hexima, and Hoth Therapeutics.This article has no funding source.Rhiannon Miller contributed to chart review, literature review, consenting the patient, and writing/revision of the manuscript. Dr. Lipner contributed to the diagnosis/treatment of the patient, chart review, literature review, and writing/revision of the manuscript.All data generated or analyzed during this study are included in this article. Further enquiries can be directed to the corresponding author."} +{"text": "Conducting everyday activities out-of-home may accumulate a large share of older adults' daily physical, especially if active transportation is used. Environmental features in home neighborhood may motivate for higher physical activity, but the role of features around destinations is less known. Our goal was to study 1) clustering of older adults' reported activity destinations, and 2) whether transport mode to a destination was associated with characteristics of destination clusters.Data comprise AGNES study participants combined with geospatial data. Using digital mapping, participants located frequently used destinations for shopping, services, and social and spiritual activities on a map, and reported transport mode (active/passive) for each. Geographic information system was used to define distance from home to each destination, to identify spatially clustered destination areas, and to assess destination areas' characteristics . Based on their characteristics, destination areas were hierarchically categorized to area types. In mixed model, active transportation (vs. passive) was regressed for area type and adjusted for distance, car use possibility, walking difficulty in 2km, age, sex, and MMSE score.Of reported destinations within 2km from home (1278 destinations for 642 participants), 81% clustered spatially in 23 destination areas and 19% remained separate. Hierarchical clustering resulted three area types: 1) city centre (versatile activities and nature), 2) less serviced areas (versatile activities and less nature), 3) shopping areas (shopping/service activities and less nature). The proportion of destinations visited using active transportation was 63% in city centre, 68% in less serviced areas, 69% in shopping areas, and 56% for separate destinations outside the areas. Based on mixed model results, the odds for active transport use were higher when destinations located in city centre or in shopping areas compared to visiting locations outside spatially clustered destination areas.Majority of older adults' activity destinations locate as spatially clustered. Varied destinations close to one another may promote active transport."} +{"text": "Among the participants who reported gambling activity (n\u2009=\u2009113), 85.8% were not problematic gamblers, 8.9% were at-risk gamblers, and 5.3% were pathological gamblers. Only 0.2% of all subjects met the criteria for both pathological gambling and pathological video game use. The findings indicate that video gaming and gambling are common leisure times among adolescent students. However, a small but significant minority of these adolescents met the criteria for either severe problem gaming or gambling or both.Adolescence is characterized by emotional instability and risk-taking behaviours that can lead to, among other things, an increased risk of developing pathological video-gaming and gambling habits. The aim of this Study is to assess the prevalence and type of video gaming and gambling habits in adolescent students attending Italian upper-secondary schools. The cross-sectional study was conducted via an online survey using validated questionnaires. The primary outcome measures were the prevalence of past-year video gaming and gambling activities. The sample consisted of 502 adolescent students from first- and second-grade secondary schools. A total of 40.8% of participants were video gamers, 4.8% were gamblers, 17.8% were both video gamers and gamblers, and the remaining 36.6% were not players. Among participants who reported video gaming activity ( Adolescence is characterized by emotional instability and risk-taking behaviours that can lead to, among other things, an increased propensity to develop pathological video-gaming and gambling habits.The eleventh edition of the International Statistical Classification of Diseases and Related Health Problems (ICD-11), which was produced by the World Health Organization, defines gaming disorder as a pattern of recurrent or persistent gaming behaviour manifested by impaired control over gaming, exaggerated priority given to gaming (which takes precedence over daily activities as well as other life interests), and perpetuation or even intensification of gaming despite the occurrence of negative consequences. Furthermore, it defines gambling disorder using the same criteria but referring to gambling instead of gaming behaviours.Growing empirical evidence suggests that each of these two disorders is positively associated with adolescents\u2019 mental health issues , 2, subsTherefore, it is not surprising that pathological use of video gaming and pathological gambling have become an emerging public health problem , 9. HoweThis is a cross-sectional study with convenient sampling. The participants were recruited from five first-grade secondary public schools (\u2018middle school\u2019) and five second-grade secondary public schools (\u2018high school\u2019) located in Brescia Province . Data collection was carried out from February 2020 until March 2021 through an online survey. A detailed description of the study protocol was published previously .The Video-Gaming Scale for Adolescents (VGS-A) and the Gambling Behavior Scale for Adolescents (GBS-A) were used to assess video gaming and gambling behaviours, respectively, that occurred during the last year. They classify the respondents as nonproblem, at-risk, or disordered gamer/gambler. Sociodemographic and educational information were also collected. For a detailed description of the measures, see , 12.Descriptive analyses were performed using R version 4.0.2 .n\u2009=\u2009294), 68.0% were classified as nonproblem gamers, 24.5% as at-risk gamers, and 7.5% as disordered video gamers. On the other hand, among the respondents who reported gambling activity (n\u2009=\u2009113), 85.8% were not problematic gamblers, 8.9% were at-risk gamblers, and 5.3% were pathological gamblers. Only 0.2% of all subjects met the criteria for both pathological gambling and pathological video game use. The demographic information and prevalence rates of video gaming and gambling activities of adolescent responders to the survey are reported in Table A total of 502 adolescent students completed the assessments. The mean age of the participants was 15.9 (SD\u2009=\u20091.93). Most of the participants were female (67.7%), attended high school (79.7%), and had never failed a school year (85.9%). The results indicate that 40.8% of participants were video gamers, 4.8% were gamblers, 17.8% were both video gamers and gamblers, and the remaining 36.6% were not players. More specifically, among participants who reported video gaming activity of these adolescents met the criteria for either severe problem gaming, severe problem gambling or both. The evidence presented here is consistent with international literature , 8 and wThe major limitations of this study are the cross-sectional design, the use of self-report tools, and a limited sample size that did not allow the use of logistic regression analysis to determine the specific odds for various vulnerability and protective factors.Future studies should expand the sample size and include adolescents who do not attend school and represent different parts of the country. Assessing the prevalence of problematic video gaming use and gambling in adolescents would help to increase awareness about these emergent public health issues and take specific measures for preventing, identifying, managing, and treating these disorders."} +{"text": "Colon screening programs have reduced colon cancer mortality. Population screening should be minimally invasive, safe, acceptably sensitive, cost-effective, and scalable. The range of screening modalities include guaiac or immunochemical fecal occult blood testing and CT colonography and colonoscopy. A number of carefully controlled studies concur that second-generation capsule endoscopy has excellent sensitivity for polyp detection and a high negative predictive value. Colon capsules fulfill the screening expectation of safety, high sensitivity for polyp detection, and patient acceptance, and appear to straddle the divide between occult blood testing and colonoscopy. While meeting these criteria, there remains the challenges of scaling, capsule practitioner training, resource allocation, and implementing change of practice. Like CT colonography, capsule screening presents the clinician with a decision on the threshold for colonoscopy referral. Overall, colon capsules are an invaluable tool in polyp detection and colon screening and offer a filter that determines \u201cwho needs a colonoscopy?\u201d. Colorectal cancer (CRC) represents a leading cause of cancer-related death in men and women globally, causing 600,000 deaths each year . Almost Population screening should be minimally invasive, safe, acceptably sensitive, cost-effective, and scalable. In some healthcare settings, colonoscopy is the preferred screening modality. The procedure is the recognized gold standard for the diagnosis of colon polyps and early-stage cancer but fails the criteria for acceptable and widespread population screening . The proIn 2000, Gavriel Iddan and colleagues published the first use of a wireless capsule endoscope designed to illuminate and transmit images of the small intestine. Microelectronics freed the device from external cabling and fiber-optic bundles, and the capsule was small enough to swallow with a sip of water. The images were transmitted using radiotelemetry and stored on an external recording device. Successive generations of hardware and software innovation followed, resulting in progressive improvements in image resolution, power consumption, and ease of use .Minimally-invasive colon capsule endoscopy (CCE) offers a tantalizing option for patients undergoing screening, surveillance, and investigation of lower gastrointestinal symptoms. Straddling fecal occult blood and FIT testing and colonoscopy, the investigation is painless, easily administered, allows direct visualization of the colonic mucosa, and is almost free of serious procedure related adverse events. However, the potential of CCE screening presents a number of challenges, including extending battery life to ensure study completion rates equivalent to those expected of colonoscopy, the requirement for consistent high-quality colon cleansing, and the need to rapidly train large numbers of capsule readers.This review summarizes key CCE publications and discusses the possible role of this new colon imaging device in CRC screening.In 2006, the first-generation of colon capsule CCE-1 [Given Imaging ] was introduced ,8. This Rokkas et al. reported a meta-analysis of polyp detection with CCE-1 in detecting colonic polyps. The pooled data showed per-patient CCE sensitivity of 73% and specificity of 89% . For polyps >6 mm in size or 3 or more polyps of any size, the respective values were 69% and 86% . Spada eWhen compared to colonoscopy, this first-generation capsule revealed poor sensitivity and specificity. This spurred the development of a second-generation capsule (CCE-2), which was re-designed to address the shortcomings of CCE-1. Launched in 2009, CCE-2 was slightly larger (31.5 mm \u00d7 11.6 mm) with the camera at each end being capable of surveying a field of 172\u00b0, thereby achieving an overall coverage of almost 360\u00b0. The integration of a bidirectional information flow algorithm linking the capsule with the DR3 data recorder allowed modulation of the frame rate at either 4 or 35 frames per second, depending on whether the capsule was stationary or moving. The adaptive frame rate, together with a \u201csleep\u201d mode in the stomach, resulted in the extension of battery life to around 14 h . The tecIn 2009, Eliakim et al. reported the first controlled CCE-2 study, which comprised 98 patients. Each patient underwent a colonoscopy, followed within 10 h by a CCE-2 examination. The per-patient CCE-2 sensitivity for polyps \u22656 mm was 89% , and for \u226510 mm it was 88% , with specificities of 76% and 89% , respectively . In 2011In one of the largest studies to date, Rex et al. reported the accuracy of CCE-2 in detecting polyps that are 6 mm or larger in an average-risk screening population. Among 695 patients analyzed, CCE-2 identified subjects with at least one polyp \u22656 mm with 81% sensitivity and 93% specificity , and polyps \u226510 mm were identified with 80% sensitivity and 97% specificity . Notably, CCE-2 identified individuals with at least one adenoma measuring at least 6 mm or larger with 88% sensitivity and 82% specificity , and ones measuring 10 mm or larger with 92% sensitivity and 95% specificity .In 2016, Spada et al. conducted a systematic review and meta-analysis of the accuracy of first- and second-generation CCE in the detection of colorectal polyps. The report included 14 studies comprising data from 1128 individuals assessed with CCE-1 and 1292 with CCE-2. CCE-2 detected polyps \u22656 mm with a sensitivity of 86% and specificity of 88.1% . Considering polyps \u226510 mm, CCE-2 demonstrated an 87% sensitivity and 95.3% specificity . This meta-analysis established clear evidence that unlike CCE-1, CCE-2 achieved acceptably high detection rates .In a more recent 2021 systematic review and meta-analysis, the diagnostic accuracy of CCE was compared with colonoscopy in polyp detection. The mean 95% CI sensitivity, specificity, and diagnostic odds ratio were: 0.85 (0.73\u20130.92), 0.85 (0.70\u20130.93), and 30.5 (16.2\u201357.2), respectively, for polyps of any size; 0.87 (0.82\u20130.90), 0.95 (0.92\u20130.97), and 136.0 (70.6\u2013262.1), respectively, for polyps \u2265 10 mm; and 0.87 (0.83\u20130.90), 0.88 (0.75\u20130.95), and 51.1 (19.8\u2013131.8), respectively, for polyps \u2265 6 mm. These findings illustrated that CCE had a high sensitivity and specificity for per-patient polyps that was comparable with standard colonoscopy .In another interesting systematic review and meta-analysis of clinical trials, the high diagnostic accuracy of CCE was once again confirmed in adequately-cleaned bowels. The pooled sensitivities and specificities for polyps \u2265 6 mm were 87% (95% CI: 83\u201390%) and 87% (95% CI: 76\u201393%) in 8 studies, respectively. For polyps \u2265 10 mm, the pooled estimates for sensitivities and specificities were 87% (95% CI: 83\u201390%) and 95% (95% CI: 92\u201397%) in 9 studies, respectively . The recLastly, in 2022, Vuik et al. reported the prevalence of gastrointestinal abnormalities in 462 asymptomatic patients that were invited to undergo CCE. In 46 (10.2%) of these asymptomatic individuals, there were significant findings in the colon, i.e., colonic polyps\u2014or CRC in one . This stThere are few reports regarding the accuracy of CCE in the detection of non-polypoid lesions such as flat polyps, lateral spreading tumours, diverticulosis, angiodysplasia, and inflammatory colitis.Flat polyps are of special interest since these lesions may harbor a higher risk of early malignant transformation ,60,61,62A single center study performed by Igawa et al. attempted to evaluate the sensitivity and specificity of CCE for detecting lateral spreading tumors (LST). The authors performed a prospective study comparing CCE-2 with optical colonoscopy in 21 patients with LSTs diagnosed during a 3-month period prior to capsule endoscopy. The sensitivity and specificity of CCE-2 for detecting LSTs was 81% and 100%, respectively. For detecting LST-granular type and LST-non-granular type, the sensitivity and specificity were 71% and 100% and 86% and 100%, respectively. The authors concluded that CCE-2 was less sensitive in detecting LSTs than optical colonoscopy, especially for LSTs located in the right colon. Nevertheless, the study was limited to a small sample size . All these studies assessing the accuracy of CCE in diagnosing colonic polypoid lesions clearly demonstrate that CCE-2 has sufficient sensitivity and specificity for its use to be considered for colon polyp screening and surveillance and determining who needs an interventional colonoscopy.Colon screening programs designed to detect adenomas and early-stage cancer have been widely adopted and the optimal age to initiate screening has progressively decreased, adding to demand for screening services. Current consensus recommends that for average-risk individuals, screening should start after the age of 45 or 50 years, varying between different governing bodies and scientific societies ,68,69,70Population screening should be safe, readily available, cause minimal discomfort, free of serious adverse events, repeatable, and affordable. Colonoscopy is not an ideal screening modality. While considered the gold standard for polyp detection, polyp miss rates of 22\u201328% have been reported . SeriousOccult blood testing using the FIT is simple to administer and is currently implemented as the primary screening modality for early detection of advanced colorectal neoplasia . A positIn a 2014 publication, Holleran et al. calculated that for every million participants in the UK FIT screening program, referral for colonoscopy would result in 6000 negative studies. They suggested the model of a \u201cfilter test\u201d, which would act as an intermediary between a positive stool test and colonoscopy. The filter would need similar detection rates as colonoscopy but would be minimally invasive and readily accessible. As CCE-2 fulfills these parameters, a prospective study was undertaken to assess the value of CCE-2 followed within 24 h by conventional colonoscopy in individuals returning a positive FIT \u2265 100 ng Hb/mL. CCE detected polyps (any type) in 69% of patients. Overall, the sensitivity, specificity, PPV, and NPV of CCE for any polyp compared with optical colonoscopy was 95%, 65%, 79%, and 90%, respectively . The autIn 2020, Pecere et al. examined the diagnostic accuracy of CCE-2 for the detection of advanced neoplasia in 178 FIT positive individuals, all of whom underwent traditional colonoscopy within 24 h of completing the capsule study . AdvanceIn 2021, Vuik et al. reported a systematic review of CCE, comprising 13 studies and 2485 patients. The polyp detection rate for CCE-2 was 24\u201374%. For polyps \u2265 6 mm, the sensitivity of CCE was 79\u201396% and the specificity was 66\u201397%. For polyps \u2265 10 mm, the sensitivity of CCE was 84\u201397%. Notably, the CRC detection rate for completed CCEs was 93% . These sIn the interim analysis of the Danish CareForColon2015 trial, the initial 234 CCEs were evaluated for quality, safety, and completion rate. The completion rate for CCEs was 67.9% and the rate of conclusive investigations was 80.3%. The polyp detection rate was 73.5%, and six suspected cancers were identified (2.6%). The authors discussed the satisfactory outcomes, but concluded that the lower-than-expected proportion of suspected cancers would be followed-up, and explored ways to improve the completion rate .Participation rate is pivotal in population-based screening programs. The desirable threshold set in the European guidance is >65%. Offering FIT-based screening in 21 European countries, the overall participation was 49.5% ,80. ThisWhen evaluating CCE as a diagnostic modality, the completion rate and quality of bowel preparation require consideration. In their 2016 meta-analysis, Spada et al. reported an 81% rate of adequate cleansing for CCE-2 and a 90.5% completion rate . In theiConversely, in a prospective French study involving 689 CCEs, the completion rate and adequate bowel preparation was less promising. In particular, less than 50% of the examinations were both complete and with adequate bowel preparation; and the authors concluded that improvement would be needed to increase the reliability of CCE, since most of the missed colonic advanced neoplasia were due to incomplete CCE with distal neoplasia location . In analThe Danish group investigated whether the prokinetic prucalopride, increases the completion rate of CCE. They found that the completion rate was 74.9% in the prucalopride group and 56.7% in the control group (standard preparation group). Additionally, the mean CCE transit time was 2 h and 8 min faster in the prucalopride group. This did not appear to negatively affect the detection rate of CCE: 589 polyps (mean 2.9) were found in the prucalopride group compared to 522 polyps (mean 2.6) in the control group .Although most cases of missed colon lesions were linked to inadequate bowel preparation or incomplete examinations, MacLeod et al. recently described an interesting case of a patient that underwent CCE. The CCE reported 17 polyps. Notably, a 40-mm cecal pole tumor, which was not detected by the CCE, was identified at follow-up colonoscopy, and this was surgically resected, thereby confirming a moderately-differentiated adenocarcinoma. The tumor was not definitively identified on retrospective review of the CCE images either .Few colon capsule practitioners have fulfilled the recommendations for formal capsule endoscopy training . Buijs eWhile CCE is safe, has high patient acceptability, and ever improving sensitivity and specificity for polyp detection, there are further limitations that need consideration. It has already been discussed that inadequate bowel preparation and/or completion rate still pose a challenge and would require further optimization. Additionally, most of the studies conducted to date involved non-Asian participants, and this should be acknowledged. In analogy to this, CCE\u2019s usage range was different in different areas, such as having less usage in Asia.Additionally, the relatively long reading time of CCE should also be taken into consideration. The reading speed is dictated by the overall circumstances. The realistic overall average reading time is between 30 and 60 minutes, and a second opinion may be wise and welcome for difficult frames . It is lThe procedure remains a relatively expensive examination, especially in the absence of shifting manpower resources from traditional endoscopy to frontline CCE examination. An older study attempted to provide a model to assess the cost-effectiveness of population-based screening for CRC using CCE and to compare the cost-effectiveness with that of a colonoscopy screening program. The incremental cost-effectiveness (compared with no screening) of colonoscopy and capsule endoscopy was $16,165 USD and $29,244 USD per life-year saved, respectively. Nevertheless, one should consider that these data likely cannot be extrapolated to the current CCE-2 era. Additionally, the authors discussed that simulating an initial compliance to capsule endoscopy was 30% better than colonoscopy, thus capsule endoscopy became the more effective and more cost-effective option . FurtherRegarding clinically-significant adverse events, in their 2016 meta-analysis, Spada et al. demonstrated that CCE is extremely safe, with no serious adverse events occurring in over 2000 subjects. They reported a cumulative adverse-event rate of 10.4%, which was mostly linked to bowel preparation (cumulative rate 9.7%), while those directly associated with CCE yielded a cumulative rate of 0.33% . In theiThere have been a series of studies that have resulted in recognition that CT colonography (CTC) is an acceptable modality for colon polyp diagnosis, especially in the setting of incomplete colonoscopy ,99,100. p = 0.08). Both CCE and CTC identified all patients with cancer. CCE detected more patients with any lesion than CTC . The authors concluded that both techniques are similar in detecting advanced colorectal neoplasia, but CCE is more sensitive for the detection of any neoplastic lesion [The VICOCA study reported a randomized trial of 290 FIT positive individuals that were referred for colonoscopy who agreed to undergo either CCE or CTC prior to colonoscopy. The sensitivity, specificity, and positive and negative predictive values for clinically-significant polyps were 98.1%, 76.6%, 93.7%, and 92.0% in the CCE group and 64.9%, 95.7%, 96.8%, and 57.7% in the CTC group. The detection rate for advanced colorectal neoplasm was higher in the CCE group than in the CTC group vs. CTC following incomplete colonoscopy. The polyp yields of CTC and CCE were 10% and 37% for polyps of any size, 13% and 21% for polyps \u22655 mm, and 4% and 9% for polyps \u226510 mm polyps. Overall, the diagnostic yield of CCE for polyps of any size was almost fourfold compared to CTC .In summary, published studies concur that compared to CTC, second-generation CCE has comparable or even superior accuracy in detecting colonic polyps, and that both are preferred by patients to conventional colonoscopy. Both CCE and CTC are almost free of serious procedure-related adverse events, although radiation exposure may be a long-term consideration. CCE-2 has been endorsed by some major scientific societies and governing bodies. The US Food and Drug Administration has approved CCE-2 as an adjunctive test in patients following incomplete colonoscopy and in the diagnostic evaluation of patients with suspected lower gastrointestinal bleeding . RecentlThere is consensus that CCE contraindications are the same as those for small bowel capsule endoscopy. The examination should not be performed in patients with swallowing difficulty, those likely to be intolerant of the bowel cleansing and booster preparations, and individuals with known or suspected gastrointestinal obstruction, stricture, or fistula. Relative contraindications include patients fitted with cardiac pacemakers, or other implanted electromedical devices, and pregnant women .A number of carefully controlled studies concur that CCE-2 has excellent sensitivity for polyp detection and a high negative predictive value. Like CTC, capsule screening presents the clinician with a decision on the threshold for colonoscopy referral. Pickardt et al. reported a carefully constructed CTC decision analysis that is readily extrapolated to CCE . The modIn a literature review of diminutive and small colon polyp management, Coe and Wallace concluded that both retrospective and prospective studies indicate that in colorectal polyps < 10 mm in size, there is an exceptionally low prevalence of advanced pathology . In addiPopulation-based stool occult blood testing followed\u2014if positive\u2014by colonoscopy has made a considerable impact on colon cancer mortality. The test fulfills the criteria for population screening; primary screening using colonoscopy offers diagnostic accuracy and the advantage of immediate polyp removal. However, primary colonoscopy screening fails to meet the acceptable criteria for population screening. The procedure, in asymptomatic individuals, requires day-case admission, causes discomfort sufficient to require analgesia and sedation, and is rarely associated with devastating complications. While considered the gold standard for detecting colorectal neoplasia, this is balanced by large numbers of negative procedures required to diagnose a single advanced neoplasm.CCE is a new device in gastroenterology with potential to change the colorectal screening landscape. Ambulant individuals swallow the capsule with a sip of water, the procedure is pain free, and, after taking the capsule, individuals can return home unaccompanied, where the capsule can complete its mouth-to-toilet journey. CCE is currently well placed to straddle the current models of occult blood testing and colonoscopy. This minimally invasive procedure asks and answers the question, \u201cwho needs a colonoscopy?\u201d, and offers patients a safe, effective, and gentler screening option."} +{"text": "Extracellular vesicle (EV) biomarkers have promising diagnosis and screening capacity for several cancers, but the diagnostic value for pancreatic cancer (PC) is controversial. The aim of our study was to review the diagnostic performance of EV biomarkers for PC.We performed a systematic review of PubMed, Medline, and Web Of Science databases from inception to 18 Feb 2022. We identified studies reporting the diagnostic performance of EV biomarkers for PC and summarized the information of sensitivity, specificity, area under the curve (AUC), or receiver operator characteristic (ROC) curve) in according to a pre-designed data collection form. Pooled sensitivity and specificity was calculated using a random-effect model.We identified 39 studies, including 2037 PC patients and 1632 noncancerous, seven of which were conducted independent validation tests. Seventeen studies emphasized on EV RNAs, sixteen on EV proteins, and sixteen on biomarker panels. MiR-10b, miR-21, and GPC1 were the most frequently reported RNA and protein for PC diagnosis. For individual RNAs and proteins, the pooled sensitivity and specificity were 79% (95% CI: 77\u201381%) and 87% (95% CI: 85\u201389%), 72% (95% CI: 69\u201374%) and 77% (95% CI: 74\u201380%), respectively. the pooled sensitivity and specificity of EV RNA combined with protein panels were 84% (95% CI: 81\u201386%) and 89% (95% CI: 86\u201391%), respectively. Surprisingly, for early stage (stage I and II) PC EV biomarkers showed excellent diagnostic performance with the sensitivity of 90% (95% CI: 87\u201393%) and the specificity of 94% (95% CI: 92\u201395%). Both in sensitivity and subgroup analyses, we did not observe notable difference in pooled sensitivity and specificity. Studies might be limited by the isolation and detection techniques of EVs to a certain extent.EV biomarkers showed appealing diagnostic preference for PC, especially for early stage PC. Solving the deficiency of technologies of isolation and detection EVs has important implications for application these novel noninvasive biomarkers in clinical practice.The online version contains supplementary material available at 10.1186/s12885-022-09463-x. Pancreatic cancer (PC) is the seventh cancer related mortality worldwide, contributing 32, 000 deaths in 2018 . SurgicaExtracellular vesicles (EVs), mainly classified exosomes and microvesicles, are as membrane-bound vesicles with biologically active molecules including proteins and nucleic acids and can be released from tumor cells to transport these molecules from parental cells to recipient cells to mediate tumor initiation, progression, and metastasis \u201321. EVs The systematic review and meta-analysis followed a preferred protocol and is reported according with the PRISMA guidelines .We performed an electronic search of PubMed, Medline, and Web of Science databases to identify relevant studies assessing circulation EV biomarkers for PC detection up to 18 Feb 2022. The search strategy used the following keywords combination: . Duplicates were removed.We initially screened all titles and abstracts and studies matched any of the following criteria were excluded: (1) non-English articles; (2) non-original articles; (3) not pancreatic cancer articles; (4) non-human studies; (5) not relevant to the topic. Two authors (Erna Jia and Na Ren) reviewed all potentially relevant full texts, the following studies were included: (1) studies that investigated EV biomarkers in plasma, serum, blood, or peripheral blood in PC patients; (2) PC patients were diagnosed as pancreatic ductal adenocarcinoma depending on the cytological or histological examination; (3) studies that reported the diagnostic performance of EV biomarkers for PC had relevant data , or receiver operator characteristic (ROC) curve); (4) control groups containing healthy people or benign disease. Any discrepancies were resolved by discussion.P Value. Risk of bias and application for each study was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) checklist [The two reviewers independently extracted available information from eligibility studies in according to a pre-designed data collection form and resolved any disagreements by discussion again. We extracted key information on first author, year of publication, country, study design, population characteristics , type of blood-based specimen, PC stage, population composition of control groups, names or panels of target biomarkers, detection methods of target biomarkers, preparation approaches of EVs, sensitivity, specificity, AUC, and hecklist . Publicahecklist .We calculated mean age and sex distribution of eligibility studies using statistical software R if relevant data was not obtained but raw data was available. If the values of sensitivity, specificity or AUC were not reported, we estimated these diagnostic indicators based on ROC curve using OriginPro software (version 9.0) according to maximum Youden\u2019s index.I2 value), with P\u2009<\u20090.05 or I2\u2009>\u200950% as statistically significant heterogeneity. We performed sensitivity analysis for studies considered at low risk of bias and low concern for applicability to give convincing diagnostic performance of EV biomarkers for PC based on the assessment of QUADAS 2 using Review Manager 5.3. We also applied subgroup analysis to pool the sensitivity and specificity of individual EV miRNAs and individual EV RNAs detected using qPCR for PC diagnosis.We combined the sensitivity and specificity of EV biomarkers in studies reporting the relevant data to obtain a pooled diagnostic performance for PC using Meta-DiSc version 1.4 by the random-effect model (DerSimonian-Laird method). If noncancerous groups were consisted of healthy controls and/ or benign diseases, we studied them as a whole if the relevant data was reported, or we studied the healthy controls if not. We investigated heterogeneity between studies using Cocharan\u2019s Q test and the inconsistency index analysis , 78, 85,analysis , 84\u201386.TThe isolation and detection methods of EVs were diversity, 15 studies used the commercial kits , 83\u201385, We judged the risk of bias and applicability concerns of the included studies using QUADAS-2 evaluation tool, which were grouped four domains: participant selection, index test, reference standard, flow and timing. The outcomes of our assessment of methodological quality were summarized in Fig.\u00a0 P\u2009=\u20090.78) did not provided any evidence of publication bias. The funnel plot showed reasonably symmetrical, which also supports the results of egger\u2019s test were reported more than one times. Among them, miR-21 and miR-10b were the highest frequently reported RNA which was reported in 6 times. The expression direction of most EV miRNAs were up-regulate, apart from miR-122 , miR-19bA total of 177 EV proteins reported in 13 studies were statistically significant for PC diagnosis, 19 EV proteins were included in panels. GPC1 was the most frequently reported EV protein with median sensitivity and specificity of 72% (from 43 to 100%) and 86% (from 52 to 100%), respectively, which was reported in nine times. And the following were EphA2, EGFR, and EPCAM for early stage (stage I-II) PC, two of individual biomarkers were conducted independent validation tests. And across these two validation studies, both the sensitivity and specificity of EV biomarkers for early stage (stage I-II) PC was more than 85% . The medStudies that reported individual EV biomarkers for PC diagnosis were performed meta-analyses. Overall, 32 individual EV RNAs investigated in 16 studies and 16 individual EV proteins investigated in 13 studies were included in the meta-analyses. The sensitivity and specificity for each individual EV RNAs and each individual EV proteins were depicted in the corresponding forest plots. The pooled sensitivity and specificity of individual EV RNAs was 79% (95% CI: 77\u201381%) and 87% (95% CI: 85\u201389%), respectively Fig.\u00a0A. The povs those of the whole RNAs (79% (95% CI: 77\u201381%) and 87% (95% CI: 85\u201389%)). We also found the similar pooled sensitivity and specificity between RNAs detected by qPCR (80% (95% CI: 78\u201382%) and 84% (95% CI: 81\u201387%), Fig.\u00a0Sensitivity analysis in according to the high quality studies failed to demonstrate a change in the pooled sensitivity and specificity (RNAs: 81% 95%CI: 78\u201383%) and 84% (95%CI: 80\u201386%), Fig.\u00a08\u201383% andA systematic understanding of diagnosis performance of tumor-related moleculars in circulation EVs is critical for PC screening and earliest detection. The present systematic review and meta-analysis has assembled the diagnostic performance of 183 EV RNAs, 177 EV proteins, and 172 EV biomarker panels based on serum/plasma for diagnosing PC in 39 studies from 2015 to 2022. The control groups selected noncancerous population containing healthy population, benign pancreatic disease, IPMN, serious cystadenoma, and nonpancreatic benign diseases. MiR-21 and miR-10b were the highest frequently reported EV RNA for PC diagnosis. GPC1 and EphA2 were mostly reported EV proteins for PC diagnosis. Both the EV RNAs and the EV proteins in high quality studies showed moderate diagnostic values and the EV panels revealed good diagnostic values for PC. Especially, the EV RNA combined protein panels had great diagnostic performances for PC with the pooled sensitivity of 84% and specificity of 89%. Surprisingly, for early stage PC the EV biomarkers showed excellent diagnostic performance, the sensitivity and specificity were 90% and 94%. Respectively. Overall, available studies highlighted the diagnostic performance of EV biomarkers to differentiate PC from noncancerous and further researches will be needed to validate the diagnostic value of EV biomarkers as noninvasive, effective, specific screening tools for PC diagnosis in general population.EV GPC1 and EV EphA2 were the mostly frequent reported diagnostic proteins for PC in present study. GPC1 was discovered in two prospective studies , 75, oneEV miRNAs recently have raised more interest as novel noninvasive biomarkers for malignant tumors. In our subgroup analysis EV miRNAs appeared powerful diagnosis capacity for PC with both sensitivity and specificity exceeded 80%, which was consistent with that of the whole EV RNAs. EV miR-21 was the most frequency reported miRNA and was significantly high expressed in PC with consistent direction in all five studies. EV miR-21 performed outstanding specificity for PC diagnosis, excepting in study by Goto et al. the specificity was 81%, the specificity value was all greater than 90% in the remaining studies and even two studies showed a specificity of 100% , 62, 84.In present study, we found EV biomarker panels showed high diagnosis value for PC, the pooled sensitivity and specificity was 80% and 86%, respectively, which showed a small advantage diagnosis performance than the whole individual EV RNAs and individual EV proteins. In previous studies, compared with the corresponding individual markers the diagnostic accuracy of either protein panels or miRNA panels was not to show any advantage , 79, 82.Due to high stability and providing specific information from original tumor of RNAs and proteins in EVs, EV RNAs and proteins have attracted considerable attention as noninvasive biomarkers for cancer diagnosis. By far, the analysis of EVs was separated into isolation and detection two steps. Multistep ultracentrifugation is the recommended standard method for EVs isolation, which increased the complexity of the operational process and was time-consuming and expensive, and the centrifugation time and force was nonuniform inducing major difference of EV purity and isolation rate . Most inThe heterogeneity of the present study ranged from mild to severe, neither subgroup analysis nor sensitivity analyses failed to reduce the degree of heterogeneity. Furthermore, we analyzed the pooled diagnostic value of EV biomarkers for early stage PC, the results also did not have impact on heterogeneity. We hypothesized that the sources of heterogeneity might be related to the various methods of EVs isolation and detection, sample selection protocol, and demographic or geographic different of study populations. In addition, the number of samples of case and control groups widely ranged from 6 to 284, which also contributed to the heterogeneity. Although the heterogeneity might limit the reliability of the pooled results in present study, the results of our systematic review and meta-analyses have a certain guide to pick up noninvasive and effective early diagnosis biomarkers for PC.In this systematic review and meta-analysis, we found circulation based EV biomarkers exhibited considerable diagnosis performance for PC. EV RNAs combined with EV proteins showed appealing higher diagnosis efficiency. Especially, for early stage PC the EV biomarkers revealed excellent diagnostic performance. However, the deficiency of technologies that can effectively isolation and detection EV biomarkers limit the application of EV biomarkers in clinical practice to some extent, highlighting the need for high-quality reproduction researches in this area as well a need for promising accuracy EV biomarkers for PC diagnosis and screening in larger sample prospective cohort.Additional file 1. Protocols of blood exosomes detection.Additional file 2. Summary of studies reporting significant associations of RNAs in pancreatic cancer.Additional file 3. Summary of studies reporting significant associations of proteins in pancreatic cancer.Additional file 4. Pooled sensitivity and specificity of EV biomarker panels for pancreatic cancer diagnosis."} +{"text": "The aim was to evaluate the impact of anastomotic leak (AL) after colon cancer (CC) and rectal cancer (RC) surgery on 5-year relative survival, disease-free survival (DFS), and disease recurrence.AL after CC and RC resection is a severe postoperative complication with conflicting evidence whether it deteriorates long-term outcomes.Patients with stage I to IV CC and RC who underwent resection with primary anastomosis were included from the Netherlands Cancer Registry (2008\u20132018). Relative survival, measured from day of resection, and multivariable relative excess risks (RERs) were analyzed. DFS and recurrence were evaluated in a subset with stage I to III patients operated in 2015. All analyses were performed with patients who survived 90 days postoperatively.A total of 65,299 CC and 22,855 RC patients were included. Five-year relative survival after CC resection with and without AL was 95% versus 100%, 89% versus 94%, 66% versus 76%, and 28% versus 25% for stage I to IV disease. AL was associated with a significantly higher RER for death in stage II and III CC patients. Stage-specific 5-year relative survival in RC patients with and without AL was 97% versus 101%, 90% versus 95%, 74% versus 83%, and 32% versus 41%. AL was associated with a significantly higher RER for death in stage III and IV RC patients. DFS was significantly lower in CC patients with AL, but disease recurrence was not associated with AL after colorectal cancer resection.AL has a stage-dependent negative impact on survival in both CC and RC, but no independent association with disease recurrence. Anastomotic leakage (AL) is the most feared complication following colorectal cancer (CRC) resection. The incidence of AL varies between 3% and 20%, depending on the type of resection, anastomosis location, neoadjuvant treatment, and sex.8Although it is widely recognized that AL is associated with poor short-term outcomes, the association with long-term outcomes is ambiguous.Evidence is also inconclusive regarding the impact of AL on disease-free survival (DFS) and disease recurrence.Investigating the impact of AL on long-term oncological outcomes can provide an important basis for future studies to investigate diagnosis strategy and treatment strategy. This nationwide study aimed to evaluate the impact of AL on 5-year relative survival, DFS, and disease recurrence after restorative CC- and RC resection.This population-based observational study included CRC patients diagnosed between January 1, 2008 and December 31, 2018 from the Netherlands Cancer Registry (NCR), which is maintained by the Netherlands Comprehensive Cancer Organization (IKNL). The following patient, tumor, and treatment characteristics are extracted from medical files: sex, age, American Society of Anesthesiologists (ASA) classification, body mass index, tumor location, pathological tumor stage, (neo)adjuvant therapy, type of surgical resection, and surgical approach. Registered postoperative outcomes consisted of AL, readmission <60 days and mortality. Follow-up regarding vital status was completed on January 31, 2020 and was captured by linking of the NCR to the Municipal Personal Records Database. Additional patient record review was performed to collect data on disease recurrence for patients diagnosed with stage I to III CRC between January 1, 2015 and June 30, 2015. Approval was obtained by the scientific board of the Prospective National Colorectal Cancer Cohort and the privacy review board of IKNL. Ethical approval and informed consent was not required according to the Dutch law.http://links.lww.com/SLA/E116).Patients with CRC stage I to IV who underwent surgical resection with formation of a primary anastomosis were included. Patients were excluded if no primary anastomosis was created . Patients who died within 90 days after surgery were also excluded from analyses, to prevent bias from death due to surgical complications , depending on the distribution. \u03c7Baseline characteristics are presented in Table P<0.01). Incidence of AL was significantly different between pathological tumor stages (I\u2013IV), surgical approaches and types of resection. In the stage III CC group, 48% (466/966) of the patients with AL received adjuvant chemotherapy compared with 67% of the patients without AL (P<0.01). The total incidence of AL after RC resection was 8.3% . After excluding patients who died within 90 days postoperatively it was 7.9% . Male sex, age below 70 years and neoadjuvant radiotherapy were associated with AL after RC resection (P<0.01).The total incidence of AL after CC resection was 5.6% . After excluding patients who died within 90 days postoperatively it was 4.8% . Male sex and age below 70 years were associated with a higher AL rate after CC resection (P=0.78), 89% versus 94% for stage II , 66% versus 76% for stage III , and 28% versus 25% for stage IV , 90% versus 95% for stage II , 74% versus 83% for stage III , and 32% versus 41% for stage IV .In 2015, 10,139 CRC patients underwent a resection with formation of a primary anastomosis, of whom 5387 were operated in the first semester of 2015. After excluding stage IV patients (1036), and patients who died within 90 days (102), a total of 4249 patients remained . Multivariable cox proportional hazard regression demonstrated that AL was not associated with disease recurrence compared with patients without AL . Multivariable cox proportional hazard regression revealed that AL was not associated with disease recurrence radiotherapy. However, neoadjuvant (chemo)radiotherapy itself is associated with AL.CC patients with AL and treated with adjuvant chemotherapy had a significantly worse survival compared with patients without AL. Stormark et alSurgical resection for stage IV CRC can be performed as intentional curative treatment in combination with local treatment of metastases, or to prevent or treat tumor complications. Previous studies demonstrated that palliative resection of the primary tumor can improve overall survival in stage IV CRC patients.DFS was significantly decreased in CC patients with AL, however, no association between AL and disease recurrence was found. Previous smaller cohort studies reported contradictory results on disease recurrence after CRC resection.This study has strengths and limitations. A large number of patients who underwent CRC surgery with a primary anastomosis were included and separate analyses for both entities were performed. However, AL was only registered if a reintervention or readmission was required within 60 days after primary surgery and a considerable number of patients develop AL thereafter. This phenomenon is mainly observed in patients who received a diverting ileostomy, which is known to diminish the severity of AL.In conclusion, AL was associated with a negative impact on survival in stage II and III CC patients, and in stage III and IV RC patients. DFS was significantly decreased in CC patients with AL, but no association was found between AL and disease recurrence in CRC patients. To mitigate the negative impact of AL on long-term outcomes after CRC surgery, nonrestorative surgery can be considered in patients at high risk of AL. Further studies have to elucidate the pathophysiological mechanism of AL, to develop early detection techniques and to investigate treatment strategies to reduce the impact of AL on oncological outcomes."} +{"text": "Gay, bisexual, and other men who have sex with men (MSM) have been disproportionately affected during the 2022 U.S. monkeypox outbreak, with Black or African American (Black) MSM being the most affected demographic group were administered. Two thirds of doses were administered before the festival and one third during the event. Overall, 2,886 (67%) doses were administered at 22 routine vaccination events at health department clinics, 702 (16%) doses at 20 mobile, community pop-up events, and 694 (16%) doses at one fixed location (a Georgia DPH-sponsored mass vaccination event). Among vaccine recipients, 93% were male, 55% were aged 30\u201349 years, 48% were Black, and 8% were Hispanic . The proMonkeypox virus and ending the outbreak (Vaccinating communities disproportionately affected by the monkeypox outbreak is important in stopping spread of"} +{"text": "Results: The overall accuracy rate was 69%, with minor and major discrepancy rates of 21% and 10%, respectively. There was an insignificant increase in overall accuracy with increased years of training, despite a reduction to 58% accuracy among Year 3 trainees. The accuracy level increased between Year 1, Year 2 and Year 4 by 70%, 71% and 75%, respectively (p > 0.05). The accuracy rates for both the adult and pediatric age groups were not statistically significant. The mobile radiographs showed lower accuracy rate of reporting than the plain radiographs. Conclusion: The radiological trainee interpretations for plain radiographs had an average rating with low discrepancy rates. The Year 3 trainees had the lowest accuracy compared to the other trainee groups. However, the present study suggests the need for further research to determine if the current outcomes are outliers or are indicative of a real phenomenon.Introduction: The primary communication between the radiologist and referrer is through the radiological report. However, there are incidents of misinterpretation during radiologist training. Therefore, the present study aimed to evaluate the accuracy level and incidence of interpretation errors for plain radiographs among radiology trainees at our institution. Materials and Methods: The present study retrospectively reviewed 508 reported plain radiographs for one year, and two radiologists subsequently evaluated these plain radiographs. The initial diagnosis by the trainee was compared with the radiologists\u2019 evaluation, and the results were categorized as either \u2018accurate\u2019, \u2018minor discrepancy\u2019, or \u2018major discrepancy\u2019. The data were analyzed concerning the overall performance, year of trainee, anatomic area, patient age group, and radiograph type. A chi-square test was performed, with Plain radiography remains the most common form of radiological imaging performed in any medical institution despite advanced radiological modalities. Advantages of plain radiography include its low radiation dose, availability, affordability, and simplicity . The plaWith an increased volume of radiographic reading and reporting, trainees gain valuable experience in detecting abnormalities. This is also the case with other modalities, such as ultrasound, fluoroscopy, computed tomography, and magnetic resonance imaging (MRI). The trainee\u2019s initial interpretation provides the basis for the patient\u2019s immediate management, especially when on-call or after office hours ,3. EveryPreviously, there has been no formal study conducted at our institution to assess trainee interpretations of plain radiographs. In order to maintain high-quality practice within our radiology department, performance must be systematically monitored, analyzed, and improved ,5. ThereThe hospital ethics committee approved the present cross-sectional study. The patients\u2019 consent was waived due to the retrospective nature of this study. Five hundred eight plain radiograph reports were randomly selected from the radiology information system (RIS) for one year. Twenty-five radiograph reports were selected every second and fourth Monday of the month, alternating between general and mobile radiography. Unreported radiographs and irretrievable images were excluded.\u00ae). A list of patients, along with the dates and times of their plain radiographs, was given to two consultant radiologists for blinded review. They were instructed to indicate their findings and primary diagnosis for each patient. Any discrepancies between the two radiologists\u2019 reports were deliberated upon until a consensus was reached.The radiograph images were reviewed via Picture Archiving, Communication System, Digital Imaging, and the Communications in Medicine systems. The radiographs were interpreted and reported in a local reporting system called the Integrated Radiology Information System test to calculate the correlation between the accuracy and discrepancy rates, and p < 0.05 was considered statistically significant. The information was then compiled based on the following: date, request number, patient name, medical registration number (MRN), patient age and date of birth, anatomic area, clinical data, verification of trainee\u2019s report, term year of trainee, radiologists\u2019 reports, and final report categorization. The patient\u2019s data were kept confidential. Statistical analysis was performed using the chi-square (This study included 508 radiographs taken from a 1-year period. First-year trainees reported 122 radiographs (24%); second-year trainees reported 96 radiographs (19%); third-year trainees reported 113 radiographs (22%); fourth-year trainees reported 177 radiographs (35%).n = 351) of the reports made by the trainees. The remaining 31% of reports contained discrepancies, with minor discrepancies in 21% of cases (n = 107) and major discrepancies in 10% of cases (n = 50). The radiologists agreed with 69% (n = 85), Year 2 at 71% (n = 68), and Year 4 at 75% (n = 132). Unfortunately, there was reduced accuracy in Year 3 relative to the other groups, with 58% (n = 66). Hence, this led to an insignificant statistical value of p = 0.958 , Year 2 had 29% (n = 28), and Year 4 had 26% (n = 45). Results indicate that Year 3 had the highest level of total discrepancies, at 42% (n = 47). The variance level of minor discrepancies did not progressively decrease, with 22% (n = 27) among Year 1, 18% (n = 17) among Year 2, 28% (n = 32) among Year 3, and 18% (n = 31) among Year 4, for an average of 21.5% between the four groups from Year 1 to Year 4, as Year 1 had 30% (r groups . Major d= 0.953) . In shorp > 0.05 . n = 287). Spine and knee radiographs constituted 9.3% (n = 47) and 5.3% (n = 27), respectively. The rest of the anatomic areas accounted for the remaining 5%. The orthopantomogram (OPG) was the least-performed radiograph, as it represented only 0.2% (n = 1).The largest portion of radiographs performed were images of the chest, accounting for 56.5% radiograph had the highest incidence level, at 25%. Foot, abdomen, and skull radiographs demonstrated the second-worst value, at 20.3%. Major discrepancies were low for shoulder, wrist, chest, ankle, and spine radiographs, ranging from 17% to 4% in descending order. The trainees made no statistically significant major discrepancies for the humerus, elbow, radius/ulna, hand, knee, femur, tibia/fibula, pelvis, or OPG radiographs. The present study included 445 total radiographs (87.5%) for the adult age group and 63 radiographs (12.5%) for the pediatric age group. The accuracy levels for the two age groups were not significantly different, at 70% for the adult age group and 63% for the pediatric age group. Minor discrepancies made by trainees were less common among the adult age group than for the pediatric age group, at 9% and 17%, respectively.The major discrepancies made by trainees for both age groups were not significantly different, with an average of 20%.n = 248), than it was for mobile radiographs, at 58% (n = 103). The discrepancy rate for general radiographs was lower than for mobile radiographs, at 25% (n = 81) and 42% (n = 73), respectively. Some examples of major discrepancies in the mobile group consisted of missing the following diagnoses: pneumothorax, pneumomediastinum, pulmonary venous hypertension, and pneumonia. Examples of such cases are demonstrated in In this study, there were a total of 329 general radiographs (64.8%) and 179 mobile radiographs (35.2%). The accuracy rate was higher for general radiographs, at 75% , 26% minor discrepancy (n = 73), and 11% major discrepancy (n = 32). The accuracy of trainee chest radiograph reporting was low compared to other studies, and we discovered that the major discrepancies were generally due to missed diagnoses. The majority of missed diagnoses involved pneumonia and congestive cardiac failure. Infrequently, they involved lung mass, pneumothorax, pneumomediastinum, respiratory distress syndrome, and transient tachypnea in newborns. A study by Grasvenor et al., found 93% agreement between radiologists and trainees, but 11% (of 200) reports led to immediate changes in patient management [Our study showed that the chest radiograph is the most frequently performed radiological investigation. There were a total of 287 chest radiographs included in the present study, and they were interpreted with 63% accuracy chest radiograph interpretations found a significant inter-observer variability of 22%, for which the most frequent sources of disagreement were in the reporting of patchy and perihilar changes . SeveralMobile radiographs are mainly performed for bedridden patients, with mobile chest radiographs being the most common. The image quality for portable radiographs is significantly lower than that general radiographs, due to the projection of the radiograph, , unsatisfactory positioning of the patient, the image being taken when the patient is under inspiration, and poor patient exposure. One study revealed that the overall accuracy of chest radiographs in diagnosing pneumonia in bedridden patients was 69%, sensitivity and specificity were 65% and 93%, respectively, and positive and negative predictive values were 83% and 65%, respectively . These fThe present research has several limitations that could have affected our findings. The first limitation is found inherently in the nature of a retrospective study, in which there are delays in both the interpretation of results and identification of trends. During our research, trainees of varying levels reported the radiographs randomly, and junior trainees only sought help from senior trainees when they encountered difficulty interpreting the radiographs. At present, mobile radiograph reports are only allowed by senior trainees who are given the responsibility to verify all the radiographs interpreted by a first-year trainee. The quality of radiographs is significantly increased when junior and senior residents are paired. Ref. MultipleThe present study\u2019s second limitation was its relatively small sample size, with only 508 radiographs being included. Previous studies by Branstetter et al., Cooper et al., and Ruutiainen et al., had 1499, 93,132, and 33,024 cases, respectively ; the casIn order to reduce major discrepancies, we have now summoned our radiologists to verify preliminary radiographs reported by the residents, and we encouraged them to give feedback when major discrepancies are encountered. Following the study, this has become our practice and has resulted in remarkable improvement in residency training, and the residents have indicated that they value the feedback. Although recent literature has discussed that artificial intelligence is comparable with the preliminary report of radiology resident in interpreting radiographs , we stilIn the present study, we found that the accuracy level of the plain radiograph interpretations among trainees in our facility is lower than that in other facilities. Several factors could be contributing to this lower accuracy. To avoid this issue in the future, we have since implemented new procedures requiring radiologists to verify the preliminary radiograph reports of the residents."} +{"text": "Haemophilus influenzae type b vaccine (Hib), hepatitis B vaccine (HepB), polio vaccine (Pol), and rubella-containing vaccine (RCV). The COVID-19 pandemic has resulted in disruptions to routine immunization services worldwide. Full recovery to immunization programs will require context-specific strategies to address immunization gaps by catching up missed children, prioritizing essential health services, and strengthening immunization programs to prevent outbreaks established the Expanded Programme on Immunization in 1974 to protect infants against six diseases through vaccination and 5.9 million more than in 2019 (19.1 million); 18.2 million (73%) had received no doses, and 6.8 million (27%) were incompletely vaccinated with DTPcv. The number of zero-dose children was unevenly distributed by WHO region, economic classification,Global MCV1 coverage remained stable during 2015\u20132019 (85%\u201386%) but decreased to 83% in 2020 and to 81% in 2021. The largest declines in MCV1 coverage during 2019\u20132021 occurred in the South-East Asia Region (from 94% to 86%) and the Western Pacific Region (from 95% to 91%) . During Global coverage during 2019\u20132021 decreased for all of the following recommended childhood vaccines: BCG, from 88% to 84%; the completed Hib series, from 73% to 71%; RCV, from 69% to 66%; 3-dose HepB series, from 85% to 80%; HepB birth dose, from 44% to 42%; and the third Pol dose, from 86% to 80%. Global coverage with first dose of HPV vaccine among females declined from 20% in 2019 to 15% in 2021, and with the last dose, from 14% in 2019 to 12% in 2021. Global PCV3 coverage was stagnant , and coverage with the final dose of rotavirus vaccine series increased from 40% in 2019 to 49% in 2021.*** Since the start of the COVID-19 pandemic in 2020, a widespread decline in childhood vaccinations has occurred globally, putting millions of additional children at risk for vaccine-preventable diseases. Global DTPcv3 coverage declined by 5 percentage points during 2019\u20132021, meaning that at least 22.9 million children in 2020 and 25.0 million children in 2021 did not access or fully utilize routine immunization services. Immunization outreach services were particularly affected that did not report immunization coverage data for 2021 by July 7, 2022, estimated coverage for 2020 was used.Reversing worrisome vaccination trends and extending previous gains in coverage beyond prepandemic levels will require targeted and context-specific approaches to eliminate barriers to vaccination, particularly in communities with large populations of zero-dose children. WHO has published strategies and guiding principles for implementing catch-up vaccination and recovering essential immunization services (High routine childhood vaccination coverage achieved during 2015\u20132019 declined globally for most vaccines during 2019\u20132021 because of COVID-19 pandemic disruptions.In 2021, the estimated global coverage with 3 doses of diphtheria-tetanus-pertussis\u2013containing vaccine as well as the first dose of measles-containing vaccine decreased to 81%, the lowest level since 2008. Globally, 25.0 million children were unvaccinated or incompletely vaccinated in 2021, 5.9 million more than in 2019.Reversing declining vaccination trends and addressing immunity gaps, as well as extending previous gains in vaccination coverage beyond prepandemic levels, requires targeted and context-specific approaches that prioritize routine vaccination as an essential health service and improve access to vaccination across the life span."} +{"text": "A previous report found that the percentages of Hispanic persons who received HIV care, were retained in care, and were virally suppressed were lower than those among non-Hispanic White persons with HIV , 81% were male, 66% identified as White, 13% identified as Black, and 4% identified as AI/AN . Thirty-https://stacks.cdc.gov/view/cdc/121706).The overall median HIV stigma score among Hispanic persons with HIV was 31.7 . HIV stihttps://stacks.cdc.gov/view/cdc/121707). Among those who experienced health care discrimination, 62% felt that a doctor or nurse was not listening to what they were saying, 48% felt they were treated with less respect than others, and 48% perceived they were treated with less courtesy than others persons with HIV experience disparities in health outcomes compared with other racial and ethnic groups. Eliminating stigma and discrimination, which are barriers to HIV care and treatment, is a national priority.Hispanic persons with HIV commonly reported HIV stigma and health care discrimination. Among Hispanic persons with HIV, HIV stigma was highest among women (median stigma score = 35.6 of 100) and American Indian or Alaska Native persons (median stigma score = 32.7); health care discrimination was experienced more frequently by men than by women (23% vs. 18%) and by Black or African American Hispanic persons than by White Hispanic persons (28% vs. 21%).Culturally appropriate efforts to reduce stigma and discrimination among Hispanic persons with HIV should consider disparities by gender and race."} +{"text": "This analysis aimed to investigate how age, race/ethnicity, and geographical location contributed to vaccine hesitancy in a sample of New York City (NYC) Metropolitan Transit Authority (MTA) workers. Transport Workers Union, Local 100 members completed online surveys in August 2020 about their COVID-19 history, workplace protections and policies, fear of COVID-19 exposure, vaccination attitudes, and sociodemographic and health characteristics. We conducted univariate and bivariate analyses, followed by multivariate logistic regression, to determine the association between respondent age (younger than 50 vs. 50+) and vaccine hesitancy (willing vs. unwilling/unsure). We also produced spatial visualizations to examine these factors by participants\u2019 zip codes. Of 645 respondents, 59% were 50 years or older, 53% were non-White, and 71% expressed vaccine hesitancy. MTA workers ages 50+ were 46% less likely to be vaccine hesitant than their younger counterparts . Compared to Whites, non-Whites and those who did not report their race were significantly more likely to be vaccine hesitant. Those who were not concerned about contracting COVID-19 in the community had 1.83 greater odds of being vaccine hesitant than those who were concerned. Spatial visualizations revealed that the oldest respondents tended to reside in Queens. Zip codes with high vaccine hesitancy were clustered in Brooklyn, where non-White respondents tended to reside. The trends observed in COVID-19 vaccine hesitancy based on race and age persist in a population of high risk, non-healthcare essential workers."} +{"text": "Researchers often prefer different accelerometers for measurement of sleep and physical activity (PA) in older adults, but wearing multiple accelerometers increases costs and participant burden. We tested the hypothesis that the Actiwatch-2, commonly used to measure sleep, and the ActiGraph GT9X Link, commonly used to measure PA, yield comparable sleep parameters among 331 participants who wore them simultaneously for 7+/-1.6 nights in the BLSA. Compared to the Actiwatch-2, the ActiGraph estimated 50% greater wake after sleep onset, 89% longer wake bout length, 18% lower sleep fragmentation index (SFI), 5% lower total sleep time (TST) and 5% higher sleep efficiency. Yet, despite yielding different absolute values of TST and SFI, the devices generated similar between-person (relative) differences in TST and SFI. These devices may only be interchangeable for measurement of some relative sleep parameters in older adults. Studies with both devices and gold-standard polysomnography are needed."} +{"text": "Since March2019, successive waves of the COVID-19pandemic have challenged the mental health of frontline healthcare workers, who have been shown in numerous studies to be at increased risk for characterized psychiatric disorders. However, healthcare professionals who were not directly involved in the care of patients withCOVID-19 were often not investigated. In Morocco, the literature dealing with the psychological impact of the pandemic on backline health professionals is still scarce.The purpose of our survey is to assess the stress, anxiety, and depression of health workers who were not on the front lines of care forCOVID-19 patients.It is a survey developed on googleforms and disseminated via social networks targeting groups of health professionals in Morocco, during June2020. We used the DASS21 scale. The results were analyzed using the JAMOVI application.out of80 participants: 54%are men, 56%are aged between 31 and 40years old, 38%have been in practice for less than 5years of exercise, 66%are married, 41%are specialists 36%are residents and 21%are nurses, 44% work in psychiatric ward. Psychiatric symptoms: 64%have worries, 64% tired, 63% irritability, 59% sadness, 53% insomnia and 51% somatic complaints. 6.3%report substance use. DASS-21: 50%of participants have depression , 48.75%have Anxiety and 30%report Stress .The high level of job stress during the early months of the pandemic exposed health workers who were not on the front line of care forCOVID-19 patients to an increased risk of psychological decompensation.No significant relationships."} +{"text": "What outcomes are associated with direct oral anticoagulant (DOAC) reversal agents in intracranial hemorrhage (ICH)?In a meta-analysis of 32 studies including 1832 patients with ICH, 4-factor prothrombin complex concentrate (4F-PCC), andexanet alfa (AA), and idarucizumab were associated with a successful anticoagulation reversal in 77%, 75%, and 82% of patients, respectively; all-cause mortality rates were 26%, 24%, and 11%, respectively; and thromboembolic event rates were 8%, 14%, and 5%, respectively. A direct retrospective comparison of 4F-PCC with AA showed no differences in successful anticoagulation reversal, all-cause mortality, or thromboembolic events.In this study, factor Xa inhibitor reversal agents for ICH had similar safety profiles and outcomes, but the lack of head-to-head comparison warrants cautious interpretation. This systematic review and meta-analysis evaluates the safety and outcomes of direct oral anticoagulation (DOAC) reversal agents among patients with intracranial hemorrhage (ICH). Direct oral anticoagulant (DOAC)\u2013associated intracranial hemorrhage (ICH) has high morbidity and mortality. The safety and outcome data of DOAC reversal agents in ICH are limited.To evaluate the safety and outcomes of DOAC reversal agents among patients with ICH.PubMed, MEDLINE, The Cochrane Library, Embase, EBSCO, Web of Science, and CINAHL databases were searched from inception through April 29, 2022.The eligibility criteria were (1) adult patients (age \u226518 years) with ICH receiving treatment with a DOAC, (2) reversal of DOAC, and (3) reported safety and anticoagulation reversal outcomes. All nonhuman studies and case reports, studies evaluating patients with ischemic stroke requiring anticoagulation reversal or different dosing regimens of DOAC reversal agents, and mixed study groups with DOAC and warfarin were excluded.Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines were used for abstracting data and assessing data quality and validity. Two reviewers independently selected the studies and abstracted data. Data were pooled using the random-effects model.The primary outcome was proportion with anticoagulation reversed. The primary safety end points were all-cause mortality and thromboembolic events after the reversal agent.I2\u2009=\u200955%); all-cause mortality, 26% , and thromboembolic events, 8% . For AA, anticoagulation reversal was 75% ; all-cause mortality, 24% , and thromboembolic events, 14% . Idarucizumab for reversal of dabigatran had an anticoagulation reversal rate of 82% , all-cause mortality, 11% , and thromboembolic events, 5% . A direct retrospective comparison of 4F-PCC and AA showed no differences in anticoagulation reversal, proportional mortality, or thromboembolic events.A total of 36 studies met criteria for inclusion, with a total of 1832 patients . The mean age was 76 years, and 57% were men. For 4F-PCC, anticoagulation reversal was 77% (95% CI, 72%-82%; In the absence of randomized clinical comparison trials, the overall anticoagulation reversal, mortality, and thromboembolic event rates in this systematic review and meta-analysis appeared similar among available DOAC reversal agents for managing ICH. Cost, institutional formulary status, and availability may restrict reversal agent choice, particularly in small community hospitals. This group\u2019s risk factors for morbidity and mortality include older age, higher hematoma volumes, and hematoma expansion.9The US Food and Drug Administration (FDA) has approved the direct thrombin inhibitor (DTI) dabigatran and factor Xa inhibitors rivaroxaban, edoxaban, and apixaban for nonvalvular atrial fibrillation (NVAF) to prevent stroke and systemic embolism and for prophylaxis of venous thromboembolism (VTE) for coronary artery disease (CAD) or peripheral artery disease to reduce the risk of major cardiovascular events.11 In 2015, the FDA approved the use of idarucizumab to reverse the effects of dabigatran,12 which marked the introduction of the first specific reversal agent for DOACs. In 2018, andexanet alfa was approved to reverse factor Xa inhibitors (FXaI).13 While the safety data from these landmark trials were promising, head-to-head trials have not compared the safety and outcomes of idarucizumab or andexanet alfa (AA) with traditional nonspecific reversal agents . Such comparisons are limited to data generated from case series and cohort studies. This systematic review summarizes the safety and anticoagulation reversal success of non-specific and targeted DOAC reversal agents in patients with DOAC-related ICH.Initially, nonspecific DOAC reversal agents such as fresh frozen plasma (FFP), activated prothrombin complex concentrate (A-PCC), and 4-factor PCC (4F-PCC) showed promising safety and anticoagulation reversal in DOAC-related bleeding.PRISMA) statement independently selected and abstracted data from eligible studies on study design, patient demographic characteristics, anticoagulation reversal, mortality, and thromboembolic events. Discrepancies were resolved by discussion and consensus. The results were reviewed by senior investigators (A.N.A. and R.D.M.). The eligibility criteria were (1) adult patients (age \u226518 years) with ICH being treated with a DOAC, (2) reversal of DOAC, and (3) thromboembolic, mortality, or anticoagulation reversal outcomes. All nonhuman studies and case reports, studies with patients with ischemic stroke requiring anticoagulation reversal, studies evaluating different dosing regimens of reversal agents, and mixed study groups with DOAC and warfarin were excluded. Abstracts, conference presentations, editorials, reviews, expert opinions, and literature published in languages other than English were excluded.The primary outcome was the successful reversal of anticoagulation. The primary safety end points were all-cause mortality and thromboembolic events after administration of the DOAC reversal agent.15Qualitative bias evaluation was performed using the following key parameters for each study: (1) clear definition of the study population; (2) clear definition of outcomes and outcome assessment; (3) independent assessment of outcome parameters, and (4) identification of important confounders and prognostic factors. In the absence of randomized clinical trials, the risk of bias for all included cohort studies was assessed using the Newcastle-Ottawa Scale.17 If any bias was observed, further bias quantification was measured using the Begg-Mazumdar test,18 Egger test,16 and Duval-Tweedie trim-and-fill method.19 Sensitivity analyses were performed to assess the contribution of each study to the pooled estimate by excluding studies one at a time.Publication bias was estimated visually by funnel plots.20 The restricted maximum likelihood estimator21 was used to calculate the heterogeneity variance \u03c42. Knapp-Hartung adjustments22 were used to calculate the confidence interval around the pooled effect estimate. Relative risk (RR) was computed for the subanalysis comparing 4F-PCC with AA for the primary and safety end points. We evaluated the heterogeneity of effects using the Higgins I2 statistic with mild, moderate, and significant heterogeneity defined as 25%, 50%, and 75%, respectively.23 Meta-analysis was performed using R version 3.5.3 and RStudio version 1.2.5003 (RStudio).We anticipated considerable between-study heterogeneity, so a random-effects model using the generalized linear mixed models was used to pool effect sizes.45; 17 studies with 525 participants evaluated AA52; and 5 studies with 340 participants evaluated idarucizumab,56 consisting of a total of 1832 patients with ICH while receiving treatment with a DOAC. Eight studies had data on more than 1 agent.44 The characteristics of the studies are in the Thirty-six studies were included in the meta-analysis , and 57% were men. Individual characteristics of patients with ICH were unavailable for most studies . For AA, it was 75% , and for idarucizumab for dabigatran reversal, it was 82% .I2\u2009=\u200968%; 95% CI, 40%-88%). For AA, it was 24% , and for idarucizumab for dabigatran reversal, it was 11% .I2\u2009=\u200941.3% 95% CI, 0%-71.8%). For AA, it was 14% , and for idarucizumab, it was 5% .31 with 17 patients. Patient-level data were unavailable to compare the primary and safety outcomes of 4F-PCC for reversing DTI. After the exclusion of these 2 studies, the data on the comparison of 4F-PCC and AA were derived from 8 retrospective studies.44 We found that 4F-PCC had a comparable proportion of successful anticoagulation reversal , proportional mortality , and thromboembolic event rate when used for the reversal of FXaI in patients with ICH and AA for patients with ICH, including the subanalysis with direct comparison of 4F-PCC with AA . While mortality rates were likewise similar for 4F-PCC and AA , there may be a higher anticipated thromboembolic event rate following reversal with AA (14% vs 8%). However, the subanalysis comparing 4F-PCC with AA did not differ in all-cause mortality or thromboembolic rates. Idarucizumab, the reversal agent specific to dabigatran, achieved anticoagulation reversal in 82% of patients with ICH, with low mortality and thromboembolic complications .57 In NVAF trials, ICH rates were 0.10%/y to 0.44%/y for DOACs vs 0.38%/y to 0.90%/y for warfarin.59 In VTE trials, ICH rates were very low for patients receiving both DOAC (0%/y to 0.1%/y) and warfarin (0.2/y to 0.4%/y).61ICH is an often-catastrophic complication of long-term anticoagulant therapy. The potential for ICH has long been limiting the widespread implementation of anticoagulation for patients with firm treatment indications, such as atrial fibrillation. In the absence of anticoagulant therapy, older adults who are most at risk of falling and suffering intracranial hemorrhage are also those at the most significant risk for thrombotic events. Fortunately, the risk of ICH is lower with DOAC than with warfarin. In a recent meta-analysis, dabigatran, apixaban, and rivaroxaban reduced ICH risk by 60%, 57%, and 41%, respectively, compared with warfarin.63 Despite the availability of proven reversal strategies for warfarin, these mortality rates were similar for DOACs and warfarin .Nevertheless, the consequences of ICH while taking a DOAC are considerable. In the preantidote era, 30-day mortality rates of 35% to 48% were noted.Compared with FFP, 4F-PCCs contain approximately 25 times more vitamin K\u2013dependent clotting factors . Rapid administration time, low volume infusion, leukocyte-free product, minimal risk for transfusion-related lung injury, and safety in heart failure all made 4F-PCCs favorable over FFP, and 4F-PCC was used for FXaI-related bleeding reversal before specific DOAC reversal agents were approved.8 evaluated the use of 4F-PCC in 146 patients with DOAC-related ICH across 19 tertiary care centers in Germany in a retrospective cohort design. Of these, 131 patients were receiving FXaI , 15 were receiving dabigatran, and subsequently, 103 patients received 4F-PCC. Imaging evidence of hematoma enlargement (4F-PCC vs no 4F-PCC) was 33.3% vs 31.0% in rivaroxaban group, 46.2% vs 50.0% in apixaban group, and 22.2% vs 16.7% in the dabigatran group . The mortality rate was 19.9% at discharge and 29.5% at 3-month follow-up, with no significant differences between patients with and without PCC treatment. In another study, Coleman et al36 included 170 patients with DOAC-related ICH and reported a mortality rate of 25.3% in the 4F-PCC treatment cohort in 45 US hospitals.36The RETRACE II study investigators45 Albeit with significant heterogeneity, our meta-analysis found a combined proportion of anticoagulation reversed of 77%, a mortality rate of 26%, and a thromboembolic event rate of 8% and safety .te of 8% -3.13 that enrolled 171 patients with FXaI-associated ICH and reported an anticoagulation reversal rate of 80.7%, a mortality rate of 14%, and a thromboembolic complication rate of 10%. Since then, multiple small retrospective studies in patients with ICH52 have reported rates of anticoagulation reversal between 50% and 91%; mortality, between 9% and 39%; and thrombotic complications, between 0% and 31%. Our meta-analysis showed a combined proportion of anticoagulation reversal of 75%, a mortality rate of 24%, and thromboembolic event rate of 14% , and the thromboembolic event rate was 0.9% in this study. Confounding by disease severity was a major limitation affecting the interpretation of the study . They also showed that idarucizumab use was associated with a reduced length of stay and higher hospitalization costs . Other smaller studies have shown a proportional anticoagulation reversal rate of 89% to 100%, a mortality rate of 0% to 15%, and a rate of thrombotic complications of 0% to 6%.56 Our meta-analysis found a combined anticoagulation reversal rate of 82%, a mortality rate of 11%, and a thromboembolic event rate of 5%.The FDA approved idarucizumab in 2015 to reverse the anticoagulant effects of oral dabigatran. RE-VERSE AD64 However, anti\u2013factor Xa levels specific to a given DOAC are unlikely to be available or will not be performed in a time frame that will affect decision-making at the bedside in the emergency setting in most institutions. As such, a generic chromogenic anti\u2013factor Xa activity can rule out a meaningful level of any FXaI. A normal thrombin time usually helps exclude supratherapeutic anti-FXaI levels.66 Additionally, the measures of viscoelastic hemostatic assays, such as rotational thromboelastometry and thromboelastography, need to be further explored in emergencies.70 When available in a timely fashion, these assays may be especially useful in determining the need for a specific reversal agent in patients who have received 4F-PCC from a transferring facility.The individualization of the reversal strategy for DOACs in patients with ICH should consider (1) confirmation of the presence and extent of anticoagulation with DOACs, (2) pragmatic selection of patients, and (3) availability of specific DOAC reversal agents at the treating facility. For all FXaIs, the anti\u2013factor Xa activity level can reliably assess the degree of anticoagulation, qualitatively and quantitatively, provided that the instruments are calibrated for the specific agents.71 More sensitive assays for monitoring dabigatran activity include thrombin time, diluted thrombin time, and ecarin thrombin time. A normal thrombin time virtually excludes dabigatran presence. Although no international reference exists for calibration, mass spectrometry methods are considered the criterion standard for measuring dabigatran. However, these analyses require specialized laboratories, which often preclude their utility in life-threatening emergencies.Screening tests, such as the prothrombin time and activated partial thromboplastin clotting time, have high variability and are insufficient to exclude the presence of dabigatran.Pragmatic patient selection for DOAC reversal should include both severity of ICH and the time window for reversal. The factors for patient selection include ICH severity, anticipated risk of hematoma expansion, immediate need for surgical decompression, time since the last dose of DOAC, and creatinine clearance. The time window should be individualized based on clinical presentation and the patient\u2019s rate of deterioration.Finally, the availability of specific DOAC reversal agents in the treating facility warrants review and consideration. In a community setting with limited availability of AA and/or idarucizumab, non-specific reversal agents may be the only option. Other scenario-specific approaches may include activated charcoal (to remove the unabsorbed drug if the last ingestion was recent) and hemodialysis .NCT03661528) compares AA with usual care (expected to include administration of 4F-PCC in most cases) in patients with acute ICH associated with FXaI. Enrolling since January 2019, this study is expected to complete in 2023 and enroll approximately 900 participants. The primary outcome includes hemostatic efficacy at 12 hours. The secondary outcome comprises a change in baseline anti\u2013factor Xa activity. This trial will provide more robust evidence of the relative benefit of the 2 DOAC reversal strategies for ICH.An ongoing randomized clinical trial , differing mechanisms (traumatic and nontraumatic), and insufficient information to determine the risk of hematoma expansion (higher risk in patients with more severe ICH and particularly in those who present early after symptom onset). These factors should be specifically addressed in future research. Additionally, reversal agent effectiveness and safety profile for patients requiring emergent surgical decompression (craniotomy or ventriculostomy) should be examined.72 some studies used prespecified adjudication criteria or did not provide details of the criteria used to define the stability of ICH on repeated imaging (eAppendix 6 in the 74Our study has several limitations. First, patient-level data were not available for analysis. Second, smaller cohorts of case series and retrospective studies were included. Third, no comorbidities-matched head-to-head comparative trials are available between different reversal agents. Fourth, although most studies used the International Society of Thrombosis and Hemostasis criteria for assessing the effectiveness of major bleeding management,In this study, we evaluated the safety and anticoagulation reversal success measures of the available DOAC reversal agents to improve the understanding of their risk-benefit profile. Among patients presenting with ICH, the decision to reverse DOAC-associated anticoagulation and choice of agent should be individualized. Among the reversal agents, idarucizumab and AA are specific for the reversal of dabigatran and FXaIs, respectively. On the other hand, 4F-PCC is a nonspecific reversal agent studied predominantly in the reversal of FXaI. Overall, the proportion of anticoagulation reversed, mortality, and thromboembolic event rates appear similar between 4F-PCC and AA for FXaI reversal. However, the lack of head-to-head comparison warrants cautious interpretation.75 Randomized clinical trials directly comparing the effectiveness and safety of 4F-PCC with specific reversal agents, ie, idarucizumab or AA, are needed to determine the optimal reversal strategies for patients with DOAC-related ICH. Additional research is needed to optimize patient-centered best practices and improve outcomes for those requiring reversal therapy for ICH.4F-PCC is more readily available in some community settings and cheaper."} +{"text": "Staphylococcus aureus was the main microorganism isolated (70%) from blood cultures. Thirty patients (49%) underwent heart surgery: thirteen had aortic valves, eleven had mitral valves, and six had tricuspid valve interventions. IE in PWIDs was relatively common, and patients with native valve right-sided IE had a better prognosis, with a low rate of surgical interventions.Intravenous drug use is a predisposing condition for infective endocarditis (IE). We report the clinical features of IE, taken from the Italian Registry of IE, in people who inject drugs (PWIDs). The registry prospectively collected epidemiological, clinical, in-hospital, and follow-up data on patients with IE from 17 Italian centers. A total of 677 patients were enrolled, and 61 (9%) were intravenous drug users (IDUs). Most PWIDs were male (78.6%), and aged between 41 and 50 years old (50%). The most frequent comorbidities were HIV (34.4%) and chronic liver disease (32%). Predisposing factors for IE were present in 6.5% of the patients, and 10% had minor valvular abnormalities. IE had occurred previously in 16.4% of the patients, and 50% of them had undergone heart surgery. Overall mortality was 9.8% in IDUs and 20% in patients with recurrent IE. IE in PWIDs mostly affected the native valves (90%). The echocardiographic diagnosis of IE was based on the detection of vegetation in 91.82% of cases. Intravenous drug use is a predisposing condition for infective endocarditis (IE) and represents a minor diagnostic criterion for diagnosis . In the Currently, IE in the general population remains a relatively rare disease, with a high in-hospital mortality rate, ranging from 15 to 26% depending on the case series and an even greater morbidity rate, due mainly to heart failure or valvular vegetations with high embolic potentials . PrognosData recently published by the Italian Registry of Infective Endocarditis (RIEI) indicated that, despite continuous epidemiological changes, IE in PWIDs still represents 9% of IE enrolled in the RIEI . We repoRIEI prospectively collected epidemiological, clinical, in-hospital, and follow-up data on patients with IE established according to the modified Duke criteria from 17 RIEI has prospectively enrolled consecutive cases of infective endocarditis in every participating center, analyzing diagnostic and therapeutic data from a real world practice perspective. No experimental interventions were proposed, and treatments were entirely decided by treating physicians. Enrollment required the following features: (1) high clinical suspicion of acute and/or active infective endocarditis (definite or highly possible infective endocarditis according to Duke criteria), (2) consecutive recruitment and prospective evaluation at presentation, (3) sufficient data availability to fulfill enrolment and follow-up records, and (4) enrollment of consecutive cases and strict monitoring of suspected cases in the laboratory of echocardiography as well as in the microbiology laboratory for identification of microorganisms. For the purposes of the present study, only cases with definite IE according to modified Duke criteria and complete echocardiographic data have been included.Complete methods and data acquisition and storage methods, together with definitions and procedures, have already been published .Of the 677 patients enrolled in the RIEI, 61 were intravenous drug users (IDUs) (9%). The main clinical characteristics and comorbidities, compared with the remaining patients in the RIEI registry, are reported in Previous cases of IE had occurred in 16.4% (10) of patients, and 50% of them underwent heart surgery. Overall mortality was 9.8% in IDUs, but it rose to 20% in patients with recurrent IE.3.IE in PWIDs mostly affected the native valves , especially the left-side valves . Prosthetic valve IE was reported in 6.5% of patients and in two cases with endocavitary devices. Twenty-one PWIDs (34.42%) were HIV-positive, and 33% of them had a CD4 level <200/mmThe most prominent sign was a fever of >38 \u00b0C, which was present in 100% of IE cases. Clinical vascular embolic events were found in 18% of patients upon physical examination, while imaging studies disclosed pulmonary infarction in 21% of patients. An acute clinical course led to immediate hospital admission in 40% of patients, and within 7 days in 31% of patients. In both instances, the rate of hospital admission after medical consultation was faster than for the other patients in the RIEI. Echocardiographic diagnoses of IE were based on the detection of vegetation in 91.82% of patients and on a myocardial abscess in 13%.Staphylococcus aureus was the main microorganism isolated (70%), with a methicillin resistance rate of 12.5% , usually occurring in patients with poor oral hygiene (78%). Infections were mostly community-acquired , and only six cases (9.8%) were nosocomial.The second most frequent microorganism was Thirty patients (49%) underwent heart surgery: thirteen with aortic valve replacements , eleven with mitral valve interventions (four repairs) of which two were associated with tricuspid valve replacement, and six with further tricuspid valve interventions (four replacements). The indications for tricuspid valve surgery were pulmonary embolism with a large residual vegetation in two cases, bacteremia or persistent infection in two cases, and severe tricuspid regurgitation and large vegetation in two cases. All patients undergoing tricuspid valve surgery had severe valvular insufficiency. Many of the 22 cases undergoing left-sided valve surgery had multiple indications; severe or moderate-severe valvular insufficiencies and vegetations > 10 mm occurred in 17 cases (77%). In addition, 13 patients (59%) had heart failure, 10 (45%) had previous embolic events, 5 (22%) presented with myocardial abscesses, and 3 (13%) had persistent bacteremia. Pulmonary infarction was found in 26% of PWID cases, occurring more frequently than in IE cases in the general population .Twenty-six patients had right-side IE . In this group, all patients had high fever, but none had neurological symptoms. Three had systemic embolic events, seven presented with heart failure , ten had septic pulmonary infarction, ten presented with severe tricuspid valve insufficiencies, and eight (30%) underwent tricuspid valve surgery (three plastic repairs). None had pulmonary oedema. There was only one death in this group (3.8%) observed in a HIV-positive patient with low CD4+ lymphocyte count.Ten out of the twenty-one HIV-positive patients presented with heart failure , which was severe in five cases. In-hospital complications occurred in 14 patients, mostly with stroke, followed by systemic embolic events and septic pulmonary infarction. Eleven of the twenty-one patients underwent cardiosurgery (52%), mostly for aortic or mitral valve replacements . The in-hospital mortality rate for this group was 19%.Even in the absence of heart disease, IDU is considered a predisposing condition for IE in developed countries, but the epidemiology and clinical manifestations of IE in PWIDs are continuously evolving ,3. PWIDsIn contrast to some reports, but in agreement with other studies, the overall prognosis of IE in PWIDs is still variable, despite the high frequency of heart surgery 49%). It is slightly lower than in the general IE population, with a mortality rate of 9.8%, rising to 20% in relapsing events ,9. As re%. It is Our data highlight some new features of IE in PWIDs, such as the increasing median age of patients; they are older than previously reported (41 to 50 years old), probably because they are being referred to care later in life when comorbidities may be present. Indeed, 6.1% of patients already had IE, 10% had prosthetic heart valves, and two patients had endocavitary devices. Notably, more than 30% of cases are HIV-seropositive, with poor responses probably due to a lower compliance with treatment. In our study, HIV-positive PWIDs with IE were up to 50 years old and had a prolonged history of intravenous drug use and more advanced heart disease than in the past . These fIn conclusion, IE in PWIDs was relatively common in our registry, and patients with native valve right-sided IE had a better prognosis, with a low rate of surgical interventions. The mortality rate was high in patients who experienced a relapse due to prolonged use of injected opioids, left heart involvement, or a positive HIV status. Our preliminary data add to the growing body of evidence demonstrating increasing concerns about substance misuse and injection-mediated risk and suggest the need for public health interventions and clinical policies to manage drug abusers. Further analyses are needed to complete the evaluation of these preliminary findings."} +{"text": "Patients with asthma are treated in primary healthcare facilities (PHCFs) in Taiwan, where the asthma control status associated with acute exacerbation (AE) and use of oral corticosteroids (OCS) and short-acting \u03b22-agonist (SABA) inhalers remains unclear. A cross-sectional, close-ended, face-to-face questionnaire survey invited board-certified physicians who treat adult asthma patients in PHCFs. The contents of the questionnaire included three parts: rescue OCS to treat AE, regular OCS for asthma control, and AE-related adverse outcomes. There were 445 out of 500 physicians who completed the questionnaire, with 61% of them being non-pulmonologists. A substantial proportion of asthma patients needed rescue OCS or regular OCS each month, or \u22653 canisters of SABA inhalers per year. Approximately 86% of physicians reported their patients with \u22652 AE-related unscheduled visits to clinics or emergency departments in the past year. A total of 41% of physicians reported their patients receiving intubation or intensive care in the past year. A total of 92% of physicians prescribed rescue OCS \u2264 40 mg/day. A total of 92% of physicians prescribed rescue OCS for a duration of \u22647 days for AEs. A total of 85% of physicians prescribed regular OCS \u2264 10 mg/day for asthma control. This is the first study to present the perceptions of asthma-treating physicians on the use of OCS in PHCFs. In summary, 31% of physicians reported \u2265 6% of their patients needed OCS for asthma control and 41% of physicians reported their patients with adverse outcomes in the past year. Thus, the need to improve asthma control in Taiwan is suggested by our study results. Asthma is one of the most serious health concerns worldwide. According to the World Health Organization, asthma affected an estimated population of 262 million people in 2019 and caused 461000 deaths [Oral corticosteroids (OCS) are considered the most effective short-term treatment for AE of asthma and long-term management for uncontrolled severe asthma (SA) despite their significant side effects . RecentlAccording to a survey that was conducted in the UK to investigate the asthma population in primary care practices, frequent exacerbators, are defined as those requiring \u2265 2 rescue OCS courses for AEs in the past 12 months, ranging from 4% to 14% . AccordiIn Taiwan, more than 80% of asthmatics were treated by physicians in primary healthcare facilities (PHCFs), while 12% were treated by pulmonologists . TherefoThe study was designed as a cross-sectional, close-ended questionnaire survey to colleA simple, short questionnaire was developed by the study team based on a literature review, consisting of appropriate items relevant to the current practices involving asthma AEs and the use of OCS. The questionnaire comprises 15 questions and is categorized into two parts\u2014the backgrounds of the physicians and the physicians\u2019 perspectives on asthma management. The entire questionnaire is presented in the p value < 0.05.Data were analyzed using the statistical software SPSS . Associations between categorical data, including clinical settings, medical specialty, and proportion of responses to questions were analyzed using the chi-squared test. Differences were considered significant at This study was conducted between 20 May and 31 August 2021. A total of 445 participants in PHCFs were invited, and all completed the interviews. The responding documents were valid, without any significant missing data. In this survey, the leading medical specialty was pulmonology (39.1%), followed by family medicine (18%) and pediatrics (17.8%). The medical practice was divided into doctors\u2019 offices (64.3%)- and community hospitals (35.7%) . Most puApproximately 55.5% of physicians reported that >6% of asthma patients experienced AEs that required OCS treatment every month. Moreover, 8.8% of physicians reported that >20% of asthmatics required rescue OCS A. In addApproximately 90.5% of physicians prescribed regular OCS for asthma control in \u226410% of asthmatics per month A. ApproxWhile considering the percentage of asthmatics experiencing \u22652 unscheduled visits to the clinic or ED due to AEs in the past year, physicians reported that only 13.7% of asthmatics were event-free A. Of theFrom the physicians\u2019 perspectives based on medical specialty, pulmonologists rated their asthmatics with a higher proportion of rescue and regular OCS use, more unscheduled visits, more ICU admissions, a higher proportion of SABA over-users, and higher confidence in biologics-related benefits, when compared to non-pulmonologists .In this study, we discovered that the majority of asthma-treating physicians (60.9%) in PHCFs were non-pulmonologists. From the physicians\u2019 perspectives, there was a substantial proportion of asthmatics who require rescue OCS or regular OCS per month, or overuse SABA inhalers per year and experience poor asthma outcomes based on AE-related unscheduled visits to the ED, intubations, or ICU admissions. For the first time, we presented the perceptions of asthma-treating physicians in PHCFs, and these results indicate the need to improve asthma control in Taiwan.In our previous study, based on the NHIRD between 2000 and 2005 asthma mIn this study, up to 84.6% of the physicians reported that their asthmatics had undergone \u22652 AE-related unscheduled visits to the clinic or ED, as well as 40.9% reported their asthmatics had experienced \u22651 intubation or ICU admission in the past year. As per the National Health Interview Survey in the USA conducted from 2011 to 2016, 44.7% of adult asthmatics experienced \u22651 AE and 9.9% had \u22651 AE-related ED visit in the past year . In the In the early large-scale randomized controlled trial (FACET study) examining the effects of ICS with or without long-acting \u03b22 agonists on asthma control in European countries, the rate of severe AE requiring OCS ranged from 19% to 39% in different treatment arms during the 1-year follow-up period ,19. ReceAs per current guidelines, regular OCS as part of maintenance treatment in asthma control is only recommended for those failing conventional treatment despite adequate inhaler use and management of comorbidities . The proIt is estimated that SA may affect 5\u201310% of asthma patients , and patIt is questionable whether pulmonologists reported worse asthma control status in this survey. Based on patient-level data, the characteristics of asthmatics treated by pulmonologists showcased higher asthma severity, more anti-asthmatic medication consumption, more comorbidities, and greater healthcare utilization than those treated by non-pulmonologists ,27,28. IIt may be argued that physicians in community hospitals were included and regarded as primary care physicians. Moreover, outpatients in hospitals in Taiwan are quite different from those in other countries because Taiwan has a unique healthcare system. Taiwan has a government-run, single-payer health insurance system, which is characterized by mandatory coverage for all citizens , convenient accessibility, low costs, and almost complete coverage of medical services. The system has neither a gatekeeper role nor restrictive referral regulations. That is, any outpatient has the freedom to choose any specialist/subspecialist in any hospital without a referral . The TaiThis study has some limitations. This study was based on a questionnaire survey that did not include patient-level data. Therefore, we could not exclude recall bias. Moreover, the different medical specialties and practice settings of the participating physicians might have some impact on the response results. The results might indirectly reflect the current status of asthma control in PHCFs, with a lack of precise data regarding important asthma control outcomes, such as SABA dispensing data, the rates of ED visits, hospitalizations, and ICU admissions.A substantial proportion of asthmatics in PHCF are frequent exacerbators, SABA over-users, and potentially inappropriate OCS users. Both patients and physicians need to be educated on advanced asthma management. In particular, physicians in PHCFs need better recognition of SA patients and arrange timely referrals to optimize asthma control."} +{"text": "We examined racial disparities in household food insecurity among low-income Americans with and without vision impairment in the National Health Interview Survey, years 2011-2018. Among 257,620 U.S. adults below a threshold of 150% poverty, 15% of White, 16% of Black, and 8% of Asian Americans, and 18% of American Indians and Inuits reported vision impairment. In analyses adjusted for sociodemographic variables, vision impairment was associated with >100% greater odds (95% CI=2.01-2.31) of 30-day food insecurity, as compared to no vision impairment. Further, odds of household food insecurity were higher among Black Americans , and American Indians and Inuits than White Americans, while Asians had lower odds . These findings highlight that low-income adults with vision impairment and racial minorities experience food disparities and dietary inadequacy, an area of disadvantage that can influence overall health, in a nationally representative sample in the U.S."} +{"text": "This retrospective study was performed over 6 months, including newborns with a gestational age between 34\u201336 weeks and 6 days in the Department of Obstetrics, Gynecology and Neonatology, Alessandrescu-Rusescu National Institute of Mother and Child Health. The following variables were assessed: infants' gestational age, delivery mode, respiratory morbidity, and the need for respiratory support. During the mentioned period, 112 late preterm infants were born, out of whom 9.8% represented late preterm infants conceived by in vitro fertilization. The delivery mode of late preterm infants conceived by in vitro fertilization was exclusively by C-section (100%) compared to those conceived spontaneously (44.5%). 18.1% of IVF late preterm infants developed transient tachypnea of the newborn. In the non-IVF group, respiratory distress syndrome was present in 5.9% and transient tachypnea in 33.6% of cases. No IVF late preterm infant required hospitalization in neonatal intensive care for more than 3 days, compared to 19.8% of naturally conceived late preterm infants. Respiratory distress syndrome very seldom occurs in late preterm IVF infants due to prenatal prophylactic treatment with corticosteroids. Respiratory pathology is rarely present due to very careful monitoring during pregnancy, the presence of a neonatal team in the delivery room for possible resuscitation, and providing proper care according to the good state of health during the short, one-week hospitalization.This study aimed to identify the incidence of In vitro fertilization (IVF), a method of assisted reproduction techniques (ART), was perfected by the British Scientist Professor Robert Geoffrey Edwards, allowing on July 25th 1978, in London, the birth of Louise Joy Brown, the first child conceived through this method. IVF is considered one of the greatest medical achievements of the 20th century, \u201cone of the fastest growing areas of medicine, having expanded far beyond the imaginations of those who pioneered the technique that led to the birth of Louise Brown\u201d [e Brown\u201d .Preterm birth is defined as the birth of a child before 37 fulfilled weeks of gestation and is the leading cause of neonatal mortality . New gloThe British Medical Journal defines prematurity categories based on gestational age (GA) (weeks-w): extreme prematurity <28w), severe prematurity (28\u201331w), great prematurity (32\u201333w), and late prematurity (34\u201336w). This classification was necessary because LPT represent 8\u20139% of the newborns and 74% of the preterm neonates, their incidence rising by 20% since 1990 . Late-prw, severein vitro fertilization of late preterm newborns (IVF-LPT) and the presence of respiratory pathology in this category of preterm newborns compared with those conceived naturally (non-IVF newborns).The objective of this retrospective study was to identify the incidence of The retrospective study was performed in 2019 for 6 months at the Department of Obstetrics, Gynecology and Neonatology, Alessandrescu-Rusescu National Institute of Mother and Child Health, Bucharest, Romania. We included 112 IVF and naturally conceived infants admitted to our department. The following were monitored: infants' gestational age, delivery mode, respiratory morbidity, the need for respiratory support, and mortality. Data were collected from medical records and analyzed using IBM SPSS Statistics v20.0.0, performing descriptive statistics.During the mentioned period, there were 44 IVF infants recorded, 61.4% of whom were born preterm. Late preterm infants (LPT) accounted for 25% of the total number of IVF infants and 40.7% of those who were born preterm .During the study period, 112 preterm infants were born at a gestational age of 34\u201336 weeks and 6 days (LPT). LPT conceived by IVF accounted for 9.8% of the total number of LPT recorded during the study. According to gestational age, in both groups, LPT infants, in most cases, were born at 36 weeks of gestational age .vs. 93.1% in the non-IVF group; the breech presentation was 45.5% in the IVF-LPT group vs. 6.9% in the non-IVF LPT infants.The incidence of IVF LPT newborns by gender was: female \u2013 81.8%, male \u2013 18.2%. In the non-IVF group, 51.4% were female, and 48% were male newborns. Regarding birth weight (BW), 54.5% of IVF-LPT infants had a BW over 2500 grams and 45.4% between 2000\u20132500 grams. In the non-IVF-LPT group: 52.4% had BW >2500 grams, 40.5% 2000\u20132500 grams, 5.2% between 1500\u20131999 grams and 1.9% were under 1500 grams. A big difference was registered regarding fetal presentation: the percentage of cranial presentation in IVF-LPT infants was 54.5% There were differences in the Apgar score between the two groups: IVF-LPT infants had an Apgar score under 7, compared to the non-IVF group in which 5.9% had an Apgar score between 4\u20136 and 1.9% had an Apgar score under 3 .Resuscitation at birth was not required in IVF-LPT infants, in contrast to the non-IVF-LPT infants who required resuscitation at 10.9%.in vitro fertilization, according to the results of studies in other countries, are more likely to require respiratory support, require more aggressive respiratory support and receive surfactant indicative of true respiratory distress syndrome [Respiratory pathology in LPT remains at higher risk when compared with term infants . This insyndrome . In our The low incidence of respiratory pathology and required oxygen therapy in IVF-LPT newborns was probably due to the prophylactic corticoid therapy on 100% of the pregnant IVF patients and very well-supervised IVF pregnancies .versus 5.9% in the non-IVF group , resuscitation at birth, and being prone to RDS.IVF late preterm infants have an increased risk for respiratory morbidity, inversely proportional to gestational age. LPT newborns are at increased risk for respiratory distress syndrome (RDS), transitory tachypnea of the newborn (TTN), apnea, pulmonary hypertension (PPHN) and pneumothorax compared with newborns delivered at term .Even if concerns have been raised over the past years, IVF has been used more frequently in recent years. Further research is needed to effectively evaluate IVF newborns and their risk.In our study, respiratory distress syndrome rarely occurred in late preterm IVF infants due to prenatal prophylactic treatment with corticosteroids. Respiratory pathology is rarely present due to careful monitoring during pregnancy, the presence of the neonatal team in the delivery room for possible resuscitation and providing proper care during the short hospitalization."} +{"text": "These results highlight the complexity of HIV care and the important prevalence of comorbidities. Personalized health care that integrates care and prevention of all comorbidities with HIV, with attention to social determinants of health, is necessary to optimize health and well-being of women living with HIV.Life expectancy for people living with HIV has increased, but management of HIV is now more complex due to comorbidities. This study aimed to measure the prevalence of comorbidities among women living with HIV in Canada. We conducted a cross-sectional analysis using data from the 18-months survey (2014\u20132016) of the Canadian HIV Women\u2019s Sexual and Reproductive Health Cohort Study (CHIWOS). Self-report of diagnosed conditions was used to measure lifetime prevalence of chronic physical conditions, current mental health conditions, and disabilities. We examined frequency of overlapping conditions and prevalence stratified by gender identity, ethnicity, and age. Among 1039 participants, 70.1% reported a physical health diagnosis, 57.4% reported a current mental health diagnosis, 19.9% reported a disability, and 47.1% reported both physical and mental health comorbidities. The most prevalent comorbidities were depression (32.3%), anxiety (29.5%), obesity (26.7%, defined as body mass index >30 kg/m The introduction of antiretroviral therapy (ART) has reduced complications associated with AIDS-defining illness and has significantly increased the life expectancy of people living with HIV . As lifeThe mechanisms resulting in high prevalence of comorbidity in people with HIV are multifactorial and may be linked to the HIV virus itself, long-term toxicity of ART, immune activation, chronic inflammation, and the intersection of unfavorable social determinants of health ,7. For eWithin a global context, traditional gender roles may also impact treatment and adherence to ART ,14,15. WThe objective of this study was to measure the prevalence of comorbidities among women living with HIV in Canada overall, stratified by gender identity, and by age and ethnicity.www.chiwos.ca, last accessed on 5 July 2022) [We conducted a cross-sectional analysis using data from the 18-months survey (2014\u20132016) of the Canadian HIV Women\u2019s Sexual and Reproductive Health Cohort Study (CHIWOS). CHIWOS is a multi-site, longitudinal, community-based research study conducted across Canada ly 2022) . Data we . Data wly 2022) . All parParticipants self-reported their gender identity, and sex at birth. Although all participants in CHIWOS identified as women, for the purposes of this article, gender was dichotomized as transgender women and cisgender women .2. Although we recognize that some of these conditions can present as more acute than chronic , these conditions often require lifelong attention in healthcare; therefore, they were included in the questionnaire.Prevalence of a chronic physical condition, a current mental health condition, or a current disability was determined via self-reported responses to the 18-month surveys. We used the 18-month survey data, rather than baseline, as it contained the most comprehensive questions regarding comorbidities. Prevalence of physical health conditions was measured for multiple chronic diseases. We asked: \u201cHave you ever been diagnosed with any of the following health concerns?\u201d The participant could then select one or more of the following responses: asthma/Chronic Obstructive Pulmonary Disease (COPD), thyroid problems, coronary artery disease, cardiac arrhythmia, osteoporosis/osteopenia/decreased bone density, fractures, stroke, deep vein thrombosis and pulmonary embolism, high cholesterol, hypertension, irritable bowel disease, renal problems, arthritis and osteoarthritis, chronic pain, and cognitive impairment. Self-reported height and weight was also used to identify obesity, defined as a body mass index (BMI) of >30 kg/mFor previous history of cancers, we asked: \u201cHave you ever been diagnosed with any form of cancer or pre-cancer?\u201d If a participant answered yes, they could select one of more of the following responses: oral or pharynx, thyroid, skin, lung, breast, liver, stomach or small bowel, colon or rectum, anal, ovarian, endometrial , cervical, vulvar, lymphoma/leukemia, bladder, kidney, high-grade cervical pre-cancer , high-grade vulvar or vaginal pre-cancer , high-grade anal pre-cancer , and other (please specify). Note that since the time period we designed the questionnaire, the preferred terminology to designate high-grade precancer changed to high-grade squamous intraepithelial lesion (HSIL) , which iFor mental health conditions, we asked: \u201cWhich, if any, of the following mental health conditions are you currently living with? Please only include conditions that have been diagnosed by a health care provider\u201d. Participants could select one or more of the following options: alcohol addiction, anxiety, anorexia or bulimia nervosa, bipolar disorder, personality disorder, dementia, depression, drug addiction, obsessive compulsive disorder, post-traumatic stress disorder (PTSD), schizophrenia, and sleep disorders.For disabilities, we asked: \u201cDo you have any of the following disabilities?\u201d. Participants could select one or more of the response options: partial deafness, complete deafness, partial blindness, complete blindness, physical difficulty to walk , physical difficulty to walk (requiring wheelchair), speech difficulty, physical difficulty moving one or both arms, other (specify), don\u2019t know, or prefer not to answer.Descriptive statistics were performed to present sociodemographic characteristics of the study participants including age , ethnicity , or other), country of birth , gender identity (cisgender or transgender), education level ( 30 kg/m2) in 26.7%, followed by asthma/COPD in 23.3%, arthritis/osteoarthritis in 20.9%, cancer or pre-cancer in 19.9%, chronic pains for other causes than arthritis/osteoarthritis and requiring medication in 19.1%, hypertension in 17.2%, high cholesterol in 13.4%, osteoporosis or osteopenia in 11.6% (9.4% reported previous fractures), thyroid problems in 10.3%, diabetes in 8.7%, HIV/AIDS wasting syndrome in 6.8%, and 6.2% reported a previous diagnosis of cardiac arrhythmias. The other physical conditions were selected by less than 5% . Transgender women participants were a little younger , but the difference with cisgender participants was not statistically significant. However, the groups were statistically different in terms of ethnicity with a higher proportion of transgender women identifying as Indigenous (25.0% vs. 16.4%) or other , but a lower proportion identified as ACB (15.6% vs. 36.7%) or white (28.1% vs. 40.2%). There was no statistically significant difference in prevalence reported by transgender women participants as compared with cisgender women participants, although a lower proportion of transgender women reported arthritis/osteoarthritis (12.5% vs. 21.2%), cancer or pre-cancer (9.4% vs. 20.3%), hypertension (6.3% vs. 17.6%), and a higher proportion reported cardiac arrythmia (15.6% vs. 5.9%) or strokes (9.4% vs. 3.6%).n = 596, 95% CI 54.3\u201360.4) of participants. As presented in the second section of At least one current mental health diagnosis was reported by 57.4% of participants reported living with a physical disability. Partial deafness was reported by 8.8%, and difficulty walking and requiring regular use of an assistive device such as a cane or walker was reported by 7.8% , but only 24 reported cervical high-grade squamous intraepithelial lesions (HSIL). Because human papillomavirus (HPV) related cancer and pre-cancer (defined as HSIL) can be difficult to distinguish for participants, they are reported together to reduce the risk of misclassification. A previous diagnosis of cervical cancer or HSIL was reported by 10.0% , anal cancer or HSIL was reported by 0.8% , and vulvar or vaginal cancer or HSIL was reported by 0.2% . For other cancers, the most commonly reported were skin , endometrial , breast , ovarian , and lymphoma or leukemia , bone , colon or rectum , oral or pharynx , thyroid, and lung. Other cancers were reported by less than 0.2% of participants .The most common type reported was cervical cancer, reported by 10.0% and age categories . Only stn = 332, 95% CI 29.1\u201334.9) reported both mental and physical health conditions (without disability); 19.5% reported a concurrent physical health condition ; 15.1% reported a concurrent physical, mental health and disability conditions; 9.3% reported a concurrent mental health condition ; 3.5% reported both physical health and disability conditions ; and 1.3% reported a disability with or without a concurrent mental health condition . Finally, only 19.2% (n = 200) reported the absence of any comorbidity in addition to HIV.Among Canadian women living with HIV, there is a significant burden of concurrent comorbidities in addition to HIV, with 70% currently living with at least one concurrent physical health condition, 20% living with a disability, and 57% living with at least one mental health condition. As a result, 81% of women living with HIV require health care attention for at least one condition other than HIV. Most physical health and disability conditions increased with age, but the prevalence of mental health conditions remains more stable across age groups. Obesity is the most prevalent physical comorbidity, and while ACB women aged 50 or more had the highest prevalence, younger groups had the highest prevalence amongst Indigenous and white/other women. Depression and anxiety are also very common, as they currently affect a third of our study population. The burden of many conditions varies widely across ethnicities and should be considered when caring for women living with HIV. Our data confirms that age, ethnicity, and gender identity are associated with differences in prevalence of comorbidities among a cohort of women living with HIV. These should not be seen as causal factors but should be used by clinician as guides to increase their index of suspicion when treating patients of these gender, age, and ethnicities. Our findings further support that all of a person\u2019s life context, including their social determinants of health, must be considered when caring for women living with HIV. HIV primary care must also include integrated/coordinated care for the prevention and management of all comorbidities that may further impact health and wellbeing.The high prevalence of comorbidities among women living with HIV in our cohort aligns with results of other studies, most conducted in United States ,26. CompThe results of this study have important preventative and primary care implications. The development of several chronic health conditions has been linked to decreased quality of life and a shorter life expectancy . The resThere are several limitations to this study. Self-reporting of diagnosed conditions may lead to misclassification in different directions. Cervical cancer may be overreported due to the confusing precancer terminology. Osteopenia might be underreported if discussions with the physicians were understood as an absence of osteoporosis. Absence of diagnosis may be due to lower interaction with medical care, but it does not always indicate the absence of conditions. Conditions may be present but undiagnosed, leading to a lower estimated prevalence. This may be the case for some ACB women who were not born in Canada and who have immigrated more recently. Lifetime report means these conditions may have been diagnosed before HIV diagnosis, meaning causality of HIV cannot be assessed. Social desirability bias might have decreased self-reporting of cigarette smoking, drug use, weight (used for BMI), and mental health conditions; however, the questionnaires were administered by peer research associates rather than health professionals which was expected to reduce social desirability bias. Still, the self-reported prevalence of mental health conditions remains concerning. Recall bias for mental health diagnoses was reduced by conducting analyses on conditions participants were currently living with and should not affect the reporting of chronic physical health condition or disabilities. The external generalizability of our results is limited to women already engaged in care, and even though CHIWOS recruited approximately 10% of all women living with HIV in Canada, women were not sampled randomly and may not be representative of all women living with HIV in Canada. Finally, although we drew from the 18-month survey whose responses pertaining to comorbidities were more complete, this survey is affected by selection bias of participants remaining in the study. Indeed, the participants lost to follow-up were younger but had more unfavorable determinants of health, making it possible that our results underestimate the burden of comorbidities in the entire population of women living with HIV in Canada. Finally, our sample of transgender women was very small and out study is likely underpowered to detect differences in comorbidity prevalence.Our results highlight the need for personalized HIV care that integrates the prevention and management of comorbidities. Considering women living with HIV are living longer due to more effective therapies, personalized HIV care must consider the dynamic nature of social determinants of health across the lifespan. Person-centered and stigma-free approaches are essential to consider the different risk factors for different health conditions experienced by women living with HIV. Clinicians\u2019 index of suspicion should also be adapted to the socio-demographic profile of patients to ensure conditions are not missed and the care meets the needs of each person. Obesity, depression, and anxiety are particularly concerning, each affecting a quarter to a third of women participating in the CHIWOS study, but close to half for certain specific age and ethnic groups. These findings also justify the need for multidisciplinary health care teams to optimize the health and wellbeing of women living with HIV."} +{"text": "The COVID-19 pandemic created new barriers to accessing primary care services, particularly among older adults who has faced barriers related to access to care, transportation, health literacy, and social isolation. Nova Southeastern University South Florida Geriatric Workforce Enhancement Program (NSU SFGWEP) partnered with primary care clinics and a local community partner to conduct wellness calls to older adult patients identified through clinic EHR. This project aimed to provide educational and telehealth support to vulnerable adults with limited resources in the Tri-County region of Florida. Wellness calls were made to determine educational and technical support needs of the older adults designated as underprivileged. We identified 44 participants to receive telehealth devices. Samsung tablets were mailed with educational resources, developed by NSU SFGWEP related to COVID-19 pandemic. The information included health, vaccine education, and instructions to access telehealth services. They had the tablets for six months. We conducted bi-weekly calls to offer peer training to access the educational materials. The participants were asked a series of questions to assess the effectiveness of the peer training support. Among participants, 36% (n=16) found the education materials impactful. Most participants, 89% (n=39), used the tablet, and 23% (n=10) reported using it daily. 11% (n=5) used it for telehealth, 7% (n=3) to connect with friends and family, and 7% (n=3) to connect with faith. This pilot project suggests that tablets were beneficial in assisting the participants in accessing education materials and resources encouraging the use of telehealth appointments and eliminating some of the social isolation."} +{"text": "In 1995, the United States was the first country to introduce universal childhood varicella vaccination. High vaccine coverage was attained among young children, \u2265 90% since 2007. In 2007, the policy was changed from 1-dose to a 2-dose program. We describe the impact of 25 years of the U.S. varicella vaccination program on varicella disease nationally.We reviewed published data and analyzed overall and age-specific trends for rates from the pre-vaccine period (1990\u20131994) through 2019 for varicella incidence using National Notifiable Diseases Surveillance System data, hospitalizations using National Inpatient Sample data, and deaths using National Center for Health Statistics data. We present trends in persons aged < 50 years, which captures most varicella burden and avoids misclassified herpes zoster in older people. Outbreak characteristics were assessed for 1995\u20132019 and were informed by published data and analysis of surveillance data reported to CDC.Within the 10 years of the 1-dose program, varicella incidence, hospitalization, and mortality rates declined dramatically (71%\u201390%) vs. pre-vaccine. However, limited transmission continued in school settings which informed the change to a 2-dose policy. By 2019, declines reached > 97% for incidence and 94% and 97% for hospitalizations and deaths, respectively. The greatest decline occurred among persons aged < 20 years, born during the varicella vaccination program, with 99%, 97%, and > 99% reduction in incidence, hospitalizations, and deaths, respectively. The 2-dose program further reduced the number, size, and duration of outbreaks vs. the 1-dose program; over the entire program, the proportion of outbreaks with < 10 cases increased from 28% to 73%.The varicella vaccination program significantly reduced varicella morbidity and mortality in the U.S. Twenty-five years into the program, pediatric varicella hospitalization has become a rare event and varicella deaths in persons aged < 20 years are practically eliminated in the U.S. Annually, > 3.8 million cases, 10,500 hospitalizations, and 100 deaths from varicella are now prevented in the United States due to the varicella vaccination program.All Authors: No reported disclosures."} +{"text": "Excessive antimicrobial use contributes to the development of antimicrobial resistance. In the Eastern Mediterranean region (EMR), there is dearth of information on the prevalence of antimicrobial use in patients hospitalized in acute healthcare settings, clinical indications, types of antimicrobials prescribed, and quality indicators for prescriptions. Between September and December 2019, seven countries in the EMR conducted a standardized point prevalence survey. All patients present in the hospital wards at 8 a.m. on the day of the survey constituted the sample population. We collected data, including patient characteristics, antimicrobials received, therapeutic indication according to predefined lists, and markers of prescribing quality. The survey included data from 139 hospitals in seven countries. Among the 19,611 inpatients surveyed, 11,168 patients received at least one antimicrobial {crude prevalence: 56.9% (95%CI: 56.2\u201357.6%). The top three classes of antimicrobials prescribed were third-generation cephalosporins (26.7%), beta-lactam penicillins (18.1%), and imidazole derivatives . Carbapenems were most frequently prescribed for the treatment of healthcare-associated infections. Compliance with quality indicators of antimicrobial use was limited where treatment guidelines were available for 41% of antimicrobial prescriptions and targeted antimicrobial treatment represented 21% of therapeutic indications. Overall hospital antimicrobial use was high in countries of the EMR, pointing to the need to design and implement context-specific antimicrobial stewardship programs to optimize antimicrobial use and reduce antimicrobial resistance. Antimicrobial resistance (AMR) poses a major global threat to human health around the world. In 2019, the Global Burden of Disease project of the Institute for Health Metrics and Evaluation (IHME) estimated that drug-resistant bacterial infections were associated with 4.95 million deaths, including 1,270,000 deaths attributable to AMR . In 2015AMS programs are one of the key actions that identify targets for quality improvement and improve the clinical outcomes of patients. AMS is one of three pillars of an integrated approach to health system strengthening, including infection prevention and control and medicine and patient safety. In 2017, the WHO developed the AWaRe classification as a simple stewardship tool to monitor prescribing patterns of antibacterials of different spectra at local, national, and global levels. AWaRe classifies antibacterials into 3 categories: Access (narrow-spectrum), Watch (broad-spectrum), and Reserve (last resort), taking into account the impact of different antibiotic classes on antimicrobial resistance to emphasize the importance of their appropriate use. The WHO set a 60% national target of total antibiotic consumption in the Access category by 2023 [Acinetobacter spp. at 70.3% (IQR 62.4\u201381.3%), followed by Klebsiella pneumonia resistant to 3rd-generation cephalosporins [Data on antimicrobial use are scarce in the EMR, particularly in LMIC; however, high levels of antimicrobial resistance are increasingly reported, where the median proportion of bloodstream infections (BSI) in 2019 was highest for carbapenem-resistant IQR 62.4\u20131.3%, folSeven countries participated in the point prevalence survey studies, including 139 acute care hospitals with a total number of 42,976 hospital beds. Public sector hospitals accounted for 50%, while 26% were private and 24% were from academia. From September to December 2019, 19,611 inpatients were included. Of these, 11,168 patients received at least one antimicrobial {56.9% crude prevalence (95% CI: 56.2\u201357.6%)}. Across countries, the prevalence of antimicrobial use was heterogenous. The median proportion of patients prescribed antimicrobials ranged from 46.5% (interquartile range (IQR) 35.4\u201361.5%) in Tunisia to 82.3% (IQR 61.6\u201390.5%) in Pakistan . The 11,Of 16,885 antimicrobials prescribed, 38.5% (6495) were prescribed for community-acquired infections, 21.8% (3699) for surgical prophylaxis, 15.7% (2658) for medical prophylaxis, and 11.4% (1940) for the treatment of healthcare-associated infections (HAIs). The proportion of antimicrobials prescribed for the treatment of CAIs ranged between 23% in Pakistan to 57.9% in Tunisia. For surgical prophylaxis, Pakistan had the highest proportion of prescribed antimicrobials (32.9%), followed by Iraq (24.8%) and Lebanon (23.2%). Pakistan also had the highest proportion of prescribed antimicrobials (30.1%) for medical prophylaxis, and Tunisia the lowest (4%). For HAIs, Lebanon reported the highest proportion of prescribed antimicrobials (19.9%) and Iraq the lowest (4.4%) . Third-gOf 16,885 antimicrobial prescriptions, antibacterials accounted for 95.2% while antimycobacterial, antimycotics for systemic use, antiprotozoals and systemic antivirals represented only 4.8%. Of 16,071 antibacterials prescribed, 34.1% were from the Access group (5470), 64.1% from the Watch group , and 1.8% from the Reserve group (293). Tunisia had the highest reported proportion of the Access group (46.7%), followed by Sudan (36%) and Iraq (33.4%). For the Watch group, Jordan (70.5%), Pakistan (67.2%), and Iraq (66.4%) were almost the same .Local treatment guidelines were available for 41% (6841) of antimicrobial prescriptions ranging from 7% in Iraq to 82% in UAE, while the overall compliance with guidelines was 74%. The reason documented for antimicrobial use was reported in 61% of prescription, and was highest in UAE (87%), followed by Lebanon (74%) and Tunisia (62%), and was lowest in Iraq (12%). The stop or review date of antimicrobial treatment was only available for 30% of documented antimicrobial prescriptions ranging from 3% in Pakistan to 72% in UAE. Out of 16,763 antimicrobial doses prescribed, 14,480 (86%) were injections, ranging from 74% in UAE to 92% in Sudan and Pakistan. Out of 9179 prescriptions indicated for therapeutic purposes, targeted antimicrobial treatment based on culture results represented only 21% with the highest in UAE (32%) and the lowest in Pakistan (6%) .Overuse and misuse of antimicrobials facilitates the emergence of multidrug resistant organisms. The literature shows that antimicrobial stewardship programs are effective in optimizing antimicrobial use and therefore key to preventing the emergence of resistance while IPC programs prevent spread ,3. This Multiple factors drive the use of antimicrobials in a country. These depend on the disease burden estimates within a country and the cultural context related to increased patient demands for antibiotics. Physicians tend to overprescribe antimicrobials in countries with poor regulations on antimicrobial use and weak antimicrobial stewardship programs . The impDespite differences in the prevalence of antimicrobial use among countries, our analysis identified some patterns. CAIs were the most common reason for hospital antimicrobial use in most countries studied, as well as several countries in Africa and Europe 49.5%), accounting for approximately 40% of all antimicrobial treatment .5%, acco. AntimicEscherichia coli and Klebsiella pneumoniae, causing bloodstream infections from 2017 (58%) to 2019 (65.4%) [The high use of third-generation cephalosporins in Jordan, Iraq, Sudan, and Pakistan (ranging from 25\u201338.4%) is a source of concern. They were commonly prescribed for surgical and medical prophylaxis, against recommendations from the WHO . The hig (65.4%) ,26,27. S (65.4%) ,28.Acinetobacter spp. and Klebsiella pneumoniae in several countries in EMR [In our report, the overall use of the antibacterials from the Access group fell short of the 60% target set by the WHO, ranging from 28.8% in Jordan to 46.7% in Tunisia . Severals in EMR . Colistis in EMR . The lims in EMR ,33.Our quality indicators could be used to set country-specific benchmarks for quality improvements and opportunities for AMS programs. First, the existence of national treatment guidelines was limited in most countries. Lack of clear guidance in clinical settings may explain the high antimicrobial prescription of treating physicians. However, compliance with hospital treatment guidelines\u2014if available\u2014was relatively high at 74%, which is higher than the compliance reported from Latin America, west and central Asia, and Africa . Fourth,Our study suffers from a number of limitations. First, we measured the prevalence of antimicrobial use using unique point estimates, which limits inferences. Second, the results were not corrected for difference in healthcare facility factors, patient case mix, variations in resistance levels, or institutional factors, all of which can influence antimicrobial use patterns. Third, not all countries conducted a nationally representative sampling design, which limited our capacity to make comparisons across countries. Between October and December 2019, we conducted cross-sectional point prevalence surveys in seven countries in the region using a standardized WHO Eastern Mediterranean protocol designed from the WHO protocol . CountriFour countries\u2014Tunisia, Lebanon, Jordan, United Arab Emirates (UAE)\u2014selected a nationally representative sample of acute care hospitals. Three countries used a convenient sample . Each country completed the survey within 3 weeks among all participating hospitals and collected data for each hospital ward on the same day.Each country assigned a national coordinator who provided general oversight to complete the survey and ensure appropriate good-quality data collection. Each participating hospital assigned a hospital coordinator supported by an investigator team composed of hospital infection control staff, clinical pharmacists, and medical doctors. WHO trained all staff engaged with data collection on the use of the study protocol, data collection procedures, data entry, and medical ethics. Hospital teams collected information on hospital affiliation , hospital size, admission specialty, age, and gender. For patients receiving an antimicrobial agent, the teams collected information from the medical records on the type, dose, indication for prescription, and site of infection. We classified antimicrobial indications as: (i) treatment of community-acquired infection (CAI) if symptoms were present on admission; (ii) treatment of hospital-acquired infection (HAI) if symptoms started 48 h after admission; (iii) medical prophylaxis (MP), which includes prevention of bacterial infections in patients with late-stage cirrhosis, upper gastrointestinal bleeding, and acute necrotizing pancreatitis and prevention of opportunistic infections in immunocompromised patients ; (iv) surgical prophylaxis (SP); (v) other; and (vi) unknown.We collected five prescribing quality indicators including (i) availability and compliance with hospital treatment guidelines , (ii) documentation of the reason for antimicrobial use, (iii) stop/review date of antimicrobials, (iv) route of administration , and (v) targeted or empirical treatment.We developed an electronic application to facilitate automated data entry and reporting and reduce errors by including built-in complex validation and skip logic rules. The hospital coordinators monitored the progress in data collection and validated and revised the quality of data entered before final submission to the national team.We analyzed the data using STATA version 16 . We estiWe classified the antibacterials prescribed according to the WHO Access, Watch, Reserve (AWaRe) classification, where the Access group contains narrow-spectrum antibacterials recommended as first and second choice for most common clinical infection syndromes. The Watch group contains broader spectrum antibacterial classes. The Reserve group consists of last-resort antibacterials for targeted use in multidrug-resistant infections . We used box-and-whisker plots to present the proportion of patients prescribed antimicrobials per country, where the horizontal line inside the box showed the median proportion of patients prescribed antimicrobials and the upper and lower end of each box provide the 75th and 25th interquartile ranges. The area between the different parts of the box indicated the degree of dispersion and skewness of data. The ends of the whiskers represented the minimum and maximum percentage of patients that were prescribed antimicrobialsThe high prevalence of antimicrobial prescription among hospitalized patients with use of broad-spectrum antibiotics with no clear indications reflects the infancy of AMS programs in several EM countries. None of the countries achieved the target of 60% antimicrobial use from Access group, with a high prescription of Watch antimicrobials, and there is low compliance with several quality indicators of antimicrobial prescribing. The situation calls for ministries of health leadership to enhance the design and implementation of national and facility stewardship programs and provide the necessary human and financial resources for country-wide implementation. Countries must use their data on the prevalence of antimicrobial use together with other national consumption and resistance data to design and implement tailored antimicrobial stewardship programs with specific quality improvement targets. They should adopt the AWaRe classification as a stewardship tool into essential medicine lists and national treatment guidelines to increase the utilization of narrow-spectrum antibiotics and preserve the precious Reserve group. While the development and implementation of national standardized treatment guidelines for infectious diseases seem to be an overall priority for countries, additional AMS strategies must also be implemented, e.g., education and training of physicians on appropriate prescribing practices is crucial. Changing practices and prescribing patterns of health care providers will take time, but investment is critical as a long-term solution. Regular point prevalence surveys should monitor the impact of antimicrobial stewardship interventions. Strong infection prevention and control programs must prevent the spread of resistance, and the surveillance of antimicrobial resistance must be sustained."} +{"text": "All registries were approved by national or institutional ethical review boards. All patients gave written informed consent. The P-SCAD case series consisted of 82 patients . Patients were alive at the time of enrollment and presented with SCAD confirmed on invasive angiography occurring during pregnancy or within 12 months of delivery, miscarriage, or termination. The pregnancy after previous SCAD series consisted of 37 pregnancies in 28 patients with angiographically confirmed SCAD who reported a subsequent pregnancy, whether ending in live birth, miscarriage, or termination. Data on 13 patients who did not survive P-SCAD were collected from the MBRRACE-UK audit of maternal deaths.The timing of SCAD in the P-SCAD case series is shown in the Figure. Few (n = 5) SCAD events occurred during pregnancy, with the peak time of vulnerability the first month after delivery. One patient had P-SCAD 4 months after miscarriage during her first trimester. Another had P-SCAD 3 weeks after medical termination.Patients with P-SCAD had high-risk features at presentation , with 49% (40/82) presenting with ST-segment\u2013elevation myocardial infarction. On angiography, 38% (31/82) involved proximal coronary segments, with 19% (15/81) multivessel and 57% (46/81) multisegment disease.The proportion of patients managed conservatively with respect to revascularization was 56% . A total of 12% (10/82) were referred for coronary artery bypass surgery, and 32% (100/315) had percutaneous coronary intervention. When stents were needed, the median number of stents used was 3 . The most common stented artery was the left anterior descending coronary artery. Of patients undergoing percutaneous coronary intervention, 40% (11/27) had complications during intervention .Of the 5 women whose SCAD occurred before delivery, 2 gave birth vaginally and 3 by cesarean section (2 were planned cesarean sections because of the recent SCAD and 1 was an emergency cesarean section because of unsuccessful labor induction) with a median gestation at birth of 39 weeks .In the cohort of patients with pregnancy after SCAD, the estimated time of conception was a median of 30 months after the most recent SCAD event. Of the 28 patients who became pregnant after SCAD, in 12 cases the index SCAD event was P-SCAD. Of 37 pregnancies, 3 women opted for medical termination and 7 spontaneous miscarriages occurred in 3 patients. Of women proceeding to birth, median gestation at delivery was 39 weeks . A total of 41% gave birth by cesarean section. The median birthweight was at the 30th percentile, with 16% of infants small for gestational age. A total of 17 of 35 patients were taking \u03b2-blockers during pregnancy. Three pregnancy-associated major adverse cardiovascular and cerebrovascular events occurred among the 37 patients (8%). One occurred during pregnancy and 2 angiographically confirmed recurrent SCAD events occurred within 12 months of delivery. There were no maternal or neonatal deaths as a consequence of these events.Of 13 maternal deaths in MBRRACE-UK attributable to SCAD, 3 occurred during pregnancy and 10 occurred postpartum . Twelve women had an out-of-hospital cardiac arrest. Three women underwent angiography, including the woman presenting alive to the hospital and 2 women who had angiography during active resuscitation. None underwent revascularization. Three women are recorded as having reported symptoms before cardiac arrest. At postmortem examination, sites of coronary dissection were mostly proximal , with the left anterior descending the most common coronary location . One-quarter had multivessel dissections. Histopathologic evidence of myocardial necrosis or infarction was seen in 8 of 11 (2 not reported), with evidence of extracoronary arteriopathy reported in one.The data, analytic methods, and study materials will be made available to other researchers on reasonable request to the corresponding author for purposes of reproducing the results. The data presented are observational. We acknowledge the potential for selection bias.P-SCAD predominantly occurs in the first 6 months postpartum, with few cases occurring during pregnancy. Although P-SCAD has an aggressive phenotype, many women are managed conservatively with favorable outcomes. Most deaths in P-SCAD result from sudden fatal arrhythmia with little apparent opportunity for medical intervention. Pregnancy after SCAD carries a modest recurrence risk, which should be discussed as part of individualized preconception counseling.The authors thank the patients; their clinical colleagues throughout Europe; the leadership of the European Society of Cardiology\u2013Association for Acute Cardiovascular Care spontaneous coronary artery dissection study group; Jenny Middleton, Jane Plume, Donna Alexander, Daniel Lawday, and Andrea Marshall for their support for spontaneous coronary artery dissection research; and Alberto Boi, MD, Cardiology Division, Azienda Ospedaliera Brozzu, Cagliari, Italy; Italo Porto, MD, PhD, Cardiology Division, Ospedale San Martino, Genova, Italy; and Annamaria Nicolino, Cardiology Division, Ospedale Santa Corona, Pietra Ligure, Italy, for support.This study was supported by the British Heart Foundation (grant PG/13/96/30608), the National Institute for Health and Care Research rare disease translational collaboration, the Leicester National Institute for Health and Care Research Biomedical Research Center, and Beat SCAD. Dr Knight is a National Institute for Health and Care Research Senior Investigator. The views expressed are those of the authors and not necessarily those of the National Health Service, the National Institute for Health and Care Research, or the Department of Health.Dr Adlam has received research funding from Abbott Vascular to support a clinical research fellowship and AstraZeneca for unrelated research and has performed consultancy for General Electric to support research funding. The other authors report no conflicts."} +{"text": "The theme of the St. Gallen International Breast Cancer Conference 2021 held virtually for the first time, due to the COVID-19 pandemic, was on tailoring therapies for patients with early breast cancer. A monkey survey that included an Egyptian Panel voted on most of the questions of the original St. Gallen consensus, and some added new questions most relevant to oncology practice in the country, to be able to compare voting results that reflect differences in breast cancer management and decision making.https://www.surveymonkey.com. The survey included 130 questions. Results were then analyzed, tabulated, and compared to the voting results of the original St. Gallen consensus.The panel included 74 Egyptian scientists from different oncology specialties. Management issues including controversial diagnostic and therapeutic interventions were prepared by a small committee and then projected using the online monkey survey website: Voting questions and resulting percentages of answers from the Egyptian panel were summarized. There was no consensus between the Egyptian and the original St. Gallen panels on 28/130 statements. They mostly included genetic and pathologic aspects, specifically the routine use of gene signature assays and a few queries involving surgical, radiotherapeutic, and systemic interventions. Probably, available resources and healthcare system differences in Egypt compared to European and the USA were the cause of these differences. This would also be applicable to other low- and low-middle-income healthcare scenarios present in many countries, especially with the present constraints of the COVID-19 pandemic. The 17th St. Gallen International Breast Cancer Conference that was convened in March 2021 aimed to provide clinical guidance on appropriate management of different aspects of early breast cancer addressing imaging, biomarkers, local management, systemic therapy, survivorship, and different issues related to COVID-19 and to weigh the balance between the benefit of adjuvant treatments and treatment burden including many aspects beyond toxicity, e.g., unaffordable costs of some drugs, or lack of experienced facilities [In view of the current situation of the COVID-19 restrictions, for the third time , a panelhttps://www.surveymonkey.com. The survey included 130 questions. The answers were reported in percentages. Voting percentages were modified after excluding abstained voters.Questions for the survey were prepared by a steering committee composed of scientists from different oncologic subspecialties, who have the ability and experience in managing breast cancer cases, and are up to date about recent advances in the field. The chosen questions were adapted from the 17th St. Gallen consensus by Thomssen et al. , as wellResults were then analyzed, tabulated, and compared to the voting results of the original St. Gallen consensus. As expected, voting highlighted both, differences as well as similarities in treatment recommendations for early breast cancer compared to the original Saint Gallen voting and recommendations. Survey data are presented as follows:When the panel was asked about the value of MRI as a standard procedure, in case of patients with human epidermal receptor 2 (HER2)-positive or triple-negative breast cancer (TNBC) planned to receive neoadjuvant therapy, 76% agreed that MRI being a standard modality to evaluate patients who might be chosen for breast conservation. However, this percentage dropped to 68% in case of estrogen receptor (ER)-positive disease.In case of the presence of microcalcifications detected by preoperative mammogram, 67% of the panel agreed to perform postoperative mammography after breast-conserving surgery (BCS).Ninety-six percent of the panel preferred to test the genetic panels for hereditary breast cancer in women if they have > 10% risk for hereditary mutation, in algorithms based on family history, age at diagnosis, and tumor subtype . About tWhile the refusal to perform a prophylactic mastectomy in patients with PALB2 mutation was clear (73%), the refusal to add tamoxifen or aromatase inhibitors in the same patients did not have the same clarity (56% refused).Although the panel was divided regarding the determination of the Ki-67 threshold that would justify chemotherapy in node-negative, hormonal-positive, and HER2-negative breast cancer as 35% of them decided that the threshold is not known, while only 47% set a threshold level of at least 30% to be the cutoff Fig. , they moWhen they were asked about Ki-67 testing after neoadjuvant endocrine treatment (NET) to assess its response, 57% agreed, while 43% refused. Sixty percent of the panel confirmed that estimation of prognosis for NET in hormonal-positive, HER2-negative ductal breast cancer could be done using Ki-67 two or more weeks after starting the treatment [Patient\u2019s gender: In male patients, 27% agreed for all males, and 52% agreed only in selected cases. Fifty-seven percent of the panel accepted the statement in all female patients, and 43% accepted only in selected patients.Menopausal status: 50% agreed in all premenopausal patients, while 44% agreed but in selected ones. These results were almost the same when the panel was asked about postmenopausal patients, as an agreement in all patients was 47% and 50% agreed in selected patients.Nodal status: As the number of positive lymph nodes increases, the percentage of the panel who were accepting to use of multigene signatures to decide on giving chemotherapy decreases. In node-negative tumors, 62% of the panel agreed with all patients and 33% agreed with selected ones. In (1\u20133 positive lymph nodes) tumors, 37% agreed in all patients and 44% agreed in selected ones. In \u22654 positive lymph node tumors, most of the panel (75%) refused to use the assay.Tumor grade: Grade 1 and grade 2 tumors were a point of debate to the voters as 45% and 49% agreed in all patients respectively, also they agreed in selected grade 1 (38%) and 2 (43%) tumors. The area of more debate was the grade 3 tumors as 38% rejected the statement, 35% accepted it in all patients, and 27% reserved the acceptance to selected patients.The panelists were asked if the multigene signatures could be used to decide on giving chemotherapy to ER-positive and HER2-negative breast cancer with a 1\u20133-cm tumor size. The answers varied according to the clinicopathologic factors , but 36% preferred to test it in all patients, also TLIs were preferred to be tested in selected patients (55%); however, 25% of panelists voted to test it in all patients, while 20% refused testing it at all.In patients with age \u2265 70 years, 87% of the panel advised not to give radiation therapy for ductal carcinoma in situ (DCIS). This was similar to an updated analysis with a median follow-up of 12.6 years of a previous CALGB 9343 study comparing lumpectomy with whole breast radiation or lumpectomy alone, both with tamoxifen for five years in clinical stage 1, ER-positive breast cancer patients 70 years of age or older [To prevent DCIS recurrence, most of the voters (80%) preferred to use tamoxifen 20 mg daily, this was like the NSABP B-24 trial which found a benefit from tamoxifen for women with DCIS after treatment with BCS and radiotherapy . AromataThe panelists differed in their opinion regarding the appropriate time and sequence of reconstruction and postmastectomy radiotherapy (PMRT). While 41% preferred delayed reconstruction after radiotherapy, the others split between delayed immediate (expander) (17%), immediate autologous reconstruction (11%), and immediate implant in 1 or 2 stages (10%) with 21% abstaining.Mastectomy\u2014as a standard procedure for ipsilateral local recurrence after conservative surgery\u2014was the preferred option by 65%, while 32% preferred to do another BCS, then give radiotherapy if the lead time was > 5 years. Factors that would favor a second BCS are low-risk tumors (75%) or intermediate risk defined as elapse of 5 years interval since the first diagnosis (72%). Mastectomy was also the standard procedure for ipsilateral local recurrence after BCS if irradiation was not an option (93%). Surgery should not be omitted after neoadjuvant therapy in case of clinical and radiological complete remission (91%). Richter et al. reportedIn case of the presence of macrometastasis (63% with).In case of the presence of micrometastasis, 57% were influenced by IBCSG 23-01 trial , so theyIn case of the presence of isolated tumor cells (ITCs) .In case of the presence of 1\u20133-positive sentinel lymph nodes (SLN) .We asked the panelists in which cases they should perform axillary lymph node dissection (ALND) after neoadjuvant therapy. The answers were Fig. :In case Sixty-three percent of voters agreed that in case of the presence of initial positive lymph node status (pN1) and good clinical response, a biopsied and clipped lymph node at baseline would be sufficient to avoid ALND, if 3/3 SLNs were negative. Thirty-seven percent of the voters could not avoid it for up to negative 3 out of 3 SLNs. ALND was necessary for initial (pN1) tumors if there was no or minor response (97%). Fifty-nine percent of the voters would endorse targeted ALND for favorable biologic subtypes compared to 69% who would recommend it for cN1 tumors clipped nodes that had become cN0.Removing more than 10 axillary lymph nodes would not add any benefits, for example, in case of more than 5 nodes affected, in view of 60% of the panel. Also, 96% agreed that intercostobrachial nerves should be preserved as a surgical standard.In case of (cN0), axillary surgery should be avoided if the patient's age was more than 70 (46%). Twenty-five percent of the panel preferred to avoid it only in patients older than 80 years, while 23% believed that age is not a cause of an axillary surgery omission.Re-sentinel excision with frozen section and ALND were the preferred procedures from the panel\u2019s point of view (58%), in ipsilateral breast recurrence with negative nodes by imaging techniques in previously treated patients with BCS and SLN mapping. However, 27% preferred to do complete axillary node dissection.While hypofractionated radiotherapy for the breast cancer could be considered without any restrictions by 56% of voters, 29% and 15% Fig. of the pThe panel was not sure when to recommend partial breast irradiation, as 77% abstained from voting, while 9% would keep it for patients under the age of 40.Sixty-one percent of panelists did not recommend RNI for patients with triple-negative or HER2-positive breast cancer with pathological complete response (pCR) after neoadjuvant treatment. Seventy-two percent consider it mandatory for stage 2 and (cN1) triple-negative or HER2-positive breast cancer with pCR, while 28% believed that it is mandatory only in stage 3. RNI is necessary for patients with PMRT in case of TNBC (90%), while in luminal A tumors, 33% recommended it in comparison to 67% who considered it unnecessary.Genomic signatures including Oncotype DX\u00ae, MammaPrint\u00ae, PROSIGNA\u00ae\u2026 etc. would not be used to help decide RNI (87%), PMRT (83%), or irradiation omission (80%).Boost irradiation of the excision site, in case of invasive duct carcinoma (IDC), could be endorsed for high-risk group only -positive tumors, TNBC, or HER2-positive tumors) was endorsed by 57% of the panel. This is compatible with data from the START trials \u201313; althAfter BCS, omission of radiotherapy is not indicated in more than 70-year-old female patients (62%), node-positive disease (70%), or tumors more than 2.5 cm (70%). We asked them if they might consider radiation omission after BCS in women with less than 2.5 cm tumor size in case of low grade or low genomic score tumors, 52% refused the omission; but, 48% accepted it.Initially cN0, in patients without macroscopic nodal involvement: 57% and 54% accepted in case of (1\u20133 SLN) with micrometastasis or with ITCs, respectively; although, 43% and 45% refused in the same cases respectively.HER2-positive tumors and available TDM-1 therapy: 75% refused, while 25% accepted.ER-positive tumors and available endocrine therapy: 68% refused, while 32% accepted.TNBC and available capecitabine therapy: 85% refused, while 15% accepted.Performing axillary radiation instead of ALND was the subject of some questions to the panel. The answers varied according to the clinical situation:Classically, pCR has been considered as a surrogate endpoint for drug approval in for early stages of breast cancer. Asked about this statement, 59% of the panel voted in favor of this approach if the regimens given achieved a great improvement in pCR rates, i.e., 50% higher than the control. The remaining 41% of panelists suggested that neoadjuvant pCR rates as encouraging, but only improvements in event-free survival (EFS) and overall survival (OS) rates are needed to define \u201cstandard\u201d regimens. While 43% of panelists recommended giving neoadjuvant treatment to all patients based only on the initial diagnostic biopsy, 57% of panelists did not agree that this is an appropriate recommendation.For postmenopausal patients having low-grade and/or low-risk genomic signature disease, 98% did not agree with giving chemotherapy for these patients. In addition, 70% of the votes were in favor of asking for genomic signature assays on core biopsies to decide on giving neoadjuvant chemotherapy versus endocrine therapy to patients with ER-positive breast cancers.In a case of women with HER2-positive, node-negative breast cancer, 66% of the panel did not favor anthracyclines in patients receiving taxane-based chemotherapy and anti-HER2 antibodies. However, in the case of node-positive cancer, 88% of them would give anthracyclines. Furthermore, in the presence of positive axillary lymph nodes on clinical examination, 49% chose anthracycline-containing regimen, while 51% favored giving platinum- and pertuzumab-containing treatment.In stages II and III with node-negative axilla, and HER2-positive disease, 60% of the panel agreed to give anthracyclines and pertuzumab in addition to taxane and trastuzumab, while 40% would add pertuzumab and platinum to taxane and trastuzumab.When treating triple-negative disease, 51% would not add an immune checkpoint inhibitor to the neoadjuvant chemotherapy treatment. Sixty-five percent believed that PD1/PDL1 testing is actually needed to be done to recommend the use of immune checkpoint inhibitors in the neoadjuvant therapy.Eighty-seven percent of the voters agreed that for HER2-positive breast cancer with pCR after neoadjuvant therapy, the baseline stage and tumor subtype still affect patients\u2019 prognosis.In patient with cN+ HER2-positive breast cancer when pCR is achieved, 52% of the voters would give trastuzumab and pertuzumab adjuvant treatment of choice regardless of baseline stage, and 32% would favor trastuzumab and pertuzumab but only in baseline stage 3, while 16% would give only trastuzumab.When pCR was achieved with trastuzumab and pertuzumab in patients presenting with cN0, HER2-positive cancer, 67% would favor giving trastuzumab alone as adjuvant treatment, and 21% would agree to consider pertuzumab and trastuzumab if patients had baseline stage 1 or 2 and 12% would give both agents with baseline stage 2 only.Eighty percent of the voters would offer trastuzumab-emtansine to all patients with residual disease, while the panel was equally split, whether they would offer trastuzumab emtansine also to anti-HER2 treatment in patients with excellent clinical response and <5 mm residual disease.If pCR is achieved in TNBC, the panel did not agree by a clear majority (81%) to give immune checkpoint inhibitors in the adjuvant setting while a strong majority (97%) would favor adjuvant capecitabine to women having residual disease after neoadjuvant treatment.For patients with ER-positive disease after neoadjuvant endocrine, the panelists did not agree (68%) to offer adjuvant chemotherapy if they had excellent clinical response short of pCR and node-negative residual cancer, but if there were 4 or more residual lymph nodes, 88% of them would give chemotherapy. If there were any residual positive lymph nodes, 70% would offer adjuvant chemotherapy. If residual tumor size was >5 cm, 87% would give adjuvant chemotherapy. In case of the presence of baseline high-grade tumor and/or intermediate-range genomic signature, 83% would offer adjuvant chemotherapy.To recommend endocrine adjuvant treatment, for hormone receptor-positive patients, the panel was asked to choose between ER threshold level \u22651 vs. \u226510% tested by IHC; the panel was equally split 50/50, while 97% of votes recommended endocrine treatment with any tumor size that include microinvasive disease for patients having luminal A and B like lesions.In cases having ER-positive, HER2-positive disease, 51% of the panelists agreed to give anti-HER2 therapy in case of tumor size equal or more than 5 mm or 6 mm (30% of votes), but 19% suggest giving such treatment in smaller lesions. The consensus was less clear to give anti-Her2 therapy to patients having negative ER and positive HER2 disease; votes were 41% for tumor size 5 mm, 32% for 6 mm, and 27% for tumors less than 5 mm to consider anti-HER2 therapy. Results are shown in Fig. In premenopausal patients with ER-positive early-stage disease with favorable biological features, 53% of the panel considered the contribution of chemotherapy-induced ovarian function suppression (OFS) to the total effect of chemotherapy to be at least 25\u201350% Fig. . In thosIn case of premenopausal with ER-positive, HER2-negative lesions with features necessitating adjuvant chemotherapy, 95% would consider adding OFS, if those patients remain premenopausal after finishing chemotherapy treatment .If premenopausal women are characterized as having a disease node-negativity and low-risk genomic signature , most of the panelists 75%) would give only OFS with tamoxifen or AIs, while only 25% voted to add chemotherapy. In low-risk patients with 1\u20133 positive lymph nodes and low recurrence score genomic signature, 48% would add chemotherapy to the endocrine treatment, 38% favored adding chemotherapy to endocrine treatment but at the same time would consider endocrine therapy alone without chemotherapy as a reasonable treatment, while only 14% favored endocrine therapy alone recommended OFS to all patients.In patients with luminal A-like tumors and positive lymph node disease, 99% of the voters agreed to consider a prolonged endocrine therapy; 34% considered additional 2\u20133 years, and 65% voted for a total of 10 years. After giving 5 years of OFS and tamoxifen, 68% of the panel recommended OFS together with AIs and 32% agreed to give only tamoxifen for 5 years. This applied to cases of high-risk patients.A majority of the panel (94%) voted that in case of stage \u2264 II, positive ER, negative HER2 disease with low-risk signature assays , patients should not receive chemotherapy. For higher anatomical stages , 97% decided to give chemotherapy, and only 3% would withhold it.For postmenopausal cases having high anatomical stage , positive ER, negative HER2 breast cancer, voters agreed by 97% that for patients having \u226510 infiltrated lymph nodes (with very high stages), regardless of biomarkers (95%), even with recurrence score <25 (88%) to give combined chemotherapy and endocrine therapy. However, for some situations, e.g., grade 1, low level of Ki-67, recurrence score <11, or lobular cancer, 91% rejected the idea of giving chemotherapy as well.In patients with positive ER, stage I disease, and negative lymph nodes who are assigned to receive adjuvant chemotherapy, 89% chose to give shorter combinations, such as EC or TC. However, 10% of the panelists voted for a standard dose of the combination of anthracycline/cyclophosphamide /taxane.With higher-stage disease or higher tumor burden, 66% of panelists recommended a standard dose anthracycline/cyclophosphamide/taxane combination, while 29% voted for the dose-dense combination.In TNBC, the optimal tumor size to start adjuvant or neoadjuvant chemotherapy was 5mm or more by 62% of panelists, while 32% recommended it with microinvasive disease.Women with negative lymph node, and positive HER2 disease are not eligible to receive adjuvant pertuzumab plus trastuzumab in view of 78% of the panel. Fifty- two percent of the panel agreed to offer an adjuvant neratinib after (neo) adjuvant trastuzumab/pertuzumab and/or trastuzumab emtansine-based therapy.For patients having stage I, and positive HER2 disease, 62% did not agree to routinely use trastuzumab-emtansine instead of a combination of paclitaxel/trastuzumab; however, 36% considered justifying the use of T-DM1 in certain situations.When the panel was asked if abemaciclib should be recommended in EBC with positive ER and negative HER2 cases having >3 positive nodes. The Panel did not agree (68%).In other possible situations as for women having positive 1\u20133 nodes or other unfavorable prognostic factors like grade III, T3 tumor size, or high level of Ki-67, only 52% of the panel agreed to recommend the application of abemaciclib while 39% refused. The panel did not agree (77%) to consider Ki-67 level evaluation to indicate anti-CDK4/6 therapy.Seventy-four percent of panelists did not agree to give women having either stage II or also stage III triple-negative breast cancer (who have not been treated by neoadjuvant but receiving adjuvant chemotherapy) anti-PD1/PDL1 therapy.The panel did not agree (74%) to recommend olaparib in case of women having stage II or III triple-negative breast cancer, who have not been treated by neoadjuvant, but receiving adjuvant chemotherapy. A summary of the voting results on the role of systemic therapy in the management of early breast cancer is shown in Tables Survivorship is now recognized as a phase of cancer that requires ongoing specialized care. Significant genitourinary or sexual health symptoms during the AIs are of concern for some women. Fifty-five percent of the voters answered yes, and 45% would not recommend intravaginal estrogens due to safety concerns.Chemotherapy-induced alopecia may influence the quality of life and psychological well-being. The panel agreed by a 67% majority on the use of cold caps.Complementary therapies include a broad range of mind and body practices, natural products, and many lifestyle modifications and are commonly used by breast cancer survivors . The majEvidence is emerging that in some patients with \u201coligometastatic disease,\u201d often defined as five or fewer metastases diagnosed on imaging, aggressive metastasis-directed therapy with surgery, and/or hypo fractionated image-guided radiation therapy improves outcomes and may even be curative .The great majority voters (95%) endorsed for the first-time curative intention for oligometastatic breast cancer , while only 65% endorsed for the first-time curative intention after multiple metastases had responded well to primary systemic therapy.Most of the panelists (90%) voted for endorsing COVID-19 vaccination for all patients before receiving chemotherapy and for all caregivers (99%).When the panel was asked about prioritizing COVID-19 vaccination, they answered that it should be offered primarily to all women with newly diagnosed breast cancer (49%) and patients with recently completed chemotherapy/radiotherapy (28%). However, vaccination of those with ongoing chemotherapy/radiotherapy was considered less priority (23%).The main aim of this work was to illuminate both, differences, and similarities in the management concepts of early breast cancer of Egyptian oncologists compared to the original Saint Gallen panel, putting into consideration economic, social, healthcare facilities, and disease patho-biologic factors that are present between breast cancer patients in western countries and most low- or middle-income countries including Egypt.Out of 130 questions asked to 74 Egyptian scientists, there were major differences in 28 answers (21.5%) between the Egyptian and the St. Gallen panel. These 28 different answers included 11 in biologic and pathologic aspects, 9 in systemic therapy, 3 in surgery, 3 in radiotherapy, and 1 in each of imaging and DCIS (Tables As shown by Thomssen et al , severalOn the other hand, the panel denied the idea of omitting surgery after a good response to neoadjuvant therapy, the importance of pCR for approving new treatments, the use of checkpoint inhibitors for patients with triple-negative stage 2 or 3 disease that have not been treated in the neoadjuvant setting, but receiving adjuvant chemotherapy, and finally adding pertuzumab for node-negative HER2-positive breast cancer.It is worth mentioning that the Egyptian panel agreed on 4 of above 7 statements. The other 3 statements include their preference in still considering mastectomy as the standard approach after ipsilateral recurrence, probably since most breast cancer patients in Egypt usually present with more advanced local disease than in Europe or the USA. Also, they agreed on the importance of pCR for approving new treatments by a close majority of 59%. Lastly, the Egyptian panel did not recommend offering abemaciclib in ER-positive HER2-negative patients with more than 3 positive axillary lymph nodes but recommended adding anthracyclines and pertuzumab in addition to taxane and trastuzumab in case of stage 2 and 3 clinically node-negative HER2-positive diseases. Based on this survey, possible summary statement guidelines need to be formulated to help in clinical decision-making for Egyptian health authorities and oncology professionals.There were clear differences in consensus percentages between the Egyptian and the original St. Gallen panels. Mostly, these differences reflect breast cancer management concepts in Egypt compared to other countries as well as available general healthcare infrastructure as well as oncology management governance, especially with the present COVID-19 pandemic."} +{"text": "We aimed to measure the baseline mental health literacy in Foundation Doctors in the Yorkshire and Humber area, identify any gaps in knowledge with the purpose of addressing these within the new foundation psychiatry teaching program, developed by North Yorkshire Health Education England.In January 2021, a questionnaire comprising of O'Connor's Mental Health Literacy Scale was sent electronically to all Foundation Doctors in the York and Humber area, that were in a placement at that time. The O'Connor's Mental Health Literacy Scale (MHLS) has been used since its publication in 2015 and is a 35 item, univariate scale that demonstrated good internal and test-retest reliability. It covers the following attributes: a) ability to identify disorders, b) knowledge about seeking information, risk factors and etiology, self-treatment, resources and support available, c) attitudes about mental disorders and seeking professional help. The anonymized data were collected and analysed in Microsoft Excel.In total, we received 49 responses to the questionnaire. Overall, 85% of respondents demonstrated good mental health literacy. Breaking this down further, 91% demonstrated knowledge of core psychiatric diagnostic criteria, 68.4% were literate in etiology and risk factors, 92% and respectively 95.9% understand what resources for treatment and professional help are available. Importantly when looking at attitudes about mental disorders overall 17% of respondents showed a degree of stigma and barriers in seeking professional help. For example, 2% strongly agreed that mental health conditions are not real illnesses, 34.7% were unsure whether people with mental illness are dangerous, 40.9% neither agreed nor disagreed they would move next door with someone with a mental illness and 14.3% would not be willing to have someone with a mental illness marrying into the family. When looking at barriers to seeking help, 12% answered they would not tell someone if they had a mental health problem, with 16.3% unsure whether they would tell someone if they had a mental health problem.Overall, our survey demonstrated good mental health literacy in our cohort, however, there are areas of improvement, the main ones being etiology, risk factors, and attitudes towards mental health. It is important to recognize these deficits, as they have been linked with poor health outcomes and barriers in seeking and providing care. Moving forward, standardization of teaching programs and anti-stigma training could be an evidence-based approach to tackling these issues."} +{"text": "The classification of brain tumors (BT) is significantly essential for the diagnosis of Brian cancer (BC) in IoT-healthcare systems. Artificial intelligence (AI) techniques based on Computer aided diagnostic systems (CADS) are mostly used for the accurate detection of brain cancer. However, due to the inaccuracy of artificial diagnostic systems, medical professionals are not effectively incorporating them into the diagnosis process of Brain Cancer. In this research study, we proposed a robust brain tumor classification method using Deep Learning (DL) techniques to address the lack of accuracy issue in existing artificial diagnosis systems. In the design of the proposed approach, an improved convolution neural network (CNN) is used to classify brain tumors employing brain magnetic resonance (MR) image data. The model classification performance has improved by incorporating data augmentation and transfer learning methods. The results confirmed that the model obtained high accuracy compared to the baseline models. Based on high predictive results we suggest the proposed model for brain cancer diagnosis in IoT-healthcare systems. Because of its critical nature, brain tumours are one of the most dangerous types of brain cancer. Compared to other cancers from brain cancer less number of people are suffering2. Meningioma, Glioma, Pituitary, and Acoustic Neuroma are examples of brain tumors. In medical observation, the rates of Meningioma, GLioma, and Pituitary tumours in all brain tumors are 15%, 45%, and 15%, respectively3. A brain tumor has long-term and psychological consequences for the patient. Brain tumors are caused by tissue abnormalities that develop within the brain or the central spine, interfering with normal brain function. There are two types of brain tumors: benign and malignant. Benign brain tumors are not cancerous and grow slowly. They do not spread and are not common. Malignant brain tumours contain cancer cells and grow rapidly in one region of the brain and spread to other parts of the brain and spine.Brain tumor (BT) is a series medical problem, and many people are suffering from it globally4. The CNNs model can extract more related features from data for accurate image classification6. Furthermore, data augmentation and transfer learning techniques can also improve the predictive capability of deep learning models to effective classify the brain tumors and diagnosis brain cancer in IoT healthcare industries7.The diagnosis of brain cancer is significantly necessary for early stage for effective treatment and recovery. In this regards to classify brain tumors and identify brain cancer, different non-invasive are developed in literature by researchers and medical experts in Internet of Things (IoT) healthcare industries. In the deigning of computer automatic diagnostic systems (CADS) for brain cancer detection Machine Learning (ML) and Deep Learning (DL) models are commonly used. The diagnosis of brain cancer using images data using the DL Convolution neural network (CNN) model has grown in popularity, and the CNN model is commonly used for image classification and analysis, particularly for medical image data analysis8 designed a brain cancer diagnosis system to classify various grades of Glioma employing SVM and KNN machine learning model and respectively achieved 85% and 88% classification accuracy. Cheng et al.9 proposed a classification approach for brain tumor classification and augmented the tumor region for improving the classification performance. They employed three techniques for feature extraction such as Gray level co-occurrence matrix, a bag of words, and an intensity histogram. Their proposed method obtained 91.28% classification accuracy.In the literature, various methods have been proposed for brain cancer diagnosis using ML and DL learning approaches by different scholars. Zacharaki et al.6 proposes an AI-based intelligent integrated framework (CNN-LSTM) for brain tumors classification and diagnosis in the IoT healthcare industry. In the integrated framework design, they have incorporated the CNN model to extract features from medical MRI data automatically. The extracted features are passed to Long short-term memory (LSTM) model to learn the dependencies in the features and finally predict the class for the tumor. Further they applied brain MRI data sets for the assessment of the proposed integrated model. Massive data is one requirement for an effective deep learning model. Since the size of our original data set is small, they utilized data augmentation approaches to increase the data set size, thereby improving the model result during training. Also used the train-test splits Cross-validation approach for hyperparameter tuning and best model selection to ensure proper model fitting. For model assessment, used well-known evaluation measures. They compared the predictive outputs of the proposed CNN-LSTM model with previous methods in the Medical Internet of Things (MIoT) healthcare industry and the model obtained high predictive performance.Haq et al.4 employed axial brain tumor images for convolution neural network training. In the proposed method they used two convolution layers, two max-pooling layers, and lastly, two fully connected layers for the final classification process. The proposed approach obtained 91.43% classification accuracy. El-dahshan et al.10 designed a brain tumors classification method for 80 brain images MRI classification. They used discrete wavelet transform and PCA algorithms for reducing dimensions of data. To classify the normal and abnormal tumors, they used ANN and KNN machine learning classifiers. The classifiers ANN and KNN, achieved 97% and 98% classification accuracy respectively.Paul et al.11 proposed a brain tumor classification method employing a capsule network that combined MRI images of the brain and coarse tumor boundaries and 90.89% accuracy achieved by the proposed method. Anaraki et al.12 developed an integrated framework for brain tumor classification, and in the proposed technique, they integrated CNN and GA, and designed GA-CNN framework and obtained 94.2% accuracy. Khan et al.13 proposed brain tumors classification method employing transfer learning techniques (CNN-Transfer learning) and achieved 94.82% accuracy14. The proposed multi-classification method employing ensemble of deep features and ML algorithms and obtained high performance.In another study, Afshar et al.According to the review of the literature, current brain cancer diagnosis techniques still lack a robust predictive capability in terms of accuracy to correctly diagnose brain cancer for proper treatment and recovery. To address this issue, a novel robust method for accurately diagnosing brain cancer for proper treatment and recovery in IoT healthcare industries is required. Furthermore, the artificial intelligence based brain cancer diagnosis systems also reduce the financial costs of healthcare department.In this study, we created an improved CNN model for the classification of brain MR images to diagnosis brain cancer in IoT healthcare industries. In the development of the proposed model, we used Convolution neural network model to classify brain tumors types employing MR images data. The CNN model is more suitable for the Meningioma, Glioma, and pituitary classification using brain tumors images data and its extract more deep features from images data for final classification. To further improve the CNN model predictive capability, we have incorporated a transfer-learning (TL) techniques for proper training of the CNN architecture, the brain MR images data is insufficient. In transfer learning, we used the well-known pre-trained models ResNet-50, VGG-16, Inception V3, DenseNet201, Xception, and MobilleNet. The weights generated of these pre trained models individually transferred to CNN architecture for effective training o CNN model. For the fine-tuning process, the model was trained with brain MR images data set. The generated weights of pre trained models improving CNN model final predictive performance. Additionally, the data augmentation technique is incorporated to increase the data set size for effective training of the model. We also used held-out cross-validation (CV) and performance evaluation metrics. The performance of the model compared with base lines models. The experimental results confirmed that the proposed model generated higher predictive results and it could be applied in IoT-healthcare systems easily.In IoT healthcare systems, an improved model based on CNN and TL for classifying brain tumors using MR image data is proposed for diagnosis of brain cancer.To increase the predictive accuracy of the CNN model, TL techniques are used because the brain tumor image data is insufficient for effective training of the CNN model. Pre-trained models ResNet-50, VGG-16, Inception V3, DenseNet201, Xception, and MobilleNet are used to train with the well-known ImageNet data set for generating trained parameters (weights). The weights of these pre tained models are individually transfer to CNN model effective training. Fine-tuning the model CNN with brain tumor images data along with transferred weights final classification.To improve model performance, the data augmentation technique is used to increase the size of the data set for effective model training.When compared to baseline methods, our model has a high predictive performance.Innovations of this study summarized as follows:The rest of the paper is organized as follows: In \u201c9, and new versions in 2017 have been published. T1-Weighted Contrast-Enhanced images (TWCEI) of 233 subjects with meningioma, glioma, and pituitary tumours are included in this data set. The data set is freely accessible via the Kaggle repository15. We also used the Brain MRI Images Data Set (BMIDS) for cross dataset validation, which contains 253 MRI brain images. The tumor class in the data set has 155 images, while the non-tumor class has 98 images16.We used a brain tumor data set (BTDS) from China\u2019s Nanfang hospital and general hospital, as well as Tianjing medical university, in this study (2005 to 2010)17. Convolutions can capture translation invariance, which means that the filter is independent of position that significantly reduces the number of parameters. The CNN model have Convolutional, Pooling, and fully connected layers. Different functions are accomplished by these layers, such as dimensionality reduction, feature extractors, and classification. During the convolution operation of the forward pass, the filter is slide on the input shape and compute the map of activation, which computing the point-wise value of each output. Further add these output to achieve the activation of that point. Designed a Sliding Filter (SF) using convolution as a linear operator, and expressed as a dot product for fast deployment. Let consider x and w are input and the kernel function, the convolution process t can be mathematically expressed in Eq. . In addition, we have used the optimization algorithm Stochastic Gradient Descend (SGD)20. The CNN architecture is given in Fig. The CNN model has significant applications in the classification of medical images21, cancer sub-type recognition22 and medical images filtering23. In this work, we used the transfer learning ResNet-50, VGG-16, Inception V3, DenseNet201, Xception, and MobilleNet models to enhanced the predictive performance of the proposed CNN model. The ResNet-50, VGG-16, Inception V3, DenseNet201, Xception, and MobilleNet pre-train models were trained on imageNet data set and transferred the trained parameters weights of these models individually to CNN model for effective training, and fine-tuned the model using the brain tumor augmented MR images data set for final classification of the CNN model.To improve CNN model predictive accuracy, we employed Data augmentation (DA) and Transfer learning (TL) techniques. The data augmentation can resolve the problem of insufficient data for model training. To expand the data amount, the zooming technique is used on original image data to produce images data with the similar label. The new created data set is used for fine tuning of the model. Th The transfer learning (TL) techniques widely used in image classification tasks25 mechanism was used for training and validation of the model. In hold out CV data is randomly assign to two sets 29 are used for model evaluation.The holdout cross-validation31 techniques are incorporated. We have used transfer learning pre-trained models ResNet-50, VGG-16, Inception V3, DenseNet201, Xception, and MobilleNet along with data augmentation technique zooming. The imagesNet data set has been employed for pre-trained of ResNet-50, VGG-16, Inception V3, DenseNet201, Xception, and MobilleNet models, and the generated weights (trained parameters) of these models were transferred for the effective training of the CNN model individually. Brain tumor MRI data set was used for fine-tuning of CNN model and for final classification of the model in IoT healthcare system.NCNN models are now popular for image classification problems. A large image data set is more suitable for the CNN model\u2019s effective training, as it allows the model to extract more related features during the training process for accurate image classification. The CNN model\u2019s performance suffers as a result of the scarcity of large image data sets, particularly in the medical domain. However, to enhance the proposed CNN classifier performance, data augmentation and transfer learning20 technique was used to augment the original dataset by using the zooming method, which improves the model generalisation capability. The integration of data augmentation and transfer learning greatly enhanced the predictive accuracy of the CNN model. The evaluation criteria of the model different assessment metrics have used.Furthermore, the proposed CNN model was trained and tested on a data set of brain tumour MR images, and its performance was compared to that of the transfer learning technique. A heldout cross-validation mechanism is used in the proposed method for model training and testing, with 70% used for training and 30% for model validation. The data augmentationX embedded into the CNN classifier,We used data transformations to increase the size of the data set so that we could train the model. Furthermore, the number of epochs E, model parameters w, Learning Rate (LR) b, and the number of layers in both CNN were configured accordingly. For the optimization of our model parameters, we have used the stochastic gradient descent algorithm (SGD). The pseudo-code of the proposed model is given in algorithm 1 and flow chart in Fig. The data set entclass1pt{minima20 has used to augment the original data set. Data augmentation technique (zooming) is used, and all three types of images are zoomed horizontally and vertically and added with existing images. The new augmented data set image size of three kinds of images is 6128. Held out technique is used for model training and validation, and respectively 70% and 30% data are employed for training and validation of the model for all experiments. To effectively optimize the model SGD Optimization algorithm is used20. In addition, other parameters such as learning rate (LR) We conducted various experiments to test the feasibility of our proposed model in IoT healthcare system. The proposed model was tested using a brain tumour image data set in this study. To improve the proposed CNN model predictive performance, we have employed CNN pre trained models with imagenet dataset to produce high trained parameters (weights) and then transferred trained parameters weights of pre trained models to the CNN model individually for effective training of the model. For fine-tuning the CNN model, the brain tumor images data set was employed for final classification. The brain tumor data have 233 subjects and 3064 slices, which belong to three classes, i.e., Meningioma, Glioma, and Pituitary. This data set is very Small for effective training of the CNN model. In addition to tackle the problem of small brain tumor data method of data augmentationAll experiments used a laptop and a Google collaborator with GPU. All experiments required Python v3.7, and the CNN model was created using Keras framework v2.2.4 as a high-level API and Tensor flow v1.12 as the back end. All experiments were repeated numerous times to obtain consistent results. All experiment results were tabulated and graphed.15. T1-weighted contrast-enhanced images of 233 meningioma, glioma, and pituitary tumour patients are included in this data set. The Brain Tumor data contains 233 subjects and 3064 slices, with meningioma subjects accounting for 82 with slices 708, glioma subjects accounting for 91 with slices 1426, and pituitary subjects accounting for 60 with slices 930. Thus, the total number of subjects in the data is 233, and the total number of slices is 3064. In order to reduce the dimension of The brain tumor data set (BTDS) is obtained from the Kaggle repository20 method to augment the original dataset by using random zooming. All slices are being zoomed, and a new data set with 6128 slices has been created. The ratio of samples in an original data set is shown in Fig. To handle imbalance problem in data set because Brain tumor data set has the different number of three subjects slices. The distribution of the data is different, and it creates a problem of over fitting the model. To balance the meningioma, glioma, and pictutitary in the data set, we incorporate the data augmentationWe also used the Brain MRI Images Data Set (BMIDS) for cross dataset validation, which contains 253 MRI brain images. The tumor class in the data set has 155 images, while the non-tumor class has 98 images.The performance of the proposed CNN model is evaluated using the original and augmented brain tumour MR image data sets. The CNN model is configured with essential hyper-parameters such as optimizer SGD with a Learning Rate (LR) of 00.0001, epochs 100, and size of batch was 120. The 70% data for training and 30% for the testing of the model is used. Different evaluation matrices were used for model performance evaluation. The input image size Table On the other hand, the CNN model gained very excellent performance when trained and evaluated on an augmented data set. The CNN model obtained 98.56% accuracy, 100.00% specificity, 98.09% sensitivity, and 98.00% MCC when trained and evaluated on an augmented data set. The accuracy of the model improved from 97.40 to 98.56% which demonstrated the importance of the data augmentation process. Also, it illustrated that model needs more data for effective training of the CNN model.From the experimental results, we concluded that the proposed CNN model effectively classified the brain tumor types, and the augmentation process further improved the model CNN performance because the CNN model more data for extract more related features for classification. The high accuracy of the proposed CNN model might be due to the suitable architecture of the CNN model and proper fitting of essential parameters of the model and data augmentation.We have evaluated the predictive performance of CNN model with independent cross dataset. We trained the proposed CNN model with original and augmented brain tumor data set and validated with independent Brain MRI Images Data Set (BMIDS). The model is configured with essential hyper-parameters such as optimizer SGD with a Learning Rate (LR) of 00.0001, epochs 100, and size of batch was 120. Different evaluation matrices were used for model performance evaluation. The input image size Table Other other side the model achieved 98.97% accuracy, 99.89% specificity, 99.39% sensitivity, 98.89% Precision, 99.40% MCC, and 99.30% F1-score when trained with augmented data set (BTDS) and validated with independent data set (BMIDS). Hence, from experimental results we observed that model predictive and generalization capability improved when trained and validated with independent data sets.The performances of transfer learning models have checked on original and augmented data sets. Theses models have configured other essential hyper-parameters such as optimizer SGD with learning rate 0.0001, the number of epoch 100, batch size 120. The input image size Table The predictive Performance of transfer learning model ResNet-50 very high when model trained and evaluated with augmented data set. According to Table The VGG-16 model with original and augmented data sets obtained 94.77% accuracy, 96.30% specificity, 94.67% sensitivity, 93.43% precision, 91.90% MCC, 96.61% F1-S, and 95.97% accuracy, 96.95% specificity, 99.40% sensitivity, 96.84% precision, 92.98% MCC, and 96.80% F1-S respectively.Inception V3 obtained 93.23% accuracy, 96.89% specificity, 95.00% sensitivity, 96.08% precision, 95.56% MCC, and 97.87% F1-s, with original data set. While on augmented data set Inception V3 obtained 96.03% accuracy, 97.03% specificity, 97.00% sensitivity, 97.01% precision, 96.05% MCC, 98.00% F1-S. DenseNet201 model obtained 96.76% accuracy on original data set and increase it 97.43% accuracy with augmented data set.The Xception model with original data set achieved 93.00% accuracy, 97.03% specificity, 98.00% sensitivity, 97.09% precision, 99.32% MCC, 97.23% F1-S and obtained 95.60% accuracy, 98.98% specificity, 96.00% sensitivity, 98.04% precision, 99.98% MCC, and 98.00% F1-S with augmented data set. MobilleNet model obtained 96.76% accuracy with original data set and 97.87% with augmented data set. Among all models the ResNet-50 model performance in terms of accuracy is high with augmented data set. The model improved accuracy from 95.30 to 98.07% with data augmentation. The other evaluation metrics values also improved with data augmentation. From the experimental results, we concluded that the data augmentation process increased the training of ResNet-50 and model effectively classified the brain tumor types.The integrated frameworks performances have checked on original and augmented data sets. Furthermore, we have incorporated the TL ResNet-50, VGG-16, Inception V3, DenseNet201, Xception, and MobilleNet CNN architectures with imageNet data set to generate high weights and then transferred trained parameters weights of these pre trained models to the CNN model individually for effective training of CNN model. For fine-tuning of the CNN model, the brain tumors original and augmented data sets have used for final classification. The models have configured with concern hyper-parameters such as optimizer SGD with learning rate 0.0001, the number of epoch 100, batch size 120. The proposed framework performance has been evaluated employing various matrices. The input image size Table On the other hand, the model obtained very high performance when it trained and evaluated on the augmented data set. The integrated CNN and transfer learning model (ResNet-50-CNN) obtained 99.90% accuracy, 99.08% specificity, 96.13% sensitivity, and 99.10% MCC when trained and evaluated on augmented data set.The VGG-16-CNN model with original and augmented data sets obtained 96.78% accuracy, 99.23% specificity, 95.00% sensitivity, 96.99% precision, 98.93% MCC, 97.98% F1-S, and 97.88% accuracy, 98.00% specificity, 100.00% sensitivity, 96.98% precision, 98.79% MCC, and 99.00% F1-S respectively.Inception V3-CNN model obtained 97.00% accuracy, 99.00% specificity, 99.87% sensitivity, 98.92% precision, 95.76% MCC, 98.09% F1-S with original data set. While on augmented data set Inception V3 obtained 98.02% accuracy, 100.00% specificity, 98.67% sensitivity, 97.56% precision, 99.00% MCC, and 97.30% F1-S.DenseNet201-CNN model obtained 97.00% accuracy on original data set and increase it 97.90% accuracy with augmented data set. Hence, the integrated model DenseNet201-CNN improved accuracy 97.00\u201397.90%\u00a0= 0.90% with data augmentation process.The Xception-CNN model with original data set achieved 98.20% accuracy, 98.88% specificity, 97.40% sensitivity, 99.00% precision, 99.10% MCC, 98.65% F1-S, and obtained 98.97% accuracy, 99.00% specificity, 98.60% sensitivity, 97.24% precision, 97.99% MCC, 99.30% F1-S with augmented data set. MobilleNet-CNN model obtained 98.08% accuracy with original data set and 98.56% with augmented data set. The improved accuracy 98.08% to 98.56% when model fine tuned with augmented data set.From above anlaysis we conculded that among all the ResNet-50-CNN, VGG-16-CNN, Inception V3-CNN, DenseNet201-CNN, Xception-CNN, and MobilleNet-CNN, the predictive performance of ResNet-50-CNN model is high in terms of accuracy. The accuracy of the model improved from 99.10 to 99.90% which is illustrated the importance of the data augmentation and transfer learning process. Hence we concluded that the ResNet-50-CNN model effectively classify the brain tumor types. The high accuracy of the proposed integrated diagnosis framework might be due to the suitable architecture of the model and proper fitting of essential parameters of the model and data augmentation. In addition, the proposed integrated model (ResNet-50-CNN) accuracy has compared with CNN model and transfer learning ResNet-50 model in Table We have compared our ResNet-50-CNN (ResNet-CNN) model performance in terms of accuracy with state-of-the-art methods in Table Also, in Tables 32, especially convolutional neural networks. The CNN model is mostly used for medical image classification19. The CNN model extracts deep features from image data, and these features played an important role in final image classification. For the diagnosis of brain cancer, various methods have been proposed by researchers using brain MR image data and deep learning models. However, these existing methods have lack of accuracy of diagnosis. In order to tackle this problem, a new method is necessary to diagnose the disease accurately and efficiently IoT healthcare systems.Brain Tumor Classification using MR images are critical in the detection of brain cancer In IoT healthcare systems. Artificial intelligence (AI) based computer automatic diagnostic systems (CAD) can effectively different diagnose diseases in IoT healthcare system. Deep learning techniques are widely used in CAD systems to diagnose critical diseasesIn this study, we have proposed a CNN model for the accurate classification of brain tumor using Brain MR images. In the design of the proposed method, we have applied the deep learning CNN model for the classification of tumors meningioma, gLioma, and pituitary. The CNN model extracts more deep features from image data for final classification. To further improve the CNN model predictive capability, we have incorporated a transfer learning mechanism because, for proper training of the CNN architecture, the brain MR images data is insufficient. In transfer learning, we have used the well-known pre-trained models with big imageNet data set to generate high parameters (weights). These generated weights of models individually transferred to CNN model for effective training. For the fine-tuning process, the model was trained with brain MR images data set. Also, the data augmentation method is employed to increase the data set size for effective training of the model. Furthermore, we have used held-out cross-validation and performance evaluation metrics. We also used cross data set for cehcking the propoed CNN model predictice performance.According to Tables For accurate medical image classification, the CNN model is played a significant role, and in most CAD systems CNN model is used for the analysis of medical image data. In research study, we have proposed a deep learning-based diagnosis approach for brain tumor classification. In the proposed method, we have used a deep CNN model for the classification of tumor types Meningioma, Glioma, and Pituitary employing brain tumor MR images data. To enhance the predictive capability of the CNN model, we have incorporated transfer learning and data augmentation techniques. The experimental results show that the proposed integrated diagnosis framework ResNet-CNN has obtained 99.90% accuracy as compared to baseline methods. The high predictive outcomes of the proposed method might be due to the effective pre-processing of data and the adjustment of other parameters of the model such as numbers of layers, optimizer and activation functions, transfer learning, and data augmentation. Due to the high performance of the proposed ResNet-CNN model, it could be applicable for the classification of brain tumors and diagnosis of brain cancer in IoT-Healthcare. In the future, we will use other brain tumors datasets and other deep learning techniques to diagnose brain tumors."} +{"text": "The prevalence of chronic kidney disease (CKD) is increasing worldwide; black patients have an increased risk of developing CKD and end stage kidney disease (ESKD) at significantly higher rates than other races.between September 2019 to March 2020. Demographic and clinical data were extracted from the ongoing kidney outpatient clinic records and interviews, and were filled in a questionnaire. Patients provided blood and urine for laboratory investigations as standard of care, and data were descriptively and inferentially entered into REDcap and analysed using STATA version 17. Multivariable logistic regression analysis was used to identify demographic and clinical variables associated with advanced CKD.A cross sectional study was carried out on black patients with CKD attending the kidney outpatient clinic at Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) in South Africa, 2, serum bicarbonate 22 (IQR 20\u201324), haemoglobin 12.9 (IQR 11.5\u201314.0) g/dl and serum uric acid 0.43 (IQR 0.37\u20130.53). The prevalence of metabolic acidosis was 62.4%, anemia 46.4% and gout 30.9% among those with advanced CKD, while the prevalence of metabolic acidosis and anaemia was 46.6% and 25.9% respectively in those with early CKD. Variables with higher odds for advanced CKD after multivariable logistic regression analysis were hypertension , diabetes mellitus , severe proteinuria , angina , anaemia , hyperuricemia , and metabolic acidosis . Other associations with advanced CKD were loss of spouse (widow/widower) , low transferrin , hyperkalemia , use of allopurinol and doxazosin .A total of 312 black patients with CKD were enrolled in the study with a median age of 58 (IQR 46\u201367) years; 58% patients had advanced CKD, 31.5% of whom had grossly increased proteinuria, 96.7% had hypertension, 38.7% had diabetes mellitus and 38.1% had both hypertension and diabetes mellitus. In patients with advanced CKD, the median age was 61 (IQR 51\u201369) years, eGFR 33 (30\u201339) mL/min/1.73 mHypertension and diabetes mellitus were strongly associated with advanced CKD, suggesting a need for primary and secondary population-based prevention measures. Metabolic acidosis, anemia with low transferrin levels, hyperuricemia and hyperkalemia were highly prevalent in our patients, including those with early CKD, and they were strongly associated with advanced CKD, requiring clinicians and dietitians to be proactive in supporting the needs of CKD patients in meeting their daily dietary requirements towards preventing and slowing the progression of CKD. A total of 24 potential variables were identified after performing univariate logistic regression analyses. Backward elimination reduced this to 15 parameters; the factors associated with advanced CKD after adjusting for age and sex on multivariate logistic regression analysis included: hypertension , diabetes mellitus , angina , severe proteinuria , moderate proteinuria , hyperuricemia , anaemia , metabolic acidosis, allopurinol and doxazosin , low transferrin , hyperkalemia and, widow/widower (We divided the patients into two subgroups according to their CKD stages [early CKD (eGFR \u2265 45 ml/min/1.72m= 0.006) .This study evaluated the demographic and clinical profile of black patients with CKD attending the CMJAH kidney outpatient clinic in Johannesburg, South Africa. There were 42% with early CKD and 58% with advanced CKD; 93.6% had hypertension and 33.0% diabetes mellitus, and 32.3% had both hypertension and diabetes. The prevalence of hypertension among patients with CKD is high and it is strongly associated with advanced CKD and CKD progression , 31, theMetabolic acidosis is common in CKD and it can lead to dysfunction of many organs and systems including the kidney resulting in CKD progression , 43, theStudies have shown that the incidence of cardiovascular events increases with worsening kidney function , 57; 22.Hypertension and diabetes mellitus were strongly associated with advanced CKD, suggesting a need for primary and secondary population-based prevention measures. Metabolic acidosis, anaemia with low transferrin levels, hyperuricemia and hyperkalemia were highly prevalent in our patients, including those with early CKD, and they were strongly associated with advanced CKD. This calls for the proactive role of clinicians and dietitians in supporting the needs of CKD patients in meeting their daily dietary requirements towards preventing and slowing the progression of CKD. Further studies on the role of diet including plant-based proteins, vegetables and fruits in preventing and slowing CKD progression and other metabolic complications of CKD are warranted."} +{"text": "Sepsis is a leading cause of pediatric mortality. Little attention has been paid to latent and reactivated viral infection in critically ill children with sepsis. We report a large multi-center study of viral DNAemia and herpesvirus seropositivity in pediatric patients with severe sepsis.We enrolled 401 pediatric patients from 9 Pediatric Intensive Care Units (PICUs). Patient samples were tested via qPCR for EBV, CMV, HSV, adenovirus, HHV6, BK and parvovirus B19 DNA. CMV, EBV, HSV and HHV6 IgG were also measured to classify patients as having no infection (IgG-negative without DNAemia), acute infection (IgG-negative with DNAemia), reactivated infection (IgG-positive with DNAemia), or latent infection without reactivation (IgG-positive without DNAemia).55% of enrolled patients were male, 39% previously healthy, and 27% immunocompromised. 56% had documented infection(s) on enrollment . 11% died in the PICU.Viral DNAemia was detected in 61% of immunocompromised patients and 46% of non-immunocompromised patients. DNAemia with 2 or more viruses on study, detected in 21% of patients, was independently associated with increased mortality in both immunocompromised and non-immunocompromised patients . Viral detection was due to reactivated infection in 91% of patients with EBV DNAemia, 63% with CMV, and 100% with HSV and HHV-6, making acute infection rare.Viral seropositivity and latent infection were both common. Adjusted mortality was higher in patients seropositive for EBV compared to those seronegative for EBV. For HHV-6, mortality was higher in patients with viral reactivation compared to latent infection . Mortality in patients with no detected viral infection (IgG-negative without DNAemia) was low (\u2264 5% for each virus).Pediatric Sepsis Mortality and Viral DNAemiaICU mortality was significantly associated with the number of viruses detected during ICU stay in both non-immunocompromised patients (light grey bars) and immunocompromised patients (dark grey bars). In patients with 0 viruses detected, morality was less than 10% in both groups. If 1 virus was detected, mortality was 6% in non-immunocompromised patients and 14% in immunocompromised patients. In the 47 non-immunocompromised patients in which 2 or more viruses were detected, mortality was almost 25% and in the 31 immunocompromised patients mortality neared 40%.Among all patients, additional viral detection of 3, 4 or more viruses by PCR continued to increase risk of death, with mortality nearing 45% in patients who had 4 or more viruses detected during their ICU admission.Viral DNAemia was common and associated with mortality in pediatric patients with severe sepsis. DNAemia with 2 or more viruses increased mortality risk, even in previously healthy patients. EBV seropositivity was strongly associated with PICU mortality, independent of concurrent viral DNAemia.Andrew H. Walton, MS, RevImmune: Grant/Research Support|Thermo Fisher: Spouse employed by Thermo Fisher."} +{"text": "Huntington\u2019s disease (HD) is a rare (1-9/100 000), inherited disease characterized by an elongated CAG repeat on chromosome 4p, leading to a degeneration of neurons. Also, psychiatric symptoms are very common in the early stage and may appear before motor symptoms.To characterize neuropsychiatric symptoms in a group of individuals with manifest or pre-motor Huntington\u2019s disease in Medell\u00edn, Colombia.Data obtained from clinical records of individuals with HD (motor-manifest or pre-motor with triplets count) evaluated for ENROLL-HD project in the Group of Neuroscience of Antioquia. We explored variables related to substances abuse, neuropsychiatric symptoms, the respective age of onset, sex, and triplet count when available.Twenty-six (53%) were women, 8% had a familiar history of psychotic illness in a first-degree relative and 88% presented motor symptoms. Also, 59% had a history of depression, 53% irritability, 57% aggressiveness, 34% apathy, 29% perseverative/obsessive behavior, 14% psychosis, and 30% mild cognitive impairment. Ten individuals (20%) had motor without neuropsychiatric symptoms. Also, thirty-seven individuals (76%) presented motor and neuropsychiatric symptoms; of these, 41% had neuropsychiatric symptoms before motor symptoms. No psychiatric symptoms were associated with the use of alcohol, cigarettes, or drugs of abuse.Neuropsychiatric symptoms are highly prevalent among individuals with HD and studies oriented to create relevant knowledge for the development of advice oriented to people with this disease are necessary.No significant relationships."} +{"text": "Background: Understanding the epidemiology and risk factors for nosocomial infections with vancomycin-resistant enterococci (VRE) is necessary for the prevention and control of VRE infections in the hospital setting. We sought to determine the incidence of nosocomial infections of VRE and to ascertain predictors associated with nosocomial infection. Methods: In this retrospective cohort study, data were collected from patients with VRE infection from January 2019 to December 2020 at a tertiary-care center in northern California. VRE infections were designated as hospital onset (HO) if the specimen was collected >3 days after hospital admission or community onset (CO) if the specimen was collected \u22643 days after admission. Associations between HO infections with time, unit, and specimen were identified. Results: Over the 2-year period, 214 unique VRE infections were identified in hospitalized patients; 115 infections were CO and 99 were HO. HO-VRE were associated most frequently with stay in medical/telemetry units (68%), followed by oncology\u2013transplant units (15%) and ICUs (12%). There were ~4.7 and ~3.6 HO-VRE infections per month in 2019 and 2020, respectively. No differences were identified between HO-VRE infections in 2 medical units regarding glycopeptide and cephalosporin use in those units. The sources of VRE infections were urinary 45%, bloodstream 15%, stool 10%, and other 30%. Of the 45 infections in urine, 51% were identified from catheters (Foley and straight) and 27% were identified from clean-catch urine. Interestingly, 71% of patients with VRE identified from urine did not report urinary tract infection (UTI) symptoms at the time of collection. Urine was most often collected for urinalysis and culture from patients with nonspecific symptoms such as fever, leukocytosis, hypotension, tachycardia, or altered mental status. All urine collected from patients who reported UTI symptoms grew >100,000 CFU/mL in culture, while only 75% of cultures from patients without symptoms grew >100,000 CFU/mL. The most common antibiogram was resistance to ampicillin, cefazolin, levofloxacin, minocycline, penicillin, tetracycline, and/or vancomycin (42% of cases) and susceptibility to both daptomycin and linezolid (60% of cases). Conclusions: HO-VRE infections were frequently identified with urinary sources and were often associated with catheter use. However, the frequent lack of concurrent UTI symptoms suggests VRE colonization rather than infection in many cases. Understanding the epidemiology and risk factors for HO-VRE infections is essential for developing infection prevention protocols to reduce the incidence of those infections.Funding: NoDisclosures: None"} +{"text": "Annual seasonal influenza vaccination in healthcare workers prevents nosocomial transmission to patients, coworkers, and visitors, and reduces absenteeism. This study aimed to describe knowledge, attitudes, and practices (KAP) of seasonal influenza vaccine among public healthcare workers attending patients in Costa Rica.We conducted a cross-sectional survey of healthcare personnel attending patients in public hospitals in 2017\u20132018. Frequency distributions of demographics, vaccination KAP, sources of information, clinical manifestations and reasons for non-vaccination were reported. Logistic regression was used to analyze associations between exposures of interest and self-reported influenza vaccination.We surveyed 747 healthcare workers in 2017\u20132018. Of 706 participants who knew their vaccination status, 55.7% were vaccinated for seasonal influenza. Only 20.7% of participants knew the influenza vaccine was an inactivated virus, and 94.6% believed the vaccine causes flu-like symptoms. Factors associated with current influenza vaccination were vaccination in previous year and believed influenza vaccination may be harmful . Reasons for non-vaccination included fear of adverse effects and access limitations.Suboptimal influenza vaccination among healthcare workers may be attributed to misconceptions about the vaccine and limited engagement strategies focusing on healthcare workers. Appropriate interventions are needed to increase healthcare worker vaccination rates and improve their knowledge and beneficence, which would improve patient safety in hospitals. Influenza is a highly infectious respiratory disease that is usually mild or moderate at presentation, but may cause serious pulmonary, neurological and cardiac complications or death, particularly among risk groups . InfluenVaccination is the most effective measure to prevent new infections and reduce seasonal influenza-associated morbidity and mortality ,7. VacciThis study was a cross-sectional KAP survey regarding seasonal influenza vaccination among healthcare workers who attended patients in public hospitals of the Costa Rican Social Security Fund (CCSS).2, conformed by 7 provinces and 82 cantons [Costa Rica has an area of 51,100 km cantons . It has cantons . The lif cantons . Costa R cantons . CCSS ha cantons . CCSS inA questionnaire was adapted from the U.S. Centers for Disease Control and Prevention influenza survey . The queA close-ended survey was conducted to healthcare personnel attending patients in hospitals between 26 June and 11 August 2017 and between 17 September and 26 October 2018, antedating the peaks of influenza A and B epidemics in Costa Rica . SurveysThe lowest administrative vaccination coverage for influenza (PAHO) was used to calculate the sample size of healthcare workers: 38% . The numTwo-stage stratified cluster sampling was used to select samples of healthcare workers who worked in hospitals of CCSS. Stratification was based on hospital health network location . In stage one, we identified conglomerates in each stratum by probability proportional to the number of healthcare workers attending patients in each healthcare facility. In stage two, we identified healthcare workers in each selected conglomerate by simple random sampling within each group of healthcare professionals. Healthcare facilities were located in five of the seven departments of Costa Rica . Healthcp < 0.10 from unadjusted analyses were included in step-wise multivariable logistic regression models to evaluate associations with influenza vaccination status. Variables associated with vaccination at p<0.05 were retained in the final model. Tolerance values were used to assess collinearity among all independent variables and Hosmer-Lemeshow to assess the final adjusted model\u2019s goodness-of-fit. SAS V.9.4 was used for all analyses.Frequency distributions of demographics were reported. Frequency distributions and 95% confidence intervals (CI) for knowledge and attitudes of influenza virus, transmission, and vaccination; sources of information for vaccination; clinical manifestations seven days after vaccination; and reasons for non-vaccination were also reported. Results were reported for all participants and stratified by survey year as KAP regarding influenza vaccination and the environment may have differed between survey years. Pearson Chi-square tests were used to evaluate associations between demographics, knowledge, attitudes, sources of information, clinical manifestations, and reasons for non-vaccination, and survey year. Logistic regression was used to analyze associations between demographics, information sources, knowledge, and attitudes about the influenza vaccine, and self-reported influenza vaccination for 1) all participants, 2) participants in 2017, and 3) participants in 2018. These analyses excluded people who did not know or did not provide their vaccination status and those who did not respond to knowledge or attitude questions. Statistical significance was evaluated through the Wald Chi-square test. Variables found to be significant at This study was approved by the Research Ethics Committee of UVG (Protocol number 156-11-2016) and Center for Strategic Development and Information on Health and Social Security of CCSS (study code AB-1513-17). It was registered with the National Health Research Council of Costa Rica. Written informed consent was obtained for all participants.A total of 747 healthcare workers who attended patients in nine CCSS hospitals were surveyed: 553 in 2017 and 194 in 2018. The median age of all participants was 37 years (interquartile range: 31\u201348 years) and median years in profession was 11 years (interquartile range: 7\u201320 years) . Of all p-values \u2264 0.03) , but 38.1% did not recognize influenza may be transmitted from birds or pigs to people . Further \u2264 0.03) .p-values \u2264 0.01) and 439 from informal information at the healthcare facility (58.8%) . A great \u2264 0.01) .In 2017, 279 of 516 healthcare workers self-reported vaccination for seasonal influenza (54.1%) . In 2018Unadjusted analyses of all participants demonstrated the odds of self-reported current influenza vaccination were 8.64 times higher for healthcare workers who self-reported vaccination in previous year (95% CI: 6.02\u201312.40), 1.46 times higher for those who believed the influenza vaccine was composed of inactivated viruses (95% CI: 1.01\u20132.11), and 51% less for those who believed the influenza vaccine may cause harm (95% CI: 0.36\u20130.67) . Resultsp = 0.52). Tolerance values for independent variables were > 0.97. Final model results restricted to participants in 2017 were similar reported mild or moderate untoward reactions after vaccination, including vaccination site pain, flu-like symptoms, and general discomfort .Among 313 unvaccinated healthcare workers, the main reasons for non-vaccination were fear of side effects or developing disease (49.5%) and access limitations (26.5%) . There wIn this study of 747 healthcare workers of public hospitals in Costa Rica, seasonal influenza vaccine coverage was 54.1% in 2017 and 60.0% in 2018, lower than the coverage reported by PAHO for the same period and . HoweverDirect physician recommendations have been shown to be associated with seasonal influenza vaccination among risk groups, including pregnant women , older aThe finding that healthcare workers who believed everyone has the same risk of getting sick from influenza were less likely to have been vaccinated for influenza in 2018 is consistent with other studies ,35. ThisDespite suboptimal influenza vaccination coverage, 96.1% of participants agreed healthcare personnel should be vaccinated for influenza annually and 86.5% would do so if the vaccine was easily accessible. Consistent with other studies, vaccination in the previous year had the strongest association with the current vaccination ,42,43. OThis study had several limitations. First, surveys were completed during two time periods to meet new requirements of the National Health Research Council of Costa Rica. As KAP of influenza and the environment may have differed between years, we reported overall results and results stratified by survey year, which had lower statistical power. Second, this study focused on healthcare workers attending patients in hospitals and may not be generalizable to other clinical settings. Third, this was a cross-sectional study, so causal inferences may not be drawn from results. Fourth, influenza vaccinations were self-reported, which may overestimate vaccination coverage, although other studies have shown strong concordance between self-reported influenza vaccination and medical records . Fifth, 1"} +{"text": "In 2016, WHO launched the Global Health Sector Strategy on STIs, 2016\u20132021 (GHSS) to provide guidance and benchmarks for country achievement by 2020 and four global targets for achievement by 2030.A country survey jointly developed by experienced technical personnel at WHO Headquarters (HQ) and WHO regional offices was reviewed and distributed by WHO regional advisors to 194 WHO Member States in September-March 2020. The survey sought to assess implementation and prioritization of STI policy, surveillance, service delivery, commodity availability, and surveillance based on targets of the GHSS.A majority of countries returned a completed survey reflecting current (2019) STI activities. The regions with the highest survey completion rates were South-East Asia Region , Region of the Americas and Western Pacific Region . Having a national STI strategy was reported by 64% (72/112) and performing STI surveillance activities by 88% (97/110) of reporting countries. Availability of STI services within primary health clinics was reported by 88% of countries (99/112); within HIV clinics by 92% (103/112), and within reproductive health services by 85% (95/112). Existence of a national strategy to eliminate mother-to-child transmission of HIV and syphilis (EMTCT) was reported by 70% of countries (78/112). Antimicrobial resistance (AMR) monitoring for gonococcal infection (gonorrhoea) was reported by 64% (57/89) of reporting countries with this laboratory capacity. Inclusion of HPV vaccine for young women in the national immunization schedule was reported by 59% (65/110) and availability of cervical cancer screening was reported by 91% (95/104). Stockouts of STI medicines, primarily benzathine penicillin, within the prior four years were reported by 34% (37/110) of countries.Mechanisms to support improvements to STI service delivery through national-level policy, commitment, programming and surveillance are needed to operationalize, accelerate and monitor progress towards achievement of the 2030 global STI strategy targets. In 2019, the World Health Organization (WHO) estimated that 376 million cases of four curable sexually transmitted infections (STIs) occurred annually [2020 WHO STI Strategy Milestones:70% of countries have sexually transmitted infection surveillance systems in place that are able to monitor progress towards the relevant targets70% of countries have at least 95% of pregnant women screened for syphilis; and 95% of syphilis-seropositive pregnant women treated with at least one dose of intramuscular benzathine penicillin70% of key populations for HIV have access to a full range of services relevant to sexually transmitted infection and HIV, including condoms70% of countries provide sexually transmitted infection services or links to such services in all primary, HIV, reproductive health, family planning, and antenatal and postnatal care services70% of countries deliver HPV vaccines through the national immunization programmeN. gonorrhoeae70% of countries report on antimicrobial resistance in 90% national coverage sustained and at least 80% in every district in countries with the human papillomavirus vaccine in their national immunization programme2030 WHO STI Strategy Targets:T. pallidum incidence globally ;90% reduction of N. gonorrhoeae incidence globally ;90% reduction in 50 or fewer cases of congenital syphilis per 100 000 live births in 80% of countries;Sustain 90% national coverage and at least 80% in every district in countries with the human papillomavirus vaccine in their national immunization programme.To evaluate and report on national implementation of recommendations in the STI Strategy for the 74th World Health Assembly in 2021, WHO performed a national survey. This survey aimed to assess national level implementation and prioritization of STI control programming and achievement of the 2020 milestones in the STI Strategy as a measure of progress towards achievement of the 2030 global targets.In August 2019, a survey instrument in the form of a questionnaire for country completion was jointly developed by experienced technical personnel at WHO Headquarters (HQ) and WHO regional offices. The survey was made available in five languages: English, French, Spanish, Russian, and Portuguese.N. gonorrhoeae; and (6) number of countries including human papillomavirus (HPV) vaccination among girls within national immunization schedules, as a proxy for delivery of this vaccine. The survey also assessed programme service delivery, including use and availability of diagnostics and medications, and captured technical assistance needs in STI programming and surveillance (The survey sought to assess progress towards achievement of the following 2020 milestones within the STI Strategy: (1) number of countries with a STI surveillance system in place; (2) number of countries with a national policy for universal screening of pregnant women for syphilis as a first step in signifying countries\u2019 intent to achieve the milestone of at least 95% of pregnant women attending antenatal care being screened for syphilis; (3) percentage of key populations to the HIV epidemics with access to STI and HIV services; (4) number of countries providing STI services or links to such services; (5) number of countries reporting on antimicrobial resistance (AMR) of eillance .During October 2019 to March 2020, national STI, HIV or reproductive health programme directors or managers, national sexual and reproductive health officers or directors, national programme officers for maternal and child health, national disease surveillance coordinators, national laboratory surveillance officers or managers, WHO country programme officers, or other UN agency HIV, STI or sexual and reproductive health officers completed the questionnaires. These staff were encouraged to liaise with programme managers with responsibility for HIV, reproductive health, immunization and commodities to gather the non-STI information needed to complete the survey. Three email reminders were sent to non-responding countries.Regional office participants were made aware in the invitation to participate and on the survey cover page that results would be used to inform WHO and the World Health Assembly on progress towards globally recommended STI programme implementation . Partici\u2122 [Completed questionnaires were returned through WHO regional offices to WHO HQ. Data were compiled and entered in Open Clinica\u2122 during FDescriptive analyses included frequency and percentages calculations for each survey question, using the number of completed responses as the denominator. Analyses were based on the overall responses received from reporting countries. Missing responses were not included in the denominator for percentage calculations. Analyses were reported for the six WHO regions and by World Bank income classifications . ResponsOf the 194 WHO Member States to which the survey was distributed, 112 58%) submitted a survey response . The reg8% submitNinety-two percent 103/112) of the reporting countries were familiar with the GHSS, 2016\u20132021 and 64% (72/112) had a national STI strategy, ranging from 37% (10/27) of countries in the European Region to 77% (20/26) of countries in the African Region of HIV and syphilis 70%, 78/112) (Tables 12 Table. AlthougAvailability of STI surveillance was reported by 87% 97/110) of countries responding to this entry (Tables 10 of couN gonorrhoeae. Only 56% (62/110) of responding countries reported overall STI surveillance to be a high priority STI intervention and only 34% (38/110) ranked surveillance for AMR in N gonorrhoeae to be of high priority of responding countries reported conducting antimicrobial susceptibility testing. Only 89 countries responded to the survey question related to gonococcal antimicrobial susceptibility testing. Of these 64% (57/89), primarily high-income countries, reported conducting this surveillance provide STI care at primary health care services, 91% (103/112) within HIV services, 85% (95/112) in reproductive health clinics, 77% (86/112) in family planning clinics, 89% (100/112) in antenatal/postnatal clinics. and 85% (95/112) in specialized STI clinics. These results suggest achievement of the STI Strategy milestone of 70% of countries providing STI services or links to such services in primary, HIV, reproductive health, family planning, and pre- and post-natal care services.Countries reported the highest priority STI services as EMTCT of HIV and syphilis , STI screening among persons with HIV , STI screening among high-risk populations of men who have sex with men (MSM) and sex workers (SW) , condom distribution and HPV vaccination for young women .Availability of HIV and syphilis testing was reported by the highest proportion of countries while the proportion of countries reporting the availability of chlamydia, HPV, and herpes testing was lower at 59% (66/111), 56% (62/111) and 54% (60/111), respectively.For pregnant women, screening was routinely offered by 94% (103/110) of countries for HIV, 96% (107/111) for syphilis, 74% (81/110) for hepatitis B, 28% (31/110) for hepatitis C, 27% (30/110) for gonorrhoea, 20% (22/110) for chlamydia, 17% (19/110) for HPV, and 15% (17/110) for herpes.For key populations, 83% (93/112) of countries reported providing HIV screening to MSM, 74% (83/112) for syphilis, 50% (56/112) for gonorrhoea, 41% for chlamydia (46/111) and 54% (60/111) for hepatitis B. For SW, 81% (90/111) of countries reported providing screening for HIV, 73% (81/111) for syphilis, 49% (54/110) for gonorrhoea, 44% (48/110) for chlamydia and 49% (54/110) for hepatitis B. These results describe screening services available towards the milestone achievement of 70% of key populations having access to a full range of services relevant to sexually transmitted infections and HIV.Recommended treatment for syndromic management of urethral discharge in males included azithromycin in 85% (91/107) of reporting countries and ceftriaxone in 83% (89/107). Recommended treatment for vaginal discharge included azithromycin in 76% (80/106) and ceftriaxone in 73% (77/105) of reporting countries. For presumptive treatment of genital ulcer disease syndrome, benzathine penicillin was used by 89% (93/105) and acyclovir by 78% (82/105) of reporting countries.STI medication stock outs during 2015\u20132019 were reported by 34% (37/110) of countries. The most frequent medication stock out was benzathine penicillin, reported by 34% of countries (37/110) followed by ceftriaxone 15% (17/111), acyclovir 14% (16/111), and cefixime 14% (15/110). Recent stock outs of any STI medication were reported by 10 countries in 2018 and by seven countries in 2019. Stock outs of syphilis test kits were reported by 57% (30/53) of responding countries.The HPV vaccine was reported to be included in the national immunization schedule of 59% 65/110) of reporting countries and is recommended for both adolescent girls and boys in 31% (20/111). The HPV vaccine is recommended for persons living with HIV in 28% (18/65) and for MSM in 18% (12/65) of reporting countries. Of the countries with a vaccination program for boys , only 7 (35%) also include HPV vaccination for MSM. Populations included for HPV vaccination varied by World Bank income classification .Of reporting countries, 94% (102/109) reported availability of cervical cancer screening for general populations of women between the ages of 35 and 55. Among these countries, the tests in use included PAP smear in 91% (95/104), HPV test 48% (49/102), and visual inspection with acetic acid testing 53% (53/100).Methods of treatment of cervical pre-cancerous and cancerous lesions reported by countries included: loop electrosurgical excision procedure , surgical removal , cryotherapy , and thermal ablation .WHO technical assistance was requested by 75% (82/109) of countries. The areas of technical assistance need included: development of national strategy , STI treatment , STI surveillance , EMTCT , AMR of gonorrhoea , and HPV prevention and treatment . Countries reported the main technical partners or agencies that supported STI prevention and control services to include the US Centers for Disease Control and Prevention, European Center for Disease Control (ECDC), the Global Fund, WHO, UNAIDS and other UN agencies . The main sources of funding support for implementation of STI-related prevention and control programmes were reported as national governments and the Global Fund.The STI Strategy urges countries to define and implement national strategies to prevent and control STIs, informed by national STI surveillance and programme data. Among the 112 countries that responded to the survey, only 64% reported having a national STI strategy. EMTCT of HIV and/or syphilis emerged as a common goal based on availability of national strategies, prioritization, and service delivery. A higher percentage of responding countries reported conducting STI surveillance or monitoring (87%), demonstrating the opportunity for development of national STI strategies guided by national STI monitoring and STI service delivery. A majority (70%) of countries reported providing STI services or links to STI services in primary care, HIV, reproductive health, family planning, and pre- and post-natal care services and for key populations. Medication and test kits stock outs, primarily of benzathine penicillin and syphilis test kits suggest that efforts to control adult, maternal and congenital syphilis may have been compromised in recent years. HPV vaccination recommendations, cervical cancer screening, and treatment of cervical lesions indicate opportunities for improved service delivery. Delivery of these and other STI services varied by country income classification. Guided by surveillance, concerted efforts to expand and improve the delivery of STI clinical services for general and key populations are needed to reach the 2030 targets of the Global STI Strategy. Direct technical assistance by WHO was requested by over 70% of surveyed countries and will be needed to accelerate progress in these areas.As of December 2021, WHO has validated 15 countries as having achieved elimination of mother-to-child transmission of HIV and/or syphilis and has N. gonorrhoeae [Although a majority of countries reported conducting STI surveillance, in most settings surveillance primarily reflects case reporting. In countries with limited laboratory-based diagnostic testing, case reports will reflect syndromic diagnosis of the common STI clinical presentations of urethral and vaginal discharge and genital ulcer disease . Due to orrhoeae , 14. WHOorrhoeae , 15\u201319.A majority of countries reported the availability of STI clinical services or links within other clinical settings such as primary care, HIV, reproductive health, family planning, and pre- and post-natal care services. STI screening among key populations of MSM and SW as well as pregnant women was primarily focused on HIV and syphilis with fewer countries reporting hepatitis B, chlamydia, and gonorrhoea screening. Quality STI services rely on appropriate diagnosis and treatment. Availability of diagnostic testing for the general population was reported by 96% of countries for HIV and syphilis but far fewer countries in comparison reported available testing for chlamydia, gonorrhoea, HPV, and herpes. These findings reflect the need for expanded availability of STI diagnostics and transition from syndromic management to etiological testing to improve diagnostic accuracy and efficacy of treatment. Although STI services may be available at multiple access points, the quality of these services may be compromised if etiologic testing is not available and treatment is not based on updated syndromic management guidelines , 21.Cervical cancer is the fourth leading cancer among women globally, claiming the lives of over 300,000 annually . In AuguN. gonorrhoeae, a greater number of high- and high-middle income countries are known to perform this surveillance [The response rate of 58% 112/194) of surveyed WHO Member States should be considered when interpreting these data. This analysis was conducted using number of reporting countries as the denominator. Countries that did not report (particularly low-middle- and low- income countries) may not have comparable implementation. The proportion of responding countries from high, and upper-middle income countries , and low-middle- and low- income countries was equal to the overall proportion of WHO Member States within these World Bank income designations of 59%, (115/194) and 41% (79/194) respectively. Nonetheless, these survey results may over or underestimate implementation of STI response activities at country, regional, and global levels. We specifically note the limited representation of two specific groups of countries: (1) only one of nine Portuguese-speaking countries completed the survey despite translation and outreach to these countries by a Portuguese-speaking staff member and (2) few countries in the Eastern Mediterranean Region completed the survey. We did not include individual country responses, instead grouping responses by World Bank income classification and WHO region. For some surveillance activities such as AMR monitoring for 4 of surveillance . SimilarIn 2019, an interim assessment of progress towards achieving the milestones for the three interlinked global strategies for HIV, hepatitis and STIs concluded that limited progress on STI prevention and elimination had been made compared to progress for HIV and hepatitis . ResultsS1 File(PDF)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table* Elimination of mother-to-child transmission of HIV and syphilis. **16 between 2020\u20132023.(DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file.S5 Table(DOCX)Click here for additional data file.S6 Table(DOCX)Click here for additional data file.S1 Checklist(DOCX)Click here for additional data file."} +{"text": "To estimate the fraction of anaemia attributable to malaria and sickle cell disease (SCD) among children aged 6\u201359 months in Nigeria.Cross-sectional analysis of data from Nigeria\u2019s 2018 Demographic and Health Survey (DHS).Nigeria.11 536 children aged 6\u201359 months from randomly selected households were eligible for participation, of whom 11 142 had complete and valid biomarker data required for this analysis. Maternal education data were available from 10 305 of these children.Haemoglobin concentration.We found that 70.6% (95% CI: 62.7% to 78.5%) of severe anaemia was attributable to malaria compared with 12.4% (95% CI: 11.1% to 13.7%) of mild-to-severe and 29.6% (95% CI: 29.6% to 31.8%) of moderate-to-severe anaemia and that SCD contributed 0.6% (95% CI: 0.4% to 0.9%), 1.3% (95% CI: 1.0% to 1.7%) and 10.6% (95% CI: 6.7% to 14.9%) mild-to-severe, moderate-to-severe and severe anaemia, respectively. Sickle trait was protective against anaemia and was associated with higher haemoglobin concentration compared with children with normal haemoglobin (HbAA) among malaria-positive but not malaria-negative children.This approach used offers a new tool to estimate the contribution of malaria to anaemia in many settings using widely available DHS data. The fraction of anaemia among young children in Nigeria attributable to malaria and SCD is higher at more severe levels of anaemia. Prevention of malaria and SCD and timely treatment of affected individuals would reduce cases of severe anaemia. This study uses individual-level data from a large, nationally representative survey that includes haemoglobin concentration, malaria testing and sickle cell testing.The relatively simple approach used here could be applied to Demographic and Health Survey and similar surveys.The data do not include measures of iron or inflammation, which would be needed to identify iron deficiency, a major cause of anaemia.We treated malaria rapid diagnostic test results, which are imperfect, as a proxy for malaria infection.http://ghdx.healthdata.org/gbd-results-tool), there were 8.3 million (95% CI: 5.5 to 12.1 million) years lived with disability worldwide among children under 5 years old due to anaemia in 2019, the majority of which were due to moderate or severe anaemia. The highest rates of anaemia (adjusted haemoglobin concentration <110 g/L) and severe anaemia (<70 g/L) among preschool-aged children are reported from sub-Saharan Africa (SSA).1 2Anaemia is a major cause of morbidity and mortality among children. According to Global Burden of Disease (GBD) models , children may have several concurrent causes for their anaemia, each requiring a different treatment strategy, for example iron supplementation, chemotherapy, transfusion, antimalarials or deworming.6http://ghdx.healthdata.org/gbd-results-tool). Because most studies of anaemia are based on relatively small populations, national and regional estimates often need to extrapolate data from these geographically scattered studies to cover the rest of the population. Here, we have explored how Nigeria\u2019s 2018 Demographic and Health Survey (DHS), a large, and uniquely detailed data source, could shed light on the contribution of Plasmodium falciparum (P.f.) malaria and sickle cell disease (SCD) to anaemia. For the first time in DHS history, this Nigerian survey not only tested a population-representative sample of children for malaria infection, but also tested them for haemoglobin subunit beta (HBB) type, including the alleles associated with sickle cell trait and disease.vs rural residence, maternal education) risk factors, we can provide a better estimate of the contribution of malaria and SCD to anaemia and explore the inter-relationships between SCD and trait, malaria and anaemia.Nigeria is Africa\u2019s most populous country and experiences a high childhood anaemia burden. Previously, 60% of Nigeria\u2019s moderate and severe anaemia among children under 5 years old has been attributed to iron deficiency and only 12% and 2% to malaria and sickle cell disorders, respectively (P.f. (HRP-II) malaria rapid diagnostic test (RDT), yielding 11 173 (96.9% of eligible children) RDT results. The same finger or heel prick was also used to evaluate HBB type using SickleSCAN point-of-care test from BioMedomics, yielding 11 186 results (97.0% of eligible children). This test determined the presence of the HbS and HbC alleles, allowing us to determine which children had normal HBB (HbAA), SCD (HbSS or HbSC), sickle cell trait (HbAS) or haemoglobin C trait (HbAC). The nine children who had a recorded HBB type of \u2018other\u2019 were excluded. In total, 11 142 children (96.6% of eligible children) with all three biomarker measurements were included in our analyses. Maternal education was not available for all of these children, so analyses that included maternal education had 10 305 (92.5%) of the children with all three biomarkers. The survey was approved by the National Health Research Ethics Committee of Nigeria and the ICF Institutional Review Board.We obtained data from Nigeria\u2019s 2018 DHS.The DHS includes sample weights based on the survey design and on household response rates.We studied the relationships between anaemia and other factors using three thresholds for adjusted haemoglobin concentration: <110 g/L (anaemia), <100 g/L (moderate-to-severe anaemia) and<70 g/L (severe anaemia).82 approximation for the other characteristics .All the demographic and socioeconomic data came from the DHS. To compare demographic characteristics between children with and without moderate-to-severe anaemia, we applied the Wilcoxon rank-sum test to determine if the distribution of ages was significantly different and a proportions test with \u03c7https://r-survey.r-forge.r-project.org/survey/html/svyglm.html). The primary sampling unit is the cluster and the strata are the DHS-defined strata . When there were no observations of one of the outcomes in a category , we do not report the odds of the outcome. This effect did not have an impact on the model estimates for the other categories. To compute the effect of sickle cell status among RDT-positive children, we fit models using RDT-positive children with HbAA as the reference group rather than RDT-negative children.We fitted multivariate quasibinomial logistic and multivariate linear generalised linear models to predict anaemia status and haemoglobin concentration, respectively. We used the svyglm package to fit these models using survey weights , 67.9% were anaemic (adjusted haemoglobin concentration <110 g/L), 41.1% had moderate or severe anaemia (<100 g/L) and 3.0% had severe anaemia (<70 g/L) . Childre10.1136/bmjopen-2022-063369.supp1Supplementary dataChildren with moderate-to-severe anaemia were significantly younger and had lower proportions of females, malaria RDT+, HbSS, rural residence, lower three wealth quintiles and lower maternal education compared with children with mild-to-no anaemia .Malaria RDT positivity, HBB type, age and wealth quintile were significantly associated with all degrees of anaemia . Among cWe found the fraction of anaemia attributable to malaria to increase with the severity of anaemia, from 12.4% (95% CI: 11.1% to 13.7%) of overall anaemia (adjusted haemoglobin concentration <110 g/L) to 29.6% (95% CI: 29.6% to 31.8%) of moderate-to-severe anaemia (<100 g/L) and to 70.6% (95% CI: 62.7% to 78.5%) of severe anaemia (<70 g/L) . The fraAlthough RDT positivity is a major risk factor for anaemia at all levels of severity , malariaChildren with HbSS or HbSC were at high risk of anaemia , but somIf the information about HBB type is not used by the regression models used for prediction , then thEach year of age was associated with an increase in haemoglobin of 2.74 g/L . Among chttp://ghdx.healthdata.org/gbd-results-tool). We found that higher levels of household wealth and maternal education were associated with reduced risk of anaemia and higher average haemoglobin concentration in children, which is consistent with earlier analyses of the same datasetWe found that malaria RDT positivity and SCD were associated with a high risk of anaemia among children participating in Nigeria\u2019s 2018 DHS. Our results support the hypothesis that malaria and SCD play a larger role in more severe compared with mild anaemia. Our estimate of the contribution of malaria to moderate-to-severe anaemia among young children in Nigeria of 30% is substantially higher than the GBD\u2019s estimate of 12% , our analysis attributes 10.6% of severe anaemia (haemoglobin concentration <70 g/L) to SCD. We note that 11.6% of children with severe anaemia had HbSS or HbSC. Ideally all children with SCD should be identified through a newborn screening programme. However, such programmes are scarce in Africa but as an interim measure our findings indicate that, because SCD is so prevalent in our population-representative sample of children with severe anaemia, screening all young children with severe anaemia with a point-of-care test could identify undiagnosed SCD. Active management could then be started, which would improve their intellectual and physical development and could reduce their need for transfusions.16et al found a clinical malaria incidence rate ratio of 0.66 between children with HbAS versus HbAA, with protection peaking around 3\u20136 years of age20Although sickle trait was associated with an increased risk of mild anaemia, it was associated with protection against anaemia among malaria-positive children, with a greater degree of protection against severe anaemia. This is consistent with observations that sickle trait protects against severe malaria more than mild malaria illnessP. falciparum malaria were available in the DHS, not on P. vivax, though falciparum comprises most infections is in Nigeria. Even with additional data, the causes of anaemia are complex and can be interrelated, making it difficult to assign aetiology. Calis et al 2008 used structural equation modelling to account for these relationships.Our study has several limitations. Although we found that increasing age was associated with a reduced risk of anaemia, this finding could be partially attributed to the fixed thresholds used to define anaemia for all children regardless of age. Haemoglobin concentrations increased with age, which has been observed in healthy, disease-free children.Our analyses highlight the importance of malaria and SCD in the more severe stages of anaemia among young children in Nigeria. The majority of children in the DHS survey had mild-to-severe anaemia, most of which was not due to malaria or SCD. At the more severe end of the anaemia spectrum, malaria appears to be linked to 70.6% of severe cases and SCD to 10.6%. There are many ways to prevent or mitigate anaemia early, which could avert the development of severe anaemia and the need for blood transfusions. Malaria control has been observed to reduce anaemia prevalence."} +{"text": "Fusarium spp. , but low for Penicillium spp. and Alternaria spp. . This study underlines the improvement in diagnostic yield by fungal primary-specimen-DNA PCR/sequencing in the event of a negative or contaminated culture, as well as its significance for the diagnosis of dermatophyte and non-dermatophyte onychomycosis. Molecular mycology methods like PCR and DNA sequencing should complement conventional diagnostics in cases of equivocal findings, suspected NDM onychomycosis or treatment-resistant nail pathologies.Rapid and reliable fungal identification is crucial to delineate infectious diseases, and to establish appropriate treatment for onychomycosis. Compared to conventional diagnostic methods, molecular techniques are faster and feature higher accuracy in fungal identification. However, in current clinical practice, molecular mycology is not widely available, and its practical applicability is still under discussion. This study summarizes the results of 16,094 consecutive nail specimens with clinical suspicion of onychomycosis. We performed PCR/sequencing on all primary nail specimens for which conventional mycological diagnostics remained inconclusive. In specimens with a positive direct microscopy but negative or contaminated culture, molecular mycology proved superior and specified a fungal agent in 65% (587/898). In 75% (443/587), the identified pathogen was a dermatophyte. Positive cultures for dermatophytes, yeasts and non-dermatophyte molds (NDMs) were concordant with primary-specimen-DNA PCR/sequencing in 83% (10/12), 34% (22/65) and 45% (76/169), respectively. Among NDMs, agreement was high for Onychomycosis is the most common cause of abnormal-appearing nails with an estimated mean prevalence of 4\u20139% in the general population ,2,3. TheTrichophyton rubrum and Trichophyton mentagrophytes Na2S (Sigma), 25% [vol/vol] ethanol) without fluorochrome. After centrifugation at 8000\u00d7 ed water ,28. Fung2 coupled with large-subunit of forward fluorescently labelled primer LSU1 (5\u2032-GATAGCGMACAAGTAGAGTG-3\u2032) and reverse primer LSU2 (5\u2032-GTCCGTGTTTCAAGACGGG-3\u2032) [28S ribosomal DNA (rDNA) was amplified by PCR using ReadyMix Taq PCR Mix with MgClzerland) . ExtractDNA sequence analysis of the amplified 28S rDNA was performed for species identification on an FLX Genome Sequencer . The fungal species was determined by comparing the sequence obtained with those in the NCBI database. The data were collected and stored in a MOLIS laboratory information system .Absolute and relative frequencies are provided for nominal variables. Median and interquartile range (IQR) are computed for metric variables. To investigate the relation between culture and PCR/sequencing results, the absolute frequencies and conditional frequencies of the culture results conditioned on the PCR/sequencing results are reported. These distributions are visualized with bar charts.n = 16,094) and subset of specimens, which in addition to the standard conventional methods also underwent primary-specimen-DNA PCR/sequencing in parallel. The latter will be referred to as the \u201cPCR/sequencing group\u201d (n = 1148). Baseline characteristics of the two groups are presented in Statistical analyses were obtained for two main groups: For the whole study population and negative in 4,951 (30.8%) cases, resulting in an overall concordance of 58.4%. The majority of discordant results resulted from samples with positive direct microscopy, but negative fungal culture: overall, 59.5% of the specimens with detection of fungal elements by fluorescence microscopy showed a negative fungal culture.Trichophyton rubrum being the most prevalent, followed by NDMs (29.1%), yeasts (21.8%) and mixed infections (1.2%).Among the patients with a positive culture, dermatophytes were the most commonly identified fungi (47.9%) with In 1148 cases, the fungal standard diagnostic with fluorescence microscopy and fungal culture was insufficient or inconclusive and, therefore, was complemented by sequencing of the amplified fungal DNA extracted from the primary nail specimen. Given the high specialization and expertise of the mycology laboratory in Lausanne, fungal elements were detected in 99.7% of these samples by fluorescence microscopy. While fungal culture remained of low sensitivity and only detected a fungal pathogen in 21.8%, molecular mycology clearly outperformed it as PCR/sequencing yielded positive results in 63.5% of the cases .Fusarium spp. were the most prevalent NDM detected by PCR/sequencing and accounted for 43.2% (98/227) of NDM cases. The distribution and comparison of culture and PCR/sequencing results are shown in In the PCR/sequencing group, the positive conventional culture results were distributed as follows: NDMs 67.6%, yeasts 26%, dermatophytes 4.8% and mixed infections 1.6%. Molecular mycology results in the same group differed as dermatophytes were the most prevalent (63.5%), followed by NDMs (31.1%) and yeasts (5.3%). PCR/sequencing detected a total of 463 dermatophyte infections. Of these, only 2.2% were also identified as dermatophyte infections by fungal culture, whereas without molecular mycology, the majority of clinical specimens were considered negative/contaminated 95.7%; . By contWhen conventional fungal culture and molecular mycology (primary-specimens-DNA PCR/sequencing) were compared based only on positive or negative/contaminated results, there was a match in 48.9% of the cases. Concordance decreased to 26% when agreement to the species level was requested .Trichophyton rubrum 37%, Trichophyton interdigitale 7%), NDMs 14% and yeasts 1%. Additionally, in cultures contaminated by fungi or bacteria, molecular mycology still identified a causative fungal agent in 72% . Overall, PCR/sequencing could disclose a fungal agent in 65% (587/898) of specimens with negative or contaminated culture and 75% (443/587) of these were dermatophytes.Of interest, only 40.5% (190/469) of all negative cultures also showed a negative PCR/sequencing result . In 59.5Trichophyton rubrum (83%) or Fusarium spp. (80%), it was low (<50%) when Aspergillus spp., Acremonium spp., Candida parapsilosis, Penicillium spp. or Alternaria spp. was detected when the culture was positive for detected . OverallThis large-scale study demonstrated the improvement in diagnostic yield in onychomycosis by molecular diagnostics like primary-specimen-DNA PCR/sequencing. PCR/sequencing could confirm the suspected onychomycosis and identify the causative fungi in a high number of cases despite inconclusive standard diagnostics, especially in terms of a negative or contaminated fungal culture. The concordance rate at the species level between the cultural and corresponding PCR/sequencing results differed among the culturally detected fungi.Trichophyton rubrum and dermatophytes in general were the most prevalent fungal agents in our whole study population, which is well in line with the currently available study data [Fusarium spp. was the most prevalent NDM identified by PCR/sequencing and its total number reached 21% of that of dermatophytes. Compared to previous data, in which Fusarium spp. accounted for 15% of the number of dermatophytes, this also indicates a continued increase in Fusarium spp. onychomycoses, which can be associated with poor treatment response [Regarding epidemiological findings, udy data ,33,34,35udy data ,36, NDMsudy data ,15. Fusaresponse ,13,28,37If fungal culture remained sterile despite positive direct microscopy and/or highly suggestive clinical findings, PCR/sequencing could eventually identify a fungal agent in 59.5% of the cases. Upon fungal culture contamination with positive direct identification and/or evocative clinical manifestations, PCR/sequencing detected a causative fungus in 72%. Similarly, other authors reported detection of fungi by molecular methods in up to 91.3% of samples with negative or contaminated culture ,34,36,38However, differences between diverse molecular techniques in sensitivity and specificity as well as in their ability to detect NDMs, yeasts and mixed infections need to be considered in clinical practice ,34. AccoThe current study elucidates the significance of PCR and fungal DNA sequencing in the diagnosis of NDM nail infections, which is known as challenging regarding the discrimination of actual NDM nail infection and frequently occurring contamination of fungal cultures by NDMs. A positive cultural result for an NDM was confirmed by subsequent PCR/sequencing in merely 45% of cases, whereas 41% showed a negative result. In contrast, among cultures diagnosed as contaminated by NDMs, fungal sequencing detected NDMs in 16% and, therefore, might indicate actual NDM nail infection rather than contamination. Additionally, PCR/sequencing detected NDMs in 14% of negative cultures. Similarly, one study reported poor agreement for culture and PCR for the detection of NDMs with single samples in 167 patients with suspected onychomycosis .Trichophyton spp., Fusarium spp. and Scopulariopsis spp. were frequently confirmed by PCR/sequencing, whereas this was rarely the case for Alternaria spp. (5%) or Pencillium spp. (20%). Similar agreement rates were reported in previous studies [Trichophyton spp. 93.8%, Fusarium spp. 84%, Scopulariopsis spp. 50%, Aspergillus spp. 46.4%, Acremonium spp. 80%, Penicillium spp. 18%, Candida spp. 59% and Alternaria spp. 5%. It is reasonable to assume that concordant NDM detection by culture and PCR/sequencing indicates actual NDM nail infection; nevertheless, repeated detection remains the gold standard in the diagnosis of NDM onychomycosis [Trichophyton rubrum or Fusarium spp. increases the likelihood of a clinically significant result.In our study, the concordance rate of culture and corresponding PCR/sequencing results differed depending on the culturally identified fungus. Positive cultures for studies ,36. For As a limitation of the recent study, the missing information on antifungal pretreatment must be considered, as recent application of antifungals significantly decreases the sensitivity of fungal culture but to a lesser extent with molecular methods . In addiIn conclusion, the presented data shows that especially in patients with clinically suspected onychomycosis but equivocal standard diagnostics, molecular methods can significantly contribute to the correct diagnosis. This finding is important as confirming the diagnosis of onychomycosis is essential to establish correct treatment and increases patient compliance for a commonly months-lasting therapy. Given the high prevalence of onychomycosis in the general population, molecular methods might not be currently available in the first place for all those confronted with onychomycosis. Furthermore, the advantages obtained with PCR methods for routine analysis must be weighed against the price of molecular biology reagents and equipment , and the expenditure of time required from trained personnel to perform the laboratory procedures. However, clinicians should be aware of the high risk of a false negative and contaminated fungal culture; and molecular methods should be added when conventional diagnostics are inconclusive, NDM onychomycosis is suspected or in the case of a treatment-resistant course of disease."} +{"text": "P = .02) and residing in Mukono district . Overall, 114 (28.1%) participants had cognitive deficit; 9 (2.2%) dementia and 105 (25.9%) impaired cognition. Cognitive deficit was independently associated with female gender , formal employment , age 70\u201374 , and \u2265 75 years . Prevalence of seizures among participants with cognitive deficit was 5.3% (6/114). Among older persons attending a medical clinic in Uganda, almost one-third had cognitive deficit with seizure prevalence being higher among these individuals.There is limited data on the prevalence of seizures and dementia among older persons in Uganda. We evaluated cognitive functioning, and the prevalence and factors associated with seizures among older persons attending an outpatient medical clinic in Uganda. We randomly selected older adults (60 years and above) attending Kiruddu National Referral Hospital medical outpatient clinics between October 2020 and March 2021. We excluded individuals with a history of head injury, brain tumors, mental retardation, co-morbidity with HIV and patients who have had recent brain surgery. Cognitive functioning was assessed using the Identification for Dementia in Elderly Africans (IDEA) tool. We enrolled 407 participants, with a median (inter-quartile range) age of 67 (64\u201373) years. Majority were female . The prevalence of seizure was 1.5% . All 6 participants reported generalized tonic-clonic seizure type. Self-reported seizure was associated with being female (adjusted prevalence ratio [aPR]: 0.79, 95%CI: 0. 67\u20130.93, Epilepsy is the third most common neurological disorder affecting older adults after stroke and dementia. Considering the increasing aging population in sub-Saharan Africa, the overall incidence and prevalence of epilepsy is expected to increase with majority of the patients with newly diagnosed epilepsy being older adults.\u20135 Furthermore, the characteristic symptoms of seizures in the elderly are different from those in younger patients.,7Neurological non-communicable diseases such as dementia and epilepsy are increasingly recognized in the developing world in tandem with the aging population.,9 The estimated prevalence of epilepsy in Uganda is about 3% of the general population. However, no national surveys have been conducted, however, studies report an estimated prevalence ranging from 0.2% to 3.4% in different villages across the country. Epilepsy has significant economic implications in terms of health-care needs, premature death, and lost work productivity. The mortality of individuals with epilepsy is 2 to 3 times higher than that of the general population.,13 People living with epilepsy have various diverse and complex effects on the overall well-being or subjective quality of life.,15 Epilepsy is associated with profound physical, psychological and social consequences, and its impact on a person\u2019s quality of life can be greater than that of some other chronic conditions.Epilepsy accounts for 0.75% of the global burden of disease and in 2012 epilepsy was attributed to approximately 20.6 million disability-adjusted life years lost. It is estimated that by 2030, the number of people aged 60 years and above will rise to over 67 million in sub-Saharan Africa. The prevalence of dementia within sub-Saharan Africa has been reported to range from 1.41% in an Ibadan community to 21.60% using the 10/66 diagnostic criteria compared to a prevalence rate of 6.40% when diagnosis was based on the DSM-IV criteria. The prevalence of dementia reported from 21 global burden of disease regions across the world ranges between 2.1% and 8.5% for those aged 60 years or older.Alzheimer\u2019s disease and related dementias (AD/ADRD), occur most frequently in the older adults. AD/ADRD may also co-exist in the same individual with several other neurological non-communicable diseases conditions, 1 Ugandan study reported that 20% of stroke survivors had severe forms of dementia. Elderly individuals (aged at least 60 or older) represent a rapidly growing segment of the population in Uganda.,23 However, data on epilepsy and AD/ADRD information is scanty in Uganda. This study aimed to determine cognitive functioning and the prevalence of seizure and associated factors among older persons in Uganda.Whereas the burden of AD/ARD in Uganda is not well established, few studies point to the existence of AD/ADRD with varying prevalence.This was a cross-sectional study conducted at the medical outpatient clinics of Kiruddu National Referral Hospital (KNRH), Kampala, Uganda between October 2020, and March 2021. KNRH draws a broad population, including substantial numbers of rural residents from across Uganda.Participants were drawn from the medical outpatient clinics at KNRH. Eligible study participants were adults aged 60 years and more at the time of recruitment.We included only persons of 60 years or older who provided written informed consent. Individuals with past medical history of head injury, brain tumors, mental retardation, co-morbid with HIV, and patients who had recent brain surgery were excluded from the study.A standardized questionnaire was used to collect demographic, behavioral and medical history information, including ethnic group, marital status, and place of birth, residence, occupation, alcohol, and tobacco consumption. The IDEA cognitive screen has been validated for use in populations with low levels of formal education within sub-Saharan Africa. The IDEA screen includes delayed recall, orientation, 2 measures of frontal lobe function, verbal fluency and abstract reasoning, praxis, and long-term memory. An assessment of ability for new learning is also possible from performance on the 10-word learning list. No items are included requiring reading, writing, drawing or calculation to reduce possible educational bias. The maximum possible score is 15 and the minimum 0, with a higher score indicating better cognitive function. Those who have low scores were objectively evaluated for dementia using Addenbrooke\u2019s Cognitive Examination III performed. An Addenbrooke\u2019s Cognitive Examination III score <82 suggested dementia.Brief dementia screening was conducted with the Identification for Dementia in Elderly Africans (IDEA) previously tested in SSA samples.Seizure types were classified as focal seizures, focal to bilateral generalized tonic-clonic seizures, and tonic-clonic seizures of unknown onset or unclassified based on semiology and interictal electroencephalogram findings.Sample size estimates: In projecting statistical power, as there are no competing epilepsy studies in this setting and the MakCHS experience with the epilepsy. For the quantitative study, we will enroll a sample of size 400, we will have power of at least 0.80 for a 2-sided test of interaction effect with Type I error of 0.05. This assumes a prevalence of 50% due to lack of prior studies and adjusted for 10% non-response to the study.P values of <.2 to a multiple GLM and built the model using a backward elimination method while checking for multicollinearity. Results from multivariate analysis are presented as adjusted estimates. All the analyses were performed using STATA version 14.We used frequencies and proportions expressed as percentages to summarize categorical variables and median to summarize continuous variables. Except age, all the other variables were categorical. The prevalence of seizure in the past 30 days was estimated with 95% confidence interval (CI) and presented overall and by all categorical variables. Also, we analyzed the cognitive levels of the study participants by estimating the proportions with normal, impaired, and abnormal (dementia) cognitive function. The proportions with the 3 different cognitive function levels were presented overall and by demographic characteristics and compared between different categories using Fisher\u2019s exact test. Due to small numbers of participants with dementia (9 out of 405 assessed for cognitive function), these were combined with those who were abnormal, and we referred to this category as cognitive deficit. The prevalence with cognitive deficit was estimated with 95% CI and presented overall and by demographic characteristics. To determine factors associated with seizure prevalence and cognitive deficit, a generalized linear model (GLM) with family binomial and a log-link function was used. Using the GLM, we estimated prevalence ratios (PR) with 95% CIs and used these to quantify the magnitude of the associations. Both bi-variate and multi-variate analyses were performed using the GLM. We subjected all factors with bi-variate The study protocol was approved by the Makerere University School of Medicine Research and Ethics Committee (SOMREC), approval number: 2020-172 and the Uganda National Council for Science and Technology, approval number: HS970ES. All patients or their caregivers provided written informed consent to participate in the study.Of the 452 participants screened, a total of 407 participants, with a median (inter-quartile range) age of 67 (64\u201373) years met eligibility criteria and were enrolled into the study Fig. . Of thesP = .02), Seizure prevalence did not significantly differ across age groups over the past 30 days by age and sex; see Figure Overall, the prevalence of seizure among the study participants was 1.5% (95% CI: 0.7\u20133.3). All those who experienced seizures were unemployed. The prevalence of seizure was significantly higher among males compared to female participants . The prevalence of seizures was nearly 17-fold higher in participants from Mukono districts compared to participants from Kampala city , Table The prevalence of seizures was 92% lower among female participants compared to their male counterparts had a cognitive deficit; 9 (2.2%) dementia, and 105 (25.9%) impaired cognition, Figure P = .053). The prevalence of dementia and cognitive impairment were significantly higher in participants aged 75 years or older . Also, a higher proportion of participants with dementia (88.9%) and impaired cognition (77.1%) were unemployed. The observed difference was statistically significant (P < .001). A significantly higher proportion of participants with dementia had attended post-primary education (66.7%) compared to those with impaired cognition (33.6%) and those with normal cognition (41.6%).At univariable analysis Table , there wP = .003), formal employment , age between 70 and 74 years , and 75 years or older .At multivariable analysis Table , cogniti,20 In this study, we report 2 main findings. First, we found a prevalence of seizure of about 1.5%, will all participants self-reporting have generalized tonic-clonic seizures. This finding is consistent with our recent systematic review which showed a pooled seizure prevalence of about 0.8% among a population of over 10,000 older persons in 4 sub-Saharan African countries. In this systematic review, seizure prevalence ranged from 0.02% to 3.2% across individual studies. Two studies conducted in Tanzania reported seizure prevalence of 0.02% in a community setting and 3.2% in the hospital setting. Two other studies from west African countries, both hospital-based cross-sectional studies reported seizure prevalence of 1.4% in Senegal and 1.35% in Niger. These few studies highlight the relatively higher prevalence of seizure in hospital-based, compared to community-based studies. This is consistent with our finding which showed a comparable prevalence. In hospital settings, patients are likely to be attending health-facilities for various reasons such as strokes, diabetes mellitus and various other co-morbidities which may increase the risk for seizures in this population.This study investigated cognitive functioning and the prevalence and factors associated with seizure and cognitive deficits among older persons attending an outpatient medical clinic in Uganda. Primary data on the prevalence of seizure disorders and cognitive deficits among older persons in sub-Saharan Africa still remains scarce. In Uganda, a few studies have reported on the prevalence of cognitive deficits in diverse populations. Among older persons in western Uganda, severe cognitive impairment was observed in 28% of the participants. Another study from rural Uganda reported a dementia prevalence of 20% among the general population of persons older than 60 years. On the other hand, Mukisa and colleagues reported a 20% prevalence of dementia among patients who recently recovered from stroke.Secondly, we found cognitive deficits in about 28.1% of the participants, with an overall prevalence of dementia at 2.2%. The prevalence of dementia is consistent with a previous estimate of dementia prevalence of about 1-3% among older persons in sub-Saharan Africa.,21,30,31 In this study, all cases of seizures were reported in patients with cognitive deficits.Several factors contribute to cognitive deficits in older persons. In the present study, female gender and formal employment were protective, meanwhile, advancing age significantly predicted higher prevalence risk of seizure. These observations are consistent with previous reports from Uganda and beyond. However, other population studies found that neither disease duration nor age of onset were significant risks for seizures in AD patients.\u201335 One possible explanation is that dementia severity, rather than disease duration, may be associated with risk of seizures. In prospective studies of patients with probable AD of mild severity, seizures occurred in 1.5% to 16% of patients over 1 to 8.5 years of follow-up.,34 Dementia severity or worse performance on tests of orientation and information have been reported to be associated with an increased risk of seizures in AD patients.Seizures may relate to disease severity and/or duration of dementia illness. In some studies, seizures noted after the onset of dementia were more likely to occur in later stages of the disease.This study has some limitations. First, the sample size is small to generalize the results to the elderly population in Uganda. Secondly, we relied on self-reported description of the seizures by next of kin, which may not be accurate and may be influenced by recall bias. Thirdly, we did not collect data on other underlying medical co-morbidities such as diabetes mellitus, rheumatic diseases etc which may have confounded on the cognitive functioning and seizure prevalence. Fourthly, we did not explore the age at onset of seizure and some cases might have had seizure onset before the age of 60 years. However, this is a baseline study which provides insights into the burden of seizures among older persons and guides future studies.In summary, among older persons attending an outpatient clinic in Uganda, we found about 28% participants to have cognitive deficits with up to about 2.2% having dementia. The overall prevalence of seizure was 1.5% and was 3.5-fold higher in participants with cognitive deficits compared to those with normal cognitive functioning. The high prevalence of cognitive deficits is of public health significance and merits further studies to inform routine screening for this disorders among in medical outpatient departments.Mark Kaddumukasa and EK conceptualized the study. Mark Kaddumukasa, FB, Micheal Kiyingi, LM, EK and MS designed the study. Mark Kaddumukasa, Micheal Kiyingi and FB curated the data. Mark Kaddumukasa and LM analyzed the data. Mark Kaddumukasa and FB drafted the manuscript. EK and MS critically reviewed the manuscript for intellectual content and supervised the study. All authors read and approved the final manuscript.Conceptualization: Mark Kaddumukasa, Felix Bongomin, Micheal Kiyingi, Elly Katabira, Martha Sajatovic.Data curation: Mark Kaddumukasa, Felix Bongomin, Levicatus Mugenyi, Micheal Kiyingi, Elly Katabira, Martha Sajatovic.Formal analysis: Mark Kaddumukasa, Felix Bongomin, Levicatus Mugenyi.Funding acquisition: Mark Kaddumukasa, Elly Katabira, Martha Sajatovic.Investigation: Micheal Kiyingi.Methodology: Mark Kaddumukasa, Felix Bongomin, Levicatus Mugenyi, Micheal Kiyingi, Martha Sajatovic.Project administration: Mark Kaddumukasa.Supervision: Martha Sajatovic.Writing \u2013 original draft: Mark Kaddumukasa, Felix Bongomin, Levicatus Mugenyi, Micheal Kiyingi.Writing \u2013 review & editing: Mark Kaddumukasa, Felix Bongomin, Levicatus Mugenyi, Elly Katabira, Martha Sajatovic."} +{"text": "To estimate the extent of suboptimal statin use for the secondary prevention of atherosclerotic cardiovascular disease (ASCVD) at different stages of the treatment pathway and identify patient groups at risk of suboptimal treatment.National retrospective cohort study using linked National Health Service Scotland administrative data of adults hospitalised for an ASCVD event (n=167 978) from 2009 to 2017. Proportions of patients initiating, adhering to, discontinuing and reinitiating statins were calculated. We separately examined treatment following myocardial infarction (MI), ischaemic stroke and peripheral arterial disease (PAD) hospitalisations. Multivariable logistic regression and Cox proportional hazards models were used to assess the roles of patient characteristics in the likelihood of initiating and discontinuing statins.Of patients hospitalised with ASCVD, only 81% initiated statin therapy, 40% of whom used high-intensity statin. Characteristics associated with lower odds of initiation included female sex (28% less likely than men), age below 50 years or above 70 years , living in the most deprived areas and history of mental health-related hospital admission. Following MI, 88% of patients initiated therapy compared with 81% following ischaemic stroke and 75% following PAD events. Of statin-treated individuals, 24% discontinued treatment. Characteristics associated with discontinuation were similar to those related to non-initiation.Statin use remains suboptimal for the secondary ASCVD prevention, particularly in women and older patients, and following ischaemic stroke and PAD hospitalisations. Improving this would offer substantial benefits to population health at low cost. Despite national clinical guidelines recommending the use of statin for the secondary prevention of atherosclerotic cardiovascular disease (ASCVD), previous studies have found that use of statin therapy among individuals with established ASCVD is suboptimal.However, knowledge regarding the extent of, and underlying risk factors for, suboptimal medication use at different treatment stages to inform on the full extent of statin use across the treatment pathway, different populations and disease types, is limited.This national study in Scotland, from 2009 to 2017, improves on previous studies by examining in detail all stages of the patient treatment pathway, namely the initiation of, adherence to, discontinuation and reinitiation of statin therapy for the secondary prevention of ASCVD, in order to estimate the full extent of suboptimal statin use across different patient populations and disease types.Only 81% of patients initiated statin therapy after hospitalisation for ASCVD and, of those who did, 24% later discontinued statin therapy. Use of intensive statin therapy was also suboptimal.Statin treatment following peripheral arterial disease (75% initiated and 29% discontinued statin therapy) and ischaemic stroke was worse than treatment following myocardial infarction .Women and patients aged <50 years or \u226570 years were systematically undertreated in terms of statin initiation and discontinuation.Improvements in use of statin therapy in patients with ASCVD would provide substantial benefits to population health. As many as 6%\u201310% of subsequent ASCVD events could be avoided.Particular focus is needed to improve statin treatment use in women and older patients, and in patients who suffer ischaemic stroke and peripheral arterial disease events, as these individuals remain systematically undertreated.Individuals with established atherosclerotic cardiovascular disease (ASCVD) are at significantly increased risk of future vascular events.Despite these recommendations, previous studies have found that use of statin therapy among individuals with ASCVD is suboptimal.This study assessed the extent of suboptimal statin therapy use for the secondary prevention of ASCVD in Scotland overall and across subgroups of individuals by age, sex, types of ASCVD and other characteristics. We examined associations between these patient characteristics and statin treatment at different stages of the pathway. This was achieved by using linked and anonymised population-wide administrative National Health Service (NHS) Scotland data for all individuals hospitalised for an ASCVD event in Scotland between October 2009 and July 2017.NHS Scotland provides comprehensive free healthcare to all people living in Scotland. This retrospective cohort study used large-scale population-wide individual patient data for all individuals hospitalised for ASCVD composed of four linked and anonymised routine healthcare datasets: (1) hospital admissions, (2) specialty mental health admissions, (3) national death records and (4) prescribing information. Individuals were followed between 1 October 2009 and 31 December 2017 .10.1136/heartjnl-2022-321452.supp1Supplementary dataAll Scottish residents aged 18 years or older were included if they had a main discharge diagnosis for an ASCVD event between 1 October 2009 and 3 July 2017, and therefore should have been offered statin treatment according to SIGN\u2019s and NICE\u2019s clinical guidelines for the secondary prevention of cardiovascular disease.The hospital admissions data were used to identify individuals hospitalised for an acute ASCVD event, categorised into myocardial infarction (MI), ischaemic stroke, peripheral arterial disease (PAD) and other ASCVD including events with a hospital length of stay of less than 1 day . FollowiStatin therapy use was asseStatins were further grouped into two intensity categories in line with NICE\u2019s definition: statins that reduce low-density lipoprotein cholesterol (LDL-C) by \u226440% and >40% were categorised as low/medium and high intensity, respectivelyThe following characteristics were assessed: sex, age at index event date, deprivation quintiles, number of comorbidities, previous mental health hospitalisation, history of previous ASCVD event and/or previous statin use and discharge calendar year .The proportions of individuals who did not initiate therapy, were not adherent, discontinued treatment and did not reinitiate therapy were calculated. Multivariable cross-sectional logistic regression models were used to study the association between patient characteristics and discharge calendar year and the likelihood of initiating statin therapy, and the likelihood of initiating high-intensity statin therapy versus low/medium-intensity therapy. For individuals who initiated statin therapy, a Cox proportional hazards modelBetween 2009 and 2017, 167 978 individuals were hospitalised for ASCVD. Baseline demographics at discharge for index ASCVD events are presented in Out of these individuals, 136 855 (81%) initiated statin therapy . Uptake Of patients who initiated statin, 40% initiated high-intensity therapy, with the remainder (60%) prescribed medium or low-intensity statin treatment. Within 12 months from initiation, 5% of initiators uptitrated to high-intensity statin therapy, 2% downtitrated to low/moderate intensity and 93% remained on the intensity initially prescribed. As a result, within 12 months since index prescription, 43% of statin initiators were using high-intensity statin therapy and 57% low/moderate-intensity therapy. The proportion of statin initiators using high-intensity statins within 12 months since index prescription almost doubled since 2009, increasing from 33% in 2009\u20132011 to 57% in 2015\u20132017 (p<0.001) . High-inWomen were 28% less likely to initiate statin than men (OR 0.72 (0.70\u20130.74)), largely irrespective of age, with 9% lower odds in the case of PAD, 22% for MI and ischaemic stroke and 33% for other atherosclerotic disease. Compared with individuals aged 60\u201369 years, those below the age of 50 years and those older than 69 years were significantly less likely to initiate statin, with the likelihood of initiation also decreasing as age increased beyond 70 years (<50 years: (OR) 0.74, 95% CI 0.70 to 0.78; 70\u201379 years: 0.78 (0.75 to 0.81); 80\u201389 years: 0.51 (0.49 to 0.53); 90 years or older: 0.23 (0.22 to 0.25)). Patients living in the most deprived areas were 8% less likely to initiate statin compared with those in least deprived areas (OR 0.92 (95% CI 0.88 to 0.96)). In addition, those with previous mental health hospitalisations were only half as likely to initiate treatment as those without similar medical histories (OR 0.50 (95% CI 0.46 to 0.54)). A higher number of comorbidities was associated with a lower likelihood of individuals initiating statin. For example, MI and stroke patients with three or more comorbidities had, respectively, 60% and 42% lower odds of initiating statin compared with individuals without comorbidities (MI: OR 0.40 (95% CI 0.37 to 0.44); stroke: OR 0.58 (95% CI 0.53 to 0.64)) . Please While on treatment, 91% of users were adherent. However, 24% of statin users discontinued treatment at some point in time and, of those who discontinued, half (50%) did so within 1.5 years since initiation, and 80% within 3.5 years . DiscontPatient characteristics associated with the discontinuation of statin were similar to those related to not initiating therapy. Specifically, women had a 17% higher hazard of statin discontinuation than men . A U-shaped association with age was observed: compared with individuals aged 60\u201369 years, those below the age of 50 years and those aged 70\u201379 years had, respectively, a 22% (HR 1.22 (95% CI 1.17 to 1.28)) and 27% (HR 1.27 (95% CI 1.23 to 1.31)) higher hazard of discontinuation, with the hazard increasing up to 3.5-fold in the case of patients aged 90 years or older (HR 3.48 (95% CI 3.27 to 3.71)). An increase in the number of comorbidities was associated with an increased hazard of statin discontinuation. For example, MI and stroke patients with three or more concomitant conditions had a 50% higher hazard of statin discontinuation than those without comorbidities (MI: HR 1.50 (95% CI 1.39 to 1.61); stroke: HR 1.47 (95% CI 1.35 to 1.60)) .This nationwide study of individuals hospitalised for ASCVD in Scotland demonstrates that use of statin therapy remains suboptimal in these very high-risk individuals. Nineteen per cent of individuals did not initiate statin therapy. While the majority of those who initiated statins were adherent while on treatment, about a quarter (24%) discontinued treatment at some point. Of those patients who stopped treatment, only 38% reinitiated treatment at a later time. Overall, about 25% of patient-years were left untreated after the index ASCVD event. A substantial number of subsequent ASCVD events might therefore have been prevented in these patients with much better statin use. Based on data from the Cholesterol Treatment Trialists\u2019 (CTT) Collaboration ,Our analyses demonstrate that certain groups of patients are at particular risk of suboptimal treatment. Strikingly, women with ASCVD were 28% less likely to commence a statin and 17% more likely to stop than men. Some previous studies have observed that women were less likely than men to be prescribed statin on hospital discharge,Individuals with a history of hospital admission for specialist mental care, who are known to be at very high cardiovascular risk, had 50% lower odds of initiation and 84% higher hazard of discontinuation of statin therapy compared with individuals without such a history. It is reasonable to propose that patients with milder mental health conditions treated in primary care, such as anxiety and moderate depression, may also be suboptimally treated for the prevention of ASCVD. Mixed findings on the association between mental health and statin use have been reported in previous large studies,There was also considerable variability in statin initiation and discontinuation rates by ASCVD type. Treatment rates for PAD and ischaemic stroke were poor compared with MI. For instance, only 75% of PAD patients and 81% of stroke patients initiated statin therapy, compared with 88% of MI patients. Among PAD patients 29% discontinued treatment, compared with 26% of stroke and 23% of MI patients. Similar findings were reported in previous observational studies using national registry and prescribing information.A meta-analysis of cardiovascular outcomes trials has shown that the further 0.5 mmol/L reduction in LDL cholesterol obtained with higher intensity statin therapy produces about a 16% further reduction in the incidence of heart attack, revascularisation or ischaemic stroke compared with moderate intensity statin therapy.The dataset has major strengths in that it captures the entire population of Scotland and all healthcare received under a single provider that is free at the point of care and is therefore highly representative. It allowed for a detailed analysis into the extent of statin use. Several limitations should be acknowledged. The data only included prescribing information for individuals who were both prescribed and dispensed treatment in a primary care setting, and therefore, we could not differentiate between treatment not being prescribed or being prescribed but not dispensed. Furthermore, we had data only on medication being collected but not whether patients actually used it, although patients who regularly collect but not use treatment are likely rare. Patient characteristics were derived from hospital records only, which do not capture patients\u2019 full medical history and diagnoses. Similarly, it was not possible to fully account for individuals who were not prescribed or who were asked to discontinue treatment on clinical grounds, such as terminal illness. To mitigate this limitation, the analyses excluded all individuals who died within 150 days of hospital discharge. Lastly, further patient characteristics that may be relevant, such as patients\u2019 ethnicity and marital status, could not be studied due to large numbers of missing observations. The data also cannot provide insights into clinicians\u2019 characteristics and management of a patient, clinicians\u2019 and patients\u2019 beliefs, preferences or risk perceptions of statin therapy.The treatment of patients with statin therapy following an ASCVD event remains suboptimal, particularly in women and older patients and following ischaemic stroke and PAD events. Effective approaches to improve statin use are likely to yield important reductions in the burden of cardiovascular disease and at low cost."} +{"text": "However, the causes remain unclear in half of NIHF cases following current standard assessment. The application of prenatal chromosomal microarray analysis (CMA) and exome sequencing (ES) can improve the identification of the etiologies. This study aimed to investigate the etiologies of NIHF in the era of next-generation sequence (NGS) following a unified prenatal work-up flow for diagnosis. (2) Methods: A retrospective analysis was conducted on NIHF cases that were collected prospectively to explore the underlying etiologies according to a unified prenatal diagnosis work-up flow at Shanghai First Maternity and Infant Hospital between Jan 2016 and Dec 2019. The medical records for all NIHF cases were reviewed, and the causes of NIHF were classified as confirmed (diagnostic), suspected, or unknown. (3) Results: Prenatal and postnatal medical records for a total of 145 NIHF cases were reviewed, 48.3% (70/145) of the cases were identified to be with confirmed etiologies, and 10.3% (15/145) with suspected etiologies. Among 85 cases with confirmed or suspected etiologies, 44.7% were diagnosed with genetic disorders, 20% with chylothorax/chyloascites diagnosed postnatally, 12.9% with fetal structural anomalies, 12.9% with fetal anemia, 7% (6 cases) with fetal arrhythmia, and 2.3% (2 cases) with placenta chorioangioma. In cases with genetic disorders, 8 aneuploidies were detected by CMA, and 30 cases had single-gene disorders identified by ES (29/30) or targeted gene panel (1/30). There were still 41.4% cases (60/145) with unknown causes after this unified prenatal diagnostic work-up flow. (4) Conclusions: In the era of NGS, the causes of NIHF were identified in 58.6% of cases, with genetic disorders being the most common ones. NGS is helpful in determining the genetic etiology of NIHF when CMA results cannot explain NIHF, but 41.4% of cases were still with unknown causes under the unified prenatal diagnostic work-up flow in this single-center study. Hydrops fetalis occurs in approximately 1 in 1700 to 3000 pregnancies and is diagnosed by prenatal ultrasound when at least two abnormal fetal fluid collections are present . The etiA standard work-up for the evaluation of NIHF etiologies prenatally was recommend by the Society for Maternal-Fetal Medicine (SMFM) in 2015 . FollowiTherefore, we aimed to assess the proportion and distribution of confirmed etiologies in strictly defined NIHF cases in a fetal treatment center that provides CMA and ES for all cases and to explore the value of prenatal CMA and ES for aiding clinical counseling.This was a retrospective analysis of 145 single NIHF cases prospectively collected that were referred to the Department of Fetal Medicine & Prenatal Diagnosis Center at Shanghai First Maternity and Infant Hospital of Tongji University between January 2016 and December 2019. Prenatal diagnostic criteria for fetal hydrops are at least two abnormal fluid collections in fetal cavities or soft tissue, including pleural effusion, ascites, pericardial effusion, or skin edema. After ruling out maternal red-cell alloimmunization, NIHF was diagnosed.The study was approved by the ethics committee of Tongji University (registration number: 2018yxy13), and informed consent was obtained from the patients.Data were prospectively collected from the medical record, including maternal characteristics, previous adverse pregnancy history , gestational age at diagnosis, ultrasound manifestations, and pregnancy outcomes. Chinese NIHF guidelines refer to the SMFM and SOGC NIHF guidelines and make some necessary modifications ,15. AccoThe sources of DNA samples for genetic testing included prenatal samples from chorionic villi, amniotic fluid, or umbilical cord blood or postnatal samples from fetal tissues. We provided CMA with or without karyotyping for genetic assessment as the first step. For cases without diagnostic disorders for NIHF, i.e., CMA results were negative or CNVs detected by CMA could not explain fetal hydrops, namely unexplained NIHF, ES was provided for further evaluation.http://exac.broadinstitute.org, accessed on 10 September 2022), the Exome Sequencing Project , the 1000 Genomes Project , and an internal database. The remaining phenotype-related variants were then assessed under the protocol issued by the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines [SNP array analysis was performed using CytoScan 750 k . The copy number variations (CNVs) were shown according to the human Feb. 2009 (GRCh37/hg19) assembly. ES was performed using the Agilent SureSelect v6 kit and sequenced with an Illumina Hiseq X Ten . Variants were annotated and filtered by Ingenuity Variant Analysis . Common variants were filtered by the databases of the Exome Aggregation Consortium (ExAC) fetal structural anomalies, including congenital pulmonary airway malformation (CPAM) and Galen aneurysm without genetic anomalies, fetal arrhythmia, and placenta chorioangioma; (2) genetic disorders, including aneuploidies, pathogenic CNVs, and single-gene disorders; (3) fetal anemia that was not associated with genetic disorders and confirmed by FBS; (4) etiologies confirmed by postnatal investigations, including chylothorax, chyloascites, and meconium peritonitis. In the present study, cases with genetic causes that were accompanied by abnormal ultrasonic phenotype were classified as genetic anomalies.Suspected etiologies were those that may explain NIHF, including: variants with unknown significance (VUS) of already known genes detected by ES; fetal anemia confirmed by FBS; fetal structural anomalies such as right cardiac dysplasia syndrome, and multiple structural abnormalities that may cause NIHF, but the genetic assessment was not performed due to insufficient DNA samples.The rest were categorized as cases with unknown causes.The primary outcomes were the proportion of cases with clearly confirmed etiologies and their distribution. The secondary outcomes were the detection rate of pathogenic (P) and likely pathogenic (LP) variants that can explain NIHF by CMA and WES.SAS 9.3 software was used to perform data analysis. For continuous variables, mean and standard deviation (SD) or median (range) were adopted according to their distribution. For categorical variables, number and proportion/rate were used to describe their distribution.A total of 145 NIHF cases were included during the study period. The demographics and clinical characteristics of the cohort are presented in Overall, 48.3% (70/145) of the cases were identified to be with confirmed (diagnostic) etiologies, 10.3% (15/145) with suspected etiologies, and 41.4% (60/145) with unknown etiologies. Among the 85 cases with confirmed or suspected etiologies, 44.7% (38/85) were diagnosed to be with genetic disorders, including 8 aneuploidies and 30 single-gene diseases, 20% (17/85) with postnatally diagnosed chylothorax/chyloascites, 12.9% (11/85) with fetal anemia, 12.9% (11/85) with fetal structural anomalies, 7% (6/85) with fetal arrhythmia, and 2.3% (2/85) with placenta chorioangioma .A total of 70 cases were diagnosed with confirmed etiologies, of which 45.7% (32/70) were genetic disorders including 8 aneuploidies and 24 single gene disease of which 23 were detected with ES; 1 case was diagnosed with Bart\u2019s hydrops fetalis using a thalassemia gene panel, 24.3% (17/70) with postnatally diagnosed chylothorax/chyloascites, 11.4% (8/70) with explained fetal anemia, 7.1% (5/70) with fetal structural anomalies; 6 cases were fetal arrhythmia, and 2 were placenta chorioangioma. Among the 15 cases with suspected causes, the etiologies in overall descending order of frequency were ultrasound anomalies , single-gene disorders , and fetal anemia . Of the 60 cases with unknown etiology, 68.3% (41 cases) completed ES assessment, but the cause was still unknown.The detection rate of CMA was 7.6% (11/144). Among them, 8 cases (5.6%) were aneuploidies, including 6 cases with trisomy 21, 1 with Turner syndrome, and 1 with trisomy 13. In addition to aneuploidies, CMA identified 3 cases (2.1%) with P/LP CNVs but could not explain NIHF.Exome sequencing was performed in 96 cases, of which 24 cases received ES prenatally, and 72 cases did so postnatally using stored fetal DNA samples. P/LP gene variants were detected in 23.9% (23 cases), among which 8 were recurrent hydrops ; 15 were non-recurrent NIHF . Six cases of recurrent NIHF had recessive inheritance patterns, of which four were lysosomal storage disorders. Autosomal dominant inheritance accounted for 73.3% (11/15) of non-recurrent NIHF, and Noonan syndrome was the most common one .In addition to LP or P variants, 6 (6.3%) cases were found to have gene variants with potential clinical significance but did not meet the criteria for P or LP and were considered suspected causes. Among the six cases, RAPSN gene variants were found in three cases with recurrent NIHF, PROC gene variants in one recurrent NIHF case, and PIEZO1 gene variants were found in two patients (one was recurrent NIHF).After careful evaluation, among 67 cases with normal WES results, 23 cases were identified with confirmed etiologies, including 8 cases of fetal anemia, 13 cases of postpartum chylothorax/chyloascites, 1 case of Galen aneurysm, and 1 case of SVT. There were three cases with suspected etiologies, including one with multiple structural abnormalities, one with right ventricular dysplasia, and one with intracranial structural abnormalities. Even after the completion of ES, there were still 41 cases with unknown etiology.Among 40 cases that did not perform ES, 15 had confirmed etiologies . There were three cases with suspected fetal anemia diagnosed by FBS and three cases with suspected ultrasound anomalies . Still, ES was not performed due to insufficient DNA sample. The remaining 19 cases were assigned to the unknown etiology group, where no ultrasound abnormality could explain NIHF, and their DNA samples were insufficient for ES.This prospective study showed the distribution of the etiologies in NIHF, of which 48.3% were identified with clearly confirmed etiologies, while 10.3% had suspected etiologies, and 41.4% remained unknown etiologies. Among the confirmed and suspected etiologies, the frequency in descending order were genetic diseases, chylothorax/chyloascites, fetal structural anomalies, and fetal anemia. CMA did not yield any pathogenic CNVs related to NIHF beyond aneuploidies. In NIHF cases with unexplained CMA results, ES could identify P or LP gene variations in 23.9% of the cases and potentially diagnostic variants in an additional 6.3% of the cases.In this strictly defined NIHF cohort study, the percentage of NIHF with confirmed etiology was similar to Sparks\u2019s 48% vs. 44%) but was % vs. 44%Genetic disorder (26%) was the most common cause of NIHF in this study. Different from SMFM guidelines for NIHF, due to the high incidence of thalassemia in southern China, thalassemia screening is included in the Chinese guidelines as a routine procedure. Since the diversity of Shanghai\u2019s population, only one case was diagnosed with Bart\u2019s hydropic fetalis. CMA did not identify any pathogenic CNVs related to NIHF beyond aneuploidies, which was consistent with previous studies ,8. The pThe incidence of confirmed ultrasound abnormalities that could explain NIHF was also smaller than in Khalil\u2019s study (8.9% vs. 24%), which may be due to the different definitions of confirmed ultrasound abnormalities. We only defined ultrasound anomalies rarely associated with genetic variations as confirmed ultrasound anomalies, including congenital pulmonary airway malformation, fetal arrhythmias, and placental chorioangioma ,21,22, sThere are several strengths of this study. It was a large cohort of prenatally diagnosed singleton NIHF cases focused on the distribution of genetic and non-genetic etiologies of NIHF, which was helpful for clinical counseling and the management of NIHF in a fetal therapy center. We had a relatively large sample size that performed exome sequencing, which made our results more robust and reliable. Furthermore, the present study included only singleton NIHF cases in which the etiologies would be more easily clarified.However, this study was not without limitations. This was a single-center prospective cohort study, and the etiologies\u2019 distribution could not represent the complete profile of all NIHF. Cases with confirmed aneuploidies that were identified in other institutions might terminate the pregnancy before referral. In addition, about 70% of cases chose termination of the pregnancy after evaluation due to concerns about poor prognosis, the information of their postpartum diagnosis, and their natural course was unable to obtain.In conclusion, 58% of the prenatal NIHF cases could be identified with etiologies, while 42% remained with unknown etiologies. The frequency of etiologies by descending order were genetic disorders, chylothorax/chyloascites, fetal structural anomalies, and fetal anemia. CMA did not yield the detection of pathogenic CNVs, while ES improved the identification of genetic disorders with a detection rate of 24% in explained NIHF. Whole-genome sequencing or other genetic tests may be recommended to identify the etiology in NIHF cases with negative ES results."} +{"text": "Leisure activity engagement in older adults\u2019 daily lives is well-documented, however, relatively few studies include participant-reported activities using prospective daily diary methods. The goal of the study was to examine the proportion of three types of reported leisure activities and how physical health moderated such activities. Two weeks of self-reported leisure activities examined among healthy sedentary community-dwelling adults from the Cognitive and Physical Exercise Study . Each day, participants listed leisure activities performed, estimated time spent on each activity, and labeled the activities as cognitive, physical, and/or social. Physical health was assessed by the SF-12 at baseline. Across 14 days, 25.14% of reported activities were labeled as cognitive activities, 26.61% were labeled as social activities, and 22.97% were labeled as physical activities. Multilevel models indicated participants\u2019 engagement in different domains of activities were not influenced by physical health and did not change over time."} +{"text": "On May 17, 2022, the Massachusetts Department of Health announced the first suspected case of monkeypox associated with the global outbreak in a U.S. resident. On May 23, 2022, CDC launched an emergency response .During May 17\u2013October 6, 2022, a total of 26,384 monkeypox cases were reported to CDC by all 50 states, the District of Columbia, and Puerto Rico. Daily case counts peaked during mid-to-late August . Among 2https://stacks.cdc.gov/view/cdc/121989). Among 13,997 cisgender men with information reported on recent sexual or close intimate contact, 10,440 (75%) reported MMSC during the 21 days preceding symptom onset. The percentage of cases in cisgender men who reported recent MMSC decreased over time, from 80% during May 17\u2013July 17 to 67% during July 18\u2013October 6 of 25,569 cases in persons with known age who were aged \u226518 years and for whom information on gender was available, 23,683 (95%) occurred in cisgender men. Cisgender men accounted for up to 99% of cases during the week of June 5; this percentage declined to 80% by the week of October 2 persons with monkeypox, among whom 13,871 (98%) experienced a rash, most frequently on the face , genitals , and arms . Among 5,017 (20%) cases in persons aged \u226518 years with reported information on HIV infection status, 2,876 (57%) had HIV infection. Information on hospitalization was reported for 11,204 (43%) persons with monkeypox, 1,870 (17%) of whom were hospitalized. Six deaths were reported. Information on smallpox or monkeypox vaccination status was provided by 9,197 (35%) persons; 2,882 (31%) had received a vaccine, among whom 1,676 (58%) provided the vaccination date. Among those, 1,670 (99.6%) were vaccinated during the 2022 outbreak . Among those vaccinated during the outbreak with race and ethnicity data available , 38% were White, 32% were Black, and 23% were Hispanic. Date of vaccination and date of symptom onset was available for 1,317 (5%) patients, 625 (48%) of whom were vaccinated after symptom onset and 692 (52%) before symptoms began.Within 1 week of announcement of the first suspected case of monkeypox in a U.S. resident by the Massachusetts Department of Public Health in mid-May, CDC launched an emergency response for monkeypox . In addiLaboratory and diagnostic support. As a result of smallpox preparedness efforts, an FDA-approved polymerase chain reaction laboratory test capable of detecting nonvariola orthopoxviruses was prepositioned through the Laboratory and Response Network (LRN) before the monkeypox outbreak began. In May 2022, 69 LRN laboratories had capacity to test approximately 6,000 specimens per week, and a positive orthopoxvirus test result was sufficient for clinicians and public health departments to initiate patient isolation and contact tracing. On June 10, CDC received FDA clearance to run the same test with a higher throughput extraction platform. To further increase national testing capacity, CDC provided technical assistance to expand testing to five nationwide commercial laboratory companies who began testing during July 2022, increasing the total U.S. testing capacity more than twelvefold, to 80,000 specimens per week was approved for treatment of smallpox in children and adults during 2018 under FDA\u2019s animal rule, which permits efficacy findings from well-controlled animal studies to support an FDA approval when doing so is not feasible or ethical to conduct a human efficacy trial,Provider and public outreach. CDC uses a variety of mechanisms to disseminate information to public health partners and health care providers about the monkeypox outbreak. On May 20, 2022, CDC released the first Health Alert Network Health Advisory on the monkeypox outbreak,CDC\u2019s community engagement strategy focuses on harm reduction messaging for populations disproportionately affected by the monkeypox outbreak. Building on existing partnerships from CDC\u2019s initiative to end the HIV epidemic by 2030, CDC has engaged with advocates, experts, and groups focused on sexual health of MSM, transgender, non-binary, gender-diverse, queer, and persons of other sexual identities to directly reach and hear from populations disproportionately affected by monkeypox. For example, on October 20, 2022, staff members from CDC\u2019s Monkeypox Response cohosted an Instagram Live session to promote the Vaccine Equity Pilot Program to agencies that serve racial and ethnic minority lesbian, gay, bisexual, transgender, queer or questioning, intersex, asexual, and others (LGBTQIA+) youth organizations. CDC developed communication resources to facilitate conversations about safer sex and social gatherings, which aim to reduce stigma and aid in making informed choices when persons are in situations or places where monkeypox is more likely to spread. CDC has also supported pilot programs to ensure that vaccines reach populations that have historically faced health disparities and inequity and might continue to face additional barriers to access.Before the 2022 outbreak, monkeypox cases were primarily reported in central and western Africa.Monkeypox continues to disproportionately affect gay, bisexual, and other MSM. However, the large proportion of cases with missing data on recent sexual or close intimate contact makes generalization of this report\u2019s findings challenging. Tailored, nonstigmatizing communicationThe current outbreak also continues to disproportionately affect persons with HIV infection (Multiple strategies exist that can help prevent and reduce transmission of monkeypox. Two vaccines, JYNNEOS and ACAM2000, can be used to prevent infection with monkeypox. During this outbreak, JYNNEOS has been used nearly exclusively because of its favorable adverse event profile overall as well as its favorable outcomes in persons who might be immunosuppressed or have other risk factors for severe monkeypox disease such as atopic dermatitis, heart disease, or a serious vaccine component allergy (The findings in this report are subject to at least three limitations. First, a substantial amount of case data is missing, which might reduce representativeness of findings reported here. Only 59% of adult cases had information on both gender identity and reported recent sexual or close intimate contact. Second, the percentage of missing data is higher in certain jurisdictions; thus, these findings might overrepresent cases from states with more complete data. Finally, mild cases might be underrepresented in this analysis because affected persons might not have sought testing or treatment.Monkeypox virus exposure and prioritize populations most affected by the current outbreak, including MSM, Black and Hispanic persons, and persons who are immunocompromised. Efforts should also focus on reducing stigma when communicating about monkeypox transmission and ensuring equitable access to testing, vaccination, and treatment options to reduce health disparities.CDC continues to evaluate new evidence and intervention strategies for monkeypox prevention and control based on available data. Public health prevention efforts should emphasize vaccination for persons at high risk for An earlier analysis of 2,891 U.S. monkeypox cases found that up to 99% occurred in men, 94% of whom reported male-to-male sexual contact.CDC\u2019s emergency response focused on surveillance, laboratory testing, medical countermeasures, and education. A total of 26,384 U.S. monkeypox cases were reported during May 17\u2013October 6, 2022. Among 59% of persons with data on gender and recent sexual or close intimate contact, 70% reported recent male-to-male sexual contact. Black and Hispanic persons continue to be disproportionately affected.Public health monkeypox prevention efforts, including vaccination, should continue to prioritize gay, bisexual, and other men who have sex with men, Black and Hispanic persons, and persons who are immunocompromised."} +{"text": "Immunocompromised individuals (ICI) are at high risk for infections, some of which are preventable by vaccines. The Israeli MOH recommends PCV13 and PPSV23 vaccines for ICI, but vaccine coverage is suboptimal. The aim of this study was to assess the effectiveness of a project to improve pneumococcal vaccination (PV) rate among ICI in outpatient settings.An automated validated, population-based registry of patients with ICI was developed in an Israeli health organization, Maccabi Healthcare Services, serving over 2.5 million members. Included in the registry were patients aged 18 and above, receiving immunosuppressive therapy (IT); patients living with HIV (PLWH); solid organ and bone marrow transplant recipients (TR); patients with advanced kidney disease (AKD); and patients with asplenia. Based on the registry and the Israeli MOH vaccination guidelines, a nationwide quality improvement project aimed at improving PV was implemented which began in October 2019. As part of the project, ICI were waived the need for preapproval for PCV13. During an eligible patient visit, physicians and nurses were prompted with an EHR alert reminding them to consider providing pneumococcal vaccine. In addition, eligible patients were invited via their patient health record (both desktop and mobile) to vaccinate. Vaccination rates during pre- and post-intervention periods were compared using the Chi square test.A total of 32,297 ICI were identified. Of them, 22,721 were on IT, 1651 PLWH, 1829 were TR ,5267 had AKD, and 1920 were asplenic. During the period October 2019 to October 2021, PCV13 vaccination rates went up from 12% to 54.1% (p< 0.0001), and PPSV23 vaccination rate improved from 44.7% to 62.6% (P < 0.0001).Using one of the first real-world automated registries for ICI and implementation of targeted automated patient and provider alerts, markedly improved pneumococcal vaccine uptake was observed in this vulnerable population. Similar interventions may be used to increase the adherence for other vaccines, including COVID-19 vaccines.Shirley Shapiro Ben David, MD, pfizer: Grant/Research Support Limor Adler, MD, pfizer: Grant/Research Support."} +{"text": "Background: The ratio of the difference between neighboring RR intervals to the length of the preceding RR interval (x%) represents the relative change in the duration between two cardiac cycles. We investigated the diagnostic properties of the percentage of relative RR interval differences equal to or greater than x% (pRRx%) with x% in a range between 0.25% and 25% for the distinction of atrial fibrillation (AF) from sinus rhythm (SR). Methods: We used 1-min ECG segments with RR intervals with either AF or SR from the publicly available Physionet Long-Term Atrial Fibrillation Database (LTAFDB). The properties of pRRx% for different x% were analyzed using the statistical procedures and metrics commonly used to characterize diagnostic methods. Results: The distributions of pRRx% for AF and SR differ significantly over the whole studied range of x% from 0.25% to 25%, with particularly outstanding diagnostic properties for the x% range of 1.5% to 6%. However, pRR3.25% outperformed other pRRx%. Firstly, it had one of the highest and closest to perfect areas under the curve (0.971). For pRR3.25%, the optimal threshold for distinction AF from SR was set at 75.32%. Then, the accuracy was 95.44%, sensitivity was 97.16%, specificity was 93.76%, the positive predictive value was 93.85%, the negative predictive value was 97.11%, and the diagnostic odds ratio was 514. The excellent diagnostic properties of pRR3.25% were confirmed in the publicly available MIT\u2013BIH Atrial Fibrillation Database. In a direct comparison, pRR3.25% outperformed the diagnostic properties of pRR31 , i.e., so far, the best single parameter differentiating AF from SR. Conclusions: A family of pRRx% parameters has excellent diagnostic properties for AF detection in a range of x% between 1.5% and 6%. However, pRR3.25% outperforms other pRRx% parameters and pRR31 . The exquisite pRRx% diagnostic properties for AF and its simple computation make it well-suited for AF detection in modern ECG technologies in long-term monitoring. The diagnostic properties of pRRx% deserve further exploration in other databases with AF. Many various heart rate variability (HRV) parameters are used alone or in combinations to distinguish atrial fibrillation (AF) from sinus rhythm (SR) ,2,3. We The difference between the durations of consecutive cardiac beats (x) at least 50 ms is one of several possible x values. After studying a wide range of such x differences between 7 ms to 195 ms, we recently demonstrated that other pRRx parameters had better diagnostic properties for AF detection than pRR50. In over 60,000 electrocardiograms (ECGs) of 1-min duration with either SR or AF, pRR31, i.e., pRRx for x = 31 ms, was the most effective for AF diagnosis. We reported that the diagnostic odds ratio (DOR) in AF detection was 194 for pRR31, which significantly outperformed pRR50 (DOR of 173) [pRRx quantifies the percentage of consecutive RR intervals differing by at least x ms, where x is the absolute difference between two consecutive RR intervals. As Instead of measuring the absolute difference between two consecutive RR intervals with x, it is possible to use a relative measure of such difference, the ratio of the difference to the duration of the preceding RR interval (x%). The percentage of relative RR interval differences equal to or greater than x% (pRRx%) describes this measure. pRRx% indicates how many RR intervals differed from the previous RR interval by at least x% of its length.In the past, RRx% (from which pRRx% is derived) has been occasionally studied. Ewing et al. proposedIn this study, we aimed to investigate the diagnostic properties of pRRx% for AF detection in a wide range of x% in 1-min ECGs with either SR or AF. Additionally, we directly compared pRR31 and the best-found pRRx% to better discriminate between SR and AF.The threshold values x of pRRx% parameters investigated in the paper ranged from 0.25% to 25% of the previous RR interval. The step of changes was 0.25% which gives 100 parameters in total. We used the same dataset of RR intervals as in our previous publication. We used data from the Long-Term Atrial Fibrillation Database (LTAFDB) ,8, whichTo minimize unidentified technical artifacts, we removed RR intervals shorter than 240 ms (corresponding to HR > 250 beats/min) or longer than 3000 ms (corresponding to HR < 20 beats/min). Altogether, 0.45% of all RR intervals were removed. We have also used another rejection criterion for each of the 1-min segments. If the total length of the removed RR intervals in a 1-min segment exceeded 6 s, we excluded the whole segment from the analysis.https://github.com/simonbus/prrx_af (accessed on 11 January 2023).We used Python programming language for all the analyses. For receiver operating characteristic analysis, we used scikit-learn library (version 1.3.3) . The souWe used the d\u2019Agostino\u2013Pearson test to formally analyze the data distribution of pRRx% for each x% in the range of 0.25% to 25%. Neither the SR nor the AF data had normal distributions of pRRx%. We plotted selected percentiles of the pRRx% distributions in AF and SR as functions of the threshold x%. We then used receiver operating characteristic (ROC) analysis to compute the area under the curve (AUC) for AF detection for all studied pRRx% and identified the optimal cutoff value using Youden\u2019s index to maximize the sum of sensitivity and specificity for AF/SR discrimination ,12. For The values of AUC for the AF/SR distinction, shown in t-test to compare the distributions for different parameters. All the differences were statistically significant, except for the difference between PPV for pRR3.25% and pRR2.75% .The metrics of AF detection with a single pRRx% parameter and the optimal cutoff value were estimated with the nonparametric bootstrap. t-test. All the differences were statistically significant, except for the differences between pRR2.25% and pRR1.5% and between pRR3.25% and pRR4.25% . In the latter case, it means that both pRR4.25% and pRR3.25% may be equally considered as having the highest DOR, i.e., 514.48 and 514.40, respectively.In The nonparametric bootstrap was used to compare the distributions of classification metrics for pRR31 and pRR3.25%. This study demonstrated that the pRRx% family could effectively discriminate AF from SR in 1-min ECGs across a wide range of x%. The pRRx% in the range of 1.5% to 6% showed exceptional diagnostic properties, with pRR3.25% outperforming other pRRx% in this range. pRR3.25% had better diagnostic properties than pRRx for x = 31 ms, which has previously been the best-performing HRV index for distinguishing AF from SR. The median accuracy of pRRx% for x% in the range of 1.5% to 6% exceeded 95%. pRR3.25% had one of the highest areas under the curve (AUC) at 0.971 and the highest accuracy. An AUC close to 1 indicates that a particular parameter is nearly perfect for diagnostic or predictive purposes. Therefore, pRR3.25% appears to have excellent properties for AF diagnosis in 1-min ECGs. If the number of successive RR intervals differing by more than 3.25% exceeds 75.32% in a 1-min ECG, it is most likely to be AF rather than SR. The median accuracy for the 75.32% threshold is 95.44%, with sensitivity at 97.16%, specificity at 93.76%, positive predictive value (PPV) at 93.85%, negative predictive value (NPV) at 97.11%, and a diagnostic odds ratio of about 514. No other HRV indices studied to date have shown similar diagnostic properties for AF detection.As shown in HRV indices have been used for automatic AF detection and screening in ECGs or photoplethysmography signals of arterial pressure waveforms. They have become helpful in various medical and non-medical technologies, e.g., wearable devices recording ECG continuously or on demand. Newer Holter ECG recorders may record ECG for up to 14 days, whereas the in-hospital monitoring systems work for the whole patient\u2019s stay. Various implantable devices, such as implantable loop recorders, pacemakers, implantable cardioverter-defibrillators (ICDs), and cardiac resynchronization therapy devices (CRTDs) continuously monitor intracardiac electrograms for arrhythmias. They store suspicious ECG segments based on real-time analysis with built-in algorithms. Most photoplethysmography-based devices for HR monitoring use HRV algorithms to detect AF. Several international consensus documents and guidelines have accepted the newer technologies, based on HRV analysis, for the screening and detection of AF ,23,24,25Mobile and wearable technologies using single-lead ECG (from touch ECG recorders or selected smartwatches) or photoplethysmographic signals have shown sensitivities of 91.5\u201399% and specificities of 76\u2013100% for AF detection, compared to standard 12-lead ECG . HRV indNewer wearable technologies have several advantages over standard 12-lead ECG. They may be used in special conditions, such as during physical work, training, or competitive sports. The ECG recording might last up to several weeks. However, these technologies also have some disadvantages. Less evidence supporting their clinical utility exists. Such recordings have more, usually motion-related, technical artifacts. A massive amount of data collected by long-term recorders has become an analytical challenge .The 12-lead ECGs are typically 8 to 12 s long. The 12-lead ECG is considered the gold standard for diagnosing AF, but only if it is acquired during an AF episode. The 24-h ECG Holter monitoring is the preferred method if AF is paroxysmal. Unfortunately, AF occurs infrequently in many patients. Longer ECG monitoring, up to 4 weeks, may be necessary, like in patients with cryptogenic stroke.AF identification from a standard short 12-lead ECG is usually instant for clinicians. Visual inspection and analysis of 24\u201348 h of Holter ECG data typically take 10\u201330 min. It is practically impossible to use a similar approach for recordings lasting several days, weeks, or even months. On average, a 24-h ECG contains between 80,000 and 120,000 RR intervals, whereas longer recordings contain millions of RR intervals, falling into the realm of Big Data. Thus, the automatic screening of suspicious ECG segments and their preselection for human visual inspection is a fundamental necessity. We are in the early stages of using Big Data analysis in clinical medicine, and there is a need for fast and easily applicable computational algorithms to analyze such data.mobile and wearable devices, such as ECG patches, vests, and Holter ECG recorders with built-in algorithms;monitoring systems analyzing online ECGs in hospitals or remotely via telemetry;algorithms in smartphones and smartwatches analyzing short-event ECGs on demand;portable ECG machines for medical staff, recording ECGs at the point of care;implantable devices continuously monitoring ECGs and searching for specific events, such as implantable loop recorders, pacemakers, ICDs, and CRTDs.The computation of pRRx% is straightforward, making it particularly well-suited for the following applications:Using pRRx% might increase the AF detection performance in ECG recordings of any length, from minutes to weeks. It might also simplify the complexity of software or hardware solutions. We acknowledge that the utility of pRRx% for AF detection should be prospectively investigated on a large scale, preferably in multicenter studies.Our study has several limitations. It is an observational and retrospective analysis using ECG recordings from a single database (LTAFDB) . For verWe have previously used the same data, consisting of RR intervals from over 60,000 1-min ECG segments with either AF or SR, in our studies ,3. In 22, we selAnother limitation of this study is the arbitrary choice of 1-min ECGs. Recently, we also investigated the diagnostic properties of various HRV parameters based on RR interval analysis for ECGs of lengths between 5 and 300 s and found that some HRV parameters had improved diagnostic properties for AF detection in longer ECG recordings . HoweverWe have demonstrated that the pRRx% parameters are excellent for differentiating AF from SR using RR intervals from 1 to min ECGs. Additionally, we found that pRRx% is superior to pRRx, at least for 1-min ECGs. Older studies reported that pRR50 is better than other HRV parameters for distinguishing AF from SR. Recently, we found that pRR31 is better than pRR50 for this purpose.However, with this study, we demonstrate that the pRRx% family even further improves the diagnosis of AF. Of all pRRx%, pRR3.25% currently appears to be the best single HRV-based parameter for differentiating AF from SR. Although the pRRx% parameters show promising results in differentiating AF from SR, further research is needed to confirm their effectiveness in various populations, settings, and medical and non-medical devices."} +{"text": "The rapid spread of coronavirus has forced the healthcare systems in Tunisia to reorganize its structures, thus mobilizing all caregivers. Their professional and emotional burden was put to the test.To evaluate the level of anxiety and to study coping strategies among caregivers during this pandemic.A cross-sectional descriptive and analytical study among150 caregivers in two hospitals in Sfax in Tunisia; during April 2020. We used anonymous questionnaire, the Spielberger State Anxiety Scale(STAI) to assess tension felt at anxiety-producing situations; and the Coping Inventory Scale for Stressful Situations (CISS): to assess coping strategies.The average age was 30.33\u00b1 6,93 years and the sex-ratio M/W = 0,29. Caregivers followed the news of this pandemic with these means of communication: 96% Facebook, 80%TV. The increase of the time spent in front of media:84% Sleep disorders were present in 64.7%: insomnia (36%), chopped sleep(34%). Caregivers used sleeping pills in 12% of case. STAI: The mean ascore =48.85 and a high anxiety level was noted in72% of case. CISS: Task-oriented coping strategies : a mean score= 47.90 and Emotion-centered coping : a mean score = 40,49 High anxiety was correlated with: age>40 years old (p=0.042). The increase of the time spent in front of media, chopped sleep and use of sleeping pills are correlated respectively with an emotionally focused coping strategy.Health professionals had a painful psychological experience with significant anxiety. Strengthening prevention strategies, management of health crises should be a priority of our health-system."} +{"text": "Dictyocaulus, Muellerius, Protostrongylus, and Cystocaulus are common helminths of domestic and wild ruminants with substantial veterinary and economic importance. Several studies have assessed the presence and prevalence of lungworm infections in ruminants in Iran. This report compiles the available scientific information about the occurrence of lungworms in domestic and wild ruminants in Iran between 1931 and June 2022 to give an insight into their epidemiology, and where possible to describe drug treatment efficacy. For this purpose, national and international scientific databases were searched. Overall, 54 publications comprising 33 articles in peer-reviewed journals, 8 conference papers, and 13 dissertations were evaluated regarding prevalence data; and an additional 4 peer-reviewed articles were evaluated regarding drug efficacy. Seven species of lungworms, namely Dictyocaulus filaria, Dictyocaulus viviparus, Dictyocaulus eckerti, Protostrongylus rufescens, Protostrongylus raillietti, Muellerius capillaris, and Cystocaulus ocreatus have been recorded from different ruminant hosts in Iran. Thirty-three studies conducted on small ruminant (sheep and goat) lungworms reported prevalences of lungworm infection of 11.6%, 45.81% and 66.29% using abattoir meat inspection, Baermann technique and fecal flotation, respectively. Eight studies conducted on large ruminants reported prevalences of infection of 14.83%, 13.98% and 5% using abattoir meat inspection, the Baermann technique and fecal flotation, respectively. The prevalence of infection in wild ruminants was variable across examined species; 38% in urial, 37% in wild goats, 5% in goitered gazelles and 67% in red deer, in addition to a single case report in roe deer. There are few contemporary studies assessing the efficacy of currently available broad-spectrum anthelmintic compounds against lungworms in Iran. The high prevalence of multiple lungworm species in Iran, combined with a lack of information about drug efficacy, supports the need to improve the understanding of these important nematode parasites and inform the development of sustainable control strategies. The aim of this review and meta-analysis is to provide a baseline for future conventional parasitology and next generation molecular epidemiological studies of lungworm infection in pastoral ruminants in Iran.Lungworms of the genera Dictyocaulus viviparus is of major importance in bovines and Dictyocaulus filaria in small ruminants. Dictyocaulus species lungworms have direct life cycles in which the first-stage larvae (L1) are shed in faces where they develop into infective third-stage larvae (L3) in the environment. L3 are ingested by ruminants while grazing and migrate to the respiratory system, where they mature into dioecious adults within the lumen of bronchi and bronchioles. Females shed eggs, which embryonated in the lungs, and hatch within the gastrointestinal tract, before being shed in feces. Diagnosis can be supported by larvoscopy to identify L1 in feces most often using the Baermann technique , 8 conference papers , 11 D.V.M. theses by veterinary students , and 2 Master\u2019s theses [in Persian with English abstract]. In addition, four peer-reviewed articles [4 in English] were used to assess the efficacy of anthelmintic drugs against lungworms in large and small ruminants. No record of infection of ruminants was found in 13 provinces, in 12 of which, veterinary faculties are not present, i.e., the University of Zabol in Sistan-va-Baloochestan province has a veterinary faculty A.D. filaria, D. viviparus, D. eckerti, P. rufescens, P. raillietti, M. capillaris, and C. ocreatus, reported in domestic sheep, goats, cattle, buffaloes and wild ruminants, namely urial , wild goats (Capra aegagrus), goitered gazelle (Gazella subgutturosa), roe deer (Capreolus capreolus), and red deer (Cervus elaphus) B.Thirty-three publications reported lungworm infection in sheep and goats in Iran, including 21 peer-reviewed articles, 12 dissertations , and 6 conference papers. These reports depicted infection in different regions of Iran, including 17 of the 31 provinces. The first record of lungworms is the 1931 report by a French veterinarian who wrote that verminous bronchopneumonia is prevalent in sheep in Iran . Since then, in total, 28,964 animals were examined for the presence of infection. The majority of animals had their respiratory system examined at necropsy, and 19.4% of cases (5615) were diagnosed by microscopy-based fecal diagnostic tests on apparently healthy animals. Prevalence rates of lungworm infection were 11.6%, 45.8% and 66.3% using abattoir meat inspection, Baermann technique, and fecal flotation, respectively . One draDictyocaulus filaria, P. rufescens, C. ocreatus, and M. capillaris were reported in small ruminants in decreasing order of the cases were examined at abattoir meat inspection, 38.4% (433) were examined using the Baermann technique and 10.6% (120) were examined using fecal flotation. For the diagnosis in buffaloes, 34.6% (100) of the cases were examined at abattoir meat inspection and 65.4% (189) were examined using the Baermann technique. In total, 12.5% (54/433) and 5% (6/120) of tested cattle were found infected by the Baermann technique and fecal flotation, respectively and 17.5% (33/189) water buffaloes were found infected by the Baermann technique . In 6 stnd goats ,63 , chinkara (Gazella bennettii), wild goat (C. aegagrus) and urial ) and three species of the family Cervidae , red deer (C. elaphus) and European roe deer (C. capreolus)). These species they are generally under protection in national parks or protected areas, and subject to close monitoring. The parasitic fauna of wild ruminants in Iran is poorly studied. Five peer-reviewed journal articles, one Master\u2019s dissertation, and one conference paper contained information on lungworms of wild ruminants. Overall, 587 wild ruminant individuals belonging to five species were examined with an overall infection of 38.7% (227/587). 38% of urial, 37% of wild goats, 5% of goitered gazelles and 67% of red deer were reported to be infected with lungworms belonging to four genera of Dictyocaulus, Protostrongylus, Cystocaulus and Muellerius. A single case report described Dictyocaulus lungworm infection in a roe deer. 53.1% (312/587), 21.1% (124/587) and 17.2% (101/587) of cases were examined postmortem, by Baermann technique and fecal flotation, respectively. Urial have been studied more than the other wild ruminant species i.e., 367 urial were examined in four studies followed by 133 wild goats in three, 56 goitered gazelles in two, and 30 red deer in one studies. In one case report a single European roe deer was examined (C. ocreatus (94%), D. filaria (78%), and Muellerius sp. (70%) were reported in a study of Kaboodan Island on Urmia Lake, where animals are living in an isolated area without any external source of infection from domesticated animals [Seven wild ruminant species are present in Iran, namely four species of the family Bovidae showed 83% efficacy [P. rufescens were 97% (goats), 90% (goats), 91% (goats) and 100% (sheep), respectively [Muellerius spp. in sheep were 56%, 26% and 28%, respectively; while the efficacies of thiabendazole (100 mg/kg PO), emetine hydrochloride (1 mg/kg PO) and emetine hydrochloride (3 mg/kg PO) against Muellerius spp. in goats were 46%, 68%, and 99%, respectively [C. ocreatus in sheep [D. viviparus in cattle, and reported efficacy of 99% [Four studies, including 3 on sheep and goat lungworms and 1 on cattle lungworms have evaluated the efficacy of 9 anthelmintic active compounds . Historiefficacy . The effectively . The effectively . Fenbendin sheep . These aD. filaria, P. rufescens, and M. capillaris [Dictyocaulus filaria was also reported in 0.4% and 8.3% of sheep and goats, respectively, in the Chiltan National Park, Balochistan, Pakistan [D. viviparus in cattle ranged between 0.3% and 70% [D. viviparus infection in cattle and buffaloes was 4.8% and 5.1%, respectively [Dictyocaulus viviparus lungworms present in Iran can have a major impact on cattle milk yields and growth rates, and cause death [Muellerius and Protostrongylus spp. present in Iran also impact livestock production, in particular through the rejection of plucks at abattoir meat inspection [Around the world, lungworms are important causes of production inefficiency in pastoral livestock systems; albeit there has been a lack of critical evaluation of the impact of and rationale for control strategies in Iran. This study shows a high prevalence of lungworm in those provinces from which diagnostic information is available, consistent with the situation in neighboring countries, with similar climates, environments and pastoral animal management. For instance, in a study in Nangarhar, Afghanistan, 21.8% of 504 sheep examined in an abattoir were infected with lungworms , albeit pillaris . DictyocPakistan . In TurkPakistan ,82. Rega and 70% , and in ectively . Dictyocspection . This stspection under loD. viviparus in cattle, and D. filaria, Muellerius and Protostrongylus spp. in sheep. The accuracy of species determination, in particular in mixed infections, must be interpreted with caution due to indistinct morphological traits of L1 [3; possibly accounting for the low prevalence of infection.This study shows the presence of 7 species of lungworm in Iran, and the high prevalence of ts of L1 . The scaDictyocaulus spp. infective L3 can be introduced by windborne spread, or survive for prolonged periods in the soil, while knowledge concerning the intermediate snail host specificity and distribution is lacking for Protostrongylus and Muellerius spp. The fundamental principal for control of Dictyocaulus spp. is to allow the establishment and maintenance of host immunity, which is rapidly acquired but requires lifelong boosting [3 challenge. In some countries, this is complimented by vaccination [3 [Muellerius and Protostrongylus spp., control strategies are limited to the periodic use of anthelmintic drug treatments. Knowledge of drug efficacy against lungworm species is therefore, needed.The control of lungworm infections in livestock is more challenging than that of gastrointestinal nematodes, not least because boosting . This uscination . Howeveration [3 . In the 4 and adult stages of Dictyocaulus spp. in sheep and cattle [Muellerius and Protostrongylus lungworms. Currently, different anthelminthic products in forms of oral solution , oral bolus (mebendazole) and injectable solution are labelled for treatment of lungworms in ruminants in Iran. This study included a single recent report of high efficacy of an ivermectin pour-on formulation against D. viviparus in cattle, and a historic report of high efficacy of an oral benzimidazole drug against D. filaria and P. rufescens in sheep. The no longer available, toxic and narrow spectrum anthelmintic drugs showed poor efficacy against Muellerius spp. (The modern-broad spectrum benzimidazole, imidazothiazole and macrocyclic lactone anthelmintic drugs are effective against Ld cattle . In mostius spp. . There iDictyocaulus viviparus resistance to pour-on macrocyclic lactone drugs has been suggested, but not proven [Poor drug efficacy may indicate anthelmintic resistance; the emergence of which threatens the efficiency of food production from livestock irreversibly . Dictyoct proven . In Irant proven ,95. Manyt proven ,96. Thert proven . Strategt proven ,99.Varestrongylus and Elaphostrongylus parasitize the respiratory tracts of wild and domestic ungulates within the families Bovidae and Cervidae [This study highlights the presence of lungworm infection in wildlife in Iran. It is important as wild species could act as reservoirs of infection for co-managed livestock . While oCervidae ,102 thesThis work provides a framework for the development of effective and sustainable lungworm control strategies, and identifies areas of need for further research. Studies are needed to identify the environmental, climatic and management conditions that play a key role in the epidemiology of lungworm infection in Iran. These studies require the integration of conventional parasitology and molecular diagnostic methods for species level identification of lungworms, to inform cross-host species transmission, and reveal cryptic biodiversity. Large-scale studies should be designed to determine the prevalence of lungworm infection in Iran, to ensure the sustainability of control programs and mitigate against associated economic losses."} +{"text": "Using data investigation, the microbiology of bacterial infection in patients with pulmonary infection was discussed, and its clinical characteristics were analyzed. The clinical data of 160 patients with pulmonary infection in our hospital from March 2019 to March 2021 were collected and analyzed. Blood samples were collected and cultured, and the pathogens were identified. The distribution, constituent ratio, and drug resistance of pathogens in elderly patients with pulmonary infection were analyzed. Logistics regression analysis was adopted to analyze the risk factors of pulmonary infection. Klebsiella pneumoniae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Serratia marcescens), 28 strains of Gram-positive bacteria , and 88 strains of fungi . Regarding Klebsiella pneumoniae in elderly patients with pulmonary infection, the drug resistance rates were 59.72% for amoxicillin-clavulanate potassium, 52.78% for ampicillin sodium-sulbactam sodium, and 51.39% for cefazolin sodium. Regarding Pseudomonas aeruginosa, the drug resistance rates were 29.31% for ticarcillin sodium-potassium clavulanate, 27.59% for piperacillin sodium, and 24.14% for gentamicin. Regarding Stenotrophomonas maltophilia, the drug resistance rates were 79.55% for ceftazidime, 38.64% for chloramphenicol, and 31.82% for levofloxacin. Regarding Serratia marcescens, the drug resistance rates from high to low were 74.42% for cefotaxime, 72.09% for moxifloxacin, and 69.77% for gentamicin. Regarding Staphylococcus aureus in elderly patients with pulmonary infection, the drug resistance rates were 100.00% for penicillin, 61.54% for erythromycin, 61.54% for clarithromycin, and 61.54% for azithromycin. Regarding Candida albicans, the drug resistance rates from high to low were 22.41% for caspofungin, 15.52% for itraconazole, and 9.09% for fluconazole. The results of univariate analysis of pulmonary bacterial infection indicated that there were no significant differences in sex and body mass index between nonbacterial infection group and bacterial infection group (P > 0.05). There were significant differences in terms of dust or harmful gas exposure, family member smoking, chronic lung disease history, age, smoking, family cooking, hospital stay, and indwelling catheter (P < 0.05). Exposure to dust or harmful gases, family cooking, age, history of chronic lung disease, indwelling catheter, and length of hospital stay were risk factors for pulmonary bacterial infection (P < 0.05). Of the 160 patients with pulmonary infection, 107 were males (66.88%) and 53 were females (33.13%). The age ranged from 12 to 97 years old, with an average of 63.82\u2009\u00b1\u200912.64 years old. Sevent-six patients (47.50%) were over 65 years old. Urban patients accounted for 71.88%, and rural patients accounted for 28.13%, of which workers accounted for 46.25%, and farmers and cadres each accounted for about 4%. 85.62% of smokers have smoked for more than 4 years. Eighty-five patients had chronic diseases such as coronary heart disease, hypertension, diabetes, and cerebrovascular disease. Heart failure occurred in 10.00%, old tuberculosis in 11.25%, and new tuberculosis in 5.63%. The average hospital stay of the patients was 14.93 days, and the improvement rate was 91.25%. Eleven patients died. Among the 160 patients with pulmonary infection, COPD, pneumonia, and lung cancer accounted for the highest proportions, and idiopathic pulmonary fibrosis, bronchitis dilatation, tuberculosis, and bronchial asthma also played an important role. Pathogenic bacteria were detected in 104 of the 160 elderly patients with pulmonary infection, and the detection rate was 65.00%. A total of 444 strains of pathogenic bacteria were detected, including 328 strains of Gram-negative bacteria (73.87%, mainly Gram-negative bacteria are the main pathogens in elderly patients with pulmonary infection. Antibiotics should be administered reasonably according to the results of the drug sensitivity test. Older age, history of chronic lung disease, catheter indwelling, and length of stay are the risk factors for pulmonary bacterial infection. Pulmonary infection is a common respiratory disease in hospitalized patients . Due to \u03b2-lactams, quinolones, and macrolides are the most adopted , and the chi-square test is used. Logistic regression analysis was adopted to analyze the influencing factors, and meaningful ones were included in the multi-factor logistic regression model. P < 0.05 indicates that the difference exhibits statistically significant.SPSS12.5 software was used for statistical analysis. The counting data are presented as [First, we analyzed the general data of 160 patients with pulmonary infection who were admitted to our hospital from March 2019 to March 2021, including 107 males (66.88%) and 53 females (33.13%). The age range was from 12 to 97 years old, and the average age was 63.82\u2009\u00b1\u200912.64 years old. The age of 76 patients (47.50%) was over 65 years. Most of the patients came from urban areas (71.88%), while those from rural areas accounted for 28.13%, where the majority were workers (46.25%), and farmers and cadres each accounted for about 1/4. 85.62% of smokers have smoked more than 4 years. Of the 160 patients, 85 had chronic diseases such as coronary heart disease, hypertension, diabetes, and cerebrovascular diseases; 10.00% of had heart failure; 11.25% had old pulmonary tuberculosis; 5.63% had new tuberculosis. The average hospital stay of the patients was 14.93 days, and the improvement rate was 91.25%. Eleven patients died. All the results are indicated in We analyzed the distribution of pulmonary diseases in 160 patients. COPD, pneumonia, and lung cancer accounted for the highest proportion, and idiopathic pulmonary interstitial fibrosis, bronchitis dilatation, tuberculosis, and bronchial asthma also played an important role. The specific results are indicated in Klebsiella pneumoniae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Serratia marcescens. Twenty-eight strains of Gram-positive bacteria and 88 strains of fungi . All the results are indicated in Figures 1One hundred and four of 160 elderly patients with pulmonary infection had positive pathogens, with a detection rate of 65.00%. A total of 444 strains of pathogenic bacteria were detected, of which 328 strains (73.87%) were Gram-negative bacteria, including Klebsiella pneumoniae in elderly patients with pulmonary infection, the drug resistance rates were 59.72% for amoxicillin-clavulanate potassium, 52.78% for ampicillin sodium-sulbactam sodium, and 51.39% for cefazolin sodium. The resistance rates of Pseudomonas aeruginosa to ticarcillin sodium-potassium clavulanate, piperacillin sodium, and gentamicin were 29.31%, 27.59%, and 24.14%. The resistance rates of Stenotrophomonas maltophilia to ceftazidime, chloramphenicol, and levofloxacin were 79.55%, 38.64%, and 31.82%. Regarding Serratia marcescens, the drug resistance rates from high to low were 74.42% for cefotaxime, 72.09% for moxifloxacin, and 69.77% for gentamicin.. The specific results are indicated in We analyzed the drug resistance rate of Gram-negative bacteria in elderly patients with pulmonary infection. Regarding Staphylococcus aureus in elderly patients with pulmonary infection, the drug resistance rates were 100.00% for penicillin, 61.54% for erythromycin, 61.54% for clarithromycin, and 61.54% for azithromycin. Regarding Candida albicans, the drug resistance rates from high to low were 22.41% for caspofungin, 15.52% for itraconazole, and 9.09% for fluconazole. The specific results are indicated in Tables We analyzed the drug resistance rate of Gram-positive bacteria and fungi in elderly patients with pulmonary infection. Regarding P > 0.05), but there were significant differences in smoking, household cooking, exposure to dust or harmful gases, family smoking history, hospitalization time for chronic lung disease, and age of indwelling catheter (P < 0.05). The specific results are indicated in We analyzed the single factor of pulmonary bacterial infection. One hundred and four cases of pathogens were detected in 160 patients with pulmonary infection as bacterial infection group, and the rest were nonbacterial infection group. No significant difference was found in sex and body mass index between nonbacterial infection group and bacterial infection group and 53 females (33.13%). The age range was from 12 to 97 years old, and the average age is 63.82\u2009\u00b1\u200912.64 years old. 47.50% were over 65 years old, which caught our attention . AccordiIn this group, up to 160 patients with coronary heart disease, hypertension, diabetes, cerebrovascular disease, and other chronic diseases are related to the high proportion of elderly cases. For elderly patients, the disease is often accompanied by aging. In the elderly, the reserve function of various organs is reduced or lost, the response to stress decreases, and the disease of one organ may lead to damage to another organ. For example, long-term bed rest or coughing in patients with cerebrovascular disease can easily lead to aspiration pneumonia, heart failure, which is closely related to pulmonary infection, and the probability of pulmonary infection in patients with diabetes increases. We should attach great importance to the previously mentioned situation.The symptoms of pulmonary infection in the elderly are often not obvious, which increases the difficulty of clinical diagnosis, so laboratory examination is of great significance for the diagnosis and treatment of pulmonary infection in the elderly . ExtensiPseudomonas aeruginosa was the most common, followed by Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and Haemophilus influenzae. In this group of data, there are 28 strains of Gram-positive bacteria, accounting for 6.30% of the bacteria in this group, mainly staphylococci and enterococci [Pseudomonas aeruginosa were studied [Acinetobacter baumannii infection with sulbactam (18 cases) and amoxicillin-sulbactam (24 cases), and 39 cases were cured [Gram-negative bacilli were the main pathogens of pulmonary infection in inpatients. Some data indicates that it is 70%\u223c90% , 20. Graerococci . Due to studied . A total studied . From 19ulbactam cases, a\u03b2-lactamase inhibitors can be administered in noncritically ill patients without the risk of multiple drug resistance MDR. For noncritically ill patients with MDR risk, \u03b2-lactamase inhibitors against Pseudomonas aeruginosa, cephalosporins, and carbapenem can be administered [Pseudomonas aeruginosa. For patients at risk for MRSA, a combination of glycopeptides or linezolid can be used. Tigecycline or polymyxin can be adopted in patients at risk of infection with pan-resistant bacteria (susceptible only to classes 1 or 2 antibiotics) [Anti-infective therapy is the most important treatment for pulmonary infection in the elderly. As most of the elderly are complicated with multiple underlying diseases, with concealed onset, rapid progress, and high mortality, empirical anti-infective treatment should be administered as soon as possible once pulmonary infection is diagnosed . The chonistered . For cribiotics) . When thKlebsiella pneumoniae in elderly patients with pulmonary infection were amoxicillin-clavulanate potassium, ampicillin sodium-sulbactam sodium, and cefazolin sodium [Pseudomonas aeruginosa had a high resistance rate to ticarcillin sodium-potassium clavulanate, piperacillin sodium, and gentamicin and were sensitive to Amikacin, polymyxin E, and polymyxin B. They were resistant to other antibiotics. Stenotrophomonas maltophilia had a high resistance rate to ceftazidime, chloramphenicol, and levofloxacin and were sensitive to compound sulfamethoxazole and minocycline. Serratia marcescens had a high resistance rate to cefotaxime, moxifloxacin, and gentamicin and were sensitive to piperacillin sodium-tazobactam sodium, cefoperazone sodium-sulbactam sodium, and ceftazidime [Candida albicans from high to low were caspofungin, itraconazole, and fluconazole, and they were more sensitive to flucytosine, amphotericin B, and voriconazole. When selecting antibiotics in the clinical treatment of elderly patients with pulmonary infection, we should pay attention to the results of drug sensitivity test and adjust the use of drugs in time.In this study, drugs with a high resistance to n sodium . Pseudomtazidime . StaphylP < 0.05). The infection rate of bacteria in the lungs of hospitalized patients who often cook at home and often encounter dust or harmful gases is also higher, mainly because there are more harmful substances in the kitchen, such as carbon monoxide, nitrogen, and sulfur oxides. These are all pathogenic factors that cause respiratory diseases. In addition, from the results of this study, catheter indwelling and length of stay in hospital are also closely related to pulmonary infection, which may be because longer hospital stays and catheter indwelling will increase patients' contact with pathogens, thus increasing the risk of bacterial infection.Recently, great attention has been paid to the risk factors of pulmonary bacterial infection in inpatients . EpidemiKlebsiella pneumoniae is the main pathogen of pulmonary bacterial infection in inpatients in our hospital. Older age, history of chronic lung disease, exposure to dust or harmful gases, family cooking, long indwelling catheter, and long hospital stay are the risk factors of Klebsiella pneumoniae in patients staying at our hospital. Actively controlling the primary disease and increasing the frequency of lung detection can reduce the incidence and reduce the bacterial infection of the lung.Conclusively,"} +{"text": "Failure of second-generation tyrosine kinase inhibitors (2GTKI) is a challenging situation in patients with chronic myeloid leukemia (CML). Asciminib, recently approved by the US Federal Drug Administration, has demonstrated in clinical trials a good efficacy and safety profile after failure of 2GTKI. However, no study has specifically addressed response rates to asciminib in ponatinib pretreated patients (PPT). Here, we present data on responses to asciminib from 52 patients in clinical practice, 20 of them (38%) with prior ponatinib exposure. We analyzed retrospectively responses and toxicities under asciminib and compared results between PPT and non-PPT patients.After a median follow-up of 30\u00a0months, 34 patients (65%) switched to asciminib due to intolerance and 18 (35%) due to resistance to prior TKIs. Forty-six patients (88%) had received at least 3 prior TKIs. Regarding responses, complete cytogenetic response was achieved or maintained in 74% and 53% for non-PPT and PPT patients, respectively. Deeper responses such as major molecular response and molecular response 4.5 were achieved in 65% and 19% in non-PPT versus 32% and 11% in PPT, respectively. Two patients (4%) harbored the T315I mutation, both PPT.In terms of toxicities, non-PPT displayed 22% grade 3\u20134 TEAE versus 20% in PPT. Four patients (20% of PPT) suffered from cross-intolerance with asciminib as they did under ponatinib.Our data supports asciminib as a promising alternative in resistant and intolerant non-PPT patients, as well as in intolerant PPT patients; the resistant PPT subset remains as a challenging group in need of further therapeutic options. In recent years, chronic myeloid leukemia (CML) marked a major milestone in cancer targeted therapies after the development of tyrosine-kinase inhibitors (TKIs), with imThe further development of new-generation TKIs set a new era for precision medicine: initially second-generation TKI (2GTKI) such as dasatinib, nilotinUnfortunately, an important proportion of patients fail all currently available TKIs, due to resistance or intolerance: approximately 50% of patients with first line imatinib will develop intolerance or resistance, whereas for 2GTKI, 30\u201340% will need a change of therapy. In thisAlthough asciminib has recently been approved in the USA, there is still a lack of information regarding its use in the real-world setting, including the benefit of asciminib in patients previously exposed to ponatinib. Accessibility of this information would be key in the context of the release of the drug, helping clinicians and hospitals tailor this new therapeutic option with accuracy for the patients in need.Our aim is to discern differences in safety and efficacy in patients under asciminib with and without prior ponatinib treatment in real-world practice setting.We gathered data from 52 CML patients treated with asciminib between October 2018 and July 2021 in 33 Spanish institutions joined to the Spanish CML group (GELMC). Asciminib was provided by a managed-access program (MAP) allowed by Novartis. MAP requests were independently reviewed by licensed treating physicians to confirm that the following criteria were met: treatment need of a serious or life-threatening disease lacking commercially available options, patients had to be ineligible or unable to participate in a clinical trial, and the request should be in alignment with all applicable local laws and regulations. The study was approved by the Spanish Drug Agency and the Ethics Committee of the Hospital Universitario Ram\u00f3n y Cajal , with informed consent being obtained from all patients. BCR::ABL1 analysis was not centralized, but all samples were analyzed in EUTOS accredited laboratories. Mutational status tests were performed in all patients after switching to a second line of TKI; no mutational status studies were performed during or after asciminib treatment.Response analysis was performed following the European Leukemia Net 2020 recommendations. TreatmeThe baseline characteristics of the study series are displayed in Table Switching to asciminib was mainly due to intolerance in the non-PPT group (75% of cases), while in the PPT group it was balanced as half intolerant and half resistant.In the whole series (PPT and non-PPT), cumulative response rates of complete hematological (CHR), complete cytogenetic (CCyR), and major molecular response (MMR) were 92%, 66%, and 52%, respectively.After excluding patients in CCyR or MMR at baseline, the cumulative rates of CCyR and MMR were 42% (11/26) and 40% (15/38), respectively. In resistant and intolerant patients, probabilities to obtain CCyR were 41% (7/17) versus 35% (6/17) and for MMR: 79% (26/33) versus 61% (20/33), respectively.Considering prior exposure to ponatinib Table , rates oMoreover, probability of improving baseline responses was 53%, 57%, and 19% towards CCyR, MMR, and MR4.5 for the non-PPT versus the PPT group reaching 27%, 20%, and 11%, respectively.Comparing probabilities for maintaining or improving responses regarding prior resistant or intolerant status: in the non-PPT group, intolerant patients displayed: 87% CCyR, 74% MMR, and 26% MR4.5, whereas resistant non-PPT showed 38% CCyR, 38% MMR, and 0% MR4.5, respectively. In the PPT group, prior intolerant patients displayed: 60% CCyR, 30% MMR, and 10% MR4.5, whereas resistant patients showed: 44% CCyR, 33% MMR, and 11% MR4.5, respectively.Considering patients with lack of response, the resistant group displayed the worst outcomes, regardless of prior ponatinib use. Ponatinib use per se does not seem to have an impact on response in our group, unlike the unresponsiveness of the whole resistant group.Concerning baseline mutational status Table , 6 patieTwo patients (4%) harbored the T315I mutation, both in the PPT-resistant group. One patient improved the depth of response from MR4 to MR4.5, whereas the other lost CHR and discontinued asciminib.Overall, half of the patients suffered from any TEAE, while 19% (10 patients) had grade 3\u20134 TEAE, with thrombocytopenia being the most common presented the same type of TEAE with asciminib: grade 4 thrombocytopenia, grade 3 pancreatitis, grade 1 anemia, and grade 1 lumbar pain.Discontinuation rate of asciminib was higher in PPT patients (45% in PPT versus 13% in non-PPT). As shown in Fig.\u00a0After a total follow-up period of 30\u00a0months (Fig.\u00a0Ponatinib is a very potent TKI capable of overcoming resistance to multiple BCR::ABL1 mutations, such as T315I. Consequently, ponatinib-resistant patients have very limited treatment alternatives. We beliIn a previous report, we showed promising preliminary results in a cohort of 31 patients treated with asciminib in the real-life setting. In the Overall, our data demonstrates a higher efficacy of asciminib in non-PPT patients, who displayed globally better outcomes than PPT: CCyR 74% versus 53% and MMR 66% versus 32%, respectively. Importantly, these differences impacted in EFS. However, after analyzing the responses rates in different cohorts, the group that benefited the most from asciminib was the non-PPT intolerant. Of interest, as it might be expected, a higher response rate was not observed in resistant non-PPT patients compared to the resistant PPT group. These data, due to the low number of patients included in each group, should be taken with caution, warranting to be further researched in subsequent studies. Considering mutational status, PPT-resistant patients did not display BCR::ABL1 mutations more often than other subgroups, apart from the T315I mutation. This can be due to the heterogeneity of the mutational spectrum in our sample and may hint that some resistance mechanisms are not exclusively explained by BCR::ABL1 mutations.Our response rates are comparable to those of the prior phase I clinical trial including 150 CML patients switching to asciminib due to resistance or intolerance to other TKIs, with 24 patients having been exposed to ponatinib. OverallThe T315I mutation has a significant impact on CML prognosis. With ponatinib as the only available drug up to now effective against this mutation, asciminib and its allosteric inhibition mechanism may prove promising. Data from the phase I trial with asciminib showed how only 1/7 patients harboring the T315I mutation with previous exposure to ponatinib obtained MMR. Thus far, in our sample the two patients with T315 mutation showed disparity, one deepening response whereas the other lost it despite receiving full dosing. Though very limited in numbers, this data may indicate that T315I remains as a negative risk factor with difficulties to be taken under control. Future directions to tackle this issue may include combinations of ponatinib and asciminib to maximize efficacy in these patients.Regarding toxicities, we found lower incidences of TEAEs compared to mentioned clinical trials. These differences are probably related to the retrospective design of our study. In contrast, treatment discontinuation related to AEs is similar in the phase I and III trials.Cross-intolerance happened in 4 PPT patients, as previously described. Favorably, no cardiovascular events happened in the PPT group, nor in those who had discontinued ponatinib due to such side effects. While cross-intolerance rarely occurs, likely to its different mechanism of action and higher kinase selectivity, it is important to highlight the relative short follow-up period in CML patients exposed to asciminib.Main limitations of the study are the relative low number of patients and the retrospective design; nevertheless, ponatinib pretreated patients are well represented in our sample, with larger proportions than those in the phase I trial. Close monitoring with longer follow-up is mandatory to better establish the safety profile of the drug.Asciminib is now available for CML patients previously treated with two or more TKIs after the results of the phase III ASCEMBL trial. While a"} +{"text": "Dear Editor,Suicide amongst the military veteran population is a significant public health problem in the United States. The National Veteran Suicide Prevention Annual Report revealed that 6261 died by suicide in 2019 [In 2019, firearms accounted for 69.2% of veteran suicides, followed by 19.9% suffocation, 8.4% poisoning, and 5.4% other methods [Limiting access to over-the-counter medications is another important area of means restriction to consider . VeteranLethal means restriction is effective in preventing suicides , 4. StudMedical practitioners who treat military veterans must make a conscious effort to regularly conduct suicide screens and assess for lethal means. Restricting access to lethal means such as firearms and medications is an effective way to mitigate suicide risk, and should be a focus of suicide prevention interventions in the military veteran population."} +{"text": "Background: The coronavirus disease 2019 (COVID-19) pandemic, which started in 2019, has created unprecedented public health problems, mental health crises, and economic and social problems. These effects have been studied by numerous researchers on the general population but none on hospitalized and discharged COVID-19 patients.Aim: To assess psychological and social problems among hospitalized and discharged COVID-19 patients.Methods: During lockdown and post-lockdown in India, we interviewed 500 COVID-19 patients admitted at our tertiary care center during their hospitalization and post-discharge period for psychological and social problems.Results: The common psychological issues in hospitalized patients during lockdown were anxiety and misconceptions about COVID-19, while insomnia, anxiety, and frustration were common during the post-lockdown period. The typical social problems in hospitalized patients during the lockdown were containment-related issues, discrimination, longer wait for repeat COVID-19 tests, and boredom; whereas issues related to employment and financial matters were common during post-lockdown. Psychological problems comparatively decreased whereas social problems increased after discharge.Conclusion: Unrehearsed mitigation strategies at the beginning of the pandemic unknowingly led to various psychological and social problems. It was further aggravated by a lack of information and miscommunication. The coronavirus disease 2019 (COVID-19) pandemic is a global health and economic crisis. COVID-19 started in Wuhan, China, in early December 2019, came into the news in late December to early January 2020, and later was declared as an emergency in the third week of January 2020. The World Health Organization (WHO) declared this a Public Health Emergency of International Concern (PHEIC) on January 31, 2020, and was finally declared a pandemic on March 11, 2020 [As per the WHO report 2020, only 46% of countries and territories had COVID-19 preparedness and response plan by March 1, 2020 [In India, a nationwide lockdown was implemented on March 25, 2020, following which the initial response was \u201ccoronaphobia\u201d and \u201cmass hysteria\u201d comprising extreme panic, desperate hoarding, a social boycott of COVID-19 patients, and discriminatory behavior towards healthcare and other frontline workers . With thSimilarly, many unforeseen social issues like quarantine, social isolation, and uncertainty begat various psychological problems like loneliness, impaired self-care, maladaptive coping strategies, and difficulty handling the parallel \"infodemic\" . VentrigThere are many studies and online surveys conducted in India and worldwide, mainly studying the general population and healthcare workers for psychological and social issues during the pandemic; however, no epidemiological data on psychological and social problems of hospitalized and discharged COVID-19 patients are available from India. The management of any pandemic is insufficient and incomplete if psychological and social components, very crucial yet often overlooked health determinants, are not given the necessary attention.This retrospective analysis was conducted to assess psychological and social problems among 500 hospitalized and discharged COVID-19 patients of Nandkumar Singh Chouhan Government Medical College (NSCGMC), Khandwa, Madhya Pradesh, India. The study was done over a period of six months, from April 2020 to September 2020. Institutional ethics committee permission was obtained .In India, the initial strategy to tackle the pandemic was to establish three-tier COVID-19 care facilities namely: COVID-19 care centres (CCC) for mild cases, dedicated COVID-19 health centres (DCHC) for moderate cases, and dedicated COVID-19 hospitals (DCH) for severe cases. Our facility had all three types. Since the outset of the pandemic, many admitted COIVD-19 patients were having various psychological issues. A few incidences of non-cooperation, aggression, absconding from COIVD-19 wards and threatening behaviour were also reported. To minimize psychological burden and to provide psychological support, teleconsultation service was started by the Psychiatry department of NSCGMC from April 2020 till September 2020, as per instructions by the administration. The detailed records of psychological and social problems of admitted and discharged patients and their management were entered in Microsoft Excel spreadsheets . These records were maintained for reporting purposes and for communicating with other established response teams for effective and holistic pandemic management at our place.During the six-month period, a total of 516 patients were consulted and counselled during their hospitalization and till 15 days after discharge. It was a convenience sampling of 500 patients (61 from DCH and 439 from CCC and DCHC); as the records of 16 patients were either incomplete or couldn\u2019t be followed up, hence they were excluded. Demographic details of admitted COIVD-19 patients, such as name, age, sex, address, date of admission, contact number of patient and their relatives were collected at the time of admission only, by the record-keeping department of NSCGMC. Additionally, other clinical information like past psychiatric history and date of discharge were collected from patients and their relatives. These patients were consulted daily by psychiatrists/authors via audio or video calling. A few cases were consulted in person, such as those who were reluctant to talk on the phone, agitated and psychotic patients, or when the treating doctor requested for in-person psychiatric consultation. During the hospital stay and post-discharge period, each patient was interviewed at least once a day by either psychiatrist, comprising more than 10,000 interviews during the study period of six months.The assessment for the psychological and social problems was done by open-ended interviews, without using any specific structured questionnaire or scale. Corroborative details whenever needed, for assessment of behavioural or psychological problems, were collected through on-duty, treating, or ward in-charge doctors and nursing staff.\u00a0Psychiatry diagnosis was made clinically as per the International Classification of Diseases, 10th revision (ICD-10) and Diagnostic and Statistical Manual of Mental Disorders, fifth edition (DSM-5),. Whenever needed, supportive counselling was done and if necessitated, psychiatric treatment was provided. These patients were interviewed by two psychiatrists; hence, the chances of subjective bias in diagnosis, transference, and countertransference were minimal.The recorded data were entered in a Microsoft Excel spreadsheet and analyzed using descriptive statistics. The data were presented as frequencies and percentages.In our study, we retrieved and analyzed the data of 500 COVID-19 patients. The mean age of the study participants was 38.29 \u00b1 17.5 years; most patients belonged to the age group of 21-30 years. A total of 121 participants were above 50 years of age and 79 were below 20 years of age. A total of 303 participants were male and 80.4% were living in urban areas was the most common psychological problem, followed by insomnia (12.8%) and depression (3.8%). Substance use-related issues were found in 2.4% of the patients, somatic symptoms in 3%, and grief in 1.4% of patients. The majority of patients didn't fulfil all the diagnostic criteria for a psychiatric disorder according to guidelines (ICD-10 and DSM-5). However, common themes or patterns of concern were found such as 11.4% of patients showed behavioural issues like anger, frustration, irritation, and non-cooperation, 10.8% had misconceptions about COVID-19 infection, and 9% were excessively worried about their family members isolated at home. Of all, 37.6% needed supportive counselling and 23.8 % needed treatment, either short or long-term of family members like calling repeatedly for updates on the patient\u2019s health and needing reassurance repeatedly. Various containment-zone-related issues like non-access to daily necessities by their family were reported by 13.6% of hospitalized patients, 11% of patients reported significant distress due to a longer wait for the report of repeat COVID-19 test, 10% of the patients, mainly females, reported concern that nobody else is there at home to do house chores. Stigma and discrimination were reported by 6.4% of patients. Among the various social issues, 7% of patients showed mistrust and misbehaviour towards medical staff such as being non-compliant with the treatment, spreading rumours or false videos, being verbally abusive, or showing physical aggression. Disobeying COVID-19 protocols like mask wearing and social distancing was found in 3.4% of patients. Delayed result and a longer waiting period for the report of COVID-19 test of close contacts and family members was reported by 6.2 % of patients , were anxiety and misconception about COVID-19. While problems faced during July-September 2020 (post lockdown) were insomnia, anxiety, and frustration , of which 10.8% was related to job/financial matters. Somatic symptoms, excessive concern for minor bodily symptoms, and worry for recurrence were found in 17% of patients. Behavioural and emotional issues of frustration, feeling of rejection, loneliness, being locked up at home, and social restrictions were found in 14.6%. Insomnia was found in 5.6% of patients.Social ProblemsThe most common social problem after discharge was containment-related issues (30%), of which 4.6 % were related to the inability to get daily necessities such as milk and vegetables and 25.4% due to containment lasting longer than expected. Issues related to social restrictions were reported by 18% of patients. Financial matter-related issues were reported by 17.4% of patients and stigma and discrimination by 5.8% of patients. A few patients (5.6%) needed the medical certificate for various purposes such as exemption or to appear in exams, and to join the workplace. Difficulty in social isolation due to few rooms at home was reported by 4.4% of patients and domestic issues like difficulty getting help for household chores were reported by 2.4% of patients.The most common psychological issues after discharge, during lockdown and post lockdown, were similar; these were somatic symptoms and emotional reactions to social restriction. The social issues faced during lockdown were financial problems, containment-related issues, stigma, and discrimination.With the outbreak of COVID-19 pandemic, almost all the countries had adopted various strategies such as lockdown, travel restrictions and containment to curtail the spread of infection. India also imposed a lockdown quite early , within two weeks of the declaration of COVID\u201119 as a pandemic. Although at the inception, these strategies were presumed to be the best possible options against the rampant rise in COVID-19 cases. However, little was known about the additional burden these were going to create on the already existing COVID-19 burden. They had a widespread impact on the psyche and daily living of the people, especially those who were suspected or diagnosed with COVID-19 infection and were kept in isolation. In this regard, our study was planned to evaluate the psychological and social problems faced by patients infected with COVID-19, who are presumed to be most likely affected.We searched various studies assessing psychological and social problems among COVID-19 patients but very few were available. Most of the researchers from India conducted online surveys on the general population -15, or aIn our study, as presumed, elderly patients commonly presented with serious conditions and needed intensive care. Hence, most were not available for routine psychiatric interviews. Psychiatric consultation of such patients was done only on as and when needed basis. Consequently, most of our participants were in their third decade of age. Another possible argument can also be that India has a mostly young population (65% aged <35 years) .During hospitalization, 422 patients 84.4%) had psychological problems and 347 (69.4%) reported social problems. Grover et al. conducted an online survey of the psychological impact of COVID-19 among the general population in India during the lockdown and found that about 70% of participants had poor mental well\u2011being 4.4% had . Our samThe most common psychiatric issue during hospitalization was anxiety (27%). Of the patients with anxiety, 16.4% were having reactive anxiety, which could be explained as a psychological response to unexpected, unpredictable stressors i.e. COVID-19 infection and the remaining 10.6% of the anxiety patients were worried well, which reflects high illness anxiety and maladaptive coping mechanisms in the early phase of the pandemic. Grover et al. also found moderate anxiety in 23.7% of the general population . SimilarApart from this, 9% of our admitted patients, mostly middle-aged, were worried for their family members. The main concerns were fear of the spread of infection to others, various COVID-19 and non-COVID-19 related health needs, non-access to daily necessities, and financial troubles, especially among daily wagers. Anxiety disorders decreased from 27% during admission to 20% after discharge, possibly due to the change in stressful environment in the hospital to a more emotionally supportive and caring environment at home. Of these discharged patients, 10.8% were anxious mainly due to financial matters, which was expected owing to lockdown, and halting of major economic activities. Joshi found similar concerns among a sample of 348 callers . The autInsomnia was found in 12.8% of admitted patients, mostly the elderly, where pre-existing age-related sleep problem was aggravated by the sudden stressors of COVID-19 diagnosis, confinement in a hospital environment, and digital illiteracy resulting in an inability to connect with relatives. Roy et al. also found insomnia in 12% of the participants . Most ofDuring hospitalization, 11.4% of patients showed behavioural issues like anger, frustration and non-cooperation, 10.8% had misconceptions about covid-19 infection, and 9% were excessively worried about their family members isolated at home. Joshi also described similar concerns, themes and subthemes in their study .We found depression in 3.8% of hospitalized patients; mostly reported stressors like a recent death in the family or multiple family members infected with COVID-19. Depression was common in patients with chronic co-morbidities. These are proven predisposing or precipitating risk factors for depression. Grover et al. also found moderate to severe depression in 3% population [Somatic symptoms in hospitalized patients (3%) increased significantly to 17% after discharge. This could be attributed to the novel nature of COVID-19 infection, frequently-changing government guidelines, and difficulty in access to medical services at home, leading to preoccupation and frequent exaggeration of minor bodily symptoms and hypervigilant behaviour .There wasn\u2019t much difference in behavioural issues during hospitalization (11.4%) and after discharge 14.6%), as behavioural issues were mostly found among young or middle-aged patients, due to the reasons of social restrictions and financial problems which didn't change much even after discharge. As Ventriglio and Bellomo have stated, restrictions and changing norms can lead to confusion, anger, and defiant behaviours [%, as behThe common psychological issues noted during lockdown were anxiety, insomnia and misconceptions about COVID-19 infection, which was quite expected due to the fear of the unknown and \u201ccoronaphobia\u201d, superadded by the rumours, misinformation, etc. Shigemura et al. mentioned that overwhelming and sensational news headlines and images and absence of information and rumours cause anxiety and fear . Common The prominent social problems of \u201chigh expressed emotions\u201d (17%) by the patient\u2019s relatives during hospitalization could be due to the novel nature of COVID-19 infection, uncertain and frequently changing clinical picture, and diagnostic and treatment guidelines. Grover et al. also found family members 38.8%) have anxiety .8% have .Social problems related to containment zones like non-access to daily necessities were reported by 13.6% of hospitalized patients and 30% of discharged patients. With the progression of the pandemic and the spread of infection, more patients were diagnosed with COVID-19 resulting in the formation of more containment zones. Often, sequential infection of multiple family members one after another led to non-removal of the containment zone, hence prolonging its duration, consequently 25.4% of discharged patients reported problems of containment lasting longer than expected and 18% of discharged patients reported social/physical restriction, quarantined at home resulting in a feeling of boredom and loneliness. It was an interesting finding that boredom and loneliness were equally reported by both youth and the elderly. Grover et al. also reported feelings of loneliness in 21.3% of participants . In addiAs predicted, the government\u2019s efforts for financial support and food security will be insufficient ; in our Social problems of discrimination and stigma were reported by 6.4% of hospitalized patients and 5.8% of discharged patients. It can be proposed that once patients were labelled as COVID-19 positive, they remained so even after discharge or being COVID-19 negative on repeat testing. Grover et al. also reported that 10% of participants face stigma [An isolated and peculiar social problem of a longer wait for the report of repeat COVID-19 test before discharge was reported by 11% of hospitalized patients. It was noted during the early pandemic when repeat COVID-19 testing was advised before discharge. Since our institutional laboratory was recently established and was also catering to the needs of adjoining districts hence overloaded which led to this issue. Accordingly, 6.2% of patients reported late results of family members or contacts. In the same line, 5.6% of discharged patients requested for medical certification for various purposes such as to appear in exams, fitness for jobs, or travelling. As with all over the world, our medical and non-medical staff was also already working ways beyond their capacity and were overburdened, therefore such non-emergency requests could not be addressed immediately. Many studies have corroborated this finding. Khasne et al. reported that 52.8% of healthcare workers had pandemic-related burnout . The docDuring hospitalization 10% of patients, mainly females, were distressed because nobody else was there at home to take care of household chores. This decreased to 2.4% after discharge. This can be explained on the basis of prevalent gender-assigned roles and possible gender discrimination in India. A similar socio-economic factor of poverty was mirrored in 4.4% of discharged patients who reported difficulty isolation due to less number of rooms at home. This is important as implementing public health measures is difficult in places with overcrowded living conditions and inadequate hygiene and sanitation .During hospitalization, 7% of patients misbehaved with medical staff. Some of them were spreading rumours and making fake videos about the hospital administration, and being abusive and physically aggressive. Similarly, 3.4% of patients didn't follow COVID-19-related protocols. All of these can be explained as a result of lack of trust in the healthcare system, misinformation, rumours, lack of education and irresponsible media reporting. Panigrahi et al. in their online survey found that 64.8% of participants felt the steps of the government were inadequate for the prevention and control of COVID-19 .We recommend from our learning from this study that while preparing and managing the pandemic, planners and policymakers must keep a holistic approach. The psychological and social dimensions are important determinants of health; therefore while planning confinement strategies during pandemics or outbreaks, various social and psychological issues must be thought about and addressed timely. Psychological and social health-related information must be considered in guidelines, to minimize myths and misconceptions. The day-to-day difficulties faced by citizens, patients, or family members should be addressed by setting up command and monitoring cells.The main strength and distinguishing feature of our study was that we studied the psychological and social problems encountered by the patients infected with COVID-19 during hospitalization and after discharge from the hospital. These patients were directly interviewed by the psychiatrists daily during the hospitalization and post-discharge period. No such studies have been done in India. However, there are certain limitations. This was a retrospective study and the data was pre-recorded; hence, a few other important information may have been missed. Being a single-centre, hospital-based study, the findings may not be generalizable.The present study observed the significant burden of psychological and social issues in hospitalized COVID-19 patients even after their discharge from hospital. Often psychological and social health is overlooked, which may be more so during pandemics as found in our study. These overlooked issues may pre-dispose, precipitate, complicate, or even present as physical symptoms or medical illnesses. If not identified and addressed adequately, these may hinder the management and pose an additional burden on individual, community, and administration levels. It may also act as an unidentified healthcare burden, further weakening the healthcare system, especially in countries like India. Additionally, various unrehearsed mitigation strategies, such as lockdown, quarantine, social isolation, containment zone, etc., to curtail pandemics may unintentionally lead to various psychological and social problems. Future pandemic preparedness should seek lessons from the current COVID-19 pandemic."} +{"text": "General practitioners (GPs) are the first point of contact for most people in Australia seeking medical attention. They play an important role in the prevention, early detection, and management of both acute and chronic diseases. In Australian general practice, antibiotics are commonly prescribed for respiratory tract infections (RTIs) despite evidence of limited efficacy ,2. A preIn mid-March 2020, the Australian government implemented the expansion of telehealth services covered by Medicare in response to the COVID-19 pandemic. Subsequently, many GPs shifted care delivery from face-to-face consultations to telehealth (telephone or video-conference consultations). A study conducted in the early stage of the pandemic showed lower rates of medication prescriptions via telehealth compared to face-to-face consultations in Australian general practice ; howeverThis retrospective study used data from the Population Level Analysis and Reporting (POLAR) platform . POLAR cFor the analysis, we examined the mean weekly percentage of consultations with antibiotic prescribing between April 1, 2020, and November 30, 2021. We also determined the patient-level probability of an antibiotic being prescribed during consultations in the periods June to November 2020 and June to November 2021, using generalized estimating equations with the Huber-White standard error, adjusted for patient factors and a sampling effect within the general practices. Active patients were defined based on the definition from the RACGP as individuals who had attended the practices 3 or more times in the past 2 years at the time of visit .Ethics approval was obtained from the Macquarie University Human Research Ethics Committee (#52020675617176).Between April 2020 and November 2021, a total of 105,719 individuals had an RTI diagnosis and attended 141,444 consultations: 92,318 (65.3%) face-to-face visits and 49,126 (34.7%) telehealth consultations .In 2020, the weekly mean antibiotic prescribing rates for RTIs were 56.7% (95% CI 54.2%-59.3%) for face-to-face consultations and 40.8% (95% CI 37.2%-44.4%) for telehealth . In 2021At the patient level, the probability of receiving an antibiotic prescription through a telehealth consultation also increased from 59.3% (95% CI 57.6%-61.0%) in 2020 to 65.7% (95% CI 64.4%-67.0%) in 2021 . The proAntibiotic prescribing via telehealth increased over time, with rates initially much lower than face-to-face consultations; however, the prescribing rates between the two consultation modalities became equivalent toward the end of 2021.While telehealth offers some advantages such as less travel time and prevention of infectious disease transmissions, the caveats include limited physical examination capabilities. Such limitations may potentially impact the adequacy of medication prescribing, particularly in populations like children who have difficulty verbalizing symptoms.Considering that high antibiotic prescribing rates for RTIs by Australian GPs is a long-standing public health concern, the findings from this study highlight the need for monitoring the impacts of telehealth on medication prescribing in general practice. Further, studies on telehealth decision-making processes for antibiotic prescribing that evaluate prescribing adequacy appear critical."} +{"text": "One scope of the Active and Healthy Ageing framework is to increase awareness on elderly-related topics. The year 2020 has seen an upheaval across the world caused by the COVID-19 emergence, even higher to older persons.In Italy, data gathered by the PASSI d'Argento behavioural surveillance system on general population aged 65+ in the timeframe 2016-2019 describe health conditions, lifestyles and care needs for elderly.Basing on physical activity recommended by the WHO globally, 33% of non-physically impaired older persons reaches out those levels, 27% are partially active, 40% is sedentary. 9% fell down within 30 days prior the interview, accessing hospital was necessary in 19% of cases; 64% of falling occurred at home, 20% outdoor. 61% refers at least one infrastructural housing issue, 15% perceive higher neighbourhood insecurity. 35% reported difficulties in accessing essential services, especially to local health premises and for necessities. About 19% lives socially isolated, 21% had not any contact (neither by phone) with anyone in a typical week, 71% do not attend collective meetings, such as at a club or church. Nearby 1 out of 3 (29%) represents an asset to the own family/community: 19% looks after cohabiting people, 14% relatives or friends not living together with, 6% engage in volunteering. Participation in training courses or social events (trips/stays organised) regards little more than 2 over65 out of 10: 5% partakes in learning courses, 23% enjoyed those latest occasions. Such low social connectedness is observed even among \u00abyounger elderly\u00bb (aged 65-74). Nearly 19% referred frailty impacting on their own families mainly, 94% of frail elderly is given help from relatives, 20% from professional caregivers, 12% from acquaintances. All these factors suffer from socio-economic and territorial differences. Among elderly reporting many economic difficulties, social isolation is 31%, frailty 28%, difficult access to services 58%, falling 15%, with a geographic gradient at the expense of the Southern Regions.COVID-19 is a clear threat to older persons: in Italy, monitoring ageing dimensions under the pandemic scenario represents even a greater opportunity to have scientific data which describe the impact of health emergency on elderly."} +{"text": "Penicillin allergy is reported in approximately 10% of the US population and is one of the most frequent medication allergies in children. Penicillin allergy labels are associated with more expensive care and adverse outcomes, such as MRSA and C. Diff infection. Studies suggest up to 90% of these patients could safely tolerate this class of drugs. Our team at M Health Fairview University of Minnesota Masonic Children\u2019s Hospital (UMMCH) implemented an allergy assessment tool for inpatient use in January of 2020 to create an effective and accessible path for delabeling pediatric patients with penicillin and cephalosporin allergies.Our pharmacists conducted the allergy assessment on inpatient pediatric patients with penicillin/cephalosporin allergies. Those deemed low to moderate risk for having a true IgE-mediated allergy by our assessment were recommended for outpatient allergy testing. Those deemed no risk were recommended for immediate delabeling. We performed manual chart reviews to describe pediatric patient risk stratification, allergy label status after assessment, outpatient allergy follow-up, and status and results of allergy testing.From January, 2020 to present, 140 patients received a pharmacist allergy assessment. During the 2020 calendar year, 51 allergy assessments were performed on 49 patients. 58 allergies were recorded, with penicillins as the most common (62%), followed by cephalosporins (24%), and penicillin combination drugs (14%). 1.9% of allergies were high risk, 68.8% moderate, 15.7% low, 9.8% no risk, and 3.8% difficult to determine. Of 42 patients deemed low to moderate risk, 8 (17%) were seen by an outpatient allergist. Of these, 5 proceeded with allergy testing and were found to be not allergic. Out of 58 allergy labels, 9 (15.5%) were removed, 5 after allergy testing, 2 immediately due to no risk, and 2 after further history review.Our preliminary data show allergy assessments can inform pediatric allergy risk prior to outpatient allergy testing and assist with imminent delabeling. Next steps include analysis of our 2021 assessments as well as patient caregiver surveys to assess perception of the allergy assessment process and to elucidate on barriers to testing/delabeling.Beth K. Thielen, MD, PhD, Horizon: Advisor/Consultant|Horizon: Honoraria|Merck: Grant/Research Support."} +{"text": "Conclusions: In patients treated for acute STEMI, acute %SAS is associated with post-infarct LVR. Therefore, we suggest performing such evaluations on a routine basis to identify, as early as possible, STEMI patients at higher risk.Background: Measures of global left ventricular (LV) systolic function have limitations for the prediction of post-infarct LV remodeling (LVR). Therefore, we tested the association between a new measure of regional LV systolic function\u2014the percentage of severely altered strain (%SAS)- and LVR after acute ST-elevation myocardial infarction (STEMI). As a secondary objective, we also evaluated the association between %SAS and clinical events during follow-up. Methods: Of 177 patients undergoing echocardiography within 24 h from primary percutaneous coronary angioplasty, 172 were studied for 3 months, 167 for 12 months, and 10 died. The %SAS was calculated by dividing the number of LV myocardial segments with \u2265\u22125% peak systolic longitudinal strain by the total number of segments. LVR was defined as the increase in end-diastolic volume >20% at its first occurrence compared to baseline. Results: LVR percentage was 10.2% and 15.8% at 3 and 12 months, respectively. Based on univariable analysis, a number of clinical, laboratory, electrocardiographic and echocardiographic variables were associated with LVR. Based on multivariable analysis, %SAS and TnI peak remained associated with LVR (for %SAS 5% increase, OR 1.226, 95% CI 1.098\u20131.369, Left ventricular remodeling (LVR) is a complication of acute myocardial infarction (MI). It has a negative prognostic value and is the main cause of heart failure in acute MI survivors ,2. SeverIn this study, we sought to verify whether a new measure of regional longitudinal strain\u2014the percentage of severely altered strain (%SAS)\u2014evaluated by STE during the acute phase of ST-elevation MI (STEMI) is associated with subsequent development of LVR and is better than the other echocardiographic predictors. The rationale underlying the use of %SAS is that it represents the amount of acute severely injured myocardium, without including mildly injured, normal or hypercontractile LV areas, thus avoiding a fundamental limitation of global LV function indices.Patients were referred to the catheterization laboratory of the Cardiac Unit of the University Hospital of Ferrara for primary PCI for suspected STEMI between September 2015 and 2017. The diagnosis of STEMI was made according to standard clinical and electrocardiographic criteria and confThis was a single-center observational study. According to the follow-up program for STEMI patients treated at the Ferrara Cardiac Unit, all patients were scheduled for echocardiography 3 months (T1 time) and 12 months (T2 time) after discharge.The primary objective of the study was to verify whether acute %SAS (at T0) is associated with the development of LVR. Because LVR is a progressive phenomenon detected echocardiographically up to 1 year from the acute event , the 12-To provide information about the clinical value of acute %SAS, we also verified whether this measure was associated with clinical events during follow-up (secondary objective). For this purpose, death from any cause and re-hospitalization for heart failure or acute coronary syndrome were chosen as clinical events and grouped into a composite endpoint. Outcome status was assessed by review of the medical records through the hospital medical informatic platform. If a patient had more than one clinical event, the first one that occurred temporally was considered. The median duration of follow-up from STEMI occurrence was 43 months (interquartile range: 36\u201351 months).(A) Image acquisition. The 2D echocardiographic examination was performed using commercial echo scanners equipped with a 3.5 MHz phased-array transducer. All Doppler and echocardiographic acquisitions were obtained at held end-expiration. Sector width was optimized to allow visualization of the whole LV myocardium in the 3 standard apical views and to maximize frame rate (which varied between 60 and 100 fps). (B) Image analysis. Analysis of the echocardiographic images was performed off-line using a commercially available software . LV end-diastolic volume (EDV), ESV, EF and left atrial volume index (LAVI) were calculated using the biplane Simpson\u2019s method . WMSI waAfter testing for normal distribution with the Kolmogorov\u2013Smirnov test, continuous variables were expressed as median values with 25th and 75th percentiles. Categorical variables were expressed as percentages. Variables of patients with and without LVR or with and without clinical events were compared using the Mann\u2013Whitney U test or the chi-square test, when appropriate. Values of continuous variables at T0, T1 and T2 were compared using the Friedman test, and pairwise comparisons were performed with a Bonferroni correction.For the primary objective, a univariable logistic regression, including the clinical and echocardiographic variables, was performed to evaluate the association with LVR. For the multivariable analysis, the following variables were selected a priori: time from symptoms\u2019 onset to STEMI diagnosis \u2265 3 h, peak of TnI, ST-resolution, use of MRAs at discharge, LV ESV, EF, GLS, WMSI, %WMA, and %SAS. Except for %SAS, all of these variables are known to be associated with LVR from previous studies ,17,18,19For the secondary objective, we performed a univariable and a multivariable Cox analysis. The hazard ratio (HR) for each statistically significant variable was calculated together with the 95% CI. For the multivariable Cox analysis, it was decided a priori to include in the model LVR those variables significantly associated with LVR in the multivariable analysis for the primary objective.p value < 0.05 was considered statistically significant.Intra and interobserver variability for %SAS measurement were assessed in 20 randomly selected patients at T0 using the interclass correlation coefficient (ICC) and the Bland\u2013Altman analysis, calculating bias and limits of agreement (LOAs). The statistical analysis was performed using the IBM SPSS Statistics software, v. 25 . A n = 303) or died before hospital discharge (n = 11). Of the 234 remaining patients, another 57 were excluded: 8 had atrial fibrillation at T0 echocardiography, 22 had inadequate echocardiographic image quality, and 27 were lost to follow-up. Therefore, 177 patients constituted the final study cohort. Five of these patients died before echocardiography at T1 and 5 before echocardiography at T2.Five-hundred forty-eight patients referred to the catheterization laboratory with STEMI diagnosis confirmed by coronary angiography were initially considered. Then, 314 patients were excluded because they were transferred to other hospitals of the Ferrara STEMI network after PCI patients had LVR; 18 (60%) of them had first evidence of LVR at T1 and 12 (40%) at T2. One patient with LVR at T1 died before T2, and another one showed reversed LVR at T2. The percentage of LVR was 10.2% (18/177) at T1 and 15.8% (28/177) at T2. Of the 28 patients with LVR at T2, 12 (43%) did not show LVR at T1.The main clinical characteristics of patients are reported in No significant differences were observed between patients with and without LVR in terms of age, gender, body surface area, body mass index, cardiovascular risk factors, systolic blood pressure, heart rate, site of infarction, culprit coronary artery, final TIMI flow, time from first medical contact to PCI and staged PCI during hospitalization . LVR patBaseline, T1 and T2 echocardiographic characteristics are reported in In patients without LVR, EDV did not change and ESV progressively decreased over time. Global and regional measures of LV systolic function improved. %SAS reduced markedly. LAVI had a modest, although significant, increase. MR severity decreased at T1 and was maintained at T2. E/e\u2019 ratio decreased progressively. Compared to non-LVR patients, at baseline patients with LVR did not differ in terms of EDV but had lower EF and GLS , and higher ESV, WMSI, %WMA and %SAS. LAVI, MR severity and diastolic measures did not differ. In patients with LVR, EDV and ESV progressively increased over time, and LV-EF improved only mildly. GLS improved, and WMSI did not vary. Regional measures of LV systolic function, such as %WMA and %SAS, declined during follow-up, especially at T2. LAVI increased at T2. MR severity remained similar over time and worse than that in patients without LVR at T1 and T2.In the univariable analysis, time from symptoms\u2019 onset to STEMI diagnosis \u2265 3 h, time from first medical contact to PCI, infarct site, ST-resolution, peak of TnI, peak of CK-MB, glycated hemoglobin, use of MRAs at discharge, LV ESV, EF, GLS, WMSI, %WMA, and %SAS were associated with LVR . A multip < 0.0005) while for peak of TnI, the OR was 1.025 . The ROC curve analysis of this multivariable model showed an AUC of 0.82 (p = 0.483 vs. %SAS), respectively. Optimal baseline cut-off values were 44% for %SAS and 49 ng/mL for peak of TnI (p < 0.0005). Model 1 excluded WMSI and %WMA . In this 0.0005) A; AUC ofity 61%) B,C. CorrModel 2 and 3 excluded %SAS and included WMSI and %WMA separately . NeitherDuring the median follow-up period of 43 months, 11 patients died, 15 were re-hospitalized for heart failure, and 15 for acute coronary syndrome as first clinical event, for a total of 41 first events in 41 patients (23% of the entire patient cohort). Because 11 patients had more than one clinical event, the overall clinical events were 55. Survival probability free of clinical events is shown in p = 0.003), TnI at T0 was not different between patients with and without clinical events.Clinical and echocardiographic characteristics of patients with and without clinical events are reported in p = 0.015). In addition to LVR, multivariable Cox analysis included %SAS and peak of TnI and LVR were associated with occurrence of clinical events during follow-up, while peak of TnI was not .Baseline variables associated with clinical events in univariable Cox analysis are reported in nsidered , model 1As regards the intraobserver variability of %SAS calculation, the ICC was 0.993, bias \u22120.2%, and LOAs 5.4 and \u22125.9%; as regards the interobserver variability, the ICC was 0.975, bias \u22120.1%, and LOAs 8.7 and \u22129.9%.This study explored, in patients treated for STEMI, the association between acute echocardiographic measures of LV systolic function and LVR (primary endpoint) and clinical events during follow-up (secondary endpoint). The main findings were: (1) in patients treated for STEMI, acute %SAS was associated with LVR; (2) this association was not observed for conventional echocardiographic measures of global LV function in the multivariable analysis, while it was observed for peak of TnI; (3) acute %SAS was also associated with an unfavorable clinical outcome, while peak of TnI was not; (4) a significant proportion (43%) of patients with LVR at 12 months did not have LVR at 3 months; (5) LVR at its first occurrence was associated with clinical outcome. All of these findings have implications for the acute evaluation and follow-up strategy of patients who experience a STEMI.Investigations performed in the decade between 1996 and 2006 reported a rate of LVR of 16\u201331% between 6 and 12 months after revascularized acute STEMI ,9,10. MoWe observed a percentage of LVR of 10.2% at 3 months and 15.8% at 1 year. In our opinion, this lower LVR prevalence compared to previous studies could be related to the effectiveness of contemporary STEMI treatments . On the other hand, the persistence of a significant number of patients with LVR also evidences that development of post-infarct LVR is still affected by determinants not fully controlled by current therapeutic strategies .In our patients, LVR was significantly associated with an unfavorable clinical outcome in univariable and multivariable analysis. This confirms previous observations ,14 and uVarious echocardiographic measures of LV global systolic function, including LV-EF, ESV, WMSI and GLS, have been proposed over the years to predict, during the early phase of STEMI, subsequent development of LVR or outcome ,6,15,16.In our study, LV-EF, ESV, and WMSI were not associated with LVR. GLS was significantly associated with LVR only when %SAS was not included in the multivariable analysis . A possiA different approach to prediction of LVR is the evaluation of regional LV systolic function. This approach has been shown to predict LVR in previous investigations based on conventional and STE Of note, in LVR patients, the baseline %SAS was high (54% on average). This could be related to the very early evaluation of %SAS in the acute phase of STEMI, when infarct size is still far from stabilization. Additionally, because a larger acute infarct size is associated with the presence of microvascular obstruction , the higp = 0.483; In our patient cohort, peak of TnI was also significantly and independently associated with LVR. This finding agrees with that of other authors, showing that patients with LVR after STEMI were characterized by higher levels of peak TnI . The assFirst, multiple Tn assays are needed after the STEMI diagnosis to identify the peak value of Tn, whereas %SAS is a single evaluation, and this may facilitate very early prediction of LVR. Second, the correlation between serum Tn after STEMI and infarct size is impaired in case of slow or incomplete reperfusion and renal insufficiency, which delay peak of Tn , while kIn our patient cohort, %SAS progressively decreased over time after the acute STEMI, with a parallel increase in GLS . This isIn our investigation, the %SAS decrease occurred both in patients with and without LVR, but in those with LVR, the magnitude of reduction was much less . This caFinally, in LVR patients, the median %SAS at 12 months was 12%. This represents the residual infarct size, that is, the non-viable myocardium with transmural scar tissue .The %SAS is an objective measure of regional LV systolic function. This is an advantage compared to other parameters, such as WMSI and %WMA, based on visual interpretation of myocardial contraction. Further, calculation of %SAS is simple and relatively fast with current echocardiographic technology. In fact, the number of segments with severe alteration of strain can be easily obtained just by looking at the LV polar plot automatically provided by the echo scanner .This study was a single-center investigation. This implies a limited number of STEMI patients but had the advantage of a homogeneous approach to treatment and follow-up strategy. In general, patients transferred rapidly after primary PCI to the other hospitals of the STEMI network were clinically more stable or had less residual coronary disease needing deferred PCI. This may have introduced a bias at baseline selection of the patient cohort, but it could not be avoided in a STEMI network organization. Although patients with previous MI were not excluded, they were not significantly different in the LVR and non-LVR subgroups. Because our study did not include cardiac magnetic resonance, we were unable to determine the direct influence of microvascular obstruction and presence of myocardial hemorrhage on LVR. Myocardial strain evaluation was performed using echo scanners of a single vendor; because inter-vendor strain calibration is still lacking ,32, studIn patients treated for STEMI, acute %SAS is significantly and independently associated with development of LVR within 1 year and is better than other echocardiographic LVR predictors; acute %SAS is also associated with unfavorable clinical outcome. Thus, assessment of %SAS after primary PCI could be a helpful routine evaluation to identify very early those STEMI patients at higher risk. Prospective multicenter studies on a wider cohort of STEMI patients are needed to confirm our observations."} +{"text": "Background: During this pandemic, the public has struggled to navigate the abundance of COVID-19 vaccine misinformation, and it is unclear how this misinformation has affected medical providers and their recommendations for patients. We sought to understand differences in COVID-19 vaccine knowledge, beliefs, and attitudes among Oregon healthcare provider types and regions of practice . Methods: A 36-question survey was constructed using Qualtrics with consultation from a survey methodologist. The survey was reviewed and approved by OHSU IRB and distributed via listserv or social media posting to provider societies in Oregon, including nurse practitioners (NPs), naturopathic doctors (NDs), physician assistants (PAs), doctors of medicine (MDs), doctors of osteopathic medicine (DOs), or practioners with a bachelor of medicine\u2013bachelor of surgery (MBBS), and via the Oregon Health Authority (OHA) immunization practice listserv. The survey accepted responses from July 9 to August 12, 2021. Participants were volunteers and responses were anonymous. Results: We collected 101 responses. Among them, 87 participants completed 100% of survey questions. Survey respondents were predominantly White females aged 41\u201350 years with an MD, DO, or MBBS. The overall COVID-19 vaccination rate of respondents was 94.6%. The vaccination rate was highest among the 4 NDs and 7 PAs at 100%, followed by 78 MDs, DOs, and MBBSs at 96.2%, and 12 NPs at 75%. Of NP respondents, 67% practiced rurally; 25.6% of MDs, DOs, and MBBSs practiced rurally; and 25% of NDs and 28.6% of PAs practiced rurally. In total, 22% of NPs did not feel comfortable recommending the COVID-19 vaccine to patients, compared to 1% of MDs, DOs, and MBBSs and 0% of NDs or PAs. All provider types had high rates of disagreement with the statement that the COVID-19 pandemic had increased their trust in vaccine safety: 44% of NPs; 29% of PAs; 25% of NDs; and 7% of MDs, DOs, and MBBSs. Among 19 rural providers, 19% indicated mistrust in public health to ensure that vaccines are safe versus 3% in suburban areas and 0% in urban areas. Conclusions: COVID-19 vaccine hesitancy is prevalent among healthcare providers and may be higher in NPs and those practicing rurally. Unfortunately, the response rate of NPs was low. Future research should focus on these providers to better understand their knowledge, beliefs, and attitudes about COVID-19 vaccines. These results can also inform future targeted vaccine education to healthcare providers during public health crises.Funding: NoneDisclosures: None"} +{"text": "Despite its importance in guiding public health decisions, studies on COVID-19 vaccination acceptance and its determinants in South East Asia (SEA) are lacking. Therefore, this study aims to determine the prevalence of COVID-19 vaccine acceptance and the variables influencing the vaccine\u2019s acceptance. This review is registered under PROSPERO CRD42022352198. We included studies that reported vaccination acceptance from all SEA countries, utilising five academic databases , three Indonesian databases , two pre-print databases (MedRxiv and BioRxiv), and two Thailand databases . The analysis was conducted using STATA 17.0 with metaprop commands. The prevalence for COVID-19 vaccination acceptance in SEA was 71% . Myanmar achieved the highest COVID-19 vaccination acceptance prevalence, with 86% (95%CI 84\u201389), followed by Vietnam with 82% and Malaysia with 78% . None of the ten determinants studied were significantly associated with acceptance. This result will be useful in guiding vaccination uptake in SEA. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a strain that caused coronavirus disease in 2019 (COVID-19), was discovered almost three years ago, and it is still causing a pandemic worldwide ,4,5,6 anNumerous medical treatments have been proposed to combat COVID-19 ,12, yet A vaccine can only be successful if it is administered adequately in a population. However, due to misinformation and misunderstandings, COVID-19 vaccination hesitancy or outright refusal rose and impeded COVID-19 vaccination ,21. It hVaccine acceptance, hesitancy, and refusal are described as a state of a continuum with complex interplay and variables involved that influence them. Contextual determinants , individual determinants , organisational determinants are some of the factors that affect vaccine hesitancy and refusal . The reaHowever, numerous pieces of literature do not seem to agree on what determinants influence vaccine acceptance. Numerous pieces of literature mention age, previous history of COVID-19 infection, hospitalisation due to COVID-19, belief in the safety and efficacy of COVID-19 vaccination, jobs, body mass index, knowledge, education status, marital status, possessing health insurance, sex, having chronic conditions, and living together as determinants that affect COVID-19 vaccine acceptance. Nonetheless, the results are conflicting, with one study mentioning the positive impact of one determinant while other studies will find an opposite or null effect of that same determinant ,28,29,30Despite numerous meta-analyses studying the prevalence of COVID-19 vaccination acceptance, we could not identify a single one focusing on South East Asia (SEA) ,31,32,33With the non-existent studies focusing on SEA regarding COVID-19 vaccination acceptance and its determinants, despite its importance in guiding public health decisions, we decided to conduct a systematic review and meta-analysis. This study aims to determine the prevalence of COVID-19 vaccine acceptance, with a secondary aim of determining the variables that influence its acceptance.The authors adhered to The Preferred Reporting Items for Systematic Review (PRISMA) 2020 guidance . The proThe studied population consisted of everyone eligible for COVID-19 vaccination, including children and pregnant women. We included studies that reported vaccination acceptance. The primary outcome of this study is to calculate the point prevalence of COVID-19 vaccine acceptance in SEA countries. A sub-group analysis would be conducted according to types of paper , the timing of vaccine rollout relative to when the study was conducted, questionnaire type, whether the study was referring to COVID-19 vaccine boosters or not, sampling methodology, data collection method, quality of the study, and risk of bias. If studies were conducted in two different years , the year with more calendar days in which the study was conducted would be chosen\u2014The readiness to receive vaccinations, acceptability of a vaccine, desirability, demand, and favourable sentiments regarding the administered vaccines are all definitions of vaccine acceptance used in this meta-analysis . The incThe literature search started on 25 August 2022 and ended on the same day. We searched five academic databases: Pubmed, MEDLINE, Cochrane Library, Science Direct, and Google Scholar. Three Indonesian-specific databases were also utilised in order to increase literature saturation: the Indonesian Scientific Journal Database (ISJD), Neliti, and Indonesia One Search. Medrxiv and Biorxiv were scoured for grey literature that was not peer-reviewed yet. Studies from these two databases were searched for the peer-reviewed version before confirming the grey literature status. Two Thailand-specific academic databases, ThaiJo and Thai-Journal Citation Index, were also utilised. The search was conducted using English and Bahasa Indonesia. The keywords used were related to COVID-19 , vaccine stances , and countries . The Medical Subject Heading (MeSH) terms for each database can be seen in Data extraction was carried out independently by two authors separately (GSO and LRYH), and then reviewed by the third author (CV) in order to ensure accuracy. We extracted relevant information such as study identification (author and year of publication), study characteristics , and vaccine acceptance rate . When studies used different theoretical vaccine efficacy to determine vaccine acceptance, we chose those with the highest suggested vaccine efficacy in each study. However, one study had a 100% vaccine acceptance rate with 80% vaccine efficacy; therefore, we opted for the second-highest theoretical vaccine efficacy level .The Newcastle\u2013Ottawa scale (NOS) for cross-sectional studies was implemented in order to assess the quality of the studies. A score of 7\u20139 on NOS implied the study indicated a good quality, 4\u20136 indicated a moderate or fair quality, and a score of 0\u20133 meant that the study had poor quality . If one We computed the point prevalence by dividing the number of respondents who identified themselves as vaccine accepting by the total number of subjects in that study . The anaWe identified 173,361 manuscripts, and 1826 of these articles were duplicates. A total of 166,749 records were eliminated after the title and abstract assessment, with 4786 articles sought for a full assessment. A total of 71 articles were included in the analysis. We also found 40 articles from citation-searching and hand-searching, which resulted in an additional 38 datasets. In total, 109 studies were available for systematic review and meta-analysis . The NOSThere were 1,166,275 respondents included in this review, and 798,850 respondents identified themselves as COVID-19 vaccine acceptors. There were a total of 135 datasets, with Malaysia contributing the most datasets (n = 26), followed by Indonesia, with 25, and Thailand, with 22. There was only one study in Brunei Darussalam, while no studies were found in Cambodia. There were 111 datasets published in peer-review journals, while 24 were published in grey literature, such as websites, government documents, or posters .Most datasets published came from studies which were conducted before the vaccine rollout (n = 71) and studied the first two vaccine shots (n = 126). The majority used a non-probability (n = 106) sampling methodology, and 118 datasets were obtained with questionnaires that were not administered directly by researchers. Many datasets had good NOS (n = 67) and JBI (n = 70) scores.2 99.87%, PI: 68.6\u201373.5). Myanmar achieved the highest COVID-19 vaccination acceptance prevalence, with 86% (95%CI 84\u201389), followed by Vietnam with 82% and Malaysia with 78% . Brunei Darussalam only achieved 59% (95%CI 59\u201359), the lowest prevalence of COVID-19 vaccine acceptance amongst other SEA countries in 2020 to 71% (95% CI 68\u201374) in 2021, and plunged to 56% (95%CI 45\u201368) in 2022. Singapore is the only country with an upward trend of COVID-19 vaccine acceptance (65% [95%CI 42\u201388] in 2020 to 69% [95%CI 59\u201379] in 2021). Malaysia showed an initial 4% upward trend of COVID-19 vaccine acceptance between 2020\u20132021, before the acceptance rate fell to just 43% (95%CI 40\u201346) in 2022 . StudiesSubgroup analysis of prevalence was conducted amongst types of papers, with a higher prevalence amongst studies published in peer-reviewed journals compared to grey literature, with 65% (95%CI 60\u201370). When the type of vaccination (booster or not booster) was assessed, the prevalence was higher amongst non-booster vaccines, with 72% acceptance (95%CI 70\u201374). Vaccine acceptance was also higher amongst studies conducted before vaccine rollout , using mixed-methods sampling , questionnaires not administered by researchers , as well as in studies with moderate NOS criteria and moderate JBI risk . Studies using the Likert scale yielded the same vaccination acceptance rate as those using yes or no questions .Having chronic diseases , being iThe COVID-19 vaccination rate in SEA countries is 71%. This number is lower compared to one meta-analysis, which discovered a vaccination acceptance rate of 70% in Europe (30 studies) and 74.6% in Asia (10 studies) . AnotherSallam concluded in his meta-analysis that Malaysia (94.3%) and Indonesia (93.3%) had the highest COVID-19 vaccination acceptance in the world . Their dVietnam achieves the second-highest COVID-19 vaccination acceptance prevalence, at 82%. It is well known that Vietnam is a model success story regarding COVID-19 vaccination uptake . The Wor\u00ae controversy. This event shows that once the public hesitates about vaccines, it becomes a mountainous challenge to win back the public\u2019s trust and confidence in the vaccine vs. 62.5% completely vaccinated [CV]), Malaysia (78% VA vs. 81.9% CV), and Vietnam (82% VA vs. 85% CV). Some countries have large disparities, such as in Thailand (67% VA vs. 75% CV) and Singapore (68% VA vs. 92% CV) . Other vLastly, a sub-group analysis is a valuable tool for assessing the difference between the two groups, but it is not a confirmatory method that eliminates bias. Even though we have tried our best to assess the outcome according to variables that may affect the prevalence, we advise our readers to interpret these findings cautiously.2 index, the PI is narrow and within the confidence interval. The PI tells us what the results will be when future studies are conducted, which is more clinically useful. The I2 index does not generally represent heterogeneity per se, and PI represents heterogeneity better than the I2 index [There are, however, some strengths of our study. This meta-analysis is the first to study the prevalence of COVID-19 vaccine acceptance in South East Asia exclusively, yielding 125 datasets and 1,166,275 respondents. Aside from its large sample size, we also identified studies published in grey literature and included them in our meta-analysis. Although there are controversies surrounding grey literature, such as the fact that the quality of such publications tends to be lower compared to peer-reviewed journals, grey literature is an essential resource in systematic reviews . TherefoI2 index .The COVID-19 vaccination acceptance rate in SEA countries may not be adequate to achieve herd immunity. Although vaccine acceptance does not equal vaccine uptake, some of these rates translate to the current vaccination rate in some countries. Therefore, unless external forces such as government intervention or increasing access to COVID-19 vaccination are incorporated, the vaccination rate trajectory will slow down eventually .There is no single variable that is significantly associated with COVID-19 vaccination acceptance. In line with this finding, we agree that COVID-19 vaccination acceptance is influenced by many complex interplays of factors specific to a particular country or region due to differences in religion, culture, or beliefs . Researc"} +{"text": "Myocarditis is a challenging diagnosis due to the heterogeneity of clinical presentations. Myocarditis can present with a mildly raised cardiac enzyme to severe myocarditis leading to congestive heart failure, arrhythmias, cardiogenic shock, and death. It is a predictor of morbidity and mortality in dengue-infected patients. The exact prevalence of dengue myocarditis and its outcomes are unknown in Pakistan.We aim to study the prevalence and association of myocarditis with the length of stay in the hospital and mortality of dengue-infected patients.A retrospective observational study done at a tertiary care hospital. We reviewed hospital record files of 1008 consecutive patients with dengue viral infection admitted from November 2018 to November 2019.Out of 1008 dengue-infected patients, 55.4% of patients were older than 35 years and 68.4% were males. Hypertension (HTN) was the most common comorbid condition. The prevalence of myocarditis in hospitalized dengue-infected patients was 4.2%. All (100%) of dengue myocarditis patients had raised cardiac troponin I (cTn-I), 59.5% of patients had at least one electrocardiography (ECG) change, and 24% had reduced ejection fraction (EF) (defined as EF < 55%). On multivariable analysis, patients with raised cTn-I levels : 2.16\u201312.96]) and abnormal echocardiography (ECHO) had a prolonged hospital stay (>3 days). Raised cTn-I levels was significantly associated with in-hospital mortality.Raised cTn-I is the predictor of length of stay and in-hospital mortality in dengue-infected patients. Atrial fibrillation, diabetes mellitus, hypertension, low serum bicarbonate, high serum creatinine, and any abnormality on echocardiography were associated with adverse outcomes in dengue-infected patients. Viral illnesses are frequently complicated by cardiovascular manifestations such as arrhythmia, myocarditis, and myocardial injury. Dengue fever is known to be associated with myocarditis. The complex interplay of pro-inflammatory cytokines, T-cell activation, and release of vasoactive substances and vascular injury leads to increased vessel wall permeability and capillary leakage. Consequently, there is a reduction in effective preload and myocardial tissue edema. This leads to a variety of cardiac manifestations of dengue fever ranging from an asymptomatic elevation of cardiac enzymes to cardiogenic shock and, arrhythmias .Cardiac manifestations of Dengue fever can present with a mildly raised cardiac enzyme to severe myocarditis leading to congestive heart failure, arrhythmias, cardiogenic shock, and death 3. CardiaThe definitive diagnosis of myocarditis depends on an endomyocardial biopsy. However, the clinically suspected diagnosis is based on history, clinical examination, and biochemical and radiological profile. The European Society of Cardiology (ESC) 2013 consensus statement suggested the presence of at least one clinical and one diagnostic criterion for the diagnosis of clinically suspected myocarditis. Clinical criteria include acute new-onset, or worsening dyspnea, palpitations, and/or unexplained shock. The diagnostic criteria include ECG or Holter changes, raised cardiac biomarkers, functional and structural abnormalities on cardiac imaging, and tissue characterization on cardiac magnetic resonance (CMR) imaging 6.The exact prevalence of dengue myocarditis is unknown. It is essential to recognize the burden of cardiac manifestations in dengue fever. There is a need for preparedness at the physician\u2019s end for early recognition and prompt management for patients with dengue fever being complicated by cardiovascular manifestations. Additionally, determining prognostic factors is essential for the risk stratification of patients. With dengue fever continuing to be a major health care concern, more studies are needed to predict in-hospital outcomes and mortality. In this retrospective study, we looked at the prevalence and outcomes of myocarditis in hospitalized patients admitted with dengue fever.It was a retrospective observational study done at the Aga Khan University hospital which is a 700-bedded multidisciplinary tertiary care hospital, located in the largest city of Pakistan. All patients (age more than 18 years) admitted with a clinical diagnosis of dengue viral infection from November 2018 to November 2019, were enrolled in the study. Data was retrieved from the electronic medical record system of the hospital. A positive dengue antigen or anti-dengue immunoglobulin M (IgM) assay was used as the inclusion criteria with patient\u2019s LOS beyond three days persisted in the adjusted model and became stronger relative to the bivariate analysis as shown in After adjusting the results of multivariable analysis for age, gender, platelet count, echo findings, and DM, the result demonstrated a statistically significant association of raised cTn-I , echocardiographic abnormality and female gender with increased in-hospital mortality as shown in There are several predictors of outcomes in dengue fever, such as extremes of age, hypertension, diabetes mellitus, nutrition status, and superadded infections . In addiOur study showed a myocarditis prevalence of 4.2%. Majumdar et al. estimated the prevalence of myocarditis in 300 dengue patients during an epidemic and found it to be 20% . During In our study, 100% of dengue myocarditis patients had raised cTn-I, 59.5% of patients had at least one ECG change, and 24% had reduced EF (defined as EF < 55%). In the characterization of 201 dengue myocarditis patients in China, Yingying et al. demonstrated that 24% had positive cardiac biomarkers, 8.63% had echocardiographic changes, 8.46% had ECG changes, 22.58% had both positive cardiac biomarkers and echocardiographic changes, and 21% had both positive cardiac biomarkers and ECG changes .ECG abnormalities can be frequently encountered in viral fever. This can include a variety of arrhythmias such as heart block, ectopic beats, and incessant tachyarrhythmias 1314. The13In our study, fever was the most common clinical presentation in dengue myocarditis patients (85.7%), followed by fatigue (78.6%), dyspnea (42.9%), and hypotension (28.6%), palpitation (9.5%) and syncope (2.4%). Cardiogenic shock was present in 9.5% of our myocarditis patients. In a cohort of 128 dengue-infected patients admitted to a multidisciplinary hospital in Pakistan, the prevalence of dengue myocarditis was 18.75% (24 out of 128 dengue patients). In this cohort of dengue myocarditis patients, fever (100%), dyspnea (100%), and fatigue (100%) were the most common clinical features on presentation. All patients had raised cardiac biomarkers, globally reduced ejection fraction, and hypotension. The shock was classified as cardiogenic in 19.67% of patients. This cohort carried a very high in-hospital mortality (83.3%). Sinus tachycardia (87.5%) was the most common ECG finding followed by atrial fibrillation (8.3%) and ventricular ectopic (4.1%) .In our study, 24% of dengue myocarditis patients had reduced EF (defined as EF less than 55%). The mean EF was 50.8% (range from 15% to 55%). Sengupta et al. studied 2D speckle tracking echocardiograms of patients with dengue hemorrhagic fever (DHF) and compared them to control. It was found that patients with DHF had lower EF and significantly attenuated subendocardial peak longitudinal strain. Lower strain predicted LOS of DHF patients . AdditioPrognostic outcomes in myocarditis due to any reason include gender, cardiac enzymes level, NYHA class, and creatinine clearance or incidence of acute kidney injury . Dengue Our study is not free of limitations. It is a retrospective observational study, conducted in a single center and the sample size is small which may not represent the whole Pakistani population. There is no long-term follow-up. We suggest prospective randomized studies to predict the long-term outcomes of Dengue myocarditis patients in our region.Dengue fever complicated by myocarditis has prognostic implications. Physicians should be cognizant of the chances of higher mortality and prolonged hospital stay in patients presenting with dengue fever and any degree of myocarditis. This further helps identify patients who would require telemetry monitoring and in-hospital cardiology consultation.The additional file for this article can be found as follows:10.5334/gh.1129.s1Dataset."} +{"text": "Among aAmong adults aged \u226518 years interviewed during November\u2013December 2022, 84.2% had completed a COVID-19 primary series, and 23.2% were up to date with COVID-19 vaccination . Among ahttps://stacks.cdc.gov/view/cdc/124394). Among adults who were open to or unsure about booster vaccination, 41.1% and 28.7%, respectively, received a provider recommendation for booster vaccination , and 83.1% and 54.5% of adults, respectively, were confident about COVID-19 vaccination safety and unsure about booster vaccination (6.6%) reporting difficulty than did those who were already vaccinated (3.6%) . The mosoncerns) . Among aFrom interviews conducted during November\u2013December 2022, approximately 20% of adolescents aged 12\u201317 years and approximately 30% of adults who had completed a primary COVID-19 vaccination series had received a bivalent booster dose since it was recommended on September 1, 2022. However, a large percentage of adults and parents of adolescents reported intent to receive booster vaccination for themselves or their children, indicating that booster vaccination coverage could substantially increase with appropriate interventions tailored to these reachable populations.,Reduction in disparities in completion of primary COVID-19 vaccination by race and ethnicity likely contributed to a reduction in the disparities in COVID-19 age-adjusted mortality rates that were observed early in the pandemic . Although survey weights were calibrated to COVID-19 vaccine administration data to mitigate possible bias from incomplete sampling frame, nonresponse, and misclassification of vaccination status, bias in estimates might remain after weighting. Second, COVID-19 vaccination was self-reported and might be subject to recall or social desirability bias. Third, respondents were not specifically asked about bivalent boosters, and all boosters received after September 1, 2022, were assumed to be bivalent boosters, which might have overestimated bivalent booster coverage if some persons had received a monovalent booster after September 1, 2022. Finally, the survey sampled noninstitutionalized U.S. adults via mobile telephone; therefore, adults who were incarcerated or nursing home residents might not be represented in the sample.,A large proportion of persons who have completed a primary COVID-19 vaccination series have not received the bivalent booster but are open to vaccination or have parents who are open to getting a booster vaccination for their child. Ongoing monitoring of intent to receive a booster vaccination (or to have one\u2019s child vaccinated with the booster vaccine), barriers to vaccination, and differences in bivalent booster vaccination coverage by demographic factors will be helpful for improving and expanding tailored strategies to improve vaccination coverage. To improve coverage, communities should partner with medical providers, schools, and community organizations to administer bivalent booster vaccination onsite or provide a referral for vaccination, reduce barriers to receipt of vaccination, employ trusted messengers to discuss vaccine safety and effectiveness with adults or parents and guardians of adolescents, and emphasize the importance of staying up to date with their COVID-19 vaccination (COVID-19 bivalent booster vaccination has been recommended for persons aged \u226512 years since September 1, 2022.Based on interviews conducted during November\u2013December 2022, only 27.1% of adults and 18.5% of adolescents who had completed a COVID-19 primary series received a bivalent booster, and coverage was lower among Black and Hispanic persons. An additional 39.4% of adults were open to booster vaccination, and an additional 52.0% of adolescents had parents who were open to booster vaccination for their children. Those in rural areas had much lower primary series completion rate and up-to-date vaccination coverage.Health care provider recommendations for booster vaccination, dissemination of information about the safety of vaccine by trusted messengers, and reducing barriers to vaccination could improve COVID-19 booster vaccination coverage."} +{"text": "I2 = 100%). The actual uptake of the booster dose in eight studies involving 12,995 subjects was 31% , while the intention to have the booster dose of the vaccine was 79% . The acceptance of the booster dose of COVID-19 vaccines among HCWs was 66% (95% CI: 58\u201374%), I2 = 99%). Meta-regression revealed that previous COVID-19 infection was associated with a lower intention to have the booster dose. Conversely, previous COVID-19 infection was associated with a significantly higher level of booster dose actual uptake. The pooled booster dose acceptance in the WHO region of the Americas, which did not include any actual vaccination, was 77% . The pooled acceptance of the booster dose in the Western Pacific was 89% , followed by the European region: 86% , the Eastern Mediterranean region: 59% , and the Southeast Asian region: 52% . Having chronic disease and trust in the vaccine effectiveness were the significant predictors of booster dose COVID-19 vaccine acceptance. The global acceptance rate of COVID-19 booster vaccine is high, but the rates vary by region. To achieve herd immunity for the disease, a high level of vaccination acceptance is required. Intensive vaccination campaigns and programs are still needed around the world to raise public awareness regarding the importance of accepting COVID-19 vaccines needed for proper control of the pandemic.The World Health Organization (WHO) recommended coronavirus disease 2019 (COVID-19) booster dose vaccination after completing the primary vaccination series for individuals \u226518 years and most-at-risk populations. This study aimed to estimate the pooled proportion of COVID-19 vaccine booster dose uptake and intention to get the booster dose among general populations and healthcare workers (HCWs). We searched PsycINFO, Scopus, EBSCO, MEDLINE Central/PubMed, ProQuest, SciELO, SAGE, Web of Science, Google Scholar, and ScienceDirect according to PRISMA guidelines. From a total of 1079 screened records, 50 studies were extracted. Meta-analysis was conducted using 48 high-quality studies according to the Newcastle-Ottawa Scale quality assessment tool. Using the 48 included studies, the pooled proportion of COVID-19 vaccine booster dose acceptance among 198,831 subjects was 81% : 75\u201385%, Coronavirus disease 2019 (COVID-19) is a highly communicable infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,4,5. As Despite the timely development of effective and safe COVID-19 vaccines, hesitancy to get vaccinated emerged as a major hindrance to preventive efforts ,9,10. InCurrently, the WHO recommends that individuals aged 18 years or older have a booster dose of COVID-19 vaccines 4\u20136 months following the completion of the primary vaccination series . As of 8It has been shown that the prevalence of the behavioral intention to receive a COVID-19 booster dose among the general population is variable in different countries with a range of 62\u201367% in the U.S., 67\u201371% in Poland, and 94% in China ,26,27. MThe current systematic review and meta-analysis aimed to address the acceptance of the general population of the booster dose of COVID-19 vaccination and to identify its associated determinants. Through identifying the main predictors of booster dose vaccine acceptance, public health authorities could be able to increase the acceptance and uptake rates of booster doses, resulting in higher vaccination coverage and population immunity with proper control of the ongoing COVID-19 pandemic.The primary study measure was the estimation of the pooled proportion of COVID-19 vaccine booster dose acceptance and actual uptake. Acceptance of the booster dose of COVID-19 vaccination was defined as the willingness to receive the vaccine as opposed to vaccine reluctance or rejection.The secondary study measures included: (1) identification of the determinants of COVID-19 vaccine booster dose acceptance; (2) assessment of COVID-19 vaccine booster dose vaccine acceptance among healthcare workers (HCWs); and (3) evaluation of the differences in COVID-19 booster dose vaccine acceptance across different WHO regions.This meta-analysis was guided by the 2020 Cochrane Handbook of Systematic Review and Meta-Analysis, with respect to the preferred reporting items of the systematic review and meta-analysis (PRISMA) checklist ,30. To aAll studies reporting the acceptance of a COVID-19 vaccine booster dose were included with no language restriction or vaccine-type restriction. Abstract-only papers, proposals, conference proceedings, editorials, author responses, reviews, case reports, case series, books, and duplicate records were excluded.https://docs.google.com/spreadsheets/d/1PyffvdDMqXJuzgy4T6WSIl3qJ1Uyf748/edit?usp=sharing&ouid=104751321858570795359&rtpof=true&sd=true (accessed on 9 October 2022) [The PRISMA flow chart for the different steps of the current meta-analysis is depicted in er 2022) .I2) was used to assess and measure heterogeneity between studies [0% to 40%: might not be important;30% to 60%: may represent moderate heterogeneity;50% to 90%: may represent substantial heterogeneity;75% to 100%: considerable heterogeneity.Cochrane\u2019s Q test was based on the Newcastle-Ottawa Scale quality assessment tool customized for cross-sectional and cohort studies . The quaThe statistical analyses were conducted using the R 4.2.1 software . Due to the heterogeneity between the studies, a random effect model was used for illustrating the pooled proportion of booster dose COVID-19 vaccine acceptance. To explain the statistical heterogeneity between the included studies, meta-regression analysis was conducted. Sensitivity analysis was performed using leave-one-out analysis to identify the influential studies and to recalculate the pooled proportion a number of times, removing an influential study at each time .Subgroup analysis was conducted for the assessment of total COVID-19 booster dose vaccine acceptance among different WHO regions and among HCWs based on the intention to get a booster dose of the vaccine and the actual booster dose vaccination uptake .The primary search using the aforementioned databases identified 1079 records, from which 949 studies were screened using the title and abstract, after excluding 130 duplicates by the EndNote X8 software. We excluded 613 irrelevant studies (those that did not report COVID-19 vaccine booster dose acceptance or uptake), 13 review articles, and 250 duplicates that were detected manually during title and abstract screening. After full-text screening, 1 unavailable citation was excluded, and 28 articles were irrelevant. Then, 44 articles were eligible for data extraction in addition to 6 records found through manual search and track citations. After QA, 2 studies were excluded because of their unsatisfactory score ,35. FinaOut of the 50 included studies, 32 were published in 2022, while 18 were published in 2021. The total number of participants among the 50 included studies was 194,410 subjects from 23 different counties across 6 WHO regions, with only 1 study conducted across 2 different regions . Most stp = 0.670) and the funnel plot, which did not indicate the presence of funnel plot asymmetry . The highest acceptance rate was 98% (95% CI: 97\u201398%) [The pooled proportion of COVID-19 vaccine booster dose acceptance for the eligible 48 studies with 193,831 participants was 81% , while t 97\u201398%) ,61,66,73I2 = 100%), ranging from 2% (95% CI: 2\u20133%) [2 = 0.46 (SE = 0.48). The most fitted model revealed that previous COVID-19 infection increases the actual booster dose acceptance significantly: 0.002 ; being employed: \u22122.27 ; vaccine type: \u22122 ; and large sample size greater than 1000 having a significant negative effect on the actual vaccination: \u22121.49 . Being HCWs and the study setting in a high-income country had no significant effect on the uptake of the booster dose: \u22120.31 and 1.28 , respectively.The attitude of 12,995 participants included in 8 studies was analyzed. The pooled proportion of the actual uptake of a COVID-19 vaccine booster dose was 31% to 74% (I: 2\u20133%) , ranging between 23% (95% CI: 21\u201324%) [2 = 0.749 (SE = 0.293). The most fitted model revealed that previous COVID-19 infection decreased the intention for booster dose: \u22120.001 ; being employed increased the intention for booster dose vaccine acceptance: 0.800 ; being HCWs had no significant effect on the intention for booster dose: 0.018 ; and the study setting in the Western Pacific region increased the intention to receive the vaccine booster dose: 2.23 ; nevertheless, the studies conducted in the Americas, Europe, Eastern Mediterranean region, or Southeast Asia did not show such an effect: 1.25 , 1.52 , 0.86 , and 0.35 , respectively.Of the 190,609 participants included in 45 studies, the pooled proportion of intentional booster dose vaccine acceptance was 79% and 97% 21\u201324%) ranging from 36% (95% CI: 31\u201342%) [Among the 15 studies that included HCW participants, 13,420 HCWs were asked about their attitude towards booster dose, but only 13 studies with 12,616 HCWs reported the acceptance proportion among HCWs. The pooled proportion of COVID-19 vaccine booster dose acceptance among HCWs was 66% to 90% ( 31\u201342%) , while the pooled estimation of actual booster dose vaccination was 69% , \u22121.23 , and \u22121.75 , respectively. A study setting in the Americas, Eastern Mediterranean region, or Western Pacific region had a statistically significant effect on booster dose acceptance among HCWs: 3.86 , 4.19 , and 3.48 , respectively. The European region as a study region, being fully vaccinated, and employment had no statistically significant effect on booster dose acceptance among HCWs: 1.95 , 0.54 , and 0.31 , respectively.The meta-regression for the pooled proportion of COVID-19 vaccine booster dose acceptance among HCWs, including the actual vaccination and intention to be vaccinated, explained 52.47% of the result. This meta-regression revealed that previous COVID-19 infection, large sample size greater than 1000 participants, and high-income country as the study setting had a significant effect on booster dose acceptance among the HCWs: 0.001 , ranging from 93% (95% CI: 90\u201395%) [The pooled acceptance of booster COVID-19 vaccination in the Americas Region, which did not include any actual uptake of booster doses, was 77% to 41% ( 90\u201395%) , ranging from 97% (95% CI: 95\u201399%) [The pooled acceptance of booster dose COVID-19 vaccination in the European region was 86% to 62% ( 95\u201399%) , while the intention to receive the booster dose in the European region was 79% .The subgroup analysis for the European region revealed that actual vaccination was 25% , ranging from 94% [The pooled acceptance of the COVID-19 booster dose of the vaccine in the Western Pacific region was 89% , ranging from 71% (95% CI: 69\u201373%) [The acceptance of booster COVID-19 vaccination in the Eastern Mediterranean region was 59% to 43% ( 69\u201373%) , and the subgroup revealed that the actual vaccination was 28% (95% CI: 8\u201366%), while the intention to have the booster dose, as reported in a single study, was 41% (95% CI: 39\u201343%). A single study reported the actual and intentional acceptance of the booster dose of COVID-19 vaccination in the African region and 6548 . This rate was higher compared with the recent and earlier estimates of COVID-19 vaccine acceptance, which ranged from 60% to 75% in various meta-analyses ,94. ThisThe intention to accept a COVID-19 vaccine booster dose as estimated in this review was 79% (95% CI: 72\u201385%), while the actual booster dose vaccine uptake was 31% (95% CI: 19\u201346%). This observed disparity can also be linked to the timing of the studies included, where booster vaccination was not widely available, as well as the prioritization of high-risk groups. In this review, the acceptance of a booster dose among HCWs was 66% (95% CI: 58\u201374%), which is in line with the previous pooled estimates among health professionals worldwide . FurtherIn this review, the pooled acceptance of booster dose vaccination in the Americas, which did not include any actual uptake of booster vaccination, was 77% (95% CI: 66\u201385%). Higher rates of booster dose acceptance were reported in the Western Pacific and in the European region . On the other hand, the lowest rates were reported in the Eastern Mediterranean region and the Southeast Asian region . Thus, the high rates of COVID-19 vaccine hesitancy in the Middle East, which was shown previously, extended to involve hesitancy to booster doses as well .The regional variability in COVID-19 booster dose vaccination can be attributed to the issues of vaccine equity and the implementation of different vaccine mandates . SeveralA noteworthy finding of the current review was the scarcity of reports addressing COVID-19 booster dose vaccine acceptance in the African region. Besides the issue of vaccine equity and vaccination hesitancy that hinder the successful implementation of vaccination campaigns in the continents, lack of studies can be considered another obstacle that should be addressed urgently ,103,104.It was worthy to note that the overall acceptance rate of booster doses of COVID-19 vaccination was relatively high. However, the actual acceptance rate was relatively below the intentional acceptance rates. A potential explanation of this high acceptance rate is perceived safety of the currently available vaccines and perceived severity of COVID-19. In addition, the increase in trust in health authorities over the world can effectively affect the acceptance of vaccination . A recenTo the best of our knowledge, our review is among the earliest and largest reviews to systematically assess COVID-19 vaccine booster dose acceptance at this scale involving the general public and health professionals; thus, we compared our findings with meta-analyses on vaccine acceptance. Our findings were higher than the results of previously published meta-analysis by Norhayati et al., which reported a pooled proportion of COVID-19 vaccine acceptance from 170 studies in 50 countries of 61% (95% CI: 59\u201364%) . A recenInterestingly, the acceptance rate of booster dose vaccination among HCWs was relatively lower than the average acceptance estimate. About one-third of HCWs were reluctant to receive booster doses. This finding is very crucial as HCWs play a key role in guiding local communities\u2019 attitudes toward vaccination . In addiIn a recent study by Dziedzic et al., nearly three-quarters of those polled preferred receiving COVID-19 vaccine booster doses, while 17.6% and 7.9% expressed rejection and uncertainty, respectively . In the In this study, the main identified predictors of booster dose acceptance were trust in vaccine effectiveness and the presence of a chronic disease among participants with increased vaccine acceptance linked to a history of a chronic disease. Such a result can be attributed to low levels of complacency among individuals with a chronic disease with high levels of perceived severity of COVID-19. Predictors such as age, gender, and fear of unknown adverse effects were insignificant predictors of booster dose acceptance.In the context of the included studies, having a chronic illness increased the odds ratio of booster dose vaccine acceptance by 1.4 in the Algerian population . LikewisThe acceptance rate of the COVID-19 vaccine across WHO regions varied significantly, being the highest in the Western Pacific and the lowest in the Southeast Asian region. The pooled proportion of COVID-19 vaccine acceptance ranged across WHO regions from 52% in Southwest Asia to 89% in the Western Pacific. On the other hand, Norhayati et al. found that the pooled proportion of COVID-19 vaccine acceptance was the highest in Southeast Asia at 74% and the lowest in the Eastern Mediterranean region at 52% , which wThe strengths of this review besides being the largest with such an aim and wide scope included: (1) the search was not limited to articles published in English, which may have allowed the generalizability of the review results. In addition, (2) we included studies with satisfactory, good, and very good quality of data based on the assessment of the risk of bias. Additionally, (3) we included preprints to increase the power of our study. Finally, (4) we searched many databases to find most, and possibly all, published studies addressing the acceptance and uptake of a booster dose of COVID-19 vaccines. The main limitation was that most of the records included in this review were cross-sectional studies, which can be thought of as snapshots of vaccine hesitancy status in each country/region. The included studies had different sampling strategies, variable survey instruments, and different assessment tools, which may explain some of the differences in vaccine acceptance rates reported in different studies from the same country. As a result, the findings should be regarded with caution, as these results cannot forecast future changes in vaccine acceptance rates.The global acceptance rate of COVID-19 booster dose vaccination was found to be relatively high; however, the intention to have a booster dose was higher compared with the actual uptake of the booster dose. The relatively low acceptance rate of booster doses among HCWs is an alarming finding that should be studied in future studies. There is an observed difference in booster dose acceptance rates across WHO regions, which may shed light on the issue of vaccine inequity, besides possible links to cultural and regional differences in vaccine acceptance. To sum up, in order to achieve herd immunity against COVID-19, a high level of vaccination acceptance is required. Many vaccination campaigns and programs are still needed around the world to raise public awareness and acceptance of COVID-19 vaccines, including booster doses. These campaigns should consider the issues of effective coordination, engaging the public, and focusing on the safety and efficacy of the currently available vaccines ,114. In"} +{"text": "Periorbital infections lead to severe condition of the orbital abscess, and eventually to sight loss, and even death. Current study aims in reviewing the literature regarding orbital abscess in adult patients and presenting 2 original cases. A surgical intervention to drain the abscess and a revision of the orbital was required. A review of literature is also reported focusing on aetiology and treatment options dealing with an orbital abscess. Periorbital infections lead to severe condition of orbital abscess, and eventually to sight loss, and even death , 2. TheyIn 1970, Chandler et al. proposed the classification of orbital complications depending on its extention: I\u2014preseptal cellulitis; II\u2014orbital cellulitis; III\u2014subperiosteal abscess; IV\u2014orbital abscess; V\u2014cavernous sinus thrombosis . CurrentStreptococcus pyogenes susceptible to empirical therapy, Staphylococcus aureus, Staphylococcus epidermidis. The patient was discharged from the clinic on day 9 in good general condition. There were no visual disturbances in the left eye. The only permanent consequence was scarring of the facial skin after surgical access .The first literature case reports of orbital abscess originated in 1884 , 6. HoweOrbital abscess formation occur in 8% of patients with retroseptal orbital cellulitis .The most frequently encountered signs and symptoms include periorbital edema, restricted ocular movement, orbital pain, proptosis, periorbital erythrema, chemosis and vision deterioration\u2014Table Streptococcus spp. 49]. On tOcular ultrasonography provides immediate assessment of an orbit and opportunity to follow treatment outcomes without unnecessary exposure to radiation , 21. HowNumerous conditions present similar symptoms as orbital abscess, possibly misleading the diagnosis, for instance: neoplasms\u2014osteoma of the ethmoid sinus, , small cAccording to current review, surgical treatment was necessary in 94% of cases. Abscess drainage is achieved via multiple approaches depending on its localisation: transculuncular, lateral or anterior orbitotomy, Caldwell-Luc approach, intranasal endoscopy, needle aspiration guided by ulstrasound, lower eyelid incision, subcilliar incisio, incision in four quadrants of the orbit. If it is necessary, surgical debridement of necrotic tissues is performed, as well as enucleation or exenteration. Antibiotic therapy is both, initial and supplementary to surgical treatment. Only two cases resolved with alone antibiotics administration\u2014Table Complete recovery succeed in 49% of cases, whereas 11% of patients recovered with vision loss, 9% with vision deterioration, 6% with persistent movement restrictions, 3% with exenteration, 3% with enucleation, 3% with residual enophatomos, 3% with residual proptosis, and 3% with corneal scarring. Exact results were not presented in 14% of cases. Fortunately, any patient died in the investigated reports \u201328, 30,,30, 32\u2013, 42. TaTable 3St"} +{"text": "Resilience to stressors is a major component of biological aging and may mediate the onset of multimorbidity in older adults. The Wake Forest Non-Human Primate Radiation Survivor Cohort (RSC) provides a novel opportunity to study aging and resilience in 250 rhesus macaques (Macaca mulatta) with single-dose radiation exposures 0\u201315 years prior and 50 controls with semi-annual clinical, imaging, and biomarker measurements taken over their lifespan. Multimorbidity is extremely common among irradiated animals. Only 38% of animals have none of 20 common chronic diseases, falling to 16% of animals over age 8 and 11% over age 10 . 70% of animals have 5 or more diagnoses in this oldest cohort. The presence of any one disease increases the likelihood of having a second, co-morbid condition. Nevertheless, some animals continue disease-free until late in life, highlighting substantial variability in resilience. To identify patterns of multimorbidity, survival curves for each diagnosis were generated for age and time since radiation and k-median clustered resulting in four groupings of aging-associated morbidities. Bone, brain, and gastrointestinal disorders arise 3.5 years after radiation on average, followed by skin, heart, and cataracts. At 4.65 years, animals are at increased risk of being underweight and overweight and developing diabetes, hypertension, and hepatic dysfunction. Tumor, lung, and kidney disorders arise approximately 6 years after exposure. In all cases, these age-related disorders occur significantly earlier in irradiated animals than controls. These findings highlight the clustering of multimorbidities in aging, radiation-challenged primates and the potential of the RSC in studying resilience."} +{"text": "Free text documents in healthcare settings contain a wealth of information not captured in electronic healthcare records (EHRs). Epilepsy clinic letters are an example of an unstructured data source containing a large amount of intricate disease information. Extracting meaningful and contextually correct clinical information from free text sources, to enhance EHRs, remains a significant challenge. SCANR was set up to use natural language processing (NLP) technology to extract structured data from unstructured sources.IBM Watson Content Analytics software (ICA) uses NLP technology. It enables users to define annotations based on dictionaries and language characteristics to create parsing rules that highlight relevant items. These include clinical details such as symptoms and diagnoses, medication and test results, as well as personal identifiers.To use ICA to build a pipeline to accurately extract detailed epilepsy information from clinic letters.We used ICA to retrieve important epilepsy information from 41 pseudo-anonymized unstructured epilepsy clinic letters. The 41 letters consisted of 13 `new' and 28 `follow-up' letters (for 15 different patients) written by 12 different doctors in different styles. We designed dictionaries and annotators to enable ICA to extract epilepsy type , epilepsy cause, age of onset, investigation results , medication, and clinic date. Epilepsy clinicians assessed the accuracy of the pipeline.The accuracy of each concept was: epilepsy diagnosis 98% , focal epilepsy 100%, generalized epilepsy 98% , medication 95% , age of onset 100% and clinic date 95% .Precision and recall for each concept were respectively, 98% and 97% for epilepsy diagnosis, 100% each for focal epilepsy, 100% and 93% for generalized epilepsy, 100% each for age of onset, 100% and 93% for medication, 100% and 96% for EEG results, 100% and 83% for MRI scan results, and 100% and 95% for clinic date.ICA is capable of extracting detailed, structured epilepsy information from unstructured clinic letters to a high degree of accuracy. This data can be used to populate relational databases and be linked to EHRs. Researchers can build in custom rules to identify concepts of interest from letters and produce structured information. We plan to extend our work to hundreds and then thousands of clinic letters, to provide phenotypically rich epilepsy data to link with other anonymised, routinely collected data."} +{"text": "Introduction. The objective of this study is to compare perspectives of young adults toward advance directives (ADs) and their preferences for life-sustaining treatment and care options. Methods. Participants include graduate students (n=30) attending a New York State university. Data were collected using a structured survey questionnaire, the Medical Orders for Life-Sustaining Treatment (MOLST) form and the Five Wishes form. Summary statistics were performed to address the study aim. Results. Of the participants, the average age was 24 years . In Five Wishes, participants who are close to death, 70% wanted all or some forms of life support; when in a coma (47%), or with permanent and severe brain damage (36.6%) chose similar options. In MOLST, without pulse and/or breathing, 87% want CPR; while with pulse and breathing, 96% want artificially administered fluids and nutrition, 90% want mechanical ventilation, 67% want to be hospitalized, 67% want antibiotics, and 53% want unlimited interventions. Conclusion. (1) The majority of participants had not previously completed an AD; however, they were capable of making decisions about their life-sustaining treatments. (2) The discrepancies in treatment preferences may be due to the language of advance directives. Further studies in this respect are warranted."} +{"text": "The purpose of this study was to establish an algorithm for measuring bone erosions at metacarpophalangeal (MCP) joints using high-resolution peripheral quantitative computed tomography (HR-pQCT), to investigate the precision of measurements, and to assess longitudinal changes in bone erosions among patients with rheumatoid arthritis (RA).The 2nd and 3rd MCP joints were scanned at a voxel size of 60.7 \u03bcm using second-generation HR-pQCT. Bone erosions on MCP joints were identified using a semi-automated algorithm we developed, and each erosion parameter was measured. Measurement reproducibility was evaluated in 19 healthy subjects using intraclass correlation coefficients (ICCs) and root mean square percent coefficient of variance (RMS%CV). Finally, longitudinal changes in bone erosions over a period of 12 months were assessed in 26 patients with RA based on the calculated least significant change (LSC).3); repair, 34% (-0.85 mm3); no change, 40%).Reproducibilities for measurement parameters regarding bone erosions with our algorithm were good . No erosion parameters showed significant changes after 12 months of treatment in terms of median values in all erosions, while both progression and repair of erosions were observed individually (e.g., erosion volume: progression, 26% (+0.62 mmThe measurement algorithm developed for bone erosions at MCP joints showed good reproducibility. Both progression and repair of bone erosions were observed in patients with RA even after 12 months of appropriate treatment. Our algorithm may be useful to investigate the etiology of RA and assess drug efficacy. Rheumatoid arthritis (RA) is a systemic chronic inflammatory disease that causes cartilage and bone destruction in association with polyarthritis and leads to disability . Bone erIn recent clinical practice, computed radiography (CR) has been widely used to assess bone erosions . Magnetiin vivo analysis of bone microarchitecture at peripheral sites with high spatial resolution [High-resolution peripheral quantitative computed tomography (HR-pQCT) allows solution , 7. Currsolution , 9.Research regarding RA using HR-pQCT has been increasing since around 2010 . In partThe main purposes of this study were to: 1) establish methods for analyzing bone erosions in metacarpophalangeal (MCP) joints using second-generation HR-pQCT; 2) verify the precision of parameters for measuring bone erosions using this algorithm; and 3) assess longitudinal changes in bone erosions over 12 months in RA patients applying this algorithm.Forty-eight healthy women with no history of finger arthritis were recruited to verify the precision of our algorithm in this study. Another 26 patients with RA fulfilling the 2010 American College of Rheumatology/European League Against Rheumatism (ACR/EULAR) classification criteria [Information on age, sex, height, weight, body mass index (BMI), disease duration, Disease Activity Score in 28 joints (DAS28), and the kind of medical treatment were recorded at baseline. At the same time, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), rheumatoid factor (RF), and anti-citrullinated protein antibodies (ACPA) were also measured. In addition, CRP, ESR, and DAS28 at follow-up were evaluated.This study protocol was approved by Nagasaki University Hospital Clinical Research Ethics Committee (registration numbers: 16020828 and 18021923) and complied with the principles of the 1975 Declaration of Helsinki, as revised in 2000. Written informed consent was obtained from all participants prior to enrolment.The 2nd and 3rd MCP joints of one hand were scanned using a second-generation HR-pQCT system with reference to the scan protocol recommended by The Study group for xtrEme Computed Tomography in RA (SPECTRA) . The domIn healthy subjects, the same hand was scanned three times with repositioning on the same day, to verify the precision of our algorithm. In patients with RA, the affected hand was scanned at baseline and at the 12-month follow-up. Image quality was evaluated according to the motion artifact grading , and imaIn this study, erosions at the MCH and phalangeal base (PB) of the 2nd and 3rd MCP joints were analyzed using bone microstructure measurement software .3, which is a standard value for trabecular bone in second-generation HR-pQCT . Widths Additional procedures are necessary for some erosions, as shown in First, the step shown in Second, the steps shown in Third, the adjustment of rotation in the axial view may be necessary if a certain degree of difference in rotation exists in the longitudinal analysis. As shown in Intra-reader reliability for each bone erosion parameter using our algorithm was evaluated using the intraclass correlation coefficient (ICC) and root mean square percent coefficient of variance (RMS%CV) . Least sThe Wilcoxson signed-rank test was used to assess longitudinal changes of bone erosions between baseline and 12 months follow-up in patients with RA. Er.BMD was evaluated only for bone erosions identified at baseline.In addition, cumulative probability plots were created to analyze longitudinal changes of individual bone erosions in patients with RA. LSCSD calculated for each parameter was applied to these plots, and the percentages of the three categories of \u201cprogression\u201d, \u201crepair\u201d and \u201cno change\u201d were calculated based on each LSCSD we regard as cut-off values. Similarly, percentages of these three categories for Er.BMD were calculated based on LSCSD for this parameter.p<0.05 were considered significant.All statistical analyses were performed using JMP version 14 and values of 3 for Er.V and 14.7 mg/cm3 for Er.BMD, and 0.13\u20130.18 mm for width and depth of bone erosions.Twenty-five erosions were identified in 19 of 48 healthy subjects using our algorithm, and 15 erosions showing motion artifact of grade 1\u20133 in three scans in a row were use2. RF-positive results were seen in 88% of patients, and ACPA-positive results in 50%. Mean parameters at baseline and follow-up were 0.69 and 0.11 mg/L for CRP, 33.9 and 15.9 mm/h for ESR, and 3.7 and 1.7 for DAS28-CRP, respectively. Methotrexate was being administered to 54% of patients, and biologics to 81%. In addition, 27% of patients were using low-dose glucocorticoids.Characteristics of patients with RA at baseline are shown in Longitudinal changes of bone erosions between baseline and follow-up (12 months) in patients with RA are shown in 3), repair in 34% (-0.85 mm3), and no change in 40% for Er.V, progression in 18% (+0.61 mm), repair in 24% (-0.36 mm), and no change in 58% for Er.D; progression in 21% (+0.43 mm), repair in 32% (-0.39 mm), and no change in 47% for Er.D-2; progression in 29% (+0.43 mm), repair in 16% (-0.61 mm), and no change in 55% for Er.W; progression in 37% (+0.39 mm), repair in 26% (-0.36 mm), and no change in 37% for Er.L; and increase in 42% (+60.2 mg/cm3), decrease in 25% (-36.5 mg/cm3), and no change in 33% for Er.BMD. Representative images for longitudinal changes in bone erosions are shown in Longitudinal changes of each bone erosion are shown in In this study, MCP joints were scanned using second-generation HR-pQCT , and a semi-automated analysis algorithm was established for bone erosions. In addition, the precision of each parameter regarding bone erosions was verified, revealing good reproducibility . Finally, longitudinal changes of bone erosions after 12 months in patients with RA were investigated. Each parameter showed no significant changes in the total cohort, while both progression and repair of erosions were observed on an individual despite appropriate treatment.Because HR-pQCT enables detailed analysis of bone erosions, changes of bone erosion volume (progression and repair) are the most commonly used indicators for disease activity or treatment efficacy in RA. However, methods for analyzing bone erosions currently vary between different research groups.One method was to estimate erosion volume from an ellipsoid formula based on manual measurements of depth and width for a visually identified erosion. This approach has been in wide use from the beginning of RA research using HR-pQCT , 23. In In terms of the measurement reproducibility of bone erosions in the present study, RMS%CV was 3.97% and ICC was 1.00 in terms of the intra-reader reliability of our algorithm for assessing bone erosion volume. These results were comparable with those for the other two algorithms. One of the strengths for our algorithm is the measurement of depth and width based on the VOI. Although seemingly the same as the manual measurement mentioned above, the VOI clearly delineates sites of bone erosion in our algorithm. The RMS%CV of depth and width was thus less than 5%, indicating high precision.Regarding longitudinal changes of bone erosions in this study, no parameter for bone erosions showed significant changes between baseline and follow-up for the total cohort, while both progression and repair of erosions were observed at the individual level. In particular, the results in this study showed progression in 26%, repair in 34%, and no change in 40% for erosion volume.Existing studies have reported variable results regarding longitudinal changes in bone erosion volume on follow-up after approximately 1 year in patients with RA. T\u00f6pfer et al. reported that erosions increased in 15%, decreased in 20% and were stable in 65% after an average of 1.2 years . Peters We expect that the algorithm described here will contribute to pathological analyses of RA or the effects of specific pharmacotherapies. Some studies have already verified the effects of specific pharmaceutical agents such as denosumab and tocilizumab , 21, andThis study has several limitations. First, we verified the precision of bone erosion measurement in healthy subjects, not in RA patients, due to the need to scan several regions such as the fingers, wrist, radius, and tibia on the same day, in consideration of the problems of scan time and radiation dose. Bone erosions in healthy subjects were considered similar to those in patients with RA, as shown in In conclusion, we established an analytical algorithm for bone erosions on MCP joints using second-generation HR-pQCT. Good reproducibility was obtained with our algorithm for measurement parameters regarding bone erosions. We observed both progression and repair of bone erosions at the individual level with longitudinal follow-up after 12 months in patients with RA, despite appropriate treatment. We believe that our algorithm allows precise assessment of bone erosions and may be useful for investigating the pathogenesis of RA and the effects of treatment."} +{"text": "Antibiotic stewardship programs optimize antibiotic use in hospitalized children, but most do not routinely review antibiotic prescriptions at discharge. Up to 30% of discharged children receive additional days of antibiotics, and one single-center study found that 27% of discharge prescriptions were suboptimal.We conducted a retrospective cohort study to evaluate duration of therapy (DOT) and antibiotic choice for children < 18 years admitted to 4 children\u2019s hospitals from January 1, 2019 - December 31, 2019 and prescribed antibiotics at discharge for uncomplicated community-acquired pneumonia (CAP), skin and soft tissue infection (SSTI), or urinary tract infection (UTI). We excluded children with complex medical conditions, > 1 infection requiring antibiotics, > 7 day hospital stay, or intensive care unit stay. The primary outcomes were the percentage of subjects prescribed optimal (1) total (inpatient plus outpatient) DOT , and (2) antibiotic choice ; UTI: cephalexin, amoxicillin, amoxicillin-clavulanate, TMP/SMX, or nitrofurantoin) based on current national guidelines and available evidence.2105 encounters were included: 783 CAP, 916 SSTI, and 406 UTI. Median age was 4 years and 49% were female. DOT for each condition are shown in Figure\u00a01 and antibiotic choice in Figure\u00a02. Antibiotic choice was optimal for 66% with CAP, 98% with SSTI, and 88% with UTI. DOT was optimal for 11% with CAP, 4% with SSTI, and 21% with UTI. Both DOT and choice were optimal for 2% with CAP, 4% with SSTI, and 19% with UTI. For all indications, antibiotic choice was optimal for 84% and DOT was optimal for 10%, while only 6% of antibiotic courses included both optimal DOT and antibiotic choice.Total duration of therapy for 2105 children discharged with antibiotics for community-acquired pneumonia, urinary tract infection, and skin and soft tissue infection.Discharge antibiotic choices for 2105 children with community-acquired pneumonia, urinary tract infection, and skin and soft tissue infection.At 4 children\u2019s hospitals with established antimicrobial stewardship programs, 94% of discharge antibiotic courses for CAP, UTI, and SSTI were suboptimal either by choice of antibiotic or duration of therapy. Discharge antibiotic prescribing represents a significant opportunity to improve antibiotic use in children.Jason Newland, MD, AHRQ: Grant/Research Support|Merck: Grant/Research Support|NIH: Grant/Research Support|PEW Charitable Trust: Grant/Research Support|Pfizer: Grant/Research Support."} +{"text": "Compared to the HPV infection rate of women aged 56\u201365, that in women aged 35\u201345 and 46\u201355 decreased significantly. To conclude, risk factors of HPV infection among female patients include high school age and below, initial sexual encounter at age \u2264 19 years, number of sexual partners > 1, ASCUS and above, non-condom contraception, nationalities other than Han nationality and rural population. Collectively, this study provides insights for the improved prevention and treatment of cervical cancer.The different human papillomavirus (HPV) strains cause warts in various regions of the body. However, considering that the status and genotype distribution of HPV infection in women in Shenyang remain unknown, herein, we investigated the epidemiological characteristics of high-risk HPV (HR-HPV) infection in women in Shenyang, as well as the current state of HPV infection in Shenyang, to provide a theoretical basis for the prevention and treatment of cervical cancer. From December 2018 to December 2021, 6,432 urban and rural women from the Liaoning Cancer Hospital and the Sujiatun Women and Infants\u2019 Hospital were assessed via the Thinprep cytology test (TCT) and HR-HPV detection. Of the 5,961 women enrolled, 739 were HPV positive (12.40%) and 562 were TCT positive (9.43%). Statistical analyses identified the following HPV risk factors: high school education or lower [OR = 1.426 (1.199\u20131.696), In women, cervical cancer ranks fourth among all cancers in incidence (13.1%) and mortality (6.9%), only after breast cancer, colorectal cancer, and lung cancer . In 2020Human papillomavirus (HPV), a double-stranded circular DNA virus, is a papillomavirus belonging to the family Papillomaviridae. To date, more than 100 HPV genotypes have been characterized, forty of which are associated with human reproductive tract infections via uncontrolled induction of squamous epithelia proliferation within the mucosa . HPV repSignificant differences have been reported in HPV infection rates and types among people in different regions . For exaFrom a clinical point of view, epidemiological studies investigating HPV infection among women in different regions have been conducted to help reduce the prevalence of infection among women. However, to date, no study has reported on the status and genotype distribution of HPV infection in women in Shenyang. Therefore, the current cross-sectional study examines the prevalence and high-risk factors of HPV infection within women in Shenyang. Moreover, the epidemiological characteristics of HR-HPV in women in this region are assessed, and a novel strategy for the prevention and treatment of cervical cancer is proposed.This study was approved by the Ethics Committee of the Liaoning Cancer Hospital (ethics batch number: 20180106), and informed consent was obtained from all participants included in this study.From April 2018 through December 2021, 6,432 women in Liaoning were screened for cervical cancer at the Liaoning Cancer Hospital and the Shenyang Sujiatun District Women\u2019s and Infant Hospital. The women selected for this study had an average age of 51.56 \u00b1 6.621 years and a median age of 51 years. Community population and hospital outpatient opportunistic screenings were employed to evaluate whether participants met the following inclusion criteria: (1) the screening participants were selected by the community (village committee) and did not represent a single occupational group; (2) women from urban and rural populations with high incidence rates and mortalities and good population compliance were selected as the target population; (3) only participants with a registered residence in their regions were screened; (4) women with a history of sexual life, aged between 35 and 65 years old (subject to the date of birth on the ID card); and (5) women with no serious organ dysfunction or mental disease, who voluntarily participate in and can accept the questionnaire survey. Exclusion criteria for screening objects included the following: (1) Women who have been diagnosed with a tumor; (2) women who are currently being treated for other serious internal and external diseases; (3) women who have had a hysterectomy; and (4) women who are pregnant and lactating.The Thinprep cytology test (TCT) was combined with HPV detection technology to screen cervical lesions. Each medical examiner took the stone cutting position. The vulva was fully disinfected and the cervix exposed with a vaginal dilator. Next, the cervix was wiped with a sterile cotton swab to remove excess cervical secretions. Finally, a disposable cervical cell sampling brush was rotated ten times within the scaly columnar junction of the cervix, removed, and stored in a cell preservation solution.A TCT (Thinprep cytologic test purchased from Hologic.lnc 20160621) test was used to obtain materials for production. The accompanying report was prepared based on The Bethesda System (TBS) for Reporting Cervical Cytology (2014). Abnormal results included negative for intraepithelial lesion or malignant tumor (NILM), atypical squamous cells of undetermined significance (ASCUS), atypical squamous cells cannot exclude high-grade squamous intraepithelial lesion (ASCH), low-grade squamous intraepithelial lesion (LSIL), high grade squamous intraepithelial lesion (HSIL), squamous cell carcinoma (SCC), and atypical glandular cells (AGC). A positive TCT diagnosis included patients with ASCUS, ASC-H, LSIL, HSIL, SCC, or AGC.The E6/E7 mRNA detection kit \u2014an FDA-approved assay for detecting HPV\u2014was used to detect 14 HR-HPV-mRNA causing cervical cancers . The results for HPV type 16 and 18 detection can be made available to provide clinical guidance. The kit detects E6 and E7, rather than L1, mRNAs of the HR-HPV virus to avoid the missed diagnosis of high-level lesions and cancer. Moreover, the test avoids cross-reactivity with low-risk HPV types, has fewer false positives, and avoids unnecessary colposcopy and overdiagnosis.Cervical exfoliative cells were examined using cervical liquid-based TCT. The diagnostic criteria are based on the TBS classification as outlined above . ColposcFor quality control purposes, 20% of the positive cervical exfoliative cell smears and 5\u201310% of the negative smears were randomly selected. All selected smears were rechecked by experts. The qualified rate of smear results reached 80%. Quality control of colposcopy samples entailed a spot check for 10% of the normal reports and 20% of abnormal reports, as well as subsequent analysis by experts. The standard rate of the report results reached 90%. Quality control of histopathological examination entailed a spot check of 10% of the pathological sections, subsequently rechecked by experts. The coincidence rate of the diagnostic results reached 90%.Analysis was performed on the basic population information, as well as the living habits, physiological indicators, psychological and emotional conditions, screening willingness, and other high-risk factors. The questionnaire posed question regarding demographic characteristics and risk factors that may be associated with HR-HPV infections. Additionally, participants answered questions meant to reflect their level of knowledge about, and overall attitudes toward, cervical cancer, HPV, and the correlation between the two. All questions were answered directly by each participant or by dictating answers to a study nurse.2) test. The influencing factors were analyzed using univariate and multivariate logistic regression to evaluate the correlation between the relevant factors mentioned in the questionnaire and HPV infection.Statistical analysis of the relevant data was conducted using the statistical package for the social science (SPSS) version 19.0 software. The count data rate (%) was analyzed using the chi-square , 941 were 41\u201345 years old (15.79%), 1,581 were 46\u201350 years old (26.52%), 1,443 were 51\u201355 years old (24.21%), 1,115 were 56\u201360 years old (18.70%), and 619 were 61\u201365 years old 10.38%; .Menarche age occurred between 12 and 18 years old in 97.94% of the participants. Menopause had occurred in 52.86% of the participants, most of whom were over 50 years of age. Moreover, 83.14% of the participants had a history of breast-feeding, and 71.26% breast-fed for more than 6 months. The population with multiple sexual partners accounted for 8.92 and 3.00% of the participants were aged < 19 years old at the time of their first sexual encounter. A total of 71.25% had a history of abortion; those with lover\u2019s redundant prepuce and sexual bleeding accounted for 5.54 and 6.46%, respectively. A total of 22.18 and 17.55% women had a history of gynecological diseases and family histories of tumors, respectively .Current smokers accounted for 8.37% of all participants, while those who had quit smoking accounted for 1.21%. Passive smokers accounted for 62.44 and 82.17% of them were exposed to cooking oil smoke almost every day. Additionally, 11.06% of the participants had a history of alcohol consumption, and 1.02% reported current alcohol consumption. Moreover, 85.82% did not often participate in outdoor physical exercise, and 92.70% did not drink tea. More than 50% of the women had an insufficient intake of fresh vegetables and fruits with vegetable intake < 5 kg per week, and fruit intake < 2.5 kg per week. Approximately 70% of women did not meet the dietary guideline requirements set forth for Chinese residents .Of the participants, 60.69% had a good health status or self-rated their health status as good. An additional 9.21% had a history of hypertension, 3.62% of diabetes, 11.84% of hyperlipidemia, and 0.22% of mental health illness. Moreover, 20.33% of the participants experienced negative life events, 32.52% had depression or anxiety symptoms, and 35.31% had poor sleep quality .A total of 22.38% of the participants believed they could easily develop cancer, while 31.74% had been previously screened for cancer. Cancer screening for 27.38% of the participants was paid for by the government. Moreover, 28.07% indicated that they would fully accept cancer screening. Those who did not accept cancer screening listed time concerns and no conscious symptoms.In the case of abnormal inspection results, most women were willing to be re-inspected and felt they were able to cover the associated expenses. However, the acceptance rate for self-paid expenses was typically below 200 Yuan. Moreover, 92.35% of the participants indicated that they were willing to accept a follow-up visit in the case of abnormal results. The primary reason preventing participants from accepting subsequent appointments was the time requirement.Additionally, 91.01% of the participants indicated that they were willing to try new, more effective screening technologies, with acceptable out-of-pocket expenses for these technologies concentrated below 200 Yuan. The participants who were unwilling to accept new, more effective screening technologies, primarily showed concern for the scientific validity and safety of the new methods .All participants completed gynecological examinations for cervical cancer screenings . The detin situ, and adenocarcinoma were not detected. Moreover, TCT-/HPV + accounted for 7.68% of the cases, TCT+/HPV- for 4.71%, and TCT + /HPV + for 4.71%.Of the 6,432 participants, 471 were excluded from the survey results. The remaining 5,961 participants were screened for cervical cancer and included in the statistical analysis . The aveOf the 5,961 participants, 739 (12.40%) tested positive for HPV , of whicThe 5,961 participants that were enrolled for TCT and HR-HPV screening from December 2018 to December 2021 were divided into six age groups, and the positive detection rates were determined for each. It was found that 35\u201340, 41\u201345, 46\u201350, 51\u201355, 56\u201360, and 61\u201365 year old participants had TCT positive detection rates of 9.92, 10.51, 10.94, 9.36, 7.71, and 6.95%, respectively . The prep < 0.05; A total of 28 potential risk factors may be related to HR- HPV infection. Univariate logistic analysis showed that HPV infection was correlated with different age groups, educational level, age at first sexual encounter, number of sexual partners, contraceptive methods, TCT positivity, nationality, and population , p = 0.046], number of sexual partners > 1 , assigned TBS classification of ASCUS or above , non-condom-based contraception , other nationalities except Han , and rural residence were risk factors for HPV infection (p = 0.001] and 46\u201355 were significantly reduced.The results of the multivariate unconditional logistic regression analysis showed that high school education or lower [odds ratio (OR) = 1.426 (1.199\u20131.696), nfection . Comparein vivo, typically occurs over a span of approximately 10 years. Hence, interrupting the early stages of HPV infection, or early stages of cervical lesion formation may effectively prevent, or delay, the occurrence and development of cervical lesions and cervical cancer.Currently, cervical cancer is the second most common female malignant tumor after breast cancer. The incidence rate of cervical cancer has increased significantly and has become increasingly prevalent in younger women. As such, establishing effective preventative and therapeutic strategies for cervical cancer has become increasing important. Various studies have repA recent study found thAge differences were also observed with regard to HPV infection rate, in the current study. Previous studies have reported that HPV infection is more common in elderly women . Here, wPrevious studies have reported that first sexual encounters occurring before the age of 19 years represents an independent risk factor for HR-HPV infection. The cervical epithelial repair function and autoimmune function of women under 19 years of age are not yet fully mature, rendering them susceptible to HR-HPV . MoreoveConsistent with other studies , the curThis study also found that living in rural areas represents a high-risk factor for HPV infection, which may be due to a lack of cervical cancer screening services, poverty in rural areas, and poor education. Indeed, An international study conducted by IARC in 2011 showed that compared to those who never smoked, the risk of cervical cancer for current smokers was OR = 1.94 ; howeverCurrently, HPV vaccine research (preventive and therapeutic) has significantly increased. A study in the United States found that HPV preventive vaccines are safe and have preventive and protective effects . HoweverThe occurrence and development of cervical cancer is a multi-factor, complex, and progressive biological process. Currently, the relationship between HPV infection, cervical cancer, and precancerous lesions is clear. Through cervical screening of female HPV infection rate, this study identified that a high school education or lower, age at first sexual encounter \u2264 19 years, number of sexual partners > 1, TBS classification of ASCUS or above, non-condom-based contraception, other nationalities except Han, and rural population serve as risk factors for HPV infection. It is, therefore, necessary to establish and improve the cervical cancer screening system according to the relevant factors affecting the incidence of cervical cancer, screen out and follow-up with high-risk groups, strengthen public education on prevention and treatment of cervical cancer, and improve awareness of cancer prevention among the general population. Moreover, targeted improvement measures for women in different regions are fundamental to reducing the positivity rate of HPV infection. Improving the living environment, improving education level, expanding health education, developing beneficial health habits, and actively preventing and treating HPV infection are the basic and effective ways to reduce the positive rate of HPV infection. Only by providing a large amount of epidemiological data can we carry out effective vaccine research and development while also optimizing the cost-effectiveness of vaccinating the Chinese population. Collectively, the results of this study provide epidemiological data for the development of an HPV vaccine, to effectively reduce the incidence of cervical cancer in Shenyang.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.This study was approved by the Ethics Committee of the Liaoning Cancer Hospital (Ethics batch number: 20180106), and informed consent was obtained from all participants included in this study. The patients/participants provided their written informed consent to participate in this study. Written informed consent was obtained from the individual(s) for the publication of any potentially identifiable images or data included in this article.HP and CW designed and supervised the project. DY, JZ, and XC collected the clinical data samples. DY collected and processed the data, performed the data analysis, and drafted the manuscript. JM translated and edited the manuscript. All authors reviewed, discussed and edited version of the manuscript, and agreed with the final manuscript."} +{"text": "To the Editor: Pityriasis rosea (PR) is a common papulosquamous disease; however, its epidemiology is not well established. Single-center studies, conducted mostly outside the United States, have estimated the prevalence of PR to be 0.39-4.80%All of Us database, a recently launched initiative by the National Institutes of Health that strives to include communities that have been historically underrepresented in research .All of Us database by identifying patients with a diagnosis of PR using ICD-9-CM code 696.3 and ICD-10-CM code L42. Electronic medical records of each patient with PR were then analyzed to collect data on age, sex, and self-identified race. We utilized the Wald method with 95% confidence intervals (CI) to calculate the overall prevalence of PR.This study was deemed IRB exempt by the University of Pennsylvania. We performed a cross-sectional analysis of the All of Us database has enrolled 327,654 participants. We identified 687 patients with PR, representing an overall prevalence of 0.21% . The aveGiven similar prevalence among all ethnicities, we might expect educational materials to depict PR equally in all skin types. However, recent analysis of educational resources has found PR less well represented in dark skin compared to light skin.All of Us database is organized by billing codes, we likely missed cases of PR simply coded as \u201crash\u201d; thereby, our prevalence calculation likely represents an underestimate of true PR prevalence. In addition, our data set did not include patients younger than 18\u00a0years of age. Furthermore, the All of Us database is 54% white, 21% Black, and 18.5% Hispanic, while the United States population is currently 60% white, 13.4% Black, and 18.5% Hispanic.All of Us.Our analysis has limitations. As the Altogether, our data suggest PR is a common dermatosis prevalent across all racial groups. Given the prevalence observed in Black patients, we advocate for greater educational representation of PR in darker skin types. Further epidemiologic studies that are not restricted by billing codes and include pediatric patients may validate our findings.None disclosed."} +{"text": "The COVID-19 pandemic strongly impacted older people, not only in terms of clinical outcome but also in care provision. Investigating trends of changes in healthcare services access among older subjects during the pandemic, along with studying potential determinants, is of utmost interest to identify the most at-risk individuals. We used data from LOST in Lombardia, a cross-sectional study conducted on a representative sample of 4,400 older adults (aged 65 or more) in autumn 2020. Data were collected about lifestyles, mental health, and access to healthcare services before and during the pandemic. To investigate potential determinants of changes in healthcare access, we presented prevalence ratios (PRs) estimated through multivariable log-binomial regression models. Twenty-one per cent of the participants increased telephone contacts with general practitioner (GP), 9.6% specialist visits for a fee, while 22.4% decreased GP visits, 7.5% ED access, 6% hospitalisations, 12.3% outpatient visits, 9.1% diagnostic exams. The prevalence of the cancellation or delay of medical appointments by the patient's decision was 23.8%, with higher proportions among men, among individuals aged 75 or over as compared to those aged 65-74, and among individuals with a higher self-reported economic status . People with comorbidities more frequently cancelled or postponed visits, reduced ED access or hospitalisations. Moreover, individuals with worsened mental health status showed a higher prevalence to cancel or delay visits and to reduce ED access. The decrease in healthcare provision and consultations could result in mortality and morbidity excess. Our results should inform targeted intervention to bridge the gaps and overcome the health inequalities that the pandemic has deepened. Exploring the underlying reasons and determinants for healthcare avoiding or delaying among the most vulnerable groups is crucial for epidemic preparedness and planning future interventions."} +{"text": "The dysphagia prevalence among elderly nursing home residents evaluated by SSA was 58.69% and by the Gugging Swallowing Screen test (GUSS) test was 53.60% . The prevalence of dysphagia in hospitalized older adults screened by the 10-item Eating Assessment Tool was 24.10% , which was significantly lower than those assessed by V-VST or GUSS tests of 47.18% . Conclusions: Dysphagia is prevalent in the elderly, affecting approximately one in three community-dwelling elderly, almost half of the geriatric patients, and even more than half of elderly nursing home residents. The use of non-validated screening tools to report dysphagia underestimates its actual prevalence.Background: This systematic review and meta-analysis aimed to estimate the pooled prevalence of dysphagia in older adults, subgrouping by recruitment settings and varying dysphagia assessment methods. Methods: Five major databases were systematically searched through January 2022. A random-effects model for meta-analysis was conducted to obtain the pooled prevalence. Results: Prevalence of dysphagia in the community-dwelling elderly screened by water swallow test was 12.14% (95% CI: 6.48% to 19.25%, I Average life expectancy has risen steadily worldwide from 66.8 years in 2000 to 73.4 years in 2019 ,6,7,8. AThis systematic review and meta-analysis followed the 2009 Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines . The seaStudies were eligible if they were observational studies published in English, which assessed the prevalence of dysphagia in older adults (\u226560 years old) . StudiesA systematic literature search was conducted from inception through January 2022 of Pubmed, Excerpta Medica dataBASE (EMBASE), Web of Science, Cumulative Index of Nursing and Allied Health Literature (CINAHL), and Virtual Health Library Portal (VHL) libraries. The following search terms were primarily utilized: Dysphagia, Swallowing Disorders, Deglutition Disorders, Prevalence, Elderly, Older Adults, Older Individuals, Older People. The specific search terms for each library are detailed in The Joanna Briggs Institute\u2019s Critical Appraisal (JBIC) Checklist was utilized to estimate the methodological quality of the included studies. The JBIC Checklist encompasses nine items with four options: Yes, No, Unclear, and Not applicable. Studies scored of at least five are considered adequate quality .We extracted the required information and summarized in tables, for each study that met eligibility criteria, the study characteristics , settings used to recruit participants, sample size, the average age of participants, gender ratio, tools to report dysphagia, and the prevalence of dysphagia.2 statistics were used to assess and quantify the magnitude of heterogeneity among studies. I2 values ranging between 25% and 50% were classified as low, between 50% and 75% as moderate, and 75% or above as high heterogeneity [p < 0.05.Statistical software RStudio Version 1.4.1717 was used to analyze the data. It was expected that the heterogeneity among studies would be considerable. Thus, a random-effects model was chosen to obtain the pooled prevalence. We calculated the overall prevalence of dysphagia in the elderly. Subgroup analyses were conducted to investigate the sources of heterogeneity among studies. Hedges Q and Iogeneity . StatistThe systematic search strategy on five electronic libraries yielded a total of 955 abstracts: 101 from PubMed, 422 from Embase, 122 from CINAHL, 186 from Web of Science, and 124 from The Virtual Health Library. A manual search of the references cited in relevant studies yielded no additional articles. After removing 216 duplicates, of the 739 studies remaining, 642 studies were excluded by screening title and abstract, 97 full-texts were assessed for eligibility in accordance with the inclusion and exclusion criteria. Subsequently, 65 studies were excluded because of reasons as follows: 1 study included participants less than 60 years old, 1 study did not mention assessment tool for dysphagia, one study did not report prevalence rate, eight studies recruited participants with specific diseases, 1 review article, 4 non-English articles, 15 conference abstracts with no full text, 25 papers with duplicated data, and 9 studies used dichotomous question to determine dysphagia. Finally, a total of 32 studies were collected in this systematic review, of which 30 studies were synthesized in meta-analyses. The study selection process is shown in Of the 32 included studies, 12 studies were from Europe and North America ,43,44,45Study quality was assessed by the Joanna Briggs Institute\u2019s Critical Appraisal Checklist, with the scores ranging from 6\u20139, suggesting that the methodology of the included studies was moderate to high. Study methodology evaluations are detailed in 2 = 99%, p < 0.001) (2 = 95%), 46.98% , and 37.98% , respectively. Because of the high heterogeneity in meta-analyses of each setting, we conducted further subgroup analyses under the methods for measuring swallowing function.Based on the random-effect model, the estimated overall prevalence of dysphagia in the elderly was 32.83% . We cond2 = 68%, p = 0.07). The estimated prevalence of 17.34% was obtained by combining seven studies assessed dysphagia using questionnaires. Two studies using the water swallow test made up the prevalence of 12.14% of dysphagia in community-dwelling elderly was reported using Standardized Swallowing Assessment (SSA), followed by the prevalence of 27.17% reported by using V\u2212VST. Due to the similarity in the description of these two assessments, we grouped the two studies in one subgroup with a combined prevalence of 30.52% .2 = 0%, p = 0.44). Pooled prevalence of dysphagia based on the the Gugging Swallowing Screen (GUSS) test and water swallow test were 53.60% and 47.47% , respectively. Combined prevalence from three studies screened dysphagia by the 10-item Eating Assessment Tool (EAT\u221210) was 36.11% .2 = 0%, p = 0.84). While, the higher combined prevalence of 47.18% was found when pooled four studies assessing multiple consistency tests (three studies examined dysphagia using V\u2212VST and one study using GUSS test). Whereas, high discrepancy existed between two studies performing water swallow tests with pooled prevalence of 47.61% .The purpose of this study is to systematically identify the totality of existing literature to estimate the prevalence of dysphagia in the geriatric population and to analyze the influence of different assessment methods on the reported prevalence. Of note, the accurate epidemiological data of dysphagia in the elderly is problematic to ascertain, which depends upon a variety of factors, including the recruited population in particular settings, different medical conditions, especially inconsistent methods and assessment procedures employed to define its presence in different epidemiological studies. Based on the included studies, the main findings of the current review were (1) the prevalence of dysphagia is high in older adults, and (2) the use of non-validated screening tools to report dysphagia underestimates its actual prevalence in older adults.In clinical practice, a comprehensive swallowing assessment often includes a review of the patient\u2019s socio-psychological and medical history, self-reported symptoms, cognitive-linguistic assessment, oral-peripheral examination, trials with different consistencies of food and liquids or a review of usual eating patterns, and intervention trials ,66. WhilRegardless of subgroups classified by different recruitment settings, the prevalence of dysphagia among the older population estimated by using non-validated methods was significantly lower than those assessed by validated methods. When considering subgroup analyses with SSA, V-VST, or GUSS as the assessment method only, up to 30% of community-dwelling elderly have dysphagia, it presents in almost half of hospitalized elderly and more than half of nursing home residents. In people aged 80 and over, the prevalence of dysphagia has been found to be even much higher ,41. NeveThere appears to be a scarcity of studies investigating the prevalence of dysphagia in the elderly by instrumental assessments such as VF or FEES. Studies should be further developed to bridge this gap. Further comparative studies pertaining to the assessment methods of dysphagia are needed to identify whether these approaches affect the secondary consequences of dysphagia. Much remains to be done to establish an international consensus on screening dysphagia in the elderly in community as well as early detection and management of dysphagia in residential care and clinical settings.We acknowledge several potential limitations of this systemic review and meta-analysis. Firstly, we may have missed relevant studies that were (1) not published; (2) abstracts without full text; (3) published in other languages than English. Secondly, there is significant heterogeneity, even after subgroup analyses, due to multifactorial nature of dysphagia assessment including differences in (1) assessments; (2) recruitment settings; (3) health conditions; (4) assessors. Due to this limitation, only subgroups were analyzed. Finally, dysphagia can be caused by a variety of diseases and disorders, such as stroke, Parkinson\u2019s disease or dementia, and so on, which are common among the elderly. In this review, in addition to the exclusion of studies assessing dysphagia in specific medical conditions, several collected studies also excluded individuals with neurological diseases or other medical conditions in their investigations, which might underestimate the true prevalence of dysphagia in the older population.In conclusion, dysphagia is prevalent in older adults. It affects around 30% of community-dwelling elderly, almost 50% of geriatric patients, and above 50% of nursing home residents. The use of non-validated screening tools to report dysphagia underestimates its actual prevalence. Given the high prevalence and associated poor outcomes, there is a need to better standardize how studies assess and report dysphagia. This is needed to advance research in this highly important field as well as potentially improve patient outcomes."} +{"text": "To evaluate the quality of linkage carried out by operators in the Trusted Third Parties (TTPs) in Public Health Scotland (PHS) and National Records of Scotland (NRS).To compare results with a PHS automated production system.To produce individual reports to feedback results to operators, informing areas for improvement.A test dataset containing names, dates of birth, sex and postcode, was derived from hospital episodes and additional synthetic records added. For a proportion of records, some variables were perturbed. The true reference index number was retained to compare against the indexes returned by operators from matching to the population spine.A run of the Medical Record Linkage (MRL) system was executed without clerical review, to provide a benchmark for the TTPs.Recall, precision and F-measures were calculated to compare results.There were 5 reports produced, including the MRL run. NRS contributed a single run, and PHS-TTP offered 3. Quality overall was excellent, with some variation dependent on operator, methods, and spine used. The MRL run was ranked 3rd overall for F-measure, with overall precision of 99.69% and 97.36% recall. Where data had been unperturbed precision was 99.92% with 99.90% recall. The best ranked run was carried out by a member of PHS TTP, with 99.72% precision (99.93% unperturbed) and 98.77% recall (99.94% unperturbed). NRS results showed precision of 99.56% (99.91% unperturbed) and 96.71% recall (99.80% unperturbed).Individual reports were produced and tailored to highlight the types of perturbations where each operator performed strongly or otherwise, encouraging operators to learn and adapt processes in future.Data Linkage in Scotland has evolved over 5 decades, more recently with the introduction of TTPs as key support services for research projects. However, little evaluation of the quality of linkage has been conducted. The results demonstrated by this exercise provide re-assurance to researchers that linkage quality remains high"} +{"text": "The COVID pandemic afforded financial scammers with new opportunities to target older adults. This paper presents data from a telephone survey conducted June\u2013September, 2020 with 380 participants from a larger National Institute of Aging study examining financial exploitation among older adults. The survey assessed COVID-related scams in three areas: (1) products, testing, treatments; (2) financial assistance ; and (3) charities. Questions focused on scam exposure / attempts, mode of contact, responses, and whether the older adult reported it to someone. The sample was 64% female; mean age = 73.6; and 47% White, 41% African American, 12% Hispanic. Across all scam types, 18.4% reported scam attempts / exposure; 24% of those exposed engaged / responded without getting scammed (11%); or were actually scammed (13%); and 40% told someone about it. The most frequent modes of contact were: telephone (54%), internet / email (40%), or mail (29%). Controlling for socio-demographics, participants from NYC were more likely to be exposed ; as were those reporting more loneliness ; and those reporting that COVID had worsened their emotional well-being to a greater extent . Older adults who were more socially isolated / lonely were also more likely to have been scammed and less like to tell anyone about it. Psychosocial factors play an important role in exposure and response to scams during pandemics. Implications for policy, intervention, and general scam susceptibility are discussed."} +{"text": "Knowing vaccine effectiveness (VE) against variants of concern (VOCs) in the real-world setting is essential for public health decision-making. A systematic landscape of the VE against a series of clinical outcomes caused by the VOCs in the real-world setting is needed. We systematically searched for studies that evaluated VE against VOCs in the real-world setting and collected individual data. We identified 113 studies meeting the eligibility criteria. We found full vaccination provided strong protection against each clinical outcome with summary VE ranging from 86.8% to 96.0% Alpha, moderate protection against infection caused by Beta, Gamma and Delta with summary VE ranging from 70.9% to 72.8%, strong protection against severe disease caused by Delta with summary VE ranging from 84.9% to 90.3%, limited protection with summary VE of 23.5% against infection and moderate protection with summary VE ranging from 56.5% to 82.4% against severe diseases caused by Omicron. Booster vaccination can provide a substantial improvement in protection against Delta and Omicron, but not as much as the Delta. The meta-regression analysis showed that the VE against the Omicron wanned over time, and the VE against hospitalization declined relatively slowly, compared to against infection. Those findings supported the need for public health measures, increasing booster vaccination coverage in response to current and new infectious waves driven by variants and developing broadly protective vaccines to confront virus evolution. The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact worldwide, with over 584 million cases and 6.41 million COVID-19-related deaths reported globally as of 11 August 2022 [The COVID-19 vaccination campaign is the most essential component of the current response to the pandemic, helping to reduce the COVID-19 disease burden, facilitate a safer reopening of societies and a recovery of the economy. As of 4 June 2022, 32 COVID-19 vaccines have been approved for use and 129 are in clinical trials . HoweverThe performance of COVID-19 vaccines in the real-world setting is a critical assessment of evidence-based public health decisions. Although some studies have reported the real-world effectiveness of COVID-19 vaccines against VOCs, the results reported by various studies are controversial . Meta-anThis systematic review and meta-analysis were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines . The proUsing the keywords \u201cCOVID-19,\u201d \u201cSARS-CoV-2,\u201d \u201cvaccine,\u201d and \u201cvariant\u201d (supplementary table S3 for search strategy), we systematic searched for literature published on PubMed, Cochrane Library, Embase before 5th Aug 2022. To ensure the validity of study results, studies published on preprint servers without peer review were not retrieved and included. Additionally, we reviewed the references from the included studies to identify any missed potentially relevant records.Observational studies that evaluated the VE against VOCs including B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) and B.1.152.9 (Omicron) were included. Clinical trials, studies on immunogenicity and antibody neutralization, estimation of comparative or marginal effectiveness and hybrid immunity , studies on non-VOCs, case reports, conference abstracts, cross-sectional and ecological studies and mathematical modelling analysis studies were excluded. The adjusted VE or estimates of effect size in various vaccination statuses against a series of clinical outcomes caused by VOCs with corresponding 95% confidence intervals (CIs) was extracted preferentially. We also extracted the first authors\u2019 name, VE at each time interval, publication year, specific VOCs type, clinical outcomes reported in each article, study design, country and sample size according to a predetermined proforma in Microsoft Excel spreadsheet.The methodological quality of each study was assessed independently by two authors using the original Newcastle-Ottawa Scale (NOS) for case\u2013control and cohort studies . The NOSWe estimated the summary VE against a range of clinical outcomes caused by VOCs in line with the vaccination status . VE was obtained from the effect size defining as (1-effect size) \u00d7100%. Summary estimates and 95% CIs were calculated using DerSimonian and Laird random-effects meta-analysis. We used the meta-regression based on a linear mixed model to estimate the change of VE over time to focus on the most concerned Omicron variant. Predetermined subgroup analysis was performed stratifying by vaccine product and study population to explore the VE in specific populations and the performance of various vaccine products. Heterogeneity between included studies was assessed by the I-square statistics using the following interpretation: 0\u201350%, 50\u201375% and >75% were considered to be low, moderate and high heterogeneity respectively. The forest plot was used to present the results of summary VE and subgroup analyses against each clinical outcome caused by VOCs and the corresponding study heterogeneity. To ensure the robustness of the results, we did not perform summary estimation for clinical outcome or subgroup with less than three studies. Publication bias was assessed by visual inspection for funnel plot asymmetry and by the Egger\u2019s test. When publication bias was examined based on either Egger\u2019s test of bias or visual inspection for funnel plot asymmetry, we used the trim-and-fill method to re-estimate the pooled effect size. Additionally, the sensitivity analyses of all outcomes were performed to assess the influence of included study on the results. All calculations and graphs were conducted using R software version 4.1.2 .For this literature review, we identified 11,402 potentially relevant records from the literature databases, 4391 were excluded as duplicates and 5308 irrelevant studies based on title and abstract were excluded, 315 published articles were evaluated at the full-text level. In total, 113 articles including 51 test-negative case\u2013control studies, 51 cohort studies, and 11 case\u2013control studies were included from 27 countries . Of the Thirty-three, five and seven studies evaluated the VE of full vaccination against infection caused by Alpha, Beta and Gamma variant, with a summary VE of 86.8% , 72.8% and 71.9% respectively. In the analyses of summary VE estimation against hospitalization, the summary VE was 90.4% for Alpha variant and 78.4% for Gamma variant. Owing to limited evidence, only three studies evaluated the VE against ICU admission and severe disease caused by Alpha variant, and the summary VE was 96.0% and 92.2% respectively. Five and three studies provided VE estimation of full vaccination against death caused by Alpha and Gamma variant, giving a summary VE of 94.2% and 82.2% . In addiSeven, eleven and three studies provided VE estimation of booster vaccination against infection, hospitalization and ED or UC caused by Delta variant among the general population, with summary VE of 93.3% , 92.8% and 92.7% respectively. The VE against severe disease was evaluated in 3 studies, 2 among the general population and 1 among the elderly, giving a summary VE of 93.8% . The summary VE of full vaccination was 70.9% against infection, 84.9% against hospitalization, 78.5% against ED or UC, 88.2% against ICU admission, 88.8% against severe disease and 90.3% against death against infection, 83.4 against hospitalization, 78.1 against ED and UC, 95.5 against severe disease and 94.9 against death . SubgrouTwelve studies evaluated the VE over time against infection and hospitalization caused by Omicron variant, among which were 5 vaccines . The summary VE of full vaccination against infection was 44.4% (95% CI 38.6\u201350.2) at first month and subsequently declined, with VE of 6.0% at sixth month. In comparison, the summary VE against hospitalization was 71.9% at first month and declined slowly to 59.2% at sixth month. Booster vaccination showed a relatively high protective effect but also wanning, declining from 62.9% at first month to 38% at fourth month. Compared with this, the summary VE against hospitalization still remained higher, wanning from 90.2% at first month to 72.9% at fourth month .Figure t\u2009=\u2009\u22122.97, P value\u2009=\u20090.0054) in the analysis of VE for partial vaccination against infection caused by Alpha variant and we corrected the results using trim-and-fill method. No significant publication bias was identified in the remaining primary analyses, either qualitatively based on funnel-plot or visually based on funnel-plot. The sensitive analysis revealed that the results of primary and subgroup analyses were stable.Publication bias was found with Egger\u2019s test reduction in the odds of developing symptomatic infection 2 weeks or more after homologous or heterologous booster vaccination compared to 25 weeks or more after a primary series during the dominance of the Omicron variant . The stuMeta analysis of neutralizing antibody responses showed results that are generally consistent with the real-world study. Antibody in vaccine-induced serum was largely retained neutralizing response against Alpha variant. Nevertheless, the neutralizing response against Beta, Delta and Gamma variants was significantly reduced compared with wild type . The assAt present, the booster vaccination is being carried out globally, and several studies indicated that booster vaccination can effectively induce B cells and strengthen T cell response to recognize VOCs . FurtherVaccine-induced neutralizing antibody titres appear to be a powerful predictor of VE against VOC. Studies based on in vitro neutralization assays showed that neutralizing antibody titres required to prevent severe disease were sixfold lower than symptomatic infections ,29, whicAnother finding in our study is that the performance of vaccines in high-risk populations was less effective than that among the general population. Studies of immunogenicity assessment reveal that age differences can affect vaccine efficacy, with lower geometric mean titres (GMT) among the elder group compared to the young group, suggesting that the young group had better immunogenicity . A studyIn addition, we also found that the VE of mRNA vaccine was relatively higher than that of other vaccine products. The evidence from clinical trials further supported our findings that mRNA vaccines are found to be better immunogenicity, with higher GMT and stronger cell responses compared to viral vector platforms ,34. The This study has several limitations. Firstly, studies evaluating each VOC are out of proportion, and we did not evaluate VE against certain clinical outcomes caused by VOCs limited by the available evidence. For example, only six studies covered the Beta variant, and we only evaluated the effectiveness of the vaccine against infection. This was also used for subgroup analyses by study population and vaccine product. Second, the identification of vaccination status showed subtle differences in the studies we included. Most studies defined full vaccination as receipt of the second dose of COVID-19 vaccines (the first dose of Ad26.COV2.S\u2009\u2265\u200914 days) before the testing or other clinical outcomes occur. However, there were still a few studies that define 7 days or more instead of 14 days as full vaccination. The previous study reveals that this slight difference in follow-up time does not differ in evaluation of VE . InitialIn conclusion, our findings indicate that full vaccination provided strong protection against Alpha, moderate protection against infection caused by Beta, Gamma and Delta, strong protection against severe disease caused by Delta, limited protection against infection and moderate protection against severe diseases caused by Omicron. Booster vaccination can provide a substantial improvement in protection against Delta and Omicron, but not as much as the Delta. Meta-regression analysis showed that the VE against the Omicron wanned over time, and the VE against hospitalization declined relatively slowly compared to against infection. In the context of a global expansion of the omicron variant and infectious wave driven by new variants in the future, those finding supported the need for public health measures, increasing booster vaccination coverage and developing vaccines against a wide range of variants to confront virus evolution.Click here for additional data file."} +{"text": "ProSAVE (NCT04158804) is the first prospective interventional RCT to address the effect of procalcitonin (PCT)-guidance in the setting of antimicrobial stewardship (ASP) oversight on clinical outcomes and antibiotics usage for patients admitted with pneumonia.Analysis of the pilot cohort from a multicenter trial was conducted enrolling subjects admitted with pneumonia at three clinical sites . Subjects meeting eligibility criteria were randomized 1:1 between the standard of care (SoC) versus PCT-guided ASP oversight (PCT arm); subjects were monitored daily by chart review for up to 30 days. An FDA-approved PCT algorithm was used to guide antimicrobial usage.95 patients were enrolled as ITT of which 60 patients were assigned per-protocol who were adherent to the PCT algorithm (30 in SoC and 30 in the PCT arm). Primary study endpoints were antimicrobial usage and composite safety comprising readmission, death, intubation, septic shock, renal failure, and pneumonia complications such as empyema and abscess up to day 30.Baseline subject characteristics were similar between both arms; median age 73y , and diabetes (23% SoC vs. 29% PCT arm). Early antimicrobial cessation by day 4 of hospitalization was achieved more often in the PCT arm as compared to SoC . In addition, antimicrobial prescription at discharge was lower in the intervention arm . A substantial statistically significant improvement of safety was observed in the PCT arm compared to SoC (reduction by 18.3% (95%-CI: 2.3% \u2013 36.3%) from 23.3% to 3.3% in PP, similar in ITT) . Readmission was the main driver for fewer safety events in the intervention arm (SoC 50% vs. PCT arm 33%).In this pilot cohort of ProSAVE, the introduction of PCT-guided, ASP intervention to medical teams proved to be a successful aid for resourceful antibiotic management decisions resulting in shorter antibiotic durations and significantly lower adverse event rates.Michael Mansour, MD, PhD, ThermoFisher Scientific: Grant/Research Support."} +{"text": "Lung cancer screening saves lives, but implementation is challenging. We evaluated two approaches to early lung cancer detection\u2014low-dose computed tomography screening (LDCT) and program-based management of incidentally detected lung nodules.A prospective observational study enrolled patients in the early detection programs. For context, we compared them with patients managed in a Multidisciplinary Care Program. We compared clinical stage distribution, surgical resection rates, 3- and 5-year survival rates, and eligibility for LDCT screening of patients diagnosed with lung cancer.P = .0005); 47%, 42%, and 32% had curative-intent surgery (P < .0001); aggregate 3-year overall survival rates were 80% versus 64% (60 to 68) versus 49% (46 to 53); 5-year overall survival rates were 76% (67 to 87) versus 60% (56 to 65) versus 44% (40 to 48), respectively. Only 46% of 1,858 patients with lung cancer would have been deemed eligible for LDCT by US Preventive Services Task Force (USPSTF) 2013 criteria, and 54% by 2021 criteria. Even if all eligible patients by USPSTF 2021 criteria had been enrolled into LDCT, the Nodule Program would have detected 20% of the stage I-II lung cancer in the entire cohort.From 2015 to May 2021, 22,886 patients were enrolled: 5,659 in LDCT, 15,461 in Lung Nodule, and 1,766 in Multidisciplinary Care. Of 150, 698, and 1,010 patients diagnosed with lung cancer in the respective programs, 61%, 60%, and 44% were diagnosed at clinical stage I or II, whereas 19%, 20%, and 29% were stage IV (LDCT and Lung Nodule Programs are complementary, expanding access to early lung cancer detection and curative treatment to different-risk populations. Implementing Lung Nodule Programs may alleviate emerging disparities in access to early lung cancer detection. However, most patients diagnosed with lung cancer in the Nodule Program would have been ineligible for LDCT by standard screening eligibility criteria.RelevanceLDCT and Lung Nodule Programs have great complementarity in identifying early-stage lung cancer in diverse populations, when curative-intent treatment is more likely, safer, and less expensive. Implementing Lung Nodule Programs may expand access to early lung cancer detection, potentially reducing disparities.5 Annual LDCT was recommended by the US Preventive Services Task Force (USPSTF) in 2013 for patients age 55-80 years with a 30 pack-year history of smoking within 15 years.6 The USPSTF extended eligibility in 2021 to individuals as young as 50 years, with the smoking intensity as low as 20 pack years, but retained the requirement for active smoking or cessation within 15 years.8 These criteria do not capture the full spectrum of individuals at risk for lung cancer.11 Screening rates in eligible US adults only increased from 3.3% in 2016 to 5% in 2018.12 Furthermore, eligibility for, access to, and participation in LDCT are rapidly expanding health care disparities.15 Current eligibility criteria underestimate the risk in women and racial minorities11; there is a geographic mismatch between per-capita lung cancer mortality rates and availability of lung cancer screening facilities.15Low-dose computed tomographic screening for lung cancer (LDCT) saves lives.16 Lung nodule management guidelines exist,19 but are infrequently followed.22 Guideline-concordant management of incidentally detected lung nodules requires infrastructure.23 The potential for synergy between such Lung Nodule and LDCT Programs is unclear, especially in high lung cancer incidence, granuloma-endemic regions such as the Mississippi Delta.Irrespective of indication, radiologic tests often reveal potentially malignant lung lesions.We compared individuals diagnosed with lung cancer through concurrently deployed LDCT and Lung Nodule (early detection) Programs and those managed in a Multidisciplinary Thoracic Oncology Program. We hypothesized that the characteristics of lung cancer would be similar between the early detection programs; they would have synergy by reaching different-risk populations; patients diagnosed through both programs would have earlier stage and better outcomes than those diagnosed outside them.24We constructed a prospective observational cohort, Detecting Early Lung Cancer (DELUGE) in the Mississippi Delta, using routinely generated clinical data of all patients managed through the LDCT or Lung Nodule Program with approval of the Baptist Memorial Health Care Corporation (BMHCC) Institutional Review Board. We compared DELUGE participants with participants in the Multidisciplinary Thoracic Oncology Program at BMHCC. BMHCC, a community-based health care system with institutions across Eastern Arkansas, Mississippi, and Western Tennessee, provides care to populations in 111 counties, including counties in Southwestern Kentucky, Southeastern Missouri, and Northwestern Alabama. These counties have some of the highest per-capita lung cancer incidence and mortality rates in the United States; 44% are persistent poverty counties in the Delta Regional Authority, whose 252 counties and parishes are designated by the US Congress as the most socioeconomically distressed.LDCT Program in 2015 for consenting apparently healthy individuals who met USPSTF 2013 lung cancer screening eligibility criteria.6 We used the American College of Radiology Lung Imaging Reporting and Data System (Lung-RADS) to categorize patients' risk and triage care.26 Data from the LDCT program are prospectively reported to the American College of Radiology Registry.28We implemented the Lung Nodule Program in 2015 as a safety net when radiologic studies, irrespective of indication (other than known or suspected cancer), revealed a potentially malignant lung lesion. Patients were automatically captured daily from radiology reports that included a standardized statement . Trained navigators used Fleischner Society Lung Nodule Management Guidelines for risk stratification.19We concurrently implemented a The provider who ordered the radiologic study was notified of the radiologist's concern and offered assistance with further management in the Nodule Program. Patients whose physicians accepted this offer were directly contacted and given the recommendations for subsequent care . Patients for whom an invasive procedure was recommended were evaluated by a pulmonologist or general thoracic surgeon in a Lung Nodule Clinic and also presented in the Multidisciplinary Thoracic Oncology Conference. Patients whose physicians refused the offer of support were not contacted by the program staff.30 Patients from within and outside the health care system with suspected lung cancer could be referred for discussion.In 2011, we implemented a weekly Multidisciplinary Thoracic Oncology Conference involving thoracic surgeons, radiation oncologists, pulmonologists, medical oncologists, pathologists, radiologists, nurse navigators, and clinical research coordinators.Each program had its own specific, structured database. From 2011 onward, data on all patients presented in the Multidisciplinary Conference were captured in a database. From 2015 onward, information on patients with any radiologic test in which the standardized statement was used was captured in the Lung Nodule Program database; information on patients who underwent LDCT from across the health care system (identified through procedure code 71271) was entered into the LDCT database.32 Data abstraction, management, and updates followed prespecified standard operating procedures .Trained data managers prospectively abstracted information from the electronic health record of all patients evaluated within each program. Data on clinical events were abstracted from routinely generated clinical records. Study data were collected and managed in research electronic data capture (REDCap), a secure, web-based software platform for research studies.33For this analysis, we included patients in the LDCT or Nodule Program databases from 2015 to May 2021. The Multidisciplinary Care cohort included patients from 2015 to December 2020, who were not registered in either early detection database. Rurality was determined by the Rural-Urban Commuting Area code of the patient's zip code of residence at diagnosis.Death information was obtained from prospective review of the electronic health record and from the institution's tumor registries at six-month intervals.34 Statistical analyses were performed using R Studio 4.7 and SAS Version 9.4 . We followed the Strengthening the Reporting of Observational Studies in Epidemiology reporting guidelines.We summarized patient characteristics, care delivery and outcomes with frequencies, percentages, medians, and interquartile ranges (IQRs) and used chi-squared tests, Fisher's exact tests, and type III overall F tests from analysis of variance for comparisons across programs. We estimated overall survival using the Kaplan-Meier method and compared it across programs using the log-rank test. We further evaluated the survival impact of the two early detection programs using Cox proportional hazard regression to estimate pairwise hazard ratios, with 95% CI comparing each program. We used unadjusted models and multivariable models adjusted for age, sex, race, insurance, rurality, smoking status, and Charlson comorbidity index. Survival information was censored on August 31, 2021, and patients with missing mortality data were excluded. We set the alpha level at .05 and applied the false discovery rate approach to account for multiple comparisons.P < .0001). The quit duration was a median of 7 years (IQR: 4-11) in the LDCT, 17 years (7-32) in the Nodule, and 12 years (5-25) in the Multidisciplinary Program (P < .0001).The cohort included 5,659 patients in LDCT, 15,461 in the Lung Nodule, and 1,766 in the Multidisciplinary Care Programs although only 1%, 3%, and 6% had previously had lung cancer. A family history of lung cancer was identified in 13%, 8%, and 18%. In the LDCT cohort, 84% were initially categorized as Lung-RADS 1 or 2, 7% as 3, and 7% as 4 or uninsured (4% v 1%). They were also more likely to have quit smoking (40% v 28%); in addition, 13% had never smoked. Similarly, 14% of patients diagnosed with cancer in the Multidisciplinary Program had never smoked. By contrast, 72% of LDCT enrollees diagnosed with cancer still actively smoked.Cancer was diagnosed in 156 of 5,659 (3%) patients in the LDCT, 772 of 15,461 (5%) in the Nodule, and 1,139 of 1,766 (65%), in the Multidisciplinary Programs (Table P < .0001). Similar proportions of patients in the three programs had a personal history of cancer: 26% versus 30% versus 32% (P = .1763); but LDCT enrollees were least likely to have previously had lung cancer\u20141% versus 5% versus 7%, respectively (P = .020). Twenty-four percent, 20%, and 20% of patients diagnosed with cancer from each respective program had a family history of lung cancer. The first Lung-RADS scores of LDCT enrollees were 1 in 6%, 2 in 9%, 3 in 9%, and 4 in 70%. Results were similar in the Lung Nodule Program cohort age 50-80 years (Appendix Table AThe median quit duration was 8 (IQR: 3-11) years in the LDCT, 16 7-28) years in the Nodule Program, and 11 (4-24) years in the Multidisciplinary Program cohort diagnosed with cancer .One hundred fifty, 698, and 1,010 patients had lung cancer and those from the Nodule Program had 0.74 (0.59 to 0.921) compared with the Multidisciplinary Program . This reveals great complementarity between LDCT and Lung Nodule Programs, tandem deployment of which can extend the possibility of early detection of lung cancer to a wider spectrum of the population than LDCT alone. The programs reached different demographic segments of the population, potentially providing a means of overcoming the looming problem of access disparity to lung cancer screening, which threatens to widen racial, sex, and socioeconomic and geographic disparities in lung cancer mortality.42Even if all eligible patients were enrolled into LDCT, 46% of patients diagnosed with lung cancer would have been deemed ineligible. In reality, given the prevailing low levels of adoption, only 8% of patients with lung cancer in this cohort received LDCT screening; 38% were detected through the Nodule Program, including 44% of patients diagnosed with localized disease and lower-than-expected proportion of patients with stage IV (29%) as compared with the US distribution (15% early stage and 40%-50% stage IV).LDCT and Lung Nodule Programs have great complementarity in redistributing lung cancer to early stage when curative-intent treatment is more likely, safer, and less expensive. Lung Nodule Programs may expand access to hard-to-reach individuals and may be less susceptible to multilevel implementation barriers."} +{"text": "This predictive model for preterm birth based on aberrant microRNA expression profile was further improved via implementation of maternal clinical characteristics , and presence of any kind of autoimmune disease ). With this model, 69.81% of pregnancies destined to deliver before 37 gestational weeks were identified with a 10.0% FPR at early stages of gestation. When other clinical variables as well as those mentioned above\u2014such as positive first-trimester screening for early preeclampsia with onset before 34 gestational weeks and/or fetal growth restriction with onset before 37 gestational weeks using the Fetal Medicine Foundation algorithm, as well as positive first-trimester screening for spontaneous preterm birth with onset before 34 gestational weeks using the Fetal Medicine Foundation algorithm\u2014were added to the predictive model for preterm birth, the predictive power was even slightly increased to 71.70% with a 10.0% FPR. Nevertheless, we prefer to keep the first-trimester screening for any type of preterm birth occurring before 37 gestational weeks in the absence of other pregnancy-related complications as simple as possible.The goal of the study was to establish an efficient first-trimester predictive model for any type of preterm birth before 37 gestational weeks (spontaneous preterm birth (PTB) or preterm prelabor rupture of membranes (PPROM)) in the absence of other pregnancy-related complications, such as gestational hypertension, preeclampsia, fetal growth restriction, or small for gestational age. The retrospective study was performed in the period from 11/2012 to 3/2020. Peripheral blood samples were collected from 6440 Caucasian individuals involving 41 PTB and 65 PPROM singleton pregnancies. A control group with 80 singleton term pregnancies was selected on the basis of equal sample-storage time. A combination of only six microRNAs (miR-16-5p, miR-21-5p, miR-24-3p, miR-133a-3p, miR-155-5p, and miR-210-3p; AUC 0.812, Spontaneous preterm birth (PTB) is characterized as delivery before the completion of 37 gestational weeks induced by regular uterine contractions along with cervical changes. Preterm prelabor rupture of membranes (PPROM) is defined as leakage of amniotic fluid that precedes the onset of labour by at least 2 h ,2,3.An algorithm for the prediction of PTB with onset before 34 gestational weeks in the early stages of gestation exists that is based only on maternal characteristics combined with previous obstetrics history ,6,7,8,9.Recently, we demonstrated that a set of 12 microRNA biomarkers can predict any type of preterm delivery that is uncomplicated by hypertensive and/or growth-restricted pregnancy disorders. This set of microRNA biomarkers revealed 52.83% of pregnancies destined to deliver before 37 gestational weeks with a 10.0% FPR in early stages of gestation [p < 0.001, 70.75% sensitivity, 78.75% specificity, cut-off > 0.652, 52.83% of cases with a 10.0% FPR) [Similarly, we have shown that a combination of a minimal number of microRNAs can also predict any type of preterm delivery before 37 gestational weeks in the absence of other pregnancy-related complications in early stages of gestation with similar discrimination power in the absence of hypertensive and/or growth-restricted pregnancy disorders or gestational diabetes mellitus. Since other pregnancy-related complications have already been reported to be associated with an altered expression profile for cardiovascular disease-associated microRNAs by our research group ,12,13, fWe were interested in whether the predictive model for any type of preterm birth before 37 gestational weeks (PPROM or PTB) in the absence of other pregnancy-related complications based on an aberrant microRNA expression profile could be further improved via implementation of other maternal clinical characteristics.This study was performed in a retrospective manner for the period from 11/2012 to 3/2020. The peripheral blood was sampled from 6440 singleton Caucasian pregnancies during the first-trimester prenatal screening. A total of 4469 pregnancies had complete medical records. Ultimately, 41 pregnancies were diagnosed as PTBs, and 65 pregnancies were confirmed to have diagnoses of PPROM, among which 29 preterm births occurred before 34 gestational weeks and 77 after 34 gestational weeks. Only those pregnancies that occurred in the absence of other pregnancy-related complications were involved in the study.n = 80) consisted of normal-term pregnancies and was selected with regard to the equality of gestational age at the time of peripheral blood sampling and the equality of biological sample-storage time.A control group and of early PE before 34 gestational weeks, FGR before 37 gestational weeks, and PTB before 34 gestational weeks was produced by Astraia Software gmbh, Germany (Astraia Obstetrics Programme), in close collaboration with the Fetal Medicine Foundation (FMF) .n = 106) were predicted to develop early PE before 34 gestational weeks and/or FGR before 37 gestational weeks. In compliance with the ACOG 2018 guidelines [Ten women from the group with preterm pregnancies were predicted to be at risk of PTB before 34 gestational weeks. The risk of PTB was below the cut-off value of 1:100. Four of these twenty-seven women were simultaneously found to be positive for early PE before 34 gestational weeks and/or FGR before 37 gestational weeks in first-trimester screening. ASA was ultimately given to two of these four women. Simultaneously, 6 out of 80 control term-pregnancies (7.50%) were also identified to be at risk of PTB before 34 gestational weeks.Furthermore, 27 women (25.47% cases) from the group with preterm pregnancies . Reverse transcription was performed with a total reaction volume of 10 \u00b5L using miRNA-specific stem loop primers and a TaqMan MicroRNA Reverse Transcription Kit ,17,18,19MicroRNA gene expression was assessed using the delta-delta Ct method as previously described ,18,19,20\u2217Power Version 3.1.9.6, Franz Faul, University of Kiel, Germany). To achieve a power of 0.805, 51 cases and 51 controls needed to be tested. Similarly, to achieve a power of 0.902, 70 cases and 70 controls needed to be tested.Initially, power analysis was performed to calculate the minimum sample size required . Afterwards, Benjamini\u2013Hochberg correction was applied.Receiver operating characteristic (ROC) curve analysis was performed for each individual microRNA biomarker to assess the area under the curve (AUC), the cut-off point-associated sensitivity, specificity, positive and negative likelihood ratios , and sensitivity at 90.0% specificity ) .To select microRNA combinations, logistic regression and ROC curve analyses were applied .To assess the detection rate of pregnancies with preterm birth before 37 gestational weeks on the base of a combination of microRNA biomarkers dysregulated in early stages of gestation and maternal clinical characteristics, logistic regression with subsequent ROC curve analyses were again applied .Concerning the microRNA expression studies only, both pilot and validation studies with two independent cohorts of patients were initially performed.n = 65) and PTB (n = 41) were reported [n = 65) and PTB (n = 41). Model validation studies would have been beneficial and desirable but would have required further long-term collection of samples within the framework of routine first-trimester prenatal screening to achieve a sufficient number of cases.Then, experimental microRNA expression data obtained from a larger independent cohort of patients with histories of PPROM , the presence of any kind of autoimmune disease , and positive first-trimester screening for early PE before 34 gestational weeks and/or FGR before 37 gestational weeks using the FMF algorithm, together with positive first-trimester screening for PTB before 34 gestational weeks, represent independent significant risk factors for the subsequent onset of any type of preterm birth before 37 gestational weeks (PTB or PPROM).p < 0.001, 73.58% sensitivity, 88.75% specificity, cut-off > 0.642930). It revealed, in early stages of gestation, 69.81% of pregnancies destined to deliver before 37 gestational weeks with a 10.0% FPR , and the presence of any kind of autoimmune disease ) and six dysregulated microRNA biomarkers demonstrated very good accuracy for the identification of pregnancies destined to deliver before 37 gestational weeks . It revealed, in early stages of gestation, 66.98% of pregnancies destined to deliver before 37 gestational weeks with a 10.0% FPR , and the presence of any kind of autoimmune disease ) combined with 12 dysregulated microRNA biomarkers also demonstrated very good accuracy for the identification of pregnancies destined to deliver before 37 gestational weeks . It revealed, in early stages of gestation, 71.70% pregnancies destined to deliver before 37 gestational weeks with a 10.0% FPR , the presence of any kind of autoimmune disease , positive first-trimester screening for early PE before 34 gestational weeks and/or FGR before 37 gestational weeks using the FMF algorithm, and positive first-trimester screening for PTB before 34 weeks of gestation using the FMF algorithm) with six dysregulated microRNA biomarkers showed the highest possible accuracy for the early identification of pregnancies destined to deliver before 37 gestational weeks . It revealed, in early stages of gestation, 73.58% of pregnancies destined to deliver before 37 gestational weeks with a 10.0% FPR , the presence of any kind of autoimmune disease , positive first-trimester screening for early PE before 34 gestational weeks and/or FGR before 37 gestational weeks using the FMF algorithm, and positive first-trimester screening for PTB before 34 gestational weeks using the FMF algorithm) and 12 dysregulated microRNA biomarkers also showed the highest possible accuracy for the early identification of pregnancies destined to deliver before 37 gestational weeks targets.It is also generally accepted that progesterone plays an important role in the maintenance of uterine quiescence until the perinatal period. Progesterone maintains uterine quiescence and reduces uterine contractility through the mediation of multiple actions involving membrane ion channels, expression of receptors and agonists, intracellular cAMP and protein kinase A (PKA) signaling, calcium signaling, and contractile proteins . At the A set of 12 microRNA biomarkers alone demonstrated similar discrimination power in predicting during early stages of gestation any type of preterm delivery (PTB or PPROM) occurring before 37 gestational weeks in the absence of hypertensive and/or growth-restricted pregnancy disorders or gestational diabetes mellitus as the set of six microRNA biomarkers alone . Both combinations of microRNAs alone were able to predict preterm delivery occurring before 37 gestational weeks in 52.83% of cases with a 10.0% FPR. Therefore, the combination of six microRNAs was considered sufficient to for implementation as a fundamental variable in a model for the prediction in early stages of gestation of the occurrence of any type of preterm delivery (PTB or PPROM) occurring before 37 gestational weeks in the absence of other pregnancy-related complications, such as GH, PE, FGR, or SGA.The implementation of other essential maternal clinical characteristics in this predictive model, such as maternal age and BMI at early stages of gestation, infertility treatment with assisted reproductive technology, the occurrence of preterm delivery before 37 gestational weeks in previous pregnancy(ies), and the presence of any kind of autoimmune disease, could significantly improve the detection rate of any type of preterm birth (PTB or PPROM) occurring before 37 gestational weeks in the absence of other pregnancy-related complications, such as GH, PE, FGR, or SGA. This model was able to identify 69.81% of cases with a 10.0% FPR at early stages of gestation.The implementation of other variables in this predictive model for preterm birth, such as positive first-trimester screening for early PE with onset before 34 gestational weeks and/or FGR with onset before 37 gestational weeks and positive first-trimester screening for PTB with onset before 34 gestational weeks, both using the FMF algorithm, would be possible but is not necessary. It slightly increased the detection rate to 71.70% of cases with a 10.0% FPR.The novel predictive model for any type of preterm birth (PTB or PPROM) occurring before 37 gestational weeks in the absence of other pregnancy-related complications, such as GH, PE, FGR, or SGA, was based on the combination of the expression profiles of six microRNA in whole peripheral blood samples and basic maternal clinical characteristics, such as maternal age and BMI at early stages of gestation, infertility treatment with assisted reproductive technology, the occurrence of preterm delivery before 37 gestational weeks in previous pregnancy(ies), and the presence of any kind of autoimmune disease. It was able to predict 69.81% of cases in the early stages of gestation with a 10.0% FPR.The implementation of additional variables in this predictive model, such as positive first-trimester screening for early PE with onset before 34 gestational weeks and/or FGR with onset before 37 gestational weeks and positive first-trimester screening for PTB with onset before 34 gestational weeks, both using the FMF algorithm, increased the detection rate of preterm births to 71.70% of cases with a 10.0% FPR.Consecutive large-scale studies involving other ethnic groups and multiple pregnancies are needed to verify the data resulting from this pilot study. Future work will also involve the use of machine-learning techniques for predicting preterm labor, measurements of heart rate variability, and electrohysterography, a noninvasive procedure to monitor contractions during pregnancy.National patent application\u2014Industrial Property Office, Czech Republic (patent n. PV2021-562)."} +{"text": "Premenstrual syndrome (PMS) is a physiologic process in women where mood swing is one of the symptoms influencing the psycho-emotional, physical, and behavioral reactions exhibited by women during menstruation. This study elucidates the effect of mood swing, confounding factors and healthcare-seeking behaviors of women in an educational environment.Exactly 328 women who were within reproductive ages 16 and 35 years participated in this study. A survey method was adopted; validated and standardized questionnaires were administered to confidentially assess the effect of mood swing via PMS. All data were analyzed with SPSS 25.0; descriptive method was adopted and results were expressed in percentages.Mood swing was discovered as a symptom overlapping with psycho-emotional, physical, and behavioral symptoms during menstruation. The overall PMS prevalence was 67.4% while PMDD prevalence was 25.6%. Psycho-emotional symptoms: anger, irritability, depression. Physical symptoms: coldness, paleness, food craving, breast tenderness, digestive changes. Behavioral symptoms: social withdrawal, nocturnal social activity, absenteeism, poor work or academic performance, increased libido. Confounding factors include stress, gynecological conditions such as endometriosis, uterine fibroid, ovarian cyst, pelvic adhesion, and polycystic ovarian syndrome. Also, 22.9% had a family history of bipolar disorder (BD) while 30.2% had previous diagnosis. Severe pain was a major factor for seeking treatment; Paracetamol, and Piroxicam were frequently used drugs.Severe PMS triggers mood swing and can badly affect academic or work activities; victims either endure the pain due to socio-cultural and financial factors or take unsuitable medications where abuse is inevitable. Menstruation is a normal, repetitive, reproductive physiological process in women characterized by the shedding of the upper endometrium which begins at puberty and stops at menopause , 2. ThisThe aetiology of PMS remains unknown but some factors attributed to nutrition such as amino acids, calcium, magnesium and vitamin B deficiencies; sex hormones as observed in the interplay of oestrogen and progesterone, also the excitatory and inhibitory roles of both serotonin and gamma-aminobutyric acid (GABA) are possible parameters for PMS development , 8. Othe6, exercising, yoga, and stress reduction programs . The questionnaire's reliability testing was done using Cronbach's alpha and a value of 0.7 or higher was considered reliable. The overall frequencies were expressed as the mean frequencies in percentages (%).Ethical clearance: The ethical clearance was obtained from the Research and Ethics Committee of the Faculty of Basic Medical Sciences (DELFBMS/0234).The reliability test revealed Cronbach's alpha to be 0.863; the overall prevalence of PMS and PMDD were 67.4% (221) and 25.6% (84) respectively as shown in Also, 22.9% (75) had a family history of bipolar disorder, while 30.2% (99) had previous diagnosis of bipolar disorder as shown in Results in The overall pain prevalence was 69.5% (228) experienced at different threshold , where 2As shown in Moreover, 26.5% (87) used Paracetamol; 14.3% (47) used Piroxicam; 4.3% (14) used Ibuprofen; 3.0 % (10) used Ladinax; 2.7% (9) used Aspirin while 9.1% (30) used other pain medications . ReasonsIn the present study, the observed Cronbach's alpha 0.863) was greater than 0.7 standard statistical values, indicating that the instrument was valid and reliable. Also, Mood swing was discovered as a symptom overlapping with psycho-emotional, physical, and behavioural symptoms in women during menstruation, suggesting that these symptoms are relatively associated. The overall PMS prevalence was 67.4% which was slightly higher than but comparable to 67% reported from Ethiopia was grea, far belThe recorded array of prevalence of psycho-emotional symptoms physical and behavioural symptoms in the present study agrees with other reports from Saudi Arabia, Nigeria, and Japan respectively even though, they were categorized differently , 12, 22.The observed 25.6% PMDD prevalence was lesser, but comparable to 34.7% prevalence reported from Ethiopia, while it was far below 47.6% and 61% reported from Nigeria and Japan respectively . This diMoreover, 30.2% had previous diagnosis of bipolar disorder (BD) while 22.9% had a family history of bipolar disorder, suggesting a critical factor for mood swing, which may be aggravated by menstrual cycle. This finding agrees with a review among females with BD where 45% to 68% experienced premenstrual mood symptoms while women with PMDD have higher chances of bipolar disorder diagnosis . AnotherIn this study, stress was observed to contribute to high prevalence as studying or working in academic/clinical environment comes with associated stress in Nigeria , 11, 22.The findings that 12.5% participants had endometriosis, 14.9% had uterine fibroid, 12.8% had pelvic adhesion, while 14.0% had ovarian cyst and polycystic ovarian syndrome respectively, suggests that there may be an association between these gynaecological conditions and premenstrual symptoms like anxiety, dysmenorrhea, menorrhagia, abnormal vaginal bleeding and pain threshold which may trigger the healthcare-seeking behaviour in women. Endometriosis usually presents symptoms such as menstrual bleeding (menorrhagia), painful periods (dysmenorrhea), painful intercourse (dyspareunia), painful defecation (dyschezia), painful urination (dysuria) as well as pelvic pain, all of which vary in women, and largely agrees with this study . FurtherSevere pain and its interference with academic/work performance was observed in to be the major reason for seeking healthcare. The overall pain prevalence was 69.5%, this agrees with 68.7%, 66.9%, and 73.6% previously reported from China, India and Ethiopia respectively, another study reported that nearly two-thirds with chronic acyclic pain undergoing laparoscopy had endometriosis , 28, 29.Reasons for taking drugs include headache (13.7%), paleness (22.3%) and other types of pain (24.1%). Paleness, as observed in this study suggests that some women may have heavy menstruation resulting into severe anaemia. Gynaecological conditions as well as genotype of the patient may account for increased predisposition of women to severe anaemia during menstruation.The frequency of most commonly used pain medications concur with previous studies (19. 28. 30). However, not all subjects who used pain medications got relieved and this may be due to the choice of drug, underlying health conditions such as paleness associated with anaemia, financial ability, the educational and/or professional background of the patient.In conclusion, PMS and PMDD prevalence among young girls and women is relatively high. Mood swing was observed as a symptom overlapping with psycho-emotional, physical and behavioural symptoms. Underlying diseases such as bipolar disorders, previous history of bipolar disorder and gynaecological diseases like endometriosis, uterine fibroid, ovarian cysts and post cystic ovarian syndrome are the major culprits for mood swing thereby causing the exacerbation of PMS resulting into PMDD. Additionally, stress is another confounding factor aggravating PMS in both women with or without underlying conditions, resulting in PMDD. Consequently, PMDD can trigger mood swing and can badly affect academic/work activities when accompanied with severe pain. Victims either ignorantly endure the pain due to socio-cultural and financial factors or take unsuitable medications and drug abuse is inevitable. Hence, there is need for the government and relevant institutions to educate young girls and women about menstruation, how to manage some of the symptoms and when to consult medical personnel."} +{"text": "Papillary thyroid carcinoma (PTC) is the most common form of thyroid cancer. Several studies have proposed serum microRNAs (miRNAs) as novel biomarkers for diagnosing PTC. In this study, we conducted a meta-analysis aiming to investigate the overall diagnostic accuracy of serum miRNAs in PTC detection. Three online databases including PubMed, EMBASE, and Cochrane Library were searched up to 1 May 2021. We systematically reviewed studies evaluating the value of serum miRNAs in diagnosing PTC, and then summarized the area under receiver operating characteristics curve (AUROC), sensitivity, specificity, and diagnostic odds ratio to assess the accuracy of serum miRNAs for the discrimination between patients with PTC and patients with benign thyroid nodules and healthy controls. We included 32 studies from 6 articles. Overall, there were 463 PTC patients, 334 patients with benign thyroid nodules, and 104 healthy controls. The results showed that the summary sensitivity and specificity were 76% and 86% (95% CI: 80-91%), respectively, and that the summary AUROC was 0.89 (95% CI: 0.86-0.91), when serum miRNAs were used for discriminating between PTC patients and those with benign nodules. On the other hand, the summary sensitivity and specificity of serum miRNAs for discriminating between PTC patients and healthy controls were 82% (95% CI: 77-86%) and 84% (95% CI: 76-90%), respectively, and the summary AUROC was 0.89 (95% CI: 0.86-0.92). We found that serum miRNAs have good diagnostic performance for the discrimination between patients with PTC and patients with benign nodules and healthy controls, and thus have considerable potential as novel minimally invasive tools for detecting PTC. Over the past three decades, the global incidence of thyroid cancer has increased markedly, ranking sixth among all malignant tumors ,2. AmongFine needle aspiration biopsy (FNAB) is considered to be the most reliable method to evaluate thyroid nodules . As a thMicroRNAs (miRNAs) are a class of endogenous non-coding RNA molecules that regulate transcription and translation, which have gained tremendous attention in research in the last two decades given their ability to regulate gene expression ,10. ThroIn contrast, samples of blood are easily available, essentially noninvasive, and can be collected at lower cost, all of which make blood samples attractive to explore for potential biomarkers . CirculaMolecular biomarkers have exhibited promising results in cancer, which may improve the preoperative management of patients . In thisThe preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed for reporting this systemic review and meta-analysis . In our The articles were included if they met the following criteria: (1) the study assessed the diagnostic accuracy of circulating serum miRNAs for the detection of PTC; (2) the study used pathological examination as the reference standard; and (3) sufficient data from the study was reported to construct a 2 \u00d7 2 table for test performance, including true positives, false positives, false negatives, and true negatives. The exclusion criteria were: (1) articles were abstracts, reviews, letters, case reports, and comments; (2) duplicate publications; (3) lack of sufficient data; (4) simple descriptive studies without control groups; and (5) not in English.Two researchers (CYP and DBT) independently screened the literature and extracted the data according to the inclusion and exclusion criteria described above. We extracted primary data from the studies, including first author, publication year, region, study design, patients\u2019 age, patients\u2019 gender, method of serum miRNAs detection, the target miRNAs, and the expression of miRNAs. In addition, the performance indices of different detected miRNAs were also extracted from each included article, including cutoff values, sensitivity, specificity, and area under the receiver operating characteristic curve (AUROC) values. In the present meta-analysis, if an article studied more than one miRNAs tests, we considered each miRNA test to be an independent study. Using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tool , the qua2 was calculated and then used to qualify the amount of non-threshold heterogeneity when an I2 \u2265 50%, heterogeneity may be assumed. To explore the potential sources of heterogeneity, we then performed meta-regression analyses using the following covariates: (1) Region ; (2) publication year ; (3) study design (prospective vs. retrospective); (4) sample size ; (5) miRNA profiling (single miRNAs vs. combination miRNAs); and (6) internal reference (miR-16 vs. cel-miR-39). Publication bias was assessed using the Deeks\u2019 funnel plot.The heterogeneity of the results between serum miRNAs studies was evaluated using the Cochrane-Q test. The inconsistency index IThe data were extracted from the included studies and then used to construct a series of 2 \u00d7 2 tables . First, the summary sensitivity and specificity, the summary positive likelihood ratio (PLR), negative likelihood ratio (NLR), and the summary diagnostic odds ratio (DOR) were calculated to examine the diagnostic accuracy of circulating serum miRNAs in PTC detection. In addition, the data from different studies included in our analysis were simultaneously used to construct the summary AUROC curves. Statistical analysis was performed using Stata 15.0 .The main characteristics of the included studies are summarized in A total of 21 studies investigated serum miRNAs for discriminating between PTC patients and those with benign thyroid nodules. Overall, 463 PTC patients and 334 patients with benign thyroid nodules were included for evaluation. On the other hand, 11 studies examined the performance of serum miRNAs in discriminating between PTC patients and healthy controls. A total of 463 PTC patients and 104 healthy controls were included for evaluation. As is shown in Notably, several kinds of miRNAs, including miRNA-146b, miRNA-221, and miRNA-222, have been extensively studied. We examined the performance of serum miRNA-222 in discriminating between PTC patients and those with benign thyroid nodules, showing pooled sensitivity and specificity of 70% and 90%, respectively, and a summary AUROC of 0.946. In addition, the summary DOR and PLR of serum miRNA-222 were 22.55 (95% CI: 11.59-43.87) and 7.01 (95% CI: 4.44-11.06), respectively. Results are shown in I2 = 91.60%) and specificity (I2 = 83.13%). Meta-regression analysis was then conducted (I2 = 72.88%) and specificity (I2 = 65.97%).Substantial heterogeneity was observed in serum miRNAs studies . When seonducted . We founp = 0.41). In addition, no evidence of publication bias was demonstrated for serum miRNAs for discriminating between PTC patients and healthy controls (p = 0.65).In this study, we conducted a meta-analysis with the aim to systematically review the current published data on the diagnostic accuracy of circulating serum miRNAs for PTC detection. We included 32 studies from 6 articles. Overall, a total of 463 PTC patients, 334 patients with benign thyroid nodules, and 104 healthy controls were included in the present meta-analysis for evaluation.Our study revealed that circulating serum miRNAs have good diagnostic performance to diagnose PTC and distinguish PTC patients from patients with benign thyroid nodule. The results showed that the summary sensitivity and specificity were 76% (95% CI: 68-83%) and 86% (95% CI: 80-91%), respectively, and the summary AUROC value was 0.89 (95% CI: 0.86-0.91), when serum miRNAs were used for discriminating between PTC patients and those with benign thyroid nodules. Similarly, the summary sensitivity and specificity of serum miRNAs for discriminating between PTC patients and healthy controls were 82% (95% CI: 77-86%) and 84% (95% CI: 76-90%), respectively, and the summary AUROC value was 0.89 (95% CI: 0.86-0.92). Our findings thus indicated that serum miRNAs can be used as novel, promising, and minimally invasive diagnostic tools for detecting PTC in clinical practice.The incidence of thyroid cancer has increased \u00adprogressively worldwide . In clinSimilarly, Xu et al. investigThere is an urgent need to develop novel and noninvasive markers for tumor detection, prediction, and prognosis for the management of cancer . In thisNoticeably, substantial statistical heterogeneity was present in our meta-analysis. Thus, we conducted meta-regression and subgroup analyses in order to explore the confounding factors. The results demonstrated that region, publication year, study design, and miRNA profiling could be the reasons for the heterogeneity in the summary sensitivity and specificity of serum miRNAs for discriminating between PTC patients and those with benign thyroid nodules; however, other covariates including sample size and internal reference were not significant factors. It is noteworthy that the results of subgroup analysis in terms of number of miRNAs showed that the combined miRNAs were better than single miRNAs in distinguishing PTCs from benign thyroid nodules, with a summary sensitivity of 84% vs 75%, specificity of 92% vs. 85%, AUROC of 0.94 vs. 0.87, and DOR of 69 vs. 16. The findings are in agreement with previous study focusing on thyroid cancer detection by Xu et al. [We acknowledge that some limitations still exist in our meta-analysis. First, we only focused on the full articles published in English, which may bias the results to some extent. Second, the number of articles on circulating serum miRNAs for the diagnosis of PTC was not adequate, so we could not set more stringent inclusion criteria. Furthermore, all included studies were conducted in China and Italy, which limited our conclusions for other ethnic populations. Future large prospective studies will, therefore, be needed. Third, cutoff values of serum miRNAs varied across the included studies because of the heterogeneous internal references and the different distribution stages of PTC in the experimental group, which can cause heterogeneity. Finally, our study may have several inherent limitations, such as the inability to identify optimal thresholds for serum miRNAs to detect PTC and the heterogeneity that may exist.Our results demonstrated that serum miRNAs have good diagnostic performance for the discrimination between patients with PTC from patients with benign thyroid nodules and healthy controls. Serum miRNAs can, therefore, be considered as novel, promising, and minimally invasive diagnostic tools for PTC in clinical practice. Additional studies with larger patient samples focusing on combination miRNAs will be needed to further validate their accuracy in PTC detection."} +{"text": "Background: Information on immune responses in cancer patients following mRNA COVID-19 vaccines is still insufficient, but generally, patients had impaired serological responses, especially those with hematological malignancies. We evaluated serological response to COVID-19 mRNA vaccine in cancer patients receiving chemotherapy compared with healthy controls. Methods: In total, 195 cancer patients and 400 randomly selected controls who had been administered a Pfizer-BioNTech or Moderna COVID-19 vaccines in two doses were compared. The threshold of positivity was 4.33 BAU/mL. Patients were receiving anticancer treatment after the first and second dose of the vaccines. Results: a TOTAL OF 169 patients (87%) had solid tumors and 26 hemolymphopoietic diseases. Seropositivity rate was lower in patients than controls (91% vs. 96%), with an age/gender-adjusted rate ratio (RR) of 0.95 (95% CL = 0.89\u20131.02). Positivity was found in 97% of solid cancers and in 50% of hemolymphopoietic tumors. Both advanced and adjuvant therapy seemed to slightly reduce seropositivity rates in patients when compared to controls . Conclusions: the response to vaccination is similar in patients affected by solid tumors to controls. On the contrary, hemolymphopietic patients show a much lower response than controls. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive sense, enveloped RNA beta coronavirus that emerged in Wuhan, China, in December 2019. It is the cause of the clinical disease known as COVID-19. It is plausible that the susceptibility of cancer patients to severe forms of COVID-19 is related more to a poor general status and comorbidities than to the cancer or therapies ,4. NeverDifferent therapies have been proposed to mitigate infective symptoms or post-viral sequelae of COVID-19 infection, including anticoagulants, anti-inflammatory drugs, antibodies contained in the plasma of convalescent patients, SARS-CoV-2-neutralizing monoclonal antibodies, stem cell-based therapies, and biological drugs, but the different spectrum of disease severity does not permit to identify a unified therapeutic strategy ,7. ThereCOVID-19 vaccines represent a major issue to decrease the risk of severe forms of the COVID-19 and to maintain a normal cancer care ,14. NeveHigh-risk patients with cancer who are candidates for priority access to vaccination are those treated by chemotherapy. The very high-priority population includes patients with curative treatment and palliative first- or second-line chemotherapy as well as patients requiring surgery or radiotherapy involving a large volume of lung, lymph node, and/or hematopoietic tissue .However, cancer patients, like other vulnerable subpopulations, may respond in a different way to vaccines and are less likely to mount an optimal immune response necessary to confer immunity. This potential limited response must be balanced against the vulnerability of patients receiving chemotherapy and the risk of serious adverse outcomes from COVID-19.Information on how novel mRNA vaccines elicit immune responses in cancer patients is still low, but generally, it has been shown that cancer patients had impaired serological responses respect to healthy individuals. In addition, the seroconversion rate was inferior in those with hematological versus solid cancers, particularly those following highly immunosuppressive therapies ,22,23,24For this reason, it is necessary to implement cohorts with immunological and clinical monitoring of vaccinated cancer patients on active treatment.In this observational study, we evaluated serological response to COVID-19 vaccination with mRNA vaccine in patients with solid and hematologic tumors receiving cancer chemotherapy in a real-world setting and compared it with the antibody production in healthy people who received same vaccines at the same time.The study included a group of 195 cancer patients (cases) followed in two hospitals in Genova (Villa Scassi and Micone) and 400 subjects randomly selected from a group of 3736 healthcare workers (controls) who had been intramuscularly administered a Pfizer-BioNTech BNT162b2 or Moderna mRNA-273 SARS-CoV-2 vaccine in two doses given 3 weeks apart by 12 February 2021. A mass vaccination program against COVID-19 in healthcare workers has been introduced in the hospitals, while vaccines have been administered to eligible oncologic patients starting with those over 65 years of age. All participants completed the full vaccination.Cases had a higher percentage of males (42.1% vs. 25.8%) and wereThe majority of cases had solid tumors (86.7%) with a greater prevalence of cancers of the breast (25.6%), colon-rectum (17.4%), lung (11.3%), and prostate (5.1%). Twenty-seven percent of patients had miscellaneous tumors: esophagus (2), stomach (5), pancreas (6), bladder (3), uterus , ovary , testis (2), and mesothelioma (6). In addition, there was one case for each of the following tumor types: gastrointestinal stromal (GIST); papilla of vater, bilio-pancreatic, neuroendocrine, vulva, head, and neck; liposarcoma, sarcoma, Kaposi sarcoma, kidney, anus, thymus, melanoma, and of unknown primary origin.Twenty-six cases had hemolymphopoietic (HLP) diseases, in particular: 3 Hodgkin\u2019s lymphomas (HL), 10 non-Hodgkin\u2019s lymphomas (NHL), 2 chronic lymphocytic leukemias (CLL), 3 myelomas, 2 essential thrombocythemia, and 6 of other histology, namely acute myeloid leukemia (AML), myelodysplasia, Waldenstrom macroglobulinemia (WM), monoclonal peak, plasmacytoma, and polycythemia vera (PV).Adjuvant therapy was given to 27.7% of cases, advanced therapy to 71.8% , and allPfizer and Moderna vaccines were administered to 56% and 44% of subjects, respectively, in equal proportion between cases and controls. Cancer patients were receiving active anticancer treatment after the first and second dose of the vaccines.Blood samples were taken on average 24.9 days after administration of the second dose. Serum samples were analyzed with immunoassays CLIA , which use an automated platform Maglumi 800 for the detection of IgG against segment S-RBD (Receptor Binding Domain) of S1 protein, specific for SARS-CoV-2. Results are calculated referring to a calibration curve and expressed in BAU/mL (Binding Antibody Unit). The threshold of positivity was 4.33 BAU/mL in accordance with the manufacturer\u2019s instructions. Samples higher than the limit of linearity (433 BAU/mL) were considered as highly positive.The study was approved by the Ethical Board of National Infectious Diseases Spallanzani Institute, Rome, Italy, and was conducted in accordance with the Declaration of Helsinki and good clinical practice. Informed consent was obtained from all subjects involved in the study.Baseline characteristics of cancer patients (cases) and healthy subject (controls) were explored and summarized using descriptive statistics. In particular, all categorical variables were expressed in terms of absolute and relative frequencies (percentages). In addition, age at vaccination was considered as a four-category factor using 50, 55, and 60 years as cutoff points.The distribution of IgG levels was described through geometric mean (GM) and corresponding 95% confidence limits (95% CL). Differences in IgG distribution in subgroups of subjects were assessed using the nonparametric Kruskal\u2013Wallis test.In order to evaluate the relationship between IgG levels and subjects\u2019 characteristics, antibody concentration was transformed into two binary serologic outcomes using 4.33 BAU/mL and 433.0 BAU/mL as cutoff values to define a positive or highly positive response, respectively, and a modified Poisson regression model was applied to both outcomes . Next, sAll analyses were performed using Stata .All cases were negative for prior COVID-19 infection.Overall, patients had lower antibody response , and IgG concentration tended to halve with age, from 323.1 BAU/mL (95% CL = 273.0\u2013382.4) for subjects < 51 years to 194.7 BAU/mL (95% CL = 150.5\u2013252.0) for those > 60 years. Additionally, a higher response rate was observed among females. n = 22, 95% CL = 177.9\u2013373.2) for lung cancer to 311.6 BAU/mL for colorectal tumors. Lower concentration of antibodies was found for HLP malignancies and particularly for non-Hodgkin\u2019s lymphomas . Among these tumors, the lowest values were found in single patients with monoclonal peak (0.82 BAU/mL), acute myeloid leukemia (1.16 BAU/mL), plasmacytoma (2.86 BAU/mL), and WM (2.94 BAU/mL). Patients with solid tumors had a GM concentration ranging from 257.7 BAU/mL , while advanced therapy seemed to induce a slightly more discernible reduction , Model 3When an IgG titer of 433.0 was used as a threshold of seropositivity (highly positive response), no reduction in response was observed for age . As already observed in the previous analysis, gender does not appear to play any noteworthy role , Model 1In this context, cases experienced a seropositivity rate remarkably lower than controls , Model 1Additionally, on this occasion, both chemotherapeutic regimens administrated at the time of vaccination seemed to play a role in attenuating seropositivity with similar response rates around 65%, which corresponded to a mean relative reduction in seroconversion of about 25% , Model 3We evaluated antibody response after a second dose of the Pfizer\u2013BioNTech BNT162b2 SARS-CoV-2 or Moderna mRNA COVID-19 vaccines in two groups subjects: 195 cancer cases and 400 healthcare workers (controls).With a cutoff value for positive serologic finding of 4.33 BAU/mL, no differences were observed for gender, while response decreased with age. Positivity was found in 96% of controls, in at least 90% of solid cancers and in only 50% of patients with HLP tumors. Compared to controls, response was lower in patients undergoing advanced therapy. When considering a major cut-off of 433 BAU/mL, response was significantly lower both for carcinomas and for HLP tumors, with a positivity rate ranging from 59% to 90% for solid tumors and of 19% for HLP tumors.Whether patients with a neoplastic disease are at higher risk of severe SARS-CoV-2 infection with inferior clinical outcomes and death is still uncertain . Some stThe outbreak of COVID-19 has led to the development of different types of vaccines, including mRNA vaccines produced by Pfizer\u2013BioNTech (BNT162b2) and Moderna (mRNA-1273), which are the first mRNA vaccines authorized for use in the general public setting .Two doses of the vaccine achieved a 94.8% and 94.1% efficacy, respectively, and were found to be safe, effective, and efficient in preventing COVID-19, including severe disease in the general population, as demonstrated in clinical trials ,34,35.Patients with neoplastic diseases are prioritized for vaccination , but so Generally, antibody response to two doses of mRNA vaccine was found in patients with the most common solid tumor types also undergoing chemotherapy or in patients with B-cell malignancies distant from therapy or in remission even if the level of the humoral response may be lower than those for general population ,37,38,39Individuals with hematologic malignancies, especially patients with B-cell-depleting agents or those treated with cellular therapies, are at risk of developing severe COVID-19 and are less likely to show protective immune responses to vaccination than the general population because of disease-related or treatment-related immunosuppression ,38,39,41A recent meta-analysis (heterogeneity index = 55%) showed that the pooled response for hematological malignancies was 64% (95% CL = 59%\u201369%) vs. 96% (95% CL = 92%\u201397%) for solid cancer and 98% (95% CL = 96%\u201399%) for healthy controls. Outcome was different across hematological malignancies, with a response of 50% for chronic lymphocytic leukemia, of 58% to 61% for aggressive and indolent non-Hodgkin\u2019s lymphoma, of 76% for multiple myeloma, and reaching 83% for myeloproliferative neoplasms and 91% for Hodgkin\u2019s lymphoma .In our series, response to vaccine was similar among male and females, but immunogenicity decreased after age 60 years. Contrary to our results, antibody titers were slightly higher in the female population of some studies ,44.Older age was associated with lower antibody titers in some papers ,45, but Our results confirmed the previous findings on the role of COVID-19 vaccines in oncologic patients even when considering the differences in the assays used to define immunogenicity and the adoption of different thresholds to define seroconversion. Nevertheless, there are some limitations. The major remark is that we know that no patient had a prior COVID-19 infection, but we were unaware of serologic status of controls before the vaccine, so we cannot exclude the possibility that the higher seropositivity rate among controls may be due to a former COVID-19 exposure. Nevertheless, we think that results are still indicative of a lower seroconversion in oncologic patients with hematopoietic diseases. If controls had been positive for SARS-CoV-2 infection, the higher antibody titer could be attributable to the disease; nevertheless, antibodies titers in hematopoietic patients are lower also when they are compared with the other patients with solid tumor who had not have COVID-19 infection, with a 50% reduction in response when considering the cut-off of positivity of 4.33 BAU/mL.Second, cancer patients were older and had a higher percentage of males than the cohort of healthcare workers population. Third, we do not have information on the health status and of possible use of drugs of controls.As shown by some authors, results of the study showed that response to vaccination is similar in patients affected by solid tumors to controls. On the contrary, hemolymphopoietic patients show a much lower response than controls when both thresholds of positivity were used. In addition, we observed a decrease of response to vaccines with age but only with the cut-off of positivity of 4.33 BAU/mL. In this context, the antibody levels resulted to be about 5% lower in subjects older than 60 years when compared to younger ages.Guidelines are in favor of vaccination for most of cancer patients . It seem"} +{"text": "Background: Human serum albumin (HSA) is a commonly used medication for the treatment of sepsis. However, there is no conclusive evidence as to whether different concentrations of HSA are associated with patient prognosis. This study aimed to evaluate the association between different concentrations of HSA and 28-day mortality in patients with sepsis.Methods: The data for this retrospective study were collected from the Medical Information Mart for Intensive Care IV database. Patients with sepsis were divided into two groups according to the concentration of HSA received: 25% and 5% HSA. The primary outcome of this study was the 28-day mortality in patients with sepsis. To ensure the robustness of our findings, we used multivariate Cox regression, propensity score matching, double-robust estimation, and inverse probability weighting models.Results: A total of 76,943 patients were screened, of whom 5,009 were enrolled. 1,258 and 3,751 patients received 25% and 5% HSA, respectively. The 28-day mortality rate was 38.2% for patients in the 25% HSA group and 8.7% for patients in the 5% HSA group. After propensity score matching, 1,648 patients were identified. The inverse probability weighting model suggested that 5% HSA received was associated with lower 28-day mortality . Subgroup and sensitivity analysis confirmed the robustness of the results.Conclusion: In patients with sepsis, 5% HSA received may be associated with a lower risk of 28-day mortality than 25% HSA. Further randomized controlled trials are required to confirm this association. Sepsis is a public health problem characterized by life-threatening organ dysfunction caused by a dysregulated host response to infection . A recenThe 2016 Surviving Sepsis Campaign (SSC) guidelines suggested that HSA may be used as a supplemental resuscitation fluid . The safBased on the above studies, we hypothesized that different concentrations of HSA may have different effects on the prognosis of sepsis. In this study, we aimed to compare the difference between 25% and 5% HSA on the 28-day mortality in patients with sepsis. Additionally, we used propensity score matching to minimize potential bias in the baseline characteristics between the 25% and 5% HSA groups. Based on this approach, the results of this study are more reliable.The data used in this retrospective study were extracted from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database , which cTo screen participants for this study, participants who met the following criteria were included in the study: 1) participants with a diagnosis of sepsis . 2) age HSA use was defined as the documented use of HSA during ICU admission. Patients receiving 5% HSA during ICU stay were categorized as low concentration of HSA group and those receiving 25% HSA were categorized as high concentration of HSA group.2), temperature, white blood cells (WBC) count, hemoglobin, platelet, blood urea nitrogen (BUN), serum creatinine (Scr), albumin, anion gap, bicarbonate, glucose, sodium, potassium, chloride, prothrombin time (PT), activated partial thrombin time (APTT), lactate, urine output, ventilator use, vasopressor use, renal replacement therapy (RRT) use, and comorbidities . The average values of laboratory parameters and vital signs within 24\u00a0h of ICU admission were used in this study (We extracted the data of the following variables from the MIMIC-IV (version 2.0) database on the first day of ICU admission: sex, age, weight, ethnicity, Simplified Acute Physiology Score II (SAPS II), SOFA score, Charlson Comorbidity Index, mean blood pressure (MBP), systolic blood pressure (SBP), diastolic blood pressure (DBP), respiratory rate, heart rate, pulse oximeter oxygen saturation . Non-normally distributed data were expressed as medians (interquartile range [IQR]). Categorical variables were expressed as frequencies or percentages. To compare the baseline characteristics of the two groups, t-tests or one-way ANOVA were used for continuous variables, and the chi-square test or Fisher test was used for categorical variables.2, temperature, WBC, hemoglobin, platelet, BUN, Scr, albumin, anion gap, bicarbonate, glucose, sodium, potassium, chloride, PT, APTT, lactate, urine output, vasopressor use, ventilator use, RRT use, and comorbidities. A matched caliper (0.2) was used to match the patients between the two groups, and a standard deviation of 10% was considered sufficient to balance out the distribution between the two groups. Propensity scores were calculated from Cox regression models, along with the hazard ratios (HRs) and 95% confidence intervals (CIs) for each estimate.Propensity score matching (PSM) and Cox regression analysis were used to balance between-group confounders to reduce the effect of potential bias as much as possible . PSM incTraditionally, when applying regression analysis or propensity score models to estimate causal effects, these methods are unbiased only if both statistical models are correctly specified. The doubly robust estimation approach combines a multivariate regression model with a propensity score model to estimate the association and causal effect of exposure on the outcome , which cp < 0.05 was considered to be statistically significant.To further validate the robustness of the 5% HSA and the association with 28-day mortality after PSM, an extended Cox regression model approach was used to adjust for different covariates . SurvivaTo assess the robustness of the results and how the application of various correlational inference models affects our conclusions, we performed a subgroup analysis of several relevant covariates and described them as forest plots. In addition, we performed two sensitivity analyses. First, patients with liver disease may have hypoproteinemia, which is a common reason for requiring HSA infusion. After excluding patients with liver disease from the data, the first sensitivity analysis was performed. In addition, considering that baseline serum albumin is an important covariate reflecting the nutritional status of the patient. We performed a second sensitivity analysis after excluding patients with missing values of serum albumin.The MIMIC-IV database (version 2.0) contains data on 76,943 adult ICU admissions. In the study cohort, we identified 5009 patients with sepsis based on inclusion criteria, of whom 1258 received 25% HSA, while 3751 received 5% HSA . After p2, hemoglobin, BUN, Scr, albumin, anion gap, bicarbonate, sodium, potassium, chloride, PT, APTT, lactate, urine output, vasopressor use, ventilator use, RRT use, atrial fibrillation, hypertension, CAD, liver disease, renal disease, and malignancy between the two groups. After PSM, 824 pairs matched. The standardized differences of covariates between the 25% HSA group and the 5% HSA group were less than 10%, except for platelets and CAD. For patient disease severity scores, including SAPS II, SOFA score, and Charlson Comorbidity Index, there was no difference between the two groups. There was a tendency that the patients in the 5% HSA group to use more ventilators, vasopressors, and RRT, although it was not statistically significant.The baseline characteristics of all participants are presented in p < 0.001). After adjusting for confounding factors, the HR for 5% HSA group in the Cox proportional hazards regression was 0.52 . The 28-day mortality in the 5% HSA group was 8.7% , compared with 38.2% for the 25% HSA group . Compare< 0.001) .p = 0.001) and in-hospital mortality were still lower in the 5% HSA group than in the 25% HSA group, and patients in the 5% HSA group had shorter lengths of hospital stay and ICU stay (p =0.004), IPTW and double robust analysis models all demonstrated that 5% HSA group had lower 28-day mortality (p = 0.0034) . The resortality . After tortality , extende 0.0034) .p = 0.001).The subgroup analysis indicated a negative association between 5% HSA and 28-day mortality . In the n = 5,009), after excluding 1,026 patients with liver disease, 3,983 patients remained. We performed multiple analyses of the data using doubly robust models, IPW models, propensity score matching models, and Cox regression based multivariate analysis models. The results demonstrated that the association between 5% HSA and 28-day mortality was robust . However, this study only enrolled 202 ICU patients receiving HSA, and this effect was not significant after adjustment for APACHE III . In another RCT, the SWIPE trial randomly assigned low (4%\u20135% HSA) and high (20% HSA) concentrations to 321 ICU patients, including medical and surgical patients . After adjusting for potential confounders using multiple methods, a stable association was found between receiving 5% HSA and decreased 28-day mortality.Similar to our results, a previous meta-analysis included 58 randomized controlled trials involving 26,351 patients, 14,659 of whom had sepsis. The results demonstrated that low concentrations of HSA may reduce mortality compared with high concentrations of HSA, OR = 0.90 (95% CI 0.68\u20131.18) . Howeverpatients . The SWIA randomized clinical trial is the best way to investigate whether there is an association between any therapeutic intervention and outcome because it maximizes two major problems in observational studies: unmeasurable confounding and bias. In this observational cohort study, we used multiple methods to try to minimize possible confounding, including PSM, double robust estimation, inverse probability weighting analysis and extended Cox regression models. The primary analysis demonstrated a significant association between 5% HSA received and decreased 28-day mortality in patients with sepsis. The results of the other two sensitivity analyses were similar. Notably, we found a significant interaction by sex in further subgroup analyses. A decrease of 28-day mortality with 5% HSA with sepsis was observed only in men. However, the result should be interpreted with caution due to the small number of cases and wide confidence intervals.It is still unclear the mechanism by which different concentrations of HSA are associated with reduced 28-day mortality in patients with sepsis. The following issues may need to be considered. First, different concentrations of HSA may have different effects on patients with sepsis. Low concentrations of HSA accumulate more fluid during fluid resuscitation in sepsis , and a pThis study has several limitations. First, owing to the retrospective design, there were unmeasurable confounding factors, such as the etiology of sepsis, antibiotic therapy, and clinician preference. We adjusted for baseline characteristics between groups by PSM and further investigated the primary study endpoint with multiple subgroup analyses to minimize the bias in the results caused by confounding factors. Second, we were unable to review the appropriateness of the indication for infusion of HSA since the basis for the physician\u2019s decision was not documented. However, we believe that our study population met the true clinical profile of HSA infusion in patients with sepsis based on inclusion and exclusion criteria. Third, in the MIMIC-IV database, we were unable to accurately identify whether septic shock was present on the day of ICU admission and may not accurately reflect the severity of the patient\u2019s condition. However, the SAPS II score, SOFA score, and vasopressor use on the first day of ICU admission were included in our study. Finally, our results suggest that 5% HSA is associated with decreased 28-day mortality in sepsis. These findings are hypothesis-generating and should be considered exploratory. We believe that a carefully designed, multicenter prospective study is needed to validate our results.Compared to those receiving 25% HSA, patients with sepsis receiving 5% HSA had lower 28-day mortality. Because our study was retrospective, the findings are preliminary, and a prospective randomized controlled study is needed to obtain greater validity."} +{"text": "Nearly 50% of Guatemalans are Indigenous Maya, yet few studies have examined the prevalence of modifiable cardiovascular disease (CVD) risk factors in Indigenous Maya populations. Therefore, we sought to estimate the prevalence of modifiable CVD risk factors in two Indigenous Maya areas in Guatemala.We conducted, between June 2018 and October 2019, a population-representative survey of adults aged 18 years and older in two rural Indigenous Maya municipalities in Guatemala. Our primary outcomes were five modifiable CVD risk factors: diabetes, hypertension, obesity, smoking, and alcohol use. We estimated the crude and age-standardized prevalence of each outcome. We also constructed multivariable logistic regression models to assess prevalence over covariates including age, sex, education level, ethnicity, and poverty. Sampling weights adjusted for nonresponse, and appropriate survey commands were used in all analyses.The crude prevalence of diabetes was 12.5% , hypertension 20.3% (95% CI 17.1% to 23.9%), obesity 23.7% (95% CI 19.4% to 28.6%), smoking 10.7% (95% CI 7.8% to 14.5%), and high alcohol use 0.9% (95% CI 0.5% to 1.6%). Age-standardized prevalence of each outcome was similar to the crude prevalence. The prevalence of multiple CVD risk factors increased between the age groups 18\u201329 years and 50\u201359 years before decreasing among older age groups. Men had twenty-fold higher smoking prevalence than women and women had nearly double the age-adjusted prevalence of obesity as men .There is a substantial prevalence of modifiable CVD risk factors in rural, Indigenous populations in Guatemala, in particular hypertension, diabetes, obesity (among women), and smoking (among men). These findings can help catalyze policy and clinical investments to improve the prevention, management, and control of CVD risk factors in these historically marginalized communities. Cardiovascular disease (CVD) is the leading cause of global mortality . Studies234569Guatemala is a Central American country of 17 million people of whom nearly 50% are Indigenous Maya . CVD is 141516172223Knowledge of the prevalence of CVD risk factors in Indigenous populations in Guatemala can identify important disparities and inform future policy and program initiatives. Therefore, the objective of this analysis was to estimate the prevalence of CVD risk factors using data from a population-representative survey in two predominantly Indigenous municipalities in Guatemala.We conducted a cross-sectional, population-representative survey between June 2018 and October 2019 in two rural municipalities in Guatemala. We previously have published the survey\u2019s primary outcomes relating to chronic kidney disease (CKD) , and in The survey sampled non-pregnant adults aged 18 years or older living in each municipality. We planned to sample at least 700 people from 350 households. As noted above, our primary goal in designing the survey was to measure CKD in Indigenous communities in Guatemala. We calculated sample size by hypothesizing a 10% prevalence of CKD, a margin of error of 0.35, 10% refusals, and a design effect of 2 to account for household clustering with at least two eligible residents per household .We have previously described our novel satellite-based sampling methodology . BrieflyThe data collection team interviewed participants using a survey containing items on sociodemographic information, medical history, and physical and biochemical measurements. Interviews were conducted in either Spanish or a Mayan language depending on respondent preference. For physical measurements, height, weight, and blood pressure were taken following standardized methods 27. We esOur primary outcomes for this analysis were five modifiable risk factors for CVD: diabetes, hypertension, obesity, smoking, and alcohol use. These outcomes were chosen based on the overlap between data available in our survey and the modifiable CVD risk factors defined in the Prospective Urban Rural Epidemiology (PURE) study, a longitudinal cohort study of CVD risk factors and mortality among adults in 21 low-, middle-, and high-income countries. The PURE definitions of CVD risk factors align with most clinical guidelines . We defiWe defined diabetes as either glycated hemoglobin (HbA1c) \u22656.5% or a self-reported history of diabetes 32. Our dHypertension was defined as either systolic blood pressure (SBP) \u2265140 mmHg, diastolic blood pressure (DBP) \u226590mmHg, or a self-reported history of hypertension or self-reported use of anti-hypertension medications. Guidelines from the World Health Organization (WHO) package of essential non-communicable (PEN) disease interventions for primary health care recommend these blood pressure thresholds . In a se2, healthy weight as BMI \u226518.5 kg/m2 but <25 kg/m2, overweight as \u226525 kg/m2 but <30 kg/m2, and obesity as \u226530 kg/m2. We used obesity as a proxy for abdominal obesity, which differs from the PURE study\u2019s use of waist-to-hip ratio.We defined categories of body mass index (BMI) according to conventions used by the WHO and US National Institutes of Health 37. We deSmoking was self-reported using a tobacco use frequency questionnaire with categories of current daily, current less than daily, past, and never smoker. We defined smoking status as current tobacco use and, in a sensitivity analysis, as any lifetime tobacco use.Alcohol use was also self-reported using a frequency questionnaire. Questions included categorical variables for days of consumption per week over the last 12 months. We defined high alcohol consumption as alcohol use more than two days per week. While the PURE study quantified alcohol use in terms of number of drinks per week, we did not quantify the number of drinks consumed and therefore defined alcohol use in terms of frequency alone.svy commands to account for stratification between the two municipalities. We used Stata version 17.0 for all analyses.First, we generated descriptive statistics in the overall sample and the gender-stratified sample. Second, we estimated the crude and age-standardized prevalence of each outcome. Age-standardized prevalence of outcomes was estimated using direct standardization to the WHO reference population . Third, Out of 806 participants surveyed, most were women . In the sensitivity analysis of hypertension using an alternative threshold of SBP \u2265130 mmHg, DBP \u226580 mmHg, or self-reported history of diagnosis or use of anti-hypertensive medication, we observed a prevalence of 37.4% (95% CI 32.6% to 42.4% Supplementary Table S1), which was higher than crude prevalence in our primary analysis of 20.3% (95% CI 17.1% to 23.9%). The overall crude prevalence of current smoking in our primary analysis was 10.7% (95% CI 7.8% to 14.5%); in the sensitivity analysis broadening the definition of smoking to any lifetime tobacco use, we observed a higher prevalence of 32.2% (95% CI 27.8% to 37.0%) and notable gender-based differences .In this population-representative survey of modifiable CVD risk factors among adults in two rural Indigenous municipalities in Guatemala, we found that approximately one in eight individuals had diabetes, one in five had hypertension, one in four were obese, and one in ten were current smokers. We also found that, across all age groups, 40% or more of adults had at least one modifiable CVD risk factor. Our findings reveal the imperative to implement clinical and public health programs to address the substantial burden of modifiable CVD risk factors in Indigenous communities in Guatemala where there is a historic underinvestment in health care infrastructure and programs.The findings in our subgroup analyses also merit further consideration. First, similar to the 2014\u20132015 Demographic and Health Survey (DHS) , we foun4143Our study contributes particular value in further understanding the epidemiology of diabetes and hypertension among Indigenous populations in Guatemala. The most well-known national survey program in Guatemala, the DHS series of surveys, does not assess either of these conditions, and there have only been a few prior diabetes or hypertension population surveys in Indigenous areas of the country. Our estimate of a diabetes prevalence of 12.5% was similar to a 2015 survey conducted in Indigenous towns surrounding Lake Atitl\u00e1n . However46Regarding hypertension in predominantly Indigenous areas of Guatemala, our prevalence of 20.3% was similar to Santiago Atitl\u00e1n , higher 4319502). Moreover, we observed that most CKD was associated with diabetes and hypertension [53Our study was focused on the most common CVD risk factors. However, it is also notable how these shared risk factors can contribute to morbidity and mortality for non-CVD outcomes. For example, in our prior study assessing CKD prevalence, we found that about 4% of respondents had chronic kidney disease , and smoking (among men). These findings can help catalyze policy and clinical investments to improve the prevention, management, and control of CVD in these historically marginalized communities.https://doi.org/10.7910/DVN/KHWHPU). Survey data will be made available pursuant to the NIH data sharing policies.Statistical code is available at the Harvard Dataverse (The additional file for this article can be found as follows:10.5334/gh.1171.s1Appendix.Supplemental Methods and Results."} +{"text": "A high percentage of patients with non-severe (17.9%) and severe (2.9%) atypical pneumonia do not display pulmonary tomographic findings upon hospital admission; furthermore, lesion associated with COVI-19 are peripherally distributed in a multifocal ground-glass pattern, as well as displaying an irregular consolidation pattern, with a posterior or lower lobe predilection. The main objective of this study was to identify the pulmonary radiological patterns in patients diagnosed with SARS-CoV-2 pneumonia, the factors associated with the need for mechanical ventilation, as well as their survival rates at 30 days.We report the pulmonary tomographic findings of 490 consecutive patients with severe and critical pneumonia due to SARS-CoV-2. The patients were classified according to the tomography and demographic findings, sepsis severity prognostic scales, Charlson comorbidity index (CCI), the Sequential Organ Failure Assessment (SOFA), and the Acute Physiology and Chronic Health Evaluation (APACHE IV). The Kaplan-Meier method was used to calculate survival distributions.2\u00a0=\u00a07.00, p\u00a0=\u00a00.008).89.80% of patients had ground-glass opacities, 81.63% radiologic consolidation sign, 42.45% vascular thickening pattern, 37.55% lymphadenopathies, 14.90% pleural effusion, and 2.65% pulmonary thrombosis; meanwhile, 91.02% had bilateral lesions, 85.51% had peripheral lesions, and 75.92% had basal lobe lesions. APACHE IV , SOFA , and CCI , as well as the pulmonary damage severity index , predict the need for invasive mechanical ventilation. Only moderate ARDS patients with mild and severe lung disease showed different 30-day mortality distributions with a higher pulmonary damage severity index died within 30 days of hospital admission, while only 25.91% with moderate lung damage and 2.42% with mild lung damage. \u2022Mortality at 30 days was 84.35% for patients with a high pulmonary damage.\u2022Mortality at 30 days was 25.91% for patients with moderate lung damage.\u2022Mortality at 30 days was 2.42% for patients with mild lung damage.\u2022Most patients with COVID-19 had ground-glass opacities and radiologic consolidation sign. The recThe use of computed tomography should be considered as the first option for imaging diagnosis in patients with suspected pneumonia ; highlig2ClinicalTrials.gov identifier: NCT04499378. Abiding by the Declaration of Helsinki, patient anonymity was guaranteed.An observational and retrospective study was conducted that included a consecutive case series of patients with SARS-CoV-2 pneumonia at the internal medicine department of our hospital from June 2020 to March 2021. The inclusion criteria included: 1) patients older than 18 years; 2) both sexes; 3) patients with contrasted chest computed tomography at the time of taking the sample to make the confirmatory diagnosis by PCR ; 4) patients with a PCR positive test for SARS-CoV-2 ; and 5) patients with a complete file with progress notes up to 30 days of hospitalization. The exclusion criteria were: 1) patients with a negative PCR test for SARS-CoV-2; 2) patients with a diagnosis of pulmonary neoplasia or evidence of a pulmonary metastatic process; 3) patients with autoimmune disease ; 4) patients with a previous medical diagnosis of interstitial disease ; 5) pregThe images were processed with a Toshiba 16 multislice tomograph and by a Siemens 16 multislice tomograph, which is scaled to 32 multislice. The pixel spacing of CT images was 0.72 mm and 0.85 mm for the uCT and Siemens scanner , respectively. The slice thickness was 5 mm for both scanners, all scans were evaluated by two radiologists. A nasopharyngeal sample was collected for each patient at the time of admission to the emergency department with a RT-qPCR SARS-COV2 kit Superscript III platinum one-step quantitative RT-PCR system .2/FiO2, arterial gases, D-dimer, lactate dehydrogenase, platelets, leukocytes, liver function enzymes, creatinine, albumin, hemoglobin, C-reactive protein), and therapeutic management were extracted from the medical file. Sepsis severity was assessed with the chronic health status through the Charlson comorbidity index (CCI), the Sequential Organ Failure Assessment (SOFA), and the Acute Physiology and Chronic Health Evaluation (APACHE IV).Demographical variables such as sex, age, weight, height, body mass index, as well as clinical variables such as length of stay in the hospital, intra-hospital stay, vital signs, comorbidities, heart failure, acute kidney failure, acute respiratory failure, laboratory work-up respiratory failure requiring mechanical ventilation; 2) shock; and 3) other organ failures requiring Intensive Care Unit (ICU) monitoring ); furthermore, as the pulmonary damage severity index increased and APACHE IV increased , the risk of mechanical ventilation did as well. Conversely, the fewer comorbidities the lower the risk of needing mechanical ventilation . After evaluating the risk factors associated with the need for invasive mechanical ventilation a survival analysis was performed. The overall survival between patients who required mechanical ventilation and those who did not were compared, with no statistically significant differences observed . The group means of all four severity scales were different between patients who required ventilation and those who did not . After assessing between-differences among the type of pneumonia a mortality analysis was performed, with no statistical differences were observed in the survival distributions of patients with severe and critical pneumonia . Furthermore, the overall survival analysis at 30 days as a function of the degree of acute respiratory distress syndrome was assessed. No statistically significant differences were observed in the overall survival distributions between the four ARDS classifications .The group means of all four severity scales were different between patients with different levels of acute respiratory distress upon admission to the critical care unit . Out of 124 patients with mild lung damage, 3 died within 30 days, while 57 patients out of the 220 with mild lung damage died and 123 out of 146 patients with severe lung damage perished within 30 days. The association between ARDS, the pulmonary damage severity index, and survival at 30 days, was also assessed and is reported in 2\u00a0=\u00a07.00, p\u00a0=\u00a00.008, Finally, when the survival distributions among the different levels of lung damage are considered, no differences in survival distributions are observed and the findings most frequently observed were consolidation, bilateral involvement and peripheral, \u201cCrazy-paving\u201d ground-glass and reverse halo sign . A studyThe main factor associated with disease severity and worst outcomes among COVID-19 patients was respiratory compromise upon hospital admission . A compa9One of the major limitations of this study is the lack of radiological follow-up, which limits the interpretability of the results as we can only make inferences about the initial radiological evaluation and not about disease progression. Another major limitation of this study was that some of the patients included received prior treatment with antibiotics and corticosteroids that could modify the tomographic findings. Associated with this limitation, we did not assess the role of coinfections in our sample, as a coinfection could confound the CT results. Furthermore, no lung biopsies were performed to confirm tomographic findings. A limitation associated with the analysis was the skewness of the pulmonary damage severity index scores, as a vast majority of the participants included in this study had a high severity index score, thus limiting the interpretability of the results presented here. Furthermore, as no statistically significant differences were observed in the survival distributions a Cox regression was not performed to determine the factor associated with the increased mortality.10All four disease severity scales were associated with the need for invasive mechanical ventilation. We also report a frequency of 89.80% for ground-glass opacities, 81.63% for radiologic consolidation sign, 42.45% for vascular thickening pattern, 37.55% for lymphadenopathies, 14.90% for pleural effusion, and 2.65% for pulmonary thrombosis. We observed that 84.25% of patients with severe lung damage, 25.91% of patients with moderate lung damage, and 2.42% of patients with mild lung damage died within 30 days, and only in patients with moderate ARDS had different survival distributions between mild and severe lung damage. The survival distributions were similar between patients who needed invasive mechanical ventilation versus those who did not, between severe and critical pneumonia, and between different levels of ARDS.None of the authors report conflicts of interest. This research did not receive any specific grant from funding agencies in the commercial sector."} +{"text": "With the COVID-19 pandemic, telehealth has been increasingly used to offset the negative outcomes of social isolation and functional decline in older adults. Crucial to the success of telehealth is end user adoption.This study aims to investigate perception and acceptability of digital technology among Asian older adults.The Healthy Ageing Promotion Program for You (HAPPY) dual-task exercise was conducted virtually to participants aged \u226560 years. Questionnaires were administered digitally and collected data on demographics, perceptions of digital technology and evaluation of HAPPY, the 6-item Lubben Social Network Scale, intrinsic capacity using the Integrated Care for Older People tool, and a functional screening with the FRAIL scale and five chair rises. Descriptive analysis was used.A total of 42 participants were digitally interviewed. The mean age was 69.1 (4.7) years. Hearing, vision, and 3-item recall difficulty were present in 14% (n=6), 12% (n=5), and 24% (n=10) of participants, respectively. Of the participants, 29% (n=12) had possible sarcopenia and 14% (n=6) were prefrail. Around 24% (n=10) were at risk of social isolation. Most of the participants agreed that technology is good, and 79% (n=33) agreed that technology would allow them to be independent for longer. Over three-quarters of participants agreed that they have the necessary knowledge, and 91% (n=38) had technological assistance available. However, 57% (n=24) were still apprehensive about using technology. Despite 71% (n=30) of older adults owning their devices, 36% (n=15) felt finances were limiting. Through digital HAPPY, 45% (n=19) of participants reported feeling stronger, 48% (n=20) had improved spirits, and 40% (n=17) and 38% (n=16) had improved mood and memory, respectively.The majority of older adults in this study believed in digital technology and had the necessary knowledge and help, but almost half still felt apprehensive and had financial barriers to adopting technology. A digitally administered exercise program especially in a group setting is a feasible option to enhance intrinsic capacity in older adults. However, more work is needed in elucidating sources of apprehension and financial barriers to adopting technology. State-mandated lockdowns during the COVID-19 pandemic, while necessary to curb spread, has led to social isolation, reduced physical activity, and functional decline . There aThe success of telehealth depends on end user adoption. Age is often quoted as a barrier to accepting new technology. Several themes and predictors have been identified in the perception and readiness of using digital technology including\u00a0self-efficacy, digital literacy, obstacles to using technology, prior experience, frequency of use, sources of support, performance expectancy, perceived usefulness, social influence, computer anxiety, perceived security, and physician\u2019s opinion ,6. SeverOur paper describes technology acceptability in older adults who were undergoing an on-site frailty intervention that subsequently transited into digital form. The Healthy Ageing Promotion Program for You (HAPPY) dual-task exercise program was first rolled out in 2017. The program was adapted from Cognicise and is a group multicomponent exercise focusing on cognition and physical function, originating from the National Center for Geriatrics and Gerontology in Nagoya, Japan. Prior to the COVID-19 pandemic, this program was ongoing in more than 50 different sites with at least 700 participants across Singapore and has shown to reverse frailty and improve cognition Figure .On-site HAPPY was conducted by health coaches and peer leaders who were trained to perform dual-task exercise by Japanese physiotherapists. The training program consisted of 3 sessions of theoretical training and cocreation of dual-task exercise and 8 hours of on-site training as assistant instructor and assessment . DigitalDuring the COVID-19 lockdown, the program was delivered virtually through the Zoom platform. More than 100 participants including their peers continued to participate. In the early phase of the national lockdown in April 2020, about 40% of participants agreed to participate in digital HAPPY, but only 14% eventually participated. As the nation remained in a semilockdown state, efforts to encourage more older adults to join the virtual platform persisted. Since March 2021, more than 700 participants now participate in digital HAPPY .Initial recruitment and evaluation were focused on those who were prefrail or had underlying cognitive impairment, but anyone in the community could join in the program . An inviLittle is known on the perception and acceptability of digital technology among Asian older adults, which is critical in increasing the uptake of telehealth. In addition, due to decline in sensory input and mobility with aging, it is less clear if tele-exercise has a perceived positive impact on older adults. Hence, as our frailty intervention underwent transition from on-site to digital, it was timely for us to study the acceptability of technology and perceived self-reported benefit of tele-exercise in our community-dwelling older adults during the pandemic lockdown.This is a cross-sectional descriptive study on technology acceptability in older adults, nested as part of a larger study\u2014the HAPPY program previously described.All existing participants of digital HAPPY aged \u226560 years were invited via WhatsApp to participate in the digital survey regarding technology acceptability between September and December 2020. Positive responders were sent the weblink. Consent was taken online. Participants needed to have access to technology, defined as older adults who had devices , internet connection, and ability to use WhatsApp and Zoom.The questionnaire can be found online , includiAs this was an exploratory descriptive study, no sample size calculation was performed. Due to the small sample size, descriptive analysis was conducted.Ethics approval was obtained from the National Healthcare Group Domain Specific Review Board (reference number: 2020/00668). Reporting is in accordance with the STROBE checklist.Only 42 (14%) of the participants who participated in the first 3 months agreed to be interviewed digitally, as many were apprehensive about digital consenting. The mean age was 69.1 (SD 4.7) years; 93% (n=39) of participants were female and 29% (n=12) of participants had up to 6 years of education, with 91% (n=38) being from the Chinese ethnic group. Only 7% (n=3) were employed, 62% (n=26) were retired, and 55% (n=23) had two or more chronic illness. Hearing, vision, and the 3-item recall difficulty was present in 15% (n=6), 12% (n=5), and 24% (n=10), respectively. Functionally, 29% (n=12) had possible sarcopenia, 15% (n=6) were prefrail, and 19% (n=8) had 1 or more falls in the past year. Slightly more than 1 in 5 were at risk of social isolation. Of the social media platforms, 93% (n=39) used WhatsApp, 79% (n=33) used YouTube, 21% (n=9) used WeChat, 19% (n=8) used Telegram, and 12% (n=5) used Instagram. Only 71% (n=30) owned their own device.On the acceptability of technology , 91% had attended on-site HAPPY exercises before. With digital HAPPY, 45% (n=19) reported feeling stronger than before, 48% (n=20) reported improvement in spirits, 40% (n=17) improvement in mood, and 38% (n=16) reported improvement in memory .Our study is particularly relevant during the current COVID-19 pandemic, with the reinforcement of social distancing especially among older adults. More than three-quarters of the seniors had the necessary knowledge to use the system. COVID-19 has accelerated technology adoption among older adults not only in the health care sector but also on social platforms, education, grocery and food delivery, socialization, and tele-exercise. Almost all the older adults used WhatsApp and more than three-quarters used YouTube.Odeh and colleagues found thWhile the majority had access to technology, finance was an issue for more than half. The digital divide can be affected at four different levels including motivational access, material access, skills access, and use access . Nearly There has been emerging research on digitally administered social activities and exercise for improving strength and reducing falls and loneliness, and studies have shown that uptake was influenced by perceived usefulness, enjoyment, social influence, gender, experience, and ease of use among other factors . One in To summarize, our study indicates that older adults are more than happy to adopt digital technology, and tele-exercise can feasibly be used to prevent and delay functional decline and loneliness. More work needs to be done on improving electronic interfaces that can be user friendly to older adults who have multiple sensory impairments and joint disability. While these efforts in reducing the digital divide and improving access to telehealth and digital technology are still underway, in certain population groups such as those with sensory or cognitive impairment, in-person clinic or home visits would still be the mainstay.The majority of older adults believe in digital technology and have the necessary knowledge and help, but almost half still feel apprehensive and have financial barriers to adopting technology. A digitally administered exercise program especially in a group setting is a feasible option to improve function.Our participants are not representative of a community sample, as they were preselected themselves to participate in digital HAPPY, and those who agreed for the digital interview already had the necessary knowledge. Despite that, more than half of the participants were apprehensive and cited financial barriers to access technology. While our study population is small, it did show that tele-exercise is beneficial in improving physical and cognitive function. Further population studies are needed to identify the areas of apprehension to and benefits of initiatives and taking up Seniors Go Digital.Digital technology including telehealth is increasingly important in this COVID-19 era. Older adults are generally accepting of technology, with top barriers being technology specific, and they are willing to adopt and adapt. However, more studies are needed to elucidate the source of their apprehension and to guide interventions to boost telemedicine infrastructure. Tele-exercise has the potential to be a useful modality to reduce functional decline and social isolation in older adults."} +{"text": "We estimated real-world vaccine effectiveness among skilled nursing facility healthcare personnel who were regularly tested for SARS-CoV-2 infection in California, USA, during January\u2012March 2021. Vaccine effectiveness for fully vaccinated healthcare personnel was 73.3% (95% CI 57.5%\u201383.3%). We observed high real-world vaccine effectiveness in this population. We matched case-patients to controls on specimen collection date and SNF county by using simple random sampling (without replacement) and a 1:1 ratio. We applied conditional logistic regression to estimate vaccine effectiveness for partial and full vaccination (compared with no vaccination).We defined partial vaccination as Because of the density-based selection of the control series, in which controls are time-matched to case-patients, drawing from a risk set of persons who are at risk for becoming case-patients at the time the case is detected, the odds ratio approximates the incidence rate ratio without reliance on the rare disease assumption as potenhttps://www.sas.com). This study received an exempt determination from the California Committee for the Protection of Human Subjects.We performed the analysis before and after excluding case-patients and controls who had previously confirmed positive test results within 90-day and 180-day windows . We perfhttps://www.pfizer.com) and 8.5% received Moderna vaccine (https://www.modernatx.com). Among the partially vaccinated, 54% received Pfizer-BioNTech vaccine, 45% received Moderna vaccine, and <1% received a combination of 2 different vaccines . All Johnson & Johnson/Janssen vaccine (https://www.janssencovid19vaccine.com) recipients, representing 1.7% of participants matched to a vaccination record, were classified as unvaccinated because the vaccination date was after the specimen collection date.Of the 4,238 study participants, 28.9% were partially or fully vaccinated; 71.1% were classified as unvaccinated, including 47.8% who did not have a California Immunization Registry COVID-19 vaccination record and 23.3% (989) who were vaccinated on or after specimen collection date. A higher proportion of controls than case-patients were partially or fully vaccinated . Among tVaccine effectiveness was 73.3% (95% CI 57.5%\u201383.3%) for full vaccination . We obseA major strength of our study is that SNF HCP were tested regularly irrespective of symptoms or known exposure, enabling us to capture their infection status and estimate vaccine effectiveness for prevention of COVID-19, including asymptomatic infection. The unchanged vaccine effectiveness estimate after adjustment for HPI score reflects that COVID-19 vaccination efforts for SNF HCP engaged persons regardless of their residential community. One limitation is that the study period was before the Delta or Omicron virus variants became dominant. Because serial testing of vaccinated SNF HCP in California stopped during July 2021, the study period could not be expanded to examine effectiveness against later variants or changes in vaccine effectiveness over time since vaccination. In addition, a higher proportion of case-patients and controls were classified as partially vaccinated, rather than fully vaccinated, during the study period, and we did not have sufficient follow-up time to assess waning of vaccine effectiveness. Some residents could have been misclassified as HCP, but the age selection criteria limiting age group helped minimize this factor. Finally, misclassification of vaccination status is possible, but most likely is nondifferential, which we would expect to bias the odds ratio toward the null.In conclusion, we observed high real-world effectiveness of COVID-19 vaccination in SNF HCP in California. Our methods can guide future studies evaluating vaccine effectiveness.Additional information on estimating COVID-19 vaccine effectiveness for skilled nursing facility healthcare personnel, California, USA."} +{"text": "Crohn\u2019s disease (CD) is a chronic inflammatory condition which can affect the entire gastrointestinal tract with a wide variety of potential complications which may require endoscopic or surgical interventions. Small bowel CD beyond the reach of standard endoscopy poses a diagnostic obstacle and relies on cross sectional imaging \u2500 such as computed tomography enterography (CTE) \u2500 and balloon assisted endoscopy (BAE). BAE is the current diagnostic gold standard allowing for direct mucosal visualization as well as therapeutic capabilities; however, remains limited by access, cost, and requires specialized training. Alternatively, CTE in small bowel in CD is widely available, and less invasive than BAE. The diagnostic accuracy of CTE against the gold standard of BAE remains unclear.We aim to assess the sensitivity and specificity of CTE vs BAE in the diagnosis and evaluation of small bowel CD.Patients with an established diagnosis of Crohn\u2019s disease who underwent a CTE and a BAE within 6 months between 2011 and 2018 were reviewed. Relevant findings of active inflammation , long-segment disease (\u2265 15 cm active disease), skip-segments, number of strictures, and presence of high-grade strictures were extracted from both reports and images of CTE and BAE by two independent reviewers. Sensitivity and specificity for each finding on CTE was calculated using BAE as the gold-standard diagnostic test.A total of 42 patients with 65 corresponding CTE and BAE were identified between 2011 and 2018. CTE was found to be most sensitive for assessing presence of active inflammation and number of strictures at 75.6% and 71.4% , respectively. CTE was highly specific for findings of long-segment inflammation, skip lesions, number of strictures, and high-grade stricture with a specificity of 89.3% , 74.1% , 100% , and 84.4% respectively. CTE showed poor specificity for active inflammation 45.0% [23.1-68.5%], and poor sensitivity for high grade strictures 54.5% [36.4-71.9] and skip lesions 54.5% [23.4-83.3]CTE is relatively sensitive in detecting active inflammation and number of strictures compared to BAE, but showed suboptimal sensitivity in detecting long segment inflammation, skip lesions, and high-grade strictures. CTE showed high specificity in identification of long segment inflammation, number of strictures, and high-grade strictures, but not active inflammation overall. CTE and BAE are complementary to one another and based utilized in combination to improve diagnostic accuracy. Future directions include prospective validation prospective studies to validate the results of this study looking at a broader population of Crohn\u2019s disease patients.NoneNone Declared"} +{"text": "In the United States, 10% of HIV infections diagnosed in 2018 were attributed to unsafe injection drug use or male-to-male sexual contact among persons who inject drugs (PWID) were ineligible, and 230 (2%) were excluded because data were incomplete.Among HIV-negative PWID, 26% receptively shared syringes, 68% had condomless vaginal sex, 23% had condomless heterosexual anal sex, 72% had either condomless heterosexual sex or shared syringes, and 43% had more than one opposite sex partner . ReceptiIn the previous 12 months, among HIV-negative PWID, 57% received an HIV test, 33% participated in an HIV behavioral intervention, 55% received syringes from SSPs, and 56% used medication for opioid use disorder . Among PThis report provides updated weighted prevalence estimates of HIV infection and behaviors associated with HIV infection since the last NHBS survey among PWID in 2015 , but a substantial decrease in SSP use among Black PWID (from 51% to 40%), and significantly lower use of SSPs in 2018 among Black PWID compared with Hispanic and White PWID was observed. Lower SSP use among Black PWID in the context of disproportionally higher rates of HIV diagnoses in Black communities in 20 U.S. metropolitan statistical areas was 7%.In 2018, estimated HIV prevalence among PWID remained unchanged, and although overall syringe service program use did not significantly change, a substantial decrease in their use occurred among Black PWID.Low-barrier access is needed to comprehensive and integrated needs-based syringe service programs that include provision of sterile syringes and safe syringe disposal, HIV and hepatitis C virus testing and referrals for treatment, HIV preexposure prophylaxis, and treatment for substance use and mental health disorders for PWID."} +{"text": "P < 0.001). Critical care and pediatric wards had the highest proportion of antibiotic users. Amoxicillin/clavulanate was the most frequently used antibiotic at KNH , and ceftriaxone was most used at CPGH and MTRH . Forty-three percent (326/756) of all antibiotic prescriptions had at least one missed dose recorded. Forty-six percent (204/489) of patients on antibiotics had a specific infectious disease diagnosis, of which 18% (37/204) had soft-tissue infections, 17% (35/204) had clinical sepsis, 15% (31/204) had pneumonia, 13% (27/204) had central nervous system infections and 10% (20/204) had obstetric or gynecological infections. Of these, 27% (56/204) had bacterial culture tests ordered, with culture results available for 68% (38/56) of tests. Missed antibiotic doses, low use of specimen cultures to guide therapy, high rates of antibiotic use, particularly in the pediatric and surgical population, and preference for broad-spectrum antibiotics suggest antibiotic use in these tertiary care hospitals is not optimal. Antimicrobial stewardship programs, policies, and guidelines should be tailored to address these areas.Antimicrobial stewardship encourages appropriate antibiotic use, the specific activities of which will vary by institutional context. We investigated regional variation in antibiotic use by surveying three regional public hospitals in Kenya. Hospital-level data for antimicrobial stewardship activities, infection prevention and control, and laboratory diagnostic capacities were collected from hospital administrators, heads of infection prevention and control units, and laboratory directors, respectively. Patient-level antibiotic use data were abstracted from medical records using a modified World Health Organization point-prevalence survey form. Altogether, 1,071 consenting patients were surveyed at Kenyatta National Hospital , Coast Provincial General Hospital and Moi Teaching and Referral Hospital . The majority were \u226518 years and 53% (563/1071) were female. Forty-six percent were receiving at least one antibiotic. Antibiotic use was higher among children <5 years than among other age groups (40%, 339/847; Antimicrobial resistance (AMR) is a major public health concern that is global in scope , 2. It iOveruse and misuse of antimicrobials are considered important drivers of AMR. In the United States, about 30% of antimicrobial therapy is considered inappropriate . In AfriAntibiotic prescribing patterns and antimicrobial stewardship efforts in Kenya are not widely documented. We conducted a point-prevalence survey to describe the antibiotic use prevalence, common antimicrobial drug types, prescribing patterns, and indications for antibiotic use among inpatients, and existing AMS activities in three large public referral hospitals located in three geographically distinct regions of Kenya.This point-prevalence survey was conducted at Kenyatta National Hospital and at Moi Teaching and Referral Hospital (MTRH) in March\u2013April 2018. According to the WHO protocol for point-prevalence studies \u2014which waModified versions of the World Health Organization (WHO) point-prevalence survey (PPS) forms were useP < 0.05 considered statistically significant. The survey protocol was approved by the relevant institutional review board (IRB) committees . Written informed consent was obtained from adult respondents and from guardians of children prior to their enrollment. No incentives were provided to study respondents.When not explicitly indicated, antibiotic use for prophylaxis was inferred for patients who had undergone surgeries for which prophylactic antibiotics are recommended, and for HIV-infected patients receiving co-trimoxazole. Diagnoses/indications for which antibiotics were prescribed were recorded following prespecified PPS indication codes, The survey lasted eight days at the Kenyatta National Hospital (KNH) in Nairobi, six days at Coast Provincial General Hospital (CPGH) in Mombasa and ten days at the Moi Teaching and Referral Hospital (MTRH) in Eldoret. KNH reported having 2,075 beds with 83,138 total admissions in 2016, CPGH had 700 beds with 24,205 total admissions (2016) and MTRH had 939 beds with 44,229 total admissions (2016). Of 1,071 patients included in the study, P = 0.26). Antimicrobial use was higher among children <5 years compared to other age groups (70% (150/224) vs 40% (339/847); P < 0.001 Forty-six percent (489/1071) of all patients received at least one antibiotic at the time of the survey, P > 0.05) at CPGH and 33% at MTRH. There was some variability in the antibiotics used by the surveyed hospitals. Amoxicillin/clavulanate was the most used antibiotic at KNH while ceftriaxone, a third-generation cephalosporin, was the most used at CPGH and MTRH , Seven-hundred and fifty-six (756) separate antibiotic prescriptions were recorded . Forty-four percent (167/383) of antibiotics prescribed at KNH had at least one missed dose recorded, compared with 52% of antibiotic prescriptions were in pediatric wards, where benzylpenicillin , gentamycin and ceftriaxone were the most prescribed antibiotics, P < 0.01), 41% , and 42% of those who did not have a catheter insertion, tube insertion or surgical procedure, respectively, were using an antibiotic. Among surgical patients receiving antibiotics, 71% (130/182) had undergone an invasive surgery during the current admission, while 22% (40/182) and 7% (12/182) had minimally invasive- and non-invasive surgeries, respectively. Of the 484 patients whose HIV status were documented, 61% (50/82) of those with a HIV-positive status were receiving an antibiotic compared with 45% of HIV-negative patients.More than half of all patients with a documented catheter insertion , tube insertion , or surgical procedure during the current admission were on an antibiotic. Comparatively 22% had a single documented diagnosis, 8% (39/489) had two diagnoses and 2% (8/489) had three diagnoses. Twenty-two percent (95/442) of patients with a single diagnosis were given antibiotics for prophylaxis and 32% (143/442) for an unspecified infectious condition . The remaining 46% (204/442)\u2014who constituted 86, 68 and 50 patients at KNH, CPGH and MTRH, respectively\u2014were taking antibiotics for the treatment of a specified/documented infectious diagnosis. The five most common infections were soft-tissue infections , clinical sepsis , pneumonia , central nervous system infections and obstetric or gynecological infections .P > 0.05). Thirty-four samples were collected for culture from the 29 patients at KNH, 21 from the 18 patients at CPGH and 10 from the 9 patients at MTRH, for a cumulative 65 samples. Cerebrospinal fluid and pus swabs were collected most frequently across all hospitals. Other common samples included blood , urine , stool and sputum .Twenty-seven percent of patients receiving an antibiotic and with a single specified infectious diagnosis had culture tests ordered. There were more tests ordered at KNH than at CPGH or MTRH but the differences were not statistically significant , pneumonia , soft-tissue infections , and clinical sepsis . For these conditions, culture results were available for 67% (10/15), 73% (11/15), 79% (11/14), and 50% (3/6) of samples submitted for the above diagnoses, respectively. Antibiotic susceptibility testing data were not collected during the survey at KNH and were scant at CPGH and MTRH, and were, therefore, excluded from the analysis.All hospitals had a clinical microbiology laboratory staffed with Kenya Medical Laboratory Technicians and Technologists Board-certified microbiologists. KNH microbiology laboratory conducted 3,930 specimen cultures and 1,509 antibiotic susceptibility tests (ASTs), in the 3-month period preceding the survey compared with 518 cultures and 185 ASTs at CPGH, and 1,200 culture tests and 650 ASTs at MTRH. Only CPGH reported experiencing periodic stockouts of AST reagents.P < 0.023). At the time of the study, no hospital required antimicrobial prescription pre-approval from another physician or pharmacist before administration or required that medical records include a rationale for antibiotic prescriptions. Further, no hospital conducted audits or reviews on the choice and duration of surgical antimicrobials used for prophylaxis. None of the hospitals\u2019 laboratories produced an antimicrobial susceptibility report for the year preceding the survey.KNH and MTRH had Infection Prevention and Control (IPC) committees, and minutes available from meetings held within the six months preceding the survey. Only KNH had an antimicrobial stewardship committee. It was led by an infectious disease physician and provided formal guidelines to assist clinicians in making empirical decisions about antibiotic use. No hospital required clinicians to provide a rationale for prescribing antibiotics or to re-assess antibiotic prescriptions after 48 hours of the initial order. At KNH, 28% (106/383) of antibiotic prescriptions had no \u201cstop\u201d or \u201creview\u201d dates indicated, compared to 37% (70/189) at CPGH and 72% (133/184) at MTRH was lower than reports from other facilities in Kenya and Africa but higher than what is reported in high income countries/other regions. Recent point-prevalence survey results in two public referral hospitals in Kenya reported 68% and 55% The beta-lactam antibiotics amoxicillin/clavulanate and ceftriaxone were the most used antibiotics in this survey, as has been reported in other surveys in Kenya , 18 and We found substantive evidence that antibiotic use may not be optimal in the surveyed hospitals. Missed antibiotic doses, low use of specimen cultures to guide therapy, relatively high numbers of antibiotic prescriptions, particularly in the pediatric and surgical populations, and prescription of a broad-spectrum antibiotic like ceftriaxone without providing a rationale or reviewing these prescriptions were prevalent. Addressing all of these areas will be challenging, particularly given the limited resources for stewardship activities. Use of CDC and WHO We also identified several areas for improvement that may be less resource intensive. The lack of locally generated antibiograms and use of clinical guidelines might be contributing to sub-optimal clinical care and worsening rates of AMR; development of locally appropriate treatment guidelines can help. While it is not possible from this study to determine the impact of oversight committees , clarifying the committees\u2019 roles and responsibilities in optimizing antibiotic use within these hospitals could contribute to improvements in AMS.An aspect that stood out from the survey was the infrequent use of laboratory diagnostics to guide prescribing practices; few patients with suspected infectious syndromes had a culture ordered. Given that patients bear the cost of diagnostic testing and that fewer than 20% have health insurance coverage , cliniciOur survey had several limitations. Firstly, we focused on large government tertiary facilities whose data may not be generalizable to smaller or private facilities within Kenya. Secondly, we did not collect data from some wards and cannot determine the exact percentage of the hospital population included in the study. We, therefore, caution against extrapolating these findings to wards that were excluded. Thirdly, for about half of the surveyed participants, we could not link specific antibiotics with a diagnosis or identify the rationale for their use either due to poor documentation or limited sample sizes for some comparisons.This descriptive study contributes to the growing data on antibiotic use in tertiary care hospitals in Kenya and can be used by health facilities and the Ministry of Health to institute or improve AMS programs, policies, and guidelines. It also highlights important considerations that may be relevant in other low- or middle-income countries. Future research should focus on exploring the rationale underlying antibiotic use by specialties or specific classes of antibiotics, evaluating the appropriateness of antibiotic prescriptions, and identifying the determinants of effective AMS programs, drug and therapeutics committees and infection prevention and control strategies.S1 File(DOCX)Click here for additional data file.S2 File(DOCX)Click here for additional data file.S3 File(XLSX)Click here for additional data file.S4 File(DOCX)Click here for additional data file.S1 Table(DOCX)Click here for additional data file."} +{"text": "Management of large colorectal polyps is increasingly complex with the expansion of endoscopic techniques, including endoscopic submucosal dissection (ESD), endoscopic mucosal resection (EMR), and endoscopic full thickness resection. Adjudicating lesions in an effort to select the optimal resection method is hugely dependent on the information included within the referral. At our institution, a referral pathway based on photo and/or video documentation was created to facilitate the timely assessment and treatment of large colorectal polyps. To date, little is known about quality of referrals for endoscopic resection of large colorectal polyps.Our study aimed to assess the adjudication process and quality of referrals for endoscopic resection of large colorectal polyps at our advanced endoscopy referral center.We conducted a single-center prospective study of consecutive colorectal polyps referred for EMR from March 2021 to March 2022. Cases selected upfront for ESD were excluded. Referral information, intraprocedural data and histology was captured. No procedural and histology data were captured if EMR does not occur after adjudication. The outcome was defined as the frequency of adequate referrals. A referral was deemed adequate if it contained: sufficient photo or video documentation, description of any characteristics that increase the difficulty of endoscopic resection, accurate polyp localization/size estimate , and description of any endoscopic features of advanced dysplasia (AD), including HGD/IMCa, or submucosal invasion (SMI).During the study period, 213 referrals were received for colorectal polyps and underwent adjudication for EMR: 211 underwent EMR; 2 underwent ESD despite being triaged for EMR. Only 5% (10/213) of referrals were deemed to be adequate. Only 34% (73/213) contained any photo or video documentation and only 13% (28/213) photos/videos were of sufficient quality for adjudication. Difficult location or polyp characteristics, if present, were accurately described in 86.7% of referrals (183/211) of referrals. The accurate polyp location was described 80.6% of the time (170/211). Polyp size was estimated in 50.2% (107/213) of referrals. Amongst referrals with size estimated, the size was accurate in 73.8% of the time (79/107). On histological evaluation, 35.1% (74/211) of polyps had AD or SMI. Amongst polyps with AD or SMI, 48.6% (36/74) had endoscopic appearance suggestive of HGD/IMCa/SMI but only 69.4% (25/36) of these polyps with high-risk endoscopic features were accurately predicted based on the referral information.Referrals for large colorectal polyps often lack important clinical information. This significantly impairs the ability to adjudicate polyps for triage and resection and may negatively impact patient outcomes. To improve referral adequacy and patient outcomes, we plan to evaluate the impact of polyp adjudication on EMR success.NoneNone Declared"} +{"text": "Influenza vaccination can reduce the incidence of cardiovascular disease (CVD) in the US. However, differences in state-level trends in CVD and sociodemographic and health care characteristics of adults with CVD have not yet been studied.In this repeated cross-sectional study, we extracted 476,227 records of adults with a self-reported history of CVD from the Behavioral Risk Factor Surveillance System from January 2011 through December 2020. We calculated the prevalence and likelihood of annual influenza vaccination by sociodemographic characteristics, health care characteristics, and CVD risk factors. Additionally, we examined annual trends of influenza vaccination by geographic location.The annual age-adjusted influenza vaccination rate among adults with CVD increased from 38.6% (2011) to 44.3% (2020), with an annual average percentage change of 1.1%. Adults who were aged 18 to 44 years, male, non-Hispanic Black/African American, or Hispanic, or had less than a high school diploma, annual household income less than $50,000, and no health insurance had a lower prevalence of vaccination. The odds of vaccination were lower among non-Hispanic Black/African American and non-Hispanic American Indian/Alaska Native compared with non-Hispanic White adults. Only 16 states achieved a vaccination rate of 50%; no state achieved the Healthy People 2020 goal of 70%. Nonmedical settings gained popularity (19.2% in 2011 to 28.5% in 2018) as a vaccination setting.Influenza vaccination among adults with CVD improved marginally during the past decade but is far behind the targeted national goals. Addressing existing disparities requires attention to the role of social determinants of health in determining access to vaccination, particularly among young people, racial and ethnic minority populations, people who lack health insurance, and people with comorbidities. Influenza vaccination has been shown to reduce cardiovascular illness and death, and routine annual influenza vaccination is recommended by the Centers for Disease Control and Prevention.We found marginal improvement in influenza vaccination during the past decade among adults with cardiovascular disease, lagging far behind the Healthy People 2020 goal. Vaccination prevalence is influenced by social determinants of health such as race and ethnicity, access to preventive services, and geographic location.We can achieve Healthy People 2030 goals for vaccine-preventable disease only if we prioritize socially vulnerable populations and look beyond clinical settings as a place of vaccination.During the past 2 decades, annual influenza vaccination has been a cornerstone of national efforts such as Healthy People to achieve a target vaccination rate of 70% and protect against influenza . The AmeThe efficacy of influenza vaccination in preventing AMI has been estimated at 15% to 45%, which is comparable to the documented efficacy of traditional CVD prevention measures such as smoking cessation (32%\u201343%), statins (19%\u201330%), and antihypertensive therapy (17%\u201325%) . HoweverWe abstracted data from the Behavioral Risk Factor Surveillance System (BRFSS), a nationwide annual telephonic health survey of noninstitutionalized adults aged 18 years or older living in the 50 US states, the District of Columbia, and US territories on health-related risk behaviors, chronic health conditions, and use of preventive services , or stroke. Approximately 6.4% of respondents with CVD were missing information on influenza vaccination and were excluded from our analytic sample. The final sample comprised 476,227 adults with CVD and accounted for 8.5% of the BRFSS survey sample conducted from 2011 through 2020. Median survey responses ranged from 45.1% to 49.9% for the study period.Annual influenza vaccination was defined as receipt of an influenza vaccination within 12 months before the interview date. Sociodemographic covariates include age , sex , race and ethnicity , education level , annual household income , marital status , and US Census\u2013defined geographic region . Health care characteristics were having any health insurance (yes/no), having a personal doctor or health care provider (yes/no), and time since the most recent visit to the personal health care provider for a routine checkup. Primary risk factors for CVD included diabetes, obesity (body mass index >30.0), and smoking status .2 test to compare the distribution of these characteristics among participants with and without a history of CVD.The survey procedures (svyset) in Stata version 17.0 (StataCorp LLC) were used to account for the complex sampling design and BRFSS survey weights and to determine national and state-level population estimates. To compute direct age-adjusted estimates, we used 2010 US Census population proportions for groups aged 18 to 44 years, 45 to 64 years, and 65 years or older. We first performed a descriptive analysis of sociodemographic characteristics, health care characteristics, and CVD risk factors, and we used a \u03c7P value of <.05 was considered significant.For our primary analysis, we examined the age-adjusted frequency distribution of annual influenza vaccination coverage among adults with CVD each year from 2011 through 2020. We used Joinpoint trend analysis software version 4.9.1.0 ; health department; another type of clinic or health center ; senior, recreation, or community center; store ; hospital (inpatient); emergency room; workplace; some other kind of place; school; received vaccination in Canada/Mexico; don\u2019t know/not sure; and refused. We combined categories into the following: doctor\u2019s office (including HMO), other health care facility , hospital/emergency room, store, workplace, and other . This analysis was performed by using the core questionnaire module for the years 2011, 2012, 2015, and 2018. Because of limited years of data for place of vaccination, we did not perform trend analysis and reported only age-adjusted prevalence.P value of .05 was used to determine significance.Multivariate logistic regression models were weighted to estimate the adjusted odds ratios (AOR) and 95% CIs of influenza vaccination associated with each sociodemographic characteristic, health care characteristic, and CVD risk factor. Furthermore, to account for possible state-level differences and temporal trends in vaccination rates, we generated year and state fixed-effects logistic regression models. A 2-sided Adults with CVD were more likely than adults without CVD to be aged 65 years or older (51.2% vs 16.9%), male (55.4% vs 47.8%), non-Hispanic White (71.5% vs 64.3%), and a high school graduate or less (52.0% vs 40.3%), and have an annual household income of less than $50,000 (69.4% vs 50.4%) . The oveIn 2020, the age-adjusted influenza vaccination rate among adults with CVD ranged from 22.6% in Puerto Rico to 64.0% in South Dakota . From 20Doctors\u2019 offices remained the most common place for annual influenza vaccination among US adults with CVD, despite consistently declining vaccination rates from 2011 (49.4%) to 2018 (47.3%); we observed similar declines for other health care facilities. In contrast, the preference for stores such as supermarkets or drug stores as vaccination sites steadily increased from 19.2% in 2011 to 28.5% in 2018 .Compared with adults with CVD aged 18 to 44 years, adults aged 45 to 64 years and adults aged 65 years or older had greater odds of getting an influenza vaccination . Women hP < .001) than among adults without a history of angina/CHD. In contrast, odds were marginally lower among adults with a history of stroke compared with adults with no history of stroke and adults with diabetes (compared with adults without diabetes) had a greater likelihood of influenza vaccination, consistent with previous literature on the general population ,16. SmokIn 2020, 44.3% of adults with CVD received an influenza vaccination in the US, and more than half of states are above this national average, which was the highest in any year during the study period. This relatively high prevalence was likely due to the surge in influenza vaccination uptake as protection against COVID-19 . During Our findings have important implications for state and national COVID-19 vaccination goals. The current administration has taken an active role in administering and distributing COVID-19 vaccinations. However, rollout responsibilities have still largely been borne by states, and our findings demonstrate that much work must be done to address the issue of vaccination acceptance among diverse population groups, especially among racial and ethnic minority populations, people with low socioeconomic status, people who lack health insurance, and people with comorbidities.The primary strength of our study is that, to our knowledge, it is the largest and most current survey to report the national prevalence of influenza vaccination with validated survey questions on vaccination receipt . MoreoveThese findings highlight significant disparities in influenza vaccination rates among adults with CVD and underline the relevance of social determinants of health toward achieving target vaccination rates , particu"} +{"text": "Older drivers are expected to make up about 25% of licensed U.S. drivers by 2050. Describing early predictors of driving difficulty can identify interventions that might delay driving cessation or support successful transition to driving retirement. In this exploratory study, we analyzed nationally representative data from the longitudinal National Social Life, Health, and Aging Project (NSHAP) conducted in 2005\u201306, 2010-11, and 2015-16. Our purpose was to ascertain mental health and physical functioning correlates of increased nighttime driving difficulty, which often precedes daytime difficulties. The sample included 1,454 drivers with observations at all 3 waves aged 57 to 85 at baseline. By wave three, adjusting for non-response and sampling bias, 59% reported no driving difficulty, 23% reported some or much difficulty, and 17% reported no longer being able to drive at night. Results of mixed-effect ordinal logistic models, adjusting for demographics, showed increased inability to drive at night was associated most strongly with self-report of poor or fair physical health , considering oneself \u201cnot at all active\u201d , and being unable to balance heel-to-toe for 10 seconds . Although generalized self-reported mental health was not associated with increased nighttime driving difficulty, each additional depressive symptom (CESD-11) increased the odds of having greater driving difficulty by 12% . This study found early predictors of increased nighttime driving difficulty and retirement, providing opportunity to inform interventions to reduce roadway risk to older adults and others."} +{"text": "Among those with diabetic foot ulcers, rural patients identifying as Black face at least 10% greater risk of major amputation or death compared to the US as a whole. As specialty care is associated with lower risk of major amputation, this difference could be driven by specialty care access. We hypothesize that rural patients and, particularly, rural patients identifying as Black, receive less inpatient specialty care compared to the overall cohort.2 tests were performed on observed frequencies.We built a cohort of all Medicare patients hospitalized with diabetic foot ulcers (2013\u20132014). Rurality was measured using Rural Urban Commuting Area codes. Race was categorized using the Research Triangle Institute algorithm. Specialty care was defined as receiving inpatient care from at least 1 of 6 relevant specialties to address diabetes, infection, biomechanics or vascular disease, per National Provider Taxonomy codes: endocrinology, infectious disease, orthopedic surgery, plastic surgery, podiatry, and vascular surgery. We reported observed differences in specialty care, overall and stratified by rurality, identifying as Black, and ulcer severity. Pearson X2 = 36.2, p \u2264 0.001) and 26.2% for rural patients identifying as Black . Among those with osteomyelitis, 54.3% of the cohort received specialty care, while only 49.5% of rural patients, 50.8% of patients identifying as Black, and 37.6% of rural patients identifying as Black received specialty care; the disparity for rural patients identifying as Black was greater than the sum of rural and racial disparities . Notably, only 2.7% of patients presenting with osteomyelitis were seen by an infectious disease specialist. This proportion decreased to 2.5% for rural patients.Overall, 32.2% of the cohort received inpatient specialty care. This proportion decreased to 29.6% for rural patients (XObserved Proportions of Patients Receiving Specialty Care Stratified by Rurality, Identifying as Black, and Ulcer SeverityA smaller proportion of rural patients received specialty care, and rural patients identifying as Black were half as likely to receive specialty care than the overall cohort. Improving specialty access for these high-risk patients may reduce disparities in major amputations.All Authors: No reported disclosures."} +{"text": "The Bacille-Calmette\u2013Guerin (BCG) vaccination remains the primary strategy to prevent severe disseminated TB in young children, particularly in high TB-burden countries such as Ethiopia. Accurate knowledge of vaccination coverage in small geographical areas is critically important to developing targeted immunization campaigns. Thus, this study aimed to investigate the spatiotemporal distributions and ecological level determinants of BCG vaccination coverage in Ethiopia.Bacille-Calmette\u2013Guerin immunization coverage and geographical information data were obtained from five different Demographic and Health Surveys, conducted in Ethiopia between 2000 and 2019. Data for independent variables were obtained from publicly available sources. Bayesian geostatistical models were used to predict the spatial distribution of BCG vaccination coverage in Ethiopia.The overall national BCG vaccination coverage between 2000 and 2019 was 65.5%. The BCG vaccine coverage was 53.5% in 2000, 56.9% in 2005, 64.4% in 2011, 79.6% in 2016, and 79.0% in 2019. BCG vaccination coverage increased by 47.6% in Ethiopia from 2000 to 2019, but substantial geographical inequalities in BCG coverage remained at sub-national and local levels. High vaccination coverage was observed in northern, western, and central parts of Ethiopia. Climatic and demographic factors such as temperature, altitude, and population density were positively associated with BCG vaccination coverage. Whereas, healthcare access factors such as distance to health facilities and travel time to the nearest cities were negatively associated with BCG vaccine coverage in Ethiopia.Despite substantial progress in national BCG vaccination coverage, marked spatial variation in BCG coverage persists throughout the country at sub-national and local levels. Healthcare access and climatic and demographic factors determined the spatial distribution of BCG vaccination coverage. Maintaining a high level of vaccination coverage across geographical areas is important to prevent TB in Ethiopia.The online version contains supplementary material available at 10.1186/s12879-022-07547-4. Mycobacterium bovis that can prevent severe forms of TB such as meningitis and disseminated TB and 2019 . Altitude was also positively associated with BCG vaccine coverage in 2019 . Furthermore, the population density was positively associated with BCG vaccine coverage in all EDHSs. Whereas travel time to the nearest cities in minutes and distance to health facilities were negatively associated with BCG vaccine coverage in all EDHS (Table Widely Applicable Information Criterion (WAIC) statistic was used to check the model fitness, the model which contains all the covariates was the best-fitting model for BCG immunization coverage in all EDHS surveys 2000-2019, B) 2000, C) 2005, D) 2011, E) 2016 and F) 2019. Table S1. Covariate correlation result of variables included in this study. Table S2. Odds ratio with 95% Confidence Intervals (CI) of covariates included in a Bayesian spatial model with Binomial response for the BCG vaccination coverage in Ethiopia. Table S3. Watanabe-Akaike information criterion (WAIC) values corresponding to different model specifications. Table S4. Data sources and definitions of covariates."} +{"text": "The COVID-19 pandemic and related restrictions have affected the wellbeing of school children worldwide. Specific problems evolving during the pandemic, their extent and duration have\u0144t been sufficiently explored yet. We aimed at describing school childre\u0144s psychosocial and behavioral parameters and associated factors during the COVID-19 pandemic in Berlin, Germany.Our longitudinal study included students from 24 randomly selected Berlin primary and secondary schools, assessing psychosocial wellbeing and behaviors at four time points between June 2020 and March 2021. We analyzed temporal changes in the proportions of anxiety, fear of infection, reduced health-related quality of life (HRQoL), physical activity and social contacts, as well as sociodemographic and economic factors associated with anxiety, fear of infection and HRQoL.Of initially 384 recruited students, 324 still participated in the fourth study round after nine months. During the observation period, presence of anxiety symptoms increased from 26.2% (96/367) to 34.6% (62/179), and fear of infection from 28.6% (108/377) to 40.6% (73/180). The proportion of children with limited social contacts (<1/week) increased from 16.4% (61/373) to 23.5% (42/179). Low physical activity (<3 times sports/week) was consistent over time. Low HRQoL was observed among 44% (77/174). Factors associated with anxiety were female sex, increasing age, secondary school attendance, lower household income, and presence of adults with anxiety symptoms in the student's household. Fear of infection and low HRQoL were associated with anxiety.A substantial proportion of school children experienced unfavorable psychosocial conditions during the COVID-19 pandemic in 2020/2021. In particular, students from households with limited social and financial resilience require special attention.Berlin school childre\u0144s anxiety increased significantly during the pandemic months between June 2020 and March 2021 and was associated with anxiety in the family and lower household income.Almost half of the schoolchildren in our study reported low health-related quality of life after the second pandemic lockdown in March 2021."} +{"text": "In March 2020, policymakers, healthcare providers, and public health professionals shifted their resources toward covid-19 prevention and mitigation. This reallocation came at the expense of other essential healthcare services, including cancer prevention and treatment. Delaying cancer services will increase the burden and cost of cancer treatment in the coming years, but the extent of these delays is unknown. As the country continues to move forward, a better understanding of how cancer services were impacted will help policymakers prioritize strategies to mitigate the adverse effects of delayed cancer prevention and treatment.This study is among the first to use the newly released 2020 Behavioral Risk Factor Surveillance System (BRFSS) questionnaire. BRFSS is a phone-based survey and is representative of the U.S population. The BRFSS questionnaire asks about cancer screening, vaccination, and treatment services within the past year. I compared the total weighted responses in Q1, 2020 with the total weighted responses in Q4, 2020. With the latter group being exposed to six months of the covid-19 pandemic, these results serve as a baseline or \u201cfloor\u201d estimate of how much cancer prevention and detection service patterns changed in the United States.v Q4 = 20,403,265), pap smears declined 1.3% , colorectal cancer screenings declined 9.9% . While there was no estimated change in adults diagnosed with cancer, the number of adults currently receiving cancer treatment declined by 5.3% .Mammographies declined 4.7% (Q1 = 21,407,433 The covid-19 pandemic forced Americans to delay critical cancer prevention and treatment services. Fewer breast cancer, cervical, colorectal cancer screenings in 2020 will undoubtedly lead to more cancer diagnoses in the coming years, likely at more advanced and aggressive stages. Meanwhile cancer patients seemed to have delayed cancer treatment, but such delays cannot be sustained. Policymakers can mitigate the potential strain on cancer control systems by advancing cancer screening initiatives."} +{"text": "Sistem Informasi Tuberkulosis Terpadu, SITT) based on a previously published patient pathway analysis frameworkDear Editor, Gender influences routine TB diagnoses,2 tests were conducted to test statistical differences between variables. Most respondents of the IDHS were women, one-third of whom were 35\u201344 years of age. Within SITT data\u2019s diagnostic phase, women comprised 45% of the 14,625 patients reported to have TB diagnostic access. Additionally, 74% of patients within SITT sought diagnostic care in public facilities, whereas 26% did so in private facilities (where 53% of patients were in Level 1 private and public facilities combined). Within SITT data\u2019s treatment phase, women comprised 42% of the 24,648 patients reported to receive treatment. Additionally, 72% of all patients received treatment in public facilities, while 28% did in private facilities (where 48% of patients were in Level 1 private and public facilities combined) and public vs. private facilities. Level 0 refers to community-based care; Level 1 to primary healthcare offering outpatient care delivered by health professionals; Level 2 to primary health facilities offering advanced inpatient and outpatient care with a wider range of diagnostic and treatment options; and Level 3 refers to specialised hospitals with advanced capabilities, including referral and teaching hospitals.ombined) .n = 16,377) of women sought care at Level 1 private facilities, whereas 30% of men sought care at Level 0 private facilities. As demonstrated by a study in Indonesia, 73% of Level 1 public facilities, 73% of Level 2 public facilities and 59% of Level 2 private facilities have adequate diagnostic capacity.n = 16,377) and 29% of men initially sought care. Likewise, for 32% of women and 30% of men who preferred Level 0 private facilities for initial care-seeking in our sample, diagnosis is likely to be unavailable. Thus, for those who initially sought care at private Levels 0 and 1, 65% of women and 59% of men were unlikely to be diagnosed at their first point of care.We observed a higher tendency for women to seek care in private primary clinics compared to men, who opted for Level 0 pharmacy visits: 33% n = 1,377 of wn = 6,076) and 73% for men and women, respectively. These findings align with a previous study regarding the location of diagnostic equipment.n = 10,492, 73%; women: n = 7,249, 71%). When disaggregated by level, a greater percentage of men and women were treated at Level 1 public facilities. The NTP is heavily dependent on public facilities. Patients accessing care at private facilities may suffer from out-of-pocket expenditure for TB drugs unless their facility is engaged in the NTP\u2019s PPM programme, potentially deterring patients from receiving care at private facilities or leading to treatment discontinuation. Furthermore, the national health insurance scheme mandates that uncomplicated TB cases should be treated within Level 1. Although this mandate does not exclude Level 1 private facilities, our study found that most TB cases were referred to public facilities. Expanding treatment access to private facilities could reduce treatment transfers and allow patients to remain at preferred points of care. To note, men and women over 65 were more likely to seek treatment at Level 2 facilities , suggesting that engaging Level 2 facilities to systematically search for TB among older people may increase case-finding. Furthermore, integrating TB services with geriatric clinics within Level 1 may provide added value of care for older people and improve coverage.At the point of diagnosis, our data suggest a higher proportion of patients accessed care in public facilities than in private facilities \u2013 at 75% n = ,076 and P < 0.001). Providing treatment adherence support to male patients could improve treatment success.Indonesia aims to successfully treat at least 90% of all cases to reach the End TB goal of TB elimination by 2030.Our case study has several limitations. Data were drawn from six districts, which may not be representative of Indonesia, nor generalizable. Our findings (generated via a proxy) operated on assumptions of TB service availability, which may not reflect actual conditions. Moreover, our analysis was limited to understanding general care-seeking patterns and was unable to deduce reasons for patients\u2019 shifting behaviour along the care continuum. Despite these limitations, the study provides preliminary insights into gender differences along the TB care continuum."} +{"text": "Ulcerative colitis (UC) is a type of inflammatory bowel disease (IBD) that affects people in their reproductive years of life. Surgical treatment for medically refractory UC involves surgery over 2-3 stages, which includes a subtotal colectomy followed by creation of an ileal pouch-anal anastomosis (IPAA), known as a \u201cJ pouch\u201d. The IPAA allows preservation of fecal continence and avoids the psychosocial impacts of a stoma. The IPAA procedure is a deep pelvic surgery, which may impact pregnancy outcomes. Caesarean section (C-section) delivery is often performed to avoid anal sphincter and J pouch damage from vaginal delivery. However, literature demonstrates conflicting results regarding the risks of C-section compared to vaginal delivery, including the impact on pouch function. Surveys of clinicians also report varying delivery recommendations.To describe the delivery methods, pregnancy outcomes and postpartum course of IBD patients with IPAA at Mount Sinai Hospital.t-test or chi-squared test.A retrospective chart review is being performed for female patients at Mount Sinai Hospital with a diagnosis of IBD and an IPAA. Eligible patients completed a pregnancy from January 1, 2002-February 1, 2021 post-IPAA surgery and had variables of interest accessible in their electronic medical record. Variables of interest include demographics, pregnancy history, IBD characteristics, IPAA surgery details, pregnancy outcomes, mode of delivery and characteristics, and postpartum complications. Clinical data will be presented as means, medians and frequencies. Differences between variables of interest will be evaluated with Student\u2019s Three avenues of patient identification yielded 1113 patients to be screened. Inclusion criteria were met for 71 patients and chart review is complete for 36 patients who had a total of 53 pregnancies and delivered 56 babies. Most patients (49%) had a two-stage IPAA surgery, 21% required a three-stage surgery and 30% were undocumented. Most patients\u2019 (55%) IPAA was created through laparotomy, while 13% was through laparoscopic procedure and 32% was undocumented. Seventy-four percent of deliveries were through C-section (75% of primiparous), 69% of which were indicated to protect the patient\u2019s J pouch and 31% for an obstetrical indication. The remaining 26% of deliveries were vaginal, 29% of which were assisted with forceps or vacuum, 57% had tears and 50% had an episiotomy.At Mount Sinai Hospital, most IBD patients with an IPAA who completed a pregnancy had a history of laparotomy to create their IPAA. Most patients (74%) with IBD and an IPAA are delivering through C-section, and mainly to protect their J pouch, which is in line with reports in the literature. Most patients had a tear or episiotomy during vaginal delivery. Rates of third-degree tears may be higher than in the general population. Trends will be further elucidated with advancement of the study.None Declared"} +{"text": "As automated echocardiographic analysis is increasingly utilized, continued evaluation within hospital settings is important to further understand its potential value. The importance of cardiac involvement in patients hospitalized with COVID-19 provides an opportunity to evaluate the feasibility and clinical relevance of automated analysis applied to limited echocardiograms.In this multisite US cohort, the feasibility of automated AI analysis was evaluated on 558 limited echocardiograms in patients hospitalized with COVID-19. Reliability of automated assessment of left ventricular (LV) volumes, ejection fraction (EF), and LV longitudinal strain (LS) was assessed against clinically obtained measures and echocardiographic findings. Automated measures were evaluated against patient outcomes using ROC analysis, survival modeling, and logistic regression for the outcomes of 30-day mortality and in-hospital sequelae.Feasibility of automated analysis for both LVEF and LS was 87.5% (488/558 patients). AI analysis was performed with biplane method in 300 (61.5%) and single plane apical 4- or 2-chamber analysis in 136 (27.9%) and 52 (10.7%) studies, respectively. Clinical LVEF was assessed using visual estimation in 192 (39.3%), biplane in 163 (33.4%), and single plane or linear methods in 104 (21.2%) of the 488 studies; 29 (5.9%) studies did not have clinically reported LVEF. LV LS was clinically reported in 80 (16.4%). Consistency between automated and clinical values demonstrated Pearson's R, root mean square error (RMSE) and intraclass correlation coefficient (ICC) of 0.61, 11.3% and 0.72, respectively, for LVEF; 0.73, 3.9% and 0.74, respectively for LS; 0.76, 24.4ml and 0.87, respectively, for end-diastolic volume; and 0.82, 12.8 ml, and 0.91, respectively, for end-systolic volume. Abnormal automated measures of LVEF and LS were associated with LV wall motion abnormalities, left atrial enlargement, and right ventricular dysfunction. Automated analysis was associated with outcomes, including survival.Automated analysis was highly feasible on limited echocardiograms using abbreviated protocols, consistent with equivalent clinically obtained metrics, and associated with echocardiographic abnormalities and patient outcomes. The use of artificial intelligence (AI) as a method for automating medical image analysis has the potential to transform patient care . In echoContinued assessment of automated analysis using real-world data is essential to evaluate potential feasibility and relevance to clinical practice. In cases of severe infection, coronavirus disease 2019 (COVID-19) patients frequently present with prognostically significant cardiac involvement . EchocarIn this multi-site, retrospective study, we sought to evaluate (1) the feasibility of automated quantification of LV systolic function using limited echocardiograms from COVID-19 patients; (2) the agreement between automated quantification and clinical findings; (3) the association of automated assessment of the LV with in-hospital patient outcomes.This study was approved by the Institutional Review Boards and conducted among consecutive inpatient adults diagnosed with COVID-19 (positive antigen or polymerase chain reaction test) who underwent clinically indicated transthoracic echocardiography at six institutions: Beth Israel Deaconess Medical Center, Harvard Medical School (Boston); Temple University Hospital (Philadelphia); Einstein Medical Center (Philadelphia); Ochsner Medical Center (New Orleans); The University of Pittsburgh Medical Center; and Mayo Clinic Health System sites across Minnesota, Wisconsin, Florida, and Arizona, between February and December 2020. Only the first transthoracic echocardiogram performed during the hospital admission for COVID-19 was considered. Echocardiographic studies were included in the analysis if either an apical 4-chamber or apical 2-chamber image clip was available for analysis. Those with insufficient image quality to assess LV ejection fraction (EF) clinically and to evaluate the AI derived contours of the LV were excluded.Patient baseline characteristics, medical history, and in-hospital outcomes were obtained at each site from review of electronic health records. These included patient demographics, presenting signs/symptoms, comorbidities at the time of initial hospital presentation, in-hospital sequelae, and echocardiographic findings. Outcomes included 30-day all-cause mortality, incident acute coronary syndrome (ACS), congestive heart failure (CHF), acute kidney injury, and major adverse cardiovascular and cerebrovascular events (MACCE), defined as the composite of ACS, CHF, stroke, coagulation disorder (disseminated intravascular coagulation or other acquired bleeding disorder), myocarditis, or pericarditis. Coronary artery disease (CAD) was defined as prior myocardial infarction (MI), coronary revascularization, or angiography showing stenosis >50% diameter. Echocardiographic variables were obtained from echocardiography reports and included (where available) qualitative assessment of cardiac function .As echocardiographic data was collected predominantly during the first wave of the pandemic, abbreviated and focused protocols were frequently utilized to minimize scan times and staff exposure risk , sometimQuantitative assessment of LV function was obtained from clinical echocardiographic reports. The method of LVEF quantification was recorded. Protocols for echocardiographic acquisition and quantification were conducted according to local procedures and clinical standards in place at the time of data collection.Quantitative assessment of LV function was obtained from automated AI driven echocardiography analysis algorithms . LV LS was calculated as the average of the end-systolic longitudinal strain from apical 4- and 2-chamber views. Where one view was unavailable, single view longitudinal strain values were calculated. LV volumes and LVEF were determined using the Simpson's biplane method of disks. Where biplane LVEF was not feasible with both apical 4- and 2-chamber views, a single plane LVEF was calculated when feasible. The AI algorithms process apical 4- and 2-chamber images to automatically select cardiac cycles, contour the endocardial border, and calculate volumes, ejection fraction and longitudinal strain . Data foThe endocardial border of apical 4- and 2-chamber images were automatically contoured by EchoGo Core and were presented to operators for approval. All operators held professional qualifications in echocardiography . All studies were processed through EchoGo Core, irrespective of image quality. A study was considered feasible for AI analysis if operators approved either apical 4- or 2-chamber views. Studies where AI analysis was not feasible were included in the feasibility evaluation but not in the final analysis.t-test or the Wilcoxon rank sum test, as appropriate. Categorical data was presented as counts and percentages and compared using the \u03c72 test. Pairwise comparisons of continuous and categorical data were conducted using paired t-tests and McNemar's test, respectively. Agreement analysis was conducted using Bland Altman statistics, linear Deming regression root mean square errors (RMSE), Pearson's correlation coefficients, and intraclass correlation coefficients (ICC). For agreement of LVEF between AI and clinical values, the analysis was conducted using comparable methods . Discordance between automated and clinically assessed LVEF was defined by an inter-method difference of >10%, which has been reported as the minimum detectable difference between observers or medians and interquartile ranges (IQR). Continuous data were compared between groups based on automated LS and EF using the Student's bservers , 34. Forbservers , 35, 36.bservers , 35, 36.bservers with potbservers , 38. AllOf 558 patient echocardiograms with at least one apical cardiac cycle, automated analysis of both LVEF and LS was feasible in 488 (87.5%). AI feasibility was 93.7% for the Mayo Clinic, 80.8% for Beth Israel Deaconess Medical Center, 100% for the University of Pittsburgh, 91.5% for Ochsner Medical Center, 72% for Temple University Medical Center and 89.7% for Einstein Medical Center . ReasonsOf the 488 accepted studies, AI analysis was performed with biplane method in 300 (61.5%) and single plane apical 4- or 2-chamber analysis in 136 (27.9%) and 52 (10.7%) studies, respectively. Clinical assessment of LVEF was recorded in 459 (94.1%) of the 488 studies at the time of the echocardiogram. Clinical LVEF was assessed using visual estimation in 192 (39.3%), biplane methods in 163 (33.4%), and single plane or linear methods in 104 (21.2%). LV LS was clinically reported in 80 (16.4%) patients.Baseline patient characteristics, demographics, and clinically derived echocardiographic parameters are reported in Comparison of the AI derived assessment to the values obtained from clinical echocardiography reports is reported in The relationship of AI derived assessment and reported echocardiographic abnormalities was examined . AI derip = 0.11) or LS . Automated and clinical assessment of LS and LVEF demonstrated inter-method agreement in 70.0 and 79.6% of cases, respectively, when identifying LVEF <50% or LS >\u201316%, respectively. For LVEF, there were 61 (13.3%) cases where the automated assessment was <50% but the clinical values were >50% and 33 (7.2%) cases where the automated assessment was >50% and the clinical assessment was <50%. AI reported LVEF was different by a margin of more than 10% in 164 patients (36%) with 73% of these occurring in patients where the clinical assessment was performed using linear or manual methods. For LS, there were 11 (13.8%) of 80 cases where the automated assessment was >\u201316% and the clinical assessment was < \u201316% and 13 (16.3%) cases where the automated assessment was <\u201316% but the clinical assessment was >\u201316%. When comparing patients identified by clinically derived LVEF and LS, automated assessment characterized a significantly smaller proportion as abnormal [AI vs. clinical: LVEF: 56 (12.2%) patients vs. 89 (19.3%) patients, p < 0.001, LS: 18 (22.5%) patients vs. 31 (38.8%) patients, p < 0.001, ROC analysis of the ability of AI LVEF and LS to identify clinical systolic dysfunction achieved an area under the curve of 0.894 and 0.863, a sensitivity of 85.7% and 81.3%, and a specificity of 78.6% and 83.1%, respectively . Pairwisp = 0.025, LS p = 0.03), ACS , CHF , acute kidney injury , and MACCE during hospital admission . Automated LVEF and LS were associated with mortality using Cox regression to account for increased risk over longer durations of hospitalization and MACCE, but not in-hospital death or acute kidney injury . Clinical LVEF (p < 0.001) but not LS (p =0.118) was associated with ACS. Cox regression of clinical LVEF and LS was associated with mortality for LVEF (p = 0.019) but not for LS , acute coronary syndrome in 39 (8%), congestive heart failure in 49 (10%), and MACCE in 117 (24.0%). Using logistic regression adjusted by site , automatp > 0.05). Kaplan Meier analysis demonstrated increased risk of death for those with abnormal LVEF, relative to normal LVEF, for both clinical (log-rank p = 0.004) and automated (log-rank p = 0.01) assessment. Relative to borderline LVEF, patients with abnormal LVEF demonstrated increased likelihood of death for clinical assessment (log-rank p = 0.01) but not for automated assessment (log-rank p = 0.19).When categorized into hyperdynamic, normal, borderline, and abnormal classes based on LVEF, survival rates were 77.6, 83.3, 85.1, and 71.1%, respectively, for clinical LVEF and 81.7, 84.8, 80.0, and 71.6%, respectively, for automated LVEF . When caThis study has evaluated the feasibility and clinical relevance of automated echocardiographic analysis software on a multi-site COVID-19 cohort, with an ethnically diverse population (50% non-Hispanic white), using limited echocardiographic studies. The main findings are: (1) Automated analysis of limited echocardiograms was feasible in 87.5% of patients in which at least one apical cardiac cycle was obtained, even under abbreviated protocols, with biplane analysis of LVEF and LS possible in 61.5% of patients; (2) Automated LVEF, LS, and volumes had good to excellent agreement with clinically derived values; (3) Automated LVEF and LS were able to stratify individuals with cardiac dysfunction, including clinically reported echocardiographic abnormalities; (4) Automated LVEF and LS were associated with adverse in-hospital and 30-day outcomes and were comparable to clinically derived assessment. These findings suggest that automated assessment of LV function is highly feasible under abbreviated protocols and provides prognostically relevant information while increasing the data available for risk stratification.During the COVID-19 pandemic, it was quickly reported that cardiac complications were common in cases of serious infection and were associated with poor patient outcomes \u201341. WhilIn addition to high feasibility, the ability to provide clinically relevant information to assist in patient risk stratification is a core requirement for medical devices. In the present study, patients with an automated LS of >\u201316% or LVEF of <50% were more likely to present with clinically identified cardiac abnormalities such as LV hypertrophy, regional wall motion abnormalities, and left atrial enlargement. Furthermore, both LS and LVEF were significantly associated with poor patient outcomes, with LS identifying patients with a 29% increased risk of MACCE per 1% increase (less negative) in LS. The risk of adverse in-hospital outcomes when stratified by LVEF or LS was largely consistent between clinical and automated assessments, providing further evidence of the validity of automated analysis. These findings are in line with recent work reporting that abnormal systolic LV function, as defined by AI derived LVEF and/or LS, are associated with adverse cardiac events and death , 18. ImpTechnological advances in both computing and instrumentation have steadily increased the availability of quantitative echocardiographic assessment in routine practice. Such assessment, including LS, have consistently demonstrated value for patient risk stratification and prognostication in a range of conditions \u201347. HoweAn important finding of this study was the discordance between automated and clinical characterization of abnormal systolic function by LVEF and LS. Automated and clinical assessment were discordant in 20 and 30% of cases for LVEF and LS, respectively. When comparing those deemed to have abnormal LVEF and LS using clinical assessment as the reference, classifications using automated assessment identified a significantly smaller population as abnormal . However, this investigation did not demonstrate significant differences in relationship to overall mortality when stratified using clinical or automated assessment; thus, the clinical implications of such discrepancies are unclear. Such differences may reflect a bias from clinical interpretation of echocardiograms, where additional information can support differential diagnosis while the use of only apical views for automated assessment may underestimate patient risk. Indeed, the use of limited methods in the clinical estimation of LVEF contributed to 73% of the observed differences of more than 10% between AI and the clinical interpretation. Although no differences were observed in patient outcomes between AI and clinical methods, limited sample size and a relatively low event rate precluded further investigation of the clinical implications of discordance between the AI and the clinical interpretation. Further work is required to understand the relationship between automated assessment and clinical interpretation for risk stratification.This study has several limitations. The retrospective nature of the investigation limits the generalizability of the findings to routine practice and further work is required to understand the real-time implications of the AI technology in varied populations. In addition, the clinical assessment of LVEF or LS was limited and as such, a comparison of AI feasibility to clinical feasibility was not possible. The limited sample of clinical LS values is a significant limitation when evaluating the association with patient outcomes. Automated assessment of RV function was not conducted and may have provided further prognostic information , 37. SecIn a multi-center study conducted during a pandemic, automated analysis of ultrasound images was highly feasible, correlated with clinical observation, and associated with outcome.The anonymized and aggregate raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The studies involving human participants were reviewed and approved by Mayo Clinic Institutional Review Board. Written informed consent for participation was not required for this study in accordance with the national legislation and the institutional requirements.PP, WH, and GW designed the study. PP and WH drafted the manuscript. CS and WH organized the database and performed statistical analysis. JS and GP-H obtained local approval and data collection for Beth Israel Deaconess Medical Center. MK and BK obtained local approval and data collection for Temple Heart and Vascular Center. SQ and AT obtained local approval and data collection for Ochsner Health System. FG and EP obtained local approval and data collection for Einstein Medical Center. RT and SW obtained local approval and data collection for University of Pittsburgh. DM and TN obtained local approval and data collection for Mayo Clinic Scottsdale Arizona. PP oversaw local approval and data collection for Mayo Clinic Rochester Minnesota. All authors contributed to manuscript revision and read and approved the submitted version.GW and WH are employed by Ultromics Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. This study received funding from Ultromics Ltd. The funder had the following involvement with the study: The AI measurements in this study were performed by Ultromics Ltd.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "To describe antimicrobial resistance before and after the COVID-19 pandemic in the Dominican Republic.Retrospective study.The study included 49 outpatient laboratory sites located in 13 cities nationwide.Patients seeking ambulatory microbiology testing for urine and bodily fluidsEscherichia coli isolates from urine and Pseudomonas aeruginosa (PSAR) from bodily fluids between January 1, 2018, to December 31, 2021, from deidentified susceptibility data extracted from final culture results.We reviewed antimicrobial susceptibility reports for E. coli and 2,111 bodily fluid cultures with PSAR were included in the analysis. On average, resistance to ceftriaxone was present in 25.19% of E. coli isolated from urine each year. The carbapenem resistance rates were 0.15% for E. coli and 3.08% for PSAR annually. The average rates of E. coli with phenotypic resistance consistent with possible extended-spectrum \u03b2-lactamase (ESBL) in urine were 25.63% and 24.75%, respectively, before and after the COVID-19 pandemic. The carbapenem resistance rates in urine were 0.11% and 0.20%, respectively, a 200% increase. The average rates of PSAR with carbapenem resistance in bodily fluid were 2.33% and 3.84% before and after the COVID-19 pandemic, respectively, a 130% percent increase.In total, 27,718 urine cultures with E. coli after the COVID-19 pandemic is rising. These resistance patterns suggest that ESBL is common in the Dominican Republic. Carbapenem resistance was uncommon but increased after the COVID-19 pandemic.Resistance to carbapenems in PSAR and Low- and middle-income countries (LMICs) have unique challenges that may contribute to AMR. In many LMICs, antimicrobials can be purchased without prescriptions and are widely available. These factors may be driving an increase in antimicrobial use (AU) and AMR in LMICs over the past decade. The COVID-19 pandemic has further compounded this challenge, increasing AU in both inpatient and outpatient settings.Antimicrobial resistance (AMR) is a major global threat.Developing antimicrobial stewardship programs (ASPs) in LMICs is critical to help optimize antimicrobial use and curb AMR. Understanding local susceptibility patterns is a key first step toward the development of treatment guidelines for ASPs. The lack of local susceptibility data to guide therapy could lead to spiraling empiricism, furthering antimicrobial pressure and worsening AMR. Data are lacking on local susceptibility in the Dominican Republic and the impact of the COVID-19 pandemic on AMR. We sought to describe resistance in the Dominican Republic and the impact of the COVID-19 pandemic.Escherichia coli and Pseudomonas aeruginosa (PSAR) isolates from an outpatient clinical laboratory in the Dominican Republic. A report was developed for E. coli isolates from urine and PSAR isolates from bodily fluids processed between January 1, 2018, and December 31, 2021. Isolates processed between January 1, 2018, and December 31, 2019, were considered prepandemic isolates. Isolates processed between January 1, 2020, and December 31, 2021, were considered postpandemic isolates. These 2 groups reflect the annual antibiograms before and after COVID-19. The bodily fluid category represented samples from any abscess, body cavity, or anatomical site. The report included adults and children and was generated from deidentified susceptibility data extracted from all final culture results during the study period. The University of Illinois at Chicago Institutional Review Board approved this study.We performed a retrospective review of antimicrobial susceptibility reports for Amadita Laboratories is a private commercial laboratory company that provides outpatient services nationwide in the Dominican Republic. There are 49 outpatient laboratory sites across the Dominican Republic, representing 13 urban areas and all geographic regions of the country and advanced expert systems (AESs) for initial analysis. The VITEK 2 XL and VITEK 2 Compact are used for the initial testing. VITEK 2 XL uses the AST-GN67, AST XN05, and AST XN08 susceptibility cards, and VITEK 2 Compat uses the AST-GN67, AST XN05, and AST XN08 cards. VITEK MS is used for matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF MS) analysis of organisms. AES software versions 8.0 and 9.2 were used for analysis and interpretation of the antibiogram. Additional confirmatory testing was performed using the Kirby-Bauer method via the MASTDISCS Combi AMP-C, ESBL ID MAST GROUP, and MASTDISCS Combi CARBA PLUS discs . Sensitivity discs for individual carbapenems and the E-test for meropenem were used to confirm resistance.E. coli, a minimum inhibitory concentration (MIC) of \u22654 to ceftriaxone was considered resistant and possible extended-spectrum \u03b2-lactamase (ESBL) whereas an MIC of \u22658 \u03bcg/mL to meropenem was considered resistant . For PSAR, an MIC of \u226532 \u03bcg/mL to ceftazidime was considered resistant and possible ESBL while an MIC of \u22658 \u03bcg/mL for meropenem was considered resistant (carbapenem-resistant Pseudomonas auriginosa or CR-PSAR). Thresholds for resistance were based on Clinical and Laboratory Standards Institute (CLSI) M100.For E. coli were reviewed from 2018 to 2021. On average, 6929.5 urine cultures were performed per year. For E. coli, the resistance rates to ceftriaxone were 25.21% in 2018, 26.05% in 2019, 24.84% in 2020 and 24.65% in 2021 (Table\u00a0E. coli with ceftriaxone resistance rates were 25.63% and 24.75% before and after the COVID-19 pandemic, respectively (Fig.\u00a0E. coli with CRE were 0.11% and 0.20% before and after the COVID-19 pandemic, respectively (Fig.\u00a0E. coli occurred.In total, 27,718 urine cultures with In total, 2,111 bodily fluid cultures with PSAR were reviewed from 2018 to 2021. On average, 527.75 cultures were performed per year. For PSAR, the resistance rates to ceftazidime were 11.79% in 2018, 13.48% in 2019, 15.19% in 2020 and 15.13% in 2021 (Table\u00a0E. coli isolated from urine samples and rising resistance to carbapenems in PSAR from bodily fluids. On average, resistance to ceftriaxone was present in 25.19% of E. coli isolates from urine each year. These resistance patterns suggest that ESBL is common in the Dominican Republic, at levels comparable to other countries in Latin American. Carbapenem resistance was rare in both E. coli and PSAR, averaging 0.15% and 3.08% each year, respectively. However, an increase was seen after the COVID-19 pandemic, particularly in PSAR from bodily fluids. With bodily fluids as a source, this increase may be in more complex patients than those from urine samples and raises the concern of a similar effect in hospitalized patients.In conclusion, we detected high levels of resistance in Antibiotic use increased in hospitalized and ambulatory patients alike, despite efforts from professional societies to discourage their use. Reports showing an increase in AMR in Latin America after the pandemic are emerging. This finding mirrors a rise of AMR in the United States, where nosocomial infections by ESBL increased by 32%, CRE increased by 35% and AMR PSAR increased by 132% in the first year of the pandemic.In Latin America, the use of azithromycin for COVID-19 was widespread. In the Dominican Republic, antimicrobials can be purchased without prescriptions and are available in pharmacies and stores. Aminopenicillins are commonly used and may contribute to high rates of ESBL. Studies have reported ceftriaxone resistance in >24% of E. coli at a pediatric hospital and 46% in hospitalized adults. Circulating ESBL genotypes in the Dominican Republic include blaCTX and blaTEM. Future ASP interventions must focus on both ambulatory and hospital settings. Treatment guidelines reflecting local susceptibilities reported herein can be an important patient safety and stewardship tool.Excess antibiotic use is a significant problem in LMICs. High inoculum can occur in severe infections and may have an impact on MICs. Ceftazidime resistance may indicate ESBL in PSAR. However, genes other than ESBL may also contribute to ceftazidime nonsusceptibility in PSAR. The lack of patient specific information, such as comorbidities or prior antibiotic use, is another weakness in our study. Despite these weaknesses, we have reported susceptibilities using the same methodology used in routine clinical practice and may provide valuable information for empiric antimicrobial selection and the development of local treatment guidelines.A strength of our study was the large number of samples and wide geographic representation of samples in the Dominican Republic. These samples may provide a valuable portrait of susceptibilities in these communities. The study also had several limitations. All cultures performed during the study period were included; thus, patients with recurrent infections may be overrepresented. The large number of isolates in the study may balance this weakness. Inferring resistance based on phenotypic resistance patterns rather than genotypes is the main limitation of our study. Ceftriaxone nonsusceptibility without ESBL genes can occur. MIC accuracy can be affected by bacterial inoculum, antimicrobial dilutions, and differing enzyme expression."} +{"text": "This review assesses the effect on intra- and postoperative patient outcomesof the timing of neck dissection in relation to transoral surgery. Outcomemeasures include postoperative bleeding, intra- and postoperative fistulaformation, and disease-specific and overall survival.A search was conducted across the MEDLINE, Embase, US National Library ofMedicine, and Cochrane databases with search terms in July 2021.Articles that conformed with specified inclusion criteria were included.Included articles were scanned for bias with the ROBINS-I tool.Nineteen articles were selected for qualitative analysis, including 546patients who had neck dissection in conjunction with transoral roboticsurgery/transoral laser microsurgery (TORS/TLM). Seventy-one (18%) patientshad neck dissection prior to TORS/TLM, 39 (10%) had neck dissectionperformed after TORS/TLM, and 281 (72%) had concurrent procedures. Inpatients with neck dissection before TORS/TLM, 3% experienced majorpostoperative bleeding, and fistula rates were 0%. In the cohort with neckdissection after TORS/TLM, 3% experienced minor postoperative hemorrhage,and 8% had intraoperative fistulae. In the concurrent cohort of patients, 1%had major postoperative bleeds and 0.3% had minor bleeds, while 4% developedintraoperative fistulas and 0.3% developed postoperative fistulas.Current evidence indicated that there appears to be no correlation betweentiming of neck dissection and complications. This systematic review foundinsufficient data to comment on whether the timing of neck dissection inrelation to TORS/TLM affects the outcomes of patients. Currently, there are no universally accepted guidelines or consensus forND timing in patients undergoing TORS for OPSCC.6In the last few decades, there has been a shift of treatment paradigm from nonsurgicaltreatment to transoral surgical resection in patients with human papillomavirus\u2013associated OPSCC. Improved outcomes of transoral robotic surgery (TORS)/transorallaser microsurgery (TLM) procedures and achieving primary resection with minimalmorbidity are factors driving the increased popularity of these procedures.7 Performing ND before primary resection allows vessel ligationbefore the TORS/TLM procedure, which may reduce hemorrhage intra- andpostoperatively.8 It has been hypothesized that performing ND after TORS/TLMresection reduces fistula formation.9 Moreover, it provides anopportunity to address any close or positive resected margins in the histopathologyreport.8ND has been performed concurrently, before, or after the primary tumor resection. Eachtechnique is thought to have its own advantages and drawbacks , overall survival (OS), and recurrencerates.Cochrane Handbook for Systematic Reviews of Interventions. Aprotocol was developed and peer reviewed locally before being registered on thePROSPERO database (CRD42021233780).The systematic review is reported in accordance with the PRISMA guidelines via methodology describedin the A search was conducted across the MEDLINE, Embase, US National Library ofMedicine, and Cochrane databases with the search terms indicated (The articles filtered by the search strategy were considered in conformance withthe following inclusion criteria:Primary studiesWritten in the English language (or provided English translations)Patients treated for a primary oropharyngeal cancerPatients undergoing TORS/TLM for primary resection in conjunction with anNDND performed conventionally and not as robot-assisted proceduresTiming of the ND specified as concurrent, before, or after TORS/TLMResults include surgical complications and functional patient-relatedoutcomesStudies describing TORS/TLM and ND in the salvage setting were excluded, and casereports were included. The main outcome measures were rates of postoperativehemorrhage, intra- and postoperative fistula formation, DSS, OS, andrecurrence.10 and disagreement wasresolved by discussion. ROBINS-I tool assesses bias within articles according to7 domains:Two reviewers (J.P.R. and A.B.-G.) were involved in the study selection processto ensure that no articles were missed. Any disagreement was resolved bydiscussion. Data from all the included articles were scanned independently byJ.P.R. and A.B.-G. for bias per the ROBINS-I tool,Bias due to confoundingBias in selection of participants into the studyBias in classification of interventionBias due to deviations from intended interventionsBias due to missing dataBias in measurement of outcomesBias in selection of resultsCochraneHandbook.11This was in accordance with guidance from the Timing of ND in relation to TORS/TLM was divided into 5 categories: before,concurrent before, concurrent, concurrent after, and after . Five articles did not specify the primary cancer site.29 while nodal staging (N)was noted in all but 1 study.29 Across all studies, 41%of patients had T1 disease, 48% had T2 disease, 7% had T3 disease, and 5% had T4disease (n = 397). Nodal disease was 33%, 16%, 48%, and 3% for N0, N1, N2, andN3 staged disease, respectively (n = 298). Overall cancer staging was reportedin 7 studies and also showed large heterogeneity.1824 The most common stage ofdisease was IV with 61% of patients being treated with this staging. A further12% of patients were treated for stage I disease, while 14% were treated forstage II and 13% for stage III (n = 311).The stage of disease was reported according to the seventh edition of theAmerican Joint Committee on Cancer\u2019s TNM classification. Tumor size (T) wascited in all but 2 studies,20; 3 asconcurrent before procedures26; 10 as concurrentprocedures132729; 2 as concurrent afterprocedures25; 1 as a separate procedure after TORS/TLM16; and 1 asbefore, after, and concurrently to TORS/TLM.6Two articles described ND as a separate procedure before TORS/TLM1323 This accounted for 279patients, of which 13% had I to IV, 32% had I to V, 51% had II to IV, and 4% hadII to V. The ND was described in 11 studies as being unilateral orbilateral.132128 Within these studies, 86%of patients had unilateral ND and 14% had bilateral ND (n = 333).Of the 19 studies, 8 cited the level of ND.24 In 2020, Tsukahara etal20 reported a patient having 2 episodes of severe pharyngealbleeding, both requiring readmission. The second bleed led to hemorrhagic shock.There were 3 episodes of minor hemorrhagic bleeding across 2 studies.26Postoperative hemorrhage was divided broadly into major and minor bleeding. Majorhemorrhage required surgical intervention while minor bleeds recovered with conservative management. Of the 13 studiesthat recorded postoperative hemorrhage as an outcome, 4 cited major episodes ofpostoperative hemorrhage.1229 Of these, 12% hadintraoperative fistulae, and 1% sustained postoperative fistulae. Allintraoperative fistulae were managed in theater, with local flapreconstructions. However, in the study by Moore et al, 6 patients withintraoperative fistulae went on to develop postoperative fistulae.29Altogether 15 studies with a total of 468 patients recorded fistula formation asa patient outcome.Of the 431 patients undergoing concurrent ND, 2 (0.5%) had grade IIIcomplications, 66 (15%) were classified as grade II, and 6 (1%) patients hadgrade V complications. Of the 39 patients with ND performed after transoralsurgery (including the concurrent after and after cohorts), 3 (8%) had grade IIcomplications and 1 (3%) had grade V. Seventy-six patients had ND prior totransoral surgery (including the before and concurrent before cohorts). Ofthese, 1 patient (1%) had grade IV complications, 2 (3%) were grade II, and 6(8%) had grade V.28 Three studies with a 2-year follow-up period found DSSto be 95%, 89%, and 78% while OS was at 100%, 100%, and 94%.19 Dabas etal24 cited a DSS of 88% and OS of 92% at a mean follow-up timeof 29 months, and Jackel26 reported DSS and OS at80% with a mean follow-up of 24.8 months. Ten studies (192 patients) recorded arecurrence rate, which was 5% on average.182628 Five studies described norecurrence.28Ten studies described DSS and OS, with varying follow-up times. Five studiescited DSS and OS as 100% for 13 patients at follow-up times ranging from 2months to 1 year.Across the studies, 12% had concurrent before procedures; 4% had concurrent afterprocedures; 2% had ND as a separate procedure before (minimum 8 days and maximum1 month before TORS/TLM); 3% had ND as a separate procedure after (minimum 10days and maximum 8 weeks after TORS/TLM); and 79% patients had a concurrentprocedure. The timing of ND was not mentioned in this cohort (n = 546).In patients with ND before TORS/TLM (including concurrent before and beforecohorts), 3% experienced major bleeding and 1% experienced minor bleeding, whilefistula rates were at 0% (n = 76). Of patients with ND after TORS/TLM (includingconcurrent after and after cohorts), 3% experienced minor hemorrhage, and 8% hadintraoperative fistulae (n = 39). In the concurrent cohort of patients, 1%experienced major bleeds and 0.3% had minor bleeds. A further 13% developedintraoperative fistulae and 2% developed postoperative fistulae (n = 431).Recurrence rates were 4% in patients who had ND before TORS/TLM and 11% inpatients who had ND after TORS/TLM. In the cohort of concurrent ND and TORS/TLM,the recurrence rate was 1%.10 with casereports classified as \u201csevere\u201d bias.28 Selection bias in diseaseseverity and stage, different inclusion and exclusion criteria, lack of commonoutcome measures and varying lengths of follow-up were identified as some of thefactors increasing the bias levels in the articles.The articles in this review were predominantly nonrandomized studies and werereviewed for bias with the ROBINS-I tool assessing timing of NDin conjunction with transoral surgery, although prospective and retrospectivestudies on this topic have been performed.2729 Of theremaining patients who had concurrent ND, 3% had major bleeds and 3% had minorbleeds recorded,13 with an overall bleeding rate of 5% (n = 80). In bothinstances of major bleeding, vessel ligation was not performed during theinitial procedure. In patients with ND performed after TORS/TLM, 3% experiencedminor bleeding (n = 39).6 In patients with ND performed before TORS/TLM, 3% had amajor bleed,24 and 1% had a minor bleed (n = 75).26 In thecase report by Tsukahara et al,20 external carotid arteryligation did not occur until the patient was readmitted for the second episodeof pharyngeal bleeding. In the majority of patients with major bleeding, vesselligation did not occur regardless of ND timing. In all 4 episodes of majorhemorrhage, bleeding was stopped with readmission and vessel ligation.24There were insufficient data from the studies in this review to draw meaningfulconclusions about whether the timing of ND affects postoperative hemorrhagerates. Six studies (352 patients) did not identify hemorrhage as anoutcome.28 Of the concurrent cohort of patients, 13% hadintraoperative fistulae, and 2% had postoperative fistulae (n = 429). There wereno recorded fistulas in patients with ND before TORS/TLM (n = 19). In patientswith ND after TORS/TLM (including concurrent after), 16% reported intraoperativefistulae16 and no postoperative fistulae were noted (n = 19). Due tothe variability in the sample size of each cohort, definitive conclusions cannotbe made about fistula formation. However, the trends identified in this study(increased fistula rate in patients with concurrent ND) are in keeping withpublished literature.Four studies (79 patients) did not include fistula rates as outcomemeasures.29 found that 29% of patients developed intraoperativecommunications and that 4% resulted in delayed fistula formation in patientsundergoing concurrent transoral surgery and ND (n = 148). Their results showedthat fistulae occur regardless of T stage but generally correlate withadvanced-stage neck disease, suggesting that there is an increased probabilityof fistulae formation when treating stage III and IV oropharyngeal disease.Moore et al29 In studies reporting DSS and OS for concurrent ND, themean DSS was calculated to be 96% and mean OS was 99%, with a follow-up periodranging from 2 to 29 months.28 One study cited DSS andOS rates of 89% and 100% at 2 years, respectively, for patients undergoing NDafter TORS/TLM.16 Three studies described mean DSS and OS rates of 89%and 91% at a follow-up ranging from 1 year to 29 months in 58 patientsundergoing ND before (including concurrent before) TORS/TLM.26 It isimportant to note that while we have reported DSS and OS, interpretation ofthese data should be cautious due to the lack of TNM-stratified survival rateswithin the studies in this review. The number of studies reporting DSS and OS asoutcomes for each category of ND was too smallto draw definitive conclusions.Long-term patient outcomes such as DSS and OS were not mentioned in 9studies.18 Performing level I ND in patients with OPSCC carriesadded risk of creating PCF intra- or postoperatively. Moreover, the rate ofoccult level I metastases based on preoperative evaluation is estimated to be3%,32 which is below the threshold to indicate standard inclusionof this level according to standard UK practice. The current guideline forsurgical management of these patients in the United Kingdom is that ND shouldinclude levels II to IV and possibly level I.33 This is reflected in theresults of our study, with 100% of patients having ND of levels II to IV and 64%having ND of level I, while 36% had level V. In 2003, Doweck et al34 performeda study of 76 patients, looking at the extent of ND required in oropharyngealcancer. They concluded that surgical management of oropharyngeal cancer shouldinclude a selective ND of levels II to IV and that without radiologic andclinical evidence of positive nodes in level I and V, these levels could bespared.Besides ND timing, one variation identified among studies in this review is thelevel of ND performed. Most authors recommended a selective ND of levels II toIV for OPSCC treatment.A major issue encountered when performing this review was interpreting thefindings of the studies. The literature search did not identify any RCTs, whichlimited analysis. In addition to the 19 articles in the review, only 5 wereprospective studies. Therefore, the articles reviewed showed variation in designand outcome measures, and the lack of control arms in the studies added to theheterogeneity among the articles. This limited statistical analysis as ameta-analysis could not be performed. Individual patient-level analysis was notpossible to extract from many of the studies.We declare no biases in the construction of this review. A thorough search wasconducted by 2 independent reviewers; the search was limited to the Englishlanguage. Articles studying cancers outside the oropharynx , modalities other than TORS/TLM, and those failing to distinguish NDtiming as a feature in the results were excluded.The evidence presented in this review is insufficient to draw definitiveconclusions surrounding ND timing and patient outcomes. As such, practice shouldcontinue to reflect the decision-making process of the multidisciplinary team.More research should be conducted, including RCTs, to allow for a more thoroughreview to be completed before any conclusive decisions arise regarding NDtiming. In addition, other factors should be considered when looking at NDtiming, including cost-effectiveness of performing staged ND, the level of ND,anaesthetic risk to the patient with having 2 procedures, and the effects ofpotentially having delayed adjuvant treatment.In conclusion, transoral surgery, TORS in particular, has become a well-establishedmodality for treating oropharyngeal carcinoma. Given the increasing rates of thesecancers, the role of TORS/TLM is becoming more relevant.This review demonstrates the lack of robust literature when analyzing ND timing inrelation to TORS/TLM for oropharyngeal carcinoma. There should be a focus onproducing more evidence for patient outcomes surrounding TORS/TLM with concurrent orstaged ND. Wherever possible, this evidence should be in the form of RCTs orprospective studies, although it is acknowledged that these would raise ethicalconcerns regarding patient allocation to particular treatment armsprospectively.Due to the heterogeneity of existing studies and the lack of comparator arms,meta-analysis could not be performed. Pooled analysis was conducted for certainoutcomes, where this was possible. There are insufficient data to comment on whetherthe timing of ND in relation to TORS affects the outcomes of patients. However,within the limitations of the current evidence base, there seems to be nocorrelation between timing of ND and complications.Finally, heterogeneity was identified in the extent of ND routinely performed fororopharyngeal carcinoma. Therefore, a dedicated systematic review on this topicwould likely be beneficial in providing the best possible quality evidence forclinicians in assessing the necessity of level I ND in patients with oropharyngealcancer.Jai Parkash Ramchandani, wrote manuscript, involved in study design,data acquisition and analysis, drafting, final review of the manuscript prior tosubmission, study supervision; Aina Brunet-Garcia, wrote manuscript,involved in study design, data acquisition and analysis, drafting, final review ofthe manuscript prior to submission; Nikoleta Skalidi, involved in studydesign, data acquisition and analysis, critical review of manuscript and finalreview prior to submission; Jack Faulkner, involved in critical reviewof manuscript and final review prior to submission; Aleix Rovira,involved in critical review of manuscript and final review prior to submission;Ricard Simo, involved in critical review of manuscript and finalreview prior to submission; Jean-Pierre Jeannon, involved in criticalreview of manuscript and final review prior to submission; Asit Arora,involved in critical review of manuscript and final review prior to submission.Competing interests: None.Sponsorships: None.Funding source: None."} +{"text": "Data on burden of peripheral artery disease (PAD) and its attributable risk factors are valuable for policymaking. We aimed to estimate the burden and risk factors for PAD from 1990 to 2019.We extracted the data on prevalence, incidence, death, years lived with disability (YLDs), and years of life lost (YLLs) from the Global Burden of Disease Study 2019 to measure PAD burden. Moreover, the attributable burden to PAD risk factors was also estimated.Globally, in 2019, 113,443,017 people lived with PAD and 10,504,092 new cases occurred, resulting in 74,063 deaths, 500,893 YLDs, and 1,035,487 YLLs. The absolute numbers of PAD prevalent and incident cases significantly increased between 1990 and 2019, contrasting with the decline trends in age-standardized prevalence and incidence rates. However, no statistically significant changes were detected in the global age-standardized death or YLL rates. The burden of PAD and its temporal trends varied significantly by location, gender, age group, and social-demographic status. Among all potentially modifiable risk factors, age-standardized PAD deaths worldwide were primarily attributable to high fasting plasma glucose, followed by high systolic blood pressure, tobacco, kidney dysfunction, diet high in sodium, and lead exposure.PAD remained a serious public health problem worldwide. More strategies aimed at implementing cost-effective interventions and addressing modifiable risk factors should be carried out, especially in regions with high or increasing burden. Peripheral artery disease (PAD) is characterized by atherosclerosis of the peripheral arteries which results in insufficient blood flow to the affected limb and subsequent ischemia. Most patients with PAD are asymptomatic, but many have experienced experience classic intermittent claudication, critical limb ischemia, occasionally acute limb ischemia, and the associated adverse cardiovascular events \u20133. PAD iUp-to-date epidemiological information is essential in public health policy making. As of 2010, ~202 million people worldwide lived with PAD, almost 70% of them living in low-income or middle-income countries . With thThe Global Burden of Disease study (GBD), an ongoing effort to estimate the global epidemiological trends of 369 diseases and injuries, provides a unique opportunity to understand the landscape of PAD. Sampson et al. reported the global landscape of PAD mortality using the data derived from the GBD study 2010 , while nhttp://ghdx.healthdata.org/gbd-results-tool). The informed consent was waived because GBD 2019 used de-identified and aggregated data.GBD 2019, conducted by Institute of Health Metrics and Evaluation (IHME), was designed to provide a systematic estimation of health loss due to diseases and injuries across 204 countries and territories, seven super-regions and 21 regions from 1990 to 2019 . And assPAD was defined as having an ankle-brachial index <0.9, and intermittent claudication was defined clinically. All cardiovascular diseases coded as 440.2, 440.4 and 443.0\u2013443.9 in the 9th revision of the International Classification of Diseases and Injuries (ICD-9) or I70.2\u2013I70.8 and I73\u2013I73.9 in the ICD-10 were recognized as PAD. Years lived with disability (YLDs) were calculated as the prevalence of each severity level and the corresponding disability weight. Disability weight reflects the severity of the disease on a scale from 0 to 1 (death). Years of life lost (YLLs) due to PAD were calculated using the number of deaths and a standard life expectancy according to age. Detailed descriptions of the estimation process are presented in the SDI was used to group countries with similar development status. SDI is composed of lag distributed income per capita, mean education in the population over age 15, and total fertility rate under 25 years, with a value range of 0 (worst) to 1 (best) \u201312. We dA comparative risk assessment approach was used to estimate the proportion of PAD attributable to 84 environmental, occupational, metabolic, and behavioral risk factors. Detailed process for quantifying the percentage contributions of different risk factors to disease burden has been published previously , 13. RisPrevalence, incidence, death, YLDs, and YLLs were the main parameters evaluating the burden of PAD. Counts and age-standardized rates per 100,000 people, with 95% uncertainty intervals (UIs) were calculated to quantify the burden of PAD across gender, age group, year, location, and SDI. To avoid the interferences of population change and age distribution difference, age-standardized rates were also used and calculated by direct standardization to the global age structure. The population attributable fractions (PAFs) were calculated to quantify the percentage contributions of risk factors to age-standardized PAD deaths. The 95% UIs were determined by the 2.5 and 97.5 centile values of 1,000 draw-level estimates after ordering them from the smallest to the largest. A 95% UIs, excluding 0, was considered to be statistically significant. Besides, we analyzed the correlation between SDI and age-standardized rates by Pearson's correlation test model. All statistics were based on the R program (Version 3.6.1).In 2019, PAD affected 113,443,017 people worldwide, increasing by 72.5% (95% UI 70.2% to 74.7%) compared to 1990 . There wPAD contributed to 74,063 deaths globally in 2019, having an increase of 145.5% (95% UI 96.5% to 176.2%) between 1990 and 2019 . AdditioGlobally, the numbers and age-standardized rates of prevalent cases, incident cases, and YLDs of PAD were all higher in females than in males across all years . ConversAcross 21 GBD regions, Andean Latin America had the lowest age-standardized incidence and death rates of PAD in 2019; whereas High-income North America had the highest age-standardized incidence rate and Eastern Europe had the highest age-standardized death rate . Among aFrom 1990 to 2019, the age-standardized incidence rate of PAD sharply decreased in regions with relatively high-income, with the greatest decrease seen in High-income Asia Pacific [\u221239.3% (95% UI \u221240.2 to \u221238.4)], followed by Australasia, Western Europe, and High-income North America . Canada,Among all risk factors quantified in GBD study 2019, the global age-standardized death of PAD was primarily attributable to high fasting plasma glucose [26.8% (95% UI 22.8% to 31.0%)], followed by high systolic blood pressure [25.3% (95% UI 18.1% to 34.0%)], tobacco [24.2% (95% UI 17.5% to 31.0%)], kidney dysfunction [12.3% (95% UI 7.3% to 16.9%)], diet high in sodium [2.6% (95% UI 0.5% to 7.1%)], and lead exposure [1.1% (95% UI 0.4% to 1.9%)]. In addition, The present study has evaluated the global PAD burden from 1990 to 2019, with attention paid to the comparisons across different age groups, sex, locations and attributable risk factors. In 2019, 113,443,017 individuals lived with PAD and 10,504,092 new PAD cases occurred globally, contributing to 74,063 deaths, 500,893 YLDs and 1,035,487 YLLs. In addition, compared with GBD 2010 can be found in the article/JL and SX contributed to conception and design of the study. JL and YC performed the statistical analysis. JL, NJ, and ZL wrote the first draft of the manuscript. SX reviewed and edited the manuscript. All authors contributed to the article and approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Using a sample of 4,182 UK adults aged 50 and above, this study explored the association of changes in health behaviours with weight and obesity during UK lockdown in Jun/Jul and Nov/Dec 2020. Over 30% adults reported more sitting, more TV watching or less exercise. Around 20% adults were engaged in eating more or sleeping less. More alcohol drinking happened in 12.3% adults. Results suggested that more sedentariness, more TV watching, less exercise, more eating and more alcohol drinking were associated with a significant increase in weight. Meanwhile, less sedentariness or less eating significantly reduced weight in Nov/Dec 2020. A higher risk of obesity was found in adults sitting, eating, or sleeping more than usual. Considering potential health risks associated with obesity in older population, weight management is necessary nationwide."} +{"text": "Introduction:\u00a0As many\u00a0Americans are becoming overweight or obese, increased body mass index (BMI) is fast becoming normalized.\u00a0There is a need for more research that highlights the association between pre-pregnancy obesity and adverse pregnancy outcomes.Aim: To determine the association between increasing pre-pregnancy BMI and adverse pregnancy outcomes.Methods: We utilized the United States Vital Statistics records to collate data on all childbirths in the United States between 2015 and 2019. We determined the association between increasing pre-pregnancy BMI and adverse pregnancy outcomes using multivariate analysis. Neonatal outcomes measures include the five-minute Apgar score, neonatal unit admission, neonates receiving assisted ventilation > six hours, neonatal antibiotics use, and neonatal seizures. Maternal outcomes include cesarean section rate, mothers requiring blood transfusion, unplanned hysterectomy, and intensive care unit admission. In addition, we controlled for maternal parameters such as race/ethnicity, age, insurance type, and pre-existing conditions such as chronic hypertension and prediabetes. Other covariates include paternal race, age and education level, gestational diabetes mellitus, induction of labor, weight gain during pregnancy, gestational age at delivery, and delivery weight.Results: We studied 15,627,572 deliveries in the US Vital Statistics records between 2015 and 2019. Among these women, 3.36% were underweight, 43.19% were with a normal BMI, 26.34% were overweight, 14.73% were in the obese class I, 7.23% were in the obese class II, and 5.14% were in the obese class III. Increasing pre-pregnancy BMI was associated with significant adverse outcomes across all measures of maternal and neonatal outcomes.Conclusion:\u00a0A strong association exists between increasing pre-pregnancy BMI and adverse maternal and neonatal outcomes. The higher risk of adverse pregnancy outcomes among overweight and obese women remained even after controlling for other traditional risk factors of adverse maternal and neonatal outcomes. In 2016, over 1.9 billion adults were overweight globally, with 650 million of this population being obese [Overweight and obesity are a state of excess or abnormal fat accumulation that may impair health. The World Health Organization (WHO) defines overweight as a body mass index (BMI) > 25-29.9 kg/mng obese . ObesityGlobally, 40% of women were overweight in 2016, and 15% of women were obese in the same year . The annMaternal obesity is associated with an increased risk of type 2 diabetes, hypertension, and cardiovascular disease. In addition, obese women have an increased risk for pregnancy complications such as gestational diabetes, preeclampsia, labor induction, cesarean section, and wound infection. Furthermore, their fetuses risk macrosomia and fetal distress .Healthy People 2020 reported that maintaining a healthy body weight can reduce complications in obese women during pregnancy. The Healthy People 2020's obesity target was 30.5% from a baseline of 33.9% among adults aged 20 years and above in 2005-2008. However, the obesity rate increased to 38.6% in 2013-2016 . HutchesThis study aims to investigate the association between pre-pregnancy BMI and adverse pregnancy outcomes. Reducing the incidence of adverse pregnancy outcomes requires intervention directed toward\u00a0obese and overweight women before they conceive.This article was previously posted to the Research Square\u00a0preprint server on August 4, 2022.Study design and data sourcesWe extracted the data for this study from the US Vital Statistics Records 2015-2019. The National Vital Statistics Records database provides complete information regarding births and deaths in the United States .We explored the association between different classes of obesity and nine measures of maternal and neonatal pregnancy outcomes. Since the database is de-identified and publicly available, ethical clearance or Institutional Review Board approval was unnecessary.Study populationWe studied 15,627,572 deliveries recorded in the United States Vital Statistics records between January 2015 and December 2019. The study cohort included women of all races/ethnicities. However, women with missing vital information such as maternal race/ethnicity, BMI, age, and measured pregnancy outcomes were excluded from the study.Patient characteristics and risk factorsCovariates utilized in this study were identified based on existing literature, including maternal and paternal demographics and obstetric and medical history. These factors included maternal race/ethnicity defined as non-Hispanic White (White), non-Hispanic Black (Black), Hispanic, and non-Hispanic other (other), maternal insurance types , and uninsured), and maternal education level defined as either high school, college, or advanced education. Other factors included in the study are maternal age, paternal race/ethnicity, paternal age, paternal education level, pre-pregnancy diabetes, hypertension, pre-pregnancy obesity, cesarean section\u00a0and previous cesarean section (PCS), augmentation and labor induction, and delivery weight.Definition of study outcomesThere were nine primary measures of pregnancy outcome. The maternal parameters were cesarean section, mothers requiring blood transfusion during labor or delivery , unplanned hysterectomy, and maternal admission to the intensive care unit . The neonatal outcomes included a low fifth-minute Apgar score (defined as Apgar score < 7), neonatal intensive care unit (NICU) admissions, neonates receiving assisted ventilation for \u2265 six hours after delivery, neonatal antibiotics use, and neonatal seizures.Statistical analysisWe expressed categorical variables as frequencies and percentages and continuous variables as mean \u00b1 standard deviations. Chi-square and independent sample t-tests were utilized to compare categorical and continuous variables. Using chi-square, baseline characteristics were stratified across the different classes of pre-pregnancy BMI . With a significant association, a post hoc analysis was performed between all groups to define the source of statistical significance. Unadjusted odds ratios (ORs) and 95% CIs for the association of study variables with pregnancy outcomes were calculated from bivariate logistic models.We adjusted for maternal age, maternal race/ethnicity, maternal education, maternal insurance types, paternal race/ethnicity, paternal age, paternal education level, pre-pregnancy diabetes, chronic hypertension, weight gain in pregnancy, PCS, induction of labor, delivery weight, and gestational age at delivery in our final multivariate analysis. We then determined the association between different classes of pre-pregnancy BMI and maternal and neonatal pregnancy outcomes. A two-tailed p-value < 0.05 was regarded as statistically significant. All statistical analyses were performed using STATA 16 .We conducted a retrospective analysis of 15,627,572 deliveries. Of the women,\u00a03.4% were underweight with a BMI < 18.5, 43.2% were with a normal pre-pregnancy BMI (18.5-24.9), and 26.3% were overweight (25.0-29.9), with 14.7% in the obesity class I group (30.0-34.9), 7.2% with obesity class II (BMI 35-39.9), and 5.1% with obesity class III.Table There was a significant association between maternal age, race/ethnicity, maternal education, insurance type, and the different classes of pre-pregnancy BMI. Among women with normal pre-pregnancy BMI, 6.09% were less than 19 years, 76.86% were between 20 and 34 years, 17.03% were between 35 and 49 years, and 0.02% were more than 50 years. However, among women with obesity class III pre-pregnancy BMI, about 2.56% were below 19 years, 80.04% were between 20 and 34 years, 17.39% were between 35 and 49 years, and 0.01% were above the age of 50 years.Among women with normal pre-pregnancy BMI, 56.53% were Whites, 10.82% were Blacks, 20.85% were Hispanics, and 11.80% belonged to other races. However, among women with class III obesity, 49.05% were Whites, 24.37% were Blacks, and 21.71% were Hispanics. While the proportion of Whites and other races (mainly Asian/Pacific Islanders and Native Americans) reduces as the BMI increases, the proportion of Blacks and Hispanics increases dramatically with increasing pre-pregnancy BMI. Considering the population distribution in the United States, according to the latest census data, Whites were underrepresented in the obese group while Blacks were overrepresented.Among women with normal pre-pregnancy BMI, 34.51% had high school education as their highest level of education, 49.74% had a college education, and 15.75% had advanced education. Among the women with morbid obesity, 44.4% had a high school education as their highest level of education, 50.2% had college degrees, and only 5.4% had advanced degrees. As the BMI increases, there seems to be a sharp increase in the proportion of women with high school education, while there was a drastic reduction in the proportion of women with an advanced degree.Among the women with normal pre-pregnancy BMI, 54.00% had private insurance, 37.23% utilized Medicaid, and 4.86% were uninsured. However, among women with class III obesity, 41.32% had private insurance, 53.87% had Medicaid, and 1.88% were uninsured. As the BMI increased, there was an increase in the proportion of women with Medicaid insurance. At the same time, there was a corresponding reduction in the proportion of women with private insurance or those who were uninsured.The prevalence of comorbidities such as prediabetes, chronic hypertension, and incidence of gestational diabetes mellitus increases across the different classes of BMI.Table Table 2 [Our main finding in this study was that increasing pre-pregnancy BMI\u00a0is strongly associated with adverse maternal and perinatal\u00a0outcomes. This association remained significant even after adjusting for independent risk factors for adverse pregnancy outcomes. This is in keeping with a meta-analysis of 13 studies that showed a linear relationship between pre-pregnancy BMI and all adverse pregnancy outcomes [2 .2 had an increased risk of a cesarean section after labor induction [In our study, increasing pre-pregnancy BMI was associated with increased cesarean section rates, which was significant even after controlling for traditional risk factors like PCS and birth weight. A study done in Canada showed that a higher BMI was also associated with earlier decisions to perform a cesarean section in the second stage of labor . A recennduction . Obesitynduction . This imWe found that excessive gestational weight gain, gestational diabetes, hypertensive complications, cesarean delivery, and increased infant weight were higher among women with pre-pregnancy obesity than women with a normal BMI. This was also in keeping with the literature and had Interestingly, in the present study, increasing maternal BMI was associated with a decrease in the need for maternal blood transfusion during labor or delivery. A study showed that the association between hemorrhage and BMI might be affected by the mode of delivery. With a vaginal delivery, overweight and obese women had up to 19% increased odds of hemorrhage or atonic hemorrhage. In contrast, women in any obesity class had up to 14% decreased odds of severe hemorrhage after cesarean delivery. The authors concluded that maternal obesity did not have a clinically significant impact on postpartum hemorrhage risk and that the direction of the association between hemorrhage and BMI may differ by mode of delivery . The difWe found that the odds of unplanned hysterectomies were higher among overweight mothers, and this increase showed a dose-dependent trend between obesity classes. Baranco et al. found that although the risk of severe maternal morbidity was increased in women with morbid obesity, the rate of unplanned hysterectomy remained unchanged . Our stu2) had the highest risk of ICU admission [In terms of maternal ICU admissions, underweight and overweight women had no difference in risk compared to women with normal pre-pregnancy BMI. Still, this risk increased across obesity classes, with women in obesity class III having the highest risk of ICU admission. This is in keeping with a study on ICU admission among obstetric patients in whom 82% had a cesarean delivery. Although ICU admission was rare, women with super obesity increases across the BMI classes, with women in obesity class III having the highest risk even after controlling for other risk factors. Furthermore, a systematic review conducted in 2015 revealed that maternal obesity was associated with low Apgar scores at five\u2009minutes and large for gestational age neonates, post-term delivery, and stillbirths . This haThe risk of neonates requiring assisted ventilation > six hours increased as their mother's pre-pregnancy BMI increased. The highest risk was seen in women with class III obesity, while underweight mothers showed no increased risk. A similar study showed that infants born to obese level III mothers were much more likely to require assisted ventilation > six hours and NICU admission. These obese mothers also had a higher risk of pregestational and gestational diabetes and cesarean delivery . Even afIt has also been shown that maternal obesity is independently associated with an increased incidence of neonatal sepsis and a combination of neonatal morbidities in full-term newborns, including patent ductus arteriosus (PDA), which occurs most commonly in premature babies, and necrotizing enterocolitis . Our obs2 [Finally, the present study found the highest incidences of neonatal seizures in class II obese women. In general, neonates born to overweight and obese women had a higher incidence of neonatal seizures. For example, a study in Sweden listed maternal obesity among the risk factors for neonatal seizures with an odds ratio of 2.6 for women with a BMI above 40kg/m2 . This haStudy limitationsIn the United States Vital Statistics records, the quality of reporting varied widely by state.\u00a0Multiple data sources, such as discharge summaries and Medicaid claims data, are needed to accurately supplement birth certificate data to understand seizure prevalence in all three US birth settings.Though the United States outspends every country in the world on health care, it continues to lag behind the developed world in maternal and child healthcare indices. A significant reason for this may be the astronomical prevalence of obesity in the population and among women of reproductive age. A strong association exists between increasing pre-pregnancy BMI and adverse maternal and neonatal outcomes. The higher risk of adverse pregnancy outcomes among overweight and obese women remained even after controlling for other traditional risk factors of adverse maternal and neonatal outcomes. Since pre-pregnancy BMI is a modifiable risk factor, significant efforts should be directed at obesity prevention, especially among women of reproductive age group, to improve women\u2019s health and pregnancy outcomes."} +{"text": "Public acceptance, trust, and actual uptake of COVID-19 vaccines are crucial to stem the pandemic. Although roll out of vaccines was high in KSA, the public response was not sufficiently studied. We aimed to investigate knowledge level, acceptance, and trust in COVID-19 vaccination and related predictors among adults in Makkah, KSA.A web-based cross-sectional survey using a snowballing sample was carried on 507 adult Saudi population living in Makkah city. The survey was developed based on literature search. In the logistic analysis, the dependent variables included acceptance rate and trust in effectiveness and safety of COVID-19 vaccines, while the independent variables (predictors) were sociodemographics and level of knowledge.OR = 2.07; CI: 1.24\u20133.48 for acceptance and OR = 2.67; CI: 1.58\u20134.51 for trust), higher educational level , previous seasonal flu vaccination , female sex , and history of COVID-19 infection were among significant predictors for both vaccine acceptance and trust in vaccine effectiveness.The survey included 507 participants, aged 18\u201378 years, 55.8% were females, and 36.7% had (or one of their family members) previously been exposed to COVID-19 infection. Their knowledge about COVID-19 vaccination was satisfactory (86.2%) with 71.2% intended to receive COVID-19 vaccination, and 56.4% was confident of the vaccine effectiveness. Vaccine efficacy, duration of protection, schedule of vaccination, and recommendation by authorities may favor their decision to accept or decline COVID-19 vaccines. Good knowledge about vaccines (Adult Saudi population in Makkah city showed satisfactory knowledge about COVID-19 vaccination with moderate rate of vaccine acceptance and a relatively low rate of confidence in vaccine effectiveness. Better understanding of public acceptance and trust in COVID-19 vaccines and addressing barriers to vaccination are recommended to improve vaccine coverage and to reinforce some communication characteristics of the current vaccination campaign. The world is currently facing one of the biggest challenges, the coronavirus disease COVID-19), which rapidly spread all over the world within a very short period to be declared by the World Health Organization (WHO) a worldwide pandemic. It led to economic loses, social ramifications, and a heavy load on healthcare sector 9, which .Before availability of COVID-19 vaccines, the only effective preventive measure was to avoid exposure. Measures like social distancing, curfew, and mass economic shutdowns resulted in severe deterioration of psychosocial and physical wellbeing and a great decline in global economy . COVID-1For a vaccination program to be successful, authorities should consider many factors such as public acceptance, facilities for wide coverage, impact of infodemics, and trust in authorities. In addition, many inquiries surround COVID-19 vaccination including short- and long-term side effects, need for frequent vaccinations, and long-term protection, and its ability to protect against different genetic variants should be considered .Vaccine acceptance may be affected by demographic, behavioral, and health predictors , 7. VaccA large study analyzing 15 surveys in low- and middle-income countries (LMIC) and Russia and the USA showed tIn Saudi Arabia, the acceptance rate among adult Saudi population at different regions ranged from 48 to 65% \u201314. Limi> 18 years who were social media users and agreed to take part in this survey.An analytical cross-sectional web-based survey using a snowballing sample was designed. Enrolled participants were adult Saudi population living in Makkah city aged The minimum sample size required was 385 according to Raosoft sample size calculator based on 95% confidence level, 5% margin of error, and anticipated response of 50%. To reduce the sampling error, the sample size was increased to around 500.The dependent variables were acceptance rate and trust in effectiveness and safety of COVID-19 vaccines among adult population, while the independent variables (predictors) were sociodemographics and level of knowledge.An electronic survey was developed for wider and rapid distribution and to reach the target population who conform to regulations of avoiding social contact from 14 to 28 February 2021. The survey was developed in Arabic after a thorough search in the literature and manuscripts with similar aims and questionnaires , 5\u201315. IA pilot study was conducted on forty participants to test objectivity and validity of questionnaire or any needed modifications, and it was finalized after a series of group discussions with estimated completion time of about 5\u201310 min.The survey was uploaded via Google online survey platform and distributed through different social media platforms within Makkah city. In addition, personal communications helped rapid distribution on the Internet. Participants were able to see the survey and answer the questionnaire by just clicking the relevant link.\u25aa The questionnaire included the following: sociodemographics of participants, sources of information about COVID-19, history of seasonal flu vaccination, chronic illness, or any type of hypersensitivity. Participants were asked to indicate if they or one of their family members had previously been exposed to COVID-19 infection.\u25aa Knowledge about COVID-19 vaccines was assessed using a 9-item MCQ and three-way scales. These include hearing about vaccines, free availability, the presence of several types, age restrictions, adverse effects, administration, official registration, place for vaccination, and need for vaccination after recovery. One point was given for correct answers and 0 for incorrect/do not know answers. The total knowledge score was 9 (range 0\u20139). Participants with scores above 75% (7\u20139) were considered to have good knowledge.\u25aa Acceptance of COVID-19 vaccines was assessed by intention to receive vaccines, and they were also asked to indicate confidence in vaccine effectiveness .\u25aa Factors that may favor their decision to accept or decline the vaccine were based on 10 items. These include efficacy of vaccines, duration of protection, schedule of vaccination, recommendation by authorities, mode of administration, immediate side effects, long-term negative health consequences, local availability, country of manufacture, and others.It was obtained from the Local Committee for Bioethics and Medical Ethics at Umm Al-Qura University . An electronic informed consent from anonymous participants was added as an initial cover page before answering the online survey with emphasis on voluntary participation and withdrawal without justification.It was carried out using SPSS package . Mean \u00b1 SD were used for quantitative variables, while frequency and percentage were used for qualitative variables. Chi-square or Fisher exact tests were used to assess differences in frequencies of qualitative variables while Mann-Whitney or Kruskal-Wallis tests were used for continuous nonparametric variables. Logistic regression analysis was used to predict the factors associated with vaccine acceptance and trust. Odds ratios (OR) and 95% confidence intervals (CI) were measured in the univariate analysis, and only significant independent variables were entered in the logistic analysis. Statistical methods were verified, assuming a significant level of < 0.05.The study included 507 participants fulfilling inclusion criteria with mean age of 45.2 \u00b1 13.9 years ranged from 18 to 78 years, 55.8% were females, 30% resides in rented houses, 36.7% were married, 86.2% were university students/graduates, about one-third had governmental work, and 29.4% had monthly income less than 5000 SAR. More than one-third (35.3%) had history of previous seasonal influenza vaccination, 12.4% of chronic diseases, 10.1% of any type of hypersensitivity, and 36.7% of participants, or one of their family members had previously been exposed to COVID-19 infection.The vast majority (99%) of participants heard about COVID-19 vaccines, 97.6% knew that the vaccine is freely available in the kingdom, and 94.3% knew that, at the time of the survey, there were several types of vaccine. The suitable and safe age groups for vaccination were known by 86.2%, vaccines can cause mild side effects, and given by injection were known by 88.2% and 97.2%, respectively. Only 8.5% did not know that they have to register in \u201cSehhaty\u201d application to get vaccine, more than half of participants (54.8%) did not know the available places for vaccination, \u061cwhile 30.6% did not know that they should take vaccine after recovery from infection and social media (59%), while 43% and 32.3% relied on websites and TV, respectively. Only 13% relied on magazines and newspapers.More than 70% 71.2%) of participants intended to receive COVID-19 vaccination, and 56.4% were confident of vaccine effectiveness. Their level of knowledge about COVID-19 vaccination was satisfactory where 86.2% had good knowledge that was significantly higher with increased age, among those with university education/graduates, governmental workers, those with higher monthly income, had history of previous seasonal influenza vaccination, had or one of their family members previously been exposed to COVID-19 infection, those with intent to receive vaccine, and those who believe in vaccine effectiveness. On the other hand, knowledge level was not affected by sex, lodging type, marital status, or having chronic disorder or any type of hypersensitivity (92.7%), ( 89.2%), and ( 87.4%), respectively. About three-forths considered recommendation by authorities, and more than half of them considered mode of administration (56.2%) and immediate side effects (55.2%). Factors less likely to favor their decision were local availability, country of manufacture, and long-term negative health consequences, and others and trust in vaccine effectiveness including age (higher ages), sex , and education (university/graduate). Other\u00a0significant factors include history of previous seasonal flu vaccination or COVID-19 infection and having good knowledge about vaccines.\u00a0In addition, those with history of previous seasonal flu vaccination or COVID-19 infection and had good knowledge about vaccines. Higher family income significantly affects participants\u2019 intent to receive vaccines Table .Table 3ROR = 2.07; CI: 1.24\u20133.48 for acceptance, and OR = 2.67; CI: 1.58\u20134.51 for trust), higher educational level , previous seasonal flu vaccination , female sex , and history of COVID-19 infection that may enhance or hamper herd immunity and are critical for planning effective health communications to encourage mass immunization .The majority of participants (86.2%) had good knowledge about COVID-19 vaccination, and those intended to receive vaccines and had trust in their effectiveness had significantly higher knowledge. Our findings were comparable with other research assessing public knowledge about COVID-19 vaccination: 90.9% in Egypt , 79% in Good knowledge among participants was significantly related to increased age, high educational and financial levels, governmental workers, those who had history of previous seasonal influenza vaccination, and those who had or one of their family members had previously been exposed to COVID-19 infection. Similarly, Shafiq et al. found that US participants 55 years and older and those with higher educational background reported a higher average COVID-19 knowledge score . Also, GThe literature on gender and COVID-19 vaccine acceptance is mixed, with most studies indicating higher male acceptance, e.g., in France , the UK,Intent to receive vaccines was reported by 71.2% of participants with only 56.4% were confident of vaccine effectiveness. This finding is notable considering the potential hesitancy associated with new vaccines.Our results were higher than those reported among Saudi population in different regions. Al-Mohaithef and Padhi found that, among adult Saudi in major cities and other minor cities, 64.7% intended to uptake the hypothetical COVID-19 vaccine, only 7% reported hesitancy, and 28.2% were reported \u201cnot sure\u201d about their intention . AlshahrThe higher rate of vaccine acceptance among Makkah population may be attributed to population dynamics , literacy levels, experience in management of vaccine preventable disease (particularly with Hajj and Umrah), and other factors. In addition, \u201cintervention fatigue\u201d among the community could be a possible explanation. However, this has not been studied and needs further evaluation.In nearby Arab countries, variable levels of public acceptability of COVID-19 vaccines were noticed with higher willing in Iraq (88.6%) and Egypn = 36,220) from all the 23 Arab countries and territories and Arabs who live in 122 other countries including Europe, North America, Turkey, and others. A significant rate of vaccine hesitancy was reported among Arabs in and outside the Arab region . The most cited reasons for hesitancy were concerns about side effects and vaccine safety, distrust in health care policies, and vaccine expedited production [A large-scale multinational study measured vaccine hesitancy among Arab-speaking subjects with moderate rate of vaccine acceptance (71.2%) and a relatively low rate of trust in vaccine effectiveness (56.4%) among adults living in Makkah. Factors as vaccine efficacy, duration of protection, schedule of vaccination, and recommendation by authorities favored their decision to accept or decline vaccines. The strongest predictors for vaccine acceptance and trust were good knowledge about vaccines, higher educational level, previous seasonal flu vaccination, female sex, and history of COVID-19 infection. Our findings can help to design larger nationwide representative studies of Saudi population to better understand public acceptance and trust of COVID-19 vaccines, to handle the issue of vaccine hesitancy, and to address barriers to vaccination in order to improve vaccine coverage among the population and to reinforce some communication characteristics of current vaccination campaigns."} +{"text": "Background: Globally, the COVID-19 pandemic has had a negative impact on individuals, education, and the economy. During its peak, the pandemic forced school closures. Although there is currently no cure for corona virus, non-pharmaceutical measures can help prevent its spread. Among these preventive measures are regular handwashing with soap and water or the use of hand sanitizers, avoiding touching the mouth, nose, and eyes, social distancing, and the use of face masks. As a result, this study investigated COVID-19 prevention practices among Durban University of Technology staff and students in South Africa. Methods: Using a cross-sectional study design, data were gathered online via self-administered, structured questionnaires from 5849 university students and staff members between May 2020 and March 2021. Utilizing descriptive statistics, the characteristics of the study sample were reported. Using logistic regression models, the relationship between demographic characteristics and the overall level of COVID-19 preventive practices was evaluated. Results: The multivariate logistic regression model showed statistically significantly associations for COVID-19 preventive practices by: male compared to female participants, single participants compared to other marital categories, and those in the faculty of Health Sciences compared to other faculties. Conclusions: Overall, the study\u2019s preventive practices were commendable; they were also influenced by socio-demographic factors such as age, gender, marital status, and university faculty. Increasing age was associated with reduced compliance with COVID-19 preventive practices. In addition, men demonstrated greater caution than women. The COVID-19 pandemic is the fifth pandemic and comes 100 years after the last, in 1918 . It starAs a response to the deadly global COVID-19 pandemic, countries around the world took a variety of measures to stop the spread of this virus and lessen its negative impact . Non-phaStudy site/design: This is a cross-sectional study that was conducted in DUT, South Africa. The university is in the top five of all universities in the country and has over 33,000 students in all its campuses situated in both Durban and Pietermaritzburg [ritzburg . It alsoritzburg .Study population and sampling: Applying a convenient sampling method, all consenting staff and students in DUT were eligible to participate in the study. Data collection and management: An online semi-structured questionnaire was designed using Google forms and piloted. The questionnaire consisted of questions on demographics, position in DUT and preventive practices towards COVID-19 transmission. After necessary revision from the pilot exercise, data was collected from consenting staff and students at the university through self-administration. Data management involved exporting data from Google forms to MS Excel for cleaning and further analysis with Statistical Package for Social Sciences (SPSS) version 20.0. Data analysis: Analysis involved both descriptive statistics to report the characteristics of the study sample and inferential statistics (logistic regression). In measuring the overall level of preventive practices of COVID-19 transmission among participants, nine (8) preventive practice questions were asked, and scoring was done based on a poor and good/adequate answer methodology. The scores were summed for all participants. The overall good/adequate preventive practices of COVID-19 transmission were scored from 6\u20139 and poor preventive practices of COVID-19 transmission were scored \u22645. Bivariate and multivariate logistic regression models were used to assess the association between demographic characteristics and overall preventive practices of COVID-19 among the study participants.The study participants included 3351 females (57.29%), 2495 males (42.61%), and six \u201cothers\u201d (0.10%) who did not provide information about their gender. The mean age was 23.67 \u00b1 6.47. The highest percentage, 80.55% (4729), was found among those aged 17\u201326; the second highest percentage, 14.57% (852), was found among those aged 27\u201336. The lowest percentage, 4.59% (268), was of those within the age range of 37 and more . The vasThe majority of the respondents were students, 96.14% (562), located across the seven campuses of the university, and with more than 75% located in three of the campuses: Ritson, ML Sultan and Steve Biko Campus. They were from the faculties of Management Sciences, 30.19% (1766), Accounting and Informatics, 22.77% (1332), Engineering and the Built Environment, 18.19% (194), while Arts & Design, Applied Sciences and Health Sciences accounted for the rest. The university accommodation facility housed 29.66% (1735), while 70.34% (4116) lived outside the university, as shown in Twenty-five percent of respondents (1501) reported visiting a busy area within the previous week; 97.97% (5730) wore facemasks; 40.50% (2369) wore gloves; 98.07% (5736) used hand sanitizer; and 94.61% (5534) routinely cleaned their hands after contacting surfaces. Those who kept their hands away from their mouths, eyes, and noses made up 87.86% (5139); those who covered their noses with tissue paper or cloth when they sneezed in public or at home, 94.58% (5532); those who observed appropriate social distance when in public spaces, 97.11% (5680); and 73.73% of respondents said they would accept the COVID-19 vaccine if it were developed (4249) (as shown in p = 0.015), 37\u201346 years , 45\u201356 years , 57\u201366 years and \u2265 67 years showed a statistically significant increased likelihood for having good/adequate preventive practices of COVID-19 transmission, with those within the age groups 47\u201356 and 57\u201366 years having the strongest relationship with preventive practices of COVID-19 transmission , and female study participants , showed a statistically significant reduced likelihood of having good/adequate preventive practices of COVID-19 transmission, with male participants having a more reduced likelihood than female participants (p = 0.002) and married study participants , showed a statistically significant reduced likelihood for having good/adequate preventive practices of COVID-19 transmission, with single participants having a more reduced likelihood than married participants , Arts & Design , Applied and Health Sciences showed a statistically significant reduced likelihood for having good/adequate preventive practices of COVID-19 transmission, with participants in the Health Sciences having the most reduced likelihood having an eight-times stronger relationship with preventive practices of COVID-19 transmission than female participants , single participants , and those in the Faculty of Health Sciences as shown in After adjustment for other factors in the model, the multivariate logistic regression model showed statistically significantly higher odds for gender, with male participants (AOR: 9.815, 95% CI: 1.721\u201355.959, The variable age, after adjusting for confounding variables, showed statistically significantly lower odds with preventive practices of COVID-19 transmission in all age groups, as shown in The majority of respondents were single females. Very few of the total study population were university staff or both staff and students. In other comparable studies conducted in Egypt, China, and Jordan, the higher proportion of females ranged from 61 to 70% ,17,18,19This cross-sectional study did not examine cause-and-effect relationships, as is typical for such research. In addition, the knowledge and preventive practices of university students and faculty were self-reported online data that were susceptible to recall and information bias.The study revealed that respondents take adequate and effective preventive measures. Sociodemographic factors such as age, gender, marital status, and university faculty were significant predictors of adequate and good adherence to COVID-19 preventive practices. Appropriate interventions to enhance COVID-19 prevention adherence must be context-specific and take into account the identified sociodemographic facilitators of COVID-19 prevention adherence.COVID-19 can be transmitted through respiratory droplets from an infected person to another when coughing and sneezing.Preventive practices can protect against COVID-19 transmission.People above the age of fifty years do have good preventive practice towards COVID-19.Females do not practice preventive measure against COVID-19 as much as males."} +{"text": "Staphylococcus aureus is the primary cause of bacteremia, and methicillin-resistant S. aureus bacteremia is associated with a high mortality rate. Methicillin-resistant S. aureus clones are widespread worldwide, and molecular epidemiological studies are important. Therefore, this study aimed to determine the characteristics of patients who died due to methicillin-resistant S. aureus bacteremia and microbiological characteristics of methicillin-resistant S. aureus strains in a tertiary teaching hospital. This single-center, retrospective study included patients with methicillin-resistant S. aureus isolated from blood bacterial culture performed at Kyoto Prefectural University of Medicine Hospital, from October 2016 to May 2019. The data analyzed included patient background, clinical strain characteristics, and molecular epidemiology. Of 41 patients with methicillin-resistant S. aureus bacteremia were men), and 7 (17%) died due to methicillin-resistant S. aureus bacteremia. The median age of those who died in the methicillin-resistant S. aureus bacteremia group was predominantly higher than that of those in the alive group (p = 0.03). The most common cause of methicillin-resistant S. aureus bacteremia was endovascular devices, which occurred in 20 (49%), 18 (53%), and 2 (29%) patients in the total, alive, and died groups, respectively. Bacteriological characteristics showed that type IV Staphylococcal Cassette Chromosome mec genotype was most frequently detected in the total (n = 34 [83%]), alive (n = 29 [85%]), and died (n = 5 [71%]) groups. In the molecular cluster analysis, CC8, ST8, staphylococcal Cassette Chromosome mec type IV, and community-acquired-methicillin-resistant S. aureus formed the largest groups. The diversity of methicillin-resistant S. aureus clones is evident, and it is possible that clones with new virulence factors may still emerge. In the future, it will be crucial to monitor the epidemiological trends of methicillin-resistant S. aureus to respond quickly to changes in pathogenic and clonal factors, to clarify the gene expression network by identifying old and new virulence factors. Staphylococcus aureus, a major cause of bacteremia in developed countries and a common cause of community-acquired (CA) and healthcare-associated (HA) bloodstream infections, has an incidence of 20\u201330 cases per 100,000 population per year in high-income countries [S. aureus (MRSA) is widely recognized as one of the most common drug-resistant pathogens causing hospital- and community-acquired infections.Infections caused by drug-resistant bacteria result in worse outcomes . Althougmec IV (USA300 clone), ST1-SCCmec IV (USA400 clone), ST30-SCCmec IV (Southwest Pacific clone), ST59-SCCmec V (Taiwan clone), and ST80-SCCmec IV (European clone), are widespread worldwide [Currently, international MRSA clones, such as ST8-Staphylococcal Cassette Chromosome (SCC) orldwide ,11. Furtorldwide . This eporldwide . Thus, torldwide . We knowmec, multilocus sequence typing (MLST), and PCR-based ORF Typing (POT), to characterize MRSA bacteremia at a tertiary teaching hospital.The purpose of this study was to determine the background characteristics of patients who died from MRSA bacteremia and microbiological characteristics of MRSA clinical strains from 2016 to 2019. We also conducted molecular epidemiological analysis based on various DNA sequences, such as SCCS. aureus, SCCmec typing, MLST, POT type, and pathogen analysis, strains stored at -80\u00b0C were incubated in Tryptic Soy agar plates at 37\u00b0C for 18 h.Between October 2016 and May 2019, the first clinical isolates of MRSA were obtained from blood bacterial cultures of patients whose physicians deemed blood bacterial culture tests to be necessary when they visited the emergency department or were admitted to a hospital ward. Blood bacterial cultures performed at the Department of Clinical Center, University Hospital, Kyoto Prefectural University of Medicine. Duplicate strains were excluded. Strains were stored at -80\u00b0C. Twenty-four hours prior to drug susceptibility testing, antibiotic susceptibility of This retrospective cohort study, conducted at the Kyoto Prefectural University of Medicine Hospital in Japan, was approved by the Medical Ethics Committee . Informed consent for publication of this study was obtained via an opt-out form on the website. We examined the medical records of patients to obtain information on age, sex, presence of MRSA carriage, history of surgery, Charlson Comorbidity Index , source https://anesth-kpum.org/research/mrsa%e6%84%9f%e6%9f%93%e7%97%87%e3%81%ae%e7%96%ab%e5%ad%a6%e3%81%ae%e5%a4%89%e9%82%84%e3%81%a8%e6%96%b0%e3%81%9f%e3%81%aa%e6%b2%bb%e7%99%82%e6%b3%95%e3%81%ae%e9%96%8b%e7%99%ba/.This study was a clinical study of retrospective study. We used only medical information, without any medical invasion and intervention on the patients. Therefore, we used opt-out consent from patients. We published information on the website of the Department of Anesthesiology of Kyoto Prefectural University of Medicine about the purpose and conduct of the study, and further guaranteed that patients had the opportunity to refuse. The opt-out web address for this clinical study is MRSA bacteremia was defined as the presence of one or more positive blood cultures from a patient with clinical symptoms of infection, such as sweats, chills, and fever. MRSA bacteremia-related death was defined if the cause of death was an acute complication related to MRSA bacteremia, endocarditis (complications of heart failure due to endocarditis), or both underlying disease and MRSA bacteremia.In this study, target strain DNA was extracted from isolates using the CicaGeneus\u00ae DNA Extraction Reagent Kit according to the manufacturer\u2019s recommendations. This template DNA was used for all analyses.Antibiotic sensitivity was determined using the minimum inhibitory concentration (MIC). The MICs complied with the Clinical and Laboratory Standards Institute (CLSI) . The bremec typing synthesized primers were used in a previously reported multiplex polymerase chain reaction (PCR) method [mec types-I (415 bp), II (937 bp), III (518 bp), IV (937 and 415 bp), and V (518 and 359 bp) targeting the genes ccrA2-B, ccrC, IS1272, and mecA-IS431. SCCmec types I, II, and III were defined as HA-MRSA, while types IV and V were defined as CA-MRSA [Eight SCC) method . We detep), III 5 bp, IV , shikimic acid dehydrogenase , glycerol kinase , guanylate kinase , phosphate acetyltransferase nucleotide sequence , triose phosphate isomerase , and acetyl coenzyme A acetyltransferase [http://www.mlst.net).In MLST, we created primers specific for each of the following genes to amplify seven housekeeping genes required for 516 bp) . We analmec element region; POT2, prophage-based ORF; and POT3, prophage-based ORF [We performed POT analysis for all MRSA isolates based on the Cica Geneus\u00ae Staph POT KIT . Two sets of multiplex PCRs were performed according to the manufacturer\u2019s instructions. The presence of 23 open reading frames (ORFs) was determined from agarose electrophoresis images and the POT type. The POT score resulted in three POT numbers: POT1, SCCased ORF .lukF-PV) by PCR [We analyzed the expression of the gene encoding Panton-Valentine leukocidin by PCR .The normality of the distribution of continuous variables was tested using the Kolmogorov-Smirnov method. Variables with a normal distribution are presented as means and standard deviations, and variables with a non-normal distribution are presented as medians (interquartile ranges) and were compared using the Mann\u2013Whitney U test. Categorical variables are shown as numbers (%), and the difference between the alive and died groups was tested using Fisher\u2019s exact test. The significance of the relationships was determined using Spearman\u2019s rank correlation coefficient. The test was two-tailed. The significance level was set at \u03b1<0.05. We did not calculate the statistical sample size. However, using the reported mortality rate of MRSA bacteremia as 34% and the MRSA strains were isolated from 41 bacteremia patients. Seven patients (17%) died due to MRSA bacteremia. The characteristics of patients who were alive or had died of MRSA bacteremia are shown in mec was type IV and type II . There were no significant differences in SCCmec genotypes I to V between the two groups (p = 0.34). Bacteriological CA-MRSA accounted for 85% (n = 35) of the total cases. There was no expression of lukF-PV in any of the strains. The strains were resistant to the following antibiotics: ABPC, PC, and CEZ ; CPFX ; EM ; and tetracycline . Resistance to tetracycline was significantly higher in the dead group than in the alive group (The most isolated genotype of SCC = 0.04) . All strMLST analysis showed that the most common sequence type was ST8 , followed by ST764 . The most common clone complex (CC) was CC8 , followed by CC1 and CC5 . Six patients died of CC8 (85%). In addition, there was one new strain for which ST and CC could not be detected in the MLST database.Twenty-six different POT types were detected, with four types identified multiple times; the most frequently isolated POT type was 106-137-80 with 12 strains (29%), followed by 106-183-37 with 5 strains (12%) . Some stThe results of the MLST and POT type analyses showed seven clusters of MRSA clinical strains with a dissimilarity of 200 . ClusterThis is one of the few studies on MRSA bacteremia in designated medical institutions for Class 1 infectious diseases in Japan. The main findings of this current study are as follows: dead patients with MRSA bacteremia were significantly older and had a 2.8 times longer time to administration of susceptible and appropriate antimicrobial agents than those in the alive group. Approximately 50% of MRSA bacteremia occurred among those with intravascular devices. The microbiological characteristics of the MRSA clinical strains demonstrated that high resistance occurred more with MINO in the dead group compared with the alive group. Molecular immunology analysis suggested that 83% of all MRSA strains were SCCmec type IV, with ST8 and CC8 being the most common. Surprisingly, we observed that 85% of the pathogenic bacteria in hospital-acquired infections were bacteriological CA-MRSA.S. aureus bacteremia is 20%\u201330%, the mortality rate due to MRSA bacteremia is even higher (20%\u201350%), and the cure rate for MRSA infections is 50%\u201360% [Escherichia coli is high because of healthcare cost, and the burden due to MRSA is 3.6 times higher than that in Europe [The mortality rate due to 50%\u201360% \u201324. In o 50%\u201360% \u201327. Our 50%\u201360% , includi 50%\u201360% , >35,000 50%\u201360% . In addi 50%\u201360% . Early a 50%\u201360% . In Japan Europe . Howevern Europe . Therefon Europe . In thisn Europe ,38. In amec type IV. In the past, type II, frequently found in HA-MRSA, accounted for approximately 75% of cases [The microbiological characteristics of MRSA revealed greater resistance against MINO among those in the dead group than among those in the alive group. Worldwide, the overall use of antimicrobial agents has increased by 65% over the past 16 years . In Japaof cases . At thatof cases \u201343. The of cases , and it of cases . We conslukF-PV gene-positive strain that increased dramatically in the United States in the first half of 2000 [In this study, CC8 and ST8 were most prevalent in the MLST analysis. The major representative of CA-MRSA is the CC8 clone (USA300) . USA300 of 2000 ,47 and w of 2000 .lukF-PV gene-negative, and we concluded that some were the Japanese-intrinsic CA-MRSA (CA-MRSA/J) genetically similar to the USA300 type [In this study, all MRSA strains were 300 type .lukF-PV gene has made no difference in virulence; thus, we suggest that there are pathogenic factors other than the lukF-PV gene [S. aureus [lukF-PV gene and other virulence factors, it is useful for infection control by monitoring antibiotic susceptibility and the course of the disease. The POT method detects ORFs, which are the mobile regions of the DNA chromosomes. Therefore, the POT index can be altered by genetic mutations [In Japan, CA-MRSA/J has increased . It incl-PV gene . High dr. aureus . The POT. aureus ,55. Althutations \u201358. FurtIn this study, we combined MLST analysis with the POT method for cluster analysis to improve the resolution of MRSA; in groups 5, 6, and 7, in contrast to other groups, the antibiogram showed CLDM and MINO antimicrobial susceptibility. CA-MRSA is highly susceptible to CLDM, MINO, quinolones, and aminoglycoside . HoweverThere are some limitations to our study; first, it is a review of retrospective studies of blood isolates at a single center only. Second, we classified the patients into two groups: alive and dead, although the data were unbalanced, and the sample size and analyzing power were small. In the future, it will be necessary to include multiple-center large-scale studies and verify the correlation by adding clinical analysis of blood data.To the best of our knowledge, our study is one of the few studies that have focused on understanding MRSA bacteremia. We have revealed the characteristics of MRSA in specific regions. The diversity of MRSA clones is remarkable, and it is possible that clones with new virulence factors will appear in the future. Therefore, it is very important to clarify the gene expression network by identifying old and new virulence factors and monitor the epidemiological trends of MRSA clones continuously and carefully and respond quickly to changes."} +{"text": "Cognitive reserve (CR) refers to the capacity of the brain to withstand changes due to age or disease-related pathology, showing how flexibly and efficiently the individual makes use of available brain resources. This study aims to explore the contributions of the CR to understanding successful aging (SA).(Project-Conacyt-256589)Population based, random sample included n=656 community-dwelling older adults 60-years and older . CR was measured by their main indicators: education, life-long learning, being bilingual, participation, use of information and communications technology. Objective SA was operationalized as no important disease, no disability, physical functioning, cognitive functioning, and being actively engaged. Subjective was an appreciation if they considered themselves as successful agers. Sociodemographic and health data were also asked. Pearson\u2032s correlation test and MANOVAs were performed.In total 11.2% met the criteria for SA, although 76% considered themselves as successful agers. CR was significantly related to subjective and objective criteria of SA(p<.000), except to no-important diseases. CR explains in general 20% of the variance in objective SA, specifically explains 28% of variance in the criteria of high cognitive function, 18% of the variance in disability, 11.3% of life engagement, 8% of physical functioning, and 2% of disease-free criteria. Also, CR explains 10% of the variance in subjective SA. This study has shown that CR the is related to SA, this set possible targets for cognitive interventions to promote resiliency of the brain not only for preventing cognitive pathologies, but also for encouraging successful and healthy aging in older adults."} +{"text": "Acute kidney injury (AKI) that develops during pregnancy results from pregnancy-induced hypertension, hemorrhage, and sepsis, associated with morbidity and mortality in the fetus and mother. This meta-analysis was conducted to evaluate the incidence of pregnancy-related AKI (PR-AKI) and adverse clinical outcomes.PubMed and Scopus were systematically searched for studies published between 1980 and 2021. We included cross-sectional, retrospective, and prospective cohort studies that reported the incidence of PR-AKI as well as adverse fetal and maternal clinical outcomes. A random-effects model meta-analysis was performed to generate summary estimates.The meta-analysis included 31 studies . The pooled incidence of PR-AKI was 2.0% . Only 49.3% of patients received antenatal care. The most common cause of PR-AKI was preeclampsia . The proportion of patients requiring hemodialysis was 37.2% (95% CI 26.0\u201349.9). More than 70% of patients had complete recovery of renal function, while 8.5% (95% CI 4.7\u201314.8) remained dependent on dialysis. The pooled mortality rate of PR-AKI was 12.7% (95% CI 9.0\u201317.7). In addition, fetal outcomes were favorable, with an alive birth rate of 70.0% (95% CI 61.2\u201377.4). However, the rate of abortion and/or stillbirth was approximately 25.4% (95% CI 18.1\u201334.4), and the rate of intrauterine death was 18.6% (95% CI 12.8\u201326.2).Although the incidence of PR-AKI is not high, this condition has a high impact on morbidity and mortality in both fetal and maternal outcomes. Early prevention and treatment from health care professionals are needed in PR-AKI, especially in the form of antenatal care and preeclampsia medication. The diagnosis and treatment of AKI during pregnancy is challenging. The risk profiles and geographic distribution of pregnancy-related AKI may be different in various parts of the world\u20136 and between different regions within the same country. The reported incidence of PR-AKI in developing countries, such as India and Pakistan, is 0.02% to 71.5%.\u201310 Data from South Asia suggest that PR-AKI accounts for 10% of total AKI cases. However, in high-income countries, PR-AKI is rare.Acute kidney injury (AKI) that develops during pregnancy results from such as pregnancy-induced hypertension, hemorrhage, and sepsis, associated with morbidity and mortality in the fetus and mother.,13 in contrast to developed countries, where chronic hypertension, renal disease, and preeclampsia are important causes of this condition.,15 The maternal and fetal outcomes that are of concern include permanent damage to the kidney, maternal survival, rate of renal recovery, dialysis dependence, rate of live births, stillbirths, and intrauterine death. This systematic review and meta-analysis of observation studies aimed to evaluate the overall incidence of PR-AKI and its prognostic value for fetal and maternal adverse clinical outcomes.In developing countries, sepsis and hemorrhage account for >50% of cases of PR-AKI,http://links.lww.com/MD/G956).We performed a literature search in MEDLINE and SCOPUS (from 1989 to March 2021) to identify eligible studies using the Medical Subject Heading and text keywords \u201cacute renal failure\u201d, \u201cacute kidney injury\u201d, \u201cacute renal insufficiency\u201d, combined with all spellings of \u201cpregnancy\u201d and \u201cpregnant.\u201d The search was limited to the English language. Reference lists of the obtained articles were also searched for relevant publications. Only officially published papers were considered for inclusion in the present meta-analysis. Studies were required to meet the following inclusion criteria: original article including cross-sectional, retrospective, or prospective cohort studies, and reported pregnancy outcomes and kidney outcomes in women with PR-AKI. Narrative reviews, case reports/series, conference abstracts, and registry databases were excluded. We followed the preferred reporting items for systematic review and meta-analysis and meta-analyses Of observational studies in epidemiology guidelines to report the meta-analysis using a standardized approach. Disagreement between the 2 investigators was recorded and adjudicated by a third reviewer (P.S.). Data on country of origin, number of patients, patient age, number of parities, trimester, causes of AKI, and underlying diseases were recorded. We also extracted data on maternal and fetal outcomes, number of patients who required renal replacement therapy, recovery of renal function, and subsequent dependence on dialysis. The other maternal outcomes included death; preeclampsia; hemorrhage during and after delivery; and hemolysis, elevated liver enzymes, and low platelet count (HELLP) syndrome. Fetal outcomes, including perinatal death, abortion, stillbirth, and preterm delivery, were also recorded.The quality of the cohort studies was evaluated by using the Newcastle-Ottawa Scale, which allocates a maximum of 9 points for quality of the selection, comparability, and outcome of study populations. Study quality scores were defined arbitrarily as poor (0\u20133), fair (4\u20136), or good (7\u20139).I2 index. The I2 index describes the percentage of total variation across studies due to true heterogeneity rather than chance, with a value of >75% indicating medium-to-high heterogeneity. To examine the effect of developed vs under developed countries on the incidence of AKI, we conducted random-effects subgroup. We also performed subgroup analysis on the AKI definitions by using the RIFLE or Kidney Disease Improving Global Outcomes (KDIGO) vs other definitions including biochemical/urine output/dialysis requirement-based definitions/administrative codes for AKI derived from the International Classification of Diseases, 9th or 10th Revision, Clinical Modification methodology. We explored the robustness of interested outcomes by sensitivity analysis and subgroup analysis based on study quality. Publication bias was formally assessed using the Egger test. We performed the meta-analyses using Comprehensive Meta-Analysis .Random-effects model meta-analyses were conducted to generate pooled incidence rates of AKI, caused of AKI, fetal, and maternal outcomes. All pooled estimates are provided with 95% confidence intervals (95% CIs). Heterogeneity was assessed using the The literature search yielded 2775 articles; 1681 studies were retrieved for detailed evaluation, among which 31 fulfilled the inclusion criteria level by approximately 1.5 times from baseline or decrease in urine output to<400\u2009mL; 6 studies defined AKI based on the KDIGO criteria; 5 studies defined AKI according to the RIFLE classification, 1 study defined AKI based on the Acute Kidney Injury Network classification; 7 studies defined PR-AKI according to the level of creatinine, 3 studies defined PR-AKI as Scr level>1.0\u2009mg/dL, 1 study defined PR-AKI as Scr level >1.5\u2009mg/dL, 1 study defined PR-AKI as Scr level >1.8\u2009mg/dL, and 2 studies defined PR-AKI as Scr level >2.0\u2009mg/dL. The remaining 11studies did not specify criteria for diagnosing AKI.I2 = 98.5%). By meta-analysis, 36.1% of patients were primigravida, while 56.9% of patients were multigravida. In term of onset of AKI, 12.6% , 15.7% , 69.0% , and 48.6% of patients presented with PR-AKI during the first trimester, second trimester, third trimester, and postpartum period, respectively. Only 49.3% of patients received antenatal care .In the meta-analysis of 31 studies, the pooled mean age of the participants was 28.2 years patients had preeclampsia and hypertensive disorders during pregnancy, 21.0% had septic abortion, 16.6% had other causes or unknown causes of abortion, 15.1% had antepartum hemorrhage, 14.1% had acute gastroenteritis, 13.3% had HELLP syndrome, 13.2% had postpartum hemorrhage, 5.8% had acute pyelonephritis, 4.5% had acute fatty liver of pregnancy, and 3.5% had glomerular disease.The incidence of AKI during pregnancy and puerperium was 1.95% (95% CI 1.01\u20133.73) using data from 31 studies Fig. . By metaIn the meta-analysis of 25 studies, the pooled mortality rate was an average of 12.7% , 10.0% required peritoneal dialysis (PD), and 8.2% required both HD and PD due to inadequate ultrafiltration by PD alone. The indications for HD included oligo/anuria, hyperkalemia, uremia, metabolic acidosis, and acute pulmonary edema.By the meta-analysis, 70.0% of patients had live births Table . The incIn subgroup analysis according to developed vs underdeveloped countries (definition by World Economic Situation and Prospects) on the incidence of AKI, the pooled incidence of PR-AKI in developed countries was 0.14% after excluding the study that had poor and fair quality. The high incidence of PR-AKI was observed in poor and fair study quality.As the Egger test results, most of the interested outcomes were mainly insignificant Table .,18In this meta-analysis of >58 million pregnancies, the incidence of AKI during pregnancy was 2%. AKI during pregnancy is associated with increased morbidity in the mother and fetus. The incidence of AKI varies based on the geographical area, with most studies conducted in the Indian subcontinent. Since the time span of study inclusion was >30 years, various definitions of AKI were used. Recently, the KDIGO criteria have been widely adopted by professional societies as the standardized criteria for AKI. The criteria provide a much higher estimated incidence (10-fold increase) of AKI than Code-Classification AKI. In previous studies, the incidence of PR-AKI was 7% to 9 % in the Indian subcontinent, 2.5% in China, and 1% to 28% in developed countries. Our meta-analysis demonstrated that the pooled incidence of PR-AKI in developed countries was only 0.14%. Unfortunately, the high pooled incidence of PR-AKI (4.11%) was observed in underdeveloped countries. Only 49.3% of patients received antenatal care. Therefore, antenatal care should be emphasized in public health care to prevent septic abortion and pregnancy-induced hypertension, especially in underdeveloped countries.The physiological changes and increase in glomerular filtration rate with the reduction in Scr levels during pregnancy are associated with increased difficulty for early and accurate diagnosis of PR-AKI. reported that 74.5% of patients developed PR-AKI during the postpartum period. However, most of the studies showed predominant incidence of PR-AKI in the trimester. In our meta-analysis, the pooled AKI during the first trimester, second trimester, third trimester, and postpartum were reported at 12.6%, 15.7%, 69%, and 48.6%, respectively. Improvements in antenatal care and early referral to nephrologists to decrease the risk of kidney injury in PR-AKI should be highlighted. The mean age of our patients was 28.2 years.\u201326 In a study by Kabbali et al, age >38 years was significantly associated with unfavorable outcomes and increased perinatal complications. Therefore, the pooled incidence of PR-AKI in this meta-analysis might be underestimated, especially in advanced maternal age.In this study, approximately 50% of patients developed postpartum PR-AKI. Similarly, Sivakumar et al; however, most patients with this condition do not develop AKI. The frequency of AKI in preeclampsia varied between 24% and 35% in different centers in India.,29 This was the most frequent cause of PR-AKI in this meta-analysis. Preeclampsia is also the main cause of severe PR-AKI and typically occurs during the third trimester and postpartum period. The frequency of preeclampsia ranges between 2% and 7% in healthy nulliparous women and increases substantially in women with multiple gestations, chronic hypertension, diabetes mellitus, and chronic kidney disease. The effect of preeclampsia on endothelial injury and vasoconstriction, which would be expected to lower the glomerular filtration rate,,33 may affect long-term renal function. The causes of PR-AKI have changed over time from septic abortion in the past to preeclampsia and hemorrhagic shock in the present era due to increased attention of health care professionals to prenatal cases.Preeclampsia and pregnancy-related hypertension were responsible for 36.6% of PR-AKI cases in our study. Preeclampsia is one of the most important causes of AKI during pregnancy, especially in Indian studies and up to 54% to 60% of severe cases. The HELLP syndrome is considered a continuum of preeclampsia. In our study, HELLP syndrome accounted for 13.3% of total PR-AKI cases, which was a similar rate associated with other causes, such as acute gastroenteritis, septic abortion, postpartum hemorrhage, and acute pyelonephritis.The HELLP syndrome is a serious disorder in pregnancy, accounting for 15% to 40% of all cases of PR-AKI2I = 96.3%), which likely resulted from a higher incidence of sepsis, the main cause of maternal mortality, in developing countries. In contrast, developed countries had a higher incidence of pregnancy-induced hypertension and favorable socioeconomic factors, leading to lower maternal mortality. The mortality rate was approximately 23% to 33%,,29 mostly in developing countries, while it was 2.7% to 4.3% in developed countries. Maternal mortality also decreased based on the time period and location of the study. The overall mortality rate declined from 20% in the 1980s to 5.79% in 2013\u20132014AKI during pregnancy was associated with a higher risk of maternal death. In our study, the mortality rate was 12.7%. The heterogeneity was quite high \u2014only 8.5% of patients were dependent on dialysis after delivery and 14.7% had subsequent chronic kidney disease. Early prevention and treatment should focus more on reducing risk in antenatal care and consider preeclampsia medication in high-risk populations.In previous studies, 16% to 73% of pregnant women with AKI required dialysis treatment. The results of the literature reviews in China showed that the incidence of stillbirth or neonatal mortality can reach 30%. The incidence of abortion and stillbirth in this study was nearly equivalent to that reported in previous studies; therefore, improvement in maternal and fetal health is needed.The fetal outcome was satisfactory, with survival in 70% cases. There were 28.5% cases of preterm delivery, 18.6% cases of intrauterine death, and 25.4% cases of perinatal infant mortality. Previous studies revealed fetal lost deliveries of 81.3%.The merit of the present study is the accumulation of various studies over a long period of time (>30 years), which encompassed >57 million pregnancies. Several meta-analyses have investigated PR-AKI; however, most studies have focused on pregnancy outcomes, such as kidney, maternal, and fetal outcomes. In the present meta-analysis, we attempted to demonstrate the incidence of PR-AKI in a pooled analysis of 40,428 PR-AKI cases. The outcomes in various aspects, especially kidney outcomes, were emphasized. The incidence of PR-AKI in different parts of the world should be considered in the future to help reduce the global burden of AKI.The following are the limitations of this study. Differences in the definition of AKI due to changes in criteria from different time points and follow-up time contributed to heterogeneous results. In addition, since this study aimed to explore the incidence of PR-AKI, we did not perform subgroup analysis of each variable. Most of the included studies were from the Indian subcontinent, which is associated with a publication bias. Additionally, we were unable to assess long-term kidney-related endpoints.In conclusion, data obtained from our meta-analysis show that the overall rate of PR-AKI is decreasing worldwide, indicating improvements in and increased awareness of antenatal care. Although the maternal, fetal, and kidney outcomes were favorable, the absolute numbers of deaths and percentage of patients with irreversible kidney damage remained unacceptably high. The most common causes of PR-AKI, including pregnancy-induced hypertension, hemorrhage, and septic abortion/abortion could be prevented, early identified, and treatment. Our analysis serves to encourage future studies to investigate improvements in antenatal care and perform early referral to nephrologists to increase patient safety and mitigate the risk of further kidney injury in PR-AKI.www.editage.com) for English language editingThe authors would like to thank Dr Thanaphan Thitivichienlert for helping with data extraction. We would like to thank Editage (Conceptualization: TT, PSMethodology: PSValidation: TT, PSFormal analysis:PSResource: TN, TT, PSWriting manuscript: TT, PSProject administration: TT"} +{"text": "Diplopia was most common in patients previously operated on for orbital wall fractures (100%), and least common in patients who reported trauma after interpersonal violence (15%) and road traffic accidents (11%). Exophthalmos appeared only in 1% (six cases); whereas it did not appear in 99% (396 cases). Enophthalmos was present in 4% (sixteen cases), most commonly in interpersonal violence cases (two cases). The frequency of orbital complications in patients with zygomaticomaxillary complex and isolated orbital walls fractures suggests how diplopia remains the most common pre-surgical orbital side effect.Zygomaticomaxillary complex and isolated orbital walls fractures are one of the most common fractures of the midface, often presenting orbital symptoms and complications. Our study was born with the aim of understanding the trend in the incidence of orbital presurgical symptoms, specifically diplopia, enophthalmos and exophthalmos, in the Campania Region in southern Italy. We conducted a retrospective, monocentric observational study at the Maxillofacial Surgery Unit of the Federico II University Hospital of Naples, enrolling 402 patients who reported a fracture of the zygomaticomaxillary complex and orbital floor region from 15 June 2021 to 15 June 2022. Patients were evaluated by age, gender, etiology, type of fracture, preoperative orbital side effects and symptoms. Pre-surgical side effects were studied, and 16% of patients ( In the field of cranio-maxillofacial traumatology, zygomaticomaxillary complex and isolated orbital walls fractures are one of the most common fractures of the midface, and account for around 27% of all facial fractures, being second only to nasal fractures . Injury The study was conducted at the Maxillofacial Surgery Unit of the Federico II University Hospital, Regional Referral Center for Cranio-Maxillo-Facial Traumas . It was a retrospective, monocentric observational study. The sample size consisted of 402 patients who reported a fracture of the zygomaticomaxillary complex and orbital floor. All clinical investigations and procedures were conducted according to the principles expressed in the Declaration of Helsinki. Ethical approval to access and use the data was obtained from the Federico II/Cardarelli Research Ethic Committee (81/2022). Patients were evaluated by age, gender, etiology, type of fracture, preoperative orbital side effects and symptoms. Blind/visually impaired patients, patients suffering from osteoporosis/osteomalacia or psychiatric disorders were excluded. Patients admitted in this study did not suffer from any globe injuries, the management of which would take priority over any maxillofacial procedures. All data were extrapolated from medical records from 15 June 2021 to 15 June 2022. Definitive diagnosis was obtained by performing computed tomography (CT) .Preoperative side effects were evaluated through accurate ophthalmic clinical examinations by the same operator and using the same instrument . In the same way, all patients took the Hess-Lancaster screen or Hess-Lancaster red-green test to better diagnose any defect in ocular motility. The considered variables were summarized considering frequency and percentage for each category.The most affected patients were men, representing 77% of the total number of cases (out of a sample of 308 men and 94 women). The most represented age group was between 13\u201325 years with 22% (90 cases), followed by the 25\u201337 age group with 19% (76 cases), the 37\u201349 age group (76 cases) with 19%, the 49\u201361 age group with 16% (64 cases), the 61\u201373 age group with 12% (48 cases), the 73\u201385 age group with 8% (34 cases), and, finally, the 85\u201397 age group with 3% (14 cases). The mean age reported was 46 years.From the data obtained, we analyzed the mechanism of the trauma that caused the fracture. In our series, the most frequent causes were accidental falls in 37% (148 cases), road accidents in 36% (144 cases) and interpersonal violence in 16% (66 cases). Among the minor causes, on the other hand, syncopal episodes were found in 4% (sixteen cases), sports accidents in 2% (ten cases), previous fracture outcomes in 3% of cases (fourteen cases), and, finally, 1% were workplace accidents (four cases). From the analyzed data, we noticed that mostly women reported accidental falls, in 60% of cases, and reported road accidents in 30%. Men mostly reported having road accidents (37%), then accidental falls (30%), followed by interpersonal violence (21%).The fractures were stratified according to the presence or absence of the involvement of the orbital frame, as impure in 64% (258 cases) and in pure in 36% (144 cases), with a frequency ratio of 1.8:1.These fractures were then further classified according to the area of impact :Zygomatic orbital fractures, the most frequent, in 60% (242 cases)Fractures of the orbital floor in 26% (104 cases)Fractures of the medial wall in 9% (38 cases)Fractures of the lateral wall in 3% (12 cases)Fractures of the orbital roof in 1% (6 cases)Among the orbital side effects, we found the following :Diplopia: 84% of patients did not report double vision (336 cases), 16% reported diplopia (66 cases).Exophthalmos appeared only in 1% (6 cases), while it did not appear in 99% (396 cases).Enophthalmos was present in 4% (16 cases), while it was not present in 96% (386 cases).n = 44); in 17% of lateral wall fractures diplopia (n = 2) was reported, in 16% of medial wall fractures diplopia (n = 6) was reported, and in 6% of zygomaticomaxillary fractures diplopia (n = 14) was reported.Correlating the type of fracture with the orbital side effects , we founn = 2) and in 2% of zygomaticomaxillary fractures (n = 4).Considering exophthalmos, it was found in 2% of orbital floor fractures (n = 10), and in 11% of medial orbital wall fractures (n = 4).Enophthalmos was reported in 10% of orbital floor fractures (n = 14), 40% while practicing sports (n = 4), 15% occurred in interpersonal violence cases (n = 10), 14% in accidental fall cases (n = 20), 13% in syncopal episode cases (n = 10) and 11% in road traffic accident (n = 16), while none occurred in a workplace setting.Correlating the cause of the trauma and the orbital complications , it was n = 2), 3% in interpersonal violence cases (n = 2) and in 1.3% of road traffic accidents (n = 2).Exophthalmos in the considered cohort were pren = 6), 12% in interpersonal violence cases (n = 8) and in 1.3% of accidental falls (n = 2).Enophthalmos were preFractures of the orbitozygomaticomaxillary complex are among the most common fractures of the midface and account for approximately 27% of all facial fractures. Impure orbital fractures are more common than pure orbital fractures ,2,11.Isolated orbital wall fractures account for 4% to 16% ,12.Early recognition of ocular injuries is fundamental in mid-facial fracture cases. The management of globe injuries often takes precedence over the treatment of mid-facial and orbital fractures. Every surgeon who addresses orbital trauma must consider how to handle an emergency surgery, whereas the fracture pattern leads to optical nerve damage and then vision loss .Diagnosis is essential to permit early treatment, as various symptoms, such as diplopia and enophthalmos, may persist even after surgical treatment, especially if the diagnosis is delayed ,14. It iExophthalmometry is used to measure the position of the globe, while graphic radiographic visualization with coronal CT makes it possible to detail soft tissue not visible with conventional X-rays; Coronal CT scans of 1.5 to 3 mm visualize antral soft tissue densities, such as prolapsed orbital fat, extraocular muscle and hematoma .Diplopia is one of the most common post-traumatic symptoms of orbital fractures . Post-trThe aim of the study conducted was to show the epidemiological distribution of pre-operative orbital symptoms presented by patients who suffered from zygomaticomaxillary complex or isolated orbital wall fractures enrolled in the Oral and Maxillofacial Operative Unit of AOU \u201cFederico II\u201d.n = 242) of the 402 patients involved in this study had a zygomaticomaxillary complex fracture.The results found in this study agree with the literature, as zygomaticomaxillary complex and isolated orbital walls fractures are the most frequent midface maxillofacial trauma ,18. IndeThe male/female ratio was 3,4:1, with male involvement representing 77% of total cases, with a mean age reported at 46 years. The fractures were stratified according to the presence or absence of the engagement of the orbital frame, as impure in 64% (258 cases) and as pure in 36% (144 cases), with a frequency ratio of 1.8:1; therefore, the incidence is comparable to other clinical studies .In our series, the most common cause was represented by accidental falls, with 148 cases , 92 of which were men and 56 were women. From the analyzed data, we noticed that mostly women reported accidental falls, with 60% among female cases, and then road accidents with 30%. Men mostly reported having road accidents (37%), accidental falls (30%), followed by interpersonal violence (21%). Among the minor causes, on the other hand, syncopal episodes were found in 4% of cases, sports accidents in 2%, previous fracture outcomes in 3% of cases and, finally, 1% were workplace accidents. This result may be related to a greater tendency in the Campania region to use private means of transport compared to public transport. This trend has been found in similar studies conducted in other Western countries, where it is common for a family to own at least one motor vehicle .In our series, we noted sixty-six patients suffering from pre-operative diplopia (16% of the sample), six patients affected with exophthalmos (1% of the sample) and sixteen patients suffering from enophthalmos (4% of the sample). These findings are not completely supported by the literature, as Bartoli et al. reported diplopia to be a main preoperative complication in 20.2% of patients, followed by enophthalmos (2.3%) and exophthalmos (1.7%), whereas Shin et al. stated diplopia was present in 42.3% of patients .In our sample, 42% of patients suffering from preoperative diplopia reported an orbital floor fracture, while 6% reported diplopia suffering from zygomaticomaxillary complex fractures; 16% had medial wall fractures and 17% had lateral wall fractures. No patients with orbital roof fractures reported diplopia. These outcomes agree with most of the international literature that reported orbital floor fractures as typically coinciding with preoperative diplopia. Ramphul et al. 2017), in their review of 126 patients with orbital floor fractures, underlined that 66.6% of the total sample suffered from preoperative diplopia 17, in th. HigashiOur results indicated that 2% of patients with orbital floor fractures showed exophthalmos and another 10% of patients with orbital floor fracture displayed enophthalmos; 2% of patients with zygomatic-maxillary complex fracture exhibited exophthalmos, 1% of presented enophthalmos and no patients with orbital roof, midwall or lateral wall fractures presented exophthalmos. An interesting observation was that enophthalmos, while it was absent in patients with orbital roof and lateral wall fractures , was found in 11% of patients with midwall fractures.The symptoms of medial orbital wall fractures are usually less severe than those of inferior wall fractures because less muscle incarceration takes place, and the bony structure is multiply overlapped . Since mCorrelating the cause of the fracture with the pre-surgical orbital symptoms, in this study, it was found that 100% of patients who previously underwent surgery for orbital wall fractures presented diplopia, while 38% reported enophthalmos, 40% of patients who experienced trauma while practicing sports reported diplopia and none reported exophthalmos or enophthalmos.Additionally, 15% of patients who reported an interpersonal violence accident were described as having diplopia, 33% had exophthalmos and 50% had enophthalmos.In accidental fall cases, 14% of patients described having diplopia, 13% had enophthalmos and none described suffering from exophthalmos.Cases correlated with syncopal falls reported diplopia in 13% of cases, and 33% reported exophthalmos.Over a period of 1 year, 402 patients who sustained a fracture in the zygomaticomaxillary complex and isolated orbital walls fractures received a full ophthalmological examination within 1 week of injury.n = 242) of patients enrolled in this study had a zygomaticomaxillary complex fracture and 26% (104 cases) had an orbital floor fracture.A total of 60% (n = 66) developed diplopia. Diplopia was most common in patients who had previously undergone surgery for orbital wall fractures (100%), and was least common in those who had experienced interpersonal violence (15%) and road traffic accidents (11%). Exophthalmos only appeared in 1%, whereas it did not appear in 99% of patients. Enophthalmos was present in 4% of patients, and was more common in interpersonal violence cases.Pre-surgical side effects were studied, and 16% of patients (The frequency of orbital complications in patients with zygomaticomaxillary complex and isolated orbital walls fractures complex has never been assessed before in the literature, and our findings suggest that, in patients under evaluation for orbital trauma, the observation of diplopia remains the most common orbital side effect before surgery."} +{"text": "COVID-19 has threatened health care for many individuals. Restriction of resources, redeployment of staff, and patient reluctance to make clinic appointments disrupts continuity of care of existing patients and limits access to care of new ones. To overcome this, our HIV clinic aggressively promoted a telehealth, MyChart (MC) application, and provided smart phone technology to those in need. Despite these efforts, we found that utilization of telehealth accounted for 4.7% of HIV clinic visits, compared to 25% in internal medicine clinics. In this report, we sought to obtain reasons why our patients were reluctant to use telehealth even in the midst of a pandemic.All Ryan White (RW) people living with HIV (PLWH) at Henry Ford Hospital that were initiated in our telehealth pilot program were surveyed on the underutilization of MC. Utilization was determined by if PLWH responded to a MC notification sent by the telehealth navigator. Activity level was established on MC , and if PLWH did not respond, they were called as a follow up for survey answers.From 10/2020 \u2013 01/2022, 206 PLWH were enrolled into our pilot program and given telehealth education. Of those successfully enrolled: 83.7% were black, 73% male, 57% were older than 45 years, 88% lived in Wayne County, and 27 needed and received pre-loaded smart phones. When contacted, 90 (44%) interacted on MC, 61 (29%) were unable to be reached and 55 (27%) successfully completed the survey . When asked why telehealth was not utilized, 27 (49%) stated they preferred in-person visits .Telehealth programs can help overcome barriers to HIV care and maintain patient engagement when crises interrupt traditional care models. However, our study suggests that our PLWH preferred and felt safe engaging with in-person visits despite telehealth education and smartphone supplementation even in a pandemic. As the future of medicine moves towards telehealth management, we must not forget our vulnerable populations and find opportunities to safely engage with in-person visits.Indira Brar, MD, Gilead: Grant/Research Support|Gilead: speakers bureau|Janssen: Grant/Research Support|Janssen: speakers bureau."} +{"text": "Several individual studies from specific countries have reported rising numbers of pediatric COVID-19 cases with inconsistent reports on the clinical symptoms including respiratory and gastrointestinal symptoms as well as diverse reports on the mean age and household exposure in children. The epidemiological characteristics of COVID-19 in children are not fully understood, hence, comprehensive meta-analyses are needed to provide a better understanding of these characteristics.2 statistic and Egger\u2019s/Begg\u2019s tests.This review was conducted in Medline, Scopus, Cochrane library, Embase, Web of Science, and published reports on COVID-19 in children. Data were extracted by two independent researchers and a third researcher resolved disputes. STATA software and the random-effect model were used in the synthesis of our data. For each model, the heterogeneity between studies was estimated using the Q Cochrane test. Heterogeneity and publication bias were calculated using the I2 of 98.36%. The proportion of household exposure was calculated to be 50.99% (95% CI: 20.80%\u201380.80%) and the proportion of admitted cases was calculated to be 45% (95% CI: 24%\u201367%). Additionally, the prevalence of cough, fatigue, fever and dyspnea was calculated to be 25% (95% CI: 0.16\u20130.36), 9% (95% CI: 0.03\u20130.18), 33% (95% CI: 0.21\u20130.47) and 9% (95% CI: 0.04\u20130.15), respectively. It is estimated that 4% (95% CI: 1\u20138%) of cases required intensive care unit admission.The qualitative systematic review was performed on 32 articles. Furthermore, the meta-analysis estimated an overall rate of involvement at 12% (95% CI: 9\u201315%) among children, with an IThe pediatric clinical picture of COVID-19 is not simply a classic respiratory infection, but unusual presentations have been reported. Given the high incidence of household transmission and atypical clinical presentation in children, we strongly recommend their inclusion in research and population-based preventive measures like vaccination as well as clinical trials to ensure efficacy, safety, and tolerability in this age group.The online version contains supplementary material available at 10.1186/s12887-022-03624-4. COVID-19 is a highly contagious viral illness which has birthed several mutations thereby making it difficult to bring an end to the current pandemic. According to research, SARS-CoV-2 requires the ACE2 receptor to enter human cells, and ACE2 is found in a variety of organs across the body . SARS-CoWith current immunization methods focusing mainly on adults, the pediatric population remains vulnerable to COVID-19 infection , 11. HenPrevious studies have reported some unique characteristics in pediatric COVID-19 cases such as lower mortality rate, longer incubation period, and longer respiratory and fecal shedding with high RNA load (83%) . FurtherHence, this study will attempt to delineate the rate of pediatric involvement in COVID-19, demographic features of the affected children, the proportion of severe cases, and the rate of household exposure as well as future recommendations on pediatric COVID-19 cases based on current epidemiological evidence. It will further address the aspect of clinical presentation, whether affected children present with symptoms of classic viral pneumonia or rather present with gastrointestinal (GI) manifestations.This systematic review and meta-analysis were performed per the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist . The comth, 2020 until April 30th, 2021. Two independent researchers (F.V. and P.S.) performed a primary search simultaneously, and in cases of difference in opinion, they referred back to the selection protocol. If the dispute remained, a third individual (MSY) made the final decision. Keywords included (Pediatric OR children OR child) AND (COVID-19 OR SARS-COV-2). A revisit to the database was conducted by the first author at 9 AM on May 10th, 2021. Furthermore, our data were scrutinized by checking the Worldometer reports [We conducted an extensive search in Medline (indexed by PubMed), Embase, Scopus, Cochrane library, and Web of Science databases on published studies from January 20 reports and theith, 2020 until April 30th, 2021, including registries [\u2022 Review articles, editorials, commentaries, opinions, or any studies with no original data.\u2022 Ongoing projects \u2022 Non-human studies.\u2022 Duplicated results in databases.This study includes peer-reviewed published studies from January 20gistries , 24\u201328, gistries , 29\u201334, gistries \u201343, whicFurthermore, relevant references to the included studies were annexed. For countries with no relevant published studies, available national registry data were used.Cross-sectional observational studies that met the aforementioned criteria underwent bias assessment using the Newcastle\u2013Ottawa Quality Assessment Scale (NOS) was reported and standard error was estimated by P-values of 0.05 or less were considered significant. Furthermore, publication bias funnel plots for analysis of the proportion of pediatric cases and mean age were drawn , Review articles about the infection (62), Erratum: (2), Irrelevant to our study (68), and no full text (1)). Full texts of 308 published articles and 5 available national registry data on pediatric COVID-19 were studied, which resulted in the exclusion of 281 more articles . Publication bias funnel plots for analysis of the proportion of pediatric cases and mean age are shown in Figs.\u00a02 values for the proportion of pediatric cases (childhood corona and 0\u20139\u00a0years old), the proportion of male cases, and mean age is depicted in each of the corresponding forest plots and 9.83\u00a0years (95% CI: 8.67\u201310.98), respectively statistic was 99.66% and 99.75%, respectively.The proportion of household exposure was calculated to be 50.99% (95% CI: 20.80%\u201380.80%) among the five studies that reported household exposure Fig.\u00a0a and 4b.The prevalence of comorbidity was estimated to be 31% (95% CI: 0.16\u20130.48) according to the meta-analysis. The prevalence of cough, fatigue, fever and dyspnea was calculated to be 25% (95% CI: 0.16\u20130.36), 9% (95% CI: 0.03\u20130.18), 33% (95% CI: 0.21\u20130.47) and 9% (95% CI: 0.04\u20130.15), respectively articles were of good quality, with no significant publication bias. We found that the overall prevalence rate of COVID-19 among pediatric patients was 12% (95% CI: 9\u201315%). The frequency of pediatric COVID-19 increased to 19.0% as of 7 April 2022 in the US . MoreoveOur study found 50.99% of household exposure among the eight studies that reported household exposure. A previous investigation by Cheng-Xian et al. found that family clustering was a major (66%) transmission route for pediatric COVID-19 . This stAs in all previous investigations, fever and cough were the main symptoms that could be associated with gastrointestinal symptoms such as nausea, vomiting, and diarrhea, and other symptoms like sore throat, dizziness, headache, and myalgia. The prevalence of cough, fatigue, fever, and dyspnea were 25%, 9%, 33%, and 9% respectively. Our study found the prevalence of cough (25%) between other studies which recorded 32.4% , (62%) , (67%) and 19% Since many children do not show the classic picture of viral pneumonia, physicians must have a high level of suspicion not to miss COVID-19 in a child. Moreover, there have been some reports of unusual clinical presentations such as skin rash and neurConsidering the high household rate of COVID-19 exposure for children, physicians are encouraged to investigate more into the family history and contacts of the child presenting with symptoms. It also signifies the importance of social distancing the infected household members from children. We were unable to perform a meta-analysis on the duration of incubation period or shedding of the virus in children but there are reports that botCOVID-19 cases in children showing a systemic inflammatory syndrome have been reported in at least 8 states in the US . CurrentFever is a prominent sign of both Kawasaki Disease (KD) and COVID-19 infection. Due to the COVID-19 pandemic, the first differential diagnosis to have in mind in a child with fever is probably COVID-19 infection or its combination. There are a few reports on this subject , 58. KD We did not have access to certain published papers. Due to insufficient data, we were not able to perform a meta-analysis on some aspects of the disease such as the percentage of children with comorbidities, duration of the incubation period, and some symptoms like abdominal pain. Our investigation did not include laboratory and radiographic findings and we recommend future research into these. Future studies need to be performed on the COVID-Kawasaki syndrome to determine risk factors for poor outcomes in children. There is a possibility of publication bias in some reports, especially for mean age, and we recommend the creation of a global registry on pediatric COVID-19.This investigation described the characteristics of epidemiological characteristics of COVID19 in pediatric patients. Furthermore, the analyzed data from minors under the age of 19 shows that they are less prone to developing severe COVID-19 disease but are equally at risk of contracting the infection. Similar to previous investigations, the presentation of SARS-CoV-2 infection is somewhat different from the adult population. For example, children have longer incubation and shedding periods than adults, an epidemiological phenomenon that places pediatric age groups as potential hosts of the infection and capable of infecting many people. This evidence shows that children might be spreaders of COVID-19 more than we ever thought, and for the pandemic to stop, all children should be involved in mass preventive measures like vaccination programs, social distancing, and masking. In addition, it is encouraged to involve children in various clinical trials for COVID-19 vaccines and drugs to generate sufficient safety and efficacy profiles for this age group.Children are not safe from COVID-19 infection. About 37% of those diagnosed will need admission or end up with a severe form of the disease. The pediatric clinical picture of COVID-19 is not simply a classic respiratory infection but unusual presentations have been reported. Mortality among children with COVID-19 is rare. Given the high incidence, we propose a global registry on pediatric COVID-19 cases be developed to help identify disease characteristics, similar to what was done previously for pediatric cancer. Considering the potential of children to act as reservoirs and spread the coronavirus, we strongly recommend the inclusion of children in population-based preventive measures like vaccination as well as clinical trials to ensure efficacy, safety, and tolerability in this age group.Additional file 1: Supplementary Table 1.\u00a0Quality assessment of the articles included in the final analysis of the study using the Newcastle-Ottawa Quality Assessment Scale (NOS). Supplementary Figure 1.\u00a0Graphical representation of the quality assessment of included studies based on checklist items."} +{"text": "Descending necrotising mediastinitis is one of the most lethal and least frequent forms of mediastinitis. It is a life-threatening infection most frequently originating from an oropharyngeal or odontogenic infection. A retrospective study of 6 patients diagnosed and treated for descending necrotising mediastinitis between 2015 and 2020 is reported. All patients were male, mean age of 34.83 years; 66% were smokers. 83% had an orocervical infection and 34% had initial mediastinal spread. All patients were treated initially with empirical broad-spectrum antibiotics and surgical drainage, with subsequent admission to the Intensive Care Unit; only one of them required tracheostomy. The mean hospital stay was 27.37 days. After a mean follow-up of 6 months, 100% of the cases had a complete recovery. Early diagnosis and surgical treatment combined with improved life-support treatment in intensive care units and broad-spectrum antibiotic therapy leads to a decrease in associated mortality. Key words:Odontogenic infection, cervical abscess, acute mediastinitis, descending necrotizing mediastinitis, mortality rate. Mediastinitis is defined as an inflammation or infection in the connective tissue surrounding the mediastinum. One of the most lethal and rarest forms of this clinical entity is descending necrotising mediastinitis (DNM) , which oMediastinal spread from the oro-cervical space occurs through the deep cervical fascia, which has 3 lamellae delimiting the cervical spaces through which the infection advances -6 Fig. .et al. defined the diagnostic criteria for this disease , clinical debut, odontogenic source, empirical and specific antibiotic treatment, surgical interventions, need of surgical tracheostomy, ICU hospitalization, days of hospital admission, follow-up, and mortality.The following inclusion criteria were established:1) Oro-cervical infection of odontogenic origin that subsequently developed mediastinal infection, with space-time relationship between both entities.2) Patients over 18 years of age.3) Cervico-thoracic CT scan as diagnostic imaging test.4) Need for surgical procedure for drainage of collections.5) Sample collection. Culture and antibiogram, following the measures established by the Microbiology Department of our center.Exclusion criteria were:1) Other descending necrotizing mediastinitis different from odontogenic cause 2) Failure to find information on some of the variables studied.A total of 132 patients with a diagnosis of odontogenic abscess requiring hospital admission were selected, of which 6 were complicated by subsequent mediastinitis and met the inclusion criteria.All patients were male, ranged in age from 22 to 48, with a mean of 34.83 years old. None of the patients had drug allergies or impaired immunity. 66% of the sample were active smokers .In all patients the cause of the odontogenic foci was the 2nd or 3rd lower molar. 2 of the cases had undergone a mandibular molar extraction in the previous days, without subsequent antibiotic therapy.The most frequent initial symptom in our series was odontalgia of several days of evolution, with progressive swelling at the para- and/or submandibular region. Other less common associated symptoms and signs were trismus, odynophagia with or without dysphagia and floor of mouth swelling.All patients underwent a blood test and cervical CT scan with intravenous contrast as initial diagnostic studies. All blood tests showed inflammatory parameters such as leukocytosis with neutrophilia and elevated C-reactive protein (C-reactive protein).In 83% of the patients (5 cases), orocervical infection with organized collection was present. In the other patient, an orocervical cellulitis without obvious collection was diagnosed. In 33% (2 patients) of the patients, initial mediastinal extension was also noted, and a thoracic CT scan was requested. .All patients were hospitalized, empirical broad-spectrum intravenous antibiotics were prescribed, and surgery was considered. 83% were firstly treated with amoxicillin-clavulanic Acid 2g/200mg 8-hourly, and 17% with meropenem 1g 12-hourly and clindamycin 600mg 8-hourly, as the last patient had taken a cycle of antibiotics with amoxicillin-clavulanic acid 875/125mg 8-hourly.In 66% of the patients (4 patients), drainage of the orocervical collection and exodontia of the causal teeth was performed under general anesthesia. 34% (2 patients) of the cases were also initially treated by the Hospital's Thoracic Surgery Department due to the mediastinal extension of their infection. The other mediastinal drainage procedures (66%) were performed on a second surgical time due to the infection's progression.1 patient (17%) underwent tooth extraction under local anesthesia and the other one (17%) was closely monitored, as 2 molars had been previously extracted and no collection was visible in the diagnostic CT scan.Reintervention was required in 83% of patients due to disease progression, with both clinical and radiological worsening .Streptococcus viridans, present in 100% of the samples. The second most common microorganism was Candida albicans (34%); other microorganisms found in the samples were Actynomices odontolyticus, Finegoldia magna, Eubacterium lentum, Prevotella denticola, Prevotella bucae. Antibiogram was performed on all samples and treatment was adjusted according to antibiotic sensitivity. The next antibiotic combinations were used: meropenem 1g 8-hourly plus linezolid 600mg 12-hourly, meropenem 1h 8-hourly plus clindamycin 600mg 8-hourly, meropenem 1g 8-hourly plus vancomycin 1g 8-hourly, fluconazole 400mg 24-hourly plus erythromycin 150mg 6-hourly, piperaziline-tazobactam 4g 8-hourly, meropenem 1g 8-hourly plus fluconazole 400mg 24-hourly.In all patients, microbiological cultures were obtained and subsequently analyzed by the Hospital's Microbiology department. Aerobic and anaerobic microorganisms were isolated; the most frequently isolated germ was In the first postoperative days, 34% n=2) of patients presented with chest pain associated with dyspnea and desaturation. An additional 34% (n=2) of patients developed pain and local deterioration. In all of them, progression of the infection towards the mediastinum was suspected by mediastinal widening in simple thoracic x-ray, and cervico-thoracic CT with intravenous contrast was done to verify the clinical suspicion. of them.During admission, 66% (n=4) of patients were diagnosed with one of the following complications: bacteremia, oral candidiasis, acute hepatitis, atelectasis, and repeated syncope of non-cardiogenic cause.The mean length of hospital admission was 27.17 days, ranging from 17 to 42 days.All patients were discharged from hospital and were followed up for a mean of 6 months (1-11 months) by the Thoracic and Maxillofacial Surgery Departments, with no deaths at the end of the study.DNM is a rare polymicrobial infection originated by aerobic and anaerobic microorganisms, which can cause tissue necrosis, perpetuate a suiTable environment for anaerobic microorganisms and lead to cervical fascial plane dissection with subsequent dissemination towards the mediastinum ,11. The The most frequent route way of dissemination of DNM is through the retropharyngeal space (70%), which communicates with the posterior mediastinum, followed by the perivascular space . The remaining 10% of infectious processes progress through the pretracheal space, also causing involvement of the anterior or middle mediastinum . The medThe diagnosis of this clinical entity is based on laboratory tests (notably leukocytosis with neutrophilia), elevated acute phase reactants such as CRP and fibrinogen, and radiological imaging test, with cervico-thoracic CT with intravenous contrast being the test of choice. All our patients underwent an initial blood test, in which leukocytosis with neutrophilia and elevated other inflammatory parameters were observed, as well as a cervical CT scan on admission to our center. Thoracic CT scan should be performed initially if mediastinal spread is suspected, for example, in case of dyspnea, chest pain, pathological cardiopulmonary auscultation, ... Only one patient required a thoracic CT scan on admission to the emergency department. In the remaining patients a chest scan was performed during admission due to clinical worsening.Treatment should be early and aggressive, based on tooth extraction , surgical drainage, exhaustive irrigation of oro-cervical and mediastinal collections and broaet al has gained importance ,8,14, whSome authors consider that prophylactic tracheostomy is a good option in the management of the patient's airway ,15,16. Het al. reported an overall mortality in their series of 33,3% (et al. reported a 11,1% of mortality rate (Mortality in DNM is high, ranging from 11% to 40%, despite early treatment. Pearse described a 35% mortality in patients who had undergone surgical treatment, compared to 85% mortality in patients in whom drainage of collections was not performed . Other aof 33,3% and Riddity rate . The higDNM is a rare clinical entity with a potentially high mortality rate that requires early diagnosis and treatment. Diagnosis should be based on analytical and imaging studies, with contrast-enhanced cervicothoracic CT being the CT scan of choice.Aggressive treatment based on broad-spectrum antibiotic therapy, surgical drainage, and good management of life support measures in intensive care units may lead to a decrease in mortality of this disease."} +{"text": "Comorbid substance misuse in mental illness presents a significant challenge to mental health services. It may lead to higher rates of relapse, hospital admissions and poorer treatment outcomes. Up to 47% of inpatients in Irish mental health units may experience substance misuse. Despite the Irish government\u2019s \u2018Vision for Change\u2019 policy (2006), access to specialised services remains variable.Evaluate: -prevalence of substance misuse at an Irish mental health unit. -quality and detail of the recorded substance misuse history. -access to specialised services for patients experiencing substance misuse.A retrospective chart review of inpatients in a mental health unit over 12 months, was completed. Information recorded included: demographic details, diagnosis, substance use history; access to substance misuse services. Microsoft Excel was utilised for data input and analysis.267 patients were admitted over twelve months. Substance misuse was the primary diagnosis of 6% and the secondary diagnosis of 67%. 46% of patients reported current substance misuse, 52% reported historical substance misuse. Frequency and quantity of use was documented in 65% and 48% of cases respectively. 4% of patients with a substance misuse history were in current contact with addiction services.Although 46% of patients reported substance misuse, only 4% were in contact with specialised addiction services. This highlights a significant unmet need. There was variability in the quality of the recorded substance misuse history. In order to fully understand comorbid substance misuse, this be addressed. The addition of a more formatted substance misuse section, to admission proformas, may help to alleviate this issue."} +{"text": "Klebsiella pneumoniae (32.4%), Pseudomonas aeruginosa (17.8%), Acinetobacter baumannii (14.4%), Escherichia coli (10.4%), and Staphylococcus aureus (2.5%) were common. We observed high levels of drug resistance in AECOPD patients admitted to ICU (87.8%) and non-ICU (86.5%). A Cox proportional hazard analysis, observed infection with Acinetobacter baumannii and female sex as independent predictors of mortality. Acinetobacter baumannii had 2.64 : 1.08\u20136.43) higher odds of death, compared to Klebsiella\u00a0pneumoniae. Females had 2.89 (95% CI: 1.47\u20135.70) higher odds of death, compared to males. A high proportion of bacterial AECOPD was due to drug-resistant bacteria. An increasing trend in drug resistance was observed among females.Exacerbation due to antimicrobial-drug-resistant bacteria among chronic obstructive pulmonary disease (AECOPD) patients contributes to mortality and morbidity. We examined the prevalence of the bacterial organisms and trends in drug resistance in AECOPD. In this retrospective study, between January 2016 to December 2020, among 3027 AECOPD patients, 432 (14.3%) had bacteria isolated. The regression and generalized estimating equations (GEE) were used for trends in the resistance patterns over five years, adjusting for age, gender, and comorbidities. Haemophilus influenzae, Pseudomonas aeruginosa, Streptococcus pneumoniae, and Moraxella catarrhalis.Chronic obstructive pulmonary disease (COPD) is a common, preventable, and treatable disease, characterized by persistent respiratory symptoms and an airflow limitation due to airway and/or alveolar abnormalities usually caused by exposure to noxious particles or gases . The higAntibiotic resistance is rising to dangerously high levels in all parts of the world, threatening our ability to treat common infectious diseases . Our armThis paper describes a retrospective study conducted to identify the prevalence of bacterial species causing severe AECOPD and their trend in drug resistance patterns. The observations made in this study could help us develop tailored empirical antibiotic use strategies and prevent the emergence of drug resistance by improving our antimicrobial stewardship programs.p = 0.002). The most common co-morbidity was hypertension (33.8%), followed by nearly one-in-five patients with diabetes mellitus (25.5%), and corpulmonale (23%) (le (23%) .Klebsiella pneumoniae (32.4%) was the most frequent organism isolated, followed by Pseudomonas aeruginosa (17.8%), Acinetobacter baumannii (14.4%), Escherichia coli (10.4%) and Staphylococcus aureus (2.5%), which together accounted for 77.5% of the total isolates. The remaining 22.5% of the isolates were other PPMs (10.6%), and non-PPMs (11.8%). Males had a higher frequency of infection with PPMs (90%) than females (82.4%) (p = 0.036). Over the five years, the number of Acinetobacter baumannii and Escherichia coli isolations decreased while the number of Klebsiella pneumoniae and Pseudomonas aeruginosa isolations increased = 1.06; 95% CI ], Acinetobacter baumannii , Escherichia coli isolates was observed . Of the top five organisms which accounted for 77.5% of the total isolates, 57.6% were MDR, 26% were drug-resistant, 3.6% were XDR, and 12.8% were sensitive to all the drugs tested , adjusted for the patient characteristics . No Staphylococcus aureus was isolated in 2020 .Over the five years, an increasing trend in drug resistance was observed among all of the organisms , and Pseudomonas aeruginosa (17.8%) had 2.64 (95% CI: 1.08\u20136.43) higher odds of death, compared to Klebsiella pneumoniae. Following the adjustment for drug resistance (model 2), the odds of death increased to 2.88 (95% CI: 1.18\u20137.03) .Klebsiella pneumoniae was the most frequent organism isolated, followed by Pseudomonas aeruginosa, Acinetobacter baumannii, Escherichia coli, and Staphylococcus aureus, among patients with AECOPD. Of major concern, over five years, of the top five bacterial species that accounted for 77.5% of all isolates, 57.6% were MDR, 26% SDR, 3.6% XDR, and only 12.8% were susceptible to all drugs tested. The mortality rate among AECOPD patients infected with drug-resistant bacteria was 12.7%, compared to 4.7% among drug-sensitive patients. Females had a significantly higher risk of mortality, as compared to males . Females also had higher death rates with (21.2%) and without (14.3%) drug resistance, compared to males with (10.2%) and without (2.8%) drug resistance. Both males and females had an increasing trend of drug resistance, however, females had a steeper increase in drug resistance over the five years. Eighty-five percent of isolates from ICU were drug-resistant in 2016, which marginally increased over five years. In contrast, drug resistance in isolates from non-ICU was 75% in 2016 which increased to more than 90% over the five years.Our study found that Bacterial superinfections cause substantial morbidity and mortality among AECOPD patients worldwide. Bacteria are isolated from sputum in 40% to 60% of AECOPD patients . Other fHaemophilus influenzae, Pseudomonas aeruginosa, Streptococcus pneumoniae, and Moraxella catarrhalis. A review conducted by Rodrigo-Troyano et al. found that Klebsiella pneumoniae (in Asia) and Pseudomonas aeruginosa (in Europe) were the most common Gram-negative bacteria isolated in AECOPD patients [Klebsiella pneumoniae, Streptococcus pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii [Klebsiella pneumoniae (1% to 58%), Pseudomonas aeruginosa (1.2% to 29.1%), Acinetobacter baumannii (0.8% to 14%), Escherichia coli (0.4% to 11%), and Staphylococcus aureus (0.1% to 26%). The high isolation rates of Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii in the present study are in contrast to the studies from regions outside of India, while they resemble those reported in other Indian studies. It is unclear whether this is related to the differences in broad-spectrum antibiotic use, exposure to hospital flora during their visits to the hospital, or the geographical variations in bacterial distributions.Globally, the top four common bacteria causing AECOPD include patients . Previouaumannii ,15,16. FKlebsiella pneumoniae as a predominant bacterium causing AECOPD, is seen mostly in Asian and Indian studies. Globally, the drug resistance in Klebsiella pneumoniae, especially to carbapenems, is increasing, which poses a serious threat to patients because of its association with increased fatality. In our study, the carbapenem resistance of Klebsiella pneumoniae increased from 11.1% to 33.3%, between 2016 and 2020. In India, Pseudomonas aeruginosa was usually found to be the second most common bacteria causing AECOPD after Klebsiella pneumoniae but in some studies, it is the most predominant [Acinetobacter baumannii and Escherichia coli are, in general, not commonly associated with AECOPD [Acinetobacter baumannii was prominent in one prospective study among ICU patients [dominant ,18. Globh AECOPD ,20. In Ipatients with AECpatients .Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus isolates). Few Indian studies that have evaluated tigecycline, have observed a sensitivity rate of 66.7% to 100%. Globally, for non-Pseudomonas aeruginosa infections, tigecycline has not been commonly used. Among tetracyclines, doxycycline has been used with a sensitivity rate of 12.5% to 77.8% [Pseudomonas aeruginosa was intrinsically resistant to tigecycline (90% of isolates) and was most sensitive to aminoglycosides (88.3). Similarly, aminoglycosides (50% to 100%) and fluoroquinolones (47.4% to 100%) were the most appropriate antibiotics for pseudomonal infections, globally [In our study, the highest susceptibility of the AECOPD-associated bacteria, was to tetracycline and glycylcycline , due to both biological and sociocultural issues ,27,28,29Escherichia coli, followed by Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus. In India, a sustained rise in antimicrobial resistance has been observed [Klebsiella spp. are commonly seen with a case fatality rate of about 50% [Klebsiella spp. have polymyxin resistance, the case fatality rate is approximately 70% [The highest consumer of antibiotics in the world is India . Accordiobserved . Globallobserved . The morobserved . In the bout 50% and whentely 70% .Globally, the mortality due to bacterial infections in AECOPD patients, varied from 2.32% to 50% ,20. In IWe observed high levels of drug resistance in AECOPD patients admitted to both the ICU (87.8%) and non-ICU (86.5%). While the high rates of drug resistance in ICU are expected, almost similar rates of drug resistance in non-ICU settings were unexpected and need urgent investigation. Possible reasons include, that AECOPD patients are prescribed three times more antibiotics than the general public , antibioTo our knowledge, this is the first study examining the trends in drug resistance among infections of AECOPD patients across gender, ICU, and non-ICU admissions in India. We used advanced statistical methods, including GLM and GEE, to identify trends after adjusting for the confounders. This is one of the few comprehensive studies conducted in LMICs that have evaluated the impact of gender on AECOPD-associated mortality. The limitation of the study includes a lack of generalizability, due to data collection happening on one site. Information on the frequency and type of antibiotic used over the last few years was not available for many cases and could not be used in the analysis. As it is a retrospective study, data on patient readmissions and previous admissions were also not collected. No information on exacerbation, caused by viruses and fungi or mixed organisms was collected.This retrospective study was carried out with data collected from patients with AECOPD, admitted to a university-affiliated 1800-bed tertiary care hospital catering to the healthcare needs of patients from the Mysore District, JSS Medical College & Hospital, India, between January 2016 and December 2020. The hospital information system (HIS) uses the ICD-10 coding system and all subjects with AECOPD (J44.1 and J44.9) were screened for demographic characteristics (age and sex), comorbidities, length of hospital stay (LOS), and admission to ICU, or non-ICU, during the study period, and mortality. The information on the bacterial pathogen species and their drug susceptibility patterns were collected. We identified 3027 COPD patients who were admitted to the tertiary care hospital, from January 2016 to December 2020, which constituted the Mysuru COPD (MYCO) Cohort. Four hundred and thirty-two patients had bacterial infections and were included in the study. The COPD patients without bacterial exacerbations were excluded. Any additional secondary diagnoses were defined, according to the ICD10 coding system.AECOPD was defined as the acute worsening of respiratory symptoms that result in additional therapy . Charlso\u00ae 2 system All of the clinical and demographic data of the subjects included in the study was collected from HIS for screening. Based on the organism isolated, we classified the bacteria into potentially pathogenic microorganisms (PPMs) and non-PPMs, as described by Cabello et al. [Sputum samples that were received in the Microbiology laboratory for routine diagnosis were included in the study. The samples were processed, according to the departmental standard operating procedures. In brief, the samples that were received were subjected to gram staining to assess the quality of the sputum sample, and those samples with Bartlet scores that are 0, \u22121, and \u22122 were excluded from the study. Sputum samples with Bartlet scores of +1, and +2 were included and were inoculated onto Blood agar and Mac Conkey agar for the isolation of the pathogens, and the media was incubated at 37 degrees Celsius overnight. The growth was further identified and antibiotic susceptibility testing of the isolates was determined by the Viteko et al. .Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Escherichia coli, Staphylococcus aureus, Acinetobacter junii, Acinetobacter lwoffii, Acinetobacter ursingii, Citrobacter freundii, Citrobacter koseri, Citrobacter species, Enterobacter aerogenes, Enterobacter cloacae complex, Haemophilus influenzae, Klebsiella oxytoca, Proteus mirabilis, Pseudomonas fluorescens, Pseudomonas putida, Serratia marcescens, Stenotrophomonas maltophilia, and Streptococcus pneumoniae.The microorganisms recognized as agents causing respiratory infections were classified as PPMs, whether or not they belonged to the gastrointestinal or oropharyngeal flora. Organisms classified as PPMs consisted of Aeromonas species, Alpha Haemolytic Streptococci, Beta Haemolytic Streptococci, Burkholderia cepacia, Coagulase-negative Staphylococcus, Group A Streptococci, Sphingomonas paucimobilis, Staphylococcus capitis, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis ssp hominis, Staphylococcus saprophyticus, Staphylococcus sciuri, Staphylococcus warneri, and Streptococcus species.The microorganisms that are not usually involved in respiratory infections in non-immune deficient patients were classified as non-PPMs belonging to gastrointestinal or oropharyngeal flora. Organisms classified as non-PPMs included From January 2016 to December 2020, a total of 432 bacteria isolated, were subjected to antibiotic susceptibility testing, which includes aminoglycosides (amikacin and gentamicin), carbapenems , other cephalosporins , fluoroquinolones for gram-negative bacteria and penicillin\u2019s , macrolides (erythromycin), tetracycline (minocycline), glycylcycline (tigecycline), glycopeptides (vancomycin and teicoplanin), sulfonamides (trimethoprim/sulfamethoxazole), lipopeptide (colistin), phenicol (chloramphenicol), nitrofurantoin, and oxazolidinones (linezolid) for gram-positive bacteria.The eligible subjects were identified by the ICD-10 codes J44.1 and J44.9. Male and female subjects \u226540 years of age, diagnosed with AECOPD, who tested sputum culture-positive, were included in the study. Other respiratory samples, subjects with no bacterial growth, and relevant missing data, were excluded from the study.t-test for continuous variables and the chi-squared test for the categorical variables were compared through a univariate analysis to assess the statistical significance. Statistical analyses were performed with SPSS software v.22 and the Stata 16 version . All statistical tests were two-tailed, and the factors were considered statistically significant at p < 0.05 and were included in the generalized linear model (GLM) and used a generalized estimating equation (GEE) if they were found to be statistically significant on a univariate analysis. Figures were generated with Microsoft Excel\u00ae and GraphPad Prism software . The antibiotic activity of the bacterial isolates was recorded as responses, with other covariates as the explanatory variables. The proportion of each type of antibiotic resistance was summarized as drug-sensitive, SDR, MDR, and XDR. We adjusted the frequencies of the patient\u2019s characteristics and type of admissions to understand the relationship of the GLM with binomial error, and logit link. We further used a GEE to explore the linear trends between the rate of antibiotic resistance and the top five bacterial species isolates over a time span of five years (2016\u20132020). In this study, we used the GEE model with the binomial link, and p-values, less than 0.05 were considered statistically significant. The GEE was used to account for the repeated measure and scanty data. As such, we analyzed the five most common bacterial species isolates that accounted for approximately 80 percent of any or all drug resistance. We looked for interactions between admissions to different hospital units , yearly. The multivariate Cox regression analysis was used to identify the independent risk factors associated with mortality.The descriptive data were presented as the mean (\u00b1standard deviation) of continuous variables and as frequencies of discrete variables. The student This study was approved by the Institutional Ethics Committee of JSS Medical College, Mysuru . Informed consent was waived because this was a retrospective study.Klebsiella pneumoniae was the most common organism causing bacterial AECOPD, followed by Pseudomonas aeruginosa and Acinetobacter baumannii. Over five years, an increasing trend in drug resistance was observed in AECOPD hospital admissions. Female sex and Acinetobacter baumannii were independent risk factors for mortality and drug resistance. Antimicrobial stewardship with the judicious use of antimicrobial agents is essential to prevent the emergence of resistant, MDR, XDR, and PDR bacteria in AECOPD patients.A high proportion of COPD bacterial exacerbations were found to be drug-resistant both in the ICU and non-ICU settings."} +{"text": "The coronavirus disease 2019 (COVID-19) pandemic has caused major sanitary crisis worldwide. Frontline healthcare workers face many difficulties, such as: direct exposure to patients with high viral load, physical exhaustion, reorganization of workspaces, face the unusually high number of deaths among patients, colleagues or relatives and ethical issues in a tense health system.Provide up-to-date information of Burnout syndrome associated with exposure of healthcare workers to the COVID-19 pandemic, after almost 20 months of the declaration of pandemic by the World Health Organization.A cross-sectional study was carried out that included 84 healthcare workers from Spain in October 2021, through an anonymous, voluntary and multiple response type online survey which included questions about sociodemographic aspects and the Maslach burnout inventory62% were doctors and 29% were nurses. 70% work on the front line of Covid-19. 38% report not having been able to enjoy their vacations when they wanted. 8% admit to having had suicidal ideas. Almost 52% admit low personal fulfillment, 38.6% admit a high depersonalization count, and 45% report high emotional exhaustion. Of the total sample, 17 respondents have burnout syndrome.It is necessary create strategies to promote mental well-being in health professionals exposed to COVID-19 after 20 months of active work. Protecting and identifying health care professionals who could be at high risk for developing a mental health pathology or detecting Burnout syndrome in them should be the priority of public health post pandemic.No significant relationships."} +{"text": "This interprofessional study conducted by faculty in Occupational Therapy, Social Work and Public Health explored older adult technology use (or nonuse) by 216 Genesee County Michigan residents. Three professional lenses informed survey development, implementation and data analysis. Occupational therapy emphasized accessibility, how physical or cognitive impairments hinder technology use, and role of technology to complete daily living activities. Social work focused on technology use to facilitate social connectivity, decrease risks for mental health problems, and resource access. Public health explored if technology use or nonuse impacts health. Results indicated that 14% of participants want to learn to obtain transportation via the internet, 13% stated they wanted to learn how to use technology to access medical records, 12.5% to attend on-line appointments, 11% reported they would engage in additional technology-based social activities (e.g. communicating with family/friends), 10% to order/refill medications, and 9% of older adults surveyed had difficulty accessing technology due to a physical, cognitive or sensory impairment. Researchers found the questions provided an integrated view of factors influencing older adult use or nonuse of technology and provided a guide for designing collaborative interventions to facilitate older adult access and use of technology to result in positive holistic health outcomes."} +{"text": "Since February 2020, the outbreak of COVID-19 has spread to several countries worldwide, including Italy, leading to an uptake of telework.We aim to evaluate the psychopathological impact of teleworking during the COVID-19 pandemic in Italy, identifying mental health determinants among home-based workers.804 participants completed an online survey, including the psychometric scales \u201cDepression, Anxiety and Stress Scale \u2013 21 items\u201d (DASS-21) and the \u201cInsomnia Severity Index\u201d (ISI). Teleworkers were also asked to provide information about their current work routine, home environment and clinical history.At the DASS-21, 30% of the participants presented pathological levels of depression, 20.8% of anxiety and 30.7% of stress. At the ISI, 5% appeared to suffer from insomnia. Respondents with psychological and physical frailties, greater social isolation or inadequate working spaces manifested higher levels of psychiatric symptoms. Moreover, we also find a correlation of these symptoms with occupations in education. Telework was broadly appreciated and 87% of respondents expressed a willingness to maintain access to this arrangement.Our results document that about a third of our sample manifested psychopathological symptoms while teleworking during the COVID-19 outbreak in Italy. However, telework itself does not seem to be directly associated with increased psychiatric symptoms, which were instead exacerbated by COVID-19-related stressful circumstances, as well as by constitutional and social determinants of health. Going forward, authorities should promote adequate measures in order to guarantee a healthy approach to teleworking.No significant relationships."} +{"text": "Gastric cancer is the fourth leading cause of cancer-related deaths globally. There is a paucity of national studies examining gastric cancer mortality in relation to treatment status. This study evaluated the survival trends in gastric adenocarcinoma and all gastric cancers stratified by treatment in Finland during 1987\u20132016.This population-based, nationwide, retrospective cohort study included all gastric cancer patients registered in the Finnish Cancer Registry and Patient Registry. The survival rates were calculated for 1, 3, and 5\u00a0years, stratified by treatment. Prognostic factors were determined using Cox regression.A total of 18,713 non-cardia gastric adenocarcinoma, and 3617 cardia adenocarcinoma patients were included. Surgical treatment decreased for non-cardia adenocarcinoma and remained constant for cardia adenocarcinoma. In non-cardia adenocarcinoma, the 5-year survival declined from 17% to 16% from 1987\u20131991 to 2012\u20132016. In surgically treated patients, survival increased from 29% to 38%, while an increase from 4% to 7% in those undergoing chemotherapy and decrease from 6% to 3% in those not receiving any treatment were observed. In cardia adenocarcinoma, the 5-year survival increased from 10% to 18% in all patients, 16% to 40% in surgical patients, 0% to 5% in patients receiving chemotherapy, and from 5% to 9% in patients receiving no treatment. Earlier calendar periods, older age, male sex, and higher comorbidity were risk factors for poor prognosis.Gastric non-cardia adenocarcinoma survival declined, limited to advanced stage patients not receiving any treatment. Gastric cardia cancer survival seems to have improved over time in Finland.This study evaluated survival trends of gastric cancer in Finland during 1987\u20132016 and established that the 5-year survival is declining in non-cardia adenocarcinoma but improving in all gastric cancers.The online version contains supplementary material available at 10.1007/s10120-022-01326-5. Helicobacter pylori infection [H. pylori has shown a potential to reduce incidences of gastric cancer [Gastric cancer is the fifth most common cancer and the fourth leading cause of cancer-related death around the world . Gastricnfection \u20137. Prevec cancer , 8, but c cancer .Although gastric cancer incidence is declining and survival is improving in most countries, the survival of patients after curative surgery is poor. In Europe, despite the decline in incidence and improvement in survival, gastric cancer remains a highly fatal disease with a poor prognosis. The 5-year survival rate of gastric cancer in Europe fluctuates between 10% and 30% . In SwedThis study was a population-based, nationwide, retrospective cohort study of all gastric cancer patients identified in Finland during the period 1987\u20132016, based on Finnish national registries. The study was approved by the Northern Ostrobothnia ethical committee EETMK 115/2016) and relevant governmental bodies. Informed consent was not required for registry research , 15./2016 andAll patients with gastric cancer were identified from the Finnish Cancer registry (FCR) and the Finnish Patient Registry (HILMO) using respective ICD-9 151) and ICD-10 C16) codes. Personal identification numbers assigned to all residents in Finland were used to combine registry data. The FCR provided data on incident cancers, date of diagnosis, cancer histology type, location, cancer stage, as well as the age of patients at diagnosis and sex of patients. FCR also provides data on whether patients had chemotherapy. HILMO was used to identify incident cancers and patients undergoing surgical resection and to calculate comorbidity in all identified gastric cancer patients, as previously defined. Surgical codes from the patient registry helped identify surgical procedure types which included gastrectomy, esophagectomy, esophagogastrectomy, endoscopic mucosal resection (EMR), and endoscopic submucosal dissection (ESD). Both open and laparoscopic surgery was included , 15. FCR1 and ICD codes. PAll analyses were based on a prior study protocol. Data on all patients diagnosed with gastric cancer from 1987 to 2016 were retrieved from FCR and HILMO registries. The patients were then grouped according to 5-year periods , age groups , sex, Charlson Comorbidity Index score , surgery status (yes and no), chemotherapy , and stage . For survival analysis, 1-year, 3-year, and 5-year survival rates were calculated for both non-cardia and cardia gastric adenocarcinoma separately, as well as stratified further by treatment: surgery, or no surgery; surgery, chemotherapy only, or no treatment; as well as by cancer stage: local, locally advanced, or advanced. Survival analysis was conducted using the life table method and plotted using Kaplan\u2013Meier curves. Cox regression was used to calculate hazard ratios (HR) of mortality with 95% confidence intervals (95% CI) for each stratified variable which are considered prognostic factors associated with gastric cancer mortality. Finally, a separate analysis for all gastric cancer types was done to evaluate whether the survival trends were similar to trends of gastric adenocarcinoma. Analyses were carried out using IBM SPSS 26 .Of the total 22,330 gastric cancer patients, 18,713 (83.8%) had non-cardia cancer and 3617 (16.2%) had cardia cancer during 1987\u20132016. After exclusion of 797 neuroendocrine tumors, 518 other types of tumors such as squamous cell carcinoma, melanoma, mesenchymal cancer, and gastrointestinal stromal tumor, and 3275 patients without any information on histology available, there were 18,713 histologically confirmed gastric non-cardia adenocarcinomas, and 3617 gastric cardia adenocarcinomas included in the analysis. The number of both cardia and non-cardia adenocarcinoma patients decreased over time. Most gastric adenocarcinomas occurred at the age of 70\u201379\u00a0years. There were more men with gastric non-cardia (52.6%) and cardia adenocarcinoma (70.0%) than women. Most gastric adenocarcinoma patients did not undergo chemotherapy and the majority had advanced cancer stages gastric adenocarcinoma patients underwent surgical treatment. For gastric non-cardia adenocarcinoma, the proportion of surgical treatment was larger 8293 (44.3%) than for gastric cardia adenocarcinoma , older age groups , higher comorbidity score , and male sex were observed to be associated with an increased risk of mortality. The risk factors were similar in patients undergoing surgery and not undergoing surgery, with the exception that comorbidity was not a risk factor for mortality in those not undergoing surgery , older age groups , male sex , and high comorbidity score , which wThe survival patterns of gastric adenocarcinoma prognosis in several European countries have been assessed previously. A Dutch study on gastric adenocarcinomas showed that 5-year survival for gastric non-cardia adenocarcinoma decreased from 22% to 14% . A SwediThe recent trends of cardia adenocarcinoma prognosis have been previously studied in the Netherlands (stable at 10% from 1990 to 2005) . The preIn a larger context, the prognosis of non-cardia gastric cancer of any histology has improved from 19% in 1987\u20131991 to 24% in 2012\u20132016, and from 11% in 1987\u20131991 to 24% in 2012\u20132016 for gastric cardia cancer. This is in line with registry studies from the United States (improvement from 26% to 29% during 2000s) , Europe H. pylori is, however, the most detrimental risk factor associated with poor prognosis in both sexes [In addition to earlier calendar periods, older age groups, comorbidity, and male sex were observed to be risk factors for poor prognosis of both gastric non-cardia and cardia cancers. While the other factors are largely in line with the previous studies, the finding on the association of sex difference in poor prognosis of gastric cancer was rather unexpected. In the subgroup analyses, sex was associated with prognosis in only surgical gastric non-cardia and cardia adenocarcinoma. In Sweden, which is a relatively similar population compared to Finland, there was no difference in prognosis between male and female gastric non-cardia adenocarcinoma patients . The higth sexes \u201331. Estrth sexes \u201334. ThesThis study has several research and clinical implications. First, the declining prognosis in gastric non-cardia adenocarcinomas highlights the need for actions, such as further centralization of gastric cancer care, and evaluation and research of treatment options such as immunotherapies or cytoreductive surgery to further improve the prognosis of the disseminated disease. Second, the discrepancy in survival trend patterns between non-cardia and cardia cancers need further studies to understand the reasons these two cancer types are behaving differently. Finally, the differences in prognostic trends between gastric adenocarcinomas and all gastric cancers may indicate that optimistic estimates of survival trends may be obtained by studying gastric cancers without taking into account cancer histology.In conclusion, this population-based, nationwide study on survival trends of gastric cancer in Finland indicates that the 5-year survival in patients with gastric non-cardia adenocarcinoma is declining but improving for cardia adenocarcinomas. However, the overall survival in all gastric cancers has improved during the last 3 decades in Finland. Earlier calendar period, older age, male sex, and higher comorbidity scores were poor prognostic factors for both gastric non-cardia and cardia cancer.Supplementary file1 (DOCX 2123 KB)Below is the link to the electronic supplementary material."} +{"text": "After multivariate analysis, reactive HIV status , positive attitude of healthcare workers , excellent services offered at the healthcare facility and few people seeking care became independent significant determinants of successful treatment outcome. The study concluded that reactive HIV status, positive attitude of healthcare workers, few people seeking healthcare, and excellent service provided were all factors that contributed to successful treatment outcomes.Tuberculosis (TB) is one of the oldest human diseases, and preventing treatment failure is critical. This is because TB cases pose a risk to the immediate and remote communities due to the potential for spread, particularly for multidrug-resistant (MDR) strains that have been associated with higher morbidity and mortality rates. Hence, this study looked at the factors that influence TB treatment outcomes in Southwest Nigeria. We conducted a cross-sectional study with 712 TB patients from 25 directly observed treatment short course (DOTS) centers, out of which 566 (79.49%) were new treatment cases, and 102 (14.33%) were retreatment cases. The outcome variable was computed into successful treatment where \u2018Yes\u2019 was assigned to TB treatment completed and cured, and \u2018No\u2019 was assigned to all the remaining outcomes following the standard TB definition. Independent variables included in the analysis were the patient\u2019s socio-demographic characteristics , clinical and facility parameters . Bivariate analysis showed that HIV status (OR: 3.53, 95% CI: 1.83\u20136.82; Tuberculosis remains a major public health concern, particularly in underdeveloped countries with weaker health systems . As a reTuberculosis (TB) is a highly contagious disease mainly caused by Mycobacterium tuberculosis (MTB) and typically affects the lungs (pulmonary tuberculosis) and other parts of the body (extrapulmonary tuberculosis) . GeneralA greater risk of infection has been observed in individuals with constant and prolonged close contact with individuals already infected with TB ,11,12. IIn most African countries, up to 80% of TB patients are HIV seropositive, suggesting that TB is the most important opportunistic infection in HIV-infected individuals worldwide ,17. ThisWhile the number of laboratory-confirmed cases of drug-resistant tuberculosis has decreased, with incidence falling from 2300 cases in 2017 to 2275 cases in 2018, the projected cases have increased from 5400 in 2017 to 21 000 in 2018 . HoweverIn 1993, the World Health Organization (WHO) declared TB a global public health emergency. In 1995, the directly observed treatment short course (DOTS) regimen was adopted as the key strategy in resolving this global problem . By 2005Early detection of tuberculosis and prompt initiation of treatment have been found to contribute to successful treatment. Late TB diagnosis could lead to increased infectivity, disease burden, and death ,32. AlthIbadan is the capital city of Oyo State, in Nigeria, with over 3 million people . There aA cross-sectional study was conducted among 712 TB patients in twenty-five (25) DOT centers using a semi-structured interviewer-administered questionnaire. This study was conducted from June to October 2016. Eligible participants recruited included all TB patients treated at all selected DOTs centers.All TB patients who consented to participate in the study.Patients age 18 years and above.These are TB patients who do not provide their consent to participate in the study.The National Tuberculosis and Leprosy Control Program (NTBLCP) diagnostic algorithm encourages a suspected TB case to undergo multiple bacteriological investigations -swab microscopy or/and Xpert MTB/RIF) for early diagnosis . This prDrug-sensitive TB treatment consists of two phases: the two-month intensive treatment phase and the four-month continuation phase for new patients. In accordance with WHO guidelines, the current anti-tuberculosis regimen begins with a two-month intensive phase treatment with four fixed-dose combinations (FDC), namely rifampicin (R), isoniazid (H), pyrazinamide (Z), and ethambutol (E), and four-month follow-up phase with two FDC (isoniazid and ethambutol) /4(EH)) ,38. RifaThe outcome variable was computed into successful treatment where \u2018Yes\u2019 was assigned to TB treatment completed and cured, and \u2018No\u2019 was assigned to all the remaining outcomes following the standard TB definition ,38,39.Independent variables included in the analysis were the patient\u2019s socio-demographic characteristics and clip-values \u2264 0.05 were reported for all statistically significant results. All statistical analyses were performed using Stata software version 12 .Descriptive statistics were employed to describe the respondent\u2019s trajectory (the number of times patients have received TB treatment) by socio-demographic and health and healthcare facility factors. The association between the outcome and independent variables was assessed by employing a multivariate binomial backward stepwise logistic regression model. Odds ratios (OR) with 95% confidence intervals (CIs) and Overall, a total of 712 participants were recruited for the study. The majority were 31\u201340 years, 30.10% (87), females, 61.74% (439), secondary level of education, 41.99% (299), and of middle social economic status, 58.85% (419). Almost two-thirds of the participants, 73.46% (523), live within 10 km distance from the health facility they take treatment. Almost 70% (495) of the respondents were married or cohabiting, with the majority in a monogamous home 64.99% (453), as shown in The overwhelming majority, 89.60% (629), of the participants use the government health facility as their primary place of access to healthcare, are new treatment cases, 79.49% (566), and have non-reactive status for HIV, 86.22% (582). Two-fifths, 41.89% (284), had a successful treatment outcome, while more than half, 58.11% (394), had unsuccessful treatment outcomes. Among the participants, those that take their drugs daily were in the majority 73.31% (522), and among the major reasons why they attended a primary healthcare center for their previous treatment contact were trusted, 39.47% (281), belief, 29.92% (213), and proximity, 29.63% (211). Most of the participants stayed six months and more at their first treatment site, 56.74% (404), experienced less than 30 min waiting time, 82.33% (559), received counseling as a service, 74.02% (527), and were of the opinion that the healthcare worker\u2019s attitude was positive, 89.33% (611), as shown in p = 0.001), healthcare worker attitude , and number of people seeking care were associated with successful treatment outcome with statistical significance. Other variables that had an association with successful treatment outcomes with statistical significance were services offered at the healthcare facility and appearance at the healthcare facility , as shown in The bivariate analysis showed that HIV status , positive healthcare worker attitude , excellent services offered at the healthcare facility , and few people seeking care , as shown in Multiple logistic regression analysis was performed to control confounding variables after which significant determinants of treatment outcome were reactive HIV status (aOR: 3.37, 95% CI: 1.67\u20136.80; The findings of this research shed light on what makes a TB treatment successful. Successful treatment outcomes were linked to a positive healthcare worker attitude, HIV status, the presence of a low number of patients seeking care, excellent service, and an attractive healthcare facility.Although age has no significant relationship with successful treatment outcomes in this study, assessment of the age distribution shows that the TB burden was most prevalent in young adults and middle-aged people. Many researchers have reported comparable results ,42,43. EAnother finding in this study was that females sought treatment 1.5 times more frequently than males. Women in Sub-Saharan Africa account for 63% of all new HIV infections in 2020, making them the most at risk of developing active TB and more likely to develop drug resistance . Doctor Barely than 40% of the participants in this study had a successful treatment outcome, defined as those who completed their treatment and those who were declared cured. This is significantly lower than the WHO\u2019s global treatment success estimates of 75% and 86% for Nigeria in 2019 , EthiopiThe HIV status of the participants revealed that 86% were negative, which is higher than the national estimate of 76% and supports the reported national incidence rate of decrease . The majThe aforementioned predictors of successful treatment outcomes, which included reactive HIV status, a positive attitude among healthcare workers, and a low number of people seeking care at the healthcare center, are similar to findings from the study by Tola et al. and ZeenAfter controlling for confounders, the predictive determinants of successful treatment outcomes were reactive HIV status, positive healthcare worker attitude, excellent service at the facility, and a low number of people seeking healthcare. This means that people with HIV coinfection have more than three times the chances of successfully completing treatment, regardless of healthcare workers\u2019 attitudes or the number of people seeking care at the facility. Furthermore, those who experience a positive attitude of healthcare workers and the presence of few people seeking healthcare have twice the likelihood of recording successful treatment, with each determinant independent of the other. It is well understood that having both TB and HIV implies a poor prognosis. This could be explained by their adherence to their treatment regimen and successful treatment.The study did not examine some clinical characteristics of the patients, such as weight and height, that could be used to assess one of the key indicators of clinical improvement. In addition, the study is limited by not exploring socio-cultural variables that can impact the outcome of treatment.The study concluded that reactive HIV status, positive attitude of healthcare workers, few people seeking healthcare, and excellent service provided were all factors that contributed to successful treatment outcomes. With a poor treatment success rate, there is a need to understand these factors. It is therefore recommended that improved policy on patient-centered care, including upgrading healthcare facilities and continuous training of healthcare workers, should be provided."} +{"text": "IRB # AAAS9652) that included symptomatic adult patients (21 years or older) who presented to our emergency room and tested positive for COVID-19 and were either admitted or discharged with at least one chest CT from 11 March 2020 through 1 July 2020. CT scans were ordered by the physicians caring for the patients; our COVID-19 care protocols did not specify the timing for chest CT scans. A scoring system was used to document the extent of pulmonary involvement. The total CT grade was the sum of the individual lobar grades and ranged from 0 (no involvement) to 16 (maximum involvement). The distribution of lung abnormalities was described as peripheral (involving the outer one-third of the lung), central (inner two-thirds of the lung), or both. Additional CT findings, including the presence of pleural fluid, atelectasis, fibrosis, cysts, and pneumothorax, were recorded. Contrast-enhanced CT scans were evaluated for the presence of a pulmonary embolism, while non-contrast chest CT scans were evaluated for hyperdense vessels. Results: 209 patients with 232 CT scans met the inclusion criteria. The average age was 61 years (range 23\u201397 years), and 56% of the patients were male. The average score reflecting the extent of the disease on the CT was 10.2 . Further, 73% of the patients received contrast, which allowed the identification of a pulmonary embolism in 21%. Of those without contrast, 33% had hyperdense vessels, which might suggest a chronic pulmonary embolism. Further, 47% had peripheral opacities and 9% had a Hampton\u2019s hump, and 78% of the patients had central consolidation, while 28% had round consolidations. Atelectasis was, overall, infrequent at 5%. Fibrosis was observed in 11% of those studied, with 6% having cysts and 3% pneumothorax. Conclusions: The CT manifestations of COVID-19 can be divided into findings related to endothelial and epithelial injury, as were seen on prior post-mortem reports. Endothelial injury may benefit from treatments to stabilize the endothelium. Epithelial injury is more prone to developing pulmonary fibrotic changes.Purpose: To describe the imaging findings of COVID-19 and correlate them with their known pathology observations. Methods: This is an IRB-approved retrospective study performed at Columbia University Irving Medical Center ( The Radiology Society of North America (RSNA) has provided guidelines for reporting imaging findings in patients with coronavirus disease 2019 (COVID-19). The typical appearance of COVID-19 includes bilateral, basilar-predominant, peripheral ground-glass and/or consolidation, and vascular enlargement . A crazyPost-mortem examinations provide valuable information regarding the pathology of COVID-19. Prior reports reveal two main microscopic patterns of lung disease identified in COVID-19 decedents. Intravascular fibrin and/or platelet-rich aggregates (IFPAs) were found in small and large pulmonary vasculature in as many as 84 to 90% of the lungs examined post-mortem . Acute lThe purpose of this study is to interpret the chest CT manifestations of COVID-19 in light of the known autopsy findings. We aim to correlate the aforementioned microscopic patterns with their radiologic equivalents and evaluate their evolution over time radiographically by identifying the date of symptoms for each chest CT. By doing so, we hope to non-invasively assess how the virus affects the lungs at various stages of the infection.IRB #AAAS9652). The requirement for informed consent for this retrospective review was waived.This retrospective study was approved by the internal review board of Columbia University Irving Medical Center (Inclusion criteria were symptomatic adult patients (21 years or older) who presented to our emergency room and tested positive for COVID-19 and were either admitted or discharged with at least one chest CT from 11 March 2020 through 1 July 2020. The age and sex of each patient were documented. In addition, we documented the number of days since symptom onset at the time of the CT scan by review of the patient medical record. Zero days means that the patient had a CT scan on the day of onset of symptoms.Iohexol 350 mg/mL at an average rate of 4 cc per second per our protocol. Scanning was triggered when the average Hounsfield unit of the pulmonary artery reached 100.CT scans were ordered by physicians caring for the patients; our COVID-19 care protocols did not specify the timing for chest CTs. Chest CT scans were performed using one of five commercial GE 64-slice CT scanners at our site. CT acquisition parameters were as follows: 120 kVp, smart mA tube current modulation (range 80\u2013600 mA), noise index 16, pitch 1.375:1, and table movement 35 mm/rotation. Two axial reconstructions were generated for each scan: one with adaptive statistical iterative reconstruction (ASIR) at 40% value and reconstructed slice thickness of 1.25 mm with standard kernel and the other with ASIR 40% at a slice thickness of 5 mm with lung kernel. Pulmonary embolism studies were performed using no more than 100 cc of intravenous non-ionic contrast agent A scoring system was used to document the extent of pulmonary involvement. The lung was divided into 4 quadrants, with the right upper lobe and right middle lobe graded as one quadrant. The left upper lobe, right lower, lobe, and left lower lobe were each considered a separate quadrant. Each quadrant was graded from 0\u20134; Grade 0 indicated no involvement; Grade 1, 1\u201325% involvement; Grade 2, 25\u201350% involvement; Grade 3, 51\u201375% involvement; and Grade 4, 76\u2013100% involvement. The total CT grade was the sum of the individual lobar grades and ranged from 0 (no involvement) to 16 (maximum involvement).The distribution of lung abnormalities was described as peripheral (involving the outer one-third of the lung), central (inner two-thirds of the lung), or both. Discrete peripheral Hampton\u2019s humps and round consolidations were noted. Additional CT findings, including the presence of pleural fluid, atelectasis, fibrosis, cysts, and pneumothorax, were recorded. Contrast-enhanced CT scans were evaluated for the presence of pulmonary embolism, while non-contrast chest CT scans were evaluated for hyperdense vessels.In total, 209 patients with 232 CT scans met the inclusion criteria; 23 patients had two CT scans. The average age was 61 years (range 23\u201397 years), and 56% of the patients were male. The average score reflecting the extent of the disease on the CT was 10.2 . Further, 73% of the patients received contrast, which allowed the identification of a pulmonary embolism in 21%. Of the 27% without contrast, 33% had hyperdense vessels, which might suggest a chronic pulmonary embolism, 47% had peripheral opacities, and 9% had a Hampton\u2019s hump. Additionally, 78% of the patients had central consolidation, and 28% had round consolidations. Atelectasis was, overall, infrequent, occurring in 5% of the patients. Fibrosis was observed in 11% of those studied, with 6% having cysts and 3% pneumothorax .The average age was 60 years, and 58% were male. Pulmonary embolism, hyperdense vessels, and Hampton\u2019s humps were present in 16%, 25%, and 23%, respectively. Peripheral opacities were very common, affecting 55% of the patients. Central consolidations and round consolidations were also frequent at 55% and 39%, respectively. Fibrotic changes were present in only one patient and were pre-existing .The average age was 62 years, and 48% were males. Pulmonary embolism and hyperdense vessels occurred in 14% and 38%, respectively. Peripheral opacities were very common, affecting 60% of the patients. Central and round consolidations were also frequent at 78% and 35%, respectively. Fibrotic changes were present in 5% of the patients and likely represented pre-existing disease .The average age was 62 years, and 66% were males. Pulmonary embolism and hyperdense vessels remained common at 33% and 40%, respectively. Peripheral opacities were very common, affecting 55% of the patients. Central and round consolidations were also frequent at 85% and 26%, respectively. The greatest average extent of disease was found at this stage. Fibrotic changes were more common, affecting 10% of the patients .The average age was 61 years, and 56% were males. Pulmonary embolism, hyperdense vessels, and Hampton\u2019s humps were observed in 11%, 32%, and 8%, respectively. Peripheral opacities were less common, affecting 27% of the patients. Central and round consolidations persisted at 80% and 17%, respectively. Fibrotic changes were present in 22% of the patients .The published results of post-mortem examinations identified two main microscopic patterns of lung disease: IFPAs were identified in as many as 90% of the patients and ALI in 75% of the lungs. These two patterns of disease, representing pulmonary endothelial and epithelial injury, respectively, can be diagnosed radiographically.The CT manifestations of a pro-coagulant microenvironment caused by an endothelial injury are typically pulmonary emboli, as is seen in patients with cancer and prolonged immobility ,15. HoweALI is secondary to alveolar epithelial damage caused by the viral infection. The angiotensin-converting-enzyme type 2 receptor is located on type 2 alveolar epithelial cells, making them vulnerable to viral infection with COVID-19 . EpithelEndothelial cell dysfunction with COVID-19 has been described ,22,23. EHampton\u2019s hump is a radiographic sign of pulmonary infarction and is rare due to the dual pulmonary and bronchial arterial supply of the lungs. Patients with COVID-19 may be predisposed to infarction due to the concurrent viral infection of bronchial arteries . HamptonA large meta-analysis showed a pooled incidence rate of PE of 16.5%, similar to our study . In our Hyperdense vasculature on a non-contrast CT scan is a radiographic sign highly diagnostic of a long-standing pulmonary embolism 27,28],,28,27,28Epithelial cell dysfunction in COVID-19 includes alveolar flooding due to leaky capillaries and inflammatory cell infiltrates, with the potential for progression to acute respiratory distress syndrome (ARDS) with diffuse alveolar damage and hyaline membrane formation . CentralRound consolidation, likely representing organizing pneumonia, was a feature of early disease and decreased during the persistent and chronic phase of the disease ,35. AtelPulmonary fibrosis occurs not infrequently following severe COVID-19 infection, especially if mechanically ventilated . In a stEfferocytosis is the removal of apoptotic cells by macrophages. Impaired efferocytosis is associated with many pulmonary diseases, including cystic fibrosis, chronic obstructive pulmonary disease, bronchiectasis, and asthma . A recenThe cause of cyst formation in COVID-19 is unknown ; howeverThe results of our study support the importance of both an endothelial and epithelial injury in many patients with severe COVID-19 infection and that a CT scan can facilitate the differentiation of the primary site of involvement and its evolution over time, which has implications for the management of patients."} +{"text": "In non-dense breasts, DBT showed significantly higher sensitivity than ultrasound , but no differences in specificity , PPV or AUC . Around 73% (74% dense and 71% non-dense) and 77% (81% dense and 72% non-dense) of lesions assigned a RANZCR 3 by DBT and ultrasound, respectively, were benign. Conclusion: DBT has higher sensitivity, but lower specificity and PPV than ultrasound in women with dense breasts recalled for assessment. Most lesions rated RANZCR 3 on DBT and ultrasound are benign and may benefit from short interval follow-up rather than biopsy.Background: To compare the diagnostic efficacy of digital breast tomosynthesis (DBT) and ultrasound across breast densities in women recalled for assessment. Methods: A total of 482 women recalled for assessment from January 2017 to December 2019 were selected for the study. Women met the inclusion criteria if they had undergone DBT, ultrasound and had confirmed biopsy results. We calculated sensitivity, specificity, PPV, and AUC for DBT and ultrasound. Results: In dense breasts, DBT showed significantly higher sensitivity than ultrasound (98.2% vs. 80%; Breast cancer screening using two-dimensional 2D) mammography is currently the primary standard of care . In womeD mammogrWomen with dense breasts are three to six times more likely to develop breast cancer than women with non-dense breasts ,10. ImpoDBT is becoming more widely used, and there is growing evidence that it can significantly reduce false positive diagnosis when compared to DM alone. DBT minimises anatomical noise by creating pseudo cross-sectional images of the breast, which reduces the overlap of breast tissue, allowing for improved differentiation between normal and pathological tissues, and improving visualisation of lesions . HoweverDespite the widespread use of DBT and ultrasound tools, only a few studies ,26,27 han = 144 patients), or if their breast density was not reported (n = 14 patients). After applying inclusion and exclusion criteria, data of 482 patients were selected for the study. The demographic information of these patients is summarised in Within the Australian breast screening program, women recalled for assessment may undergo clinical breast examination, mammography spot views, DBT, ultrasound, and, if necessary, a percutaneous biopsy. For the current study, a total of 640 recalled women were identified in the BreastScreen database. Women met the inclusion criteria if they had undergone both DBT and ultrasound examinations and had confirmed biopsy results . Patients were excluded from the study if their specimens were not available or inadequate, had atypical/equivocal biopsy results , equipped with a 12L4 linear array transducer (12\u20134 MHz). Colour Doppler was also used for characterisation of breast lesions. Where a lesion was detected on ultrasound, the sonographic features were described. The descriptions included indeterminate mass, cystic mass, solid mass (probably benign), solid mass and axillary lymph nodes. Lesions detected on DBT and ultrasound were also rated using the RANZCR breast imaging lesion classification scale. Information such as lesion size, lesion location, tumour grade, patient age and personal/family history of breast cancer were retrieved from the database. Both DBT and ultrasound were interpreted by one radiologist depending on the digital mammographic findings.All cases graded as equivocal, suspicious, or malignant were biopsied using needle core biopsy or FNA with image guidance, e.g., ultrasound or mammography, as part of the BreastScreen Australia program. Needle core biopsy was the procedure of choice, while FNA was limited to simple cysts and lymph nodes. Needle core biopsy provided histological confirmation of malignant status , cancer type, and tumour grade in breast malignancies.p-value \u2264 0.05 was considered statistically significant. These statistical analyses were conducted via the open-source Jamovi software (1.6.22) and R statistical software (4.0.3).Using these data, we calculated the diagnostic performance of DBT and ultrasound in terms of sensitivity, specificity, positive predictive value (PPV) and the area under the curve of the receiver operator characteristics (AUC) curve across dense and non-dense breasts. For the analysis, the RANZCR breast imaging lesion classifications of 1 and 2 were considered as negative findings, and classifications of 3, 4, and 5 were considered positive findings. For breast density, cases categorised as BI-RADS A and B were considered non-dense breasts, and those classified as BI-RADS C and D were considered dense breasts. The difference between cancer sizes in dense and non-dense breasts were compared using a Mann\u2013Whitney U test. McNemar\u2019s test was used to compare the sensitivity and specificity of DBT and ultrasound in dense and non-dense breasts. The Two Proportion Z-Test was used to compare the PPVs of DBT and ultrasound in dense and non-dense breasts. The method for paired sample design, devised by Delong et al. was emplp < 0.001). In dense breasts, the median size of the breast cancers was 1.4 cm (range: 0.4\u201310 cm), with 34.3% of the cancers \u22641 cm. In non-dense breasts, the median size of the breast cancers was 1.1cm (range: 0.3\u201313 cm); 49% of breast cancers were \u22641 cm. A total of 492 breast lesions from 482 women , who received both DBT and ultrasound followed by histopathological tests, were examined. The needle biopsy revealed 296 breast cancers and 197 benign lesions. Approximately 38% of invasive breast cancers detected were Grade 2. The sizes of breast cancers significantly differed between dense and non-dense breasts (p < 0.001). The specificity of DBT was 15.4% , significantly lower than that of ultrasound . The PPVs of DBT was 61.3% , significantly lower than that of ultrasound . DBT poorly discriminated between malignant and benign lesions , significantly lower than the discriminatory power of ultrasound, which was 0.671 (95% CI: 0.607\u20130.735), (p = 0.001).n = 107) in their mammograms, the sensitivity of DBT was 100% (95% CI: 93.4\u2013100), significantly higher than that of ultrasound . The specificity of ultrasound was 92.5% (95% CI: 82\u201398), significantly higher than DBT . The PPVs of DBT was 51% , significantly lower than that of ultrasound . Ultrasound performed better in discriminating between calcified benign and malignant lesions than DBT .For women recalled due to the presence of calcification(s) (n = 183) , DBT and ultrasound achieved similar performance in sensitivity , specificity , PPVs and AUCs .For women recalled due to other radiologic features (p = 0.14), PPV or AUC . However, the sensitivity of DBT was significantly higher than that of ultrasound .In non-dense breasts, there were no significant differences between DBT and ultrasound in specificity , the sensitivity of DBT was 100% (95% CI: 75.3\u2013100), significantly higher than that of ultrasound . The specificity of DBT was 0% , significantly lower than that of ultrasound . There were no significant differences between DBT and ultrasound in PPV or AUC .For women recalled due to the presence of calcification in their mammograms (n = 171), DBT also achieved significantly higher sensitivity than ultrasound . However, the specificity of DBT was 16.3% , significantly lower than that of ultrasound . There were no significant differences between DBT and ultrasound in PPV or AUC .For women recalled due to other radiologic features should be balanced against its disadvantages, which include low specificity and PPV, particularly in dense breasts. Given the high prevalence of calcifications in the screening population, reasonable positive thresholds are required to increase both specificity and PPV for DBT. A previous work shows that DBT improves diagnostic accuracy in suspicious calcification features, with an excellent AUC of 0.903 in dense breasts and 0.904 in non-dense breasts . We founFurthermore, we observed that ultrasound underestimated most calcification features, classifying them as RANZCR grade 1. This RANZCR rating suggests that the calcifications may have been missed or dismissed on ultrasound, particularly in dense breasts, where the sensitivity was only 37%. It has been shown that Cooper\u2019s ligaments and ductal walls may mimic calcifications, particularly in fibrocystic changes ,42, and In noncalcified lesions, DBT was comparable to ultrasound in dense breasts, but showed significantly higher sensitivity in non-dense breasts. Noncalcified lesions are mostly hypoechoic; the contrast between hypoechoic tumour and echogenic dense tissue may contribute to the high sensitivity of ultrasound in dense breasts ,44. The Recalling lesions with a low probability of cancer using thWe found that DBT changed lesion classification in 36% of cases rated RANZCR 3 on DM, with an upgrade in 22% (86% of which had breast cancer) and a downgrade in 14% (90% of which were benign). Whereas ultrasound changed the classification in 71% of lesions rated RANZCR 3 on DM, with an upgrade in 29% (68% of which had breast cancer) and a downgrade in 42% (72% of which were benign). Another interesting finding was that the benign rate of lesions where DBT and ultrasound led to no change in classification (RANZCR 3) was much higher than the cancer rate. Biopsy results revealed that around 73% (74% dense and 71% non-dense) and 77% (81% dense and 72% non-dense) of lesions assigned a RANZCR 3 by DBT and ultrasound, respectively, were benign . Thus, cThis study is not without limitations. All radiologists had prior knowledge of the original mammographic findings when interpreting subsequent DBT and ultrasound images. This factor could influence the radiologists\u2019 decision-making, leading to the increased false-positive rates for both modalities. Furthermore, our data is from a single centre. Larger multi-centre studies are needed to verify and translate the results of our study. Conversely, our data represents real-life clinical experience of using DBT and ultrasound for assessment of mammography recalled women and account for the independent double reading system practiced in Australia, which has been associated with increased breast cancer detection . To our Digital breast tomosynthesis has higher sensitivity, but lower specificity and positive predictive value than ultrasound in women with dense breasts recalled for assessment. Both DBT and ultrasound demonstrate significant limitations in the assessments of calcifications, with DBT limited in correctly characterising benign calcifications and ultrasound underestimating the malignant potential of many malignant calcifications. Most lesions rated RANZCR Grade 3 on DBT and ultrasound assessments are benign and may benefit from short interval follow-up rather than biopsy. Therefore, optimising the assessment of calcifications and lesions rated RANZCR 3 as well as the thresholds for biopsy recommendations for these lesions may reduce unnecessary biopsies and improve the management of women with such lesions."} +{"text": "Subjective age (SA) has been found to be a biopsychosocial marker of aging. This study examined the associations between SA and frequency of technology usage of older adults.Data were collected via an online survey conducted in 2020. The study analyzed participants aged 65 to 89 years resided in Japan . SA was indexed by asking participants to specify in years how old they felt. Proportional discrepancy scores (PDS) / chronological age) were calculated to indicate younger or older SAs and used as an independent variable. Participants were asked about the frequency of computer, smartphone, flip phone, and SNS use.Nearly 90% reported using computers for more than 2-3 days a week, 64.3% smartphones, 22.9% flip phones, and 36.6% SNS. Logistic regression analyses revealed that lower PDS was associated with a significantly higher frequency of smartphone use after adjusting for age, gender, education, and subjective health. No such association was found for computer, flip phone, and SNS use. Implications: Older adults who use smartphones daily may feel younger than those who do not. Since the present study was administered during the COVID-19 pandemic, the daily use of smartphones may have helped older adults stay in touch with friends and family members and obtain information they need. The use of smartphones possibly contributed to better mental health outcomes while practicing social distancing."} +{"text": "PICU inpatients are likely to be at increased risk of having unmet SRH needs due to barriers to accessing services. Since May 2018, an in-reach SRH assessment has been available to all psychiatric inpatients on ES1 ward, if referred. Analysis of referrals over 15 months identified only 24 had been made during this time.To assess the SRH needs of women admitted to ES1 PICU, the feasibility of providing a SRH in-reach clinic, and the acceptability of delivering a nurse lead referral programme.A bi-monthly SRH in-reach clinic and a nurse led SRH referral pathway were implemented on ES1 over a seven-month period. A staff training needs assessment was performed followed by training, a protocol was developed, staff attitudes were explored, and patient engagement was sought.A total of 41% (32/77) of patients were referred, which was a 29% increase. 53.1% (17/32) of the total referrals had a true SRH need, equating to a 10% increase and 22% (17/77) of all PICU admissions. 90% of referrals were made by nursing staff. A staff focus group (n15) highlighted the acceptability and perceived importance of offering SRH care in PICU, if interventions were appropriately timed and the patient\u2019s individual risk profile was considered.Results identify that SRH needs for PICU admissions are greater than previously realised. Providing a nurse led referral pathway for an SRH in-reach clinic is acceptable, feasible and beneficial for PICU patients. This project has resulted in service improvements including offering asymptomatic STI testing to all PICU admissions.No significant relationships."} +{"text": "Mental disorders are a major public health concern. Genetic and environmental factors, both reflected in family health histories, jointly contribute to the onset of mental disorders. We examined the intergenerational transmission of mental disorders using objectively-measured family health histories from three generations.A population-based cohort study was conducted using administrative healthcare databases from Manitoba, Canada. The cohort included offspring who were 18 years or older between 1977 and 2020 with linkage to 1+ parent and 1+ grandparent. Mental disorders were identified using diagnosis codes from hospitalization and outpatient physician visit records and included mood and anxiety, psychotic, and substance use disorders. Logistic regression models were mutually adjusted for mental disorder history in grandparents, parents and/or siblings in addition to offspring demographics: sex, region, decade of birth and income quintile, and comorbidity. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were estimated.Out of 125,070 individuals, 59.1% were females and 57.8% were urban residents. 41,552 (33.2%) had a mental disorder during study period and 108,682 (86.9%) had a family member with a mental disorder history. Individuals were more likely to have a mental disorder if they had a family history: mother , father , sibling , grandparent . Compared with other mental disorders, psychotic disorders had the strongest association with family history: mother , father , sibling . However, there was no association between psychotic disorders and grandparent history .We observed a strong association between mental disorders family history across three generations and the risk of the mental disorders in offspring. This association was observed for all the investigated mental disorders. This work highlights the value of multigenerational data linkage in understanding the intergenerational transfer of mental disorders."} +{"text": "The COVID-19 pandemic has been shown to cause enormous psychological burden among health care workers, including first responders. However, psychological well-being of first responders, essential in the fight against COVID-19 pandemic, has often been ignored. We performed the first meta-analysis to explore the prevalence of 1) depression, 2) anxiety, and 3) stress among first responders for medical emergencies during the COVID-19 pandemic.2, and 2I statistics were used to examine heterogeneity. Sub-group analysis was conducted to identify moderator variables.A comprehensive search was conducted in Embase, CINAHL, Web of Science, PsychInfo, PubMed, and the WHO COVID-19 database from 2020. The Freeman-Tukey double-arcsine transformation model in R-software determined the pooled prevalence and Comprehensive Meta-Analysis for associated factors of depression, anxiety, and stress with corresponding 95% confidence intervals (CI). The Cochrane Q, \u03c4We identified 765 records, from which 17 studies were included with 8096 first responders. The pooled prevalence was 31% (95% CI\u2009=\u200921%-41%) for depression; 67% (95% CI\u2009=\u200964%-70%) for mild depression, 24% (95% CI\u2009=\u200917%-31%) for moderate depression, and 16% (95% CI\u2009=\u20094%-34%) for severe depression. The pooled prevalence for anxiety was 32% (95% CI\u2009=\u200920%-44%); 60% (95% CI\u2009=\u200946%-73%) for mild anxiety, 27% (95% CI\u2009=\u200914%\u201342%) for moderate anxiety, and 14% (95% CI\u2009=\u20097%-22%) for severe anxiety. The pooled prevalence for stress was 17% (95% CI\u2009=\u20094%-34%); 58% (95% CI\u2009=\u200938%-77%) for mild stress, 22% (95% CI\u2009=\u20095%-44%) for moderate stress, and 19% (95% CI\u2009=\u20095%-37%) for severe stress. The prevalence of depression was 37% (95% CI\u2009=\u200925%-52%) for paramedics, 28% (95% CI\u2009=\u200912%-54%) for EMS personnel and 22% (95% CI\u2009=\u200913%-33%) for police. Similarly, the prevalence of anxiety was 38% (95% CI\u2009=\u200920%-60%) for paramedics, 28% (95% CI\u2009=\u200911%-53%) for EMS personnel, and 19% (95% CI\u2009=\u200910%-32%) for police. Married responders were likely at risk for depression and anxiety , while unmarried responders were less likely at risk for depression and anxiety .High prevalence of depression, anxiety, and stress during the COVID-19 pandemic among first responders for medical emergencies emphasizes the need for monitoring their psychological well-being. Early assessment and management of mild depression, anxiety, and stress among first responders are crucial in preventing progression into moderate and severe types. The COVID-19 pandemic has been a major public health concern globally, causing significant physical, physiological, and psychological negative health outcomes in all countries . First rPrevious research findings have demonstrated increased levels of depression, insomnia, anxiety, chronic fatigue, and stress among health care workers during previous epidemics of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) -8. DespiThe study protocol was registered with PROSPERO: CRD42022301213 and the reporting of the meta-analysis adhered to the Meta-Analysis of Observational Studies in Epidemiology (MOOSE) and PRISMA statement updated 2020 guidelines ,11. A coThe study inclusion criteria followed the PICOS framework: 1) population: first responders ,4, 2) exGH and KJB independently performed the data extraction from the included studies using standard data extraction forms with the following categories: author, year of publication, age, country, sample size, gender, occupation, type of first responders, study design, assessment method, and psychological outcomes .The primary outcome was pooled prevalence of depression, anxiety, and stress among first responders for medical emergencies using validated assessment tools. The secondary outcomes were associated factors including 1) being a first responder, including paramedics and EMS, 2) gender , and 3) marital status (married and unmarried).The quality of the included studies was examined using Hoy\u2019s Risk of Bias assessment tool for prevalence studies . The tooi as the proportion estimate from study i in the analysis . The pooled prevalence estimate of depression, anxiety, and stress pi was calculated as pi\u2009=\u2009ei/ni, with ei being the number of participants with depression, anxiety, and stress, and ni being the total sample size of first responders in the included studies. The model also calculates weighted pooled estimates and performs back-transformation on the pooled estimates to stabilize the within-study variance by using a binomial distribution. Publication bias was examined by Egger\u2019s Regression method and visual inspection of the funnel plots [The Freeman-Tukey double-arcsine transformation model was used to estimate the pooled prevalence rate of depression, anxiety, and stress among first responders for medical emergencies during the COVID-19 pandemic with the metaprop package in R software ,14. The el plots .The DerSimonian-Lard random and fixed-effects model in Comprehensive Meta-Analysis (CMA), Version 2.0 software was used2X-based test using Cochran's Q statistic (P\u2009=\u20090.10), \u03c42 statistic, and the 2I statistic quantified heterogeneity with a score of 25% as low, 50% as moderate, and 75% as high [Heterogeneity depression assessment and anxiety prevalence estimates were done to account for variations regarding individual and methodological factors among the included studies. Statistical heterogeneity was examined using an as high .Moderator analysis was performed among the included studies using pre-specified individual and methodological factors to account for identified statistical heterogeneity . Sub-groNo ethical approval was required for the current meta-analysis, as it used secondary data from previously published studies in which informed consent was sought from the participants.We identified 765 studies from PubMed, Web of Science, CINAHL, Embase, WHO COVID-19 database, and PsychInfo from which a total of 17 studies publisheFor the study outcomes, 14 studies examined depression, 16 studies examined anxiety, and three studies examined stress. The prevalence of depression ranged from 11.4% to 77.8%. Depression was measured using the Depression, Anxiety and Stress Scale-21 (DASS-21), Patient Health Questionnaire-9 (PHQ-9), Patient Health Questionnaire-8 (PHQ-8), Patient Health Questionnaire-4 (PHQ-4), Patient Health Questionnaire-2 (PHQ-2), Hospital Anxiety and Depression Scale (HADS), Self-Reporting Questionnaire-20 (SRQ-20), and Overall Depression Severity and Impairment Scale (ODSIS). The prevalence of anxiety ranged from 9.8% to 85.2%. Anxiety was measured using Generalized Anxiety Disorder-7 (GAD-7), GAD-2, DASS-21, HADS, PHQ-4, and Overall Anxiety Severity and Impairment Scale (OASIS). The prevalence of stress ranged from 7.6% to 33.3%. Stress was measured using DASS-21 and Impact of Event Scale-Revised (IES-R) (P\u2009=\u20090.578) and the funnel plot showed no evidence of publication bias with 67% for mild depression, 24% for moderate depression, and 16% for severe depression. We observed statistical heterogeneity among the included studies (P\u2009=\u20090.257) and the funnel plot showed no evidence of publication bias ; 60% for mild anxiety, 27% for moderate anxiety, and 14% for severe anxiety. We observed statistical heterogeneity among the included studies ; 58% for mild stress, 22% for moderate stress, and 19% for severe stress. We observed statistical heterogeneity among the included studies was significantly associated with depression, while gender and being a first responder (including paramedics and EMS personnel) were not. Married first responders were more likely to be depressed, while unmarried first responders were less likely. First responders were non-significantly associated with being depressed compared to other health care workers. Among first responders, paramedics and EMS personnel were non-significantly associated with being depressed. Considering gender, male first responders with were non-significantly associated with a reduced risk of being depressed while female first responders with were non-significantly associated with increased risk of being depressed.Similarly, the study findings showed that marital status (married and unmarried) was significantly associated with anxiety while gender and being a first responder (including paramedics and EMS personnel) were not. Married first responders were more likely to be anxious, while unmarried first responders were less likely. First responders were non-significantly associated with being anxious compared to other health care workers. Among first responders, paramedics were non-significantly associated with being anxious, while EMS personnel were non-significantly associated with reduced risk of being anxious. Male first responders with were non-significantly associated with a reduced risk of being anxious while female first responders were non-significantly associated with increased risk of being anxious (P\u2009=\u20090.0007), structured interviews had a prevalence of 33% compared to a prevalence of 16% for unstructured interviews. Study quality showed to be a significant moderator (P\u2009=\u20090.0005), as moderate quality studies had a prevalence of 43% compared to a prevalence of 20% for high-quality studies. Regarding sample size (P\u2009=\u20090.006), studies with sample sizes <200 had a prevalence of 39% compared to a prevalence of 21% for studies with sample sizes \u2265200. Regarding study type (P\u2009=\u20090.069), web-based studies had a prevalence of 34% compared to a prevalence of 18% for interview-based studies. The country status prevalence rates (P\u2009=\u20090.825) were 28% for high income, 31% for middle income, and 29% for low-income countries. The prevalence rates by setting (P\u2009=\u20090.719) were 31% for urban and rural and 27% for urban settings. Regarding assessment tools (P\u2009=\u20090.200), studies that used Patient Health Questionnaire had a prevalence of 34% compared to a prevalence of 23% for studies that used other types of assessment tools. Concerning the number of cases and mortality rate (P\u2009=\u20090.859), top-5 countries had a prevalence of 31% compared to a prevalence of 29% for non-top-5 countries, respectively.The results of subgroup analysis for the prevalence of depression demonstrated that type of interview, study quality, sample size, and study type were significant moderator variables while country status, setting, and assessment tool were not. Regarding the type of interview (P\u2009=\u20090.0012), structured interviews had a prevalence of 33% compared to a prevalence of 13% for unstructured interviews. Study quality showed to be a significant moderator (P\u2009=\u20090.014), moderate quality studies had a prevalence of 42% compared to a prevalence of 18% for high-quality studies. Regarding sample size (P\u2009=\u20090.0005), studies with sample sizes <200 had a prevalence of 48% compared to a prevalence of 17% for studies with sample sizes \u2265200. Regarding study type (P\u2009=\u20090.293), web-based studies had a prevalence of 26% compared to a prevalence of 44% for face-to-face studies. The country status prevalence rates (P\u2009=\u20090.921) were 30% for high-income and 29% for middle-income and low-income countries. The prevalence rates by setting (P\u2009=\u20090.847) were 29% for urban and rural and 31% for urban. For the assessment tool (P\u2009=\u20090.228), studies that used GAD questionnaire had a prevalence of 31% compared to a prevalence of 22% for studies that used other types of assessment tools. Accounting for the number of cases and mortality rate (P\u2009=\u20090.675), top-5 countries had a prevalence of 27% compared to a prevalence of 32% for non-top-5 countries, respectively , and work-related factors .The current meta-analysis shows a substantial higher prevalence of depression, anxiety, and stress among first responders during the COVID-19 pandemic. Early assessment and management of mild depression, anxiety, and stress should be encouraged to prevent the development of moderate and severe types in order to ensure psychological well-being among first responders. Essential support initiatives and interventions for the management of depression, anxiety, and stress among first responders should be developed to prevent short-term and long-term consequences of these negative psychological outcomes. Future high-quality studies with larger sample sizes reporting individual-related and work-related factors should be encouraged to provide a comprehensive view into the nature of depression, anxiety, and stress among first responders."} +{"text": "With increasing awareness and reduction of stigma associated with Mental Health issues, referrals to services are increased, pushing specificity of commissioning and therefore declining patients of services when referrals are inadequate. Standards would be improved by better inclusion of information necessary for the Single Point of Access process (SPOA) in the Bolsover Community Mental Health Team (CMHT) to make prompt, effective decisions on allocating care.A Quality Improvement project in a Mental Health Team was devised to improve standards, and acceptance rate, of appropriate referrals to the Bolsover CMHT from General Practitioners (GPs). This would encourage GPs to refer patients whose mental health difficulties do not meet CMHT thresholds to alternative services. A higher acceptance rate and lower rejection rate would indicate that the proportion of suitable referrals had increased.Using the Plan, Do, Study, Act (PDSA) model, Driver diagrams were used to create a template with the crucial information necessary for GP referrals to psychiatry/SPOA. Data were collected to check aims of the referral, sufficient information of the presenting complaint, personal & family history, safety concerns, protective factors, comorbidities, medication and substance misuse. The outcome of each referral was recorded and categorised as either Community Psychiatric Nurse Assessment, Outpatient Appointment, Referral Rejected, Referred Elsewhere or No Patient Response.All referrals in September and October 2021 were analysed to assess whether enough information had been included for each variable. The September and October data were compared to check if the template had been associated with improved quality of referrals.Pre-template, 17.4% of referrals were accepted, 13.0% received a SPOA assessment, 17.4% were rejected, 39.1% were re-referred elsewhere and 21.8% did not respond to the CMHT. After the template was circulated, 28.0% were accepted, 36.0% received a SPOA assessment, 4% received joint Doctor-SPOA care, 8% had a medication review and 12% were waiting for an MDT decision when data were analysed. The results for SPOA assessment and rejection were statistically significant (p < 0.05), while results for other outcomes were not.Information on presenting complaint , personal history and aims increased, while other information did not change in a statistically significant manner.The template led to an increased proportion of accepted referrals and a decreased proportion of rejected referrals. However, information on variables did not necessarily improve in the same manner. The template is useful to improve decision-making in SPOA."} +{"text": "Headache and migraine adverse events are common concerns in the administration of intravenous immune globulins (IVIG). Trials of IVIG for primary immunodeficiency (PI) are typically small and have reported headache and migraine data inconsistently.\u00ae 5% and 10% in PI . The trials were pooled in a retrospective analysis that included two 12-month open-label non-comparative trials of the 5% IVIG product and one 6-month open-label crossover bioequivalence trial comparing the 5% IVIG and 10% IVIG products. The population included adult and pediatric patients, who received IVIG infusions of 300-800 mg/kg/infusion every 21 or 28 days using a 15-minute rate escalation protocol.We analyzed headache and migraine in pooled data from three pivotal trials of GammaplexIn total, 1482 infusions were administered to 123 patients, with 94.6% of infusions achieving the maximum infusion rate. At least one product-related headache was reported in 6.1% (90/1482) of infusions. At least one product-related migraine was reported in 0.5% (7/1482) of infusions. Headache rates were higher for adults vs pediatric patients, females vs males, and 21-day vs 28-day dosing schedules, but were similar for the 5% and 10% IVIG products. Most headaches and migraines occurred during or within 72 hours of the infusion. Rates decreased after the first few infusions.Patients receiving this IVIG product on a 15-minute rate escalation protocol had low rates of headache and migraine for both the 5% and 10% formulations. IVIG \u00ae (immune globulin intravenous [human]) is an intravenous immune globulin available in both 5% and 10% formulations. In the United States, both formulations are indicated for treatment of patients with primary immunodeficiencies (PI) and chronic immune thrombocytopenic purpura (ITP), and have been investigated in four pivotal clinical trials, three in PI and one in ITP for the treatment of PI. This retrospective pooled analysis did not directly engage any patients. All trials included in the analysis were approved by an institutional review board/ethics committee at each study center and obtained written informed consent from each participant to participate in the study. Participants from the included studies agreed to have their results published.2.1p-values are descriptive.Infusion and adverse event data were pooled across three Gammaplex studies . Summaries of infusion protocol were generated to identify the proportion of infusions following the 15-minute rate escalation protocol and reaching the maximum infusion rate. Adverse events were documented based on direct observation during each infusion, interviews with the patient, and/or diary entries. Summaries of tolerability were generated to identify the proportion of infusions associated with product-related AEs. Product-related AEs were defined as those considered possibly, probably, or definitely related to administration of the product by the investigator. Infusion-associated AEs were defined as those occurring during or within 72 hours of the end of the infusion, specifically headaches and migraines. When assessing infusion protocol and tolerability, 95% confidence intervals for the proportion of infusions were calculated using the Clopper-Pearson (exact) method. Differences in tolerability across product formulation, dose categories, infusion order, and PI diagnosis were summarized using a 95% confidence interval for difference of proportions. All analyses were produced using SAS 9.4. All Exploratory subgroup analyses were conducted by gender , age (adult vs pediatric), product formulation (5% IVIG vs 10% IVIG), infusion schedule (every 21 days vs every 28 days), and dose tertile . Exploratory bivariate analyses were conducted for age and product formulation, age and gender, and gender and product formulation. Data were analyzed both by infusions and by patients to evaluate the extent to which a subset of patients accounted for headache and migraine events.2.2In all trials, infusion of the IVIG product was started at an initial infusion rate for 15 minutes , then advanced every 15 minutes if tolerated to a maximum of 0.08 mL/kg/min, using the protocols shown in 3The analysis included all Gammaplex infusions administered during the PI clinical trials (1482 infusions administered to 123 patients). Of these, 1234 infusions of the 5% IVIG formulation were administered to 108 patients and 248 infusions of the 10% IVIG formulation were administered to 47 patients. Both adult and pediatric patients participated in the 5% and 10% studies. Key patient, disease, and treatment characteristics for each trial are summarized in 3.1p\u2009<\u20090.0001), higher for males than for females , higher for the 5% IVIG formulation than for the 10% IVIG formulation , and lower for patients receiving infusions every 21 days than for patients receiving infusions every 28 days . Although statistically significant, these differences are likely explained by large sample sizes within groups and are unlikely to represent clinically meaningful differences. Breaking down the results by age and product formulation, the probability of achieving the maximum rate was not different for the 5% and 10% IVIG formulations in adults , but was higher for the 5% formulation than the 10% formulation in pediatric patients .The maximum infusion rate was achieved in 94.6% (1402/1482) of infusions Figure\u00a013.2p\u2009=\u20090.0140), lower for males than females , similar for the 5% IVIG product and the 10% IVIG product , and higher for patients receiving infusions every 21 days vs patients receiving infusions every 28 days .Product-related, infusion-associated headache was reported in 6.1% (90/1482) of all infusions Figure\u00a02p\u2009=\u20090.8702) and for pediatric patients . In the age-by-gender breakdown, infusions with headache were less likely with adult males than adult females , but rates were similar for pediatric males and pediatric females .In the age-by-product breakdown, the percentage of infusions with at least one product-related, infusion-associated headache was similar for the 5% IVIG product and the 10% IVIG product in adults , lower for males than females , similar for the 5% IVIG product and the 10% IVIG product , and similar for patients receiving infusions every 21 days vs patients receiving infusions every 28 days .Product-related, infusion-associated migraine was reported in 0.5% (7/1482) of all infusions Figure\u00a023.3p\u2009=\u20090.9999). Most adult and pediatric patients did not report a headache . Adults reported headache in 72 infusions. Four infusions were associated with two headaches each, for a total of 76 headaches. Pediatric patients reported headaches in 18 infusions. One infusion was associated with two headaches, for a total of 19 headaches.Headache and migraine were reported by 28.5% (35/123) and 4.1% (5/123) patients, respectively. The percentage of patients reporting at least one product-related headache was similar for adults and pediatric patients , showed a non-significant trend toward higher rates with the 5% IVIG formulation than the 10% IVIG formulation , and higher for patients receiving infusions every 21 days vs patients receiving infusions every 28 days . Breaking down the results by age and product formulation, the percentage of patients reporting at least one product-related headache was non-significantly larger for the 5% IVIG formulation than for the 10% IVIG formulation in adults , and for pediatric patients . Adult males were less likely to report at least one headache than adult females , but rates were similar for pediatric males vs pediatric females . The percentage of patients reporting at least one headache did not differ markedly across dose tertiles .The percentage of patients reporting at least one headache was lower for males than females of patients. Of the seven reported migraines, six were reported by four adult female patients, with four migraines associated with infusion of the 5% IVIG formulation and two with the 10% IVIG formulation. The remaining migraine was reported by one male pediatric patient who was receiving the 10% IVIG formulation. The percentage of patients reporting at least one product-related migraine was significantly lower for males than females and all migraine events occurred within 72 hours of the start of the infusion Figure\u00a034Headache is clearly associated with IVIG therapy for PI, but not with PI itself. In this retrospective analysis, we analyzed pooled data from three clinical trials of a single IVIG agent to confirm and extend our understanding of headache and migraine associated with IVIG infusions. Our analysis provides a systematic evaluation of infusion times and rates of headache and migraine in a large population of patients receiving IVIG treatment for PI. Pooled analyses can be used to reaffirm data present in individual trials or to understand new concepts that may be better represented in a larger data set \u201337. To oAlmost all patients achieved the maximum infusion rate specified in the product labeling, utilizing an infusion protocol with 15-minute rate escalation increments. Recent trials of other IVIG products have reported achieving per-protocol infusion rates in >90% of infusions, but with longer rate escalation increments , 24. In The observed rates of product-related headache and migraine occurred with 94.6% of patients achieving the maximum infusion rate, and use of a 15-minute rate escalation protocol. To place these results in context, headache rates reported in recent studies of IVIG in PI range from 2% to 22% on a per-infusion basis, and from 8% to 50.8% on a per-patient basis , 32, 38.Despite short (15-minute) escalation increments in the infusion protocol, rates of product-related headache were not significantly different for the 5% and 10% formulations in the entire population, the adult subgroup, and the pediatric subgroup, whether calculated at the infusion level or on a per-patient basis. In contrast to our results, 10% IVIG formulations have historically been associated with increased adverse event rates compared to 5% IVIG formulations , 6, 11. With IVIG therapy, first doses have been associated with more reported AEs than subsequent doses , 14, 26.Product-related headache and migraine were concentrated in a minority of patients, and only a small proportion of the total number of infusions were preceded with premedications. This finding should serve as a reminder that many patients may tolerate these infusions without difficulty and without the need for premedications. Perhaps greater emphasis on selecting patients most at risk for AEs would result in more judicious use of premedication.Rapid IVIG infusion is generally considered to be a risk factor for IVIG-related headache . One retThis pooled analysis is limited by the open-label design of the studies that were pooled for the analysis, the retrospective nature of the analysis, and the relatively small number of patients included, although the data set includes a large number of infusions. The pediatric patients included in trials GMX04 and GMX07 may not have reported their headache and migraine complaints appropriately. Lack of randomization increases the risk of bias in the subgroup analyses. In addition, the data are drawn from clinical trials rather than routine practice. Because of these limitations, the results should be considered suggestive rather than conclusive. However, the information presented here may help clinicians mitigate headache and migraine AEs in patients receiving IVIG infusions for PI.In summary, this retrospective data analysis found in patients being treated with IVIG for PI, rates of headache (6.1%) and migraine (0.5%) were low for adult and pediatric patients and for both the 5% and 10% formulations. A large majority of infusions (94.6%) achieved the maximum infusion rate. Either formulation of this IVIG product can be administered using a 15-minute rate escalation protocol without excessive rates of headache or migraine.The datasets presented in this article are not readily available because the datasets generated during and/or analyzed during the current study are not publicly available because they containing information that could compromise research participant privacy/consent. Reasonable requests as appropriate and permissible will be considered by the corresponding author. Requests to access the datasets should be directed to Kim Clark, Kim.Clark@bpl.co.uk.The studies involving human participants were reviewed and approved by the institutional review board/ethics committee at each study center. The 3 trials each involved multiple centers. Participants from the included studies agreed to have their results published. Written informed consent to participate in this study was provided by each participant or the participants\u2019 legal guardian/next of kin as applicable and appropriate.EW, KC, and BG contributed substantially to data collection, analysis, manuscript writing, and editing. ME conducted data analysis. All authors contributed to the manuscript and approved the submitted version."} +{"text": "This cross-sectional study examines racial and ethnic disparities in health insurance coverage among Black and Hispanic adults vs White adults aged 60 to 64 years. We assessed potential for expanding Medicare to reduce existing coverage disparities among Black and Hispanic adults vs White adults aged 60 to 64 years. We hypothesized that sizeable coverage disparities remain, particularly among adults with low income in Medicaid nonexpansion states, which could be reduced through an expansion of Medicare.One reform under consideration by Congress, termed Medicare-for-more, would lower the age threshold for Medicare to age 60 years from 65 years.STROBE) reporting guideline.We analyzed the 2019 American Community Survey, which reports demographic, residential, and insurance information. We used self-reported race and ethnicity to categorize respondents as Black, Hispanic, or White. The University of Pittsburgh institutional review board waived study review and informed consent because this analysis used deidentified data. We followed Strengthening the Reporting of Observational Studies in Epidemiology were female, 12.3% were Black, 11.6% were Hispanic, and 76.1% were White. Among adults aged 60 to 64 years who were uninsured in 2019 across all states and income levels, 6.9% were Black, 15.1% were Hispanic, and 7.0% were White. Uninsurance among Black adults exceeded 10% in 17 states, and among Hispanic adults it exceeded 10% in 38 states .P\u2009<\u2009.001) (P\u2009=\u2009.007). We did not detect significant Black-White coverage disparities in expansion or nonexpansion states.In Medicaid expansion states, 18.0% of Hispanic adults and 11.5% of White adults aged 60 to 64 years with incomes less than 138% FPL were uninsured, representing a coverage disparity of 6.6 percentage points . In none4 Evidence from the ACA suggests that broader coverage in middle age may yield health gains, including reductions in mortality among low-income adults.5Our results suggest potential for lowering the threshold for Medicare to 60 years of age to reduce existing coverage disparities among adults aged 60 to 64 years, particularly among low-income Hispanic adults in nonexpansion states. These findings are consistent with a recent study that found reductions in coverage disparities among adults acquiring coverage at Medicare\u2019s current age threshold.6 Thus, our results may conservatively reflect the current extent of coverage disparities among older adults.One limitation of our analysis is that it uses 2019 data, the most current, which predates the COVID-19 pandemic. Emerging evidence suggests coverage disparities during the pandemic widened in nonexpansion states."} +{"text": "Falls are one of the major health issues faced by older adults, and they can result in physical harm, eventual loss of independence, and even death. Herein, we investigated the prevalence, alongside the main risk factors and resulting injuries, of falls among older adults.We employed a descriptive cross-sectional approach. Data were collected between February and July 2021 from 403 older adults aged 60 years or above via an online self-reported questionnaire. Basic activities of daily living (BADLs) and instrumental activities of daily living (IADLs) were also recorded.The prevalence of falls among community-dwelling older adults was 47.4%. Among those who had experienced a fall, 36.2% incurred injuries, 25.3% had fractures, and 23.1% required walking aids. Age between 95-104 years, female sex, participants on anti-hypertensive medications, history of hip or knee replacement surgery, and presence of a caregiver, were significantly more likely to have had a previous history of falls (p < 0.05). Furthermore, having a previous history of stroke, osteoporosis, lower limb weakness, dizziness, using wheelchairs as walking aids, and living with the fear of stumbling or slipping were significantly associated with history of previous falls (p < 0.05).The prevalence of falls is high among community-dwelling older adults in Jeddah. Physicians should identify older adults with higher falling risk and provide them with appropriate interventions. Public health strategies could significantly reduce falls and fall-related injuries in older adults. KSA:Kingdom of Saudi ArabiaBADLs:Basic activities of daily livingIADLs:Instrumental activities of daily livingSPSS:Statistical Package for the Social Sciences\u03c72:Chi-squared testFalls are one of the most serious health concerns faced by older adults worldwide. A fall is defined as an unintentional incident that results in an entity coming to rest on the ground or floor or other lower-level surface.3Multiple risk factors have been found to increase the risk of falls among older adults. These factors include chronic conditions such as cardiac disease and diabetes.Falls could also be linked to a variety of environmental hazards such as inappropriate styles of steps, poor lighting, clutter, slippery floors, and movable mats.12The financial burden of falls on health care and social systems is significant.15Multiple studies have evaluated the prevalence and associated risk factors of falls among older adults. However, to our knowledge, no such studies have been carried out in Jeddah, Saudi Arabia. Therefore, the objectives of this study were 1) to determine the prevalence of falls among community-dwelling older adults aged \u2265 60 years in Jeddah and 2) to identify the main factors associated with falls.This cross-sectional study was conducted in Jeddah, Saudi Arabia, between February and July 2021. Older adults aged 60 years or above were surveyed for this study. A data collection Form was developed as a tool for questioning the participants. This was a four-page questionnaire consisting of 43 questions grouped under three main sections: demographic questions , health status-related questions , and fall-related questions .The Katz Index was used to evaluate independence in the Basic Activities of Daily Living (BADL). It is a reliable tool for evaluating the functional status of older adults.17The Lawton Scale was used to evaluate independence in Instrumental Activities of Daily Living (IADLs). It is a standardized, validated tool used to determine the ability of older adults to care for themselves.19Participants\u2019 data were collected using a standardized anonymous questionnaire, which was administered online in an electronic form to older adults living in Jeddah city. The sample size was calculated using the Roasoft online calculator. The calculation was based on a 50% response distribution, 5% margin of error and 95% confidence interval. The calculated sample size was 384 patients. Data were analysed using Statistical Packages for the Social Sciences (SPSS) version 25 software.Qualitative data are expressed as frequencies or percentages, and the Chi-squared test (\u03c72) was used to analyze the relationship between variables. Quantitative data are expressed as mean with standard deviation (mean \u00b1 SD), and the Mann-Whitney test was used to analyze non-parametric variables. Binary logistic regression analysis was used to determine the independent predictors (risk factors) of falls among participants . A p-value of < 0.05 was considered statistically significant.The study was conducted in accordance with all local regulations and followed the principles of the Helsinki declaration. Informed consent for data collection was sought from participants before they answered the questions. Ethical approval was obtained from the Research Ethics Committee of King Abdulaziz University (Ref. No.: 51-21).A total of 403 participants completed our questionnaire. The greatest proportion of the participants aged 60\u201364 years (48.6%), were female (67.2%), and had a Saudi nationality (94.5%). 2.Around 7.2% of the participants smoked cigarettes or shisha, 53.1% took between 1\u20134 drugs daily, and the most common medications taken were vitamin D (65.5%), anti-hypertension (HTN) (52.4%), and anti-diabetic medications (51.1%). About one-third (30.3%) of the participants had past surgical histories: mostly cataract surgery (40.2%), followed by orthopaedic surgery (17.6%) and heart procedures (11.4%). About 45% of the participants had a caregiver, and 82.4% owned their own residence. Most participants (66.7%) lived on a high floor, 38% had an elevator, and 40.4% were overweight with a mean body mass index (BMI) of 29.46 \u00b1 6.45 kg/mIn terms of functional status, more than 70% of the participants were able to dress and feed themselves, count, use the toilet independently, bathe, transfer, make telephone calls, and take their medication by themselves. Only 27% participated in exercises regularly; among them, 23.1% were able to walk, 15.1% participated in daily exercises for \u2265 30 minutes, and 8.4% exercised \u2265 5 times weekly. The most prevalent chronic diseases included poor vision (53.8%), osteoarthritis (51.9%), back pain (51.6%), HTN (50.6%), and diabetes mellitus (50.4%). Most participants (64.5%) did not use walking aids, and 20.8% used walking sticks.In regard to falls, 47.4% of the participants had a previous history of falls; 28.5% of them had fallen only once . As illuThe female sex, being 95\u2212104 years old, having a middle educational level, and having a household income less than SAR5000 were all associated with a significantly higher risk of having a previous fall (p < 0.05). Participants on anti-hypertensive medications, who have a surgical history of hip or knee replacement surgery, who have a caregiver, and who have a rented residence were significantly more likely to have had a previous history of falls (p < 0.05).In relation to function, participants who were able to bath, do shopping, do transportation, to cook food, to take medication, do housework, laundry, and accounting were significantly less likely to have history a previous fall (p < 0.05). Furthermore, having a previous history of stroke, osteoporosis, lower limb weakness, dizziness, using wheelchairs as walking aids, and living with the fear of stumbling or slipping were significantly associated with a history of previous falling (p < 0.05). However, a non-significant association (p > 0.05) was found between previous history of falls and other chronic diseases and the possibility to perform other tasks or practice physical exercises, irrespective of the duration, frequency, or type of exercise.The binary logistic regression analysis was used to determine the independent predictors (risk factors) of falls among participants. It showed that age between 95\u2013104 years, the female sex, recurrent stumbling or slipping, living in a rented residence, the presence of a caregiver, and the inability to use transportation devices were all independent predictors (risk factors) of fall among the participants .Falls are common among older adults and could lead to serious injuries, significantly impacting morbidity and mortality.21The results of the present study showed that the prevalence of falls among older adults in Jeddah was 47.4%. Similar studies have shown that 49.9% and 42.4% of older adults in Saudi Arabia and Canada had a history of falls, respectively.22Remarkably, a variation in prevalence rate was reported in multiple countries, 34%, 34%, 32%, 28%, 27.6%, 19%, 16%, 11%, and 4% in Canada, Qatar, USA, England, Brazil, Hong Kong, Japan, China, and Malaysia, respectively.In our study, 51.3% of female participants had a history of falls compared to 39.4% of older males. This finding is consistent with that of a study in Unaizah, Saudi Arabia (KSA), which showed a prevalence of 34.5% and 28.5% among older females and older males, respectively. The higher prevalence in females could be due to lack of education and low-income level, both of which have been shown to have a significant correlation with a history of falling.24In this study, chronic diseases were found to be a risk factor for falls, as demonstrated in previous studies.25Not surprisingly, participants with lower-limb weaknesses in this study had a significantly higher risk of falling. These results are in line with previous studies.25The present study also revealed a significant association between a hip or knee replacement surgery and risk of falls. These results concurred with those observed in earlier studies.Moreover, older age was found to be a factor associated with falls in our study, as reported in several previous studies carried out in developed countries.Additionally, the present study revealed a high prevalence of falls among older adults with a low educational level. This finding is also consistent with the results of other studies.It was also found that participants who lived in a rented home had a considerably greater risk of falling (p<0.05). This finding matches the results of a study in Riyadh, KSA.9First, we used a one-year recall period, which is susceptible to inducing recall bias. Second, other associated factors, such as postural hypotension, cognitive impairment, and malnutrition, were not included in our survey; it may be useful to evaluate these other factors in future studies.Falls were highly prevalent among community-dwelling older adults in Jeddah. Advanced age, female sex, use of anti-hypertensive medications, history of hip or knee replacement surgery, having a caregiver, previous history of stroke, osteoporosis, lower limb weakness, dizziness, using wheelchairs as walking aids, and living with the fear of stumbling or slipping were significantly associated with falls. These findings corroborate the findings of a previous study conducted in Riyadh.SHA, WHA, and RSA conceptualized and designed the study, developed the questionnaire, and drafted the manuscript. They also assisted in data collection and shared in statistical design and analysis.NMA and RDA participated in the study planning and assisted in data collection and entry.RAG and WAA helped with data interpretation and manuscript editing.SHA, RAG and WAA were responsible for the overall accuracy of this project.All authors contributed to the final revision of the manuscript and approved it for publication."} +{"text": "Complex skin disorders including Stevens-Johnson Syndrome (SJS) / Toxic Epidermal Necrolysis (TEN), Ritter's Disease , and Erythema Multiforme are uncommon, but result in significant injury to pediatric patients. Skin necrosis and desquamation occurs, which in some cases affects mucosa. Gynecologic, ophthalmologic, and dermatological complications also occur. The purpose of this work is to describe epidemiology and management trends in these cases.Records were reviewed for all pediatric patients with skin disorders from 2006 - 2019 to evaluate trends in occurrence, age, length of stay, survivability, types of consultants, causative agent, and wound care strategies.One-hundred percent of pediatric patients were transferred from other hospitals for definitive management by the burn service. The incidence in pediatric patients was 21% compared to 79% in adults. Males were most often affected at 67% compared to 33% in females. The age range was 2-17 years, with an average of 9.2 years. The type most frequently seen was SJS/TEN at 60% of the cases. The total body surface affected ranged from 10-95%. Management of wounds commonly required operative management for dressing changes in children with large body surface area involvement, in addition to ophthalmologic and gynecologic procedures in patients with mucosal involvement. In the subset of patients with SJS / TEN, 100% had ophthalmology consults and 50% were seen by gynecology. The average hospital length of stay was 11.3 days. All children survived.Complex skin disorders in pediatric patients require a multidisciplinary team approach to care and wound management and benefit from burn service care. Early transfer is beneficial in order to definitively diagnose the specific disorder and prioritize strategies in care such as nutrition, wound care, and psychosocial support."} +{"text": "The meta-analysis showed that malaria and leptospirosis co-infections occurred by chance . The prevalence of malaria in leptospirosis co-infection among febrile patients in the included studies was low. Co-infection was likely to occur by chance. However, as clinical symptoms of leptospirosis patients were non-specific and not distinguishable from symptoms of malaria patients, clinicians caring for febrile patients in an area where those two diseases are endemic should maintain a high index of suspicion for both diseases and whether mono-infections or co-infections are likely. Recognition of this co-infection may play an important role in reducing disease severity and treatment duration.Malaria and leptospirosis are important cosmopolitan infections that have emerged with overlapping geographic distribution, especially in tropical and subtropical regions. Therefore, co-infection with malaria and leptospirosis may occur in overlapping areas. The present study aimed to quantify the prevalence of malaria and leptospirosis co-infection among febrile patients. The association between malaria and leptospirosis infections was also investigated. Relevant studies that had reported malaria and leptospirosis co-infection were identified from PubMed, Scopus, and Web of Science. The risk of bias of the studies was assessed using the Joanna Briggs Institute (JBI) Critical Appraisal Tool. The pooled prevalence of malaria and leptospirosis co-infections among febrile patients and the pooled prevalence of leptospirosis infection among malaria patients were estimated using random effect models. The association between malaria and leptospirosis infection among febrile patients was estimated using random effect models. The outcomes of each study were shown in a forest plot in point estimate and 95% confidence interval (CI). Heterogeneity among the included studies was assessed using Cochran\u2019s Q and quantified using I-squared statistics. For leptospirosis, subgroup analyses of countries, diagnostic tests, and participants\u2019 age groups were performed to specify prevalence in each subgroup. Publication bias was assessed by funnel-plot visualization. Of the 2370 articles identified from the databases, 15 studies met the eligibility criteria and were included for qualitative and quantitative syntheses. Most of the included studies were conducted in India , Thailand , and Cambodia . Most of the enrolled cases were febrile patients (5838 cases) and malaria-positive patients (421 cases). The meta-analysis showed that the pooled prevalence of malaria and leptospirosis co-infection (86 cases) among febrile patients was 1% (95% CI: 1\u20132%, I Plasmodium spp.: P. falciparum, P. vivax, P. malariae, P. ovale curtisi, P. ovale wallikeri, and P. knowlesi [P. cynomolgi might be a cause of malaria in humans in Cambodia [P. falciparum infection; however, a lesser proportion of severe malaria could also be caused by other Plasmodium spp. [Malaria in humans is caused by one of six knowlesi . Recent Cambodia , ThailanCambodia , and MalCambodia ,5,6. TheCambodia . SymptomCambodia . If leftium spp. ,11,12,13ium spp. ,15.Leptospira [Leptospirosis is one of the most important zoonotic diseases caused by pathogenic species of the spirochete bacteria ptospira ,17. Thisptospira ,19. Nowaptospira ,21. Prevptospira . At leasptospira . The iniptospira ,23. Thisptospira . Therefoptospira . Severe ptospira ,19. Tranptospira . Howeverptospira ,25. RiskMalaria and leptospirosis are important cosmopolitan infections that have emerged with overlapping geographic distribution, especially in tropical and subtropical regions . TherefoThe protocol of this systematic review was registered at PROSPERO with ID CRD42021255898. Reports of the systematic review followed the PRISMA 2020 statement .Potentially relevant articles were searched in PubMed, Scopus, and Web of Science by using keyword combinations specific for malaria and leptospirosis, as provided in All types of study designs that reported malaria and leptospirosis were considered. Studies were selected according to the following eligibility (inclusion/exclusion) criteria: (1) Cross-sectional studies, longitudinal studies, case-control studies, cohort studies, and observational studies were included. The inclusion of all types of studies allowed us to maximize the number of included studies to represent the pooled prevalence of co-infection globally and (2) only human studies with malaria and leptospirosis infections by laboratory diagnosis, such as microscopic diagnosis, culture, molecular diagnosis, rapid diagnostic test (RDT), and serology, were included. The following studies were excluded: diagnosis of malaria and leptospirosis infection by clinical diagnosis only , animal studies, in vitro studies, assay performance, review articles, case reports, and case series. The participant/population (P), outcome of interest (I), and contexts (Co) were applied to the key question.Study selection was based on the eligibility criteria. Articles were retrieved from the databases using the search strategy. All articles were imported into Endnote software for management. All studies were reviewed by two independent authors (MK and WM). First, duplicates were screened and removed. Second, the titles and abstracts of the articles were reviewed. Unrelated articles were excluded and then the remaining articles were examined for full texts. Studies that met the eligibility criteria were included and those that did not were excluded, with the explained reasons. For any discrepancies between the two authors during study selection, another author (PW) served as a third author to create consensus.The two authors (MK and WM) extracted data from each included study to the pilot Excel datasheet before data analysis. The following data were extracted: name of the first author, year of publication, country, year study conducted, study design, characteristics of participants enrolled, age, gender, number of patients with co-infection, number of patients with malaria, number of patients with leptospirosis, diagnostic test(s) for malaria, and diagnostic test(s) for leptospirosis. The data were cross-checked by another author (PW) to assure the accuracy of the method.The risk of bias in the studies was assessed independently by two reviewers (MK and WM) according to the Joanna Briggs Institute (JBI) Critical Appraisal Tools for cross-sectional study . Any disThe data extracted from all of the included studies were narratively synthesized to provide a qualitative account of the data extracted from the included studies. The qualitative syntheses involved an explanation of the characteristics of the included studies, including study design, participants, study location, age, number of patients with co-infections, number of patients with malaria, number of patients with leptospirosis, and diagnostic tests for both malaria and leptospirosis. The quantitative synthesis involved the use of statistical analysis to pool the outcome. The first outcome of this study was the pooled prevalence of malaria and leptospirosis co-infections among febrile patients. The secondary outcome was the pooled prevalence of leptospirosis infection among malaria patients. The tertiary outcome was the pooled odds of malaria and leptospirosis co-infections among febrile patients. All outcomes were estimated using the random effect models and assumed that heterogeneity existed among the included studies. The outcomes of each study were shown in the forest plot in the point estimate and their 95% confidence interval (CI). The summarized outcome of interest was also shown in the forest plots. The heterogeneity among the included studies was assessed using Cochran\u2019s Q and quantified using I-squared statistics. In the presence of substantial heterogeneity, the outcomes were pooled using the random effect model. For leptospirosis, the subgroup analyses of countries, diagnostic tests, and participants\u2019 age groups were performed to specify the prevalence in each subgroup. Publication bias was assessed by visualizing a funnel plot. The meta-analysis was conducted using Stata ver. 14 .Overall, 2370 articles were retrieved from three databases: 542 from PubMed, 1232 from Scopus, and 596 from the Web of Science. After duplicates were removed, 1487 studies were screened for titles and abstracts. After 247 non-relevant articles were excluded, 125 articles were examined for full texts. Of the 125 articles examined for full text, 111 articles were excluded for the following reasons: 55 had no data on co-infection of malaria and leptospirosis, 25 had no malaria cases, 13 were review articles, 9 were case reports or case series for malaria and leptospirosis, and 9 had no leptospirosis cases. Fourteen articles ,39,40,41Fifteen studies included in the present study were prospective observational studies ,34,37,41The quality of the included studies was assessed using the checklist see for anal2: 85.2%), 1% , and 6% (95% CI: 3\u201312%), respectively , 0% in Jamaica (95% CI: 0\u20131%), 1% in Colombia (95% CI: 0\u20135%), and 1% in India . Overall, the pooled prevalence of malaria and leptospirosis co-infection (86 cases) among febrile patients was 1% , 2% in Tanzania (95% CI: 1\u20134%), 1% in Thailand .2: 0%), 9% , 9% (95% CI: 4\u201316%), 6% (95% CI: 3\u201312%), and 8% (95% CI: 5\u201312%), respectively , 11% in Thailand , 9% in Cambodia (95% CI: 7\u201311%), 8% in Tanzania (95% CI: 4\u201316%), 7% in Jamaica (95% CI: 4\u201312%), and 4% in Venezuela (95% CI: 2\u20138%) , 25% in Colombia (95% CI: 5\u201370%), 12% in India .2: 99.3%), 7% in adults , and 24% in all age groups . Overall, the pooled prevalence of leptospirosis infection (186 cases) among malaria patients was 13% .The odds of malaria and leptospirosis co-infections (86 cases) among febrile patients (5838 cases) were estimated using the data of 10 studies ,39,40,41Publication bias among studies that included analysis of the pooled prevalence of leptospirosis infection among malaria patients was performed using funnel plot, Egger\u2019s test, and Contour enhanced funnel plot. The funnel plot between effect size and standard error of the ES (seES) showed the asymmetrical distribution of the outcomes of two studies .p: 0.07, coefficient: 2.75, standard error: 1.38, t; 1.99). The contour-enhanced funnel plot showed missing studies in non-significant areas (p > 0.01) indicating that the cause of funnel plot asymmetry may more likely be due to publication bias . However, the subgroup of countries showing highest co-infection was in Bangladesh (5%) and lower in Tanzania (2%), Thailand, Jamaica, Colombia, and India. In addition, the pooled prevalence of leptospirosis infection among malaria patients was high (13%). However, the heterogeneity of the prevalence was subsided by the subgroup of countries that showed the highest prevalence in Bangladesh (75%) and lower in Colombia 25%), India (12%), Thailand (11%), Cambodia (9%), Tanzania (8%), Jamaica (7%), and Venezuela (4%). The high prevalence of leptospirosis infection among malaria patients in Bangladesh could be explained by the seropositivity for leptospirosis being stable throughout seasonality, while malaria had a peak in the rainy season when conditions for the vector seem to be favorable. In addition, high proportions of asymptomatic malaria-positive adults were identified in this country, indicating a greater probability for semi-immunity by increasing age . Moreovenfection . While tnfection . The titnfection ,43. In anfection . ELISA i%, India nfection . Techniq32 genes ,45. Real32 genes . Nested serovars .Leptospira from rodents to humans [Subgroup analysis of age groups showed that that the pooled prevalence of leptospirosis infection among malaria patients was highest in all age groups (24%), while lower prevalence was demonstrated in studies that enrolled specific groups, such as children (8%) and adults (7%). This result was consistent with the report showing severe leptospirosis occurred more among adolescents than children and adults Moreovero humans or exceso humans . In Bango humans . Therefoo humans .The present study had limitations. First, the limited number of studies reported concurrent malaria and leptospirosis infection. Therefore, the limited data, such as clinical laboratory characteristics and also the outcome of coinfected patients that might differ from malaria or leptospirosis mono-infection, could be used to investigate using a meta-analytical approach. Secondly, the pooled prevalence of malaria and leptospirosis co-infection among febrile patients or the pooled prevalence of leptospirosis infection among malaria patients were demonstrated with high prevalence heterogeneity across studies or countries. Therefore, the pooled prevalence of co-infection might not be estimated precisely and should be interpreted with the prevalence of an individual study.In conclusion, the low prevalence of malaria in leptospirosis co-infection among febrile patients occurred among the included studies. Co-infection was likely to occur by chance. However, clinical symptoms of leptospirosis patients were non-specific and not distinguishable from symptoms of malaria patients. Therefore, clinicians caring for febrile patients in an area where these two diseases are endemic should maintain a high index of suspicion for both diseases, particularly during the peak incidence seasons and whether mono-infections or co-infections are likely. The recognition of co-infection may be an important factor in reducing disease severity and treatment duration."} +{"text": "Oral hypofunction, resulting from a combined decrease in multiple oral functions, may affect systemic-condition deterioration; however, few studies have examined the association between oral hypofunction and general health among older adults. In this cross-sectional study, we examined the relationship between oral hypofunction and sarcopenia in community-dwelling older adults. We included 878 adults . Tongue coating index, oral moisture, occlusal force, oral diadochokinesis , tongue pressure, mas-ticatory function, and swallowing function were evaluated as indicators of oral hypofunction. Grip strength, gait speed, and skeletal muscle mass index were measured as diagnostic sarcopenia parameters. The association between oral hypofunction and sarcopenia was examined via logistic regression using sarcopenia as the dependent variable. Oral hypofunction prevalence was 50.5% overall, 40.3% in men, and 54.9% in women. The prevalence of sarcopenia was 18.6% overall, 9.7% in men, and 22.5% in women. A logistic regression showed oral hypofunction, age, body mass index, higher-level functional capacity, and serum albumin level were significantly associated with sarcopenia. Sarcopenia occurred at an increased frequency in patients diagnosed with oral hypofunction ; accordingly, oral hypofunction appears to be significantly associated with sarcopenia. Japan has a rapidly aging population. As the population ages, the number of people in need of nursing care, and the cost of social security benefits increase correspondingly . TherefoIn 2016, the Japanese Society of Gerodontology (JSG) recognized oral hypofunction as a new disease in the oral field . As of 2Decreases in individual levels of oral function have been shown to influence general health deterioration ,6,7,8,9.In this study, we focused on sarcopenia as an outcome of oral hypofunction, as it is a principal geriatric syndrome, and malnutrition is a risk factor for its development ,12, as iThis cross-sectional study used data collected in 2018 for \u201cThe Otassha Study\u201d, a cohort study that evaluated comprehensive health examination data conducted by the Tokyo Metropolitan Institute of Gerontology. Data was collected from people aged 65 years or older living in Itabashi city, Tokyo. Potential participants were informed of the date, time, and venue of the health examination in advance by letter, and the health examination was conducted for those who appeared on the allotted date. The purpose and content of the health examination were explained to all participants in writing and orally, and written consent for participation in the study was obtained from all study participants. Individuals with missing survey data were excluded. All health examination evaluators received training on measurement methods and the use of evaluation instruments in advance, and evaluation criteria were standardized. This study was approved by the Ethics Committee of the Tokyo Metropolitan Institute of Gerontology , and was conducted in accordance with the Strengthening the Reporting of Observational Studies in Epidemiology Statement .Numbers of present and functional teeth were evaluated via an intra-oral examination by dentists and dental hygienists . PresentTo diagnose oral hypofunction, the degree of tongue coating, oral moisture, occlusal force, tongue-lip motor function, tongue pressure, masticatory function, and swallowing function were evaluated by dentists and dental hygienists. The presence or absence of seven items including poor oral hygiene, oral dryness, reduced occlusal force, decreased tongue-lip motor function, decreased tongue pressure, decreased masticatory function, and deterioration of swallowing function were assessed, and participants who experienced decreased functionality of least three items were diagnosed with oral hypofunction based on diagnostic criteria published by the JSG in 2016 [Degree of tongue coating was evaluated using the tongue coating index (TCI). To determine TCI values, the tongue was divided into nine blocks, and the degree of tongue coating of each block was visually inspected . Poor orThe degree of oral moisture was assessed using an oral moisture checker ,17. The Occlusal force was measured using a pressure-sensitive sheet scanned using an image scanner ,19,20. PTongue-lip motor function was measured based on the dexterity of the tongue and lips using an automatic counter . Sounds Tongue pressure was assessed using a tongue pressure measurement device ,23. To eMasticatory function was evaluated using gummy jelly ,25. PartSwallowing function was assessed using a 10-item Eating Assessment Tool , which iTo diagnose sarcopenia, parameters including grip strength, gait speed, and appendicular skeletal muscle mass of participants were measured by researchers with expertise in physical functions assessed. Using the Asian Working Group for Sarcopenia 2019 (AWGS2019) algorithm as a reference, sarcopenia was diagnosed if the participant had either low appendicular skeletal muscle mass and muscle strength levels or low appendicular skeletal muscle and low physical performance. Sarcopenia was considered severe if participants were determined to be positive for both sarcopenia indicators .To evaluate muscle strength, the grip strength of the dominant hand was measured using a Smedley-type hand dynamometer . Participants were required to grip of the hand dynamometer in a standing position with their arms lowered at a position that felt natural. Measurements were obtained twice, and the higher value was used to record handgrip strength. A handgrip strength < 28 kg and <18 kg for men and women, respectively, were defined as low muscle strength .Gait speed was measured to evaluate physical performance. Participants were instructed to walk at a normal pace along a straight 11-m walkway with 3-m and 8-m points marked with tape on a flat floor. Time needed to walk the 5-m distance between tape marks was measured to determine gait speed . A gait 2 and <5.7 kg/m2 for men and women, respectively, indicated low appendicular skeletal muscle mass [Appendicular skeletal muscle mass was measured using bio-electrical impedance analysis . Each measured appendicular skeletal muscle mass value was divided by the square of the height (m conversion) of each participant to calculate skeletal muscle mass index (SMI). An SMI value of <7.0 kg/mcle mass .Other survey items included the following: age; years of education; body mass index (BMI); drinking and smoking habits; living situation; depression assessed with a questionnaire ; higher-Patients with sarcopenia and severe sarcopenia were included in the sarcopenia group when performing statistical analyses. Between-group comparisons of continuous variables were performed using the Mann\u2013Whitney U test, and categorical variables were analyzed with the chi-squared test. The association between oral hypofunction and sarcopenia was examined via logistic regression analysis using the forced entry method, with sarcopenia as the dependent variable. Inclusion of variables in the model was based on existing knowledge of risk factors for sarcopenia. Statistical analyses were performed using IBM SPSS version 27 . As this was a secondary study of the Otassha Study, no prior sample size calculations were performedA flowchart detailing the design of this study is shown in p < 0.001). The prevalence of sarcopenia and severe sarcopenia was 14.4% and 4.2% overall, 7.2% and 2.2% in men, and 17.4% and 5.1% in women, respectively. The prevalence of sarcopenia (both severe and not severe) in men and women significantly differed (p < 0.001). When sarcopenia and severe sarcopenia were considered collectively, sarcopenia prevalence was 18.6% overall, 9.7% in men, and 22.5% in women. The prevalence of oral hypofunction between the robust not diagnosed with sarcopenia and sarcopenia groups was 45.3% and 73.0%, respectively, and the values were determined to significantly differ (p < 0.001). Among subordinate symptoms of oral hypofunction considered, rates of reduced occlusal force (p < 0.001), decreased tongue-lip motor function (p < 0.001), decreased tongue pressure (p < 0.001), decreased masticatory function (p < 0.001), and deterioration of swallowing function (p = 0.028) were significantly higher in patients of the sarcopenia versus robust group.Characteristics of the study population and survey item differences according to sex, and presence of sarcopenia and oral hypofunction are shown in Results of the multivariable logistic regression analysis in which sarcopenia was the dependent variable are shown in In this study, we focused on sarcopenia ,12 as anOral function evaluation may help confirm the effectiveness of treatment, and predict future general-health deterioration . It is aA strength of this study is that we analyzed a comprehensive set of oral-health and function variables. To the best of our knowledge, this was the first study to demonstrate that oral hypofunction, diagnosed in strict accordance with criteria published by the JSG, was associated with sarcopenia in community-dwelling older adults. One previous study reported an association between oral hypofunction and sarcopenia . AlthougIn our study, the prevalence of oral hypofunction based on diagnostic criteria published by the JSG was 50.5% overall, 40.3% among men, and 54.9% among women. Previous reports have indicated that the prevalence of oral hypofunction among older adults living in different regions of Japan is 43.6\u201361.6% overall, 39.0\u201362.6% among men, and 46.9\u201363.1% among women ,39,40,41The prevalence of sarcopenia in our study population was 18.6% overall, 9.7% among men, and 22.5% among women. The prevalence of sarcopenia in older Asians using AWGS2019 criteria has ranged from 16.4 to 22.8% overall, 11.5 to 21.8% among men, and 16.7 to 23.1% among women ,43,44. TThe results of the logistic regression analysis showed that age, BMI, JST-IC representing higher-level functional capacity, and serum albumin level reflecting nutritional and inflammatory status were significantly associated with sarcopenia. Age and BMI reportedly have a clear association with sarcopenia . Low serThis study revealed a significant association between oral hypofunction and sarcopenia, even after adjusting for effects of multiple variables. Numerous studies have shown that decreased oral function leads to poor nutritional status ,20,49. IAs this was a cross-sectional study, it was not possible to determine the direction of the association between oral hypofunction and sarcopenia. To date, few longitudinal studies have examined the impact of various oral function parameter decreases on sarcopenia . LongituIn this study, we found a significant association between oral hypofunction and sarcopenia among community-dwelling older adults. The prevalence of oral hypofunction based on diagnostic criteria published by the JSG in 2016 was 50.5% overall, 40.3% in men, and 54.9% in women. The prevalence of sarcopenia based on diagnostic criteria of AWGS2019 was 18.6% overall, 9.7% in men and 22.5% in women. Multidisciplinary action is needed to establish comprehensive measures for managing the oral health of patients with oral hypofunction, especially as a means to avoid future general-health deterioration."} +{"text": "Gastrointestinal cancers cause over 2.8 million deaths annually worldwide. Currently, the diagnosis of various gastrointestinal cancer mainly relies on manual interpretation of radiographic images by radiologists and various endoscopic images by endoscopists. Artificial intelligence (AI) may be useful in screening, diagnosing, and treating various cancers by accurately analyzing diagnostic clinical images, identifying therapeutic targets, and processing large datasets. The use of AI in endoscopic procedures is a significant breakthrough in modern medicine. Although the diagnostic accuracy of AI systems has markedly increased, it still needs collaboration with physicians. In the near future, AI-assisted systems will become a vital tool for the management of these cancer patients.Gastrointestinal cancers are among the leading causes of death worldwide, with over 2.8 million deaths annually. Over the last few decades, advancements in artificial intelligence technologies have led to their application in medicine. The use of artificial intelligence in endoscopic procedures is a significant breakthrough in modern medicine. Currently, the diagnosis of various gastrointestinal cancer relies on the manual interpretation of radiographic images by radiologists and various endoscopic images by endoscopists. This can lead to diagnostic variabilities as it requires concentration and clinical experience in the field. Artificial intelligence using machine or deep learning algorithms can provide automatic and accurate image analysis and thus assist in diagnosis. In the field of gastroenterology, the application of artificial intelligence can be vast from diagnosis, predicting tumor histology, polyp characterization, metastatic potential, prognosis, and treatment response. It can also provide accurate prediction models to determine the need for intervention with computer-aided diagnosis. The number of research studies on artificial intelligence in gastrointestinal cancer has been increasing rapidly over the last decade due to immense interest in the field. This review aims to review the impact, limitations, and future potentials of artificial intelligence in screening, diagnosis, tumor staging, treatment modalities, and prediction models for the prognosis of various gastrointestinal cancers. Artificial intelligence is described as the intelligence of machines compared to natural human intelligence. It is a computer science field dedicated to building a machine that simulates the cognitive functions of humans, such as learning and problem solving ,2. RecenAs per the WHO report, nearly 5 million new gastrointestinal, pancreatic, and hepatobiliary cancers were recorded worldwide in 2020. Gastrointestinal cancers include esophageal, colorectal (colon and rectum), and gastric cancer. Colorectal cancer (CRC) is the most common cancer of all gastrointestinal cancers. Overall, CRC is the second in terms of mortality and third in incidence after breast and lung cancers globally . AlthougEsophageal cancer, comprising esophageal adenocarcinoma and esophageal squamous cell carcinoma (ESCC), is the ninth most common cancer globally by incidence and sixth by cancer mortality, with an estimated over 600,000 new cases and half a million deaths in 2020 . Even thRetrospective studies included non-magnifying and magnifying images and real-time endoscopic videos of normal or early esophageal lesions to measure the diagnostic performance of AI models 23\u201324). One of the earliest retrospective studies conducted by Liu et al. with white light images used joint diagonalization principal component analysis (JDPCA), in which there are no approximation, iteration, or inverting procedures. Thus, JDPCA has low computational complexity and is suitable for the dimension reduction of gastrointestinal endoscopic images. A total of 400 conventional gastroscopy esophagus images were used from 131 patients, which showed an accuracy of 90.75%, with an area under the curve (AUC) of 0.9471 in detecting early esophageal cancer [\u201324. One Further retrospective analyses have been performed to analyze the role of different AI models, including supervised vector machines, convolutional neural networks on various diagnostic methods such as white light endoscopy, NBI, and real-time endoscopy videos. Cai et al. developed a computer-aided detection (CAD) using a deep neural network system (DNN) to detect early ESCC using 2428 esophageal conventional endoscopic white light images. DNN-CAD had sensitivity, specificity, and accuracy of 97.8%, 85.4%, and 91.45%, respectively, with a ROC of >96% when tested on 187 images from the validation dataset. Most importantly, the diagnostic ability of endoscopists improved significantly in sensitivity (74.2% vs. 89.2%), accuracy (81.7% vs. 91.1%), and negative predictive value (79.3% vs. 90.4%) after referring to the performance of DNN-CAD . In anotThe definitive treatment of ESCC varies from endoscopic resection to surgery or chemoradiation depending on the level of invasion depth, so it is very important to determine it. In a study conducted in Japan, 1751 retrospectively collected training images of ESCC were used to develop an AI-diagnostic system of CNN using deep learning technique to detect the depth of invasion of ESCC. The AI-diagnostic system identified ESCC correctly in 95.5% of test images and estimated the invasion depth with a sensitivity of 84.1% and accuracy of 80.9% in about 6 s, which is higher than endoscopists . IntrapaMany prospective analyses have also been performed to further assess the application of AI in the diagnosis of esophageal cancer. Struyvenberg et al. conducted a prospective study to detect Barrett\u2019s neoplasia by CAD using a multi-frame approach. A total of 3060 VLE images were analyzed using a multi-frame analysis. Multi-frame analysis achieved a much higher AUC (median level = 0.91) than a single frame one (median level = 0.83). CAD was able to analyze multi-frame images in 3.9 s, which, traditionally, is a time-consuming and complex procedure due to the subtle gray shaded VLE images . Thus, oWith the promising results from retrospective and prospective studies conducted on endoscopic images, studies were designed to evaluate the role of AI for in vivo analysis to aid the diagnosis of Barrett\u2019s during endoscopies. A prospective study developed and tested a CAD system to detect Barrett\u2019s neoplasm during live endoscopic procedures. The CAD system predicted 25 of 33 neoplastic images and 96 of 111 non-dysplastic BE images correctly and thus had an image-based accuracy, sensitivity, and specificity of 84%, 76%, and 86%, respectively. Additionally, the CAD system predicted 9 of 10 neoplastic patients correctly, resulting in a sensitivity of 90%. So, this study showed high sensitivity to predict neoplastic lesions with the CAD system. However, it is in vivo single center, so further large multicenter trials are needed . p < 0.05) [Shiroma et al. conducted a study to examine AI\u2019s ability to detect superficial ESCC using esophagogastroduodenoscopy (EGD) videos. A CNN through deep learning was developed using 8428 EGD images of esophageal cancer. The AI system performance was evaluated using two validation sets of a total of 144 videos. The AI system correctly diagnosed 100% and 85% ESCC in the first and second validation sets, respectively. Whereas endoscopists detected only 45% of ESCC and their sensitivities improved significantly with AI real-time assistance compared to those without AI assistance ( < 0.05) . In a re < 0.05) .Systematic reviews and meta-analyses of 21 and 19 studies, respectively, were conducted to test the CAD algorithm\u2019s diagnostic accuracy to detect esophageal cancer using endoscopic images. It showed that the pooled AUC, sensitivity, specificity, and diagnostic odds ratio of CAD algorithms for the diagnosis of esophageal cancer for image-based analysis were 0.97 (95% CI: 0.95\u20130.99), 0.94 (95% CI: 0.89\u20130.96), 0.88 (95% CI: 0.76\u20130.94), and 108 95% CI: 43\u2013273), respectively. The pooled AUC, sensitivity, specificity, and diagnostic odds ratio of CAD algorithms for the diagnosis of esophageal cancer depth of invasion were 0.96 (95% CI: 0.86\u20130.99), 0.90 (95% CI: 0.88\u20130.92), 0.88 (95% CI: 0.83\u20130.91), and 138 (95% CI: 12\u20131569), respectively. There was no heterogeneity or publication bias on meta-regression . Table 1\u2013273, resThe available literature provides strong evidence that the utilization of CAD in esophageal cancer can prove beneficial for early diagnosis, which remains crucial to prevent the significant morbidity and mortality of the patients . While lGastric cancer is the sixth most common cancer worldwide by incidence with over 1 million new cases and the third leading cause of cancer-related death in 2020 . The diaChronic, untreated H. Pylori infection is strongly associated with chronic gastritis, ulceration, mucosal atrophy, intestinal metaplasia, and gastric cancer . On endop < 0.01). Thus, this study showed a higher accuracy of H. pylori infection diagnosis with BLI and LCL with AI systems than WLI [A single-center prospective study compared the accuracy of the AI system with endoscopy images taken with white light imaging (WLI), blue laser imaging (BLI), and linked color imaging (LCL) in 105 H. pylori-positive patients. The AUC for WLI, BLI, and LCL were 0.66, 0.96, and 0.95, respectively for the computer-aided detection of chromoendoscopy abnormal frames. It is a hybrid approach of local and global texture descriptions. The G2LCM texture features and the support vector machine classifier were able to classify abnormal from normal frames with a sensitivity of 91%, a specificity of 82%, an accuracy of 87%, and an AUC of 0.91 . In anotA systematic review and meta-analysis of 16 studies were performed to understand AI efficacy in endoscopic diagnosis of early gastric cancer. The use of AI in the endoscopic detection of early gastric cancer achieved an AUC of 0.96 (95%CI: 0.94\u20130.97), pooled sensitivity of 86% (95% CI: 77\u201392%), and a pooled specificity of 93% (95% CI: 89\u201396%). For AI-assisted depth distinction, the AUC, pooled sensitivity, and specificity were 0.82 (95% CI: 0.78\u20130.85), 72% (95% CI: 58\u201382%), and 79% (95% CI: 56\u201392%), respectively .Most of the available literature currently focuses on AI applications in diagnosing gastric cancer rather than on the treatment response and prediction. Joo et al. constructed and studied the application of a one-dimensional convolution neural network model (DeepIC50), which showed accuracy in pan-cancer cell line prediction. This was applied to approved treatments of trastuzumab and ramucirumab, which showed promising predictions for drug responsiveness, which can be helpful in the development of newer medication .While many studies have been conducted independently, there is a need for larger prospective trials studying the application of AI in the entirety of gastric cancer diagnosis and treatment to better assess its efficacy and application in clinical practice. Colorectal cancer (CRC) is the fourth most common cancer diagnosed in the United States . Its incp < 0.001). All studies had a higher polyp detection rate in the AI group than the standard colonoscopy alone group [A recent systematic review and meta-analysis reported a pooled sensitivity and specificity of 92% and 93%, respectively, with 92% accuracy using still and video images from colonoscopy in over 17,400 patients. When using video frames or images, the pooled sensitivity and specificity were higher compared to studies that used still images alone, reporting a pooled sensitivity and specificity of 84% and 87%, respectively, for AI in the detection of colon polyps. Most of the studies were retrospective in design . The typne group . Recent ne group ,76. Laizp < 0.001). The absolute improvement in adenoma detection ranged from 6% to 15.2% for AI compared to colonoscopy alone in the studies. All RCTs utilized ANN- or CNN-based AI systems using video streams from colonoscopy [A pooled analysis of 20 studies that used AI to predict the histology of a polyp detected on colonoscopy revealed a sensitivity and specificity of 94% and 87% with 91% accuracy in detecting an adenomatous polyp. SVM was the most common AI in these studies, followed by DNN, CNN, and other DL methods . A meta-onoscopy . Table 3onoscopy ,97,98,99p < 0.001). Analyzing patients who underwent the endoscopic resection of T1 tumors, the LN metastases rate was higher for the AI system compared to guidelines , signifying a potential role for AI in detecting patients who may need further nodal sampling after the endoscopic resection of early-stage colon cancer [Lymph nodal metastases in colon cancer confer a lower survival and prognosis than patients with no nodal metastases in early-stage colon cancer, with 5-year survival dropping from over 90% to 72% in the presence of nodal metastases in early-stage colon cancer . Kudo etn cancer . Ichimasn cancer .Overall, AI has shown considerable promise to be an excellent addition to a gastroenterologist\u2019s armamentarium to not only detect small polyps with higher accuracy but also to be able to differentiate adenomas from other histologies and identify patients with early-stage T1 colon cancer who may benefit from or may be able to avoid additional nodal surgery.Pancreatic cancer is an aggressive cancer with a dismal 5-year overall survival of <10%. The incidence is rising globally, and it has the highest mortality rate amongst all major cancers . SurgicaLiu et al. using a faster region-based CNN model reported an AUC of 0.96 for the recognition of pancreatic cancer based on contrast-enhanced CT images. In contrast, Li et al. reported an accuracy of only 72.8% of differentiating various pancreatic cysts based on CT images using densely connected convolutional networks ,105. UsiAI application has been challenging in MR images for the recognition of pancreatic neoplasms. Kaisiss et al., using the ML model, reported an AUC of 0.93 with the sensitivity of 84% and specificity of 92% for the recognition of pancreatic cancers. In comparison, Corral et al. reported an efficacy of 78% using a DL model with a sensitivity of 92% and a specificity of 52% for recognizing malignant IPMNs ,110.Several studies have reported excellent accuracy of detection of pancreatic cancer from the normal pancreas. Ozkan et al. studied ANN and reported an accuracy of 91.66% in patients over 60 years old, while Mayra et al. and Tonozuka et al. studied CNN with a reported ROC AUC of 0.94 and 0.957, respectively, to identify pancreatic cancer from the noncancerous pancreas ,112,113.The presence of chronic pancreatitis complicates the diagnosis of pancreatic cancer, where standard EUS has low specificity, and cytology remains the mainstay of diagnosis. AI has been shown to improve the diagnostic capability of EUS to differentiate cancer from chronic pancreatitis compared to cytology. Zhang et al. showed an accuracy of 94% with 93% specificity to differentiate cancer from chronic pancreatitis using a support vector machine model of AI in a retrospective analysis of 388 patients using still EUS images . Three pKuwahara et al. showed that the CNN model of AI had a 94% accuracy in differentiating malignant from benign IPMNs. They also reported very high sensitivity, specificity, PPV, and NPV of 96%, 93%, 92%, and 96%, respectively. However, this study was a small retrospective analysis of still EUS images from 50 patients .Non-invasive biomarkers such as CA19-9 are non-specific in the diagnosis of pancreatic cancer. MicroRNA expressions are found to be unique in different gastrointestinal cancers, and their small size, stability, and easy detection in serum, make them potentially attractive for the early diagnosis of pancreatic cancer ,120. YanOverall, AI has shown considerable promise in the early detection of pancreatic malignancies and may become a useful adjunct to interventional gastroenterologists in the near future. Studies with CT scans and MRI showed a range of sensitivities and specificities, while a custom model of AI with PET/CT images showed promise. Endoscopic studies using AI in EUS imaging analysis showed higher sensitivities and specificities than traditional EUS to recognize pancreatic malignancies, and AI combined with miRNA also shows promise. If successful, they may help establish a diagnosis of pancreatic cancer in a non-invasive manner without cytological confirmation.Hepatocellular cancer (HCC) is a common hepatic tumor that can be diagnosed with specific radiological criteria without the need for tissue biopsy in the appropriate patient population . Less thVirmani et al. used the SVM technique to obtain a classification accuracy of 88.8% . Wu et aCao et al. utilized a deep neural network (DNN)\u2014automated multiphase convolutional dense network (MP-CDN) in 375 patients with 517 lesions to classify liver lesions into four groups . They reported that the AUCs for differentiating each category from the others were 0.92, 0.99, 0.88, and 0.96, respectively, for HCC, metastases, benign non-inflammatory lesions, and abscesses . Yasaka Hamm et al. applied the CNN model to multiphasic MRI images in 494 hepatic lesions and compared the performance of the AI model to radiologists. The CNN model showed a sensitivity and specificity of 92% and 98%, respectively, compared to 82.5% sensitivity and 96.5% specificity for radiologists reading the same cases. The overall accuracy of AI was 92%, with a false positive rate of 1.6% and an ROC of 0.992 . OestmanOverall, AI has shown considerable progress in application with US, CT-scans, and MRIs to increase HCC diagnosis accuracy and early detection, with some studies showing better sensitivities and specificities than radiologists. AI has the potential to become an excellent adjunct to radiology techniques in diagnosing HCC in the future.Several studies have explored the role of AI in assisting with pathological diagnosis of GI cancers. Of all AI methodologies, CNN has been the most widely studied with regards to applications in the pathological diagnosis of cancer. If well built, it has the potential to ease the pathologist\u2019s workload and increase the efficiency of pathological diagnosis ,134. WhiThis review outlined the current published literature on the AI application in gastrointestinal, pancreatic, and hepatocellular cancers. AI is considered an instrumental tool in changing the future of healthcare, especially oncology. AI may become a useful tool in screening, diagnosing, and treating various cancers by accurately analyzing diagnostic clinical images, identifying therapeutic targets, and processing large datasets. Although the diagnostic accuracy of AI systems has markedly increased, it still needs collaboration with physicians. Robertson et al. proposed a five-step process that they foresee can help integrate AI with clinical practice, namely, Quality improvement, Productivity improvement, and Performance improvement, followed by Evaluation (step 4) where AI replaces human analysis and the results can be reviewed by the gastroenterologist before being reported to the final step 5, Diagnostic, where AI may replace the diagnostician for simple pathologic results releasing them to the patients without review . However"} +{"text": "Streptococcus pneumoniae as an etiologic agent. Vaccination is the primary method of preventing bacterial meningitis and therefore its complications. There are three vaccine preventable causes: Haemophilus influenzae type b (Hib), S. pneumoniae, and Neisseria meningitidis. Starting antibiotics without delay is also critical to reduce the risk of neurological complications. Additionally, early adjuvant corticosteroid use in Hib meningitis reduces the risk of hearing loss and severe neurological complications.Bacterial meningitis is a devastating infection, with a case fatality rate of up to 30% and 50% of survivors developing neurological complications. These include short-term complications such as focal neurological deficit and subdural effusion, and long-term complications such as hearing loss, seizures, cognitive impairment and hydrocephalus. Complications develop due to bacterial toxin release and the host immune response, which lead to neuronal damage. Factors associated with increased risk of developing neurological complications include young age, delayed presentation and Acute bacterial meningitis is the most common bacterial central nervous system (CNS) infection. It is a devastating illness, especially in neonates (age < one month) and infants (age < one year). Bacterial meningitis has a high case-fatality rate of up to 30% ,2,3,4,5,The incidence of bacterial meningitis in children differs by age group and is highest in infants aged younger than two months ,12. In tHaemophilus influenzae type b (Hib), Neisseria meningitidis and Streptococcus pneumoniae over the last three decades has led to a drastic decrease in the incidence rate of bacterial meningitis beyond the neonatal period in countries with these vaccines included as part of their routine infant and children immunization programs [The most common organisms causing bacterial meningitis vary by age group . Introduprograms . Howeverprograms ,18,19,20S. pneumoniae has become the leading cause of bacterial meningitis outside the neonatal period, except in some European and Sub-Saharan African countries, where it is the second most common cause in this age group after N. meningitidis [Escherichia coli remain the leading causes of bacterial meningitis in neonates with little change in incidence rates over time [Listeria monocytogenes is an uncommon cause, it should be considered in neonates.Hib was the leading cause of bacterial meningitis in the 1990s, but became uncommon in countries that introduced Hib immunization. However, it is still a frequent cause of bacterial meningitis in the countries were Hib vaccine is not universal or in unvaccinated children due to vaccine hesitancy . In counngitidis . Group Bver time ,12. Intrver time ,29. AlthMeningitis develops after the pathogen invades the CNS either though hematogenous route (bacteremia) or by direct extension secondary to sinusitis or mastoiditis and multiplies in the subarachnoid space. The presence of bacteria in the subarachnoid space leads to activation of the immune response, resulting in bacterial lysis. The presence of bacterial particles triggers a further inflammatory response with on-going migration of neutrophils across the blood\u2013brain barrier and continuous cytokine and chemokine release 7,30,31,33,34,35There are many complications that are associated with bacterial meningitis. These include short-term complications such as seizures, focal neurological deficits and subdural effusions, and long-term complications such as hearing loss, cognitive impairment, hydrocephalus, learning disability, and epilepsy ,36,37,38S. pneumoniae and N. meningitidis [Subdural effusions occur in 20\u201339% of children with bacterial meningitis ,51,52. SFocal neurological deficit refers to a set of signs and symptoms resulting from a lesion localized to a specific anatomical site in central nervous system . ExampleAcute focal neurological deficits after bacterial meningitis are usually due to ischemic stroke, but can also occur due to subdural empyema, cerebral abscess or intracranial bleeding . Focal nS. pneumoniae (14\u201332%), compared with N. meningitidis (4\u201323%) and H. influenzae (20%) [Sensorial hearing loss is the most widely reported neurological sequelae of bacterial meningitis ,57,58,59ae (20%) ,60. Chilae (20%) and speeae (20%) , and areae (20%) .Reversible deafness has been documented in long term follow up of children with pneumococcal meningitis ,61. For Due to the irreversible neuronal damage that occurs during bacterial meningitis, the risk of developing long-term cognitive deficits and learning difficulties are significant ,48. The In a Dutch study, 680 children between the age of 4 and 13 years who survived bacterial meningitis were followed up for 6 years after their meningitis episode. The study followed their educational, behavioral and general health issues. The survivors were compared to a control group of healthy school-age siblings and peers, with similar socioeconomic background. It was found that 30% of children with meningitis had problems with school achievement or concentration. Additionally, these children repeated a school year twice as often as the control group (16% vs. 8%). Moreover, the post-meningitis group were referred to special-needs school four times more frequently compared to control group .In a Danish nationwide population-based cohort study, adults who had a bacterial meningitis in childhood were compared to control group that included a general population of the same age and sex, their siblings and the siblings of meningitis patients. Adults who had childhood bacterial meningitis had lower educational achievements and economic self-sufficiency compared to control group. By the age of 35 years, 11%, 10.2% and 5.5% fewer had completed high school in meningococcal pneumococcal, and Hib meningitis, respectively. Additionally, 7.9%, 8.9% and 6.5% fewer had obtained a higher education in meningococcal pneumococcal, and Hib meningitis, respectively. Additionally, 3.8%, 10.6% and 4.3% had lower economic self-sufficiency in meningococcal pneumococcal, and Hib meningitis, respectively . In a stFinally, psychiatric disease including anxiety and depression is likely under-recognized and underreported in meningitis survivors and contributes to cognitive difficulties and overall quality of life . One of the clinical presentations of bacterial meningitis is seizures ,66. In cE. coli (41% vs. 25%) [In a neonatal bacterial meningitis study seizures have been more commonly associated with GBS then vs. 25%) . 71% of vs. 25%) .Hydrocephalus incidence is around 7% of bacterial meningitis in children and it iThere are many risk factors associated with neurological complications in bacterial meningitis .In general, infants are at higher risk of developing neurological complications compared to older children ,9,23. 71S. pneumoniae meningitis have a higher risk of developing neurological complication (75% of S. pneumoniae meningitis cases) compared to N. meningitidis (25%) and Hib (20%) [S. pneumoniae compared to N. meningitidis and Hib is associated with higher risk of symptomatic seizures, hydrocephalus, hearing loss and mental retardation [S. pneumoniae as an etiologic agent were associated with increased risk of neurological complications in both HIC and LMIC settings [In bacterial meningitis, delayed presentation to hospital increase the risk of subdural effusion, hydrocephalus, hearing impairment and seizure disorder . Althougib (20%) . S. pneuardation . Delay iardation . In summsettings ,76,77,78N. meningitidis and 23 of the >90 serotypes of S. pneumoniae [H. influenzae, and is given as three or four doses before 18 months of age [N. meningitidis: Conjugate vaccines against capsular groups A, C, W, and Y and protein vaccines against group B. There are two types of vaccines against S. pneumoniae: Pneumococcal conjugate vaccines and polysaccharide vaccine against 23 serotypes which is not routinely used in healthy children [The most effective prevention of neurological complications from bacterial meningitis is preventing the infection though infant and childhood vaccination programs. Despite the development of multiple vaccines against the organisms causing bacterial meningitis, there continue to be many meningitis outbreaks caused by vaccine-preventable organisms ,80. Thereumoniae ,15. Hib s of age . There achildren .Routine vaccination can lead to development of community protection by indirect effect prevention of transmission within a population . Since tS. pneumoniae accounted for 65% of acute bacterial meningitis cases in Malawi, while the rates of N. meningitidis have remained constant at <5% [The highest rate of meningococcal disease worldwide is in the Sub-Saharan Africa, specifically in the \u201cmeningitis belt\u201d region where major epidemics occur every 5\u201312 years . After tt at <5% .S. pneumoniae and N. meningitidis. Ampicillin should be added to cover L. monocytogenes in very young children; some guidelines recommended for younger than 3 months, others recommended this for those younger than 1 month [It is important to have a high clinical suspicion of bacterial meningitis and start appropriate treatment without delay ,94. The 1 month ,96. Neuronal damage due to acute bacterial meningitis is not only due to bacterial invasion to the subarachnoid space, but also due to the host\u2019s inflammatory response to this invasion . The onlH. influenzae meningitis who received dexamethasone were less likely to have neurological sequelae compared to a placebo group (27% vs. 40%) [H. influenzae is confirmed or strongly suspected.In infant and children with Hib meningitis, administration of dexamethasone with antibiotics has shown a significant reduction in neurological sequelae rate 17%) compared to antibiotic only (23.4%) ,59. Addivs. 40%) . Therefo7% comparvs. 40%) ,96 when On the other hand, the use of dexamethasone in infants and children with pneumococcal meningitis is controversial as it has not been clearly proven to change the outcome ,36,98,99Better understanding of specific microbial and host factors contributing to CNS infection and inflammatory response may help in identification of new therapeutic targets and specific immunomodulatory regimens.All children who are diagnosed with meningitis should have a hearing assessment done before discharge or 1 month within discharge; even if hearing loss is not clinically suspected ,61. It iChildren with seizure disorders require antiepileptic medication and should ideally have long-term follow up by a neurologist ,8,67,70.E. coli). For children diagnosed with bacterial meningitis, starting antibiotic therapy without delay is critical for a good prognosis and to reduce the risk of developing neurological complications. So far, steroids are the only drug that can control inflammatory response, but effectiveness is limited to specific situations.Children with bacterial meningitis are at risk of developing neurological complications that include focal neurological deficits, subdural effusion, hearing loss, cognitive impairment, seizure disorder, and hydrocephalus. There is a need to optimize utilization of available vaccines and to develop vaccines for pathogens implicated in neonatal meningitis (GBS and"} +{"text": "Transplant candidates and recipients are at increased risk of infectious complications of vaccine-preventable diseases due to their longstanding immunosuppressive regimens. We assessed the rates of vaccination in our liver transplant patients at University Hospital (UH) in Newark, NJ. > 18 years old who underwent liver transplantation at UH for a 3-year period from 01/01/2017 to 07/20/2020. Data collected included demographics, clinical outcomes, eligibility and receipt of vaccinations before and after transplantation, protection titers after administration of hepatitis vaccinations and presence of an ID outpatient consultation. We looked at the following receipt of vaccinations: Prevnar-13, Pneumovax-23, Influenza, TDaP, Shingrix, Varivax, Havrix and Engerix/Heplisav. Characteristics of study participants was analyzed using descriptive statistics and Chi-Square/Fisher\u2019s Exact tests were used to test associations. Retrospective chart-review including patients 119 unique medical charts were reviewed and no patients were excluded. Of those patients who were eligible to receive Hepatitis A vaccination, only 44.8% were documented to receive vaccination and of those eligible to receive Hepatitis B vaccination, only 47.8% received it. Influenza vaccination pre-transplantation was 46% and 66.1% in post-transplant recipients. For the other vaccinations, during the pre-transplant period, 17.6 % of patients received Prevnar-13, 36.1% Pneumovax-23 and 20.2% TDaP and 26.1% received Shingrix. Patients who had ID consultation were significantly more likely to receive appropriate Hepatitis A and Hepatitis B vaccinations . We are not meeting national vaccination standards set by the American Society of Transplantation (AST) for optimal vaccination in this population. Our study can inform of possible solutions to increase vaccination rates in this population such as the simple addition of a smartphrase within EMR notes to remind providers to order appropriate vaccinations and eventually, a more long term solution of creation of a dedicated vaccination clinic and/or routine ID pre-transplant evaluations for all transplant candidates. All Authors: No reported disclosures"} +{"text": "People who use drugs (PWUD) remain at significantly high risk for HIV infection. It is estimated that the majority of all new HIV infections are through injection drug use, with an estimated 2,500 new infections occurring annually among people who inject drugs. Although new HIV infections have been quickly rising over the past year, the Center for Disease Control and Prevention (CDC) preliminarily reported a 50% to 70% intra-pandemic decline in HIV testing. Within Kentucky, an ultra-high-risk state, multiple health departments reported all HIV testing stopped during the early stages of the COVID-19 pandemic (March-July 2020). Once testing resumed, appointments were sparse.To address low rates of HIV testing among PWUD, we evaluated the acceptability of a HIV self-testing program implemented at a health department in Louisville, Kentucky that services PWUD. Descriptive statistics were calculated for testing location, testing self-efficacy, reasons and motivations, ease of use, and preferences for future services.From May to June 2021, a total of 230 PWUD engaged with the program (average of 18 per day). Most participants (87.8%) self-tested at the health department with the help of study staff, while the other 12.2% tested at home and returned at a later time. Approximately 77% of participants reported the self-test kit made them feel better able to keep track of their HIV status compared to standard testing methods. The most common reasons for testing were wanting to know their status (85%), the test was free (37%), fast results (31%), more privacy (23%), and recent high-risk drug use and sexual behaviors (17%). Virtually all (97%) reported the test kits were very easy to use. For future availability of self-test kits through the health department, 33% reported they would use them monthly, 28% every three months, 22% every six months, and 17% annually. In terms of preference for future testing modality, 72% indicated a preference for taking the kits home, while the other 28% indicated a desire to test at the health department with help from staff.Program participants found the self-test kits to be acceptable and easy to use. Implications for program implementation and future research will be discussed.Michelle Rose, MBA, Gilead Sciences Inc. (Grant/Research Support) Laura Guy, BS, CCRC, GILEAD Sciences"} +{"text": "Dengue is a major public health problem in Thailand, but data are often focused on certain dengue-endemic areas. Methods: To better understand dengue epidemiology and clinical characteristics in Thailand, a fever surveillance study was conducted among patients aged 1\u201355 years, who presented with non-localized febrile illness at Bang Phae Community Hospital in Ratchaburi province, Thailand from October 2011 to September 2016.Among 951 febrile episodes, 130 were dengue-confirmed. Individuals aged 10\u201314 years were mostly affected, followed by those 15\u201319 years-of-age, with about 15% of dengue-confirmed cases from adults 25 years and older. There were annual peaks of dengue occurrence between June-November. Most prevalent serotype in circulation was DENV-2 in 2012, DENV-3 in 2014, and DENV-4 & -3 in 2015. Among dengue cases, 65% were accurately detected using the dengue NS1 RDT. Detection rate was similar between secondary and primary dengue cases where 66% of secondary vs. 60% of primary dengue cases had positive results on the NS1 RDT. Among dengue cases, 66% were clinically diagnosed with suspected dengue or DHF, prior to lab confirmation. Dengue was positively associated with rash, headache, hematemesis and alterations to consciousness, when compared to non-dengue. Dengue patients were 10.6 times more likely to be hospitalized, compared to non-dengue cases. Among dengue cases, 95 were secondary and 35 were primary infections. There were 8 suspected DHF cases and all were identified to be secondary dengue. Secondary dengue cases were 3.5 times more likely to be hospitalized compared to primary dengue cases. Although the majority of our dengue-positive patients were secondary dengue cases, with few patients showing manifestations of DHF, our dengue cases were mostly mild disease. Even among children < 10 years-of-age, 61% had secondary infection and the rate of secondary infection increased with age.While the majority of dengue-confirmed cases were children, almost three-quarters of dengue-confirmed cases in this study were secondary dengue. Our study results consistent with previous data from the country confirm the hyperendemic transmission of DENV in Thailand, even in the non-epidemic years. With various interventions becoming available for dengue prevention and control, including dengue vaccines, decision-making on future implementation strategies should be based on such burden of disease data. Dengue is a well-known public health problem in Thailand. To identify epidemiologic and clinical patterns of dengue in Thailand, we studied 951 febrile patients with fever, aged 1\u201355 years, who attended Bang Phae district hospital in Ratchaburi province, Thailand. Patients were tested with a rapid test for dengue, and further tests were carried out on paired blood samples taken 10\u201321 days apart. Overall, 14% of the febrile episodes identified between October 2011 and September 2016 were dengue-confirmed. Teenagers were mostly affected with only few adults. Dengue peaks occurred between June-November, but there was no large epidemic during the study period. DENV type 2 was the main serotype in circulation in 2012, DENV type 3 in 2014, and DENV types 4 and 3 in 2015. Dengue cases were 11 times more likely to be hospitalized than non-dengue cases. Dengue patients were more likely to present with rash, headache, hematemesis and alterations to consciousness, compared to non-dengue. Two thirds of the dengue cases were clinically diagnosed with suspected dengue or DHF, even without lab confirmation. Secondary dengue cases were about three times more common than primary cases. Even among children < 10 years-of-age, 61% of the patients were of secondary infection. Among dengue cases, 65% were accurately detected using the dengue RDT. This was not different between secondary and primary dengue cases. All 8 patients clinically diagnosed with DHF were secondary dengue cases. Although most of our dengue-positive patients were secondary dengue cases, we only observed few patients showing DHF. Thus, we concluded that our dengue cases were mostly of mild dengue illness. Our study results support the previous data confirming the high burden of dengue in Thailand and such information would help to make decisions on future implementation of various tools for dengue prevention and control. Dengue fever (DF) is a mosquito-borne flavivirus infection caused by four related but antigenically distinct dengue viruses . The global burden of dengue has experienced a dramatic increase in recent years ,3. With As a major public health problem in Thailand, despite mosquito control efforts, DF/DHF has steadily increased in both incidence and range of distribution in the country. All four serotypes are in circulation and it has now spread to all provinces, districts, and sub-districts ,8. DHF iThere is a considerable amount of dengue burden data from Thailand based on epidemiological studies including those following dengue vaccine trials. However, often existing data are focused on hospitalized cases, despite that outpatient dengue accounts for the greatest burden of disease, both epidemiologically and economically. Thus, there continues to be a lack of data on dengue among non-hospitalized cases ,12. AlsoIn order to better understand epidemiologic and clinical patterns of symptomatic dengue in Bang Phae, a passive facility-based fever surveillance study was conducted in a catchment area among residents of Bang Phae district, Ratchaburi province, Thailand. The study served two objectives. First, dengue-confirmed cases were compared to non-dengue cases, to identify significant epidemiologic and clinical features associated with dengue-confirmation, including assessing patterns related to dengue rapid diagnostic test (RDT) results and clinical diagnosis. Secondly, among dengue-confirmed patients, differences between secondary and primary cases were assessed.The study protocol obtained ethical approvals from the Institutional Review Boards (IRBs) of the International Vaccine Institute (2011\u2013007), the Ethics Committee of the Faculty of Tropical Medicine, Mahidol University (MUTM2011-031-06), and the Ethical Review Committee in Human Subjects (Ref.no.31/2554) of the Ministry of Public Health, Thailand.All adult subjects provided written informed consent, and a parent or guardian of any child participant provided written informed consent on the child\u2019s behalf with written assent from the child aged between 7 and 18 years.In site selection, the factors such as reported incidence, cases, outbreaks in the literature, available seroprevalence studies, and adequate research infrastructure were considered \u201317. Ratc2 (2017) and the specificity of 99.8% (95% CI: 99.1 to 99.9%).While non-dengue patients were almost 3 times more commonly prescribed with antibiotics than dengue-confirmed patients (30.1% of non-dengue patients vs. 10.8% of dengue-confirmed patients prescribed with antibiotics), mean duration of antibiotic use was significantly longer for dengue-confirmed patients than for non-dengue patients . Most ofParacetamol was given to all enrolled subjects and mean duration of paracetamol use was longer among dengue-confirmed patients, compared to non-dengue patients. Ibuprofen was rarely prescribed, to about 1% of enrollees.From univariable analyses , variablTo the clinical variables selected by the model, a priori adjustments were included in the final multivariable logistic regression model. Clinical diagnosis of suspected dengue (vs. undifferentiated fever or non-dengue) and positivity on RDT were initially considered potential confounders. However, they were too closely related to dengue-confirmation status as well as to signs and symptoms and were not entered in the final model. The final model, adjusted for a priori adjustments, showed that, there were 4.8 and 2.4 times greater odds of dengue-confirmed cases presenting with rash and headache, respectively, compared to non-dengue cases . Also, dThe majority of dengue-confirmed cases, 73% (n = 95), were identified to be secondary dengue infection. There was no statistically significant difference observed in age distribution between secondary and primary dengue patients . Also, tAmong hospitalized patients, 86% (44/51) were secondary dengue patients. Patients with secondary dengue infections were 3.5 (95% CI: 1.37\u20138.67) times more likely to be hospitalized, compared to those with primary dengue infection. Duration of hospitalization was measured among 49 patients and the mean duration was significantly longer for those with secondary (4.17 days) vs. primary dengue infection (3.71 days).Secondary dengue infections were more likely to be diagnosed as suspected dengue, but the difference in proportions was not statistically significant, when compared against primary dengue infections. Furthermore, all those clinically diagnosed with DHF among dengue-confirmed cases (n = 8) had secondary dengue and all of these secondary cases were hospitalized.Among secondary dengue cases, 66.32% (95% CI: 55.89% - 75.69%) had positive results on the NS1 kit of RDT, compared to 60.0% (95% CI: 42.11% - 76.13%) in primary dengue cases. However, the difference was not statistically significant (p = 0.504). In terms of symptomatic presentation, secondary dengue cases were significantly more likely to present fatigue (O.R = 2.7 times), nausea/vomiting (O.R = 3.0 times), loss of appetite (O.R = 2.7 times), and muscle pain (O.R = 4.1 times), compared to primary dengue cases. There were no hemorrhagic signs that were found significantly more among secondary dengue cases, compared to primary dengue cases.Dengue is well studied in many of Southeast Asian countries, including Thailand. There have been extensive studies conducted to assess epidemiologic patterns and burden of dengue disease in the country. Our study results showed consistent data with previous studies. We found 14% (n = 130) of 951 enrolled febrile patients to be dengue-confirmed. Similarly, Sabchareon et al. reported 2.7% to 10.2% of the febrile episodes to be dengue-confirmed among primary school students in Muang district of Ratchaburi province between 2006 and 2009 .While there are dengue epidemics that occur every 2\u20134 years, during our study period, there was no large epidemic of dengue in Bang Phae district. Nonetheless, Also, as previously documented, there were annual peaks of dengue occurrence between June-October/November ,35. TherIn terms of age, more than 50% of the febrile patients enrolled at BPCH were under 15 years of age. More than 50% of those dengue-confirmed were 10\u201319 years of aged. A study conducted in Photharam Hospital in Ratchaburi in 2005\u20132015 also showed similar age patterns where 40% of dengue patients were found to be between 10\u201318 years of age with those between 10\u201314 years mostly affected . SimilarWith the majority of these dengue-confirmed patients as secondary dengue cases, our data showed that there was no statistically significant difference in age distribution between secondary and primary dengue cases. Among patients with secondary dengue infections, the youngest individual was 2 years old (PCR confirmed with DENV-1) and reached up to 45 years-of-age. Such patterns with respect to age are consistent to what have been reported from other studies conducted in Thailand ,36,38.In our studied population, we observed a high index of clinical suspicion of dengue with 66% of dengue-confirmed patients clinically diagnosed with dengue infection. The large majority of non-dengue cases had respiratory infections, including URI, viral syndrome, bronchitis. While these may seem atypical manifestations of dengue, our surveillance only excluded febrile patients if they have an obvious localized infection.While clinical diagnosis of suspect dengue was made prior to lab confirmation, the RDT test results were available during visit 1. With the NS1 kit of the dengue RDT demonstrating 65% sensitivity and specificity of 99%, clinical judgement would have been made in the presence of knowledge of the dengue RDT results. When we consider either IgM or NS1 results on the RDT, of 87 patients with RDT positive results, 92% (n = 80) were diagnosed with suspected dengue or DHF. In terms of specificity of clinical diagnosis, 98% (n = 844) of 864 patients with RDT negative results were diagnosed with non-dengue. When clinical diagnosis of dengue was compared against lab-confirmation of dengue, sensitivity was quite high at 65.38% (95% C.I = 56.54\u201373.51) and specificity was even higher at 98.17% (95% C.I = 97.00\u201398.97). Even if aided by RDT results, in our studied population, we observed clinical diagnosis to perform well in detection of dengue cases.Furthermore, dengue RDTs have been reported to be more sensitive for primary than secondary infections . HoweverIn the current study, we referred to only the NS1 results for assessment of the test performance of the dengue RDT. However, to compare with the clinical diagnosis, we referred to positivity either based on IgM and/or NS1 kit of the RDT and there may be concerns of cross-reactivity between flaviviruses reported in antibody assays and tests for dengue NS1 antigen ,41. HoweIn terms of treatment, all patients were given paracetamol and the period of prescription was not significantly different between dengue and non-dengue patients. For antibiotics, prescription was more common among non-dengue (30%), than dengue-confirmed cases (11%). The mean duration of antibiotic use was almost twice longer for dengue-confirmed than non-dengue patients. Of 14 dengue-confirmed cases, the reasons for doctors giving antibiotics were negative RDT results and suspected bacterial infection including URI (n = 8).In terms of symptomatic presentation, the final model reported that dengue-confirmed cases were significantly associated with increased odds of presenting with rash, headache, hematemesis and alterations to consciousness, while dengue-confirmed patients were significantly associated with decreased odds of presenting with rhinorrhea and cough, compared to non-dengue patients. In addition to being part of the 2009 WHO case definition of probable dengue, our results were consistent to what was commonly reported symptoms observed among patients with dengue fever in Thailand ,44\u201346. DIn addition to these signs and symptoms, our model reported that dengue-confirmed cases were more likely to present with higher body temperature \u2265 38.3\u00b0C at enrollment than non-dengue cases. This was found statistically significant even after adjusting for fever duration days prior to visit and supported by other previous studies ,45.Hospitalization due to dengue illness is a common indicator of morbidity and numbOther indicators of possible severe outcomes of dengue could be the warning signs . The 199Given the hyperendemicity of dengue in Thailand, it is expected that most of the cases are secondary dengue infections. Our data showed a significantly higher rate of admission, 3.5 times more likely, and a significantly longer mean duration of hospitalization among secondary cases compared to primary dengue cases in the studied population. However, given that our data did not have many cases with warning signs or cases diagnosed with DHF, most of patients in the studied population showed to have mild disease of dengue.We recognize variability of dengue epidemiology over time and by region. While the surveillance continued for 5 years and BPCH is the main hospital serving the studied population, due to resource constraints, subject recruitment was only at one facility. In addition, depending on the transmission volume of dengue or other co-circulating pathogens, there may have been cases of co-infection. There is documented co-circulation of multiple arboviruses, such as chikungunya virus (CHIKV), and Zika virus (ZIKV), observed in Thailand . HoweverAn important potential source of bias is under-ascertainment due to the community residents with relevant symptoms not seeking care. In its passive design, our study may miss those eligible patients seeking for care at other healthcare providers than the facility under surveillance. Also, we did not recruit more mild patients who may seek care at private clinics. So, there may have been limitations in capturing of the wide spectrum of clinical manifestations of dengue by only involving a district-level hospital. We recognize that there may be limited generalizability due to these limitations.Our findings confirm the hyperendemicity of dengue with all 4 serotypes in circulation in Bang Phae, Ratchaburi province, Thailand, even in the times without large reported epidemics. While mild illness was observed in the majority of our dengue patients, we found more secondary cases than primary dengue cases even in teenagers. Given the importance of the burden data in making decisions on interventions, our results could contribute to facilitate decision-making on implementation of interventions, especially given that more options are becoming available for preventive and control measures, including vaccines.S1 Table(DOCX)Click here for additional data file.S1 Strobe Checklist(DOCX)Click here for additional data file."} +{"text": "Use of prescription pain medication after burn injury is commonly required. However, little is known about long-term pain medication use and its association with outcomes. Therefore, the purpose of this study is to assess patterns of prescription pain medication use after discharge and the association between these medications and quality of life outcomes.Data from the Burn Model System National Longitudinal Database (2015-2021) were analyzed. Pain medication use was assessed at pre-injury , discharge and follow-up . Outcome measures included: VR-12 Physical and Mental Component Summary scores (PCS and MCS), Community Integration Questionnaire (CIQ), Posttraumatic Stress Disorder Checklist (PCL), Satisfaction with Life Scale (SWLS), and NeuroQOL Stigma. The population was divided into two groups, those taking and not taking prescription pain medications at one year. Regression analyses examined associations between prescription pain medication use and outcomes at 12 months, controlling for age, gender, race, ethnicity and burn size.Of the 645 participants, 15% reported prescription pain medication use prior to their burn. At discharge, 81% reported use of an opioid and 46% reported use of a neuropathic pain medication. At 12 months, 32% of individuals indicated prescription pain medication use. The pain medication group exhibited larger burn size (24.0% vs 15.2%) and longer hospital stays (40.4 vs 25.0 days) than the non-pain medication group . Additionally, 25% of individuals who reported pre-injury pain medication use also reported use at 12 months. Regression analyses demonstrated that pain medication use was associated with worse physical health mental health , stigma , and satisfaction with life at one year. Additionally, pain medication use was associated with 45% decreased odds of being employed and approximately 3 times greater odds of having post-traumatic stress disorder at 12 months .There are significant associations between prescription pain medication use and worse physical, mental and employment outcomes at twelve months. This information may be used to trigger screening and manage long-term recovery outcomes."} +{"text": "This cross-sectional study examines within-area physician-level variations in decision-making in common clinical scenarios where guidelines specifying appropriateness or quality of care exist. To what extent do physician-level variations in the appropriateness or quality of care exist within metropolitan areas, notably among specialists?In this cross-sectional study of 8788 physicians across 7 specialties in 5 US metropolitan areas, sizeable physician-level practice pattern variations were evident across 14 common clinical scenarios where practice guidelines and clinical evidence can help discern, on average, the appropriateness or quality of clinical decisions. Variations were robust to adjustment for patient and area-level characteristics, and measure reliability was generally high.Within-area physician-level variations in practice patterns were qualitatively similar across clinical scenarios, despite practice guidelines designed to reduce variation. While variations in quality of care have been described between US regions, physician-level practice pattern variations within regions remain poorly understood, notably among specialists.To examine within-area physician-level variations in decision-making in common clinical scenarios where guidelines specifying appropriateness or quality of care exist.This cross-sectional study used 2016 through 2019 data from a large nationwide network of commercial insurers, provided by Health Intelligence Company, LLC, within 5 metropolitan statistical areas (MSAs). Physician-level variations in appropriateness and quality of care were measured using 14 common clinical scenarios involving 7 specialties. The measures were constructed using public quality measure definitions, clinical guidelines, and appropriateness criteria from the clinical literature. Physician performance was calculated using a multilevel model adjusted for patient age, sex, risk score, and socioeconomic status with physician random effects. Measure reliability for each physician was calculated using the signal-to-noise approach. Within-MSA variation was calculated between physician quintiles adjusted for patient attributes, with the first quintile denoting highest quality or appropriateness and the fifth quintile reflecting the opposite. Data were analyzed March through October 2021.Fourteen measures of quality or appropriateness of care, with 2 measures each in the domains of cardiology, endocrinology, gastroenterology, pulmonology, obstetrics, orthopedics, and neurosurgery.A total of 8788 physicians were included across the 5 MSAs, and about 2.5 million unique patient-physician pairs were included in the measures. Within the 5 MSAs, on average, patients in the measures were 34.7 to 40.7 years old, 49.1% to 52.3% female, had a mean risk score of 0.8 to 1.0, and more likely to have an employer-sponsored insurance plan that was either self-insured or fully insured (59.8% to 97.6%). Within MSAs, physician-level variations were qualitatively similar across measures. For example, statin therapy in patients with coronary artery disease ranged from 54.3% to 70.9% in the first quintile of cardiologists to 30.5% to 42.6% in the fifth quintile. Upper endoscopy in patients with gastroesophageal reflux disease without alarm symptoms spanned 14.6% to 16.9% in the first quintile of gastroenterologists to 28.2% to 33.8% in the fifth quintile. Among patients with new knee or hip osteoarthritis, 2.1% to 3.4% received arthroscopy in the first quintile of orthopedic surgeons, whereas 25.5% to 30.7% did in the fifth quintile. Appropriate prenatal screening among pregnant patients ranged from 82.6% to 93.6% in the first quintile of obstetricians to 30.9% to 65.7% in the fifth quintile. Within MSAs, adjusted differences between quintiles approximated unadjusted differences. Measure reliability, which can reflect consistency and reproducibility, exceeded 70.0% across nearly all measures in all MSAs.In this cross-sectional study of 5 US metropolitan areas, sizeable physician-level practice variations were found across common clinical scenarios and specialties. Understanding the sources of these variations may inform efforts to improve the value of care. While efforts to improve the value of health care have adopted a national scope, most health care decisions remain local. Patients and families typically choose among physicians and hospitals close to home. Employers and insurers contract with local physicians and hospitals for their insurance networks. Yet patients, purchasers, insurers, and health care delivery organizations face a common challenge: variations in the appropriateness or quality of care between physicians are generally unknown.1 Following this seminal work, the Institute of Medicine also noted substantial variation within regions and recommended that efforts to improve the value of care focus on differences in clinical decision-making rather than geographic variation.3 Early surveys using clinical vignettes focused on primary care physicians revealed varying clinical preferences among physicians between high- and low-spending regions.6 Direct measurement of low-value care, also focused on primary care physicians, has found large variations between physicians, including within regions.10 However, the evidence on within-region physician-level variations in appropriateness or quality remains scant\u2014especially for specialists whose services play an important role in determining health care spending and patient outcomes.To date, variations in quality and spending have been largely described between regions, notably by the Dartmouth Atlas of Health Care.13In this cross-sectional study, we examined within-area physician-level variations in appropriateness and quality across 14 sentinel clinical scenarios pertaining to 7 specialties. As a proof of concept, we hypothesized that clinically meaningful variations in claims data are measurable with rigor among similar patients across physicians of the same specialty within a metropolitan area. Measuring physician-level variations may inform quality improvement efforts and stimulate local competition on quality that benefits patients. It may also help patients, employers, and insurers choose physicians and design insurance benefits beyond word of mouth or historically contracted networks.14 where included insurers had high market penetration. To protect confidentiality, all data were deidentified and HIPAA compliant. Moreover, we omitted MSA names and instead reported them as Southeast MSA 1, Southeast MSA 2, South Central MSA, Midwest MSA, and West MSA. Institutional review board approval was obtained from Harvard Medical School and Embold Health, and need for informed consent was waived owing to the use of deidentified data. This work followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guidelines for cross-sectional studies.15We analyzed the 2016 through 2019 claims and enrollment data from a national network of insurers provided by Health Intelligence Company, LLC. We examined physicians in 5 metropolitan statistical areas (MSAs), each of which contains at least 1 urban area of 50\u2009000 inhabitants,17 These scenarios were defined by eligible patients with certain diagnoses, specified via International Statistical Classification of Diseases and Related Health Problems, Tenth Revision, diagnosis codes, who received a given service, defined through the Common Procedural Terminology or drug codes, that reflected care of high or low appropriateness or quality. Physician performance in a measure was the share of patients whose care met the definition for appropriateness or quality, or reflected a continuous variable such as rates.We constructed quality measures for 14 common clinical scenarios based on current measures in the public domain, clinical guidelines from professional societies, appropriate use criteria, and established end points from the clinical literature.The clinical scenarios pertained to 7 specialties and included 2 scenarios each in cardiologist coronary artery disease care (stress tests and statin therapy), endocrinologist diabetes care (kidney function testing and drug therapy), gastroenterologist gastrointestinal tract care (polyp detection and appropriate endoscopy), pulmonologist chronic obstructive pulmonary disease care (drug therapy and spirometry), obstetrician prenatal and delivery care , orthopedist joint care (preoperative care and arthroscopy), and orthopedic surgeon or neurosurgeon spine care . Within each measure, patients were attributed to the physician who was plausibly most directly accountable for the care in that measure. Attribution to proceduralists was based on a triggering event . Attribution to nonprocedural specialists was through the plurality of clinical encounters in that specialty over a 3-year period. Rare ties in attribution were broken by attributing to the most recent specialist the patient saw.19 Recognizing these limitations, we focused on the narrow set of 14 measures for which guidelines and prior literature provide clear distinctions on appropriateness and quality. The guidelines and evidence behind each measure are provided in eMethods 1 in the The measures were designed to assess variations in physician-level decision-making in standardized clinical scenarios where, on average, more appropriate or higher-quality care could be plausibly distinguished from less appropriate or lower-quality care among similar patients in similar situations across physicians of the same specialty. Deriving measures of appropriateness or quality from claims data is challenging owing to potentially unobserved aspects of the patient or clinician that may affect the quality of clinical decisions.21 These specifications have gone through rigorous review and are commonly used by Medicare and commercial insurers. References to these measures in the public domain are provided in eFigures 1 through 7 in the To support measure validity, 9 of the 14 measures adhered to measure specifications from the National Quality Forum, the National Committee for Quality Assurance\u2019s Healthcare Effectiveness Data and Information Set, the Agency for Healthcare Research and Quality (AHRQ), or the Centers for Medicare & Medicaid Services.24 we identified patients without previous evidence of knee or hip pain who had incident osteoarthritis without meniscal abnormality. Within these patients, we measured rates of arthroscopy performed by their orthopedic surgeons in the subsequent year. The specifications for these measures are similarly provided in eFigures 1 through 7 in the For the 5 measures not currently in the public domain, we used detailed claims analyses to similarly restrict to patients in a specific clinical situation where rigorous guidelines exist. For example, in the measure of arthroscopic surgery for new hip or knee osteoarthritis, which has been demonstrated in multiple randomized clinical trials to lack benefit and is not recommended in such patients in guidelines,To further examine and improve measure validity, 3 of the investigators conducted a series of internal validation exercises by comparing the claims-based measure outputs and claims-based physician attribution to those obtained from a random subset of patient electronic medical record data. In these exercises, we selected a random subsample of patients in a given measure and constructed the measure output de novo by hand using medical record data. In essentially all cases, we found concordance between the 2 methods in physician attribution and measure output.25 The covariance parameter estimate serves as the between-physician variation; the within-physician variation was calculated by the sum of the squared residuals from the model, divided by N(N\u2009\u2212\u20091). Standards for acceptable reliability (a reflection of consistency and reproducibility) depend on a measure\u2019s specification and its intended use.27 Consistent with AHRQ methodology, we considered a reliability greater than 0.7 to be high and 0.4 to 0.7 to be acceptable.24 To improve reliability, physicians with fewer than 10 attributed patients in a measure were excluded. We reported the average number of patients per physician in each measure.Measure reliability for each physician was calculated using the signal-to-noise approach, which examines the ratio of the variation between physicians and total variation within a measure\u2014the latter comprising between-physician and within-physician variation. A linear random effects model was fit to estimate the clinical event of interest, with the physician as the independent variable alongside a random intercept.In unadjusted analyses, we calculated mean physician performance with 95% CIs reflecting uncertainty around the mean after adjustment for case volume. These reveal the observed variation in a transparent manner but do not account for patient factors or practice patterns that may explain between-physician differences.28 Without patient-level data on social determinants of health in claims, this index helps address, though does not resolve, concerns about claims-based quality measurement noted in the Institute of Medicine report,3 such as differences in health care access, patient preferences, and other unobserved factors.In adjusted analyses, we estimated physician performance using a multilevel model that adjusted for patient age, sex, diagnostic cost group risk score, index of socioeconomic status, and physician random effects with observations clustered within physicians. The diagnostic cost group risk score is driven by clinical diagnoses and is commonly used by insurers in risk adjustment. The socioeconomic status index was constructed using 7 US Census variables on education, income, housing, poverty rate, and unemployment rate from the patient\u2019s zip code of residence following AHRQ methods , we did not conduct individual statistical tests for each difference in mean performance. We used 95% CIs to convey the uncertainty around mean differences in performance. Sensitivity analyses tested alternative specifications. For additional details, please see eMethods 2 in the Physician performance in each measure and MSA was shown graphically with physicians ordered by mean performance, accompanied by 95% CIs. We then compared mean physician-level performance between quintiles of physicians in each measure, comparing quintile 1 to those in each subsequent quintile. We estimated between-quintile differences at the patient level with patients assigned to physicians and quintiles based on the random effects model. The coefficient of interest captured the difference in mean performance between physicians in quintile 1 and those in a subsequent quintile of a measure, adjusted for patient age, sex, risk score, and index of socioeconomic status derived from the 7 US Census variables based on the patient\u2019s zip code of residence, according to the methodology of AHRQ.29 This was motivated by the question of whether physicians whose episode-level spending was lower on average tended to be physicians whose patients also received more clinically appropriate care in the situations we measured. Second, in 1 MSA where we had data on physician organizational affiliations, we explored physician-level variations within organizations and across organizations. Analyses were performed using R software, version 4.0.5 (R Foundation).Finally, we conducted 2 exploratory analyses. First, we explored the correlation between average physician performance across the 2 measures in a specialty and average spending on the corresponding episode of care within that specialty attributable to the physician . Spending reflected insurer-standardized negotiated prices using the HealthPartners standardized costs of care measures.A total of 8788 physicians across the 7 specialties and 5 MSAs, comprising about two-thirds of all specialists in these MSAs, were included in the 14 measures. The characteristics of patients are shown in Physician decision-making varied substantially across MSAs . For exaMeasures of endocrinologists, gastroenterologists, and pulmonologists exhibited similar variations within each MSA. However, the extent of within-MSA physician variation differed across MSAs. For example, annual kidney function testing in patients with diabetes ranged from 84.9% (quintile 1) to 22.6% (quintile 5) among endocrinologists in the West MSA, whereas it ranged from 93.2% (quintile 1) to 69.8% (quintile 5) in the South Central MSA. The average measure reliability similarly exceeded the AHRQ threshold of 70.0% for all measures and MSAs to 30.9% to 65.7% (quintile 5) within MSAs, and the proportion of low-risk pregnancies with cesarean delivery (on average less appropriate) ranged from 5.0% to 17.3% (quintile 1) to 51.0% to 61.5% (quintile 5) within MSAs. Average measure reliability ranged from 71.1% to 91.8% across the MSAs was received by 19.1% to 64.8% of patients among orthopedists in quintile 1 compared with 3.9% to 16.6% in quintile 5, with measure reliability averaging 62.5% in the Southeast MSA and exceeding 80.0% elsewhere. The proportion of patients with new hip or knee osteoarthritis who underwent arthroscopic surgery (on average not indicated) ranged from 2.1% to 3.4% among orthopedists in quintile 1 to 25.5% to 30.7% among those in quintile 5, with average measure reliability also exceeding 75.0% in all MSAs ranged from 5.6% to 22.5% among spine surgeons in quintile 1 to 57.3% to 79.2% among those in quintile 5. Measure reliability averaged 85.0% or higher in all MSAs. The proportion of patients with cervical spine pain who received any physical therapy was 51.4% to 65.4% in quintile 1 compared with 5.7% to 29.6% in quintile 5 of surgeons. Average measure reliability similarly exceeded 70.0% in all MSAs , and other social determinants of health not captured in the present data may have influenced the results. Our efforts to carefully define the clinical scenarios and the patients in them, along with sensitivity analyses, suggest that these factors likely would not qualitatively change the results. However, for any given situation or patient, the potential for confounding could not be fully eliminated.4 It builds on earlier efforts to measure physician-level differences in patient outcomes such as surgical report cards, as well as the seminal Dartmouth Atlas of Health Care literature on between-region variations in quality.37 For consumers, employers, and insurers, within-region physician-level variations may be useful because moving or shifting enrollees across regions is less practical. We caution that heterogeneity in delivery systems, incentives, and other within-MSA differences still exist and could partially explain the variations.7 However, we found that between-physician variations within physician organizations were generally larger than between-organization variations in 1 MSA.This evidence adds to the Institute of Medicine recommendation to focus on within-region variations in clinical decision-making as a target of policy and quality improvement.38 If conveyed in a collaborative and nonpunitive way , such evidence may lead clinicians and their organizations to explore practice patterns relative to peers and identify areas of improvement.39 Understanding why some guidelines are followed more uniformly than others may further inform clinical education and training.This study demonstrates that measuring variations in decision-making at the clinician level using carefully defined clinical situations is possible in large claims data. It provides basic examples of clinical scenarios where evidence-based guidelines could be expected to have reduced such variations. Owing to imperfect risk adjustment and potential confounders, we consider this work a proof of concept and believe that between-physician comparisons can be improved with further data . Nevertheless, these findings are illustrative in showing the extent of variation that remains among plausibly similar patients in similar clinical scenarios. Moreover, rigorous approaches to measure reliability can help improve on earlier efforts to study physician-level variations.Evidence of local practice pattern variations may also encourage employers, insurers, and clinicians to collaborate on quality improvement efforts. Such evidence may eventually help patients and purchasers choose among local physicians or design insurance plans in a higher-value way. Today, to the extent data are used at all by employers and insurers to nudge patients toward higher-value clinicians, only differences in prices or spending are typically used, partly owing to the challenges of measuring physician-level quality and appropriateness of care. While clinician resistance to such measurement might be expected, measures that adhere closely to accepted clinical guidelines, address clinical scenarios with large sample sizes, and include adequate risk adjustment might garner more physician support.40 exacerbating inequalities ,42 and contributing to physician administrative costs and burnout.43Even so, attaching direct financial incentives to such measures in a pay-for-performance context may produce unintended consequences. Various pay-for-performance programs in recent years that tied financial rewards to quality measures have not achieved meaningful or sustained quality improvement. On the contrary, unintended consequences have been common, such as gaming behavior ,44 Thus, we advocate caution in individual physician comparisons. Third, because care is frequently team based, measures may misattribute decision-making to the specialist. Notably, in measures concerning chronic disease management , primary care physicians may influence performance, though it was difficult to discern whether decisions originated from specialists (such as through recommendations) or from primary care physicians. Similarly, we could not disentangle physician effects from hospital or organization-level effects. Although statistical models could accommodate additional random effects for the hospital or organization, physician-level effects are not easily distinguishable from them.45 Finally, commercially insured populations may not generalize to other populations, although prior studies of low-value care and regional variations have shown correlations between payer populations.46We emphasize several limitations. First, the 14 measures captured limited dimensions of quality or appropriateness in these specialties. Second, the data lacked further observable patient characteristics , which limited our ability to adjust for additional confounders. Moreover, claims data may not fully capture the preceding symptom burden that may have triggered subsequent testing and therapies. To the extent that unobserved patient complexity may explain sorting of patients to physicians or the contributions of patient demand to clinical decision-making, the present results may overestimate differences attributed to physician decision-making. Evidence of substantial residual confounding after risk adjustment exists.In this cross-sectional study of physicians in 5 US metropolitan areas, sizeable physician-level practice pattern variations were found across specialties and common clinical scenarios. In addition to payment reform, understanding physician-level variations in decision-making may provide a complementary direction for improving value that is more clinically nuanced."} +{"text": "Time elapsed between trauma and treatment greatly influences the prognosis of traumatic dental injuries (TDIs). The aim of this study was to analyze clinical and radiographic findings related to complications of TDIs among patients seeking delayed treatment of such injuries. 123 permanent teeth with a history of previous TDIs were included in the study. Clinical findings analyzed were the type of fracture, type and number of injured teeth, crown discoloration, and pulpal status of the injured tooth . The radiographic findings analyzed included pulp canal obliteration (PCO), root resorption (RR), and periapical radiolucency (PR). Statistical analysis included descriptive analysis. Tooth discoloration was the most common presenting complaint (53.65%), while fall (48.78%) was the most frequent cause of trauma. The range of time duration between trauma and presentation for treatment was 5 months to 30 years (average time 12.82 years). Pulp necrosis (PN) was the most common complication (90.24%). Almost half of the teeth with PN had fracture injury and discoloration along with a high frequency of PR (78.37%). Even teeth with a normal appearance were found to have a high incidence of PN (76.92%) and PR (53.84%). The crown discoloration was the second most frequent finding (48.78%). Many teeth (41.66%) with vital pulp were also discolored. Most of the teeth (79.31%) with yellowish discoloration and all teeth with brownish discoloration were nonvital. A high frequency of PN (90%) and PR (78.33%) was found in teeth with discoloration. PR was the most common radiographic finding (69.10%), while PCO and RR were observed in 17.88% and 21.13% of teeth, respectively. The findings of this study support the fact that delayed treatment of TDIs leads to increased complications. PN was the most common complication followed by tooth discoloration, RR, and PCO among patients seeking delayed treatment after TDIs. Traumatic dental injuries (TDIs) are one of the most common causes of tooth loss and hence are a well-known public dental health problem. The main objective of the treatment of TDIs is the healing of the dental pulp and periradicular tissues .Time elapsed between trauma and treatment is an important factor that greatly influences the prognosis of TDIs \u20135. SimilDelayed treatment of TDIs has an unfavorable effect on the prognosis of injured teeth, which can cause loss of pulp vitality and thus poor prognosis , 10, 11.However, treatment of TDIs is frequently neglected or delayed, which leads to various complications , 8. TreaAlthough healing of dental pulp and adjacent tissue is the most favorable outcome of TDIs, complications such as pulp necrosis (PN), infection of the root canal system, pulp canal obliteration (PCO), crown discoloration, root resorption (RR), bone resorption, and ankylosis have frequently been associated with TDIs , 4. ThesTherefore, the aim of this study was to analyze clinical and radiographic findings related to complications of TDIs among patients seeking delayed treatment of such injuries.This study was conducted at the Department of Conservative Dentistry and Endodontics, School of Dental Sciences, Chitwan Medical College, Nepal, between January 2018 and December 2019, for a period of two years. It included patients coming for delayed treatment of teeth with a previous history of TDIs to permanent dentition. Informed consent was taken according to ethical principles. This study was approved by the Institutional Review Board of the Chitwan Medical College .A total of 123 permanent teeth with a previous history of TDIs were evaluated in this study. The study included 82 patients comprising 47 males (57.31%) and 35 females (42.68%). The ratio between male and female is 1.34\u2009:\u20091. The age of the patient ranged from 14 to 53 years (mean age was 28.03 years).A thorough clinical and radiographic examination was conducted using a digital intraoral periapical radiograph exposed with a paralleling technique and an exposure time 0.125 seconds at 60\u2009kV and 7\u2009mA. The patient's name, age, gender, chief complaint (reason for seeking treatment), time elapsed between trauma and presentation for treatment, and the etiology of trauma were investigated.Findings from the clinical examination and tests, as well as radiographic examination, were documented. The clinical findings analyzed were type of fracture injury, type and number of injured teeth, crown discoloration, intraoral sinus, swelling, and pulpal status of the injured tooth . The radiographic findings analyzed were PCO, RR, and periapical radiolucency (PR).The diagnosis of PN was made based on clinical and radiological findings. The tooth was diagnosed as PN when clinical findings were observed along with radiographic findings (PR and or RR) . PCO andTeeth with a previous history of treatment were excluded from the study. Similarly, teeth without a previous history of TDIs were also excluded from the study.The data collected were subjected to descriptive analysis and chi-square tests were applied for association analysis. Statistical analysis of the obtained data was performed using Statistical Package for the Social Sciences ). The level of significance was set at 5%.p > 0.05). The distribution of TDIs with respect to age groups, gender, and etiology is shown in p > 0.05).The most frequently observed history of TDIs was in the age group 14\u201320, followed by the age group 21\u201325. Comparison of the frequency of TDIs between genders and age groups found no significant difference , followed by the maxillary left central incisor (23.57%). Maxillary teeth (74%) were more frequently involved than mandibular teeth (26%). The distribution of the affected tooth type is presented in The range of time duration between trauma and presentation for treatment was 5 months to 30 years. The average time of presentation after trauma was 12.82 years (within a year\u2009=\u20093 (3.65%), 2\u20134 years\u2009=\u200916 (19.51%), 5\u20137 years\u2009=\u200913 (15.85%), 8\u201310 years\u2009=\u200915 (18.29%), 11\u201315 years\u2009=\u200921 (25.60%), 16\u201320 years\u2009=\u20096 (7.31%), 21\u201325 years\u2009=\u20094 (4.87%), and 26\u201330 years\u2009=\u20094 (4.87%)).Vital pulp was detected in (9.75%) teeth upon diagnosis. Among them, 33.33% of teeth had a fracture, whereas 41.66% of teeth had discoloration. Similarly, on radiographic examination and 50% of teeth had PCO, and 16.66% of teeth had RR. Similarly, nonvital pulp (PN) was diagnosed in 90.24% of teeth. Among them, 44.14% of teeth had a fracture, and 49.54% of teeth were discolored. Likewise, 78.37% of teeth were associated with PR, 13.51% of teeth had PCO, and 20.72% had RR on radiographic evaluation. The tooth distribution, clinical and radiographic findings associated with pulpal diagnosis are shown in Likewise, on clinical examination, 21.13% of teeth had a normal appearance (NA). Among them, 76.92% of teeth were diagnosed as having PN. 53.84% of teeth were related to PR, 38.46% of teeth had PCO, and 19.23% had RR on radiographic findings. Enamel fracture (E#) was seen in 8.13% of teeth, of which 90% of teeth had PN. PR was found in 90% of teeth, while 10% had PCO and 50% had RR. Enamel dentin fracture (ED#) was observed in 26.01% of teeth. Among them, 84.37% teeth were diagnosed to have PN. Also 75% teeth had PR, and 28.12% of teeth were associated with RR. Similarly, all teeth with complicated crown fractures were diagnosed with PN. Among them, 72.72% of teeth were linked to PR on radiographic examination.Tooth discoloration was a frequent finding (48.78%) in this study. Among them, 48.33% of teeth had yellowish discoloration. 79.31% of teeth with yellowish discoloration had PN. Also, 68.96% of teeth were associated with PR and 27.58% of teeth had PCO and 31.03% had RR. All teeth with brownish discoloration (51.66%) were nonvital. 87.09% of teeth with brownish discoloration had PR, while only 3.22% of them had PCO and RR 16.12%. Overall, a high incidence of PN and PR (78.33%) was found in teeth with discoloration. However, the frequency of RR (23.33%) and PCO (15%) observed was low in teeth with discoloration. The tooth distribution, pulpal diagnosis, and clinical and radiographic findings related to clinical examination are shown in Upon analysis of radiographs, 13% of teeth had normal radiographic findings (NRF). Among them (25%) were discolored, whereas (56.25%) had fracture injuries. Also, 50% of teeth with NRF were nonvital.PR (69.10%) was the most common radiographic finding. 52.94% of teeth had discoloration, and 48.23% of teeth had fracture injury among the teeth with PR. All teeth with PR were nonvital, while 22.35% teeth had RR and 8.23% teeth had PCO.PCO was detected in 17.88% of teeth. Among them, half were discolored. The yellowish discoloration was found in 72.72% of teeth, whereas only 27.27% of teeth had brownish discoloration. Also, 63.63% of teeth with PCO were nonvital. On radiographic examination, 31.81% of teeth were associated with PR and 27.27% of teeth had RR in teeth with PCO.Likewise, 21.13% of teeth were found to have RR on radiographic evaluation. Among them, 88.46% of teeth had PN, 50% of teeth were discolored, while 73.07% of teeth had PR and 26.92% of teeth had PCO. The tooth distribution, pulpal diagnosis, and clinical and radiographic findings according to radiographic examination are shown in Immediate treatment after dental trauma significantly improves the prognosis of the injured tooth and is equally important for preventing and reducing complications. Late presentation for treatment after TDIs was identified as the reason for higher frequency of complications in a recent study . Timely Many patients with TDIs do not seek treatment as long as it remains asymptomatic . Tooth dPatients generally seek immediate treatment for severe injuries due to road traffic accidents, assaults, or sports. However, traumas due to impact and fall injury are considered mild injuries and are often neglected since they are seldom severe or symptomatic. Hence, patients tend to delay or ignore treatment for these kinds of injuries. This may explain the findings of this study, where fall (48.78%) was the most frequent cause of trauma. Most of the TDIs were due to fall and impact injury .PN has been found to be the most frequent posttraumatic complication in all types of TDIs , 14, 21.The prevalence of PN is very low in enamel-fractured and dentin-fractured teeth without an associated luxation injury. However, the risk of PN is higher in teeth with dentin fracture compared to teeth with enamel fracture , 18, 22.PN in uncomplicated crown fractures is rare and ranges between 2% and 5%. However, PN is very common in fractured teeth without treatment. Since complications can arise from the invasion of bacteria into the dentinal tubules, an increased PN is found even in the absence of luxation injuries, particularly in teeth with delayed treatment , 22, 23.PN was also a common finding in fractured teeth among patients seeking delayed treatment in another previous study . TherefoPN, PCO, RR, and ankylosis are important complications linked to luxation injures. Luxation injuries due to the damage to the neurovascular bundle are associated with a higher incidence of PN . Many stConcussion and subluxation injuries have a low risk of PN, whereas lateral luxation and intrusion have a high rate of PN , 31\u201333. Time period of development of PN after dental trauma varies depending on the type of injury. Although most of the PN developed within 12 months of trauma, the incidence of PN within 3 months was significantly higher in a study . TherefoPCO is a pulpal healing complication commonly found in teeth with luxation injuries, root fracture, and reimplanted teeth , 35, 36.Although very rare, PN can occur in teeth with PCO. PN is a late complication associated with PCO and ranges from 1% to 16% , 37. HowTeeth with PCO generally have discoloration, which is clinically seen as a yellowish discoloration of the crown . YellowiTooth discoloration, a long-term complication of dental trauma, is a frequent finding in a traumatized tooth. Grayish and brownish discoloration of a traumatized tooth indicates PN, while yellowish discoloration is a sign associated with PCO. Patients with mild injuries such as concussion and subluxation usually have negligible symptoms and hence seek treatment only when it becomes symptomatic. These patients with discolored teeth often come for delayed treatment . Tooth dUpon further evaluation, most of the teeth (79.31%) with yellowish discoloration were nonvital with a high incidence of PR (68.96%). A very high frequency of PN was also seen in teeth with brownish discoloration. All teeth with brownish discoloration were nonvital. Most of the teeth with brownish discoloration have been associated with periapical lesions , 39. A hPR was the most common radiographic finding (69.10%) . Almost RR is an important periodontal healing complication of TDIs. RR was observed in (21.13%) of teeth with a high rate of PN (88.46%) and PR (73.07%). Half of the teeth with RR were also discolored .Surprisingly, RR was not detected in teeth with a complicated crown fracture in this study since RR is mostly associated with luxation injury. RR was more frequently associated with intrusive luxation (93%), followed by avulsions (89%), lateral luxation (80%), and extrusive luxation (77%) in a recent study . This isOther periodontal complications related to TDIs such as marginal bone loss, mobility, transient apical breakdown, and cervical-invasive resorption, however, were not evaluated in this study.Early diagnosis of complications is very important since management of such tooth is difficult. Therefore, timely treatment and follow-up of an injured tooth, according to guidelines, are important for ensuring a favorable outcome, protecting pulp vitality, and reducing complications . SimilarKnowledge about the various consequences in teeth with TDIs can help to provide better treatment and reduce complications. Likewise, information regarding the timeline of the development of possible complications of TDIs is also essential to anticipate and prevent them.A traumatized tooth can have multiple signs and symptoms related to complications. Information from this study may help to predict the possibility of various likely complications related to TDIs and identify these complications early. Outcomes of this study may additionally assist in monitoring and follow-up of such teeth as well. Future studies related to the management of complications of TDIs with follow-up of the patients can be conducted, which might be valuable in better understanding of these complications linked to TDIs.The findings of this study support the fact that delayed treatment of TDIs leads to increased complications. Pulp necrosis was the most common complication followed by tooth discoloration, root resorption, and pulp canal calcification among patients seeking delayed treatment after TDIs in this study."} +{"text": "Cumulative mortality rates were highest among persons of Black, Asian, other, or mixed ethnicities and in socioeconomically deprived areas.Of the 58,186 coronavirus deaths among adults in England during March\u2013December 2020, 77% occurred in hospitals, 93% were in patients Reliable ascertainment and description of mortality rates is vital in monitoring the public health response to coronavirus disease (COVID-19). Disparities between population subgroups provide critical insights into which groups are most affected, directly informing the public response. In England, COVID-19 was first detected on January 30, 2020; the first COVID-19 death occurred on March 2, 2020. We describe trends in COVID-19 mortality rates by age group, sex, ethnicity, residential region and socioeconomic deprivation, time from positive specimen date to death, and place of death during the first 9 months after the first known COVID-19 death in England.>18 years of age from 3 sources: hospital trusts using the COVID-19 Patient Notification System; local PHE Health Protection Teams ; and the National Health Service Demographic Batch Service, which matches of all laboratory-confirmed COVID-19 cases against registered deaths records. Data from each source were combined daily into a single dataset, the COVID-19 Specific Mortality Surveillance System (COSMOSS) receives daily reports of the date of death, the date the specimen is taken for COVID-19 testing, and laboratory results for adults COSMOSS data are matched using a unique patient identifier to death registrations from the Office for National Statistics were reported.Social distancing measures were announced nationally on March 23, 2020, 3 weeks after the first death. The number of COVID-19 deaths peaked on April 8, \u22482 weeks after social distancing began , 2, grad>60 years of age, and 57% occurred in men of deaths in adults occurred in persons d in men ; 64% of ulation) . During ulation) .Place of death was available for 86% of decedents. Overall, 77% of deaths occurred in hospitals, 18% in residential care homes, and the remainder elsewhere . The median time from specimen date to death was 8 days (interquartile range 4\u201315 days); 91% died within 28 days of the specimen date. Of those dying in hospital, 96% died within 28 days of the specimen date, compared with 86% in residential care homes and 84% elsewhere.When we compared first 4.5 month period with the second, the demographic profile of decedents did not change substantially by sex (57% vs. 57% were men), ethnicity (87% vs. 89% White), place of death , or time to death (91% vs. 91% within 28 days of specimen date). However, region of death became less London-focused , and the>60 years of age. Men, Black persons, Asian persons, persons of other or mixed ethnic groups, and residents in deprived areas also experienced higher cumulative mortality rates compared with White persons and persons in less deprived areas. Almost 1 of 10 persons died >28 days after their specimen date, and 1 of 4 persons died outside hospital.In the 9-month period after the first COVID-19 death in England, \u224858,000 adults died of COVID-19 that show older age is associated with higher COVID-19 mortality rates was developed rapidly, is comprehensive, and captures deaths daily in all settings (Further analyses using multivariate models are underway and will better measure the clinical and demographic risk factors for COVID-19 deaths. Furthering understanding of the characteristics of those who die and the context in which they are living is the only way we can reduce COVID-19 mortality overall and address the factors that are driving the inequalities observed across England."} +{"text": "Sexually transmitted diseases (STDs) are a major cause of morbidity in the United States, with an estimated $15.9 billion in lifetime direct medical costs. Although the majority of STDs are diagnosed in the private sector, publicly funded STD clinics have an important role in providing comprehensive sexual health care services, including STD and HIV screening, for a broad range of patients. In certain cases, STD clinics often are the only source of sexual health care for patients, particularly among gay, bisexual, and other men who have sex with men (MSM).2010\u20132018.The STD Surveillance Network (SSuN) is an ongoing sentinel surveillance system for monitoring clinical information among patients attending STD clinics. SSuN is a collaboration of competitively selected state and city health departments that conduct facility-based sentinel surveillance in STD clinics. Information routinely collected through the course of patient encounters is obtained for all patients seeking care in the participating STD clinics. This information includes demographic, behavioral, and clinical characteristics . This report presents 2010\u20132018 SSuN data from 14 STD clinics in five cities to describe the patient populations seeking care in these STD clinics. Estimated numbers and percentages of patients receiving selected STD-related health services were calculated for each year by using an inverse variance weighted random-effects model, adjusting for heterogeneity among SSuN jurisdictions. Trends in receipt of selected STD-related health services were examined and included HIV screening after an acute STD diagnosis among persons not previously known to have HIV infection, annual chlamydia screening among adolescent and young females, and extragenital chlamydia and gonorrhea screening among MSM.During 2010\u20132018, the total number of annual visits made in the 14 participating STD clinics decreased 29.8% , and the total number of unique patients examined in the clinics decreased 35.1% . Decreases in the number of unique patients occurred both among men who have sex with women only and among females . The decreases in the number of female patients were observed across all age groups, although they were more pronounced among females aged \u226424 years . In contrast, the number of patients identified as MSM increased 44.0% , with the greatest increase among MSM aged \u226525 years . Among visits during which an acute STD was diagnosed, the percentage of visits during which an HIV test was performed within approximately 14 days of the STD diagnosis increased from 58.2% in 2010 to 70.2% in 2018. Among those patients tested, 1,672 HIV infections were identified, of which 84.0% were among MSM. Among females aged 15\u201324 years, the percentage screened for chlamydia in any calendar year increased from 88.6% in 2010 to 90.6% in 2018. However, because fewer females aged 15\u201324 years attended these clinics during the study period, the crude number of adolescent and young females tested for chlamydia decreased from 14,249 in 2010 to 4,507 in 2018. During 2010\u20132018, the percentage of females retested after their first positive chlamydia diagnosis during the same year ranged from 11.4% to 13.3%. During 2010\u20132018, the percentage of MSM tested for rectal chlamydia and rectal gonorrhea increased . During the same period, increases were noted in the percentage of MSM with diagnosed rectal chlamydia (from 15.5% in 2010 to 17.7% in 2018) and rectal gonorrhea (from 13.3% in 2010 to 17.1% in 2018). In contrast with pharyngeal chlamydia, pharyngeal gonorrhea screening was more common (from 69.5% in 2010 to 74.6% in 2018), and the percentage positive doubled during the study period (from 7.3% in 2010 to 14.8% in 2018). Pharyngeal chlamydia testing also increased (from 50.3% in 2010 to 72.9% in 2018), with concurrent decreases in positivity (from 4.2% in 2010 to 2.6% in 2018).During 2010\u20132018, changes occurred in the demographic composition of patients attending STD clinics participating in SSuN. Understanding trends in the demographic profile of STD patients and services provided can help identify addressable gaps in STD control efforts and direct public health action. Overall, fewer females, especially those aged 15\u201324 years, accessed care in these STD clinics during the study period. Untreated STDs among adolescent and young females can have serious consequences, including pelvic inflammatory disease and infertility. Additional efforts to monitor where adolescent and young females seek care and to ensure they are receiving quality STD-related health services are needed, especially considering increases in reported cases of STDs among females. Increases in the number of MSM attending STD clinics present a unique opportunity to reach this population with STD and HIV prevention services. Although a large percentage of STD cases are diagnosed outside of STD clinics, publicly funded STD clinics are an important safety-net provider of STD-related health services and provide vital STD-related health services for patient populations at risk for the consequences of STDs and HIV infection.STD-related health services represent effective strategies for preventing STD and HIV transmission and acquisition or STD-related sequelae. Ensuring that all persons receive quality HIV and STD prevention and treatment services is vital for an effective public health approach to reducing STDs. STD clinics provide crucial safety-net services for preventing STD-related morbidity, including timely identification and treatment of curable STDs such as chlamydia, gonorrhea, and syphilis. Increases in the numbers of MSM attending STD clinics participating in SSuN provide additional opportunities for linking patients to high-impact HIV preventive services , and the clinics are positioned to facilitate initiation or resumption of treatment among persons living with HIV. Reported cases of sexually transmitted diseases (STDs) continue to increase, and STDs remain a major cause of morbidity in the United States. In 2018, a record 2.4 million combined cases of chlamydia, gonorrhea, and syphilis were reported to CDC , enhanced surveillance in sentinel sites, including STD clinics, provides for monitoring trends among populations at risk for the consequences of STDs and HIV infection. Understanding who seeks care in STD clinics and the patterns of STD-related health services provided by those clinics is important for planning and monitoring STD and HIV prevention and control program activities. In addition, funding priorities have shifted, and a reduction in the number of STD clinics has been observed nationwide, which might have resulted in reduced access to STD-related care for certain populations (The STD Surveillance Network (SSuN) comprises state and city health departments that receive funding for facility-based surveillance activities. These departments collect and report to CDC the demographic, behavioral, and clinical data about patients seeking STD-related health services at participating STD clinics. During SSuN cycle 1 (2005\u20132008), six jurisdictions were funded primarily for conducting genital wart and gonorrhea surveillance. During SSuN cycle 2 (2008\u20132013), funding was expanded to 12 collaborating state and city health departments, and data collection for facility-based surveillance encompassed the full census of STD clinic patients, not just those with selected diagnoses. SSuN cycle 3 (2013\u20132018) followed similar methods as cycle 2, continuing the core functions of the network in monitoring the incidence of STDs and care-seeking behaviors among all patients at participating STD clinics. Because cycles 2 and 3 used similar methods, data were included from the overlapping five jurisdictions with 14 STD clinics that participated in SSuN cycles 2 and 3 and that transmitted data for the entire 9 calendar years (2010\u20132018).State and local health departments applied to participate in the SSuN cycles 2 and 3 as part of the funding opportunity announcements STD Surveillance Network CDC-RFA-PS08-865 and STD Surveillance Network CDC-RFA-PS13-1306. Five state and city health departments providing data from 14 STD clinics submitted SSuN facility data during 2010\u20132018: Baltimore, Maryland (two clinics); New York City, New York (eight clinics); Philadelphia, Pennsylvania (two clinics); San Francisco, California (one clinic); and Seattle, Washington (one clinic). SSuN is not designed to be nationally representative; rather, sites are competitively selected to fulfill the objectives and scope of the project across multiple geographic settings as outlined by the notices of funding opportunity. The 14 STD clinics in the five cities represent clinics with large numbers of patients, including MSM, adolescents, and young adults.Visit-level demographic, behavioral, and clinical data were collected from the full census of patients seeking services in participating SSuN STD clinics as documented in each clinic\u2019s electronic medical records; these data also were collated across patient visits each year. Clinic visits that were classified as express visits were not included in this analysis. The term \u201cvisit\u201d is defined as a single nonexpress visit to the STD clinic. For cycles 2 and 3, SSuN collaborators in each of the funded jurisdictions and CDC\u2019s principal investigators defined data elements. All the data collected for this project were ascertained through routinely collected electronic health records from a clinic visit. The investigators did not conduct patient interviews. Extracted data for this analysis included age, race/ethnicity, sex/gender identity, sex of sex partners, HIV status, previous HIV screening and results, STD diagnoses, and laboratory screening and results. Unique patient and clinic or event identifiers were established to provide longitudinal monitoring of multiple visits by patients within each clinic. SSuN jurisdictions, in conjunction with data management staff members at the participating STD clinics, produced three main data sets. The first of these was a visit file containing demographic, behavioral, and self-reported HIV infection status information collected at that visit. The second file contained visit-level STD-related diagnoses. The third file contained visit-level laboratory tests and results. Participating SSuN jurisdictions completed data verification and validity checks on each of the files and transmitted deidentified data to CDC through a secure data portal. When CDC received the files, additional data verification and validity checks for quality assurance, including consistency checks to ensure that data in the records were internally rational, were performed. All three files were linked by the unique patient and visit or event identifiers allowing for deduplication. Errors, including duplicate patient or event identifiers, were submitted to the jurisdictions, and the jurisdictions were asked to fix the errors before retransmission to CDC. After the processing of data, the files were merged into the national SSuN data sets for analysis. Jurisdictions upheld the Data Security and Confidentiality Guidelines for HIV, Viral Hepatitis, Sexually Transmitted Diseases, and Tuberculosis Programs HIV screening among persons not known to be living with diagnosed HIV infection who received a diagnosis of an acute STD, 2) chlamydia screening among adolescent and young females and rescreening at 8\u201316 weeks among those who had a documented chlamydial infection, and 3) extragenital chlamydia and gonorrhea screening among MSM. Annual counts were based on either the number of unique patients or the number of visits, depending on the selected characteristic being analyzed.The estimated percentages might have varied across clinics, and simply aggregating the data across jurisdictions could lead to biased estimates if heterogeneity were not considered. In addition, clinics provided data for a full census of patients, and simple aggregation would be biased toward clinics with the largest numbers of patients. Therefore, for each of the demographic and STD-related health service estimates, jurisdiction-specific estimates for each year were calculated and combined by using an inverse variance weighted random-effects model. The random-effects model incorporated heterogeneity across the jurisdictions by allowing each jurisdiction to have a different true prevalence. SAS was used to conduct all analyses.Trends in five demographic and clinical characteristics of patients were described: sex/gender identity, race/ethnicity, age, sex of sex partners, and HIV status. Sex/gender identity categories were male, female, transgender, and unknown. Race/ethnicity was categorized as non-Hispanic (NH) White, NH Black, Hispanic, NH Asian/Native Hawaiian and other Pacific Islander (NHOPI), or NH other . Age was based on age at last clinic visit of each year and was grouped into categories of \u226424 years and \u226525 years, except for the analysis of chlamydia screening . Patients were categorized as MSM, men who have sex with women only (MSW), females, and males with unknown sex of sex partners. Classification of male sexual behavior/orientation was based on the sex partner\u2019s reported or self-identification of sexual orientation as reported by the patient. Sexual orientation and sex of sex partner data were collected for female patients, and the majority identified as heterosexual women and reported only sex with men. However, due to small sample sizes among the female groups who identified as homosexual or bisexual or among those with missing information, results stratified by sexual orientation were not shown. Hence, females without regard to the sex of their sex partners were reported. Patients were categorized as known to be living with diagnosed HIV infection if a laboratory-documented positive HIV antibody test was included in their clinic records or the record contained a self-reported HIV diagnosis. All other patients were categorized as HIV uninfected or status unknown.The U.S. Preventive Services Task Force (USPSTF) recommends routine HIV screening among all persons requesting testing for STDs . However, fluctuations were noted in trends in unique patients by age group. For example, decreases occurred in the percentages of patients aged \u226424 years (33.6% in 2010 versus 21.3% in 2018), concurrent with increases in the percentage of patients aged \u226525 years (66.4% in 2010 versus 78.7% in 2018) . Overall, the number of patients known to be living with diagnosed HIV infection who were accessing care in participating SSuN clinics increased , whereas the number of visits decreased .During 2010\u20132018, a total of 713,380 unique patients sought care at 14 STD clinics from five jurisdictions with continuous participation in SSuN during this time frame . The numhttps://stacks.cdc.gov/view/cdc/110780). In addition, clinic visits by MSM increased 76.3% (https://stacks.cdc.gov/view/cdc/110780). During 2010, unique MSM patients accounted for 17.9% of the clinic populations; however, by 2018, MSM accounted for 30.9%. (https://stacks.cdc.gov/view/cdc/110780). During 2010\u20132018, the percentage of MSM who were NH Black decreased (from 38.8% in 2010 to 29.0% in 2018), as did the percentage who were NH White (from 37.5% in 2010 to 33.1% in 2018) . Concurrent increases occurred in the percentages of MSM who were Hispanic (from 14.8% in 2018 to 20.7% in 2019 ), NH Asian/NHOPI (from 5.1% in 2010 to 6.5% in 2018), and NH other race (from 3.8% in 2010 to 10.7% in 2018). Among MSM, the percentage aged \u226525 years increased (from 77.1% in 2010 to 85.0% in 2018) (data not shown). The number of MSM visiting participating clinics who were known to be living with diagnosed HIV infection increased , although the overall percentage of MSM who were known to be living with diagnosed HIV infection decreased (from 22.5% in 2010 to 17.7% in 2018) .The number of unique MSM patients seeking care at the 14 participating STD clinics increased 44.0% . Overall, the percentage of patients who were MSW decreased from 39.4% in 2010 to 34.3% in 2018 (https://stacks.cdc.gov/view/cdc/110780). Among MSW, the percentages decreased among those who were NH White (from 25.2% in 2010 to 20.5% in 2018) and NH Black (from 54.8% in 2010 to 50.8% in 2018). Concurrent increases occurred in the percentages of MSW who were Hispanic (from 12.2% in 2010 to 13.5% in 2018), NH Asian/NHOPI (from 3.6% in 2010 to 5.0% in 2018), and NH other race (from 4.2% in 2010 to 10.2% in 2018). During 2010\u20132018, the percentage of MSW aged <25 years decreased from 28.8% in 2010 to 18.8% in 2018. The percentage of MSW patients who were known to be living with diagnosed HIV infection visiting participating SSuN clinics was stable (1.1% in 2010 versus 1.0% in 2018) .During 2010\u20132018, the number of unique MSW patients seeking care at the 14 participating STD clinics decreased , as did the number of clinic visits by MSW (Supplem in 2018 (Supplemhttps://stacks.cdc.gov/view/cdc/110780). Overall, the percentage of males with unknown sex of sex partners visiting participating clinics increased, from 4.8% in 2010 to 5.2% in 2018 .During 2010\u20132018, the number of unique male patients with unknown sex of sex partners seeking care at the 14 participating STD clinics decreased 59.9% . Clinic visits made by males with unknown sex of sex partners also decreased (Supplemhttps://stacks.cdc.gov/view/cdc/110780). Overall, females accounted for a decreasing percentage of all patients (from 34.7% in 2010 to 26.4% in 2018) (https://stacks.cdc.gov/view/cdc/110780). Among females, the percentages of those who were NH Black and NH White decreased . Increases occurred in the percentages of females who were Hispanic (from 12.0% in 2010 to 13.9% in 2018), NH Asian/NHOPI (from 6.3% in 2010 to 7.1% in 2018), and NH other race (from 5.9% in 2010 to 10.3% in 2018). Among females, the percentage of those aged \u226424 years decreased (from 44.8% in 2010 to 30.4% in 2018 [data not shown]). The percentage of female patients visiting participating SSuN clinics who were known to be living with diagnosed HIV infection remained stable (0.9% in 2010 and 1.0% in 2018) .During 2010\u20132018, the number of unique female patients seeking care at the 14 participating STD clinics decreased , as did the clinic visits by females (Supplemin 2018) (Supplemhttps://stacks.cdc.gov/view/cdc/110780). Overall, among all patients, the percentage of transgender patients increased (from 0.2% in 2010 to 0.6% in 2018) . Among transgender patients, decreases occurred in the percentages who were NH Black (from 38.1% in 2010 to 21.1% in 2018) and NH White (from 26.6% in 2010 to 22.8% in 2018). During 2010\u20132018, concurrent increases occurred in the percentages of transgender patients who were Hispanic (from 26.8% in 2010 to 31.3% in 2018), NH Asian/NHOPI (from 5.7% in 2010 to 7.8% in 2018), and NH other race (from 2.8% in 2010 to 17.0% in 2018). When stratified by age group, the percentage of transgender patients aged \u226424 years decreased (from 25.1% in 2010 to 18.1% in 2018). The percentage of transgender patients visiting participating clinics who were known to be living with diagnosed HIV infection increased (from 10.9% in 2010 to 13.0% in 2018) .The number of unique transgender patients seeking care at the 14 participating STD clinics increased (from 123 patients in 2010 to 299 patients in 2018), with a corresponding increase in the number of clinic visits by transgender patients (from 301 visits in 2010 to 662 visits in 2018) (Supplemhttps://stacks.cdc.gov/view/cdc/110780). However, HIV screening coverage was higher among MSM than among MSW and females throughout the period (https://stacks.cdc.gov/view/cdc/110780).During 2010\u20132018, the overall percentage of unique patients with a diagnosed acute STD at least once during the calendar year increased (from 9.0% in 2010 to 12.9% in 2018), although the absolute number of clinic patients with at least one acute STD diagnosis annually decreased . Overall, the percentage of patients with an acute STD diagnosis who were not known to be living with diagnosed HIV infection screened for HIV within \u226414 days of the STD diagnosis increased (from 58.2% in 2010 to 70.2% in 2018). HIV screening among persons with an acute STD diagnosis increased for MSM, MSW, and females . The number of females screened for chlamydia decreased during the study period because of decreases in the number of adolescent and young females seeking care in the participating 14 clinics. In 2010, a total of 14,249 females aged 15\u201324 years were screened for chlamydia, compared with 4,507 screened in 2018, representing a 68.4% decrease throughout the study period. The overall percentage of females with at least one positive chlamydia test during any calendar year increased (from 16.2% in 2010 to 19.9% in 2018) (https://stacks.cdc.gov/view/cdc/110780).The percentage of females aged 15\u201324 years screened for chlamydia at least once during a calendar year was 88.6% in 2010 and 90.6% in 2018) (Supplemin 2018) (Supplemhttps://stacks.cdc.gov/view/cdc/110780). Higher chlamydia screening coverage was observed among females aged 20\u201324 years (from 90.7% in 2010 to 93.8% in 2018). When stratified by age group, females aged 15\u201319 years (from 21.5% in 2010 to 30.5% in 2018) had consistently higher positivity than those aged 20\u201324 years (from 13.5% in 2010 to 15.6% in 2018) .https://stacks.cdc.gov/view/cdc/110780). However, chlamydia positivity varied, with higher positivity among females who were NH Black and NH other race noted across all years, compared with females who were NH White, Hispanic, or NH Asian/NHOPI (https://stacks.cdc.gov/view/cdc/110780).When stratified by race/ethnicity, the percentage screened for chlamydia each year ranged from 80% to 93% in all racial/ethnic groups during the study period (Suppleman/NHOPI (Supplemhttps://stacks.cdc.gov/view/cdc/110780). Each year, rescreening positivity (23.0% in 2010 versus 27.1% in 2018) was higher than overall screening positivity (16.2% in 2010 versus 19.9% in 2018). Because of the small sample size, stratification by age group or race/ethnicity among females who were rescreened was not performed.Rescreening at 8\u201316 weeks among adolescent and young females after their first positive chlamydia test varied by year . In 2010https://stacks.cdc.gov/view/cdc/110780). Because gonococcal and chlamydial infections are usually detected using a single diagnostic nucleic acid amplification test (NAAT), a similar increase was noted among those screened for rectal gonorrhea (from 55.0% in 2010 to 58.4% in 2018). Absolute numbers of MSM screened increased for both rectal chlamydia and rectal gonorrhea . Throughout the study period, positivity among MSM also increased for rectal chlamydia (from 15.5% in 2010 to 17.7% in 2018) and rectal gonorrhea (from 13.3% in 2010 to 17.1% in 2018) .https://stacks.cdc.gov/view/cdc/110780). During the same period, pharyngeal gonorrhea positivity doubled among MSM (from 7.3% in 2010 to 14.8% in 2018). Pharyngeal chlamydia screening among MSM also increased (from 50.3% in 2010 to 72.9% in 2018). Pharyngeal chlamydia positivity decreased during the study period (from 4.2% in 2010 to 2.6% in 2018) , with a corresponding increase in the annual number of MSM patients screened (Supplemin 2018) .,,\u2013Historically, publicly funded STD clinics have served as a crucial safety-net provider for certain populations . HIV and other STDs share sexual and other risk factors. Moreover, being infected with STDs such as syphilis and gonorrhea can lead to an increased risk for HIV infection. For these reasons, since 1987, U.S. clinical guidelines have recommended routine HIV screening of persons with STDs in all clinical settings. Screening STD patients for HIV identifies substantial numbers of HIV infections. For example, among all sites, states, and independently funded jurisdictions receiving CDC support for HIV screening in 2011, STD clinics conducted 19% of tests performed in health care settings and identified 26% of all new HIV cases , chronic pelvic pain, infertility, and life-threatening ectopic pregnancy. Because chlamydial infections are largely asymptomatic among females, screening is a principal component of comprehensive chlamydia prevention and control activities and can reduce the incidence of PID . Because of the substantial decrease in females seeking care in STD clinics, further study is warranted to ensure they are still accessing health care and are being screened and rescreened as recommended for chlamydia and other STDs.Although overall annual chlamydia screening coverage was high, the decreases in the number of young females screened for chlamydia is notable. First, ACA expanded access to health insurance for certain adolescents and young adults beginning in 2014, offering opportunities for them to access preventive services, including chlamydia screening, from different types of health care providers. However, this cannot entirely explain observed trends, especially because the decreases were observed before ACA was fully implemented. Second, funding for public health has been declining, resulting in budget and staffing reductions and closures of clinics providing STD services (. During the study period, the percentage of MSM screened for rectal and pharyngeal gonorrhea and chlamydia increased modestly; however, with the substantial increases in the number of MSM seeking care in STD clinics, the crude number of MSM screened for either pathogen doubled. Extragenital gonococcal and chlamydial infections often are asymptomatic and can be readily passed to an uninfected partner, contributing to an increased risk for HIV acquisition or transmission (Increases in diagnoses of extragenital chlamydial and gonococcal infections were also observed. Increases in disease incidence might account for this, although other explanations, such as increases in disease detection and increased screening, are possible. First, in 2010, STD treatment guidelines recommended using NAATs to routinely screen for rectal and pharyngeal chlamydial and gonococcal infections among MSM (The findings in this report are subject to at least seven limitations. First, estimates of unique patients, patient visits, and use of selected STD-related health services in the 14 clinics are not representative of all U.S. STD clinics or of other clinical and health care settings that serve populations at risk. Second, classification of sexual orientation and sex of sex partners was based on patient self-reported sex/gender identity or reporting of sex of sex partners, which might have led to misclassification. Third, although participating jurisdictions followed standardized protocols for abstracting data from electronic medical records and sending data to CDC, the data presented were not validated against clinics\u2019 complete medical records. In addition, medical and laboratory records are inherently complex and potentially susceptible to errors or omissions. Fourth, patients might have had STD or HIV screening at another health care facility or might have been offered screening but refused, indicating that these STD-related health measures are minimum estimates. Fifth, symptom status was not uniformly collected and screening might not be differentiated from diagnostic testing. This might have resulted in an overestimate of screening coverage. Sixth, because treatment data were not available, the analysis of chlamydia rescreening coverage was based on the 3 months after the initial positive chlamydia testing visit. In addition, guidelines also suggest that if rescreening at 3 months is not possible, clinicians should retest in the 12-month period after initial treatment. Hence, the rescreening rates in this analysis are more conservative because it was not possible to look across a 12-month time frame. Finally, regarding extragenital screening, a clinical history of sexual exposure by anatomic site was not collected; therefore, certain MSM included in the denominators of this metric might not have been exposed at a specified anatomic site and might not have been candidates for extragenital screening. Consequently, the percentage screened for extragenital infections is likely an underestimate of screening coverage.Ensuring that all persons receive quality HIV and STD prevention and treatment services is a vital part of an effective public health response to increasing STD rates (STD clinics have a principal part in an effective public health care system by focusing resources on priority problems and populations. An example of this is the implementation of express STD testing models for triaging patients to identify those who need to see a medical provider for a comprehensive examination versus asymptomatic patients who can just have laboratory samples submitted for STD testing (Although STD clinics continue to screen adolescent and young females for chlamydial infection at a high rate, a limited percentage was rescreened after a chlamydia diagnosis, resulting in missed opportunities for enhancing service provision. The asymptomatic nature of extragenital chlamydia and gonorrhea, in conjunction with a high prevalence identified among this clinic population, further supports the need to continue screening all anatomic sites of exposure among MSM. With the increasing incidence of STDs and renewed focus on ending the HIV epidemic at the national level, STD clinics are well positioned to offer vital care and prevention services to populations at risk, including MSM, adolescent and young females, and sexual/gender identity minorities. Moreover, describing the trends in health services provided in STD clinics can help develop a better understanding of the clinics\u2019 role and capacity for providing STD- and HIV-related health services as well as opportunities for program improvement.A core component of Ending the HIV Epidemic: A Plan for America is to provide HIV diagnoses for all persons with HIV infection as early as possible ("} +{"text": "The Democratic Republic of Congo\u2019s free TB care policy and recent progress with universal health coverage are insufficient to remove barriers to TB care access and adherence. As there were no nationally representative data on the economic burden borne by TB patients, the TB programme conducted a national survey to assess the proportion of TB patients facing catastrophic costs, which could also serve as a baseline for monitoring progress.A national survey with retrospective data collection and projection, following WHO methods, was administered to 1,118 patients in 43 treatment zones. Each patient was interviewed once on costs, time loss, coping measures, income, household expenditure and asset ownership. Total costs were expressed as a percentage of annual household expenditure.In 2019, 56.5% of households affected by TB experienced costs above 20% of their annual household expenditure. Mean costs amounted to respectively US$400 (range: 328\u2013471) and US$1,224 per episode of first-line and drug-resistant TB. The risk of catastrophic costs increased with hospitalisation, drug resistance status and lower economic status. Half of households resorted to coping strategies and experienced food insecurity. Only 7.5% received social support.TB-affected households incur on average a cost of US$549, despite free TB care policy. Mitigating this burden with medical cost reductions, social and labour market measures will be key. Assessing the economic burden borne of patients affected by TB and establishing progress towards zero suffering from catastrophic costs target are key to monitoring progress towards global and the Democratic Republic of Congo\u2019s strategy to end TB.4* kills 1 in 2000 infected, and was the third cause of mortality in 2019.10DR Congo were randomly sampled, and facilities selected with probability proportional to cases notified in 2017. Per facility, 26 patients were then consecutively sampled. All adults and children on treatment for TB for at least 14 days either in intensive or continuation phase from July to October 2019 were eligible, following WHO design.11From July to October 2019, 31 trained interviewers administered paper or electronic questionnaires, adapted from the WHO generic instrument,14Direct medical , non-medical and indirect costs were estimated per TB-affected household. Following WHO methods,Annual household expenditure was used as the primary method for determining household ability to pay. Collected self-reported income pre- and post-disease were not used as the main measure for household ability to pay nor as indirect cost measure; instead, annual household expenditure and time loss valued at a fixed hourly wage rate were used. Income loss was estimated using the human capital and equality of wages method, whereby hours lost in care were multiplied by minimum wage of CDF814 per hour.The patient\u2019s costs were compared against their household\u2019s annual expenditure. Each household was given a binary value representing whether or not they incurred catastrophic total costs due to their TB disease. Sensitivity analysis was conducted using alternative thresholds and alternative cost indicators . We did not test alternative ability to pay (denominator) measures, as this would have required imputation of missing self-reported income estimates and more comprehensive asset ownership reporting.The study collected and analysed the occurrence of coping strategies to compensate for costs faced for TB care, perceived social impact and self-assessed financial impact.In accordance with WHO reporting standards,P > 0.1). Statistical analyses and data visualisations were performed using Stata v15.0 and R v4.0.1 .The odds of TB-affected households incurring catastrophic costs were evaluated against the patient\u2019s sociodemographic and clinical characteristics using univariate and multivariate analysis. We present the unadjusted odds ratios (ORs) from univariate regressions and the adjusted odds ratios , Kinshasa, DR Congo (IOR G0008558/IRB) and the WHO African Region Ethics Review Board (AFR/ERC/2019/08.01). Written informed consent was obtained from adults and children\u2019s guardians prior to each interview.The study protocol was approved by the National Health Ethics Committee . Sampled patients included 59.6% male and 12.5% under age 15 or above 65, in line with routine surveillance patterns.Patients were interviewed at a health centre (71.5%), hospital (25.7%) or dispensary (2.8%); 5% of sampled patients were hospitalised at the time of interview and 10.9% during the treatment phase for an average of 13.3 days (95% CI 4.2\u201322.5) . HospitaOf all survey respondents, 50% were the main income earners prior to the disease . Annual Pre-disease levels of poverty in 2019 were 85.7% (95% CI 83\u201388) in all TB-affected households, 74% (95% CI 61\u201384) in the wealthiest quintile, 81.4% (95% CI 69\u201390) in DR-TB and 86.7% (95% CI 83\u201390) in DS-TB patients.On average, patients lost 428 hours in TB care; this was three-fold higher for DR-TB than for DS-TB , in particular in the continuation phase (Supplementary Table S1).The total TB episode costs incurred by affected households in 2019 averaged US$549 (95% CI 427\u2013670), including respectively US$74 (95% CI 46\u2013102), US$246 (95% CI 189\u2013302) and U$229 (95% CI 155\u2013303) for medical, non-medical and indirect costs. Patients with DR-TB incurred higher total costs than DS-TB patients . High mean episode costs among DR-TB were largely attributed to post-diagnostic travel costs and food outside normal diet . Detailed mean and median costs are presented in * as poverty levels decreased, so did the proportion of households experiencing catastrophic costs, declining from the poorest to the wealthiest from 76.8% (95% CI 65\u201386) to 34.3% (95% CI 21\u201350). On sensitivity analysis, 16% , 19.3% (DR-TB: 95% CI 11\u201333) and 15% (DS-TB: 95% CI 11\u201321) of affected households experienced direct medical out-of-pocket spending (OOP) higher than 10% of their annual household expenditure in 2019 (Supplementary Table S3).The proportion of TB-affected households experiencing costs higher than 20% of their annual household expenditure as per the WHO global monitoring indicatorHouseholds affected by drug resistance, poverty and hospitalisation had higher odds of incurring catastrophic costs than drug-susceptible, wealthiest and non-hospitalised households. The risk increased five-fold according to drug resistance status , ten-fold if in the poorest quintile and 22 times if hospitalised . Other factors explored were not statistically significant .The impact of TB on employment was drastic: employment of any form among patients dropped from 65% employment to 43% while in care, with informal employment dropping from 45% to 31%, presumably due to lower licensure or sick leave protection ; 23% of DR Congo relies heavily on out-of-pocket spending to finance health,With 86% of TB patients in 2019 below global poverty levels prior to entering TB care and 56.5% of TB-affected households experiencing catastrophic costs, policies are needed geared to increase access to care and social protection among the poorest. The higher annual household expenditure among DR-TB patients and their greater access to patient support (14% vs. 6% for DS-TB) may indicate that the poorest affected by DR-TB might not be accessing care or patient support, reinforcing previous findings on utilisation of services by Laokri et al.10Survey results can be compared to recent national surveys conducted in seven African countries from 2015 to 2020.2Several countries have successfully used this survey evidence as entry point for multisectoral actions.Survey evidences TB care delivery could potentially improve by shortening care-seeking time down from 10 weeks and US$1,224 per episode of first-line and drug-resistant TB, while 56.5% (95% CI 49\u201363.7) experience catastrophic costs, posing a barrier to TB diagnosis and treatment access. Reducing OOP and designing, social and labour market measures to mitigate these costs will be needed to achieve End TB targets. The relatively higher proportion of direct medical costs in DR Congo is likely a result of the use of the national minimum wage to value time loss. DR Congo\u2019s minimum wage is among the lowest in sub-Saharan Africa."} +{"text": "Empiric use of vancomycin is common in clinical practice. Currently there is strong evidence to support the use of MRSA nasal screening to predict the absence of MRSA in respiratory infections; however, minimal data exists regarding its utility as a de-escalation tool beyond pulmonary indications. Furthermore, MRSA nasal PCR has been shown to be a more efficient way to detect the presence of MRSA colonization than traditional culture methods. The purpose of this study was to evaluate the correlation between results of MRSA nasal PCR assays and blood or bone/soft tissue cultures.This was a retrospective study of patients who presented to any of three hospitals part of an integrated health system in Des Moines, Iowa, from March 1, 2019 to February 29, 2020. Included patients were those who underwent MRSA nasal PCR screening and had a clinical culture obtained within 3 days of the MRSA nasal PCR. Data on age, sex, diabetes mellitus and dialysis were collected. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for all cultures, and blood and bone/soft tissue cultures separately were estimated. A total of 1989 patients were included in the study. Of these patients, 1953 patients had a blood culture obtained and 171 patients had a bone/soft tissue culture obtained. The median age was 66 years, and 1086 (54.6%) patients were male. At baseline, 33.1% and 3.8% of patients had diabetes or were on dialysis, respectively. The overall prevalence of MRSA colonization was 12.3%. The sensitivities of the MRSA nasal PCR screening were 67.5% for all clinical cultures, 81.8% for blood cultures, and 55% for bone/soft tissue cultures. Specificities were 88.8%, 88.5%, and 92.7% for all cultures, blood cultures, and bone/soft tissue cultures, respectively. The PPVs were 11%, 7.5%, and 50% for all cultures, blood cultures, and bone/soft tissue cultures, respectively, and the NPVs were 99.3%, 99.8%, and 92.7%, respectively.MRSA nasal PCR screening showed high NPV across blood and bone/soft tissue cultures. These results indicate the clinical utility of MRSA nasal PCR assays beyond respiratory infections and can further support antimicrobial stewardship activities.All Authors: No reported disclosures"} +{"text": "The primary variables studied were BMI, BMI Z-score BMI-SDS and, additionally, the secondary variables studied were nutritional status and physical and mental health. In 72% of the interventions presented, positive effects were seen on the reduction of BMI, including in parents and their children. The interventions were carried out mainly by nutritionists in health centers. The duration of the 29 interventions was \u22646 months and \u226512 months, in 59% and 41% of the studies, respectively. 57% of the studies reported post-intervention results. 86% of the interventions included a physical activity component, 80% included a nutrition component, 66% included a behavioral therapy component and 55% included an education component. Concerning the effects of the intervention on the primary outcome, in interventions with a duration equal to or less than six months, the most effective interventions included recreational activities, education, and nutritional programs. In interventions lasting 12 months or more, the most effective interventions included physical activity recommendations, nutritional and physical exercise programs, and cooking classes. Conclusions: This systematic review analyzed the effectiveness of, and characterized, multicomponent interventions lasting for 6 and 12 months, aiming to treat childhood obesity in extremely cold climates. The most frequently used units of measurement were also analyzed and summarized. Evidence derived from RCT. These results can be useful for designing future interventions to treat childhood obesity in territories with an extremely cold climate.Aim: To analyze the characteristics of multicomponent interventions to reduce childhood overweight and obesity in territories with an extremely cold climate. Methods: A systematic review was conducted following the PRISMA statement. MEDLINE, PsycNet, SciELO, and grey literature databases were reviewed in the period between 2010 and 2020. Results: 29 articles were included ( The World Health Organization (WHO) has consistently reported that overweight and obesity are causing a significant deterioration in the health of the world\u2019s population . These cRegarding the global prevalence of obesity, it has almost tripled. Specifically, in 2019 the estimation was that 38.2 million children under the age of five were overweight or obese. This is a problem in high-, middle- and low-income countries, particularly in urban settings . BesidesThe consequences of childhood obesity are increased school absences and doctor visits , so chilTreatment strategies for childhood obesity have been carried out in multiple ways. Modifying the obesogenic environment and ensuring the acquisition of healthy lifestyle habits has been suggested for more than a decade . InterveIt has been reported that there is an association between extreme cold weather and childhood overweight or obesity. Thus, it has been shown that cold environments favor the development of obesity since it could influence hormones related to hunger, increasing the appetite towards excessive intake, and promote inactivity ,17. FurtAmong the coldest countries in the world are Russia, Canada, USA (north), Iceland, Finland, Estonia, Norway, Sweden, Denmark, Latvia, France, and New Zealand (south) . ScotlanIn Punta Arenas, Chile, winds of 80 miles per hour are common during the southern hemisphere summer. The temperature varies around an average of 6.5 \u00b0C, with the lowest temperature of \u221216.4 \u00b0C in Winter, June and July, and the highest of 29.9 \u00b0C in summer, January and February .The collected data on extreme cold weather are relevant for designing intervention strategies aimed at reducing overweight or obesity in children in these climates. To date, no systematic reviews have been reported that specify the characteristics of the interventions in children with overweight and obesity in territories with extremely cold climate characteristics.Therefore, the objective of this review is to analyze the characteristics of multicomponent interventions aimed at reducing overweight and obesity in children in territories with an extremely cold climate.This systematic review was carried out in accordance with the standards established by the PRISMA declaration .We reviewed the MEDLINE databases using PubMed, PsycNet, SciELO, and grey literature. The objective was to identify studies that carried out interventions for the treatment of overweight and obesity in children in extremely cold climates. The search covered the period from January 2010 to January 2020 taking as reference the Global Action Plan for the Prevention and Control of NCDs in the Americas. For this search, we used The MeSH terms: \u201cTherapy\u201d, \u201cTherapeutics\u201d, \u201cRehabilitation\u201d, \u201cObesity\u201d, \u201cOverweight\u201d and \u201cChild\u201d. The search strategy followed the Peer Review of Electronic Search Strategies (PRESS) . The seaStudies that met the following inclusion criteria were selected: (a) Country: interventions carried out in countries with extremely cold climates ; (b) Sample: boys and girls between 6 and 12 years old; (c) Methodological Design: randomized controlled clinical trial; (d) Period: between 2010 and 2020. Exclusion criteria were: reviews, editorial documents, protocols, and doctoral thesis .First, we used the Mendeley tool to look for duplicates. As no duplicates were found, then the articles that met the inclusion criteria were selected. When decisions could not be made considering only the title and abstract of the article, the full text was retrieved . We usedTo assess the methodological quality of the studies included in this review, we used the \u201cCochrane Handbook of Systematic Reviews of Interventions\u201d , evaluatThe main information of the included studies is presented in summary tables and figures. In the discussion, the most relevant methodological and applicability aspects are analyzed and some suggestions for future research are given.29 articles were included in this review, whose interventions were carried out in the following countries considered as extreme cold climate zones: Sweden, Canada, Denmark, United States, Iceland, Germany, Norway, Switzerland, England, Finland, Holland, and China. Considering all the studies, the total number of subjects at baseline was 4434, with an average adherence of 86%. The adherence to the programs, depending on the type of the intervention, was: (1) Physical activity and nutrition: 100%; (2) education: 93%; (3) behavioral and education: 93%; (4) physical activity and education and nutrition: 87%; (5) behavioral and nutrition: 86%; (6) physical activity and behavioral: 86%; (7) physical activity and behavioral and education and nutrition: 84%; (8) physical activity and behavioral and nutrition: 81%. Of these studies, 93% reported losses in their sample, the main reasons being categorized as follows: lack of time (10%), personal reasons (24%), attendance (41%), health (20%), not meeting criteria during the development of the intervention (17%), did not wish to continue (27%) and unspecified (34%). 58% of the studies recruited children from health centers, 27% from educational centers, and 51% from the community. The mean age was 9.3 years. Concerning gender distribution, 56% were women and 44% men. Regarding the prevalence of diseases, only two studies detailed this information: one included a child with asthma, and the other only healthy children. The main inclusion criterion (90%) was the BMI value corresponding to overweight or obesity, while in 3% of the studies it was the value of weight for height and 7% did not specify this information. 51% of the interventions were carried out in health centers, 13% in educational centers, 13% in university centers, and 13% in community centers. Of these studies, 13% did not specify this information .The risk of bias analysis revealed that the distribution of biases classified as \u201clow risk\u201d or \u201cunclear risk\u201d was similar, except for detection bias, in which 66% of the studies presented \u201cunclear risk\u201d, and reporting bias, in which 100% of the studies presented \u201clow risk\u201d. Among the four types of bias, studies classified as \u201chigh risk\u201d were only for \u201cperformance bias\u201d, where more than 10% (22%) of the studies presented \u201chigh risk\u201d .The studies presented as main result six variables related to childhood overweight and obesity: 38% reported BMI z-score, 34% reported BMI-SDS (standard deviation), 24% considered BMI (kg/m2) and 10% considered other variables, these being the percentage of body fat, body weight according to height and BMI-p (percentile). Regarding the main post-intervention result, 72% of the interventions presented significant changes, while 28% did not present significant post-intervention changes. Only nine studies analyzed the maintenance of this effect over time, obtaining statistically significant maintenance in 77% of cases. One of the inclusion criteria of 38% of the studies was that at least one of the parents was overweight or obese. In relation to the subjects who underwent the intervention, 4% included only parents, 6% only children, 52% included parents and children, and 34% included the entire family. In 59% of the studies, the duration of the intervention was equal to or less than 6 months, and in 41% it was equal to or greater than 12 months. 57% of the studies presented follow-up of post-intervention results. Of these, 43% followed up for a period equal to or less than 6 months, while 57% followed up for a period equal to or greater than 12 months. Regarding the professionals who participated in the interventions, 52% were nutritionists, 34% qualified professionals in exercise prescription , 32% doctors, 27% psychologists, 27% other types of professional , 23% included a nurse, 2% a social worker and 9% did not specify this information. The interventions were based on four components: (1) physical activity, (2) education, (3) behavioral therapy, (4) and nutrition. The physical activity component was included in 86% of the interventions, being implemented in 55% of cases as recommendations , in 16% of cases as physical exercise programs , and in 23% of cases as recreational activities (mainly games). Of the interventions. 55% included an education component, which was implemented mainly as healthy lifestyle recommendations focused on health promotion. Regarding behavioral therapy, 66% of the interventions included this component through cognitive-behavioral strategies: stimulus control, self-monitoring, coping strategies, dealing with problems, positive reinforcement, planning, goal setting, behavior skills, and parenting skills. Finally, 80% of the interventions included a nutrition component, which was implemented in 45% of cases as recommendations focused on healthy eating , in 34% of the cases as food plans using mainly the \u201ctraffic light system\u201d, and in 6% of cases healthy eating workshops were included .Duration equal to or less than six months: Considering all types of interventions, 77% obtained significant effects for the primary outcome. All the interventions that included the physical activity component showed significant effects on the primary outcome with the recreational activities modality, while with the recommendations modality they obtained significant effects in 59% of cases, and 83% of cases using the physical exercise program modality. All the interventions that included education had significant effects on the primary outcome, whereas those that included behavioral therapy had significant effects in 65% of cases. Finally, 100% of the interventions that included a nutrition component showed significant effects on the primary outcome when using the diet program modality, 63% with the recommendation\u2019s modality, and 50% when using the healthy cooking workshop modality. Furthermore, considering that all the interventions included at least two components, they all presented significant effects when they included the physical activity component in the form of recreational activities. However, the interventions that combined physical activity (recommendations approach), behavioral therapy, and nutrition component (recommendations approach) only presented significant effects when they also included the education component,Duration equal or more than twelve months: of the interventions, 89% had significant effects on the primary outcome. 67% of interventions that included a physical activity component presented significant effects with the recreational activities modality, 100% with the recommendations modality, and 100% with the physical exercise program modality. Regarding interventions that included education, 92% presented significant effects on the result. The interventions that included behavioral therapy had significant effects in 91% of cases. Finally, 100% of the interventions that included a nutrition component showed significant effects on the primary outcome with the diet program modality, 75% with the recommendations modality, and 100% with the healthy cooking workshop modality. Furthermore, only two interventions (11%) did not present significant effects, having in common that both included the nutrition component in the modality of recommendations .The variables studied in the different studies were grouped into three categories: nutritional status, physical and health condition, and psychological variables.This category was considered in 100% of the studies and included eight variables: BMI z-score (86% of studies), BMI (79%), waist circumference (44%), body composition , waist-to-height ratio (14%), skinfold (10%), hip circumference (6%) and neck circumference (3%) a.This category was considered in 76% of the studies and included eight variables: physical activity level (48% of studies), food intake (41%), blood pressure (34%), health biomarkers (31%), sedentary behavior (20%), aerobic fitness (17%), eating behavior (10%), muscular strength (3%) b.This category was considered in 24% of the studies and included seven variables: health-related quality of life (17% of studies), self-perception (6%), self-esteem (6%), mood (3%), anxiety (3%), depression (3%), and strengths and difficulties perceived by parents (3%) c.The instruments used in the studies were grouped into three categories: nutritional status, physical and health condition, and psychological variables.To assess these variables, six instruments were used: tape measure (34% of studies), anthropometry measurement (17%), bio impedance measurement (13%), dual-energy x-ray absorptiometry (DXA) (13%), caliper (6%), and the three-component model of body composition (3%) a.To assess these variables, 20 instruments were used, and were sub-grouped into four categories:Nutrition: to assess this category, the instruments used were food frequency questionnaire (17% of the studies), 3-day diet recall form (10%), 24h-dietary recall (3%), Block Kids questionnaire (3%), Dutch eating behavior questionnaire for children (DEBQ-C) (3%), The Family Eating and Activity Habits questionnaire (FEAH) (3%), Day in the life questionnaire (DiLQ) (3%) and 2-day nutritional dietary record (3%) b.Level of physical activity and sedentary behavior: to assess this category, the instruments used were non-validated questionnaire for dietary, physical activity and sedentary behaviors (33% of studies), accelerometers (13%), pedometer (6%), Physical activity questionnaire for children (PAQ-Q) (6%), Leisure Score Index (LSI) (3%) c.Physical condition: to assess this category, the instruments used were walking test (6% of studies), handgrip strength test (3%), ergo-spirometry test (3%), jumping test (3%) d.Cardiovascular risk: 31% of the studies took blood samples, while 13% measured blood pressure with a manual blood pressure cuff, and 20% with an automatic sphygmomanometer e.Ten instruments were used to assess these variables, and were sub-grouped into two categories:Psychological health: to assess this category, 6% of studies used the self-perceptions profile questionnaire for children (SPPC), 6% the children\u2019s depression scale (CDS), 6% the questionnaire of strengths and difficulties of the child reported by the parents (SDQ), 3% used the child and youth physical self-perception profile questionnaire (CY-PSPP), 3% the scale of intrinsic versus extrinsic orientation in the classroom, and 3% the multidimensional anxiety scale for children (MASC) f.Health-related quality of life: of the studies, 6% used the pediatric quality of life questionnaire (PedsQL), 3% the child health questionnaire, Dutch version (CHQ-PF50) and 3% the quality of life questionnaire for children between 7 and 13 years old (KID-KINDL-R) g.The main finding of this review is that interventions that are effective for the management of childhood overweight and obesity are those that combine the components of physical activity, diet, education, and behavioral therapy, and that involve children and parents as participants in the intervention. Specifically, the most effective interventions with a duration equal to or less than six months included recreational activities, education, and nutritional programs. The most effective interventions lasting 12 months or more included physical activity recommendations, nutrition programs, physical exercise programs, and cooking classes.For more details, the findings of this review are organized into four categories: the general characteristics of the studies, the assessment of the risk of bias, the main characteristics of the interventions, and the variables studied, as well as the assessment instruments used. Their importance and possible implications are discussed below.In this review, 12 countries belonging to North America, Europe, and Asia were included, where interventions were developed for the management of obesity in children between 6 and 12 years of age with overweight, or obesity in geographic areas with extremely cold climates. Childhood overweight and obesity are a global problem , with a The distribution of biases classified as \u201clow risk\u201d or \u201cunclear risk\u201d was similar, except for detection bias, which presented a 66% \u201cunclear\u201d risk. Detection bias is related to the blinding of the assessors to the study results, and although the Cochrane manual states that their blinding does not ensure success, lack of blinding could bias the study results . In any Most of the studies considered BMI as the main outcome to assess the effects of the interventions. Although this is logical, since it was the main inclusion criterion to classify overweight and obesity, some authors question its use because it is less sensitive to weight change in children with higher body weight . A changThe nutritional status variables were present in all studies, with BMI being the most studied variable despite its limitations, such as not allowing the distinction between fat mass and lean mass. It has also been observed that some children with normal BMI have fat mass values in the obesity range . Only abA limitation of this study is not having found, in the literature, interventions carried out in other representative countries in areas of extreme cold climate such as Russia, or southern Chile and Argentina. However, studies from 12 countries on three different continents were included, allowing a broad view of the characteristics of interventions to combat childhood overweight and obesity in geographic areas of extreme cold climate. This study can serve as a guide to implement interventions in areas with these characteristics, knowing which ones are the most effective, concerning the components addressed and their duration.The interventions that were effective in the management of childhood overweight and obesity were those that combined the components of physical activity, diet, education, and behavioral therapy and that involved both children and their parents as participants in the interventions. In interventions with a duration equal to or less than six months, the most effective included recreational activities, education and nutritional programs. In interventions lasting 12 months or more, the most effective included recommendations for physical activity, nutritional and physical exercise programs, and cooking classes. This demonstrates that the effectiveness of these programs requires a combination of components, with a multi-professional approach, aimed at implementing strategies that favor a healthy lifestyle in children, involving parents as active participants in the process. The results of this review serve as a reference to design future effective interventions in the management of childhood obesity in extremely cold climates."} +{"text": "Parascaris spp. remains the most important parasite infecting foals and weanlings. Anthelmintic resistance is highly prevalent in cyathostomins and Parascaris spp. worldwide and it must be factored into treatment decisions. To assess anthelmintic efficacy in Northern Italy, we sampled 215 horses from 17 sport and horse-breeding farms. Fecal egg count reduction tests (FECRT) were used to assess anthelmintic efficacy. Copromicroscopic analysis was performed using MiniFLOTAC before treatment with fenbendazole, pyrantel pamoate or ivermectin, and repeated 14 days post-treatment. Strongyle-type eggs were detected in 66.91% of horses (CI95% 61.40\u201373.79%), while Parascaris spp. was detected in 2.79% (CI95% 1.94\u20135.95%). Reduced efficacy against cyathostomins was observed for fenbendazole in 55.56% of the treated animals (CI95% 41.18\u201369.06%), and for pyrantel pamoate in 75% of animals (CI95% 30.06\u201395.44%). Ground-based actions must be set in place to promote the uptake of state-of-the-art worm control plans that will prevent clinical disease while minimizing the selection pressure of resistant parasites.Nematodes are an important cause of disease and loss of performance in horses. Changes in the parasitic fauna of horses have occurred in the past few decades, making cyathostomins the major parasites in adult horses, while large strongyles have become less prevalent. Strongylus spp. [Resistance is a mechanism determined according to genetic base, defined as the ability of a parasite within a population to survive treatments that are generally effective against the same species and stage of infection . Today, lus spp. , as a relus spp. . Among olus spp. . The firlus spp. , and nowlus spp. ,9,10. Whlus spp. ,12,13, mlus spp. ,15,16,17lus spp. . In factlus spp. . Animal lus spp. , comparelus spp. .Parascaris spp. and cyathostomin infections in the field [The fecal egg count reduction test (FECRT) is recognized as the gold standard for defining the anthelmintic susceptibility of both he field . We therA questionnaire was administered to the farm manager/veterinarian prior to enrollment to establish history of anthelmintic drug usage. Specifically, we collected information on frequency of treatment, active principles used as well as treatment criteria (selective vs. strategic vs. symptomatology-based treatment) .n = 2, maximum enrolled horses n = 39, proportionally divided by age class) were subjected to FECRT [Only facilities for which detailed information on anthelmintic drug usage was available for the 3 years prior to the beginning of the study were included. Eligible facilities must have used the same anthelmintic product for 2 consecutive treatments to be enrolled. From each facility, 25% of the horses present suggested for each drug category by Nielsen et al. . Horses Coprocultures were performed on all positive samples at T0 and repeated, if positive, at T14 post-treatment. Individual samples (10 g) were incubated in Petri dishes for 10 days in a stove at 23\u201325 \u00b0C to obtain infective L3 larvae. The larvae were isolated using the Baermann technique and 10 larvae per sample were identified to larval type by morphology ,25,26,272) confidence intervals at 95% and odds ratio (OR) and generalized linear models (GLM) were used to assess the influence of management practices and horse individual characteristics on parasite load and reduced efficacy. Differences were considered significant at p < 0.05.Statistical analysis was performed using R3.4.4 . Chi-squn = 166 horses from 13 facilities), followed by FBZ (n = 45 horses from 3 facilities) and PYR (n = 4 horses from 1 facility). A total of 215 horses were sampled . The horses were 38% geldings, 13% stallions and 49% mares and were distributed in three age classes . FEC at T0 detected intestinal strongyle eggs in 66.91% of the tested animals (CI95% 61.40\u201373.79%). Infection in each positive facility ranged from 16.67% (CI95% 4.70\u201344.8%) to 100% (CI95% 34.24\u2013100%) while all horses from one recreational center tested negative , while management was shown to highly influence parasite load. Horses housed exclusively on paddocks showed greater FEC than those housed in boxes or on pastures . Frequent (once or more per week) manure removal was significantly associated with lower FEC . The mean EPG value for strongyle eggs at T0 was 515 from four facilities . As expected, animals under 1 year of age were significantly more infected with Parascaris spp. compared to older age categories and Parascaris spp. was detected in 100% of the facilities where foals were present. Parascaris spp. FECRT results showed a 100% reduction in all infected animals. In animals treated with PYR, the efficacy of treatment against strongyles yielded an FECR lower than the expected cutoff [p < 0.05). PCR for the beta-tubulin codon 200, differentiating the codon TTC/TAC polymorphism, carried out on FBZ-resistant horses from stud farm 2, showed the presence of the resistant homozygote variant (RR) in 20 subjects, while the remaining five showed the heterozygote variant (Rr). PCR of pooled samples allowed determination of the presence of the resistance allele R in all samples from all studied facilities. Coproculture of positive T14 samples allowed the identification of three different cyathostomin larval types, namely type A (including Cylicocyclus nassatus (NAS), Cylicostephanus goldi (GLD), Cyathostomum catinatum (CAT), Cylicostephanus longibursatus (LNG), Cylicocyclus insigne (INS) and Coronocyclus coronatus (COR)), type C (including Cyathostomum pateratum (PAT) and Cylicostephanus calicatus (CAL)), and type D including Cylicocyclus ashworthi (ASH), while Strongylus edentatus (EDN) was detected in one individual sample. For each of the identified larval types at T0, we reported the distribution among sampled facilities , and on the implementation of selective treatment strategies to reduce selection pressure for resistance . GuideliParascaris spp. showed no resistance, regardless of the type of anthelmintic used. For strongyles, FECRT evidenced no resistance phenomena in any of the facilities where macrocyclic lactones were used. In the literature, recent studies detected reduced efficacy of IVM in horses from the UK [IVM was the most frequently used anthelmintic product, as it was used by 12 recreational facilities and by one breeding center. m the UK , Italy [m the UK ,35, the m the UK . FBZ wasm the UK ,37. In Em the UK , the UK m the UK ,39, Germm the UK , Switzerm the UK , Sweden m the UK , Denmarkm the UK and the m the UK , while rm the UK , Denmarkm the UK , the UK m the UK , Finlandm the UK and Germm the UK .p < 0.05).Molecular determination of FBZ resistance-related alleles allowed determination of the presence of resistance allelic variants in all enrolled facilities, including those where FBZ had not been used for at least 3 years. Once acquired, resistance is permanent, even in populations of cyathostomins that remain unexposed to anthelmintic treatment for decades . This fiOur study accurately demonstrated the reduced efficacy of FBZ and PYR against strongyles, although some limitations are present. As previously reported from other countries , horse fWe observed higher prevalence of strongyle eggs in horses housed in paddocks if compared to those housed in boxes and pasture. Access to grass (either pasture or paddock) has been only weakly associated with cyathostomin infection and indiGiven the increasing importance of anthelmintic-resistant cyathostomins in horse management, it will be essential to promote the uptake of sustainable practices among veterinary practitioners, farm managers and horse owners in order to improve the collaboration between them and to establish an integrated parasitic control plan based on the correct use of anthelmintic drugs, adequate pasture hygiene and periodic FEC analysis."} +{"text": "Patient self-assessment via a mobile app detects actionable symptoms and has been shown to detect lung cancer relapses early, thereby lengthening survival.The purpose of this study was to assess the incidence of chief symptoms associated with the main tobacco-induced pathologies in both current and ex-smokers through a self-assessment smartphone app and to evaluate the app\u2019s capacity to encourage users to quit smoking or reduce consumption, as well as its impact on early lung cancer stages at the time of diagnosis.Current and ex-smokers were recruited through an advertising campaign in Sarthe county (France) proposing the free download of a smartphone app. App users were asked to answer 13 questions related to symptoms associated with tobacco-induced diseases . In the event of any positive answer, a message was displayed recommending the user to consult a physician. In addition, they were asked about smoking cessation intention before and after answering these 13 questions. Finally, incidence of stage 1 or 2 lung cancers diagnosed during the launch period of our application was evaluated by comparing data from various sources to those from the same period during the previous year.P<.001). The most frequent symptoms triggering the notifications were fatigue , cough , dyspnea , and persistent chest pain . Of the current smokers, 14.0% (515/3679) showed symptoms suggesting COPD, 15.5% (571/3679) showed symptoms suggesting stable angina, 12.4% (455/3679) probably had lower extremity artery disease, and 6.8% (249/3679) had possible cancer. Of the users, 36.5% (1343/3679) claimed that they thought about quitting smoking, and 48.7% (1795/3679) had thought about reducing their consumption. Surgery-eligible stage 1 and 2 lung cancer incidence was 24% (14/58) during the study period versus 9% (5/54) during the previous year in Sarthe county (P=.04), whereas it remained unchanged in the neighboring county of Maine-et-Loire.Of the 5671 users who were eligible for evaluation, an alert was sent to the majority , with a higher incidence for current smokers (2833/3679, 77.0% vs 1298/1992, 65.2%; A majority of current and ex-smokers showed worrying symptoms, and the use of a self-assessment smartphone app may drive a majority of smokers toward the intention of smoking cessation or decreasing consumption. A randomized study should be performed to confirm this intention and to support the potential increase of symptomatic lung cancer detection at early, surgery-accessible stages.ClinicalTrials.gov NCT04048954; https://www.clinicaltrials.gov/ct2/show/NCT04048954 Lung cancer is the most frequent cancer worldwide (2.09 million new cases in 2018) and the leading cause of death by cancer (1.76 million deaths in 2018) [In addition, tobacco consumption may also result in other tumoral diseases (22% of deaths by cancer), cardiovascular diseases (CVD), and chronic pulmonary diseases such as chronic obstructive pulmonary disease (COPD), extremely frequent yet underevaluated pathologies (80% of the concerned patients ignore their status) related to tobacco consumption in 85% of cases. Nonspecific symptoms are commonly disregarded by patients even thoYet, despite tobacco-cessation strategies ranging from awareness-raising campaigns to nicotine-replacement therapies, and\u2014more recently\u2014electronic cigarettes, long-term tobacco-cessation rates remain low .New information and communication technology services in the form of mobile health have become a cornerstone in oncology. Various clinical studies have demonstrated longer survival in patients treated by chemotherapy and earlA study conducted in England in 2015 showed that reaching smokers with persistent cough through a simple poster advertising campaign led to the diagnosis of 9% more lung cancers over the campaign period and an increase in good-prognosis, surgery-eligible stage I cancer diagnosis by 3 percentage points. The tagline was \u201cbeen coughing for 3 weeks or more? Tell your doctor\u201d . CurrentA dedicated self-assessment app provides regular analysis of symptoms in relation to tobacco consumption reported by patients on their smartphones and notifies them to consult their general practitioner (GP) in the event of suspicious symptoms. Knowledge about symptoms possibly indicating COPD, CVD, or lung diseases may help patients to reduce tobacco consumption or even quit smoking .The purpose of this prospective study was to assess the incidence of the main symptoms associated with the leading tobacco-related diseases, evaluate the capacity of the app to encourage smokers and ex-smokers to quit smoking or reduce tobacco use, and evaluate its impact on the incidence of symptomatic surgery-eligible lung cancer.Current and ex-smokers who quit smoking during the past 5 years were recruited via an advertising campaign on social media, newspapers, and public posters in the city of Le Mans and in Sarthe county (France). The campaign was held between June 3, 2019 and June 20, 2019. County GPs also received information on the app and were encouraged to propose it to their patients.The self-assessment smartphone app was available for free download on Android and Apple app stores. After entering personal anonymous data , current smokers were asked whether they considered quitting or did not wish to at all. Both current and ex-smokers were then requested to answer 13 simple questions linked to symptoms possibly corresponding with the following diseases: cancer , COPD, lower extremity arterial disease (LEAD), and angina. In the event of a positive answer to any of the mentioned points, a notification was sent recommending the user to consult his or her GP about the suspicious symptoms.Symptoms were selected by a board of experts according to specific semiology of each disease ,11.In addition, once the questionnaire was filled out, current smokers were asked whether they considered reducing tobacco consumption or quitting. In addition, a toll-free telephone number was provided for patient counseling on smoking cessation therapy.For the purpose of this study, participants were included based on the following criteria: aged 16 years or older, being a current or former smoker (cessation within the past 5 years), informed consent on data use.Exclusion criteria were a lack of consent and nonuse of the app.The study was approved by the French National Health Data Institute, which reviews ethical issues in human research, data confidentiality, and safety.We focused on the diagnosis of cancer in the 2 counties as data were available through the registries of thoracic surgical oncology, unlike information regarding COPD or arteritis. In addition, surgery remains the main curative treatment for lung cancer.We first assessed the number of users presenting with symptoms. We then evaluated the impact on smoking cessation intention after using the app and compared the rate of symptomatic lung cancer eligible for surgery in Sarthe county and neighboring Maine-et-Loire during the app roll-out period with the same period in 2018. Analysis of new cases started 12 weeks after launching the app to allow time for required examinations . This evaluation was conducted on the basis of private and public pathology laboratories\u2019 records in both Sarthe and Maine-et-Loire counties, thus providing 100% of documented lung cancer cases. Records from multidisciplinary team thoracic oncology meetings in both counties were analyzed to obtain the number of symptomatic lung cancers eligible for surgery.P<.05 considered to be statistically significant.Fisher and Mac-Neymar tests were used for descriptive analyses, with The app was downloaded 6835 times between June 3, 2019 and December 31, 2019, and 5671 users were eligible. Among them, 3679 (64.9%) were current smokers, and 1992 (35.1%) were ex-smokers. Median age was 39 years, 57.8% (3276/5671) were men, and 42.2% (2395/5671) were women. Regarding smoking history, 3425 had a 20 pack-year smoking history, and 4450 had been smoking for at least 20 years. The app was downloaded by 944 users in Sarthe county and 104 in neighboring Maine-et-Loire . In stepP<.001). The most frequently detected symptoms were unusual tiredness , persistent cough , dyspnea , and persistent chest pain . Current smokers were notified significantly more often than ex-smokers .Indeed, 78.0% (3213/4118) of the patients who received a notification had a smoking history of over 20 years, while 22.0% (905/4118) had less than 20 years of smoking history (P<.001).On average, users who received a notification had 1.93 symptoms. Current smokers had 2.13 symptoms, whereas former smokers had 1.57 symptoms .Associated symptoms that may be indicators of COPD, such as a persistent cough for 3 weeks with dyspnea or a need to expectorate, was reported by 14% (515/3679) of current smokers as well as 7.5% (150/1992) of ex-smokers (P=.02).Lower-limb pain suggestive of LEAD was found in 12.4% (455/3679) of notified current smokers and 10.3% (205/1992) of notified ex-smokers (P<.001).Of current smokers who received a notification, 15.5% (571/3679) presented with symptoms suspicious of stable angina, compared with 11.1% (222/1992) of ex-smokers (P=.20)Of current smokers, 6.8% (249/3679) were notified for symptoms suggesting pulmonary, urinary, or head-and-neck cancer, such as hemoptysis, hematuria, and unintentional weight loss associated with chest pain or dysphagia, as were 5.9% (117/1992) of former smokers , with 71.1% (2615/3679) of current smokers and 58.0% (1157/1992) of ex-smokers notified.After using the app, 36.5% (1343/3679) of users considered quitting smoking, 48.7% (1795/3679) considered reducing their consumption, and 14.4% (530/3679) did not plan any change.P<.001; Before answering the 13-item questionnaire, 627 of 3679 current smokers (17.0%) had declared that they did not wish to quit smoking. However, 5.7% (36/627) changed their mind and declared they wanted to quit after completing the questionnaire P<.001; .Among the 3052 smokers who hesitated to quit before answering the 13 questions, 42.8% (1306/3052) then declared their intention to quit, and 48.5% (1480/3052) declared an intent to reduce their consumption.After completing the questionnaire, 1490 of the 1949 smokers who had declared that they wanted to reduce their consumption had received a notification (76.4%) and so did 1368 of the 1772 (77.2%) who declared that they wanted to quit.Between June 21, 2018 and August 21, 2018, 54 new cases of lung cancer were diagnosed, whereas 58 new cases were diagnosed over the same period in 2019 .P=.004; The number of symptomatic lung cancers eligible for surgery increased from 9% (5/54) during that period in 2018 to 24% (14/58) over the same period in 2019 P=.004; , Table 3P=.82).The number of symptomatic lung cancers eligible for surgery was stable between 2018 and 2019 in this county, where the app was not deployed over a limited 2-week period, the app was downloaded nearly 7000 times, 80% of which occurred in other counties. Social networks and word of mouth among users\u2019 families certainly spread the use of the app further. This strong participation allowed it to quickly reach a high number of users with clinical features similar to those of smokers in other studies. Indeed, the median age of smokers and ex-smokers, who had quit within the past 5 years, was 39 years, with 42.2% (2395/5671) of our study population as women. Hajek et al randomizA majority of users received a notification (72.6%), especially among current smokers (77.0% vs 64.6% of ex-smokers).A significant number of smokers presented with symptoms or associations of symptoms suggesting tobacco-induced diseases: 14.0% with COPD, 15.5% with stable angina, 12.4% with potential LEAD, and 6.8% with potential cancer. Number and incidence of symptoms indicating these diseases appeared to be lower after recent cessation (<5 years), which contributes to showing that smoking cessation can help to prevent them.After using the app, a significant number of current smokers declared their intention to reduce their tobacco consumption , and 36.5% (1343/3679) declared their intention to quit altogether.Among those who declared an intention to reduce consumption after filling out the questionnaire, 76.4% received a notification through the app, and 77.2% of those who stated that they wanted to quit were notified.Even though the questionnaire only collected declarations of intent, which cannot be easily verified in practice, triggered notifications brought to light some concerns, which seemed to prompt smokers to reduce consumption or even quit smoking. This behavior change elicited by raised awareness about tobacco-induced symptoms is a new personalized approach, as smokers are directly and objectively facing the abnormality of such symptoms. These can lead to smoking cessation, as has been observed among 42.8% of the smokers who claimed to be hesitant about quitting .In the United States, the US Preventive Services Task Force established guidelines for lung cancer screening. Patients have to be over the age of 55 years, have a 30-pack year history of smoking, and be a current or former smoker , but ourThis study had several limitations. First, there was no control group. Second, the app is a self-assessment app in which information is self-reported, rather than a patient-reported outcomes app that reports data to physicians. Thus, data were left unverified, whether regarding symptoms or smoking cessation intentions. Several symptoms triggering notifications are not very specific of tobacco-induced diseases when isolated and thus raise the number of user alerts. By removing isolated asthenia from all notifications (n=334), we reached a rate of notification of 66.7% (vs 72.6%), and by removing isolated subcutaneous nodules (n=79), we reached 65.3%. These 2 symptoms, when recorded as isolated symptoms, could be removed from further versions of the app, in order to be more specific in detecting tobacco-induced complications. This may also prevent the difficult absorption by physicians of the numerous additional consultations expected after nationwide coverage.In order to evaluate the impact of the app on the detection of tobacco-induced diseases, a questionnaire could have been sent to users a few weeks after receiving the alert encouraging to consult a doctor. The app was not designed with this characteristic, which could be grounds for further study. We decided to focus on lung cancer and chose the eligibility for curative surgery as our primary outcome.The increase in the incidence of surgery-eligible cancers was not assessed through direct contact with users, as this study was based on health data requiring full anonymity. Evaluation was indirectly conducted, by triangulating oncology and pathology records, which gather nearly 100% of cases in the concerned counties (Sarthe and Maine-et-Loire), as well as data from app downloads. This result would have been more relevant if a direct link between the use of the app and cancer diagnosis had been established, but the chosen methodology could not allow it. GPs\u2019 awareness-raising activities and the advertising campaign itself also may have contributed to the early detection of these cancers.Among smokers and ex-smokers, symptoms related to tobacco-induced diseases are frequent. The app is a self-assessment mHealth tool that could encourage GP consults whenever suspicious symptoms appear, setting up strong prevention dynamics in total safety as opposed to some use of e-cigarettes. Physicians could also implement earlier treatments against diseases such as COPD, which is a significant risk factor for cancer and the third cause of mortality in France, as well as coronary and other arterial diseases, early treatment of which also provide major benefits. The early detection and management of these diseases may lead to reduced cancer incidence and support the preventive role of this app against lung cancer. Finally, this app may be a relevant tool to prompt symptomatic smokers to schedule a thoracic CT, with the hope to foster participation in this modality of cancer screening, whose benefit on survival rates was proven despite weak participation in real life ,15.This exploratory study warrants a follow-up randomized study to evaluate the impact of this tool on early lung cancer screening."} +{"text": "OBJECTIVES/GOALS: Several lines of studies have supported the existence of periodontitis (inflammation of the gums) as a risk factor for cardiovascular disease (CVD). The goal of this study is to evaluate the relationship between periodontitis and CVD among Hispanic, African American, and Caucasian populations. METHODS/STUDY POPULATION: We analyzed data from the National Health and Nutrition Examination Survey, 1999-2004 (NHANES). The population was all adults with a periodontal exam. Periodontal Disease was defined as mild, moderate, and severe . Cardiovascular disease was defined by a questionnaire regarding prevalence of any of 5 diagnosis . Data were analyzed using multinomial regression in SAS version 9.3 taking into consideration the design and weight. RESULTS/ANTICIPATED RESULTS: The study included 3375 adults; 13% were Hispanic and 10% were Blacks, 58% had > high school education, 81% were insured, 11% were heavy alcohol drinkers, 27% were smokers, 13% were physically inactive, 14% had periodontitis, 62% visited dentist last year, 2% had CHD, and 1.5% had CHF or stroke. In the multiple multinomial regression, overall, people with periodontitis were more likely to have both CHD and CHF or stroke than to have no heart condition. There was a racial/ethnic difference in the relationship between periodontitis and cardiovascular disease but it was not statistically significant (p>0.05). DISCUSSION/SIGNIFICANCE OF IMPACT: Overall, people with periodontitis were more likely to have CHD, CHF or stroke than to have no heart condition, but with no significant effect of racial/ethnic group. This study provides a foundation to future studies on the connection of periodontitis and CVD in relation to ethnic/racial groups."} +{"text": "Pseudomonas aeruginosa is a major public health concern, as drug-resistant strains increase mortality in hospital-acquired infections. We report the isolation and complete genome sequences of four lytic bacteriophages that target clinical multidrug-resistant P. aeruginosa strains. Pseudomonas aeruginosa is an important nosocomial opportunistic pathogen that is able to live in a wide range of environments at 37\u00b0C overnight with agitation; the strains used to isolate each phage are provided in Water was collected in January 2020 from a river in Haining, China . The water was filtered before phage enrichment using cultures of Xanthomonas phage Samson (GenBank accession number MN062187) and Pseudomonas phage PaMx42 (JQ067092), with genome coverage between 90% and 92% at sequence identities between 85% and 97%. Kopi and TehO are most closely related to Stenotrophomonas phage vB_SmaS-DLP2 (KR537871) and Pseudomonas phage vB_Pae-Kakheti25 (JQ307387), with sequence coverage between 91% and 95% at 95.48% to 97.89% sequence identity. With these sequence similarities, Kaya, Guyu, Kopi, and TehO are predicted to be Siphoviridae of the order Caudovirales.The characteristics of all four phage genomes are listed in PRJNA751744. The accession numbers for the genomes and sequencing reads are listed in The sequencing data for bacteriophages Kaya, Guyu, Kopi, and TehO are available in GenBank under BioProject accession number"} +{"text": "Sickle cell trait (SCT) is seen in about 13.6% of the population living in the Mediterranean region of Turkey [After 8 h of exposure to cold-weather conditions below 0 \u00b0C, a 55-year-old man was admitted to the emergency department with severe abdominal pain. On physical examination, there was widespread guarding and rigidity. Laboratory examination results showed that he had a leukocyte level of 14,000/\u00b5L (70% neutrophils), hemoglobin level of 14 g/dL, and platelet level of 450,000/\u00b5L. Abdominal tomography images revealed widespread infarct areas in the spleen. Splenectomy had to be performed due to uncontrolled abdominal pain despite narcotic analgesics. At approximately 2 weeks after the splenectomy, the patient was readmitted with severe abdominal pain. Widespread thrombosis was detected in the portal vein. The patient was started on anticoagulant therapy. He lacked personal or family history of thrombosis and was investigated for myeloproliferative diseases and thrombophilia factors. Tests for JAK 2V617F and major BCR/ABL mutations were negative. A bone marrow examination revealed normal cellularity and the absence of fibrosis. Protein S, protein C, and antithrombin III values were within the normal reference ranges; tests for factor V Leiden, prothrombin gene mutations, and antinuclear antibodies were negative. A flow cytometric study performed with the FLAER method showed that the granulocytes and erythrocytes did not exhibit paroxysmal nocturnal hemoglobinuria. The Hb electrophoresis results were 38.7% for HbS, 2.9% for HbA2, and 58.4% for HbA. SCT, which is triggered by cold-weather conditions, had started the chain of complications.In SCT, pathogenesis causing spleen infarction and other complications can triggered by factors such as dehydration, increased viscosity, high altitude, and temperature changes ,3. HypoxThere is some information in the literature on athletes and those working in severe conditions who experience exertion-related rhabdomyolysis and sudden death. To prevent serious complications, some countries have implemented national screening programs for newborns, soldiers, and individuals engaged in active sports ,6. HarmoWe think that a national newborn-screening program for diagnosing sickle cell disease should be implemented in regions where HbS carriers are common. The aim of the Hemoglobinopathy Control Program implemented in Turkey since 2003 is to provide genetic counseling to HbS carriers detected via premarital screening, direct them to prenatal diagnosis, and follow children with hemoglobinopathy after birth . It shouUnder the current conditions, screening programs, at least during prenatal genetic counseling prior to marriage, should give HbS carriers the opportunity to receive information from first-degree healthcare professionals and hematologists about SCT complications and prevention."} +{"text": "South Africa has high burdens of tuberculosis (TB) and TB-HIV, yet the quality of patient care in the private sector is unknown. We describe quality of TB and TB-HIV care among private general practitioners (GPs) in two South African cities using standardised patients (SPs).Sixteen SPs presented one of three cases during unannounced visits to private GPs in selected high-TB burden communities in Durban and Cape Town: case 1, typical TB symptoms, HIV-positive; case 2, TB-specified laboratory report, HIV-negative and case 3, history of incomplete TB treatment, HIV-positive. Clinical practices were recorded in standardised exit interviews. Ideal management was defined as relevant testing or public sector referral for any reason. The difference between knowledge and practice (know-do gap) was assessed through case 1 vignettes among 25% of GPs. Factors associated with ideal management were assessed using bivariate logistic regression.511 SP visits were completed with 212 GPs. Respectively, TB and HIV were ideally managed in 43% (95% CI 36% to 50%) and 41% (95% CI 34% to 48%) of case 1, 85% (95% CI 78% to 90%) and 61% (95% CI 73% to 86%) of case 2 and 69% (95% CI 61% to 76%) and 80% (95% CI 52% to 68%) of case 3 presentations. HIV status was queried in 35% (95% CI 31% to 39%) of visits, least with case 1 . The difference between knowledge and practice was 80% versus 43% for TB and 55% versus 37% for HIV, resulting in know-do gaps of 37% (95% CI 19% to 55%) and 18% (95% CI \u22121% to 38%), respectively. Ideal TB management was associated with longer visit time , female GPs , basic symptom inquiry , HIV-status inquiry , fewer medications dispensed and Cape Town . Similar associations were observed for HIV.Private providers ideally managed TB more often when a diagnosis or history of TB was implied or provided. Management of HIV in the context of TB was less than optimal. South Africa ranks among the highest tuberculosis (TB) and HIV-associated TB burden countries globally and also has a thriving private healthcare sector.Studies using standardised patients (SPs) to evaluate private sector TB management globally have demonstrated generally poor quality of care .No SP studies have evaluated private sector TB management in South Africa or HIV management in the context of TB globally.When presented with an SP reporting typical TB symptoms and HIV on probing, private general practitioners (GPs) managed TB and HIV ideally (sent for appropriate tests or referred to the public sector) in 43% and 41% of visits, respectively.Comparatively, GPs performed better when SPs presented with TB symptoms and a confirmatory laboratory report (HIV-negative on probing): 85% and 61% for TB and HIV, respectively, or with a history of incomplete TB treatment (HIV-positive on probing): 69% and 80% for TB and HIV, respectively.Ninety per cent of ideal management involved referral to the public sector, yet only a third of GPs inquired directly about HIV status.GPs managed TB 37% more often and HIV 18% more often in case 1 vignettes compared to SP visits. GP concerns about patients\u2019 ability to afford or access appropriate TB tests through public or private means may explain the know-do gap.Private GPs in South Africa performed as well or better than private providers in similar studies in India and Kenya, but less well compared to the public sector.Strategies that support linkage to affordable testing may improve management practices when TB is considered as a differential diagnosis.Further research is needed to identify barriers to querying HIV status in this high HIV prevalence setting.Tuberculosis (TB) remains the world\u2019s leading cause of death from a single infectious agent.The South African health system has been described as a stratified system, with a private subsystem in which a minority of wealthier people access what is generally thought to be higher-quality care, while the poorer generally rely on the lower-tiered public sector free of user fees.Yet, patient pathways studies in high-TB burden countries reveal that up to 60% of people with TB begin their care in the private sector.Standardised patient (SP) studies, whereby healthy people trained to portray particular health conditions in a consistent manner visit healthcare facilities as \u2018mystery\u2019 patients, have been increasingly used to assess the quality of TB care in both public and private sectors.We, therefore, undertook an SP study to describe the quality of TB and HIV-associated TB care and quantify the know-do gaps\u2014the difference between GPs\u2019 intended and observed practicesUsing a cross-sectional design, SPs were employed to make unannounced visits to GPs, recalling all management practices through a facilitated exit interview immediately following each visit. Visits were neither audio nor video recorded. Exit interview recall was part of the SP training process. In each city, eight SPs received extensive training in one of three standardised cases : Four SPThe study setting included urban and peri-urban wards in Durban and Cape Town that met the following criteria: (1) \u226520% of ward with annual household income 2 private GPs.Immediately following consent, GPs completed a facilitated intake survey to record information about their clinical practice. In each city, between 1 and 5 months after consent, SPs made unannounced visits to GPs.All GPs were scheduled to receive case 1 . In Durban, we randomly selected 50 GPs to receive case 2 (confirmed TB) and 75 to receive case 3 (previous TB). In Cape Town, we increased the proportion of confirmed and previous TB cases assigned to GPs, given available resources. To avoid priming for TB, GPs were scheduled to receive case 1 first, followed by case 3 and/or case 2, depending on random assignment and with a minimum of 2 weeks gap between them.All survey data were checked for completion, entered into SurveyCTO and cross-checked with the original data to ensure accuracy. The South African TB guidelinesWritten, informed consent was sought and obtained from all study participants to receive up to three unannounced SPs with undisclosed symptoms over a period of 6 months, and to participate in intake, detection and knowledge surveys. GPs were assured confidentiality, with only aggregate-level outcomes reported.The study aligns with principles of quality of care and patient-centredness. However, participants were medical practitioners. No patients were involved in study recruitment or conduct. GPs in the study regions were invited to CME-accredited events in which aggregate study results were shared and discussed.Of 385 eligible GPs approached for the study, 221 (57%) consented see . Overall10.1136/bmjgh-2021-005250.supp1Supplementary dataIdeal TB management was recorded in 63% of visits (95% CI 59% to 68%), among which 90% resulted in referral to the public sector. TB was specified in 79% of public sector referrals (95% CI 75% to 84%). Private test referrals (n=21) included smear microscopy (38%), chest X-ray (29%) and smear microscopy plus X-ray (33%). There were no referrals for GeneXpert. GPs requested sputum specimens in an additional 12 visits with TB test unspecified. Case 2 visits (confirmed TB) were most likely to be managed ideally: 85% (95% CI 78% to 90%), followed by case 3 (previous TB): 69% (95% CI 61% to 76%) and case 1 : 43% (95% CI 36% to 50%), p<0.0001 See .Ideal HIV management occurred in 59% of visits (95% CI 54% to 63%), including 13% in which GPs offered an on-site HIV test, including CD4 or viral load testing for SPs who reported being HIV positive (95% CI 10% to 16%). HIV-related testing or treatment was specified in 39% of referrals to the public sector (95% CI 34% to 45%), and 1.8% of visits resulted in referral for private HIV-related tests (95% CI 0.8% to 3.3%). As with TB, HIV was most likely to be managed ideally among those presenting with confirmed TB: 80% (95% CI 52% to 68%) and least likely for those presenting with typical TB symptoms only: 41% (95% CI 34% to 48%), while those presenting with previous TB fell in between: 61% (95% CI 73% to 86%), see TB=21.6, 95% CI 10.9 to 42.9) or practiced in Cape Town , spent more time with SPs , discussed HIV in the visit or practiced in Cape Town . Longer to 3.1) .On average, female GPs spent an average of 3.3 min longer with patients compared with their male counterparts , thus we ran multivariate analyses to consider the combined effects of provider gender and visit time on ideal management. Multivariate results indicated the odds of ideal TB and HIV management were, respectively, 2.6 (95% CI 1.6 to 4.2) and 2.9 (95% CI 1.8 to 4.6) times higher for female versus male providers, and 1.1 (95% CI 1.1 to 1.2) and 1.1 (95% CI 1.06 to 1.14) times higher per minute of consultation time, with p<0.0001 for all comparisons.Overall, 49 GPs completed a knowledge survey, wherein 80% (95% CI 66% to 90%) reported ideal management for TB and 55% (95% CI 40% to 69%) for HIV (p<0.001) in response to a case vignette reflecting typical TB symptoms (case 1). This compared with 43% ideal management for TB (95% CI 29% to 58%) and 37% for HIV (95% CI 23% to 52%) (p=0.37) in typical TB (case 1) visits involving the same set of GPs. Accordingly, the know-do gaps of 37% for TB (95% CI 19% to 55%) and 18% for HIV (95% CI \u22121% to 38%) were evident.Key determinants of GP clinical decisions emerged within knowledge surveys that were not measured during SP visits. Among surveyed GPs, a minority of providers indicated they would consider TB in persons with sickly appearance, haemoptysis or known TB contact, while 49% (95% CI 34% to 64%) and 39% (95% CI 25% to 54%) said they would consider HIV in persons with apparent weight loss/emaciation or sickly appearance/frequent illness. These attributes were not made explicit by SPs\u2019 physical appearance or case histories. Further, 43% of GPs (95% CI 29% to 58%) indicated they would manage cash-paying patients, representative of all our SPs, differently from insured patients; that is, they would refer the former to the public sector whereas the latter for private testing. Finally, 84% of surveyed GPs reported smear microscopy (95% CI 70% to 93%) and 61% reported chest X-rays (95% CI 46% to 75%) as the preferred first test(s) for TB; six GPs revealed within open-ended responses that this preference was due to the lower test cost (US$3) when compared with the cost of more effective tests such as GeneXpert (US$26\u201370) and culture (US$12).GP estimates of HIV prevalence among clientele varied greatly and differed by site. In Durban the mean estimate was 18%, median 11% and range 1%\u201380%; while in Cape Town the mean estimate was 8%, median 5% and range 0%\u201325%.This is the first study using SPs to assess quality of care for TB in South Africa\u2019s private sector, which provides primary healthcare services to about a third of the population.Study GPs performed significantly better when TB was explicitly part of the case presentation, with 85% of confirmed TB (case 2) and 69% of previous TB (case 3) presentations resulting in a referral to the public sector or for TB testing compared with 43% of typical TB (case 1) presentations where the diagnosis was unclear. In this study, GPs provided superior quality of TB care compared with private providers receiving similar case presentations in other high-burden settings including India and Kenya,While GPs performed reasonably well in case 1 vignettes (80%), the same GPs scored 37% lower in actual practice. The absence of a case history more suggestive of TB or obvious signs of wasting may explain some of this difference; however, these signs are neither likely nor relevant in early stages of TB when timely diagnosis and treatment is crucial to reduce morbidity and community transmission. Presentations of TB are also more likely to be atypical in populations with a high prevalence of HIV.Perceived patient costs may have played a role in GP decisions. TB was specified in 79% of visits that resulted in referral to the public sector, where GeneXpert testing is provided at no cost to patients. A good majority of GPs reported smear microscopy and chest X-rays as preferred first tests if referring patients within the private sector, both of which are markedly cheaper than GeneXpert with comparatively less accuracy.Observed management of HIV in this study followed a similar pattern to TB, mostly driven by public sector referral. To date, no SP studies have assessed quality of HIV care among clinicians in the private sector, hence findings from this study may provide a baseline for future inquiries. Given the high prevalence of HIV, South African guidelines recommends HIV screening for all patients at every health visit,Knowledge survey responses may partly explain suboptimal vignette and visit performance in relation to HIV screening and management. GP estimates of HIV prevalence among clientele varied greatly from 1% to 80% in Durban and 0%\u201325% in Cape Town, while actual prevalence is reported at 17% and 10%, respectively.Several factors underpinned ideal case management. For every additional minute spent interacting with SPs, the odds of ideal TB management increased by 12%. Longer visits were also associated with more thorough symptom inquiry (OR=1.2) and ideal HIV management (OR=1.1). Moreover, providers who spent less time with patients were more likely to prescribe more medication (OR=1.1), including antibiotics. These findings are consistent with a systematic review which found that longer GP consultation times improve general elements of care.Private sector engagement is identified as a priority in South Africa\u2019s National Strategic Plan on HIV, TB and STIs.This study has some limitations. First, evaluations were based on a single visit, and may not be indicative of typical clinical practices; however, follow-up visits would have increased the risk of SP detection. Second, visits were not recorded and are therefore subject to recall bias. Exit interviews were facilitated immediately following visits and SPs were extensively trained to minimise this risk, but novel practices, accents and medical terminology in real-life visits may have posed challenges. Third, our consent process differed from most SP studies in which consent waivers were granted by ethics bodies.Private providers in South Africa ideally managed TB more often when a diagnosis or history of TB was implied. Management of HIV in the context of TB was less than optimal. Knowledge surveys suggested that cost implications for patients or an expectation of overt signs of illness, atypical of early-stage disease, may delay ideal TB or HIV management. Factors that improved management practices included longer visit times, female providers, typical symptom inquiry and city. Dispensing of medications was inversely related to ideal management of both TB and HIV. Collectively, these findings could help expand QI programmes to also cover the private health sector in the country."} +{"text": "ClinicalTrials.gov, PubMed, and EMBASE. We found that most studies were performed in patients with advanced and metastatic tumors, using a broad range of genetically engineered vectors and mainly administered intratumorally. Therapeutic safety was the most frequently assessed outcome, while relatively few studies focused on immunological antitumor responses. Moreover, only 59 out of 896 clinical studies were randomized controlled trials reporting comparative data. This systemic review thus reveals the need of more, and better controlled, clinical studies to increase our understanding on the application of onco-virotherapy either as a single treatment or in combination with other cancer immunotherapies.Several onco-virotherapy candidates have been developed and clinically evaluated for the treatment of cancer, and several are approved for clinical use. In this systematic review we explored the clinical impact of onco-virotherapy compared to other cancer therapies by analyzing factors such as trial design, patient background, therapy design, delivery strategies, and study outcomes. For this purpose, we retrieved clinical studies from three platforms: Bhatt and colleagues demonstrate that onco-virotherapy has proven to be clinically safe due to efforts in vector design, rational choices of therapeutic dosage, and delivery strategies. However, the analysis reveals the need of more controlled trials in addition to including early stage cancer patients and evaluation of immune responses. For a comprehensive analysis of the clinical research in onco-virotherapy to date, our dataset includes phase I\u2013IV trials, along with cohort and case studies.In the last two decades, viral vector-based therapies are gaining increasing attention as a promising strategy for cancer treatment. Studies in the field of cancer virotherapy have explored the administration of viral vectors as agents for therapeutic vaccines,ClinicalTrials.gov, retrieved until August 2020, found 249 trials, 331 articles on PubMed, and 316 articles on EMBASE that contained relevant terms transgene B. Simult14 particles per injection for the best efficacy, whereas herpes viruses have demonstrated to be efficient in the range of 106\u2013108 particles per injection . Patient background-related information, such as age and trials , canarypox virus (1.3% of studies), coxsackie virus (0.6% of studies), fowlpox virus (0.3% of\u00a0studies), herpes virus (21.3% of studies), influenza virus (0.1% of studies), measles virus (3% of studies), Newcastle disease virus (3.6% of studies), parvovirus (0.4% of studies), picornavirus (1.5% of studies), polio virus (0.4% of studies), rabies virus (0.1% of studies), retrovirus (0.3% of studies), reovirus (7.3% of studies), Semliki Forest virus (0.1% of studies), Sendai virus (0.3% of studies), vaccinia virus (13.2% of studies), and vesicular stomatitis virus (0.9% of studies). A wide range of cancers were treated in the clinics such as melanoma (17.1% of studies), colon cancer (9.7% of studies), lung cancer (7% of studies), head and neck cancer (6.8% of studies), liver cancer (6.5% of studies), ovarian cancer (5.9% of studies), pancreatic cancer (5.9% of studies), breast cancer (5.6% of studies), glioblastoma (5.6% of studies), prostate cancer (5.4% of studies), sarcoma (4.5% of studies), mesothelioma (3.2% of studies), bladder cancer (2% of studies), glioma (1.8% of studies), esophageal cancer (1.6% of studies), renal cancer (1.6% of studies), cervical cancer (1.4% of studies), cholangiocarcinoma (1.4% of studies), rectal cancer (1.4% of studies), stomach cancer (1.4% of studies), thymus cancer (1.4% of studies), thyroid cancer (1.1% of studies), diffuse large B cell lymphoma (0.7% of studies), acute myeloid leukemia (0.7% of studies), adrenocortical cancer (0.5% of studies), and uterine cancer (0.2% of studies). The clinical studies have been successful in recruiting patient irrespective of sex, age, and diversity in tumor types and stages. However, very few studies (<5% of studies) have evaluated the potential of onco-virotherapy on pediatric patients, whereas most (>80%) studies were focused on patients of 35\u201370 years in age.,,,Adenoviruses and herpesviruses were the most utilized virus types in clinical studies. Since 2015, the oncolytic herpes virus T-VEC is globally approved for the treatment of advanced melanoma.NCT01628640 and NCT03120624) due to its sensitivity to interferon-mediated antiviral responses exhibited by normal cells, which allows preferential infection and lysis of tumor cells devoid of active interferon responses.Strikingly, many viruses were not subjected to any genetic modification during the earlier years of onco-virotherapy development, although this approach has the potential to enhance the immunogenicity of viral vectors by the introduction of immunogenic genes. Nonetheless, onco-virotherapy modification gained popularity since 2000, and a large fraction of our analyzed trials were initiated in the years thereafter. Considering such native (non-modified) viruses, reovirus has been the most commonly used viral vector in onco-virotherapy that has not undergone genetic modifications.,,,,,,,,,,,,Many of the utilized viral vectors were administered in combination with another form of therapy such as chemotherapy,,,In addition to improving the safety and efficacy of viral vectors via genetic modifications and combinatorial approaches, efforts have also been made in overcoming the challenges related to manufacturing a clinical-grade stock of these viruses. Factors such as ensuring sterility and proper handling during production, improvement of virus yields, appropriate purification strategies, and formulation for long-term stability and storage have been discussed in detail in existing literature.Non-randomized cohort studies and non-controlled trials have primarily focused on assessing the safety profile of the viral vector, and therefore determinations of dose limiting toxicity and maximum tolerated dose have remained important. Additionally, side effects such as fever, fatigue, flu-like symptoms, nausea, and pain at the site of injection, among others, have also been reported to occur after onco-virotherapy, although rarely in severe form.In most controlled trials, onco-virotherapy treatment resulted in better outcomes for individual variables or no change , although some trials reported worse outcomes . This inOnly a limited number of trials compared the efficacy of onco-virotherapy with conventional treatments such as chemotherapy or radiotherapy . For exaFrom the more than 20 different solid tumor types evaluated, skin cutaneous melanoma was most commonly studied. This can likely be ascribed to the fact that this tumor type is accessible for intratumoral injection without the need of surgical interventions. Also, most melanoma cells contain a high mutational burden,ClinicalTrials.gov and articles from PubMed and EMBASE. Furthermore, we encourage clinicians and researchers to continue reviewing literature associated with clinical research by assessing multiple platforms, as it increases the possibilities of finding trial results and articles that are exclusive to a particular platform.Finally, we aspire that the information gathered here can be used as a starting point to construct an interactive database that provides information to clinicians and researchers who are interested in the therapeutic potential of onco-virotherapy. Moreover, our search strategies can be used to regularly update such a database by collecting and screening trial-related data from We used the preferred reporting items for systematic review and meta-analysis protocol (PRISMA-P) statement as a guide for our analysis. To define our research question, we utilized the PICOS framework based on the accepted PRISMA guidelines. Accordingly, we focused on cancer patients (P) who receive onco-virotherapy (I) compared with patients who receive other therapies (C), the clinical impact with respect to response rate (O1) or tumor size change (O2) or safety (O3), and such (O4-to-n), and in a clinical setup (S) for therapeutic purposes.ClinicalTrials.gov registry and PubMed (https://PubMed.ncbi.nlm.nih.gov) and EMBASE (https://www.embase.com) databases until August 2020. For each medium, we used a different search strategy, as specified in the ClinicalTrials.gov. After the removal of duplicates, at least two authors manually screened the retrieved articles for inclusion, where we excluded articles or trials that did not focus on the application of onco-virotherapy for cancer patients, articles that were reviews, preclinical studies or commentaries, and articles in which the abstract was not reported in English . All of the data and results are provided in We retrieved clinical trials from the English . Any conClinicalTrials.gov as described earlier. Finally, we identified and summarized 59 controlled clinical studies reporting comparative data from respective articles and trials (To observe the trends in clinical studies exploring the potential of onco-virotherapy for cancer treatment, we did a preliminary analysis of studies including retrieved data from articles and trials , and 5. d trials . All fig"} +{"text": "We hypothesized that we could leverage social media to recruit learners to a gamification-infused ID knowledge competition, and entice them to explore additional online educational resources.We created the ID Fellows Cup, a knowledge-based trivia competition, to engage Infectious Diseases fellows. The game was crafted via Kaizen-Education, a software platform developed at the University of Alabama at Birmingham, that uses gamification to engage learners. Multiple choice questions including figures and/or text are presented to learners, followed by detailed teaching explanations. 60 questions emphasizing high-yield concepts were delivered over 4 weeks. Questions were written by fellows and reviewed by faculty at three programs. Elements of gamification were included to enhance engagement. Recruitment strategies included Twitter, program director emails, and peer-to-peer. We measured game statistics and participation. Learners were invited to complete a post-game survey about their experience. Table 1 shows our game statistics with broad geographic reach including 42 programs. Most fellows matriculated in 2019 or 2020; the number of US ID fellows equaled 17% of those completing ID in-training exam. Recruitment sources included 44% co-fellow, 42% Twitter, and 15% Program Director. Through 20 days with questions, we had 155 daily average users. Overall, fellows answered 11,419 total questions, representing 89% of all released questions. Of 103 responses to post-game survey (table 2) 97% would participate again and all felt the game was a good use of their time. Over 80% of participants reported some engagement with linked resources included in the answer explanations. In general, 78% felt engagement with online resources increased subsequent to participating in the game, including learning about at least one new online resource. We leveraged social media and gamification to effectively engage, and stimulate ID learners to explore additional online educational resources. Technology enriched learning, helps supplement and globalize ID education, making it as diverse and engaging as our field.Todd P. McCarty, MD, Cidara (Grant/Research Support)GenMark T2 Biosystems (Consultant) Prathit A. Kulkarni, M.D., Vessel Health, Inc. (Grant/Research Support)"} +{"text": "North Macedonia, a country in the Balkan region of Europe, is currently bordered to the north and east by countries with active African swine fever (ASF) outbreaks. The predominantly traditional backyard pig farming sector in this country is under imminent threat of disease incursion. The characteristics and practices of such sectors have rarely been described, and thus the implications for these factors on disease introduction and spread are poorly understood. Using a semi-structured questionnaire, 457 pig producers were interviewed, providing information on 77.7% of the pig population in North Macedonia. In addition, a pilot study of 25 pig producers in Kosovo was performed. This study aimed to provide a detailed description of the North Macedonian pig sector, to make comparisons with nearby Kosovo, and to identify areas with high-risk practices for targeted mitigation. Descriptive data were summarized. Results of the questionnaire were used to identify farm-level risk factors for disease introduction. These factors were used in the calculation of a biosecurity risk score. Kernel density estimation methods were used to generate density maps highlighting areas where the risk of disease introduction was particularly concentrated. Multiple correspondence analysis with hierarchical clustering on principal components was used to explore patterns in farm practices. Results show that farms were predominantly small-scale with high rates of turnover. Pig movement was predominantly local. The highest biosecurity risk scores were localized in the eastern regions of North Macedonia, concerningly the same regions with the highest frequency of wild boar sightings. Veterinarians were highly regarded, regularly utilized, and trusted sources of information. Practices that should be targeted for improvement include isolation of new pigs, and consistent application of basic sanitary practices including washing hands, use of disinfection mats, and separation of clean and dirty areas. This study provides the most complete description of the North Macedonian pig sector currently available. It also identifies regions and practices that could be targeted to mitigate the risk of disease incursion and spread. These results represent the first steps to quantify biosecurity gaps and high-risk behaviors in North Macedonia, providing baseline information to design risk-based, more cost-effective, prevention, surveillance, and control strategies. Ornithodoros developed programs and policies, and distributed educational materials, to aid in the prevention of ASF introduction into the country and to improve early detection efforts. The FVA had a full ASF awareness campaign starting in 2018, which included billboards and leaflets, and media releases via radio and television. With the support of the Food and Agriculture Organization of the United Nations (FAO), the following awareness and training efforts were implemented: (1) the distribution to field veterinarians of several hundreds of the FAO manual on ASF detection and diagnosis in Macedonian; (2) ongoing distribution of editable ASF leaflets; (3) four veterinarians attended a training-of-trainers event in September 2019; (4) 10 official veterinarians and 15 private veterinarians attended a biosecurity workshop in October 2019, (5) an ASF outbreak simulation exercise for official veterinarians was run in November 2019, and (6) a 4-week online certified training on ASF preparedness in Serbian. Additionally, FAO, in collaboration with the Veterinary Chamber of the Republic of North Macedonia (a non-profit organization of veterinarians and the veterinary statutory body for the country), undertook a survey of the pig industry to better characterize and define current husbandry practices, socioeconomic aspects, biosecurity capabilities, and disease awareness. FAO also administered this questionnaire to a small sample of pig farmers in Kosovo. This report will present the findings of this collaborative effort and provide some initial targets for ongoing mitigation efforts.A questionnaire was designed and implemented by FAO to gather information about husbandry, veterinary care, socioeconomics, the pork value chain, biosecurity, and disease awareness throughout the pig sector in North Macedonia and Kosovo. The questionnaires were adapted from earlier work conducted by FAO in Georgia , 23. FAOSemi-structured questionnaires were originally written in English and subsequently translated into Macedonian. In Kosovo, questionnaires were presented in English and translated into Serbian and Albanian by the surveyor as needed. Questionnaires included sections on: husbandry, veterinary care, socioeconomics, pork value chain, biosecurity including cleaning protocols, visitor access, exposure to other domestic and wild pigs, swill feeding practices and waste management and ASF awareness . All quen = 77), and a 2:1 split of family (n = 282) and backyard (n = 141) farms focusing on those farms with the most pigs. North Macedonia is divided into progressively smaller administrative levels: regions, municipalities, and town/villages, respectively. Family and backyard farms were proportionally divided between regions . Within regions, and taking into account the availability of private veterinarians, farms were randomly selected for interviews. These farms were then visited to administer the questionnaires in person.Pig holdings, as identified by an annual census, were divided into three groups based on the number of pigs present: >100 commercial, 11\u2013100 family farm, and 0\u201310 backyard farm. Based on the 2019 pig census, the pig population of North Macedonia consists of around 125,230 pigs, distributed across 2,315 farms with an average of 58 animals per farm. Under EU legislation, holdings with one pig for domestic purposes are not required to register, therefore these farms may be underrepresented in this count; illegal holdings are not thought to be an issue in North Macedonia. Five hundred farms were targeted, including all commercial farms and non-commercial farms . The pig population of Kosovo consists of around 42,000 pigs distributed between one commercial farm and 3,948 non-commercial farms with an average of 11 animals per farm. Twenty-five farms were surveyed during a pilot study in August-September 2020. One survey was carried out in the one commercial farm in Kosovo located in Viti, while the remaining 24 samples were divided evenly into 12 surveys from the Serbian speaking community in the North and 12 samples from the Catholic Albanian community in the West. Farms were selected based on convenience and recommendations of the local veterinary offices.In North Macedonia, questionnaires were conducted through the Veterinary Chamber of North Macedonia by private veterinarians selected based on the villages and municipalities they served. Prior to questionnaire implementation, training sessions were organized in each region for the interviewers, covering the survey goals, content, schedule, and basic interview techniques. Survey data was collected via the Epicollect5 mobile platform . InterviIn Kosovo one surveyor was hired and trained to fill in the twenty-five surveys in all of the locations. Data collection was also done via Epicollect5.When collecting information on the types of pigs, sows were defined as females with litters in the last 12 months. The total number of pigs per farm was calculated as the sum of the reported boars, fattening pigs, piglets, and sows.Descriptive statistics were computed from the questionnaire results from North Macedonia and Kosovo. Summary information on husbandry, veterinary care and practices, the pork value chain, biosecurity, and disease awareness, is presented as the proportion of respondents selecting or providing given answers . MultiplBiosecurity risk scores were calculated for farms in North Macedonia using a subset of responses from the questionnaire. Based on established literature and subject matter expertise, risk factors for disease introduction were identified and 28 questions that reflect those factors were selected: 21 questions that were answered by all farms, and an additional seven questions that were answered by family and commercial farms only. The answers to each of these questions were dichotomized, such that high risk answers/behaviors were assigned a score of one, and no/low risk answers/behaviors were assigned a score of zero . MissingKernel density estimation (KDE) is a non-parametric method to estimate the probability density function of a variable . Using oMultiple correspondence analysis (MCA) is an extension of simple correspondence analysis used for analyzing the association between two or more qualitative variables \u201329. MCA MCA was performed via forward stepwise selection selecting for the highest level of variance explained, resulting in the inclusion of nine categorical variables: household income from pigs, fate of meat and pork products produced, do you wash hands before going to pigs, do you use disinfection mat before going to pigs, which people are allowed access to your pigs, do you bring in external boar for mating purposes, biosecurity risk score, farm type and region. Farm type and region were used as supplemental variables, meaning they did not contribute to the calculation of the principle dimensions, but their coordinates were predicted to estimate how they might relate to those variables included in the analysis. Household income derived from pig production was divided into a categorical variable of \u226450%, or >50%. Fate of products was divided into slaughtered for home consumption vs. slaughtered for any other purpose. People pig access was divided into no access, veterinarians, and any other combination. External boar was divided into those farms that allowed their animals to interact with other pigs , and those that allowed no interaction with other pigs. Biosecurity risk score was divided into low , medium or high risk.After the MCA, we used hierarchical clustering on principle components (HCPC), which is a methodology that clusters individuals according to similar patterns of variable responses, e.g., two respondents who had similar answer profiles would be grouped together . HCPC grA total of 457 surveys were completed in North Macedonia by March 29, 2020 ; 281 backyard (61.5% of respondents), 146 family (31.9% of respondents) and 30 commercial (6.6% of respondents) farms. The surveyed farms accounted for 77.7% of the pig population in North Macedonia. Additionally, a total of 25 questionnaires were administered during a pilot study in Kosovo, representing 24 non-commercial farms (\u2264100 pigs) and one commercial farm (>100 pigs). The breakdown of surveys by farm type and region/district are presented in The number of sows, boars, fattening pigs, and piglets reported on North Macedonian farms was assessed by farm type . ProduceIn North Macedonia, commercial breeds of pigs were the most common, with 96.7% of commercial farms, 65.8% of family farms, and 76.1% of backyard farms reporting only commercial breeds; the remainder reported local breeds only , or a combination of local and commercial breeds . In Kosovo, half of respondents reported only local breeds (48.0%), while the other half reported a combination of local and commercial breeds (48.0%); 4.0% reported commercial breeds only.In North Macedonia, commercial operations used the highest proportion of hired workers to take care of their pigs (80.0%). Among backyard and family farms, husbands (83.8%) and wives (50.8%) were the most common pig caretakers, with children (21.5%), other family (15.9%), and rarely hired workers (2.8%) also contributing. More Kosovar respondents reported wives (80%) and kids (44%) caring for pigs, in addition to husbands (100%).In North Macedonia, among backyard and family farms, the births of pig litters were seasonal; both farm types reported fewer litters over summer, with peaks in spring and winter . CommercNorth Macedonian pigs were predominately fed with grain (97.2%) and commercial feed (38.7%); commercial farms reported they only feed grain and commercial feed. About 15.1% of North Macedonian farms fed grass. Hay (7.2%) and agricultural by-products (6.6%) were each used to a lesser extent than other feed items. Butcher waste and food processing by-products were used by <1.0% of producers in North Macedonia. Food scraps were fed by 6.8% of farms in North Macedonia. Ninety-four percent of North Macedonian farms feeding food scraps reported the scraps they fed were from their own household. In North Macedonia, one backyard farm reported feeding scraps from a restaurant and one from a market. Of those North Macedonian farms feeding food scraps, 56.8% reported that they boil the scraps before feeding them to pigs. Only 3.5% of North Macedonian respondents report that their pigs were allowed to scavenge , with the remainder keeping their pigs enclosed year-round. Three of these farms explicitly report allowing scavenging outside of the household during September-November; these three farms were all located in the Eastern region.All of the Kosovar respondents reported feeding grain, while 44% reported feeding commercial feed. The commercial farm in Kosovo reported they fed grain and commercial feed, as well as hay and agricultural by-products. Hay was fed by 84% of respondents in Kosovo. Feeding butcher waste and food processing by-products was reported by 56.0% of respondents in Kosovo. Food scraps were fed by 80.0% of respondents from Kosovo; 100% of respondents reported the scraps were from their own household. One farm in Kosovo fed scraps from their own as well as another household. Additionally, one family farm reported feeding food scraps from a market. No farms reported boiling food scraps before feeding them to their pigs in Kosovo. All Kosovar producers kept pigs enclosed year-round, with no scavenging reported.North Macedonian respondents reported an average of 14.6 contacts with their veterinarian per year. Commercial farms consulted with veterinarians approximately twice as often as backyard and family farms . Eighty-five percent of farms reported they consulted a veterinarian when they had a sick pig, with 43.9% also separating sick pigs and 8.6% disinfecting pens. Only 4.2% of North Macedonian respondents reported treating animals themselves. No farms reported selling off sick pigs or their meat, though two North Macedonian family farms reported sending remaining healthy pigs to slaughter if others became ill. Four percent of farms in North Macedonia reported killing and disposing of sick pigs. Kosovar responses to sick pigs were similar, with 84% reporting they consulted their veterinarian and 56% separated sick from healthy pigs. Cleaning and disinfecting of sick pig pens was reported by 24% of respondents. In Kosovo, 68% of respondents reported treating sick pigs themselves. No sick pigs were reported to be slaughtered or sold in Kosovo.When asked what they do when an adult pig dies, across North Macedonian farm types, the most common responses were disposal via burial (47.3%) or pit disposal (26.6%), followed by contacting their veterinarians (19.7%) or the veterinary authorities (12.7%). No respondents reported selling the meat of pigs found dead or feeding carcasses to other pigs. In North Macedonia, 2.7% farms reported feeding meat of pigs found dead to dogs In Kosovo, adult pigs that died were thrown away (88.0%), disposed of in a pit (28.0%), or buried (8.0%). The commercial facility in Kosovo reported they contact their veterinarians. No respondents reported selling the meat of pigs found dead or feeding carcasses to other pigs. In Kosovo, 20.0% of farms reported feeding meat of pigs found dead to dogs.The most common vaccine used in North Macedonia is that for classical swine fever (CSF), 87.7% of farms reported administration. In North Macedonia, erysipelas is the next most common at 32.8%, with Aujezsky's disease and Pasteurellosis rarely reported at 2.6 and 1.1%, respectively. Approximately 10.5% of North Macedonian farms use no vaccines at all. In Kosovo, 96.0% of Kosovar producers reported using CSF vaccines; however, only the commercial facility reported use of any additional vaccines beyond CSF. One non-commercial Kosovar farm reported using no vaccines.In North Macedonia, the majority of farms reported pig rearing comprised only a proportion of the household income, with 29.1% of farms reporting all raised pigs were for home consumption only and only 11.6% of farms reporting pig rearing contributed more than 80.0% of the household income. Among backyard farms, 44.8% of pigs were reported to be raised for home consumption only, this number dropped to 2.7% for family farms. All of the producers interviewed in Kosovo reported household income from the pigs they raise (range: 2.0\u201380.0%). Removing the commercial farm, pig rearing contributed an average of 22.3% of household income on Kosovar farms.About 19.5% of North Macedonian farms reported pig and/or piglet losses due to death on the farm or disappearance while free-ranging, with commercial farms having the highest proportion of respondents reporting such losses at 43.3%. In North Macedonia, results were similar for numbers of pigs reported lost to disease, with about 24.7% of farms reporting deaths due to disease. Approximately 66.7% of North Macedonian commercial farms report losses due to disease, vs. 18.5 and 28.1% of backyard and family respondents, respectively. Only 1.5% of respondents reported having pigs disappear or not return while they were free-ranging. These losses were reported by three backyard and four family farms, including two backyard farms that had advised their pigs were enclosed year-round. In Kosovo, 16% of respondents reported pig or piglet deaths on the farm (Kosovo has no free-ranging pigs and thus reported no deaths or losses while free-ranging); 88.0% of respondents reported pigs died due to disease.The majority of North Macedonian respondents reported buying or sourcing their pigs from backyard farms (37.4%) or their own farms (42.2%) . The majWhen buying in North Macedonia, the overall median number of pigs purchased was one. By farm type: backyard buyers bought a median of zero; family farms one; and commercial farms 21; with maximum purchases of 50, 200, and 25,000 for backyard, family, and commercial, respectively. Piglets for fattening (48.1%) and replacement sows (40.5%) were the most common types of pigs bought in North Macedonia . CommercThe majority of backyard and family farms slaughtered their pigs at home, with 76.1% of North Macedonian farms reporting slaughter on-site by a family member (54.0%) or someone else (22.1%). North Macedonian farms slaughtering pigs at home overwhelming reported that they owned all the equipment used for slaughter or that the slaughterman brought everything needed. Only 2.1% of farms slaughtering pigs at home reported they borrowed all or only owned some equipment. Inedible materials from slaughter were primarily disposed of via offsite burial (33.6%) and pit disposal (26.1%) in North Macedonia. Sixteen percent of respondents in North Macedonia reported feeding inedible parts to dogs and cats. No respondents reported feeding parts to pigs. Fattened pigs were predominately slaughtered at the end of the year, with November the most common month across farm types, while the slaughtering of piglets had two peaks\u2014April-May and November-January. Regarding the fate of pork products slaughtered at home, 90.2% of North Macedonian respondents reported the meat and products they produced were for home consumption, while most of the product from commercial farms ended up at butcher shops or with middlemen . BackyarAbout 64.8% of North Macedonian respondents answered questions regarding selling live pigs, suggesting there is a large segment of farms that do not sell pigs . The pigs sold in North Macedonia were primarily ready-to-slaughter pigs (50.9%) and piglets for fattening (69.4%). In a given year, North Macedonian commercial sites reported selling a median of 1,128 pigs , compared to backyard and family farms with medians of 1.0 and 27.5 pigs sold, respectively.All responses from Kosovo reported slaughter on-site, with approximately half of slaughter performed by family (47.8%) and half by someone else (52.2%). Having all the equipment needed for slaughter was reported by 39.1% of respondents, while 47.8% borrowed or shared with neighbors. In Kosovo 95.7% of respondents reported inedible materials from slaughter were fed to dogs and cats, 43.5% disposed of via pit disposal and/or 39.1% thrown offsite. The commercial farm in Kosovo reported off-site burial or collection. No respondents reported feeding parts to pigs. Fattened pigs were reportedly slaughtered in October (25%), November (100%) and December (50%). Piglets were slaughtered in May (18.2%), June (77.3%) and July (45.5%). Pork products from homeslaughter were predominantly for home consumption (100.0%), or sold or given to relatives, friends and family (80.0%); however, pork products were also reportedly sold to middlemen (32.0%) and restaurants or bars (16.0%). Sale of pork products was primarily local, sold in the same village (100.0%), same municipality (95.4%), or adjacent municipality (52.4.0%). Pork products were also sold Skopje (28.6%). Fresh meat (100.0%), dried/smoked/salted meat (81.1%), fresh fat (38.1%), and sausage (14.3%) were the most commonly sold or gifted pork products.About 44.0% of Kosovar respondents answered questions regarding selling live pigs. Among those selling pigs, 81.3% reported selling to backyard farms, followed by middlemen (54.5%) and family farms (27.3%). No respondents reported selling pigs to commercial farms or markets. The majority of pigs sold in Kosovo were ready-to-slaughter pigs (63.6%), piglets for fattening (54.5%) and pigs fattened halfway (45.5%). Pigs were primarily sold during October-November and April-June.Producers were asked about a variety of biosecurity and sanitation practices on their farms. Over 90.6% of North Macedonian producers reported that their home or farm was fenced, with 98.2% reporting that their pig pens were fenced. Only 23.4% of North Macedonian producers reported isolating newly purchased pigs; of those who do isolate, the mean time was 24.9 days . Even among commercial farms, the isolation of new pigs was not reported to be consistently practiced (46.7%). Equipment lending or borrowing between neighbors was reported by only 3.7% of respondents in North Macedonia, with commercial farms never lending or borrowing equipment. Changing shoes (94.1%) or clothes (92.8%) before going to the pigs was common in North Macedonia, with hand washing before going to the pigs being slightly less consistent (87.1%). Disinfection mats were used less reliably (68.5%). In general, commercial farms were the most consistent with their biosecurity practices, with all farms reporting fenced properties, fenced pig pens, and consistent practices of changing shoes and cloths, washing hands and using disinfection mats before going to pigs.In Kosovo, 100% of respondents reported their farm/home was fenced; 92% reported their pigs were kept in a pen or fenced in. Among Kosovo respondents 40.0% reported isolating new pigs. Sharing of equipment was reported by 72.0% of respondents. In Kosovo, changing clothes (40.0%) and washing hands (28.0%) were performed less frequently than in North Macedonia; only the commercial farm used disinfection mats.Next, producers were asked about the exposure of their pigs to people visiting the farm and pigs from other premises. Veterinarians were the most common persons allowed access to pigs at 86.7% in North Macedonia. Twenty-three percent of North Macedonian farms had restricted access, with no one allowed near the pigs. Friends (9.0%), neighbors (8.5%), and buyers (8.1%) were each allowed in at a low rate. Slaughtermen had access at 4.2% of farms in North Macedonia. Only 1.8% of North Macedonian farms allowed fellow pig farmers access to their pigs. Commercial farms were generally the most restrictive, with 36.7% allowing no access and 56.7% only allowing access to veterinarians; one North Macedonian commercial farm reported allowing fellow pig farmers and one allowed buyers onsite. In Kosovo, veterinarians were allowed on 100.0% of farms. Among Kosovar respondents 28.0% allowed neighbors, 36.0% allowed buyers, and 28.0% allowed slaughtermen, to access their pigs. Fellow pig farmers were allowed access by 76.0% of Kosovar respondents.Bringing in external boar to cross with sows was reported by 8.6% of respondents in North Macedonia, including three commercial facilities. Most North Macedonian farms reported either using artificial insemination (35.9%) or owning their own boars (35.9%). Only 2.9% of farms, and only backyard and family farms, reported taking their sows offsite for breeding. Of the Kosovar farms assessed, 40.0% did not have breeding animals on-site; among those who did, 32.0% brought in an external boar, 12.0% sent their sows offsite, and 12.0% had their own boar. Artificial insemination was only reported by the commercial farm in Kosovo.In North Macedonia, only 3.9% of farms reported having seen wild boar in the proximity of the farm in the last 12 months, with most sightings occurring late in the year. Wild boars were reported throughout the year in the Northeastern region, in November in the Eastern region, and in October and December in Vardar. Those farms who had seen wild boar were all in the eastern regions of the country. Among pig producers, 2.4% in North Macedonia reported hunting wild boar. Only one farm in Kosovo reported seeing wild boar. Hunting wild boar was reported by 8.0% of Kosovar respondents.Most farms in North Macedonia reported their household waste was collected by the municipality (77.2%). In North Macedonia, burning (9.2%) and throwing/dumping household waste off-site (8.1%) were the next most common disposal routes, with on-site burial of waste rarely reported (3.1%). All but one commercial farm report waste removal by the municipality. No farms reported burying off-site or discarding household waste on their premises. One third of North Macedonian farms reported that there was no disposal site available for household waste in their village. In North Macedonia, most village disposal sites were fenced sites (46.8%), with unfenced sites less common (11.1%). Burial (2.5%) or burning (5.8%) of household waste at village disposal sites was rare. In Kosovo, 68.0% of respondents reported household waste was collected by the municipality, with discarding household waste offsite the next most common form of disposal (36.0%). One farm reported burning some of their household waste. No disposal site available for household waste in the village was reported by 80.0% of Kosovar respondents; 12.0% reported a fenced disposal site, 4.0% a non-fenced disposal site, and 4.0% burial at the disposal site. No burning of waste at village disposal sites was reported.Manure was most commonly disposed of in unfenced (49.2%) or fenced (27.8%) gardens or fields, or stored on-site (36.5%) in North Macedonia. Rarely manure was disposed of at a dumpsite (8.3%). It was very uncommon to sell or give away pig manure (1.3%) in North Macedonia. In Kosovo, manure disposal was highly variable: 84.0% dump off-site, 36.0% spread in unfenced fields, 32.0% sell or give away, 20.0% store in a pit, and 8.0% spread in fenced fields.A second series of biosecurity questions was targeted at family and commercial farm operations: 39.2% of farms reported having a double fence; 55.5% reported having separate clean and dirty areas for employees; and 42.1% reported restricting the kind of food products employees could bring on-site for their own consumption. No commercial farms allowed workers to keep their own pigs at home, with 86.8% of all respondents reporting workers could not keep pigs. Similarly, all but one commercial farm reported their workers were not allowed to hunt in their free time, with 91.1% of all respondents not allowing workers to hunt.When asked about having detailed disinfection protocols, 55.3% reported protocols for vehicles, 68.8% for equipment, and 65.2% for people. Eighty-nine percent of commercial farms reported protocols in place for vehicles, equipment and people, compared to 41.2% of family farms.About one third of farms report never re-assessing their biosecurity procedures. However, 27.1% were reassessing each month, with 18.6% doing so every 3 months, and 10.9% twice a year. Commercial farms were more likely to reassess more often.Forty-three percent of farms reported never organizing events to educate workers about ASF; however, 14.6% did so each month, 12.3% every 3 months, 15.4% every 6 months, and 14.6% once a year. Commercial farms organized training more often.Producers were asked a series of questions regarding where they get information on animal diseases, their level of concern, and to test their knowledge of ASF. The most common sources of animal health information in North Macedonia were veterinarians (96.3%), television (75.6%), the internet (39.4%), and leaflets (29.8%). No one reported getting animal health information at church. These responses were consistent with responses about where producers heard about ASF. One percent of North Macedonian producers report not having heard of ASF\u2014this represents three backyard farms, three family farms and one commercial farm. Reported sources of animal information were similar in Kosovo: veterinarians (96.0%), television (72.0%), local authorities (48.0%), newspapers (32.0%), leaflets/posters (20.0%). Among the Kosovo respondents, 32.0% reported not having heard of ASF.Given a list of pig diseases\u2014ASF, Aujezsky's disease, classical swine fever (CSF), foot-and-mouth disease (FMD), porcine reproductive and respiratory syndrome virus (PRRS), swine influenza, Seneca Valley virus \u2014producers were asked to rank the top three diseases of most concern. African swine fever (85.6%), CSF (85.3%) and swine influenza (41.4%) were the predominant diseases of concern in North Macedonia. While ASF and CSF were consistently of concern, the remaining diseases showed some regional variation. In Kosovo, 68.0% of farms did not list ASF in their top three disease of concern, rather CSF (92.0%), swine influenza (92.0%), and FMD (68.0%) predominated.In recognizing the signs of ASF, the most commonly reported signs from North Macedonian producers were: hemorrhages on the skin (60.6%), reduced appetite (60.0%), fever (60.0%) and sudden death (52.1%). Only 2.4% reported not knowing the signs of ASF, consistent with the previous numbers who had reported not hearing of ASF. Only 1.5% of producers thought ASF was zoonotic. The most common North Macedonian responses regarding the ways their pigs might contract ASF were: introduction or exposure to diseased animals (87.1%), fomites, e.g., infected boots or cloths (49.9%), and feeding infected pork products (39.2%). Twenty-four percent were concerned about transmission routes not relevant to ASF, such as 20.4% mosquitoes, 3.5% wind and 1.8% bad vaccines. In Kosovo, the most commonly reported clinical signs related to ASF were fever (68.0%), diarrhea (64.0%), reduced eating (44.0%), and sudden death (40.0%). Kosovar respondents reported diseased animals (76.0%), feeding infected pork products (28.0%), and fomites (20.0%) as paths of ASF transmission. Twenty percent of respondents did not know how ASF could infect their pigs.When it comes to reporting suspect ASF cases, 76.4% of producers in North Macedonia reported they would quickly report ASF to veterinary authorities if they suspected it on their farms. Twenty-three percent in North Macedonia advised they would wait a few days to report due to concerns about it being a false report. In North Macedonia, only two farms would wait a few days to report to the veterinary authorities due to concern for financial losses. In Kosovo, 48.0% of respondents said they would quickly report suspect ASF, 12.0% would wait a few days due to concerns about a false report, and 40.0% would wait due to concern for financial losses.Finally, when asked why an owner may not report ASF, producers in North Macedonia reported not knowing how to report (39.6%), being unclear about what might happen after reporting (31.1%), the culling of their pigs (27.8%), the subsequent restriction of sale of their pigs (24.3%), damaged reputation (15.1%), and no compensation (9.8%), as the top reasons. Only 2.4% said the owner would prefer to deal with the disease themselves. Reporting being too time consuming was only cited by 0.8% of respondents. In Kosovo, 60.0% reported not knowing how to report, 64.0% were concerned about post-reporting unknowns, 36.0% were concerned about banned sales, 28.0% felt reporting was too time consuming, 20.0% were concerned about their reputations and 16.0% were concerned about their pigs being culled.A subset of survey questions was selected to reflect the biosecurity practices and associated risk level of each farm in North Macedonia. The responses to these questions were dichotomized into low/no risk or contributing risk based on whether a farm performs or does not perform certain activities, e.g., vaccinating vs. not vaccinating pigs . The disMost farms have low biosecurity risk scores\u2014indicating low risk of disease introduction and good biosecurity . When evRisk maps generated using the all-farm biosecurity risk scores, identified areas of high risk for ASF introduction in the Northeastern, Southwestern, and Southeastern regions of North Macedonia . When foMCA grouped not washing hands, allowing access to external boar, allowing access to people other than veterinarians, and not using a disinfection mat as variables highly correlated with dimension 2 and high biosecurity risk scores . Low andThis study provides the most complete profile of the pig industry in North Macedonia available, covering 77.7% of the pig population in the country, thanks to the large sample size and the comprehensive survey responses from pig producers on their husbandry practices, the pork value chain, biosecurity practices, and disease awareness. The recent ASF introductions into Bulgaria, Greece, and Serbia, highlight the need to better understand the pig sector in this region and to inform future targeted interventions. Like other countries in the Balkans, North Macedonia and Kosovo have numerous risk factors for ASF introduction including many low biosecurity small holder farms, free ranging pigs, farms practicing swill feeding, high wild boar suitability, and high connectivity to ASF positive countries through international travel , 34. ThiNorth Macedonian farms had a high rate of turnover among their pigs; this is consistent with census data that shows a relatively large proportion of small farms do not maintain pigs year-to-year, making registration of, and outreach to, these small holder farms a challenge. The predominant use of commercial feed (97.2%) and grain (38.7%) suggests sites selling pig feed may provide good venues to access producers. The reports of feeding scraps and inedible parts to dogs and cats poses a zoonotic concern, not for ASF, but for other diseases such as pseudorabies or echinococcosis. Education on the risks of feeding food scraps to pets, and their role in the transmission of zoonoses, could be added to materials targeting swill feeding.The North Macedonian pig sector seems to make good use of their veterinarians and to trust them as an information source (96.3%). However, only a third of producers called their veterinarians or the veterinary authority when they had pigs die. This should be highlighted as a major gap in current passive surveillance, a critical element for early detection and eradication. Burial and pit disposal predominated as methods of dead pig disposal; depending on the depth of burial, these methods should limit the access of wildlife to carcasses. The last outbreak of CSF in North Macedonia occurred in 2008 , yet vacA large number of households report raising pigs for home consumption and as a source of supplemental income. This reliance on pigs to feed families, as well as contribute to household income, highlights the extent to which an ASF introduction would impact the food and financial security of these producers. Adequate indemnity programs and education about these programs will be needed to support producers and get buy-in on timely disease reporting. Commercial farms reported higher rates of death and disease than backyard and family producers. These systems should be evaluated for potential husbandry, health and biosecurity interventions that may reduce these losses.The pork value chain is predominantly localized, which may limit disease spread if ASF is introduced . The salBiosecurity is highest among commercial farms, but sanitary practices were in general fair to good. The primary areas that could consistently be improved upon would be the use of disinfection mats, the creation of separate clean and dirty areas, and the implementation of consistent disinfection protocols. The efficacy of disinfection mats and boot baths is dependent on removal of visible debris before use, and the use of appropriate disinfectants at adequate concentrations and for enough time , 37. WhiAddressing hurdles to timely reporting is critical to a country's disease detection. Kosovar producers reported a high level of concern about the financial implications of reporting, suggesting the need for clear messaging and planning around indemnity for animals culled to control disease. In both North Macedonia (39.6%) and Kosovo (60%), producers reported not knowing how to report suspect ASF, while about a third of respondents in each country were concerned about post-reporting unknowns, culling, and restricted sale of pigs. Concern about reputation or attempting to control disease oneself, was less commonly reported than previous studies in the region have shown . These rOur biosecurity risk scores and KDE maps highlight specific areas for targeted intervention. On the KDE maps we observe diminishment of the foci in the Southeast and Eastern regions, while retaining the foci in the North and West, when focusing on family and commercial farms vs. focusing on all farms, indicating that high biosecurity risk scores from family and commercial farms were contributing to high risk of ASF introduction in the North and Southwest, while backyard farms likely have a more important role for risk in the South and East. While the highest biosecurity risk scores were focused in the East, Southeast and West, our KDE maps register the highest risk areas in the West and North. This may be due to the small number of farms with high biosecurity risk scores and KDE being influenced by the number of farms in an area, particularly in the North; future work could consider standardizing biosecurity risk in a region by the number of farms in that region. Outreach for backyard farms at high risk of ASF introduction should be targeted in the East, particularly in Southeastern region. More general campaigns to reach all farm types are warranted in Southwestern, Northeastern and Eastern regions. Primary areas in which improvements could be made include: isolating/separating new pigs, using disinfection mats, and limiting access of visitors to pigs. Among family and commercial farms, investment in double fencing, separate clean and dirty areas, and educational training would improve current biosecurity risk scores.MCA and HCPC divided farms into three groups\u2014dimension 1 which captured commercial farms, dimension 2 which captured farms with high-risk practices, and a third group made up of the remaining farms. Our analysis suggests that farms with certain high-risk behaviors were likely to have profiles that demonstrated multiple risky behaviors resulting in an overall high biosecurity risk score profile. The specific behaviors that were highly correlated with dimension 2\u2014not washing hands, allowing visitors including friends, neighbors, buyers, and slaughtermen, and external pigs onto the farm, and not using a disinfection mat\u2014were correlated with high-risk biosecurity risk scores. This grouping generated a profile of responses to this subset of questions. Farms with similar responses are expected to have poor biosecurity practices, and thus high biosecurity risk scores, and should be targeted for education and improved biosecurity, i.e., a farm that does not practice regular handwashing before working with their pigs likely has other poor biosecurity habits, will likely have a high biosecurity risk score, and should be targeted for intervention.The Kosovo pilot study was intended to gain awareness of practices in their pig sector to support the expansion of FAO activities, including biosecurity training that is actively under development. The low sample size from the pilot study in Kosovo implies we should interpret these results with caution. However, a few marked contrasts between North Macedonia and Kosovo, that may impact the risk of ASF spread, should be noted. Kosovo has good, consistent practices around keeping pigs confined and not allowing scavenging. However, Kosovar pig producers reported a much higher rate of swill feeding, and not treating food scraps that were fed to pigs. These responses indicate that while swill feeding is banned in surrounding European Union countries, it is still widely practiced in this region and should be highlighted as a topic for education campaigns . In geneWith data collected via a questionnaire, this study is subject to reporting bias by the respondents. In North Macedonia in particular, with questionnaires being administered by veterinarians, producers may have been more likely to report higher usage of veterinarians, higher levels of care, and stricter biosecurity practices. Additionally, outreach and educational campaigns targeting ASF awareness have been ongoing since 2018, which may have led producers to change or at least report higher quality practices. FAO training did occur in September, October, and November of 2019, while the initial phases of the survey were underway; however, these trainings were primarily targeted at veterinarians vs. producers and are not thought to have had much impact on the respondents. Survey responses are being used to inform updates and development of training materials for producers in the region. In the calculation of the biosecurity risk scores, non-answers were assigned a value of zero. This practice may have resulted in an underestimation of the biosecurity risk scores for some farms.Overall, this study has provided a thorough review of the practices of the pig sector in North Macedonia, highlighting some similarities and contrasts with neighboring Kosovo, and discussing the potential strengths and vulnerabilities regarding the risk of ASF introduction and spread. We have highlighted some specific aspects (and regions) for improvement via additional and targeted educational campaigns and risk reduction interventions. This information will be of great value to inform risk assessments of ASF introduction/exposure, and modeling of ASF spread, if it is eventually introduced into the country. Ultimately, all of these tools will contribute to better prevention, early detection, and control efforts for ASF in North Macedonia and Kosovo.The raw data supporting the conclusions of this article will be made available upon request.KO'H performed the initial draft preparation, data curation and validation, development of the R-code, and formal analysis under supervision of BM-L. DB-A, MH, and BT developed the questionnaire and initiated recruitment of farms included in the study, collected and organized the raw data, and contributed to data cleaning and validation. BM-L supervised the development, implementation and interpretation of the analytic approach. All authors contributed to the project conceptualization and critical and extensive review and editing of the submitted manuscript.Data collection was conducted by FAO through the Technical Cooperation Programme (TCP) (TCP/RER/3704 and TCP/KOS/3703). Data analysis was supported by The Ecology and Evolution of Infectious Diseases Program, Grant No. 2019-67015-28981 from the USDA National Institute of Food and Agriculture and the UC Davis Graduate Group in Epidemiology.The views expressed in this paper are those of the author(s) and do not necessarily reflect the views or policies of FAO.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer EK declared a past co-authorship with one of the authors BM-L to the handling editor.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.Frontiers Media SA remains neutral with regard to jurisdictional claims in published maps and institutional affiliations."} +{"text": "How did health insurance enrollment rates compare for Medicaid vs subsidized marketplace coverage among low-income adults in Colorado 2014 to 2015?In this cross-sectional study with a regression discontinuity analysis of 87\u2009542 US adult enrollees in Medicaid and private insurance, marketplace enrollment was 81.3% lower than Medicaid enrollment in 2014 and 88.6% lower in 2015 among those close to the eligibility threshold. The drop-off in marketplace enrollment was largest among younger adults.Substantial gaps in publicly subsidized private coverage may have existed for those with incomes just beyond the reach of Medicaid expansion, especially among younger adults. This cross-sectional study assesses the association between income eligibility for Medicaid vs marketplace coverage and insurance enrollment among adults with low income in Colorado. The Affordable Care Act created 2 new coverage options for uninsured adults: Medicaid expansion, which in most states provides comprehensive coverage without premiums and deductibles; and private marketplace coverage, which requires a premium contribution and cost-sharing, though with generous federal subsidies at lower incomes. How enrollment rates compare in the marketplace vs Medicaid is an important policy question as states continue to weigh alternative coverage options such as Medicaid buy-in programs, enrolling Medicaid-eligible populations into marketplace plans, or creating a public option.To assess the association between income eligibility for Medicaid vs marketplace coverage and insurance enrollment among low-income adults in Colorado.Using 2014 and 2015 all-payer claims data from Colorado and detailed income eligibility information, we used a regression discontinuity design to assess the difference in Medicaid and marketplace enrollment just below and just above 138% of the federal poverty level (FPL), the eligibility threshold between the 2 programs. The sample included nonpregnant adults aged 19 to 64 years with incomes between 75% to 400% FPL. We stratified our analysis by age, sex, chronic condition status, and urban vs rural residence. Analysis was conducted from January to October 2020.The main outcome was total enrollment in either Medicaid or marketplace coverage during marketplace\u2019s Open Enrollment period. Income-based health insurance eligibility was assessed as a percentage of FPL at the time of initial application for coverage.The primary analytical sample included 32\u2009091 enrollees in 2014 and 55\u2009451 in 2015, with incomes ranging from 120% to 156% FPL. Most enrollees were women , resided in urban areas , and had no chronic conditions . For age, in 2014 and 2015, respectively, 13.22% and 13.93% were aged 19 to 25 years, 27.85% and 28.54% were aged 26 to 34 years, 23.58% and 24.34% were aged 35 to 44 years, 18.35% and 17.75% were aged 45 to 54 years, and 17.00% and 15.44% were aged 55 to 64 years. Marketplace enrollment was 81.3% lower than Medicaid enrollment in 2014 and 88.6% lower in 2015 among those close to the 138% FPL eligibility threshold. The drop-off in marketplace enrollment was largest among younger adults, aged 26 to 34 and 35 to 44 years: relative drop off \u221288.7% and \u221287.8% in 2014, and relative drop off \u201391.9% and \u221293.0% in 2015, respectively.In this cross-sectional study using a regression-discontinuity analysis, meaningful gaps in insurance enrollment may have existed for those with incomes just above the eligibility threshold for Medicaid expansion, especially among younger adults. Policies expanding Medicaid income eligibility or zero-dollar premium marketplace plans are likely to be more effective at inducing enrollment than subsidized private plans with premium requirements. Individuals with incomes between 138% and 400% FPL can purchase private marketplace coverage, which requires a premium contribution and cost-sharing, but includes income-based tax credits and cost-sharing subsidies from the federal government.The Affordable Care Act (ACA) created 2 important coverage options for uninsured adults beginning in 2014.2 For those with incomes above the expanded Medicaid eligibility threshold, marketplace coverage has also decreased the uninsured rate and improved access to care for low-income adults without employer-sponsored insurance (ESI).3Since then, 39 states (including the District of Columbia) have expanded Medicaid and almost 20 million low-income adults have gained health insurance.4 Research suggests that lack of affordability may deter enrollment for those eligible for marketplace coverage.5 Although premiums for low-income individuals are subsidized,6 marketplace plans often include high deductibles and point-of-care cost sharing. Previous studies of insurance indicate modest premiums and higher cost sharing are barriers to coverage among low-income individuals.8 Various subgroups may differ in their price sensitivity for coverage, with low-income individuals, younger adults, and the self employed potentially more sensitive to premiums.10 This may be compounded by administrative hurdles to enrolling in marketplace coverage, and confusion related to ACA complexity and misinformation campaigns.12Despite these coverage gains, almost 30 million people remained uninsured in 2019, and over 7 million of them were likely eligible for marketplace tax credits.13; expanding Medicaid\u2019s low-cost comprehensive coverage with a subsidized premium buy-in; or replacing eligibility for the Medicaid expansion in some populations with private insurance.15 Evidence on factors driving differential enrollment rates could provide key insights on ways to insure those with the greatest need.Recent federal and state proposals to address these gaps included options, such as improving private coverage and marketplace affordability through increased subsidies and reduced cost sharing16 In this study, we assess an important question that was not explored in our prior research, the overall likelihood of enrollment in these 2 types of coverage.In this Colorado-based analysis, we compare individuals near the eligibility threshold of 138% of FPL to assess the association between eligibility for Medicaid vs Marketplace coverage and public insurance enrollment among low-income adults and whether enrollment differs by age, sex, chronic condition status, or residence. With this data set, we previously compared health care costs, quality, and utilization between Medicaid and Marketplace enrollees across the expanded Medicaid eligibility threshold. We found modest differences in quality, significantly higher costs among Marketplace enrollees, and higher emergency department visits among Medicaid enrollees.Using all-payer claims data (APCD) from Colorado and detailed income eligibility information provided by the state\u2019s Medicaid agency and marketplace, we assessed the difference between Medicaid and Marketplace enrollment just above and below the 138% FPL cutoff, using a sharp regression discontinuity design (RD) . Because most individuals below the 138% FPL threshold were covered by Medicaid and those above, by marketplace, we compare the enrollment differences across the threshold by coverage rather than income. The analysis was conducted from January 2020 to October 2020, using STATA statistical software .International Classification of Diseases, Ninth Revision, Clinical Modification and (ICD-9) and ICD-10 codes) and urban vs rural residence using scatterplots of enrollment in each bin of family income as a percentage of the FPL. We analyzed enrollment using 2 sets of RD models and modeled the association between income and enrollment as a polynomial, allowing for linear, quadratic, and cubic terms. As in the local linear model, we allowed this association to vary above and below the 138% threshold.2 analyses , we tested for significant differences between enrollment estimates for each subgroup.We use a generalized linear model with a negative binomial distribution and log link, and present estimated coefficients as incidence rate ratios, which allowed for direct comparisons of the relative reduction in enrollment between subgroups. We repeated stratified analyses for year, age, sex, chronic condition status, and urban vs rural residence. Using simultaneous covariance matrices with cross-model \u03c7We also conducted 2 sensitivity analyses (1) replicating our methods using linear regression models; and (2) examining any discontinuities in income for the Colorado population using data from the American Community Survey , resided in urban areas and had no chronic conditions . For age, in 2014 and 2015, respectively, 13.22% and 13.93% were aged 19 to 25 years, 27.85% and 28.54% were aged 26 to 34 years, 23.58% and 24.34% were aged 35 to 44 years, 18.35% and 17.75% were aged 45 to 54 years, and 17.00% and 15.44% were aged 55 to 64 years .Our primary regression results are from the local linear model using the optimal bandwidth, with incomes between 120% and 156% FPL. The relative drop-off in total enrollment in ACA-related coverage between 138% and 139% FPL was \u221281.3% in 2014 and \u221288.6% in 2015 in the local linear model .Subgroup analyses also showed significant drop-offs in enrollment for those above 138% FPL.P\u2009<\u2009.001 for all age groups compared with those aged 55-64 years).In both years, differences in enrollment varied most widely by age group. Younger enrollees\u2014those aged 26 to 34 years and 35 to 44 years\u2014had the largest enrollment drop-offs: \u221288.7% and \u221287.8% in 2014, and \u221291.9% and \u221293.0% in 2015, respectively Table 3Table 3. P\u2009<\u2009.001), but not in 2014 (P\u2009=\u2009.57).The relative drop-off in ACA-related enrollment above 138% FPL was slightly larger for women than for men in both years, \u221281.6% in 2014 and \u221289.5% in 2015 for female enrollees, compared with \u221280.7% in 2014 and \u221287.3% in 2015 for male enrollees eFigure. These dP\u2009=\u2009.24), but the gap widened in 2015, with drop-offs of \u221289.1% for urban residents and \u221283.1% for rural residents (P\u2009=\u2009.02).In 2014, urban and rural residents experienced similar drop-offs in enrollment above 138% FPL, \u221281.3% and \u221282.0% , respectively and \u221288.5% compared with \u221288.7% (\u221290.9% to \u221286.0%) in 2015 (P\u2009=\u2009.65), respectively, but these differences were not statistically significant compared with \u221281.9% in 2014 if some patients with these conditions did not obtain medical care resulting in a billed diagnosis. Similarly, information on substance abuse disorders in the database was limited owing to federal privacy laws, which also may have contributed to an underestimate of chronic conditions in our study.Finally, our sample includes Colorado residents only, which may limit the generalizability of these findings to other states.14 However, zero-premium marketplace plans, such as the public option proposed by policymakers for nonexpansion states, have been shown to improve marketplace enrollment, especially for low-income adults.33 Automatic enrollment, another part of this proposal, would likely have similar effects34 and may promote continuity of coverage36; together, these options could significantly improve effectuated enrollment for this population by removing both administrative and financial barriers to coverage.37These findings indicate that low-income adults in Colorado appear over 80% less likely to enroll in ACA-related health insurance coverage when the option is marketplace insurance rather than Medicaid. As policymakers consider various approaches to enrolling more individuals in insurance, zero-premium comprehensive coverage in Medicaid offers a substantial advantage in enrollment compared with highly subsidized private insurance requiring a premium. This suggests the proposals by states, such as Massachusetts, to move some Medicaid beneficiaries into private coverage, could produce large losses in insurance.19 Other policymakers have proposed benchmarking marketplace premium tax credits to gold plans to increase the overall subsidy, which could offer similar affordability improvements by reducing premiums on plans with higher cost-sharing assistance.Meanwhile, models that offer coverage to those above the 138% income cutoff in programs more similar to Medicaid, such as the Basic Health Program in New York and Minnesota, may have greater success at covering uninsured populations. Out-of-pocket costs in marketplace are substantially higher than in Medicaid, which may lead to disenrollment.38 which for many also meant a loss of their ESI. Although a significant proportion may obtain coverage from Medicaid or the marketplaces, with Medicaid enrolling most, studies have predicted anywhere from 3.5 to 7 million will be left without insurance.40 Though unemployment rates are changing with different COVID-19 restrictions, layoffs continue to disproportionately affect younger adults, with those aged 25 to 34 years experiencing increases in unemployment at roughly 1.5 times the rate of those aged 45 years and older.41 In the context of these findings, newly unemployed younger low-income adults may be at high risk for becoming uninsured if they do not qualify for Medicaid\u2019s premium-free coverage and if this pattern of discontinuity persists.Amidst the coronavirus 2019 (COVID-19) pandemic, coverage gaps for low-income adults are increasingly relevant for policymakers. Between January and May 2020, more than 40 million individuals lost their jobs,In this cross-sectional study using a regression discontinuity analysis, our findings showed that significant enrollment differences in public health insurance existed for Coloradoans with incomes just above the expanded Medicaid eligibility threshold in 2014 and 2015, particularly for younger adults. Policies extending Medicaid or zero-dollar premium plans are likely to be more effective at inducing enrollment for this population than subsidized private plans with premium requirements. Policymakers should be aware of enrollment differences between Medicaid and subsidized private insurance and focus on implementing changes that could substantially increase enrollment and curtail age disparities for low-income adults."} +{"text": "Transportation is an increasingly meaningful concern for older adults as physical, cognitive, and psychological changes in older adulthood impact mobility and accessibility. While several studies have examined the modes of transportation used among older adults, few have explored specifically how older adults are accessing primary care/medical care services. As such, this study aimed to determine the specific modes of transportation used among older adults for primary care visits. Data were derived from the 2018 National Health and Aging Trends Study (NHATS), an annual longitudinal panel survey of older adults aged 65 and older living in the United States. Descriptive analyses were conducted to examine the prevalence of several modes of access and logistic regression models were used to predict the likelihood of using the two most prevalent transportation modes, based on sociodemographic and socioeconomic factors. Results showed that 70% of older adults drive themselves to their doctor, 34.8% rely on a family member, friend, or paid person, 2.4% have a home visit, 2.1% use public transportation, 1.5% walk to their doctor and 1.1% use a taxi. Additionally, having higher income, being of younger age, being White, and having post-secondary education was associated with driving oneself to the doctor. These results indicate that while most older adults are still self-reliant on transportation to medical providers, those with lower socioeconomic status are particularly at risk of losing driving independence. Transportation-related interventions should therefore consider targeting individuals with lower economic capital by proving financial assistance, ride-share programs, and other innovative approaches."} +{"text": "Background: Co-infection with malaria and chikungunya could exert a significant public health impact with infection misdiagnosis. Therefore, this study aimed to collect qualitative and quantitative evidence of malaria and chikungunya co-infection among febrile patients. Methods: Potentially relevant studies were identified using PubMed, Web of Science, and Scopus. The bias risk of the included studies was assessed using the checklist for analytical cross-sectional studies developed by the Joanna Briggs Institute. The pooled prevalence of malaria and chikungunya co-infection among febrile patients and the pooled prevalence of chikungunya virus (CHIKV) infection among malaria patients were estimated with the random effect model. The odds of malaria and chikungunya co-infection among febrile patients were also estimated using a random effect model that presumed the heterogeneity of the outcomes of the included studies. The heterogeneity among the included studies was assessed using the Cochran Q test and I2 statistics. Publication bias was assessed using the funnel plot and Egger\u2019s test. Results: Of the 1924 studies that were identified from the three databases, 10 fulfilled the eligibility criteria and were included in our study. The pooled prevalence of malaria and chikungunya co-infection (182 cases) among febrile patients , stratified by diagnostic tests for CHIKV infection, was 10% : 8\u201311%, I2: 99.5%) using RDT (IgM), 7% (95% CI: 4\u201310%) using the plaque reduction neutralization test (PRNT), 1% using IgM and IgG ELISA, and 4% (95% CI: 2\u20136%) using real-time RT-PCR. When the prevalence was stratified by country, the prevalence of co-infection was 7% in Nigeria, 1% in Tanzania, 10% (95% CI: 8\u201311%) in Sierra Leone, 1% (95% CI: 0\u20134%) in Mozambique, and 4% (95% CI: 2\u20136%) in Kenya. The pooled prevalence of CHIKV infection (182 cases) among malaria patients (8317 cases), stratified by diagnostic tests for CHIKV infection, was 39% using RDT (IgM), 43% (95% CI: 30\u201357%) using PRNT, 5% using IgM and IgG ELISA, and 9% (95% CI: 6\u201315%) using real-time RT-PCR. The meta-analysis showed that malaria and chikungunya co-infection occurred by chance . Conclusions: The prevalence of malaria and chikungunya co-infection varied from 0% to 10% as per the diagnostic test for CHIKV infection or the country where the co-infection was reported. Hence, the clinicians who diagnose patients with malaria infections in areas where two diseases are endemic should further investigate for chikungunya co-infection to prevent misdiagnosis or delayed treatment of concurrent infection. Chikungunya is one of the most common vector-borne infectious diseases caused by the chikungunya virus (CHIKV) ,2. The cThis systematic review and meta-analysis were performed as per the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines . This syPotentially relevant studies were identified through PubMed, Web of Science, and Scopus without any restrictions by language or publication date. The combination of the search terms with Boolean operators \u201c AND Chikungunya\u201d was used to search for the studies. The Medical Subject Heading database was used to check the search terms for accuracy as well as to search for further studies to be included in the present analysis. The search terms and search strategy are shown in Studies were included as per the inclusion and exclusion criteria. The inclusion criteria were based on the participants (P), outcome of interest (I), and contexts (Co) (PICo): P represented febrile participants or malaria patients; I represented malaria; chikungunya represented co-infection or CHIKV infection; Co represented the global prevalence. All types of study designs, including observational, cohort, and case-control designs, that reported the co-infection of both pathogens were considered. Case reports, case series, letters to editors, comments, reviews, systematic reviews, meta-analyses, studies without full text, and studies from which the data could not be extracted were excluded.Following the identification of potentially relevant studies from the databases, the duplicates were removed, and the remaining studies were screened for titles and abstracts. The unrelated studies were excluded, and the remaining studies were examined for their full texts. The studies that did not fulfill the eligibility criteria were excluded, with the reasons noted. The studies that fulfilled the eligibility criteria were included for further data extraction and quality assessment. Studies were selected independently by two authors (MK and WM). Any disagreement between the two reviewers was resolved by the third author (PW).Data regarding the following aspects were extracted from the included studies: the name of the first author, the year of publication, the site of the study, the year of the study, the design of the study, the number and characteristics of participants, the age of the subjects, the sex of the subjects, the number of co-infections, the number of malaria mono-infections, the number of CHIKV infections, and the diagnostics tests for malaria and CHIKV infections. Data were extracted by two authors (MK and WM) and were cross-checked by the third author (PW). The extracted data were recorded in the pilot standardized datasheet for further analyses.The bias risk in the included studies was assessed using the checklist for analytical cross-sectional studies that was developed by the Joanna Briggs Institute . The risThe primary outcome of the present study was the pooled prevalence of malaria and chikungunya co-infection in febrile patients. The secondary outcome was the pooled prevalence of CHIKV infection in malaria patients. The third outcome was the odds of malaria and chikungunya co-infection in febrile patients.2 statistics. A Cochran Q test with p < 0.1 or an I2 statistic >25% indicated substantial heterogeneity in the outcome of the included studies. The subgroup analyses of countries and diagnostic tests for CHIKV infection were performed to explore the source of the outcome heterogeneity. All the analyses were performed using Stata version 14 .The qualitative and quantitative collection of evidence from the literature has been described elsewhere ,12,13. TA total of 1924 studies were identified from the following 3 databases: 441 from PubMed, 876 from Scopus, and 607 from Web of Science. After the duplicates were removed, 1173 studies were screened through the titles and abstracts; thereafter, 1045 studies were excluded because they were irrelevant. The remaining 128 studies were examined through their full texts. Of these, 119 studies were excluded because they were reviews (29), only reported on chikungunya (25), only reported on malaria or chikungunya mono-infection 21), were in vitro studies (12), performed assays (8), were case reports or case series (7), reported on malaria only (5), were animal studies (5), were systematic reviews (4), involved mathematical models (2), or did not have full text (1). Thus, 9 studies ,21,22 th, were inAll the characteristics of the included studies are shown in The risk of bias among the included studies was assessed using the checklist for analytical cross-sectional studies that was developed by the Joanna Briggs Institute (11). Most of the included studies had a moderate bias risk level , while 2 had low bias risk levels , Table 12: 99.5%) in Nigeria, 1% in Tanzania, 10% (95% CI: 8\u201311%) in Sierra Leone, 1% (95% CI: 0\u20134%) in Mozambique, and 4% (95% CI: 2\u20136%) in Kenya in febrile patients was estimated using 8 studies . The results showed that the prevalence of co-infection stratified by country was 7% using RDT (IgM), 7% (95% CI: 4\u201310%) using PRNT, 1% using IgM and IgG ELISA, and 4% (95% CI: 2\u20136%) using real-time RT-PCR in studies that enrolled patients of all age groups, 1% in studies that enrolled only pediatric subjects, and 1% (CI: 0\u20134%) in the study that enrolled only adult subjects (2: 96.4%).When the prevalence was stratified as per age groups, the prevalence of malaria and chikungunya co-infection was 6% in Nigeria, 4% in Tanzania, 41% (95% CI: 36\u201347%) in Sierra Leone, 6% (95% CI: 3\u201310%) in Venezuela, 6% (95% CI: 2\u201319%) in Mozambique, and 9% (95% CI: 6\u201315%) in Kenya among malaria patients 8317 cases) was estimated using 9 studies [ cases wa2 cases ain Kenya .2: 99.7%) using RDT (IgM), 43% (95% CI: 30\u201357%) using PRNT, 5% using IgM and IgG ELISA, and 9% (95% CI: 6\u201315%) using real-time RT-PCR in studies that recruited patients in all age groups, 5% (95% CI: 2\u20138%) in children, 6% (95% CI: 2\u201319%) in adults, and 6% (95% CI: 3\u201310%) in the study that did not specify the patient age (2: 97.3%).When the prevalence of CHIKV infection in malaria patients was stratified by age group, the prevalence of CHIKV infection in malaria patients was 23% in febrile patients were estimated using 8 studies 2 cases i,20,21,22: 78.5%) .p: 0.954, coefficient <0.001, standard error: 0.002). The meta-regressions with sex as a covariate for the pooled prevalence of chikungunya co-infection in patients with malaria showed that sex did not confound the effect estimate .Meta-regressions with sex as a covariate for the effect estimates were performed. The meta-regressions with sex as a covariate for the pooled prevalence of malaria and chikungunya co-infection in febrile patients showed that sex did not confound the effect estimate overall pooled prevalence of malaria and leptospirosis co-infection. The subgroup of countries showed that the prevalence ranged from 1% to 10% in several countries within Africa, including Sierra Leone, Nigeria, Kenya, Tanzania, and Mozambique. The results were consistent with those that previously reported a prevalence of 0.02\u201315% for the co-infection of malaria and chikungunya in Africa . These pMalaria and chikungunya co-infection are rare; however, single infections share similar clinical symptoms with other febrile illnesses, which leads to misdiagnosis at the early stages of infection ,2. In EtAnopheles mosquitoes, while chikungunya is transmitted via the bite of Aedes mosquitoes. However, lower odds of co-infection were demonstrated in the studies conducted in Nigeria [The meta-analysis showed that malaria and chikungunya co-infection occurred by chance. This could be explained by the fact that these two diseases were transmitted through two different vectors. Malaria is transmitted by the female Nigeria , Tanzani Nigeria , and Sen Nigeria . The res Nigeria ,8. In adThe present study has certain limitations. First, a limited number of studies reported malaria and chikungunya co-infection; thus, only a single outcome of the meta-analysis could be estimated: the pooled prevalence of the co-infection. Second, some studies might have been missed during study selection. However, we performed searches on other sources, such as Google Scholar, and reviewed the reference lists of the included studies to prevent overlooking relevant studies. Third, differences based on clinical data, laboratory alterations, or treatment outcomes could not be assessed due to the unavailability of data; therefore, future prospective studies should examine these differences to provide relevant data to clinicians that can enable treatment decisions for patients with co-infection.The prevalence of malaria and chikungunya co-infection ranged from 0% to 10%, as per diagnostic tests for CHIKV infection or the country where the co-infection was reported. Hence, clinicians who diagnose patients with malaria in areas that are endemic for these two infections should further investigate for chikungunya co-infection to prevent misdiagnosis or delayed treatment of concurrent infection."} +{"text": "Infections are the main cause of death in patients with hematologic malignancies. This study aims to determine the microbial profile of infections in patients with hematologic malignancies and to determine the antimicrobial resistance patterns for these pathogens.A retrospective descriptive cross-sectional study was conducted from January 2018 to December 2019 at a large hematological center in Palestine. The medical data of hematologic malignancy patients with positive cultures were collected from the hematology/oncology department using the hospital information system, and data regarding the microbial isolates and their antimicrobial resistance were collected from the microbiology laboratory.Pseudomonas aeruginosa , followed by Escherichia coli (E. coli) . Fourteen isolates (24.6%) of GPB were Staphylococcus epidermidis followed by Enterococcus faecium and Staphylococcus hemolyticus . The most frequent fungal pathogens were Candida species . GNB were found to be resistant to most antibiotics, mainly ampicillin (79.3%). Pseudomonas aeruginosa exhibited high resistance to ciprofloxacin (60%) and imipenem (59.3%). Among GPB, high resistance rates to oxacillin (91.1%) and amikacin (88.8%) were found. All isolated strains of Staphylococcus epidermidis were resistant to cephalosporins and oxacillin. Approximately half of the GNB isolates were multi-drug resistant organisms (MDRO), and 16.7% (11 isolates) were difficult-to-treat resistance (DTR). Furthermore, 68.4% (39 isolates) of GPB were MDRO. The proportion of staphylococci (CoNS and S. aureus) resistant to oxacillin was 91.7%, while 88.6% of enterococci were resistant to vancomycin.A total of 144 isolates were identified from different types of specimens, mostly blood samples. Of all isolates, 66 (45.8%) were gram-negative bacteria (GNB), 57 (39.6%) were gram-positive bacteria (GPB), and 21 (14.6%) were fungal isolates. The GNB that were most frequently isolated were The findings of this study confirm the predominant microorganisms seen in patients with hematologic malignancies, and show a high percentage of antibiotic resistance. Policies regarding antibiotic use and proper infection control measures are needed to avert the ever-growing danger of antimicrobial resistance. This may be achieved by developing antibiotic stewardship programs and local guidelines based on the hospital's antibiogram. In recent decades, major developments have been made in the care of cancer patients that have significantly improved patient survival. However, despite these developments, patients with hematologic malignancies remain at an extraordinarily high risk of infections. This is the result of a complex interaction between basic immunodeficiency and therapeutic practices such as surgery, radiation, and chemotherapy \u20134.Previous studies have reported that the prevalence of bacterial bloodstream infections among patients with hematologic malignancies ranges from 11 to 38%, and the rough mortality rate reaches up to 40% \u20137. FurthE. coli was the most common isolated organism, followed by coagulase-negative staphylococci (CoNS) [A study in India showed that i (CoNS) . Anotheri (CoNS) . Howeveri (CoNS) .Staphylococcus aureus, and high resistance to penicillin (40.4%) in Streptococcus pneumonia [In Palestine, cancer is the third leading cause of death after heart disease and cerebrovascular disease, accounting for 10.3% of total deaths . Howeverneumonia . HoweverAntibiotic resistance is a growing concern in global health \u201320. OverThis study provides information on the spectrum of microbial isolates and their antimicrobial resistance patterns in patients with hematologic cancer at An-Najah National University Hospital. This study is the first to evaluate bacterial and fungal resistance patterns among hematological malignancies in Palestine. This information will help decrease morbidity and mortality by helping to establish empirical treatment guidelines and antibiotic stewardship programs. These will reduce antibiotic overuse and, subsequently, decrease hospitalizations. This study also highlights the immense effect and burden of multi-drug resistant organisms.A retrospective cross-sectional study was conducted to determine the frequency of microbial isolates and patterns of antimicrobial resistance in patients with hematologic malignancies.Data were collected from the medical laboratory department and the hematology department of An-Najah National University Hospital. The hospital has a bed capacity of 169, with approximately 40 beds for adult hematology/oncology patients .All patients with hematologic malignancies who had a positive culture from January 2018 to December 2019 at An-Najah National University Hospital.Demographic and medical data were obtained from the hospital information system. Information on the sources of specimens, types of microorganisms, and antibiotic susceptibility was collected from the microbiology laboratory. Importantly, cefepime is available in the hospital, but its use is very restricted because it requires a special request from an infectious disease specialist. Furthermore, ceftolozane / tazobactam is not available in Palestine.All patients with hematologic malignancies who had positive cultures during the study period at An-Najah National University Hospital were included.Patients who did not have a positive culture and those who had solid tumors were excluded.The proposal was reviewed and accepted on September 22, 2019, with the permission of An-Najah National University Hospital. The approval of the Institutional Review Board (IRB) Committee of An-Najah National University was obtained on July 24, 2019 (Archived number: AN4June2019).Data were entered and analyzed using version 21 of the Statistical Package for Social Sciences (SPSS) program. For continuous variables, data were expressed as means\u2009\u00b1\u2009standard deviation (SD) and as frequencies and percentages for categorical variables.A total of 144 cancer patients were included in the study. Of these, 77 (53.5%) were women and 67 (46.5%) were men. The mean age\u2009\u00b1\u2009SD of the study participants was 40.8\u2009\u00b1\u200916.6\u00a0years, ranging from 17 to 84\u00a0years old. The most common hematologic malignancy was acute lymphoid leukemia (ALL) , followed by Hodgkin\u2019s lymphoma , acute myeloid leukemia , multiple myeloma , non-Hodgkin lymphoma , chronic lymphoid leukemia , Waldenstrom macroglobulinemia and Langerhans cell histiocytosis . Most of these patients were actively on the chemotherapy protocol or had had bone marrow transplantation , while others had finished their treatment or had not received any cancer treatment at the time their samples were collected . It should be noted that most of the patients were febrile and a portion had died at the end of the study ; , urine and sputum . A smaller portion was isolated from fluid , stool and cerebrospinal fluid .There were 144 positive cultures; 66 (45.8%) isolates were GNB, 57 (39.6%) GPB, and fungal infections were positive in 21 (14.6%) samples.Pseudomonas aeruginosa was predominant, followed by E. coli which can be divided into non-extended-spectrum beta-lactamase-producing Escherichia coli (non-ESBL-EC); , and ESBL-producing Escherichia coli (ESBL-EC); . These were followed by both Acinetobacter baumannii and Klebsiella pneumonia , followed by Enterococcus faecium and Staphylococcus hemolyticus , Staphylococcus hominis , Enterococcus faecalis , and Staphylococcus aureus with only one (4.8%) Saprochaete capitate . The vast majority were The vast majority of antimicrobials were used in combinations. Among those used in combination, amikacin was the most popular antibiotic for empiric therapy, since it was used in 45 cases out of 144 organisms , followed by vancomycin , meropenem , piperacillin-tazobactam , colistin and tigecycline . On the other hand, the least frequently used antimicrobials were azithromycin, clindamycin, and caspofungin , followed by colistin , tigecycline , vancomycin and amikacin . Meanwhile, the antibiotics used most frequently were linezolid , followed by amoxicillin-clavulanate were ESBL and 23 isolates (31.8%) were CRE (carbapenem resistant Enterobacteriaceae). The most common isolated GNB, Pseudomonas aeruginosa, had a high resistance rate to ciprofloxacin (60%), imipenem (59.3%), piperacillin (54.2%), meropenem, and gentamicin (48% each). Furthermore, resistance rates against cephalosporins, cefepime, and ceftazidime were 16% and 24% respectively. E. coli isolates were highly susceptible to amikacin (95%), while they were highly resistant to trimethoprim-sulfamethoxazole and fluoroquinolones. Regarding the six isolates of Acinetobacter baumannii, the highest resistance rates were towards carbapenems (80% for meropenem and 83.3% to imipenem), piperacillin-tazobactam (83.3%) and gentamicin (66.7%). Only four isolates were tested for sensitivity to colistin and all showed 0% resistance. Finally, the six isolates of Klebsiella pneumonia were highly susceptible to piperacillin-tazobactam, carbapenems, fluoroquinolones ceftazidime and cefepime. The antimicrobial resistance profiles of the most frequently isolated GNB are reported in Table In general, the highest resistance rates for GNB were 79.3% for ampicillin, 73.3% to levofloxacin, 65.7% for ceftriaxone, 61.8% to piperacillin, and 59.3%, 56.5% and 59.4% for cefuroxime, ciprofloxacin, and tobramycin, respectively. Meanwhile, the lowest resistance rates were 3.6% for ertapenemS. epidermidis, hemolyticus, hominis, sciuri, and capitis while none of the Enterococcus faecalis isolates were VRE. 40% of Enterococcus faecium isolates were resistant to streptomycin, 30% were resistant to gentamicin, and 11.1% were resistant to tigecycline. Meanwhile, Enterococcus faecalis species had 80% resistance to streptomycin, 50% resistance to gentamicin, and 33.3% resistance to tigecycline. However, none of the Enterococcus faecalis or Enterococcus faecium isolates were resistant to linezolid. Overall, the highest resistance rates of GPB were 91.1% to oxacillin, 88.8% to amikacin, 86.9% to cefuroxime, 85.1% to erythromycin, and 84.8%, 82.6%, 77.4 to penicillin, ceftriaxone, amoxicillin-clavulanic, respectively. Meanwhile, the lowest resistance rates were 0% to linezolid, 4.2% to tigecycline, 11.5% to quinupristin-dalfopristin, and 16.1% to vancomycin. The antimicrobial resistance profiles of the most frequently isolated GPB are reported in Table Among the CoNS isolated in our study , whereas among GPB, CoNS had the highest rate (81.3%) Table .Table 7FA. baumannii\u00a0only), and aztreonam (not applicable to A. baumannii), when results are available [Pseudomonas aeruginosa, 5 (83.3%) were Acinetobacter baumanni (6) and 1 (5%) was E. coli was the predominant bacterium among GNB, followed by E. coli that can be divided into non-ESBL and ESBL-E. coli . These were followed by Acinetobacter baumannii and Klebsiella pneumonia, with six isolates each (9.7%). These results are in conjunction with other studies conducted in India and Pakistan. In the former, they reconfirmed the predominance of GNB in patients with hematologic cancers, with E. coli, Pseudomonas, and Klebsiella having the largest shares [Pseudomonas aeruginosa was the most frequent bacteria, followed by E. coli, Klebsiella, Proteus, and Shigella [E. coli was the most frequent organism, followed by Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterobacter cloacae [E. coli represented the most frequently isolated bacterium among GNB, followed by Pseudomonas aeruginosa [Klebsiella pneumoniae followed by E. coli [In our study, t shares In the lShigella . These r cloacae . In anotruginosa . Meanwhicoli 20, .3% that Enterococcus faecium , Enterococcus faecalis and Staphylococcus aureus . These results are comparable to the aforementioned Italian study, where CoNS were the most common species, followed by Enterococcus spp., viridans group streptococci (VGS) and Staphylococcus aureus (11). In the Indian study, the most frequent GPB isolates were CoNS, then Staphylococcus aureus, Streptococcus spp., and Enterococcus spp. (14).Regarding GPB, CoNS represented the most frequent species isolated in our study , followed by Pseudomonas aeruginosa (22%), E. coli (16.3%), and Staphylococcus epidermidis (11.4%), followed by Enterococcus faecium and Staphylococcus haemolyticus (8.1% each), and then Klebsiella pneumonia, Acinetobacter baumanii, and Staphylococcus hominis (4.9% each). In comparison, when looking at patients with hematologic malignancies in Japan, E. coli was the most commonly seen bacterium, followed by Klebsiella spp., Pseudomonas aeruginosa, Staphylococcus aureus, Enterobacter spp. Citrobacter spp., and Acinetobacter spp. [In our study, the bacteria most commonly isolated were ter spp. .Aspergillus and Candida\u2014are the leading infectious cause of mortality in patients with myelosuppression due to chemotherapy [Candida had the highest share of fungal infections, in contrast to a study in Italy where most infections were caused by Aspergillus spp., followed by Candida [Hard to spot but lethal if missed, invasive fungal infections\u2014predominantly caused by otherapy . In our Candida .Pseudomonas aeruginosa exhibited high resistance to ciprofloxacin (60%), in concordance with numbers found in similar Italian studies [Pseudomonas aeruginosa isolates in our study also had high resistance to carbapenems, including imipenem (59.3%), meropenem (48%), and gentamicin (48%). These numbers resemble those found in another study where the resistance rate to carbapenems was 60% [Pseudomonas aeruginosa isolates, piperacillin resistance was found to be 54.2%, while in a previously mentioned study it was found to be 24% [In our study, studies , 36, and studies . Pseudom was 60% . However was 60% . Also amo be 24% , to avoio be 24% , 41.E. coli isolates to amikacin was only 5%, similar to the results of another study where 85.2% of E. coli isolates were found to be sensitive to amikacin [E. coli exhibited 100% resistance to both cephalosporins and ampicillin, similar to previous research, where the vast majority of ESBL-producing isolates were resistant to all generations of cephalosporins [E. coli in our study also exhibited high resistance to levofloxacin and TMP-SMX , similar to the results found in a previous study [Among GNB, 21 CRE (31.8%) were detected, more than that seen in febrile neutropenic patients with hematological cancer in Japan . In our amikacin . On the osporins . E. colius study . This cous study .Acinetobacter baumannii, the highest resistance rates were observed to carbapenems (80% to meropenem and 83.3% to imipenem) and piperacillin-tazobactam (83.3%) similar to a related study held in Turkey [Acinetobacter baumannii were susceptible to colistin [Klebsiella pneumonia were 100% susceptible to piperacillin/tazobactam, carbapenems, fluoroquinolones, ceftazidime, and cefepime. In other studies, 55.8% of Klebsiella isolates were resistant to piperacillin/tazobactam [Regarding the six isolates of n Turkey . Isolatecolistin . Finallyzobactam , 44.9% wzobactam , 69.8% wzobactam , and 20%zobactam .Enterococcus faecium isolates and the 5 Enterococcus faecalis isolates, 90% of Enterococcus faecium isolates were VRE while none of the Enterococcus faecalis isolates were VRE. Regarding Enterococcus faecium, 40% of isolates were resistant to streptomycin, 30% were resistant to gentamicin, and 11.1% were resistant to tigecycline. Meanwhile, Enterococcus faecalis species had 80% resistance to streptomycin, 50% resistance to gentamicin, and 33.3% resistance to tigecycline. In particular, none of the Enterococcus faecalis or Enterococcus faecium isolates was resistant to linezolid, in agreement with prior research [Among the 10 Staph. epidermidis, hominis and haemolyticus), no isolates were resistant to vancomycin or linezolid, while 93.3% were resistant to oxacillin, similar to the results of a previous study [Staphylococcus epidermidis, all were resistant to penicillin and cephalosporins, and 54.5% were resistant to trimethoprim-sulfamethoxazole. Regarding the four isolates of Staphylococcus aureus, 75% were resistant to oxacillin, a high percentage compared to patients in Italy (36.4%) [Among the CoNS (us study . Regardi (36.4%) . Additio (36.4%) .Candida infections in patients with hematologic malignancies, a study showed that 27.6% [Candida were resistant to voriconazole and 5% were resistant to caspofungin [Regarding antifungal resistance rates, all were sensitive to caspofungin, comparable to a similar study in which caspofungin resistance rates were 5% . All werat 27.6% were respofungin .Acinetobacter baumanni had the highest rate of MDRO (83.3%), whereas among GPB, CoNS had the highest rate (81.3%). Meanwhile, in a similar study in which MDROs were isolated in 13% of patients, the most frequently isolated MDRO was Klebsiella pneumoniae, followed by MRSA, Acinetobacter baumanni, Pseudomonas, E. coli, and VRE [51.5% of GNB and 68.4% of GPB in this study were MDRO. Among GNB, and VRE .This study is the first in Palestine to determine the microbial profile of infections in patients with hematological malignancies. However, there were some limitations to our study. First, not all data were written in the patient\u2019s medical reports such as white blood cell counts, absolute neutrophil counts, and patient temperatures at the time of culture, so we could not assess neutropenic fever and its relationship with other variables. Furthermore, some data were not collected, such as the last time a patient received a chemotherapy session. Second, our data were collected from only one center that may not be representative of other centers. Third, some patients died or left the hospital before the culture results were ready, so they did not receive any treatment other than empirical antibiotics. Finally, the study did not assess increases in antibiotic resistance year over year.Pseudomonas aeruginosa and E. coli, while coagulase-negative staphylococci and Enterococcus faecium were the most common among GPB. Our study showed alarming rates of resistance to the most widely used antibiotics, thus highlighting the need to develop local guidelines for antimicrobial use based on local resistance patterns of these organisms. This study also emphasizes the need to develop antimicrobial stewardship programs in local hospitals. Enforcing the implementation of infection control policies would help curb the spread of these MDROs and reduce the morbidity, mortality, and economic burden of these serious infections.Patients with hematologic malignancies are at risk for a variety of serious infections that cause significant morbidity and mortality. The most common bacterial isolates among GNB were"} +{"text": "Salmonella Typhi, is fatal in 12%\u201330% of patients not treated with appropriate antibiotics. In 2016, a large outbreak of extensively drug-resistant (XDR) Typhi infections began in Pakistan with cases reported globally, including the United States. In 2021, the Centers for Disease Control and Prevention (CDC) issued a health advisory on XDR infections among U.S. residents without international travel. We describe resistance of Typhi infections diagnosed in the United States to help guide treatment decisions. Typhoid fever, caused by Typhoid fever is a nationally notifiable disease. Health departments report cases to CDC through the National Typhoid and Paratyphoid Fever Surveillance system. Isolates are submitted to the National Antimicrobial Resistance Monitoring System for antimicrobial susceptibility testing (AST) using broth microdilution. AST results are categorized by Clinical and Laboratory Standards Institute criteria. We defined XDR as resistant to ceftriaxone, ampicillin, chloramphenicol, and co-trimoxazole, and nonsusceptible to ciprofloxacin.During 2008\u20132019, of 4,637 Typhi isolates, 52 (1%) were ceftriaxone resistant (axo-R); 71% were ciprofloxacin nonsusceptible, 1 azithromycin resistant (azm-R), and none meropenem resistant. XDR was first detected in 2018, in 2% of 474 isolates and increased to 7% of 535 in 2019. Of the 52 axo-R isolates, 46 were XDR, of which 45 were from travelers to Pakistan, and one from a non-traveler; 6 were not XDR, of which 4 were linked to travel to Iraq. In preliminary 2020 reports, 23 isolates were XDR; 14 were from travelers to Pakistan, 8 from non-travelers, and 1 from someone with unknown travel status. Among those with XDR infection, median age was 11 years (range 1\u201362), 54% were female, and 62% were from 6 states. Ceftriaxone-resistant Typhi infections, mostly XDR, are increasing. Clinicians should ask patients with suspected Typhi infections about travel and adjust treatment based on susceptibility results. Carbapenem, azithromycin, or both may be considered for empiric therapy of typhoid fever among travelers to Pakistan or Iraq and in uncommon instances when persons report no international travel. Ceftriaxone is an empiric therapy option for travelers to countries other than Pakistan and Iraq.All Authors: No reported disclosures"} +{"text": "P. aeruginosa to help guide empiric antibiotic coverage. The aim of our study was to determine the prevalence of P. aeruginosa as the causative organism for adult patients admitted to a large urban academic medical center with community acquired pneumonia (CAP).IDSA/ATS guidelines regarding pneumonia diagnosis and treatment changed in 2019. Guidelines recommend determining local prevalence of MRSA and A report of urine streptococcus antigen tests collected January 1st-December 31st in 2019 was generated. Six hundred charts were reviewed and two hundred subjects met inclusion criteria (figure 1). Inclusion criteria were age >18, hospital admission, and documented suspicion of pneumonia by a physician.P. aeruginosa were identified. The most commonly isolated organisms were Influenza A and pneumococcus. 66% of cases had age >65yo, 25% were from long term care facilities, 34% had structural lung disease, 20% had dementia, 15% were hospitalized in the prior 90 days and received IV antibiotics, and 30% of cases met severe CAP criteria (table 2).The average age was 70 and half of the cases were women. The causative organism was identified in 60/200 cases (table 1). No cases of Figure 1. WorkflowTable 1. Organisms IdentifiedTable 2. Risk FactorsP. aeruginosa may not be needed at our center in this cohort of older patients with clinical characteristics sometimes thought to be risk factors for P. aeruginosa.Limitations include a low prevalence of renal failure in the study population, and lack of a standardized respiratory infection evaluation. Our results suggest that empiric coverage for Wendy Szymczak, PhD, Premier, Inc (Consultant)Qiagen Gregory Weston, MD MSCR, Allergan (Grant/Research Support)"} +{"text": "The diagnosis of cholangiocarcinoma depends on several factors, including growth pattern and location. Previous studies have evaluated the diagnostic accuracy of endoscopic retrograde cholangiopancreatography based tissue sampling and endoscopic ultrasound with either fine-needle aspiration or fine-needle biopsy, reporting values < 80% for each procedure. Here, we describe the performance of both methods in a group of patients with a stricture of the biliary tract suspicious for cholangiocarcinoma. Our analysis confirms the high diagnostic accuracy of the procedures when performed together in distinguishing between a primary malignant or benign biliary stenosis. Differentiating between benign and malignant biliary stenosis (BS) is challenging, where tissue diagnosis plays a crucial role. Endoscopic retrograde cholangiopancreatography (ERCP)-based tissue sampling and endoscopic ultrasound (EUS) with fine-needle aspiration (FNA) or biopsy (FNB) are used to obtain tissue specimens from BS. The aim of this retrospective study was to evaluate the diagnostic yield of EUS-FNA/B plus ERCP with brushing or forceps biopsy in BS. All endoscopic procedures performed in patients with BS at our gastroenterology unit were reviewed. The gold standard for diagnosis was histopathology of surgical specimens or the progression of the malignancy at radiological or clinical follow-up. A total of 70 endoscopic procedures were performed in 51 patients with BS. Final endoscopic diagnosis was reached in 96% of the patients and was malignant in 61.7% and benign in 38.3% of cases. Sensitivity, specificity, and diagnostic accuracy were 73.9%, 100%, and 80%, respectively, for EUS-FNA/B; 66.7%, 100%, and 82.5% for ERCP; and 83.3%, 100%, and 87.5% for both procedures carried out in the same session. The combination of EUS and ERCP tissue sampling seems to increase diagnostic accuracy in defining the etiology of BS. Performing both procedures in a single session reduces the time required for diagnostic work-up and optimizes resources. Biliary stenosis (BS) is a frequent, common, clinical condition in patients hospitalized for jaundice, caused by a narrowing of the biliary tree due to several conditions. Malignant BS (MBS) often results from pancreatic adenocarcinoma or cholangiocarcinoma (CCA). CCA is a tumor arising from the epithelial cells lining the biliary tree and is the second most frequent primary liver malignancy worldwide. From an anatomical point of view, CCA is classified as either intrahepatic cholangiocarcinoma ; perihilar cholangiocarcinoma , also called Klatskin tumor; or distal CCA (involving the common bile duct). Based on macroscopic growth patterns, CCA can be further classified as either mass-forming (presence of a nodular lesion in the hepatic parenchyma), periductal-infiltrating , or intraductal (polypoid or papillary tumor growth toward the duct lumen) ,2,3. TheDifferentiating between MBS and BBS is crucial, as a misdiagnosis of BS leads to unnecessary surgery or delay in the treatment of malignant strictures. Despite recent improvements in imaging and endoscopic techniques, differential diagnosis of BS still represents a clinical challenge, with indeterminate BS (IBS) accounting for up to 20% of all BS . IBS is The location of BS is crucial to choosing the most accurate method to obtain tissue for differential diagnosis between MBS and BBS, as well as the optimal time sequence in which to use the diagnostic tools available. Tissue sampling may be accomplished by endoscopic retrograde cholangiopancreatography (ERCP)-based tissue collection with brushing or biopsy and endoscopic ultrasound (EUS) with fine-needle aspiration (FNA) or fine-needle biopsy (FNB). When used in the same or sequential sessions, these endoscopic procedures are used to study the site and extent of the stenosis in two different ways, reveal the presence of liver or pancreatic nodules suspicious for malignancy, and obtain tissue for histopathological diagnosis. Following tissue sampling, biliary drainage can be performed by positioning a plastic or metallic stent during ERCP or during EUS when ERCP is not feasible or in patients with hilar obstruction . Currently, the overall diagnostic yield of ERCP-based histopathological diagnosis is estimated to reach a maximum of 75% , whereasThe aim of our study was to evaluate the diagnostic yield of EUS-FNA/B and ERCP-based tissue sampling in primary strictures due to cholangiocarcinoma involving the proximal or distal biliary tract.All patients referred to our gastroenterology unit with jaundice due to BS suspicious for CCA and who underwent ERCP or EUS from November 2015 to September 2021 were considered eligible for the study. The suspicion of BS was based on clinical history and investigations, including abdominal computed tomography (CT) and magnetic resonance imaging (MRI). The exclusion criteria were previous evidence of pancreatic head mass, a clearly protruding-type ampullary cancer, or the lack of adequate follow-up. The diagnostic work-up for each patient was defined by a multidisciplinary team, including gastroenterologists, oncologists, radiologists, surgeons, and pathologists.TM, Boston Scientific) or EUS-FNB . The needle was moved back and forth at least 10 times without a syringe. At least three passes were performed for each patient. In the last five years of the study period, we used only FNB to collect tissue samples during EUS. The tissue collected during ERCP and EUS was immediately put in formalin, and the adequacy of the material was evaluated in all patients by gross inspection by the operator, as rapid on-site evaluation (ROSE) was not available. All brushing samples were sent for cytological examination in special tubes with fixative liquid. In the case of procedures carried out on the same day, EUS with tissue sampling always preceded ERCP. Cytological and histological findings were defined by the pathologist as either negative, positive for malignancy, or nonconclusive due to inadequacy of the tissue sample. In the case of strong suspicion of malignancy and nonconclusive histopathological findings, the EUS or ERCP procedure was repeated. The gold standard for diagnosis was the histopathology of surgical specimens or clinical outcomes . Patients with no neoplastic findings from the endoscopic procedures were followed for at least one year. Any complications during or following the procedures were recorded. All ERCP examinations were performed using a side-viewing scope . Cholangiography and endoscopic sphincterotomy were carried out after cannulation and before tissue sampling. Endoscopic transpapillary tissue sampling was performed with forceps , and at least three samples were collected. Brushing cytology was achieved with at least 10 passes of a brush on guidewire in the bile duct. Forceps biopsy and brushing were performed after biliary duct dilatation, if indicated, in the last year of the study period. After tissue sampling, endoscopic biliary stenting was carried out. EUS was performed with a linear array echoendoscope equipped with a 7.5 MHz transducer . Tissue sampling was carried out using EUS-FNA with a 22-gauge needle were calculated based on the final gold-standard diagnosis. Parameters of diagnostic yield were calculated for each endoscopic procedure and for the two procedures performed in combination, both at first attempt and after repetition. BS site and repetition of the same procedure were considered factors influencing the performance of EUS-FNA/B and ERCP tissue sampling. Statistical analysis was calculated using MedCalc software .During the study period, 51 patients with BS underwent endoscopic evaluation with EUS or ERCP. We excluded 4 patients because of insufficient follow-up; the analysis of the results therefore refers to 47 patients (28 men (59.6%), median age 73 years (range 49\u201394)). The characteristics of the patients and procedures are summarized in A total of 70 endoscopic procedures with tissue sampling for histological and cytological analysis were carried out: ERCP with brushing/biopsy in 40 patients and EUS-FNA/B in 30 patients (EUS-FNA in 4 patients and FNB in 26 patients). Twenty-four patients underwent ERCP with brushing/biopsy only, fourteen patients underwent EUS-FNA/B only, and sixteen patients underwent both ERCP with brushing/biopsy and EUS-FNA/B performed in the same session. Six patients with nonconclusive histological and cytological diagnoses repeated the endoscopic procedure: three patients underwent two ERCPs, one patient three ERCPs, and two patients two EUS-FNBs. One case of mild post-ERCP bleeding and one case of mild post-ERCP pancreatitis were reported. No adverse events were reported after EUS-FNA/B.Malignancy was finally diagnosed in 29 patients (61.7%), while the remaining 18 patients (38.3%) had BBS. Of the 29 patients with malignancy, 27 (93.1%) were diagnosed by ERCP- or EUS-based tissue sampling, while the remaining 2 patients were diagnosed by surgery. Of the two patients with surgical diagnoses, one had previously undergone both ERCP with brushing cytology and transpapillary biopsies and EUS-FNB, while the other had only undergone EUS-FNB. Both of these patients underwent a Whipple procedure after the first nonconclusive histopathological result without repetition of tissue sampling because of a strong clinical and radiological suspicion of MBS, deemed operable at clinical and radiological staging. The histology of surgical specimens revealed an infiltrating distal CCA. A total of 13 patients underwent surgery . No surgery was performed for benign disease based on the histology of surgical specimens. After a negative histological and cytological report, a final diagnosis of BBS was confirmed with clinical and radiological follow-up after a minimum of 6 months .The diagnostic yield of ERCP with brushing/biopsy and EUS-FNA/B of BS is shown in Single ERCP with brushing/biopsy\u2014On the first attempt, the sensitivity, specificity, and diagnostic accuracy were 63.2% (95% CI: 38.4\u201383.7%), 100% (95% CI: 79.4\u2013100%), and 80% (95% CI: 63.1\u201391.6%), respectively. Due to nonconclusive histological findings, ERCP was repeated for four patients repeated (one patient underwent three ERCPs), which revealed MBS in two patients and BBS in the remaining two. Considering the repeated procedures, the overall sensitivity, specificity, and diagnostic accuracy of ERCP with brushing/biopsy were 66.7% (95% CI: 43.0\u201385.4%), 100% (95% CI: 82.4\u2013100%), and 82.5% (95% CI: 67.2\u201392.7%), respectively.Single EUS-FNA/B\u2014On the first attempt, the sensitivity, specificity, and diagnostic accuracy were 72.7% (95% CI: 49.8\u201389.3%), 100% (95% CI: 54.1\u2013100%), and 78.6% (95% CI: 59.5\u201391.7%), respectively. Due to nonconclusive histological findings, the procedure was repeated for two patients repeated, which revealed BBS in one patient and MBS in the other. Notably, in the latter patient, we performed an EUS-FNB of perihilar adenopathy after a previous ERCP-based brushing and EUS-FNB of hilar stricture, both of which failed to diagnose malignancy. Considering the repeated procedures, the overall sensitivity, specificity, and diagnostic accuracy of EUS-FNA/FB were 73.9% (95% CI: 51.6\u201389.7%), 100% (95% CI: 59.1\u2013100%), and 80% (95% CI: 61.4\u201392.3%), respectively. In six patients, we performed EUS-FNB of the primary (biliary tree) and potentially secondary (lymph nodes) sites of the disease, which was positive for malignancy in only one patient. Combined ERCP- and EUS-FNA/B-based tissue sampling\u2014Sixteen patients underwent both EUS and ERCP sampling in the same session . The comDiagnostic yield of ERCP with brushing or biopsy and EUS-FNA or EUS-FNB according to location of BS is shown in Distal BS was observed in 31 patients, all of whom underwent ERCP with brushing or biopsy except 1, who was operated on a few days after EUS-FNB with a definite histological diagnosis of malignancy, without performing ERCP. The sensitivity, specificity, and diagnostic accuracy of ERCP in these cases of distal BS were 69.2% (95% CI: 38.6\u201390.1%), 100% (95% CI: 73.5\u2013100%), and 84% (95% CI: 63.9\u201395.5%), rising to 73.3% (95% CI: 44.9\u201392.2%), 100% (95% CI: 78.2\u2013100%), and 86.7% (95% CI: 69.3\u201396.2%), respectively, after repetition of the procedure in the case of nonconclusive findings at first attempt. Fourteen of the thirty-one patients with distal BS underwent EUS-FNA/B, which showed a sensitivity, specificity, and diagnostic accuracy of 44.4% (95% CI: 13.7\u201378.8%), 100% (95% CI: 47.8\u2013100%), and 64.3% (95% CI: 38.4\u201388.2%), respectively.Proximal BS was observed in 16 patients, 10 of whom underwent ERCP with brushing/biopsy and 12 of whom underwent EUS-FNA/B. The sensitivity, specificity, and diagnostic accuracy were 50% (95% CI: 11.8\u201388.2%), 100% (95% CI: 39.8\u2013100%), and 70% (95% CI: 34.7\u201393.3%) for ERCP and 90.1% (95% CI: 58.7\u201399.8%), 100% (95% CI: 2.5\u2013100%), and 91.7% (95% CI: 63.9\u201399.8%) for EUS-FNA/B, respectively. CCA is the second most common primary liver tumor, exhibiting poor prognosis and resistance to chemotherapeutic drugs, and is responsible for the majority of BS. pCCA and iCCA represent >90% of all CCA ,2,3. CT Tissue sampling histology is necessary to obtain a definitive diagnosis of primary liver cancer and to exclude metastatic localization of other tumors. In the case of the radiological diagnosis of CCA and evidence of surgical resectability, when extrahepatic secondary localization of the disease has been excluded, the patient may undergo surgical resection without a prior histological diagnosis in selected cases. In the case of unresectable neoplasia, tissue diagnosis is mandatory for choosing the most appropriate treatment. ERCP-based tissue sampling and EUS-FNA/B are the most common methods used to collect tissue for a differential diagnosis of BS, whether associated with liver mass or not. EUS-FNA/B is the method of choice with distal biliary stenosis due to pancreatic mass , which iThe diagnostic power of these endoscopic procedures for the diagnosis of malignancy is influenced by the expertise of the operator, the site of the lesion, and the growth pattern of the disease; a wide range of sensitivity values are reported as being 21\u201372% for ERCP brushing ,16,17,18In our study, we excluded patients with BS secondary to pancreatic cancer in order to analyze data relating to a more homogeneous population. Overall, the sensitivity of EUS-FNA/B was slightly higher than that of ERCP-based sampling, considering both brushing and forceps biopsy tissue acquisition . A key finding of this study is that repeating EUS or ERCP-based tissue sampling increases the diagnostic power of both procedures, reducing the risk of referring a non-neoplastic patient to the surgeon for biliary resection. This result is in line with our previous experience and withThe location and growth patterns of CCA may affect the performance of endoscopic tissue sampling procedures. In a subanalysis focusing on the location of the disease, we found that ERCP-based tissue sampling had a higher diagnostic yield than EUS-FNA/B in distal BS, in contrast with previous studies ,12,28. TOur study confirmed that the combination of EUS and ERCP improves diagnostic performance in BS. In a subgroup of 16 patients undergoing both endoscopic procedures, we observed a rise in the diagnostic accuracy of combined procedures of up to 90%. This finding is in line with those of a previous study reportinThe diagnostic and therapeutic complexity of BS due to CCA requires a multidisciplinary approach in tertiary centers equipped with all the diagnostic tools currently available. Over the years, technological advancements have made it possible to obtain more adequate tissue sampling for diagnostic purposes. We hope that in the near future, the development of other approaches, such as the use of biohumoral markers, may facilitate early diagnosis and provide possible predictors of response to therapy.Our study has several limitations. First, it is a retrospective investigation, even if the data were prospectively recorded. The number of patients is relatively small, limiting a statistically significant comparison between the two procedures in terms of diagnostic accuracy. Only 16 patients underwent combined EUS and ERCP-based tissue sampling, as we only started to routinely perform both procedures in the last two years of the study period. In addition, we began using EUS-FNB instead of EUS-FNA in 2017. We cannot exclude that this change in the diagnostic work-up may have influenced the performance of the endoscopic procedures analyzed here.A strength of our study is the selection of patients. We evaluated a homogeneous group of patients with jaundice and evidence of BS, excluding cases of BS due to pancreatic cancer or metastatic disease. To the best of our knowledge, very few studies have evaluated the role of ERCP and EUS sampling in patients with a disease involving exclusively the biliary tract. Our specificity was higher with no false positive samples. However, the pathologist was not blinded because all patients were discussed in a multidisciplinary team meeting before the endoscopic procedure. Nevertheless, our study provides useful insights supporting previous evidence regarding the advantage of combining the two endoscopic procedures in the same session to obtain a more rapid, accurate, and definitive histopathological diagnosis. The diagnostic accuracy of EUS-FNA and ERCP tissue sampling in BS is influenced by the growth patterns and the location of the disease, as well as by the presence of liver mass. The combination of EUS-FNB and ERCP-based tissue sampling increases the diagnostic power of each procedure when performed alone. A multidisciplinary approach plays a crucial role in defining neoplastic biliary disease and in tailoring the most appropriate treatment."} +{"text": "A faulty prosthesis can cause damage more than relief. Poor people who cannot afford specialty treatment prefer to go to unregistered dental practitioners who are less expensive. Therefore, it is of interest to record the presence and type of old faultyprosthesis and its effect on surrounding structures. In this study 983 case sheets were reviewed from the record management system at the Saveetha Dental College, India using keyword search. Results show that 33% of faulty prosthesis leads to periodontallycompromised abutments, 26% to decay of abutment tooth, 20% to gingival inflammation, 13% to denture stomatitis, 6.6% to non-vital abutment tooth. Faulty prosthesis damages abutment tooth and the surrounding structure of oral mucosa. Thus, damage to theperiodontium in fixed prosthesis is common and prevalent. Hence, faulty dental prosthesis construction should be discouraged through awareness programme. A dental prosthesis is a protheis used to restore residual ridge defects, missing teeth, missing structure of teeth and associated structures around it . A fixedThe retrospective analysis was an institutional study from the already existing patients data. Two examiners were involved in this study. The data was collected from the RDBMS database at the Saveetha Dental College, India. The database stores records ofpatients with their intra-oral and extra-oral photographs (taken with consent of the patients), their demographic details, personal history, medical history and the Dental findings. The data was collected for nine months from June 2019 to March 2020 from theinternal database. We used keywords such as faulty prosthesis, damaged prosthesis, ligated prosthesis, faulty acrylic, ligated acrylic, removable prosthesis faulty to retrieve the required data. The search identified 34 cases and further refinement selected 12case sheets with the exact match for the analysis. Collected data was verified with photographs obtained from the digital documentation. The inclusion criteria for search included faulty prosthesis and damaged prosthesis. Data was imported to the SPSS 23.0software for statistical analysis. Independent variables include age, gender, and faulty prosthesis. Both descriptive and inferential statistics were done. Frequency distribution for age and gender was completed. Chi square test was completed to find theassociation at a significance level of 0.05.The collected data was imported in SPSS software version 23 for chi-square test. Data analysis shows that 26.6% male and 6.6% female patients had periodontally compromised abutments, 20% male and 6.6% female patients had decay in their abutments, 6.6% maleand 13.3% female patients had gingival inflammation in their abutments. Data also shows that 6.6% male had non-vital abutments. However, 6.6% male and 6.6% female patients had denture stomatitis. Nevertheless, this was not statistically significant (p>0.05).Thus, there is no significant association between gender and condition of abutment teeth . AssociaData shows that FPDs were the most faulty prosthesis followed by TPDs and CDs. Faulty prosthesis causes damage to the abutment tooth and the surrounding structure like the periodontium or oral mucosa. Thus, ill oral health caused by faulty prosthesis andquackery could be controlled by awareness.All the authors contributed equally for the research."} +{"text": "In the United States, racial and ethnic minorities are disproportionately affected by COVID-19, with persistent social and structural factors contributing to these disparities. At the intersection of race/ethnicity and gender, women of color may be disadvantaged in terms of COVID-19 outcomes due to their role as essential workers, their higher prevalence of pre-existing conditions, their increased stress and anxiety from the loss of wages and caregiving, and domestic violence.The purpose of this study is to examine racial and ethnic differences in the prevalence of COVID-19 outcomes, stressors, fear, and prevention behaviors among adult women residing in the United States.Between May and June 2020, women were recruited into the Capturing Women\u2019s Experiences in Outbreak and Pandemic Environments (COPE) Study, a web-based cross-sectional study, using advertisements on Facebook; 491 eligible women completed a self-administered internet-based cross-sectional survey. Descriptive statistics were used to examine racial and ethnic differences on COVID-19 outcomes, stressors, fear, and prevention behaviors.Among our sample of women, 16% (73/470) reported COVID-19 symptoms, 22% (18/82) were concerned about possible exposure from the people they knew who tested positive for COVID-19, and 51.4% (227/442) knew where to get tested; yet, only 5.8% (27/469) had been tested. Racial/ethnic differences were observed, with racial/ethnic minority women being less likely to know where to get tested. Significant differences in race/ethnicity were observed for select stressors and prevention behaviors . Although no racial/ethnic differences emerged from the Fear of COVID-19 Scale, significant racial/ethnic differences were observed for some of the individual scale items .The low prevalence of COVID-19 testing and knowledge of where to get tested indicate a critical need to expand testing for women in the United States, particularly among racial/ethnic minority women. Although the overall prevalence of engagement in prevention behaviors was high, targeted education and promotion of prevention activities are warranted in communities of color, particularly with consideration for stressors and adverse mental health. The COVID-19 pandemic has shed light on racial and ethnic disparities in the United States . Among 4Contributing factors to racial and ethnic disparities in COVID-19 outcomes include social and structural vulnerabilities and pre-existing health conditions, affecting socially marginalized populations ,7. ResidThe continuation of the COVID-19 pandemic has led the US government to recommend prevention behaviors, including staying at home except for essential activities, physical distancing from nonhousehold members, wearing a face mask in public, avoiding nonhousehold groups, and frequent handwashing . CompliaGiven the lack of published findings on COVID-19 outcomes by race/ethnicity among women in the United States, our paper describes the prevalence and racial/ethnic differences among COVID-19 outcomes, stressors, fear, and prevention behaviors among an ethnically diverse sample of US adult women.Between May and June 2020, we conducted the Capturing Women\u2019s Experiences in Outbreak and Pandemic Environments (COPE) Study, a web-based cross-sectional study of COVID-19 outcomes, testing, and prevention behaviors among adult women in the United States. Our study included participants who were 18 years or older, cisgender or transgender female, living in the United States, and able to understand English. We excluded participants who did not reside within the United States, were younger than 18 years, were male, or did not understand English.Recruitment occurred through Facebook advertisements, designed to recruit adult women currently residing in the United States. We aimed to collect at least 400 survey responses. Interested women accessed a digital consent form within the REDCap (Research Electronic Data Capture) survey platform. The consent form included the purpose of the study and participant risk, burden, rights, and compensation. Participants who provided documented consent were directed to a screening survey. Screening questions included age, gender, and state of residence. Of 682 users who clicked on an advertisement, 633 (92.8%) provided informed consent and answered screener questions. Among the 633 participants, 7 participants were not eligible for the study. Eligible participants (n=626) were directed to the survey, which took 15 to 20 minutes to complete. Of 626 eligible participants, 491 (78% response rate) completed the full web-based survey. Participants received a US $20 Amazon e-gift card via email. The COPE Study procedures were approved by the University of California, San Diego Human Research Protections Program Institutional Review Board.Race/ethnicity were self-reported by using the following categories: White ; Asian, Native Hawaiian, or other Pacific Islander (API); Black ; Hispanic, Latina, or Spanish origin ; AIAN ; and multiracial or some other race, ethnicity, or origin. \u201cOther race, ethnicity, or origin\u201d included 7 women who self-identified as Middle Eastern or North African. Other demographics included age, education, employment status, sexual orientation, relationship status, parenthood, household composition and type of occupants, type of residential community , current living situation, and household income.We modified COVID-19 measures developed by the World Health Organization (WHO) for rapid behavioral studies about COVID-19 . We asseWe assessed nine COVID-19 stressors as outlined by the WHO . ExampleCOVID-19 prevention behaviors examined were: washing hands, avoiding touching face, using disinfectants (including hand sanitizer), staying home except for essential activities, covering mouth when coughing, physical distancing from nonhousehold members, physical distancing if sick, isolating oneself if sick, public face mask use, public glove use, avoiding crowds, and not leaving home . ResponsP value was used. Individual pairwise comparisons by race/ethnicity were conducted when the Kruskal-Wallis test or chi-square test had a P<.05. The Dwass-Steel-Critchlow-Fligner test was used when the Kruskal-Wallis test was significant (P<.05), and individual chi-square tests between each of the racial/ethnic groups were examined when the overall chi-square was significant (P<.05). To account for potential confounding, COVID-19\u2013related outcomes, stressors, and prevention behaviors that were significantly associated in bivariate analyses were included in multivariable binary logistic regressions. Each regression was adjusted for age, education, income, and type of residential community , with race as the independent variable and the outcome, stressor, or prevention behavior as the dependent variables. All analyses were performed using SAS, version 9.4 (SAS Institute).Excluding participants without reported race/ethnicity, the sample was 473 women. We computed descriptive statistics of all variables overall and by race/ethnicity. We report medians and IQRs for nonnormally distributed continuous variables and frequencies and proportions for categorical variables. For race/ethnicity comparisons, we used Kruskal-Wallis tests and chi-square tests. If subgroups had expected values less than 5, Fisher exact test or a Monte Carlo estimate for Fisher exact Of 473 women, 51% (n=241) were White, 13.5% (n=64) API, 12.7% (n=60) Black or African American, 10.1% (n=48) Hispanic or Latinx, 5.7% (n=27) AIAN, and 7% (n=33) multiracial or \u201cother\u201d . The medApproximately 46% (211/461) of women lived alone. Of 250 living with others, 55.2% (n=138) and 53.2% (n=133) lived with their partner and family members, respectively. The median number of children in the household was 2. Almost 44% (193/447) had a household income of US $50,000 or more, with White individuals more likely than all racial/ethnic groups, except Latinx. Almost 50% (212/466) of women lived in an urban environment and 17.6% (82/466) in a rural environment.P<.001, P=.01, and P=.01, respectively), and Black women more likely than API and AIAN women . A total of 2% (8/469) of women were diagnosed with COVID-19, of which 50% (4/8) were hospitalized; 22% (18/82) of women were concerned that they were exposed to COVID-19 by the people they know. No significant differences by race/ethnicity were found for either.Approximately 16% (73/470) of women reported COVID-19 symptoms; the highest prevalence was among White and multiracial or other women, and the lowest prevalence was among API women ; 67.1% (55/82) identified a diagnosed friend, and 42.7% (35/82) identified diagnosed family. Of the 82 women, 42.7% (n=35) knew someone hospitalized, with Black women more likely than White women (P<.001); family members and friends were the most frequently reported relationships. Black women were more likely than White women to report a family member hospitalized (P=.01). Of the 82 women, 22% (n=18) knew someone who had died of COVID-19; most were a friend or family member .A total of 18% (82/469) of women knew someone diagnosed with COVID-19, with White and Black women more likely than API women ; API women were more likely than Latinx women (P=.046) to not have enough food. Approximately 20% (91/473) did not have enough money for rent; White women were less likely to not have enough money for rent than API, Black, Latinx, and AIAN women . Of 20.9% (99/473) who reported homeschooling children, White women were more likely than API and AIAN women , and Black and Latinx women were more likely than AIAN women . Of 28.1% (133/473) unable to have a doctor or telemedicine appointment, White women were more likely than API and AIAN women . For the remaining stressors, 36.6% (173/473) of women reported loss of income, 15.4% (73/473) were essential employees, 4.7% (22/473) were unable to obtain medication, and 9.9% (47/473) were caregivers for sick family without or with COVID-19.Racial/ethnic differences emerged for four COVID-19 stressors . A totalP=.01 and P=.02, respectively). White women reported more agreement with becoming nervous or anxious when watching media about COVID-19 compared to API women (P=.001). Latinx women agreed with experiencing clammy hands when thinking about COVID-19 more than White and multiracial or other women (P=.02 for both); AIAN women agreed more than White, Black, and multiracial or other women . AIAN women agreed more with sleep loss due to worrying about getting COVID-19 compared to White, Black, and multiracial or other women ; API women agreed more than Black women (P=.02). AIAN women also had more agreement with experiencing their heart racing when thinking about getting COVID-19 compared to Black women (P=.04).Although no racial/ethnic differences emerged for the Fear of COVID-19 Scale, significant differences were observed for individual items. Higher agreement with the statement \u201cI am very afraid of coronavirus\u201d was found among White women compared to API and multiracial or other women . Of 60.0% (284/473) who self-isolated if sick, API women were more likely than White, Black, and multiracial or other women . Of 40.2% (190/473) who publicly used gloves, API, Black, and AIAN women were more likely than White women ; API women were more likely to publicly use gloves than Latinx and multiracial or other women (P<.001 for both); AIAN women were more likely to publicly use gloves than Black, Latinx, and multiracial or other women . Of 43.6% (206/473) who did not leave home at all, White women were less likely than API, AIAN, and multiracial or other women ; API women were more likely to not leave home at all than Black and Latinx women ; AIAN women were more likely to not leave home at all than Latinx women (P=.02). Approximately 80% (374/473) of women avoided face touching, 87.1% (412/473) used disinfectants, 88.6% (419/473) stayed home except for essential activities, 82.2% (389/473) covered mouths when coughing, 86.5% (409/473) physically distanced from nonhousehold members, 59.8% (283/473) physically distanced from others if sick, 79.7% (377/473) publicly used a face mask, and 81.8% (387/473) avoided crowds.Significant differences in race/ethnicity were observed for four COVID-19 prevention behaviors . Of 95.6To account for potential confounding, COVID-19\u2013related outcomes, stressors, and prevention behaviors that were significantly associated with race or ethnicity in bivariate analyses were identified for inclusion in multivariable binary logistic regressions. Each regression was adjusted for age, education, income, and type of residential community . Results of these regressions are available in To our knowledge, this is the first study to describe COVID-19 outcomes, stressors, fear, and prevention behaviors among a sample of US women and to examine racial/ethnic differences. Our data showed that 1 in 6 women had COVID-19 symptoms. Troublingly, although 51.4% (227/442) of women knew where to get tested for COVID-19 and 22.0% (18/82) were concerned about possible exposure to COVID-19, only 5.8% (27/469) had been tested.White women were the most likely to know where to be tested for COVID-19, despite experiencing a lower burden of COVID-19 among family and friends compared to Black women. This may be due to persistent medical mistrust due to legacies of abuse, mistreatment ,23, and A total of 18% (82/469) of women knew someone close to them diagnosed with COVID-19\u2014often family or friends\u2014with White and Black women being more likely than API women. Black women were more likely than White women to know someone hospitalized for COVID-19 and report them as family. This demonstrates a high burden of COVID-19 morbidity and mortality among Black families and their social circles; further, this implies a potential burden of adverse mental health associated with loss and trauma.Racial/ethnic differences were observed for select stressors. White women were less likely than all others to lack food and money for rent, possibly because White women were more likely to have a household income over US $50,000, ensuring the ability to sustain food and housing expenses. White women were also more likely than API and AIAN women to be unable to go to the doctor or have a telemedicine appointment and report homeschooling children. Collectively, plausible explanations are that White women had competing responsibilities due to living with other family members and having a higher median number of household residents, which prevented in-person appointments with their doctor. Additionally, White women may have had privacy concerns with engaging in a phone or video telemedicine visit with their provider due to more family members or household residents being present.Although significant differences by race/ethnicity were not identified by summed scores for the Fear of COVID-19 Scale, there were significant differences in many of the individual items, showing dimensionality within experiences of fear of COVID-19. White women consistently agreed with statements regarding psychological experiences of fear (being \u201cvery afraid\u201d or \u201cnervous or anxious\u201d) relating to COVID-19, while API, Latinx, and AIAN women consistently endorsed agreement with physical manifestations of fear . Black women did not fall into these patterns, endorsing most agreement with being very afraid and experiencing anxiety relating to media about COVID-19. This may reflect differential conceptualization of fear and stress, including antidisclosure socialization and stigma around mental health -27 or inOverall, we found high prevalence of implementation of CDC-recommended prevention behaviors. Prevalence of staying home except for essential activities was 88.6% (419/473) compared to a rate of 77.3% among US adults surveyed in May 2020 . LikewisSelf-isolation at home if sick was more likely among API women, possibly due to customary traditions of preventing illness. Handwashing with soap was more likely among White and API women than AIAN women. This may be due to White and API women\u2019s increased access to education on preventing COVID-19, primarily disseminated through television and the internet. Of further importance is the possibility of performative practice of prevention behaviors among API women, in response to COVID-19\u2013related xenophobia; individuals of Asian descent have been the targets of hate speech and crime based on the origination of COVID-19 in China . Among AAPI women were more likely than Black and Latinx women to not leave home for any activities, possibly due to API increased partner cohabitation, allowing them to remain indoors and rely on a partner for essential activities. Consistent with existing data, Black and Latinx populations are overrepresented in essential service industries, limiting the ability to shelter at home ,12. BecaSupplemental analyses to assess confounding confirmed statistically significant variation between racial/ethnic groups in binary logistic regressions after adjustment for age, education, income, and type of residential community, in comparison to White participants. All adjusted odds ratios were in the expected directions and consistent with bivariate findings. However, the variation in relationship between race/ethnicity and COVID-19\u2013related outcomes, stressors, and prevention behaviors indicate a need for further research to assess the nuanced experiences of women of all racial and ethnic identities, which was beyond the scope of this analysis, to ensure culturally responsive and appropriate public health programming.The primary limitation of our research was the use of nonprobability sampling methods with recruitment through online social media, resulting in a lack of generalizability of our study findings. Thus, our sample is not representative of adult women in all US states. Our sample was younger to middle-aged, primarily resided in urban environments, and did not consist of racial/ethnic groups and other demographics such as age, education, and income that were proportionate to each US state population\u2019s demographics. Specifically, 17.6% (82/466) of our sample resided in a rural environment, slightly underrepresenting the 19.3% of the US population in rural areas . AlthougLimitations notwithstanding, our data highlight racial/ethnic differences in COVID-19\u2013related outcomes among adult US women. Our ability to recruit an ethnically diverse sample of women that comprised 41 US states and Washington, DC using online recruitment methods within a short time frame demonstrates the willingness of women to share their experiences on COVID-19. Future studies are needed that use probability sampling methods and longitudinal cohort study designs to examine trends over time in racial/ethnic disparities of COVID-19 outcomes and elucidate underlying factors fueling these disparities among a representative sample of adult US women.The lower knowledge of testing availability, actualized testing, and prevention behaviors among Black, Latinx, and AIAN women compared to their White and API counterparts will serve to exacerbate the high rates of COVID-19 mortality already demonstrated among these populations. Meanwhile, stressors, physical manifestations of fear, and adverse mental health associated with loss of family and friends to COVID-19 may compound existing toxic stress, culminating in increasingly negative chronic health outcomes. It is vital that public health interventions for COVID-19 focus on these communities, ensuring testing, health care, and support services\u2014including mental health, economic, and social services\u2014are accessible and acceptable, rather than allowing for disparities to persist and worsen."} +{"text": "This study is a systematic review and meta-analysis of international literature on the achievements of various performance indicators for colorectal cancer screening programs. We systematically summarized performance indicators of organized colorectal cancer screening that used fecal immunochemical test as a primary screening modality, and colonoscopy as a subsequent confirmatory test, from 93 studies involving nearly 90 million people-times, and reported their pooled achievements based on random-effects models. We also performed meta-regression and subgroup analyses to explore the heterogeneity. Our findings could help to identify the areas that could be improved and finally optimize the organized colorectal cancer screening programs.(1) Background: To summarize the achievements of the performance indicators of colorectal cancer (CRC) screening programs that used the fecal immunochemical test (FIT) as a primary screening modality and colonoscopy as a subsequent confirmatory test. (2) Methods: PubMed, Ovid MEDLINE, Embase, and Cochrane were searched from inception to September 2020. We included original articles published in English, and performed hand searching for relevant national reports. We generated pooled achievement estimates of the performance indicators by \u201cmetaprop\u201d (R software 3.6.3). Meta-regression analyses and subgroup analyses were also conducted. (3) Results: We included 93 studies involving nearly 90 million people-times. The participation rate ranged from 6.80% to 95.98%, which was associated with study type, continents, FIT number, age, and round. The pooled FIT invalid rate and positivity rate were 1.08% and 7.28%, respectively. The pooled estimates of FIT detection were 2.26% for adenoma, 1.26% for advanced adenoma, and 0.28% for CRC. In addition, only seven studies reported that their colonoscopy compliance rate reached 90% among 69 studies. The colonoscopy completion rate (21/40 studies > 95%) and the complication rate (18/27 studies < 0.5%) were acceptable. (4) Conclusions: Our findings could help to identify the areas that could be improved and finally optimize the CRC screening programs. Worldwide, colorectal cancer (CRC) is the third most common cancer, and it was responsible for 10.2% of all new cancer cases and 9.4% of cancer-related deaths in 2020 , 28% [4]A large body of systematic reviews have summarized the performance indicators of different screening tools in CRC screening and diagnosis. They mainly described the comparison between gFOBT and FIT , factorsThis study is a systematic review and meta-analysis that was conducted in compliance with the Meta-analysis of Observational Studies in Epidemiology (MOOSE) and was registered on PROSPERO International prospective register of systematic reviews (CRD42020142617).We searched PubMed, Ovid MEDLINE, Embase, and Cochrane for articles published in English, from their inception to 8 September 2020. The keywords and MeSH terms used are shown in Population-based CRC screening programs that used FIT as a primary screening test and colonoscopy as a confirmatory test were eligible in this review. The exclusion criteria included the following: (1) randomized controlled trial and cost-effectiveness analysis; (2) studies on opportunistic screening, screening restricted in clinics, and screening targeting at special groups (people who were disabled or suffered from chronic diseases); (3) programs that included the use of other screening tools ; (4) studies that examined outcomes other than performance indicators, such as CRC incidence or mortality; and (5) literature reviews, abstracts, or articles in other languages. If there were identical populations or overlapped study periods in different studies, we included the articles with the largest sample size.The literature search was conducted by two independent qualified reviewers (J.L. and Z.X.) based on screening titles and abstracts. Disagreements were resolved by a third reviewer (H.D.). The full texts were reviewed and appraised if the title and abstract were identified as eligible for inclusion. We extracted data including first author, year of publication, study location, project period, number of registered subjects, number of screening participants, age range, screening round, screening tools, the number of FIT used, the cut-off value of FIT, the number of subjects who submitted valid and invalid FIT, the number of subjects who were tested positive FIT, the number of subjects who attended colonoscopy appointment, quality of bowel preparation, number of individuals who completed colonoscopy procedure, complications due to colonoscopy, the number of subjects identified as having adenoma (including non-advanced adenoma and advanced adenoma), advanced adenoma, and CRC. Discrepancies in data extraction were resolved by group discussion.We evaluated the quality of included articles by the Appraisal of cross-sectional studies (AXIS) . There a2 and I2 of 25%, 50%, and 75%, which indicated low, medium, and high heterogeneity, respectively [p value < 0.05 was considered statistically significant. Meta-regression random-effects models were performed to investigate the heterogeneity of the main pooled estimates. Subgroup analyses were also conducted in terms of the type (article and report), sample size , continents , the number of FIT used (one and two), age groups , the FIT cut-off value , and screening round . All statistical analyses were performed by R software (version 3.6.3) and the function \u201cmetaprop\u201d was adopted to conduct the meta-analysis of rates to generate pooled estimates.We included the participation rate, the FIT invalid rate, the FIT positivity rate, the adenoma/advanced adenoma/CRC detection rate of FIT, PPV for adenoma/advanced adenoma/CRC, the colonoscopy compliance rate, the adequate quality rate of bowel preparation, the colonoscopy completion rate, and the colonoscopy complication rate the as the outcome variables. Each performance indicator was defined according to what was specified in the guidelines ,21. Meanectively . Egger\u2019sA total of 12,253 citations were identified from the literature search. A total of 7721 citations remained after the removal of duplicates, of which 7380 citations were further excluded in the first stage of screening based on titles or abstracts. In the second stage of screening, 341 full-text articles were assessed for eligibility and 22 reports were collected from national websites by hand searching. After the comprehensive review, a total of 93 studies from 63 articles and 22 reports were included in this meta-analysis .The characteristics of all eligible studies are presented in 2 = 100%; p < 0.05). In the univariate subgroup analyses, articles reported higher participation rate than reports (p < 0.001). The studies with a larger sample size reported the lower participation rates . In multivariate meta-regression, the study type, continents, FIT number, age, and round were associated with the participation rate, which could explain 86.98% of heterogeneity between studies . Meanwhile, the positivity rate showed a decreasing trend with an increasing cutoff value, which was more pronounced in screening with one FIT , which showed significant publication bias. Seventy-four studies presented a FIT positivity rate that ranged from 1.09% to 30.01%. The pooled FIT positivity rate was 7.28% (95% CI: 6.81\u20137.76%), while the Ias 99.9% . The conas 99.9% . The pos one FIT .The pooled detection rates for adenoma, advanced adenomas and CRC were 2.26% (95%CI: 2.00% to 2.53%), 1.26% (95% CI: 1.10% to 1.44%), and 0.28% (95% CI: 0.25\u20130.31%), respectively . The adeThe pooled PPV for adenoma, advanced adenoma, and CRC was 44.79% (95% CI: 41.8\u201347.79%), 27.13% (95% CI: 24.39\u201329.97%), and 5.48% (95% CI: 4.96\u20136.02%), respectively . After pA total of 69 studies were included to estimate the colonoscopy compliance rate, involving 1.3 million participants. The wide variability of the compliance rate was 31.42\u201396.01%, and only seven studies reported that the compliance rate was higher than 90%. Fourteen studies described the quality of bowel preparation, four of which adopted the Boston Bowel Preparation Scale, and two studies used the original/modified Ottawa Scale. Only one study (65.20%) did not reach 85%. Among 40 studies that involved a completion rate, half of studies achieved 95% and three-quarter studies reached 90%. A total of 27 studies reported the complication rate (0.00\u20131.23%), 18 of which were less than 0.5% .To the best of our knowledge, this is the first large-scale literature review that summarized quantitative data on the performance of organized CRC screening programs worldwide. Quality indicators of FIT and colonoscopy were based on definitions from guidelines, which confirm the comparability of all indicators. Meanwhile, all FIT-related indicators were pooled and we performed a meta-regression using the random-effects model to interpret the heterogeneity. Furthermore, our subgroup analyses adjusted the covariates of indicators according to significant associations.Our overall results were similar to current benchmarks or evidence, while our findings showed a wider variability as this is a worldwide systematic review. Most included CRC screening programs used quantitative FIT rather than qualitative FIT, as the former allows for the adjustment of cut-off values tailored to a country\u2019s colonoscopy resources . A higheContinents and age groups also contributed to the heterogeneity between studies. According to the epidemiology of CRC, Europe and America had a higher incidence than the Asia Pacific , which lMost studies showed that the initial (first screening) tests had a better performance than the subsequent (screening performed by participants who have tested in the previous round) tests, ,20 whileThe colonoscopy compliance rate represents important determinants of the effectiveness of screening programs on CRC-related mortality reduction. The European guidelines recommended over 90% as the satisfactory rate of compliance with colonoscopy attendance in patients with positive fecal tests . FurtherAccording to our results, the performance of global CRC screening showed large variability. In this case, a fixed benchmark may not provide enough evidence in consideration of the local conditions. Besides the overall estimates, we conducted several subgroup analyses to stratify the indicators, which may provide a specific reference for future CRC screening programs. The meta-regression in our study may help policymakers to consider the impact of factors and choose a suited screening strategy to balance the health resources and expected performance.There are some limitations to the study. Firstly, we only included studies using FIT as the initial screening tool, followed by colonoscopy after a positive FIT, because in many studies, FIT was consistently proven to be better than gFOBT ,32. FurtOverall, we summarized the achievements of various indicators from population-based CRC screening programs using FIT and subsequent colonoscopy on a global scale, and explained the wide variability of these indicators in terms of screening modalities. These findings could help to identify the processes that can be improved and can finally optimize the CRC screening programs."} +{"text": "Those <50 years were also less accepting of vaccination. Subsequent vaccine uptake was 99% in non-hesitant participants. For those who were unsure, preferred not to answer, or answered \u201cno\u201d, vaccination rates were 80% , 78% , and 52.7% , respectively. These findings suggest that initial intent did not correlate with vaccine uptake in our cohort.Coronavirus Disease-2019 (COVID-19) vaccine acceptance is variable. We surveyed participants in the COVID-19 Community Research Partnership from 17 December 2020 to 13 January 2021 to assess vaccine receptiveness. Vaccine uptake was then monitored until 15 May 2021; 20,232 participants responded to the receptiveness survey with vaccination status accessed in 18,874 participants via daily follow-up surveys . In the initial survey, 4802 (23.8%) were vaccine hesitant. Hesitancy was most apparent in women (Adjusted RR 0.93, Three COVID-19 vaccines have been approved for Emergency Use Authorization (EUA) in the United States by the Food and Drug Administration (FDA) ,3. In NoTo assess the extent of vaccine hesitancy in North Carolina, we conducted a survey between 17 December 2020, and 13 January 2021, of 20,232 individuals affiliated with five medical centers from differing geographic regions of North Carolina. This was followed by a daily survey of respondents from the same cohort to determine subsequent vaccine uptake rates. This report presents the key findings from those two surveys.The COVID-19 Community Research Partnership (CCRP) is a multi-site, prospective study combining daily electronic symptom surveillance, longitudinal serologic surveillance, and electronic health record capture . DemograBasic demographic data captured for all CCRP participants included age, sex, previous COVID-19 diagnosis status, community of residence, and race/ethnicity. Counties of residence were characterized as urban, suburban, or rural utilizing the North Carolina rural center counties map. Densities were calculated based on the 2014 census population estimates Participp-values < 0.001 were considered significant.To correlate the association of demographic characteristics with vaccine intent, binomial regression was implemented. Vaccine intent responses were categorized into two groups for this analysis: Yes and No/Undecided. To assess how demographic characteristics were associated with vaccine receptiveness, multivariate binomial regression was used with a log link function. The resulting coefficient estimates were exponentiated (eb) to calculate relative risk. The relative risk of responding \u2018Yes\u2019 was calculated for each demographic variable, along with 95% confidence intervals. Previous COVID-19 Diagnosis was self-reported information included as a part of the enrollment questionnaire . The impIn addition to the vaccine attitudes survey, daily CCRP survey data through 15 May 2021, was used to assess which participants reported receiving at least one COVID-19 vaccine dose. The vaccine rate was stratified by the vaccine intent and participants\u2019 characteristics . UnvacciA total of 20,232 people completed the initial mini-survey . The follow-up survey was completed by 18,874 respondents of the same cohort. This decrease in number of participants was due to exclusion of unvaccinated individuals who did not complete the daily follow-up survey 30 days or more prior to 15 May 2021.In the initial survey, 76.2% of participants indicated their intent to get the vaccine. Participants were grouped by race, gender, age, residence locale, healthcare worker status, and previous COVID-19 infection . Comparap < 0.0001) vaccine uptake among those that were undecided, 77.6% uptake among those that preferred not to answer, and a 52.7% uptake among those that answered \u201cno\u201d to getting the vaccine in the initial survey.The follow-up survey revealed some interesting data about vaccine uptake in these groups. Overall, of the 18,874 individuals that participated in the daily survey until 15 May 2021, 17,461 (92.5%) obtained a COVID-19 vaccine. Among the participants that had intent to get the vaccine, there was a 98.5% vaccine uptake. Of those who did not answer \u201cyes\u201d to the initial survey, there was a 70% vaccine uptake . Within Interestingly, Black Americans who were the least likely to accept the vaccine based on expressed pre-vaccination attitudes had an 88.9% vaccine uptake . There wMultiple surveys have looked at COVID-19 vaccine hesitancy ,7,8,9,10There are several potential limitations of this study. First, our data represent responses from North Carolinians enrolled into an ongoing research study through regional healthcare systems and may not be representative of national data. Our study volunteers are likely to be better connected to a healthcare system and more comfortable with electronic communication than the general community. Second, this survey provides only a snapshot in time and, as demonstrated by out follow-up survey, attitudes do change over time. Third, the demographics of our survey participants may not reflect national demographics. Fourth, our finding of more hesitancy among suburban residents may simply reflect limitations in our method for characterizing counties as it is difficult to accurately describe many counties in North Carolina as entirely urban, suburban, or rural. Fifth, we did not detail the reasons why our participants had a change in attitude trending towards increased acceptance. Finally, survey results might not be comparable to other national or state polls or surveys due to potential differences in survey methods, sample population, and questions related to willingness to get the vaccine.In conclusion, this survey examined attitudes towards the COVID-19 vaccine in the initial phases of the vaccine rollout, and then followed the same cohort over subsequent months looking at uptake. Initial intent did not correlate with uptake in our North Carolina cohort. Vaccine uptake in participants that did not answer \u201cyes\u201d to the initial survey was 70% which offers some insight that broader acceptance of vaccination may continue to evolve over time."} +{"text": "Morbidity and mortality amongst extremely low birth weight (ELBW) and extremely low gestational age neonates (ELGANs) in developing nations has not been well studied.Evaluate survival until discharge, short- and long-term morbidities of ELBW and ELGANs in LMICs.CENTRAL, EMBASE, MEDLINE and Web of Science.Prospective and retrospective observational studies were included.Four authors extracted data independently. Random-effects meta-analysis of proportions was used to synthesize data, modified QUIPS scale to evaluate quality of studies and GRADE approach to ascertain the certainty of evidence (CoE).192 studies enrolling 22,278 ELBW and 18,338 ELGANs were included. Survival was 34% (95% CI: 31% - 37%) (CoE\u2013low) for ELBW and 39% (34% - 44%) (CoE\u2014moderate) for ELGANs. For ELBW neonates, the survival for low-income (LI), lower middle-income (LMI) and upper middle income (UMI) countries was 18% (11% - 28%), 28% (21% - 35%) and 39% (36% - 42%), respectively. For ELGANs, it was 13% (8% - 20%) for LI, 28% (21% - 36%) for LMI and 48% (42% - 53%) for UMI countries. There was no difference in survival between two epochs: 2000\u20132009 and 2010\u20132020. Except for necrotising enterocolitis [ELBW and ELGANs\u20148% (7% - 10%)] and periventricular leukomalacia , rates of all other morbidities were higher compared to developed nations. Rates of neurodevelopmental impairment was 17% (7% - 34%) in ELBW neonates and 29% (23% - 37%) in ELGANs.CoE was very low to low for all secondary outcomes.Mortality and morbidity amongst ELBW and ELGANs is still a significant burden in LMICs. CoE was very low to low for all the secondary outcomes, emphasizing the need for high quality prospective cohort studies.CRD42020222873).PROSPERO ( Prematurity is one of the leading causes of childhood mortality, rates of which are on the rise across the globe \u20134. AvailThe quantum of impact on decreasing the neonatal mortality rate (NMR) is more pronounced when community based interventions targeting the late preterm and term neonates are implemented successfully across LMICs . It is eEvery Newborn action plan by WHO envisages reducing national NMR to 12 per 1000 live births by the year 2030 . HistoriThe protocol for the systematic review was registered with PROSPERO (CRD42020222873) . The repst January 2000 till 21st November 2020. There were no language restrictions. Google translate was used for translating non-English literature. Studies published in Urdu and Persian were translated with the help of a translator as there were some limitations in Google translate for these languages. Studies published as abstracts were also eligible for inclusion. Only published data was used in this systematic review. Four authors conducted the literature search independently in pairs of two using Rayyan-QCRI software [Electronic databases: MEDLINE, EMBASE, Web of Science and Cochrane CENTRAL were searched from 1software . The seaRetrospective as well as prospective observational studies that had reported on outcomes of ELGANs (born at less than 28 weeks\u2019 of gestation) and / or ELBW neonates (birth weight of less than 1000 grams) from a LMIC as per the World Bank country classifications by income levels (2020) were eligible for inclusion . Randomith centile at 36 weeks\u2019 PMA), any NDI (as defined by authors) and cerebral palsy of any severity, both assessed at 18\u201324 months\u2019 corrected age.The primary outcome of the review was proportion of neonates who had survived until discharge. Secondary outcomes included prevalence of intraventricular hemorrhage (IVH) (> grade II) , perivenThe risk of bias assessment was done using a modified QUIPS scale . Four paThe data for relevant outcomes were extracted using a pre-specified proforma by two authors independently . Statistical analysis was done using the R-Software. Meta-analysis of proportions was used for synthesis of data. Raw data was used if the proportions were between 0.20 to 0.80. Otherwise, data was logit transformed. Freeman-Tukey Double arcsine transformation of data was preferred over logit transformation when there were many proportions with 0 or 1 values. \u2018Metaprop\u2019 package in R-software was used for meta-analysis of proportions. \u2018Metaprop\u2019 can analysis meta-analysis of raw data based on proportions as well as convert raw data to logit transformation or Freeman-Tukey Double arcsine transformation and re-transform to proportions by default for meaningful interpretation. A random effects model was chosen as significant heterogeneity was anticipated as reported in prior studies on newborn survival . An inve2 value was used to adjudge significant heterogeneity. Imprecision was evaluated based on the point estimate and the 95% confidence interval. If these were to cross a decision threshold to intervene, the CoE was downgraded by one level for imprecision. Though publication bias assessment in meta-analysis of prognosis studies is a contentious topic, we assessed publication bias using funnel plots and Begg\u2019s rank test based on GRADE working group guidelines [CoE was assessed using a modified GRADE approach . Outcomeidelines , 25.The following sensitivity analyses were performed for the primary outcomeCategorizing studies from countries based on three income levels\u2013low income (LI), lower middle-income (LMI) and upper middle-income (UMI).Categorizing studies based on geographical regions where they are situated.Excluding studies with low sample size (less than 50 subjects).Comparison of survival between two time periods\u2014epoch 1: 2000\u20132009 and epoch 2: 2010\u20132019.Analyzing studies which had evaluated neonates with varying baseline sickness.A total of 21,535 studies were identified from the literature search, of which 2157 full texts were assessed for eligibility after removal of duplicates as well as title, abstract screening and 192 studies were included in the final synthesis Status, Apgar scores and Level of NICU care. 83 studies had a prospective study design. The risk of bias of included studies is given in S2 Table in The overall survival was 34% (95% CI: 31% - 37%). There was significant heterogeneity in the survival rates between studies. Sub-group analysis to address the heterogeneity was done by analyzing studies based on the income status, region and country of origin. While there were widely varying survival rates between countries of similar economic status as well as region of origin, it was much lesser when studies were analyzed according to the country of origin.For ELBW neonates, the survival for LI, LMI and UMI countries was 18% (11% - 28%), 28% (21% - 35%) and 39% (36% - 42%), respectively . It was 13% (8% - 20%) for LI, 28% (21% - 36%) for LMI and 48% (42% - 53%) for UMI countries. Similar to ELBW survival, there was considerable variation between countries of similar economic classification and geographic region and 7% (4% - 11%), respectively. For ELGANs, while the overall rate of severe IVH was 14% (11% - 19%). it was 6% (5% - 7%) for PVL . Meta-analysis of five studies revealed a NDI prevalence of 29% (23% - 37%) for ELGANs. The prevalence of CP in ELGAN population was 3% (1% - 9%) for ELBW neonates and 50% (35% - 65%) for ELGANs for ELBW neonates and 75% (65% - 84%) for ELGANs . One study from South Africa had reported a relatively lower rate of 17% (6% - 33%). The overall prevalence of BPD was 37% (29% - 47%) in ELGANs. Three centers from China, India and Turkey had reported a higher rate of more than 60% and 28% (21% - 35%), respectively. Rates of any and culture proven sepsis in ELGANs was 40% (25% - 57%) and 21% (12% - 32%), respectively for ELBW neonates as well as ELGANs. Publication bias was detected for studies reporting on NEC in ELBW neonates , 24% (19% - 30%) and 18% (12% - 27%), respectively. One study each from India, Iran and Pakistan had reported severe ROP rate of more than 50%. Also, some reports from China, Turkey and Jordan had ROP requiring intervention rates of more than 30%.In ELGANs, any stage ROP, severe ROP and ROP requiring intervention was reported in 53% (46% - 59%), 22% (16% - 30%) and 20% (13% - 29%) of neonates, respectively. Single center reports from Thailand and Brazil had rates exceeding 40%.Data related to ROP is given in S37-S48 Figs in 4a. Excluding studies with low sample size. Analysis of survival outcome after excluding studies with low sample size did not result in any significant changes in the effect estimate when compared to the primary analysis for both ELBW neonates and ELGANs and ELGANs. and ELGANs survival was 37% (28% - 47%) for RDS. While 41% (28% - 56%) of ELBW neonates who underwent invasive ventilation survived, the survival rate was 23% (9% - 48%) for ELGANs.CoE for the primary outcome measure of survival until discharge for ELGANs was moderate and for ELBW neonates was low. While most of the included studies reporting on the primary outcome measure were prospective in design and started with high CoE, they were downgraded for serious inconsistency by one level. The outcome of survival until discharge for ELBW neonates was further downgraded by one level for publication bias. The CoE for other secondary outcomes were very low to low, with retrospective study design and heterogeneity being reasons for downgrading the CoE. The CoE is given in This systematic review and meta-analysis included 192 studies from LMICs situated in different geographical regions across the globe. To the best of our knowledge, this is the only systematic review evaluating survival and morbidities in ELGANs or ELBW neonates from LMICs.The primary outcome of the review was the proportion of neonates who had survived until discharge. The results of this study indicate that the overall survival until discharge of ELBW neonates was 34% and ELGANs was 39%, with significant heterogeneity between studies based on the income status, region as well as country of origin. These survival rates are much lower than that reported from HICs . MyrhaugThere was significant variation in survival between LMICs as well. Similar findings are also seen in the studies published from HICs . While sSensitivity analysis indicated that there was no significant differences in the survival rates between the two epochs (epoch 1: 2000\u20132009 and epoch 2: 2010\u20132019). Similar findings were noted in the meta-analysis by Myrhaug et al. for HICs . HoweverThis systematic review had some limitations. There was considerable heterogeneity in the various outcome measures despite performing multiple sensitivity and sub-group analyses to address the same. The analysis might be limited by denominator bias as survival rates could not be assessed based on different denominators such as live births versus NICU admissions, due to inconsistent reporting in studies. Accurate gestational age assessment is still a major issue in LMICs and might have influenced our final estimates. Further, analysis by stratification on the basis of gestational age or birth weight could not be performed for ELGANs and ELBW neonates. Important confounders determining survival such as antenatal corticosteroid use, multiple gestation, SGA status, gender, chorioamnionitis and level of NICU care were not reported by majority of the included studies, thus precluding any sensitivity analysis based on these parameters. The overall CoE was very low to low for all the secondary outcomes. Finally, though the literature search included the standard databases as recommended by the Cochrane group, studies from LMICs might be more likely to be published in alternative databases as well.Mortality and morbidity of ELBW neonates and ELGANs is still a huge burden in LMICs, with significant differences in their occurrence between countries of similar economic status and geographical region of location. For ELBW neonates, the survival for LI, LMI and UMI countries was 18% (11% - 28%), 28% (21% - 35%) and 39% (36% - 42%), respectively. For ELGANs, it was 13% (8% - 20%) for LI, 28% (21% - 36%) for LMI and 48% (42% - 53%) for UMI countries. These are significantly lower than the survival rates reported from HICs. The CoE for most of the outcomes was very low to low, emphasizing the need for surveillance and high quality prospective cohort studies from LMICs on this sub-group of vulnerable neonates. Such studies should provide data related to still births, live births, delivery room deaths, important baseline characteristics such as antenatal corticosteroid use, multiple gestation status, SGA, gender, chorioamnionitis and level of NICU care, and sub-group data on different gestational ages or birth weights for ELGANs or ELBW neonates. Such data would not only quantify the burden of mortality and morbidity in these preterm infants, but also enable evaluating the post-implementation impact of important public health interventions.S1 Checklist(DOC)Click here for additional data file.S1 File(PDF)Click here for additional data file."} +{"text": "Home health care is the most commonly used home- and community-based service to older adults \u201cAging in Place\u201d. Patient experience of healthcare services is a critical aspect of patient-centered care. Indeed, policymakers have linked patient-rated quality of care to payment to healthcare providers. This study aimed to examine the association between patient-rated care performance of home health agencies and risk for hospitalization among Medicare beneficiaries. This study used several national datasets from 2016 and included 491,718 individuals from 8,459 home health agencies. Home health agencies\u2019 performance was measured using patient experience star rating from the Home Health Consumer Assessment of Healthcare Providers and Systems (HHCAHPS). Propensity score matching was used to balance the differences in patient characteristics at baseline between those receiving care from high-performing home health agencies and those in lower-performing agencies. On average, patients were 80.5 years old, 65% female, 81% White, 10% Black, and 6% Hispanic, with 90% taking 5 or more medications. Patients had a mean score of 1.73 (SD=1.69) on the Charlson Index. Respectively, 10% and 16% of patients were hospitalized within 30 and 60 days of home health care initiation. Estimates of logistic regression after propensity score matching found that patients receiving care from lower-performing agencies were at similar risk for both 30-day and 60-day hospitalization following the start of home health care, compared to those in high-performing agencies. Our findings suggest discrepancies (or no relationship) between patient experience and objective outcomes of home health care."} +{"text": "ABSTRACT IMPACT: Within three EDs in a regional health system in Connecticut, African American race, male gender, non-Hispanic ethnicity, lack of private insurance, and homelessness were associated with significant odds of being physically restrained during a visit. OBJECTIVES/GOALS: Agitated patient encounters in the Emergency Department (ED) are on the rise, and physical restraints are used to protect staff and prevent self-harm. However, these are associated with safety risks and potential stigmatization of vulnerable individuals. We aim to determine factors that are associated with odds of being restrained in the ED. METHODS/STUDY POPULATION: We conducted a retrospective cohort analysis of all patients (\u226518 yo) placed in restraints during an ED visit to three hospitals within a large tertiary health system from Jan 2013-Aug 2018. We undertook descriptive analysis of the data and created a generalized linear mixed model with a binary logistic identity link to model restraint use and determine odds ratios for various clinically significant demographic factors. These include gender, race, ethnicity, insurance status, alcohol use, illicit drug use, and homelessness. Our model accounted for patients nested across the three EDs and also accounted for multiple patient visits. RESULTS/ANTICIPATED RESULTS: In 726,417 total ED visits, 7,090 (1%) had associated restraint orders. Restrained patients had an average age of 45, with 64% male, 54% Caucasian and 29% African American. 17% had private insurance, 36% endorsed illicit substances, 51.4% endorsed alcohol use and 2.3% were homeless. African Americans had statistically significant odds of being restrained compared to Caucasians with adjusted odds ratio (AOR) of 1.14 . Females and Medicare had increased odds compared to the privately insured. Illicit substance use , alcohol use had increased odds of restraint use. DISCUSSION/SIGNIFICANCE OF FINDINGS: We showed statistically significant effects of patient demographics on odds of restraint use in the ED. The increased odds based on race, insurance status, and substance use highlight the potential effects of implicit bias on the decision to physically restrain patients and underscores the importance of objective assessments of these patients."} +{"text": "Evidence-based digital health applications (apps) offering comprehensive lifestyle therapies for inflammatory bowel disease (IBD) patients are limited in Canada.www.lyfemd.ca).The aims of this study were to explore the Canadian IBD digital app landscape and review preliminary data from a recently launched digital app for IBD, LyfeMD. \u201d were searched by one team member (BC) on the App Store. Apps were included if they offered any type of lifestyle therapy, including education. The mobile application rating system (MARS) was used to evaluate each app and is a validated tool used to assess the quality of mobile health apps. For the LyfeMD app, 35 IBD users completed a baseline assessment survey to identify: 1) physical activity, sitting, and screen time, and; 2) stress, sleep, depression and anxiety. Eleven participants completed in-depth user experience evaluations after 4 weeks. Survey scores were calculated using published scoring protocols and descriptive data were prepared.2, 57% were meeting 150 minute/week activity guidelines, 49% had high sitting time, 100% had high screen time, 69% had a moderate to high level of stress, 100% experienced sleep problems, 69% reported depression, and 49% reported anxiety. Eleven people completed the detailed user experience evaluations. They reported the app helped them identify behaviour changes to improve overall wellness; most often what they eat (64%), overall well-being (64%) and physical activity (46%).The LyfeMD and My IBD Care app scored highest on the MARS with a total score of 4.8/5. Of the other eight apps identified, scores ranged from 2.4 to 4.6 . LyfeMD differentiated itself from other apps by providing lifestyle programs to improve nutrition, physical activity and mental health. Of the LyfeMD users, 74% had CD and 26% had ulcerative colitis , 60% had a BMI \u226525 kg/mTwo IBD apps available in Canada had a high MARS rating, however only the LyfeMD app offered comprehensive lifestyle therapies. The growing literature supports benefit for lifestyle therapies in IBD, and the LyfeMD app may be effective to identify areas amenable to lifestyle modification.Ascend, Alberta Innovates"} +{"text": "To perform a systematic review of design and reporting of imaging studies applying convolutional neural network models for radiological cancer diagnosis.A comprehensive search of PUBMED, EMBASE, MEDLINE and SCOPUS was performed for published studies applying convolutional neural network models to radiological cancer diagnosis from January 1, 2016, to August 1, 2020. Two independent reviewers measured compliance with the Checklist for Artificial Intelligence in Medical Imaging (CLAIM). Compliance was defined as the proportion of applicable CLAIM items satisfied.\u03c1 = 0.15, p = .04) and journal H-index . Clinical journals demonstrated higher mean compliance than technical journals .One hundred eighty-six of 655 screened studies were included. Many studies did not meet the criteria for current design and reporting guidelines. Twenty-seven percent of studies documented eligibility criteria for their data , 31% reported demographics for their study population and 49% of studies assessed model performance on test data partitions . Median CLAIM compliance was 0.40 (IQR 0.33\u20130.49). Compliance correlated positively with publication year for cancer diagnosis frequently omit key clinical information including eligibility criteria and population demographics.\u2022 Fewer than half of imaging studies assessed model performance on\u00a0explicitly unobserved test data partitions.\u2022 Design and reporting standards have improved in CNN research for radiological cancer diagnosis, though many opportunities remain for further progress.\u2022 The online version contains supplementary material available at 10.1007/s00330-021-07881-2. Recent years have seen an increase in the volume of artificial intelligence (AI) research in the field of cancer imaging, prompting calls for appropriately rigorous design and appraisal standards \u20136. EvaluEQUATOR was founded to improve the quality of scientific research through standardisation of reporting guidelines , 14. EstCLAIM aims to promote clear, transparent and reproducible scientific communication about the application of AI to medical imaging and provides a framework to assure high-quality scientific reporting. Current conformity to these standards has not been formally quantified to date. Consequently, a need exists for a contemporary evaluation of design and reporting standards in the domain of cancer imaging AI research.Following ImageNet 2012 , convoluThe article evaluates a CNN model for radiological cancer diagnosis in humans.The model receives a radiological image as its sole input.The article was published in a peer-reviewed journal between January 1, 2016, and August 1, 2020.The article is published in the English language.The model addresses a non-diagnostic task such as pre-processing, segmentation or genotyping.The model receives non-radiological images such as histopathology, dermoscopy, endoscopy or retinoscopy.The article presents experiments on animal or synthetic data.The article primarily addresses economic aspects of model implementation.The article is published in a low-impact journal.The article is unavailable in full-text format.PubMed, EMBASE, MEDLINE and SCOPUS databases were searched systematically for original articles from January 1, 2016, to August 14, 2020, for articles meeting our inclusion and exclusion criteria. Search queries for each database are included in the Data items were defined to measure compliance with CLAIM proposal and previously published proposals , 18. ComArticles were read and annotated by R.O.S. and A.S., and disagreements were resolved by consensus. Articles were read in random order, using a fixed sequence generated in R . JournalStatistical analysis was conducted using R version 3.5.3 and RStut test. All code and data required to support the findings of this research are available from the corresponding author upon request. As a methodological review assessing study reporting, this study was not eligible for registration with the PROSPERO database.Temporal change in CLAIM compliance was evaluated by two-sided test of Spearman rank correlation between CLAIM score and year of publication. Association between journal impact factor and compliance was evaluated with a two-sided test of Spearman rank correlation between journal H-index and CLAIM score. The difference in mean CLAIM compliance between clinical and technical journals was evaluated with a two-sided Six hundred fifty-five articles were identified in the primary database search, of which 267 were duplicates. One hundred twenty articles were excluded during title screen, and 82 articles were excluded during abstract screening. One hundred eighty-six articles were included in the final analysis. A flow diagram for the literature search process is provided in Fig. Compliance for items 1\u201313 is shown in Fig. Thirty-three percent of studies documented a retrospective or prospective timeframe . Of these, 87% were retrospective , 10% were prospective and 3% used both retrospective and prospective data . Twenty-five percent of studies specified a goal .Ninety-four percent of studies documented their data sources . Of these, 45% used publicly available datasets only , 49% used local data only and 6% combined public datasets with locally collected data . Seventy-two percent of studies documented the centres from which the data was sourced . Of these, 50% used data from multiple centres . Fifty-one percent of studies detailed the imaging equipment used . Of these, 53% employed equipment from multiple vendors . Image acquisition parameters were documented in 37% of studies . Amongst studies which collected local data, 83% documented institutional review board approval and 26% documented participant consent . In studies of publicly available data, 9% documented institutional review board approval and 8% documented participant consent . Twenty-seven percent of studies documented eligibility criteria for their data .Pre-processing was documented in 69% of studies , though only 53% provided a reproducible methodology . Data subsetting was applied in 42% of studies , of which 95% included methods . As per our inclusion criteria, all studies employed convolutional neural network models, which define predictor features autonomously. We also required an outcome in the domain of radiological cancer diagnosis. Therefore, relevant data elements were defined in 100% of included studies . Nineteen percent of studies performing local data collection documented data anonymisation , though only 3% detailed the methodology . Eighty-four percent of studies performing local data collection documented data anonymisation, institutional review board approval or both . Three percent of studies of publicly available data documented data anonymisation , and none detailed the methodology. Missing data procedures were documented in 17% of studies . Case exclusion was the only strategy employed to manage missing data in these studies .Compliance for items 14\u201327 is shown in Fig. Forty percent of studies documented image annotation by a radiologist with relevant subspecialist expertise . A further 32% documented annotation by a radiologist with unspecified expertise and 4% used other clinicians . Of the studies which utilised histopathological ground truth, 8% specified annotation by a pathologist with relevant subspecialist experience . Twelve percent of studies documented the software tools used for image annotation . Eighteen percent of studies provided inter-rater or intra-rater variability statistics , and 27% provided their aggregation strategy , though only 16% provided both .Eighty-seven percent of studies reported the number of images modelled , though only 1% provided a power calculation . Seventy-two percent specified the number of study participants in their dataset . Of these, a median of 367 participants were included (IQR 172\u20131000). Seven studies served only to validate existing models and were exempted from criteria pertaining to model development and data partitioning. Seventy-six percent of modelling studies defined data partitions and their proportions , though 32% specified the level of partition disjunction .Sixty-six percent of modelling studies provided a detailed model description and 20% of modelling studies provided access to source code . Sixty-eight percent documented the development software , though only 41% included the software version . Sixty-eight percent of modelling studies reported model initialisation parameters . Of these, 52% employed transfer learning and 3% compared transfer learning with random initialisation .Sixty-five percent of modelling studies reported data augmentation , though only 54% documented reproducible methodology . Sixty-one percent of modelling studies documented the optimisation algorithm , 61% documented learning rate , 44% documented loss function and 52% documented batch size . Model selection strategies were documented in 69% of modelling studies . Of 30 studies which employed model ensembling, 93% reported their aggregation methodology .Compliance with CLAIM items 28\u201342 is shown in Fig. Forty-nine percent of studies assessed model performance on test data which was explicitly disjunct from training and validation data . Forty-five percent of studies mentioned only two data partitions ; their reported results may have represented validation rather than test performance. A further 6% failed to document any data partitions ; their reported results may have represented training performance. Forty-one percent of studies benchmarked models against other computational methods . Seventeen percent of studies benchmarked their model against radiologists with relevant subspecialist expertise . Five percent of studies benchmarked their model against radiologists without specifying expertise and 1% employed other clinicians .Case flow diagrams were provided in 8% of studies . Thirty-one percent of studies reported demographic and clinical characteristics of their population . However, only 10% described separate distributions for each data partition . Fifteen percent of studies reported performance metrics on test data from another institution . Thirty-four percent used test data from the same institution . Diagnostic accuracy was reported with confidence intervals in 40% of studies . Twenty-four percent of studies discussed misclassified examples .Forty-six percent of studies discussed limitations and 37% clinical implications of their findings .Study registration numbers were provided in 7% of studies , and study protocols in 1% . Funding was documented in 65% of studies though only 3% included the role of the funding institution . A further 6% of studies stated that they did not receive funding . Compliance for items 1\u201342 is provided in Supplementary Table \u03c1 = 0.15, p = .04) and journal H-index . Clinical journals demonstrated higher mean compliance than technical journals . Compliance distribution is visualised with respect to publication year, journal H-index and journal category in Fig. Median CLAIM compliance was 0.40 (IQR 0.33\u20130.49). Compliance correlated positively with publication year . Training data is used for model learning, validation data for model selection and test data to assess performance of a finalised model , 48. HalEvidently, CLAIM has also introduced requirements which depart from current norms. Few studies satisfied item 12, which requires the documentation of data anonymisation methods, an issue which has developed with image recognition capabilities , 49, 50.Our findings concur with previous reviews of design and reporting standards in both clinical and general-purpose AI research. A review of studies benchmarking AI against radiologists identified deficient documentation of data availability, source code, eligibility and study setting . ReviewsWe note several limitations to this systematic review. First, as scope was limited to studies published in English, findings were susceptible to language bias. Second, although reporting standards were directly measurable, items relating to study design were only measurable if reported. Consequently, design compliance may have been underestimated in poorly reported studies. This is a general limitation of reviews in this field. Third, articles were read sequentially and therefore readers were potentially susceptible to anchoring bias. The effect of anchoring on the trend and subgroup analyses was minimised by randomisation of the reading order.Design and reporting standards have improved in CNN research for radiological cancer diagnosis, though many opportunities remain for further progress. The CLAIM guidance sets a high standard for this developing field, consolidating clinical and technical research requirements to enhance the quality of evidence. Our data supports the need for integration of CLAIM guidance into the design and reporting of CNN studies for radiological cancer diagnosis.ESM 1(DOCX 89 kb)"} +{"text": "The goal of this study was to evaluate feasibility and acceptability of a remote Tai Chi program in diverse older adults with multisite pain and risk for falls during the COVID-19 pandemic. Adults aged \u226565y living in diverse Boston neighborhoods were invited through mailed letters to participate in a recruitment and screening survey. Eligible adults were re-contacted to join a 4-week Tai Chi or light exercise program offered online twice weekly. We conducted pre- and post-interviews to assess pain characteristics, fall risk, computer use, and satisfaction with the program. Primary outcomes were class attendance, experience, and program safety. Among 335 survey respondents, 105 (31%) were eligible based on multisite pain and fall history or cane/walker use. Of the eligible respondents, average age was 74y, 75% were women, 62% were Black, and 31% had high school education or less. We assigned 32 participants to 4 Tai Chi (Yang-style Tai Chi tailored to older adults with pain) or 2 light exercise (stretching and strength exercise) groups conducted via zoom; of these, 24 (75%) completed the program. Overall, 79% attended \u22656 of 8 classes. There were no adverse events reported. Regarding experiences with remote exercise, 67% reported it was very easy to join, 88%, very easy to see the instructor and 83%, very easy to participate. For future planning, 29% prefer remote classes, 33% prefer in-person classes, and 38% could do either. In conclusion, remote exercise programming is safe and feasible for diverse older adults who have multisite pain and risk of falls."} +{"text": "COVID-19 restrictions and fear dramatically changed the use of medical care. Understanding the magnitude of cancelled and postponed appointments and associated factors can help identify approaches to mitigate unmet need.To determine the proportion of medical visits cancelled or postponed and for whom. We hypothesized that adults with serious medical conditions and those with higher anxiety, depressive symptoms, and avoidance-oriented coping would have more cancellations/postponements.Four nationally representative cross-sectional surveys conducted online in May, July, October, and December 2020.59,747 US adults who completed 15-min online surveys. 69% cooperation rate.Physical and mental health visits and cancer screening cancelled or postponed over prior 2 months. Plan to cancel or postpone visits over the next 2 months. Relationship with demographics, medical conditions, local COVID-19 death rate, anxiety, depressive symptoms, coping, intolerance of uncertainty, and perceived COVID-19 risk.N = 34,868) with a medical appointment during the 2 months before the survey, 64% had an appointment cancelled or postponed in May, decreasing to 37% in December. Of the 41% of respondents with scheduled cancer screening, 20% cancelled/postponed, which was stable May to December. People with more medical conditions were more likely to cancel or postpone medical visits and cancer screening . Race, ethnicity, and income had weak associations with cancelled/postponed visits, local death rate was unrelated, but anxiety and depressive symptoms were strongly related to cancellations, and this grew between May and December.Of the 58% (Cancelled medical care and cancer screening were more common among persons with medical conditions, anxiety and depression, even after accounting for COVID-19 deaths. Outreach and support to ensure that patients are not avoiding needed care due to anxiety, depression and\u00a0inaccurate perceptions of risk will be important.The online version contains supplementary material available at 10.1007/s11606-021-07254-x. Prior reports suggest that 20\u201350% of adults had cancellations of medical care4 with declines in emergency services6 and more cancellations for those with pre-existing medical conditions.3 Studies show substantial decreases in admissions for serious medical conditions.8COVID-19 has upended myriad aspects of life, particularly receipt of usual medical care. Early in the pandemic, many health care providers cancelled elective procedures and visits9 Early data suggest fewer early cancer diagnoses10 and portend worse outcomes.12 Further, missed appointments and treatments among patients with existent cancer are expected to result in increased cancer mortality.13Increased levels of non-COVID-19 death have been reported during these periods of medical care avoidance.To plan for medical care as restrictions ease, it is important to understand the developing level of unmet need for clinical care, trends over time, and patient characteristics associated with cancelled or postponed medical appointments and cancer screening. We surveyed cross-sectional national samples at four time points in 2020 to examine missed medical care and cancer screening in the setting of COVID-19. We hypothesized that in addition to the local death rate from COVID-19, people at greater risk of adverse outcomes from COVID-19, those with higher anxiety and depressive symptoms, those more intolerant of uncertainty, and those more likely to cope with the pandemic through avoidance would be more likely to have cancelled and postponed medical care including cancer screenings.We fielded four 15,000-person cross-sectional surveys between May and December of 2020. Surveys were conducted online with samples provided by the market research firm Lucid. Samples are constructed to match a set of demographic quotas on age, gender, race, ethnicity, region, income, and education. The resulting survey data are weighted to be representative of the US adult population as descrThe survey asked about missed medical appointments as follows: \u201cOver the last two months, have any of your healthcare providers cancelled or postponed scheduled visits or services for physical or mental health?\u201d Response options were Yes, No, I did not have anything scheduled, and Not sure. Respondents also were asked if they had cancelled or postponed scheduled visits or services. These two items were combined to describe whether the respondent had a medical visit that was cancelled or postponed, had no appointment scheduled, attended a medical visit, or was unsure. Concerning cancer screening, the survey asked: \u201cOver the last two months, have you cancelled or postponed getting routine cancer screening ?\u201d with the same response options. Concerning the future, respondents were asked \u201cIn the upcoming two months, do you plan to cancel or postpone getting routine cancer screening ?\u201d and the same question was asked concerning visits or services for physical or mental health.15 divided into approach-oriented coping by tercile and avoidant coping dichotomized, anxiety,16 depressive symptoms,17 three items from the Intolerance of Uncertainty Scale,18 perceived COVID-19 risk, region, and time (survey wave). COVID-19 deaths in the county of the respondent 2 weeks before each survey were obtained from nytimes/covid-19-data, https://github.com/nytimes/covid-19-data/tree/master/excess-deaths.Independent variables included age, gender, race/ethnicity, education, household income (by tercile), political party, number of significant medical diagnoses , respondent or household member believes they had COVID-19, coping with \u201cthe COVID-19 experience\u201d (yes/no items based on commonly used measures)The data include 14,636 interviews conducted in May 11\u201324, 14,936 interviews in July 9\u201322, 14,946 interviews in October 1\u201317, and 15,229 interviews in December 4\u201316. Weighted proportions of the respondents had a medical appointment during the 2 months prior to survey, and this increased slightly from May through December. Of the people with a physical or mental health appointment, 51% did not attend because the appointment was cancelled or postponed. This fraction decreased across the first three waves from 64.6% in May to 53.5% in July and 36.8% in October, before stabilizing at 37.6% in December in December. The nearly 20% cancellation rate of retrospective cancer screening was stable across survey waves . The proportion of respondents with cancer screening appointments increased steadily across the four waves\u2014indicating people\u2019s return to activities over the course of the year\u2014from 36.4% in May to 47.0% . Of those with appointments, 15% planned to cancel or postpone. Similarly, concerning future cancer screening, 42% had screening scheduled and 16% planned to cancel or postpone.Comparing reports of past appointment cancellations or postponements across survey waves to plans to cancel or postpone future appointments shows that retrospective reports far exceed anticipated cancellations or postponements for general medical care, whereas the difference between past and future cancellations or postponements is smaller for cancer screening. While physical and mental health appointment cancellations or postponements decreased and then plateaued, cancer screening cancellations were stable. Anticipated cancellations or postponements were stable for physical and mental health appointments and also cancer screening Table .p < 0.001). Those with an appointment and with medical conditions were more likely to experience a cancellation or postponement relative to those with appointments and no medical conditions . Patients with pre-existing heart and lung disease experienced the highest rates of cancelled or postponed appointments were more likely to have a scheduled appointment within the 2 months prior to their interview and cancer screenings ESM 2(PDF 489 kb)"} +{"text": "People join a customer-driven organization with motivations that may not be static over time, an important issue for long-term organizational viability. In this study, we examined motivations among members of ShareCare, the first Village for older adults in the U.S. Using qualitative data from a random sample of 91 members, we compared motivations for becoming a member and for continuing membership. Motivations to join and continue membership are not necessarily the same. Motivations were categorized as: instrumental, social, and altruistic motivation. We categorized length of membership as short-term: 8-years or less (51.63%) and long-term: 9-years and more (49.37%). While 36% of members joined only for instrumental motivation, 59% continued membership only for instrumental motivation. While about 52% joined with multiple motivations, only 35% of members mentioned multiple motivations when continuing their membership. Finally, 18% of short-term members mentioned altruistic motivation when continuing their membership, while 28% of long-term members mentioned altruistic motivation when continuing their membership. While people\u2019s motivation might change over time, altruistic motivation may be the greatest motivating factor for long-term memberships. Long-term members may identify themselves as supporters rather than users of the organization and cultivate stronger connections with other members over time. Our findings inform how to recruit and retain members in Villages, and customer-driven organizations for older adults more broadly."} +{"text": "This study presents the cardiology referral model adopted at the University of S\u00e3o Paulo-Hospital das Cl\u00ednicas complex during the initial period of the coronavirus disease (COVID-19) pandemic, main reasons for requesting a cardiologic evaluation, and clinical profile of and prognostic predictors in patients with COVID-19.In this observational study, data of all cardiology referral requests between March 30, 2020 and July 6, 2020 were collected prospectively. A descriptive analysis of the reasons for cardiologic evaluation requests and the most common cardiologic diagnoses was performed. A multivariable model was used to identify independent predictors of in-hospital mortality among patients with COVID-19.Cardiologic evaluation was requested for 206 patients admitted to the ICHC-COVID. A diagnosis of COVID-19 was confirmed for 180 patients. Cardiologic complications occurred in 77.7% of the patients. Among these, decompensated heart failure was the most common complication (38.8%), followed by myocardial injury (35%), and arrhythmias, especially high ventricular response atrial fibrillation (17.7%). Advanced age, greater need of ventilatory support on admission, and pre-existing heart failure were independently associated with in-hospital mortality.A hybrid model combining in-person referral with remote discussion and teaching is a viable alternative to overcome COVID-19 limitations. Cardiologic evaluation remains important during the pandemic, as patients with COVID-19 frequently develop cardiovascular complications or decompensation of the underlying heart disease. Cardiology referral is an essential occupation area and a good opportunity for the technical training of cardiologists. It consists of support to other medical specialties in managing cardiovascular problems associated with primarily non-cardiac diseases such as infectious, respiratory, or systemic diseases and in preparation for non-cardiac surgeries . CardiolIn the initial period of the coronavirus disease (COVID-19) pandemic, the University of S\u00e3o Paulo School of Medicine\u2019s Hospital das Cl\u00ednicas complex (HC-FMUSP) was restructured to attend only the suspected or confirmed COVID-19 cases in its 900-bed Central Institute to optimize care, reduce intra-hospital contamination, and meet the growing demand of the Unified Health System for isolation beds.During this period, cardiology referral also underwent changes, since there was a greater demand associated with the cardiovascular complications of COVID-19. A significant increase in the number of patients requiring intensive care, new challenges imposed by the need to restrict the movement of personnel, and the rational use of personal protective equipment were important challenges during this phase. In this scenario of relocation for assistance, it was also necessary to continue supervision and guidance of resident physicians in cardiology.This study aimed to report the referral model adopted in our service and the main reasons for requesting a cardiologic referral for hospitalized COVID-19 patients. We also characterized the clinical profiles and prognostic predictors of the COVID-19 patients hospitalized at the HC-FMUSP for whom cardiology referrals were requested.The main objective of the present study is to describe how cardiology consultation was performed in a quaternary university hospital in terms of patient care and medical training during the COVID-19 pandemic. All referral requests between March 30, 2020 and July 6, 2020 were eligible for inclusion in our study and encompassed suspected and confirmed COVID-19 patients. In this observational cohort, data were obtained and managed prospectively using the REDCap tool. Initial bedside assessments were performed by cardiology residents of the Heart Institute who were organized in pairs on a monthly rotation basis and supervised in person by attending physicians without risk factors for developing the most severe forms of the disease. This team was exclusively dedicated to care for COVID-19 patients.via a joint decision of the group.A daily videoconference was held among regional physicians dedicated to COVID-19 care and other physicians allocated to areas without infected patients through the InCor platform for telemedicine to ensure confidentiality of information. Clinical, laboratory, and imaging data of the most severe cases were reviewed during the videoconference and the best treatment plan was selected The reasons for cardiologic evaluation request were defined according to the referral by the assisting team and not the final cardiologic diagnosis.The diagnosis of COVID-19 was confirmed using laboratory criteria (positive reverse transcription-polymerase chain reaction [RT-PCR] or serology test result) or clinical criteria . Patients without a confirmed diagnosis of COVID-19 were excluded from the analysis of clinical characteristics, cardiovascular manifestations, complementary examinations, and main clinical outcomes.Troponin elevation was defined as the level of high-sensitive cardiac troponin T above the 99th percentile of normality, which characterizes myocardial injury. Troponin elevation was considered acute if there was an increase or decrease in its levels and chronic when the elevated levels plateaued. Diagnosis of infarction was established according to the Fourth Universal Definition of Acute Myocardial Infarction .Descriptive statistics included the reasons for the cardiologic evaluation request. For exploratory data analysis, we presented the primary clinical, demographic, and laboratory characteristics and clinical outcomes during hospitalization according to in-hospital mortality outcomes. The variables included sex, age, previous comorbidities, use of medications, laboratory tests at admission , and main electrocardiographic presentations. The clinical outcomes considered for analysis included the need for hemodialysis, need for mechanical ventilation, use of vasoactive drugs, sepsis, acute heart failure, arrhythmias, troponin elevation, and acute myocardial infarction (AMI).p<0.05) were included in this model. All tests were performed using PASW Statistics for Windows, version 18.0 , with a significance level of 5%, two-tailed probability, and a confidence interval of 95%.Continuous variables with normal distribution are presented as means and standard deviations, while variables with skewed distribution are presented as medians and interquartile ranges. In the univariate analysis, the unpaired t-test was used to compare the means of continuous variables between patients who died during hospitalization and those who were discharged. The Mann-Whitney test was used for variables with a skewed distribution. The chi-square test was used to compare frequencies of categorical variables with respect to death during hospitalization. Pairwise deletion was applied to remove cases with missing data. A multivariable logistic regression model was used to identify independent predictors of mortality. It consisted of variables that could be measured at hospital admission. Variables identified as significant in the univariate analyses . Overall, 12.6% of the patients tested negative for COVID-19 after clinical and laboratory re-evaluation, mainly with an alternative diagnosis of acute heart failure. Analysis of the prognosis and clinical and laboratory characteristics was performed for 180 patients with confirmed COVID-19.The mean age was 62 years (60.8% men). The most frequent comorbidities were hypertension (77.2%), diabetes (42.2%), heart failure (39.4%), and coronary artery disease (32.8%). The most commonly used medications during hospitalization were antibiotics (85.2%), oseltamivir (42.9%), corticosteroids (16.3%), and hydroxychloroquine (4.9%). For anticoagulation, 56.3% of the patients received low molecular weight or unfractionated heparin in a prophylactic dose, while 32.5% received full doses. Intermediate dose regimens of anticoagulants were used in 4.9% of the cases.Missing data at admission included those of the following laboratory variables: troponin (16.6%), brain natriuretic peptide (48.3%), D-dimer (22.2%), CRP (15%), hemoglobin (3.3%), lymphocytes (9.4%), and platelets (5.5%).The cardiology referrals revealed cardiologic complications in 77.7% of the patients diagnosed with COVID-19. The most frequent complications were decompensated heart failure, arrhythmias, and acute myocardial injury . There wThe most frequent comorbidities noted among patients with COVID-19 and cardiologic manifestations were systemic arterial hypertension (76.2%), previous heart failure (43.4%), diabetes mellitus (43.4%), stable coronary artery disease (30.1%), and obesity (20.3%). Only 6.3% of the patients had no known comorbidities.Among the 70 patients with acute heart failure, 15.7% had been diagnosed with heart failure with preserved ejection fraction and 48.6% had been diagnosed with heart failure with reduced ejection fraction.Altogether, 84 cases of troponin elevation were noted. Among these, 25% had AMI, 57.1% had non-ischemic acute myocardial injury, and 17.9% had chronic myocardial injury. Among patients with acute myocardial injury (ischemic or non-ischemic), 40.6% had been previously diagnosed with chronic coronary artery disease.All patients diagnosed with AMI underwent transthoracic echocardiography during hospitalization. Among these, 47.6% had ventricular ejection fraction below 50% with segmental dysfunction. Invasive stratification was performed using cineangiocoronariography for 13 patients, revealing plaque instability and/or intraluminal thrombus in 77% of the cases. The angiographic characteristics are shown in The triple-vessel atherosclerotic involvement pattern was found in 46.1% of the patients who underwent coronary angiography. The single-arterial pattern was observed in 23% of the patients, while 15.4% exhibited the two-arterial pattern. Angioplasty was performed in nine patients (42.8%), while others remained under medical treatment.Non-cardiac complications were frequent, highlighting the need for mechanical ventilation (39.9%), sepsis (33.7%), hemodialysis (16.3%), and use of vasoactive drugs (42.7%).On worsening of the clinical condition, 65% of the cases required intensive care unit admissionand 20.6% of the evaluated patients died. p=0.021), greater need for ventilatory support on admission , and pre-existing heart failure .For the multivariable analysis, we considered only parameters that could be measured at hospital admission. The following variables were included in the logistic regression model: age, pre-existing heart failure, chronic need for dialysis, degree of need for ventilatory support, lymphocytes, platelets, and initial troponin level . The varversus benefit ratio for patients and healthcare professionals.In the present study, we demonstrated our experience in maintaining specialized cardiology care for patients with COVID-19, ensuring supervision and teaching of resident physicians, and minimizing the risk of contamination between teams and patients. The need for isolation of COVID-19 patients involves restricting movement of patients and personnel and rationally using protective equipment. These factors hinder the usual format of in-person bedside visits by residents, preceptors, and attending physicians. In this scenario, auxiliary use of telemedicine has played an essential role in optimizing care and safeguarding health teams . Among sOur experience with referral for patients with COVID-19 enabled residents\u2019 practical and theoretical training in pathologies highly relevant to clinical practice such as acute coronary syndrome, arrhythmias, and heart failure, demonstrating that training can be achieved safely and effectively with proper adaptations ,9.In daily practice of cardiology consultation during a pandemic, challenges begin with the appropriate diagnosis of COVID-19. RT-PCR for the diagnosis of COVID-19 has exhibited an approximate sensitivity of 86% and a specificity of 96% . In pativersus 4.5%) as well as a higher incidence of severe acute respiratory syndrome (58.5% versus 14.7%), mechanical ventilation (22% versus 4.2%), and acute kidney injury (8.5% versus 0.3%) when compared with COVID-19 patients with normal troponin levels (Acute myocardial injury and differential diagnosis of acute coronary syndrome were among the most frequent reasons for referral requests. Acute myocardial injury was observed in 38.3% of the confirmed cases of COVID-19, and only a quarter of patients with troponin elevation were diagnosed with AMI. Reportedly, the general incidence of acute myocardial injury was approximately 17% among hospitalized patients and up to 59% of these patients died . Acute tn levels . The impIn the present study, AMI was confirmed in 21 patients. Altogether, 62% of patients underwent invasive stratification and only two patients did not exhibit obstructive lesions, confirming the validity of early specialized evaluation of critically ill patients with COVID-19. A Brazilian study evaluated 152 patients diagnosed with infarction and COVID-19 and demonstrated multivessel disease in 69% of the patients, with a mortality rate of 23.7%. ST-segment elevation was observed in 54.6% of the cases, and 18.4% of them had a previous diagnosis of coronary artery disease (The greatest strength of the present study is utilization of an efficient model of cardiologic referral practice in a teaching hospital. This model involved referrals for complex cases of COVID-19, with due consideration to medical care for patients as well as medical training of the residents. The exploratory statistical analysis was limited to a small inpatient population diagnosed with COVID-19. Thus, its conclusions should not be extrapolated to the majority of the population infected with SARS-CoV-2, which remains outside the hospital environment. Moreover, this study was conducted before the availability of vaccines against SARS-CoV-2, which might modify the clinical parameters and outcomes of these patients.A hybrid model involving in-person referrals with remote discussion and teaching is a viable alternative for reducing the movement of patients and personnel. It helps maintain the wellbeing of patients and health teams with less burden on care providers and ensures practical and theoretical training of cardiology residents. Patients with COVID-19 frequently present with new cardiovascular involvement or decompensation of the underlying heart disease. Specialized cardiologic evaluation is vital to assist in the management of such cases.Calderaro D was responsible for the study design. Santorio NC, Cardozo FAM, Miada RF, Pitta FG, Tavares CAM, Habrum FC, Pinesi HT, Menezes MCS and Magalh\u00e3es IR collected the data. Santorio NC, Cardozo FAM, and Miada RF were responsible for data retrieval and manuscript drafting. Calderaro D performed statistical analyses. Calderaro D and Caramelli B were responsible for reviewing the manuscript. All of the authors have approved the final version of the manuscript."} +{"text": "Black women are disproportionately diagnosed with obesity (BMI \u2265 30 kg/m2). Obesity is a preventable but complex, public health problem that is multifaceted, chronic, and approximately 58% of Black women 60 years and older are classified as obese, compared to 38% of their White counterparts. This 12 week, pre/post, 2-group study aimed to determine if a peer-informed physical activity (PA) intervention with peer support would be feasible among community- dwelling, obese, older Black women to promote regular PA. Forty-eight potential participants were screened, 24 categorized as obese were enrolled and completed the study. The mean age was 64 (SD 3.0) years. Steps were measured by a Fitbit-Inspire with data successfully collected on 98% of days with the treatment group averaging a daily increase of 700-steps more than the control. Evaluation of intervention\u2019s acceptability revealed that 100% enjoyed the study and using the Fitbit device. Text message readability was 100% and 95% said the study was motivational. Additionally, 8.3% said daily prompts were too frequent, 12% indicated that future studies should include additional social support, and 88% did not comment on the Fitbit community option for support, suggesting that this feature was not practical. Findings demonstrated that this intervention meets the criteria of being scalable, low cost, feasible, and acceptable for the older Black women. Using self-monitoring techniques in combination with at least one other behavioral strategy, such as our TOSS messages (cues for motivation) as the delivery channel for health promotion messages are a promising approach to increase PA behaviors."} +{"text": "What is the percentage of asymptomatic individuals with positive test results for SARS-CoV-2 among tested individuals and those with confirmed COVID-19 diagnosis?In this systematic review and meta-analysis of 95 unique studies with 29\u2009776\u2009306 individuals undergoing testing, the pooled percentage of asymptomatic infections was 0.25% among the tested population and 40.50% among the population with confirmed COVID-19.The high percentage of asymptomatic infections from this study highlights the potential transmission risk of asymptomatic infections in communities. This systematic review and meta-analysis evaluated the percentage of asymptomatic COVID-19 infections among individuals undergoing testing and those with confirmed infections. Asymptomatic infections are potential sources of transmission for COVID-19.To evaluate the percentage of asymptomatic infections among individuals undergoing testing (tested population) and those with confirmed COVID-19 (confirmed population).PubMed, EMBASE, and ScienceDirect were searched on February 4, 2021.Cross-sectional studies, cohort studies, case series studies, and case series on transmission reporting the number of asymptomatic infections among the tested and confirmed COVID-19 populations that were published in Chinese or English were included.This meta-analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Random-effects models were used to estimate the pooled percentage and its 95% CI. Three researchers performed the data extraction independently.The percentage of asymptomatic infections among the tested and confirmed populations.Ninety-five unique eligible studies were included, covering 29\u2009776\u2009306 individuals undergoing testing. The pooled percentage of asymptomatic infections among the tested population was 0.25% , which was higher in nursing home residents or staff , air or cruise travelers , and pregnant women . The pooled percentage of asymptomatic infections among the confirmed population was 40.50% , which was higher in pregnant women , air or cruise travelers , and nursing home residents or staff .In this meta-analysis of the percentage of asymptomatic SARS-CoV-2 infections among populations tested for and with confirmed COVID-19, the pooled percentage of asymptomatic infections was 0.25% among the tested population and 40.50% among the confirmed population. The high percentage of asymptomatic infections highlights the potential transmission risk of asymptomatic infections in communities. Presymptomatic transmission will also make temperature screening less effective.6 Only extensive testing and close contact tracing could lead to identification of more asymptomatic infections.7COVID-19, the disease caused by SARS-CoV-2, was first reported in December 2019.6 A previous study8 showed that the upper respiratory viral loads in asymptomatic patients were comparable to those in symptomatic patients. Meanwhile, the highest viral load in throat swabs at the time of symptom onset indicated that infectiousness peaked on or before symptom onset.9 Moreover, studies showed that asymptomatic infections might have contributed to transmission among households, nursing facilities, and clusters.13 As the pandemic has been contained in many countries and regions, travel restrictions have been lifted and public places have reopened. Asymptomatic infections should be considered a source of COVID-19 infections that play an important role in the spread of the virus within community as public life gradually returns to normal. The management of asymptomatic carriers was essential for preventing cluster outbreaks and transmission within a community.Unlike SARS, which had little known transmission from asymptomatic patients, evidence showed that asymptomatic patients were a potential source of transmission of COVID-19.11 varied considerably owing to different study design and study population. Thus, we conducted a meta-analysis to better understand the global percentage of asymptomatic infections among the tested and confirmed COVID-19 populations. Our results could be useful for strategies to reduce transmission by asymptomatic infections.However, comprehensive evaluation of the percentage of asymptomatic infections among the tested population and the population with confirmed COVID-19 (confirmed population) is limited. Current results from different studiesPRISMA) guideline. This review was not registered. Three researchers searched the published studies on February 4, 2021, through PubMed, EMBASE, and ScienceDirect without language restriction. The search terms used included COVID-19, coronavirus, SARS-CoV-2, asymptomatic transmission, asymptomatic infection, asymptomatic proportion, asymptomatic case, asymptomatic cases, asymptomatic contact, asymptomatic ratio, asymptomatic people, asymptomatic patients, and asymptomatic patient. The detailed search strategies are shown in eMethods 1 in the We conducted the meta-analysis following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses studies reporting the number of asymptomatic infections, tested population, and confirmed population and (2) cross-sectional studies, cohort studies, case series studies, and case series on transmission. Exclusion criteria consisted of (1) reviews, systematic reviews, and meta-analysis; (2) duplicate publications; (3) preprints; (4) multiple studies reporting on overlapping participants (the study with more information was included); (5) articles with ambiguous definition of asymptomatic infections; and (6) articles not written in English or Chinese.Asymptomatic individuals with positive test results for SARS-CoV-2 (asymptomatic infections) were defined as those who did not present any symptoms at the time of SARS-CoV-2 testing or diagnosis.15 for cross-sectional studies and the Newcastle-Ottawa scale16 for cohort studies (eMethods 2 in the 17 Two researchers (Q.L. and L.K.) performed the quality assessment independently. Disagreements were resolved by 2 other reviewers (W.J. and Y.W.). Outcomes of interest included the percentages of asymptomatic infections among the tested and the confirmed populations.Three researchers performed the data extraction independently. Data were extracted for the first author, date of publication, study location, number of tested individuals, number of individuals with confirmed COVID-19, and number of asymptomatic infections. The ratio of male to female individuals (MFR) and mean age of study participants were gathered if available. The quality of studies included in the meta-analysis was assessed using the Joanna Briggs Institute Prevalence Critical Appraisal Tool18 were used to calculate the pooled percentage and its 95% CI. The heterogeneity among studies was assessed using I2 values.19 We performed subgroup analyses by study location , countries\u2019 development level (developed vs developing), study population , publication period (June 2020 and earlier vs July 2020 and later), sample size for the tested population , sample size for the confirmed population , study design , study quality , MFR , and mean age . Publication bias was assessed by funnel plot and the Egger regression test.20 We performed 3 sensitivity analyses to test the robustness of our results, by using the Knapp-Hartung adjustments21 to calculate the 95% CIs around the pooled effects, by excluding 3 studies with a tested population more than 200\u2009000 and studies with low quality. Two-sided P < .05 indicated statistical significance. All analyses were performed using R, version 4.0.0 .We performed a meta-analysis to estimate the pooled percentage of asymptomatic infections among the tested and confirmed populations. Untransformed percentages and DerSimonian and Laird random-effects models115 were cross-sectional studies, 41 (43.16%) were cohort studies, 7 (7.37%) were case series, and 3 (3.16%) were case series on transmission studies. Thirty-five studies (36.84%) were conducted in Europe; 32 (33.68%), in North America; and 25 (26.32%), in Asia. Seventy-four studies (77.89%) were conducted in developed countries. Thirty-seven studies (38.95%) were conducted among health care workers or in-hospital patients; 17 (17.89%), among nursing home residents or staff; 14 (14.74%), among community residents; 13 (13.68%), among pregnant women; 8 (8.42%), among air or cruise travelers; and 6 (6.32%), among close contacts. Twenty-one studies (22.11%) were published in June or before; 74 (77.89%), in July and after. Forty-nine studies (51.58%) had sample size of 100 to 1000. Fifty-three studies (55.79%) were assessed as low quality; 17 (17.89%), high quality; and 25 (26.32%), moderate quality . For croI2\u2009=\u200999%; P\u2009<\u2009.001) , with high heterogeneity among studies in nursing home residents or staff, 2.02% in air or cruise travelers, 2.34% in pregnant women, 1.46% in close contacts, 0.75% in health care workers or in-hospital patients, and 0.40% in community residents. The pooled percentage of asymptomatic infections was 0.90% in Europe, 0.47% in North America, and 0.05% in Asia. The pooled percentage was higher in developed countries , studies published in July or later , studies with a sample size of less than 100 , and cohort studies . In studies with MFR of 0.5 to less than 1.0, the pooled percentage was higher . The pooled percentage was higher when the mean age of the study population was 60 years or older .108 The remaining 77 studies were included in the meta-analysis for the percentage of asymptomatic infections among the confirmed population,115 covering 19\u2009884 individuals with confirmed COVID-19, among whom 11\u2009069 had asymptomatic infections. The pooled percentage of asymptomatic infections among the confirmed population was 40.50% , with high heterogeneity among studies in pregnant women, 52.91% in air or cruise travelers, 47.53% in nursing home residents or staff, 39.74% in community residents, 30.01% in health care workers or in-hospital patients, and 26.94% in close contacts. The pooled percentage of asymptomatic infections was 46.32% in North America, 44.18% in Europe, and 27.58% in Asia. The pooled percentage was higher in developed countries , studies published in June or earlier , studies with sample size of 500 or greater , and cross-sectional studies . The pooled percentage was slightly lower for cohort studies . Among studies with MFR of 1.0 to less than 1.5, the pooled percentage was higher . The pooled percentage was higher when the mean age of the study population was younger than 20 years or 20 to 39 years .After using the Knapp-Hartung adjustments, the pooled percentage of asymptomatic infections among the tested population was 0.25% , and the 95% CI of the pooled percentage became slightly larger , which was higher than the original results. The percentage of asymptomatic infections among the confirmed population was 39.37% , which was slightly lower than the original results. After excluding 53 low-quality studies, the pooled percentage of asymptomatic infections among the tested population was 0.24% , and the percentage of asymptomatic infections among the confirmed population was 41.71% . Both percentages were similar to the original results.After excluding 3 studies with tested populations of more than 200\u2009000,z\u2009=\u200943.1725; P\u2009<\u2009.001) and for the percentage of asymptomatic infections among the confirmed population indicated that there might be publication bias.Funnel plots are shown in 36 In the sensitivity analyses, we found that the pooled percentage of asymptomatic infections among the tested population was higher than the original results after excluding studies with large sample sizes. This indicated that studies with different sample sizes were very heterogeneous. Owing to severe outcomes among older patients with COVID-19, more studies were conducted among nursing home residents or staff. Thus, asymptomatic individuals were more likely to be tested among this population. As more and more countries conducted expanded screening, studies concerning the percentage of asymptomatic infections among the general population would increase in the future.In this meta-analysis, we found that the pooled percentage of asymptomatic infections among the tested population was 0.25% , and the pooled percentage of asymptomatic infections among the confirmed population was 40.50% . At present, there are only a few meta-analyses for the percentage of asymptomatic infections among the tested population. We found that the percentage of asymptomatic infections was highest among the tested population in nursing homes and lowest among community residents. Because the percentage of asymptomatic individuals varies as a function of community prevalence, it was not available in all studies. This might be a potential driver of heterogeneity across studies. Furthermore, the percentages of asymptomatic infections among the tested population were different between studies conducted in different locations. Studies in Asia had the lowest percentage, whereas studies in other locations had higher percentages. This lower percentage in Asia might be related to the large city-wide SARS-CoV-2 nucleic acid screening program in China.14 Thus, the percentage of asymptomatic infections was lower in cohort studies, because some patients with presymptomatic findings were identified during follow-up. There were limited case series of great interest in the first months of the pandemic; however, these studies mostly traced and tested limited contacts, which contributed limited value to the evidence of the percentage of asymptomatic infections.17 Several meta-analyses concerned the percentage of asymptomatic infections among the confirmed population. Chen et al5 conducted a meta-analysis that included 104 published studies and preprints before May 13, 2020. They found that the percentage of asymptomatic individuals among those with COVID-19 was 13.34% . Unlike our study, Chen et al5 searched a Chinese database. Thus, the percentage of Chinese studies was higher in their study than in the present study. He et al14 searched PubMed and Embase before May 20, 2020, and included 41 published studies. More than 50% of the studies were from China, and the pooled percentage of asymptomatic infection was 15.6% . In our study, we only included published studies. The percentage of countries excluding China was higher than the previous meta-analysis.14 This might be the reason for the higher percentage of asymptomatic infections found in our study compared with studies conducted by Chen et al5 and He et al.14 Another meta-analysis conducted by Yanes-Lane et al17 included published studies and preprints before June 22, 2020. After quality assessment, 28 studies were of high or moderate quality and were included in the meta-analysis. The percentage of asymptomatic infection among persons with confirmed COVID-19 varied among different study populations, with the highest observed in obstetric patients .In this study, the pooled percentage of asymptomatic infections among the confirmed population was 40.50%. The pooled percentage of asymptomatic infections was 40.96% among cohort studies, which was slightly lower than that among cross-sectional studies (44.47%). The patients who developed symptoms later were mistakenly classified as having asymptomatic infection in cross-sectional studies because the observation time was not long enough.25 In addition, we found that the percentage of asymptomatic infections among the tested population was relatively low among community residents. However, the percentage of asymptomatic infection among confirmed individuals was 39.74% in communities. These findings suggest that asymptomatic infections might contribute to the transmission of SARS-CoV-2 within the community. To prevent further transmission in communities, asymptomatic individuals among the general population should be tested. If resources are limited, workers in specific industries such as air transportation should be routinely tested. In addition, we found that approximately one-third of individuals with confirmed COVID-19 were asymptomatic among health care workers or in-hospital patients. Because asymptomatic health care workers might contribute to disease spread in and out of hospitals, surveillance of asymptomatic individuals is important for infection control and transmission reduction in health care settings and community.117 Meanwhile, hand hygiene and personal protective equipment were necessary for hospital visitors.117 A previous study showed that most asymptomatic patients belong to younger groups,3 which was consistent with the findings of our study. The percentage of asymptomatic infections was higher among groups younger than 39 years than in other age groups, possibly because the young adults were more likely to show only mild or moderate clinical symptoms.5 This indicated that young adults who often presented mild or no symptoms were a potential source of transmission in the community.In our study, the percentage of asymptomatic infections among the confirmed population was 54.11% in pregnant women and 52.91% in air or cruise travelers. The percentage was 47.53% in nursing home residents or staff. This finding of a high percentage of asymptomatic infections among air or cruise travelers suggests that screening and quarantine on airport arrival is important for reducing community transmissions, especially in countries without local transmission.In the meta-analysis, we included studies published before February 3, 2021, providing the most updated pooled percentage of asymptomatic infections among tested and confirmed populations. We included countries in Africa, Asia, Europe, North America, and South America and estimated the percentage of asymptomatic infections for different populations. Our results could raise awareness among the public and policy makers and provide evidence for prevention strategies.This study has several limitations. First, we did not include preprints and therefore may have missed some relevant studies; however, we thought that the results of published studies were more reliable. Second, some relevant articles written in Chinese may not be included because we did not search Chinese literature databases such as China National Knowledge Infrastructure. Third, most studies did not follow up to identify presymptomatic and covert infections. Future studies should evaluate the percentage of these 2 types of asymptomatic infection among the confirmed population. Fourth, most studies were conducted in a specific population; thus, our findings might not be generalizable to the general population. Fifth, the heterogeneity between studies was high, which might be related to different study location, period, population, and sample size. Sixth, the Egger regression test suggested potential publication bias in this study. Because studies that did not detect asymptomatic infections were less likely to be published, our pooled percentage of asymptomatic infections might be overestimated.In this systematic review and meta-analysis, we found that the pooled percentage of asymptomatic SARS-CoV-2 infections among the tested population was 0.25%. Among the confirmed population, 40.50% of individuals had asymptomatic infections. The high percentage of asymptomatic infections highlights the potential transmission risk of asymptomatic infections in communities. Screening for asymptomatic infection is required, especially for countries and regions that have successfully controlled SARS-CoV-2. Asymptomatic infections should be under management similar to that for confirmed infections, including isolating and contact tracing."} +{"text": "Pregnancy and postpartum are critical periods for patients with neurological complications. In this study, we aimed to evaluate the clinical characteristics and outcome of pregnant women with neurological conditions. This cross-sectional study reviewed pregnant women with neurological signs and symptoms, who were registered in the Medical Care Monitoring Center (MCMC) database of Shiraz University of Medical Sciences 2013-15. A questionnaire was designed to record each patient\u2019s information including demographic variables, past medical history, clinical presentation, obstetric profile, and fetal/maternal outcomes. Totally, 332 mothers were registered in the database. The main neurological complaints in our population were headache, seizure, unilateral neurological symptoms, multiple sclerosis, neuromuscular disorder, and brain tumor. More than half of the patients (54%) experienced headache during the pregnancy and postpartum period. Evaluating the neurological disorders separately, based on the time of symptom onset indicates the importance of follow-up of mothers during peripartum. Our findings suggest that decisions for pregnancy in women with neurological disorders should be based on risks outweighing for the mother and the fetus, particularly regarding the pharmacological side effects. Pregnancy and postpartum are critical periods in developing neurologic complications. These periods are associated with significant physiological and hormonal changes in women, which might cause relapse or remission of previous neurological disorders or cause a new one , 2; apprThis cross-sectional study was performed among high-risk mothers with neurological signs or symptoms while pregnant or six weeks postpartum. We collected the data from the MCMC registry system, which was launched in 2012 to record and promote the health of at-risk pregnant women. A pregnancy in which the risk of maternal and fetal mortality and disability is more than normal, considered as a high-risk pregnancy. In this system, demographic and clinical features of all pregnant women with positive free-beta-human chorionic gonadotropin (free-beta-hCG) test and a fetal/maternal life-threatening disease that required hospital admission (previous or newly diagnosed disorders) was recorded. We designed a questionnaire including set of demographic variables, obstetric profile , past medical history, clinical characteristics , as well as fetal and maternal outcomes . In addition, patients were followed-up for 6 weeks after delivery, using a phone call or in-person interviews in case if they were accessible. Before commencing the study, verbal consent was obtained from all participants. Variables were analyzed using statistical package for Social Sciences, version 16.0 and presented as counts and percentages.A total of 705\u00a0at-risk pregnant women had registered in MCMC from April 2013 till November 2015, out of which, 332 patients had the inclusion criteria. The mean age of patients was 29.32 years old. More than half of the patients (54%) experienced headaches during their pregnancy and postpartum period. Sixty-six percent developed primary headaches (mainly migraine and tension headaches). The remaining headaches were secondary to infection and preeclampsia (34%). Twenty percent of all headaches occurred during the first trimester, 20% in the second and 28% in the third trimester. Also, 1% occurred at the time of giving birth or after birth, and finally 31% during their postpartum period. Gestational hypertension and gestational diabetes were the most common pregnancy complications in patients with headaches, which was observed in 19.5% and 10%, respectively. Regarding maternal and fetal outcomes, 80% of infants were born healthy at term gestation, while 20% were aborted. Also, 83% of the pregnant women with headaches gave birth at term gestation, out of which, 65% were delivered by cesarean\u00a0section (C/S) and the reaming (35%) were born via normal vaginal delivery (NVD). Three percent of mothers experienced decreased levels of consciousness or coma. The prevalence of preterm labor in mothers with headache was 8%. Amongst these mothers, stillbirth and congenital anomalies were observed in 0.6% of newborns.The seizure was observed in 17.2 % of pregnant women, and 67% of patients with seizures had the previous history of epilepsy. Regarding seizure occurrence time, 27% of women experienced seizure in their postpartum period. The rate of seizure in the first, second, and third trimester was 3%, 19%, and 22%, respectively. Eclampsia accounted for 16% of these seizures, 9% was drug-induced, and 4% occurred without any specific cause. Hypertensive disorder of pregnancy and gestational diabetes were observed in 25% and 9% of patients with seizure. About 73% of neonates were born healthy at term. The rate of NVD and C/S was 37% and 63%. Abortion, preterm birth, and stillbirth occurred in 5.5%, 2%, and 11% of our study population.About 12% of pregnant women in our study were hospitalized due to unilateral neurological symptoms, of which, 73% had cerebral venous sinus thrombosis (CVST), 7.5% had ischemic stroke and 20% had cerebral hemorrhage . Gestational hypertensive disorders and diabetes were observed in 15% and 7.5% of the patients. About 13% of pregnant women with unilateral neurological symptoms were presented with a decreased level of consciousness or coma. About 73% of neonates were born healthy at term. Twenty-one percent of neonates were born by NVD and 79% via C/S. Abortion, preterm delivery, and stillbirth occurred in 2.5%, 5%, and 7.5% of our patients, respectively. The rate of these symptoms in the first, second, and third trimester was 8%, 19.5%, and 26%, respectively. About 5% of these symptoms occurred during delivery and 50% in postpartum.About 4.5% of pregnant women in this study had MS. Near 13% of them were new cases and all were diagnosed in the first trimester of pregnancy. Gestational diabetes was observed in 7% of these patients, but none had gestational hypertension. The rate of abortion was 20% and no stillbirth, preterm delivery or congenital anomalies were observed amongst our patients. Eighty percent of the infants were born at term, out of which, 67% were born via C/S and 33% by NVD.via C/S and one by NVD. No neonatal and maternal complications were observed in this group.About 4.5% of our patients suffered from peripheral neuromuscular diseases. Four patients had myasthenia gravis (MG), and one had Guillen-barre syndrome (GBS). Neither Carpal tunnel syndrome (CTS) nor Bell\u2019s palsy was observed in our population. About half of these patients (50%) reported having a positive history of neuromusculardisorders before pregnancy and the remaining developed neuromusculardisorders symptoms in the second trimester of their pregnancy for the first time. Symptoms of the newly diagnosed patients were exacerbated during six months follow-up. All the infants were born healthy at term. Four neonates were born Two cases in our population had brain tumor, and one had gestational diabetes. One infant was delivered at term while the other was delivered preterm, and both were delivered via C/S. The onset of symptoms was in the first and the second trimesters for both patients.et al. (2004) and in a study by Brook et al. (2001), deterioration of GBS during postpartum follow-up were reported, too [In this study, major neurological complaints were classified as headache, seizure, unilateral neurological symptoms, multiple sclerosis, neuromuscular disorder, and brain tumor. Amongst mothers, the headache was the most common neurologic symptom, referring to Shiraz health centers. Primary headache was observed in two-third of mothers, that were alleviated during pregnancy with minimum intervention. Secondary headaches occurred in one-third of patients while infection and preeclampsia were the main causes. Typically, primary headaches diminish during pregnancy, but in many cases, headaches begin or worsen in this period . As prevted, too , 29. MG ted, too , 31. TwoNeurological disorders are frequent during pregnancy. Migraine, seizure, benign intracranial hypertension and cerebral venous and sinus thrombosis are the most common neurological disorders in this period. The investigation, diagnosis, and management of neurological disorders during pregnancy is particularly challenging and requires multidisciplinary team, including neurologist, obstetrician and gynecologist, neurosurgeon, and pharmacologist.This study was financially supported by\u00a0Shiraz University of Medical Sciences\u00a0(grant number:\u00a01396-01-67-16182). The authors wish to thank Mr. H. Argasi at the Research Consultation Center (RCC) of Shiraz University of Medical Sciences for his invaluable assistance in editing this manuscript.The authors declare no conflict of interest in this study."} +{"text": "Indications for repositioning included acute flap dislocation (35.7%) and visually significant striae (64.3%). High myopia and patient age over 50 years were the strongest risk factors for these complications. Prior to flap repositioning, uncorrected distance visual acuity (UDVA) of 20/20 or better and 20/40 or better occurred in 19% and 57% of eyes, respectively. After repositioning, a final UDVA of 20/20 or better and 20/40 or better occurred in 78% and 98% of eyes, respectively. After repositioning, one line of UDVA was lost in two eyes (2.8%) and two lines were lost in one eye (1.4%). Risk factors for acute flap dislocation included high myopia and age over 50 years. Flap repositioning was effective in salvaging visual outcomes.Although the use of femtosecond lasers instead of mechanical devices has decreased the incidence of flap complications following laser-assisted in situ keratomileusis (LASIK), dislocations and striae still occur. Flap repositioning is an effective intervention to improve visual outcomes after acute flap complications in both microkeratome-assisted and femtosecond-assisted LASIK. This retrospective case series included patients undergoing flap repositioning secondary to acute flap dislocation and/or visually significant striae within the first two weeks following femtosecond LASIK (FS-LASIK) from 2015 to 2020 at a single institution. Preoperative, intraoperative, and postoperative de-identified data were analyzed for incidence, risk factors, and visual acuity outcomes. The incidence of flap repositioning was 0.35% in 21,536 eyes ( Laser-assisted in situ keratomileusis (LASIK) is currently the most commonly performed refractive surgery in the United States, and visually significant complications are rare. Studies on the quality of life after LASIK surgery have shown that 96% of patients have an uncorrected distance visual acuity (UDVA) of 20/20 or better three months after surgery. Flap complications may require additional intervention to restore baseline corrected distance visual acuity (CDVA). The most common visually significant flap complications in the early postoperative period are striae and acute flap dislocation ,2.Technological advances in LASIK surgery, such as replacing the microkeratome with femtosecond lasers (FS-LASIK) for flap creation, have increased the precision of flap creation ,4, increRetrospective chart review of all patients who underwent LASIK or enhancement of a prior LASIK procedure at Hoopes Vision between 1 January 2015 and 1 June 2020 was completed. Four different surgeons performed the LASIK procedures at a single site. The creation of the corneal flap was performed using the following femtosecond lasers based on surgeon preference: WaveLight FS200 , Zeiss VisuMax , or AMO iFS . This study involved de-identified patient data, adhered to the tenets of the Declaration of Helsinki, and was approved by the Hoopes Vision Ethics Review Board. The patients signed an informed consent for the use of their data in research prior to surgery. Brany IRB approved the exemption for this retrospective study.Eyes requiring FR in the acute postoperative period were retrospectively identified. Only patients with a history of acute flap dislocation or visually significant striae who underwent FR within 14 days of the initial procedure were included in this study. Therefore, patients requiring FR secondary to post-LASIK trauma, interface debris, or diffuse lamellar keratitis (DLK) were excluded from this study. For patients who required bilateral FR, each eye was considered independently in data analysis. Indications for FR included visually significant microstriae, macrostriae, flap wrinkles, asymmetrical gutter, flap misalignment, flap dislocation, and flap dislodgement. Mechanical complications were classified into two groups: acute flap dislocation and striae. Slit lamp findings of flap wrinkles, asymmetrical gutter, misalignment, and dislodgement were all considered stages of flap dislocation when followed by FR procedures. Additionally, a large-volume control cohort composed of eyes undergoing LASIK from 1 January 2015 to 1 June 2020 at our facility without acute flap dislocations or striae was used for comparing preoperative and intraoperative risk factors. Some of the eyes in the control group did have other complications, including traumatic flap dislocation, epithelial ingrowth, and DLK. For age analysis, the control cohort was limited to patients aged 20 to 59 years.The AMO iFS , WaveLight FS200 , and Zeiss VisuMax femtosecond laser systems were used for flap creation, while the WaveLight EX500 excimer laser system was used for stromal ablation with a 6.0\u20136.5 mm central optical zone and blend zone to 8.5\u20139.0 mm. Flap diameter was between 8.5 and 9.0 mm, and flap thickness was between 100 and 115 \u00b5m with the creation of a superior hinge. The postoperative treatment protocol included ofloxacin 0.3% or moxifloxacin 0.5% four times a day for one week. Patients were instructed to apply prednisolone acetate 1% every 1\u20132 h while awake for the first 24 h. On the first postoperative day, the prednisolone was decreased to four times daily for one week and subsequently discontinued.The flap edge was identified at the slit lamp using a Sinskey hook. The patient was taken to the operating microscope where they underwent draping with sterile technique. The flap was lifted and reflected superiorly with non-toothed forceps. A cellulose sponge was used to reflect any encroaching epithelium from the exposed stromal bed. Using a 27-gauge LASIK cannula, the flap was placed in the appropriate position and refloated to remove any debris and ensure proper alignment. For patients with significant macrostriae, the epithelium was debrided over the affected area. An 8.4 mm base curve bandage contact lens was placed after the procedure and then removed one week postoperatively. Patients were then strongly encouraged to avoid touching their eyes and to remain compliant with eye shield use.Preoperative clinical data that were collected included the date of LASIK, age, sex, pre-LASIK medical and ophthalmic conditions, pre-LASIK systemic and ophthalmic medications, smoking status, pre-LASIK manifest refraction, UDVA, CDVA, uncorrected near visual acuity (UNVA), keratometry, and pachymetry. Age, sex, pre-LASIK UDVA, pre-LASIK CDVA, and manifest refraction were analyzed as possible risk factors for dislocation by comparison with the control cohort consisting of a random collection of eyes with no postoperative complications during the same time frame. Intraoperative parameters included femtosecond laser used, flap diameter, flap thickness, and surgery end time. Postoperative UDVA, CDVA, UNVA, and manifest refraction were recorded at one, three, six, and twelve months after LASIK.2 test were used to compare nominal outcomes when appropriate. A two-sided p-value of less than or equal to 0.05 was deemed statistically significant. Variables potentially associated with an increased likelihood of FR were investigated in a multivariable logistic regression. A p-value of less than or equal to 0.05 was deemed statistically significant. We used the standard nine graphs to report outcomes following refractive surgery.Statistical analysis was performed using Microsoft Excel and R Statistics . The nonparametric Mann\u2013Whitney test for independent samples was used to compare continuous outcomes. Fisher\u2019s exact test and \u03c7n = 64) , 70 eyes required FR due to acute flap dislocation and striae for an overall incidence of 0.35%. The incidence of visually significant striae was 0.21%, and that of acute flap dislocation was 0.12%. The median age of the patients undergoing FR was 35 years . At the n = 64) .p < 0.001) , but the range of the sphere and SEQ was greater in the control cohort, indicating that eyes with greater degrees of myopia did undergo FS-LASIK surgery without complications (p = 0.001). No other measured factors, including gender, laterality of affected eye, different femtosecond laser used, performing surgeon, preoperative keratometry, or diopters of cylinder, showed a statistically significant difference between the FR group and the control group.< 0.001) . The aveications . Table 2p = 0.001) (p = 0.001) (= 0.001) . Patient= 0.001) .Preoperative CDVA of 20/20 or better was seen in 98% of eyes. At diagnosis of flap dislocation, 16% of eyes had an UDVA of 20/20 or better, with 53% having an UDVA of 20/40 or better. One month following FR, 67% of eyes had an UDVA of 20/20 or better, with 100% having an UDVA of 20/40 or better. Three months following FR, 65% of eyes had an UDVA of 20/20 or better, with 96% having an UDVA of 20/40 or better. A final UDVA of 20/20 or better and 20/40 or better was reached within 12 months in 74% and 98% of FR eyes with a plano target, respectively A. SEQ wiThis study adds to the literature on the visual outcomes of eyes undergoing a flap repositioning procedure for acute flap dislocation and striae secondary to FS-LASIK ,9,10,11.It is worth noting that the criteria for diagnosis and classification of flap dislocation and striae can vary widely among clinicians. We included asymmetrical gutter, flap misalignment, flap dislocation, and flap dislodgement, but other studies have additionally included buttonholes, torn flaps, and flap dislocations outside of the time period measured in this study . There aIn this study, there was no significant difference in the incidence of acute flap dislocation or striae from year to year. In contrast, Mimouni et al. described inter-surgeon variability in complication rates and decreasing complication rates year to year as they performed more FS-LASIK procedures .In our population, there was also no statistical difference in dislocation rates between surgeons or between different femtosecond laser models . This isHigh myopia is an established risk factor for acute flap dislocation, although dislocations remain rare even among high myopes . Our datPatients 50 years and older were significantly more likely to suffer acute flap dislocations . PreviouThe correlation between the incidence of dry eye and age is well documented in the literature ,28,29,30Changes in the ability of the flap to adhere may also contribute to flap dislocation. Keratocytes play a crucial role in corneal wound healing by secreting growth factors and producing collagen ,33,34,35Flap repositioning procedures following FS-LASIK successfully salvaged CDVA equal to or better than that measured preoperatively in 94.5% of patients suffering from acute flap dislocation or striae. This rate is similar to that seen in a study on LASIK using a microkeratome, in which a 92.6% safety index was achieved [In our study, four eyes (5.7%) lost one or more Snellen lines of CDVA, with one eye losing two lines of CDVA and three eyes losing one line of CDVA. Of these four eyes, two had a preoperative CDVA of 20/15 with a postoperative CDVA of 20/20. However, it is important to note that the examiner may not always check beyond the 20/20 Snellen line, which could account for the apparent reduction in CDVA in eyes with a preoperative CDVA of 20/15. It is also important to note that a large angle of error of refractive astigmatism was found in three out of four of these eyes, which could account for the reduction in perceived CDVA. Overall, we conclude that patients suffering acute flap dislocation or visually significant striae following FS-LASIK are unlikely to lose visual acuity if the flap is repositioned.In our study, 69% of eyes undergoing FR had an efficacious outcome, defined as final UDVA equal to or better than pre-LASIK CDVA B. Our reThe external validity of this study may be limited due to the data collection occurring at only one center and possible inter-patient variability between study groups. Another limitation in our study is that 27% of our patients were lost to follow-up before reaching the 12-month postoperative mark. Further directions include performing a multivariate analysis of total ablation depth and percent tissue altered in FS-LASIK as potential risk factors for flap dislocation. Flap repositioning led to satisfactory visual outcomes in cases of acute non-traumatic flap dislocation following FS-LASIK. Significant risk factors for acute dislocation were high myopia (greater than \u22126.0 D) and age over 50 years. No other preoperative, intraoperative, or postoperative risk factors were associated with increased risk of acute flap dislocation."} +{"text": "Background & Objectives: Anaemia has been reported to be associated with adverse pregnancy outcomes, especially when presenting in the last trimester. In addition to prevalent common causes of anaemia in pregnant women, poor replenishment of iron stores after a pregnancy event is specific to women with higher birth orders. Anaemic women presenting in the third trimester are more prone to maternal complications such as infections, toxaemia, antepartum haemorrhage, cardiac failure, pre-eclampsia as well as fetal hazards too such as low birth weight, pre-term deliveries, developmental anomalies, and even neonatal death. When presented near term there are higher chances of feto-maternal morbidity and mortality. In the current study, analysis is done of feto-maternal outcomes, routes of delivery of women, causes of anaemia in multigravida women in the third trimester suffering from moderate to severe anaemia in a tertiary care centre of Western Rajasthan of India.Methods: A prospective observational clinical study was conducted on patients attending Geetanjali Hospital over a period of 18 months. A total of 70 consecutive multigravida pregnant women having moderate to severe anaemia in the third trimester were selected. Statistical analysis of the data collected was done and a p-value <0.05 was taken as significant.Results: Moderate and severe anaemia in the study population were 44.28% and 55.71%, respectively. The mean haemoglobin level of all study groups was 7.0 gm%. Pre-eclampsia, placenta praevia, postpartum haemorrhage (PPH), congestive cardiac failure (CHF), neonatal intensive care unit (NICU) admission, preterm birth (PTB), low birth weight (LBW), intrauterine death (IUD), low Appearance, Pulse, Grimace, Activity, and Respiration (APGAR) score, and birth asphyxia records were investigated. Of the patients studied, 18.57% had PPH, 15.71% had pre-eclampsia, 8.57% had IUD, and 37.14% newborns were LBW.Interpretations and Conclusion: Multiparity itself is a major risk factor of anemia. Anemia presenting in the third trimester of pregnancy is a proxy indicator of care received by gravid women in the early antenatal period. In combination, a multigravida in the third trimester with less time to restock iron and vitamin stores\u00a0may result in considerable maternal as well as perinatal mortality and morbidity. Anaemia is defined by the WHO as haemoglobin level \u2264 11 g/dl in pregnant women [Factors contributing to anaemia in obstetrics are: increased physiological and fetal demands, inadequate intake, poor absorption due to endemic diseases, viz., malaria, hookworm infestation, and blood loss because of multiple pregnancy losses or during and after labour\u00a0. All iroAnaemia in pregnancy gives rise to a plethora of maternal and fetal health issues. It can lead to multiple abortions, pre-eclampsia, recurrent infections, antepartum haemorrhage, cardiac failure in the antenatal period. Post-partum haemorrhage (PPH), wound gaping, delayed involution, and puerperal sepsis diminish the joy of the postpartum period. Few among the multitude of hazards faced by the foetus are intra-uterine growth retardation, intrauterine death (IUD), preterm birth (PTB), low birth weight (LBW), neonatal morbidity , and even neonatal mortality. There is a paucity of studies focussing on third-trimester anaemia in multigravida women. The current study analyses causes, risk factors, frequency, and feto-maternal outcomes of moderate to severe anaemia (according to WHO guidelines) in third-trimester multigravida pregnancy\u00a0.This was a hospital-based prospective and observational analytical study conducted in the department of Obstetrics and Gynaecology at Geetanjali Medical College and Hospital, Udaipur. Out of 93 women enrolled for this probe, 23 women were lost to follow-up. A total of 70 multigravida\u00a0women reporting to the antenatal clinic in the third trimester having clinical/laboratory signs of moderate to severe anaemia were taken as study subjects. The study duration was 18 months from February 2019 to July 2020. Human Research and Ethics Committee, Udaipur, Rajasthan, issued approval GU/HREC/EC/2019/606.The study aimed to study the frequency, causes, risk factors, maternal and fetal outcome of moderate to severe anaemia in third-trimester multigravida pregnancy. Out of the total patients during the study duration, the current study included all the women who fulfilled the inclusion criterion: multigravida females (gravida 3 and more) of 28 to 40 weeks of gestation having clinical features suggestive of moderate to severe anaemia with Hb 7.1 - 9 gm% (moderate) and \u2264 7 gm% (severe) anaemia, giving informed consent to participate in the study. Exclusion criteria were antenatal females of <28 weeks of gestation not willing to follow up. The women were interviewed in their own language in full detail regarding age, literacy, socioeconomic status , diet, etc. Proforma was prepared in English, which was clinician-administered and translated to local language while delivering. It was validated internally. Pregnancy details regarding significant past and family history were noted. A thorough general physical, systematic, and obstetrical examination was conducted for each subject.\u00a0The approach to anaemia included identification of the type of anaemia. History of poor dietary intake, strictly vegetarian diet, smoking, alcoholism, pagophagia, bleeding haemorrhoids, gastric bypass surgery, any chronic illness such as tuberculosis/malaria/diabetes/chronic kidney disease, intake of drugs such as deworming agents, phenytoin, phenobarbitone, and trimethoprim-sulphamethoxazole, and complaints of easy fatiguability or weakness was elicited. Previous pregnancy ailments were interrogated such as anaemia, puerperal sepsis, pre-eclampsia, and blood transfusion. Pallor, glossitis, splenomegaly, jaundice were noticed on general physical examination. RBC indices - haemoglobin/hematocrit level, mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC) simultaneous with peripheral blood film were analysed. In peripheral blood film (PBF), microcytic hypochromasia, anisopoikilocytes, megaloblasts, target cells, Howell-Jolly bodies, sickle-shaped cells, and malarial parasite were searched for. Raised serum transferrin level pointed towards iron deficiency anaemia and low serum Iron levels taken were <60 microgram/mL. When iron levels were found high, haemoglobin electrophoresis was done together with PBF to draw a distinction between thalassemia and sickle cell disease. Serum ferritin levels <30 micrograms/L\u00a0taken as the earliest marker of depleted iron stores. Also, it aided to differentiate between anaemia of chronic disease from\u00a0iron deficiency anaemia. Plasma bilirubin and plasma haptoglobin were sent to identify haemolytic anaemia. Urine microscopy was done. Stool examination for occult blood was conducted for hookworm infestations. Leukocyte count, RBC count, platelet count and reticulocyte count helped to discern leukaemias. The fetal wellbeing was ensured by obstetrical examination as well as ultrasonogram on admission.All the study subjects were carefully followed in the antepartum, intrapartum, and postpartum periods . Dietary sources of iron were discussed in detail and assertions were made for regular use of hematinics. Enquiries were made regarding new symptoms, which were confirmed by clinical examination or laboratory investigations to detect the obstetrical and neonatal difficulties due to anaemia at the earliest. Women\u00a0in labour were carefully monitored and progress of labour was noted. They were also\u00a0watched for any obstetric or medical complexity, which was dealt with efficiently. Blood transfusion was the commonest mode of treatment resorted to in severe anaemia cases and was done in antepartum, intrapartum, or postpartum periods. Utmost care was exercised to prevent the complications of blood transfusion. Blood components were used in all the cases. Finally, the mode of delivery, operative intervention, maternal morbidity and mortality were recorded in all the study subjects.Breastfeeding was encouraged immediate post-partum. Emphasis was laid on the maintenance of personal hygiene and early ambulation to avoid complications in the puerperium. The perinatal outcome were taken note of. The weight of newborns and their Appearance, Pulse, Grimace, Activity, and Respiration (APGAR) scores at one and five min were documented. The neonate was attended by the paediatrician to detect the complications of severe anaemia. The outcome was judged by analysis of the above data.Need for sterilization was addressed during antenatal visits in all females. Willing participants were guided accordingly. Advice was given regarding the need for continuous use of haematinics for a minimum period of six months post-partum.\u00a0Importance of the same was explained to the patient as well as available family members.Data entry was done in Microsoft Excel Windows 10 . Data Analysis was done with IBM SPSS Statistics for Windows, Version 21.0 . Analysis of data was\u00a0done with percentage, proportion, mean, and using Chi-square test and Fischer exact test. p-value <.05 is taken as significant.As shown in Table Menstrual cycle was regular in 78.57% of the cases. In the present study, menstrual history was not taken as significant. This was because some\u00a0women in the study group were not able to tell history accurately due to general ill health or lack of menstrual cycles with lactational amenorrhea continuing as pregnancy amenorrhea.In terms of diet, 71.43% of subjects were vegetarian and around 29% were non-vegetarian or with mixed dietary habits. Symptoms suggestive of fatigue was experienced by 64.29% of the anaemic women. The common symptoms were loss of appetite (52.86%), fever (52.86%), dyspnea/palpitation (47.14%), pedal edema (45.71%) and headache/giddiness (40%). In the study subjects, moderate anaemia was 44.28% and severe anaemia was 55.71%. The mean haemoglobin level of all study groups was 7.0 gm%. Maximum haemoglobin value was 8.4 gm% and minimum was 4.6 gm%Complete blood count with peripheral blood smear in 34.29% was analysed as iron deficiency anaemia and dimorphic anaemia in 61.42%. The current study reported no case of megaloblastic anaemia. G6PD deficiency is not routinely screened, and the current probe encountered no patient with it. Significant bacteriuria was found in 17.14% of study subjects. Anaemia decreases the immunity of the mother and therefore predisposes to infections. Hookworm/roundworm infestations were seen in 5.71%. They were given deworming doses of anthelmintic agents. As shown in Table Of the babies, 35.71% had PTB, 37.14% were LBW, 8.57% had IUD, 15.71% had low APGAR at one minute, 14.28% had low APGAR at five minutes, 7.14% had birth asphyxia, 8.57% had meconium aspiration syndrome (MAS), 17.14% had respiratory distress syndrome (RDS), 47.14% had NICU\u00a0admission, mostly with severe anaemia . No maternal mortality was reported in the study. Fetal morbidity following the same pattern was more with severe anaemia (53.84%).Anaemia in pregnancy is an important preventable cause of feto-maternal\u00a0morbidity and mortality. Studies have demonstrated differences in outcomes in iron deficiency as compared to physiological anaemia of pregnancy. In India, especially in low socioeconomic settings, it is common to see patients with anaemia presenting late in pregnancy with no prior antenatal care. The same was evident in this study, where a vast majority of women were anaemic at delivery. As it is estimated by WHO, there are over 6.3 million\u00a0perinatal deaths per year globally, almost all of\u00a0which occur in developing countries, and 27% of them in the least developed countries alone [In the present study, the majority of the study subjects belonged to the age group of 30-34 years (37.14%). Omote et al. observed maximum participants in the 31- 40 years category [In our study, 64.28% of the women belonged to the lower socioeconomic status group. In the study by Devi et al.,\u00a088.82% of study subjects were of lower socioeconomic class . AlthougThe present study found the commonest type of anaemia to be microcytic hypochromic anaemia mainly followed by dimorphic anaemia. Similar results were found with Singh et al. . A predoIn the current study, 50% of women had a caesarean section and 47.14% had a vaginal delivery. Indications of caesarean section were obstetric only: cephalo-pelvic disproportion, fetal distress, malpresentation, mal-rotation, and non-progress of labour. Strangely, among all severe anaemic women, 53.84% were delivered vaginally. This confirms that the mode of delivery in anaemia is\u00a0dependent only on obstetric indications.In the present study, 70% (49/70) subjects were given blood transfusion (46 of these 49 blood transfusions were given to mothers having severe anemia) and 32.85% were given IV iron. The majority (44.28% (31/70)) had blood transfusion due to moderate and severe anaemia in the antepartum period. It is important to highlight here that our institution is designated to aid in blood transfusions to pregnant women as per state government maternal health schemes. Also, a specific group of multiparous women in the third trimester was investigated. At the same time, despite belonging to lower socioeconomic status with high illiteracy, the current research had a higher antenatal booking. Moderate to severe anaemia in close proximity to delivery interval mandates transfusing blood for optimum feto-maternal outcomes. Similarly, a study by Catherine Smith et al. observed more transfusions in moderate to severe anaemia [Preterm labour was experienced by 40% of women. It is comparable from the data of Devi et al. in which 44.68% had preterm labour .Talking about the maternal outcomes, 15.71% had pre-eclampsia, which was comparable with Singh et al. (16.1%) ; 4.28% hAs there is reduced oxygen-carrying capacity due to low haemoglobin, fetal distress ensues. Due to the activation of hypothalamo-pituitary axis of the foetus, the onset of labour occurs, mostly before term. It was observed that 35.71% of the deliveries were PTB and consequently LBW (37.14%). Figueiredo et al. found similar results with a 38% higher risk of having children with low/insufficient weight at birth in pregnant women with anaemia . Our obsFoetus, as well as neonates of anaemic mothers, suffer from a myriad of conditions due to low haemoglobin/low oxygen intrauterine habitat. Distress in utero was evident by birth asphyxia (7.14%), MAS (8.57%), RDS (17.14%), which was comparable with the study of Miglani et al. in which 8.6% had birth asphyxia, 7.5% had MAS, and 13.9% had RDS . SuryanaThe limitations of the current analysis are that it is a single hospital-based study. Also, the place of study is a tertiary care setting which usually gets complicated pregnancies, which might be a bias. Future recommendations are to conduct a community-based survey.Secondary prevention in multiparous antenatal women can be made possible by early diagnosis and treatment of anaemia. Efforts must be made to diagnose and treat anaemia in the third trimester to decrease length of hospital stay and reduce maternal and neonatal morbidity and mortality. Strategies such as food fortification, mandatory iron, and folic acid supplementation, deworming, and diligent applications of national health programmes should be done. Counseling women, spouses, families, and society on the causes and outcomes of anaemia during pregnancy and after childbirth may help the cause in the long run and enhance public health."} +{"text": "Our study outlines the prevalence of nutritional deficiencies in an orthopaedic trauma population and identifies areas for possible targeted supplementation to decrease wound complications.Macro- and micronutrients play important roles in the biological wound-healing pathway. Although deficiencies may potentially affect orthopaedic trauma patient outcomes, data on nutritional deficiencies in orthopaedic trauma patients remain limited in the literature. The purpose of this study was to (1) evaluate the prevalence of macro- and micronutrient deficiencies in orthopaedic trauma patients with lower extremity fractures and (2) evaluate the impact of such deficiencies on surgical site complications. This retrospective study identified 867 patients with lower extremity fractures treated with surgical fixation from 2019 to 2020. Data recorded included albumin, prealbumin, protein, vitamins A/C/D, magnesium, phosphorus, transferrin and zinc, as well as wound complications. Nutritional deficiencies were found for prealbumin, albumin and transferrin at 50.5%, 23.4% and 48.5%, respectively. Furthermore, a high prevalence of micronutrient deficiencies was observed. We also recorded a statistically significant difference in wound complications in patients who were deficient in prealbumin (21.6% vs. 6.6%, The important role of nutrition in wound healing has been well documented in the literature, with macro- and micronutrients considered vital at every step of the wound healing pathway ,2,3. UnfPrevious literature has demonstrated that malnutrition, as defined by hypoalbuminemia, is common in the orthopaedic trauma population . MoreoveEven fewer studies have looked at the prevalence of micronutrient deficiencies in orthopaedic trauma patients. Among elderly hospitalized patients, vitamins C and D are commonly deficient ,16; howeThe purpose of this study is to (1) evaluate the prevalence of macro- and micronutrient deficiencies in orthopaedic trauma patients with lower extremity fractures and (2) evaluate the impact of such deficiencies on surgical site complications in patients with high-risk lower extremity fractures. Our hypothesis is that deficiencies are common in the orthopaedic trauma population, and these deficiencies may be associated with an increase in surgical site complications in high-risk lower extremity fractures.This study is a retrospective database analysis of orthopaedic trauma patients undergoing surgical fixation of their lower extremity fractures treated at a university-based level 1 trauma center between the years of 2019 and 2020. The study protocol was approved by our Institutional Review Board, and data collection, methods and analysis were performed in accordance with their rules and regulations. Inclusion criteria were patients over 18 years old with a minimum of 3 months follow-up and lower extremity fractures, identified through our electronic medical record system using the coding database. Patients were identified using the OTA classification system to include femur, tibia, tibia/fibula, fibula, talus, calcaneus and foot fractures. Subjects were excluded if they were under 18 years old, mentally or cognitively impaired, prisoners, or if they presented with a pathologic fracture, as well as those with less than 3 months follow-up.Demographic data included age, gender, race/ethnicity, BMI, and the American Society of Anesthesiologists scale , as wellSecondary clinical outcome measures were tracked through a review of inpatient and outpatient charts and included data on wound complications and surgical complications .The statistical analysis was performed using SAS software version 9.4 . Categorical variables are summarized as count and percent. Chi-squared and Fisher\u2019s exact test were used to calculate differences for categorical variables. All tests were conducted at the alpha level of 0.05.We identified 867 patients who met the inclusion criteria. Of these patients, 28.7% were age 65 or older. There were slightly more male patients (56.9%) compared to female patients. A majority of patients identified as White (95.6%) or Hispanic/Latino (62.1%). Finally, nearly 40% of patients were obese, as defined by BMI \u2265 30 .Albumin was measured for 745 patients, and of these, 23.4% were malnourished, as defined by albumin < 3.5 g/dL. Approximately half of the patients were deficient in prealbumin (50.5%). Finally, nearly half of the patients (48.5%) were deficient in transferrin.Of those patients who had micronutrient data measured, 35.4% were deficient in vitamin A, 54.4% were deficient in vitamin C, and 75% were deficient in vitamin D. Over half of the patients were deficient in zinc (56.5% of patients). We did not observe significant deficiencies in magnesium, selenium or vitamin K .p = 0.0153). A similar trend was recorded with age and albumin, where 37% of patients over 65 years old were deficient, compared to 17.7% of patients under 65 years old (p < 0.0001). Compared to younger patients, patients over 65 years old were also at increased risk of deficiency in serum protein and transferrin . With regards to age-related differences in micronutrients, patients over 65 years old were not at increased risk of deficiency in vitamins A, C, or zinc. Additionally, advanced age was protective against vitamin D deficiency, as 84.7% of younger patients had vitamin D deficiency, compared to 59.0% of patients over 65 (p < 0.0001).There were significant differences in nutritional deficiencies between demographic groups. Of the patients 65 and older, 83.3% were deficient in prealbumin, compared to only 46.0% of patients younger than 65 years old (p = 0.0015). Micronutrient data showed that Hispanic patients were more likely to be vitamin D deficient than non-Hispanic patients . We did not observe statistically significant differences between these demographic groups in the remaining serum markers.Females were more likely to be deficient in albumin (29.2%) compared to males . Vitamin C deficiency was also associated with wound complications; where 56.8% sustained a wound complication, compared to only 28.6% with normal vitamin C levels (p = 0.0236).To measure the rate of wound complications, we assessed the data at the fracture level, identifying 1008 individual lower extremity fractures, 181 (18.0%) of which had a wound complication. Low prealbumin was associated with a statistically significant difference in wound complications. We found that 21.6% of fractures with a prealbumin deficiency had a wound complication, compared to 6.6% of those with normal prealbumin levels understand the prevalence of this issue and (2) perform targeted interventions, which may lead to improvement in outcomes. Our data suggest that nutritional deficiencies have a high prevalence in orthopaedic trauma patients. Furthermore, macro- and micronutrient deficiencies may be associated with wound complications, most notably prealbumin and vitamin C deficiency.There were some limitations to our study. One limitation was its retrospective design; this resulted in limited data for some of the studied micronutrients. Also, expanded micronutrient data collection was at the discretion of the treating surgeon at the time of hospital presentation. This led to variability in which nutritional markers were drawn for each patient. This may have contributed to the underrepresentation of certain micronutrients and difficulties in identifying other surgical complications, such as malunion/nonunion. Also, these data are from our local orthopaedic trauma population, which may lead to geographic variation in deficiency patterns.Previous studies demonstrated improved outcomes with nutritional supplements in the geriatric population ,20 and eWe have demonstrated profound malnutrition rates, including a hypoalbuminemia rate of 23.4%, which is slightly lower than previously found in this population . Over half of our patients were deficient in prealbumin, which more closely correlates with perioperative nutritional deficiency, given its shorter half-life . PrealbuOur study reinforces prior literature on the prevalence and impact of hypoalbuminemia in an orthopaedic trauma population ,26 and cIn summary, our study demonstrates a high prevalence of macro- and micronutrient deficiencies in an orthopaedic trauma patient population with lower extremity fractures. Deficiencies in prealbumin, and vitamins C, D and zinc were common, with over half of patients in our study group proving to be deficient. We also identified demographic risk factors for malnutrition, such as age, sex and ethnicity. Finally, we demonstrated that prealbumin and vitamin C may be associated with wound complications. This study lays the groundwork for identifying targeted supplement and nutritional interventions that may reduce the risk of surgical site complications. The reversal of these deficiencies in the perioperative period has the potential to improve patient outcomes and reduce hospital costs."} +{"text": "Orthoptera), silkworm, and earthworm are the commonly used insect meals in broiler and laying hen diets. This paper summarizes the nutrient profiles of the insect meals and reviews their efficacy when included in poultry diets. Due to the differences in insect meal products, and breeds of poultry, inconsistent results were noticed among studies. The main challenge for proper utilization, and the promising prospect of insect meal in poultry diet are also addressed in the paper. To fully exploit insect meal as an alternative protein resource, and exert their functional effects, modes of action need to be understood. With the emergence of more accurate and reliable studies, insect meals will undoubtedly play more important role in poultry feed industry.Shortage of protein feed resources is the major challenge to the world farm animal industry. Insects are known as an alternative protein source for poultry. A wide range of insects are available for use in poultry diets. Insect larvae thrive in manure, and organic waste, and produce antimicrobial peptides to protect themselves from microbial infections, and additionally these peptides might also be functional in poultry feed. The feed containing antimicrobial peptides can improve the growth performance, nutrient digestibility, intestinal health, and immune function in poultry. Insect meal contains a higher amount of essential amino acids compared to conventional feedstuffs. Black soldier fly, mealworm, housefly, cricket/Grasshopper/Locust ( Fish meal and soybean meal are the conventional protein sources in poultry feed. In poultry production, feed cost is approximately 60% to 80% of the total cost. A possible solution to reduce poultry feed costs is finding available, efficient, and inexpensive alternative feed sources. Insects are natural foods for poultry. Chickens can be found picking worms, and larvae from the grass, soil, and litter where they walk.Insects are capable of consuming animal manure, and food wastes, and reducing pollution, and providing protein (larvae), and fertilizer (frass). Insects convert waste into proteins, and reduce total nitrogen excretion, odors, and methane emission, thus reduce up to 80% of waste mass \u20133.The use of insects in poultry feed is a potential solution to improve the sustainability of poultry diets. A wide range of insects are available for use in poultry diets . Insect Escherichia coli, Salmonella, and Salmonella enterica serovar Typhimurium in broiler chickens [Hermetia illucens) does not carry any disease-causing agent; however, housefly is a carrier of Entomophthora spp. fungus, house cricket (Acheta domesticus) is a carrier of Metarhizium sp. fungus and cricket paralysis virus, and mealworm (Tenebrio molitor) is a carrier of Beauveria bassiana fungus [The exoskeleton of insects mainly consists of chitin, which improves the immune system of chicken ; howeverchickens ,14. Furtchickens . Howeverchickens . Black sa fungus . Insect a fungus ,17. Morea fungus ,19. Insea fungus . In addia fungus . Furthera fungus \u201324. In aa fungus .Insect meal in poultry diets increases the palatability for chickens and chickens fed on insect meal are highly preferable by consumers . Insect Black soldier fly meal (BSFM) is a good source of protein, and energy, enriched with essential, and nonessential amino acids, saturated, monounsaturated, and polyunsaturated fatty acids (PUFA), vitamins, and minerals ,28,29. TIn addition, BSF larvae reduces manure mass by 50%, and total nitrogen concentration by 62% . The rapEnterobacteriaceae count; 8% BSFM had better growth performance, and 10% BSFM increased drip loss, and decreased the gizzard weight [Salmonella Gallinarum, and decrease of the bacteria count in the tissues of liver, spleen, bursa, and cecum [Considerable studies showed that BSFM is the superior insect protein to improve growth performance, carcass composition, and meat quality in broiler chickens. Diet containing 2.6% BSFM with extended amino acids supply in the diet of Ross 308 broiler chickens improved the growth performance and nitrogen balance in starter phase . Cobb brd weight . Indigend weight . Diet cod weight . BSFM atnd cecum .The effects of BSFM on broiler chicken were affected by the dietary ratio between methionine and cysteine. Ross 308 male broiler chickens fed on the diet containing 23%/21% BSFM (starter/grower phase) with 50:50 methionine cysteine ratio improved feed efficiency, increased net protein utilization and body crude fat deposition; diet with 40:60 methionine cysteine ratio reduced the growth performance, methionine precaecal digestibility, and net protein utilization; diet containing 60:40 methionine cysteine ratio increased amino acids precaecal digestibility; however, diet with 55:45 methionine cysteine ratio only increased the cysteine precaecal digestibility .Black soldier fly meal can be used to replace fish meal and/or soybean meal or even soybean oil in broiler diet. Fish meal was successfully replaced by BSFM up to 15% in the diet of domestic chickens . Cobb 50There were few studies regarding the effects of BSFM in laying hens, and variable results were observed. Hy-Line Brown laying hens fed on 3% BSFM improved the growth performance, apparent digestibility of CP and crude fat, immunoglobulin A and glutathione peroxidase . Laying Mealworms are the brown worm-like larvae of the darkling beetles. Mealworms can be found throughout most of the world where they prefer warm, dark, and damp places like under decaying logs and leaves. Mealworms are designed for burrowing and eating and will feast upon the grains, vegetation, spoiled food, and many other types of fresh or decaying organic matter.The concentration of CP in MWM ranged from 27% to 54%, and fat ranged from 4% to 34%. Reported values for CP concentration in MWM are 46.44% , 51.93% Escherichia coli count [Salmonella enteritidis and Escherichia coli, fed on the diet containing 0.4% MWM resulted in increased feed intake, serum IgA, and reduced mortality and cecal Escherichia coli; however, 0.4% super MWM increased the body weight, weight gain, serum immunoglobulin G, and reduced FCR, bursa of fabricius percentage, cecal Salmonella spp. [Arbor Acres broiler chickens fed on diet containing 2.5% MWM improved the weight gain (1 to 10 d) and reduced the albumen globulin ratio; however, 5% MWM reduced the albumen globulin ratio and intestinal li count . Diet coli count . Mealworli count and incrli count . Higher li count . Label Hli count . Shaver li count . Ross 70li count . Diet coli count . Ross 70li count . In addili count . Chickenli count . Ross 30lla spp. .Corn gluten meal in diets of female label Hubbard hybrid free-range chickens, was successfully replaced by 7.5% MWM without any effect . Diet coThe HF can be found in all countries and in any climates. It is commonly associated with animal feces and can be found feeding on animal manure and food wastes. The concentration of CP in HF meal (HFM) ranged from 40% to 64%, and crude fat in HFM ranged from 2.5% to 28%. HFM contains about 53.3% CP , 54.36% Housefly meal can be used as a substitute for fish meal or soybean meal, and HFM can improve the production performance ,86,90\u201392Everything has pros and cons. There are opinions that using maggot meal in poultry diets can enhance the risk of disease transmission. Houseflies are recognized as a carrier of diseases; they carry disease causing agents on their legs and hairs that cover their bodies. But the maggot itself doesn\u2019t contain any disease-causing agent because maggot therapy has been used for decades for the treatment of septic injuries.Oxya hyla hyla) contains about 64.67% CP, 2.58% crude fat [Acanthacris ruficornis) contains about 50.5% CP and 18.8% crude fat, desert locust (Schistocerca gregaria) contains about 50.9% CP and 20.5% crude fat, and wild edible grasshopper contains about 52% CP and 21.4% crude fat [Ornithacris cavroisi) grasshopper contains about 47.73% CP and 12.23% crude fat [Acrida cinerea) contains about 65.4% CP and 8.3% crude fat [Cricket/Grasshopper/Locust (Orthoptera) meal (OTM) is a rich source of protein, amino acids, fatty acids, minerals, and vitamins ,98. The rude fat , reared rude fat . Howeverrude fat . Chineserude fat .Ornithacris cavroisi) meal as a replacement for fish meal had improve Haugh unit, and diet containing 75% grasshopper (Ornithacris cavroisi) meal improved the egg yolk color [Ruspolia nitidual) meal as replacement for fish meal improved the FCR and EE apparent digestibility, and diet containing 100% wild edible grasshopper meal improved the CP apparent digestibility; However, diet containing higher levels (above than 25%) of wild edible grasshopper meal as a replacement of fish meal resulted in reduced feed intake in indigenous chickens [Arbor Acres broiler chickens fed on the diet containing 50% (5% in diet) or 100% (10% in diet) grasshopper meal as fish meal replacer exhibited improved growth Table 2Table 2. lk color . Indigenchickens .However, chitin and chitosan in OTM are not easily absorbed and utilized. Cobb 500 male broiler chickens fed on the diet containing 0.05% cricket chitosan or 0.05% cricket chitin displayed a negatively affected intestinal morphology and a downregulated mRNA expression of some nutrient transporters .The silkworm is the larva or caterpillar of a moth. The larvae spins the silk to make a cocoon where it pupates to the adult moth. Silkworms eat mulberry leaves and were native to northern China. The culture of silkworms is called sericulture. Silkworm meal is a good source of protein, fatty acids, amino acids, minerals and vitamins \u2013107. SilDifferent content of silkworm meal (SWM) can be used in poultry feed to replace fish meal or soybean meal. Silkworm meal successfully substituted for fish meal or soybean meal in the diet of broiler chickens with no significant effect \u2013109. SoySonali chickens fed on the diet containing 25% SWM as replacement of soybean meal increased the weight gain, feed intake, heart percentage, breast meat yield, and reduced breast meat protein percentage and ash percentage; 50% SWM increased the meat pH, and n-3 PUFAs, and reduced the n-6 PUFAs of breast meat . In addiEisenia foetida) [Lumbricus rubellus) contains 6.89% CP and 2.25% crude fat [Earthworm meal (EWM) is rich source of protein, energy, and amino acids \u2013115. Thefoetida) ,118, 7.2foetida) , 57.85% foetida) , and 41.foetida) , and repfoetida) , 9.2% [1foetida) , and 3.5foetida) . Fresh erude fat . It is gLumbricus rubellus) diet improved the quality of meat for thigh and breast; in addition, diet containing 100% EWM as a replacement for fish meal reduced the fat content of breast, and thigh meat, and exhibited the higher acceptability of drumsticks [Feeding broilers with feed supplemented with 1% EWM and 1% vermi-humus has a negative impact on the growth performance of broilers, although the immune functions were improved . But theumsticks . Ningdu umsticks .Eudrilus eugeniae) improved the body weight gain, and diet containing 5% EWM improved the FCR and increased meat pH; and diet containing 7% EWM improved aroma, juiciness, residues, and flavor of the meat in Cobb 500 broiler chickens [Diet containing 3% EWM (chickens . Ross 30chickens . It was chickens (Table 4Sclerotized macropterous) meal contains about 42.33% CP after Sun drying and 47.34% CP after roasting, and about 41% crude fat [Termite were successfully substituted in dry or fresh form in the diet of indigenous chickens without any effect [Glyptotermes montanus) extracted endo-\u03b2-D-1,4-glucanase, avicelase, \u03b2-D-1,4-mannanase, \u03b2-D-1,4-xylanase and \u03b2-D-1,4-glucosidase enzymes in poultry diet can improve digestion in poultry [Termites (y effect . Inclusi poultry .Bee slum contains about 9.37% CP and 54.9% crude fat . Bee proRoss 308 broiler chickens fed on the diet containing 0.025% bee propolis and 2% bee pollen increased carcass yield and reduced drip loss, skin yellowness, breast meat yellowness: and 0.05% bee propolis increased carcass yield and reduced drip loss, skin yellowness, breast meat yellowness . DietaryRoss 308 broiler chickens fed on the diet containing 0.04% bee pollen resulted in increased body weight and carcass weight . Diet coLohmann LSL laying hens fed on the diet containing 0.025% and 0.05% bee propolis increased the egg mass, egg production, Haugh unit, albumen height, yolk height, yolk index, yolk weight, blood total protein, blood globulin, hemoglobin, lymphocytes and reduced FCR, yolk diameter, blood cholesterol, heterophil, heterophil lymphocyte ratio . Diet coAlthough considerable studies have been conducted in broilers and laying hens, there are still some obstacles to the proper and efficient utilization of insect meal in poultry industry. The quality and nutrient profile of insect products varied with the differences in insect species, rearing medium, environment, and processing method. The absence of large-scale production and stable supply of insect meal do not favor the accurate evaluation of metabolizable energy and effective nutrient availability. Furthermore, the processing method needs to be updated for cost reduction of insect products, and risk reduction of pathogenic contamination and disease spreading. With the availability of quality and stable insect meals, more reliable efficacy studies may be performed to evaluate the health, immunomodulatory and functional effects of insect meals compared with the alternative protein feedstuffs.In the current environment with studies of insect meal in broiler and laying hens, BSFM, MWM, and HFM exhibit the most promising industrialization prospects. However, earthworm, silkworm, and locust swarms can be effectively utilized in poultry feed. Because insects are used as medium of medicines for centuries, it is reasonable to believe that insects can be used in poultry diet to replace antibiotics because of their antimicrobial properties. Insect meal can also be used in low CP diets for amino acids adjustment as insects are enriched in essential amino acids. With the emergence of more accurate and reliable studies, insect meal will inevitably play a greater role in the poultry feed industry."} +{"text": "Diabetes mellitus is associated with changes in soft tissue structure and function. However, the directionality of this change and the extent to which either tissue thickness or stiffness contributes to the pathogenesis of diabetes-related foot ulcerations is unclear. Hence, this systematic review aims to summarise the existing evidence for soft tissue structural differences in the feet of people with and without diabetes.In compliance with MOOSE and PRISMA guidelines, AMED, CINAHL, MEDLINE, ProQuest Health & Medical Collection, ProQuest Nursing & Allied Health Database, and Web of Science electronic databases were systematically searched for studies published from database inception until 1st October 2020 [Prospero CRD42020166614]. Reference lists of included studies were further screened. Methodological quality was appraised using a modified critical appraisal tool for quantitative studies developed by McMaster University.A total of 35 non-randomised observational studies were suitable for inclusion. Within these, 20 studies evaluated plantar tissue thickness, 19 studies evaluated plantar tissue stiffness, 9 studies evaluated Achilles tendon thickness and 5 studies evaluated Achilles tendon stiffness outcomes. No significant differences in plantar tissue thickness were found between people with and without diabetes in 55% of studies (11/20), while significantly increased plantar tissue stiffness was found in people with diabetes in 47% of studies (9/19). Significantly increased Achilles tendon thickness was found in people with diabetes in 44% of studies (4/9), while no significant differences in Achilles tendon stiffness were found between people with and without diabetes in 60% of studies (3/5).This systematic review found some evidence of soft tissue structural differences between people with and without diabetes. However, uncertainty remains whether these differences independently contribute to diabetes-related foot ulcerations. The heterogeneity of methodological approaches made it difficult to compare across studies and methodological quality was generally inadequate. High-quality studies using standardised and validated assessment techniques in well-defined populations are required to determine more fully the role of structural tissue properties in the pathogenesis of diabetes-related foot ulcerations.The online version contains supplementary material available at 10.1186/s13047-021-00475-7. Diabetes-related foot ulcerations (DFUs) are one of the most challenging complications of diabetes mellitus. They are associated with high morbidity and mortality , 2, withHistological changes have been observed in the plantar soft tissues , 8 and AIncreased tissue stiffness , particuAs a separate entity, increased Achilles tendon stiffness (ATS) reduces ankle joint motion and is associated with increased forefoot plantar pressures . The AT Altogether, these changes bear the potential to reduce shock-absorbing capacity of the plantar tissues thus lowering the threshold for which integrity of the skin is breached, while at the same time magnify biomechanical stresses at localised sites, thereby considerably increasing the individual\u2019s propensity to ulceration. However, the extent to which tissue thickness and stiffness contributes to DFU pathogenesis is unclear. Ulcerations and their recurrence are frequent sequelae , 21, yetThis systematic review was conducted in compliance with the Meta-analyses Of Observational Studies in Epidemiology (MOOSE) and the Six electronic databases were systematically searched by the first reviewer (B.K.) for studies published from database inception until 1st October 2020. The databases were: EBSCOhost , ProQuest , and Web of Science. No date restrictions were imposed, however, studies were restricted to those published in English and in peer-reviewed journals\u00a0only. Boolean operators and relevant MeSH terms were used and keywords were adapted for each database Population: cohorts comprised of adults 18\u2009years old and above were included; experiments conducted on animals, artificial tissues, cadavers or minors below 18\u2009years old were excluded. (2) Interventions: no restrictions set. (3) Comparison: studies which had made a comparison between cohorts with and without diabetes were included; non-comparative studies, specifically studies which had not included a control group of otherwise healthy adults, were excluded. (4) Outcomes: in-vivo assessments of either thickness and/or stiffness of plantar soft tissues and/or the AT were included; in-vitro studies, studies which assessed other body parts or internal body organs, or technical studies solely evaluating the physics or engineering of the measurement technique were excluded. (5) Type of study: quantitative primary research studies published in peer-reviewed journals were included; qualitative studies, case reports, commentaries, conference proceedings, narrative reviews, and studies published in non-peer reviewed journals were excluded.All articles retrieved in the search were first exported to RefWorks for removal of duplicates and subsequently exported to Covidence. Two reviewers (B.K. and R.B.) independently screened all titles and abstracts against pre-established inclusion and exclusion criteria. Articles which appeared to be eligible were retrieved in full and assessed by both reviewers. Upon mutual agreement for inclusion, the reference lists of included articles were additionally screened. This iterative process was performed until no further articles could be included. Where full-text articles could not be accessed, university library services were employed and authors contacted directly; this was successful on six occasions. Throughout this process, discrepancies were first resolved by consensus between the two reviewers (B.K. and R.B.) with adjudications sought from a third reviewer (J.W.) where required.All included studies were appraised for their methodological quality using a modified critical appraisal tool for quantitative studies developed by McMaster University . This moThe sample description was deemed as limited if participant inclusion or exclusion criteria, and/or baseline characteristics of body mass index (BMI), duration of diabetes or HbA1c levels of the cohort were not reported. This lack of detail limits the reviewers\u2019 attempts to establish comparability of diabetes, DPN and DFU cohorts within studies. Potential confounders were identified a priori as age, sex and BMI due to their known effects on soft tissue thickness \u201328 and sStudies which had either tested for or cited previous works demonstrating the reliability or validity of their chosen assessment tool for the relevant outcome measures were recognised to have addressed these domains. Where reliability or validity was addressed for other assessment techniques within the study, but not those relating to PTT, PTS, Achilles tendon thickness (ATT) or ATS outcomes, or was not mentioned at all, the study was deemed to not have addressed this domain.p\u2009<\u20090.05.Data extraction was performed independently by the first reviewer (B.K.) and checked for accuracy by the second reviewer (R.B.). A pre-specified data extraction sheet was used to extract data from all studies, which includes: (1) Article information: title, authors and year of publication; (2) Methods: study design, setting, participant demographics, participant inclusion and exclusion criteria, type of assessment tool utilised, outcome metric, and method of measurement for thickness or stiffness; and (3) Main findings. Within studies, statistical significance was defined as A descriptive synthesis was conducted using summary data from individual studies to identify the directionality of PTT, PTS, ATT and ATS changes in people with diabetes when compared to their controls. Absolute values for PTT and ATT were further extracted. Where sufficient data permits, subgroup analysis was undertaken to identify the presence of any anatomical variations across the plantar aspect of the foot and the length of the AT, and to explore how findings may compare across cohorts with different diabetes-related complications. This includes people with DPN or people with either an active or history of DFUs.The search strategy yielded a total of 668 articles, from which 68 full-text articles were screened Fig.\u00a0. 33 artiStudies were published across three decades (1985 to 2020), with sample sizes ranging from 8 to 190 participants. The mean age of participants with diabetes was 58.5\u2009years and their mean BMI was 27.3. The mean age of controls was 51.6\u2009years and their mean BMI was 26.0. Participant comparison groups included healthy controls, people with diabetes but without DPN, people with DPN, and people with either an active or history of DFUs.From 35 included studies, 20 studies evaluated PTT outcomes , 55\u201361, All 35 papers included were non-randomised observational studies assessed to be of low quality. Overall, the degree of reporting was deemed to be inadequate for the following components of methodological quality: study design, sample size justifications, strategies to reduce confounding, reliability and validity of outcome measures utilised, and assessment techniques Table\u00a0.Table 2The purpose of the study and supporting background literature was generally well reported. Even though study designs were explicitly stated in only 43% of studies (15/35), the designs were considered appropriate.Consecutive , 65 or cReliability of outcomes measures was reported in 40% of studies (14/35). For PTT, reliability was reported for computed tomography (CT) , magnetiWithin these studies, a coefficient of variance between repeated measurements was found to be less than or equal to 5% in six studies , 57, 68 Validity of outcome measures was reported in 11% of studies (4/35). All four studies had cited previous works in demonstrating the validity of their chosen assessment tools for their specified outcome measure(s). Two studies , 55 haveFor PTS, 18 different outcome metrics were adopted across 19 studies\u00a0Table . Of thesFrom 20 studies investigating PTT, five different assessment tools were used. 80% of studies (16/20) utilised US-based measures , 58\u201361, From 19 papers assessing PTS, six different assessment tools were used. 47% of studies (9/19) utilised US-based measures , 58, 62,From nine studies assessing ATT, two different assessment tools are used. 89% of studies (8/9) utilised US-based measures, with 78% utilised US , 65\u201367 aPTT was measured as the distance between skin and bone in 70% of studies (14/20) , 55\u201360. Some uniformity was noted in the method of measurement for ATT across papers. ATT was measured as the anteroposterior diameter across the examined AT portion(s) in 56% of studies (5/9) , 47, 48.Across 20 studies examining PTT, 30% examined the hallux, 60% examined the first metatarsal head (MTH), 45% examined the\u00a0second MTH, 45% examined the\u00a0third MTH, 30% examined\u00a0the fourth MTH, 40% examined the\u00a0fifth MTH and 60% examined the heel. Robertson et al. (2002) did not Across 19 studies examining PTS, 37% examined the hallux, 58% examined the first MTH, 26% examined the\u00a0second MTH, 32% examined the\u00a0third MTH, 5% examined the\u00a0fourth MTH, 26% examined\u00a0the fifth MTH, 11% examined the medial and lateral midfoot, and 84% examined the heel. 16% of studies had merged their findings for the third to fifth MTHs , 51, 52.Across 10 studies which had investigated either ATT and/or ATS, 20% of studies (2/10) had differentiated their measurements between all three portions of the AT. Both studies , 38 concThe main findings for PTT, PTS, ATT and ATS outcomes are tabulated in Table\u00a0Across 20 studies examining PTT, no significant differences were found between people with and without diabetes across all examined anatomical site(s) in 55% of studies (11/20) , 59 . Of these, 26% of studies 5/19) noted significantly increased PTS across all examined site(s) in cohorts with diabetes when compared to their healthy controls , 55, 58 /19 notedAcross nine studies that analysed ATT, 44% (4/9) found a significant increase across all examined portion(s) in people with diabetes when compared to healthy controls , 41, 66 Across five studies that measured ATS, 60% (3/5) found no significant differences across all examined portion(s) between people with and without diabetes , 38, 41.Seven studies investigating PTT , 55, 58,Eight studies investigating PTT , 59, 60,Brink (1995) and ThomIn studies which compared findings across subgroups with different diabetes-related foot complications, no significant differences in PTT were found between people with diabetes and those with DPN , 41, as Changes to plantar tissue sub-structures are seldom reported. Chao et al. (2012) measuredRegional variations in PTS were observed in only one out of all other examined sites in 26% of studies 5/19) , 51, 52./19 , 51,Only two studies distinguished their findings between the three segments of the AT , 38, botThis systematic review investigated the evidence for differences in plantar soft tissue and AT thickness and stiffness in people with and without diabetes. The general consensus among studies was that diabetes is associated with a significant increase in PTS, however the differences in PTT is not significant. Studies also found that diabetes is associated with a significant increase in ATT, however the differences in ATS is not significant.Extensive methodological heterogeneities and deficiencies was a key finding of this systematic review. Sample sizes were seldom justified . Additionally, reporting was generally inadequate across the domains of study designs and the reliability and validity of outcome measures. Case definition for participants with diabetes and subgroups formed on the presence and history of DFU or DPN were often absent or inadequately defined. Furthermore, the risk of selection bias cannot be eliminated in the majority of studies as only 6% of studies adopted a consecutive sampling method for recruiting people with diabetes; the remaining 94% of studies (33/35) made no mention of their sampling strategy for their cohorts with diabetes.No gold standard assessment techniques have been established for tissue thickness and stiffness assessments and this was reflected in the diverse approaches reported in this review. Studies that employed novel biomedical technologies and tissue engineering outcomes are additionally not easily reproduced and are not well understood in clinical settings. Ultrasound-based techniques were favoured \u2013 utilised by 80% of studies (16/20) investigating PTT, 47% of studies (9/19) investigating PTS, 89% of studies (8/9) investigating ATT, and 100% of studies (5/5) investigating ATS \u2013 but standardisation in its usage is lacking. Ultrasound-based techniques are also known to be highly dependent on the knowledge, experience and skill of the operator . TherefoStudies further differed in their measurement techniques. Using PTT for example, while the majority of studies measured PTT as the distance between skin and bone, overall six different methods of measurements were observed. Combined with the use of different assessment techniques and examination of different anatomical sites, these wide-ranging methodological heterogeneities made it difficult to compare and synthesise results across studies. The lack of standardisation also renders derivation of normal and diagnostic cut-off values extremely challenging and hampers routine clinical utility for at-risk screening, detection and longitudinal monitoring.On the plantar aspect of the foot, areas at high risk of ulceration are the apices of the toes, metatarsal heads, medial aspect of the midfoot and the heel . This syThe lifetime incidence of DFUs is estimated to be up to 35% . DFU recAchilles tendon changes in diabetes are recognised to potentially alter ankle biomechanics , increasThickening in tendons are often regarded as pathological clinically , 72. WhiAsymptomatic AT pathologies are common in athletic and general populations \u201376. WhilIt is further unclear to what extent baseline factors such as age, sex, BMI, duration of diabetes and glycaemic control are associated with soft tissue changes in diabetes. In this systematic review, the differences between groups with diabetes and control groups in age, sex and BMI were statistically not significant in 40% of studies which appears to reduce the potential for confounding. However, studies reviewed have documented poor correlations between age with PTT , 40, PTSThis systematic review has several strengths. The review included all studies published to date on the topic, including a body of knowledge from the biomedical technology field where assessment techniques were utilised in cohorts of people with diabetes and associated risk factors for DFU. Extensive search strategies were employed with detailed, careful and critical assessment to identify risk of bias. The review is, however, limited by the methodological deficiencies of included studies. The critical appraisal tool by McMaster University has alsoThis systematic review found some preliminary evidence supporting differences in soft tissue properties in the feet of people with and without diabetes. However, uncertainties remain largely due to methodological heterogeneities and deficiencies. Tissue thickness and stiffness are putative risk factors for DFU and may be a viable treatment target. High-quality studies using standardised and validated assessment techniques in well-defined populations are required to advance our understanding and to determine more fully the role of soft tissue thickness or stiffness changes in the pathogenesis of DFU. Should soft tissue compromise be indicative of imminent tissue breakdown in the diabetic foot, this has the potential to aid clinical triage and inform the timely adoption of targeted preventive measures.Additional file 1. Database search strategy.Additional file 2. Reasons for article exclusion.Additional file 3. Plantar tissue thickness values.Additional file 4. Achilles tendon thickness values.Additional file 5. Directionality of findings for plantar soft tissues.Additional file 6. Directionality of findings for Achilles tendon."} +{"text": "Infectious diseases account for the third most common cause of neonatal deaths. Globally, antibiotic resistance (ABR) has been increasingly challenging neonatal sepsis treatment, with 26 to 84% of gram-negative bacteria resistant to third-generation cephalosporins. In sub-Saharan Africa, limited evidence is available regarding the neonatal microbiology and ABR. To our knowledge, no studies have assessed neonatal bacterial infections and ABR in Central-African Republic (CAR). Therefore, this study aimed to describe the pathogens isolated and their specific ABR among patients with suspected antibiotic-resistant neonatal infection admitted in a CAR neonatal unit.This retrospective cohort study included neonates admitted in the neonatal unit in Bangui, CAR, from December 2018 to March 2020, with suspected antibiotic-resistant neonatal infection and subsequent blood culture. We described the frequency of pathogens isolated from blood cultures, their ABR prevalence, and factors associated with fatal outcome.p\u00a0=\u20090.002). Gram-negative bacteria were isolated in 87.9% of positive samples; with most frequently isolated bacteria being Klebsiella pneumoniae (39.4%), Escherichia coli (21.2%) and Klebsiella oxytoca (18.2%). All tested bacteria were resistant to ampicillin. Resistance to third-generation cephalosporins was observed in 100% of tested Klebsiella pneumoniae, 83.3% of isolated Klebsiella oxytoca and 50.0% of tested Escherichia coli. None of the tested bacteria were resistant to carbapenems. Approximately 85.7 and 77.8% of gram-negative tested bacteria were resistant to first-line (ampicillin-gentamicin) and second-line treatments, respectively. In hospital mortality, adjusted for blood culture result, presence of asphyxia, birth weight and sex was higher among neonates with positive blood culture , male sex , asphyxia and very low birth weight (1000\u20131499\u2009g) .Blood cultures were positive in 33 (26.6%) of 124 patients tested (17.9% for early-onset and 46.3% for late-onset infection; Overall, 77.8% of confirmed gram-negative neonatal infections could no longer effectively be treated without broad-spectrum antibiotics that are not routinely used in sub-Saharan Africa referral hospitals. Carbapenems should be considered an option in hospitals with surveillance and antibiotic stewardship.The online version contains supplementary material available at 10.1186/s12887-021-02911-w. Staphylococcus aureus, Klebsiella spp. and Escherichia coli \u2009=\u20091.6\u20139.6). Neonates with EONI were more likely to be resuscitated at birth , have meconium-stained amniotic fluid at birth , and have a diagnosis of asphyxia . The occurrence of EONI was more likely associated with maternal fever/chorioamnionitis and a final \u201cdiagnosis\u201d of neonatal infection . In contrast, neonates with LONI were more likely to have a diagnosis of preterm-related condition and abdominal distension , which can be a clinical sign of necrotizing enterocolitis. Moreover, neonates with LONI were more likely to present with low birth weight (LBW) and have preterm birth than those with EONI.During the study period, 2365 patients were admitted to Castor\u2019s neonatal unit. One-hundred-twenty-six blood cultures were performed for 124 patients with suspected antibiotic-resistant neonatal infection. For two patients, blood cultures were performed as follow up after a first positive result to prove the efficacy of treatment. Blood cultures were positive for 33 (26.6%) of 124 patients tested. Eighty-one patients (65.3%) had early onset neonatal infection (EONI) and 41 (33.1%) had late onset neonatal infection (LONI). Table Klebsiella pneumoniae (44.8%), Escherichia coli (24.1%) and Klebsiella oxytoca (20.7%). In neonates with EONI, Klebsiella pneumoniae and Escherichia coli were the most frequent gram-negative pathogens (41.7% each), and in those with LONI, Klebsiella pneumoniae was the most frequent gram-negative pathogen (47%), followed by Klebsiella oxytoca (35.3%) and Escherichia coli (11.8%). We found 4\u2009gram-positive bacteria: 2 Staphylococcus aureus and 2 Coagulase negative Staphylococci (CoNS). The 2 patients with CoNS isolated in blood culture received first and seond-line treatment. They both recovered, one was considered in the final diagnosis infected with CoNS, for the other we did not know if the CoNS was considered pathogen or contaminant.Table Klebsiella pneumoniae, 80% of tested Klebsiella oxytoca and 85.7% of isolated Escherichia coli. Both isolated Staphylococcus aureus and half of the two strains of isolated Enterobacter cloacae were resistant to gentamicin. Resistance to third generation cephalosporins was observed in 100% of tested Klebsiella pneumoniae, 83.3% of isolated Klebsiella oxytoca, 50% of tested Escherichia coli and 50% of isolated Enterobacter cloacae. Only 14.3% of all gram-negative tested bacteria were sensitive to first-line treatment (ampicillin + gentamicin) and 22.2% were sensitive to second-line treatment . Moreover, resistance to amikacin was observed in 33.3% of isolated Klebsiella oxytoca and in none of the other tested bacteria. Reduced susceptibility to ciprofloxacin was observed in 88.9% of tested Klebsiella pneumoniae, 83.3% of isolated Klebsiella oxytoca, 80% of tested Escherichia coli and 100% of isolated Enterobacter cloacae. Only 13.6% of the gram-negative tested bacteria were sensitive to ciprofloxacin. None of the tested bacteria was resistant to carbapenems. Among the two isolated Staphylococcus aureus strains, one was resistant to cefoxitin (both tested) and one was resistant to ciprofloxacin (only one tested). Additional\u00a0file\u00a0Table Table Klebsiella pneumoniae Klebsiella oxytoca and Escherichia coli) accounting for over 80% of the identified pathogens. All the identified pathogens were resistant to at least one antibiotic. All the tested bacteria were resistant to ampicillin, and more than 80% of the gram-negative tested pathogens were resistant to both antibiotics of the ampicillin-gentamicin combination, which is the first line treatment for neonatal sepsis as per the WHO [In 26.6% of neonates with suspected antibiotic-resistant neonatal infection in Castor\u2019s neonatal unit, an underlying pathogen was identified from blood culture, with gram-negative bacteria were isolated in 87.9% of positive culture samples, which is higher than that described in the central African region [Klebsiella spp. 21%, Escherichia coli 10% and Staphylococcus aureus 25%) [Streptococcus (GBS) was not isolated in our retrospective cohort, whereas 6\u20138% of GBS was reported in the literature in the central African region [Klebsiella spp. and 85.7% versus 26% for Escherichia coli) [Klebsiella spp. and 0% of Escherichia coli) [Klebsiella spp. and 0% of Escherichia coli) [Escherichia coli and Klebsiella pneumoniae in our study population. Klebsiella oxytoca showed no carbapenems resistance but was resistant to amikacin in 33.3% of cases. In sub-Saharan Africa, ciprofloxacin resistance varies widely, with ciprofloxacin resistance of Klebsiella spp. ranging from 14% in the east African region to 92% in the central African region and that of Escherichia coli ranging from 4% in the east African region to 64% in the southern African region [The proportion of neonates with positive blood cultures (26.6%) in our study population is similar to that in a previously described sub-Saharan neonatal cohort . Gram-nen region ; howevern region . UnfortuThe case fatality rates of all neonates with suspected antibiotic-resistant neonatal infection (23.9%) and those with blood culture-confirmed sepsis (38.7%) were slightly lower than the case fatality rates reported by other authors . This suE. coli and 38 Klebsiella spp.); therefore, our study can add to this sparse evidence despite its relatively small number of isolated bacteria. Furthermore, other studies from the central-African region are also similarly small scaled [This study has some limitation. First, we had a small number of isolated bacteria. However, the currently accepted estimation of the aetiology and prevalence of ABR in central African region reported by Okomo et al. is basedl scaled \u201331. Secol scaled . Consequl scaled . Howeverl scaled ; therefoKlebsiella pneumoniae Klebsiella oxytoca and Escherichia coli) in almost 9 of 10 positive samples (with similar percentages in EONI and LONI), a proportion that is higher than what has been described elsewhere in sub-Saharan Africa. We also detected a comparatively higher profile of gentamicin resistance in our study population, and most of the isolated pathogens showed resistance to first- and second-line treatments. This study highlights that carbapenem could be considered as second line treatment for neonatal infection in critically ill patients. Blood cultures should be done prior to commencing new antibiotics. However further larger, multicentered studies are warranted in low middle-income countries. For settings that are similar to those of Castor\u2019s Maternity , we recommend carbapenem use as second-line treatments for neonatal sepsis, at least for specific groups of patients. Future studies are warranted to identify such groups. We further recommend that ABR prevalence in neonates with first-line treatment failure be studied routinely to further inform the medical community about the use of carbapenems as a possible second-line option. Carbapenems should not be used as empirical routine second- or third-line treatment options in facilities where blood culture is not routinely performed in neonates with failure of first and/or second line antibiotic treatment.A major finding of this study was the isolation of gram-negative bacteria (mostly Additional file 1.Additional file 2.Additional file 3."} +{"text": "The 2019 coronavirus disease (COVID-19) epidemic is a global health emergency which has been shown to pose a great challenge to mental health, well-being and resilience of healthcare workers, especially nurses. Little is known on the impact of COVID-19 among nurses in sub-Saharan Africa.A cross sectional study was carried out between August and November 2020 among nurses recruited from the Aga Khan University Hospital, Nairobi. The survey questionnaire consisted of six components- demographic and work title characteristics, information regarding care of COVID-19 patients, symptoms of depression, anxiety, insomnia, distress and burnout, measured using standardized questionnaires. Multivariable logistic regression analysis was performed to identify factors associated with mental health disorders.Of 255 nurses, 171 (67.1%) consented to complete the survey. The median age of the participants was 33.47 years, 70.2% were females and 60.8% were married. More than half, 64.9% were frontline workers directly engaged in COVID-19 care. Only 1.8% reported a prior history or diagnosis of any mental health disorder. Depression, anxiety, insomnia, distress, and burnout were reported in 45.9%, 48.2%, 37.0%, 28.8% and 47.9% of all nurses. Frontline nurses reported experiencing more moderate to severe symptoms of depression, distress and burnout. Furthermore, females reported more burnout as compared to males. Multivariate logistic regression analysis showed that after adjustment, working in the frontlines was an independent risk variable for depression and burnout.This is one of the few studies looking at mental health outcomes among nurses during the COVID-19 pandemic in Kenya. Similar to other studies from around the world, nurses directly involved with COVID-19 patients reported higher rates of mental health symptoms. Burnout threatens to exacerbate the pre-existing severe nursing workforce shortage in low-resource settings. Cost-effective and feasible mitigating strategies, geared to low-middle income countries, are urgently needed to help cope with mental health symptoms during such a pandemic. According to the World Health Organization (WHO), Kenya, in 2020, confirmed over 95,000 COVID-19 cases with about 1,655 deaths [The Kenyan health system is defined by the following 6 levels of care provided to patients: level 1: community services, level 2: dispensaries and clinics, level 3: health centres, level 4: sub-county hospitals, level 5: county referral hospitals and large private hospitals and level 6: national referral hospital and large private teaching hospitals. Kenya\u2019s health budget accounts for 4% of the total budget and the funds are primarily used for curative services. Government funds are solely distributed to the sub-county and government clinical facilities and hospitals [Nurses remain a critical part of the work force in Kenya often on the frontline providing initial and key services to patients. There are approximately 51,649 nurses below the age of 60 with majority being female between the ages of 21\u201330 years. Majority of the nursing training institutions are government sponsored and may offer three levels of training programs including: certificate, diploma and a bachelor\u2019s degree. A majority of the nurses (65%) in Kenya are diploma holders [Prior to the COVID-19 pandemic, the Ebola pandemic nearly demolished an already fragile healthcare system in West Africa. Healthcare workers were 20\u201330 times more likely than the general population to contract the virus, and mortality among healthcare workers was reported as high as 69% . DespiteThe pandemic has been linked to various psychological disorders especially in healthcare workers involved in the direct care of COVID-19 patients, with many studies showing increased levels of depression, anxiety, stress and burnout most notably among frontline nurses \u201318. A stUnfortunately, one year into the pandemic, little is known about the effects of COVID-19 on mental well-being of healthcare workers especially nurses in SSA. Due to the paucity in data and limited resources, including mental health care in sub-Saharan Africa when compared to western countries, we sought to explore the mental wellbeing of nurses taking care of COVID-19 patient at a tertiary healthcare facility in Kenya.We carried out a cross sectional survey between August and November, 2020. Email invitations with a link to a voluntary, de-identified survey was sent to all the nurses at the Aga Khan University Hospital, Nairobi (AKUHN). Email reminders were sent out twice a week from REDCap for participation in the survey. The link to the survey could only be used once. Responses from the nurses remained anonymous, Approval for this study was obtained from the Institutional Ethics and Review Committee AKHUN and online survey data was collected through the Research Electronic Data Capture\u2014REDCap platform .There was a steady increase in COVID-19 cases from October into November. Kenya recorded the highest number of cases in a single month in November 2020. Based on the 7-day average from John Hopkins University data dashboard, the peak of the first wave occurred in early August whereas the peak of the second wave occurred in mid-November in Kenya .The survey questionnaire, in English, consisted of demographic characteristics, job title, experiences providing care to patients with COVID-19, symptoms of depression, anxiety, insomnia, distress and burnout. The mental health symptoms were measured using validated questionnaires that would allow for comparison across different populations: the 9-item Patient Health Questionnaire (PHQ-9) , the 7-iCategorical data was presented as frequencies and percentages whereas continuous data was presented as medians with interquartile ranges (IQR). Normality tests were employed using the Shapiro-Wilk test. Kruskal-Wallis test and Fisher\u2019s Exact test was utilized to compare the continuous and categorical variables. Logistic regression analysis was performed, and the associations between risk factors and outcomes are presented as odds ratios (ORs) and 95% CIs, after adjustment for confounders, including age, gender, and marital status. Data analysis was performed using SPSS statistical software version 20.0 (IBM Corp). The significance level was set at \u03b1 = .05, and all tests were 2-tailed.Between August 2020 and November 2020, 255 nurses from AKUHN were invited to participate in the study and 171 (67.1%) consented to complete the survey. The median age of the participants was 33.47 years (IQR: 29.80\u201335.82). Majority of the nurses were females (70.2%) and married (60.8%). A total of 111 nurses (64.9%) were frontline workers directly engaged in COVID-19 care. Majority of the nurses (64.0%) had cared for about 5\u201320 patients and 66.7% had lost a patient to COVID-19. Approximately, 60.0% of the nurses reported having enough resources to care for COVID-19 whereas 71.2% reported to have been adequately trained for COVID-19. Only 1.8% had reported a prior history or diagnosis of any mental health disorder.Depression, anxiety, insomnia, distress, and burnout were reported (mild to severe) in 45.9%, 48.2%, 37.0%, 28.8% and 47.9% of all nurses. Frontline nurses reported experiencing more moderate to severe symptoms of all the mental health disorders than the second line nurses. Moderate to severe; depression among frontline vs second line nurses was 17.3% vs 3.4% (p = 0.026); anxiety among frontline vs second line nurses was 11.1% vs 5.1% (p = 0.681); insomnia among frontline vs second line nurses was 9.1% vs 0.0% (p = 0.052); distress among frontline vs second line nurses was 20.4% vs 11.9% (p = 0.039); burnout among frontline vs second line nurses was 56.1% vs 32.8% (p = 0.005) . ContinuOn comparing the differences between gender and mental health symptoms, females reported experiencing more symptoms of all the mental health disorders than males. However, only burnout was found to be statistically significantly higher in females ) .Multivariate logistic regression analysis showed that after adjustment, working in the frontlines was an independent risk variable for depression and burnout .To the best of our knowledge, this is the first study of its kind looking at the mental wellbeing of nurses taking care of COVID-19 patient in a tertiary healthcare facility in Kenya. Comparable to other studies, we found over 40% of front-line nurses at our facility who took care of COVID-19 patients suffered from mild to severe depression , 29, 30.Our study also aligns with a number of other studies showing that front-line nurses, especially females, suffer from poor sleep, depression and anxiety , 33, 34.Tu and colleagues looked at sleep quality and mood symptoms in front-line nurses in Wuhan, China during the COVID-19 outbreak and found that 60% had poor sleep, 46% suffered depression symptoms and 40% reported anxiety symptoms . SimilarSimilar to other studies , 35\u201337, Shechter and colleagues in their study looking a psychological distress among New York healthcare workers during the COVID-19 pandemic found 57% of their participants screened positive for acute stress. In addition, nurses and advanced practice providers had a higher percentage of psychological symptoms compared to attending physicians . In contOur study has several limitations. All the participants were from one institution and this limits the generalization of our findings to other healthcare institutions in Kenya. In addition, psychological outcomes among nurses could certainly have been more pronounced if the study had been conducted in a larger cohort for a longer duration. Thirdly, an online survey is often skewed by a selective population that is technologically familiar with the use of internet and email. Finally, even though our response rate was 67%, response bias may still exist especially if the nurses who did not respond were either too stressed to respond or not stressed at all to respond to the survey.The current pandemic is weighing heavily on our healthcare workforce. In Kenya, this burden is particularly concerning given the acute shortage of nurses\u2019 even prior to the pandemic. As many countries in SSA struggle with limited medical resources and fragile health care systems amidst the COVID-19 pandemic, the mental health burden on all healthcare workers especially in resource-limited settings must be appropriately measured and addressed. Our study sheds light on the mental well-being among nurses in Kenya and similar to other studies reflects on the psychological burden that frontline nurses are encountering during this pandemic. However, further research to understand the long-term effects of COVID-19 on the mental well-being of nurses, especially in sub-Saharan Africa, are warranted. Our study has major implications including the need for cost-effective and easy to implement strategies across the healthcare system to support the mental well-being of healthcare workers especially nurses.S1 File(XLSX)Click here for additional data file."} +{"text": "ABSTRACT IMPACT: Identifying racial disparities in septic shock mortality, a common and lethal condition, can inform future research and policy efforts aimed at understanding the drivers these disparities and addressing the underlying factors in order to reduce disparities and improve health. OBJECTIVES/GOALS: Septic shock is a major public health problem with significant mortality. Existing data indicate racial disparities in sepsis incidence, but evidence is limited on differences in septic shock outcomes. Our objective was to determine the association between race and septic shock mortality in a statewide cohort while controlling for clinical factors. METHODS/STUDY POPULATION: This was a retrospective analysis of septic shock patients in the One Florida Data Trust between 2012-18. Data was collected regarding age, sex, race, insurance status, and selected comorbid conditions . To account for severity of illness, we assigned Sequential Organ Failure Assessment scores for components based on laboratory values (labSOFA), and collected data on mechanical ventilation use and initial lactate.The primary outcome was 90-day mortality. The Least Absolute Shrinkage and Selection Operator (LASSO) method was used for variable selection for the multivariable regression model. RESULTS/ANTICIPATED RESULTS: There were 13,932 septic shock patients with a mean (SD) age of 61(16) years. Of these, 68% identified as white, 28% as black, 2.1% as Hispanic, and 2.0% as other races. 90-day mortality was 32% and 59% required mechanical ventilation. Significant independent predictors of mortality in the regression model were age , black race , lactate , mechanical ventilation , labSOFA , history of liver disease , hypertension , COPD , CHF , HIV , and the interaction between age and black race. Black patients had 1.72 times the odds of mortality compared to white patients. For every one-year decrease in age, black patients had a 1% increased odds of mortality . DISCUSSION/SIGNIFICANCE OF FINDINGS: Black patients have increased odds of dying from septic shock compared to white patients after controlling for age, selected comorbid conditions, and markers of illness severity. Future work is needed to move beyond demonstrating septic shock disparities and towards understanding the underlying factors."} +{"text": "Escherichia coli (32%) and Enterococcus spp. (21%) were the most common isolates. Other Gram-negative, Gram-positive, and atypical pathogens accounted for 22%, 20%, and 5%, respectively. Resistance was <15% for piperacillin/tazobactam and carbapenems (both Gram-negative and -positive pathogens); <5% for glycopeptides against Gram-positive; 7%, 14%, and 20% for aminoglycosides, fosfomycin, and macrolides against Gram-negative pathogens, respectively; 10% for amoxicillin/clavulanate against Gram-positive pathogens; <20% for cephalosporins and fluoroquinolones against to Gram-negative pathogens (higher against Gram-positive pathogens); none for macrolides against atypical pathogens, but 20% and 27% for fluoroquinolones and tetracyclines. In West Africa, the resistance rates were generally higher, although the highest rates for ampicillin, cephalosporins, and fluoroquinolones were observed in the Gulf area. Lower rates were observed in Southeastern Europe. Conclusions: Resistance to antibiotics is a health problem requiring local health authorities to combat this phenomenon. Knowledge of the spectrum of pathogens and antibiotic resistance rates is crucial to assess local guidelines for the treatment of prostatitis.Objective: To evaluate spectrum and resistance rates to antibacterial agents in causative pathogens of bacterial prostatitis in patients from Southern Europe, the Middle East, and Africa. Materials: 1027 isolates from cultures of urine or expressed prostatic secretion, post-massage urine or seminal fluid, or urethral samples were considered. Results: Escherichia coli is the most frequent pathogen in acute prostatitis. Other Enterobacteriacae may be causative, while Pseudomonas aeruginosa is less frequent, usually secondary to recent urological instrumentations. The rate of Gram-positive pathogens is approximately 5% [Infection is microbiologically proven in approximately 10% of patients presenting with prostatitis-like symptoms . Mid-strately 5% .E. coli and other Enterobacteriacae are the most common pathogens isolated in chronic prostatitis [Enterococci, are increasingly reported [Chlamydia trachomatis, Ureaplasma spp., and Mycoplasma spp.) is still debated [Chronic bacterial prostatitis can present with varied clinical scenarios, including urinary symptoms, perineal, pelvic and genital pain, and sexual symptoms. Mid-stream urine cultures are positive in only a few cases. Other sources utilized for diagnosis include cultures of samples obtained through the four- or two-glass test , and culstatitis , althougreported . The rol debated . Acute p debated . Parente debated .Chronic prostatitis therapy requires the administration of drugs with high penetration in the prostatic tissue, which must be administered for long periods, preferably via the oral route, and must have good tolerability ,8,9.Drugs must be lipid-soluble, have favorable size and shape, and result in minimal serum protein binding to favor diffusion across biological membranes. In recent years, basic drugs such as trimethoprim, macrolides, and tetracyclines have been preferred, although fluoroquinolones are now more often used .Fluoroquinolones still remain the best available drug for the treatment of chronic bacterial prostatitis, although resistance rates to these antibiotics have increased in recent years. Recently, doubts have been raised about the tolerability of these drugs, and empirical use for prostatitis has been discouraged ,11.The effectiveness of fluoroquinolones can be enhanced by combining with macrolides , which, Fosfomycin is another possible alternative to fluoroquinolones for the treatment of prostatitis ,15,16.Nitrofurantoin retains a favorable resistance profile, but its pharmacokinetic characteristics are not ideal for the treatment of prostate infections .Glycopeptides could be an option for the treatment of Gram-positive pathogens, but these agents are not orally absorbed, and we have limited knowledge about their use in prostatitis\u2014although, in selected cases of severe, multi-resistant Gram-positive prostatic infections, the efficacy of glycopeptides has been reported .The effectiveness of the antibiotic treatment of bacterial prostatitis depends on the rates of microbial resistance to antibiotics commonly used to treat prostatic infections, which may change in different geographical areas as a result of environmental and sociocultural characteristics, and how infections are diagnosed and treated and the local use of antibiotics in people and animals.The aim of this study was to assess the microbial spectrum in bacterial prostatitis cases in selected centers in Southeastern Europe, Africa, and the Gulf area, as well as their resistance pattern to commonly used antimicrobials.M. hominis and U. urealyticum were performed using the Mycoplasma IST 2 kit (bioMerieux). C. trachomatis was detected by direct immunofluorescence . For each sample, the isolated pathogen, the source, and the antibiotic resistance pattern exhibited in the antibiogram were recorded. Each class of antibiotics was considered inactive on a specific bacterial strain only if it demonstrated resistance to all of the tested antibiotics of that class . Strains demonstrating intermediate susceptibility were not considered resistant. Resistance to a combination of quinolones\u2013macrolides or amoxicillin/clavulanate-aminoglycosides was also assessed. The combination was classified as \u201cresistant\u201d if the pathogen was resistant to both agents.A study was initiated by U-merge, an association that unites urologists around the world. Eight centers from seven countries, namely, Bulgaria, Greece (two centers), Italy, Qatar, Bahrain, Mali, and Nigeria, participated in this study. The results of microbiological investigations of patients with prostatitis-like symptoms were studied retrospectively. Age and type of clinical presentation were recorded. Cultures of urine, prostatic secretions expressed by prostate massage (EPS), urine evacuated after prostate massage (VB3), seminal fluid and urethral specimens were analyzed. Isolates were identified at the laboratory of each participating center using conventional methods according to local guidelines. Undiluted urine samples were cultured in blood and on MacConkey agar plates. Identification of traditional pathogens was performed by conventional methods or the Vitek-2 Compact system. Isolates were tested for antimicrobial susceptibility using custom broth microdilution panels or disk diffusion. Minimum inhibitory concentration (MIC) values were evaluated according to guidelines of the Clinical and Laboratory Standards Institute (CLSI) (in most extra-European countries) or the European Committee for Antimicrobial Susceptibility Testing (EUCAST) . The local interpretations of antimicrobial susceptibility testing, reported as S, I, or R, were considered for the analyses, as quantitative data were not provided by the participating laboratories. Different antimicrobial agents were included on the panels at each laboratory, according to the local guidelines, with appropriate dilution ranges. The identification and semi-quantitative assay for p-value of <0.05 was considered as statistically significant. Post-hoc analysis was carried out with the Bonferroni test. Contingency tables were built (i) to compare the frequency of pathogens in different countries, (ii) to compare their antibiotic resistance rates, and (iii) to estimate how often different antibiotics were tested in the countries and for pathogens classified as Gram-negative, Gram-positive, and atypical pathogens. Differences between proportions were assessed with the chi-squared test or with a two-tailed Z-test for independent proportions.The mean ages of patients in different countries were calculated, and any difference was analyzed with an ANOVA test. A N = 60) and chronic (N = 924) bacterial prostatitis were considered. Patients were diagnosed in Bahrain (N = 50), Bulgaria (N = 202), Greece (N = 184), Italy (N = 409), Mali (N = 36), Nigeria (N = 30), and Qatar (N = 73). The average age was 46 \u00b1 13 years. The mean ages were higher in Qatar (64 \u00b1 11 years) than in Bahrain (43 \u00b1 8 years), Bulgaria (44 \u00b1 11 years), Greece (46 \u00b1 12 years), Italy (45 \u00b1 13 years), Mali (45 \u00b1 14 years), and Nigeria (44 \u00b1 10 years). The prevalence of acute prostatitis was higher in Mali (47%), Qatar (29%), Nigeria (27%), and Bahrain (14%), while a lower rate was observed in Greece (4%). No cases of acute prostatitis were reported from Bulgaria and Italy. The average age of patients with acute prostatitis was not significantly higher than those with chronic prostatitis . Overall, 1027 pathogens were isolated: A single pathogen in 942 patients, two pathogens in 41 patients, and three pathogens in one patient.A total of 984 patients with acute . Klebsiella spp. was more frequent in acute prostatitis than in chronic prostatitis . The rates of Proteus spp. (3% vs. 4%), P. aeruginosa (3% vs. 2%), other Enterobacteriacae (5% vs. 4%), and other Gram-negative bacteria (5% vs. 4%) were similar in the two groups (p > 0.05). Enterococci , Staphylococci , Streptococci (3% vs. 5% p > 0.05), and other Gram-positive pathogens (0% vs. 2% p > 0.05) were less frequent in acute compared to chronic prostatitis. Atypical pathogens (6%) and fungi (0.1%) were isolated only from chronic prostatitis specimens , Mali (55%), Bahrain (46%), Qatar (40%), Greece (35%), Bulgaria (32%), and Italy (23%). Proteus spp. were less frequent (3\u20134%), except in Nigeria (13%). P. aeruginosa (0\u20132%) was also less prevalent, except in Qatar (11%). Klebsiella spp. ranged between 3% and 8% in Bahrain, Bulgaria, Greece, and Italy, but higher rates were observed in Qatar (26%), Nigeria (23%), and Mali (19%). Rates of other Enterobacteriacae (1\u20138%) and other Gram-negative pathogens (1.5\u20136%) were low in all countries. Gram-positive bacteria were frequently isolated in Greece, Bulgaria, and Italy (41\u201351%) with Enterococci being the most frequent isolate. Lower rates of Gram-positive pathogens were observed in Qatar (17%), Bahrein (27%), Nigeria (0%), and Mali (14%). Atypical pathogens were observed in Greece (4%) and Italy (11%) (ly (11%) .The most frequently tested antibiotics were amoxicillin/clavulanate (57\u2013100%), cephalosporins (60\u2013100%), fluoroquinolones (79\u2013100%), aminoglycosides (41\u2013100%), carbapenems (37\u201374%), and piperacillin\u2013tazobactam . Some antibiotics were not tested, or only tested in a few cases in some countries: In Bahrain, ampicillin in 4% and tetracyclines and fosfomycin in none; in Qatar, glycopeptides in 9% of cases and macrolides, tetracyclines, and fosfomycin in none; in Mali, trimethoprim sulfamethoxazole (TMP/SMX) in 3% and glycopeptides in none; in Nigeria, piperacillin/tazobactam, glycopeptides, macrolides, tetracyclines, and fosfomycin were never tested.The antibiotic resistance rates in different countries are shown in Antibiotics tested in both Gram-negative and Gram-positive pathogens were ampicillin (69% and 82%), amoxicillin/clavulanate (87% and 67%), fluoroquinolones (96% and 80%), and aminoglycosides (79% and 78%). Gram-negative pathogens were tested for piperacillin\u2013tazobactam (64%), cephalosporins (98%), carbapenems (84%), fosfomycin (50%), TMP-SMX (63%), and nitrofurantoin (35%). Less than half of Gram-negative pathogens were tested for glycopeptides (10%), macrolides (8%), and tetracyclines (14%). Gram-positive pathogens were tested for glycopeptides (88%), macrolides (69%), cephalosporins (54%), and carbapenems (50%). Less than half of Gram-positive isolates were tested for piperacillin/tazobactam (46%), tetracyclines (44%), fosfomycin (24%), TMP-SMX (41%), and nitrofurantoin (33%). Atypical pathogens were tested for macrolides, tetracyclines, and quinolones.The antibiotic resistance rates of pathogens are reported in Only 13% of pathogens were simultaneously resistant to quinolones and macrolides, while resistance was ascertained to one of them in 37%.In 4% of pathogens, there was simultaneous resistance to amoxicillin/clavulanate and aminoglycosides, while resistance to one of them was present in 38%.E. coli is the most common isolate in prostate infections, although the frequency of E. coli was higher in acute prostatitis (46%) than in chronic prostatitis (31%).In general, our data confirmed that Enterococci, in chronic prostatitis cases [In our series, Gram-positive bacteria were isolated in 17% of acute prostatitis, but in 42% of chronic prostatitis, in congruence with recent reports of increasing incidence of these pathogens, particularly is cases ,20.E. coli was higher in West African countries (55\u201363%) and in the Gulf countries (40\u201346%) than in European countries (23\u201335%) due to the different acute to chronic infections ratio. In fact, acute infections were more frequently reported in West Africa (27\u201347%) and the Gulf area (14\u201329%) than in Southeastern Europe. Conversely, Gram-positive bacteria were more frequently isolated in Greece, Bulgaria, and Italy (41\u201351%) compared to Qatar (17%), Bahrain (27%), Nigeria (0%), and Mali (14%). Atypical pathogens were researched and observed only in Greece (4%) and Italy (11%).The frequency of Cumulative resistance rates to some antibiotics, such as carbapenems and piperacillin/tazobactam, are still low in both Gram-negative and -positive pathogens. The resistance rates of Gram-positive pathogens also remained low for glycopeptides and amoxicillin/clavulanate. Conversely, the resistance rates to cephalosporines and fluoroquinolones in Gram-negative pathogens were approximately 20%, but higher in Gram-positive pathogens . Finally, the resistance rates of atypical pathogens were 20% and 27% for fluoroquinolones and tetracyclines, while no resistance was observed for macrolides.The rates of antibiotic resistance were different in different geographical areas. Three different geographical scenarios with similar environmental and sociocultural characteristics and healthcare system organization were observed .In West African countries, citizens are eligible for subsidized public healthcare\u2014some have private health insurance, while some are not insured at all.The study cohort from West Africa mainly comprised patients with acute prostatitis and severe symptoms seeking medical attention. Chronic infections seem to be unattended or self-managed. The panel of antibiotics utilized and tested for susceptibility in these countries is limited. Additionally, resistance rates for antibiotics are much higher than in other countries.E. coli isolates, resistance was reported in 74.5\u201381% for ampicillin, 38.8\u201352.5% for amoxicillin/clavulanate, 26\u201347.7% for ceftazidime, 9.3\u201337.7% for gentamicin, 11.7\u201324% for ciprofloxacin, and 60.4\u201381% for TMP/SMX. Ouedraogo et al. [Our findings confirm those of a systematic review of studies focused on urinary tract infections demonstrating high rates of antibiotic resistance in West Africa . Among Eo et al. attributE. coli resistance to ceftazidime from 9% to 22.7% and to ciprofloxacin from 19.9% to 34.8%. The resistance rates for TMP/SMX and ampicillin were already high in 1999\u20132002, while the resistance rates for imipenem (0\u20130.1%), gentamicin (11.1\u201317.7%), and piperacillin/tazobactam (2.1\u20134.9%) remained low. Self-medication seems to be one of the main causes of this increase in resistance. A study in Abu Dhabi [Persian Gulf countries have health systems of high standard freely accessible for citizens, but not expatriates, who should rely on private health insurance or pay out the expenses for health services and medications themselves. The microbiological epidemiology in this area was somewhat similar to that in West Africa, although the panel of antibiotics tested was larger and the resistance rates lower. Increasing antibiotic resistance has been previously reported in the Gulf area . In the bu Dhabi confirmeSoutheastern European countries have universal government-funded or mixed public\u2013private health systems covering diagnostic services, as well as medications.Data from Southeastern Europe are mostly related to chronic prostatitis, which requires more complex and expensive diagnostics and prolonged therapies. Access to diagnostics and the treatment of chronic diseases at no direct cost to the patient could explain the greater number of these cases seeking medical attention in European countries with universal health systems. A larger number of antibiotics were tested with a high resistance pattern, although the resistance rates were lower than those observed in other countries of the survey.Resistance rates <20% were assessed for carbapenems, piperacillin/tazobactam, aminoglycosides (excluding Bulgaria), cephalosporins (excluding Bulgaria), fluoroquinolones, and fosfomycin .Other studies ,27 have International guidelines recommend the empirical treatment of acute bacterial prostatitis with parenteral administration of high doses of bactericidal antimicrobials, such as broad-spectrum penicillins, a third-generation cephalosporin, or fluoroquinolones, that may be combined with an aminoglycoside . CarbapeAccording to our data, this option seems to be feasible in Southeastern Europe or the Gulf area, where resistance to piperacillin\u2013tazobactam is less than 10% and to the association between amoxicillin/clavulanate with an aminoglycoside is <5%.The scenario is more critical in West Africa, where the resistance rate to piperacillin/tazobactam in Mali has been reported to be 58%, and the drug was never tested in Nigeria. The resistance to the amoxicillin/clavulanate and aminoglycoside combination is <10% in Mali, but very high in Nigeria, where the resistance rates to amoxicillin/clavulanate are 100% and to aminoglycosides are 60%.The guidelines still recommend fluoroquinolones as first-line agents in the empirical treatment of chronic bacterial prostatitis, despite the increasing resistance rates of uropathogens to fluoroquinolones.According to our data, the resistance rates in Southeastern Europe for fluoroquinolones are 15%, while much higher rates have been observed in the Gulf area and in West Africa. On the contrary, TMP-SMX, macrolides, and tetracyclines showed resistance rates > 20% in most countries.The association between fluoroquinolones and macrolides may represent an alternative option to be used with caution due to the risk of cardiotoxicity. The microbiological data looks promising in most countries, although susceptibility to macrolides was not tested in Qatar or Nigeria.Fosfomycin is another possible alternative to fluoroquinolones for the treatment of prostatitis. In our study, the resistance rates to fosfomycin were less than 10% in Greece and Bulgaria and 23% in Italy. A high resistance rate was observed in Mali, while susceptibility to the antibiotic was not tested in the Gulf area or Nigeria.A limitation of our study is the possible discrepancy resulting from microbiological investigations in different laboratories using different methodologies and guidelines for clinical breakpoints of antibiotic susceptibility. As a result, the interpretation of antimicrobial susceptibility testing results may vary, at least for resistance estimates close to the breakpoints.On the contrary, the main objective of our study was not a comparison between the resistance rates in different countries, which requires a more rigorous methodology with standardization or centralization of the investigations, but rather a description of the epidemiological aspects based on the microbiological diagnostics available in real life. The data obtained are certainly preliminary, but can be used to plan subsequent investigations that become mandatory due the globalization of health problems.The results of this survey provide us some information about the microbiology and resistance rates of pathogens of prostatic infections, although caution should be exercised when comparing resistance rates across countries, because of differences in sample collections and testing methods. Taking into account these limitations, data from this study may be useful to clinicians to formulate their policies for the empirical treatment of prostatitis; to clinicians in planning treatment of migrant patients or patients resident in other countries for long time; to local health authorities in creating appropriate guidelines based on the microbiological epidemiology of their countries and to put in place medical and veterinary policies to reduce the emergence of further resistance, particularly for those few drugs that still retain high levels of efficacy; to international health organizations in building antibiotic stewardship programs that will limit antibiotic multi-resistant strains."} +{"text": "Current information regarding bacteriemia in patients with solid tumors is scarceTo assess the etiology, clinical features and outcome in patients with solid tumors and bacteremia, we carried out a prospective multicenter study. Episodes of bacteriemia in adult cancer patients in 9 centers, from May 2014 to February 2021, were recorded. To identify factors associated with 30-day mortality, variables with p < 0.05 in univariate analysis were included in a logistic regression model for multivariate analysisStaphylococcus aureus 33%) and polimicorbial 11%; 20% were multidrug resistant organisms (MDR-O), being 88% of them GNB (MDR-GNB). ESBL and KPC carbapenemase producing were the most frequent mechanisms of resistance. Mortality at day 7 and day 30 was 16% and 27%, respectively. In the univariate analysis, the risk factors for 30-day mortality were Charlson index, refractory underlying disease, use of steroids, polimicrobial bacteremia, Staphylococcus aureus, GNB resistant to carbapenems, APACHE and Pitt scores, hypotension, respiratory source and ICU admission. In multivariate analysis, risk factors for 30-day mortality were refractory underlying disease, GNB resistant to carbapenems and ICU admission, while 7-day clinical response was associated with lower mortalityThree hundred and thirty-two episodes of bacteremia were included, with 51% being women (mean age 59). The state of underlying disease was: recent diagnosis 27%, remission 27%, relapsed 29% and refractory 17%. Seventy-three percent had received chemotherapy in the last 30 days, 25% were receiving steroids. Neutropenia was present in 23% (mean duration 3 days). The most frequent sources were: abdominal 39%, urinary tract 21%, respiratory 15%, catheter 10% and skin and soft tissue 9%. The microorganisms were: Gram negative bacilli (GNB) 67% , Gram positive cocci 36% (Bacteremia is a serious complication in cancer patients, with high mortality. The state of underlying disease, infection caused by GNB resistant to carbapenems, and the severity of presentation are associated with increased mortality. Our results stress the importance of infection control measures and antibiotic stewardship to prevent colonization with MDR-OAll Authors: No reported disclosures"} +{"text": "Prostate cancer (PCa) is one of the most frequent causes of cancer death worldwide. Historically, diagnosis was based on physical examination, transrectal (TRUS) images, and TRUS biopsy resulting in overdiagnosis and overtreatment. Recently magnetic resonance imaging (MRI) has been identified as an evolving tool in terms of diagnosis, staging, treatment decision, and follow-up. In this review we provide the key studies and concepts of MRI as a promising tool in the diagnosis and management of prostate cancer in the general population and in challenging scenarios, such as anteriorly located lesions, enlarged prostates determining extracapsular extension and seminal vesicle invasion, and prior negative biopsy and the future role of MRI in association with artificial intelligence (AI). Prostate cancer is the most frequent cancer worldwide in men. Although it is usually considered a slow growing tumor, it remains the third cause of cancer death in the male population. According to Globocan statistics approximately 1,414,259 new cases are diagnosed every year worldwide. The lifetime probability of a man developing PCa is 1 in 9 and the number of estimated deaths caused by PCa in the world during 2020 was 375,304. The regions with higher incidence of PCa are Northern Europe, North America, Caribbean, Australia, and New Zealand [Historically, when PCa was suspected, diagnosis was based on an elevated prostate-specific antigen (PSA), abnormal digital rectal examination, and transrectal ultrasound (TRUS) images, all known to have low sensitivity and specificity for cancer diagnosis. Then a systematic TRUS-guided biopsy was indicated that sampled the main six areas of the peripheral zone of the prostate. However, due to its random nature, this approach has several limitations, such as overall low cancer detection rates as well as a high percentage of detection of indolent prostate cancer. This can lead to overtreatment of a group of patients. During the past few years, the use of MRI as a diagnostic tool has gained momentum with increasing roles in diagnosis, staging, treatment decision, and follow-up of prostate cancer. This review summarizes the importance of MRI in prostate cancer history, its actual recommendations in clinical practice, and the future role of MRI in combination with artificial intelligence.In 1971, Damadian et al. first explored the application of MRI in the diagnosis of cancer in six normal tissue samples and two malignant solid tumors in murine animals. Malignant tissues could be differentiated according to the T1 and T2 relaxation times, as such parameters were outside the range of values when compared with the normal tissues . It was In terms of MRI guided biopsy for suspicious lesions, various sampling techniques are used to secure targeted biopsies, i.e., in-bore MRI-guided biopsy, cognitive biopsy, and MRI-TRUS fusion-guided biopsy. Each technique has strengths and limitations. Cognitive MRI targeted biopsy is a less expensive and time-consuming biopsy and does not require software-based platforms but needs operator expertise on MRI lesion localization. In-bore MRI-guided biopsy provides direct visualization of lesions, with fewer cores needed. However, the length of the procedure is longer, which increases the cost of the technique. p = 0.13), and neither for FUS-TB compared with COG-TB (p = 0.11) [A meta-analysis compared three different techniques for MRI targeted biopsy (in-bore MRI target biopsy (MRI-TB) , MRI-tra = 0.11) . Guideli = 0.11) ,8.The use of MRI in detection of PCa has been validated in different clinical settings. PROMIS and PRECISION trials reported the diagnostic accuracy of the use of MRI in detection of PCa. In the PROMIS study, 740 men were enrolled and 576 men were randomized to multiparatric MRI (mpMRI) targeted biopsy group versus standard biopsy. Clinically significant cancer was detected in 40% in the MRI-TB group, compared to 26% in the standard-biopsy group. Furthermore, mpMRI with or without targeted biopsy was non inferior to standard biopsy, and the 95% confidence interval indicated the superiority of this strategy over standard biopsy [p = 0.005). In terms of both sensitivity (93% vs. 48%) and negative predictive value (89% vs. 74%) mpMRI was superior to the standard approach and could identify a quarter of men who might safely avoid an unnecessary biopsy. Additionally, the PRECISION study reported that mpMRI had a 29% detection rate of clinically significant (CS) PCa (defined as Gleason Score \u2265 3 + 4 = 7) for PIRADS 3 lesions, 40% for PIRADS 4, and 31% for PIRADS 5 [The PRECISION trial showed that mpMRI was more accurate than TRUS-biopsy for PCa detection. This trial randomized 500 patients with elevated PSA and suspicion of PCa to either mpMRI or standards biopsy. For those men who underwent mpMRI if they were diagnosed with a suspicious lesion \u2265 3, a targeted biopsy of the lesions was performed. Prostate cancer was detected in 95 men (38%) in the MRI-targeted biopsy group, as compared to 64 of 248 (26%) in the standard-biopsy group [The use of MRI in patients with prior negative biopsy has also been studied with interesting results by Vourganti et al. who assessed cancer detection rates for this group of patients when using mpMRI and FUS-TB in 195 men with previous negative biopsies. The authors reported that 73 (37%) men were found to have cancer and high-grade cancer (Gleason score \u2265 8) was detected in 21 (11%) of them. Furthermore, 55% of high-grade cancers were missed by standard transrectal ultrasound biopsy. Pathological upgrading occurred in 28 men (38.9%) as a result of mpMRI- FUS-TB vs. standard transrectal ultrasound biopsy . Anotherp = 0.4) Results MRI has also shown to improve cancer detection in patients with no prior biopsy. A meta-analysis including 29 studies with 13,845 patients compared the use of mpMRI and targeted biopsy to standard biopsy. 15% higher rate of any PCa diagnosis was reported in the mpMRI targeted biopsy group. Diagnoses of clinically significant and high-grade PCa were more common in the mpMRI imaging targeted biopsy group while there was no difference in diagnosis of clinically insignificant PCa .Another important contribution of MRI is to be able to differentiate between benign and malignant tissue. In terms of factors predicting for benign pathology on mpMRI, Troung et al. developed a nomogram that considered the use of parameters such as age, prostate-specific antigen, prostate volume, and PIRADS score to predict benign pathology on mpMRI. The authors described the results with 2 different thresholds: cutoff 0.7 and 0.4. With a cutoff probability of 0.4, 36.5% of patients would have avoided unnecessary biopsy. However, 6.3% of CS PCa would have been missed. When the cutoff of \u22650.7 was used, 21.4% of patients would have avoided an unnecessary biopsy, and CS PCa would have been missed in only 1.4% of cases .Increasing evidence supports the use of mpMRI for anteriorly located lesions which are usually underdiagnosed. These lesions are often missed by conventional standard TRUS-guided biopsy given their anterior location is not easily reached by conventional techniques. In a study by Volkin et al. of 499 patients undergoing MRI-TRUS fusion-guided biopsy, 162 patients had anterior lesions. PCa was detected in 121 anterior lesions (50.2%) identified on mpMRI and 40.2% of these lesions were diagnosed by targeted biopsy compared with 25% diagnosed by the standard TRUS-guided biopsy approach .Another trial included 39 patients with previous negative TRUS-guided biopsy who underwent prostate mpMRI including DWI. Patients with a suspicious anterior lesion on mpMRI underwent targeted anterior gland TRUS-guided biopsy with cognitive fusion technique. Anterior gland prostate adenocarcinoma was diagnosed in 46.2% on targeted cores, and CS PCa was diagnosed in 13 patients (33.3%). Biopsies were positive in 90% of patients with overall PIRADS 5 lesions, and 33% of patients with PIRADS scores of 4 . These s3. Detection rate was 77% for prostate glands less than 30 cm3, and 61%, 47% and 34% for glands 30 to less than 38.5, 38.5 to less than 55, and 55 to 160 cm3, respectively (p = 0.001) [Standard systematic TRUS-guided biopsy cancer detection rates decrease with increasing prostate volume. In this setting, mpMRI-targeted biopsy appears to increase the accuracy of PCa detection. MRI FUS-TB represents a promising solution for patients with suspicion of PCar and an enlarged prostate. In a trial of 649 patients with a mean whole prostate volume of 58.7 cc the overall cancer detection rate of the MRI FUS-TB was 55%. For prostates < 40 cc the detection rate was 71.1% compared to 57.5% for standard systematic TRUS-guided biopsy, 46.9%, 46.9% 33.3%, 36.4%, and 30.4% for glands 40 to 54.9, 55 to 69.9, 70 to 84.9, 85 to 99.9, 100 to 114.9, and 115 cc or greater, respectively. Inverse association of mpMRI volume with PCa detection, controlling for age and prostate-specific antigen was also reported . Similar= 0.001) . These sThe role of this imaging technique has expanded beyond detection of cancer, including staging of tumors with evaluation of extracapsular extension (ECE) and seminal vesical invasion (SVI), as well as improved characterization of possible candidates for active surveillance. Accurate staging is one of the fundamentals in oncology in order to determine the best therapeutic alternative for patients. mpMRI has demonstrated high specificity and negative predictive value for predicting pathologic ECE and SVI. In a trial of 79 patients that were studied with mpMRI, 28% patients had ECE, 5% SVI, and 4% lymph node involvement (LNI) in mpMRI. p = 0.3 and 71.8% vs. 61.3%, p < 0.001). Performance of the nomogram with regards to SVI was comparable in terms of discrimination , and a net benefit for probability threshold above 7.5% validating a nomogram predicting ECE and SVI in patients diagnosed with mpMRI-targeted biopsy [Tools such as Memorial Sloan Kettering Cancer Centre and Partin tables have been used to predict ECE or SVI. Recently a nomogram including mpMRI parameters and mpMRI-targeted biopsy was developed. Performance of the nomogram in comparison with the Memorial Sloan Kettering Cancer Center (MSKCC) model and Partin tables, was evaluated. Regarding ECE prediction, the nomogram showed high discrimination men in the non-MRI arm and 98 (77%) continued on active surveillance. Median follow-up was two years. This trial demonstrated that mpMRI before targeted biopsy resulted in fewer men with active surveillance failure (19% vs. 35%), and there were fewer men with CS PCa detected at two years after follow-up biopsy in the MRI arm (9.9% vs. 23%) thus confirming the role of mpMRI in men with PCa undergoing this treatment approach. No significant differences in progression free survival (PFS) and radical intervention were documented .MRI guided biopsy has also been studied to determine the risk of pathologic upgrading in patients on active surveillance on confirmatory biopsy. In a retrospective cohort study, 332 patients with prostate cancer ISUP group of 2 or lower were included in confirmatory biopsy protocol using MRI FUS-TB. The protocol established performing MRI FUS-TB at 12\u201324 months. 11.7% of patients were upgraded to ISUP 3 during follow up and those with a PSA density \u2265 0.15 ng/mL were at higher risk for upgrade on confirmatory biopsy. Therefore, the combination of confirmatory biopsy with MRI and PSA density could be an interesting combination tool to explore in prospective trials . SimilarMRI in PCa is an evolving tool which has contributed to the field of diagnosis, staging, and determination of treatment options for this disease. However, a concerning limitation for wide implementation of this technique has been inter-reader variability and experience which is known to affect its performance ,37,38,39AI in PCa has been applied in different settings such as assessment of benign/malignant lesions, to distinguish significant versus non-significant cancer, defining active surveillance candidates, staging, prediction of response to treatment, and recurrence among others ,48,49,50p < 0.1), and with Gleason score in the transition zone [Kwak et al. investigated the association between mpMRI and digital histopathologic analysis (DHA). They used machine learning models in 40 patients to compare the mpMRI and DHA. In their study, DHA correlated positively both with specific regions containing benign versus malignant tissues , and radiologic assessment for characterizing benign versus malignant lesions. Quantitative measurement of the ADC significantly had a 62% specificity and a 90% sensitivity which had similar performance with radiomic machine learning and outperformed clinical assessment .p = 0.0007 < 0.001) [Interestingly, Bulten et al. developed a deep-learning system to be able to reduce the inter-observer variability for determining Gleason grade. A total of 1243 patients were included in this retrospective study performed in the Netherlands in which 5759 biopsy specimens were collected. The deep learning automated system demonstrated an AUC of 0.990 for differentiating between benign and malignant lesions and outperformed 10 of the 15 pathologist in determining Gleason grade, with high agreement with the reference standard (quadratic Cohen\u2019s kappa 0.918 95% CI 0.891\u20130.941) . Further< 0.001) .PCa is an heterogenous disease in terms of aggressiveness and currently there are no effective biomarkers available to predict the nature and progression of the disease. A retrospective study of 64 patients with PCa found 14 radiomics features that correlated with the Gleason score and 31 histogram and texture characteristics that correlated with different gene signatures. Although prospective trials are required, radiomics features with machine learning prediction models are promising markers for cancer aggressiveness .Another possible key application for AI models is to assist in reducing unnecessary biopsies in certain clinical scenarios to decrease the overload of healthcare systems, especially where specialists are not easily available ,67. A reAI has also been studied in terms of response to treatment in patients with metastatic castration resistant prostate cancer. Deng et al. implemented a model based on 78 different features that included laboratory abnormalities, patient characteristics, and clinical and oncological history. Prediction performance was evaluated by area under the curve models in 1600 patients. Determination of 10 important features in an implemented model demonstrated that early discontinuation of treatment can be predicted from clinical information of the patients .mpMRI technique has evolved in the past years from T1-weighted and T2-weighted sequences to modern sequences such as DWI, DCE, and magnetic resonance spectroscopy imaging which have improved the diagnosis of prostate cancer in the general population in multiple clinical scenarios ,72,73,74"} +{"text": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seropositivity was assessed for 3,066 individuals visiting hospitals in St. Louis, Missouri, during July 2020, November 2020, or January 2021. Seropositivity in children increased from 5.22% in July to 21.16% in January. In the same time frame, seropositivity among adults increased from 4.52% to 19.03%, prior to initiation of mass vaccination.IMPORTANCE This study determined the percentage of children and adult samples from the St. Louis metropolitan area in Missouri with SARS-CoV-2 antibodies during three collection periods spanning July 2020 to January 2021. By January 2021, 20.68% of the tested individuals had antibodies. These results show the evolution of the SARS-CoV-2 pandemic in St. Louis, Missouri, and provide a snapshot of the extent of infection just prior to the start of mass vaccination. Accurate estimates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection rates are vital in understanding viral spread and death rates and in planning vaccine distribution. Reported coronavirus disease 2019 (COVID-19) cases likely underestimate true prevalence due to a large number of mild and asymptomatic cases. Seroprevalence studies test for the presence of antibodies rather than virus for adult patients presenting to Barnes-Jewish Hospital in St. Louis, Missouri, in April-May 2020 results were aggregated with previously published April 2020 data (2). DurWithin the adult cohort, the estimated seroprevalence rate of our samples increased from 3.11% in April 2020 to 4.52% , 6.09% , and then 19.03% in July 2020, November 2020, and January 2021, respectively. Within the pediatric cohort, the estimated rate in April 2020 was 1.72% . The rate increased to 5.22% , 15.56% , and finally 21.16% in July, November, and January .P = 0.0057). Additionally, during the April 2020 collection period, we previously found a significantly lower positivity in young children (less than 5\u2009years) than in adults (P > 0.204).Our results do not provide evidence for seroprevalence rate differences based on sex during the first three collection periods but show significantly higher rates in males than females during January 2021 ; thus, vaccination is unlikely to have substantially impacted the seropositivity rate. To experimentally assess whether the adult January 2021 seroprevalence rate we report was affected by vaccines, we also tested these samples for reactivity to nucleoprotein (NP) (see P = 0.78).Vaccination in St. Louis, Missouri, began on 14 December 2020. During the final adult collection window, ranging from 25 December 2020 through 5 January 2021, 0.96% to 2.05% of the St. Louis population had received at least one vaccine and 0% to 0.11% had received both doses , largely overlapping with the seroprevalence rate we estimated using the spike assay, 19.03% . Therefore, while some vaccinated individuals may be included in our cohort, the low vaccination rate during the collection window and NP-based seroprevalence rate suggest that any potential effect of vaccination would be minimal.Our study estimates the prevalence of SARS-CoV-2 IgG antibodies in residual serum/plasma samples collected during three collection windows between July 2020 and January 2021, prior to mass vaccination in St. Louis, Missouri. We report seroprevalence rates for adult and pediatric cohorts during July 2020, November 2020, and January 2021 collection windows, aggregated with previously reported rates for April 2020.Our study has several limitations. Samples are collected from patients obtaining medical care so are not necessarily generalizable to the St. Louis population. Additionally, collection dates for pediatric and adult patients are similar for each window, though not identical. Discrepancies between collection dates and inclusion criteria between pediatric and adult cohorts may limit comparative interpretation of the observed rates. Further, the kinetics of antibody waning over time is currently unclear , 4. SomeFor samples collected in January 2021, the estimated seroprevalence rates are 19.03% for adults and 21.16% for the pediatric cohort. These rates are similar to the 18.9% seroprevalence rate found in patients receiving dialysis across 43 states in January 2021 (https://slu-opengis.github.io/covid_daily_viz/index.html). Because the midpoints of adult and pediatric November collection periods occurred on November 2 and November 15, respectively, the pediatric November data may have captured more of the peak in reported cases in St. Louis than the adult data.Among pediatric samples, the greatest increase in prevalence between collection periods occurred between July and November . Howeverhttps://slu-opengis.github.io/covid_daily_viz/index.html). However, this seroprevalence rate remains substantially lower than that required to achieve herd immunity . Collection windows for pediatric specimens were 22 July 2020 to 16 August 2020, 1 November 2020 to 30 November 2020, and 24 December 2020 to 21 January 2021, and 502 to 546 samples were collected during each period. This study was approved by the Human Research Protection Office at Washington University in St. Louis (202004199 and 202004153).SARS-CoV-2 spike and NP ELISAs. Seropositivity for 3,066 samples was assessed using an in-house IgG ELISA based on spike antigen. Vaccination of adults in St. Louis, Missouri, began just prior to the January 2021 collection window so spike-positive samples were also tested for reactivity to nucleoprotein (NP). The development and validation of in-house IgG ELISAs based on NP and trimeric spike proteins were described previously method was implemented in python using the PyStan package (P values (2 discrepancy measure between generated data sets and expected values drawn from the posterior distribution. package . BayesiaP values , reflect"} +{"text": "Informed by social cognitive theory, Age-Friendly Columbus and Franklin County conducted a community-engaged mixed methods study that examined the needs and utilization of alternative transportation by older residents in three pilot neighborhoods in Franklin County, Ohio (n = 32). Participants were provided tablets and used an app (MyAmble) developed at the University of Texas-Arlington to document their traveling experiences. During a 14-day period, 1,190 trips were recorded by older adults and 71.3% of these trips were completed through driving their own personal vehicles. Participants designated 84.5% of trips as important and 72% of the trips improved their mood. Individual , environmental , and behavioral barriers and facilitators to alternative transportation use such as riding the bus, walking and biking were identified."} +{"text": "Dear Editor,Although the incidence and risk factors of venous thromboembolism [VTE] is well characterized in multiple myeloma [MM], little is known regarding the characterization of arterial thromboembolism [ATE] in the context of modern anti-myeloma therapy. Since MM is a cancer of older adults with several shared risk factors for cancer and cardiovascular disease, ATE remains an area of major concern. Notably, population-based studies from Sweden have demonstrated an increased risk of ATE in MM compared to matched controls, with an incidence of 3.8% in the first year . AnotherWe included all consecutive MM patients treated at the Cleveland Clinic from 1/1/2008 to 12/31/2018. We identified potential baseline disease-related, patient-related and treatment-related risk factors a priori and extracted from medical records. The primary endpoint was to estimate ATE incidence in the first year after treatment initiation. Secondary endpoints were to identify risk factors for ATE and association of ATE with overall survival [OS].p value.We calculated the cumulative incidence of ATE by 12 months. Death without ATE was a competing risk for ATE. Fine and Gray regression was used to identify univariate risk factors for ATE and results were reported as hazard ratio [HR] with 95% confidence intervals [CI]. We tested the following pre-treatment variables: year of treatment, age, sex, race, immunoglobulin subtype, International Staging System [ISS] stage, bone marrow plasma cell percentage, M-protein, involved/uninvolved free light chain ratio, karyotype, high-risk FISH, lactate dehydrogenase, creatinine, calcium, hemoglobin, prior ATE, prior VTE, body mass index, diabetes mellitus, chronic kidney disease, hypertension, hyperlipidemia, total leukocyte count, platelet count, liver disease, acute infection (within 90 days before treatment), erythropoietin use, clotting disorders, autoimmune disease, hyperviscosity, dexamethasone dose, doxorubicin use, multi-agent chemotherapy, smoking status, IMiD use, and concurrent anti-platelet/anti-thrombotic therapy. If HR could not be calculated, Gray test was used instead to assess association with ATE; this occurs for variables with categories that have 0% or 100% ATE events. Survival based on occurrence of ATE was assessed by landmark analyses at 6 and 12 months. For this analysis, Kaplan\u2013Meier survival estimates at 5 years were calculated for those with or without ATE by the landmark along with log-rank test A total of 1029 consecutive patients met inclusion criteria, of whom 934 patients with available data on initial anti-myeloma therapy were analyzed. The baseline clinical and demographic characteristics are summarized in Table n\u2009=\u200910; 40%], acute myocardial infarction , transient ischemic attack , peripheral artery embolism , and superior mesenteric artery thrombosis . Of 15 patients for whom response status at the time of ATE was available, 4 had very good partial response [VGPR], 7 had PR, and 4 had stable disease.A total of 25 ATE events were observed within a year of treatment initiation. The cumulative incidence of ATE at 6 and 12 months was 2.0% and 2.7% respectively. The Kaplan\u2013Meier curve for cumulative incidence of ATE, along with that of VTE for comparison, is shown in Fig. p\u2009=\u20090.038], prior ATE , diabetes mellitus , chronic kidney disease , hyperlipidemia , acute infection , and current smoker . Of note, use of IMiDs in induction therapy was not associated with an increase in ATE risk . We did not find any significant association between the use of thromboprophylactic agents and incidence of ATE.On univariate analysis, the following factors were significantly predictive of ATE: ISS stage III disease and that at 12-month landmark was 45% and 63% respectively [p\u2009<\u20090.001]. The Kaplan\u2013Meier curves for survival using landmark analysis at 6 and 12 months is shown in the figure in Supplementary Appendix Subsequently, we evaluated the association of ATE with OS. Of 25 patients with ATE events, nine were alive with a median follow-up after ATE diagnosis of 23.9 months . The 5-year OS among patients with or without ATE at 6-month landmark was 39% and 60% respectively , which is a non-modifiable risk-factor for atherosclerotic cardiovascular disease . HoweverIn summary, we show a small but significant risk of ATE in the first year after myeloma diagnosis in the current era, with several modifiable risk factors, including diabetes, hyperlipidemia, and smoking. A history of ATE was present in 12% of patients prior to myeloma diagnosis, which was the strongest risk factor for subsequent ATE. Patients with myeloma should undergo a thorough risk assessment for ATE at diagnosis. There is a paucity of data on primary prophylaxis for ATE in patients with cancer. A phase III RCT comparing LMWH (nadroparin) to placebo for prevention of VTE and ATE in solid tumor patients demonstrated a decrease in ATE risk by 50% (0.4% in nadroparin arm and 0.8% in placebo arm) . HoweverFigure LegendSupplementary Appendix A"} +{"text": "Compliance with influenza immunization in HCW remains a global challenge, uptake in the Middle East has been reported at 24.7% due to limited access and awareness (1). We aim to report a successful campaign by establishing a multidisciplinary Flu Team during ongoing COVID-19 pandemic.A multidisciplinary Flu team taskforce was assembled representing all stakeholders to include: Occupational Health, Nursing, Operations, Infomatics, Pharmacists and Administrative staff in July 2020. A pivot was made to switch location from previous year visits to an established vaccine center to a mobile campaign. From July to November 1st, the team met on a regular basis with 90 stakeholders to launch and monitor the ongoing immunizations. Electronic medical record (EPIC) tools such as One Click and Express Lane facilitated nursing check-in, documentation and immunization at one stop and eliminated previously used registration by other staff. EPIC Clarity feature facilitated reporting of compliance for managers and leadership. Ongoing education and awareness of immunization were ongoing through various platforms of communication such as huddles, phone screens, elevators, lounges, virtual grand rounds and corporate intranet communication and website videos.Of the 3578 healthcare workers, 3,399 were immunized (95%) from September 2020 until the end of October 2020. There were 86 (2.4%) employees exempted during this period due to medical reasons or excused leaves , Figure 1. Compliance differed among functions, 95.86% physicians, 97.2% clinical and nursing, 92% academics, 94.96% finance, 91.15% human resources, 92.1% infomatics, 60% legal, 80.6% operations. Only 93 (2.6%) were non-compliant.Employee Flu ImmunizationHospital Overall Compliance in 2020Compliance by Function in 2020Influenza illness adds an additional burden to the healthcare workforce during COVID-19. A multidisciplinary and collaborative team of teams approach delivered higher compliance for flu immunization than reported in the Middle East and enhanced by the use of state of the art technology. Convenience, educational awareness, free and safe access supported further the compliance with vaccination. To our knowledge, our 2020 flu campaign is the first successful experience reported in the Middle East during the current pandemic.All Authors: No reported disclosures"} +{"text": "Expanding antiviral therapy to benefit more populations and optimizing treatment to improve prognoses are two main objectives in current guidelines on antiviral therapy. However, the guidelines do not recommend antiviral therapy for inactive hepatitis B surface antigen (HBsAg) carriers (IHCs). Recent studies have shown that antiviral therapy is effective with good treatment outcomes in IHC populations. We conducted a systematic review and meta-analysis of HBsAg clearance and conversion in IHCs.We searched PubMed, Embase, Medline, and Web of Science to retrieve articles on HBsAg clearance in IHCs published between January 2000 and August 2021. Data were collected and analysed using the random-effects model for meta-analysis.A total of 1029 IHCs from 11 studies were included in this analysis. The overall HBsAg clearance rate was 47% : 31% - 64%), with a conversion rate of 26% (95% CI: 15% - 38%) after 48 weeks of Pegylated interferon (Peg-IFN) treatment. In the control group (including nucleos(t)ide analogue (NA) treatment or no treatment), the overall HBsAg clearance rate was only 1.54% (95% CI: 0.56% - 3.00%), which was markedly lower than that in the Peg-IFN group. Further analysis showed that a low baseline HBsAg level and long treatment duration contributed to a higher HBsAg clearance rate.This study showed that treatment of IHCs can be considered to achieve a clinical cure for chronic hepatitis B virus (HBV) infection. After Peg-IFN treatment, the HBsAg clearance rate was 47%, and the conversion rate was 26%, which are markedly higher than those reported by previous studies on Peg-IFN treatment in patients with chronic hepatitis B (CHB). A low baseline HBsAg level and long treatment duration were associated with HBsAg clearance in IHCs. Therefore, antiviral therapy is applicable for IHCs, a population who may be clinically cured.http://www.crd.york.ac.uk/PROSPERO, CRD): CRD42021259889. Chronic hepatitis B virus (HBV) infection is an important cause of liver cirrhosis and hepatocellular carcinoma (HCC) . To reduImmune function can control HBV DNA and maintain HBsAg at a low level in IHCs. Moreover, the cumulative number of patients receiving antiviral therapy has increased over the past decades, and the population of patients with low HBsAg levels has expanded significantly. In the past, few studies have focused on whether IHCs are eligible for antiviral therapy and how such therapy may benefit patients. In this study, we performed a literature review and meta-analysis of recent reports.http://www.crd.york.ac.uk/PROSPERO, CRD): CRD42021259889).This review was registered in the International Prospective Register of Systematic Reviews; the protocol is available online guidelines and condThe titles, abstracts, and keywords of eligible articles were screened. Next, the abstracts and the full texts were carefully read for further screening, and duplicate publications were excluded. Two researchers independently completed this process and assessed the relevance of each study and the quality of the methodology. Any discrepancy was resolved with the help of a third researcher.The inclusion criteria were as follows: (a) studies with more than 20 IHCs with HBsAg clearance data after pegylated interferon (Peg-IFN) treatment, nucleos(t)ide analogue (NA) treatment, or no treatment; and (b) studies with adequate data, including the frequency and rate of HBsAg clearance and observations with at least 24 weeks of Peg-IFN treatment, NA treatment, or no treatment. Studies with inadequate data and studies including patients with liver transplantation or HCC before HBsAg clearance or with human immunodeficiency virus (HIV), hepatitis C virus (HCV), or hepatitis D virus (HDV) coinfection were excluded.Two researchers independently extracted data from the articles with a standard form. Data collected included the author, year of publication, country/region where the study was conducted, study design, sample sizes of the Peg-IFN group and the control group, patient ages, and baseline HBV DNA levels. Outcome data included the frequency and rate of HBsAg clearance and HBsAg conversion and Peg-IFN treatment courses in different groups.In this meta-analysis, IHC status was defined as HBsAg(+) >6 months, HBsAg <1500 IU/mL, HBeAg (\u2013), anti-HBe(+) or (-), anti-HBc(+), HBV DNA < 2000 IU/mL, normal alanine transaminase (ALT), and no cirrhosis on ultrasound or FibroScan. The treatment group received Peg-IFN, and the control group received NA or no treatment. The outcome measures were HBsAg clearance and conversion after 48 weeks of treatment or follow-up. In addition, subgroup analyses were performed to evaluate the correlations between baseline HBsAg and treatment course and HBsAg clearance.Two researchers independently assessed the quality of the articles. The Newcastle-Ottawa Scale (NOS) was used to assess quality and bias . The NOS2I test and Cochrane\u2019s Q test were performed to assess among-study heterogeneity, and a funnel plot and Egger\u2019s test were used to assess any publication bias , Freeman-Tukey double-arcsine transformation was used to stabilize the variance, and the Wilson method was used to calculate the 95% confidence intervals (CIs) suggested no significant publication bias. Eight studies reported HBsAg clearance at 48 weeks in the Peg-IFN group and the control group. The results showed that Peg-IFN treatment significantly increased the HBsAg clearance rate (relative risk (RR)=16.46, 95% CI: 7.60% - 35.66%, P<0.001, 2 = I0%, Among the 11 studies on HBsAg clearance in IHCs after Peg-IFN treatment, the total sample size was 1029 patients, including 566 in the Peg-IFN group and 463 in the control group . Peg-IFN treatment lasted 24 to 96 weeks [24 weeks: n=1 ; 48 weekTo evaluate the effect of baseline HBsAg on HBsAg clearance and reduce data heterogeneity, we analysed the data of patients who completed 48 weeks of Peg-IFN treatment, with stratification based on HBsAg level. The patients were divided into five groups based on their baseline HBsAg levels: <10 IU/mL, <20 IU/mL, <100 IU/mL, <500 IU/mL, and <1000 IU/mL. Two studies with baseline HBsAg levels <1500 IU/mL were excluded from the analysis due to data bias. The results showed that baseline HBsAg was inversely correlated with the clearance rate. After 48 weeks of Peg-IFN treatment, the HBsAg clearance rates were 92% (95% CI: 79% - 99%) for HBsAg <10 IU/mL, 88% (95% CI: 77% -95%) for <20 IU/mL, 73% (95% CI: 62% - 83%) for <100 IU/mL, 60% (95% CI: 48% - 71%) for <500 IU/mL, and 39% (95% CI: 25% - 53%) for <1000 IU/mL Figure\u00a05P=0.5). This finding may be related to the small sample sizes and significant heterogeneity in the 24-week and 48-week groups.To evaluate the effect of Peg-IFN treatment courses on HBsAg clearance, we analysed the clearance rate among IHCs with baseline HBsAg <1000 IU/mL after Peg-IFN treatment. The HBsAg clearance rates were 29% (95% CI: 17% - 40%) after 24 weeks of treatment, 39% (95% CI: 25% - 53%) after 48 weeks of treatment, and 43% (95% CI: 35% - 50%) after 96 weeks of treatment , the overall clearance rate was only 1.54%, which was markedly lower than that in the Peg-IFN group, suggesting that IHCs may be clinically cured and that Peg-IFN treatment is far more effective than NA treatment in achieving this goal.The clearance rate ranged from 20% to 94% across the studies due to different baseline HBsAg levels, Peg-IFN treatment courses, and sample sizes. To minimize data heterogeneity, we first analysed factors affecting HBsAg clearance in IHCs who completed 48 weeks of Peg-IFN treatment and found that baseline HBsAg was inversely correlated with the clearance rate, which was 92% among IHCs with baseline HBsAg levels <10 IU/mL. Next, we analysed the clearance rate after different Peg-IFN treatment courses in patients with baseline HBsAg levels <1000 IU/mL and found that the HBsAg clearance rates were 29% after 24 weeks of treatment, 39% after 48 weeks of treatment, and 43% after 96 weeks of treatment. These data indicate that a low baseline HBsAg level and longer Peg-IFN treatment are favourable factors for HBsAg clearance with practical value for the clinical treatment of IHCs along with the predictive value of post-Peg-IFN treatment HBsAg and ALT. While the overall HBsAg clearance rate is substantially higher among IHCs than among CHB patients, more precise planning can enable targeted treatment to help IHCs achieve a clinical cure and an optimal outcome as early as possible and at a lower cost. Patients who do not respond to Peg-IFN treatment can discontinue treatment early to prevent adverse drug reactions, which also has pharmacoeconomic value.This study has some limitations. First, because current Chinese and international guidelines do not recommend treatment for IHCs, few prospective, multicentre cohort studies have been conducted to investigate posttreatment HBsAg clearance in IHCs, and the sample sizes in available studies are usually small. Second, all studies included in this meta-analysis were conducted in the Asia-Pacific region, without any study from Europe or the US, which is due to the regional deviation in the hepatitis B prevalence. The European and American hepatitis B guidelines do not recommend treatment for IHCs. This recommendation is primarily based on studies in Caucasian populations in Europe and the US showing that for IHCs, the HBsAg conversion rate is 15% to 45% over a 10-year follow-up period, without any significant increase in the incidence of HCC compared to that for the general population . HoweverIn short, this meta-analysis shows that IHCs may achieve a high HBsAg clearance rate (47%) after Peg-IFN treatment. Given the very large IHC population and the high response rate, IHCs should be treated with antiviral therapy, as they have the potential to be clinically cured.The original contributions presented in the study are included in the article/AS, XL, and XC conceived and designed the protocol and study. JL and SR identified studies to be screened. ZC and HL identified studies for eligibility, extracted data, and assessed the methodological quality of the included studies. AS performed the analysis with assistance from SZ, ZH, CS, and XC. All authors contributed to the article and approved the submitted version.This work was supported by the Thirteenth Five-Year Major Science and Technology Projects , the Capital Health Research and Development Projects (2020-1-2181), the Beijing Municipal Administration of Hospitals Clinical Medicine Development of Special Funding Support (ZYLX202125), and the Key R&D and Transformation Plan in Qinghai Province (No. 2017-SF-159).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Our study examined the effects of COVID-19 pandemic and public health measures on family caregivers (FCGs) of frail older adults; specifically, their care work, anxiety, and loneliness all of which are associated with decreased wellbeing. Approximately 604 FCGs completed the survey and findings evidenced COVID-19 creating two solitudes. First, 73% of FCGs for individuals living with them were providing significantly more care during COVID-19. Second, those caring for residents in congregate settings were unable to care. Both situations, community-dwelling and congregate care, increased FCG distress and decreased wellbeing. Anxiety significantly increased from 36% pre COVID-19 to 54% during COVID-19. Loneliness increased from 46% to 85%. FCGs report their mental (58%) and physical (48%) health deteriorated. The detrimental impact of the pandemic and public health measures on FCGs caring at home and in congregate care, and their related needs, need immediate attention from both the health and social systems of care."} +{"text": "COVID-19 outbreaks have been reported in homeless shelters across the United States (Through conversations with public health and housing assistance partners, CDC identified sixFull COVID-19 vaccination coverage among persons experiencing homelessness ranged from 18.6% to 44.5% in the six jurisdictions compared with 43.6% to 59.8% in the general population in each jurisdiction or corresponding area . In eachThese estimates highlight relatively low COVID-19 vaccination coverage among persons experiencing homelessness compared with coverage in the general populations in a convenience sample of six jurisdictions. Estimating vaccination coverage for persons experiencing homelessness is challenging because housing status is not routinely collected in vaccination records. In addition, because homelessness could be temporary, estimating population size is difficult. Some health departments have overcome these challenges by fostering relationships with health clinics and homeless service providers. The use of integrated data systems to link deidentified, individual-level records across housing, health care, and public health systems is an emerging potential solution.The findings in this report are subject to at least three limitations. First, because of varying data collection methods, comparison across jurisdictions was not possible. Second, the systems used for estimating homelessness rely on use of homeless services, and not all persons experiencing homelessness access these services, particularly persons living unsheltered. Finally, because of nonrandom selection and inclusion of only six jurisdictions, these findings are not generalizable to all persons experiencing homelessness in the United States, particularly in rural areas.Given low COVID-19 vaccination coverage and increased risk for infection with SARS-CoV-2, the virus that causes COVID-19, in congregate settings ("} +{"text": "Emergency departments (EDs) serve as sentinel settings for diagnosing sexually transmitted infections (STIs), including HIV and syphilis. We aimed to assess performance and patient acceptability of a point-of-care (POC) test, the Chembio Dual Path Platform (DPP\u00ae) HIV-Syphilis Assay, in an urban ED in Baltimore.170 patients were enrolled via convenience sampling from Oct 2019 \u2013 March 2020 and Jan 2021 \u2013 June 2021. Patients eligible were < 70 yrs, men who have sex with men, pregnant without care, had STI concerns, or history of drug use. Subjects received standard of care (SOC) HIV and syphilis testing under institutional laboratory algorithms. Subjects were then tested with the finger-stick POC test and completed a survey, both before and after the POC test to assess subjects\u2019 attitudes about the POC test.Comparing the SOC and POC results, 165/170 (97.1%) were test concordant. 3 syphilis POC results were false negative, but reported successful treatment over 10 years prior to enrollment . 1 HIV result was false negative and 1 was false positive. Overall the sensitivity and specificity of the HIV POC test were 96.8% and 99.3% , and for syphilis were 85.7% or 100% , if excluding 3 persons having been successfully treated, and 100% respectively.The pre-test survey found 67% and 77% of participants were comfortable with a finger-stick test and agreed the POC test result would be as good as the SOC test result, which increased to 96% and 86% in the post-test, respectively, (p< 0.05). At post-test, 86% reported they would feel confident to perform this test at home and 81% would use it at least once per year if it were available. 97% reported they were more likely to seek treatment if receiving a positive result during their ED visit and 91% reported it would reduce their stress/anxiety if receiving a negative test result in the ED.Our findings demonstrated satisfactory performance and high patient acceptability of the Chembio DPP\u00ae HIV-Syphilis Assay. Given the test is FDA approved, implementation studies are needed to determine whether adoption of this POC test will benefit patients and be consistent with ED workflows.Richard E. Rothman, PhD, MD, Chem bio (Grant/Research Support)"} +{"text": "We assessed coronavirus disease vaccination and intent and knowledge, attitudes, and beliefs among essential workers during March\u2013June 2021. Coverage was 67%; 18% reported no intent to get vaccinated. Primary concerns were potential side effects, safety, and lack of trust in vaccines, highlighting the importance of increasing vaccine confidence in this population. We examined sociodemographic characteristics, including age group, sex, race and ethnicity, annual household income, health insurance status, marital status, urban versus rural status, and underlying conditions (Appendix).We assessed vaccination status, intent, and KABs by worker group (Appendix). We categorized respondents as reachable or reluctant; reachable respondents said they probably would get or were unsure about getting a vaccine, whereas reluctant respondents said they probably or definitely would not get a vaccine. We assessed the following KABs about COVID-19 vaccination: reasons for not getting vaccinated, barriers to getting vaccinated, motivators for getting vaccinated, concerns about getting vaccinated, and concerns about vaccine side effects.We weighted all surveys to ensure US population representation (Appendix). We used contrast tests for differences in percentages to compare reachable versus reluctant groups among each of the worker categories. This activity was reviewed by the Centers for Disease Control and Prevention and was conducted consistent with applicable federal law and Centers for Disease Control and Prevention policy (Appendix).Vaccination coverage among essential workers increased from 25.5% in March 2021 to 69.8% in June 2021 . AverageAmong all unvaccinated essential workers, reasons for not getting vaccinated included concern for possible side effects (58.0%), vaccine safety (42.9%), and distrust of the vaccine (41.9%) . Higher Concern about COVID-19 disease was lower (38.5%) than concern about side effects from the vaccine (46.4%) among all essential workers (Appendix Table 2). Among reachable groups, 42.5% reported concern about getting COVID-19 compared with 21.8% of those in reluctant groups. Among HCP, 85.5% of reachable respondents were concerned about vaccine side effects compared with 68.8% of those in reluctant groups.Among all essential workers, the main motivators for getting vaccinated were protection from spreading COVID-19 to family and friends (51.4%), receiving more information on effectiveness of COVID-19 vaccines (44.4%), and reducing spread of COVID-19 in the community (41.9%) . Motivat>1 vaccine dose by early June 2021, similar to the 69% of all adults in the sample population during the same time period (data not shown). Over the 6 waves of data collection, HCP had the highest vaccination coverage (66.6%); those in the other essential worker group had the lowest vaccination coverage (45%) during March\u2013June 2021, and one quarter were reluctant to get COVID-19 vaccinations. Consistent with another study (Despite their increased risk for COVID-19 exposure, only about 70% of essential workers included in the sample received The first limitation of our study is that although the panel recruitment survey methodology and data weighting were designed to produce nationally representative results, respondents might not be fully representative of the general US adult population. Vaccination coverage among respondents was self-reported and could be subject to recall or social desirability bias. Data were combined across multiple survey waves, which might overaverage any recent changes in vaccination coverage and intent. Finally, state-specific vaccine prioritization varied during the data collection period, which might have affected vaccination coverage responses to items related to attitudes, behaviors, and perceptions.Among essential workers in this sample, predominant motivators for getting vaccinated were protecting family and friends, gaining more information about the safety and effectiveness of vaccinates, and preventing community spread. These data suggest that clear, consistent messages from healthcare providers, public health officials, and immunization partners about the safety and effectiveness of the vaccine could increase vaccination coverage and vaccine confidence more broadly (Among unvaccinated essential workers, nearly 60% were worried about vaccine side effects. Connecting employers and employees to credible resources on vaccine safety and expected side effects might improve vaccination coverage among essential workers. Implementing interventions to mitigate barriers to vaccination, such as flexible scheduling, paid time off for vaccination and illness resulting from side effects, on-site vaccination, and walk-in clinics, also could improve vaccination coverage. In conclusion, our findings suggest public health officials and other leaders should differentiate between continued challenges in accessing vaccines for all populations from behavioral factors associated with vaccination. To reach vaccination goals for essential workers and everyone in the community, healthcare providers, public health officials, and immunization partners should consider KABs when tailoring messages and strategies to increase vaccination uptake and confidence, especially at local community levels.Additional information on coronavirus disease vaccination coverage, intent, and knowledge, attitudes, and behaviors among healthcare workers, United States."} +{"text": "Accurate data on HIV-related mortality are necessary to evaluate the impact of HIV interventions. In low- and middle-income countries (LMIC), mortality data obtained through civil registration are often of poor quality. Though not commonly conducted, mortuary surveillance is a potential complementary source of data on HIV-associated mortality.During April-July 2019, we assessed HIV prevalence, the attributable fraction among the exposed, and the population attributable fraction among decedents received by two high-volume mortuaries in Kisumu County, Kenya, where HIV prevalence in the adult population was estimated at 18% in 2019 with high ART coverage (76%). Stillbirths were excluded. The two mortuaries receive 70% of deaths notified to the Kisumu East civil death registry; this registry captures 45% of deaths notified in Kisumu County. We conducted hospital chart reviews to determine the HIV status of decedents. Decedents without documented HIV status, including those dead on arrival, were tested using HIV antibody tests or polymerase chain reaction (PCR) consistent with national HIV testing guidelines. Decedents aged less than 15 years were defined as children. We estimated annual county deaths by applying weights that incorporated the study period, coverage of deaths, and mortality rates observed in the study.The two mortuaries received a total of 1,004 decedents during the study period, of which 95.1% (955/1004) were available for study; 89.1% (851/955) of available decedents were enrolled of whom 99.4% (846/851) had their HIV status available from medical records and post-mortem testing. The overall population-based, age- and sex-adjusted mortality rate was 12.4 per 1,000 population. The unadjusted HIV prevalence among decedents was 28.5% : 25.5\u201331.6). The age- and sex-adjusted mortality rate in the HIV-infected population (40.7/1000 population) was four times higher than in the HIV-uninfected population (10.2/1000 population). Overall, the attributable fraction among the HIV-exposed was 0.71 (95% CI: 0.66\u20130.76) while the HIV population attributable fraction was 0.17 (95% CI: 0.14\u20130.20). In children the attributable fraction among the exposed and population attributable fraction were 0.92 (95% CI: 0.89\u20130.94) and 0.11 (95% CI: 0.08\u20130.15), respectively.Over one quarter (28.5%) of decedents received by high-volume mortuaries in western Kenya were HIV-positive; overall, HIV was considered the cause of death in 17% of the population (19% of adults and 11% of children). Despite substantial scale-up of HIV services, HIV disease remains a leading cause of death in western Kenya. Despite progress, increased efforts remain necessary to prevent and treat HIV infection and disease. Although estimated deaths from human immunodeficiency virus (HIV) disease have been declining globally since 2006 , HIV remEstimates from the Kenya National AIDS and Sexually Transmitted Infections (STI) Control Program (NASCOP) indicated that HIV prevalence among adults aged 15\u201349 years reduced from 7.1% in 2007 , and to The HIV epidemic in Kenya is heterogeneous across the country\u2019s 47 counties. HIV prevalence among people aged 15 years and above in Kisumu County (17.5%) is more than three times greater than the national prevalence . Kisumu Over the past three decades, studies in Cote d\u2019Ivoire, the Democratic Republic of Congo, and Kenya have estimated HIV-associated mortality by testing adult decedents \u201320. The This study was approved by KEMRI\u2019s Science and Ethical Review Committee (#KEMRI/RES/7/3/1), Jaramogi Oginga Odinga Teaching and Referral Hospital (JOOTRH) Ethics Review Committee (#ERC.IB/VOL.1/615), and the University of California, San Francisco\u2019s Committee on Human Research (#230355).Informed consent was waived by the ethical review committees. This project was reviewed under CDC human research protection procedures. The CDC investigators did not interact with living human subjects or have access to identifiable data or samples for research purposes. Results of HIV testing were not linked back to living family or next of kin of decedents.Kisumu County, located in the Nyanza region of western Kenya, had an estimated population of 1,155,574 in 2019 . The citThis was a cross-sectional study conducted in the two high-volume mortuaries attached to two referral hospitals in Kisumu County (JOOTRH and KCRH). Decedents admitted to the two mortuaries between April and July 2019 were consecutively enrolled. Data from the mortuaries were used to obtain medical records of decedents who died within the two hospitals. Chart reviews were done to establish if HIV infection was documented in medical records. Blood was collected by transthoracic cardiac puncture from decedents without documented HIV status in the medical records, including those dead on arrival, or whose latest HIV-negative result was older than three months. Death was considered to be due to HIV/AIDS if HIV or AIDS was listed as the underlying cause of death.All decedents with intact bodies, including children (0\u201314 years), received by the two mortuaries between April through July 2019 were eligible for enrollment into this study. We excluded decedents from whom blood could not be collected due to deterioration, burns, or embalming, stillbirth, and those who had been dead for \u226548 hours.The age and sex distribution of the county population was obtained from the 2019 Housing and Population Census Report . The 201Demographic variables included age, sex, place of birth, date of birth, date of death, and place of death . Clinical and laboratory variables collected for hospital deaths from paper-based medical records included date of admission, clinical diagnosis, date of diagnosis, time of death, cause of death (COD) based on postmortem results if available, sample collection date, HIV test results, and viral load (VL) (copies/milliliter [mL] of plasma).\u2122 HIV-1/HIV-2\u00ae as the screening assay, and First Response\u00ae as the confirmatory test. Samples that were reactive on Determine\u00ae and First Response\u00ae were considered positive. Samples that were reactive on Determine\u00ae and non-reactive on First Response\u00ae were considered discordant and retested by a different technician. After retesting, samples that remained discordant were tested using reverse transcriptase PCR (RT-PCR) to confirm the final HIV status. HIV-positive samples were further tested for viral load by RT-PCR using the AbbottTM system . The use of rapid test kits in this study is supported by previous studies showing that HIV antibodies remain detectable in serum for up to 58 days after death [For each decedent, a 6 mL non-clotted blood sample was collected and transferred into sterile ethylene diamine tetra-acetic acid (EDTA) sample tubes and transported in a cool box to the Kenya Medical Research Institute (KEMRI) HIV research laboratory in Kisumu within 4 hours of collection. HIV testing was conducted in compliance with the 2015 Kenya HIV Testing Services guidelines ,27. Samper death ,29 and ter death ,30\u201332.Primary outcomes were the prevalence of HIV infection among decedents, attributable fraction among the HIV-exposed, and the population attributable fraction. We calculated the overall HIV prevalence among decedents stratified by age, sex, and place of death. HIV-associated mortality was defined as death in an HIV-infected person documented in the medical records or confirmed through HIV testing. We adjusted the number of deaths observed over the study period (87 days) to estimate the number of county deaths expected over 365 days by multiplying them by 365/87 and adjusting for coverage . Mortality rates were calculated per 1000 people by dividing the annualized deaths by the 2019 population for Kisumu County by HIV status, age, and sex. Pooled HIV positivity and mortality rates were then computed weighted by the projected population size by age, sex and HIV status.The standardized mortality rate difference and standardized mortality rate ratio were calculated using Stata\u2019s epitab package . The standardized mortality rate difference was calculated by subtracting mortality rates in the HIV-uninfected population from mortality in the HIV-infected population standardized to the HIV-infected population by age and sex. To obtain SMRR, we divided mortality rates for HIV-infected decedents by mortality rates of HIV-uninfected decedents standardized to the age and sex distribution of the HIV-infected population. Attributable fraction among the exposed (HIV-infected decedents) and population attributable fraction were calculated by dividing standardized mortality rate difference by mortality rates of HIV-infected decedents and mortality rates in the population, respectively . We testOf 1,004 decedents received by the two mortuaries during the study period, 95.1% were potentially available for the study, 89.1% (851/955) of whom were enrolled . Of 104 Children accounted for 18.9% (161/851) of enrolled decedents. About half, 49.7% (80/161) of decedent children were under 1 year old, 28.0% (45/161) were aged 1 to 4 years, while the age groups 5 to 9 and 10 to 14 years each accounted for 11.2% (18/161). Most decedent children, 82.0% (132/161), were inpatients in the two hospitals before death, 16.2% (26/161) were dead on arrival, and 1.2% (2/161) died in the outpatient departments. One decedent 0.6% (1/161) was brought in as a police case.Adolescents and adults accounted for 81.1% (690/851) of enrolled decedents; 9.9% (58/690) of adolescent and adult decedents were aged 15 to 24 years, 19.0% (131/690) were aged 25 to 34 years, 17.0% (117/690) were 35 to 44 years old, and 55.7% (384/690) were aged 45 years and above. Males accounted for 52.5% (362/690) of decedent adolescents and adults. Most adolescent and adult decedents, 54.8% (378/690), were inpatients in the two hospitals, 33.0% (228/690), were dead on arrival, 6.2% (43/690) died within outpatient departments, and 5.9% (41/690) were police cases.Among the 119 decedents with documented HIV-infection, 58.8% (70/119) had medical records indicating they were on ART during the hospitalization preceding death, 16.0% (19/119) were not, and 25.2% (30/119) had no documented ART status . Among tAccording to the 2019 Kenya Housing and Population Census, the population of Kisumu County in 2019 was 1,155,574 . Using SAdjusted for age and sex, the mortality rate among PLHIV was thrice higher than that among HIV-uninfected people . The staData on mortality due to HIV can help evaluate the impact of ART programs and guide efforts to strengthen HIV care. Despite the high ART coverage among PLHIV documented through population-based surveys , we deteThe adjusted HIV positivity among decedents in this study was higher than observed in Nairobi but loweIn this study, the first of its kind to include children from a high HIV prevalence setting, children living with HIV were over ten times more likely to die than their HIV-uninfected counterparts. The attributable fraction among the exposed, above 90%, indicates that HIV was the cause of death in most of these children. Previous studies have documented a larger gap in HIV diagnosis, ART initiation, and viral suppression in children than in adults \u201344. LateThe population attributable fraction for adolescents and adults observed in our study was similar to that reported by the Nairobi mortuary study 17% vs. 16%) . The sim% vs. 16%Unlike the Nairobi study, which tested all decedents, our study explored the abstraction of HIV status from medical records, a more convenient approach to HIV surveillance among decedents. However, we noticed that documentation of HIV and ART status in medical records was poor. Although we successfully obtained HIV infection information for half of all HIV-infected decedents from medical records, critical information was missing. This may have been caused by the segmental nature of handling medical records in this setting. Often, HIV programs maintain electronic health records (EHR) within comprehensive care centers that are not readily available to other service delivery points such as inpatient departments. Expansion of EHRs to other service delivery points could increase the quality of HIV information available in the medical records and contribute to better patient outcomes.Our study had several limitations. It was conducted exclusively in public-sector mortuaries. Not all deaths in the community are captured by mortuaries of any kind. Nonetheless, we believe our data are representative. Our two study hospitals receive 70% of decedents in Kisumu, with the other 30% shared by private and other public facilities. We used data from three months to estimate annual mortality. This approach may have introduced bias from seasonal differences in mortality. We utilized HIV status from medical records for hospital deaths when available as advised by the ethical review committee, but this precluded viral load testing for HIV-positive decedents thus identified. Abstracting ART status from medical records could have led to misclassification of decedents and testing of blood for ART metabolites was not possible. . ObtainiOur study documented a higher than expected prevalence of HIV infection among decedents received by two high-volume mortuaries in western Kenya. The majority of HIV-infected decedents with viral load measurements were not virally suppressed. The fraction of mortality in the population attributable to HIV infection was high, 17% (17%). Preventing HIV-attributable mortality could substantially reduce overall mortality in this high-HIV-prevalence population.S1 Fig* viral load were not abstracted from the inpatient/outpatient hospital records, they are usually recorded in comprehensive care center records that were not reviewed as part of this protocol.(TIF)Click here for additional data file.S1 Data(DTA)Click here for additional data file."} +{"text": "With military personnel in Iraq and Afghanistan surviving what were previously fatal injuries, there is ongoing discussion about how to provide care for them and support their families. Parents frequently provide care for their unmarried, injured adult children, especially those returning with polytraumatic injuries, PTSD, or Traumatic Brain Injury (TBI). Parents (n=160) of combat injured adult children who participated in a DoD-funded behavioral intervention study are described. Parents were mainly mothers, average age 60.2 years, with ages ranging from 45 to 79. The veterans had functional limitations, and only 9.2% were employed. Parents, on average, had been caregivers for 6.6 years and daily spent 7.7 hours providing care and 17.2 hours on duty, primarily focused on supervision and daily life management rather than physical care. Average caregiver burden score approached high and was related to veteran TBI diagnosis, aggressive behavior toward others, and functional limitations. Few parents (22.7%) worked full-time; 85.3% had decreased personal spending, 84.0% dipped into personal savings, and 58.9% reduced retirement saving. These findings are similar to those of aging parent caregivers of adult children with serious mental illness or developmental disabilities in amount of care provided to their adult children, their level of burden, financial and career cost to themselves, and concern about their future and their children\u2019s future. As these parents and their adult children age, providing care and resources will present greater challenges for them, for the military and veteran care systems they rely on for support, and for society."} +{"text": "The COVID-19 Pandemic led to many restrictions in health care services, and as a consequence, an expansion of telehealth capabilities. In order to meet the needs of PLWH along the Care Continuum, we developed a process to promote the use of our MyChart app. This HIPAA-compliant app allows patients to view their medical records, communicate with their providers, make appointments, and have video visits on their smart devices. This report describes our preliminary findings. PLWH enrolled in the Ryan White Program, in the Infectious Diseases Clinic at Henry Ford Hospital who had not used telehealth services were asked to sign up for our MyChart initiative. A telehealth Navigator interviewed and taught PLWH how to download and use MyChart, and supplied pre-loaded phones, as needed, to make virtual visits accessible. We collected demographic and clinical information and reasons for not using telehealth services.3). When asked why they were not using telehealth services, 29% reported a lack of technology or capability to install MyChart on their phones, 27% needed further education, and 18% and had not prioritized installation of the application.From October 2020 to May 2021, 209 PLWH were enrolled into our pilot program (Table 1). Of these: 48% were 45-64 years old (yo), while 21% were >/+ 60 yo and 3% < 25 yo; 75% were male, 85% Black; 48% MSM, and 84% virally suppressed (HIV RNA < 200 copies/mmThe crises created by the COVID-19 pandemic revealed a new role for telehealth services. Although available to all PLWH in our RW program, many had never used telehealth services. Over half lacked compatible devices or needed help to download or use the app. Compared to younger PLWH, older individuals were more likely to need assistance. Further work is needed to understand and promote digital parity.All Authors: No reported disclosures"} +{"text": "To determine the characteristics of adult patients referred to a Liaison Psychiatry service in a general teaching hospital in London, UK with 950 inpatient adult beds.All referrals for adult inpatient psychiatric consultation made during a period of 9 months were reviewed; those that involved a patient with a diagnosis of diabetes were analysed. Descriptive statistics were used; data were collected on demographic characteristics and physical and mental health parameters, including type of diabetes, number of years since diabetes diagnosis, glycaemic control, presence of diabetes-related complications, reason for Psychiatry consultation request, psychiatric diagnosis, psychotropic medication, frequency of admissions to general hospital, psychiatric risk issues and outcome of psychiatric consultation.Pilot results indicate that 30 diabetic patients were referred for a psychiatric consultation in 9 months. Of those, 9 had type 1 diabetes, 17 had type 2 diabetes and 1had pre-diabetes 3 were unknown. 13 were male and 17 were female; the median age was 46 (range 18 to 68); the ethnicities were 6 White, 15 Black, 1 Asian and 8 other.Diabetes-related complications were present in 77% . 6% had comorbid cardiovascular disease. 10% were on dialysis and 3% had had amputations.The main reason for referral for psychiatric consultation was low mood and self harm; other reasons were recurrent DKA, anxiety and self neglect. Psychiatric risk issues included 20% risk of self-harm/suicide; 13% risk of violence; 10 risk of self-neglect. The outcomes of liaison psychiatry consultation were: 30% received an assessment that led to recommendations to the general medical team and did not require further psychiatric input; 27% received continued psychiatric follow-up during the admission. With regards to treatment, 36% had psychiatric treatment (including medication) reviewed; 47% received general treatment recommendations, including recommendations for new laboratory or radiological investigations or change in level of nursing care. 20% required transfer to an inpatient psychiatric unit, with 33% discharged to care of community mental health.Our findings indicate the scope of practice for a Liaison Psychiatry service with regards to adult hospital inpatients with diabetes. Our data suggest that patients with type 2 diabetes are the majority of inpatients with diabetes that require psychiatric consultations, and that the majority of those are patients already known to psychiatric services due to long-term severe mental disorders, particularly schizophrenia, schizoaffective disorder or bipolar disorder. Most of those patients have medical comorbidities and severe diabetes-related complications. Patients with type 1 diabetes, despite making up a smaller proportion of referrals for psychiatric consultations, also tend to have recurrent hospital admissions and features of self-neglect."} +{"text": "Hsp70 (heat shock protein 70) plays a key role in carcinogenesis and cancer progression. However, the relationship between the Hsp70 expression level and the colorectal cancer patient survival is unknown. This study is aimed at investigating the relationship between Hsp70 and the prognosis of colorectal carcinoma patients. PubMed, Web of Science, and Embase were used for systematic computer literature retrieval. Stata SE14.0 software was used for quantitative meta-analysis. Besides, data was extracted from selected articles. Relationships between Hsp70 expression level and prognosis were further studied. The hazard ratios (HRs) and 95% confidence intervals (95% CIs) were also computed. A total of 11 potentially eligible studies with 2269 patients were identified in 10 tumors from PubMed, Web of Science, and Embase. Hsp70 overexpression was associated with poor overall survival (OS) and disease-free survival (DFS) in colorectal carcinoma patients and 0.77 (95% CI: 0.23-1.32), respectively). Hsp70 overexpression can predict poor survival in colorectal cancer patients. Colorectal cancer (CRC) is a serious health problem worldwide. The response and overall survival of advanced colorectal cancer patients are very poor compared with the early stage. While colorectal cancer can be treated through surgery, tumor recurrence develops in about 25% to 40% of patients . SurgicaHsps are well-maintained molecules overexpressed in cells subjected to various stress stimuli (heat shock or disruption of homeostasis). Hsps act as molecular chaperones assisting protein folding in normal metabolic conditions and promoting protein repair and stabilization during molecular stress . Hsps arStudies have shown that Hsp70 expression is upregulated in various carcinoma tissues and could be a potential biomarker \u201310, esopStudies published between July 9, 1989 and July 9, 2020 were downloaded from PubMed, Web of Science, and Embase. Text word and MeSH strategy were used for the retrieval. The following terms were used: heat shock protein 70 OR Hsp70 AND colorectal AND cancer OR carcinoma OR malignant OR neoplasm OR tumor. Besides, the reference lists of the retrieved studies were manually screened for additional literature retrieval.in vitro or animal studies. Besides, only English researches were included.Two researchers independently extracted the studies. The inclusion criteria were as follows: (a) studies showing the relationship between the Hsp70 expression level and OS or DFS in colorectal carcinoma, (b) studies describing the relationship between clinicopathological parameters and Hsp70 expression levels in human carcinoma tissues, (c) studies grouping patients (two groups) based on Hsp70 expression level, and (d) if hazard ratios and 95% confidence intervals could be calculated. The exclusion criteria were as follows: (a) studies with insufficient information to compute hazard ratios and 95% confidence intervals or (b) letters, case reports, expert opinions, and reviews or (c) Two authors (GY and ZY) extracted data from identified articles that complied with the standards, and a third researcher resolved different opinions. The first author, country, year of publication, tumor type, sample size, study design, cut-off value, follow-up time, methods used, and the outcome were recorded. Hazard ratios with 95% confidence intervals for overall survival or disease-free survival were also determined. Engauge Digitizer version 4.1 was used to calculate prognosis after drawing the Kaplan-Meier curves .P value and I2. Furthermore, I2 > 50% indicated significant heterogeneity. The random-effects model was used to determine the total hazard ratios. A fixed-effects model was used when I2 \u2264 50% (moderate heterogeneity). The Stata 14.0 software was used for all data analyses.The prognostic value of the Hsp70 expression level in colorectal cancer patients was determined by estimating the hazard ratios between the upregulated and downregulated Hsp70 tissue groups for overall survival or disease-free survival. The 95% confidence intervals and the heterogeneity were also calculated and evaluated based on The research procedure is shown in I2 = 0%) in the identified studies.Systematic meta-analysis was used to assess the relationship between the Hsp70 expression level and OS in colorectal cancer patients. Meta-analysis of nine articles with 1917 colorectal cancer patients showed that Hsp70 expression was significantly associated with OS . The upregulated Hsp70 was associated with poor disease-free survival .The relationship between Hsp70 expression and disease-free survival of 352 cancer patients was also investigated . A fixedBegg's and Egger's tests were used to evaluate the publication bias via funnel plot symmetry estimation. There was no significant asymmetry of the funnel plots. Therefore, this study has no significant publication bias Figures and 5. AIn recent years, potential prognostic biomarkers have been identified to improve the efficacy and survival rate. However, the prognosis of most cancers is relatively low. Therefore, high/positive tissue Hsp70 expression could be associated with the prognosis of colorectal carcinoma patients. Furthermore, previous studies have concluded that Hsp70 expression has biological and clinical significance. However, various cancers have different results. Hsp70 is significantly upregulated in gastric, breast, and prostate carcinoma compared with the normal tissues. In contrast, some articles have indicated that Hsp70 is significantly downregulated in cancer tissues compared with normal tissues in malignant melanoma, colon cancer, and urothelial bladder cancer. The different results could be due to the various interactions between Hsp70 and other human gene products in different organs. Recent articles have verified that Hsp70 overexpression is associated with poor survival in breast cancer, colorectal cancer, melanoma, gastric cancer, hepatocellular carcinoma, non-small-cell lung cancer, ovarian cancer, and testicular cancer. Besides, Hsp70 overexpression is not associated with esophageal adenocarcinoma and esophageal squamous cell cancer, while it is associated with better survival in urinary bladder cancer and pancreatic cancer. Sun et al. reported no significant relationships between Hsp with sex or age of patients, tumor site, Duke's stage, growth pattern, or differentiation . Shotar Notably, this study has several limitations. First, some survival statistics from digital computer technology should be carefully considered. Besides, non-English articles were excluded. Second, only 11 articles with 2269 patients were included. There were no enough articles for subgroup analyses on disease-free survival. Third, different studies had different definitions of Hsp70 expression. Therefore, more researches are needed for more inclusive conclusions.Hsp70 overexpression is significantly associated with poor overall survival and disease-free survival in colorectal carcinoma patients. Several such studies can provide mechanistic, pathophysiological, and epidemiological evidence complementing the findings of the current clinical trials on Hsp70 inhibitors."} +{"text": "To evaluate the risk profile of noncompliant patients in relation to adherence to supportive periodontal therapy in order to identify factors associated with this profile, and be able to prevent the abandonment of periodontal therapy. This cross-sectional observational and comparative study was carried out on the patients who attended the Periodontics department of a University in Valencia 220 patients were interviewed and gave their informed consent and data release permission before taking part in the study, which was approved by the Ethics Committee (UCV/2019-2020/048).48.84% of self-reported patients were regular compliers, in contrast with 10.62% of referred patients. Those with acute symptoms were greater adherent than those patients who didn\u00b4t present symptoms. Regarding patients undergoing surgical procedures, significant results were obtained: 69.70% showed adherence, in contrast with 18.67% patients with basic treatment. Results between men and women were similar. However, the age of the non-compliant patients was slightly older.Self-reported patients presented a significantly higher degree of adherence to periodontal supportive therapy than the referred patients. Patients with acute symptoms presented higher adherence than those without them. Patients who underwent surgery presented a significantly higher degree of adherence than patients who received basic periodontal treatment. No conclusive data have been found regarding sex and age. Key words:Awareness, periodontal disease, compliance, SPT. Periodontal diseases can be defined as inflammatory disorders caused by bacteria that affect the periodontium, which is composed of the gum, periodontal ligament, cementum and alveolar bone. There are two main types of periodontal diseases: gingivitis, a mild and reversible form, and periodontitis, when inflammation progresses deeper into the tissues with the formation of periodontal pockets and irreversible destruction of the periodontal ligament and bone damage which, in advanced cases, can lead to tooth loss ,2.Periodontal disease (PD) is considered a public health problem due to its high prevalence , its impPeriodontal treatment It includes behavioral change techniques, such as: oral-hygiene instructions; smoking-cessation and dietary intervention ,6. TheseA problem facing periodontal treatment is the low adherence undergoing SPT once patients have completed the active part. Moreover, PD has been seen to be difficult to diagnose by patients making them not even start the treatment. The ability of patients to determine if they have PD known as \u2018\u2019self-reported\u2019\u2019 patients is crucial, as recognition of the symptoms and/or signs of PD enables patients to seek help and treatment . WarningOnce a patient has been diagnosed with PD, great attention has been paid to identify the variables that affect treatment adherence like behavioral, cultural and economic factors. In addition, factors such as age, gender, type of treatment and patient satisfaction have been seen that could affect patient behavior -19.Adherence is defined by the World Health Organization (WHO) as \u201cthe extent to which the patient follows medical instructions\u201d and inclAs it has been found, periodontal awareness influences daily oral hygiene practices and routine periodontal care . BecauseThis prospective observational and comparative study was carried out following the Strengthening the Reporting of Observational studies in Epidemiology (STROBE) criteria on a total of 196 patients who were diagnosed with PD in the clinics of the Catholic University of Valencia from September 2016 to April 2019. Treatment follow-up was assessed by the clinical history in addition to a questionnaire to the patient about the reason for consultation and knowledge about PD. Participants gave their informed consent and data release permission before taking part in the study, which was approved by the Ethics Committee: UCV/2019-2020/048 where a favorable report was agreed.Inclusion criteria were patients over 18 years of age, who had received basic active periodontal treatment (R.A.R) or surgery, from September 2016 to April 2020 and had been undergoing SPT for at least one year. Exclusion criteria were having any type of mobility impairment due to lack of dependability, terminally ill patients, pregnant women and patients with diseases that could affect the immune system such us HIV.- Adherence to the SPT The main variable to be examined was the degree of adherence to the SPT; this information was obtained by accessing to each patient\u2019s clinical history. The patients were classified according to the pattern of adherence to the SPT appointments: . Regular- Reason for consultation The reason for consultation was obtained by means of a validated patient questionnaire in which all the information was completed and the patients were classified into two groups: self-reported: patients- Secondary variables Other variables that were evaluated were the absence or presence of pain, where patients were classified as having acute pain or being asymptomatic . They we- Sample size calculationIt was calculated that a random sample of 206 individuals would be sufficient to estimate, with a 95% confidence interval (CI) and a precision of +/- 0.45 units, a population mean using this questionnaire, which was predicted to show a standard deviation of about 4 units. The replacement rate needed was predicted to be 20%.- Statistical analysis p-value obtained is less than 0.05, so that if the p-value is less than 0.05 we reject the null hypothesis. Chi-square, Anova and Bonferroni test(s) were used for carry(ing) out the comparison of proportions.The statistical analysis was carried out using the SPSS 23 computer program using a confidence level of 95% and considering statistically significant those comparison results for which the - Descriptive results A total of 250 patients were selected, of those, 199 patients finally completed the study, applying the inclusion and exclusion criteria. Fifty-four patients were regular compliers (27.14%), 53 were erratic compliers (26.63%) and 92 were non-compliers (46.23%). According to the reason for consultation 86 were self-reported (43.22%) while 113 (56.78%) were referred. Patients that had no pain numbered 176 (88.44%) while 23 (11.56%) did feel pain. A number of 166 patients (83.42%) received nonsurgical periodontal treatment while 33 patients (16.58%) also underwent surgery. Half of the participants were male 99 (49.75%) and the other half female 100 (50.25%). The mean age of the sample was 54 years old. There were 66 patients in the 18 to 40 range, which is 33.16% of the sample, 68 in the 41-55 range (34.17%) and 65 patients over 55 (32.66%) .-Comparative analysis of the study variables- Reason for consultation: The results we obtained in relation to the SPT were that, referring to the reason for consultation in the case of self-referred patients, 48.84% were regular compliers, 29.07% were erratic compliers and 22.09% were non-compliers in attending periodontal treatment support therapy. These self-referred patients (86 patients) 69.77% presented bleeding, 25.58% mobility, 24.42% halitosis, 24.42% gingival recession, 24.42% pain, 18.60% pockets, 18.60% sensitivity and 4.65% bad taste. In the case of referred patients (those who attended for any other reason not related to PD) 10.62% were regular compliers, 24.78% were erratic compliers and 64.60% were non-compliers in attending periodontal treatment support therapy . 28,28% of men were regular compliers, and it was 26,00% in the case of women. In the erratic compliers category, we obtained 26,26% of men and it was 27,00% of women. In the non-compliers category, we obtained 45,45% of men and 47,00% of women , in which statistical evidence was obtained to show that older patients were less adherent where much less compliant. Talking about gender, we didn\u2019t find conclusive data between men and women. Lastly, we obtained a slight difference between older patients being less compliant than younger ones."} +{"text": "The proportion of MLST sequence type (ST) 117 peaked in 2018, at 78.2% (n = 190/243). The major role of these emerging strains in invasive infections in central Europe requires novel strategies for their diagnosis, treatment, and prevention.Vancomycin-resistant enterococci (VRE) pose a public health challenge worldwide. While VRE bloodstream infections (VREBI) increase in Germany and Europe, population-based molecular data are scarce. We aimed to analyze the molecular epidemiology, demographic aspects, and geographical distribution of VREBI in the German Federal State of North-Rhine\u2013Westphalia (NRW), located in the German\u2013Dutch\u2013Belgian border area, representing over 20% of Germany\u2019s population. VREBI isolates were collected from hospitals across NRW between 2016 and 2019. Demographic data were gathered and anonymized upon sample collection. Multilocus sequence typing (MLST) and identification of glycopeptide resistance were carried out. Epidemiological analysis and geographical mapping were performed. Single VREBI isolates from 755 patients were analyzed. In total, 38.9% were female, and 80.0% were aged \u2265 60 years. The VREBI incidence per 100,000 inhabitants nearly tripled, from 0.52 (2016) to 1.48 (2019), particularly in male patients aged \u2265 50 years. The proportion of Enterococcus faecium has substantially increased in recent years [Since their first description three decades ago ,2, vancovan-operons. These comprise several variants and may be located either in chromosomal regions or in mobile genetic elements [vanA and vanB are the most relevant resistance determinants, encoding a combined resistance against vancomycin and teicoplanin or solely against vancomycin, respectively [vanA has predominated over vanB in Europe, Asia, and the Americas, with vanA-positive strains accounting for over 89% of all VRE isolates [vanB-positive VRE isolates has been described recently in studies carried out in Europe [vanA-positive strains have been historically most prevalent, the German National Reference Centre (NRC) for Staphylococci and Enterococci reported a shift in the vanA/vanB ratio for the first time in 2016 [vanB in the following years [vanB-positive VRE strains, mainly collected from rectal swabs upon admission [Phenotypic resistance against glycopeptides , is genetically encoded by resistance determinants designated as elements , renderielements . In the ectively . In the isolates ,13,14,15n Europe ,17. In G in 2016 and confng years . Studiesdmission or in hodmission . HoweverIn cooperation with local public health offices, a state-wide network of 31 microbiology laboratories in chargAll patients diagnosed with VREBIs within the study area were included. Isolates were collected between 1 January 2016 and 31 December 2019. Only the first received isolate from each patient was analyzed. The study area comprised healthcare facilities in any of the 53 administrative districts of NRW.https://www.landesdatenbank.nrw.de/ldbnrw/online/data?operation=table&code=12411-01i&levelindex=0&levelid=1597225839095#astructure, accessed on 17 January 2021). Incidence was calculated for each year of the study period employing the mid-year population of NRW and each of the districts from which VRE isolates were received. To visualize the geographical distribution of the VREBI cases, results were mapped according to the location of the treating hospitals in the different administrative districts.Information on the sex and age of patients was collected directly at the treating hospital and anonymized before sample submission for molecular analysis. Regional demographic data were obtained from databases made available by NRW\u2019s statistical office . Glycopeptide resistance determinants were identified using a qPCR assay, the GenoType Enterococcus\u00ae line probe, according to the manufacturer\u2019s instructions .Sequence types (STs) of VRE strains were determined employing a multilocus sequence typing (MLST) scheme, performing amplification of housekeeping genes by PCR and subsequent sanger sequencing of the PCR products, as previously described . ObtaineData were processed using the Stata statistical software version 16 . Categorical data were compared using the chi-squared test.In total, 755 isolates were included in the study . The nump < 0.001), accounting for 61.1% (95%CI: 59.3\u201362.9%) of the subjects included, while females represented 38.9% (95%CI: 37.1\u201340.7%) of the group. Sex distribution did not vary significantly over the course of the four-year study period ; >79 years ; 60\u201369 years . Up to 80% of all analyzed VRE strains were isolated from patients aged \u2265 60 years. No significant variation was observed in the age distribution throughout the study period , ST80 , ST203 , ST192 , and ST17 . vanB was identified in 71.4% (n = 539/755) of the samples, while vanA was detected in the remaining 28.6% (n = 216/755). No coexistence of both resistance determinants was found.All VRE isolates were identified as Raw incidence of VREBIs in NRW rose continuously, from 0.52 in 2016 to 1.48 in 2019, showing a biphasic pattern: It increased by 162% between 2016 and 2018 and by 54% between 2018 and 2019 a,b. The vanA predominated over vanB . In 2017, a clear inversion of these proportions was observed of all isolates were identified as ST117, subsequently increasing until peaking at 78.2% in 2018. By 2019, this proportion represented almost three-quarters of the isolates collected that year . The incidence of ST117 showed a development nearly identical to that of vanB in 2016 to 94.4% in 2019 (n = 25/42) of all ST117 strains carried the vanB operon in 2016, this proportion had reached 95.4% in 2019.The most commonly detected ST was ST117, with an increasing incidence throughout the study period a,b,d. In of vanB b. The pr in 2019 d. Similan = 18/93) of all isolates in 2016. This proportion decreased to 11.5% (n = 28/243) in 2018, finally reaching 18.9% (n = 50/265) in 2019. This followed the trend observed for the incidence of vanA isolates (n = 90/118) of all ST80 isolates carried the vanA resistance determinant.After ST117, the second most common ST was ST80, accounting initially for 19.4% of the samples analyzed by the NRC in 2016, with stool and rectal swabs, most likely from patients colonized but not infected, accounting for 43.5% (n = 808) of the samples [vanB strains was larger in NRW (81.1%), as compared with the NRC reports (68%) [vanB display an enhanced ability to cause bloodstream infections, as only 10.6% of all strains analyzed by the NRC were isolated from blood cultures [A remarkable change in the epidemiological panorama of VREBIs was observed in NRW in 2017, marked by an inversion of the ear 2016 . This on samples . Considets (68%) . This dicultures .vanB-positive strains, the incidence of vanA isolates remained stable during the study period , which show no sex predominance [vanB/ST117 VRE strains leads to VREBIs more commonly in male patients aged \u2265 50 years. This finding is relevant for risk profiling and improvement of empirical therapy of suspected enterococcal bloodstream infections in at-risk patients.Matched demographic and molecular data indicate that the drastic increase in VREBI cases observed within the study period was mainly determined by the occurrence of bloodstream infections among male patients aged \u2265 50 years, caused by ominance . Assuminhttps://www.it.nrw/70-jahre-amtliche-statistik-fuer-nordrhein-westfalen-jubilaeumsveroeffentlichung-mit-vielfaeltigen, accessed on 9 December 2021). Hence, the epidemiological relevance of NRW transcends its own borders and can thus be considered an indicator for Germany and neighboring countries. Given the controversy that continues to surround VRE and the need for special infection control measures to prevent their spread [vanB increase with a predominance of ST117 in recent years.The main strengths of this work are the large study population, the regional relevance of the study area, as well as the inclusion of samples obtained exclusively from invasive infections. Due to its location, NRW constitutes a regional hub with dynamic border-crossing traffic in central Europe . Almost r spread , data rer spread ,28. HaviStaphylococcus aureus [The fact that sample submission by laboratories participating in the study was achieved on a voluntary basis and the lack of official statistics on the total incidence of VREBIs in Germany that allow the contextualization of our data represent the main limitations to this study. However, this represents a general problem related to the national notification strategies. A feasible strategy to tackle underreporting would be the mandatory notification of VREBI cases, such as in the case of invasive infections caused by methicillin-resistant s aureus .vanB as a predominant resistance determinant, appropriate therapeutic options must be considered [vanB strains, indicate that the lower degree of resistance of these strains against vancomycin can pose a challenge for the identification of VRE in clinical samples, potentially leading to the misclassification of resistance strains as sensitive [In light of the observed emergence of oplanin) . Aspectsensitive .The observed changes in VREBI resistance patterns and molecular distribution must be considered for the development of diagnostic, therapeutic, and prevention strategies in order to effectively tackle the increasing incidence of these invasive infections. The future development of trends in VREBI resistance patterns and molecular distribution warrant further prospective, continuous data collection, and interpretation."} +{"text": "BackgroundPeripheral artery disease (PAD) may be a useful tool to predict\u00a0coronary artery disease (CAD) in patients undergoing coronary angiography. If proven that PAD can be a good predictor of CAD, it can help in early and cost-effective diagnosis of CAD.MethodologyThis observational study was conducted from January 2020 to February 2021 in the cardiology unit of a tertiary care hospital. Participants older than 40 years, with a history of uncontrolled hypertension and unstable angina, who warranted the need of angiography were enrolled in study. After enrollment and recording history, these cases were assessed for the presence of PAD based on ankle brachial index (ABI). ABI values less than 0.9 were labelled as participants with PAD. Then these cases underwent coronary angiography at the same institute, and the presence of greater than 50% stenosis of any coronary vessel on angiography was taken as positive CAD.ResultsIn this study, PAD was identified in 152 (62.8%) participants. A total of 165 (68.1%) participants had greater than 50% stenosis on angiography. Out of 152 participants with ABI less than 0.9, 140 had greater than 50% stenosis on angiography. In total, 90 participants had ABI more than 0.9, of which 35 participants had greater than 50% stenosis.\u00a0Sensitivity of PAD in predicting coronary artery stenosis was 80.0% , specificity was 82.09% (95% CI: 70.80%-90.39%), and accuracy was 80.58% (95% CI: 75.02%-85.37%).ConclusionsOur study demonstrated that the sensitivity, specificity, and accuracy of PAD in predicting coronary artery stenosis were significant. Hence, we conclude that PAD can be an excellent predictor of CAD by helping in early and cost-effective diagnosis of CAD. Peripheral artery disease (PAD) is an occlusive disease affecting the arterial supply of the lower limb ,2. It afThis observational study was conducted from January 2020 to February 2021 in the cardiology unit of a tertiary care hospital. Participants older than 40 years, with a history of uncontrolled hypertension and unstable angina, who warranted the need of angiography were enrolled in study. A total of 242 participants were enrolled in the study via consecutive convenient non-probability sampling from the outpatient department. The detailed demographic data such as age, gender, and presence of comorbidities were noted in a self-structured questionnaire. After enrollment and recording history, these cases were assessed for PAD based on ABI. ABI values less than 0.9 were labelled as participants with PAD. Then these cases underwent coronary angiography at the same institute. The presence of greater than 50% stenosis of any coronary vessel on angiography was taken as positive CAD.Statistical Package for Social Sciences\u00ae software version 23.0 \u00a0was used for data analysis. For numerical variables, data such as age were expressed as mean \u00b1\u00a0standard deviation. Frequencies and percentages were used for categorical variables. An online calculator was used to calculate the sensitivity, specificity, positive predictive value, and negative predictive value for PAD in predicting coronary stenosis.The mean age of participants in the study was 50 \u00b1 11 years. Hyperlipidemia was the most common comorbidity (66.9%), followed by type two DM (46.3%). Overall, 13.2% participants mentioned a past history of myocardial infarction participants. In total, 175 (72.3%) participants had greater than 50% stenosis in angiography. Sensitivity of PAD in predicting coronary artery stenosis was 80.0% , specificity was 82.09% (95% CI: 70.80%-90.39%), and accuracy was 80.58% (95% CI: 75.02%-85.37%) . Hur et The high prevalence of PAD with CAD and the high positive predictive value of ABI suggest that a patient with PAD could be screened for CAD with high suspicion and pretest probability. However, the diagnosis of CAD is highly dependent on tests including electrocardiogram, stress electrocardiogram, myocardial perfusion imaging, coronary angiography, and other cardiac imaging modalities. ABI can add to the pretest probability of CAD, but it cannot substitute any of the above testing modalities.Our study suggests that routine determination of ABI and correct diagnosis and supervision of patients with PAD can help in the early and cost-effective diagnosis of CAD and prevent any coronary stenosis-related event in the future. Therefore, the diagnosis of PAD in patients should prompt the clinicians to have a high clinical index of suspicion for possible CAD, especially if they have hypertension, dyslipidemia, diabetes, and other risk factors.This study has its limitations. Because it was a single-center study, the sample was less diverse and limited. Keeping in mind the aforementioned facts, further large-scale studies are required to establish the correlation between PAD and CAD.Our study demonstrated that the sensitivity, specificity, and accuracy of PAD in predicting coronary artery stenosis was significant. Hence, we conclude that with a high positive predictive value, PAD can be an excellent predictor of CAD. It can help in the early and cost-effective diagnosis of CAD. However, further large-scale, multi-centered studies are needed to study their correlation."} +{"text": "Reduced physical activity and mental health were the top qualitative themes that emerged regarding reasons for weight change. These findings suggest that RDN professional practice skills may have conferred some personal health benefits, as evidenced by smaller weight gains, the maintenance of healthy habits, and fewer reporting psychological effects relative to the general population and other health professionals, thereby limiting the impact of pandemic-induced work and life disruptions.The COVID-19 pandemic introduced an unprecedented health crisis, requiring many Registered Dietitian Nutritionists (RDNs) to expand their duties and services, while other RDNs faced unemployment, reduced hours, and changes to their work environment. This study evaluated whether the pandemic impacted RDNs\u2019 weight, eating behaviors, and psychological factors, and whether professional training as an RDN was perceived as a protective factor in maintaining healthy habits. A 57-item, cross-sectional, online questionnaire including open-ended questions was distributed to RDNs residing in the United States. Over two months (January 2021 to February 2021), 477 RDNs completed the questionnaire. Among RDNs, 68.5% reported no weight change, 21.4% reported weight gain greater than 5 pounds, and 10.3% reported weight loss greater than 5 pounds. Approximately 75% ( The COVID-19 pandemic triggered a global health crisis that prompted a cascade of abrupt life and work adaptations with numerous health and professional consequences. While it is well documented that stressful life events can cause a variety of health effects such as shifts in eating patterns, diet quality, physical activity, and mental health, research continues to build on and explore the immediate and far-reaching impact of COVID-induced home, work, and overall lifestyle disruptions ,5,6,7,8.Forced to step out of their comfort zones to face new daily challenges, healthcare workers have experienced and have been impacted by the COVID-19 pandemic in numerous ways. Some healthcare workers have been thrust onto the frontlines of care while placing themselves at risk for contracting the COVID-19 virus. Specifically looking at the role of registered dietitian nutritionists (RDNs) during the pandemic, many RDNs have been expected to take on additional responsibilities as credentialed practitioners, including the screening, treatment, and care of COVID-19 patients . DespiteCompromised well-being at work has been associated with maladaptive psychological consequences such as heightened anxiety and stress, as well as unhealthy coping practices such as smoking, drinking, overeating, and lack of exercise ,11. StreDespite growing attention to the pandemic\u2019s impact on the well-being of healthcare workers, no study to date in the United States or worldwide has identified and described the pandemic experience\u2014from impact to adaptation\u2014from RDNs\u2019 own perspectives. RDNs are nutrition experts who play an integral part in maintaining the health of individuals and communities, but stressful circumstances can present challenges to even those who are well-equipped with a strong foundation in nutritional knowledge. Studies have identified barriers to nutrition care practice and reported on changes in the work environment as well as resilience levels of dietitians during the COVID-19 pandemic. However, research evaluating the impact of the pandemic on the personal health of dietitians is lacking ,17. Thisxm LLC system [This exploratory and cross-sectional study investigated changes in health habits, lifestyle, psychological factors, and professional practice among RDNs during the COVID-19 pandemic. RDNs residing in the United States were recruited using a pre-existing electronic listserv of 4984 RDNs from January 2021 to February 2021. These months represented a time in the United States when new COVID cases peaked, and many parts of the country saw its highest rates since the beginning of the pandemic. Eligible participants were invited to complete a 57-item questionnaire anonymously through the QualtricsC system . InteresThis cross-sectional research methodology included an online questionnaire. All subjects participating in the project were informed of the aims and type of research and completed electronic consent to participate in the survey. Ethical review and approval were granted for this study from the Villanova University Institutional Review Board . The study was conducted in accordance with the Declaration of Helsinki.Participants completed quantitative self-report measures about eating patterns, physical activity, and weight changes, along with demographic characteristics, employment status, professional practice setting, and years in professional practice. The research team developed these questions. Psychological factors were assessed using validated scales such as General Anxiety Disorder GAD-7 and InsoQualitative questions provided a unique opportunity to understand personal aspects of the pandemic experience. For example, the qualitative question Q1 explored reasons for changes in weight during the COVID-19 pandemic by asking, \u201cIf your weight changed during the height of the pandemic period, please describe why you think your weight changed.\u201d Qualitative question Q2 provided a rich perspective to Q1 by asking, \u201cIf you would like, feel free to share more about how the COVID-19 pandemic affected your eating habits, food purchasing habits, physical activity, weight or general health.\u201dResearchers exported data from Qualtrics into SPSQ1 was analyzed using AtlasTi9 with a content analysis approach ,25. Fourn = 457; 95.8%), had an average age of 43.96 (\u00b115.04), and were predominantly White/Non-Hispanic , with the majority possessing a Master\u2019s degree . The mean body mass index (BMI) was 24.77 kg/m2; 2.5% were classified as underweight, 61.5% were classified as normal weight, 22.2% were classified as overweight, and 13.8% were classified in the obesity category. See A total of 477 RDNs responded to the email invitation, yielding a 9.57% response rate. Participants were primarily women , portion sizes (73.2%), caffeine intake (67.5%), alcohol intake (54.7%), fruit intake (75.9%), vegetable intake (70.0%), fast food or take out (49.9%), or snacking/grazing (45.7%) were reported. In contrast, roughly half increased snacking/grazing (44.45%) and increased meal preparation at home (53.7%) see .Survey questions asked respondents to assess current physical activity levels by asking, \u201cOn average, how many minutes/hours a day are you currently engaging in moderate-intensity activities?\u201d Of the respondents, 29.1% of RDNs reported engaging in 30\u201345 min daily, 27.0% engaging in 15\u201330 min daily, and 19.1% engaged in <15 min daily see . A validated scale, GAD-7, was used to measure anxiety among the survey respondents. A total of 53% of respondents met the criteria for minimal anxiety, 31% for mild anxiety, 9% for moderate anxiety, and 7% for severe anxiety. When asked about general health conditions, it is worth noting that 70.2% reported no anxiety, while 28.9% indicated a health professional had informed them that they had anxiety. A validated scale, ISI, was used to measure insomnia among the survey respondents. A total of 63.9% of respondents\u2019 scores indicated no clinically significant insomnia, and 31.2% met the criteria for subthreshold insomnia. Moderate-severity and severe insomnia were reported by 4.1% of respondents and 0.9%, respectively. Of note, when asked about general health conditions, 89.3% reported no sleep problems, and only 9.9% indicated a health professional had informed them that they had sleep problems see .p < 0.001), indicating that those who reported higher anxiety also reported having higher levels of insomnia.Additionally, relationships between the GAD-7 and ISI scales were examined using Pearson correlation analysis. It was found that those with higher GAD-7 scores were positively correlated with higher ISI scores reported that the pandemic did not significantly affect family or caretaking responsibilities. Although 26.4% noted a significant impact, most respondents (82.3%) did not think these changes resulted in significant food intake/behavior changes.Over half of respondents (55.3%) had a master\u2019s degree, and the most common practice settings were hospitals (20.3%), outpatient clinics (17.4%), or long-term care facilities (15.5%). A total of 65.0% worked full-time, with 65.6% working typical weekday hours. While 34.4% reported significant changes in responsibilities due to the pandemic, over half (55.3%) experienced no or only slight changes in work responsibilities. In addition, 56.8% reported their professional training as an RDN equipped them to handle pandemic-related changes at work. Of the RDNs, 75.5% and 62.3%, respectively, reported their professional training equipped them with the skills needed to maintain healthy eating behaviors and physical activity. However, of note, 17.6% and 25.2%, respectively, reported that despite having the appropriate skills, the pandemic made it challenging to put healthy eating and physical activity skills into practice consistently.Of 477 participants, 255 answered open-ended Q1, yielding a 53% response rate. Two-hundred and three participants provided Q2 responses, yielding a 42.6% response rate. Participant responses from Q1 were coded into eight themes that emerged: reduced physical activity, increased physical activity, unfavorable eating habits, improved eating habits , change in alcohol use, job/family/schedule disruption, mental health, and health/medical conditions. Q2 invited participants to further explain their responses to Q1. Over 40% indicated that reduced physical activity was the primary reason for weight change, followed by mental health concerns at 25.5%. In contrast to these negative health effects, the qualitative data also reveals positive health adaptations, such as increased physical activity and improvements in eating habits, which are data not commonly seen during the COVID era of research. See The COVID-19 pandemic triggered a global health crisis that sparked a cascade of abrupt life and work adaptations with numerous health and professional consequences. During the COVID-19 pandemic, healthcare workers were undoubtedly susceptible to increased levels of stress, anxiety, and emotional fatigue ,9. StudyWhile dietitians are often asked to advise the public about healthy weight or weight management, this is the first questionnaire study to our knowledge that explored RDNs\u2019 perceptions relating to maintaining their own health behaviors during the COVID-19 pandemic. This study requested that RDNs self-reflect on personal health behaviors and health preservation abilities. Key results indicated that RDNs\u2019 specialized knowledge and experience conferred some level of protection from pandemic-related disruptions in healthy eating patterns and unintentional weight gain compared to other healthcare workers and the general population. RDNs are not immune to work and life stressors, and while clear causal relationships cannot be established, this study suggests that professional training and skillsets may equip RDNs with strategies to adapt to changing circumstances. During the pandemic, RDNs\u2019 work and life experiences were subject to changes based on each of his/her distinctive roles. Some RDNs in the clinical setting were charged with COVID-19-specific role changes, such as identifying and addressing malnutrition in treating and preventing further adverse health outcomes from COVID-19 infection . For othSelf-reported weight gain (weight gain >5 lbs.) was noted in 21.4% of study respondents. This was a significantly lower weight gain compared to reports of the general population . In a reTrends noted in both eating and physical activity habits were demonstrated by 75.5% and 62.3% of participants, respectively, who reported that their RDN professional training equipped them with the skills needed to maintain these habits. Regarding physical activity, 42.6% of respondents maintained physical activity levels of at least 30 min daily, compared to other studies, which reported decreases of up to 46% for moderate-intensity activity and ranges of 32\u201343% for overall physical activity ,30. In aRegarding psychological factors, GAD-7 results revealed that while 16% of participants met criteria for moderate to severe anxiety, over 80% of the respondents did not. In comparison, the National Center for Health Statistics (NCHS) Household Pulse Survey conducted during the same frame as our study revealed that, on average, 35.8% reported significant anxiety symptoms based on the GAD-2, an abbreviated version of GAD-7, with a range of 28.1\u201341.2% when separated by race/ethnic groups . When anAccording to the ISI, most RDNs in our study experienced no significant levels of insomnia, with less than 5% meeting the criteria for moderate or severe insomnia. In comparison, a 2021 systematic review and meta-analysis found a pooled estimated prevalence of sleep problems to be 31% among healthcare professionals and 18% among the general population . Other sThree-quarters of respondents reported that their professional training equipped them adequately for maintaining healthy eating habits during the pandemic, and nearly two-thirds indicated that professional training left them adequately equipped to maintain physical activity habits. This finding is not surprising, as the pathway to becoming an RDN provides a solid foundation in many areas of nutrition, health promotion, obesity prevention and treatment, lifestyle, behavioral changes, and adapting nutritional needs for a multitude of lifestyle needs or medical conditions. COVID-19 restrictions may have afforded RDNs with more time to spend on activities or commit to habits they value, which, by nature of being an RDN, may be assumed to be health related. However, knowledge, practice, and understanding of the value of health do not guarantee perfect adherence. Stressful circumstances can present challenges to even those well-equipped, as indicated by the 17.6% of respondents who indicated that pandemic-related circumstances made it difficult to consistently put healthy eating into practice, and 25.2% reported that pandemic circumstances made it difficult to meet goals for physical activity. Thus, additional support may be warranted, even for those who are well-trained in nutrition. There were several strengths to this study. First, to our knowledge, this is the first study that captures experiences of RDNs across the United States during the COVID-19 pandemic peak of winter 2021 and the impact of pandemic-related changes on weight, eating behaviors, physical activity, and psychological factors. With well over 100,000 RDNs in the United States, it is essential for their experiences to be understood, especially those relating to lifestyle, physical, and mental health . Given RThis study is not without its limitations. First, the data presented represent self-reported measures by a subset of RDNs at one-time point, and therefore, generalizability to other groups is limited. The research team developed the quantitative assessment questions that gathered data on eating patterns, physical activity, and perceived physical and mental health data; these questions lacked validation. Next, responses to the GAD-7 and ISI were not verified by a clinical diagnosis. Additionally, most survey respondents were working full-time and had a regular weekday schedule, and therefore, those RDNs working erratic schedules or subject to other significant stressful work scenarios may have been underrepresented. Other factors that were not controlled for or not captured by this research must also be considered. Finally, the demographic breakdown of our RDN respondent pool lacked diversity, which may also limit generalizability .These findings suggest that the professional practice skills of RDNs may have conferred some personal health benefits, as evidenced by smaller weight gains, the maintenance of healthy habits, and smaller numbers reporting psychological effects compared to the general population and other health professionals, thereby limiting the impact of pandemic-induced disruptions. However, any changes that may disrupt eating patterns, physical activity, or overall lifestyle may impact overall health if sustained long-term. Therefore, future research that focuses on supporting the healthful eating habits of all individuals beyond the acute pandemic effects is essential. In addition, implementing ongoing health promotion strategies to ensure these dietary changes are not permanent may benefit the health and wellness of all populations."} +{"text": "To ascertain the cumulative incidence of acute organ failure and intensivecare unit admission in cancer patients.This was a single-center prospective cohort study of adult cancer patientsadmitted for unscheduled inpatient care while on systemic cancertreatment.Between August 2018 and February 2019, 10,392 patients were on systemictreatment, 358 had unscheduled inpatient care and were eligible forinclusion, and 285 were included. The mean age was 60.9 years, 50.9% weremale, and 17.9% of patients had hematologic cancers. The cumulative risk ofacute organ failure was 39.6% (95%CI: 35 - 44), and that of intensive careunit admission among patients with acute organ failure was 15.0% (95%CI: 12- 18). On admission, 62.1% of patients were considered not eligible forartificial organ replacement therapy. The median follow-up time was 9.5months. Inpatient mortality was 17.5%, with an intensive care unit mortalityrate of 58.8% and a median cohort survival of 134 days (95%CI: 106 - 162).In multivariate analysis, acute organ failure was associated with 6-monthpostdischarge mortality .The risk of acute organ failure in cancer patients admitted for unscheduledinpatient care while on systemic treatment was 39.6%, and the risk ofintensive care unit admission was 15.0%. Acute organ failure in cancerpatients was an independent poor prognostic factor for inpatient hospitalmortality and 6-month survival. The secondary endpoints were the probability of resuming antineoplastictreatment after discharge, survival of cancer patients who developed AOF whileundergoing systemic antineoplastic treatment and postdischarge mortality, which wasdefined as deaths that occurred after hospital discharge. All included patients weretreated according to institutional guidelines and local best practices. Datacollection for this study was performed after each patient\u2019s hospital discharge.Data were collected with a standardized case report form. This form included patientdemographic data, Charlson Comorbidity Index (CCI) variables, cancer-relatedinformation , main diagnosis on inpatient admission criteria, theoccurrence of AOF syndrome, the administration of artificial organ replacementtherapy (AORT), admission to the ICU, patient health status upon discharge andoutcomes. All patients were followed until the end of June 2019.14). All patients consented to participate in this study by providingsigned consent forms.The baseline characteristics of the included subjects at inpatient care admissionwere described using descriptive statistics as indicated. Two main subgroupswere considered, namely, those who had AOF at admission or during the inpatienthospital stay and those who did not have AOF. An exploratory comparison of thebaseline characteristics between these subgroups was performed using parametricand nonparametric tests, as appropriate.The cumulative risk of AOF was calculated as the proportion of patients with AOFat admission or during the inpatient stay out of all patients included in thestudy. The cumulative risk of admission to the ICU was calculated as theproportion of patients admitted to the ICU out of all patients included in thestudy.The outcome of cancer patients who develop AOF while undergoing systemicantineoplastic treatment was evaluated by inpatient hospital mortality,postdischarge mortality and median survival using the Kaplan-Meier method. Theoutcome data for subjects admitted to the ICU were the mortality rate during theICU stay and 30 days after discharge from the unit, and the median survival wascalculated by Kaplan-Meier method.Exploratory analyses of the impacts of other baseline characteristics wereperformed with univariate and multivariate Cox proportional hazard models. Ananalysis of potential confounders of AOF was performed with a Cox proportionalhazard model with the following parameters: age \u2265 60 years old, adjustedCCI \u2265 3, hematologic or nonhematologic malignancy, curative or palliativetreatment intent, first or more than 1 line of antineoplastic treatment andadmission cause. The proportional hazards assumption was tested using graphicaldiagnostics based on the scaled Schoenfeld residuals.No correction for multiple hypothesis testing was established, as this analysiswas exploratory and hypothesis generating. All data were analyzed usingStatistical Package for Social Sciences (SPSS), version 25.0.From August 2018 to February 2019, 10,392 patients were on systemicanti-neoplastic treatment, 358 had unscheduled inpatient care and were eligiblefor inclusion, and 285 were included . The cohThe baseline characteristics at the time of acute inpatient admission aredescribed in The median time from the diagnosis of the neoplasia to inpatient admission was 15months (range 0 - 253), and the median time since the last administration ofantineoplastic treatment was 13 days (range 0 - 56). Antineoplastic treatmentwas prescribed with curative intent in 76 patients (26.7%). The most frequentcauses for acute inpatient admission were infections , followedby uncontrolled pain and respiratory insufficiency notattributable to infectious causes . Of the 116 patients admittedwith fever, 56.9% (n=66) had no infection focus identified at admission. Themost frequent sites of infection were respiratory ,gastrointestinal , cutaneous and other sites . At inpatient hospital admission, 62.1% (n = 177) of patients wereconsidered not eligible for artificial organ replacement therapy.The cumulative risk of AOF at admission for inpatient care was 29.5% , and the cumulative risk of AOF (atadmission or during inpatient care) was 39.6% (95%CI 35 - 44). For thosepatients with artificial life support criteria indications at admission, thecumulative risk of AOF was 50.0% (95%CI 41 - 59).The cumulative risk of the intensive care unit admission of patients with AOF was15.0% (95%CI 12 - 18). For those patients meeting artificial life supportcriteria, the cumulative risk of intensive care unit admission of the patientswith AOF was 31.5% (95%CI 23 - 40).versus 45.3%, p = 0.04) and a higherprevalence of hematologic malignancies . Most patients with AOF were in receiving first-line antineoplastictreatment , and there were nodifferences between the two groups in the intent of treatment . The most frequent inpatient admission cause of AOF was infection. Of those patients whodeveloped AOF, 34.3% were considered to not benefit from artificial organreplacement therapy.The characteristics of and comparisons between patients undergoing systemicantineoplastic treatment who presented with AOF and those who did not aredescribed in Of the 17 patients admitted to the ICU, 23.5% (n = 4) had hematologic cancers,17.6% (n = 3) had digestive tract cancer, 17.6% (n = 3) had breast cancer, 17.6%(n = 3) had male genital cancer, 11.8% (n = 2) had lung cancer, 5.9% (n = 1) hadhypopharyngeal cancer, and 5.9% (n = 1) had small intestine neuroendocrinecancer. Antineoplastic systemic treatment was administered with curative intentto 8 patients (47.1%). Acute organ failure was present at hospital admission in13 patients (76.5%). The main diagnosis on ICU admission was infection , febrile neutropenia , sepsis or septic shock , and noninfectious respiratory insufficiency ; there was onecase each of neurologic dysfunction, cardiac insufficiency, acute renal failure,carcinoid syndrome and perforated hollow viscus.Overall, in-hospital mortality was 17.5%, and among those patients admitted tothe ICU, in-hospital mortality was 58.8%. Of those patients discharged home,63.8% resumed antineoplastic treatment. Of the patients who required ICU care,57.1% resumed antineoplastic treatment. In univariate analysis, the probabilityof resuming systemic therapy was higher among those patients being treated withcurative intent for their cancer, those who had improved health status at thetime of discharge and those with hematologic cancers . The medPatients who developed AOF had a median survival duration of 87 days (95%CI 41 -133), which was significantly lower than that of patients without AOF . Acute o7,8).16) score for the prediction of ICUand hospital mortality in critically ill cancer patients, with better prognosticaccuracy than SIRS for both parameters.20) and specialty.23)( In future, we intend to design and study theapplicability of a protocol with pre-established admission criteria for criticallyill cancer patients in the ICU.Overall, in-hospital mortality was 17.5%, and the survival of these patients waspoor, with a median survival duration of 4.5 months among all patients and 2.5months among those admitted for ICU care. The occurrence of AOF was associated witha 3-fold increase in mortality and a 2-fold increase in mortality after hospitaldischarge even after adjustment for age and comorbidity. This higher mortality forpatients who developed AOF is probably not directly related to the acute event butrather inherent to the patient\u2019s condition or subsequent treatment decisions.Patients with a previous episode of AOF while receiving treatment may be atincreased risk of subsequent hospitalizations, with a higher likelihood of a seriousadverse event and death. On the other hand, the occurrence of AOF may lead tochanges in the patient\u2019s therapeutic plan, with dose reductions and changes in orthe suspension of treatment, which may be associated with decreased survival.Despite the worse prognosis of patients who developed AOF while receiving systemicmedical treatment, patients undergoing potentially curative therapy and those withadvanced cancer with predictable long-term survival may benefit from ICUadmission.In this single-center prospective cohort study, cancer patients who requiredunscheduled inpatient medical care had a cumulative risk of acute organ failure of39.6% and a 15% risk of the need for intensive medical care treatment. Acute organfailure was associated with increased mortality both during the hospital stay andafter discharge.The datasets generated and analyzed during the current study are not publiclyavailable due to Union European General Data Protection Regulations but areavailable from the corresponding author upon reasonable request after approvalby the institutional ethics committee and by the local government responsiblefor assessing the impact of data protection."} +{"text": "Due to patient hesitancy surrounding the COVID-19 vaccination initiative, the public needs accurate and timely education that encourages partnership with medical professionals.This study assessed the impact of online patient/caregiver education on knowledge, confidence and intent to act. The educational intervention consisted of 4 activities published on a dedicated COVID-19 learning center on WebMD Education portal from April-May, 2021. The activities were comprised of text and integrated visuals, with 3 of the activities being further customized with a patient or healthcare professional (HCP) video commentary. Demographic questions were asked prior to each activity. Knowledge questions were asked both before and after to assess learning gains. Intent to change and confidence questions were asked at the end of each activity. Absolute improvements were calculated for pre/post questions. An initial data pull was conducted on 6/7/2021 for the purpose of this abstract, and data for the complete analysis will be collected until approximately 8/7/21. To date, 14,911 learners of which responded to the pre/post questions) have participated in the activities, and have demonstrated improvements in knowledge and high levels of confidence and intent to act . Activity 1: COVID-19 Vaccines: Covering the Basics. Demographics (n=155): 50% male; 41% White, non-Hispanic, 30% Asian; 52% over the age of 54. Activity 2: Understanding the Why, Who, and When of COVID-19 Vaccines. Demographics : 66% female; 51% White, non-Hispanic, 18% Asian; 54% over the age of 54. Activity 3: What to Expect When You Get the COVID-19 Vaccine. Demographics (n=500): 66% female; 49% White, non-Hispanic, 22% Asian; 56% over the age of 54. Activity 4: What Have You Heard about Herd Immunity and COVID-19. Demographics (n=599): 63% female; 53% White, non-Hispanic, 25% Asian; 53% over the age of 54.The metrics and outcomes gathered in this assessment are a strong indicator that online patient/caregiver activities on WebMD Education improved knowledge and confidence and prompted intent to act related to COVID-19 vaccines. These findings highlight the potential for well-designed online education to overcome vaccine related challenges of the COVID-19 pandemic. All Authors: No reported disclosures"} +{"text": "The HIV cascade of care is a framework for monitoring HIV care, identifying gaps and informing appropriate interventions. This study aimed to describe the cascade of care in Oman in 2019 and highlight disparities at the sub-population level.We used the UNAIDS Spectrum modelling software to estimate the number of people living with HIV. A national HIV surveillance database was used to identify Omani people (\u226513 years old) diagnosed with HIV from 1984 through December 2019. We calculated the cascade indicators as of 31 December 2019 stratified by sex, age, HIV risk factor, residence, and region of HIV care. We also performed multivariate logistic regression to determine the predictors of attrition at linkage, retention, on ART, and viral suppression.As of December 2019, the estimated number of people living with HIV in Oman was 2440. Out of the estimated number of people living with HIV, 69% were diagnosed, 66% were linked to care, 61% were retained in care, 60% were on ART, and 55% were virally suppressed. Of the 1673 diagnosed individuals, 96% were linked to care, 88% were retained in care, 87% were on ART, and 81% were virally suppressed. People who received HIV care outside Muscat had the largest attrition (11% loss) in the transition from linkage (97%) to retention (86%). Similarly, people aged 13\u201324 years had the largest attrition (13% loss) from \u201con ART\u201d (88%) to viral suppression (75%). Logistic regression showed that both not reporting a specific HIV risk factor and receipt of HIV care outside Muscat independently predicted attrition at each cascade stage from linkage to care through viral suppression.Our findings identified substantial disparities across various subpopulations along the cascade of care in Oman. This analysis will be invaluable in informing future interventions targeting patient subgroups who are at the highest risk of attrition. HIV infection remains a significant global public health threat, despite the substantial gains in the fight against the HIV epidemic. The Joint United Nations Programmes on HIV/AIDS (UNAIDS) recently published report showed that the estimated number of people living with HIV at the end of 2019 was 38 million (1). New HIV infections and AIDS-related deaths in 2019 were estimated at 1.7 million and 690, 000, respectively. As of December 2019, 81% of the estimated people living with HIV knew their HIV status, 67% were on antiretroviral therapy (ART), and 59% were virally suppressed. The UNAIDS report indicated that all global targets for 2020 would be missed and called for addressing the entrenched inequalities that continue to drive the HIV epidemic [The HIV cascade of care (referred to as the cascade hereafter) is a framework for monitoring HIV care; the importance of its role in identifying gaps and informing appropriate interventions is increasingly recognised . The comOur group has recently reported the 2018 cascade of HIV care in Oman. The estimated number of people living with HIV in Oman was 3030; 1532 (50.6%) of whom were diagnosed [The Sultanate of Oman is located in the Arabian Peninsula, with a total population of 4,601,706 of whom 2,022,470 (44%) are non-Omanis . The HIVWe used a national HIV surveillance database. The Ministry of Health has been collecting individual-based HIV data since 1984. Public health law for communicable diseases in Oman mandates notifying HIV infection within seven days of diagnosis. Data on notification forms include demographics, HIV risk factors, the reason for HIV testing, baseline CD4 cell count, baseline HIV VL, and ART details. The CPHL shares the HIV VL testing data with the NAP on a bimonthly basis. Staff at the NAP regularly collect follow-up clinical data from all HIV clinics.Omani people (\u226513 years old) diagnosed with HIV from 1984 through December 2019. We excluded patients who were known to have died (n = 28) or who had emigrated (n = 7). Non-Omani patients were also excluded.HIV diagnosis: positive HIV serology or point-of-care test, which was confirmed by a positive Western blot or nucleic acid-based test.Linkage to care: receiving HIV-related services (CD4 cell count or HIV VL test) after HIV diagnosis.Retention in care: having at least one clinical care episode with documented HIV VL measurement in 2019.On ART: having evidence of ART prescription and dispensing in 2019.Viral suppression: achieving a plasma HIV VL <1,000 copies/mL at the most recent measurement in 2019.The key variables used for univariate (descriptive) analysis were sex, age as of 31 December 2019 , risk factor , other and unknown), residence (Muscat and outside Muscat) and region of HIV care (Muscat and outside Muscat). \u201cOther\u201d HIV risk category included people who inject drugs (PWID), vertical transmission, and blood transfusion. The risk factor was categorised as \u201cunknown\u201d when patients did not report any specific risk factor for HIV infection. Other variables included marital status, the reason for HIV testing, year of HIV diagnosis, hepatitis B and C status, baseline CD4 cell count, baseline HIV VL, most recent HIV VL, ART details, and time on ART (years).We performed a cross-sectional analysis to calculate the cascade indicators as of 31 December 2019. We conducted a descriptive univariate analysis for sociodemographic and clinical parameters for people diagnosed with HIV; categorical variables were reported as frequency and percentage, and continuous variables were reported as medians and interquartile ranges. We used the UNAIDS Spectrum modelling software to estimWe performed multivariate logistic regression to determine the predictors of attrition at linkage, retention, on ART, and viral suppression. We adjusted models for the following variables: sex, age, HIV risk group, residence, and region of HIV care. We included all predictor variables in the multivariate model irrespective of their statistical significance in the univariate analysis. The adjusted odds ratio (aOR) was reported at a 95% confidence interval (CI). We analysed data using R Software.We used programme data collected for routine patient care. Permission to use the data was obtained from the DGDSC, at the Ministry of Health, who deemed the study as a public health programme evaluation. Hence, institutional review board approval and informed consent were not sought. There was no interaction with human subjects, and the conduct of the study did not expose patients to any risk. The data were not accessed by any other third party other than the study team. We strictly maintained anonymity and confidentiality throughout the study by using non-personal identifiers such as the patient\u2019s index number in the NAP registry.As of 31 December 2019, a total of 1673 people were living with HIV in Oman. The majority were males (69%), with a median age of 39 years . Patients aged 25\u201349 years accounted for 73% of the total cohort; only 6% aged 13\u201324 years . Most inp value 0.115.Based on Spectrum modelling for Oman, there are an estimated 2440 people living with HIV, 69% (95% CI: 57\u201390) were diagnosed. Out of the estimated number of people living with HIV, 66% (95% CI: 50.49\u201379.73) were linked to care, 61% (95% CI: 46.47\u201373.38) were retained in care, 60% (45.94\u201372.53) were on ART, and 55% (95% CI: 42.5\u201367.1) were virally suppressed. The proportion of women who knew their HIV infection was 71% (524/740) compared with 68% (1149/1700) in men; p value 0.055. The percentage of women with viral suppression was 85% compared with 79% in men; p value 0.007.Of the 1673 diagnosed individuals, 96% were linked to care, 88% were retained in care, 87% were on ART, and 81% were virally suppressed . Out of p value 0.347. By contrast, the rate of viral suppression increased with age. The percentages of persons aged 13\u201324, 25\u201349, and \u2265 50 years with viral suppression were 75%, 80%, and 84%, respectively. p value <0.001 and 11% vs. 6%; p value <0.001, respectively) .Compared with patients receiving care in Muscat, those who received care outside Muscat had a lower percentage of viral suppression and larger attrition in the transition from linkage to retention . ResidenBased on the Spectrum analysis of HIV data for Oman in 2019, 69% of the estimated people living with HIV were aware of their infection, 66% were on ART, and 55% were virally suppressed. Among diagnosed individuals, the overall retention in care (88%) and viral suppression (81%) rates were favourable; however, the former ranged from 75% to 93%, and the latter ranged from 64% to 87% in various stratifications. People who received HIV care outside Muscat had the largest attrition (11% loss) in the transition from linkage to retention. Similarly, people aged 13\u201324 years had the largest attrition (13% loss) from \u201con ART\u201d to viral suppression. Both receipt of HIV care outside Muscat and not reporting a specific HIV risk factor independently predicted attrition at each cascade stage.The proportion of people living with HIV who were aware of their HIV infection in Oman is well below the global average of 81%, yet it exceeds the regional average of 52% . Given tThe suboptimal viral suppression rate among young persons in this study might be attributed to drug resistance and poor adherence to ART, as a result of mental health problems \u201320 HIV-rAmong all patient subgroups, individuals who did not report a specific risk factor for HIV infection had the worst outcomes at all cascade steps. People who chose not to disclose their HIV risk behaviour could belong to key populations, such as MSM and sex workers, and fear of judgment, privacy breaches, HIV stigma, violence, and criminal prosecution might deter them from revealing their HIV risk , 24. A pThe regional (outside Muscat) HIV treatment centres are staffed by general physicians and not as well-resourced as clinics in Muscat, which are led by consultants with easier access to diagnostics and ancillary services, such as mental health support. These provider-related elements might explain the observed disparities in performance between regional and central clinics; however, patient-related factors, including psychosocial aspects, might have contributed too. Besides, fear of confidentiality breaches and HIV-related stigma and discrimination could hinder engagement with HIV services and adherence to ART in smaller communities , 26. It The main strength of our analysis is the ability to calculate prevalence-based cascade, which has identified a high proportion of undiagnosed HIV in the country. Moreover, we used population-based, with individual-level, data derived from a national HIV surveillance system with input from all 14 HIV treatment centres, and the CPHL in the country. A limitation of this study is the limited comparability of its findings to similar published cascades because of the heterogeneity in data sources and definitions of cascade elements . For insIn summary, our data demonstrate substantial disparities in retention in care and viral suppression among various subpopulations and will be invaluable in informing future interventions. Strategies targeting patient subgroups who are at the highest risk of attrition, including young persons, those denying HIV risk behaviours and those receiving HIV care outside Muscat are required."} +{"text": "Conclusion: In our cohort, the baseline comorbidities that were significantly associated with in-hospital mortality were diabetes, underlying cardiac disease, and underlying kidney disease. Additionally, the factors that independently influenced mortality among critically ill COVID-19 patients were high Activated Partial Thromboplastin Time (aPTT )and international normalization ratio (INR), acidosis, and high ferritin.Background: SARS-CoV-2 infection has a high mortality rate and continues to be a global threat, which warrants the identification of all mortality risk factors in critically ill patients. Methods: This is a retrospective multicenter cohort study conducted in five hospitals in the Kingdom of Saudi Arabia (KSA). We enrolled patients with confirmed SARS-COV-2 infection admitted to any of the intensive care units from the five hospitals between March 2020 and July 2020, corresponding to the peak of recorded COVID-19 cases in the KSA. Results: In total, 229 critically ill patients with confirmed SARS-CoV-2 infection were included in the study. The presenting symptoms and signs of patients who died during hospitalization were not significantly different from those observed among patients who survived. The baseline comorbidities that were significantly associated with in-hospital mortality were diabetes (62% vs. 48% among patients who died and survived ( Coronavirus disease (COVID)-2019 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) . The firGiven the high contagiousness of the virus, especially with the emergence of highly transmissible variants such as the Delta variant; the presence of asymptomatic and subclinical cases, especially among the vaccinated population; and significant differences in susceptibility to COVID-19 morbidity and mortality among the different age groups and types of population, knowledge on COVID-19 pathophysiology, management, complications, and the underlying risk factors for mortality is a top priority for researchers in order to help health care providers to direct their resources and deliver care according to the predicted outcomes and take the most appropriate measures to improve clinical outcomes among the different types of patient populations. Studies that addressed recovery and mortality from COVID-19 disease have shown wide variability worldwide . Multiple studies have addressed clinical outcomes in COVID-19 patients: many of them have shown a correlation of mortality with advanced age and male gender; some have shown an association with smoking and certain chronic comorbidities, such as underlying diabetes mellitus, chronic renal insufficiency, chronic obstructive lung disease, and cardiovascular diseases; some have addressed clinical parameters, such as the severity of respiratory failure and acutThe prevalence rate of COVID-19 among the Saudi population was 6.1%, corresponding to an incidence of 879.7 per 100,000 population and a case fatality of 2.0% between March and August 2020. Advanced age, male gender, hypoxia on presentation, underlying cardiovascular disease, and malignancy were highly associated with mortality as per one of the previous largest studies . Most ofThis urged us to conduct this multicenter retrospective cohort study to identify the factors associated with mortality in a group of patients that was characterized to have worse outcomes, critically ill patients, who were admitted to all five participating intensive care units (ICUs) in the KSA.This retrospective cohort study was performed in five hospitals and health institutions in the KSA , all of which are specialist centers that receive patients with a confirmed diagnosis of COVID-19. The need for consent was waived, as this was retrospective and anonymous study.We enrolled all patients with confirmed SARS-COV-2 infection admitted to any of the ICUs in these hospitals between 20 March 2020 and 27 July 2020, which was the time when the peak number of COVID-19 cases was recorded in the KSA. Patients for whom significant data were missing were excluded. All participating institutions used the same visual triage checklist for acute respiratory infection in suspected cases. The diagnosis of SARS-COV-2 infection was made using real-time reverse transcription polymerase chain reaction analysis of nasopharyngeal secretions, sputum, or endotracheal aspirate. We included all data from paper and electronic health records that were deemed to be clinically relevant based on the published literature and expert opinion. The dataset consisted of demographic data ; presenting symptoms and signs; history of recent contact with a confirmed positive case of COVID-19; initial triage and COVID-19 score at presentation; initial physiological status and hospital course prior to ICU admission; findings on chest radiography; need for and duration of noninvasive or invasive mechanical ventilation; evidence of electrocardiographic abnormalities; evidence of infection; inflammatory markers, including leukocytosis or leukopenia, neutropenia, lymphopenia, high C-reactive protein, troponin, and ferritin; disturbance of the coagulation profile; and details of medications received.We also recorded comorbidities, namely, diabetes, hypertension, asthma, renal impairment, cardiac disease, hematological or oncological disease, and post-transplant immunosuppression. The initial physiological status and its impact on the outcome was assessed using Sequential Organ Failure Assessment and COVIRenal function was assessed by the baseline creatinine level, baseline estimated glomerular filtration rate (eGFR), highest creatinine level, and lowest eGFR recorded during the initial 7 days of admission. We also calculated the urine output. The eGFR was calculated using the modified Schwartz formula . The basp-value of 0.05 and the 95% CI.Dichotomous variables are summarized as the proportion and continuous variables as the mean. The proportion and 95% confidence interval (CI) of in-hospital mortality in patients admitted to the critical care unit with confirmed COVID-19 were estimated. Factors associated with in-hospital mortality were determined using the Chi-square test. Age, sex, and other variables for which significant associations were found were entered into a multivariable logistic regression model to determine the factors that were independently associated with mortality. All statistical analyses were performed using Stata statistical software . Statistical significance was determined by a In total, 229 critically ill patients with confirmed COVID-19 infection were included in the study. Baseline demographic and disease characteristics are shown in p = 0.046)), underlying cardiac disease (38% vs. 19% (p = 0.001)), and underlying kidney disease (32% vs. 12% (p < 0.001)) . The presenting symptoms and signs of patients who died during hospitalization were not significantly different from those observed among patients who survived . The bas 0.001)) . The morp < 0.001)), hypernatremia (70% vs. 36% (p < 0.001)), hyperkalemia (73% vs. 38% (p < 0.001)), anemia (71% vs. 38% (p < 0.001)), leukocytosis (92% vs. 67% (p < 0.001)), thrombocytopenia (69% vs. 25 (p < 0.001)), high APTT (96% vs. 71% (p < 0.001)), high INR (64% vs. 26% (p < 0.001)), acidosis (85% vs. 49% (p < 0.001)), high troponin (85% vs. 49% (p < 0.001)), and high ferritin (87% vs. 27% (p < 0.001)) ) .p = 0.035)), high INR ), acidosis ), and high ferritin ) ) .In this study, the in-hospital mortality rate was 37% in patients with COVID-19 who required admission to an ICU in the KSA. Diabetes, cardiac disease, and underlying kidney disease were associated with increased mortality. A meta-analysis of 24 studies that included 10,150 patients and was published in 2020 found a mortality rate of 41.6% in those admitted to an ICU . A higheOur finding that diabetes, underlying cardiac disease, and underlying kidney disease were risk factors for mortality in critically ill patients with COVID-19 is similar to that in a meta-analysis of 48 studies, which identified diabetes, cardiovascular disease, renal disease, respiratory disease, malignancy, hypertension, older age, and smoking to be associated with mortality . We alsoWe also found that hypernatremia was associated with mortality. This is in line with previous reports showing that dysnatremia (hypernatremia or hyponatremia) is a risk factor for mortality in patients with COVID-19 ,31. The Acute kidney injury (AKI) with the rapid deterioration of renal function was significantly more common in nonsurvivors in our cohort and has already been found to be a risk factor for mortality in patients hospitalized with COVID-19 . Other sAcute myocardial injury and complications were also more common in nonsurvivors in this study. Acute cardiac injury, as defined by troponin elevation, occurs in approximately 16% of patients with COVID-19 and is associated with increased mortality and a prolonged length of stay ,39,40.This study has some limitations, in particular, its retrospective design and small study population, which means the result of the study was not powered to show the causality on general population. However, it was a multicenter study and examined the risk factors for mortality in patients with COVID-19 in detail and showed that there are some important comorbidities that were significantly associated with in-hospital mortality and other clinical factors that independently influenced mortality in critically ill patients with COVID-19, which may help to categorize these patients and these factors as high-risk and might improve the outcome.Patients with COVID-19 requiring ICU admission have a high mortality rate. Underlying comorbidities increase the risk of mortality in these vulnerable patients. In our cohort, the baseline comorbidities that were significantly associated with in-hospital mortality were diabetes, underlying cardiac disease, and underlying kidney disease. Factors that independently influenced mortality in our critically ill patients with COVID-19 were high aPTT, high INR, acidosis, and a high ferritin level."} +{"text": "During rollout of coronavirus disease vaccination, policymakers have faced critical trade-offs. Using a mathematical model of transmission, we found that timing of vaccination rollout would be expected to have a substantially greater effect on mortality rate than risk-based prioritization and uptake and that prioritizing first doses over second doses may be lifesaving. In December 2020, the US government issued emergency use authorization for two 2-dose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines, both estimated to be >94% efficacious in preventing symptomatic coronavirus disease (COVID-19) .Focusing on Austin, Texas, USA, we projected COVID-19 deaths over 8 months for both an infection-blocking vaccine that prevents infection upon exposure (assuming 95% reduction in susceptibility in vaccinated persons) and a symptom-blocking vaccine that prevents symptoms upon infection (assuming 95% reduction in symptomatic ratio in vaccinated persons). Vaccination would begin on January 15 or February 15, with 10,000 vaccines administered weekly and allocated to cities pro rata. We compare 3 strategies: no priority groups; 1 of 3 priority groups vaccinated before the general public ; and 10 phases that vaccinate age\u2013risk groups in order of risk for severe COVID-19 outcomes. Stochastic simulations assumed that 7.6% of the overall population of the Austin\u2013Round Rock Metropolitan Statistical Area were immunized by infection before January 15.If a perfectly risk-prioritized (10-phase) rollout of an infection-blocking vaccine were to begin January 15, we estimated that 52% (95% CI 47%\u201356%) of deaths would be averted relative to the baseline of no vaccines, assuming 50% uptake, or 56% (95% CI 51%\u201360%) of deaths averted assuming 90% uptake , panel AExpected differences are magnified with a symptom-blocking vaccine. For a January 15 start and 50% uptake, the risk-prioritized 10-phase strategy would avert 40% (95% CI 35%\u201345%) of deaths, whereas unprioritized rollout would avert 32% (95% CI 25%\u201337%). If a single dose with 82% efficacy Table 1.These projections validate prioritizing high-risk groups. In a pessimistic scenario in which a symptom-blocking vaccine rollout began in February 2021 with 50% uptake, prioritizing high-risk adults and adults >65 would avert \u224817,000 more deaths in the United States than a nonprioritized campaign. Given the state of the pandemic in early 2021, we expected vaccine delays to cost more lives than either imperfect prioritization or vaccine hesitancy. The United Kingdom and Belgium have prioritized first doses over second doses Figure 7We assumed that vaccines provide lasting immunity and block either infection or symptoms, whereas the reality may be a hybrid of both .Risk prioritization is a valid approach for maximizing the impact of vaccines, but not at the expense of vaccination speed. Our projections suggest 2 immediate strategies: hybrid distributions that combine active outreach to priority groups with passive distribution to the general public; and distribution of single doses to as much of the population as possible, foregoing plans to hold second doses in reserve.Additional information about modeled effects of coronavirus vaccination and prioritization on mortality, United States."} +{"text": "Cervical cancer remains a common cancer affecting women in Canada. While cervical cancer incidence and mortality in Canada have declined for several decades due to the success of organized, provincial cervical cancer screening programs, further decreases will require enhancement of primary, secondary, and tertiary prevention efforts. The present commentary provides a historical overview of cervical cancer trends in Canada, presents current statistics on cervical cancer incidence, mortality and survival, and discusses future directions in relation to cervical cancer elimination. While cervical cancer incidence in Canada has declined for several decades due to the success of organized cervical cancer screening, cervical cancer continues to impact the lives of women, and all people with a cervix, across Canada . Women uFollowing the call to action in 2018, in 2020, the World Health Organization launched a global strategy to accelerate the elimination of cervical cancer. Specifically, the goals call for improved early detection, diagnosis, and treatment, prioritizing vaccination, and expanded research . The CanAge-standardized incidence rates (ASIRs) were obtained from Statistics Canada Table 13-10-0747-01, which includes data from the Canadian Cancer Registry . Data reAge-standardized mortality rates (ASMRs) were calculated using direct age-standardization from mortality counts and population estimates data. Cervical cancer mortality counts among all Canadians were obtained from Statistics Canada Table 13-10-0392-01, which includes data from the Canadian Vital Statistics Death Database . PopulatCervical cancer incidence has steadily declined since the 1970s, with annual percentage changes (APC) ranging from \u22128.8% to \u22120.33% [Similar trends have been observed internationally as well\u2014in the United States, incidence rates declined steadily from 1975\u20131982 from 14.8 to 10.6 per 100,000, remained stable through 1990 and declined until 2006, after which rates remained stable at around 6.8 per 100,000 . In AustIt is now well established that a persistent infection with an oncogenic genotype of the human papillomavirus (HPV) is necessary for the development of cervical cancer and there are substantial prevention opportunities with the availability of HPV vaccines . As in oThe age-standardized mortality rate (ASMR) for cervical cancer was estimated to be 2.0 per 100,000 persons in 2019 . OverallThere were a total of 2026 deaths related to cervical cancer between 2015 and 2019, averaging 405 deaths per year [Cervical cancer was the third most common cancer among women aged 25\u201334 years, accounting for 10.1% of all cancers . It remaA total of 5710 women in Canada (excluding Quebec) were diagnosed with cervical cancer from 2014\u20132018, at an average of 1142 cases per year [Presently in Canada, cervical cancer is more likely to be diagnosed at an early stage, reflective of the positive impacts of organized cervical cancer screening programs. Overall, 54.4% of cervical cancers are diagnosed at stage I, 13.4% at stage II, 16.5% at stage III and 11.8% at stage IV . The disThe 5-year net survival, or probability of survival for the specific outcome of cervical cancer, is 72% in Canada . This isDespite the existence of publicly funded cervical cancer screening programs across Canada, inequities in access to screening services persist. Decreases in incidence rates are related to the success of organized, provincial cervical cancer screening programs in most provinces . All proOf those diagnosed with invasive cervical cancer in Canada from 2011\u20132013, 37% had last undergone pap screening more than 5 years ago, or never, suggesting the need to reach under-screened populations . Under-sThe WHO set an ambitious \u201c90/70/90\u201d target to be achieved globally by 2030 in order to be on track for cervical cancer elimination by 2040: 90% of girls vaccinated against HPV by age 15, 70% of women screened using high-precision testing by age 35 and 45, and 90% of cervical cancers identified and treated [For Canada to achieve these goals, a combination of strategies must be considered that improve primary, secondary, and tertiary prevention. In terms of primary prevention, efforts are required to increase uptake of HPV vaccination. Expansion of the HPV vaccine to broader cohorts, with population-based monitoring of vaccine uptake can help accelerate elimination. Enhanced efforts are required to better understand and address vaccine hesitancy . HesitatElimination of cervical cancer will not be reached among all groups in the population if existing inequities are not addressed. More work is needed to better understand and address current sociodemographic differences in cervical cancer screening participation, incidence, treatment and mortality.Cervical cancer incidence in Canada has declined overall; however, the downward trend has slowed. Further decreases in incidence require improving HPV vaccine uptake, incorporating novel HPV-based screening technologies, increasing participation in cervical cancer screening and addressing inequities in access to and availability of screening services between population groups."} +{"text": "Optimal medical therapy after myocardial infarction with nonobstructive coronary arteries is uncertain. We evaluated variability in discharge prescription of angiotensin-converting enzyme inhibitors / angiotensin receptor blockers (ACEI/ARB) and beta-blockers (BB) to MINOCA patients between hospitals to assess physician equipoise about secondary prevention.Patients with MINOCA between 2007\u20132014 were identified in the NCDR Chest Pain\u2013MI Registry. Those with prior revascularization or missing demographic, angiographic, or medication data were excluded. Analysis was limited to high-volume hospitals with \u226520 MINOCA total discharges. Discharge prescriptions for ACEI/ARB and BB after MINOCA were analyzed for each hospital. Clinical data on left ventricular ejection fraction (LVEF), glomerular filtration rate (GFR), and diabetes mellitus status were extracted to identify other indications for ACEI/ARB or BB.Clinical data were available for 17,849 MINOCA patients, of whom 8,752 (49%) had LVEF <40%, GFR \u226460 mL/min, and/or diabetes. 5,913 patients without one of these indications for ACEI/ARB or BB were discharged from 156 high-volume hospitals. At discharge, ACEI/ARB was prescribed to between 16.0% and 88.8% of MINOCA patients and BB to between 28.0% and 97.5% .There is marked variability between hospitals in the proportions of patients receiving ACEI/ARB and BB after hospitalization for MINOCA, suggesting clinical equipoise about the routine use of these agents. Randomized clinical trials are necessary to establish the benefit of ACEI/ARB and BB to improve outcomes after MINOCA. Myocardial infarction (MI) with nonobstructive coronary arteries (MINOCA) accounts for approximately 6% of all MI . PatientOptimal medical therapy for secondary prevention of cardiovascular events after MINOCA is uncertain, because no randomized clinical trials have been conducted in this population. In particular, the role of angiotensin-conversing enzyme inhibitors (ACEI/)/angiotensin receptor blockers (ARB) and beta-blockers (BB) is not clear. These agents are typically prescribed with the goal of mitigating consequences of left ventricular dysfunction after MI, such as heart failure, adverse remodeling, and sudden cardiac death. These are less common after MINOCA than MI-CAD . Observath and 75th percentiles), and range . Histograms were generated to illustrate the frequency distribution of the proportion of patients discharged on ACEI/ARB and BB by hospital. A waiver of written informed consent and authorization was granted by Chesapeake Research Review Incorporated. The Duke Clinical Research Institute served as the data-coordinating center and analyzed de-identified patient data.Data were obtained from the American College of Cardiology (ACC) National Cardiovascular Data Registry (NCDR) Chest Pain MI Registry . The regThere were 18,363 patients with MINOCA during the study period, among whom discharge therapy included aspirin in 85.3%, P2Y12 inhibitors in 27.2%, statins in 71.2%, ACEi/ARB in 57.9% and beta-blocker in 77.0% [Data on LVEF, eGFR, and DM status were available for 17,849 MINOCA patients, among whom 8,754 (49%) had LVEF < 40%, CKD, and/or DM. Among patients who did not have one of these indications for ACEI/ARB and/or BB, 5,913 patients were discharged from 156 high-volume hospitals. These patients represent the final study cohort.Fig 1). These same hospitals prescribed BB to anywhere between 28.0% and 97.5% of MINOCA patients, with a median of 74.1% (IQR of 64.7% to 80.0%) .At discharge, participating high-volume hospitals prescribed ACEI/ARB to anywhere between 16.0% to 88.8% of MINOCA patients without DM, CKD or reduced LVEF, with a median frequency of 45.6% (IQR 38.0% - 56.5%) clinical trial, which is currently ongoing in Sweden and Australia to evaluate the clinical benefit of these agents in MINOCA . In contThere are some limitations of this analysis. The NCDR Chest Pain MI registry only includes patients referred for coronary angiography at centers in the United States, and prescribing patterns may vary internationally. Since all participating hospitals enroll in the registry voluntarily, the study cohort may not be representative of all hospitals. We were unable to review medical records to verify presumed MINOCA diagnoses; however, the directions for inclusion in the NCDR Chest Pain MI registry require a clinical diagnosis of MI, and the proportion of MI patients with MINOCA in this cohort is similar to multiple previously published large studies , 17 AddiIn conclusion, marked variability between hospitals in the proportions of patients receiving ACEI/ARB and BB after hospitalization for MINOCA suggests clinical equipoise about the routine use of these agents. Randomized clinical trials are necessary to establish the benefit of ACEI/ARB and BB to improve outcomes after MINOCA."} +{"text": "Among all single-antibiotic prescriptions, 91.5% are broad-spectrum. Two-thirds of the prescriptions contain medicines for symptom management. The overall guideline compliance rate of acute bronchitis treatment for adults is 31.0%. Prescribing antibiotics, especially broad-spectrum ones, for acute bronchitis is commonly observed in Chinese PHSs. Targeted interventions are urgently needed for Chinese primary clinicians, especially in western rural areas.Inappropriate prescribing for acute bronchitis in primary healthcare settings (PHSs) is commonly seen worldwide. Here we describe the prescribing patterns and antibiotic use for acute bronchitis in PHSs across China. We conduct a nationwide cross-sectional survey to collect outpatient prescriptions from PHSs in 2017. Patients diagnosed with acute bronchitis without other infections are eligible for this study. Generalized estimating equations are used for analysis. Overall, 10,678 prescriptions for acute bronchitis from 214 institutions are included. The antibiotic prescription rate is 44.5% for total prescriptions, and differs significantly by region and urban/rural status ( It is estimated that every year, 5% of the general population report an episode of acute bronchitis, 90% of whom seek medical advice3. Acute bronchitis is a self-limited condition caused by virus in at least 90% of cases, in which antibiotics have no role in treatment5. However, studies show that most patients with acute bronchitis are treated with inappropriate or ineffective therapies6. Antibiotics are inappropriately prescribed for acute bronchitis up to 70% of the time, accounting for 44% of all outpatient antibiotic prescriptions in the US4. Unnecessary antibiotic prescriptions provide no clinical improvement3, increase the prevalence of antibiotic resistance7, and healthcare costs8. Symptoms of acute bronchitis, such as acute cough and sputum production, generally last for 2\u20133 weeks5. Clinicians are challenged with providing evidence-based and effective symptom control therapies as the viral syndromes progress.Acute bronchitis, an inflammation of the lower respiratory tract manifested by acute cough, is among the commonest clinical condition responsible for primary healthcare consultations12. Previous study showed that 93.5% of acute bronchitis visits in Chinese primary healthcare settings involved an antibiotic prescription, among which more than 50% were inappropriate9. However, studies are limited on the rates of antibiotic use and antibiotic selection for acute bronchitis in primary healthcare settings in China, as well as the detailed symptom treatment strategies for acute bronchitis. Therefore, we designed this study to evaluate outpatient antibiotic utilization, predictors of antibiotic use, and overall prescribing patterns for acute bronchitis at primary healthcare in China.Reducing overprescribing of antibiotics for respiratory infections has been emphasized in China in the past decade to tackle antibiotic resistanceA total of 10,678 prescriptions for acute bronchitis from 214 Chinese primary healthcare settings in 37 cities in eight provinces were eligible for inclusion in our study (Table p\u2009=\u20090.039). The facilities in cities of the highest economic status had lower adjusted APR (41.1%) than those in the lowest economic status (50.3%) although the difference was not statistically significant . Facilities located in eastern region (41.3%) had significantly lower adjusted APR than those in central region and non-significantly lower APR than western region . Economic status, patient gender, and patient age were not the significant predictors of antibiotic prescribing.After weighting to better reflect the national income and urban/rural distribution, the antibiotic prescription rate (APR) for acute bronchitis was 44.5% (unadjusted for other variables). After further adjustment Table , clinicip\u2009=\u20090.000). Among all single-antibiotic prescriptions, 91.5% were broad-spectrum. Township hospitals had significantly higher rate of broad-spectrum antibiotics than community centers . The most commonly prescribed antibiotic classes in urban areas were second-generation cephalosporins (31.8%), macrolides (19.8%), and third-generation cephalosporins (19.6%). In contrast, third-generation cephalosporins (23.1%) were identified as the most commonly used antibiotic in rural areas, followed by macrolides (19.4%) and broad-spectrum penicillins (16.9%). In both urban and rural areas, the most commonly used second-generation cephalosporins were cefuroxime and cefaclor . The most commonly used third-generation cephalosporins were cefixime, cefdinir, and ceftazidime in urban areas , and ceftazidime, cefotaxime, and ceftriaxone in rural areas .Of all the antibiotic prescriptions for acute bronchitis, 12.0% contained more than one antibiotic . The overall compliance rates of Chinese primary healthcare prescribers following clinical guidelines of the US and the UK were 18.5% and 27.4%, respectively.Overall, 17.3% of the adult patients in our sample were prescribed only antibiotics for acute bronchitis, while 36.1% were prescribed only symptom management drugs, 29.1% were prescribed both antibiotics and symptom management drugs, and 17.5% were not prescribed with drugs for acute bronchitis Table . The oveIn light of the paucity of studies investigating detailed outpatient treatment patterns for acute bronchitis in primary healthcare settings in China, we evaluated prescribing patterns of antibiotics and symptom management medications for patients with acute bronchitis treated in 214 primary healthcare settings across China.13, US (74%)14, Belgium (69.0%)15, Spain (58.6%)16, Japan (52.8%)17, and Netherlands (51.0%)18, and was also lower than previous studies in China (77.5\u201395.2%)11. However, our rate was slightly higher than the rate showed in the study conducted in Swiss (41.5%)19. One study conducted in England found that 82% of the consultations for acute bronchitis resulted in an antibiotic prescription on the same day, among which only 13% of the patients was necessary for antibiotic treatment according to guidelines and expert elicitations20. Another study showed that 85.6% of the antibiotic treatment duration exceeded guideline recommendations in primary care in England7. The relatively lower prevalence in our study could be due to the changing patterns of antibiotic use in China21, or to our limiting inclusion of acute bronchitis cases without any other infectious diagnosis. The higher rates of antibiotic prescribing in previous studies may be driven by misconceptions of clinicians and patients23. A Cochrane review suggested that antibiotics were minimally effective for acute bronchitis, with a half-day reduction in cough and no reduction in functional impairment compared to placebo, as well as increasing rates of adverse events3. Public perception/misconception of antibiotic efficacy drove inappropriate demand for utilizing antibiotics in the primary outpatient setting in China24. Surveys showed that 60% of the population believed that antibiotics were effective for the treatment of acute bronchitis25, a belief that varied by educational level26. This may partially explain the higher antibiotic prescribing rate in rural and the less developed western region in our study.Our results indicated that, in 2017, Chinese primary healthcare clinicians prescribed antibiotics for nearly half of outpatients with acute bronchitis, which was a lower rate than those in the studies conducted in Italy (73.5%)10. This preference for broad-spectrum cephalosporins was also found in the US and European countries27. As noted in previous studies, cephalosporins should be avoided when a narrow-spectrum antibiotic would be effective28. Inappropriate antibiotic use accelerated the development of antibiotic resistance such as methicillin-resistant staphylococci29. Cephalosporin overuse in Chinese primary healthcare outpatient settings may be largely due to the requirement of mandatory skin testing before prescribing either oral or injectable penicillins for all patients30. Ideally, skin testing can increase the number of incidents in which penicillin can be safely administered rather than alternative broad-spectrum antibiotics31. However, in clinical practice, overestimation of penicillin allergy rates33, along with the inconvenience and unreliable results of penicillin skin testing, may actually impel some primary healthcare clinicians to replace penicillins with cephalosporins or other broad-spectrum antibiotics33.Among all single-antibiotic prescriptions, 91.5% were broad-spectrum formulations, and second- and third-generation cephalosporins were the most prescribed categories. This was consistent with previous findings in Chinese hospitals for treating respiratory tract infections34. Our study provided a comprehensive overview of prescribing patterns of symptom management drugs for acute bronchitis patients in Chinese primary healthcare settings; however, evidence supporting these symptomatic therapies was limited according to national clinical guidelines35. For example, inhaled or systemic corticosteroids for cough management were not recommended as there were no data to support their therapeutic effect for acute cough caused by acute bronchitis36. Insufficient quality data were support to recommend the routine use of Chinese herbs for acute bronchitis and other respiratory conditions according to a Cochrane review37.Supportive care and symptom management were the mainstay of treatment for adult patients with acute bronchitis38. Second, even if familiar with evidence-based practice, primary healthcare clinicians may have difficulties getting access to updated clinical guidelines, as most of the guidelines were published in academic journals and cannot be obtained for free. Third, Chinese guidelines were sometimes vaguer in expression and more liberal in medication selection than those in other countries .We systematically selected community healthcare centers in urban areas and township hospitals in rural areas across China. First, we classified all 408 cities in China into four levels of economic status according to GDP per capita in 2016. We then selected nine provinces out of 31 provinces in mainland China to conduct the survey. Among these provinces, 42 cities were randomly selected according to the four economic strata. Finally, in each selected city, two community healthcare centers and nine township hospitals were selected randomly based on the ratio of these two facility types nationally in 2017 . Narrow-spectrum antibiotics consisted of narrow-spectrum penicillins, first-generation cephalosporins, nitroimidazoles, tetracyclines, and sulfonamides. Broad-spectrum antibiotics included broad-spectrum penicillins, advanced-generation cephalosporins, macrolides, quinolones, lincosamides, aminoglycosides (except for streptomycin), and other antibiotics 45.We classified antibiotics according to Anatomical Therapeutic and Chemical classification J01 .STATA 14.0 was used for all statistical analysis. We used generalized estimating equations to generate population-weighted comparisons, standardized margins to calculate mean adjusted proportions, and chi square test to compare the urban\u2013rural differences. We weighted sample estimates to reflect the distribution of economic level and urban\u2013rural status in the national population. The level of statistical significance was defined as Further information on research design is available in the Supplementary InformationReporting Summary"} +{"text": "OBJECTIVES/GOALS: This study has two primary aims: 1) evaluate points of success and failure in connecting hepatitis C virus (HCV) positive homeless patients to care following a preliminary positive rapid HCV test result, and 2) describe the barriers cited by patients who drop out at each step in the care continuum. METHODS/STUDY POPULATION: A retrospective longitudinal analysis of adult (18 years or older) homeless individuals accessing shelter at six homeless shelters in New Orleans, LA was conducted. Every patient who came through a testing site received a survey collecting information on demographics, barriers to healthcare, and recent utilization of health services. A retrospective chart review of hospital and homeless clinic medical records was used to track patient linkage to care and their progress through the HCV care continuum. We defined successful linkage to care as attendance at the first scheduled follow-up appointment for treatment with a primary care physician. RESULTS/ANTICIPATED RESULTS: A total of 1719 unique patients were identified from August 2016 through August 2019 which included 36% self-identified as African American/Black, 55% identified as White and 8% identified as mixed-race or other. A total of 24% of individuals reported no insurance coverage while 66% of patients reported having insurance. Overall, 85 patients reported they experienced no barriers to healthcare. Of those who reported barriers, 44% reported trouble with finances or insurance, 22% transportation, 18% personal drug use, 9% personal alcohol use, and 7% reported a distrust of healthcare providers or the system. Other barriers included long wait times, distance, and recent incarceration. DISCUSSION/SIGNIFICANCE OF IMPACT: Although screening for HCV is readily available, barriers exist which prevent diagnosis and treatment. We implemented a HCV testing and linkage-to-care program between local homeless shelters and health centers in New Orleans in an effort to reduce HCV-related morbidity and mortality."} +{"text": "Public health officials are concerned that adults may refuse to be vaccinated with an approved COVID-19 vaccine thereby limiting the community health benefit. Here, we studied the self-reported intent to be vaccinated of persons in North Carolina (NC) and then measured whether they did or did not get vaccinated. The Community COVID-19 Research Partnership (CCRP) is a large prospective study exploring COVID-19 epidemiology and sequelae in participants of several mid-Atlantic and Southern States. All participants complete an online daily survey where they are asked questions about COVID-like symptoms, infections, and their vaccination status. In addition to the daily survey, in December 2020, we implemented a short online cross-sectional survey questioning NC participants on whether they intended to be vaccinated. After completing the cross-sectional survey, we used daily survey data through 15 May 2021 to see if participants reported receiving vaccine. Unvaccinated participants who did not complete the daily survey 30 days or more prior to 15 May 2021 were excluded.18,874 participants completed the cross-sectional survey and reported vaccination status. Of these participants, 90% were white, 68% were female, 26% were healthcare workers, and 2% self-reported COVID-19 diagnosis The median age was 54 years (IQR: 41 \u2013 65). 79%, 13%, 9%, and 2% answered yes, unsure, no, and prefer not to answer, respectively, about intention to be vaccinated (Table). 99% of the participants who intended to receive the COVID-19 vaccine reporting being vaccinated. Those who were unsure or intended not to get vaccinated had vaccination rates of 80% and 53%, respectively. 78% of the participants who preferred not to answer were vaccinated. Vaccine intent versus vaccine status \u2013 COVID-19 Community Research Partnership, North Carolina, December 2020 \u2013 May 2021More than three-quarters of NC participants intended to get vaccinated and by mid-May 2021, the vast majority had received at least one dose. Similarly, those who were unsure or preferred not to say were mostly vaccinated. Even among those who reported they would not get vaccine in January, more than half had received vaccine by May. The nature of our sample makes it difficult to generalize results to the population of NC; nevertheless, further investigation as to the causes of the shift in attitudes is warranted. All Authors: No reported disclosures"} +{"text": "OBJECTIVES/GOALS: The Mayo Clinic Clinical and Translational Science (CTS) Predoctoral program aims to develop independent researchers capable of leading multi-disciplinary teams to accelerate the translation of discovery to application. Here, we detail the outcomes of our graduates over the past ten years (2010-2019). METHODS/STUDY POPULATION:): A survey was fielded with all CTS graduates whose degrees were conferred since the program\u2019s inception to 2019. Items addressed their current position, whether they were still involved in research, what type of research they were involved in, and whether they stayed involved with education. They also submitted a recent CV, from which data were collected about publications and grants. A subset were then contacted for a semi-structured interview. Items included questions addressing motivation for pursuing a PhD in CTS, whether the program prepared them for their current work, gaps they felt they had in training, and whether they felt they were making a difference in the lives of patients. RESULTS/ANTICIPATED RESULTS: Of the 41 alumni, 34 responded (83% response rate). Of these, 19 (56%) are at Mayo Clinic, 9 (26%) work for other academic institutions, and 6 (21%) do not work for an academic institution. Most have remained in research . The majority are involved in clinical research, 30% (10/33) in basic science, and 24% (8/33) in healthcare delivery research. Most are engaged in educational activities. When asked about changes they have led, 67% (18/27) led quality improvement projects and 44% (12/27) designed a new research method. Several hold leadership positions either in their organization or in a professional organization . DISCUSSION/SIGNIFICANCE OF IMPACT: The CTS Predoctoral program successfully prepares scholars for careers involving clinical and translational research; furthermore, alumni remain in research-oriented careers after graduation. We will continue to gather longitudinal data alumni move forward in their careers."} +{"text": "In a recent commentary, Bradbury and colleagues raise concerns regarding the potential influence of preexisting helminth infections on Coronavirus Disease 2019 (COVID-19) disease severity in helminth-endemic regions [In response, Hays and colleagues offer thAscaris lumbricoides and Ancylostoma sp., reaches 45% to 95% [An important caveat for consideration is that caution should be exercised when interpreting data from endemic areas due to possible lags in reporting. Evidence from some prospective surveillance studies in Africa suggest that the number of COVID-19 cases is underreported . Further% to 95% , but wit% to 95% . In Vene% to 95% . This poConversely, data from Lucas and colleagues regarding patterns of immune response to SARS-CoV-2 infection may help clarify why activation of the canonical helminth-driven Th2 phenotype could instead be deleterious . In theiAncylostoma duodenale and Necator americanus cause blood loss, anemia, pica, and wasting. Roundworms can also cause malabsorption, compete for nutrients, or cause intestinal or biliary tract obstruction, or in some cases, dysentery or diarrhea [Lastly, it is essential to remember the manifold negative effects of intestinal parasitosis. The hookworms diarrhea . In regi"} +{"text": "OBJECTIVES/GOALS: There is not much known on how to improve informed consent understanding and there are no effective interventions that have been identified to improve understanding rates of information. This study seeks to assess participants understanding of the informed consent. METHODS/STUDY POPULATION: We studied a non-probability sample of 245 participants, 57% female, with age range from 6 to 84, currently enrolled in clinical trials conducted at an urban city, multi CTSA institution. A self-administered questionnaire approved by IRB was utilized. Redcap database was utilized for data entry. The items in the questionnaire reflected understanding of the informed consent . Participants completed the survey during their first visit to the research centers or on a follow-up visit. Data were collected from July 2018 to November 2019. Data were analyzed descriptively by summary statistics. RESULTS/ANTICIPATED RESULTS: African Americans were 44%, Non-Hispanic Whites were 36%, Hispanic 6%. Others 13%. 52% married, 12% completed High school, 74.8% completed College, 13% less High school. 91% read the form themselves. 99% knew the purpose of the study; 99% knew they could quit the study at any time. While (113) 47% indicated knowledge of the potential risk, only (12)10.6% could not list any associated risk. 98% stated they had information on who to call with questions regarding the study. (204)86% knew of a potential benefit, only (11)5% could not name some study benefit. 38% were unsure/did not know the total number of visits study required of them. 74% knew the duration of the study. DISCUSSION/SIGNIFICANCE OF IMPACT: Extended discussion and more time on one-one by the study teams in this CTSA tend to increase trust. This approach has been reported to be most effective in improving participant understanding of informed consent process and may result in the positive experience."} +{"text": "Elder mistreatment (EM) is often underreported, making potential screening a valuable tool. There is limited literature on the screening utility, especially for minority populations. This abstract aims to study sensitivity and specificity of a commonly used 10-point EM screener compared to a detailed EM questionnaire among Chinese older adults. This study used data from a representative sample of 3,157 community-dwelling U.S. Chinese older adults 60+. Chi-squared test was conducted between VASS 10-questionare screener and EM measured by 56 items on psychological, physical and sexual mistreatment, caregiver neglect and financial exploitation subtypes. Sensitivity and specificity was calculated using the Bayes Theorem. In this sample, average age was 72 and 59% female. 637 (20.30%) reported any EM while 475 (15.14%) older adults screened positive for EM. Of participants reporting any EM, 365 (57.30%) did not screen positive for EM. The screener had a sensitivity of 42.70% and specificity of 91.88% for all EM subtypes. Gaps between reported EM and negative EM screener is smaller in psychological and physical EM subtypes, but much larger in financial exploitation and neglect . The VASS screener demonstrates poor sensitivity but acceptable specificity rate for any EM. The screener showed better sensitivity and specificity for physical and psychological mistreatment, but performed worse for more common forms of mistreatment like financial exploitation and neglect. Modifying this screener may improve sensitivity and specificity in identifying EM."} +{"text": "Studies conducted at the beginning of Covid-19 precautions suggested that older adults were stressed, but hopeful. Less is known how coping has changed for older adults after experiencing months-long pandemic precautions. We explore differences in coping between the initial pandemic declaration in March 2020, and 9 months later, via an internet survey fielded in November 2020 (n= 781). We present summary data, using chi-square tests for subgroup analyses. A majority of respondents were women (64%) and White (94%). When asked to compare their feelings to the beginning of the pandemic, 44.8% were more frustrated, 38.7% were more stressed, and 32.7% were more anxious. However, 38.3% were more appreciative. Women were significantly more likely than men to report increases in feeling frustrated, angry, scared, stressed, sad, and hopeless. Introverts were significantly more likely than extroverts to report an increase in loneliness and stress. Since the first few weeks of the pandemic, respondents reported more communication through video calls (45.2%), texting (40.2%), and phone calls (28.8%). Additionally, 61.5% spent more time on computers/tablets, 47.2% spent more time watching TV, and 24.5% spent more time praying. Extroverts were significantly more likely than introverts to report an increase in time with TV, phones, and computers/tablets. Women were significantly more likely than men to report increased texting and praying. These data provide further understanding of the impact of long-term pandemic precautions on older adults and suggest particular subgroups of older adults may benefit from public health and mental health interventions."} +{"text": "Reducing diagnostic delay is key toward decreasing tuberculosis-associated deaths in people living with human immunodeficiency virus. In tuberculosis patients with retrospective urine testing, the point-of-care Fujifilm SILVAMP TB LAM (FujiLAM) could have rapidly diagnosed tuberculosis in up to 89% who died. In FujiLAM negative patients, the probability of 12-week survival was 86\u201397%. Tuberculosis (TB) is the leading infectious cause of death worldwide and contributed to approximately 300 000 deaths related to human immunodeficiency virus (HIV) in 2017. Diagnostic delay remains a key factor contributing to mortality in HIV-associated TB, 5. AlthWe recently published findings on a next-generation urine LAM assay, Fujifilm SILVAMP TB LAM (FujiLAM), demonstrating its superior sensitivity and similar specificity to AlereLAM in hospitalized PLHIV . FujiLAMpost hoc mortality analysis, we utilized outcome data from 2 prospective cohorts of the previously published diagnostic accuracy study [For this cy study . Both stcy study . \u201cCohortcy study . Both coMycobacterium tuberculosis in any clinical specimen using culture or Xpert. In Cohort A, \u201cclinically confirmed TB\u201d was defined as those without a microbiological diagnosis of TB but where the nonstudy clinical team had started TB treatment based on clinical and/or radiological features of TB, as per the primary diagnostic accuracy study [The demographic and clinical details of patients were recorded at study entry. TB or alternative diagnoses were based on a comprehensive laboratory work-up including Xpert and/or mycobacterial culture in sputum, blood, urine, and other clinically indicated samples, along with clinical examination and follow-up, as previously described , 9, 10 . FujiLAMcy study . In Cohocy study , as thisThe proportion of TB patients who died who could have been rapidly diagnosed by each LAM assay with or without the addition of sputum Xpert was calculated. Kaplan-Meier plots were generated to investigate the cumulative mortality risk by FujILAM and AlereLAM test result. Negative predictive values (NPV) for death with Wilson 95% confidence intervals (CIs) were calculated for each LAM assay, by dividing the total number of LAM-negative survivors at 12 weeks by the total number of LAM-negative patients. The NPV represents the probability that those with a negative LAM result survive 12 weeks. Whether patients were treated for TB or any delays in treatment initiation were not factored into outcome analyses. Analysis was done using R (version 3.6.0).Overall, 983 patients were included in this analysis: 410 from Cohort A and 573 from Cohort B . The medAmong TB patients, 18/175 (10.3%) in Cohort A and 101/496 (20.4%) in Cohort B died within 12 weeks. In TB patients who died in Cohort A, FujiLAM could have diagnosed TB in 88.9% versus 66.7% by AlereLAM . All TB In TB patients who died in Cohort B, FujiLAM could have rapidly diagnosed TB in 80.2% versus 43.6% by AlereLAM . The comKaplan-Meier mortality curves stratified by FujiLAM-status for all patients in Cohorts A and B, and by subgroups, are shown in When assessing the NPV of FujiLAM for 12-week mortality, the probability of survival to 12 weeks was 89.9% (95% CI: 85.7\u201392.9) in unselected FujiLAM-negative patients from Cohort A and 97.0% (95% CI: 89.6\u201399.2) in the TB patients of Cohort A . The propost hoc analysis of 2 South African cohorts of hospitalized PLHIV, we found that FujiLAM would have rapidly detected TB in up to 89% of patients who died within 3 months. Furthermore, in TB patients, a negative FujiLAM result was associated with between 86 and 97% probability of survival to 3 months.In this AlereLAM-based diagnosis in combination with rapid TB treatment initiation has already been shown to reduce mortality in high-risk PLHIV and the association between detection of urinary LAM and mortality is not novel , 5. HoweStrengths of this study include analysis of 2 well-characterized large cohorts, with low rate of loss-to-follow-up. With retrospective urine testing, we cannot assess the real-world feasibility of FujiLAM, or whether it could have changed TB treatment practices or patient survival. Although the results suggest that there is room for benefit due to improved sensitivity, we also recognize the slightly lower specificity noted in our previous study with the FujiLAM assay, even though this difference was not statistically significant and might be a result of the imperfect reference standard . The risOur results suggest that in addition to the superior sensitivity of FujiLAM in comparison to AlereLAM, FujiLAM also has greater prognostic value. The clinical impact, including the potential survival benefit of FujiLAM, should be prospectively assessed in different real-world settings and more diverse populations\u2014including outpatients, children, and HIV-uninfected patients.Clinical Infectious Diseases online. Consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author.Supplementary materials are available at ciaa024_suppl_Supplementary_MaterialClick here for additional data file."} +{"text": "Objective: To determine the nationwide prevalence of malignant neoplasms (excluding hepatocellular carcinoma-HCC) in hospitalized liver transplant recipients and to study the hospital utilization, and mortality to the incidence of malignancies. To the best of our knowledge, few epidemiological studies addressed outcomes in post-liver transplant patients, such as the annual number of hospitalizations, mortality, patient characteristics regarding malignancies.Methods: NIS database was queried between 2016 and 2018 to retrieve records of patients admitted with a principal or secondary diagnosis of liver transplant following the International Classification of Diseases, tenth Revision (ICD-10). The population was divided into case and control groups according to the presence and absence of malignant neoplasm (MN) except for HCC. We also compared the incidence of MN in LTX patients and non-LTX matched cohort.Results: A total of 7.28% admissions were associated with malignant neoplasms (except HCC) in LTX patients. Lymphomas, respiratory, gastrointestinal (excluding HCC), leukemia, and head/neck were commonest cancers with estimated admission rates of 0.97%, 0.90%, 0.80%, 0.53%, and 0.49%, respectively. Lung cancer was the most frequent malignant neoplasm among White and Black racial/ethnic groups (15.78% and 14.8%), whereas lymphoma was pervasive among Hispanics (20.3%). Lung cancer had the highest in-hospital mortality (10.55%), followed by the cancer of the nervous system (9.09%). The LTX and non-LTX cohort comparison showed that LTX patients are at increased risk of head and neck cancers, skin cancers, lymphomas, tumors, and Myelodysplastic syndrome. According to a multivariate analysis, a statistically significant association existed between malignant neoplasms in LTX patients and the following factors: increasing age (P < .001), higher mortality (P < .001), females with 29% lesser odds than males (P < .001), Black race and Hispanic ethnicity with 20% and 26% lesser odds as compared to White (P < .05). Clinical factors included smoking, Alcoholic cirrhosis, Hepatitis B, and Hepatitis C, were statistically significant risk factors of post-liver transplantation malignancies.Conclusions: Malignancies were frequent among elderly patients and predominantly in males. Lymphoproliferative diseases were the most prevalent malignancy types, followed by respiratory/lung cancer- which showed the highest mortality risk of all cancers. LTX patients are at increased risk of head and neck cancers, skin cancers, lymphoma, tumors, and Myelodysplastic syndrome compared to non-LTX patients. This study aimed to determine the nationwide prevalence of malignant neoplasms, and the associated trends, clinical risk factors, patient demographics in hospitalized LTX patients. In addition, we aimed to compare the incidence of malignancies in LTX and non-LTX patients.International Classification of Diseases, tenth Revision) code of Z944. All malignant neoplasms were also identified with ICD-10 codes and categorized into Head and Neck, Gastrointestinal (excluding Liver), Bone, Skin, Breast, Reproductive system, Urinary system, Nervous system, Endocrine system, Lymphoma, Leukemia, Myeloma, Tumors, Myelodysplastic Syndrome, Cancer of other sites and Secondary malignancies. The NIS database houses more than 8 million records per year. It is the largest all-payer dataset from the Healthcare Cost and Utilization Project (HCUP), maintained by the Agency of Healthcare Research Quality (AHRQ) We used the National Inpatient Sample (NIS) database of hospitalized patients in the United States with data collected between January 2016 and December 2018, and we only selected data on patients with a primary or secondary diagnosis of liver transplant (LTX) based on an ICD-10 and controls . HCC is considered a common indication for LTX, so we excluded it from the data analysis to avoid bias. The secondary outcomes analyzed the hospital utilization, including discharge status, inpatient mortality, length of stay (LOS), and inpatient hospital-related total cost of care for all malignant neoplasms. The secondary outcome also includes a comparative analysis of the incidence of malignancies among LTX and non-LTX patients.The statistical analyses were performed using the SAS statistical software . We used mean (\u00b1standard deviation-SD) or median (interquartile range-IQR= Q3-Q1) for continuous variables such as age, total charges, and length of stay (LOS). Percentages denoted categorical variables. We performed group comparisons based on sociodemographic characteristics using Student t-test (for continuous variables) and Chi-square tests . We used t-tests to calculate the difference in LOS and total charges. Age was categorized into five groups for group-level comparisons . A multivariate model developed from the stepwise logistic regression was used to test the predictor variables' association with malignant neoplasms. This regression model selected the most relevant variables to retain at a significant effect level of entry of 0.15 and a level of staying of 0.10, removing other variables not fitting this effect criterion. We calculated odds ratios from logistic regression models, examined covariates' effects on the predictor variables, and adjusted these odds ratios (adjusted aOR) for confounders such as age, gender, and race. We selected a non-LTX matched group based on age, sex, and race using the 1:1 ratio nearest neighbor (greedy) propensity score method. The goodness of fit model was evaluated with Pearson's Chi-square. All hypothesis testing used a two-tailed p-value with the significance level set at 0.05. The missing data on race, primary payer, median household income, discharge status, hospital location, and hospital teaching status were labeled with \u201cother\u201d or \u201cUnknown\u201d.A total of 26225 hospital admissions occurred between 2016 and 2018 with liver transplant status, of which 1909 (7.28%) entries were associated with malignant neoplasms (except HCC)- thus constituted our group of cases of hospitalized LTX patients.Figure 1).Lymphomas were the most prevalent cancer among LTX patients, followed by respiratory cancers, gastrointestinal cancers (excluding liver or HCC), leukemia, and head/neck cancers with estimated admission rates of 0.97%, 0.90%, 0.80%, 0.53%, and 0.49%, respectively. Cardiac cancers were the least prevalent, followed by cancers of the nervous system and bone (SD \u00b115.08) and among males (68.73% among cases vs. 59.20% among controls) than females (31.27% for cases vs. 40.80% for controls) (Table 1). Respiratory cancer was the most prevalent malignant neoplasm among White patients (15.78%), followed by lymphoma (14.33%) and gastrointestinal cancer (12.29%). Among Black patients, respiratory cancer (14.81%), reproductive system cancer (12.96%), and leukemia (11.11%) were the most reported. Among Hispanics, lymphoma (20.27%) and gastrointestinal cancers (13.51%) prevailed .Malignant neoplasms with LTX were more frequent in older patients with a mean age of 61.21 years , p < .05, hepatitis B (3.09% among cases vs. 1.69% among controls) , p < .01, hepatitis C (12.94% among cases vs. 9.83% among controls) , p < .01, and opioids (3.72% among cases vs. 2.94% among controls), p =0.05. Immunosuppressants, HIV and Primary sclerosing cholangitis (PSC) were also more frequent in patients with LTX but was found to be statistically not significant.Malignant neoplasms with LTX were more frequent in patients with smoking (37.56% among cases vs. 32.10% among controls), Table 2 showed the univariate and multivariate regression analyses and some selected sociodemographic and clinical risk factors of malignant neoplasms in hospitalized LTX patients. The multivariate logistic regression showed that female patients were 29% less likely to develop cancers compared to males . Compared to patients aged 17 years or less, the odds of cancers in patients aged 18-49 were the same; however, in patients aged 50-59, the odds of cancers were 1.68 times higher ; p < .001), 2.1 times higher in patients aged 60-69 , and 2.69 times higher in those aged over 70 . In terms of race, compared to White patients, Black patients had 20% and Hispanic patients had 24% lesser odds of developing malignant neoplasms. Asian or Pacific Islander and Native American odds were not statistically significant. The median household income using national quartiles ranging from 1 (lowest median income) to 4 (highest median income) was utilized in the regression model as a proxy measure reflecting patients' socioeconomic status based on their communities' zip codes. Compared to median household income in quartile 1, the odds of cancers in patients with median household income in quartile 3 were 1.28 times , and 1.16 times in quartile 4.aOR, 1.121; 95% CI, 1.013 - 1.240; p < .05), 30% greater odds with alcoholic cirrhosis , 54% greater odds with hepatitis B , 24% greater odds with hepatitis C , and 36% greater odds with opiods .LTX Patients have 12% greater odds to develop cancers with smoking , and 27% more likely to get admitted to medium hospitals as compared to small , and higher likelihood to get admitted into large hospitals (47%) than to small . In our study, the hospital's teaching status and its region failed to show a statistically significant association with risk for malignant neoplasm. Regarding discharge characteristics, cases were 34% more likely to transfer to home health care (HHC) as compared to routine discharges , and had 3.9 times greater odds of in-hospital mortality . The mean differences in total length of hospital stay (LOS) and hospital inpatient charges were found to be higher in LTX patients with malignant neoplasms and , respectively.Patients with malignant neoplasms had 73% greater odds of elective admissions than non-elective admissions (p < .01), 3.2 times higher in skin cancer , 1.4 times higher in lymphoma's , 1.58 times higher in Myelodysplastic syndrome , and 1.55 times higher in tumors .Table p < .001, more patients admitted on weekdays- 80% compared to around 20% during weekdays and weekends, respectively in both cases and controls (p < .001). In both groups, more than 65% of patients got admitted to large hospitals (68.88% of cases vs. 65.10% of controls) compared to 21% to medium hospitals and 10% to small hospitals (p < .001). In terms of hospital teaching status, most patients with LTX preferred admission to an urban teaching hospital (84.60% for cases and 84.40% for controls) than urban nonteaching and rural hospitals (Table 1). Patients with LTX and malignant neoplasms (cases) had a higher length of stay (LOS) compared to LTX patients (controls), M = 6.45 days (SD \u00b18.54) vs. M = 5.56 days (SD \u00b17.94), respectively (Table 4). Similarly, Table 4 showed that cases had a higher inpatient hospital cost of care than controls with a respective mean total charge of $77,127 vs. $64994 . Patients admitted with bone, gastrointestinal, head, neck, and myeloma cancers had a higher mean length of stay (LOS) than other cancers - except for nervous system cancers and myeloma Figure .Most hospital admissions were non-elective (78.24% among cases vs. 86.16% among controls) as compared to elective (21.76% among cases and 13.84% among controls), de novo malignancies de novo malignancy or recurrence of hepatocellular carcinoma in-vitro studies Previous studies demonstrated that liver transplant recipients were at risk of developing Our study showed that the risk of developing malignant neoplasms in LTX patients increases with age. Also, malignant neoplasms were more common in males than females . Black and Hispanic patients were at lower risk than Whites. Our study also showed that smoking is a significant risk factor associated with higher odds of malignant neoplasms in LTX patients. 12% greater odds to develop cancers with smoking .Our study revealed that the most common malignancies present among hospitalized LTX patients are lymphomas, followed by respiratory cancers. Gastrointestinal cancers, excluding hepatocellular carcinoma, marked the third top malignancy. In our population dataset, lymphomas accounted for 0.97% of admissions in post-liver transplant patients, with the highest incidence among Hispanics 20.27%). lymphomas or lymphoproliferative disorders in the post-transplant phase could correlate with inadequate immune response toward the EBV virus .27%. lymRespiratory malignant neoplasms are the second leading in our LTX patient's cohort. Often lung cancer is seen in lung transplant patients or heart transplant recipients de novo malignancy Gastrointestinal cancers, excluding hepatocellular carcinomas, ranked third as the most common malignancies in our study population. Out of all the GI malignancies, colorectal malignancies in LTX patients were the most studied. Previous studies showed that the incidence rate of colorectal cancer is 0.4 to 0.54 % in the United States Other cancers observed in LTX patients included head and neck, genitourinary, nervous system, bone, skin, leukemia, myeloma, breast, and endocrine cancers. Data on admissions with cardiac cancers were missing. Head, neck, and bone cancers had lesser admission rates (0.49% and 0.13%), but their inpatient hospital charges were higher, and their length of stay was more extended than more prevalent cancers like lymphomas.Our study revealed that LTX patients are at increased risk of head and neck cancers, skin cancers, lymphoma, tumors, and Myelodysplastic syndrome compared to our non-LTX hospitalized patient cohort. The highest on the list is skin cancer with 3.2 times higher odds, which aligns with the previous studies' results This study highlighted that most admissions of LTX patients with malignancy were elective and were on weekdays. Patients preferred sizeable urban teaching hospitals over small urban non-teaching hospitals. LTX patients with malignant neoplasms had a longer length of stay with a mean of 6.45 days as compared to 5.56 days of LTX patients with no malignancies. This longer length of stay can be attributed to more comorbidities and complications in this patient population. Our results showed that bone cancers had the most extended length of stay, possibly because of widespread metastasis and malignancy complications. In-hospital mortality was 3.3 times higher in LTX patients with malignant neoplasms than in those without malignancy. Respiratory cancers accounted for the highest inpatient mortality. Inpatient hospital cost of care was higher in LTX patients with malignant neoplasms secondary to more complicated hospital courses and expensive chemotherapy treatment regimens- thus increasing the health care burden. Out of all malignancies, bone cancers recorded the highest utilization of hospital charges. This finding is in line with our previously mentioned observation of bone cancer patients' most extended length of stay.We used the National Inpatient Sample database with data collected between January 2016 and December 2018. With more than 7 million records per year, the NIS administrative database could be prone to selection bias and coding errors. Our study encountered multiple limitations; for instance, liver donor information was lacking from the database, and one of the significant risk factors of malignancy in post LTX patients includes EBV seropositivity in the donor.Another limitation was the missing data regarding the length of time between transplantation and the incidence of diagnosis of malignancy. In addition, the duration and dosage of immunosuppressant drugs were not available. Moreover, since this database housed inpatients data only, we could not evaluate any outpatient follow-up and previous cancer screening. Therefore, the calculated mortality from malignant neoplasms reflects only that for the inpatient sample and does not account for outpatient mortality rates; therefore, it could be that our data present an underestimation of malignancy-associated mortality rates post liver transplant.This study remains unique because it highlights the impact of malignancy post-liver transplant using a large and diverse cohort of patients with national data from all United States regions compared to previous studies of specific geographical areas or centers. In addition, we compared the LTX patients with a non-LTX matched cohort and compared the incidence of various cancers. To the best of our knowledge, it is the first study from the National Inpatient Sample database to analyze hospital utilization and the discharge status of all liver transplant patients. Despite the inherent pitfalls of using an administrative database to study clinical outcomes, still, the NIS database houses a plethora of national data that provide a rough estimation of the cumulative prevalence of malignancy post-liver transplant at the national level; thus, its utilization can be harnessed to generate new hypotheses for prospective controlled experimental studies.The number of post-liver transplantation complications is on the rise. Therefore, our study aimed to observe the incidence of malignancies in hospitalized liver transplant patients. Among these hospitalized LTX patients, lymphoproliferative diseases followed by respiratory cancers were the most reported malignancies. Moreover, our research found that LTX hospitalized patients are at increased risk of head and neck cancers, skin cancers, lymphoma, tumors, and Myelodysplastic syndrome than non-LTX patients.This study highlights a clear trend in the patient sociodemographic and discharges characteristics. Advanced age, being White, and being male were significantly associated with a higher likelihood of malignant neoplasms in liver transplant patients. Patients aged 70 and up were 2.7 times more likely to develop malignancy than young patients; females had 29 % lesser odds of malignancy than males.In our research, factors like smoking, Alcoholic cirrhosis, Hepatitis B, Hepatitis C were statistically significant risk factors of post-liver transplantation malignancies. Moreover, our study also found opioids linked with a higher rate of post-liver transplantation malignancies.Respiratory cancer had the highest risk of mortality among all cancers, accounted for 10.5% of all reported mortalities. Cancers of the nervous system, myelodysplastic syndrome, and breast cancer admission rates were lower, but their mortality was higher than other cancers with 9.1%, 8.75%, and 8.3%. Although head, neck, and bone cancers were uncommon in LTX patients, they had a longer length of stay and hospital charges than more frequent cancers like lymphomas and respiratory. Most of the patients had routine discharge, followed by transfer to home health care, other facilities , or short-term hospitals.To conclude, regular cancer screening in liver transplant patients is crucial as early detection helps in enhancing treatment responsiveness. Therefore, clinicians should proactively seek to diagnose these aggressive cancers post-liver transplantation as early as possible to reduce morbidity and mortality, hospital burden, and improve patients' outcomes and quality of life.The authors confirm contribution to the paper as follows:Study conception and design: Author, Maryam Bilal Haider (corresponding author). Data collection and statistical analysis: Author, Syed M Haider. Interpretation of results: Author, Rana Ismail. Draft manuscript preparation: Author, Maryam Bilal Haider, and Anusha Bapatla. Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved: Author, Rana Ismail, Ahmed J Chaudhary, and Sana Iqbal.All authors reviewed the results and approved the final version of the manuscript."} +{"text": "Evidence on how body mass index (BMI) influence cardiometabolic health remains sparse in Chinese children and adolescents, especially in south China. We aim to investigate the effect of overweight and/or obesity on high blood pressure (HBP), dyslipidemia, elevated serum uric acid (SUA) and their clustering among children and adolescents in an island in South China.Using multi-stage cluster sampling method, 1577 children and adolescents aged 7\u201318 in Hainan province, south China, participated in the survey. The association between body mass index and cardiometabolic indexes were explored. Overweight and obesity were classified according to criteria of World Health Organization for children and adolescents aged 5 to 19. Restricted cubic spline models were used to examine the possible non-linear association between BMI and cardiometabolic profiles. Multivariable logistic regression models were fitted to examine the effect size of BMI on cardiometabolic disorders including HBP, elevated SUA and dyslipidemia. Comorbidity of at least two cardiometabolic abnormalities was defined as clustering of cardiometabolic risk factors.Comparing with normal weight and underweight subjects, overweight/obese youths had higher levels of BP, SUA, triglyceride, low-density lipoprotein but lower level of high-density lipoprotein. Overweight/obese youth had higher risk of dyslipidemia , HBP and elevated SUA , respectively, than their counterparts. The sex-, age-adjusted prevalence of abnormalities clustering was 32.61% (95% CI: 20.95% to 46.92%) in overweight/obesity group, much higher than in the under/normal weight group .Excess adiposity increased the risk of elevated serum uric acid, serum lipids, blood pressure and their clustering among children and adolescents in south China. Cardiometabolic risk factors in childhood, such as high blood pressure, elevated serum uric acid, dyslipidemia, are associated with earlier onset and greater risk of chronic diseases in adults \u20133.ExcessSince cardiometabolic disease develops gradually, it is important to identify children and adolescents who are in high risk and have already had abnormalities. There are previous studies exploring the association between excess adiposity and pediatric cardio-metabolic risk factors \u201316, whicThe present study is cross-sectional design and based on data collected in Hainan province, which is an island in southernmost China. The sampling method is the same with our previous studies , 18. BriAs in this study, several cardiometabolic disorders were measured, we used the lowest prevalence among these disorders to ensure the statistical power. Based on our previous analysis, the prevalence of dyslipidemia and high blood pressure among children and adolescents were 20% and 7% , 18, resq equals 1-p, and d was the error tolerance. To reach a significant level of 0.05 and error tolerance 0.2\u2009\u00d7\u2009p, the estimated minimum sample size was 1276. An additional 20% to the minimum sample size was added factoring in possible non-compliance rate and targeted 1532 subjects. Finally, 1609 children and adolescents participated in the study.Alpha (\u03b1) was the significant level, p was the prevalence of HBP, 2). Using a digital blood pressure measuring device with children customized cuff size, systolic blood pressure (SBP) and diastolic blood pressure (DBP) were measured on the right arm of individual after at least 5\u00a0mins in a sitting position in the study morning. The average value of the three measures were recorded. A 9\u00a0ml (at least 8\u00a0h fasting overnight) venous blood sample from each participant was draw by qualified nurses for serum lipids and uric acid tests by Chemistry Analyzer . For each day of the survey, the samples were kept in a portable, insulated cool box with ice packs to maintain their temperature at 0\u20134\u2103 for up to 3\u00a0h before being transported to the laboratory of local center for disease control and prevention (CDC) for immediate processing. Serum lipid tests included total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C).A standardized questionnaire interview was conducted face-to-face by fixed trained staff to collect information on demographic characteristics at community health centers or village clinics in the study sites. Height was measured to the nearest 0.1\u00a0cm using a fixed stadiometer by the same staff to avoid measurement system error. Body weight were measured barefooted with light clothes using a body composition analyzer with decimal accuracy. BMI was calculated as weight in kilograms divided by the square of height in meters for children and adolescents aged 5 to 19[National Heart, Lung, and Blood Institute (NHLBI) cholesterol screening guidelines and cut points backed by the American Academy of Pediatrics [Serum lipid disorders were defined according to the diatrics , and hasdiatrics .Fourth Report on the Diagnosis, Evaluation, and Treatment of High Blood Pressure in Children and Adolescents [Blood pressure was classified into normal BP and high blood pressure based on the updated guidelines of the lescents . As therlescents .Comorbidity of at least two cardiometabolic abnormalities was defined as clustering of cardiometabolic risk factors.After excluding subjects with missing data on main risk factors , data on 1577 youths were analyzed.Summary results were presented as mean (SD) for normally distributed continuous data, median for continuous data in-normally distributed, and counts for categorical data. T-test or U Mann-Whitsney test was used to compare continuous data between two groups. Chi-square test was used to compare grouped data. Two-way analysis of covariance or quantile regression models were used to compare cardiometabolic profiles among body weight groups after adjusted for potential confounders. Partial correlation analysis was performed to understand the correlation between BMI and cardiometabolic indexes by adjusting potential confounders. Scatter plots were presented to show these correlations. Factors that were associated with both BMI and cardiometabolic indexes, such as age and residential areas, were set as covariates in the adjusted regression models, to avoid the potential confounding caused by these factors.Logistic regression models were used to calculate the multi-variable adjusted prevalence of elevated SUA, HBP and dyslipidemia among different body weight groups . Restricp-value\u2009<\u20090.05 (two-tailed) was considered statistically significant. Because of the limited number of obesity in both sexes, obesity was combined with overweight as one group, presented as overweight/obesity in the present study. All statistical procedures were performed using SAS 9.4 .A The demographic and basic clinical information were presented in Table The correlation between BMI and SUA, blood pressure and serum lipids, stratified by sex, were presented as scatter plots in Fig.\u00a0p\u2009<\u20090.001 in girls). For blood pressure, only in girls, the overweight/obesity group had higher SBP (p\u2009<\u20090.001). No difference was tested in DBP. In both boys and girls, overweight/obesity group had higher level of TG, LDL-C, but lower HDL-C than their counterparts (P\u2009<\u20090.05).The comparison between underweight, normal weight and overweight/obesity on SUA, blood pressure and serum lipids were presented in Table P\u2009<\u20090.001) and dyslipidemia (P\u2009<\u20090.001) were observed. Neither linear nor non-linear significant association between BMI and HBP was tested by RCS (P\u2009>\u20090.05). When took BMI as grouped variable to fit the logistic regression model by sex, increased risk of cardiometabolic disorders in the overweight/obesity group were observed. In the overall model, overweight/obese youth had 1.89, 1,81, and 1.49 times higher risk of dyslipidemia, HBP and elevated SUA, respectively, comparing with the under/normal weight youths , 38.29% (95%CI: 35.42% to 41.25%) and 60.00% (95%CI: 46.87% to 71.83%); 4.93% (95%CI: 2.73% to 8.73%), 5.28% (95%CI: 4.14% to 6.72%) and 13.46% (95%CI: 6.44% to 26.02%); 15.74% (95%CI: 11.46% to 21.23%), 18.43% (95%CI: 16.32% to 20.74%) and 38.99% (95%CI: 27.10% to 52.37%).The sex-specific crude prevalence and adjusted prevalence of elevated SUA, HBP and dyslipidemia in different BMI groups were presented in Fig.\u00a0The crude prevalence of the clustering of at least two cardiometabolic abnormalities in under/normal weight and overweight/obesity groups were 9.21% and 23.88%, respectively Fig.\u00a0-A. AfterIn this study, based on a representative population sample, we explored the association between body mass index and cardiometabolic profiles, especially take elevated serum uric acid as one of the components of cardiometabolic abnormalities, in a southernmost island of China. Our findings revealed that BMI was linked with multiple cardiometabolic abnormalities and their clustering. The prevalence of cardiometabolic abnormalities increased with elevated BMI, and the level of serum lipids, blood pressure and serum uric acid were associated with overweight and/or obesity regardless of sex.The epidemic of overweight and obesity is increasing in Chinese children , 11 and The relationship between excess adiposity and cardiometabolic diseases in children and adolescents has been acknowledged by previous studies \u201315, 29. Our study revealed that, increased BMI was linked with elevated SUA, and this effect varies on sex. Boys had much higher SUA level than girls and the correlation between BMI and SUA was also stronger than girls. The negative association between SUA and BMI groups in boys may be due to the limited sample size and the cut-off value of serum uric acid. SUA and other metabolic components has complicated interactions. Elevated SUA can also influence other cardiometabolic risk factors and vice versa , 22, 35.Elevated body weight was also associated with increased risk of serum lipid disorders , 40, andOverweight and obesity are important risk factors for HBP in children , 46. In Few studies explored the clustering of cardiometabolic abnormalities. Seo et al. investigated the cardiovascular disease risk factors clustering (CVD-RFC) among Korean children and adolescents aged 6\u201315 , in whicThe investigation of co-morbidity of high blood pressure, serum lipids and SUA could provide more comprehensive estimation on disease risk and clues for risk factors prevention among children and adolescents. Several studies have reported the cardiovascular risk factors clustering in Chinese children and adolescents , but theThe strength of our study is the representative large sample size and the co-mobility estimation of cardiometabolic abnormalities clustering among children and adolescents. Given the limited data of cardiometabolic abnormalities clustering, especially the clustering of elevated SUA and other risk factors among Chinese children and adolescents, this study could provide evidence on disease burden estimation in youth in South China. In addition, in this study we used both linear and non-linear models to understand the association between excess adiposity and cardiometabolic abnormalities in multi-aspects. Nonetheless, the limitation of the current study should also be acknowledged. Firstly, using cross-sectional data, we cannot make causal inference between excess adiposity and cardiometabolic abnormalities. Given that both epidemiological and Mendelian randomization study have improved the causal role of overweight/obesity in the disease onset of cardiometabolic disorders , 51, andIn summary, with representative community-based sample, vigorous methodology, we find that excess adiposity increased the risk of elevated serum uric acid, serum lipids, blood pressure and their clustering among children and adolescents in a southernmost island of China. This study highlights the risk of overweight and/or obesity on multiple cardiometabolic abnormalities and would be helpful for policy makers as well health practitioners to learn the current situation of local childhood disease burden and risk factors, and further useful for early intervention."} +{"text": "In 2021, during the COVID-19 response, the Council of State and Territorial Epidemiologists (CSTE) conducted its seventh periodic Epidemiology Capacity Assessment (ECA), a national assessment that evaluates trends in applied epidemiology workforce size, funding, and epidemiology capacity at state health departments.The ECA questionnaire instrument was updated in 2021 to include new epidemiology program areas for generalists and COVID-19 specialists and the revised EPHS , followed by state funds (12%) and other sources (3%). As part of the federal funding for epidemiology activities, 39% was designated for COVID-19 activities with time-limited funding. The federal government funds 85% of epidemiology personnel positions, with 33% of these funds designated specifically for COVID-19 personnel. The remaining epidemiology personnel positions are funded by state government (15%) and other sources of funding (2%). Federal funding supports approximately 80% of epidemiology positions for COVID-19 response, preparedness, and substance use. In contrast, state and other sources of funding support approximately 50% of informatics, environmental health, generalist, and vital statistics positions.Among program areas, infectious disease accounted for 1,498 (36%) of the 4,136 epidemiology positions, followed by COVID-19 response (24%) and MCH (7%) . ProgramThe largest absolute and relative increases between 2017 and 2021 were in informatics, where 103 positions were added, representing a 107% increase . Since 2Participating state epidemiologists expressed the need for an additional 2,196 epidemiologists to deliver the EPHS, a 53% increase over the current number . The larIn 2021, 75% of jurisdictions had substantial-to-full capacity for monitoring health status (EPHS 1) and 88% capacity for diagnosing and investigating health problems and hazards (EPHS 2); both represented declines from 2017 . Substantial-to-full capacity to conduct research and evaluation (EPHS 9) was 43%.When overall capacity was examined by program area, substantial-to-full capacity was highest for infectious diseases (88%), MCH (70%), chronic diseases (66%), vital statistics (54%), substance use (52%), injury (50%), and preparedness (50%) . States Despite achieving the largest applied epidemiology workforce since tracking began in 2001, reported decreases in current staffing levels and an increased need for staff members by state health departments are concerning. Decreases in the number of staff members have important impacts on the ability of public health agencies to detect, investigate, and respond . Second, data on public health capacity are subjective; the data reflect the jurisdiction\u2019s needs at the time of fielding, which might be biased toward immediate priorities, such as the COVID-19 response, rather than toward routine public health activities and planned strategic priorities or the resources to support public health transformation.The Coronavirus Aid, Relief, and Economic Security Act has authorized $500 million for public health data surveillance and analytics infrastructure modernization.The COVID-19 response has strained the U.S. public health system. Although the state health department epidemiology workforce has increased since 2017, workforce and capacity needs remain unmet.From 2017 to 2021, the number of epidemiologists in state health departments increased 23%, primarily because of those supporting the COVID-19 response. The epidemiology workforce remains substantially understaffed, and core program areas have experienced staffing declines. Temporary federal funding has increased to support 85% of epidemiology activities and 83% of personnel. Overall capacity to deliver essential public health services has declined.More epidemiologists and sustainable resources are needed to deliver essential public health services consistently and effectively."} +{"text": "Hepatitis B virus (HBV) infection is a significant global public health problem. Health care providers and medical students in developing countries including Ethiopia are at an increased risk of contracting HBV due to the high burden of this infection. The most effective way of prevention against HBV infection is vaccination of health care providers. However, there is a paucity of data on the HBV vaccination coverage among students of health science in Ethiopia. Therefore, this study aimed to determine HBV vaccination coverage and associated factors, level of knowledge, attitudes, and practices (KAP) towards HBV among students of medicine and health science at Wolkite University.A cross-sectional study was conducted at Wolkite University among 417 study participants from November to December 2020. The study participants were recruited by using a simple random sampling technique. Data were collected using a self-administered structured questionnaire and analyzed using SPSS version 21. A binary logistic regression model was used to determine the factors associated with full-dose vaccination status. Statistical significance was set at P-value <0.05.Out of the 417 study participants, 5.8% (95%CI: 3.8\u20137.9) received a full-dose of the HBV vaccine in this study. Unavailability and high cost of the vaccine were frequently mentioned reasons for not being vaccinated against HBV. About 73.6%, 36.2%, and 47% of participants had good knowledge, positive attitudes, and good practices towards HBV, respectively. Being male gender , rural residence , positive attitude , good practice , medicine department , being second-year student , third-year student , and fourth-year student were significantly associated factors with full-dose vaccination status.Our study revealed that only small proportions (5.8%) of study participants received full-dose HBV vaccination. Vaccinations of students before starting clinical attachments, provisions of training for students on infection prevention mechanism and universal precautions particularly on HBV, increasing the uptake of the HBV vaccine, creating awareness on attitude and practice of students towards HBV to enhance uptake of the vaccine are recommended. Hepatitis B virus infection is a global public health problem, a study indicated 3.61% of the overall burden of HBV infection globally with a higher burden reported from the African 8.8%) and western pacific region 5.26%) .8% and wTransmission of HBV in a health care setting occurs through contact with blood, blood products, body fluids, needlestick, and sharps injury from HBV carrier , 10. MedThe most effective and efficient way of prevention mechanisms against HBV infection is vaccination of health care workers, which provides more than 90% protection . The WorSeveral epidemiological studies conducted in Ethiopia showed varying rates of full-dose HBV vaccination among health care workers \u201315. The Determination of HBV vaccination coverage and its associated factors among medicine and health science students was an aid to design and implement effective intervention mechanisms such as vaccination of students before starting their clinical attachments and intervene on associated factors. Assessing the level of knowledge, attitudes, and practices (KAP) of medicine and health science students towards HBV was important to design and implement awareness creation on standard safety precautions towards the prevention of HBV infection. Planning, designing, and implementation of effective interventions were based on the available and updated information. However, there is limited information on the HBV vaccination coverage and associated factors among health science students in Ethiopia despite the increasing burden of the infection. Therefore, this study aimed to determine HBV vaccination coverage and associated factors, level of KAP towards HBV among students of medicine and health science at Wolkite University, southwest Ethiopia.A cross-sectional study was conducted at Wolkite University in Gurage zone, South Nation Nationality and Peoples Regional State (SNNPR), Ethiopia. The University is located in the Gubriye sub-city, 13km far away from the zonal town, Wolkite which is located 158km from the capital city of Ethiopia, Addis Ababa. The University provides teaching, research, and community service in its six colleges. College of medicine and health sciences has five departments . In this college, there were 1,739 students, out of those 530, 271, 313, 321, and 304 were in medicine, public health officers, nursing, medical laboratory science, and midwifery department respectively. Most of the health science students received 4 years of training except for the students of medicine (6 years). The study was conducted in medicine and health sciences students from November to December 2020 in the college of medicine and health science at Wolkite University, southern Ethiopia.2p(1-p)/d2] with an assumption of 95% confidence level, 5% margin of error (d), 44.3% proportion (p) of HBV vaccine coverage in medicine and health science students at Makerere University, Uganda received a full dose of the HBV vaccine in this study. The majority of the study participants 310 (74.3%) have never received the hepatitis B vaccine and 107 (25.7%) had received one or two doses of the HBV vaccine. The most frequently mentioned reasons for not being vaccinated against HBV were unavailability of the vaccine 320(81.4%), high cost of the vaccine 54(13.7%), lack of knowledge about vaccine 16(4.1%), and fear of side effects 3 (0.8%). Forgot to receive follow-up dose 216(55%), busy schedule, 47(12%), and having obtained the immunity 130(33.1%) were the common reason for not receiving a full course of vaccination among the study participants.The majority of the study participants 307 (73.6%) had good knowledge about HBV infection, mode of transmission, and prevention. Among the study participants, 364 (87.3%) knew that HBV infection causes liver cancer. The majority of the study participants 384(92.1%) and 400(95.9) reported contact with contaminated blood and body fluid of HBV carrier, and unsterilized syringes, needles, and surgical equipment were the main mode of transmission for HBV respectively. Regarding knowledge on vaccination, 349(83.7%) participants were aware of the HBV vaccine and it provides protection against HBV infection, and also 199(47.7%) of participants knew that there is post-exposure prophylaxis for HBV .Among the study participants, 151 (36.2%) had positive attitudes towards HBV infection and risk perceptions. About 313 (75.1%) study participants agreed that following infection control guidelines would protect them from being infected at work, and 286(68.6%) were aware that the HBV vaccine is safe and effective against HBV infection .Among the study participants, 196(47%) had good practice towards the prevention of HBV. Out of the 417 study participants, only 161(38.5%) had screened for HBV, 107(25.5%) had been vaccinated against HBV. However, out of the vaccinated participant, 24(5.4%) had completed the recommended three doses. About 153(36.5%) reported they had encountered needle stick injury and 278(68.8%) reported they would always change gloves for each patient during procedures .Association between full-dose vaccination status and independent variables were tested with binary logistic regressions. By considering P-value <0.25 in bivariate analysis, gender, age, residence, academic year, department, attitude, and practice were identified candidates variables for multivariate analysis. Then, multivariate logistic regression analysis was performed to control for confounders and identify significantly associated factors with the full-dose vaccination status. After multivariate analysis, male gender, rural residence, academic years, medicine department, good attitude, and practices were significantly associated with full dose vaccination status .Being male gender , rural residence , being second year student , third year student , fourth year student , medicine department , positive attitude and good practice were significantly associated with full-dose vaccination status .The current study attempted to determine HBV vaccination coverage and associated factors, and level of KAP towards HBV among students of medicine and health science at Wolkite University, southwest Ethiopia. World Health Organization estimated 18\u201339% coverage of HBV vaccine among healthcare providers in developing countries and 67\u201379% in developed countries . HoweverThe 5.8% full-dose vaccination rate among our respondents was low, given their increased risk of contracting HBV. In this study, the most commonly reported reason for not receiving a full course of vaccination among the study participants was forgot to receive a follow-up dose (55%) and having a busy schedule (12%). This finding was in agreement with studies conducted in Gondar University Hospital, Ethiopia and ChinThis study revealed that 25.7% of study participants had been vaccinated at least once against HBV. This result was comparable with studies reported from different areas. For instance, a similar study conducted in Ghana reported 22.5% of participants were vaccinated against the hepatitis B virus . AnotherThe current study revealed that 74.3% of study participants have never received the hepatitis B vaccine. Frequently mentioned reasons for not being vaccinated against HBV among study participants were unavailability of the vaccine (81.4%) and followed by the high cost of the vaccine (13.7%). A similar finding was reported from Gondar University Hospital, Ethiopia , and MakMale study participants were 12% less likely to take full-dose hepatitis B vaccination than females study participant. This finding was consistent with the study conducted in Wolayita hospital in Southern Ethiopia , and ShaThe study participants who were rural area residents were 64% less likely to receive full-dose vaccination against HBV as compared to urban residents. This might be due to a lack of awareness of the infectious disease, inaccessibility, and unavailability of the HBV vaccine. In the current study, full-dose vaccination status was significantly associated with the academic years of the study participants. This result was in agreement with a study conducted among students in Ho, Ghana , and MakBeing in a medicine department was significantly associated with the full-dose vaccination status in this study. This was consistent with the studies conducted in Gondar University Hospital, Ethiopia and ChinDespite the different professional backgrounds of the study participants, our finding revealed that 73.6% of study participants had a good level of knowledge regarding HBV, its mode of transmission, and prevention. This finding was consistent with the previous studies reported from Makerere University, Uganda (74.6%) , Kochi, Regarding the attitude of students towards HBV and its vaccination, 36.2% of study participants had positive attitudes regarding HBV. The majority (75.1%) of the participants were aware that following infection control guidelines will protect them from the risk of contracting HBV at the workplace and 68.6% of them believe that the HBV vaccine is effective and safe. Several previous studies reported comparable results with the current study. The study conducted in Senegal among 315 medical students reported that 32.4% of students had positive attitudes regarding HBV. Whereas, it was lower than the study finding reported from Kochi, India 84.3% and KancIn the current study, 47% of the participants had good practices against hepatitis B. This finding was higher than the study reported from Senegal 32.4% . But it Despite extensive efforts that have been made to minimize possible shortcomings of this study, the findings of this study were interpreted by considering the following limitations. HBV vaccination status was assessed based on self-report, we did not measure the anti-hepatitis B surface antibody titer of the participants, and did not confirm the information regarding HBV vaccination because the study participants came from different parts of the county. The cross-sectional nature of the study does not confirm a cause-and-effect relationship. There was also a possibility of admitting recall bias because of the self-reported vaccination status. Despite the limitations, the findings of this study highlighted that there was a critical need for vaccination of students against this highly contagious infection before they start clinical attachments, provisions of training on prevention mechanisms, and universal precautions regarding blood-borne pathogens before enrolling in professional practice.Our study revealed that only small proportions (5.8%) of study participants received full dose vaccination against HBV. Gender, residence, academic years, type of profession, attitude, and practices towards HBV were significantly associated factors with full dose vaccination status. Unavailability and high cost of the HBV vaccine were frequently mentioned reasons among study participants for not being vaccinated against HBV. Our finding showed that students are at a very high risk of contracting HBV infection during their clinical training owing to the low HBV vaccine uptake rate. Thus, we recommend that all students in the health care professional should be vaccinated before they enter into clinical attachments, provisions of training for students on infection prevention mechanisms, and universal precautions particularly on HBV, increase uptake of the HBV vaccine, and creating awareness on attitudes and practices of students towards HBV to enhance uptake of the vaccine.S1 File(DOCX)Click here for additional data file.S2 File(SAV)Click here for additional data file."} +{"text": "Pet ownership is common in most countries, but few published studies have addressed pet owners\u2019 knowledge of zoonoses, pet contact practices, or awareness of zoonotic disease risks posed by pets. The aim of this study was to assess household knowledge, attitudes, and risks related to pet ownership and zoonoses in northern Portugal. A questionnaire was developed to gather information regarding participants\u2019 demographic characteristics; household pet types and their importance to the family; pet contact-related attitudes; knowledge of zoonoses, high-risk groups, disease transmission pathways, and disease protection measures. It was observed that most participants considered pets an important part of the family. Nevertheless, high-risk practices were recurrent and pet owners\u2019 knowledge was limited. These results reinforce the importance of further studies to better understand the existing gaps in knowledge of pet ownership and zoonoses and strengthens the need to adopt the One Health concept.p = 0.036); 73.1% allowed their pets to live an indoor/outdoor life; 41.3% denied sharing the bed with their pets while 29% assumed they did it daily; 20.3% reported never kissing their pets/pets licking their faces. Furthermore, 73.6% considered animals as potential sources of human diseases, but only 25.9% reported knowing the definition of zoonoses; 96.9% considered the role of veterinarians important in protecting public health. The low level of knowledge of pet owners and the occurrence of high-risk behaviors indicates a need to strengthen communication between veterinarians, physicians, pet owners, and the general public towards reduce the risk of acquisition and transmission of zoonoses.Pet ownership is common in modern society. In Portugal, 38% and 31% of all households own at least one dog or cat, respectively. Few studies have ascertained the knowledge of pet owners on pet ownership and zoonoses, and none have been carried out in Portugal. The aim of the present study was to assess household knowledge and practices related to pet ownership and zoonoses in northern Portugal. A face-to-face questionnaire was completed by 424 pet owners, from November 2019 to February 2020. Most respondents (97.2%) considered pets as an important part of the family, especially women ( Pet ownership is common in modern society, although differences exist on a continent and country basis ,5,6,7,8.Several studies have reported that animal ownership or interaction with animals may contribute to improve overall quality of life including physical, social and psychological health ,11,12,13The number of emerging infections from companion animals is low . HoweverZoonotic agents can infect healthy people, for example through occupational exposure. In fact, occupational zoonoses frequently occur through close contact between animals and humans due to specific settings and professional activities . TherefoIt is unrealistic to eliminate the possibility of acquiring a zoonotic disease but rather the aim should be to reduce the risk. To this end, personal hygiene measures should be applied, such as hand washing, proper animal handling, diet and health care, as well as educational measures and awareness on zoonoses prevention for pet owners, children and immunocompromised people. This, helps them make informed choices and, hopefully, interact safely with animals ,23,28.The One Health concept has become an international standard for expanding interdisciplinary collaboration between professionals in all aspects of human, animal, and environmental health, working at the local, regional, national and global levels . The adoTo date, few studies have assessed basic knowledge of pet-associated zoonoses among pet owners and there are few longitudinal studies detailing this issue ,36,37,38A cross-sectional voluntary study on zoonoses and pet ownership was conducted from November 2019 to February 2020 among a convenience sample of pet owners in northern Portugal . Portugal is a medium-sized country on a European scale and the northern region is its most densely populated area. It represents 35% of the Portuguese population which corresponds to around 3.6 M citizens, 22% of the total area of continental Portugal, and 30% of the municipalities in mainland Portugal . Individ2 test was conducted for each variable in the study looking at gender and ownership differences. The t-test was conducted in order to examine the owners\u2019 gender differences relative to the importance attributed to knowledge and practices regarding pet animals and zoonoses. Statistical significance was based on a p-value < 0.05.Data were entered into an Excel database and exported and analyzed using SPSS version 27.0 . For descriptive purposes, the Pearson \u03c7n = 309), followed by cats , birds , turtles , fish , rabbits , exotic animals , horses , and livestock species . Cats and dogs were owned by 97.6% of respondents (414/424).In the period in which the survey was applied, 424 individuals responded. Dogs were the most frequently reported owned species were female and 25.9% (n = 110) male. In relation to academic background, 49.5% (n = 210) had higher education (attended or completed), 25.5% (n = 108) secondary education (up to the 12th school year), 10.6% (n = 45) the 3rd cycle of basic education (up to the 9th school year), 5.9% (n = 25) the 2nd cycle of basic education (up to the 6th school year), and 8.5% (n = 36) the 1st cycle of basic education (up to the 4th school year). Regarding occupation, 28.5% (n = 121) were students, 39.9% (n = 169) had an essentially physical professional activity, 19.1% (n = 81) an essentially mental activity, and 12.5% (n = 53) no occupation (unemployed or retired). Most respondents lived in urban areas and 41.5% (n = 176) rural areas and 46% adults (>35 years of age). Regarding gender, 74.1% , with most individuals of this opinion being dog owners .Most respondents considered pets as an important part of the family were asked to assign a level of importance that their animals constituted for their family, where 1 was the minimum level and 5 the maximum. Most respondents considered them extremely important or very important . Level 3 of importance was chosen by 20.3% (n = 86) of participants, followed by level 2 and level 1 , which correspond to little importance and very little importance, respectively.Participants (n = 319) of the participants considered that benefits of having a pet outweighed the potential health risks. This opinion prevailed among women and younger respondents , while 16.7% (n = 71) of all respondents had no opinion.In this study, 75.2% (n = 324) considered that having no pets (or reducing the number of pets in the household) would negatively affect their family. In contrast, 8.5% expressed no opinion.Most participants, of the companion animals lived an indoor/outdoor life; 79.7% of participants stated that their animals never ate or licked the dishes, in contrast to 2.1% of the respondents who reported that this occurred daily. In addition, 24.1% of owners admitted washing the pet food containers together with other dishes . Moreover, 20.3% of respondents reported that they never kissed their pets, or their animals never licked their faces. However, the majority admitted doing this, particularly among female owners .n = 231) of owners declared that their pets had contact with other animals. About half of the owners who answered affirmatively considered that these animals could be a risk for the acquisition of diseases.In relation to contact with other animals, 54.5% (n = 184) of participants answered that they would provide food and shelter. Respondents who did not have dogs at home reported having this attitude more frequently as well as female respondents . Only 7.1% (n = 30) would take the animals to the vet to assess their health status for deworming and/or vaccination. Moreover, 37.3% (n = 158) would communicate to the responsible entities or to non-governmental entities . This attitude was statistically associated with having a dog . In this study, 31.3% of the participants would not act, which implies that they would not help the animal or try to resolve the situation. Most of those who would not act were the older respondents .When asked about their attitude towards a dog or cat that they frequently found close to home, 43.4% (n = 362) of the respondents considered that stray dogs should be collected and treated . Most participants who had this opinion were female . Only 1.2% (n = 5) considered that stray dogs should be euthanized because of their potential for disease transmission. For 6.4% of respondents, stray dogs should be left freely on the streets if they were first neutered, vaccinated, and dewormed. The remaining 7% had no opinion.The majority took their pet to the veterinarian while 6.8% (n = 29) did not. Most reported taking their animals to the vet for vaccination or deworming or due to illness , particularly female respondents . More than half did not take their animals to routine consultations . Only 6.8% (n = 29) declared going to the vet for guidance on issues related to estrus, pregnancy, and pet-offspring. In addition, only 13.2% of participants answered taking their pets for bathing and shearing. Four participants (0.9%) reported other motives, such as cutting nails, bee stings, and oral hygiene procedures, such as scaling and trimming rabbits\u2019 teeth.Participants were asked to state in what situations they took their animal to the vet within a list of options. Most owners . Of these, 44.1% (n = 187) dewormed their animals every six months; 26.6% dewormed frequently than every six months; 20.3% (n = 86) annually, and 9.4% (n = 40) declared not doing so.Most participants reported internally deworming their pets of participants reported protecting their animals against external parasites. Of these, 37.5% (n = 159) performed prevention for external parasites every six months; 42.5% (n = 180) applied antiparasitic drugs for external parasites more often than every six months; 13.9% (n = 59) prevented external parasites annually, and 6.1% (n = 26) did not perform preventive measures for external parasites.Regarding external application of antiparasitic drugs, 93.9% (n = 249) were comfortable with their level of knowledge in relation to the potential diseases that may arise from contact with animals, which prevailed among the younger respondents .More than half of respondents followed by respondents who reported having some knowledge , little knowledge , a lot of knowledge and excellent knowledge .Participants were asked to assign their perception of the level of their knowledge on this topic. Most participants reported having no knowledge considered animals as potential sources of human diseases. However, 8.5% (n = 36) answered negatively and 17.9% (n = 76) admitted not knowing. Interestingly, only 25.9% (n = 110) of respondents reported knowing the definition of zoonoses while in contrast, 74.1% (n = 314) acknowledged not being aware of this concept.Most participants , brucellosis , toxoplasmosis , leishmaniosis , scabies , dermatophytosis , tuberculosis , salmonellosis ; leptospirosis , babesiosis , tick fever , dengue , giardiosis , yellow fever , avian chlamydiosis , bovine spongiform encephalopathy , colibacillosis , and malaria . Others included Q fever , taeniosis , West Nile disease , avian influenza , COVID-19 , cryptococcosis , Ebola , ehrlichiosis , heartworm , hydatidosis/echinococcosis , Lyme disease , rickettsiosis and trichinellosis .Examples of zoonoses were requested. The frequencies of the responses were as follows: rabies , this was through academia followed by conversations with veterinarians , media , or family and friends , with only 0.9% (n = 4) through physicians.Participants were asked how they obtained information about zoonoses. For 20.3% (n = 290) were aware of groups of people who are at greater risk of contracting zoonotic diseases, while 22.2% (n = 94) admitted not knowing what to answer, and 9.4% (n = 40) considered that there are no high-risk individuals. The degree of risk assigned is shown in Most participants . Of these participants, 75.9% (n = 208) considered feces as a means of transmitting zoonotic diseases, and this option was more frequently chosen by female owners while 64.2% (n = 176) considered that transmission could occur through insect bites with female owners again more frequently selecting this option .The option \u201cblood\u201d was chosen by 56.7% (n = 155) of the respondents, followed by \u201cphysical contact\u201d while 48.2% (n = 132) considered that transmission could occur through coughing and sneezing with male owners choosing this option more frequently . Additionally, 43.1% (n = 118) recognized the food route as a means of transmitting zoonotic diseases, followed by vomit and 38.3% (n = 132) deemed it possible to transmit zoonotic diseases through fur, brushes and blankets of the animals.Participants were asked if they knew how animals could transmit diseases to humans and the majority responded affirmatively responded affirmatively. Subsequently, the respondents had to assign the level of knowledge they thought they had. The majority admitted not having knowledge followed by having some knowledge , little knowledge , a lot of knowledge and excellent knowledge .Participants were asked if they felt comfortable with their knowledge in relation to preventive measures against zoonotic diseases and 52.1% was assigned to primary hygiene care (41.5%), followed by frequent hand washing (38.9%) and people vaccination (33.3%) .2 = 13.545; p = 0.019) and not feeding raw meat to pets . The results are shown in Subsequently, the participants who considered themselves comfortable with their level of knowledge, had to assign a level of importance for preventive measures directly associated with animals. Female owners attributed a higher level of importance for two preventive measures: treatment of sick animals (\u03c7n = 236) declared being concerned about the possibility of their pets transmitting diseases to themselves or to some family member. Those who answered affirmatively were asked to attribute a level of concern and the majority admitted being concerned , followed by those being just a little concerned , very concerned and extremely concerned .When their animals become ill, 55.7% (n = 17), while 26.4% (n = 112) of the participants answered not knowing, and the majority responded that their animals never had such diseases. Those who answered affirmatively declared their animals suffered from: dermatophytosis (n = 11), scabies (n = 2), babesiosis (n = 1), leishmaniasis (n = 1), leptospirosis (n = 1) and parasitism (n = 1).Owners were questioned whether their pets ever had a disease that could be transmitted to humans. According to the results, few animals contracted zoonotic diseases of pet owners confirmed that they had some diseases transmitted by animals, which were dermatophytosis (n = 6), parasitism (n = 3), brucellosis (n = 1) and scabies (n = 1).In this survey, 2.6% (n = 369) of respondents would like to obtain more information about zoonotic diseases but 7.5% (n = 32) had no opinion.In this study, 87.0% (n = 247) would like to have it through the media , 64.7% (n = 239) through veterinarians, 34.1% (n = 126) through physicians, and 33.3% (n = 123) through flyers.Of the participants who answered affirmatively, 66.9% (n = 411) of the participants considered the role of veterinarians important in protecting public health, although 3.1% (n = 13) had no opinion. No participant responded negatively.In this study, 96.9% (n = 240) attributed the maximum level of importance. For 32.1% (n = 136), the role of veterinarians is very important (level 3), followed by the owners who attributed them some importance and minimum importance . Female owners assigned the highest score values as well as the younger respondents .Those who answered affirmatively were asked to assign a level of importance in which 1 represented minimum importance and 4 maximum importance. More than half . The same scenario was seen in relation to the role of veterinarians in protecting public health . Regarding the mean score, the This study aimed to characterize household knowledge, attitudes and practices related to pet ownership in northern Portugal. Despite the considerable increase in the number of households with pets, the close interaction of animals with household members and the growing recognition of the potential benefits and risks pets posed, few studies have addressed this topic ,43,44,45Animal ownership patterns observed were consistent with the FEDIAF report on Portugal with most respondents having dogs, followed by cats and birds. Most participants considered their animals an important part of the family and believed that benefits of pet ownership outweigh disease risks. Indeed, several studies have reported cardiovascular benefits , especiaIt is crucial to emphasize that few studies have ascertained the level of knowledge of pet owners about zoonoses and their prevention ,34,43,45Pet owners, for the most part, were comfortable with their level of knowledge of zoonotic diseases although 40.8% admitted not having knowledge. To assess zoonotic disease knowledge, respondents were asked about the definition of zoonoses. Interestingly, most respondents did not know the meaning of the word or its definition. However, they considered animals as a potential source of diseases. This finding is in line with that of other studies, which reported a lack of knowledge of pet owners and/or general public ,38,45,68Pet owners who claimed to understand the term \u201czoonoses\u201d were asked for examples. Rabies was the most frequent zoonotic disease reported, in agreement with other world studies ,33,43. PT. gondii. Moreover, the study reported that risk factors for T. gondii infection in women were participating in soil-related activities without gloves, consumption of unwashed raw vegetables or fruit, and consumption of smoked or cured (non-cooked) processed pork products [Statistically significant differences existed regarding the gender of the participants who referred to toxoplasmosis as an example of zoonoses. In fact, only one male mentioned this zoonosis, which may suggest that women are more aware of this disease, perhaps because they are more informed that childbearing women constitute a risk group. However, given the small sample and the type of questionnaire performed, it is not possible to conclude this assumption. Gargat\u00e9 et al. referredproducts .A recent study conducted in Italy which aiMost of the participants who declared knowledge of zoonoses admitted having acquired it through their academic path, contradicting other studies which reported veterinarians as the main source of zoonotic disease information for pet owners ,28,33. HFindings from this study are consistent with those of others regarding the role of physicians in transmitting information about zoonoses. In fact, the limited involvement of physicians in questioning the detention of pets by their patients, advising on protective measures and discussing potential zoonotic diseases has been described ,79,80,81The One Health concept is in vogue. It is essential that the veterinary and human fields join efforts to bridge the communication and information gaps that have been reported over the years . These fYersinia pestis (plague\u2019s agent), Bartonella henselae (cat scratch disease), Methicillin-resistant Staphylococcus aureus [Capnocytophaga canimorsus [Pasteurella multocida [Helicobacter spp. [The growing importance of pets, especially in industrialized countries, has led to increasingly close contact with their owners . Some sts aureus and a fenimorsus and Pastultocida have beeter spp. and periter spp. have beeEscherichia coli and Listeria monocytogenes are increasing [Salmonella serotypes [Salmonella shedding by healthy reptiles and high incidence of human salmonellosis attributed to contact with reptiles have been described, especially among children younger than five years old [Apart from the abovementioned risk factor, more than 70% of respondents admitted that their pets had free access to the interior of the house and could roam indoors. Some participants reported household husbandry practices that increase zoonotic disease risk, such as allowing their pets to eat or lick their dishes, washing pet food containers with other dishes, or allowing their pets to be in contact with potentially disease-carrying animals. Other studies reported these practices, but also high-risk habits, such as feeding their animals with raw meat, eggs, and animal product treats, washing their pets in the kitchen sink, and removing pet feces from the garden/backyard/litter box weekly or less often ,40,91. Icreasing ,99. Pet creasing ,98. It sears old ,103,104.ears old ,70,102.Overall, more than 90% of respondents took their pets to the veterinarian with the most common reasons being for vaccination, antiparasitic preventive treatment or health-issues. A similar scenario was reported in other studies ,105,106.Most participants declared that their pets were annually subjected to two to four preventive treatments for gastrointestinal parasites and external parasites. A study developed in Portugal by Prata showed ePet-human contact is frequent, but for most people, such contact does not translate into a high health risk situation . HoweverYounger children are recognized for their hand-to-mouth behavior. Additionally, children and people with some developmental disabilities are more prone to poor hygiene care or higher risk contact with animals, which makes them particularly exposed to infection ,35,36. TToxocara spp. on dog\u2019s fur is low although it should not be neglected [Toxocara eggs were found in fur but not in feces. These results prove that the presence of eggs in fur is not always due to self-contamination. The significantly higher prevalence in dogs compared to cats may be due to their behavior: dogs tend to have greater soil contact while cats have extreme grooming habits that lead to the removal of possible existing eggs [When questioned about the possibility of disease transmission from animals to humans, more than half (64.6%) of the pet owners in the present study responded affirmatively. However, given a list of possible pathways of transmission, it was found that participants rarely chose all options, which proves some lack of knowledge on the topic. It was encouraging to note that most of the respondents were aware that feces, arthropods, and blood were important means for transmitting zoonotic diseases. Nonetheless, it was worrying to realize that only less than half were conscious of physical contact (scratches and bites), food route and fur as potential transmission pathways. It was previously mentioned how raw meat and close physical contact between owners and pets constitute an animal and public health risk. In relation to fur, both dogs and cats regularly lick the anus and thereafter the fur, increasing the odds of Enterobacteriaceae on their fur or footpads . The preeglected . A surveeglected reporteding eggs .Contrarily to Steele and Mor who repoFurthermore, few (4%) in the present study reported that their animals contracted zoonotic diseases in the past. A similar answer was obtained when asked about themselves (2.6%). These results are similar to a Canadian study in which 4% of households reported getting a disease from their pet and to tRoutine preventive veterinary care and husbandry practices are important to reduce zoonotic diseases ,36. WhenSome studies ,38,45,68The aim of this study was to gather information on pet owners from northern Portugal. The survey was conducted with a convenience sample and estimated proportions may not be representative of all pet owners from this region. The higher response proportion by females most likely relates to their willingness to participate in paper-and-pencil surveys .In retrospect, the present study could have included questions about the existence of high-risk individuals in the households in order to understand whether this condition would interfere with knowledge and willingness to learn more about zoonotic diseases. Additionally, open questions about preventive measures could have been performed to really look at what measures respondents apply on a daily basis and finally, owners could have been asked about specific common zoonoses rather than just being asked for the definition and some examples. In this way, it would be possible to verify in depth the knowledge of the participants about the zoonoses they had referred to.Knowledge and practices may vary by species owned. However, since cats and dogs were owned by most of the pet owners (97.6%) and other species were seldom reported, the potential bias was minimal.This study revealed a lack of knowledge and understanding of zoonoses among northern Portuguese pet owners. Veterinarians and physicians must be proactive in their public health responsibilities, implementing the One Health concept and strengthening communication between both professions as well as with their clients/patients. Different methods should be used to draw people\u2019s attention to the topic of zoonoses and their prevention. Addressing the subject during consultations is essential, but not completely effective. Free online educational programs, audiovisual presentations, and flyers can promote better educational mediums for people of different ages, academic backgrounds, and willingness to listen and assimilate the information provided. These educational vectors must contain information about the most common zoonoses, transmission pathways, risk behaviors, preventive measures and high-risk groups . Medical and veterinary school students should be exposed to the One Health concept from the beginning of their career, improve their knowledge on current zoonotic disease risks, foster their team spirit, collaboration and interprofessional dialogue. From the scientific point of view, more questionnaires, pilot studies and cross-sectional studies should be developed to frequently update eventual progress. All the above-mentioned measures are efforts that must be taken to disseminate knowledge and, consequently, reduce pet-associated disease risks to the public."} +{"text": "We investigated the prevalence of SBP, positive ascitic fluid cultures, and risk factors for mortality. (2) Methods: A retrospective analysis of all patients with cirrhosis hospitalized or in follow-up in a single center between 1996 and 2020. The clinical data, long-term complications, and mortality of SBP patients were compared with those of non-SBP patients. Ascitic fluid positive culture was compared with those without growth. (3) Results: We included 1035 cirrhotic patients, of which 173 (16.7%) developed SBP. Ascitic fluid culture growth was found in 47.4% of the SBP cases, with Escherichia coli bacteria detected in 38%, 24.4% grew ESBL-producing bacteria, and 14.5% displayed multidrug resistance. In a Cox regression model, SBP, male sex, prolonged INR at diagnosis, and hepatocellular carcinoma were found to be risk factors for mortality in cirrhotic patients. The long-term all-cause mortality was 60% in non-SBP and 90% in SBP patients. (4) Conclusions: Only a minority of cirrhotic patients developed SBP, 47.4% of which had positive ascitic fluid cultures with high antibiotic resistance. Growth of ESBL and multidrug resistant organisms is becoming more frequent in the clinical setting, reaching SBP mortality of 90%. Infection is one of the most important causes of acute decompensation and death in liver cirrhosis (LC) . It is wA number of general risk factors and specific risk factors for resistant infections have been identified in cirrhosis patients ,3. ThereAscitic fluid infections can be difficult for infectious disease specialists and clinicians to characterize and treat. There are several known risk factors for SBP, including upper gastrointestinal bleeding, low ascitic protein concentration (<1.5 g/dL), and a history of prior episodes, however, ascitic fluid cultures are frequently negative in patients with suspected SBP .In this study, we aimed to investigate the prevalence of SBP, clinical characteristics, long-term outcomes, and risk factors for ascitic fluid culture growth, and the evolution of antimicrobial resistance profiles throughout the last 24 years. For this retrospective study, demographic and clinical data were retrieved from computerized databases of internal medicine departments and the clinic of gastroenterology and hepatology at Soroka University Medical Center (SUMC) between the years 1996 and 2020. Data included etiologies of cirrhosis, laboratory values, complications, and death. The Child-Pugh score for severity of cirrhosis in each patient was calculated retrospectively for time of diagnosis, and again at the time of data collection or time of death if the patient already expired at the time of data collection. Patients were diagnosed as suffering from cirrhosis based on liver biopsy, fibroscan, fibrotest, or the presence of typical clinical findings of cirrhosis, such as ascites or esophageal varices.3 in the aspirated ascites fluid. Microbiological data was collected and included resistance patterns to antibiotics according to the CLSI classification , multidrug-resistant bacteria were defined as non-susceptible to at least one antimicrobial agent in three or more drug classes, and extended spectrum beta lactamase (ESBL) was defined as resistant to 3rd generation cephalosporins [SBP was defined by the presence of a polymorphonuclear (PMN) cell count over 250/mmosporins . We exclt test for continuous variables. Continuous variables that were not normally distributed were compared in the Kruskal Wallis test. p-values less than 0.05 were considered statistically significant, and variables found to be significantly associated with mortality were gradually added to a COX regression model, where hazard ratio (HR) was calculated for each. Statistical analysis was performed using \u2018R statistics\u2019 with the packages \u2018lubridate\u2019, \u2018dyplr\u2019, \u2018survival\u2019, and \u2018ggplot2\u2019. The study was carried out in accordance with the principles of the Helsinki Declaration, approval and a waiver of informed consent was granted by the Institutional Review Board (0285-18-SOR). We described patient characteristics as mean \u00b1 SD for continuous variables and as percentages for categorical variables. To compare groups, we used the chi-squared test for categorical variables and Student\u2019s 82 (47.4%) had positive ascitic fluid cultures. The demographic and clinical characteristics of our study populations are summarized in Our cohort of cirrhotic patients included 1035 patients, of which 173 (16.7%) were diagnosed with SBP according to neutrophil count in ascitic fluid. Of those, only p < 0.001), respectively. No significant differences were found regarding gender, age, age at diagnosis, ethnicity, or cause of cirrhosis, between the two groups. However, esophageal varices and esophageal variceal bleeding were more common among SBP patients compared with non-SBP patients; 71% vs. 53% and 41% vs. 26% (p < 0.001). Significantly higher all-cause mortality was found among SBP patients compared with non-SBP patients; 91% vs. 60% (p < 0.001). Lower hemoglobin, platelets, albumin, and higher bilirubin and INR were found among the SBP group (p = 0.018), younger age at diagnosis , and esophageal varices bleeding . No significant differences between groups were found regarding etiology of cirrhosis, HCC, or death. Laboratory values are summarized in The data of patients with positive ascitic fluid cultures compared with those who did not grow any bacteria in cultures is presented in E. coli, found in 31 (37.8%) patients, followed by coagulase-negative staphylococci in 13 (16%) patients. Other bacteria were less common of cirrhotic patients develop SBP. Second, ascitic fluid culture growth was found in only 47.4% of patients with SBP. Third, as in previous studies, In our cohort of 1035 cirrhotic patients, only 173 (16.7%) were diagnosed with SBP, and 81 (47%) had acute renal failure as an acute complication of the SBP. There were 82 (47.4%) SBP patients that had positive ascitic cultures and 91 (52.6%) had culture-negative neutrocytic ascites. In a prospective multinational study including 46 centers (1302 patients), the prevalence of SBP was 27% among hospitalized cirrhotic patients, and 39% had positive cultures .In the present study, we investigated several risk factors which could affect the frequency of bacterial growth in the ascitic fluid, including hospitalization, ICU admission, and antibiotic therapy or surgery within six months prior to the SBP episode; all these were not found to be risk factors for bacterial growth. However, the relatively small size of our cohort of 82 patients with bacterial growth makes it difficult to draw conclusions regarding these risk factors. E. coli, in particular), our study showed growth of E. coli in about 38% of positive ascitic fluid cultures, 52% (16 of 31) being ESBL-positive and 42% (13 of 31) displaying quinolone resistance. ESBL resistance is of particular interest, since third generation cephalosporins are recommended as first-line empirical treatment for SBP, per international guidelines [Consistent with other studies ,14, wheridelines ,16. In tidelines . In contidelines . In our idelines ,14, awarWith respect to mortality, individuals with advanced and decompensated liver cirrhosis with SBP are an extremely vulnerable population. Upon long-term follow-up, we found that mortality of cirrhotic patients with SBP was significantly higher (90%) in comparison to non-SBP patients (60%). Previous studies investigating short-term mortality of cirrhotic patients (with follow-up of one to six months) have reported mortality ranging between 24\u201349% . The expSBP is the most common bacterial infection and one of the feared complications in patients with ascites, which is associated with increased mortality . In our The strengths of our study are the large size of our cohort of cirrhotic patients in a single center and the long-term follow-up of complications and mortality. However, this study also has several limitations, including its retrospective design, lack of data regarding SBP treatment in the course of hospitalization, and that the data included all-cause mortality and not liver-related mortality. A minority of cirrhotic patients in our cohort developed SBP, of which only 47% had positive ascitic fluid cultures with relatively high antimicrobial resistance. Policy for empirical treatment of SBP should be addressed and reevaluated regularly on a local level, especially when a high rate of ESBL producing pathogens is observed. SBP, male sex, prolonged INR at diagnosis, and HCC are all significant risk factors for mortality in cirrhotic patients, with mortality up to 90% among SBP patients, compared with 60% among non-SBP patients."} +{"text": "The percentage of individuals who reported consuming fast-food meals \u22653 times/week decreased from 37.7% before the pandemic to 33.3% during the pandemic. The percentage of heavy drinkers (\u22655 times/week) increased from 20.9% before the pandemic to 25.7% during the pandemic. Among smokers, heavy smoking (\u226511 cigarettes/day) increased from 5.8% before the pandemic to 7.9% during the pandemic. We also identified subgroups who were more vulnerable to adverse influences from the pandemic, including racial/ethnic minority groups and young adults. Conclusions: The COVID-19 pandemic had negative impacts on multiple lifestyle behaviors among Americans. Mitigating such negative impacts of COVID-19 requires effective interventions, particularly for some vulnerable subgroups.Objective: To investigate the impact of the COVID-19 pandemic on multiple lifestyle changes among adults in the United States (USA). Methods: We conducted a survey, the Health, Ethnicity, and Pandemic (HEAP) Study, in October 2020 among USA adults. Participants were selected from the United States using 48 sampling strata, including age, race, ethnicity, education, and gender, and were asked to report five lifestyle behaviors before and during the COVID-19 pandemic. The associations of sociodemographic factors with each lifestyle change were estimated using weighted multivariable logistic regression models. Results: All 2709 HEAP participants were included in this study. Compared to pre-pandemic, the time spent on exercise decreased (32.06 vs. 38.65 min/day; The novel coronavirus disease COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a worldwide pandemic since March 2020. SARS-CoV-2 is a single-stranded RNA virus and the third coronavirus 2012)) that has caused severe diseases in human in the past two decades 9, induce.In the 2003 Severe Acute Respiratory Syndrome (SARS) pandemic, several studies documented changes of health behaviors in people living in the most infected areas, such as China ,6. DurinSince the beginning of the COVID-19 pandemic, several studies from different countries have observed undesired lifestyle changes among their populations, such as less exercise, more sedentary behavior, unhealthy dietary patterns, and increased alcohol consumption and cigarette smoking in Canada , Italy ,9, BraziThe objective of our study was to investigate the impact of COVID-19 on multiple lifestyle behaviors in USA adults and to identify sub-groups who were more adversely impacted by the COVID-19 pandemic, using a nationally representative, population-based sample.This analysis was conducted using the data from the Health, Ethnicity, and Pandemic (HEAP) Study. HEAP is survey designed by a consortium of investigators from several universities in the USA, led by the Center for Reducing Health Disparities at the University of Nebraska Medical Center. The HEAP survey was carried out by the National Opinion Research Center (NORC) at the University of Chicago with the sample randomly drawn from NORC\u2019s AmeriSpeak Panel and Dynata panel. AmeriSpeak is a probability-based mixed-mode panel designed to be representative of the USA non-institutionalized population using a multi-stage address-based sample design. Participants were selected using 48 sampling strata, including age, race, education, and gender following the American Association for Public Opinion Research guidelines. Detailed information regarding the panel recruitment and selection methodology can be found in the previous publication . Figure The HEAP is a cross-sectional study in design and the survey included questions related to mental health, lifestyle changes, racial discrimination, financial status, and healthcare utilization. Lifestyle changes were assessed using five questions asking participants to report the following behaviors before and during the pandemic: (1) number of minutes spent on exercise per day; (2) the number of fast-food meals consumed per week; (3) the number of hours spent on screen time per day; (4) the number of cigarettes smoked per day; and (5) the number of alcoholic drinks consumed per week . The survey also collected sociodemographic variables such as age, sex, race/ethnicity, educational attainment, marital status, annual household income, and health insurance coverage.All statistical analyses were performed with poststratification weighting to account for the complex survey design and sampling procedures. Each lifestyle behavior, before or during the pandemic, was reported as weighted mean for continuous variables or weighted percentage for categorical variables. Differences in these behaviors during the pandemic were compared to behaviors before the pandemic using the Wilcoxon Signed Rank Test for continuous variables and Bhapkar\u2019s Test for categorical variables. The prevalence of missing data ranged from 3.1 to 3.8% (including the response categories \u201cDon\u2019t know\u201d and \u201cPrefer not to answer\u201d) for measures of lifestyle/behaviors. Changes in lifestyle behaviors were calculated (during pandemic\u2013before pandemic) and categorized as \u201cdesired change\u201d or \u201cundesired change\u201d for each behavior. The \u201cundesired change\u201d category refers to decreased exercise, increased screen time, increased numbers of fast-food meals, increased cigarettes smoking, or increased alcohol drinking during the pandemic as compared with before the pandemic, respectively, for each behavior. Associations of sociodemographic factors with changes in lifestyle behaviors were estimated using logistic regression models. Sociodemographic factors included as independent variables in the logistic regression models were age , sex , race/ethnicity , or Alaska Natives or Others vs. Non-Hispanic Whites), educational attainment , marital status (widowed/divorced/separated or never married vs. married/living with a partner), annual household income , and health insurance before the pandemic . All statistical analyses were performed with SAS statistical software .All 2709 HEAP participants were included in this study. Among them, 20.5% were aged between 18\u201329 years, 25.5% between 30\u201344 years, 24.2% between 45\u201359 years, and 29.8% \u2265 60 years. The study population reflected the USA racial/ethnic composition, and the majority were Non-Hispanic Whites (61.3%), followed by Hispanics (16.7%), Non-Hispanic Blacks (11.9%), and Asian and Pacific Islanders (6.4%). Of all participants, 51.7% were female, 34.3% had a bachelor\u2019s degree or higher, 58.2% were married or living with a partner, 58.6% had an annual household income \u2265$50,000, and 52.7% had private health insurance .p < 0.001), and screen time increased during the pandemic. Before the pandemic, 15.3% of individuals reported zero exercise time, and this proportion increased to 20.9% during the pandemic. The proportion of individuals who exercised \u226530 min per day also decreased from 56.4% before the pandemic to 45.4% during the pandemic. Individuals with screen time \u22654 h per day also increased from 59.5% pre-pandemic to 79.8% during the pandemic. For fast-food meals, the average consumption level was 1.41 times/week before the pandemic and decreased to 0.96 time/week during the pandemic. The percentage of zero consumption increased from 15.0% before the pandemic to 25.0% during the pandemic, and the percentage of consuming three or more fast-food meals per week decreased from 37.7% before the pandemic to 33.3% during the pandemic. The average alcohol drinking level among drinkers increased from 3.01 drinks/week before the pandemic to 4.24 drinks/week during the pandemic (p < 0.001). Non-alcoholic beverage drinking was unchanged during the pandemic (50.6% vs. 49.8%), but the percentage of heavy drinkers (\u22655 drinks/week) increased from 20.9% before the pandemic to 25.7% during the pandemic. The average cigarette smoking level among smokers increased slightly from 9.29 times/week before the pandemic to 9.80 times/week during the pandemic (p < 0.001). The percentage of non-smokers was similar before and during the pandemic (82.9 vs. 82.4%). Quitting behavior was not statistically significant before and during the pandemic (only 0.2% of smokers became non-smokers). However, among smokers, heavy smoking (\u226511 cigarettes/day) increased from 5.8% pre-pandemic to 7.9% during the pandemic. The relationship between sociodemographic factors and undesired changes in the five lifestyle behaviors are presented in In this large study among USA adults with multiple racial/ethnic groups, we found that the COVID-19 pandemic resulted in undesired changes in multiple health-related lifestyle behaviors. On average, USA adults decreased their time spent on exercises, but increased their screen time during the COVID-19 pandemic compared to before. The percentage of heavy alcohol drinkers and cigarette smokers also increased during the pandemic. Our findings corroborate results from several recent studies conducted in other countries. We also identified subgroups who were more vulnerable to unfavorable lifestyle changes during the pandemic. The most critical findings are for age and racial groups. Compared to Non-Hispanic Whites, Non-Hispanic Blacks and Hispanics were more likely to have undesired changes in multiple lifestyle behaviors, including exercise, screen time, fast food intake, and alcohol drinking; American Indians and those in the \u201cother\u201d racial category were more likely to decrease their exercise time and increase consumption of fast-food meals; while Asian Americans were less likely to increase alcohol drinking and cigarette smoking. The clustering of negative lifestyle changes among racial and ethnic minority groups, as revealed in this study, is consistent with findings from previous studies documenting the disproportionate exposure to and suffering from the COVID-19 pandemic by these groups ,18,19,20It is no surprise that the pandemic resulted in a decline in exercise time and a rise in screen time. Indeed, 20.9% of individuals did not do any exercise during the pandemic (vs. 15.3% before) and 79.8% of individuals had screen time \u22654 h per day (vs. 59.5% before). The proportion of individuals who exercised \u226530 min per day also decreased to 45.4% during the pandemic (vs. 56.4% before). On average, the daily time spent on exercise decreased from 38.65 min in pre-pandemic to 32.06 min during the pandemic and screen time increased from 5.06 to 6.79 h. These findings are consistent with studies from other countries and populations . For exaWe found that the COVID-19 pandemic had a negative impact on alcohol drinking and cigarette smoking among USA adults, which is in line with findings from studies conducted in the USA ,15 and oThe observed decrease in fast food consumption is likely due to the stay-at-home order and the closure of fast-food restaurants during the pandemic. The average level of fast-meal consumption decreased from 1.41 times/week before the pandemic to 0.96 times/week during the pandemic. The percentage of individuals who reported consuming fast-food meals \u22653 times/week also decreased from 37.7% before the pandemic to 33.3% during the pandemic. Although the majority of study participants (77.4%) decreased or did not see a change in their fast-food meal consumption, there were still 22.6% that increased their fast-food meal consumption during the pandemic. In previous studies assessing different perspectives on eating, people reported more unhealthy dietary behaviors during the pandemic, including increased consumption of unhealthy foods , snacks, and the overall number of main meals ,11,12. NThe strengths of this study include a large, nationally representative sample, which is based on a population of USA adults with adequate numbers from each racial/ethnic group, and the timing of the data collection. Our study sample included over 1000 Asian Americans, who are commonly underrepresented or excluded in other studies. The study survey was designed and carried out in fall 2020 at the peak of the USA COVID-19 pandemic; thus, the survey responses are timely and likely to reflect the acute impacts of the pandemic. This study has several noteworthy limitations. First, the survey data were only collected at the one-time point during the pandemic. Therefore, the changes in lifestyle behaviors may only reflect the peak of the pandemic. Second, we were only able to collect limited information for each lifestyle behavior due to the concerns regarding participant time and burden. For dietary intake, we only focused on the consumption of fast-food meals.In this large study conducted during the peak of the COVID-19 pandemic in the USA, we found that regulations to restrict non-essential activities and the stay-at-home order during the pandemic had profound impacts on multiple lifestyle behaviors in American adults. We found a marked increase in sedentary behaviors, alcohol consumption, and cigarette smoking and a decline in exercise. These negative changes in lifestyle disproportionately impact racial and ethnic minorities who also bear a higher disease burden of COVID-19. Our findings corroborate results from several recent studies conducted in other countries. Collectively, the observed undesired lifestyle changes may have a negative impact on both physical and mental health outcomes. Future studies investigating whether such lifestyle changes persist as the pandemic continues and whether the quality of life and health well-being are subsequently affected, are warranted. Resources and supports that can help people maintaining healthy lifestyles during the pandemic are urgently needed, and different strategies may be needed for different sub-groups."} +{"text": "Systemic Sclerosis (SSc) is a chronic disease associated with a 1.5-fold increase in cancer risk, including lung cancer, hematological malignancies, and breast cancer (BC). This is a retrospective study aiming to explore the clinical and pathological features of BC developed by SSc patients. A total of 54.5% of patients developed BC before SSc , whereas 45.5% of patients developed BC after SSc (median delay: 8 years). A total of 93.1% of patients were diagnosed with an early stage tumor. Among invasive carcinomas, 70.8% presented with a low Mib1, 8.3% with a tubular histotype, and 42.8% with a Luminal A-like phenotype. A total of 66.6% of patients underwent breast-conserving surgery and 55.5% RT. A total of 40% of patients developed interstitial lung disease after RT and 20% diffuse cutaneous SSc. The cause of death of the six deceased patients was PAH. A significant association was observed between the use of immunosuppressive therapy and diffuse skin extension, negative ACA, positive Anti-Scl-70, and interstitial lung disease, but not BC status. SSc patients developed BC at a good prognosis, suggesting a de-escalation strategy of cancer therapies. In particular, ionizing radiation and chemotherapeuticals should be limited to higher-risk cases. Finally, proper screening is mandatory in order to allow for early cancer detection in SSc patients. Systemic Sclerosis (SSc) is a chronic disease characterized by vascular dysfunction, specific autoimmune alterations, and fibrosis of the skin and internal organs, such as lungs and heart. However, gastrointestinal and kidney involvement is also well known ,2. PreviThe relationship between BC and SSc has long been debated. Previous research has been contradictory and inconclusive on this matter, and breast is one of the organs not directly involved by the tissue alterations that characterize SSc. Overall, several authors described the association between SSc and BC ,14,15,16To our knowledge, nevertheless, no study has evaluated the clinical and pathological features of BC developed by SSc patients and their correlations with SSc features. The aim of our project was to analyze clinical and pathological features of BC in 33 SSc patients attending two Rheumatology/SSc Units in the north of Italy.This is an observational retrospective multicenter study performed at Modena University Hospital and Reggio Emilia Hospital in northern Italy. We enrolled women affected by both SSc and BC in their lifespan, regardless of which disease was developed first. Women affected by SSc with a personal history of BC were identified at two Rheumatology/SSc Units in the north of Italy between January 2017 and December 2019. Clinical and pathological characteristics of BC were evaluated in terms of particular age at diagnosis, menopausal status, histotype, estrogen receptor status (ER), progesterone receptor status (PR), Mib1 and HER2 expression, clinical and pathological stage at diagnosis, metastatic sites, type of loco-regional treatment (surgery and radiotherapy), type of systemic treatment (neoadjuvant/adjuvant chemotherapy and endocrine treatment), other cancers, and time from the diagnosis of the first disorder to the second one. Moreover, clinical\u2013rheumatological features related to SSc were collected: age at disease onset; smoking habits (with packs/year); skin extension of the disease (limited/diffuse); presence of skin ulcers, calcinosis, and telangiectasia; presence of gastro-intestinal and kidney involvement; interstitial lung disease (at HR-CT); forced vital capacity (FVC) evaluation at pulmonary function tests and diffusing capacity of the lungs for carbon monoxide through the single-breath technique (DLCO SB); ECG abnormalities; echocardiographic assessment of pulmonary arterial hypertension (PAH) with measurement of pulmonary artery systolic pressure (PAPs); SSc pattern at videocapillaroscopy; autoantibody profile; exposure to immunosuppressive and vasoactive therapies; status at last follow-up evaluation; and cause of death. Oncological and rheumatological characteristics were then compared with data available in the literature for each disease.ER, PR, and HER2 expression were determined according to the national pathology guidelines, which closely adhere to international standards. ER and PR were defined as positive with immunohistochemical staining of at least 1% of nuclei. Triple negativity was defined as immunohistochemical staining of less than 1% of nuclei for both ER and PR, and an immunohistochemical result (DAKO score) of 0 or 1+ for HER2/neu.p < 0.05 was considered statistically significant. Statistical analysis was performed using SPSS . Fisher\u2019s exact test was applied. Approval for this study was obtained from the local \u2018Area Vasta Emilia Nord (AVEN)\u2019 Ethics Committee and written informed consent was obtained from all subjects included in the study.Between January 2017 and December 2019, 33 patients affected by SSc with a personal history of BC were identified. Clinical\u2013pathological characteristics of the overall population are listed in p = 0.015), negative ACA status (p = 0.036), positive Scl70 status (p = 0.017), and presence of interstitial lung disease at HR-CT (p = 0.036) was observed. Vasoactive agents were used to treat 25 patients (75.7%); in particular, iloprost in 18 patients, calcium channel blockers (CCBs) in 12 patients, bosentan in 3 patients, and sildenafil in 2 patients.The rheumatological characteristics of the overall SSc population are listed in At the end of December 2019, 22 patients (66.7%) were recorded as still alive, with 5 patients (15.1%) lost at follow up. In all six deceased patients, the cause of death was PAH (in one case with concomitant lung cancer).p = 0.030). No other statistically significant associations were observed between BC pathological stage, Mib1 level or ER expression, and skin extension of the disease, the presence of skin ulcers, calcinosis, teleangectasia, gastro-intestinal and kidney involvement, interstitial lung disease (at HR-CT), FVC and DLCO SB values, echocardiographic assessment of PAH with PAPs measurement, ECG abnormalities, SSc pattern at videocapillaroscopy, and autoantibody profile .Several authors have described the association between SSc and BC ,14,15,16Overall, 54.5% of these patients developed BC before SSc with a median time between the two diagnoses of 5 years, whereas 45.5% of patients developed BC after their SSc diagnosis with a median delay of 8 years. Our findings diverge from the previous studies that showed a close temporal relationship between SSc and BC onset. In particular, in a retrospective cohort of 65 SSc patients affected by BC, Scope et al. reported that 75% of scleroderma and BC cases were diagnosed within 3 years of each other and in 44% of cases, scleroderma appeared before or simultaneously with the BC diagnosis . MoreoveIn line with data from the general population, 75% of invasive tumors were hormone receptor positive, 28.6% were HER2 positive, and 19% were triple-negative. Nevertheless, it is worth noting that 93.1% of BC patients were diagnosed with a clinical stage I or II tumor. Among invasive carcinomas, 70.8% presented with a low Mib1 proliferative rate, and 8.3% with a special histotype at a very good prognosis (tubular), while 42.8% presented with a Luminal A-like phenotype. According to such good prognostic features, only 10.3% of patients underwent neoadjuvant chemotherapy, 37.9% adjuvant chemotherapy, 66.6% breast-conserving surgery, and 55.5% underwent RT after surgery. Interestingly, 40% of SSc patients that underwent RT developed interstitial lung disease and 20% diffuse cutaneous forms of SSc.As is well known, pulmonary involvement is one of the most important features of SSc and often the leading cause of exitus. Interstitial lung disease and pulmonary hypertension together account for 60% of SSc-related deaths ,33. AddiIn 2007, Derk et al. found that SSc patients affected by BC presented with pulmonary fibrosis more frequently than other patients without malignancy . In 2012In a recent cohort analysis on cardio-pulmonary involvement in SSc , we intePossibly due to the small sample size, besides positive ER status and normal SSc pattern at videocapillaroscopy, no statistically significant associations were observed between any oncological characteristic and rheumatological features such as skin extension of the disease, presence of skin ulcers, calcinosis, teleangectasia, and gastro-intestinal and kidney involvement. Similarly, interstitial lung disease at HR-CT, pulmonary function test values, echo assessment of PAH, ECG abnormalities, SSc videocapillaroscopic pattern, and autoantibody status revealed no significant correlations with the BC characteristics mentioned above.Overall, confirming previous research in systemic rheumatic diseases , the SScOn these grounds, proper screening of SSc patients is mandatory in order to allow for early detection of tumor development. Further investigations on larger numbers of patients are needed, yielding substantial benefits at various levels. First of all, they would further clarify the intriguing relationship between BC and SSc. Secondly, they would help us explore the common biological and molecular pathways at the basis of SSc and BC development, with the aim of improving BC diagnosis and prognostication and personalizing oncological targeted treatments in this specific subset of multimorbid patients."} +{"text": "During the COVID-19 pandemic, we realized the importance of limiting in-clinic interactions with patients who were stable on antiretroviral therapy to promote social distancing. Our HIV clinic adopted telemedicine practices, in line with the HHS Interim Guidance for COVID-19 and Persons With HIV. Several HIV clinics reported lower viral suppression rates during the pandemic. We aim to describe the implementation process as well as year one outcomes of telemedicine at our clinic.In March 2020, we created telemedicine protocols; we also designed and continuously updated algorithms for determining patient eligibility for telemedicine based on recent viral loads and last clinic visit. We monitored outcomes through electronic medical record chart reviews between May 1, 2020, and April 30, 2021. We collected patient demographics, and federal poverty level (FPL) information. We collected baseline and post-intervention rates of viral load suppression , medical visit frequency and lost to care .We conducted a total of 2298 ambulatory medical visits; 1642 were in person and 656 (29%) were telemedicine visits. Out of those, 2177 were follow up visits . There was no difference of telemedicine utilization based on race (28% in African Americans vs. 32% in Whites); ethnicity (30% in Hispanic vs. 30% in Hon-Hispanic); gender ; or FPL (28% in FPL < 200% vs. 31% in FPL >200%). By the end of April 2021, overall clinic VLS rate was 94%, MVF was 48%, and there were 40 patients LOC compared to 92%, 49%, and 43 patients in April 2020, respectively.Telemedicine was a safe alternative to routine in-person HIV care during the COVID-19 pandemic. We observed similar rates of utilization across demographic and FPL status. Applying selection criteria, viral suppression and retention in care rates were not adversely impacted by shift to telemedicine modality. All Authors: No reported disclosures"} +{"text": "We aimed to compare the effects of using high-fat (HF) and advanced glycation end-products (AGEs)containing diets to induce obesity and diabetes on sperm function in mice.In this experimental study, twenty-five 4-week old C57BL/6 mice were divided into 5groups and were fed with control, 45% HF, 60% HF, 45% AGEs-HF, or 60% AGEs-HF diet. After 28 weeks, fastblood sugar, glucose intolerance, insulin concentration, homeostatic model assessments (HOMA) for insulin resistance (IR) and HOMA for beta cells (HOMA beta) from systematic blood were assessed. In addition, body weight,morphometric characteristics of testes, sperm parameters, DNA damage (AO), protamine deficiency (CMAA3), andsperm membrane (DCFH-DA) and intracellular (BODIPY) lipid peroxidation were measured.Body mass and fasting blood sugar increased significantly in all experimental groups compared to the controlgroup. Insulin concentration, glucose intolerance, HOMA IR, and HOMA beta were also increased significantly withhigher levels of fat and AGEs in all four diets (P<0.05). The changes in the 60% HF-AGEs group, however, were moresignificant (P<0.001). Morphometric characteristics of the testis, sperm concentration, and sperm morphology in thediet groups did not significantly differ from the control group, while sperm motility and DNA damage in the 45%HFwere significantly low. Although for protamine deficiency, both 60% HF-AGEs and 45% HF showed a significantincrease compared to the control, the mean of sperm lipid in the 45% HF group and intracellular peroxidation in the60% HF-AGEs group had the highest and the lowest increases, respectively.Our results, interestingly, showed that is the negative effects of a diet containing AGEs on examined parameters are less than those in HF diets. One possible reason is detoxification through the activation of the protectiveglyoxalase pathway as the result of the chronic AGEs increase in the body. Twentyfive 4-weeks old healthy non-obese and non-diabeticC57BL/6 male mice were selected from Institute forBiotechnology and housed under controlled conditions; temperature of 21 \u00b0C (\u00b1 2%), 65%humidity (\u00b1 5%), 12\u2010hours light/12\u2010hours dark cycles,and an ad libitum access to food and water. After oneweek of acclimatization in special cages, mice wererandomly divided into five groups . Preparing the formulation of the diets was based on previousstudies . Four tyFasting blood sugar was measured from the tail veinby animal glucometer after 6 hours of fasting, following28 weeks of keeping the mice on the special diets. Tolerance test was also performed after 28 weeks of keeping the mice on the special diets. After 6 hours of fasting,D-glucose was injected intraperitoneally , 13 and The mice were euthanized under combined administration of xylazine (10 mg/kg body mass per mouse) andketamine (80 mg/kg body mass per mouse). For assessing the insulin concentration, heart blood was collectedimmediately after scarification. Following centrifugation of the collected blood at 4500 rpm for 5 minutesat 4\u00b0C, the insulin level in the serum (ng/dL) was quantified using Ultra-Sensitive Mouse Insulin ELISA kit according to the manufacturer\u2019sinstructions.HOMA IR, a surrogate marker of IR was assessed usingfasting glucose and insulin concentration according to thefollowing formula :equationHOMA-beta assesses the function of \u03b2-cells using insulin concentration according to the following formula:equationFollowing the sacrifice of mice, weight and morphometric measurements of the testes were performed. The cauda segment was separated from the leftepididymis and cut into pieces and incubated in 2 mlof sperm washing media+10% serum at 37\u00b0C for 30minutes to retrieve spermatozoa. After analyzing thesperm parameters, the spermatozoa were washed withphosphate-buffered saline forfurther evaluation.Sperm concentration (million/ml) and sperm motility (% motile) were measured using a sperm counting chamber undera light microscope. The collected sperm was stained bythe Eosin-Nigrosin method as described previously formorphological evaluations . AbnormaHistone replacement by protamine occurs during the latestages of spermatogenesis. We evaluated the protaminedeficiency using the chromomycin A3 (CMA3) stainingmethod as described previously . For thiThe DNA damage was evaluated by acridine orange(AO) staining, as described previously . For thi6 spermatozoa and incubated at 37\u00b0C for30 minutes and the percentage of lipid peroxidation was assessed using the FACSCaliburflow cytometer . A positive control for each sample was obtained byadding H2 O2 to sperm suspensions.Sperm membrane lipid peroxidation was assessed using the BODIPY probe as describedpreviously . Briefly2O2 to sperm suspensions.DCFH-DA staining was used to detect cytosolic ROS and peroxidation as describedpreviously . BrieflyAll data in the present study were analyzed by the Statistical Package for the Social Sciences for Windows, version 25 . All the parameters had a normal distribution, and a one\u2010way analysisof variance (ANOVA) was used to compare the sperm parameters, lipid peroxidation, and chromatin status. Datawere presented as mean \u00b1 standard error of the mean, andP<0.05 was considered significant.The initial and final mean body mass of the mice in thefive studied groups is presented in Table 2. All the groupsgained weight significantly compared to the control groupafter 28 weeks of being fed with the special diets. In addition, we assessed morphometric characteristics of testesand found that none of them showed any significant differences in the mean values compared to their corresponding control group. On the other hand, unlike the 45% HFgroup , the mean weight of theleft testis in the 60% HF , 45%HF-AGEs , and 60% HF-AGEs groups significantly increasedin comparison to the control group (0.084 \u00b1 0.004). Additionally, the mean weight of the left testis in the 60% HF-AGEs group increased compared to the 45% HF group(P<0.05).Glucose tolerance was dropped along with the increasein fat and AGEs content in the diet of the different studied group, so that the 60% HF-AGEs was the most intolerant group to glucose compared to the control group(P<0.001). The results of fasting blood sugar showed asignificantly increased level of this parameter in all fourgroups with a special diet in comparison to the control(P<0.05).As shown in Table 3, the results of insulin concentration, HOMA-IR, and HOMA-beta were significantlyhigher in all groups with a special diet compared to thecontrol group . Fastingblood sugar insulin concentration and IR were higher in60% HF-AGE compared to the other groups. Therefore,we considered 60% HF-AGE and 60% HF groups as type2 diabetes, and pre-diabetes groups, respectively.6 /ml), the mean percentage of sperms with totalabnormal morphology as well as abnormal head and tail were not significantly affected byHF and HF-AGEs diets for 28 weeks. However, the mean motility of the sperms in the 45% HFgroup decreased compared to the control (P<0.05), whilst the mean motility of thesperms in the 45% HF-AGEs (P=0.004) and 60% HF-AGEs (P<0.05) groups increasedcompared to the 45% HF group.Conventional sperm parameters are demonstrated as bar charts in Figure 1. The meansperm concentration , 60% HF (P=0.02), 60% HF-AGEs (P=0.004),and 45% HF-AGEs (P=0.08) groups.The results of protamine deficiency in different groupsare depicted in Figure 2B. The mean of this parameter wassignificantly higher in the 45% HF (P=0.05) and 60% HF-AGEs (P=0.006) groups compared to the control group.According to Figure 2C, the mean percentage of lipidperoxidation of the sperm membrane in all the different diet groups experienced an increase in comparisonto the control counterpart and the differences of 45%HF (P<0.001), 60% HF (P=0.02), and 45% HF-AGEs(P=0.004) groups was significant. In addition, the mean ofthis parameter was lower in the 60% HF-AGEs (P=0.07)group in comparison to the 45% HF group, although itwas not statistically significant (P>0.05).As can be seen in Figure 2D, the means percentage ofintracellular ROS of the sperms in four out of five groupswith HF and HF-AGEs diets were higher than that in thecontrol group (P<0.001). In contrast, the mean of this parameter was lower in the 60% HF-AGEs group (P=0.07)compared to the 45% HF group, although the differencewas not statistically significant. AGEs are produced through a non-enzymatic reactionknown as glycation/Maillard, using reducing sugars (suchas glucose and fructose) in combination with proteins,lipids, or nucleic acids. The AGEs content in the 45%HF and 60% HF diets in our study was not significantlydifferent from the control diet. In contrast, the AGEscontent in the 45% HF-AGEs and 60% HF-AGEs werehigher than the standard rodent diet due to the hightemperature heating process .Fasting blood sugar analysis of the HF and HF-AGEsgroups showed increased levels of blood glucose comparedto the control group. Interestingly, de Assis et al. reportedIn this research, there were no significant differencesamong the studied groups in terms of neither spermconcentration nor abnormal sperm morphology. Despitethe pathologic conditions of diabetic men, numerousstudies have reported that diabetes and obesity may haveno direct effects on sperm parameters, but could indirectlyimpair sperm functions , 21-23. Unlike the HF-AGEs diets, the obesity-inducing HF dietshad significantly negative effects on sperm motility. The HFdiet could result in an abnormal level of blood lipid knownas dyslipidemia, which could trigger metabolic syndromeand have toxic effects on the reproductive system and semenquality , 24, 25.in vitro research by Portela et al. (Based on the literature, more deleterious effects on sperm parameters and functions wereinitially expected with the concomitant rise of saturated fat and AGEs content in the mousediet. Ironically, instead of showing more reduction of sperm motility in the 60% HF or AGEsgroup, it was even restored to the control when compared to the 45% HF group. We believethat this discrepancy can be explained by the adaptation mechanism, which is explained inthe below paragraphs, although, the literature on this topic is still controversial. Ana et al. suggesteDue to the fact that glucose and fructose are abundant ingerm cells, and sperms are full of polyunsaturated fatty acids,they are prone to glycation reaction and AGEs formation.Chen et al. believe Lipid peroxidation is one of the major consequencesof AGEs-induced ROS production in cells, whichwas significantly increased in both HF and HF-AGEsdiets compared to the control group. A high level ofpolyunsaturated fatty acids in the sperm membrane isextremely vulnerable to excess ROS. Karimi et al. ,21 haveDespite the above explanation on the toxic effects of HFand AGE, both lipid peroxidation and ROS productionwere high in the 45% HF group compared to the othergroups, which were expected to have a more toxic effect.One of the reasons that the percentage of sperm lipidperoxidation, and ROS production were lower whilepercentage of sperm motility was higher in the 60% HFdiet compared to the 45% HF diet could likely be relatedto the adaptation of mice to 60% diet. In the adaptationstage, the overall situation of blood glucose, insulin level,HOMA-IR, and HOMA beta function are more similarto the control group, therefore, it is not surprising to seebetter sperm motility, with reducing lipid peroxidation,intracellular ROS production, and reduced DNA damage in the 60% HF vs. 45% HF group.Despite the results of earlier studies on diabetes thathave linked the AGEs augmentation to complicationslike spermatogenesis impairment, our results showedthat although the HF-AGEs diets had higher glucoseconcentrations and induced the diabetes complications morethan the HF diets, they had significantly fewer negative effectson sperm motility, intracellular ROS and lipid peroxidation.Interestingly, Mallidis et al. reportedin vitro study by Antognelli et al. (Methylglyoxal is known as a precursor of AGEs produced from fructose and glucose followinga high sugar intake. Methylglyoxal level is increased in pre-diabetic and diabeticindividuals and it leads to disruption of the insulin signaling pathway , 30. A rIn this context, the trend of decreased DNA damage,lipid peroxidation, intracellular ROS production withconcomitant improved motility in the 60% HF, 45%HF-AGEs and 60% HG-AGEs diets compared to the45% HF diet, suggest that an adaptation is taken placefollowing the increased levels of glucose and insulin,which probably activated a detoxification mechanism orthe glyoxalase pathway as an anti-glycation defense in thetestes and epididymis. In this regard it has been shown thatmethylglyoxal is converted to D-Lactate, which is less toxic. InteresDue to the limitations of DNA repair mechanismsin sperms, DNA damage could occur at any step ofspermatogenesis, which is a common finding in diabeticpatients , 36, 37.Surprisingly, our results indicated that the 60% HF-AGEsdiet induces severe sperm protamine deficiency comparedto the control group while it results in a minimum amountof DNA damage in comparison to the HF diets. However,AGEs exert their deleterious effects directly by modifyingproteins, lipids, and DNA or indirectly by interacting withtheir specific receptors in cell surface known as RAGE. Inthis context, protein carbonylation is the worst consequenceof AGEs. ROS also reacts strongly with amino acid residuesrich in carbonyl groups like arginine, cysteine, and lysine.In humans, almost 85% of histones are exchanged withprotamines during spermatozoa maturation, which is rich inamino acid residues like arginine and cysteine. Other studieshave reported that such amino acids, especially arginine, areextremely vulnerable to glyoxal and methylglyoxal that areknown as reactive glycating agents . RegardiTo sum up, although the sperm concentration,morphology, and morphometric characteristics of thetestes were not significantly affected in the C57BL/6male mice fed with saturated fat- and AGEs-rich dietsfor 28 weeks, sperm motility, DNA fragmentation, andprotamine deficiency as well as membrane and cytoplasmicperoxidation were negatively affected by the HF and HF-AGEs diets. A noteworthy finding in our results was thatthe adverse effects of the HF diets were more severethan those rich in AGEs, which could be the result of theactivation of a protective glyoxalase pathway following theAGEs increase. However, the milder synergistic effect ofobesity and diabetes in mice fed by an AGEs-rich diet couldmislead our appreciation of the negative hidden effects ofthese compounds, which demands further studies on themechanism of action of AGEs and detoxification throughthe glyoxalase pathway in the body."} +{"text": "Conclusion: The rate of hospitalisation due to IHD has decreased in England and Wales during the past two decades. Hospitalisation due to IHD was strongly and negatively correlated with the increase in the rates of dispensing of IHD-related medications. Other factors contributing to this decline could be the increase in controlling IHD risk factors during the past few years. Future studies exploring other risk factors that are associated with IHD hospitalisation are warranted.Objectives: The aim of this study was to explore the trend of ischemic heart disease (IHD) admission and the prescriptions of IHD medications in England and Wales. Methods: A secular trends study was conducted during the period of 1999 to 2019. We extracted hospital admission data for patients from all age groups from the Hospital Episode Statistics database in England and the Patient Episode Database for Wales. Prescriptions of IHD medications were extracted from the Prescription Cost Analysis database from 2004 to 2019. The chi-squared test was used to assess the difference between the admission rates and the difference between IHD medication prescription rates. The trends in IHD-related hospital admission and IHD-related medication prescription were assessed using a Poisson model. The correlation between hospital admissions for IHD and its IHD medication-related prescriptions was assessed using the Pearson correlation coefficient. Results: Our study detected a significant increase in the rate of cardiovascular disease (CVD) medication prescriptions in England and Wales, representing a rise in the CVD medications prescription rate of 41.8% in 2004 to 764,584.55 in 2019 prescriptions per 100,000 persons), with a mean increase of 2.8% per year during the past 15 years. This increase was connected with a reduction in the IHD hospital admission rate by 15.4% (from 838.50 (95% CI = 836.05\u2013840.94) in 2004 to 709.78 (95% CI = 707.65\u2013711.92) in 2019 per 100,000 persons, trend test, Cardiovascular diseases are the leading cause of mortality globally, accounting for an estimated 17.9 million deaths in 2016 . The preLike in many other countries, IHD is the number one cause of mortality in the United Kingdom (UK). In 2014, 10% of female mortality and 15% of male mortality was due to IHD, contributing to 69,000 deaths [Despite the fact that females usually have a lower probability of developing CVDs compared to males, they have poor prognosis and a higher rate of mortality following an acute cardiovascular episode . CardiovAlthough the death rate from cardiovascular disease (CVD) is decreasing, it remains the principal cause of death in the world ,11. ThisWe conducted a secular trends study using publicly available data extracted from the Hospital Episode Statistics (HES) database in England and the Cardiovascular disease-related medication prescription data in England and Wales were extracted from the Prescription Cost Analysis database for the available period of April 2004\u2013March 2019 . The Brip < 0.05 was considered statistically significant. All analyses were performed using SPSS software version 25 .The rates of hospital admission with their 95% confidence intervals (CIs) were calculated using the number of IHD admissions for each age group divided by the mid-year population of the same age group of the same year. IHD medication prescription rates were calculated using the number of IHD medication prescriptions divided by the total mid-year population during the same year. The chi-squared test was used to assess the difference between the admission rates in 1999 and 2019 and the difference between IHD medication prescription rates in 2004 and 2019. The trends in IHD-related hospital admission and IHD-related medication prescription were assessed using a Poisson model. The correlation between hospital admissions for IHD and its IHD medication-related prescriptions was assessed for the duration between 2004 and 2019 using the Pearson correlation coefficient. Only a subset of IHD-related medications was selected for correlation analysis with IHD-related disease based on clinical relation/indication. A two-sided p < 0.01). The most common IHD-related hospital admission reasons were chronic IHD, acute myocardial infarction, and angina pectoris in 1999 to 709.78 (95% CI = 707.65\u2013711.92) in 2019 per 100,000 persons, trend test, pectoris .Over the last two decades, the hospitalisation rates for the other acute IHDs category, acute myocardial infarction, and chronic IHD increased by 12-fold (1175.0%), 56.3%, and 6.8%, respectively. On the contrary, the rate of hospital admission due to subsequent STEMI and NSTEMI, certain current complications following STEMI and NSTEMI, and angina pectoris decreased by 90.8%, 63.5%, and 59.1%, respectively .p < 0.001). The IHD-related hospital admission rate among patients aged 15\u201359 years decreased by 14.8% (from 351.07 (95% CI = 349.00\u2013353.14) in 1999 to 299.23 (95% CI = 297.40\u2013301.05) in 2019 per 100,000 persons, trend test, p < 0.001). The IHD-related hospital admission rate among patients aged 60\u201374 years decreased by 25.9% (from 2462.48 (95% CI = 2450.95\u20132474.02) in 1999 to 1825.19 (95% CI = 1816.56\u20131833.82) in 2019 per 100,000 persons, trend test, p < 0.001). The IHD hospital admission rate among patients aged 75 years and above increased by 6.5% (from 2777.18 (95% CI = 2760.90\u20132793.46) in 1999 to 2957.84 (95% CI = 2943.11\u20132972.58) in 2019 per 100,000 persons, trend test, p < 0.001) in 1999 to 0.61 (95% CI = 0.46\u20130.75) in 2019 per 100,000 persons, trend test, < 0.001) . Betweenp < 0.05). The IHD-related hospital admission rate of males decreased by 2.3% (from 985.39 (95% CI = 981.55\u2013989.23) in 1999 to 962.52 (95% CI = 958.99\u2013966.05) in 2019 per 100,000 persons, trend test, p = 0.24) in 1999 to 466.87 (95% CI = 464.43\u2013469.31) in 2019 per 100,000 persons, trend test, = 0.24) .p < 0.05) .The rate of certain current complications following STEMI and NSTEMI was higher among the 60\u201374-year age group than those aged 75 years and above during the years 1999/2000, 2007/2008, and 2016/2017. Furthermore, the rate of chronic IHD was higher among the 60\u201374-year age group than the 75-year age group from 1999 to 2010, after which the rate of chronic IHD became higher again in those aged 75 years and older from 2010 to 2019 .p < 0.001) . CVD medication prescription rates increased by 41.8% in 2004 to 764,584.55 in 2019, prescriptions per 100,000 persons, trend test, < 0.001) (detaile< 0.001) section.p < 0.01).A strong negative correlation was found between the prescription of beta-adrenoceptor blocking drugs, antihypertensive therapy, nitrates, calcium channel blockers and potassium channel activators, lipid-regulating drugs, and hospital admission rates for angina pectoris (p < 0.05).A strong negative correlation was found between the prescription of positive inotropic drugs, diuretics, anti-arrhythmic drugs, and hospital admission rates for acute myocardial infarction (p < 0.05).A negative correlation was found between the prescription of beta-adrenoceptor blocking drugs, antihypertensive therapy, nitrates, calcium channel blockers and potassium channel activators, anti-fibrinolytic drugs and haemostatics, lipid-regulating drugs, and hospital admission rates for subsequent ST elevation (STEMI) and non-ST elevation (NSTEMI) myocardial infarction (p < 0.01).A strong negative correlation was found between the prescribing of beta-adrenoceptor blocking drugs, antihypertensive therapy, nitrates, calcium channel blockers and potassium channel activators, anti-fibrinolytic drugs and haemostatics, lipid-regulating drugs, and hospital admission rates for certain current complications following ST elevation (STEMI) and non-ST elevation (NSTEMI) myocardial infarction (within the 28-day period) (p < 0.05).A negative correlation was found between the prescribing of beta-adrenoceptor blocking drugs, antihypertensive therapy, nitrates, calcium channel blockers and potassium channel activators, lipid-regulating drugs, and hospital admission rates for chronic ischemic heart disease , which is consistent with a previous study ,23. In aThe prevalence and incidence of IHD increase with aging ,23,29,30The same study found that the hospitalisation rates for chronic IHD decreased slightly in patients <65 years and increased in patients \u226565 years between 1998 and 2007. This is contrary to our study, which showed that the chronic IHD-related hospital admission rates increased for all age groups between 1999 and 2007 . In the IHD hospitalisation rates decreased in the Netherlands in the last few years, with a significant decrease in acute myocardial infarction hospital admission rates, while chronic IHD hospitalisation rates increased . RegardiThe prevalence rate of angina pectoris in England dropped from 4.8% to 3.2% in males and 3.4% to 2.1% in females in the years 2003 and 2017, respectively . This deIn England, cigarette smoking among adults decreased from 27% in 1993 to 17% in 2017. Additionally, the percentage of children (aged 8 to 15) who had ever smoked declined from 19% to 5% in the same period . BetweenIn England, the percentage of adults diagnosed with hypercholesterolemia decreased from 67% in 1998 to 48% in 2017 . The sigThe proportion of adults with untreated hypertension decreased from 16% in 2003 to 11% in 2017 in females and from 20% to 12% in males . As showA previous study infers a parallel rise in rates of dysglycaemia hospital admission and rates of dispensing antidiabetic medication in England and Wales between 1999 and 2016 . In EnglConsistent with other studies, the use of anti-anginal medications, such as beta-blockers, calcium channel blockers, and disease-modifying medications like anti-platelets, and lipid-lowering medications, are negatively correlated with IHD-related hospital admission rates. These medications are mainly maintenance therapy and have been shown to improve symptoms and prolong survival in many studies ,36,37,38Previous studies revealed that obesity is an independent predictor of the future risk of hospital admissions due to IHD. For example, Murphey et al. predicted an additional 14 admissions per 100 men and women over the next 20 years if the prevalence of obesity continues to rise . AlthougOver the past two decades, many factors may have influenced the trend of admission rates due to IHD. For instance, the introduction of coronary computed tomography angiography (CCTA) and coronary artery calcium score (CACS) and their wide use since 2011 as an anatomical diagnostic tool has completely changed the diagnostic approach of coronary artery disease (CAD). Most major adverse cardiac events (MACEs) requiring hospitalisation take place in non-obstructive plaques, particularly in women , and theIHD prevalence continues to increase despite the decreasing IHD incidence. This is likely due to the implementation of public health measures and the recent efforts to tackle cardiovascular risk factors, coupled with the increased cardiovascular medication prescription rate . We obseTo the best of our knowledge, this is the first study to explore trends in the rates of IHD-related hospitalisation and the prescription of IHD-related medications worldwide and in England and Wales without restricting the study to specific inclusion/exclusion criteria. Our study provided detailed hospital admission rates for all types of IHD stratified by age and gender, giving a comprehensive description of the hospitalisation profile for this group of patients over 20 years. Our study has several limitations. Since it is a secular trends study, it lacks information at the individual levels. Having a family history of CVD, personal lifestyle, overweightness/obesity, alterations in lipid metabolism, and lack of physical activity are also variables that can impact the incidence or prevalence of IHD/CVD. Because of the study\u2019s nature, the correlations between IHD-related hospital admission rates and IHD-related medication prescription rates cannot be confirmed. Innate to ecologic studies, they cannot establish causality or associations. Identified temporal variability could be related to potentially non-medical causes, such as updated coding guidelines. These artificial changes may introduce temporal correlation among diagnoses inferred from routine data, violating the assumptions of frequently used statistical methods .In correlation analysis, there is a lack of information on the temporal relation between the drugs and associated IHD complications. Moreover, data are not available at the individual level. Hence, statistically significant results do not necessarily imply causality. They may indicate possible causality, reverse causality, or confounded association. Accounting for confounding association remains crucial in interpreting the analysis, as the care of patients with IHD has improved in multiple ways, and many innovations have been introduced during the last 20 years. Moreover, many medications are used after an IHD complication occurs, resulting in a positive association, which is defined as reverse causality. When looking at the overall changes during the study period in admission and prescription rates without considering the weight of group and IHD-specific type STEMI and NSTEMI contribute to only 0.1% of the total number of admissions) from the total number of prescriptions/admissions, overweighting may lead to overestimated rates, which could affect the interpretation of the study findings. Admission data include admission and readmission at the same time. Therefore, our admission rate estimates could be overestimated, as some proportion of them could be drug-use related re-admission . Thus, CVD medications that decreased the IHD hospitalisation rate could increase it.The rate of hospitalisation due to IHD has decreased in England and Wales during the past two decades. This decrease could be explained partly by the increase in the CVD medication prescription rate. Other reasons that likely decreased IRHAs include the decrease in IHD incidence, increase in controlling IHD risk factors, and improved IHD treatments. Future studies exploring other risk factors that are associated with IHD hospitalisation are warranted."} +{"text": "Prospective cohort studies show that higher intakes of ultra-processed food (UPF) increase the risk of obesity and obesity-related outcomes, including cardiovascular disease, cancer and type 2 diabetes. Whether ultra-processing itself is detrimental, or whether UPFs just have a lower nutritional quality, is debated. Higher UPF intakes are inversely associated with fruit, vegetables, legumes and seafood consumption. Therefore, the association between UPFs and poor health could simply be from excess nutrient intake or from a less healthful dietary pattern. If so, adjustment for dietary quality or pattern should explain or greatly reduce the size of the significant associations between UPFs and health-related outcomes. Here, we provide an overview of the literature and by using a novel approach, review the relative impact of adjusting for diet quality/patterns on the reported associations between UPF intake and health-related outcomes in prospective cohort studies. We find that the majority of the associations between UPFs, obesity and health-related outcomes remain significant and unchanged in magnitude after adjustment for diet quality or pattern. Our findings suggest that the adverse consequences of UPFs are independent of dietary quality or pattern, questioning the utility of reformulation to mitigate against the obesity pandemic and wider negative health outcomes of UPFs. Obesity is a leDiet has long been a cornerstone of weight management, with dietary policies being a core feature of government and health organisation strategies to reduce obesity worldwide. Indeed, poor diets are a leading cause of preventable obesity-related death and NCD, including cancer, cardiovascular disease (CVD) and type 2 diabetes (T2DM), accounting for 11 million deaths annually ,6. As suDespite the importance of specific nutrients and food groups within overall dietary patterns for health, it is becoming increasingly clear that other dimensions of diets are important . In receWhether ultra-processed diets are detrimental to health simply because they are of a poor nutritional quality, or whether the nature and extent of processing itself has health consequences is an ongoing debate . SeveralSeveral classification systems have been developed to categorise food and drink based on levels of processing, including the International Food Information Council, International Agency for Research on Cancer and NOVA classifications . The mosIn recent decades, the contribution of UPFs to diets worldwide has been increasing year on year . In the Systematic reviews and meta-analyses of prospective cohort studies and cross-sectional studies show that UPF consumption is associated with an increased risk of weight gain, overweight and obesity ,36,37,38There is increasing evidence showing that UPFs are linked with obesity and other adverse health-related outcomes. However, the potential mechanisms that lead to these adverse health outcomes are diverse, and still largely debated . From a nutrient perspective, UPFs have on average a higher energy density and lower nutrient density than minimally processed foods ,46. UPFsHowever, aspects of ultra-processing may also increase the risk of obesity and other adverse health-related outcomes. Textural and structural changes to the food matrix as a result of ultra-processing can also allow for UPFs to be consumed more quickly ,50,51. RBeyond nutrients and ultra-processing, behavioural aspects of UPFs and the local, environmental and systemic drivers influencing food choice are also important . The heaActions to reduce the risks associated with UPF intake have largely been either reformulation to improve the nutrient profile of UPFs, or avoidance of UPFs altogether. Whether experts support UPF reformulation or UPF avoidance is dependent on the views regarding which mechanisms link UPFs with poor health.Both those in favour of limiting UPFs , and thoIndeed, many UPFs are nutritionally poor and energy dense, but not all are. Studies demonstrate that UPFs tend to relate with existing nutrient profile indices, based on saturated fat, added sugar and sodium content . In compGiven that particular UPFs, such as reformulations, can be considered to be of a similar or greater nutritional quality than some MPFs, it has been suggested that these UPFs are therefore healthy and nutritious ,76. ExpeIn summary, there is agreement that energy dense foods high in saturated fat, sodium and added sugar are harmful to health and should be limited. Such foods also tend to be ultra-processed, but not all are ,74. DespOne of the main criticisms against the NOVA classification is that UPFs simply capture nutrient poor foods high in saturated fat, sodium and added sugar ,73. FurtMany prospective studies in adults have performed dietary adjustments, with only a small proportion not adjusting for aspects of dietary quality ,89,90,91Across 37 studies, 87 health-related outcomes were assessed using 91 models. Of the 66 models that demonstrate a significant association between UPF and a health-related outcome, 64 remained significant following adjustment for diet quality or diet pattern. In total, 136/142 dietary adjustments did not explain the significance of the association between UPF intake and a health-related outcome. Across four studies, all four models demonstrated higher UPF intakes were significantly associated with all-cause mortality ,104,105.Within the NutriNet-Sant\u00e9 cohort, several studies have performed dietary adjustments for the associations between UPF intake and all-cause mortality, CVD, overweight/obesity incidence, T2DM, cancer and functional gastrointestinal disorders ,127,129.p = 0.04) and 10% increased risk of CVD, CHD and cerebrovascular disease, respectively [Srour et al. reported a 12% , 13% and 11% increased risk of CVD, coronary heart disease (CHD) and cerebrovascular disease, respectively, per 10% increase in UPF in the diet . Multiplectively . Third, ectively .In a separate study, Srour et al. reported a 15% increased risk of T2DM with each 10% increase in UPF in the diet, which included adjustment for dietary quality using the FSA-NPS-DI . Again, Fiolet et al. reported a 12% and 11% increased risk of all cancer and breast cancer, respectively, per 10% increase in UPF in the diet . Adjustm2 ) and increased risk of overweight ) or obesity ), per 10% increase in UPF in the diet [2 ), or increased risk of overweight ) or obesity ), and neither did adjustment for saturated fat, sugar, sodium and dietary fibre intake, which also resulted in a greater BMI gain ), and increased risk of overweight ) or obesity , per 10% increase in UPF intake [Beslay et al. reported a greater BMI gain (odds ratio (OR): 1.24 ) and functional dyspepsia ) when comparing the highest vs. lowest quartiles of UPF intake . AdjustmFour studies within the Seguimiento Universidad de Navarra (SUN) cohort have adjusted for fat, added sugar and sodium intake, or for dietary pattern. Rico-Campa et al. demonstrated that the highest vs. lowest quartile of UPF intake was associated with a 62% increased risk of all-cause mortality . AdjustmLlavero-Valero et al. reported that the highest vs. lowest tertile of UPF intake was associated with a 53% increased risk of T2DM, which was unaltered ) after adjusting for Mediterranean diet pattern adherence .G\u00f3mez-Donoso et al. found a 41% increased risk of incident depression in the highest vs. lowest quartile of UPF intake, which was still associated with a 33% higher risk of incident depression after further adjustment for other covariates, including Mediterranean diet pattern adherence .Leone et al. identified an increased risk of gestational diabetes in females aged 30 and over ), which was unaltered after adjustment for Mediterranean diet pattern adherence ) .p-trend = 0.001) [In the US Third National Health and Nutrition Examination Survey (NHANES III) cohort, there was a 31% increased risk of all-cause mortality in the highest vs. lowest quartile of UPF intake, which remained significant after further adjustment for dietary quality score using the HEI-2000 (= 0.001) . HoweverIn the Italian Moli-sani cohort, the highest vs. lowest quartile of UPF intake was associated with a 32% higher risk of all-cause mortality, 65% higher risk of CVD mortality, and a 63% higher risk of ischemic heart disease (IHD)/cerebrovascular mortality . AdjustiIn the Framingham Offspring cohort, each additional serving of UPF per day was associated with a 5% , 9% , 7% and 9% increased risk of overall CVD, CVD mortality, hard CVD and hard coronary heart disease, respectively . FurtherIn the US Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial cohort, the highest vs. lowest quintile of UPF intake was associated with a 50% increased risk of CVD mortality, and a 68% increased risk of heart disease mortality . MultiplIn the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, each additional standard deviation (SD) increment in UPF intake per day was associated with a 0.12 kg greater increase in weight over 5 years of follow-up, which was unaltered after further adjusting for Mediterranean diet score ) . In sensIn the China Nutrition and Health Survey (CNHS), consuming \u226550 g of UPF per day was associated with an increased risk of overweight/obesity ) and central obesity ), when compared to no UPF intake. Adjustment for traditional and modern dietary patterns did not alter the increased risks , central obesity, OR: 1.50 ) .In the Seniors Study on Nutrition and Cardiovascular Risk in Spain (Seniors-ENRICA-1), Sandoval-Insausti et al. found an increased risk of abdominal obesity in the highest vs. lowest tertile of UPF intake, which was unaltered after adjustment for Mediterranean diet adherence and fibre and omega-3 fatty acid intake ) .Donat-Vargas et al. identified an increased risk of hypertriglyceridaemia ) and low-HDL cholesterol ), as well as a significant increase in blood triglycerides ) when comparing the highest vs. lowest tertile of UPF intake . Adjustm2 greater gain in FMI from ages 6 to 11, per 100 g daily increase in UPF intake [2 from age 6 to 11, per 100 g daily increase in UPF intake [In the Pelotas-Brazil 2004 Birth Cohort, Costa et al. found a 0.09 kg/mF intake . AdjustmF intake .2 and 0.03 kg/m2 greater yearly increase in BMI and FMI, respectively, from the age of 7 to 24 [2/year ) or FMI ) [In the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort, the highest vs. lowest quintile of UPF intake was associated with a 0.06 kg/m 7 to 24 . Adjustm, 0.05)) .Koniecnzna et al. conducted a prospective analysis of the PREDIMED-Plus trial over the course of 12 months. Each 10% increment in UPF intake was associated with increases in total ) and visceral ) fat mass z-scores. Adjusting for overall repeated measures of saturated and trans fat, sodium, glycaemic index, alcohol and fibre intake across the 12 month study did not alter the significant association between UPF intake and increases in total and visceral ) fat mass z-scores per 10% increase in daily UPF intake . AdjustiIn the Tianjin Chronic Low-grade Systemic Inflammation and Health (TCLSIH) Cohort Study, the highest vs. lowest quartile of UPF intake was associated with a 17% higher risk of non-alcoholic fatty liver disease (NAFLD) in the age, sex and BMI adjusted model. After adjustment for other confounders including for a healthy diet score based on fruit, vegetable, red meat and fish intake, the increased risk associated with the highest vs. lowest quintile of UPF intake was 19% .Zhang et al. found a 21% increased risk of hyperuricaemia in the highest vs. lowest quartile of UPF intake, which was still associated with a 17% increased risk of hyperuricaemia after adjustment for dietary pattern .In a separate study, Zhang et al. reported that each 10% increment in UPF in the diet was associated with a \u22120.30 kg and \u22120.0043 kg/kg weight yearly reduction in absolute and weight-adjusted grip strength, respectively . AdjustmIn a combined analysis of the Nurses\u2019 Health Study, the Nurses\u2019 Health Study II and the Health Professionals Follow-up Study, Lo et al. found a 75% increased risk of Crohn\u2019s disease in the highest vs. lowest quartile of UPF intake after adjusting for age, cohort and calendar year. The increased risk was unchanged after further covariate adjustments, including for diet quality defined by the AHEI-2010 ) .In the Prospective Urban Rural Epidemiology (PURE) cohort, Narula et al. identified an 82% increased risk of inflammatory bowel disease (IBD) and a 450% increased risk of Crohn\u2019s disease in those consuming five or more UPF servings per day, compared with those consuming less than one serving per day. Adjustment for AHEI-2010 still resulted in a 92% increased risk of IBD and a 490% increased risk of Crohn\u2019s disease .In the Norwegian Mother, Father and Child Cohort Study, Borge et al. reported that each 1 SD increase in maternal UPF intake was associated with an increase in absolute ) and relative ) measures of child attention deficit hyperactivity disorder (ADHD) symptoms at age 8, using the Parent Rating Scale for Disruptive Behaviour Disorders . AdjustmThree studies have considered the impact of diet quality and dietary pattern using alternative methods. In the ATTICA cohort, each additional weekly serving of UPF was associated with a 10% increased risk of CVD. Kouvari et al. then performed sub-group analysis based on Mediterranean diet pattern adherence. Participants with moderate to high adherence to the Mediterranean diet had an attenuated ) risk of CVD per weekly serving of UPF, whereas participants with low adherence to the Mediterranean diet had an even greater risk of 19% , per weekly serving of UPF .p for interaction = 0.034) in the Moli-sani cohort [Bonaccio et al. identified that diet quality (defined by the FSA-NPS-DI) was only significantly associated with all-cause mortality in high UPF consumers , but not in low UPF consumers (i cohort . The intp = 0.047).In the ENRICA study, the highest vs. lowest quartile of UPF intake had a 44% increased risk of all-cause mortality . InsteadTwo studies have simultaneously adjusted for fat, sodium and carbohydrate intake and for dietary pattern, which are reported in Adjibade et al. identified a 21% higher risk of depressive symptoms per 10% increase in UPF in the diet in the NutriNet-Sant\u00e9 cohort . After aSome studies have adjusted for one or two components of fat and/or sugar and/or sodium intake, rather than all three components. One study adjusted for carbohydrate intake, rather than sugar intake . These aOther measures used for dietary adjustment are provided in p = 0.031) increase in android:gynoid fat ratio z-score during 12 months of follow-up [To date, only two studies have performed dietary adjustments that explain the association between higher UPF intakes and adverse health-related outcomes. In the PREDIMED-Plus study, each 10% increase in UPF in the diet was associated with a 5% higher risk of other cause mortality . However, after adjusting for Mediterranean diet score, this became non-significant ) . As noteAn ultra-processed diet has been shown to increase energy intake in comparison with a minimally processed diet . Energy Adjustment for energy intake can be achieved using several methods ,146. HowBesides being included as a covariate within models, formal mediation analysis can be used to determine whether dietary components mediate the association between UPF intake and adverse health-related outcomes ,150. Fewp < 0.001) of IHD/cerebrovascular mortality risk, but did not account for all-cause mortality , p = 0.14) or CVD mortality , p = 0.15) risk. Sugar content alone accounted for 23.2% , p < 0.001), 18.0% , p = 0.003) and 36.3% , p < 0.001)) of the associated risk between UPF intake and all-cause mortality, CVD mortality and IHD/cerebrovascular mortality, respectively. Saturated fat or sodium content did not account for any of the associated risks.Bonaccio et al. examined the mediating role of nutrients and energy content on all-cause mortality, CVD mortality and IHD/cerebrovascular mortality . All diep > 0.05) [Fiolet et al. performed mediation analyses for sodium, total lipids, saturated fat, monounsaturated fat, polyunsaturated fat, carbohydrate and for Western dietary pattern, with all mediation effects for the association between UPF intake and overall cancer being less than 2% .Koniecnzna et al. found that repeated measures of saturated fat, trans fat and fibre explained 11\u201330% of the associations between UPF intake and increases in measures of central and overall adiposity over 12 months of follow-up . Repeate2 ) of the association between UPF intake and the increase in FMI from age 6 to 11 in children was mediated by energy content, with the remaining 41.8% being either a direct effect of ultra-processing, or as a result of unmeasured variables [Costa et al. identified that 58.2% or processed , which may result in the misclassification of foods with the dietary assessment methods used. Furthermore, other important dietary aspects may have not been captured or suitably adjusted for. Most studies have adjusted for fat, sugar and sodium intake or for overall dietary patterns, which are important dietary factors for health, and proposed to be explanatory factors for the associations between UPF intake and health outcomes.Experts for and against the NOVA classification have often focussed on nutrient quality as an important explanatory link between UPFs, obesity and adverse health-related outcomes. However, many of the prospective studies published to date have performed analyses adjusting for nutrient content and overall dietary patterns. These adjustments do not explain the association between UPFs, obesity and adverse health-related outcomes, with estimates remaining significant. These findings raise important questions regarding current policy and future research needs, suggesting that the nature and extent of processing is an important dietary dimension, and whether UPF reformulations can sufficiently address the growing transition towards high UPF diets and the associated risk of obesity and poor health."} +{"text": "Although the prevalence of sarcopenic obesity is increasing, nowadays a universally accepted definition still does not exist. Because, this clinical entity is defined as the combination of obesity and sarcopenia, the diagnosis appears to be strictly linked to criteria used for sarcopenia and the available prevalence data are not uniform. To investigate the prevalence of sarcopenic obesity in older persons according to EWGSOP2 and FNIH criteria. Second, to evaluate the prevalence of diabetes in patients with sarcopenia diagnosed by the two definitions.Observational multicenter study performed in 2014 on older patients admitted to 12 Italian hospitals (GLISTEN Study). Data were collected through standardized questionnaires, which assessed: socio-demographic data, cognitive status, functional abilities, pharmacological therapy, comorbidities, and blood tests. Moreover, muscle mass and strength and physical performance were evaluated.p\u2009=\u20090.101); otherwise, using FNIH criteria, 36.3% of sarcopenic and 26.9% of non-sarcopenic patients were diabetic (p\u2009=\u20090.030). After adjustment for potential confounders, diabetic patients had a 73% higher probability of being sarcopenic according to FNIH criteria .Six hundred and ten were included in the analyses. Among sarcopenic patients, the prevalence of sarcopenic obesity was 30.8% with FNIH and 0% with EWGSOP2 criteria. According to EWGSOP2 criteria, 23.7% of sarcopenic and 30.8% of non-sarcopenic patients were affected by diabetes (The EWGSOP2 and FNIH sarcopenia criteria are differently related to the prevalence of obesity and diabetes. The EWGSOP2 criteria seem to be not suitable to identify people with sarcopenic obesity. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL Selected demographic and clinical characteristics of enrolled patients are shown in Table n\u2009=\u200945), whereas, no patients were defined as obese in the sarcopenic group based on EWGSOP2 criteria .The prevalence of FNIH defined sarcopenic obesity was 7.4% , 23.7% of sarcopenic and 30.8% of non-sarcopenic patients were affected by diabetes (p\u2009=\u20090.101), whereas, after standardization by BMI (FNIH criteria), the prevalence of diabetes was 36.3% in sarcopenic subgroup and 26.9% in non-sarcopenic one (p\u2009=\u20090.030) , whereas diabetes was not associated to sarcopenia prevalence when defined according to EWGSOP2 criteria . Adjustment for functional status and comorbidity did not modify the relationship between diabetes and sarcopenia having very low sensitivity for intercepting patients with sarcopenic obesity. Previous studies had already shown that EWGSOP2 and FNIH criteria have different construct and identify different patients: therefore, it is well known that they cannot be used interchangeably [The method used for appendicular muscle mass standardization significantly affects the association of sarcopenia with obesity and type 2 diabetes, with standardization for heightangeably , 31, 32."} +{"text": "Diabetes Mellitus (DM) is an epidemic in the US that complicates the treatment of burn injuries. Lower extremity burns in diabetic patients, particularly the feet, are challenging problems with predictably unfavorable outcomes, as demonstrated by single-institution studies. National evaluations are absent, especially with regard to limb salvage. We aim to characterize lower extremity burns in persons with DM and evaluate the likelihood of amputation. We hypothesize that the incidence of DM associated foot burns is increasing in the US, and these patients are more likely to undergo lower extremity amputation than those without DM.th Edition codes. DM is a predefined comorbidity within the NTDB, allowing for cohort comparisons. Logistic regression modeled predictors of lower extremity amputation. Patient covariables included age, sex, race/ethnicity, and comorbidities. Burn covariables included % burn total body surface area (TBSA), mechanism, and region of burn center. Poisson regression evaluated for significance in temporal changes in DM foot burns.The National Trauma Data Bank (NTDB) was queried from 2007-2015 extracting encounters with primary burn injuries of the feet using International Classification of Diseases (ICD) 9There were 116,796 adult burn encounters of which 7,963 (7%) had foot burns. Of this group, 1,308 (16%) had DM. DM foot burn encounters were older, more likely to be male, and had more comorbidities than non-DM foot burn encounters . DM foot burn encounters were more likely to sustain a scald injury (compared to flame) and had smaller %TBSA . Additionally, 5.6% of encounters with DM foot burns underwent amputation compared to 1.5% of non-DM encounters (p< 0.001). Independent predictors of lower extremity amputation included DM , alcohol use, smoking, chronic kidney disease, burn size >20%, African American/Black race, male sex, and age >40 years . The incidence of DM foot burns increased over the study period with an incidence rate ratio (IRR) of 1.09 .In the largest cohort study to date, DM was associated with nearly a 4-fold increase in amputation after adjusting for available confounders. Furthermore, the incidence of DM foot burns is increasing. Strategies for optimizing care in persons with DM foot burns are need to improve limb salvage."} +{"text": "In an online survey exploring older Canadians\u2019 experiences during the COVID-19 pandemic, 3989 respondents aged 55-99 indicated whether they had discussed their future care preferences and with whom, prior to and since the outbreak. Pre-pandemic, 62% had held such discussions; since the pandemic 43% did so, 11% for the first time. Rates were significantly higher among white respondents than among persons of color, women than men, and those 65+ than younger respondents. Respondents were most likely to have talked, respectively, with their spouse , family , and friends \u2014with higher rates for white, women and older respondents. Surprisingly, only 4% before and 2% since the pandemic had discussed their care preferences with a doctor. Initiation of some new discussions was encouraging but there were fewer than expected, perhaps due to denial, superstition, or disbelief of pandemic severity. Advance care planning remains an under-utilized resource."} +{"text": "The primary source of information about COVID-19 was social networking (38.9%). Pharmacists were committed to social distancing (86.5%) and wearing masks (76.2%). They expressed levels of agreement to their role in decreasing COVID-19 spread (94.2%) and correcting false information (94.5%); they expressed levels of expectation toward concern about a second COVID-19 wave (83%) that would be more severe than the previous one (43.4%). Pharmacists expected that an influenza vaccine might be helpful in decreasing severity and spread of the COVID-19 pandemic (56.9%). Pharmacists expected COVID-19 vaccine development within 6 months of administering our study survey (84.9%) and that vaccination might be effective in preventing COVID-19 (93%) infection. Conclusion: Pharmacists expressed positive roles on COVID-19 spread through exemplary actions, self-commitment to protection measures, and public health awareness. Social media as a source of health information should be cautiously investigated, and pharmacists should always refer to evidence-based sources. The role of pharmacists is particularly important for the upcoming era of COVID-19 vaccination administration and awareness.Objectives: To analyze the role of pharmacists during the COVID-19 pandemic, to measure pharmacists\u2019 attitude toward COVID-19 safety measures , and explore their perspectives regarding a second wave of the virus. Methods: This cross-sectional online survey study was conducted in Jordan during the COVID-19 outbreak in July 2020 to discuss Jordanian pharmacists\u2019 awareness of safety at their workplace during the COVID-19 outbreak, their sources of information, and their predictions for COVID-19 vaccination. Results: The participants ( Coronavirus (CoV) infections are caused by emerging respiratory viruses and are known to cause illness ranging from common cold-like symptoms to severe acute respiratory syndrome (SARS) . CoV areFake news and rumormongering are popular in a wired world because of the increase in internet and social media use, especially during a pandemic . A confuPharmacists, as healthcare providers, could be the first point of contact for many people with the healthcare system to discuss their health problems or when they simply need information. In these circumstances, the pharmacists\u2019 function is not limited solely to ensuring sufficient stocks of medicines and protective equipment, but also to play an important role in minimizing transmission to the population by increasing public knowledge ,11. BaseThis is a descriptive, cross-sectional online study using a self-reporting survey distributed during July 2020 designed through Google forms platform. The survey was administered in Arabic, the official language of Jordan. A list of pharmacists was provided by the Jordan Pharmacists Association (JPA), which is the official and only syndicate for pharmacists in Jordan, established in 1957 with obligatory membership for pharmacists to gain their license to practice pharmacy in Jordan. The JPA has around 15,000 pharmacist members across Jordan. Considering the absence of similar measures of our study variables in Jordan, the response distribution was assumed as 75% and a sample size of at least 283 pharmacists was expected to express 95% confidence level with 5% error using the Raosoft sample size calculator.Social media (mainly WhatsApp and Facebook) was used to spread the survey to reach pharmacists all over Jordan through groups that only included pharmacists. Close-ended questions were designed to measure our goals using predefined answers. The research proposal and tools were reviewed and approved by the Institutional Review Board (IRB) at Al-Balqa Applied University, Al-Salt, Jordan (code: 492/1/3/26). Participation in the study was completely voluntary and posed no risk upon participants. Completion of the study survey was deemed as an informed consent for participation in the study. Eligibility to participate included that participants were a pharmacist, while those who did not consent to participate or did not complete the questionnaire were excluded.Validation of this study\u2019s survey items for comprehension was carried out prior to launch using a random pilot sample of 20 independent pharmacy professionals, mainly serving as community pharmacists. Feedback regarding the clarity and comprehension of the pilot survey were conveyed to the research team and discussed thoroughly, then incorporated where appropriate produce a final version of the survey. All items of our study survey were based on current literature ,13,14, aDemographic data of participants includes: their residence area, gender, age, level of education, and place of work. We also asked the participants about their primary source of information during the pandemic.Our survey included questions to measure the pharmacist\u2019s opinion on their role during the COVID-19 pandemic. The study survey included questions to measure pharmacist\u2019s commitment to follow protective procedures and the use of protective equipment as per regulations of the pandemic, including social distancing, wearing masks, and wearing gloves. Moreover, several questions seek to assess pharmacists\u2019 perceptions toward their role in decreasing COVID-19 spread and correcting false information about the COVID-19 pandemic. Additionally, this survey challenges pharmacist\u2019s knowledge by assessing their ability to differentiate between COVID-19, influenza, and Spanish influenza. A question was also included to measure perception of pharmacists\u2019 ability to collect samples for COVID-19 testing.Pharmacists\u2019 expectations related to current and future COVID-19 pandemics were also assessed. Pharmacists were asked for their expectation of a second COVID-19 pandemic wave in terms of presence, relative severity to the first wave, and timing. Our survey also including pharmacists\u2019 expectations about a COVID-19 vaccine, in terms of development and effectiveness in resolving the ongoing pandemic. Their expectation of whether immunization against influenza might decrease severity and the spread of COVID-19 was also assessed from the perspective of participating pharmacists in our study.All data were generated automatically to Microsoft Excel by Google forms then coded and analyzed using Statistical Package for Social Sciences . Descriptive statistics with corresponding 95% confidence intervals (CIs) were constructed. Differences between various categorical variables were evaluated using the chi-square test.Data were collected from 311 participants, all pharmacists. A total of 45.0% of participants in this study were aged between 23\u201330 years old, 33.1% were aged between 31\u201340 years old, 15.8% were aged between 41\u201350 years old, and 6.1% were aged above 50 years old. Around 83.0% of the sample were females. In terms of education, 77.2% were university graduates with a bachelor\u2019s degree, 17.7% with a master\u2019s degree, and 5.1% held a doctoral degree. For residence location, most of the participants (38.3%) were in Amman, the capital city, while the rest of participants were distributed as living in the middle area of Jordan(35.0%), living in northern area (14.8%), and living in the southern area (11.9%). Among participants, most reported social networks as their primary source of information about the COVID-19 pandemic (38.9%), while other sources reported were TV newscasts (23.8%), specialized scientific journals (18.6%), personal readings (15.4%), and other sources (3.2%). Pharmacists in our study were mostly community pharmacists (39.5%), while 5.8% were hospital pharmacists, and 54.0% had work elsewhere to the defined place of work, Participating pharmacists in our study expressed commitment at all times to social distancing measures (86.5%), while 10.9% reported occasional commitment; only 1.3% self-reported non-commitment. Moreover, most participants, 76.2%, reported commitment at all times to wearing masks, while 16.7% reported occasional commitment, and only 6.4% reported non-commitment. Regarding their commitment to wearing gloves, most of our study participants reported commitment at all times (58.8%), while 28.9% reported occasional commitment, and only 12.2% reported non-commitment.Most participants (48.9%) confirmed that pharmacists do have a role in decreasing the COVID-19 pandemic, while 45.0% believed they might have such a role, and only 5.8% denied having such a role. Participants mostly believed that pharmacists knew the difference between influenza and COVID-19 (84.6%), while 10.6% believed they might know, and only 4.5% denied such beliefs. Additionally, participants mostly believed that pharmacists might know the difference between the Spanish influenza of 1918 and the COVID-19 pandemic (33.4%), while 29.3% had never heard of the 1918 pandemic, 24.4% believed they did know the difference, and only 12.5% denied such belief of pharmacist\u2019s knowledge. Most participants reported that pharmacists correct false information about the COVID-19 pandemic (76.2%), while 18.3% believed they might have such a role, and only 5.5% denied this role. Regarding pharmacist\u2019s ability to take samples for COVID-19 testing, most participants believed that pharmacists are not competent for such a role (54.7%), while 23.8% believed they might be for such a role, and only 21.5% believed they do have such an ability.Regarding their expectation of a second COVID-19 wave, most participants confirmed such expectation (48.6%), while 33.8% believed this might happen, and only 17.0% denied a second wave. Moreover, most participants expected that a second wave of COVID-19 would be more severe compared to the first one (43.4%), while 35.0% expected it to be less severe, 12.2% expected there was no relation of severity between both waves, and 8.7% expected the second wave to be of similar severity to the first one. Additionally, 58.5% of participants expected the second wave to happen within 3 months, while 23.2% expected it within one year, 3.2% expected it within two years, and 12.9% expected it after more than two years, A total of 56.9% of participants expressed varying levels of agreement toward the ability of an influenza vaccine to decrease the severity and spread of COVID-19: , although 43.1% clearly denied such ability of an influenza vaccine. Regarding expectation of developing a COVID-19 vaccine within 6 months of administering our study survey, 55.6% of participants believed this is expected, while 29.3% might expect this, and only 14.8% denied such expectation. Moreover, the efficacy of a COVID-19 vaccine was mostly expected by our study participants (60.8%), while 32.2% believed this might be expected, and only 7.1% denied its effectiveness, p-value = 0.013). Regarding pharmacists\u2019 role in decreasing COVID-19 spread, several participant segments expressed more significant involvement for such a role, including male participants , participants living in the middle area of Jordan , and hospital pharmacists (0.048). Female pharmacists significantly believed more of their knowledge of the difference between influenza and the COVID-19 pandemic . Pharmacist knowledge of similarities between the COVID-19 pandemic and the Spanish influenza of 1918 expressed varying significant uncertainties, as pharmacists in the 23\u201330 age group , and pharmacists with bachelor\u2019s degree were both more uncertain of such knowledge.Factorial associations were established between several demographic characteristics of participants with other variables in our study. Pharmacists in hospital settings were more committed toward wearing gloves . Participants holding master\u2019s or doctoral degrees significantly expected a more severe second COVID-19 wave and they also significantly expected the occurrence of a second wave within three months . Low expectation was significantly noted by pharmacists living in the capital regarding the ability of an influenza vaccine to decrease the severity and spread of COVID-19. Lastly, pharmacists in the 23\u201330 years old age group significantly believed that a COVID-19 vaccine would be effective in COVID-19 prevention, Expectation of a second COVID-19 wave was more significantly noted by pharmacists living in the middle area of Jordan using an online survey. Our study uncovered several roles of pharmacists related to their knowledge, attitudes, and practices during the COVID-19 pandemic. These included pharmacists\u2019 commitment to protective measures and health education, which both honor the pharmacist\u2019s role of leading by example and spreading evidence based scientific information regarding this newly emerging virus, ultimately altering community response to pandemics such as COVID-19. Additionally, this study assessed several expectations of pharmacists about current and future COVID-19 pandemics.Healthcare staff, including pharmacists, have a reported increased risk of positive COVID-19 testing . This shPharmacists are pillars of a more safe and effective healthcare service. In our study, pharmacists believed they had an influential role in decreasing COVID-19 spread, and the role of hospital pharmacists was particularly prevalent. Our findings are consistent with a previous independent study completed by Mukattash. T. et al., which revealed a positive role of Jordanian pharmacists during the COVID-19 pandemic, particularly ones related to patient safety and satisfaction . HussainPharmacists are probably the most accessible members of a healthcare team , and witOur study identified specific knowledge gaps related to COVID-19 among pharmacists, as it seems like the younger aged holding bachelor degrees had uncertainties about COVID-19 pandemic having similarities to the Spanish influenza of 1918. Some perceptions in our study revealed gender variations, particularly male pharmacists believed more that they had a role in decreasing COVID-19 spread, while female pharmacists believed they knew more about the difference between influenza and the COVID-19 pandemic. Several studies tried to establish relationship between an influenza vaccine and COVID-19, especially the concept of trained immunity ,23. In oPharmacists expressed high expectation of a second COVID-19 wave, but as we dug into our findings, pharmacists with higher education degrees believed more that the second wave will be more severe and the second wave was to be expected within three months by the time they filled out our survey. Nevertheless, pharmacists in our study believed more that the coronavirus vaccine will be effective in COVID-19 prevention. Our findings are consistent, in terms of positive intentions, with a study among French healthcare workers, including pharmacists who were motivated to get the novel COVID-19 vaccine .Pharmacists\u2019 role as professional frontline healthcare members must be supported considering the accumulated evidence of pharmacist\u2019s role as health educators, and interprofessional communicators for the better health of patients and sustainability of health care system, especially during crises and pandemics, such as COVID-19.Limitations of this study include the involvement of an online survey instead of in-person encounters, causing a small number of respondents due to poor response rates; the reliability and authenticity of the study data might be affected since it was obtained through social network platforms (Facebook and WhatsApp). Nevertheless, these social network platforms are considered official ways of communication in Jordan. Considering the physical and social distancing measures during the current COVID-19 pandemic, using such methodology was the best possible approach. Other alternative and more authentic approaches could have been used but we had concerns of reduced engagement with participants as they might not frequently check their emails. Data representation of our study population might pose a limitation, since most participants are from the capital of Jordan, Amman, where most healthcare facilities are located.Pharmacists are part of the healthcare team and have a great responsibility toward public health during crises and pandemics such as COVID-19. By their exemplary actions, pharmacists in Jordan are committed in using protection measures to minimize the spread of COVID-19 to self and others. Health education and public health awareness are both crucial positive roles of pharmacists, and so comes great responsibility upon pharmacists to stay updated in order to provide evidence-based information to the public and other professionals. Media streaming of health-related information should not be taken lightly, and future measures are recommended to ensure their validity and credibility, which is directly reflected on public and professional common knowledge of our health and diseases."} +{"text": "Promising technologies, which are simple, portable, quick, non-invasive, and inexpensive, may open new horizons on fall risk assessments and provide important information for older adults. We used a mixed-methods approach to examine the feasibility and acceptability of technology-based fall risk assessments, including the BTrackS Balance System, Bioelectrical Impedance Analysis, and activity monitoring devices among older adults. Data were collected via a Qualtrics survey and interviews. The acceptability was measured by the Senior Technology Acceptance (STA) and semi-structured interviews with 15 participants. The STA consists of four domains with 14 items, and the semi-structured interview includes three main questions related to experiences about balance performance tests, body composition, and activity monitoring. One hundred twenty-four community-dwelling older adults completed the online survey, and 15 older adults participated in the interviews. The majority of participants were female, and 72% had no history of falls. Race and ethnicity were 17% Hispanic, 7% African Americans, and 3% Asian Americans. About 7% had COVID-19 positive, 31% reported fear of COVID, and 14.5% were afraid of losing their life to COVID. The word-of-mouth strategy and key person approach were used and had an incredible impact on the recruitment process. None of the participants had ever had their fall risk and fear of falling assessed before agreeing to participate in this study. The technology-based fall risk assessments were feasible and acceptable. About 78% of participants liked the idea of using technology to assess falls risk, and 79% agreed that using technology would enhance their effectiveness in daily activities."} +{"text": "Promising technologies, which are simple, portable, quick, non-invasive, and inexpensive, may open new horizons on fall risk assessments and provide important information for older adults. We used a mixed-methods approach to examine the feasibility and acceptability of technology-based fall risk assessments, including the BTrackS Balance System, Bioelectrical Impedance Analysis, and activity monitoring devices among older adults. Data were collected via a Qualtrics survey and interviews. The acceptability was measured by the Senior Technology Acceptance (STA) and semi-structured interviews with 15 participants. The STA consists of four domains with 14 items, and the semi-structured interview includes three main questions related to experiences about balance performance tests, body composition, and activity monitoring. One hundred twenty-four community-dwelling older adults completed the online survey, and 15 older adults participated in the interviews. The majority of participants were female, and 72% had no history of falls. Race and ethnicity were 17% Hispanic, 7% African Americans, and 3% Asian Americans. About 7% had COVID-19 positive, 31% reported fear of COVID, and 14.5% were afraid of losing their life to COVID. The word-of-mouth strategy and key person approach were used and had an incredible impact on the recruitment process. None of the participants had ever had their fall risk and fear of falling assessed before agreeing to participate in this study. The technology-based fall risk assessments were feasible and acceptable. About 78% of participants liked the idea of using technology to assess falls risk, and 79% agreed that using technology would enhance their effectiveness in daily activities."} +{"text": "Burnout is a psychological syndrome that emerges in response to emotional and interpersonal work-related stressors. Its main manifestations are exhaustion, depersonalization, and inefficiency . The preThe following factors are associated with a higher prevalence of burnout among physicians: female gender, young age, long work hours, low job satisfaction, and conflicts between professional and personal life . Other fBurnout negatively affects patient care and healthcare systems, decreasing patient satisfaction, increasing medical errors and job switching, and leading to early retirements . It permth, 2020, the World Health Organization (WHO) reported that an unprecedented coronavirus strain (Sars-CoV-2) caused the outbreak of viral pneumonia, Covid-19, in Wuhan, China. On January 30th, 2020, with 98 confirmed cases of the disease in 18 countries other than China, WHO Director-General declared the global outbreak of Covid-19 a public health emergency of international concern .st, 2020, and each urologist was asked to send it to their teammates. The physicians agreed to the informed consent form before filling the questionnaire. We closed collections on July 30th, 2020.Brazilian urologists practicing during the Covid-19 pandemic and six months prior were eligible for the study. An anonymous questionnaire on the Google Forms platform was sent to Brazilian urologists on July 1We developed the questionnaire to assess the prevalence of burnout, stress, and poor sleep quality among Brazilian urologists during the pandemic. It consisted of demographic and clinical practice questions , and the following questionnaires: Copenhagen Burnout Inventory (CBI), Perceived Stress Scale - 10 (PSS-10), and Pittsburgh Sleep Quality Index (PSQI).We assessed burnout using the CBI, which consisted of 19 questions divided into three domains: personal burnout, work-related burnout, and patient related burnout. We considered burnout significant when the score was greater than or equal to 50% in each domain or on average. We assessed stress perception using the PSS-10, which consisted of ten questions and whose final measure is classified as low (0-13), moderate (14-26), or high (27-40). We assessed sleep quality through the PSQI, which comprised seven components. When the sum was greater than five, we considered this to indicate poor sleep quality.We assessed the association between qualitative variables using the Fisher's exact test. We used the Mann-Whitney U test for independent samples with two categories to compare the means, and the Kruskal-Wallis test for samples with more than two categories. We tabulated the data in a Microsoft Office Excel spreadsheet and analyzed it using the IBM Statistical Package for the Social Sciences (v.20.0). The significance level was 5% (p <0.05).A total of 165 urologists answered the questionnaire, namely 127 men (77%) and 38 women (23%). Physicians from throughout Brazil participated, with a predominance of the Southern region , followed by the Southeastern region . Out of all questionees, 52.8% (87) work in an academic institution, and 45.5% (75) work exclusively in non-academic institutions. Additionally, 83.9% (125) work in teams with other urologists, 67.9% (112) spent less than 20 hours a week in hospitals, and 48.5% (80) dedicated less than six hours a week to surgical practice during the pandemic.Regarding the CBI results, 7.87% experienRegarding the PSS-10 results, 57.57% (95) of the urologists showed a moderate to high perceived stress during the pandemic, with a significant association with gender (p=0.043): 73.68% (28) of women and 52.75% (67) of men had a moderate to high perceived stress.Regarding the PSQI results, 44.84% (74) of the urologists had a poor sleep quality, with 60.5% of womenThere was a significant association between sleep quality and overall burnout (p=0.008) , work-reOurs is the first study that evaluated burnout, stress and sleep disorders among Brazilian urologists. Burnout rates in urology gained prominence when Dr. Shanafelt published an update to his 2011 study with 2014 data, demonstrating a significant increase in burnout rates - which were already high - among urologists over this period (greater than 20%) . AccordiThe rates found in our study are lower than those previously published with U.S. data , 3, evenWhen comparing the average levels of burnout between men and women, our study found significantly higher personal burnout (p=0.005) and work-related burnout (p=0.001) in women. When assessing stress levels, women also had significantly higher levels of stress than men p=0.043). These findings are compatible with previous publications that indicate higher levels of burnout among women in surgical specialties, confirming that the female gender is a risk factor for burnout among physicians. However, the study carried out with American urologists in the AUA census does not present the same association of the urologists had poor sleep quality during the pandemic, with no significant difference between genders. We found an association between sleep quality and levels of overall (p = 0.008), work-related (p = 0.009), and personal (p <0.001) burnout. This finding is consistent with studies showing that poor sleep quality is a risk factor for burnout of urologists had poor sleep quality and 57,57% (95) of urologists had moderate to high perceived stress levels. Additionally, we also found an association between stress levels and overall (p <0.001), work-related (p <0.001), and personal burnout (p <0.001) levels. The individual's control under daily life circumstances impacts their perceived stress. During a pandemic, there is a decrease in the predictability of events, especially among health professionals, who had their work routines significantly changed, including the telemedicine's emergency implementation to maintain urological care quality and avoid the risk of disseminating Covid-19 (A positive aspect of our study is that it is the first of its kind to assess aspects of mental health in Brazilian urologists. Despite the limitations of a survey study, we obtained a representative sample of Brazilian urologists working during the pandemic. Additionally, it is the first study to evaluate burnout, stress and sleep disorders in urologists during the pandemic.Burnout prevalence in Brazilian urologists during the Covid-19 pandemic was lower than previous U.S findings but consistent with the burnout rates among Brazilian physicians. We found a high level of stress and poor sleep quality and also a significant association between stress and poor sleep quality with burnout levels among urologists."} +{"text": "The experience of the COVID-19 pandemic may vary widely by race. This study examined race differences in pandemic-related stress, social isolation and the implications for well-being. Participants included 1260 adults (45% women) ages 18 to 97 from the May and June 2020 nationally representative Survey of Consumers and 562 who completed a 6 month follow up in November/December. A total of 76% were White, 10% were Black, 3% were Asian, and 11% were Hispanic. Participants reported experiences of pandemic-related stress, social isolation and depressive symptoms in the last month. Analyses showed that minority groups reported greater pandemic related stress that had negative implications for depressive symptoms over time. The implication of social isolation for the stress-depressive symptoms link also varied by race. Overall this study showed racial inequities in the implications of COVID-19 pandemic and that reducing social isolation may only be beneficial for certain racial/ethnic groups."} +{"text": "Since the first confirmed case being identified in January 2020, authorities in Hong Kong have implemented various measures in an attempt to control the spread of the disease. These measures include compulsory quarantining of infected persons and those suspected of exposure, temporary closure of high-risk premises, and suspension of public activities and services, encouraging work-from-home arrangement etc. These measures, however, may exacerbate the impact of known risk factors and create new avenues for elder mistreatment. Life stress, financial strains and work-from-home arrangements increase chances of family conflicts, cessation of public services increases burden in the already stressed caregivers. This study examines the changing intergenerational family relations in the midst of the pandemic. A total of 1200 community dwelling senior citizens participated through responding to a telephone survey. Information was collected on participants\u2019 demographic characteristics, perceived disruptions brought about by COVID-19, family relations, physical and mental health, etc. Family conflicts and abuse were commonly reported: 27.8% reported family conflicts, 14.5% psychological abuse, 3.1% physical abuse, 3.9% financial abuse. A large proportion of participants (41.8%), however, also reported improved family relations during the pandemic. Results of logistic regression indicate that advanced age, female gender, poor financial situation were significant predictors for family conflicts and abuse. Contrary to our expectations, pandemic related disruptions in daily lives and perceived safety in the community were not associated in family conflicts and abuse in the present sample."} +{"text": "Methods: This is a longitudinal survey-based study conducted on 1138 adult South African pilgrims in two phases (during and post-Hajj). Data on demographics, vaccination status, underlying health conditions, pre-Hajj training, health promotion, travel history, and health issues during and post-Hajj were collected using pre-designed questionnaires. Results: Participants had a mean age of 49.2 years , with a male: female ratio of 1.2:1. The majority of pilgrims were married (88.2%), of Indian/Asian background (73%), and literate (>99%). Nearly all pilgrims were vaccinated against meningococcal disease and yellow fever, but only 23.7% were vaccinated against Influenza. Hypertension, diabetes, and elevated cholesterol levels were the most common underlying health conditions reported by 22.6%, 13.2%, and 11.5% of pilgrims, respectively. One month after return to South Africa, nearly 65% of pilgrims reported illness during Hajj, while 40% reported falling ill post event upon return to South Africa. Nevertheless, only a few were admitted to hospitals (12 during Hajj and 15 post-Hajj). Among ill pilgrims, respiratory symptoms were the most commonly experienced symptoms during (70.2%) and post-Hajj (82.2%). Other symptoms such as walking-related symptoms include symptoms directly related or mainly caused by walking , dehydration, and gastrointestinal tract symptoms reported during Hajj. Medication to treat respiratory symptoms and antibiotics were the most commonly used medications during and post-Hajj. Having an underlying health condition was an independent predictor of falling ill during or post Hajj. Conclusion: Our study indicates that a sizable proportion of South African pilgrims are elderly with underlying health conditions and most contract respiratory tract infections during and post Hajj. Our study highlights the need for systematic collection of prospective pilgrims\u2019 demographics and health data and more attention to post-Hajj health follow-ups of pilgrims.The Hajj mass gathering annually attracts over two million Muslim pilgrims worldwide to the Kingdom of Saudi Arabia (KSA). We aimed to establish demographics and health profiles for the South African pilgrims performing the 2017 Hajj. Hajj is an annual religious mass gathering in Makkah, Saudi Arabia (KSA) and attracts over two million Muslim pilgrims. Although the actual Hajj rite does not last for more than five days, many pilgrims extend their stay in Makkah and the surrounding cities, usually arriving early, departing late, or both for various reasons. Pilgrims originate from over 180 different countries with varying ethnicities, cultures, languages, and socio-economic and health backgrounds . These hMass gatherings such as the Hajj pose significant public health challenges and stress the host\u2019s health system. Therefore, timely and appropriate planning for the event is crucial. KSA authorities employ a well-established system for planning, communication, public health, and Hajj safety issues . This inWe aimed to collect data on South African pilgrims and their health pre, during, and post Hajj to determine their demographics and health profiles and the impact of Hajj on their wellbeing.This longitudinal survey-based study was conducted in two phases, through which data was collected from pilgrims who agreed to participate, using pre-designed questionnaires. The questionnaire was in English administered through trained investigators. The questionnaire was developed reviewing available publications in the literature but was tailored for the study objectives and Hajj setting ,16,17,18Hajj phase: Data on pilgrims\u2019 demographics , vaccination status, underlying health conditions, pre-Hajj training, and health promotion, as well as travel history, was collected during Hajj in KSA from the 23rd of August to the 20th of September 2017.Post-Hajj phase: Pilgrims were followed-up, one month after their return to South Africa from Hajj, through phone call interviews. Data was collected on health issues during and post-Hajj in South Africa from the 13th of October 2017 to the 5th of February 2018. This included information on illness symptoms, symptoms, diagnosis, medications prescribed and visits to healthcare facilities or hospitals\u2019 admissions.Our study targeted all adult South African pilgrims (>18 years old) who attended the 2017 Hajj and consented to participate. A total of 1138 pilgrims were enrolled in this study.p-value of <0.05 was considered statistically significant. Odds ratios with 95% CIs were computed to assess the presence and degree of association between the dependent versus independent variables. Variables with p-value <0.05 at the bi-variate analysis were taken for multivariate analysis. All analyses were performed using IBM SPSS Statistics version 25.0 .The study population\u2019s characteristics were summarized as frequencies and percentages for categorical variables and means, range, and standard deviations (SDs) for quantitative variables. The association between explanatory variables and outcomes was evaluated by the Chi-Square test or Fisher\u2019s exact test, as appropriate . All sigAll study participants were briefed about the study and gave verbal consent before enrolment. The study was approved by the King Fahad Medical City Ethics Committee, the Institutional Review Board (IRB log: 17-244E), and the Biomedical Research Ethics in the University of KwaZulu-Natal, South Africa (IRB log: BE491/17).Of the 2500 South African pilgrims who attended the 2017 Hajj, 1138 (45.5%) were eligible and agreed to participate in the study; among participants, 80.5% was the response rate for post hajj follow up. The participants had a mean age of 49.2 years , with a male:female ratio of 1.2:1. Most pilgrims, 91% (1000/1098), had at least a secondary education, and nearly all could read 99.7% (1124/1127) and write 99.6% (1108/1112). The age and level of education distribution by gender are presented in A large proportion of pilgrims, 73% (476/652), were of Indian/Asian background , and theThe majority of pilgrims 98.4% (1113/1131) reported being vaccinated against meningococcal disease using the quadrivalent conjugate vaccine. About 95.2% (1082/1137) were vaccinated against yellow fever, 23.7% (241/1019) received the influenza vaccination, and only 4.7% (48/1019) were vaccinated against pneumococcal disease. Hypertension, diabetes (mainly Type 2), and elevated cholesterol levels were the most common health conditions reported by 22.6% (239/1057), 13.2% (139/1057) and 11.5% (122/1057) of pilgrims, respectively. Allergy was reported in only 8% (84/1058) of pilgrims , while chronic respiratory illnesses were reported in 6.8%. (72/1055) . The disRegarding training and health promotion before arrival to KSA, 90.5% (1019/1126) of pilgrims declared that they had received training on the Hajj journey and rituals. Similarly, most pilgrims reported that they knew where to seek medical care in KSA 76.6% (863/1126) and the location of their medical missions during Hajj 66.3% (738/1113). About 66.5% (733/1103) of pilgrims reported having been briefed about possible health risks to expect during their stay in KSA, mainly related to heat and respiratory illnesses . Most ofOver 25% (273/1086) of the participants mentioned suffering from a cough upon arrival to Saudi Arabia, 9% (89/1083) mentioned having a fever , and 9.7% (105/1083) reported having diarrhea. Vomiting appeared in only 2.3% (25/1056) of participants and lasted for less than three days in most cases, while 11% (119/1088) reported suffering from a headache, mostly for less than a week.p-value = 0.00). Only 12 participants were admitted to the hospital during Hajj, most 66.6% for only one day. Post-Hajj, 15 pilgrims were admitted to hospitals in South Africa for a mean duration of 6.4 days (SD = 5.7).About 65.1% (596/916) of the participants had fallen ill during Hajj, and 31.6% reported suffering at least two illness episodes during the pilgrimage. The mean duration of illness episodes during Hajj was 3.5 days (SD = 2.9). Nearly 40% (365/915) of pilgrims also reported that they got sick post-Hajj, displaying symptoms on average four days (SD = 5.6) after returning home. There were significantly more pilgrims who fell ill during Hajj than post Hajj . Among ill pilgrims, respiratory symptoms were found to be significantly higher post-Hajj than during Hajj, with 70.2% (413/588) and 82.2% (287/349), respectively . On the other hand, gastrointestinal tract (GIT) symptoms were significantly more common during Hajj compared to post Hajj (5.4% (32/588) vs. 1.4% (5/349), p-value = 0.002). Similarly, dehydration was only reported during Hajj in 10.9% of ill pilgrims. Walking-related symptoms and injuries were reported in 10% (59/588) of ill participants during Hajj and in 7.1% (25/349) post-Hajj .Respiratory symptoms were the most commonly experienced symptoms among the pilgrims during and post-Hajj (p = 0.003) and not having previously performed Hajj were significantly associated with increased risk of falling ill during Hajj. In the multivariate analysis, pilgrims with underlying health conditions were 1.6 times more likely to fall ill during Hajj . Similarly, pilgrims with underlying health conditions were 1.4 times more likely to fall ill post-Hajj .In the bivariate analysis, having an underlying health condition .Regarding medical diagnosis, our study results showed that diagnosis with respiratory and hypertension as well as muscle-related illness were all significantly more common in Hajj than post Hajj . Respirap-value = 0.000).The South African Medical Mission Clinic was the most visited healthcare provider during Hajj (87.7% (522/596)), while private hospitals were the most visited post-Hajj in South Africa 57% (208/366). Furthermore, self-treatment was significantly higher post-Hajj compared to during Hajj (37.5% (137/569) vs. 17.1 (102/366) Our study aimed to collect data on demographics and the health of South African pilgrims pre, during and post Hajj. The study enrolled all adult pilgrims who agreed to participate, encompassing nearly half of all the South African pilgrims who participated in the 2017 Hajj. Hence, giving the best representation of the demographics and health profile of South African pilgrims to date. The study also reports on health issues experienced by pilgrims during and post Hajj and highlights the high rates of respiratory tract infection and antibiotic use during and post pilgrimage.We report that South African pilgrims represent the general Hajj population in relation to gender, age, and underlying health conditions. The General Hajj population has a slightly higher proportion of males, is dominated by older pilgrims, many with underlying health conditions ,20,21,22Additionally, our study revealed a very high literacy level among South African pilgrims, with a large proportion (91.1%) having a secondary of higher education. Reported levels of education among pilgrims varied depending on the studied populations. One study among pilgrims from South Africa, Nigeria, Pakistan, Egypt, Iraq, and Indonesia in 2017 found that 83.7% had secondary or higher education . A similIn this study, 40% of respondents had at least one underlying health condition, with 22.6% having hypertension and 13.2% being diabetic. These results are in accordance with other reports showing that a sizable proportion of Hajj pilgrims have underlying health conditions, with diabetes and hypertension being the most common . StudiesGiven the potential for the rapid spread of infectious diseases during Hajj, the Hajj health requirements for pilgrims are focused on vaccination to minimize the risk of disease and outbreaks during and post event. Meningococcal vaccination has been compulsory for all pilgrims, including South Africans since 1988 . BesidesWe investigated the impact of Hajj on pilgrims\u2019 health through tracing developed symptoms, visits to healthcare facilities, medical diagnosis, and dispensing of medications during and after the event. Our study results confirm previous reports that respiratory infections are the most common diseases experienced by pilgrims and are among the main reason for visits to healthcare facilities and dispensing of medications during Hajj, including among South African pilgrims ,12,24,25The pattern of medication prescribed to pilgrims pre-and post-Hajj was in accordance with symptoms experienced by pilgrims. Given infections were the most common illnesses among pilgrims, medications to relieve symptoms of such infections and well as antibiotics were commonly prescribed. Besides, vitamins likely used to boost the pilgrims\u2019 nutrients and immune system, as well as analgesic medications were also commonly prescribed. A recent study on medication prescribing patterns among outpatients in Hajj found that the most common classes of prescribed drugs were anti-inflammatory medicines, analgesics and antipyretics, antibacterials, cough, and cold preparations, antihistamines, and drugs for acid related disorders . SimilarHajj is a unique experience and pilgrims need to be adequately informed about all aspects of the pilgrimage prior to arrival to KSA, including health risk and how to access medical services during the event. In our study, while a sizable proportion of pilgrims had visited KSA and performed Umrah previously, for most of them, it was their first time performing Hajj. While these two mass gatherings take place in the same location, they different in many aspects including crowdedness, duration, rituals, and health risks , which hAdditionally, given the Hajj location and a heat-vulnerable pilgrim population, heat-related illnesses are considered public health threats during the event, especially when it is held in the summer months, as was the case during our study period . HoweverGiven the international nature of the Hajj, the crowded conditions at the event and the constant movement of pilgrims during the Hajj journey, tracking pilgrims\u2019 health and provision of health services can be challenging. Active and real-time surveillance are applied during Hajj, including a recently implemented syndromic and event-based health early warning system ,50. HoweThis study has some limitations. Although we systematically invited all eligible pilgrims to participate, only 45.5% of pilgrims agreed and were enrolled. Additionally, we used questionnaires and interviews to collect information from pilgrims during and post Hajj. As such, responses obtained are prone to information bias, particularly recall bias. Nevertheless, our study is the first to collect information on the health of nearly half of the South African pilgrim population pre- during and post Hajj and reporting on Hajj\u2019s impact on the health of these pilgrims. Future studies should investigate a more significant number of pilgrims from more countries with larger pilgrim populations, such as India and Indonesia.In summary, our study indicates that the South African Hajj population is representative of the general Hajj population in terms of gender composition and age and that of the South African (in particular the Indian/Asian) population in terms of socio-economic status and underlying health conditions. Pilgrims appear to have been informed about where to seek medical assistance during Hajj and about some of the leading health risks during Hajj. Additionally, pilgrims did adhere to the required vaccinations for the pilgrimage. Around two-thirds of pilgrims had fallen ill during Hajj and one-third reported suffering illness post event. In both instances, respiratory infections were by far the most common cause of illness. A pattern of medication prescribing both during and post Hajj was in accordance with illnesses and symptoms reported by pilgrims, with frequent use of antibiotics and medications to relieve symptoms of respiratory illnesses. Our results highlight the need for a unified data sharing platform for Hajj pilgrims among Hajj stakeholders that capture pilgrims\u2019 demographics and health information pre, during and post event . As such"} +{"text": "Atrial fibrillation (AF) is the most commonly diagnosed arrhythmia, and ECG remains the gold standard for diagnosing AF. Wrist-worn technologies are appealing for their ability to passively process near-continuous pulse signals. The clinical application of wearable devices is controversial. Our systematic review and meta-analysis qualitatively and quantitatively analyze\u00a0available literature on wrist-worn wearable devices and their sensitivity and specificity in detecting AF compared to conventional methods.\u00a0Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed, yielding nine studies .\u00a0Observational studies assessing the sensitivity and specificity of wrist-worn wearables in detecting AF in patients with and without a history of AF were included and analyzed using a fixed-effect model with an inverse-variance method.\u00a0In patients with a history of AF, the overall sensitivity between device groups did not significantly differ . Specificity significantly differed between Apple, Samsung, and KardiaBand . The effect size for this analysis was highest in the Samsung device group. Two studies (n = 796) differentiated cohorts to assess device sensitivity in patients with known AF and device specificity in patients with normal sinus rhythm (NSR) 93.85%-97.59% and specificity: 98.82%; CI:97.46%-99.57%). Wrist-worn wearable devices demonstrate promising results in detecting AF in patients with paroxysmal AF. However, more rigorous prospective data is needed to understand the limitations of these devices in regard\u00a0to varying specificities which may lead to unintended downstream medical testing and costs. Atrial fibrillation (AF) is the most commonly diagnosed arrhythmia in clinical practice . It is eWhile AF typically presents with palpitations, dyspnea, chest pain, and fatigue, it is estimated that a 10-40% incidence of AF is asymptomatic . SubclinInterpretation of a 12-lead electrocardiogram (ECG) by a trained cardiologist or heart rhythm specialist is the gold standard for detecting AF . The 201While it is clear that more evidence is needed to illustrate the advantages of early screening protocols, studies have demonstrated that active screening for undiagnosed AF has proven to be effective starting at an age of 40 years . FurtherAn increasing number of individuals use commercially available wearable technology, which has paralleled innovation in the mobile health space. mHealth has been an avenue for expanding AF detection beyond traditional cardiac telemetry. Currently, mHealth technology utilizes electrocardiographic or photoplethysmographic (PPG) signal processing to detect AF . While EObjectiveObservational clinical studies measuring the accuracy of wearable devices in detecting AF demonstrate\u00a0promising outcomes. This novel development has garnered significant interest in the field of cardiology over the past five years due to the recent FDA clearance of multiple mobile technologies for AF detection . HoweverTo date, there are several reviews that look at the use of wearable devices for the detection of AF -15. OnlyMethodsThis systematic review and meta-analysis was conducted using the PICO method and followed the framework outlined in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines .Search strategyA comprehensive search of several databases from each database\u2019s inception to July 27th, 2020, English language, was conducted. The databases included Ovid MEDLINE(R) and Epub Ahead of Print, In-Process & Other Non-Indexed Citations, and Daily, Ovid EMBASE, Ovid Cochrane Central Register of Controlled Trials, Ovid Cochrane Database of Systematic Reviews, and Scopus. The search strategy was designed and conducted by an experienced librarian with input from two authors (S.B and W.W). Controlled vocabulary supplemented with keywords was used to search for data collection accuracy of wearables and their efficacy in predicting outcomes in AF.Study selection criteriaStudies were included for review if they met the following criteria: involve human subjects, collect EKG data, assess the accuracy of wrist-worn wearables, diagnose atrial fibrillation, and published within the past five years (2016-2020), due to the increase in digital health technologies since the FDA\u00a0approval for the AliveCor Kardia device as the first wearable technology to detect AF . StudiesQuality assessmentThe quality of outcomes was assessed using the GRADE methodology, while studies\u2019 quality of evidence was assessed using the modified Newcastle-Ottawa Scale ,19.Data extractionEligible studies were pooled according to the aforementioned inclusion and exclusion criteria. Data extraction from articles, tables, and figures was pulled by one reviewer (S.B) and accuracy of data entry was verified by a second reviewer (W.W). Data collected included: study author, year of publication, type of device used, sample size, number of recorded events, method of AF verification, true positive, true negative, false positive, false negative, specificity, and sensitivity Table .Statistical analysisA meta-analysis of diagnostic test specificity and sensitivity was conducted, with results represented as effect sizes (ES) with corresponding 95% confidence intervals (CIs). A fixed-effect model with an inverse-variance method\u00a0was used -31. HeteResultsSearch ResultsOur search strategy yielded a total of 2113 unique articles. After removal of 1263 articles that were published prior to 2016 and 39 articles that concerned a pediatric population, inclusion/exclusion criteria were applied to abstracts of the remaining 814 articles. This resulted in 28 articles that underwent full-text analysis, of which nine met the predefined eligibility criteria and were included in the qualitative and quantitative synthesis , and three regarding Samsung devices -28. In tSensitivityThe overall sensitivity between device groups was not statistically significant P = 0.276). Apple devices had an average sensitivity of 97.9% (95% CI: 96.1% to 99.7%), KB with 96.9% (95% CI: 94.7% to 99.2%), and Samsung devices with 95.5% (95% CI: 93.1% to 97.8%). Overall sensitivity across all devices was 97.0% (95% CI: 95.8% to 98.2%) . Apple devices had an average specificity of 99.61% (95% CI: 98.9% to 100.32%), KB with 81.13% (95% CI: 75.19% to 87.08%), and Samsung devices with 97.96% (95% CI: 96.71% to 99.22%). Overall sensitivity across all devices was 99.02% (95% CI: 98.41% to 99.63%) . Our results also indicate that the sensitivity was sustained across all three devices .However, this research demonstrates that specificity differs significantly between device groups . A specificity funnel plot revealed that there might be some publication bias with regards to the KardiaBand studies. Furthermore, a specificity forest plot revealed a wide confidence interval for one of the included Apple studies. This forest plot also demonstrated that the mean of both KardiaBand studies fell short of the overall average Figure .Clinical significance and future directionsThis study demonstrates clinical significance with regards to specificity between device groups, indicating that there is some discrepancy between how these device groups interpret \u201cnormal sinus rhythm\u201d (NSR) or \u201cnot normal sinus rhythm.\u201d This type of diagnostic information can add value as a screening tool for patients who are either at risk for AF or patients who have had a stroke and are seeking to understand whether it may have been of cardiac origin.The majority of the studies included patients with some form of cardiac medical history, such as AF. It is important to test these devices in patients who were never diagnosed with AF. This will provide more accurate information on the potential for these devices to be used as a diagnostic screening tool.LimitationsThere are limitations that should be considered with this study. First, an indirect comparison was performed for this meta-analysis. Second, given the sample sizes, a small number of true negatives and false positives may have influenced the specificity. With this in mind, a number of false positives may have artificially inflated the specificity. Lastly, one of the studies included in this analysis was from Apple, Inc but it was not published in a peer-reviewed journal.In conclusion, this research demonstrates that wrist-worn wearable devices offer promising results in detecting AF in patients with paroxysmal AF. However, caution is needed in all three devices regarding the use of this technology to detect NSR in patients with and without a history of AF. This research suggests that more rigorous prospective data is needed to understand the limitations of these devices in regard\u00a0to varying specificities which may lead to unintended downstream medical testing and costs."} +{"text": "The main aim of this study was to investigate whether the EIT access and waiting time standard (>60% of people experiencing first episode psychosis (FEP) are treated with a NICE-approved care package within two weeks of referral) was being met within Liverpool EIT.We also wanted to understand the pathway to treatment within EIT services, identify delays in the process of triage/assessment/MDT/medical review and implement changes to reduce delays.This study was a retrospective cross-sectional audit of all patients accepted on to the FEP pathway following MDT discussion in the Liverpool EIT Teams across May and June 2020.Case notes were analysed for delays in referral, engagement with assessment and care-coordinators, as well as prescriber review offering medication. The data were collated and analysed before implementing changes.40 patients presented as FEP in May and June 2020, 6 were excluded due to an extended inpatient stay.Within the remaining patient cohort (n = 34), 64.7% of patients were engaged with a care package within 14 days. Only 14.7% of patients received an offer of medication within 14 days, the mean time to be offered medication was 39 days.26% of patients first contact within MerseyCare Trust was with EIT, 74% presented elsewhere. 24% instead presented to liaison psychiatry from A&E departments, 18% to the single point of access team, 9% to criminal justice liaison team (CJLT) and 9% to North West Ambulance Service triage car.29% of referrals came from the community (GP and counselling services), 15% from CRHT (crisis resolution and home treatment team), 14% from CJLT, 12% from urgent care team, 9% from liaison psychiatry.The Access and Waiting time standard was met. However, this study showed that patients were not being referred to EIT at first point of contact. This study shows 26% of service users first presented to liaison psychiatry, yet only 1/3 of those were immediately referred to EIT, the remainder being later referred by other services e.g. CRHT.In addition to referral delays, lack of medical practitioner availability caused significant delays in arranging medical reviews, delaying patients access to medication.The changes implemented to address these issues included educating MerseyCare services in the early recognition of psychosis to increase early referral. Non-medical prescribers\u2019 roles were developed to perform initial medical reviews in addition to doctors, allowing patients earlier medication access. This allowed \u2018urgent slots\u2019 to be developed, time set aside for emergencies enabling prompt review of urgent cases."} +{"text": "Capsicum annum, Melia azedarach, Citrus reticulata and Quercus infectoria, the plant extracts showed urease inhibition activities in soils, the extent of which was lower as compared to that observed in jack bean urease though. Maximum urea hydrolysis inhibition (70%) was noted with Vachellia nilotica which was 40% more than that of hydroquinone (50%) followed by that of Eucalyptus camaldulensis (24%). The extracts of V. nilotica and E. camaldulensis were coated on urea and applied to soil in the next step. At 21st day, 239% and 116% more urea-N was recovered from soil treated with V. nilotica and E. camaldulensis extracts coated urea, respectively, as compared to uncoated urea. Conclusively, these results indicated that the coating of V. nilotica and E. camaldulensis extracts on urea prills prolonged urea persistence in soil owing to minimum urea hydrolysis, probably, the extracts of V. nilotica and E. camaldulensis showed their urease inhibition potential. The results of this study provide a base line for the identification of new soil urease inhibitor compounds from plant materials in future.Urea is the most popular and widely used nitrogenous fertilizer. High soil urease activity rapidly hydrolyses applied urea to ammonia which contributes to soil nitrogen (N) losses and reduces N use efficiency of crop plants. The ammonia losses can be minimized by the inhibition of soil urease activity which has been explored using various potential chemical inhibitors. However, the soil urease activity inhibition potential of plant extracts is rarely explored to date. In the present study, extracts of 35 plant materials were taken and evaluated against jack bean urease. Eleven extracts, showing >50% jack bean urease inhibition, were selected and further investigated in 13 soils collected from various districts of Punjab, Pakistan. Interestingly, except Owing tactivity . This raactivity , and libactivity , which iactivity . High coactivity . Furtheractivity .According to an estimation, excessive soil urease activity in different soils can lost 20\u201333% applied urea-N on an average which can reach up to 70% . MoreoveStudies involving preventing of rapid urea hydrolysis through soil urease inhibition aims to increase nitrogen use efficiency of crop plants . An incrHelicobacter pylori infection in human stomach [Acacia decurrens, seed kernel powder of Azadirachta indica and bark of Acacia caven have also been reported to inhibit ureases in different soils [Ureases are nickel-dependent proteinaceous metalloenzymes widely distributed in bacteria, fungi, algae, invertebrates and plants . These a stomach ,20,21. Hnt soils .The use of reported urease inhibitors is limited to certain areas of the world owing to the reasons like cost ineffectiveness, toxicity to crop plants, and variation in effectiveness with soil type, climate and crop management . TherefoThis work has proposed a systematic screening for natural soil urease inhibitors starting from the extraction of thirty-five plant materials. Twelve out of these thirty-five extracts have been reported to demonstrate inhibitory activities against jack bean urease, but none has been reported to show inhibition of soil urease activity to date. The study has also optimized the dose of key selected plant extracts for urea coating by studying the impact of coated urea on urea-N stay in soil.Leaves, stem bark, heart wood, fruits, fruit peel and bagasse of thirty-five plant materials were selected based on their ease of availability and cost effectiveness . Some ofDried and powdered plant materials (10 g) were transferred to conical flasks containing 100 mL of acetone each, and shaked on reciprocal shaker at 200 rpm for 48 hours to obtain extracts. The contents of the flasks were filtered using Whatman filter paper grade 1 and the filtrates were concentrated by solvent evaporation at 70\u00b0C to about 3 mL volume that was diluted to 100 mL with distilled water. The extracts were stored maximum up to three days at 4\u00b0C if not used immediately in urease inhibition assay.Jack bean urease inhibition assay was carried out following Nabati et al. with sli3-N) in the assay mixtures was determined by following the procedure of Nelson [3-N in the aliquot was estimated from the curve of NH3-N standards. Urease inhibition by a plant extract was calculated by the following formula [After 30 minutes of incubation, ammonia nitrogen is the percent urease inhibition, T and C are NHThirteen soil samples were collected from Lahore, Sheikhupura, Gujranwala, Jhang, Narowal, Okara, Khanewal, Sahiwal and Multan districts of Punjab, Pakistan. These soils have already been classified to subgroup level by Soil Survey of Punjab, Pakistan. Textures of the soils were estimated by hydrometer method . Soil or-1 and urease activity from 36 to 673 \u03bcg urea-N hydrolyzed g-1 2h-1. Ammonium acetate extractable K, Na, Ca, and Mg were varied from 0.07 to 0.27, 0.06 to 0.39, 1.30 to 5.51 and 0.41 to 1.56 mg g-1, respectively over 100 g of urea prills rotating in a rotary mixing container till uniform application of the extract over the surface of the prills. The coated urea prills were then removed from the container and dried in shade.In soil assays, maximum urea hydrolysis inhibition was noted with extract of V. nilotica and E. camaldulensis was applied at 225 mg urea-N kg-1 soil in triplicate. The pot soil was irrigated with tap water and moisture level was maintained to field capacity. The pots were placed in an open corridor at natural temperature for 21 days. Variations in daily minimum and maximum temperatures are presented in Surface field soil of 0\u201315 cm depth (soil no. 1 in Urea from the soil (2 g dry matter) was extracted with 2 M KCl-PMA (KCl-phenyl mercuric acetate) solution. A known volume of the extract was then incubated at 85\u00b0C for 45 minutes with a 5:2:100 mixture of diacetyle monoxyme (DAM) solution, thiosemicarbazide (TSC) solution and acid reagent in test tubes. After incubation the test tubes were immediately cooled in running tap water and red color intensity of the contents was measured using spectrophotometer at 527 nm .The data of all the experiments were subjected to analysis of variance and means were compared by Tukey\u2019s HSD test. All the statistical analyses were performed by Statistix-8.1 software.V. nilotica and Prunus armeniaca, (both 95%), which was comparable to that of hydroquinone (94%), followed by that of E. camaldulensis (92%) and Melia azedarach (89%) , C. sinensis (black tea), Coffea Arabica, Citrus reticulata also showed more than 50% inhibition of jack bean urease (Maximum inhibition of jack bean urease was noted with ch (89%) . The extn urease .C. annum, M. azedarach and C. reticulata, increased urea hydrolysis instead of inhibition in all thirteen soils. Quercus infectoria extract increased urea hydrolysis in seven soils and inhibited it slightly up to 14% in other six soils. The data of these four extracts which stimulated urea hydrolysis in most of the soils were neither subjected to analysis of variance nor presented in this manuscript. Other seven extracts inhibited soil urease without showing any variation in their inhibition potential among the soils. Vachellia nilotica extract demonstrated maximum inhibition (70% on an average) in all thirteen soils which was 40% more than that showed by hydroquinone (49.5%). The extracts of E. camaldulensis, C. sinensis (green) and P. armeniaca followed V. nilotica and showed urease hydrolysis inhibitions of 24%, 22% and 20%, respectively, on average. Nicotiana tabacum showed 3.5% inhibition on average basis is presented in V. nilotica extract coated urea significantly increased urea recovery at all three sampling times. Recovery of urea, coated with extract of 10 g dry leaves per 100 g urea, was 16, 27 and 168% more than that of uncoated urea at 7th, 14th and 21st DOI, respectively. Coating with extract of 20 g V. nilotica leaves increased urea recovery to 23% at 7th, 45% at 14th and 239% at 21st DOI. Coating of extracts taken from 50 and 100 g leaves did not further increase urea recovery in comparison to extract of 20 g leaves increased urea recovery at any of the sampling times (Difference in urea-N recovery between uncoated and coated urea with extract of 10 g leaves of ng times .The extraction of plant materials, to study their urease inhibition potential, is carried out mostly through water, methanol or acetone as extracting solvents ,31. In oQ. infectoria, Saccharum officinarum, Allium cepa, Mentha arvensis, Santalum album, Cinnamomum verum, Olia europaea and Myristica fragrans inhibited activity of jack bean urease by 98%, 35%, 53%, 93%, 59%, 84%, 72%, and 78% respectively [N. tabacum, V. nilotica, C. sinensis and Psidium guajava showed jack bean urease inhibition comparable to or greater than that reported in literature [Twelve out of 35 investigated plant materials, in this study, are already reported to have inhibition potential against jack bean urease. In our study, most of these materials did not perform the same way as reported in literature. According to literature 50% methanolic extracts of ectively . Howeverterature ,31. Thesterature . Other fterature stage ofterature , method terature ,31.In comparison to jack bean urease, reduction in inhibition potential or failure of some plant extracts in soils was, perhaps, due to the fact that soil ureases being a mixture of plant, fungal and bacterial ureases are different from pure jack bean urease. As plant and fungal ureases are monotrimers or hexamers of about 90 kDa subunits, while bacterial ureases are multimers of two or three subunits complexes ,40. FurtThe screening through jack bean urease, in comparison to soil, is easier, free from interferences and gives precise results . These fV. nilotica and E. camaldulensis can be extracted with acetone to coat urea, particularly in the regions where these species are in abundance. These coatings can delay urea hydrolysis minimum up to three weeks to increase urea-N efficiency in alkaline soils. Further investigations regarding any possible allelopathic effects of extracts coatings on different crop plants are needed in future.The results of the experiments provide a base line for the identification and extraction of new urease inhibitor compounds from the effective plant extracts. Leaves of"} +{"text": "Trichomonas vaginalis (TV) has a prevalence of 26% in Baltimore and is associated with preterm delivery (PTD). Yet screening and treatment of TV is not advised due to conflicting data on harms. Our goal is to investigate the association between asymptomatic TV treatment and PTD. METHODS/STUDY POPULATION: This is a retrospective cohort study of women who delivered a child at The Johns Hopkins Hospital between 7/1/16 \u2013 11/19/19. Exclusion criteria included multiple gestation, stillborn, miscarriage, diabetes, hypertension/ preeclampsia, HIV, and history of PTD. Chart review and ICD-10 diagnosis codes were used to collect data on demographics, STI test results, lab encounter diagnoses, STI treatment during pregnancy, and labor encounter diagnoses. Preliminary analysis for crude incidence of PTD in asymptomatic and symptomatic women treated for TV was performed using TriNetx, a global research network compiling all de-identified data within the Hopkins system. RESULTS/ANTICIPATED RESULTS: Three hundred and eighty women were tested for TV, 240 (63%) were asymptomatic and 140 (37%) women were symptomatic. Mean ages were 26 (SD:5) and 26 (SD:5) years, respectively. Black women comprised 87% of the asymptomatic cohort and 93% of the symptomatic cohort. Women of Hispanic ethnicity were represented by 4% of the asymptomatic cohort and 7% of the symptomatic cohort. Crude incidence of PTD was 4.1% among asymptomatic women and 7.1% among symptomatic women. Incidence ratio comparing asymptomatic PTD incidence to symptomatic PTD incidence was 0.58 with 95% CI . DISCUSSION/SIGNIFICANCE OF IMPACT: Preliminary data from our study suggests there is no difference in PTD between asymptomatic and symptomatic women treated for TV. Future steps include multiple linear regression using a larger dataset. These preliminary data suggest TV should be considered for screening during pregnancy.OBJECTIVES/GOALS:"} +{"text": "ABSTRACT IMPACT: The existing literature describing immune-related adverse events (irAE) has predominantly focused on clinical trial populations, which may not be representative of the broader population receiving immune checkpoint inhibitors (ICI), so we sought to perform a comprehensive evaluation of irAE in a real-world population of cancer patients being treated with ICI. OBJECTIVES/GOALS: With a cohort of patients with malignancy treated with ICI, we characterized incidence, severity, timecourse of ir-AE. We sought to inform providers who prescribe ICI to recognize the clinical burden of irAE in an effort to more effectively communicate the benefits and risks of ICI with patients. METHODS/STUDY POPULATION: After obtaining approval from the institutional review board, we used a pharmacy database to identify adult cancer patients treated with an ICI between January 2014 and October 2018. We used electronic medical records to obtain baseline variables. Each patient was followed at each clinic visit for 12 months for development of a physician-reported irAE.For irAE, site and grade were recorded as documented by the provider. At diagnosis and each follow-up visit, we collected: 1) adjustments to ICI, immunosuppression, and hormone therapy.Continuous variables were summarized using mean and standard deviation (SD) or median and interquartile range (IQR). Categorical variables were summarized using frequencies and percentages. Time to development and resolution of irAE were calculated using Kaplan-Meier curves. RESULTS/ANTICIPATED RESULTS: Among 131 patients, two-thirds were men, and 60% were Caucasian with a mean age was 65 years. Nearly 40% had an Eastern Cooperative Oncology Group performance score of 2 or higher. A small proportion (3.1%) had an autoimmune disorder. Nearly half had lung cancer (49.6%), and several had received radiation (33.6%). Over 70% were former or current smokers. In total, 57 patients (43.5%) developed an irAE, resultng in a total of 95 irAE, at a median of 208 days . The most common irAE included dermatitis, thyroiditis, pneumonitis, and hepatitis. Of 95 irAE, half were grade 1, 30% were grade 2, and nearly 20% were grade 3 or higher. Median time to resolution was 85 days (56-183 days). DISCUSSION/SIGNIFICANCE OF FINDINGS: This study demonstrates that irAE are clinically impactful in this relatively unfit, medically complex population, which may be a more accurate reflection of patients receiving ICI in everyday practice. This study showcases that this population is susceptible to irAE, although this needs to be examined in larger, prospective trials."} +{"text": "Access to infectious disease (ID) providers has been heavily impacted by COVID-19. Telemedicine (TM) has been viewed as a promising solution to the challenges in care delivery posed by this pandemic. However, perceptions of TM among ID providers remain unclear. This study investigated the impact of TM on outpatient ID during the COVID-19 pandemic, efficacy of TM in ID clinics, which clinical conditions within ID that TM may be best suited for, and influences on provider attitudes toward TM. We conducted online surveys of outpatient ID providers via the IDSA Idea Exchange and by reaching out to large ID private practices via email. Data was collected October 2020 - April 2021 and recorded through REDCap (Research and Electronic Data Capture). Associations were calculated using Hmisc in R and p-values adjusted using B-H. Missing values were imputed by median. 108 respondents completed the survey. 70.4% were attendings, 63% were under age 50, and 65.7% practiced in academic centers. 55.7% somewhat or strongly agreed there was a decline in outpatient visits. A median of 40% of outpatient visits during COVID were reported to be conducted via TM, divided equally between telephone and televideo (TV). 71.9% of providers somewhat or strongly agreed that TV visits were more effective than telephone visits. Reasons cited for TM as less effective than in person visits included lessened ability to examine the patient, diminished rapport, and inability to perform labwork. 85.2% somewhat or strongly agreed that patients responded favorably to TM. 89.8% of providers somewhat or strongly agreed they will continue to conduct TM visits when appropriate after COVID-19. Plans to continue TM after COVID were significantly associated with perceptions of patient response to TM. Respondents mentioned specific problems less suited to TM: new HIV patients, skin, soft tissue, and joint infections, fever, abdominal pain, transplant evaluations, rash, and wounds.The majority of providers felt their patients responded favorably to TM. Most providers plan to conduct TM visits after COVID-19. These plans are associated with views of patient response and comparability to other visit types. Specific diagnoses were cited as better suited for TM. All Authors: No reported disclosures"} +{"text": "The etiology and optimal clinical management of acute febrile illness (AFI) is poorly understood.Blood samples taken from study participants with acute fever (\u226537.5\u00b0C) or a history of fever and recruited into the previous Typhoid Fever Surveillance in Africa (TSAP) study were evaluated using a polymerase chain reaction (PCR)-based TaqMan-Array Card designed to detect a panel of bacterial, viral, and parasitic pathogens. Clinical metadata were also assessed.Plasmodium spp., accounting for 47% (25 of 53), 2.2% (8 of 364), and 45% (90 of 198) of AFI at the respective sites. In Madagascar, dengue virus was the most prevalent pathogen (10.2%). Overall, 69% (357 of 516) of patients with clinical diagnoses of malaria, respiratory infection, or gastrointestinal infection were prescribed a World Health Organization guideline-recommended empiric antibiotic, whereas only 45% (106 of 237) of patients with pathogens detected were treated with an antibiotic exerting likely activity.A total of 615 blood samples available for analysis originated from Burkina Faso (n\u2005=\u200553), Madagascar (n\u2005=\u2005364), and Sudan (n\u2005=\u2005198) and were taken from participants ranging in age from 0\u201319 years. Through the TaqMan-Array Card, at least 1 pathogen was detected in 62% (33 of 53), 24% (86 of 364), and 60% (118 of 198) of specimens from Burkina Faso, Madagascar, and Sudan, respectively. The leading identified pathogen overall was A PCR approach for identifying multiple bacterial, viral, and parasitic pathogens in whole blood unveiled a diversity of previously undetected pathogens in AFI cases and carries implications for the appropriate management of this common syndrome. Children and adolescents with acute febrile illness at 3 African sites underwent testing for multiple bacterial, viral, and parasitic pathogens in whole blood, revealing a diversity of pathogens with important implications for appropriate management of this common syndrome. In African and other low- and middle-income countries, up to 80% of children who visit a healthcare facility present with an acute febrile illness (AFI) . AFI is Salmonella Typhi and invasive nontyphoidal Salmonella through blood culture. In this study, we investigate the presence of pathogens in whole blood specimens collected from children and adolescents enrolled in the TSAP study using a multiple polymerase chain reaction (PCR) approach with the goal of obtaining additional insights into the etiology of AFI.The Typhoid Fever Surveillance in Africa Program (TSAP) was a multisite fever surveillance study conducted prospectively in 10 sub-Saharan African countries . The proWe analyzed venous blood samples collected at the time of enrollment into TSAP between 2011 and 2013 for which sufficient volume was still available; samples had been maintained at \u201380\u00b0C and were shipped on dry ice for testing in 2018. Samples were available from Burkina Faso, Sudan, and Madagascar , and we 6 copies) and MS2 bacteriophage (107 copies) were added to monitor extraction and amplification efficiency. One extraction blank control was included for each batch to exclude contamination [The PCR-based TaqMan Array Card (TAC) system used in mination , 20. No mination . Cards wz scores for height for age were generated using WHO growth standards [P values <.05 were considered statistically significant.Analyses were performed using STATA statistical package and SPSS version 26. When evaluating hemoglobin values, the site-specific altitude was used to adjust the values according to World Health Organization (WHO) guidelines , 23. Agetandards , 25. BodWe tested 615 blood samples from individuals who presented with AFI; 8.6% (53 of 615) of patients from Burkina Faso, 59.2% (364 of 615) from Madagascar, and 32.2% (198 of 615) from Sudan. Study participants ranged in age from 0 to 19 years. Clinical characteristics of the participants are listed in We assessed the subset of individuals tested in this project against those published in the TSAP study. Participants of our subset were, in comparison, older, had a lower temperature, and had less anemia than the others in the TSAP . Further species-specific assays showed that 92% were P. falciparum, 2% were mixed infections, and 6% were unspeciated. At the Madagascar sites, dengue virus was recovered from 10.2% (37 of 364) of samples, followed by cytomegalovirus (CMV) with 5.5% (20 of 364), Bartonella with 2.5% (9 of 364), and Plasmodium spp. with 2.2% (8 of 364). At the Sudanese site, at least 1 pathogen was identified in 60% (118 of 198) of samples; these included dengue virus, Candida spp., Coxiella burnetii, Escherichia coli, Klebsiella pneumoniae, Aeromonas spp., and Staphylococcus aureus , CMV in 15% (8 of 53), dengue virus in 11% (6 of 53), and E. coli in 4% (2 of 53). Four Bartonella-positive samples from Madagascar were able to be further speciated by sequencing to be Bartonella quintana. At all sites, Schistosoma mansoni was found.Overall, the TAC system identified at least 1 pathogen in 39% (237 of 615) of the specimens evaluated . In totas aureus . There wPlasmodium falciparum was the most common coinfecting pathogen (36 of 51 coinfections), followed by dengue virus (19 of 51 coinfections) and CMV (15 of 51 coinfections). Malaria smears were reported positive in 98 specimens, among which TAC detected Plasmodium in 70% (69 of 98). Plasmodium quantitative PCR quantities were higher in these smear-positive (Cq\u2005=\u200519.4\u2005\u00b1\u20054.1) vs smear-negative detections . The quantities of pathogens were not appreciably different between countries (Multiple pathogens were identified in 51 samples (22% of positive samples). Two pathogens were found in 16% (38 of 237) of specimens, 3 pathogens in 5% (12 of 237), and 5 pathogens in 1 patient, 0.4% (1 of 237). ountries .Candida spp. was associated with abdominal pain and constipation . Klebsiella pneumoniae was positively associated with cough , while Plasmodium spp. was negatively associated with cough .We sought to determine how the clinical presentation and management of patients correlated with the pathogens that were identified. The respective associations are shown in Plasmodium spp. Specifically, 52% (87 of 168) of clinical malaria diagnoses had Plasmodium spp. detected, whereas among other clinical diagnoses, only in 8% (36 of 447) was Plasmodium spp. identified . Furthermore, the Plasmodium spp. quantity was greater when malaria was the primary clinical diagnosis .We then examined the clinical diagnoses and their relationships to the pathogens, the only significant association was between clinical malaria and the detection of P\u2005<\u2005.01); however, both of these rates were quite low. We also assessed malaria. From the 168 clinically diagnosed malaria cases, 123 were confirmed to harbor Plasmodium spp. parasites; 61% of them (75 of 123) received an artemisinin-based or quinine therapy, as is appropriate.We retrospectively determined whether the antibiotics prescribed empirically were in line with the guidelines for the particular clinical diagnosis or for the pathogen detected. Overall, in 69% (357 of 516) of patients with a primary clinical diagnosis of malaria, respiratory tract infection, or gastrointestinal infection, an antibiotic aligned with WHO guidance was prescribed . By contThis study provides an important epidemiologic characterization of AFI in 3 sub-Saharan African countries to complement previous work , 28, 29.E. coli, K. pneumoniae, S. aureus, Aeromonas, and Coxiella. In Burkina Faso and Sudan, Plasmodium was the prevailing pathogen, followed by dengue virus and Candida. An important finding was substantial dengue prevalence at all 3 sites, even though dengue is understudied in Madagascar, with only 1 report from 2006 [Findings from the Sudanese site contrasted with results from the original TSAP study, whereby a pathogen could be detected by blood culture in only 2% 16 of 644) 6 of 644 . Our prerom 2006 . Future There were several limitations to this study. First, we could not assess disease outcomes, so we could not determine the benefit of particular clinical diagnoses or specific therapies. We noted a wide range of antibiotics prescribed. Sometimes these choices were not in line with WHO recommendations for the respective disease. This practice of antibiotic treatment that is not in line with recognized guidelines is common and exists in all countries, rich and poor , 33. TheE. coli, K. pneumoniae, and S. aureus) and unnecessary antibiotics . For instance, of 40 cases of dengue monoinfection, 88% received antibiotics. Whether improved pathogen-specific diagnosis and management can improve outcomes is an important area for future investigation.There were examples of both inactive antibiotics (eg, undertreatment of common bacterial pathogens such as Plasmodium spp., as asymptomatic parasitemia without disease may occur frequently. A quantitative case definition of a few thousand parasites per microliter has been used frequently to enhance clinical specificity [Plasmodium parasites fits this notion. Applying this cutoff, the prevalence of Plasmodium in these 3 countries would drop to 32%, 1%, and 30% for the 3 sites. How frequently asymptomatic nucleic acid detection in blood occurs for other pathogens is less clear. Certainly, CMV detection is often not sufficient evidence for clinical disease. Beyond Plasmodium and CMV, PCR is a gold-standard clinical diagnostic for most of the pathogens in this study, such as dengue virus, Bartonella, Coxiella, and Rickettsia [A second limitation was that there were no blood specimens from clinically healthy patients to serve as controls. This is particularly an issue for cificity , which cckettsia . For culckettsia , as was ckettsia . TherefoA third limitation was that we could only test specimens in small amounts of residual blood conserved from the underlying TSAP study. This skewed the population age to older children compared with the parent study. It also could have enriched for less sick individuals. However, in general, these were outpatient individuals and thus not severely ill. Nonetheless, our findings are likely most generalizable to the adolescent population. Finally, since malaria smears were performed under routine conditions and not under a research protocol, we expect this explains some of the malaria smear\u2013PCR mismatch.Shigella and Campylobacter should be pursued. Of course clinical judgment is complex and does not always align with guidelines [The optimal clinical management of AFI is uncertain. WHO guidelines recommend assessing fever for malaria with rapid antigen or smear testing, with empiric treatment if positive. If there are respiratory symptoms, antibiotics for pneumonia should be considered. If bloody diarrhea exists, antibiotic treatment to cover idelines . For allIn summary, this TAC study leveraged systematic AFI surveillance to provide a granular picture of prevailing pathogens. This work showed a substantial pathogen diversity missed by blood culture and should be considered when conducting future assessments of disease burden. The impact of these molecular detections and implications on management require further study.Clinical Infectious Diseases online. Consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author.Supplementary materials are available at ciab289_suppl_Supplementary_Table_S1Click here for additional data file.ciab289_suppl_Supplementary_Table_S2Click here for additional data file.ciab289_suppl_Supplementary_Table_S3Click here for additional data file."} +{"text": "Infection and prolonged inflammation in deep partial-thickness burns can lead to inadequate healing. In addition to their role in hemostasis, activated platelets also contain granules with anti-inflammatory properties which may impact wound healing. However, portability and storage of platelets remain a challenge. Synthetic platelet-mimetics (SPM) avoid these difficulties, but like natural platelets, SPM have vesicles that can transport bioactive agents, such as antibiotics. We sought to evaluate wound healing outcomes in deep partial-thickness burns treated topically with SPM.A total of 30 circular, deep partial-thickness burns were created on the dorsum of 2 porcine models. Each wound measured 5cm in diameter and was standardized using a thermocoupled burn device. Sets of six wounds were randomized into five groups: SPM, gentamicin alone, SPM with gentamicin, a vehicle control , or dry gauze . Additionally, two separate 5cm diameter circular areas were demarcated to serve as normal skin controls. Wounds were assessed at post-burn days 3, 7, 14, 21, 28, 60 and 90 with a variety of non-invasive imaging and punch biopsies. Treatments were re-applied at each assessment. The primary outcome was the amount of wound re-epithelialization, measured histologically, at post-burn day 28. Secondary outcomes consisted of the percentage of wound contraction, amount of superficial blood flow, and mean bacterial load.The amount of wound re-epithelialization in wounds treated with SPM was 96% whereas those treated with the SOC measured only slightly less at 92% (p = 0.56). The percentage of wound contraction was 39% in the SPM with gentamicin group, while in the SOC group contraction was higher at 45% (p = 0.20). Moreover, superficial blood flow in the SPM group was measured to be 168% of normal skin controls, while wounds in the SPM with gentamicin group were slightly lower at 160%, and in wounds treated with the SOC blood flow was 110% of normal skin controls (p = 0.27). The mean bacterial load in each group was measured at post-burn day 3 and notably consisted of bacterial load being the lowest in wounds treated with gentamicin alone at 17/100, meanwhile in wounds treated with the SOC or those in the SPM with gentamicin group, mean bacterial loads were significantly higher at 43/100 and 47/100, respectively (p = 0.02).SPM applied to deep partial-thickness burns did not significantly improve measured outcomes over the SOC. Although numerical improvements were shown in all measured outcomes, no significant differences were noted. The theoretical and observed potential for SPM to improve wound healing deserves additional evaluation in larger preclinical studies."} +{"text": "Previous studies concerning older adults have focused on whether cannabis use leads to positive or negative outcomes. In this study, we identified clusters of negative health outcomes associated with medical cannabis use. In total, we examined eight health outcomes: pain, sleep, falls, memory, digestive issues, mental health conditions, exercise, and general productivity reported by 2,968 persons over 60 who participated in the Illinois Medical Cannabis Program. We used association analysis to simultaneously identify groups of negative outcomes reported by participants. The distribution of non-positive outcomes shows a bell-shaped curve: 1.4% of participants responded that cannabis use improved all outcomes, while 4.1% of participants answered that cannabis use did not. When looking at negative outcomes, 86% of participants reported none worsened, and 11% reported one of the outcomes was affected. Only a small fraction of the participants (3%) claimed more than one negative outcomes after cannabis use."} +{"text": "Breastfeeding was initiated in 98% of infants, but the duration of exclusive breastfeeding to six months was less than 1%. Nearly 40% of children continued to receive breastmilk beyond one year, with 10% of toddlers receiving breastmilk at two years. One-quarter of infants were introduced to solid foods between 4 to 5 months, and nearly all infants had received solid foods by 7 months. New guidelines encourage the early introduction of potential food allergens to reduce the risk of allergy, and by 12 months, over 90% of children had been given eggs and peanuts. One-third of children received no breastmilk substitutes during their first year. One-third of infants first received breastmilk substitutes following birth and before discharge from the hospital. Of these infants, 30% ceased breastmilk substitute use after discharge. Our findings suggest a high rate of continued breastfeeding with 44% receiving breastmilk beyond 1 year. One approach to increase the duration of exclusive breastfeeding is to reduce breastmilk substitute use while in hospital.The Australian Feeding Infants and Toddler Study 2021 (OzFITS 2021) is a nationwide survey of Australian caregivers\u2019 infant and toddler feeding practices. Here, we describe breastfeeding rates and duration, use of breastmilk substitutes, and introduction of complementary (solid) foods, including common food allergens. Caregivers ( The Australian National Health and Medical Research Council (NHMRC) Infant Feeding Guidelines recommend exclusive breastfeeding for the first six months to optimize infant growth, development, and health ,2,3. AftDespite the importance of early infant feeding, there is very little data on breastfeeding practices and the timing of solid food introduction of Australian caregivers. The 2010 Australian National Infant Feeding Survey (ANIFS) providesIn their 2012 Infant Feeding Guidelines, the NHMRC advised Here, we provide recent nationwide data on breastfeeding initiation, duration of exclusive, and the use of breastmilk substitutes among Australian caregivers. We also provide new data on the timing of introduction to solid foods, including early exposure to common food allergens. n = 1140) were surveyed between April 2020 and 2021. The methods for OzFITS 2021 are described in detail elsewhere in this supplement . BrieflyQuestions regarding initiation of breastfeeding and feeds in the early neonatal period were consistent with the ANIFS : \u201cWhat wAge definitions adopted were based on completed months, consistent with the ANIFS . The defThe OzFITS 2021 cross-sectional survey enrolled 1140 caregivers with children in four age bands: 0\u20135.9 months; 6\u201311.9 months; 12\u201317.9 months; and 18\u201323.9 months. A feature of the data when looking at events such as exclusive breastfeeding, predominant breastfeeding, and introduction to solid foods are censored responses: children who had not yet experienced the relevant event at the time of the survey. Kaplan\u2013Meier survival analysis was used to estimate the cumulative proportion surviving at each event time and associated 95% confidence intervals. We estimated one minus the cumulative proportion of surviving at each event for solid food introduction. We were interested in the proportion who have experienced the event rather than the proportion who have experienced a disqualifying event . Statistical analyses were completed using SPSS 28.0 [Exclusive breastfeeding was initiated in 93% of infants; however, only 59% were exclusively breastfed to one month, and 39% were exclusively breastfed to four months. Less than 1% of infants were exclusively breastfed to six months . The maiThe median duration of any breastfeeding was 11.0 months (95% CI 10.2 to 11.8). Breastfeeding was initiated in 98% of infants, and at six months of age, 68% (95% CI 65 to 71) were breastfed. Nearly 40% of children were breastfed beyond 12 months, and at 20 months of age, 10% of toddlers were still receiving some breastmilk. n = 455) of infants consuming breastmilk substitutes in their first month of life, 78% (350/455) received these in hospital soon after birth. Of the infants who began breastmilk substitutes in the hospital, 33% (116/350) ceased consuming breastmilk substitutes after hospital discharge and received only breastmilk. Another 58% (202/350) continued to receive both breastmilk and a breastmilk substitute, and only 9% (32/350) received breastmilk substitutes alone. In contrast, of the children introduced to breastmilk substitutes at home by one month of age, 9% (9/105) ceased breastmilk substitutes and then only received breastmilk for a period; 81% (86/105) received both, and 10% (10/105) received only breastmilk substitutes. By six months of age, just over half of the infants had been given breastmilk substitutes, with 40% of infants introduced during the first month of life. By age one, 35% of children had never received breastmilk substitutes . Of the n = 13) started solid foods before 4 months. Of these, one child (<1 month of age) was given honey on their pacifier, one child (1\u20132 months) of age had pureed food at 4 weeks, and the remainder (n = 11) started solid foods at around 3 months and 3 weeks of age. Delayed food introduction beyond seven months was observed among 3% of infants . Reasons for delaying the introduction to solid foods included prematurity n = 5; food intolerances or allergy n = 3; n = 22 parents gave no specific reason. The median age at first introduction to solid foods was 5 months (95% CI 4.9 to 5.1). One-quarter of all children were introduced to solid foods between 4 and 5 months, 33% commenced solids between 5 and 6 months, and by 6 to 7 months, 97% were introduced to solid foods. A small number who had started solid foods, caregivers reported medically diagnosed IgE mediated food allergy, which was confirmed by allergen testing in 77/922 children (8.5%). Of these, IgE-mediated egg allergy was reported in 2.4% (22/922), and peanut allergy was reported in 1.6% (15/922) of children.Amongst the children state-wide perinatal indicators report where 29% of infants were given breastmilk substitutes in hospital . FurtherDespite the short duration of exclusive breastfeeding in OzFITS 2021, breastfeeding duration to one year was high, with many children breastfed into their second year of life. Our finding of long breastfeeding duration is consistent with other Australian cohorts and surveys ,14. In tThe Australian NHMRC infant feeding guidelines recommenIn OzFITS 2021, infants were introduced to common allergens such as egg and peanut by one year of age, consistent with results reported elsewhere ,18,19. WA strength of this study is that it provides contemporary Australian data with a sample proportionate to the population size within each state. Questions were adapted from the ANIFS but included more comprehensive questions regarding the timing of solid foods and common food allergens. Limitations include the retrospective nature of the feeding survey data collected, specifically for the older age group. We used convenience sampling, which is more subject to response bias than purposeful sampling. In our case, participants were more highly educated and had a higher family income than the Australian population ,22. DespIn conclusion, for OzFITS 2021, we report exclusive breastfeeding rates at 4 and 6 months compared with the ANIFS 2010. Most caregivers commenced solid foods at around 6 months of age, according to the NHMRC Infant Feeding Guidelines, and most infants were exposed to common allergens in the first year of life. Perhaps the most worrying finding is the early introduction to breastmilk substitutes in hospitals, affecting exclusive breastfeeding rates. Many caregivers surveyed breastfeeding, ceased breast milk substitutes, and gave their infant only breastmilk, possibly suggesting they intended to exclusively breastfeed their babies Strategies that support exclusive breastfeeding while in hospital are needed."} +{"text": "To assess the learning impact of e-curriculums on healthcare professionals (HCPs). The second objective was to report the screening, detection and clinical features of patients with obstructive lung diseases (OLD) through an integrated care program at The Indus Hospital & Health Network (IHHN), Karachi, Pakistan.A retrospective, observational study was conducted in the Family Medicine outpatient department from January 2019 till July 2021. HCPs were trained on the diagnosis and management of OLD through e-learning. Patients were screened clinically for OLD and had spirometry performed if suspect. Baseline characteristics, patient-reported outcome measures (PROMs), spirometry and treatment modalities were collected. Univariate analysis was done on Excel and paired t-testing was performed on Stata 16.Online training on clinical aspects of OLD was completed by 33 HCPs, amongst whom 77.9% demonstrated improved post-test evaluations of 26.8% (p=0.000). Of 1896 patients screened, 60.8% were diagnosed as OLD. Asthmatics accounted for 66.5% . In 84.5% of patients who completed PROMs, poor control of symptoms was reported. Inhaler technique was taught in 66.5%. Breathless patients, with a high modified Medical Research Council score , were referred for pulmonary rehabilitation in 92% of cases. Tobacco cessation advice was delivered to 61.1% of all current users (n=229).The OLD program uses capacity building, gold standard diagnostics and updated management strategies in primary care, allowing earlier diagnosis of suspected patients and implementation of evidence-based interventions, aiming to improve their morbidity and mortality. Non-communicable diseases (NCD) are gaining recognition globally, and are a major public health challenge. In a ten-year review, the World Health Organization (WHO) declared chronic respiratory diseases (CRD), affecting the lungs and airways, one of the four most detrimental NCDs.In low-middle-income countries (LMICs), the prevalence of COPD and asthma cannot be fully understood due to underdiagnosis,15Only 20% of the estimated asthma and COPD cases are currently being identified and diagnosed in primary care in Pakistan.An e-learning platform, Canvas, was used to train relevant healthcare professionals (HCP) in four modules: spirometry, COPD, asthma and inhalers. Bespoke modules were developed based on internationally accepted guidelines.Each module consisted of a (1) thirty-minute pre-course assessment, (2) overview, (3) main objectives, (4) marking criteria, (5) course content and (6) thirty-minute post-course assessment. Illustrations, algorithms and quizzes were added to enhance the course content.Both pre- and post-course assessments involved ten questions in a case-based format. Marking criteria stipulated scores greater than 70% as passing and eligible for completion certificates while lower scores are offered a re-attempt option to be completed within the same week.The module learning cycle had a four-week format:Week zero: Pre-course assessment,Week one and two: HCPs read through course content,Week three: Post-course assessment,Week four: Pre- and post-course assessment results compiled and distributed; re-attempts offered where necessary.Learning was supported by online and selected in-person interactive sessions where needed. Nurses further shadowed Consultant Pulmonologists in outpatients to become Specialist Lung Health nurses.A retrospective, observational study was conducted at the Family Medicine outpatient department at The Indus Hospital \u2013 Korangi campus from January 2019 to July 2021. Patients with breathlessness, wheeze, cough and other clinical features suggestive of OLD were referred for evaluation. Characteristics including demographics, occupation, comorbidities, biomass exposure and tobacco status were captured. Spirometric data with reversibility was used to diagnose asthma and COPD and to assess severity of obstruction using Forced Expiratory Volume in first second (FEV1) values. Patient-reported outcome measurements were used to assess control of disease, CAT \u2265 10 and ACT \u2264 19 showing poor control . NumbersAn electronic data collection tool, REDCap, was used for data collection. Excel was used for univariate analysis. Quantitative data was expressed as percentage and median (interquartile range (IQR)) where appropriate. Stata 16 was used for statistical testing (paired t-test) with significance set at p<0.01. Ethical approval was obtained from the Institutional Review Board IRD_IRB_2020_05_013 and IRD_IRB_2021_05_021.A total of 33 HCPs (30 primary care physicians and three nurses) enrolled in the online training modules . Each phSince 2019, a total of 1896 patients were screened on first visit. Of these, 60.8% were diagnosed as OLD on both spirometric and/or clinical grounds. Asthma was more common in females (60.8%) with a median (IQR) age of 39 (28-50) years and COPD in males (79.1%) with a median (IQR) age of 60 (50-67) years . By occuBaseline spirometry was offered to all suspected OLD cases (n=1154). A diagnosis of OLD was based on spirometry in 845 cases (73.2%) whilst clinical diagnosis alone accounted for 309 (26.8%). Airflow obstruction ranged from severe to very severe intensity in 42.6% of COPD and 32.5% of asthma cases. Using mMRC, 45.2% of OLD patients scored two or above. CAT scores in COPD showed 88% had poor symptom control whilst ACT scores demonstrated uncontrolled asthmatic disease in 77% .Staging for COPD patients showed 11.6% at GOLD stage A , 31.3% stage B , 1.3% stage C and 55.8% at stage D . Two or more exacerbations requiring increased therapy were seen in 42% of OLD patients.Of 1129 OLD patients, 54% had inhaled therapy prescribed. This included combined inhaled corticosteroid and long-acting beta 2-agonists , short-acting beta2-agonists and long-acting antimuscarinics (10.2%). Montelukast (31.4%) was prescribed as an add-on oral therapy. Inhaler technique was taught in 66.5%. Those with mMRC score of two and above (n=234) were referred for PR in 96.2% of cases. Advice on tobacco cessation was delivered to 61.1% of all current users (n=229).Integration of the OLD program into Family Medicine through training and formal diagnostics showed that (1) e-curriculums enable improved HCP knowledge of OLD, (2) asthma was more common than COPD, was associated with more co-morbidities and was predominant in females. In this population, a high prevalence of biomass exposure and both smoking and smokeless tobacco use was noted in both asthma and COPD. Spirometry revealed advanced disease in over half the patients with OLD.The OLD program is an integrated care program where CRDs, namely asthma and COPD, are diagnosed and managed in primary care and to our knowledge is the first of its kind in Pakistan. Implementation strategies for interventions in lung health in LMICs have been suggested by Brakema and colleagues.Through our e-learning platform, HCPs were introduced to updated, evidence-based learning material covering all aspects of OLD in a flexible and accessible manner. In Pakistan, a precedent for e-learning was reported by The Aga Khan University. Their massive open online course on Drug Discovery was well received by participants.22In our experience, limitations to training were seen as HCP turnover interrupted the e-curriculum format and created lag time. Internet access was variable. Training time was often compromised by other clinical activity during the work day, delaying completion. Importantly, whilst pre- and post-test evaluations demonstrate improved learning, we cannot conclude a clear link with improved diagnosis of OLD within the constraints of this work. This is similar to the e-learning strategy reported in the UK, teaching fundamentals of prescription writing and causes of prescription errors. Whilst pre and post course assessments done on general practitioners and pharmacists demonstrated scores increased by 17.4%, the impact on patient outcomes could not be established.23Our data collection methods were online and easily accessible. This information can be interrogated to provide important epidemiological data on these poorly documented NCDs. Notably the population selected for confirmation of OLD were likely suspects of disease, so true incidence and prevalence figures cannot be reliably interpretated. Patients with OLD are more likely to abuse tobacco, we identified 34% were smokers of our patient, higher than the national average.Amongst patients who were screened for OLD, 16.2% were unable to perform spirometry in their first visit. Technicians performing spirometry have an important role in appropriate coaching but factors such as worsened breathlessness, coughing or communication issues can still limit outcomes. Where spirometry provides a gold standard for diagnosis, its absence relies on clinical judgement and we noted 26.8% of diagnosed OLD patients had no spirometry performed. Meanwhile, despite careful HCP training, we found inadequate inhaler therapy prescription in some patients. Our program could not evaluate the causes of this, which may include unaffordability, lack of compliance or need for remedial training of HCPs. Advice on tobacco cessation was missing in 59% eligible cases, possibly demonstrating a gap in training.Spirometry completely halted in April 2020 in view of the COVID pandemic, as it is an aerosol generating procedure likely to spread disease. This limitation inevitably impacted program performance and data collection. Since August 2020, services were restarted with careful verbal screening by technical staff who were otherwise in full personal protective equipment and were relocated to ventilated areas. A pragmatic approach to continue services, as done worldwide, was therefore adapted.The programmatic requirements of extensive data collection and highly trained resources for each patient may serve as a limitation by proving expensive and difficult to further integrate. However, the program provides an evidence-based package, impacting both the patient and their health ecosystem. Patients may have improved self-awareness and slower decline in lung function. Meanwhile, the health system may have a reduced burden of emergency visits and hospitalizations. A complete cost-benefit analysis is warranted to evaluate this further. Other potential areas of development include development of home-based support both in the medical and non-medical sectors, completing the cycle and becoming truly integrated practice units and integrated care programs.The Obstructive Lung Disease program has shown itself to be a useful primer for establishing a sustainable and scalable integrated care program within primary care. It has used innovative training models, dealt with implementation challenges and provided learning opportunities on how to develop further. Providing evidence-based care for common NCDs begins to address the Sustainable Development Goals within Pakistan. Further expansion is planned to protect the health of our communities.SS: Conception and design, program development, drafting the manuscript, revision for accuracy an is responsible for integrity of the study.MS: Educational module development, data interpretation, manuscript drafting, revision for accuracy.RA: Design of data collection tools and acquisition of data, computations and analysis, manuscript drafting, revision for accuracy."} +{"text": "Stratification by continents and by GDP per capita also showed huge heterogeneity. The Middle East had the weakest total prevalence with 10% (6% to 14%), and Oceania the strongest with 35% (21% to 50%). Despite the prevalence of breastfeeding in general increasing with GDP per capita , the prevalence of non-exclusive breastfeeding follows more of a U-curve with the lowest and highest GDP per capita having the highest percentages of breastfeeding . Conclusion: Breastfeeding after RTW is widely heterogeneous across the world. Despite economic status playing a role in breastfeeding after RTW, cultural aspects seem influential. The lack of data regarding breastfeeding after RTW in most countries demonstrates the strong need of data to inform effective preventive strategies.Background: The benefits of breastfeeding are widely known; however, continuation after returning to work (RTW) is not. We aimed to conduct a systematic review and meta-analysis to assess the prevalence of breastfeeding after RTW. The secondary objectives were to compare the economic statuses between continents. Method: PubMed, Cochrane Library, Base, and Embase were searched until 1 September 2020, and two independent reviewers selected the studies and collated the data. To be included, articles needed to describe our primary outcome, i.e., prevalence of breastfeeding after RTW. Results: We included 14 studies, analyzing 42,820 women. The overall prevalence of breastfeeding after RTW was 25% , with an important heterogeneity (I Breastfeeding provides multiple health advantages for the child and their mother (breast cancer) ,2,3,4, wTherefore, we aimed to conduct a systematic review and meta-analysis to evaluate the prevalence of breastfeeding after RTW (primary aim). The secondary objectives were to evaluate the differences between continents or their level of development, as well as putative influencing variables such as sociodemographics ,22,23, bWe reviewed all studies involving breastfeeding after returning to work. Specifically, the inclusion criteria for the search strategy were the prevalence of breastfeeding and/or exclusive breastfeeding after RTW, using the following keywords: Breastfeeding AND work per capita), month of RTW, breastfeeding practices , and characteristics of the individuals .An assessment of the methodological quality was performed using the Newcastle\u2013Ottawa Scale (NOS) for cohort studies and modip-Values less than 0.05 were considered statistically significant. We stratified these meta-analyses by continents and by economic status of the countries (GDP per capita). All of these meta-analyses were computed for global, exclusive, and non-exclusive breastfeeding. Heterogeneity in the study results was evaluated by examining forest plots and confidence intervals (CIs) and by using formal tests for homogeneity based on the I2 statistic, which is the most common metric for measuring the magnitude of between-study heterogeneity and is easily interpretable. I2 values range between 0% and 100% and are typically considered low for <25%, modest for 25%\u201350%, and high for >50% [Statistical analysis was conducted using Stata software ,39,40,41for >50% . For exafor >50% . When pon = 383) and applying the selection criteria reduced these articles reporting the prevalence of breastfeeding after RTW to 14 studies .Type of occupation: Nine studies included all working mothers with no job specification [fication ,53,54,55fication ,57. One fication . One stufication . One stufication .Country of breastfeeding: Two studies were conducted in Europe (France [ (France and the (France ), two st (France and Egyp (France ), three , and th France ,55,56).,56.CountGross domestic product per capita: We retrieved the GDP per capita by country and year of the included studies using data from the World Bank database [database .Other characteristics: Characteristics such as education [ducation ,54,56,57ducation ,52,53,55ducation ,52,53,55Working mothers were the shared inclusion criterion for the 14 studies ,55,56,57The primary outcome of the included articles was the prevalence of breastfeeding after RTW for six studies ,50,53,56Seven studies had a cross-sectional prevalence survey design, analyzing breastfeeding amongst working mothers ,50,56,57Method of assessment: Breastfeeding after RTW was measured via a questionnaire [ionnaire ,50, semiionnaire ,48,49,57ionnaire ,56, or aionnaire ,51,53. Tionnaire ,54.Type of breastfeeding: Seven studies investigated both exclusive and non-exclusive breastfeeding [tfeeding ,55,56,57tfeeding ,48, and tfeeding ,49,51,52Return to work: RTW after birth ranged from <1 month [<1 month to 12 mo<1 month ,50,55. T2 = 98.6%)\u2014the prevalence of breastfeeding after RTW ranging from 2% [Our meta-analysis demonstrated an overall prevalence of breastfeeding after RTW of 25% , with an important heterogeneity (I from 2% to 61% [ from 2% . Stratif2 > 90%), with a mean overall prevalence of breastfeeding after RTW of 21% (14% to 28%) and 28% (23% to 32%), respectively. Stratification by continents demonstrated similar results, with Middle Eastern countries having the weakest prevalence (5% (3% to 7%) and 14% (8% to 19%), respectively) and Oceania countries the strongest (26% (4% to 47%) and 42% (29% to 55%), respectively). Stratification by GDP did not show an increase in exclusive or non-exclusive breastfeeding with the economic status of countries. For example, for non-exclusive breastfeeding, the highest prevalence of breastfeeding was for the lowest and highest GDP (47% (41% to 54%) for GDP under US$5000 per capita and 50% (45% to 55%) for GDP higher than US$50,000, whereas the prevalence was 20% (17% to 22%) between US$5000 and US$30,000 and 28% (20% to 36%) between US$30,000 and US$50,000) . Funnel plots of these meta-analyses demonstrated a wide heterogeneity , precludThe main finding was that the prevalence of breastfeeding after RTW is widely heterogeneous across the world. Despite the review demonstrating that economic status may play a role in breastfeeding after RTW, cultural aspects seem an important determinant. We did not find an effect of putative influencing variables.This study is the first meta-analysis analyzing breastfeeding prevalence after RTW. As stated by the WHO, breastfeeding confers various benefits for infants and mothers . HoweverInterestingly, whatever their economic status, some countries have strong breastfeeding policies, especially after RTW . AustralWe did not find other factors that influenced breastfeeding prevalence after RTW. Obviously, the literature showed that early RTW negatively affected breastfeeding initiation and duraAll meta-analyses have limitations . Meta-anDespite the scarcity of data, the prevalence of breastfeeding after returning to work is 25% and widely heterogeneous across the world. Even if economic status plays a role in breastfeeding after return to work, cultural aspects seem an important determinant, influencing public health policies and workplace breastfeeding support. We also showed the lack of data regarding breastfeeding after returning to work in most countries, with no data available from some continents such as Africa, demonstrating the strong need for data in these countries to inform effective preventive strategies."} +{"text": "Independent variables included weight status, trimester, smoking, stress, education, employment, race, and age. Dependent variables were high (consuming \u2265 1 serving/day) versus low consumptions of SSB, ASB, and 100% FJ. Multivariate logistic regression modeling was performed to examine factors associated with beverage consumption. Out of the sample, 48.2%, 6.7%, and 31.3% reported high SSB, ASB, and 100% FJ consumption, respectively. SSB consumption was associated with smoking , education , and race . Artificially sweetened beverage consumption was not associated with any factors examined. One hundred percent FJ consumption was associated with stress and race . Clinicians may advocate for reductions in SSB and 100% FJ consumption tailored to client consumption characteristics.This study examined consumption proportions and factors associated with sugar-sweetened beverages (SSBs), artificially sweetened beverages (ASBs), and 100% fruit juice (FJ) consumption. We recruited Non-Hispanic Black ( Approximately 70% of American pregnant women consume higher than recommended amounts of added sugars [Beverage intakes, such as sugar-sweetened beverages (SSBs), artificially sweetened beverages (ASBs), and 100% fruit juice (FJ), are modifiable factors affecting a pregnant women\u2019s health ,3, increSimilarly, high ASB consumption during pregnancy has been associated with increased risks of the infant being overweight , whereasCurrently, relatively few studies have examined factors associated with SSB, ASB, and 100% FJ consumption. Health status (such as weight status and trimester), individual behavior (such as smoking), and social factors might affect the three types of beverage consumption among pregnant women. Available data on pregnant women have shown associations between weight status and SSB consumption . HoweverBiology and genetics (such as age) might also influence the three types of beverage consumption. Currently, only two studies of pregnant women examined associations between age and SSB consumption and have yielded mixed results ,15. The This study investigated the proportion of SSB, ASB, and 100% FJ consumption among low-income overweight or obese pregnant women. We also applied four categories of health determinants .This cross-sectional study utilized convenience sampling. Participants were recruited from 4 WIC clinics located in western and southern Michigan. WIC provides a nutrition education and food voucher/package to pregnant, postpartum, and lactating women and children under 5 years old from low-income environments. Detailed descriptions of study recruitment have been previously published . BrieflyDemographics and BMI. Participants self-reported the following: smoking , education , and employment . Participants also reported race/ethnicity, age, and last menstrual cycle, which was used to calculate trimester status. Moreover, participants self-reported height and weight, both of which were used to calculate BMI.. The Perceived Stress Scale (9 items) with reported validity and reliability (Cronbach Alpha = 0.84\u20130.86) [Perceived Stress 84\u20130.86) was used84\u20130.86) . Partici84\u20130.86) . ResponsR2 = 0.52\u20130.95, p < 0.001), validated using 24-hour dietary recalls, was used to measure beverage consumption [SSB, ASB, and 100% FJ Consumption. A beverage intake survey with acceptable validity and reliability did not fill out any beverage intake survey questions because they had to leave. Of the data collected, only the beverage intake survey had missing data (<0.1%). Hot Deck imputation was applied to impute missing data. Statistical software SAS version 9.4 was used for all analytical procedures. Descriptive analysis was performed to examine demographics and the proportion of the 3 types of beverage consumption. One serving of beverage intake, defined as 12 fl oz, was used as a cut-off value [2 prior to pregnancy). More than one-third of participants were in the second trimester. r = 0.27, p < 0.001), between SSB and 100% FJ consumption , and between ASB and 100% FJ consumptions .p < 0.001) was associated with high SSB consumption. In terms of social factors, higher levels of stress were associated with low 100% FJ consumption, and at least some college education was associated with low SSB consumption. However, being Black was associated with high SSB and 100% FJ consumption . Biology and genetics were not associated with high consumption of any of the three types of beverages.This study examined consumption proportion and factors associated with daily SSB, ASB, and 100% FJ consumption among low-income, overweight, or obese pregnant women. Our study findings partially supported our hypotheses: current smoking, lower education, and Black race were associated with higher SSB consumption. In addition, Black race was associated with higher consumptions of 100% FJ.In the 2009 WIC food package, policy makers reduced the 100% FJ allotment to align with the Dietary Guidelines for Americans . CurrentOur results showed that almost half of the sample reported high SSB consumption, which is about 2.5-times higher than a previous study of pregnant women that included all weight status and income levels . The pre2, the previous study included all weight statuses and treated weight status as a continuous variable. Thus, associations between weight status and beverage consumption in previous work might have reflected the larger range of weight status included in the study. We found that current smokers were more likely than nonsmokers to report high SSB consumption, which is consistent with prior studies [We found no significant associations between weight status and any of the three types of beverage consumption, a finding that contradicts findings of a previous study of pregnant women across all income levels . The inc studies ,13. HoweThe study findings revealed that stress was only associated with 100% FJ consumption but not with consumption of the other 2 types of beverages. Comparison of our stress findings to previous studies is not feasible because we are unaware of other studies of pregnant women that investigated such associations. Our findings revealed that women with at least some college education were less likely to report high SSB consumption than women with high school or less education. This finding is consistent with a prior study of pregnant women , but it The present study has several limitations. The cross-sectional design precludes any cause\u2013effect conclusions. The secondary nature of the analysis means that the study was not originally designed with tests of independent variables of beverage consumption in mind. Our study is limited in the number of individual behavior or social factors that might influence the study outcomes. The selection of possible factors was limited by the original design purposes (that were not primarily to address beverage consumption patterns). Data were collected via self-report, all of which are subject to potential inaccuracy of dietary recall. Low-income women and individuals with higher weight status are more likely to under-report their dietary intake . The datThe present study has some strengths. We collected frequency and the amount of beverage consumption. Thus, we were able to report daily consumption amount. We also used reliable and valid surveys to measure perceived stress and beverage consumption. The study included a homogenous but vulnerable sample: low-income overweight or obese pregnant women.Based on our findings, future prospective studies are needed in order to examine the associations between high SSB and 100% FJ consumption, dietary quality, and gestational weight gain among low-income, overweight, or obese pregnant women. Moreover, focus group discussions and future prospective studies might consider identifying factors influencing Black pregnant women\u2019s SSB and 100% FJ consumption. Moreover, lifestyle intervention studies promoting healthy pregnancies among low-income pregnant women might consider including reductions in SSB and 100% FJ consumption. In 2018, WIC served 675,227 pregnant women nationwide . Registe"} +{"text": "Severe bacterial infections (SBI) associated with intravenous drug use have been increasing in frequency in the U.S. over the last decade. This mixed methods study aims to identify the risk factors associated with SBI in hospitalized individuals with recent injection drug use.We conducted 34 quantitative and 15 qualitative interviews between August 2020 and June 2021 at Bellevue Hospital in New York City. Eligible participants were (1) >/= 18 year of age, (2) admitted with a SBI, and (3) reported injection drug use within the 90 days prior to admission. Quantitative and qualitative data was obtained using a quantitative survey and in-depth, semi structured interviews of participants respectively. Analysis was performed to examine trends and explore common themes potentially contributing factors to SBI.Staphylococcus aureus as the sole organism. Discharges against medical advice occurred in 35%. Daily injection drug use in prior 30 days was 95% with a median of 10 injections per day. In the 30 days prior to admission, 50% reported an increase in injection frequency, 80% reported reusing needles and/or syringes, 75% reused cookers, 65% reused cottons. Analysis of qualitative interview data revealed high risk injection behaviors. Participants were not practicing and unaware of strategies to reduce their risk of drug injection-related SBI. Prior hospitalizations for SBI did not impact on this knowledge deficit on what constitutes bacterial infection risk and how to prevent it. Of the 34 participants included, the median age was 37.5, 85% were male, 53% white, and 65% reported being homeless within the past 3 months. Endocarditis was the most common primary diagnosis (65%). Median length of hospital stay was 24 days and 35% required ICU level care during admission. A causative microorganism was identified in 85% of participants and 50% had Study findings highlight the complexity of the injection drug use process and the potential social and physiological pathways leading to SBI. Multiple domains at the structural, network, and individual level that impact drug injection practices and provide context by which these factors predispose and lead to physiological tissue damage and the development of SBI among PWID. Benjamin Eckhardt, MD, MS, Gilead Sciences (Grant/Research Support)"} +{"text": "Pain has been shown to be undertreated in the older population. At the same time, the increased opioid use is of concern in the Western world. This study analyzes temporal trends in pain management among home-dwelling people aged 75 to 95 using cross-sectional cohort data spanning 20 years. The Helsinki Aging Study recruited random samples aged 75, 80, 85, 90, and 95 in 1999, 2009, and 2019. In total, 5,707 community-dwelling people participated in the questionnaire survey. Participants reported their medical diagnoses, regular prescription medications, and the presence of back pain or joint pain within the last 2 weeks . We compared analgesics use in people reporting musculoskeletal pain and in people not reporting pain in 1999, 2009, and 2019. Of participants, 57\u201361% reported intermittent or daily musculoskeletal pain. The percentage of people taking a daily analgesic increased from 9% in 1999 to 16% in 2019. The use of NSAIDs decreased from 1999 to 2019, while the use of paracetamol increased from 2% to 11%. Of participants, 3% took daily opioids in 2019. Of those reporting daily musculoskeletal pain, 20% in 1999, 35% in 2009 and 32% in 2019 took regular pain medication. Pain remains undertreated in the older population, although the use of regular prescribed analgesics increased from 1999. The use of NSAIDs diminished, while the use of paracetamol increased. Daily opioid use remained modest from 1999 to 2019."} +{"text": "Purpose: Immunotherapy has created a paradigm shift in the treatment of metastatic non-small cell lung cancer (NSCLC), overcoming the therapeutic plateau previously achieved by systemic chemotherapy. There is growing interest in the utility of immunotherapy for patients with resectable NSCLC in the neoadjuvant setting. The present systematic review and meta-analysis aim to provide an overview of the existing evidence, with a focus on pathological and radiological response, perioperative clinical outcomes, and long-term survival. Methods: A systematic review was conducted using electronic databases from their dates of inception to August 2021. Pooled data on pathological response, radiological response, and perioperative outcomes were meta-analyzed where possible. Results: Eighteen publications from sixteen studies were identified, involving 548 enrolled patients who underwent neoadjuvant immunotherapy, of whom 507 underwent surgery. Pathologically, 52% achieved a major pathological response, 24% a complete pathological response, and 20% reported a complete pathological response of both the primary lesion as well as the sampled lymph nodes. Radiologically, 84% of patients had stable disease or partial response. Mortality within 30 days was 0.6%, and morbidities were reported according to grade and frequency. Conclusion: The present meta-analysis demonstrated that neoadjuvant immunotherapy was feasible and safe based on perioperative clinical data and completion rates of surgery within their intended timeframe. The pathological response after neoadjuvant immunotherapy was superior to historical data for patients who were treated with neoadjuvant chemotherapy alone, whilst surgical and treatment-related adverse events were comparable. The limitations of the study included the heterogenous treatment regimens, lack of long-term follow-up, variations in the reporting of potential prognostic factors, and potential publication bias. The emergence of immune checkpoint inhibitors (ICIs) transformed the landscape of treatment pathways for patients with metastatic non-small cell lung cancer (NSCLC) after encouraging results were reported from randomized controlled trials . For patDue to the relative paucity of robust clinical data, there is an urgent need to assess the existing literature to analyze the feasibility, safety, and efficacy of neoadjuvant immunotherapy. The primary aims of the present systematic review and meta-analysis were to identify the pathological and radiological response rates of neoadjuvant ICIs. Secondary endpoints included perioperative mortality, surgical morbidity, treatment-related adverse events, delays in surgery, and the overall long-term and disease-free survival outcomes.Our methods adhered to the guidelines set forth in the Preferred Reporting Items for Systematic Review and Meta-Analyses: The PRISMA Statement. A systematic review was performed using online databases from their dates of inception to August 2021, including EMBASE, Ovid Medline, and all EBM Reviews. Search terms included neoadjuvant* and and as either Medical Subject Headings or keywords. Reference lists of all retrieved full texts were screened for further identification of potentially relevant studies.Selected studies included those in which patients with histologically proven NSCLC were treated with ICI prior to surgical resection and provided data on radiological and pathological response. Publications were limited to human subjects and written in English. Case studies involving 10 or fewer patients, conference abstracts, and poster presentations were excluded. Two investigators (A.G. and A.L.) independently reviewed each retrieved article. Discrepancies between the two reviewers were resolved by discussion and consensus after review by the senior investigator (C.C.).2 statistic was used to estimate the percentage of total variation across studies due to heterogeneity rather than chance. Thresholds for I2 values for low, moderate, and high heterogeneity were considered as 0\u201349%, 50\u201374% and \u226575%, respectively. Specific analyses considering confounding factors were not possible because raw data were not available. All p-values were 2-sided, and \u22640.05 were considered statistically significant. All statistical analyses were conducted with Review Manager Version 5.1.2 or R Version 4.0.2 .Meta-analysis of proportions or means was performed for categorical or continuous variables via generalized linear mixed models, as appropriate . A randoA total of 4143 references were identified through the electronic search; 2914 potentially relevant articles remained for screening after the removal of duplicated studies. After applying the selection criteria, 33 studies remained for full assessment, and 18 publications from 16 studies were selected for quantitative analysis ,20,21,22In total, 548 patients were treated with at least one cycle of neoadjuvant immunotherapy, with 507 patients (96%) undergoing subsequent surgery. The overall incidence of male patients was 73.7%, and the interquartile range of age across different studies was 61.5\u201365.5. Overall, 81.7% of patients were either former or current smokers. Histologically, 56.6% of patients had squamous cell carcinoma, 36.9% had adenocarcinoma, and 4.2% had other subtypes. The clinical stage was reported according to either the 7th or 8th edition of the TNM staging system, with 78.0% of patients reported as clinical stage IIIA and 1.0% of patients as stage IIIB ,24. FurtThe most common type of resection was lobectomy (67.5%), followed by bilobectomy (12.1%), and pneumonectomy (8.6%). Surgical access was performed with minimal invasiveness through a video-assisted or robotic-assisted approach in 47.4% of operations, but 12.4% patients underwent a conversion to open thoracotomy after an intended minimally invasive approach. Overall, thoracotomy was performed in 51.7% of all operations. A complete microscopic resection (R0) was reported in 97.3% of all patients. The interquartile time interval from the final dose of immunotherapy to the time of operation was 27\u201332 days, and 2.0% of patients were delayed from their intended time of operation after treatment with neoadjuvant immunotherapy. The interquartile range of operative duration was 171\u2013239 min. A total of 11 transfusion events occurred in 417 patients (6.9%). A summary of surgical details is presented in Radiological response outcomes were consistently reported according to the Response Evaluation Criteria in Solid Tumors (RECIST) criteria . Overall2 = 73%) of patients who underwent surgery following neoadjuvant immunotherapy achieved MPR, 24% achieved pCR of the primary lesion, and 20% achieved pCR of both the primary lesion as well as the sampled lymph nodes. A summary of radiological and pathological response rates is presented in Pathological response outcomes were reported as \u2018major pathological response\u2019 (MPR) when less than 10% of the viable tumor was identified in the primary lesion, and \u2018complete pathological response\u2019 (pCR) when no viable tumor was identified. However, some studies specifically reported pCR when both the primary lesion as well as the sampled lymph nodes were free from any viable tumor ,17,19,22Overall, four deaths (0.6%) were reported within 30 days of surgery from all selected studies. However, some studies reported deaths within the same admission beyond 30 days . AdverseSix studies provided survival data in the form of Kaplan\u2013Meier graphs, but a statistical summary of these data was not possible due to different timeframes of survival calculation ,11,12,22The present systematic review and meta-analysis aimed to provide an overview of the existing evidence for patients who underwent neoadjuvant immunotherapy for resectable NSCLC. The key findings of the study identified a major pathological response rate of 52% and a complete pathological response of 24%. These values compared favorably to historical data for chemotherapy, which reported estimated rates of MPR and pCR as 22% and 4%, respectively ,27. WhenSurgical resection was performed by open thoracotomy in 51.7% of all cases, including in 12.4% patients who were converted from an intended minimally invasive approach. These findings compared favorably to outcomes reported by the National Cancer Data Base, which reported a thoracotomy rate of 73.2% and a conversion rate of 18.9% for VATS and 10.3% for robotic VATS . For patSeveral limitations should be acknowledged from the present study, and results should be interpreted with caution. Some endpoints were inconsistently reported by studies identified in the present systematic review. Most importantly, a complete pathological response was defined as \u2018no viable tumor within the resected specimen\u2019, but there was variable reporting on whether the resected lymph nodes were also assessed. Travis advocated for a systematic approach to evaluate sampled nodes, particularly in the context of clinical trials, to confirm an absence of a tumor within the nodes (ypN0) after neoadjuvant systemic therapy . SeveralMany challenging questions remain about the utility of immunotherapy for patients with resectable NSCLC. The potential prognostic value of PD-L1 (programmed death-ligand 1) was evaluated at separate cut-off points and measured against different surrogate endpoints such as MPR and pCR ,7,8,9,22"} +{"text": "To identify intramuscular rapid tranquilisation (IMRT) events in all >65 years inpatients in Sussex Partnership NHS Foundation Trust (SPFT) and to establish whether accompanying documentation meets SPFT guidelines. This is a re-audit, initial data were collected in 2016. Multimodal intervention has been implemented since initial data collection. In psychiatric inpatients IMRT should be administered as a last resort to calm acutely disturbed patients after verbal de-escalation and an offer of oral medication has failed. IMRT can cause physical health complications and impact therapeutic relationships. Quality improvements made since initial data collection were: an IMRT treatment algorithm for >65s, a teaching package for staff, IMRT prescription area on medicine cards and post IMRT physical monitoring forms \u2013 in line with updates to trust IMRT policy.Retrospective case note audit cycle of 119 patients. Electronic and paper records were reviewed for inpatients >65 years on 1/9/2019. Records were examined for instances of IMRT\u2013 the following features were noted: diagnosis; verbal de-escalation; oral medication offered prior to IMRT; IMRT prescription location; and post-IMRT monitoring. Descriptive statistics were performed. This audit was approved by the trust audit committee.There were 34 RT events in 17 patients, reduced from 83 RT events in 20 patients in 2016. De-escalation was attempted in 62% versus 34% in 2016, oral medication offered first in 71% versus 59% in 2016. Physical monitoring was fully completed in 50% of instances in 2019, an improvement from 23% in 2016.Education, a new treatment algorithm, medicine card changes, and IMRT physical monitoring forms have improved adherence to trust standards. There was a 49% reduction in IMRT events in 2019 versus 2016. De-escalation is being performed more frequently, and oral sedation offered in more cases. The physical monitoring of patients has improved."} +{"text": "Due to the availability of effective combination chemotherapies such as gemcitabine/nab-paclitaxel (GNP) or FOLFIRINOX, neoadjuvant treatment of borderline resectable (BRPC) and locally advanced pancreatic cancer (LAPC) has been increasingly investigated in recent years. However, due to toxicity, FOLFIRINOX is only available for selected patients and data on GNP are scarce. The aim of this systematic review and meta-analysis, which is to our knowledge the first addressing this question, is to evaluate the value of GNP in patients with BRPC and LAPC. We provide a comprehensive overview on data of 21 studies, comprising 950 patients treated with neoadjuvant GNP. The pooled overall and R0 resection rates were 36% and 26%, respectively. Resection rates were higher in BRPC (49%) compared to LAPC (16%). With acceptable toxicity and a median overall survival rate ranging from 12 to 30 months, neoadjuvant GNP has considerable value in this setting, with more prospective trials being warranted.Therapy with gemcitabine and nab-paclitaxel (GNP) is the most commonly used palliative chemotherapy, but its advantage in the neoadjuvant setting remains unclear. Accordingly, our aim is to evaluate the impact of first-line neoadjuvant therapy with GNP in patients with borderline resectable (BRPC) and locally advanced pancreatic cancer (LAPC). A systematic search for published studies until August 2020 was performed. The primary endpoint included resection and R0 resection rates in the intention-to-treat population. Secondary endpoints were response rate, survival and toxicity. Among 21 studies, 950 patients who received neoadjuvant GNP were evaluated. Treatment with GNP resulted in surgical resection and R0 resection rates as follows: 49% (95% CI 30\u201368%) and 36% (95% CI 17\u201358%) for BRPC and 16% (95% CI 7\u201326%) and 11% (95% CI 5\u201319%) for LAPC, respectively. The objective response rates and the median overall survival (mOS) ranged from 0 to 67% and 12 to 30 months, respectively. Neutropenia (range 5\u201377%) and neuropathy (range 0\u201322%) were the most commonly reported grade 3 to 4 adverse events. Neoadjuvant chemotherapy with GNP can be performed safely and with valuable effects in patients with BRPC and LAPC. The utility of GNP in comparison to FOLFIRINOX in the neoadjuvant setting requires further investigation in prospective randomized trials. The incidence of pancreatic ductal adenocarcinoma (PDAC) is steadily increasing in the Western world. Current estimates project a disease rate of 60,500 cases in the United States in 2021 ,4. HowevResection is the only possible chance for a cure, but due to the lack of screening methods and early symptoms, surgery is only feasible in 15\u201320% of the cases. The remaining patients with PDAC are either borderline resectable (BRPC), locally advanced (LAPC) or metastatic. After successful resection, adjuvant therapy has been shown to improve survival. A better understanding of therapy selection, initiation of therapy after resection and supportive options such as enzyme replacement and nutritional therapy resulted in increased median survival of up to 4.5 years in selected patient groups ,8.Compared to other gastrointestinal malignancies, neoadjuvant therapy (NAT) to date is of limited value in PDAC. Nevertheless, there is an important rationale for NAT in BRPC and LAPC to increase the chance for complete resection and decrease the risk of local or systemic recurrence by local downstaging and elimination of micrometastases. In addition, NAT enables identification of patients with aggressive tumor biology despite systemic therapy who do not benefit from surgery . In accoWith regard to combination chemotherapy in the neoadjuvant setting, most studies were performed with FOLFIRINOX . Meta-anMost studies to date have indicated greater efficacy and associated longer survival for FOLFIRINOX compared to gemcitabine +/\u2212 nab-paclitaxel ,4. HowevIn the past few years, several studies investigating the efficacy and safety of GNP in the neoadjuvant setting have been published and the body of evidence is growing. However, no systematic analysis of existing data has been performed yet. To provide a comprehensive overview of current evidence, we performed a systematic review and meta-analysis of published literature to evaluate the overall resection rate, R0 resection rate, toxicity and survival outcomes after neoadjuvant chemotherapy with GNP in patients with BRPC or LAPC.A systematic search for eligible articles was performed in PubMed/MEDLINE, Cochrane Library/Cochrane Central Register of Controlled Trials/CENTRAL, Google Scholar, Web of Science and LIVIVO for published studies either in English or German until August 3rd, 2020. The search terms were \u201cPancreas\u201d, \u201cCancer\u201d, \u201cNab-paclitaxel\u201d, \u201cGemcitabine\u201d and relevant variants. The study protocol has been registered at the International Prospective Register of Systematic Reviews (PROSPERO CRD42019135326).We included only randomized controlled trials and studies with prospective or retrospective observational design. Duplicates, case reports, letters, reviews and studies with no details on resection rates or studies including minors were excluded. We screened the title and abstract for each retrieved study for eligibility. If abstract screening indicated relevant content for the research question, the full text was further assessed. Studies reporting the use of first-line GNP as a neoadjuvant treatment in BRPC or LAPC with the intention to perform a resection of the tumor regardless of subsequent other treatments were selected. Studies that investigated the combination of GNP with other chemotherapy agents or radiotherapy in a neoadjuvant setting were also eligible. The reference lists of all included articles were manually searched for the identification of potentially missed studies. Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines were followed when reporting results . The floTwo reviewers (M.D. and B.B.) independently screened articles to determine eligibility. If there were disagreements, a third reviewer (R.M.) was consulted. The following information was extracted: first author, year of publication, country, study design, study population , patient groups , tumor stage , diagnostic work-up , type of intervention radiation, type and percentage of additional chemotherapy agents), surgical resection rates, R0 resection rates, duration of follow-up, overall survival (OS), progression-free survival (PFS), objective response rate (ORR) and grade 3/4 adverse events. Corresponding authors were contacted when data were missing or could not be extracted from the article. The primary outcomes were overall resection rates and R0 resection rates after first-line neoadjuvant chemotherapy with GNP. Additional outcomes were median PFS, median OS, ORR and rate of G3/G4 toxicity.I2 test, significant when p < 0.05. Publication bias was explored using funnel plots and symmetry of the funnel plot was analyzed with visual inspection. Quality assessment of studies was performed using the Newcastle-Ottawa Scale (NOS) [The meta-analyses were performed using STATA 15.0 statistical software using the package metaprop . Pooled le (NOS) and the le (NOS) . Two revAmong 2131 identified records, 77 full-text articles were assessed for eligibility and 21 studies were included in the qualitative and quantitative synthesis ,44,45,46In total, the 21 studies involved 2570 patients undergoing different neoadjuvant chemotherapy regimens in patients with resectable, borderline resectable and locally advanced PDAC .Nine studies had a prospective design and 12 were retrospective cohort studies. The prospective studies comprised one phase 2 single-center randomized open-label study with two treatment arms , one phaResectability status was based on NCCN criteria in 17 out of 21 studies. Criteria of MD Anderson Cancer Center (MDACC) and AmerMost of the studies (19/21) were intention-to-treat analyses, whereas two studies just included resected patients ,32.n = 1360), no neoadjuvant therapy (n = 173), patients with resectable PDAC and patients who were included in more than one study were excluded.For qualitative synthesis, patients with neoadjuvant therapies other than GNP Overall, 950 patients who received first-line neoadjuvant gemcitabine plus nab-paclitaxel were included in qualitative synthesis . Among t2 and nab-paclitaxel 125 mg/m2 at day 1, 8 and 15 whereas in three phase I studies different dose levels were investigated [n = 3) received additional FOLFIRINOX [n = 50) in two studies [n = 16) received S1 in the study of Kondo et al. [n = 277, refs. [In most studies (16/21), application of neoadjuvant GNP followed the standard protocol, which consisted of gemcitabine 1000 mg/mstigated ,39,46. Istigated and one stigated . The medLFIRINOX , and add studies , and allo et al. . Patient7, refs. ,36,38,43Radiological response after neoadjuvant therapy according to RECIST was available in 11/21 studies. The objective response rate (ORR) and disease control rate (DCR) ranged from 0 to 67% and from 57 to 100%, respectively. Of note, no patient showed complete response (CR) after therapy with GNP.The median overall survival (mOS) was reported in 13/21 studies and ranged from 12 to 29.9 months in studies with an ITT population. The mOS ranged from 19.8 to 43.6 months for patients undergoing secondary resection and from 10.2 to 16 months for non-resected patients. In six studies, the median progression-free survival (mPFS) was reported as ranging from 8.2 to 14.8 months, while 15 studies did not provide PFS information. Six studies reported data on mOS separately for BRPC or LAPC. The mOS in ITT analysis for patients with BRPC ranged from 14.5 to 27.9 and with LAPC from 15.7 to 19.9 months.Only 8/21 studies reported data on the toxicity of neoadjuvant GNP. The overall incidence of G3 and G4 adverse events ranged from 5 to 90% . Data onFor quantitative synthesis, 19 studies comprising 739 patients treated with neoadjuvant GNP were eligible. Two studies comprising 211 cases that only included resected patients were excluded ,32. Of 7n = 224) received additional radiotherapy and 9% received additional chemotherapy . Pooled proportions of prospective studies (n = 396) showed an overall resection rate of 42% (95% CI 24\u201361%) and an R0 resection rate of 22% (95% CI 10\u201336%) of the patients underwent surgical resection. In 26% (95% CI 15\u201338%) of all patients who underwent treatment, R0 resection was achieved . Of note 10\u201336%) .n = 444) showed overall resection and R0 resection rates of 16% (95% CI 7\u201326%) and 11% (95% CI 5\u201319%). Based on resected patients, the pooled R0 resection rates were 85% (95% CI 68\u201397%), 89% (95% CI 69\u2013100%) and 77% (95% CI 51\u201397%) for all patients, BRPC and LAPC, respectively. In prospective studies, R0 resection was achieved in 74% (95% CI 55\u201390%) of the resected patients.Among 282 patients with BRPC, surgical resection and R0 resection rates were 49% (95% CI 30\u201368%) and 36% (95% CI 17\u201358%), respectively . PatientOf note, there was heterogeneity of R0 definition among the studies: 9 of 19 studies provided information on definition of R0 resection. In six studies, absence of tumor at the margin (UICC definition), and in three studies, a minimum distance between tumor and margin of >1 mm (College of American Pathologists (CAP) definition) were defined as R0 resection .Overall, the systematic review comprised 13 retrospective cohort studies and 8 clinical trials. The retrospective cohort studies were assessed for quality using the Newcastle-Ottawa scale (NOS). Our analysis assessed four studies as having good quality, eight as having moderate quality and one was assessed as a poor-quality study . Using tTo our knowledge, this is the first systematic review and meta-analysis specifically addressing outcomes of neoadjuvant gemcitabine and nab-paclitaxel (GNP) in patients with BRPC or LAPC. With a pooled overall resection rate of 36% , a pooled R0 resection rate of 26% and a median overall survival rate ranging from 12 to 30 months in ITT analysis, our data indicate that neoadjuvant treatment with GNP has considerable beneficial value.In many other solid tumors of the gastrointestinal tract such as esophageal, gastric and rectal cancers, neoadjuvant or perioperative therapies represent an established therapeutic concept. In PDAC, however, this approach has not been implemented as standard treatment. So far, the standard in resectable disease is surgery with macroscopic complete resection followed by standard-of-care adjuvant therapy. In the non-metastatic setting, resection and in particular R0 resection are the ultimate goals since both are major determinants of long-term survival ,48. HoweIn the present meta-analysis, over 80% of the included studies assessed resectability status according to the NCCN guidelines, indicating that these recommendations have now been widely accepted . DespiteIn our meta-analysis, as expected, the overall and R0 resection rates were higher in patients with BRPC compared to patients with LAPC. However, they were significantly lower than in the most recently published meta-analyses by Janssen and Chen ,16. SixtFirst, in parallel with studies in the palliative setting, it must be assumed that the application of FOLFIRINOX is associated with a strong patient selection bias, especially in retrospective cohort studies. On average, patients receiving FOLFIRINOX are 10 years younger than the average age of the PDAC population ,3. ThereSecond, the exact protocols and the duration of neoadjuvant chemotherapies, as well as the proportion of additional (chemo-) radiation (CRT) performed, varied considerably between the studies. In the meta-analyses of Chen, Xu and Janssen et al., the median number of neoadjuvant FOLFIRINOX cycles ranged from 3 to 11.5 ,16,51. TAdditional (chemo-) radiation is widely used in the neoadjuvant setting, as it was applied in 57% of the studies with GNP and in 70\u201371% of the studies with FOLFIRINOX ,51. BefoThird, different or unclear definitions of resectability or R0 resection in the studies impede the comparability of the results. While in our analysis most of the studies followed the NCCN guidelines, up to seven different classifications of resectability were used in a total of 24 studies in the meta-analysis of Janssen et al. . In addiThe recent NEOLAP study was published after our systemic literature search was completed and was therefore not included in our analysis. However, these data have provided additional insights into many open questions in the search for the optimal chemotherapy regime. In patients with LAPC, which was the target population, neoadjuvant therapy consisting of four cycles of GNP versus two cycles of GNP plus four cycles of FOLFIRINOX was investigated . The seqThe ultimate goal is to determine whether the effect of neoadjuvant therapy followed by resection also has a positive impact on overall survival. Irrespective of categorization into BRPC and LAPC, our meta-analysis showed strong heterogeneity with variations for mOS of 12\u201330 months for the entire cohort. Previous patient-level meta-analyses of ITT populations showed a mOS of 22 and 24 months for BRPC and LAPC treated with neoadjuvant FOLFIRINOX, respectively ,15. InteThe NEOLAP study achieved a mOS of 18.5 months in the GNP group and 20.7 months in the sequential GNP/FOLFIRINOX group, which was not significantly different and altogether lower than expected from previous studies . HoweverNo data exist on the impact of adjuvant therapy after neoadjuvant pretreatment and resection. Two-thirds of the patients in the NEOLAP study received adjuvant therapy with no difference between the groups. Compared to historical data on adjuvant therapy alone after curative resection, neoadjuvant therapy does not affect capability to receive adjuvant therapy ,60.p = 0.06) [In our meta-analysis, 11/21 studies provided information on adjuvant therapy which was applied in 30\u201396% of the resected patients. Gemenetzis and colleagues showed that there was no significant difference in postoperative PFS or OS between patients with adjuvant therapy and patients without . In cont = 0.06) . HoweverIn the present meta-analysis, the most commonly reported grade \u2265 3 adverse events for neoadjuvant GNP were neutropenia and neuropathy. The occurrence of febrile neutropenia was reported with \u22644% in most of the studies. No deaths were attributed to GNP. These results are comparable to the findings of the phase III landmark trial conducted in the palliative setting . The ratSome limitations of our analysis need to be considered. More than half of the included studies were retrospective, which increases the risk of selection bias. Furthermore, two-thirds of the trials with a prospective design were phase I studies with small sample sizes. Some studies also demonstrated a limited follow-up period, among which mOS data should be interpreted tentatively. In addition, quality assessment revealed that only 30% (4/13) of the retrospective studies had good quality, and almost all of the clinical trials had high risk of bias, which might impair the validity of the observed results. Although most of the studies followed NCCN criteria for resectability, there was substantial heterogeneity, probably due to differences in patient characteristics, duration and dosage of neoadjuvant chemotherapy, such as variations in therapy additives. Similarly, the interpretation of outcomes might be hampered in part due to the lack of important information, such as data regarding the extent and impact of adjuvant therapy or how R0 resection was defined.Promising studies in the field of neoadjuvant therapy, such as NEONAX (adjuvant vs. perioperative GNP in resectable PDAC), CONCO-007 (neoadjuvant chemotherapy vs. chemoradiation in LAPC) and PREOPANC-2 (neoadjuvant FOLFIRINOX vs. chemoradiation in resectable PDAC and BRPC) are currently ongoing and are eagerly awaited. Moreover, a randomized phase III study comparing neoadjuvant GNP with modified FOLFIRINOX in patients with BRPC/LAPC (NCT0461782) with planned enrollment of 300 participants and estimated completion in 09/2023 will hopefully fill the current evidence gap on the role of GNP in BRPC and LAPC.In conclusion, this systemic review and meta-analysis demonstrates the feasibility of neoadjuvant GNP in patients with BRPC or LAPC, representing a reasonable alternative in this setting, when comorbidities preclude the use of FOLFIRINOX. However, more data from randomized prospective trials are needed."} +{"text": "To describe health care providers\u2019 knowledge about lung donation anddonor lung management.Sociedad Argentina de Terapia Intensiva.A descriptive, cross-sectional study based on an anonymous survey wasconducted between March and September 2018 among health care professionalsregistered to 2O. For 85% of the health care providers, the type ofapnea test chosen was disconnection from the ventilator, and only 18.5% useda lung management protocol. The most frequent interventions used in the caseof arterial oxygen partial pressure/fractional inspired oxygen < 300were positive end expiratory pressure titration, closed-circuit endotrachealsuctioning, and recruitment maneuvers.Of the 736 respondents, the mean age was 40.5 years (standard deviation 8.9),and 61.3% were female. Sixty percent were physicians, 21.5% were nurses, and17.9% were physiotherapists. Seventy-eight percent considered themselvesappropriately informed about organ procurement, and 79.8% stated that theyknew potential organ donor critical care management. The lung donor criteriawere answered correctly by 71.3% of the respondents. However, after thedonor\u2019s brain death, 51% made no changes to ventilator parameters,22.9% were not aware of which parameters to reprogram, and 44.5% selectedtidal volume of 6 - 8mL/kg and positive end expiratory pressure of5cmHHealth care professionals surveyed in Argentina correctly answered most ofthe questions related to lung donor criteria. However, they lacked detailedknowledge about ventilatory settings, ventilatory strategies, and protocolsfor lung donors. Educational programs are key to optimizing multiorgandonation and should be focused on protecting the donor lungs to increase thenumbers of organs available for transplantation. The high demand for transplant organs does not match thenumber of actual organ donors, and this shortage of organs is the leading cause ofdeath among patients on transplant waiting lists.2,3), incomparison to other countries such as Spain (46.9 DPMP).4,5) criteria, and donormanagement.9,10).The research questions are as follows: does the lack of knowledge regarding donormanagement impact the number of donor organ procurements? Do the multiorgan donormanagement protocols impact donor lung retrieval?This study aims to describe lung donor knowledge and management among HCPs inArgentina.Appendix -Supplementary material). This instrument wasreviewed by two experts in the field. A pilot test of the instrument wasperformed at the author\u00b4s hospital and the questions were then modifiedaccording to the respondents\u2019 feedback. The study was approved by the localInstitutional Ethics Committee through resolution 3493. This research wasconducted pursuant to the ethical principles described in national andinternational rules and regulations on human health research, in accordance withregulation 1480/2011 by the Argentine Ministry of Health, the Declaration ofHelsinki, the Declaration of Istanbul, and the Good Clinical Practice (GCP)standards issued by the National Institutes of Health. All anonymous data werehandled with strict confidentiality. Access was limited to authorized personnelonly for research purposes, pursuant to Act 25.326/00 and Act 26.529/09. Since answering the questionnaire impliedactive participation, it was assumed that respondents agreed to participate.A descriptive, cross-sectional study based on an anonymous survey was conductedbetween March and September 2018. After identifying and reviewing questionnairesalready available in Spanish, which did not cover the range of informationrequired for our study, the authors created a new self-administered instrument,the DonAR survey (Sociedad Argentina de Terapia Intensiva (SATI) is a nationalvoluntary professional organization. It includes professionals from across thecountry who work in adult, pediatric and neonatal critical care units in publicor private hospitals and emergency services, both of which are potential areasfor POD detection and donor organ procurement in Argentina.The Health care professionals responsible for the care of PODs in Argentina.All health care professionals in the SATI database were invited to participate bycompleting an online questionnaire sent by email. Biochemists, veterinarians andpharmacists were excluded from the study.The study variables were grouped into four categories: variables related todemographic characteristics - age, gender, profession, speciality, year ofgraduation from university, organ procurement region, kind of institution andworkplace, and ability to diagnose BD in the workplace; variables related toknowledge - level of knowledge, training in organ procurement and/or PODmanagement, definition of BD and detection, reporting and critical caremanagement of PODs, as well as knowledge of donation criteria for lung donors;variables related to professional experience: prior experience with patientswith potential BD - apnea testing and types of tests, engagement in PODmanagement and POD protocols; ventilation setting parameters - tidal volume (Vt)and positive end expiratory pressure (PEEP), besides POD ventilation strategy:interventions in cases of low oxygenation and types of strategies used in suchcases; types of recruitment maneuvers and PEEP titration; use of closed-circuitendotracheal suctioning and pneumonia prevention measures.Categorical variables are shown as numbers and percentages. Continuous variablesare presented as the mean and standard deviation (SD) or median andinterquartile range, according to their distribution. To determine thedistribution of the sample, histograms, skewness and kurtosis parameters, theShapiro-Wilk test was used. The analysis was performed with Stata 13.0.The questionnaire could be completed in approximately ten minutes and coveredthree domains: demographic data; general knowledge about the definition of BD,its diagnosis and lung donor criteria; and professional experience in potentiallung donor (PLD) management.A total of 751 completed questionnaires were received, and 15 were excluded. Among the surveyed health careprofessionals, the mean age was 40.5 years (SD 8.9). Overall, 61.3% were women,and physicians were the most represented professionals (60.6%), particularlyphysicians working in intensive care (72.2%). Other professionals were nurses(21.5%) and physiotherapists (17.9%), and 78.03% of the latter specialized inrespiratory critical care or cardio-respiratory care. Most respondents (74.2%)graduated after 2000, and the percentage of those working at public or privateinstitutions was similar. According to the results, 65.9% worked in adultintensive care units (ICUs), and 16.2% worked in pediatric ICUs. The responserate from the City of Buenos Aires (30.4%) was higher than that from othercities, and among regions, Pampeana had the highest response rate . A totalIn relation to organ donation, 77.6% of surveyed professionals consideredthemselves to be appropriately informed. Only 27% of respondents describedreceiving instruction on organ procurement and/or donor management processesduring their graduate studies, and 66.4% described receiving this trainingduring their postgraduate studies.To 7.2% of the respondents, BD did not imply patient death. A total of 24.3% ofrespondents identified a neurocritical patient as a POD when the Glasgow ComaScale was 7 or lower, while 70.5% of respondents considered the patient apotential organ donor only when BD diagnostic criteria were met.According to the results, 79.8% of surveyed professionals stated that they werefamiliar with POD critical care management, and 71.3% correctly identified whichoptimal conditions a PLD must fulfill.InstitutoNacional Central \u00danico Coordinador de Ablaci\u00f3n eImplante (INCUCAI) to report a patient with potential BD. A totalof 97.2% of respondents had had at least one patient with potential BD, and69.7% of respondents hadparticipated in the procurement and/or management process of a POD. Of these,88.8% had performed an apnea test at least once, with the traditional method forapneic oxygenation being the preferred choice. The main findings related to PLDmanagement are detailed in 2O. However, 22.9% were not familiar withappropriate parameters to ventilate a PLD.More than half of the professionals (54.6%) had contacted the 2O for 40 seconds ; and a pressurecontrol-continuous mandatory ventilation mode with an inspiratory pressure of20cmH2O and an incremental increase in PEEP to 20 -30cmH2O .In the case of a PLD with low oxygenation, defined as the ratio of arterialoxygen partial pressure to fractional inspired oxygen less than < 300, 84.1%of respondents reported making some kind of intervention. The most frequentlychosen type of PEEP titration was the PEEP/Compliance Protocol .The choice of recruitment maneuver was heterogeneous, and the most frequentmaneuvers performed were an incremental increase in PEEP to 40cmH2O, followed byan incremental decrease ; a continuous positive airway pressure(CPAP) of 40cmHFinally, most respondents used closed-circuit endotracheal suctioning (91.8%) andmaintained ventilator-associated pneumonia prevention measures.The main findings of this study were that although most of the professionals surveyedanswered lung donor criteria correctly and claimed knowledge of POD management,nearly a quarter did not know which ventilation parameters to select for PLDs, andalmost half of them did not choose the recommended ventilatory strategy for PLDs;most used disconnection from the ventilator as an apnea test, and just a few usedPLD management protocols.17)( Thus, concerns about donor organshortages can be turned into actions, and actions into procurement. Despitelimitations arising from the size and the selection of the sample, the results ofthis study revealed that there is a lack of specific knowledge about ventilationstrategies as well as an underidentification of POD and a need for PLD managementprotocols.The results help us to understand some barriers that may be overcome by changingoverall organ procurement processes, especially lung procurement processes, inArgentina. Strategies to mitigate the unmet demand for transplant organs must targethealth care teams working with neurocritical patients at risk for BD, who canidentify, report, and manage potential donors.Teaching and training health care professionals in Argentina to improve the currentlylow lung donation rates is key. The challenge is to cultivate a multidisciplinaryteam that succeeds in treating multiorgan donors with a focus on protecting thelungs to increase donor lung availability for transplantation, thus saving a greaternumber of lives."} +{"text": "OBJECTIVES/GOALS: While there are many well-documented factors for racial/ethnic variation in discharge destination, less is known about the role hospital processes play. We hypothesize that variation in hospital processes -defined as the patient length of stay (LOS) adjusted for known confounders - explains racial/ethnic variation in discharge destination. METHODS/STUDY POPULATION: Our sample was 176,686 discharges from 165 hospitals in 2014 using the New York State Inpatient Dataset from the Healthcare Cost and Utilization Project, merged with the 2014 American Hospital Association Annual Survey to build a file of inpatient discharges with patient, disease and socio-economic characteristics. We excluded patients under 18 years, those with LOS of zero, those who died, those admitted to critical access hospitals, and patients from hospitals that lacked sufficient number of minority patients. We used a generalized linear mixed effects model to create an in-hospital risk-adjusted LOS by modelling the relationship between the interaction of race and discharge destination and LOS, controlling for known confounders such as patient, disease and between-hospital characteristics. RESULTS/ANTICIPATED RESULTS: Mean age of sample was 56.5 years, 57.3 % female, 54.9% white, 18.9% black and 13.1% Hispanic; 64.3% were discharged home, 15.8% to a skilled nursing or other intermediate care facility, 15.5% to home with home care and 2.4% left against medical advice. The top 3 discharge diagnoses were vaginal delivery (6.3% of discharges), psychosis (4.7%), and major joint replacement (2.9%). In adjusted analysis compared to white patients, black and Hispanic patients did not have an risk of increased LOS after being discharged to non-home destinations vs. discharged home, . However, being black compared to white and discharge to non-home destinations significantly increased LOS. DISCUSSION/SIGNIFICANCE OF IMPACT: In this large sample of patients admitted for inpatient care in 2014 in New York, we found no independent effect between race and discharge destination on a patient\u2019s LOS after controlling for patient, disease and between-hospital characteristics. However race/ethnicity increased LOS, suggesting its effect may play a role on in-hospital processes CONFLICT OF INTEREST DESCRIPTION: Dr. Ghosh has no relevant relationships with commercial interests to disclose Dr. Ibrahim has no relevant relationships with commercial interests to disclose"} +{"text": "Particle irradiation is suitable for resistant histologies owing to a combination of improved dose delivery with potential radiobiologic advantages in high linear energy transfer radiation. Within the head and neck, adenoid cystic carcinoma and mucosal melanoma are two such histologies, being radioresistant and lying closely proximal to critical structures. Here, we review the use of particle irradiation for adenoid cystic carcinoma and mucosal melanoma of the head and neck. Particle irradiation is suitable for resistant histologies, owing to a combination of improved dose delivery with potential radiobiologic advantages in high linear energy transfer (LET) radiation. Within the head and neck (H&N), adenoid cystic carcinoma (ACC) and mucosal melanoma (MM) are 2 such histologies, radioresistant and lying closely proximal to critical structures . Here, wThe benefits of particle therapy are more clearly noted when compared with conventional irradiation and vary with the particle employed . Three dNeutron irradiation bears a similar dose distribution to conventional radiotherapy but with notably higher LET. Consequently, increased direct nuclear damage is seen in target tissue, with an effective RBE for fast neutrons between 2 and 4 , 9. Due ClinicalTrials.gov were conducted on August 5, 2020 is uncommon, accounting for approximately 1% of malignant H&N tumors . ACC is Much of the data regarding proton treatment of ACC comes from Massachusetts General Hospital. A total of 23 patients with newly diagnosed ACC with skull base extension were treated with combined proton and photon therapy from 1991 to 2002. With a median of 75.9 GyE, the 5-year local control (LC) was 93% . SimilarReviewing patients from MD Anderson Cancer Center, Bhattasali et al presenteMorimoto et al reportedMost recently, Pelak et al reviewedProton therapy has also been used with some success in case reports and small retrospective studies for treating cutaneous ACC of the cavernous sinus , eyelid Proton irradiation has been used successfully in the setting of reirradiation. Sixty-one patients with second primary tumors following previous radiotherapy were reviewed. Of the analyzed patients, 16.4% had ACC. Median dose was 66 GyE to microscopic disease, and 70.2 GyE to gross residual. The 2-year OS was 32.7% with a median OS of 16.5 months for all histologies. Grade-3+ acute toxicity was seen in 14.7% of patients and late toxicity in 24.6%, including 3 treatment-related grade-5 toxicities .Massachusetts General Hospital is currently comparing intensity-modulated radiation therapy (IMRT) with proton radiotherapy in a phase II trial across H&N malignancies, including ACC (NCT01586767). Memorial Sloan Kettering has a phase II trial investigating endoscopic resection followed by adjuvant concurrent proton therapy and cisplatin for sinus and nasal tumors, including ACC (NCT03274414).In 2004, the University of Heidelberg reported the early results of 21 patients treated with combination photon and carbon-ion radiotherapy (CIRT) for unfavorable ACC. Notably, the 3-year LC was 62% with no grade-3+ toxicity . The firIn Japan, Mizoe et al reportedThe Japan Carbon-Ion Radiation Oncology Study Group (J-CROS) conducted a retrospective review of 69 patients, including 33 patients with ACC, finding 3- and 5-year LC rates of 81% and 74%, respectively. No acute grade-4+ toxicity was seen, although 10% experienced grade-3 mucositis and 10% experienced grade-3 dermatitis. Two patients experienced grade-3 late toxicities, with one having dysphagia and another having a brain abscess .Sulaiman et al followedSinonasal disease tends to be particularly aggressive and near critical organs at risk, including the optic structures. Hagiwara et al analyzedCIRT has demonstrated efficacy and tolerability in other disease sites, including the larynx , lacrimaCIRT has further shown efficacy for reirradiation. At Heidelberg, Combs et al reportedRecently, the Italian National Center of Oncological Hadrontherapy (CNAO) reported on 51 patients with inoperable recurrent salivary gland tumors treated with CIRT as part of the phase II CNAO S14/2012C protocol. Approximately 75% of patients had ACC. With a median follow-up of 19 months, 41% of patients had stable disease and 59% had progression at time of last follow-up, with a 2-year PFS of 52% .Currently, multiple investigators are conducting clinical trials on the role of CIRT for ACC . The phaParticle therapy is also being investigated in combination with different systemic therapies. In Heidelberg, the ACCEPT trial is a phase I/II feasibility trial of combined IMRT with CIRT boost and cetuximab (NCT01192087). Apatinib is being investigated for combination with particle radiotherapy for H&N ACC at the Shanghai Proton and Heavy Ion Center. In this phase II study, patients were randomized to 56 GyRBE proton followed by 15 GyRBE CIRT boost with or without apatinib 0.5 g daily (NCT02942693).Although fast neutron therapy (FNT) was a promising technique, the availability is currently limited in the United States due to challenges with funding and modern national experience. Similar to other particles, neutrons have a relatively high LET, with a maximum RBE as high as 26 when treating bone marrow ; the inaMost prominently, the randomized RTOG/MRC FNT study evaluated 32 patients with inoperable, recurrent, or unresectable salivary gland tumors, randomizing between FNT and photon therapy in the United States and Scotland. The complete tumor clearance was 85% for neutrons and 33% for photons . At 10 yThe most recent retrospective cohort study was reported in 2019 by Timoshchuk et al . A totalWhen taken together, particle therapy provides excellent 5-year LC of approximately 65% to 90% for ACC. For instance, Samant et al reportedThe comparison of these results is limited, however, by the heterogeneity in both radiation technique and use with concurrent chemotherapy. For instance, studies involving ACC are often pooled with other histologies and disease sites over a prolonged period, making analysis of only ACC with a given radiation technique implausible. Regardless, particle therapy appears to have superior results to conventional photon-based irradiation, and further randomized clinical trials are unlikely to be powered effectively due to the rarity of the disease.Accounting for less than 1.3% of all melanomas, MMs are notably rare. Half arise in the H&N, typically in the nose, paranasal sinuses, oral cavity, pharynx, and/or larynx. Notable epidemiologic variation exists between races, with MMs encompassing 8% of all melanomas in Japanese patients vs 1% in white patients, with concentration in men and ties to tobacco usage . Owing tFuji and colleagues reportedZenda and colleagues presenteIn 2014, Demizu and colleagues presenteProton therapy has also been used with success in adjuvantly treating MM of the palatine tonsil after partial pharyngectomy with left level I-V neck dissection. This patient was free of disease 11 months after surgery and 8 months after RT .In the United States, Christopherson and colleagues reviewedIn 2004, Mizoe et al conducteP = .007). They concluded that CIRT may be preferential in radioresistant disease, while proton appears to match the best conventional results with less frequent toxicity [In a 2010 systematic meta-analysis, Ramaekers and colleagues comparedtoxicity .In 2014, Demizu et al conducteIn 2016, Mohr and colleagues from theKoto et al conducteIn 2017, Naganawa and colleagues retrospeTakayasu and colleagues at GunmaKoto et al , in collLiao and colleagues at the ULike ACC, comparison of results with MM with particle therapy and conventional photon therapy is limited by the generally low number of patients, as well as the heterogeneity of treatment techniques and pooled cohorts of various anatomic sites. For instance, treatment with surgical resection before adjuvant radiation and the use of chemotherapy confound comparison. Studies of photon-based treatments estimate a 5-year LC of 35% to 79% and 5-year OS of 16% to 45% , 85\u201389.A complete analysis of toxicity using photon-based techniques is limited given the heterogeneity of photon technology and toxicity reporting. Hallemeier et al reportedACC and MM are notably rare diseases, and the paucity of cases with geographical and demographic biases limits the generalizability of definitive treatment data. Many publications are pooled analyses, and overlap of patient cohorts between reports is likely. Similarly, patient course was noted to be heterogeneous between trials, with varying adjuvant and salvage approaches incorporated that may have gone underreported. Additionally, direct comparison between the different types of particles is impractical given the limited availability of centers treating with CIRT and neutron therapy.Nonetheless, particle therapy appears a viable means by which to improve disease control, with the high-LET and conformal carbon-ion beam demonstrating unique promise in critical-adjacent radioresistant disease. Summarized, proton therapy and carbon-ion therapy provide excellent 5-year LC rates, ranging from 73% to 90% for ACC and 62% to 84% for MM; survival remains limited by systemic disease control. Currently, routine use of particle therapy for ACC and MM is limited primarily by the low number of centers treating with particles. Consideration for a phase III trial is complicated by disease rarity and consideration of clinical equipoise versus conventional treatment; in the absence of a prospective and randomized approach, propensity-standardized comparative exploration is warranted, and ongoing retrospective multi-institutional updates should be released as follow-up time course accrues."} +{"text": "Information from these records was used to calculate incidence and mortality and corresponding 95% confidence intervals (CIs) by population group. Population estimates were calculated using data from the U.S. Census Bureau.During March 1, 2020\u2013February 28, 2021, in Hawaii the COVID-19 incidence was 1,477 per 100,000 population and mortality rate was 32 per 100,000 population . In aggrAmong Asian persons, there was also substantial variation in incidence among subgroups after disaggregation . The highest incidence of cases among Asian persons were among Filipino persons and Vietnamese persons ; incidence among Japanese persons was 568. Among Asian subcategories, crude mortality rates ranged from 20 deaths per 100,000 population among Chinese persons to 33 among Japanese persons.Disaggregation of COVID-19 data in Hawaii revealed substantial disparities in COVID-19 case and mortality rates during March 1, 2020\u2013February 28, 2021, among Native Hawaiian, Pacific Islander, and Asian persons that were obscured in the aggregate data. Detailed information on disparities in COVID-19 cases and deaths among Marshallese persons has been reported , and supported community outreach . Prevention messaging incorporated cultural values and highlighted messages of protecting community; alternative strategies were encouraged for engaging in important cultural traditions and practices . These efforts complemented efforts by advocate organizations and grassroots initiatives within Native Hawaiian, Pacific Islander, and Filipino communities.The findings in this report are subject to at least six limitations. First, these data could underestimate COVID-19 case rates because of undetected cases and the exclusion of 18% of cases because data on race were missing. Second, case information was not available on characteristics such as occupation, income, and education, which can influence COVID-19 outcomes, and nativity and generational status, which might be associated with access to services and other social determinants of health. Third, the examination of disparities among specific combinations of categories was not possible because detailed U.S. Census data to calculate these rates were not available. Fourth, differences in the collection of race information between the case surveillance system and U.S. Census forms might have led to overestimation of rates among some race subgroups. For some races, race information was collected using explicit check-box options during case investigations, and in the U.S. Census, race information was collected through written-in free text that was later coded.Substantial disparities in COVID-19 incidence and mortality rates during March 1, 2020\u2013February 28, 2021, were identified through community-informed data disaggregation among Native Hawaiian, Pacific Islander, and Asian subgroups in Hawaii. The disparities identified among Marshallese, Other Micronesian, Samoan, Filipino, and Vietnamese persons, which were obscured in aggregated analysis, highlight the importance of partnering with these populations to develop culturally responsive outreach teams and tailored public health interventions and vaccination campaigns to more effectively address health disparities.Aggregated race data can obscure health disparities among subgroups.During March 2020\u2013February 2021, community-informed data disaggregation in Hawaii indicated Pacific Islander persons, who account for 5% of the Hawaiian population, represented 22% of COVID-19 cases and 22% of COVID-19\u2013related deaths. Among Asian populations, the highest COVID-19 incidences occurred among Filipino and Vietnamese persons.Disaggregating race data can aid in identifying racial disparities among specific subpopulations and highlights the importance of partnering with communities to develop culturally responsive outreach teams and tailored public health interventions and vaccination campaigns to more effectively address health disparities."} +{"text": "Background andObjectives: This 10-year multicenter retrospective study reviewed the clinical manifestations, diagnostic tests, and treatment modalities of tubercular uveitis (TBU), including direct infection and indirect immune-mediated hypersensitivity to mycobacterial antigens in Taiwan. Materials and Methods: This retrospective chart review of patients with TBU was conducted at 11 centers from 1 January 2008 to 31 December 2017. We used a multiple regression model to analyze which factors influenced best-corrected visual acuity (BCVA) improvement. Results: A total of 79 eyes from 51 patients were included in the study. The mean age was 48.9 \u00b1 16.4 years. The mean change of LogMAR BCVA at last visit was \u22120.21 \u00b1 0.45. Diagnostic tools used include chest X-ray, chest computed tomography, Mantoux test, interferon gamma release test (QuantiFERON-TB Gold test), intraocular fluid tuberculosis polymerase chain reaction, and bronchial alveolar lavage. The clinical manifestations included 48% posterior uveitis and 37% panuveitis. In the sample, 55% of the cases were bilateral and 45% unilateral. There was 60.76% retinal vasculitis, 35.44% choroiditis, 21.52% serpiginous-like choroiditis, 17.72% vitreous hemorrhage, 12.66% posterior synechiae, 6.33% retinal detachment, and 3.80% choroidal granuloma. Treatment modalities included rifampicin, isoniazid, pyrazinamide, ethambutol, oral steroid, posterior triamcinolone, non-steroidal anti-inflammatory drugs, vitrectomy, and immunosuppressants. BCVA improved in 53.2% of eyes and remained stable in 32.9% of eyes. In the final model of multiple regression, worse initial BCVA, pyrazinamide, and receiving vitrectomy predicted better BCVA improvement. Ethambutol was associated with worse visual outcomes. Seven eyes experienced recurrence. Conclusions: This is the largest 10-year multicenter retrospective study of TBU in Taiwan to date, demonstrating the distribution of clinical manifestations and clinical associations with better treatment outcomes. The study provides a comprehensive description of TBU phenotypes in Taiwan and highlights considerations for the design of further prospective studies to reliably assess the role of ATT and vitrectomy in patients with TBU. Tuberculosis (TB) is an airborne disease mostly caused by Mycobacterium tuberculosis (MTB). It is a slowly progressive, chronic, necrotizing or non-necrotizing, and granulomatous or nongranulomatous infection, which usually infects the lungs. Only 10% of infected individuals become symptomatic. Moreover, 90% of those with latent TB remain infected without manifesting diseases. Alveolar macrophages acquire phagocytic and bactericidal functions and may limit the pulmonary infection. However, some organisms may escape through lymphatics or blood resulting in seeding of other organs, such as the cardiovascular system, gastrointestinal system, musculoskeletal system, genitourinary tract, central nervous system, skin, and eyes .Ocular TB encompasses any impact by MTB in the eye, around the eye, or on its surface. It can be acquired by direct infection or an indirect immune-mediated hypersensitivity response to mycobacterial antigens, and is a great mimicker of various uveitis entities ,4,5. PriThere are two possible pathophysiological mechanisms of TBU: one is active spread via blood circulation and direct invasion of MTB into intraocular tissues, such as choroidal granuloma, and the other is delayed hypersensitivity immunological response to MTB perched other places in the body, not associated with local replication of the pathogen, like in serpiginous choroiditis. Therefore, combined anti-infectious and anti-inflammatory treatment are necessary.The definite diagnosis of TBU is challenging due to the difficulty in demonstrating acid-fast bacilli on smears or histopathology in intraocular specimens. The paucity of available intraocular tissue is another issue. Molecular diagnostic techniques such as polymerase chain reaction (PCR) from aqueous or vitreous humor have low sensitivity due to the low bacterial load in ocular fluids and the thick cell wall of MTB ,9,10,11.This 10-year multicenter retrospective study reviews the clinical manifestations, diagnostic tests, and treatment modalities of TBU in Taiwan. We also use multiple regression model to analyze which factors will influence best-corrected visual acuity (BCVA) improvement.This retrospective chart review of patients with TBU was conducted at 11 Taiwan medical centers from 1 January 2008 to 31 December 2017 in compliance with the tenets of the Declaration of Helsinki. IRB approval was obtained for all sites. Standardization of uveitis nomenclature scoring of anterior chamber cell and flare; anterior and posterior synechiae; lens opacity or precipitates; and vitreous haze score (standardized Nussenblatt scheme) were recorded. The clinical manifestations of TBU in this study include anterior uveitis , intermediate uveitis , posterior uveitis , panuveitis, neuroretinitis, and optic neuropathy. Rubeosis iridis, neovascular glaucoma, retinal detachment, and vitreous hemorrhage were also recorded.The guidelines for diagnosis of TBU are as follows: (1) exclusion of other uveitis diagnoses; (2) a clinical history and signs compatible with TBU; (3) ocular examinations revealing direct evidence, positive acid fast bacilli, positive culture of MTB, or positive PCR of ocular fluid for MTB; 4) systemic investigations as corroborative evidence, including positive Mantoux test, positive IGRA (QuantiFERON-TB Gold test), positive chest images, or confirmed active extrapulmonary TB; and 5) positive therapeutic response to anti-TB therapy (ATT) [ systemic positiveThe clinical manifestations, diagnostic tests, and treatment modalities of TBU were reviewed and recorded. Because this was a 10-year retrospective multicenter chart review study, the treatment strategy with regards to treating patients as active TB or latent TB could not be standardized across all centers. A multiple regression model was used to analyze which factors influenced BCVA improvement. As for the statistical methods, SAS 9.4 was used for analysis in this study. For comparison of cross-section data, one-way ANOVA was used for continuous data and Fisher\u2019s exact test was used for categorical data. For comparison of serial data, principle of generalized linear mixed model (GLMM) was applied with use of GLIMMIX procedure in SAS.To build a prediction model to find possible factors that might influence functional outcome (BCVA), multiple regression was performed with Proc Reg in SAS. The outcome was final change of LogMAR BCVA and the predictors (independent variables) included age, gender, location, initial BCVA, existence of co-morbidities, vitreous hemorrhage, posterior synechiae, choroidal granuloma, choroiditis, neovascular glaucoma, retinal detachment, retinal vasculitis, rubeosis iridis, serpiginous-like choroiditis, recurrence of uveitis and treatment modalities. The selection method was stepwise with entry significance level setting at 0.05 and stay significance level setting at 0.05.A total of 79 eyes from 51 patients were evaluated in this study. The study group consisted of 24 males and 27 females, and the mean age was 48.9 \u00b1 16.4 years (range 10\u201382). The mean LogMAR BCVA at presentation was 0.57 \u00b1 0.61. The mean LogMAR BCVA at last follow-up was 0.35 \u00b1 0.58. The mean change of LogMAR BCVA at last visit was \u22120.21 \u00b1 0.45. The mean follow-up period was 18.20 \u00b1 24.05 months. Seven eyes experienced recurrence .The clinical manifestations comprised of 48% (38 eyes) posterior uveitis, 37% (29 eyes) panuveitis, and 15% (12 eyes) intermediate uveitis. In the sample, 55% cases were bilateral and 45% unilateral. There was 60.76% retinal vasculitis, 35.44% choroiditis , 21.52% serpiginous-like choroiditis , 17.72% vitreous hemorrhage, 12.66% posterior synechiae, 6.33% tractional retinal detachment, and 3.80% choroidal granuloma. No rubeosis irides or neovascular glaucoma was recorded . VitreouThe diagnostic tools utilized include chest X-ray, chest computed tomography (CT), Mantoux test, IGRA, intraocular fluid real-time PCR assay for MTB DNA, and bronchial alveolar lavage. The percentage of positive rate for individual diagnostic test were 3.8% bronchial alveolar lavage, 5.06% intraocular fluid MTB PCR, 7.59% Mantoux test, 27.85% chest CT, and 27.85% chest X-ray. The most sensitive test was IGRA with sensitivity up to 84.81%. The most frequent diagnostic patterns include 51% only IGRA positive; 11% both IGRA and chest CT positive; 9% IGRT, chest CT, and chest X-ray positive .The treatment modalities included 70.89% rifampicin, 68.35% isoniazid, 56.96% pyrazinamide, 50.63% ethambutol, 43.04% oral steroid, 19.83% posterior triamcinolone, 16.46% non-steroidal anti-inflammatory drugs (NSAIDs), 10.53% vitrectomy, and 4.11% immunosuppressants . Some auBCVA improved in 53.2% of eyes, remained stable in 32.9% of eyes, and worsened in 13.9% of eyes. The mean LogMAR BCVA significantly enhanced from 0.57 to 0.35 after treatment . We use In the literature, clinical manifestations of TBU include granulomatous or nongranulomatous acute anterior uveitis, broad-based posterior synechiae, iris nodules, ciliary body tuberculoma, granulomatous or nongranulomatous intermediate uveitis, posterior uveitis, panuveitis, neuroretinitis, and optic neuropathy ,4,12,13.This 10-year retrospective chart review study showed that the clinical manifestations of TBU in Taiwan contain retinal vasculitis, choroiditis, serpiginous-like choroiditis, vitreous hemorrhage, posterior synechiae, tractional retinal detachment, and choroidal granuloma. Although anterior segment manifestations could occur simultaneously, posterior segment involvement is the more common form of TBU in Taiwan. Retinal vasculitis is the most frequent form of posterior involvement, along with choroiditis and vitreous hemorrhage.In Asian populations, retinal vasculitis is a common presentation of TBU; however, in a study of a referral eye center in Iraq, vitritis was a universal finding, while multifocal choroiditis was the most common fundus lesions . In someMost diagnoses of TBU in our study were based on ocular signs consistent with TBU and positive IGRA. The majority of cases with TBU did not have any history or symptoms of other systemic TB, and the majority of patients (72.1%) had a negative finding in their chest X-ray.The Mantoux test is one of the few investigations from the 19th century . A posit. It has been recommended to initiate early ATT in patients with positive IGRA results and high suspicion of TBU.Real-time polymerase chain reaction (PCR) assay has been applied for the detection of MTB complex in clinical specimens. The inherent difficulties in obtaining adequate intraocular histopathological samples for TB PCR limit its use ,9,10,11.The methods used for TBU diagnosis showed great variety of sensitivity in Taiwan. The leading positive rate for individual diagnostic test was 27.85% chest CT, 27.85% chest X-ray, and 84.81% IGRA. We further analyzed the patterns of positive diagnostic tests for individual eyes. The most frequent patterns were 51% only IGRA positive followed by 11% IGRA and chest CT positive, and 9% IGRT, chest CT, and chest X-ray positive. Therefore, the majority of TBU diagnoses in the study was based on clinical manifestations and positive IGRA.Tuberculous retinal vasculitis (TRV) is typically an obliterative periphlebitis, resulting in retinal nonperfusion, which may induce proliferative retinopathy. Long-term complications of TBU with peripheral neovascularization and recurrent vitreous hemorrhage may lead to retinal detachment and/or macular pucker . Close mWhen investigating patients with uveitis, it is not uncommon for there to be no identifiable systemic disease, with the only positive test being an IGRA ,30. In sThe COTS consensus statements for the initiation of ATT in TBU is treatment with fixed dose combination anti-tubercular treatment (Rifafour e-275), which includes rifampicin, isoniazid, pyrazinamide, and ethambutol hydrochloride for the first 2 months . HoweverIn our present study, about 70% of patients received rifampicin and isoniazid. Around half of the patients received pyrazinamide and ethambutol. Steroid, immunosuppressants , and NSAThe mean LogMAR BCVA significantly increased from 0.57 to 0.35 after treatment. Therefore, we use multiple regression analysis to see which factors will influence the degree of improvement of BCVA. In the final model of multiple regressions, worse initial BCVA, pyrazinamide, and receiving vitrectomy predicted better BCVA improvement.Pyrazinamide is bactericidal for MTB. It is largely absorbed from the gastrointestinal tract and penetrates most tissues, including cerebrospinal fluid (CSF). Pyrazinamide and isoniazid are fairly lipophilic small molecules and therefore optimal drugs for the management of central nervous system (CNS) infections . It appeWe also found use of ethambutol to be associated with worse visual outcome. Ethambutol is a bacteriostatic drug and has significant ocular toxicity, especially in patients with pre-existing ophthalmic disease, such as TBU. Optic neuritis is the most common complication and could happen in axial and periaxial forms. Axial optical neuritis manifests with decreased central visual acuity and green color perception and is associated with macular degeneration. Periaxial optic neuritis results in paracentral scotomas with normal vision and color perception. Other ocular side effects consist of extraocular muscle paresis, photophobia, and toxic amblyopia ,36.Although it would be statistically easier to manage single eye data from single patient, using eye-level data or individual-level data for ophthalmology study has been a long-standing debate. A very thorough review by Murdoch mentions many shortcomings and possible biases that might come from single-eye-per-individual data: (1) Unless we are certain that the disease has absolutely no laterality, choosing single eye has the risk of potential bias. (2) The major disadvantage of this approach is the loss of information. As the author described, the data might be statistically valid, but the power and precision of the analysis are less than optimal. (3) Another disadvantage of this approach is the potential for biases arising through the choice of which data to use .Often, if data are only available on a single eye in an individual because of incomplete data or for other reasons, that single eye is included in the analysis. Bias could occur if some individuals have data on both eyes, only one of which is \u201crandomly\u201d selected for analysis, while other individuals have data on only one eye which is automatically included . The non-random selection of eyes can introduce bias. Similar caveats apply to the choice of the first eye with disease, worse/better eye, or operated eye.They also mentioned some disadvantages of pooling or averaging results from right and left eyes. Meanwhile, in their review, there were up to 20% of qualitative studies which used data from all eyes (eye-level data). Because pros and cons exist for both types of data utilization, the author provided a formula to calculate the intraclass correlation coefficient and it is identical to kappa statistic. They suggested if this indicator is less than 0.3, the correlation between eyes can be treated as acceptable. The formula is: (P2eyes-Peye^2)/(Peye (1-Peye)). Where P2eyes is the proportion of individuals with the finding in both eyes and Peye is the proportion of eyes with the finding. The result of this coefficient from our data is \u22120.29.Therefore, we opine that it is acceptable to use eye-level data for analysis in our study.The 1-year follow-up of the COTS-1 of TRV showed no significant therapeutic effects of ATT . NeverthThere are some limitations of this study. First, some diseased eyes came from the same patients. This might induce some bias for clinical manifestations that could be influenced by personal characteristics. However, because of the very low incidence of this disease entity, we opine that only including a single diseased eye from each person might also possibly exclude many valuable information that might be person-independent and also weaken the power of this study by further decreasing sample size. We treated our study as an innovative but preliminary one, which will inspire more stringent large-scaled intervention studies in the future. The other limitations of this study are the retrospective methodology, the lack of control group analysis, and the lack of standardized treatment protocols, which led to missing data and inability to account for severity of inflammation in outcomes analyses. However, this is the largest data set of TBU to date in Taiwan using 10-year data collected from 11 tertiary referral ophthalmology centers. The current study addresses the multicenter data and standardized criteria for inclusion and treatment outcomes.Based on this study of TBU in Taiwan, IGRA is a helpful diagnostic tool in uveitis patients and it should be covered by Taiwan national health insurance reimbursement in the future. The presence of active typical ocular inflammation and a positive IGRA, with or without other systemic signs, could be considered as possible TBU.In this long-term multicenter retrospective study, BCVA showed significant improvement after treatment. The final model of multiple regression showed that worse initial BCVA, pyrazinamide therapy, and receiving vitrectomy predicted better BCVA improvement. Use of ethambutol was associated with worse visual outcome after treatment. The current study provides a comprehensive description of TBU phenotypes in Taiwan and highlights considerations for the design of further prospective studies to reliably assess the role of ATT and vitrectomy in patients with TBU."} +{"text": "Area Agency on Aging (AAA) senior and adult day centers closed due to COVID-19, causing many older adults to lose an important source of connection and engagement, leading to social isolation. To combat negative consequences, iN2L and a Florida AAA partnered on an innovative program providing iN2L tablets to AAA-supported older adults to use at home. The tablets have a simple interface, content specifically designed for older adults , and video call capability. Participants included 51 independent older adults (mean age 77) and 39 family caregivers (mean age 59) of people with dementia. Participants completed phone surveys with AAA case managers at baseline and 3 months, including UCLA Loneliness Scale (3 item) and questions about their tablet experiences. Findings show positive trends for loneliness and well-being in both groups. At 3 months, lonely participants decreased from baseline by 25% for independent older adults and 18% for family caregivers. Over 80% of independent older adults agreed the tablet engages them in meaningful activities, provides daily enjoyment, and helps with relaxation. For family caregivers, 79% agreed the tablet is another tool in their caregiver toolkit and about 70% agreed the tablet adds daily enjoyment, helps with relaxation, and provides engagement in meaningful activities for their family member. Approximately 50% of caregivers felt happier, less stressed, and less irritable since using the tablets. This work has implications for the utility of technology in promoting engagement and connection, alleviating negative effects of social isolation, and the effectiveness of industry-AAA partnerships."} +{"text": "The United States (US) is one of the most affected countries by the COVID-19 pandemic. A disproportionate burden of COVID-19 deaths is seen in Black, Asian, and Latinx groups. COVID-19 vaccines are the primary mitigation strategy to reduce morbidity and mortality. However, vaccine hesitancy is high in these communities due to factors such as low health literacy, language barriers, and other health inequities. Our objective was to implement a culturally sensitive, multi-lingual, community outreach model to promote vaccine education and facilitate vaccine administration.Community healthcare workers or \u201cpromotoras\u201d were deployed to high traffic areas such as supermarkets, laundromats, churches, and commercial hubs from February-May 2021. The promotoras provided culturally sensitive vaccine counseling to individuals in their preferred language and facilitated vaccine appointments at our hospital. Our data was compared with publicly available data from other facilities organized by ZIP codes defined by the Department of Public Health as low, medium, or high-vulnerability to COVID-19.A total of 109 outreach workers were hired, of which 67% (73) were Latinx, 27% (29) Black and 6% (7) Asian. Overall, 8,806 individual encounters led to 6,149 scheduled appointments and 3,192 completed first doses . A total of 14,636 individuals were vaccinated. Average age was 45.5 (range 12-98). Preferred language was 54% Spanish, 38% English, and 8% Chinese. Ethnicity was mostly Hispanic (66%) with race mostly white (54%) . High and medium-risk ZIP codes represented 69.4% of vaccinations at our facility .Figure 1. Education encounters and appointments made by community outreach workers and associated vaccinations.Figure 2. Racial distribution of vaccinated individuals at our facilityFigure 3. Comparative vaccinations by zip codes from hospitals in our area.We successfully implemented a culturally sensitive community outreach model which resulted in higher vaccination rates from at risk ZIP codes when compared to other hospitals. Promotoras encouraged vaccination in native languages, thereby increasing vaccine awareness and appointment faciliation. Barriers to vaccine access remain in these vulnerable communities. This model educated the community via its own members and may help reduce barriers, increase vaccine awareness and vaccination rates.All Authors: No reported disclosures"} +{"text": "Understanding how recent alcohol or drug use among older adults involved in car crashes can inform emergency care team on the morbidity and mortality risks. This study aimed to assess the odds of worsened health outcomes among older adults with evidence of alcohol or drug ingestion. This cross-sectional analysis used crash census data from the National EMS Information System. The outcome variable was the health outcome after EMS care, measured on a four-point ordinal scale: lower acuity, emergent, critical, and dead. The predictor variable was alcohol/drug use (present/not present). Age, race, gender, part of the body injured, and the revised trauma score of the patients were used as confounders. Odds ratio were calculated using proportional ordinal logistic regression. A total of 42,992 individuals, aged 65 years and older, were involved in car crash events, which required EMS activation. About 22.9% needed emergent care, 4.4% were classified as critical, and 0.4% died without resuscitation efforts. At the time of crash, 3.8% of the older population had evidence of alcohol or drug use. After adjusting for age, gender, race, injury location and revised trauma score of the crash patients, alcohol/drugs were associated with 54% increased odds of worse clinical outcome . The adjusted odds remained elevated in urban and suburban and not significantly elevated in rural areas. Study findings can inform EMS service and emergency room care as well as policies that strengthen the urban and suburban EMS."} +{"text": "Viruses are responsible for a large proportion of acute respiratory tract infections (ARTIs). Human influenza, parainfluenza, respiratory-syncytial-virus, and adenoviruses are among the leading cause of ARTIs. Epidemiological evidence of those respiratory viruses is limited in the East Africa Community (EAC) region. This review sought to identify the prevalence of respiratory syncytial virus, parainfluenza, and adenoviruses among cases of ARTI in the EAC from 2007 to 2020.2 statistic, and Cochran\u2019s Q test, and further we did subgroup analysis. This review was registered with PROSPERO under registration number CRD42018110186.A literature search was conducted in Medline, Global Index Medicus, and the grey literature from public health institutions and programs in the EAC. Two independent reviewers performed data extraction. We used a random effects model to pool the prevalence estimate across studies. We assessed heterogeneity with the IA total of 12 studies met the eligibility criteria for the studies documented from 2007 to 2020. The overall pooled prevalence of adenoviruses was 13% , respiratory syncytial virus 11% , and parainfluenza was 9% . Pooled prevalence of reported ARTIs, all ages, and locality varied in the included studies. Studies among participants with severe acute respiratory disease had a higher pooled prevalence of all the three viruses. Considerable heterogeneity was noted overall and in subgroup analysis.Our findings indicate that human adenoviruses, respiratory syncytial virus and parainfluenza virus are prevalent in Kenya, Tanzania, and Uganda. These three respiratory viruses contribute substantially to ARTIs in the EAC, particularly among those with severe disease and those aged five and above. Acute respiratory tract infections (ARTIs) are among the five most common causes of morbidity and mortality globally, accounting for approximately 3.9 million deaths annually. Most of these deaths occur among young children in developing countries . VirusesGlobally, non-influenza respiratory viruses have received less attention respiratory virus surveillance programs, hence few studies are available in the published literature . NeverthIn Sub-Saharan Africa, recent annual incidence data of community-acquired pneumonia is estimated to be 131 million, with significant proportion of these aetiologies due to viruses . A studyThe World Health Organization Regional Office for Africa (WHO-AFRO) 2012 country profiles indicated that acute lower respiratory infections (ALRTIs) were amongst the top three causes of death in the East African Community (EAC). In EAC partner states, the proportionate mortality from lower respiratory tract infections (LRTIs) was: Tanzania (8.7%), Kenya (12.3%), Uganda (9.6%), South Sudan (12%), Rwanda (10%) and Burundi (12.5%). Amongst these EAC states, Kenya, Tanzania, Uganda, and Rwanda have established surveillance programs for influenza and other respiratory viruses which are recognized by the WHO . The EACA large number of programs for surveillance of influenza-like illness (ILI) and severe acute respiratory illness (SARI) were established in order to strengthen health security after the establishment of the 2005 International Health Regulations. However, such programs have primarily estimated the occurrence of influenza viruses and have either not assessed or not reported other (non-influenza) viruses . This leThis review considered studies that reported laboratory-confirmed infections caused by HRSV, HPIV, and HAdV in all age groups. These three respiratory viruses are among those frequently reported to cause respiratory tract infections other than influenza. In addition, the review included a broad range of study participants, including those with acute respiratory tract infections (ARTIs), influenza-like illnesses (ILIs), severe acute respiratory illnesses (SARIs), and other syndromes including pneumonia. Studies reporting asymptomatic infections were excluded in this review.st January 2007 and 31st December 2020 were included.The review considered observational studies, including prospective and retrospective cross-sectional and cohort studies that were either descriptive, analytical, or both. Case series, individual case reports, letters to editors, reviews, commentaries, and qualitative studies were excluded. Only studies published in English, including those from unpublished reports from the grey literature, were included. Published studies and unpublished reports documented in the period between 1An initial unlimited search was conducted in Medline that allowed more refined search strategies tailored for Global Index Medicus. The initial search was performed by verification of the text words contained in the title and abstract of the index terms, which were used to describe the articles using keywords and Medical Subject Heading (MeSH) terminologies . This inTo obtain information from the grey literature, inquiries regarding these viruses were made directly to the ministries of health. We also searched the databases of government medical research institutions, teaching hospitals, and university libraries in EAC partner states. Electronic database search or author correspondence was performed with the Kenya Medical Research Institute (KEMRI) and Kenyatta National Hospital (KNH) for Kenya; National Institute for Medical Research (NIMR) for Tanzania; Uganda Virus Research Institute (UVRI) and Makerere University (MAK), and Mulago Hospital (MUH) for Uganda; Institut National de Sante Public (INSP) for Burundi; and Rwanda Biomedical Center (RBC) for Rwanda. In addition, other non-government public health research programs in the East African Community were contacted.All identified citations were collated and uploaded into Zotero software, version 5.0, and duplicates were removed. Titles and abstracts were re-screened against the eligibility criteria, and studies that met the eligibility criteria were retrieved in full and their details imported into JBI SUMARI . The full texts of selected studies were assessed in detail against the eligibility criteria by two parallel reviewers, and any disagreements were resolved by a third investigator.www.jbisumari.org.Prior to data extraction, all selected studies were critically appraised for methodological quality. This was accomplished with a standardized critical appraisal instrument from the Joanna Briggs Institute by two independent reviewers. This review followed the guideline of systematic reviews of prevalence and incidence manual with the use of JBI SUMARI software available at //All data extracted from the selected studies were included in the review using a standardized data extraction tool in JBI SUMARI software. Extracted data consisted of: name of the primary author, year of publication, locality, age categories of participants, clinical characteristics, study design, length of the study period, specimen type, laboratory test type, number of cases, and total population. Age categories were reported as under five years only, five and above only, or all ages. Clinical conditions or syndromes were recorded as influenza-like illness (ILI) only, severe acute respiratory illness (SARI) only, or acute respiratory tract infections (ARTIs) for studies which investigated both ILI and SARI. Pneumonia was categorized as a severe acute respiratory illness (SARI). Study durations were classified as five months or less, six to twelve months, and more than twelve months.The risk of bias was assessed in the selected studies through the use of an eight variable rating scale \u201327. Each\u00ae13 . The dataset was re-organized and coded for analysis, and further meta-analysis was performed using the \u201cmetaprop\u201d package in STATA program [Data were analysed using Stata program . Initial2 statistic, Cochran\u2019s Q test, and subgroup analysis were used to assess heterogeneity [2 expressed the variation of in-between studies differences as a percentage, simplifying the interpretation with the \u201crule of thumb\u201d [2 >50%, whereas a tentative categories of minimal (I2< = 25%), low (I2 = 25\u20134950%), moderate (I2 = 50\u201375%), and high (I2> = 75%)[To ensure that studies with very small or large prevalence were kept in the overall estimates, the Freeman-Tukey double-arcsine transformation technique was performed using the metaprop command . This progeneity . The staf thumb\u201d , 34. Gen2> = 75%), 35. A f2> = 75%). The Egg2> = 75%)\u201339.Prevalence of infection was described by country, age group, and clinical conditions. In addition, pie charts were used to display the prevalence of HRSV, HPIV and HAdV infections in the region with quantum geographical information system (qGIS). Subgroup analyses were performed on variables of public health importance including: clinical condition , age groups , and locality . We followed guidelines for systematic reviews of prevalence and incidence from the Joanna Briggs Institute to accomplish this review. In addition, the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guided the report writing . This reIn this review, we found 1005 records in published databases and 5 reports from unpublished sources. After filtering based on the defined study period (2007\u20132020), 995 (990 published and 5 unpublished) studies were retained. A total of 299 (294 published and 5 unpublished) were retained after removing 188 duplicates. After screening using the abstract and title, we excluded 508 which did not meet eligibility criteria. The remaining 26 studies were assessed for full article eligibility, and 14 were excluded for different reasons shown . Twelve In this review, qualified studies were documented from 2009 to 2018 . A largeThe overall pooled prevalence of HRSV was 11% (95% CI: 7\u201315) reported from 10 studies with a total population of 22,627 participants .The estimated overall pooled prevalence of 9% (95% CI: 7\u201311) HPIV was estimated from 8 studies with 28,363 participants .HAdV overall pooled prevalence was 13% (95% CI: 6\u201321) recorded in 9 studies with 28,829 participants .Substantial heterogeneity in the pooled prevalence of the three viruses was seen in the included studies, according to severity of illness, age group, and locality. Prevalence of the three viruses differed in the three countries .A pooled prevalence of 10% was found for HRSV, 9% for HPIV, and 12% for HAdV when restricting the analysis to the studies that investigated ARTIs. Prevalence estimates from ILI studies only found HRSV, HPIV and HAdV prevalences of 5% , and 3% (95% CI: 3\u20133.5) respectively. In contrast, estimates from SARI studies only were higher for all three viral pathogens at 22% (95% CI: 20\u201323) for HRSV, 16% (95% CI: 12\u201321) for HPIV and 18% (95% CI: 16\u201319) for HAdV.Studies which considered participants of all ages had an estimated prevalence of 9% (95% CI: 5\u201314), 9% (95% CI: 6\u201312) and 12% (95% CI: 4\u201324) for HRSV, HPIV, and HAdV, respectively. Prevalences of 10% (95% CI: 2\u201324) for HRSV, 6% (95% CI: 4\u20139) for HPIV, and 15% (95% CI: 13\u201316) for HAdV were reported in studies that enrolled participants who were under five years of age. In the studies that involved individuals five years and above, HSRV prevalence was similar at 10% (95% CI: 6\u201315), whereas the prevalence of HPIV and HAdV was much higher at 14% (95% CI: 9\u201321) and 30% (95% CI: 23\u201337) respectively.For studies carried out in Kenya, prevalences of HRSV, HPIV and HAdV were 10% (95% CI: 6\u201315), 9% (95% CI: 7\u201311) and 14% (95% CI: 7\u201325) respectively. In Tanzania, estimated prevalence of HAdV and HPIV were similar at 9% (95% CI: 6\u201312) and 10% (95% CI: 7\u201314), whereas HRSV prevalence was higher at 29% (95% CI: 24\u201335). In the studies conducted in Uganda, the corresponding prevalences of HRSV, HPIV, and HAdV were lower at 3% (95% CI: 2\u20136), 6% (95% CI: 4\u20139), and 8% (95% CI: 5\u201312).There was no publication bias suggested by the funnel plot and or the Egger\u2019s test . WhereasMost of the EAC partner states have, in collaboration with WHO, established programs for surveillance for ILI and/or SARI in order to strengthen global health security under the 2005 IHR. Kenya was the first country to initiate an influenza surveillance program in 2006, followed by Uganda (2007), Rwanda (2008), and Tanzania (2009) , 41. TheThe overall pooled prevalence of HRSV was 11%, 9% for HPIV and 13% for HAdV, but there was substantial heterogeneity by severity of illness, age group, and location. Overall, most (80%) of the reported studies were done in Kenya. Most studies were assessed as low risk for bias, and no publication bias was evident.et al. [et al. [In this meta-analysis, the overall prevalence of HAdV was 13%. This prevalence is slightly higher than the 9.8% reported in individual studies in the Eastern Mediterranean region . A study [et al. in 2018 [et al. . The difIn this systematic review, the pooled prevalence of HRSV was 11%, which is similar to a previous estimate of 14.6% among people with ARTIs in Africa . In a 20The overall prevalence of HPIV in this review was 9%. Previous studies have reported generally similar prevalence estimates of HPIV. In Cameroon, HPIV prevalence of 7.5% was reported in 2012 among ILI patients , which w2 values.This systematic review is subject to several limitations. The systematic searches performed in this review were limited to the most accessible and widely used databases of medical literature, including Medline and Global Index Medicus. In addition, the search was complemented with unpublished literature from major public health institutions and research programs in the EAC. We identified several significant sources of heterogeneity in the estimates of pooled prevalence of HRSV, HPIV, and HAdV, including disease severity, age group, and location. Heterogeneity may also be influenced by other factors, including measured factors such as the length of the study period, study design, and laboratory technique. For example, while most studies used highly sensitive and specific diagnostic PCR tests to detect these viruses, studies which used less sensitive diagnostic methods likely underestimated prevalence. Heterogeneity may also have been influenced by unmeasured factors. Selection of participants may also have been different among the studies, likely resulting in higher prevalence among studies in which patients with more severe illness were enrolled, such as SARI as compared to ILI patients. Additionally, the sample size of studies eligible for inclusion in this analysis was small, limiting the power to detect differences, particularly in subgroup analysis. For example, not all countries of the EAC were represented, and Tanzania and Uganda only had one study each. The small sample size may be due to various factors including limited funding, government policy and priorities, the challenges of information sharing, lack of documentation, inaccessibility of databases, and difficulties with publication of data. Further, the presence of extreme values of prevalence introduced computational complexity which limited our ability to report confidence intervals for the IFinally, this review only included studies in which patients were selected based on defined medical conditions such as ILI and SARI or ARTIs in general. Studies that included asymptomatic participants were excluded. Asymptomatic patients would likely have had lower prevalence of these viruses than the symptomatic populations used in our study. Therefore the results of this review cannot be generalized to the general population. The exclusion of asymptomatic cases was considered necessary to avoid overdiagnosis of patients who were colonized or carriers of viruses which may not have ever caused disease.Despite these limitations of the study, this study had several strengths. We have documented the first systematic review and use of meta-analysis to estimate the pooled prevalence of selected non-influenza viruses in the EAC. This systematic review and meta-analysis simultaneously reported HRSV, HPIV, and HAdV prevalence with a pre-defined protocol, used robust search strategies, and involved two independent investigators. Selected studies were all assessed for well-defined study characteristics to assess study heterogeneity and bias. There was no significant publication bias detected, and most of the included studies had a low risk of study bias. Sensitivity analysis yielded similar results to crude estimates, further supporting the robustness of this systematic review and meta-analysis.Respiratory illness surveillance programs in the EAC have enhanced the detection of both influenza and non-influenza viruses for over a decade. However, there are no platforms for systematic information sharing in the region. It is vital to establish national and regional information-sharing platforms for non-influenza respiratory viruses to guide future research, policy, and development. Our findings indicate that human adenoviruses are the most common sources of ILI and SARI other than influenza infection, followed by the human respiratory syncytial virus and parainfluenza virus. Future studies or research could identify the prevalence of HRSV, HPIV, and HAdV using standardized methods and populations to increase comparability among studies and to account for sources of misclassification and heterogeneity. Additional studies should be considered among older populations, among populations from EAC countries from which no data were found, and asymptomatic populations. In addition, the literature search could include additional databases used in biomedical research. Finally, other emerging respiratory pathogens could be studied and further molecular characterization could be carried out to assess transmission.S1 File(PDF)Click here for additional data file.S2 File(PDF)Click here for additional data file.S3 File(TIF)Click here for additional data file.S4 File(PDF)Click here for additional data file."} +{"text": "Little is known about mental health risk factors in medical residents and doctors in Sub-Saharan Africa. Residents are at a greater risk of developing depression, stress and substance abuse than the general public owing to the stressful nature of their medical training. Poor mental health in residents leads to decreased clinical efficiency and training satisfaction; it can also lead to substance dependence, self-harm and suicide.Our primary aim was to ascertain depression prevalence among medical residents in Kenya's largest national teaching and referral hospital. Secondary aims were to analyze how depression was associated with perceived stress, perceived social support, substance use, and educational environment.Self report questionnaires were administered in this cross-sectional survey to 338 residents covering eight specialties . In addition to key sociodemographics, the Centres for Epidemiology Depression Scale - Revised, Perceived Stress Scale, Multidimensional Scale of Perceived Social Support, Alcohol, Smoking and Substance Involvement Screening Test, and Postgraduate Hospital Educational Environment Measure were used.The mean participant age was 31.8 years and 53.4% were males. Most residents (70.4%) reported mild/no depressive symptoms 12.7% had moderate, and 16.9% had severe symptoms.High social support (71.8%) and moderate stress (61.6%) were reported by most residents. Almost half (46.3%) rated their educational environment as being more positive than negative. Out of 238 respondents 11.3% were at moderate risk of health and other problems due to cocaine use, while 13.3% (out of 240 respondents) were at risk due to alcohol. On bivariate analyses, we found significant correlations between depression, perceived stress, substance use, perceived social support, and educational environment. Multivariate analysis revealed that depression was strongly associated with: fewer hours of sleep , high perceived stress and low perceived social support .High perceived social support, low perceived stress, and less sleep were significantly associated with lower depression scores. A large proportion of residents were at risk of developing depression (29.6%). There were high levels of perceived social support (71.8%). A concerning proportion of residents used substances like alcohol and cocaine. This work is one of few that describe the mental health of an important and understudied population group in an LMIC. Priority must be given to protect and promote the mental health of such a vulnerable group.Data collection and analysis were funded by Kenyatta National Hospital."} +{"text": "The detection reference standard was the Mycobacterium tuberculosis complex culture, and for resistance detection, it was phenotypic drug susceptibility testing. The median age of 474 participants was 39 years. On decontaminated sputum, Xpert Ultra had a sensitivity of 91%, compared to 77% for RT-MTB, with a difference of +14% . On raw sputum, Xpert Ultra exhibited a sensitivity of 89% and Xpert one of 88%, compared to 80% for RT-MTB, exhibiting differences of +10% and +8.6% , respectively. Specificity was \u226598% for all tests. All three tests showed high sensitivity and specificity for detection of rifampin resistance. Abbott assays may have lower sensitivity than Xpert and Xpert Ultra for TB detection but similar performance for detection of resistance. The differences in TB detection may be attributable to differences in testing of frozen (Abbott) versus fresh (Xpert) samples. Studies in compliance with manufacturer\u2019s instructions are required to compare performance.High-throughput centralized testing for tuberculosis (TB) and drug resistance is important, but comparative data are limited. In this retrospective cross-sectional study, participants were recruited from Johannesburg, South Africa, and Tbilisi, Georgia. The index tests, Abbott RealTiIMPORTANCE In 2019, 10 million people fell ill with tuberculosis (TB), of whom 1.4 million died. There are few comparative studies of diagnostic assays, particularly those aiming to be used in high-throughput laboratories. One such assay is the Abbott RealTime MTB (RT-MTB) and RealTime MTB RIF/INH (RT-MTB RIF/INH), which uses the m2000 platform already in use in many settings for HIV load testing and allows the diagnosis of TB and resistance to two first-line drugs, rifampin and isoniazid. Our study compared the RT-MTB and RT-MTB RIF/INH to the WHO-recommended Xpert MTB/RIF Ultra and Xpert MTB/RIF. The study is the largest comparative study to date and was performed independent of the manufacturer. The study results suggest that the Abbott RealTime MTB may have a lower sensitivity, but the study may have placed the Abbott test at a disadvantage by using frozen samples and comparing the results to those for fresh samples for the Xpert. As the m2000 platform is designed for central laboratories, optimal performance requires skilled and experienced technicians with appropriate training and resistance detection. These platforms should be suitable for national or regional referral laboratories, where cost savings and higher efficiency may be expected due to a high volume of samples and multidisease testing. The RealTiA recent meta-analysis identifiThree studies in the systematic review performed head-to-head comparisons with Xpert, with one also including Xpert Ultra . The study comparing Xpert Ultra with RT-MTB found greater sensitivity of Xpert Ultra than RT-MTB, with sensitivities of 88.9% and 77.8 , respectively . A singlTo complement these relatively few studies, our study aimed to compare the accuracy of the RT-MTB and RT-MTB RIF/INH assays against Xpert Ultra and Xpert in two high-TB-incidence settings, one with low HIV prevalence and the other with high HIV prevalence.3 . Overall, culture-positive TB prevalence was 136/474 (29%), of which 105/136 (77%) were smear positive were recruited in Tbilisi, Georgia, while 223 (47%) were recruited in Johannesburg, South Africa . There wpositive .Full results of sensitivity and specificity for the main outcome and subgroups are presented in Among unprocessed sputum samples (sputum 4 RT-MTB versus sputum 1 Ultra and Xpert), 307 patients provided samples for both, with 93 samples being culture positive (30%). Xpert Ultra and Xpert exhibited a sensitivity of 89% and 88% , compared to 80% for RT-MTB, for differences of +10% and +8.6% , respectively. For both Xpert and Xpert Ultra, specificity was 100% , while specificity for RT-MTB was 98% .For both analyses, the removal of \u201ctrace\u201d results for Xpert Ultra resulted in reduced sensitivity with minimal improvement in specificity. With the inclusion of a repeated Xpert Ultra test after an invalid test result, more valid results were available for analysis without affecting the estimated sensitivity and specificity (Table S2).A higher sensitivity for Xpert Ultra than for RT-MTB was observed across all subgroups (Table S3). In the same S2 sputum comparison among smear-negative participants, the sensitivity of Xpert Ultra was 59% compared to 22% for RT-MTB, with similar findings in the across sputum (S4 versus S1) comparison . Xpert Ultra also exhibited higher sensitivity than the RT-MTB assay among HIV-positive individuals for the same sputum comparison (89% [75% to 96%] versus 68% [51% to 80%]) and the across-sputum comparison (89% [67% to 97%] versus 72% [49% to 88%]). Among patients with prior TB history, sensitivity in the same sputum comparison was reduced for both Xpert Ultra and RT-MTB assays at 80% and 60% , but specificity was high for both at 97% and 98% , respectively. Specificity was \u226597% for all subgroups for Xpert Ultra, Xpert, and RT-MTB assays. There was no difference in sensitivity or specificity by study site.3 , lower than the average in the cohort . Compared to Xpert Ultra, RT-MTB identified fewer true positives correctly in the smear-negative, scantily positive, and HIV-positive subgroups.A further analysis of test results by smear status and HIV status is presented in Table S4. Most false-negative results in the RT-MTB assay were observed in smear-negative and HIV-positive patients. Of 8 HIV-positive, smear-negative participants with TB, none were detected by RT-MTB; conversely, among HIV-negative, smear-positive participants with TB, only 1/27 (4%) had a false-negative result. Among the 12 HIV-positive with false-negative results by RT-MTB, the median CD4 count was 108 cells/cmIn a subgroup analysis of whether the duration of the freezing step may have altered the sensitivity of RT-MTB, confidence intervals were widely overlapping between grouped duration, suggesting no differences in sensitivity (Table S5).In the same sputum comparison, of 65 samples that underwent drug susceptibility testing (DST), 7 samples were identified as rifampin (RIF) resistant, while 58 were RIF susceptible . Both XpOn sputum 2 testing, RT-MTB MTB/RIF recorded 27/473 invalid results, compared to 16/473 invalid results for Xpert Ultra. On sputum 4 testing, RT-MTB recorded 4/328 invalid results. On sputum 1 testing, Xpert Ultra showed 16/473 invalid results, while Xpert had 11/473 invalid results.Mycobacterium tuberculosis DNA should be present even if the freezing step results in cell lysis. However, data on the effect of freezing from the manufacturer are available only for temperature ranges of \u221225 to \u221213\u00b0C for up to 90\u2009days greater sensitivity of Xpert Ultra when tested fresh over RT-MTB when tested after freezing for the diagnosis of culture-positive TB. This estimate must be interpreted with caution, as the Xpert Ultra test was performed on fresh samples, while RT-MTB was done on frozen samples for which storage was outside the manufacturers\u2019 recommendations. Freezing samples should not affect the RT-MTB, as the 90\u2009days .When different unprocessed sputum samples provided by the same patient were compared, Xpert Ultra demonstrated a +10% (+3.3 to +18%) higher sensitivity while Xpert demonstrated an +8% (+2.4 to +17%) higher sensitivity when tested on fresh samples compared to RT-MTB tested on frozen samples. This could suggest that the combination of decontamination and a freezing step results in a disproportional reduction of detectable DNA, thus explaining the larger difference between the RT-MTB and Xpert Ultra on the decontaminated sputum. Specificity across all three assays for both processed and unprocessed samples was \u226598%, demonstrating high specificity across all assays.Our findings are in keeping with the sensitivity estimates of Xpert Ultra and RT-MTB previously reported in the only head-to-head comparison . The poi3 compared to 220 in Johannesburg and 85/223 [38%] in Tbilisi) or the participant self-reporting as HIV positive or negative , with preference given to the HIV test result in case of conflicting data (2 cases).All data were initially recorded on paper case report forms before being transferred to a dedicated electronic database using double entry.The 95% confidence intervals for simple proportions were calculated by Wilson\u2019s method . The 95%The study protocol of the Ultra study was reviewed and approved by ethics committees at the study sites and included the use of remnant samples for further analyses. Written informed consent was obtained from all study participants. Study participation did not affect the standard of care."} +{"text": "The mental health needs of older adults are largely unmet, a finding even more prevalent within culturally diverse older adult populations. Added to this is the high rate of social isolation. Research has indicated increased connection to mental health services when services are embedded within physical health care settings. For those attending community centers, 85% indicate that they are socially isolated, 68% indicate they are lonely, and 53% have a mental health need . The need for innovative programming is evident. When examining the needs of diverse older adults, it is increasingly important that new and innovative approaches address social isolation, loneliness, and mental health problems experienced by this cohort. Utilizing this knowledge an innovative model of embedding and integrating mental health services, provided by bilingual and bicultural clinicians, into congregate sites (older adult centers) was implemented. Those that participated were mainly female (72.1%), 68.5% English-speaking, 14.5% Spanish-speaking, 13.6% Chinese-speaking and 3.4% other. Spanish-speakers had more depression than English-speakers and both had more depression than Chinese-speakers. English and Spanish-speakers reported more social isolation and Chinese-speakers compared were more likely to participate in engagement. Chinese-speakers were less likely to be in clinical services with a positive screen compared to English-speakers. Overall, 75% engaged in treatment; 37.3% and 41% showed a 3-month improvement of depression and anxiety, respectively. This presentation focuses on the innovative components of this model, how to engage diverse older adults to utilize treatment, steps needed for replication, and policy implications around integrated mental health treatment."} +{"text": "To characterize the functional impairments of a cohort of patients undergoing inpatient rehabilitation after surviving severe COVID-19 illness, in order to better understand the ongoing needs of this patient population.th to May 22nd, 2020. Patient demographics, clinical characteristics and complications from acute hospitalization were examined. Measures of fall risk , endurance , gait speed , mobility (transfer and ambulation independence), cognition, speech and swallowing were assessed at rehabilitation admission and discharge.This study consisted of a retrospective chart review of consecutive patients hospitalized for COVID-19 and admitted to a regional inpatient rehabilitation hospital from April 29The study population included 29 patients and was 70% male, 58.6% white and with a mean age of 59.5. The mean length of acute hospitalization was 32.2 days with a mean of 18.7 days intubated. Patients spent a mean of 16.7 days in inpatient rehabilitation and 90% were discharged home. Patients demonstrated significant improvement from admission to discharge in measures of fall risk, endurance, gait speed, mobility, cognition, speech and swallowing, (p< 0.05). At discharge, a significant portion of the population continued to deficits in cognition , balance (55%) and gait speed (97%).Patients admitted to inpatient rehabilitation after hospitalization with COVID-19 demonstrated deficits in mobility, cognition, speech and swallowing at admission and improved significantly in all of these domains by discharge. However, a significant number of patients exhibited residual deficits at discharge highlighting the post-acute care needs of this patient population. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a novel coronavirus that causes coronavirus disease 2019 (COVID-19) , stroke Patients that survive severe COVID-19 illness develop a myriad of functional deficits that impact their ability to return home from the acute care hospital. Cardiopulmonary symptoms include reduced aerobic capacity, orthostatic hypotension and arrhythmias , 8, 9. TThere is not much data on the rehabilitation course and functional outcomes following prolonged hospitalization for COVID-19. It has been shown that a large proportion of patients have persistent symptoms that impact quality of life . Patientth and May 22nd, 2020. Demographic, clinical and outcomes data were collected by retrospective chart review using a standardized data extraction form.The study consisted of a convenience sample of consecutively admitted patients to an inpatient rehabilitation facility (IRF) in Boston, MA, following hospitalization for COVID-19 between April 29All subjects received standard of care inpatient rehabilitation. Rehabilitation therapy treatments are performed by physical therapists, occupational therapists and speech and language pathologists at least three hours per day, five days per week. There was not a standardized treatment protocol for post-COVID patients. Interventions were tailored to each patient\u2019s individual needs.Functional measures were assessed at IRF admission and discharge. Outcomes assessed included fall risk ), endurance ), gait speed ), mobility (transfer and ambulation independence), as well as cognition, speech and swallowing ). The BBS is a validated 14 item assessment that evaluates static balance and risk of falls . The 6MWThis study included 29 patients, who were 70% male, 58.6% white and had a mean age of 59.5 years. The most common preexisting medical conditions were hypertension (76%), obesity (62%) and hyperlipidemia (55%). All patients required intubation. The mean length of intubation was 18.7 days and acute hospital stay was 32.2 days. Dysphagia (86.2%), weight loss (79.3%) and delirium (69%) were the most common complications. Tracheostomy was performed in 20.7% of patients, while gastrostomy was performed in 13.8% of patients. Significant weight loss occurred in 79.3% of patients with a mean loss of 12.5% of premorbid body weight compared to weight at IRF admission. Pressure injuries occurred in 37.9% of patients, which included common locations from lying supine (sacrum/ankles) and uncommon location from lying prone on the ventilator (face/abdomen) .The mean length of inpatient rehabilitation was 16.7 days. Most patients (90%) were discharged home. No patients were discharged to a skilled nursing facility. Two patients had planned readmissions for surgical treatment of pressure injuries. One patient had an unplanned admission for a hospital acquired pneumonia .This study describes the clinical characteristics of a cohort of patients who underwent inpatient rehabilitation following hospitalization with severe COVID-19. Multidimensional functional deficits in mobility, cognition, speech and swallowing were pervasive at the time of admission to rehabilitation. Although the study population demonstrated significant improvements in all domains examined, deficits remained in domains of fall risk, gait speed and cognition at rehab discharge. This study highlights the prevalence of persistent functional deficits after severe COVID-19 that will require ongoing treatment and may, in some cases lead to longer-term impairments.Information on the long-term effects of COVID-19 infection is limited. At approximately two months after onset of symptoms, fatigue and dyspnea are common . ComplicSimilar to sepsis survivorship initiatives, a large-scale registry to facilitate trials and detailed longitudinal follow-up is needed to advance understanding of COVID-19 recovery . Of noteStudy limitations include small sample size, single center, retrospective design and lack of standardized rehabilitation protocol for COVID-19 patients. Baseline functional status and psychiatric complications were not evaluated in this study. Despite these limitations, this study begins to illuminate the multidimensional functional impairments and post-acute care needs of this population.S1 Data(XLSX)Click here for additional data file."} +{"text": "E. coli accounted for most infections (56% (1994/3558)), followed by E. faecalis, with a prevalence of 17% (609/3558). The prevalence of K. pneumoniae was 5% (193/3558), 5% (186/3558) for S. agalactiae, and 5% (179/3558) for P. mirabilis. Ninety-five percent (1827/1927) of the E. coli and 99% of the E. faecalis (301/305) isolates were susceptible to nitrofurantoin. Common uropathogens showed high susceptibility to first-line antibiotics, gentamicin and nitrofurantoin, as recommended for use in primary healthcare settings. Overall, our study provided an indication of the level of antimicrobial resistance in the four facilities. In South Africa, uncomplicated community-acquired UTIs (CA-UTIs) are treated empirically; however, the extent of antibiotic resistance among these pathogens is not well known. We conducted a descriptive cross-sectional study of women attending ANCs at four tertiary public-sector hospitals in Gauteng. Female patients aged 15\u201349 years, with urine cultures performed between January 2015 and December 2019, were included. A case of culture-confirmed UTI was defined as any woman with \u22642 uropathogens with a bacterial count of \u2265105 colony-forming units per ml for at least one pathogen. We identified 3558 cases of culture-confirmed UTIs in women with a median age of 30 years . Antimicrobial resistance (AMR) is a growing global public health concern as it threatens the effective control and treatment of bacterial infections . AMR patCommunity-acquired UTIs (CA-UTIs) are the second most common infection in primary care . CompareTo determine the etiologic agents and their susceptibility profiles among patients with UTIs, urine culture is the method of choice . HoweverIn resource-limited settings, syndromic treatment approaches are introduced for uncomplicated system organ infectious diseases, however, continuous monitoring of etiology and antimicrobial susceptibility testing of bacterial pathogens is required to prevent the development of antimicrobial resistance. We aimed to determine the etiology and susceptibility patterns of uropathogens circulating in the community, analyzing pregnant women attending antenatal clinics (ANCs) in Gauteng with culture-confirmed UTIs. We anticipated that our study findings would provide information to guide the empiric treatment of all women with UTIs in primary healthcare.A total of 51,139 laboratory records were retrieved over the five-year period; 36,944 (63%) were excluded based on age, sex, other specimen types and duplication, and the remaining 14,195 urine cultures were submitted from 13,955 women. The positivity rate was 50% and the contamination rate was 25% . Among all positive urine cultures, 50% (3558/7078) represented cases of culture-confirmed UTIs, and 2% (83/3558) of these were polymicrobial infections (two uropathogens) . Most caE. coli (56% (1994/3558)) and E. faecalis (17% (609/3558)) , with 5% (179/3 558) for P. mirabilis and 5% (193/3558) for K. pneumoniae. Other Gram-negative uropathogens accounted for 8% (298/3558) of the infections, and these included, but were not limited to, Klebsiella spp. (3% (111/3558)), Enterobacter spp. (2% (67/3558)), and Acinetobacter spp. (0.4% (14/3558)). The prevalence of other Gram-positive uropathogens was 3% (99/3558), and the most predominant species among these were Staphylococcus spp. (2% (86/3558)) and Enterococcus spp. (0.3% [10/3558]). Candida spp. accounted for 0.2% (6/3558) of the uropathogens. E. coli and E. faecalis remained the most dominant uropathogens throughout the analysis period ) . The pres period .E. coli isolates were susceptible to amoxicillin/clavulanic acid and 88% (95% CI 86\u201388 (1626/1852)) were susceptible to ciprofloxacin. Ninety-five percent (95% CI: 94\u201396 (1827/1927)) of the E. coli isolates were susceptible to nitrofurantoin and 93% (95% CI 92\u201394 (1835/1970)) to gentamicin. E. coli isolates were less susceptible to ampicillin/amoxicillin ) and trimethoprim/sulfamethoxazole ). E. coli demonstrated reduced susceptibility to cefuroxime ) and cefazolin ), while susceptibility to cefotaxime/ceftriaxone was 93% (95% CI 91\u201394 (1805/1948)) and 95% (95% CI 93\u201395 (1880/1988)) for cefepime. The majority of K. pneumoniae isolates were susceptible to ciprofloxacin ), gentamicin (95% CI 90\u201397 (178/188)) and trimethoprim/sulfamethoxazole ). Forty percent (95% CI 34\u201348 (80/198)) of the K. pneumoniae isolates were susceptible to nitrofurantoin. Among the K. pneumoniae isolates, 89% (95% CI 83\u201392 (165/186)) were susceptible to cefuroxime, 91% (95% CI 86\u201395 (177/194)) to cefotaxime/ceftriaxone, 92% (95% CI 87\u201395 (185/201)) to cefepime and 97% (95% CI 84\u2013100 (31/32)) to cefazolin.Susceptibility testing of the predominant uropathogens is shown in P. mirabilis isolates tested, 98% (95% CI 94\u201399) and 99% (95% CI 96\u2013100) were susceptible to amoxicillin/clavulanic acid and ciprofloxacin, respectively, and only 51% (95% CI 43\u201358) were susceptible to ampicillin/amoxicillin. E. faecalis showed high susceptibility to ampicillin/amoxicillin ) and nitrofurantoin ). Thirty-seven percent (95% CI 24\u201351 (20/54)) of the E. faecalis isolates were susceptible to trimethoprim/sulfamethoxazole. Of the 176 n = 134) were E. coli.Overall, 4% (155/3558) of the cases were infections with MDR uropathogens , 87% of which [E. faecalis was the second most prevalent uropathogen in our study, with a prevalence of 17%. This was in contrast to previous community-based South African studies, one including all women, and one including only pregnant women. In these studies, E. faecalis accounted for 4% of the UTIs, despite being the most common Gram-positive uropathogen [Candida spp. were the predominant pathogens [As is consistent with a number of other studies in patients with CA-UTIs, ur study ,19. The al (54%) ,20. The pathogen ,22. Pregathogens . E. coli was susceptible to nitrofurantoin (96%) and, to a lesser extent, to ciprofloxacin (88%). Although the proportion of E. coli isolates that were susceptible to ciprofloxacin was high, resistance among E. coli isolates was above the 10% threshold set by the Infectious Diseases Society of America (IDSA) for treatment modification [Overall, there was high susceptibility to those antibiotics recommended for first-line treatment in primary care settings , although this differed by the common pathogen. In a laboratory-based study between 2015 and 2017 at CMJAH, susceptibility to ciprofloxacin and nitrofurantoin was 71% and 70%, respectively . This lofication . Above tfication . K. pneumoniae (40%) and P. mirabilis isolates. Regarding P. mirabilis isolates, we need to emphasize that Proteus spp. are intrinsically resistant to nitrofurantoin, and it should not be considered as a treatment option [E. coli was between 6\u20137% and 8\u20139% in K. pneumoniae. This finding was consistent with studies reporting increasing ESBL production among strains isolated from urine [Although the overall susceptibility to nitrofurantoin was high in our study, this was an exception with t option . We examom urine . The preom urine ,28,29. Aom urine . These dom urine . E coli for reporting nitrofurantoin according to the guidelines of both the CLSI and European Committee on Antimicrobial Susceptibility Testing (EUCAST), which means it should not be recommended to clinicians. We did not have data on fosfomycin, as susceptibility testing was not routinely performed for this antibiotic in the NHLS laboratories. However, resistance to nitrofurantoin was low in our study, suggesting that it remains a suitable first-line treatment for CA-UTIs and for the treatment of MDR infections. Compared to MDR pathogens isolated from patients in the healthcare setting, community-acquired pathogens have no antibiotic resistance phenotype, and they are more stable in the absence of antibiotic pressure normally found in healthcare settings [In our study, the prevalence of MDR uropathogens was low, as we described a specific population and included a first episode of UTI. Fosfomycin and nitrofurantoin are suitable for treating UTIs with MDR uropathogens, and nitrofurantoin is more suitable for pregnant women . We needsettings ,32. TherThe findings of our study should be interpreted in the context of the study limitations. First, our study included only pregnant women attending antenatal care, thus findings may not be generalizable to other population groups. In addition, we limited our analysis to Gauteng, and our results may not represent resistance patterns in other parts of South Africa. However, the strength of our study was that it included women attending antenatal clinics at large public-sector facilities that offer services to individuals from all parts of the province, and thus was likely to be representative of antimicrobial susceptibility patterns of the pathogens circulating in communities in Gauteng Province.This was a descriptive cross-sectional study including women attending antenatal clinics (ANC) with culture-confirmed UTIs, in four tertiary-level facilities in Gauteng; Charlotte Maxeke Johannesburg Academic Hospital (CMJAH), Rahima Moosa Mother and Child Hospital (RMMCH), Steve Biko Academic Hospital (SBAH) and Chris Hani Baragwanath Academic Hospital (CHBAH). We conducted secondary data analysis using laboratory data from the National Health Laboratory Service Corporate Data Warehouse (NHLS CDW), which stores all laboratory results of urine cultures performed in public-sector facilities. We obtained urine culture results from 2015 to 2019 and used laboratory-defined ANC test codes to identify urine specimens from patients seen at antenatal clinics at the four facilities. Limited patient information, including dates of birth and sex, and laboratory results, including bacterial colony-forming unit counts, organisms cultured, and antimicrobial susceptibility testing (AST) results were retrieved. Standard operative procedures for urine cultures and AST were used at the NHLS laboratories, and interpretation AST results were performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines throughout the study period .A case of culture-confirmed UTI was defined as any woman of childbearing age (15\u201349 years) with a positive urine culture consisting of \u22642 uropathogens with an organism growth of \u2265100,000 colony-forming units per ml for at least one of the isolated organisms. We used the Centers for Disease Control and Prevention National Healthcare Safety Network (CDC NHSN) guidelines to distinguish uropathogens from contaminants among positive cultures . MDR uropathogens were defined as organisms resistant to three or more classes of antimicrobials , includiAdditional urine cultures from the same patient that met the case definition and were collected within six months of the first urine culture were regarded as part of the initial UTI episode and were excluded. Male patients, women patients aged <15 years and >49 years, and those with non-urine specimen types were excluded. Patients with missing information on study inclusion criteria, such as date of birth or age, sex, specimen type and collection date, and organism name, were also excluded.The positivity and contamination rates were calculated. We determined the urine positivity rate by dividing the number of urine cultures where any organism was isolated by the total number of urine cultures performed. We determined the contamination rate by dividing the number of urine cultures that yielded a non-uropathogen by the total number of urine cultures. For each antimicrobial, susceptibility was determined by dividing the number of antimicrobial susceptible uropathogens by the total number of uropathogens with AST results.This study provides updated profiles of infectious causes of UTIs and antimicrobial susceptibility, and may be used to guide empirical UTI treatment for female outpatients in Gauteng. Additional studies including other population groups, such as non-pregnant women, patients seeking care in private facilities, and patients in other regions of the country, could be considered for better representation. In conclusion, there is a need for regular community-based surveillance of antimicrobial resistance patterns for empirical treatment recommendations at the primary healthcare level."} +{"text": "Pre-exposure prophylaxis (PrEP) is a highly effective biomedical strategy to decrease Human Immunodeficiency Virus (HIV) acquisition. Effectiveness of oral PrEP is linked to medication adherence. In 2018, Grady Health System (GHS) launched a PrEP program to increase PrEP access among un- and underinsured individuals living in metro Atlanta, Georgia. The purpose of this study is to determine PrEP medication adherence, PrEP discontinuation rates, and associated individual factors of patients enrolled during the first 18 months of the program\u2019s implementation. A single-center, retrospective chart review was conducted on patients enrolled in the GHS PrEP program between June 1, 2018 and February 29, 2020 who received more than one monthly PrEP prescription. Adherence was estimated using the medication possession ratio (MPR). The primary outcome was mean adherence to PrEP. Secondary outcomes include rate of high percent adherence (MPR > 80%), median time of engagement in care, PrEP discontinuation rates, rates of PrEP re-engagement, and individual factors associated with PrEP discontinuation and low adherence. This study included 154 patients, 70.8% of them were Black, 62.3% were cisgender men, 59.1% were uninsured, and the mean age was 34. The majority of patients identified as men who have sex with men (51.9%). Mean PrEP adherence was 89.2%; 77.3% of patients demonstrated a high rate of adherence. No individual or social factors were associated with low adherence, but younger age was associated with higher rates of PrEP discontinuation (p< 0.0061). At the end of the follow up period on October 30, 2020, 53.8% of patients were active in the program and 12.7% of those who discontinued had re-engaged with the program. The average length of program engagement was 9.8 months.Table 1. Baseline socio-demographic characteristics (N=154)Table 2. PrEP Adherence and Discontinuation at the GHS PrEP Program from 2018 to 2020 (N=154)Table 4. Multivariate analysis of individual factors associated with PrEP discontinuation and low adherenceMean PrEP adherence at a safety net PrEP program in Atlanta was high and PrEP discontinuation rates were comparable to other PrEP clinics nationwide. We found no association with individual factors previously linked to lower adherence, including Black race, younger age, and insurance status. Program-related factors that may have impacted these findings need to be investigated. Other future areas of research include strategies to optimize engagement in care in younger patients. Bradley L. Smith, Pharm.D., AAHIVP, Gilead Sciences, Inc (Advisor or Review Panel member)"} +{"text": "Background: Older people often receive multiple medications for chronic conditions, which often result in polypharmacy (concomitant use of 5\u20129 medicines) and hyperpolypharmacy (concomitant use of \u226510 medicines). A limited number of studies have been performed to evaluate the prevalence of polypharmacy, hyperpolypharmacy, and potentially inappropriate medication (PIM) use in older people of developing countries. The present study aimed to investigate regional variations in the prevalence of polypharmacy, hyperpolypharmacy, and PIM use in older people (60 + years) in India.Methods: Studies were identified using Medline/PubMed, Scopus, and Google Scholar databases published from inception (2002) to September 31, 2020. Out of the total 1890 articles, 27 were included in the study.Results: Overall, the pooled prevalence of polypharmacy was 49% , hyperpolypharmacy was 31% , and PIM use was 28% among older Indian adults. Polypharmacy was more prevalent in North-east India , whereas hyperpolypharmacy was prevalent in south India . Region-wize estimates for the pooled prevalence of PIM use in India were as follows: 23% (21\u201325) in East, 33% in West (24\u201342), 17.8% in North (11\u201323), and 32% (26\u201338) in South India. The prevalence of PIM use in adults aged \u226570\u00b0years was 35% (28\u201342), in those taking more medications (\u22655.5/day) was 27% (22\u201331), and in adults using a high number of PIMs (\u22653) was 29% (22\u201336). Subgroup analysis showed that cross-sectional studies had a higher pooled prevalence of polypharmacy 55% (44\u201365) than cohorts 45% (37\u201354). Hyperpolypharmacy in inpatient care settings was 37% (26\u201347), whereas PIM use was higher in private hospitals 31% (24\u201338) than government hospitals 25% (19\u201331).Conclusion: Polypharmacy and hyperpolypharmacy are widely prevalent in India. About 28% of older Indian adults are affected by PIM use. Thus, appropriate steps are needed to promote rational geriatric prescribing in India.Systematic Review Registration: https://clinicaltrials.gov, identifier [CRD42019141037]. There were 703 million people aged 65\u00b0years or over in the world in 2019. The number of the older people is projected to double to 1.5 billion by 2050, with a more prominent increase in developing countries . AccordiIn general, older people often receive multiple medications for chronic conditions, which often result in polypharmacy (concomitant use of 5\u20129 medicines) and hyperpolypharmacy (concomitant use of \u226510 medicines) . ResearcThe term PIM is defined as medications that have adverse effects and, when used by older adults, may outweigh the clinical advantages of the drug, such as mental and functional decline, adverse drug events, drug interactions, unplanned hospitalization, morbidity, and mortality . Higher-Several systematic reviews and meta-analyses on the prevalence of polypharmacy and PIM use in the older population, using data from developed countries , indicatThe study was performed according to the MOOSE guidelines . The resWe comprehensively searched Medline/PubMed, Scopus, Google Scholar, and bibliographic databases from inception (2002) to September 31, 2020. The search process was initiated in april 2019 and updated until September 31, 2020. We used combinations of Medical Subject Headings (MeSH) and free text words to identify the relevant studies related to the exposure , PIMs, and to search terms related to outcomes . Complete details about the search terms used in various databases have been listed in The studies met the following criteria; observational on the older population (aged 60 and older), conducted in India, and reported prevalence of polypharmacy, hyperpolypharmacy, and PIM use, using any explicit criteria to assess the appropriateness of drugs prescribed. The following articles were excluded; duplicate studies, abstracts, letters, editorials, conference proceedings, review articles, meta-analyses, non-population-based studies, and interventional studies.Three reviewers independently screened the titles and abstracts of the initially identified studies to determine whether each study met the predefined eligibility criteria. Full-text articles were retrieved for selected titles. References of the retrieved articles were also screened to identify the additional eligible articles. Any disagreements regarding selection were resolved through discussion, consensus, or consultation with other team authors .Full texts of included studies were read, and three reviewers extracted the relevant data from the selected studies. The extracted data included author details, year of publication, geographic origin, study design and settings, patient sampling, participant characteristics , measurements (explicit criteria), and information on outcomes . Prevalence estimates of PIM use were stratified to provide specific estimates of the subsets .The methodological quality of the included studies was evaluated using the Newcastle Ottawa Scale (NOS) for cross-sectional and cohort studies . The NOSI2 statistic , and Tau2 (method of moments estimate of between-study variance) was used for each of the pooled estimates. I2 values range between 0 and 100%, and is considered low for I2 <25%, modest for 25\u201350%, and large for >50% , and p-value resulting from Cochran\u2019s Q test. A p-value of <0.10 was considered statistically significant for Cochran\u2019s Q test with corresponding 95% confidence intervals (CI). The pooled prevalence estimates of outcome variables were calculated using regional population size weights. The magnitude of heterogeneity between the studies was assessed using the for >50% . As difffor >50% . In cases Q test . The risn = 92) due to various reasons is presented in A total of 1890 references were initially identified through electronic databases. After removing 165 duplicates, a total of 1835 titles and abstracts were screened to determine if they met the inclusion criteria, as described in the methodology section. Full-text assessment of 119 potentially relevant articles resulted in 27 eligible studies , as showAll the studies included in the present study were published between 2010 and 2019. Sample size varied on regional basis from 90 to 1,510, making a total of 11,649 patients. All the studies included both women and men ; howeverThe quality assessment of included studies was assessed using NOS for the cross-sectional and cohort studies. The highest quality score was 9, and the lowest was 4. The average score of the NOS scale was 7.4, indicating high quality. In the risk of bias assessment, four studies (14.8%) were of lower quality, with a NOS score of <7. Based on NOS criteria, three studies were of lower quality based on criteria 1 (representativeness of the exposure group or sample representation), seven studies based on criteria 2 (selection of non-exposure group or sample selection), and three studies based on criteria 3 (not report the definition of the exposure); only four of eight cross-sectional studies performed appropriate statistical tests (criteria 7). Detailed results on the NOS quality assessment are presented in n = 10,146, 95% CI: 42\u201356; I2 = 98.2%, p < 0.01, \u03c42 0.03). Region-wize data showed significant differences in the prevalence of polypharmacy between different regions of India ranging from 39% in Northern states to 52% in East India. Studies from West India , and North-east India reported higher prevalence of polypharmacy . Moreover, the majority of studies were conducted in South India . The data on the prevalence of polypharmacy in other regions is summarized in Out of 27 publications, twenty-one studies, comprising 9,391 participants, reported a prevalence of polypharmacy among older adults. The pooled prevalence of polypharmacy in India, after weighing the regional population size, was 49% . Region-wize data on the prevalence of hyperpolypharmacy among older adults showed considerable variations with 36% prevalence was seen in East India (95% CI: 27\u201344), 35% in West India (95% CI: 28\u201341), 23% in North India (95% CI: 8\u201339) and 33% (95% CI: 17\u201348) in South India, as shown in Q = 2.08, df = 3; p = 0.560).Fourteen studies investigated the prevalence of hyperpolypharmacy among the older population in India . The pooI2 = 97.3; p < 0.01; \u03c42 0.0117), which indicated substantial heterogeneity, as shown in Q = 18.8, df = 4; p < 0.01). West India and South India demonstrated a relatively higher pooled prevalence of 33% and 32% , respectively, while North India and East India had a lower pooled prevalence of 17 and 23%, respectively. The variations in the pooled prevalence of PIM use are further illustrated in the forest plot in All the 27 studies provided PIM estimates among the older population in India . The pooQ = 26.4, df = 3; p < 0.01). Regarding PIM use, studies conducted before 2013 had a lower pooled prevalence (22%) than those conducted between 2013 and 2016 (31%); however, the pooled prevalence slightly decrease for studies conducted after 2017. Grouping the studies by various subgroups did not reduce heterogeneity, and no significant difference was observed between the groups . However, significant differences in the heterogeneity were observed between low-quality and high-quality studies .A stratified meta-analysis of the prevalence of polypharmacy, hyperpolypharmacy, and PIM use in India is summarized in Subgroup analysis by geographic region, study design, type of hospital, and study settings did not influence the prevalence estimates of polypharmacy, hyperpolypharmacy, and PIM use, as shown in p = 0.034) and PIM use (Egger test: p = 0.027 & Begg\u2019s test: p = 0.001). Visual examination of the funnel plots showed asymmetry and suggested publication bias, as shown in The Egger\u2019s and Begg\u2019s tests indicated statistically significant publication bias for the polypharmacy estimates reported a higher prevalence of polypharmacy (49%), hyperpolypharmacy (31%), and PIM use (28%) among the older population in India. Region-specific estimates showed that polypharmacy is widely prevalent in Northern India (72%), hyperpolypharmacy in the eastern and western parts of India (36%), and PIM use (33%) in Western states. Furthermore, polypharmacy is more frequently observed in outpatient settings (57%) and hyperpolypharmacy in inpatient settings (37%). Stratified analysis showed variations in PIM exposure across subsets, and governmental hospitals showed a lower prevalence of PIM use than private hospitals (25 vs. 27%). Considerable variations in polypharmacy and hyperpolypharmacy are seen among cross-sectional studies in comparison to cohort studies.Sharma et al. study demonstrated the differences in the prevalence of polypharmacy in the Indian states and reported that Uttaranchal (93.1%) from North India and Southern states, such as Telangana (82.8%) and Karnataka (84.6%), had the highest prevalence of polypharmacy compared to Northeast -West Bengal (5.8%), Tripura (East India) (6.8%), Madhya Pradesh (8.3%) and Goa (West India) (13.8%) . While tPolypharmacy and hyperpolypharmacy are proxy indicators for PIM use in older populations, leading to adverse clinical outcomes. The findings of the current study revealed an increasing incidence of hyperpolypharmacy. The pooled estimates showed a much higher prevalence of hyperpolypharmacy (31%) in India than the developed countries like the United States of America (1%) , New ZeaOur findings on the pooled prevalence of PIM use showed that 28% of older patients in India are affected by PIM; a similar trend was observed over the years in high-income countries (33.3%) . This stFindings from this study demonstrate the prevalence of polypharmacy, hyperpolypharmacy, and PIM use in Indian states and highlight the urgency to address inappropriate medication use in the older population. Therefore, future studies with a multi-pronged approach should be conducted, focusing on comprehensive geriatric medication reviews by clinical pharmacists, computerized clinical decision support systems, and prioritizing rational geriatric prescribing at the national level. Moreover, multifaceted randomized controlled trials are needed to evaluate the effects of the intervention on clinically relevant outcomes such as hospitalization, medication costs, and health-related quality of life.This is the first systematic review and meta-analyses to consolidate the quantitative evidence on the wide-ranging impact of polypharmacy, hyperpolypharmacy, PIM use in various states of India. We also thoroughly assessed the risk of bias in each of the 27 observational studies. We further conducted meta-analyses stratified according to the suspected potential source of heterogeneity between the studies and subgroups.2 test statistics) and I2. More studies were conducted in South India than in any other region. Third, publication bias was present in the selected studies and has been known to affect heterogeneity. We performed a more stratified subgroup analysis to explore the source of heterogeneity and differences within the subsets.The study findings are subject to some limitations. First, factors like geographic areas, cultures, and practices vary widely across the states in India, which may influence the results. Second, higher heterogeneity in the outcomes may be due to differences in sample size (ranging from a few hundred to a few thousand). Low power and precision may produce higher Cochran Q (heterogeneity xThe prevalence of polypharmacy and hyperpolypharmacy among older Indian adults is relatively high. Almost a quarter of the older people are affected by PIM use in India. Significant regional differences exist in the prevalence of polypharmacy, hyperpolypharmacy, and PIM use. These findings highlight the need for urgent steps to promote rational geriatric prescribing and prioritize pharmacist-led comprehensive medication reviews to reduce medication-related problems among older people in India."} +{"text": "Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae. Our hospital, Rambam Health Care Campus (RHCC), was one of the medical centers affected by this outbreak. We aimed to investigate the changing epidemiology of CPE at RHCC since 2006.Israeli hospitals were confronted with a major national outbreak of carbapenemase-producing Enterobacterales (CPE) starting in 2006, caused predominantly by monoclonal This was a retrospective observational cohort study performed in Northern Israel (Haifa) at RHCC, which is a primary tertiary acute care academic hospital. The study included all patients who had acquired CPE at RHCC between January 2005 and December 2020.K. pneumoniae dropped from 100% of all CPE in the first years to 28% (37/134) in 2020. In 2014, the carbapenemase in 94% of all CPE patients (89/95) was KPC. This decreased to 56% in 2020, while New Delhi metallo-\u03b2-lactamase (NDM) and OXA-48 carbapenemases increased from 4% and 2% to 29% (39/134) and 12.7% (17/134) of CPE, respectively.The proportion of patients infected with K. pneumoniae to involve different Enterobacterales and carbapenemases. Our results are a microcosm of the current global epidemiology attesting to globalization in bacteriology. The results have implications for infection control and antibiotic treatment of CPE infections.The CPE epidemic evolved from KPC-producing Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-\u03b2-lactamase (NDM), imipenemase (IMI), oxacillinases (OXA)-48, and Verona integron-encoded metallo-\u03b2-lactamase (VIM). Israeli hospitals confronted a major national outbreak starting in 2006, caused predominantly by monoclonal KPC-producing Klebsiella pneumoniae.2Carbapenem-resistant Enterobacterales (CRE) are amongst the major challenges that have been facing healthcare institutions throughout the world in the last two decades.K. pneumoniae; from January 2006 to April 2007, all 88 carbapenem-resistant K. pneumoniae patient isolates carried KPC.3Our medical center, Rambam Health Care Campus (RHCC), located in Northern Israel, was among the affected hospitals. The prevalence of CRE at RHCC increased from 2006, reaching a peak of 186.6 new acquisitions per 100,000 hospital-days in 2008.Some of the carbapenemases are chromosomal, but most often, and notably, the KPCs are found on plasmids, hence they are able to move between bacterial species. Indeed, with time, KPC spread to different Enterobacterales, and the introduction of diverse carbapenemases was noted. The aim of this study was to describe the introduction of new carbapenemases at RHCC and the spread of carbapenemases among Enterobacterales.The study was conducted at RHCC, a 1,000-bed primary and tertiary university hospital in Northern Israel. All patients who acquired CPE at RHCC between January 2005 and December 2020 were included in the study. At RHCC, CPE was considered as acquired if the positive sample was taken \u226572 hours after admission, within 72 hours after any discharge, or within one month after discharge, if the patient was not hospitalized in another healthcare facility. Patients who acquired CRE before admission to RHCC were excluded.blaKPC/blaNDM/blaOXA-48/blaVIM, have been detected routinely using polymerase chain reaction (PCR)-based multiplexed assays specific for these genes.5Rectal swab screening samples were cultured prior to 2019 on PD420 CHROMagar KPC plates; since 2019, samples were cultured on PD517 MSUPERCARBA plates . The latter medium was used because of its higher sensitivity to non-KPC CPE. Carbapenemase-producing Enterobacterales was defined as Enterobacterales of any type resistant to all tested carbapenems using the Clinical and Laboratory Standards Institute (CLSI) M100S guidelines definition of MIC>1. We extracted DNA from suspected CRE colonies using the Qiamp DNA mini kit in accordance with the manufacturer\u2019s instructions. Since 2014, \u03b2-lactamase (bla) carbapenemase genes, i.e. K. pneumoniae. Starting in 2009, the proportion of patients carrying CRE with other strains increased gradually, reaching 72% (97/134) in 2020, while the proportion of K. pneumoniae decreased to 28% (37/134) in 2020 of all CPE acquired at RHCC possessed the KPC gene. Only 6% (6/95) of isolates possessed other resistance genes. This proportion decreased to 56% (75/134) in 2020 . The proK. pneumoniae, spread of carbapenemases to other Enterobacterales strains was reported in RHCC as early as 2010.K. pneumoniae, and less than half possessed the KPC gene. Carbapenemases spread to many different Enterobacterales, and new carbapenemases were introduced.We examined the changing epidemiology of CPE in terms of pathogens and resistance mechanisms in one Israeli institution (RHCC) endemic for CPE. Starting from an outbreak confined to KPC-producing K. pneumoniae in North Carolina, USA, in 1996,K. pneumoniae has spread to many locations worldwide.8Since the first description of KPC-producing Our findings are consistent with this spread, which has a major impact on infection control. The diversity of isolates and resistant genes may indicate that, besides clonal transmission of CRE in the hospital, alternative transmission occurs through horizontal spread of mobile genetic elements and plasmids. Modalities to prevent transfer of carbapenemases between Enterobacterales are necessary, possibly avoiding certain antibiotics, such as carbapenems which are direct drivers of carbapenem resistance. While previously all CRE carriers could be cohorted, separate isolation according to the type of carbapenemase is currently necessary. The diverse resistance mechanisms also affect our choice of empirical and definite antibiotic treatment, since the new \u03b2-lactamases are carbapenemase-specific.Our study has some limitations. First, it was conducted in one medical center that was endemic for CPE. Second, we included only CPE acquired in RHCC due to lack of microbiological data and molecular studies on isolates acquired elsewhere. However, 95% of CPE carriers hospitalized in RHCC during the study period had acquired CPE there. This study does not analyze the mechanisms leading to this spread of carbapenemases among bacteria and the reasons leading to the introduction of new carbapenemases to RHCC; only the CPE epidemiology at RHCC over time is described. Similar changes are most likely occurring in other Israeli hospitals. Data published in the 2019 national report for all CPE found in Israeli hospitals reported that only 47% were KPC, 33% were NDM, 12% OXA, 5% VIM, and 3% other; it is likely that these CPE circulate within and among hospitals.12In conclusion, we demonstrate the change in carbapenem resistance mechanisms in one Israeli hospital, the introduction of new carbapenemases, and the spread of carbapenemases across Enterobacterales. These findings, if representative of global epidemiology, are of great concern. Irrespective of location, infection control efforts are essential to prevent the further spread of carbapenemases and CPE."} +{"text": "L-Arginine has been shown, in human breast cancers, to increase protein synthesis and the number of cells in the growth phase of the cell cycle. L-Arginine, therefore, may potentiate the response of breast cancers to cell cycle-specific cytotoxic agents. This phase II pilot study assessed the clinical, radiological and pathological responses in 44 patients with breast cancers > 4 cm in diameter , who received oral L-arginine 30 g day-1 for 3 days prior to each cycle of CHOP chemotherapy, followed after 4-6 cycles by radiotherapy. Following this treatment, 95% of patients had a clinical response: complete response in 30% and partial response in 65%. Imaging, ultrasound and mammography revealed response rates of 91% and 76% respectively. Surgery was performed in 43 patients. Histological examination revealed that in 18% of cases there was no residual evidence of tumour. Furthermore, if residual tumour was identified, the degree of destruction was graded as 'severe' in 36% and 'moderate' in 30% of cases. Further studies are now required to evaluate the potential beneficial use of nutritional pharmacology in combination with existing treatment regimens."} +{"text": "We characterized the prevalence of cockroach allergen exposure in a nationally representative sample of U.S. homes and assessed risk factors for elevated concentrations.We used data from the National Survey of Lead and Allergens in Housing, a population-based cross-sectional survey.Participants were residents of 831 U.S. homes in the survey.We analyzed allergen, questionnaire, and observational data of 831 U.S. homes.Cockroach allergen (Bla g 1) concentrations exceed 2.0 U/g, a level associated with allergic sensitization, in 11% of U.S. living room floors and 13% of kitchen floors. Concentrations exceed 8.0 U/g, a level associated with asthma morbidity, in 3% of living room floors and 10% of kitchen floors. Elevated concentrations were observed in high-rise apartments, urban settings, pre-1940 constructions, and households with incomes < $20,000. Odds of having concentrations > 8.0 U/g were greatest when roach problems were reported or observed and increased with the number of cockroaches observed and with indications of recent cockroach activity.Household cockroach allergen exposure is characterized in a nationally representative context. The allergen is prevalent in many settings, at levels that may contribute to allergic sensitization and asthma morbidity.Likelihood of exposure can be assessed by consideration of demographic and household determinants. Asthma, a chronic respiratory disease characterized by episodes of airway inflammation and narrowing, represents a significant public health problem. The prevalence of asthma in the United States has increased considerably since 1980 , coincidIt has been clearly established that exposure to cockroach allergen is one such risk factor. Many studies have demonstrated this association, including some that have found that levels of cockroach allergen in homes are one of the strongest risk factors predictive of allergic sensitization and asthma morbidity in children . It has Previous studies examining levels of cockroach allergens and associated characteristics in U.S. homes have targeted specific populations such as single metropolitan areas and inner-city neighborhoods . Such stThe weighted NSLAH population is, by design, comparable with the U.S. population of eligible housing units: 28% in urban areas with population > 1 million, 39% with children < 18 years of age, 80% white, 8% Hispanic, and 80% above the poverty level.The objectives of this research are to provide the first nationally representative estimates of cockroach allergen prevalence within households and to identify demographic factors and housing characteristics associated with high cockroach allergen levels. Achieving these objectives will provide a characterization of household cockroach allergen exposure on a nationwide basis, assist clinicians in assessing the likelihood of a patient\u2019s exposure, and influence research hypotheses for intervention studies.The NSLAH was a cross-sectional survey of the U.S. population of 96 million permanently occupied, noninstitutional housing units that permit resident children, and was carried out in 1998\u20131999. A complex, multistage design was used to sample and gain participation from 831 housing units containing 2,456 individuals. The staged design involved the selection of 75 primary sampling units across the United States, followed by the sampling of segments (defined as contiguous blocks) within each primary sampling unit, and then the sampling of housing units within each segment. Among 1,984 housing units initially selected to be recruited into the study, 980 were determined to be eligible during screening, 229 were found to be ineligible, and 775 did not complete sufficient screening to determine eligibility. Assuming that the eligibility rate among these 775 is the same as the rate among households of known eligibility, the surveyed population of 831 housing units constitutes a response rate of 52% of an estimated 1,608 eligible units. Demographic comparisons with both the American Housing Survey and the Dust samples used in this analysis were collected from the kitchen floor, living room floor, upholstered living room furniture, a randomly selected bedroom bed, and bedroom floor, using a Eureka Mighty-Mite 7.0-A vacuum cleaner . A 19 mm \u00d7 90 mm cellulose extraction thimble was placed in the distal end of the vacuum\u2019s extension tube, sealed with a rubber O-ring, and covered with a clean crevice tool. Defined floor areas or perimeters, upholstery surfaces, and bedding layers were vacuumed over specified time intervals. Details of dust collection protocols are described elsewhere .At the laboratory, dust samples were sieved through 425-\u03bc m pore grating, weighed, and divided into 100-mg aliquots of fine dust. Dust aliquots were extracted in borate-buffered saline and clarified by centrifugation. Supernatants were decanted and stored at \u201320\u00b0C. Cockroach allergen was measured by a two-site, monoclonal antibody enzyme-linked immunosorbent assay . AllergeF-test statistics. We developed standard errors (SE), CIs, and p-values in accordance with the complex survey design using Taylor series linearization methods. Statistical analyses were conducted using SAS software and SUDAAN .We selected factors for analysis on the basis of hypothesized relevance gleaned from the literature or other sources. All percentages, correlations, means, percentiles, and odds ratios (ORs) were weighted to represent the U.S. population of permanently occupied, noninstitutional housing units that permit resident children. The statistical weighting included the application of a nonresponse adjustment factor to the weights of the surveyed housing units, to ensure that they also represent the eligible housing units that did not participate in the survey. A detailed description of the statistical weighting for the NSLAH can be found elsewhere . We calc2) and the highest median weight of sampled dust (459 mg). Samples of comparable median dust weight were collected from the living room floor (290 mg) and the bedroom bed (287 mg); thus, the higher median cockroach allergen load seen in living room floors is mostly a function of higher concentrations in that location.Among samples containing detectable cockroach allergen from locations with recorded collection areas, the bedroom floor exhibited the highest median load across the sampling locations and endotoxin .To investigate associations between cockroach allergen and various demographic factors, we compared the distributions of concentration across levels of the factors shown in The highest prevalence of elevated concentrations was observed in high-rise apartments. Generally, higher concentrations were also observed in homes built before 1940, urban areas, low-income households, and multifamily structures. Some differences were also seen according to geographic region of the United States, with somewhat higher living room floor levels in the Northeast and Midwest. However, results obtained using dust sampled from the kitchen floor were reversed from those in Detectable concentrations were generally prevalent in all demographic categories; the lowest rate of detection was 29.9% among western households.With regard to income in particular, patterns seen in In contrast and as mentioned above, generally higher kitchen floor cockroach allergen concentrations were observed in the South and West. Among southern homes with household incomes < $20,000, 31.9% of kitchen floors exceeded 2.0 U/g and 24.2% exceeded 8.0 U/g. Results for low-income western homes were similar . All such results were lower in low-income northeastern (17.2% and 7.6%) and midwestern (18.1% and 18.1%) homes.After accounting for demographic factors, specific household characteristics were analyzed to investigate their ability to predict higher levels of living room floor cockroach allergen relative to two thresholds: 2.0 U/g and 8.0 U/g. Results are displayed in Cockroach allergen in dust sampled from the kitchen floor yielded results generally comparable with those displayed in Restating our results in terms of positive and negative predictive value, 86% of residents reporting problems with cockroaches did in fact have detectable concentrations at one or more sites, with 58% > 2.0 U/g and 38% > 8.0 U/g. Only 16% of residents indicating no such problems had detectable levels > 2.0 U/g, and 4% > 8.0 U/g. Although 100% of residents who reported seeing > 50 cockroaches/day had detectable levels > 8.0 U/g, resident reporting of between 5 and 50 cockroaches per day was also a strong predictor of levels > 2.0 U/g and 8.0 U/g . Other useful predictors of exceeding these thresholds included resident reporting of cockroaches seen within the past week (77.9% and 58.7%) or month (74.3% and 53.1%) and field staff reports of roach stains or live or dead roaches in at least one location in the home (71.2% and 52.5%).In this article we provide the first nationally representative estimates of household cockroach allergen prevalence and find that 11% of U.S. living room floors and 13% of kitchen floors exhibit elevated concentrations relative to a 2.0-U/g threshold previously established as related to allergic sensitization . We alsoIn the National Cooperative Inner-City Asthma Study, children with sensitivity to cockroach allergen who were exposed to bedroom levels > 8.0 U/g had asthma hospitalization rates that were 3.7 times higher than sensitive children with lower levels of exposure . On a naElevated cockroach allergen levels are most prevalent in high-rise apartments, urban settings, pre-1940 constructions, and households with incomes < $20,000. However, the allergen is not restricted to low-income environments; levels > 2.0 U/g were detected on the living room floors of 7% of households with annual incomes > $60,000.Although there are some regional differences in magnitude, the same demographic factors are generally associated with elevated cockroach allergen levels in each geographic region. Demographic distributions themselves provide one possible explanation for the greater prevalence of elevated living room floor cockroach allergen in the Northeast compared with the South, because the Northeast target population includes relatively more pre-1946 constructions (43% vs. 14%) and more households in large urban areas (34% vs. 23%).After accounting for the demographics, elevated exposure risk is most strongly associated with reported or observed cockroach activity and increases consistently with more recent or more prevalent activity. This is particularly informative in the context of cockroach allergen abatement studies that have focused on the impact of cleaning and insecticide application . Our resCockroach allergens are derived from several sources, including secretions, excretions, dead bodies, and associated debris. Airborne cockroach allergens are associated primarily with larger particles than are animal allergens, and after disturbance they fall and settle rapidly . The genThe major strength of this study is its national representativeness. The weighted characteristics of the surveyed homes compared favorably with those of other national housing surveys . Our resThe major limitation of the study is its cross-sectional design. Dust samples were collected at a single point in time because repeated visits to the home were not feasible. However, this was the most efficient method for achieving the stated objective of estimating and characterizing indoor allergen levels on a national scale. Sampling was conducted across seasons so as to mitigate any possible seasonal bias.Blattella germanica, a small organism responsible for the primary U.S. exposure. The estimated prevalence of detectable Bla g 1 concentrations in 63% of homes is consistent with other research that found 52% prevalence in a regional sample of child care facilities (This study surveyed homes for the Bla g 1 allergen from the German cockroach cilities . NeverthThis study characterizes the prevalence of cockroach allergen in U.S. homes and illustrates factors influencing the risk of exposure to elevated concentrations. These results may help clinicians to assess whether a patient is likely to be exposed and suggest measures to reduce this exposure. Our results also lend important context to the potential impact of abatement studies of cockroach allergen."} +{"text": "The relationship between physical activity and health status has been thoroughly investigated in several studies, while the relation between physical activity and socio-economic status (SES) is less investigated. The aim of this study was to measure the extra-curricular physical activity of adolescents related to the socio-economic status (SES) of their families.The survey was carried out by submitting an anonymous questionnaire to junior high school students in the following Regions: Lazio, Abruzzo, Molise, Campania, Puglia, during the school year 2002\u20132003. Extra-curriculum physical activity was evaluated considering whether or not present and hours of activity weekly conducted. 2411 students agreed to participate in the study.Participants were 1121 males (46.5%) and 1290 females (53.5%), aged between 11 and 17 years (median age: 12 years). 71.1% of the students reported to practice extra-curricular physical activity. Parents' educational levels and work activities play an important role in predicting students' physical activity, with the more remunerative activities and higher educational levels being more predictive.The results confirm the relationship between adolescents' physical activity and their families' SES. In particular, a positive relationship between participation in extra-curricular physical activity and their families high SES was found.These data will be useful for school administrators and for politicians in order to reduce the gap between adolescents from the least and most disadvantaged families. The relationship between physical activity and health status has been described extensively in several studies. Active lifestyles are often associated with better health status and quality of life -8, howevIn Italy there isn't an individual SES classification available, territorial data (ISTAT data) is based on personal economic consumption rather than income and education. Another possible classification of personal income comes from the Italian financial acts and the different levels of income tax rates. However, this data is not easily inferable from statistical sampling including adolescents.The aim of the present study was to investigate the relationship between adolescents' extra-curricular physical activity and the SES of their families.The survey was carried out by submitting an anonymous questionnaire junior high school students randomly selected in the following regions: Lazio, Abruzzo, Molise, Campania, Puglia, during the school year 2002\u20132003. Sample size calculations suggested to sample 2502 students. We obtained informed consent for interviewing minors in our study from their parents. Students absent during the first submission were given the questionnaire in the days following.2411 students agreed to participate in the study. The research was conducted according to the Helsinki Declaration.The questionnaire, already validated in a pilot study ,18, cont- scholastic physical activity- extra-curricular physical activity- physical activity attitudes- lifestyle habits- parents' physical activity, education and work activity- students' socio-demographic dataAs far as concerns physical activity of the adolescents the questionnaire investigated whether or not extra-curricular physical activity is conducted, which type of physical activity is chosen by, how many hours per week are devoted to this activity.Concerning attitudes toward physical activity, it was asked if physical activity is considered useful in preventing obesity, in socialising, and in character- building.Moreover, we collected information on the following lifesyle habits, as dichotomous variables (yes/no): cigarette smoking, coffee and alcohol drinking.The following data from students' parents were collected: weekly physical activity, described as intense (more than two times per week), regular (two times per week), scarce (once per week) and abstent; educational levels, indicating the level reached: Degree, Senior High school, Junior High school, Primary school; regarding work activities we used a classification cited in another study : ManagerCertain information about family income was impossible to obtain from the students, therefore, SES was estimated considering parents' educational levels and work activities. A socio-economic family index, derived from the combination of parents' work activities, was calculated, using the matrix described in Fig. Data from the questionnaires was collected in a suitable relational database and analysed with SPSS statistical package.2) and chi-square for trend test for qualitative variables and Student t-test for quantitative variables were applied to test the differences between the groups, considering p < 0.05 as statistically significant.Chi-square , sex , educational level of both parents (reference group: primary school), father's job (reference group: unemployed), parents' physical activity , student's opinions about sport as a means of socialisation, character-building and prevention of obesity (reference group: negative responses).The second regression analysis model evaluated the influence of the same covariates used in the first model (with the exception of the father's job) and that of socio-economic level (reference group: low socio-economic level) on the variable \"extra-curricular physical activity\". Analysis was performed using the Hosmer and Lemeshow method, with a p < 0.10 level for the insertion in the regression model of covariates considered for univariate analysis.Participants were 1121 males (46.5%) and 1290 females (53.5%), aged between 11 and 17 years (median age 12 years). 33.7% of the students attended the first class, 38.5% the second and 27.8% the third one.86.4% of them participated in school-based physical activity for two hours per week and 13.6% for three hours per week or more.The types of school-based physical activity undertaken were as follows: 71.1% did gymnastics; 81.7% volleyball; 37.8% basketball; 10.7% football; 36.8% handball; 22.3% long jump; 21.6% high jump and 48.8% running.71.1% of students declared to participate in extra-curricular physical activity with the following breakdown: 20.2% for one-two hours per week, 23.8% for three-four hours per week, while 56% stated they did five hours or more per week.Concerning extra-curricular sports, 30.1% of the students played football, 19.7% did dancing/aerobics/gymnastics, 14.5% swam, 14.2% played volleyball, 5.8% played basket ball, 5.4% did fitness/body-building, 3.9% did martial arts, and 1.8% cycled.370 students (15.3%) state to take nutritional supplementation before or after physical activity. 68.2% of students practising extra-curricular physical activity stated that they paid a monthly fee.Concerning attitudes toward physical activity, 79.9% of participants considered constant physical activity useful in preventing obesity, 5.6% did not and 14.5% were unsure. 82.7% of students considered physical activity important in socialising, 5.9% did not and 11.6% remained unsure. 56.1% of responders considered physical activity important in character- building, 15.8% did not and 19.1% did not know.As for unhealthy lifestyles, 37.8% stated that they were smokers or had started smoking, 43.8% drank coffee and 43.4% drank alcohol, especially beer, wine, alcoholic lemon drinks and vodka.Table 2 = 15.41; p = 0.0015). However, there were not significant differences between parental education .With regards to parental physical activity levels, fathers were significantly more active than mothers and Non-skilled workers (34.3%) for fathers and Housewives (59.3%) and Office workers (28.3%) for mothers. According to our SES classification adolescents' families were categorised in the following way: very high 16.8%, high 14.5%, middle 37.2%, middle-low 30.1% and low 1.4%.2 = 64.764; p < 0.0001) Fig. than tho2 = 35.421; p < 0.0001). 86.7% of students with fathers graduated with a Degree considered constant physical activity helpful in socialising, versus 84.5%, 88% and 75.5% respectively, of students with fathers holding a diploma, a secondary school-leaving certificate, a primary school/leaving certificate .86.3% of students with fathers graduated with a Degree considered constant physical activity helpful in preventing obesity, compared to 85.2%, 80.7% and 69.4%, of students respectively, with fathers holding a diploma, a secondary-school leaving certificate or a primary school-leaving certificate and undertook physical activity, for more than three hours per week , than those whose mothers have a lower educational level.Mother's educational level also seemed to considerably influence the determinants of the student's physical activity Fig. and the 2 = 12.817; p = 0.046).86.4% of students with mothers graduated with a Degree and 86.5% of those whose mothers have a diploma considered physical activity important in socialising, compared to 84.6% and 78.1%, respectively, of students whose mothers have a secondary-school leaving or a primary school-leaving certificate .83.5% of students with graduated mothers considered constant physical activity useful in preventing obesity, compared to 85.3%, 80.4% and 77%, respectively, of students with mothers holding a diploma, a secondary-school leaving certificate, a primary school-leaving certificate .Furthermore, extra-curricular physical activity is related to the parents' work activity Fig. . Student2 = 64.319; p < 0.0001). Adolescents with mothers who are Non-skilled workers/Housewives or Unemployed undertake less extra-curricular physical activity than those with mothers who were Managers/Professionals or Office-workers/Skilled workers and even more so for the mothers .Weekly hours of extra-curricular physical activity show a similar trend Fig. : percentTable The second model, which considers socio-economic family index, confirms the results of the first one. Moreover it shows an association between extra-curricular physical activity and SES (with ORs ranging from 1.63 and 1.96 for the indexes of High to Very high levels).Similar results were found considering in the logistic regression models the outcome \"percentages of students practising physical activity for three hours per week or more\" (data not shown).Several studies show evidence of a relationship between socio-economic level and health status. As demonstrated by Lowry et al. , higher The likelihood of undertaking adequate physical activity is low for subjects who have a low family income and for Studies on the relationship between physical activity and parents' educational level -23,25,26Results of our study confirm the relationship between family socio-economic, parents' educational levels and physical activity of adolescents.Moreover the classification of socio-economic index used in this survey, derived by the combination of the parents' work activities , appears to be comparable to the distribution of family income levels as reported in the Italian Financial Acts [Given these results, which are in agreement with other international surveys conducted in USA , South AFamilies with high SES consider physical activity useful both in preventing chronic and degenerative diseases and for socialisation, essential for the correct physical and psychological development of adolescents.SES is therefore clearly related to parents' educational levels, and parents' low educational levels and low remunerative work activities can negatively influence the participation of children in extra-curricular physical activity.In addition, it must be considered the inadequate knowledge about benefits of physical activity, related to low socio-economic and cultural levels .The presents study has some limitations. As far as concerns internal validity, we sampled randomly the participants, and used a validated questionnaire. Misclassification bias could arise if incorrect information on both exposure (SES status) and outcome (PA). The accuracy of self-reported physical activity of adolescents, should have been avoided, given the reliability of the tool we used, which had been validated in previous studies ,18. MoreAs far as external validity a potential selection bias could have been avoided, even if we used a cross-sectional type of study design. Finally, the precision of the estimates is comparable with that had been designed for.Neverthless, to our knowledge this is the first attempt in Italy to evaluate the relationship between SES, based either on a family income index and parents' educational status, and adolescents' extra-curricular physical activity.In our study parents' physical activity is a good predictor of adolescents' extra-curriculum physical activity, accordingly to previous studies. In a recent review on correlates of physical activity of children and adolescents, Sallis and coll. demonstrThe author(s) declared that they have no competing interests.All of th authors partecipated in the establishment of the research, and all read and approved the manuscript. GLT, DM and WR wrote the initial draft of the manuscript, which GLT edited.The pre-publication history for this paper can be accessed here:"} +{"text": "Nitrite inhalants (\"poppers\") are peripheral vasodilators which, since the beginning of the epidemic, have been known to increase risk for acquiring HIV infection among men who have sex with men (MSM). However, few studies in recent years have characterized use. From 1999 to 2004, new HIV diagnoses among MSM in British Columbia increased 78%, prompting us to examine the prevalence and correlates of this modifiable HIV risk factor.Self-administered questionnaires were completed between October 2002 and May 2004 as part of an open cohort study of HIV-seronegative young MSM. We measured nitrite inhalant use during the previous year and use during sexual encounters with casual partners specifically. Correlates of use were identified using odds ratios.Among 354 MSM surveyed, 31.6% reported any use during the previous year. Nitrite inhalant use during sexual encounters was reported by 22.9% of men and was strongly associated with having casual partners, with greater numbers of casual partners (including those with positive or unknown serostatus) and with anal intercourse with casual partners. Nitrite inhalant use was not associated with non-use of condoms with casual sexual partners per se.Contemporary use of nitrite inhalants amongst young MSM is common and a strong indicator of anal intercourse with casual sexual partners. Since use appears to increase the probability of infection following exposure to HIV, efforts to reduce the use of nitrite inhalants among MSM should be a very high priority among HIV prevention strategies. Nitrite inhalants (\"poppers\") are peripheral vasodilators used by men who have sex with men (MSM) to facilitate and enhance sexual intercourse . ThroughAmong MSM studied in San Francisco between 1985 and 1991, the prevalence of poppers use varied annually from 29.9% to 35.9% . ConsistDetailed studies of nitrite use among MSM during the past 5 years are scarce. One random digit dial survey conducted in 2003 reported that poppers were used during the previous six months by 18.6% of HIV-seronegative MSM residing in Seattle, Washington . Use wasThe substantial contribution of nitrite inhalants to contemporary HIV infections among MSM is well established. Remarkably, in recent years mention of nitrite inhalants in HIV prevention messages has become exceedingly rare. Risk reduction counselling guidelines do not include clear and specific messages about the increased risk for acquiring HIV infection associated with nitrite use ,12. IndeIn the province of British Columbia, annual reports of new HIV diagnoses among MSM from 1999 and 2004 increased 78% (from 95 to 169) ,14.This tremendous increase in HIV infections among MSM in BC, the importance of poppers as a modifiable risk factor for HIV seroconversion, and the scarcity of recent related research prompted us to study the prevalence and correlates of contemporary nitrite inhalant use among young MSM in Vancouver.The Vanguard Project was a prospective, open cohort study of HIV incidence and risk behaviours among young MSM ,16. BrieResults from our previous study showed the association of substance use and unprotected anal intercourse (UAI) depends on the type of drug-use measure , type of sexual partner and sexual position (insertive vs. receptive) ; therefoWe compared men who did and did not report use of nitrite inhalants using Pearson's chi-square, Fisher's exact, and Wilcoxon rank-sum tests. Correlates of use were identified using odds ratios (OR) with exact 95% confidence intervals (CI) computed using PEPI for Windows software Version 4.18 .Among 354 MSM study participants, 66.4% were white, 13.6% were Canadian-Aboriginal, 51.3% had completed college, 51.1% were employed full-time, and 7.0% were HIV-seropositive. Use of poppers during the previous year was reported by 112 men (31.6%). Compared to non-users, men who used poppers were younger , more likely to have stable housing (92.0% vs. 83.2% p = 0.032), and more likely to report an annual income greater than CDN$10,000 . Previous-year use of poppers was not significantly associated with race-ethnicity, having completed high school or college, full time employment, or HIV serostatus.Compared to men who did not report nitrite inhalant use, users were more likely to also report previous-year use of other substances, including alcohol (96.4% vs. 82.4%), marijuana (73.2% vs. 53.7%), ecstasy (48.2% vs. 21.5%), crystal methamphetamine (39.5% vs. 21.1%), gamma hydroxybutrate (GHB) (28.0% vs. 7.5%) and ketamine (22.2% vs. 8.8%) , as well as cocaine . Men who did and did not report use of poppers were not significantly different with regard to previous-year use of cigarettes, crack cocaine, amphetamines , lysergic acid (LSD), or heroin. Compared to non-users, men who used nitrite inhalants were more likely to have met sexual partners in bars (53.6% vs. 34.0%), on the Internet (45.5% vs. 27.1%), and in bathhouses (37.5% vs. 17.6%) .Among 349 men (99%) who answered the question, previous-year use of poppers during sexual encounters was reported by 80 (22.9%). In the sample overall, men who used poppers during sexual encounters were significantly more likely to report unprotected receptive anal intercourse with a casual partner . However, this association could indicate that men who use poppers during sexual encounters are more likely to have a casual partner, or are more likely to have anal intercourse with a casual partner, or are more likely to have receptive than insertive intercourse with a casual partner, or are less likely to use a condom during anal receptive encounters with casual partners. To explore each of these possibilities, we progressively restricted the sample to examine each association in turn.Compared to non-users, men reporting nitrite inhalant use during sexual encounters had a 17-fold increased likelihood of having casual partners and with engaging in anal intercourse with casual partners. However, among men who reported anal intercourse with casual partners, use of poppers during these encounters was not significantly associated with non-use of condoms during these encounters.With regular partners, associations between the use of poppers and unprotected sexual behaviours were markedly different. In the overall sample, use of poppers during these encounters was associated with neither insertive nor receptive unprotected anal intercourse . Similarly, in analyses progressively restricted like those used to examine sexual behaviours with casual partners, use of poppers during encounters with regular partners was not associated with any of the behaviours measured, except for a negative association with unprotected insertive anal intercourse or with use of condoms during specific acts of sexual intercourse. The latter limitation is common to all but a handful of studies that relate high-risk sexual behaviours and drug use .In summary, we report a disturbingly high prevalence of nitrite inhalant use among young MSM during a period of rapidly increasing HIV incidence in British Columbia. Our results, together with those from previous studies, suggest nitrite inhalant use by MSM is associated with a synergy among risks for HIV seroconversion. Use of poppers is associated with an increased likelihood of engaging in anal intercourse with an infected partner and in addition, a higher probability of infection following each such exposure. Rapid assessments are needed to determine whether MSM are aware of HIV-related risks associated with use of poppers. Efforts to reduce the use of nitrite inhalants during sexual encounters should be considered a high-priority HIV prevention strategy for MSM.The author(s) declare that they have no competing interests.TML conceived and designed the study, supervised data analyses and revised drafts of the manuscript. KM reviewed literature, produced the first draft of the manuscript and, with KC, performed data analyses and manuscript revisions. RSH reviewed a draft of the manuscript. All authors read and approved the final version of the manuscript.The pre-publication history for this paper can be accessed here:"} +{"text": "Matrix metalloproteinase (MMP) expression was investigated in patients with prostatic adenocarcinoma and benign prostatic hyperplasia (BPH). Forty-one men were studied: 26 had histologically proven prostate cancer, with 14 (54%) showing metastatic disease; 15 patients had BPH. Prostatic tissue was obtained from transurethral resection and needle core biopsies; gelatinolytic activity was determined by zymography. Seven gelatinolytic bands were detected, with molecular weights ranging from > 100 kilodalton (kDa) to 29 kDa. Nine of 14 patients (64%) with skeletal metastases had 92 kDa activity, present in only two of 12 patients (17%) with a negative bone scan, and absent in BPH. The 92 kDa gelatinolytic activity was expressed in 73% of aneuploid tumours compared with 20% of diploid tumours. A 97 kDa gelatinase was expressed in 80% of BPH samples and 23% of carcinoma patients. Enzyme bands of 72, 66 and 45 kDa were equally expressed in malignant tissue, irrespective of metastatic status, but were expressed in fewer BPH patients. The 97, 92, 66 and 45 kDa enzymes were identified as being pro-MMP-9 sequences by Western blotting, using a specific antibody directed against the pro sequence of the mature protein. MMP activity appeared to be increased in malignant prostatic tissue compared with BPH. Pro-MMP-9, in its 92 kDa form, was shown to be exclusively expressed by malignant prostatic tissue, and in particular by tumours that exhibited the aggressive and metastatic phenotype."} +{"text": "Dipyridamole and dobutamine stress echocardiography testing are most widely utilized, but their sensitivity remained suboptimal in comparison to routine exercise stress echocardiography. The aim of our study is to compare, head-to-head, exercise, dobutamine and dipyridamole stress echocardiography tests, performed with state-of-the-art protocols in a large scale prospective group of patients.Dipyridamole-atropine (Dipatro: 0.84 mg/kg over 10 min i.v. dipyridamole with addition of up to 1 mg of atropine), dobutamine-atropine (Dobatro: up to 40 mcg/kg/min i.v. dobutamine with addition of up to 1 mg of atropine) and exercise were performed in 166 pts. Of them, 117 pts without resting wall motion abnormalities were enrolled in study . Tests were performed in random sequence, in 3 different days, within 5 day period under identical therapy. All patients underwent coronary angiography.Significant coronary artery disease was present in 69 pts and absent in 48 pts. Sensitivity (Sn) was 96%, 93% and 90%, whereas specificity (Sp) was 92%, 92% and 87% for Dobatro, Dipatro and Ex, respectively (p = ns). Concomitant beta blocker therapy did not influence peak rate-pressure product and Sn of Dobatro and Dipatro (p = ns).When state-of-the-art protocols are used, dipyridamole and dobutamine stress echocardiography have comparable and high diagnostic accuracy, similar to maximal post-exercise treadmill stress echocardiography. Exercise stress echocardiography is more sensitive and specific for detecting inducible ischemia than exercise electrocardiography testing alone -4. DipyrBetween January and July 2004, 166 consecutive patients referred for coronary angiography were evaluated. Of them, only 117 patients without resting wall motion abnormalities were enrolled in the study. Exclusion criteria were: presence of left ventricular wall motion abnormality at baseline, heart failure, left bundle branch block, unstable angina, congenital or valvular heart disease, severe hypertension (systolic \u2265180 mmHg and diastolic pressure \u2265110 mmHg), serious arrhythmias and chronic obstructive pulmonary disease.Informed consent was obtained from all patients. They underwent exercise, and pharmacological stress echocardiography. Previous non-transmural myocardial infarction was present in 32 patients, 69 had angina pectoris and 16 patients experienced atypical chest pain.The study was approved by the Institutional Review Board of the Institute of Cardiovascular Diseases in Belgrade.Concomitant beta blockers were used in 34% (40/117), calcium antagonists in 37% (44/117) and nitrates in 45% (53/117) of patients. Teophylline, caffeine-containing products, and dipyridamole preparations were not allowed for at least 12 hours before testing.Patients performed stress testing in 3 different days in random sequence within 5 day period, at least 14 days after uncomplicated myocardial infarction.Exercise echocardiography (Ex) was performed according to maximal Bruce treadmill protocol.Dobutamine was infused in 3-minutes dose increments, starting from 5 to 40 mcg/kg/min. In echocardiography negative patients, atropine was added (in 4 divided doses up to a maximum of 1 mg of atropine) to the continuing 40 mcg/kg/min dobutamine infusion .Dipyridamole was infused at a dose of 0.56 mg/kg over 4 min, followed with 4 min of no dose and then, if the test was still negative, 0.28 mg/kg in 2 min. In dipyridamole echocardiography negative patients, 3 min after the end of infusion, atropine was given in 4 divided doses up to a maximum of 1 mg of atropine .The test was considered positive in the presence of obvious left ventricular regional wall motion abnormality. The other reasons for test interruption were: peak atropine dose , achievement of maximal age predicted heart rate, significant ST segment depression or elevation, severe chest pain, exercise-limiting dyspnea, fatigue and/or claudication, symptomatic hypotension (decrease in systolic blood pressure >20 mmHg) or hypertension (>220/120 mmHg), severe arrhythmias or intolerable side effects of administered drugs. Intravenous aminophylline (250 mg) was given after cessation of Dipatro test, and beta blockers (metoprolol 5 mg) or nitroglycerin if required.A 12-lead electrocardiogram monitoring was performed continuously and recorded at baseline, at the end of each stage and during recovery period accompanied with blood pressure recordings. Rate pressure product was calculated by multiplying systolic blood pressure and heart rate.Two-dimensional echocardiography was performed with the patient in the left lateral decubitus position. Standard apical and parasternal views were recorded, facilitating the analysis from the off line digitized videotapes . We used 16-segment left ventricular model . SegmentAll patients underwent selective coronary angiography according to Judkin's technique, within one week of stress echocardiography tests. Angiograms were analyzed using quantitative coronary angiography by observers unaware of the patient's data. Significant coronary artery stenosis was considered as \u226550% diameter stenosis present in at least one major epicardial coronary vessel.t test where appropriate, whereas dichotomous variables were compared using chi-square (McNemar-s test for paired proportions). A coefficient of correlation (r) was used to compare peak wall motion score index of different tests. Confidence intervals were calculated according to standard formulas (95%CI) as well as sensitivity, specificity and diagnostic accuracy.The data are expressed as mean \u00b1 SD. Comparison of continuous variables was performed using ANOVA As, Newman-Keuls procedure and Calculation of sensitivity, specificity and diagnostic accuracy were performed according to standard formulas. A p value less than 0.05 was considered statistically significant.Coronary artery disease was present in 69 patients: one-vessel coronary artery disease was present in 57 patients, 12 patients had multi-vessel coronary artery disease. The distribution of lesions were: left anterior descending \u2013 50 patients, circumflex artery \u2013 15 patients, and right coronary artery \u2013 16 patients.Feasibility was 95% and 97% for Dobatro and Dipatro (p = ns), respectively. Limiting side effects occurred in 6 and in 4 patients during Dobatro and Dipatro, including non-sustained ventricular tachycardia and short run of supraventricular tachycardia in the absence of myocardial ischemia. They disappeared after cessation of the test or after administration of specific antidote.Limiting side effects occurred in 17 patients (14%) during Ex in the absence of diagnostic end point and consisted of serious ventricular and supraventricular rhythm disturbances, severe chest pain, hypertensive response and fatigue. Thus, feasibility of Ex was 85%. There was no significant difference in feasibility of all three tests . There were no late complications in the ensuing hours after finishing the tests.Hemodynamic changes during stress echocardiography tests are presented in Table Atropine was added to dobutamine in 69% 81/117) of patients and to dipyridamole in 68% (80/117) of patients. Stress-induced wall motion abnormalities appeared in 70, 68 and 68 patients during Dobatro, Dipatro and Ex, respectively. The sensitivity was 96%, 93% and 90% for Dobatro, Dipatro and Ex in detection of myocardial ischemia (p = ns for Ex vs. Dobatro vs. Dipatro) , with significant correlation (p < 0.0001) of peak WMSI between all tests.Single vs. multivessel CAD: The sensitivity of stress in detection of one-vessel coronary artery disease was 95% for Dobatro and 95% for Dipatro and 93% for Ex . The sensitivity for detection of multivessel coronary artery disease was 100% for Dobatro and Dipatro and 92% for Ex (p = ns).Forty (34%) patients received concomitant beta blocker therapy (34 with coronary artery disease). There was significant difference between patients with (BB+) and without beta-blocker therapy (BB-) in the peak heart rate for Dob, Dip, and Ex (p < 0.001), whereas addition of atropine excluded significant influence of beta-blocker therapy on peak heart rate. Rate-pressure product at baseline and peak stress tests in patients with (BB+) and without (BB-) concomitant beta-blocker therapy are presented in Table Atropine was added to dobutamine in 75% of patients in BB+ (34/40) and in 61% in BB- group (47/77), and to dipyridamole in 85% of patients in BB+ (34/40) and 60% (46/77) in BB- group. Addition of atropine resulted in similar sensitivity . However, sensitivity of Ex was significantly affected by beta-blocker therapy an increase in oxygen demand, exceeding the fixed supply \u2013 dobutamine and exercise; and b) flow maldistribution, due to inappropriate coronary artery vasodilatation. Atropine superimposes a marked chronotropic stress to dipyridamole and dobutamine increasing oxygen demand, decreasing, at the same time, myocardial oxygen supply by shortening the diastole whose duration is important for perfusion in the presence of maximal vasodilatation and incrSeveral meta-analytic comparisons of echocardiographic stressors have been performed in the past -23. TheyThe study group was derived from patients referred for coronary angiography and angioplasty, so large majority of patients had the one-vessel coronary artery disease. The use of a qualitative assessment of wall motion during stress echocardiography is a limitation of this technique, although qualitative assessment of regional wall motion by trained observers remains the only clinically applied method in stress echocardiography.When state-of-the-art protocols are used, dipyridamole and dobutamine stress echocardiography have comparable and high diagnostic accuracy, similar to maximal post-exercise treadmill stress echocardiography. In addition, dipyridamole-atropine and dobutamine-atropine stress echocardiography testing overcome the effects of concomitant beta-blocker therapy reaching high and comparable diagnostic value.The author(s) declare that they have no competing interests.We would like to report specific contribution of each author of the manuscript: IN made the concept, performed stress echocardiography tests and participated in the echocardiographic analysis. MO participated in the design of the study and interpretation of data. BB performed quantitative coronary angiography and help to draft the manuscript. ADD carried out the stress echocardiography testing. JS performed stress echocardiography tests and participated in its interpretation. MN performed coronary angiography. SS performed coronary angiography and quantitative coronary angiography analysis. GS participated in the interpretation of data. JS helped in quantitative coronary angiographic analysis. ZP carried out the selection of patients. VG participated in the statistic analysis. PM participated in the design of study and helped to draft the manuscript.All authors read and approved the final manuscript."} +{"text": "Of 150,000 new coccidioidomycosis infections that occur annually in the United States, \u22481% disseminate; one third of those cases are fatal. Immunocompromised hosts have higher rates of dissemination. We identified 8 patients with disseminated coccidioidomycosis who had defects in the interleukin-12/interferon-\u03b3 and STAT3 axes, indicating that these are critical host defense pathways. Coccidioides immitis. The Centers for Disease Control and Prevention reported 22,401 cases in 2011, an increase from 2,265 cases reported in 1998 . These cases highlight the importance of the interleukin (IL)\u201312/interferon (IFN)\u2013\u03b3 and signal transducer and activator of transcription 3 (STAT3) pathways in host defense. Dissemination of this typically self-limited pathogen should prompt consideration of underlying host genetic factors.>2 extrapulmonary affected sites.Our systematic literature search resulted in 370 case reports of disseminated coccidioidomycosis (DC) published during 1975\u20132014 . DC was Coccidioides spp. with race/ethnicity, sex, pregnancy, and immune status . Of total deaths, 75% occurred among women during their third trimester; fetal or infant death occurred in 40% of reported cases. Although one third of pregnant women affected were black, survival did not differ by race.The rate of DC is higher for pregnant woman than for the general population . CMRs were lower, but still substantial, for patients receiving steroids . In HIV-infected exogenously immunocompromised patients, coccidioidomycosis was similar to that in persons without HIV/AIDS. CMRs were lower for persons who were able to stop exogenous immunosuppression. Patients with exogenous immunosuppression were 37% white, 20% Hispanic, and 11% black , similar to the racial/ethnic distribution in DC-endemic areas was \u224850% for persons immunocompromised by HIV, cancer, organ transplantation, antigraft rejection medications, antiinflammatory biologicals, or chemotherapy . Additionally, osteomyelitis was more common among blacks (82%) than whites (29%); central nervous system (CNS) infection was more common among whites (59%) than blacks (13%). Hispanics and Asians also had higher rates of osteomyelitis and lower rates of CNS dissemination than whites . In contrast, among patients with exogenous immunosuppression, differences in rates of osteomyelitis and CNS infections by race were much smaller (44% of blacks with osteomyelitis vs. 24% of whites and 33% of blacks with CNS infection vs. 21% of whites). These data suggest that different immunologic factors that track with race might variably control susceptibility to DC, osteomyelitis, and CNS disease. However, exogenous immunosuppression apparently overrides these racial/ethnic variations.Most (84%) patients with multisite infection were male, and the number of blacks was double that of any other race . Overall, blacks had more single-site osteomyelitis than whites (64% vs. 41%), and whites had more CNS infection than blacks (17% vs. 2%) . Thus, despite the lower CMR in single-site disease, racial/ethnic differences in infection site were largely consistent between those with single-site and multisite infection.Consistent with the demographic characteristics of patients with multisite disease, 83% of those with single-site infection were male donors. In vivo, 3 patients with DC improved substantially after therapy with IFN-\u03b3. Immune function studies in 2 of those patients showed blunted IFN-\u03b3\u2013mediated responses , pregnancy, race/ethnicity, and discrete genetic defects. Although racial/ethnic associations with DC were evident in patients without known underlying risks, they were submerged by exogenous immunosuppression.Coccidioides. We identified mutations affecting these pathways in 8 patients with especially severe or refractory DC, some of whom responded to IFN-\u03b3 therapy. Younger patients with severe DC or patients whose illness relapses should be considered for genetic screening for discrete primary immune defects. The discrete defects demonstrated here clearly do not account for all occurrences of coccidioidomycosis in the general population but highlight the importance and nature of genetic control.Functional and genetic studies indicate that the IL-12/IFN-\u03b3 axis and STAT3-mediated immunity are central to protection against Coccidioides most likely exploits a very narrow vulnerability. The demonstration that DC has an underlying genetic predisposition indicates that the advent of newer genetic techniques, such as whole exome/genome sequencing, will inevitably identify coccidioidomycosis-specific genetic factors. These, in turn, should enable us to better understand, preempt and treat coccidioidomycosis.Coccidioidomycosis is distinguished by its geography and relative virulence in many persons who otherwise appear immunologically competent. Because most persons in whom DC develops are previously healthy, Additional methods for study of risk factors for disseminated coccidioidomycosis and IL-12/IFN-\u03b3 signaling pathway."} +{"text": "Acute coronary syndrome (ACS) can complicate acute ischemic stroke, causing significant morbidity and mortality. To date, literatures that describe poststroke acute coronary syndrome and its morbidity and mortality burden are lacking. This is a single center, retrospective study where clinical characteristics, cardiac evaluation, and management of patients with suspected poststroke ACS were compared and analyzed for their association with inpatient mortality and 1-year all-cause mortality.p < 0.05), lower mean peak troponin levels , and lower mean length of stay compared to those who underwent stent or CABG. Troponin levels were significantly associated with 1-year all-cause mortality. Of the 82 patients, 32% had chest pain and 88% had ischemic ECG changes; mean peak troponin level was 18, and mean ejection fraction was 40%. The medical management group had older individuals (73 versus 67 years, Age and troponin level appear to play a role in the current clinical decision making for patient with suspected poststroke ACS. Troponin level appears to significantly correlate with 1-year all-cause mortality. In the management of poststroke acute coronary syndrome, optimal medical therapy had similar inpatient and all-cause mortality compared to PCI and/or CABG. Acute coronary syndrome can complicate acute ischemic stroke. In the Randomized Trial of Tirilazad Mesylate in Patients with Acute Stroke , cardiac ischemia was found to occur in 6% of patients, with 1% being life-threatening . CardiacNeurologic events are known to cause myocardial injury and dysfunction. Cardiac injury after an acute stroke has been shown to occur even in the absence of underlying coronary artery disease . There iGiven the lack of guidelines and literature for poststroke ACS patients, the objectives of this study were to describe the demographics and comorbidities of patients with poststroke acute coronary syndrome, including their presenting symptom, peak troponin level, presence of ischemic electrocardiogram (ECG) changes, 2D-echocardiograms, and cardiac catheterization results. We compared the clinical characteristics and cardiac evaluation of patients who were medically managed and those who underwent any invasive intervention with percutaneous coronary intervention (PCI) or coronary artery bypass graft surgery (CABG). We sought to determine if there is a difference in inpatient mortality and 1-year all-cause mortality among these patients.This is a retrospective cohort study on adult patients who were admitted for acute ischemic stroke at Albert Einstein Medical Center from January 2003 to December 31, 2013, and developed acute coronary syndrome within 72 hours after ischemic stroke. Acute coronary syndrome referred to patients who fulfilled the third universal definition criteria of elevated cardiac biomarkers of at least one value above the 99th percentile upper reference limit and one of the following: symptoms of ischemia, development of pathologic Q waves in the electrocardiogram, new or presumed new significant ST-segment-T-wave (ST-T) changes or new left bundle branch block (LBBB), and imaging evidence of new loss of viable myocardium or a new regional wall motion abnormality. We excluded the patients with age < 18 years, patients with intracerebral hemorrhage, subarachnoid hemorrhage, hemorrhagic contusions, epidural hemorrhage, subdural hemorrhage, and other brain lesions, and patients with end stage renal disease on hemodialysis.Baseline demographic data and comorbidities such as preexisting coronary artery disease, hypertension, hyperlipidemia, diabetes mellitus, chronic kidney disease, congestive heart failure (systolic and/or diastolic heart failure), coronary artery disease equivalents , and smoking history were collected. Results of cardiac evaluation such as peak troponin level, ECG changes, 2D-transthoracic echocardiograms, and cardiac catheterization were also obtained. The primary outcomes of the study were inpatient mortality and 1-year all-cause mortality from the time of the acute ischemic stroke. The mortality information was acquired using social security database index (SSDI).t-test to test for differences between independent continuous variables and the chi-square test to test for differences between categorical variables. For continuous data that are not normally distributed, a nonparametric test will be used. For example, a rank-sum test will be used instead of t-test. In a 2 \u00d7 2 table, if one of the cells contains an expected value of less than 5, Fisher exact test will be used instead of chi-square test. To measure the association between an outcome variable and selected exposure variable, such as peak troponin level, ischemic changes in ECG, and intervention, the relative risk will be computed. The chi-square or Fisher exact test will be used to determine the significance of the association.For data analysis, categorical data were presented as numbers and percentages and continuous data as mean \u00b1 standard deviation. The demographic characteristics, comorbidities, and cardiac evaluation results of those who were medically managed versus those who underwent cardiac catheterization and subsequent stent placement or CABG were compared using Student's Among adult patients admitted to Albert Einstein Medical Center from 2003 to 2013, there were 82 patients who had an acute coronary syndrome after an acute ischemic stroke. The mean age was 72 years; 52% were female. Sixty-two percent of the patients in the study were African American, 30% were Caucasian, 6% were Hispanic, and 2% were Asian .Most of the patients in the study were found to have hypertension (96%). The next most common comorbidities were diabetes mellitus (56%), hyperlipidemia (45%), known coronary artery disease (44%), and congestive heart failure (46%). One-third of the population had a body mass index above 30 or chronic kidney disease. Around 20% were smokers or had coronary artery disease equivalents .Surprisingly, among patients who had acute coronary syndrome after an acute ischemic stroke, only 32% complained of chest pain. Other criteria for acute coronary syndrome occurred more frequently. Ischemic ECG changes were found 88% of the time. The most common ischemic ECG change was new T-wave inversion (78%). Mean peak troponin level was 18. Wall motion abnormalities on 2D-echocardiograms occurred in 43% of the patients with 88% in coronary artery territories corresponding to the ischemic ECG changes. The mean ejection fraction of the patients in the study was 40% .Although the patients had acute coronary syndromes, 67% did not undergo cardiac catheterization and were managed conservatively. Of the 33% who underwent cardiac catheterization, 15% had no significant coronary artery disease, 26% had 1-vessel disease, 15% had 2-vessel disease, and 44% had 3-vessel disease. Overall, out of the 82 patients, only 16% underwent placement of stents or CABG. The remaining 84% were managed medically. Medical management was in accordance with the guideline-directed medical therapy for acute coronary syndromes and congestive heart failure by the American College of Cardiology/American Heart Association guidelines that include aspirin, clopidogrel, and beta-blockers. For those with reduced ejection fraction, ACE inhibitors, beta-blockers, hydralazine/nitrates, and so on were given. The mean length of stay was 14 days .p < 0.05) and had a significantly lower length of stay . In term < 0.05) . As for < 0.05) .p > 0.05). The 1-year all-cause mortality, however, was similar , lower mean peak troponin levels (12 versus 49), and lower mean length of stay (12 versus 25 days). Troponin levels revealed being significantly related to 1-year all-cause mortality, but not to inpatient mortality. Optimal medical therapy had similar inpatient and all-cause mortality compared to PCI and/or CABG.Given the retrospective nature of our study, variables like severity of stroke, MRI findings for the location of the stroke, patient frailty, and other related variables were missing in our patient records and were not included in the study. Sixty-seven percent of the patients in the study also did not undergo cardiac catheterization. Finally, it is possible that the elevated troponin levels seen in our patient group were secondary to catecholamine surge caused by the stroke."} +{"text": "Accounting for justifiable variance is important for fair comparisons of treatment quality. The variance between general practices in treatment quality of type 2 diabetes (T2DM) patients may be attributed to the underlying patient population and practice characteristics. The objective of this study is to describe the between practice differences in treatment, and identify patient and practice level characteristics that may explain these differences.The data of 24,607 T2DM patients from 183 general practices in the Netherlands were used. Treatment variance was assessed in a cross-sectional manner for: glucose-lowering drugs/metformin, lipid-lowering drugs/statins, blood pressure-lowering drugs/ACE-inhibitor or ARB. Patient characteristics tested were age, gender, diabetes duration, comorbidity, comedication. Practice characteristics were number of T2DM patients, practice type, diabetes assistant available. Multilevel logistic regression was used to examine the between practice variance in treatment and the effect of characteristics on this variance.Treatment rates varied considerably between practices (IQR 9.5\u201313.9). The variance at practice level was 7.5% for glucose-lowering drugs, 3.6% for metformin, 3.1% for lipid-lowering drugs, 10.3% for statins, 8.6% for blood pressure-lowering drugs, and 3.9% for ACE-inhibitor/ARB. Patient and practice characteristics explained 19.0%, 7.5%, 20%, 6%, 9.9%, and 13.4% of the variance respectively. Age, multiple chronic drugs, and \u22653 glucose-lowering drugs were the most relevant patient characteristics. Number of T2DM patients per practice was the most relevant practice characteristic.Considerable differences exist between practices in treatment rates. Patients\u2019 age was identified as characteristic that may account for justifiable differences in especially lipid-lowering treatment. Other patient or practice characteristics either do not explain or do not justify the differences. Quality assessment frameworks have been introduced in several countries with the goal to ensure appropriate and evidence-based healthcare for patients . Within In heterogeneous populations, it is to be expected that healthcare provider\u2019s treatment decisions are influenced by differences in patient characteristics. For example, patients with type 2 diabetes (T2DM) commonly have multiple conditions and risk factors which may require individualized treatment plans. A recent review concluded that patient characteristics, such as marital status and BMI, affect outcome measures for diabetes but no consistent patterns were observed for process measures , 4, gendWe conducted a cross-sectional study to assess treatment quality in 2012 in a large diabetes care group in The Netherlands, which included more than 80% of all general practices in the province of Groningen. Diabetes care groups have been formed after the introduction of bundled payment in 2007 . They arData were collected from the GIANTT database. This regional longitudinal database contains anonymized data extracted from electronic medical records of almost all type 2 diabetes mellitus (T2DM) patients (<1% opted out) managed in general practice . The datTreatment quality was defined as current treatment status, that is, if a patient was treated or not with guideline recommended drug treatment, similar to many of the prescribing measures currently in use in The Netherlands . We focuTo explain the differences in treatment between practices, the following patient level characteristics were included as dichotomous variables: age , gender, duration of diabetes (\u22652 years), overweight , history of cardiovascular comorbidity , history of peripheral vascular comorbidity , diabetes complications , nephropathy , history of malignancy , history of psychological disorders , treatment with 5 or more other chronic drug classes , treatment with 3 or more glucose lowering drug classes, treatment with 4 or more blood pressure lowering drug classes, and treatment with 2 or more lipid lowering drug classes. The cutoff levels for age were based on the Dutch guideline where leThe treatment quality rates were described at practice level as mean percentages with standard deviation, or median percentages with interquartile ranges. Descriptive statistics were also used to describe the distribution of patient characteristics across general practices.Multilevel logistic regression analysis was conducted for each of the six treatment measures separately to assess the variance that is attributed to general practice level and the part of this variance that can be explained by patient and practice characteristics. Two level random intercept models were estimated with patients at level 1 nested within general practices at level 2. In these models the probability for the treatment outcome can vary across practices but the effect of the patient characteristics is assumed to be the same (fixed) for all practices.First, the variance in treatment at practice level was estimated in an empty multilevel model. Second, multilevel univariate analyses were conducted for each patient and practice level explanatory variable. Next, three multivariate models were built using backwards selection for including variables that were potentially associated with the treatment measure (p<0.2); (i) model 1, with patient level characteristics only, (ii) model 2, with general practice characteristics only, (iii) model 3, with patient and practice characteristics together.2 measure was used to estimate what part of the variance at practice level could be explained by including patient and general practice characteristics [2 were calculated for each model compared to the empty model, expressing the part of the practice level variance that can be explained by the included characteristics.The pseudo Reristics , 26. ForIn The Netherlands, according to the Code of Conduct for the use of data in Health Research , no ethics committee approval was needed for this research using data from anonymous medical records.A cohort of 24,628 patients with T2DM managed in 183 general practices was eligible, after excluding 974 patients for incomplete follow-up and 27 patients for missing or invalid diabetes onset dates. Of the 183 general practices, 90.7% had a diabetes assistant and 45.4% were practices with a single general practitioner . The medFor glucose lowering drugs, patient and practice characteristics together reduced the practice level variance with 1.4%, and thereby explained 19.0% of the observed practice level variance in treatment . Each ofFor lipid-lowering drugs and statins, patient and practice characteristics together reduced the practice level variance with 0.6% each, and thereby explained 20% and 6% of this variance respectively . Age, trFor blood pressure-lowering drugs and RAAS-blockers, patient and practice characteristics together reduced the practice level variance with 2.1% and 0.5% respectively, and thereby explained 9.9% and 13.4% of this variance . A histoWe observed considerable between practice differences in treatment with glucose-lowering, lipid-lowering, blood pressure-lowering drugs, and RAAS-blockers (IQR ranges of 10% or more) in T2DM patients. Smaller between practice differences in treatment were observed in treatment with metformin and statins (IQR ranges less than 8%). Not more than 10% of the observed differences, however, could be attributed to practice level, indicating that a significant part of the differences may be due to patient-level differences or random variance. Of these differences attributed to practice level, between 6% and 25% could be explained by the patient and practice level characteristics included in our study. Patient characteristics explained almost 10% of the differences in lipid-lowering treatment compared to less than 10% for the other treatments. Practice characteristics explained more than 15% of the differences in glucose-lowering treatment compared to less than 10% for the other treatments.Several studies have described differences in treatment rates between general practices, showing sometimes wide ranges \u201331. One A recent review looking at patient characteristics associated with diabetes performance indicators did not find any consistent impact of demographics, complications, comorbidity, geography or care-seeking behavior . They hoPractice characteristics explained at least 15% of the between practices differences for treatment with glucose-lowering drugs, and less than 10% for treatment with lipid-lowering and blood pressure-lowering drugs. Between practice differences in health care quality of patients with diabetes and the role of patient and practice characteristics in these differences were examined previously \u201338. ThesThe primary care system organization in the Netherlands is comparable with other West-European countries . The popMeasuring the quality of treatment at practice level is part of various quality improvement initiatives \u201350. In sS1 Appendix(PDF)Click here for additional data file.S2 Appendix(PDF)Click here for additional data file."} +{"text": "Accurate data on CMR practice patterns is a prerequisite for planning strategies to grow clinical volumes within existing CMR clinical services, increase the number of hospitals that offer these services, and improving reimbursement.Data analysis was performed on a cloud-based system that is currently receiving de-identified searchable data from electronically-signed clinical reports with full DICOM datasets for 23,275 consecutive CMR exams performed at four geographically diverse U.S. medical centers from Jan 1, 2010 through Dec 31, 2014. At the time of abstract submission, 8,242 datasets have been analyzed, and analysis of all 23,275 is expected by the end of 2015. All data fields were derived from CMR reports that had been electronically signed by board-certified physicians with Level 3 CMR training. We analyzed: 1) patient characteristics and clinical indications for CMR scans; 2) use and complication rates for contrast agents; 3) use and complication rates for stress testing; and 4) billing data based on CPT codes.The median age of patients undergoing CMR was 59 years (IQR 20 years), 57% were male, 20% had a history of diabetes mellitus, 58% had a history of hypertension, 45% had a history of hyperlipidemia, and 9% were active smokers. Seventy-eight percent were outpatients and 22% were inpatients. The top reason for CMR scanning was CHF/cardiomyopathy, followed by ischemia evaluation, vascular disease, and valve assessment Figure . ContrasCMR is clinically viable in the United States with the most common indications: heart failure/cardiomyopathy, ischemia evaluation, vascular disease, and valve assessment. CMR vasodilator stress testing appears remarkably safe in clinical practice."} +{"text": "Acute coronary syndrome accounts for more than 15% of the chest pains. Recently, Hess et al. developed North American Chest Pain Rule (NACPR) to identify very low-risk patients who can be safely discharged from emergency department (ED). The present study aimed to validate this rule in EDs of two academic hospitals.A prospective diagnostic accuracy study was conducted on consecutive patients 24 years of age and older presenting to the ED with the chief complaint of acute chest pain, during March 2013 to June 2013. Chest pain characteristics, cardiac history, electrocardiogram findings, and cardiac biomarker measurement of patients were collected and screening performance characteristics of NACPR with 95% confidence interval were calculated using SPSS 21.From 400 eligible patients with completed follow up, 69 (17.25 %) developed myocardial infarction, 121 (30.25%) underwent coronary revascularization, and 4 (2%) died because of cardiac or unidentifiable causes. By using NACPR, 34 (8.50%) of all the patients could be considered very low- risk and discharged after a brief ED assessment. Among these patients, none developed above-mentioned adverse outcomes within 30 days. Sensitivity, specificity, positive prediction value, and negative prediction value of the rule were 100% (95% CI: 87.35 - 100.00), 45.35 (95% CI: 40.19 - 50.61), 14.52 (95% CI: 10.40 \u2013 19.85), and 100 (95% CI: 97.18 - 100.00), respectively.The present multicenter study showed that NACPR is a good screening tool for early discharge of patients with very low-risk chest pain from ED. Acute c from ED -8. This Study design and settingA consecutive prospective diagnostic accuracy study was conducted on adult patients who presented to the EDs of Imam Khomeini and Shariati Hospitals, Tehran, Iran, with chest pain as their primary complaint during March 2013 to June 2013. Informed consent was obtained from every patient and the data were kept confidential. The Institutional Review Board of the hospitals and ethic committee of Tehran University of Medical Sciences approved the study protocol. ParticipantsAll adults older than 24 years with chief complaint of anterior chest pain presenting to ED were enrolled. As in Hess et al. study, patients were excluded if there was ST segment elevation at least in two contiguous leads on the initial ECG, hemodynamic instability (persistent heart rate greater than 100 beats/min or less than 50 beats/min or systolic blood pressure persistently below 90 mmHg), an unreliable clinical history, a chest pain caused by trauma, a documented history of cocaine abuse , a non-cardiac terminal illness, pregnancy, previous enrollment within the past 30 days, or inability to receive follow-up by telephone . Studied hospitals were tertiary-care university-affiliated centers with more than 600 beds each. They have an annual ED visit rate of approximately 40,000 patients. All diagnostic tests and therapeutic procedures were performed at the discretion of the attending physician, according to routine ED practice. Patients presenting to the ED with definite signs and symptoms of developing ACS (e.g. ST-elevation or elevated cardiac biomarkers) were consulted with a cardiologist and admitted directly to the coronary care unit afterwards. Other patiens were admitted and observed in the ED. Serial ECGs and cardiac markers were obtained and further decisions were made according to the results. A team of well-trained research assistants worked in a scheduled set of shifts and enrolled eligible patients. Data gatheringet al. study, past history of CAD was defined as at least 50% coronary stenosis on angiography; demonstrated ECG changes, perfusion defects, or wall motion abnormalities on exercise, pharmacologic, or rest imaging studies; or previous documentation of acute myocardial infarction were recorded on specific data collection forms by research assistants. As in Hess farction . Accordifarction . In ordeAssigning patients to one of NACPR groups was done retrospectively and no intervention was performed to implement the rule during admission. All the ECGs were reviewed by two investigators blinded to final outcome , and a third investigator (MJ) resolved disagreement. The definition in Hess et al. study was used to define ECG abnormality . By consOutcomesMyocardial infarction (ST-elevation and non ST-elevation), coronary revascularization, cardiac death, and no other definite cause found in investigation were considered as 30 days outcomes. Outcomes were defined same as original derivation study of NACPR . The menNACPRAccording to NACPR, two groups of patients are eligible for early discharge. The first group includes patients younger than 40 years of age with a normal primary ECG, reporting very low-risk chest pain characteristics, and without history of ischemic chest pain. The second group of patients consist of patients 41-50 years of age with normal troponin level 6 hours after the pain onset, in addition to the criteria mentioned for the first group .Statistical analysisMinimum sample size required for the present study was calculated to be 400 cases, considering 100% sensitivity of NACPR (95% CI: 97.1 -100), 20.9% specificity (95% CI: 16.9 \u2013 24.9), 0.06 p value, and 0.048 desired precision . Therefore, a total of 409 patients were finally enrolled. 400 of which had follow-up completed . ReviewiBaseline characteristic of patientsThe mean age of the 400 enrolled patients was 56.77 \u00b1 12.52 (25 - 87) and 213 (53.3%) cases were male. The baseline characteristics of patients are summarized in Screening characteristics of ruleBased on the results of screening with NACPR, 34 (8.5%) cases were in very low-risk group for developing 30 day adverse outcomes and were eligible to be discharged from ED. Based on the results of the present study, NACPR has 100% sensitivity and negative predictive value in predicting very low-risk patient for developing 30 day adverse outcomes of MI, revascularization, and death among those presenting to ED with chest pain. Having used NACPR, 34 patients (8.50%) would have been eligible to be included in the very low-risk group and could be discharged from the ED. None of the 166 patients who developed aforementioned outcomes within 30 days would have been included in the very-low-risk group by implementation of this rule. In our study, sensitivity and negative likelihood ratio were similar to those found by Hess et al. and Mahler et al. (100% and 0%). The specificity in our study (14.53%) was lower than the original study 20.90%) but higher than Mehler et al. study (5.6%) , 9. This0% but hiClinical decision rules are developed in order to facilitate the decision making process in common and important clinical conditions. Acute chest pain has a high prevalence, which calls attention to develop rules. These rules use easily obtainable elements in history, clinical examination, and simple tests, to safely rule out hazardous conditions . Data in the United States showed that approximately 2% of patients with ACS are misdiagnosed and inappropriately discharged from the EDs . FurtherIn 1990s, some rules for cardiac care unit admission were developed based on observation with 3% misrate , 12. LatIn a prospective study, Hess et al. derived a clinical decision rule for identification of patients with very low-risk chest pain who could be safely discharged from ED without further objective cardiac testing such as stress tests . By adheRecently Vancouver Chest Pain Rule was developed according to methodological standards by utilizing biomarkers . ChristeJalili et al. found sensitivity of 95.1% and specificity of 56.3% for Vancouver Chest Pain Rule. The PPV and NPV were fairly similar . In addition to having lower yields in comparison to NACPR, there are some debates over this rule. For example, Hess et al. study showed that some elements in Vancouver Chest Pain Rule have insufficient inter-observer reliability . RecentlLimitationsOur study faces some limitations. Although this rule assesses chest pain, like Hess et al. study, we did not study unstable angina independently. In addition, non-chest pain presentation of cardiac origin was not included in the rule, which precludes its application in these patients. During the study period, inter-observer agreement was not assessed in our study in regard to gathering patient information by research assistants and ECG assessment by HM and SV, which in turn may increases the risk of performance bias. As shown in the Hess et al. study, several other factors such as presence or absence of observation units can also affect the costs. However, due to lack of accurate and detailed financial records, we were not able to determine the use of financial resources and find out if costs had been minimized by early discharge of very-low-risk patients. Another limitation in our result interpretation is 10% failed enrollment or follow up. In addition, even the most accurate rules are unlikely to be applied in practice if they are not considered reasonable by the end-user, therefore, these rules should consist of simple and sensible elements . End-useIn summary, our study proved that the prediction rule proposed by Hess et al. is a sensitive decision tool for diagnosing very-low-risk chest pain patients who can be discharged early from the ED."} +{"text": "Geosocial networking (GSN) smartphone apps are becoming the main venue for sexual encounters among Brazilian men who have sex with men (MSM). To address the increased HIV incidence in this population, preexposure prophylaxis (PrEP) was recently implemented in the Brazilian public health system in the context of combined HIV prevention.This study aimed to describe the characteristics of MSM using GSN apps for sexual encounters, their awareness of prevention strategies, and willingness to use PrEP.This study was an online cross-sectional study conducted in 10 Brazilian state capitals from July 1 to July 31, 2016. The questionnaire was programmed on SurveyGizmo and advertised in two GSN apps used by MSM to find sexual partners (Hornet and Grindr). Inclusion criteria were >18 years of age, cisgender men, with an HIV-negative status. Eligible individuals answered questions on: demographics; behavior; and knowledge, preferences, and willingness to use PrEP, nonoccupational postexposure prophylaxis (nPEP), HIV self-testing (HIVST), and condoms. Logistic regression modeling was performed to assess the factors associated with daily oral PrEP willingness.During the study period, 8885 individuals provided consent and started the questionnaire. Of these, 23.05% (2048/8885) were ineligible, 6837 initiated, and 5065 completed the entire questionnaire and were included in the present analysis. Median age was 30 years (interquartile range: 25-36), most self-declared as MSM , white , middle income , and had 12 or more years of schooling . The majority of MSM scored >10 points (high risk) on The HIV Incidence Risk for MSM Scale, but only 21.39% (1083/5064) had a low perceived likelihood of getting HIV in the next year. Daily use of apps for sex was reported by 35.58% (1798/5054). Most MSM reported testing for HIV at least once in their lifetime and 9.16% (464/5065) used nPEP in the previous year. PrEP, nPEP, and HIVST awareness was reported by 57.89% (2932/5065), 57.39% (2907/5065), and 26.57% (1346/5065) of participants, respectively. Half of all respondents were willing to use daily oral PrEP, and this finding was associated with higher numbers of male sexual partners , condomless receptive anal intercourse , sex with HIV-positive partner versus no HIV-positive partner , daily use of apps for sexual encounters , high and unknown perceived likelihood of getting HIV in the next year , sexually transmitted infection diagnosis , stimulant use , PrEP awareness , and unwillingness to use condoms .Our results evidenced high-risk scores in the studied population, suggesting the importance of PrEP use. Those individuals presenting risky sexual behaviors were more willing to use PrEP. Nonetheless, only 58% (2932/5065) of individuals had heard about this prevention strategy. Efforts to increase awareness of new prevention strategies are needed, and mobile health tools are a promising strategy to reach MSM. Brazil has the largest population of individuals living with HIV and acquired immune deficiency syndrome (AIDS) in Latin America , represePreexposure prophylaxis (PrEP) with tenofovir/emtricitabine is now a key component of prevention packages for MSM. The efficacy of treatment for this population has been shown with both once daily and on-demand use in clinical trials and open-label studies -9, and dWith expanded access to the Internet via mobile phones, geosocial networking (GSN) smartphone apps are becoming the main venue for casual sexual encounters -32. MSM This was a cross-sectional online study targeting MSM from 10 Brazilian capitals : Bel\u00e9m and Manaus (North); Salvador and Recife (Northeast); Bras\u00edlia and Goi\u00e2nia ; Florian\u00f3polis and Porto Alegre (South); and Rio de Janeiro and S\u00e3o Paulo (Southeast). According to the 2010 Brazilian Population Census, these are the cities with the greatest number of MSM couples from each region . IndividThe questionnaire was programmed on SurveyGizmo and the Age was categorized into three brackets: (1) 18-to-24 years; (2) 25-to-34 years; and (3) >35 years. Skin color/race was dichotomized into \"white\" or \"non-white\" . Schooling was dichotomized into \"<12 years\" and \">12 years\" . Family monthly income was grouped into \"<3\" (low income), \"4-to-10\" (middle income), and \">10\" minimum (high income) wages (Brazilian minimum wage was 880 BRL or US $267 dollars in July 2016). Sexual orientation was dichotomized into \"MSM\" or \"other\", and the options for a question regarding their friends with the same sexual orientation were \"none\", \"a few\", and \"majority\". Individuals were asked if they had a steady partner and the options were \"yes/no\", \"male\" and \"female\".Any substance use in the prior six months considered the use of any of the following: tobacco (cigarettes), stimulants , 4-hydroxybutanoic acid (GHB), marijuana or hash, and hallucinogens , which were displayed in a predefined list of all substances.Binge drinking was evalHornet, Grindr, and other. Although the project was advertised only on Hornet and Grindr, the link to the survey could be copied and exchanged through other media . The use of apps for sexual encounters was categorized into \"never\", \"sometimes\" , \"daily\", and \"only when traveling or vacations\".The variable \u201cApps\u201d was created based on the question, \u201cWhere did you hear about this questionnaire?\u201d (with response format as open text) and was categorized into The HIV Incidence Risk for MSM Scale, which is a 7-item questionnaire developed by Smith et al ). Analyses were performed using PROC GENMOD available in the Software SAS ). Afterwards, a backwards stepwise logistic regression modeling approach was used to identify the factors independently associated with daily oral PrEP willingness . Variablware SAS .During the 30 days of the online survey, 8885 individuals provided informed consent. Of these, 23.05% (2048/8885) were ineligible, 6837 initiated the questionnaire, and 5065 completed the questionnaire and were included in the present analysis . DiffereAmong all individuals who accessed the questionnaire and completed questions regarding HIV serostatus (n=6664), HIV prevalence was 12.27% (818/6664). Considering ineligible respondents (n=2048), 2.29% (47/2048) self-declared as cisgender women, 1.56% (32/2048) as transgender women or transvestites, 1.95% (40/2048) as transgender men, and 9.33% (191/2048) as other genders.Among those included in this analysis (n=5065), most participants were from southeast Brazil and accessed the survey through the Hornet app , and a total of 4618 respondents used apps for sexual encounters. The median age of the cohort was 30 years old (interquartile range: 25-36), 63.06% (3194/5065) were white, 68.13% (3541/5065) reported middle-to-high income, and 61.36% (3106/5062) reported more than 12 years of schooling. Most respondents identified themselves as MSM and reported having friends with the same sexual orientation . Only 20.48% (1029/5024) of respondents reported a male steady partner and 3.97% (198/4986) reported a female steady partner .Binge drinking and tobacco use in the last six months were reported by 71.79% (3636/5050) and 32.60% (1651/5065) of individuals, respectively . MarijuaThe HIV Incidence Risk for MSM Scale (high HIV risk) and fall into the category of individuals who should undergo evaluation for PrEP use. Conversely, only 21.39% (1083/5064) of participants had high HIV risk perception and 9.16% (464/5065) reported nPEP use in the last 12 months. Among those that used PEP, 81.68% (379/464), 12.72% (59/464), 2.59% (12/464), and 3.02% (14/464) reported nPEP use once, twice, three times, and more than three times in the past 12 months (respectively).In the previous 6 months, only 236 respondents reported having no sexual partners. Condomless receptive anal sex prevalence was high . Approximately 10% of respondents reported having had sex with one HIV-positive partner, 2.19% (111/5064) with more than one partner, and 18.62% (943/5064) reported that they did not know how many HIV-positive partners they had sex in the prior six months. Regarding the number of times they were the insertive partner without a condom with an HIV-positive partner, 18.90% (957/5064) of participants reported one to four times and 8.87% (449/5064) reported five times or more. Reported prevalence of STIs in the previous 6 months was 12.06% respondents had never performed an HIV test and one of the main reasons was the fear of having an HIV-positive result . Compared to those who had been tested before, these respondents were younger , had less years of schooling , had lower income , and almost half self-reported as white . Almost half of the respondents believed that the best testing venue is at home and most would be comfortable with picking up the HIVST somewhere else , 57.39% (2907/5065), and 26.57% (1346/5065) of respondents, respectively. Willingness to use different HIV prevention methods is depicted in In the final multivariate model , variablOur findings provide important insights about the characteristics of Brazilian MSM based on two popular GSN apps for sexual encounters, and their preferences amidst the HIV prevention strategies. This information can potentially guide and support national prevention programs. Over half of the respondents would be willing to use daily oral PrEP if available through SUS, which is lower than previously reported in Brazil . This fiOur study showed that, in addition to daily oral PrEP, a high proportion of respondents were also interested in other PrEP formulations, such as injectable PrEP . Long-acting injectable PrEP can be very beneficial among individuals for whom adherence to a daily oral regimen is challenging ,49,50. CAlthough nPEP has been available at no cost through SUS since 2009, awareness, willingness, and use were lower than expected. This problem is highly concerning given that almost half of our sample reported unprotected anal sex. Similar results have been described from other settings with MSM-concentrated epidemics ,54.Few of the respondents had heard about HIVST; however, half of them would be willing to use it and this strategy, which could increase serostatus awareness and facilitate integration into HIV care . The accAlthough smartphones became the main devices used for Internet access, especially in lower income families , it is hThe HIV Incidence Risk for MSM Scale, most of the sample should be further evaluated for PrEP use, but perceived likelihood of getting HIV in next year was low. Moreover, rates of unprotected anal intercourse reported by study participants was high, which has also been found to be high among MSM who use Grindr in studies conducted in the United States [Considering d States ,65 and ad States . The CDCd States ,67. Almod States , but mucd States ,69. Knowd States -72, usind States . Disclosd States . This beBinge drinking and tobacco and substance use were high in the study population, compared with the general population , which iMoreover, our results provide evidence that MSM reporting higher risk behaviors were more willing to use daily PrEP, as observed in other studies ,82-87. AUnequivocally, this study has limitations. First, online studies are not probabilistic sampling strategies, thus precluding the generalizability of the findings. Given the cross-sectional nature of the data, causality and the direction of association may not be inferred. All collected data were self-reported by participants and may be subjected to bias, including social desirability bias. Our data were also subjected to recall bias due to 6-month or 12-month recall periods. There is also a concern about participants taking the survey multiple times. To avoid this issue, the first question of the survey was, \u201cAre you answering this survey for the first time?\u201d (4% of participants answered \u201cno\u201d and were excluded from the study). Finally, we have measured intention to use PrEP, nPEP, condoms, and HIVST as a proxy of willingness. There are different methods for accessing PrEP willingness, as reviewed by Young and McDaid , and as In summary, our observed high HIV risk scores suggest that most MSM would be eligible for PrEP, and that those who present risky sexual behaviors were more willing to use it. Notwithstanding, only 58% (2932/5065) of individuals were aware of this prevention strategy. Additionally, awareness, willingness, and use of nPEP\u2014which has been available in Brazil since 2009\u2014were low. Efforts to increase awareness of new prevention strategies are urgently needed to create demand among those at the highest risk for HIV infection. Mobile health tools are a promising strategy to reach high risk MSM in Brazil."} +{"text": "Bacillus (39.60%), coagulase-negative Staphylococcus (29.95%), Streptococcus species other than Streptococcus agalactiae (25.74%), coagulase-positive Staphylococcus (3.96%), and Streptococcus agalactiae (0.74%). Isolates were most susceptible to Gentamicin (95.8%), followed by Tetracycline (90.5%), Kanamycin and Chloramphenicol (each at 85.3%), Sulphamethoxazole (84.2%), Co-trimoxazole (82.1%), Ampicillin (78.9%), and finally Streptomycin (76.8%). This translated to low resistance levels. Multidrug resistance was also reported in 30.5% of the isolates tested. Even though the antibiotic resistance demonstrated in this study is low, the observation is significant, since the few resistant normal flora could be harboring resistance genes which can be transferred to pathogenic bacteria within the animal, to other animals' bacteria and, most seriously, to human pathogens.This study was designed to determine antimicrobial resistance profiles of bacteria isolated from the nasal cavity of healthy camels. A total of 255 nasal samples (swabs) were collected in Isiolo, Samburu, and Nakuru counties, Kenya, from which 404 bacterial isolates belonging to various genera and species were recovered. The bacterial isolates included Among the animals reared in the arid and semiarid areas of Kenya, camels are most suited to the harsh environmental conditions which are a characteristic of these areas. They play an important role in support of livelihood and culture of pastoral communities in the country . Despite Klebsiella pneumoniae and diplococci from camel pneumonic lungs in India. Chauahan et al. [Isolation of bacteria from the respiratory system of both healthy and diseased camels has been reported by a number of researchers; Arora and Kalra reportedn et al. reportedn et al. in Somaln et al. reportedn et al. identifin et al. , Ethiopin et al. , and Somn et al. . Despiten et al. with nonn et al. .Noting that respiratory infection is one of the emerging diseases of camels , studiesAntibiotics are commonly used for treatment and prevention of diseases as well as growth promotion in domestic animals , 17. OveKenya is experiencing antibiotic resistance with high resistance rates being reported in microorganisms causing respiratory, enteric, and hospital-acquired infections . OveruseA few studies on antibiotic resistance in Kenya in domestic animals have been documented; for example, bacterial isolates from chicken and swine have been reported to be resistant to Tetracycline and Sulphonamides. Also other bacteria isolated from pork tissues have demonstrated resistance to Ampicillin, Streptomycin, Tetracycline, and Chloramphenicol .The existence of bacteria in the nasal cavities of apparently healthy camels in Kenya has not been documented previously. The sensitivity of these bacteria to commonly used antibiotics is also not known, a fact that cannot be ignored as antibiotic use not only targets pathogenic bacteria but also exerts selective pressure on normal flora (bacteria), leading to maintenance of antibiotic resistance in these bacteria . This stSamburu, Isiolo, and Nakuru counties were selected for the study, specifically Naimaralal and Opiroi locations of Samburu, Burat and Isiolo west locations (Isiolo), and Gilgil area of Nakuru.The areas were purposively selected as treatment of animal diseases in the pastoral communities of Kenya is mostly done without the benefit of laboratory testing as laboratories are almost nonexisting or dormant in most of these areas. This could contribute to the spread of antibiotic resistance due to misuse of commonly used antibiotics .A total of 255 nasal swab samples were collected using the method described by Mohamed et al. . BrieflyThis was done according to standard procedures , 32. NasAntibiotic susceptibility testing was done using disk diffusion method as described by Clinical and Laboratory Standards Institute . 95 isolIsolates were grown on blood agar for 24 hours; 5 colonies were picked from each plate and suspended in 5\u2009ml of sterile normal saline which was then adjusted to a density approximately equal to McFarland Opacity Standard number 0.5. A dry sterile cotton swab was then placed inside the suspension; excess liquid from the swab was expressed against the wall of the tube and the swab used to spread the bacterial suspension evenly on the surface of Mueller-Hinton agar in order to get confluent growth. Antibiotic disks were then placed on the surface of the inoculum and incubated for 18\u201324 hours. Zones of inhibition were measured to the nearest millimeter and interpretation as to whether the bacterium was resistant or susceptible to the particular antibiotic was done according to specifications defined by Clinical and Laboratory Standards Institute (CLSI 2006).245/255 samples (96%) showed positive bacterial growth yielding different genera and species of bacteria. 404 isolates were isolated from the 245 positive samples. Bacillus at 39.6% (160/404), coagulase-negative Staphylococcus at 29.95% (121/404), Streptococcus species other than Streptococcus agalactiae at 25.74% (104/404), and coagulase-positive Staphylococcus at 3.96% (16/404) and Streptococcus agalactiae was the least isolated at 0.74% (3/404). Organisms belonging to the genus Bacillus' species were the most frequently isolated in Isiolo at 56.07% (60/107), followed by Samburu at 40.85% (67/164) and Nakuru at 24.81% (33/133). Coagulase-negative Staphylococcus was most frequently isolated from Nakuru at 36.84% (49/133), followed by Samburu at 29.27% (48/164) and Isiolo at 22.43% (24/107). Streptococcus species other than Streptococcus agalactiae were the highest isolated from Nakuru at 35.34% (47/133), followed by Samburu at 21.95% (36/164) and Isiolo at 19.63% (21/107). Coagulase-positive Staphylococcus (Staphylococcus aureus) was the highest isolated from Samburu at 6.1% (10/164), followed by Nakuru at 3% (4/133) and Isiolo at 1.87% (2/107). Streptococcus agalactiae was isolated from Samburu at 1.83% (3/164); none was isolated from both Nakuru and Isiolo counties , Tetracycline at 90.5% (86/95), Kanamycin and Chloramphenicol at 85.3% (81/95), Sulphamethoxazole 84.2% (80/95), Co-trimoxazole at 82.1% (78/95), Ampicillin at 78.9% (75/95), and Streptomycin at 76.8% (73/95) . Thus, tAlthough in this current study most isolates showed resistance to one antibiotic, some of the bacterial isolates in different genera and species showed multidrug resistance (resistance to more than one antibiotic), with respect to the antibiotics used. Generally, out of the 95 isolates tested, 29 (30.5%) showed resistance to more than one antibiotic used in this study.Camel keeping in Kenya, including the study areas, is commonly kept under traditional pastoral production system which is characterized by low production inputs and herd/household mobility which is necessitated by search of pasture, water, mineral licks, and community feuds . VaccinaThis study shows that diversity of bacterial species can be found in the nasal cavity of apparently healthy camels. The organisms could have reached the nasal cavity through inhalation, direct or indirect contact, or during drinking. However, the normal flora in apparently healthy camels can be altered by several factors such as bad sanitation, stress due to transportation, sudden change in feed, low herd health status, and immunosuppression. This could end up lowering the resistance of the respiratory system to infection ; thus, t Staphylococcus aureus, Corynebacterium pyogenes, coagulase-negative Staphylococcus, Bacillus species, Streptococcus pyogenes, diphtheroids, E. coli, Klebsiella pneumoniae, and Diplococcus pneumoniae from nasal swabs collected from camels in Sudan.Isolation of diverse bacteria in this study has been supported by other authors who demonstrated presence of diverse bacterial species in the nasal tract of the apparently healthy camels from nos Staphylococcus aureus and Streptococcus agalactiae were also reported to show marked resistance to Co-trimoxazole, Sulphamethoxazole, and Ampicillin [Generally, in this study, most of the isolates were sensitive to the antibiotics used. The susceptibility percentages of the organisms in the descending order were as follows: Gentamicin at 95.8% (91/95), Tetracycline at 90.5% (86/95), Kanamycin at 85.3% (81/95), Sulphamethoxazole and Chloramphenicol at 84.2% (80/95), Co-trimoxazole at 82.1% (78/95), Ampicillin at 78.9% (75/95), and finally Streptomycin at 76.8% (73/95). Gitao et al. reportedpicillin . A variepicillin , 41. Simpicillin , where b Staphylococcus aureus had the highest susceptibility to Gentamicin, Chloramphenicol, and Kanamycin followed by Tetracycline and Sulphamethoxazole, followed by Ampicillin, followed by Co-trimoxazole and Streptomycin. These results agreed to some extent with those of Abdulsalam [ Staphylococcus aureus to be highly sensitive to Ampicillin, Doxycycline, Streptomycin, Gentamicin, and Neomycin. A study by Gitao et al. [ Staphylococcus aureus from mastitic milk in camels to be resistant to Ampicillin, Co-trimoxazole, and Sulphamethoxazole.In this study,dulsalam ; he founo et al. reported Staphylococcus in this study was least in Ampicillin and Tetracycline; a study by Al-Thani and Al-Ali [ Staphylococcus species to be resistant to Tetracycline, Penicillin, and Ampicillin in different Qatari farms. However, the same study reported the organisms being very susceptible to Cephalothin, Norfloxacin, and Co-trimoxazole.The susceptibility of coagulase-negatived Al-Ali reportedStreptococcus organisms had the highest susceptibility to Tetracycline followed by Ampicillin; they were also sensitive to Chloramphenicol and Gentamicin, followed by Sulphamethoxazole and then Co-trimoxazole, and they were least susceptible to Streptomycin and Kanamycin. This was in agreement with results obtained by Abdulsalam [ Streptococcus isolates were sensitive to Ampicillin and Doxycycline. However, Abdulsalam [ Streptococcus organisms that were highly susceptible to Streptomycin at 100%.dulsalam , where Sdulsalam reported Staphylococcus showed resistance to multiple drugs.Overuse and improper use of antibiotics have contributed to development of multidrug resistance in bacteria , 19. In Staphylococcus organisms from surgical wounds. This presents a great threat as these organisms are commonly associated with a good number of animal and human infections. Bhatt et al. [This was also reported in other studies , 43. Bhat et al. also rept et al. reportedThe fact that some of the isolates showed some resistance to the antibiotics used, in this study, is important as it shows that normal flora/resident bacteria can harbor resistance genes to antibiotic(s). Transfer of resistance in bacteria has been documented to occur between different animal species, within humans, from animals to humans, and from humans to animals . This ma"} +{"text": "Although substantial improvement in survival from this disease has been reported in high-resource countries, the risk continues to increase, yielding high mortality rates in middle- and low-income countries.2 Within the Eastern Mediterranean Region (EMR), cancer is the fourth-ranked cause of death, after cardiovascular diseases, infectious diseases, and injuries.3 According to WHO classification, the EMR comprises 21 member states in the Middle East, North Africa, and Central Asia. The included nations are Afghanistan, Bahrain, Djibouti, Egypt, Iran, Iraq, Jordan, Kuwait, Lebanon, Libya, Morocco, Palestinian territory, Oman, Pakistan, Saudi Arabia, Somalia, Sudan, Syria, Tunisia, United Arab Emirates, and Yemen. The International Agency for Research on Cancer (IARC) estimated that 292,677 cases of cancer were newly diagnosed among the female population in EMR during 2012, and 176,139 died of the disease.1 The five most commonly recorded cancers in women were those of the breast, colorectum, cervix, ovary, and non-Hodgkin lymphoma. Overall, 99,000 cases were registered as breast cancer in that region.Breast cancer is the most frequent malignancy among women worldwide, accounting for 25% of all cancers, with an estimated 1.57 million new cases in 2012.9In addition to being the most important cancer, other features that justify increasing efforts for breast cancer control in the EMR include the exponential rise in the incidence and the higher prevalence of affected young women presenting at advanced stages of disease. These factors led to low 5-year survival rates from breast cancer in many countries within the region as compared with high-income settings.9 It has been the highest-ranked malignancy among the Iraqi population in general since 1986. The latest Iraqi Cancer Registry8 revealed that among an estimated population size of 32,500,000, a total of 21,101 new cases of cancer were registered in 2012; 9,268 were in men and 11,833 were women.8 The crude incidence of all cancers was 61.69 per 100,000 (53.31 in men and 70.59 in women). During that year, 4,115 cases of breast cancer were reported, accounting for 19.5% of all newly diagnosed malignancies and 34% of the registered female cancers, with an incidence approximating 22 per 100,000 female population. The highest frequency was observed in middle-aged women (45-49 years old), whereas the peak age-specific incidence was reported in women 50-54 years old. It has been documented that there is a tendency for the disease to be diagnosed at advanced stages, with a likely prevalence of poorly differentiated tumor forms illustrated in significantly high rates of nuclear aneuoploidy, thus yielding a mortality incidence of approximately 60%.10Breast cancer has become a major threat to female health in Iraq, where it is the leading cause of death after cardiovascular diseases among women, with a cancer-related mortality rate of 23%.4 Although 90.6% of those patients detected the lumps by themselves, only 32% sought medical advice within the first month. Approximately one-third of those patients were diagnosed in their fifth decade of life, 47% presented at advanced stages of disease, and 16% recalled a positive family history.4 Another survey that was conducted to explore the level of knowledge, attitude, and practice toward breast cancer and breast self-examination (BSE) among educated Iraqi women demonstrated in 2012 that almost half of the participants had low knowledge scores.11 Although 90% of the respondents have heard about BSE, only 43% actually practiced the technique. By multiple logistic regression analysis, researchers found that the level of knowledge among a university-affiliated population in northern Iraq and participants\u2019 age were significantly associated with performing BSE.12At the Main Training Center for Early Detection of Breast Cancer in Baghdad, it was reported in 2010 that breast cancer was diagnosed in 19.8% of women presenting with palpable breast lumps.13The outcomes of those studies obviously illustrate significant knowledge gaps about the relative importance of breast cancer among the Iraqi community and emphasize the urgent need for practical policy decisions to promote early detection through elevating the level of awareness. In general, the poor survival in less-developed countries, including Iraq, is mainly attributed to the lack of strategic, well-designed diagnostic policies coupled with inadequate treatment facilities.14WHO, in collaboration with IARC, organized a consultative Regional Meeting on Cancer Control and Research Priorities in Doha, Qatar, in October 2013. The following recommendations were made: strengthening cancer registration and surveillance, conducting priority research on cancer etiology, and strengthening screening and early detection of priority cancers. It was concluded that the most common cancers amenable to early detection in EMR are those of the breast, colorectum, and cervix, and it was emphasized that strengthening needs to be built on the best international evidence and existing regional experience, taking into consideration the available resources, challenges, and opportunities.15 Evaluating such processes inevitably demands ensuring the provision of an appropriate sustained database operated by trained personnel. Within hospital records, in the majority of countries belonging to EMR, there is improper documentation of critically important clinical factors such as tumor size, nodal status, stage of breast cancer at initial diagnosis, hormonal receptor status, frequency of distant metastasis, prevailing treatment modalities, and survival. In fact, most of the national cancer registries lack data regarding stage distribution and survival rates.In the context of breast cancer control, information on the putative risk factors for breast cancer and the clinical profile of patients are of utmost importance.10 An online information system supervised by IARC has been provided to collect data systematically from patients attending targeted breast cancer facilities belonging to eight member nations.In an attempt to address these information needs in the clinical profile of patients with breast cancer, and to emphasize the role of research as one of the basic pillars in the adoption of a national cancer control strategy, a national breast cancer research program was established in Iraq in 2009. Under supervision of the IARC Screening Unit, the author developed a comprehensive information system database for Iraqi patients diagnosed with breast cancer. In 2011, the WHO Eastern Mediterranean Regional Office proposed using that model to compare the demographic characteristics, clinicopathologic presentations, and management outcomes among patients in the EMR affected with the disease through implementing a regional comparative breast cancer research project.In Iraq, a preliminary analysis of the relevant database findings belonging to 855 patients, diagnosed and treated for breast cancer, documented the following results. Overall, 24.6% of the patients were illiterate, 70.8% sought medical consultation within the same year after detecting abnormal signs or symptoms, and 46% were in their premenopausal age, whereas 35% were diagnosed in the 45-54 year age group. Interestingly, 86.3% were married, merely 7% had their first childbirth after the age of 35 years, and only 8.5% were nullipara. History of lactation and hormonal therapy was reported in 48% and 20.5%, respectively. Overall, 35% documented a positive family history of malignancy, and 18.5% confirmed having relatives with breast cancer. The main presenting signs were palpable breast lumps (94%), skin changes (9.8%), and bloody nipple discharge (4.7%). Bilateral breast cancer was reported in 4.6%. According to TNM classification, 9.8% presented with stage I disease, and 46% were diagnosed in stages III and IV. Infiltrative ductal carcinoma was the most common pathology (67%), followed by intraductal carcinoma (13.6%) and lobular carcinoma (18.5%). Less than 7% of malignant tumors were well differentiated. More than two-thirds of the patients (65.5%) had positive lymph node involvement at the time of initial diagnosis. Immunohistochemical assays demonstrated that estrogen, progesterone and Her2 receptors were positive in 67%, 69%, and 49.2% of specimens, respectively. The majority of patients (92.3%) were provisionally treated by modified radical mastectomy, 35.2% received palliative treatment, hormonal therapy was prescribed to 54.2%, and recurrence was registered in 9.4%.16 Nevertheless, Iraq, categorized as a middle-income country by WHO/Eastern Mediterranean Regional Office,17 documents far better prognostic indicators than those recorded in low-resource settings such as Eritrea in eastern Africa, where two-thirds of the cases are detected in advanced stages; the mean duration from the onset of symptoms to the time of seeking medical advice approaches 3 years.18Comparing our statistics with those reported in high-resource settings , obvious significant differences are displayed specifically regarding the stage distribution of the disease, with 61%, 32%, and 6% of breast cancer cases present at localized, regional, and distant stages, respectively.In general, these findings justify increasing efforts to establish comprehensive breast cancer control programs in Iraq, focusing provisionally on promoting education and early diagnosis as major approaches to controlling the disease. The striking patterns of breast cancer among women in our region highlight the urgent need to consider early detection a priority."} +{"text": "Objective:to analyze the efficiency of (NACT) followed by concurrent radiochemotherapy (RCT) in patients with locally advanced cervical cancer, 5-year overall, specific and disease-free survival and the prognostic factors correlated with the response and survival.Materials and methods:207 patients with cervical carcinoma stages IIB-IIIB, who received 2-4 cycles of neoadjuvant chemotherapy followed by concurrent chemoradiation were retrospectively analyzed for an objective response (OR), overall survival (OS), and disease-specific survival (DSS) rate. All patients received platinum-based NACT followed by concurrent RCT to a total dose (TD) of 46 Gy/pelvis when patients were evaluated for surgery. Patients with favorable parametrial response optionally underwent surgery. The rest of the patients continued radiochemotherapy exclusively.Results:The baseline characteristics were: median age at diagnosis - 52 years; 82% squamous and 12% adenocarcinoma histologies; 67 patients (32.4%) with FIGO stage IIB, 87 (42%) with stage IIIA and 53 (25.6%) with stage IIIB. The OR rate was 56.5% post-NACT and the complete response (CR) after exclusive RCT was 19.7% while pathological complete response (pCR) in patients that underwent surgery was 61.2%. The median follow-up was 58.3 months. Overall and disease-specific survivals at 5 years were 78% and 84%, respectively. The OS for stages IIB and IIIA was 84%, and 61% for stage IIIB while the DSS rates were 90% for stage IIB, 86% for stage IIIA and 72% for stage IIIB. The disease-free intervals (DFS) rates were 88%, 76% and 69% for stages IIB, IIIA and IIIB, respectively. Conclusions:Neoadjuvant chemotherapy followed by concurrent chemoradiation produces higher response rates and improvements in disease-specific survival and disease-free survival rates compared to RCT. In Romania, cervical cancer accounts for 15% of all malignant tumors, being the first cause of female death in women in female genital cancers and third after breast cancer and colorectal cancer in other types of cancers. Unfortunately, our country ranks first in Europe regarding cervical cancer mortality [2].Cervical cancer is ranked 4th in the world regarding malignant tumors in women, accounting for 12% of all cancers in women. 85% of cases occur in developing countries, where they are the leading cause of death from cancer among women. The global annual incidence of cervical cancer in 2012 was 528.000. In 2012, 266.000 deaths from cervical cancer worldwide were estimated, accounting for 7.5% of all female cancer deaths [3]. Neoadjuvant chemotherapy (NACT) prior to surgery or radiotherapy has been investigated as a new therapeutic strategy for a voluminous or locally advanced disease. The reasons for using neoadjuvant chemotherapy (NACT) are several. Reducing the size of the tumor can later facilitate local therapy, either radiotherapy or surgery. This reduction can convert inoperable tumors to resectable ones. It has also been suggested that NACT increases the radiosensitivity and decreases the fraction of hypoxic cells. Moreover, NACT treats the micrometastatic disease, preventing a significant proportion of relapses. Finally, the NACT response was identified as an important prognostic factor in several studies [4][5].Concomitant radiotherapy and chemotherapy (CRCT) are considered the standard combination of treatment for locally advanced cervical cancer. With 5-year overall survival ranging from 60% to 65% for stage IIB and from 25% to 50% for stage III, new therapeutic strategies are investigated in order to improve these results treated at the Institute of Oncology \u201cProf. Dr. Ion Chiricuta\u201d Cluj- Napoca between November 2010 \u2013 December 2013. Clinical staging was performed using pelvic examination by an experienced gynecologic oncologist and a radiation oncologist. Before treatment, all patients underwent several investigations as part of the initial workup: hematology and biochemistry profiles, chest X-ray, abdominal and pelvic computed tomography. All patients signed the informed consent before treatment. After diagnosis, patients recieved two to four cycles of NACT, two regimens of Paclitaxel 175mg/m2 and Carboplatin AUC 5 (PC) or Topotecan 0.75mg/m2 and Cisplatin 50mg/m2 (TC) administered every three weeks. Three weeks after the completion of the last NACT cycle, patients started RCT. The radiosensitizer chemotherapeutic agents administered concurrently with external beam radiation therapy (EBRT) were two regimens of Cisplatin (20mg/m2 for 5 days every three weeks \u2013 for 92.8% (192/207) of the patients) or 40mg/m2 weekly \u2013 4.8%(10/207)] or Carboplatin AUC 2 \u2013 2.4% (5/207).The patients included in this study had histologically confirmed stage IIB-III cervical cancer (FIGO staging modified by MD Anderson Cancer Center) defined as complete response-CR, partial response-PR, stable disease-SD and progressive disease-PD by a pelvic examination three weeks after the administration of the last NACT cycle, before RCT and at the end of RCT. For the operated patients, the tumor response was confirmed by the pathological outcome. Pathological CR was defined as the absence of tumor cells in the cervix, parametrium, vaginal cuff and pelvic lymph nodes. Patients were followed up periodically. Follow-up was scheduled at 3 months for the first year after treatment, every 6 months for the next 2 years, then once a year thereafter. The follow-up was performed at a multidisciplinary consultation (by both a gynecologic oncologist and a radiation oncologist). Local and distant control was evaluated at every visit by gynecologic and general clinical examination. Medical imaging was performed if recommended.Tumor response was evaluated according to the RECIST v1.1 criteria with radiochemotherapy. The NACT associated with RCT improves DSS and DFS compared to the standard treatment , Manci et al. [12] showed a 15.8% pCR and 73.7% pPR after the administration of three consecutive cycles of NACT. In a phase II study of dose-dense neoadjuvant chemotherapy (NACT) with paclitaxel and carboplatin before radical chemoradiation (RCT), McCormack et al.showed a complete/partial response rate of 70% at the end of NACT, and 85% after completing RCT [13].The tumor size is an important prognostic factor in cervical carcinoma. Large tumors tend to be less radiosensitive as they have relatively large hypoxic tumor cell population and are thus likely to respond poorly to radiotherapy. To overcome these shortcomings, NACT followed by concurrent chemoradiation is being adopted for a bulky locally advanced disease. Several studies showed that the neoadjuvant chemotherapy is effective in reducing the tumor size, expediting the elimination of micrometastasis, improving operability and surgical downstaging. Even though there are many published trials with NACT before surgery, and recent data from several trials of NACT before RCT became available, no NACT regimen emerged [15][16][17][18][19][20].In two studies, the outcome was inferior in the NACT group [21][22]. In their study, McCormack et al. achieved an overall and progression-free survival rate at 3 years of 67% (95% CI: 51\u201379) and 68% (95% CI: 51\u201379) [12].In a retrospective study of NACT followed by RCT in locally advanced cervical cancer (stage IB-IVA), Harsh et al. [23] showed that 5-year OS and DFS rates were 79.7% and 76.6% for stage II-B, 67.6 and 59.5% for stage III-A, 48.4 and 41.9% for stage III-B.Between 1990 and 2000, a number of non-randomized and randomized studies explored the use of neoadjuvant chemotherapy (NACT) prior to radiation in patients with locally advanced cervix cancer (IIB\u2013IVA). A variety of chemotherapy regimens have been evaluated for use in NACT. Cisplatin-based combinations were used in 8 randomized studies. An improvement in progression-free and overall survival compared to radiation alone has failed to be shown in these studies [24], confirmed the superiority of cisplatin-based RCT compared to RT alone with 5-year survival rates of 74% vs. 64% (p <0.05). The association of surgery with RCT achieved an 86% OS rate. Another institutional randomized study, published in 2012 [8], comparing two radiochemotherapy (RCT) regimens revealed a 75% DSS and 71% DFS at 5 years. The 5-year DSS was 83% in stage IIB, 69% in stage IIIA, and 63% in stage IIIB, while DFS was 83%, 64%, and 53%, respectively. The addition of NACT to standard treatment seems to bring a benefit in DSS and DFS . A randomized trial is necessary to confirm these data.In our study, the 5 year OS, DSS and DFS were 78%, 84% and 79%, respectively. The OS for stages IIB and IIIA was 84%, and for stage IIIB 61%. DSS rates were 90% for stage IIB, 86% for stage IIIA and 72%for stage IIIB, while DFS rates were 88%, 76% and 69% for IIB, IIIA and IIIB, respectively. Our randomized study, published in 2009 [The role of surgery in advanced stages is rarely analyzed in the literature. In our study, superior results were obtained by RCT associated with surgery with regard to survival and local control, but it must be mentioned that the patients in stage IIB were optionally operated but in stage III, only the patients with a favorable local response underwent surgery. The evaluation of a surgery combination with RCT is necessary in a randomized study.Neoadjuvant chemotherapy followed by concurrent radiochemotherapy seems to bring better results regarding DSS and DFS compared to RCT, but a larger number and long-term evaluation trials are necessary in order to confirm these data.DisclosuresThe authors declare that there is no conflict of interest."} +{"text": "Bifidobacterium bifidum, B. breve, Lactobacillus casei, L. plantarum, and L. bulgaricus) on bone microarchitecture in a mouse model of age-related osteoporosis. Groups (n = 7 each) of 10-month-old male mice were fed one of six diets for 6 months: 10% grape powder with sugar corrected to 20%; 20% grape powder; 1% probiotic with sugar corrected to 20%; 10% grape powder + 1% probiotic with sugar corrected to 20%; 20% grape powder + 1% probiotic; 20% sugar control. Femur, tibia and 4th lumbar vertebrae from 10-month-old mice served as comparator baseline samples. Bone microarchitecture was measured by micro-computed tomography and compared across diet groups using analysis of variance. Aging exerted a significant effect on tibia metaphysis trabecular bone, with baseline 10-month-old mice having significantly higher bone volume/total volume (BV/TV) and trabecular number measurements and lower trabecular spacing measurements than all 16-month-old groups (p < 0.001). Neither grape nor probiotic enrichment significantly improved bone microarchitecture during aging compared to control diet. The combination of 20% grape + 1% probiotic exerted detrimental effects on tibia metaphysis BV/TV compared to 10% grape + 1% probiotic, and trabecular number and trabecular spacing compared to 10% grape + 1% probiotic, 1% probiotic and control groups (p < 0.05). Femur metaphysis trabecular bone displayed less pronounced aging effects than tibia bone, but also showed detrimental effects of the 20% grape + 1% probiotic vs. most other diets for BV/TV, trabecular number, trabecular spacing and trabecular pattern factor (p < 0.05). Tibia and femur diaphysis cortical bone displayed neither aging nor diet effects (p > 0.05). Vertebrae bone showed age-related deterioration in trabecular thickness and trabecular spacing and a trend toward preservation of trabecular thickness by grape and/or probiotic enrichment (p < 0.05). These findings demonstrate no benefit to bone of combined compared to independent supplementation with probiotics or whole grape powder and even suggest an interference of co-ingestion.Nutrition is a primary modifiable determinant of chronic noncommunicable disease, including osteoporosis. An etiology of osteoporosis is the stimulation of bone-resorbing osteoclasts by reactive oxygen species (ROS). Dietary polyphenols and probiotics demonstrate protective effects on bone that are associated with reduced ROS formation and suppressed osteoclast activity. This study tested the effect of dietary enrichment with powdered whole grape and probiotics (composed of equal parts Bone protection is paramount as people are living longer and must maintain optimal skeletal health into advanced age. A 2015 analysis of US National Health and Nutrition Examination Survey data reports the prevalence of low bone mass as 48% and osteoporosis as 16% in adults over age 65 years ,4. StrikNutrition intervention offers an inexpensive, readily accessible, preventive strategy against osteoporosis that is most effective when adopted early in life . ObservaGrapes are one of the most concentrated sources of dietary polyphenols and theyA novel strategy to enhance the bone-protective effects of grape consumption is to increase the production of bioactive grape polyphenol metabolites in the gastrointestinal tract. Intestinal bacteria (microbiota) metabolize dietary polyphenols to compounds that are absorbed into the body and exert beneficial biologic effects ,39,40. Bn = 6) of mice was used to provide bones for baseline reference measurements to which age- and diet-related changes in 16-month-old mice were compared. The remaining groups (n = 7) were fed one of six diets for 6 months (to age 16 months): 10% grape powder with sugar corrected to 20%; 20% grape powder; 1% probiotic with sugar corrected to 20%; 10% grape powder + 1% probiotic with sugar corrected to 20%; 20% grape powder + 1% probiotic; and 20% sugar control. The experiment was performed in strict accordance with the Guide for the Care and Use of Laboratory Animals prepared by the National Institutes of Health. The use of animals and the study protocol were approved by the Idaho State University Animal Care and Use Committee on 21 July 2016 under protocol number 743. Male 8-month-old ND4 Swiss Webster retired breeder mice were purchased from Envigo, Indianapolis, IN and were housed individually in one environmentally controlled room under a 12-h light-dark cycle and fed standard chow for two months. At age 10 months, a group modified with freeze-dried grape powder made from whole grapes and probiotics, . Grape pBifidobacterium bifidum, B. breve, Lactobacillus casei, L. plantarum, and L. bulgaricus at a concentration of 1011 cfu/g. These strains were selected because they demonstrate growth and polyphenol metabolite production when cultured in polyphenol medium [8 cfu/g diet, or 5 \u00d7 108 cfu/day for a mouse consuming 5 g diet/day, a dose effective in producing bone improvements in mice in our laboratory\u2019s previous study [The probiotic was a mixture of equal parts l medium ,46,52,53us study . Fresh bus study ,56.Mouse body weight and food intake were measured weekly. At the conclusion of the feeding experiment, mice were euthanized using carbon dioxide and femur, tibia and 4th lumbar spine vertebra were excised. Bones were cleaned of muscle, fixed in 10% formalin for 48 h, and stored in 70% ethanol at 4 \u00b0C until micro-computed tomography scanning.High-resolution \u00b5CT scans were performed at the University of Utah Small Animal Imaging Core Facility. Bones were scanned on a Siemens Inveon tri-modality (CT/PET/SPECT) system by a trained technician dedicated to the project. The energy settings used were 150 uA/80 kEv, with an exposure time of 2300 ms. The scans used a full rotation step-and-shoot acquisition with 600 total projections. The reconstructions from the acquired projections resulted in images with an isotropic spatial resolution of 20.49 \u00b5m with a matrix size of 1024 \u00d7 1024 \u00d7 3968.One operator performed all of the analysis. Reconstructed images were loaded into Siemens Inveon Research Workstation or IRW software and checked for artifacts, such as motion artifacts and beam hardening effects. Once the reconstructed image quality was deemed acceptable, the desired bone regions were cropped and analyzed separately as follows. For the femur, the medial notch superior to the condyles was used as a mean to rotate the femur such that the condyles aligned with the horizontal axis. The tibia was rotated such that the flat posterior side was aligned with the horizontal axis whereas the vertebrae was aligned such that its anterior side was aligned with the horizontal axis. For cortical bone analyses, the femur and tibia were analyzed at the 50% mid-shaft whereas the vertebra was analyzed at the 50% mid-vertebrae region. For the data to reflect the area, a range of 21 slices (\u00b110 slices from the 50% slice) was segmented. Trabecular bone analyses for the femur were performed in the distal femoral metaphysis region defined at 0.1 mm proximal to the distal femoral growth plate extending 1 mm towards the mid diaphysis. Tibia trabecular analyses were performed in the proximal tibia metaphysis defined at 0.1 mm distal to the growth plate of the proximal tibia extending 1 mm towards the diaphysis. Two additional regions were analyzed for the vertebrae, namely the regions at the 25% and 75%, for these additional ranges of interest (ROIs), a range of 15 slices was chosen however the bone morphometric (including the trabecular measurements) results were averaged to accurately reflect the entire vertebra. Measurement for each of the three ROIs was based on the total length of the vertebra measured from the cranial end following orientation. For the purposes of segmentation, a thresholding value based on the image volume histogram that selected 65% of the brightest of pixels was used. This value clearly differentiated the cortical bone from the trabecular bone and bone marrow and was kept consistent from specimen to specimen. \u22121), representing the proportion of bone surface available for remodeling; trabecular thickness ; trabecular number , in which a higher number suggests stronger bone structure; trabecular spacing , in which a smaller number indicates better structure; and trabecular pattern , which is a measure of connectiveness of trabecular structures and a smaller number indicates more connected bone. Cortical wall thickness for each of the bones was measured manually using a transparency placed over the images, centered on the medullary area of each slice from the 50% region. Eight measurements were collected from the medial, lateral, anterior and posterior planes and the average was calculated to provide one measurement. Whole-bone measurements of each parameter were calculated using the average of the regional measurements. Once each region was segmented, the Siemens IRW software calculated bone morphometric measurements which included the ratio of total trabecular bone volume to total tissue (bone + marrow) volume ; the ratio of trabecular bone surface area to trabecular total bone volume ,59 betweData were examined for normal distribution and equality of variances using the Shapiro\u2013Wilk test and analysis of means for variances with Levene test, respectively. Data that were not normally distributed were transformed to log normal prior to analyses. One-way analysis of variance (ANOVA) followed by Tukey\u2013Kramer HSD post-hoc multiple comparisons were used to compare group means when variances were equal. Nonparametric one-way ChiSquare test followed by Wilcoxon nonparametric comparisons for each pair were used when variances were not equal. Descriptive data are reported as means with standard deviations. Percent body weight gain was calculated as: body weight\u2014initial (age 10 mo) body weight)/initial body weight \u00d7 100. Feed efficiency was calculated as ), using kcals/g for each diet as indicated in p = 0.99, 0.51, and 0.66, respectively), p < 0.0001), with 10% grape + 1% probiotic and 10% and 20% grape groups weighing more than 1% probiotic , and 10% grape and 10% grape + 1% probiotic weighing more than control , Initial body weight, final body weight and % change in body weight were not significantly different across diet groups (p < 0.0001 for both), p = 0.0003, p < 0.0001 and p = 0.0002, respectively). Although mice in the 1% probiotic group ate the most food per day, feed efficiency was significantly less in the 1% probiotic vs. 10% grape, 10% grape + probiotic and 20% grape + probiotic groups .Food intake was significantly different across diet groups when analyzed by one-way ANOVA of average intake during the entire experiment and ANOVA with repeated measures across the 24 weeks of the experiment (p < 0.0001), with 10% grape + 1% probiotic and 10% and 20% grape groups weighing more than 1% probiotic , and 10% grape and 10% grape + 1% probiotic weighing more than control .Mixed models ANOVA with repeated measures showed a significant main effect of diet group on body weight (BW in g) across weeks (p < 0.001) (p < 0.05). Tibia cortical bone showed no significant effects of aging or diet (p > 0.05).Aging exerted a significant effect on tibia metaphysis trabecular bone, with baseline 10-month-old mice having significantly higher BV/TV and trabecular number measurements and lower trabecular spacing measurements than all 16-month-old groups (< 0.001) . Neitherp > 0.05) (p < 0.05). Femur cortical bone showed no significant effects of aging or diet (p > 0.05).Femur trabecular bone did not demonstrate significant aging effects when comparing 10-month-old mice to 16-month-old mice fed control diet ( > 0.05) . Neitherp = 0.0394) and the largest trabecular thickness .Vertebrae trabecular bone showed limited effects of aging and diet. The baseline 10-month-old mice displayed the smallest vertebrae trabecular spacing (group main effect lactobacillus and bifidobacteria strains metabolize polyphenols to bioactive metabolites [lactobacillus and bifidobacteria strains, augment the health benefits of polyphenol-rich food consumption [The hypothesis tested in this study, that probiotics would enhance bone-protective outcomes of grape-enriched diets, was not supported by these data. Results show that combining probiotics with 10% and 20% grape diets exerted either a null or an interfering effect on bone microarchitecture measures in comparison to independent probiotic and grape dietary enrichment. The underlying rationale for the hypothesis was based on evidence showing that polyphenol-rich diets protect bone from age- and post-menopausal-related loss ,49,50,57abolites ,63,64,65sumption ,66,67,68sumption ,22 and bsumption ,24,27,28sumption ,70,71,72sumption showed tsumption . Bacillus subtilis CU1. Hakansson et al. [lactobacillus and bifidobacteria probiotics compared to without probiotics. Similarly, reductions in tissue and blood inflammatory markers resulting from a 4% powdered green tea leave diet fed to mice were augmented by co-ingestion of L. plantarum [L. plantarum was added to a bilberry-enriched diet, their data do not indicate antagonism of the probiotic on bilberry-associated bioactivity. Interestingly, their study demonstrated that adding L. plantarum to bilberry- and chokeberry-enriched diets prevented reductions in colonic lactobacillus counts caused by the berry diets. The authors suggested that L. plantarum, which possesses enzymatic activity toward polyphenols [lactobacillus. Modification of the intestinal microbiota by polyphenols has been documented in multiple human and animal studies as well as in vitro models [lactobacillus and bifidobacteria concentrations are increased in response to feeding of red wine polyphenols and flavanol-enriched cocoa powder [Several studies suggest a beneficial synergism between probiotics and polyphenol-rich diets. Duoeonne et al. describen et al. reportedlantarum . While Jlantarum showed nyphenols ,76, may o models ,80,81,82a powder ,84.Reasons for the absence of an observed improvement in bone integrity with the combined probiotic + grape diets in this study may include an interaction between the probiotic strains and commensal gut bacteria, leading to impaired production of polyphenol metabolites that are beneficial to bone. Interactions between polyphenols and other dietary components have been previously reported. Blanton et al. describeAnother possibility is that a positive effect of grape oligosaccharides and fiber on bone architecture was inhibited by co-ingestion of probiotics. Higher dietary and specifically fruit fiber intake has been shown to protect against femoral neck bone loss in men . Mechanilactococcus garvieae-fermented soy germ showed superior bioavailability to intact soy isoflavones [A different strategy of using probiotics to metabolize polyphenols to bioactive compounds prior to consumption has also been tested. Lambert et al. demonstrflavones . ConsumpLactobacillus acidophilus, Lactococcus lactis lactis and fructooligosaccharides. McCabe et al. [Lactobacillus reuteri for four weeks. These improved bone outcomes were associated with lower intestinal expression of TNF-\u03b1, a marker of inflammation. The investigators also demonstrated that L. reuteri supplementation suppressed bone resorption and preserved femur trabecular bone parameters in ovariectomized mice [L. reuteri treatment preserved osteoblast function and protected femur trabecular and cortical parameters against loss. Lastly, Lactobacillus paracasei and a mixture of Lactobacillus strains, including L. plantarum, prevented femur cortical loss and reduced the expression of femur TNF-\u03b1 in ovariectomized mice [The lack of a significant beneficial effect of the 1% probiotic compared to control diet on bone microarchitecture in this study is not consistent with previous findings and may be related to differences in probiotic strains used. Blanton et al. reportede et al. showed szed mice . Using azed mice showed tzed mice . It is important to recognize the differences among animal models of osteoporosis in the site-specificity and rate of bone loss, which might impact treatment effects. Age-related osteoporosis, as modeled in the current study, is characterized by a reduced rate of bone turnover ,98, wherL. reuteri. Similarly, Karlsson et al. [L. plantarum vs. plain water. Our laboratory previously found no significant effects of synbiotic- or probiotic-containing diets in body weight, food intake, or feed efficiency in male rats [Lactobacillus species on weight change, with L. plantarum, a probiotic used in the current study, promoting weight loss [The lower body weight, higher food intake, and lower feed efficiency in the 1% probiotic mice are consistent with prior findings from some rodent studies but contrary to those from others, particularly experiments in commercial production animals. McCabe et al. reportedn et al. showed sale rats ,56. A meght loss . Probiotght loss ,107. In conclusion, dietary co-enrichment with grape powder and probiotics does not produce a synergistic beneficial bone response in aging mice. Moreover, the data suggest an interaction between grape and probiotics that exerts negative bone effects compared to independent dietary enrichment with either supplement."} +{"text": "Evaluation of estrogen receptor (ER), progesterone receptor (PR), and Her-2 on core needle biopsies (CNBs) is increasingly in use to diagnosis early breast cancer, but its concordance with surgical excision (SE) is not well documented.The study included 100 formalin fixed, paraffin-embedded specimens of invasive breast carcinoma archived in Pathology Department of Cancer Institute, Tehran, Iran, from 2011 to 2014. Immunohistochemistry was applied to detect ER, PR, and Her-2.ER expression. The correlation between CNB and SE specimens was estimated as 81% and 97.3% for PR and Her-2, respectively.The current study findings indicated a significant correlation of 90% between CNB and SE specimens for .CNB can be performed confidently to determine ER and Her-2. For PR, results obtained from CNB should be considered Breast cancer is one of the most frequently diagnosed neoplasms among females , and alsNowadays, increasing screening programs lead to the discovery of clinically occult lesions , and deaCNB has an undeniable role to diagnose both palpable and impalpable lesions ,2,6, andER and PR expression profiles are introduced as important parts of breast cancer pathologic evaluation as their statuses describe the ensuing hormonal treatment efficacy , progesterone receptor (PR) have essential roles in ascertaining an effective treatment plan . efficacy .On the other hand, although the overexpression of Her-2 is associated with patients\u2019 worse prognosis , recentlPrevious studies showed variable consistency rates of hormonal receptor status between CNBs and surgically excised specimens . TherefoSamplesER, PR, and Her-2 expression. The current cross sectional, retrospective study was conducted in the second half of 2015 on a total of 100 formalin fixed, paraffin-embedded specimens definitely diagnosed as invasive breast carcinoma archived in Pathology Department of Cancer Institute, Tehran, Iran,from2011 to 2014.Thestudy was approved by the Ethics Committee of Tehran University of Medical Sciences, and the routine paraffin block-included study rules, such as preservation of adequate specimen for further evaluations, were considered. Both lobular and ductal carcinoma with different grades were incImmunohistochemical staining2O2 in methanol for 20 minutes to block the endogenous peroxidase activity. Then, slides were washed with distilled water and heated for 20 minutes at 120\u00baCwith citrate buffer in an autoclave to retrieve the antigens. Slides were, then, put in phosphate-buffered saline (PBS), H2O2, distilled water, and again PBS, respectively. Next step was incubation with ready-to-use primary antibodies . Then, Novo link Polymer RE 7150-k kit was used for horse anti-mouse IgG secondary antibodies and 3,3'-diaminobenzidine(DAB) as chromogen. Washing with Tris-buffered saline (TBS) was done after each step. Finally, counter staining with the Mayer hematoxylin, dehydration and mounting with DPX mountant were performed. The current study used normal breast tissue as positive controls, and negative controls were obtained by replacing the primary antibody with nonimmune IgG. Briefly, 5-\u00b5m thick sections, prepared from samples, were incubated at37\u00baCand 54\u00baC for 24 hours and 30 minutes, respectively. Slides were deparaffinized and rehydrated using xylene and ethanol 100%, 96% and 70%, and incubated with 0.5% HImmunohistochemical staining evaluationER and PR expression as follow: no staining (0), 1% to 25% stained cells (1), 26% to 50% (2), 51% to 75% (3), > 75% (4) . Percentage of stained cells (nucleus staining) in five high power fields were figured, and quick score system was used to evaluate 75% (4) . For staER, PR, and Her-2 are shown in A total of 100 patients with the mean age of 50.44 years, ranged from 28 to 75 years, were included in the current study. The immunohistochemical expression of ER expression in core needle biopsy and surgically excised specimensER expression, 89%of positive CNBs were confirmed by SE specimens and also 92%of negative CNBs were followed by the same findings of SE specimens and negative (96.7%) cases of CNBs were confirmed by SE specimens for ER, PR, and Her-2, respectively. Assessment was done by Allred scoring. They presumed CNB as a reliable method to perform IHC staining ,Omranipour et al. , and ZidTamKi et al. performed a comprehensive study on 353 breast cancer patients, using clone 6F11 , clone 6 Ab (Ventana), and a standard immunohist-ochemistry(IHC) kit for ER,PR, and Her-2. They reported that concordance rate for ER and PR was 94.1% to 96% and 86.1% to 89.5%, respectively, while Her-2 had 64% to 96% concordance . Some reLower correlation rates for PR compared to ER, could be explained by the focal and heterogeneous expression pattern of PR that can affect the results ,20. In aThe current study had no case with CNB negative hormonal profile and SE positive results or vice versa, but there was one case that was weakly positive on CNB and strongly positive on SE; therefore the idea of decision-making separately about each patient was supported, and although the results showed the ability of CNB to predict patients' hormonal profile, at least the negative cases require more conservative interpretations. For surgical excisions, a delay between surgery and specimen delivery to a pathologic lab and a gap to pass the specimen can cause autolysis and advert the hormonal profile results ,17,21.Brenner et al. showed that for CNB, five specimens are enough to diagnose any lesion , but in .CNB can be performed confidently to determine ER, or Her-2 status of the tumors. For PR, results obtained from CNB should be utilized with consideration"} +{"text": "Objective: The objective of this standardised experimental study was to investigate the antimicrobial efficacy of the combination of chlorhexidine digluconate (CHX) and the anti-inflammatory pro-vitamin dexpanthenol, which stimulates wound-healing, in the form of Bepanthen\u00ae Antiseptic Wound Cream, in order to rule out possible antagonistic combination effects of CHX and the alcohol analogue of pantothenic acid (vitamin B5) dexpanthenol.Method: Testing was carried out using the quantitative suspension test at conditions simulating wound bio-burden. Test strains included Enterococcus hirae (ATCC 10541) and Candida albicans (ATCC 10231) in accordance with the standard methods of the German Hygiene and Microbiology Society with the following three organic challenges: i) cell culture medium MEM with Earle\u2019s salts, L-glutamine and 10% foetal calf serum (CCM); ii) 10% sheep\u2019s blood; iii) or a mixture of 4.5% albumin, 4.5% sheep\u2019s blood and 1% mucin. For methodological reasons, the wound cream was tested as a 55% dilution, prepared with 1% Tween 80 . CHX 0.275% was tested as control in an aqueous solution and in 1% Tween 80. Additionally, 1% Tween 80 was tested in order to rule out an interfering effect of the dilution medium. A combination of 3% Tween 80, 3% saponin, 0.1% histidine, 0.3% lecithin, 0.5% Na-thiosulphate and 1% ether sulphate was identified as the most appropriate neutraliser during the experiments.Results: Exposed to CCM or 10% sheep\u2019s blood, the tested wound cream fulfilled the requirements for a wound antiseptic against both test species with \u22653 log reduction at 10 minutes. Even at the the worst-case challenge test with 4.5% albumin, 4.5% sheep\u2019s blood and 1% mucin, the requirement for a \u22653 log reduction was met after 24 hours of exposure. Interestingly, the aqueous solution of 0.275% CHX tested as control did not achieve the antimicrobial efficacy of the combination of CHX and 5% dexpanthenol. 1% Tween 80 was ineffective against both test species.Conclusion: Bepanthen\u00ae Antiseptic Wound Cream achieves the in vitro bactericidal and fungicidal efficacy required for a wound antiseptic under three different challenges, despite dilution to 55% of the original preparation. So far, the addition of dexpanthenol was intended to support wound healing. However, our results indicate that the antiseptic efficacy of CHX is synergistically increased by adding 5% dexpanthenol. Acknowledging the antimicrobial and residual efficacy of CHX, and bearing in the mind the contraindications to CHX , the tested wound cream should be regarded as better suitable to be used as wound antiseptic than preparations on basis of CHX alone. Pantothenic acid vitamin B5) and its biologically active precursor D-dexpanthenol activates the proliferation of fibroblasts, promotes the formation of collagen fibres, stimulates the regeneration of damaged tissue, and has an anti-inflammatory and antioxidative effect , 2], , , [5], . N. NA. nidctively) , which wctively) in respe\u00ae Antiseptic Wound Cream achieves the in vitro bactericidal and fungicidal efficacy required for a wound antiseptic with three different organic challenges, including a worst-case scenario. Taking account of recent findings from the literature on the microbicidal and residual effect of CHX, and bearing in mind the contraindications for CHX , the wound ointment may be regarded as suitable for use as a wound antiseptic under real challenging conditions. The microbicidal efficacy is enhanced by the addition of 5% dexpanthenol, which additionally supports wound healing.As BepanthenThe study was initiated and financed by Bayer Vital GmbH, Leverkusen/Germany. Editorial support for this publication was also provided by Bayer Vital GmbH; final responsibility for the English version of this article rests with its authors.No funds were received for this work."} +{"text": "Despite having higher sensitivity as compared to conventional troponins,sensitive troponins have lower specificity, mainly in patients with renalfailure.Study aimed at assessing the sensitive troponin I levels in patients withchest pain, and relating them to the existence of significant coronarylesions.\u00ae TnI-Ultra assay was used. The ROC curve analysis was performed toidentify the sensitivity and specificity of the best cutoff point oftroponin as a discriminator of the probability of significant coronarylesion. The associations were considered significant when p < 0.05.Retrospective, single-center, observational. This study included 991 patientsdivided into two groups: with (N = 681) and without (N = 310) significantcoronary lesion. For posterior analysis, the patients were divided into twoother groups: with (N = 184) and without (N = 807) chronic renal failure.The commercial ADVIA CentaurThe median age was 63 years, and 52% of the patients were of the male sex.The area under the ROC curve between the troponin levels and significantcoronary lesions was 0.685 (95% CI: 0.65 - 0.72). In patients with orwithout renal failure, the areas under the ROC curve were 0.703 (95% CI:0.66 - 0.74) and 0.608 (95% CI: 0.52 - 0.70), respectively. The best cutoffpoints to discriminate the presence of significant coronary lesion were: inthe general population, 0.605 ng/dL ;in patients without renal failure, 0.605 ng/dL ; and in patients with chronic renal failure, 0.515 ng/dL.In patients with chest pain, sensitive troponin I showed a good correlationwith significant coronary lesions when its level was greater than 0.605ng/dL. In patients with chronic renal failure, a significant decrease inspecificity was observed in the correlation of troponin levels and severecoronary lesions. The coronarylesion was considered significant when \u2265 70% on coronary angiography.Chronic renal failure was defined as a creatinine level > 1.5 mg/dL.The patients were divided into two groups: with (N = 681) and without (N = 310)significant coronary lesion. For Receiver Operating Characteristic (ROC) curveanalysis, the patients were divided into two other groups: with (N = 184) andwithout (N = 807) chronic renal failure.\u00ae TnI-Ultra assay was used for current sensitivetroponin with a 99th percentile value of 0.04 ng/mL. The flowchart ofthe management of all patients with chest pain met the criteria established bythe last American Heart Association guideline.9Non-ST-elevation acute coronary syndrome was defined as presence of chest painassociated with electrocardiographic changes or troponin elevation/drop onadmission or, in the lack thereof, clinical findings and risk factors compatiblewith unstable angina . The highesttroponin level during hospitalization before coronary angiography was consideredfor analysis, following the every 6-hour marker collection protocol of theinstitution.The commercial ADVIA CentaurThe following data were obtained: age, sex, presence of diabetes mellitus,systemic arterial hypertension, smoking habit, dyslipidemia, family history ofearly coronary artery disease, chronic coronary artery disease, previous acutemyocardial infarction, creatinine, ST-segment depression or T-wave inversion onthe electrocardiogram.This study was submitted to the Ethics Committee in Research and approved by it.All patients provided written informed consent.The ROC curve analysis was performed to identify the sensitivity and specificityof the best cutoff point of troponin as a discriminator of the probability ofsignificant coronary lesion, and 95% confidence interval (CI) was used. Thatanalysis was performed for the general population and separately for patientswith and without chronic renal failure.th percentile of the method and the best cutoff point found inthis study) were entered into the univariate analysis. Comparison betweenpatients with versus without significant coronary lesion wasperformed.Descriptive analysis of the categorical variables was performed by use ofpercentages. Continuous variables with non-normal distribution were expressed asmedians and interquartile intervals, and those with normal distribution, asmeans and standard deviations. The comparison between groups was performed byuse of the chi-square test for categorical variables. The continuous variables,when the Kolmogorov-Smirnov test showed normal distribution, were assessed byusing the unpaired T test, and when the distribution was not normal, theMann-Whitney U test was used. Both troponin cutoff points analyzed (the99th percentile of the method and the bestcutoff point found in this study).Multivariate analysis was performed with logistic regression, p < 0.05 beingthe significance level adopted. All baseline characteristics listed in The calculations were performed with the SPSS software, version 10.0.th percentile) showedsensitivity of 93.7% and specificity of 23%. For patients with chronic renal failureto reach a specificity of 67% , an elevation in thetroponin level to 1.58 ng/dL was necessary.The median age was 63 years, and 52% of the patients were of the male sex. The areaunder the ROC curve between the troponin levels and significant coronary lesions was0.685 (95% CI: 0.65 - 0.72). In patients with or without renal failure, the areasunder the ROC curve were 0.703 (95% CI: 0.66 - 0.74) and 0.608 (95% CI: 0.52 -0.70), respectively. The best cutoff points to discriminate the presence ofsignificant coronary lesion were: in the general population, 0.605 ng/dL; in patientswithout renal failure, 0.605 ng/dL ; and in patients with chronic renal failure, 0.515ng/dL . In the Troponin was negative in 143 patients, and, in 40.6% of them, significant lesionswere observed on coronary angiography. In addition, 10.5% of those patients withnegative troponin showed ST-segment depression/T-wave inversion onelectrocardiogram. Using the gold-standard procedure of cardiac catheterization, theacute coronary syndrome diagnosis was confirmed in 68.7% of the patients admitteddue to chest pain. In 9.1% of those without significant coronary lesion on coronaryangiography and with positive troponin, the acute coronary syndrome diagnosis wasconfirmed by cardiac magnetic resonance. The baseline characteristics of thepopulation studied and the univariate analysis between the groups are shown in th percentile of the method,there were significant differences between the groups with and without coronarylesion regarding smoking habit , ST-segment depression/T-waveinversion and troponin positivity , respectively. However, when considering the best troponin cutoff pointfound in this study, there were significant differences between the groups with andwithout coronary lesion regarding the male sex , smoking habit, ST-segment depression/T-wave inversion and troponin positivity , respectively. Themultivariate analysis results are shown in In multivariate analysis, considering the 99th percentile of the method. When assessingthe subgroup with renal failure, that level is even higher, hindering its correctinterpretation.The results of this study in the Brazilian population are in accordance with those ofrecently published literature. Troponin positivity without association with coronaryangiographic findings was observed in 31.3% of the patients. In addition, betterspecificity values were only achieved with a troponin cutoff point of 0.605 ng/dL,approximately 15 times the 9912 That prevalence of troponin positivity not relatedto acute coronary artery disease is similar to that found in our study, although weassessed specifically patients with chest pain.In a study published in 2012 derived from the Scottish Heart Health Extended Cohort,blood samples were collected and high-sensitivity troponin I levels were measured.The results showed that, in a population of 15340 individuals, 31.7% of the men and18.1% of the women had high high-sensitivity troponin with no clinical manifestationat the time of blood collection, highlighting the problem of the specificity of themethod. Positivity and worse prognosis were correlated in the long run (p <0.0001), as reported in other studies.13Likewise, a prospective cohort study of 6304 patients with chest pain presenting tothe emergency department has reported positive high-sensitivity troponin T in 39% ofthe cases diagnosed as non-coronary.14 have conducted anobservational multicenter study with 1181 patients hospitalized because ofnon-cardiac causes, 15% of whom had positive high-sensitivity troponin T. Of themajor factors related to that unexpected elevation, the presence of kidneydysfunction was identified as a significantly influencing factor. In addition, onceagain, patients with elevated troponin were at higher risk for death .14Irfan et al.15That specificity value can be greater than ours found in the general population,probably because of the inclusion of more patients with other heart diseases,because we belong to a referral tertiary cardiology center.In individuals older than 75 years, high-sensitivity troponin T was assessed in thecontext of chest pain, being measured at baseline and 3-4 hours. Approximately 27%of the patients were classified as having acute coronary syndrome. The sensitivityand specificity found in that population were 88% and 38%, respectively. The greaterthe initial level or the increase (mainly absolute) in the subsequent measures, thehigher the specificity found.1The concept of variation in the levels of sensitive troponin and high-sensitivitytroponin in different measurements has been studied, and establishing a correlationbetween the amplitude of variability and the probability of coronary artery diseasehas been consecutively attempted. In addition, amplitude can be relative (expressedas percentages) or absolute, with possible implications and distinctinterpretations.16A retrospective study published in 2014, including 1054 patients with chest pain,assessed the variability related to high-sensitivity troponin T. Approximately 40%of the patients showed alteration in at least one measurement. Even with a variationgreater than 20% as compared to the initial level, the specificity did not exceed70%.17 publisheda study comparing current sensitive troponin I versushigh-sensitivity troponin I in 381 patients with chest pain at the emergencydepartment. Those authors found sensitivity values for the two assays of 94% and97%, and negative predictive values of 98% and 99%, respectively, with nosignificant difference.17 Anothersimilar study of 1807 patients with non-ST-segment elevation acute coronary syndromehas shown no significant difference regarding prognosis when comparing thepositivity of current sensitive troponin I versus high-sensitivitytroponin I.18 Differently from thefindings of those studies and using the same assay, ours showed lower sensitivityand specificity of 23% when using the 99th percentile of the method. Thatshows the importance of assessing each center\u2019s population, respecting theirspecific individualities.Assessing specifically the same current sensitive troponin assay used in this study,in 2013 Bonaca et al.2In alignment with that, the meta-analysis published in 2014 with 17 studies and 8644patients with chest pain compared the use of high-sensitivity troponin with that ofconventional troponin. There were differences regarding sensitivity and specificity , respectively.Despite that increase in sensitivity with high-sensitivity troponin, the number ofpatients with the final diagnosis of myocardial infarction and the need foradditional tests for ischemia did not differ between the groups, showing noadditional clinical advantage with the use of high-sensitivity troponin.20 The studyconducted in 2015 compared seven assays of current sensitive troponins andhigh-sensitivity troponin in 2813 patients with chest pain, and with (16%) orwithout kidney dysfunction. Of the patients with nephropathy, in only 45-80% ofthose with positive troponin, the final diagnosis was myocardial infarction. Theoptimal cutoff point varied from 1.9 to 3.4 times that of the general population todetect acute coronary artery disease. Assessing only the same current sensitivetroponin assay used in this study, in 27% of those with positive troponin, the finaldiagnosis of myocardial infarction was ruled out. The area under the curve ofaccuracy of that assay decreased from 0.92 to 0.87 (p = 0.013), comparing thegeneral population with the patients with kidney dysfunction.19 That cutoff point elevation is inaccordance with our findings, showing a clear specificity reduction in the group ofpatients with nephropathy.Finally, some studies have validated the new troponin assays.Despite the large case series, this is a retrospective single-center study, with a much higher number of patients withoutchronic renal failure than with it. In addition, we used only one troponinassay, and most patients were of the male sex.In the study population of patients with chest pain, sensitive troponin I showed agood correlation with significant coronary lesions when its level was greater than0.605 ng/dL. In patients with chronic renal failure, a significant decrease inspecificity was observed in the correlation of troponin levels and severe coronarylesions."} +{"text": "In 2012, the percentage of adults with a dental visit within the past year increased with increasing income. Approximately 44% of adults with family income <200% of the poverty threshold had a dental visit in the past year, increasing to 60% of those with family income from \u2265200 to <400% and 79% for those with family income of \u2265400% of the poverty threshold. The percentage of women with a dental visit in the past year was higher than men within each income group.Source: National Health Interview Survey, 2012. Available at http://www.cdc.gov/nchs/nhis.htm.Reported by: Brandy Lipton, PhD, blipton@cdc.gov, 301-458-4318; Sandra Decker, PhD."} +{"text": "All grains provided 278 kcal/day or 14% of all energy in the total diet, ranking as the 4th largest contributor of energy compared to 15 main food groups. All grain foods ranked 1st for thiamin (33%) and niacin (23%) intake relative to 15 main food groups. The grain foods category ranked 2nd highest of 15 main food groups for daily dietary fiber (23%), iron (38%), folate (40%), and magnesium (15%) and was the 3rd largest food group contributor for daily calcium intake (13%). When considering nutrients to limit as outlined by dietary guidance, main group of grains contributed 6% total fat, 5% saturated fat, 14% sodium and 9% added sugar. Breads, rolls and tortillas provided 150 kcal/day or 8% of all energy in the total diet, ranking as the 2nd largest contributor of energy compared to 46 food subcategories. Breads, rolls and tortillas ranked 1st of 46 foods for daily thiamin (16%) and niacin (10%) intake and 2nd for dietary fiber (12%), iron (12%), folate (13%), and magnesium (7%). Breads, rolls and tortillas ranked 3rd largest food group contributor for daily calcium (5%) intake. Ready-to-eat cereals provided 47 kcal/day or 2% of all energy in the total diet, ranking as the 20th largest contributor of energy compared to 46 food subcategories. All ready-to-eat cereals ranked 1st for daily iron (19%), 1st for folate (21%), 5th for dietary fiber (7%), 3rd for niacin (9%), 8th for magnesium (4%), and 13th for calcium (2%) intake. Given all grain foods and specific subcategories of grain foods provided a greater percentage of several underconsumed nutrients than calories , grain foods provide nutrient density in the American diet of the older adult.Previous data demonstrate grain foods contribute shortfall nutrients to the diet of U.S. adults. The 2015\u20132020 Dietary Guidelines for Americans have identified several shortfall nutrients in the U.S. population, including fiber, folate, and iron (women only). Intake of some shortfall nutrients can be even lower in older adults. The present analyses determined the contribution of grain foods for energy and nutrients in older U.S. adults and ranked to all other food sources in the American diet. Analyses of grain food sources were conducted using a 24-hour recall in adults (\u226551 years old; Food sources of energy and nutrients research in the United States (U.S.) has shown that the grain category can play an important contributory role in the diet of all children, adolescents and adults ,2. SpeciIndeed, healthy aging is multifactorial, however, nutrition is one of the key determinants of successful aging, as it has been documented to promote health and functionality . Thus, aAs data in all children and adults support grain food contributions to nutrient density in U.S. dietary patterns and since several nutrients in grains play a distinct role in healthy aging, the objective of the present analyses was to determine sources of energy and nutrients in all grains, and in commonly consumed grain foods and rank relative to all other foods in U.S. older adults (\u226551 years old) using data from NHANES, 2011\u20132014. The NHANES is a nationally-representative, cross-sectional survey of U.S. non-institutionalized, civilian residents. NHANES data are collected by the National Center for Health Statistics of the Centers for Disease Control and Prevention. Written informed consent was obtained for all participants or proxies, and the survey protocol was approved by the Research Ethics Review Board at the National Center for Health Statistics. Data from two NHANES datasets were combined for the present analyses in adults \u226551 years old .In the current analyses, each grain food and all other foods reported in WWEIA/NHANES is placed in one of the mutually-exclusive food subcategories by linking each food code contained in FNDDS to one WWEIA category . Mixed gAll statistical analyses were performed using SAS software . SAS PROC SURVEYMEANS was used for all statistical calculations, including means and percentages. Survey weights were used to generate nationally-representative estimates for U.S. adults, which were also adjusted for the complex sample design of NHANES. Mean and standard errors of energy, macronutrients and micronutrients for the daily total diet and from food groups were determined (nutrients from dietary supplements were not considered). Percentages of total energy and nutrient intake contributed from food sources were tabulated by ranked order.Food sources of energy and nutrients for main food groups are shown in Tables 1\u201321, which appear in this article. Food sources of energy and nutrients for USDA food subcategories are shown in Energy contribution of main food groups and subcategory of foods groups are presented in The highest ranking main food group contributors, providing 94.31% of dietary fiber in the diet, were grains (23.1%), mixed dishes (19.0%), vegetables (18.3%), fruit (11.7%), snacks and sweets (11.7%), and protein foods (10.6%) . The topThe largest ranking main food group contributors of dietary folate providing 60.3% of folate in the diet, were grains (40.5%), and mixed dishes (19.9%) . The topThe top ranking subcategory foods, collectively providing 37.4% of dietary fiber to the total diet, were vegetables, excluding potatoes (13.6%), breads, rolls and tortillas (12.0%) and fruits (11.7%) . When coTwo grain food groups were the two largest contributors of dietary folate as Dietary Folate Equivalents (DFE) providing 34.4% of folate in the diet, namely ready-to-eat cereals (21.0%), and breads, rolls and tortillas (13.4%) . SimilarProtein foods, mixed dishes, snacks and sweets were the source for nearly 77% of total fat in the diet . Mixed dWhile no one subcategory of food contributed \u226510% of all total fat in the dFour main food groups contribute nearly 78% of all thiamin in the diet, with the leading main food group being grain foods, providing 32.6% of thiamin in the total diet . For niaTwo grain subcategories were the largest contributors (\u226510% for each food) of thiamin in the diet, collectively providing more than a quarter of thiamin in the total diet . Breads,Americans of all ages are continuously not meeting nutrition recommendations even as previous and currCurrent and preceding dietary guidance ,8 for AmMany older Americans are not meeting recommendations for several key nutrients, many of which are contributed by grain food products. Thus, maintaining both whole- and refined/enriched grains, as part of a healthy dietary pattern, may prove to benefit nutrient intakes in a substantial portion of the U.S. older population. The 2015\u20132020 DGAs identified shortfall nutrients in all Americans 2 years of age, however, intake of shortfall nutrients can be even lower in older adults. A recent NHANES analysis examining food and supplement use in various age groups found significant differences in the proportion of the population with intakes below EAR. Adults \u226571 years of age had a higher prevalence of inadequacy for calcium, magnesium, and most B vitamins compared to middle-aged and younger adults. Overall, when considering food consumption alone, the data showed that older adults had lower intake and higher prevalence of inadequacy for most nutrients relative to younger adults, with use of dietary supplements being associated with the greatest benefit in older adults . An IrisThe current analyses have a limitation inherent in observational research and has previously been reported in similar research designs. The results are dependent on self-reported dietary data for foods, which may involve study participants under- or over-estimating food consumption, leading to inaccuracies in energy and nutrient intakes. Data were also obtained using a 24-hour dietary recall, which relies on study participant memory, and while validated methods are used to gather the data, recall information is subject to inaccuracies and bias from memory challenges and other potential measurement errors experienced in epidemiological investigations . CautionAlthough existing dietary guidance recommends an increase in shortfall nutrients and nutrients of public health concern, predominantly through food consumption, gaps in nutrient intakes persist in older U.S. adults. The current sources of energy and nutrients analyses show that cumulatively, a variety of grain foods, regularly consumed by older American adults, in addition to other nutrient-dense foods, including fruits and vegetables, help contribute to nutrient density in the total diet. Specifically, grain foods are contributors of the 2015\u20132020 DGA under-consumed shortfall nutrients and nutrients of public health concern, including dietary fiber, folate, magnesium, calcium and iron, vitamin A, vitamin E, vitamin B12, niacin, and thiamin. The subcategory of breads, rolls and tortillas are contributors of daily thiamin, niacin, dietary fiber, folate, and iron, while ready-to-eat cereals contribute iron, folate, thiamin, vitamin B6, and vitamin B12. Based on the current data presented, encouraging certain grain food patterns in older U.S. adults, including selecting a mix of whole-, enriched- and fortified-grains, from breads, and cereals, may improve nutrient intakes and minimize gaps in shortfall nutrient intakes. In contrast, eliminating grains, especially refined grains, from the diet may lead to unintended nutrient intake consequences. Developing dietary strategies that are mindful of recommended caloric needs, while monitoring nutrients to limit can benefit from the inclusion of refined/enriched and whole grain selections in the U.S. diet."} +{"text": "As access to Xpert expands in high TB-burden settings, its performance against clinically diagnosed TB as a reference standard provides important insight as the majority of childhood TB is bacteriologically unconfirmed. We aim to describe the characteristics and outcomes of children with presumptive TB and TB disease, and assess performance of Xpert under programmatic conditions against a clinical diagnosis of TB as a reference standard.Retrospective review of children evaluated for presumptive TB in Mbeya, Tanzania. Baseline characteristics were compared by TB disease status and, for patients diagnosed with TB, by TB confirmation status using Wilcoxon rank sum test for continuous variables and the Chi-square test for categorical variables. Sensitivity and specificity were calculated to assess the performance of Xpert, smear, and culture against clinical TB. Kappa statistics were calculated to assess agreement between Xpert and smear to culture.Among children (N\u2009=\u2009455) evaluated for presumptive TB, 70.3% (320/455) had Xpert and 62.8% (286/455) had culture performed on sputa. 34.5% (157/455) were diagnosed with TB: 80.3% (126/157) pulmonary TB, 13.4% (21/157) bacteriologically confirmed, 53.5% (84/157) HIV positive, and 48.4% (76/157) inpatients. Compared to the reference standard of clinical diagnosis, sensitivity of Xpert was 8% (95% CI 4\u201315), smear 6% (95% CI 3\u201312) and culture 16% (95% CI 9\u201324), and did not differ based on patient disposition, nutrition or HIV status.Despite access to Xpert, the majority of children with presumptive TB were treated based on clinical diagnosis. Reflecting the reality of clinical practice in resource limited settings, new diagnostics such as Xpert serve as important adjunctive tests but will not obviate the need for astute clinicians and comprehensive diagnostic algorithms.The online version of this article (doi:10.1186/s12879-017-2236-9) contains supplementary material, which is available to authorized users. In 2014, one million cases of childhood tuberculosis (TB) resulted in 140,000 pediatric deaths worldwide , 4. MoreFirm diagnosis and confirmation of childhood TB remain challenging due to bacteriologic confirmation by culture, the universally acknowledged reference standard, being suboptimal in children. In children, the sensitivity of culture varies range 1.5%\u201365%) depending on age, disease severity, number of specimens collected and disease prevalence of the setting %\u201365% dep. The intMycobacterium tuberculosis infection. The use of a clinical TB diagnosis as a reference standard against which to evaluate the performance of diagnostic tests is an imperfect approach, but it affords an important perspective on test performance in this setting. As Tanzania and other high TB-burden countries roll out Xpert technology across expanding levels of care, its performance in programmatic conditions must be continually evaluated to effectively inform policy makers. Upfront Xpert testing in children has shown superior yield over smear microscopy compared to clinically diagnosed TB cases were diagnosed with TB. Baseline characteristics and diagnostic tests performed among those diagnosed with and without TB did not differ, with the exception of FNA being performed more often in those with TB compared to without [8.3% (13/157) vs 3.7% (11/298), Ninety-nine percent (155/157) of children with a TB diagnosis were initiated on ATT, with one child dying and one child lost-to-follow up (LTFU) before treatment could be initiated. Sixty-nine percent of children (109/157) showed treatment success, 7.0% (11/157) were not evaluated/transferred out, 7.6% (12/157) died and 15.9% (25/157) were LTFU Table\u00a0. All chin\u2009=\u2009320), 2.8% of children had a positive Xpert and 2.2% of children had a positive smear , 8% (95% CI 4\u201315), and 6% (95% CI 3\u201312), respectively. The sensitivity of culture, Xpert and smear did not significantly vary by inpatient versus outpatient disposition or by HIV-status , compared to HIV negative children. There were no differences in CXR or FNA performed between the two groups.TST and CXR was performed in 89.5% (407/455) and 62.2% (283/455), respectively, of children with presumptive TB. Overall, 13.5% (55/407) of TSTs were positive and 23.3% (66/283) of CXR were resulted as \u2018abnormal \u2013 suspicious for TB\u2019 , Xpert was half as sensitive as culture (16% sensitivity). Large proportions of children with presumptive TB presented in a severely compromised state with multiple comorbidities . This likely lowered clinicians\u2019 thresholds for empiric TB treatment and contributed to the high numbers of clinical TB diagnoses (86.7% of TB cases). Our findings demonstrate that even with access to Xpert, TB treatment decisions rely heavily on clinical diagnosis, particularly in critically ill children.The effect and interplay between Xpert and empiric TB treatment remains complex , and ourEmerging evidence suggests under-diagnosis of TB may be common in children with severe acute malnutrition (SAM) and/or HIV and their mortality is high , 24, 25.The impact of any new diagnostic test \u2013 such as Xpert \u2013 depends greatly on how it is implemented outside of research settings and on the context in which it is implemented . Two recOur study was limited by its retrospective approach assessing TB care at a single site. Despite clinical practice following national guidelines, there was variability in the diagnostic tests performed per patient, reflecting the reality of clinical practice in TB high burden, resource constrained settings. This variability provided unique and realistic insights regarding the incorporation of new diagnostics into clinical care. Our site received many referrals, contributing to potential referral bias that lowered clinicians\u2019 thresholds to treat empirically. High levels of empiric treatment may limit the performance of Xpert against clinical practice. Although there were few bacteriologically confirmed cases, our study benefited from long follow up of at least six months of all patients to ensure that clinically diagnosed TB cases improved on ATT and \u2018not TB\u2019 cases improved without ATT. Our study did not specifically look at impact of Xpert on clinician behavior or favorable patient outcomes, but provided the basic foundation for such future research. Overall, these findings emphasize the importance of evaluating new diagnostics in children against clinical diagnosis as reference standards.Despite access to Xpert technology, the majority of childhood TB cases presenting to a pediatric referral centre in a resource limited setting were diagnosed clinically, thus limiting the contribution of Xpert to clinical decision making under our programmatic conditions. Recognizing the paucibacillary nature of childhood TB and high risk of rapid disease progression in children, new diagnostics such as Xpert serve as important adjunctive tests but will not obviate the need for astute clinicians and comprehensive diagnostic algorithms. Care should be taken to carefully balance allocation of scarce resources between new diagnostic technologies (e.g. Xpert) and educational efforts to foster traditional components of the diagnostic algorithm for childhood TB in resource limited settings."} +{"text": "Behavioral and Psychological Symptoms of Dementia (BPSD) are relevant since theyare frequent and cause distress to caregivers. However, they may not be reportedby physicians due to the priority usually attributed to cognitive symptoms.To verify whether BPSD is being systematically investigated by physicianseven in specialized settings and whether their records on medical files areaccurate.Assessment of records on medical files of BPSD reported by caregivers to 182patients assisted in atertiary-care behavioral neurology outpatient clinic (BNOC) who also hadappointments in other clinics of the same hospital. Alzheimer\u2019s disease(37.9%) and vascular disease (19.2%) were the most frequent causes ofdementia.Report/appointment ratios were 0.58 in BNOC, 0.43 in other neurological, 0.93in psychiatric and 0.20 in non-neurological, non-psychiatric clinics. BPSDmost frequently recorded in BNOC were insomnia, aggressiveness,agitation/hyperactivity, visual hallucinations, apathy, inadequate behaviorand ease of crying. Sorted by psychiatrists, categories associated to moreBPSD were affect/mood, thought and personality/behavior. affect/mood andsensoperception symptoms were the most frequently reported. Sorted accordingto Neuropsychiatric Inventory (NPI), categories associated to more BPSD weredepression/dysphoria, delusion and apathy/indifference. depression/dysphoriaand agitation/ aggression symptoms were the most frequently reported.BPSD reported by caregivers were very diverse and were not systematicallyinvestigated by physicians. Notes in medical files often containednon-technical terms. This heterogeneity reflectsdifferent pathophysiologic states of cerebral regions and different underlyingpsychopathological mechanisms2. Despitetheir interrelationship, behavioral and cognitive symptoms are different and independentto some extent4.Non-cognitive symptoms occurring in dementia patients constitute a major problem forfamily members and caregivers. As symptoms are frequent and diverse, the term behavioraland psychological symptoms in dementia (BPSD) was proposed by the InternationalPsychogeriatric Association7. Although behavioral and psychological symptoms areubiquitous in all dementias, their frequency and distribution may vary according totype8 severity ofdementia11 and ethnic group12.BPSD are very frequent in dementia patients in both developed and developingcountries17. The occurrence of BPSD considerably increases theeconomic and social costs of dementia management18.These symptoms have crucial relevance since they are the most important cause of distressto caregivers and family members, usually leading to institutionalization of patients.The magnitude of burden caused to caregivers and its consequent distress depends onsymptom severity, type and also ethnicityDespite their high occurrence and importance, behavioral and psychological symptoms maynot be reported by physicians due to the priority usually attributed to theinvestigation of the cognitive symptoms in dementia. In this study, we reviewed thereports of BPSD by caregivers in tertiary care outpatient clinics of a teaching hospitalaccording to the physicians' annotations.The objective of this study was to verify whether BPSD is being systematicallyinvestigated by physicians even in specialized settings and check whether their recordson medical files are accurate and adequate.19. In the BNOC,diagnoses of Alzheimer\u2019s disease, vascular dementias, Lewy body dementia andfrontotemporal dementias are made in accordance with internationally acceptedcriteria23. In this outpatient clinic, dementia severity israted using the Clinical Dementia Rating (CDR)27. The study wasapproved by CHFMRP Ethics Committee through its branch Section of Medical Files. Dueto the nature of the study, it was not necessary seek Informed Consent.We reviewed the medical files of all dementia patients assisted in the BehavioralNeurology Outpatient Clinic (BNOC) during a 3-year period of follow up (1997-1999).BNOC, which has been described elsewhere, is a tertiary care facility of a teachinghospital, the Clinics Hospital of the Ribeir\u00e3o Preto Faculty of Medicine(CHFMRP)We actively looked up physicians\u2019 annotations in reports on BPSD by their informantcaregivers at appointments made in the BNOC. All appointment records of each patientwere reviewed. By informant caregivers we assumed those who were present in theappointment and routinely involved with patient care, comprising mostly familymembers.Additionally, we sought physicians\u2019 annotations on reports of BPSD by those BNOCpatients' informant caregivers during appointments made in other neurologicaloutpatient clinics, psychiatric outpatient clinics and other non-neurological,non-psychiatric outpatient clinics ofthe same hospital. As all patients were BNOC patients, we performed searches inother clinic appointments in the same way they were done in BNOC appointmentannotations.29.Initially, we took the literal annotation by the physicians in the reports onbehavioral and psychological disorders given by the caregivers. Subsequently, theseliteral terms were transposed by three of the authors to a moretechnical, closer to the psychopathological terminology. In this manner, some 60reported symptoms were listed. Next, they asked 22 psychiatrists of CHFMRP to sortthose symptoms into five categories of disturbances: affect and mood, thought,sensoperception, personality and behavior and other behaviors that did not fit underin any of these categories. Finally, three of the authors managedto sort those symptoms according to the categories of the Neuropsychiatric Inventory(NPI), although this instrument had not been applied to these patientsWe present a descriptive analysis of the reports on BPSD by informant caregiverswhich were annotated by the physicians during the appointments in the BNOC and inother outpatient clinics of a tertiary care, teaching hospital.We studied 182 patients , age range 29-93 years (mean age67.6\u00b113.5 years). The age of onset of dementia symptoms ranged from 26 to 91years (mean age of 64.7\u00b114.0 years). Alzheimer's disease (AD) was the mostfrequent cause, accounting for 37.9% of cases (6.0% of those constituting ADassociated with vascular dementia). Vascular dementia (VaD) accounted for 19.2% ofcases, other non degenerative dementias for 19.1% , other degenerative dementia for 9.2% , mixed dementiasexcept AD associated with VaD represented 5.8%. The etiology was not clear in 8.8%of cases. Dementia severity was staged as mild in 23.1% of cases, moderate in 34.1%and severe in 42.8%.On the whole, we observed that these symptoms were not systematically investigated bythe physicians in the course of various appointments. Also, annotations were ofteninaccurate and frequently written in non-technical, lay terms.BPSD reported by the informant caregivers most frequently annotated by physicians inBNOC appointments were insomnia (8.38%), physical aggressiveness (8.30%),agitation/hyperactivity (7.71%), visual hallucinations (6.69%), apathy (6.35%),inadequate behavior (5.42%) and ease of crying (4.83%). These percentage figuresrepresent report frequencies of each symptom in relation to the overall number ofreports. BPSD least annotated by physicians were: ideoaffective dissociation,increased libido, multiple complaints, illusion, arrogance, leave home aimlessly,rummaging and sundowning (0.08% each); hopelessness, ideas of abandonment,pessimism, rumination of ideas, other hallucinationsand childish behavior (0.17% each); anhedonia, lack of interest , solitude, delusion of jealousy and delusion of theft (0.25%each); euphoria and tachylalia/verbosity (0.34% each); indifference, jocosity(improper laughs and jokes) and suicidal attempt (0.42% each).19. A possible bias inthe discussion of our data is that it lacks the level of education of the informantcaregivers, and education may be a factor influencing the perception and report ofbehavioral and psychological symptoms. In a previous paper, mean schooling of theBNOC dementia patients was 2.96\u00b13.17 years (19) and hence it might also beinferred that the level of education of caregivers was also low.The percentage distribution of the etiology does not reflect that of populationalstudies, since this is a casuistry taken from tertiary care outpatient clinics of ateaching hospital. In this setting, the frequency of cases are mostly made up ofreferrals by primary and secondary care physicians and by physicians from otherspecialty outpatient clinics in the hospital, as was described elsewhere for theBNOCConcerning the frequency of reports of BPSD by caregivers in the appointments, astaken from the physicians annotations in the medical files, the report/appointmentratios varied among different clinics. The highest report/ appointment ratio (0.93)occurred in psychiatric outpatient clinics probably due to the nature of symptoms.However, even in this context, 7.0% of appointments lacked annotation of BPSD,possibly because they went uninvestigated by the physicians. By taking 0.93 as a\u201cgold standard\u201d in this casuistry, the report/appointment ratio in BNOC (0.58) mightbe considered low since it is a specialized neurological clinic attending dementiapatients. The ratio was even lower in other neurological clinics (0.43) but thatcould be accounted for the occurrence of other relevant neurological symptoms to bereported in their appointments. The lowest ratio occurred in other non-neurological,non-psychiatric outpatient clinics, as one might expect. All these outpatientclinics are practices with medical residences, and trainee physicians may not beaware of the importance of investigating BPSD even in neurological settings.6, studies highlighting different symptoms as beingthe most frequently reported, namely depression11, aberrant motorbehavior13 andapathy14.The most generally reported BPSD by informant caregivers in the BNOC annotated by thephysicians were insomnia, physical aggressiveness and agitation/hyperactivity. Ratesof BPSD vary according to setting and ascertainment14hallucinations and disinhibition14as being amongst the least reported.The least reported symptoms, all with less than 0.50% of occurrence each, wereideoaffective dissociation, increased libido, multiple complaints, illusion,arrogance, leave home aimlessly, rummage, sundowning, hopelessness, ideas ofabandonment, pessimism, rumination of ideas, other hallucinations, childish behavior, anhedonia, lack of interest , solitude, delusion of jealousy, delusion of theft, euphoria,tachylalia/verbosity, indifference, jocosity (improper laughs and jokes) andsuicidal attempt. Rates of the least reported behavioral and psychological symptomsvary due to the same reasons as for the most reported ones, studies have indicatedeuphoriaAccording to the sorting of BPSD by psychiatrists, the category under which mostsymptoms were assigned was affect/mood disturbances (55.0 of symptoms), followed bythought disturbances (16.7%) and personality/behavior disturbances (13.3%).Affect/mood disturbance symptoms were also the most frequently reported but here the secondplaced category is sensoperceptiondisturbances (27.8%).In reference to the sorting of BPSD reported by informant caregivers according to NPIcategories, one must stress that it was merely an attempt to add information andenrich the discussion because this instrument was not applied to the patients ofthis casuistry. Presently, the BNOC dementia patients have been assessed using theNPI, to be reported in a coming paper. Several BPSD reported could be sorted intomore than one category; however the authors chose the most suitable categories bytaking into consideration the structure and the set of questions of the NPI. Also,some BPSD reported did not fit under any NPI category . The categories assigned most symptoms weredepression/dysphoria (25.0% BPSD reported), delusions (13.3%) andapathy/indifference (10.0%). with regard to the frequency of reports of symptoms,the most important categories were depression/ dysphoria and agitation/aggression (18.2%).16.In this casuistry, BPSD reported by informant caregivers were more diverse. They werenot systematically investigated by the physicians. Despite being an important causeof distress for family members and caregivers, such symptoms were not alwaysproperly described in the medical files whereas the annotations were also inaccurateand written with the use of non-technical terms. On the other hand, this highlightsthe need for systematically looking out for behavioral and psychological symptomswhen examining patients with cognitive disorders and dementias, perhaps possiblewith the aid of appropriate questionnaires and inventories"} +{"text": "To evaluate the sensitivity and specificity of optical coherence tomography angiography (OCTA) in differentiating polypoidal choroidal vasculopathy (PCV) from age-related macular degeneration (AMD). Fundus color photographs, spectral-domain optical coherence tomography, and fluorescein angiography (step 1) and OCTA (step 2) of 50 eyes that had PCV or AMD were presented to two ophthalmologists. The final diagnoses of PCV were masked. Sensitivity and specificity were calculated and compared to the 2-step approach (before and after OCTA) in detecting PCV. The limitations were also evaluated. Of the 50 eyes, 31 were PCV and 19 were non-PCV. The sensitivity increased from 69.5% to 90% after OCTA; however, there was no significant improvement in specificity after OCTA. 70.9% of the eyes with PCV had clear or obvious branching vascular nets (BVNs) in OCTA with high sensitivity (97.5%) after OCTA. Contrarily, 29.1% had insignificant BVNs with a low sensitivity (72.5%) after OCTA. 27% of the occult choroidal neovascularization (CNV) cases were overdiagnosed as PCV when OCTA was applied. OCTA based on clear BVNs at the choroidal level increased sensitivity of diagnosis of PCV by 20%. However, the false-positive rate also increased in occult CNV. Several limitations for a correct diagnosis of PCV were noted. Idiopathic polypoidal choroidal vasculopathy (PCV) was first described by Yannuzzi et al. and is characterized by recurrent subretinal and subretinal pigment epithelium bleeding , 2. PCV The fundus characteristics of PCV include subretinal red or orange nodules and hemorrhagic or exudative pigment epithelial detachment (PED) , 4. MostOCT angiography (OCTA) is a new imaging tool used to diagnose PCV. The polyps appear as hypoflow round structures, whereas the BVNs are detected as hyperflow vascular networks . HoweverWe retrospectively collected images of patients who had macular subretinal fluid with or without pigment epithelial detachment (PED) or hemorrhage attributable to either PCV or AMD from January 2015 to February 2016 in a tertiary medical center in Taiwan. The images included color fundus photographs, SD-OCT , OCTA , FA, and ICGA . Patients with retinal vascular occlusion, myopic CNV, and other secondary CNVs, diabetic retinopathy, and central serous chorioretinopathy were excluded. Poor quality images such as those with a hazy medium or poor fixation of OCTA were also excluded. The patients with a history of treatment including photodynamic therapy (PDT) or intravitreal injections of antivascular endothelial growth factor (VEGF) therapy were not excluded. The OCTA images were not further refined or modified even if autosegmentation was not perfectly aligned, and the cross-sectional picture with the segmentation line was provided , bottom.At the first step, one color image of the macula, three FA images , and two cross-sectional SD-OCT images of all cases were provided to the two graders who wereP < .05 was considered statistically significant.Statistical analyses were performed with PASW Statistics for Windows, Version 18.0 , using McNemar chi-square test. Among the 50 eyes, 31 were confirmed to have PCV and 19 to not have PCV by ICGA . In comparison, an average of 32 eyes were diagnosed as PCV and 18 as non-PCV by the two graders. An average of 87.5% (28/32) were true positive, 12.5% (4/32) were false positive, 83.4% (15/18) were true negative, and 16.6% (3/18) were false negative.p = 0.046); however, the specificity did not (p = 0.856).The sensitivity increased from 69.5% to 90% for both graders from step 1 to step 2 after OCTA . Figure Six PCV cases were misdiagnosed as being non-PCV after providing OCTA images, all of which had unclear or insignificant BVNs in the OCTA images. Therefore, we further classified all of the PCV cases into two groups based on whether or not they had clear and obvious BVNs in the OCTA images. The results showed that 70.9% of the PCV cases (22/31) had clear or obvious BVNs and that this feature was the most sensitive to make an accurate diagnosis (sensitivity 97.5%). On the other hand, 29.1% of the PCV cases (9/31) had insignificant BVNs, all of which had a lower sensitivity of 72.5%.Among the 11 cases of occult CNV, an average 27.2% were overdiagnosed as PCV after OCTA. Other false-positive cases included one mixed-type CNV and one classic CNV. All false-positive cases had a BVN-like shape in OCTA.p < 0.05). This increase in sensitivity was mainly due to the presence of BVNs in OCTA. Without manually adjusting for the segmentation line, BVNs were found in 70% and polyps in only 42% of our 31 cases with PCV. Unlike BVNs that resides within the Bruch's membrane, polyps are located on a more anterior and variable plane above BVNs and are identified in OCTA in less than half of cases [Our results showed that after providing color, FA, and cross-sectional SD-OCT images, OCTA increased the sensitivity of a diagnosis of PCV from 69.5% to 90% cases had been treated before, which increased the difficulty of the diagnosis of PCV. However, we believed that the OCTA images were more representative of daily clinical practice and that postimage manual adjustments or processing was not available before the introduction of the automated retinal layer segmentation algorithm. In conclusion, by identifying BVNs in OCTA at a choroidal level, the sensitivity of diagnosing PCV with color, SD-OCT, and FA images increased by 20%. Future studies should investigate how well OCTA can identify polyps with more sophisticated analysis of imaging data in a cohort of patients with AMD and increase the diagnostic accuracy of PCV compared to ICGA."} +{"text": "The demographics, clinical characteristics and management of patients presenting at the Nairobi Hospital with acute myocardial infarction have not been documented in the past. There is a paucity of studies on this subject in this region.A retrospective, hospital-based study was carried out, examining data of patients presenting at Nairobi Hospital with acute myocardial infarction between January 2007 and June 2009. The data collected were patient demographics, coronary artery disease (CAD) risk factors, clinical presentation, GRACE score risk stratification, coronary anatomical findings on angiography, interventions and outcomes during hospitalisation.Sixty-four patients were recruited (mean age 56.7 years). The CAD risk-factor profile included systemic hypertension in 71.9% of patients, age over 55 or 65 years in men and women, respectively in 42.2%, 35.9% of subjects were smokers, low high-density lipoprotein cholesterol levels in 25%, diabetes mellitus in 25%, family history of premature coronary artery disease in 8%, prior acute coronary syndrome in 18.8%, ST-segment elevation myocardial infarction (STEMI) in 60.9% and non-ST-segment elevation myocardial infarction (NSTEMI) in 39.1% of patients. In the STEMI arm, 79.5% of patients underwent thrombolysis, 17.9% had rescue percutaneous coronary intervention (PCI) and 2.6% had no reperfusion therapy. Medical management was carried out in 29% of the patients, 19.1% had a coronary artery bypass graft and 40.4% had PCI. The mean duration of hospitalisation was 6.69 days. The in-hospital mortality rate was 9.4% and mean in-hospital probability of death according to the GRACE risk score was 16.05%. Discharge medication was a \u03b2-blocker in 84.5% of patients, an ACE inhibitor or angiotensin receptor blocker in 48.3%, low-dose aspirin in 96.6%, clopidogrel in 96.6% and statins in 93.1%.The risk-factor assessment in our population, albeit small, was in keeping with the traditional risk factors for coronary artery disease. There is, however, room for improvement in reconciling the gap between actual and recommended patient care. The demographic and clinical characteristics of patients presenting with acute myocardial infarction at the Nairobi Hospital have not been documented in the past. Abnormal lipid levels, smoking, hypertension, diabetes mellitus, abdominal obesity, psychosocial factors, low consumption of fruit and vegetables, alcohol abuse, and no regular physical activity account for most of the risk factors for myocardial infarction worldwide in both genders and all ages in all regions.3Over the past 20 years, there has been considerable progress with improved outcomes in the treatment of acute coronary syndromes (ACS). These include the establishment of coronary care units and the development of antiplatelet therapy, refinement of anticoagulation strategies and introduction of fibrinolytic therapies. Percutaneous coronary intervention (PCI) has become the intervention of choice in the acute setting in ST-segment elevation myocardial infarction (STEMI). Early invasive intervention in non-ST-segment elevation myocardial infarction (NSTEMI) is also advocated.8Randomised clinical trials in STEMI patients have shown that efficient triaging and early reperfusion therapy decreases mortality rates. Early thrombolysis is effective in improving outcomes in acute STEMI. Although timely performance of primary PCI is more effective in the restoration of patency, and for lower re-occlusion rates, improved residual left ventricular function and better clinical outcomes, this benefit diminishes with any delays.9The initial strategy in NSTEMI is to alleviate ischaemia and symptoms by using anti-ischaemic agents, antiplatelets, anticoagulants, IIb/IIIa inhibitors, to monitor the patient with serial ECGs, and carry out repeat measurements of markers of myocardial necrosis. The invasive coronary approach has been shown to reduce mortality rates in NSTEMI patients.12The GRACE risk model has been validated to establish the in-hospital mortality risk in patients with STEMI and NSTEMI. In this model, the risk factors predicting early mortality include age over 70 years, prior myocardial infarction, Killip class at admission, anterior myocardial infarction, and the combination of hypotension and tachycardia. The GRACE risk model assists in risk profiling and hence prioritising care.14The Nairobi Hospital has a well-equipped emergency department and intensive care unit (ICU), and a modern cardiac catheterisation laboratory with well-trained staff. At the Nairobi Hospital, fibrinolytic therapy is the treatment of choice for STEMI. Primary PCI is increasingly used however it is not yet available timeously and consistently at all hours, due to various logistical factors.This was a retrospective study of the Nairobi Hospital ICU and high-dependence unit (HDU) in-patient records to describe the demographics, risk factors, clinical characteristics, management and outcomes of patients diagnosed with acute myocardial infarction admitted to the Nairobi Hospital ICU and HDU from January 2007 to June 2009.The hospital ethics committee gave consent for the study.The in-patient patients\u2019 records were retrieved and a cardiologist verified the diagnosis of STEMI and NSTEMI, after which the pre-specified data variables were retrieved and filled into a pre-designed study pro forma.Patients who presented with a diagnosis of acute myocardial infarction and were over 18 years were included. STEMI was defined according to the European Society of Cardiology guidelines, as patients with acute chest pain and persistent (> 20 minutes) ST-segment elevation at the J-point in two contiguous leads with the cut-off points: \u2265 0.2 mV in men or \u2265 0.15 mV in women in leads V2\u2013V3 and/or \u2265 0.1 mV in other leads. For the purposes of reperfusion strategy, true posterior myocardial infarction was considered in patients with ST-depression in the anterior leads or new prominent R waves on the same leads.16NSTEMI was defined as patients with chest pain but without persistent ST elevation, new horizontal or down-sloping ST depression \u2265 0.05 mV in two contiguous leads; and/or T inversion \u2265 0.1 mV, flat T waves and pseudo-normalisation of T waves in two contiguous leads with prominent R wave or R/S ratio or no ECG changes at presentation. The confirmation of acute myocardial infarction was made based on elevated cardiac biomarkers.We analysed the demographic data, mode of transport to the accident and emergency department, first medical contact, time of arrival after onset of chest pain, door-to-first ECG time, and ECG-to-cardiologist time. The GRACE risk score of each patient on admission was documented as per the parameters at admission.The risk factors for coronary artery disease analysed included age > 55 years in men and > 65 years in women, male gender, current smoking, low high-density lipoprotein cholesterol (HDLC) level < 40 mg/dl (1.04 mmol/l), systemic hypertension (blood pressure > 140/90 or on antihypertensives), diabetes and family history of premature coronary artery disease.The initial medication given at the accident and emergency department, the type of myocardial infarction and the reperfusion treatment for STEMI were noted. The door-to-needle time and fibrinolytic agent used were both recorded. The coronary anatomy and TIMI grade for coronary blood flow were documented as per the cardiologist\u2019s notes and confirmed by an interventional cardiologist who studied the digital images of the coronary angiogram. The in-hospital complications, duration of hospitalisation, in-hospital deaths and discharge medications were noted.The extracted data were entered into the Statistical Package for Social ScienceTM (SPSS) version 13.0 for Windows statistical software to check for errors and perform the requisite statistical tests. Data were analysed using the same software. Descriptive analysis was performed to characterise the number and type of patient outcomes. To obtain insight into the social demographic factors of the patients, frequency tables were used with accompanying percentages.Bivariate comparisons of continuous symmetric characteristics, such as duration of time between onset of chest pain/ symptoms and arrival at hospital, door-to-first ECG time and ECG-to-cardiologist time were performed using the Student\u2019s t-test and Mann\u2013Whitney test for non-symmetric characteristics for patients with independent variables . Fisher\u2019s exact test and the chi-squared test, as appropriate,were used for comparison of categorical characteristics, such as gender, coronary artery anatomy and in-hospital complications with patients\u2019 in-hospital outcomes.Correlations between variables were tested using the Pearson\u2019s correlation co-efficient. Prevalence of risk factors was calculated with accompanying 95% confidence intervals. Statistical significance was defined as a two tailed p-value \u2264 0.05.Sixty-four patients fulfilled the criteria for STEMI and NSTEMI from January 2007 to June 2009 and 87.5% were male. The mean age was 56.7 years. Of the study population, 60.9% were from the community, while 26.6% were referrals from other health facilities; 28.1% were brought by ambulance but mode of transport was not documented in 67.2% of the cases. Five per cent of the patients were already hospitalised and 89.1% had their first medical contact in hospital. Among the patients, 17.2% arrived within one hour of onset of chest pain, whereas 40.6% arrived at the emergency department more than 12 hours after the onset of chest pain.The presence of coronary artery risk factors in this population was as follows: systemic hypertension was found in 71.9% of patients, 42.2% were over 55 or 65 years in men and women, respectively, 35.9% were cigarette smokers, 25% had a low HDL-C level, 25% had diabetes mellitus, 8% had a documented family history of premature coronary artery disease, 18.8% hada previous history of acute coronary syndrome and 9.4% had chronic kidney disease.The documented door-to-ECG time was less than 10 minutes in only 10.9% of patients and the ECG-to-cardiologist time was less than 30 minutes in 36.5%. Both aspirin and clopidogrel were received by 96.9% of patients on arrival at the emergency department. A loading dose of aspirin was given in 53.2% of patients, whereas 62.9% received a loading dose of clopidogrel; 89.1% received enoxaparin and only 9.4% received unfractionated heparin; 67.2% had transthoracic echocardiography during their hospital stay, of whom 76.9% had a left ventricular ejection fraction (LVEF) > 40%.For type of acute myocardial infarction, 60.9% had a diagnosis consistent with STEMI and 39.1% had NSTEMI. In the NSTEMI arm, 44% of the patients received IIb/IIIa inhibitors, mainly eptifibatide infusion, and 68% had a coronary angiogram done before hospital discharge. The coronary anatomy was consistent with significant atheromatous lesions in 79% of the patients. Of those who had no coronary angiography, 60% had non-invasive testing for myocardial ischaemia before discharge.In the STEMI arm, 79.5% of patients received thrombolysis, 17.9% underwent rescue PCI and 2.6% did not receive reperfusion therapy. None of the patients underwent primary PCI. The door-to-needle time was less than 120 minutes in 45.2% of the thrombolysis patients and 38.7% had no documentation of door-to-needle time. The thrombolytic agent was tenecteplace in 80.6% and steptokinase in 6.5% of patients. Only 51.6% of the thrombolysis patients had an ECG done at 90 minutes post thrombolysis, of whom 56.3% had achieved reperfusion. Of the patients who did not achieve reperfusion, 66.7% underwent rescue PCI. The coronary anatomy was consistent with significant atheromatous lesions in 82.1% of the patients who underwent angiographic studies.Of the patients who underwent coronary angiography, 29% were managed medically, 19.1% were referred for coronary artery bypass grafting (CABG), and 40.4% had PCI with 84.2% receiving drug-eluting stents. Of the patients who underwent PCI, 87.5% achieved TIMI flow of grade 2 to 3.Cardiogenic shock occurred in 17.2% of patients, new atrial fibrillation in 6.3% and cardiac arrest in 3.1%. Sustained ventricular tachycardia or ventricular fibrillation occurred in 5.3%, atrioventricular block in 4.7% and acute kidney injury (creatinine > 200 \u03bcmol/l) in 6.3%.The mean duration of hospitalisation was 6.69 days. In-hospital mortality rate was 9.4%. The mean in-hospital probability of death according to the GRACE risk score was 16.05%.Upon discharge from hospital, 84.5% were prescribed \u03b2-blockers, 48.3% were on ACE inhibitors or angiotensin receptor blockers (ARBs), 96.6% were on low-dose aspirin, 96.6% on clopidogrel and 93.1% on statins.Cardiovascular risk factors have been determined from several landmark studies, mostly performed in the Western world. The African forum has recently embarked on some local studies.The patient population in our study was similar in age and gender to that of other African studies on traditional cardiovascular risk factors in patients with confirmed coronary artery disease.18Emergency medical systems were not in place in our local setting at the time we carried out this study, therefore first medical contact was at the emergency department. Most patients arrived after three hours from onset of chest pain. The initial triage at the emergency department was not optimal with regard to door-to-ECG, ECG-to-cardiologist and door-to-thrombolysis times going beyond the recommended door-to-needle time of 30 minutes. The hospital is currently looking at a system that will allow for immediate interactive communication with the concerned cardiologist to advise on the management of these patients.The thrombolytic agent used most frequently was tenecteplace. Almost all patients received antiplatelet and antithrombin co-therapy as per the current guidelines. The gold standard of acute management of ST-elevation myocardial infarction is primary PCI, with thrombolytic therapy being effective when given early. Thrombolysis was the standard approach in this study.Most patients in our study had an echocardiogram performed during their hospital course. It is generally indicated that echo assessment of cardiac anatomy and function be done in the first 24 to 48 hours after acute myocardial infarction.4Our data showed that the in-hospital mortality rate of patients with a diagnosis of acute myocardial infarction was 9.4%. Despite the small size of the study population, this is comparable to data derived from European studies. The mean probability of in-hospital death in our study according to the GRACE risk score was 16.05%.Secondary preventive medication was prescribed for most patients as per the standard recommendations. However ACE inhibitors or ARBs were prescribed in less than 50% of patients.The risk-factor assessment in our population of patients, albeit small, was in keeping with traditional risk factors for coronary artery disease found in other studies. The risk for acute myocardial infarction was found to increase with higher income and educational level in our black African population, in contrast with findings in other African groups. With advances in the field of cardiology, the local emergency medical system will improve and timely invasive management of patients presenting with acute myocardial infarction will be available. Currently, there is room for improvement in reconciling the gap between actual and recommended patient care. There is also a need to develop local management protocols for patients with acute myocardial infarction, based on local specialist experience and the available facilities. The Nairobi Hospital is committed to putting in place facilities to allow for primary PCI and early thrombolysis."} +{"text": "The aim of this study was to assess the prevalence of multiple chemical sensitivities (MCS), its co-occurrence with asthma and fragrance sensitivity, and effects from exposure to fragranced consumer products.n\u200a=\u200a1137) was surveyed in June 2016.A nationally representative cross-sectional population-based sample of adult Americans (Among the population, 12.8% report medically diagnosed MCS and 25.9% report chemical sensitivity. Of those with MCS, 86.2% experience health problems, such as migraine headaches, when exposed to fragranced consumer products; 71.0% are asthmatic; 70.3% cannot access places that use fragranced products such as air fresheners; and 60.7% lost workdays or a job in the past year due to fragranced products in the workplace.Prevalence of diagnosed MCS has increased over 300%, and self-reported chemical sensitivity over 200%, in the past decade. Reducing exposure to fragranced products could help reduce adverse health and societal effects. Previous studies have found that MCS often co-occurs with asthma,4 as well as fragrance sensitivity,5 characterized by adverse health effects from exposure to fragranced consumer products.6Multiple chemical sensitivities (MCS) is a medical condition characterized by adverse health effects from exposure to common chemicals and pollutants, from products such as pesticides, new carpet and paint, renovation materials, diesel exhaust, cleaning supplies, perfume, scented laundry products, and air fresheners.3 MCS follows a two-step process of (i) initiation of the disease, often from exposure to petrochemical products, and then (ii) triggering of symptoms when exposed to problematic chemicals, often at low levels.7 While significant efforts have been devoted to developing case definitions and diagnostic criteria,9 a single internationally agreed-upon standard for prevalence studies is not yet established. Nonetheless, prior population-based studies of MCS, using specific and often different definitions and criteria, offer useful data on the extent and severity of the condition.While MCS is perhaps the most common term, the condition is also known by other terms, such as chemical intolerance or environmental illness .4 and 2005 to 2006,5 investigated the prevalence of MCS by using the key question developed by the California Department of Health Services (CDHS)10: \u201cCompared to other people, do you consider yourself allergic or unusually sensitive to everyday chemicals like those in household cleaning products, paints, perfumes, detergents, insect spray and things like that?\u201d This criterion reflects self-reported chemical sensitivity. To ascertain a medical diagnosis of MCS, the survey asked, \u201cHas a doctor or health care professional ever told you that you have multiple chemical sensitivities?\u201d This criterion reflects medically diagnosed MCS. These two USA studies found (respectively) a prevalence of 11.1% and 11.6% self-reported chemical sensitivity and 2.5% and 3.9% medically diagnosed MCS.In the USA, two previous nationally representative studies, conducted in 2002 to 200310 found a prevalence of 15.9% self-reported chemical sensitivity and 6.3% medically diagnosed MCS. A survey of 1583 metropolitan Atlantans in 1999 to 2000,1 also using the CDHS criteria, found a prevalence of 12.6% self-reported chemical sensitivity and 3.1% diagnosed MCS. A survey of 1027 individuals in North Carolina in 1993,7 using a question similar to CDHS, found a prevalence of 33% chemical sensitivity.At the state and regional level in the USA, using the CDHS criteria, a survey of 4046 Californians in 199511 an investigation of 1387 adults in Sk\u00f6vde found a prevalence of 33% of self-reported general odor intolerance, or being bothered by strong or pungent odors, such as perfume, cleaning agents, or flower scents.12 Also in Sweden, a survey of 3406 adult respondents from V\u00e4sterbotten found 12.2% reported chemical intolerance to odorous pungent chemicals, such as perfumes and cleaning agents, and 3.3% were physician-diagnosed with chemical intolerance.In Sweden, using the chemical sensitivity scale for sensory hyperreactivity (CSS-SHR),13 using a variation of the CDHS question, found a prevalence of 15.9% of self-reported chemical sensitivity and 1% medically diagnosed MCS. In Japan, a national survey of 7245 adults,14 using the Quick Environmental Exposure and Sensitivity Inventory (QEESI) questionnaire,9 found a prevalence of 7.5% for chemical intolerance. In Korea, a survey of 379 adults, also using the QEESI, found a prevalence of 16.4% for chemical intolerance.15In Australia, a population-based survey of 4009 adults in South Australia in 2001 to 2002,While these studies provide useful context, we lack recent nationally representative data in the USA. A primary objective of this study is to provide a current estimate of the prevalence of MCS in the American population. Also, given previous studies indicating connections, a second objective is to investigate the co-occurrence of MCS with asthma and with fragrance sensitivity. Finally, because fragranced products are a common trigger, a third objective is to investigate the effects of exposure to fragranced products for individuals with MCS, which points to ways to reduce potential adverse effects.n\u200a=\u200a1137, 95% confidence level, 3% margin of error), drawn from a large national panel held by Survey Sampling International. The survey instrument was developed and tested over a 2-year period before full implementation in June 2016. Response rate was 95%, and all responses were anonymous. To assess the prevalence and effects of MCS, an online survey was conducted with a random national cross-sectional sample of the adult US population, representative of age, gender, and region 6 while the present study focuses specifically on effects on the subpopulations of individuals with MCS or chemical sensitivity.Specific exposure contexts were air fresheners or deodorizers used in public restrooms and other environments, scented laundry products coming from a dryer vent, being in a room after it was cleaned with scented cleaning products, being near someone wearing a fragranced product, entering a business with the scent of fragranced products, fragranced soap used in public restrooms, and ability to access environments that used fragranced products. The survey also investigated effects of fragrance exposure in the workplace, access to public places that used fragranced products, and preferences for fragrance-free environments and policies. Data on fragranced product exposures and effects were derived from a survey of the general population,5 the prevalence of diagnosed MCS has increased over three times and self-reported chemical sensitivity has increased over two times in a little over 10 years.A national prevalence of 12.8% medically diagnosed MCS, 25.9% self-reported chemical sensitivity, and 27.5% either or both, was assessed by the survey and with chemical sensitivity is relatively similar.In addition, 71.0% of those with MCS are asthmatic: diagnosed with asthma (40.0%), an asthma-like condition (34.5%), or both. Also, 59.2% with chemical sensitivity are asthmatic: diagnosed with asthma (35.0%), an asthma-like condition (26.2%), or both , migraine headaches (46.9%), mucosal symptoms (46.9%), skin problems (37.9%), and asthma attacks 31.7%). Similarly, 81.2% of those with chemical sensitivity report one or more types of health problems when exposed to fragranced products , scented laundry products coming from a dryer vent (57.9%), being in a room recently cleaned with scented products (67.6%), being near someone wearing a fragranced product (65.5%), and in general fragranced consumer products 73.1%) , asked by the question: \u201cDo any of these health problems substantially limit one or more major life activities, such as seeing, hearing, eating, sleeping, walking, standing, lifting, bending, speaking, breathing, learning, reading, concentrating, thinking, communicating, or working, for you personally?\u201dFragranced products also restrict access in society: 58.6% of individuals with MCS are unable to use public restrooms that have an air freshener, deodorizer, or scented product; 55.2% are unable to wash their hands in a public place if the soap is fragranced; 63.4% enter a business but then want to leave as quickly as possible due to a fragranced product; and 70.3% have been prevented from going someplace because of the presence of a fragranced product that would make them sick . Previous national prevalence studies in the US found instead a slight female bias. Relative to gender and age, the highest bias is male 25 to 34 (+12.7%) .In addition, among individuals with MCS, 86.2% report adverse health effects from exposure to fragranced consumer products. Thus, individuals with MCS are proportionally more likely to be fragrance sensitive than individuals without MCS .18 a practical step in the meantime would be to reduce exposure to the products. For instance, 71.0% of those with MCS would support fragrance-free policies in the workplace, and 82.1% would prefer fragrance-free health care facilities and professionals, as would a majority of the US general population.6As a consequence, individuals with MCS are prevented from accessing restrooms, businesses, workplaces, and public places due to risk of adverse health effects\u2014some potentially disabling\u2014from fragranced consumer products. Notably, exposure to fragranced consumer products is associated with lost workdays or a job, in the past year, for 11.0% of the adult population with MCS or chemical sensitivity, representing an estimated 22 million Americans. While researchers continue to investigate which chemicals or mixtures of chemicals in fragranced consumer products could be associated with adverse effects,Limitations of the study include the following: (a) data were based on self-reports, although a standard and accepted method for epidemiological research, and consistent with prior prevalence studies of MCS; (b) only adults (ages 18 to 65) were surveyed; (c) all possible fragranced products and health effects were not included, although the low percentages for responses in the \u201cother\u201d category indicates the survey captured the primary products and effects; and (d) MCS and chemical sensitivity lack standard diagnostic criteria, although the survey replicated questions from prior large-scale USA prevalence studies to promote comparability.The prevalence of MCS has increased across the American population, and it frequently co-occurs with asthma and fragrance sensitivity. Moreover, fragranced consumer products, such as air fresheners and scented cleaning products, trigger significant adverse health and societal effects among individuals with MCS. Reducing exposure to fragranced products, such as through fragrance-free policies, would be an important practical step to reduce the adverse effects."} +{"text": "General surgeons are often asked to evaluate acute abdominal pain which has an expanded differential diagnosis in women of childbearing age. Acute appendicitis accounts for many surgical emergencies as a common cause of nongynecologic pelvic pain. In some rare instances, acute appendicitis has been shown to occur simultaneously with a variety of gynecologic diseases. We report a case of concurrent acute appendicitis and ruptured ovarian endometrioma. General surgeons are often asked to evaluate acute abdominal pain; however the differential diagnosis must be expanded in women of childbearing age. Acute appendicitis accounts for 27.5% of abdominal surgical emergencies and is the most common cause of nongynecologic pelvic pain . In some\u03bcL with 80.7% neutrophils. Her urinalysis was normal, and her urine pregnancy test was negative. Computed tomography (CT) scan of abdomen and pelvis with intravenous and oral contrast revealed a mildly dilated appendix, measuring 7.5\u2009mm in diameter, and mild wall thickening consistent with acute appendicitis is present in 80% of cases; however, leukocytosis alone has a low specificity. An elevated WBC count in conjunction with neutrophilia and elevated C-reactive protein level, however, has a sensitivity of 97 to 100%. Ultrasound (sensitivity: 83%) with a noncompressible appendix > 6\u2009cm diameter and CT scans (sensitivity: 90%) identifying periappendiceal inflammatory changes are used to aid in diagnosis [Acute appendicitis carries a lifetime risk of 7% with a peak occurrence between the ages of 10 and 30 years and accounts for 27.5% of surgical emergencies [Endometriomas, also known as chocolate cysts or endometrioid cysts, contain dark reddish, brown degenerated blood products. They occur during reproductive years in 17\u201344% of all women with endometriosis. Infertility and dysmenorrhea occur as the cysts are most often found in the ovaries and less commonly in anterior/posterior cul-de-sac, the uterosacral ligaments, uterus, or colon. Physical exam findings include tenderness or nodules in the cul-de-sac or uterosacral ligaments, pain with uterine movement, enlarged adnexal masses, or fixation of adnexa or uterus in a retroverted position. Plain X-rays can show calcified endometrioma 10% of the time. Transvaginal US, CT, and magnetic resonance imaging (MRI) can aid in diagnosis. On US, 50% classically appear as a unilocular cyst and less commonly a multiloculated cyst, a cystic-solid lesion (15%), purely solid lesion (1%), or anechoic cyst (2%) in postmenopausal patients [\u03b2-human chorionic gonadotropin (\u03b2-hCG) and pelvic US aid in the diagnosis.Ectopic pregnancy can occur in the fallopian tube, cervix, ovary, or abdomen with an incidence of 60,000 per year in the United States [Pelvic inflammatory disease (PID) may lead to endometritis, salpingitis, oophoritis, peritonitis, perihepatitis, and tubo-ovarian abscess. PID has an incidence of 1,000,000 women per year in the United States. Common findings include vaginal discharge, urinary symptoms, history of PID, tenderness outside the right lower quadrant, cervical motion tenderness, and positive urinalysis . Pelvic Hemorrhagic corpus luteal cysts commonly occur in women of childbearing age between days 20\u201326 of the menstrual cycle or during the first trimester of pregnancy, accounting for hospital admissions in 4% of women before age of 65. Ruptured cysts are associated with sudden onset of unilateral lower abdominal pain, nausea and vomiting, vaginal bleeding, weakness, syncope, and shoulder tenderness. Ultrasound, CT, and MRI may identify the hemorrhagic ovarian cyst or an adnexal mass associated with high attenuation pelvic fluid representing hemoperitoneum .Ovarian torsion occurs when ovarian cysts or neoplasms, usually \u22655\u2009cm, twist around the vascular pedicle compromising blood flow and resulting in ischemia of the ovary, which can lead to necrosis, hemorrhage, or peritonitis . OvarianAppendiceal endometriosis occurs as a separate entity with an incidence between 0.054% and 0.8% . It may This case illustrates how concomitant gynecologic disorders can occur in patients with acute appendicitis. Our patient presented with an acute onset of epigastric pain that radiated to the right lower quadrant, tenderness at McBurney's point, and leukocytosis which are classic findings in acute appendicitis. However, her low hematocrit and suprapubic pain were atypical. Interestingly, she had no cervical motion tenderness or palpable adnexal mass. Imaging reported acute appendicitis and endometrioma. This serves as a reminder that an atypical clinical picture in women should also promote imaging studies with a goal of increasing diagnostic accuracy. We were able to appropriately treat this patient with a multidisciplinary approach. Such an approach can help to prevent system failures and improve patient safety and outcomes."} +{"text": "Once-daily tenofovir/emtricitabine-based pre-exposure prophylaxis (PrEP) can reduce HIV acquisition in men who have sex with men (MSM), by 44% in the iPrEx trial, and reaching up to 99% with high adherence. We examined the potential population-level impact and cost-effectiveness of different PrEP implementation strategies.We developed a dynamic, stochastic compartmental model of HIV transmission among the estimated 57,400 MSM in Toronto, Canada. Parameterization was performed using local epidemiologic data. Strategies examined included (1) uniform PrEP delivery versus targeting the highest risk decile of MSM (with varying coverage proportions); (2) increasing PrEP efficacy as a surrogate of adherence (44% to 99%); and (3) varying HIV test frequency (once monthly to once yearly). Outcomes included HIV infections averted and the incremental cost ($CAD) per incremental quality-adjusted-life-year (QALY) gained over 20 years.Use of PrEP among all HIV-uninfected MSM at 25, 50, 75 and 100% coverage prevented 1970, 3427, 4317, and 4581 infections, respectively, with cost/QALY increasing from $500,000 to $800,000 CAD. Targeted PrEP for the highest risk MSM at 25, 50, 75 and 100% coverage prevented 1166, 2154, 2816, and 3012 infections, respectively, with cost/QALY ranging from $35,000 to $70,000 CAD. Maximizing PrEP efficacy, in a scenario of 25% coverage of high-risk MSM with PrEP, prevented 1540 infections with a cost/QALY of $15,000 CAD. HIV testing alone (Q3 months) averted 898 of infections with a cost savings of $4,000 CAD per QALY.The optimal implementation strategy for PrEP over the next 20 years at this urban centre is to target high-risk MSM and to maximize efficacy by supporting PrEP adherence. A large health benefit of PrEP implementation could come from engaging undiagnosed HIV-infected individuals into care. In Cak groups \u201311. The k groups , and phak groups . More rek groups . To infok groups , and PREDynamic mathematical models of the population impact of PrEP on HIV spread among MSM have been developed on both national and sub-national scales in high- \u201319 and lTo address these gaps, we developed a mathematical model of HIV spread in Toronto MSM using the best available, regional epidemiologic data. Our aim was to evaluate the impact of different strategies of PrEP delivery in Toronto MSM on the following outcomes: reduction in the total number of diagnosed and undiagnosed HIV infections, total number of HIV-related deaths averted, incremental costs and cost per quality-adjusted life year (QALY) gained, over a 20-year period. Strategies examined included targeting PrEP at the highest risk MSM (with varying proportions of coverage) and varying the frequency of HIV screening in those on PrEP. We further assessed the sensitivity of outcomes to varying rates of adherence.We developed a dynamic, deterministic-stochastic hybrid compartmental model of HIV spread among MSM in Toronto, Canada. The model was represented by a combined deterministic-stochastic model of state3 as early disease; (3) CD4 200 to 500 representing late HIV and (4) CD4<200 representing AIDS. The model represented an open population of MSM. HIV-uninfected men entered the model at a rate maintaining 1% population growth. HIV-uninfected and HIV-infected MSM left the modelled population at compartment-specific rates, with mortality dependent upon the stage of infection.The sexual behaviour of high-risk MSM was drawn from the annual number of sexual partners taken from regional empiric data . These data were collected from MSM undergoing anonymous HIV testing at a downtown Toronto sexually transmitted infection clinic in Spring 2013 and suggested that the highest decile of MSM had a mean of 36 partnerships in the last year . The remHIV serostatus was based on an individual's awareness of his diagnosis of HIV. We assumed that HIV infectivity decreased after a diagnosis of HIV infection, based on behaviour change observed in population-based studies . The redHIV transmission between compartments was a function of the following variables : (1) theIndividuals who were diagnosed with HIV could initiate ART at a rate that varied depending upon CD4 stage, as described below. Similarly, individuals who were on ART could discontinue treatment and return to the diagnosed, infected, but untreated population with CD4>500. In the intervention scenarios, PrEP could be initiated among HIV-uninfected individuals. If taking PrEP, the likelihood of acquiring HIV infection per act was reduced by 44% . If individuals became infected with HIV while on PrEP, they were infectious while undiagnosed (with no effect of PrEP on HIV infectivity). Once diagnosed, they moved into the diagnosed HIV category. We did not incorporate the potential impact of PrEP use on emergence of antiretroviral drug resistance.Toronto-specific epidemiologic data was used wherever possible for parameters and initial conditions . BaselinCost-effectiveness analysis was conducted from the health-systems perspective and included costs associated with inpatient and outpatient clinical care and diagnostics. PrEP, ART and HIV/AIDS related care costs were drawn from previous studies based on Canadian estimates, and included physician-visit and nursing costs, acute hospitalization costs, diagnostic testing and prescription costs ,37. SpecWe calibrated the model at an equilibrium state against the following historical estimates using acceptance-rejection sampling: (1) a stable annual HIV diagnosis rate (330 to 400 cases per annum) and (2) a stable annual HIV-attributable mortality . Parameti.e., the average of a large number of stochastic realizations), we performed 150 stochastic realizations per parameter set to ensure the mean incidence of diagnosed and undiagnosed HIV infections varied less than 1% with each additional simulation.We used the accepted parameter sets to simulate the baseline scenario (without PrEP), and different strategies of PrEP delivery. PrEP was introduced at an HIV-equilibrium state and outcomes were measured at 20 years. Because we were interested in the mean outcome per parameter set targeting all MSM versus only high-risk activity MSM alone, with varying proportions of coverage; (2) varying the frequency of HIV testing in those taking PrEP including the scenario in which screening is performed without PrEP use and (3) increasing PrEP efficacy (as a surrogate for adherence) based on pharmacokinetic analyses from the iPrEx trial, from 44% risk reduction (corresponding to fewer than two doses per week), to 76% (two doses per week), 96% (four doses per week), and 99% risk reduction (seven doses per week) . We thenIn the absence of PrEP, the model estimated 8378 new HIV infections and 1567 HIV-attributable deaths over 20 years. Of the new HIV infections, 30% were acquired by high-risk MSM. The prevalence ratio of high to low-risk was 3, in keeping with the increased risk of infection in the high-risk population .Over 20 years, PrEP use in 25, 50, 75 and 100% of MSM prevented 1970, 3427, 4317, and 4581 new HIV infections, and 110, 182, 222, and 236 HIV-associated deaths. The estimated cost of implementing PrEP increased as more men used PrEP, from $1.36 billion CAD with 25% PrEP coverage to $4.37 billion CAD with 100% PrEP coverage. Total QALYs gained varied from 2673 to 5430, and cost per QALY gained varied from $495,175 to $792,763 CAD with 25% to 100% PrEP coverage, respectively .In contrast, restricting PrEP to the highest risk decile of HIV-uninfected MSM at 25, 50, 75 and 100% coverage was estimated to prevent 1166, 2154, 2816, and 3012 new HIV infections, and 70, 117, 137, and 140 HIV-associated deaths over 20 years. The cost of targeting PrEP at the highest risk MSM increased from $80 million CAD with 25% PrEP coverage to $269 million CAD with 100% PrEP coverage. Total QALYs gained varied from 1417 to 2951, and cost per QALY gained varied from $34,999 to $68,203 CAD with 25% to 100% PrEP coverage respectively . IncremeIncreasing PrEP coverage in high-risk MSM under the assumption of 99% efficacy prevented more infections , prevented more HIV-associated deaths , led to more QALYs gained and produced improved cost per QALY .To evaluate the impact of HIV testing frequency and PrEP efficacy among PrEP users, we assumed a baseline scenario in which 25% of high-risk MSM used PrEP. When keeping efficacy fixed at 44%, changing the frequency of HIV testing in those on PrEP had minimal influence on the number of HIV infections prevented over 20 years . Similarly, costs and cost-effectiveness did not significantly change with variation in testing frequency . HoweverIn this regional model of HIV transmission, we found that PrEP implementation in all MSM, irrespective of risk profile, provides important reductions in HIV infections and mortality. Increasing the frequency of HIV testing in susceptible individuals on PrEP resulted in minimal improvement in the number of infections averted, even when testing monthly. When compared to established cost-effectiveness thresholds , generalFocusing PrEP on the highest risk HIV-uninfected MSM was a more efficient strategy than targeting all high and low risk at comparable levels. Specifically targeting a fraction of highest risk MSM (25% coverage) was the most cost-effective option, with a cost per QALY of approximately $35,000 CAD, similar to values previously described in the literature for comparable populations ,16. ThisIncreasing the frequency of HIV testing in susceptible individuals on PrEP resulted in minimal improvement in the number of infections averted, even when testing monthly. This is because most new infections still occur in non-users when PrEP efficacy is moderate to high. Decreasing the frequency of testing (outside of guideline recommendations of every three months) suggests minimal cost savings and modestly more infections. There has also been documented drug resistance in breakthrough infections . TogetheGiven the cost savings of approximately $4,000 CAD per QALY of HIV testing alone in high-risk populations, our findings suggest a potentially large collateral health benefit of PrEP programmes via engaging more high-risk MSM in routine HIV testing, even if they do not ultimately take PrEP. This is likely occurring due to both behavioural changes in those who are diagnosed with HIV and early initiation of ART, both of which will lead to reduced transmission. Some of the barriers to HIV screening among MSM include a belief that they are not at risk for infection, fear of a positive test and fear that other people might find out they are infected \u201347. PartOf note, with increased HIV testing in a PrEP programme, the fraction of undiagnosed men with HIV declines, and the number of new HIV diagnoses can outpace incident HIV infections. Since HIV diagnoses are used for surveillance and assessing response to interventions, this could misinterpret the population-effectiveness of PrEP programmes. There may be increased HIV cases diagnosed due to increased HIV testing, especially early in the PrEP programme. Similarly, observed declines in new diagnoses may underestimate true declines in new HIV infections.While a strength of this study is its regional focus, using a city with epidemic features similar to other urban MSM HIV epidemics ,48, the Important next steps include an evaluation of the impact of PrEP use on rates of ART resistance accumulation among those who become infected while taking PrEP, as has preliminarily been explored in some models . FurtherProviding once-daily PrEP for HIV prevention among MSM in a large, urban city could be associated with important reductions in HIV infections and deaths from the use of PrEP itself, and from newly engaging MSM in HIV care through PrEP-related screening. The most efficient approach to PrEP delivery would involve identifying high-risk MSM and aiming for modest PrEP coverage, with a focus on maximizing PrEP adherence over more frequent HIV testing.Click here for additional data file."} +{"text": "Schizotypal disorder has been linked to conversion to schizophrenia, with a quarter to half of patients converting over a course of two to five years. Substance use disorders are common in patients with schizotypal disorder, and cannabis has been shown to be a risk factor for developing schizotypal disorder. Cannabis has also been linked to an increased risk of schizophrenia. Other substance use disorders, in particular alcohol, may also increase risk of later schizophrenia. These previous results suggest that substance use, in particular cannabis, may predict conversion to schizophrenia in people with schizotypal disorder.We used the nationwide, unselected Danish registers. The study population was all people born since 1981 in Denmark with incident diagnosis of schizotypal disorder, without previous diagnosis of schizophrenia. Information on substance use disorders was combined from five different registers. Cox regression using time-varying information on substance use disorders and antipsychotic medication, and adjusted for parental history of mental disorders, sex, birth year, and calendar year were used to estimate hazard ratios (HR) and 95% confidence intervals (CI).After two years, 16.3% (95% CI 14.8%-17.8%) of the people with schizotypal disorder had converted to schizophrenia. After 20 years, the conversion rate was 33.1% (95% CI 29.3\u201337.3) overall, and 58.2% (95% CI 44.8%-72.2%) in those with cannabis use disorders. In fully adjusted models, any substance use disorder predicted conversion to schizophrenia . Dividing by substances, cannabis use disorders , amphetamine use disorders , and opioid use disorders predicted conversion to schizophrenia. These associations were not explained by concurrent use of antipsychotic medication, functional level before incident schizotypal disorder, or parental history of mental disorders.Substance use disorders, in particular cannabis, amphetamines, and opioids, are important predictors of conversion from schizotypal disorder to schizophrenia. However, conversion rates are high even in those without substance use disorders, indicating a need for both universal and substance-targeted prevention in people with schizotypal disorder."} +{"text": "Healthy People 2020objective is to increase health care provider counseling for physical activity orexercise among adults with arthritis.Arthritis affects an estimated 54 million U.S. adults and, as a common comorbidity, cancontribute arthritis-specific limitations or barriers to physical activity or exercisefor persons with diabetes, heart disease, and obesity and 2014 .Changes in age-adjusted prevalence of counseling for exercise were examined across the 5years in which both arthritis and counseling forexercise questions were included on the survey. All analyses included adjustment for themultistage complex survey design, including applying sampling weights to make estimatesrepresentative of the U.S. civilian, noninstitutionalized population. Estimates wereage-standardized to the 2000 projected U.S. population using three age groups.Healthy People 2020 age-standardized target of57.4% for adults with arthritis, with the exception of non-Hispanic other races (53.8%),underweight/normal weight persons (50.0%), current smokers (56.9%), inactive persons(56.7%), and persons without a primary care provider (50.7%). In 2002 and 2014,age-adjusted prevalences of health care provider counseling for exercise among adultswith arthritis who were inactive were 47.2% and 56.7%, respectively, representing a20.1% increase (p = 0.001) . In 2014= 0.001) . OverallIn both 2002 and 2014, adults with arthritis who did not receive health care providercounseling for exercise had a higher age-adjusted prevalence of physical inactivity.Compared with the referent group of active persons, the prevalence for 2002 was 41.4%,compared with 34.7% , and for 2014 was 36.8% compared with 30.5%.Among adults with arthritis, the prevalence of reported health care providercounseling for exercise increased from 51.9% in 2002 to 61.0% in 2014. However, itshould be noted that, in a 2014 report, fewer than one third of primary carephysicians said they provide exercise counseling for arthritis during office visits,Physical Activity Guidelines forAmericansHealth care providers and adults with arthritis agree that physical activity hasimportant benefits for managing arthritis, and federal physical activity guidelineshave been found reasonable for adults with arthritis might introduce response bias, although the sampling weights atleast partially adjust for this potential bias. Finally, the exercise counselingquestion does not address the quality or frequency of the counseling.Prevalence of health care provider counseling for exercise among adults witharthritis has increased significantly over more than a decade, but the prevalence ofcounseling remains low for a self-managed behavior (exercise) with proven benefitsand few risks (The American College of Rheumatology\u2019s osteoarthritis managementguidelines recommend exercise as a first-line, nonpharmacologic strategy tomanage arthritis symptoms. An estimated 54 million adults in the UnitedStates are affected by arthritis.Healthy People2020 target of 57.4%.The prevalence of receiving health care provider counseling for exerciseamong adults with arthritis increased 17.6% from 51.9% in 2002 to 61.0% in2014. However, nearly 40% of adults with arthritis still do not receivehealth care provider counseling for exercise. In addition, subgroupsincluding non-Hispanic persons of other races, underweight/normal weightpersons, current smokers, inactive persons, and persons without a primaryhealth care provider, are still below the Health care provider education and training in exercise counseling,electronic medical record prompts, and connections to community programsmight help increase health care provider counseling for exercise amongadults with arthritis."} +{"text": "Gay, bisexual, and other men who have sex with men (collectively referred to as MSM) represent approximately 2% of the U.S. population tests, was assessed at \u22641 and \u22643 months after diagnosis of HIV infection. Receipt of care (any care and retention in care) and viral suppression were assessed among MSM with HIV infection diagnosed by December 31, 2013, and who were alive and resided (based on the most recent known address) in any of the 38 jurisdictions as of December 31, 2014 . Any care (defined as having one or more CD4 or VL tests), retention in HIV care (defined as having two or more CD4 or VL tests \u22653 months apart), and viral suppression (defined as a VL of <200 copies/mL at most recent test) were assessed for 2014. HIV data routinely are statistically adjusted by using multiple imputation techniques to account for missing HIV transmission categories reported through December 2016 from 38 jurisdictions (37 states and the District of Columbia)In 2015, in the 38 jurisdictions, 19,170 MSM received a diagnosis of HIV infection . Blacks Among the 19,170 MSM with HIV infection diagnosed in 2015, 14,328 (74.7%) were linked to care within 1 month after diagnosis . The perAmong 358,151 MSM living with diagnosed HIV infection at year-end 2014, a total of 265,280 (74.1%) received any care, 206,523 (57.7%) were retained in care, and 219,043 (61.2%) were virally suppressed . The lowAmong MSM aged \u226513 years with HIV infection diagnosed in 2015, 19.1% of infections were classified as stage 3 at the time of diagnosis. This suggests that one in five MSM have advanced immunosuppression at the time of diagnosis, highlighting the urgent need for screening. The percentages of MSM linked to care within 1 month and 3 months after diagnosis of HIV infection, were 74.7% and 84.0%, respectively. Among MSM living with HIV diagnoses at year-end 2014, 57.7% were retained in care and 61.2% had achieved viral suppression; these percentages fall short of the national goals for persons living with HIV infection of 85% linkage to care within 1 month after HIV diagnosis, 90% retention in care, and 80% viral suppression of HIV diagnoses classified as stage 3 among black MSM suggests that, compared with other racial/ethnic groups, blacks might receive testing sooner after infection, leading to a lower percentage of infections classified as stage 3 at the time of HIV diagnosis.Percentages of linkage to care and viral suppression were lowest among younger MSM, and all care and treatment outcomes were least favorable for black MSM. Compared with 2010 findings based on data from 19 jurisdictions represent approximately 2% of the U.S. population, yet in 2015 MSM accounted for 70% of all diagnoses of human immunodeficiency virus (HIV) infection, including 3% who also were persons who inject drugs. National goals for persons living with HIV infection include linkage to care for 85% within 1 month of diagnosis, retention in care for 90%, and viral load suppression for 80% by 2020.In 2015, 19% of HIV infections diagnosed among MSM were classified as stage 3 (acquired immunodeficiency syndrome), and 75% of MSM with diagnoses of HIV infection were linked to care within 1 month. MSM who were black or African American and MSM aged <25 years were less likely to be linked to care within 1 month of diagnosis of HIV infection compared with other racial/ethnic and age groups. Among MSM living with diagnosed HIV infection at year-end 2014, 74% received any care, 58% were retained in care, and 61% had achieved viral suppression. Retention in care and viral suppression were low in all MSM, particularly black or African American MSM.Tailored strategies for MSM that increase care and achieve viral suppression, particularly among young MSM and black or African American MSM, are needed to reduce HIV infections, improve health outcomes for persons living with HIV infection, and reduce HIV-related health disparities."} +{"text": "Salmonella infections were identified through PulseNet, the national molecular subtyping network for foodborne disease surveillance. Many ill persons in each of these clusters reported contact with live poultry, primarily chicks and ducklings, from a single mail-order hatchery; therefore, the clusters were merged into a single investigation. During February 3\u2013October 14, 2014, a total of 363 persons infected with outbreak strains of Salmonella serotypes Infantis, Newport, and Hadar were reported from 43 states and Puerto Rico, making it the largest live poultry-associated salmonellosis outbreak reported in the United States.In early 2014, five clusters of human Among the ill persons, 35% (122 of 353) were aged \u226410 years, and 33% (76 of 233) were hospitalized; no deaths were reported. Among those interviewed, 76% (174 of 230) reported live poultry contact in the week before illness onset. Among the ill persons who provided supplemental information on live poultry exposure, 80% (94 of 118) reported chick exposure and 26% (31 of 118) reported duckling exposure. Among 96 (81%) ill persons who were exposed to live poultry at their residence, 28 (29%) reported keeping poultry inside their home instead of outdoors, and 26 (27%) reported no direct contact with their poultry.Salmonella infection outbreaks ; 27 (36%) reported illness onset within 14 days of purchase. Hatchery source information was available for 69 purchases, of which 58 (84%) came from a single mail-order hatchery in Ohio. This same Ohio hatchery was previously linked with multiple, large human \u2013730 daysSalmonella prevention and control programs are needed at all hatcheries and associated breeder farms to prevent outbreaks.The U.S. Department of Agriculture\u2019s National Poultry Improvement Plan, a collaboration between industry and state and federal agencies, provides guidance on management and sanitation practices for mail-order hatcheries, including a Best Management Practices Handbook.Salmonella transmission from live poultry (Salmonella outbreaks, including outbreaks associated with live poultry, is available from CDC (The possibility of environmental contamination of the home by live poultry, suggested by the 27% of respondents who reported no direct contact with their poultry, illustrates a need for additional educational information advising customers on how to reduce the risk for poultry to humanfrom CDC . A compr"} +{"text": "In recent years, major changes in health care policy have affected oncology practice dramatically. In this context, we examined the effect of practice structure on volume and payments for radiation oncology services using the 2013 Medicare Provider Utilization and Payment Data: Physician and Other Supplier Public Use File (POSPUF) for New York State radiation oncologists.The Medicare POSPUF data was queried, and individual physicians were classified into freestanding office-based and hospital-based practices. Freestanding practices were further subdivided into urology, hematology-oncology, and other ownership structures. Additional variables analyzed included gender, year of medical school graduation, and Herfindahl-Hirschman Index (HHI). Statistical analyses were performed to assess the impact of the above-mentioned variables on reimbursements.There were 236 New York State radiation oncologists identified in the 2013 Medicare POSPUF dataset, with a total reimbursement of $91,525,855. Among freestanding centers, the mean global Medicare reimbursement was $832,974. Global Medicare reimbursement was $1,328,743 for urology practices, compared to $754,567 for hematology-oncology practices and $691,821 for other ownership structures (p < 0.05). The mean volume of on-treatment visits (OTVs) was 240.5 per year, varying by practice structure. The mean annual OTV volumes for urology practices, hematology-oncology practices, other freestanding practices, and hospital-based programs were 424.6, 311.5, 247.5, and 209.3, respectively. After correcting for gender, physician experience, and HHI, practice structure was predictive of freestanding reimbursement and on treatment visit volume.Higher Medicare payment was significantly predicted by the type of practice structure, with urology-based and hematology-oncology practices accounting for the highest total reimbursement and OTV volume. Radiation therapy represents one of the three pillars of cancer treatment. With the rapidly aging population, the demand for radiation therapy is projected to increase significantly . Broad aEconomic constraints, competition, growing administrative burden, and proliferation of cost-containment programs have been cited as pressures on independent oncology practices that are driving practice consolidation . While tThe 2014 release of the Medicare Provider Utilization and Payment Data: Physician and Other Supplier Public Use File (POSPUF)\u00a0allows for unprecedented opportunity to investigate factors associated with healthcare expenditure attributable to radiation therapy. The POSPUF datafile contains information on nearly all Medicare Part B services provided by individual physicians. Analysis of Medicare spending using POSPUF data has been detailed for multiple specialties, including ophthalmology, plastic surgery, urology, general surgery, and radiation oncology -15. HoweSince Medicare accounts for approximately 50% of all patients diagnosed with cancer , we perfwww.CMS.gov. These files contain a comprehensive summary of Medicare Part B payments to individual physicians. To protect patient confidentiality, billing codes of procedures performed on fewer than 10 patients per physician were embargoed. Data from these files include billing codes, the location of service, total submitted services, and total payment amount. This study was deemed to be exempt from review by the Institutional Review Board.We queried the 2013 Medicare Provider and Utilization and Payment Data: POSPUF for radiation oncologists in New York State, obtained from Quality assurance and post-processing of the raw data were performed to ensure that all analyzed physicians were accurately classified as practicing New York State radiation oncologists. We identified several radiation oncologists, misclassified as diagnostic radiologists and hematology oncologists and vice versa. Additionally, several physicians, classified as New York-based radiation oncologists, practice other specialties or worked in another state. Physicians who were known to have changed practices in 2013 were excluded. These physicians were often identified as having a large variation in Medicare reimbursement, compared to 2012. Physicians with less than $20,000 in Medicare Part B payments were presumed to be part-time and excluded from the analysis. A total of 236 radiation oncologists in 88 practices met the inclusion criteria for this analysis.Practices were grouped into freestanding practices that billed according to the Medicare Physician Fee Schedule (MPFS) and hospital practices that billed through the hospital outpatient prospective payment system (HOPPS). A small cohort of physicians worked in practices that billed through both MPRS and HOPPS.Among practices that billed MPFS, we considered three subgroups, including majority urology practices, majority hematology-oncology practices, and \u201cother\u201d practice structures, which included traditional single specialty radiation oncology practices, multispecialty practice\u00a0, and national radiation oncology chains. Among practices that billed HOPPS, no attempt was made to separate out programs by type of institution.Treatment codes for radiation treatment delivery, simulation, planning, weekly treatment management, brachytherapy, and stereotactic radiation were extracted Table . For eacVitals.com.The Herfindahl-Hirschman Index (HHI) is a standard measure of economic competition that has been extensively applied to health policy research . The HHIOne-way analysis of variance (ANOVA) tests were performed to look at differences in reimbursement and key metrics of clinical activity between practice types and year of medical school graduation groups. Post-hoc pairwise comparisons between groups were made with Bonferroni adjustment for multiple comparisons. R-squared statistics were reported to describe the proportion of variance explained by the models. Wilcoxon rank-sum tests/independent sample t-tests were performed to look at differences in reimbursement and clinical activity by gender and HHI category , as appropriate.Three multivariable generalized estimating equations (GEEs) models were performed for the outcomes of 1) reimbursement, 2) OTVs), and 3) IMRT utilization, using practice type, gender, year of medical school graduation, and HHI as predictors in the multivariable models. The GEE models provided robust standard errors due to the potential correlation between radiation oncologists in the same practice. Similarly, because the proportion of Medicare Advantage participants within the\u00a0county could influence outcomes, subsequent GEEs for all three outcomes were constructed, clustering by county and the results served to confirm the original models with respect to practice setting . AnalyseA total of 236 New York State radiation oncologists were identified, with a total payment of $91,525,855 from Medicare. Of this group, 176 were males, and 60 were females. The average year of medical school graduation was 1989 (range 1954\u20132007) 709,269 to 956,678; median $711,586) with significant variation by practice type Figure . UrologyIn New York State, 58% of physicians worked in hospital-based practices with professional billing attributed to the physician. In this structure, technical billing is performed by the institution and not available for analysis. Professional reimbursement averaged $115,588 .The number of OTVs\u00a0is a standard benchmark for physician productivity in radiation oncology. This metric fails to capture physician work related to stereotactic radiation, brachytherapy, image-guided radiation therapy, or IMRT. With these caveats, this is a measure of productivity for physicians working in both freestanding and hospital-based settings.The mean number of OTVs per physician was 240.5 per year . The mean number of OTVs per physician was 424.6 per year for urology practices compared to 311.5 per year for hematology-oncology practices, 247.5 per year for other freestanding practices and 209.3 per year for hospital-based programs Figure . PracticFor freestanding centers, there are granular data on the percentage of patients receiving external radiation therapy fractions delivered via IMRT. The formula used is the number of patients with code 77418 divided by the number of patients with codes 77402 through 77418. Overall, 55% (95% CI 49% to 60%) of patients were treated with IMRT. For urology centers, 80% (95% CI 75% to 85%) of patients were treated with IMRT compared to 22% (95% CI 12% to 31%) of hematology-oncology centers and 55% (95% CI 49% to 62%) for other freestanding practices.To compare IMRT utilization with hospital-based practices, we utilized IMRT planning codes that were shared across practice settings. IMRT\u00a0utilization was estimated by dividing the number of patients with code 77301 divided by the number of patients with codes 77295 plus 77301. To validate the use of IMRT planning codes to estimate IMRT utilization, the Pearson\u2019s correlation coefficient for IMRT treatment delivery vs. IMRT\u00a0planning codes was 0.91 for freestanding centers. Overall, 49% (95% CI 45% to 53%) of patients were treated with IMRT. IMRT\u00a0was used for 58% (95% CI 52% to 64%) of freestanding centers vs. 43% (95% CI 39% to 47%) of hospital-based centers.For urology centers, 76% (95% CI 69% to 82%) of patients received IMRT compared to 32% (95% CI 18% to 46%) of hematology-oncology centers, 58% (95% CI 52% to 64%) of other freestanding centers and 43% (95% CI 39% to 47%) of hospital-based programs Figure . PracticNeither gender nor year of medical school graduation had a significant impact on global Medicare reimbursement, OTV volume, or IMRT utilization on univariate analysis (p > 0.05). Above average HHI was not associated with differences on global Medicare reimbursement or IMRT utilization but was associated with higher volumes of OTVs (p = 0.02). Physicians practicing in highly competitive markets averaged 225.4 OTV compared to 295.9 for physicians practicing in less competitive markets.In multivariable modeling, urology practices demonstrated significantly greater Medicare reimbursement, compared to hematology-oncology and other freestanding practices. The biggest difference was found between urology and other freestanding practices, with physicians in urology practices receiving on average $618,746.00 more reimbursement than physicians in other freestanding practices (p < 0.001) Table .Similarly, urology practices demonstrated significantly greater OTV than other freestanding\u00a0and hospital-based practices. The biggest difference was found between urology and hospital-based practices, with physicians in urology practices having on average 207 more OTVs than physicians in hospital-based practices (p < 0.001). Additionally, physicians with an HHI above the mean had on average 65 more OTVs than physicians with an HHI below the mean (p = 0.012) Table .Lastly, urology practices demonstrated significantly greater IMRT utilization than hematology-oncology, other freestanding, and hospital-based practices. The biggest difference was found between urology and hematology-oncology practices, with physicians in urology practices treating on average 43% more patients with IMRT than physicians in hematology-oncology practices (p < 0.001) Table .A total of 41 physicians treated more than 10 patients with stereotactic radiation. For high volume stereotactic radiation practices, the median number of patients treated was 21 (range 11 to 174). High volume stereotactic radiation practices were more likely to be hospital-based practices than freestanding practices .In contrast, there were only 13 physicians who treated more than 10 patients with brachytherapy.\u00a0For high volume brachytherapy practices, the median number of patients treated was 16 (range 11 to 42). High volume brachytherapy practices were uncommon in both hospital-based and freestanding practices .Through the release of Medicare Provider Utilization and Payment Data, patterns of practice can be identified. Limiting the scope of the study to New York State allowed investigators to perform post-processing to classify physicians accurately to various practice structures and to enrich the database by including gender, year of medical school graduation, and Herfindahl-Hirschman Index. These efforts allowed for a more extensive and robust analysis than prior efforts .We demonstrated that physicians working at urology practices generate increased revenues by combining high patient volumes with increased IMRT utilization. This report supplements and extends earlier work documenting practice patterns for combined urology and radiation oncology groups . Our stuWhile improper variation in IMRT utilization can increase costs without improving outcome, appropriate use of IMRT can be highly beneficial. For instance, a recent study demonstrated that increased use of lung IMRT reduced the likelihood of hospitalization for dehydration or pulmonary toxicity . ImproviThere are several disadvantages to inherent in claims-based datasets. Since the SEER registry does not cover New York State, this analysis could not consider patient level data. Therefore, it is impossible to consider differences in patient populations treated at various practice settings. It was not feasible to systematically account for physicians working part time or those heavily engaged in research or administration. Analysis of Medicare data does not necessarily correlate to practice patterns for other payers. Importantly, this cross-sectional analysis represents a retrospective snapshot in time of a highly fluid healthcare marketplace.Although the Medicare public data set did not capture low volume codes, it is important to recognize that most patients are treated with high volume codes. For instance, RT delivery to three or more areas (77412-77416) + IMRT (77418) accounts for 99.4% of external beam treatment delivery codes, suggesting that excluding low volume codes would not materially change conclusions .Despite the increasing prominence of direct to patient marketing and highly integrated multispecialty group practices, successful referral-based physician practices are still judged by ability, availability, and affability . Grit, mA deep dive into Medicare Part B provides useful insight into recent practice patterns. This information could assist physicians and administrative leaders to develop strategic plans in radiation oncology."} +{"text": "Saudi Arabia has reported >80% of the Middle East respiratory syndrome coronavirus (MERS-CoV) cases worldwide. During April 2015\u2013February 2016, Saudi Arabia identified and tested 57,363 persons with suspected MERS-CoV infection; 384 (0.7%) tested positive. Robust, extensive, and timely surveillance is critical for limiting virus transmission. Middle East respiratory syndrome (MERS) coronavirus (CoV) causes severe respiratory illness in humans, with death occurring in >35% of reported cases . In addition to suspected cases, testing is recommended for close contacts of persons with confirmed MERS-CoV infection, regardless of symptoms, and can also be requested at the discretion of an infectious disease consultant. Tests are performed on respiratory specimens at 5 regional laboratories using real-time PCR . When a suspected case-patient is identified for testing, the referring hospital reports demographic and basic clinical data to HESN . After s<14 years of age, respectively tested positive . Among tectively . The monectively , and theAmong tested persons for whom the reason for testing was known, 89.0% met the clinical case definition for suspected MERS . The remMost tested persons were reported in the course of routine surveillance through a local HAD. Nationwide, 18.4 persons/10,000 inhabitants were tested, and 1.2/100,000 were MERS-CoV\u2013positive . Rates oIn addition, surveillance during the annual Hajj pilgrimage included 888 tested persons during September 2015, representing 4.5 tested persons/10,000 among 1,952,817 pilgrims. None tested positive for MERS-CoV.<14 years of age, 10 (0.1%) tested positive, including 5 who were <1 year of age. At least 7 of the 10 children were tested because of exposure to a MERS case-patient. The number of tests among children <14 years of age temporarily dropped after the case definition revision in June 2015, which introduced more stringent criteria for testing.Among 8,032 children Surveillance and testing for MERS-CoV infection is extensive and widespread in Saudi Arabia. During our study, an average of >5,000 persons per month were identified as being at high risk for infection due to clinical or epidemiologic criteria and were subsequently tested. MERS was first recognized in 2012, and as of November 3, 2016, Saudi Arabia has reported 80.9% of the cases reported worldwide .<14 years of age tested positive for MERS-CoV; this was the lowest rate among all age groups. Most MERS-CoV\u2013positive children <14 years of age were tested because of high-risk exposures, not because they met clinical criteria. Although the proportion of positive tests was highest among persons >35 years of age, the number of tests was highest among persons 18\u201334 years of age, perhaps because of widespread testing of healthcare workers during outbreaks.Only 0.1% of children The largest number of tests was conducted in November, coinciding with the winter respiratory virus season. In comparison, the proportion of positive tests peaked in May and August, coinciding with outbreaks that occurred in Ahsa (Our analysis had limitations. Variations were probably present in the reporting practices of the various data reporters, in the clinical diagnostic practices used across Saudi Arabia, and among investigation teams. Such variations could affect the completeness, accuracy, and timeliness of the data used for this assessment.Surveillance and testing for MERS-CoV throughout Saudi Arabia is extensive, as documented by HESN; in a single month during this study, >9,000 patients at high risk for MERS were investigated. A continued robust approach to the early detection of patients with MERS is critical for the prompt implementation of infection-control precautions and the prevention of healthcare-associated transmission of MERS-CoV.Definitions for suspected cases of Middle East respiratory syndrome coronavirus in Saudi Arabia."} +{"text": "Candida chorioamnionitis is rare but can lead to neonatal infection, high mortality, and neurodevelopmental impairment. We aimed to investigate maternal clinical features and perinatal outcomes and discuss future management strategies. We reviewed the medical records of women with Candida chorioamnionitis at our hospital over a 10-year period (n = 9) and previous published case reports and case series. The most prevalent Candida species was C. albicans . The most prevalent predisposing condition was preterm premature rupture of membranes , followed by pregnancy with a retained intrauterine contraceptive device and pregnancy after in vitro fertilization . Preterm labor was the most common symptom , and only 13% of cases involved fever. Of the infants, 27% of the singletons and 23.8% of the twins were born before 22 gestational weeks, while 60% of the singletons and 76.2% of the twins were born at 22\u201336 weeks. The median birth weight of the babies born after 22 weeks was 1230\u2009g. The mortality rates of the singletons and twins born after 22 weeks of gestation in the year 2000 or later were 28.6% and 52.4%, respectively. Antenatal treatment for Candida chorioamnionitis has not been established. Candida species rarely cause chorioamnionitis. A recent neonatal study demonstrated that chorioamnionitis is an important risk factor of invasive early-onset candidiasis in extremely low-birth-weight infants, which leads to high mortality (71%) and neurodevelopmental impairment rates (86%) ), C. tropicalis (3% [3/101]), C. lusitaniae (2% [2/101]), C. parapsilosis (2% [2/101]), C. famata (1% [1/101]), and C. kefyr of cases in this study were antenatally diagnosed using amniotic fluid culture obtained through transabdominal amniocentesis. A recent case report also showed that the collection of amniotic fluid sludge succeeded to detect C. albicans [The presence of an IUCD during pregnancy, an established risk factor of intra-amnioticnfection , 93, shok factor , 91. How methods . Howeverwith IVF . Our studied yet . A case nionitis . The insnionitis , 57. Amnalbicans . Thus, w Candida colonization in vagina was missing in most cases of the literature review, we were unable to evaluate the effect of Candida colonization in vagina on Candida chorioamnionitis in this study. A recent study, which showed recurrent vaginal colonization with C. albicans in early pregnancy was a risk factor for preterm delivery and low birth weight, indicates that the routine screening and consequent treatment for Candida colonization can be useful to improve pregnancy outcomes [ Candida is associated with Candia chorioamnionitis, we also suggest that the screening and treatment for Candida colonization in vagina in early pregnancy is a reasonable strategy to prevent ascending infection.Since the information ofoutcomes . AlthougAlmost 30% of singletons and 50% of twins born after 22 weeks died, even after the year 2000. Immaturity and severe fetal inflammation could be causes of the high mortality rate. As shown in Candida chorioamnionitis is challenging. Although the maternal administration of various antifungal agents via various routes has been conducted, only half of cases resulted in the delivery of live infants. Fluconazole was the most popular agent used in seven cases. However, fluconazole has less activity against C. glabrata, the second most prevalent species, and whether fluconazole crosses the placenta is unknown [ C. glabrata. One case report showed that intravenous amphotericin B treatment resulted in pregnancy extension by 4 weeks and the delivery of live infants with no signs of inflammatory changes in the placenta or umbilical cord [Antenatal treatment for unknown . The use unknown , 98, alt unknown . Thus, a unknown , and is cal cord , althougcal cord , 87, 88.cal cord . Some cacal cord , 71. Tracal cord . Transabcal cord , 101. Thcal cord .Candida chorioamnionitis may manifest as preterm labor, pPROM, or cervical incompetence without fever. Therefore, Candida chorioamnionitis should be considered in pregnant women with these symptoms, even in the absence of fever, especially in those with early gestation with a retained IUCD, pregnancy after IVF, a history of amniocentesis, or cervical cerclage and preterm delivery. The preterm birth and fetal/neonatal mortality rates are high, and antenatal treatment has yet to be established."} +{"text": "In 1988, when an estimated 350,000 cases of poliomyelitis occurred in 125 countries, the World Health Assembly resolved to eradicate polio globally. Transmission of wild poliovirus (WPV) continues uninterrupted in only three countries through routine immunization services was 85% in 2016 (the most recent year for which data are available). World Health Organization (WHO)/United Nations Children\u2019s Fund estimates for Pol3 coverage in 2016 were 73% in the African Region, 92% in the Region of the Americas, 80% in the Eastern Mediterranean Region, 94% in the European Region, 87% in the South-East Asia Region, and 95% in the Western Pacific Region, with heterogeneity in coverage among countries in all regions.Following certification of the eradication of WPV type 2 (WPV2) in 2015, a global, synchronized withdrawal of trivalent OPV , and switch to bivalent OPV , was completed by the end of April 2016 were conducted in five WHO regions, during which approximately two billion total OPV and IPV doses were administered , includiIn 2017, 172 SIAs were conducted in five WHO regions, during which approximately 1.79 billion total OPV and IPV doses were administered, including 1,110,923,756 (62%) doses administered during national immunization days, 672,091,158 (38%) during subnational immunization days, and 5,696,917 (0.3%) during mop-up activities. Of the administered doses, 95% were bOPV, 3.9% were mOPV2, 0.5% were IPV plus bOPV, and 0.2% were IPV alone.Surveillance for acute flaccid paralysis (AFP) is the means of detecting polio cases caused by WPV or cVDPV, confirmed by stool specimen testing through the Global Polio Laboratory Network. The performance of AFP surveillance is assessed through two main indicators: sensitivity and completeness of case investigation. An annual nonpolio AFP rate of \u22651 case per 100,000 population aged <15 years for countries in the WHO regions certified as poliofree, or \u22652 for all other countries is considered sufficiently sensitive to detect a case of polio, should it occur. Case investigation is considered to be sufficiently complete if at least 80% of reported AFP cases have adequate stool specimens collected . In 2016, among the four countries reporting polio cases, three met both performance indicators and one (Laos) did not. Among the five countries reporting polio cases in 2017, four met both performance indicators and one (Syria) did not. Although Nigeria and DRC meet AFP surveillance indicators nationally and subnationally in most provinces, both countries are affected by substantial issues in population accessibility and other impediments to AFP surveillance . In 2016, 54% of WPV1 cases in Afghanistan were reported from Paktika province in the southeastern region. In 2017, 50% of WPV1 cases were reported from Kandahar province in the southern region. During January 1\u2013March 30, 2018, seven WPV1 cases were detected , compared with three WPV1 cases detected during the same period in 2017.Pakistan reported a 60% decrease in the number of WPV1 cases, from 20 cases in four districts in 2016 to eight cases in seven districts in 2017. During January 1\u2013March 30, 2018, one WPV1 case was reported , compared with two reported during the same period in 2017. WPV1 continues to be isolated from environmental surveillance sites in five provinces of the country .Nigeria reported four WPV1 cases in 2016. No WPV1 cases were reported in 2017 and none to date in 2018.Countries reporting cVDPV cases and isolations. In 2016, five cVDPV cases were reported from three countries has not been interrupted in Afghanistan, Nigeria, and Pakistan. A global, synchronized switch to bivalent oral poliovirus vaccine was completed in April 2016.Compared with 2016, the number of WPV1 cases overall decreased in 2017. Some transmission of circulating vaccine-derived poliovirus type 2 (cVDPV2) has been identified more than 1 year following the switch to bOPV in 2016.What are the implications for public health practice?Interruption of transmission of WPV1 and of cVDPV2 will require addressing persistent challenges to vaccinating every missed child. Until poliovirus eradication is achieved, all countries must maintain high population immunity and sensitive poliovirus surveillance."} +{"text": "HIV acquisition in pregnancy and breastfeeding contributes significantly toward pediatric HIV infection. However, little is known about how sexual behavior changes during pregnancy and postpartum periods which will help develop targeted HIV prevention and transmission interventions, including pre-exposure prophylaxis (PrEP).Cross-sectional study in HIV-infected and uninfected pregnant and postpartum women in Cape Town, South Africa. Interviewers collected survey data on demographic, sexual behaviors, and alcohol use among pregnant and post-partum women. We report descriptive results of sexual behavior by trimester and postpartum period, and results of multivariable logistic regression stratified by pregnancy status.We enrolled 377 pregnant and postpartum women . During pregnancy, 98% of women reported vaginal sex vs. 35% and 88% during the periods 0\u20136 and 7\u201312 months postpartum, respectively (p<0.05). More pregnant women reported having >1 partner in the past 12-months compared to postpartum women . Sex frequency varied by trimester with greatest mean sex acts occurring during first trimester and >6-months postpartum . Pregnant women had increased odds of reporting condomless sex at last sex and ever having condomless sex in past 3-months adjusting for age, HIV status, and sex frequency compared to postpartum women.We identified that sexual behaviors and risk behaviors were high and changing during pregnancy and postpartum periods, presenting challenges to primary and secondary HIV prevention efforts, including PrEP delivery to pregnant and breastfeeding women. The risk of HIV acquisition during pregnancy remains high in South Africa despite increased access to and initiation of antiretroviral therapy (ART) \u20133, and mHIV-infected pregnant women are at risk of transmitting HIV, not only to their infants, but to their sex partners. In addition, HIV-infected pregnant women are particularly vulnerable to potential re-infection, viremia and sexually transmitted infection (STI) which may increase the risk of both vertical and horizontal HIV transmission \u20138. A recOur study evaluated sexual behaviors across trimester and between pregnancy and postpartum periods among HIV-infected and uninfected women during pregnancy and postpartum to determine risk factors associated with increased HIV acquisition and transmission risk. Those findings have the potential to improve the implementation of counseling, risk reducing messages, and primary and secondary prevention interventions among HIV-exposed HIV-uninfected women who are pregnant, post-partum, or seek to get pregnant in South Africa and beyond.Between July and December 2016, we enrolled consenting pregnant or postpartum women attending primary care services to participate in a 30-minute survey. Women received information about the study during their antenatal or postnatal care visit from the study counselor, who counseled them about the risks and benefits of participating in the study. We selected a convenience sample of 2 to 5 pregnant and post-partum women per day depending on the patient flow and capacity of the counselors. Participants received reimbursement for transportation and a snack . All surveys were conducted in private rooms by trained study counselors in the local dialect, isiXhosa.We enrolled pregnant and postpartum women (child was \u2264 18 months old) who were attending primary care services at a large primary care health facility in Cape Town, South Africa. A study counselor provided information on the study and consented participants who were willing to participate in the 30-minute survey. All consenting mothers participated in an interviewer administered questionnaire which investigated participant and partner demographics, sexual behaviors during and after pregnancy, and alcohol use during pregnancy. Inclusion criteria included: (1) \u226518 years old, (2) seeking antenatal care in a health facility or post-natal mothers with infants 6\u201318 months old), (3) willingness to participate in the study (approximately 30-minute quantitative interview. Exclusion criteria included: (1) younger than 18 years old, (2) not pregnant, (3) not during post-natal period (with infant >18-months old), (4) not willing to participate in the study. Any ethnic or language group were eligible to participate, as long as they could provide informed consent.We received institutional review board approval from University of Cape Town and University of Los Angeles, California. Interviews were held in private rooms with a closed door at the clinic to ensure that privacy is protected. All study tools were coded and anonymous. Study counselors were trained on how to consent patients, and how to minimize undue influence using non-judgmental tones and probing questions to preface each section of the survey and encourage honest responses. All study staff were monitored regularly by the researcher teama priori covariates including mother\u2019s age, relationship status and education. Separate analyses were performed for pregnancy vs. postpartum, and HIV-infected vs. uninfected women. Data analysis was carried out using STATA/SE statistical software package version 14.0 .We describe continuous variables as means with standard deviations where normally distributed, and as medians and inter-quartile ranges (IQR) if non-normally distributed. Binary variables were described using frequencies and percentages. Logistic regression modelling was used to analyze risk factors of HIV acquisition and transmission. We created multivariable models controlling for Exposures: maternal age, maternal and paternal HIV status, stage of pregnancy (self-reported), stage of postpartum period , employment status, cohabitation status, number of previous pregnancies, number of live children, and alcohol use during pregnancy , including quantity of alcohol use and what quantified a drink .Outcomes: condomless sex with partner at last sex act, frequency of sex (and condomless sex) during those periods, any condomless sex during pregnancy, frequency of sex acts per month during and after pregnancy, having a partner of unknown serostatus, and multiple partners in year prior to study enrollment.We enrolled 212 pregnant women and 165 postpartum women, of which 40% were HIV-infected (37% of pregnant women and 44% of postpartum women). Median age was 28 years . Overall fewer than half of women were married or cohabiting with the father of the index pregnancy/child (48% of pregnant women vs. 40% of postpartum women) and more HIV-infected pregnant women reported being married or cohabiting more than HIV-uninfected women (56% vs. 44%). More pregnant women reported not knowing the serostatus of the father of the index pregnancy/child (44% vs 32% of postpartum women) and fewer reported being serodiscordant with their father of the index pregnancy/child (7% vs. 10% respectively). HIV-uninfected women reported being in sero-concordant relationships more than HIV-infected women (58% of HIV+ pregnant women and 73% of postpartum HIV+ women). Two-thirds of women reported being unemployed, higher among postpartum vs. pregnant women . Overall, 33% of women did not want to get pregnant and 7% were unsure with no difference by serostatus. Twenty-nine percent of pregnant women reported any alcohol use during pregnancy, and 27% of women reported drinking alcohol 4 or more times a month and 2% reported drinking 2 or more times a week (no different by serostatus) .During pregnancy, 98% women reported vaginal sex (n = 369 of 376 women)), 23% female to male oral sex (n = 86), 21% male to female oral sex (n = 79), and 8% anal sex (n = 30). Though 98% of women reported vaginal sex during pregnancy, of the 165 postpartum women, 35% reported vaginal sex 0 to 6-months after birth (n = 58) and 88% of women reported sex 7 to 12-months after birth (n = 145). Most of the postpartum women reported having sex after giving birth, 8% reported resuming postpartum sex within 30-days of giving birth (n = 13), 10% reported resuming sex 1-2-months after birth (n = 17), 46% reported resuming sex 2-4-months after birth (n = 76), and 37% reported resuming sex later (\u22655-months postpartum) (n = 61). About half of the postpartum women reported using a condom with first postpartum sex . Overall, 15% of women reported having sex with another partner who was not the father of the index pregnancy/child in the past 12-months (n = 58), including 18% of pregnant women (n = 37) and 13% of postpartum women (n = 21). In all women who reported sexual activity (both pregnant and postpartum women), sex frequency per month varied by trimester with greatest mean sex acts occurring during first trimester (mean sex act = 12.8 in the first trimester vs. 8 in the second trimester and 4.2 in the third trimester) and increased again in postpartum period (mean sex acts = 7.2 from 0\u20136 months and 17 in 7\u201312 months) .HIV-infected pregnant women were slightly older than HIV-uninfected women and reported having no relationship with the father of their child more than HIV-uninfected pregnant or postpartum women (13% vs. 6% in pregnant women and 20% vs. 9% in postpartum women). HIV-infected pregnant women reported being employed 31% vs. 42% of HIV-uninfected women. There was no difference in alcohol use reporting by HIV status. Condom use at last sex was higher in HIV infected pregnant women (36%) and postpartum women (55%) compared with HIV-uninfected pregnant women (11%) and postpartum women (37%). HIV-infected women reported less anal sex in pregnancy (3%) and postpartum (8%) vs. HIV-uninfected pregnant (8%) and postpartum (13%) women. Approximately 21% of pregnant and postpartum women reported male-to-female oral sex Half of the pregnant and postpartum women interviewed reported sex within the past week before study enrollment and 69% reported condomless sex at last sex . Over 70% of pregnant or postpartum women who reported anal sex also reported condomless sex. More pregnant women reported having >1 sex partner compared to postpartum women (18% vs. 13% of postpartum women). Further, 36% of women suspected their partners of having other sex partners, and 24% were unsure whether their partner had other partners. Similarly, condom use varied by trimester, postpartum period and serostatus .In multivariable models, pregnant women had increased odds of reporting condomless sex at last sex during pregnancy and ever having condomless sex during pregnancy/postpartum period compared to postpartum women, adjusting for age, HIV status and relationship with partner. Pregnant women had increased odds of reporting heavy alcohol use (\u22655 drinks on more than one occasion) compared with postpartum women adjusted for age and HIV status .Our study identified behavioral risk for HIV transmission (to sex partners and infants) and acquisition during pregnancy and postpartum periods including heavy alcohol use, multiple partners, frequent condomless vaginal and anal sex with serodiscordant partners, and partners of unknown serostatus. Sexual risk behaviors changed significantly across pregnancy and postpartum periods. Reported sex frequency was highest during the first two trimesters of pregnancy and lowest for the third trimester and the first 6-months post-birth, but increased again after 6-months postpartum. Further, reported condomless sex was highest during pregnancy and lower during postpartum sex, which may reflect the desire to prevent pregnancy. Importantly, less than half of pregnant and postpartum women reported being married or cohabiting with the father of the index pregnancy/child, and 39% of women did not know their partner\u2019s status and 15% reported more than one partner. Couple HIV testing and male partner HIV counseling and testing is important in the context of pregnant women because of the increased risk of HIV acquisition in pregnancy and risk of MTCT following seroconversion during pregnancy and breastfeeding periods. South Africa has several interventions to increase male testing and couples counseling and testing including self-testing and partner notification. Further, lack of marital or cohabiting relationship combined with multiple partners and lack of knowledge of partner\u2019s serostatus have implications for the effectiveness of PMTCT programs, including regular HIV testing and condom promotion.Our study demonstrated that among African pregnant and postpartum women sexual behaviors and risk changed significantly between trimester and between pregnancy and postpartum periods , 17\u201319. Our study demonstrated that alcohol use in pregnancy was high (~30%) compared to other studies among pregnant African women. Further, 6% of women reported heavy or binge drinking, including consuming alcohol 6+ times in one occasion 2 or more times per week. Those results are important given the association of alcohol use and HIV acquisition in women . One-fifFor HIV-infected women, at-risk sex was reported in pregnancy and postpartum periods including multiple partners, condomless vaginal and anal sex, and heavy alcohol consumption. Only 56% of HIV-infected pregnant women were cohabiting or married, 13% were not in a relationship, and 18% reported having more than 1 sex partner in the past 12-months. Almost half of HIV-infected women did not know the serostatus of her partner and 18% were in serodiscordant relationships. Despite this lack of knowledge and serodiscordance, only 36% of women reported using a condom at last sex. Prior studies have demonstrated the risk of STIs and viremia during pregnancy on vertical HIV transmission [Our study was cross-sectional, so it did not allow us to study the same women across time. We used self-reported data that may be biased because of recall or respondent bias, and further research is needed to collect biomarkers to validate sex behavior and substance use among pregnant and breastfeeding women.Despite these limitations, as efforts to eliminate vertical transmission intensify, it will become increasingly important to prevent primary HIV acquisition before (during peri-conception), during, and after pregnancy (during breastfeeding exposure). In addition, interventions are needed to prevent HIV transmission to sex partners during and after pregnancy. Interventions such as repeat HIV testing during antenatal and postnatal visits (including immunization visits), testing pregnant and breastfeeding women for acute HIV testing, testing male partners and couples testing , and conPregnant and breastfeeding women are at risk of HIV acquisition, and HIV acquisition currently significantly increases the probability of mother to child transmission of HIV. Our study identified that sex frequency, condomless sex, heavy alcohol use, and multiple partners varied across pregnancy and postpartum periods. Changing sexual risk presents previously unrecognized challenges to prevention efforts, including PrEP delivery. Access to female controlled interventions like PrEP, for which use may vary depending on sexual activity, is necessary."} +{"text": "Rural populations in the United States have well documented health disparities, including higher prevalences of chronic health conditions , and the U.S. territories. BRFSS, designed to provide national and state-level estimates, collects data on health-related risk behaviors and chronic health conditions. Among the 2015 BRFSS respondents surveyed in the 50 states and DC, complete information on age, county, and arthritis diagnosis was available for 426,361 (98.2%). The median combined response rate for the 2015 BRFSS was 47.2% and ranged from 33.9% in California to 61.1% in Utah.Counties were classified into six urban-rural categories using the National Center for Health Statistics 2013 Urban-Rural Classification Scheme for Counties,Unadjusted overall, age-specific, and age-standardized prevalence with CIs were estimated for arthritis and AAAL by urban-rural categories. Age-standardized prevalence by urban-rural categories was further stratified by selected demographic and health characteristics. Estimates were age-standardized to the 2000 U.S. standard population aged \u226518 years using three age groups .In the most rural areas (noncore) nearly 1 in 3 adults reported having doctor-diagnosed arthritis . Age-speAAAL affected about half of adults with arthritis in all urban-rural categories; unadjusted overall prevalence ranged from 47.8% to 55.3% . Age-speIn 2015, rural U.S. residents experienced a high prevalence and negative impact of arthritis. In the most rural areas, nearly 1 in 3 adults had arthritis and among adults with arthritis, approximately half reported being limited by arthritis. Prevalence of arthritis and AAAL was particularly high among rural residents with a functional or work disability. Rural populations might have higher prevalence of arthritis and AAAL because of recognized rural risk factors including older age, obesity, and lower socioeconomic status services.The findings in this study are subject to at least four limitations. First, arthritis is self-reported and the diagnosis was not confirmed by a health care professional; however, this case definition has been validated for public health surveillance report having a diagnosis of arthritis, and the prevalence of arthritis-attributable activity limitation has increased 20% from 35.9% in 2002 to 42.8% in 2015.In rural areas, arthritis affects nearly 1 in 3 adults. Rural residents with arthritis are likely to be limited by their arthritis, with approximately half reporting arthritis-attributable activity limitation. In rural areas, arthritis prevalence followed patterns previously reported for all adults with arthritis: higher prevalence among women, older adults, smokers, adults with less education, adults who are less physically active, or adults with higher body mass index.Because of the high prevalence of arthritis in the rural adult population, rural residents should be targeted for interventions including physical activity and self-management education programs that help adults with arthritis manage their condition and reduce symptoms. Health care providers and community organizations can help residents participate in these helpful interventions."} +{"text": "To develop cancer antigen-targeted immunotherapeutic strategies for malignant pleural mesothelioma (MPM), we investigated the individual and coexpressions of the cancer-associated antigens mesothelin (MSLN), cancer antigen 125 (CA125), and Wilms tumor 1 (WT1) in both epithelioid and non-epithelioid MPM.All available hematoxylin and eosin-stained slides from patients who were diagnosed with MPM (1989-2010) were reviewed. We constructed tissue microarrays from 283 patients . Intensity and distribution for each antigen were assessed by immunohistochemistry.Positive expression of MSLN, CA125, and WT1 were demonstrated in 93%, 75%, and 97% of epithelioid MPM cases, and 57%, 33%, and 98% of non-epithelioid MPM cases, respectively. Triple- and double-positive antigen coexpressions were demonstrated in 72% and 23% of epithelioid MPM cases and 29% and 33% of non-epithelioid MPM cases, respectively. Complete absence of expression for all three antigens was demonstrated in <2% of MPM cases. More than two-thirds of MPM cases had \u226550% distribution of MSLN-positive cells and, among the remaining third, half had \u226550% distribution of WT1-positive cells. CA125/MSLN coexpression was observed in more than two-thirds of epithelioid MPM cases and one-third of non-epithelioid MPM cases.A limited number of cancer-associated antigens can target almost all MPM tumors for immunotherapy. Malignant pleural mesothelioma (MPM) is an aggressive malignancy with a median survival of 9 to 12 months , its benFor other thoracic malignancies, such as lung cancer, variable driver mutations have been discovered and corresponding targeted molecular agents have been applied in clinical practice. Recent comprehensive genomic analysis of transcriptomes and exomes from patient MPM samples have identified significantly mutated genes, recurrent mutations, gene fusions, and splicing alterations . HoweverDespite poor prognosis for patients with MPM, tumor-infiltrating immune cells have been investigated and have been shown to be prognostic indicators \u201315. ReceMSLN is overexpressed in a broad spectrum of solid tumors including mesothelioma and lung cancer \u201324. Our CA125 overexpression was initially recognized in ovarian cancer and has recently been reported in several other cancers such as pancreatic , 27. PriWT1 is a nuclear protein that is involved in tumor growth and overexpressed in multiple malignancies , 39. SinTo develop personalized immunotherapeutic strategies for the treatment of MPM, we aimed to investigate the individual and coexpressions of MSLN, CA125, and WT1 in both epithelioid and non-epithelioid MPM. Heterogeneity of cancer-associated antigen expression in solid tumors allows for therapy resistance via antigen escape and is a known challenge for immunotherapies \u201345. In aAmong all 283 patients, 234 patients were diagnosed with epithelioid mesothelioma, 26 with biphasic mesothelioma, and 23 with sarcomatoid mesothelioma. Of the 234 patients with epithelioid mesothelioma, 39 patients were classified as having pleomorphic mesothelioma. The median age of patients with epithelioid mesothelioma and non-epithelioid mesothelioma (biphasic or sarcomatoid) were 63 years and 66 years range, 41-79 years), respectively. The majority of patients were male , positive for asbestos exposure (42% and 53%), smokers (58% and 57%), never received induction chemotherapy before surgery (70% and 80%), and were diagnosed with late-stage disease , 226 (97%), and 226 (97%) cases of epithelioid MPM, respectively. For non-epithelioid MPM patients, evaluation of all 3 antigens was completed for 49 (100%) cases. Among epithelioid MPM cases, MSLN expression was positive in 93%, CA125 expression was positive in 75%, and WT1 was positive in 97% of cases. Distribution \u226550% of MSLN-, CA125-, and WT1-positive tumor cells were observed in 84%, 20%, and 72% of epithelioid MPM cases, respectively. Antigen expression intensity was: (1) strong in 35% and moderate in 34% of cases for MSLN expression; (2) strong in 9% and moderate in 27% of cases for CA125 expression; and (3) strong in 31% and moderate in 43% of cases for WT1 expression epithelioid MPM cases and 49 (100%) non-epithelioid MPM cases. Triple antigen coexpression was demonstrated in 72% of epithelioid MPM cases and double antigen coexpression was demonstrated in 23% of epithelioid MPM cases. Triple and double antigen coexpressions were demonstrated in 29% and 33% of non-epithelioid MPMs, respectively. Only 1% of epithelioid and 2% of non-epithelioid MPM cases demonstrated complete absence of expression of any of the three antigens . Subsequently, patients with MSLN distribution <50% were sorted by WT1 distribution. The blue background represents patients whose tumors had \u226550% MSLN distribution and the green background represents patients whose tumors had both <50% MSLN distribution and \u226550% WT1 distribution. Patients whose tumors had no antigen with \u226550% distribution have no background color associated with them.For non-pleomorphic epithelioid MPM cases (n = 185), 161 (87%) patients had \u226550% MSLN distribution and 18 (10%) patients had \u226550% WT1 distribution without \u226550% MSLN distribution. For pleomorphic epithelioid MPM cases (n = 35), 24 (69%) patients had \u226550% MSLN distribution and 3 (9%) patients had \u226550% WT1 distribution without \u226550% MSLN distribution. For biphasic MPM cases (n = 26), 9 (35%) patients had \u226550% MSLN distribution and 8 (31%) patients had \u226550% WT1 distribution without \u226550% MSLN distribution. For sarcomatoid MPM cases (n = 23), 3 (13%) patients had \u226550% MSLN distribution and 7 (30%) patients had \u226550% WT1 distribution without \u226550% MSLN distribution. For all patients (n = 269), 197 (73%) patients had \u226550% MSLN distribution and 36 (13%) patients had \u226550% WT1 distribution without \u226550% MSLN distribution.In our study, we demonstrated that >98% of epithelioid and non-epithelioid MPM cases had positive expression of at least one of the three cancer-associated antigens. Positive expression included strong antigen expression, high frequency of double and triple antigen expressions, and high distribution of antigen-positive tumor cells. These findings, combined with the survival benefits shown in MPM patients with MSLN-, CA125-, and WT1-specific immune responses, provide the rationale for the development of targeted therapies. Additionally, the expression of these three antigens on normal tissue is very low , 34, 41 Previous studies have reported that non-epithelioid subtypes were associated with worse prognosis compared with the epithelioid subtype in patients with MPM who were with surgery . AdditioThe pathologic and prognostic role of CA125 in MPM has not been elucidated. Previous studies have suggested that there is an interaction between MSLN and CA125 that may affect solid tumor metastatic potential \u201331. TherOne limitation of our present study is the use of a tissue microarray (TMA) that may not identify tumors that are focally positive on whole-tissue block staining. Despite this, we selected six TMA cores from six different areas in each tumor. We think that the frequency of each antigen overexpression and the distribution of antigen-positive cells in each patient will not be significantly changed if a whole-tissue block were used to confirm these results.In conclusion, more than two-thirds of MPM patients have \u226550% distribution of MSLN-positive cells within whole tumor cells and, among the remaining one-third, half have \u226550% distribution of WT1-positive cells. CA125/MSLN coexpression was observed in more than two-thirds of epithelioid and one-third of non-epithelioid MPM patients. These results provide the rationale for developing personalized immunotherapeutic strategies for MPM patients that target these three cancer-associated antigens.The current retrospective study was approved by the Institutional Review Board (WA-0436-10) of Memorial Sloan Kettering Cancer Center (MSK). We reviewed all 620 patients who were diagnosed with MPM at MSK between 1989 and 2010. From this cohort, we reviewed 395 MPM cases with available hematoxylin and eosin (H&E)-stained slides. All slides were re-reviewed by two pathologists; this yielded 301 epithelioid, 59 biphasic, and 35 sarcomatoid MPM cases. Of these, 283 had tumor blocks available for construction of TMAs. Clinical data were collected from the prospectively maintained MPM database.Histologic evaluation was performed using an Olympus BX51 microscope with a standard 22-mm diameter eyepiece. All tumors were classified as either epithelioid, sarcomatoid, or biphasic according to the 2015 World Health Organization classification . For epiFormalin-fixed, paraffin-embedded tumor blocks were used for construction of TMAs. For epithelioid tumors, six to nine representative tumor areas were marked on H&E-stained slides. For biphasic tumors, six tumor areas were selected from a predominantly morphologic sarcomatoid lesion. Cylindrical 0.6 mm tissue cores were arrayed from the marked areas of corresponding paraffin blocks onto a recipient block using an automated tissue arrayer ; this resulted in five TMA blocks.Sequential paraffin 4 \u03bcm-thick sections were cut from the TMA blocks and deparaffinized. Sections were stained using a Ventana Discovery XT automated immunohistochemical stainer for MSLN , 23, CA1CA125 and MSLN expressions were mainly observed in the membrane of tumor cells and WT1 expression was observed in the nucleus. We evaluated the overexpression of these antigens by intensity of antigen expression and distribution of positive cells. The intensity of antigen expression for each core was determined by the pathologist as follows: 0 for no expression; 1 for weak; 2 for moderate; and 3 for strong. The intensity scores of six cores for each patient were averaged and rounded up to the next integer to obtain a mean intensity grade for each patient: 0 for no expression; 1 for weak; 2 for moderate; and 3 for strong. The distribution of antigen-expressing positive cells was determined as a percentage of the total number of cells, which is estimated in 10% increments. The antigen distribution of six cores for each patient was calculated and rounded up to the next 10% increment ."} +{"text": "Saline-irrigated radiofrequency ablation, which has been widely used for surgicaltreatment of atrial fibrillation in recent years, is 80-90% successful in achievingsinus rhythm. In our study, our surgical experience and mid-term results in patients whounderwent mitral valve surgery and left atrial radiofrequency ablation wereanalyzed.Forty patients underwent surgery for atrial fibrillation associated with mitral valvular disease. Allpatients manifested atrial fibrillation, which started at least six months before thesurgical intervention. The majority of patients were in NYHA classIII; 34 (85%) patients had rheumatic heart disease. In addition to mitral valve surgeryand radiofrequency ablation, coronary artery bypass, DeVega tricuspid annuloplasty, leftventricular aneurysm repair, and left atrial thrombus excision were performed. Followingdischarge from the hospital, patients' follow-up was performed as outpatient clinicexaminations and the average follow-up period of patients was 18\u00b13 months.st year follow-up examination.While the incidence of sinus rhythm was 85.3% on the first postoperative day, it was80% during discharge and 71% in the 1Radiofrequency ablation is an effective method when it is performed by appropriatesurgical technique. Its rate for returning to sinus rhythm is as high as the rate ofconventional surgical procedure. The prevalence of AF wasreported as 0.16% in the 40-59 age group, and 2.16% in patients over 60 years of age, inTurkey.Atrial fibrillation (AF) is an arrhythmia observed in 0.4-1% of the population, with thisrate rising up to 10% in advanced ages (over 65 years of age). It has an incidence of 40-60%in patients with mitral valvular disorders, and 5-10% in patients with aortic valvulardisorders,4. However, since the procedureis technically difficult, the cardiopulmonary bypass and operation times are long, and therisks for complications such as postoperative bleeding are high, thus, simpler and easiertechniques, which are developed by using different energy sources, have gained widespreadapplicability. Irrigated radiofrequency ablation is one of the frequently implementedablation methods, and it is used as monopolar and bipolar radiofrequency (RF) ablation inour clinic. In this study, our aim was to analyze our surgical experience and results inpatients who had undergone mitral valve surgery and left atrial RF ablation.Medical treatment may be insufficient in controlling the rate of AF, or intolerance maydevelop against antiarrhythmic agents, due to their side effects. Additionally, AF is knownto reduce the life quality of patients due to causes such as heart failure, hemodynamicinstability, palpitations, and thromboembolic events. For this reason, in patients with AFundergoing openheart surgery, surgical ablation is performed in order to provide sinusrhythm (SR) and avoid AF-related complications that may develop in the postoperative period.Surgical ablation techniques intend to achieve SR by terminating AF, together with regainingatrioventricular synchronization and atrial contractility function. The method, described byDr. Cox, in 1980, and developed as 'Maze I' thereafter, is the gold standard in surgicaltreatment of AF, with a success rate of 99% todayForty patients underwentsurgery for AF associated with mitral valvular disease. All patients manifested AF, whichstarted at least six months before the surgical intervention. In addition to mitral valvesurgery and RF ablation, coronary artery bypass, DeVega tricuspid annuloplasty, leftventricular aneurysm repair, and left atrial thrombus excision were performed. Withoutconsidering performed surgical procedures, irrigated-monopolar RF ablation was used in 35patients and irrigated-bipolar was used in five patients. The performed surgical procedureswere as follows: mechanical valve replacement in 10 patients, bioprosthetic mitral valvereplacement in 5 patients, mechanical mitral valve replacement and tricuspid commissurotomyin 2 patients, mechanical mitral valve replacement and left atrial thrombectomy in 3patients, bioprosthetic mitral valve replacement and DeVega tricuspid annuloplasty and leftatrial thrombectomy in 1 patient, bioprosthetic mitral valve replacement and splenectomy in1 patient, bioprosthetic mitral valve replacement and tricuspid annuloplasty in 7 patients,mechanical mitral valve replacement and tricuspid annuloplasty in 3 patients, single-vesselcoronary artery bypass and mechanical mitral valve replacement in 2 patients, triple-vesselcoronary artery bypass and bioprosthetic mitral valve replacement and tricuspid annuloplastyin 1 patient, mechanical mitral valve replacement and aortic wrapping in 1 patient,mechanical mitral valve replacement and Bentall procedure in 1 patient, bioprosthetic mitraland aortic valve replacement in 1 patient, mechanical aortic and mitral valve replacement in1 patient.In the preoperative period, the left atrium (LA) size was measured as 53.5\u00b16.2 mm,in average (range 33-63 mm); in seven patients, LA was 60 mm or over. The preoperativepulmonary artery pressure (PAP) was 49.8\u00b116.4 mmHg, in average (range 30-100 mmHg);in 57 (72.2%) patients, PAP was 40 mmHg or over. In the preoperative period, EuroSCORErevealed that the standard EuroSCORE 2 value was 2.9\u00b12.4, in average (range 0-9), andthe logistic EuroSCORE 2 value was 3.1\u00b12.1%, in average (range 0.8%-16.8%).In one patient, mitral valve replacement and splenectomy were performed due to infectiveendocarditis.TM ablation system composed of a power generator and an ablation clamp . In two patients in whom theheart rate slowed down, amiodarone administration was terminated and temporary pacemakersupport was provided. In patients in whom PR interval was prolonged in electrocardiography(ECG), the infusion dose of amiodarone was reduced. Patients who received inotropic agentsfor any reason (even with low-dose or short-term) were considered as supported byinotropes.rd month of thepostoperative period, besides echocardiography and ECG controls, 24-hour Holter ECG was alsoperformed. All antiarrhythmic agents were discontinued in patients who had sinus rhythm inthe control examination performed in the 3rd month.In all patients, amiodarone treatment was used for three months postoperatively. Followingsurgery, with the aim of rhythm control, beta-adrenergic blockers (metoprolol) or digoxinwas added to the treatment of patients. The first evaluations of patients' rhythm statuswere made by ECG during their ICU follow-up. Following discharge from the hospital, theywere followed-up by control examinations in the outpatient clinic. Patients were followed-upby ECG in the first week and in the first month. In the 3P value of less than 0.01.Kaplan-Meier analysis was performed to determine the probability of survival, andsurvival curves were compared using the log-rank test. All values were considered to bestatistically significant with a Forty patients underwent surgery for AF associated with mitral valvular disease. None of the patientsrequired permanent pacemaker. The average duration of perfusion and cross-clamping time were111\u00b110.2 min (range 54-159 min) and 81.3\u00b119.6 min (range 33-139 min),respectively. The average durations for ICU and hospital stay were 1.9\u00b11.3 days(range 1-11 days) and 9.6\u00b12.5 days (range14-21 days), respectively.P=0.50). Of those patients, many had recurrence of atrialtachyarrhythmias within the first or second week after the Maze procedure. The New YorkHeart Association (NYHA) functional class had improved by the last follow-up as comparedwith the preoperative class in all patients Immediately after the operation, SR was restored in 85.3% of the patients patients and AF was identified in 12 (30%) patients in their3. There has been a demandfor less invasive procedures, such as manipulation only in the pulmonary veins andintraoperative ablation of atrial walls with alternative energy sources , and thoracoscopy procedures using RF and ultrasoundcatheters from the epicardium in on-pump surgeries. With ensuring SR and effective atrial contraction, myocardialremodeling and heart failure due to tachycardia are prevented. Forlani et al. reported that ensuring SR increased the survival rate and decreased themorbidities significantly in patients. For this reason, in patients having chronic AFrhythm, if cardiac surgery is planned, addition of ablation treatment is suggested. On theother hand, AF, which is present approximately in 5% of patients with coronary arterydisease, may continue following recovery of myocardial ischemia. Since AF was shown to reduce the long-term survival ratefollowing coronary bypass procedures, surgical ablation is recommended in thesepatients. AF ablation has shown arapid progress by utilization of various energy sources such as RF, microwave, laser,ultrasound, and cryoablation. Nevertheless, the success rates vary between 76% and 92% insurgical ablation methods excluding Maze. There are many studies comparing the RF ablation treatment of AF withpatients in whom this procedure was not performed. Khargi et al. reported that at the end of the first year, 80% of patientsin whom RF was performed and 20% of patients in whom only mitral valve repair was performedhad SR. Melo et al. found that, in thefirst month, SR was present in 7% of patients in whom RF ablation was not performed.Jessurun et al. found sinus,paroxysmal AF and chronic AF rhythms preoperatively in 162 patients, 71% of patients withSR, 34% of patients with paroxysmal AF, and 4% of patients with chronic AF were in SR. Brick& Braile analyzing studies withimmediate results (n=5), the percentage of return to SR ranged from 73% to 96%, while thosewith long-term results (n=20) (from 12 months on) ranged from 62% to 97.7%. Even withpostoperative antiarrhythmic drug treatment and electrical cardioversion, returning to SRwas found below 25% in the long-term follow-up. Early postoperative AF originates from delayed healing processes ofatrial lesions, inflammatory processes related to the procedure, and tiny macro re-entries,which have responded perfectly to the antiarrhythmic treatment; for this reason, amiodaronetreatment with a dose of 200 mg/day is used during the first postoperative three months.In patients with chronic AF, the rate of returning to SR following mitral valve operationis under 10% showed that thromboembolic complications were met with lessfrequency in AF patients who underwent Cox-Maze operation, when compared to the patients whodid not undergo this operation. In our study, also, no thromboembolic event was observed inany of the patients.One of the most important purposes of returning the patients who were in AF preoperativelyto SR is to provide atrial contraction and atrioventricular electromechanical synchrony, andadditionally to reduce the risk of cardiac embolus. Waldo et al.. Permanent pacemaker requirement is considered more frequentin patients having large LA diameter and sick sinus syndrome in the preoperative period.Postoperative drug treatments were mainly for rhythm control. We observed that in patientsthat SR was acquired, life quality during their daily living improved with medicaltreatment. The heart rates of patients having AF rhythm were observed to be under controland episodes of disturbing tachycardia were not present.It is suggested that the variations observed in results are related to patientcharacteristics, ablation lines, and technical variables. In some patients, permanentpacemaker may be required following ablation procedure. The frequency of requirement forpacemaker generally varies between 5-10% in publicationsIn conclusion, the early postoperative results of monopolar and bipolar RF ablation inpatients undergoing mitral valve surgery were successful in terms of providing atrialtransport function and it was observed that these procedures did not lead to additionalcomplications in the postoperative period. Therefore, we suggest that, in patients with AFwho are planned to undergo mitral valve surgery, RF ablation for AF is an effective andreliable method for eliminating postoperative risks related to AF and for increasingbenefits of surgery."} +{"text": "Fiscal interventions are promising strategies to improve diets, reduce cardiovascular disease and diabetes , and address health disparities. The aim of this study is to estimate the impact of specific dietary taxes and subsidies on CMD deaths and disparities in the US.Using nationally representative data, we used a comparative risk assessment to model the potential effects on total CMD deaths and disparities of price subsidies on fruits, vegetables, whole grains, and nuts/seeds and taxes on processed meat, unprocessed red meats, and sugar-sweetened beverages. We modeled two gradients of price-responsiveness by education, an indicator of socioeconomic status (SES), based on global price elasticities (18% greater price-responsiveness in low vs. high SES) and recent national experiences with taxes on sugar-sweetened beverages (65% greater price-responsiveness in low vs. high SES).Each price intervention would reduce CMD deaths. Overall, the largest proportional reductions were seen in stroke, followed by diabetes and coronary heart disease. Jointly altering prices of all seven dietary factors would prevent 23,174 CMD deaths/year, corresponding to 3.1% (95% UI 2.9\u20133.4) of CMD deaths among Americans with a lower than high school education, 3.6% (95% UI 3.3\u20133.8) among high school graduates/some college, and 2.9% (95% UI 2.7\u20133.5) among college graduates. Applying a 30% price change and larger price-responsiveness (65%) in low SES, the corresponding reductions were 10.9% (95% UI 9.2\u201310.8), 9.8% (95% UI 9.1\u201310.4), and 6.7% (95% UI 6.2\u20137.6). The latter scenario would reduce disparities in CMD between Americans with lower than high school versus a college education by 3.5 (95% UI 2.3\u20134.5) percentage points.Modest taxes and subsidies for key dietary factors could meaningfully reduce CMD and improve US disparities.The online version of this article (doi:10.1186/s12916-017-0971-9) contains supplementary material, which is available to authorized users. Cardiovascular disease (CVD) remains the leading cause of disability and death in the US and globally , with asA suboptimal diet is a major cause of CMD . Among sWe utilized nationally representative US data in a comparative risk assessment framework. We incorporated national data from 2012 on the consumption of selected food items, by age, sex, and SES; estimates of etiological effects of these foods on CMD, by age; observed national CMD deaths, by age, sex, and SES; and estimated impact of pricing changes on dietary habits, by SES. Because data on income is not routinely collected in US mortality datasets, we used educational attainment as a measure of SES. Using the National Health and Nutrition Examination Survey (NHANES) , the incCurrent dietary intakes were obtained from NHANES , combiniWe defined seven foods based onWe obtained the impact of pricing changes on dietary intakes from a meta-analysis of prospective observational and interventional studies , allowinFinally, we considered a 10% price change in taxes or subsidies and, similarly, a higher scenario of a 30% price change. We modeled the direct effects of the price changes at the consumer level, rather than the specific policies required to attain them, in order to minimize assumptions in translating the latter to consumer prices.http://www.cdc.gov/nchs/deaths.htm). We excluded foreign residents and those with missing information on age (0.017% of deaths) or educational level (2.1%). We included deaths from coronary heart disease (ICD 10: I20\u2013I25), ischemic stroke , I69.3, G45), hemorrhagic , unidentified and other non-ischemic/hemorrhagic stroke , diabetes mellitus , and hypertensive heart disease (I11). For each stratum, the corresponding size of the US population by age, sex, and educational levle was estimated from the 2012 American Community Survey microdata sample including 2.15 million weighted records [The numbers of disease-specific deaths in 2012 by age, sex, and educational level were obtained from the National Center for Health Statistics Division of Vital Statistics is the RR at dietary intake level x, P(x) is the current stratum-specific distribution of dietary intake, P\u2019(x) is the alternative stratum-specific distribution of dietary intake following the intervention, and m is the maximum dietary intake level.where In addition to the estimation of the effect of individual food targets, we also considered a potential joint effect, for example, as part of a tax-subsidy framework or similar incentive-disincentive system. Because summation of PIFs overestimates their joint effects, the joint impact for multiple dietary changes was estimated within each age-, sex-, and education-specific stratum based on the following formula:PIFjoint is the joint potential attributable fraction, r denotes each individual dietary factor, and R is the number of dietary factors. We recognized that certain dietary intakes may be correlated among individuals within each stratum, which could slightly overestimate the true joint effect. All inputs to the model were prepared using Stata SE version 14, College Station TX, and analyses were conducted using R version 3.1.0 [where on 3.1.0 . A detaiThe selected dietary factors, current consumption levels, price-responsiveness, and estimated etiologic effects are shown in Table\u00a0The estimated number of CMD deaths preventable by each price intervention are shown in Table\u00a0Per year, 111 CMD deaths per million US adults could be potentially prevented by a 10% price change in all seven dietary targets, whereas 303 deaths/million could be potentially prevented by a 30% price change , disparities in CMD deaths were evident was estimated to prevent 9.2% of all CMD deaths. None of the pricing scenarios significantly increased disparities; all would reduce disparities in diabetes deaths and, given a higher SES price-responsiveness, each would also reduce disparities in CHD, and stroke mortality. The largest impact was observed for decreasing prices of fruits and vegetables, and increasing the price of SSBs. By cause of death, reductions in stroke mortality were most effectively achieved by subsidies for vegetables and fruits, and in diabetes mortality by taxes on SSBs. These results are in line with previous modeling studies in South Africa and India, where a 20% SSB tax was estimated to reduce diabetes prevalence by 4% over 20\u00a0years , 34.Many governments have already implemented fiscal measures to increase the price of unhealthy foods. One of the earliest was a 2011 Danish tax on saturated fat, later rescinded in 2013 due to controversy but estimated to have reduced national saturated fat intake by 4% . Taxes eGiven the growing inequities in diet and CMD in the US , our finBoth nutrient- and food-specific taxes could be implemented by policy-makers. A recent report estimated that a sugar (nutrient) tax would have a larger impact on nutrition than a product-specific (SSB) tax, based on the broader base of products influenced by the former . We focuWe modeled final retail price changes of foods, which could be achieved by a range of potential strategies. Lower prices could be achieved by subsidies for agricultural practices, research and development or tax incentives for food manufacturers, retailers, and restaurants, or direct subsidies to wholesalers, retailers, or consumers . In paraOur study has a number of strengths. We used nationally representative datasets on demographics, education, dietary habits, CVD risk factors (blood pressure and BMI), and cause-specific deaths, making our results generalizable to the US adult population. We limited our estimates of etiologic effects to a small number of specific dietary factors with the greatest evidence from meta-analyses, supported by consistency, dose-response, and plausible biology. Our model incorporates stratum-specific heterogeneity in underlying characteristics and intervention effects by age, sex, and education, increasing the validity of our results. We quantified uncertainty using Monte Carlo simulations, increasing interpretability and identifying the range of plausible effects.Potential limitations should be considered. Dietary estimates were based on self-report, which could introduce errors into our estimates. We minimized this by using the average of two 24-h recalls per person and adjusting for both energy intake and within-person variation. The etiologic effect of each dietary factor on CMD was obtained from meta-analysis of mostly prospective observational data, which may be impacted by residual confounding (causing overestimation of effects) and by measurement error and regression dilution bias (causing underestimation of effects). However, these effects are supported by mechanistic evidence as well as a large randomized clinical trial that demonstrated reductions in CVD and diabetes highly comparable to the predicted effects from observational studies . While cStrategies introducing modest price changes on key dietary factors could reduce cardiovascular disease and diabetes burdens and disparities in the US. Policy-based strategies targeting disparities will require considering both baseline dietary habits as well as price responsiveness in specific population subgroups. The findings of our study have broad implications for policy-makers targeting fiscal measures to reduce CMD burden."} +{"text": "To evaluate if the outcomes of IVF/ICSI in frozen-thawed embryo transfer andfresh embryo transfer cycles differ in relation to cleavage and blastocyststages.Retrospective cohort study to compare IVF/ICSI outcomes between fresh embryotransfer and frozen-thawed embryo transfer cycles, according to the stage ofembryo development. Analysis was carried out on 443 consecutive embryotransfer cycles performed between January 1st and December 31st, 2014. Womenaged up to 38 and submitted to embryo transfer cycles with fresh (n = 309)or frozen-thawed (n = 134) embryos at a private center for assistance inhuman reproduction were considered for analysis. Results in each group werestratified according to the stage of embryo development: cleavage stage andblastocyst stage. Main outcome measures were implantation rate, clinicalpregnancy rate, ongoing pregnancy rate and live birth rate per cycle.p= 0.0005); clinical pregnancy rates were 34% and 64% (p =0.0057); the ongoing pregnancy rates were 30% and 61% (p =0.0046) and live birth rates were 28% and 55% (p = 0.0148).There were no significant differences in the rates between cleavage andblastocyst stages in the frozen-thawed group, neither between fresh andfrozen-thawed cleavage embryo transfers nor between fresh and frozen-thawedblastocyst transfers.In the fresh embryo transfer group, for cleavage stage versus blastocyststage, respectively, implantation rates were 22% and 47% (Our results confirm that blastocyst transfer is better than cleavage stage infresh embryo transfer cycles. In frozen-thawed cycles, cleavage orblastocyst stages seem to offer similar reproductive outcomes. In Assisted Reproductive Techniques (ART), successful implantation depends not onlyon embryo quality, but also on endometrial receptivity . The analysis was carried out on 443 consecutive ET cycles performedbetween January 1st and December 31st, 2014. The main outcomes were implantationrate, clinical pregnancy rate, ongoing pregnancy rate and live birth rate percycle.We studied the women aged up to 38 and submitted to ET cycles with fresh (n = 309) orfrozen-thawed (n = 134) embryos at a private center for assistance in humanreproduction. Results in each group were stratified according to the stage of embryodevelopment: cleavage stage (from day 2 to day 4) and blastocyst stage (days 5 and6). The Institutional Clinical Committee approved the study. Patients gave writtenconsent for assisted reproduction technology treatment, and an oral consent wasobtained for confidential data use for research purposes. A specific writteninformed consent was not considered necessary for this study, since the data wasobtained exclusively from patient files, respecting anonymity.p < 0.05 inall analyses.The statistical analysis was performed using GraphPad Prism software, version 5.00. Fisher's exact test was used to compare ratesbetween groups. The level of significance was set at p = 0.0005), respectively; clinicalpregnancy rates were 34% and 64% (p = 0.0057), ongoing pregnancyrates were 30% and 61% (p = 0.0046) and live birth rates were 28%and 55% (p = 0.0148). There were no significant differences inrates between cleavage and blastocyst stages in the frozen-thawed ET group in those cycles may be highly effective inequalizing the results for embryos at any stage of development.There are several factors that explain why supraphysiological steroid levels impairembryo implantation. First of all, controlled ovarian stimulation (COS) leads toadvancement of pinopodes appearance and histological features linked toimplantation, resulting in an embryo-endometrium asynchrony (Another point is the evidence that COS causes deregulation of more than 200 genesrelated to implantation, in comparison to natural cycles. The altered geneexpression profile leads to an aberrant endometrium, which probably impairs theideal intrauterine microenvironment for embryo implantation (Moreover, elevated estrogen concentration may increase uterine contractions. Thiseffect is more important for cleavage ET, since the contractility decreasesprogressively, reaching a nearly quiescent status at the time of the blastocysttransfer (Based on the obtained data, we were not able to find significant differences in ratesbetween fresh and frozen-thawed cleavage ET or between fresh and frozen-thawedblastocyst ET. Previous studies have demonstrated similar results for cleavage stageembryos (The existence of biases related to the retrospective design of our study cannot beexcluded and our results must be considered with caution. Statistical analysisdemonstrated a small but significant difference in the numbers of embryostransferred between frozen-thawed cleavage and blastocyst transfers; thus,implantation rates may be misleading . Also, oBesides, our study design limited exploration of other factors that may influencereproductive outcomes, such as body mass index, etiopathogenic diagnosis ofinfertility, primary versus and secondary infertility, pregnancy in a previous freshcycle, type of luteal support, precocious progesterone elevation.In conclusion, our study suggests that blastocysts are the best option for fresh ET.However, in frozen-thawed ET, no significant differences in reproductive outcomeswere found between cleavage and blastocyst stages."} +{"text": "Genomic sequences are described from five novel viruses and divergent strains of Brejeira and Guaico Culex viruses from mosquitoes collected in Pantanal, Brazil, in 2010. We describe here the genomes of five novel viruses and divergent strains of Brejeira (BRJV) and Guaico Culex (GCXV) viruses isolated from pooled mosquitoes captured with CDC light traps from Pantanal, Mato Grosso do Sul state, in west-central Brazil, in April 2010. Genomic sequences were derived from mosquito cell cultures by Illumina technology 13 Table\u00a0.Culex (Culex) spp. yielded 99% identity among themselves, but 88% to 90% identity with a BRJV isolated in northern Brazil, indicating the detection of a divergent strain of this recently described Negevirus-like virus (Four BRJV isolates from ke virus .Culex (Culex) spp. pool number 407 aligned with coverages from 78% to 87% and identities from 97% to 100% with published sequences. A second isolate from pool number 313, also Culex (Culex) spp., was the same strain, based on partial sequences (data not shown). In Brazil, the first detection of a Jingmenvirus was from tick collections in southeast Brazil, and called Mogiana tick virus . Translated nucleotide identities ranged between 32% and 73% to known viruses. The following abbreviations are suggested for the novel viruses: TERV, OFAV, KADV, KAIV, and GUTV.Mansonia spp. pool aligns with viruses of a newly described genus within Bunyaviridae called Phasmavirus with M\u00e9no virus, recently described within the family Culex (Culex) spp. most closely align with a recently described virus from China called Wuchang Cockroach virus 3. The three isolates of GUTV are 99% identical to each other, whereas KAIV and GUTV are 30% divergent at the nucleotide level. These viruses consistently accompanied isolates of BRJV. Whether the accompaniment of these viruses is coincidence, or they derived from coinfected mosquitoes within each pool, is unknown. However, KAIV and GUTV genomes could in fact be independent genomic segments within a multisegmented genome that includes BRJV.GUTV and KAIV isolated from To evaluate the host range of these virus isolates, attempts to generate cytopathic effect (CPE) were made with human, monkey, frog, bat, mosquito, and tick cell cultures. A clear CPE was observed only in mosquito cells. However, the capacity of these novel viruses to cause CPE in vertebrate and invertebrate cells was not fully evaluated.Pantanal\u2019s biodiversity has recently produced other mosquito-borne viruses, and may be useful for studying virus evolution \u201314.\u2013The sequences have been deposited in GenBank under the accession numbers listed in"} +{"text": "Arthritis is among the most common chronic conditions among veterans and is more prevalent among veterans than nonveterans ,2. ConteBRFSS is an annual, cross-sectional, random-digit\u2013dialed telephone (landline and cell phone) survey of the 50 U.S. states, territories, and the District of Columbia (DC). BRFSS is designed to collect data that are representative of the noninstitutionalized adult civilian population in each state. All analyses used combined 2011, 2012, and 2013 BRFSS data. Median state-specific BRFSS response rates, based on American Association for Public Opinion Research definition no. 4, were 49.7% in 2011, 45.2% in 2012, and 45.9% in 2013.CDC estimated annualized crude and age-specific prevalence of doctor-diagnosed arthritis stratified by veteran status and sex, age-standardized overall and sex-specific prevalence by veteran status across categories of race/ethnicity, highest educational attainment, employment status, income, and body mass index , age-standardized prevalence overall and by sex among veterans for the 50 states, DC, Guam, and Puerto Rico. Data were analyzed using software that accounted for the complex sampling design, including application of sampling weights so that estimates were representative of the noninstitutionalized adult civilian population in each state. Variance was estimated with 95% confidence intervals (CIs) that accounted for the clustered design using the Taylor series linearization method. The 2000 U.S. Projected Population, in three age groups was used for age-standardization.\u2020Veterans had a higher overall prevalence of reported arthritis than nonveterans, 25.6% (CI = 25.2%\u201326.1%) versus 23.6% (CI = 23.4%\u201323.7%). For both men and women, arthritis prevalence was higher among veterans than nonveterans . Among mAmong the 50 states and DC, the median state-specific arthritis prevalence among veterans was 25.4% (range = 19.7% in DC to 32.7% in West Virginia) , Figure.Veterans reported arthritis frequently and more often than nonveterans among both men and women and across all sociodemographic groups. Although a high level of physical fitness and good health are required for entry into military service, traumatic and overuse injuries are common during active duty . A recenOne of the few previous population-based studies of arthritis prevalence among veterans was a small study based on 2010 BRFSS data from men in five states health system services indicated that three in four 77.6% in 2008) had arthritis veterans (40.3% among women and 36.0% among men) but also among younger veterans indicating that arthritis and its effects need to be addressed among male and female veterans of all ages. Reducing the impact of arthritis among younger adults might help to stem its debilitating effects in later life.The findings in this report are subject to at least five limitations. First, arthritis was based on self-report. Although recall bias is possible, a validation study among health plan enrollees found that this definition had a positive predictive value of 74.9% among persons aged 45\u201364 years and a 91.0% positive predictive value among persons ages \u226565 years and is aWhat is already known on this topic?Arthritis is a common chronic condition among veterans, and at least two population-based studies have reported a higher prevalence of arthritis among veterans compared with nonveterans. These arthritis prevalence studies of veterans were conducted before the Persian Gulf War, were small, or examined men only.What is added by this report?To assess the prevalence of doctor-diagnosed arthritis among male and female veterans, CDC analyzed Behavioral Risk Factor Surveillance System survey data from 2011, 2012, and 2013. The analysis found that 25.6% of veterans reported having arthritis (25.0% among men and 31.3% among women) and that prevalence was higher among veterans than nonveterans across most sociodemographic categories. State-specific, age-standardized arthritis prevalence among veterans ranged from 18.8% in Hawaii to 32.7% in West Virginia.What are the implications for public health practice?The high prevalence of arthritis, combined with the large number of persons affected, indicate that strategies are needed to reduce the adverse effects of arthritis. Interventions to improve the quality of life of persons with arthritis include providing access to affordable physical activity and self-management education classes.The contemporary, state-specific arthritis prevalence estimates provided in this report indicate that veterans with arthritis represented a sizeable portion (with a median of approximately one in six) of adults with arthritis in each state. Because most veterans use health systems other than the VA system , strateg"} +{"text": "Whether neutropenia has an impact on the mortality of critically ill cancer patients remains controversial, yet it is widely used as an admission criterion and prognostic factor.Systematic review and meta-analysis. Studies on adult cancer patients and intensive care units were searched on PubMed and Cochrane databases (2005-2015). Summary estimates of mortality risk differences were calculated using the random-effects model.2 = 50%). The admission period was not associated with how neutropenia affected mortality. Mortality significantly dropped throughout the study decade [\u221211% (\u221213.5 to \u22128.4)]. This mortality drop was observed in non-neutropenic patients [\u221212.1% (\u221215.2 to \u22129.0)] but not in neutropenic patients [\u22123.8% (\u22128.1 to +5.6)].Among the 1,528 citations identified, 38 studies reporting on 6,054 patients were included. Median mortality across the studies was 54% \u201364, withSensitivity analyses disclosed no differences in underlying malignancy, mechanical ventilation use, or Granulocyte-colony stimulating factor use. Seven studies allowed the adjustment of severity results . Although pooled risk difference estimates were similar to non-adjusted results, there was no significant impact of neutropenia on mortality Although the unadjusted mortality of neutropenic patients was 11% higher, this effect disappeared when adjusted for severity. Therefore, when cancer patients become critically ill, neutropenia cannot be considered as a decision-making criterion. The intensive care unit (ICU) admission of patients with cancer has long been controversial. Studies performed in the early 1990s demonstrated high mortality rates in cancer patients admitted to the ICU, especially among those with respiratory failure who required mechanical ventilation, those with neutropenic sepsis, and in hematopoietic stem cell transplant (HSCT) recipients . Over thDespite these results, the prognostic impact of neutropenia remains controversial. Hence, although meaningful survival has been described in neutropenic patients , 8, neutThe aim of this study was to assess the influence of neutropenia on the outcome of critically ill cancer patients. Secondary objectives included assessing the influence of neutropenia on the outcome of critically ill patients in pre-specified subgroups .Our initial search yielded 1,528 citations, of which 38 were excluded for duplication. Among these records, 706 were excluded as irrelevant to the scope of this review. For the 784 remaining records, abstracts were carefully checked, and 135 full-text articles focusing on critically ill cancer patients' prognosis were scrutinized for further evaluation. Finally, 38 studies with a total of 6,054 patients fulfilled our eligibility criteria and were included . Ten were prospective cohort studies, and five were multicentric cohort studies . All stuMedian mortality across all studies was 54% (45%\u201364%). Median mortality in neutropenic and non-neutropenic patients was of 60% (53%\u201374%) and 47% (41%\u201368%), respectively.Overall mortality was 54.1% . The mortality of neutropenic and non-neutropenic patients was 62.8% and 49.5% , respectively.P - 0.0002; Figure Funnel plot analysis failed to identify publication bias Figure . OverallN - 428), hematological malignancy , or both , respectively , 8% (95%CI: 0% \u2013 +15%), and 12% (95%CI: 6% \u2013 17%) in patients with solid tumors . The mortality of neutropenic patients was 64.1% . The mortality of non-neutropenic patients was of 54.9% (95%CI: 52.7%\u201357.1%) before 2005 vs. 42.8% after 2005 .Mortality according to the inclusion period is displayed in Figure vs. 10% [95%CI: 3%-17%]).The time of admission, therefore, did not modify the influence of neutropenia on the outcome reported on the use of G-CSF. Use of G-CSF ranged from 8% to 100% of neutropenic patients, and evaluation of the influence of neutropenia in these studies was impaired by the lack of statistical power in this analysis .P - 0.48; Overall, seven studies including 1,350 patients (642 patients with neutropenia) reported the adjusted influence of neutropenia on mortality. Although pooled risk difference estimates were similar to non-adjusted results, the overall influence of neutropenia was non-statistically significant and in non-neutropenic patients according to a study inclusion period. Conversely, study inclusion period had little influence on critically ill neutropenic patients. Although, inclusion period in the included studies was too wide to allow for any definite conclusions, which may suggest that the survival gain suggested by previous studies [Another interesting finding of our results is related to the changes in overall mortality according to the study period. Hence, a significant decrease in overall mortality was noted during the decade in the overall population in neutropenic critically ill cancer patients. Neither underlying malignancy, period of admission, use of mechanical ventilation, or use of G-CSF significantly influenced this result. Additional studies are needed to confirm our findings and to identify room for improvement in the management of these patients. Meanwhile, the meaningful survival of neutropenic patients in the reported studies strongly suggest that ICU admission denial based upon neutropenia should be discouraged.http://www.prisma-statement.org/). The study was registered in the PROSPERO database (CRD42015026347).This systematic review and meta-analysis were performed according to the guidelines of the Meta-analysis of Observational Studies in Epidemiology and the The aim of this meta-analysis was to determine the prognostic impact of neutropenia on the outcome of critically ill cancer patients.First, public-domain databases PubMed and the Cochrane databases were searched using exploded medical subject headings and the appropriate corresponding keywords: \u201cNEOPLASM\u201d or \u201cMALIGNANCY\u201d or \u201cCANCER\u201d AND \u201cINTENSIVE CARE UNIT\u201d or \u201cICU\u201d. The research was restricted to articles in English and studies involving humans and published from May 2005 to May 2015. Abstracts were carefully checked, and studies focusing on children or patients aged lower than 18 years, case reports, and studies failing to focus on critically ill patients were excluded.All remaining references were then downloaded for consolidation, elimination of duplicates, and further analysis. Four authors independently evaluated the eligibility of all studies identified in the initial research. Lastly, studies with explicit redundancies were only included once.Four authors performed data extraction, working in pairs. Disagreements were resolved by discussion among authors and by adjudication of a third evaluator in case of persistent disagreement.For each included trial, information was extracted on the following items: study design, study setting, follow-up period, study population, the proportion of HSTC recipients, the proportion of allogeneic HSCT recipients, the number of included patients, the number of patients with neutropenia, the outcome of patients with and without neutropenia.ICU admission period was defined as the median inclusion year.http://methods.cochrane.org/bias/sites/methods.cochrane.org.bias/files/uploads/Tool%20to%20Assess%20Risk%20of%20Bias%20in%20Cohort%20Studies.pdf).Risk of bias was assessed using the Cochrane's Tool to Assess Risk of Bias in Cohort Studies . Overall mortality of included patients and mortality in included studies are reported as medians (interquartile ranges). Publication bias was assessed by visually inspecting the funnel plot and summary estimates of risk differences were calculated using the random-effects model.To enable data comparison, we transformed illness severity scores (SAPS II and APACHE III) into the equivalent APACHE II score, using a previously described methodology .Four subgroup analyses were preplanned, and they included the influence of neutropenia according to underlying malignancy , median ICU admission periods in the included studies, the use of mechanical ventilation, and the use of G-CSF. The last subgroup analysis on the duration of neutropenia could not be performed because this variable was unreported in most of the selected manuscripts.P value of less than 0.05 was considered statistically significant. Cochran's Chi2 test and I2 test for heterogeneity were used to assess inter-study heterogeneity [2 test assesses whether observed differences among results are compatible with chance alone, and the I2 describes the percentage of the variability in effect estimates that results from heterogeneity rather than from sampling error. An I2 test for heterogeneity above 0.25 was considered to indicate moderate heterogeneity. Statistically significant heterogeneity was considered present at Chi2P < 0.10 and I2 > 50%.A ogeneity . The Chihttps://www.r-project.org/), Metafor package (https://cran.r-project.org/web/packages/metafor/metafor.pdf).Last, since significant heterogeneity was observed, a post-hoc meta-regression was undertaken in way to identify factors that may be associated with the observed heterogeneity. This analysis was performed using R software ("} +{"text": "Chronic obstructive pulmonary disease (COPD) accounts for the majority of deaths from chronic lower respiratory diseases, the third leading cause of death in the United States in 2015 and the fourth leading cause in 2016.The National Center for Health Statistics (NCHS) 2013 Urban-Rural Classification Scheme for Counties, which uses 2010 U.S. Census population data and the February 2013 Office of Management and Budget designations of metropolitan statistical area, micropolitan statistical area, or noncore area codes 490\u2013492 or 496 or ICD-10-CM codes J40\u2013J44.Medicare enrollment records and data from 100% of Part A claims in 2015 were obtained from the Centers for Medicare & Medicaid Services. Analyses were limited to 30,212,024 living Medicare Part A enrollees aged \u226565 years who were eligible for fee-for-service hospitalizations on July 1, 2015, and all 335,362 fee-for-service inpatient hospital claims with a first-listed diagnosis of COPD that were submitted in 2015 for Medicare Part A enrollees aged \u226565 years. COPD was defined by Mortality data for all ages were analyzed using CDC WONDER, an interactive public-use Web-based tool.Age-adjusted prevalence of diagnosed COPD for persons aged \u226518 years, Medicare hospitalization rate for persons aged \u226565 years, death rate for all ages, and 95% CI for each estimate were calculated by urban-rural classification and state. For BRFSS analyses, statistical software was used to account for the complex sampling design. Differences in COPD prevalence among rural respondents compared with those of other urban-rural subgroups were determined by t-tests. Urban-rural differences in Medicare hospitalizations and death rates were determined by the Z-test. All two-sided tests were considered statistically significant at \u03b1\u00a0=\u00a00.05.In 2015, approximately 15.5 million adults aged \u226518 years had self-reported diagnosed COPD. County-level estimates of COPD prevalence ranged from 3.2% to 15.6% . U.S. coAge-adjusted prevalence of diagnosed COPD among adults aged \u226518 years increased with less urbanicity from 4.7% among populations living in large metropolitan centers to 8.2% among adults living in rural areas . MedicarOverall 5.9% of U.S. residents lived in rural counties in 2015. State-specific percentages of rural residents ranged from zero percent in Connecticut, Delaware, District of Columbia, New Jersey, and Rhode Island to 34.7% in Montana . State-sIn 2015, rural U.S. residents experienced higher age-adjusted COPD prevalence, Medicare hospitalizations for COPD as the first-listed diagnosis, and deaths caused by COPD than did residents in micropolitan or metropolitan areas. In addition to the major risk factors for COPD, which include tobacco smoke, environmental and occupational exposures, respiratory infections, and genetics, correlates include older ages, low socioeconomic status, and asthma history might have affected current COPD prevalence. Sixth, Medicare claims should not be interpreted as unique prevalent cases because some might reflect readmissions; however, these COPD estimates do reflect the actual Medicare burden for hospital facilities, pulmonary rehabilitation services, health care providers, caregivers, and other resources. Seventh, both Medicare hospital claims and death certificates might be subject to reporting preferences for certain diseases as the first-listed or underlying cause if there is a consistent regional or urban-rural preference. Finally, although the data reported here show higher COPD hospitalization and death rates for rural populations, they do not assess whether hospitalization and death rates among patients with COPD vary by urbanicity. Higher burdens of COPD among rural U.S. residents highlight needs for continued tobacco cessation programs and policies to prevent COPD and improve pulmonary function among smokers. Known barriers to care in rural areas suggest a need for improved access for adults with COPD to treatment strategies (pulmonary rehabilitation and oxygen therapy) and comprehensive chronic disease self-management programs. Health care providers and community partners who serve rural residents can help adults with COPD increase access to and participation in health care interventions. Federal agencies are promoting collaborative and coordinated efforts to educate the public, providers, patients, and caregivers about COPD and improve the prevention, diagnosis, and treatment of COPD. The COPD National Action PlanChronic obstructive pulmonary disease (COPD) is a leading cause of death and has been diagnosed in 15.5 million adults in 2015 in the United States. Risk factors include tobacco exposure, occupational and environmental exposures, respiratory infections, and genetics. In 2015, rural U.S. residents had higher age-adjusted prevalence of COPD, of Medicare hospitalizations, and deaths caused by COPD than did residents living in micropolitan or metropolitan areas. Several states with the highest percentages of rural populations also had the highest estimates for all three measures.Additional efforts are needed to prevent risk factors and overcome barriers to early diagnosis, and the appropriate treatment and management of COPD. Improving access to such health care might improve quality of life and reduce hospital readmissions among COPD patients and reduce COPD mortality."} +{"text": "Background: Hospital Acquired Infection (HAI) burden patients, complicate treatment, prolong hospital stay increase costs and can be life threatening.Several studies showed that HCAI affect 4.6% to 9.3 % of hospitalized patients. Adequate Hand hygiene among health care personnel could prevent an estimated 15-30% of HCAI. Numerous studies over last few decades have shown that hand hygiene compliance rate is generally less than 50% of all opportunities Ineffective communication with staff or employee during transition of care is potential cause of non- compliance with hand hygiene practice by health care personnel.Aim of the study: The study used was directed for effective communication with continuous feedback about performance.Methods: As communication is the ability to convey information both effectively and efficiently. We combined multiple tools of communications. We started to use four types of effective communication in this study.Visual communication, .Verbal communication (Recorded video messages).Non-verbal communication.Written communication: .Results: Improvement and increase hand hygiene compliance rate in ER reaching 74% after intervention. Compliance rate was 55% in October 2017 before implementing the study then it reached 64% after one month and recently it reached 74% in February 2018 with implementation of effective communication tools.Conclusion: Simple measures to enhance communication through getting employee attention about the importance of hand hygiene by high impact alert messages, high visual screen saver, tickers survey and quizzes.Background: The emergence of different infections caused by penicillin-resistant strains of Streptococcus pneumoniae has become a worldwide concern. The magnitude of the problem in South West Saudi Arabia was not investigated.Methods: Laboratory data on pneumococcal isolates was collected retrospectively from January 2010 to December 2014 from hospitalized patients in the main tertiary care hospital of Al Baha, South West Saudi Arabia. Minimum inhibitory concentrations (MICs > or = 2 mg/L) was used to detect the resistance isolates.Results: During the five year duration, a total of 201 S pneumoniae isolates were identified, most of which (61%) 124/201 were isolated from respiratory specimens , followed by eye swabs (15%) 30/201, blood (12%) 25/201, ear swabs (7%) 15/201 and CSF (3.4%) 7/201. The resistance rate of S pneumoniae was 71 % (43/60) on year 2010, 76% (35/46) on year 2011, 61% (22/36) on 2012, 68% (20/29) on 2013 and 66% (21/30) on 2014 respectively with an overall resistance of 70% (141/201).Conclusions: The data confirm the presence of penicillin -resistant S pneumoniae in South West Saudi Arabia. This is in agreement with other studies that covered other parts of the country. The high resistance identified might indicate a potential concern and warn of further spread among individuals. Thus good penicillin control with periodical antibiotic surveillance may improve the current situation and attempt to slow down the accelerating problem of resistance to penicillin.Background: There are limited studies conducted in Saudi Arabia to assess the knowledge, attitude and safety practice of the college students regarding nutrition labeling.Objectives: The purpose of the study were to assess knowledge, attitudes and practice (KAP) about nutrition labeling among university students.Method: A cross sectional survey was planned to assess knowledge, attitudes and practice (KAP) about nutrition labeling among students of University of Hail. The subjects were surveyed through a previously standardized self-administered questionnaire for questions related to their favorite food, nutrient content, knowledge, attitudes and practice of using nutrition labels. In addition, self-reported weight and height was collected and body mass index was calculated. The statistical analysis was done using Statistical Package for Social Sciences software (version 16.0).Results: There was a significant difference (p < 0.05 or 0.000) between the mean scores of knowledge, attitude and practice between the nutrition and non-nutrition students. The nutrition students reported a very good knowledge on nutrient content , total calories , cholesterol , expiry date , food poisoning stated in the nutrition labeling of the foods and was statistically highly significant(P<0.000). The attitudes of the nutrition students on reading information, making healthy food choice (\u03c72=12.729), taste , checking ingredients and packaging, food allergies, food safety(\u03c72=9.562) were all found to be highly significant (P<0.01 or 0.000). The practices of nutrition students on reading list of ingredients (\u03c72=7.320), serving size(\u03c72=12.335), health claims(\u03c72=8.809), vitamins and mineral content (\u03c72=11.904), and checking the hygiene (\u03c72=8.717) was statistically significant .Conclusion: Nutrition labels and its awareness were more useful tools for students and had an direct impact on the health status of the students. It is suggested to perform successfully designing, organizing and implementing the nutrition education programs in the institutions which will promote the level of knowledge about nutrition and nutrition labels thereby improving their food habits and lifestyle.Juniperus excelsa leaves extract, to be used as alternative agents against multidrug-resistant bacteria. The synergistic effect of AgNPs with antibiotic was also studied. Multi-drug resistant bacteria were collected from Taif hospitals patients with skin infections. Phenotyping, biotyping and molecular characterization using 16S rRNA gene analysis of nonrepetitive multidrug-resistant (MDR) bacterial isolates were studied. The formation of later nanoparticles was characterized using FTIR, XRD, UV-VIS spectrophotometer and TEM. The antimicrobial studies were initially carried out by the determination of inhibition zone (ZIN), the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). The biomolecules in the aqueous Juniperus excelsa leaves extract function as both safeties reducing and capping agents for biosynthesis of AgNPs. The shapes of AgNPs were spherical and hexagonal. The particle sizes ranged from 16.08-24.42 nm. The antimicrobial effect of AgNPs and their synergistic effect with antibiotic were studied against Methicillin- resistant Staphylococcus aureus (MRSA) and Proteus mirabilis. MICs of AgNPs against tested MDR bacteria ranged from 48-56 \u03bcg/ml, while MBCs of AgNPs against tested strains ranged from 72-96 \u03bcg/ml. Synergistic effects of AgNPs with cephalosporines, ampicillin and erythromycin, and showed 3 folds increase in the inhibition zone against tested strains. Consequently, we suggest that phyto-synthesized AgNPs are good alternatives in the treatment of diseases because of the presence of bioactive agents. Also, it showed a strong synergistic effect of AgNPs with antibiotic on tested bacteria. Consequently, it may be used to activate the antibiotics. These results indicate that AgNPs and AgNPs with antibiotic showed strong antibacterial properties on multi-drug resistant bacteria, which could be exploited in developing better dressings for wounds.There is worldwide concern about the rapid emergence of resistant bacteria and their resistance to commonly used antibiotics. Nowadays, the need for innovative strategies for developing antimicrobial drugs is becoming a necessity against antibiotic multi-resistant bacteria that have become of critical concern in public health. To overcome this multidrug-resistance problem, we studied for the first time a green, simple, and low-cost synthesis of silver nanoparticles using Foodborne diseases outbreaks continue to be problem indicating the failure of population to adhere to safe practices during food preparation. Thus, this study aimed to assess the knowledge, attitude, and practices (KAP) of food safety awareness among public Saudi population. This study involved 136 persons from Taif Saudia Arabia. The food safety KAP among 136 Saudi population was assessed using a questionnaire. The study involved 54.4% females and 45.6% males, 56.6% work outside health field and 43.4% in health care field ,82.4% from urban area and 17.6% from rural area and 81% within the age group from 21-30 years old. 75.7% of the population had good attitude and practice towards health and food safety and washing hands before eating. Further population had low attitude on other related items such as unimportance of expire date in food safety 44.8% , unimportance of reading the instruction label on the caned food 59.5%, unimportance of checking the refrigerator temperature 77.9%, and unimportance of changing the cutting knife used between meat and vegetables cutting 66.9% . As regard knowledge , 61.8% of population had good knowledge about best temperature for bacterial growth which is between 4 to 50 \u00b0C and .About 73.5% of population had good knowledge about diseases that could be transmitted through food, but only 30.9% of population had knowledge about best method of meat thawing.In conclusion, the suggestion of this study was that Saudi population had adequate food safety knowledge, but perceived knowledge failed to be translated into practices, therefore necessary to hold training programs through workshops or to include courses in the schedule of ministry of health.Background: Methicillin resistant Staphylococcus aureus (MRSA) is a critically important pathogen in neonatal intensive care units (NICUs) population and has been associated with both endemic and epidemic infections. Staphylococcus aureus nasal colonization is a well-known independent risk factor for infection.Purpose: To decolonize neonatal MRSA organisms admitted to NICU at King Faisal Medical Complex, TAIF.Methods: Eighty-three nasal swab samples were screened for MRSA during October \u2013 November 2017. Staphylococcus aureus were identified as round white colonies positive to Gram stain, catalase and slide agglutination tests. Methicillin-resistant phenotype was confirmed according to British Society for Antimicrobial Chemotherapy (BSAC) standards using the Vitek2 system . An isolate is considered methicillin resistant when the minimum inhibitory concentration (MIC) breakpoint of oxacillin is >2 mg/L and of cefoxitin >4 mg/L. MRSA decolonization was performed using nasal mupirocin ointment three times / day for 5 days. To confirm decolonization, cultures were taken after 2 days of stopped treatment. For prevention measures: hand hygiene, education program and cohort isolation were implemented during the study period.Results: Eleven patients were colonized with MRSA and successfully decolonized after treatment with mupirocin ointment cream 2% for five days. Central line-associated bloodstream\u2013MRSA infection was reported, treated with vancomycin, cured and discharged home.Conclusion: Periodical assessment of MRSA is needed depends on the prevalence of hospital-onset-MRSA to control spread of organisms and maintain health and safe environment.Background: Human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS) by destroying \u201chelper T cells\u201d. In healthy individuals, helper T cells organize immune responses that protect the body from infection. Survival rates among patients have improved since the introduction of antiretroviral therapy (ART) in HIV management. Studies suggests that supplementation of prebiotics and probiotics is beneficial for (ARV)-treated HIV patients.Aim: Objective of study is to assess knowledge of female students of Hail University about probiotics, prebiotics and their effective role with antiretroviral drugs in treatments of HIV patients. Also, provides knowledge about probiotics, prebiotics and their relationship to HIV disease.Method: A cross sectional survey was planned to evaluate knowledge about HIV-infection and its relation to probiotics among female students of Hail University through a previously standardized self- administered questionnaire. Then, comparing degree of knowledge between literature and scientific colleges.Result: there is a highly significant differences among levels of knowledge at P < 0.05 or P < 0.01. Statistical analysis for the degree of knowledge showed that there is a high significant differences in degree of knowledge between students of literature colleges (58.93\u00b1 11.73) and students of scientific colleges (73.20 \u00b1 9.08). Results indicate that students of scientific colleges have higher level of knowledge than literature colleges at P < 0.05 or P < 0.01.Conclusion: Study provides an update and a discussion on the influence of prebiotics and probiotics in the management of HIV infections. The results provide perspective for discussing potential future therapeutic strategies focused on modulating the gut microbiota to abate HIV disease progression. These findings should encourage consumption of fermented dairy products and vegetables & fruits as part of the total daily food consumption. That they contain probiotics and prebiotics.Background:Klebsiella species are found everywhere in nature leading to a wide range of diseases including pneumonia, septicemia, meningitis and soft tissue infections. Recently, pathogens have developed resistance to antibiotics posing serious threats to human health globally.Objectives: This work highlights comparatively the incidence and pattern of antibiotic resistance for clinical Klebsiella isolates in 2010 and 2017.Methods: Fifty-five Klebsiella isolates (20 in 2010 and 35 in 2017), from blood of patients admitted to ICU, were tested for their sensitivity to fifteen antibiotics including Amoxicillin/ Clavulanic acid, Ampicillin/ Sulbactam, Piperacillin/ Tazobactam, Aztreonam, Meropenem, Imipenem, Cefotaxime, Ceftriaxone, Ceftazidime, Cefoperazone/Sulbactam, Amikacin, Tobramycin, Gentamicin, Trimethoprim/Sulfamethoxazole and Doxycycline.Results: In 2010, the resistance percentages to the tested antibiotics ranged from 0-30%, however this percentage increased by 2-3 folds in 2017 especially towards tobramycin, cefotaxime, ceftriaxone, ceftazidime, piperacillin/tazobactam, cefoperazone/sulbactam and ampicillin/sulbactam.Conclusion: The change in pattern and incidence of resistance among pathogens is alarming requiring collaborative efforts among health sector partners to combat this phenomenon.Background: Accidental occupational exposure of healthcare workers to blood and body fluids after skin injury constitutes a risk for transmission of blood-borne pathogens.Aim: To assess pattern and risk factors of sharp object injuries in two tertiary hospitals were affected more than male 33 (25.2%). Mean age was 31 \u00b1 6.6. Most affected employee were young (20-30years constitute 73 (55.7%). Most injuries occurred in Emergency room 26 (19.8%) followed by Surgical word 20(15.3%), OR 16(12.2%). Nurses were more affected 74(56.5%), doctor 23(17.6%) housekeeping 18 (13.7%). According to type of exposure high exposure due to needle prick 104 (79.4%), cut wound 15(11.5%). Most devices caused injuries were bore hollow needle 63(48.1%), suture needle 18 (13.7%), cannula and insulin syringe each 13 (9.9%). Regarding circumstances of injury, most during operation 23 (17.6%) , during waste collection 15 (11.5%) , cannulation 12 (9.2%) and giving injection 12 (9.2%) . Exposure to HBV, HCV and HIV were 4(3.1%), 3(2.3%) and 3 (2.3%) respectively. No seroconversion among employee was documented.Conclusion: There is increase in incidence of sharp needle injuries from 2016 to 2017.Female were more exposed than males. The younger and nurses were more affected. Emergency department was the most affected area. Bore hollow needle was the most device causing sharp injuries. Sharp injuries during operation were the most circumstances during which exposures occurred followed by waste collection.Background: Health care-associated infections (HAIs) increase mortality, length of hospital stay, costs of care, bacterial resistance, antibiotic usage, and other adverse events. Monitoring HAI indicators is one of patient safety component. We describe the distribution of HAIs in three hospitals in Taif, Saudi Arabia.Methods: A retrospective study was conducted on three acute care hospitals during the year 2017. Patient population, surveillance, calculation of incidence rate and ratio, benchmarking and interpretations were conducting according to National Safety Healthcare Network (NHSN) USA.Results: Incidence rates of ventilated associated pneumonia (VAP) were high (> 90 percentile) with median utilization ratio (50-75 percentile) followed by catheter urinary tract infections (75-90 percentile) with median utilization ratio (50-75 percentile) in adult intensive care units (ICU). Incidence rate of central line associated bloodstream infections (CLABSI) was high (>90 percentile) despite of low utilization ratio (10-25 percentile) in adult ICU of post graduate teaching hospital. However, the incidence rate of CLABSI was (25-50 percentile) with the same utilization ratio (25-50 percentile) in ICU of graduate teaching hospital. Incidence rate and ratio of VAP, CAUTI and CLABSI were high (>90 percentile) in medical/surgical department of post graduate teaching hospital. Incidence rate of CLABSI and CAUTI were high (> 90 percentile) with low utilization ratio in ICU and Medical/Surgical department of pediatric non- teaching hospital. Incidence rates of Appendix (APPY) and cesarean section (CSEC) infections were low positive. Out of the 50 isolates we noted theexistence of 46 profiles and 74% of isolates are considered as multi-drug resistance strains. Distribution of antibiotic resistance genes realized by Polymerase Chain Reaction (PCR) showed that the genes aac(3)-IV and blaSHV were identified in 33.33% of isolates. In addition, the genes qnrA, blaCMY and dfrA1 were founded in 37.25%, 19.60% and 17.64% of the isolates respectively. In total, 17 different genotypes were detected and 12 isolates (24%) do not include any genes in their genomes.In this work, 50 clinical Background: Hand hygiene is a cost-effective method in preventing infection transmission. Hand hygiene practices have been found to be faulty in most healthcare settings. We conducted a study to evaluate the awareness, and compliance of hand hygiene among undergraduate medical students during their clinical phase in Taif University Medical College, Saudi Arabia.Methods:A questionnaire based on World Health Organization's concept of \u201cFive Moments for Hand Hygiene\u201d was used to evaluate the awareness of the indications for hand hygiene and compliance was observed during Objective Structured Clinical Examination (OSCE) sessions. Sixty students including thirty-six males (60%) and twenty-four females (40%) participated voluntarily in the study.Results: The average awareness regarding the positive indications of hand hygiene was 56%. Rest of the 44% of students was either not sure or unaware of the indications of hygiene. Only 29% of students were able to identify all the five indications for hand hygiene in the questionnaire. Compliance as assessed during OSCE sessions was only 17% with no significant difference between the genders.Conclusion: It was concluded that serious efforts are needed to improve the hand hygiene practices among medical students.Introduction:Escherichia coli is commonly found in intestinal tracts and, as a result of fecal contamination or contamination during food animal slaughter, is often found in foods of animal origin.Objectives: This study was conducted to determine the antibiotic sensitivity pattern of E. coli isolated from different types of animal original foods collected randomly from street-vendors and super-markets in Giza.Methods: Thirty-one isolates of Escherichia coli recovered in 2007 and twenty-seven isolated recovered in 2015 were examined to better understand the prevalence of antimicrobial resistance among these organisms. Antimicrobial susceptibility testing was performed using 15 antimicrobials including chloramphenicol, ampicillin, amoxicillin-clavulanic acid, cephalothin, ceftiofur, ceftriaxone, gentamicin, sulfamethoxazole, trimethoprim-sulfamethoxazole, nalidixic acid, ciprofloxacin, tetracycline, and cefoxitin. The antibiotic susceptibility test was performed using the agar disk diffusion test.Results: The results indicated that. There was an increase in the frequency of resistance to a majority of antimicrobials tested. The overall incidence of drug resistant E. coli was 18% in 2007 increased to 62% in 2015. Extended Spectrum \u03b2-Lactamase (ESBL) producers were more detected in 2015.Conclusion: Multidrug resistant strains of E. coli are a matter of concern as resistance genes are easily transferable to other strains in the human and might pose a potential health risk to the consumer. Therefore, in order to avoid this, good hygienic practices during handing and processing of these foods are necessary.Background: Enterobacteriacea are gram negative rods causing serious infections in intensive care units (ICUs) of hospitals. They are glucose fermenter, catalase positive and oxidase negative. These organisms are showing resistance to several classes of antimicrobials and resistance genes are spreading by acquired plasmids in bacterial population. Resistance to carbapenem group of antimicrobials is an emerging problem for clinicians and surgeons. Because after this class of antibiotics, no other treatment regimen is left workable to treat infections.Methods: This research was a descriptive, cross sectional study. A proforma was used as a tool for data collection. Eighty three isolates of CRE from intensive care units samples were processed in 9 months duration from July 2015 to March 2016.This study was conducted in department of Pathology, Microbiology, Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad.Data was collected through samples coming from ICUs. And organisms were cultured on blood and Mac Conkey agar. Organisms were identified, confirmatory tests were done and sensitivity of drugs was checked by Kirby Bauer disc diffusion method according to CLSI manual 2014. Resistant organisms to imipenem and meropenem were preserved in glycerol broth at -800C. MIC of imipenem was checked by using E-strips. Their molecular characterization was done using the conventional PCR targeting NDM, KPC, VIM and IMP genes.Results: Minimum age of patient was 2nd day of life while maximum age of patient was 80 years of life.There were 36 (43%) females and 47 (57%) males. Out of 83 samples, 22 (26.5%) were from urine, 22 (26.5%) were from endotracheal tube tip, 12(14%) were from blood, 11 (13%) were from pus, 11 (13%) were from tracheal secretions, 3(4%) were from fluids and 2(3%) were from catheter tip.In this study, out of 83 samples of CRE,62(75%) were klebsiella pnemoniae, 14(17%) were e.coli, 2(2.25%) were klebsiella specie, 2(2.25%) were enterobacter agglomerans, 2(2.25%) were enterobacter cloacae and 1(1.25%) were klebsiella oxytoca.From total of 83 samples isolated from intensive care units, 83(100%) were found sensitive to Tigecycline, and Polymxine B 34 (41%) were sensitive to Chloramphenicol, 14 (16.9%) were sensitive to Aztreonam, 12(14.5%) were sensitive to Amikacin. There were 0(100%) resistance to Imipenem, Meropenem, Ertapenem, Amoxicillin+Clavulanic acid, Ceftriaxone, Ceftazidime, Tazobactam+Pipercillin, Ciprofloxacin, Gentamicin,Tobramycin, Sulfamethoxazole+Trimethoprim, Nitofurantoin, Nalidixic Acid. The minimum inhibitory concentration of imipenem were between ranges of 4 \u03bcg/ml to more than 32 \u03bcg/ml. NDM was isolated in 56% isolates. VIM, KPC, IMP was not found in any study isolates.Conclusion: CRE are 100% resistant to Imipenem, Meropenem, and Ertapenem in this study. Tigecycline and polymxin B are parental drug which is found effective against CRE isolates.14.5% of CRE isolates were sensitive to Amikacin in our study. MIC of imipenem showed 100% resistance for CRE isolates. NDM gene was present in 56% samples. Whereas VIM gene, KPC gene, IMP genes were not detected in our CRE samples. NDM positive isolates were 48% Klebsiella pneumoniae."} +{"text": "To investigate the values of Computed Tomography (CT) in diagnosing postoperative pancreatic surgeryabdominalinfection and its efficacy and to provide a reasonable method for the diagnosis of abdominal infection.Seventy-two patients who were confirmed as resectablepancreatic carcinoma by physical examination, CT, positron emission tomography (PET)/CT, endoscopic retrograde cholangiopancreatography (ER-CP), endoscopic ultrasonography and mesenteric angiography and were admitted to the Binzhou People\u2019s Hospital, Shandong, China, from July 2013 to July 2015 were randomly selected. The plain CT images and clinical data of the patients were retrospectively analyzed.Among 72 patients, 32 patients were diagnosed as abdominal infection by CT, three patients were misdiagnosed , and 2 patients were wrongly diagnosed as suppurative abdominal inflammation. As regards distribution of CT imaging positive performance, the number of patients with intestinal loop abscess accounted for 41.7%, subphrenic abscess for 16.7%, pelvic abscess for 33.3%, the existence of septation for 25%, and emphysema sign for 16.7%. As to the distribution of CT findings of intestinal obstruction, 46.1% of patients had dilatation of intestine, 30.8% for bowel wall thickening, 7.7% had abnormal enhancement, 11.1% had density abnormality, and 15.4% had mesenteric effusion. CT features of purulent peritonitis showed 57.1% of patients had peritoneal thickening, 42.9% had peritoneal effusion, 42.9% had free intraperitoneal air, 14.3% had intestinal walls edema, and 28.6% had mesenteric edema.The diagnosis of postoperative abdominal infection of patients with pancreatic carcinoma using CT is quick and efficient showing the pattern and distribution of collection and the gross reaction to the exciting infection. Pancreatic carcinoma is one of the commonly seen malignant tumors in the digestive system and also one of the malignant tumors with poor outcome. Pancreatic carcinoma can occurr in any site of pancreas, and pancreatic head has the highest incidence, with 60%~70%. Patients with pancreatic carcinoma show no obvious specific performance but clinical symptoms such as abdominal pain, jaundice, anorexia, body mass loss, nausea and emesis. The surgery associated mortality of pancreatic carcinoma patients is high; more than 90% of pancreatic carcinoma patients who have not underwent treatment died one year after definite diagnosis, and the average survival period is less than 6 months; therefore, the early pick up and diagnosis of pancreatic carcinoma is the key for improving curative effect.This study evaluated the values of CT in diagnosing postoperative pancreatic surgery abdominal infection and its efficacy and determined the infection frequency and CT patterns of different infections, aiming to provide a reasonable method for the diagnosis and treatment of abdominal infection.Seventy-two patients who were diagnosed as pancreatic carcinoma by surgery and pathological slides in the Binzhou People\u2019s Hospital from July 2013 to July 2015 were randomly selected. Their clinical performance mainly included upper abdominal pain, lacking in strength, jaundice and loss of appetite. Thirty-six patients had radiative pain on shoulder and back, 25 patients showed loss of appetite, and 11 patients were observed with mass in abdomen. All the patients had no organ infection, diabetes, hypertension and cardia-cerebrovascular disease before surgery. Moreover, they were confirmed as pancreatic carcinoma by physical examination, CT, positron emission tomography (PET)/CT, endoscopic retrograde cholangiopancreatography (ER-CP), endoscopic ultrasonography and mesenteric angiography. Patients successfully underwent laparoscopic resectionduring hospitalization, and their clinical data were preserved completely.CT axial plain scan and enhancement scan were performed on all the cases using SOMATOM sensation 16 spiral CT machine . Scanning parameters were as follows: slice thickness: 5 mm, tube current: 320 mA, tube voltage: 120 KV, reconstruction slice thickness: two mm, reconstruction interval: two mm, scanning scope: from diaphragmatic dome to pubis. Enhancement scan including dual scan with 35 s and 70 s delay was carried out after the injection of contrast agent. According to the CT performance of patients and the clinical symptoms, relevant factors such as gastroenteric function were further analyzed. The incidence of abdominal opportunistic infection after surgery was recorded. The clinical data and various parameters of the patients before and after abdominal opportunistic infection were sorted.Data were processed and statistically analyzed using SPSS ver. 20.0. Difference was considered statistically significant if P<0.05.Among 72 patients with pancreatic carcinoma, 32 patients were confirmed as abdominal infection by one1 case of intraperitoneal abscess; two cases were wrongly diagnosed as purulent peritonitis. The accuracy of the diagnosis was 84.4%.There were 13 cases of intestinal obstruction, 12 cases of intraperitoneal abscess and 7 cases of purulent peritonitis .The CT imagingof 13 cases of intestinal obstruction included dilatation of intestine, intestinal wall thickening and intestinal effusion; enhancement scan suggested abnormal enhancement of intestinal loop . The CT For patients with pancreatic carcinoma, suboptimal nursing can induce postoperative infection and various complications after surgery. The common complications which occur after pancreatic carcinoma surgery include pancreatic fistula, intestinal fistula, abdominal bleeding and infection, intraperitoneal septicemia and hepatic failure; some patients may have gastroperesis and septic shock after surgery.Multi-slice spiral contrastenhanced scanning as a mature imaging examination method has been extensively used in examining the organs in the abdomen including the pancreas.Abdominal infection after pancreatic carcinoma surgerymanifests as intraperitoneal abscess, intestinal obstruction and purulent peritonitis under CT.16In conclusion, abdominal infection has a high incidence after pancreatic carcinoma surgery and suggests multiple imaging manifestations. The diagnosis of abdominal infection after pancreatic carcinoma surgery by CT is of great clinical values to the early diagnosis of abdominal infectionassociated complications, beneficial to the improved control of complications, and can help the correct postoperative diagnosis and timely determination of treatment schemes.YZM, GSL & LLZ: Study design, data collection and analysis.YZM, GSL & LLZ: Manuscript preparation, drafting and revising.GSL: Review and final approval of manuscript."} +{"text": "This study explored spatial-temporal variation in diagnoses of gonorrhoea to identify and quantify endemic areas and clusters in relation to patient characteristics and outcomes of partner notification (PN) across England, UK.Endemic areas and clusters were identified using a two-stage analysis with Kulldorff\u2019s scan statistics (SaTScan).p<0.0001). After controlling for age, gender, ethnicity and deprivation rank, 4 endemic areas were identified including 11,047 diagnoses, 86% of which occurred in London. 33 clusters included 17,629 diagnoses and spanned 21 locations, some of which were dominated by heterosexually acquired infection, whilst others were MSM focused. Of the 53,547 diagnoses, 14.5% were the result of PN. The proportion of patients who attended services as a result of PN varied from 0% to 61% within different age, gender and sexual orientation cohorts. A third of tests resulting from PN were positive for gonorrhoea. 25% of Local Authorities had a higher than expected proportion for female PN diagnoses as compared to 16% for males .Of 2,571,838 tests, 53,547 diagnoses were gonorrhoea positive (positivity = 2.08%). The proportion of diagnoses in heterosexual males was 1.5 times that in heterosexual females. Among index cases, men who have sex with men (MSM) were 8 times more likely to be diagnosed with gonorrhoea than heterosexual males (The English gonorrhoea epidemic is characterised by spatial-temporal variation. PN success varied between endemic areas and clusters. Greater emphasis should be placed on the role of PN in the control of gonorrhoea to reduce the risk of onward transmission, re-infection, and complications of infection. Neisseria gonorrhoeae, the causative agent of gonorrhoea, is the second most common bacterial sexually transmitted infection (STI) diagnosed in England. Gonorrhoea diagnoses reached their nadir in the early 1990s , rose to 41,262 (2015) and subsequently fell to 36,244 in 2016 [1,262 201 and subs in 2016 . In addi in 2016 \u201312.In England, sexual health services for the confidential diagnosis, treatment and management of STIs are provided free of charge. Partner notification (PN), including provider referral and outcome follow-up, is an essential control strategy as it reduces the risk of onward transmission, re-infection, and complications ,14. SincAll commissioned sexual health services are required to report STI tests and diagnoses to Public Health England (PHE) through GUMCAD. The latest iteration of GUMCAD includes reporting through community pharmacies and internet testing; however, when this project was undertaken testing activity and diagnoses made through such services were not captured unless patients were referred to a commissioned or specialist service for ongoing management. Diagnoses of gonorrhoea were extracted from GUMCAD for 2012 and 2013 . This psClinic and patient location were analysed at two geographic area levels: Middle Super Output Area and lower tier Local Authority . PopulatDiagnoses, including repeat infections (restricted to one positive diagnosis every 42 days), were stratified by gender, age, ethnicity, sexual orientation, region of birth, and HIV status. During the study period some individuals transitioned between age groups. Consequently, 2,489,334 subjects were identified across the age groups compared to 2,420,090 unique individuals. To explore gonorrhoea positivity (proportion of tests which tested positive) the dataset was restricted to those attending for gonorrhoea tests.th 2014 (Project ID: 7578).Analyses were based on de-identified surveillance data held by PHE. In its role providing infectious disease surveillance, PHE has permission to handle data obtained by GUMCAD under Regulation 3 of the Health Service (Control of Patient Information) Regulations 2002. The London School of Hygiene and Tropical Medicine Research Ethics Committee granted ethical approval on June 5The crude diagnosis rate (not controlled for covariates) was calculated for each LA. To be comparable with the demarcations used in PHE STI profiles in previous years, areas with a diagnosis rate 20% above the England average were classified as having a high rate of infection, whereas those 20% below had a low rate [To examine spatial-temporal patterns the data were classified by quarter. The expected quarterly diagnosis rate was derived from the total diagnosis rate for 2012 and 2013 and was assumed to be evenly distributed. Gonorrhoea clusters were investigated by MSOA regions to provide greater detail on spatial-temporal patterns that were otherwise masked at the LA level. The proportion of PN diagnoses in each LA was calculated by comparing the number of PN diagnoses per LA to the national total of all gonorrhoea diagnoses. The observed proportion of PN diagnoses within each LA was then compared to the expected proportion of 0.045% .Endemic areas consisted of MSOAs that had a high diagnosis rate for every six month period in 2012 and 2013. To avoid large endemic areas masking small clusters a two-stage procedure was used . After eBetween 2012 and 2013, 2,420,090 patient attendances were recorded in GUMCAD . Of the The crude diagnosis rate was 100.8/100,000 individuals. Highest diagnosis rates were seen in LAs within cities, including London, Manchester, Newcastle-upon-Tyne, Brighton, Bedford, and Leeds . DiagnosThe expected average quarterly diagnosis rate for England was 12.6/100,000 individuals. LAs in London, Brighton, Manchester, and Newcastle-upon-Tyne had persistently high diagnosis rates across quarters whereas diagnoses in surrounding LAs fluctuated . Spatialp<0.0001). Approximately a third of PN diagnoses were gonorrhoea positive, which is consistent with PHE annual data tables [Of the 53,547 positive gonorrhoea tests, 45,772 (85.5%) were index cases and 14.5% were diagnosed as a result of PN. Among index cases, the proportion of gonorrhoea positive males was 3.2 times higher than females within 4 cities: London, Brighton, Birmingham and Manchester . These ep = 0.84). Among females, the proportion of PN positive diagnoses ranged from 1.4% (Liverpool) to 47.9% (Bedford) and from 0% (Bradford) to 61% (Bedford) in heterosexual males (The average age (year) of females, heterosexual males, and MSM was 24.4, 28.4, and 32.7, respectively, across the 4 endemic areas and 23.4, 27.6 and 32.4 across the 33 clusters. The proportion of gonorrhoea diagnoses due to PN was similar between individuals with HIV (15.6%) and without HIV (16.5%). Diagnoses seen in heterosexual males and females were similar across clusters Click here for additional data file.S1 FigRegions are separated by local authority (LA). Regions are compared to the English average as higher, similar or lower. Similar regions were denoted as those within 20% above or below the English average .(TIF)Click here for additional data file.S2 FigRegions are grouped by LA. Regions are compared to the English average as higher, similar or lower. Similar regions were denoted as 20% above or below the English average .(TIF)Click here for additional data file.S3 FigRegions are compared to the English average as higher, similar or lower. Similar regions were denoted as those within 20% above or below the English average .(TIF)Click here for additional data file.S4 FigRegions are compared to overall English average proportion of positive partner associated gonorrheoa diagnoses spread evenly across all 326 LAs (0.045% expected per LA). Similar regions were denoted as those within 20% above or below the average per LA (0.036%-0.045% and 0.045%-0.053% partner related diagnoses for a given gender).(TIF)Click here for additional data file.S1 Tablep<0.05. The cluster numbers correspond to the clusters in Endemic regions were chosen by locations that were participating in a high rate cluster every six months. Outbreak clusters were selected based on a statstical level of (DOCX)Click here for additional data file."} +{"text": "This study describes patterns of cigarette smoking by sociodemographic, household, and chronic disease characteristics and correlates among US adults receiving housing assistance from the US Department of Housing and Urban Development (HUD) during 2007\u20132012. Estimates were generated from 4,771 adults by using National Health Interview Survey and HUD-linked data. Overall, 48.4% of HUD-assisted adults were never smokers, 33.0% were current smokers, and 18.6% were former smokers; smoking status varied by sex, age, race/ethnicity, whether children were living in the household, and chronic disease status. These estimates could inform tobacco control interventions to improve the health and well-being of HUD-assisted residents. Assisted housing is an important platform for improving the health and well-being of residents through evidence-based tobacco control interventions . Nearly The National Center for Health Statistics (NCHS) linked HUD administrative data to data from respondents of the National Health Interview Survey (NHIS), a cross-sectional household survey conducted by using multistage area probability design to capture a statistically representative sample of the civilian, noninstitutionalized US population ,4. The NSmoking status was assessed by asking, \u201cHave you smoked at least 100 cigarettes in your entire life?\u201d and \u201cDo you now smoke cigarettes every day, some days, or not at all?\u201d Current smokers reported smoking at least 100 lifetime cigarettes and now smoking every day or some days; former smokers reported smoking at least 100 lifetime cigarettes and now smoking not at all; never smokers reported not smoking at least 100 lifetime cigarettes.t tests, with P < .05 indicating significance. For constructs with more than 2 comparisons , Bonferroni adjustments were implemented to account for multiple hypothesis testing.Data were weighted to account for the complex survey design, and weights were adjusted for linkage eligibility by using a model-based calibration approach . The perDuring 2007\u20132012, 48.4% of HUD-assisted adults were never smokers, 33.0% were current smokers, and 18.6% were former smokers . The perSmoking status also varied by the number of chronic conditions among HUD-assisted adults . OverallBefore release of the linked NHIS\u2013HUD data, no data sources existed to provide national estimates of smoking status among HUD-assisted residents. This study complements a previous report on current smoking and health outcomes among HUD-assisted adults by proviThis study indicates that former and never smokers comprise the majority 67%) of HUD-assisted residents. These people are susceptible to secondhand smoke exposure in their homes; approximately one-third of multiunit housing residents who prohibit smoking in their personal living units experience secondhand smoke incursions from elsewhere in their building \u20137. These% of HUD-Our study has limitations. First, approximately 60% of 2007\u20132012 NHIS adults were linkage eligible, which may introduce selection bias if those who were linkage-eligible differed from those who were not linkage-eligible. However, linkage-adjusted weights were used to account for differences between these groups by sex, age, and race/ethnicity . Second,These data can help inform the development, implementation, and sustainment of evidence-based strategies , includi"} +{"text": "To assess the performance of symptom-based screening for tuberculosis (TB), alone and with chest radiography among people living with HIV (PLHIV), including pregnant women, in Western Kenya.Prospective cohort studyPLHIV from 15 randomly-selected HIV clinics were screened with three clinical algorithms , underwent chest radiography (unless pregnant), and provided two or more sputum specimens for smear microscopy, liquid culture, and Xpert MTB/RIF. Performance of clinical screening was compared to laboratory results, controlling for the complex design of the survey.Overall, 738 (85.6%) of 862 PLHIV enrolled were included in the analysis. Estimated TB prevalence was 11.2% . Sensitivity of the three screening algorithms was similar . Sensitivity of the WHO algorithm was significantly lower among HIV-infected pregnant women [28.2% ] compared to non-pregnant women [78.3% ] and men [77.2% ]. Chest radiography increased WHO algorithm sensitivity and negative predictive value to 90.9% and 96.1% , respectively, among asymptomatic men and non-pregnant women.Clinical screening missed approximately 25% of laboratory-confirmed TB cases among all PLHIV and more than 70% among HIV-infected pregnant women. National HIV programs should evaluate the feasibility of laboratory-based screening for TB, such as a single Xpert MTB/RIF test for all PLHIV, especially pregnant women, at enrollment in HIV services. Tuberculosis (TB) remains the leading preventable cause of morbidity and mortality among people living with HIV (PLHIV) . In 2015In 2010, WHO conducted meta-analysis of existing data on TB screening among PLHIV in 2010 in order to identify an evidence-based clinical screening algorithm. This meta-analysis identified the presence of current cough of any duration, fever, night sweats, or weight loss as the best performing screening rule, with an overall sensitivity of 78.9% for TB among all PLHIV and 90.1% among those screened in clinical settings and a negative predictive value of 95.3% among PLHIV with a 10% prevalence of TB . Based oWe conducted a prospective cohort study in Western Kenya to evaluate the performance of clinical screening for TB among adults and older children living with HIV using the WHO TB ICF algorithm . AdditioDetailed study procedures have been described elsewhere . BrieflyAll PLHIV received standard medical care per Kenya MOH guidelines, which included TB screening at entry into care using the 2009 Kenya MOH ICF algorithm a physical examination, and CD4 count analysis to determine antiretroviral treatment (ART) eligibility , 16, 17.Mycobacterium tuberculosis complex (MTBC) by Ziehl-Neelson acid fast bacilli (AFB) microscopy and either the Capilia TB Neo or the MGIT TBc ID immunochromatographic assay. The Hain Genotype CM line probe assay was used to further identify culture isolates with non-tuberculous mycobacteria.Sputum specimens were collected at study sites and transported to the Kenya Medical Research Institute (KEMRI)/U.S. Centers for Disease Control and Prevention (CDC) reference laboratory for smear microscopy, mycobacterial culture, and Xpert MTB/RIF . LaboratPLHIV who reported any symptom or sign in the algorithm suggestive of TB were defined as having \u201cpresumptive TB\u201d (previously known as a \u201cTB suspect\u201d) by that algorithm . PLHIV wDemographic information, clinical symptom screening, and physical examination findings were documented in paper-based medical records by clinicians at each site. Study personnel entered these data into an SQL database, which was merged with the KEMRI/CDC laboratory SQL database. Data were analyzed using SAS version 9.3 and Stata 13.1 . Symptom screening results were reviewed and recoded for internal consistency so that, for example, patients reporting cough lasting for 2 weeks or longer were also reported as having any cough. We calculated the sensitivity, specificity, negative predictive value, and positive and negative likelihood ratios of the three TB screening algorithms compared to laboratory-confirmed pulmonary TB. Analyses were weighted and controlled for the complex design of the survey . Analyses incorporated the use of a finite population correction (FPC) factor to account for the large sampling fraction. The chi-squared tests incorporated a Rao-Schott second order correction to account for the survey design. Differences in age and CD4 (square root transformed) were assessed using survey adjusted t-tests.Funding for this study was provided by the U.S. President\u2019s Emergency Plan for AIDS Relief through Cooperative Agreement 5U19GH000041 from CDC and by the United States Agency for International Development. Ethical approval was obtained from the KEMRI Ethical Review Committee and the CDC Institutional Review Board. We received a waiver of formal written informed consent for participation in this study because (1) the data and specimen collection were not experimental ; (2) the study activities posed no more than minimal risk to study participants; (3) participation did not adversely affect the welfare or rights of the patients in any way; and (4) to require formal written consent would have imposed an undue burden on the clinical staff of these busy clinics.Between May 2011 and June 2012, 1,157 PLHIV were enrolled in HIV care and treatment at the 15 study sites. Of these, 880 (76.1%) were eligible for enrollment, of which 862 (98.0%) were enrolled . After eAmong PLHIV evaluated for TB at enrollment into HIV services, 83 ) were diagnosed with bacteriologically-confirmed pulmonary TB. The median age of enrolled PLHIV was 30 years ; 20 PLHIV were younger than 15 years and 487 PLHIV were female. The median CD4+ cell count was 343 per \u03bcL . Compared to PLHIV in whom no TB diagnosis was made, PLHIV with TB disease had a significantly lower median CD4+ cell count and were significantly more likely to have an abnormal chest radiograph at enrollment .Documentation of TB screening using the WHO screening algorithm was complete for 696 [94.3% (unweighted proportion)] of 738 PLHIV. Overall, 53.2% of PLHIV screened at enrollment reported having at least one symptom in the WHO screening algorithm . Among Por an abnormal chest radiograph were classified as screening positive increased sensitivity compared to WHO symptom screening alone [90.9% versus 74.1% ], slightly increased negative predictive value [96.1% versus 93.8% ], but decreased specificity [32.0% versus 49.5% ] ] received chest radiography. Adding a chest radiograph to the screening algorithm so that PLHIV with any symptom 1\u201353.9)] . Among POverall, 50.1% of all PLHIV reported having at least one of the symptoms in the MOH TB screening algorithm, with weight loss remaining the most commonly reported symptom (66.0% of PLHIV). This algorithm performed as follows: sensitivity 77.5% , specificity 49.4% , and negative predictive value of 94.7% . The ID-TB/HIV algorithm performed similarly, with a sensitivity of 72.5% , specificity 56.5% , and negative predictive value of 94.3% [data not shown].Among the 487 women enrolled in this study, 134 (27.5%) were pregnant women identified at enrollment into PMTCT services. These pregnant women represented 18.2% of all PLHIV in this study and had a median age of 25 years . TB prevalence among pregnant women was lower than among both non-pregnant women and men . Pregnant women with TB did not have a significantly different baseline median CD4+ cell count than pregnant women without TB . Only 33 (24.6%) pregnant women reported having at least one of the symptoms in the WHO screening algorithm compared to 195 (55.2%) non-pregnant women and 143 (57.0%) men; night sweats was most commonly reported [57.6% of symptomatic pregnant women] and weight loss was least commonly reported [36.1% of symptomatic pregnant women]. The sensitivity of the WHO algorithm was significantly lower among pregnant women, 28.2% compared to 78.3% for non-pregnant women and 77.2% for men .In this study, the prevalence of bacteriologically-confirmed TB among PLHIV enrolling in HIV services was 11.2%. This is consistent with findings from a multi-country study that found a 12% TB prevalence among PLHIV not on ART in four countries in sub-Saharan Africa ; the TB The prevalence of TB varied across the districts, and likely reflects the burden of disease in those districts. Given the substantial burden of TB among PLHIV at enrollment in HIV care, TB case finding should be a priority intervention in HIV care and treatment and PMTCT settings. Although implementation of routine ICF is expanding, only 7 million (19%) of the 36.9 million PLHIV worldwide in 2014 were reported to be screened for TB . Our stuOur results confirm that the performance of the WHO TB ICF algorithm varies with the level of immunocompromise , 23. CliApproximately two-thirds of PLHIV enrolled in this study were women, which is consistent with findings from a review of ART programs which found that the female-to-male new ART enrollee ratios were 2.10 in countries in East Africa, partially because of access to HIV testing and ART as part of antenatal services for pregnant women . Our stuIn this study, TB prevalence among pregnant women living with HIV was approximately half that of non-pregnant women and men living with HIV. National TB surveillance systems do not routinely report pregnancy status of TB cases. However, a recent study estimated that the global burden of TB in pregnancy was substantial, with 216,500 cases in 2011, 41% of which occurred in the WHO AFRO region . Data frStrategies to optimize the performance of TB screening include expanding the number of symptoms and signs included in the screening algorithm, assessing for TB contact status, and adding chest radiograph. In our study, we found that the Kenya MOH TB screening algorithm, which included a combination of six symptoms and close contact with a person with TB disease, only marginally increased sensitivity, suggesting that expanded clinical screening likely has limited value. Including chest radiography as part of the WHO symptom screening algorithm improved case finding and should be considered as feasible, keeping in mind that this increase in sensitivity was associated with a decrease in specificity. This decrease in specificity is not surprising given that PLHIV commonly have non-TB related lung changes which in some cases can complicate radiologic TB diagnosis, especially in early stages of disease .This study had multiple limitations. Symptom screening was conducted as part of routine clinical services and clinical symptoms were not independently verified by study staff. Additionally, under these routine practice conditions, we were unable to obtain complete data on all patients. Clinical information, such as baseline CD4+ cell count and chest radiograph results, was missing for a subset of patients. Approximately 5% of PLHIV enrolled in the study were excluded from the final analysis because they were unable to provide more than one sputum specimen or provided specimens that could not be examined due to culture contamination. Of the 40 excluded PLHIV, 2 (5%) were found to have TB disease by Xpert MTB/RIF or culture of one sputum specimen; exploratory analysis with differing exclusion criteria did not result in substantive differences in the performance of the clinical screening algorithms (data not shown). However, the true prevalence of TB among the other PLHIV with culture contamination is unknown. Finally, while our study was designed to be representative of the Kisumu, Siaya, and Bondo Districts of Kenya as defined at the time of study inception, our study was not designed to be nationally-representative or generalizable to other settings in Kenya or sub-Saharan Africa.This study confirms that the WHO TB ICF algorithm performs as predicted among PLHIV newly enrolling in HIV services in this high HIV and TB burden region of Kenya. However, as half of all PLHIV reported symptoms consistent with TB disease, use of this clinical screening algorithm would lead to diagnostic evaluation of a large number of PLHIV without TB disease and would additionally miss asymptomatic PLHIV with TB disease. Given the poor performance of clinical screening among pregnant women, national HIV and PMTCT programs should evaluate the programmatic feasibility and cost implications of laboratory-based screening for TB disease at the initial presentation for HIV care, such as requesting a single Xpert MTB/RIF test for all HIV-infected pregnant women and potentially all PLHIV, enrolling in HIV services. Additional analyses are needed to determine the performance of WHO screening at follow-up visits, strategies to improve the sensitivity and negative predictive value of clinical screening algorithms, optimal intervals for screening, and to assess whether different clinical or laboratory-based (e.g. Xpert MTB/RIF) screening algorithms are more sensitive among pregnant women living with HIV."} +{"text": "We retrospectively investigated the incidence of acute graft-versus-host disease (GVHD) in the lower gastrointestinal (GI) tract and the diagnostic accuracy of endoscopy. Of 1231 patients who underwent allogeneic hematopoietic stem cell transplantation between January 2005 and December 2014, 186 of whom underwent colonoscopy and biopsy and had no cytomegalovirus infection. The endoscopic findings and histologic diagnosis from these 186 patients were retrospectively analyzed. Based on the histopathological findings, 171 patients were diagnosed with GVHD, accounting for 13.9% of all transplant recipients. Useful endoscopic findings for the diagnosis of GVHD were atrophy of the ileocecal valve and villous atrophy in the terminal ileum and tortoise shell-like mucosae, edema, and low vascular permeability in the colon. Even when no mucosal abnormality was observed, the incidence of GVHD was 78.9% in the terminal ileum and 75.0% in the colon. Furthermore, patients with mucosal exfoliation, although infrequent, were all diagnosed with grade 3/4 GVHD. It is important to perform endoscopy proactively for the early diagnosis of GVHD, and biopsy should be performed even when no abnormality is observed. In addition, because patients with mucosal exfoliation are extremely likely to have grade 3/4 GVHD, early treatment should be initiated. Early diagnosis and treatment are essential for graft-versus-host disease (GVHD), which is a serious complication that influences the prognosis of patients after allogeneic transplantation . HoweverIn this study, we therefore retrospectively investigated the incidence and endoscopic features of GI GVHD that had occurred within 100 days of hematopoietic stem cell transplantation and analyzed the association between the endoscopic features and histopathological GVHD.Of 1231 patients who underwent allogeneic hematopoietic stem cell transplantation between January 2005 and December 2014, 523 developed GI symptoms indicative of GVHD such as diarrhea and poor appetite and 222 subsequently underwent colonoscopy. After excluding 35 patients with cytomegalovirus (CMV) infection, 186 patients who had also undergone biopsy for histopathological assessment were enrolled in this study . Some pa3.In each case, various endoscopic findings were extracted retrospectively , and theBased on histopathological findings in the lower GI tract, GVHD was diagnosed in 171 patients, accounting for 91.9% of the patients who had undergone endoscopy and 16.4% of all transplant recipients. Sixty patients had GVHD only in the lower GI tract and not in other organs.Endoscopy was performed in 122 men and 64 women within approximately 41.3 (13\u2013100) days after transplantation. The primary disease was acute leukemia in 120 patients, malignant lymphoma in 38, myelodysplastic syndrome in 16, chronic myelogenous leukemia in 5, and other in 7. The source of stem cells for transplantation was umbilical cord blood in 125 patients, bone marrow in 36, and peripheral blood from a relative in 25. All patients underwent additional treatment to prevent GVHD, such as combination therapy with tacrolimus (FK506) and mycophenolate mofetil (MMF) in 72 patients; combination therapy with methotrexate (MTX), MMF, and FK506 or cyclosporin A (CyA) in 57; and monotherapy with CyA in 57. Biopsies were conducted at 4.9 sites on average . In addiHistopathological severity of GVHD was grade 1 in 52 (28.0%) patients, grade 2 in 36 (19.4%), grade 3 in 45 (24.2%), and grade 4 in 38 (20.4%).The rate of positive biopsy by a GI region was 90.4% for the terminal ileum and 94.4% for the colon . More spGVHD was present in the terminal ileum of 122 patients, one of whom was diagnosed based on the assessment of the terminal ileum alone. Frequent endoscopic findings were atrophy of the ileocecal valve (68.0%) and villous atrophy (49.6%). No abnormal findings were observed in 30 (22.2%) patients. Sensitivity toward GVHD was low for every endoscopic feature, but specificity and positive predictive value were 100% for villous atrophy, ulcer, and mucosal exfoliation and \u226580% for edema, redness, and erosion. In addition, GVHD was diagnosed in 80% of the patients with no abnormal findings. Reanalysis of grade 3/4 GVHD cases showed a high positive predictive value of approximately 90% for mucosal exfoliation .GVHD was detected in the colon of 170 patients. Frequent endoscopic findings were low vascular permeability (80.0%), edema (73.3%), and tortoise shell-like mucosae (67.6%). Specificity was 100% for ulcer and mucosal exfoliation and 93.3% for erosion, and positive predictive value was \u226590% for all endoscopic findings, showing high diagnostic performance. GVHD was diagnosed in 75% of 12 patients with no abnormal findings. Analysis of grade 3/4 GVHD cases revealed a high positive predictive value of 93.3% for mucosal exfoliation and 81.3% for ulcer .Treatment efficacy was observed in 75.4% of all patients. Potent therapy with, for example, antithymocyte globulin (ATG) or infliximab tended to be indicated for histopathologically severe GVHD, showing a correlation with actual clinical practice. A comparison by a disease stage showed that treatment efficacy was as high as 92.3% in grade 1 GVHD but decreased gradually to 86.1% in grade 2, 80.0% in grade 3, and markedly to 36.8% in grade 4 . ComparaGVHD is a disease caused by donor lymphocytes recognizing host histocompatibility antigens as foreign and attacking them immunologically. In definition, GVHD occurs within 100 days of transplantation . PrimaryThe incidence of acute GI GVHD is estimated to be 30\u201360% of all transplant recipients .Biopsy is essential in making a diagnosis of GVHD, and specimens are taken from organs such as the skin, liver, and GI tract. The rate of positive biopsy was 46% for the skin but was as high as 58% for the upper and lower GI tract, indicating the validity of GI endoscopy in diagnostic biopsy [GVHD is histopathologically characterized by the apoptosis of crypt epithelial cells accompanied by the infiltration of lymphocytes . The epiCandida and other fungal enteritis [The differential diagnosis includes regimen-related toxicity, CMV and other viral infections, TMA (thrombotic microangiopathy), bacterial enteritis such as pseudomembranous enterocolitis, and nteritis . Before nteritis . After aIn this study, 16.4% of the 1231 transplant recipients developed GVHD in the lower GI tract. The known common sites of lower GI GVHD are the terminal ileus, cecum, and ascending colon [The known characteristic endoscopic features of GVHD in the terminal ileum are villous atrophy, redness, edema, erosion, and shallow and wide ulcer-like lesions , but theThe known characteristic endoscopic findings of GVHD in the colon are orange peel appearance and tortoise shell-like mucosae , the latAlso in this study, 26 patients had mucosal exfoliation . Despite the relatively low incidence rate, the positive predictive value of mucosal exfoliation was as high as 92.3% for grade 3/4 GVHD, indicating that this endoscopic feature is an extremely important predictor of severe GVHD. Indeed, only about 50% of the patients with mucosal exfoliation responded to treatment in this study. Therefore, when endoscopic findings include mucosal exfoliation, early intervention should be initiated even before obtaining biopsy results.In addition, attention must be paid to patients with no abnormal endoscopic findings because in a previous study, GVHD was histopathologically diagnosed in the areas appearing virtually normal in endoscopy . Also inIn this study, we also investigated whether the deep insertion of a colonoscope is necessary. In clinical practice, it is often difficult to insert a colonoscope all the way to the terminal ileum in transplant recipients because of poor general conditions and insufficient bowel preparation. In this study, lower GI GVHD was diagnosed at a rate of 91.2% based solely on biopsy assessment of the left-side colon, suggesting that colonoscopy should be performed regardless of patient performance status. However, because the terminal ileum is often most severely affected by GVHD, colonoscopy should include the terminal ileum if possible.This study has several limitations. First, this is a retrospective single-institution study with a limited number of patients. Secondly, the interpretation of endoscopic findings was performed by one examiner. Thirdly, GI endoscopy was not performed in all transplant recipients, generating sampling bias. Therefore, we plan to perform a prospective study with a large number of patients in the future.In summary, lower GI GVHD was diagnosed histopathologically in 91.9% of the patients who had undergone endoscopy and 13.9% of all transplant recipients. Useful endoscopic findings for the diagnosis of GVHD were atrophy of the ileocecal valve and villous atrophy in the terminal ileum and tortoise shell-like mucosae, edema, and low vascular permeability in the colon. In addition, although rare, mucosal exfoliation was highly correlated with grade 3/4 GVHD, necessitating the initiation of early intervention even before obtaining biopsy results."} +{"text": "Secondary AH has a prevalence of 3-5%. The treatment of the cause can cure AH orimprove BP control. 1 As CKD advances, AH increases progressively,affecting 90% of stage 5 patients.2Chronic kidney disease is defined by a GFR < 60 mL/min or abnormal findings inurinalysis and/or kidney morphology for 3 months.3 . Additional investigation includes renalUS for all.3 Other exams can be necessary. Kidney biopsy is indisputably indicatedin the presence of rapid decline in glomerular filtration or proteinuria >3.5 g/g of urine creatinine.4Arterial hypertension accelerates the progression of CKD5 and BP reduction attenuates CKDcourse.6 The treatmentgoals and most indicated medications for BP control in patients with CKD aredescribed in Chapter 8. For CKD patients on dialysis, BP reduction decreasesmortality,7 and loopDIUs are indicated in the presence of residual renal function, as well asultrafiltration, in selected cases.8All patients with AH should have plasma creatinine measured, their GFR calculatedand urinalysis performed to screen for CKD.9 Its majorcause is atherosclerosis (90%), followed by renal artery fibromusculardysplasia,10Takayasu's arteritis being the less frequent.9 Regardless of its cause, it is an important determinantof CV morbidity and mortality.10Renovascular hypertension (RVAH) is secondary to partial or total, uni- orbilateral stenosis of the renal artery or of one of its branches, triggered andmaintained by renal tissue ischemia. The RVAH prevalence is 5% of hypertensivepatients.11314 list the main steps.The diagnosis and assessment of the extent of involvement with TOD are essentialfor the choice of treatment. A cost-effective investigation requires properselection of candidates, and anatomical and functional assessment of thestenosis, in addition to methods to correct the anatomical and functionaldefect.15 Regardingpatients with RVAH due to fibromuscular dysplasia, 82-100% of them have BPcontrol, and 10%, restenosis.11 . Regarding atherosclerotic RVAH withoutcomplications, three randomized studies have shown no benefit of stentimplantation as compared to optimized clinical treatment in BP control, kidneydisease progression, and occurrence of clinical events and mortality.18 For patients with atherosclerotic renal artery stenosisand controlled BP with clinical treatment, without heart complications andstable kidney function for 6-12 months, the mechanical intervention is notrecommended, clinical treatment being the first option. .The indication for the therapeutic option should consider the etiology andclinical conditions associated with renal artery stenosis, such as AH, ischemicnephropathy and accelerated CVD. Evidence of benefit of the percutaneous orsurgical mechanical treatment is restricted to situations, such as progressiverenal function loss, APE and difficulty to control BP, that cause irreversibleTOD.19 There is evidence that OSAHS is related to thedevelopment of AH regardless of obesity.21 Theprevalence of OSAHS in patients with AH is 30-56%,23reaching 64-83% in those with resistant AH (RAH).25OSAHS contributes to TOD26 andacceleration of atherosclerosis in hypertensives.27Obstructive sleep apnea-hypopnea syndrome is characterized by recurring upperairway obstructions during sleep, causing reductions in intrathoracic pressure,intermittent hypoxia and sleep fragmentation.28 can beused to screen for OSAHS,23but does not seem useful in patients with RAH.29 Changes in the physiological BP decreaseduring nocturnal sleep can indicate the presence of OSAHS.30 Polysomnography or homerespiratory polygraphy confirms the diagnosis with the finding of at least fiveepisodes of apnea and/or hypopnea per hour of sleep (apnea-hypopnea index -AHI), and an AHI \u226515 events/hour seems to have a higher impact onAH.31The risk factors for OSAHS are age, male sex, obesity and MS. The Berlinquestionnaire31 Meta-analyses have shown a small effect ofCPAP in reducing BP, but they have limitations because they included studies onindividuals with normal BP and controlled hypertensives.34 Most randomized studies38 onpatients with OSAHS and RAH have shown more significant reductions in BP thanthose of patients with non-resistant AH. Body weight loss in combination withCPAP has resulted in greater BP reduction than each isolated intervention inobese individuals with OSAHS.39 Mandibular advancement with mobile orthodontic devices formild to moderate OSAHS can also reduce BP,34 but further studies are necessary.34 Although severalantihypertensive classes have been tested,40 there is no definitive conclusion about the best drugfor hypertensives with OSAHS.41The treatment of choice for moderate or severe OSAHS is the use of continuouspositive airway pressure (CPAP) during sleep.42 (Aldo), caused by bilateraladrenal hyperplasia or unilateral Aldo producing adenoma (APA), and, morerarely, unilateral adrenal hyperplasia, adrenal carcinoma or genetic origin(monogenic or chimeric gene). The prevalence of PHA in hypertensives is 3-22%,being higher in stage 3 and/or resistant hypertensives.43Primary hyperaldosteronism (PHA) is a clinical condition characterized byexcessive, inappropriate and autonomous production of aldosterone43Primary hyperaldosteronism is suspected when AH is associated with: spontaneousor DIU-induced hypokalemia; adrenal incidentaloma; RAH; family history of AH orCbVD before the age of 40 years; and MS. The prevalence of hypokalemia in PHA is9-37%.43 Suppressed plasma renin activity (PRA) and Aldo > 15ng/dL, with an Aldo/PRA ratio > 30, indicate the diagnosis of PHA.Confirmatory testing is recommended when Aldo > 15 ng/dL and < 25 ng/dL,with an Aldo/PRA ratio > 30 and < 100. The furosemide and captopril testshave higher diagnostic accuracy than the saline infusion test.44 In the furosemide uprighttest, the patient should remain lying down for at least 30 minutes, then receive40 mg of furosemide (IV), and renin should be measured after 2 hours of walking.The test is positive if PRA < 2 ng/mL/h. In the captopril challenge test, 50mg of captopril are administered orally after the patient remained seated or inthe upright position for at least 1 hour. Renin and Aldo should be measured atthe times 0, 60 and 120 minutes. The test is positive if there is no drop >30% in plasma Aldo or if it remains > 12 ng/dL. In the saline infusion test,2 liters of 0.9% saline are administered (IV) in 4 hours. The Aldo measurementwill be \u2265 5 ng/dL.Laboratory tests do not require suspension of antihypertensive agents, except forspironolactone for 4-6 weeks.43Catheterization of the adrenal veins is indicated when, on CT, the adrenalglands are normal, have bilateral abnormalities (thickening or micronodules) ora unilateral lesion in patients > 40 years.44 The dexamethasone suppression test isindicated to investigate PHA suppressible with glucocorticoid in patients withPHA and AH beginning before the age of 40 years.44For APA or hyperplasia to be detected, thin-sliced CT or MRI of the adrenalglands is indicated.43 preferably with previous treatment with spironolactoneup to 3-4 weeks.45 Clinicaltreatment of hyperplasia requires spironolactone, 50-300 mg/day, if welltolerated.45 Cure ofAH with surgery is observed in 35-60% of the patients.45Laparoscopic surgery is indicated in APA,46 Of PHEOs, 10% to 15% are extraadrenal(paragangliomas), 10% are bilateral, and 10% are malignant.47 Familial forms have thedominant autosomal trait or are part of syndromes with known genemutations.47Pheochromocytomas (PHEO) are tumors of chromaffin cells of the sympatheticadrenomedullary axis that produce catecholamines.46 is indicative of the disease, and concomitance of theclassic triad with HC has sensitivity of 89% and specificity of 67% for the PHEOdiagnosis.46Presence of persistent or paroxysmal AH (50%), paroxysmal headache, excessivesweating and palpitations (classic triad)48but because of its higher cost, urine metanephrine isolated or associated withplasma catecholamines is indicated in cases of high likelihood.48 The measurement of urinevanillylmandelic acid has good specificity, but the lowest sensitivity of allmethods, being indicated only when the other tests are not available.48 If the diagnosis is notcertain, clonidine suppression test is indicated in hypertensives, and glucagonstimulation test, in individuals with normal BP levels.47Laboratory diagnosis is based on the measurement of catecholamines and theirmetabolites in blood and urine. Free plasma metanephrine has the highestsensitivity and specificity,49The MRI is superior to identify paragangliomas. MIBG whole body scan is usefulin extraadrenal, bilateral PHEOs, and metastases and relapses.50 Octreoscan, bone scan andpositron-emission CT can be indicated when the localizing exams cited arenegative or when investigating malignancy.51The imaging tests to locate adrenal tumors are CT and MRI, with sensitivity of89% and 98%, respectively.52 The chronic pharmacological treatment includesalpha1-blockers, BBs , CCBs, ACEIs and central action agonists.52 The paroxysmal HC of PHEO is aHE, and should be treated with SNP or injectable phentolamine and volumereplacement, if necessary.46The preferential treatment is surgery, whose preoperative preparation shouldinclude alpha1-blockers (doxazosin or prazosin) and appropriate hydration for atleast 2 weeks before surgery.49 For malignant PHEOs withunresectable metastases, the following are indicated: chemotherapy,embolization, radiotherapy, and, if possible, ablation with MIBG-131.47 Clinical, biochemical andradiological follow-up of the patients is essential to detect recurrences ormetastases, in the malignant form, and other tumor in familial syndromes.Total and early removal of the neoplasm usually determines total remission ofsymptoms and cure of AH.53 The diagnosis isestablished by finding high TSH levels and gradual decrease in free T4. Themost common clinical findings are weight gain, hair loss and muscleweakness. The treatment is initiated with thyroid hormonereplacement,53and, if AH persists, antihypertensive drugs are indicated. .In hypothyroidism, AH occurs in 20% of hypothyroid patients.54 The most important signs are exophthalmos,hyperthermia, hyperreflexia and humid skin.54 The diagnosis is confirmed by low TSHlevels and high free T4 levels. The treatment usually normalizes BP.Beta-blockers are the first choice to control the adrenergic symptoms. .In hyperthyroidism, AH is a frequent finding in hyperthyroidism, and theclinical presentation mimics hyperadrenergic findings. The main symptoms arepalpitation, tremor, fatigue, increased sensitivity to heat, hyperactivity,weight loss and emotional lability.55 It can be caused by an adenoma or hyperplasia of theparathyroid glands. Secondary hyperparathyroidism results from a situationthat induces hypocalcemia, CKD being the major cause. The most commonsymptoms are depression, thirst, polyuria, renal lithiasis, osteoporosis,lethargy, muscle weakness, muscle spasms, and renal function reduction.Arterial hypertension is present in up to 75% of the patients, and can beresistant.43 Thediagnosis is established with plasma calcium and PTH measurement. Surgicalcorrection of hyperparathyroidism can cure or reduce BP inhypertensives.56In hyperparathyroidism, there is excessive secretion of parathormone (PTH) bythe parathyroid glands, with consequent hypercalcemia andhypophosphatemia.57 It canresult from adrenal tumors with autonomous cortisol production , adrenal hyperplasia, excessive adrenocorticotropin(ACTH) production, or ectopic tumor.57 The prevalence of AH in CS is 80% in adults and 47%in children.57 The majorsigns and symptoms are decreased libido, central obesity, moon face, striae,muscle weakness, and hirsutism.58 The confirmatory tests are: 24-hour urine freecortisol; nocturnal salivary cortisol; dexamethasone suppression test;dexamethasone combined with corticotropin-releasing hormone test; and ACTHmeasurement.58Pituitary MRI shows an adenoma in 35% to 60% of patients.58 Surgical removal of thetumor can cure AH, but 30% of the patients maintain SAH, and 25%,DAH.59 The AHduration before surgery correlates with postoperative AHpersistence.59Thiazides and furosemide should be avoided, because they can worsenhypokalemia, ACEIs and ARBs being recommended.59Cushing's syndrome (CS) is a disorder caused by excessive cortisol levelsassociated with a deficiency in the control mechanism of thehypothalamus-hypophysis-adrenal axis and of the cortisol secretion circadianrhythm.60 Inacromegaly, AH has a 35% prevalence, and contributes to increase thedisease's morbidity and mortality. Acromegalic cardiomyopathy contributes toraise BP, and can be aggravated by the coexistence of AH. The treatment ofacromegaly reduces BP in parallel with GH reduction.60Acromegaly is usually caused by a pituitary adenoma that secrets growthhormone (GH) and insulin-like growth factor type 1 (IGF-1). It manifests asprogressive excessive growth of the hands, feet and facial bones, increasedinterdental spacing, mandibular prognathism, macroglossia, excessivesweating, and respiratory, CV, metabolic-endocrine and skeletal-musclechanges.63Coarctation of the aorta is the aortic constriction close to the ductusarteriosus or ligament, found mainly in children and young adults. Clinicalsuspicion is based on symptoms and physical exam .62The imaging exams include: chest X ray ; echocardiogram ; angiography with MRI . The MRI is the best method forassessment and post-intervention follow-up in young individuals, and doesnot require preoperative angiography. Invasive angiography is indicated whenother imaging methods do not provide visualization of the coarctation, andto older individuals who can have CAD. The definition of significantcoarctation requires pre- and post-coarctation pressure gradient > 20 mmHg.Patients who do not undergo surgery have a higher incidence of CV events. Thetreatment is always interventional: endovascular procedure or surgery (hypoplasia of the aortic arch and/orneed for coarctation resection). The BP response to interventional treatmentdepends on the duration of AH prior to surgery and the patient's age. Thecure of AH occurs in up to 50% of patients, but AH can reoccur later,especially if the intervention is performed at advanced age. The drugs ofchoice for both the preoperative period and residual AH after surgery areBBs and ACEIs."} +{"text": "Recent review about functional magnetic resonance imaging (fMRI) in first episode psychosis (FEP) concluded that there is an abnormal connectivity involving the frontal temporal pathway similar to found in chronic schizophrenia . Besides, thalamic circuits were also altered in chronic schizophrenia patients . The present work gives a wider review of studies using functional magnetic resonance imaging techniques (fMRI) on first-episode psychotic patients, specifically focus on the main areas involved.The review was made in accordance with the PRISMA guidelines . For each study, the following factors were extracted: anatomical location of the main finding and type of functional abnormality (hypo and hyperactivation). A total of 3 different databases were reviewed. Thirty-five of 643 (from 2000 to 31st October 2017) neuroimaging papers were analyzed.We found that the dorsolateral prefrontal cortex (DLPFC) showed 52% of activity abnormalities (55% was hypoactivation). Temporal lobe showed 51% of functional activity altered (61% was hypoactivity). The ventrolateral prefrontal cortex (VLPFC) presented 28% of aberrant fMRI (75% was hyperactivity). Thalamus presented alteration activity with 20% (71% was hypoactivity). The Cingulate was also altered during activation with 20% of patients (85% was hypoactivity). Finally, functional alterations of the Amygdala were present in 14% of the selected patients (80% was hypoactivation).This larger review suggests that there are several possible areas apart from fronto temporal pathways , that have to be taken into account at the early course of psychosis, such as lymbic system, thalamo-cortical networks and cingulate. These functional activation abnormalities seem to be different to the reported in the previous review. The different results seem to be clearly influenced by the kind of paradigm. Moreover, our finding is not in concordance with the suggestion that thalamic alterations became only prominent at the chronic phase of psychosis .1. Moher, D et al., Preferred reporting items for systematic reviews and meta-analyses: The Prisma statement. PLoS Med, 2009, 6, 1000097.2. Mwansisya, T et al., Task and resting-state fMRi studies in first-episode schizophrenia: A systematic review. Schizophrenia Research article in press, 2017.3. Li, T et al., Brain-wide analysis of functional connectivity in first episode and chronic stages of schizophrenia: Schizophrenia Bulletin 2016, 43, 436\u2013448."} +{"text": "We aimed to determine the frequency, type, and etiology of infections and the risk factors for infections and mortality in hospitalized cancer patients.We prospectively enrolled adult cancer patients hospitalized in the internal medicine wards of a tertiary care academic center between January and August 2004. Patients were followed during their hospitalization periods for neutropenia, infections, culture results, and mortality.We followed 473 cancer patients with 818 hospitalization episodes and 384 infection episodes in total. Seventy-nine percent of the infections were nosocomial, and febrile neutropenia (FN) was observed in 196 (51%) of the infection episodes. Bacteremia was found in 29% of FN episodes and in 8% of nonneutropenic patients. Gram-positive bacteria were the leading cause of bacteremia in both neutropenic and nonneutropenic cases . Presence of an indwelling central catheter increased bacteremia risk by 3-fold. The overall mortality rate was 17%, whereas 34% of the patients with bloodstream infections died. Presence of bacteremia and advanced disease stage increased overall mortality by 6.1-fold and 3.7-fold, respectively.Nearly half of the cancer patients developed an infection during their hospital stays, with gram-positive bacteria being the predominant etiologic microorganisms. This demonstrates the changing trends in infections considering that, until 2004, gram-negative bacteria were the most predominant microorganisms among cancer patients in our institute. Infections have become the leading cause of mortality and morbidity of cancer while supportive and curative treatment strategies prolong life ,2. CancePredominant infectious pathogens have been variable in time with changing cancer treatment strategies, antibacterial prophylaxis practices, and emerging resistance patterns in bacteria. Until the 1980s, the leading microorganisms in cancer patients were enteric gram-negative bacteria and Pseudomonas aeruginosa. As of the 1980s, gram-positive bacteria became the most common pathogens in these patients . However, recently, nonfermenting gram-negative bacteria have emerged as the leading pathogens in cancer patients.It is important to know the risk factors for infections, changing epidemiology, and resistance patterns of pathogenic microorganisms for the proper management of infections in cancer patients. In this study, we aimed to determine the frequency, type, and etiology of infections and the risk factors for infections and mortality in hospitalized cancer patients.This study was done in the internal medicine wards of a tertiary care university hospital. The institutional review board approved the study and adult cancer patients hospitalized between January and August 2004 were enrolled and followed prospectively. Demographic data, cancer type and stage, previous stem cell transplantation history and type, comorbidities, and presence of antibacterial utilization in the previous month were recorded upon admission. Presence of indwelling catheters , presence of parenteral nutrition, requirement of intensive care unit and mechanical ventilation, therapy for cancer , vital signs, infections, antibiotic usage, culture results, and neutrophil counts were recorded throughout the admission episode. Descriptive data and further analyses were done based on the admission episodes unless otherwise specified. One patient might have had more than one admission. The infectious diseases department followed the patients and the researchers did not intervene in the diagnostic and therapeutic processes.Neutropenia was defined as an absolute neutrophil count below 500/mm3 or below <1000/mm3 and expected to decline rapidly. Neutropenic infections were classified as clinically or microbiologically documented infection, bloodstream infection (BSI), or fever of unknown origin [All the cultures were collected from different parts of the body according to the presumed infections. They were inoculated onto suitable media and incubated at 37 \u00b0C for 24-48 h. Catheter cultures were studied quantitatively. For blood cultures, a BD BACTEC 9000 Blood Culture System was used. All the microorganisms were identified by gram staining, conventional microbiological tests , and the Phoenix System (Becton Dickinson Diagnostic Systems). Antibiotic susceptibility tests were conducted with the Phoenix System and for Streptococcus pneumoniae by E-test . Results were evaluated according to the Clinical and Laboratory Standards Institute 2004 standards.Data were analyzed by SPSS 11.5 for Windows . Distribution of data was analyzed by Kolmogorov-Smirnov test. Normally distributed data are presented as mean \u00b1 standard deviation, while abnormally distributed data are presented as median (minimum-maximum). Categorical variables were compared by chi-square test and Fischer\u2019s exact test where appropriate, and continuous variables were analyzed by Student\u2019s t-test. Risk analysis was performed by Fisher\u2019s exact chi-square test and parameters that were found to be significant were introduced into a multivariate logistic regression model. Relative risk was computed for possible risk factors with 95% confidence interval and p<0.05 was accepted as statistically significant.During the study period, 473 cancer patients between 16 and 82 years of age were enrolled and 818 hospitalization episodes were followed prospectively. Of these patients, 286 (60%) were male and the mean age was 51 years (16-82 years). Chronic diseases accompanying admission episodes were as follows: 4.8% coronary artery disease, 2.7% chronic renal failure, 10.2% diabetes mellitus, and 13.4% hypertension. Solid organ cancer was seen in 254 (53%) patients while the remaining had hematological diseases . HematopIn the course of 818 hospitalization episodes, a total of 384 (46%) infection episodes were observed and 79% of these were nosocomial. Febrile neutropenia (FN) was observed in 126 patients having 196 (51%) infection episodes. Acute myeloid leukemia was the most common underlying disease in patients with FN. Mean duration of neutropenia was longer in patients with an infection (16.2 days) when compared to those without an infection (8.2 days) (p=0.002). Bacteremia was found in 29% of FN episodes and in 8% of nonneutropenic infections (p<0.05). Sites of infections in neutropenic and nonneutropenic patients are shown in Fluconazole as antifungal prophylaxis was given in 63 (7.7%) episodes as a part of the stem cell transplantation regimen. Corticosteroids were used in 215 (26.4%) of the admission episodes. Radiation therapy was performed in 5.1% (42) of hospitalization episodes. Unfortunately, we had no data about granulocyte colony-stimulating factor use in this study.Nonneutropenic episodes constituted 71.4% of all the hospitalization episodes and in 77.3% of these cases an immunosuppressive treatment, including corticosteroids, was used. As expected, there was an immunosuppressive treatment in 94% of neutropenic episodes (p<0.001). Among the nonneutropenic episodes, infections were more frequently seen in those patients receiving any immunosuppressive treatment than in episodes with no immunosuppressive treatment (p<0.001). However, there was no difference in terms of mortality (p=0.111).At least one pathogenic microorganism was isolated from culture specimens obtained from patients during 187 (48.6%) infection episodes. Blood cultures were positive in 29.6% of all the patients and in 60.6% of neutropenic patients. Gram-negative microorganisms were the most common (51%) isolates among all the specimens, whereas gram-positive microorganisms were the most common (65%) among blood culture isolates . Fungi wThe resistance patterns of Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Klebsiella spp., and Pseudomonas spp. are listed in Possible risk factors for infection in cancer patients were analyzed by univariate analysis and then the risk factors found to increase the occurrence of an infection were introduced into a multivariate logistic regression model . We founThe overall mortality rate was 17%, whereas 34% of patients with BSIs died (p<0.05). Among patients with FN, the mortality rate was 18.4%, and the occurrence of a BSI increased the mortality rate to 41%. Presence of bacteremia increased overall mortality 6.1 times and advanced disease stage increased overall mortality 3.7 times. On the other hand, usage of prophylactic antifungal therapy decreased mortality 3.3-fold, but the p-value was found to be statistically insignificant (p=0.055) . ComorbiThis study is a landmark study to show the shift of infectious etiologies in cancer patients from gram-negative to gram-positive bacteria. Afterwards, a long-term multicentric study was established in Turkey for microbiological surveillance of FN patients. Such surveillance studies are valuable to implement systemic changes in individual institutions and countries.In this prospective observational study we found that 46% of all cancer patients developed at least one infection and 85% of neutropenic patients developed at least one FN attack during their index hospital stay. Among the neutropenic attacks, 65% were documented clinically or microbiologically, and the BSI rate was 29% among the FN attacks, comparable to that reported in numerous other studies ,8,9. ComMethicillin-resistant coagulase-negative staphylococci (MR-CoNS) were the most commonly isolated microorganisms from overall and blood culture specimens. The predominance of gram-positive bacteria and MR-CoNS in BSIs in this cohort was parallel to findings in the literature. In cancer patients BSIs were due to gram-negative enteric bacteria and Pseudomonas aeruginosa in the 1960s and 1970s, but by the middle of the 1980s gram-positive bacteria had become predominant ,13. MemoRecent studies revealed that in hematological malignancies gram-negative microorganisms have again become the most relevant microorganisms in BSIs. Cattaneo et al. reported a predominance of gram-negative bacteria (57.3%) in hematological malignancies between 2004 and 2010 . Gudiol In this study ESBL-positive E. coli (55%) and Klebsiella spp. (50%) were more frequent in neutropenic cases than nonneutropenic cases. A literature review revealed that ESBL positivity in cancer patients ranged from 12% to 75% for E. coli and K. pneumoniae in different studies ,27,28,29We found that patients who were neutropenic for 7 or more days were prone to infection 3.9-fold more so than others. Poor prognosis and advanced stage solid or hematologic cancers were also related to an increased infection risk by 3.1-fold. Radiation was another risk factor for infection. This might be explained by the characteristics of the patient group that received radiotherapy: poor performance status, palliation in advanced disease, advanced age, or total body radiation prior to stem cell transplantation.Indwelling central catheter was a risk factor for BSIs. In the last 30 years, increased use of persistent indwelling catheters has brought about an increased infection risk, especially for CoNS BSIs ,12,32,33Antifungal prophylaxis was part of the prophylaxis regimen in HSCT patients and it seemed to lower the mortality, although we could not show statistical significance. There are some reports showing azole-resistant breakthrough fungemia, but a recent study from the EORTC revealed that antifungal prophylaxis was protective in fungemia in cancer patients . As therNearly half of the cancer patients developed an infection during their hospital stays, with gram-positive bacteria being the predominant etiologic microorganisms. This demonstrates the changing trends in infections considering that, until 2004, gram-negative bacteria were the most predominant microorganisms among cancer patients in our institute. Each patient must be evaluated individually for risk factors, and while antibiotic treatment is being planned, current local surveillance data and the resistance patterns of the microorganisms should be taken into account along with individual risk factors.A part of this study was presented as a poster presentation at the Febrile Neutropenia Symposium, February 2005, Ankara, Turkey, and the Interscience Conference on Antimicrobial Agents and Chemotherapy, December 2005, Washington, DC, USA.Ethics Committee Approval: LUT 05/15; Informed Consent: It was taken."} +{"text": "Entrobacteriaceae in the University of Gondar Referral Hospital environments.This study aimed at assessing the magnitude, distribution, and the antimicrobial susceptibility of the extended spectrum beta-lactamase producing Entrobacteriaceae, where 42.10% Klebsiella pneumoniae, 35.09% Escherchia coli and 7.01% Proteus mirabilis were the predominant isolates. Most ESBL producing isolates, that is, 24.56, 22.8, and 22.8% were found from waste water, sinks and bedside tables respectively. All ESBL producing Entrobacteriaceae were found to be resistant to ceftriaxone, ceftazidime, cefpirome, cefpodoxime, and amoxicillin with Clavulanic acid. Resistance rate was also high for non-beta-lactam antimicrobials, like chloramphenicol (70.18%), cotrimoxazole (64.91%), norfloxacin (42.10%), ciprofloxacin (43.86%), and gentamicin (19.30%).Out of a total of 384 samples, 14.8% were ESBL producing Hospital environment is a potential source of nosocomial infections, since it houses both patients with diverse pathogenic microorganism and a large number of susceptible individuals \u20133.The ever-increasing bacterial resistance to antibiotics is one of the most thought-provoking tasks of medical issues today . A persiEntrobacteriaceae, and their resistance increased mainly due to the spreading of ESBL and the emergence of different genes [Entrobacteriaceae are Escherichia coli, Klebsiella pneumoniae and Proteus species. However, all other clinically relevant Entrobacteriaceae species are also common ESBL producers. The distribution of ESBL depends on geographic locality, hospital wards, groups of patients and the type of infection [An extended spectrum beta-lactamase production has been observed mostly in nt genes \u201311. The nfection \u201316.Entrobacteriaceae becomes common in any other area of the hospital indicating a high possibility of horizontal gene transfer among strains of different genera within the hospital environment [The resistance patterns of ESBLs were initially considered as a problem related to nosocomial outbreak, mainly in Intensive Care Units, surgical procedures, bladder catheterization, long-term hospitalization, and frequent exposure of broad spectrum antimicrobials. However, the distribution of ESBL producing ironment \u201321.Entrobacteriaceae at hospital environments in northwest Ethiopia are limited. Thus, this study was carried out to assess and determine the rate of ESBLs producing Entrobacteriaceae and their antimicrobial susceptibility patterns in the hospital environment at the University of Gondar Referral Hospital.Reports about ESBLs producing A hospital-based cross-sectional study was conducted at the University of Gondar Referral Hospital from January to June 2014. The hospital provides surgical, medical, gynecologic and obstetric, and ophthalmologic services to over 5 million inhabitants. It has different wards with 465 beds and outpatient departments.Seven sample selection sites were identified prior to data collection. The simple random sampling technique was applied. Out of the 2508 total population, 384 were included in the study based on the single population proportion formula.Samples were collected from bed frames, bedside tables, door handlers, floors, sinks, waiting chairs, walls, and the waste water of the hospital which have direct contact with patients, their families, and health care providers. Medical wards, surgical wards, the Gynecology and Obstetrics ward, the Fistula clinic, the Eye clinic, the hospital caf\u00e9, and hospital sewages were the study sites. Sterile cotton tipped swabs moistened with normal saline were rotated against the surfaces of inanimate objects to obtain specimens, and waste water was collected from the hospital sewage by a sterile screw capped bottle and transported to the microbiology laboratory. Each sample was transferred to the selective media, Hicrome ESBL agar base, to assess the ESBL production in 2\u00a0h. The species was differentiated by specific colony color and again by a biochemical test , 23. AntThe descriptive statistical analysis was performed by using SPSS version 20 software program.Entrobacteriaceae, namely Escherchia coli, Klebsiella pneumoniae, Klebsiella ozenae, Proteus mirabilis, Entrobacter cloceae, Entrobacter aerogens, Citrobacter and Providencia stuarti were isolated from the samples. The predominant species were Klebsiella pneumoniae (42.10%), Escherchia coli (35.09%) and Proteus mirabilis (7.01%). Escherchia coli and Klebsiella pneumoniae were found in all the selected types of samples. However, Klebsiella ozenae were found in sinks; Proteus mirabilis in bed frames, floor and sinks; Entrobacter cloace in bed frame; Entrobacter aerogens in bed tables and bed frames; Citrobacter in floor and sinks and Providencia stuarti in bed frames and sinks , bed tables (22.80%), waste water (15.79%) and less than 5% were found in bed frames, door handles, floors, walls, and waiting chairs. However, no isolates were found from hospital cafe chairs.The highest number of ESBL producing Entrobacteriaceae were found to be 100% resistant to cefpirome, cefpodoxime, ceftazidime, ceftriaxone, and amoxicillin with clavulanic acid. However, 70.18, 64.91, 42.10, 43.86, and 19.30% were resistant to chloramphenicol, cotrimoxazole, norfloxacin, ciprofloxacin, and gentamicin, respectively.All ESBL producing Klebsiella pneumoniae were resistant to 91.7% cotrimoxazole, 66.7% chloramphenicol, 45.8% norfloxacin, 45.8% ciprofloxacin, and 25.0% gentamicin. Escherchia coli was also resistant to chloramphenicol (55.0%), cotrimoxazole (35.0%), norfloxacin (25.0%), ciprofloxacin (30.0%), and gentamicin (20.0%).Proteus mirabilis, only 25.0% strain was resistant to norfloxacin, ciprofloxacin, and cotrimoxazole. But, all isolates were susceptible to gentamicin.All isolates of Klebsiella ozenae were resistant to chloramphenicol, and cotrimoxazole, whereas all isolates were sensitive to norfloxacin, ciprofloxacin, and gentamicin.Of the total ESBL producing Entrobacteriaceae isolates demonstrated multiple non-beta lactam antibiotics resistance against ciprofloxacin, norfloxacin, gentamicin, chloramphenicol, and cotrimoxazole, of which Klebsiella pneumoniae (58%) and Escherchia coli (40%) showed a high level of multiple drug resistance. Despite the fact that the number of isolates was small; Entrobacter cloceae, Entrobacter aerogens, Citrobacter, and Providencia stuart were multidrug resistant.More than 56% of the ESBL producing Entrobacteriaceae is one of the most important causes of nosocomial and community acquired infections where Beta-lactam antibiotics are the first choice for treatment of infections caused by Entrobacteriaceae. However, they produce extended spectrum beta-lactamases (ESBLs) that cause high resistance to the beta-lactam antibiotics. Of the different genera of Entrobacteriaceae, Escherichia coli is the leading urinary tract pathogens with septicemic potential, Klebsiella pneumonia causes lobar pneumonia and often outbreaks in hospital settings, Proteus mirabilis cause urinary tract infections, chronic ear infection and septicaemia, Klebsiella ozane cause atrophic rhinitis, Enterobacter causes urinary tract infection & sepsis and Citrobacter Causes urinary tract infection, sepsis, wound infection, osteomyelitis in elderly hospitalized patients and neonatal meningitis [The rise of bacterial pathogens in hospital environment is associated with an increasing in nosocomial infections. ningitis .Entrobacteriaceae at the University of Gondar Referral Hospital environments. The data presented in this study will provide information of immediate public health importance to clinicians on the selection of antimicrobial agents for patients suffering from infections caused by ESBL Entrobacteriaceae in northwest Ethiopia.Routine ESBLs detection is not common in many developing countries including Ethiopia. Hence, assessing the prevalence and the drug susceptibility of ESBL producing bacteria is very important to develop guideline for the management of infections associated with such organisms. This study was carried out to examine the prevalence and rate of antimicrobial drug resistance of ESBL producing Entrobacteriaceae were 14.8% of which the predominant isolate was Klebsiella pneumoniae (14.7%) which is in line with a study finding in Alexandria, Egypt (14.9%) [Escherchia coli (12.3%) which is higher than those of studies conducted in France (5%) and Algeria (4%) [Entrobacter cloceae (1.2%) was lower than those of a research carried out in Algeria\u2019s Intensive Care Unit of the hospital (11%) [According to this study, the total ESBL producing (14.9%) but lowe (14.9%) , 29 and (14.9%) . these vria (4%) , 29. Howria (4%) , 30. TheEntrobacteriaceae respectively, the overall distribution of ESBL producing Entrobacteriaceae in different sections was higher than the report in France [In our findings, inanimate objects in the hospital OPD, wards, surgical room, delivery room, waiting area, and the waste water from different sewage systems were variously contaminated by multiple drug resistant ESBL producing bacteria. Moreover, medical wards, sewage, and the surgical ward had 52.6, 24.6, and 10.5% of ESBL producing n France . This maKlebsiella pneumoniae than ESBL producing Escherchia coli in an Entrobacteriaceae family [Different studies also showed that the proportion of organisms which cause environmental contamination is directly associated to the number of patients who visit the hospitals. According to this and a previous study more hospital environment contamination was caused by ESBL producing e family , 31, 32.Entrobacteriaceae were 100% resistant to cefpirome, cefpodoxime, ceftazidime, ceftriaxone and amoxicillin with clavulanic acid which is much higher than reports from Poland, cefpodoxime(73.5%) and ceftazidime(81.6%) [Klebsiella pneumonia (95.5%) for ceftazidime and Escherchia coli (91.4%) for ceftazidime [In an antimicrobial susceptibility test, all isolates of ESBL producing e(81.6%) , and Upptazidime .Entrobacteriaceae demonstrated an alarming rate of resistance. In this finding, the rate of resistance to Klebsiella pneumoniae was 25.0% gentamicin and 45.8% ciprofloxacin which is lower than that of a study done in Upper Egypt where gentamicin was 84.4% and ciprofloxacin 77.7% [Escherchia coli isolates showed 20% resistance to gentamicin and 30% to ciprofloxacin. This result shows a lower resistance rate compared to the study done in Upper Egypt (42.8%) to gentamicin and (68.5%) to ciprofloxacin [Even though the rate of resistance was low for non-beta lactam antibiotics compared to beta-lactam antibiotics, ESBL producing in 77.7% . Moreovefloxacin .Entrobacteriaceae are the development of multiple drug resistance (Resistant to two or more drugs). There is a report on co-resistance of ESBL producing Entrobacteriaceae, but not to more than three antibiotics [The most challenging condition in the management of infectious diseases associated with ESBL producing ibiotics . HoweverBased on our findings, the hospital should install a proper hygiene and rational use of antimicrobial activities in order to control and prevent the possibility of spreading of infectious diseases in the compound. Moreover; the sewage system of the hospital should be managed to decrease environmental contaminations.Entrobacteriaceae in hospital environment, it would be better assessing all types of the hospital environments. It would have a better figurative if the study was conducted in different hospitals that are found in north-west Ethiopia.Some type of hospital environments were not included in the study. So to get good distribution of ESBLs"} +{"text": "Background: Non-alcoholic fatty liver disease (NAFLD) is a leading cause of liver disease in developed countries. The association of NAFLD with conduction defects is unknown. The aim of our study was to find whether an association exists between conduction defects and NAFLD.Methods: This is a case-control retrospective study of 700 patients admitted to Orange Park Medical Center, Orange Park, Florida from 2009 to 2015. Patients with a history of alcohol use, congenital heart disease, infiltrative malignancy, and myocarditis were excluded from the study. NAFLD was diagnosed by detection of hepatic steatosis on abdominal ultrasound or computerized tomography (CT) scan. Electrocardiograms (EKGs) were performed on all 700 patients and were interpreted by a cardiologist. Univariate logistic regression was used to assess the association between NAFLD and the variables of demographics, clinical characteristics, medicine use, EKG changes, and conduction defects, while multivariate logistic regression with backward elimination method was performed to determine if NAFLD is one of the most important risk factors for conduction defects.Results: The study population included 408 patients with NAFLD and 292 patients with No-NAFLD. A total of 155 conduction defects occurred in 140 patients; conduction defects included 25.7% (36) patients with first degree block, 2.1% (three) patients with Mobitz type 1 block, 41.4% (58) patients with right bundle branch block (RBBB), 17.9% (25) patients with left bundle branch block (LBBB), 11.4% (16) patients with bifascicular block, and 12.1% (17) patients with nonspecific intraventricular block. Multivariate logistic regression with backward elimination method identified six risk factors for conduction defects; these included NAFLD (odds ratio (OR) 2.38; 95% confidence interval (CI) 1.51-3.73, p<0.0001), hypertrophy , congestive heart failure (CHF) , male sex , diabetes mellitus , and age .Conclusion: NAFLD is associated with conduction defects. Prospective randomized trials are needed to demonstrate that NAFLD causes conduction defects. Non-alcoholic fatty liver disease (NAFLD) is defined as fatty infiltration of the liver in the absence of alcohol use or infection with viral hepatitis. NAFLD is a common disorder, affecting 25% of the world population and almost 24%-32% of the population in the western world . In the To date, there has been one retrospective study to ascertain the association of NAFLD with conduction defects\u00a0. The stuThe study protocol was approved by the OPMC Graduate Medical Education Research committee as a minimal risk study because the study is a retrospective chart review with no patient contact.This\u00a0was a retrospective case-control study designed to test the association between NAFLD and conduction defects Figure . NAFLD wThe study population included adult patients (>18 years of age) admitted to the OPMC from 2009 to 2015. All patients had abdominal imaging and EKG studies ordered. Based on abdominal imaging, the population was divided into NAFLD versus No-NAFLD cases. Patients were excluded if there was a history of alcohol use, defined as >21 drinks/week for men and >14 drinks/week for women. Other exclusions included acute viral hepatitis, chronic viral hepatitis, congenital heart disease, infiltrative malignancy, myocarditis or cardiac surgeries. Also, patients who did not have an abdominal USG, CT scan abdomen or EKG were excluded from the study.Baseline demographic characteristics collected included age, gender, race, obese, chronic conditions (asthma/chronic obstructive pulmonary disease (COPD), congestive heart failure (CHF), diabetes mellitus, hypertension) ischemic heart disease, NAFLD, medication use , cirrhosis, thyroid disorders, smoking, cocaine use Table . We did Conduction defect\u00a0identified on EKG was the primary outcome variable. The EKG changes for conduction defects were determined by reviewing EKG tracings already verified by a cardiologist. Secondary outcomes for this study included the presence of other EKG changes , premature ventricular contractions (PVCs), axis deviation, low voltage, prolonged QTc interval, hypertrophy, and ST wave changes).Univariate logistic regression analysis was used to assess the association between NAFLD, baseline demographics, clinical characteristics, medicine use, EKG changes, and conduction defects Table . MultivaA total of 700 patients were included in the study. NAFLD was identified on abdominal imaging in 408 patients. In the No-NAFLD group, there were 292 patients. The median age was 58 years (standard deviation (SD)=15.3 years). There were 293 males (41.9%), and 407 females (58.1%). Most patients were Caucasian . Other baseline characteristics are listed below identified a positive association with NAFLD . Atrial fibrillation showed no association with NAFLD Table .The proportion of patients with a conduction defect on EKG was higher in patients with NAFLD 107/408, 26.2%) compared to the No-NAFLD group , . When conduction defects were further stratified , hypertrophy , CHF , male sex ,\u00a0diabetes mellitus , and age (Table The major finding of this study is that patients diagnosed with NAFLD showed a significant association with conduction defects. This association was independent of numerous other risk factors after adjusting for confounders.Prior studies have shown associations between NAFLD and CAD -13. HoweThe underlying pathophysiological mechanism responsible for the association between NAFLD and conduction defect is not well understood. NALFD might be a marker for ectopic fat deposition in myocardium and pericardium that promotes cardiovascular disease. A recent study has shown an association between intra-hepatic and myocardial triacylglycerol content and that increased pericardial fat is associated with increased prevalence of atrial fibrillation -15. FurtThis study has several limitations. First, NAFLD was diagnosed by USG or CT scan, instead of tissue biopsy, the gold standard. Studies have shown that USG has a sensitivity of 60% to 94% and specificity of 84% to 95%, while CT scan has a sensitivity of 82% and specificity of 100%; so neither USG nor CT scan is able to reliably detect hepatic lipid content that is less than 30% -24. HencSeveral studies have demonstrated increased cardiovascular morbidity and mortality in NAFLD patients -26. It iThe role of NAFLD as a novel risk factor for cardiac disease has been extensively researched in the last decade. Previous studies have shown an association between NAFLD and structural and metabolic cardiac changes. Still, the data is relatively scarce for the association between NAFLD and arrhythmogenic cardiac abnormalities.\u00a0Our study suggests that NAFLD is associated with conduction defects. Larger studies are needed to find out the causal relationship as well as the pathophysiological pathways that connect NAFLD and arrhythmogenic abnormalities of the heart."} +{"text": "Kikuchi-Fujimoto disease is a rare, self-limited, histiocytic, necrotizing lymphadenitis first described in Japan in 1972. Necrosis of lymph node tissue is caused by apoptosis and may be virally induced. It commonly presents with cervical lymphadenitis and fever. Despite its low incidence, Kikuchi-Fujimoto disease should be considered in patients with persistent lymphadenopathy. Originally thought to occur only in young Asian women, it is now recognized in other geographic regions. We report a 30-year-old white woman with Kikuchi-Fujimoto disease. We discuss the clinical features, differential diagnosis, radiography, pathology, and outcome. Kikuchi-Fujimoto disease (KFD), also known as histiocytic necrotizing lymphadenitis, is an uncommon, self-limited, benign, systemic lymphadenitis of unknown etiology. By the late 1960s, members of the Pathology Reference Center and FujiA 30-year-old white woman presented to the emergency department with a 4-day history of a left anterior cervical mass. She reported that swelling in her upper neck had been waxing and waning. In the 36 hours before her presentation, the swelling had decreased the range of motion in her neck. The mass was causing severe pain and tenderness over the sternocleidomastoid muscle, and she also had mild trismus. She reported intermittent fevers up to 39\u00b0C and denied any airway compromise or otalgia. She was a nonsmoker with an unremarkable medical history, except for Hashimoto thyroiditis. Her medical regimen included levothyroxine sodium and azithromycin. 9/L and consisted of 77% neutrophils, 8% monocytes, 14% lymphocytes, less than 1% basophils, and less than 1% eosinophils. Her hemoglobin level was 8.4\u2009g/dL, , and her platelet count was 157 \u00d7 109/L . A chest radiograph was negative for any masses or lymphadenopathy. A computed tomographic (CT) scan revealed a 2\u2009cm mass in the left jugular digastric region (level 2) with peripheral enhancement that are more prevalent in Asian KFD patients [HLA-DPB1 allele appears with considerably higher frequency in Asians when compared with whites [The incidence of KFD is unknown. It has been observed in patients aged 19 months to 75 years . KFD is The etiology of KFD has not been identified. Necrosis of the lymph nodes appears to be caused by apoptosis . Recent Despite the low incidence, KFD should be considered in patients with persistent lymphadenopathy, and an early diagnosis from biopsy findings can prevent unnecessary investigations and treatments. Most patients 80%) present with cervical lymphadenitis, although any lymph node region may be involved 0% presen. Other aRadiographic findings specific to KFD have not been established, and reports of KFD in the medical literature have largely focused on the disease pathology. Chest radiography should be included in the diagnostic evaluation to eliminate the possibility of malignancy or tuberculosis. CT and ultrasonography are common and often helpful before obtaining a biopsy specimen. Ultrasonography frequently shows lymph nodes with a hypoechoic center and a hyperechoic rim , 12. CT The radiographic diagnosis of KFD is broad and includes Hodgkin and non-Hodgkin disease, metastatic tumor, tuberculosis, nontuberculous mycobacterial infection, SLE, human immunodeficiency virus infection, infectious mononucleosis, cat-scratch disease, mucocutaneous lymph node syndrome (Kawasaki disease), and toxoplasmosis. In 1 series, 29% of patients with KFD were initially misdiagnosed as having Hodgkin or non-Hodgkin disease .There are no specific assays available to confirm the diagnosis of KFD, but laboratory tests are used to eliminate other causes of cervical lymphadenopathy. Peripheral blood tests indicate 25.0% to 58.3% of KFD patients had leukopenia, and 25.0% to 31.1% of patients had atypical lymphocytes . ExtensiPatients suspected of having KFD often undergo fine-needle aspiration before an excisional biopsy is performed. Aspiration was not performed on our patient because ultrasonography indicated that the mass was solid. The definitive diagnosis of KFD is made through lymph node excision biopsy and histologic examination. There are several classic histologic features of KFD. The affected lymph nodes have patchy necrotizing regions (the degree of necrosis varies widely among patients), mainly in the paracortical areas . They ofThe differential diagnosis of a slow-growing neck mass is extensive and includes malignant lymphoma, systemic lupus erythematosus (SLE), Hodgkin disease, toxoplasmosis, metastatic carcinoma, infectious mononucleosis, acquired immunodeficiency syndrome, cat-scratch disease, and angioimmunoblastic lymphadenopathy . To diffIn 80% of patients, KFD is self-limited and resolves within 1 to 6 months without specific treatment . PatientKFD is a self-limited and typically benign lymphadenitis of unknown etiology now recognized in multiple geographic regions and races. The clinical suspicions of the otolaryngologic surgeon, in conjunction with the pathology findings, are critical for an accurate diagnosis. Understanding the characteristic clinical presentation and histologic findings of KFD help exclude malignant disorders and nonneoplastic conditions that require specific therapy."} +{"text": "The serum diagnostic value of the foeto-acinar pancreatic protein (FAP protein), an oncofoetal pancreatic antigen, was tested in 201 patients. Of these, 112 suffered from malignant disease and 89 had benign disease (49 patients with hepato-pancreato-biliary disease and 40 with other benign disease). FAP protein was measured by a competitive radioimmunoassay. In this technique, the normal cut-off level was 10% inhibition. This was deducted from values in 32 normal sera. FAP protein levels superior to 10% inhibition were found in 86% of patients with pancreatic cancer, in 31% with non-pancreatic malignancy, in 69% with benign hepato-pancreato-biliary disease and in 20% with other benign diseases. Accordingly, sensitivity of FAP protein for pancreatic carcinoma was 86% and specificity, 66%. However, high FAP protein levels (greater than 30% inhibition) were almost exclusively seen in patients with pancreatic cancer. At this cut-off level, specificity increased to 95% but sensitivity decreased to 51%. Determination of the carbohydrate antigen CA19/9 was made in parallel by a commercially available assay. At the cut-off level of 37 u ml-1, CA19/9 in our serum panel had a sensitivity of 74% for pancreatic carcinoma and a specificity of 88%. In pancreatic cancer 55 out of 57 patients had elevated levels of either FAP protein or CA19/9 ."} +{"text": "Prostate leiomyosarcoma is an extremely rare and highly aggressive neoplasm that accounts for less than 0.1% of primary prostate malignancies. We present a patient with primary leiomyosarcoma of the prostate and review 54 cases reported in the literature to discuss the clinical, diagnostic and therapeutic aspects of this uncommon tumor. Median survival was estimated at 17 months (95% C.I. 20.7\u201343.7 months) and the 1-, 3-, and 5-year actuarial survival rates were 68%, 34%, and 26%, respectively. The only factors predictive of long-term survival were negative surgical margins and absence of metastatic disease at presentation. A multidisciplinary approach is necessary for appropriate management of this dire entity. Prostate leiomyosarcoma is an extremely rare neoplasm that accounts for less than 0.1% of primary prostate malignancies . We presAn 80-year-old man presented with frequent micturition, dysuria, poorurinary stream, and nocturia of approximately 12-month duration. He reported nohematuria or perineal pain and denied any constitutional symptoms. There was nofamily history of genitourinary cancer. He was a heavy smoker, drank alcoholsocially, and reported no exposure to hazardous chemicals. Rectal examination revealed a firm nodular mass, 3 to 4 cm in diameter, involving the left lobe of the prostate and extending to the edge of the gland. The right prostatic lobe was diffusely firm. There was no palpable lymphadenopathy, and the rest of his physical examination was unremarkable. Prostate specific antigen(PSA) at presentation was 2.7 ng/mL, and his creatinine was normal. His lastPSA, obtained 3 years earlier by his primary care physician as part of routine annual physical examination, was the same.Patient underwent transurethral resection of the prostate (TURP), and pathologyrevealed a dominant population of neoplastic spindle cells intermingled withgiant neoplastic cells and multifocal necrosis that involved almost the entiretumor Figures . ImmunohComputed tomography (CT) of the abdomen demonstrated two hypodense liver lesions, and CTscan of the chest showed multiple pulmonary nodules and mediastinal and lefthilar lymphadenopathy, all considered suspicious for metastatic disease. CT ofthe brain and bone scan was negative for metastatic disease.Patient denied any intervention and was treated symptomatically. Three months later, hepresented with urinary retention and acute renal failure. A permanent urinarycatheter was placed, and a palliative external beam radiotherapy wasrecommended. Patient denied any treatment and was discharged home with hospice.He died 2 weeks later.The information for the 54 cases included in this review was compiled using the PubMed and Medline databases for articles published in the last 20 years until March 1, 2008. The seaThe median age of the 54-patient cohort included in this review was 63.8 years (rangingfrom 40 to 80). The most common presenting manifestations includedobstructive urinary symptoms in 89.4% and perineal or rectal pain in 25.6% ofthe patients. Less frequent manifestations wereburning on ejaculation andhematuria, both presented as initial symptoms inonly 5.2% of the patients . The diaA sizeable proportion of patients (23.5%) had metastatic disease at the time of diagnosis.Lungs were the most common sites of metastatic disease accounting for 17.6% ofthe cases, followed by liver (11.7%), and bone (5.8%) . Only twP = .018), and patients with microscopic or gross residual disease after surgery had worse overall survivalthan those with microscopically negative margins after surgery .Among 55 patients (including our patient), clinical outcome data were available for 34patients. Median survival was 17 months (95% CI 20.7\u201343.7 months) andthe 1-, 3-, and 5-year a ctuarial survival rates were 68%, 34%, and 26%, respectively. Our analysis in this 34-patient cohortdemonstrated that the only factors predictive of long-term survival were absent from metastaticdisease at presentation and negative surgical margins Figures , resp.. Primary prostate sarcomas arise from nonepithelial mesenchymal components of theprostate stroma and account for less than 0.1% of primary prostate tumors .Leiomyosarcoma most commonly presents with signs and symptoms of urinary obstruction, as well as hematuria, perineal and/orrectal pain, constipation, burning on ejaculation, and constitutional symptomssuch as weight loss \u20137. In thPhysical examination reveals nonspecific enlargement of the prostate, while serum PSA istypically within normal limits , 3, 7. DThe majority of leiomyosarcomas are high-grade hypercellular lesions composed ofintersecting bundles of eosinophilic spindle-shaped cells with increasedmitotic activity and moderate to severe nuclear atypia . High-gThe local extent of prostatic leiomyosarcoma is determined by CT or MRI scans, which provideclear delineation of the tumors from surrounding normal tissues and areimportant in assessing whether they are surgically resectable. A significantproportion of these neoplasms presents with metastatic disease. In the54-patient cohort, lungs were the most common sites of metastatic spread followedby liver and bone. In that regard, chest CT constitutes an important componentof the metastatic evaluation of prostatic leiomyosarcomas. Since brain metastasesare uncommon, imaging of the brain should not be performed routinely, unlessthere is high-clinical suspicion , 3.Multimodality treatment combinations including surgery, pre- or postoperative radiationtherapy, and neoadjuvant or adjuvant chemotherapy have been used in themanagement of leiomyosarcomas of the prostate, but there are no standard treatmentrecommendations \u20134, 7, 11Surgeries with curative intent include radical retropubic prostatectomy, radicalcystoprostatectomy, suprapubic prostatectomy, and pelvic exenteration \u20134, 11. VThe clinical outcome of patients with prostate leiomyosarcoma is poor. The 17-month mediansurvival estimated in our retrospective analysis renders prostateleiomyosarcoma as one of the most aggressive prostate malignancies, similar toother histologic subtypes of prostate soft-tissue sarcomas, more aggressivethan prostate adenocarcinoma, albeit somewhat less aggressive than prostatecarcinosarcoma, which is associated with an actuarial risk of death of 20%within 1 year of diagnosis and frequent widespread metastases to bones, liver,and lungs. When compared to other urologic leiomyosarcomas, prostateleiomyosarcomas are associated with significantly worse survival than renal andbladder leiomyosarcomas , 19. OurIn conclusion, leiomyosarcoma of the prostate is a rare neoplasm that usually presentswith metastatic disease and typically follows an aggressive course. A multidisciplinary approach that includes urology, radiation,and medical oncology consultations should be employed for appropriatemanagement of this devastating malignancy."} +{"text": "Patients in the ICU have encountered an increasing emergence and spread of antibiotic-resistant pathogens. We examined patterns of antimicrobial susceptibility in gram-negative isolates to commonly used drugs in an adult ICU at a tertiary care hospital in Riyadh, Saudi Arabia.A retrospective study was carried out of gram-negative isolates from the adult ICU of King Fahad National Guard Hospital (KFNGH) between 2004 and 2009. Organisms were identified and tested by an automated identification and susceptibility system, and the antibiotic susceptibility testing was confirmed by the disk diffusion method.Acinetobacter baumannii, followed by Pseudomonas aeruginosa, Escherichia coli, Klebsiella pnemoniae, Stenotrophomonas maltophilia, and Enterobacter. Antibiotic susceptibility patterns significantly declined in many organisms, especially A baumannii, E coli, S marcescens, and Enterobacter. A baumannii susceptibility was significantly decreased to imipenem (55% to 10%), meropenem (33% to 10%), ciprofloxacin (22% to 10%), and amikacin (12% to 6%). E coli susceptibility was markedly decreased (from 75% to 50% or less) to cefuroxime, ceftazidime, cefotaxime, and cefepime. S marcescens susceptibility was markedly decreased to cefotaxime (100% to 32%), ceftazidime (100% to 35%), and cefepime (100% to 66%). Enterobacter susceptibility was markedly decreased to ceftazidime (34% to 5%), cefotaxime (34% to 6%), and pipracillin-tazobactam (51% to 35%). Respiratory samples were the most frequently indicative of multidrug-resistant pathogens (63%), followed by urinary samples (57%).The most frequently isolated organism was Antimicrobial resistance is an emerging problem in the KFNGH ICU, justifying new more stringent antibiotic prescription guidelines. Continuous monitoring of antimicrobial susceptibility and strict adherence to infection prevention guidelines are essential to eliminate major outbreaks in the future. Multidrug-resistant organisms (MDROs) are resistant to one or more classes of antimicrobial agents, such as \u03b2-lactams, including penicillins, cephalosporins, and monobactams, carbapenems, fluoroquinolones, and aminoglycosides. The severity and extent of disease caused by these pathogens varies by the population(s) affected and by the institution(s) in which they are found, but the prevention and control of MDROs should be a national priority.2Enterobacteriaceae family of gram-negative bacilli, particularly Klebsiella spp., E coli, and Proteus mirabilis; however, other gram-negative bacilli have been documented to produce such enzymes, including Enterobacter spp., P aeruginosa, Citrobacter freundii, Morganella morganii, and S marcescens. P aeruginosa has a strong tendency to become a multidrug-resistant pathogen. Usually, this process occurs as a result of both cross-infection with resistant strains and acquisition of drug resistance during treatment. Klebsiella spp. that produce a carbapenemase known as KPC are a serious concern because of high-level resistance against most antibiotics. The KPC enzymes are a class A, group 2f \u03b2-lactamase that efficiently hydrolyze carbapenems, as well as other \u03b2-lactam antibiotics.3Extended-spectrum \u03b2-lactamases (ESBLs) are often found in the A baumannii infections have become increasingly common among critically-ill patients in intensive care units (ICUs) worldwide.A baumannii clinical isolates are frequently resistant to most antimicrobial agents, and evidence of pan-drug resistance among A baumannii isolates has been reported. Data suggest that infections caused by S maltophilia have high mortality and that the risk factors associated with mortality are related to the initial clinical condition and patient type.5These facts constitute an alarming development in the field of infectious diseases, with major public health implications. More intensive efforts are urgently required to elucidate the epidemiological and infection control issues related to these organisms and to improve the management of patients with such infections.6Previous antimicrobial use is one of the strongest risk factors associated with the development of resistant pathogens. There should be monitoring of bacterial etiologies and infection patterns in order to take the necessary steps to treat infection, prevent resistance development, and lower hospital acquired cross infection. Knowledge of susceptibility patterns is helpful in selecting empirical therapy and improving the likelihood of a satisfactory outcome for the patient. The object of this study was to examine patterns of antimicrobial susceptibility of gram-negative isolates to commonly used drugs in ICU patients at a major tertiary care hospital.A retrospective review was conducted of all reports of gram-negative isolates from the general adult ICU of King Fahad National Guard Hospital (KFNGH) between January 2004 and June 2009. KFNGH is an 800-bed tertiary care referral hospital in Riyadh. Gram-negative organisms were identified and tested and results were interpreted according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI).E coli ATCC 25922, E coli ATCC 35218, P aeruginosa ATCC 27853, and Enterococcus faecalis ATCC 29212 to check the thymidine level on Muller Hinton Agar.8The following antimicrobial agents were tested either by the breakpoint method (with the MicroScan system) or by the Kirby-Bauer disk diffusion method using the following disks on (Muller Hinton Agar Plate): amikacin (30-mg disks), ampicillin (10-mg disks), ceftazidime (30-mg disks), ceftriaxone (30-mg disks), ciprofloxacin (5-mg disks), gentamicin (10-mg disks), imipenem (10-mg disks), trimethoprim-sulfamethoxazole , and nitrofurantoin (300-mg disks). Quality control was performed by testing these same antimicrobials on P values were two-tailed. P value <.05 was considered as significant. Open Epi software was used for all statistical analyses.The proportion of susceptible isolates was calculated as the sum of susceptible organisms (neither intermediately susceptible nor resistant) relative to the total number of organisms tested. Multidrug resistance was defined as resistance to three or more antimicrobials . The trend in the susceptibility rate over a 6 years period (between 2004 and 2009) was calculated and analyzed to identify a statistically significant increasing or decreasing trend using chi-square for linear trend analysis. Associations between categorical variables were tested using the chi-square test. The percent of change of antibiotic susceptibility was calculated as the difference between the later (e.g. 2009) and earlier (e.g. 2004) susceptibilities percentages divided by the earlier one. All Acinetobacter spp. , followed by P aeruginosa , E coli , K pneumonia , S maltophilia , Enterobacter spp. , Proteus spp. , and 35 isolates of Citrobacter spp. and Serratia marcescens each (1.25% each). We included only samples sent to rule out infection and did not include all surveillance or screening samples, which may represent colonization rather true infection.Of 4192 isolates taken from clinical specimens between 2004 and 2009, 2792 (66.6%) were gram-negative organisms and 1400 (33.4%) were gram-positive organisms. The number of gram-negative isolates were 310 in 2004, 481 isolates in 2005, 339 isolates in 2006, 386 isolates in 2007, 851 in 2008, and 424 in as of June 2009. The most common bacteria isolated were A baumannii susceptibility markedly decreased to imipenem , meropenem , ciprofloxacin , and amikacin , ceftazidime (69% in 2004 to 44% in 2009), and ciprofloxacin (67% to 49%) , ceftazidime , cefotaxime , cefepime , and ampicillin exhibited ESBL. The rate of ESBL in E coli increased gradually from 9% in 2004 to 16% in 2009. Of 285 K pneumonia isolates, the ESBL rate increased from 12% in 2004 and to 21% in 2009. The increase could have been related to better screening and detection, which was introduced to our laboratory in 2007. All of our ESBL-producing isolates were susceptible to carpabenems except one case of K pneumonia carpabenemase that is still under further genotypic investigation. S marcescens susceptibility was markedly decreased to cefotaxime , ceftazidime , and pipracillin-tazobactam . Enterobacter susceptibility was markedly decreased in vitro to ceftazidime , cefotaxime , and pipracillin-tazobactam . Gentamicin effectiveness in S maltophilia decreased dramatically, while trimethoprim-sulfamethoxazole remained the most effective antimicrobial agent . P aerug to 49%) . E coli P=.723) . Of 392 al agent . The mosEach year, healthcare-associated infections affect an estimated two million Americans, including 500 000 intensive care unit (ICU) patients, resulting in an estimated 90 000 deaths and $4.5 billion in excess health care costs.10E coli (7.7%-15.5%), and P aeruginosa (10.8%-22.3%) being most common in three of the five countries following only S aureus. The gram-positive genus Enterococcus, either as E faecalis, E faecium, or unspeciated isolates accounted for <10% of isolates in most countries.A baumannii in addition to E coli and P aeruginosa that were also common as in other western countries. We also noted the presence of S maltophilia in the Saudi isolates, which is less frequent than isolates in the Western ICUs.Jones et al assimilated in vitro susceptibility data from over 220000 isolates from ICUs in five countries over the period 2000 to 2002.K pneumoniae is naturally resistant to aminopenicillins (ampicillin). Multiresistant A baumannii are defined as resistant to aminoglycosides and cephalosporins: some of our isolates are also resistant to imipenem or meropenem. Rates of resistance to ceftazidime in Europe range from 15% to 97% and to imipenem from less than 1% up to 85%. S maltophilia is intrinsically resistant to carbapenems; however, the majority of strains are susceptible to ticarcillin-clavulanate. S maltophilia is frequently resistant to all aminoglycosides. Most strains of Enterobacter species that are resistant to third-generation cephalosporins produce an AmpC \u03b2-lactamase, which can inactivate most cephalosporins and the cephamycins. In P aeruginosa, a number of acquired \u03b2-lactamases can hydrolyze carbapenems and all other \u03b2-lactams with the exception of aztreonam. However, the frequent presence of other \u03b2-lactamases in these bacteria usually results in resistance to aztreonam.The resistance of some of the isolates are due to inherent resistance of the microorganisms. For example, Klebsiella isolates had increased from 7% to 9%, imipenem resistance among P aeruginosa strains had increased from 12% to 19%, quinolone resistance in P aeruginosa had increased from 12% to 23%, and resistance to third-generation cephalosporins among Enterobacter strains had increased from 34% to 37%. Our data showed significant resistance of cefotaxime to Enterobacter (66%-94%) and E coli (24%-54%). Pipracillin-tazobactam also exhibited increased resistance in Citrobacter (8%-25%) and Enterobacter (49%-68%).A review of the 1999 National Nosocomial Infection Surveillance (NNIS) survey data from the CDC,P aeruginosa, K pneumonia, E coli, and Enterobacter were most commonly isolated, with imipenem, ciprofloxacin, and amikacin showing greatest efficacy. Another study comparing ICU isolates from Saudi Arabia and KuwaitE coli and Klebsiella spp. demonstrated multidrug resistance to monobactams, cephems, and aminoglycosides. The Kuwaiti Pseudomonas spp. were more sensitive to imipenem (100% vs. 68%). They concluded that the higher number of resistant bacteria seen in Saudi Arabia might be due to greater antibiotic consumption. Another study carried out at a tertiary care hospital in RiyadhP aeruginosa, E coli, S aureus, K pneumonia, and S marcescens. In this analysis, we found that imipenem inhibited 98% of all isolates, and we had a significant overall reduction in the antibiotic susceptibility pattern in vitro.There have been relatively few studies of antibiotic use in ICUs in Saudi Arabia. EltahawyP aeruginosa, E coli, Acinetobacter spp., and Klebsiella spp. The most commonly encountered ICU infections were ventilator-associated pneumonia, bacteremia, urinary tract infection, and wound infection. A study of clinical isolates from 19 medical centers in Canada showed that S aureus (MSSA and MRSA), E coli, P aeruginosa, H influenzae, Enterococcus spp., S pneumoniae, and K pneumoniae are the most common isolates recovered in Canadian ICUs. Acinetobacter spp. and S maltophilia are less prevalent in Europe and North America, but appear more significant in Saudi Arabia.1819In the 1995 European Prevalence of Infection in Intensive Care (EPIIC) Study, the most frequently reported gram-negative pathogens were Epidemiological information will help to implement better infection control policies in ICUs and help collaboration between different ICUs as more knowledge is gained. Therefore, developing nationwide antibiotic policy and guidelines is essential nowadays due to increasing resistance patterns. Also, developing a local antibiogram database will improve the knowledge of antimicrobial resistance patterns in Saudi Arabia and will also help to improve treatment strategies based on unit-specific data."} +{"text": "The epidemiology of diarrheal disease in Botswana, an HIV endemic region, islargely unknown. Our primary objective was to characterize the prevalentbacterial and parasitic enteropathogens in Gaborone, Botswana. Secondaryobjectives included determining corresponding antimicrobial resistancepatterns and the value of stool white and red blood cells for predictingbacterial and parasitic enteropathogens.Shigella spp. and Salmonella spp.,isolated from 4.0% (180 of 4485) and 3.9% (175 of4485) of specimens, respectively. Escherichia coli (22 of4485) and Campylobacter spp. (22 of 4485) each accountedfor 0.5% of pathogens. Comparing antimicrobial resistance amongShigella spp. and Salmonella spp.between two periods, February 2003 to February 2004 and July 2006 to July2008, revealed an increase in ampicillin resistance amongShigella spp. from 43% to 83%(p<0.001). Among Salmonella spp., resistance tochloramphenicol decreased from 56% to 6%(p<0.001). The absence of stool white and red blood cells correlatedwith a high specificity and negative predictive value.A retrospective cross-sectional study examined laboratory records of stoolspecimens analyzed by the Botswana National Health Laboratory in Gaborone,Botswana from February 2003 through July 2008. In 4485 specimens the mediansubject age was 23 [interquartile range 1.6\u201334]years. Overall, 14.4% (644 of 4485) of samples yielded apathogen. Bacteria alone were isolated in 8.2% (367 of 4485),parasites alone in 5.6% (253 of 4485) and both in 0.5%(24 of 4485) of samples. The most common bacterial pathogens wereShigella spp. and Salmonella spp.were the most common bacteria; Isospora spp. andCryptosporidium spp. were the most common parasites.Resistance to commonly used antimicrobials is high and should be closelymonitored.Most gastroenteritis stools were culture and microscopy negative suggestingthat viral pathogens were the majority etiologic agents in this Botswanacohort. Diarrheal disease is a serious cause of mortality and morbidity in Sub-SaharanAfrica, accounting for an estimated 16% of deaths in Africa amongchildren <5 years of ageA broad range of etiologic agents are responsible for acute and chronic diarrhealdisease, and the prevalence of such agents varies greatly by geographic region,season, patient age, immune status, and socioeconomic conditions. The dynamicvariability of etiologic agents has been shown in studies throughout southern AfricaSalmonella spp. and Shigella spp., andto determine the sensitivity, specificity, positive predictive value and negativepredictive value of stool white blood cells (WBC) and red blood cells (RBC) forbacterial and parasitic enteropathogens.The primary objective of this study was to determine the prevalence of bacterial andparasitic enteropathogens in Gaborone, Botswana in stool samples from both inpatientand outpatient adult and pediatric populations. Secondary objectives were todescribe antimicrobial susceptibilities of the most frequently occurring bacterialpathogens, This study was reviewed and approved by the institutional review boards of theBotswana Ministry of Health , Princess Marina Hospital, and The Children's Hospital of Philadelphia. A waiver of informed consent was granted by all reviewboards given that the study represented a de-identified, retrospective study ofroutine clinical practice with no more than minimal risk to subjects.A retrospective, cross-sectional study of stool specimen records collectedbetween February 1, 2003 and July 31, 2008 was performed at the BotswanaNational Health Laboratory (BNHL) in Gaborone, Botswana. The BNHL, which servesa population of 500,000, is the reference microbiology laboratory for the publichealth facilities in and those surrounding Gaborone, Botswana. Stool samplesreceived from Princess Marina Hospital (PMH), the largest tertiary care referralcenter in Botswana, as well as from clinics and smaller hospitals within a 30 kmradius of Gaborone were eligible for inclusion. Specimens were excluded if theycame from a patient without gastroenteritis. Botswana has the second highestprevalence of HIV in the world. In 2007, an estimated 23.9% ofBatswana aged 15\u201349 years were HIV positive Salmonellaspp. and Shigella spp. for susceptibility to ampicillin,trimethoprim-sulfamethoxazole, gentamicin, trimethoprim, tetracycline,cefotaxime, and ampicillin-sulbactam. From October 2003, BNHL adopted the WorldHealth Organization (WHO) recommended panel of susceptibility testing toampicillin, trimethoprim-sulfamethoxazole, ciprofloxacin, chloramphenicol, andnalidixic acid Stool samples were subjected to microscopy, culture, and antimicrobialsusceptibility testing. Routine laboratory practice for stool samples at theBNHL during the study period followed a standard operating procedure including a24 hour turn-around-time for stool microscopy and processing of all stoolsamples within 24 hours of collection. All samples were assessed by a qualifiedlaboratory technologist who was supervised by a laboratory scientist. Weekendcoverage included a technologist on duty until 4 pm each day. Antimicrobialsusceptibility patterns of isolates were determined by disk-diffusion methodaccording to Clinical Laboratory Standards Institute (CLSI) guidelinesstFebruary 2003 through 27th February 2004 and 1st July 2006through 31st July 2008. For the period 28th Feb 2004 to30th June 2006, records were available for 11 (39.3%)of 28 months. This period contributed 308 (6.9%) of 4485 studyspecimens. While the overall analysis included all specimens analyzed fromFebruary 2003 through July 2008, the two selected study periods were compared todetermine whether changes in antimicrobial susceptibility patterns occurred overtime. Overall proportions of different pathogens found in stool were calculatedand stratified as a measure of disease burden.Electronic and paper-based records of the BNHL were reviewed to identify stoolsamples meeting study inclusion criteria. Demographic data abstracted includedage, sex and, for inpatient samples only, ward location. Results ofantimicrobial susceptibility testing were recorded when available. In addition,exposure to antibiotics in the 2 weeks before the stool sample was submitted wasrecorded as antibiotic exposure in this period may have influenced theantimicrobial susceptibilities of bacterial pathogens. Consistent and completestool records were available for two selected study periods: 1Data were analyzed using STATA version 9.2 .Categorical variables were compared using Fisher exact tests. Sensitivity,specificity, positive predictive value and negative predictive value werecalculated to determine the accuracy of stool white blood cells and red bloodcells in predicting bacterial and parasitic infections.During the study period, 90.4% (4485 of 4960) of stool samples metinclusion criteria. Samples were excluded because no result was recorded (205 of4960) or the sample came from a patient without gastroenteritis (270 of 4960).Outpatient services accounted for 70.5% (3162 of 4485) ofspecimens included in this study. Samples from inpatients at PMH accounted for26.7% (1197 of 4485) of specimens. The location was unknown for2.8% (126 of 4485) of specimens. The demographic characteristics ofpatients from which samples were received are described in Shigella spp. andSalmonella spp., isolated from 4.0% (180 of 4485)and 3.9% (175 of 4485) of all specimens, respectively.Escherichia coli (22 of 4485) andCampylobacter spp. (22 of 4485) each accounted for0.5% of all specimens. Of the Shigella spp.,S. flexneri was the most common, accounting for63.3% (114 of 180) of all Shigella isolates,followed by S. sonnei (15.6%), S.dysenteriae (11.1%), and S. boydii(7.2%). Data for specific serotypes of Salmonellaspp. were not available, other than for two cases of S. typhi.Overall, 14.4% (644 of 4485) of samples yielded a pathogen. Bacteriaalone were isolated in 8.2% (367 of 4485), parasites alone in5.6% (253 of 4485) and both parasites and bacteria in 0.5%(24 of 4485). Of the 367 samples that isolated bacteria alone, 8 samplesisolated two types of pathologic bacteria. Because of this, the total number ofbacterial isolates is 399 (367+24+8). The most commonbacterial pathogens were Isospora spp. andCryptosporidium spp., found in 2.5% (113 of4485) and 2.2% (99 of 4485) of all specimens, respectively. Othercommon parasites were Giardia lamblia (0.8%) andTaenia spp. (0.6%).The most common parasites were Individual pathogens were stratified by patient age and selected study period asillustrated in Shigella spp. isolates and a significant decrease inresistance to chloramphenicol among Salmonella spp. isolatesover time. No Salmonella spp. or Shigella spp.isolates were resistant to ciprofloxacin, while 0% (0 of 10) and22% (2 of 9) Campylobacter spp. were resistant tociprofloxacin in the earlier and later selected study periods, respectively.When all bacterial isolates were pooled together, significant findings were anincrease in ampicillin resistance (p<0.001), and decreased resistance totrimethoprim-sulfamethoxazole (p\u200a=\u200a0.028) andchloramphenicol (p\u200a=\u200a0.001).Susceptibility data were available for 87.7% (350 of 399) of positivebacterial isolates. Because data were most consistently available forsusceptibility to ampicillin, trimethoprim-sulfamethoxazole, chloramphenicol,and nalidixic acid within the two selected study periods, resistance patterns tothese antimicrobials for all bacterial isolates were compared . Of these, 24% (33 of 139) wereexposed to antimicrobials within 2 weeks as follows: cefotaxime 33%(11 of 33), trimethoprim-sulfamethoxazole 30% (10 of 33), andmetronidazole 24% (8 of 33).Shigella spp. and Salmonella spp. were the mostcommon bacteria, while Isospora spp. andCryptosporidium spp. were the most common parasites. We alsoidentified important trends in antimicrobial susceptibility among common agentsresponsible for gastroenteritis in southern Africa. The proportion of resistance toampicillin and trimethoprim-sulfamethoxazole among common pathogens was high,supporting the utility of nalidixic acid as empiric therapy for suspected bacterialdysenteric gastroenteritis. Although significant changes in resistance to nalidixicacid were absent, susceptibility to this agent should be closely monitored.Our study reports a high proportion of stool specimens with no identifiablepathogenic bacteria or parasites. When pathogens were identified,Compared with previous studies of diarrheal disease in the region, our data showed amarkedly lower overall proportion of bacterial and parasitic isolates. Thesedifferences could be partially attributed to the fact that few other regionalstudies comprehensively evaluated a similar breadth of pathogens, and most wererestricted to children. In our study, if we restricted the proportion analysis ofbacterial pathogens to children younger than 5 years of age, the rate increases to11.1% (143 of 1288), although this is still lower than other regionalstudies. Studies from Zimbabwe, Mozambique, South Africa, and Kenya have reportedbacterial pathogens in 22% to 32% of specimens from patientswith diarrheal disease Shigella spp. was alsosubstantially lower than most other estimates in the region, which ranged from10\u201316% Shigella spp. of 0.2% Shigella isolatesare similar to those previously reported from the region with ranges of resistancereported at 77\u201397% for ampicillin, 90\u201397%for trimethoprim-sulfamethoxazole, 27\u201388% for chloramphenicol,0\u20133% for ciprofloxacin, and 0\u20132% fornalidixic acid The proportion of specimens positive for Salmonella spp. was similarto other estimates from the region, which ranged from 1.4\u20135.8%Salmonella isolates was similar toregional studies with ranges of 13\u201362% for ampicillin,4\u201388% for trimethoprim-sulfamethoxazole,3\u201336% for chloramphenicol, 0\u20131% forciprofloxacin and 3\u201333% for nalidixic acid) In the present study, the proportion of Campylobacter spp.,E. coli, Isospora spp.,Cryptosporidium spp., and G. lamblia, thanhave been seen in other studies in the region. For these pathogens, otherSub-Saharan Africa studies have indicated ranges of: Campylobacterspp. (1\u20139%), E. coli(2\u201323%), Isosporaspp.(12%), Cryptosporidium spp.(0.5\u201316%), and G. lamblia(1\u20137%) We also reported a lower overall proportion of The calculated sensitivity, specificity, positive predictive value, and negativepredictive value of WBC and/or RBC in determining the presence of bacteria werewithin reported ranges of previous studies examining acute infectious diarrhea Shigella spp. in that study was higher than thepresent study ; 89% of isolates wereresistant to ampicillin and 39% were resistant totrimethoprim-sulfamethoxazole. The prevalence of Salmonella spp.,was similar to that found in our study and, in contrast to our results, allSalmonella spp. were sensitive to ampicillin andtrimethoprim-sulfamethoxazole. While prospective, the Urio et alstudy was limited to a five month period, did not examine antimicrobial resistancein enteropathogens other than Salmonella orShigella and reflects a single clinic pediatric experience in a lowsocioeconomic setting The only similar study concerning diarrheal disease in Gaborone included 221 childrenwith diarrhea enrolled prospectively from July through November, 1998 at a singleclinic serving a relatively socioeconomically poor area Shigella,Campylobacter) and many parasites are sensitive to desiccation whenleft in the specimen container for an extended period of time. This bias would causeus to underestimate the prevalence of some pathogens, but would not impact theinterpretation of susceptibility data. Because Botswana has one of the highest HIVprevalence rates in Africa There are several possible explanations for the discrepancy in enteropathogenprevalence rates between this study and others previously discussed. The majority ofspecimens in this study are from outpatient clinics, while many previous studieswere restricted to inpatient admissions. Inpatient samples may select for moresevere cases of diarrhea and thus bias those studies toward a higher prevalence ofbacterial pathogens Salmonella and Shigella were submitted todifferent susceptibility testing panels before and after October 2003. It has alsobeen laboratory practice not to routinely differentiate Cyclosporafrom Cryptosporidium; thus, the prevalence ofCryptosporidium may be lower than reported in this study.However, there have been few reported cases of Cyclospora inSub-Saharan Africa, and we believe this contribution to be negligible This study had several limitations. Our retrospective and descriptive design makesour results susceptible to all limitations and potential biases of studies ofsimilar design. We were unable to account for multiple specimens from the samepatient, which precluded incidence rate calculation. Data on recent antimicrobialexposure were not routinely available, although those samples for which data wereavailable indicated that the percentage of specimens previously exposed toantimicrobials was relatively low. Due to the retrospective study design, standardlaboratory techniques and data recording practices shifted over the course of thestudy period. Because of changes in laboratory practices, isolates ofShigella spp. and Salmonella spp. were themost common bacteria; Isospora spp. andCryptosporidium spp. were the most common parasites. Resistance tocommonly used antimicrobials among enteropathogens in Gaborone, Botswana and thesurrounding area is high. Nalidixic acid may provide the best alternative forempiric therapy in a patient with dysentery, although such use should be closelymonitored as resistance to nalidixic acid is also increasing.In summary, this study demonstrates a high prevalence of samples negative forbacteria and parasites, likely indicating a high prevalence of viral illnessalthough further prospective studies are needed to confirm such findings."} +{"text": "Bartonella species were isolated from 49% of 128 cattle from California and Oklahoma, 90% of 42 mule deer from California, and 15% of 100 elk from California and Oregon. Isolates from all 63 cattle, 14 deer, and 1 elk had the same polymerase chain reaction/restriction fragment length polymorphism profiles. Our findings indicate potential for inter- and intraspecies transmission among ruminants, as well as risk that these Bartonella spp. could act as zoonotic agents."} +{"text": "Information about the availability and effectiveness of childhood obesity training during residency is limited.We surveyed residency program directors from pediatric, internal medicine-pediatrics (IM-Peds), and family medicine residency programs between September 2007 and January 2008 about childhood obesity training offered in their programs.The response rate was 42.2% (299/709) and ranged by specialty from 40.1% to 45.4%. Overall, 52.5% of respondents felt that childhood obesity training in residency was extremely important, and the majority of programs offered training in aspects of childhood obesity management including prevention , diagnosis , diagnosis of complications , and treatment . However, only 18.1% (N = 54) of programs had a formal childhood obesity curriculum with variability across specialties. Specifically, 35.5% of IM-Peds programs had a formal curriculum compared to only 22.6% of pediatric and 13.9% of family medicine programs (p < 0.01). Didactic instruction was the most commonly used training method but was rated as only somewhat effective by 67.9% of respondents using this method. The most frequently cited significant barrier to implementing childhood obesity training was competing curricular demands (58.5%).While most residents receive training in aspects of childhood obesity management, deficits may exist in training quality with a minority of programs offering a formal childhood obesity curriculum. Given the high prevalence of childhood obesity, a greater emphasis should be placed on development and use of effective training strategies suitable for all specialties training physicians to care for children. Childhood obesity is an epidemic problem in the United States. In 2003-2006, approximately one-third of children in the U.S. were overweight or obese . These cPerrin et al. demonstrated improvement in confidence, ease and frequency of obesity-related counseling with an intervention for pediatric residents and community pediatricians , and GonWe conducted a survey of all U.S. pediatric, IM-Peds, and family medicine residency program directors to characterize resident training related to childhood obesity. We also sought to assess teaching methods used and their perceived effectiveness, to identify barriers to implementation, and to assess attitudes toward the importance of training residents regarding childhood obesity. We further sought to evaluate whether residency program characteristics were associated with presence of a formal childhood obesity training curriculum. We hypothesized that a minority of pediatric, IM-Peds, and family medicine residency programs in the U.S. would have a formal childhood obesity curriculum but that family medicine programs would be more likely than pediatric programs to have a formal curriculum because of the specialty's emphasis on primary care.The survey was sent to all residency program directors from pediatric, IM-Peds, and family medicine programs in the U.S. identified using the American Academy of Family Physicians public Directory of Family Medicine Residency Programs, the Association of Pediatric Program Directors public database, and the American Medical Association public Fellowship and Residency Electronic Interactive Database (FREIDA) database -27. OnlyA 24-item survey instrument was developed to address the study aims. Respondents were asked whether their residency program has a formal childhood obesity curriculum, defined as a comprehensive or systematic program that has formal educational goals and either a written curriculum or identified methods for resident education in childhood obesity. Respondents also answered questions regarding resident training in childhood obesity prevention, diagnosis, treatment and diagnosis of complications. Respondents were asked about teaching methods and their perceived effectiveness, barriers to implementation of obesity training, and attitudes toward the importance of childhood obesity training during residency.Survey development was informed by discussions with childhood obesity experts, primary care physicians managing overweight children, pediatric residency program directors, and a literature review. The survey was pre-tested with assistant residency program directors, a former pediatric residency program director, an internal medicine residency program director, and chief residents at Children's Hospital Boston.The survey was anonymous and designed for administration via internet or mail. The survey indicated that $1 would be donated toward a campership for a child with type 2 diabetes for each completed survey, and the maximum amount would be donated with receipt of 75% or more completed surveys. A copy of the survey instrument is available upon request.The survey was fielded between September 2007 and January 2008. Altogether, 711 program directors were sent initial surveys representing 194 (27.3%) pediatric, 76 (10.7%) IM-Peds, and 441 (62.0%) family medicine programs. Initially, 566 (80%) were emailed and 145 (20%) were mailed. Nonrespondents were sent up to three follow-up surveys.2, or Fisher's exact. Logistic regression was used to evaluate the relationship between specialty and presence of a formal childhood obesity curriculum. The model was adjusted for program characteristics associated with specialty and presence of a formal childhood obesity curriculum in bivariate analyses at p < 0.2. Respondents who were \"unsure\" about the presence of a formal curriculum were excluded from analyses with that outcome. For questions regarding methods used for training, a missing response was considered \"not used.\" For barriers to implementation of childhood obesity training, respondents rated items on a scale of 1 to 10 with 1 labeled \"not at all a barrier\" and 10 labeled \"major barrier.\" We defined a \"significant barrier\" as a response of 8-10. Statistical significance was considered p < 0.05. Analysis was performed using SAS .Data are presented as mean and standard deviation or proportions. Bivariate analyses were performed using t-tests, ANOVA, \u03c7There were 711 surveys fielded. Two program directors had invalid email and mailing addresses, and 299 consented and returned completed surveys. Therefore, the overall response rate was 42.2% (299/709) and ranged by specialty from 40.1% to 45.4%. There were 88 (29.4%) pediatric, 34 (11.4%) IM-Peds, and 176 (58.9%) family medicine programs represented. One respondent (0.3%) did not indicate a specialty. Additional characteristics are presented in Table Overall, only 18.1% (N = 54) of respondents indicated that their program currently had a formal childhood obesity curriculum. Of these, 79.6% were started in the prior three years. However, most respondents reported resident training in prevention , diagnosis , diagnosis of complications , and treatment of childhood obesity. Overall, one-third (32.8%) reported that residents receive \u22645 hours of childhood obesity training during residency, and 19.4% reported that residents receive >15 hours.2, p < 0.01). IM-Peds programs were more than three times as likely to have a formal childhood obesity curriculum as family medicine programs . However, the significance of this relationship was attenuated by adjustment for the proportion of residents entering primary care . Pediatric programs were not significantly different from other specialties. In bivariate analyses, U.S. geographic region, community setting, location for majority of resident clinical pediatric training, proportion of residents entering primary care, and the size of the program were not significantly associated with the presence of a formal childhood obesity curriculum.Differences were noted across specialties Table . Whereas2, p < 0.0001).For training in individual aspects of obesity management, a significantly lower proportion of family medicine respondents reported training residents in treatment and diagnosis of complications of childhood obesity Table . In addiAmong programs offering training in prevention, diagnosis, diagnosis of obesity complications, and/or treatment of childhood obesity, didactic instruction was the most commonly used training method (92.3-97.9%) followed by teaching on inpatient wards (69.5-77.5%). Despite the common use of didactic instruction, 67.9% of respondents using this method rated it as only \"somewhat effective,\" and only 18.9% rated it as \"very\" or \"extremely effective.\" Compared to other methods, when used, participating in a specialty clinic that focuses on obesity was reported to be \"very\" or \"extremely effective\" by the greatest proportion of respondents (59.4%). Additional training methods included precepted patient care in a primary care clinic with focus on obesity, structured individual study with selected reading or educational CD, providing resource lists of texts, providing online materials, elective offerings, and other methods such as community offerings, school-based programs, computer-based education programs, working with a nutritionist, doing obesity-related research, using electronic medical records with prompts for body mass index calculation, attending national obesity conferences, and participation in subspecialty clinics.Respondents rated the importance of including childhood obesity training in a curriculum for successfully training residents to care for children on a scale from \"not at all important\" to \"extremely important.\" Overall, 52.5% felt that childhood obesity training was extremely important. However, whereas, 70.6% of IM-Peds respondents rated childhood obesity training as extremely important, only 62.1% of pediatric and 45.9% of family medicine respondents answered similarly . Respondents were then asked to rate, relative to childhood obesity, the importance of required content areas for pediatric residencies identified by the Accreditation Council for Graduate Medical Education (ACGME), which include both specialties and skills. Childhood obesity training was felt to be equally as important as training in advocacy, developmental pediatrics, injury prevention, and school health by at least 50% of respondents and more important than training in genetics, intensive care, and palliative care by at least 50%. Slightly less than half (44.5%) also felt that childhood obesity training was more important than training in subspecialty care.2, p = 0.02) compared to the other specialties combined; whereas, lack of administrative support and inadequate financial resources for program development were significant barriers in a significantly lower proportion.Overall, the most frequently cited significant barrier to implementing obesity training was other competing curricular demands (58.5%), followed by lack of insurance reimbursement for childhood obesity interventions (44.8%), and inadequate financial resources for program development (40.1%). While these three issues were the top significant barriers in each specialty, their order of importance varied, and other differences across specialties were noted Table . For fam2 p < 0.0001) and faculty surveys .About half (54.2%) of programs use resident feedback to evaluate childhood obesity training, and a minority use faculty (12.4%) or patient (2.7%) feedback. However, a significantly greater proportion of programs with a formal obesity training curriculum compared to those without use resident feedback . While the response rate for programs in the Northeast and Midwest were approximately 50%, only approximately one-third of programs in the South and West responded. A response bias may exist if those returning the survey were more likely to be from programs interested in childhood obesity management. If present, such a bias might overestimate the prevalence of residency training related to childhood obesity. Given that only 18.1% of programs reported a formal curriculum, availability of such curricula may be even more limited than suggested here if such a bias were present. With representation from all U.S. geographic regions (Table In summary, in a U.S. sample of pediatric, IM-Peds, and family medicine residency programs, we have extended what is known about the availability, methods and perceived effectiveness of resident training programs in childhood obesity. Our findings suggest that, while most residents receive training in some aspects of childhood obesity management, deficits may exist in training quality. Given the high prevalence of childhood obesity in the U.S., greater emphasis should be placed on development of effective training strategies suitable for the multiple specialties that train physicians to care for children.IM-Peds: Internal medicine-pediatrics; FREIDA: Fellowship and Residency Electronic Interactive Database; ACGME: Accreditation Council for Graduate Medical EducationER was formerly Chief Medical Officer for Pediatric Weight Management Centers, LLC's Great Moves! Program, which was privately owned and operated in collaboration with the physicians of Children's Hospital Boston. ER neither had nor has any equity or other economic interest in the business. ER also received salary support from an unrestricted, philanthropic grant from the New Balance Foundation to DL at Children's Hospital Boston. MW and DL have no competing interests to disclose.MW conceived of the study and participated in its design and coordination, the acquisition of data, analysis and interpretation of data, and drafting of the manuscript. ER participated in the study design and coordination, the acquisition of data, analysis and interpretation of data, and drafting of the manuscript. DL participated in the development of the study design, analysis and interpretation of data, and critical revision of the manuscript. All authors have read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1472-6920/10/18/prepub"} +{"text": "We investigated a focus of highly endemic Echinococcus multilocularis infection to assess persistence of high endemicity in rural rodents, explore potential for parasite transmission to domestic carnivores, and assess putative exposure versus infection frequency in inhabitants of the region. From spring 1993 to spring 1998, the prevalence of E. multilocularis in rodents was 9% to 39% for Arvicola terrestris and 10% to 21% for Microtus arvalis. From June 1996 to October 1997, 6 (7%) of 86 feral dogs and 1 of 33 cats living close to the region tested positive for intestinal E. multilocularis infection. Testing included egg detection by coproscopy, antigen detection by enzyme-linked immunosorbent assay (ELISA), and specific parasite DNA amplification by polymerase chain reaction. Thus, the presence of infected domestic carnivores can increase E. multilocularis exposure risk in humans. A seroepidemiologic survey of 2,943 blood donors in the area used specific Em2-ELISA. Comparative statistical analyses of seroprevalence and clinical incidence showed an increase in Em2-seroprevalence from 1986 and 1996-97 but no increase in clinical incidence of alveolar hydatid disease."} +{"text": "We reviewed all serologically confirmed cases of leptospirosis from 1985 to 1999 in Israel, where the disease is endemic. There were 59 cases, with an average annual incidence of 0.05/100,000. The dominant serogroup, Leptospira icterohemorrhagica, occurred in 29% of patients; in an earlier study (1970-1979), it accounted for only 2%. Serogroups that occurred mainly in rural areas accounted previously for 79% but had declined to 32%."} +{"text": "Survival and prognostic factors were analysed in 150 patients with histologically confirmed epithelial ovarian cancer stage IA-IIA. The relapse-free and overall survival rates were, respectively, 81% and 88% after 3 and 74% and 84% after 5 years. The analysis of various prognostic factors indicates as the main factor the grade differentiation of the tumour."} +{"text": "Intracranial germinoma has usually been treated with radiation doses of 50 Gy or more, but it is unclear whether such doses are actually necessary to cure this radiosensitive tumour. At our institution, the standard radiation dose for intracranial germinoma was 60 Gy in the 1960s, but the dose has prospectively been reduced stepwise to 40-45 Gy. In this paper, the treatment outcome was assessed in 84 patients enrolled in both prospective and retrospective series. The 5 and 10 years survival rates for all 84 patients were 88% and 83% respectively, and the corresponding relapse-free survival rates were 88% and 85%. The 10-year relapse-free survival rate was 88% for 31 patients receiving 19-47 Gy (median 42 Gy) to the primary tumour, 92% for 28 patients receiving 48-52 Gy (median 50 Gy), and 83% for 25 patients receiving 54-62 Gy (median 60 Gy), and there was no significant difference among the three groups. In-field local recurrence only developed in one patient who received 40 Gy over a protracted period and one patient who received 60 Gy. A tumour size < 3 cm and treatment in the post-computerised tomography era were associated with a better prognosis according to univariate analysis, while age, sex, tumour site, treatment volume, the radiation dose to both the primary and the spinal cord and the extent of surgical resection did not influence the prognosis. In contrast, none of these factors had a significant influence in multivariate analysis. In conclusion, intracranial germinomas < or = 4 cm in size can usually be cured with 40-45 Gy of radiation, thus avoiding the major adverse effects of brain irradiation."} +{"text": "Objective: A study was carried out to compare 3 treatment regimensfor vaginal candidiasis. Methods: A total of 150 women with clinical and mycological evidence of vaginal candidiasis wererandomized to receive 50 mg of oral fluconazole daily for 6 days (50 women), a single oral 150 mg dose of fluconazole (50 women), or 100 mg of intravaginal clotrimazole daily for 6 days (50 women). They were assessed at 5\u201315 days (short-term assessment) and again at 30\u201360 days (long-term assessment) after the completion of treatment.Results: Candida species were completely eradicated from the vagina in 88% or 80% in the 6-day oral fluconzaole group, 76% or 70% in the single oral fluconazole group, and 72% or 60% in the intravaginal clotrimazole group at short-term or long-termassessment, respectively. The rates of clinical effectiveness were 92% or 88% in the 6-day oral fluconzaole group, 80% or 76% in the single oral fluconazole group, and 72% or 58% in the intravaginal clotrimazole group at the short-term or long-term assessment, respectively. Treatment-related side effectswere not found in any group. Conclusions: This study suggests that the treatment of vaginal candidiasis with oral fluconazole is effective and that a single oral fluconazole dose might be one choice in the treatment of vaginal candidiasis."} +{"text": "Age could influence the prognosis of multiple myeloma patients treated with conventional chemotherapy. Between January 1987 and March 1990, 341 consecutive previously untreated patients with multiple myeloma received chemotherapy within the prospective, multicentre, randomized Protocol MM87. Survival was evaluated in patients aged > or < or = 66 years (the median age for the whole series) and in a subgroup of patients aged < 55 years. These groups were similar for main clinical characteristics, including results of cytostatic treatment. As of May 1996, 271 (79%) of the 341 patients had died, and median follow-up of the 70 (21%) living patients was 82 months. Overall, younger patients survived longer than older ones. In fact, in patients > and < or = 66 years, median survival was 31 and 44 months (P < 0.00095) and the percentage of patients surviving over 72 months was 17% and 32% (P = 0.0018) respectively; in patients < 55 years, these figures were 57 months and 35% respectively . In all groups, about 50% of the patients surviving over 72 months had stage I disease. For multiple myeloma patients treated with chemotherapy, survival is favourably affected by relatively young age and early stage of disease."} +{"text": "The outbreak of the pandemic flu, Influenza A H1N1 (Swine Flu) in early 2009, provided a major challenge to health services around the world. Previous pandemics have led to stockpiling of goods, the victimisation of particular population groups, and the cancellation of travel and the boycotting of particular foods (e.g. pork). We examined initial behavioural and attitudinal responses towards Influenza A, H1N1 (\"Swine flu\") in the six days following the WHO pandemic alert level 5, and regional differences in these responses.328 respondents completed a cross-sectional Internet or paper-based questionnaire study in Malaysia (N = 180) or Europe (N = 148). Measures assessed changes in transport usage, purchase of preparatory goods for a pandemic, perceived risk groups, indicators of anxiety, assessed estimated mortality rates for seasonal flu, effectiveness of seasonal flu vaccination, and changes in pork consumption26% of the respondents were 'very concerned' about being a flu victim . 36% reported reduced public transport use , 39% flight cancellations . 8% had purchased preparatory materials , 41% Malaysia (15% Europe) intended to do so (p < .001). 63% of Europeans, 19% of Malaysians had discussed the pandemic with friends (p < .001). Groups seen as at 'high risk' of infection included the immune compromised (mentioned by 87% respondents), pig farmers (70%), elderly (57%), prostitutes/highly sexually active (53%), and the homeless (53%). In data collected only in Europe, 64% greatly underestimated the mortality rates of seasonal flu, 26% believed seasonal flu vaccination gave protection against swine flu. 7% had reduced/stopped eating pork. 3% had purchased anti-viral drugs for use at home, while 32% intended to do so if the pandemic worsened.Initial responses to Influenza A show large regional differences in anxiety, with Malaysians more anxious and more likely to reduce travel and to buy masks and food. Discussions with family and friends may reinforce existing anxiety levels. Particular groups are perceived as at greater risk, potentially leading to increased prejudice during a pandemic. Europeans underestimated mortality of seasonal flu, and require more information about the protection given by seasonal flu inoculation. Medical interest in Influenza A, H1N1 has been considerable . During th April [th May 2009. We collected data from 30th April 2009 (at which time there had been 9 deaths and 212 confirmed cases worldwide) until 6th May 2009 . By 6th May there had been 27 confirmed cases in Europe, but none in Asia.The international threat posed by H1N1 calls for a necessary pooling of international data, both by medical teams and by social scientists. Particular concern has been expressed about the pandemic spreading to Asia, and the potential for mixing with other variants, such as avian influenza . Our teath April , a mass Our study sought to gather a snapshot of the attitudinal and behavioural responses during the early stages of a pandemic, knowledge about the differences between seasonal and pandemic flu, and those groups seen as most 'at risk' from infection. Understanding such attitudes and levels of knowledge may have important public health implications for information campaigns aimed at encouraging appropriate precautions against infection, while comprehending risk perceptions can help identify those groups most likely to be at risk of stereotyping and prejudice during a pandemic.th April and 6th May 2009 from 158 respondents via an online questionnaire in English or Portuguese, linked to the website http://www.swinefluquestionnaire.com. The website link was pasted onto a variety of general, non-health networking websites (e.g. 'I love London'). Respondents were primarily from the UK and Portugal but also included 30 respondents living outside these countries and resident in Finland (19 respondents), Poland (6 respondents), Malta (3 respondents) and France (2 respondents). Ten non-European based residents were then removed from the online survey before analysis.Following ethical approval by the relevant University ethics boards in London and Malaysia, data was collected from a total of 328 respondents . A paper version of the questionnaire was distributed in Malaysia, with students recruiting 180 respondents from their own classes, and community members from residential areas and local offices in Kuala Lumpur , 59% female)). Response rate was generally good, with 180 out of 200 approached to participate (90%) completing the questionnaire. In Europe, data was collected between 30comparative risk were analysed for a number of group members associated with risk in previous pandemics. We included these 'high risk' groups on the basis of previous research on representations and reactions to HIV/AIDS, the Ebola virus and SARS [more at risk than me, the same risk as me or less at risk than me.Respondents were asked to complete a questionnaire 'about perceptions of swine flu' which comprised a number of closed and open-ended format questions. Beliefs about and SARS ,9,12-14.and SARS , while tand SARS led us tand SARS meant wevery concerned to not at all concerned), as well as questions assessing friends and families' estimates of the risk . We used closed format questions for two questions assessing the purchase, or intention to purchase, specific items, such as face masks anything in preparation for a swine flu epidemic ?\" (yes/no responses). We accompanied this with an open-ended question for those who indicated they had/intended to purchase an item (\"what have you bought?\") with responses categorised for frequency in Malaysia and Europe, with the most common categories reported below. We also assessed whether respondents expected to modify their public transport use as a result of the threat , and whether respondents intended to cancel or delay travel plans (yes /no). An open-ended question asked 'how can you protect yourself from infection?' with the most frequent responses coded into categories by our research team in Malaysia and Europe.Anxiety indicators were assessed through two closed-format questions assessing personal worries about catching the virus , and the precautionary desire for anti-viral drugs at home ). We asked about the mortality rate in ordinary, seasonal flu , as well as whether the symptoms of swine flu differed from seasonal flu, and whether seasonal flu vaccination provided immunity against swine flu (both yes/no answers). Throughout, statistical analysis for structured questions was through chi-square analyses and Pearson product moment correlation.In Europe only, we asked additional closed-ended questions about stopping or reducing eating pork as a result of the pandemic (x2 (1) = 21.91, 49.20, both p < .001). Few had already bought products (25/328), but 41% (74/180) of our Malaysians were preparing to do so (x2 (1) = p < .001 for differences between Malaysia and Europe). Most likely to be purchased were masks and food . Asked in the free response question how to avoid infection, 37% (121/328) of our respondents cited washing hands and good hygiene, 28% (92/328) wearing a mask, 13% avoiding infected others and 12% (39/328) shunning crowded places.As shown in table x2 (2) = 68.03, 11.44, 31.82, and 12.10, p < .001 for each), Europeans were more likely to see the elderly and those with weakened immunity at risk (respective x2 (2) = 8.27, 3.49, p < .05). Whilst around half (165/325) of our respondents reported they were at least 'somewhat concerned' about being a victim of the pandemic, this anxiety was stronger in Malaysia, where 71% (127/178) indicated they were at least 'somewhat concerned' (x2 (3) = 91.67, p < .001). Nearly three quarters of our overall respondents (241/325) felt they had at least some control over whether they were infected. Europeans were more likely to have discussed their fears with their friends (90/142) (x2 (1) = 66.56, p < .001). Across the sample, personal perceptions of risk about the pandemic were related to those of families and friends . Those most anxious about personally being a victim of the outbreak were the most likely to reduce their use of public transport (r (320) = .48, p < .001) and cancel/delay air travel (r (322) = .37, p < .001).Five groups were seen as particularly at risk by more than half of our respondents: those with weakened immunity, pig farmers, the elderly, the homeless and prostitutes/highly sexually active. Malaysians were more likely to see pig farmers, general farmers, homosexuals and prostitutes as at greater risk data, respondents underrated the dangers of ordinary season flu, with 64% (95/148) claiming that this killed under 100,000 worldwide . 26% were judged to be at relatively high risk of infection, with Malaysian respondents particularly likely to emphasise the infection risk in these groups. Such judgements of risk may have important implications for the equitable treatment of socially marginalised group, particularly as the pandemic continues to accelerate worldwide.The authors declare that they have no competing interests.RG, SH and LM designed conceived the overall project, and analysed the data along with SH and FN. LM and SH helped in data interpretation and all the authors were involved in final article drafting.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2334/9/166/prepub"} +{"text": "To estimate HIV prevalence and characterize risk factors among young adults in Asembo, rural western Kenya.Community-based cross-sectional survey.From a demographic surveillance system, we selected a random sample of residents aged 13-34 years, who were contacted at home and invited to a nearby mobile study site. Consent procedures for non-emancipated minors required assent and parental consent. From October 2003 - April 2004, consenting participants were interviewed on risk behavior and tested for HIV and HSV-2. HIV voluntary counseling and testing was offered.Of 2606 eligible residents, 1822 (70%) enrolled. Primary reasons for refusal included not wanting blood taken, not wanting to learn HIV status, and partner/parental objection.Females comprised 53% of 1762 participants providing blood. Adjusted HIV prevalence was 15.4% overall: 20.5% among females and 10.2% among males. HIV prevalence was highest in women aged 25-29 years (36.5%) and men aged 30-34 years (41.1%). HSV-2 prevalence was 40.0% overall: 53% among females, 25.8% among males. In multivariate models stratified by gender and marital status, HIV infection was strongly associated with age, higher number of sex partners, widowhood, and HSV-2 seropositivity.Asembo has extremely high HIV and HSV-2 prevalence, and probable high incidence, among young adults. Further research on circumstances around HIV acquisition in young women and novel prevention strategies are urgently needed. African youth are disproportionately affected by the global HIV pandemic. Of 10 million HIV-infected persons aged 15-24 years, 62% live in sub-Saharan Africa; the majority are female. In Nyanza Province, the Kenya Medical Research Institute (KEMRI) and the U.S. Centers for Disease Control and Prevention (CDC) have conducted infectious disease research since 1988 in Asembo, a rural community. In 2003, KEMRI, CDC, ITM, and the London School of Hygiene and Tropical Medicine (LSHTM) initiated the first HIV-specific study in Asembo to measure the prevalence of HIV and sexually transmitted infections (STIs), identify factors associated with HIV infection, provide a baseline to evaluate a new adolescent prevention intervention, and inform sample size calculations for a prospective HIV-incidence cohort. We present HIV and HSV-2 prevalence and associated factors for 13-34 year old Asembo residents.Before study initiation, ethical approval was obtained from the Kenya Medical Research Institute (KEMRI), the U.S. Centers for Disease Control and Prevention (CDC), the Institue of Tropical Medicine (ITM), and the London School of Hygiene and Tropical Medicine (LSHTM) Ethics Review Committees/Institutional Review Boards.Asembo is a rural, subsistence farming community in Nyanza. The entire population of approximately 65,000, over 95% of whom are Luo, participates in an ongoing DSS maintained by KEMRI/CDC. et al, Based on Kisumu data from Buv\u00e9 Written informed consent was obtained from all adults and mature minors before study participation. Minors (<18 years of age) were classified as \u201cmature\u201d or \u201cnon-mature\u201d using legal definitions. Mature minors were married, pregnant, or a parent and could consent to study participation, as they can for HIV voluntary counseling and testing in Kenya. Data were collected from October 2003 through April 2004. Trained interviewers visited compounds to obtain informed consent from potential study participants. Participants were invited to a nearby site on a specified day for the interview and specimen collection. Study clinicians conducted physical examinations to diagnose acute illnesses or symptomatic STIs and confirm male circumcision.All participants underwent pre-test HIV counseling by certified counselors before venipuncture. Participants could obtain their HIV results and post-test counseling confidentially through study counselors at community health facilities. Adult participants were encouraged to share their HIV results with sexual partners and minors with their parent/guardian.Participants received free clinical care for common, acute ailments including STIs and were referred for free tuberculosis diagnosis and treatment. Sexual partners of participants with STIs were offered free STI treatment. HIV care and support services were provided through existing infrastructure developed collaboratively between the Ministry of Health and CDC's Global AIDS Program.Initially, the HIV testing algorithm used Determine and Unigold rapid tests in parallel. Discordant results were resolved with Capillus . Concordant negatives were tested with the sensitive Murex enzyme immunoassay . Negative Murex results were considered negative for HIV-infection. All Murex HIV-positive samples were further run on Western blot and read according to CDC criteria. For efficiency and cost, halfway through the study we changed to parallel testing by ELISA using Vironostika HIV Uniform II plus O kit and Enzygnost . Concordant results were final. Discordant results were run on Western blot . No statistical adjustments were made with this change in the HIV testing algorithm because a number of systematically selected specimens that had been tested with the original HIV testing algorithm were retested with the second algorithm with consistent results.HSV-2 was screened using an HSV-2 type-specific IgG ELISA with a reported sensitivity of 92.3% and specificity of 97.7% in African populations. Urine pregnancy tests were conducted on-site for all consenting females not visibly pregnant using Randox, Inc. latex monoclonal agglutination test and First Sign HCG One Step .Data were collected on optical character recognition enabled forms that were completed in the field through face-to-face interviews, transported to the research station, scanned into a database using Teleform version 8 , and exported into Access 2000. Questionnaires contained embedded internal consistency and validity checks. Data cleaning and statistical analyses using survey procedures were performed in SAS versions 8.2 through 9.13 and STATA 8.2 .HIV prevalence and univariate aggregate data were weighted to the population from which the study sample was drawn. Standard errors were computed that accounted for the sampling design and the individual's sampling probability from the sampling strata. Analyses that are descriptive of the sample attributes are not weighted. Analyses that are descriptive of the population are weighted and are labeled as such. All logistic regression models used weights to account for the probability of selection by age and sex strata. Separate analyses were conducted for females and males. Due to gender differences in age of life events (e.g. marriage), females were age-group adjusted by 13-19 and 20-34 years and males by 13-24 and 25-34 years. Because of the strong association between HIV infection and marriage, bivariate and multivariate analyses were conducted separately for sexually active participants and those who had ever been married. Mutlivariate analyses were conducted with SAS's Proc SurveyLogistic.Marriage was defined as a legal, religious, or customary agreement or a man and woman living together as married. Having ever been married included those who were currently married, separated, divorced, or a widow/widower. Anyone who had ever had sexual intercourse was considered sexually active. Polygamy, widow inheritance, and cultural rituals involving sex are part of Luo culture. p-value \u22640.2 on bivariate analysis. First, sociodemographic variables were entered into the model beginning with the most significant covariate on bivariate analysis. Upon finalization of the sociodemographic tier, the same approach was used to add sexual behavior, other HIV risk factors, and finally STI-related covariates. Once a covariate was significant within its tier, it was retained in the final model. Because STI-related covariates affected most models, we present the four models with and without STI covariates. The likelihood ratio test was used to compare statistical models. Although not significant on bivariate analyses, male circumcision was included in all male models because of the protection conferred against HIV. We evaluated factors associated with HIV infection through logistic regression modeling using software that incorporated the sampling weights. Using the forward stepwise selection method, four hierarchical models were constructed: ever sexually active females and males and ever-married females and males. Each model included all covariates with a p<0.0001). Primary reasons for refusal included not wanting blood taken (37%), partner/parental objection (19%), and not wanting to be tested for or learn one's HIV status (18%).Of 3960 randomly selected individuals, 2606 (66%) were eligible for enrollment; almost all others, 1261/1354 (93%), were ineligible because they had left Asembo. Of the eligible 2606, 1822 (70%) enrolled, 447 (17%) refused, and 337 (13%) consented at home but did not come to the study site. Enrollment rates were similar for males and females (70%) but higher among those aged <20 years (75%) than those aged \u226520 years of females and 8/189 (4.2%) of males, were in polygamous marriages. Additionally, 63.9% (39/61) of widows had been inherited, and 2.8% (6/214) of ever-married men had inherited a widow. Of sexually active participants, 102/1202 (8.4%) had participated in ritual sex. Only 13.2% (77/583) of sexually active males were circumcised. There was high mobility with only 18% of female and 48% of male sexually active participants having lived their entire lives in Asembo.The median number of lifetime sexual partners for sexually active participants in our sample was 3 for females and 4 for males. Over half of sexually active females, 327/619 (52.8%), had sex in exchange for gifts; 45/619 (7.3%) reported having ever been forced to have sex. Condom use during the last sexual intercourse was equally low between never-married males and females (25%). Among ever-married participants, condom use during the last sexual intercourse with spousal or non-spousal partners was rare in females (3.3%) and males (6.9%). Of currently married individuals, 3.7% (12/328) of females and 23.8% (45/189) of males reported having had sex with a non-spousal partner in the previous six months.The population, HIV prevalence for the study area, based on 1762 participants who provided blood specimens and complete data, weighted by age group and sex was 15.4% overall, 20.5% among females, and 10.2% among males. Of 309 females who denied ever having had sexual intercourse in our sample, 4 (1.3%) were HIV-positive and 5 (1.6%) were pregnant; 2/249 (0.8%) males who denied having had sexual intercourse were HIV-positive.After adjustment for age group and stratification by sex, several demographic and risk variables were associated with HIV prevalence among sexually active participants . Among sAmong sexually active males , factorsMarital status was an effect modifier necessitating separate analyses by gender and marital history. Because few never-married individuals were HIV-infected, we were unable to conduct adequate multivariate analyses in this group. For ever-married participants, univariate analyses of factors associated with HIV infection are presented in Limited data were available on circumstances around injections. Of 458 sexually active individuals who reported receiving an injection in the previous six months in our sample, 87% received it from clinicians, 9% from community health workers, and 4% from traditional healers/herbalists. Those aged 30-34 years comprised the highest proportion receiving an injection (42.1%); 15-19 year olds were the lowest (35.2%).This population-based study in rural Nyanza Province, Kenya, found a high prevalence of HIV infection among those aged 13-34 years. Despite a decreasing trend in Kenya's national HIV prevalence, HSV-2 may also play a role. The strong association we found between HIV and HSV-2 infection confirms findings from other studies. Including HSV-2 infection in the multivariate model attenuated the positive association between HIV and a higher lifetime number of sexual partners. Although under-reporting of lifetime number of sexual partners is a possible explanation, HSV-2 infection, particularly in young people, may be a more accurate marker of sexual activity than reported sexual behavior. Marriage has been associated with risk for HIV infection in sub-Saharan Africa. The potential contribution of unsafe injections to HIV transmission has been raised HIV infection in Africa has been associated with urban-to-rural and intra-rural human mobility. Recent randomized clinical trials of male circumcision resulted in an approximate reduction of HIV acquisition by half. Ritual sex around funerals, polygamy, and widow inheritance are traditional Luo practices that can facilitate HIV transmission. et al. present HIV prevalence data from a 2006 general population survey in Kisumu city, the capital of Nyanza Province, conducted to evaluate antiretroviral therapy-related attitudes and beliefs. Although an urban setting, they found a similar over HIV prevalence of 25% in women and 16% in men aged 15-49 years. Other data regarding HIV prevalence in Nyanza Province include a second cross-sectional study with different sampling methodology and age distribution was conducted from 2004-2005 in the neighboring community of Gem. This study of volunteers aged 15-34 years showed a weighted HIV prevalence of 28.2% among females and 14.8% among males. Study limitations exist. Risk factor data in cross-sectional studies are associations and cannot identify causality. There is potential for selection bias from migration, because 30% of selected individuals had moved out of Asembo between the DSS survey round and study enrollment (<8 months). Ill individuals may have left the area seeking health care or returned home to die. Healthy individuals may have left seeking employment or returned to care for ill relatives. By requiring participants to visit a nearby site, we may have selected for healthier individuals. Since study participation took up to four hours, we may have selected for individuals who were wealthier, unemployed, or had time. As the first HIV-specific research conducted in Asembo, individuals with self-perceived low HIV risk may have self-selected to participate. Most of these potential biases would have resulted in lower HIV prevalence estimates. However, if the individuals aged \u226520 years who refused study participation did so because they engaged in risky sexual behavior and did not want to know their HIV status, their non-participation might have resulted in an underestimation of HIV prevalence.Recall bias due to illness, gender, or age can occur when describing sexual histories or risk behaviors. Sexual behavior interviews are limited by the accuracy of self-reporting, and women, particularly adolescent females, frequently underreport sexual experiences. Our study shows a large HIV-burden in this area of rural Nyanza. High HIV transmission rates are probable given the rapid increase in age-specific HIV prevalence among adolescent females. Without massive and drastic prevention and treatment efforts, AIDS will continue to devastate Asembo. Community-wide delivery of HIV counseling and testing with HIV/AIDS treatment provision merits exploration. Alterations in cultural perceptions and practices are needed to delay sexual debut, reduce the number of sexual partners, promote mutual faithfulness to known seronegative partners, implement 100% condom use with casual partners, and discourage inter-generational and transactional sex. Community elders and opinion leaders are urged to encourage non-sexual substitutions for ritual sex and empower widows refusing to be inherited. In an area with such high HIV prevalence, key life decisions should be made based on known HIV serostatus.Qualitative data are required to better elucidate circumstances around individual HIV transmission/acquisition events and identify behaviors driving the epidemic in this area. Interventions to achieve high male circumcision rates are needed along with continued research on additional HIV prevention strategies including HIV vaccines, microbicides, pre-exposure chemoprophylaxis, and vaccine and chemotherapeutic agents against HSV-2."} +{"text": "Objective: The objectives of this study were to assess the efficacy of medical management for vulvar vestibulitis and to examine several historical variables and determine their predictive values as to which treatments will be most successful.Methods: Seventy-four patients diagnosed with vulvar vestibulitis were evaluated. Each patient was treated using a sequence of consecutive medical therapies for vulvar vestibulitis. These therapies were topical aqueous 4% lidocaine with intercourse, topical corticosteroid therapy, oral amitriptyline, topical low-dose 5-fluorouracil (5-FU) cream, intralesional alpha-interferon, and a low-oxalate diet in combination with oral calcium citrate. The patients were followed over 3\u201330 months and their responses to therapy were assessed. In addition, a statistical analysis was performed to determine the positive predictive values of certain historical variables and specific treatment successes.Results: Forty-nine patients reported positive responses to one of the initiated therapies. More specifically, 18.1% of the patients who used lidocaine, 33.8% who used topical corticosteroids, 57.1% who used amitriptyline, 16.7% who used 5-FU, none who received interferon, and 50% who tried a low-oxalate diet had positive responses to therapy. No historical variables were predictive of which therapies would have the most successful outcome.Conclusions: Medical management is effective in alleviating the symptoms of vulvar vestibulitis. Various aspects of a patient's history are not helpful in selecting the therapy that will be most effective."} +{"text": "The outcome and prognostic factors of 217 women with invasive lobular carcinoma (ILC) and those of 1121 women with invasive ductal carcinoma (IDC) of the breast were compared. The patients were followed up for 10-43 years. Women with ILC had axillary nodal metastases less frequently than those with IDC , although there was no difference in the primary tumour size between the groups. ILCs were more frequently of low grade, had lower mitotic counts and had less tumour necrosis. Furthermore, ILCs had lower S-phase fractions and were more often DNA diploid in flow cytometric analysis than IDCs . The 5- and 30-year corrected survival rates of women with ILC were 78% and 50%, respectively, compared with 63% and 37% for women with IDC (P = 0.001). Small pT1NOMO ILCs (n = 41) had 100% 10-year and 83% 20-year corrected survival rates. In a multivariate analysis, a large primary tumour size, the presence of axillary nodal metastases, a high mitotic count and the presence of tumour necrosis all had an independent prognostic value in ILC. We conclude that ILC is associated with better survival than IDC."} +{"text": "Injection drug use (IDU) is one of the major modes of HIV transmission in China. Drug use is illegal in China, all identified drug users are registered by Public Security Bureau, and most were sent to detention; most detainees engaged in high risk behaviours. In order to well understand the HIV/AIDS knowledge among detainees, a survey was conducted in different detention settings in Hunan province in 2008 to assess knowledge and attitudes about HIV among detainees and to provide useful information for HIV prevention and intervention strategies in detention centers.A cross-sectional survey was conducted in 10 detentions in Hunan province, China, and demographic information along with knowledge and attitude of HIV/AIDS was collected through standardized interviews. Descriptive statistics were used to describe HIV knowledge, attitudes, and education services among detainees.There were 956 detainees interviewed from 10 detention centers. The male to female ratio was 2.24:1. The majority detainees received nine years of compulsory education, accounting for 51.5%. There were nine questions to assess HIV/AIDS knowledge of detainees, and 35.7% of those surveyed answered all nine questions correctly. There were 92.3% (882/956) who consented to be informed about the HIV antibody test results when tested, and 81% (774/956) elected that their family members were also informed. All detention centers had an organized HIV/AIDS education program.This study gives us an overview about HIV/AIDS knowledge in detention in Hunan province, and all detention sites in the study provided HIV/AIDS intervention services among detainees that focused on HIV/AIDS knowledge, attitude, and health behaviors. Injection drug use (IDU) is one of the major modes of HIV transmission in China . Drug usThe Chinese government has issued a series of laws and regulations to response to the HIV/AIDS epidemics and injection drug use. Prevention and intervention campaigns have addressed drug dependency and HIV, such as greatly expanding methadone maintenance therapy (MMT) and clean needle exchange programs. By the end of October 2007, 397 MMT clinics were open in 22 provinces, autonomous regions, and municipalities with 88,313 participants in the MMT treatment program. In 2006, a total of 729 needle exchange stations were established in 204 counties or districts in 17 provinces. By the third quarter of 2007, about 49,108 IDUs had participated in clean needle exchange programs -8.While in detention centers, most detainees engaged in high risk behaviours, and some special characteristics of detention centers contribute to HIV transmission, such as crowded space, almost all the same gender, fighting, and other factors -16. TherIn order to better understand the trends of HIV epidemic and knowledge, attitudes and practices (KAP) about HIV among high-risk population groups, China created an HIV sentinel surveillance system in 1995, focusing efforts on groups including drug users, female sex workers, sexual transmitted diseases (STD) clinic clients, Men who have sex with men (MSM), male long distance truck drivers and students . SentineThe aim of our study is to describe the results of survey among detainees in Hunan province in China conducted in 2008, to assess HIV knowledge and practices among detainees, and to provide useful information for HIV prevention and intervention strategies in detention centers.This investigation involved the public security and justice system. Specifically, the public security system included obligatory detoxification centers and custody houses, and the justice system included labor re-education centers and prison.Detention centers were selected using stratifying sampling method, detoxification centers and custody houses were selected in the public security system, and prison and re-education centers were selected in the justice system. A Multi-level random sampling method was used to recruit individuals in different detention centers. Ten centers were randomly selected according to the system, and then at least 110 individuals were selected in every single detention center. A self-reported questionnaire was used to collect needed information.The survey was conducted from 13 October to 30 October, 2008. Anonymity and confidentiality were guaranteed to the detainees when they participated in the survey. Under the approval of the protocol \"HIV Surveillance Protocol\" by the national ethical committee of China , informed consent from participants in behavioral surveillance was required during survey .Different types of detention canters were selected in order to gain better representativeness, such as centers only for women, obligatory detoxification centers, custody houses, labor re-education centers, and prison. Variables used in this study included sample source, gender, age, marital status, resident place, ethnic groups, education background, profession, time of entry detention, time space of detention, cause of detention, AIDS information, intervention and prevention services, and others.All detention centers had an organized HIV/AIDS education program. Activities included seminars, workshops, and training for security staff; non-profit activities; some volunteer and some students gave courses or health education, such as \"No Drug\", \"Health Behavior\", and others. Video courses and notice boards, as well as posters, were also used for promotion of HIV/AIDS knowledge. In some detention centers, peer education and counseling were also used.Most detention centers attempt to implement comprehensive HIV management. In one labor re-education center, Xinkaipu, a \"caring center\" for HIV positives started in July 2008; Baimalong established \"HIV prevention unit\" in July 2008. In prison, no HIV positive individuals were identified, and in a female prison, few HIV positive individuals were identified, and an established isolation caring center was implemented to provide case management collectively.The sample size included 979 samples from 10 detention centers. Epidata was used for data entry and database management. First, data cleaning was conducted, in which 23 samples were deleted. After data cleaning, a total of 956 records were included in the analysis. SPSS software was used to analyze the dataset.There were 660 male, and 296 female, so the male to female ratio was 2.24:1. Local Hunan residents were 920, accounting for 94.4% of the sample size; transient detainees from other provinces without local permanent residence permission were 52, which accounted for 5.4%. The participants were predominantly Han Chinese, which accounted for 96.9%, 3.1% were minority ethnic groups. 47.7% samples were single, 30.6% samples married, and the remaining people were cohabiting, divorced or widowed.The major part of detainees received nine years of compulsory education, accounting for 51.5% of the total sample size. Those with primary school or high school education were 20.0% and 21.4%, respectively. The illiteracy was 2.0%. See Table Illegal drug use was the cause of detention for 47% (449/956) of the study participants; commercial sex or other reasons accounted for 51.5% (492/956).There were nine questions to assess the HIV/AIDS knowledge of detainees, 35.7% of the participants answered all 9 questions correctly. The lowest correct answer rate of the nine questions was \"does mosquito bite can transmit HIV virus?\" (63.1% answered correctly). See Table There were 67.4% (644/956) of study participants who received HIV/AIDS information materials. The proportion of participants who received condom distribution and Voluntary Counseling and Testing (VCT) was 31.2% (298/956) and 49% (468/956), respectively.There were 204 participants who had been tested for the HIV antibody before being sent to detention, which accounted for 21.3% (204/952). Of these 79.4% (162/204) knew the test results, and 36 samples were aware of HIV positive results. Most of the HIV antibody tests were conducted in a Center for Disease Control (CDC) or in other detention centers.The total number of participants tested for HIV antibodies inside detention was 580, which accounted for 60.7% (580/951). Of these, 41.4% (240/580) participants were drug users; and 29.8% (173/580) samples knew the results. Of the 47 HIV positive participants, 36 were drug users. There were no HIV positive individuals identified among commercial sex workers.There were 92.3% (882/956) who wished to be notified about the test results if tested, and 81% (774/956) indicated that they wished that their family members were also notified. Of those participating in the survey, 23.4% (224/956) indicated that they would like to live with HIV positive individuals, while 55.1% (527/956) indicated that they did not like living with HIV positive individuals. There were 89% (851/956) of participants who wanted to be informed directly after the test. See Table Of those interviewed in re-education centers and detoxification centers, all participants have drug use history; however, in custody houses and prisons, only a few people have a drug use history. Most drug users once shared needles, but most reported that this typically occurred at the beginning of drug use. After receiving HIV/AIDS information, needle sharing behavior almost stopped completely. Needles were typically bought in drug stores by individuals, not in clean needle exchange centers, because most clean needle exchange centers are far, and it is possible to be arrested by police. Individuals in higher social economic status (SES) levels reported using drugs at home, and did not report Needle sharing practices.Most male detainees reported commercial sex use, and also reported sexual activity with heterosexual drug partners. Most detainees used condoms with commercial sex workers, but did not use condoms with established sex partners.This study gives us an overview about HIV/AIDS knowledge in detention in Hunan province, China, but information about the HIV/AIDS risk behavior among detainees was still limited. Random sampling methods is very difficult or nearly impossible. Because of the characteristics of this population group and the operational difficulties of such investigation, legal and ethical issues should be considered ,12-15. PAll detention sites in our study provided HIV/AIDS intervention services among detainees, and it improved HIV/AIDS knowledge, attitudes, and health behaviors among detainees. However, intervention should take action as early as possible in order to be effective and prevent further transmission ,23. ProvSince the emergence of the HIV epidemic, China has launched an HIV prevention and harm reduction program. A comprehensive program to prevent the further transmission of HIV among drug users has been implemented that includes community based harm reduction programs, primarily a methadone maintenance treatment and needle-syringe program. In 2003, China announced a national AIDS control policy, \"Four Frees and One Care\" , free Prevention of Mother to Child Transmission (PMCT) and free education for AIDS orphans, and provision of social relief and care for HIV patients) .This study gives us an overview about HIV/AIDS knowledge in detention in Hunan province, and all detention sites in the study provided HIV/AIDS intervention services among detainees that focused on HIV/AIDS knowledge, attitude, and health behaviors. These efforts are likely to require an infrastructure that not only provides operational and financial support, but also creates an environment in which at-risk populations feel comfortable and safe in seeking help and non-discrimination.The authors declare that they have no competing interests.XW, WZ, XC and FL designed and conducted the analysis, WZ conducted the analysis and wrote the final version of the text. XC, FL and XW developed the questionnaire; XW collected the raw data on sites. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2458/10/221/prepub"} +{"text": "Active Bacterial Core surveillance (ABCs) is a collaboration between the Centers for Disease Control and Prevention and several state health departments and universities participating in the Emerging Infections Program Network. ABCs conducts population-based active surveillance, collects isolates, and performs studies of invasive disease caused by Streptococcus pneumoniae, group A and group B Streptococcus, Neisseria meningitidis, and Haemophilus influenzae for a population of 17 to 30 million. These pathogens caused an estimated 97,000 invasive cases, resulting in 10,000 deaths in the United States in 1998. Incidence rates of these pathogens are described. During 1998, 25% of invasive pneumococcal infections in ABCs areas were not susceptible to penicillin, and 13.3% were not susceptible to three classes of antibiotics. In 1998, early-onset group B streptococcal disease had declined by 65% over the previous 6 years. More information on ABCs is available at www.cdc.gov/ncidod/dbmd/abcs. ABCs specimens will soon be available to researchers through an archive."} +{"text": "Administration of 0.125% formylhydrazine in drinking water to 6-week-old randomly bred Swiss albino mice for life, induced lung tumours. Compared to untreated controls, the lung-tumour incidence rose from 15 to 94% in the females and from 22 to 100% in the males. The treatment had no detectable tumorigenic effect in other organs."} +{"text": "To the Editor: Infectious diseases can spread rapidly by air travel, as did severe acute respiratory syndrome (SARS) in 2003. Public health measures at airports might protect passengers and employees from such diseases and delay spread into the general population. The SARS epidemic was contained largely through traditional public health interventions to European destinations, and from Zurich Airport to Asian or North American destinations during the summer of 2007. Data were collected by a pretested, self-administered, 23-item questionnaire , which was distributed to all adult passengers in the departure waiting areas. Information was analyzed by basic statistical methods, \u03c7A total of 2,633 passengers were approached and asked to participate. The response rate was 71%. Most passengers who refused to participate did so because of language difficulties. After we excluded passengers <18 years of age, data for 1,880 participants were analyzed. Mean (SD) age was 39.8 (14.7) years; 54% were female, 58% had a university degree, 97% were currently feeling healthy, 30% were traveling alone, 37% were traveling for business reasons, 30% were residents of Switzerland, 42% were residents of other European countries, and 15% were residents of the Americas.Passengers were asked about acceptance of public health measures in a hypothetical severe respiratory disease pandemic. Results are shown in the There were no differences in questionnaire responses between the 2 airports. Other questions concerned information status and seeking. In a pandemic, 93.5% of passengers would acquire information before departure about the situation and preventive measures; 67% would consult the Internet, 59% their family doctor, 49% the media, 37% health authorities, 25% their travel agent, 23% travel medicine centers, 20% the airport, and 17% friends and relatives. For their current trip, 22.4% sought pretravel advice on infectious diseases. This seeking of advice was more frequent in those departing to overseas destinations from Zurich Airport. Information sources were the family doctor (38%), the Internet (34%), the media (26%), friends and relatives (22%), a travel agency (19%), health authorities (11%), travel medicine centers (10%), and the airport (7%). A total of 17.4% noticed the official posters regarding avian influenza.Because the study was conducted when no major international disease outbreaks were occurring, passengers answered hypothetical questions about an imaginary future pandemic. Therefore, attitudes and behavior might be difficult to predict from these results and would depend on perceived severity of the pandemic disease. Similar surveys among the general population showed comparable results. During an influenza pandemic, 75% of Europeans would avoid public transportation in Haut-Rhin, France, and 782 air passengers at Zurich Airport (ZK) in Kloten, Switzerland."} +{"text": "Human monkeypox is a zoonotic smallpox-like disease caused by an orthopoxvirus of interhuman transmissibility too low to sustain spread in susceptible populations. In February 1997, 88 cases of febrile pustular rash were identified for the previous 12 months in 12 villages of the Katako-Kombe Health Zone, Democratic Republic of Congo . Seven were active cases confirmed by virus isolation. Orthopoxvirus- neutralizing antibodies were detected in 54% of 72 patients who provided serum and 25% of 59 wild-caught animals, mainly squirrels. Hemagglutination-inhibition assays and Western blotting detected antibodies in 68% and 73% of patients, respectively. Vaccinia vaccination, which protects against monkeypox, ceased by 1983 after global smallpox eradication, leading to an increase in the proportion of susceptible people."} +{"text": "In 3 years, 118 patients with Hodgkin's disease have completed chemotherapy with chlorambucil, vinblastine, procarbazine and prednisolone (Ch1VPP). The complete remission rates were 90% for 29 patients previously treated with radiotherapy, 67% for 73 patients previously untreated and 44% for 16 patients with prior chemotherapy. The 3-year survival rates for the first 70 patients in the series were 83% for previously irradiated patients, 84% for previously untreated patients and 67% for those with prior chemotherapy. Forty-seven previously untreated or previously irradiated patients in this group achieved complete remission. The 3-year disease-free survival rates for these patients were 71% and 67% respectively. This regimen gives complete remission and survival rates comparable with results obtained with combinations including nitrogen mustard, while producing fewer side-effects."} +{"text": "A meta-analysis of six randomised trials demonstrated that intensive followup in colorectal cancer was associated with an absolute reduction in all-cause 5-year mortality of 10% : 4\u201316) \u2013 however, only two percent (95% CI: 0\u20135) was attributable to cure from salvage re-operations. We postulate that other factors, such as increased psychological well-being and/or altered lifestyle, and/or improved treatment of coincidental disease may contribute to the remaining lives saved, and form important future research questions. Approximately two-thirds of patients presenting with colorectal cancer undergo resection with curative intent, and most subsequently enter protocols for long-term followup . The ratwww.christie.man.ac.uk/profinfo/departments/surgery/default.htm. The key features were:Updated search strategy (to December 2003) using Cochrane methodology.Inclusion criteria were: randomised controlled trial; patients with colorectal cancer treated surgically with curative intent; randomisation at or shortly after surgery, and availability of 5-year survival data.Data were extracted independently by two investigators .Important components of methodological quality, namely adequacy of concealment of patients' allocation to treatment groups, double-blinding, and withdrawals, were assessed.The search strategy, inclusion and exclusion criteria, data extraction, and study quality assessment have been published elsewhere , with fuvs conventional followup were performed and pooled estimates expressed as risk ratios (RR) and 95% confidence intervals (95% CIs). Second, estimates of the proportion of overall lives gained, and lives gained through to salvage re-operation, were calculated using absolute risk differences (and 95% CIs) for intensive 95% CIs) . The difThere were six randomised controlled trials , but re-operation rates favoured those intensively followed . For both arms, the proportions successfully salvaged were low \u2013 4 and 2%, respectively.There were 268 (31%) deaths in patients followed intensively compared with 328 (40%) for those followed by conventional regimens, giving a pooled RR estimate of 0.76 (95% CI: 0.67\u20130.86) . The recP=0.009), which, after exploration, was mainly due to the vs 6%). After excluding this study, the absolute risk difference for all lives gained was 9% ; that for lives gained through salvage was 1% .The estimate of absolute risk difference for overall lives gained from intensive followup was 10% (95% CI: 4\u201316), but only 2% (95% CI: 0\u20135) was attributable to cure from salvage re-operation . The difThe findings of this study add to earlier meta-analyses increased psychosocial support and well-being; (ii) altered dietary and lifestyle factors and (iii) improved treatment of coincidental disease. For the first postulate, there is evidence that psychological therapies improve outcome in some cancer types (If the hypotheses developed from this study are true, the implications for future health resources and research are considerable. For decades, the majority of colorectal cancer followup was performed by clinicians within surgical and/or oncology clinics. Alternatives to this are emerging, and include colorectal nurse specialists working in parallel with colorectal cancer specialists using protocol-driven protocols ("} +{"text": "Interestingly, Main et al. did note that approximately 12% and 18% of breast milk samples and placentas, respectively, were obtained from diabetic Finnish mothers of cryptorchid boys, compared with 0% of controls , but the"} +{"text": "Since 1975, 191 patients with Hodgkin's disease have been treated with a combination of chlorambucil, vinblastine, procarbazine and prednisolone (ChlVPP). Complete remission rates were 73% for previously untreated patients, 91% for patients previously treated with radiotherapy and 55% for patients previously treated with chemotherapy. In 59 patients with advanced disease who received no other treatment, a 5-year survival rate of 66% was comparable with that achieved by more toxic mustine-containing combinations. ChlVPP has few side effects, is easily given to outpatients, and can be combined with elective radiotherapy in selected patients."} +{"text": "Proc. Natl. Acad. Sci. U.S.A. 100:12343\u20138] and identified 3 differentially expressed serum proteins for the diagnosis of ovarian cancer (OC) , namely, apolipoprotein A-I (apoA-I), transthyretin (TTR) and transferin (TF). The objective of the present study is to determine the efficacy of the three OC biomarkers for the detection of early stage (ES) OC, in direct comparison to CA125.We have previously analyzed protein profiles using Surface Enhanced Laser Desorption and Ionization Time-Of-Flight Mass Spectroscopy (SELDI-TOF-MS) , obtained through the GOG and Cooperative Human Tissue Network. Following statistical analysis, multivariate regression models were built to evaluate the utility of the three OC markers in early detection.mucinous histological subtype showed that collectively, CA125, TTR, TF and apoA-I, were able to distinguish normal samples from mucinous LMP with 90% sensitivity, and further distinguished normal samples from early stage mucinous ovarian cancer with a sensitivity of 95%. In contrast, in serum samples from patients with mucinous tumors, CA125 alone was able to distinguish normal samples from LMP and early stage ovarian cancer with a sensitivity of only 46% and 47%, respectively. Furthermore, collectively, apoA-I, TTR and TF (excluding CA-125) distinguished i) normal samples from samples representing all histopathologic subtypes of LMP, with a sensitivity of 73%, ii) normal samples from ESOC with a sensitivity of 84% and iii) normal samples from LSOC with a sensitivity of 97%. More strikingly, the sensitivity in distinguishing normal versus mucinous ESOC, utilizing apoA-I, TF and TTR (CA-125 excluded), was 95% .Multiple logistic regression models (MLRM) utilizing all biomarker values from all histological subtypes distinguished normal samples from LMP with 91% sensitivity (specificity 92%), and normal samples from ESOC with a sensitivity of 89% (specificity 92%). MLRM, utilizing values of all four markers from only the These results suggest that the biomarker panel consisting of apoA-I, TTR and TF may significantly improve early detection of OC. Ovarian cancer has the highest mortality rate of all the gynecologic malignancies worldwide. With no adequate screening tests, early diagnosis\u2014the most significant prognostic factor\u2014continues to elude the clinician. Presently, over 85% of patients with ovarian cancer are diagnosed with Stage III or IV disease .Serum cancer antigen 125 (CA125), a high molecular weight glycoprotein, is currently the best clinical marker for papillary serous adenocarcinoma of the ovary in the postmenopausal age group. However it is a consistently poor diagnostic tumor biomarker in premenopausal women, non-serous histologies, and early stage diseases. Only 50%\u201360% of women with early stage ovarian cancer will demonstrate elevated serum levels of CA125 . The ideProteomic-based approaches have been utilized in an attempt to detect early-stage ovarian cancer patients, and monitor biologic responses to therapy , 5]. Se. Se5]. SSerum samples were obtained through the Gynecological Oncology Group (GOG) and Cooperative Human Tissue Network. Samples were collected preoperatively following the standard GOG protocol (GOG 199 protocol) from patients with benign, borderline and malignant ovarian tumors. The 392 serum samples utilized in the present study included 82 women with normal ovaries (N), 24 women with benign ovarian tumors (B), 85 women with ovarian tumors of low malignant potential (LMP), 126 women with early stage ovarian cancer (ESOC), and 75 women with late stage ovarian cancer (LSOC). The age and pathology distribution of the samples are provided in The levels of each individual protein marker were measured on all serum samples. The Immulite 1000 was used to measure CA125 level by using chemiluminescence technology and the Hitachi 912 was used to measure apoA-I, TTR and TF levels based on immunoturbimetry technology. The reagents were purchased from Diagnostics Product Corporation and Roche. A separate dataset was compiled for external-validation purposes from serum collected from patients with breast cancer, colon cancer and atherosclerosis.Statistical analysis of the levels of each of the individual markers was performed using the Kruskal-Wallis non-parametric rank sum test and Mann-Whitney U tests to compare marker levels across ovarian cancer stage. Multivariate logistic regression models (MLRM) were built to predict N vs. low malignant potential (LMP) and N vs. ESOC and LSOC. Model prediction \u2018cut-points\u2019 were also determined by maximizing specificity and sensitivity with equal weight. We then compared MLRM sensitivity, specificity and area under the receiver operator curve (AUC). AUC is a cut-point independent measure of predictive value.Age-matched (51.5 \u00b1 7.5) sera from a separate dataset that included normals, patients with early stage ovarian cancer, breast and colon cancers, and atherosclerosis were then standardized based on the normals in each dataset, assuming a scalar multiplier for each type of measurement . To compute the standardization, multipliers and perform multivariate statistical tests, extreme outliers were removed using a standard outlier detection procedure , 11]. T. T11]. Tmucinous tumors, CA125 was able to distinguish normal samples from LMP and ESOC with a sensitivity of only 46% and 47%, respectively . Collectively, the four markers distinguished normal samples from LMP with 91% sensitivity , normal samples from ESOC with a sensitivity of 89% ; and normal samples from LSOC with a sensitivity of 97% .mucinous histology subgroup, the results suggested greater sensitivity and specificity in the ability of the biomarkers to distinguish serum from normal subjects versus patients with ESOC . In contrast, these four biomarkers when used together, distinguished serum samples from normal subjects versus patients with early stage mucinous ovarian cancer with a sensitivity of 95% .mucinous early stage ovarian cancer, utilizing apoA-1, TF and TTR (CA125 excluded), was 95% .To further validate the disease-specificity of the three biomarkers, we examined serum levels for apoA-I, TTR and TF in 71 additional subjects that included normal (18), breast cancer (18), colon cancer (8), atherosclerosis (9), and early stage OC (18) . MultivaThe majority of patients with ovarian cancer are diagnosed with Stage III or IV disease. Unfortunately, there are no adequate screening tests for the early detection of ovarian cancer and as a result, the diagnosis of ovarian cancer eludes the clinician. Not surprisingly, ovarian cancer is associated with the highest mortality rate among gynecologic malignancies. .Serum cancer antigen 125 (CA125), a high molecular weight glycoprotein, is currently the best clinical marker for papillary serous adenocarcinoma of the ovary in the postmenopausal age group. However it is a consistently poor diagnostic tumor biomarker in premenopausal women, non-serous histologies, and early stage diseases. Only 50%\u201360% of women with early stage ovarian cancer will demonstrate elevated serum levels of CA125 . The idemucinous subsets were analyzed, CA125 levels distinguished N from LMP and ESOC with a sensitivity of 46% and 47% respectively (mucinous subtype by 44% and 48%, respectively, compared to normal subjects (Since CA125 is the gold standard biomarker for ovarian cancer, we measured CA125 levels in all the study samples. CA125 levels alone distinguished N from LMP with a sensitivity of 62% and N from ESOC with a sensitivity of 76% . Furtherectively . These nectively . More imsubjects . These rInterestingly, there exists a link between OC and each of the three biomarkers, apoA-I, TTR and TF , 14], , . ApoA-I In order to evaluate the direct efficacy of the three biomarkers, apoA-I, TTR, and TF, in detecting OC, we reevaluated the specificity, sensitivity and AUC values without CA125 levels. We noted an improvement of 11% in sensitivity for the detection of LMP (compared to CA125 alone, More recently, to evaluate these markers in an independent study population, postdiagnostic/pre-treatment serum samples were studied as part of the National Cancer Institute Immunodiagnostic Serum Bank; levels of various posttranslationally forms of transthyretin and apolipoprotein A1 were measured in addition to CA125. The mean levels of five of the six forms of transthyretin were significantly lower in cases than in controls. The specificity of a model including transthyretin and apolipoprotein A1 alone was high, 96.5%, but sensitivity was low, 52.4%. A class prediction algorithm using all seven markers, CA125, and age maintained high specificity, 94.3%, but still relatively low sensitivity, 78.6% . It is iFinally, our data also suggest that apoA-I, TTR, and TF, when analyzed collectively, are unique to ovarian cancer and thusThree serum biomarkers, ApolipoproteinA-I, Transthyretin and Transferrin, combine with CA125 can be used to significantly improve detection of early stage ovarian cancer over CA125 alone."} +{"text": "The purpose of this study was to compare urate-lowering (UL) efficacy and safety of daily febuxostat and allopurinol in subjects with gout and serum urate (sUA) \u2265 8.0 mg/dL in a six-month trial.Subjects were randomized to febuxostat 40 mg or 80 mg, or allopurinol 300 mg . Endpoints included the proportion of all subjects with sUA <6.0 mg/dL and the proportion of subjects with mild/moderate renal impairment and sUA <6.0 mg/dL. Safety assessments included blinded adjudication of each cardiovascular (CV) adverse event (AE) and death.P < 0.001). Achievement of target sUA in subjects with renal impairment was also superior with febuxostat 80 mg compared with febuxostat 40 mg (50%) or allopurinol (42%), but febuxostat 40 mg showed greater efficacy than allopurinol (P = 0.021). Rates of AEs did not differ across treatment groups. Adjudicated (APTC) CV event rates were 0.0% for febuxostat 40 mg and 0.4% for both febuxostat 80 mg and allopurinol. One death occurred in each febuxostat group and three in the allopurinol group.Comorbidities included: renal impairment (65%); obesity (64%); hyperlipidemia (42%); and hypertension (53%). In febuxostat 40 mg, febuxostat 80 mg, and allopurinol groups, primary endpoint was achieved in 45%, 67%, and 42%, respectively. Febuxostat 40 mg UL was statistically non-inferior to allopurinol, but febuxostat 80 mg was superior to both , which were comparable. In subjects with mild/moderate renal impairment, both febuxostat doses were more efficacious than allopurinol and equally safe. At the doses tested, safety of febuxostat and allopurinol was comparable.NCT00430248 Gout is an increasingly common disorder -5 characSeveral recent publications -11,16-18Febuxostat, a non-purine analogue XO inhibitor , has recHere we report results of the CONFIRMS trial, a Phase 3, double-blind RCT further examining the comparative UL efficacy and safety of febuxostat and allopurinol in a greater number of gout subjects than the total participating in prior comparative trials ,35. The Subjects aged 18 to 85 years with a diagnosis of gout fulfilling American Rheumatology Association preliminary criteria and sUA Exclusion criteria included: secondary hyperuricemia ; xanthinuria; severe renal impairment ; alaSubject screening evaluations included: physical examination and vital signs; medical history, a pre-specified CV history/risk form; laboratory tests ; echocardiogram; assessment for tophi and gout flare; and concomitant medication use. With the exception of tophus assessment, these elements, along with compliance, were repeated at bimonthly visits during the six-month treatment period. sUA was blinded after baseline determination at Day-4.An Interactive Voice Response System was utilized by site personnel during screening visits to initiate double-blind randomization. Subjects were randomized 1:1:1 on Day 1 to receive daily febuxostat 40 mg, febuxostat 80 mg, or allopurinol . Randomization was stratified by baseline renal function and prior completion of either of two open-label extension trials ,14. AmonDuring a 30-day washout period for subjects receiving prior ULT, and throughout the subsequent six-month treatment period for all subjects, prophylaxis for gout flares was given either as colchicine, 0.6 mg daily or naproxen, 250 mg twice daily . All subjects receiving naproxen prophylaxis also received lansoprazole 15 mg daily . Choice of prophylaxis regimen was made by the investigator and subject, taking into account prior drug tolerance and prophylaxis experience. In addition, subjects with eCLcr <50 ml/minute were not to receive naproxen. Gout flares were regarded as expected gout manifestations rather than as AEs.While 2,269 subjects were randomized to receive at least one dose of febuxostat 40 mg, febuxostat 80 mg, or allopurinol Figure , one subThe primary efficacy endpoint was the proportion of subjects in each treatment group with sUA <6.0 mg/dL at the final visit. Prior febuxostat RCTs have demonstrated maintenance of efficacy across last three study visits ,35. A maA total of 750 subjects per treatment group was required to achieve 90% power to meet the non-inferiority criteria between febuxostat 40 mg and allopurinol for the primary efficacy variable, and to detect a 10% difference between febuxostat 40 mg and allopurinol for the primary efficacy variable, and between febuxostat 40 mg and 80 mg for the primary efficacy variable.Secondary efficacy variables included: the proportion of subjects with mild or moderate renal impairment and final sUA <6.0 mg/dL; and the proportion of subjects with sUA <6.0 mg/dL, <5.0 mg/dL, and <4.0 mg/dL at each visit. Pairwise comparisons were made between treatment groups with Fisher's exact test.In subgroup analyses, the primary endpoint was stratified by baseline sUA, renal functional status, presence of tophi at baseline, and prior participation in a ULT trial ,14. A seSafety analyses were carried out on the results from all 2,269 subjects. AEs were summarized using Medical Dictionary for Regulatory Activities (MedRA) terminology and reported by count (n) and percentage of subjects reporting any event for that term. Pairwise comparisons between treatment groups were made using Fisher's exact test. As pre-specified, all deaths and AEs considered by investigators to be potentially CV-related were reviewed by a CV Endpoints Committee, composed of three blinded expert adjudicators. The Committee determined if the AE met Antiplatelet Trialists Collaboration (APTC) criteria ,40 for tOf the 2,269 subjects randomized, 757, 756, and 756 subjects received at least one daily dose of febuxostat 40 mg, febuxostat 80 mg, or allopurinol, respectively Figure . Among a2; 64%) persons who acknowledged the use of alcohol (68%). Of the total cohort, 276 had previously completed a three- to five-year open-label ULT trial with either febuxostat or allopurinol [P < 0.001); prior participant and non-participant groups did not, however, differ significantly in the proportion of subjects with mild or moderate renal impairment (data not shown).There were no significant differences across treatment groups in demographic, gout-related, or comorbid characteristics of the subjects enrolled Table . As in popurinol ,14. ThesMild or moderate renal impairment was identified in 65% of all subjects. Other comorbid conditions included hypertension (53%), hyperlipidemia (42%), hypercholesterolemia (7%), and diabetes (14%). The majority of subjects (87%) reported use of concomitant medications, including medications acting on the renin-angiotensin system (36%), lipid-modifying agents (31%), and anti-inflammatory and anti-rheumatic products (29%). Greater than 90% adherence to treatment was recorded for 80% of the subjects.P < 0.001).The proportions of subjects achieving a final visit sUA <6.0 mg/dL, were 45.2%, 67.1%, and 42.1% in the febuxostat 40 mg, febuxostat 80 mg, and allopurinol groups, respectively. UL by febuxostat 40 mg was non-inferior to that by allopurinol: but the difference in the response rates between the two groups was not significant. However, the greater UL response rate with febuxostat 80 mg compared with either febuxostat 40 mg (21.9%) or allopurinol (24.9%) was significant . In addition, among the total group of subjects with renal impairment, the UL response rate in the febuxostat 40 mg group was significantly higher than that in the allopurinol 300/200 mg group (P = 0.021).Among subjects with any (mild or moderate) renal impairment, the UL response rate in the febuxostat 80 mg group significantly exceeded those observed in the febuxostat 40 mg and allopurinol groups (P < 0.001). Greater proportions of subjects in the febuxostat 40 mg group than the allopurinol group achieved sUA <6.0 mg/dL and <5.0 mg/dL , but significant differences were not seen at other visits, including the final visit. There were no differences between febuxostat 40 mg and allopurinol groups in achievement of sUA <4.0 mg/dL.At any sUA endpoint and at any scheduled visit, a significantly higher proportion of subjects receiving febuxostat 80 mg achieved the target endpoint than subjects receiving febuxostat 40 mg or allopurinol (P < 0.001) and independently affected achievement of the primary endpoint: higher sUA and tophi were associated with lower rates of endpoint achievement, and subjects with mild renal impairment had uniformly higher rates of reaching goal sUA than subjects with normal renal function .Among the 276 subjects who had maintained long-term goal range sUA over three to five years in prior ULT trials ,14, sUA P \u2264 0.001 for each comparison).Rates of flare requiring treatment occurred in 10% to 15% of subjects in all treatment groups during each of the first two months of treatment but declined slowly over the subsequent course of the trial Figure . Of partAEs were reported by 56% of subjects . Occurrence rates did not differ among treatment groups Table , nor didRates of AEs in subjects with mild or moderate renal impairment were similar to those in the overall study population: 56% (268/479), 54% (270/503), and 58% (289/501) of subjects in the febuxostat 40 mg, febuxostat 80 mg, and allopurinol groups, respectively, reported at least one AE. The most frequently reported AEs in subjects with renal impairment were the same as those reported for all subjects. Although not significant, rates of abnormal liver function tests were lower among subjects with mild (6% to 7%) or moderate renal impairment (3% to 6%) compared to subjects with normal renal function (9% to 10%) in all treatment groups. Rates of diarrhea were higher among subjects with moderate renal impairment receiving febuxostat (8% to 10%), compared with subjects with moderate renal impairment receiving allopurinol (7%).Most frequently reported serious AEs were non-specific bacterial infections, coronary artery disease, ischemic coronary artery disorders, lower respiratory tract infections, and prostate cancer. Five subjects died during the study: one subject each receiving febuxostat 40 mg (anaphylactic reaction after 50 fire ant stings) and febuxostat 80 mg (brain edema and chronic obstructive pulmonary disease); and three subjects receiving allopurinol . No deaths were judged by investigators to be related to a study drug.Differences among treatment groups in premature discontinuation rates due to AEs occurring during the study were not significant and are detailed in Figure Rash AEs were reported by 6%, 6%, and 7% of subjects receiving febuxostat 40 mg, febuxostat 80 mg, and allopurinol, respectively. The most frequently reported rash AEs were dermatitis and eczema and rashes, eruptions, and exanthems . With the exception of contact dermatitis, no specific rash was experienced by >1% of subjects in any treatment group, and differences in incidence between groups were not significant. Eighteen subjects withdrew prematurely due to a rash AE, including one subject, receiving allopurinol, who had a severe desquamating eruption requiring parenteral corticosteroid therapy.Rates of liver function abnormalities are shown in Table At least one CV AE was investigator-reported in 5% of all subjects: 5%, 5%, and 6% of subjects in the febuxostat 40 mg, febuxostat 80 mg, and allopurinol groups, respectively. No difference between treatment groups in specific CV AEs was detected. Pre-specified adjudication of all deaths and all AEs reported to be CV system-related identified a total of six subjects experiencing an adjudicated APTC event: three in the febuxostat 80 mg group and three in the allopurinol group Table . All subIn a previous RCT in subjects with gout , the UL If goal range urate levels are not achieved and maintained with febuxostat 40 mg daily or allopurinol, the current data suggest that dose titration to febuxostat 80 mg would be a rational alternative to increasing allopurinol doses beyond 300 mg. In fact, RCT evidence to support the safety and efficacy of allopurinol administered at doses exceeding 300 mg daily is limited to a recent four-month trial in which 13 of 17 subjects (eCLcr \u2265 50 ml/minute) failing to achieve sUA <5.0 mg/dL while receiving allopurinol 300 mg daily safely reached this efficacy endpoint when treated with 600 mg daily .Failure to achieve sUA <6.0 mg/dL among individuals with or without renal impairment receiving guideline-recommended doses of allopurinol has been documented . The comThe prior RCTs comparing febuxostat and allopurinol ,35 did nIn all treatment groups, rates of gout flares requiring treatment diminished slowly after Month 2 and did not affect more than 15% of subjects per month after Week 8 of the study and for Biocryst Pharmaceuticals, Regeneron Pharmaceuticals, Proctor & Gamble, Inc., and URL Pharma . LRE has received consulting fees from Takeda Global Research & Development Center, Inc. . HRS has received consulting fees from Takeda Global Research & Development Center, Inc., Savient Pharmaceuticals, Regeneron Pharmaceuticals, Pfizer, Inc., Xoma, Centocor, Inc., and has received research grants from Takeda Global Research & Development Center, Inc., CherryPharm, and Wyeth Pharmaceuticals . AFW has served as a consultant for Takeda Global Research & Development Center, Inc., Abbott Laboratories, Amgen, Inc., Bristol-Myers Squibb Company, Centocor, Inc., Eli Lilly and Company, GlaxoSmithKline, Pfizer, Inc., Wyeth Pharmaceuticals, and Genetech, Inc. . PM and EL are currently employees of Takeda Global Research & Development Center, Inc., Deerfield, IL, USA. They were employees of TAP Pharmaceutical Products Inc. at the time of the study conduct and analysis. CL was an employee of TAP Pharmaceutical Products Inc. at the time of the study conduct and analysis.MAB and PM made substantial contributions to the conception and design of the study; acquisition, analysis and interpretation of the data; drafting and revising of the manuscript; and gave final approval for publication. HRS participated in the analysis and interpretation of the data; drafting and revising of the manuscript; and gave final approval for publication. LRE and AFW were involved in drafting and revising the manuscript; and gave final approval for publication. EL and CL contributed to the conception and design of the study; analysis and interpretation of the data; drafting and revising of the manuscript; and gave final approval for publication."} +{"text": "We applied period analysis to data from the nationwide Finnish cancer registry to provide up-to-date estimates of 5-, 10-, 15- and 20-year relative survival rates (RSR) achieved by the end of the 20th century. For most forms of cancer, period estimates of long-term survival are much higher than corresponding traditional survival estimates which suggests that for these cancers there has been ongoing major progress in survival rates in recent years which so far has remained undisclosed by traditional methods of survival analysis. For example, period analysis reveals that 10 year RSR have come close to (or even exceed) 80% for cancer of the corpus uteri and melanoma, 75% for breast cancer, 70% for bladder cancer, 65% for cancer of the cervix uteri, and 55% for cancer of the colon and prostate. Period analysis further reveals that 20 year RSR have now come close to (or even exceed) 75% for endometrial cancer and melanoma, 60% for breast cancer and cervical cancer, 55% for colon cancer and bladder cancer, and 40%\u201350% for cancer of the rectum, the ovaries, kidneys and nervous system. \u00a9 2001 Cancer Research Campaign"} +{"text": "Neuroblastomas (NBs) were assessed according to INSS recommendations including MIBG scan and extensive bone marrow staging to eliminate metastatic spread. Patients with unresectable tumour received primary chemotherapy including two courses of carboplatin-etoposide (CE) and two of vincristine-cyclophosphamide-doxorubicin (CAdO). Post-operative treatment was to be given only in children over 1 year of age at diagnosis who had residual disease or lymph node (LN) involvement. Between 1990 and 1994, 130 consecutive children were registered. In comparison with resectable primaries, these tumours were more commonly abdominal, larger and associated with N-myc amplification (NMA). Complete, very good and partial response to CE were, respectively, 1%, 7% and 44%, overall response rate (RR) to two courses of CE and two courses of CAdO was 71%, and the tumour could be removed in all but four of the children. The toxicity was manageable. The 5-year overall survival (OS) and event-free survival (EFS) were, respectively, 88% and 78% with a median follow-up of 38 months. In multivariate analysis, only NMA and LN involvement adversely influenced the outcome, particularly NMA. Children with unresectable NBs and no NMA fared as well as children with resectable ones as OS were, respectively, 95% and 99% and EFS 89% and 91%. Our data show encouraging results in localized but unresectable NBs as 90% of children may be considered as definitely cured, especially those without NMA."} +{"text": "The androstenedione derivative, exemestane (FCE 24304), is a new orally active irreversible aromatase inhibitor. Fifty-six post-menopausal advanced breast cancer patients entered this study to evaluate the activity of four low exemestane doses in reducing oestrogen levels. The drug's tolerability and clinical efficacy were also assessed. Exemestane was orally administered to four consecutive groups at daily doses of 25, 12.5, 5 and 2.5 mg, and the changes in oestrogen, gonadotrophins, sex-hormone binding globulin and dehydroepiandrosterone sulphate levels were evaluated. Drug selectivity was studied by measuring 17-hydroxycorticosteroid urinary levels. After 7 days of treatment, mean oestrone and oestradiol levels had decreased by respectively 64% and 65% (a decrease which was maintained over time); in the 2.5 mg group, oestrone sulphate levels also decreased by 74%. Gonadotrophin levels were significantly higher, whereas no changes in the other serum hormone levels or any interference with adrenal synthesis were detected. Treatment tolerability was satisfactory: nausea and dyspepsia were reported in 16% of patients. The overall objective response rate was 18%. In conclusion, exemestane is effective in reducing oestrogen levels at all of the tested doses and shows interesting clinical activity."} +{"text": "Acanthamoeba for 12.13%, fungi for 8.16%, and virus for 2.93%. The most frequent agent identified was Corynebacterium macginleyi (18.41%), followed by Staphylococcus aureus (17.78%), Streptococcus pneumoniae (9.41%), and Pseudomonas aeruginosa (9.00%). We identified at least one ophthalmologic risk factor in 410 patients (85.77%). Trauma and contact lens wear were the most common risk factors found, accounting for 34.94% (n\u2009=\u2009167) and 33.47% (n\u2009=\u2009160) of cases. Sensitivity to fluoroquinolones and aminoglycosides was tested in all bacterial isolates, presenting values of 96.66% and 98.12%. In our region, the most common bacteria are Staphylococcus aureus, Streptococcus pneumoniae, and Pseudomonas aeruginosa, and they showed high sensitivity rates to first-line antibiotics, without any modification or emergence of antibiotic resistance trends during the 10 years of the study. For this reason, we decided to maintain the same internal protocol in our tertiary centre.The microbiological profile of infectious keratitis has shown great differences across the world. Due to the continuous shifting trends in microbiological profile and antibiotic resistance patterns reported in several studies, constant local updates are crucial to provide an adequate treatment. The propose of this study was to analyze the incidence of infectious keratitis, possible changing trends in microbiological profile, and bacteria sensitivity to commonly used antibiotics, in our tertiary center, in the last 10 years. A retrospective study was performed, based on the survey review of electronic medical records of all patients with presumed infectious keratitis, between January 1, 2009, and December 31, 2018. Microbial cultures were performed, and patients were treated according to an internal protocol. A total of 1360 samples were included. We obtained a 35.1% culture-positive rate. Bacteria accounted for 76.78% of all positive scrapes (53.34% were Gram positive and 23.44% were Gram negative), Infectious keratitis is a serious and frequent cause of ophthalmology consultation and one of the greatest causes of visual impairment worldwide , 2. The Infectious keratitis is associated with significant morbidity, carrying a high risk of corneal scar, corneal perforation, endophthalmitis, and vision loss.Contact lens usage and ocular trauma are the major risk factors to develop infectious keratitis. However, other conditions such as ocular surface diseases (blepharitis and dry eye) and systemic disorders are also strongly associated with the onset of this disease .Clinically, it manifests as eye pain, photophobia, blurred vision, and ciliary injection.The microbiological profile of infectious keratitis has shown great differences across the world, but bacteria triumph as the leading cause of infectious keratitis, followed by fungi . Virus and protozoa are less frequent agents , 7.Having in mind this etiological pattern, broad-spectrum antibiotics are used as empiric first-line treatment for presumed infectious keratitis, after obtaining corneal scrapes . HoweverThe propose of this study was to analyze the incidence of infectious keratitis, possible changing trends in microbiological profile, and bacteria sensitivity to commonly used antibiotics, in our tertiary center, in the last 10 years.2 in size with or without epithelial defect.This retrospective study was performed in a Portuguese tertiary center, based on the survey review of electronic medical records of all patients with presumed infectious keratitis, between January 1, 2009, and December 31, 2018. Presumed infectious keratitis was defined by the presence of a corneal infiltrate >1\u2009mmMycobacterium and Acanthamoeba, were used.All samples were collected in the emergency room, under topical anesthesia. Every time, scrapes were obtained from two different locations and then inoculated onto Amies Agar Gel . Finally, they were sent to the Microbiology Department for culture and antibiotic sensitivity testing. In clinically suspicious or nonresponsive cases, selective media and stains for aerobic and anaerobic bacteria, Patients were treated according to an internal protocol, using an empiric third- or fourth-generation fluoroquinolone and an aminoglycoside, hourly. If a fungi etiology was suspected (soil contamination or trauma with vegetable matter), topical clotrimazole was added to the treatment regimen.Patients were assessed for age, gender, presence of risk factors , sample results, and antibiotic sensitivity test results. The study was therefore divided into 2 periods for analysis: from 2009 to 2013 and from 2013 to 2018.t-test, logistic, and multiple regression were performed, as appropriated. P < 0.05 was considered significant.Statistical analysis was performed using SPSS software, version 22 . To compare differences between groups, chi-square test, n\u2009=\u20091360) samples were included. Patients' mean age was 46.88\u2009\u00b1\u200920.327 years (range 2\u201398), and 50.3% of them were males. Over the years, we observed an increase in the number of suspected cases of infectious keratitis, with the value doubling in 10 years. We obtained a 35.1% (n\u2009=\u2009478/1360) culture-positive rate. The percentage of positive microbiological cultures per year ranged from 31.31 to 42.22%. Per period, this value was 37.76% and 33.71% in 2009\u20132013 and 2014\u20132018, respectively, without significant statistical differences (P > 0.05).A total of one thousand three hundred and sixty of all positive scrapes (53.34% were Gram positive and 23.44% were Gram negative), or 2.93% .Corynebacterium macginleyi (18.41%), followed by Staphylococcus aureus (17.78%), Streptococcus pneumonia (9.41%), and Staphylococcus epidermidis (4.39%). No significant statistical changes were observed in the microbiological profile in both periods. The most frequent Gram-negative agents were Pseudomonas aeruginosa, Serratia spp., Moraxella spp., and Haemophilus influenzae . Again, no significant statistical changes were observed in the microbiological profile in both periods.Gram-positive bacteria accounted for 55.50% of all positive scrapes in 2009\u20132013 and 51.80% in 2014\u20132018, while Gram-negative bacteria accounted for 20.50% and 25.54% in 2009\u20132013 and 2014\u20132018, respectively, without significant statistical changes . The mosAcanthamoeba accounted for 11% and 12.95% of positive scrapes in 2009\u20132013 and 2014\u20132018, respectively, without significant statistical differences in both periods. The same was observed with fungi and virus . Candida specimens, Fusarium specimens, and Aspergillus specimens accounted for 4.18%, 1.46%, and 1.26% of all positive scrapes. The distribution of microbial profile is shown in n\u2009=\u200984). Trauma and contact lens wear were the most common risk factors found, accounting for 34.94% (n\u2009=\u2009167) and 33.47% (n\u2009=\u2009160) of cases. The distribution of the risk factors is demonstrated in We identified at least one ophthalmologic risk factor in 410 patients (85.77%). Additional systemic disorders were present in 17.57% and to aminoglycosides (gentamicin and tobramycin), 89.41% and 98.82%, respectively. Two cases were methicillin-resistant Staphylococcus aureus (MRSA), being sensitive to vancomycin and linezolid only. All Streptococcus pneumonia isolates were sensitive to fluoroquinolones and aminoglycosides, and only a small proportion (4.44%) was resistant to tetracyclines. 85.72% of Staphylococcus epidermidis isolates were sensitive to fluoroquinolones and the same proportion to aminoglycosides, but resistance to tetracycline was observed in 38.09% of cases.Pseudomonas aeruginosa presented a sensitivity of 95.35% to fluoroquinolones and aminoglycosides, and 27.91% demonstrated resistance to cotrimoxazole. Besides, 4.35% of cases showed multidrug resistance (resistance to at least three different classes of antibiotics), being sensitive exclusively to cefepime and colistin. All Serratia specimens and Moraxella catarrhalis isolates were sensitive to fluoroquinolones and aminoglycosides. No differences were observed in sensitivity to antibiotics in both periods analyzed.Considering the widespread use of broad-spectrum antibiotics, antibiotic resistance among bacterial microorganisms in general is a real concern nowadays, and ocular pathogens are no exception. Therefore, constant local updates of microbiological profiles and antibiotic resistance patterns are crucial to wisely choose the most appropriate topical treatment to ocular infections.Infectious keratitis is a serious condition that can lead to a poor visual outcome or even loss of the eyeball. The diversity of the clinical presentation constitutes a huge challenge to an accurate diagnosis and treatment. Untreated keratitis can lead to opacification and/or perforation of the cornea, as well as to other equally fearsome complications such as secondary glaucoma, corneal thinning, uveitis, and endophthalmitis. Due to this rapidly progressive and potentially devastating course, an appropriate treatment with effective empirical topical antibiotics is mandatory.It is well known that the epidemiological pattern of infectious keratitis significantly varies between countries and even among regions of the same country \u201313. TherIn this study, we analyzed a total of 1360 corneal scrapes obtained from patients diagnosed with infectious keratitis, admitted to a tertiary hospital in Portugal.n\u2009=\u2009478/1360) culture-positive rate, a result in agreement with similar studies published in the literature [We obtained a 35.1% , followed by Staphylococcus aureus (17.78%), Streptococcus pneumoniae, (9.41%) and Pseudomonas aeruginosa (9.00%). In the literature, some studies showed Pseudomonas aeruginosa as the most frequent agent [Staphylococcus aureus is the main causal agent [Corynebacterium macginleyi was considered by the Microbiological Department as a scrape contaminant. Nevertheless, it seems to actively contribute to the pathophysiology of blepharitis, and thus, it can potentially play a role in the genesis of infectious keratitis, particularly if some risk factors are present [The most frequent agent identified was nt agent , 16, 18,al agent , 14, 16. present . For thi present \u201322.Acanthamoeba accounted for 12.13% of positive scrapes, and this value is located between the ranges published in the literature (1.6% and 16.9%) [d 16.9%) .Candida spp. being the most frequent. However, the incidence of fungi is much higher in some countries such as Brazil (30%) or India (23\u201336%) since these microbiological agents are more frequent in tropical and subtropical regions than in the temperate regions [Fungi represented 8.16% of positive scrapes, regions , 25.Globally, fluoroquinolone sensitivity was high (96.66%), and the same was observed with aminoglycoside sensitivity (98.12%). Although these results are similar to several other series already published, \u201316, 18 rInfectious keratitis caused by MRSA is an alarming issue all around the world due to its poor response to conventional antibiotic treatment \u201329. Our Corynebacterium macginley was considered a scrape contaminant. In the first reports in the literature, this agent was highly sensitive to common topical antibiotics, but this scenario has now changed, and high levels of resistance to fluoroquinolones have been already reported [In our Microbiological Department, reported \u201337.Staphylococcus aureus, Streptococcus pneumoniae, and Pseudomonas aeruginosa, and they showed high sensitivity rates to first-line antibiotics, without any modification or emergence of antibiotic resistance trends during the 10 years of the study. For this reason, we decided to maintain the same internal protocol in our tertiary centre.Some of the differences found in our study, compared to others already published, can be explained by factors such as the geographic location and associated climate and the extent and type of empirical antimicrobial therapy instituted before corneal scrapes. In our region, the most common bacteria are"} +{"text": "Over 10 million people with Alzheimer\u2019s disease or related dementias (ADRD) live in China. In Shanghai, the prevalence of ADRD is about 3-4% among aged 60 or older, and approximately 70-85% have never been diagnosed. This study reported the pilot testing results of a dementia management model launched by Shanghai Mental Health Center to build dementia friendly communities. The dementia management model links screening, diagnosis, care planning, treatment, and services, to improve dementia literacy and standard diagnosis rate. About 3,786 senior residents were screened using the AD 8 and MoCA scales. The cognitively intact group was suggested for annual check-up, while at -risk groups were referred to formal diagnosis and intervention. About 125 older adults with a mild cognitive impairment diagnosis were provided referrals for cognitive training, and 109 diagnosed with dementia were provided medical and social interventions. This management model adds to dementia awareness and education."} +{"text": "Poly-trauma patients often sustain complex head/neck injuries requiring prolonged hospitalizations and multiple operations. Few studies have evaluated the associated injury patterns and risk factors for poor clinical outcomes.Consecutive poly-trauma patients with operative maxillofacial fractures treated at a level 1 trauma medical center between 1995 and 2013 were evaluated. Concomitant head/neck injuries to identify potential injury patterns were numerated. Lastly, a multivariate analysis was performed to determine independent risk factors for complications during the acute hospitalization period.p<0.01) and older patients had a 4.5% increase in complication rate (p<0.05) for every year of increased age. Totally, 232 poly-trauma patients presented with operative maxillofacial fractures, while 38.8% of patients had a secondary maxillofacial fracture, 16.4% had intracranial hemorrhage, 23.7% had skull fractures, and 12.1% had spinal fractures. The rate of complication during admission was 28.3%. Multivariate analysis revealed advanced patient age and increased number of operations to predict the rate of complication. Patients requiring more than one operation had a 1.8-fold increase in complication rate (Poly-trauma patients have a high incidence of secondary maxillofacial fractures, concomitant head/neck injury, and inpatient complication rate. Knowledge of associated injury patterns can help increased awareness and can guide physician decision-making to avoid missed/delayed injuries. Maxillofacial injuries are often associated with high rates of secondary head/neck injury following trauma, however, are often overlooked during initial assessments. Vles 8,9 To this end, identifying potential injury patterns can help guide evaluation and treatment to prevent missed/delayed diagnosis in this vulnerable patient population. Poly-trauma patients often present with maxillofacial fractures and are known to have increased rates of complication during hospitalization.7,10-12Inadequate clinical assessment, truncated radiologic workup, delayed presentation of injury, and poor mental status can contribute to missed injuries/diagnoses.9,13-17 Etiology of complications in the trauma population is multifactorial and dependent on multi-organ injury, the severity of injury, prolonged hospital stay, numerous invasive diagnostic/therapeutic procedures, amongst others.14,15 While, few authors have evaluated risk factors related to complications, a comprehensive analysis evaluating patient and surgery-related factors has yet to be explored.Complication rates for trauma patients admitted to the ICU are estimated at 17.0-31.2%, whereas complication rates following traumatic facial fractures range from 12.0-50.3%.Accordingly, the objective of the current study was (i) to identify the relationship between operative maxillofacial fractures and the presence of secondary head/neck injuries and (ii) to identify patient and surgical risk factors for complication. Increased awareness of risk factors, associated injuries, and complications following maxillofacial trauma can help improve clinical outcomes for this complex patient population.In the current study, a retrospective, cross-sectional analysis was performed to investigate consecutive polytrauma patients treated at a Level 1 trauma medical center.Polytraumapatients included a subset of patients requiring inpatient hospitalization for multisystem injury. A cohort of patients presenting with maxillofacial fractures using ICD9 diagnosis codes was identified. The patients who underwent surgical intervention for maxillofacial fractures by the plastic surgery department using CPT codes and chart review were sub-selected. They were cross-compared with ICD9 codes for secondary spinal fracture, intracranial hemorrhage, and skull fracture. Patient charts were evaluated for variables related to socio-demographics, surgery, injury presentation, and complication rate. Next, the associated injury patterns concomitant with maxillofacial fracture were numerated to identify potential injury patterns. Finally, a multivariate analysis was performed to evaluate sociodemographic and surgery related variables to identify the risk factors for increased complications.Patients who underwent operative repair for maxillofacial injuries were identified based on ICD9 and CPT codes. Patient charts were evaluated for sociodemographic variables including age, gender, race/ethnicity, comorbidities, toxicology screen, and insurance type. Race was categorized as Caucasian, Asian, African American, Hispanic, and Other. Insurance types were categorized as Private, Medicare, Medicaid, self-pay, and no insurance. We evaluated variables related to the trauma including the mechanism of injury, number of injuries sustained, need for ICU admission, and number of surgeries performed. Finally, the complication rates occurring during the acute hospitalization period were evaluated.16,17 a multivariate analysis was performed to identify independent risk factors for complications. Patients who suffered operative maxillofacial injuries were numerated and compared to identify secondary head/neck injuries including spinal fractures, ICH, and skull fractures. Next, univariate and multivariate regression analyses were performed to identify the variables influencing complication rates during the acute hospitalization period. First, a univariate analysis was performed to identify predictors of complications across each categorical or continuous variable using ANOVA. Given the high incidence of complications following poly-trauma cited in literature,p-values<0.05 with all tests two-sided. All statistical analyses were conducted with IBM SPSS software. Approval for this study was obtained from the Human Research Protection (HRP) and Institutional Review Board at the University of California, Irvine Medical Center.After identifying the significant predictors of complication on univariate analysis, these variables were included into a multivariate linear regression analysis and identified the predictors of complication while simultaneously controlling for confounding variables. Statistical significance was set at Between 1995 and 2013, 232 poly-trauma patients received operative management of their maxillofacial fractures by the plastic surgery department. Patient characteristics are summarized in The incidence of maxillofacial fractures was numerated and found 232 operative facial fractures occurred with 90 fractures occurring in association with a secondary maxillofacial fracture . Next, tAn analysis of the injuries sustained by these patients revealed that 18.1% of patients had 1-3 injuries, 34.9% had 4-6 injuries, 28.9% had 7-10 injuries, and 18.1% had greater than 10 injuries. Next, the operative management of the injuries rendered and found 43.5% of patients required 1-2 surgeries, 28.9% required 3-4 surgeries, and 27.6% of patients required more than 4 surgeries.To identify potential fracture patterns, the incidence of secondary maxillofacial fracture was evaluated. As shown in p<0.01). With respect to patient age, patients had a 4.5% increase in complications for every year of older age .The remaining patient demographics , mechanism of injury, or number of injuries were not significant predictors of complications.The overall complication rate during the acute hospitalization period for the study cohort was 28.3%, with sepsis, respiratory failure, and pneumonia/pnuemonitis being the most common. After controlling for sociodemographic and injury/disease related variables in our multivariate modeling , the num16 In the current study, we evaluated poly-trauma patients who underwent operative repair of facial fractures and found a high rate of secondary maxillofacial fractures (38.8%). Associated injuries also included intracranial hemorrhage (16.4%), skull fractures (23.7%), and spinal fractures (12.1%). Maxillofacial fracture is a common finding in poly-trauma patients and one that often presents with multiple concomitant injuries and significant morbidity, mortality, and complication.p<0.05). The presence of medical comorbidities or number of injuries incurred failed to influence complication rates. Maxillofacial fractures often present with an incidence of associated life-threatening injuries.17We found a complication rate of 28.3% during the acute hospitalization period and revealed that patients who underwent multiple operations, as well as those who presented with advanced age, were more likely to suffer a complication , skull fractures (23.7%), and spinal fractures (12.1%). Rates of associated injuries vary from 1.9-19% for skull fractures,19,22-25 11.0% to 43.7% for brain injury,9,24 and 0.8-24% for cervical spine injury.27,28 The relative lack of protection of the head and neck in these high-impact settings make the face vulnerable to injury.26 The coexistence of head and neck injury following maxillofacial fractures is likely secondary to the proximity of the cranial/spinal bones to the facial bones and the ability to transmit direct traumatic impact to the cranium and spine via sutural attachments.24,27Similar to previous reports,et al. found that ~3% of patients with facial fractures and no neurological abnormalities exhibited intracranial hemorrhage on computed tomography (CT) scans.28 Similarly, Davis et al. found diagnosis of cervical spine injury was missed or delayed in 4.6% of patients-often due to inadequate or misread cervical spine imaging.29 Recognizing the frequency of multiple injuries and identifying maxillofacial fracture patterns can help alert physicians to potential concomitant injuries that may otherwise be under-evaluated.Further, these significant injuries can be missed or delayed. Kloss 16,17 whereas, others have found complication rates of 12.0-50.3% for traumatic facial fractures.9,19,20 Studies have shown age, gender, traumatic CNS injury, chronic alcohol use, the type of intensive care unit, and number of operations to influence complication rates.16,17,21,30,31In the present study, we found a complication rate of 28.3% in the acute hospitalization period for poly-trauma patients presenting with operative maxillofacial fractures. Previous studies have estimated the complication rate of trauma patients admitted to the ICU to be 17.0- 31.2%,21 inflammatory response induced by surgical intervention itself, and others. While each operative intervention may be necessary and responsible for the decrease in mortality of trauma patients, clinicians must evaluate the necessity of additional operations, its timing, and the possibility of performing surgery on a delayed basis. In the current study, we found patients requiring more than one operation had a 1.8-fold increase in complication rate. This may reflect added anesthesia risks, risks for DVT/PE inherent to surgery, infectious risks associated with incision,et al. revealed elderly patients are at increased risk of dying following poly-trauma after finding patients >80 years had a 46% inpatient mortality rate vs. 10% in patients 66 to 79 years old.32 Similar previous studies have shown the associated increased mortality, length of stay, and cost of treatment with advancing patient age.33-35Advanced age is a demographic variable that influences numerous medical and surgical outcomes. In this study, we found age to be an independent predictor of complication during the acute hospitalization period. While mortality rates have improved overall, Lonner 36 decreased functional reserve for recovery, and multisystem changes that occur with age. Ultimately, a more conservative approach for older patients may prove beneficial as would delay non-urgent surgical intervention. Further, physicians must be informed about the risks associated with advanced age and encouraged to be proactive with planning of services, such as rehabilitation, to improve clinical outcomes.37This likely reflects increased comorbidities of the elder population,This study has several limitations. First, this study was a retrospective cross-sectional study, and was therefore subject to potential uncontrolled and unmeasured biases. Although we were able to identify risk factors and predictors of complication, the study was unable to establish a causal-effect relationship. Further, the present study included data from a single institution in a single urban setting. A different geographical area may represent different patient populations, etiologies for traumatic injury, and access to trauma centers. Further, our study did not evaluate timing of surgical intervention or the duration of operations, which may have affected complication rates. Despite these limitations, our study was able to evaluate the incidence of secondary maxillofacial and head/neck injuries and identified risk factors for complications to help guide clinical decision-making.Poly-trauma patients have a high incidence of secondary maxillofacial fractures, concomitant head/neck injury, and inpatient complication rate. Knowledge of associated injuries is necessary to comprehensively evaluate, treat, and avoid missed/delayed injuries. Older age and number of operations can contribute to higher complications during the acute hospitalization period. Delaying non-urgent operative intervention after the initial hospitalization period as well as providing more conservative management for older patients may decrease complication rates and improve outcomes.The authors declare no conflict of interest."} +{"text": "Strongyloides stercoralis and Schistosoma sp. and viral infections among sub-Saharan Africans (SSA) and Latin Americans (LA) in Switzerland's largest pretrial prison. We carried out a cross-sectional prevalence study using a standardized questionnaire and serological testing. Among the 201 participants, 85.6% were SSA and 14.4% LA. We found the following prevalence ratios: 3.5% of HIV , 12.4% of chronic HBV , 2.0% of viraemic HCV , and 8.0% of strongyloidiasis . The serological prevalence of schistosomiasis among SSA was 20.3% (not endemic in Latin America). Two infections were simultaneously detected in SSA: 4.7% were coinfected with schistosomiasis and chronic HBV. Four other coinfections were detected among SSA: schistosomiasis-HIV, HIV-chronic HBV, HIV-HCV, and schistosomiasis-strongyloidiasis. To conclude, the high prevalence rates of persistent viral and parasitic infections and their potential coinfections among SSA and LA detained migrants highlight the need to implement control strategies and programs that reach people in detention centers in nonendemic countries.In Swiss prisons, more than 70% of detained people are foreigners and over one-third originate from sub-Saharan Africa or Latin America. These two regions are endemic for various tropical diseases and viral infections, which persist after migration to nonendemic countries. Parasitic infections and cooccurrent viral infections , and hepatitis C (HCV)) are especially of concern for clinical care but have been neglected in empirical research. These diseases often remain silent for years before causing complications, especially if they occur concomitantly. Our research aimed to study the prevalence rates and coinfections of two neglected tropical diseases, namely, The global prevalence rate of human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) approximates, respectively, 0.8%, 3.6%, and 1%, although their specific disease burden varies considerably between and within countries and regions . Owing pSimilarly, other infectious pathologies, including helminthiasis such as strongyloidiasis and schistosomiasis , can represent a persistent health problem among people who have migrated from endemic countries \u20139. HowevStrongyloidiasis is endemic in tropical and subtropical regions. In immunocompetent persons, chronic intestinal infection usually remains paucisymptomatic for decades. In immunocompromised individuals, larvae can massively invade the gastrointestinal and pulmonary systems (hyperinfection syndrome) and other organs (disseminated strongyloidiasis). This invasion facilitates the translocation of enterobacteria leading to bacterial sepsis . Hyperin S. mansoni and S. haematobium) [S. mansoni) is endemic only in certain areas of Brazil, Venezuela, Suriname, and some Caribbean islands [S. mansoni and S. japonicum) and perivesical (S. haematobium) veins, and the deposition of eggs in host tissues provokes inflammatory and fibrotic reactions. Infected patients can present abdominal pain, diarrhea, dysenteric syndromes and/or hematuria, dysuria, secondary infections, and ureteral fibrosis (genitourinary disease). Eggs can embolize the portal spaces of the liver, causing progressive fibrosis. One of the most feared complications is an upper gastrointestinal bleeding caused by esophageal varices [Sub-Saharan Africa is the main endemic region for schistosomiasis: 93% of world's cases occur in this continent (mainlyatobium) . In Lati islands . Adult w varices . Pneumocystis carinii [Patients coinfected with viral and NTDs may have a more severe clinical course . Coinfec carinii . Data onIn Europe, immigrants represent a high proportion of the correctional population. In 2012, non-European citizens accounted for 21% of the estimated 1.73 million people detained in the prisons of the 47 Member States of the Council of Europe. A large majority of foreign detainees originated from low-income countries. In Switzerland, inmates of non-Swiss nationality represent 73% of the correctional population, which is among the highest proportion of foreigners in detention in Western European countries. In the largest pretrial prison of Switzerland, 28% of detainees were SSA and 9% LA , 28. PeoThe prevalence rates of blood-borne viruses are reported to be higher in prison settings than in the community. The main risk factors include history of injecting drug use, unprotected sexual intercourse, and unsafe tattooing . There iTherefore, our study aimed to explore the epidemiologic profile of strongyloidiasis, schistosomiasis, HIV, HBV, and HCV among people from sub-Saharan Africa and Latin America who are detained in the pretrial detention center in Geneva, Switzerland.We used a cross-sectional study, which took place in 2015 at the pretrial detention center of Champ-Dollon (Geneva), the largest correctional center in Switzerland. The report of our study findings are based on the STROBE statement. Through an information campaign conducted in the detention center, all adults originating from Latin American or sub-Saharan African countries were invited to participate in the study. Interested individuals received information about the research and signed an informed consent form before study inclusion. A trained researcher administered a standardized questionnaire to each participant, whereupon a nurse collected a blood sample of circa 10 ml. We calculated the sample size according to the expected prevalence rates of strongyloidiasis and schistosomiasis, the core focus of the study. The expected prevalence rates for strongyloidiasis and schistosomiasis were estimated at 10% and 15% using a pilot study at Geneva correctional center \u201336. WithParticipants answered a standardized questionnaire in Spanish, Portuguese, English, or French (the interviewer was competent in these languages) for parasitic diagnoses. Serum samples were tested for HBV surface antigen (HBsAg), antibodies against HBV core antigen (anti-HBc), and surface antigen (anti-HBs), anti-HIV, and anti-HCV using commercial immunoenzymatic assays (Abbott Laboratories SA). Anti-HIV were systematically confirmed by INNO-LIA\u2122 HIV I/II Score . Anti-HCV reactivity was systematically confirmed by INNO-LIA\u2122 HCV Score and quantitative HCV RNA measurements . The presence of these three positive tests signaled an active HCV infection. HBsAg positivity signaled a chronic HBV infection. The presence of anti-HBc antibodies and negative HBsAg indicated a resolved infection. Among participants with a serological pattern compatible with a resolved HBV (anti-HBc pos/HbsAg neg), occult HBV infections were not excluded. Since these cases are rare, underevaluation of chronic HBV prevalence rate in the study population would be very limited . Schistosoma mansoni and Schistosoma haematobium with a specificity of 94% in patients also coinfected with other helminths [ Strongyloides stercoralis has a sensitivity of 91% and a specificity of 94% among a composite population, which includes individuals from tropical areas who are coinfected with other parasitic infections [Screenings for strongyloidiasis and schistosomiasis were done using two ELISA commercial kits . Bordier-ELISA kits for the diagnosis of schistosomiasis are reported to detect 94% of bothelminths , 40. Scrfections . All serAll participants with confirmed HIV, HBV, HCV, schistosomiasis, and strongyloidiasis underwent a clinical evaluation. In cases of HIV, chronic HBV, and HCV, patients were referred to the Geneva university hospitals for specialized care. Antiparasitic treatments were given to participants who were positive for schistosomiasis and for strongyloidiasis . Vaccination against HBV was proposed to susceptible participants .The data were compiled into an Excel spreadsheet see Dataset.The research project protocol was approved by the Ethics Committee of Geneva .Out of 403 inmates invited, 201 consented to participate in the study, answered the questionnaire, and completed blood analyses (participation rate: 49.9%). A total of 85.6% were SSA (23 countries) and 14.4% were LA (12 countries). A large majority of SSA participants originated from West or Central Africa (94.8%) .With regard to factors potentially related to parasitic infections, the sanitation conditions before migration differed among participants from different regions: 96.5% of LA and 52.8% of SSA had indoor toilets (p<0.01) and 96.5% of LA reported having indoor tap water compared to 40.8% of SSA (p<0.01). versus 11.8%, p<0.001), as well as body piercing . A history of blood transfusion was reported by 4.7% of the participants. In terms of sexual risk factors, 45.2% of males reported a history of transactional sex (against money or other favors). Half of the participants (49.8%) reported using condoms most of the time or always. Among the 156 male participants who reported being sexually active prior to detention, 98.7% reported being solely heterosexual.Regarding factors potentially related to viral infections, only one SSA participant (0.6%) and one LA (3.5%) reported a history of injecting drugs. More LA than SSA reported having tattoos . The serological prevalence rate of schistosomiasis, calculated among participants originating from sub-Saharan Africa (endemic area), was 20.3%.Coinfections were detected only among SSA: 4.7% were coinfected with schistosomiasis and chronic HBV, 0.6% with schistosomiasis and HIV, 0.6% with HIV and chronic HBV, 0.6% with HIV and HCV, and 0.6% with schistosomiasis and strongyloidiasis.Among SSA participants, chronic or resolved HBV infection (anti-HBc-positive) was not significantly associated with age, education level, socioeconomic status, number of sexual partners, use of condom, or transactional sex Table.Among the four participants who were HCV positive, no one reported a history of injecting drugs or having tattoos or body piercing. Only one of them reported a history of blood transfusion. versus 17.9%; p=0.1). History of swimming in lakes or rivers was marginally associated with schistosomiasis see Table.This was the first study conducted in a prison setting designed to identify strongyloidiasis and schistosomiasis prevalence rates in Europe and their association with HIV, HBV, and HCV.Our study in Swiss prison showed that a high proportion of migrants in detention from these endemic regions have parasitic NTDs . These findings corroborated the results from published literature on persistent parasitic diseases among migrants , but focused on a neglected sub-group of migrants in Europe, i.e., detainees , 42\u201347. The study population's prevalence ratio was 3.5% for HIV, 12.4% for chronic HBV, and 2.0% for viraemic HCV. These prevalence rates were higher than the respective prevalence rates in the Swiss general population , 50. TheThe observed prevalence ratios of blood-borne infections among our participants were similar to the expected prevalence rates in the general population of the regions of origin. With regard to HIV, the expected prevalence rate is 3% in sub-Saharan Africa and 0.3% in Latin America and the Caribbean . We founFor chronic HBV, the expected prevalence rate is 11.2% in West and Central Africa (14.5% in our study) and 0.8% in Latin America (0% in our study) .The similarity between the prevalence rates in our study and the region of origin also applied to HCV. The global prevalence rate of viraemic HCV is estimated to be 1.5% in Western and Central sub-Saharan Africa in the general population . We idenA total of 4.7% of SSA participants had schistosomiasis and chronic HBV coinfection, and 0.6% had schistosomiasis and HIV coinfection. Detection and treatment of schistosomiasis are recommended for HIV-, HBV-, or HCV-positive persons with epidemiological risk factors. Indeed, schistosomiasis accelerates the development of liver fibrosis concomitantly with HBV or HCV infections and can increase the likelihood of HIV transmission, as well as accelerate the progression of HIV \u201325. TreaThe correctional population is characterized by higher morbidity when compared to the host community and specTwo of the participants who were HIV-positive and were not injecting drug users had concomitant infections: one with HBV (HIV/HBV coinfection) and the other with HCV (HIV/HCV coinfection). Thus, these coinfections were not frequent but could be clinically important. HIV accelerates the natural course of HBV and HCV infection, facilitating faster liver fibrosis and malignancy . Early dFirst, the relatively small sample size limited the extension of statistical analyses to test associations between variables. However, the main study objective was not to confirm well-known risk factors of viral and parasitic diseases, but to investigate at a descriptive level the prevalence rates of selected parasitic NTDs and common viral infections. Second, the relatively low participation rate may have induced some degree of selection bias: questions about sex and sexual behavior are sensitive and many African Muslim participants refused to answer such questions; individuals of Muslim faith refused blood sampling during Ramadan; and the interviewer was a woman . Therefore, there might be an underestimation of the prevalence rates of viral infections. We did not expect any influence on the prevalence rates of NTD. A third shortcoming was that the small sample size of prisoners having blood-borne and NTDs may have led to a lack of power when analyzing their associations with risk factors. Further studies using larger sample sizes should test whether migrant status and risk factors are cumulative risk factors for these diseases. In high-income countries, it would be useful to investigate whether the prevalence rates of persistent viral and NTDs among migrants in the general population correspond to that of incarcerated migrants.The prevalence rates of viral infections, strongyloidiasis, and schistosomiasis were worryingly high in the studied prison population. Therefore, persistent parasitic NTDs should no longer be overlooked in custodial settings hosting migrants from endemic regions. Control efforts should target migrants originating from highly endemic countries. Indeed, correctional settings offer an opportunity to implement infectious disease control programs for a vulnerable population who has limited access to health care. Early diagnoses and treatments limit complications and costs for both patients and the host community. Therefore, detention settings must be part of the agenda for achieving target 3.3 of the United Nations Sustainable Development Goals, as it aims to end the NTDs epidemics and combat hepatitis among others."} +{"text": "Candida. Candidemia is one of the most common healthcare\u2013associated BSIs in the United States, with all-cause in-hospitalmortality of up to 30%.Candidemia is a bloodstream infection (BSI) caused by yeasts in the genus2012\u20132016.Candida species collected from asurveillance area resident during 2012\u20132016. Isolates were sent toCDC for species confirmation and antifungal susceptibility testing. Anysubsequent blood cultures with Candida within 30 days ofthe initial positive culture in the same patient were considered part of thesame case. Trained surveillance officers collected clinical information fromthe medical chart for all cases, and isolates were sent to CDC for speciesconfirmation and antifungal susceptibility testing.CDC\u2019s Emerging Infections Program (EIP), a collaboration among CDC,state health departments, and academic partners that was established in1995, was used to conduct active, population-based laboratory surveillancefor candidemia in 22 counties in four states with a combined population of approximately 8 million persons.Laboratories serving the catchment areas were recruited to report candidemiacases to the local EIP program staff. A case was defined as a blood culturethat was positive for a Candida species.Candida albicans accounted for 39% of cases, followed byCandida glabrata (28%) and Candidaparapsilosis (15%). Overall, 7% of isolates were resistant tofluconazole and 1.6% were resistant to echinocandins, with no clear trendsin resistance over the 5-year surveillance period.Across all sites and surveillance years (2012\u20132016), 3,492 cases ofcandidemia were identified. The crude candidemia incidence averaged acrosssites and years during 2012\u20132016 was 8.7 per 100,000 population;important differences in incidence were found by site, age group, sex, andrace. The crude annual incidence was the highest in Maryland and lowest in Oregon . Thecrude annual incidence of candidemia was highest among adults aged\u226565 years followed by infants aged<1 year (15.8). The crude annual incidence was higher among males (9.4)than among females (8.0) and was approximately 2 times greater among blacksthan among nonblacks (13.7 versus 5.8). Ninety-six percent of cases occurredin patients who were hospitalized at the time of or during the week afterhaving a positive culture. One third of cases occurred in patients who hadundergone a surgical procedure in the 90 days before the candidemiadiagnosis, 77% occurred in patients who had received systemic antibiotics inthe 14 days before the diagnosis, and 73% occurred in patients who had had acentral venous catheter (CVC) in place within 2 days before the diagnosis.Ten percent were in patients who had used injection drugs in the past 12months. The median time from admission to candidemia diagnosis was 5 days(interquartile range [IQR]: 0\u201316 days). Among 2,662 cases that weretreated in adults aged >18 years, 34% were treated with fluconazolealone, 30% with echinocandins alone, and 34% with both. The all-cause,in-hospital case-fatality ratio was 25% for any time after admission; theall-cause in-hospital case-fatality ratio was 8% for <48 hours after apositive culture for Approximately nine out of 100,000 persons developed culture-positivecandidemia annually in four U.S. sites. The youngest and oldest persons,men, and blacks had the highest incidences of candidemia. Patients withcandidemia identified in the surveillance program had many of the typicalrisk factors for candidemia, including recent surgery, exposure tobroad-spectrum antibiotics, and presence of a CVC. However, an unexpectedlyhigh proportion of candidemia cases (10%) occurred in patients with ahistory of injection drug use (IDU), suggesting that IDU has become a commonrisk factor for candidemia. Deaths associated with candidemia remain high,with one in four cases resulting in death during hospitalization.C. albicans, which are generally associated withgreater antifungal resistance than C. albicans, and thepresence of substantial fluconazole resistance supports 2016 clinicalguidelines recommending a switch from fluconazole to echinocandins as theinitial treatment for candidemia in most patients.Active surveillance for candidemia yielded important information about thedisease incidence and death rate and persons at greatest risk. Thesurveillance was expanded to nine sites in 2017, which will improveunderstanding of the geographic variability in candidemia incidence andassociated clinical and demographic features. This surveillance will helpmonitor incidence trends, track emergence of resistance and speciesdistribution, monitor changes in underlying conditions and predisposingfactors, assess trends in antifungal treatment and outcomes, and be helpfulfor those developing prevention efforts. IDU has emerged as an importantrisk factor for candidemia, and interventions to prevent invasive fungalinfections in this population are needed. Surveillance data documenting thatapproximately two thirds of candidemia cases were caused by species otherthan Candida, is one of themost common opportunistic fungal infections worldwide system can change from case to case in the same person. However, demographicdata are at the patient level because characteristics such as sex and race donot change from case to case in the same person. A case of candidemia was defined as a blood culture positive for aCandida blood culture, surveillanceofficers from each site used the surveillance case definition to determine casestatus and completed a standardized case report form to gather demographic andclinical data from the medical record. Surveillance officers received detailedinstructions on completing the abstraction form and training in chartabstraction. In addition, surveillance officers performed periodic audits oflaboratory microbiology records to ensure completeness of reporting. Thecorresponding Candida species isolates were sent to CDC forspecies confirmation and antifungal susceptibility testing. Deidentified datawere sent to CDC.Clinical, reference, and commercial laboratories that serve the population in thesurveillance catchment areas were recruited to participate in the surveillanceprogram and report cases of candidemia to the local surveillance officer. Oncenotified of a positive https://stacks.cdc.gov/view/cdc/80195; 2010\u20132013 shortchart review form, https://stacks.cdc.gov/view/cdc/80196; 2014 case report form,https://stacks.cdc.gov/view/cdc/80193; and 2016 case reportform, https://stacks.cdc.gov/view/cdc/80194). The forms includeinformation on demographic data, including age at time of positive culture, sex,and race. Adults were defined as patients aged >18 years. Other variablescollected from medical chart review included underlying medical conditions andmedical comorbidities; dates of hospital admission and discharge; receipt ofantibiotics and antifungal medications; TPN in the 14 days before candidemiadiagnosis; presence of a CVC within 2 days before diagnosis; treatment receivedfor candidemia; and patient outcome .The chart review and case report forms used to collect data are available . Thirty-eight percent ofpatients were aged 45\u201364 years, and 37% were aged \u226565 years;infants aged <1 year represented 2% of cases . Fifty-tThe crude candidemia incidence averaged across sites and years was 8.7 per100,000 population (range: 8.3\u20139.1) during 2012\u20132016 . The cruThe crude incidence of candidemia also varied by age group, with the highestcrude incidence among adults aged \u226565 years , followedby infants aged <1 year . The lowest crude incidenceoccurred among persons aged 1\u201318 years . AdjustiThe crude incidence among males was higher than among females . AdjustiThe crude incidence among blacks was higher than among nonblacks . Adjustihttps://stacks.cdc.gov/view/cdc/80192).The univariable negative binomial regression estimate of the trend in incidenceover the 5-year surveillance period showed no statistically significant changein incidence. No statistically significant trend in incidence over the 5-yearperiod was found by site, age group, sex, or race of candidemia cases were in patients with diabetes, and 17% werein patients with solid-organ malignancy. Seventeen percent were in patients withliver disease, most commonly hepatitis C virus infection (10%). Sixteen percentwere in patients with chronic renal disease, and 12% were in patients who hadreceived hemodialysis in the 90 days before the candidemia diagnosis. Threepercent of cases were in patients who were infected with human immunodeficiencyvirus or had acquired immunodeficiency syndrome .Approximately one third (33%) of cases were in patients who had a surgicalprocedure in the 90 days before the candidemia diagnosis; abdominal surgery(19%) was the most common type of surgery. Four percent of cases were inpatients who had neutropenia in the 2 days before diagnosis. Most (77%) of caseswere in patients who had received systemic antibiotics in the 14 days beforediagnosis. Almost one fourth (24%) of cases were in patients who had receivedTPN in the 14 days before the candidemia diagnosis. Georgia had a higherproportion of cases in patients receiving TPN (31%) than other sites(17%\u201318%). Nearly three fourths (73%) of cases were in patients who had aCVC in place within 2 days before diagnosis. More than half (58%) of cases werein patients who had had a previous hospitalization in the 90 days before thediagnosis, and 96% were in patients who were hospitalized at the time of or inthe week after the diagnosis. More than half (56%) of the cases were in patientswho were in the ICU in the 14 days before or after the candidemia diagnosis.Ten percent of cases were in patients who had used injection drugs in theprevious 12 months. The proportion of cases related to injection drug use (IDU)was higher in Oregon (28%) and Tennessee (14%) than in other sites (3% inGeorgia and 11% in Maryland) .Sixty percent of the cases were health care\u2013onset infections, 32% werehealth care\u2013associated community-onset infections, and 8% werecommunity-onset infections .Oregon Nine percent of cases occurred in patients who had a previous episode ofcandidemia, and the median time from previous to current candidemia episode inthe same patient was 104 days (IQR: 56\u2013253 days) . Forty-oA total of 82% of 3,492 cases were treated with an antifungal for candidemia. Themost common antifungal received was fluconazole (56%), followed by echinocandins(51%) . Among cThe all-cause in-hospital case-fatality ratio was 25% for any time afteradmission and 8% for <48 hours after a positive culture. The all-causein-hospital case-fatality ratio varied by age group: 15% in infants (aged <1year), 10% in persons aged 1\u201318 years, 15% in adults aged 19\u201344years, 26% in adults aged 45\u201364 years, and 32% in adults aged \u226565years. The median time from positive candidemia culture to death was 6 days(IQR: 2\u201314) .C. albicans accounted for 39% of cases, and otherCandida species accounted for 61%; the most common specieswere C. glabrata (28%), C. parapsilosis (15%),and Candida tropicalis (9%). Four percent of cases involvedmultiple Candida species isolated on the date of the initialcandidemia blood culture or in the 30 days after. The lowest proportion ofC. albicans was in Maryland (35%), compared with40%\u201342% in the other three sites and C.albicans (0%\u20130.9%). None of the C.parapsilosis isolates were echinocandin resistant. Multidrugresistance was identified in 1.3%of C. glabrata isolates. Fluconazole resistance ranged from5.9% to 10.3% in Georgia, 4.0% to 10.8% in Maryland, 0% to 9.6% in Oregon, and1.6% to 8.6% in Tennessee than males, invasive bloodstream infections were less common amongfemales than among males. Although the reasons for differences in candidemiaincidence by sex are unknown, these differences have been found with other fungaldiseases such as paracoccidioidomycosis and coccidioidomycosis. Forparacoccidioidomycosis, the differences in incidence occur in postpubertal agegroups (approximately aged \u226512 years), and laboratory research has shown thatestrogen levels might have a role in acquisition of fungal diseases (Staphylococcus aureus (MRSA)infection found that racial disparity could partially be explained by socioeconomicfactors such as overcrowding and limited access and availability to health careservices and beaware of local antifungal resistance patterns when making treatment decisions.Drug-resistant Species-level identification and AFST are important aspects of candidemia management.However, availability of both types of testing, especially AFST, is limited inclinical laboratories have substantialtoxicity (In contrast with the 2009 Infectious Disease Society of America guidelines for thetreatment of invasive candidiasis, in which echinocandins were recommended only forneutropenic patients and patients with previous exposure to antifungals (C. auris were not detected in the surveillancesites during 2012\u20132016, ongoing transmission of C. auris hasbeen detected in several areas in the United States, primarily in Illinois, NewJersey, and New York (C. auris had been documented in the United States (Candida species, including Candidahaemulonii, Candida duobushaemulonii, andCandida rugosa, have been reported from surveillance in othercountries (Candida species will be critical in detectingrare and emerging drug-resistant species in the United States before they becomewidespread.Although cases of The findings in this report are subject to at least four limitations. First,underlying conditions and predisposing factors described in this report wereextracted from medical charts, which might have resulted in underestimates ofcertain conditions, such as IDU, which might not be systematically recorded onmedical charts. Second, although the surveillance was active, population based, andfrequently audited, certain culture-proven cases might have been missed, likelyunderestimating the number of infections. In addition, this surveillanceunderestimates the true proportion of invasive candidiasis because it only includescases positive by blood culture, which has suboptimal sensitivity, particularly forintraabdominal candidiasis, or infections in which blood cultures were not obtained.Third, surveillance data were available from 22 counties in four states representing2.5% of the U.S. population and therefore are not nationally representative.Finally, only five time points were assessed, which limits the ability to understandlong-term trends. Nevertheless, data presented in this report describe surveillanceinformation on geographically and demographically diverse populations and are thelargest data source of population-based candidemia incidence data in the UnitedStates.Candidemia remains a serious cause of illness and death in the United States, andsurveillance data are necessary to focus prevention efforts. Active surveillance forcandidemia should continue to monitor incidence trends by age and race, trackemergence of resistance and species distribution, monitor changes in underlyingconditions and predisposing factors, and assess trends in antifungal treatment andoutcomes. Surveillance was expanded to nine sites in 2017, and ongoing surveillanceefforts are expected to improve the development of treatment and preventionefforts."} +{"text": "An increased number of survivors have emerged from the 2014 West African Ebola Virus Disease (EVD) epidemic. Post-Ebola Syndrome (PES) is a group of physical and psychological symptoms affecting EVD survivors. This study aimed to estimate the prevalence of PES among EVD survivors in Montserrado County, Liberia. A cross-sectional study design was conducted to determine the prevalence of PES, types, onset, and duration among survivors. Survivors in Montserrado County were recruited using multistage sampling methods. Quantitative data was collected using semistructured questionnaire. Variables were collected on EVD survivors demographics, pre- and post-Ebola health history.Prevalence of Post-Ebola Syndrome was estimated to be 90% (242/268). PES was experienced by 67% (162/242) females. PES occurred mainly in the adult population between ages 25-34, 35% (84/242). The commonest symptoms were reported from the following systems of the human body: neurological system and musculoskeletal system . The onset of PES occurred between the first 1-12 weeks after being discharged from a treatment unit. Prevalence of PES is high. Clinical care for survivors should be strengthened. PES is In Sierra Leone when the epidemic was ongoing, a study was conducted to assess survivors. More than 50% of survivors experienced symptoms such as visual problem, joint and chest pains, headaches, extreme fatigue, and depression . These sSurvivors of the 2014 West African EVD epidemic are predisposed to many health and non-health-related problems. Although the phenomenon of PES has been identified following previous EVD epidemics, due to the high case fatality rate of previous epidemics that resulted in fewer survivors, few researches were conducted. The health problems survivors experienced during recovery post-Ebola is still not fully understood. This study was conducted to document the prevalence of PES among EVD survivors in Montserrado County, Liberia.A cross-sectional study was conducted from January to April, 2016. Data was collected on the types of PES, its onset, and duration.The study was done in Montserrado County, one of the fifteen counties in Libera. It has seven health districts, namely, Careysburg, Bushrod Island, Somalia Drive, St. Paul, Central Monrovia, Todee, and Common Wealth Districts with a population of 1,287,184 inhabitants.The study population was EVD survivors recorded in Montserrado County from the beginning of the epidemic, May 2014-March 2015. Survivors in Montserrado County were 902; this accounted for 58% of survivors in Liberia. Survivors 18 years and above were 712.The sample size (n) for the study was 300 survivors. This was calculated with stat calculator in Epi Info from a population of 712 survivors line-listed by Ministry of Health (MOH), at a 50% prevalence of PES , a signiEVD survivors \u226518 years of age.EVD survivor should be a resident of one of the seven health districts in Montserrado County.EVD survivors without a copy or photocopy of original discharge certificate.EVD survivors without a membership card of the Survivors network, Liberia.An EVD survivor that refuses consent from being a part of the study.Survivors in Montserrado County were stratified by the seven health districts based on their location, after which, selection of survivors was done proportionately to the size of each health district. We further used a simple random number table to generate the list of participants in each health district. For participants selected, they were traced using their telephone number and interviews were conducted. Other details were previously published , 9.Prior to the commencement of the study, five research assistants were hired and trained. Also, pretesting of data collection tool was carried out in both a rural and urban communities. The study protocol and instruments were approved by the University of Liberia Pacific Institute of Research and Evaluation International Review Board Monrovia, Liberia (00004982). Meetings were conducted with Ebola Survivor Network to explain the objectives and method of the study before participation of survivors. Also, a written informed consent by each participant was signed to ensure willingness, privacy, and confidentiality of information. Illiterate/incapacitated survivors were asked to thumb print using an ink pad.Prior to the selection of participants to partake in the study, the principal researcher met with the national coordinator, president, sector heads, and sector supervisors of Ebola Survivors Network in Liberia. This meeting was organized to explain the study, its importance, and the process through which participants were to be selected to take part in the study. After which, the recruitment process of participants for the study was conducted from November-December 2015. Data collection began in January 2016 and continued until April 2016. During which time participants of the study were visited at their homes, clinics, and market places in communities around Montserrado County. Data were collected through interviews with Ebola survivors using a semistructured questionnaire to determine the prevalence of PES in Montserrado County. The questionnaire was used to record survivors demographic information, individual Ebola history, and pre- and post-Ebola medical historytory.Data was entered, cleaned, coded, and analyzed with SPSS version 23.The characteristics of study participants were explained through descriptive statistics; continuous variables were presented as median and range. Categorical variables were presented in composite tables showing frequencies and percentage distributions. Graph and charts were also used to present part of the data. Post-Ebola Syndrome. Health-related problems that occurred in EVD survivors after laboratory result has proven negative. Short-Term PES. Health-related symptoms that manifest between 1 and 10 months after discharge from an ETU. Survivors. A patient subsequently recovers, after being confirmed positive with a result of RT-PCR testing for Ebola virus on anybody fluid .Of all respondents, 9.7% (26/268) had never experienced PES. The remaining 90.3% (242/268) complained of at least having experienced a health problem.The commonest symptoms observed among respondents with PES were joint pains 64% (154/242), headache 52% (127/242), eyes problem 47% (114/242), muscles pain 34% (80/242), and unusual tiredness 28% (68/242). The types of PES reported among respondents are shown in \u201cOthers\u201d represent symptoms other than the 14 listed above which includes absentmindedness, hair loss, generalized body pain, back aches, swollen feet, diabetes, hemorrhoids, ear pain, hearing loss, erectile dysfunction, heart palpitation, frequent fever, numbness of feet, liver, and heart problems. Some survivors interviewed did not have PES; hence, symptoms did not add up to 268.Within the first 3 months of recovery from EVD, the majority of survivors started experiencing musculoskeletal symptoms such as joint pain 77% (118/154), muscles pain 68.2% (60/88), chest pain 67% (38/57), and abdominal pain 62%, (38/61). In the second quarter 4-6 months symptoms with onset were chest pain 21% (12/57) of survivors, abdominal pain 19.7% (12/61), joints pain 16% (25/154), and muscles pain 17% (15/88). Symptoms with onset between 7 and 9 months were abdominal pain accounting for 13% (8/61), chest pain 8.8% (5/57), muscles pain 8% (7/88), and joints pain 0.6% (1/154). As reported in the last quarter with onset between 10 and 12 months, muscles pain accounting for 6.8% (6/88), joints pain 6.5% (10/154), chest pain 8.8% (2/57), and abdominal pain 4.9% (3/61) were reported. Testes pain was reported by 53.8% (7/13) of survivors to have started during the first 3 months after discharge; 30.7% of male survivors reported testis pain to have started by 4-6 months while during 7-9 months, testis pain was accounted for by 15.4% (2/13) of male survivors. Testis pain was not reported with onset between 10 and 12 months. Among the females survivors, 91% (29/32) had menstrual problems with onset beginning the first 3 months after discharge, while 9.4% (3/32) stated menstrual problem to have started by 10-12 months. Menstrual problems were not reported by female survivors to have started between 4 and 9 months. The menstrual problems complained of included menstrual irregularities and cessation.Itching of the skin were reported by 86% (31/36) of survivors to have started by the first 3 months, 8.3% (3/36) stated their skin started itching by the 4-6 months after discharged, while 5.5% (2/36) said they started experiencing symptoms between 7 and 9 months. Peeling of the skin was reported by 89% (41/46) of survivors between the first 3 months, while 8.7% (4/46) said they started experiencing skin itching by 6 months and 2% (1/46) with symptom onset by 9 months.Every nine out of ten survivors complained of having PES after being discharged from the ETU in Montserrado County, Liberia, and this conforms with Qureshi 2015 study which reported close to 100% symptoms in Guinea [Females account for the majority of our study participants. In Liberia, the higher number of females participants could be attributed to females constituting more than half of survivors in the country. Other studies have also reported more female survivors , 12. TheOur findings conform to other studies, which showed that the majority of survivors had reported more than one symptom , 12. ThePES was mostly experienced among the age categories of adults between ages 25-34 and 35-44 years. These are mostly people who work to earn their living whether through skilled or unskilled jobs in Liberia. Consistent with our study was a study in Sierra Leone which stated that many adult survivors reported health problems and their justification was that adults mostly perform work that demanded energy .Though pain exists without any activity in few survivors, pain intensifies when trying to carry out normal day to day activities like selling, walking distances, and doing house chores. The preliminary findings of a five-year clinical trial conducted in Liberia also recorded that joint pain was reported among approximately fifty percent of survivors visiting the Medicine San Frontier Clinic. Joints pain was described as pain in the elbows, wrist, fingers, hips, ankles, neck, back, and knee .Ocular problems occurred in less than 50% of EVD survivors. The ocular problems were blurred vision, redness, pain, and itching of eyes. In Sierra Leone, two weeks after being discharged, 14% of survivors reported ocular problems which ranged from eye pain, eye discharge, red eyes, and blurred vision . In the A range of neurological disorders were reported including headache which accounted for 50%. Headache was one of the most commonly reported symptoms . These wOut of the total EVD survivors that participated in this study, 26% suffered unusual tiredness. Thirty-two percent of EVD survivors enrolled in the clinical research had also experienced unusual tiredness, while almost 80% of EVD survivors in the United States experienced unusual tiredness .Respondents complained of depression in this study and this was consistent with other studies that reported 15% of EVD survivors had suffered depression. Also, a study in the United States shows that about half of EVD survivors experienced depression . Sleep dEar problem was reported in a small number of less than two percent of EVD survivors in this study. Ear problems as described by this study include hearing loss and ear pain. Consistent with these findings was a literature in Sierra Leone which stated that a little more than five percent of EVD survivors experienced ear problems . AnotherSkin diseases were reported by 15% of survivors and desquamation of the palm and feet has been reported by 18% of EVD survivors. The findings in this study conform with reports by the Medicine San Frontier Clinic in Liberia which stated that EVD survivors reported experiencing desquamation and dryness of skin which commonly affected the palm and soles of the feet . Also stLess than 10% EVD survivors in this study reported reproductive system complications that include erectile dysfunction and testes pain. Female survivors also experienced menstrual problems including menstrual cessation and irregularities which accounted for 11% of female survivors. Consistent with these findings is Nabena et al. study from Sierra Leone which reported that erectile dysfunction and menstrual problems accounted for less than 5% each in the population of EVD survivors studied [Finding from this study revealed that the onset of the symptoms was between the first 1 and 12 weeks after discharge from an ETU. Our finding was consistent with other studies which stated that symptoms onset began immediately after discharge or the first few weeks after , 12, 15.In this study, testicular pain and itching of the skin were less common among EVD survivors by the ninth month with less than three and ten cases recorded, respectively. Other symptoms reported by fewer EVD survivors by >10 month were menstrual problem, chest pain, abdominal pain, and depression with 17, 12, 19, and 14 percent, respectively. While symptoms that were most likely to have persisted above >10 months were eyes problems (53%), joints pain (40%), muscles pain (28%), unusual tiredness (38%), and headache (80%). This is consistent with literature published in the Democratic Republic of Congo which stated that joint pains, muscles pain, abdominal pain, and fatigue were the commonest reported during a six-month follow-up visit, while muscles and joints pain remained high among EVD survivors up to the twenty-one months after EVD .A cohort study in Uganda revealed long-term symptoms that might continue for greater than two years. Commonest symptoms reported by this cohort were blurred vision, hearing loss, difficulty in swallowing, joint pains, and sleep disorders . CommoneWe were not able to compare respondents with PES to those without PES. This is a limitation of this study given that some respondents found it difficult to discriminate true PES occurrences from other complaints not related to PES in the study population.This study indicated that the prevalence of Post-Ebola Syndrome among EVD survivors in Montserrado County, Liberia, is high. The onset of symptoms was reported between the first 1 and 12 weeks after discharged from the ETU. Commonest symptoms reported were chest pain, muscle pain, eyes problem, abdominal pain, joint pain, unusual tiredness, sleep disorder, and headache. Symptoms among survivors were often intermittent and peaked by the sixth month. By the ninth month, decline was observed in the number of symptoms reported. Notwithstanding, a few number of symptoms were shown to have persisted among survivors above ten months but with reduced severity, such symptoms include eyes problem, joints pain, unusual tiredness, and headache. Clinical care for survivors in Montserrado County remains the biggest gap; very few of survivors have received appropriate treatment for complaints suffered.Based on the findings of this study, the following recommendations were made.The Ministry of Health, Liberia, negotiated with partners to improve and maintain the care being offered to survivors by increasing the number of health care centers for survivors, hiring of specialist for the commonest reported conditions, and the building of laboratory capability for advanced testing and screening. The implementation of the WHO 2016 clinical guide by care givers at the ETU to schedule preliminary follow-up visits at clinics for survivors upon leaving the ETU before the country was declared free of EVD was ensured. This enables adequate monitoring of survivors recovery status and immediate detection of any deviation in health post-EVD to avoid long-term disabilities."} +{"text": "This study examines the degree to which hospice and palliative care staff observe or perceive inadequate, disrespectful, or abusive care to LGBT patients and family members. A cross-sectional study using an online survey completed by 865 providers, including social workers, physicians, nurses, and chaplains. Among respondents, 55% reported that LGB patients were more likely to experience discrimination at their institution than non-LGB patients; 24% observed discriminatory care; 65% reported that transgender patients were more likely than non-transgender patients to experience discrimination; 20% observed discrimination to transgender patients; 14% observed the spouse/partner of LGBT patients having their treatment decisions disregarded or minimized; and 13% observed the spouse/partner being treated disrespectfully. Findings reported also include: institutional non-discrimination policy, staff training, intake procedures, and comfort in assessing LGBT status. Implications for future research, policy, and practice will be presented."} +{"text": "Administrative healthcare databases are useful and inexpensive tools that can provide a comprehensive assessment of the burden of diseases in terms of major outcomes, such as mortality, hospital readmissions, and use of healthcare resources. However, a crucial issue is the reliability of information gathered. The aim of this study was to validate ICD-9 codes for several major cardiovascular conditions, i.e., acute myocardial infarction (AMI), atrial fibrillation/flutter (AF), and heart failure (HF), in order to use them for epidemiological, outcome, and health services research.Data from the centralised administrative database of the Umbria Region were considered. Patients with a first hospital discharge for AMI, AF/flutter, and HF, between 2012 and 2014, were identified using ICD-9-CM codes in primary position. A sample of cases and non-cases was randomly selected, and the corresponding medical charts reviewed by specifically trained investigators. For each disease, case ascertainment was based on all clinical, laboratory, and instrumental examinations available in medical charts. Sensitivity, specificity, and predictive values with 95% confidence intervals (CIs), were calculated.We reviewed 458 medical charts, 128 for AMI, 127 for AF/flutter, 127 for HF, and 76 of non-cases for each condition. Diagnostic accuracy measures of the original discharge diagnosis were as follows. AMI: sensitivity 98% , specificity 91% , positive predictive value (PPV) 95% , negative predictive value (NPV) 97% . AF/flutter: sensitivity 95% , specificity 95% , PPV 97% , NPV 92% . HF: sensitivity 96% , specificity 90% , PPV 94% , NPV 93% .The case ascertainment for AMI, AF and flutter, and HF, showed a high level of accuracy (\u2265 90%). The healthcare administrative database of the Umbria Region can be confidently used for epidemiological, outcome, and health services research. Administrative databases are considerable data repositories that are increasingly being used within healthcare systems, 2. ThesIn addition to maintaining a rigorous anonymity of patient\u2019s demographic, the most relevant data that makes these healthcare databases interesting for research purposes is the diagnosis provided to the patient at hospital discharge. This diagnosis is coded according to the International Classification of Diseases (ICD) which is a standardized diagnostic tool planned to map health conditions. When individual patient data are linked with other data (prescription and laboratory data) it is possible to explore a wide range of clinical issues, research questions as well as quality performance evaluations. To reach this target, administrative databases need to be validated, which means the diagnoses that correspond to the ICD-9 code need to be ascertained according to a defined disease criteria by consulting a reference standard which is usually the medical chart, 3, 4.Acute myocardial infarction (AMI), heart failure (HF), and atrial fibrillation (AF) are the most common cardiovascular diseases\u20137 in devAccording to our published protocol, the objDetails regarding the regional healthcare administrative database of Umbria have been reported elsewhere. BrieflyAny permanent resident in the Umbria Region aged 18 years or older that has been discharged from a hospital with the diagnosis of AMI, AF or atrial flutter, and HF was eligible for inclusion.Residents that have been hospitalised outside the regional territory of Umbria were excluded from analysis.From the entire discharge abstract database of Umbria we identified three cohorts of \u201ccases\u201d, that is patients having the ICD-9 codes located in primary position of acute myocardial infarction (ICD-9 codes 410.x), atrial fibrillation (code 427.31) and flutter (code 427.32), and heart failure (codes 428.x), between 2012 and 2014. According to Italian legislation, the primary diagnosis constitutes the main cause of the need for treatment and/or diagnostic tests, and is mainly responsible for the use of resources. We excluded estimated prevalent cases, i.e. patients discharged from hospitals with the same diagnosis in the five years before. Repeated hospital admissions were also excluded. From each cohort, we extracted a random sample of 130 cases . At the same time, we identified a cohort of \u201cnon-cases\u201d, that is patients who had been discharged in the same period of time, also with a diagnosis of cardiovascular disease (ICD-9 codes 390\u2013459), but other than AMI, AF and flutter, and HF. From this cohort of non-cases, we extracted a random sample of 80 patients. This sample of non-cases was used as control for each of the three conditions.Medical charts of the samples of cases and non-cases were selected by simple randomization method using SAS 9.4 procedures and were obtained from hospitals for case ascertainment. The following data were abstracted from the medical charts: unique patient identification code, age and sex, hospital admission and discharge dates, diagnostic procedures as well as interventions that contributed to the diagnosis of the disease. In addition, clinical, laboratory and instrumental procedures data, including the date of performance, were abstracted.Two physicians acting as chart reviewers received specific training on data abstraction. An initial chart review was then performed, with the same medical charts (n = 20) being independently examined by each reviewer. The inter-reviewer agreement was very high (\u03ba >0.9). To further ensure consistency among the reviewers, findings of this initial assessment were discussed in review; data extraction was then completed independently by each reviewer using a standardised data collection form. Reviewers were not blinded to the diagnosis due to limitation of resources. However, the validation process was not biased as the reviewers independently abstracted the data.Uncertainties were discussed and resolved through third party involvement (GA).Case ascertainment of disease within medical charts was based on symptoms, laboratory, and diagnostic tests, as described below.Criteria used for validation of the considered ICD-9-CM codes were those derived from international guidelines or systematic reviews published on these topics, as previously defined . To valiFor validation of the ICD-9 code 427.31 for AF and 427.32 for atrial flutter, we required at least one ECG tracing documenting, the presence of AF or atrial flutter, according to the ESC Guidelines .To validate the ICD-9 codes 428.x relating to HF, we considered the European Society of Cardiology Heart Failure Guidelines . These gAs reported elsewhere, for eacSensitivity and specificity, with their corresponding 95% CI, were calculated for each ICD-9-CM code by producing 2\u00d72 tables. Positive and negative predicting values were also calculated, along with their 95% CI.To ensure quality and thoroughness of reporting, this paper followed the criteria of Standards for Reporting Diagnostic Accuracy (STARD) 2015 S1 Tabl.Ethics approval has been obtained from the Regional Ethics Committee of Umbria (CEAS), registry No 2695/15 of 16/12/2015.Tables 3 show the characteristics of the patients for each disease. A minimal anonymized dataset is available as supporting information file (41%), followed by code 410.1 (24%), and by code 410.4 (17%). Two thirds of patients were males. Most patients (48%) were in the age class 60\u201379 years. Instrumental examinations performed for the diagnosis included electrocardiography, echocardiography, and coronary angiography. Troponin levels were measured in almost all patients. Sixty-two percent of patients underwent percutaneous transluminal coronary angioplasty (PTCA).We identified a cohort of 4,682 patients with AMI, from which we extracted a sample of 130 cases, 128 clinical charts were analysed . Table 2 shows the diagnostic accuracy measures for AMI: sensitivity 98% (95% CI: 94% - 100%), specificity 91% (95% CI: 83% - 97%), positive predictive value (PPV) 95% (95% CI: 89% - 98%), and negative predictive value (NPV) 97% (95% CI: 91% - 100%).Table 5. False positives were patients with troponin levels within the normal range, or not reported in the medical chart. The false negatives were non-cases actually found to have increased troponin concentration and presence of symptoms or instrumental confirmation of myocardial infarction.Misclassification of cases and non-cases is described in We identified a cohort of 2,792 patients with AF/flutter, from which we extracted a sample of 130 cases, 127 clinical charts were analysed .Table 3 shows the basic characteristics of the patients with AF/flutter. In this sample, 84% percent of patients had atrial fibrillation, while 16% had atrial flutter according to ICD codes in primary position. Fifty-three percent of patients were males. Most patients (52%) were in the age class 60\u201379 years. During hospital stay, almost all patients underwent electrocardiography, and most of them (72%) echocardiography. Twenty-nine percent of the patients underwent electrical cardioversion (Table 2)..The diagnostic accuracy measures for AF/flutter were: sensitivity 95% (95% CI: 90% - 98%), specificity 95% (95% CI: 87% - 99%), PPV 97% (95% CI: 92% - 99%), and NPV 92% (95% CI: 84% - 97%) Table 5).All patients without an ECG in the medical chart, or with ECG negative for AF/flutter, were considered false positives. All false positives had a clinical history of AF or flutter, while, between the non-cases, false negatives were patients having other cardiovascular diseases even with an ECG confirmation of AF or flutter in the medical chart .Table 4 shows the basic characteristics of patients with HF. The most common ICD-9 subgroup was code 428.0 (64%), followed by code 428.1 (left heart failure) (24%). Fifty-three percent of patients were females. Most patients (61%) were 80 years or older. The most frequent diagnostic instrumental examinations were electrocardiography, echocardiography, and chest radiography. Brain natriuretic peptide (BNP) levels were measured in 46% of patients (Table 3).Table 2).The diagnostic accuracy measures for HF were: sensitivity 96% (95% CI: 91% - 99%), specificity 90% (95% CI: 81% - 96%), PPV 94% (95% CI: 88% - 97%), and NPV 93% (95% CI: 85% - 98%) (Table 5).Patients with signs or symptoms but without instrumental or laboratory confirmation of HF in their medical chart were considered false positives. Most false positives (5/8) were patients \u2265 85 having polypathologies that during the hospital admission underwent only treatment procedures, no instrumental examinations were performed. Among the non-cases, false negatives were patients that, in addition to other cardiovascular diseases, also had signs, symptoms and instrumental examinations confirming heart failure inhibitor, angiotensin-II receptor antagonist, loop diuretic, or digoxin, and laboratory data such as BNP. Despite it is not specific to HF, Alqaisi et al suggest A systematic review included 16 studies that validated algorithms to identify AF from administrative databases . MethodsThis study evaluated the validity of the ICD-9-CM codes for cardiovascular diseases using the administrative database of the Umbria Region. For this purpose, we reviewed original source documentation available in medical charts to adjudicate cases of cardiovascular disease.Our study was based on a pre-published protocol, and no deviation from protocol occurred during study development.We followed recommended guidelines based on the STARD 2015 for the One limitation of our study is that we did not evaluate the accuracy of ICD-9 codes in secondary position. Another limitation of the present study concerns generalizability. In general, results that originate from a healthcare database are immediately applicable only to the setting in which such database has been validated, due to obvious differences that may exist with respect to demographics, ethnicity, disease prevalence, and standards of care, among different populations. In Italy, healthcare provision and management of healthcare databases are regulated at a national level, and therefore we speculate that results from our database, nonetheless, can be generalized to other regions in this country, also because we do not expect major differences in demographics and disease prevalence. However, replication of our validation study in other national settings may allow to explore and refine possible differences in accuracy results, and explore potential factors that might explain heterogeneity.In administrative databases, the diagnosis of a given disease is associated with a specific ICD code. Despite some limitations, the ICD code is an important tool designed to map health conditions to corresponding general disease categories, along with specific variations. These codes have the advantage of being widely available and require a much lower effort and cost than consulting medical charts . RecentlS1 Table(DOCX)Click here for additional data file.S1 Dataset(PDF)Click here for additional data file."} +{"text": "Objective: To establish if sleep disorders andsexual function are associated with deterioration of the quality of life (QoL)in hysterectomized and sexually active women. Methods: Across-sectional study was carried out with inhabitants from two cities of theColombian Caribbean. The pollsters invited women aged between 40-59 years toparticipate; in their communities they applied surveys with demographiccharacteristics: Female Sexual Function Index, Atenas Insomnia Scale andMenopause Rating Scale. Sexually active women were selected; then theassociation was established with logistic regression. Results: 522women were studied with an average age of 50 years: 30% oophorectomized, 59.8%Hispanic, 40.2% afro-descendants and 22.2% hormonal therapy users. 80% of themhad somato/vegetative, psychological or urogenital deterioration; 29.1% withsevere deterioration of QoL and 47.5% with insomnia. Out of 390 (74.7%) withsexual activity, 59.7% suffered from sexual dysfunction. Insomnia: OR:3.05[95%CI:1.86-4.99], sexual dysfunction OR:3.52 [95%CI:2.01-6.17], dissatisfactionabout sexuality OR:4.77 [95%CI:2.08-10.93], low or non-existent sexual desireOR:2.94 [95%CI:1.65-5.25], daytime drowsiness OR:3.15 [95%CI:1.59-6.24] anddecrease in daytime well-being OR:3.18 [95%CI:1.79-5.64]. These were factorsassociated with severe worsening of QoL, while the presence of genitallubrication was protective, OR: 0.44 [95%CI:0.21-0.93],p=0.0332. Conclusion: It was observed thatinsomnia and sexual dysfunction behaved as factors associated with three timesmore severe deterioration of the QoL in climacteric and sexually active womenpreviously hysterectomized. Hysterectomy is a common gynecologic surgery carried out to remove thepathologic uterus. QoL includes subjective and objective indicators about physicaland psychological well-being, independence, social relationships, environment andspirituality1-3.Determining the quality of life (QoL) is a priority and it has become an importantvariable to consider regarding multidisciplinary interest and the approach fromdifferent perspectives3. The evaluationshould be multidimensional and it has to take into account specific and globalcomponents. Several QoL scales have been proposed, which are suitable forms ofexploration1,3,4.The World Health Organization defines the QoL as the perception that the person hasabout his/her own life within the value system and the cultural context in whichthey find themselves with respect to their purposes, expectations andconcerns5-9. Most of the information has been obtained from Caucasian womenand the results cannot be systematically extrapolated to other communities orethnicities. There are no known studies in climacterics previously hysterectomizedColombian women, where the association among sleep, sexuality and QoL is evaluated.The objective was to establish if sleep components and sexual function areassociated with worsening of the quality of life (QoL) in hysterectomized andsexually active women.Menopausal symptoms and factors that deteriorate the QoL must be valued duringclimactericCross-sectional study carried out with sociodemographic questions and three validatedscales. This investigation is part of CAVIMEC project . The project was developed in two phases: a. Theproperly completed forms to estimate severe deterioration of QoL were involved; b.Sexually active women were chosen to establish the prevalence of sexual dysfunctionas well as the association between sexual function and sleep in the QoL. For theevaluation of sexual function and sleep disorders two scales were used: FemaleSexual Function Index for the first one and Atenas Insomnia for the second, whichare described later.Afro-descendants and Hispanic women aged between 40-59 years old, residing inCartagena or Barranquilla in the Colombian Caribbean. The pollsters, door bydoor, identified and invited to participate women with more than 12 months ofhysterectomy. Surgically intervened women for malignant or obstetric pathology,vaginal or by laparoscopy and those who did not understand the study wereexcluded. Only the completed forms were considered.4.[A] Menopause Rating Scale (MRS): specific to menopausal symptoms and QoL; it iscomposed by 11 questions that are grouped in three domains: somato/vegetativepsychological and urogenital . Eachquestion is answered from 0-4 points. The total determines the score of thedomain and the total score. Also, the scale identifies four levels of severity:none/little, mild, moderate and severe. Somato/vegetative score greater than 8,psychological greater than 6, urogenital higher than 3 and QoL greater than 16define severe compromise10.[B] Atenas Insomia Scale (AIS): psychometric instrument about sleep disturbancecomposed by 8 questions which are answered from 0-3, the sum offers the totalscore; if is higher than 5, it is a sign of insomnia11.[C] Female Sexual Function Index (FSFI-6): is a one-dimensional abbreviatedinstrument of a previous proposal. It assesses the sexual function in the lastfour weeks and identify the sexually active women. Six questions explore desire,arousal, lubrication, orgasm, satisfaction and pain. Each question is markedfrom 0-5 points. A total score equal to or less than 19 defines sexualdysfunctionhttp://www.dane.gov.co/index.php/estadisticas-por-tema/demografia-y-poblacion/censo-general-2005-1/censo-general-2005].The study had 384 participants, 50% of heterogeneity level, 5% error and 96% ofconfidence level. It has been observed in the CAVIMEC study that 30% of theinvited women refused to participate in the study due to social, cultural oreconomic reasons (unpublished data). For the aforementioned condition, 114 womenwere included and 147 (30%) were added to compensate the incomplete surveys.Therefore, 645 women were involved.The last Colombian census was carried out in 2005 and 41.468.384 peopleparticipated. The estimated impact in 2006 was 48.747.708 inhabitants,24.678.673 women, 5.660.856 between 40-59 years old, 122.067 residents inCartagena and 153.008 in Barranquilla; .The participants were able to stop filling the form if they considered itpertinent.The participation was anonymous and voluntary with signed informed consent. Thisproject was endorsed by the Ethics Committee of Universidad de Cartagena,Colombia, according to the rules for research in the health field:Resoluci\u00f3n 8430-1993, Ministerio de Salud, Rep\u00fablica de Colombia[645 women were invited, out of which 22 (3.4%) did not accept to participate. 101(16.2%) incomplete forms were discarded. In the first phase, 522 women wereincluded, 35.9% above the sample size and the distribution of data wasnonparametric. 40.2% was afro-descendants and 59.8% was Hispanic. 68.2% had neversmoked with an average age of 50. The 30.0% had bilateral oophorectomy and the 65.3%were hysterectomized during postmenopause. One out of five used hormonal therapy.p<0.0001.The 19.1% showed severe/very severe hot flashes. Eight out of ten experimented insome grade somato/vegetative, psychological, urogenital or QoL deterioration. Halfhad severe urogenital deterioration, while two out of ten experienced severepsychological worsening. The domain with minor severe compromise was thesomato/vegetative . Severep=0.2.p<0.0001.55.1% of the women had low/no sexual desire, 29.3% moderate and 15.5% high/very high.390 (74.7%) reported having sexual activity and make up the sexually active group.Among them, two out of ten considered high/very high their level of arousal. 38.4%never, almost never or only sometimes presented genital lubrication. Less than 12.0%reported having orgasm almost always. The 21.2% declared themselves satisfied withtheir sex life, while three out of ten were considered unsatisfied. The 23.3% hadcoital pain sometimes, 14.8% most of the time and 4.8% almost always . Sexual p<0.0001 ,social, educational and sanitary aspects14,15.For some communities, the uterus symbolizes femininity and sexual value, so thehysterectomized woman loses hierarchy, is vulnerable to her partner, and becomessusceptible to social signaling for the detriment of QoL15 founda similar clinical profile in other group of hysterectomized Colombian womenevaluated with MRS: 18.7% presented severe/very severe hot flashes and 25.7%severe/very severe sexual problems. These figures are high and show the need forhealth interventions.It was observed that four out of five middle-aged women had, in some grade,deterioration of those domains and the QoL. Half of them had severe urogenitaldeterioration and three out of ten had severe deterioration of QoL.Saavedra-Orozco et al.16. One third of the participants had bilateraloophorectomy in this study. Deciding to remove the ovaries with the uterus mustbe a decision supported by clinical criteria, since the removal of the gonadscauses immediate loss of estradiol, testosterone, and androstenedione13,16. Finch et al.17 found greater vasomotor,psychological, physical and sexual deterioration after bilateral oophorectomycompared with preoperative evaluation, which showed that surgical menopauseaffects negatively the health and QoL due to hypoestrogenism andhypoandrogenism.In the United States, 600,000 hysterectomies are performed annually and half ofthem include bilateral oophorectomy2,5. The Women\u00b4s Health Initiative18 informed that hysterectomy with oophorectomyis an independent factor for myocardial infarction or death by coronary heartdisease.As mentioned earlier, hormonal cessation is associated with an increase of 50% inthe risk of osteoporotic fracture, double increase in mortality after hipfracture caused by trauma and double risk of Parkinson disease and cognitivedeterioration17.Oophorectomized women had worse sexual function than those not oophorectomized,both in sexual desire, frequency and orgasmic response16.The hysterectomy with oophorectomy can trigger sudden onset of hot flashes, moodchanges and vaginal atrophy, which are related to damage of the QoL and sexualdeterioration8,19,20 have indicated that the greatest sexual deteriorationin women undergoing surgical menopause is due to the reduction of estradiol andtestosterone. The Women\u00b4s International Study of Health and Sexuality21 reported that women agedbetween 20-49 years and with surgically induced menopause had higher rates ofhypoactive sexual desire disorders compared with those who had intact gonads:26% versus 14% respectively, p<0.0001, which coincides withthe study findings where dysfunction, low desire and dissatisfaction were riskfactors for deterioration of QoL, p<0.0001.Several authors20. The decrease of estrogen isassociated with genitourinary atrophy, lactobacilli reduction, basic pH, changesin flora and vaginal dryness19,22. Women will experiment pain during sexual activity, loseinterest and avoid sexual relationships. All of the previous have negativeimpact on their QoL23. Half ofwomen with genitourinary atrophy inform that the symptoms interfere with thesexual enjoyment; 12% of the women without a couple prefer to be alone due tothese symptoms6,24.The appropriate vaginal health is important for sexuality7, 75% of women informed thatvaginal discomfort negatively affected their sexual life. Vaginal drynessinduces worse emotional well-being and social functioning5. The presence of adequatelubrication was a protective factor for deterioration of QoL in the Colombianstudied women, p=0.03.In the Vaginal Health: Insights, Views & Attitudes study8. Generally,few women reveal their sexual concerns, hence the importance of medicalthoroughness. If sexual dysfunction is suspected, the doctor must deepen intosocial and medical history with questions focused on sexuality. Discovering theetiology and identifying modifiable factors can lead to improvements in thesexuality and QoL20. Sexualdysfunction and QoL are multidimensional concepts, interrelated in both thereproductive and climacteric stages25.Many hysterectomized women can be sexually active, if they have a stable couple.Although most of them consider that sex is an important part of life, as wasobserved in the study, dissatisfaction and sexual dysfunction are highlyprevalent2.The perception, participation and expectations of the sexual partner, before orafter hysterectomy, are poorly studied. Solidarity and empathy between thecouple can reduce false expectations or preventions regarding surgery. Men tendto worry about hysterectomy impact, especially with regard to sexuality. Both,man and woman, should receive complete and precise information, always takinginto account cultural customs and sexual behaviors26.Are frequent alterations in postmenopausal women. They can be primary orsecondary to hot flashes, disorders of the state of sleep, medical conditions,psychosocial factors or intrinsic sleep disorders that, if remain untreated, cancause deterioration of the QoL. Insomnia, well-being diminution and daytimedrowsiness were factors associated with poor QoL among the Colombians womenanalyzed in this study. It has been showed that ovarian hormones have favorableimpact in the sleep27. Estrogen hasa benefit impact on sleep architecture; also, it is involved in the metabolismof norepinephrine, serotonin and acetylcholine: neurotransmitters that controlsleep, increase the total time of sleep and diminish the sleep latency and thenumber of awakenings28. Memoryloss, a recurrent complain among postmenopausal women, can be associated withpoor sleep architecture29.Progesterone stimulates benzodiazepine receptors with sedative and anxiolyticeffect30. It is difficult to identifythe beneficial effect of estrogen compared to progesterone. Both hormones seemto have independent therapeutic effects on sleep25,31. Testosterone and sleep have not beenextensively studied; apparently, they do not alter normal sleep32. However, the etiology ofsleep disorders is multifactorial; it must be evaluated and treated because itgoes deeper than menopause. The etiology may arise as part of aging and it isnot necessarily related to the decrease of estrogen levels.Having said that, the average user of hormonal therapy had fewer night awakeningsthan non-user in a study with 3000 postmenopausal womenThis research has typical limitations of cross-sectional studies. There was notevaluation of sexual dysfunction, nor daytime insomnia or sleepiness, or of QoLbefore the surgery. It is necessary to carried out mores studies with otherdesigns that allow a greater approach to causal relationships among sexualdysfunction, sleep disorders and QoL in hysterectomized women. Although onlywomen operated for benign pathology were included, the diagnosis that motivatedthe surgery, complications or subsequent evolution was not specified.The time from the intervention to the subsequent evolution was not establish inorder to determine if QoL and the identified factors are modified with the time.In spite of the results cannot be overtly extrapolated, they are the firstapproaches to the study of QoL, sleep disorders and the sexuality ofhysterectomized climacteric women in Latin America and the Colombian Caribbean.On the other hand, it has as a strength that it was carried out in the communitywith tools that measure the perception of women. The tools are widely validatedand had good statistical reliability in the population involved.Sleep and sexuality disorders must be evaluated and treated in hysterectomizedwomen. It is necessary to take into account biological, ethnic, cultural,environmental and familiar aspects.It was observed that insomnia and sexual dysfunction behaved as factors associatedwith three times more severe deterioration of the QoL in climacteric and sexuallyactive women previously hysterectomized."} +{"text": "Evidence continues to mount that sleep apnea (SA) occurs in 10-25% of Americans and is associated with significant morbidity and mortality (Schulman 2018). Among veterans, SA has been reported four times more often as compared to other non-veteran cohorts. (Wong 2015). The risk of developing dementia is increased in older individuals with OSA . The prevalence and characteristics of older adults with dementia and sleep apnea is not well known and long-term population-based studies on mortality have been lacking. Recent studies have reported overall mortality rates of 19%, in those individuals with SA, an increased rate of 1.5-3 times the mortality rate as compared to those individuals those without SA. Current recommendations support SA screening of high risk individuals including those with symptoms of snoring, fatigue, memory and concentration problems and mood changes. (Krist 2018). Despite a large number of older adults with suspected SA and comorbidities, the majority are not screened, referred, diagnosed and treated. In this VA pilot study of outpatient older male veterans with dementia and SA, N=195, mean age 75.83 years, SD=9.1, 51.3% were white, 37.5% were black. Frequently found comorbidities were: hypertension 88%, congestive heart failure 41%, Diabetes. 62% and, stroke 21%. Of note, among those who died, SA was significantly related to congested heart failure and COPD . The overall mortality rate of 27% was higher than previous reports. Further investigation is needed to better understand the relationship between comorbidities, and SA, screening, treatment and mortality."} +{"text": "EGFR mutation positive. This study aims to compare the effectiveness of first line TKIs; gefitinib, erlotinib, and afatinib in the treatment of advanced stage NSCLC patients with EGFR mutation positive in the Indonesian population.EGFR-tyrosine kinase inhibitors (EGFR-TKIs) were used to treat non-small cell lung cancer (NSCLC) patients with EGFR mutation positive treated with gefitinib (n=59), erlotinib (n=22), and afatinib (n=7) was performed in national cancer hospital in Indonesia.Inclusion criteria were stage \u2162b or \u2163 NSCLC with adenocarcinoma subtype. Subjects less than 18 years or with a history of other malignancy were excluded. Outcomes were treatment response, progression-free survival (PFS), and mortality rate.A retrospective cohort study of 88 NSCLC patients with EGFR mutation positive profile, a total of 56.8% subjects had deletion in exon 19, 42% subjects had mutation in exon 21, and rare mutation in exon 18 was found in 3.4% of total subjects. Demography and clinical characteristics had no significant association with the risk of progressive disease. The median PFS of subjects was 11 months (95%CI: 6.8-15.2 months). There was no statistical difference of PFS between treatment groups.Complete response, partial response, and stable disease were shown in 1.1%, 35.2%, and 31.8% of subjects, respectively. There were 31.8% of subjects developed progressive disease during treatment. Regarding EGFR mutation positive. Afatinib tends to be associated with longer PFS but further investigation is required.Gefitinib, erlotinib, and afatinib have similar effectiveness in advanced stage NSCLC with It was estimated that lung cancer mortality in 2035 will be 86% higher than in 2012. Throughout all types of lung cancer cases, the non-small cell lung cancer (NSCLC) accounts for 85% of them. Adenocarcinoma subtype found in more than 70% of NSCLC. In a majority of patients, NSCLC is usually diagnosed at an advanced stage where surgical therapy is no longer applicable.Despite the global health effort on smoking cessation, lung cancer still retains its high mortality rate in the developed and developing countries until presentEGFR) gene was found. EGFR mutations were found in significantly higher proportion in female patients, Asian population, and non-smokers. The most common mutations were the deletion in exon 19 and mutation in exon 21 L858R point. Several experimental studies and meta-analysis reported that EGFR-tyrosine kinase inhibitors (EGFR-TKIs) treatment has better efficacy in advanced stage of NSCLC with these EGFR mutation positive compared with conventional chemotherapy treatment-9.In 10%-35% of lung adenocarcinoma, mutations in the epidermal growth factor receptor . Then, DNA amplification using high-resolution PCR protocol followed by direct DNA sequencing was performed to determine the EGFR mutation profile.This was a retrospective cohort study at Dharmais National Cancer Hospital, Indonesia. The study was approved by the Ethical Committee of Dharmais National Cancer Hospital. To optimize the power of the research, total sampling was performed in recruiting study subjects. Subjects were advanced non-small cell lung cancer (NSCLC) patients (adenocarcinoma subtype) with proven Subjects less than 18 years or with a history of other malignancy were excluded. EGFR-TKIs treatment was administered orally with a daily dose of 250 mg for gefitinib, 150 mg for erlotinib, or 40 mg for afatinib. Treatment would be discontinued if there was evidence of progressive disease or serious adverse event.Inclusion criteria were stage \u2162b or \u2163 of lung adenocarcinoma according to American Joint Committee 2010.EGFR mutation status. We did a 60-month follow-up through the medical record to evaluate treatment response, progression-free survival (PFS), and mortality rate. Treatment response was assessed on the basis of the Response Evaluation Criteria in Solid Tumors (RECIST) guideline. Evaluation of the treatment response was performed every 3-6 cycles after starting EGFR-TKIs treatment. Clinical examination, laboratory tests, abdominal ultrasonography, and computed tomography (CT) scan were performed to determine treatment response.The demographic and clinical parameters were collected before the EGFR-TKIs treatment. These data included age, gender, body mass index (BMI), comorbidity, Statistical analysis was performed using IBM SPSS software version 24. Study outcomes were treatment response and 24-months PFS. For the survival analysis, we performed right censoring for handling loss to follow-up subjects.Chi-square test was performed. A P-value of less than 0.05 was considered statistically significant. Relative risks and their 95% confidence interval were calculated.To assess the association between type of EGFR-TKIs treatment and study outcomes, the Kaplan-Meier graph and log-rank test were performed to compare the survival probability of PFS regarding EGFR-TKIs treatment.The A total of 115 of NSCLC patients fulfilled inclusion criteria of study. However, 27 subjects had incomplete medical records, so a total of 88 subjects were included in analysis.Characteristics of subjects treated with gefitinib, erlotinib, and afatinib were comparable with respect to the demographic, clinical, and molecular variables .EGFR gene. Approximately 3% of total subjects had rare mutation in the EGFR gene (mutation in exon 18). There were two subjects having double mutations in exon 19 and exon 21.The mean age of all subjects was 60 years. There was no significant difference in gender proportion. Most subjects were at stage \u2163. The most common sites of metastasis were pleura (51.4%), bone (31.1%), and brain (10.8%). More than 50% of total subjects were found to have exon 19 deletion in Complete response (CR), partial response (PR), and stable disease (SD) were shown in 1.1%, 35.2%, and 31.8% of subjects, respectively. However, there were 31.8% of subjects who developed progressive disease during treatment of TKIs. Demography and clinical characteristics had no significant association with the risk of progressive disease .EGFR mutations had no significantly difference of risk of progressive disease than subjects with a deletion in exon 19 or mutation in exon 21.Regarding the type of EGFR-TKIs treatment, the risk of progressive disease in subjects receiving gefitinib, erlotinib, and afatinib was similar. Subjects with uncommon Log-rank test showed that there was no significant difference in PFS between these three groups of treatment (P=0.28).The median progression-free survival (PFS) of subjects was 11 months (95%CI: 6.8-15.2 months). Comparison of 24 months PFS by EGFR-TKIs treatment is shown in EGFR mutation profile. The results of our study showed that gefitinib, erlotinib, and afatinib had similar effectiveness in terms of treatment response and 24-months follow-up of PFS. Although not statistically significant, subjects receiving afatinib have marginally longer PFS compared to others receiving gefitinib or erlotinib. No progression found in patients with afatinib in 24 months follow up. Regarding EGFR mutation status, subjects with uncommon EGFR mutations had similar risk of progressive disease compared to subjects with mutation in exon 19 or exon 21 point.To our knowledge, this was the first Indonesian cohort study which compared the effectiveness of EGFR-TKIs treatment in advanced stage NSCLC patients with respect of et al. showed similar results. The study was done in Poland involving 180 NSCLC patients. They found that there was no significant in treatment response, PFS, and overall survival in NSCLC patients treated with gefitinib, erlotinib, and afatinib. There were 14.5% of subjects having progressive disease, compared to 31.8% in our study. The difference was probably due to several reasons. First, the study enrolled all subtypes of NSCLC in the Caucasian population compared to adenocarcinoma patients of the Asian population in our study. Second, there was a higher proportion of exon 19 mutation and a lower proportion of exon 21 in that study compared to ours. Patients with exon 19 deletion indicated to have a higher response rate after EGFR-TKI treatment compared patients having exon 21 mutation, 19.A retrospective study by Krawczyk et al. also reported that subjects treated with afatinib have slightly longer PFS compared to subjects receiving gefitinib or erlotinib. A large phase 2B randomized controlled trial comparing the efficacy of gefitinib and afatinib performed by Park et al. (Lung-LUX 7) supports this finding. The study showed that median PFS in the afatinib group was 11 months (95%CI: 10.6-12.9), while in gefitinib group was 10.9 months (95%CI: 9.1-11.5). However, it is important to note that there was a slightly higher incidence of serious treatment-related adverse event and fatal adverse event in afatinib group compared to gefitinib group .Similar to our study, Krawczyk et al found a different result compares to our study. Gefinitib showed superior efficacy compared to erlotinib. Subjects treated with gefinitib have longer PFS and overall survival in 1-year follow up. These differences could be due to several explanations. First, the erlotinib group in the study has a higher proportion of cachexia which could affect treatment response and overall survival. Second, there was no data on the type of EGFR mutations. So, there might be a possibility that there was a difference in the profile of EGFR mutation compared to our study population.On the contrary, a large retrospective cohort study involving 7, 222 lung adenocarcinoma patients in Taiwan by Chang et al. showed that patients' characteristics such as age, gender, staging, performance status, and smoking history did not affect one-year and two-year overall survival after multivariate cox regression analysis. Other retrospective cohort study performed by Chang et al. in Taiwan in previously treated NSCLC patients also reported that gender, comorbidities, and presence of cachexia had no association with PFS.In our study, the multivariate analysis to control all of the potential confounders was not performed due to two considerations. First, despite total sampling, the sample size was not adequate to perform a multivariate analysis. Second, the baseline characteristics between gefitinib, erlotinib, and afatinib group were comparable. Moreover, other similar retrospective study performed by Krawcyzk e.g. smoking status, history of treatment) could not be analyzed due to incomplete data. In addition, time for assessing treatment response might be varied among study subjects.Our study had several limitations. Since afatinib were not covered in Indonesia National Health Insurance during the study period, we had only small number of subjects receiving afatinib. Therefore, although they had marginally longer PFS than other groups, the result must be interpreted cautiously. Further studies with larger sample size is needed to produce more precise result. Retrospective observational study designs was another limitation to our research. All potential confounders (EGFR mutation lung adenocarcinoma patients. Afatinib tends to associate with longer PFS but further investigation is required.The result of this study provides evidence that gefitinib, erlotinib, and afatinib have similar effectiveness in advance stage"} +{"text": "After multivariate analysis, increased %MAP and %MAP > 50% (p \u2264 0.047) were still the predictors of total mortality and %MAP > 50% (p = 0.024) was still the predictor of cardiovascular mortality. In HD patients, we found that ankle %MAP and %MAP > 50% could predict total mortality and ankle %MAP > 50% could predict cardiovascular mortality in the multivariate analysis. Hence, assessment of %MAP from pulse volume recording at ankle might be helpful in identifying the high-risk group for poor prognosis in HD patients.Pulse volume recording is an accurate modality for detecting arterial occlusion in the lower extremities. There are two indexes of pulse volume recording measured at ankle, percentage of mean arterial pressure (%MAP) and upstroke time (UT). The aim of the study was to examine the ability of %MAP and UT for the prediction of overall and cardiovascular mortality in hemodialysis (HD) patients. In 197 routine HD patients, ankle %MAP, ankle UT, and ankle\u2013brachial index (ABI) were automatically measured by Colin VP-1000 instrument. Fourteen cardiovascular mortality and 29 overall mortalities were documented during 2.7 \u00b1 0.6 years follow-up. In the univariate analysis, in addition to co-morbidities and traditional clinical parameters, increased total mortality was associated with decreased ABI, ABI < 0.9, increased %MAP and UT, %MAP > 50%, and UT > 169 ms ( The prevalence of peripheral artery disease (PAD) has increased in recent years. The presence of PAD impairs quality of life and is associated with a greatly increased risk of major cardiovascular events and death . The risPulse volume recording is another accurate modality for detecting arterial occlusion in the lower extremities . There an = 6) and those with atrial fibrillation (n = 4). Finally, 197 patients were included in this study. The protocol was approved by our Institutional Review Board and all enrolled patients gave written, informed consent.The study was performed in a regional hospital in southern Taiwan from April 2016. All routine HD patients in the dialysis clinic of this hospital were included except those who refused vascular examination . Every HD session was conducted for 3\u20134 h using a dialyzer with a blood flow rate of 250 to 300 mL/min and dialysate flow of 500 mL/min.After resting in the supine position for at least 5 min, the peripheral vascular parameters and blood pressures were measured 10\u201330 min before HD using a validated device that automatically and simultaneously measures blood pressures in both arms and ankles using an oscillometric method . OcclusiDemographic and medical data including age, gender, current smoking history, and comorbid conditions were acquired from medical records and interviews with patients. The body mass index (BMI) was calculated as the ratio of weight in kilograms divided by the square of height in meters. Blood samples were obtained within 1 month of enrollment. The diagnosis of diabetes mellitus was confirmed if the fasting blood glucose level was greater than 126 mg/dL or hypoglycemic agents were used to control blood glucose. The diagnosis of hypertension was confirmed if the systolic blood pressure was \u2267140 mmHg or diastolic blood pressure \u2267 90 mmHg or anti-hypertensive agents were prescribed. Stroke was defined as a history of cerebrovascular disease including cerebral bleeding and infarction. Coronary artery disease was defined as angiographically documented coronary artery disease, a history of myocardial infarction, a history of typical chest pain with positive stress test and having undergone coronary artery bypass surgery or angioplasty. Heart failure was defined according to Framingham criteria [Cardiovascular mortality was defined as death caused by cardiogenic shock, heart failure, ischemia heart disease, lethal arrhythmia, unexplained sudden cardiac death, aortic dissection, cerebrovascular disease, and so on. Cardiovascular mortality was ascertained and adjudicated by two cardiologists, with disagreement resolved by adjudication from a third cardiologist from the hospital course and medical record. In mortality patients, they were followed until date of death. The other patients were followed until March 2019.t test and Chi-square test, respectively. The significant variables in the univariate analysis were selected for multivariate analysis. Time to mortality events was modeled using the Cox proportional forward hazards model. A Kaplan\u2013Meier survival plot was calculated from baseline to time of mortality events and compared using the log-rank test. All tests were two-sided and the level of significance was established as p < 0.05.SPSS 22.0 software was used for statistical analysis. Data were expressed as the mean \u00b1 standard deviation or percentage. Continuous and categorical variables between groups were compared by independent samples Among the 197 subjects, the mean age was 61 \u00b1 12 years. The prevalence of ABI < 0.9 was 25.4%. n = 14) and overall mortality (n = 29).The follow-up period to mortality was 2.7 \u00b1 0.6 years in all patients. Mortality events were documented during the follow-up period, including cardiovascular mortality (p = 0.002) and UT > 169 ms or not (log-rank p = 0.030). Participants with %MAP > 50% and UT > 169 ms had higher overall mortality rate.The optimal cut-off vales of %MAP and UT for the prediction of overall mortality have not been established. To find the appropriate cut-off values of %MAP and UT as predictors of overall mortality, we created several models using different cut-off values of %MAP and UT. Using the Chi-square value to select the model with the best performance, the model using %MAP > 50% and UT > 169 ms had the best performance in predicting the overall mortality. There were 24 and 99 patients with %MAP > 50% and UT > 169 ms, respectively. This study aimed to evaluate %MAP and UT measured at ankle for the prediction of overall and CV mortality in HD patients. We found that %MAP and %MAP > 50% were the predictors of total mortality and %MAP > 50% was the predictor of cardiovascular mortality in the multivariate analysis. In addition, after multivariate adjustment, the major determinants of %MAP were female gender, low ABI, high baPWV, and high UT and the major determinants of UT were low diastolic blood pressure, low ABI, and high %MAP in HD patients.In patients without PAD, pulse volume recording looks like a normal arterial wave. In contrast, in patients with peripheral arterial occlusion, the pulse waveform becomes flattened and has a delayed upstroke. A high %MAP caused by a flattened arterial wave implies the possibility of peripheral arterial occlusion . In factMitsutake et al. found that UT was significantly correlated with coronary artery calcification score based on computed tomography findings . Sheng eLi et al. demonstrated that %MAP had a positive correlation with baPWV in patients with ABI > 0.9, but UT had no correlation with baPWV in the same group . In the Several traditional cardiovascular risk factors, such as diabetes, coronary artery disease, stroke, and chronic heart failure were useful predictors of mortality in HD patients ,20,21. IThere were several limitations in this study. First, the study generality was limited because study patients were only included from one dialysis clinic in a regional hospital in southern Taiwan. Second, we did not evaluate the association of peripheral arterial occlusion disease on image studies with %MAP and UT. Therefore, the mechanism underlying the link between high ankle %MAP and mortality and no correlation between ankle UT and mortality was still unknown. Third, vascular calcification, extremely high in dialysis patients, might have affected the measurements of baPWV, ABI, %MAP, and UT. However, we did not evaluate the vascular calcification in our study patients, so the impact of vascular calcification on these parameter measurements could not be assessed in the present study. Fourth, most of our patients were receiving long-term antihypertensive treatment. For ethical reasons, we did not withdraw these medications. Therefore, we could not exclude the impact of antihypertensive medication on the present findings. Finally, because of the large number of variables in the analysis with only 29 mortality events, the possibility of a chance finding and the limited power should be considered.In HD patients, we found that ankle %MAP and ankle %MAP > 50% could predict total mortality and ankle %MAP > 50% could predict cardiovascular mortality in the multivariate analysis. Hence, assessment of %MAP from pulse volume recording of lower limbs might be helpful in identifying the high-risk group for poor prognosis in HD patients."} +{"text": "Technology presents opportunities to optimize whole person wellness and functioning. To understand tech readiness and the potential role of virtual (VR) and augmented reality (AR) to support optimal aging, we surveyed 604 participants from the nationally representative RAND American Life Panel. Participant age ranged from 50-90+, 51.5% were female, and 50% reported bachelor\u2019s education or higher. Overall, 8% of the sample identified as Hispanic, with 15% of individuals also identifying as Black, Asian, or Asian Indian or Alaskan Native. Males reported greater optimism and technology innovation and adults aged 50-64 were the most optimistic. Overall, 80% of the sample reported VR familiarity compared to 33% AR. Regarding future needs, 75% of the participants expressed specific concerns about future ADL ability. Almost half of the respondents indicated willingness to use VR and AR to maintain or improve functioning with age and increased personalization of optimal aging emerged as a significant predictor."} +{"text": "Conclusions: nfHP patients experienced an excellent survival with good therapeutic effect on pulmonary function tests with both corticosteroid initiation as well as antigen avoidance. In contrast, fHP patients experienced a dismal prognosis without any therapeutic effect of corticosteroid treatment. Whether antigen avoidance is useful in fHP patients is still unclear.Background: Although the third most frequent interstitial lung disease, hypersensitivity pneumonitis (HP) remains an enigmatic disease without clear diagnostic and therapeutic guidelines. We assessed the effect of the commonly used therapeutic interventions (i.e. exposure avoidance and corticosteroid treatment) in an HP cohort. Methods: We collected clinical data of all HP patients followed at our centre between January 1, 2005, and December 31, 2016. HP patients were stratified according to the presence of fibrosis on chest CT. Survival was analysed using the multivariate Cox proportional hazards model. Forced vital capacity and diffusing capacity of the lung for carbon monoxide evolution were analysed using linear mixed-effect models. Results: Two hundred and two HP patients were identified: 93 non-fibrotic HP (nfHP) and 109 fibrotic HP (fHP), experiencing a monthly FVC% decline before treatment of 0.93% and 0.56%, respectively. While nfHP had an excellent survival, fHP patients experienced a median survival of 9.2 years. Corticosteroid treatment and exposure avoidance did not result in survival differences. Although nfHP patients showed FVC% and DLCO% increase after corticosteroid initiation, no therapeutic effect was seen in fHP patients. FVC% and DLCO% increased in nfHP patients after exposure avoidance, while a positive numerical trend was seen for FVC% after exposure avoidance in fHP patients ( Hypersensitivity pneumonitis (HP) is the third most frequent interstitial lung disease (ILD) , charactStratification of HP patients is classically based on symptom chronicity as well as presenting symptoms ,9,10. CoFor this study, we sought to investigate the therapeutic effect on survival and pulmonary function test evolution of both antigen avoidance and corticosteroid initiation in both non-fibrotic HP (nfHP) and fibrotic HP (fHP) with the hypothesis that treatment effects would be different between these two subgroups.Combination of compatible symptoms (dyspnoea and/or cough and/or symptoms with onset shortly after exposure (max 4\u20136 h) and/or recurrent viral symptoms), suggestive CT findings (extensive ground glass opacities (GGO) and/or centrilobular noduli and/or peribronchovascular fibrosis and/or upper lobe predominant fibrosis and/or airtrapping) and\u2014if biopsy was performed\u2014suggestive pathology data -like pattern)Combination of compatible symptoms (cf supra) and suggestive CT findings (cf supra) and compatible pathology findings (any fibrosis and no other disease more probable according to the pathology report)Combination of compatible symptoms (cf supra) and compatible CT findings -like pattern) and suggestive pathology findings (cf supra).All patients presenting at the University Hospitals Leuven between January 1, 2005, and December 31, 2016, with a diagnosis of HP were included. The HP diagnosis was validated using one of the following criteria, in line with recent literature ,9,19,20:Cases not complying with one of these criteria were discussed in a multidisciplinary discussion (MDD). Reports of these MDDs can be found in Patients were divided in two HP subgroups (nfHP and fHP), based on HRCT findings ,11,12: ft-tests or Mann Whitney U-test where appropriate. For discrete variables, chi square tests and Fisher\u2019s exact tests were used, where appropriate. Baseline characteristics: Continuous variables were analysed using Student\u2019s Survival analysis: outcome was based on 10-year survival. Data were displayed as Kaplan Meier curves and analysed using Cox proportional hazards models. Patients who underwent lung transplantation were censored at the day of transplantation. In multivariate analyses, we corrected for age, gender, and baseline FVC%. All multivariate analyses are shown in PFT evolution: evolution of PFT was analysed with mixed effect models, using FVC% and DLCO% as outcome measurements with subject as a random effect and time, age, and gender were accounted for as fixed effect. Corticosteroid treatment analysis: corticosteroid use was accounted for as fixed effect, both with and without time-varying covariate. Exposure status was corrected for as fixed effect and immunosuppression use as a time-varying covariate. Antigen avoidance analysis: exposure status and corticosteroid use were corrected for with and without time-varying covariate and immunosuppression use as time-varying covariate. Informed consent and ethical approval were obtained at the University Hospitals Leuven ethical commission. Analyses were conducted according to \u2018strengthening the reporting of observational studies in epidemiology\u2019 (STROBE) guidelines . Statistp < 0.001), as presented in Two hundred and two patients met the inclusion criteria: 93 were classified as nfHP and 109 as fHP. Overview of cohort formation is presented in p = 0.75).PFT data were collected from the 202 included patients. In total, 1251 and 1604 PFTs were collected from the clinical files of nfHP and fHP patients, respectively. Throughout the first year of their follow-up (before treatment initiation), there was no difference in FVC% per month between nfHP or fHP groups and DLCO% , were more often female , and were prescribed more often second line immunosuppressive agents . Corticosteroids were used in 67 (79%) nfHP patients and 82 (80%) fHP cases. In 8 (10%)-nfHP patients and 24 (25%) fHP patients an additional immunosuppressive agent was used. Baseline characteristics according to corticosteroid treatment status and 2nd line immunosuppressive treatment status can be found in p = 0.096), as displayed in Corticosteroid treatment did not result in different survival rates in the entire cohort a. A trenp < 0.001). For DLCO% decline, no significant differences were observed (p = 0.43); however, nfHP patients showed a trend towards an immediate DLCO% increase of 3.38% after corticoid treatment initiation (p = 0.081). In contrast, no significant changes were observed for fHP . Results are shown in p = 0.57; DLCO%: p = 0.41).In nfHP, corticosteroid initiation resulted in a reversal from a monthly FVC% decline of 0.35% to an FVC% increase of 0.84% (p = 0.003). Overall, patients without known inciting agent had lower baseline FVC% , were more often female ) and more often ever-smokers and showed more often signs of fibrosis . The inciting agent remained unknown in 41 cases (20%): 11% of nfHP and 28% of fHP cases (p = 0.056), that was significant after multivariate correction , which could not be replicated in the fHP cohort (p = 0.26). No differences in DLCO% decline were observed . Throughout the entire cohort (both nfHP and fHP patients), there was a trend towards worse survival in patients without known inciting agent , as shown in Overall, bird, mould, and other exposures were found in 53%, 20%, and 7% of patients, respectively (while 20% of patients had unknown exposure). Prevalence of exposure types differed between nfHP and fHP (p = 0.057) or patients without known exposure . No differences in FVC% and DLCO% evolution could be observed.Bird-exposed HP patients had a better survival compared to mould-exposed patients and treatment with a second line immunosuppressive treatment were similar; neither were survival differences found after exposure avoidance (correcting for treatment and baseline characteristics). Similarly, DLCO% decline of 0.23% per month was reversed to a DLCO% increase of 0.37% with an additional immediate increase of 4.0% after avoidance (p = 0.04). Although the 0.06% FVC% decline before avoidance reversed to a 0.28% monthly increase in fHP patients afterwards, these differences were not statistically significant (p = 0.15). DLCO% decline did not change in the fHP group (p = 0.54). Results are shown in In nfHP patients, FVC% decline of 0.24% monthly was reversed to a 0.92% monthly FVC% increase (p = 0.482), nor symptoms chronicity (p = 0.187) had an effect on survival. Moreover both parameters did not affect FVC% evolution or DLCO% evolution .As the classical classification of HP patients into acute HP (AHP) and chronic HP (CHP) is also based on symptoms types and symptoms chronicity (i.e. for AHP: <6 months), we investigated whether these factors would influence survival and PFT evolution in the nfHP patients of the cohort. Neither symptom type : 91 without fibrosis (nfHP) and 109 patients with fibrosis (fHP). We assessed the rate of FVC decline in nfHP and fHP . Although corticosteroids and exposure avoidance have been used for many years as the first line treatment of HP, this is the first study to assess the efficacy of these treatment options in both subgroups of this disease. Corticosteroid treatment was effective in nfHP concerning FVC% and DLCO% decline. In contrast, these treatments were not effective in fHP. Furthermore, we did not observe a survival impact of corticosteroid treatment in any subgroup. While exposure avoidance was significant with both FVC% and DLCO% decline reversed in nfHP and a positive trend in the FVC% decline in the fHP subgroup, no clear impact of exposure avoidance on survival was seen. Some observations deserve further attention. FVC% and DLCO% trajectories do not fully correlate with those presented by Salisbury or MorisMorisset et al. determinWe observed worse outcome in HP patients without known antigen in multivariate analysis, which validates the data published by Fernandez-Perez et al. . We furtFinally, as symptom chronicity and symptom type did not alter clinical behaviour in nfHP patients, these results support the idea that a radiological stratification of HP patients is relevant.p = 0.096), as this trend was attenuated after correction for baseline disease severity in the multivariate analysis . Randomized controlled trials would be needed to further elucidate this question. Secondly, being an observational study of patients followed at a tertiary centre, there is a risk of referral bias, as already discussed regarding the lack of corticosteroid treatment effect in the fHP group. Thirdly, as a limited number of patients included in the cohort were treated with second line immunosuppressive drugs, the study lacked the necessary statistical power to assess the effect of this treatment option. As HP patients are not systematically treated with these therapies in many centres in Europe, this cohort might reflect this common practice in Europe.There were several limitations to this study. First, being a retrospective study, the treatment effect of corticosteroid treatment with regard to survival could be biased as patients with more severe disease were more frequently treated with corticosteroids. We believe this should be taken into account when interpreting the trend to increased mortality in fHP patients treated with corticosteroids . These data underpin the high medical need for new treatment options in fHP. In conclusion, we assessed the impact of corticosteroid treatment and antigen avoidance in a large cohort of 202 HP patients. Corticosteroid treatment increased FVC% and DLCO% in nfHP but not in fHP. Exposure avoidance was effective in nfHP, with a trend towards efficacy in fHP ("} +{"text": "Superbugs are pathogenic micro-organism and especially a bacterium that has developed resistance to the medications normally used against it. As the superbug family increases, the need for appropriate diagnostic, treatment, prevention and control strategies cannot be over emphasized. Therefore, this work determined the distribution of superbug bacteria among patients on prolonged hospital admissions in three tertiary hospitals of Kano state, Nigeria.Acinetobacter spp and other related nosocomial bacterial pathogens. Antibiotic susceptibility testing was done using Kirby-Bauer disc diffusion method.A descriptive cross sectional study was undertaken among 401 patients from medical, surgery, orthopedic and burn centre wards in a three tertiary hospitals in Kano state. A sample collected comprises wound/pus, urine, urine catheter and nasal intubation and were analysed using standard microbiological methods for Klebseilla spp, Proteus spp, Pseudomona spp and Acinetobacter spp. In-vitro antibiotic susceptibility test revealed that acinetobacter were 100% resistant to amoxicillin, co-trimoxazole, perfloxacin and imipenem.One hundred and thirty eight (138) isolates were recovered, from the studied participants. More than 80% of the nosocomial infections (NIs) were caused by Gram-negative bacteria, predominantly Escherichia coli, Acinetobacter spp) especially on prescribing antibiotics that showed 100% resistant from these studied hospitals.Superbugs (Acinetobacter species) significantly contributed to delayed hospital admissions through observed 100% resistance to used antibiotics. The healthcare managers of these hospitals and the ministry of health need to take measures against this resistant bacteria ( E. coli and other unnamed gram negative were reported to have 100% resistant to amoxicillin/clavulanate and chloramphenicol [et al [Acinetobacter baumannii isolated from the intensive care unit (ICU) of the Nigerian tertiary hospitals to ceftriaxone, amoxicillin-clavulanate, ampicillin-sulbactam, gentamicin, ciprofloxacin and ofloxacin. Resistant of some Gram positive bacteria such as Staphylococcus aureus to ampicillin ranged between 0 to 95.6% and coagulate negative showed 100% resistance to ampicillin in some part of the country. Most of the previous research on nosocomial infection and antimicrobial susceptibility from major tertiary hospital in Kano did not focus much on superbugs-related prolonged admissions despite World Health Organisation\u2019s recommendations on frequent research on these organisms [Antimicrobial resistant poses one of the most pressing public health threats worldwide . The emel [et al reportedStudy area: the study was conducted at Aminu Kano Teaching Hospital (AKTH), Murtala Muhammad Specialist Hospital (MMSH) and Muhammad Abdullahi Wase Specialist Hospital (MAWSH) microbiology laboratory of each hospital, Kano state, Nigeria. The duration of the study was 6 months (July to December 2016).Study design: this was a cross sectional descriptive hospital based which involved isolation of bacteria from urine, wound/pus, urine catheter and nasal feed tube from patients who were eighteen years and above of ages and both sexes admitted in all the above Aminu Kano Teaching Hospital (AKTH), Murtala Muhammad Specialist Hospital (MMSH) and Muhammad Abdullahi Wase Specialist Hospital (MAWSH). The isolated bacteria were subjected to antibiotic sensitivity testing using different antibiotics discs.Sample collection: samples were collected according to the method described by [ribed by . A steriIsolation and identification of bacterial pathogens: isolation of bacterial agents of urine, wound/pus, urine catheters and nasal tube was done according to the method described by [Acinetobacter media. All the media were prepared according to manufacturer's instructions. The media was sterilized at 121\u00b0C for 15 minutes. Ten percent (10%) blood agar was prepared by mixing 10ml fresh sheep blood with 90ml of blood agar base at 45\u00b0C. Twenty (20ml) of each medium was dispensed into sterile disposable plastic petridish and allowed to set. Each sample was aseptically inoculated (in triplicate) into 10% blood sheep agar, MacConkey agar and Cysteine Lactose Electron Deficient Agar (CLED) and Leeds Acinetobacter media. The plates were incubated aerobically at 37\u00b0C for 18-24h. The characteristic bacterial isolates observed on the selective media plates were aseptically sub-cultured onto freshly prepared culture media plates. Identification of bacterial isolates was done on the basis of their cultural and biochemical characteristics as described by Cheesbrough [ribed by , 12. Fouesbrough . The ideAntibiotic susceptibility study: antibiotic susceptibility was determined using Mueller Hinton (mast group limited). A small inoculum of each pure bacterial isolates was emulsified in 3ml sterile normal saline in a cleaned sterile test tube until it matched with 0.5 McFarland standards. Mueller Hilton agar plates were inoculated using sterile cotton swab in the confluent pattern as in the Kirby-Bauer procedure [Escherichia coli ATCC25922, Pseudomonas aeruginosa ATCC27853, Staphylococcus aureus ATCC29213 were used as a reference strains for susceptibility test.rocedure . Antibiorocedure . AntibioEthical consideration: ethical approvals to carry out the study were obtained from Institutional Review Boards of Kampala International University Western Campus, Health Service Management Board Kano (HMB/GEN/488/VOL.1), Ministry of Health Kano State and AKTH, Nigeria. Written informed consent prepared in local languages (Hausa) were obtained from all participants or guardians in case patients were critically ill.E. coli was the most frequently isolated bacterial nosocomial pathogens from all the studied hospitals (E. coli showed higher resistance to co-trimoxazole (94%) and less resistance to Augmentin (11%) among all antibiotics tested. Proteus spp showed higher resistance to amoxicillin (42%) with less resistance to Imipenem (8%) among all antibiotics tested. Streptococcus spp showed 40% resistance to co-trimoxazole, ceftriaxone, rocephin, augmentin, ceftazidime and ciprofloxacin with 0% resistance to tetracycline. Pseudomnas spp showed 100% resistance to amoxicillin with 0% resistance to augmentin and imipenem. Acinetobacter spp were 100% resistant to amoxicillin, co-trimoxazole, perfloxacin and imipenem with 20% resistant to tetracycline, ciprofloxacin and ceftazidime. Staphylococcus spp were 75% resistant to co-trimoxazole and perfloxacin with 25% resistance to tetracycline, ciprofloxacin and ceftazidime. Klebsiella pneumonie were resistant 100% resistant to tetracycline with 0% resistance to ciprofloxacin were in the age range of 49-58 years while the 18-28 years age group constituted the least age group (9.2%). There were 200 males and 201 females. Most of the participants were retired (54.9%) while the least were unemployed (3.2%). Most of the participants were married (45.6%) while 1.5% were widows. Out of the 401 studied participants enrolled in this study, 138 (34.42%) bacterial nosocomial pathogens were isolated. Fifty eight (58) bacterial isolates were isolated from AKTH and MMSH each. Twenty two (22) bacterial isolates were obtained from MAWSH. Among the bacterial pathogens isolated, ospitals . The resfloxacin .E. coli showed 80% resistance to co-trimoxazole with 0% resistant to imipenem. Proteus spp showed 100% resistance to tetracycline with 0% resistant to augmentin and imipenem. Streptococcus spp showed 50% resistance to co-trimoxazole, tetracycline, ciprofloxacin, ceftazidime, rocephin and ceftriaxone with 0% resistant to amoxicillin, perfloxacin, augmentin and imipenem. Pseudomonas spp were 100% resistant to amoxicillin, tetracycline and ceftazidime with 0% resistant to rocephin. Acinetobacter spp were 100% resistant to amoxicillin, co-trimoxazole and perfloxacin with 33% resistant to tetracycline, ciprofloxacin, ceftazidime and cugmentin. Staphylococcus spp were 100% resistant to co-trimoxazole, perfloxacin and augmentin with 33% resistant to ceftazidime and ceftriaxone. Klebsiella pneumonie showed 100% resistance to tetracycline with 0% resistant to Imipenem . Nwadike et al [Acinetobacter spp resistant to \u03b2-lactams, aminoglycoside antibiotics in many healthcare centres within the country which make some of the healthcare centres a reservoir of Acinetobacter spp resistant genes. Odewale et al [Acinetobacter spp isolated in Ladoke Akintola University Teaching Hospital, Osogbo, Nigeria.More than 80% of the nosocomial infections (NIs) were caused by the Gram-negative bacteria (GNB). tigators , 17. Thile et al also repAcinetobacter spp to Imipenem from AKTH. This was in line with findings of Shahcheraghi et al [Acinetobacter spp from patients at Tehran hospitals, Iran. Other Gram negative bacteria found to be 100% to some of the antibiotics tested from AKTHS and MAWSH were Proteus spp, Pseudomnas spp and Klebsiella pneumonie. The higher resistance of Gram's negative bacteria to antibiotics reported in this could be due to the higher exposure of these bacteria to these antibiotics [Streptococcus spp showed 0-40%, 0-50% and 0-70% resistant to antibiotics tested from AKTH, MAWSH and MMSH respectively. This was in line with findings of Barma et al [Staphylococcus spp showed 25-75%, 33-100% and 22-78% resistance to antibiotics tested from AKTH, MAWSH and MMSH respectively. This was in line with finding of Barma et al [Streptococcus pyogenes isolated from Intensive Care Units of the University of Maiduguri Teaching Hospital, Nigeria.The results of this study also found 100% resistance of hi et al who repoibiotics . Antibioma et al , who repma et al who repoAcinetobacter spp and other related nosocomial bacterial pathogens were 0-100% resistant to the antibiotics tested. There is need for the management of the three studied hospitals to take measures especially in antibiotics prescription by reviewing guideline to avoid prescribing antibiotics that showed 100% resistance to this bacteria.Present study determined the superbugs-related prolonged admissions in three tertiary hospitals, Kano state, Nigeria. The results showed that, Presence of some nosocomial bacterial pathogens from the three studied hospitals;Antibiotic resistant profile of some nosocomial bacterial pathogens from the three studied hospitals.Acinetobacter spp associated with other nosocomial bacterial pathogens from the three studied hospitals;Presence of Acinetobacter spp associated with bacterial nosocomial pathogens from the three studied hospitals.Antibiotic resistant profile of The authors declare no competing interests."} +{"text": "Highly pathogenic avian influenza virus (AIV) has been endemic in Cambodia since 2004, and is a major agricultural and public health concern. Cambodia is a tropical, resource poor, lower-middle income country in Southeast Asia with a large socio-economic dependence on agriculture. In 2015, 87% of Cambodian households with agricultural holdings raised poultry . CambodiMeleagris gallopavo) and geese (Anser anser domesticus) were taken, the majority were from domestic chickens and ducks (Anatidae spp), so analysis focused on these two poultry types.Between August 2017 and May 2018, 16 total sampling sessions were performed in LBMs, slaughterhouses and poultry storage facilities in Takeo, Kandal and Banteay Meanchey (BM) provinces, concurrently. Sampling on the week before, the week of, and the week after the four major Cambodian festival periods: Pchum Ben , Bon Om Touk , LNY (February 2018) and Khmer New Year with single samplings in-between . One tracheal and one cloacal swab were collected and pooled into a single tube from at least 40 individual birds/province/sampling for a total of 2129 poultry samples and tested for AIV by RT-qPCR as previously described ,4. WhileOverall, 23.3% of the poultry samples screened were positive for AIV by RT-qPCR with 20.0% and 32.6% positivity in chickens and ducks, respectively. Percentages were similar for individual provinces . Longitudinally, total AIV detection fluctuated between 4.0% and 48.3%, with highest levels the week before or the week of festivals with increased poultry consumption. Highest detection was associated with LNY followed closely by KNY (Co-infections comprised 3.2% of all AIV positive samples (As observed previously , A/H5 isOverall, AIV continues to circulate within Cambodia at high levels as previously described, correlating to festival periods when poultry production and consumption is increased . However"} +{"text": "Loop-mediated isothermal amplification (LAMP) is used to detect pulmonary tuberculosis (PTB); however, the diagnostic accuracy of the LAMP assay for extrapulmonary tuberculosis (EPTB) is unclear. We performed a meta-analysis to evaluate the performance of LAMP in the detection of EPTB.We searched PubMed, EMBASE, the Cochrane Library, China National Knowledge Infrastructure (CNKI), and the Wanfang database for studies published before Sep 16, 2017. We reviewed studies and compared the performance of LAMP with that of a composite reference standard (CRS) and culture for clinically suspected EPTB. We used a bivariate random-effects model to perform meta-analyses and used meta-regression and subgroup analysis to analyze sources of heterogeneity.Fourteen articles including 24 independent studies of EPTB were identified. LAMP showed a pooled sensitivity of 77% 68\u201385), specificity of 99% (95% CI 96\u2013100), and area under SROC curves (AUC) of 0.96 (95% CI 0.94\u20130.97) against CRS. It showed a pooled sensitivity of 93% (95% CI 88\u201396), specificity of 77% (95% CI 64\u201386), and AUC of 0.94 (95% CI 0.92\u20130.96) against culture. The pooled sensitivity, specificity, and AUC of MPB64 LAMP were 86% (95% CI 86\u201386), 100% (95% CI 100\u2013100), and 0.97 (95% CI 0.95\u20130.98), respectively, and those of IS6110 LAMP were 75% (95% CI 64\u201384), 99% (95% CI 90\u2013100), and 0.91 (95% CI 0.88\u20130.93), respectively, compared with CRS.These results suggest good diagnostic efficacy of LAMP in the detection of EPTB. Additionally, the diagnostic efficacy of MPB64 LAMP was superior to that of IS6110 LAMP. Mycobacterium tuberculosis (MTB) and is one of the most serious challenges to public health [Tuberculosis (TB) is an infectious disease caused by c health . The mosc health . DiagnosThere are many methods for diagnosis of tuberculosis. PCR tests require an expensive thermal cycler to amplify DNA fragments in multiple temperature-dependent steps. Therefore, some PCR assays, such as Xpert MTB/RIF, are very costly, which is an obstacle to application in low-income areas. Loop-mediated isothermal amplification (LAMP) is an isothermal DNA method that relies on two or three sets of primers to amplify minute quantities of DNA within a shorter period of time. Compared with other nucleic acid amplification tests, LAMP is very economical. This is a new assay with high accuracy for pulmonary TB detection , but theFor this purpose, we performed a meta-analysis to reveal the diagnostic test accuracy of the LAMP assay for EPTB using data from previous studies of the LAMP assay compared with that of a composite reference standard (CRS) and culture reference in the detection of EPTB. We analyzed the pooled sensitivity and specificity of this assay against different references. Moreover, the diagnostic efficiency of the test according to different target genes, types of samples, incubation times, condition of samples, and types of LAMP were evaluated by subgroup analysis.We followed the standard guidelines to perform this meta-analysis \u20136.We searched PubMed, EMBASE, the Cochrane Library, China National Knowledge Infrastructure (CNKI), and the Wanfang database for studies evaluating LAMP accuracy in TB published before Sep 16, 2017. The search formula AND ) was used for PubMed without any language restrictions. The search formulas for EMBASE, the Cochrane Library, CNKI, and the Wanfang database were similar to the PubMed search formula. The search strategies for each database were shown in the We included full text original studies assessing the diagnostic accuracy of the LAMP assay for EPTB using extrapulmonary site specimens. Reference standards were defined in the studies and were appropriate. Articles directly provided TP, FP, FN, and TN values for the assay, or included the data necessary to calculate these measures. Case reports, studies of fewer than 10 samples, abstracts, and conference reports without full articles were excluded.A composite reference standard (CRS) or mycobacterial culture was defined as the reference standard in the studies. Clinical manifestation, biochemical testing results, smears, histopathology, other nucleic acid amplification tests (NAATs), culture, or a response to anti-tuberculosis treatment constituted the reference standards in the CRS.Two investigators independently assessed candidate articles by reviewing titles and abstracts, then full text for inclusion. Discrepancies between the two decisions were resolved by discussion with a third investigator.The same two investigators independently extracted the necessary information from each of the included articles. We then cross-checked the information obtained by the two investigators. Discrepancies between the two data sets were settled by discussion with a third investigator, just as in the literature selection phase. Data from studies against two different reference standards or target genes were treated separately.According to the two reference standards (CRS and culture), the two investigators independently divided studies into two groups and used a revised tool for Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) to assess study quality separately . Publica2 statistics were calculated to assess the heterogeneity between studies compared with a standard reference. A value of 0% indicated no observed heterogeneity, and values greater than 50% were considered substantially heterogeneous [We first obtained the numbers of TP, FP, FN, and TN in each included study, and then calculated the estimated pooled sensitivity and specificity of LAMP associated with 95% CI against CRS or culture using bivariate random-effects models. Forest plots of the sensitivity and specificity as well as summary receiver operating characteristic (SROC) curves were generated for each study. The area under SROC curves (AUC) was likewise calculated. The Iogeneous . We explImperfect reference standards may lead to misclassification of samples in diagnostic validity studies , 12. ForEight hundred candidate articles were identified by searching the relevant databases using our search strategy, and 14 qualified articles were included according to the inclusion criteria , S2 FileWhen an article reported the use of two different standards or target genes in the same study, we considered the article to include two independent studies. In accordance with this principle, 24 independent studies were included: 16 compared LAMP with CRS and 8 with culture . The chaThe overall methodological quality of the included studies using a CRS and culture is summarized in 2 statistical values were 95% for sensitivity and 85% for specificity, suggesting significant heterogeneity in diagnostic validity between the studies. When compared to a culture reference standard , the combined sensitivity of LAMP was 93% (95% CI 88\u201396) with I2 = 49% and the specificity was 77% (95% CI 64\u201386) with I2 = 96% for 1515 specimens in 8 studies and 99% (95% CI 96\u2013100), respectively . The I2 studies . The hetWe explored the heterogeneity between the studies using hierarchical analysis on predefined subgroups of target genes, sample types, incubation time, condition of samples and types of LAMP used in the assay.2 = 3.33% and 100% (95% 100\u2013100) with I2 = 0, respectively (The pooled sensitivity and specificity of the MPB64 LAMP assay (613 samples) vs. CRS were 86% (95% CI 86\u201386) with Iectively . There w2 statistical values were 95% and 88% for sensitivity and specificity, respectively, of IS6110 LAMP. The P values of meta-regression for sensitivity and specificity of the IS6110 LAMP assay against a non-IS6110 LAMP assay in comparison to CRS were 0.16 and 0.25, respectively, suggesting that this target gene was not a source of heterogeneity in the LAMP assay. Therefore, combining different studies to assess the diagnostic performance of the LAMP assay did not significantly skew the results. Compared with culture, the pooled sensitivity of IS6110 LAMP was 89% (95% CI 81\u201394), and specificity was 79% (95% CI 62\u201390). The I2 statistical values of IS6110 LAMP were 42% and 97% for sensitivity and specificity, respectively. Heterogeneity of sensitivity among the studies was moderate. The pooled sensitivity of MPB64 LAMP was significantly higher than that of IS6110 LAMP (P<0.05); however, the difference between the specificities was not statistically significant (P>0.05), and the AUC of MPB64 LAMP was higher than that of IS6110 LAMP when assessed against CRS. Data of other target genes were too limited to analyze.When using IS6110 as the target gene, the pooled sensitivity and specificity of IS6110 LAMP compared with CRS were 75% (95% CI 64\u201384) and 99% (95% CI 90\u2013100), respectively . I2 stat2 = 97%), and pooled specificity was 99% . The P-vWhen LAMP was compared to CRS, meta-regression showed that the type of LAMP was the source of heterogeneity (P < 0.05) rather than incubation time and sample condition (meta-regression P > 0.05). The pooled sensitivity and specificity of Loopamp MTBC and in-house assays were 54% (95% CI 40\u201369) 93% (95% CI 84\u2013100) and 84% (95% CI 79\u201390), 100% (95% CI 99\u2013100), respectively. The differences between sensitivity and specificity were statistically significant . However, heterogeneity in the subgroup was still relatively significant, and the results should be treated with caution.Timely and accurate diagnosis of tuberculosis is very important for effective management of the disease and prevention of infection in the community, particularly in areas with high burdens tuberculosis. Conventional diagnostic methods, such as smears and culture, are time-consuming and not very sensitive.LAMP is an innovative point-of-care diagnostic technique with increased specificity, speed, and low cost . It can In this meta-analysis, we reviewed the diagnostic efficiency of the LAMP assay for EPTB compared with that of a CRS or culture reference. Based on AUC, the diagnostic performance of the LAMP assay was very good for EPTB, regardless of the reference standard used. However, this test was less effective than PCR assays such as Xpert MTB/RIF , 37. We For the detection of the MTB genome, several factors play important roles in standardizing a sensitive and specific LAMP assay. The target gene is an important factor, and a variety of target genes can be used in NAATs. In LAMP, the commonly used target genes are IS6110, MPB64, and IS1081, among others. Through this meta-analysis, we found that diagnostic efficacy was different when using different target genes. The IS6110 gene has been the favored target gene in studies using the LAMP assay, as multiple copies are present in the MTB genome , 39. HowHeterogeneity between the studies using MPB64 LAMP was not significant. The pooled sensitivity and specificity of IS6110 LAMP compared with those of non-IS6110 LAMP were not significantly different vs. CRS. However, heterogeneity between IS6110 LAMP studies was very significant. The pooled sensitivity and AUC of MPB64 LAMP were higher than those of IS6110 LAMP against CRS. This result was consistent with those of studies using other NAATs , 41. IncWe considered that LAMP accuracy for tuberculosis detection in EPTB specimens might vary widely according to specimen type, as it did in another systematic review and meta-analysis of EPTB diagnosis using the Xpert MTB/RIF assay . HoweverWe observed that incubation time and sample condition in LAMP assays did not affect test results. Different assay types might affect results, e.g., an in-house LAMP assay might be better than the Loopamp MTBC assay. As the heterogeneity between the studies was very significant, further studies using different types of the LAMP assay are needed to assess its sensitivity and specificity.PCR tests are considered the most effective means of diagnosis . HoweverSeveral limitations existed in our review. First, the meta-analysis was limited by the number of studies using different target genes and sample types, particularly those comparing LAMP against culture. Only two target genes and one sample type (CSF) could be analyzed through meta-analysis; the diagnostic validity of the LAMP assay for other target gene and sample types could not be assessed. Some included studies used multiple sample types, which may have led to some bias in the results. Second, the quality of some studies in this analysis was relatively poor. The heterogeneity between the studies was remarkable, and the meta-analysis results should be interpreted with caution.In this meta-analysis, we observed that the pooled sensitivity and specificity of LAMP for the detection of EPTB were 77% and 93%, respectively, when compared with a CRS, and 99% and 77%, respectively, when compared with culture. Depending on the assessment of AUC, LAMP showed good diagnostic efficacy. We also found that the diagnostic efficacy of LAMP tests varied according to different target genes; the diagnostic efficacy of MPB64 LAMP was better than that of IS6110 LAMP. The diagnostic accuracy of LAMP for different samples could not be effectively assessed, as the number of studies using different sample types was limited. Additionally, an in-house LAMP assay might be superior to the Loopamp MTBC assay. Because of its low cost, LAMP could be useful in the diagnosis of EPTB, particularly in areas where financial resources are limited and drug-resistant MTB is not prevalent.S1 File(DOCX)Click here for additional data file.S2 File(DOC)Click here for additional data file.S3 File(DOC)Click here for additional data file.S1 Table(DOCX)Click here for additional data file."} +{"text": "To evaluate the performance of Xpert MTB/RIF for lymph node tuberculosis (LNTB). We searched databases for published reports. We reviewed the studies and identified the performance of Xpert MTB/RIF with respect to a composite reference standard (CRS) and culture. We used a bivariate random-effects model to perform meta-analyses and used metaregression to analyze sources of heterogeneity. 15 independent studies compared Xpert MTB/RIF with CRS while 21 comparing it with culture were included. The pooled sensitivity and specificity of Xpert MTB/RIF were 79% and 98% compared to that of CRS, respectively, and 84% and 91% compared to that of culture, respectively. The pooled sensitivity and specificity using fine needle aspiration (FNA) samples versus CRS were 80% and 96%, whereas those against culture were 90% and 89%, respectively. The percentages while working with tissue samples versus CRS were 76% and 100%, respectively, whereas those against culture were 76% and 92%, respectively. There was no significant difference in diagnostic efficiency among the types of specimen. Xpert MTB/RIF demonstrates good diagnostic efficiency for LNTB and is not related to the type of specimen, obtained via different routes. Mycobacterium tuberculosis infection may spread to extrapulmonary sites, causing extrapulmonary tuberculosis (EPTB), LNTB being its most common type. At present, fine needle aspiration (FNA) of lymph node and biopsy are used for diagnosis, although the accuracy is relatively low, and traditional diagnostic protocols, such as Mycobacterium tuberculosis culture, are quite time-consuming. Mostly, biopsy with histopathological examination and culture are required for proper diagnosis; effective control of tuberculosis lies in its rapid diagnosis and treatment. Therefore, a rapid laboratory diagnosis of tuberculosis is an urgent necessity. The Xpert MTB/RIF assay is a rapid, automated molecular test with high accuracy in PTB and EPTB detection .\u201337.11\u201337When an article reported the use of two different standards in the same study, we considered the article to include two independent studies. In accordance with this principle, 36 independent studies were included: 15 compared Xpert MTB/RIF with CRS and 21 compared Xpert MTB/RIF with culture . Twenty-The overall methodological quality of the included studies, using a CRS and culture, is summarized in 2 statistical values were 86%. Xpert MTB/RIF specificity ranged from 72% (95% CI 57\u201384%) to 100% (95% CI 97\u2013100%). Pooled specificity of Xpert MTB/RIF assay was 98% (95% CI 94\u201399%) and I2 statistical values were 89% to 97% (95% CI 83\u2013100%). Pooled sensitivity of Xpert MTB/RIF assay for LNTB was 79% (95% CI 69\u201386%) and Iwere 89% . The het2 = 67% and specificity was 91% (95% CI 78\u201396%) with I2 = 92% for 1629 FNA or tissue specimens from 21 studies with I studies . The hetWe explored the heterogeneity among studies, using subgroup and metaregression analyses on predefined subgroups of sample types, decontamination method, sample condition, and homogenization used in the assay.2 = 90%, and the pooled specificity was 96% (95% CI 90\u201398%) with I2 = 89% to 97% (95% CI 83\u2013100%) against a CRS. The pooled sensitivity was 80% (95% CI 63\u201390%) with II2 = 89% . There wI2 = 89% . Heterog2 = 52%, and pooled specificity was 89% (95% CI 65\u201397%) with I2 = 95% with I2 = 86% to 100% (95% CI 78\u2013100%) against culture. The pooled sensitivity was 90% (95% CI 83\u201395%) with II2 = 95% . While hI2 = 86% . HeterogMetaregression analysis showed that studies with FNA samples and tissue samples, compared to a CRS, showed similar sensitivity . However, studies with FNA samples, compared to a CRS, showed lower specificity (96%) than those using tissue samples (100%); the difference was statistically significant (metaregression P < 0.01). The sensitivity of studies using FNA samples was higher than that of studies using tissue samples, compared to culture (90% versus 76%); however, the difference was not statistically significant (meta-regression P = 0.43). The specificity of studies using FNA samples was lower than that of studies using tissue samples, compared to culture (89% versus 93%); this difference was also not statistically significant (metaregression P = 0.56).Metaregression analysis showed that decontamination method (with NALC-NaOH or without), sample condition (fresh or frozen), homogenization , and patient population (high/low income) did not have any effect on Xpert MTB/RIF sensitivity and specificity (meta-regression P > 0.05), compared to that in CRS. These factors were, therefore, obviously not a source of heterogeneity across the studies.Diagnosis of EPTB, including LNTB, is very challenging, due to the characteristics of a low bacterial load. In most cases, invasive examinations are necessary. For LNTB, the most commonly used invasive procedures are FNA and biopsy. Specimens obtained by different methods have different sensitivity for the diagnosis of LNTB. Sensitivity of pathological diagnosis is the highest with the most invasive biopsy specimens . FNA is Nucleic acid detection has been widely used in the diagnosis of tuberculosis . The XpeOur research found that the pooled sensitivity and specificity of Xpert MTB/RIF for LNTB were 79% (95% CI 69\u201386%) and 98% (95% CI 94\u201399%) versus CRS and 84% (95% CI 77\u201390%) and 91% (95% CI 78\u201396%) versus culture, respectively. In a meta-analysis by Denkinger et al., Xpert MTB/RIF pooled sensitivity and specificity were 81.2% (95% CI 72.4\u201387.7%) and 99.1% (95% CI 94.5\u201399.9%) versus CRS, and 83.1% (95% CI 71.4\u201390.7%) and 93.6% (95% CI 87.9\u201396.8%) versus culture for lymph node tissues or aspirates ; FNA speSample processing of lymph node specimens, such as decontamination, sample condition, and homogenization, was variable across studies, but metaregression analysis showed that these factors did not affect the result and hence were not the sources of heterogeneity. In addition, we also found the patient's financial status to not affect the outcome.According to the findings of this study, a multistep approach could be adopted for the management of suspected LNTB: FNA should be performed as the first step due to its less invasiveness, followed by complete relevant examinations, including Xpert MTB/RIF and pathological tests to improve diagnostic sensitivity. When the inspection result of the first step is negative, a more invasive technique (like biopsy) should be performed; pathological examination may be used for further validation, rather than Xpert MTB/RIF, since the assay did not increase the sensitivity of diagnosis when performed in biopsy-obtained samples.Our meta-analysis also had several limitations. We realize that we may have missed some studies, despite the comprehensive search, and some studies that failed to distinguish specimen types. In addition, some included studies used multiple sample types, which may have led to some bias in our results. In addition, sample processing of lymph node specimens was highly variable across and within studies, since the assay, designed for respiratory samples, may slightly vary for other specimens. Additionally, the CRS standard for the studies was also different. Heterogeneity among the studies was remarkable, and the pooled estimates need to be interpreted with caution.In this meta-analysis, we observed that the pooled sensitivity and specificity of Xpert MTB/RIF were 79% and 98%, respectively, when compared with a CRS, and 84% and 91%, respectively, when compared with culture. When performed on FNA samples, the pooled sensitivity and specificity were 80% and 96% versus CRS and 90% and 89% versus culture, respectively. When performed on tissue samples, the pooled sensitivity and specificity were 76% and 100% versus CRS, and 76% and 92% versus culture, respectively. There was no significant difference in the diagnostic efficiency for specimens obtained via different routes. Xpert MTB/RIF showed a good diagnostic efficiency on LNTB and was not related to the type of specimen."} +{"text": "To describe indications, clinical outcomes and complications of flexible bronchoscopy.Hospital Israelita Albert Einstein . Demographic and medical data were analyzed. Electronic medical records with incomplete data or reporting interventional procedures were excluded. A descriptive observational study of bronchoscopies performed at the endoscopy service of Over a three-year period (2013 to 2016), a total of 1,949 bronchoscopies were performed by respiratory endoscopy team and anesthesia specialists of the hospital. The mean age of patients was 57.7\u00b121.9 years (range of 3 days to 99 years), with prevalence of males (56.4%). The procedures were mostly (86.3%) elective and 30.7% were carried out in the intensive care unit. Major indications for bronchoscopy were infection or secretion (42.4%), followed by suspected neoplasm (10.8%). Endoscopic changes were reported in 91.9% of cases, with more than one change described in approximately 6.9% of patients. Positive results were obtained via direct testing or culture in 36.3% and 53.9% of 1,399 bronchoalveolar lavages, respectively. The overall diagnostic yield was 72.6%. Mild adverse event rate was 7.2%. The rate of severe adverse events requiring additional intervention was 0.5% . Lower airway endoscopy is critical for respiratory disease assessment, diagnosis and treatment. Flexible bronchoscopy is associated with good diagnostic yield and minimal inherent risk. As from 1970, the popularization of flexible bronchoscopy over rigid bronchoscopy led to a rise in the number of procedures performed and increasing availability at hospitals and outpatient clinics. Flexible bronchoscopy, a highly versatile and effective diagnostic and therapeutic tool, plays a key role in respiratory medicine. Lower airway endoscopy is aimed at anatomical assessment for diagnostic and therapeutic purposes.Respiratory endoscopy was revolutionized by the invention of the flexible bronchoscope by Dr. Ikeda, in 1968. At first, bronchoscopy was performed using a rigid instrument in highly specialized centers.1 As fi.e ., cannula replacement and intubation), foreign body retrieval, bronchial stenosis, and transplantation.Major indications are infectious conditions, such as pneumonia, bronchitis and bronchiectasis. Bronchoscopy is useful for clearance of airway secretions, relief of related airway obstructions, for diagnosis and identification of pathogens. Other indications for respiratory endoscopy comprise thoracic neoplasm, hemoptysis, airway management The scope of indications for interventional bronchoscopy currently includes tracheal or bronchial obstruction relief, mediastinal staging, dilation and others. Bronchoscopy has also experienced major advances with the advent of novel technologies, such as endoscopic laser resection, deployment of endobronchial orthoses devices, brachytherapy catheters, electrocauterization techniques aimed at hemostasis or tissue resection, therapeutic and diagnostic cryotherapy, endobronchial ultrasound (EBUS) and electromagnetic scanning, among others.,,5Limited availability is still a significant constraint for application of these novel technologies in Brazil. Also, national respiratory endoscopy data are lacking and the number of expert professionals is low.3To describe major indications, outcomes and complications of flexible bronchoscopy.Hospital Israelita Albert Einstein , in S\u00e3o Paulo (SP). Data compiled over a 36-month period (3 years), from April 2013 to April 2016, were analyzed.An observational descriptive study based on a prospective database of bronchoscopies carried out at the endoscopy service of Hospital Albert Einstei n \u2013 Morumbi unit. Electronic medical records with incomplete data or reporting interventional procedures, such as tumor resection, endoscopic ultrasound and airway dilation, were excluded.The sample comprised bronchoscopic procedures carried out at the endoscopy service of Demographic and medical data were also investigated.Hospital Israelita Albert Einstein approved this study; CAAE: 52243515.4.0000.0071.This study was limited to descriptive analysis and did not include inferential statistics. The Ethics Committee of The total of 1,949 bronchoscopies were performed over the course of three years (2013 to 2016), by the respiratory endoscopy team of the hospital. Anesthesiologists, in compliance with the institutional protocol, assisted the procedures. Anesthetic techniques ranged from sedation with spontaneous breathing to general anesthesia delivered via endotracheal intubation or laryngeal mask. The mean age was 57.7 years . This sample comprised 1,100 (56.4%) male patients.Bronchoscopic procedures involved intensive care unit (ICU) patients, outpatients or inpatients .Most procedures (86.3%) were elective, with only 13.7% of emergency bronchoscopies. Medical indications were reported in 80% of cases. The most frequent indication for bronchoscopy was suspected infection or secretion (42.4%), followed by suspected neoplasm (10.8%). More than one indication for bronchoscopy was reported in 5.7% cases .We were able to report endoscopic alterations in 91.9% of cases, with more than one described in 6.9% of patients. Upper airway changes were described in 5.5% of cases; in that, laryngitis (4.4%) and tumor lesions, such as polyps, cysts or nodules (0.7%). Bronchoscopy was normal in most patients in this sample (21.3%). Secretion was the second most common finding reported (17.4%) .Ancillary tests requested were also analyzed , culture and others). Bronchoscopic BAL was performed in 71.8% of patients; positive results were obtained via direct testing or culture in 36.3% and 53.9% of cases, respectively. Biopsies were collected from 37.6% of patients. Overall diagnostic yield, including ancillary tests (BAL and biopsy), amounted to 72.6%. Specific tests are shown in Parainfluenzae and s yncytial virus t ype B . The following viruses were detected by polymerase chain reaction (PCR) analysis: syncytial virus (five cases), herpes virus type 1 (five cases), rhinovirus (three cases) and s yncytial virus type A .Major microorganisms detected by different BAL techniques are described in Ancillary procedures performed were as follows: 732 biopsies , 132 cannula replacements and 91 endoscopic intubations. Biopsy diagnostic yield corresponded to 49%. Among the biopsies performed, the neoplasms were diagnosed in 114 (15.6%) patients; pulmonary adenocarcinoma was the most common . Other The rate of complication was 7.2% . The most commonly reported were mild and moderate adverse events as hypoxemia (oxygen saturation level less than 85%) in 4.9% of bronchoscopies, and bleeding, in 2.1%. Severe adverse events requiring additional intervention were reported in ten cases in this sample . More than one endoscopy specialist may be required in specific, exceptional situations.Bronchoscopy is a vital, well-established tool with rising attractiveness in respiratory medicine. Bronchoscopy must be properly indicated and performed in a safe and effective manner; still, it is an operator-dependent procedure and outcomes vary according to different methods and techniques.,,6 i.e ., case reports, case series or specialist opinions). Our institutional protocol directives that bronchoscopy must be carried out by at least two physicians \u2013 one respiratory endoscopy and one anesthesiologist. Topical anesthesia with 1% lidocaine is required to help control coughing, and reduces sedating drug doses. High-standard randomized trials suggest lower lidocaine concentrations are as effective as higher concentrations for cough control during bronchoscopy (level 1 evidence). Topical nasal anesthesia is thought to be more effective when 2% lidocaine gel is used (grade A recommendation).In other services, sedation may be performed by certified endoscopy specialists. Scientific evidence supporting the need for anesthesiologist participation is limited and derived from non-analytical studies ( pinions).,,7 Age per se is not a risk factor or contraindication for bronchoscopy. Most patients (30.7%) in this study were at an intensive care unit, the hospital sector where respiratory endoscopy is more often performed, with 23% of ICU patients required bronchoscopy at some point.(-)The demographic profile of patients in this sample is consistent with literature data.,,5 Bronchoscopic BAL for infection diagnosis in patients receiving mechanical ventilation is associated with oxygenation compromise and reduced oxygen partial pressure/inspired oxygen fraction (PaO2/FiO2) ratio, regardless of BAL fluid volume. Therefore, physicians must be aware of contraindications for bronchoscopy to minimize severe complications, such as hemodynamic instability, bronchospasm, severe unresponsive hypoxemia and hemorrhage. Overall, bronchoscopy is a safe procedure, when the safety precautions are taken.Major indications for bronchoscopy in ICU were infection, obstruction by secretion and atelectasis.,-8 Bronchoscopy requires special care in ICU settings, particularly in patients receiving mechanical ventilation. Bronchoscope diameter must be consistent with endotracheal tube diameter to prevent significant airflow obstruction and increased airway resistance. In non-intubated patients, the bronchoscope occupies 10 to 15% of the tracheal cross-sectional area, in contrast with 30 to 81% of the endotracheal tube cross-sectional area in intubated patients. Hence, poor scope choice may lead to respiratory comprise and interfere with aspiration of secretion and BAL collection. Endoscopists must be aware of the ratio between the bronchoscope and endotracheal tube diameter to ensure a safe, high-quality, risk-free procedure and prevent scope damage. Examples of proportions of tube cross-sectional area obstructed by different bronchoscopes are given in ,,6 In 382 patients (21.3%), the exams were normal but it does not mean without pulmonary alterations, refers only to the endoscopic features of the bronchial tree.Most of the bronchoscopies showed endoscopic alteration, in 1,410 patients (78.7%), compatible with the consulted literature.,,5 i.e ., beyond the sixth generation of branches) can only be assessed indirectly via ancillary endoscopic or imaging modalities, such as endobronchial ultrasound and radioscopy. For example: normal endoscopic findings in patients with pulmonary infiltrate or pneumonia requiring BAL or pulmonary biopsy, in the absence of endobronchial lesions.Mechanical constraints are dictated by scope diameter. The most usually used bronchoscope is 4.9mm wide. The bronchial tree is partitioned into approximately 20 generations of dichotomous branching, extending from the initial portion of the trachea to terminal bronchioles . Therefore, bronchoscopic imaging is limited to the fourth/fifth generation of branches. Distal changes In 42.4% of patients in this sample, the bronchoscopy was indicated due to infection or secretion. Direct testing and culture were positive in 36.3% and 53.9% of cases, respectively. The sensitivity of microscopy ranges from 10 to 40%, compared to 52 to 95% of BAL culture. Some microorganisms are thought to be non-pathogenic commensals, and are not regarded as positive cultures. Bronchoalveolar lavage is a sensible and specific tool for etiologic agent identification in immunocompromised patients. The diagnostic yield of different methods is organism-specific. For example, BAL has 90% to 98% sensitivity for detection of Pneumocystis jirovecii in cases with no history of therapeutic or prophylactic antimicrobial therapy. Empirical antimicrobial therapy reduces BAL sensitivity to 64%. Bilateral BAL is associated with higher diagnostic yield compared to unilateral BAL, and samples collected from upper lobes are more sensitive compared to those collected from lower or middle lobes. Bronchoalveolar lavage is as sensitive as transbronchial biopsy, and has lower inherent risk. Therefore, BAL is the diagnostic test of choice in suspected cases of P . jirovecii infection.Bronchoscopy is indicated for non-resolving or slowly resolving pneumonia in immunocompetent patients with suspected infection, particularly in smokers or former smokers aged over 50 years.2 BronLegionella , mycobacteria, fungi ( aspergillus ) and respiratory viruses. Samples for Legionella culture must be collected using distilled water to prevent inhibition of microbial growth; in all other tests and cultures, saline solution.In immunocompromised, HIV-positive patients with pulmonary infection, BAL is thought to be associated with changes of diagnosis and antimicrobial therapy in 50% and 62% of cases, respectively. Immunocompetent and immunocompromised patients were not compared in this study; still, we believe data presented may help optimize BAL performance and results.In immunocompromised patients, PCR is used in BAL for rapid diagnosis of tuberculosis, with 85.7% sensitivity and 90.9% specificity. This diagnostic strategy is useful for detection of solution.2In imAnother interesting finding in this study was the prevalence of mycobacterial and viral infections . Isolation of such agents, although uncommon in this study, suggests special attention should be given to bronchoscopy regarding the need for rooms or environments amenable to respiratory isolation prior to and after the procedure. These measures are thought to be important to avoid cross-infections between patients and for occupational safety. According to recent evidences, the expected diagnostic yield of combined endoscopically visible lesions and bronchial biopsy amounts to 90%. A minimum of five samples are required to achieve 90% diagnostic likelihood in biopsies of visible tumors. Peripheral lesions are approached via combined bronchoscopic techniques, such as BAL, biopsy and fine needle aspiration. In these lesions, size and possibility of fluoroscopic visualization are the major determinants of diagnostic yield. Positive biopsy rates range from 14% to 50% for pulmonary nodules (\u22643cm), and 46% to 80% for pulmonary masses (>3cm). Advanced techniques, such as radial probe endobronchial ultrasonography have led to significant diagnostic yield improvement in bronchoscopy of peripheral lesions . Overall diagnostic yield of bronchoscopic biopsies in this series achieved 49%, and it is consistent with literature data (<50%). In this series, the cumulative diagnostic yield of bronchoscopic procedures (BAL and biopsy) was 72.6%. The significance of combined bronchoscopy procedures for increased diagnostic yield varied according to medical indication and patient/disease characteristics.Suspected neoplasm was the second (10.8%) more common indication for bronchoscopy. Respiratory endoscopy is admittedly useful for pulmonary neoplasm diagnosis and staging. Endoscopically visible endobronchial lesions have higher diagnostic yield as compared to peripheral lesions.,,10 Severe adverse events, such as cardiac arrhythmia requiring intervention, severe hemorrhage, myocardial infarction, pulmonary edema, pneumothorax and death are uncommon. Bleeding may be categorized as traces of blood (spontaneuos resolution without continuous suctioning); mild (spontaneuos resolution with continuous suctioning of blood from the airways); moderate ; or severe .Tachycardia, bradycardia, mild bleeding, bronchospasm, laryngospasm, cough, dyspnea, sore throat and hypoxemia are common adverse events of bronchoscopy, cough being the most common.2 Seve The adverse event rate in this series corresponded to 7.2%, including two deaths (0.1%). Death cases are always worthy of revision and reflection. The indication in critical situations should always be discussed with the clinical staff and the bronchoscopist - both aware of the limits, risks and benefits of the procedure. Deaths in this study involved critically ill patients. One patient was in the semi-intensive care unit with endocarditis, septic shock, kidney failure requiring dialysis and diffuse pulmonary infiltrate. Biopsy and BAL were requested for diagnostic purposes. Bronchoscopic biopsy collection was carried out after discussing the case with the medical team. Severe bleeding occurred upon collection of the first fragment, which was difficult to control and followed by severe hypoxia. The patient was admitted to the ICU following bleeding resolution and overall stabilization, but progressed to cardiac arrest and death. The second patient suffered from severe leukemia with compromised coagulation function and hemoptysis. Bronchoscopy was indicated for bleeding control, but hypoxia progressed during the procedure. Hemoptysis was temporarily controlled; however, hypoxia persisted and the patient died in a few hours.Adverse event rates ranged from 5% to 35%. Severe complications are expected in less than 1% of patients.In this study, the rate of adverse events corresponded to 0.5%, with 0.1% mortality. Therefore, bronchoscopy may be considered a safe procedure, provided proper techniques are used and contraindications accounted for.Lower airway endoscopy is a useful, critical tool for assessment, diagnosis and treatment of several respiratory diseases. Flexible bronchoscopy should be made widely available, given the good diagnostic yield and minimal inherent risk associated with the procedure when carried out by expert professionals."} +{"text": "Staphylococcus aureus (CA-MRSA) skin and soft tissue infections (SSTIs) recurrence ranges from 16% to 43% and presents significant challenges to clinicians, patients, and families. This comparative effectiveness research study aims to disseminate, implement and evaluate whether an existing intervention, consisting of decolonization and decontamination procedures, which has been determined to be effective in hospital intensive care unit settings, can be implemented by Community Health Workers (CHWs) or \u201cpromotoras\u201d conducting home visits prevent recurrence of CA-MRSA and transmission within their households for patients presenting to primary care with SSTIs. METHODS/STUDY POPULATION: In partnership with 3 Community Health Centers and 4 community hospitals in NYC, this study will recruit patients (n=278) with confirmed MRSA SSTIs and their household members. Participants are randomized to receive either a CHW/Promotora-delivered decolonization-decontamination intervention or usual care, which includes hygiene education. The highly engaged stakeholder team meets monthly to review interim results, identify areas for refinement and new research questions, and develop and implement strategies to improve participant engagement and retention. RESULTS/ANTICIPATED RESULTS: MRSA and MSSA were found in 19% and 21.1% of wound cultures, respectively. 59.5% with MRSA+ wound culture had one or more MRSA+ surveillance culture; 67.8% with MSSA+ wound culture had one or more MSSA+ surveillance culture. The \u201cwarm handoff\u201d approach, developed and implemented by the stakeholder team to engage patients from their initial consent to return of lab results and scheduling of the home visits, helped improve completion of baseline home visits by 14%, from 45% to 59% of eligible participants. Home visits have demonstrated that 60% of households had at least one surface contaminated with S. aureus. Of the surfaces that tested positive in the households, nearly 20% were MRSA and 81% were MSSA; 32.5% of household members had at least one surveillance culture positive for S. aureus . DISCUSSION/SIGNIFICANCE OF IMPACT: This study aims to understand the systems-level, patient-level, and environmental-level factors associated with SSTI recurrence and household transmission, and to examine the interactions between bacterial genotypic and clinical/phenotypic factors on decontamination, decolonization, SSTI recurrence and household transmission. This study will evaluate the barriers and facilitators of implementation of home visits by CHWs in underserved populations, and aims to strengthen the weak evidence base for implementation of strategies to reduce SSTI recurrence and household transmission.OBJECTIVES/SPECIFIC AIMS: Community-associated methicillin-resistant"} +{"text": "Seven urogenital specimen types obtained from 1,778 females, aged 15 to 74\u2009years, and 1,583 males, aged 16 to 82\u2009years, were tested with the Aptima Mycoplasma genitalium assay, an investigational transcription-mediated amplification (TMA) NAAT for the detection of M. genitalium 16S rRNA. Infected status for enrolled subjects was established using results obtained from testing either self-collected vaginal swab or clinician-collected male urethral swab specimens with a composite reference method consisting of three transcription-mediated amplification NAATs targeting unique regions of M. genitalium 16S or 23S rRNA. M. genitalium prevalence was 10.2% in females and 10.6% in males; prevalence was high in both symptomatic and asymptomatic subjects for both sexes. Compared to the subject infected status standard, the investigational test had sensitivity and specificity estimates, respectively, of 98.9% and 98.5% for subject-collected vaginal swabs, 92.0% and 98.0% for clinician-collected vaginal swabs, 81.5% and 98.3% for endocervical swabs, 77.8% and 99.0% for female urine, and 98.2% and 99.6% for male urethral swabs, 88.4% and 97.8% for self-collected penile meatal swabs, and 90.9% and 99.4% for male urine specimens. For all seven specimen types, within-specimen positive and negative agreements between the investigational test and the composite reference standard ranged from 94.2% to 98.3% and from 98.5 to 99.9%, respectively. These results provide clinical efficacy evidence for the first FDA-cleared NAAT for M. genitalium detection in the United States.A prospective multicenter clinical study involving subjects from 21 sites across the United States was conducted to validate the performance of a new Mycoplasma genitalium is a fastidious bacterium in the class Mollicutes. Its minute 580-kb genome is the smallest known among prokaryotes capable of self-replication . Slow grs method . Nucleic method 59. Since d rectum \u201320. An ated also . Increasfloxacin , 23, thereviewed .Mycoplasma genitalium (AMG) assay, an in vitro diagnostic (IVD) transcription-mediated amplification (TMA) assay that targets the 16S RNA of M. genitalium, has led to its experimental use to study the epidemiology and clinical outcomes associated with infection with the organism, as well as to a comparison with other molecular amplification assays and Good Clinical Practice Guidelines (cGCP) set forth by the International Conference on Harmonization (ICH-E6). The study protocol (A10109-MGENPS-CSP-01) was approved by the local institutional review board at every site. Written informed consent was obtained from each subject at the time of enrollment, prior to specimen collection. Participants were compensated for study participation.Sexually active female and male subjects of \u226514\u2009years of age with (symptomatic) or without (asymptomatic) symptoms of sexually transmitted infections (STIs) were eligible for enrollment. Subjects were enrolled at 21 U.S. sites between July 2017 and April 2018. Exclusion criteria included antibiotic treatment within 21\u2009days of enrollment or previous enrollment in this study.Four specimens were collected in the clinic from each female subject in the following order: one self-collected first-catch urine specimen, one self-collected vaginal swab specimen, one clinician-collected vaginal swab specimen, and one clinician-collected endocervical swab specimen. Three specimens were collected in the clinic from each male subject in the following order: one self-collected penile meatal swab specimen, one clinician-collected urethral swab specimen, and one self-collected first-catch urine specimen. Vaginal and penile meatal specimens were collected using Aptima multitest swabs and placed in Aptima tubes containing specimen transfer medium (STM). Urethral and endocervical specimens were collected using an Aptima unisex swab and placed in Aptima tubes containing STM. First-catch urine specimens were processed for testing using an Aptima urine specimen collection kit and placed in Aptima tubes containing urine transport medium (UTM).M. genitalium; the Alt TMA assay-1 detected a different region of the 16S rRNA than the AMG assay. All three Alt TMA assays have similar analytical and clinical sensitivities assays and three alternate (Alt) TMA assays used for the composite reference standard have been described previously . All spetivities . Alt TMAtivities . OperatoPrevalence (based on reference test result and patient infected status [PIS]), sensitivity, specificity, positive predictive value, and negative predictive value were calculated according to standard equations . ConfideM. genitalium . The PIS was based on reference (composite Alt TMA assay) results from testing of the urethral swab sample for male subjects and of the patient-collected vaginal swab sample for female subjects; based on prior studies, vaginal swab and urethral samples are the most sensitive specimen types for the detection of nitalium , 36, 37.n = 6,880) and three male specimen types .M. genitalium prevalence for each group, are shown in M. genitalium prevalence was 11.6% and 7.9% among symptomatic and asymptomatic subjects, respectively; for males, M. genitalium prevalence was 12.0% and 8.8% among symptomatic and asymptomatic subjects, respectively. The highest prevalence of infection was in young adults of both sexes aged 18 to 20\u2009years .Demographic characteristics of enrolled subjects for sex, age, and race/ethnicity, as well as symptom status and M. genitalium prevalence and the clinical performance of the investigational assay for the detection of M. genitalium are shown in M. genitalium was similar for clinician-collected vaginal swabs, patient-collected vaginal swab, endocervical swab, and female urine specimens and for urethral swab, penile-meatal swab, and male urine specimens .The M. genitalium-infected subjects was \u226590% for clinician- and patient-collected vaginal and male urethral swab specimens and male urine specimens, 88.4% for penile-meatal swab specimens, 81.5% for endocervical specimens, and 77.8% for female urine specimens. Overall specificity was \u226597.8% for all specimen types. The combination of investigational and reference assay M. genitalium results for all subjects with a conclusive PIS status and valid AMG assay results are shown in Tables S1 and S2 in the supplemental material for female and male urogenital specimens, respectively. Sensitivity and specificity estimates were similar in asymptomatic and symptomatic subjects for each specimen type. Assay performance was similar among races and ethnicities for each specimen type (Tables S3 and S4).Overall sensitivity of the investigational test for detection of M. genitalium detection for performance comparison, positive (PLR) and negative (NLR) likelihood ratios were also calculated. By symptom status, estimates of the PLR in female specimen types ranged from 39.0 for clinician-collected vaginal swab specimens from symptomatic subjects to 465.2 for female urine specimens from asymptomatic subjects. For male specimens, PLR estimates ranged from 40.0 for penile meatal swab specimens from symptomatic subjects to 747.4 for urethral swab specimens from symptomatic subjects. For all specimen types, NLR ratios were less than 0.26. Together, these results demonstrated highly relevant and statistically significant increases in knowledge based on positive and negative AMG assay results in all specimen types.In the absence of results from FDA-approved assays for To investigate the effect of the clinical specimen matrix on investigational assay performance for specimens other than the male urethral swab and self-collected vaginal swab, a comparison of AMG assay and Alt TMA assay results within the same specimen type was performed . InfecteM. genitalium in more than one specimen type . However, for both female and male subjects, a minority of subjects had positive AMG assay results in only one sample type . Most subjects had positive AMG results for two or more specimen types; 121 (55.8%) females and 138 (68%) males reported positive AMG results in all specimen types assessed.Receiver operating characteristic (ROC) curve analysis was performed on the female and male urogenital specimens . The areMycoplasma genitalium assay for detection of M. genitalium. These results provide clinical efficacy evidence for the first IVD NAAT for M. genitalium detection in the United States. Following completion of this study, the assay received FDA clearance (510k# DEN180047) for the detection of M. genitalium in patient- and clinician-collected urogenital specimens from symptomatic and asymptomatic subjects, including minors. The FDA clearance will now allow laboratories to test for M. genitalium in a wide variety of urogenital specimens without having to develop and validate laboratory-developed tests and/or diagnostic accuracy (sensitivity and specificity) estimates associated with some specimen types such as female urine may be due to anatomic site-specific infections rather than specimen matrix effects on assay performance.M. genitalium is sexually transmitted, there is wide discrepancy in the prevalence detected in the general population compared to the prevalence in patients seeking care from many types of clinics. In lower-risk populations, an M. genitalium prevalence of approximately 1% to 3% has been reported in both men and women (\u2013M. genitalium is associated with disease and the future development of adverse sequelae. In this AMES study, the prevalences in symptomatic males and females were 12% and 11.6%, respectively, whereas, in asymptomatic persons the prevalences were 8.8% and 7.9%, respectively, demonstrating a prevalence not very different from the prevalence of chlamydia in symptomatic women seen in many health care settings. There are many observational reports that disease manifestations of persistent urethritis (40\u2013M. genitalium detection in males and females. An unmet need for understanding the public health significance of infection with M. genitalium includes prospective trials that demonstrate that screening and treating asymptomatic persons prevents adverse reproductive sequelae in women and persistent urethritis and sequelae in asymptomatic men although such studies are likely to be costly.While there is little debate that nd women , 39. In nd women \u201316. The ethritis , cerviciethritis , 40\u201342, ritis 40\u2013, 43, 44 M. genitalium to azithromycin, the first-line antibiotic used to treat urogenital infections (M. genitalium, where standard syndromic treatment may fail (\u2013M. genitalium as part of the larger antibiotic stewardship efforts needed for the clinical management of all STIs.A major concern with the increasing use of diagnostic testing and treatment of infected patients is the high antibiotic resistance of fections , 31, 33.may fail \u201348. It wM. genitalium infection and transmission, and we do not have coinfection data for other STIs. Additionally, there is no information about the antibiotic resistance status of M. genitalium-positive subjects, which is an important clinical consideration (46\u2013Our study has limitations. We did not collect oropharyngeal or rectal specimens, potentially important sources of deration , 46\u201348. M. genitalium rRNAs, eliminating potential bias due to differences in sensitivities between the investigational test and reference assays (Strengths of this study include adherence to cGCP regulations to enroll a large, diverse cohort from six geographic areas of the United States, including 15 states and the District of Columbia and representing patients attending multiple clinical practice types. In addition, multiple sample types were collected from each patient, providing clinicians options for patient management. Finally, the composite reference standard used in this study consisted of a consensus result from three validated TMA assays targeting e assays .M. genitalium urogenital infections in men and women using cervical, vaginal, urethral, penile-meatal, and urine specimens. Future research will be required to further define the pathogenicity of M. genitalium, the best treatment algorithms, and its significance when detected in asymptomatic persons.In summary, we now have an FDA-cleared IVD assay that can be used to detect"} +{"text": "In a multivariable regression analysis increase in SOFA score, increased number of SIRS criteria and the use of the official sepsis screening tool were associated with antibiotic administration, however obtaining microbiology cultures was not. Our study shows that antibiotics prescription practice is not accompanied by microbiological investigations. A significant proportion of sepsis patients are still at risk of not receiving appropriate antibiotics treatment and microbiological investigations; this may be improved by a more thorough implementation of sepsis screening tools.Recent description of the microbiology of sepsis on the wards or information on the real-life antibiotic choices used in sepsis is lacking. There is growing concern of the indiscriminate use of antibiotics and omission of microbiological investigations in the management of septic patients. We performed a secondary analysis of three annual 24-h point-prevalence studies on the general wards across all Welsh acute hospitals in years 2016\u20132018. Data were collected on patient demographics, as well as radiological, laboratory and microbiological data within 48-h of the study. We screened 19,453 patients over the three 24 h study periods and recruited 1252 patients who fulfilled the entry criteria. 775 (64.9%) patients were treated with intravenous antibiotics. Only in 33.65% (421/1252) of all recruited patients did healthcare providers obtain blood cultures; in 25.64% (321/1252) urine cultures; in 8.63% (108/1252) sputum cultures; in 6.79% (85/1252) wound cultures; in 15.25% (191/1252) other cultures. Out of the recruited patients, 59.1% (740/1252) fulfilled SEPSIS-3 criteria. Patients with SEPSIS-3 criteria were significantly more likely to receive antibiotics than the non-septic cohort ( Sepsis, defined as dysregulated host response leading to life threatening organ dysfunction secondary to infection, has been thought to contribute significantly to in-hospital mortality ,2. RecenThe early administration of resuscitation bundles, including appropriate antibiotics, has been demonstrated to improve patient outcomes . This haDespite the evidence of the potential benefit of these initiatives, there is growing concern surrounding the indiscriminate use of antibiotics and omission of microbiological investigations in patient management ,12,13. AIn light of these controversies, the primary objective of the study was to investigate antibiotic prescribing practices on general wards and emergency departments (ED) in at-risk population of patients in acute hospitals in Wales. The secondary objective was analysis of outcomes of microbiological investigations of sepsis patients using our comprehensive database.Secondary analysis of patient episodes was performed on the patient population recruited into three annual 24-h point-prevalence studies on the general wards and ED across all Welsh acute hospitals in the years 2016, 2017 and 2018. In order to be entered into the study, each hospital was required to have a 24/7 consultant supervised ED and the ability to admit and treat any acutely unwell patient. We recruited patients with National Early Warning Score (NEWS) \u22653 and proven or suspected infection documented in the clinical notes. Those who were under 18, in mental health or critical care units were excluded as these patients are not covered by the NEWS system in the Welsh hospitals.Data were collected using a digital platform, the methodology and performance of which is described in detail in our previous studies ,14. The www.isrctn.com (ISRCTN86502304). Ethical approval was given by the South Wales Regional Ethics Committee (16/WA/0071). Written informed consent was gained from each patient, or by proxy for those who lacked capacity. The trial was registered prospectively at p-value < 0.05 was considered statistically significant. To identify factors associated with antibiotic administration we performed a multivariable logistic regression analysis with backwards elimination method, using antibiotic administration as a dependent variable. The likelihood ratio test was used in the backward elimination method using a significance level of p-value < 0.05. We only considered the main effects in this analysis; interaction terms were not included in the model. We determined the goodness-of-fit of the model using the Hosmer\u2013Lemeshow test. The results of the multivariable analysis are shown as odds ratios (OR) and 95% confidence interval (95% CI). All statistical tests were calculated using SPSS 25.0 .Categorical variables are described as proportions and are compared using the Chi-square test. Continuous variables are described as median and inter-quartile range. A two-tailed We screened 19,453 patients over three 24-h point-prevalence study periods in 14 acute hospitals in Wales in 2016, 2017 and 2018. We recruited 1252 patients who fulfilled the study criteria. Patient characteristics are summarised in Out of 1,195 patients, 775 (64.9%) were treated with intravenous (IV) antibiotics. Majority of patients were treated with one IV antibiotic . The antibiotics used were broad spectrum, with Piperacillin/Tazobactam (Tazocin) being the most commonly prescribed . The most frequently prescribed antibiotics are presented in E. coli (17 out of 421 cultures) and Gram-positive cocci (16 out of 421 cultures), the latter most commonly interpreted as contamination. None of the organisms were characterized as multi-resistant. Detailed microbiological results are presented in The vast majority of patients did not undergo microbiological investigations. Only in 33.65% (421/1252) of all recruited patients did healthcare providers obtain blood cultures; in 25.64% (321/1252) urine cultures; in 8.63% (108/1252) sputum cultures; in 6.79% (85/1252) wound cultures; and in 15.25% (191/1252) other cultures. The yield of the cultures was very low with positive result in only 13.06% (55/421) blood cultures, 13.71% (44/321) urine cultures, 45.37% (49/108) sputum cultures, 32.94% (28/85) wound cultures and 8.90% (17/191) other cultures. The most commonly identified organism in blood cultures was p < 0.0001) fulfilled SEPSIS-3 criteria of Sequential Organ Failure Assessment (SOFA) score of two or above. Patients with SEPSIS-3 criteria were significantly more likely to receive antibiotics than the non-septic cohort (490/740 of septic patients received antibiotics in comparison to 285/512 non-septic patients 0.0001) . Neverthp < 0.0001 and p = 0.04, respectively). No significant difference in sputum, wound or other microbiological investigations was noticed for this cohort. On the other hand, a significant proportion of patient who underwent investigations did not receive antibiotics. We found that 28.74% (121/421) of patients with blood, 35.19% (38/108) sputum, 34.65% (111/321) urine and 40.57% (71/175) other cultures were not prescribed any antibiotics. Further details on how the presumed site of infection influenced antibiotic therapy and microbiology investigations is provided in Analysing only patients who received antibiotics, we found that 49.75% (300/603) had blood cultures, 13.81% (70/507) had sputum cultures, 35.47% (210/592) had urine cultures, 9.01% (53/588) had wound cultures and 13.42% (104/775) had other microbiological investigations. We also found that patients who received antibiotics were more likely to have obtained blood and urine cultures in comparison to the patients with no antibiotic treatment (p < 0.0001) and to have blood culture (p = 0.001) but no other microbiological investigations.We also investigated whether the use of official screening tools had an impact on antibiotic prescription practice. We found that the screening tools have been completed for only 17.7% (221/1252) of patients, despite high NEWS score and documented suspicion of infection. Interestingly, the screened patients were significantly more likely to receive antibiotics in comparison to non-screened patients , increased number of SIRS criteria present and completion of the official screening tool were independently associated with antibiotic administration, however increased frailty score or microbiological sample collection was not.Our study shows that antibiotic prescription practice for patients with suspected sepsis is not accompanied by microbiological investigations. The majority of recruited patients with suspicion or confirmed infection, did not undergo microbiological investigations and were prescribed broad spectrum antibiotics.Our study highlights the current practices of antibiotics prescribing in an era when awareness of sepsis is raised and in a healthcare system which has adopted a nation-wide screening tool and escalation process for the condition . PatientThe implementation of the sepsis bundles both within the UK and internationally have highlighted a potential drawback of the \u201ctreat first, ask questions later\u201d approach, which fails to take into account the several factors which could influence the bedside clinicians, resulting in less than ideal practice ,6. FirstClostridium difficile diarrhoea [Early identification of the infectious organism could allow more targeted and effective treatment. This could also facilitate the use of antibiotics with narrower spectra or early antibiotics switching instead of using broad-spectrum antibiotics, an approach advocated in sepsis for over a decade ,25. Cliniarrhoea . In a priarrhoea . This miiarrhoea .The lack of microbiological investigations could be influenced by the low yield of detection of organisms of the gold standard\u201d microbiological investigations. In our study, the yield of blood cultures, which are a part of Sepsis Six bundle, was only 13.06%, similar to other reports ,30,32. TThe strengths of our study include the participation of centres all across Wales, including both academic and general district hospitals, as well as using prospective data collection methods, resulting in a clinically rich and complete dataset.Our study has some limitations. Firstly, patients with sepsis who had NEWS below 3 could have been missed and not recruited into our study ,34. HoweIn conclusion, a significant proportion of sepsis patients are still at risk of not receiving appropriate antibiotics treatment and microbiological investigations. This could be improved by a more thorough implementation of sepsis screening tools. In addition, adopting both SIRS and SOFA clinical criteria may help to identify the high-risk population, where microbiological investigations should accompany appropriate antimicrobial therapy."} +{"text": "This study was performed to investigate the effects of supplementing sesame seed meal (SSM) with phytase and lysine on performance, egg quality, blood biochemical and antioxidant status of laying hens.A total of 960, 56-wk-old laying hens were divided into 12 dietary groups with eight replicates per group (10 birds per replicate). A completely randomized design with factorial arrangement 2\u00d73\u00d72 consisted of two levels of lysine supplement (0% and 10% over requirement), three SSM levels with or without phytase (0 and 300 g/ton). The feeding trial lasted 10 weeks.Birds fed diets with 10% SSM had higher feed intake than groups fed 0% and 20% SSM. The addition of phytase to experimental feeds, improved feed conversion ratio, increased egg weight and mass (p<0.01). Egg quality criteria was not affected by supplementing phytase; however, supplementing 300 g/ton phytase to hens diet, led to a significant (p<0.05) increase in egg shell strength. Egg yolk cholesterol and serum low-density lipoprotein cholesterol, atherogenic index and total cholesterol were decreased (p<0.01) by diet containing 20% SSM. The high-density lipoprotein cholesterol was increased (p<0.05) in serum of hens fed 20% SSM than the other groups. It was also observed that total antioxidant capacity and total superoxide dismutase content of hens fed 20% SSM was significantly higher than control group (p<0.05).As from results, dietary supplementation of SSM and phytase had no negative effects on laying hens performance or egg quality while improving the egg oxidative stability. The main constraint racing the poultry industry is the feed cost, which approximately represents 75% of the total cost production. Soybean meal (SBM) is the main protein source in poultry rations given its high nutritional value, and most of the Asian countries, including Iran, import this feed ingredient. Therefore, cottonseed, rapeseed, sunflower and sesame meals have been suggested as alternative protein sources for poultry diet .Sesame indicum L) seed is one of the most important oil crops and is composed of 45% to 50% lipid, 15% to 20% protein, and 10% to 15% carbohydrates \u00d7100). Haugh unit was calculated with following formula where the HA is albumen height and WE is egg weight . Serum lipid peroxidation (LP) was determined using the method proposed by Kei [Antioxidant capacity, including total antioxidant capacity (T-AOC), total superoxide dismutase (TSOD) and glutathione peroxidase (GSH-Px) was determined in serum samples using RANDOX kits according to the manufacturer\u2019s instruction. Serum TSOD activity was assayed by the xanthine oxidase method , which md by Kei and Yagid by Kei , but witData were subjected to one-way analysis of variance (ANOVA) with 12 treatments and eight replicates having 10 hens in each replicate. Data obtained were submitted to ANOVA using the general linear model procedure of SAS software . Means wThe effects of experimental diets on performance and egg parameters of laying hens are shown in The findings of the present study indicate that dietary supplementation with 20% SSM decreased feed consumption of laying hens. In contrast to this study, Cheva-Isarakul and Tangtaweewipat and MampPhytase addition to diets affected on egg weight, egg mass and FCR, which is consistent with the results reported by Um and Paik who repoIn conclusion, considering the laying hens feed consumption and FCR, the most suitable SSM level in diet was 10% having also no negative effects on performance or egg quality. Further, the present findings indicated that phytase addition improved hens performance and egg quality traits. Egg yolk cholesterol level could be reduced up to 5% by supplementing 20% SSM. Therefore, based on our results, SSM at 20% is of interest as a potential egg cholesterol-lowering agent, which would be helpful for the marketing of eggs and egg products. The addition of 20% SSM to the laying hen diet led also to an increase in serum TSOD activity and T-AOC amount. At the same time, the oxidative stability of egg was improved by SSM supplementation, and this may favorably influence the shelf life of eggs."} +{"text": "Background and objectives: Chronic kidney disease (CKD)-associated pruritus is a common and disturbing condition which has a negative impact on sleep quality, as well as overall health-related quality of life of patients receiving hemodialysis. To date, no systematic review has been undertaken, and there is a lack of concise evidence that statistically quantifies the impact of pruritus based on published data. Materials and Methods: A systematic search was done for original articles published in peer-reviewed English journals from database inception on 20 December, 2018, in the following databases: PubMed, MEDLINE, EMBASE, Ovid, CINHAL, ProQuest, and Scopus. Results: A total of 9217 research articles were identified. After removal of duplicates and screening for titles and abstracts, 28 articles were selected. The prevalence of disturbed sleep was 4\u201394%, while the pooled proportion on random effect in the study was 40% (95% CI = 0.30 to 0.49); I2 = 99.8%. However, the prevalence of disturbed sleep quality and quantity due to pruritus was 9\u201376%, and the pooled proportion on random effect in the study was 50% (95% CI = 0.37 to 0.64); I2 = 99.8%. Conclusions: Patients undergoing hemodialysis who are affected by CKD-associated pruritus have a higher chance of experiencing sleep disturbances. The prevalence of disturbed sleep due to CKD-associated pruritus was found to be 9\u201376% in the included studies for patients receiving hemodialysis therapy. Chronic kidney disease (CKD) is a major public health dilemma worldwide . CKD-assDue to the impact of CKD-aP on patients, and the challenges associated with its treatment, it would seem imperative to quantify the likelihood of CKD-aP among patients undergoing hemodialysis. Moreover, it will be of great worth to explore the impact of CKD-aP on the sleep quality of patients undergoing hemodialysis. To date there is no systematic review and a lack of concise evidence that statistically quantifies the impact of CKD-aP based on published data. Our objective is to therefore evaluate the prevalence of sleep disturbance and CKD-aP among hemodialysis patients. Findings can be used to ensure that appropriate and timely measures can be planned to improve the HRQOL of these patients, a factor which is often overlooked in clinical settings . TherefoA systematic review was conducted to explore the impact of CKD-aP on the sleep quality of patients undergoing hemodialysis. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed to identify potential research articles from evidence-based scientific literature (PRISMA Statement) . The proPubMed, MEDLINE, EMBASE, Ovid, CINHAL, ProQuest, and Scopus were searched for potential papers from database inception to 20 December, 2018.The strategic search terms used medical subject headings (MeSH) and keywords, and the following text terms were combined with Boolean operators: (uremic* OR Skin Disorder OR Rash* OR Itch* OR Pruritus OR Uremia*) AND AND AND .Original research articles using observational or experimental designs, published in peer-reviewed English journals and exploring the impact of CKD-aP on sleep quality among CKD patients undergoing hemodialysis.All systematic reviews, case reports, advertisements, thesis, opinions, letters to the editor, and qualitative studies, were excluded. In addition, studies which reported on, or data on any other form of pruritus due to factors other than CKD, were excluded.Data were extracted using a standardized extraction form designed for this systematic review. The following information was extracted: author\u2019s name, publication year, study design, country, respondent\u2019s information, inclusion/exclusion criteria for the selection of respondents, sample size, statistical analysis used, and outcome measurements of the impact of CKD-aP on sleep quality and quantity. The Cochrane risk of bias criteriap-values were set at <0.05 with 95% confidence intervals. Subgroup analysis was performed to address heterogeneity. I2 statistic was used to interpret the heterogeneity at a confidence interval of 95% among the included studies.For the risk of bias, RevManger 5.3\u00ae was used to generate a graphical presentation of the included trials. A meta-analysis was performed using STATA version 14 using the random effects model. All A total of 9217 related research articles were identified. After removal of duplicates, the final count reduced to 8054. After reviewing titles and abstracts, 777 were selected, and from these, 28 articles were included in this systematic review after the application of the inclusion and exclusion criteria ,43,44,45The study characteristics are shown in 2 = 99.8% , and in clinical trials it was 74% (95% CI = 0.52 to 0.96). The pooled proportion on random effect found prevalence of sleep disturbance for studies conducted in Asia was 50% (95% CI = 0.38 to 0.62) and the heterogeneity was 99.0%; whereas the pooled proportion on random effect for studies conducted in Europe was 25% (95% CI = 0.19 to 0.32) and the heterogeneity was 80.1%. The pooled proportion on random effects revealed the prevalence of sleep disturbance in cross sectional studies was 32% (95% CI = 0.19 to 0.45); I2 = 99.3% in Europe. Subgroup analysis based on sample size showed a pooled proportion of 42% (95% CI = 0.15 to 0.70); I2 = 97.3% for sample size less than 200, while for sample size more than 200 showed a pooled proportion of 55% (95% CI = 0.38 to 0.71); I2 = 99.0%.The results of the subgroup analysis on the basis of geographical regions among selected studies ,42,43,44The quality assessment of observational studies was assessed using NOS . The mea2 = 99.8%, while in patients suffering from CKD-aP, 50% of them were observed to have sleep disturbances with a pooled proportion of 50% (95% CI = 0.37 to 0.64); I2 = 99.8%. This emphasizes the need to routinely assess CKD-aP and sleep quality. This is to allow suitable and timely interventions to be carried out to address these problems, which are very frequent among CKD patients on hemodialysis.This systematic review and meta-analysis is perhaps the first systematic and quantitative assessment to assess the impact of CKD-aP on sleep quality among CKD patients undergoing hemodialysis. Results from the meta-analysis revealed the proportion of hemodialysis patients suffering from sleep disturbance, regardless of whether they have CKD-aP or not, was 40% (95% CI = 0.30 to 0.49); IThe heterogeneity in the prevalence data may be due to the different study design, selection of participants , and the definition of CKD-aP in the included studies. Another meta-analysis on the prevalence of CKD-aP among adult hemodialysis patients also previously reported high heterogeneity in the subgroup analysis .Studies showed a high prevalence of CKD-aP with 85.4% and 53.4Therefore, from a clinical practice point of view it is important to assess patients for the severity of CKD-aP and intervene therapeutically to improve the HRQOL and overall wellbeing of the patients. CKD-aP is often overlooked by nephrologists, primary care physicians, and other health care professionals and thisThere was high heterogeneity in the pooled analysis; this could be due to varied sample size, population characteristics, race, difference in study designs, diverse tools/questionnaire used for assessment of CKD-aP as well as sleep assessment and the definition of CKD-aP in the included studies. Despite performing sub-group analysis, the heterogeneity remained high and that is the major limitation of this study.In conclusion, sleep quality is disturbed to a great extent by CKD-aP in patients receiving hemodialysis. The prevalence of disturbed sleep due to CKD-aP was found to be 9\u201376% in the included studies; establishing evidence of impaired sleep quality. More research is needed to establish suitable data using specific tools for determining CKD-aP and sleep quality for quantitative analysis. Among health care providers, CKD-aP should be treated with equal importance as other complications to improve patient\u2019s HRQOL, and to relieve itching to avoid secondary infections due to persistent scratching."} +{"text": "Since 2012, Middle East respiratory syndrome (MERS) coronavirus has infected 2,442 persons worldwide. Case-based data analysis suggests that since 2016, as many as 1,465 cases and 293\u2013520 deaths might have been averted. Efforts to reduce the global MERS threat are working, but countries must maintain vigilance to prevent further infections. Furthermore, we obtained the expected total number of cases in 2016, 2017, and through September 2018, conditional on the incidence of community-acquired cases, by simulating 10,000 times from the distribution of human-to-human\u2013transmission cluster sizes observed during 2014\u20132015. Thus, the observed incidence rates in these years could be compared with simulations to test the null hypothesis that human-to-human transmission levels remained constant since 2014\u20132015 . The intervals reported are the 2.5th and 97.5th percentiles of the simulations (95% CIs). We examined a range of mortality rates from healthcare-associated outbreaks in South Korea and Saudi Arabia . The incidence of community-acquired cases was 177 in 2016, 151 in 2017, and 86 through September 2018 Table. TThe total number of cases averted, when simultaneously taking into account reduced camel-to-human and human-to-human transmission, was estimated at 507 (95% CI 189\u2013967) in 2016, 507 (95% CI 189\u2013967) in 2017, and 451 (95% CI 191\u2013855) through September 2018, totaling 1,465 cases averted and 293 (95% CI 179\u2013433) expected deaths averted (under the assumption of a 20% CFR) from 2016 through September 2018. Assuming a 35.5% CFR, this estimate corresponds to 520 (95% CI 318\u2013769) expected deaths averted.We believe that affected countries are reducing the global threat of MERS by addressing knowledge gaps with regard to transmission, enhancing surveillance, and strengthening the ability to detect cases early and contain outbreaks through improved infection prevention and control measures in hospitals. Critical for preventing international spread and sustained transmission have been improved prevention and control measures in hospitals, restriction of camel movement in affected areas, stronger and more comprehensive investigations of cases and clusters, and improved communication.Although global efforts seem to have prevented hundreds of infections and deaths, vigilance must be maintained by all countries. More needs to be done to limit spillover infections from dromedaries, which requires stronger surveillance of dromedary populations and persons in direct contact with infected herds and accelerated development of a vaccine for dromedaries (Supplementary information about study of worldwide reduction in MERS cases and deaths since 2016."} +{"text": "Hydroxychloroquine (HCQ) retinopathy may be more common than previously recognized; recent ophthalmology guidelines have revised recommendations from ideal body weight (IBW)-based dosing to actual body weight (ABW)-based dosing. However, contemporary HCQ prescribing trends in the UK remain unknown.We examined a UK general population database to investigate HCQ dosing between 2007 and 2016. We studied trends of excess HCQ dosing per ophthalmology guidelines (defined by exceeding 6.5\u00a0mg/kg of IBW and 5.0\u00a0mg/kg of ABW) and determined their independent predictors using multivariable logistic regression analyses.p\u2009<\u20090.01). Long-term HCQ users showed similar excess dosing.Among 20,933 new HCQ users , the proportions of initial HCQ excess dosing declined from 40% to 36% using IBW and 38% to 30% using ABW, between 2007 and 2016. Among these, 47% of women were excess-dosed using IBW and 38% using ABW. Applying IBW, 37% of normal and 44% of obese patients were excess-dosed; however, applying ABW, 53% of normal and 10% of obese patients were excess-dosed ; both A substantial proportion of HCQ users in the UK, particularly women, may have excess HCQ dosing per the previous or recent weight-based guidelines despite a modest decline in recent years. Over half of normal-BMI individuals were excess-dosed per the latest guidelines. This implies the potential need to reduce dosing for many patients but also calls for further research to establish unifying evidence-based safe and effective dosing strategies.The online version of this article (10.1186/s13075-018-1634-8) contains supplementary material, which is available to authorized users. Hydroxychloroquine (HCQ) is commonly prescribed in patients with systemic lupus erythematosus (SLE) and remains a cornerstone of lupus care today , 2, and Although HCQ is generally well-tolerated, the major long-term adverse event is vision-threatening toxic retinopathy , 11. RatTo understand recent prescribing trends in the UK and to elucidate the predictors of potential excess dosing, we assessed HCQ prescribing patterns in relation to the previous and latest HCQ dosing guidelines , 20, 26 Our study cohort was derived from The Health Improvement Network (THIN), an electronic medical record (EMR) database which represents 6.2% of the UK population, including over 11 million patients. THIN database is representative of the general UK population in terms of demographics, lifestyle factors, and healthcare utilization . HealthcWe identified all subjects age 18 years or older within THIN with incident HCQ prescriptions between 1 January 2007 and 31 December 2016. We divided these cohorts into five 2-year blocks each, based on index date, determined by the date of first documented HCQ prescription. We required \u22651 year of subject inclusion in THIN prior to the index date to be considered an incident prescription.We determined information from the most recent available data prior to the index date on age, sex, lifestyle , and anthropometric characteristics . We calculated body mass index (BMI) and IBW using the commonly used Devine formula , 31, as We identified the incident HCQ prescription dose for the primary analysis. We also obtained overall HCQ prescription dose, assessing the first prescription dose in a given calendar year for each subject. We classified the weight-based excess HCQ dose according to recommended safe doses per IBW , 27, andTo examine the dosing trends according to the duration of use, we obtained the initial HCQ prescription dose and the HCQ prescription dose at 5 years of treatment for a subgroup of subjects with at least 5 years of HCQ use. We similarly classified their 1st and 5th year prescription doses according to recommended doses per ABW and IBW.We compared the baseline characteristics of individuals at the index date of their incident HCQ prescriptions according to calendar year categories. We calculated the proportion of incident HCQ prescriptions exceeding either IBW or ABW maximum safe dose over the five 2-year cohort blocks and described the secular trends. We examined the relationship between age, sex, BMI, CKD, and indication for HCQ use and the risk of prescribed HCQ dose exceeding each safe dose for IBW or ABW, respectively, using a multivariable logistic regression model. The final multivariable model was adjusted for age, sex, BMI, CKD, indication for HCQ use, smoking, tamoxifen use, diabetes mellitus, and calendar year.We calculated median and interquartile ranges for initial HCQ dose per IBW and ABW at 6-month intervals between 2007 and 2016 and performed quantile regression to assess the median value trends. Furthermore, we calculated the proportion of different HCQ dose categories comprising overall initial HCQ doses over this same timeframe. We also calculated the proportion of these dose categories comprising overall HCQ doses over this timeframe.2. RA was the most common indication for HCQ use (56%), 2257 subjects (11%) had SLE, and 1572 (8%) had CKD \u2265 stage 3.During the 10-year period between 2007 and 2016, 20,933 individuals initiated HCQ ) and from 38% to 30% per ABW-based dosing ) . Using the ABW-based recommended dose, 38% of women and 25% of men had excess dosing, which led to a multivariable OR of 1.98 (Table p\u2009=\u20090.40); 37% and 33% had excess dosing by ABW for the initial dose and at 5\u00a0years, respectively (p\u2009=\u20090.53).Of 4276 (20%) subjects prescribed HCQ for 5 years or more, the dose at 5\u00a0years of use remained largely unchanged (median 400\u00a0mg/day). There was no difference in the proportion of excess dosing between the initial dose and dose at 5\u00a0years. Of these subjects, 40% and 37% had excess dosing by IBW for the initial dose and at 5\u00a0years . We focused on prescribed HCQ doses rather than assessing actual dispensed prescriptions or other measures of effective consumed dose of HCQ as our goal for this study was to assess prescribing patterns rather than patient adherence. Finally, our aim was to describe the level of excess HCQ dosing according to the previous and current guidelines; assessing the risk of retinal toxicity was beyond the scope of the current study. As the latest guideline change has beenIn conclusion, this UK general population-based study found that according to previous and latest ophthalmology society guidelines, excess HCQ dosing is substantial, despite a modest decline over recent years. Female patients more often receive an excess HCQ dose according to these guidelines, and a similarly considerable proportion of long-term HCQ users also experience excess HCQ dosing. Over half of normal BMI individuals were excess-dosed per the latest guidelines; however, BMI had a noticeably opposite impact on the risk of excess dosing between the prior and latest weight-based guidelines. This implies the potential need to reduce dosing in many patients but also calls for further research to establish unifying, evidence-based safe-dosing strategies, balancing retinopathy risk and treatment efficacy.Additional file 1:Figure S1. Overall hydroxychloroquine prescription dose trends. (DOCX 17 kb)"} +{"text": "Owing to out-migration, decreased fertility and longer lifespans, 18.5% of Puerto Rico\u2019s population is aged 60+ -- 36% live alone and 40% are below poverty. Out-migration after Hurricane Maria may well raise the proportion of older adults to 30%. Mental health problems are among the most widespread and enduring effects of disasters. Common Mental Disorders (CMD) are most common. Before Maria, CDC data showed 38 % of persons age 65+ reported fair or poor health and 20% had been told they had a depressive disorder. In the months after Maria, the overall suicide rate rose 29%, while it more than doubled for people aged 65-69 and tripled for those aged 75- 79. This pilot study assesses the feasibility and acceptability of adapting the Friendship Bench, an evidence-based intervention developed in Zimbabwe for CMD, for use with older adults in primary care in Puerto Rico."} +{"text": "In the Philippines, one in four pregnancies are unintended and 610 000 unsafe abortions are performed each year. This study explored the association between missed opportunities to provide family planning counseling, quality of counseling and its impact on utilization of effective contraception in the Philippines.One-hundred-one nationally representative health facilities were randomly selected from five levels of the health system. Sexually-active women 18\u201349 years old, wanting to delay or limit childbearing, attending primary care clinics between April 24 and August 8, 2017 were included. Data on contraceptive use, counseling and availability were collected using interviews and facility assessments. Effective contraceptive methods were defined as those with rates of unintended pregnancy of less than 10 per 100 women in first year of typical use.849 women were recruited of whom 51.1% currently used effective contraceptive methods, 20.6% were former effective method users and 28.3% had never used an effective method. Of 1664 cumulative clinic visits reported by women in the previous year, 72.6% had a missed opportunity to receive family planning counseling at any visit regardless of level of facility, with 83.7% having a missed counseling opportunity on the day of the interview. Most women (55.9%) reported health concerns about modern contraception, with 2.9% receiving counseling addressing their concerns. Only 0.6% of former users and 2.1% never-users said they would consider starting a modern contraceptive in the future. Short and long acting reversible contraceptive methods were available in 93% and 68% of facilities respectively.Missed opportunities to provide family planning counseling are widespread in the Philippines. Delivery of effective contraceptive methods requires that wider legal, policy, social, cultural, and structural barriers are addressed, coupled with systems approaches for improving availability and quality of counseling at all primary health care contacts. Unintended pregnancies remain an important public health problem worldwide. Between 2010 and 2014, there were an estimated 62 unintended pregnancies per 1000 women aged 15\u201344 years each year, with rates ranging from 112 in East Africa to 28 in Western Europe .In 2017, the modern contraceptive prevalence rate (CPR) in the Philippines was estimated to be 40% among married women of reproductive age and 17% among unmarried sexually active women . The modWomen who are fecund, sexually active and who want no more children or to delay the next child, but are not using any method of contraception, are defined as having an \u201cunmet need for family planning\u201d. The unmet need for family planning among married women of reproductive age in Philippines was 17% in 2017, with the demand met by modern methods estimated to be 57%. Among unmarried sexually active women the unmet need increases to 49% and the demand met by modern methods falls to 22% . As a coSeveral barriers to accessing family planning services have been observed in the Philippines. A 2013 survey found that maintenance of virginity until marriage was important for 83% of women aged 15\u201324, even though 14% of 15\u201319 year-olds and 49% of those aged 20\u201324 years experienced first sexual intercourse before marriage . This soAlthough the family planning program in the Philippines began in 1971 and was one of the strongest in Asia, religious concerns, rapid decentralization and various legal interventions have restricted implementation. The Responsible Parenthood and Reproductive Health Act of 2012, designed to re-vitalize family planning service provision, was not put into place until 2017 when legal and programmatic barriers had been overcome .In response, the Department of Health in Philippines sought to identify strategies to improve family planning programming. Improvement of uptake of modern methods of contraception, especially LARCs, became an important public health priority. Experience from other countries in Asia has shown that facility-based contraceptive counseling is often poor , 10. WomA nationally representative cross-sectional survey design was used. One hundred one health facilities were selected. In first stage sampling, 23 provinces were randomly selected using probability proportionate to size based on the estimated number of sexually active women with unmet need . Within At each facility, women aged 18\u201349 years of age, who were not currently pregnant or within 6 weeks of delivery, wanting to delay or limit childbearing on the day of the visit were eligible to for the study, to avoid confounding by stage of pregnancy, place of delivery or the early post-pregnancy period on the likelihood and quality of counseling. Questions about missed opportunities to provide family planning counseling were asked about all clinic visits in the previous year. Individual interviews using structured questionnaires were conducted with 10 women per hospital and 6 per health center. Sampled women were divided into equal groups of those currently using and not using effective contraceptive methods. We defined effective contraceptive methods as those with rates of unintended pregnancy of less than 10 per 100 women in first year of typical use . We exclData were collected from women attending the outpatient primary care clinic on the day of the survey. Primary care clinics included postnatal care, reproductive health, well child, and primary care. If more than the required number of women were in attendance, systematic sampling method was used. At five sampled health facilities, the minimum number of women were not available on the day of the survey. At these facilities, 24 (2.8%) women meeting eligibility requirements for the study and living within 1 hour of the facility were identified from clinic registers for the previous days and interviewed at their homes to obtain the minimum sample size.A closed-ended questionnaire for women, interview guide and health facility assessment checklist were developed referring to previous research. These were finalized after two field pilot tests. To those women who preferred local dialects, the questionnaires and consent forms were translated into one of eight local dialects then validated by back-translation. Eight teams consisting of one team leader and one enumerator collected data from April 24 to August 8, 2017 using paper-based questionnaires. Enumerators near selected facilities were identified to minimize language differences across study sites. Data were collected using: 1) interviews with women on current, former and never use of effective contraceptive methods, concerns and attitudes towards contraception, and management of concerns at outpatient primary care clinics of health facilities; 2) facility assessments of the availability of family planning commodities and policies including hospital accreditation status for use of LARCs.Counseling was defined as any information or advice given about any contraceptive method during the woman's clinic visit. A missed opportunity was defined as a woman\u2019s clinic visit at which a staff member at the health facility did not provide any counseling. When counseling was provided, quality of counseling was measured by asking the woman whether health staff asked about her concerns on family planning, helped her to find solutions to her concerns, offered her information about how different family planning methods work, or explained side-effects or problems she might have with any method. A health concern about a family planning method was defined as any perceived undesirable health effect. Accumulated facility visits were defined as the number of visits to health facilities made by interviewed women between January 1 and December 31, 2016. Accumulated missed opportunities were defined as the total number of accumulated facility visits at which health staff did not provide any family planning counseling on the day of that visit.The team leader checked completeness and accuracy of completed paper-based questionnaires on the day of interview. Two data managers independently entered the questionnaire data into identical Excel sheets and compared using STATA version 13.1. Inconsistencies were validated with the original paper and corrected. Statistical analysis was also done using STATA.Ethical clearance was obtained by the WHO Regional Office for the Western Pacific Ethics Review Committee on 12 January 2017, and the National Ethics Committee in the Philippine Council for Health Research and Development of the Department of Science and Technology on 1 February 2017. All women were asked for informed consent. Participants were informed of their right to refuse participation in the study, or not answer specific questions should they assent to participation and were assured of the confidentiality of the collected information. All interviews were conducted in private settings and unique identifiers were used to maintain anonymity. All paper copies are maintained in a locked file cabinet.A total of 849 non-pregnant sexually active women, 18\u201349 years of age, wanting to delay or limit childbearing were included in the study. Only one woman meeting the entry criteria refused to be interviewed. Of sampled women, 51.1% (434) were currently using an effective contraceptive method, 16.5% (140) a less effective contraceptive method and 32.4% (275) no contraceptive method. Of all women, 36.7% (312) were currently using short-acting effective methods , 8.9% (76) LARCs (IUD or implants) and 5.5% (46) female sterilization. An additional 18.2% (155/849) of women had used short-acting effective methods in the past and 2.4% (20) had used LARCs in the past. An effective method had never been used by 28.3% (240) of women .Demographic characteristics of sampled current, former and never users were similar . RespondOf all women, 83.7% (711/849) reported a missed opportunity for family planning counseling on the day of the interview. Missed opportunities were high regardless of contraceptive method used, residence, age group, marital status, education, number of children, or financial protection status, but highest among those younger than 21 years old, and women living together or not married . Missed The 849 women interviewed reported 1664 accumulated primary health care facility visits including antenatal care and postnatal care before discharge, between January 1 and December 31, 2016, not including the day of the interview. Of the 1664 accumulated health facility visits, 72.6% (1211) were missed opportunities to provide family planning counseling. Missed opportunities were found for 68.6% (587/856) of visits by current effective contraceptive method users, 73.4% (235/320) by former users and 78.9% (385/488) by never users. Overall, women not currently using any effective contraceptive method had a missed opportunity in 76.7% (620/808) of all clinic visits in 2016. Missed opportunities to provide family planning counseling were reported for 85.8% (241/281) of reproductive health clinic visits, 76.8% (182/237) of antenatal care visits, 74.7% (198/265) of postnatal care before discharge contacts, 73.7% (73/99) of postnatal care visits after discharge, 71.9% (264/367) of well-child visits, 70.7% (162/229) of sick child visits and 57.1% (68/119) of primary care visits for herself. Missed opportunities were lowest for contraceptive clinic visits, at which 32.8% (23/70) women reported that family planning counseling about any method was not provided .Sixteen percent (138/849) of women received family planning counseling on the day of the interview. Of the 138 women receiving counseling, 67.4% (93) were asked if they had concerns about contraceptives, 59.4% (82) received information about how different contraceptives work and 44.9% (62) were told about possible contraceptive side-effects during the counseling. Current effective contraceptive users were more likely to receive information than former or never users. Of the 80 current users receiving family planning counseling, 75.0% (60) were asked about concerns, 66.3% (53) were given explanations about how different methods work, and 55.0% (44) were given advice about side-effects. In contrast, the same information was given less frequently to the 24 former users receiving counseling and the 34 never users receiving counseling .4, while 35.1% (199) were misperceptions. The latter included the belief that contraceptives caused uterine cancer, cysts, fetal malformations, varicose veins, and dry skin. Misperceptions accounted for 33.6% (38/113) of all concerns among current, 25.7% (44/171) former and 41.3% (117/ 283) never users. Misperceptions were particularly high about female sterilization (87.0% or 20/23 of concerns such as frequent bleeding or cause uterine cancer) and IUDs (67.6% or 50/74 of concerns were misperceptions such as movement to other organs inside the body). Misperceptions were a low proportion of concerns for implants (37.5% or 9/24 of concerns), pill (27.9% or 79/283 of concerns) and injectables (25.1% or 41/163 of concerns).Overall, 55.9% (481/849) of women reported a total of 567 concerns about any effective contraceptive method on the day of the interview. The prevalence of concerns was 72.6% (126/175) among former users, 56.0% (242/434) among current users, and 47.5% (113/240) among never users. Only two women reported concerns that were not related to health: one woman who had never used effective contraception stated that it was illegal to use sterilization and IUDs; and another currently using injectables stated that the church did not allow the use contraception. Of all 567 concerns, 64.9% (368) were medically known side effects such as changes in bleeding patterns, irritability (mood changes), headaches and weight gainOf the 481 women with a health concern about effective contraceptive methods, 16.3% (79/481) received family planning counseling on the day of interview. Regardless of contraceptive usage status, information given to women with concerns was limited, with only 2.9% (14/481) of women reporting that their concern about a specific method(s) had been addressed by the health worker during counseling . Only 0.A stock of non-expired effective short-acting contraceptive methods was available at 87.5% (42/47) of government hospitals, 95.7 (45/47) of health centers, and 100% (7/7) of barangay health stations. LARCs were available in 85.1% (40/47) of government hospitals, 60% (28/47) (61%) of health centers and 1/7 (14.3%) of barangay health stations.Of 1664 cumulative total clinic visits reported by the women wanting to delay or limit childbearing in 2016, 72.6% had a missed opportunity to receive family planning counseling at any visit regardless of level of facility or socio-economic indicators. On the day of the interview in 2017, 83.7% of women had a missed opportunity. Although 55.9% of women reported health concerns about effective contraceptives on the day of the interview, 16% with a concern received family planning counseling and only 2.9% received counseling addressing her specific concerns. Only 0.6% of former effective contraceptive method users and 2.1% never-users said they would consider starting effective contraceptive method in the future. As relatively few facilities had stock-outs, most women in our study could have received an effective contraceptive on the day of the visit, if they had received high quality of counseling, been offered a method and had decided to use it.These findings suggest that the quantity and quality of family planning counseling provided at primary care clinic contacts in Philippines to women who wish to delay or limit childbearing is inadequate and unlikely to significantly increase the use of effective contraceptive methods. Around 20% of women attending clinics in this study had previously used an effective contraceptive method, but had discontinued use, highlighting that contraceptive services must focus not only on attracting new users but also on improving continuation rates . To do tThe high prevalence of missed opportunities to provide family planning counseling found in this study is consistent with other studies in both developed and developing country settings \u201319.The World Health Organization recommends providing routine family planning counseling at antenatal care, postnatal care, and other contact points \u201323. HoweClient-centered counseling approaches are associated with improved method continuation. Women who report experiencing higher quality care have higher rates of contraceptive continuation and contraceptive use \u201333. In rMost counseling in primary care clinics in Philippines is provided by doctors, nurses and midwives. Although family planning counseling at both antenatal and postnatal care contacts is included in national policies and guidelines in Philippines , our finHowever, the RPRHA imposes a ban on the purchase of dedicated emergency contraceptives by national hospitals, and requires parental consent for minors to access contraceptives. These restrictions directly impose barriers to contraceptive use on poorer women and adolescent girls .Although many Philippine-governmental norms and standards are in agreement with adolescents\u2019 human rights to contraceptive information and services recommended by the WHO, a significant number are restrictive, reflecting the strong influence of conservative religious beliefs . In addiThere are also a number of provider perceptions that may limit counseling provision, including lack of knowledge, training, and comfort, assumptions about patient pregnancy risk, negative beliefs about contraceptive methods, a reliance on patients to initiate discussions; and limited communication with other primary care staff , 42, 43.Social norms are believed to be particularly important barriers in Philippines. These norms prevent women, especially adolescents and unmarried women, from accessing services and using methods effectively. The high value placed on virginity at marriage discourages women from admitting sexual activity and inappropriate health concerns .Women frThis study confirms that LARCs such as IUDs and implants are used less frequently than short acting methods in the Philippines despite being far more effective . AlthougIn summary, improving family planning counseling at all clinic contacts in the Philippines will require actions at several levels. Recognizing the role of effective contraception to improve the health and economic development of the country is the first step and should be reflected in national laws and policies. Legal barriers such as limitations on the availability of emergency contraception and requiring parental consent can be carefully re-considered and removed. National policies and guidelines should be reinforced at all levels to ensure they are consistent with WHO recommendations and to remove abstinence-centered and sex-negative content. Mechanisms to avoid local adaptations which bypass national policies and guidelines should be explored. Availability of LARCs can be increased by expanding the range of facilities where they can be provided and the number and categories of staff trained in their use. National policies, guidelines and standard operating procedures for primary care services can emphasize integrating family planning counseling at all contacts. Health worker awareness and counseling skills can be strengthened by incorporating skills into professional medical, nursing and midwifery pre-service training curricula and by providing on-the-job coaching of doctors, nurses and midwives; client-centered counseling approaches can address both relational and task-based communication focusing on common obstacles to use . DevelopThis study aimed to select a nationally representative sample, based on unmet need for family planning. Since the 2014 Philippine Demographic and Health Survey calculated population-based estimates of unmet need only at the regional level, provinces within a region with higher than average unmet need may be under-represented . PhilheaSince our sample was facility-based, findings may not reflect the practices of those who have less access to public clinics or seek care less regularly. In addition, adolescents under 18 years of age were excluded, because their inclusion would have required a lengthy institutional review process which could not be completed within financial deadlines. Given the high missed opportunities among adult women, omission of these groups likely meant that our findings underestimate the extent of the problem.We asked respondents about family planning services received on the day of the interview and at all clinic visits in 2016. A maximum period of 6 months has been suggested for the recall of non-significant events . HoweverAs in other low- and middle-income countries, the Philippines faces substantial barriers to improving reproductive health services. This study showed that the vast majority of women who wish to delay pregnancy, attending public health clinics, did not receive family planning counseling regardless of their current status of contraceptive use or clinic attended. Over half of these women had health concerns about effective contraceptive methods which were not addressed. This striking finding means that many women in contact with the health system continue to use no contraception, use traditional and other less-effective methods or stop using contraception altogether. As a consequence, many women are put at unnecessary risk of short-spaced high-risk pregnancies and cycles of high fertility, lower educational and employment potential and poverty \u201351. The S1 Questionnaire(PDF)Click here for additional data file.S2 Questionnaire(PDF)Click here for additional data file.S3 Questionnaire(PDF)Click here for additional data file.S4 Questionnaire(PDF)Click here for additional data file.S5 Questionnaire(PDF)Click here for additional data file.S6 Questionnaire(PDF)Click here for additional data file.S7 Questionnaire(PDF)Click here for additional data file.S8 Questionnaire(PDF)Click here for additional data file.S9 Questionnaire(PDF)Click here for additional data file.S10 Questionnaire(PDF)Click here for additional data file.S1 Minimal Dataset(XLSX)Click here for additional data file.S2 Minimal Dataset(DTA)Click here for additional data file.S3 Minimal Dataset(XLSX)Click here for additional data file."} +{"text": "Prescription opioid misuse has become a leading cause of unintentional injury and death among adolescents and young adults in the United States. However, there is limited information on how adolescents and young adults obtain prescription opioids. There are also inadequate recent data on the prevalence of additional drug abuse among those misusing prescription opioids. In this study, we evaluated past-year prevalence of prescription opioid use and misuse, sources of prescription opioids, and additional substance use among adolescents and young adults.P < 0.001), and non-Hispanic whites and blacks were more likely to have had any opioid use compared to Hispanics . Opioid misuse was reported by 1,050 adolescents and 2,207 young adults . Male respondents using opioids were more likely to have opioid misuse without use disorder compared with females , with similar prevalence by race/ethnicity. Among those misusing opioids, 55.7% obtained them from friends or relatives, 25.4% from the healthcare system, and 18.9% through other means. Obtaining opioids free from friends or relatives was the most common source for both adolescents (33.5%) and young adults (41.4%). Those with opioid misuse reported high prevalence of prior cocaine (35.5%), hallucinogen (49.4%), heroin (8.7%), and inhalant (30.4%) use. In addition, at least half had used tobacco (55.5%), alcohol (66.9%), or cannabis (49.9%) in the past month. Potential limitations of the study are that we cannot exclude selection bias in the study design or socially desirable reporting among participants, and that longitudinal data are not available for long-term follow-up of individuals.This was a retrospective analysis of the National Survey on Drug Use and Health (NSDUH) for the years 2015 and 2016. Prevalence of opioid use, misuse, use disorder, and additional substance use were calculated with 95% confidence intervals (CIs), stratified by age group and other demographic variables. Sources of prescription opioids were determined for respondents reporting opioid misuse. We calculated past-year prevalence of opioid use and misuse with or without use disorder, sources of prescription opioids, and prevalence of additional substance use. We included 27,857 adolescents (12\u201317 years of age) and 28,213 young adults (18\u201325 years of age) in our analyses, corresponding to 119.3 million individuals in the extrapolated national population. There were 15,143 respondents who used prescription opioids in the previous year, including 21.0% (95% CI 20.4\u201321.6) of adolescents and 32.2% (95% CI 31.4\u201333.0) of young adults. Significantly more females than males reported using any prescription opioid (30.3% versus 24.8%, Results from this study suggest that the prevalence of prescription opioid use among adolescents and young adults in the US is high despite known risks for future opioid and other drug use disorders. Reported prescription opioid misuse is common among adolescents and young adults and often associated with additional substance abuse, underscoring the importance of drug and alcohol screening programs in this population. Prevention and treatment efforts should take into account that greater than half of youths misusing prescription opioids obtain these medications through friends and relatives. Joel Hudgins and coworkers study reported use and misuse of prescription opioids and other substances among adolescents and young adults in the United States. Prescription opioid misuse is a leading cause of unintentional injury and death among adolescents and young adults.There is limited information on the source of prescription opioids among adolescents and young adults or whether those misusing prescription opioids engage in use of additional substances and drugs of abuse.Understanding these factors will inform strategies to ensure judicious opioid prescribing and effective treatment approaches.Using the National Survey on Drug Use and Health for the years 2015 and 2016, we determined past-year prevalence of prescription opioid use, sources of prescription opioids, and additional substance use among adolescents and young adults ages 12\u201325.We found that 27.5% of respondents, corresponding to an estimated 32.8 million individuals, used prescription opioids in the previous year, including 21.0% of adolescents and 32.2% of young adults.The prevalence of opioid misuse was 3.8% among adolescents and 7.8% among young adults.Most individuals misusing prescription opioids obtained them for free from a friend or relative or from a single prescriber.Individuals with prescription opioid misuse reported high prevalence of use of other substances, including cocaine, hallucinogens, heroin, and inhalants.The prevalence of prescription opioid use is high among adolescents and young adults in the United States despite known risks for progression to opioid and other substance use disorders in this population.Prevention and treatment efforts should take into account that adolescents and young adults misusing prescription opioids obtain these drugs most commonly from friends and relatives or from a single prescriber.Healthcare providers should consider screening all adolescents and young adults with opioid misuse for additional substance use and should have established intervention plans available to maximize the opportunity to provide substance use treatment to this population. Over the past two decades, opioid misuse and poisonings have emerged as a public health crisis in the US. Since 1999, rates of deaths secondary to opioids have tripled, and in 2017 alone, over 72,000 Americans died from opioid overdoses \u20136. OpioiAmong adults in the US, roughly 1 in 3 is estimated to use prescription opioids, with 4.7%, or 11.5 million, misusing them . Opioid There is limited information on how adolescents and young adults are obtaining prescription opioids. Studies suggest an indirect link between opioid prescriptions in adults and exposures in adolescents, suggesting that households and family members may be a contributing source ,24. In oIn this study, we analyzed data from a large, nationally representative survey collecting information on prescription opioids to measure prevalence of opioid use and misuse among US adolescents and young adults. We also determined sources of prescription opioids and characterized opioid use and misuse according to additional use of other substances and drugs of abuse.Data for this analysis were obtained from survey responses in the 2015 and 2016 National Survey on Drug Use and Health (NSDUH). The NSDUH is an annual cross-sectional survey that collects information on drug use, mental health, and other health-related issues in the US civilian, noninstitutionalized population aged 12 years and older. It is sponsored by the Substance Abuse and Mental Health Services Administration (SAMHSA) within the US Department of Health and Human Services. We used the publicly available version of the dataset, which was downloaded for use on February 16, 2018.The survey includes interviews with approximately 70,000 individuals randomly selected annually, using a multistage area probability sample for each state and the District of Columbia. Certain populations, including younger age groups , are oversampled to ensure robust estimates . InterviOur analysis was prospectively planned, including the definition of the study population, sociodemographic characteristics of interest, and outcome measures. Two modifications were made to the planned analysis. The first was our definition of young adult, which we initially defined as 18\u201323 years of age but modified to 18\u201325 years to match the NSDUH definition and data categorization. The second was the grouping of the different sources of prescription opioids, which was revised in response to peer-review comments. The study was deemed exempt from review by the Institutional Review Board at Boston Children\u2019s Hospital.We analyzed responses from adolescents 12 to 17 years of age and young adults 18 to 25 years of age. The NSDUH seeks to allocate 25% of its sample to adolescents aged 12 to 17 years, 25% to young adults aged 18 to 25 years, and the remaining 50% to adults 26 years and older [Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV), criteria for substance use disorder [We examined three outcomes based on survey questions in the NSDUH: prescription opioid use, misuse, and use disorder, sources of prescription opioids for misuse, and use of other substances and drugs of abuse. NSDUH specifically identifies prescription opioids by presenting a list of prescription opioids and pictures of prescription opioid pills to respondents, and asks about past month, year or lifetime use of these opioids. For participants providing a positive response, follow-up questions determine classification into one of three groups: use without misuse, misuse without use disorder, or use disorder. Prescription opioid misuse is defined as \u201cuse in any way that a doctor did not direct you to use them\u201d . Specifidisorder ,30.For respondents reporting misuse of prescription opioids in the past year, NSDUH collects data on where the medications were obtained. Respondents are asked to select as many responses as apply from the following options: (a) obtained from one doctor, (b) obtained from more than one doctor, (c) stole from doctor office, clinic, hospital, or pharmacy, (d) obtained from friend or relative for free, (e) bought from friend or relative, (f) stole from friend or relative, (g) bought from drug dealer or stranger, and (h) got some other way.The NSDUH also asks respondents about additional substance use and drug abuse. For our population, we examined responses to questions on tobacco, alcohol, cocaine, cannabis, heroin, inhalant, and hallucinogen use. Questions address use within the past month, past year, and lifetime. We combined use with and without use disorder for these substances and drugs.Sociodemographic characteristics collected in the NSDUH include sex, race/ethnicity , health insurance , marital status, educational attainment, and past-year family income .The reliability of the NSDUH questionnaire related to substance use and misuse has been previously assessed, with measures showing good reproducibility over time ,32. Misssvyset and svy).Data were analyzed using the person-level sample weight, which is the product of the corresponding sampling fractions at each stage in the sample design, and allows extrapolation to national population estimates. The sampling weights are adjusted using the generalized exponential model , which aP values for comparisons were calculated using chi-squared test. The study conforms to the STROBE guideline , and uideline .The NSDUH included 27,857 adolescent and 28,213 young adult respondents during the survey years 2015 to 2016, corresponding to an estimated 119.3 million individuals in the extrapolated national population (49.8 million adolescents and 69.5 million young adults). Overall, 27.5% of these respondents, corresponding to an estimated 32.8 million individuals, reported using a prescription opioid in the previous year, including 21.0% (95% CI 20.4\u201321.6) of adolescents and 32.2% (95% CI 31.4\u201333.0) of young adults .P < 0.001). Prevalence of opioid misuse without use disorder was higher in young adults compared with adolescents , with similar prevalence of opioid use disorder in the two groups. Considering both age groups together, female respondents were more likely to have had any prescription opioid use compared with males , but male respondents were more likely to have opioid misuse without use disorder compared with females . Non-Hispanic white and black respondents reported higher prevalence of past-year opioid use compared with Hispanic respondents (P < 0.001), but prevalence of misuse without and with use disorder were similar between groups. Insurance status was not a significant determinant of opioid use, but uninsured respondents were more likely to report opioid misuse without use disorder compared with those with Medicaid.Opioid misuse or use disorder in the past year was reported by 6.1% (95% CI 5.8\u20136.4) of respondents, corresponding to an estimated 1.9 million adolescents and 5.4 million young adults obtained them from the healthcare system, 55.7% (95% CI 53.7\u201357.6) from friends or relatives, and 18.9% (95% CI 17.4\u201320.5) through other means . AdolescP < 0.001) reporting use of tobacco, 90.1% use of alcohol, and 80.7% use of marijuana. For cocaine, heroin, hallucinogen, and inhalant use, differences in prevalence of use between those with opioid use without misuse and those with opioid misuse were even more pronounced. Prevalence of cocaine use increased greater than 4-fold from 7.9% (95% CI 7.1\u20138.7) to 35.5% for respondents with opioid use without misuse compared with those with opioid misuse. Similarly, the prevalence in these populations increased from 0.9% (95% CI 0.6\u20131.1) to 8.7% for heroin use, 13.1% (95% CI 12.3\u201313.9) to 49.4% for hallucinogen use, and 12.1% (95% CI 11.3\u201312.8) to 30.4% for inhalant use.Additional substance use and drug abuse associated with prescription opioid use is shown in P < 0.001), 77.4% , and 55.0 , respectively, among young adults. For cocaine and hallucinogens, lifetime prevalence of using the substance more than doubled between adolescents and young adults with opioid misuse.Among adolescents and young adults with opioid misuse, prevalence of additional substance use was significantly higher among young adults for all substances except inhalant use . These dIn this national sample of adolescents and young adults, 27.5% reported using a prescription opioid in the past year, with 3.8% of adolescents and 7.8% of young adults engaged in opioid misuse or having a use disorder. Respondents stated that opioids were obtained most frequently from friends or relatives or from a single prescriber, and much less often through drug dealers or from multiple prescribers. Adolescents and young adults with any type of opioid misuse were significantly more likely to use additional substances and drugs of abuse, with a third or more reporting prior use of cocaine, hallucinogens, and inhalants and half or more reporting past month use of tobacco, alcohol, or cannabis. Overall, young adults engaging in opioid misuse have higher rates of additional substance use and drug abuse compared with adolescents.These findings are consistent with prior research indicating that the opioid epidemic is taking a significant toll on adolescents and young adults. In one large longitudinal study of youths 13 to 25 years of age, new diagnoses of opioid use disorder increased 6-fold between 2001 and 2014 . OverallThe risk of progression to opioid use disorder and other substance abuse is well-documented for youths exposed to prescription opioids ,37\u201339. HSources of prescription opioids have not been well defined among adolescents and young adults misusing these drugs. Adults misusing prescription opioids have been found to obtain opioids both from prescribers and through friends and relatives . PreviouAdolescents and young adults misusing opioids are at high risk of abusing other substances. In addition to our findings of high prevalence of recent substance abuse, prior studies have demonstrated high prevalence of explicit co-ingestion of drugs with prescription opioids. Among high school seniors, approximately 70% report co-ingesting another drug while engaging in prescription opioid misuse, with greater than half reporting concurrent use of marijuana or alcohol, and 10% concurrent use of cocaine, tranquilizers, or amphetamines . These pOur study has several limitations. While the NSDUH had a high response rate of approximately 75% during the years analyzed, we cannot preclude self-selection bias among participants. In addition, despite sophisticated interviewing techniques, we cannot exclude socially desirable reporting among participants. The NSDUH also does not survey homeless people, active military personnel, or people in prison, which might impact findings reported for young adults in the study, especially because high rates of opioid misuse and use disorder have been identified in these populations ,49. BecaOur findings suggest that the prevalence of prescription opioid use among adolescents and young adults in the US is high despite known risks for future opioid and other drug use disorders. Prevention and treatment efforts should take into account that greater than half of adolescents and young adults misusing prescription opioids obtain these drugs from friends and relatives. Both adolescents and young adults misusing opioids demonstrate high prevalence of additional substance use and drug abuse, underscoring the importance of drug and alcohol screening programs in this population.S1 STROBE Checklist(DOC)Click here for additional data file."} +{"text": "National Gay Men\u2019s HIV/AIDS Awareness Day, September 27, directs attention to the impact of human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) on gay, bisexual, and other men who have sex with men (MSM). In 2017, MSM accounted for 67% of new diagnoses of HIV infection, and MSM who inject drugs an additional 3% use. From 2014 to 2017, in 20 urban areas, PrEP awareness among MSM increased from 60% to 90%, and PrEP use from 6% to 35% (https://www.cdc.gov/hiv/group/msm/index.html), support the linkage to and engagement of MSM in care and treatment, and reduce the risk for acquiring and transmitting HIV (https://www.cdc.gov/hiv/group/msm/bmsm.html) .CDC supports efforts to reduce HIV infection among MSM, including HIV prevention services that increase diagnosis of HIV infection ("} +{"text": "Onychomycosis is the most common affliction of the nail. It may be caused by dermatophytes, yeasts, and non-dermatophyte molds. Traditionally, oral antifungal treatments have been used to treat the fungus, although they can be accompanied by side effects and drug interactions. Topical treatments provide an alternative modality, bypassing the systemic effects of oral drugs; recent research has centered on topical drug improvement and development. Physical and laser treatments are being used in conjunction with topicals, which may help penetrate the thick nail plate. In this review, techniques from all categories are outlined: both novel experimental approaches and progress and effectiveness of recently developed treatments. More long-term studies are required to determine the efficacy of various treatments, but cure rates are improved when patients adhere to treatments and follow preventative measures to avoid disease recurrence. It is the most common nail pathology and accounts for about 90% of toenail infections worldwide1. This infection presents several problems for affected populations, including local pain, paresthesia, and reduced quality of life as its appearance may impair social interactions and daily activities2. Most onychomycoses are caused by the dermatophytesTrichophyton,Trichophyton rubrum,Trichophyton mentagrophytes, andEpidermophyton3. Infections often initiate from tinea pedis, a fungal infection on the surrounding skin of the feet3. Factors that contribute to disease progression are humidity, occlusive footwear, nail trauma, and genetic predisposition5. Patients with diabetes, poor peripheral circulation, HIV, and immunosuppression are also more susceptible, as are elderly patients10.Onychomycosis is a fungal infection occurring in the nails and may affect the adjacent skin. Typically, it manifests as discoloration of the nail, nail plate thickening, and onycholysis11. This, coupled with slow toenail growth, requires that topicals be used for 12 months or longer, ideally until a healthy nail has regrown. Traditionally, oral therapeutics have been the preferred treatment because of their accessibility and efficacy2. Terbinafine and itraconazole are US Food and Drug Administration (FDA)\u2013approved oral antifungal medications, and fluconazole is available as an off-label option in the US. Though effective, they may be accompanied by systemic side effects and drug\u2013drug interactions, which is a concern for those already taking medications for other conditions. Patients may be hesitant to take oral antifungals. It is understandable that there is demand for non-systemic treatments. At present, there are several oral, topical, and physical therapies broadening the treatment options available to patients. Additionally, combination therapy with several drug classes/modalities can be considered12. Some research groups are studying new molecules and permeation enhancers for topicals, diversifying drug targets, and improving the effectiveness of base molecules already in use. When the efficacy of these drugs is measured, commonly used outcome measures are mycological cure and complete cure. Mycological cure is defined as eradication of the fungal pathogen from the nail, confirmed by a negative potassium hydroxide (KOH) preparation (a test to differentiate dermatophytes and yeasts from other skin disorders) and negative fungal culture. Complete cure meets the goals of the patient, physician, and regulatory bodies. Complete cure is defined as 100% clear nail in addition to mycological cure13. This review will outline some of these recent developments in therapies for managing onychomycosis.Owing to its chemical composition, the nail is a formidable barrier to the permeation of drugs, and diffusion into the nail is poor relative to the skin14. It is advantageous to develop a drug delivery system that allows the drug to enter the nail plate through the transungual and subungual routes rather than just penetrating the nail plate, which is demonstrated by the application of tavaborole and efinaconazole15. Phase III clinical trials have been completed for these drugs and further studies are in progress to understand long-term efficacy14. Despite significant advances in the effectiveness of topical treatments, mycological and complete cure rates remain relatively lower than those of some of the oral agents . In two phase III randomized, double-blind, vehicle-controlled trials, tavaborole 5% solution was applied once daily for 48 weeks, and efficacy was evaluated at 52 weeks. Patients ranged from 18 to 88 years of age. Mycological cure rates (negative KOH and culture) with tavaborole 5% solution for studies 1 and 2 were 31.1% and 35.9%, respectively, significantly higher than vehicle . Complete cure rates were significantly higher for tavaborole compared with vehicle in study 1 and study 2 18. Similarly, a pooled post-study follow-up from these two trials showed that complete cure was higher in the tavaborole-treated group compared with the vehicle control group (28.6% versus 7.7%) at week 60. Additionally, at 60 weeks, mycological cure for the tavaborole group was higher than vehicle (53.1% versus 23.1%)19.Tavaborole is a novel boron-based antifungal agent that was approved by the FDA for treating onychomycosis in 2014P <0.001). Mycological cure rates (negative KOH and culture) were significantly higher with efinaconazole (55.2% in study 1 and 53.4% in study 2) compared with vehicle 22.Efinaconazole 10% solution was FDA-approved as a treatment around the same time in 2014. It is a triazole antifungal that inhibits the synthesis of ergosterol in the fungal cell wall. In phase III trials, patients with distal lateral subungual onychomycosis received the solution once daily for 48 weeks and were evaluated at 52 weeks. The results were a 17.8% complete cure rate versus 3.3% for vehicle in study 1 and 15.2% versus 5.5% in study 2 rate was significantly higher in luliconazole groups (14.9%) compared with vehicle . Similarly, the negative direct microscopy rate was significantly higher in luliconazole (45.4%) than vehicle . It is suggested that once-daily topical application of luliconazole is clinically effective and well tolerated27. Luliconazole is not approved for the treatment of onychomycosis in the US.Luliconazole was approved in 2013 for fungal infections of the skin, including tinea pedis in the US28. In a randomized, evaluator-blinded, controlled, parallel-group clinical trial, P-3051 showed statistical superiority to amorolfine after 48 weeks in complete cure in 120 patients 18 to 75 years of age with 25 to 75% nail involvement. Similarly, mycological cure (negative direct microscopy and culture) was achieved by all patients who received P-3051 compared with 81.7% who received amorolfine (P <0.001)29. In a randomized, evaluator-blinded, placebo-controlled, parallel-group clinical trial comparing P-3051 with reference ciclopirox 8% and placebo, 467 patients (mean age of 49.84 \u00b1 11.89 years) with 25 to 60% nail involvement applied the lacquers for 48 weeks, followed by a 4-week washout period and 8-week follow-up period28. Complete cure was achieved in 5.7% of P-3051 users and 3.2% for reference (P = 0.6834), whereas placebo saw no cure (P = 0.0165). P-3051 complete cure rate increased at 60 weeks (12.7%) and was greater than reference and placebo . A post-hoc analysis confirmed that severity of disease is a prognostic factor for responsiveness to P-3051 treatment and significantly affects reported efficacy data30. The population subset excluded patients with more severe disease (>50% nail involvement). P-3051 was superior to placebo and reference ciclopirox in cure and response rates at 60 weeks, and efficacy rates in the P-3051 group were higher in the groups that excluded patients with more than 50% nail involvement. Ciclopirox 8% hydrolacquer (P-3051) is not approved for the treatment of onychomycosis in the US.In Europe, ciclopirox 8% hydrolacquer (P-3051) uses a novel technology based on hydroxypropyl chitosan for the delivery of ciclopirox 8% to the nail31. A PU polymer delivered two antifungal drugs (terbinafine and ciclopirox), and a 10% PU concentration was most effective forin vitro drug release, permeation, and antifungal activity. The lacquer smooths the nail plate and reduces porosity, increasing effectiveness of the base molecule31. Finally, there are ongoing clinical trials for ME-1111 and MOB-015. ME-1111 is a new agent with potentin vitro antifungal activity and small molecular weight33. It targets succinate dehydrogenase of the electron transport chain, inhibiting it and blocking ATP production. MOB-015 is a topical formulation of terbinafine34.A study using polyurethanes (PUs) as new excipients in topical nail treatments has been conducted35. Recently, there has been insight about the use of ravuconazole and its prodrugs as new drug candidates for oral therapy. A water-soluble prodrug, mono-lysine phosphoester derivative (BFE1224), is in the advanced stages of clinical development35. A phase III randomized, double-blind, placebo-controlled study of fosravuconazole (F-RVCZ) L-lysine ethanolate, the novel oral triazole, was conducted in Japan36. One hundred fifty-three patients 20 to 75 years of age with at least 25% nail involvement were assigned 100 mg of F-RVCZ or placebo to take once daily for 12 weeks. Evaluation was carried out at week 48. The complete cure rates (0% nail involvement and negative KOH) for F-RVCZ and placebo were 59.4% and 5.8%, respectively (P <0.001). Mycological cure rate (negative KOH) was determined every 12 weeks and increased over time; the difference between F-RVCZ and placebo was statistically significant at 24 weeks and onward (P = 0.002 andP <0.001 at weeks 36 and 48). At week 48, mycological cure rates were 82.0% for F-RVCZ and 20.0% for placebo36. Fosravuconazole (F-RVCZ) is not approved for the treatment of onychomycosis in the US.Typically, oral therapeutics are reserved for severe infections because of their safety issues and drug\u2013drug interactions37. In a randomized, phase 2b study to evaluate the efficacy and safety of oral VT-1161 for onychomycosis, 259 patients 18 to 70 years of age with 25 to 75% nail involvement at baseline received 300 or 600 mg oral doses or matching placebo. Once-weekly VT-1161 at a dose of 300 or 600 mg was administered for 10 or 22 weeks following a 14-day once-daily loading period at the same dose (300 or 600 mg)38. Mycological cure (negative KOH and culture) at week 48 was shown for 61%to 72% of patients, collapsed across VT-1161 arms, whereas complete cure ranged from 32 to 40%38. Phase II clinical trials have been completed39.VT-1161 is a novel, tetrazole fungal CYP51 inhibitor designed to selectively target fungal enzymes and maintains high potency for the fungal targetet al.40 showed that repeated, daily cold atmospheric plasma treatment inhibits thein vitro growth ofT. rubrum. Recently, a pilot study demonstrated the effects of non-thermal plasma in treating onychomycosis41. Non-thermal plasma was created by using an electric insulator by short pulses (10 ns) of electric fields that ionize air molecules. This process creates ions, electrons, ozone, hydroxyl radicals, and nitric oxide, which are fungicidal and cytotoxic41. Ultimately, 13 patients 33 to 74 years of age with 25 to 50% nail involvement completed the trial, and 15.4% achieved mycological cure (negative KOH and culture). Additional studies are required because of the small sample size and varying protocols, but it is the first clinical study to report that thermal plasma may be effective against toenail onychomycosis.Heinlin42. Hollow-core photonic crystal fibers guide light from a femtosecond-pulsed laser in a focused, high-energy density beam. As it irradiates the nail, the laser creates pores (100 \u03bcm in diameter) with minimal damage to surrounding tissues. Complete poration of nails increases permeation by two to three orders of magnitude relative to an untreated nail, which in turn would increase the effectiveness of topical treatments42. Floreset al.43 coupled poration with a nanocapsule formulation of tioconazole. The nano-formulations are advantageous for topical delivery because they ensure stability of actives and act as reservoirs for extended drug delivery. Nanocapsules were composed of pullulan, a water-soluble polysaccharide that forms films44. The newer film-forming formula provided the best efficiency ofex vivo delivery, and drug payload percentages were higher than those of marketed products.Another novel physical strategy is precise laser poration46. The effectiveness of lasers as a standalone treatment is reported inconsistently, and cure rates for laser treatment are lower than those of oral and topical treatments. There is limited evidence that they can eradicate pathogenic fungi and this is due to incomplete reporting of randomization and lack of controls49. Additionally, the inclusion criteria and definitions of efficacy outcomes between drug and devices differ, preventing meaningful comparisons46. In the US, lasers are approved for the temporary increase of clear nail in onychomycosis50.Lasers are approved by the FDA because of their similarity to predicate devices. These devices improve cosmetic appearance by increasing the clarity of nail in patients with onychomycosis1. The smaller temporal pulse length in this laser is less than the thermal relaxation time of the fungi, which permits contained heating of the fungi in the nail plate while allowing dissipation of heat in the surrounding soft tissue of the toenail and fingernail. There is a lack of robust clinical data. Randomized, double-blind trials are required to determine whether they are actually fungicidal52.Commonly used lasers include neodymium-yttrium garnet lasers and Q-switched laser systems53. It is also important to treat tinea pedis, and any affected family members, early and effectively.Aside from adhering to the prescription protocol of their onychomycosis therapy, patients can perform measures to improve the effectiveness of their treatment and avoid the possibility of reinfection. They should disinfect shoes and socks, avoid walking barefoot in public places, keep feet cool and dry, and recognize the early signs of recurrence and reinfection1.There is a diverse array of therapies for treating onychomycosis, particularly centered on topical formulas as the adverse effects are limited to the application site without systemic drug interactions. Devices are being considered as an addition to antifungal therapies, which is an important step in diversifying treatment optionsFDA, US Food and Drug Administration; KOH, potassium hydroxide; PU, polyurethane."} +{"text": "The study aims to describe sociodemographic and health variable indices related to current and former tobacco use among older adults who participated in the Indonesia Family Life Survey (IFLS-5) in 2014-15. A national population-based cross-sectional study was conducted with a probability sample of 8,001 aged 50 years or older Indonesians. The overall prevalence of current tobacco use was 33.3% (62.2% in men and 6.5% in women) and former tobacco use was 9.8% (17.4% among men and 2.8% in women), of which 64.4% quit tobacco use when 50 years and older. In multinomial regression analysis, sociodemographic factors and health variables were associated with current tobacco use. In addition, being overweight or obese, having had a stroke, and other lung conditions were inversely associated with current tobacco use. Further, in adjusted analysis, sociodemographic factors and having chronic conditions were associated with former tobacco use. A high rate of current tobacco use and low rate of former tobacco use was found, particularly among men. The identified risk factors may help to better target this vulnerable population with tobacco cessation programmes. Some of the highest prevalence of tobacco use are found in low- and middle-income countries, including Indonesia . In a study among older adults (50 years and older) in six middle-income countries, the prevalence of current tobacco use ranged from 7% in Ghana to 46.5% in India . In an older local study in Indonesia, the smoking prevalence among men (65-74 years old) was 84.5% , the current tobacco use rate was 40.7% among 45-64 year-olds and 38.2% in 65 years and older individuals in the Global Adult Tobacco Survey in 2011 in Indonesia . In a systematic review in populations 65 years and older, the overall prevalence of tobacco use was 13% . Some research seem to suggest that older adults continue tobacco use at a high rate, have less awareness of potential harmful effects and may be more resistant to quit tobacco use , which emphasises the need to collect information about the tobacco use pattern among older adults and consequently develop adequate tobacco cessation strategies . Risk factors for current tobacco use among older adults include sociodemographic and health variables. Sociodemographic risk factors include, younger age , no significant decline with older age , male gender , lower socioeconomic and/or educational status , and rural residence in China, Ghana, and India, and urban residence in Mexico . Health variable risk factors for current tobacco use include chronic obstructive pulmonary disease , mental health difficulties , lower life satisfaction , poor self-rated health , insufficient fruits and vegetable consumption , and cognitive impairment . Obesity was negatively associated with tobacco use among older adults in South Africa .Similarly, factors associated with tobacco use cessation among older adults include sociodemographic and health variables. Sociodemographic variables include older age , male gender (Peltzer and Phaswana-Mafuya 2012), female gender , higher education , increasing income levels and among urban residence . Health variables associated with tobacco use cessation include higher prevalence of CVDs , transient ischemic attacks , asthma , heart trouble or angina , and mental health difficulties .There is a lack of studies that analyse the socio-demographic and health characteristics influencing current and former tobacco use behaviour among older adults in Indonesia.Therefore, the aim of this study was to assess the prevalence of current and former tobacco use and its associated factors among a national population-based sample of older Indonesians who participated in the Indonesia Family Life Survey (IFLS-5) in 2014-15.Sample and procedureData were analysed from the 2014-2015 \u201cIndonesia Family Life Survey (IFLS-5)\u201d.The IFLS-5 used a multistage stratified sampling design representative of 83% of Indonesia\u2019s population, with a response rate of over 90%; more details . In the IFLS-5, 16,204 households and 8001 50 years and older individuals were interviewed with complete tobacco use measurements. The IFLS has been approved by ethics review boards of RAND and University of Gadjah Mada in Indonesia . Written informed consent was obtained from all respondents prior to data collection.MeasuresTobacco use was assessed with two questions: 1) \u201cHave you ever chewed tobacco, smoked a pipe, smoked self-enrolled cigarettes, or smoked cigarettes/cigars?\u201d 2) \u201cDo you still have the habit or have you totally quit?\u201d . Responses were grouped into never, quitters and current tobacco users.Socio-demographic factor questions included age, gender, education , urban-rural residential status, region and subjective socioeconomic background .2 defined as overweight or obesity. Anthropometric measurements. Body weight and height were assessed with standard measures . Body mass index (BMI) was calculated, with 23 or more kg/mChronic conditionsChronic medical condition was assessed with the question, \u201cHas a doctor/paramedic/nurse/midwife ever told you that you had\u2026?\u201d , Heart attack, coronary heart disease, angina or other heart problems, Stroke, Arthritis or rheumatism, Stomach or other digestive disease\u201d) .Hypertension Based on averaged three consecutive measurements of systolic and diastolic blood pressure , \u201chypertension was defined as SBP \u2265140 mm Hg and/or DBP \u226590 mm Hg and/or current use of antihypertensive medication\u201d .The Centres for Epidemiologic Studies Depression Scale (CES-D: 10 items) was used to assess depressive symptoms, and scores 10 or more were classified as moderate to severe depressive symptoms .Self-reported health status was measured with the question, \u201cIn general, how is our health?\u201d Response options were \u201c1=Very healthy, 2, Somewhat healthy, 3=Somewhat unhealthy, and 4=Unhealthy\u201d . Those who responded somewhat unhealthy or unhealthy were defined as having poor self-rated health.Functional disability was measured by five items of Activities of Daily Living (ADL) and six items of Instrumental Activities of Daily Living (IADL) . Functional disability defined as having difficulty in one or more ADL/IADL items.Fruit and vegetable consumption was assessed with questions on, \u201cHow many days in the past week did you eat, 1a) Green leafy vegetables? 1b) carrots? 2a) banana? 2b) papaya? 2c) mango?\u201d Inadequate fruit consumptions was defined as \u201cless than three days a week, and inadequate vegetable consumption less than daily\u201d. Cognitive functioning was assessed with questions from the \u201cTelephone Survey of Cognitive Status (TICS)\u201d . Total scores ranged from 0-34; scores 13 and lower were defined as low.Data analysisDescriptive statistics were calculated to describe the sample, and current and former tobacco use levels. Multinomial logistic regression was performed to estimate associations between all independent variables and dependent variables of current and former tobacco use; with never tobacco use as reference category. Potential multi-collinearity between variables was assessed with variance inflation factors, none of which exceeded critical value. P < 0.05 was considered significant. Cross-section analysis weights were applied to make the study sample representative of the 2014 Indonesian population in the study provinces . Both the 95% confidence intervals and P-values were adjusted considering the survey design of the study. All analyses were done with STATA software version 13.0 .Sample and tobacco use characteristicsThe total sample included 8001 older adults, 50 years and older in Indonesia. The proportion of women was 51.9%, 72.1% of the sample had no or elementary education, 42.4% described themselves as having medium economic status, 52.1% resided in urban areas and 58.1% lived in Java. Regarding health variables, 46.9% were overweight or obese, 8.1% high total cholesterol or low-density lipoprotein (LDL), 58.5% had hypertension, 2.9% had a stroke, 3.6% heart attack, angina or other heart problems, 46.9% overweight or obese, 11.8% arthritis, 6.3% had diabetes, 3.4% asthma, 2.3% other lung conditions and 17.0% depression symptoms. One in three of the participants (32.9%) rated their health as poor, 31.5% had a functional disability, 29.3% low cognitive functioning and 33.5 inadequate fruit and vegetable consumption. The overall prevalence of current tobacco use was 33.3% (62.2% in men and 6.5% in women) and former tobacco use was 9.8% (17.4% among men and 2.8% in women), of which 64.4% quit tobacco use when 50 years and older. Smoking tobacco (94.4%) was the most prevalent type of current tobacco use, while smokeless tobacco use was 5.6%. Among the different tobacco users, 39.6% of women and 1.3% of men used smokeless tobacco currently. The prevalence of smokeless tobacco use increased by age group, 2.0% in the age group 50-59 years, 3.6% 60-69 years, 13.5% 70-79 years and 26.6% in the age group 80 years and older see .Associations with current and former tobacco use In adjusted multinomial regression analysis, sociodemographic factors and health variables were associated with current tobacco use among older adults. In addition, being overweight or obese, having had a stroke, and other lung conditions were inversely associated with current tobacco use. Further, in adjusted analysis, sociodemographic factors and having chronic conditions were associated with former tobacco use see .The study found a high prevalence of current tobacco use among older adults in Indonesia , which seem to be lower than in the latest (2011) Global Adult Tobacco Survey in Indonesia (more than 38%) , but higher than in many other countries . On the other hand the proportion of former tobacco use was low in this study, compared to studies in Ghana, Mexico, Russia and South Africa , but was similar to the low rates among older adults in China and India . Reasons for a possible decline of the prevalence of current tobacco use among older adults from 2011 to 2014/15 could be that a higher proportion of older adults quit tobacco use in the latest survey, which was 64.4% when they were 50 years and older, compared to a smoking quit rate of 51.5% within the past 10 years of persons 65 years and older in the 2011 survey . The study found some regional differences in the prevalence of current and former tobacco use, with higher rates in Sumatra compared to Java and major island groups. Reasons for this need further investigations. Intensified public health interventions are needed in targeting tobacco use in older adults in Indonesia.The study found that current tobacco use did not significantly decline with increasing older age, which was also found in a study in South Africa , while most studies seem to show a decline of current tobacco use with increasing age . On the other hand, older age was in this study, in agreement with previous studies associated with former tobacco use. The strong male preponderance of current and former tobacco use is also in line with previous studies , especially in low- and middle-income countries. These huge gender differences seem to reflect social norms in Indonesian or Asian culture being taboo for women to smoke . This finding is reinforced by the fact that a large proportion (39.6%) of older Indonesian women engaged in smokeless tobacco use. Although there was no significant difference in terms of age group and tobacco use, there was with ageing a significant increase in the use of smokeless tobacco, from 2.0% among 50-59 year-olds to 26.6% among individuals 80 years and older. Similar gender differences and increases of smokeless tobacco use with age have also been found in the 2011 Indonesia Global Adult Tobacco Use survey .Lower socioeconomic and/or educational status was in this study associated with current tobacco use, as found in previous studies . However, contrary to a previous study in Ghana , this study did not find an association between higher levels of education, increasing income levels and former tobacco use. Just like in several other middle-income countries , this study found an association between rural residence and current tobacco use. The prevalence of former tobacco users was in this study higher in urban than rural areas, as found in a study in Ghana , but this was statistically not significant.Several chronic conditions were in this study positively associated with current and/or former tobacco use. This has been partially also found in previous studies . Former tobacco users were significantly more likely to have five chronic conditions measured in this study, while current smokers had only three chronic conditions compared to never tobacco users. A possible reason for this is that tobacco users tend to quit after receiving a diagnosis of a chronic condition, likely to be related to tobacco use .Overweight or obesity was in this study negatively associated with current tobacco use, as also found in previous studies . Some research refers to nicotine intake as promoting satiety so that overweight development may be reduced .Having had a stroke and having other lung conditions (other than asthma) were in this study negatively associated with current tobacco use. It is possible that due to stroke and/or having lung conditions tobacco users quit tobacco use. This may be confirmed by the positive (but not significant) association between having other lung conditions and former tobacco use. Tobacco use may exacerbate existing chronic conditions in the increasingly ageing older population in Indonesia calling for a critical need for tobacco cessation programming .In agreement with several previous studies , this study found an association between insufficient fruits and vegetable consumption current tobacco use. It is possible that unhealthy behaviours such as inadequate fruit and vegetable consumption clusters with other risk behaviours such as current tobacco use. Unlike some previous studies , this study did not find an association between poor self-rated health, poor cognitive functioning and tobacco use. Limitations of the studyThe self-report of tobacco use has its limitations, especially among women and older adults. It is possible that individuals who reported not being a tobacco user misclassified their tobacco use status . Some indicators such as alcohol use and other drug use, formerly found associated with tobacco use were not assessed in this study and should be included in future investigations. In addition, this study used a cross-sectional design and therefore, we cannot ascribe causality to any of the associated factors in the study. In conclusion, this study reports high rates of current and low rates of former tobacco use among older adults (50 years and more) in Indonesia that puts them at increased risk of morbidity and mortality. Tobacco use among older adults is often under-recognized needing multilevel interventions. None declared."} +{"text": "The preAmong residents of urban areas, the prevalence of meeting the combined physical activity guidelines was higher overall during 2016\u20132017 (24.4%) than during 2008\u20132009 (19.8%), as well as across all demographic subgroups and in all Census regions . Among rSince release of the 2008 Physical Activity Guidelines for Americans, the prevalence of meeting the combined aerobic and muscle-strengthening physical activity guidelines among adults has increased in both urban and rural areas. Despite the increases, additional progress is needed. In 2017, only one in four (25.3%) urban residents and one in five (19.6%) rural residents met the combined guidelines. To continue and perhaps accelerate progress, communities can implement evidence-based approaches that make physical activity the safe and easy choice, including improvements to community design, improved access to indoor and outdoor recreation facilities, social support programs, and community-wide campaigns . Environmental differences might contribute to this finding. For example, environmental supports and nearby destinations including sidewalks, public transit, and shops can encourage physical activity, but are less common in rural than in urban areas in 2017.Since 2008, the prevalence of meeting physical activity guidelines increased from 19.4% to 25.3% among urban residents and from 13.3% to 19.6% among rural residents. Among urban residents, all subgroups reported increases, whereas among rural residents, no increases were reported among Hispanics and adults living in the South.Despite increases, physical activity prevalence remains low, especially for some rural subgroups with high incidences of chronic diseases. Incorporating culturally appropriate strategies into local, evidence-based programs might help communities build on recent progress."} +{"text": "To predict hospital admission at the time of ED triage using patient history in addition to information collected at triage.This retrospective study included all adult ED visits between March 2014 and July 2017 from one academic and two community emergency rooms that resulted in either admission or discharge. A total of 972 variables were extracted per patient visit. Samples were randomly partitioned into training (80%), validation (10%), and test (10%) sets. We trained a series of nine binary classifiers using logistic regression (LR), gradient boosting (XGBoost), and deep neural networks (DNN) on three dataset types: one using only triage information, one using only patient history, and one using the full set of variables. Next, we tested the potential benefit of additional training samples by training models on increasing fractions of our data. Lastly, variables of importance were identified using information gain as a metric to create a low-dimensional model.A total of 560,486 patient visits were included in the study, with an overall admission risk of 29.7%. Models trained on triage information yielded a test AUC of 0.87 for LR (95% CI 0.86\u20130.87), 0.87 for XGBoost (95% CI 0.87\u20130.88) and 0.87 for DNN (95% CI 0.87\u20130.88). Models trained on patient history yielded an AUC of 0.86 for LR (95% CI 0.86\u20130.87), 0.87 for XGBoost (95% CI 0.87\u20130.87) and 0.87 for DNN (95% CI 0.87\u20130.88). Models trained on the full set of variables yielded an AUC of 0.91 for LR (95% CI 0.91\u20130.91), 0.92 for XGBoost (95% CI 0.92\u20130.93) and 0.92 for DNN (95% CI 0.92\u20130.92). All algorithms reached maximum performance at 50% of the training set or less. A low-dimensional XGBoost model built on ESI level, outpatient medication counts, demographics, and hospital usage statistics yielded an AUC of 0.91 (95% CI 0.91\u20130.91).Machine learning can robustly predict hospital admission using triage information and patient history. The addition of historical information improves predictive performance significantly compared to using triage information alone, highlighting the need to incorporate these variables into prediction models. While most emergency department (ED) visits end in discharge, EDs represent the largest source of hospital admissions . Upon arPrediction models in medicine seek to improve patient care and increase logistical efficiency ,3. For eNumerous prior studies have sought to predict hospital admission at the time of ED triage. Most models only include information collected at triage such as demographics, vital signs, chief complaint, nursing notes, and early diagnostics ,14\u201319, wFurthermore, many prior studies have been limited by technical factors, where continuous variables are often reduced to categorical variables through binning or to binary variables encoding presence or missing-ness of data due to the challenges of imputation ,16,19\u201321Expanding on prior work ,12,20, wRetrospective data was obtained from three EDs covering the period of March 2013 to July 2017 to ensure a 1-year of historical timeframe from the study start period of March 2014. The represented EDs include a level I trauma center with an annual census of approximately 85,000 patients, a community hospital-based department with an annual census of approximately 75,000 patients, and a suburban, free-standing department with an annual census of approximately 30,000 patients. All three EDs are part of a single hospital system utilizing the Epic EHR and the Emergency Severity Index (ESI) for triage. The study included all visits for adult patients with a clear, recorded disposition of either admission or discharge. Individuals with any other disposition, such as transfer, AMA, and eloped, were excluded. This study was approved, and the informed consent process waived, by the Yale Human Investigation Committee (IRB 2000021295).For each patient visit, we collected a total of 972 variables, divided into major categories shown in The primary response variable was the patient's disposition, encoded in a binary variable .Demographic information, either collected at triage or available from EHR at the time of patient encounter, included age, gender, primary language, ethnicity, employment status, insurance status, marital status, and religion. The primary language variable was recoded into a binary split , while the top twelve levels comprising >95% of all visits were retained for the religion variable and all other levels binned to one 'Other' category. All unique levels were retained for other demographic variables.Triage evaluation included variables routinely collected at triage, such as the name of presenting hospital, arrival time , arrival method, triage vital signs, and ESI level assigned by the triage nurse. Triage vital signs included systolic and diastolic blood pressure, pulse, respiratory rate, oxygen saturation, presence of oxygen device, and temperature. Values beyond physiologic limits were replaced with missing values.Given the high number of unique values (> 1000) for chief complaint, the top 200 most frequent values, which comprised >90% of all visits, were retained as unique categories and all other values binned into 'Other'.The number of ED visits within one year, the number of admissions within one year, the disposition of the patient's previous ED visit, and the number of procedures and surgeries listed in the patient's record at the time of encounter were taken as metrics for prior hospital usage.ICD-9 codes for past medical history (PMH) were mapped onto 281 clinically meaningful categories using the Agency for Healthcare Research and Quality (AHRQ) Clinical Classification Software (CCS), such that each CCS category became a binary variable with the value 1 if the patient's PMH contained one or more ICD-9 code belonging in that category and 0 otherwise.Outpatient medications listed in the EHR as active at the time of patient encounter were binned into 48 therapeutic subgroups used internally by the Epic EHR system, with each corresponding variable representing the number of medications in that subgroup.A time-frame of one year from the date of patient encounter was used to calculate historical information, which included vital signs, labs and imaging previously ordered from any of the three EDs. Historical vital signs were represented by the minimum, maximum, median, and the last recorded value of systolic blood pressure, diastolic blood pressure, pulse, respiratory rate, oxygen saturation, presence of oxygen device, and temperature. Values beyond physiologic limits were replaced with missing values.Given the diversity of labs ordered within the ED, the 150 most frequent labs comprising 94% of all orders were extracted then divided into labs with numeric values and those with categorical values. The cutoff of 150 was chosen to include labs ordered commonly enough to be significant in the management of most patients , even if they were not as frequent as routine labs like CBC, BMP, and urinalysis. The minimum, maximum, median, and the last recorded value of each numeric lab were included as features. Categorical labs, which included urinalysis and culture results, were recoded into binary variables with 1 for any positive value and 0 otherwise. Any growth in blood culture was labeled positive as were urine cultures with > 49,000 colonies/mL. The number of tests, the number of positives, and the last recorded value of each categorical lab were included as features.The number of orders were counted for each of the following categories: electrocardiogram (EKG), chest x-ray, other x-ray, echocardiogram, other ultrasound, head CT, other CT, MRI, and all other imaging.A series of nine binary classifiers were trained using logistic regression (LR), gradient boosting (XGBoost), and deep neural networks (DNN) on three dataset types: one using only triage information, one using only patient history, and one using the full set of variables . All anaA randomly chosen test set of 56,000 (10%) samples was held out, then the remaining 504,486 (90%) samples split randomly five times to create five independent validation sets of 56,000 (10%) and training sets of 448,486 (80%). Hyperparameters for each model were optimized by maximizing the average validation AUC across the five validation sets. The optimized set of hyperparameters was then used to train the model on all 504,486 (90%) samples excluding the test set. Finally, the test AUC was calculated on the held-out test set, with 95% confidence intervals constructed using the DeLong method implemented in the pROC package ,31. YoudCategorical variables were converted into binary variables prior to training using one-hot encoding . The medOne key question in predictive modeling is whether additional training samples will improve performance or whether a model has reached its maximum performance given the inherent noise in its features . To testInformation gain is a metric that quantifies the improvement in accuracy of a tree-based algorithm from a split based on a given variable . We calcA total of 560,486 ED visits were available for analysis after filtering for exclusion criteria, with 13% of the samples excluded due to disposition other than admission or discharge. The visits represented 202,953 unique patients, with a median visit count of 1 and a mean visit count of 2.76 per patient during the study duration. The overall hospital admission risk was 29.7% and decreased by triage level: ESI-1 85.6%, ESI-2 55.0%, ESI-3 29.1%, ESI-4 2.2%, and ESI-5 0.4% . CharactModels trained on triage information yielded a test AUC of 0.87 for LR (95% CI 0.86\u20130.87), 0.87 for XGBoost (95% CI 0.87\u20130.88) and 0.87 for DNN (95% CI 0.87\u20130.88). Models trained on patient history yielded an AUC of 0.86 for LR (95% CI 0.86\u20130.87), 0.87 for XGBoost (95% CI 0.87\u20130.87) and 0.87 for DNN (95% CI 0.87\u20130.88). Models trained on the full set of variables yielded an AUC of 0.91 for LR (95% CI 0.91\u20130.91), 0.92 for XGBoost (95% CI 0.92\u20130.93) and 0.92 for DNN (95% CI 0.92\u20130.92). The addition of historical information improved predictive performance significantly compared to using triage information alone . NotablyFor LR, the 95% CI of the AUC of the model trained on 10% of the training set contained the AUC of the model trained on the entire training set. For XGBoost and DNN, the point at which this occurred was at 50% of the training set . All AUCVariables of importance extracted from a hundred iterations of the full XGBoost model are shown in We describe a series of prediction models for hospital admission that leverage gradient boosting and deep neural networks on a dataset of 560,486 patient visits. Our study shows that machine learning can robustly predict hospital admission at emergency department (ED) triage and that the addition of patient history improves predictive performance significantly compared to using triage information alone, highlighting the need to incorporate these variables into predictive models.In order to test whether additional training samples will improve performance, we train our models on increasing fractions of the training set and show that the AUC plateaus well below the full training set. This result suggests that we have likely maximized the discriminatory capability for our feature set. More studies will be required to develop features that may further improve performance. We expect that many of these features will be derived from free-text data in the electronic health record (EHR). Specifically, natural language processing of medical notes may provide an informative set of features that capture information absent in tabular data. Recent prediction models on outcomes ranging from sepsis to suicide have demonstrated success with these approaches ,26,40,41The ranking of information gain extracted from the gradient boosting (XGBoost) model present a number of notable features. In particular, the importance of medication counts in the model may either reflect a proxy feature for medical complexity or indicate that polypharmacy itself is a risk factor ,43. Not This study has a number of limitations. We chose to restrict patient history to information gathered from previous ED visits and anticipate that expanding the sources of historical data may improve model performance. Importing historical data from outpatient clinics or inpatient wards may present technical difficulties regarding EHR integration and differing standards of care. Furthermore, the data utilized in this study came from a hospital system that includes multiple emergency departments with a large catchment area. We anticipate difficulties extending this study to datasets from dense urban areas with multiple independent EDs, given that patients may not consistently present to the same hospital system. Ongoing progress with inter-system information sharing presents one path forward, and this study highlights the importance of those efforts ,50.Throughout this study, we predict patient disposition by using the ED provider's prior decision as our true label. In doing so, we are unable to address the appropriateness of individual clinical decisions. This and similar studies would benefit from further research into a gold-standard metric for hospital admission. Studies have suggested that such a metric will remain elusive ,52. HoweLastly, this study does not address the implementation and efficacy barriers present in clinical practice . While wS1 TableDescriptions of all 972 variables included in the study.(XLSX)Click here for additional data file.S2 TableMean information gain for top variables from 100 runs of XGBoost.(XLSX)Click here for additional data file.S1 Fig(TIF)Click here for additional data file.S1 TextDetails on the model fitting process, including the link to the de-identified dataset and R scripts.(DOCX)Click here for additional data file."} +{"text": "Database methodology was previously discussed here. We queried studies using keywords from the 24 major skin disease categories . We collected data on study design, reporting methods, and analyzed relevant data stratified by 2 time-periods (1976\u20132008 and 2009\u20132014) chosen to encompass a comparable number of studies. RESULTS/ANTICIPATED RESULTS: In total, 42 and 50 studies corresponding to the 2 time-periods were retrieved (representing 14/24 disease categories). Based on the recommended data reporting guidelines for CUAs, study quality remained largely unchanged across the 2 phases. Across the 2 time-periods, a societal perspective was used in 19% and 12% of studies, costs and QALYs were discounted in 67% and 72% of studies, a correct ICER was reported in 67% and 72% of studies, and a sensitivity analysis was included in 88% and 84% of studies, respectively. DISCUSSION/SIGNIFICANCE OF IMPACT: Our findings suggest the quality of dermatology-related CUAs, as evaluated by recommended data reporting guidelines, to be generally stable during the analyzed time-periods. However, the quality of our results may be limited by the small number of CUAs within dermatology (10/24 disease categories did not have CUAs across any time-period). Moving forward, we encourage researchers within dermatology to pursue additional investigation towards cost-effective practices while adhering closely to recommended quality reporting guidelines for CUAs.OBJECTIVES/SPECIFIC AIMS: Costs associated with the treatment of skin diseases accounted for greater than 4% of total US healthcare spending in 2013, an increase of $46 billion (170%) since 2004. Considering the increase in novel treatments and spending, cost-utility analyses (CUAs) may provide a better understanding of costs in dermatology. In this study, we conduct a systematic overview of study quality among CUAs related to dermatology. METHODS/STUDY POPULATION: We queried studies from the Tufts Medical Center Cost-Effectiveness Analysis Registry ("} +{"text": "We investigated progress towards UNAIDS 90-90-90 targets among female sex workers in Kampala, Uganda, who bear a disproportionate burden of HIV.Between April and December 2012, 1,487 female sex workers, defined as women, 15\u201349 years, residing in greater Kampala, and selling sex for money in the last 6 months, were recruited using respondent-driven sampling. Venous blood was collected for HIV and viral load testing . We collected data using audio computer-assisted self-interviews and calculated weighted population-level estimates.The median age was 27 years (interquartile range: 23 to 32). HIV seroprevalence was 31.4% . Among all female sex workers who tested HIV-positive in the survey (population-level targets), 45.5% had knowledge of their serostatus (population-level target: 90%), 37.8% self-reported to be on ART (population-level target: 81%), and 35.2% were virally suppressed (population-level target: 73%).HIV prevalence among Kampala female sex workers is high, whereas serostatus knowledge and VLS are far below UNAIDS targets. Kampala female sex workers are in need of intensified and targeted HIV prevention and control efforts. In 2014, the Joint United Nations Programme on HIV/AIDS (UNAIDS) launched three treatment targets to achieve epidemic control by 2020; that is, 90% of all people living with HIV will know their HIV status, 90% of those diagnosed with HIV infection will receive antiretroviral therapy (ART), and 90% of all people receiving ART will have viral suppression (90-90-90 targets)[Key populations such as female sex workers are considered a priority population in efforts to achieve 90-90-90 targets. Female Uganda has a mature, generalized HIV epidemic; however, sex work is likely an important driver of sexual transmission. AccordiScale-up of prevention and treatment programs could reduce HIV transmission among female sex workers, however, the effectiveness of these interventions are dependent on the extent to which Ugandan female sex workers engage in prevention and treatment services. Being tested and knowing one\u2019s HIV status is associated with a reduction in HIV risk behaviors, prevents onward transmission, and can lead to mobilization of support networks , increasFemale sex workers were recruited using respondent driven sampling (RDS), a modified form of chain-referral sampling with a mathematical system for weighting, suitable for hard-to-sample populations, 15. RecEligible and consenting women were interviewed using audio computer assisted self-interview (ACASI) in either Luganda or English. The interview\u2019s key domains included demographics, lifetime sexual characteristics, sexual behaviors in the last three months, sexual violence, and HIV testing and treatment history. Other data measures included alcohol use and drug use (including injection drug use).All HIV testing was voluntary. Ugandan ministry of guidelines for HIV counseling, testing and referral services were followed. Pre-tesrd generation and Murex HIV Ab, 3rd generation in parallel. STAT-PAK was used as a tiebreaker for discordant results. Respondents with concordent reactive results or STAT-PAK reactive results were classified as HIV seropositive. HIV seropositive specimens were further tested for viral load using COBAS TaqMan\u00ae assay. An undetectable viral load was defined as <50 copies/ml and viral load suppression was defined as <1000 copies/ml, chosen based on World Health Organization guidelines[Treponema pallidum (TP) infection, using the anti-syphilis IgG ELISA and, if reactive, the rapid plasma reagin (RPR) Syfacard-R Test . Respondents with RPR-reactive test results were classified as having active TP infection.At their initial visit, female sex workers provided a venous blood sample for HIV and syphilis testing and, if HIV-positive, for CD4+ T cell count and viral load. HIV serologic testing was conducted at the Uganda Virus Research Institute (UVRI) laboratory in Entebbe using Vironostika\u00ae Uniform II plus O2, 3uidelines. Plasma In total, 1,497 female sex workers were included in the analysis, including 2 of the 4 seeds. Two seeds were unproductive and did not recruit other female sex workers. RDS Analyst (RDS-A) v5.7 was used to generate unweighted and weighted descriptive statistics. We utilWe defined serostatus knowledge as an HIV seropositive female sex workers who reported a previous positive test result. Female sex workers were classified as on ART if she self-reported ART use among those who reported a previous positive test result. VLS was defined as <1,000 copies/ml among those female sex workers self-reporting ART use.Population-level estimates of each unconditional 90 target were calculated using all HIV seropositive FSW as the denominator, i.e., the proportion of all HIV seropositive female sex workers who reported a previous positive test, reported ART use, or were virally suppressed.Weighted logistic regression was used to examine bivariate associations between serostatus knowledge, ART use, or viral suppression and demographic characteristics, sexual behaviors, substance use, drug use, HIV knowledge, and STI history. All regression analyses were conducted using SAS 9.4 .We conducted a sensitivity analysis for population-level estimates of 90-90-90 targets by assuming that any female sex workers with viral suppression was taking ART at the time of the study, and further that all female sex workers on ART knew their serostatus. We also varied the definition of viral load suppression. We calculated population level estimates for 90-90-90 targets with viral load suppression defined as <50 copies/ml and <200 copies/ml.The study protocol and consent procedures were approved by the human subjects protection boards at Makerere University School of Public Health, the Uganda National Council of Science and Technology (UNCST), and Centers for Disease Control and Prevention (CDC). Informed consent was obtained verbally and separately for interview, blood draw and testing, as well as storage of specimens for future testing. No personal identifiers were collected; biomarker results were returned to recruits at their scheduled return visit, three weeks following the initial visit. Recruits testing positive for syphilis were offered treatment; those testing HIV-positive were referred to care and ART per national guidelines. Female sex workers between the ages of 15\u201317 years were treated as emancipated minors and provided informed consent themselves.Of 4,018 coupons issued, 1,915 (47.7%) were redeemed. Of the 1,915 redeemed, 1,501 (78.4%) women were eligible to participate and 1,497 completed the visit and were included in the analyses. Women were ineligible if they had not sold sex in the 6 months prior and were under the age of 15. Unweighted demographic characteristics and weighted population estimates are reported in The estimated HIV prevalence was 31.4% . Among aAmong HIV seropositive female sex workers, 48.7% reported a previous positive HIV test result, whereas only 7.8% perceived themselves to be HIV positive. Among seropositive female sex workers who reported a previous positive HIV test result (n = 123), 67.7% indicated they were taking ART. An estimated 51.6% of female sex workers were virally suppressed among women who self-reported ART use. The prevalence of unsuppressed viremia was estimated at 14.7% Among seropositive female sex workers, serostatus knowledge was 26.8%, 18% reported being on ART, and 35.2% were virally suppressed . Under tWhen viral load suppression was defined as <200 copies/ml, serostatus knowledge, ART use, and viral load suppression decreased to 38.8%, 30.2%, and 27.4%, respectively . When viFemale sex workers who started sex work at the age of 25 or older had 0.57 times the odds of not knowing their serostatus and 0.47st and 2nd 90\u2019s by respondents\u2019 VLS status, we still found that only a minority of HIV positive female sex workers were aware of their HIV status (45.5%), only 37.8% were on ART, and just 35.2% were virally suppressed. These estimates are much lower than UNAIDS population-level 90-90-90 targets of 90%, 81%, and 73%, respectively.HIV prevalence among Kampala female sex workers (31.4%) is more than three times the HIV prevalence of the general female population of reproductive age in Kampala (9.5%). The higThe HIV prevalence among female sex workers in Uganda is consistent with previously reported studies in 2009 , 20. SexAmong seropositive female sex workers, self-reported serostatus knowledge was low and likely to be an underestimate as demonstrated in previous studies. We atteThere was marked discordance between actual serostatus and perceived serostatus. While 48.7% of seropositive women (among those previously tested for HIV) reported a previous positive test result, only 7.8% of seropositive women believed themselves to be positive and 79.3% indicated they did not know their status. We speculate that women on ART with VLS were more likely to believe they were no longer HIV-positive. Whether women are embarrassed or frightened to acknowledge their serostatus, or believe that ART is a \u2018cure,\u2019 additional education and counseling is urgently needed.We speculate that the self-reported estimate for ART use is an underestimate. Female sex workers were only asked if they were on ART if they had previously reported a positive HIV test result. Like serostatus knowledge, we corrected our ART estimate by including women with VLS. Our estimate of 37.8% is similar to past studies in surrounding countries. In Mozambique, only 30\u201340% of eligible female sex workers self-reported ART use , and simVLS was low 35.2%) compared to other studies among female sex workers. In a 2014 Malawi study, almost half of HIV-positive female sex workers were virally suppressed . Similar.2% compaThere are number of limitations to our study. Female sex workers who received a coupon had to travel to the survey site to participate. Eligible female sex workers were then asked to provide self-reported data, which could be subject to recall bias. Social desirability bias could impact our results, as under-reporting of factors related to HIV, such as the number of clients, known serostatus, and self-reporting of ART are possible. We aimed to minimize these biases through the confidential nature of ACASI. Viral load data was not available for 29% of seropositive female sex workers and the questionnaire did not ask about the date of diagnosis, nor did it include time to treatment initiation or time since ART initiation, making qualification of VLS difficult. Additionally, HIV risk dynamics among female sex workers can vary substantially by the type and structure of the sex work and can change over time, 41. OurDespite these limitations, the high prevalence of HIV and low proportion of HIV-positive female sex workers with VLS is concerning. Reduction of barriers to service utilization among both the general population and female sex workers must be addressed. Increasing testing uptake, more effective linkage to and uptake of ART, along with condom and pre-exposure prophylaxis (PrEP) provision by increasing service awareness and flexibility will be useful. Efforts that facilitate female sex workers\u2019 ability to negotiate safer sex-work environments and criminalize abuse are urgently needed. Incorporation of community- and rights-based approaches with tailored prevention packages that included engagement of peer networks may reduce stigma and discrimination. Ongoing surveillance of HIV incidence and VLS in this population should occur to monitor trends in order to inform HIV control and prevention programs. A combination of intensified interventions promoting prevention and treatment are necessary if we are to achieve the ambitious 90\u201390\u201390 targets in Uganda."} +{"text": "Preterm birth refers to a birth of a baby before 37 completed weeks of gestation and after fetal viability. It is now the leading cause of new born deaths. Although identifying its common risk factors is mandatory to decrease preterm birth and thereby neonatal deaths, there was a dearth of studies in the study area. The aim of this study was to identify determinants of preterm birth among women who gave birth in Amhara region referral hospitals, Northwest Ethiopia, 2018. p-value <0.05 in binary logistic regression were the candidate for multivariable analyses. Finally, the statistical significance of the study was claimed based on the Adjusted Odds Ratio (AOR) with 95% Confidence Interval (CI) and its p-value <0.05. An institutional based case-control study was conducted from September 01 to December 01/2018. A total of 405 mothers (135 cases and 270 controls) were included in the study. Multistage sampling technique was employed. Data were collected using structured questionnaire through face to face interview and checklist via Chart review. Data were entered into Epi Info version 7 and export to Statistical Package for Social Sciences (SPSS) version 20 for analysis. Descriptive statics like mean, frequency and percentage was used to describe the characteristics of participants. Both bivariable and multivariable analyses were carried out. Variable having \u2009 The result of multivariable analysis show that mothers with no formal education , history of abortion , multiple gestation , hemoglobin level <11\u2009gm/dl , premature rupture of membrane and pregnancy induced hypertension had statistically significant association with experiencing preterm birth. Most of the determinants of preterm birth found to be modifiable. Thus, putting emphasis for prevention of obstetric and gynecologic complications such as anemia, premature rupture of membrane and abortion would decrease the incidence of preterm birth. Moreover, strengthening Information Communication Education about prevention of preterm birth was recommended. Preterm Birth (PTB), which refers to the birth of a baby before 37 complete weeks of gestation, poses multi-dimensional adverse consequences \u20139. GlobaPrematurity causes enormous impacts . It is nTo alleviate this burden, efforts have been taken globally. For instance, Sustainable Development Goal (SDG) 3 target 2 is planned to end preventable death of new born and CUFYs . In thisAn institutional based unmatched case-control study was conducted from September 1 to December 1/2018 in referral hospitals which is found in Amhara National Regional State (ANRS).ANRS is one of the nine national states in Ethiopia which is found on the Northwestern part of Ethiopia. The region has 67 hospitals, 734 health centers, and 2941 health posts. There are 5 referral hospitals\u2014namely Gondar University Comprehensive Specialized Hospital (GUCSH), Felegehiwot Comprehensive Specialized Hospital (FCSH), Dessie Referral Hospital (DRH), Debre-Markos Referral Hospital (DMRH) and Debre-Birhan Referral Hospital (DBRH). Each hospital serves for nearly 5 million people, poses 200\u2013400 beds, and conducts 2000\u20134000 deliveries per year and 5\u201310 deliveries per day.Three out of five of referral hospitals has been selected randomly using lottery method. These include; Felegehiwot Comprehensive Specialized Hospital (FCSH), Debre-Markos Referral Hospital (DMRH) and Debre-Birhan Referral Hospital (DBRH). All women who gave birth in the selected referral hospitals during the study period were taken as study population. Thus, all immediate postnatal women who gave live birth at the selected referral hospitals during the study period that had been included whereas those mothers who had neither certain Last Menstrual Period (LMP) nor early ultrasound (U/S) evidences, had been excluded.The sample size had been calculated through Epinfo version 7 by considering the following assumptions: ratio of control to case 2\u2009:\u20091; power 80%; confidence level 95%, precision level 5%, Odds Ratio (OR) 3.81, design effect 1.5, nonresponse rate 10%, and percent of birth defect among controls (nonpreterm births) and cases (preterm births) 5.1 and 17 respectively from the study conducted in Tigray . This prst ANC visit, frequency of ANC, history of obstetric complications (Premature Rupture of Membrane (PROM), Antepartum Hemorrhage (APH), preeclampsia/eclampsia and poly/oligohydramnios) in the index pregnancy, history of preterm birth, multiple pregnancy, history of previous multiple pregnancy, history of abortion, iron provision, duration of iron provision, onset of labour, syphilis, Hemoglobin (HGB) level, history of chronic Hypertension (HTN), Urinary Tract Infection (UTI), Sexually Transmitted Diseases (STD) including HIV, Malaria, Mid Upper Arm Circumference (MUAC), maternal height, smoking, congenital anomalies, and birth weight. Moreover, cases (preterm births) and controls (nonpreterm births) had been selected based on the Gestational Age (GA) assessment.Socio-demographic, obstetric, medical, nutritional and fetal related variables had been incorporated. These include maternal age, residence, religion, maternal occupation, marital status, spouse occupation, maternal educational status, ethnicity, family size, spouse educational status, distances from home to nearest health facility, family monthly income, parity, inter-pregnancy interval, planned pregnancy, bad obstetrics history, Antenatal Care (ANC) visit, time of 1The GA had been determined based on a certain Last Menstrual Period (LMP) date and/or early pregnancy ultrasound (U/S) established date (up to and including 20 completed weeks of gestation). When the LMP and U/S dates had not been correlated, defaulting to U/S for GA assessment was required in accordance with the American College of Obstetricians and Gynecologists (ACOG) recommendation , 26. ThoData were collected using structured questioner and check list through face to face interview and chart review respectively. Questioner and checklists were developed after reviewing of various relevant literature , 27\u201330. p-value <0.05 were fitted to multivariable logistic regression model using Backward Stepwise method. Both Crude Odds Ratio (COR) and Adjusted Odds Ratio (AOR) with the corresponding 95% Confidence Interval (CI) were computed to show the strength of the association. Finally, statistically significant association of variables had been claimed based on the AOR with its 95% CI and p-value <0.05. In addition, model fitness had been checked using Hosmer and Lemeshow goodness of a fit test (P = 0.3).Data were then entered in to Epi info statistical software version 7 and exported to SPSS version 20 for cleaning, recoding, categorizing and analyzing. Both descriptive and analytical statistical procedures had been utilized. Descriptive statistical like mean, frequency and percentage were used to describe the characteristics of participants and results presented using tables, graph and text. Binary logistic regression was used to identify factors associated with preterm birth. Finally, variables with In this study, about 405 mother-newborn pairs (135 cases and 270 controls) had been participated with the overall response rate of 94%. Majority of respondents (about 77.1% of cases and 84.1% of controls) were in the age group of 20\u201334 years with the mean (\u00b1Standard Deviation (SD)) of 28.6 (\u00b15.4) for cases and 26.5 (\u00b15.2) for controls. Most of the respondents (95.6% of cases and 91.1% of controls) were Orthodox Tewahido religion follower. Nearly all (97% of cases and 96.3% of controls) were belong to Amhara in Ethnicity. More than half (52.6%) of cases and one-third (35.2%) of controls were rural dwellers. In addition, about, 64 (47.4%) of cases and 70 (25.9) of controls had no formal education. Almost all respondents (99.3% of cases and 97% of controls) were in marriage relationship. More than four in five participants (84.4% of cases and 94.1% of controls) had total family size of \u22645. The time taken to the nearest health facility for most of the respondents (77.8% of cases and 141 89.3% of controls) observed to be \u22641 hour .st16 weeks of gestation). Of multiparous mothers, about 34 (25.2%) in cases and 43 (15.9%) in controls had one or more previous history of bad obstetric complications. Majority (86.5% in cases and 91.3% in controls) of mothers had received Iron supplementation in the index pregnancy (More than two-fifth respondents (43.7% in cases and 55.6% in controls) were primiparous. Among Multigravida mothers, considerable participants (5.9% in cases and 3.3% in controls) had history of previous PTB and significant respondents (18.5% in case and 3.3% in controls) had history of abortion. Similarly, substantial proportion of respondents (9.6% in cases in controls) had unplanned pregnancy. Large number of participants (94.3% in cases and 93.0% in controls) had ANC follow up during the most recent pregnancy. Among mothers who had ANC visit in the indexed pregnancy, majority (60.7%) in cases and nearly one-third (29.6%) in controls had incomplete ANC visits. And 42 (31.1%) of cases and 76 (30.3%) of controls had started their ANC visit timely of cases and two-third (62.2%) of controls. Most of the respondents (90.4% in cases and (95.9% in controls) had HGB level \u226511\u2009gram/deciliter. Similarly, almost all (99.3% in cases and 99.3% in controls) mothers \u2265150\u2009cm tall. On the other way, none of the respondent had history of cigarette smoking.Findings from the bivariate logistic regression analysis show that age, residence, total family size, educational status of the women, distances from home to the nearest health facility, parity, previous history of abortion, multiple pregnancy, PROM, PIH, bad previous obstetric history and HGB level were statically associated with PTB.However, in the multivariable logistic regression analysis; lower maternal educational status , low HGB level . PROM , PIH , abortion and multiple pregnancies had statistically significant association with PTB .PTB remains a leading cause of neonatal deaths in Ethiopia where lack of reliable information on predictors of PTB is common. This study was aimed at identifying determinants of PTB among women who gave birth in referral hospitals in ANRS, northwest Ethiopia. The odds of giving PTB were higher among mothers who had HGB level <11\u2009gm/dl, history of abortion, PROM in the index pregnancy, PIH in the index pregnancy, multiple pregnancies and no formal education.The result of the present study showed that the odds of PTB in women with HGB level <11\u2009gm/dl were 2.75 times higher than that in women with HGB\u2009\u2265\u200911\u2009gm/dl. Similar findings have been reported in other studies conducted in Malawi and EastIn this study, history of abortion was found to be a significant risk factor for PTB. Accordingly, mothers who had history of abortion were 2.92 times more likely to give PTB as compared to those women who had no history of abortion. Similarly, statistically significant association between history of abortion and PTB have been observed in other studies done in Brazil , Iran 3 and nortThe present study found that the risk of PTB was 4.674 folds higher in women with PIH than that in those women with no PIH. This finding is in line with the result of studies done in Wuhan China , NairobiThe result from multivariable regression analysis in the present study shows that multiple pregnancies have been associated with the increased likelihood of PTB. Thus, women with multiple pregnancies were 4.1 times more likely to experience PTB as compared to those women with singleton pregnancies. Similar results have been reported from other studies conduct in Brazil , 45, IraWe found that mothers with PROM had more than six-fold increased the likelihood of having PTB as compared to mothers with no PROM. This is consistent with the study done in Nigeria and KenyIn the current study, the odds of giving PTB were 2.3 times higher among women who had never attended formal education than those women who had ever attended. The finding is in agreement with the report of other studies conducted in Northern Albia , Brazil There might be a recall bias in some variables' measurement although attempts had been taken to minimize recall biases by informing the local events.The odds of giving PTB was higher among women with low HGB level, no formal education, history of abortion, PIH, PROM and multiple pregnancy in the index pregnancy. Most of the determinants of PTB were found to be modifiable. Thus, putting emphasis for prevention of obstetric and gynecologic complications such as anemia, PROM and abortion would decrease the incidence of PTB. Moreover, strengthening Information Communication Education about prevention of PTB has been recommended."} +{"text": "Diabetes among older people is becoming more common worldwide, and usually accompanied by polypharmacy. However, the role of polypharmacy in older people with diabetes remains uncertain. A nationally representative cross-sectional study, ELSA 2012/2013, was used and 7729 participants aged 50-109 were investigated. Polypharmacy was defined as taking five to nine long-term used medications daily for chronic diseases or chronic symptoms, while using ten or more medications was excessive polypharmacy. The presence of illness was defined as either self-reported diagnosis or being prescribed specific medications for the condition. Data showed the prevalence of polypharmacy was 21.4%, and only 3% was excessive polypharmacy. 51.6% of diabetic people reported polypharmacy and 10.2% excessive polypharmacy. These rates were significantly higher than the 16.4% polypharmacy and 1.8% excessive polypharmacy among people without diabetes (p < 0.001). Among people with three or more comorbidities, polypharmacy was present in 61.5% of people with diabetes, compared with 36.0% in people without diabetes. Significant risk factors for polypharmacy were diabetes , older age , male , more comorbidity , living with a partner , and less wealth . However, age, cohabitation, and wealth were not significantly related to excessive polypharmacy. Diabetes and the number of comorbidities were predominant risk factors for excessive polypharmacy. Current evidences confirmed both health condition and socioeconomic status were associated with medication use in older adults."} +{"text": "Purpose: To estimate the proportion of Chinese cancer survivors experienced financial hardship and then examine whether older age was associated with financial hardship. Methods: We surveyed 965 cancer survivors 30 to 64 years of age and 643 cancer survivors age >=65 years in China. Cancer survivors were asked whether (1) they have borrowed money because of cancer, its treatment, and lasting effects of treatment and (2) they have forgone some cancer-related medical care because of cost. Multi-variable logistic regression models were used to examine factors associated with financial hardship. Results: About 44% of cancer survivors older than 65 borrowed money because of cancer, and 18% had borrowed more than 20,000 CNY . In contrast, 54% of younger patients (P<0.01) had cancer-related debts, and 32% had to borrow more than 20,000 CNY. About 11% of cancer survivors have forgone cancer care in both age groups. The logistic regression analyses show that being 65 or older was 43% less likely to report cancer-related debts than younger patients . Among older cancer survivors, those who were older than 75, female, and had Urban Employee Medical Insurance and higher family income were less likely to report financial hardship. Conclusion: Older cancer survivors in China experience significant financial hardship, but not as striking as younger patients. Additional research is needed to analyze whether the finding is associated with the Chinese family structure and traditional filial piety culture."} +{"text": "Trends in Geriatric Physical Assault Injuries Treated in US Emergency Departments, 2006-2015 Older adults are common victims of assault, many of which may result in severe injuries. Our objective was to understand temporal and demographic trends in geriatric assault injuries treated at U.S. Emergency Departments (EDs) and to compare these trends to assault injuries in younger adults. We conducted an analysis of assault injuries in patients aged \u226560 compared to patients aged 18-59 treated in EDs during 2006-2015 using the National Electronic Injury Surveillance System-All Injury Program Special Study of Assaults, which collects data from a nationally representative stratified probability sample of U.S. hospitals. Total geriatric assaults seen in EDs increased from 35,135 in 2006 to 69,657 in 2015, a 98% increase. These injuries increased as a percentage of all geriatric injuries treated from 0.9% to 1.1%. Assaults in older men increased 119%, while assaults in older women increased 68%. Among age groups, the biggest percentage increases were among adults aged 60-64 (138%) and aged 65-74 (89%). ED visits for injuries associated with physical elder abuse increased from 13,241 in 2006 to 27,406 in 2015, a 107% increase. During this period, number of younger adults treated for assault did not significantly change. We concluded that geriatric assault injuries, particularly in older men in younger age groups, are dramatically increasing. Further research is needed to better understand these assaults to develop prevention strategies."} +{"text": "Pithecellobium unguis-cati, Mora oleifera, Terminalia cattapa and Thespesia populnea maintained growth rates close to those of controls at 90 % seawater. In contrast, inland species such as Minquartia guainensis, Apeiba membranacea, Ormosia coccinea and Ochroma pyramidale showed strong reductions in growth rates and high mortality. Plant height and leaf production also differed greatly between the two groups of plants. Furthermore, measurements of gas exchange parameters, i.e. stomatal conductance and maximum photosynthetic rate, were consistent with the contrasting growth responses of coastal and inland species. Our research reveals a great degree of variation in salinity tolerance among tropical tree species and demonstrates a close relationship between species habitat and the ability to thrive under increasing salt concentration in the soil, with coastal species being better adapted to withstand increased soil salinity than non-costal species.Sea-level rise will result in increased salinization of coastal areas. Soil salinity is a major abiotic stress that reduces plant growth, yet tolerance to salinity varies across environmental conditions, habitats and species. To determine salinity tolerance of 26 common tropical tree species from Panama, we measured growth, gas exchange and mortality of 3-month-old seedlings subjected to weekly irrigation treatments using five seawater solutions for ~2 months. In general, species from coastal areas were more tolerant to increased seawater concentration than inland species. Coastal species such as We examined salinity tolerance among 26 common tropical tree species found along coastal and inland wet forests of Panama. While salinity tolerance varies greatly among tropical tree species we found a close relationship between species habitat and the ability to thrive under increasing salt concentration in the soil, with coastal species being better adapted to withstand increased soil salinity than non-coastal species. Climate change is causing sea level to rise . Salt inSalinity represents a major problem for many plants, e.g. non-halophytes . In the Citrus spp. (Persea americana) (Olea europaea), pine (Pinus radiata) (Pistacia vera) , an exclusive crop of temperate zones, is achieved by combining biochemical control of osmoregulation and reactive oxygen species (ROS), and physiological and structural adaptations are widely recognized in alleviating soil salt stress when the proper mycorrhizal lines are used , eucalypgrandis) , olive tradiata) and pistCoastal marine conditions influence tree species distribution , operated and maintained by the Smithsonian Tropical Research Institute. Plants were cultivated underneath a glass-roof that prevented rainfall from entering the pots. Plants grew under close to full sunlight conditions, natural air circulation, and natural temperature and relative humidity conditions.Twenty-six species of trees native or naturalized to Panama, from coastal and inland forests, were chosen depending on seed availability. Species represent a diversity of families and distribution ranges . Seeds wWe employed a randomized design with five seawater concentrations. Plants were treated with 150 mL of 20, 40, 60 and 90 % of seawater, while control plants (0 % seawater) were irrigated with 150 mL of tap water, respectively, once a week. We used 8\u201310 replicates for each treatment . We ran experiments in consecutive phases depending on seedling availability. In addition to flushing soils with treatment solutions, plants received 50 mL of tap water every 2 days to replace water lost by evaporation and transpiration.For all 26 species we measured plant height and leaf number every 15 days. Plant height was measured from the base of the stem to the tallest bud using a metered ruler. The total number of leaves was counted during each census. In the case of species with compound leaves, leaflets were counted as leaves. We measured initial and final biomass as the sum of dry mass of leaves, stems (including petioles of the leaves) and roots after drying for 72 h at 70 \u00b0C. Total leaf area was determined using a LiCor 3000 area meter . Initial and final seedling total biomass was used to determine the relative growth rate (RGR), defined as:W1 is the initial total dry mass in g and W2 is the total dry mass at final harvest in g, and t is the time of the treatment in days.where The number of plants that was still alive at the end of experiments, 60 \u00b1 2 days, was used to determine plant survivorship across all species. A plant was considered dead after all leaves had been dropped and the stem was dry.gs) and maximum photosynthetic rates (Amax) were measured in a subset of coastal and inland species with leaves that allowed for easy insertion into the LI-6400 photosynthesis chamber (6 cm2). Coastal species included: Mora oleifera Thespesia polpunea and Cedrela odorata, while inland species included Guazuma ulmifolia, Faramea eurycarpa, Cananga odorata, Protium pecuniosum, Luehea seemannii, Ochroma pyramidale, Castilla elastica, Apeiba membranacea and Virola koschnyi. Measurements of leaf stomatal conductance (gs) and maximum photosynthetic rates (Amax) were made using a LiCor 6400 portable photosynthesis system . Both gs and Amax were obtained by illuminating a healthy, fully expanded leaf at 1000 \u03bcmol m\u22122 s\u22121 of photosynthetic photon flux density (PPFD), until a steady state of net CO2 fixation and stomatal conductance was reached. Artificial illumination was supplied to the leaf from the LI-6400\u2019s red-blue LED light source, chamber temperature was kept at 28 \u00b0C, a CO2 reference partial pressure of 400 \u03bcmol\u00b7mole of CO2 was maintained by the LI-6400 CO2 mixer and leaf chamber relative humidity was maintained above 80 %.Stomatal conductance to detect seawater concentration treatment effects among the studied species using each of the response variables independently. An additional ANOVA was done to assess species and habitat effects, possible interaction of the two and their effects on RGR and mortality. For assessing treatment effects on gas exchange parameters gs and Amax we employed a repeated measured ANOVA. A hierarchical cluster analysis was performed as an exploratory tool in order to visually rank salinity tolerance among all studied species regardless of the habitat they came from and summarize species response to salinity in a concise form using all parameters, except gs and Amax. This analysis is represented in a cladogram that shows how the 26 species ranked using their response to 90 % seawater. All ANOVA analyses were conducted using JMP v 13 . The hierarchical cluster and cladogram analyses were done using IBM SPSS Statistics version 22 . All graphs of growth and physiological responses depicting averages and standard errors were done using Sigma Plot 12.3 .Plant height, leaf number, RGR, survival percentage, F4, 25 = 14.8, P < 0.0001 ANOVA). For example, on average, regardless of species, seedlings subjected to 90 % of seawater irrigation were 40 % shorter than those under control . Just after 30 days of irrigation with 20 % seawater, plant height was significantly reduced in the inland species. Castilla was the most sensitive species among all, showing a stem height reduction near 75 % after 4 weeks of being irrigated with 20 % seawater (LSMeans Tukey HSD). Similarly, seedlings of Apeiba, a species common to inland mature tropical wet forests, showed 30 % stem height reductions after 30 days under the same seawater treatment. In contrast, coastal species such as Thespesia, Terminalia, Mora and Pithecellobium showed no reduction in stem height when compared to the control at the end of the experiment under 90 % concentration of seawater. In fact, seedlings of Pithecellobium under 20 % seawater grew 4 % more than control seedlings.Across all species, plant height was significantly reduced by seawater treatment starting at 30 days . Among inland species, seedlings of Apeiba showed a 47 % reduction in leaf number under 20 % of seawater, but all the leaves had been dropped after 4 weeks at 40, 60 and 90 % seawater treatments. Coastal species Thespesia, Terminalia and Sterculia showed no significant reduction in leaf number after 60 days across seawater treatments, including 90 % (LSMeans Tukey HSD). However, Mora and Cedrela showed reduction in leaf number after 60 days of exposure to 60 % seawater treatment.Leaf number also decreased significantly as seawater concentration increased after 30 days across all species . When compared to controls, seedlings of Virola, Apeiba and Castilla grew just 15 % under 20 % seawater, and above this treatment all plants died. In contrast, seedlings of Mora, Thespesia, Terminalia and Pithecellobium maintained above 75 % of RGR under 90 % of seawater when compared to controls. However, Cedrela, a dry forest species, showed significant reductions in RGR at 90 % of seawater [see].Relative growth rate was much less affected by salinity in the coastal species than in the inland species . However, seedling mortality depended on the interaction of species habitat and treatment . The coastal species Thespesia, Terminalia, Pithecellobium, Mora and Cedrela had 100 % plant survival, even at 90 % seawater concentration. On the contrary, seedlings of Apeiba, Virola, Castilla, Minquartia and Ochroma species showed about 100 % mortality at 90 % seawater concentrations, respectively (LSMeans Tukey HSD). Among the inland species, Guazuma, Annona and Inga showed between 33 and 38 % survival at 90 % sweater concentration . However, salinity affected species differently . Both, inland and coastal species, showed significantly lower gs after 30 days, as seawater concentration exceeded 20 % . Inland species such as Lueha, Apeiba, Ochroma and Virola suffered up to 95 % reductions in gs, after 30 days starting at 40 % of seawater followed a similar pattern than gs, decreasing as salinity increased , with species responding differently to salinity . Although Amax of inland and coastal species was significantly lowered after 30 days , the sweater concentration at which Amax was lowered differed between the two habitats. After 30 days, inland species showed significantly lower Amax when seawater concentration exceeded 20 % while for the coastal species treatment effects were detectable after 40 % seawater. Amax varied greatly across species with seedlings of inland species such as Apeiba, Virola, Castilla and Ochroma, having >95 % reductions after 30 and 60 days, regardless of treatment methodology using all response parameters under 90 % of seawater concentration, with the exception of Mora, Pithecellobium, Terminalia, Thespesia, Sterculia and Cedrela maintained above 65 % RGRs when exposed to high salinity irrigation (~30 \u2030) and 4. Aangroves , which m forests , showed Amax across all species and treatments. However, the relationship was only significant after a month under the 20 % seawater treatment, where Amax explains 30 % of the variance in RGR . In plants, salinity stress is evidenced by stomatal closure during photosynthetic CO2 uptake, whereas in the long term, as in this study, gs and Amax decrease more or less simultaneously. However, stomatal limitations due to increased ABA or hydraulic limitations via ionic unbalances deserve further attention.Reduced stomatal conductance and photosynthesis means limited carbon budgets for plant growth -fixing legume from inland dry forests (2-fixing bacteria (Rhizobium). The importance of effective N2-fixing bacteria associations among plant species has been highlighted by Rhizobium strains might significantly help plants cope with increased soil salinity. In the case of tropical trees, it remains to be investigated how salinity responses vary among N2-fixing legumes, as no clear pattern emerged from other N2-fixing inland species in this study. Erytrina appeared to be slightly more salt-sensitive than Enterolobium, but Calliandra was more tolerant than both . Further research on tropical tree salinity tolerance based the concept of adaptive strategy theory . Central American countries are predicted to experience above 30 % increment in storm surge under future climatic scenarios from the Secretar\u00eda Nacional de Ciencia Tecnolog\u00eda e Innovaci\u00f3n (SENACYT) and the support of the Sistema Nacional de Investigaci\u00f3n (SNI) awarded to O.R.L.O.R.L. and K.W. conceived and designed the study, facilitated the logistics, contributed to the analysis and final writing. A.D.S. conducted the experiments, analyzed the data and led the early writing. Y.G. contributed to the fieldwork.None declared."} +{"text": "To compare the relative effectiveness of fluorescence in situ hybridization (FISH) and cytology in diagnosing upper urinary tract urothelial carcinoma (UUT-UC) and to evaluate the advantages and potential deficiencies of FISH analysis.We performed a complete systematic review based on studies from PubMed/Medline, Embase, Web of Science, Ovid, Web of Knowledge, and Cochrane Library. We identified 2031 patients with strict criteria in 14 individual studies between January 2005 to November 2017 in accordance to preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines, we summarized the test performance using bivariate random effects models.FISH was superior to cytology in terms of pooled sensitivities . FISH and cytology were similar to each other in terms of pooled specificities, which were 89.5% (95% CI 85.3\u201392.6%) for FISH and 95.9% (95% CI 91.2\u201398.1%) for cytology.We confirm the superiority of FISH over cytology in terms of sensitivity and find similar diagnostic outcomes between them based on systematic analysis. Therefore, we demonstrate that FISH is extremely sensitive while still very reliable with a relatively low error rate for diagnosing UUT-UC. Therefore, an efficient, accurate yet non-invasive early-diagnostic technique is needed. Current diagnostic methods can be generalized into three categories, namely, cytology, imaging techniques, and endoscopy; notably, cytological examination is the most convenient and most widely applied method.Upper urinary tract (UUT) urothelial carcinoma (UUT-UC) is characterized by its wide range of grades and stages as well as its high tendency toward progression and recurrence, and cytological examination also becomes far less efficient in terms of both sensitivity and specificity when detecting low-grade UUT-UC.\u20138 More importantly, cytological examination can be subjective at times and is controversial in circumstances such as infection and inflammation.,10 The accurate diagnostic rate of cytology increases to 50% to 60% when implemented with ureteroscopy, although the procedure-related complications are often inevitable.,11 Theoretically, ureteroscopy is regarded as one of the standard methods in the diagnosis of UUT-UC. However, severe accompanying complications including infection, perforation, and hemorrhage can sometimes be unavoidable. In addition, anatomic abnormalities and a history of urinary tract reconstruction may render the ureteroscopy difficult and risky.,13The UUT-UC has to be differentiated with urinary tract trauma, infection, renal cell carcinoma, and renal metastasis, as they manifest similar symptoms at early stage, such as hematuria, flank pain, or hydronephrosis. Imaging techniques such as computed tomography urography and intravenous pyelography fail to detect small tumors, has exhibited high sensitivity and specificity in detecting UUT malignancies. Genetic mutations can be identified in the early stages of cancer development and represent important targets for clinical detection during further malignant transformation. FISH is known for its ability to analyze multiple chromosomal aberrations in a certain number of cells. Specifically, FISH detects aneuploidy in the 3rd, 7th, 9th, and 17th chromosomes in exfoliated cells collected from voided urine samples.,18 Owing to the drastically increasing diagnostic accuracy of low-grade UC, the FISH probe set serves as an excellent supplement to cytological examination.In the last decade, fluorescence in situ hybridization (FISH), which is based on genetic aberrations and is associated with reduced complications,,9 However, some of these studies have included insufficient number of patients, and the results reported in various articles differ greatly, leading to incomplete and inaccurate conclusions.,15,18 Therefore, the aim of this meta-analysis is to integrate the main parameters (sensitivity and specificity) along with secondary parameters, including PPV and NPV, to generate more reliable and authentic data.During the last decade, many clinical trials comparing the newly established FISH analysis method and traditional methods, particularly cytology, have been initiated.22.1After careful resources\u2019 searching in authenticated databases, article screening, and quality assessment process, 14 studies with high reliability, adequate sample size, and comprehensible design with accessible data and full texts were considered for this systematic review. The total number of patients incorporated was 2031. All studies were carried out in a retrospective and single-centered fashion. In terms of the nationalities and regions, 4 studies were performed in Europe, 8 in Asia, and 2 in North America. To select proper patient groups, most articles included patients with symptoms such as hematuria, hydroureterosis, or hydronephrosis and patients with suspected or readily diagnosed UUT-UC. Meanwhile, patients without adequate cell numbers in voided urine samples as required by FISH or with an insufficient follow-up duration, or patients with concomitant bladder carcinoma were excluded.2.2Supplementary Table 1 shows detailed characteristics of the 14 included articles. The sensitivity and specificity of both diagnostic techniques were carefully calculated according to the exact number of patients with true positive (TP), true negative (TN), false positive (FP), or false negative (FN) diagnostic results. The pooled sensitivity of FISH was 84.0%, ranging from 51.9% in a study with 80 participants to 100% in a study with 12 participants. The pooled sensitivity of cytology was 40.0%, varying from 20.8% to 60%, which was relatively lower than that of FISH. We also examined the distribution of diagnostic sensitivity and specificity percentages between FISH and cytology , Quadas-2,22 tools. According to the three standard article evaluating systems, the 14 included studies were ultimately defined as reliable. However, some studies failed to fully describe the gold-standard comparator which may have led to low scores in index test. The method used to select patients may also have contributed to bias.Standard quality evaluation of the 14 included studies was performed based on the Newcastle\u2013Ottawa scale2.4To perform a comprehensive comparison regarding the efficiency and applicability of the 2 diagnostic techniques, we selected 12 key parameters for evaluation, including sensitivity, specificity, PPV, NPV, TP, TN, FP, and FN values, and the alteration rate for chromosomes 3, 7, 9, and 17 as mentioned above. A forest plot was, therefore, synthesized to manifest sensitivity, specificity, TP, TN, FP, and FN values of selected studies (13 studies for FISH and 12 studies for cytology) for FISH and 95.9% (95% CI 91.2%-98.1%) for cytology, whereas the sensitivity of cytology was notably lower than that of FISH, which was 84.0% (95% CI 74.4%-90.5%) for FISH and 40.0% (95% CI 33.6%-46.7%) for cytology. The diagnostic ORs are 44.61 (95% CI 26.46\u201375.20%) and 15.47 (95% CI 7.68\u201331.17) for FISH and cytology, respectively. The LRs (+) and LRs (-) for FISH and cytology are 7.96 (95% CI 5.87\u201310.81%) vs 9.69 (95% CI 4.82\u201319.46%) and 17.9 (95% CI 11.1\u201328.9%) vs 62.6 (95% CI 56.9\u201369.0%), respectively.33.1Authenticated databases including PubMed/Medline, Embase, Web of Science, Ovid, Web of Knowledge, and Cochrane Library were extensively searched for articles written in English published from January 2005 to November 2017 . We retrieved a total of 1112 articles. Thirty relevant studies remained after removal of obvious duplicates and meticulous correlational analysis. Of these, 5 studies were excluded because their full texts were inaccessible, and 7 articles were case reports, editorials, reviews, or letters. Finally, 14 studies were qualified for further analysis according to the following criteria: included more than 15 patients; reported sensitivity and specificity values for FISH and cytology; and randomized controlled trials and any observational design, including cross-sectional, case\u2013control, and cohort designs.Three independent reviewers participated in the screening process, analyzed the full texts, and performed quality assessments. Subsequently, we performed a blinded cross-check to detect underlying discrepancies. If a discrepancy was detected, a 4th reviewer was assigned to adjudicate the conflict. The identification, inclusion, and exclusion of studies were conducted according to preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines. Figure 3.2A general data table containing 29 parameters was generated from the included articles by 3 individual reviewers simultaneously, and discrepancies were resolved through extensive discussions. The following information were extracted: title, author, nationality, department, ethnicity, study design, age and sex of the patients , enrollment year, and comparison of correlated outcomes.3.3 and the hierarchical summary receiver operating characteristic (HSROC) model. We chose to use these methods to respect the binomial structure of diagnostic accuracy data, thus jointly summarizing paired measures simultaneously, for example, sensitivity and specificity or positive and negative likelihood ratios. Also, as a random effects approach, the bivariate/HSROC meta-analysis allowed pooling results in view of knowing that heterogeneity was commonplace across included studies due to different or implicit thresholds. The said approach was carried out by metandi command in STATA 14.2 (StataCorp).Data were extracted on either an article or a study level when possible to reconstruct a 2\u200a\u00d7\u200a2 table, which was used to calculate sensitivity, specificity, PPV, NPV, ORs, and DLRs (Diagnostic Likelihood Ratio) along with the 95% CIs for each study. The forest plots were generated to display sensitivity and specificity estimates using Review Manager 5.3 (The Cochrane Collaboration). To summarize test performance, 2 methods for meta-analyzing diagnostic accuracy test have been used: the bivariate modelThis study was approved by the Ethics Committee of West China Hospital, Sichuan University 4,27,28 with the sensitivity as low as 30% to 50%.,29 Regarding the potential harmful effect of ureteroscopy, a meta-analysis published in 2018 with 3975 patients indicated that diagnostic ureteroscopy had a negative impact on oncological outcomes, especially in intravesical recurrence, which was ascertained by another systematic review.This systematic review assessing the diagnostic accuracy of FISH and cytology for UUT-UC summarizes current literature and includes 14 studies for meta-analysis. The gathered evidence shows that FISH not only fits for an ideal alternative for diagnosing UUT-UC, but also proves much superior to cytology in terms of sensitivity. Recently, the most commonly applied diagnostic method for UUT-UC cytology has been reported to exhibit insufficient value in recognizing suspicious and ambiguous foci in the UUT, However, studies aimed to clarify the advancement and efficiency of FISH in the UUT were inadequately carried out.,30,27 A study by Mian et al in 2010 with 68 patients demonstrated 100% sensitivity of FISH vs a considerably low sensitivity of 20.8% for cytology. In contrast, another study on 637 patients by Fern\u00e1ndez et al in 2012 identified a much lower disparity in sensitivity between the 2 methods. Generally, the discrepancy between the sensitivities of FISH and cytology ranges from 5.7% to 89.2% for patient group sizes varying from 16 to 637.As a novel biomolecular diagnostic technique, FISH has previously been reported to exhibit a relatively high sensitivity and specificity in detecting carcinoma in the urinary system, especially in the bladder.Following a carefully considered and standardized process, we confirmed the higher sensitivity of FISH compared to that of cytology by standard statistical integration. In the specificity analysis, we obtained similar values between FISH and cytology, although the specificity of FISH was 6.4% lower than that of cytology. Conversely, Shan et al reported that an FP FISH result may imply potential tumor development in cases with a negative endoscopy or cytology result. So far, a number of opinions have been put forward regarding the potential deficiencies of FISH analysis method. First, compared with its excellent performance in diagnosing high-grade tumors, FISH is much less sensitive in detecting low-grade tumors. A likely explanation for more FN FISH results for low-grade tumors may be that tumor chromosomes are generally diploid or nearly diploid without obvious genetic abnormalities, which resemble those of normal cells. Second, the probe for 9p21, representing the most common site of genetic abnormalities, is the smallest in terms of size. Thus, non-typical, inconspicuous abnormalities are possible to be omitted at times. Finally, FISH requires collection of sufficient cell quantities in voided urine samples, which is difficult in some patients. Low cell quantities cannot provide the minimum number of chromosomes, thus precluding FISH analysis. Therefore, future optimization of cell collection either by washing urine or from voided urine rather than advances in cellular biochemical technologies alone is crucial.Although FISH exhibits superior sensitivity and comparable specificity to those of cytology, inherent and inevitable challenges exist for FISH.In conclusion, this study pooled the largest number of UUT-UC patients to date and confirmed that FISH has higher sensitivity than cytology for diagnosing UUT-UC. However, we were unable to identify concrete differences in specificity between the 2 techniques. We acknowledge several limitations in this study. First, our study did not subgroup low- and high-grade tumors. Further studies may obtain distinct genetic aberration spectrums from different grades of tumor since they may have unique biological characteristics. Second, among the 14 eligible studies, only 4 contained detailed information regarding the alteration rates for chromosomes 3, 7, 9, and 17, and the exact numbers of chromosomal alterations evaluated varied substantially among studies. Therefore, the optimal cutoff values of specific chromosomal alterations remain to be determined.5We confirm the superiority of FISH over cytology in terms of sensitivity and found similar diagnostic outcomes between them based on systematic analysis. Therefore, we demonstrate that FISH is extremely sensitive while still very reliable with a relatively low error rate compared with cytology, which is valuable to clinical practice.Conceptualization: Hongyu Jin, Tianhai Lin, Qiang Wei.Data curation: Hongyu Jin, Jianqi Hao.Formal analysis: Hongyu Jin, Tianhai Lin.Funding acquisition: Ping Han, Qiang Wei.Investigation: Jianqi Hao, Shi Qiu.Methodology: Lu Yang, Liangren Liu.Project administration: Tianhai Lin, Qiang Wei.Resources: Peng Zhang, Zhenhua Liu.Software: Ruichao Yu, Hang Xu.Supervision: Ping Han, Qiang Wei.Writing \u2013 original draft: Hongyu Jin, Jianqi Hao.Writing \u2013 review & editing: Tianhai Lin, Sheng Sun."} +{"text": "RBS is an ideal cohort to study healthy aging in women and to examine sex differences in aging. Initiated in 1972, RBS enrolled 82% of adult residents of Rancho Bernardo, a suburb of San Diego. Residents were white, and middle to upper-middle class. Participants have been followed via 12 research clinic visits at ~4 year intervals and 32 mailed surveys. RBS contains detailed assessment of cardiometabolic disease risk factors, bone health, biomarkers, physical ability, cognitive function, health and reproductive history, medications, behaviors and psychosocial measures. Of the 6726 participants, 54% are women and 65% were aged \u226550 at enrollment. Vital status is known for 91% of the cohort; overall mortality is 71%. Death certificates have been coded for cause of death for 91% of decedents. We will discuss contributors to healthy longevity in RBS women ."} +{"text": "The Freedom of Information Act (FOIA) provides access to unreleased government records that can be used to enhance the transparency and integrity of biomedical research. We characterized FOIA requests to Department of Health and Human Services (HHS) agencies, including request outcomes, processing times, backlogs, and costs.Using HHS FOIA annual reports, we extracted data on the number of FOIA requests received and processed by HHS agencies between 2008 and 2017, as well as request outcomes. Processing times were reported in three time increments, < 1\u201320, 21\u201360, or 61+ days, and trends in backlog status were also described. Information about costs and fees collected were aggregated.Between 2008 and 2017, 69.6% of 530,094 HHS FOIA requests were received by the Centers for Medicare and Medicaid Services (CMS), 18.9% by the Food and Drug Administration (FDA), and 11.6% by all other HHS agencies. During this period, CMS processed 374,728 requests, FDA 114,938, and other HHS agencies 61,890. CMS and FDA reduced backlogged requests by 9396 (89.7%) and 4289 (65.3%), respectively, leaving backlogs of 1081 and 2279 requests at the end of 2017. CMS fully or partially granted 60.3% of requests whereas FDA fully or partially granted 72.4%. Of all requests to CMS, 82.0% were considered simple and 18.0% complex; 82.2% of simple requests and 54.9% of complex requests were processed in 20\u2009days, and 5.6% and 29.9% were processed in 61+ days. In contrast, 60.2% of requests to FDA were considered simple and 39.8% complex; 28.8% of simple requests and 9.0% of complex requests were processed in 20\u2009days, and 58.3% and 81.5% were processed in 61+ days. The costs to HHS associated with FOIA requests totaled $446.4 million ($809 per processed request), increasing from $28.1 million ($423 per request) in 2008 to $53.3 million ($1544 per request) in 2017. In total, HHS collected $8.5 million in fees .FOIA is frequently used to obtain information about HHS and its agencies. With growing costs, minimal fees collected, and lengthy processing times, HHS agencies\u2019 FOIA programs might be made more efficient through greater proactive record disclosure. The Freedom of Information Act (FOIA) can enhance transparency and accountability of biomedical research and regulatory agencies by providing access to a wide range of records held by government agencies. The Act requires federal agencies to disclose unreleased records upon request by the public, unless records fall under nine specific exemptions protecting interests such as trade secrets and other confidential commercial information, personal privacy, and national security . At the Several recent examples demonstrate the beneficial role FOIA can play. Emails obtained by the New York Times through FOIA revealed that alcohol manufacturers had funded and shaped a major study at the National Institute on Alcohol Abuse and Alcoholism (NIAAA) examining the effects of moderate alcohol consumption on cardiovascular disease . In the FOIA can also be used to provide access to clinical trial data. For example, the Treatment Action Group and the Global Health Justice Partnership used FOIA to obtain clinical trial data including clinical study reports, study protocols, and individual patient-level data, albeit heavily redacted, on the Hepatitis C drugs Sovaldi and Harvoni, enabling the research community to independently assess the safety and efficacy of the drugs . In manyDespite several examples in which FOIA requests have helped inform the clinical and scientific communities, little empirical data exists on FOIA requests to HHS. A previous evaluation of FOIA requests to the FDA focused on classifying requesters and found that of the over 10,000 requests in 2013, 75% were filed by commercial requesters, 12% by news media, and 13% by all other requesters . In addiUsing HHS\u2019s FOIA annual reports , we deteAgencies are required by statute to respond to FOIA requests within 20\u2009days for any request comporting with agency regulations, unless there are \u201cunusual circumstances,\u201d such as a need to review a voluminous number of records . RequestBetween 2008 and 2017, 69.6% of 530,094 HHS FOIA requests were received by CMS, 18.9% by FDA, and 11.6% by other HHS agencies and 30,254 (26.3%) of requests based on reasons other than exemptions, respectively, while denying 49,263 (13.1%) and 1420 (1.2%) based on exemptions, respectively.No records or withdrawn requests were the most common reasons for full denials Table\u00a0. CMS mosBetween 2008 and 2017, 82.0% of requests to CMS were considered simple and 18.0% complex; 82.2% of simple requests and 54.9% of complex requests were processed in 20\u2009days, 5.6% and 29.9% in 61+ days , including $433.4 million (97.1%) on processing and $13.0 million 2.9%) on litigation for more than three-fourths of the approximately 63,500 exemptions the agency asserted to withhold requested information. However, FDA most commonly invoked exemption 4 . Previously, researchers have suggested that FDA at times invoked exemption 4 even when withholding under that exemption is not warranted under the relevant legal standard .CMS and other HHS agencies processed more than three-fourths and one-half of requests within 20\u2009days, respectively, whereas two-thirds of requests processed by FDA took more than 61\u2009days. Requests to FDA were generally more complex than those to CMS, which likely contributed to FDA\u2019s slower processing time. In addition, FDA addressed potentially complex issues related to FOIA exemption 4 at a higher rate than CMS, and fully denied requests less frequently, which may have also contributed to FDA\u2019s slower processing speed. However, even within the simple request category, FDA required more than 61\u2009days to process over one-half of requests, compared to 5.6% at CMS and 14.5% at other HHS agencies, suggesting there may be opportunity for FDA to increase its processing speed to more closely align with other HHS agencies. To reduce delays, HHS agencies should consider hiring more personnel and devoting greater resources to responding to FOIA requests. The number of backlogged requests across HHS agencies was reduced by 76.5% over the 10-year span, suggesting that efforts implemented in response to an Obama administration instruction in 2009 to reduce federal agency FOIA backlogs have been effective . The FOIWe found that between 2008 and 2017 costs to HHS associated with FOIA requests totaled over $400 million, with requests to FDA comprising nearly 70% of overall HHS costs. The large number of complex requests FDA receives is likely a contributing factor to its disproportionate costs. Costs to HHS per FOIA request more than tripled during the 10-year span. Growth in the number of employees responsible for handling FOIA requests may have contributed to the increase in processing costs. Despite rapidly growing costs, HHS recovered just 1.9% of total costs. A possible explanation for the minimal fees HHS collected is that its agencies are simply not following FOIA fee guidelines, which require commercial use requesters to be charged for any search time, document review, and duplication; news media, educational, or scientific requesters to be charged for duplication only; and all other requesters to be charged for search time and duplication [Given growing costs, minimal fees collected, and sometimes lengthy process times, HHS agencies, and particularly the FDA, should consider expanding efforts to proactively disclose records. These efforts might both improve agency transparency and make FOIA programs more efficient. For example, FDA advisory committee materials used to be confidential until they were the subject of FOIA requests, but the FDA changed its practice to proactively release such materials, which has provided useful information for the public and saved the agency time responding to FOIA requests. Notable types of records that HHS agencies might consider proactively disclosing include for the FDA; clinical study reports, final reports of clinical trials that fulfill postmarketing requirements and commitments, and Risk Evaluation and Mitigation Strategies; for CMS, provider level claims and spending data; and for NIH and CDC, expenditures on preclinical and clinical research and development, agency-held intellectual property, and payments to and from industry , 19.This study was limited to aggregate information on FOIA requests to HHS, which did not include information on the types of entities, such as news media, academics, or commercial requesters, who requested records, the information requested and released, and the appropriateness of agencies\u2019 withholding of information. Further, we could not determine whether multiple FOIA requests were for the same materials nor the redundancy in the materials requested, which has implications for HHS\u2019s costs of processing requests.Between 2008 and 2017, over 500,000 FOIA requests were made to HHS agencies, nearly 90% of which were to CMS or FDA, demonstrating that FOIA is an important tool for obtaining information about HHS and its agencies. While nearly two-thirds of requests were fully granted and processed within 20\u2009days, one-quarter required 61\u2009days or longer. Requests to FDA were generally more complex, took longer to process, and were costlier to process than those to CMS. Given growing costs, minimal fees collected, and lengthy process times, HHS agency FOIA programs might be made more efficient through greater proactive record disclosure.Additional file 1: Table S1. Other Agencies at the Department of Health and Human Services Included in the Analysis."} +{"text": "OBJECTIVES/SPECIFIC AIMS: (1) Determine person , environment , and health and illness characteristics that are associated with outcomes . (2) Determine the association of symptom management strategies and outcomes . (3) Test person and environment characteristics as moderators of the effect of symptom management strategies on outcomes . METHODS/STUDY POPULATION: AF patients (\u226518 years of age) already enrolled in the PaTH study will be included. To date, 1026 total participants have been enrolled. Based on the enrolled participants, 92% (945) of our study population are Caucasian and 36% (362) are female. The age range of the enrolled participants is: 2% (16) 18\u221239, 4% (42) 40\u221249, 11% (108) 50\u221259, 33% (343) 60\u221269, 34% (353) 70\u221279, and 16% (162) 80+. Participants are recruited through in-person, email, phone, patient portal messaging and post mail techniques to ensure a representative sample. The PaTH study integrates electronic health record and insurance claims data with patient-reported outcome measures collected through online surveys. RESULTS/ANTICIPATED RESULTS: We hypothesize that sex, older age, low education level, living alone, absence of partner, absence of insurance coverage, high BMI, and a high number of comorbidities will be associated with lower QOL, high symptom severity, and low emotional and functional status. We further hypothesize that symptom management strategies will be associated with higher QOL, low symptom severity, and high emotional and functional status, and that these associations will be moderated by person and environment characteristics. DISCUSSION/SIGNIFICANCE OF IMPACT: The proposed research is an important first step in determining potential causes of person and environment differences in symptom severity. It will lead to tailored symptom management interventions for individuals most at risk for experiencing high symptom severity."} +{"text": "Older adults who experience social isolation have higher rates of mortality relative to their counterparts. Social interactions are an important way to combat this isolation. This research aims to better understand how social isolation in older adults living in low-income households in Richmond, Virginia (RVA) is related to their economic, physical, and psychological health status. As part of the VCU iCubed Health and Wellness Aging Core and in collaboration with the Richmond Memorial: East End Housing Coalition for Older Adults, older adults from a selected public housing unit (n=28) self-reported their financial status, experiences with physical and psycho-social health, and feelings of social isolation. Survey participants were 71.4% female, the mean age was 69.75 years, and 25% were high school graduates. Participants averaged 34 years living in the area and reported an average of $300 to spend on rent monthly. Overall, 55% (n=20) reported having two or more supports and 61% (n=22) reported hardly ever feeling isolated. However, a small subset of the sample reported having either no supports and 41.7% (n=15) lacked companionship some of the time or often. A one-way ANOVA was conducted and it was determined that participants who reported feeling left out more often were significantly more likely to report stress, anxiety, and depression . Findings support the existence of supportive communities formed in low-income areas. Findings also indicate some older individuals residing in public housing in RVA experience social isolation, linking them to poorer psycho-social health."} +{"text": "Orthopaedic surgery residency training requires 5 clinical years; fellowship subspecialty training requires an additional year. Orthopaedic surgery fellowship training has financial implications regarding potential career earnings and opportunity cost. To evaluate the effect of fellowship training on employment, 30 years of orthopaedic job advertisements were analyzed to determine fellowship requirements for academic centers, private practices, urban areas, and rural areas. It was hypothesized that subspecialty training is an important prerequisite for orthopaedic employment.Journal of Bone and Joint Surgery (JBJS Am) and Orthopedics were analyzed to determine whether fellowship training versus \u201cgeneralist\u201d positions were advertised for the years 1984, 1989, 1994, 1999, 2004, 2009, and 2014. Jobs were categorized as academic ; private practice; rural ; and urban. \u201cGeneral\u201d orthopaedic surgery job postings were defined as job advertisements that did not require fellowship training.Job advertisements in the P < 0.05). Conversely, from 1984 to 2014, the percentage of advertised jobs targeting general orthopaedic surgeons decreased from 95% to 32% (P < 0.05). Between 2009 and 2014, advertised jobs requiring fellowship surpassed general orthopaedic surgery jobs.A total of 4,720 job advertisements were analyzed. From 1984 to 2014, the percentage of advertised jobs requiring fellowship training increased from 5% to 68% (Over the past 30 years, there was a trend toward fellowship being required as part of the advertised orthopaedic jobs available to graduates of orthopaedic training programs. The reasons for increased orthopaedic training are likely multifactorial, including limited clinical duty hours during orthopaedic residency, advertisement and marketing forces emphasizing super-sub-specialty care in multispecialty orthopaedic groups, and the greater complexity of orthopaedic procedures being performed. Most orthopaedic surgery residents elect additional subspecialty fellowship training. To evaluate the effect of fellowship training on employment, 30 years of orthopaedic job advertisements were analyzed to determine fellowship requirements for academic centers, private practices, urban areas, and rural areas. It was hypothesized that subspecialty training is an important prerequisite for orthopaedic employment.Journal of Bone and Joint Surgery (JBJS Am) and Orthopedics were analyzed to determine whether fellowship training versus \u201cgeneralist\u201d positions were advertised for the years 1984, 1989, 1994, 1999, 2004, 2009, and 2014. Jobs were categorized as academic ; private practice; rural ; and urban. \u201cGeneral\u201d orthopaedic surgery job postings were defined as job advertisements that did not require fellowship training. The Cochran-Armitage trend test and Poisson regression modeling were used for statistical analysis. All analyses were performed in SAS Version 9.4, and a 0.05 significance level was used throughout this analysis.Job advertisements in the P < 0.05). Conversely, from 1984 to 2014, the percentage of advertised jobs targeting general orthopaedic surgeons decreased from 95% to 32% . Between 2009 and 2014, advertised jobs requiring fellowship surpassed general orthopaedic surgery jobs and 62.5% of rural jobs . In 1984, 17.4% of advertised academic jobs and 1.4% of advertised nonacademic jobs required fellowship training; this increased by 2014 to 83.9% of advertised academic jobs and 41.1% of advertised nonacademic jobs requiring fellowship training . Between 1999 and 2014, the job advertisements requiring fellowship training surpassed \u201cgeneralist\u201d positions in the urban, rural, and academic practice setting part 2 certifying examination database, \u201cgeneralists\u201d decreased from 44.2% to 28.7% from 1990 to 2006. Moreover, from 2003 to 2013, fellowship-trained applicants taking American Board of Orthopaedic Surgery part 2 increased from 76% to 90%.2Orthopaedic surgery residency training requires five clinical years; fellowship subspecialty training requires an additional year. Orthopaedic surgery fellowship training has financial implications regarding potential career earnings and opportunity cost.A limitation of the current study is that only two sources of orthopaedic surgery job advertisements were analyzed. Our analysis allows for consistent comparative methodology over the 30-year study period in two long-standing general orthopaedic journals. Online advertisements were not as prevalent in 1984 and would complicate analysis of trends over the study period. Furthermore, we did not delineate nonacademic positions into private groups versus hospital employed, but we speculate that these followed the overall trends seen.3 The reasons for increased orthopaedic training are likely multifactorial, including limited clinical duty hours during orthopaedic residency,5 advertisement and marketing forces emphasizing super-sub-specialty care in multispecialty orthopaedic groups,6 and the greater complexity of orthopaedic procedures being performed.Over the past 30 years, there was a trend toward fellowship being required as part of the advertised orthopaedic jobs available to graduates of orthopaedic training programs."} +{"text": "Concurrent autoimmune illnesses contribute to increased medical burden and reduced quality of life in patients with autoimmune hepatitis (AIH). The frequency of coexisting autoimmune conditions among North American patients with AIH and their families remains incomplete. Challenges associated with disease capture in the electronic medical record, high study costs, and geographic spread of patients are formidable barriers to understanding the extent of concurrent autoimmune conditions in these groups.This objective of this study was to examine the frequency of extrahepatic autoimmune diseases (EHAD) among AIH cases and healthy controls as well as their first-degree relatives using social networking sites (SNS).We developed a 53-question survey detailing the history of autoimmune diseases. A survey link was posted at routine intervals within specific Web-based cohorts on SNS. Healthy controls, without self-reported autoimmune liver disease, were recruited from Amazon\u2019s Mechanical Turk. Continuous variables were summarized using medians and P values obtained with the Wilcoxon rank-sum test. Categorical variables were compared using the chi-square test.P=.001). The most frequent EHADs among cases were thyroid disease , Sj\u00f6gren syndrome , Raynaud phenomenon , and psoriasis . Overall, 55.88% (171/306) of cases and 35.71% (1601/4484) of controls reported at least 1 first-degree relative (FDR) with a history of EHAD (P=.001). Cases had a significantly higher risk of EHAD than controls after the adjustment for age, sex, race, and body mass index: odds ratio 2.46 (95% CI 1.8-3.3); P=.001.Compared with controls (n=1162), cases (n=306) were more likely to be older (median age: 49 vs 33 years), female , and have an EHAD (128/306, 41.83% vs 218/1162, 18.76%; Patients with AIH report higher prevalence of coexistent EHAD than healthy controls, and their FDRs are also more likely to have autoimmune disorders. Autoimmune hepatitis (AIH) is characterized by T-cell-mediated inflammation of the liver and typical autoantibodies ,2. If leHLA) locus [HLA gene [The etiology of AIH remains unclear, but both environmental and genetic factors have been hypothesized despite few supporting studies. Environmental contributions are supported by varying global AIH incidence rates -6, evideA) locus and in aHLA gene . Beyond HLA gene ,14. To dGeographic barriers and lack of a nationwide medical record system have limited AIH investigation; however, the advent of Web-based social networking sites (SNS), such as Facebook and Twitter, have bridged this gap in research accessibility . Web-basWe implemented an AIH patient recruitment method using SNS for this study. We have previously described the advantages of these platforms to provide patients with AIH with access to health information, patient-directed support, and opportunities for research involvement . The AutControls without self-reported AIH were screened and recruited from Amazon\u2019s Mechanical Turk (MTurk), a crowdsourcing website for the completion of requester-directed tasks, which has been shown to approximate the demographics of American adults over the Web . MTurk wAn autoimmune disease questionnaire was created using Web-based survey development software and included key demographics, as well as 48 questions addressing personal and FDR medical history of other autoimmune diseases. The questionnaire was adapted from the Mayo Clinic Medical Questionnaire for Chronic Cholestatic Liver Diseases and took approximately 10 minutes to complete . We asseP values were obtained with the Wilcoxon rank-sum test. Categorical variables were compared using the chi-square test. Logistic regression was used to estimate the risk of concurrent EHAD and EHAD within FDR after adjusting for age, sex, race, and body mass index (BMI). Statistical analysis was completed using IBM SPSS Statistics software (version 2.0).Continuous variables were summarized using medians and the 25th and 75th percentiles, and P<.001; Compared with controls, cases were more likely to be female , older , Caucasian , and have a higher BMI (28.5 vs 25.8). At least 1 EHAD was reported in 41.83% (128/306) of cases and 18.76% (218/1162) of controls P<.001; .P<.001). Among cases with the AIH-PBC overlap, the most frequent EHAD was autoimmune thyroid disease , Sj\u00f6gren syndrome , and psoriasis . Cases with the AIH-PBC overlap were more likely than cases without the overlap to have Sj\u00f6gren syndrome and lupus . Among cases with the AIH-PSC overlap, the most frequent EHAD was Crohn diseases , ulcerative colitis , and psoriasis . Cases with the AIH-PSC overlap were more likely to have Crohn disease and ulcerative colitis than cases without the overlap. A comparison of cases with and without EHAD revealed similar demographics. Female sex , age at AIH diagnosis (47 years vs 42 years), race (88.32% vs 86.02% Caucasian) and BMI (29.2 vs 28.3) were similar between cases with EHAD and cases without EHAD, respectively.Autoimmune thyroid disease was the most common EHAD in cases and controls . The next most prevalent diseases were Sj\u00f6gren syndrome , Raynaud phenomenon , and psoriasis among cases and psoriasis , rheumatoid arthritis , and type 1 diabetes mellitus among controls. All EHADs were markedly more frequent in cases than controls, except for Crohn disease and type 1 diabetes mellitus . Both PBP=.001; P=.001; P=.001).Overall, 6080 FDR autoimmune disease histories were obtained, including 1596 FDRs in cases and 4484 in controls. Cases more frequently had an FDR with at least one autoimmune disease compared with controls , siblings , and children of cases. In total, only 3.71% (14/306) cases and 2.14% (27/1162) controls reported an FDR with AIH (P=.05). Further depiction of AIH per FDR did not reveal any differences between cases and controls, yet AIH within mothers appeared more likely among cases .P=.001) and EHAD among FDR were significantly higher among cases than among controls.A logistic regression model was used to assess the risk of concurrent EHAD and EHAD within FDRs of all participants after adjusting for current age, sex, race, and BMI. After the adjustment, both the odds of EHAD of cases and only 18.76% (218/1162) of controls reported an EHAD at the time of the survey completion. Furthermore, 55.88% (171/306) of cases and 35.71% (1601/4484) of controls reported at least one FDR with an EHAD. The assessment of AIH cases with and without EHAD did not demonstrate any demographic differences. The observation of increased EHAD in cases and their FDRs compared with controls remained statistically significant even after adjusting for current age, sex, race, and BMI.The findings of our case-control study provide a similar estimate of concurrent EHAD in AIH compared with prior descriptive European reports that document the prevalence between 26% and 42% ,13,14. IHLA region on chromosome 6. Variable alleles at this locus have been strongly associated with autoimmune disease risk, yet in some instances, other variants provide protection. The first and only AIH-specific genome-wide association study, to date, has confirmed the HLA locus at 6p21 as a region of heightened disease risk [The observation of increased EHAD within cases is not unexpected, particularly as reports within other autoimmune diseases have described an \u201cautoimmune phenotype,\u201d in which autoimmune diseases frequently coexist in an individual. For example, studies in disorders, such as thyroid disease , celiac ase risk . Assessmase risk . Future Our interrogation of FDRs of patients with AIH remains the largest interrogation ever with >6000 individual histories, as well as the only case-control assessment. We found a high percentage of EHAD within FDR cases , compared with only 2 other published reports that examined EHAD among FDR (42% in the Netherlands ). In facDespite a significant difference of any EHAD between case and control FDRs, close to 50% of the 12 assessed EHADs were no different between the FDR groups. Interestingly, the frequency of 2 autoimmune liver diseases, AIH and PBC, were also similar among case and control FDRs in this study. Further examination of autoimmune liver disease in FDRs within each respective disease may help elucidate distinct pathogenetic disparities or similarities among each . For instance, Mantaka et al and JoneSNS are attractive research tools, and if implemented cautiously, may help reduce large gaps in rare disease research. There are >1.3 billion users on Facebook alone, and many patients use this as an application for medical information and health-related support from peers ,31. ThesIn summary, this study utilized SNS as a low-cost, effective research method to examine the associations between AIH and other autoimmune diseases among patients and their FDR using a case-control study design. Our data maintain the previously observed autoimmune phenotype of patients with AIH and their family members, such that cases and case FDRs were almost twice as likely as controls and control FDRs to have been diagnosed with, at least, one EHAD. These findings lend further support to an inheritable genetic predisposition underscoring the etiology of AIH. Overall, the FDR prevalence of AIH was found to be quite low among cases, and, thus, broad FDR screening for AIH is not indicated. However, female FDRs of patients with AIH, mother-daughter pairs in particular, may be worth educating of associated symptoms, given a slightly higher risk of the disease development."} +{"text": "The percentage of hereditary neuropathies had a significant decrease (p = 0.016), while the rate of vasculitic and chronic inflammatory neuropathies increased (p < 0.0001). This is the largest Italian study addressing the yield of sural nerve biopsy. During the years, we observed a progressive refinement of the indication of this procedure, which confirms its utility for interstitial neuropathies, particularly if non-systemic vasculitic neuropathy is suspected.Nerve biopsy represents the conclusive step in the diagnostic work-up of peripheral neuropathies, and its diagnostic yield is still debated. The aim of this study is to consider the impact of nerve biopsy on reaching a useful diagnosis in different peripheral neuropathies and its changing over time. We retrospectively analyzed 1,179 sural nerve biopsies performed in the period 1981\u20132017 at Neurological Clinic of Policlinico San Martino (Genoa). We relied on medical records and collected both clinical and pathological data in a database. Biopsy provided univocal diagnoses in 53% of cases (with an increase over time), multiple diagnostic options in 14%, while diagnosis was undetermined in 33% (undetermined reports decreased during the years). In 57% of patients, the pre-biopsy suspicion was confirmed, while in 43% sural biopsy modified the clinical diagnosis. The highest yield was in axonal neuropathies (29% undetermined reports vs. 40% in demyelinating and 48% in mixed neuropathies). In 68% of patients with vasculitic neuropathy, this etiology was already suspected, whereas in 32% nerve biopsy modified the clinical diagnosis. During the years, the number of annually performed biopsies decreased significantly ( Peripheral neuropathies represent one of the main neurological diseases, with a prevalence of 2.4% in general population, reaching 8% in people older than 55 . The disClinical utility , 13, 14,We retrospectively analyzed 1,184 medical records of the sural nerve biopsies performed in the period 1981\u20132017 at the Neuropathology Laboratory of Neurological Clinic of Policlinico San Martino (Genoa). Excluding 5 missing histological reports, we analyzed 1,179 reports of sural nerve biopsy and collected both clinical and pathological data in a database Excel format , 26, we p < 0.05.We used linear regression and Spearman correlation coefficient R to analyze the decrease of the number of annually performed biopsies, the increase in the average age of patients and the reduction of the percentage of minors. We also evaluated the trend of the percentage of indeterminate reports and univocal diagnoses over the years. Finally, we considered whether certain categories of neuropathy, in particular hereditary, toxic-deficient, chronic inflammatory and vasculitic forms, showed either a decrease or an increase. Results were considered statistically significant in the presence of r2 = 0.19, p = 0.007, The total number of analyzed biopsies is 1,179. The number of annually performed biopsies has undergone a significant decrease , the cases in which biopsy provided multiple diagnostic options were 13.7% (n = 162), and indeterminate reports were 33.6% (n = 396).The univocal diagnoses were 52.7% , while the report was indeterminate in the remaining 29% (n = 114). Regarding demyelinating neuropathies, instead, histological examination provided diagnostic indications in 60.5% (n = 245) and did not contribute to the achievement of an etiological diagnosis in 39.5% of cases (n = 160). In mixed neuropathies, in which it was therefore not possible to identify whether the pathological process was initially axonal or demyelinating, the reports were indeterminate in 48% of cases (n = 106), while it was possible to formulate diagnostic hypotheses in the remaining 52% (n = 115).In axonal neuropathies, some diagnostic indication was obtained in 71% of cases . In the remaining 5 cases a double diagnostic hypothesis was formulated, i.e., hereditary neuropathy or chronic inflammatory demyelinating polineuropathy (CIDP).r2 = 0.22, p = 0.016, r2 = 0.38 and p < 0.0001 for chronic inflammatory neuropathies; r2 = 0.57 and p < 0.0001 for vasculitis, r2 = 0.22 and p = 0.0038, The proportion of hereditary neuropathies significantly decreased over time , in 190 (57.2%) clinical suspicion was confirmed by nerve biopsy, while in the remaining 142 cases (42.8%) nerve biopsy modified the clinical diagnosis.n = 283) of cases a precise etiological hypothesis was missing even before histological examination. On the contrary, considering 708 patients with an absent clinical suspicion, in 38.9% of cases (n = 275) the histological report was indeterminate, while in 61.1% of cases (n = 433) biopsy provided one or more diagnostic indications.Among 396 patients for whom nerve biopsy did not provide diagnostic indications, in 71.5% (n = 17) of cases molecular confirmation of diagnosis was obtained, in 15.6% (n = 5) molecular diagnosis was not achieved with a single genetic test, and in the remaining 31.3% (n = 10) of patients molecular diagnosis was not achieved after several tests.Regarding 52 patients with histological diagnosis of genetic neuropathy in the period from 1991 (year of identification of 17p11.2 chromosome duplication as responsible for CMT1A) , 26 to 2n = 105) of which axonal and 5% (n = 6) with mixed features of demyelination and axonal damage. Active Wallerian degeneration was highlighted in 71% of cases (n = 79), demyelination and remyelination were however present in 24% (n = 27) of patients, but always secondary to primitive axonal damage. Inflammatory infiltrates were found in 85% (n = 81) of cases, with chronic vascular changes predominating in the remaining cases . In several cases, periavventitial hemosiderin-containing macrophages were found, suggesting previous hemorrhages. Axonal regeneration clusters, suggestive of the end of the acute phase of damage, were highlighted in 46% (n = 51) of cases . Mean age at biopsy was 62 years.n = 52) vasculitis was already suspected, while in 32% (n = 24) nerve biopsy modified the clinical diagnosis.Considering 76 patients with known clinical suspicion, in 68% (n = 8), cryoglobulinemic in 4% (n = 1), associated with Churg-Strauss syndrome in 11% (n = 3), ANCA-associated with lung and peripheral nervous system (PNS) involvement in 4% (n = 1), associated with connectivity's in 11% (n = 3), involving skin and PNS in 7% (n = 2), and involving kidney and PNS in 4% (n = 1) of cases. Finally, vasculitis was limited to PNS in the remaining 30% (n = 8) of patients.Since Genoa University is a reference center, many patients come from other centers, so obtaining detailed clinical information is difficult. Among 27 cases of vasculitic neuropathy with clinical records completely available, vasculitis was: HCV-related in 30% (n = 20) of which axonal, with active Wallerian degeneration in 56% (n = 14) and regeneration clusters in 36% (n = 9) of cases. The remaining 20% (n = 5) of biopsies showed coexistence of Wallerian degeneration and segmental or paranodal demyelination. Vascular changes were noted in 40% (n = 10) of cases. Constantly found feature was the deposit of amyloid substance in the epineurium, perineurium, and endoneurium. Amyloid fibrils, stained with Congo red, show a typical apple-green birefringence under a polarized light microscope, which allows a certain etiological diagnosis.In our series, amyloidotic neuropathies are 25 , 80% , axonal (ganglioside), or Ranvier node (155 neurofascin or contactin) components radically changed the diagnostic approach. Furthermore, the percentage of hereditary neuropathies diagnosed by sural nerve biopsy has dropped down, since molecular tests, including next generation sequencing, approaches are now available in most countries . ConsistIn the first years of the study, in fact, inhalation of glue solvents (N-hexane and methyl-butyl-ketone) and exposure to other industrial toxic substances and heavy metals were certainly more frequent. In 1973 a law was issued (Article 4) for the regulation of the use of chemical reagents in industries and probably after that also the consequences to the exposure have been decreased. However, it must be considered that nerve biopsy is rarely performed in the suspicion of toxic or deficient neuropathies as diagnosis is usually achieved through careful medical history, general and neurological examination, electrophysiology, and laboratory investigations.Moreover, out data confirm the higher frequency of vasculitic neuropathies in females. This is predictable, since vasculitis is generally immune-mediated and autoimmune diseases have a higher incidence in the female sex . In otheAmong vasculitic neuropathies, inflammatory infiltrates were found in most cases (85%), but not in all samples, with prevalent chronic vascular changes in the remaining 15%. After the acute phase, inflammatory infiltrates may disappear leaving the pathological hallmarks of fibrous obliteration of lumen, calcifications, recanalization and fragmentation of internal elastic lamina. In several cases, hemosiderin-containing macrophages were found at the periavventitial level, indicating previous bleeding. At the end of the acute phase, axonal regeneration clusters often appear, but they may miss if the loss of fibers was massive. Immunohistochemistry with specific antibodies for the antigenic determinants of inflammatory cells has been frequently used and is still essential for the precise diagnosis of some dysimmune neuropathies. In contrast, direct immunofluorescence, previously used to highlight epineurial deposits of immunoglobulin, complement, and fibrinogen, has not been used in our laboratory since 2010, following the introduction of anti-MAG and anti-gangliosides antibodies plasma dosage.Non-systemic vasculitic neuropathies represent the 30% of analyzed vasculitic cases. If nerve biopsy is useful, but not always essential in patients with known systemic vasculitis, histological examination is mandatory when PNS-limited vasculitis is suspected.Regarding amyloidotic neuropathies, Congo red staining and apple-green birefringence under polarized light microscope allow a certainty diagnosis. It is interesting to note that 20% of biopsies presented mixed features of axonal and myelin damage. The presence of segmental demyelination in amyloidotic neuropathies, better evaluated by teasing, has been previously described by some authors \u201334.The diagnostic yield of nerve biopsy is still a topic of discussion. Over the 37 years examined, out of a total of 1,179 sural nerve biopsies, the univocal diagnoses were 52.7%, the cases in which the histology provided multiple diagnostic options 13.7% and indeterminate reports 33.6%. Nerve biopsy was therefore helpful in more than half of patients undergoing this test.Considering only patients with a specific clinical etiological hypothesis, histological examination confirmed the pre-biopsy suspect in 57.2%, while in the remaining 42.8% of cases nerve biopsy changed clinical diagnosis.The diagnostic yield showed a progressive improvement, with an increase in the number of univocal diagnoses. This may be explained by the refinement of cases in which a pathological exam is required and by the improving expertise of our center. In our opinion, this supports the view that biopsies should be processed and examined by expert personnel, in order to both reduce artifacts and recognize the pathological hallmarks of different diseases.Considering indeterminate reports, in 71.5% of cases a precise etiological hypothesis was missing even before biopsy. Even in a retrospective study by Deprez et al., the lowest diagnostic yield was when biopsy was performed in the absence of clinical suspicion . Deprez If we considered our cohort of vasculitic neuropathies, in 68% of patients a vasculitis was already suspected before histological examination, while in 32% of cases, the diagnosis was clarified only after the pathological exam nerve biopsy modified clinical diagnosis.These results about the diagnostic yield confirm what was already known from previous literature , 35\u201337.Our work confirms a rather high diagnostic yield of nerve biopsy, comparable to that obtained by Neund\u00f6rfer et al. and GabrThe diagnostic yield of this exam increases if patients are carefully selected. Comprehensive clinical information are also crucial since in most neuropathies a diagnosis can be obtained by combining the results of biopsy with clinical features. The importance of the choice of a clinically or electrophysiologically affected nerve to be biopsied should be reiterated, since 12% of examined nerves proved to be free of pathological changes. However, in many cases of normal sural nerve, biopsy was actually performed to exclude a peripheral neuropathic process in the context of differential diagnosis from central nervous system or motor neuron diseases.According to literature, sural nerve biopsy provides the most useful results in interstitial neuropathies, such as vasculitis, granulomatosis, amyloidosis, or atypical forms of CIDP , 22. In This is the largest Italian study evaluating the diagnostic yield of sural nerve biopsy, both for the number of biopsies and for the period considered. Over time there was a progressive refinement of biopsy prescription. Nevertheless, it remains a pivotal exam in interstitial neuropathies, such as amyloidosis and vasculitis, in particular in non-systemic vasculitic neuropathies, allowing a diagnosis and addressing an appropriate treatment.All datasets generated for this study are included in the article/http://www.ospedalesanmartino.it/ricerca-scientifica/introduzione-crb/biobanche-e-servizi.html). For this reason, the approval of the Ethical Committee was not required as per the local legislation and national guidelines.All patients signed the informed consent to the processing of the personal data and the use of biopsy samples for research purposes in relation to the laws in force during the period of the intervention, carried out for diagnostic purposes. All tissue samples taken are now stored in the neurologic biobank (Bioneuro) which was established by the Policlinico San Martino IRCCS with the aim of making tissue samples available to researchers at an international level (VP designed and supervised the study. SM collected and analyzed the data. AG, EB, and PM analyzed the genetic data. MM and EV provided patients data. GM, MG, and AS supervised the study. VP, SM, and GM wrote the article. All authors discussed the results.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Despite widespread use of fluorouracil, epirubicin, cyclophosphamide,docetaxel (FEC-D) chemotherapy in breast cancer, the optimal strategy forprimary febrile neutropenia (FN) prophylaxis remains unknown. A systematicreview was therefore performed.Embase, Ovid MEDLINE, PubMed, Cochrane Database of Systematic Reviews,Cochrane Register of Controlled Trials, and conference proceedings weresearched from 1946 to April 2016 for trials that reported the effectivenessof primary FN prophylaxis with FEC-D chemotherapy. Outcome measures wereincidence of FN; treatment-related hospitalizations; chemotherapy dosedelays, reductions, and discontinuations; and adverse events fromprophylaxis.=576), one phase IV single-arm trial (n = 69), one prospective observationalstudy (n = 37), and six retrospective studies (n = 861) were identified.Agents investigated were pegfilgrastim (n = 108), filgrastim ,and ciprofloxacin (n = 89). The heterogeneity of studies meant that anarrative synthesis of results was performed. Median FN rates for patientswho received FEC-D with and without primary prophylaxis were 10.1% and 23.9% ,respectively. In the absence of primary prophylaxis, FN was more commonduring docetaxel than during FEC. Data from six studies showed a median rateof dose reductions and delays of 6.1% and 19.3% , respectively, that occurred as a consequence of FN.Toxicity from prophylaxis itself was rarely reported.Of 2,205 identified citations, eight studies met our eligibilitycriteria. Three additional studies (n = 293) were identified from a priorsystematic review. Three randomized controlled trials (n Primary FN prophylaxis is effective in patients who receive FEC-Dchemotherapy. The paucity of prospective data makes optimal recommendationsabout the choice and timing of prophylaxis challenging. FNcan be associated with considerable morbidity, mortality, and costs5 and often results in chemotherapy dose reductions, delays, anddiscontinuations.6 In thepivotal PACS 01 III trial where primary prophylactic granulocyte colony-stimulatingfactor (G-CSF) was administered in 22.2% of patients, FEC-D was associated with an11.2% rate of FN.3 However, as itsuse expanded into routine clinical practice, reports of FN rates as high as 46.4%were reported.8 One systematic review identified that in routineclinical practice, FEC-D chemotherapy without G-CSF primary prophylaxis wasassociated with a median FN rate of 30.6% . In contrast, fortrials in the meta-analysis that used primary FN prophylaxis with G-CSF, the FN ratewas 6.8% .8FEC-D or timing of such prophylaxis. These limitations are important given theconsiderable differences in cost and toxicity between agents.Most local,To our knowledge, no high-quality evidence guides optimal FN prophylaxis with thiscommonly used chemotherapy regimen. Hence, we performed a systematic review toevaluate the incidence of FN with FEC-D (with and without primary prophylaxis), itstiming, and optimal strategies for primary FN prophylaxis. We also identified gapsin the available literature that require further study.9/L with oral temperature >38.3\u00b0C or a temperature of > 38.0\u00b0C sustained over a 1-hourperiod). Secondary outcome measures were treatment-related hospitalizations;chemotherapeutic dose reductions, delays, and discontinuations; and frequency ofadverse events from primary FN prophylaxis. Interventional or retrospective andprospective observational studies published in English were included. Animalstudies, studies in the metastatic setting, and studies that involved patientswho had received prior chemotherapy and secondary FN prophylaxis wereexcluded.This systematic review was performed to identify and evaluate the incidence andtiming of FN in the absence of primary FN prophylaxis and the effects of twostrategies (G-CSF and antibiotics) for primary FN prophylaxis in patients whoreceived six to eight cycles of FEC-D chemotherapy once every 3 weeks forearly-stage breast cancer. The population, intervention, comparator, and outcomestudy design framework was used to structure the research question and itscorresponding literature search. The population of interest was patients withbreast cancer who received FEC-D chemotherapy in the adjuvant or neoadjuvantsetting. Interventions of interest were primary FN prophylaxis G-CSF and prophylactic antibiotics of anytreatment duration. Primary FN prophylaxis was defined as prophylacticadministration of hematopoietic cell growth factors or quinoloneantibiotics to prevent the occurrence of infection. Comparators were bestsupportive care or prophylactic quinolone antibiotics. The primary outcomemeasure was the incidence of FN designed and executed an electronic literaturesearch to identify relevant citations from Embase, Ovid MEDLINE, PubMed(including in-process and other nonindexed citations), the Cochrane Database ofSystematic Reviews, the Cochrane Register of Controlled Trials, and conferenceproceedings from 1946 to April 26, 2016. Search terms and their medical subjectheading equivalents are shown in the Data Supplement.8 The screeningprocess is presented in a Preferred Reporting Items for Systematic Reviews andMeta-Analyses (PRISMA) flow diagram (17 (DataSupplement).Stage 1 screening consisted of a review of titles and abstracts identified fromthe literature search by two independent reviewers (R.F. and S.M.).Disagreements between the reviewers were discussed and resolved. A thirdreviewer was consulted if necessary to achieve consensus. Stage 2 screeningconsisted of a full-text review of all manuscripts and meeting abstracts frompotentially relevant citations identified during stage 1 screening by twoindependent reviewers .We also reviewed the relevant studies included in a previous systematicreview. diagram , and a Pv adjuvant setting, type and frequency of G-CSF, andantibiotics used), and outcomes of interest .Authors were contacted to acquire other unpublished data. The CochraneCollaboration\u2019s tool for assessing risk of bias in randomized controlledtrials was used14,15 (Data Supplement). Funding forthe current study was from internal sources, and there was no pharmaceuticalcompany funding.Data from the final set of included studies were extracted by two reviewersindependently who used a predesigned form implemented in Microsoft Excel version2010 ; discrepancies were resolved byconsensus discussion. The following information was collected from each study:publication characteristics , patientcharacteristics ,intervention characteristics ,21 filgrastim inseven ,26 andciprofloxacin in one (n = 89).23 None of the included studies reported use of interimneutrophil counts to guide G-CSF dosing.Eligible studies included three randomized trials (n = 576), one phase IVsingle-arm trial (n = 69), one prospective observational study (n = 37), and sixretrospective observational studies (n = 861). Sample sizes ranged from3220Characteristics of the individual studies are listed inOverall, we found 1,543 patients treated with FEC-D . FEC-D chemotherapy with and without primary prophylaxis wasassociated with median FN rates of 10.05% and 23.9% , respectively.21 Onestudy showed that among 32 patients treated with FEC-D who received primary FNprophylaxis with pegfilgrastim, FN developed in 5%.21 The other trial demonstrated that 9% of the 69patients treated with FEC-D experienced FN despite receipt of primaryprophylaxis with pegfilgrastim.20 Two studies provided detailed information about the use ofprimary prophylactic filgrastim.17 One trialdemonstrated that of 100 patients treated with FEC-D, 26% and 10% had FN withoutand with filgrastim prophylaxis, respectively.17 In the other study, with a cohort of 189patients treated with FEC-D, filgrastim was used in 1.8% and 9% during the FECand docetaxel phases, respectively.16With respect to each primary prophylaxis treatment, pegfilgrastim was used as aprimary prophylaxis in two prospective studies.16 In another trial of 284patients who had FEC-D without primary prophylaxis, 14 (4.9%) had FN. Overall,FN developed in 2.1% of patients during FEC cycles, whereas FN related todocetaxel occurred in 1.4% of patients.18 The third study comprised 32 patients treated withFEC-D without primary prophylaxis, where 9% and 21.8% experienced FN during theFEC and docetaxel phases, respectively.19 Finally, Rayson et al26 showed that among 37 patients without primaryFN prophylaxis, the FEC and docetaxel cycles were associated with 35% and 62% FNrates, respectively. In summary, primary prophylaxis was only used in 9% to 24%of patients, and most episodes of FN occurred during docetaxel administration. In contrast, in theabsence of primary prophylaxis, a median of 8% ofpatients experienced FN during FEC cycles.26Four studies reported the differences in FN rates between the FEC and docetaxelphases. In one study where 189 patients were treated with FEC-D, 7% and 21%experienced FN during the FEC and docetaxel phases, respectively.12 Primaryprophylaxis was not used in all the included studies . FN risk factors were identified in two studies.20 In these two studies, the percentage of patients olderthan 65 years were 33.3%16 and19%.20 Furthermore,17% of patients were found to have medical comorbidities, such as vasculardisease, diabetes, and chronic obstructive pulmonary disease.20 In one of the two studies thatreported FN rates according to a 65-year age cutoff, the risk of developing FNduring FEC was equal in patients older and younger than 65 years .16Traditional risk factors with a high/intermediate level of supporting evidencefor FN are extensive prior chemotherapy; \u2265 85% relative intensity; ageolder than 65 years; poor performance status; low albumin/high lactatedehydrogenase levels; comorbidities such as pulmonary, cardiovascular, and liverdisease; and diabetes mellitus.22Hospital admission as a result of FN occurred in 0.04% to 33.4% ofcases. The median duration of hospitalization reported was 6 days .20 Onlyone study reported chemotherapy discontinuation rates as a result of FN thatoccurred in 6.7% of patients.18 Of note, across all the studies, no deaths occurred as aresult of FN.Data from six studies reported a median number of dose reductions and delays of6.1% and 19.3% as a consequence ofFN.Clostridium difficile infection (7.6%).20Few studies reported adverse effects of primary prophylaxis. Two studies withfilgrastim reported primary prophylaxis toxicity, such as back pain (0.4%) and13 recommend the use of primary FN prophylaxis.Primary prophylaxis is usually in the form of G-CSF or antibiotic use. However,despite the considerable differences in the cost and toxicity profiles of theseagents as well as significant differences in the risk of FN depending on thechemotherapy received (docetaxel > FEC), we were unaware of high-quality datathat compared either the choice of agent or its timing .FN is an important toxicity associated with FEC-D chemotherapy and can be associatedwith significant morbidity, mortality, and costs as well as a result of chemotherapydose reductions, delays, and discontinuations. Because the proportion of FN cases inthe absence of primary prophylaxis exceeds 20% with FEC-D chemotherapy, mostguidelines28 From a cost perspective alone, thecost differences are important from a global health care standpoint, with threecycles of FEC-D being associated with direct drug costs of $CAD1,740 for filgrastimfor 10 days and $CAD2,422 for pegfilgrastim and $CAD35 for ciprofloxacin for 14days.9 These costs do notinclude the charges for a health care professional to administer the G-CSFinjections. Furthermore, from clinical experience, FN is much more commonly observedduring the docetaxel component of treatment than during the FEC cycles. Finally, thetoxicities of G-CSF differ from those of antibiotics as well as differ according toduration of use. Possible adverse effects of ciprofloxacin are nausea (> 2%)and, less commonly, diarrhea and vomiting (< 1%).29 Possible adverse effects of G-CSF (> 10%)are bone pain, headaches, irritation at the injection site, and diarrhea.30 The current systematic reviewattempts to address these questions from the synthesis of available evidence.The most effective strategy of providing FN prophylaxis is an important question notonly to the physician and patients but also to the entire health care system in boththe developed and the developing world because of its financial implications. Giventhe greater drug cost of pegfilgrastim over filgrastim, most health care funderswill cover filgrastim, even though some data suggest that pegfilgrastim is superiorand more cost-effective than filgrastim .26To our knowledge, this systematic review is the second to evaluate G-CSF andantibiotic use in patients with breast cancer who underwent FEC-D chemotherapy.Overall, median FN rates for patients who receive FEC-D with and without primaryprophylaxis are 10.05% and 23.9% ,respectively. With respect to the timing of FN, four studies showed that mostepisodes occurred during docetaxel infusion cycles compared with during FEC cycles .With respect to the choice of primary prophylaxis, pegfilgrastim (n = 108),filgrastim , and ciprofloxacin (n = 89) were used. However, variablereporting of the use of different agents at different times and as primary or secondary FN prophylaxis made it challenging to identifythe optimal strategy. In fact, none of the included studies compared bothstrategies.This systematic review had limitations. First, the included studies were mostlyretrospective in design. Second, and of note, despite the widespread global use ofFEC-D for more than a decade, a paucity of high-quality literature on the incidence,measurement, treatment, and prophylaxis of FN exists. The identified studies alsolacked detailed and consistent outcome data, two of which were published in abstractform only, which leads to a risk of bias in these trials. Finally, although we aimedto compare two FN primary prophylaxis options (G-CSF and antibiotics), we wereunable to find any such trial conducted previously.28 Unfortunately, no definitive results were available forantibiotic use. In addition, future trials could assess the timing of primary FNprophylaxis, for example, either from the start of FEC-D treatment or during thedocetaxel component only. Robust economic analyses also are needed.Future studies are needed to determine the most effective treatment strategies toprovide appropriate patient selection and individualized drug dosing and to preventand reduce treatment-related toxicities. Only one clinical trial prospectivelylooked at optimal duration of filgrastim as FN primary prophylaxis, specifically inpatients with early-stage breast cancer who underwent commonly used adjuvantchemotherapy regimens, including FEC-D.In conclusion, FN is a common toxicity of FEC-D chemotherapy. In light of the 20% FNthreshold currently recommended for primary prophylaxis, the current results suggestthat primary prophylaxis should be considered for the FEC-D regimen in routineclinical practice. Large population-based studies will help to clarify FN incidencein the real world, and randomized clinical trials are crucial to the establishmentof treatment strategies and improvement of optimal G-CSF use."} +{"text": "Due to the high morbidity of extended lymph node dissection (eLND) and the low detection rate of limited lymph node dissection (LND), targeted sentinel lymph node dissection (sLND) was implemented in prostate cancer (PCa). Subsequently, nonradioactive sentinel lymph node (SLN) detection using magnetic resonance imaging (MRI) and a magnetometer after intraprostatic injection of superparamagnetic iron oxide nanoparticles (SPIONs) was successfully applied in PCa. To validate the reliability of this approach, considering the magnetic activity of SLNs or whether it is sufficient to dissect only the most active SLNs as shown in other tumor entities for radio-guided sLND, we analyzed magnetometer-guided sLND results in 218 high- and intermediate-risk PCa patients undergoing eLND as a reference standard. Using a sentinel nomogram to predict lymph node invasion (LNI), a risk range was determined up to which LND could be dispensed with or sLND only would be adequate. In total, 3,711 LNs were dissected, and 1,779 SLNs were identified. Among 78 LN-positive patients, there were 264 LN metastases . sLND had a 96.79% diagnostic rate, 88.16% sensitivity, 98.59% specificity, 97.1% positive predictive value (PPV), 93.96% negative predictive value (NPV), 4.13% false-negative rate, and 0.92% additional diagnostic value (LN metastases only outside the eLND template). For intermediate-risk patients only, the sensitivity, specificity, PPV, and NPV were 100%. Magnetic activities of SLNs were heterogeneous regardless of metastasis. The accuracy of predicting the presence of metastases for each LN from the proportion of activity was only 57.3% in high- and 65% in intermediate-risk patients. Patients with LNI risk of less than 5% could have been spared LND, as no positive LNs were found in this group. For patients with an LNI risk between 5% and 20%, sLND-only would have been sufficient to detect almost all LN metastases; thus, eLND could be dispensed with in 36% of patients. In conclusion, SPION-guided sLND is a reliable alternative to eLND in intermediate-/high-risk PCa. No conclusions can be drawn from magnetic SLN activity regarding the presence of metastases. LND could be dispensed with according to a nomogram of predicted probability for LNI of 5% without losing any LN-positive patient. Patients with LNI risk between 5% and 20% could be spared eLND by performing sLND. Lymph node (LN) status plays a decisive role in estimating the local extent and prognosis of prostate cancer (PCa), as survival is inversely related to the number of positive nodes . Patientvia the lymphatic network using imaging agents or sentinel tracers that exhibit a lymphatic drainage from the primary tumor location (Growing evidence in the setting of recurrent PCa argues for the use of prostate-specific membrane antigen positron emission tomography\u2013computed tomography (PSMA PET/CT) for detection of LN metastasis in men with persistent PSA after RP. PSMA PET/CT imaging at primary staging might improve the detection of LN metastases compared to conventional imaging techniques, too. However, there is still a paucity of data comparing PSMA PET/CT results from primary staging with histological results from pelvic LND. Only few reports involving few patients exist pursuing this purpose. Some of these studies could show a high sensitivity in the detection of LN metastases . In prinlocation .LND can be performed as extended or limited procedures to various extents. Several studies have shown that extended LND (eLND) including the area along the common, external, and internal iliac vessels as well as the obturator fossa region has a more reliable diagnostic value and could improve biochemical recurrence-free survival compared with the limited approach . Althoug99mtechnetium (99mTc) nanocolloid as a tracer. However, the radioactive tracer is accompanied by several disadvantages, particularly the dependence on radioisotopes and exposure to ionizing radiation. Therefore, SLN detection using a magnetic tracer was established in breast cancer, as equivalent results to 99mTc nanocolloid could be shown , and receiving the surgical intervention named above .\u00ae, iron overload disease, and those with pacemakers or other implantable devices in the chest wall as well as hip prosthesis or other metallic pelvic implant.Exclusion criteria were patients with previous transurethral or open prostate surgeries, previous hormone therapies, known intolerance or hypersensitivity to iron, dextran compounds or Sienna+\u00ae system was applied to mark and detect LNs in cancer patients and is composed of a handheld magnetometer, the SentiMag\u00ae unit, and the Sienna+\u00ae magnetic tracer, which both are Conformit\u00e9 Europ\u00e9enne (CE) certified as class IIa medical devices.The SentiMag\u00ae is a suspension of superparamagnetic carboxydextran-coated iron oxide particles in injectable water. Each milliliter of Sienna+\u00ae contains approximately 28 mg of iron. The mean hydrodynamic diameter of the particles is 60 nm, just as 99mTc nanocolloid, but more homogeneous. Their functional properties are also comparable, as after interstitial injection both flow through the lymph system and get trapped in SLNs where Sienna+\u00ae subsequently forms iron deposits that can be intraoperatively identified with the handheld SentiMag\u00ae magnetometer. Another advantage of Sienna+\u00ae is that its brown color can also help identify SLNs.Sienna+\u00ae has been reviewed and tested as specified in EN 10993-1:2009 based on the specified site of injection and duration. Sienna+\u00ae is contraindicated in any patient with hypersensitivity to iron oxide or dextran compounds and should not be administered in any patient with an iron overload disease or with a metal implant close to the expected SLN location. Sienna+\u00ae is only approved for interstitial injection. When similar material to that used in Sienna+\u00ae has been injected intravenously, the following undesirable effects have been reported: common (<2%)\u2014pain at the injection site, vasodilation, paresthesia; uncommon (\u22650.1% to <1%)\u2014asthenia, back pain, injection site reactions, chest pain, nausea, vomiting, headache, taste perversion, pruritus, and rash; rare (\u22650.01% to <0.1%)\u2014hypersensitivity and anaphylaxis, hypertension, phlebitis, hyperesthesia, anxiety, dizziness, convulsion, parosmia, dyspnea, increased cough, rhinitis, eczema, and urticaria. There have been a small number of reports of inflammatory and hypersensitivity response with intradermal injection. There is no evidence of adverse reaction following interstitial injection sLND and eLND as a reference, followed by a radical retropubic prostatectomy performed by four high-volume surgeons.One day after tracer injection, all patients underwent open magnetometer-guided (SentiMag\u00ae), magnetic activity was detected, and the corresponding lymphatic fatty tissue containing the active LN and if applicable direct adherent nonactive LNs was dissected. To generate values, the magnetometer measures the difference between the local magnetic activity and the activity in the surrounding medium. For this purpose, it is necessary to calibrate the magnetometer against the corresponding medium before measuring. The measurand is \u201cunits\u201d and thus is not defined. To not disturb the magnetic field of the SentiMag\u00ae system, metal retractors were replaced with polymer retractors .Using the handheld magnetometer was performed to assess metastatic spread.in vivo magnetically active LN. Based on previous work, eLND was used as a reference standard to assess the diagnostic reliability of sLND as the index test curve.The updated nomogram developed by All subjects gave informed consent for the documentation and scientific evaluation of their data in a prospective clinical registry. The study was conducted in accordance with the Declaration of Helsinki, and the protocol was registered in an international clinical trial register (Research Registry: researchregistry4963). The study protocol was approved by the Medical Ethics Committee of the Carl von Ossietzky University Oldenburg (no. 2018-140).This study included 218 intermediate- (n = 97) and high-risk (n = 121) PCa patients who underwent magnetometer-guided sLND, eLND, and RP after intraprostatic SPION injection one day before surgery. In total, 3,711 LNs were dissected and 1,779 SLNs were found in 211 of 218 patients (diagnostic rate of 96.79%), with a median of eight SLNs. Seventy-eight patients (29.55%) were LN-positive and had 264 LN metastases (median = 2). A LN-positive patient was correctly identified by sLND with an 88.16% sensitivity, 98.59% specificity, 97.1% PPV, and 93.96% NPV Table 2.In the high-risk group (n = 121), a total of 2,074 LNs were dissected. Altogether, 967 SLNs were detected in 116 of 121 patients (95.87% diagnostic rate), with a median of eight SLNs per patient. There were 238 LN metastases (median = 2) found in 65 patients (53.72%). Patient-based sLND results had an 85.71% sensitivity, 96.55% specificity, 96.43% PPV, and 86.15% NPV Table 3.An even higher diagnostic reliability result was found for the intermediate-risk group. A total of 1,637 LNs were dissected in this risk group, and 812 SLNs were found in 95 of 97 patients, yielding a diagnostic rate of 97.94%, with a median of eight SLNs. Among the intermediate-risk patients, 13.4% (n = 13) were LN-positive and had 26 LN metastases (median = 1). All of them also had positive SLNs. Patient-based results showed 100% sensitivity, 100% specificity, 100% PPV, and 100% NPV Table 4.in vivo SLN magnetic activity and existing metastases, a mean activity of positive as well as of negative LNs in both risk groups between 184 and 323 units was revealed with a maximum of 6,000 units classified in this risk group, so that the number of dissected LNs could have been halved. In the risk range from 45.01% to 100%, both sLND and eLND showed additional diagnostic benefit, so we recommend a combination of these two to increase diagnostic reliability.With the aim of removing all pelvic LN metastases to achieve possible therapeutic benefits, patients with a risk of \u22645% could have been spared eLND, as no positive LNs were found in this risk group. In patients with an LNI risk between 5.01% and 20% , a sole sLND would have been sufficient to dissect almost all positive LNs. We recommend combined sLND with subsequent eLND for all patients with a risk between 20.01% and 100% because neither LND method alone could detect all positive LNs. Moreover, more dissected LNs seemed to increase the likelihood of finding LNI .Nevertheless, we must also note that the reduced perioperative morbidity by avoiding LND in patients with a risk of LNI \u22645% must be weighed against the improved survival by removing LN metastases. Especially in patients with minimal LNI, LND can also play a therapeutic role in addition to its diagnostic benefit .https://www.prostatakarzinomzentrum.info/vorhersagetool_fuer_lymphknotenmetastasen__nomogramm_.html) can provide support in this process.Furthermore, in clinical routine, the use of nomograms is associated with an increased preoperative effort. In addition to the respective calculation, the resulting individualized counseling of patients is more complex. However, electronic nomogram tools as the online available nomogram developed by us LND at a risk range for LNI up to 5%. Between a nomogram risk from 5.01% to 20%, sLND alone might be sufficient. However, external validation and renewed data collection with a larger number of cases are required.sLND after intraprostatic SPION injection is a reliable alternative to eLND in intermediate-risk PCa patients to correctly identify all positive patients while halving the number of dissected LNs. In high-risk PCa patients, sLND alone can also ensure the diagnostic standard if it is performed only under the condition that at least three The datasets generated for this study are available on request to the corresponding author.The studies involving human participants were reviewed and approved by Medical Ethics Committee of the Carl von Ossietzky University Oldenburg. The patients/participants provided their written informed consent to participate in this study.AW, SE, and FW conceived and designed the study. AW and FW performed a large number of the surgeries. WG evaluated data and wrote the manuscript. SE and PA performed and documented magnetic measurements. FW, HG, and JS conducted critical revision for important intellectual content. All authors helped prepare the paper and approved the final version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.AUC, area under the curve; eLND, extended lymph node dissection; FN, false-negative; FP, false-positive; GS, Gleason score; LN, lymph node; LNI, lymph node invasion; LND, lymph node dissection; MRI, magnetic resonance imaging; NPV, negative predictive value; PCa, prostate cancer; PPV, positive predictive value; PSA, prostate-specific antigen; ROC, receiver operating characteristic; RP, radical prostatectomy; SLN, sentinel lymph node; sLND, sentinel lymph node dissection; SPION, superparamagnetic iron oxide nanoparticles."} +{"text": "In 2016, 63,632 drug overdose deaths occurred in the United States, 42,249 (66.4%) of which involved opioids ( CDC funds 32 states and the District of Columbia to abstract death certificate and medical examiner and coroner data, including toxicology results, on opioid deaths, through the State Unintentional Drug Overdose Reporting System, a component of ESOOS. Data are collected on death scene investigations , circumstances occurring close in time to the death , history of substance use treatment, prior history of overdose, and demographics. For all opioid deaths classified as unintentional or of undetermined intent, states list all positive tests for opioid and nonopioid substances (\u201cpresent\u201d or \u201cdetected\u201d), and whether the medical examiner or coroner determined that the substance contributed to the overdose death (\u201cinvolved\u201d).Among 11,884 opioid deaths, 2,066 (17.4%) involved prescription opioids only, 6,975 (58.7%) involved illicit opioids only, and for 2,194 (18.5%) both prescription and illicit opioids were detected; type of opioid could not be classified in 649 (5.5%) deaths, leaving 11,235 deaths for analysis. Among deaths for which both prescription and illicit opioids were detected, medical examiners or coroners determined that both prescription and illicit opioids contributed to 59.2% of deaths, illicit opioids alone contributed to 39.8% of deaths, and prescription opioids alone contributed to 1.0% of deaths. The percentage of deaths involving different opioid types varied across states , with thAmong prescription opioid\u2013only deaths, the median age of decedents was 47 years, 51.0% were female, and 86.2% were non-Hispanic white (white). Among illicit opioid\u2013only deaths, the median age of decedents was 36 years, 73.0% were male, and 81.1% were white. Among deaths for which both prescription and illicit opioids were detected, decedents\u2019 median age was 39 years, 70.5% were male, and 83.6% were white .Evidence of injection drug use was found in approximately half of illicit opioid deaths, but only 6.6% of prescription opioid\u2013only deaths. Other drugs were frequently detected in opioid deaths . BenzodiApproximately one in 10 decedents had evidence of having been released from an institutional setting in the month preceding the fatal overdose, with the most common settings being jail, prison, or detention facilities when only illicit opioids were involved (4.9%), and hospitals when only prescription opioids were involved (4.1%). Previous drug overdose at any time before the fatal overdose was noted in 15.1% of illicit opioid\u2013only deaths, 13.5% of deaths with both prescription and illicit opioids present, and 9.3% of prescription opioid\u2013only deaths. Bystanders were reported to have been present in 44% of opioid deaths, but naloxone was seldom administered by a layperson (in approximately 4% of deaths involving only illicit opioids and 0.8% of prescription opioid\u2013only deaths).This report is one of the first to use medical examiner and coroner reports across multiple states and provides information that can be used to better inform prevention and response programs related to opioid overdose deaths. Specifically, among these 11 states, there is improved understanding of prescription and illicit opioid involvement, polysubstance use, and potential missed opportunities to intervene to prevent opioid overdose deaths. Previous efforts to differentiate illicit and prescription opioid deaths were limited by grouping within the same drug categories and by the difficulty in determining whether detection of morphine or fentanyl by forensic toxicology testing indicates the presence of prescription or illicit opioids , as well as using syringe services programs for naloxone distribution, providing access to treatment, and addressing blood borne infections might have a larger impact. To prevent prescription opioid overdose, strategies might emphasize prescription drug monitoring programs, face-to-face education of prescribers by trained health care professionals, typically pharmacists, physicians, or nurses (a process known as academic detailing), and implementation of the CDC Guideline for Prescribing Opioids for Chronic Pain opioid overdose deaths involved illicit opioids only, followed by those where both illicit and prescription opioids were detected (18.5%); 17.4% of deaths involved prescription opioids only. Bystanders to the overdose, who could potentially intervene, were documented in 44% of deaths; however, laypersons rarely administered naloxone.Development of overdose prevention programs should consider the types of opioids contributing to deaths, link persons to treatment during and upon release from an institution or after a nonfatal overdose, and expand naloxone distribution to laypersons."} +{"text": "Combination antiretroviral therapy (cART) initiation in hospital settings, where individuals often present with undiagnosed, untreated, advanced HIV disease, is not well understood. A cross-sectional study was conducted to determine a period prevalence of cART initiation within two weeks of eligibility, as determined at hospitalization. Using a pretested and precoded data extraction tool, data on cART initiation status and reason for not initiating cART was collected. Phone calls were made to patients that had left the hospital by the end of the two-week period. Delayed cART initiation was defined as failure to initiate cART within two weeks. Sociodemographic characteristics, WHO clinical stage, CD4 count, cART initiation status, and reasons for delayed cART initiation were extracted and analyzed.\u03bcl and who resided in \u22658 kilometers from the hospital were more likely to have delayed cART initiation . Overall, 386 HIV-infected adults were enrolled, of whom 289/386 (74.9%) had delayed cART initiation, 77/386 (19.9%) initiated cART, and 20/386 (5.2%) were lost-to-follow-up, within two weeks of cART eligibility. Of 289 with delayed ART initiation, 94 (32.5%) died within two weeks of cART eligibility. Patients with a CD4 cell count\u2265 50 cells/ Up to 75% of hospitalized HIV-infected, cART-na\u00efve, cART-eligible patients did not initiate cART and had a 33% pre-ART mortality rate within two weeks of eligibility for cART. Hospital based strategies to hasten cART initiation during hospitalization and electronic patient tracking systems could promote active linkage to HIV treatment programs, to prevent HIV/AIDS-associated mortality in resource-limited settings. There is global commitment to fast-track the end of the HIV/AIDS epidemic through the Joint United Nations Programme on HIV/AIDS (UNAIDS) 90-90-90 campaign to test 90% of all people living with HIV, initiate and sustain combination antiretroviral therapy (cART) for 90% of all those diagnosed HIV-infected, and have sustained undetectable viral load among 90% of cART-treated individuals . Access \u03bcL , and 20/386 (5.2%) were lost to follow-up. Of patients with delayed cART initiation, 94/289 (32.5%) died within two weeks of being found cART eligible. The median hospital stay was 8 (IQR 4-13) days, and the commonest causes of hospitalization were tuberculosis (pulmonary and extrapulmonary), followed by bacterial pneumonia . The leaPrior to the current hospitalization, majority [295/386 (76.4%)] of HIV-infected patients were aware of their HIV-infected status, yet only 132/295 (44.7%) had been enrolled into an HIV care program, yet 291/295 (98.6%) had received cotrimoxazole prophylaxis. This was the first admission within the year for 258/386 (66.8%) patients, although more than half had visited outpatient clinics five times or more during the year prior to this study.\u03bcl and patients living outside Kampala were more likely to have delayed cART initiation and , respectively of whom initiated cART after leaving hospital. Of patients with delayed cART initiation, 94/289 (33%) died within two weeks. Up to 80% of patients who died before cART initiation were still in hospital and the main reason for not initiating cART despite physicians' recommendations was postponement (by the patients and relatives) because patients were too sick. Similarly, high mortality was reported among patients that initiated cART during hospitalization in Tanzania, where the main causes of death within the first month of cART were anemia, thrombocytopenia, and severe malnutrition . It remaOur results are comparable to previous reports from an HIV testing trial on the same wards where only 62% of surviving HIV-infected participants were linked to HIV care, only 15% received cART, and 35% died, within six months of discharge from hospital . A study\u03bcl and patients living outside Kampala were more likely to have delayed cART initiation. Similarly, lengthy preparation for cART [54/195 (28%)] and failure to honor referral appointments [51/195 (28%)] were mentioned by individuals that did not initiate cART. Our data from hospitalized patients was comparable to reports from a review of observational cART cohorts in sub-Saharan Africa where patients presented to the health care system with advanced untreated HIV diseases with CD4 cell count <50 cells/\u03bcL and WHO stage IV and faitiation , and inditiation , 30, 31.itiation , 24, 32,We found that 76% of hospitalized HIV-infected patients were aware of their HIV-infection status prior to current hospitalization and had received cotrimoxazole prophylaxis but not cART, and only 45% of them had been enrolled into an HIV care program. Of the patients that did not initiate cART within two weeks of eligibility, 28% were still under preparation for cART, 26% had not honored their referral notes to ART clinics, and another 24% were still considered too weak to initiate cART. Health system challenges such as poor access to diagnostic services, prolonged patient preparation for cART, and limited tracking of referrals continue to affect the quality of health care , 28. In cART initiation was simply by patient self-report, but could not be confirmed via any tracking system. Similarly it was unclear whether patients recorded as \u201clost to follow-up\u201d had been enrolled into other HIV care facilities in or outside urban Kampala. We recommend development of a national HIV care database with unique identifiers to track patients between different HIV treatment sites. Our definition of delayed cART initiation was limited to two weeks after eligibility, as determined during hospitalization, mainly because of the evidence that early cART initiation within two weeks of eligibility reduced the rate of severe illnesses in clinical trial settings , 34.Up to 75% of hospitalized HIV-infected, ART-na\u00efve, ART-eligible patients did not initiate cART and had a 33% pre-ART mortality rate within two weeks of eligibility for cART. Hospital based strategies to hasten cART initiation during hospitalization and electronic patient tracking tools could improve linkage to HIV treatment programs and prevent HIV/AIDS-associated mortality in resource-limited settings."} +{"text": "While caregivers of older adults with dementia often report considerable levels of depressive symptoms, much less is known about depressive symptoms among family members of older adults with depression or recent delirium. As part of an ongoing randomized clinical trial testing an in-home multidisciplinary team intervention for older adults with cognitive vulnerability due to dementia, depression, and/or delirium and their caregivers, in this presentation we report baseline data from the first 211 dyads enrolled in the trial to determine how caregiver depressive symptom severity is related to: CR diagnoses; CR cognitive impairment severity; and CR depressive symptom severity. CR diagnostic groups: Depression Only (n=49); Dementia Only (n=61); Depression and Dementia Only (n=47); Delirium Plus (n=54). Depressive symptom severity was measured using the Center for Epidemiologic Studies Depression Scale; CR cognitive symptom severity was measured using the Telephone Interview for Cognitive Status. Among CR, 57% were female, mean/sd age=77/6.9, 93% White; among caregivers, 64% were female, mean/sd age=66/13.7, 91% White, 55% spouses, 25% daughters, 9% sons. In multivariate linear regression models, which included covariates caregiver gender, relationship to CR, and number of hours/week providing care, we found that caregiver depressive symptom severity was less severe among caregivers of CR with Dementia Only compared to CR with Depression Only ; not associated with CR cognitive symptom severity; and significantly associated with CR depressive symptom severity . We conclude that family members of older adults with depression deserve greater attention to address their own depressive symptoms."} +{"text": "Large disparities in preparedness measures, BLS and ALS techniques emerged among levels of expertise. Only 32% (95% CI: 29\u201336%) of respondents complied with BLS practice guidelines, varying from 49% (95% CI: 42\u201355%) of BCS to 15% (95% CI: 10\u201320%) of GPG. While incompliances in BCS, RES, and GPE were predominantly due to knowledge gaps, GPG compliance was further compromised by limitations in the resuscitation environment . Those aware of RECOVER guidelines were more likely to comply with recommended preparedness , BLS , and ALS techniques independent of age, gender, region of practice or level of expertise. We conclude that awareness of RECOVER guidelines is high in specialists and residents, but incomplete among general practitioners. This awareness positively influenced compliance with CPR guidelines, but CPR practices continue to be variable and largely not in agreement with guidelines. A widely accessible educational strategy is required to broadly improve compliance with best practices in small animal CPR.In 2012 the Reassessment Campaign on Veterinary Resuscitation (RECOVER) published evidence-based treatment recommendations for dogs and cats with cardiopulmonary arrest (CPA), to optimize the clinical practice of small animal CPR and positively impact outcomes. Six years after the release of these guidelines, we aimed to determine the compliance of small animal veterinary CPR practices with these RECOVER guidelines. To identify current CPR practices in clinically active small animal veterinarians and their awareness of the RECOVER guidelines, we conducted an internet-based survey. Survey invitations were disseminated internationally via veterinary professional organizations and their social media outlets. Questions explored respondent demographics, CPR preparedness, BLS and ALS techniques and awareness of RECOVER guidelines. Responding small animal veterinarians ( Mortality is extremely high in small animals experiencing in-hospital cardiopulmonary arrest (CPA). Survival to discharge rates range from 1.6\u20136% in dogs, and 2.3\u20139.6% in cats , whereasResults of an internet-based survey conducted in 2008 and published in 2010 evaluated the clinical practice of veterinary CPR. This study concluded that CPR was heterogeneously performed in small animal veterinary medicine , 10. TheTo address these questions, we analyzed the data from an international, internet-based survey that broadly examined the clinical practice in small animal CPR. The objectives of our study were to determine the agreement of CPR practices of clinically active small animal veterinarians with current guidelines and to quantify the association of RECOVER awareness with CPR guidelines compliance.We used an anonymous online survey to interview clinically active small animal veterinary professionals on their clinical practice of CPR after the University of Melbourne's Human Ethics Committee approved the survey procedure (Ethics ID 1546061). From the survey data that encompassed all aspects of small animal CPR, we extracted the questions that describe respondent characteristics, those that reflect specific RECOVER guidelines and those that concern respondent awareness of the RECOVER guidelines. The entirety of descriptive survey data on the current practice in veterinary CPR is published elsewhere.Survey invitations were distributed internationally via electronic mailing lists of various professional veterinary organizations and their social media outlets. These organizations were the American College of Veterinary Anesthesia and Analgesia , the Veterinary Emergency and Critical Care Society , American College of Emergency and Critical Care , the European Veterinary Emergency and Critical Care Society , the Australian and New Zealand College of Veterinary Scientists , and the Academy of Veterinary Emergency and Critical Care Technicians . The initial emails containing invitations to take part in the survey were sent on March 1, 2017, followed by reminder emails sent on March 8 and 15. The survey closed on March 31. Survey links were also made available on the social media outlets of the above organizations over the same time period. Neither the email invitations nor the text used in social media postings included the term RECOVER.We used REDCap (Research Electronic Data Capture), a software toolset for electronic collection and management of research and clinical trial data, to implement the online survey .The survey posed 36 questions regarding respondent and patient demographics, CPR statistics such as training, preparedness, equipment, drugs and technique, as well as opinions on CPR skills and RECOVER guidelines . Based oThe design of the survey only permitted those respondents indicating that they were currently providing small animal (dogs and/or cats) clinical veterinary care, access to the survey questionnaire. The initial 14 questions surveyed population characteristics, such as gender, age, current career status, and working environment. We used these questions to apply inclusion and exclusion criteria. Responses from non-veterinarians and residents or specialists in areas other than anesthesia , or emergency and critical care were excluded from analysis. Furthermore, we excluded partially completed surveys. We then divided the remaining records into four groups based on the qualifications of the individuals completing the survey, namely board-certified specialists (BCS), residents (RES), general practitioners working as emergency veterinarians (GPE), and general practitioners working in non-emergency positions (GPG). BCS and RES included respondents that were board-certified or residents, respectively, in veterinary emergency and critical care or in anesthesia. GPG referred to non-BCS veterinarians working in general practice offering an emergency service during business hours with or without an after-hours on-call service. Non-BCS veterinarians working in an after-hours emergency clinic, a 24 h emergency clinic, or an emergency/critical care center, were designated group GPE. Interns were allocated to either GPG or GPE using the same criteria.Eleven questions contained information relevant for CPR compliance in the areas of preparedness, BLS and ALS. An additional three questions at the end of the survey inquired on respondents' awareness of the 2012 RECOVER consensus guidelines and their opinion regarding the usefulness of the guidelines to improve CPR.2 but not intravascular volume expansion, and access to CPR drugs with a level I, IIa, or IIb recommendation in the RECOVER guidelines ALS compliant when the respondent's answers were in agreement with the RECOVER guidelines. Compliance in preparedness was defined as cognitive aids being displayed and a regularly maintained crash cart being present in the practice, as well as having participated in CPR training within the last 6 months. Respondents who selected the recommended chest compression and ventilation rates , for both dogs and cats were deemed BLS compliant per the RECOVER guidelines. We considered respondents with access to a defibrillator, routinely using ECG and ETCOt-test (for continuous data) or Fisher's exact test were used for comparisons of responses among two groups.We exported survey data from REDCap into a commercial spreadsheet computer programP-values for hypothesis testing. The significance level was set at an alpha value of 0.05.Individual respondent-level variables that were likely to confound the association between compliance in a specific CPR domain and awareness of RECOVER guidelines, were controlled-for using binomial logistic regression. These variables were professional group , gender, age, and region of work. The effect of each variable on compliance was expressed as odds ratios and we used the likelihood-ratio test and associated P = 0.09). The mean age of all respondents was 38 \u00b1 9 years with a significant age difference between BCS and RES (P < 0.0001) (P < 0.0001). Forty-eight percent of RES (95% CI: 37\u201359%), 38% of BCS (95% CI: 32\u201345%), and 34% of GPE (95% CI: 28\u201340%) indicated that they were directly involved in CPR more than 20 times per year, while GPG performed CPR predominantly once or 2\u20135 times per year. There was a significant difference in resuscitation team size between groups. Almost all BCS and RES and the majority of GPE performed CPR in teams of 4 or more, whereas GPG had predominantly 1 or 2 team members or 3 team members available . Residenvailable .Forty-seven percent of all respondents practiced in the USA, 24% in Europe, and 15% in Latin America. The majority of BCS (66%), RES (63%), and GPE (51%) respondents were based in the USA. A high proportion of GPG (41%) practiced in Latin America .P < 0.0001). The latter was most commonly made available in RES' and BCS' institutions, followed by GPE and GPG. Thirteen percent (95% CI: 9\u201319%) of GPG and 3% (95% CI: 2\u20136%) of GPE indicated that they did not have any of the suggested CPR preparation measures in place in their practices. More than half of RES and 48% (95% CI: 41\u201354%) of BCS had participated in CPR training in the 6 months prior to completing the survey compared with 38% (95% CI: 33\u201343%) of GPE and 21% (95% CI: 16\u201328%) of GPG.The vast majority of BCS, RES, and GPE respondents had emergency drug dosing charts displayed and crash carts available in their practices . Among aFrom the above responses, the proportion of those that responded in agreement with all preparedness items was similar in BCS (40% [95% CI: 34\u201347%]) and RES (45% [95% CI: 34\u201357%]), but significantly lower in GPE (23% [95% CI: 19\u201329%]) and further GPG (8% [95% CI: 5\u201312%]) . Non-comP < 0.0001; In dogs, 86% (95% CI: 75\u201392%) of RES, 74% (95% CI: 68\u201380%) of BCS, 55% (95% CI: 49\u201360%) of GPE, and 32% (95% CI: 26\u201339%) of GPG targeted the currently recommended chest compression rate between 100 and 120 cpm. The majority of GPG (58% [95% CI: 51\u201365%]) selected rates < 100 cpm in dogs . CompareP < 0.0001).In both dogs and cats , approximately three quarters of all respondents targeted a ventilation rate commensurate with current CPR guidelines . Of the remaining respondents, a higher percentage selected a ventilation rate that was higher than recommended compared with ventilation rates that were lower than recommended and RES respondents' answers suggested BLS compliance, whereas less than a third of GPE and only 15% (95% CI: 10\u201320%) of GPG responded in adherence to BLS guidelines . The maj2]) were widely available to BCS, RES, and GPE respondents, compared with 63% (95% CI: 56\u201370%) and 35% (95% CI: 29\u201342%) of GPG, respectively. Consequently, more than 95% of all BCS and RES respondents used ECG and capnography routinely, compared to 45% (ECG) and 23% (ETCO2) in GPG in GPG . SimilarP < 0.0001) and a similar pattern emerged regarding sodium bicarbonate. Two thirds of both GPE and GPG indicated that they routinely integrated intravascular volume expansion therapy into their CPR strategy compared with 38% (95% CI: 31\u201344%) of BCS and 45% (95% CI: 34\u201357%) of RES. RECOVER does not recommend the routine use of IV fluids during CPR in euvolemic or hypervolemic dogs or cats , 89% (95% CI: 85\u201393%) of BCS and 96% (95% CI: 88\u201399%) of RES complied with ALS guidelines compared with 43% (95% CI: 38\u201349%) of GPE and 3% (95% CI: 2\u20137%) of GPG. While disagreement with one ALS guideline explained most of the incompliance in BCS and RES, a majority of GPE respondents were incompliant due to at least two recommendations and GPG respondents deviated in several points from the guidelines (Fifty percent of BCS (95% CI: 43\u201357%) and 42% (95% CI: 31\u201354%) of RES complied with ALS guidelines compared with 17% (95% CI: 13\u201322%) of GPE and 1% (95% CI: 0\u20134%) of GPG . Lack ofidelines .n = 542; 93% [95% CI: 91\u201395%]) consulted the RECOVER guidelines, including 100% (95% CI: 97\u2013100%) of BCS, 97% (95% CI: 90\u201399%) of RES, 91% (95% CI: 87\u201394%) of GPE, and 77% (95% CI: 65\u201385%) of GPG.A total of 576 respondents indicated that they had heard of the 2012 RECOVER CPR guidelines, which included all BCS and RES , and 77% (95% CI: 72\u201381%) of GPE but only 35% (95% CI: 28\u201342%) of GPG. Of those that were aware of this resource, most (P = 0.0086) times, being BLS-compliant was 4.5 times, and being ALS-compliant was 7.8 times the odds of a non-aware respondent being compliant in these domains.All professional groups taken together, respondents that expressed awareness of the RECOVER guidelines were significantly more compliant in preparedness , BLS , and ALS compared to those not aware of the guidelines . After adjusting for the effect of respondent age, gender, region of work and professional group the odds of a respondent aware of the RECOVER guidelines being preparedness-compliant was 2.4 may require remediation. This study suggests that for BCS and RES respondents, further investments in the infrastructural environment may not be necessary as almost all had access to crash cart, ECG, capnography and defibrillator, cognitive aids, and resuscitation team sizes of 4 or more.P < 0.01) and an increase, albeit not statistically significant, in survival to discharge from 0 to 9% are associated with an increased risk of failure to achieve ROSC and were also challenged by limitations in resuscitation infrastructure. As for BCS and RES, more frequent training sessions would likely be effective in resolving most knowledge gaps and disagreements with guidelines as well as in improving CPR psychomotor skills, with more frequent training leading to better performance , 33. A R 0 to 9% . Howeveric value \u201337. Simiith ROSC . Regardiith ROSC , 39.Delivering guideline-compliant CPR requires three components: awareness of the guidelines, consultation with them and delivery of CPR according to them. All BCS and RES and 77% of GPE respondents indicated that they had heard of the RECOVER guidelines, however only slightly more than a third of GPG respondents had. Those respondents that had heard of RECOVER were, independent of age, gender, region of practice or professional group, markedly more likely to answer BLS and ALS questions in compliance with the guidelines compared to those that had not. This indicates that awareness of the guidelines may have influenced the self-reported clinical practice in CPR in a positive way. Most of those that were aware of the guidelines did in fact consult this resource. However, despite this awareness and consultation, only half of the respondents in the BCS and RES groups indicated BLS and ALS techniques in compliance with the recommendations. Even-though these findings result from knowledge assessment only, evidence in human medicine suggests that rescuers with higher theoretical knowledge of CPR guidelines are more likely to deliver guideline-compliant CPR , 31. StuThe limitations of this survey-based study require careful consideration. While advantageous in terms of time, cost and workflow efficiency, internet-based surveys are not without disadvantages and this study is no exception \u201345. SeveIn conclusion, awareness of RECOVER guidelines is high in specialists and residents, but incomplete among general practitioners. Awareness of these guidelines positively influenced compliance, but CPR practices continue to be variable and commonly not in agreement with current treatment recommendations. Widely accessible, cost- and time-effective educational and implementation strategies are required to broadly improve knowledge and application of best practices in small animal CPR. Such programs need to take into consideration the different professional environments and infrastructural constraints in which CPR is applied.The datasets generated for this study are available on request to the corresponding author.The survey procedures and questionnaire were reviewed and approved by the Veterinary and Agricultural Sciences Human Ethics Advisory Group of the University of Melbourne as a Minimal Risk Project. The consent was implied when participating to the survey. Project title: Clinical practice of small animal cardiopulmonary resuscitation after publication of standardized guidelines: an internet based survey. Ethics ID: 1546061\u00cdG designed the survey questionnaire, interpreted data, and wrote the manuscript. DF helped design the survey questionnaire and critically revised the manuscript. MS analyzed and interpreted the data and critically revised the manuscript. MB designed the study questionnaire, conducted the survey, analyzed and interpreted data, and critically revised the manuscript. All authors read and approved the final manuscript.MB and DF are co-chairs of the RECOVER initiative that released the RECOVER guidelines. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "The Alabama Department of Public Health (ADPH) conducts an annual community assessment to evaluate household preparedness and local public health concerns. In June 2017, ADPH conducted a Community Assessment for Public Health Emergency Response (CASPER), focusing on indoor air pollutants in seven neighborhoods in Madison County, Alabama, where a large percentage of homes were built before 1980. Local health partners had concerns about indoor air quality and environmental risks such as radon; however, limited information was available regarding community awareness, prevention, and mitigation measures related to potential exposures. Weighted response frequencies were calculated from assessment responses. Among 192 household interview respondents, 78.4% were aware of potential indoor lead exposures, but only 12.6% of respondents living in houses built before 1978 reported that the house had been tested for lead. Similarly, respondents in 70.2% of households had heard of radon; however, only 7.3% of houses had been tested for radon. Smoking was reported by residents of 45.7% of households; among those, 48.4% reported that smoking occurred inside the house. Identified gaps in exposure prevention and mitigation, including low lead and radon testing rates and a high prevalence of indoor smoking, were shared with the local health department, and recommendations for timely interventions and policy guidance were presented. Results of this CASPER demonstrated its usefulness and efficiency in gathering community-level data to help guide public health policies and timely interventions.According to ADPH\u2019s Radon Program, Madison County\u2019s underground geology, which allows radon gas to accumulate and more readily enter houses and other buildings above ground, places it at high risk for elevated radon levels blood lead level (weighted percentage 14.3%) .Respondents in 70.2% of households reported awareness of radon . AlthougAmong other self-reported indoor pollutant exposures, excessive dust was most commonly reported (22.4% of households) . RespondThe most frequently reported respiratory diagnoses among respondents were allergies (45.0%) and asthma (21.5%). Diagnosed chronic obstructive pulmonary disease (COPD) (5.6%), emphysema (4.0%), and lung cancer (2.6%) were also reported. These conditions were reported separately as seen in other respiratory surveys, despite clinical and pathologic overlap. In the preceding 12 months, 58.1% of household respondents reported a resident who experienced allergies .Among Madison County households at risk, interviews identified gaps in respondent knowledge and protective behaviors related to indoor air pollutants. A majority of household respondents reported being aware that lead exposure could exist in older homes; however, respondents in only a small percentage of houses built before 1978, when lead-based paint was banned for residential use, reported that their homes had been tested. Lead-based hazards from paint chips or an accumulation in dust or soil are more common in older homes is a household-level rapid assessment commonly used during disasters and emergency preparedness planning.The CASPER conducted among 192 households in Madison County, Alabama, about selected indoor air pollutants and routine emergency preparedness found the majority of residents were aware of potential indoor lead exposures and had heard of radon, but most had not tested for either. Smoking inside the house occurred among 22% of households.Using the CASPER methodology in nondisaster settings to collect community-specific data can guide targeted intervention and prevention recommendations for local public health departments and their community partners."} +{"text": "Mycobacterium leprae using skin biopsy tissues are essential for leprosy diagnosis and monitoring response to treatment. Although formalin fixation of patient tissues may not be ideal for molecular studies, biopsy samples are the most accessible material from suspected cases. Therefore, clinical molecular laboratories must be able to utilize formalin-fixed, paraffin-embedded (FFPE) material.Detection and pathology analysis of M. leprae-specific repetitive element (RLEP) gene and evaluated the results compared to those using previously established RLEP primers (372 bp).To determine the best molecular method for diagnosing and monitoring leprosy in FFPE specimens, we developed a single-tube nested PCR (STNPCR) (131 bp) and SYBRGreen PCR (101 bp) assay using primers for the FFPE biopsy samples obtained from 145 leprosy patients (during or after multidrug therapy (MDT)) and patients with 29 other confounding dermatoses were examined by the bacteria index (BI) and by simple PCR, STNPCR, and SYBRGreen PCR using primers amplifying a 372-bp, 131-bp or 101-bp fragment of RLEP, respectively.In leprosy patients receiving MDT, STNPCR showed a highest specificity of 100% and a positive predictive value (PPV) of 100%. For multibacillary (MB), paucibacillary (PB) and all leprosy patients, the highest sensitivities were 91.42%, 39.13%, and 67.92%, negative predictive values (NPVs) were 8.57%, 60.36%, and 32.07%, and the highest accuracies were 93.93%, 62.67%, and 74.81%, respectively, higher than the results of SYBRGreen PCR and simple PCR. For post-MDT leprosy patients, SYBRGreen PCR showed the highest sensitivity of 50.0%, highest specificity of 100%, a PPV of 100%, an NPV of 100% and the highest accuracy of 83.72% for MB patients, which were higher than those of STNPCR and simple PCR. STNPCR showed the highest sensitivity of 26.66% and 34.48%, highest specificity of 100% and 100%, a PPV of 100% and 100%, NPV of 72.50% and 60.21%, and highest accuracy of 75.00% and 67.24% for PB and leprosy patients, respectively, higher than those of SYBRGreen PCR and simple PCR.These findings suggest that STNPCR or SYBRGreen PCR for RLEP using FFPE specimens performs better as a diagnostic test and for monitoring response to MDT than does simple PCR based on 372-bp fragment amplification. Additionally, STNPCR showed increased sensitivity for PB diagnosis using FFPE specimens, which can be transferred remotely or retrieved from previous leprosy patients. Mycobacterium leprae. Despite being curable, leprosy is still a notorious disease, causing serious disability and a stigma generally associated with late diagnosis. The disease is challenging to diagnose because there is no gold standard method for detecting M. leprae or its cellular components . In past decades, different PCR methods were developed to amplify different M. leprae gene targets, such as the RLEP gene, with high sensitivity in leprosy diagnosis using skin biopsy and slit skin smear (SSS) specimens. However, few reports have focused on FFPE specimens. Because FFPE specimens can be transferred remotely or retrieved from previous leprosy patients, we developed and evaluated the STNPCR assay for detecting M. leprae in these specimens. Our results suggest that STNPCR of RLEP using FFPE specimens performs better as a diagnostic test and for monitoring response to MDT than does simple PCR.Leprosy is one of the oldest diseases known to humankind and is caused by Mycobacterium leprae. Recently, due to scientific advances, knowledge has increased about the pathogenesis, prognosis and treatment of this stigmatized disease. Despite being curable, leprosy is still a notorious disease, causing serious disability and a stigma generally associated with late diagnosis. The implementation of World Health Organization (WHO) multidrug therapy (MDT) has drastically reduced the number of registered leprosy cases from approximately 12 million reported in 1985 to 211,973 new cases globally in 2015 /total specimens.Data were entered into VassarStats: Website for Statistical Computation , STNPCR (131 bp) and SYBRGreen PCR (101 bp) was the same, at 13 fg DNA.M. lepraemurium was used as the template. Conversely, no primer sets amplified any region when DNA from other species of Mycobacterium or non-mycobacterial species was used as the template and 29 controls from the same endemic region were included. The basic information for each study group is summarized in Of the 174 specimens included in the present study, 145 patients were diagnosed as having leprosy based on clinical signs and symptoms, skin smears, skin biopsy, and neurophysiologic examinations according to the leprosy diagnosis criteria of China. Other confounding dermatoses were diagnosed based on 29 specimens. Of the 145 leprosy patients, 116 cases were before MDT and 29 after MDT . Using these criteria, the sensitivity, specificity, PPV, NPV, LRs and accuracy of the individual methods were calculated.The sensitivities of the BI, simple PCR, STNPCR, and SYBRGreen PCR were 60.34%, 42.24%, 67.92%, and 60.34% for leprosy patients, respectively . All of For MB patients before MDT, STNPCR showed the highest sensitivity of 91.42%, the highest specificity of 100%, a PPV of 100%, an NPV of 82.85%, and the highest accuracy of 93.93%, which were higher than those for simple PCR but lower than those for BI.For PB patients before MDT, STNPCR showed the highest sensitivity of 39.13%, the highest specificity of 100%, a PPV of 100%, an NPV of 50.87%, and the highest accuracy of 62.67%, which were higher than those of SYBRGreen PCR, simple PCR, and BI.Twenty-nine leprosy patients in this study were under MDT at the CDC and had finished MDT when enrolled in the study. The BI, simple PCR, STNPCR, and SYBRGreen PCR assays using RLEP primers were performed with specimens obtained from these patients after MDT to determine the presence of target DNA to monitor the response to MDT. There were 22 patient specimens in which the BI was zero, whereas the remaining 76 patient specimens had a positive BI. Among the 22 patient specimens (BI = 0), RLEP PCR revealed 3, 6, and 5 positive amplifications of patient specimens by simple PCR, STNPCR, and SYBRGreen PCR, respectively. Among the 6 patient specimens (BI = positive), RLEP PCR resulted in 2, 4, and 5 positive amplifications of patient specimens by simple PCR, STNPCR, and SYBRGreen PCR, respectively .Compared with STNPCR and simple PCR, SYBRGreen PCR exhibited the highest sensitivities of 50.00% for MB and 34.48% for leprosy patients and the highest accuracies of 83.72% for MB and 67.24% for leprosy patients. However, for PB patients, STNPCR showed the highest sensitivity (26.88%) and the highest accuracy (75.00%) compared with SYBRGreen PCR and simple PCR. .Early diagnosis of the disease, followed by prompt treatment with MDT, is the basis of current leprosy control strategies . To prevM. leprae and to evaluate the diagnostic performance and monitor the developed STNPCR and SYBRGreen PCR assays using primers specific for the RLEP gene in FFPE specimens.More than 100 counties, mainly in southwestern China, report incidence rates of leprosy >1/100,000 . FFPE, wM. leprae is very difficult, and traditional laboratory techniques, such as the BI, are far from sensitive and specific. In the absence of a true gold standard, PCR methods, such as quantitative PCR (qPCR), multiplex PCR, and droplet digital PCR assays, have been developed to aid the diagnosis of leprosy worldwide . However, STNPCR with the primer set amplifying the 101-bp fragment used in the present study for FFPE samples showed reasonable accuracy, whereas simple PCR methods for FFPE and BI for skin slit smear were less accurate . RLEP STNPCR was the most accurate assay compared to simple PCR and BI for PB and leprosy diagnoses.For monitoring response to MDT, the SYBRGreen PCR with the 101-bp fragment primer set used in the present study for FFPE showed reasonable accuracy, but the simple PCR methods for FFPE were less accurate . The RLEP SYBRGreen PCR was the most accurate assay for monitoring MDT response compared to the other methods for MB, whereas STNPCR had the greatest accuracy for monitoring MDT response in PB and leprosy patients after treatment. Both STNPCR and SYBRGreen PCR (101-bp fragment) showed better accuracy than simple PCR (372-bp fragment) in leprosy diagnosis and in MDT monitoring.M. leprae by conventional nested PCR using RLEP (101-bp fragment) as the target. To obtain a PCR method that is just as efficient but without the risk of contamination, we optimized STNPCR. In the case of STNPCR and SYBRGreen PCR, the internal primers (101 bp) were developed within the published primer (372 bp) region of M. leprae RLEP. We also used UNG in STNPCR, and the UNG-treated loop-mediated isothermal amplification (LAMP) assay can prevent unwanted amplification by carryover contamination of the previously amplified DNA [Conventional nested PCR is a very sensitive and specific method for the diagnosis of pathogens. However, this type of PCR is notorious for contamination problems related to the processing of the product between the first and second PCR steps . In the fied DNA . The STNThe sensitivity of RLEP PCR is reported to be 57%-80% for the diagnosis of leprosy. When evaluated using clinical specimens, AFB positivity in skin biopsy was 44% (range 10\u201385), whereas PCR positivity in skin biopsy was 70% (range 46\u201393) . When coM. leprae diagnostic studies, PCR assays using two primer sets for M. leprae RLEP were carried out to monitor the response to anti-M. leprae MDT. Therefore, FFPE specimens were collected from leprosy patients after MDT, from both BI-positive and BI-negative patients given MDT. The most common methods for monitoring the response to MDT are a progressive reduction in the number of AFBs in skin slit smears and histological examination of skin lesion biopsies. The present method using RLEP PCR can be employed to semi-quantitate M. leprae DNA to assess a patient\u2019s response to MDT.In addition to the M. leprae RLEP for the diagnosis of PB leprosy patients from a hyperendemic area of China [Our study has limitations. We tested our quantitative PCR assay for of China ,28. MoreM. leprae DNA in FFPE specimens. Moreover, we used UNG in the STNPCR assay to reduce the number of steps and prevent contamination when compared with conventional nested PCR. The detection limitation for the purified M. leprae DNA was 13 fg using simple PCR, STNPCR and SYBRGreen PCR. We also assessed the specificity of the system against other Mycobacterium and non-Mycobacterium species. Within the context of clinical evolution, amplification of the 131-bp and 101-bp fragments of RLEP in FFEP specimens from leprosy patients performs better as a diagnostic test and for monitoring response to MDT than simple PCR based on amplification of the 372-bp fragment. Despite being regarded as suboptimal material for molecular diagnosis, given their use in routine tests for suspected leprosy and their ability to be transferred remotely or retrieved from previous patients, FFPE specimens are still essential material for M. leprae identification.In conclusion, we developed an assay to amplify 131-bp and 101-bp fragments within the published 372-bp fragment of RLEP to identify"} +{"text": "Recently patients need faster treatments, and delaying restoration is not possible following bleaching treatment. The purpose of this study was to determine the effect of antioxidants, namely 10% sodium ascorbate, 10% alpha-tocopherol, 10% green tea and 10% Aloe vera extract on the shear bond strength of composite resin to enamel following extra-coronal bleaching using 40% hydrogen peroxide.Seventy premolars were randomly assigned into 7 groups of 10 each. Group 1: bleaching treatment and no antioxidants application. Group 2: composite was built-up immediately after bleaching. Group 3: bleached specimens received composite build-up delayed by 2 weeks. Group 4, 5, 6 and 7: bleached specimens received an application of 10% sodium ascorbate, 10% alpha-tocopherol, 10% green tea, and 10% Aloe vera before composite build-up. Specimens were immersed in artificial saliva, stored in an incubator 37\u00b0C (24 hours), thermocycling, and tested using a universal testing machine. Data were analyzed by one-way ANOVA and Tukey\u2019s test with 95% level of significance.p<0.05), and application of 10% sodium ascorbate, 10% alpha-tocopherol, 10% green tea and 10% Aloe vera produced significantly greater shear bond strength compared to bleached group (P <0.05). However, no significant differences occurred between antioxidant groups (P >0.05).Bleaching caused significantly reduced shear bond strength (Application of antioxidants increased the shear bond strength of composite resin to enamel following extra-coronal bleaching using 40% hydrogen peroxide. 10% sodium ascorbate, 10% alpha-tocopherol, 10% green tea and 10% Aloe vera extracts produced the same effect on the shear bond strength of composite resin to enamel following extra-coronal bleaching using 40% hydrogen peroxide. Key words:Antioxidants, shear bond strength, composite resin, extra-coronal bleaching. Increasing interest in esthetic dentistry has resulted in the widespread practice of extra-coronal bleaching or vital bleaching. Extra-coronal bleaching is considered a safe, popular, conservative and well-accepted treatment modality for discolored teeth . BleachiHowever, numerous studies have shown that bleaching can cause complications that may vary from postoperative sensitivity to pulpal irritation, tooth structure alterations or microleakage of existing restorations -7. AnothSome techniques have been suggested to solve the clinical problems related to post bleaching compromised bond strength, such as treated bleached enamel with alcohol before restoration, removal of the superficial layer of enamel, and the use of adhesives containing organic solvents ,9. HowevSodium ascorbate is a neutral, nontoxic, and biocompatible antioxidant that when used as a 10% solution and application time of 10 min can reverse the reduced bond strength of bleached enamel . Alpha-tRecently other natural products are used for antioxidant agents such as green tea and Aloe vera extracts, which have free radical scavenging ability that are more potent than sodium ascorbate and alpha-tocopherol . The greIt has been postulated that the polysaccharides in Aloe vera gel have therapeutic properties such as immune-stimulation, anti-inflammatory effects, wound healing and anti-oxidant effects . Since AHowever, no studies have been conducted to compare the effects of sodium ascorbate and alpha-tocopherol to green tea and Aloe vera extracts on the bond strength of bleached enamel. Hence, the aim of this in vitro study was to evaluate and compare the effects of 10% sodium ascorbate, 10% alpha-tocopherol, 10% green tea and 10% Aloe vera extracts on the bond strength of enamel following extra-coronal bleaching using 40% hydrogen peroxide. The following null hypotheses were tested in this study: there would be no effect of 10% sodium ascorbate, 10% alpha-tocopherol, 10% green tea, and 10% Aloe vera extracts on the shear bond strength of composite resin restoration to enamel following extra-coronal bleaching.This study was approved by Faculty of Dentistry Universitas Gadjah Mada Research Ethics Committee. Seventy extracted human premolars were collected, and stored in a distilled water following extraction. All teeth used in this study were extracted in the course of 1 months. The roots were sectioned approximately 2 mm apically of cemento-enamel junction (CEJ) using microtome . Each crown of teeth then was cut in mesial distal direction, and the buccal side of crowns were used in this study. Buccal side of crowns were embedded in an acrylic resin block, keeping only the buccal portion exposed, and were flattened with 600 grit silicon carbide paper to obtain flat and rough enamel surfaces. All specimens were observed under light microscope to verify enamel exposure rather than dentin occurred.All specimens were assigned randomly into 7 groups of 10 each. Group 1 (served as control), no bleaching treatment and no antioxidant application, specimens were immersed in artificial saliva for 2 weeks. Group 2, specimens were bleached using 40% hydrogen peroxide as manufacturer\u2019s direction. After bleaching, composite resin restorations were performed immediately. Specimens were acid etched with 37% phosphoric acid for 20 seconds, rinsed for 30 seconds and air dried for 10 seconds. A thin layer of adhesive material was applied on the etched enamel, gently spread with compressed air and light-cured for 10 seconds. The embedded specimens were mounted in an apparatus containing a split metal mold with a circular hole 3 mm in diameter and 4 mm in height. Two increments of a composite resin were inserted into the hole of the split mold and each increment was light cured for 20 seconds. Therefore, composite resin restoration attached to the buccal portion of crown. The specimens were stored in an artificial saliva for 24 hours in 37\u00baC incubator.Group 3, specimens were bleached as group 2, then were immersed in the artificial saliva for 2 weeks. After immersion, specimens were restored using composite resin as group 2. Group 4, specimens were bleached as in group 2, specimens were applied 10% sodium ascorbate as an antioxidant. Group 5, specimens were bleached as group 2, then were applied 10% alpha-tocopherol . To attain 10% sodium ascorbate, 10 g cristal of sodium ascorbate was dissolved in distilled water, and 10 g alpha-tocopherol was diluted in ethyl ethanol to make 10% solutions. Group 6, specimens were bleached as group 2, then were applied 10% green tea leaf extract . Group 7, specimens were bleached as group 2, then were applied 10% Aloe vera extract . Green tea leaf extracts were prepared by maceration method with ethanol solvent and were dilutes using distilled water to obtain 10% concentration . Same meEach specimen was loaded in universal testing machine for shear bond strength testing . The long axis of the specimen was perpendicular to the direction of the applied forces. The knife edge was loaded at the interface between the composite and enamel surface Fig. . The shep<0.05). Results revealed (p<0.05). In contrast, group 1 (control), which was unbleached, produced the highest shear bond strength compare to other groups, but this value of shear bond strength was almost similar to group 3, which was bleached and had a waiting period for 2 weeks before composite resin restoration . Among antioxidants groups, 10% alpha-tocopherol revealed the highest shear bond strength compare to other antioxidants groups, however the differences were not significant (P>0.05), whereas 10% Aloe vera extract produced the lowest shear bond strength compared to other antioxidant groups (P>0.05).One-way ANOVA showed significant differences in shear bond strength among the groups . This condition is probably caused by lower molecular weight in sodium ascorbate and alpha-tocopherol, although in this study molecular weight was not measured of each antioxidant agent. Consequently, the lower molecular weight of sodium ascorbate and alpha-tocopherol cause these antioxidants to penetrate deeply into enamel than green tea and Aloe vera extracts (The results of this present study showed that sodium ascorbate and alpha-tocopherol produced non-significant greater shear bond strength than green tea and Aloe vera extracts (extracts .Within the limitation of this study, it can be concluded that application of antioxidants increased the shear bond strength of composite resin to enamel following extra-coronal bleaching using 40% hydrogen peroxide. 10% sodium ascorbate, 10% alpha-tocopherol, 10% green tea and 10% Aloe vera extracts produced the same effect on the shear bond strength of composite resin to enamel following extra-coronal bleaching using 40% hydrogen peroxide."} +{"text": "The effect of adiposity on hypertension among Uyghur Chinese is not clear. This study aimed to compare the effect of BMI and its optimal cut-off value in identifying hypertension in Uyghur and Han adults in China. By using a multistage stratified sampling method, 3072 Uyghur and 3195 Han adults underwent questionnaire interview, physical examination, and biochemical tests. Age- and sex-standardized prevalence of hypertension was calculated. Adjusted odds ratios for adiposity associated with hypertension were estimated. ROC analyses were used for assessing the ethnic and sex specific optimal BMI cut-off values in identifying hypertension.2 and 24.9 kg/m2 , respectively, but the correspond values in Uyghur and Han females were 27.2 kg/m2 and 25.0 kg/m2. Both in Uyghur and Han, increased BMI was consistent with the elevated systolic and diastolic blood pressure. Although more Uyghur were overweight/obese, their standardized prevalence of hypertension (17.87%) was lower than that of Han (20.28%). Han adults had 1.42 times odds than Uyghur of hypertension. The adjusted ORs of overweight and obesity were 2.67 and 6.04 in Uyghur and 2.74 and 7.58 in Han. In male, the optimal cut-off values of BMI identifying hypertension in Uyghur and Han were 24.6 kg/m Adiposity had strong effect on hypertension, but this effect was less strong in Uyghur female than in Han female. World widely, hypertension is a major public health problem and is considered the greatest attributable risk factors for death . AlthougEthnic disparities in obesity could result in concurrent differential prevalence of obesity-related diseases including hypertension , and thiTherefore, in this cross-sectional study, we used data from the China National Health Survey (CNHS) to investigate the role of body mass index (BMI) as risk factor of hypertension in Uyghur and Han adults in China. We hypothesize that different genetic background, socioeconomic status, and life style between Uyghur and Han could probably lead to disparities in hypertension prevalence as well as modify the effect of adiposity as risk factor of hypertension.Details of the CNHS study design and methods have been described previously , 16. The2). For each participant, systolic blood pressure (SBP) and diastolic blood pressure (DBP) were measured three times after at least five minutes rest in a seated position, using a digital sphygmomanometer . A 9-ml fasting blood sample with at least 8 hours fasting overnight was collected. Fasting plasma glucose , serum-lipid including triglyceride , total cholesterol , high-density lipoprotein cholesterol , and low-density lipoprotein cholesterol were tested in the General Hospital of Chinese People's Liberation Army. Ethic approval was obtained from the Bioethical Committee of Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences. All participants provided written informed consent before the questionnaire interview.A comprehensive questionnaire including information on demographic and socioeconomic characteristics, personal and family medical history, and life style risk factors was administered by trained interviewers. Anthropometric measurements including height, weight, and body composition were taken using calibrated instruments with standard protocols, with participants wearing light clothing and bared feet. Weight and body composition were measured using a body composition analyzer . Standing height was obtained to decimal level precision by a stadiometer. Body mass index was calculated as weight in kilograms divided by the square of height in meters (kg/m2), overweight (25 kg/m2 \u2264BMI <30 kg/m2), and obesity (BMI \u226530 kg/m2). Hypertension was defined as individual who was measured with an average SBP \u2265 140mmHg and/or an average DBP \u2265 90mmHg, or self-reported hypertension history [Excess adiposity was measured by BMI that was separated into three categories based on World Health Organization (WHO) classification : under/n history , 18. The history , diabete history , 15.In this study, we restricted analytic sample to participants with complete information on major risk factors . This analysis included 2928 Uyghur and 3097 Han adults. 242 participants were excluded because of missing value on major risk factors.Summary results are presented as mean for continuous data and number for categorical data. Since underweight subjects accounted only for 3.52% and 3.10% in Uyghur and Han, they were integrated into one category into analysis.Scatter plots were drawn to identify the linear relationship between covariates and blood pressure. General linear regression models (GLMs) were used to perform two-way analysis of covariates (ANCOVA). For the comparison of hypertension prevalence, age- and sex-standardized prevalence was calculated by using the population census data of China in 2010. Multivariable logistic regression models were used to examine the association between excess adiposity and hypertension. Ethnic and sex specific receiver operating characteristic (ROC) curves were applied to evaluate the overall performance of BMI cut-off values in detecting excess risk for Uyghur and Han adults. The areas under the ROC curve (AUC) were calculated by logistic regression model and were used as a measure of accuracy of BMI in screening the presence of hypertension risk factors. The Youden index was calculated (sensitivity + specificity -1), and the maximum of it was considered as the optimal cut-off value for BMI.We further did several sensitivity analyses to ascertain the effects of BMI on hypertension among participants (1) who were newly diagnosed with hypertension in the survey; (2) who were not diagnosed with diabetes to avoid the possible influence on BMI by lifestyle change. We also perform the analysis using body fat percentage as a replacement of BMI to compare indexes of body composition on the association with hypertension.Statistical analysis was performed using SAS 9.4 .2928 Uyghur and 3097 Han adults aged 20-80 years were included for analysis. Both in Uyghur and Han, female participants accounted more in proportion than male, with 64.9% in Uyghur and 59.5% in Han, respectively. Uyghur and Han had significant difference in educational attainment, residential areas, cigarette smoking, alcohol drinking, and physical activity (P<0.001). In the Uyghur participants, male had higher proportion on older age, higher educational attainment, urban resident, overweight/obesity, ever-smoking, alcohol consumption, moderate or active physical activity, and hypertension. This sex difference was also seen in Han group except for residential areas (P=0.355). The demographic and clinical characteristics across categories of ethnicity and sex appeared in In Uyghur male, the mean of SBP increased from 118.30 mmHg in the under/normal weight group to 131.81 mmHg in the obesity group (P<0.001). Likewise, DBP increased from 69.97 mmHg in the under/normal weight group to 81.13 mmHg in the obesity group (P<0.001). The same trend of increasing SBP and DBP with elevated BMI categories was also observed in Uyghur female and Han male and female and DBP (P<0.001) level than Uyghur. But after the stratified analysis by sex, no statistical difference on SBP was found, but there was still higher DBP level in Han than in Uyghur (P<0.001) in both sexes.The age- and sex-standardized hypertension prevalence was 17.87% (95% CI: 16.26% to 19.48%) in Uyghur, and 20.28% (95% CI: 18.72% to 21.84%) in Han. The age-standardized prevalence in male and female was 18.59% (95% CI: 16.09% to 21.10%) and 17.13% (95% CI: 15.13% to 19.13%) for Uyghur and 23.17% (95% CI: 20.60% to 25.74%) and 17.25% (95% CI: 15.50% to 19.01%) for Han. Hypertension prevalence stratified by ethnicity and sex and age was illustrated in In the total population, overweight individuals had 2.70 times odds of hypertension compared with under/normal weight. For obese subjects, the OR was 6.62 . Han aduAUCs of BMI identifying hypertension were summarized in 2 and 24.9 kg/m2, respectively, but the correspond values in Uyghur and Han female were 27.2 kg/m2 and 25.0 kg/m2.In male, the optimal cut-off values of adiposity identifying hypertension in Uyghur and Han were 24.6 kg/mThis is the first population-based study that investigates the effect adiposity on hypertension in Uyghur. It sheds insights into a possible role of excess adiposity on blood pressure elevation among Uyghur Chinese, as well as the varied effect between different ethnic groups.In both Uyghur and Han adults, the odds ratios of hypertension appeared stronger among individuals with higher adiposity. The sensitivity analysis, where BMI was replaced by body fat percentage, provided consistent result with present findings. Previous studies have observed ethnic disparities between Uyghur and other ethnic groups in chronic diseases prevalence, such as type 2 diabetes , 12, 20,Uyghur had generally high BMIs, which might be attributable to multiple factors, including lifestyle factors and economic developments. However, interestingly, in our study, Uyghur adults had lower hypertension prevalence than Han. It suggested that the impact of excess adiposity on blood pressure may be less strong in Uyghur than in Han adults. Like populations of Central Eurasia, Uyghur Chinese are genetically related to both Caucasian and East Asian populations , 23. On Although heritability of BMI remained high over all age groups, the importance of environmental determinants for BMI increased with aging . TherefoThe adjusted means of DBP in Han were found higher than Uyghur adults. This difference was possibly attributable to genetic heterogeneity between Uyghur and Han. Since DBP was considered more strongly predicting cardiovascular disease risk in younger adulthood , hyperteAs AUCs of 0.6-0.7 are considered poor and 0.7-0.8 are fair , BMI perThis study adds evidence to previous observations indicating that excess adiposity has ethnic disparity in influencing hypertension. It implied that controlling body mass index to a normal range could have considerable potential for prevention of hypertension, which would lead to a broad public health implication. This study has several strengths. Firstly, by using a multistage stratified clustering sampling method, we selected representative samples of study population. Secondly, the strict quality control standards being implemented all through the survey guaranteed the data validity and reliability.Limitations of this study should also be acknowledged: first, participants who were diagnosed with hypertension or other chronic diseases before the survey may have some lifestyle changes, thus leading to a biased estimation of the effect. Nonetheless, in the sensitivity analysis where individuals who had been diagnosed with hypertension before the survey were excluded, the ORs for BMI of hypertension enlarged. Likewise, among participants without diabetes, the ORs remain stable. Therefore, our study provides a conservative estimation of adiposity on hypertension. Second, central obesity was not measured, thus comparisons of associations among different body composition indices with hypertension were not available. But compared with BMI, WC were not found more strongly associated with prevalence of hypertension . In this"} +{"text": "The Global Adult Tobacco Survey (GATS) is a global study to monitor tobacco use, and evaluate current measures and requisite policies on tobacco control. In this study, the key indicators from GATS Kazakhstan that address six tobacco control policies are assessed.GATS Kazakhstan was a nationally representative household survey of the adult population aged 15 yr or older implemented in 2014, in all regions of Kazakhstan. A multi-stage, geographically clustered sample design was used to obtain the key indicators of tobacco use and tobacco measures in the country. The sampling weights were employed to ensure real national representation. A household and individual questionnaire were administered through electronic devices.The majority of current tobacco users were cigarette smokers 22.2%. Overall, 19.0% of adults were exposed to secondhand smoke while at work. One third of smokers made a quit attempt in the last 12 months. Only, 74.0% of adults believed that breathing other people\u2019s smoke causes serious illness in non-smokers. Almost all current smokers (97.6%) noticed pictorial health warnings on cigarette packages. Over half (58.0%) of the current smokers had thought about quitting, having seen pictorial warning labels. Exposure to any cigarette advertisement, sponsorship or promotion had been experienced by 25.7% of adults, with the highest rate of noticing cigarette advertisements being found in stores where cigarettes are sold (14.0%). Cigarettes were largely affordable for the population.The GATS Kazakhstan results identified tobacco use indicators, as well as existing gaps in tobacco control measures. Tobacco use is the greatest cause of preventable death globally and causes 6 million deaths annually worldwide ,2. The aM-monitoring tobacco use and prevention policies; P-protecting people from tobacco smoke; O-offering help in quitting tobacco use; W-Warning about the dangers of tobacco; E-enforcement of tobacco advertising, promotion, and sponsorship bans; and R-raising taxes on tobacco products and SAS version 9.3 to obtain prevalence rates as percentages with a 95% confidence interval (CI). Standard errors were calculated using Taylor series linearization. Tests of statistical differences were performed by comparing the 95% CIs of the two estimates.Overall and gender-specific current tobacco use, current cigarette smoking, current smokeless tobacco use.Exposure to tobacco smoke at indoor workplaces and in other public spaces in the last 30 d.Tobacco cessation: attempts to quit smoking in the past 12 months, health care professionals advising to quit smoking during medical consultation in the past 12 months; interest in quitting smoking.Awareness about the dangers of tobacco: adults noticed anti-cigarette smoking information; noticed health warning labels and pictorial labels on cigarette packaging; thoughts of quitting due to health warning labels and pictorial labels on cigarette packaging; beliefs about the dangers of smoking and exposure to secondhand smoke.Noticed cigarette marketing during the last 30 d in various places.Economic indicators showing cigarette affordability: average amount spent on 20 manufactured cigarettes; average cigarette expenditure per month; Cost of 2,000 manufactured cigarettes as a percentage of per capita Gross Domestic Product (GDP).The GATS indicators that correspond to implementation of tobacco control measures are presented in the article. There are six groups of indicators :OverallOf 4611 households in the final sample, 4,451 participated in the survey and 4,425 individuals completed the individual interview. Therefore, the household response rate was 97.2%, the individual response rate was 99.4% and the overall response rate was 96.7%. By gender, there were 47.2% males and 52.8% females, by place of residence- 56.6% urban and 43.4% rural population, by education- 6.0% had primary, 24.0% -secondary education, 30.6%-secondary vocational and 39.3% higher education (the weighted data).Overall, the current tobacco use prevalence among adults was 22.9%. The majority of current tobacco users were cigarette smokers (22.2%), which represents 2,794,500 people. Cigarette smoking prevalence was far greater among males (42.2%) than females (4.2%). The current smokeless tobacco use rate was low, at 1.3% .The overall prevalence rate of secondhand smoke exposure in indoor workplaces was 19.0% in the last 30 d. The percentage of adults who visited various public places in the last 30 d and were exposed to tobacco smoke was the highest in restaurants , followed by public transportation , government buildings or offices , and health care facilities .Those Kazakhstan current smokers and former smokers abstained for less than 12 months, and visited health care providers, were asked in GATS if their health care provider had asked them about their smoking status and if the health care provider had advised them to quit. The majority (59.0%) of smokers were asked by their health care professional about smoking during a consultation in the past 12 months about smoking, and 46.6% were advised to quit smoking.In terms of cessation method used, amongst current smokers and former smokers abstained for less than 12 months, 76.5% had attempted to quit without assistance, 10.2% used counseling and advise, and 23.4% used pharmacotherapy. More than half of the current smokers (63.9%) were interested in quitting smoking.According to the GATS Kazakhstan 2014 data, 84.9% of all adults believed that tobacco smoking causes serious illness . Overall, 74.0% of adults believed that breathing other people\u2019s smoke causes serious illness in non-smokers. For current smokers, 73.0% believed that tobacco smoking causes serious illness, and only 57.3% were aware of health risks of secondhand smoke.Anti-cigarette smoking information at any location in the last 30 d was noticed by 49.5% of adults . The three major channels of antismoking information were television (with 34.6% adults noticing messages on this medium), newspapers or magazines (29.9%) and billboards (20.7%).Nearly all of the current smokers (97.6%) noticed pictorial health warnings on cigarette packaging. A majority (58.0%) of current smokers thought about quitting because of pictorial warning labels that they had encountered.According to the GATS results, 25.7% of adults in Kazakhstan were exposed to any cigarette advertisement, sponsorship or promotion . Among various places that advertisements could be, the highest rate of noticed cigarette advertisements in the last 30 d was found to be in stores where cigarettes are sold, at an overall rate of 14.0%.The average manufactured cigarette expenditure per month 23.30 USD overall, with significant difference seen in expenditure between males (24.30 USD) and females (14.30 USD). The average price paid for a pack of 20 manufactured cigarettes was 1.22 USD. The cost of 100 packs as a percentage of per capita GDP for 2014 was 1.0%.Implementation of tobacco surveys is essential for countries to track and support tobacco control measures and policies. Monitoring programs have to include indicators of different forms of tobacco use, the impact of policy interventions, as well as tobacco industry marketing practices. Article 20 of FCTC calls for surveillance of tobacco consumption indicators and the need for comparable data.In Kazakhstan, the monitoring of tobacco use has been conducted through periodic national health behavior surveys. 26.5% of adults smoked cigarettes . HoweverSecondhand smoke is responsible for over 600,000 deaths annually ,11. The The Republic of Kazakhstan has banned smoking in indoor workplaces, government buildings or offices, health care and education facilities, public transportation, and other public places. However, designated smoking areas are allowed in public catering places, at airports, rail, road and water stations, on trains, and on ships for sea and river transport. The Code of Administrative Violations includes fines and penalties for violation of the smoking ban.Overall, 33.0% of adults who visited various public places in the past 30 d were exposed to tobacco smoke. Overall, 19.0% of adults who worked indoors were exposed to tobacco smoke, and among non-smokers, the rate was 13.4% . Therefore, despite the ban on smoking in public places, adults were still exposed to tobacco smoke at work and in public places. It was due to limitations of partial smoke-free laws showing a need for existing law enforcement.People who quit smoking significantly reduced their risk of disease and premature death ,5. ArticIn Kazakhstan, chronic non-communicable disease screening procedures for the target population require practitioners to obtain information about the smoking status of a patient. Anti-tobacco resources are available in public primary health care settings. Cost-covered nicotine-replacement therapy and national tobacco quit line are not generally available. Almost a third (29.5%) of smokers had attempted to quit tobacco in the past 12 months. Along with improvements in asking patients whether they smoke or not, and providing cessation advice, improvements need to be made to increase the awareness of health care providers in terms of smoking cessation counseling and other quit-support services.Article 11 of WHO FCTC states that the adoption and implementation of effective measures should include the placement of warning labels on cigarette packages. The Guidelines for the Implementation of Article 11 of the WHO Framework Convention on Tobacco Control supports the fact that combined written and graphic health messages on the packaging of tobacco products are more likely to attract the public\u2019s attention and raise awareness on the health effects of tobacco than text warnings alone .According to Article 12 of FCTC, every party has an obligation to support and promote public awareness on tobacco control issues, health effects of tobacco use and exposure to tobacco smoke, and the health benefits of quitting tobacco use. Active and continuous anti-tobacco campaigns increase people\u2019s awareness about the harms of tobacco use, prompting the reduction in tobacco use and exposure to tobacco smoke, and increases the rates of smokers who quit . KnowledArticle 13 of FCTC calls for a complete ban on tobacco advertising, promotion, and sponsorship. The total ban for any kind of tobacco marketing can reduce tobacco consumption and protect the youth from smoking initiation ,12.Kazakhstan has a general ban on tobacco and tobacco products advertising, which extends to sponsorship and promotion too. Despite the ban, GATS showed that respondents (25.7%) had been exposed to some type of cigarette advertisement, sponsorship, or promotion. Stores, where cigarettes were sold, were a key site of cigarette marketing.Article 6 of the FCTC addresses the importance of price policy for and tax on tobacco products. An increase in cigarette tax reduces the rates of adults and youths who smoke. A 10% increase in the real price of cigarettes may cause a 3 to 5% drop in cigarette consumption in high-income countries, and an 8% reduction in low-and-middle-income countries ,13,14.Kazakhstan applies a specific excise tax. Differential rates apply (operating in a tier system) for filter and non-filter cigarettes. In 2014, the excise tax on manufactured cigarettes increased by 93.5% of the products, and since then, the annual increase in the excise tax has been 30%, up until 2016. Nevertheless, according to the results of GATS Kazakhstan 2014, cigarettes remain largely affordable for the population.The key survey limitation is related to self-reported responses of the respondents with probability of under- or over-estimation of their behavioral status or knowledge of tobacco-related situation.The first GATS Kazakhstan results provide valid and comparable data on adult tobacco use, which was previously absent for our middle-income country. People remain exposed to secondhand smoke at work and in public places, despite the existence of a law that partially prohibits smoking in certain public spaces. The recently introduced graphical warnings on cigarette packs have been noticed by nearly all smokers, and are effective in making smokers think about quitting. However, cigarettes are still widely available, and the population, especially at the point of sale, notices various forms of tobacco marketing. The results demonstrate new opportunities for research findings to transition into policy actions in Kazakhstan.Ethical issues have been completely observed by the authors."} +{"text": "The Duke Geriatric Workforce Enhancement Program aims to improve linkages between primary care practices (PCP\u2019s) and community-based organizations by developing an interdisciplinary, community-based team to consult with PCPs, identifying resources to help vulnerable older adults. The Inter-agency Care Team (ICT) includes a nurse practitioner, pharmacists, community resource specialists, geriatricians and geriatrics and advanced practice nursing fellows. PCP\u2019s refer older adults with complex care needs through the EHR for virtual consultation by the ICT. Team members review medical records and call participants and caregivers to obtain permission for the consult, gather information on function, social factors, medical problems, and their perceived needs. The ICT meets to review each case and sends written recommendations to the PCP and patient. To date, the ICT performed consultations for 73 older adults with a mean age of 76 years. 69% were female. 71% were black and 26% white. Frequently identified needs included personal/home safety (74%), medication management (64.3%), food security (63.0%), cognition (49.3%), transportation (38.4%) and advance care planning (31.5%). In the 90 days before consultation, 32.9% of patients had ED visits and 21.9% were hospitalized. In the 90 days after, 24.7% had ED visits and 13.7% were hospitalized. ICT provided virtual consultation for complex older adults with prevalent social needs and high rates of ED visits and hospitalization. The team worked with PCP\u2019s to connect these patients more directly to community resources. Further study is needed to know rates of adherence with recommendations and true impact on health outcomes."} +{"text": "Allergy Asthma Clin Immunol 2019, 15(Suppl 3)Background: Hereditary angioedema (HAE) is an unpredictable and serious genetic disorder affecting approximately 1:10,000 to 1:50,000. It is an autosomal dominant disorder due to C1 inhibitor deficiency. Clinically, it is manifested by painful, unpredictable edema of the face, larynx, abdomen, genitals and extremities. It can be debilitating and if left untreated, may be fatal. We sought to better understand the demographic profiles of patients living with HAE in Canada.Methods: In 2017, a comprehensive survey was sent out to all HAE Canada members by email to gather information on HAE in Canada. Data from respondents have been collected and analyzed using percentage of total surveys to provide data on demographics of these patients.Results: The demographic location of HAE patients living in Canada includes Ontario, Alberta, Manitoba, British Columbia, Nova Scotia, Quebec, Saskatchewan and Newfoundland and Labrador. 140 respondents indicated their relationship to HAE as; 81% are adults living with HAE, 10% are caregivers of an adult living with HAE who lives with them, 2% are caregivers of an adult living with HAE who does not live with them, 2% are adults awaiting a diagnosis, and 4% are other or unknown. 109 respondents indicated 79% are female and 21% are male. When respondents were asked about their HAE type, 60% were found to have type 1/2 C1-inhibitor protein deficiency, 26% have HAE with normal C1-inhibitor, 10% unsure, and 4% have acquired angioedema.Conclusions: This survey helps to better understand the current demographic profile of patients living with HAE and is the first national HAE survey done in Canada. However, data interpretation is limited due to uncertainty of necessary sample size required to be representative of the true population. Overall, our results demonstrate that HAE patients can be found across Canada and that the majority of patients in this survey are aware of their diagnosis.Allergy Asthma Clin Immunol 2019, 15(Suppl 3)Background: Hereditary Angioedema (HAE) is a rare genetic disorder that is characterized by episodes of unpredictable painful swelling in different body parts involving the face, larynx, peripheral limbs, abdomen and genitals. In Canada, there are approximately 400\u2013600 HAE subjects. To better understand the challenges of Canadians living with HAE we conducted the first web survey among our HAE Canada members, the objective was to gather real world data that will provide insight into the attack profiles of a HAE patient.Methods: In 2017\u20132018, data was collected through voluntary online surveys of children, youth, and adults who live with HAE and their caregivers in Canada. The following data was based solely on adult participants.Results: Among 104 participants with HAE they reported a diagnosis of: Type 1 or 2 C1-inhibitor protein deficiency (60%), HAE with normal C1-inhibitor (26%), acquired angioedema (4%), and unsure of diagnosis (10%). In the last year, 78% were symptomatic, 11% were asymptomatic, and 11% were unsure. Regarding the frequency of attacks: 61% had 7 or more attacks, 22% had 1\u20136 attacks, 6% had no attacks, and 10% were unsure. Identifiable attack triggers vary from stress (87%), typing/writing (78%), trauma (70%), illness (61%), medical procedures (61%), anxiety (55%), and Ace Inhibitors (6%). Other factors that increase HAE symptoms include menopause (9%), estrogen contraceptives (33%), and menstruation (47%). To treat these attacks, 84% use an agent, compared to 16% who do not. The most common treatment agent used was C1 esterase inhibitor (Berinert IV).Conclusions: Our findings demonstrate the majority of participants are knowledgeable in identifying their triggers and managing their attacks. Results show improvements are necessary for proper diagnosis and awareness of the disease. Since the number of people living with HAE is estimated, our data is limited to the respondents and may not represent the broader Canadian HAE population."} +{"text": "Background: the plasma D-dimer and fibrinogen which are indicators of coagulation-fibrinolysis system has been reported to be associated with survival in several types of cancers, including RCC. The aim of our study was to assess the prognostic significance of preoperative plasma D-dimer and fibrinogen levels in RCC patients.Methods: Data from 449 patients with RCC were assessed retrospectively. Cutoff value for plasma D-dimer and fibrinogen were tested by the standardized cutoff-finder algorithm. Overall survival (OS) and disease-free survival (DFS) were evaluated using the Kaplan-Meier method. Univariate and Multivariate Cox regression models were further applied for two end points.Results: Multivariate analysis identified increased plasma D-dimer and fibrinogen as independent prognostic factors for OS and DFS . Moreover, all the patients were stratified using these two factors in the following ways: (1) Low risk: both level of plasma D-dimer and fibrinogen were no more than cutoff value. (2) Intermediate risk: neither low risk nor high risk, (3) high risk: both level of plasma D-dimer and fibrinogen were higher than cutoff value. This model showed significant predictive power for OS and DFS.Conclusion: preoperatively elevated D-dimer and fibrinogen can be regard as independent predictors for patients' prognosis in RCC. Combining both plasma D-dimer and fibrinogen can improve the prognostic accuracy and easy accessibility in clinical practice. Renal cell carcinoma (RCC) comprises approximately 1.6% of all new malignancies in Chinese adults for the most recent 3 years It is evident that the plasminogen-plasmin and coagulation system is a vital component in the biology of neoplastic disease As far as we known, the plasminogen-plasmin and coagulation system are studied infrequently in RCC. In our present study, we retrospectively evaluated the relationships between the fibrinogen, D-dimer and patient survival. In the same time, we sought to determine whether preoperative fibrinogen and D-dimer are prognostic factors. Specially, we stratified all the patients based on these two factors into three cohorts and studied whether the three cohorts have different prognosis or not.This retrospective analysis included data from 912 consecutive RCC patients who underwent a curative radical or partial nephrectomy at the department of urology in sun yat-sen university cancer center (SYSUCC), Between January 2000 and December 2012. The following items are the inclusion criteria for this research: (i) diagnosed as RCC pathologically; (ii) access to complete clinical data and preoperative blood sampling for D-dimer and fibrinogen levels; (iii) effective and accurate follow-up. Of this data set, the 449 patients were included in our study. All the clinicopathological data were retrieved from the electronic patient records of our center. Informed consent was waived because of the retrospective research of the study and the analysis used anonymous clinical data.Follow-up was carried out by telephone interview and complimentary medical records review. Important follow-up data included postoperative adjuvant therapy, living status, progression and sites of tumor metastases. The last follow-up was completed in November 01, 2015, and after that, the whole data were analyzed. The primary endpoint was overall survival (OS) which defined that the interval between surgery and last follow-up or death. Secondary endpoint was disease free survival (DFS) which calculated the interval between surgery and last follow-up or recurrence or death.www.empowerstats.com, X&Y solutions, Inc. Boston MA). All tests were two-sided and a P value <0.05 was considered statistically significant.Continuous variables were presented as mean and standard deviations and categorical variables were expressed as frequencies and percentages. To evaluate the best cutoff points of D-dimer and fibrinogen to predict prognosis, we used a validated web-based software Table 1.A total of 449 patients with RCC were enrolled in our study which comprised 292 males and 157 females at a mean age of 52.06 years (SD: \u00b113.49). 361 (80.4%) had clear cell, 28 (6.2%) had papillary 23 (5.2%) had chromophores RCC and 37 (8.2%) were not otherwise specified. According to the TNM staging system, 314 (69.9%), 67 (14.9%), 43 (9.6%) and 25 (5.6%) were staged in \u2160, \u2161, \u2162 and \u2163, separately. The demographic and clinicopathologic parameters of the study cohort are shown in Figure 1). According to the cutoff values, all the patients were divided into the low and high groups, respectively (Table 1).According to the Cutoff Finder, the optimal cutoff values of the D-dimer and fibrinogen were determined to be 0.95 and 4.42 for the prognosis of RCC patients, respectively , respectively.To investigate whether the D-dimer and fibrinogen were related to the clinical outcome of RCC patients, univariate and multivariate analyses for OS and DFS were performed. The mean and median follow-up time was 58.71 and 57.72 months. For localized disease, we excluded stage \u2163 cases resulting in 424 patients with RCC. In our further study, 449 patients were analyzed for OS and 424 were analyzed for DFS. Table 2). In the same way, regarding DFS, univariate analysis revealed that BMI, blood platelet, pathologic types, Fuhrman grade, pT-stage, pN-stage, clinical stage, D-dimer and fibrinogen were associated with prognosis of RCC patients (Table 3).Univariate analysis identified BMI, blood platelet, pathologic types, Fuhrman grade, pT-stage, pN-stage, pM-stage, clinical stage, D-dimer and fibrinogen were as prognosticators of poor outcome for patients' OS (Table 2). For DFS, these clinicopathologic parameters included BMI, blood platelet, pathologic types, Fuhrman grade, pT-stage, pN-stage, D-dimer and fibrinogen brought into our multivariate analysis and we also demonstrated that D-dimer and fibrinogen were independent prognostic factors for DFS (Table 3).To determine the independent prognostic significance of the D-dimer and fibrinogen for OS and DFS, a multivariate analysis using a Cox proportional hazard model was performed. Regarding OS, in our multivariate analysis that included BMI, blood platelet, pathologic types, Fuhrman grade, pT-stage, pN-stage, pM-stage, D-dimer and fibrinogen, we identified D-dimer and fibrinogen as independent prognostic factors for OS and also including BMI, pT status, pN status and pM status . Moreover, we analysis the 1-year, 3-years and 5-year survival rate for OS and DFS. The 1-year, 3-year and 5-year OS rate for patients with high risk was 85% (95%CI: 78% to 93%), 78% (95%CI: 69% to 87%) and 61% (95%CI: 49% to 75%) compared with 100%, 82% (95%CI: 71% to 96%), 74% (95%CI: 60% to 92%) for patients with intermediate risk and 98% (95%CI: 96% to 99%), 93% (95%CI: 90% to 95%), 91% (95%CI: 88% to 94%) for patients with low risk. The Kaplan-Meier curves also revealed that the high risk group has the worsen OS than intermediate and low risk for 1-year, 3-year and 5-year survival . In the other hand, we also analysis the prognostic significance in these three cohort for DFS. The 1-year, 3-year and 5-year DFS rate for patients with high risk was 90% (95%CI: 84% to 98%), 80% (95%CI: 71% to 90%) and 78% (95%CI: 69% to 89%) compared with 96% (95%CI: 90% to 100%), 87% (95%CI: 76% to 99%), 73% (95%CI: 55% to 97%) for patients with intermediate risk and 96% (95%CI: 94% to 98%), 93% (95%CI: 90% to 96%), 93% (95%CI: 90% to 95%) for patients with low risk. The Kaplan-Meier DFS curve showed that there was significant predictive power for 3-year and 5-year survival , but not for 1-year survival .Finally, patients were categorized into different risk groups according to the level of D-dimer and fibrinogen . By the Kaplan-Meier curves and log-rank test, we demonstrated the high risk group had significantly poorer OS and DFS than the other two groups , whereas D-dimer only had negative independent prognostic value on OS Fibrinogen is synthesized in the liver, and its level is affected by in vivo infection or inflammation Our results indicate that the high and intermediate risk may inform frequency of surveillance. Patients with high risk should be close follow-up. Furthermore, according to the different year survival rate for DFS and OS, when the plasma D-dimer or fibrinogen was higher than the cutoff value, the worse trend of survival status was being seen. Given our results and the data from previous basic studies, increased coagulation and fibrinolytic activities appear to be associated with increased risks of tumor progression and metastasis among patients with RCC. Concentrations of D-dimer and fibrinogen before surgery may also offer a useful marker of recurrence and metastasis in RCC patients following resection. Furthermore, functional inhibition of fibrinogen and other coagulation factors might represent novel strategies for treating RCC. Further investigations are needed to clarify the relationships among circulating coagulation and angiogenic factors in neoplastic tissues.As with all retrospective studies, limitations of our study remain some limitations. Firstly, our outcomes originated from retrospective data. Secondly, the study cohort was small, despite being relatively large compared to other such investigations of RCC patients. Nonetheless, even considering these limitations, our data clearly indicate that increased preoperative D-dimer and fibrinogen might represent independent prognostic factors for OS and DFS in RCC patients.In conclusion, preoperatively elevated D-dimer and fibrinogen seems to represent independent predictors with respect to patients' OS and DFS in RCC. Combining both plasma fibrinogen and D-dimer can improve the prognostic accuracy and act as a select criterion for risk factor-stratified patient management in RCC."} +{"text": "Low fruit and vegetable consumption contributes significantly to the burden of disease. The study aimed to assess the prevalence and correlates of fruit and vegetable (FAV) consumption among adults in a national survey in Kenya.A national cross-sectional study based on a stratified cluster random sampling was conducted in 2015. The total sample included 4479 individuals 18-69 years, from Kenya. Sociodemographics, health risk behaviour and anthropometric data were collected using the WHO-STEPS questionnaire.On average, participants had 0.78 servings of fruits a day, 1.31 servings of vegetables a day, and 2.09 servings of FAV. Only 12.4% of respondents had two or more servings of fruit a day, 7.4% had three or more servings of vegetables a day and 94.0% had less than five servings of FAV a day. In adjusted logistic regression analysis, higher education , greater wealth , and being a Kikuyu or Luo were associated with two or more servings of fruits daily. Urban residence and being male decreased the odds, and older age and being Luo increased the odds of having three or more servings of vegetables daily. Being male and being Luo decreased the odds and urban residence increased the odds of inadequate (< five servings) FAV consumption.A high prevalence of inadequate FAV consumption was found, and risk factors identified, such as being female, lower education, urban residence, and not being Luo, that may help in guiding strategies to increase FAV consumption. Globally, 2.8% of deaths can be attributed to low fruit and vegetable (FAV) consumption . Based oData, study design and participants: A multi-stage cluster sampling method was used to select adults aged 18 to 69 years for the Kenya STEPS Survey (April to June 2015), details of sampling methodology can be found in Ministry of Health [f Health . The samf Health . The KenFAV intake were calculated from the number of servings of FAV consumed per day in a typical week. Inadequate FAV consumption was defined as less than five servings a day [Measures: Following WHO STEPS methodology three stgs a day .Physical activity level was calculated from the duration of moderate and vigorous physical activities in a typical day and week. Physical activity levels were classified into low, moderate and high, as per WHO Global Physical Activity Questionnaire [Current tobacco use was measured with two questions, \u201cDo you currently smoke any tobacco products, such as cigarettes, hand-rolled, cigars, water pipes/shisha or pipes/kiko?\u201d and \u201cDo you currently use any smokeless tobacco products such as snuff, chewing tobacco, kuber..pan?\u201d . Past month binge drinking was assessed by asking participants how many times they had six or more standard alcoholic drinks in a single drinking occasion during the past 30 days [Body Mass Index(BMI) was measured from scientific body height and weight measures, and overweight or obesity was classified as 25+ kg/m2 [ionnaire . CurrentYes, No) , p.5-1-65+ kg/m2 . Central5+ kg/m2 Data analysis: Post stratification adjustments were done to align with the population projections according to age-sex categories [tegories . DescripSample characteristics and intake of fruit, vegetables and fruit and vegetables categories: The total sample included 4479 individuals 18-69 years, from Kenya. More than half of the participants had at least completed primary education (58.7%), 14.9% were Kikuyu by ethnic group, and 51.4% resided in rural areas. Almost one in ten (9.0%) of participants had general obesity, 12.8% central obesity, 89.1% had adequate physical activity, 13.3% were currently tobacco users and 13.5% were past month binge drinkers. Only 15.3% of participants consumed fruits daily, and 50.9% had vegetables daily. The mean number of days consuming fruits per week was 2.52 and the mean number of days consuming vegetables per week was 4.96. On average, participants had 0.78 servings of fruits a day, 1.31 servings of vegetables a day, and 2.09 servings of FAV per day. Only 12.4% of respondents had two or more servings of fruit a day, 7.4% had three or more servings of vegetables a day and 94.0% had less than five servings of FAV a day. In bivariate analyses, fruit servings per day increased with being male, education, greater wealth, urban residence, having general and central obesity, and being a Kikuyu or Luo by ethnic group and decreased with age, current tobacco use and low physical activity. Vegetables servings increased with age, education, being a Kikuyu or Luo by ethnic group and central obesity and decreased with greater wealth and low physical activity. FAV consumption increased with age, education, greater wealth, being a Kikuyu or Luo by ethnic group, and central obesity and decreased with low physical activity and current tobacco use , greater wealth , and being a Kikuyu or Luo were associated with two or more servings of fruits daily. Urban residence and being male decreased the odds, and older age and being Luo increased the odds of having three or more servings of vegetables daily. Being male and being Luo decreased the odds and urban residence increased the odds of inadequate (< five servings) FAV consumption FAV consumption in adults 18-69 years) was 94.0% in 2015, which is higher than in the 2004 Kenya World Health Survey 86.7%) [ servings-69 years% servi. This fiThis would mean more effort is needed to increase the frequency of both FAV intake in order to reach recommended levels of FAV consumption. While some studies found a decline of inadequate FAV consumption with age , 10, 11,Study limitations: Apart from anthropometric measurements, a study limitation was that all the other information assessed in this analysis was based on self-reporting. It is possible that certain behaviours were over or under reported. Further, it was a cross-sectional study and causal relationships between independent and dependent variables cannot be established. Certain variables that represent barriers or facilitators such as cost and access were not assessed in this study and should be included in future studies.The study found a high prevalence of inadequate FAV consumption in a representative sample of the general adult population in Kenya. Relative to other studies, vegetable consumption was particularly low. Several risk factors, such as being female, lower education, urban residence, and not being Luo were identified to better target an increase in FAV consumption in Kenya.In the 2004 Kenya World Health Survey, the prevalence of insufficient (< five servings) fruit and vegetable consumption was 86.7%.The current (2015) study showed that the prevalence of insufficient fruit and vegetable consumption was 94.0% in Kenya;Several risk factors, such as being female, lower education, urban residence, and not being Luo were identified for insufficient fruit and vegetable consumption;Very high insufficient fruit and vegetable consumption calls for urgent health promotion programming to increase fruit and vegetable consumption in Kenya.The authors declare no competing interests."} +{"text": "To validate a morphokinetic implantation model developed for EmbryoScope onembryos with known outcome, compared to standard morphology in aretrospective single center study.Morphokinetic annotation of 768 embryos with known outcome between 2013-2015; corresponding to 116 D3 fresh embryos, 80 D6 frozen blastocysts, and572 D5 blastocysts, fresh or frozen. The embryos were ranked by the KIDScoreinto five classes, KID1-5, and grouped into four classes based on standardmorphology. Pregnancy rates, clinical pregnancy rates and live birth rateswere compared. Combinations of morphology and morphokinetics were evaluatedfor implantation rates and live births.Live birth rate increased with increasing KIDScore, from 19% for KID1 to 42%for KID5. Of all live births, KID5 contributed with 71%, KID4 with 20%, KID3with 4%, KID2 with 4%, and KID1 with 2%. For morphology, the correspondingfigure was 43% for Top Quality, 47% for Good Quality, 4% for Poor Quality,and 5% for Slow embryos. For day 3 embryos, KID5 embryos had the highestlive birth rates, and contributed to 83% of the live births; whereas thesecond best morphological class had the highest live birth rate andcontributed to most of the live births. For blastocysts, the KIDScore andmorphology performed equally well. Combining morphology and morphokineticsindicated stronger predictive power for morphokinetics.Overall, the KIDScore correlates with both implantation and live birth in ourclinical setting. Compared to morphology, the KIDScore was superior for day3 embryos, and equally good for blastocysts at predicting live births. The successful culture, evaluation and selection of embryos often determine theoutcome of infertility treatment. The desire to reduce multiple births by a singleembryo transfer has increased the burden on the clinical embryologist to choose theembryo with the highest ability to give the patient a healthy baby from a cohort ofembryos. Traditionally, the evaluation and selection of embryos is done usingmorphology, often with daily removals and evaluations outside the safer environmentof the incubator. The use of time-lapse incubators in clinical IVF laboratories hasgiven embryologists access to thousands of multifocal images of each embryo. Itprovides a solution to the 'observational dilemma' that the likelihood of selectingthe right embryo increases with the number of observations, but every observationposes a threat to the embryo as it gets exposed to sub-optimal culture conditions, and it is referred to as a parameter. Events in embryodevelopment have been linked to blastulation, implantation and chromosomal content., of which ~800 implanted and ~250 yielded live births. The time-lapse data wasgathered from a large database from 24 clinics, including both IVF and ICSItreatments, with embryo culture in both reduced and ambient oxygen levels approved the study. Our only exclusion criteria was the patient'slack of consent.2)before cumulus cells were removed and all oocytes placed in the EmbryoScope.ICSI oocytes were placed in EmbryoScope directly after microinjection. Embryos were cultured insequential media, with half media change done in the afternoon of days 2 and4.All patients had controlled ovarian stimulation with either antagonist or agonistprotocol. We adjusted the starting dose to female age, ovarian reserve andoutcome of any previous cycles. When at least 3 follicles reached 18 mm,triggering was performed using recombinant human chorionic gonadotropin. Oocyteswere retrieved 36 hours after triggering. The oocytes were fertilized bystandard gamete co-incubation (referred to as IVF) or ICSI. IVF oocytes werecultured overnight in a standard incubator was obtained from all participating patients through follow-upquestionnaires and/or phone calls.Time-lapse annotation was performed in retrospect on all embryos transferredfresh/frozen between 2013-2015. 768 transferred embryos were included . The cohort consisted of 116 D3 fresh transferred embryos, 80D6 vitrified/warmed transferred embryos, and 572 D5 blastocysts (287 fresh and287 frozen). The following parameters were annotated for each embryos; tPNa asthe time of appearance of pronuclei, tPNf as the time of fading of pronuclei.t2, t3, t4, t5, t6, t7, t8, t9+ was defined as the times for the correspondingnumber of cells. tM was defined as the first frame of the morula stage, tSB asthe first frame with presence of blastocoel, tB as the first frame of a fullyformed blastocyst, tEB as the first frame showing expansion of the zonapellucida with enlargement in size. The 'Compare and Select' feature inEmbryoViewer software with KIDScore D3 Basic was used torank embryos into KID 1-5.For statistical purposes, the embryos were categorized into morphological classesbased on their grade. The blastocysts were classified as belonging to the TopQuality Embryo (TQE) Group; blastocysts with an A for ICM and/or TD, to the GoodQuality Embryo (GQE) Group; blastocysts with B for both ICM and TD, to the PoorQuality Embryo (PQE) Group; blastocysts with a C for ICM and/or TD, or Slow;embryos with an expansion grade of 0, 1 or 2 (pre-blastocyst stage embryos).Day-3 embryos were categorized into three classes based on their morphologicalevaluation. Day-3 embryos with exactly 8 cells, less than 20% fragmentation andeven blastomeres were classified as TQE. Day-3 embryos with 6-10 blastomeres orwith more than 20% fragmentation, or uneven cells were classified as GQE. Day-3embryos with less than 6 cells, or more than 10 cells, and/or <50%fragmentation were classified as PQE.Pregnancy rate (PR) was calculated as the percentage of transfers leading to arise in beta-HCG. Clinical pregnancy rate (CPR) was calculated as percentage oftransfers leading to intrauterine gestational sacs with fetal heartbeat observedby transvaginal ultrasonography. Live birth rate (LBR) was calculated as thepercentage of live born babies. PR, CPR, LBR were calculated and compared foreach morphokinetic score and for each morphological score, with significancetesting using fishers exact t-test.The transfer of 768 embryos resulted in 380 positive pregnancy tests (PR 49.5%), 299ongoing pregnancies as detected by early ultrasound (CPR 38.9%) and 283 live births(LBR 36.8%). There was no significant difference in outcome between IVF and ICSI. Blastocyst transfers resulted in higher LBRcompared to cleavage stage embryos, and transferring D5 blastocysts resulted inhigher LBR compared to transferring D6 blastocysts. See The algorithm used to score all embryos was accessed through the EmbryoScopesoftware . RankingLooking at all embryos, the LBR increased from 18.9% for KID1, 17.9% for KID2,32.3% for KID3, 33.3% for KID4 to 42.0% for KID5. The distribution of theKIDScore classes on transferred embryos, positive pregnancy tests, ongoingpregnancies and live births show a prevalence of KID5 embryos in all categories.Of all live births, 71% originated from a KID5 embryo, 20% from KID4, and only9% from the remaining KID1-2-3. See When splitting embryos based on day of transfer, the distribution of embryos intoKIDScore classes, and their corresponding PR, CPR and LBR showed similarpatterns as for all embryos combined. For blastocysts, LBR increased from 21.2%for KID1 to 43.8% for KID5. For cleavage-stage embryos, LBR increased from 0%for KID1-2, to 33.3% for KID5. Of all live births after day-3 transfers, KID5embryos accounted for 83%. See The blastocysts were categorized into four classes- TQE, GQE, PQE and Slow-,whereas cleavage-stage embryos were categorized into only three classes - TQE,GQE, PQE. The embryo distribution was uneven, with TQE accounting for 37% of thetotal embryos, GQE for 50%, PQE for 5% and Slow 8%, respectively. Looking at allembryos, LBR decreased from 43% for TQE, 35% for GQE, 33% for PQE, and 25% forSlow. Due to the distribution of embryos, the majority of live born babies areattributed to the second highest category 'GQE' (47%) followed by TQE (43%) andonly 4% from PQE and 5% from Slow embryos. See p=0.039). However, due to thedistribution with more embryos assigned to GQE, the contributions of TQE and GQEon live births were identical (45.3%). See When splitting the embryos based on day of transfer, a different pattern is foundfor cleavage-stage embryos. Of the 116 day-3 embryos, 61% were assigned as GQE,29% as TQE and 10% as PQE. LBR was 18% for PQE, and 32% for both TQE and GQE,i.e. morphology could not identify embryos with the highest ability to result inlive birth from day-3 morphological data. The skewed distribution with the vastmajority of embryos assigned as GQE resulted in 66% of live births from day-3transfers originating from the second-best morphology class, more than doublethat of TQE (28%). For blastocysts, LBR was similar for PQE and GQE, andsignificantly higher in TQE .Prior to this validation, we performed a comparison between morphology andmorphokinetics in terms of inter-observer and intra-observer agreement. Formorphokinetics, all investigated parameters had a high agreement rate betweenobservers and between repeated measurements. When evaluating an embryo, the outcomeis independent of which embryologist annotates and when. All parameters included inthe KIDScore model had an 'almost perfect agreement' except t8, which had 'strongagreement'. The notion that the objectivity and reproducibility of morphokineticsadds value to the more subjective method of morphology, especially on day 3, isstrengthened from the findings from In contrast, morphological evaluation was capable of identifying blastocysts withhigh LBR. The embryos ranked as top quality had the highest LBR - 45.5%, but becauseGQE was the most common score, both TQE and GQE contributed equally to live births -45%. Using morphokinetics, the highest KID5 score had a LBR of 44% but contributedwith 70% of the live births, due to more embryos contained in the highest category.This is a feature of the KIDScore and a feature of deselection models in general. Itreduces the risk of scoring an embryo with a fair chance of resulting in asuccessful outcome as poor.Although a high morphokinetic score often accompanies a high morphological score, itis not always the case. Embryos with irregular division patterns, like directcleavage, can develop into morphologically excellent blastocysts. However, theirimplantation ability is substantially reduced , type ofcycle (fresh or frozen), or type of treatment (IVF or ICSI). Here we show that isfunctions as a blastocyst prediction algorithm, as implantation predictionalgorithm, and as live birth predictor in a clinical setting using sequential media,reduced oxygen, both IVF and ICSI treatments and both antagonist and agonist type ofstimulation. The differences found for IVF and ICSI morphokinetics (The clinical use of time-lapse incubators with regards to improved culture conditionsand increased ease of quality control makes them invaluable in clinical practice -even without using morphokinetics for embryo evaluation and selection. A recentmeta-analysis on morphokinetics showed increased pregnancy rates, reduction in earlypregnancy loss and increase in live births when selecting embryos using themorphokinetic embryo evaluation ("} +{"text": "Median percent of calories from polyunsaturated fat was 6.8% (5.4\u20139.6). Percent of calories from PUFA was positively and significantly associated with greater FFM% , lower FM% , and greater FFM/FM ratio . Additionally, a higher PUFA to saturated fatty acids ratio was also significantly correlated with greater FFM% , lower FM% , and greater FFM/FM ratio . DISCUSSION/SIGNIFICANCE OF IMPACT: In patients with NASH, the consumption of PUFA is associated with higher FFM and lower FM, which suggests a protective role of these nutrients on body composition. A larger study on patients with NASH is warranted to confirm our findings on PUFA consumption and body composition, as well as to determine whether these effects will improve clinical outcomes.OBJECTIVES/SPECIFIC AIMS: Nonalcoholic steatohepatitis (NASH) is a common cause of chronic liver disease in the United States characterized by fat accumulation, inflammation, and fibrosis. Higher amounts of fat-free mass (FFM) and lower amounts of fat mass (FM) have been associated with better outcomes in several chronic diseases, recently also in NASH. Body composition is highly influenced by diet. However, the role of diet on body composition in patients with NASH is largely unknown. We hypothesized that consumption of polyunsaturated fatty acids (PUFA), healthy fatty acids mainly found in fish, nuts, and some vegetable oils, is associated with improved body composition, specifically greater FFM and lower FM, in NASH patients. METHODS/STUDY POPULATION: In total, 13 patients with histologically confirmed NASH underwent body composition testing via bioelectrical impedance analysis to estimate FFM% (% of body weight), FM% (% of body weight), and FFM/FM ratio. PUFA and saturated fat consumption was determined by standardized 5-pass 24-hour dietary recall. Correlations were computed using the Spearman rank test. RESULTS/ANTICIPATED RESULTS: Median body mass index (BMI) was 35.7 kg/m"} +{"text": "Temporal trends in demographics, tumor characteristics, and survival were assessed by cohort-level analysis. The National Cancer Institute\u2019s Surveillance, Epidemiology, and End Result Program was used for external validation . Results: The number of oldest-old women aged \u226580 years significantly increased in the study period. A stage shift was observed, with stage I disease decreasing from 43.0% to 34.0% (21.0% relative decrease), and tumors with distant metastases increasing from 23.2% to 35.6% . The number of women who underwent surgical treatment decreased from 84.0% to 69.7% (17.0% relative decrease), whereas utilization of radiotherapy increased from 34.4% to 43.2% (25.7% relative increase) over time (p < 0.05). In the cohort-level analysis, the five-year survival rates significantly decreased from 2001 to 2010 (p < 0.05), specifically, 66.9% to 51.0% for progression-free survival (23.7% relative decrease), 79.5% to 67.9% for cause-specific survival (14.6% relative decrease), and 74.9% to 62.3% for overall survival (16.9% relative decrease). In the patient-level analysis, oldest-old women were less likely to undergo surgical treatment and were independently associated with decreased survival (p < 0.05). In the US cohort, the number of oldest-old women (25.2% to 27.8%) and the five-year cause-specific survival rate (81.8% to 79.9%) remained unchanged during the study period (p > 0.05). Conclusion: Demographics and outcomes of vulvar cancer in Japan significantly changed during the study period. An increasing oldest-old population and a stage shift to more metastatic disease resulted in a cohort-level decrease in survival rates.Background: To examine trends in the clinicopathological characteristics of vulvar cancer in Japan. Methods: This is a nationwide retrospective study examining consecutive women with vulvar cancer between 2001 and 2010 in Japan ( Vulvar cancer is a rare malignancy, accounting for 4% of all gynecological cancers; 65% of these cases occur in developed countries . HistoriThe population in Japan has been significantly and steadily aging. In 2017, 27.7% of Japanese was 65 years old or older, and 13.8% was 75 years old or older [Vulvar cancer has been relatively understudied worldwide, including in Japan, with no large-scale clinicopathological investigations of vulvar cancer in the past three decades. Moreover, the published studies examined small samples, which interfered with data interpretation and utilization . TherefoThe study protocol was approved by the Ethics Committee of Kurume University (protocol number: 14034), which served as the host institution, and each participating Japanese Gynecologic Oncology Group (JGOG)-affiliated institution reviewed the protocol and approved the study. The study protocol was registered at the University Hospital Medical Information Network (UMIN) (protocol number: UMIN-000017080). The study concept and participation call were initially announced at all JGOG-designated institutions (181 sites), and 109 (60.2%) sites voluntary participated in the study. The study sites, however, covered all high-volume centers in Japan.Upon completion of data collection by participating clinicians, the anonymous de-identified data sheets were transferred to the host institution. Data were then compiled into a master Excel data sheet by the research staff. The principal investigators reviewed the accuracy, consistency, and quality of the dataset, and when there was disagreement in a data element, the principal investigator and investigators at each participating institution discussed the context to achieve adjudication.Consecutive patients with invasive vulvar cancer from January 2001 to December 2010 were examined, and data curation of this retrospective observational study was conducted from August 2014 to March 2016. JGOG institutions are thought to see more patients with vulvar cancer, estimated at 5\u201310 patients per institution annually for 10 years. The inclusion criteria were a diagnosis of and treatment for invasive vulvar cancer, including patients whose initial therapy had a palliative intent and patients with primary vulvar cancer, including all histological types. Patients with malignant melanoma were excluded from the analysis. For eligible patients, information on patient demographics, tumor characteristics, surgical treatment, radiotherapy, chemotherapy, and survival outcomes was obtained from archived medical records.Patient demographics included age and year of diagnosis. Tumor characteristics included histological type , cancer stage, tumor size (2 cm increments), and surgical margin status . Surgical treatment included type of vulvar surgery , details of inguino-femoral lymphadenectomy , and reconstructive surgery . Information on perioperative complications was abstracted .Radiotherapy information included use in a neoadjuvant, adjuvant, definitive, or palliative setting. The details of radiotherapy were also abstracted, including radiation field, irradiation method , linear accelerator (LINAC), electron beam, total dose, and treatment duration. Radiotherapy-related toxicity (both early and late) was also documented. Details on regimens and cycles of chemotherapy were obtained for patients who received concurrent chemoradiotherapy. Chemotherapy information included the setting , regimen type, administered cycles, and treatment-related toxicity. Survival information included follow-up time, presence of recurrent/progressive disease, and vital status .Patients were grouped by age as non-older <60 years), young-older (60\u201379 years), and oldest-old (\u226580 years) per the World Health Organization/United Nations criteria (5). Cancer stage was reassigned based on the 2008 International Federation of Gynecology and Obstetrics (FIGO) criteria [0 years, The primary objective of this study was to outline the time-specific descriptive statistics of the clinicopathological features of invasive vulvar cancer in Japan. The secondary objective was to assess the temporal trends of survival statistics and the prognostic factors of invasive vulvar cancer in the study population.H test, as appropriate. Discrete and categorical variables are displayed with numbers and percentages per group, and the statistical significance of differences was assessed with chi-squared tests.Standard statistical methods were used to describe continuous variables as mean (\u00b1SD) or median Interquartile range (IQR) values based on normality, as assessed using the Kolmogorov\u2013Smirnov test. Significance in differences among multiple groups (more than two) was assessed using one-way ANOVA or the Kruskal\u2013Wallis For cohort-level analysis, the Joinpoint trend analysis software was used to examine temporal trends over time. Single calendar years were used as time increments, and percent frequencies with confidence intervals (CI) or observed values of 5-year survival rates with standard errors are reported. The 5-year survival time point was based on the median follow-up of the study cohort. Linear segmented regression was used to analyze temporal trends, and log-transformation was performed to determine annual percentage rate changes (APC) of the slope with 95% CI. Relative changes in outcomes were based on the modeled value in this study.For the patient-level analysis, Cox proportional hazard regression models were fitted to assess the prognostic impact of the clinicopathological factors of interest on survival, and the magnitude of statistical significance was expressed using hazard ratio (HR) and 95% CI. Specifically, on the basis of the results of the cohort-level analysis, we examined the association of patient age and survival adjusted with a priori survival factors, histology, stage, tumor size, and treatment types. The year of diagnosis was also considered in the model. This parsimonious approach was due to the relatively small sample size of our study.To examine if the cohort-level characteristics observed in the study population are unique to Japanese women, the National Cancer Institution\u2019s Surveillance, Epidemiology, and End Result (SEER) Program was used for external validation (US cohort). Briefly, the SEER database is the largest population-based tumor registry in the United States, covering approximately 34.6% of the population in the latest version . The cohp < 0.05 was considered to indicate statistical significance (two-tailed hypothesis). The Statistical Package for Social Sciences was used for all analyses.Various sensitivity analyses were performed to examine the robustness of the analysis, and trends and outcomes were assessed for stage I disease, surgery, and squamous histology. These subgroups were chosen on the basis of the rationale that vulvar cancer is more likely to exhibit squamous histology in early-stage disease, and surgical treatment remains the mainstay of treatment. In the statistical analysis, n = 768, 72.4%) and in stage I . Metastatic tumors to inguino-femoral lymph nodes or distant organs were seen in 312 (29.4%) women. Most patients underwent surgical treatment .There were 1061 women who met the inclusion criteria . The medn = 100, 12.5%). Radiotherapy with any indication was performed in 410 (38.6%) women, with definitive and adjuvant radiotherapy being the two most common indications. Among women who received radiotherapy, concurrent chemotherapy was used in 103 patients (25.1%).Regarding the surgical treatment, 273 (34.1%) patients underwent radical vulvectomy, 259 (32.4%) underwent some type of reconstructive surgery, and 494 (61.8%) underwent inguino-femoral lymphadenectomy. Tumors with close or involved surgical margins accounted for 436 (54.5%) cases. Perioperative complications were relatively infrequent , whereas the number of young-older women decreased from 64.0% to 48.8% (23.7% relative decrease) , 79.5% to 67.9% for CSS , and 74.9% to 62.3% for OS .The median follow-up of censored cases was 58.2 months , with 423 cases of recurrence or progressive disease, 280 deaths from vulvar cancer, and 349 deaths from any cause during the follow-up. Among those who died, the median time to death was 14.5 months (IQR 7.2\u201337.8). Five-year survival rates significantly decreased A: 66.9% p < 0.05). Oldest-old women were more likely to receive radiotherapy (46.1% versus 33.6\u201337.8%) and less likely to receive concurrent chemotherapy during radiotherapy (6.8% versus 28.3\u201345.2%) or systemic chemotherapy (4.7% versus 16.0\u201321.2%) than younger women .Patient demographics per age group are shown in p < 0.05). This association was also observed in subgroups with squamous tumors, stage I diseases, and surgery , the median age was 68 years (IQR 54\u201380), with 26.4% being oldest-old (n = 2683). The number of oldest-old women did not change from 2001 to 2010 .The median follow-up of censored cases was 104 months (IQR 78\u2013139), and during follow-up, there were 2046 deaths from vulvar cancer and 5433 deaths from any cause. Among those who died, the median time to death was 27 months . The five-year CSS rate remained unchanged during the study period . As the incidence of vulvar cancer in Japan was lower than that in Western countries , this maFor instance, the number of surgically treated women who underwent incomplete tumor resection in our study, evidenced by the presence of tumors in the surgical margin, was significantly higher than that reported in a recent European study (22.4% versus 9.9%) , in whicAs high surgical volume is clearly associated with improved survival in other gynecologic cancer types, centralization of hospitals treating vulvar cancer may be necessary in Japan ,20,21,22The strengths of our study include the large sample size and an external US validation cohort that showed clear contrasts. To our knowledge, vulvar cancer reports in Japan were available only for local specific geographic areas, with no national surveys ,11. We bNonetheless, our study has several limitations. First, the study has all the limitations inherent in a retrospective study. A salient unmeasured bias that can impact the outcomes includes medical comorbidity, frailty, performance status, surgeon\u2019s experience, patient compliance, and the decision-making process, all of which most likely affect treatment approach, surgical performance, and survival. Second, while this study population covers diverse areas of hospitals in Japan, not all hospitals in Japan participated, resulting in a potential selection bias. However, as described earlier, the sites that participated in the current study represent all the high-volume centers in Japan, which mitigates the possible selection bias. Third, due to the relatively long duration (10 years) of this study, there may have been changes in treatment methods, resulting in non-uniformity of treatment. A summary of these geographic disparities is shown in In summary, the demographics and outcomes of vulvar cancer in Japan significantly changed during the study period: an increasing oldest-old population and a stage shift to more metastatic disease resulted in a cohort-level decrease in survival rates. The optimization of treatment strategies and screening methods will be useful to decrease mortality due to vulvar cancer in Japan."} +{"text": "The study aimed to examine hypertension prevalence and management in China. Data were from a national survey of a probability sample of 45+ in China . Self-reported hypertension diagnosis and readings from electronic blood pressure monitors were used to create four variables: diagnosed, measured (>=140/90 as high), undiagnosed, and overall (diagnosed + undiagnosed) hypertension. Respondents with diagnosed hypertension were asked about medication use, blood pressure monitoring, and lifestyle advice from doctors; and were considered inadequate blood pressure control if having measured hypertension. Weighted descriptive statistics and multivariate logistic regression were conducted. The prevalence of diagnosed, measured, undiagnosed and overall hypertension was 27%, 37%, 14%, and 51%, respectively. Across all four, older age adults, women, and urban residents had higher rates. Among hypertensive patients, 82% took anti-hypertensive medications, 91% monitored blood pressure, 60% received lifestyle advice, and 53% had inadequate blood pressure control. Compared to the 45-54 years old, the 75+ was less likely to receive lifestyle advice and the 65-74 was less likely to have adequate control . Men were less likely to use medications but more likely to receive lifestyle advice than women. More education and urban were associated with better hypertension management and control. In conclusion, hypertension affects half of the middle-aged and older population in China. More than half of hypertensive patients have inadequate blood pressure control. People who are older, women, low-educated, and rural residents are disadvantaged in hypertension management."} +{"text": "Lesbian, gay, bisexual, transgender, and queer (LGBTQ) older adults face unique challenges in finding affordable, inclusive, and supportive housing. These challenges may be due to discrimination, income disparities, and higher rates of health problems compared to cisgender heterosexual seniors. To our knowledge, this is the first longitudinal study of the health and wellbeing of older adults who move into LGBTQ-welcoming, affordable senior housing. Participants completed a brief baseline survey at the time of their housing lottery application. Questions focused on physical, psychological, and social health and current health service use. We calculated descriptive statistics on health status at baseline. 184 participants completed the baseline survey, mean age was 68 years (SD 5.2), and nearly 75% reported an annual income under $30,000. Almost half reported a diagnosis of hypertension, 40% depression, 27% anxiety, and 25% HIV/AIDS. Around 70% reported their health as good to excellent, 21% fair, and 9% poor or very poor. However, 58% reported their physical activities were at least somewhat limited by their physical health, 43% reported difficulties with balance or walking, and 32% reported memory problems. Nearly 3% had been admitted into the hospital and 10% had visited the emergency room in the past 30 days. In terms of social wellbeing, 63% felt isolated from others at least some of the time. In summary, LGBTQ older adults seeking affordable senior housing report relatively good health, although they also experience functional and social difficulties. New forms of housing that are explicitly LGBTQ-welcoming may help address these health challenges."} +{"text": "Clostridium difficile (CD) infection, with resolution in 80% to 90% of patients. However, immunosuppressed patients were often excluded from FMT trials, so safety and efficacy in this population are unknown. Fecal microbiota transplantation (FMT) has been shown to be effective in recurrent We searched MEDLINE and EMBASE for English language articles published on FMT for treatment of CD infection in immunocompromised patients , inherited or primary immunodeficiency syndromes, cancer undergoing chemotherapy, or organ transplant, including-bone marrow transplant) of all ages. We excluded inflammatory bowel disease patients that were not on immunosuppressant medications. Resolution and adverse event rates were calculated. Forty-four studies were included, none of which were randomized designs. A total of 303 immunocompromised patients were studied. Mean patient age was 57.3 years. Immunosuppressant medication use was the reason for the immunocompromised state in the majority (77.2%), and 19.2% had greater than one immunocompromising condition. Seventy-six percent were given FMT via colonoscopy. Of the 234 patients with reported follow-up outcomes, 207/234 (87%) reported resolution after first treatment, with 93% noting success after multiple treatments. There were 2 reported deaths, 2 colectomies, 5 treatment-related infections, and 10 subsequent hospitalizations. We found evidence that supports the use of FMT for treatment of CD infection in immunocompromised patients, with similar rates of serious adverse events to immunocompetent patients. Clostridium difficile (CD) infection is the leading cause of healthcare-associated diarrheal illness in the United States, affecting nearly 500,000 patients annually .\u201356.13\u201356Patient averaged about 2.5 episodes of CD prior to first FMT. Most patients (73.7%) had received other treatments for CD infection, mainly antibiotics, before FMT, with many (48.6%) receiving 2 or more CD infection treatments prior to FMT. Treatments other than antibiotics prior to FMT included probiotics, intravenous immunoglobulin, and surgery. For patients that received antibiotics prior to FMT, antibiotics were stopped on average about 1.5 days prior to FMT procedure.Colonoscopy was the route of delivery of FMT in 76% of patients, while 21% had stool transplanted via ingestion of capsules or other upper gastrointestinal route . Retention enema was performed in 7.6 % of patients. Most patients (95%) received fresh stool, while 5% utilized commercially prepared products. Among those reporting source of stool, a related donor was employed in 75% of patients.A total of 234 patients had data on outcome and were included in the efficacy analysis. Of these, 206 (87.7%) had clinical resolution of CD infection after first FMT treatment, while 93% had resolution after 2 or more FMT attempts. Comparing rate of resolution by delivery method, colonoscopy delivered FMT had an 84% success rate, while upper gastrointestinal delivery resulted in 92% success rate (p = 0.202). In terms of number of immunocompromising conditions, patients with one condition had a success rate of 93%, while those with two or more immunocompromising conditions were resolved 78% of the time (Odds ratio (OR) 0.24, 95% CI: 0.11- 0.51, p<0.0001).All 303 patients were included in the safety analysis. There were 2 reported deaths. Both deaths were in patients with solid organ transplants. One patient died 13 days after successful FMT, with death due to progressive pneumonia, while the second patient died 1 day after FMT following aspiration pneumonitis during sedation for colonoscopy. Other reported adverse events include 2 colectomies, 5 episodes of bacteremia or infection, 10 subsequent hospitalizations, 7 otherwise unspecified life-threatening complications, and 7 flares of inflammatory bowel disease. Twenty-eight patients had other complications including abdominal pain, irritable bowel syndrome, nausea, fever, and diverticulitis post-FMT procedure. Mean time to adverse event was 26.6 days from FMT .Twenty of the included 43 case reports/studies had at least 5 patients in the original study population. Only 10 studies showed adequate reporting in all of six essential domains of study quality , with others missing 1 to 3 of these elements or occurred beyond 30 days after FMT , 37. Of Our study has the following strengths. It addresses a very specific population with CD infection that has a higher incidence of CD infection with higher risk of recurrence and would ideally benefit from FMT. In addition, we included only patients who met a standard, predetermined definition of immunosuppression. However, our study has some limitations. We reviewed case reports and series, as there were no RCTs that were identified for inclusion. Inclusion of case reports with possibility of publication bias towards positive results might account for the high success rate after a single FMT. Missing data on demographics, method of stool transplantation, volume and amount of stool, and relationships of donor and recipients were common in our review and were also noted in a similar review by Bafeta et al. . One cliIn conclusion, FMT in immunocompromised appears to have comparable efficacy and safety data to those on patients with intact immunity. However, due to heterogeneity of immunosuppression subtype, no solid conclusion can be made about any single specific immunocompromised states or a combination regarding response to FMT. Further randomized trials including these patient populations would be appropriate."} +{"text": "To determine travelers\u2019 actual and subjective knowledge about risk for Ebola virus disease, we surveyed travelers from France. Actual knowledge did not prevent irrational perceptions or promote safe behavior. Rather, readiness to adopt protective behavior depended on subjective knowledge and overconfidence in ability to self-protect. As for many other infectious diseases anonymously completed a questionnaire about their knowledge and perceptions of risk of acquiring EVD. Respondents reported their sociodemographic characteristics, destination, purpose of travel, date of departure, and date of return. Questions about EVD actual knowledge included preventive measures, transmission routes, epidemic status, affected countries, and presence of EVD in the destination country. We used correct responses to compute final scores . We usedAmong the 189 participants, 25.9% planned to travel to West Africa , 21.7% to other African countries, and 52.4% to other countries worldwide. Only 10.6% were able to correctly report the 3 countries affected by the EVD epidemic , and many were unaware of preventive measures (45%) and modes of Ebola virus transmission (39.1%). The most frequent answers for preventive measures were practice careful hygiene (24.34%), avoid contact with infected persons (23.28%), and wear protective equipment (21.16%). Answers about modes of Ebola virus transmission were body contact (31.22%), body fluids (30.16%), and aerosol . Overall, the actual knowledge about EVD was very low . Simultaneously, subjective knowledge was low performing safe behavior (Additional methods and results for study of travelers\u2019 actual and subjective knowledge about risk for Ebola virus disease."} +{"text": "While physical and mental health comorbidities have been associated with poor asthma control in this population, the potential role of allergen sensitization is unknown. This study examined the association of indoor sensitization and exposure as a risk factor for increased asthma morbidity in WTC workers. We used data from a prospective cohort of 331 WTC workers with asthma. Sensitization to indoor allergens was assessed by measurement of antigen-specific serum immunoglobulin E (IgE) levels. We used validated tools to evaluate the exposure to indoor allergens. Asthma morbidity outcomes included level of control , quality of life and acute resource utilization. The prevalence of sensitization to cat, dog, mouse, dust mite, cockroach, and mold allergens were 33%, 21%, 17%, 40%, 17%, and 17%, respectively. Unadjusted and regression analyses showed no significant relationship between sensitization and increased asthma morbidity ( Multiple studies have documented high rates of asthma prevalence among World Trade Center (WTC) rescue and recovery workers ,2. RecenAllergic sensitization is also associated with increased asthma morbidity, particularly in inner-city children ,6. MoreoIn this study, we determined the rates of sensitization to indoor allergens in a cohort of WTC workers with asthma, and assessed the relationship to asthma control and acute resource utilization.The study was conducted using data from a cohort of WTC workers with a physician diagnosis of asthma. Study participants were recruited between December 2012 and July 2016, from WTC workers who were followed by the Mount Sinai Hospital, North Shore-Long Island Jewish Health System/Queens College, and the New York University School of Medicine WTC Health Program. Criteria for recruitment into this program have been previously published ,13 and iThe current study was limited to patients with physician-diagnosed asthma who spoke English or Spanish and were \u226518 years of age at the time of enrollment. We excluded WTC workers with a prior diagnosis of chronic obstructive lung disease (COPD) and those who had history of >15 pack-years of smoking, due to the possibility of undiagnosed COPD. We also excluded workers with other chronic respiratory illnesses. Signed consent was obtained from all participants; the Institutional Review Boards of the Icahn School of Medicine at Mount Sinai, Queens College and New York University School of Medicine approved this study.Study participants underwent an in-person standardized interview in English or Spanish to collect sociodemographic information and data regarding asthma history, including onset in relation to WTC exposure and medication regimen. We obtained information about physician diagnosis of GERD, allergic rhinitis, and chronic sinusitis, as well as other comorbidities. In order to diagnose the presence of mental health conditions patients underwent a structured clinical psychiatric interview (SCID) . AccordiDermatophagoides Farinae and Dermatophagoides Pteronyssinus), cockroaches (Blatella Germanica or Periplaneta Americana), and molds (Alternaria Alternata and Aspergillus Fumigatus). Serum IgE levels were determined using the Thermo Fisher Scientific Analyzer Phadia\u2122 1000\u00ae . Home environmental exposures were ascertained using survey questions previously validated against findings from home inspections [Sensitization to indoor allergens was assessed using serum IgE levels in peripheral blood; a level >0.35 kU/L was considered indicative of sensitization ,15. The pections ,17,18. TWe used the Asthma Control Questionnaire (ACQ) to assess the level of asthma control . The ACQt-test to compare ACQ and AQLQ scores of WTC workers sensitized versus those not sensitized to each specific indoor allergen. The chi-square test was used to compare acute resource utilization according to sensitization status. The adjusted association between sensitization status, ACQ, and AQLQ scores over time was assessed using linear regression to control for sociodemographic characteristics, asthma history, asthma onset in relation to 9/11 exposure, asthma regimen, WTC exposure level, and comorbidities. The potential relationship of acute resource utilization with sensitization to each allergen was evaluated using logistic regression analysis.The means with standard deviations and percentages with 95% confidence intervals (CI) were used to describe the baseline characteristics of the study participants. We used the Power calculations showed that a total of approximately 220 patients were required for the study to have 80% power to detect a clinically significance difference of \u22650.5 units in ACQ and AQLQ scores among patients sensitized versus not sensitized to each indoor allergen. All statistical tests were performed with SAS statistical software using 2-tailed tests.Overall, 373 WTC workers with asthma were enrolled in the study; of these, 42 lacked results for specific IgE and were excluded from these analyses. The mean (SD) age of study participants was 52.7 (8) years; 73% were male; 35% white, 13% Black, and 43% Hispanic . Most WTDermatophagoides Farinae, Dermatophagoides Pteronyssines, cockroach, Alternaria Tenuis, and Aspergillus Fumigatus was 33% (95% CI: 28\u201338%), 21% (95% CI: 17\u201326%), 17% (95% CI: 13\u201322%), 34% (95% CI: 30\u201340%), 32% (95% CI: 26\u201337%), 17% (95% CI: 13\u201321%), 11% (95% CI: 7\u201314%), and 10% (95% CI: 6\u201315%), respectively. Overall, 50% of participants had cats, dogs, or birds at home, 17% reported presence of mice/rats at home, 24% had observed cockroaches, 20% observed wet spots, 25% had mold/mildew at their home, and only 34% kept windows closed during the allergy season.Overall, 56% (95% CI: 51\u201362%) of WTC workers were sensitized to at least one indoor allergen . The frep > 0.05 for all comparisons) . However, sensitization to mouse epithelium was associated with a decreased use of oral corticoids in the year before enrollment. We also found that acute asthma-related resource utilization was lower in patients sensitized to at least one allergen . Unadjusted analyses also showed no significant interaction between allergen sensitization and WTC exposure category , suggesting the effect of sensitization was not different according to the level of exposure at the WTC site.Unadjusted analyses showed no significant association between sensitization to most indoor allergen and ACQ and AQLQ scores (arisons) . Only sep > 0.05 for all comparisons) . HoweverAsthma is a common WTC-related condition that is frequently poorly controlled and associated with substantial healthcare resource utilization . In thisAlternaria [There is strong epidemiologic evidence linking allergen sensitization to increased asthma morbidity in inner-city children ,6,24,25.ternaria , have beternaria . Similarternaria . A studyternaria . Similarternaria . Conversternaria . The Eurternaria . Our stuSeveral factors may explain our findings. WTC-related asthma may be associated with a higher prevalence of airway neutrophilia . Asthma Many WTC workers have physical and/or mental health comorbidities known to increase asthma morbidity. These include GERD, chronic sinusitis, and rhinitis, as well as, PTSD, and major depression ,3,4. ThuGiven the relatively high rate of allergen sensitization in our population of WTC workers with asthma, avoidance of environmental triggers could still contribute to improved control in some of these patients, particularly those with features of eosinophilic disease. However, our findings suggest that healthcare providers should also focus on other important asthma triggers in this population, such as other medical comorbidities and occupational exposures.Dermatophagoides Pteronyssines and cockroach) with markers of decreased asthma morbidity. We used objective measures of allergen sensitization and validated cut-offs, however, we did not collect home samples to assess the actual levels of environmental exposure. Although self-reported measures may be subject to bias, we used validated items that have been correlated to direct home environmental assessments [Our study has some limitations that should be mentioned. Our data were collected between 11 and 15 years of the WTC exposure, and therefore our findings represent a narrow window in time. Despite enrolling a relatively large number of WTC workers, our cohort did not represent all populations exposed to WTC disaster, such as firefighters, local residents, and passersby. Thus, our results may not be generalizable to these groups. Our study did not include a non-WTC asthma control group to assess for potential differences in the role and the impact of allergen sensitization. WTC rescue and recovery workers are a unique population given their exposures at the WTC site, range of occupations and associated exposures prior and after 9/11, healthy worker effect, and a high prevalence of physical and mental health comorbidities, many of which are associated with worse asthma control. Thus, it is very difficult to identify a control group to perform robust comparisons of the relationship between allergic sensitization and asthma morbidity in WTC versus no-WTC populations. However, in a prior study of non-WTC asthma patients recruited from the same institution [essments ,21,22. Sessments . We founIn summary, we found no significant associations between indoor allergen sensitization and exposure to asthma morbidity in WTC workers. Given the high rates of the absence of asthma control and decreased quality of life in this population, our findings can guide providers in their management strategies for WTC workers with asthma."} +{"text": "The objective of this research was to determine the effects of growth media containing FA and FA mixed with soil on selected crop plants seedlings growth. We studied the influence of various FA concentrations in FA/soil composed media on the germination, growth, and heavy metals uptake of the following plants: barley, Sudan grass, ryegrass, rape, alfalfa, and canola. Plants were grown on Petri dishes for 14\u201321 days, harvested, dried, and weighed. Experiments have been replicated three times. The concentrations of Al, B, Ba, Co, Cr, Cu, Mo, Sr, Ti, Tl, and V in growth media were determined, and the concentrations of the same elements in young plants were analyzed. Addition of 10, 20, and 30% of FA to the soil were acceptable for most plants, as compared to FA alone used as a growth media. Barley was the only plant of plants used in our research, which was able to sustain seedlings growth on media consisting on FA alone. Preliminary results of chemical analysis of FA and harvested young plants implicate that plants do not accumulate toxic amounts of heavy metals even being grown on media containing 100% FA. Our research results indicate that coal FA might be used as a plant growth media additive. However, additional studies should be undertaken to determine the effects of FA on plants grown till maturity. Fly ash (FA) is a byproduct from burning pulverized coal in electric power generating plants . During A vegetative cover is a remedial technique to stabilize coal fly ash (FA) landfills, and to physically and chemically immobilize heavy metals present in FA. . HoweverThe use of fly ash as an amendment to agricultural soils has been investigated to explore its effects on crop growth and production .Many herbaceous plants, primarily grasses which exhibit rapid growth, are moderately resistant to environmental stress, and are therefore often used as cover crops in environmental restoration and remediation projects . HoweverCoal fly ash, used as soil amendment, or on a soil-covered fly ash landfills, can be very effective as a provider of certain essential nutrients to plants, such as B, Mg, Mo, S, and Zn . HoweverWe hypothesized that selected plants will grow on media containing FA and/or soil mixed with FA. The objective of this experiment was to study the influence of various FA concentrations in FA/soil composed media on the germination, growth, and uptake of heavy metals by several plant species.(Hordeum vulgare), Sudan grass (Sorghum bicolor), canola (Brasica campestris), rapeseed (Brassica napus), alfalfa (Medicago sativa), and perennial ryegrass (Lolium perenne).Coal FA from Montana semi-bituminous coal alone or in combinations of different soil/FA ratios have been tested as plant growth media for the following plant species: barley Adaptation of plants to coal ash based media have been presented with regard to seedlings growth, heavy metals presence in the media and accumulation of heavy metals by young plants.Plant growth media composition:90% NDSU Ash 10% Soil (90ND 10Soil)80% NDSU Ash, 20% Soil (80ND 20S)70% NDSU Ash, 30% Soil (70ND 30S)60% NDSU ASH, 40% Soil (60ND 40S)50% NDSU Ash, 50% Soil (50ND 50S)40% NDSU Ash, 60% Soil (40ND 60S)30% NDSU Ash, 70% Soil (30ND 70S)20% NDSU Ash, 80% Soil (20ND 80S)10% NDSU Ash, 90% Soil (10ND 90S)The controls of 100% Soil (100Soil), and 100% NDSU FA (100ND)Plants were grown on Petri dishes (3 replications for each plant and treatment) for 14\u201321 days, harvested, dried, and weighed. The number of seeds planted per Petri dish depended on seed size.Plant growth media were watered to the level of becoming fully-moist, but without excess standing water .After two to three weeks of growing, plants were cut at growth media level.All plants were measured, the envelopes were labeled, and the plant material was placed inside the envelopes.Samples were then placed into the oven to dry, and after two weeks the dry plant material was weighed.The dry and weighed samples were treated through an acid digestion process.The samples were then put through an inductively coupled plasma (ICP) emission spectrophotometry to determine the presence and concentration of selected elements. The concentrations of Al, As, B, Ba, Be, Cd, Co, Cr, Cu, Mo, Sr, Ti, Tl, and V in growth media have been determined, and the concentrations of the same elements in young plants have be analyzed.Effects of growth media containing different concentration of FA in soil on plant germination and weight are presented in All plants were able to germinate on growth media containing up to 40% of FA in growth media. Such concentration of FA in the media, despite still supporting germination, reduced the level of germination of all plants significantly, as compared to the control. Barley and Sudan grass expressed the lowest level of this reduction. The concentrations of FA in growth media higher than 40% were not able to sustain growth seedlings after initial germination, except for barley and Sudan grass.Barley and Sudan grass showed not only the greatest germination but also the highest seedlings weight of all tested species, despite being grown in harsh conditions, with gradually growing concentrations of FA in the media. Barley seems to be the most adaptable to the growth on FA of all plant used in our study. Barley was the only plant of plants used in our research, which was able to sustain seedlings growth on media consisting on FA alone.Ryegrass and alfalfa had the poorest growth on media containing FA.\u00a0The concentration of aluminum (Al) in all plant growth media didn\u2019t exceed the concentrations found in some American soils . DespiteThe concentration of arsenic (As) in plants was below the detection limits, despite relatively high concentration of As in FA used as growth media (up to 64 mg/kg). Such concentration meets the standards for considering plant growth media as phytotoxic .The concentration of boron (B) in all growth media containing FA reached 1230 mg/kg in FA and exceeded several times values expected to be present in the soil is found in most soils at concentrations ranging from about 15 to 3,500 mg/kg and mean values ranging between 265 and 835 mg/kg, depending on soil type (ATSDR 2007). Barium in our soil, control treatment reached the level of 1900 mg/kg, and was within acceptable limits for soils. Barium in our FA only slightly exceeded acceptable limits for soils. The concentration of Ba in plant seedlings, although strongly related to the concentration in growth media, remained within toxicologically acceptable limits.The average concentration of cobalt (Co) in soil in the United States is 7.2 mg/kg, with a range of 1\u201340 mg/kg . The conIn most soils, chromium (Cr) occurs in low concentrations (2 \u2013 60 mg/kg) and in our studies not only Cr concentration in the soil, but also in all but one FA based plant growth media Cr concentration remained within these limits .Although plant growth media supplemented with FA contained elevated amounts of copper (Cu), as compared to the soil, it didn\u2019t result in elevated concentration of Cu in plant tissues. The concentration of Cu remained almost unchanged and within average values for Cu concentration in plants .High concentration of molybdenum (Mo) is generally associated with alkaline soils. Molybdenum concentration up to 50 mg/kg dry weight has been found in agricultural soils . AlthougStrontium (Sr) is found naturally in soil in amounts that vary over a wide range, but the typical concentration is 250 mg/kg. The concentration of Sr in FA may vary depending on FA source and be as low as < 1mg/kg and as high as 3,900 mg/kg . In our Heavy clay soils, like the soil used in our experiment (Fargo clay) contain more titanium (Ti) than sandy soils , and theThe vanadium (V) content if soils is related to those of the parent rocks from which they are formed and range from 3 to 310 mg/kg . The conThe concentration of As, Be, Cd, Pb, and Tl in plants were below ICP detection limits.The additions of 10, 20, and 30 % of FA to the soil supported plant germination and growth.Preliminary results of chemical analysis of FA and harvested young plants implicate that plants do not accumulate toxic amounts of heavy metals, even grown on media containing 100% FA.These results indicate that coal FA might be used as a plant growth media supplement.Additional studies should be undertaken to better understand the effects of FA on plant growth from germination to maturity.Barley and Sudan grass expressed the highest phyto-remediatory potential for coal FA.Using our studies, application of different plant species for the revegetation of coal ash piles might be discussed."} +{"text": "The US Epidemiologic data show that past-year marijuana use rates among the 50+ age group rose more than 300% between 2002 and 2017. In 2017, 10.2% of those aged 50-64 years and 3.7% of those aged 65+ years were past-year users, and 15% of these users reported all or part of their use to have been for medical purposes. In this symposium, using findings from previous research and recent epidemiologic data, we will present both positive and adverse effects of late-life marijuana use. Marijuana may be useful for the treatment of pain (particularly neuropathic pain) and chemotherapy-induced nausea and vomiting. However, older marijuana users are often long-term users and significant proportions suffer from marijuana use disorder along with other substance use and/or mental disorders. Adverse effects also include dizziness, confusion, impairments in memory and attention, somnolence, and hallucinations, which may outweigh purported positive effects."} +{"text": "Reaching the Joint United Nations Programme on HIV/AIDS (UNAIDS) 90-90-90 targets to end the HIV epidemic relies on effective interventions that engage untested HIV+ individuals and retain them in care. Evidence on community-based interventions through the lens of the targets has not yet been synthesized, reflecting a knowledge gap. We conducted a systematic review and meta-analysis to shed light on successful community-based interventions that have been effective in contributing, directly or indirectly, towards the UNAIDS 90-90-90 targets: knowledge of HIV status, linkage to care/on treatment, and viral suppression. Linkage to care was also included in this review due to the limitations of studies.We conducted a systematic review and meta-analysis of the period 2007\u20132018. Eleven databases were searched to identify community-based interventions designed to improve knowledge of HIV status (in particular HIV testing), linkage to care/on treatment, and/or viral suppression. Eligible studies were classified by intervention, population, country income level, outcomes and success. Success was defined as interventions demonstrating statistical significance between intervention and control group or that reached any target by proportion; 90% testing, 81% linked to care/on treatment and 73% viral suppression.Of 82 eligible studies, 51.2% (42/82) reported on HIV testing (first 90), 20.7% (17/82) on linkage to care/ on treatment (second 90), and 45.1% (37/82) on viral suppression (third 90). In all, 67.1% (55/82) of studies reported success; 21 studies on the first 90, 9 towards linkage to care/on treatment, and 25 towards the third. By strategies, 36.6% deployed community workers/peers, 22% used combined test and treat strategies, 12.2% used educational methods, 8.5% used mobile testing, 7.3% used campaigns and 13.4% used technology. For HIV testing/linkage, combined test/treat interventions were often used, for viral suppression, educational interventions and technologies were commonly deployed. Our pooled analysis suggested that deployment of community health care workers/peer workers significantly improved viral suppression (pooled OR: 1.40 95% CI 1.06\u20131.86). Of the studies published after 2014, 50.0% reported metrics aligned with UNAIDS targets.Data on linkage to care/on treatment (second target) remained weak, because many studies reported successes on the first and third targets. Stratification by targets and country income levels is informative and guides adaptation of successful interventions in comparable settings. Consistent reporting of clear metrics aligned with UNAIDS targets will aid in synergy of study data with programmatic data that will help reportage. Exploration of innovative interventions, for engagement and linkage and deployment of community/ peer workers is strongly encouraged. HIV/AIDS continues to be a public health concern worldwide; over 70 million people have been infected with HIV and close to 35 million people have died as a result since the beginning of the epidemic. As of June 2017, about 37 million were living with HIV, with about 20.9 million [18.4 million\u201321.7 million] accessing antiretroviral therapy .According to the 2017 Global AIDS Update, many countries are making significant progress towards the 90-90-90 targets; some countries have reached all three targets, and many are close to reaching them . A synthCountries such as Botswana and Australia, both with very different economic backgrounds have each shown that it is possible to reach some of the targets by way of concerted efforts, when resources are less readily available , 9. ClosCommunity-based interventions have become increasingly popular, with reported decreases in HIV-related mortality, virologic failure, and other adverse health outcomes \u201313. DeceAlthough evidence on community-based initiatives has been synthesized prior to the announcement of the 90-90-90 targets, an updated, comprehensive review of community initiatives and outcomes, aligned to the UNAIDS targets was not available, precipitating a gap in understanding progress towards the targets , 18, 19.The primary objective of this systematic review and meta-analysis is to shed light on successful community-based interventions that have been effective in contributing towards the UNAIDS 90-90-90 targets, stratifying by intervention type and country income level. We also set out to determine if reporting of outcomes and/or metrics before and after the 2014 announcement of the UNAIDS targets were consistent and in line with the care continuum. With 2020 around the corner, it is vital that concise information regarding successful interventions be accessible to researchers, stakeholders and policymakers.The Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) and Cochrane guidelines were followed in reporting this review 20]..20].This review is unregistered.We searched eight databases for the period 2007\u20132018; MEDLINE via PubMed, OVID, BIOSIS, LILACS, CINAHL, Cochrane DARE, Embase and Global Index Medicus, and three conferences .The search strategy for PubMed was (\"hiv\"[MeSH Terms] OR \"hiv\"[All Fields]) OR (\"acquired immunodeficiency syndrome\"[MeSH Terms] OR (\"acquired\"[All Fields] AND \"immunodeficiency\"[All Fields] AND \"syndrome\"[All Fields]) OR \"acquired immunodeficiency syndrome\"[All Fields] OR \"aids\"[All Fields]) AND (UNAIDS[All Fields] AND/OR 90-90-90[All Fields] AND (\u201cyouth AND/OR \u201cadults\u201d) AND \u201cviral load\u201d).All experimental trials and observational studies were included. In order to be included for the review, studies had to report on any or all of the UANIDS 90-90-90 targets/outcomes, that is; knowledge of HIV status by means of HIV testing, linkage to and/or retention in treatment, or virologic suppression/ART adherence. Modelling studies, as well as reviews, narratives, trial protocols and studies that were in a language other than English were excluded. Bibliographies of chosen articles were further scanned for additional articles.Three reviewers conducted data selection and abstraction. Quality assessment was conducted by two reviewers (SD and AK).A pre-designed abstraction table was used to collect information on author, study design, study population, sample size, intervention description, HIV outcome measure, and metrics used to measure reported outcomes pertaining to 90-90-90 targets. Interventions were categorized based on country income level into high, upper middle, lower middle and low-income countries , and by type of intervention (1) Community health workers (including lay workers/peers); 2) Educational; 3) Integrated or Combined services; 4) Mobile Testing units (e.g. mobile vans); 5) Campaigns; and 6) Technology). Success was defined as reaching the proportions in either of the targets, i.e. 90%, 81%, and 73% for HIV testing, linkage to care/on treatment and viral suppression, respectfully. If statistical significance was reached between intervention and control group, it was deemed a successful intervention as well.The outcomes that capture UNAIDS 90-90-90 targets were: 1) HIV testing, 2) Linkage to care/on treatment, and 3) Viral suppression. Pooled analysis was performed for outcomes that were consistently documented among similar interventions. A random effect meta-analysis model was used to determine pooled estimate. Forest plots were made for visual representation of heterogeneity and pooled OR with 95% CI. We performed all statistical analyses using Stata/IC, V.12.Knowledge of HIV status was defined as any method of diagnosing/screening HIV, in particular HIV testing. Linkage to care/on treatment was defined as any way of linking recently diagnosed HIV+ patients to healthcare services and/or initiated on ART within a reasonable time from diagnosis. Linkage to care was included as a metric towards the second 90 subject to the limitations of different studies and variations in definitions. Viral suppression was defined as having viral levels <1000 copies/mL, or as defined by the individual studies themselves; in some cases ART adherence was a reported outcome, this was used as a precursor to viral suppression, the rationale being that sustained ART adherence will result in viral suppression.Targets were reported by metrics that varied across studies, were heterogeneous and inconsistent. Metrics varied from number of HIV tests conducted, attendance rate, linkage to care, ART adherence, pill count, viral load, CD4 count and self reported outcomes. Acceptability was defined as the willingness of participants to use community-based interventions. Feasibility was defined as the convenience of implementing such interventions. The lack of consistent reporting of outcomes and/or study design precluded pooling of measures for the majority of studies and therefore pooling was only performed where possible.Quality was assessed using the Cochrane Risk of Bias Tools and the Newcastle-Ottawa quality assessment scale, for clinical trials and observational studies respectively.Over 5000 studies were identified through the search, out of which 82 studies met our eligibility criteria .By WHO geographical location, 25.6% (21/82) of the studies were conducted in the Americas, 3.6% (3/82) in Europe, 3.6% (3/82) in the Western Pacific region, 6.1% (5/82) in the South East Asia region and 68.3% (56/82) in the African region. Classified by country income level, 26.8% (22/82) of the studies were conducted in high income countries, 25.6% (21/82) were from upper middle-income countries, 30.5% (25/82) were from lower middle-income countries and 24.3% (20/82) were conducted in low-income countries. Some studies had multiple locations varying by regions and country, thus contributing to percentages over 100%.Randomised controlled trials, comprised 29.3% (24/82) of the studies, followed by 24.3% (20/82) of cross-sectional studies and 14.6% (12/82) of feasibility studies. Quasi-experimental and cohort/case control studies were also noted. Overall by UNAIDS targets, a vast proportion of studies, (42), had interventions that targeted the first 90, while 17 studies targeted the second 90, and 37 studies targeted the third 90. A little over half ) of the studies were published after the announcement of the UNAIDS targets, out of these 50.0% (23/46) reported according to metrics aligned with the UNAIDS targets. The other 50.0% reported using metrics such as self-reporting of outcomes, first-time testers, CD4 counts or other metrics not directly aligned with the indicator measures for the UNAIDS 90-90-90 targets. This is an improvement in reporting of outcomes aligned to UNAIDS targets as only 33% of studies pre-90-90-90 announcement reported outcomes according to the targets.A summary of all included studies can be found in the Out of the 82 studies, 51.2% (42/82) documented HIV testing. This included any intervention that increased HIV testing uptake. Of the 42 studies, 21 (50%) were deemed successful based on statistical significance compared to a comparator group, or whether they reported proportions of testers reaching 90% (\u00b110%) or higher based on the first UNAIDS 90-90-90 targets.Of the 21 studies reporting positive results, 9 (42.9%) made use of link workers/community health workers, lay workers or peers to increase testing uptake. In middle income countries such as those in Southern Africa, India as well as in low income countries, successful interventions employed community health workers to conduct home-based HIV testing. In some cases couple-based HIV testing and counselling was used over individual based HIV testing and counselling . CombinaFive studies were acceptability or feasibility studies, of which three were highly acceptable interventions; integrated HIV testing in ANC settings, a national radio program that increased HIV knowledge and school based HIV testing and counselling \u201344. One Linkage to care was included and defined as those linked to HIV services , the reason for this being that smaller scale intervention studies do not directly quantify the second 90 due to study limitations and differences in definitions.Nine studies (52.9%) studies were deemed successful by either reaching statistical significance or reaching 81% by proportion linked to care/on treatment. Five studies used link workers/community health workers or lay workers, these were more common in middle income countries. A home-based HIV counselling and testing (HBHCT) initiative directed towards families of HIV positive patients in South Africa yielded 93.7% of those diagnosed HIV+ through this methods, another study also looking at HBHCT in South Africa demonstrated 76% were linked to care; another community-based health and social service centre in USA, provided support to youth regarding HIV and other STIs, reported 80.% of youth diagnosed with HIV met with a case manager to initiate care , 47, 48.A combination of interventions such as loud speakers, flyers and campaigns, treatment in antenatal care settings and test and treat strategies , 49, 50 ART adherence was defined as those adhering to ART to achieve viral suppression. Various metrics used for this target were CD4 counts, viral suppression, pill counts or self reported adherence, as these sustained behavioural changes would result in the clinical outcome of viral suppression.Twenty five studies were deemed successful, in reaching 73% adherence/suppression by proportion, within the study population. Of the 25 studies, eleven, (44%) utilized community health workers, lay workers or other forms of people (e.g peers/family) for treatment assistance. This was particularly popular in middle and low income countries compared to high income countries. Studies conducted in South Africa, Kenya, Mozambique and Peru specifically used Directly Observed Therapy (DOT), via a community worker/lay worker, a peer or even a partner, to ensure patients took ARTs and demonstrated sustained viral suppression. Other studies used community health workers, lay workers or other forms of people (e.g peers/family) to send reminders to take medication , 51\u201359.Five (20%) used a combination of interventions to target any or all of the cascade of care with the end goal of viral suppression; one study integrated food security alongside ART services, another provided incentives paid to community health centres on a per person basis in care, while others combined the use of adherence diaries, group education, counselling etc to ensure viral suppression. These were all studies conducted in middle or low income countries, with the exception of one conducted in China (which involved the cash on delivery model) , 60\u201363.Four studies (16%) involved educational sessions . All the educational-related successful interventions were conducted in middle and low income countries \u201367; fiveFor outcomes that were consistently documented, we performed a pooled analysis. The pooled estimate for the impact of community health care workers/lay workers or peers on viral suppression monitored via viral loads was 1.40 [95% CI 1.06\u20131.86] .Among the randomised control trials , while aOverall, a vast majority of the studies were observational, in particular, confounding, selection of participants and information bias were of concern. Such biases need to be minimised when determining the true effect of any intervention .Our systematic review aimed to collate community-based interventions that were successful in reaching the UNAIDS 90-90-90 targets. By categorizing interventions based on success, intervention type and stratifying by country income level, our aim was to provide information on interventions that are successful in contributing towards the UNAIDS 90-90-90 targets, such that researchers, policymakers can find value in and potentially implement modified interventions and policy changes that could work in comparable settings. The results of our review are aligned to previous reviews , 18, 19 Overall, data on the first and third 90 were strong, while data on the second 90 requires work. A greater number of initiatives focused on the first target, compared to targets 2 and 3 . According to the UNAIDS report, a greater focus on linkages was needed, and this seen in our review . In partCommunity-based interventions demonstrated success when their implementations were tailored to country or community context. For example, in a country or community where multiple concurrent partners were common, the couples voluntary HIV counselling and testing was not an ideal way to increase test uptake . IntegraFor the first 90, across all income levels, decentralized testing initiatives like mobile testing and home-based HIV testing and counselling services were able to reach vulnerable populations that may not have presented themselves to healthcare facilities for testing. Testing initiatives by members of a community and those familiar to the patients resulted in a much higher uptake of testing; this was especially true in middle and lower income countries \u201327, 74. For the second 90 (linkage to care/on treatment), community health workers/lay workers were most successful in facilitating linkages to care. Of nine studies, three did not show a positive effect with linkages to care; 2 studies reached targets for HIV testing, yet linkage to care/initiation of ART lagged, even with community HIV care providers , 26. ComDespite the WHO\u2019s recommendation on the implementation of ART for all HIV-infected people regardless of CD4 count, many lower income countries face limitations , that impedes success towards the second 90 . While tRegarding the third 90, nuanced evidence in support of the integration of linkage to care services with micro-clinics and informal social networks which are normally used for the management and prevention of chronic disease, can increase linkages and subsequent viral suppression . Task shDigital technology has become a prominent intervention in increasing ART adherence; this includes daily text messages, beepers and alarm devices that remind patients to take medications. Three studies (37.5%) using digital technology did not show positive outcomes. Nonetheless, the use of technology to improve ART adherence and viral suppression is a good alternative to the use of community health workers where patients may feel their autonomy is violated.Text message-based programs in low and middle-income populations with high rates of mobile phone usage may improve test uptake, treatment adherence rates, and increase viral suppression, but frequency of text messages heavily influences adherence levels . FurtherIn summary, using the UNAIDS 90-90-90 targets as a framework creates momentum in our populations to reach the goals, furthermore, if studies reported according to the targets, using the metrics most commonly used, direct comparisons of intervention effectiveness can be made.This systematic review provides condensed information regarding interventions successful towards each of the 90-90-90 targets within income levels and by UNAIDS targets. Strategies must be multifaceted and designed to recognize the social context of the population in question. The decentralization of testing to familiar, comfortable and non-clinical settings using peer support and community workers has been demonstrated to improve testing uptake and linkage to care rates in key populations, such as men who have sex with men, female sex workers, and injection drug users.Direct comparisons of interventions and their ability to reach the UNAIDS targets is difficult given inconsistent reporting. Metrics used to measure HIV testing, linkage to care and viral suppression must be streamlined and effectively used across interventions looking at these outcomes such that we can make direct comparisons of the effectiveness of interventions and inform the scale up of them.We have shown that reporting outcomes post 2014 will need to continue to follow the UNAIDS targets as these targets are aligned to the HIV care continuum, which will ultimately help us compare interventions and determine success.This review is unique in its framing of outcomes aligned to UNAIDS 90-90-90 targets globally , 18, 19.As with all systematic reviews, our study has limitations. Although an exhaustive literature search was carried out, by also including hand searched articles, our search strategy may have missed some articles and interventions. Furthermore, majority of the studies were observational and at high risk of various bias such as confounding and selection bias, thus decreasing our confidence in reported intervention effects. Additionally, due to the limited number of studies included in the meta-analysis, the potential risk of publication bias could not be assessed. A fewer number of studies results in a lower power of the tests to distinguish chance from real symmetry . DespiteDespite these limitations, this review draws strength from including over 80 studies, representing different interventions, populations and regions, that focused on various aspects of the UNAIDS targets, and also focused on other interventions that can help meet those targets directly or indirectly.Use of community health care/peer workers is strongly recommended. Exploration of innovative interventions for linkage to care and to engage first time testers is encouraged. Besides, reporting of studies aligned with UNAIDS targets is recommended. Stratification by targets and country income levels is informative, and guides adaptation of successful interventions in comparable socio-economic settings. Consistent reporting of clear metrics aligned to UNAIDS targets is vital to informing policy initiatives. Finally, with 2020 fast approaching, resources need to be targeted to achieve the ambitious UNAIDS targets. Including reporting of studies by UNAIDS targets simplifies policy comparisons and determination of success towards the targets. This in turn could potentially catalyze greater progress towards the UNAIDS 90-90-90 targets.S1 Checklist(DOC)Click here for additional data file.S1 Table(DOCX)Click here for additional data file."} +{"text": "Heart failure and dementia are common age-related conditions. Heart failure and associated comorbidities of hypertension and arrhythmias may impact cognition. Retrospective data of 311 patients averaging 98 (\u00b13.2) years who received treatment at the University of Arkansas for Medical Sciences were analyzed for diagnoses, prescribed medications and health conditions relevant to heart failure, hypertension, arrhythmias and dementia. 74% of the subjects were white, non-Hispanic, 24% were African American, and 2% were of unknown ethnicity. 83% were women and 17% were men. Only 251 (81%) of the reviewed charts had blood pressures recorded, of whom 43% (n=114) had systolic pressures >140mmHg. Furthermore, 50% (n=156) of patients had heart failure, and 29% (n=89) had dementia. Of those with dementia, 35% had an arrhythmia. For those without a diagnosis of dementia or any treatment for dementia, 25% had an arrhythmia. Heart failure and arrhythmias have not been well studied as an etiological factor for dementias. In our cohort, the presence of heart failure diagnoses was not different in those with dementia versus those without dementia. However, more patients with dementia had arrhythmias versus those without dementia, suggesting that arrhythmias may contribute to cognitive decline, even in the oldest old. Approximately 70% of the arrhythmias were atrial fibrillation. We did not have data on the management of these arrhythmias and whether anticoagulants were being used appropriately, especially for atrial fibrillation. Nevertheless this highlights the importance of close management of arrhythmias for maintaining cognitive health in older adults."} +{"text": "This study was carried out to evaluate the epidemiological studies of trichinellosis in five states of North East India from Apr 2016 to Dec 2017.Trichinella larvae and 1580 sera samples for detection of anti-Trichinella antibody were collected. Intensity of infection with Trichinella larvae in meat was determined by HCL: Pepsin digestion procedure and anti-Trichinella IgG in serum were detected using excretory/secretory antigens, according to validated ELISA.Overall, 865 different meat samples for detection of Trichinella larva was detected by HCL: Pepsin digestion method. However, four (0.25%) samples were seropositive for Trichinella IgG and four inconclusive results as per cut off value. The highest seroprevalence was observed in Meghalaya (0.41%) followed by Assam (0.27%) whereas no seropositive cases were recorded in Arunachal Pradesh, Mizoram and Tripura.No Trichinellosis is common in North East, India. However, it is suspected in communities where more than 75% of the population relish pork. Finally, there is a need for more research to establish the facts of trichinellosis in this region. Thus, public awareness, food hygiene, monitoring, and surveillance programme are suggested to implement for prevention of trichinellosis in this region. Trichinellosis is a zoonotic disease caused by nematode worms of the genus Trichinella , diaphragm , tongue and filet (musculus longissimus dorsi) for detection of Tripura . The bloTrichinella spp. larvae in meat were determined by pepsin digestion procedure as per OIE recommendation . No TricTrichinella. Overall seroprevalence was 0.25% and four inconclusive results as per cut off value antigen-based indirect ELISA has been reported to vary from 90.6% to 99.6% followed by Assam (0.27%). Findings of this study were different than that of the previous study where 38 pig serum samples were collected from Assam but none of the samples were found positive for 1% followMany authors have used indirect ELISA for estimating sero-prevalence of trichinellosis , 25. TheTrichinella spp. have revealed prevalence rate ranging from 0.4%\u20130.6% (Previous studies indicate a low prevalence of swine trichinellosis in India. Studies conducted on slaughtered pig carcasses to isolate .4%\u20130.6% , 19. The.4%\u20130.6% , 29. In .4%\u20130.6% . Similar.4%\u20130.6% .The parasite is still a health and food safety problem for countries worldwide . As per Human trichinellosis outbreaks following consumption of raw or undercooked wild boar meat were reported from the Uttarakhand state of India, where 11 deaths occurred from 70-suspected cases . EpidemiThis study will be useful to cover the missing epidemiologic gaps related to porcine trichinellosis in North East India where more than 75% population relish pork as a protein supplement in cheaper rate. Trichinellosis remains a rare zoonosis in North East India. However, we recommend strict monitoring and surveillance programme to generate scientific baseline data to support pig industry of this region. Furthermore, this research will also help in capacity building workshop for detection of trichinellosis in large pig consumer. Widespread studies must be carried out in wild animals like walrus, bear, deer, wild hog, etc. to recognize the reservoir hosts in this part of the country."} +{"text": "This study aims to identify the coverage rates for influenza vaccination and related factors depending on chronic disease in Korean adults aged 50 and older.The 2016 Korea Community Health Survey was used for analysis. Chi-square test was performed to investigate the coverage rates for influenza vaccination depending on chronic disease, and a multiple logistic regression analysis was used to identify the factors associated with influenza vaccination, by chronic disease.In men with \u22651 chronic disease, 39.8% of 50-64 years of age, and 86.8% of elderly (over 65 years of age) received influenza vaccination. In women with \u22651 chronic disease, 58.7% of 50-64 years of age, and 89.9% of elderly (over 65 years of age) received influenza vaccination (p<0.001). The chronic diseases associated with influenza vaccination were hypertension , diabetes in men aged 50-64, hypertension , diabetes , chronic cardiovascular disease in elderly (over 65 years of age). In women aged 50-64, hypertension , diabetes , chronic cardiovascular disease , and hypertension , diabetes in elderly (over 65 years of age).Populations in aged 50-64 are recommendation subject for vaccination or classified as high-risk group in case with chronic disease. Though subject over 60 years old is age close to the elderly, the coverage rates for vaccination was low. It is necessary to devise strategies to raise the coverage rates for vaccination. Influenza is an acute respiratory disease caused by influenza virus infection. Elderly persons and patients with chronic diseases are defined as a high-risk group as they are at high adult, Korea Community Health Survey (KCHS), Korea risk of contracting influenza or complications. The high-risk group is at high-risk of complications such as pneumonia. Some patients require hospitalization and intensive care due to severe complications and die in some cases .According to the Korea\u2019s National Health Insurance Service data 2015), there were 5,293 patients aged 65 years or older, 5,453 patients aged 50-64 years, and 6,412 patients aged 30-40, who were seasonal influenza; the number of patients hospitalized for influenza increased as age decreased [015, therVaccination is the most effective method to prevent influenza. The effect of vaccination varies by age and underlying disease. Vaccination is 70-90% effective in healthy adults, 50-60% effective for elderly patients who are hospitalized for influenza, and 80% in preventing death [In the US, the coverage rates of vaccination was 63.4% for persons aged 65 years or older and 43.6% for those aged 50-60 years. In Korea, the rate of vaccination was 81.7% for those aged 65 years or older and 28.4% for those aged 50-64 years -11. The Healthy People 2020 of the US aims to raise the rate of influenza vaccination among elderly persons aged 65 years or older and patients with chronic diseases, who are classified as high-risk groups, to 90%. Korea aims to raise the vaccination rate among elderly persons aged 65 years or older to 82% but has not clarified the target vaccination rate for patients with chronic diseases who are classified as high-risk groups. Previous studies have reported low vaccination rates among patients with chronic diseases ,13.This study was conducted to investigate the rate of influenza vaccination in patients with chronic diseases who were aged 50-64 years in 2016 and to identify the factors that affect the actual vaccination rate to ultimately obtain basic research materials for increasing the vaccination rate among persons aged 50-64 years.The original data of the 2016 KCHS were used. 56,917 men and 73,693 women who responded to an influenza vaccination questionnaire were included .In this study, the dependent variables were the variables of influenza vaccination. Persons who were vaccinated were defined as \u201cyes\u201d, and those who were not were defined as \u201cno\u201d.The socioeconomic factors of the independent variables included gender, age, city and province, family income, education level, occupation type and marital status. The variables of health behaviors included smoking, drinking, walking, and subjective health status. Chronic diseases included hypertension, diabetes, myocardial infarction or angina, and stroke. Since all chronic diseases except for hypertension were associated with a high-risk of severe influenza or complications, patients with these chronic diseases were defined as high-risk groups . For useThe KCHS data are complex sample data. Weighted values, strata, and clusters were included in each stage of analysis and analyzed using a SURVEY procedure.A chi-square test was performed to investigate significant differences in the socioeconomic factors, health behavior factors, chronic disease status, use of medical services, and influenza vaccination among the subjects. A multiple logistic regression analysis was performed to investigate the factors that affect the influenza vaccination coverage rate among subjects aged 50 years or older. Regions were divided into province, metropolis, medium cities and rural areas, and the coverage rate of influenza vaccination in subjects aged 50 years or older was investigated according to whether or not the subjects had at least one chronic disease.Data were analyzed using SAS version 9.4 .Vaccination coverage rates by age were 23.2% for men aged 50-54 years, 31.3% for women aged 50-54 years, 76.9% for men aged 65-69 years, and 83.3% for women aged 65-69 years . The higRegarding vaccination coverage rates among subjects aged 50-64 years and those aged 65 years or older, the vaccination coverage rate was 30.5% for men aged 50-64 years, 43.8% for women aged 50-64 years, 84.3% for men aged 65 years or older, and 87.8% for women aged 65 years or older; women showed higher vaccination coverage rates . In the High vaccination coverage rates were observed among men and women with hypertension, diabetes, chronic cardiovascular disease or stroke. Significant difference in the vaccination coverage rate was observed among men and women aged 50-64 years according to whether or not they had stroke . RegardiRegarding the factors affecting influenza vaccination among men, the vaccination coverage rate was 19.0% lower for men aged 50-64 years in the middle household income group . The vaccination coverage rate was 29.0% lower for men aged 50-64 years who completed high school education than those who completed middle school education or lower and was 43.0% lower for those who completed a university degree or above . RegardiFor women, the vaccination coverage rate was 14.0% lower for those aged 50-64 years with middle to high household incomes . The OR for vaccination was 1.40 times higher for those aged 65 years or older. The vaccination coverage rate was 34.0% for women aged 50-64 years who completed high school education relative to those who completed middle school education or below . The vaccination coverage rate was 47.0% lower for women who completed a university degree or above. The vaccination coverage rate was 13.0% lower for women aged 50-64 years who did manual labor. The OR for vaccination was 1.17 times higher for unemployed women aged 50-64 years and 1.70 times higher for unemployed women aged 65 years or older. Among the subjects aged 50-64 years, the OR for vaccination was 1.31 times higher for former smokers relative to current smokers, and 1.55 times higher for non-smokers relative to current smokers. Among the subjects aged 65 years or older, the OR for vaccination was 1.61 times higher and 1.73 times higher for former smokers and non-smokers relative to current smokers, respectively. The vaccination coverage rate was 16.0% lower for women aged 50-64 years who consumed alcohol and 11.0% lower for women aged 65 years who consumed alcohol. The OR for vaccination was 1.15 times higher for women aged 50-64 years who engaged in walking activities. Among the subjects aged 50-64 years, the vaccination coverage rate was 9.0% lower for those with normal health statuses and 23.0% lower for those who had good health statuses compared with those with poor health statuses. The vaccination coverage rate was 23.0% lower for women aged 65 years or older who had good health statuses. The OR for vaccination was 2.07 times higher for those aged 50-64 years and 2.36 times higher for those aged 65 years or older who had health examinations. The OR for vaccination was 1.77 times higher for those aged 50-64 years and 3.66 times higher for those aged 65 years or older who visited public health centers.Regarding influenza vaccination coverage rates by cities and provinces, South Jeolla Province had the highest vaccination coverage rate of 44.1%, and Jeju Island had the lowest vaccination coverage rate of 31.4% for those aged 50-64 years . IncheonRegarding the number of metropolis, medium cities, and rural areass that did not reach the target vaccination coverage rate of 80.0% set in 2015 for persons aged 65 years or older, 16 metropolis, 6 medium cities, and 1 rural area did not reach the target vaccination of 80.0% for persons without any chronic diseases. Five metropolis, 4 medium cities did not reach the target rate for those with at least one chronic disease .This study used the 2016 KCHS data to investigate influenza vaccination coverage rates and associated factors among subjects aged 50 years or older who responded to a questionnaire about influenza vaccination history in the last one year. The influenza vaccination coverage rates were investigated by regions and accompanying chronic diseases.In Korea, the scope of the National Immunization Program was expanded to civilian medical facilities in 2015, and its goal was set to reaching influenza vaccination coverage rates of 80.0% or higher for elderly persons aged 65 years or older [In Korea, vaccination is recommended for priority vaccination groups before an influenza outbreak occurs. Medical staff, pregnant women, persons aged 50-64 years, elderly persons aged 65 years or older, and patients with chronic respiratory diseases, chronic heart diseases, chronic liver disease, chronic kidney disease, nerve-muscle disease, hemato-oncologic disease or diabetes are included in the priority group. Of these, those with chronic diseases are classified as high-risk groups.In this study, high vaccination coverage rates were found among subjects aged 50 years who had chronic diseases compared with those who did not. Consistent with overseas and domestic research findings, vaccination coverage rates increased as the number of chronic diseases increased among subjects with at least one chronic disease ,17. In aRegarding the health-related factors, high vaccination coverage rates were observed for both unemployed men and women, and the unemployment status was identified as a factor that increased vaccination coverage rates among subjects aged 65 years or older. In a previous study, being too busy for vaccination was one of the reasons for being unable to receive vaccination ,19. It iRegarding vaccination coverage rates by regions, high vaccination coverage rates were observed in metropolitan cities than provinces. It appears that cities show higher vaccination coverage rates since they allow easier access to medical institutions. It also appears that the expansion of the free vaccination services for persons aged 65 years or older to private medical institutions has increased vaccination coverage rates for those living in cities. Subjects living in metropolis, medium cities and rural areas who had at least one chronic disease showed high vaccination coverage rates. In all counties, the target vaccination coverage rate of 80.0% set in 2015 was reached for subjects aged 65 years or older with at least one chronic disease. The high vaccination coverage rates observed in counties were consistent with previous findings . VaccinaThis study had a number of limitations. First, the influenza vaccination status was investigated using a self-report questionnaire. Therefore, the investigated vaccination coverage rates may differ from the actual vaccination coverage rates, and they may be overestimated. Second, the possibility of recall bias that may have occurred when the subjects were asked about their influenza vaccination status in the last one year in the KCHS cannot be eliminated. Third, due to the limitations of the questionnaire, vaccination coverage rates for various chronic diseases with high-risk of influenza complications could not be investigated. Fourth, although health professionals\u2019 recommendations and previous history of vaccination can significantly affect influenza vaccination among elderly persons and patients with chronic diseases, these variables could not be investigated as they were not included in the KCHS data .Despite these limitations, this study is meaningful in that it used survey data that considered regional characteristics to divide regions into metropolis, medium cities and rural areas and further divided the subjects into 50-64 and \u226565 years age groups to investigate vaccination coverage rates according to the chronic disease status and identify the factors that affect vaccination. The higher vaccination coverage rates observed for subjects aged 50-64 years who had at least one chronic disease compared to those who did not, and for subjects who lived in rural area than those who lived in medium cities indicate that active vaccination advertisements are needed to increase vaccination coverage rates among those aged 50-64 years who live in metropolis and medium cities. In addition, healthy professionals must recommend patients with chronic diseases who are aged 50-64 years to receive vaccination when they visit a health institution for a treatment."} +{"text": "Loneliness in older adults is most often attributed to marital and living status, social life factors, and physical health. Hearing impairment, however, is an understudied, potentially modifiable risk factor for loneliness. Older adults with hearing impairment experience difficulties with communication and social functioning, which also could contribute to loneliness. For this analysis, we used data from Wave 2 of the National Social Life, Health, and Aging Project. Participants were a nationally representative sample of community dwelling older adults aged 62 - 91 years. Poisson regression models with robust variance were used to model the cross-sectional relationship between self-reported hearing impairment and loneliness. We found a dose-response relationship such that individuals reporting very good/good and fair/poor hearing had a 9% [95% CI: 0.93 - 1.28] and 26% [95% CI: 1.10-1.46], respectively, higher prevalence of loneliness compared to individuals reporting excellent hearing, adjusting for chronic conditions, functional and cognitive ability, and demographic factors. Results were robust to exclusion of participants who reported hearing aid use. These findings suggest that self-reported hearing impairment is a strong factor associated with loneliness in older adults. Given the negative implications of loneliness on multiple facets of mental and physical health, functional ability, and premature mortality, efforts to further explore hearing impairment as a causal and modifiable risk factor for loneliness should be undertaken."} +{"text": "Screening reduces colorectal cancer deaths, but\u2009<50% of Asian Americans are screening up-to-date according to surveys, with variability across Asian subgroups. We examined colorectal cancer screening participation among Asian Americans overall and Asian subgroups in a large integrated health care system with organized screening.Data were electronically accessed to characterize screening in 2016 for Asians overall and subgroups relative to the National Colorectal Cancer Roundtable target of \u226580% screening and compared with non-Hispanic whites. Screening up-to-date was defined as a colonoscopy with 10 years, a sigmoidoscopy within 5 years, or a fecal immunochemical test (FIT) completed in 2016.p\u2009<\u20090.001). Almost all subgroups met the 80% target: Chinese (83.3%), Vietnamese (82.4%), Korean (82.1%), other Asian (80.3%), Filipino (78.7%), Asian Indian (79.6%), and Japanese (79.0%). Among Asians overall and non-Hispanic whites, 50.6% and 48.4% of members were up-to-date with screening by colonoscopy, and 28.0% and 28.2% were up-to-date by FIT, respectively. Across Asian subgroups, colonoscopy most frequently accounting for being screening up-to-date (range: 47.4\u201359.7%), followed by FIT (range: 21.6\u201331.5%).Among 436,398 patients, 69,826 (16.0%) were Asian, of whom 79.8% were screening up-to-date vs. 77.6% of non-Hispanic whites (In an organized screening setting, there were minimal differences in screening participation among Asian subgroups and almost all met the 80% screening target, despite differences in language preference. Screening test type differences across subgroups suggest possible preferences in screening modality, which can inform future research into tailored education or outreach. Colorectal cancer deaths can be reduced through screening, and the United States Preventive Services Task Force recommends several screening tests, including high-sensitivity guaiac-based fecal occult blood testing, fecal immunochemical testing (FIT), multi-targeted stool DNA testing, colonoscopy, computed tomography colonography, and flexible sigmoidoscopy with or without FIT2.Cancer is the leading cause of death in Asian Americans, with colorectal cancer being the third most common cause of cancer-related deaths3 it is estimated that achieving this goal would result in 19% fewer colorectal cancer deaths4. However, according to a recent estimate, only 63% of eligible United States residents, and fewer than 50% of some racial/ethnic groups, including Asians, are up-to-date with screening, leading to concern that the 80% target may not be achievable5. These findings are consistent with prior population-based surveys which reported low screening rates for Asian Americans and lower screening rates compared with non-Hispanic whites14. In addition, studies have reported disparities in colorectal cancer screening across Asian American subgroups, but little data exist regarding the influence of organized screening programs on these disparities12.The National Colorectal Cancer Roundtable set a goal of increasing the colorectal cancer screening rate in the eligible United States population to \u226580% by 2018;15, and recent studies in medically-insured populations have reported that Asians overall had colorectal cancer screening rates similar to or higher than those of non-Hispanic whites16. However, in one study, Asian Indians and Filipinos had lower screening rates, while Japanese, Chinese, Korean, and Vietnamese had similar rates to non-Hispanic whites15. Low screening participation and disparities across Asian subgroups, if widely observed, may suggest the need for more intensive or tailored approaches to screening.Access to health care is strongly associated with participation in colorectal cancer screeningThe aim of the current study was to ascertain colorectal cancer screening participation among Asians overall and Asian subgroups, relative to the 80% screening target and compared to non-Hispanic whites, in a large integrated health care system with organized screening. We hypothesized that with access to organized screening, disparities by race and ethnicity, specifically among Asians and Asian subgroups, would be minimal despite differences in English language proficiency, and that most groups would be at or near the 80% screening target and comparable in their participation to non-Hispanic whites.17.This cross-sectional study was conducted among health plan members of Kaiser Permanente Southern California (KPSC), an integrated pre-paid health care system that provides comprehensive medical services to over 4.5 million members. Individuals and their family members enroll in the health plan through their employer, individual plans, or state and federal programs such as Medi-Cal and Medicare. The membership is socioeconomically diverse and broadly representative of the underlying population living in Southern California; in 2010 specifically, Asian/Pacific Islanders comprised 11.8% of the census population in Southern California and 10.1% of KPSC membersThe study was reviewed and approved by the Institutional Review Board at KPSC, which waived the requirement for individual informed consent. The listed authors had sole responsibility for the study design, data collection, decision to submit the manuscript for publication, and drafting of the manuscript. The study was conducted within the National Cancer Institute-funded Population-based Research Optimizing Screening through Personalized Regimens (PROSPR) consortium (U54 CA163262) which conducts multisite, coordinated, transdisciplinary research to evaluate and improve cancer screening processes. Dr. Zauber is supported in part by the Memorial Sloan Kettering Cancer Center Core Grant (P30 CA008748) and Dr. J. Lee is supported by a career development grant from the National Cancer Institute (K07 CA212057).20, each year FIT kits are mailed to eligible health plan members 51\u201375 years of age who are not screening up-to-date by either a recorded colonoscopy within 10 years or sigmoidoscopy within 5 years. FIT kits are sent annually, regardless of whether prior FIT kits were previously completed, unless a patient tests positive, in which case they are referred for a diagnostic colonoscopy. The goal of the screening program is, primarily through FIT or colonoscopy, to have all eligible members up to date with screening by December 31 of each calendar year, starting the calendar year they turn 51 through 75 years of age, in accordance with the Healthcare Effectiveness Data and Information Set (HEDIS) measurement approach22. The screening outreach program includes mailed and telephone reminders, and in-reach includes reminders for members attending office or preventive health visits through best practice alerts in the electronic medical record. FIT kits are returned by mail to a regional laboratory and analyzed shortly after the return date. Those with a positive FIT are referred for a follow-up colonoscopy. In lieu of FIT screening, members can request to be screened by colonoscopy.As previously describedThe study population included health plan members 51\u201374 years of age as of January 1, 2016, enrolled in the health plan for \u2265\u20091 year prior to study entry (to ascertain screening history), and eligible for colorectal cancer screening . Asian subgroups were defined using self-identification to the health plan registrars as Filipino, Chinese, Vietnamese, Asian Indian, Japanese, Korean, or other Asian . Those self-identifying as non-Hispanic white and who otherwise met the study eligibility criteria served as the comparative group. Race/ethnicity data were available on approximately 95% of active health plan members, and Asian subgroup data were available in approximately 98% of Asians.Data on patient age, sex, race/ethnicity, membership duration, body mass index (BMI), influenza vaccinations, self-reported language preference, endoscopy procedures (colonoscopy and sigmoidoscopy), and FIT were obtained from electronically-accessible KPSC administrative, clinical, and laboratory databases.Colorectal cancer screening status among Asians overall, Asian subgroups, and non-Hispanic whites was determined as of December 31, 2016. Screening up-to-date was defined as having received a colonoscopy or sigmoidoscopy in the prior 10 years (2007\u20132016) and 5 years (2012\u20132016), respectively, or completed FIT screening in 2016.Multivariable log-binomial regression analysis was used to evaluate the association between Asian race/ethnicity and being up-to-date with screening, with non-Hispanic whites serving as the referent group. Prevalence ratios (PR) and 95% confidence intervals (CIs) were adjusted for the following covariates selected a priori: age (continuous); sex; length of health plan membership prior to cohort entry (continuous); BMI (continuous); English language preference (yes/no); and the number of influenza vaccinations in the 3 years before study entry, a surrogate for health care utilization . Tests were two-sided with a significance level of 0.05. BMI and length of membership prior to study entry were the only variables with missing data ; those with missing data were not included in the main adjusted analyses. All analyses were conducted using SAS version 9.4 .n\u2009=\u200969,826) were Asian, 84.0% were non-Hispanic white, 44.3% were 55\u201364 years of age, and 51.8% were female (Table\u00a0p\u2009<\u20090.001), have a lower BMI (p\u2009<\u20090.001), and have the influenza vaccine annually (p\u2009<\u20090.001), they were less likely to prefer English as a language (p\u2009<\u20090.001).Among 436,398 individuals in the study population, 16.0% , Chinese and Vietnamese . Asian Indians, Japanese, Koreans, and other Asians (n\u2009=\u20094498\u20136314) comprised 6.5\u20139.1% of Asians overall the National Colorectal Cancer Roundtable screening target of \u226580%, despite substantial differences between subgroups in English as a preferred language. Colonoscopy was the screening test that most frequently accounted for being up-to-date with screening, followed by FIT, regardless of race, although test choice varied moderately across Asian subgroups.14, as well as similar reports from national surveys for Asian Americans and Pacific Islanders combined8. A more recent study examined the colorectal cancer screening status of medically-insured patients in a mixed-payer outpatient health care setting in Northern California between 2012 and 2013, and reported that while all groups were below the 80% screening target, Japanese (68.3% screening up-to-date), Chinese (66.7%), Korean (66.2%), Vietnamese (65.8%), and Filipino patients (59.0%) had higher participation rates than non-Hispanic whites (63.7%), while Asian Indians (45.6%) had lower rates16. Our study significantly extends the findings of this latter study, demonstrating that, in a larger integrated health care setting with more recent screening data and a larger population of Asians, an organized screening program was associated with a near absence of disparities in screening across Asian subgroups and achieving screening rates at or near the 80% target is feasible. Our findings are also consistent with a recent report of colorectal cancer screening among 1,746,714 participants across 4 health care systems in the United States, in which Asian Americans and Pacific Islanders combined had higher odds of screening than whites 15, as well as a study that reported low racial/ethnic disparities in colorectal cancer survival within an integrated health care system in California23.Our findings contrast with those from prior survey-based studies which reported that Asians and Asian subgroups within California had screening rates well below the 80% screening target, and were less likely to be up-to-date with colorectal cancer screening than non-Hispanic whites27. The high rates of screening and relative lack of disparity in screening participation across Asian subgroups in the current study likely reflect the select nature of the Asian American population studied relative to acculturation factors and barriers to screening. For example, among Asians overall, the average duration of health plan membership was 12.4 years, and most members accessed health insurance through an employer. However, given similar screening rates have not been reported in other settings within California, the high screening participation in the current study may also be related to the integrated and organized nature of cancer screening delivery in this setting, including outreach and in-reach initiatives aimed at reducing barriers to screening, particularly annual FIT outreach. Within Kaiser Permanente Northern California (KPNC), where this has been looked at extensively, screening rates rose from approximately 39% in 2000-2005, to 66% in 2008 , to\u2009>\u200980% starting in 2011; the sharp increase in screening paralleled an increase in the uptake of FIT28. These findings are similar to what was reported among racial/ethnic groups within KPNC, including Asians/Pacific Islanders in aggregate20. Screening rates within KPSC mirror those of KPNC, although they are unpublished. Beyond the annual mailing of FIT kits, patients could opt instead for endoscopy screening (primarily colonoscopy); offering multiple screening options may increase screening uptake30. Through electronic medical record prompts, all physicians, not just primary care providers, were informed of a patient\u2019s screening status at every health care visit, and FIT kits were made available to patients not-up-to-date with screening despite mailed outreach. Also, tailored outreach materials and interpreters were utilized to explain colorectal cancer screening to patients, and patient language preference was matched to the language spoken by the physician when possible; these efforts at tailoring outreach and in-reach may help explain why English language preference did not modify the association between race/ethnicity and the likelihood of being screening up-to-date as has been reported in other studies27. Finally, screening rates across medical facilities were tracked and reported monthly as performance improvement measures. Attention to these system-, provider-, and patient-level factors may enhance more uniform access to screening for patients, despite differences in patient demographics.In prior studies, various factors have been linked to low participation in colorectal cancer screening among Asian Americans, including employment status, health insurance access, English language proficiency, health literacy, and length of residency in the United States30. Similar findings were reported for Asian/Pacific Islanders compared to non-Hispanic whites within Kaiser Permanente Northern California health plan members20. Differences in screening test usage between Asian American subgroups has not been extensively explored, but may reflect differences in barriers related to discussing health concerns and attitudes about prioritizing preventive health care 31. Further research to identify the factors driving these differences in screening modality usage may allow more tailored education or outreach.The finding of Asian subgroup variation in screening test usage, despite standardized outreach procedures, suggests there may be cultural differences in the acceptance of different screening modalities. Other studies have reported racial/ethnic disparities in screening test usage. In a cluster randomized trial of different colorectal cancer screening strategies, nonwhites were more likely to complete fecal occult blood testing than whites, whereas whites were more likely to complete colonoscopy than nonwhitesStrengths of the present investigation include the large sample of Asians overall and Asian subgroups, and the comprehensive capture of colorectal cancer screening tests, including FIT from the laboratory database, endoscopy procedures from procedure codes, and claims data for procedures performed outside the health system; in contrast, survey-based studies relying on self-reports of screening are subject to recall and social desirability biases, low response rates, and overestimation of actual screening completion. A limitation of the study is that results may not be generalizable to health care settings with limited ability to deliver colorectal cancer screening or to individuals with limited access to health care. In addition, we did not have access to some known predictors of screening, such as employment status, English language proficiency, health literacy, and length of residency in the United States, which may contribute to omitted variable bias and error in the regression estimates.In conclusion, in contrast to survey data suggesting that\u2009<50% of Asian Americans are up-to-date with colorectal cancer screening, with variation across Asian subgroups, in a setting with organized colorectal cancer screening, there was minimal variation in screening participation and all subgroups we studied were close to or exceeded the 80% screening target set by the National Colorectal Cancer Roundtable. While this study did not test an intervention, the findings suggest the potential for organized screening programs to achieve high screening rates. Further research into the variation in screening test usage across Asian subgroups may allow more tailored education or outreach approaches.National surveys report that\u2009<\u200950% of Asian Americans are up-to-date with colorectal cancer screening, with variability across Asian subgroups.The National Colorectal Cancer Roundtable screening target for the United States is\u2009\u2265\u200980% by 2018.In an organized colorectal cancer screening program, approximately 80% of Asians overall were screening up-to-date in 2016, with minimal variability across subgroups.Test use varied across Asian subgroups.Differences in screening test usage across Asian subgroups may require tailored education or outreach."} +{"text": "Rheumatoid arthritis (RA) patients have nearly twice the risk of cardiovascular disease (CVD) compared to the general population. We aimed to assess, in a predominantly Black population, the prevalence of traditional and RA-specific CVD risk factors and therapeutic patterns. Utilizing ICD codes, we identified 503 RA patients \u226518 years old who were seen from 2010 to 2017. Of them, 88.5% were Black, 87.9% were women and 29.4% were smokers. CVD risk factors were higher than in previously reported White RA cohorts. Eighty-seven percent of the patients had at least one traditional CVD risk factor, 37% had three or more traditional CVD risk factors and 58% had RA-specific risk factors < 20). CV outcomes were comparable to published reports. Higher steroid use, which increases CVD risk, and lesser utilization of biologics (decrease CV risk) were also observed. Our Black RA cohort had higher rates of traditional CVD risk factors, in addition to chronic inflammation from aggressive RA, which places our patients at a higher risk for CVD outcomes, calling for revised risk stratification strategies and effective interventions to address comorbidities in this vulnerable population. Rheumatoid arthritis (RA) is a chronic inflammatory condition that affects about 1% of the adult population, with an annual incidence rate of 40 new cases per 100,000 persons . The patIn this cross-sectional study, we utilized the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM 714.0) and the International Classification of Diseases, Tenth Revision (ICD-10-CM M06.00\u2013M06.09), to identify RA as either the principal or secondary diagnosis in the discharge summary. We included all inpatient discharges, from 1 January 2010 to 30 May 2017, that took place at State University of New York Downstate Medical Center-University Hospital of Brooklyn and New York City (NYC) Health + Hospitals/Kings County, which serve the population of Central Brooklyn, NY. Prior to the initiation of the study, the protocol was approved by the SUNY Downstate Institutional Review Board and the Office of Research Administration for implementation at NYC Health + Hospitals/Kings County. We selected patients, 18 years or older by 1 January 2010 to be included in the study. Two investigators independently reviewed the cases identified by ICD-codes to confirm RA diagnosis. We used physician entries (inpatient/outpatient notes and consultations) and the presence of disease-modifying anti-rheumatic drugs (DMARDs) in the medication reconciliation or DMARDs prescriptions. Data abstraction was performed for confirmed cases utilizing the study data collection sheet. Demographics and clinical data including history of smoking, year of RA-diagnosis (according to 2010 American College of Rheumatology criteria), comorbidities, laboratory data, hand imaging and treatment regimens were abstracted .A musculoskeletal radiologist (SK) evaluated the bilateral hand radiographs utilizing the Simple Erosion Narrowing Score (SENS) to ascertain the presence and number of erosions and joint space narrowing . The radt-test to compare between groups for continuous variables, and Chi square analysis for categorical ones.Descriptive statistics using IBM \u00ae SPSS version 23 was applied. Measures of central tendency and dispersion for continuous variables, and frequency distribution for categorical variables were used. Data is presented as the mean \u00b1 standard error of the mean (\u00b1SEM). We compared our predominantly Black RA population with the predominantly White cohort of the Consortium of Rheumatology Researchers of North America (CORRONA) to assess differences in CVD risk profiles, CVD outcomes, features of RA disease severity, and therapeutic patterns including the use of steroids, DMARDs and biologics . We used2). Women were significantly older compared to men, with a mean age of 65 \u00b1 0.67 vs. 61 \u00b1 2.19 respectively (p < 0.04) .The rates of traditional CVD risk factors in our study cohort (predominantly Black) vs. the CORRONA study cohort (predominantly White) respectively were: hypertension (66.6% vs. 29%), dyslipidemia (41.3% vs. 25%), diabetes (28.5% vs. 8%), and smoking (29.4% vs. 34%) .CVD risk factors were not significantly different between men and women in our cohort . At leasp < 0.001 or known coronary artery disease (CAD) (19.8%), which were similar to those reported in the CORRONA study . The rat < 0.001 .Utilizing SENS scoring for hand radiographs, periarticular osteopenia, joint space narrowing and joint erosions were observed in 95.2%, 69% and 66.5% respectively of our RA patients, while joint erosions were reported in 50.7% of the cohort in the 2010 CORRONA study . Our patOur predominantly Black RA population had higher rates of CVD risk factors compared to predominantly White RA cohorts of previous studies. These CVD risk factors included obesity, hypertension, dyslipidemia and diabetes. The CORRONA is a US-based registry of about 25,000 RA patients which is followed longitudinally . RA diseSimilarities between our study cohort and the CORRONA cohort include female predominance and nearly identical BMI (28.9 vs. 29.2). However, our population differs from the CORRONA patients in a number of characteristics. Lower rates of current smokers and ever smokers were found among our patients, i.e., 11.5% and 29.5% respectively (vs. 19% and 37% in CORRONA respectively), and higher rates of hypertension, dyslipidemia and diabetes. Eighty-seven percent of our patients have at least one traditional CVD risk factor present, with more than a third of them carrying three or more traditional risk factors, which supports the notion that our population is at a higher risk for CVD events and mortality.Our RA population was also found to have a higher frequency of seropositivity, as demonstrated by the presence of rheumatoid factor or anti-citrullinated antibodies (85.8% vs. 77% in CORRONA), and more than half of our patients had had RA disease for longer than 10 years. Our study includes radiological evaluation with evidence of joint damage as markers of disease severity. Furthermore, our study examined the presence of extra-articular manifestations of RA , and recorded 7.5% of patients with a BMI < 20 (rheumatoid cachexia). The aggressive nature of RA disease seen in our cohort is further supported by the frequency of elevated inflammatory markers such as CRP and ESR. We also found a statistically-significant difference between the seropositive and seronegative RA groups in the rates of RA-specific CVD risk factors, with seropositive patients exhibiting higher prevalence of joint erosions, joint space narrowing, extra-articular disease and elevated serum markers. Seronegative patients demonstrated higher rates of hypertension compared with the seropositive group (66.6% vs. 50.4% respectively); however, this finding was not statistically significant, likely due to the small sample size. Furthermore, our data demonstrates a higher burden of both traditional and RA-specific risk factors in our study cohort as compared with the CORRONA cohort revealedIncreased risk for CVD events and mortality in RA has been the subject of several meta-analyses, population studies and mechanistic experiments ,21,22). RA patients are prone to a specific form of dyslipidemia which is characterized by high levels of triglycerides, low levels of both low-density lipoproteins (LDL) and high density lipoproteinemia. This phenomenon is called \u201clipid paradox\u201d given that there is increased CV risk despite low levels of lipoproteins. High-density lipoprotein appears to be dysfunctional in RA patients, leading to inadequate clearance of lipids from the atheromatous plaque formation. This pro-inflammatory high-density lipoprotein positively correlates with elevated acute phase reactants and disease activity ,26,27,282 correlating with high disease activity and higher BMI reflecting better disease control [The obesity rates observed in our population could be explained by decreased physical activity secondary to active RA disease, which further contributes to the burden of traditional CVD risk. On the other hand, \u201cobesity paradox\u201d is also observed in RA, with BMI < 20 Kg/m control ., the higher use of prednisone among our patients, administered for disease control, adds to the CVD risk [AdditionallyCVD risk . MethotrCVD risk . In contFinally, our study is limited by the retrospective nature of the analysis, lack of available RA-specific disease activity measurements, characterization of cardiac involvement, stroke type (ischemic vs. hemorrhagic), response to therapeutic interventions and survival outcomes. Inaccuracy in coding explains the number of cases in which RA diagnosis was not found in the clinical documentation. There is also data missing at random, which we believe is harmless and does not represent a systematic bias. We plan, however, to undertake a longitudinal study to assess disease activity at presentation and at follow-up intervals, disease complications including CVD events, response to primary and secondary prevention of traditional and RA specific risk factors and outcomes. We also acknowledge the limitation of the gender comparison made in This is the first study to evaluate CVD risk in a predominately Black RA population that included radiological as well as serological assessment of disease severity, together with characterization of therapeutic patterns. We observed higher rates of traditional CVD risk factors, including obesity, diabetes, hypertension, dyslipidemia, compared to the White RA cohort. Our population had more aggressive disease with higher rates of seropositivity, joint narrowing/erosions and elevated inflammatory markers. The combination of higher rates of traditional and RA-specific risk factors confers on our patients a high risk for CVD events. Our RA population characteristics require therapeutic interventions to address disease control and targeted management of comorbidities that involve revised risk stratification aiming at reducing CVD morbidity and mortality in this highly vulnerable population."} +{"text": "Worldwide, tuberculosis (TB) is the leading cause of death from a single infectious disease agent , special studies, including TB prevalence surveys , a 1.8% decline from 2016 . IncidenThe WHO regions of South-East Asia and Africa accounted for nearly 70% of overall global TB. Although total case numbers were higher in South-East Asia, overall incidence was similar in both regions . Most hiTB preventive treatment (TPT) (most commonly daily isoniazid for \u22656 months) has been found to prevent TB disease among persons who might be infected with TB and are at risk for progressing to TB disease. Current recommendations include providing TPT to persons with HIV infection is the leading cause of death from a single infectious disease agent and the leading cause of death among persons living with human immunodeficiency virus (HIV) infection.In 2017, an estimated 10 million incident TB cases and 1.6 million TB deaths occurred, representing reductions of 1.8% and 3.9% from 2016, respectively. TB epidemiology varied by World Health Organization region.Innovative approaches to case finding, scale-up of TB preventive treatment, use of newer TB treatment regimens, and prevention and control of HIV will contribute to decreasing TB."} +{"text": "Imaging presence of the perivascular cuff is not associated with tumor persistence and resection margin infiltration (p = 0.362). Lesion enhancement and pattern homogeneity were not accurate in determining tumor persistence. IOA was generally poor to fair, except for >25 mm cut-off classification where IOA was moderate. Diagnostic accuracy is superior in consensus lecture rather than single lecture. Conclusion: Imaging methods tend to underestimate PDAC resectability after neoadjuvant-CRT. IOA is poor to fair in evaluating most of the qualitative parameters of downstaged pancreatic adenocarcinoma. Surgery should be considered for downstaged borderline resectable PDACs, independently from perivascular cuff presence, especially for tumors smaller than 25 mm.Introduction: Evaluation of pancreatic ductal adenocarcinoma (PDAC) after chemoradiotherapy downstaging is challenging due to computed tomography (CT) overestimation of tumor extension and residual vascular involvement, limiting access to surgery to some patients with potentially resectable tumors. With this study, we wanted to assess which radiological findings are most reliable at pre-operative imaging in the evaluation of PDAC after chemoradiotherapy in order to achieve complete resection. Methods: We retrospectively enrolled 71 patients with locally advanced and borderline resectable PDAC who underwent neoadjuvant chemoradiotherapy. Pre-operative CT or magnetic resonance (MR) have been evaluated by three radiologists to assess major qualitative and quantitative parameters of lesions. Accuracy, sensitivity, and specificity compared to anatomopathological results were evaluated for each parameter. Cohen\u2019s K-coefficient has been calculated to evaluate the inter-observer agreement (IOA). Both single and consensus lecture have been tested. Different dimensional cut-offs were tested to categorize tumors according to their major axis and to compare with anatomopathological diameter, tumor persistence, and margin infiltration. Results: A 25 mm cut-off was 67% sensitive, 90% specific, and 77% accurate in assessing real tumor dimension. 25 mm cut-off reported a 64% sensitivity, 78% specificity, and 69% accuracy in assessing R0 resection. Each 5 mm increment of major axis dimension there is an odds ratio (OR) 1.79 (95% CI 1.13\u20132.80, Pancreatic ductal adenocarcinoma (PDAC) represents one of the most common causes of cancer-related death in the United States and Europe, with a life expectancy of about 5% at 5 years ,2. In faWe retrospectively enrolled patients between February 2013 and July 2017 with a diagnosis of borderline resectable or locally advanced PDAC in agreement with Society of Abdominal Radiology and American Pancreatic Association criteria [2). Dynamic imaging was performed with a volumetric 3D gradient-echo pulse sequence (volume interpolated breath-hold examination) with fat saturation on the axial plane, during injection of 0.2 mL/kg of Gd-BOPTA with the same phases described for CT evaluation. CT was performed by using two multi-slice equipment 64-detector rows . Scans were acquired before and after 1.5 mL/kg intravenous injection of iodine contrast media during pancreatic arterial phase (15s after aortic bolus-tracking peak), venous phase (60\u201370s), and equilibrium phase (5 min). Section thickness was 2 mm, kV 120, and mAs 125\u2013250. MR was performed by using a 1.5T equipment , including the following pulse sequences: axial fat-suppressed T1-weighted gradient-echo; axial/coronal T2-weighted half-Fourier acquisition single-shot turbo spin-echo (HASTE); axial fat-suppressed T2-weighted turbo spin-echo; single shot HASTE MR cholangiopancreatography. Diffusion-weighted images were acquired using echo-planar imaging sequences with three b-values ; fibrosis presence; main pancreatic duct dilatation >5 mm; retroperitoneal infiltration; involvement of portal vein, celiac trunk, mesenteric artery, mesenteric vein; perivascular cuff (hypodense avascular undefined tissue around celiac trunk and major vessels). Tumor dimensions, persistence, fibrosis, retroperitoneal infiltration, and presence of surgical margin infiltration (R+) have been subsequently evaluated on the operative sample by an expert pathologist with decades of experience in pancreatic tumors.http://www.analyse-it.com/; 2009) and IBM SPSS Statistic (v.19).Imaging and anatomopathological parameters were categorized into dichotomous classes. Different dimensional cut-offs were considered with an increase of 5 mm to categorize the tumors according to their major axis. Single radiological evaluations and consensus evaluation have been tested. Consensus evaluation was considered as the most frequent measure among the three single evaluations of the same parameter for qualitative measures and as the mean value for quantitative measures. The single evaluation from pancreas-master radiologist was taken as the imaging gold standard and compared to consensus evaluation. Accuracy, sensitivity, and specificity compared to anatomopathological results were evaluated for each parameter. Chi-Square test was used to assess correlations between categorical variables. A logistic regression model was used to calculate the risk of R+ resection related to the dimensions at imaging. Cohen\u2019s K-coefficient has been calculated between single evaluations to assess the inter-observer agreement (IOA). Continue variables with normal distribution were expressed as mean \u00b1 standard deviation, while median (interquartile range) was used for non-normal distributions. Statistical analysis was performed by using Analyse-it software for Microsoft Excel and at consensus evaluation (p = 0.037). In total, 78% of lesions with R0 resections were <25 mm at pancreatic-expert radiologist evaluation, while 65% of R1 resections were >25 mm. Only 14% of tumors >25mm at imaging led to an R0 resection.The surgical resection margin R classification was statistically correlated to the size of the lesion when categorized above or below the 25 mm cut-off at imaging, both when measured by the pancreatic-expert radiologist , retroperitoneal infiltration (58%), and surgical margin infiltration (69%). Referring to R+ surgical margin infiltration, the 25 mm cut-off was 64% sensitive and 78% specific. Moreover, sensitivity and specificity for 25 mm cut-off were, respectively, 23% and 94% related to retroperitoneal infiltration, and 51% and 67% related to tumor persistence . p = 0.012) for R+ resection, with an of OR 6.56 when bigger than 25 mm. Even at consensus evaluation, lesions >25 mm reported an OR of 3.39 for a R+ resection.When measured by a pancreatic expert radiologist, each 5 mm increase in tumor dimension reported an OR of 1.79 and consensus (p = 0.098). Whereas tumor density homogeneity in venous and equilibrium phase reported an accuracy of 50% and 63% respectively in evaluating tumor persistence, tumor enhancement in both phases was not an accurate parameter . However, the presence of enhancement in the venous and equilibrium phase was found to be an accurate measure of the presence of fibrosis, with respective accuracy of 95% and 89% in consensus lecture.The presence of the perivascular cuff at imaging evaluatiConcordance values between the three radiologists are summarized in Imaging is of fundamental importance in the identification, characterization, and staging of PDAC. One of the biggest challenges in pancreatic imaging is to correctly restage a locally advanced PDAC after downstaging CRT to assess its resectability. In 2001, White et al. first nop = 0.362), therefore we suggest giving it little consideration in resectability evaluation. In the same way, as proven by Cassinotto et al. [Probably one of the most misleading causes of underestimation of PDAC resectability is the persistence of perivascular hypodense tissue after neoadjuvant-CRT. This perivascular cuff could better rely on lymphatic congestion or CRT-related fibrotic rehash than on tumor infiltration. Indeed, in our study the presence of the perivascular cuff was not accurate in assessing tumor persistence and was not statistically correlated with surgical margin infiltration and R+ resection and consensus evaluation (p = 0.037). Testing different major axis cut-offs, we found that there is no one capable of simultaneously maximizing sensitivity, specificity, and accuracy referring to anatomopathological tumor diameter, persistence, and retroperitoneal margin infiltration. Nevertheless, we found how 25 mm imaging cut-off is accurate in assessing real tumor dimension, reporting moderate IOA. Referring to retroperitoneal infiltration, 25 mm imaging cut-off is 94% specific, 58% accurate, but only 23% sensitive. However, when considering overall surgical margin infiltration, the 25 mm cut-off was 64% sensitive, 78% specific, and 69% accurate in predicting an R+ resection. These mean that about 70% of the times, the 25 mm cut-off can correctly diagnose the R0 or R+ of the surgical resection. In particular, if tumor dimensions are evaluated by an expert radiologist, each increase of 5 mm leads to a 79% increase in R+ risk (p = 0.001), reporting a higher risk for tumors >25 mm with an OR of 6.56 . More than half of our patients presented margin infiltration at histological evaluation of surgical specimen, probably due to a high component of borderline resectable PDAC in our population. However, the near totality of the R+ was R1, and therefore reported a solely microscopic surgical margin infiltration. For this reason, we could always consider the size and the extent at the anatomopathological evaluation coinciding with the real measurements of the tumors. In our study, the strong majority of R0 tumors were smaller than 25 mm, while about half of R+ tumors were >25 mm, with a significant statistical difference both at pancreatic expert radiologist (All these findings support the argument to be more aggressive in borderline resectable PDAC multimodality treatment, as previously suggested in literature, in order to not deny surgery to a potentially resectable patient ,20,21. IA final interesting fact is that IOA mostly tended to be higher between the pancreas expert and young radiologist who did all their residency period in a pancreatic institute, than between the pancreas expert and general older radiologist coming from a different non-specialized institute. Most of the time the pancreatic expert radiologist agreed with young radiologist but disagreed with the older general radiologist. For this reason, consensus evaluation often coincided with the expert\u2019s evaluation and preserves diagnostic and statistical significance. This underlines how radiological specific expertise is essential in a highly specific ambit, such as pancreatic diseases, and more important than years of working experience and is independent from overall radiological knowledge.The retrospective setting was the main limitation of the study. The moderately low number of patients who were included in the analyzes may represent an additional limitation. Further prospective studies on larger series are needed in the future to confirm the findings in this study. Furthermore, comparison studies between downstaging and upfront resection will be useful in the future, eventually considering preoperative imaging and tumor shrinkage.Common radiological criteria are not fully applicable to assess resectability of PDAC after CRT. Basically, imaging methods tend to underestimate PDAC resectability after neoadjuvant-CRT. IOA is poor to fair in evaluating most of the qualitative parameters of downstaged pancreatic adenocarcinoma. Surgery should be considered for downstaged borderline resectable PDACs, independently from perivascular cuff presence, especially for tumors smaller than 25 mm."} +{"text": "While increased healthcare engagement and antiretroviral therapy (ART) adherence occurs during pregnancy, women living with HIV (WLWH) are often lost to follow-up after delivery. We sought to evaluate postpartum retention in care and viral suppression and to identify associated factors among WLWH in a large public hospital in Atlanta, Georgia. Data from the time of entry into prenatal care until 24 months postpartum were collected by chart review from WLWH who delivered with \u226520 weeks gestational age from 2011 to 2016. Primary outcomes were retention in HIV care and viral suppression (<200 copies/mL) at 12 and 24 months postpartum. Obstetric and contraception data were also collected. Among 207 women, 80% attended an HIV primary care visit in a mean 124 days after delivery. At 12 and 24 months, respectively, 47% and 34% of women were retained in care and 41% and 30% of women were virally suppressed. Attending an HIV care visit within 90 days postpartum was associated with retention in care at 12 months and 24 months postpartum. Receiving ART at pregnancy diagnosis , viral suppression at delivery , and attending an HIV care visit within 90 days postpartum were associated with 12-month viral suppression, and older age was associated with 24-month viral suppression. Long-term retention in HIV care and viral suppression are low in this population of postpartum WLWH. Prompt transition to HIV care in the postpartum period was the strongest predictor of optimal HIV outcomes. Efforts supporting women during the postpartum transition from obstetric to HIV primary care may improve long-term HIV outcomes in women. Despite the availability of effective antiretroviral therapy (ART), many patients living with HIV in the United States do not achieve viral suppression, contributing to AIDS and non-AIDS morbidity and mortality and ongoing HIV transmission \u20134. The HThe majority of the over 280,000 WLWH in the United States live in Southern states, contributing to the nearly 8,500 WLWH who become pregnant annually \u201322. Due Data were collected by electronic medical record review of all WLWH who delivered at a large publically-funded healthcare system in Atlanta, Georgia, with at least 20 weeks gestational age, from January 1, 2011, to November 30, 2016. Supplementary data were available through August 1, 2016, from the Georgia Department of Public Health (DPH) enhanced HIV/AIDS Reporting System (eHARS) for the study population for women who did not have documented HIV follow-up within the healthcare system during all postpartum time points. Approval was obtained from the Emory University and state and institutional review boards. The study obtained a waiver of consent by the Emory University institutional review board, as it was minimal risk and did not adversely affect the rights and welfare of the subjects.Sociodemographic and clinical data were collected from the electronic medical record beginning with each patient's entry into prenatal care until 24 months after delivery, including age, race/ethnicity, year of HIV diagnosis, mode of HIV infection, ART history, HIV resistance, CD4 and HIV-1 RNA results, gravidity, parity, number of prenatal care visits, mode of delivery, gestational age at delivery, birth outcome, attendance of postpartum obstetric follow-up (within 90 days), time to first postpartum HIV care visit, and contraceptive plan and use. Subsequent pregnancy was determined for all study participants through November 30, 2016, including those that resulted in abortion or delivery at outside hospital. Transition to HIV primary care postpartum occurred at the time of the first HIV care visit or viral load measurement . For each postpartum HIV care visit, viral load, method of contraception, pregnancy status, ART regimen changes, adherence, and transfers of care were recorded. Additional CD4 count and viral load data were obtained from eHARS.Retention in HIV care was defined as two HIV care visits or viral load measurements, greater than 90 days apart . This waIn the event of multiple deliveries for a woman, the first recorded delivery was used for analysis. Descriptive statistics were used as appropriate. Bivariate analyses were conducted using t-tests, Wilcoxon rank sum, and chi-square tests as appropriate to determine the associations between the sociodemographic and clinical variables and each outcome.Separate multivariable logistic regression models were used to determine factors associated with each HIV care outcome. Covariates reported in the existing literature were initially included in the model: delivery year, age, race, perinatal HIV infection, new HIV diagnosis, number of prenatal care visits, number of prior live births, ART use before pregnancy, CD4 count at presentation, viral suppression and contraceptive plan at delivery, postpartum obstetric visit attendance, and HIV primary care visit within 3 months postpartum. Covariates which were not predictive of any outcomes in bivariate or initial multivariable analyses (p>0.05) were removed from the final model only if removal did not significantly alter associations with other variables. Model fit was assessed by Hosmer-Lemeshow test, evaluation of residuals, and predictive ability. Analyses were conducted in SAS version 9.4 . For all analyses, two-sided p <0.05 was considered significant.Overall, 245 pregnancies occurred in 207 HIV positive women; 44 women had 2 or more (range 2-4) pregnancies. Overall, 78% of women were African-American, the average age was 28.1 years; women had a median of one prior live birth .3, and 37% of women were receiving ART at time of pregnancy diagnosis, including 48% of women diagnosed with HIV before pregnancy.The majority acquired HIV sexually (59%); 11% were perinatally infected. Pregnancy occurred a median of 3 years since HIV diagnosis, and almost a quarter of women were diagnosed with HIV during the index pregnancy. Mean CD4 count at presentation for obstetric care was 413 cells/mmWomen attended a median 9 prenatal care visits, and 71% of women were virally suppressed (<200 copies/mL) at delivery .About half of the women had a vaginal delivery, and 99% of the infants tested HIV negative. Overall, 62% received a contraception method by discharge, most frequently depo-medroxy progesterone (DMPA) (30%); 10% chose condoms as their only form of contraception.Overall, 76% attended a postpartum obstetric visit. Repeat pregnancy occurred in 44 (24%) of women over a median 4.3 follow-up years. The median time between delivery and the estimated date of subsequent conception was 358 days; 23 (52%) occurred within 1 year of delivery, and 34 (77%) within 2 years of delivery.Overall, 64% of women had an HIV primary care visit within 180 days of delivery, 37% within 90 days. For women who attended a visit, the median time to HIV care visit was 124 days postpartum. At 12 months postpartum, 86 (47%) women were retained in care and 76 (41%) were virally suppressed. Among women who were not retained in care at 12 months, 26 (26%) re-entered care and completed two visits 90 days apart between 12 and 24 months. Among women who were not virally suppressed at 12 months, 12 (11%) became virally suppressed between 12 and 24 months. Using the pre-specified criteria that retention/viral suppression was required at 12 months to be considered retained/suppressed at 24 months, 52 (34%) women were retained in care and 46 (30%) were virally suppressed at 24 months postpartum . With thIn multivariable analysis , retentiRetention at 12 months was also associated with older age . Viral suppression at 12 months postpartum was associated with ART use before pregnancy , viral suppression at time of delivery , and attending an HIV care visit within 90 days postpartum (aOR 2.40 95%CI 1.12-5.16). Only age was associated with achieving viral suppression at 24 months postpartum .Given the association between long-term outcomes and attending an HIV care visit within 90 days postpartum, we additionally examined characteristics associated with transition to HIV primary care within 90 days. CD4 count at prenatal care entry , lack of contraceptive provision at delivery , and calendar year of delivery were associated with transition to HIV primary care within 90 days.Retention in HIV care and achievement of viral suppression are necessary to maximize the benefits of ART. Despite recent improvements , achieveAttending an HIV care visit within 90 days postpartum was the strongest and most consistent predictor of HIV outcomes, similar to a study which used city-wide data from Philadelphia . DespiteThe American College of Obstetricians and Gynecologists (ACOG) recently highlighted the importance of the postpartum period and transition to primary care in a set of new guidelines, stressing the need for an individualized spectrum of follow-up over the initial twelve weeks postpartum . With 50By analyzing data from a single healthcare system in which HIV primary care, specialized HIV/obstetric care, and pediatric care for HIV exposed infants occurs in close geographic proximity, we showed, despite minimization of operational barriers that may be expected from co-located services , women iTemporal changes occurred within and outside our healthcare system, such as community-based interventions, streamlined clinic enrollment procedures, and enhanced care coordination between HIV and obstetric services. As such, we observed that prompt postpartum transition to HIV primary care improved over time. Nonetheless, strong associations between prompt transition and improved long-term outcomes remained even after controlling for year of delivery in our models. As has been proposed for addressing challenges surrounding transition of adolescents living with HIV from pediatric to adult care and in ALimited evidence-based interventions exist to improve retention in care. Our findings highlight the urgent need for targeted interventions to improve outcomes in this highly vulnerable population. Previous studies have identified complex, multi-level factors associated with postpartum disengagement, such as lack of HIV disclosure, HIV-related stigma, transportation barriers, substance abuse, limited social support, and competing responsibilities such as children and work , 46, 47.Finally, repeat pregnancy occurred in one quarter of women, most within 1 year of delivery. While pregnancy intention was not captured in our dataset, the frequency and timing of repeat pregnancy and low uptake of highly effective postpartum contraception further emphasize the importance of integration of HIV and reproductive healthcare to improve long-term HIV care outcomes. Interestingly, contraceptive provision at time of delivery was associated with prolonged transition from obstetric to HIV primary care on multivariable analysis. This finding was likely due to increased DMPA provision at delivery for women in whom there was a high concern for loss to follow-up.There are limitations to this study. First, as a retrospective chart review, we relied on the accuracy and scope of electronic medical records. Thus, some socioeconomic factors were not consistently available. Second, this single center analysis may not be generalizable to postpartum WLWH in other settings. However, our use of statewide surveillance data, which provided rates of viral suppression and retention for the majority of postpartum WLWH regardless of location of follow-up, did not significantly alter our HIV outcome estimates and mitigates this limitation. Third, the small number of women achieving 24 month viral suppression reduced power to identify associated predictors.In conclusion, we characterize a contemporary description of the HIV care continuum in a population of postpartum WLWH in a large-volume healthcare system in the South, the center of the HIV epidemic in the US, and the area with the highest number of perinatal transmissions. Even in the modern ART era, retention in care and viral suppression were low 1 and 2 years after delivery despite high levels of healthcare engagement during pregnancy and even lower than a historical control population of new and out-of-care patients in the same clinic. Prompt transition to HIV primary care in the postpartum period was the strongest predictor of postpartum HIV outcomes, suggesting that targeted interventions to engage women during pregnancy and the early postpartum period may improve long-term HIV outcomes in women. Further research is urgently needed to develop targeted interventions to improve HIV care outcomes for this population."} +{"text": "Naloxone is a life-saving antidote for opioid overdoses. In June 2016, the Ontario government implemented the Ontario Naloxone Program for Pharmacies (ONPP) to enhance access to naloxone.We examined the initial uptake of naloxone through the ONPP and characteristics of the individuals receiving and pharmacies dispensing naloxone kits.We conducted a population-based study of all Ontario residents who received a naloxone kit between July 1, 2016 and March 31, 2018. This involved 1) a cross-sectional analysis of monthly rates of kits dispensed; and 2) a descriptive analysis of all individuals and pharmacies who accessed and dispensed naloxone, respectively. We stratified individuals according to their opioid exposure as: prescription opioid agonist therapy (OAT) recipients, prescription opioid recipients, those with past opioid exposure and those with no/unknown opioid exposure. We calculated a Lorenz curve comparing the cumulative percent of naloxone-dispensing pharmacies and cumulative percent of naloxone kits dispensed and the corresponding Gini coefficient.Naloxone dispensing through the ONPP increased considerably from 1.9 to 54.3 kits per 100,000 residents over the study period. In this time, 2,729 community pharmacies dispensed 91,069 kits to 67,910 unique individuals. Uptake was highest among prescription OAT recipients (40.7% of OAT recipients dispensed at least one kit), compared with 1.6% of prescription opioid recipients, 1.0% of those with past opioid exposure and 0.3% with no/unknown opioid exposure. Naloxone dispensing was highly clustered among pharmacies (Gini = 0.78), with 55.6% of Ontario pharmacies dispensing naloxone, and one-third (33.7%) of kits dispensed by the top 1.0% of naloxone-dispensing pharmacies.The ONPP launch led to a rapid increase in the number of naloxone kits dispensed in Ontario. Although the program successfully engaged people prescribed OAT, efforts to increase uptake among others at risk of opioid overdose appear warranted. Opportunities for expanding pharmacy participation should be identified and pursued. Opioid-related mortality has become a major public health concern in Canada, with approximately 4,000 opioid-related deaths occurring nationally in 2017\u20135 AlthouNaloxone is an opioid antagonist medication that can prevent death when administered during an opioid overdose with few adverse effects beyond the induction of withdrawal symptoms. Because Naloxone availability in Ontario has historically been limited to specialized clinics providing care to individuals with an opioid-use disorder, public health departments, and supervised consumption sites that target populations at high risk of an overdose. However, recent evidence suggests that approximately one-quarter of opioid-related deaths in the province involve prescription opioids only, suggestWe conducted a population-based study of all Ontario residents eligible for health insurance who were dispensed a naloxone kit between July 1, 2016 and March 31, 2018.https://www.ices.on.ca). These databases are routinely used to study the impact of policy changes related to prescription opioids.[We used the Ontario Drug Benefit (ODB) claims database, which captures individual-level information on all products dispensed from community pharmacies and reimbursed by the Ontario Public Drug Programs (OPDP), to identify all naloxone kits dispensed from community pharmacies across Ontario. The ODB database has been demonstrated to be complete and of high quality, with an error rate <1%. This dat opioids., 20We conducted a cross-sectional analysis of naloxone uptake by identifying the monthly number of kits dispensed, individuals receiving at least one kit, and pharmacies dispensing naloxone over the study period. In order to differentiate naloxone uptake among different groups at risk of an opioid overdose, we stratified individuals into one of four mutually exclusive, hierarchical pre-defined groups as follows . First, We similarly applied the hierarchical mutually exclusive stratification method for all Ontario residents to define population denominators in each month over the study period. Here, we defined prescription OAT and prescription opioid populations as those who had a prescription dispensed within the month of interest, or a prior prescription with a days\u2019 supply overlapping the month of interest. We defined individuals with past opioid exposure using 1) the first day in the month of interest to capture past opioid prescriptions and 2) the last day in the month of interest to capture history of opioid-use disorder and opioid-related harms. All remaining individuals were defined in the no/unknown exposure group population. In our primary analysis we reported population-adjusted monthly rates of naloxone dispensing per 100,000 population overall, and stratified by opioid exposure group.We identified all individuals who received a pharmacy dispensed naloxone kit over the study period, using the most recent naloxone claim date as the index date. Within this cohort, we identified demographic characteristics , and neighborhood income quintile), comorbidities associated with risk of opioid overdose , kidney disease and liver disease; see We identified characteristics of pharmacies that dispensed naloxone over the entire study period, including the number of kits dispensed, location in Ontario and whether the pharmacy dispensed OAT. We examined clustering of naloxone dispensing through Ontario pharmacies using Lorenz curves. We calculated the Gini coefficient and the corresponding 95% confidence interval for the Lorenz curve comparing the cumulative percent of naloxone-dispensing pharmacies and cumulative percent of naloxone kits dispensed.Fig 1).Between July 2016 and March 2018, 2,729 community pharmacies dispensed 91,069 naloxone kits to 67,910 unique individuals. In 2017 specifically, there were 60,375 kits dispensed to 46,610 individuals. Over the study period, the monthly rate of kits dispensed increased 29-fold from 1.9 to 54.3 naloxone kits per 100,000 population, and the rate of individuals who accessed naloxone increased 26-fold from 1.9 to 48.5 individuals per 100,000 population to 8.6% . Furthermore, of the 4,909 community pharmacies in Ontario the number that dispensed naloxone increased from 46 (0.9%) to 1,459 (29.7%) per month over the study period.Table 1). In contrast, 1.6% of prescription opioid recipients and 1.0% of those with past opioid exposure were dispensed a kit. Although only 0.3% of Ontario residents with no/unknown opioid exposure were dispensed a kit, the monthly uptake of individuals accessing naloxone in this group grew most quickly over the study period, increasing 200-fold . Therefore, despite low population-adjusted prevalence, by March 2018, 44.0% of all naloxone kits dispensed through the ONPP were provided to people with no/unknown opioid exposure.Over the study period, naloxone uptake was most prevalent among prescription OAT recipients, with 40.7% of all prescription OAT recipients having accessed naloxone at least once (Table 1). The majority of individuals dispensed naloxone over the study period accessed only one kit ; however, a greater proportion of prescription OAT recipients and those with past opioid exposure accessed multiple kits , compared with 8.7% and 10.5% of prescription opioid recipients and individuals with no/unknown opioid exposure, respectively (Table 1).Among the entire cohort of 67,910 individuals dispensed naloxone over the study period, 51.3% had no/unknown opioid exposure , nearly one-third were prescription OAT recipients and the remaining were prescription opioid recipients and those with past opioid exposure (Table 1).The median age of individuals who accessed naloxone was 38 years (interquartile range (IQR) 28 to 51) and approximately half (50.3%) were male. Most naloxone recipients resided in urban areas (89.1%) and in southern Ontario (91.2%), and approximately half resided in low-income neighborhoods (50.3% in the lowest two income quintiles). Characteristics of individuals differed by opioid exposure, with the most noticeable differences between prescription OAT recipients and the no/unknown exposure group. In comparison to prescription OAT recipients, individuals in the no/unknown exposure group were significantly more likely to be female 0.30), live in the highest income neighborhoods and have lower comorbidity rates, including alcohol-use disorder and liver disease . Furthermore, prescription opioid recipients who accessed naloxone tended to be chronically receiving opioids (76.0% with \u226511 prescriptions in the past year), treated with high daily opioid doses (47.2% with >90 MME), and receiving current benzodiazepine prescriptions . Specifically, one-third (33.7%) of naloxone kits were dispensed by the top 1.0% (N = 35) of naloxone-dispensing pharmacies, and 88.0% of naloxone-dispensing pharmacies dispensed under 50 kits over the entire study period. The majority of naloxone-dispensing pharmacies were located in urban areas (86.9%) and dispensed OAT (66.9%) (Table 2).Over the study period, 2,729 pharmacies dispensed naloxone, and among these pharmacies, naloxone dispensing was highly clustered ; In this population-based study, we found that 67,910 individuals were dispensed naloxone through a community pharmacy in the first 21 months of the ONPP. The program was most successful in providing access to prescription OAT recipients, with less uptake among prescription opioid recipients and individuals with past opioid exposure despite their risk of overdose. Furthermore, although the population-adjusted rate of dispensing was low among people with no/unknown opioid exposure, this group was responsible for more than half of all naloxone kits were dispensed over the study period. Importantly, we also found that naloxone dispensing was highly clustered, with just over half of Ontario pharmacies participating in the ONPP, suggesting that barriers to access may continue to exist.The ONPP\u2019s relative success providing naloxone access to prescription OAT recipients is important as this is a group at high risk of overdose. This finAlthough we found that the ONPP led to considerable growth in naloxone distribution in the province, there were some notable gaps. Specifically, naloxone uptake among prescription opioid recipients was only 1.6%, despite some of these individuals likely being at risk of overdose. PrescripAt the provider level, only half (55.6%) of pharmacies eligible to participate in the ONPP did so, with a small number of pharmacies dispensing the majority of kits. Importantly, we found that two-thirds of naloxone-dispensing pharmacies also dispensed OAT, which may be influenced by the launch of the program that prioritized OAT-dispensing pharmacies for naloxone distribution. These fiSeveral limitations of this study warrant discussion. First, our study did not capture the entire population uptake of naloxone in Ontario since people can access this medication from other sources, including mobile services, needle exchange and hepatitis C programs, correctional facilities, safe injection sites and public health units., 29 BetwThe launch of the ONPP led to a rapid increase in the number of naloxone kits dispensed from pharmacies in Ontario. Although the program successfully engaged a considerable proportion of people treated with OAT, efforts to increase uptake among individuals at risk of opioid overdose appears warranted, particularly those being prescribed high daily doses of prescription opioids. Further, opportunities to expand pharmacy participation should be identified and pursued, particularly in regions of the province experiencing high rates of opioid overdoses. As accessible health care professionals, pharmacists are ideally positioned to identify individuals at risk of opioid overdose to provide harm reduction interventions such as take-home naloxone. Future research evaluating the effectiveness of this program in reducing overdose mortality will help measure the impact of this harm reduction program.S1 Tableth Revision (ICD-10) codes used to define comorbidities.*ICD-10: International Classification of Diseases, 10(DOCX)Click here for additional data file.S1 Fig(DOCX)Click here for additional data file.S2 FigGini coefficient = 0.78.(DOCX)Click here for additional data file."} +{"text": "Predatory journals fail to fulfill the tenets of biomedical publication: peer review, circulation, and access in perpetuity. Despite increasing attention in the lay and scientific press, no studies have directly assessed the perceptions of the authors or editors involved.Our objective was to understand the motivation of authors in sending their work to potentially predatory journals. Moreover, we aimed to understand the perspective of journal editors at journals cited as potentially predatory.Potential online predatory journals were randomly selected among 350 publishers and their 2204 biomedical journals. Author and editor email information was valid for 2227 total potential participants. A survey for authors and editors was created in an iterative fashion and distributed. Surveys assessed attitudes and knowledge about predatory publishing. Narrative comments were invited.P<.001). Only 26.2% of authors (54/206) were aware of Beall\u2019s list of predatory journals versus 49% (21/43) of editors (P<.001). A total of 30.1% of authors (62/206) believed their publication was published in a predatory journal. After defining predatory publishing, 87.9% of authors (181/206) surveyed would not publish in the same journal in the future.A total of 249 complete survey responses were analyzed. A total of 40% of editors (17/43) surveyed were not aware that they were listed as an editor for the particular journal in question. A total of 21.8% of authors (45/206) confirmed a lack of peer review. Whereas 77% (33/43) of all surveyed editors were at least somewhat familiar with predatory journals, only 33.0% of authors (68/206) were somewhat familiar with them (Authors publishing in suspected predatory journals are alarmingly uninformed in terms of predatory journal quality and practices. Editors\u2019 increased familiarity with predatory publishing did little to prevent their unwitting listing as editors. Some suspected predatory journals did provide services akin to open access publication. Education, research mentorship, and a realignment of research incentives may decrease the impact of predatory publishing. Increased access to the Internet has allowed for open access publishing to flourish. Traditional modes of scholarly publication involve the transfer of copyright from authors to publishers, with journal fees collected to provide access to articles. Traditional publishing, whether due to cost or perceived prejudicial peer review, is not embraced by all ,2. In coSo called \u201cpredatory\u201d journals take advantage of the open access publication model to prey on unsuspecting authors . Such joDefining what is and is not a predatory journal has been a point of contention among researchers -8. BeallWhat remains unknown amid this controversy is the perspective of both editors who manage predatory journals and those choosing to publish in them. While the lay press and literature has increasingly drawn attention to this issue, these journals continue to exist ,5,13. NoBeall\u2019s list was acceA total of 350 publishers were randomly selected from this list, using a random-number generator. Eight reviewers evaluated publishers using the following criteria. First, we confirmed an active link to the publisher website. Second, we reviewed the titles of journals within the portfolio of a publisher\u2019s work to assess if any were biomedical journals in scope. Specifically, we applied the MEDLINE criteria: \u201c[Journals] predominantly devoted to reporting original investigations in the biomedical and health sciences, including research in the basic sciences; clinical trials of therapeutic agents; effectiveness of diagnostic or therapeutic techniques; or studies relating to the behavioral, epidemiological, or educational aspects of medicine\u201d . JournalSurveys for both authors and editors were created during a round-table discussion among study authors. The surveys underwent iterative testing for clarity, content, and length. Next, we invited editors and authors to participate via email. Surveys were administered using REDCap, with one reminder sent to nonresponders. We simultaneously performed a nested randomized controlled trial on incentives to encourage survey response, which is published separately . InviteePrefer not to answer were not considered incomplete responses.Surveys assessed authors\u2019 basic demographics, publication history, their recollection of the editorial process for the article in question, and their knowledge regarding predatory journals see . EditorsSummary statistics were used to describe the cohort. Means and standard deviations as well medians and interquartile ranges (IQRs) were used for continuous variables. Frequency tables were used for categorical variables. The chi-square statistic was used to compare frequencies between groups. Developed-nation status was based on the World Bank listing for high-income countries derived from gross national income higher than US $12,056 per capita . StatistConsent for publication was granted by participants when they responded to the survey in accordance with Institutional Review Board (IRB) approval. Ethical clearance was granted by the IRB of the University of California, San Francisco, CA .P<.01). Several respondents provided incomplete responses (n=40). Complete responses were collated from 206 authors and 43 editors, out of a potential 1165 and 1062, respectively, for a final response rate of 11.18% (249/2227).Journals meeting selection criteria came from 181 distinct publishers. There was a substantial range in the number of journals per publisher represented in our cohort. A total of 58.0% of publishers (105/181) were singular entities, having only a single journal in their portfolio. However, several larger publishers were also included; indeed, 52.00% of 1146/2204) journals came from just 3 out of 181 publishing companies (1.7%). Of the articles selected, 59.68% (811/1359) were published in 2018, 17.73% (241/1359) were published in 2017, and none were published before 2014. Authors and editors represented a global academic community see . Of all 4 journalResponding authors had a median age of 43 years (IQR 33-54), with 47.0% (95/202) reporting that they had been in practice for over 15 years see . A totalP=.04), with 27.2% (56/206) of total articles reportedly cited. Authors\u2019 perceptions of the journals\u2019 prestige was not impacted by whether their paper was cited. Google Scholar searching confirmed that only 16% (9/56) of those articles purported to be cited had a recorded citation. A total of 40.8% of authors (84/206) felt this particular publication was neutral in terms of career advancement and 14.1% (29/206) had published in the same journal prior to this particular publication. Most common reasons for selecting this particular journal for publication were open access , solicitation , and affordability .A total of 12.1% of authors (25/206) felt publication in their chosen journal was both prestigious and had a positive impact on their career. In addition, 19.6% of authors (39/199) noted a positive career impact if they reported their paper was cited versus 10.6% (21/199) that reported a positive impact when their paper was not cited (P<.01). These authors reporting higher expenses were not necessarily more likely from high-income countries . Authors came from 54 countries, spanning all continents except Antarctica; 23.3% (48/206) were from India and 13.6% (28/206) were from the United States.Authors that paid fees in the top quartile (>US $519) for publication had no difference in perception of journal prestige, impact on career, shorter publication times, or fewer revision requests than authors paying lower fees see . They weEditors\u2019 median age was 41 years (IQR 33-53) see . Among sA total of 40% of editors (17/43) who responded were not aware that they were listed as an editor for the particular journal in question. These editors were excluded from subsequent analysis. Among remaining editors, 96% (25/26) felt their journal was not a predatory journal and 50% (13/26) were already aware their journal was listed on Beall\u2019s list. A total of 92% (24/26) of editors reported that their journal requires peer review. Editors reported that the mean cost to publish in their journals was US $634 (IQR 75-1360). Editors\u2019 estimated, on average, that 50% of manuscripts required revisions and that 35% were rejected. A total of 54% (14/26) of editors reported that 31-45 days elapsed between submission and acceptance.P<.001) (see P<.001). A total of 30.1% of authors (62/206) believed that their publication was published in a journal that could be defined as predatory, once given the definition. Given knowledge that a journal was definitely predatory, 87.9% of authors (181/206) surveyed would not publish in the same journal in the future.Whereas 77% of all surveyed editors (33/43) were at least somewhat familiar with predatory journals, only 33.0% (68/206) of authors were somewhat familiar with them (001) see . SimilarNarrative comments were also collected via the survey. These provided surprising and conflicting insight into the attitudes and opinions of both authors and editors. Additionally, many survey respondents felt passionate enough about this topic to contact the research staff via email to share additional long-form opinions. Selected comments are presented in an anonymized fashion in We found editors were at least somewhat familiar with predatory journals, but the vast majority of authors (67%) were not. Per authors and editors, in limited cases, predatory journals seemingly provide some editorial support via revisions, rejections, and circulation that was enough to drive citations. Predatory journal authorship is a global phenomenon in our study, with higher penetrance in India and the United States. Alarmingly, 39% of editors reported not even being aware of being a journal editor for the journal in question. Several editors sent us comments stating they had previously asked that their name and contact information be removed from the journal websites, given no purposeful affiliation. After alerting authors that their recent publication was in a potentially predatory journal, 88% would avoid the same journal, demonstrating that via dissemination of knowledge regarding predatory practices, predatory publishing may decrease.On the surface, these predatory journals are providing at least some service to authors. In our cohort, authors frequently recalled a peer review and a need to submit revisions. Editors similarly stated that a peer review was performed and approximately 35% of articles were rejected. A potential marker of journal prestige and circulation is ultimately citation, reported by 27% of surveyed authors . Of noteWe found that 40% of authors were from countries designated by the World Bank as high income; prior work suggests that authors who published in predatory journals were primarily from developing nations . A predoPrior work proposed that young na\u00efve authors are the target of predatory journals, but 47% of responding authors in this study have been in practice for more than 15 years . By way A high proportion of responding authors in our cohort reported that publication is an important facet of academic advancement. There is a growing concern that the motivation to publish may supersede desires for research quality . Both auThink. Check. Submit. [Potential solutions to predatory publishing include demanding promotion committees judge faculty on the quality of publications in lieu of sheer number . Authors Submit. , an inte Submit. . Researc Submit. . AccountSome authors shared already-published concerns regarding blacklists, such as Beall\u2019s stifling of innovation in open access publishing, which is why we cross-referenced our findings with well-publicized white lists to generate a cohort of authors and editors -8. PriorA major limitation to this study is our poor response rates from both authors and editors, but particularly editors. Given that 39% of responding editors were not even aware that they were editors at the journal in question, it is not surprising that editors-at-large may have faced confusion with our survey invitation. Moreover, unlike author email addresses, the editorial email addresses often took a generic form, such as \u201ceditor@journalname.org,\u201d and may have encountered staff that did not forward the survey to the intended recipient. Our data comes from an international cohort, but we randomized the selection of publishers and not the countries of publishers. As such, some countries only contributed via a single survey response and the responses should not be seen as representative of all authors of that region. All authors published their papers in English journals. Nonetheless, English may not be a first language for respondents, limiting responsiveness or leading to response error. Due to monetary and time constraints, we did not perform survey adaptation or cross-cultural validation for global participants ,32. SurvPredatory journal authorship is a global phenomenon not unique to early-career researchers. The majority of studied authors were not familiar with predatory publishing practices, despite being published in a suspected predatory journal. Alarmingly, 39% of editors reported that they were not even aware of being an editor for the journal in question, clearly confirming the unethical practices of such journals. Education, research mentorship, and a realignment of research incentives may decrease the impact of predatory publishing."} +{"text": "Older African Americans (OAA) are at high risk for becoming frail in later life. Interventions can reverse or delay frailty, yet OAA have largely been excluded from frailty intervention research. Many interventions are also time and resource intensive, making them inaccessible to socially disadvantaged OAA. We present results of a feasibility trial of a low dose frailty prevention intervention among 60 community-dwelling, pre-frail OAA aged 55+ recruited from a primary care clinic between June 1st and October 31st 2018. Using a 2-arm RCT, participants were assigned to the intervention, which was delivered by an occupational therapist (OT) and comprised of four sessions over four months , or enhanced usual care . Feasibility criteria were set a priori at 75% for participant retention , 80% for session engagement, 2 participants/week for mean participant accrual, and 90% for program satisfaction. Participants were 65% female with an average age of 76.58 years, 51.67% of which lived alone and 51.67% lived off of less than 15K per year. Feasibility metrics were met. The study recruited 2.5 participants per week and retained 75% of participants who attended 95% of scheduled sessions. Mean satisfaction scores were 93%. The intervention was feasible to deliver. Qualitative findings from exit interviews suggested changes to the program dose, structure, and content that could improve it for future use."} +{"text": "To evaluate agreement between pre- and post-laparoscopy gynecologicaldiagnosis in order to demonstrate the rationality of this minimally invasivetechnique use in gynecological propaedeutics. Retrospective chart review study conducted between March 2010 and October2016 based on a convenience sample. 315 patients undergoing surgicallaparoscopy at the Center of Gynecologic Endoscopy and Family Planning ofBotucatu Medical School/UNESP. Pre- and postoperative diagnoses werecompared by the diagnosis agreement test considering the proportions ofevents. Laparoscopy contributed to diagnosis in 59.6% of infertility cases(P>0.05), in 93.7% of chronic pelvic pain of undetermined origin(P<0.01) and conclusively elucidated the diagnosis of acute abdomen andthe ruling out of tubo-ovarian abcess (P<0.05). Laparoscopy alsoincreased the diagnosis of pelvic-abdominal adhesions in 76.7% (P>0.05). The use of laparoscopy considerably contributed to diagnostic elucidation,especially in cases of undetermined chronic pelvic pain. It is the basis for developingan adequate treatment plan and establishing effective patient managementstrategies--,9- Over the past years, laparoscopy has become a powerful propedeutic as well astherapeutic tool of modern gynecological practice. It can reduce the number ofinnappropiate procedures and unnecessary treatments with very low complicationrates Nonetheless, in many countries, medical residency programs in gynecology do notinclude laparoscopic training, be it for surgical therapeutic or even purelydiagnostic procedures. Therefore, this study aimed to assess patients underwentlaparoscopy to evaluate the consistency of agreement between pre- andpost-laparoscopy gynecological diagnosis in order to demonstrate the rationality oflaparoscopy use in gynecological propaedeutics, and thus expand the discussion aboutthe basis of the training of future gynecologists. This retrospective chart review study was conducted to evaluale all patientsundergoing surgical laparoscopy at the Center of Gynecologic Endoscopy andFamily Planning of Botucatu Medical School/UNESP, Brazil between March 2010 andOctober 2016 . Pre- an Data, such as age, body mass index (BMI= kg/m\u00b2), parity, abortion, age atmenarche, date of last menstruation, menstrual pattern, use of hormone therapy,history of pelvic inflammatory disease (PID), presence of systemic arterialhypertension (SAH), diabetes mellitus, thiroid diseases, dyslipidemia andsmoking were transcribed into an Excel spreadsheet for analysis. Information onpatients\u2019 clinical complaints, transvaginal-pelvic ultrasound findings,anatomopathological findings, type of surgical procedures performed, and therate of complications observed before, during and after laparoscopy were alsocomparatively assessed. Descriptive statistical analysis was performed. The absolute and relativefrequencies of the study parameters were assessed. Mean, standard deviation, andminimum-maximum values of quantitative variables, as well as the absolutefrequency and percentage of qualitative variables were estimated. Pre- andpostoperative diagnoses were compared by the diagnosis agreement testconsidering the proportions of events Patient mean age was 35 years. The majority of women were overweight (BMI= 26.94\u00b15.52) and in reproductive age (84.1%) . Hormone Laparoscopy was inconclusive in 17% of the patients assessed due to infertility withno apparent cause. However, in 83% of these cases it was essential for establishingthe diagnosis of polycystic ovary (2.1%) with no other reason for infertility,ovarian endometrioma (6.4%), adhesions (17%), and endometriosis (57.5%) (P>0.05). The dia The pre-laparoscopy diagnosis of complex ovarian cyst was related with thepost-laparoscopy diagnosis of hemorrhagic corpus luteum (37.5%), ovarian tumor(ovarian teratoma on anatomopathology) (50%), and retention cyst (12.5%). In 40% ofthe cases with a preoperative diagnosis of ovarian tumor, and in 77.8% of cases witha diagnosis of adnexal mass of unknown etiology, laparoscopy detected uterine myoma,endometriosis, adhesions and tubo-ovarian abcesses, but with no statisticaldifferences . In general, laparoscopy contributed to diagnosis elucidation in 59.6% of infertilitycases (P>0.05), 93.7% of chronic pelvic pain of undetermined origin (P<0.01),87.5% of complex ovarian cyst cases (P<0.05), 40% of ovarian tumor cases(P>0.05), and 77.8% of adnexal mass of unknown etiology cases (p>0.05) . Further,,,- Compared to conventional open surgery, laparoscopy has numerous advantages, such as(1) less postoperative pain, (2) shorter hospital stay, (3) lower rates ofpostoperative complications, (4) early return to daily activities, and (5) betteresthetic effect. These benefits combined decrease the direct and indirect costsrelated to the surgical procedure,,,- To some authors, laparoscopy should be an integral part of the evaluation of womenwith pelvic pain of undetermined origin due to its safety and reliability,,- Regulatory bodies have already emphasized the need of expanding validated trainingprograms to prepare professionals for the increasing use of laparoscopy beforeprogression to real procedures,, It is estimated that 73% of programs lead off laparoscopic skills in North Americabut only 29% of residencies provide a structured surgical curriculum and only 55% ofresidency programs have facilities for training in laparoscopy in the UnitedStates In this study, after excluding the cases of adnexal and/or ovarian diseases which requirehistopathological confirmation and cannot be accurately identified surgically,diagnostic elucidation after laparoscopy occurred in 93.7% of the cases of pelvicpain of unknown etiology (P<0.01), and 59.6% of the cases of infertility with noapparent cause (p>0.05). Furthermore, laparoscopy was conclusive in the diagnosisof acute abdomen, even though there was a low number of cases with this condition inour series (P<0.05).,,,, The introduction of laparoscopy into clinical practice has opened up new avenues forthe diagnosis and management of chronic pelvic pain. It is estimated that more thanhalf of patients with a normal preoperative pelvic examination will present abnormalfindings during the laparoscopic procedure, Except in cases of endometrioma, ovarian retention syndrome and ovarian residualsyndrome, ovarian cysts are not a common cause of chronic pelvic pain. Thelaparoscopic assessment of patients with chronic pelvic pain reveals ovarian cystsin only 4% of all cases excluding endometriomas-, Similarly, endometriosis is estimated to affect up to 50% of infertile women, andits severity appears to correlate with reduced fertility,, In this study, laparoscopy also proved to aid the diagnosis of tubo-ovarian abcess(P<0.05). Despite the small number of cases, these findings corroborate the roleof laparoscopy as a specific clinical criterion for the diagnosis of complicatedpelvic inflammatory disease The use of laparoscopy can reveal treatable conditions, not detected using othermethods, with a very low rate of complications. In our study, the rate ofpotentially severe complications ranged from 0.3% to 0.6%. A survey of 6.451laparoscopic procedures showed an overall complication rate of 0.65% (42/6451).However, this rate rose to 0.80% (39/4865) when surgical laparoscopy was compared tomerely diagnostic laparoscopy that was associated with a complication rate of 0.19%(3/1586) (P<0.001) The benefits of this minimally invasive technique indicate that an in-depthdiscussion on reshaping medical residency programs is necessary as to adjust them tothe new technology available as well as to today\u2019s reality. Given its propedeuticnature and association with very low complications risks, diagnostic laparoscopyshould be routinely addressed in the training of future gynecologists. All effortsshould be made so that health policies contemplate the dissemination and increasinguse of laparoscopy, which has been demonstrated to offer numerous advantagesthroughout the medical assistance system, especially in the field of gynecology. Since it is not included in the training of resident doctors in mostservices worldwide, laparoscopy\u2019s potential for development in stillconsiderable; The propedeutic role of laparoscopy for elucidating the diagnosis ofseveral conditions of undetermined origin, notably complaintsrelated to infertility and chronic pelvic pain, should not bedisregarded; Programs of medical residency in gynecology including training inthe use of propedeutic/diagnostic laparoscopy should be encouragedby medical care improvement policies. This can bring direct andindirect benefits, besides reducing costs throughout the healthcaresystem; Training in therapeutic laparoscopy should be provided inspecialized centers because the learning curve, despite beingreproducible, takes quite long and depends on the number ofprocedures performed by the surgeon."} +{"text": "Background: The aim of this study was to evaluate the benefit of standard practice Optical Coherence Tomography (OCT) imaging, as a complement to coronary angiography (CA), for optimizing the indications, strategy, and results of percutaneous coronary interventions (PCI). Methods: We retrospectively analyzed 182 patients with OCT imaging in a single tertiary center. Results: OCT use had a low prevalence (3.1% of 4256 CAs and 1.7% of 3027 PCIs). OCT was used post-CA in 71.5% and post-PCI in 28.5% of cases, mainly in acute coronary syndromes\u201495.6%. OCT was performed for borderline lesions in 43.4% of cases; lesion severity was reassessed as severe and led to PCI in 64.5% of them. OCT was performed for nonsignificant lesions in 17% of cases; lesion severity was reassessed as severe and led to PCI in 38.7% of them. OCT provided optimal selection for PCI strategy in 11% of cases. OCT identified suboptimal PCI results in 54% left main PCIs and in 48% bifurcation PCIs with optimal CA; PCI optimization was performed. In the only seven patients with suboptimal PCI, OCT revealed an optimal result in four cases, thus avoiding unneccessary optimization. In 27.3% of patients with post-CA OCT and PCI result \u201csystematic\u201d OCT control, a PCI optimization was indicated. Conclusion: OCT supplied a major benefit in 86.2% of cases, especially by identifying significant coroanry stenosis in CA borderline and nonsignificant lesions; OCT led to PCI indication in two-thirds and, respectively, one-third of these cases. In the post-PCI context, OCT led to an indication of PCI optimization in half of the complex left main and bifurcation lesions, as well as in a quarter of \u201csystematic\u201d post-PCI OCT controls. Cardiovascular diseases represent a major health burden, with coronary artery disease (CAD) as the most important cause of morbidity and mortality ,2. EveryCoronary angiography (CA) is the gold standard invasive procedure currently used for CAD diagnosis, decision-taking and assessing efficacy of percutaneous coronary interventions (PCIs) . CA limiOptical coherence tomography (OCT) further improves invasive intracoronary imaging, offering new insights on the coronary wall and lumen, due to its high resolution (10 micrometers) ,6. OCT pOver the last ten years, fast acquisition OCT devices and software allowed this method to be used safely, in everyday practice, as a complement to CA. OCT is therefore not only a very well recognized in vivo CAD research tool ,7,8, butThe aim of this study is to evaluate the benefit of standard practice OCT imaging, as a complement to CA for optimizing the indications, strategy and results of percutaneous coronary interventions. The study covers five years of practice of a single tertiary center from Romania.This study retrospectively analyzes the indications and benefit of OCT use in 182 patients, evaluated in a single tertiary center from Romania , over a period of 5 years (January 2012\u2013September 2017). During this interval, 4256 patients underwent CA for suspected CAD, of whom, 3027 patients also had PCI.No exclusion criteria were considered. Informed consent was obtained before the invasive procedure. Clinical data and angiographic examinations were stored in the hospital database and in a dedicated catheterization laboratory database.2.Data regarding cardiovascular risk factors were obtCA was performed via right radial artery in 143 (78.6%) patients, via femoral artery in 35 (19.2%) patients and transbrachial in the remaining four (2.2%) patients, on Siemens Coroskop T.O.P and Siemens Artis Zee angiographs . Severity of coronary stenosis was assessed visually and by quantitative coronary analysis (QCA). The highest degree of stenosis severity, usually the area stenosis severity provided by QCA, was considered. After CA, coronary arteries were classified as normal (without plaques), with nonsignificant lesions (<50%), with borderline lesions (50\u201370%) or with significant stenosis (>70%).OCT images were acquired with a commercially available system , using an over the wire OCT catheter . The entire length of the region of interest was scanned using the integrated automated pullback device at 20 mm/s. During image acquisition, coronary blood flow was replaced by continuous flushing of contrast medium directly from the guiding catheter. All images were recorded digitally, stored, and analyzed using proprietary software in concordance with standard consensus of OCT use .OCT was performed by all three senior interventional cardiologists, using the predefined indications in Indications for OCT use were the ones generally accepted at the time of the investigation 5,10,16,1610,16.The study complies with the Declaration of Helsinki on human research.2 test. A two-sided p-value of 0.05 was considered significant.Categorical variables were expressed as frequencies and compared with \u03c7The investigated population includes 174 (95.6%) patients with ACS, of which 50 had ST-elevated myocardial infarction (STEMI), 39 had non-ST elevated myocardial infarction (NSTEMI), 85 had unstable angina (UA), and eight had stable CAD (SCAD). Demographic, clinical and angiographic data of OCT investigated patients are presented in OCT was performed in two main instances: first, as a complemmentary imaging method after CA\u2014130 patients (71.5% of the OCT investigations) and second, as an imaging method just used first after PCI\u201452 patients (28.5% of the OCT investigations) . Post-CAIn the \u201cdecision-making OCT group\u201d (110 patients), there were 79 patients (43.4% of the OCT investigations) with borderline (50\u201370%) CA lesions and 31 patients (17% of the OCT investigations) with nonsignificant lesions (<50%) or with a normal aspect on CA .In the 79 patients with a high clinical and electrocardiogram suspicion of CAD and with borderline CA lesions, in 77 of them with ACS and only two with SCADs an accurate decision for revascularisation could not be made based on CA alone, so OCT was performed. After performing OCT, the severity of coronary artery lesions was reassessed and graded as severe (>70%) A/a, withIn the 31 patients with nonsignificant lesions (<50%) D/d, therp = 0.013).When performed after CA, OCT led to revascularization in significantly more patients with borderline lesions than in ones with nonsignificant lesions or normal coronary arteries ; OCT proved restenosis in eight and neoatherosclerosis in two patients E/e;-selection of PCI devices features ; there were three cases of long lesions PCI F/f, two -comprehensive assessment of native lesions suspected of complications ; OCT confirmed complicated atherosclerotic plaques in all three of them, with identification of thrombus in one patient.The second main indication for OCT, after CA, was represented by patients in whom a decision for PCI revascularization was taken after CA, but OCT was still needed on top of CA, in order to provide optimal selection of PCI strategy . In thesThe \u201cpost-PCI\u201d OCT group included 52 patients, with two main indications for imaging : assessmThis group included 24 patients with LM PCI, representing 13.2% of OCT indications and 19.8% of the 121 LM PCIs performed in our center, during the investigated time interval; there were mainly ACS patients, while two had SCAD; OCT was performed for LM PCI control in cases of technically challenging procedures (15 cases), two stents technique (seven cases), and for important LM, LAD, or LCX decalibration (two cases); optimal OCT results were found in 11 patients, without need for LM PCI optimization; OCT imaging found malappositions (10 patients) G/g and eThis group included 21 patients with bifurcation PCI, representing 11.5% of OCT indications and 2.2% of the 955 bifurcation PCIs performed in our center, during the investigated time interval; there were only ACS patients; OCT was performed for bifurcation PCI control in cases of technically challenging procedures (11 cases) and two stents techniques (10 cases); optimal OCT results were found in 11 patients, without need for PCI optimization; OCT imaging found malappositions (six patients) and edge dissections (four patients), leading to a decision for PCI optimization in these 10 out of the 21 patients .-angiographic suspicion of edge dissection (three cases); only one was confirmed by OCT, leading to PCI optimization;-angiographic suspicion of extensive coronary dissection (one case)\u2014unconfirmed by OCT;-angiographic suspicion of coronary thrombus (two cases), confirmed by OCT in both cases and followed by PCI optimization;-angiographic suspicion of significant residual stenosis in the native coronary, proximal to the stented lesion (one case), unconfirmed by OCT H/h.This group included seven patients , representing only 0.23% of the 3027 PCIs performed in our center in the investigated time interval. The indication for OCT imaging was represented byIn this group, OCT imaging revealed the presence of an optimal PCI result in four of the seven patients (57.1%), thus avoiding unneccessary PCI optimization. There were only three out of seven patients (42.8%) in whom PCI optimization was really needed.-in all the 130 patients having OCT imaging as a complement to CA, for assessing the indication of revascularization and-in 27 of the 52 patients investigated post-PCI (51.9% of this subgroup).For the entire group of 182 patients investigated by OCT, intracoronary imaging had a decisive benefit for optimizing interventional cardiology indications and strategy, in 157 patients (86.2%), as followsThere also were 44 OCT investigations performed after PCI, out of 77 cases, in patients from the \u201cpost-CA\u201d group. In these patients, OCT catheter was already used before PCI, OCT investigations were therefore performed for PCI result control. In this group of patients, all post-PCI angiographic results were optimal, but OCT found suboptimal result and led to optimization in 12 cases (27.3%): 10 with balloon post-dilatation for stent underexpansion and two with new stent implantation for edge dissections.Multiple centers use OCT in a variety of clinical scenarios for diagnosis and therapeutic optimization in coronary interventions ,12,13,14In our study, OCT proves particularly useful in the clinical setting of ACS (95.6% of the investigated patients), with 71.5% of OCTs performed as a complementary imaging method to CA, representing 3.1% of CAs in our center.We mainly used OCT to provide accurate diagnosis and therapeutic decisions concerning revascularization (60.4% of the OCT investigations). A moderate proportion (43.4%) of the OCT investigations were performed for borderline lesions, and 17% for assessment of coronary arteries with nonsignificant lesions or with a normal aspect. Our approach is in consensus with the recent european recommendation of OCT uA very important finding in our study is that OCT, performed complementary to CA, in ACS, reassessed the severity of coronary lesions and led to the indication of revascularization in 64.5% of borderline lesions, and in 38.7% of nonsignificant lesions or normal coronary arteries. This result would support inclusion of OCT imaging in the practice guidelines, in this setting.In our study, OCT also proved useful for the control of LM PCI patients with optimal angiographic results, which accounted for 13.2% of OCT indications. In these patients, suboptimal OCT findings as malappositions and edge dissections led to PCI optimization in not less than 54% of the cases. This finding underlines the limits of angiography for LM PCI assessment and may support the need for a systematic OCT imaging in this setting. In our study, OCT was used in only 19.8% of LM PCI patients, with technically challenging procedures, a two-stent technique, or important LM, LAD, or LCX decalibration.This was in contrast to the survey on intravascular imaging use, where participants reported a 77% use for LM PCI guidance .OCT was useful for optimization of bifurcation PCI, in difficult, technically challenging procedures and two-stent techniques. Despite a very good angiographic result in these patients, OCT found suboptimal results in 48% of the cases, with need for optimization. These findings support the limited existing data ,20,21 reWhile other authors report that 79.6% of IVI evaluations are done for PCI strategy planing, in selected cases , this inOCT provided support in cases with suboptimal angiographic PCI results, in whom imaging proved in fact to correspond to a good PCI result, in four of the seven investigated patients. This is a rare OCT indication but its results further support that OCT imaging may overcome CA limitations.While being available during the whole 5-year period of our study, OCT was used in only 1.7% of patients undergoing PCI. Our findings are comparable to the results of a recent large observational study, which showed a 1.3% prevalence of OCT use for PCI guiding .Our relatively low prevalence of OCT use (3.1% of CA and 1.7% of PCIs) is similar to the approach of 16.6% of interventionalists in the recent clinical practice survey, that used intravascular imaging in less than 5% of their patients . It is hOur study reports that OCT, while used in a limited number of pts submitted to CA and PCI, offer a substantial benefit for 86.2% of the investigated patients, leading to optimization of interventional cardiology indications and strategy. This is true in all patients in the post-CA group and in 51.9% of the post-PCI group.Our results concerning OCT-related decision changes in the post-PCI LM and bifurcations complex lesions group (51.9%) are similar to the ones reported by the DOCTORS trial, nOur study is an observational, retrospective, single-center one, with a limited sample size, without a statistical power calculation; thereby, our results should be interpreted with caution and considered hypothesis generating. Clinical follow-up of our patients is beyond the purpose of our study. Long term clinical benefit of a dual imagistic approach, using both CA and OCT, and not only CA, for the selection of PCI indications, strategy and result assessment and optimization, would require either a randomized study, or a comparison between centers using these two approaches.The main OCT benefit is in borderline and nonsignificant lesions on CA, in whom OCT identifies significant coronary stenosis and leads to PCI indication in two-thirds and, respectively, one-third of the patients. In the post-PCI context, OCT leads to an indication of PCI optimization in half of the complex left main and bifurcation lesions, as well as in a quarter of \u201csystematic\u201d post-PCI OCT controls."} +{"text": "Children with acute lymphoblastic leukemia (ALL) in low-income countries havedisproportionately lower cure rates than those in high-income countries. AtButaro Cancer Center of Excellence (BCCOE), physicians treated patients withALL with the first arm of the Hunger Protocol, a graduated-intensity methodtailored for resource-limited settings. This article provides the firstpublished outcomes, to our knowledge, of patients with ALL treated with thisprotocol.This is a retrospective descriptive study of patients with ALL enrolled atBCCOE from July 1, 2012 to June 30, 2014; data were collected throughDecember 31, 2015. Descriptive statistics were used to calculate patientdemographics, disease characteristics, and outcomes; event-free survival wasassessed at 2 years using the Kaplan-Meier method.Forty-two consecutive patients with ALL were included. At the end of thestudy period, 19% (eight) were alive without evidence of relapse: threecompleted treatment and five were continuing treatment. Among the remainingpatients, 71% (30) had died and 10% (four) were lost to follow-up. A totalof 83% (25) of the deaths were disease related, 3% (one) treatment-related,and 13% (four) unclear. Event-free survival was 22% ,considering lost to follow-up as an event, and 26% iflost to follow-up is censored.As expected, relapse was the major cause of failure with this low-intensityregimen. However, toxicity was acceptably low, and BCCOE has decided toadvance to intensity level 2. These results reflect the necessity of adata-driven approach and a continual improvement process to care for complexpatients in resource-constrained settings. In low- and middle-income countries (LMICs),conversely, survival rates remain poor\u2014often < 35%.10 This reflects many challenges, including gaps in implementationof care, delayed or incorrect diagnosis, comorbid conditions, lack of neededtreatment components, increased relapse rates, abandonment of therapy, death fromtoxicity, and suboptimal supportive care.12Acute lymphoblastic leukemia (ALL) is the most common pediatric cancerworldwide.13 Data onsimilar models in sub-Saharan Africa are limited, but a Tanzanian cohort of 81patients following the United Kingdom Acute Lymphoblastic Leukaemia 2003 (UKALL2003)protocol had a 2-year EFS rate of 26%.14 Obstacles included availability and affordability ofchemotherapy and supply of blood products.Monitoring ALL outcomes can provide a useful metric of a program\u2019s capacity toaddress delivery of complex longitudinal oncology care. Successful models fortreating ALL in resource-limited settings have been reported in South America. Forexample, 5-year event-free survival (EFS) rates in a Brazilian hospital increasedfrom 32% to 63% from 1980 to 2002 because of improvements in clinician training,patient social support, supportive care, and treatment availability andstandardization.16 After a national consensus meetingin March 2012, BCCOE began treating patients with ALL in accordance with thegraduated intensity regimen proposed by Hunger et al,17 an approach developed specifically forlow-resource settings. Treatment facilities begin with regimen 1, a low-intensitymedication regimen, and advance to an increased medication regimen only afterdemonstrating that treatment-related toxicity is acceptably low (less than one deathfor every 25 patients). To our knowledge, no prior studies have reported on thisregimen in a low-resource setting. Therefore, the objective of this study is toreport the outcomes of using regimen 1 of the Hunger protocol on pediatric patientsat BCCOE, as well as the quantitative measures of resource demands and delays incare.Located in northern rural Rwanda, Butaro Cancer Center of Excellence (BCCOE) ishoused in the Ministry of Health\u2019s Butaro District Hospital and provides freecancer care in partnership with Partners In Health/Inshuti mu Buzima and theDana-Farber/Brigham and Women\u2019s Cancer Center. BCCOE has been described ingreater detail elsewhere.During the study period, BCCOE treated 169 pediatric oncology patients, in whomALL was the second most common diagnosis (after nephroblastoma). At the time ofthis study, BCCOE offered patients with ALL basic imaging (x-ray andultrasound), laboratory tests, bone marrow biopsy, and pathology processing. Inaddition, social services covered costs for transportation and nutritionalsupport. Pathologists at Brigham and Women\u2019s Hospital orRwandan referral hospitals or visiting pathologists at BCCOE interpreted tissuespecimens.l-asparaginase . Thisstudy was approved by the Rwanda National Ethics Committee, the Inshuti MuBuzima Research Committee, and the Institutional Review Board at PartnersHealthcare, Boston, Massachusetts.Patients were considered to start a phase of treatment once the firstchemotherapy agent was administered. A phase of treatment was consideredcomplete if documented in the medical record. Documented treatment delays werethose that postponed chemotherapy administration for any duration.Disease-related deaths were defined as occurring either before treatment beganor after relapsed or refractory disease. Relapse was confirmed by clinicalsymptoms, derangement of CBC, and presence of blasts in the peripheral bloodfilm after a period of remission. Refractory disease was defined as failure toachieve remission after completion of either induction or consolidation. Theremaining deaths were deemed either treatment related (those after initiation ofchemotherapy) or unclear . Loss to follow-up (LTFU) was strictly defined asmissing the most recent appointment.EFS from intake for all patients diagnosed with pathology was assessed at 2 yearsusing the Kaplan-Meier method. This was calculated twice. First, events weredeath from any cause, relapsed disease, and LTFU. Second, events were death fromany cause and relapsed disease; LTFU was right-censored.17 Forty-twopatients were evaluated with a new pathologically confirmed diagnosis of ALL after onset of symptoms, the most common of which werelymphadenopathy 76% (32), fever 76% (32), and malaise 57% (24). The most commonextramedullary sites of involvement were lymph nodes 80% (33), spleen 67% (28),and liver 55% (23).Disease immunophenotype was unknown for 60% 25) of patients, 21% (nine) hadB-cell, and 19% (eight) had T-cell. In addition to subtype, other information,such as CNS involvement, was often unavailable and 2. U5 of patiOf the 42 patients who began therapy for ALL, 95% (40) initiated induction, 83%(35) consolidation, and 71% (30) maintenance . At the For patients alive at time of analysis, treatment duration was a median of 699.5days . Of the 30 deaths, 83% (25) were disease related,3% (one) were treatment-related, and 13% (four) were unknown. Deaths occurredthroughout all phases of treatment, although concentrated in two periods: withinthe first 2 months after presentation, and 6 to 8 months after initiation oftherapy, most frequently during the first cycles of maintenance .3/\u03bcL . For the 40 patients who started induction therapy, 63% (25)required packed red blood cells and 50% (20) required platelets of patients of patients , and delAppendix . Medical1 and the ability to provide care for patients withALL is an essential component of oncology programs serving LMICs. However, given theduration of therapy, the recurrent periods of neutropenia, and the supportive carerequirements, including transfusions and antibiotics, delivery of care requires arobust medical infrastructure. To our knowledge, our results represent the firstpublished outcomesfrom a rural cancer center in a low-income country using thestrategy proposed by the Hunger group17 that restructures treatment into stratified levels oftherapeutic intensities. This model recommends an initial, low-intensity regimen anddata capture to assess the incidence of treatment-related deaths. Once care can bedemonstrated to be safely provided, intensity of care can be increased.ALL is the most common hematologic malignancy in children,14In North American cohorts, an estimated 5% to 25% of patients with ALL receivecranial radiation for treatment and prophylaxis of CNS lymphoma.18 In our patient cohort, 53% ofpatients experienced relapse. Given this high relapse rate in patients receivinglow-intensity treatment, it is likely the low-intensity treatment was insufficientfor long-term survival. For some critically ill patients, the precise cause ofmortality was difficult to determine when signs of infection coincided withtreatment initiation. Nevertheless, definitive treatment-related toxicity wassufficiently low to advance to the next level of therapy per Hungerguidelines.17We piloted this approach at BCCOE, a rural-based cancer center where care is providedby pediatricians, internists and general practitioners follow strict treatmentprotocols, and there is support from visiting on-site oncologists and regular remotesupport from affiliated oncologists. As expected, given the initial low-intensityand anthracycline-free regimen, relapse was the major cause of treatment failure andled to survival rates similar to the 26% estimated 2-year EFS and 8.1 month mediansurvival of a Tanzanian cohort.14 In addition, the lack ofin-country radiation therapy poses financial and operational challenges. Whendisease stratification can be achieved along with simultaneous training of hospitalpersonnel, strengthening of supportive care, and standardizing of treatmentregimens, outcomes can markedly improve, as was seen with the 63% 5-year EFS inBrazil.13 This data-drivenapproach to improving care can only be achieved in the context of collecting andanalyzing high-quality patient data, a challenge in all health care settings andparticularly in a resource-constrained environment.Intensification of treatment, however, requires disease stratification, a challengegiven the limited number of physicians, inconsistent access to CSF diagnostics,difficulties in reliably obtaining immunophenotyping, and delays in pathologyreports and 2.8,19 and 22% in El Salvador.8 Patient social support, such ascoverage of transportation and chemotherapy costs as provided at BCCOE, have helpedin similar settings and have led to lower abandonment rates of 9% inTanzania14 and 0.5% inBrazil.13 Given itsmission to provide care to all patients, both social and clinical, BCCOE has alsonoted low levels of abandonment and delays in treating other cancers, such asnephroblastoma.20Treatment abandonment, often cited as a cause of treatment failure for patients withALL, was uncommon at BCCOE. Although additional follow-up will be needed, the 10%lost to follow-up rate was modest compared with 35% in Indonesia21 At BCCOE, > 40% of patientswho started treatment required transfusions; this drastically underscores theimportance of a reliable system to provide supportive clinical care.22 Quantitativelydocumenting this need could serve as a tool to predicting and planning for futuretransfusion needs in similar settings. Some minor lapses in availability ofchemotherapeutics led to additional delays. Alterations in chemotherapy regimensbecause of lack of drug availability have led to poorer survival in bothresource-rich and resource-constrained settings,23 and, therefore,more accurate predictions and a reliable supply chain for ALL medications andtransfusions has become a crucial goal at BCCOE.In the presented approach to classifying delays, health system delays, such aswaiting for blood products and availability of chemotherapy agents, were the mostcommon in our patient population. Inconsistent sources for both blood products andsome chemotherapy Appendix weremajIn the context of Rwanda\u2019s dedication to providing cancer care, the RwandanMinistry of Health has hosted regular national consensus meetings for cancerprotocol development. The BCCOE clinical team presented these data at the pediatricprotocol meeting in the spring of 2015. After reviewing the results, the committeesupported intensifying the national ALL treatment protocol, given the high relapserate and acceptable treatment-related death rate. This data-driven approach thatfocuses particularly on resource demands of care is critical to patient outcomes inthis and other resource-constrained settings.In conclusion, this study details our experience treating patients with ALL in arural Rwandan cancer center and to our knowledge reports the first publishedoutcomesusing the lowest intensity level of the Hunger ALL protocol. As expectedwith a low-intensity regimen, a high rate of disease-related mortality occurred,interestingly clustering in two time periods. However, treatment-related toxicitywas below the threshold suggested for increasing treatment intensification. Inaddition to supplementing the limited literature on ALL care in sub-Saharan Africa,the quantification of transfusion needs and classification of treatment delays canbe used to predict challenges to care in similar settings.Overall, we have demonstrated that an iterative model of cancer care, delivered bynononcologists with remote oncological support, where implementation is followed byanalysis of outcomes and subsequent evidence-based changes for improvement of care,allows for accountable delivery of ALL treatment in LMICs using the Hunger approach.We are now risk-stratifying patients and advancing to regimen 2 for high-riskpatients after an intensive educational program for providers. These results pointto the necessity of a data-driven approach to optimize care for complex patients inresource-constrained settings."} +{"text": "OBJECTIVES/SPECIFIC AIMS: Gender affirmation is a critical aspect of the health and well-being of transgender individuals. For many transgender people, this includes changing one\u2019s physical appearance to align with one\u2019s felt gender. Some gender-affirming body modifications require medical interventions such as hormone therapies and surgeries. Other modifications, such as tucking to create a flat-appearing lower pelvis and binding to create a flat-appearing chest, require no external intervention. The published literature is slowly growing on the health effects of gender affirming medical interventions; however, other body modifications are understudied. As part of our needs assessment of the transgender community, we sought to understand the frequency and health impact of binding and tucking. METHODS/STUDY POPULATION: A quantitative online survey was developed based on qualitative interviews with 20 community-based key informants. The survey was available online, in English, for 6 months. Eligible participants were 18 years of age or older, lived in the Baltimore metropolitan area, and identified as transgender and/or a sex different from what was assigned on their original birth certificate. RESULTS/ANTICIPATED RESULTS: 139 participants provided complete data: 45% were assigned male at birth (AMAB) and 55% were assigned female at birth (AFAB). In total, 54% were Black, 40% White, and 9% Latinx. Of AFAB participants, 80% had bound their chest tissue. Of those who had bound, 51% bound 7 days/week, 62% bound 8+ hours per day, and 68% were concerned about the health effects of binding. The most common symptoms associated with binding were back pain (65%), shortness of breath (48.6%), bad posture (32%), chest pain (30%), and light-headedness (30%). Of AMAB participants, 71% had ever tucked, 85% of those tucked 7 days per week, 79% tucked 8+ hours per day, and 50% were concerned about the health effects of tucking. Most common symptoms included itching (28%), rash (21%), testicular pain (17%), penile pain (14%), and skin infections (12%). DISCUSSION/SIGNIFICANCE OF IMPACT: The majority of transgender participants used binding or tucking for gender-affirming body modification and at least half of them have concerns about associated health effects. Clinicians should ask transgender patients about binding and tucking behaviors and assess for common symptoms. More research is needed to better understand the benefits and risks of gender-affirming binding and tucking behaviors."} +{"text": "Of 795,000 strokes occurring annually in the United States, 87% are classified as ischemic strokes . Aging iAging and cerebral vasculature. The complex network of the adult brain vasculature measures approximately 370 miles, receives about 20% of total cardiac output, and exchanges 20% of total blood glucose and oxygen. With aging, both cerebral micro- and macro-circulations undergo structural and functional alterations. Age-related microcirculatory changes are presumably mediated by endothelial dysfunction and impaired cerebral autoregulation and neurovascular coupling. Whereas endothelial dysfunction promotes neuro-inflammation, impaired cerebral autoregulation may lead to microvascular injury, and impaired neurovascular coupling fosters a decline in cortical function, all potential targets for future therapeutic interventions. Aging, in otherwise healthy individuals, is associated with numerous noticeable changes in human intracranial and extracranial cerebral arteries that predict the risk of future stroke.Aging and silent cerebrovascular disease. Silent cerebrovascular disease represents structural abnormalities, presumed vascular etiology, on neuroimaging not supported by clinically recognized stroke symptoms. The prevalence of silent cerebrovascular disease increases with advancing age and is recognizable as the following parenchymal lesions: 1) Silent infarcts (silent strokes), prevalence 6% and 28%, exceeds symptomatic stroke by a ratio of 10:1, 2) white matter hyperintensity or hypodensity on neuroimaging represent microvascular disease occurring in 20% to 94% older adults, and 3) cerebral microbleeds indicate silent intracerebral hemorrhages in 38% of general population aged >80 years. These conditions are age dependent and forecast increased risk of future symptomatic strokes recommendation for aspirin use in adults aged 60 to 69 years and do not recommend its use in those aged \u2265 70 years, or statin therapy for people aged \u2265 75 years for primary prevention of cardiovascular events [r events . HoweverStroke mortality. Stroke remains the 5th leading cause of death, one of every 19 death, in the United States, despite decreased incidence rates (1987 to 2011) and age-adjusted death rates (2005 to 2015) [Conclusion. To continue the gains achieved over decades, in reducing the overall incidence and mortality associated with stroke, it is important to remain focused on not only the risk factors but also on comorbidity."} +{"text": "Chronic kidney disease (CKD) is an independent risk factor for severalunfavorable outcomes including cardiovascular disease (CVD), particularly inthe elderly, who represent the most rapidly growing segment of the end-stagekidney disease (ESKD) population. Portugal has the highest Europeanunadjusted incidence and prevalence rates of ESKD. In 2012, we started tofollow a cohort of elderly CKD patients, we describe their baselinecharacteristics, risk profile, and cardiovascular disease burden.All CKD patients aged 65 years and older referred to our department during2012 were enrolled. Baseline data included: demographic, CKD stage,medication, comorbid conditions. Estimated glomerular filtration rate (eGFR)was calculated by the CKD-EPI formula.2participated in the study. Fifty percent had diabetes (DM), 85%dyslipidemia, 96% hypertension; 26% were current/former smokers, and 24% hada body mass index > 30 kg/m2. The prevalence of CVD was 62%and higher in stage 4-5 patients; in diabetics, it gradually increased withCKD progression (stage 3a < stage 3b < stage 4-5) .A total of 416 patients, 50% referred by primary care physicians, aged 77 \u00b1 7years, 52% male, with a median eGFR of 32 mL/min/1.73mAt baseline, our CKD elderly cohort had a higher burden of CVD. Theprevalence of CVD was greater than in other European CKD cohorts. Lowerlevel of eGFR was associated with a greater burden of CVD and was morepronounced in diabetics, highlighting the importance of strategicallytargeting cardiovascular risk reduction in these patients. CHP isa tertiary-care hospital that serves a diverse population of 500 000 inhabitantsin the North region of the country.Data collection was conducted by nephrologists using electronic case reportforms. Reporting of cardiovascular disease was based on both the patients\u2019 selfreport and review of their medical records by trained staff on the same date ofthe baseline interview. The study was performed in accordance with theDeclaration of Helsinki and approved by the Institutional Review Board ofCHP.Baseline date included sex, age, body mass index (BMI), CKD stage, proteinuria,medication, and comorbid conditions, such as diabetes, dyslipidemia,hypertension, smoking status, and cardiovascular disease. Cardiovascular diseasewas defined as the history of at least one of the following: cardiac disease,cerebrovascular disease, and peripheral vascular disease. Cardiac disease wasdefined as the history of coronary artery disease, congestive heart failure, andsevere valvular heart disease with or without valvular replacement. Criteria forthe diagnosis of coronary artery disease included previous myocardialinfarction, angina pectoris, coronary artery bypass grafting, or percutaneoustransluminal coronary angioplasty with or without stent implantation.Cerebrovascular disease included previous transient ischemic attack, stroke, orcerebral hemorrhage. Peripheral artery disease was defined as the presence ofintermittent claudication, need of peripheral revascularization, oramputation.All diabetic patients met the classification criteria established by the AmericanDiabetes Association. Hypertension was considered if the patient had systolicblood pressure (BP) > 140 mmHg or diastolic BP > 90 mmHg or need forantihypertensive drugs. Dyslipidemia included total serum cholesterol > 200mg/dL, or triglycerides > 150 mg/dL, or high-density lipoprotein (HDL)cholesterol < 40 mg/dL in males and < 48 mg/dL in females, or low-densitylipoprotein (LDL) cholesterol > 100 mg/dL, or need for lipid-loweringdrugs.Glomerular filtration rate was estimated (eGFR) using the Chronic Kidney DiseaseEpidemiology (CKD-EPI) 2009 creatinine equationCognitive status was evaluated and screened using the Mini Mental StateExamination (MMSE)A modified version of the Charlson comorbidity index (mCCI)Baseline characteristics are described using mean \u00b1 standard deviation or medianwith interquartile ranges for continuous variables, while categorical data arepresented as numbers and percentages. Cardiovascular disease burden was comparedbetween CKD stages by Chi-squared test for trend for categorical variables.Statistical analyses were performed using SPSS version 22.0. P-value < 0.05was considered statistically significant.From a total of 848 patients newly referred to our Nephrology department during2012, 416 of them were 65 years and older. Of these, all were Caucasians, 52%were male, with a mean age of 77 years, and 36% of them were aged 80 years ormore. About 50% (n = 206) of the patients were diabetic. The majority (85%) ofthe study population came from urban areas.2. The most frequent etiologies of renal diseasewere ischemic nephropathy and diabetic nephropathy ; unknown causes of renal disease were 55 (13%). Only 4% (n = 17) of thepatients had a renal biopsy.Their baseline characteristics, divided by gender and by the presence or absenceof diabetes are summarized in 2). The BMI ranged from a mean value of 25.7 \u00b1 4.1kg/m2 in men without diabetes to 29.5 \u00b1 5.5 kg/m2 inwomen with diabetes.Most of patients were nonsmokers . The proportion of current orformer smokers was highest in men with and without diabetes . Overall, 24% (n = 101) of enrolled patients were obese (BMI > 30kg/mAbout 96% (n = 400) of the patients presented hypertension, with a mean BP of141/72 mmHg. In approximately 30% of the patients it was < 130/80 mmHg and inapproximately 50% it was < 140/90 mmHg; men with diabetes were the group withworst BP control . About 50% (n = 207) of the patientswere receiving two or more antihypertensive drugs (excluding diuretics), and 14%(n = 58) were under three or more antihypertensive drugs. Inhibitors of therenin angiotensin system were the drugs most frequently used : angiotensin-converting enzyme (iECA) inhibitors in 33% (n = 137),angiotensin II receptor blockers (ARB) in 41% (n = 172), and combined iECA andARB in 4% (n = 16) of the patients. The use of these agents was more frequent inmen with diabetes (77%). About 71% (n = 296) of the patients were ondiuretics.Dyslipidemia was present in 85% of the patients (n = 354) and 60% (n = 248) wereunder lipid-lowering medication. Dyslipidemia was more prevalent in patientswith diabetes .An active or previous malignancy was present in 15% (n = 62) of patients. About25% (n = 105) of the patients had a high comorbidity index (mCCI score \u2265 5),particularly men with diabetes .Supplementary Table S1), clinical anddemographic data were very similar in the three groups, with the exception of ahigher systolic BP, the use of more antihypertensive drugs, higher prevalence ofdyslipidemia, and higher proteinuria level in those with presumed diabeticnephropathy.About 50% (n = 206) of the patients were diabetic, but in only 51% (n = 106) ofthem, diabetic nephropathy was considered the etiology of renal disease; 48% ofthose patients with etiologies of CKD other than diabetic nephropathy haddiabetes. When we analyzed baseline characteristics in patients with diabetesseparately for patients with and without diabetic nephropathy in comparison topatients without diabetes of the patients were totallydependent, and 38% (n = 158) were partially dependent with no difference betweenthe groups. Cognitive impairment was present in 12% (n = 50) of the patients,with no difference between the groups.Globally, eGFR was slightly lower in men, particularly those without diabetes.The mean uPCr rate was 1.1, higher in patients with diabetes when compared topatients without diabetes.Most patients had a hemoglobin level \u2265 11 g/dL , and the percentageof patients with transferrin saturation < 20% was 38% (n = 158), and ferritinlevel < 100 was 25% (n = 104), respectively. Only 5% (n = 21) of the totalcohort was receiving erythropoiesis stimulating agents (ESA). The percentage ofpatients on oral and IV iron supplementation were 10% (n = 42) and 0.7% (n = 3),respectively.Intact parathyroid hormone was elevated in 81% (n = 337) of the patients, despitegood control of calcium-phosphorus levels. The percentage of patients beingtreated with vitamin D supplementation and phosphate binders was 7% (n = 28) and4% (n = 17), respectively.Cardiovascular disease was present in 62% (n = 256) of the patients: coronaryartery disease in 25% (n = 103), cerebrovascular disease in 24% (n = 100), andperipheral vascular disease in 19% (n = 77), respectively .Coronary artery disease was present in 31% (n = 64) of the patients withdiabetes, compared to 19% (n = 39) in patients without diabetes.Previous cerebrovascular events were more frequent in men compared to women: 28%(n = 60) and 20% (n = 40), respectively; the prevalence was only slightly higherin patients with diabetes compared to patients without diabetes: 26% (n = 53)and 22% (n = 47), respectively.Peripheral vascular disease was more prevalent in patients with diabetes comparedto patients without diabetes, 24% (n = 49) and 13% (n = 28), respectively, andin men compared to women, 23% (n = 51) and 13% (n = 26), respectively.Stratifying the CKD stages in 3a, 3b, and 4-5 the prevalence of coronary arterydisease, congestive heart failure, and peripheral vascular disease were highestin stage 4-5 patients, gradually increasing with CKD progression . The carWhen we designed our longitudinal cohort study, the main objective was to identifythe main predictors for CKD progression and death in elderly CKD patients referredto our outpatient departmentA particular characteristic of this study is that all enrolled patients were newlyreferred to our nephrology department. This gives us information on the baselinecharacteristics of the patients before they receive specific attention from thenephrologist.,In our cohort, the two most frequent causes of CKD were ischemic and diabeticnephropathy, which are considered leading causes of CKD worldwide,The prevalence of cardiovascular disease in our elderly CKD cohort was very high,present in 62% of the patients. Patients with CKD are more prone to developcardiovascular diseaseIn our cohort, many established risk factors of cardiovascular disease showed a highprevalence; with an increase in the prevalence of cardiovascular disease with worseCKD stage . The carAlthough our study was not designed to identify risk factors for CKD and forcardiovascular disease, several characteristics of the patients provided indirectevidence for several predisposing factors.First, the diabetes prevalence of 50% is almost twice as high as in thePREVADIAB-Among the traditional risk factors for CKD and for cardiovascular disease, thepresence of hypertension in our cohort was almost universal (96%), withoutsignificant differences between diabetic and non-diabetic patients. In terms ofhypertension control, blood pressure was < 130/80 mmHg in only approximatelyone-third of the patients. This gap between targets and clinical reality isconsistent with other CKD cohort studies-,Current smoking was reported in 5% of the cohort, and former smoking in 21 % , with a 2), which islower than the prevalence in other European CKD cohorts-Overall, 24% of enrolled patients were obese (BMI > 30 kg/m,Prediction of the renal and cardiovascular risks in people with CKD is likely to beimproved by the incorporation of albuminuria into kidney disease stagingDyslipidemia is also a traditional cardiovascular risk factor that is frequentlyobserved in CKD patients, with an increasing incidence with CKD progressionAnemia is also an associated factor of cardiovascular disease prevalence andmortality, and CKD progressionCKD-mineral bone disorder is a major contributor to vascular calcification andcardiovascular diseaseThe prevalence of diabetes as well as other risk factors for CKD may partly explaininternational variation in CKD prevalence. In a recent narrative review on thefactors that potentially underlie observed international differences in CKDprevalence in the elderly within EuropeThe strengths of our study include the rigorous exploration of the first PortugueseCKD cohort with patients aged 65 years and over newly referred to a nephrologyclinic. Furthermore, this was a representative group of patients, and knowing theirbaseline characteristics and cardiovascular morbidity will allow a betterunderstanding of CKD epidemiology, nephrology referral policy in our geographicalarea, and the global approach to cardiovascular risk.There are certain limitations to our research. First, this is a single-center study.Second, some misclassification bias maybe have been introduced based on thepatients\u2019 self-reporting of comorbidity. Finally, because this cohort only comprisedpatients attending the nephrology outpatient clinic, our results may not necessarilytranslate to CKD patients who are not referred to nephrologists.In summary, the characteristics of our referral CKD cohort demonstrated the heavyburden of cardiovascular risk profile and disease, and reflected an important roleof several risk factors for kidney disease development. The prevalence of diabetesand cardiovascular disease is greater than other European CKD cohorts.Lower eGFR level was associated with a greater burden of cardiovascular disease,highlighting the importance of strategically targeting cardiovascular risk reductionin these older patients. This is an important group of patients that should becharacterized and understood; our results should improve management of thesepatients over time."} +{"text": "Staphylococcus aureus (CA-MRSA) resulted in the recommended use of clindamycin and trimethoprim-sulfamethoxazole (TMP-SMX) for suspected S. aureus infections. The objective of this study was to determine the resistance to methicillin, clindamycin, and TMP-SMX in S. aureus isolates during a 10-year period.The emergence of community-associated methicillin-resistant S. aureus isolates in the outpatient and inpatient settings at Nationwide Children\u2019s Hospital from 1/1/2005 to 12/31/2014. Duplicate isolates from the same site and year and those obtained for MRSA surveillance or from patients with cystic fibrosis were excluded.Retrospective review of the antimicrobial susceptibilities of all S. aureus isolates from 2005\u20132014, 40,795 (71%) were included. In the outpatient setting, methicillin resistance decreased from 54% to 44% (p<0.001) while among inpatient isolates, no significant change was observed. From 2009\u20132014, resistance to clindamycin among outpatient isolates increased from 16% to 17% (p = 0.002) but no significant trend was observed among inpatient isolates (18% to 22%). Similarly, TMP-SMX resistance increased in outpatient S. aureus isolates from 2005\u20132014 but not among inpatient isolates. Among both inpatient and outpatient isolates, methicillin-susceptible S. aureus (MSSA) exhibited higher resistance to both clindamycin and TMP-SMX than MRSA. In addition, resistance to methicillin, clindamycin and TMP-SMX varied widely according to the site of specimen collection.Of the 57,788 S. aureus isolates were identified at a large pediatric hospital, substantial changes in methicillin, clindamycin, and TMP-SMX resistance occurred. These findings highlight the importance of ongoing surveillance of the local antimicrobial resistance in S. aureus in order to guide empiric antimicrobial therapy.In a decade where >40,000 Staphylococcus aureus (CA-MRSA) infections in the late 1990s[S. aureus (MSSA) to clindamycin, trimethoprim-sulfamethoxazole (TMP-SMX), and tetracyclines.[S. aureus isolates identified in the outpatient and inpatient settings at Nationwide Children\u2019s Hospital, Columbus, Ohio during a 10-year period. In addition, differences in antimicrobial resistance patterns by type of staphylococcal infection were determined. Such information may impact recommendations for empiric therapy of staphylococcal infections in children.The emergence of community-associated methicillin-resistant ate 1990s resultedcyclines.\u201311 Clindcyclines., 13 TherS. aureus isolates that were identified by the Microbiology Laboratory at Nationwide Children\u2019s Hospital (NCH) from January 1, 2005 to December 31, 2014. The NCH Microbiology Laboratory serves an area of over 3,000 square miles that includes the Columbus Metropolitan area as well as adjacent urban and rural counties . Before 2014, there was no protocol for empiric antimicrobial therapy for possible staphylococcal infection at NCH, the only pediatric tertiary care center in central Ohio. In 2014, the Pediatric Infectious Diseases division recommended the use of clindamycin for suspected and uncomplicated staphylococcal infections in previously healthy children greater than one year of age that were cared for in non-intensive care settings.The Institutional Review Board of Nationwide Children\u2019s Hospital approved the study with a waiver of informed consent given that the data were analyzed anonymously. This retrospective study evaluated the antimicrobial susceptibilities to methicillin, clindamycin, and TMP-SMX in all S. aureus was performed using the Laboratory Information Management System. All S. aureus isolates that grew in culture and were identified by the NCH Microbiology Laboratory from all body and tissue sites were included. Duplicate isolates from the same patient that were cultured from the same site and year, isolates from samples obtained for MRSA surveillance, and isolates from patients with cystic fibrosis who were more likely to harbor multidrug resistant bacteria were excluded.Ascertainment of all positive cultures for All staphylococcal isolates were assessed as being from an inpatient or outpatient source based on the patient\u2019s location at the time of specimen collection. Information regarding patient location was obtained using the NCH Enterprise Data Warehouse. Isolates from the Emergency Department were classified according to patient disposition. The isolates also were classified by the body site from where they were obtained: blood, musculoskeletal , respiratory tract , peritoneal fluid, urine, cerebrospinal fluid (CSF), skin and soft tissue (SST), and \u201cother\u201d sites .S. aureus isolates was performed by the NCH Microbiology Laboratory using mostly the automated VITEK-2 system for determination of the minimum inhibitory concentrations (MIC). On occasion, E-testing also was performed to confirm or verify results of the VITEK test. MICs of \u22654 \u03bcg/mL and \u22654/76 \u03bcg/mL defined resistance to clindamycin and TMP-SMX, respectively, as established by the Clinical and Laboratory Standard Institutes (CLSI). Starting in 2009, a D-test for determination of inducible clindamycin resistance was performed on all erythromycin-resistant S. aureus isolates. Therefore, trends of clindamycin resistance were analyzed only from 2009 to 2014.During the entire study period (2005\u20132014), antimicrobial susceptibility testing of 2) test and between MRSA and MSSA using Fisher\u2019s exact test. Antimicrobial resistance trends over time were analyzed using the \u03c72 test for trends. A two-sided P < 0.05 was considered to be statistically significant. Statistical analyses were conducted using GraphPad Prism, version 7.0 .Descriptive statistics were reported as frequency distributions or proportions. Proportion of resistant isolates between different sites were compared using chi-square were excluded secondary to being duplicate isolates from the same site and patient encounter , isolates identified during the same year , or isolates from cystic fibrosis patients . The 40,795 (71%) remaining S. aureus isolates were included in the analyses, with methicillin resistance identified in 52% , clindamycin resistance in 17% , and TMP-SMX resistance in 2.2% (n = 897) of the isolates. Among all MRSA isolates, 14% and 2% were resistant to clindamycin and TMP-SMX, respectively. Among MSSA isolates, 21% and 3% were resistant to clindamycin and TMX-SMX, respectively. All of the S. aureus isolates were susceptible to vancomycin.From 2005 to 2014, 57,788 S. aureus isolates. The frequency of antimicrobial resistance for isolates according to sites of infection is provided in p<0.001) and musculoskeletal sites .Information on specimen site was available on 37,070 (91%) of the 40,795 p<0.001) and SST infections .Clindamycin resistance was highest among staphylococcal isolates cultured from paranasal sinuses and lowest in those from pleural fluid . There was no TMP-SMX resistant isolates cultured from musculoskeletal, pleural fluid, and peritoneal fluid samples.Of the 40,795 staphylococcal isolates, 39,520 (97%) had patient location information linked to the isolate with 31,760 (80%) being from outpatients and 7,760 (20%) from inpatients. The number of isolates and proportion of antimicrobial resistance per year in each group are provided in Tables p<0.001). During this time period in the outpatient setting, methicillin resistance decreased from 54% in 2005 to 44% in 2014 (p<0.001) while among inpatient isolates, resistance to methicillin varied from 48% to 60% with no significant trends observed and 54% in isolates from outpatients and inpatients, respectively among outpatients and 20% among inpatients (p<0.001). In all staphylococcal isolates among outpatients, the resistance to clindamycin increased from 16% in 2009 to 19% and 17% in 2013 and 2014, respectively (p = 0.002). In addition, clindamycin resistance increased significantly in both MSSA and MRSA, and in every year from 2009 to 2014, outpatient MSSA isolates had higher clindamycin resistance than MRSA. Among all inpatient staphylococcal isolates, clindamycin resistance varied from 18% to 22% with no significant trends observed are always expressed or are induced by the presence of a macrolide antibiotic. In this study, the majority of clindamycin resistance among all staphylococcal isolates was inducible. Inducible resistance was higher in MSSA than MRSA isolates . Among all of the clindamycin resistant staphylococcal isolates , inducible resistance was higher in outpatient than inpatient isolates (p<0.001). In addition, among outpatient isolates, inducible but not constitutive clindamycin resistance increased significantly during the study period. However, among inpatient isolates, neither inducible nor constitutive clindamycin resistance changed significantly among inpatient isolates (p = 0.06). Among outpatient isolates, resistance increased in both MSSA and MRSA isolates (p<0.001) with MSSA having higher resistance than MRSA in all years. Among all inpatient staphylococcal isolates, TMP-SMX resistance varied non-significantly from 1% to 3% (p = 0.005), while there was no change in resistance among MRSA isolates.The overall resistance to TMP-SMX from 2005 to 2014 was 2% in outpatient isolates , p<0.0011% to 3% . HoweverS. aureus isolates from a U.S. pediatric hospital serving a large area in central Ohio. The analysis demonstrated significant differences in antimicrobial resistance by site of specimen collection, higher methicillin and clindamycin resistance among inpatients vs. outpatients, higher clindamycin and TMP-SMX resistance among MSSA vs. MRSA, and importantly, significant changes in antimicrobial resistance patterns during the past decade that included decreasing methicillin resistance but increasing clindamycin and TMP-SMX resistance among outpatient staphylococcal isolates.The present study reports resistance to commonly used anti-staphylococcal antimicrobial agents in 40,795 unique S. aureus plays a main role, and among SST isolates, more than 50% were due to MRSA. This proportion of MRSA among SST isolates is substantially higher than the 21% in 2003 and 41% in 2008 that was reported by Karamatsu et al.[SST infections represent the most common pediatric infections in which su et al. and the su et al. among sisu et al., 15, 16 su et al. On the osu et al.S. aureus is the most common bacterial agent that causes invasive infections in children. Among staphylococcal isolates from musculoskeletal sites in this study, MSSA was more frequent than MRSA, and nearly one fourth of the MSSA isolates were resistant to clindamycin. This finding raises important questions about the optimal empiric choice of antistaphylococcal therapy for serious osteoarticular infection in the era of vancomycin stewardship. None of the musculoskeletal staphylococcal isolates were resistant to TMP-SMX, and further study is needed on the use of TMP-SMX for osteoarthritis.[rthritis. ImportanS. aureus also can cause complicated pneumonias, especially in association with preceding viral infections such as influenza. In this study, pleural fluid isolates had the highest methicillin resistance of almost 70%, but at the same time, the lowest clindamycin resistance (<10%) among both MRSA and MSSA. For this reason, in our institution it appears that clindamycin remains a suitable choice for empiric treatment of staphylococcal pneumonia associated with parapneumonic effusions. None of the pleural fluid isolates were resistant to TMP-SMX. On the other hand, among blood staphylococcal isolates, clindamycin resistance was 29%, with MRSA and MSSA isolates exhibiting resistance rates of 40% and 21%, respectively.S. aureus significantly decreased, although only among outpatient isolates which is consistent with what has been described previously.[S. aureus isolates from multiple centers in the U.S., and particularly among isolates from the Midwest starting in 2011. More recently, Khamash et al.[During the 10 year study period, methicillin resistance in eviously., 20\u201325 Ieviously. reportedeviously. Sutter eeviously. also dessh et al. noted sish et al.Clindamycin has been recommended for empiric therapy of staphylococcal infections. Yet, a significant increase in clindamycin resistance was seen among our outpatient MRSA and MSSA isolates. Increasing proportion of MSSA isolates resistant to clindamycin has been reported previously in a study that analyzed data from 1999 to 2011, and moreS. aureus has remained highly susceptible to TMP-SMX with most studies reporting resistance rates of <3% in the era of CA-MRSA.[S. aureus isolates and in both MRSA and MSSA. CA-MRSA., 24, 28 CA-MRSA. reportedThe finding of a significant increase in clindamycin and TMP-SMX resistance only among outpatient staphylococcal isolates could be due to frequent use of these antimicrobial agents in the outpatient setting. Although the actual use of clindamycin and TMP-SMX is not known among our patients, these agents are recommended frequentlyfor empiric treatment of staphylococcal infections.\u20139 TherefThis study has other limitations, chief of which is the retrospective nature with resultant lack of patient location and specimen collection site in 9% of isolates. In addition, appropriate labeling of clinical sites may not have occurred. Importantly, the inability to separate inpatient staphylococcal isolates into those that were hospital-acquired vs. community-associated was not possible. Identification of specific staphylococcal clones that may have contributed to the observed antimicrobial resistance patterns also was not possible. However, the large number of isolates over a ten-year period and representing a large area of central Ohio adds robust and timely information on antimicrobial resistance.S. aureus isolates from 2005 to 2014, particularly among isolates obtained in the outpatient setting. These changes included a decrease in methicillin resistance and an increase in clindamycin and TMP-SMX resistance. In addition, MSSA exhibited higher resistance to clindamycin and TMP-SMX than MRSA among outpatient isolates. The increase in clindamycin resistance among outpatient S. aureus isolates likely was due to an increase in inducible rather than constitutive resistance. Lastly, resistance to methicillin, clindamycin, and TMP-SMX varied widely according to the site of specimen collection. These results highlight the need for ongoing surveillance of local resistance patterns in order to ensure appropriate empiric antimicrobial selection for the treatment of S. aureus infections.Significant changes in antimicrobial resistance patterns were observed among"} +{"text": "Delirium, or acute confusional state, affects up to 7 million hospitalized older adults annually, and is associated with increased risk of mortality, institutionalization, and cognitive and functional impairment. There has been a proliferation of both pharmacological and nonpharmacological clinical trials to reduce the incidence and sequelae of delirium. In other neuropsychiatric disorders, exclusion criteria prevent up to 75% of individuals with the condition under study from participating. It is unclear how well these trial samples represent the population of older adults with delirium. We selected all intervention trials registered at ClinicalTrials.gov containing the keyword \u201cdelirium\u201d (N=131), regardless of type of intervention. We manually examined study descriptions to restrict analysis to studies with delirium as a primary or secondary outcome (N=92). Of these 92 studies, 76% enrolled only adults, with 45% enrolling only older adults. 38% of studies were restricted to surgical units, 27% to intensive care units, and 7.6% to medical units. Only 1 study examined nursing homes and 4 studies examined palliative care. 50% of studies excluded individuals with pre-existing dementia, 28% excluded individuals with psychiatric disorders, and 30% excluded individuals with neurological disorders. 34% of studies excluded individuals with alcohol or drug abuse. Overall, many intervention studies for delirium are limited to the surgical and ICU populations, and they exclude individuals with common comorbidities associated with an increased risk of delirium. Similar to other neuropsychiatric disorders, these findings raise significant concerns about the generalizability of clinical trials in delirium to the hospitalized older adult population."} +{"text": "Hand-foot-mouth disease (HFMD) is a widespread communicable disease and has caused large epidemics in many countries. This meta-analysis aimed to analyze and evaluate the epidemiological features of HFMD outbreaks in Chinese preschools.Literature review was based on PubMed, Chinese National Knowledge Infrastructure (CNKI) and Wanfang databases from 2008 to 2015. The temporal, spatial and demographic parameters were summarized and analyzed.Overall, 19 studies with a total of 11269 HFMD cases were selected for data synthesis and analysis. April, May, June and July were detected as the peak months of HFMD outbreaks, with the pooled rate of 21% (95% CI: 12%\u201334%), 23% (95% CI: 19%\u201327%), 20% (95% CI: 17%\u201324%) and 11% (95% CI: 7%\u201315%). Urban areas were at a higher risk of suffering from HFMD outbreaks than rural areas, with the pooled rate of 65% (95% CI: 48%\u201378%) and 35% (95% CI: 22%\u201352%) respectively. The constituent ratio of children aged 37\u201348 months is the highest, accounting for 46% (95% CI: 39%\u201353%) of the total cases during HFMD outbreaks. The pooled rate of male cases (60%) was higher than that of female cases (40%).Month, residence, age, and gender may be early risk factors for potential HFMD outbreaks. Before the advent of peak months from Apr to Jul each year, measures should be taken to prevent the HFMD outbreaks among preschool children in China. Preschools located in urban areas should take priority over special prevention. HFMD surveillance should preferentially focus on children aged 37\u201348 months, especially boys in preschools. Hand, foot, and mouth disease (HFMD) is an acute communicable disease mostly happened to children. It is caused by viruses belonging to the Enterovirus genus, such as Coxsackievirus A16 (CA16) and Enterovirus71 (EV71) . HFMD isIn the past three decades, HFMD epidemic has been continuously observed across the world. Recently, HFMD has become an increasing burden in the Asia-Pacific Region including Japan, Malaysia, Singapore, Viet, China etc. \u20138. In 20HFMD outbreaks among Chinese preschool children occurred continuously since 2008 . A HFMD We performed a meta-analysis to evaluate the epidemiological features of HFMD outbreaks among preschool children. We assessed the spatio-temporal distribution of HFMD outbreaks, to identify early risk factors and provide reference for future surveillance and prevention. The results will be helpful to effectively contain the spread of HFMD.We follow the preferred reporting items for meta-analysis of observational studies in epidemiology (MOOSE) . A systeInclusion criteria for studies were as follows: publisheTwo reviewers reviewed the studies respectively, screening article titles and abstracts for possible inclusion. If the information is not sufficient enough to make a decision on whether the study should be included or not, the full text of the article was further reviewed. The results were checked and discussed by two reviewers to agree upon a final list of included studies.Data from eligible studies were extracted separately by two reviewers. For each included study, we extracted the following data from original publications: authors, year of publication, study location (province and city), study period, residence , number of HFMD outbreaks in each month, age of the patients, total number of HFMD cases and number of HFMD outbreaks in each study. Disagreements between the two reviewers during data extraction were reconciled by a third investigator.https://cran.r-project.org/). Proportion was automatically selected as a summary statistic in R software to enable forest plots. Pooled proportion and 95% confidence intervals were obtained by random or fixed effects model determined by I2. Pooled rate was gotten from pooled proportion multiplied by 100%.A published systematic meta-analysis technique was used to calculate the pooled parameters of HFMD outbreaks from all eligible studies. Meta-analysis was carried out by using the software in R version 3.2.1, downloaded from the Comprehensive R Archive Network , obviously higher than the sum of the rest months.I2=54.2%; P=0.02). To eliminate the heterogeneity between studies, subgroup analyses were conducted for sample size, geographical regions, and study year. Finally, geographical difference was found to be the heterogeneous source. Southern China (sample 2) has higher pooled rate of HFMD outbreaks than Northern China (sample 1) during peak months, and the numeral value was 78% (95% CI: 70%\u201384%) and 61% (95% CI: 55%\u201366%) respectively which could not be reduced by subgroup analyses. Therefore, the random effect model was used.As for urban areas, the pooled rate of HFMD outbreaks is high, with the numeral value of 65% (95% CI: 48%\u201378%). While in rural areas the rate is lower, which was 35% (95% CI: 22%\u201352%). There was high heterogeneity between studies . Next was the age group 49\u201360 months, with the pooled rate of 28% (95% CI: 25%\u201333%). As for the age group 61\u201372 months, the pooled rate was relatively low, which was 14% (95% CI: 10%\u201319%). The lowest was the age group 0\u201336 months, with the pooled rate of 9% (95% CI: 5%\u201315%).In addition to age distribution, impact of gender was also analyzed as part of the demographic distribution assessments. The pooled rate of male cases was 60% . In China, recurring outbreaks of HFMD among preschool children is a major public health concern. To the best of our knowledge, this is the first meta-analysis to identify epidemiological features of HFMD outbreaks in preschools across China. Month, region, age, and gender might be used as risk indicators for HFMD outbreaks. This will provide guidance for HFMD prevention and help to reduce outbreaks of HFMD in pre-schools.In temperate climate, HFMD outbreaks usually occur in warmer months of the year, whereas in tropical areas, HFMD epidemics increase in wet season . For exaSuch peak month pattern might be partly explained by climatic factors, such as temperature and humidity.In Japan, higher temperature could influence the increase of HFMD incidence . In addiThe difference in HFMD incidence between urban and rural areas has also been discussed in other studies. The rural region in Taiwan had the least incidences of severe HFMD cases . ChildreAge has been identified as a risk factor for HFMD infection in previous studies. Data from Asia countries showed that HFMD incidence rate varies widely even within the narrow 0- to 5-yr age-band. A serologic survey in Singapore children showed that seropositivity to EV71 increases rapidly from age 2 to 5 yr . In MalaAnother interesting finding in our study was that gender might be a risk factor of HFMD outbreaks among preschool children. The male-to-female ratio was 1.5:1. In a report from Singapore, there was a male predominance of HFMD cases, with a male-to-female ratio between 1.3:1 and 1.6:1 . In TaiwMonth, residence, age and gender might be early risk factors for potential HFMD outbreaks. To control future HFMD outbreaks among pre-school children, prevention measures should be taken before the advent of peak months from Apr to Jul each year. Those preschools located in urban areas should take priority over preventing and controlling the disease. Further professional protection should be given to high-risk children 37\u201348 months old, especially preschool boys. We hope that data from China could help other countries to improve the quality of HFMD prevention.Ethical issues have been completely observed by the authors."} +{"text": "To investigate the presence of intestinal parasites in tuberculosis patients who suffered from immunodeficiency disorders.Tuberculosis is an important infectious disease that is endemic in some regions of Iran. However, there is a coverage in the endemicity areas of this infection with intestinal parasites. Giardia spp., coccidian parasites and microsporidia. Stool samples were collected from 50 immunocompromised tuberculosis patients. Direct smear using the normal saline (0.85% NaCl solution) and Lugol\u2019s iodine staining were performed to detect trophozoite of parasites. Moreover, stool samples were concentrated using routine formalin-ether to detect protozoan cysts and helminth\u2019s ova/larvae. Specific staining techniques including Trichrome, Modified Ziehl-Neelsen and chromotrope 2R were employed to detect amoeba, + SD of patients was 47.88 + 10.88 years. Among the participated patients, HIV positive, cancer, organ transplant and receiving corticosteroids were seen in 13, 10, 15 and 12 subjects, respectively. The prevalence of Intestinal parasites was 34 %( 17/50). Blastocystis , and intestinal helminth (Enterobius vermicularis) were the most prevalent and less prevalent parasites, respectively. Statistical significance difference was not seen between presence of intestinal parasites and type of immunodeficiency. From 50 participants, 42 (84%) and 8 (16%) were male and female, respectively. The mean age Blastocystis. Indeed, this study suggested that due to complicated immune conditions of TB patients with immunodeficiency disorders, this group of patients are at higher risk of infection by intestinal parasites. Our findings showed the high prevalence of intestinal parasites with majority of During the years, pulmonary tuberculosis (TB) remains as one of the main reasons of death resulted from infectious diseases , 2. BaseAscaris lumbricoides, and Trichuris trichiura, respectively in immunocompromised TB patients (IC-TB) could be related with many factors such as lower CD4 T-cell count, poor hygiene, rural life, lack of nutritious foods and lack of refined drinking water -15. ImpoTherefore, concerning the endemicity of TB and IPIs and emerging of immunodeficiency disorders, there is a little data in co-existence of TB, IPIs and immunodeficiency disorders. However, the current study aimed to investigate the prevalence of intestinal parasites among pulmonary tuberculosis patients who suffer from immunodeficiency disorders. Study population The current study received the ethic permission of the Ethics Committee of the Shahid Beheshti University of Medical Science (Number: IR.SBMU.MSP.REC.1395.323). Sample collection was conducted during February 2017 to May 2018 from Masih Daneshvari Hospital . A total of 50 IC-TB patients who were registered in the TB surveillance system and were undergoing anti-MTB treatment, participated in the current study. Prescription of anti-parasitic drugs during three-month prior to sample collection was considered as exclusion criterion. Stool samples were collected in a clean plastic containers and together with filled standard questionnaire and a signed informed consent, were immediately transformed to parasitology laboratory. Fecal sample collection and parasitological analysisGiardia lamblia and Entamoeba histolytica. Modified Ziehl-Neelsen and chromotrope 2R staining were used for detection of Cryptosporidium spp. oocysts and microsporidia spores, respectively. All slides were examined under light microscopy with 10\u00d7, 40\u00d7 and 100\u00d7 magnifications.In order to detect intestinal parasites, standard methods consisted of direct smear using the normal saline (0.85% NaCl solution) and Lugol\u2019s iodine staining were performed for detection of protozoal trophozoite and cyst, respectively. Moreover, stool samples were concentrated using routine formalin-ether in order to detect protozoan cysts and helminth\u2019s ova/larvae. Specific staining including Trichrome was employed to identify intestinal protozoans such as Statistical analysis P values <0.05 were considered statistically significant. Data analysis was performed using STATA software version 14.2. The frequency and percentages of intestinal parasites and other descriptive were calculated by binomial distribution. The Chi square and Fisher's exact tests were used to compare prevalence of parasites among groups regarding socioeconomic risk factors.A total of 50 IC-TB patients including 13 HIV positive subjects, 10 cancer patients (receiving chemotherapies), 15 organ transplant recipients and 12 immunocompromised patients receiving corticosteroids participated in the current study. From 50 participants 42 (84%) and 8 (16%) were male and female, respectively with mean age (\u00b1SD) of 47.88\u00b110.88 years. Demographic data and socioeconomic factors are summarized in P value = 0.02), while there was no statistical significant association between presence of intestinal parasites and other risk factors in all groups of IC-TB patients, while only one patient in HIV-TB group was infected with intestinal helminths (Enterobius vermicularis). Moreover, the highest prevalence of IPIs was seen among those TB patients who were positive for HIV, while the less prevalence of IPIs was observed among TB patients who received immunosuppressive drugs. However, statistical significance difference was not seen between presence of intestinal parasites and type of immunodeficiency of IPIs among the patients. Accordingly, ficiency .et al. who reported the prevalence of 7.3% (TB and IPIs have been considered as public health issues in low- and middle-income countries. The results of present study showed that the total prevalence of IPIs among IC-TB patients was 34 %. This prevalence rate is approximately in accordance with previous comprehensive studies in Iran that showed the overall prevalence of IPIs among immunocompromised patients 11.7% , hemodia of 7.3% and 14.9 of 7.3% in TB pa of 7.3% , 23 and of 7.3% , 24, 25 of 7.3% . In the current study, the highest prevalence of IPIs was seen among TB patients who infected with HIV. However, there are studies that reported the role of HIV in shifting of immune response from Th1 toward Th2. Notably, defense against helminth parasites is mainly mediated by Th2 immune responses and thus, imbalance of immune response resulted from HIV, helminth parasites and/or both of them, makes human subjects more susceptible to TB , 28. On Apart from HIV that affects the immune system via an infectious agent, the other mentioned immunodeficiency disorders in the current study happened due to consumption of corticosteroids or immunesuppressor agents . HoweverFurthermore, findings of the current study showed that consumption of raw vegetables and fruits, particularly in rainy seasons, increases the risk of IPIs in susceptible subjects especially TB patients who suffer from immunodeficiency disorders. The increased risk of transmission of intestinal parasites to human via eating raw vegetable and fruits were frequently reported. Bekele and colleagues showed that 54.4% of vegetable and fruit samples were contaminated with intestinal parasites . In IranHowever, it is proposed that co-existence of TB and acquired immune deficiencies provides a complicated immune conditions that make patients more prone to intestinal parasites. In addition, socio-economic conditions, especially in developing countries can enhance the risk of co-infection of TB and intestinal parasites. Mycobacterium tuberculosis, experience complicated condition that make them more prone to particularly helminths parasites. This intricate issue would be worst if this group of patient suffers from an immunodeficiency disorder. Therefore, it seems that TB patients with immunodeficiency are probably more susceptible to gastrointestinal infections, particularly parasites. Thus, providing a suitable personal hygiene and also regular health checkup for intestinal parasites are recommended.In the current study, intestinal parasites were observed amongst 34% of TB patients who suffer from immunodeficiency disorders. In addition, the highest prevalence of IPIs was seen in TB patients with HIV. However, TB patients due to immune response to"} +{"text": "Colorectal cancer (CRC) is the third greatest cancer burden in the United States. The remarkably diverse Mountain West state of Nevada has uncharacteristically high CRC mortality compared to other Western states. We aimed to study the determinants of the CRC excess burden by using data from the Nevada Central Cancer Registry from 2003\u20132013. Five-year cause-specific age-adjusted survival from colorectal cancer was calculated and stratified by sex, race/ethnicity and region of Nevada. Cox Proportional Hazards regression modelling was used to study the impact of demographic, social, and clinical factors on CRC survival in Nevada, assessing follow-up as accurately as possible. The extent to which differences in survival can be explained by receipt of stage-appropriate treatment was also assessed. 12,413 CRC cases from 2003\u20132013 in Nevada were analyzed. Five-year CRC survival was low: 56.0% (95% CI: 54.6\u201357.5) among males and 59.5% (95% CI: 58.0\u201361.1) among females; significantly lower than national 5-year survival of 65.1% and 66.5%, respectively. Low survival was driven by populous Southern Nevada; after adjustment for all covariates, Southern Nevadans were at 17% higher risk of death than their counterparts in Northwestern Nevada . Many patients did not receive stage-appropriate treatment, although this only partly explained the poor survival, uniformly low for every race/ethnicity in Nevada. The observed disparity for this one state within a single nation merits public health attention; regardless of the state or region of residence, all Americans deserve equal opportunity for optimum health outcomes in the face of a cancer diagnosis. The current study provides baseline information critical to clinicians, public health professionals, and all relevant stakeholders as they attempt to discern why Nevada\u2019s outcomes are vastly divergent from its neighboring Western states and make plans for remediation. Colorectal cancer (CRC) is the third leading cause of cancer incidence and mortality among both men and women in the United States (US) , with anth largest by land area, comprised of only two large metropolitan areas and vast swaths of rural and frontier lands. The current population of almost 3 million reflects tremendous population growth, over 50% since 2000 [The Mountain West state of Nevada is a unique state, the 7nce 2000 , contribnce 2000 . Moreovence 2000 ; it alsonce 2000 . In addince 2000 and healnce 2000 .According to known cancer patterns, Nevada stands as an exception, with an uncharacteristically high CRC mortality rate compared to any Western state, including its five neighbors: Arizona, California, Idaho, Oregon, and Utah . HoweverTherefore, this study aims to accurately characterize colorectal cancer survival in Nevada by race/ethnicity, sex, stage at diagnosis, and region of Nevada, and compare with national survival. We also aim to identify within-state survival disparities and examine the impact of available demographic, social, and clinical factors on CRC survival. Owing to its rapidly increasing population, understanding what drives Nevada\u2019s unfavorable CRC profile is critical to meeting the cancer control and prevention needs of Nevada\u2019s burgeoning and racial/ethnically diverse population.The Institutional Review Board at the University of Nevada, Las Vegas reviewed this study, #858093\u20131, and determined it was exempt. All data were de-identified.All cases of first primary colorectal cancer, inclusive of International Classification of Diseases for Oncology (ICD-O-3) codes C18-C20 , diagnosCovariates included demographic, social, and clinical factors ascertained at date of diagnosis and assessed for their impact on colorectal cancer survival. Age was categorized into the following five groups: 15\u201344, 45\u201354, 55\u201364, 65\u201374, and 75+, according to the International Cancer Survival Standards age classification . Cases wSocial factors included were insurance type, marital status, and socioeconomic status (SES). Insurance categories included private, Medicare, Medicaid, uninsured, and unknown. Marital status categories were married, single, divorced/separated, widowed, or unknown. Since SES information is not directly collected on individual patients by the NCCR, the proportion of people living in poverty in 2011 in a patient\u2019s zip code of residence at diagnosis was used as a proxy for SES; less than 5% poverty in zip code of residence was considered high SES, between 5\u201310% was medium SES, and over 10% was low SES.Tumor stage at diagnosis was coded I, II, III, or IV, according to guidelines set by the American Joint Committee on Cancer . HoweverReceipt of stage-appropriate treatment was determined only for AJCC Stage I-III tumors by assessing whether treatments were received in accordance with guidelines developed by The American Society of Colon and Rectal Surgeons , 25, as Five-year cause-specific age-adjusted survival from colorectal cancer was calculated and stratified by sex, race/ethnicity , and region of Nevada , using the life table method. Survival time was measured in months from the date of diagnosis until either the date of death or the end of the study period, Dec 31, 2014, whichever occurred first. The presumed alive assumption was usedKaplan-Meier survival curves were developed to visualize differences in survival within the state of Nevada by stage at diagnosis (SEER summary staging), period of diagnosis (2003\u20132007 and 2008\u20132012), race/ethnicity, and region of Nevada. Log-rank tests were used to detect differences in survival curves.To calculate comparative risk of death and identify factors impacting survival, Cox proportional hazards regression models for multivariate survival analysis were constructed, adjusting for all covariates significant in univariate analyses. Hazard ratios and their corresponding 95% confidence intervals (CI) were computed. Separate models were constructed for the sub-analysis to examine risk of CRC death for cases diagnosed in AJCC stages I-III (with complete information on treatments) by region of Nevada and receipt of stage-appropriate treatment.Statistical tests were interpreted as significant against \u03b1 = 0.05. Data were analyzed with SPSS v22 and SAS 9.3.In the 11-year period of 2003\u20132013, first primary colorectal cancer tumors were identified in 12,413 patients from the Nevada Central Cancer Registry. Fifty-five percent of patients were male, 61% were over 65 years of age, 78% were non-Hispanic white and two-thirds were from Southern Nevada. Almost half were married; 73% had either private insurance or Medicare. Over 90% of tumors were some type of ADK; distribution between right colon, left colon, and rectum was approximately equal but almost 10% were colon NOS cases. For the sub-analysis, 68% of tumors (n = 8480) were diagnosed in AJCC Stages I, II, or III; of those, only 36% received stage-appropriate treatment, while 39% did not. For 26% of these cases, stage-appropriate treatment was unable to be determined due to missing treatment information .As expected, Kaplan Meier curves showed significantly better survival from CRC in Nevada for tumors diagnosed in localized and/or regional stages (p < .001). Moreover, survival was slightly higher in the more recent 2008\u20132012 time period than in 2003\u20132007 (p = .007). Significant survival differences were also seen for race/ethnicity and region of Nevada .Five-year age-adjusted colorectal-cancer-specific survival in Nevada was 56.0% (95% CI: 54.6\u201357.5) among males, significantly lower than females at 59.5% (95% CI: 58.0\u201361.1); both were significantly lower than corresponding national proportions of 65.1% and 66.5% based on the SEER-18 catchment area for the same time period. Within Nevada, non-Hispanic black males had the lowest survival of any analyzed group, at 48.3% (95% CI: 42.7\u201353.9), and Other API females had the highest at 68.8% (95% CI: 61.6\u201376.0). However, for every distinct male racial/ethnic group, CRC survival in Nevada was significantly lower than CRC survival of their counterparts nationally. Likewise, non-Hispanic white and Hispanic females had significantly lower survival compared to SEER-18 CRC patients of the same race/ethnicity .Examining by stage at diagnosis, five-year CRC survival in the entire state of Nevada for localized and regional stage tumors was significantly lower than national survival. Males and females in Nevada diagnosed with CRC at a localized stage had 5-year survival proportions of 83.3% and 86.7%, respectively, compared to national survival of 88.6% and 90.0% . Even larger survival differences were seen for males and females in Nevada diagnosed with CRC at a regional stage; 5-year survival was 61.9% and 63.2%, respectively, compared to national survival of 69.9% and 71.4% . Survival for distant stage CRC tumors was not significantly different than national survival for either sex. Notably, by geographic region of Nevada, stage-specific survival in Northwestern Nevada did not differ from national survival at any stage for both men and women. Five-year CRC survival in Southern Nevada was significantly lower than national survival for all diagnosis stages except for distant stage in men .After adjustment for all clinical, social, and demographic covariates, as well as year of diagnosis, Cox proportional hazard model estimates indicated that female CRC patients were at 11% lower risk of death than male. Southern Nevadans were at 17% higher risk than their counterparts in Northwestern Nevada . By race/ethnicity, non-Hispanic blacks and Filipinos did not differ significantly from non-Hispanic whites, while Hispanics and Other APIs had 14% and 25% significantly lower risk, respectively and . Patients with any insurance status type other than private insurance had higher risk of CRC death. Likewise, any marital status besides the referent, married, conferred significantly higher risk of death. CRC mortality risk increased inversely with socioeconomic status. For clinical factors, carcinoma NOS cases had 74% higher risk than the referent ADK morphology. By tumor sublocation, patients with colon NOS cases had an almost 50% higher risk of death than those with right-sided tumors, while risk of death from a left-sided CRC tumor was lower than from a right-sided tumor . Patients with metastatic CRC, AJCC stage IV, had a 14 times higher risk of death than those with Stage I .In the sub-analysis, restricting analysis to Nevada\u2019s CRC cases diagnosed in AJCC stages I-III and adjusting for age, sex, race/ethnicity, and year of diagnosis, patients who were identified as not receiving stage-appropriate treatment had 2.47 times the risk of death (95% CI: 2.21\u20132.76) within 5 years than those who received stage-appropriate treatment. Moreover, death from CRC at these stages after adjustment for stage-appropriate treatment was 14% and 28% significantly higher in Southern and Rural Nevada, and , respectively, than in the Northwestern region. .the lowest in the entire US. Such a disparity for one state within a single nation merits public health attention; regardless of the state of residence, all Americans deserve equal opportunity for optimum health outcomes in the face of a cancer diagnosis. Thus, the current study provides baseline information critical to clinicians, public health professionals, and all relevant stakeholders as they attempt to discern why Nevada\u2019s outcomes are vastly divergent from its neighboring Western states and make plans for remediation.Our study documented CRC survival disparities between the state of Nevada and the overall US; the proportion of patients diagnosed with CRC that survived at least five years was much lower in Nevada than the SEER-18 national survival. Based on a recent study of CRC survival in 38 US states (Nevada not included) , our datth in the nation for rates of residency and fellowship placements [th - 49th of all US states for rates of active patient care physicians, active general surgeons and active primary care physicians per capita in 2015 [The current study also documents for the first time that a striking within-state regional disparity largely explains Nevada\u2019s poor survival profile. The low CRC survival observed in populous Southern Nevada is driving the state\u2019s overall poor survival profile; taken alone, CRC survival in Northwestern Nevada is on par with national CRC survival. Unfortunately, a similar regional survival disparity has previously been documented in Southern Nevada for breast cancer and lungacements . Despiteacements , Nevada in 2015 . However in 2015 . Additio in 2015 , it had in 2015 . EffortsParticularly troubling from a clinical perspective was our finding in the sub-analysis that a significant portion of Nevadans with colorectal cancer did not receive stage-appropriate treatment, especially in Southern and Rural Nevada. Previous US studies have linked racial/ethnic minorities, lack of insurance, and low socioeconomic status to lower likelihood of receiving recommended cancer care according to guidelines . In NevaOne modifiable factor with the potential for leading to better CRC survival outcomes is colon cancer screening on a population basis, as it can detect tumors at earlier stages . ScreeniAmong Nevada\u2019s CRC cases, between 80\u201390% of each minority population (except American Indian) resided in Southern Nevada, a region shown to be disadvantaged. We found a lack of racial disparity between non-Hispanic blacks and Filipinos compared to non-Hispanic whites in Nevada for CRC survival, which runs counter to most other studies conducted in the US \u201340. HoweOther factors impacting CRC survival in Nevada were consistent with the literature. Survival was slightly better in the more recent time period. With improvements in treatment modalities as well as screening detection of tumors at earlier stages, the number of CRC survivors in the US has increased, numbering almost 1.5 million in 2016 . Also coA major strength of this study is the large sample size provided by the Nevada Central Cancer Registry, enabling the creation of stable survival estimates by sex, race/ethnicity, stage of diagnosis, and region of Nevada for comparison purposes. Matching vital status with the NDI to completely capture deaths, customarily done in some other states, enhanced the accuracy of our survival estimates.Nonetheless, this study is subject to a few limitations. Incompleteness of the data for key prognostic variables, such as stage at diagnosis, could have influenced the results of this study , 64. In In conclusion, this study accurately characterized for the first time the colorectal cancer survival profile in Nevada, revealing disproportionately poor survival compared to the US. We further identified demographic, social, and clinical factors associated with CRC survival. The identification of these determinants should help cancer prevention and control efforts, whether by seeking to intervene on modifiable determinants or providing programming to specific population groups. Certainly, CRC screening outreach efforts must continue and expand. A significant disparity between regions of Nevada was identified, disproportionately impacting rural and Southern Nevada, likely linked to access to care. Further studies are warranted in order to determine the barriers to receipt of stage-appropriate treatment for colorectal cancer patients in Nevada. Collaboratively, all stakeholders, including clinicians and researchers, must aggressively approach any opportunities not only for primary prevention of colorectal cancer, but also to maximize the survival potential, at least reaching national levels, for all patients who are diagnosed with colorectal cancer in Nevada. Certainly, Nevada should not have outcomes so vastly disparate from the rest of the American states."} diff --git a/PMC_clustering_774.jsonl b/PMC_clustering_774.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..3f641e89b55561e9b01e8e5213af1a48cf86fc98 --- /dev/null +++ b/PMC_clustering_774.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b7600a854589ce256489d9abfcc2d6069205c8ee2f8a56fe44131ea8be8ed4bc +size 52178443 diff --git a/PMC_clustering_775.jsonl b/PMC_clustering_775.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b0979ab91f1df696a447599b131b95f29c2404fa --- /dev/null +++ b/PMC_clustering_775.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:410c987b99b723e39a2798cbe8e5c19d4ff7779b5926215908d2cd46d320af29 +size 131579397 diff --git a/PMC_clustering_776.jsonl b/PMC_clustering_776.jsonl new file mode 100644 index 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0000000000000000000000000000000000000000..9fb4f8a84974e50c4b26a582ca11313833bca3bb --- /dev/null +++ b/PMC_clustering_786.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c86bd437fceb714ca747c12baf814ce498000bc42cb67bb86482c608b460ffee +size 67348926 diff --git a/PMC_clustering_787.jsonl b/PMC_clustering_787.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..d1e325ecb1f3db9b76c09313058a321417cb4087 --- /dev/null +++ b/PMC_clustering_787.jsonl @@ -0,0 +1,639 @@ +{"text": "We sought to understand intergenerational differences in the impact of the initial COVID-19 restrictions on interactions, loneliness, and stress. Data was collected via online survey from individuals ages 18 and above during the period April 7-May 8, 2020. The predominantly female, White, and well-educated sample (n = 962) included 245 younger adults (YAs) ages 18-34, 374 middle-aged adults (MAs) ages 35-64, and 343 older adults (OAs) ages 65+, with overall mean age 51.67 . Before the restrictions, 41% of these OAs infrequently/never interacted face-to-face with children, increasing to 74% after restrictions. Three quarters (77%) of YAs reported seeing OAs less often, but 42% reported increasing their connections with OAs via technology. About a third of MAs (35%) and OAs (36%) were lonely, compared to 48% of YAs (p = .003), and a higher percentage of YAs (57%) reported being \u201cmore lonely\u201d now, compared to MAs (36%) and OAs (41%). OAs reported the least stress; 42% reported low/very low levels of stress compared to YAs (9%) and MAs (20%). All generations most often identified \u201cbeing able to go places\u201d as the thing they missed most, but it increased significantly with age (p < .001), from YAs (32%), MAs (37%), to OAs (44%). More YAs (20%) than OAs (7%) reported missing \u201cstructure to their day.\u201d Results of these intergenerational comparisons suggest the resilience of older adults is helping them during the current pandemic."} +{"text": "Traffic injuries are the third leading cause of death in Iran, accounting for more than 16000 death in 2016 (death rate of 20.5 per 100000 population). It was the first leading cause of premature death and disability in Iran in 2003. East Azerbaijan province is ranked eighth among the 31 provinces in terms of the number of deaths caused by traffic injuries. Purpose: To determine the epidemiological aspects of fatal traffic injuries in East Azerbaijan province, Iran.This cross-sectional descriptive study included 758 traffic-related deaths in East Azerbaijan province between March 2016 and March 2017. The data source was the Ministry of health and medical education death registry. According to this registry, all deaths should be recorded in this system. In this study, demographic and epidemiological variables including age, sex, education, occupation, death place, and living area were collected. Data were analyzed using Excel 2013 software.Out of 758 people died in traffic injuries, 604 (80%) were male and 154 (20%) were female. The age distribution of death indicated that 354 (57%) aged 20-59 died from road traffic injuries. 667 (53.2%) road traffic death happened in the road and public places, 386 (30.3%) deaths happened in hospitals and day clinics, and 210 (16.5%) cases were unknown. In terms of living area 503 (66%) were living in urban areas, 242 (32%) in rural areas and it was unknown for 13 (2%) cases. 144 (19%) cases had primary education, 113 (14.9%) secondary education (Guidance school), 125 (16.5%) tertiary education (high school), 116 (15.3%) were uneducated, and 78 (10.3%) had academic education. In respect of occupation In terms of occupation, most jobs respectively were related to free job (36.7%) , unknown (22.8%), housekeepers (12.5%), farmers (7.4%), students (6.7%), employees/laborers (6.5%), unemployed (5%), retired (4.1%), children (2.4%), and professional drivers (1.8%).Considering that the most road traffic deaths occurred in roads, paying more attention to roads and vehicles safety should be taken into account. The high rate of death in men aged 20-59 who mostly are family breadwinners indicates the necessity of the effective behavioral interventions for this group.Road traffic injuries, Fatality, Road accident"} +{"text": "In this case series in Jiangsu Province, COVID-19 patients had less severe symptoms and had better outcomes than the initial COVID-19 patients in Wuhan. The BMI \u2265 28 kg/m2 and a known history of type 2 diabetes were independent risk factors of severe illness in patients with COVID-19.Limited data are available for clinical characteristics of patients with coronavirus disease 2019 (COVID-19) outside Wuhan. This study aimed to describe the clinical characteristics of COVID-19 and identify the risk factors for severe illness of COVID-19 in Jiangsu province, China. Clinical data of hospitalized COVID-19 patients were retrospectively collected in 8 hospitals from 8 cities of Jiangsu province, China. Clinical findings of COVID-19 patients were described and risk factors for severe illness of COVID-19 were analyzed. By Feb 10, 2020, 202 hospitalized patients with COVID-19 were enrolled. The median age of patients was 44.0 years . 55 (27.2%) patients had comorbidities. At the onset of illness, the common symptoms were fever (156 [77.2%]) and cough (120 [59.4%]). 66 (32.7%) patients had lymphopenia. 193 (95.5%) patients had abnormal radiological findings. 11 (5.4%) patients were admitted to the intensive care unit and none of the patients died. 23 (11.4%) patients had severe illness. Severe illness of COVID-19 was independently associated with body mass index (BMI) \u2265 28 kg/m 2 and a known history of type 2 diabetes were independent risk factors of severe illness in patients with COVID-19. Sustained intensive control efforts remain urgently needed to minimize the risk of COVID-19.We reported the epidemiology, clinical laboratory, radiological characteristics, treatment, and clinical outcomes of 202 confirmed cases of COVID-19 in 8 hospitals from 8 cities of Jiangsu province, China. In this case series in Jiangsu Province, COVID-19 patients had less severe symptoms and had better outcomes than the initial COVID-19 patients in Wuhan. The BMI \u2265 28 kg/m During December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China and spread among humans in China and other countries . SARS-CoSeveral studies have reported the clinical characteristics of COVID-19 patients who were hospitalized in Wuhan (the outbreak center of the infection) ,6,7. HuaAlthough several studies have reported the clinical manifestations and short-term prognosis of COVID-19, the source of cases in majority of these studies was from a single center in Wuhan. The characteristics of the disease and risk factors of severe illness among inpatients in other parts of China outside Wuhan were still lacking. Chang et al. reported early clinical features of 13 patients with confirmed COVID-19 who were admitted to hospitals in Beijing, China . In theiIn this multi-center study, we aimed to describe the clinical characteristics of COVID-19 and to identify the risk factors of severe illness among inpatients with confirmed COVID-19 in Jiangsu province, which is located in the east of China.This multi-center study retrospectively recruited 202 confirmed COVID-19 patients from 8 designated hospitals in 8 cities of Jiangsu province, China .Data of the confirmed COVID-19 patients were collected from January 22, 2020 to February 10, 2020. The 8 designated hospitals are responsible for the treatment of COVID-19 patients in Jiangsu province, China, assigned by the Chinese government. All confirmed patients were diagnosed based on the criterion of World Health Organization (WHO) interim guidance ), type 2 diabetes (19 [9.4%]), chronic lung diseases (7 [3.5%]), chronic liver diseases (4 [2.0%]), cardiovascular diseases (5 [2.5%]), cerebrovascular diseases (3 [1.5%]), and malignant tumors (2 [1.0%]).A total of 202 admitted patients who were identified as COVID-19 were included in the study. The median age of the patients was 44.0 (IQR 33.0\u201354.0) years . Six (3.Although only 3 (1.5%) patients had direct exposure to Huanan Seafood Market, 84 (41.6%) patients visited Hubei province and 92 (45.5%) patients had contact with people who visited Hubei province after the onset of the COVID-19 epidemic. 98 (48.5%) patients had known contact with suspected or confirmed cases. However, 32 (15.8%) patients did not report any known contact with Hubei. The median time from symptom onset to admission was 5.0 days (IQR 2.0\u20137.0 days).2 vs. 24.2 kg/m2, P = 0.004). Nearly half (44.4%) of the severe patients were obese (BMI \u2265 28 kg/m2) compared to only 10.4% of the non-severe patients. Furthermore, more severe patients had history of type 2 diabetes . More non-severe patients contacted with suspected or confirmed patients than severe patients .23 (11.4%) of the patients developed severe illness in our study. The age of severe patients was comparable with non-severe patients and the BMI index of severe patients was higher than non-severe patients , cough (120 [59.4%]), followed by fatigue (44 [21.8%]), sore throat (24 [11.9%]), muscle ache (21 [10.4%]), shortness of breath (19 [9.4%]), diarrhea (13 [6.4%]), and headache (12 [5.9%]) .The blood counts of patients on admission showed leukopenia (57 [28.2%]) and lymphopenia (66 [32.7%]). 87 (65.9%) of 132 patients had normal serum levels of procalcitonin on admission. 55 (38.2%) of 144 patients had increased serum C-reactive protein level . Very few patients (1.9%) had elevated cardiac troponin I (cTnI) .9/L vs. 1.2\u00d7109/L, P<0.001) and albumin (ALB) levels . However, prothrombin time was not significantly different between severe patients (median 12.3 s) and non-severe patients . The proportion of patients with CRP < 10mg/L, 10-50mg/L, and \u2265 50mg/L were 40.0%, 30.0%, and 30.0% in severe patients, while patients with CRP < 10mg/L, 10-50mg/L, and \u2265 50mg/L account for 65.3%, 30.6%, and 4.0% in non-severe patients, respectively. More patients showed elevated CRP in severe patients than non-severe patients (P<0.001). Furthermore, severe patients had higher fasting blood glucose (median 6.5 mmol/L) as compared with non-severe patients .Compared to non-severe patients, severe patients presented higher percentage of shortness of breath , lower lymphocytes patients. Out of 193 patients, 158 (78.2%) had bilateral involvement, and 149 (73.8%) had ground glass opacity . BilaterOxygen therapy was required in 109 (54.0%) patients and non-invasive mechanical ventilation was required in 9 (4.5%) patients. None of the patients required intubation and invasive mechanical ventilation. 196 (97.0%) patients received antiviral therapy . 149 (73.8%) patients were administered with empirical antibiotic treatment. Additionally, sixty-four (31.7%) patients were given corticosteroids and 31 (15.3%) patients were given gamma globulin. Common complications included respiratory failure (9 [4.5%] patients), ARDS (2 [1.0%] patients), and shock (1 [0.5%] patients) . By FebrCompared with non-severe patients, more severe patients received oxygen therapy and antibiotic therapy . Most of the severe patients received corticosteroid and more severe patients were treated with gamma globulin . Regarding patients with severe illness, 11 (47.8%) patients were admitted to the ICU and 9 (39.1%) patients required non-invasive mechanical ventilation.2), presence of type 2 diabetes, lactate dehydrogenase (LDH) > 250 U/L, CRP > 10 mg/L, and ALB < 35 g/L. However, on multivariate analysis, only the BMI \u2265 28 kg/m2 and a known history of diabetes were the independent risk factors for developing severe illness . Although some experts recommend the prudently use of short courses of corticosteroids at low-to-moderate doses for critically ill patients with COVID-19, the use of corticosteroids remains controversial in COVID-19 [23 11.4%) patients were identified as severe illness cases in our study which is lower than the previous study 15.7%) . The ICU% . The I% patient2) and a history of type 2 diabetes as two independent risk factors of severe illness, suggesting that the metabolic conditions was associated the severity of COVID-19. In the previous study, metabolic syndrome-related conditions such as diabetes and obesity were also demonstrated to be etiologically linked to middle east respiratory syndrome coronavirus (MERS-CoV) pathogenesis [Early identification of patients with severe illness is important for the management of patients with COVID-19. We conducted univariate and multivariate analysis for risk factors of COVID-19 patients with severe illness on admission. For the first time, we identified the obesity (BMI over 28 kg/mogenesis . These dogenesis ,24. Prevogenesis . WhetherThis study has several limitations. First, only 202 patients with confirmed COVID-19 were included from eight cities of Jiangsu province. It would be better to include as many as possible patients in Jiangsu province to get more comprehensive understanding of COVID-19 outside Wuhan. Moreover, we only included patients with laboratory confirmed cases. The suspected but undiagnosed cases were not included in the present study. As of February 10, 2020, 515 confirmed cased have been reported in Jiangsu province [2 and a history of type 2 diabetes are independent risk factors for severe illness of COVID-19. Sustained intensive control efforts remain urgently needed to minimize the risk of COVID-19.In conclusion, COVID-19 patients in Jiangsu province were less severe and have improved prognosis than the initial COVID-19 patients as previously reported in Wuhan indicating that mild cases might already have occurred. A BMI > 28 kg/m"} +{"text": "The surgical treatment of patients with complex ventral hernias is challenging. The aim of this study was to present an international overview of expert opinions on current practice.A survey questionnaire was designed to investigate preoperative risk management, surgical approach and mesh choice in patients undergoing complex hernias repair, and treatment strategies for infected meshes. Geographical location of practice, experience and annual volumes of the surgeons were compared.Of 408 surgeons, 234 (57.4 per cent) were practising in the USA, 116 (28.4 per cent) in Europe, and 58 (14.2 per cent) in other countries. Some 412 of 418 surgeons (98.6 per cent) performed open repair and 322 of 416 (77.4 per cent) performed laparoscopic repair. Most recommended preoperative work-up/lifestyle changes such as smoking cessation and weight loss , but the consequences of these strategies varied. American surgeons and less experienced surgeons were stricter. Antibiotics were given at least 1\u00a0h before surgery by 295 of 414 respondents (71.3 per cent). Synthetic and biological meshes were used equally in contaminated primary hernia repair, whereas for recurrent hernia repair synthetic mesh was used in a clean environment and biological or no mesh in a contaminated environment. American surgeons and surgeons with less experience preferred biological mesh in contaminated environments significantly more often. Percutaneous drainage and antibiotics were the first steps recommended in treating mesh infection. In the presence of sepsis, most surgeons favoured synthetic mesh explantation and further repair with biological mesh.There remains a paucity of good-quality evidence in dealing with these hernias, leading to variations in management. Patient optimization and issues related to mesh choice and infections require well designed prospective studies. This survey provided a good overview of current practice among difficult subjects in ventral hernia repair on which limited guidelines exist in two continents (Europe and USA). Based on the findings, the authors recommend that more attention should be paid to preoperative optimization, specifically preoperative diabetic control and adequate antibiotic prophylaxis. Prehabilitation programmes should be implemented together with patient education on the importance of risk reduction and the impact of complications. Reaching goals set to optimize patients before hernia surgery should be a quality control parameter. The use of biological mesh in ventral hernia repair should be appraised critically. To improve adherence to guidelines and protocol decision tools, guideline training, easy ways of data-sharing, feedback loops and apps may be helpful. Complexity is defined according to the criteria proposed by Slater Preoperative risk management includes patient optimization measures such as smoking cessation, controlling blood glucose in patients with diabetes, and weight reduction in obese patients to reduce complicationsversus Europe), experience and annual volume of the operating surgeon were evaluated along with results of responses compared with recommendations in clinical guidelinesIn the absence of scientific evidence, expert opinion covering these issues was sought by developing a survey questionnaire in a collaboration between the USA and the Netherlands. Differences in geographical location of practice (USA Invitations for the English web-based survey were sent to members of the American Hernia Society (AHS). A reminder was sent after 6\u00a0weeks. In addition, European hernia surgeons attending the first world conference on abdominal wall hernia surgery in Milan, Italy, in 2015 who were not members of the AHS were also offered the opportunity to take part.Appendix\u00a0S1), designed for completion in around 20\u00a0min.The survey consisted of 34 questions: 10 demographic questions, 9 knowledge questions, and 15 case vignettes . Answers were described as counts and percentages for categorical variables. Additionally, three different demographics within the preoperative risk management results, knowledge questions and the case vignettes were examined separately: geographical location of practice (USA versus Europe), experience of the surgeon (little (15\u00a0years or less) versus high (more than 15\u00a0years)) and annual volume of the operating surgeon (low (fewer than 50 per year) versus high (more than 50 per year)). The Freeman\u2013Halton test was used to compare the results of the different case vignettes. P\u00a0<0.050 was considered statistically significant for all tests.Data were anonymized and analysed using SPSSTable\u00a01. Of 408 surgeons, 234 (57.4 per cent) were practising hernia surgery in the USA, 116 (28.4 per cent) in Europe, and 58 (14.2 per cent) in other countries. Some 412 of 418 surgeons (98.6 per cent) performed open repair, 105 of 409 (25.7 per cent) at the expert level. Laparoscopic repair was performed by 322 of 416 responders (77.4 per cent), of whom 69 of 320 (21.6 per cent) were at the expert level.Questionnaires were returned by 417 surgeons, representing about 25 per cent of eligible members of hernia societies approached. Not all questions from the questionnaire were answered by all respondents, so the denominator used to calculate percentages varied. Responder demographics are listed in Table 2.Views concerning preoperative risk management are shown in 2) before surgery. Ninety-one of 146 surgeons (62.3 per cent) were willing to proceed to repair even if the target weight loss had not been reached. Some 165 of 392 surgeons (42.1 per cent) checked target haemoglobin (Hb) A1c to improve diabetes control before surgery; 68 of 156 surgeons (43.6 per cent) would operate on patients who did not reach the target HbA1c.Some 319 of 398 surgeons (80.2 per cent) agreed on the benefit of smoking cessation. Fifty-one of 396 surgeons (12.9 per cent) checked urine for nicotine and metabolites before surgery, of whom 49 of 50 (98 per cent) demanded negative results. A total of 254 of 399 surgeons (63.7 per cent) recommended a weight loss regimen in patients with a high BMI (above 40\u00a0kg/mAntibiotics at least 1\u00a0h before surgery were recommended by 295 of 414 (71.3 per cent), of whom 80 (19.3 per cent) administered further antibiotics over the next 24\u00a0h, whereas 26 (6.3 per cent) continued for more than 24\u00a0h. Only 13 of 414 (3.1 per cent) did not use prophylactic antibiotics for ventral incisional hernia repair.versus 69 of 110 (62.7 per cent) respectively; P\u2009<\u20090.001), checked urine for nicotine (47 of 223 (21.1 per cent) versus 3 of 108 (2.8 per cent); P\u2009=\u20090.001) and determined HbA1c before surgery (101 of 218 (46.3 per cent) versus 31 of 110 (28.2 per cent); P\u2009=\u20090.006). No difference was found for weight loss regimens (149 of 225 (66.2 per cent) versus 64 of 110 (58.2 per cent); P\u2009=\u20090.199) or requirement of negative test results before operation (smoking: 45 of 46 (98 per cent) versus 3 of 3 (100 per cent), P\u2009=\u20090.796; weight loss: 50 of 78 (64 per cent) versus 27 of 42 (64 per cent), P\u2009=\u20090.757; HbA1c: 44 of 99 (44 per cent) versus 11 of 25 (44 per cent), P\u2009=\u20090.523).Compared with European surgeons, significantly more American surgeons wanted patients to stop smoking (199 of 224 (88.8 per cent) versus 90 of 110 (81.8 per cent) respectively; P\u2009=\u20090.380), weight loss regimen (122 of 189 (64.6 per cent) versus 77 of 111 (69.4 per cent); P\u2009=\u20090.448), checking HbA1c before surgery (83 of 185 (44.9 per cent) versus 50 of 109 (45.9 per cent); P\u2009=\u20090.904), or requirement for negative results before operation (smoking: 21 of 22 (95 per cent) versus 21 of 21 (100 per cent), P\u2009=\u20091.000; weight loss: 48 of 72 (67 per cent) versus 29 of 48 (60 per cent), P\u2009=\u20090.561; HbA1c: 37 of 80 (46 per cent) versus 19 of 49 (39 per cent), P\u2009=\u20090.466).No difference was seen between surgeons with high or low annual volume concerning smoking cessation (145 of 189 (76.7 per cent) versus 158 of 264 (59.8 per cent) respectively; P\u2009=\u20090.036) and checked urine for nicotine more often (31 of 132 (23.5 per cent) versus 20 of 263 (7.6 per cent); P\u2009<\u20090.001). No difference was found for smoking cessation (107 of 133 (80.5 per cent) versus 211 of 264 (79.9 per cent); P\u2009=\u20091.000), checking HbA1c before to surgery (53 of 129 (41.1 per cent) versus 111 of 262 (42.4 per cent); P\u2009=\u20090.828) or requirement for negative results before operation (smoking: 30 of 31 (97 per cent) versus 19 of 19 (100 per cent), P\u2009=\u20091.000; weight loss: 34 of 55 (62 per cent) versus 57 of 91 (63 per cent), P\u2009=\u20091.000; HbA1c: 22 of 51 (43 per cent) versus 46 of 104 (44.2 per cent), P\u2009=\u20091.000).Less experienced surgeons were more likely to commence morbidly obese patients on a weight loss regimen than those with more experience (95 of 134 (70.9 per cent) Table\u00a03. Only the questions about surgical wound classification (Q3) and anatomical plane (Q6) produced consistent responses with 73.1 per cent and 80.1 per cent of respondents respectively giving the correct answer.The knowledge questions (Q1\u2013Q9) with answers and references are shown in versus 10 of 115 (8.7 per cent) of the European surgeons. In the latter group, answer a (0\u201310 per cent) was chosen more often: 29 of 115 (25.2 per cent) for European surgeons versus 16 of 231 (6.9 per cent) for American surgeons (P\u2009<\u20090.001). European surgeons considered \u2018abdominal aortic aneurysm\u2019 (answer a) more often to be an independent risk factor for recurrence (Q5) than American surgeons (30 of 108 (27.8 per cent) versus 35 of 216 (16.2 per cent) respectively; P\u2009=\u20090.001). American surgeons indicated \u2018tobacco use\u2019 (answer e) more often to be a risk factor than European surgeons (121 of 216 (56.0 per cent) versus 39 of 108 (36.1 per cent) respectively; P\u2009=\u20090.001). No differences between American and European surgeons were found for the other knowledge questions.The majority of American surgeons reported a higher percentage of repeat ventral hernia repairs (Q1) compared with European surgeons. Forty-seven of 231 (20.3 per cent) chose answer h, in which the number of repeat hernia repairs was set at 71\u201380 per cent, P\u2009=\u20090.004). No differences between surgeons with high or low annual volume were found for the other items.The majority of high-volume surgeons reported a lower percentage of surgical-site infections (Q9) compared with low-volume surgeons. Fifty-three of 107 (49.5 per cent) chose answer a, in which the percentage was set at 1.5 per cent, compared with 52 of 183 (28.4 per cent) for low-volume surgeons (versus 93 of 136 (68.4 per cent) respectively; P\u2009=\u20090.001). Conversely, less experienced surgeons answered the question about the typical maximum distance of bilateral advancement with the component separation method (Q7) correctly more often than more experienced surgeons (61 of 127 (48.0 per cent) versus 80 of 257 (31.1 per cent) respectively; P\u2009=\u20090.002). No differences between less and more experienced surgeons were found for the other items.Q2 on recurrence rate within 10\u00a0years was answered correctly more often by more experienced surgeons compared with less experienced surgeons (220 of 266 (82.7 per cent) Table 4. The most frequently provided answers for the specific case vignette are discussed below.The case vignettes with all answers are shown in In the case of a co-morbid patient , 184 (45.1 per cent) of the 408 respondents preferred open repair and 198 (48.5 per cent) preferred laparoscopic repair. Permanent synthetic mesh was used most often in open repairs . For laparoscopic ventral hernia repair, the type of mesh was not specified.In contaminated primary hernia repair, synthetic mesh was used as often as biological mesh . Primary suture repair was performed by 60 (14.5 per cent) of the 415 respondents. In case of a contaminated recurrent hernia repair, most surgeons preferred a biological over a synthetic mesh. Primary suture repair was performed by 112 (27.5 per cent) of the 408 respondents.In clean recurrent hernia repair, 359 of 413 respondents (86.9 per cent) preferred a synthetic over a biological mesh . Primary suture repair was performed by 14 (3.4 per cent) of the 413 respondents. Most preferred a permanent , macroporous or lightweight mesh in clean recurrent hernia repair.In patients with a defect larger than 6\u00a0cm and a stoma in close proximity, most respondents chose either an open repair with permanent synthetic mesh , open repair with biological mesh or laparoscopic ventral hernia repair with the type of mesh not specified .For a non-co-morbid patient during an open clean ventral incisional hernia repair with a 4-cm gap between the rectus muscles that could easily be approximated, most respondents reinforced the fascial closure with a retrorectus mesh . If the gap was 7\u00a0cm and could not be approximated during open repair, either anterior component separation or posterior component separation was added to the retrorectus reinforcement.In the case vignettes on mesh infection, the first step in treatment was to start empirical antibiotics. In mesh infection occurring after an open component separation and retrorectus placement of a biological mesh, 250 (62.0 per cent) of 403 surgeons would drain the fluid percutaneously, whereas 24 (6.0 per cent) preferred open drainage of the fluid and complete excision the mesh. In case of mesh infection after laparoscopic application of a permanent barrier composite mesh, 181 of 398 (45.5 per cent) would drain the fluid percutaneously and 62 of 398 (15.6 per cent) preferred open drainage of the fluid and complete excision the mesh. After open component separation and retrorectus placement of a macroporous synthetic mesh, 225 of 394 surgeons (57.1 per cent) would drain the fluid percutaneously, and 25 of 394 (6.3 per cent) preferred open exploration with fluid drainage and complete mesh removal.Staphylcoccus aureus (MRSA) infection, 82 of 179 respondents (45.8 per cent) continued antibiotics and left the mesh with the CT-guided drain in place until resolution of infection, and 94 of 179 (52.5 per cent) explanted the mesh.If fluid culture from the drain revealed methicillin-resistant For a patient with a history of MRSA wound infection (no current active infection) and a ventral incisional hernia greater than 6\u00a0cm, 150 of 395 respondents (38.0 per cent) chose laparoscopic repair (mesh not specified), 117 of 395 (29.6 per cent) chose open repair with permanent synthetic mesh, and 76 of 395 (19.2 per cent) selected open repair with biological mesh.In a patient with a recurrent parastomal hernia and an infected synthetic mesh without systemic sepsis, more than half of the responders would explant the mesh followed by repair with a biological mesh or primarily close the parastomal hernia without mesh .In the event of an unplanned enterotomy with minimal spillage during elective laparoscopic ventral incisional hernia repair, 237 of 375 respondents (63.2 per cent) would repair the enterotomy laparoscopically. In this situation, 148 (39.5 per cent) of 375 surgeons would then delay the hernia repair, 122 (32.5 per cent) would proceed laparoscopically, 94 (25.1 per cent) would convert to an open procedure, and 11 (2.9 per cent) did not further specify their hernia repair. If laparoscopy was continued, 69 of 120 (57.5 per cent) preferred a permanent synthetic mesh repair, 16 of 120 (13.3 per cent) preferred absorbable synthetic mesh repair, and 35 of 120 (29.2 per cent) preferred a biological repair. When converting to open ventral hernia repair, 28 of 91 (31 per cent) preferred permanent synthetic mesh repair, 11 of 91 (12 per cent) preferred absorbable synthetic repair, and 52 of 91 (57 per cent) preferred a biological mesh repair. There was no agreement about the length of delay .versus 43 of 114 (37.7 per cent) respectively; P\u2009=\u20090.004), and were more likely to use biological mesh in contaminated primary (129 of 232 (55.6 per cent) versus 33 of 115 (28.7 per cent); P\u2009<\u20090.001) and recurrent (138 of 226 (61.1 per cent) versus 51 of 115 (44.3 per cent); P\u2009=\u20090.008) hernia repair. Although both American and European surgeons preferred permanent synthetic mesh (181 of 231 (78.4 per cent) versus 107 of 115 (93.0 per cent) in clean recurrent hernia repair, significantly more American surgeons chose biological mesh (30 of 231 (13.0 per cent) versus 5 of 115 (4.3 per cent) (P\u2009=\u20090.005).American surgeons significantly preferred laparoscopic over ventral hernia repair in patients with co-morbidity compared with European surgeons (118 of 229 (51.5 per cent) versus 56 of 219 (25.6 per cent) for American surgeons; P\u2009=\u20090.030), whereas most American surgeons chose open repair with biological mesh (53 of 219 (24.2 per cent) versus 19 of 107 (17.8 per cent)) or laparoscopic repair (mesh not specified) (93 of 219 (42.5 per cent) versus 35 of 107 (32.7 per cent)) (P\u2009=\u20090.030).If a patient had a ventral incisional hernia of more than 6\u00a0cm and a stoma in close proximity, European surgeons preferred open repair with permanent synthetic mesh (44 of 107 (41.1 per cent) versus 21 of 227 (9.3 per cent) for American surgeons), whereas American surgeons more often intervened by draining the fluid percutaneously (163 of 227 (71.8 per cent) versus 50 of 111 (45.0 per cent) for European surgeons) (P\u2009<\u20090.001). A mesh infection after open component separation and retrorectus placement of a macroporous synthetic mesh was more likely to be treated conservatively by European surgeons (with antibiotics) (25 of 110 (22.7 per cent) versus 23 of 219 (10.5 per cent) for American surgeons) or open exploration with fluid drainage, leaving the mesh in place (22 of 110 (20.0 per cent) versus 23 of 219 (10.5 per cent) respectively), whereas American surgeons preferred draining the fluid percutaneously (136 of 219 (62.1 per cent) versus 56 of 110 (50.9 per cent) for European surgeons) (P\u2009=\u20090.001). With mesh infection after laparoscopic application of a permanent barrier composite mesh more European surgeons preferred conservative management (with antibiotics) (23 of 109 (21.1 per cent) versus 22 of 226 (9.7 per cent) of American surgeons), whereas American surgeons more often intervened by open drainage of the fluid and complete excision of the mesh (46 of 226 (20.4 per cent) versus 8 of 109 (7.3 per cent) of European surgeons) (P\u2009=\u20090.002).For mesh infection after open component separation and retrorectus placement of a biological mesh, European surgeons preferred conservative management (with antibiotics) (29 of 111 (26.1 per cent) versus 50 of 109 (45.9 per cent) of European surgeons; P<0.001) after removal of the infected mesh. European surgeons were more likely to close the parastomal hernia without mesh.If a patient had a recurrent parastomal hernia with an infected synthetic mesh (without systemic sepsis), American surgeons were more inclined to repair the parastomal hernia with a biological mesh (138 of 225 (61.3 per cent) versus 120 of 214 (56.1 per cent) respectively; P\u2009=\u20090.001).In the event of an unplanned enterotomy with minimal spillage during elective laparoscopic repair, more European surgeons would repair the enterotomy laparoscopically than American surgeons (79 of 102 (77.5 per cent) versus 39 of 263 (14.8 per cent)), compared with experienced surgeons who more often preferred the anterior component separation technique (52 of 130 (40.0 per cent) versus 129 of 263 (49.0 per cent) respectively) (P\u2009=\u20090.050). Both techniques used reinforcement with a retrorectal mesh.In a patient with no co-morbidity and a hernia with a 7-cm gap that could not be approximated during open repair, surgeons with less experience more often chose the posterior component separation technique (36 of 130 (27.7 per cent) versus 103 of 272 (37.9 per cent)) significantly more often than experienced surgeons, who more often chose a permanent synthetic mesh (41 of 142 (28.9 per cent) versus 102 of 272 (37.5 per cent)) (P\u2009=\u20090.003).In contaminated primary hernia repair, surgeons with little experience chose a biological mesh (72 of 142 (50.7 per cent) P\u2009=\u20090.030), who chose to continue with conservative therapy.In the case vignettes on mesh infection, both groups chose percutaneous drainage as the first step after antibiotics. If this failed, experienced surgeons preferred open drainage of the fluid and leaving the mesh in place as the next step , compared with less experienced surgeons (versus 115 of 193 (59.6 per cent); P\u2009=\u20090.040), whereas surgeons with a low annual volume more often preferred conservative management (with antibiotics) (30 of 193 (15.5 per cent) versus 11 of 114 (9.6 per cent) of high-volume surgeons) or open drainage, leaving the mesh in place (23 of 193 (11.9 per cent) versus 8 of 114 (7.0 per cent) respectively).For mesh infection, high-volume surgeons preferred percutaneous drainage significantly more often than low-volume surgeons (89 of 114 (78.1 per cent) versus 11 of 109 (10.1 per cent) for high-volume surgeons) and open exploration with fluid drainage with complete mesh removal (19 of 186 (10.2 per cent) versus 1 of 109 (0.9 per cent) respectively), and those with a high annual volume more often preferred percutaneous drainage (78 of 109 (71.6 per cent) versus 94 of 186 (50.5 per cent) for low-volume surgeons) (P\u2009=\u20090.001).In case of a mesh abscess after open component separation and retrorectus placement of a macroporous synthetic mesh, surgeons with a low annual volume more often preferred conservative management (with antibiotics) (34 of 186 (18.3 per cent) This article provides an international overview of self-reported practice on different topics in ventral hernia repair in relation to practice location, experience of the operating surgeon, and annual volume of the operating surgeon. The striking feature was the extent of variation for many responses.2), have all been recommended by European and American ventral hernia working groups,,Preoperative optimization and lifestyle measures, related to smoking cessation (more than 4\u00a0weeks before surgery), maintaining blood glucose (HbA1c below 7 per cent) in patients with diabetes, and weight-loss regimens remain based on limited data and expert opinion. In patients without sepsis, it is advised to start with conservative treatment with targeted antibiotic therapy and, if possible, local percutaneous drainageThe majority of surgeons agreed that percutaneous drainage combined with antibiotic treatment was the first step for mesh infection (abscess), independent of the type of repair or mesh used. As for the next step, American surgeons more often proposed a more aggressive approach of mesh removal, whereas European surgeons often continued conservative management with antibiotics. The same was found when comparing more with less experienced surgeons, as well as high- ,,,The results regarding unplanned enterotomy during a laparoscopic repair indicated that most would repair the enterotomy laparoscopically, in line with expert opinion stated by Silecchia et al.: \u2018if an enterotomy is recognized without spillage or contamination, a prosthetic repair can be accomplished after closing the enterotomy laparoscopically or open\u2019This study has limitations. Participants were drawn from professional associations involved in hernia surgery. The authors have no information on the proportion of complex ventral hernia surgery undertaken by surgeons in general. The response rate could not be determined accurately, and was an estimate of the proportion of conference attendees who completed the survey. The proportion of active hernia surgeons on the member list of societies approached was also unknown. As there was no definition for an expert, this level for a ventral hernia surgeon was based arbitrarily on limited data supporting the chosen thresholdBased on the findings from this survey, there is a clear need to conduct prospective research that can establish the value of preoperative optimization programmes. Better adherence to guidelines, particularly where evidence exists, such as antibiotic administration, with improved ways of data-sharing must be promotedDisclosure. The authors declare no conflict of interest.BJS Open online.zraa057_Supplementary_DataClick here for additional data file."} +{"text": "In the article titled \u201cExpression Analysis of Fibronectin Type III Domain-Containing (FNDC) Genes in Inflammatory Bowel Disease and Colorectal Cancer\u201d , there wp < 0.05) in analyzed cell lines were found regarding FNDC3A and FNDC3B (significance bars are not shown for overview purposes). In the microsatellite-unstable colorectal cancer data set (GDS4515) of human MSI CRC samples (n = 34), we analyzed the gene expressions compared to nonaffected colonic mucosa (n = 15) [31]. The expression data of FNDC3A, FNDC3B, FNDC4, and GPR116 were available and showed a small but significant downregulation of FNDC4 in MSI CRCs ), while FNDC3A (p = 0.055) and FNDC3B (p = 0.127) remained unchanged. GPR116 was significantly upregulated (p = 0.014). To test for possible confounding by age or sex, we analyzed expression data in early- and late-onset CRCs in females (n = 21) and males (n = 25), diagnosed at an age of 28-53 years (n = 27) or 69-87 years (n = 19) (GDS5232) [32]. Data were available for FNDC3A, FNDC4, and GPR116, which showed neither age- nor sex-dependent differences .Publicly available data sets of the GEO database were analyzed to complement our findings with previous comparable studies. First, the microarray expression of FNDCs in seven human colonic tumor cell lines from the NCI-60 panel was obtained (GDS4296) [30]. All FNDCs were expressed, whereas FNDC3A displayed the highest expression values (mean 2.4-fold higher) in all cell lines ). Significant expression differences ("} +{"text": "Dorysthenes granulosus (Thomson 1860) was sequenced. The 15,858\u2009bp long genome has the standard metazoan complement of 38 genes. These genes contain 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The nucleotide composition of the D. granulosus mitogenome was A: 39.5%, T: 31.7%, G: 10.9%, C: 17.9%. The A\uff0bT content was 71.2%, showing strong AT skew. Phylogenetic analysis indicated that D. granulosus have sister relationship with Dorysthenes paradoxus.The complete mitogenome sequence of an Asian longicorn beetle Dorysthenes granulosus (Thomson) (Coleoptera: Cerambycidae: Prioninae), an underground pest that mainly damages sugarcane and cassava of Nanning City . The total genomic DNA was extracted following the modified CTAB DNA extraction protocol and stored at Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety with sample number of FDSW190073798. Then library was constructed and pair-end was sequenced (2*150\u2009bp) with HiSeq . Via SPAdes (version 3.9), approximately 15.33\u2009G of raw data and 15.26\u2009G of clean data were obtained for sequence assembly and constitutive of 38 genes. These genes contain 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 control region. The nucleotide composition of the D. granulosus mitogenome was A (39.5%), T (31.7%), G (10.9%), C (17.9%). The A\uff0bT content was 71.2%, showing strong AT skew.The complete mitochondrial genome of D. granulosus had a close relationship with that of D. paradoxus (Liu et al. The phylogenetic relationship among Prioninae, Cerambycinae and Lamiinae species by Neighbor-Joining method with 1000 bootstrap replicates (Sudhir et\u00a0al."} +{"text": "Scientific Reports, 10.1038/s41598-020-60042-1, Published on 20 February 2020Correction to: The Article contains errors in Table 4 where the reported results for the \u201cMild Group (low risk)\u201d and \u201cSevere Group (high risk)\u201d are incorrect.The results for the Mild Group (low risk) should read Male 178 (85.6%), Female 30 (14.4%) and Smoking history (SMK) 163 (78.4%).The results for the Severe Group (high risk) should read Male 163 (80.7%), Female 39 (19.3%) and Smoking history (SMK) 136 (67.3%).The correct Table 4 appears below as Table"} +{"text": "Correction to: BMC Public Health (2020) 20:64https://doi.org/10.1186/s12889-019-8094-1It was highlighted that the original article containeEquation 1 (infant\u2019s exposure)Equation 2 (probability of not getting pregnant)Equation 3 (disease burden)Equation 4"} +{"text": "ApoE e4 genotype is associated with both dementia and delirium for COVID-19 severity in the UK Biobank (UKB) , dementiUKB is a community cohort currently aged 48 to 86 .n = 451,367, 90% of sample) attending baseline assessment centers in England , excluding participants who died before the epidemic . Single nucleotide polymorphism (SNP) data for rs429358 and rs7412 was used to determine ApoE genotypes: ApoE e4e4 homozygotes , e3e4 , and e3e3 genotype groups . Mean age was 68 years (SD = 8) with 176,951 females (55%). There were 622 positive COVID-19 patients compared to e3e3 homozygotes ; hypertension ; coronary artery disease or type 2 diabetes , compared to OR = 2.31 (95% CI: 1.65 to 3.24) using all the tested samples.ozygotes . The assto 3.55) , based oApoE e4e4 allele increases risks of severe COVID-19 infection, independent of preexisting dementia, cardiovascular disease, and type-2 diabetes. ApoE e4 not only affects lipoprotein function (and subsequent cardio-metabolic diseases) but also moderates macrophage pro-/anti-inflammatory phenotypes (ApoE is one of the highly co-expressed genes (ApoE genotypes to COVID-19 severity.In conclusion, the ed genes . Further"} +{"text": "The role exerted by Aquaporin 4 (AQP4) as a regulator of astrocyte immune functions has been poorly explored. A recent report demonstrates that under neuroinflammatory conditions, the expression of Aqp4 on murine astrocytes is mandatory for the effective control of acute inflammation in the central nervous system. Such an immunomodulatory function appears to be mediated by a promotion of the transforming growth factor beta 1 (Tgfb1) pathway. Here, these results are discussed in the context of neuromyelitis optica (NMO) and multiple sclerosis (MS) progressive forms. It is proposed that NMO and progressive MS might rely on opposite molecular mechanisms involving, in NMO, an acutely-defective AQP4/TGFB1 pathway and, in progressive MS, a chronically-stimulated AQP4/TGFB1 pathway. Data supporting the involvement of angiotensin II as a molecular link between AQP4 and TGFB1 are also reviewed. Aqp4) exhibit an impaired systemic and intra-cerebral synthesis of transforming growth factor-beta 1 (Tgfb1) [AQP4 does not comprise TGFB1. The same result is obtained when exploring murine microarray datasets (n = 2401). These data mining findings suggest that APQ4 may not directly impact the transcription of TGFB1. On another hand, according still to the MEM database and webtool, AQP4 tightly co-expresses with angiotensinogen (AGT) , a gene upregulated in MS spinal cords [Aqp4 tightly co-expresses with Agt . Of note, Angiotensin II, the main active metabolite of angiotensinogen, not only stimulates the transcription of TGFB1 [In a recent paper, Xue et al. established that under conditions of acute neuronal insult, mice knock out for aquaporin 4 ( (Tgfb1) . The pap (Tgfb1) ,4 but pr (Tgfb1) and exhi (Tgfb1) . While a (Tgfb1) ,8, other (Tgfb1) ,10. Sinc (Tgfb1) and a pr (Tgfb1) ,13,14. W (Tgfb1) and (ii) (Tgfb1) . The dem (Tgfb1) ,18 or de (Tgfb1) ,20. In a (Tgfb1) ,22. Whil (Tgfb1) ,24. It i (Tgfb1) shows thal cords and exteal cords ,27,28,29of TGFB1 ,29 but eof TGFB1 ,31,32, tof TGFB1 . Finallyof TGFB1 ,13,14,16Overall, although NMO and progressive MS both stem from CNS-targeting autoimmune events, the evolution of spinal cord lesions in each disease appears to follow strikingly opposite fates: uncontained inflammation and rapid extension of lesions in NMO vs contained inflammation and slowly-expanding astrocytosis in MS. It is proposed here that NMO and progressive MS might rely on the following opposite molecular mechanisms: an acutely-defective AQP4/TGFB1 pathway in NMO versus a chronically-stimulated AQP4/TGFB1 pathway in progressive MS ."} +{"text": "Due to an error during production, Equations 10), (13)\u2013(20), (23), (24) were unreadable in the published paper [0, (13)\u2013("} +{"text": "The Oklahoma Healthy Aging Initiative is a statewide health promotion program for older adults based at the University of Oklahoma. Seven staff educators and 32 volunteers delivered 2 community-based fall prevention programs, Staying Active and Independent for Life (SAIL) and Tai Chi Quan: Moving for Better Balance (TCBB) to 763 older Oklahomans in 71 sites across the state over 9 months. For both programs, twenty-four 60-90 minute classes were delivered over 12 weeks with pre and post assessments completed at the first and last class, respectively. Two hundred ninety eight participants (39%) completed at least 75% of class sessions and to date 140 completed a posttest evaluation and were included in the evaluation. Participants were mostly older (87% \u226560 years), female (86%), college educated (45%), white (87%), and most participated in TCBB (89%). Participants improved in 2 physical performance measures: mean 30-second chair stands increased from 11.5 (SD3.8) to 13.1 (SD3.4) stands (p<0.0001); and mean timed up and go time decreased from 10.0 (SD2.9) to 9.4 (SD2.9) seconds (p=0.004 ). More participants reported vigorous or moderate activity at least 3 times per week after program completion, 134 (96%) vs. 114 (81%), p=0.0001. There was no difference in measures of global health, satisfaction with social roles and activities, or companionship with participant mean scores near the upper range of these scales at baseline. Older Oklahomans participating in community-based exercise report good overall health and report high social connection. Future efforts will focus on more socially isolated older adults and diverse communities."} +{"text": "On September 16, 2020, this report was posted online as an MMWR Early Release.Pregnant women might be at increased risk for severe coronavirus disease 2019 (COVID-19) . Among 2Among 596 women with COVID-19 whose pregnancy trimester was known, 14 (2.3%), 61 (10.2%), and 521 (87.4%) were hospitalized during the first, second, and third trimesters, respectively. The reason for hospital admission was reported for 324 women: 242 (74.7%) were hospitalized for obstetric indications (including labor and delivery), 61 (18.8%) for COVID-19\u2013related illness, and 21 (6.5%) for other reasons. The most common reason for admission during the first or second pregnancy trimester was COVID-19\u2013related illness (56.8%) and during the third trimester, obstetric indications (81.9%). Among hospitalized pregnant women with COVID-19, 20.6% had at least one underlying medical condition; asthma (8.2%) and hypertension (4.3%) were the most prevalent.Overall, 272 (45.5%) pregnant women with COVID-19 were symptomatic at the time of hospital admission, and 326 (54.5%) were asymptomatic. Women hospitalized during the first or second trimester were more frequently symptomatic (84.0%) than were those hospitalized during the third trimester (39.9%). Among symptomatic women, the most commonly reported symptoms were fever or chills (59.6%) and cough (59.2%) .Among 272 hospitalized symptomatic pregnant women, 44 (16.2%) were admitted to an ICU and 23 (8.5%) required invasive mechanical ventilation. Two (0.7%) deaths were reported among symptomatic women. No asymptomatic women were admitted to an ICU, required invasive mechanical ventilation, or died.At hospital discharge, 458 women (76.6%) with COVID-19 had completed pregnancies, including 448 (97.8%) that resulted in live births and 10 (2.2%) in pregnancy losses . PregnanOne in four women aged 15\u201349 years who had a COVID-19\u2013associated hospitalization during March 1\u2013August 22, 2020 was pregnant, based on a convenience sample from COVID-NET. Approximately one half of pregnant women were asymptomatic at hospital admission. Among symptomatic pregnant women, 16.2% were admitted to an ICU, 8.5% required invasive mechanical ventilation, and two died during COVID-19\u2013associated hospitalizations; none of these outcomes occurred among asymptomatic pregnant women. Among all pregnancies completed during a COVID-19\u2013associated hospitalization, 2.2% resulted in pregnancy losses. Pregnancy losses occurred among both symptomatic and asymptomatic hospitalized women with COVID-19.Approximately 5% of women of reproductive age in the general population are pregnant at any given time and Black (26.5%) were higher than the overall proportions of women aged 15\u201349 years in the COVID-NET catchment area who were Hispanic (15.3%) or Black (19.5%).Most pregnant women with COVID-19 in this study were asymptomatic, similar to findings in settings where universal SARS-CoV-2 testing is conducted upon admission to labor and delivery units was similar to that observed in two European studies was higher than that observed in the general U.S. population in 2018 (10.0%) , mechanical ventilation (8%), and death (1%). Pregnancy losses occurred for 2% of pregnancies completed during COVID-19-associated hospitalizations and were experienced by both symptomatic and asymptomatic women.Pregnant women and health care providers should be aware of potential risks for severe COVID-19, including adverse pregnancy outcomes. Identifying COVID-19 during birth hospitalizations is important to guide preventive measures to protect pregnant women, parents, newborns, other patients, and hospital personnel."} +{"text": "Avelumab, an antiprogrammed death ligand-1 antibody, is approved as a monotherapy for treatment of metastatic Merkel cell carcinoma and advanced urothelial carcinoma, and in combination with axitinib for advanced renal cell carcinoma. We report the efficacy and safety of first-line avelumab in advanced non-small cell lung cancer (NSCLC).In a phase I expansion cohort of the JAVELIN Solid Tumor trial, patients with treatment-naive, metastatic, or recurrent NSCLC received 10 mg/kg avelumab intravenously every 2 weeks. Endpoints included best overall response, duration of response (DOR), progression-free survival (PFS), overall survival (OS), and safety.Overall, 156 patients were enrolled and treated. Median duration of follow-up was 18.6 months . The objective response rate was 19.9% , including complete response in 3 (1.9%) and partial response in 28 (17.9%). Median DOR was 12.0 months . Median PFS was 4.0 months and the 6-month PFS rate was 38.5% . Median OS was 14.1 months and the 12-month OS rate was 56.6% . Treatment-related adverse events (TRAEs) occurred in 107 patients (68.6%), including grade \u22653 TRAEs in 19 (12.2%). Immune-related adverse events and infusion-related reactions occurred in 31 (19.9%) and 40 patients (25.6%), respectively. No treatment-related deaths occurred.Avelumab showed antitumor activity with a tolerable safety profile as a first-line treatment in patients with advanced NSCLC. These data support further investigation of avelumab in the phase III JAVELIN Lung 100 study.NCT01772004; registered January 21, 2013.ClinicalTrials.gov EGFR) or anaplastic lymphoma kinase (ALK) gene defects and with \u226550% programmed death ligand 1 (PD-L1) expression on tumor cells.5\u20137Monoclonal antibodies targeting immune checkpoint proteins are established treatments for metastatic non-small cell lung cancer (NSCLC). In 2016, the antiprogrammed cell death protein-1 (PD-1) antibody pembrolizumab was approved as first-line monotherapy for patients with metastatic NSCLC without targetable epidermal growth factor receptor . General eligibility criteria for the JAVELIN Solid Tumor trial have been reported previously.12JAVELIN Solid Tumor (NCT01772004) is an international, multicohort, open-label phase I trial. In this phase Ib NSCLC expansion cohort, patients, who were unselected for PD-L1 expression, had histologically confirmed stage IV Patients received avelumab 10 mg/kg by intravenous infusion every 2 weeks until disease progression, unacceptable toxicity, or other criteria for withdrawal were met. Patients were permitted to continue treatment despite progression according to the investigator\u2019s decision and in agreement with the patient if no new symptoms appeared, existing symptoms did not worsen, Eastern Cooperative Oncology Group (ECOG) performance status did not decrease, and the investigator did not consider it necessary to administer a salvage therapy. Dose reductions were not permitted. Premedication with an antihistamine and acetaminophen was given 30 to 60 min before each infusion. Treatment was permanently discontinued for any grade \u22653 adverse event (AE) except for specified transient AEs (reported previously).Tumor assessments were performed every 6 weeks for the first year and every 12 weeks thereafter by investigators according to Response Evaluation Criteria in Solid Tumors 1.1 (RECIST 1.1) and modified immune-related response criteria.PD-L1 expression was assessed using a proprietary immunohistochemistry assay . In previous studies comparing the 73-10 PD-L1 assay with the 22C3 assay used in pembrolizumab trials, the 73-10 assay showed greater sensitivity, and the \u226580% PD-L1 cut-off for the 73-10 assay was found to be comparable to the \u226550% PD-L1 cut-off for the 22C3 assay (manuscript in press).Prespecified endpoints assessed in this expansion cohort included confirmed best overall response, duration of response (DOR), and PFS based on investigator assessment according to RECIST 1.1, best overall response based on investigator assessment according to modified immune-related response criteria, OS, PD-L1 expression, and safety .Planned enrollment was 150 patients, which was based on the anticipated sample size required to estimate and provide 95% Clopper-Pearson CIs for potential objective response rates (ORRs). Safety data were summarized using descriptive statistics. Time-to-event endpoints were estimated using the Kaplan-Meier method, while 95% CIs for medians were calculated using the Brookmeyer-Crowley method. P values for the association between PD-L1 status and ORRs were determined using the Fisher\u2019s exact test. Comparisons between other subgroups were not prespecified and are reported descriptively.EGFR and ALK mutation status were unknown in 18 (11.5%) and 16 (10.3%), respectively. At data cut-off , the median follow-up was 18.6 months . Patients received a median of 12 avelumab infusions over a median duration of 5.5 months . At data cut-off, 26 patients (16.7%) remained on study treatment. Reasons for permanent treatment discontinuation were disease progression (82 (52.6%)), AEs (24 (15.4%)), withdrawal of consent (9 (5.8%)), death (9 (5.8%)), and other reasons (6 (3.8%)).Between March 18, 2015, and November 19, 2015, 156 patients were enrolled from seven countries in North America, Europe, and Asia . The medEGFR or ALK mutation status, ORRs were 16.7% and 18.8% , respectively. Of the three patients who had a CR, two had a preceding PR. Response was ongoing in 15 of 31 patients at data cut-off had a confirmed complete response (CR) and 28 (17.9%) had a confirmed partial response (PR), resulting in an ORR of 19.9% ; 17 patients (10.9%) were not evaluable for response per RECIST , 22.6% , and 26.3% , respectively . PatientIn analyzes of response by immune-related criteria, four additional patients, who did not achieve a response according to RECIST 1.1, had an objective response, resulting in an immune-related ORR of 22.4%, including immune-related CRs in four patients (2.6%) and immune-related PRs in 31 patients (19.9%). In PD-L1 subgroups with expression levels of \u22651%, \u226550%, and \u226580%, immune-related ORRs were 23.9% , 28.3% , and 34.2% , respectively. In the overall population, median PFS based on immune-related criteria was 6.9 months .In total, 156 patients (100%) had an AE of any grade. AEs led to permanent treatment discontinuation in 31 patients (19.9%). Twenty patients (12.8%) died following an AE that was unrelated to treatment; no deaths were considered related to treatment. IRR, identified using an expanded definition, was the most common AE and occurred in 40 patients (25.6%), including grade \u22653 AEs in five patients (3.2%). Most IRRs (34 of 40 patients) occurred after the first infusion, and eight patients (5.1%) permanently discontinued treatment because of an IRR.Treatment-related AEs (TRAEs) of any grade occurred in 107 patients 68.6%; . Of 19 p10.1136/jitc-2020-001064.supp4Supplementary dataSerious TRAEs occurred in 15 patients (9.6%), and the most common (\u22652 patients) were IRR (4 (2.6%)) and pneumonitis (2 (1.3%)).Thirty-one patients (19.9%) had an irAE, of which one patient (0.6%) had a grade \u22653 irAE in which patients with treatment-naive NSCLC received pembrolizumab, the ORR was 27%, median PFS was 6.2 months, and median OS was 22.1 months; efficacy was increased in patients whose tumors had high PD-L1 expression .In summary, the results from this phase Ib study showed that avelumab monotherapy has clinical activity and acceptable safety as a first-line treatment for patients with advanced NSCLC, providing the rationale for further studies. Findings from the phase III JAVELIN Lung 100 study will help clarify the potential role of avelumab monotherapy in the NSCLC treatment landscape."} +{"text": "Thymelaea hirsuta, a wild plant from the Sinai Peninsula of Egypt, were identified and their selective cytotoxicity levels were evaluated. Phytochemical examination of the ethyl acetate (EtOAc) fraction of the methanolic (MeOH) extract of the plant led to the isolation of a new triflavanone compound (1), in addition to the isolation of nine previously reported compounds. These included five dicoumarinyl ethers found in Thymelaea: daphnoretin methyl ether (2), rutamontine (3), neodaphnoretin (4), acetyldaphnoretin (5), and edgeworthin (6); two flavonoids: genkwanin (7) and trans-tiliroside (8); p-hydroxy benzoic acid (9) and \u03b2 sitosterol glucoside (10). Eight of the isolated compounds were tested for in vitro cytotoxicity against Vero and HepG2 cell lines using a sulforhodamine-B (SRB) assay. Compounds 1, 2 and 5 exhibited remarkable cytotoxic activities against HepG2 cells, with IC50 values of 8.6, 12.3 and 9.4 \u03bcM, respectively, yet these compounds exhibited non-toxic activities against the Vero cells. Additionally, compound 1 further exhibited promising cytotoxic activity against both MCF-7 and HCT-116 cells, with IC50 values of 4.26 and 9.6 \u03bcM, respectively. Compound 1 significantly stimulated apoptotic breast cancer cell death, resulting in a 14.97-fold increase and arresting 40.57% of the cell population at the Pre-G1 stage of the cell cycle. Finally, its apoptosis-inducing activity was further validated through activation of BAX and caspase-9, and inhibition of BCL2 levels. In silico molecular docking experiments revealed a good binding mode profile of the isolates towards Ras activation/pathway mitogen-activated protein kinase (Ras/MAPK); a common molecular pathway in the development and progression of liver tumors.In this study isolates from Daphne giraldii -4,4\u2032-dione.The first flavanone is linked to the second flavanone at the C-3 and C-3`` positions, which was confirmed by comparison of the avanones and mithavanones . Further\u03b4C 82.8) . Based o2\u201310 (2) -4,4\u2032-dione; as well as nine other compounds, including five first reported dicoumarinyl ether compounds which were identified as daphnoretin methyl ether (2), rutamontine (3), neodaphnoretin (4), acetyldaphnoretin (5), and edgeworthin (6), and four previously isolated compounds, which were identified as genkwanin (7), trans-tiliroside (8), p-hydroxy benzoic acid (9) and \u03b2 sitosterol glucoside (10). Compounds 1, 2 and 5 exhibited remarkable cytotoxic activities against HepG2 cells, with IC50 values of 8.6, 12.3 and 9.4 \u03bcM, respectively. However, they exhibited non-toxic activities against the Vero cells. Additionally, compound 1 further exhibited promising cytotoxic activity against both MCF-7 and HCT-116 cells, with IC50 values of 4.26 and 9.6 \u03bcM, respectively. Compound 1 significantly stimulated apoptotic breast cancer cell death resulting in a14.97-fold increase, with 40.57% of the cell population being arrested at the Pre-G1 cell cycle stage. Finally, its apoptosis-inducing activity was further validated through activation of BAX and caspase-9, and inhibition of BCL2 levels. Molecular docking experiments with the isolates showed a high affinity to Ras/MAPK when compared to rutin and sorafenib, and support the putative molecular mechanism of action of these compounds.The phytochemical examination of the EtOAc fraction of the MeOH extract of"} +{"text": "Background/Aim: Dermatological adverse events (DAE) in hepatocellular carcinoma (HCC) patients treated with sorafenib predicts better outcome. Some turn into skin lesions (SL) requiring pathology examination. We describe incidence, characteristics and molecular profile of SL in HCC patients treated with sorafenib.HRAS, KRAS and BRAF mutations were analyzed by CAST-PCR, mutated p53 and MAPK pathway activation by immunohistochemistry and immune infiltration by hematoxylin-eosin staining.Materials and Methods: SL were prospectively collected in 311 HCC patients who started sorafenib. SL from sorafenib cohort were compared to those from a control patient group selected to match SL type and demographics. n = 4), squamous-cell carcinomas (SCC)(n = 5), basal-cell carcinomas (BCC)(n = 3) and seborrheic keratosis (n = 5). HRAS and KRAS mutations were detected in 4 SL, while no mutations showed in control SL. Nuclear pERK immunostaining was identified in 33.3% of cases versus 5.3% of controls. Most SL (90%) from patients with DAE were proliferative with intense immune infiltration (73%).Results: Eighty-eight out of 311 patients developed DAE and 7.4% SL required histological assessment. Most frequent lesions were keratoacanthomas (Conclusions: The onset of SL and their molecular profile did not impact negatively on patient\u2019s prognosis, but intense proliferation of SL may reflect compensatory activation of MAPK pathway and warrants their close monitoring. Sorafenib is an oral multitarget tyrosine kinase inhibitor directed to vascular endothelial growth factor receptor (VEGFR)-1, -2, -3, platelet-derived growth factor receptor (PDGFR)- b, c-KIT, RET, FLT-3 and BRAF. This agent demonstrated survival benefit in patients with hepatocellular carcinoma (HCC) and refrSorafenib-related dermatologic adverse events (DAE) affect approximately 40% of the patients and are notable for a wide spectrum of manifestations, including maculopapular rash, hand-foot skin reaction, alopecia, xerosis, generalized exanthema and erythema multiforme-Stevens-Johnson syndrome , 6. The Since the approval of sorafenib, case reports and small series have described the onset of proliferative and inflammatory skin lesions (SL) in patients undergoing treatment, such as squamous cell carcinoma (SCC), keratoacanthoma (KA), actinic keratosis, cystic folliculitis and basal cell carcinoma (BCC) \u201317. ThesRAS , 269 (86.5%) patients were male, 278 (89.4%) had ECOG-PS of 0, 270 (86.8%) had preserved liver function (Child-Pugh A). Nine (2.9%) were previously submitted to liver transplantation. Median follow-up was 12 months [IQR: 6.1\u201322.5], and the median duration of sorafenib treatment was 6.2 months [IQR: 2.1\u201312.5]. Grade > II DAEs within the first 60 days of treatment (eDAE) were observed in 88 (28.1%) patients .n = 20; 86.9%), alcohol and non-alcoholic steatohepatitis . Coexistence of alcohol and chronic hepatitis C was found in 5 (21.7%) patients patients developed 32 SL that were submitted to biopsy or excisional procedure, with pathologic assessment. Five patients developed more than 1 SL. The median age of the group who developed SL was 58 years-old [IQR: 52\u201366], 19 (82.6%) patients were male, 21 (91.3%) had ECOG-PS 0, 21 (91.3%) were Child-Pugh A and 3 (13%) had previous liver transplantation. Eleven (47.8%) were BCLC-C and 12 (52.2%) were BCLC-B. The main liver disease etiologies were chronic hepatitis C virus infection and the 223 patients who did not present eDAE, 16 (7.2%) (The incidence of SL was similar between the 88 patients who presented eDAE (6 (7.2%) .n = 23) was 26.5 months (95% CI 21.6\u201344) with a median treatment duration of 15.5 months [IQR: 9.5\u201323]. Patients who develop eDAE had a median overall survival of 18.2 months (95% CI 13.9\u201323.6) with median treatment duration of 9 months [IQR: 4.5\u201314]. Finally, those patients with eDAE and SL (n = 7) had a median OS of 26.5 months (95% CI 22\u201351.6) with a median treatment duration of 16.7 months [IQR: 10\u201322.6]. Detailed clinical characteristics and management are shown in Supplementary Table 1.None of the patients required definitive discontinuation of sorafenib due to SL management. The median overall survival of the patients with SL (n = 10/35.7%). The most frequent types of proliferative SL were KAs (n = 4/22.2%), SCCs (n = 5/27.7%) (n = 3/6.6%) and seborrheic keratosis (n = 5/27.7%). The whole spectrum of SL is depicted in Supplementary Table 2. Marked immune cell infiltration was observed in 15 out of the 18 proliferative lesions (83.3%).For additional pathology and molecular characterization, a total of 28 samples of SL from 19 HCC patients were available. We found that 18 of the 28 SL (64.3%) could be classified as proliferative lesions while the rest were non-proliferative entities (5/27.7%) , BCCs (nn = 11) or non-eDAE patients (n = 17) we found that the great majority of SL in eDAE group were proliferative lesions (n = 10/ 90.9% vs n = 8/47%) with higher immune infiltration (n = 8/72.7% vs n = 6/35.3%).When we divided the 28 SL according to their development in eDAE group of patients BBC and in the sebaceous hyperplasia case, HRAS Q61L in 1 (out of 3) BCC and a HRAS Q61K mutation was found in 1 out of 5 seborrheic keratosis. The latter also presented strong immunostaining for nuclear pERK, suggesting activation of the MAPK pathway. None of the samples presented BRAF V600E mutation.Briefly, we observed a Five out of 24 cases that could be analyzed (20.8%) showed immunostaining for nuclear pERK and only 1 (5.3%) control presented a weak (10%) immunostaining for pERK, suggesting that activation of MAPK pathway was more frequent in HCC patients compared to the control group.Additionally, we found 4 (16.6%) cases and 8 (42.1%) controls with immune expression of mutated p53 (in > 5% of the cells). This result evidence a higher p53 mutation in control patients compared to sorafenib-treated patients.n = 7; 8%) and those who did not present eDAE, 16 (7.2%), our study shows that 90% of the SL from patients who developed eDAE, clusters into the proliferative pattern with associated immune cell infiltration in 73% of them. Our study also shows that a more exacerbated and early \u201cskin response\u201d evidenced a longer OS for those patients with eDAE and SL (median 26.5 months 95% CI 22\u201351.6) compared to that of all eDAE patients (median 18.2 months 95% CI 13.9\u201323.6) with a higher median treatment time also for eDAE plus SL group. Of note, the longer median sorafenib duration treatment in patients developing SL together with the late onset of SL raise the \u201cchicken or egg paradox\u201d hampering any robust inference in terms of survival.We reported the largest series dedicated exclusively to patients with HCC under sorafenib focusing on the onset of SL requiring excisional procedures and their management, mutational profile and clinical outcomes. A wide spectrum of lesions was observed ranging from inflammatory to proliferative profile, with a varying range of time between treatment initiation and biopsy (2.4 to 54.1 months). Despite SL may appear early after sorafenib start, we found no difference in time to biopsy between patients with eDAE and patients without eDAE. Sporadic skin tumors and other proliferative cutaneous lesions development generally occurs with gradual accumulation of genetic mutations along years or decades. The fact that patients receiving sorafenib treatment may develop SL within months after its start, suggest that this agent may hyperactivate the pathways for keratinocyte transformation. While the incidence of SL was similar between patients who presented eDAE , and by the mechanisms behind the activation of the hedgehog signaling pathways . Time to-event data were estimated by Kaplan Meier with median and 95% Confidence Interval (95%CI). All the analysis were performed using SAS v. 9.4 ."} +{"text": "Physicians desire an electronic health record (EHR) interface to visualize data from mobile devices in rapid and unobtrusive manner. We developed an EHR interface after performing semi-structured qualitative interviews with 12 physicians. These interviews led to creating an EHR graphical interface that allowed seamless viewing of the top ranked patient attributes of pain, falls, hydration and mobility patterns. Physicians then evaluated the interface using the International Standard ISO 9241, Part 110\u2014 a survey to evaluate the design of human computer interactions. The median response for each of domains were as follows: suitability = 18.5 out of 24 (range: 9-24); conformity=34 out of 40 (range: 16-40); self-descriptiveness=25 out of 32 (range: 13-31); controllability=19.5 out of 24 (range: 8-23); error tolerance=5 out of 8 (range: 1-8). The median total score of 111.5 out of 140 (range: 88-128) indicated a relatively high level of usability of the EHR interface depicting smartwatch data."} +{"text": "On July 7, 2020, this report was posted online as an MMWR Early Release.Meat and poultry processing facilities face distinctive challenges in the control of infectious diseases, including coronavirus disease 2019 (COVID-19) for long time periods (8\u201312 hour shifts), shared work spaces, shared transportation to and from the workplace, congregate housing, and frequent community contact with fellow workers. Many of these factors might also contribute to ongoing community transmission (Twenty-eight (56%) of 50 states responded, including 23 (82%) that reported at least one confirmed COVID-19 case among meat and poultry processing workers. Overall, 239 facilities reported 16,233 COVID-19 cases and 86 COVID-19\u2013related deaths among workers . The medTwenty-one states provided information on demographic characteristics and symptom status of workers with COVID-19. Among the 12,100 (75%) and 12,365 (76%) patients with information on sex and age, 7,288 (60%) cases occurred among males, and 5,741 (46%) were aged 40\u201359 years, respectively . Among tAmong 239 facilities reporting cases, information on interventions and prevention efforts was available for 111 (46%) facilities from 14 states. Overall, 89 (80%) facilities reported screening workers on entry, 86 (77%) required all workers to wear face coverings, 72 (65%) increased the availability of hand hygiene stations, 70 (63%) educated workers on community spread, and 69 (62%) installed physical barriers between workers . Forty-oAmong seven facilities that implemented facility-wide testing, the crude prevalence of asymptomatic or presymptomatic infections among 5,572 workers who had positive SARS-CoV-2 test results was 14.4%. The pooled prevalence estimated from the model for the proportion of asymptomatic or presymptomatic infections among workers in meat and poultry processing facilities was 11.2% (95% CI = 0.9%\u201323.1%).The animal slaughtering and processing industry employs an estimated 525,000 workers in approximately 3,500 facilities nationwide COVID-19\u2013related deaths. Among cases with race/ethnicity reported, 87% occurred among racial or ethnic minorities. Commonly implemented interventions included worker screening, source control measures , engineering controls , and infection prevention measures .Targeted workplace interventions and prevention efforts that are appropriately tailored to the groups most affected by COVID-19 are critical to reducing both COVID-19\u2013associated occupational risk and health disparities among vulnerable populations."} +{"text": "Bacillus strains isolated from five different batches of fermented Napa cabbage kimchee. Strains TNC1(2019), TNC3(2019), and TNW1(2019) were identified as Bacillus subtilis, while TNC2(2019) and TNW2(2019) were identified as Bacillus velezensis.We report the draft genome sequences of five novel Bacillus strains isolated from five different batches of fermented Napa cabbage kimchee. Strains TNC1(2019), TNC3(2019), and TNW1(2019) were identified as Bacillus subtilis, while TNC2(2019) and TNW2(2019) were identified as Bacillus velezensis.We report the draft genome sequences of five novel Bacillus is a genetically and metabolically diverse genus of bacteria that have been used for the development of environmental and medicinal tools . Whole-genome sequencing was conducted at the Microbial Genome Sequencing Center, LLC , using the 151-bp paired-end read libraries designed for the Illumina MiSeq platform. We obtained a total of 3,653,401 raw reads for TNC1(2019), 3,551,954 raw reads for TNC2(2019), 3,581,451 raw reads for TNC3(2019), 3,863,404 raw reads for TNW1(2019), and 3,466,478 raw reads for TNW2(2019).To investigate the genetic diversity of de novo assembler v3.11, testing assemblies with kmer values of 21, 33, 55, 77, 99, and 127 (NCBI accession number ASM608879v1), with DDH values of 91.7%, 90.0%, and 86.8%, respectively. The three draft genomes ranged in size from 4,044,726\u2009bp to 4,080,193\u2009bp, with an average G+C content of 43.6% and median coverage of 106.7\u00d7. We found that the draft genome of strain TNC2(2019) was most closely related to Bacillus velezensis NRRL B-41580 (NCBI accession number ASM146182v1), a type strain isolated from river sediments in Spain (Bacillus velezensis FZB42 (NCBI accession number ASM1578v2), a strain formerly known as Bacillus amyloliquefaciens subsp. plantarum FZB42 and isolated from beet rhizosphere (We found that the draft genomes of strains TNC1(2019), TNC3(2019), and TNW1(2019) were most closely related to in Spain , and thaThe draft genomes and raw reads for each strain have been deposited in DDBJ/EMBL/GenBank under the accession numbers listed in"} +{"text": "During September 3\u2013November 16, 2020, daily confirmed cases of coronavirus disease 2019 (COVID-19) reported to the Wisconsin Department of Health Services (WDHS) increased at a rate of 24% per week, from a 7-day average of 674 (August 28\u2013September 3) to 6,426 (November 10\u201316) , correctional facilities (14.9%), and colleges or universities (15.0%) accounted for the largest numbers of outbreak-associated cases in Wisconsin.COVID-19 surveillance and mitigation planning should be prioritized for highly affected settings such as long-term care facilities, correctional facilities, and colleges and universities, which could represent early indicators of broader community transmission."} +{"text": "Single examples of C\u2013As and lack of C\u2013Se bond formation, involving two of the closest neighbors of P and S in the periodic table, have also been noted. Applications of the obtained \u03c0-conjugated molecules, mainly as semiconducting materials, flame retardants, and resins hardeners, designed on the basis of five- and six-membered cyclic molecules containing ring phosphorus and sulfur atoms, are also included. This comprehensive review covers literature up to August 2020.The interest in functional materials possessing improved properties led to development of new methods of their synthesis, which allowed to obtain new molecular arrangements with carbon and heteroatom motifs. Two of the classical reactions of versatile use are the Friedel-Crafts and the Bradsher reactions, which in the new heteroatomic versions allow to replace ring carbon atoms by heteroatoms. In the present work, we review methods of synthesis of C\u2013S and C\u2013P bonds utilizing Thus, phosphole has nearly six times weaker aromatic character than thiophene based on aromatic stabilization energies thienobis[1]benzothiophene reported by Sirringhaus and coworkers. The syntheses proceeded via the acid-induced intramolecular cyclization reaction of arenes containing methyl sulfoxide groups, i.e., methylsulfinylbiphenyl (9) and 3,7-bis(methylsulfinylophenyl)dibenzothiophene. The latter was prepared through the Suzuki\u2013Miyaura cross-coupling reaction of the bromide (10) and the diboronic acid (11) (The first illustration of this new methodology was synthesis of dibenzothiophene (cid (11) 10]..7) and db:4,5-b\u2019]bis[b]benzothiophenes (12), dithienobenzodithiophenes (13), and dithienothienobenzodithiophenes (14), as useful materials for organic transistors. In this synthesis, 2,5-dibromophenyl dimethyl disulfoxide (15), a cyclic boronic ester (16), or organotin compounds were applied as the corresponding substrates containing carbazole, pyrrole, or thiophene aromatic rings. A key step of these syntheses involved intramolecular triflic acid (TfOH)-mediated cyclization. The corresponding substrates for the cyclizations were prepared through the Suzuki cross-coupling reaction of 2,5-dibromophenyl dimethyl sulfoxide (15) or 1-bromophenyl methyl sulfoxides (24) with carbazole 2-boronic (25) or 2,7-diboronic acids diesters (26) and the Stille coupling reaction of 1-bromophenyl methyl sulfoxides (24) or 2,7-dibromocarbazole (27) with ditin heteroaryl derivatives or tin heteroaryl derivative (30) (The same research group synthesized heteroacenes (ive (30) 17,18].,18.19\u201323b]benzo[d]thiophene (31) and benzothienothiophene (32) from fluorenes (33), 3-bromothiophene (34), and sulfides (35) . Photoph36) through the following reaction sequence: bromination of the teraryl (37), reaction of the resulting bromo-derivative with NaSMe, oxidation with hydrogen peroxide, followed by the final cyclization using triflic acid (Liu and coworkers prepared dibenzotetrathienoacene (lic acid 21]..36) thro38) and (39) from 2- and 2,6-substituted tin derivatives (40) and (41), respectively. The latter was first reacted with 2-bromothioanizole (42) and then oxidized with hydrogen peroxide to give sulfoxides (43) and (44), respectively, and finally cyclized to the desired products (38) and (39) in the presence of triflic acid (TfOH)/phosphorus pentoxide and 45\u201347) were realized by Li and coworkers. The approaches utilized a coupling of pyrene derivatives (48\u201350) with 2-iodothioanisol (51) or boronic acids (52)/(53), and subsequent oxidation to afford sulfoxides (54\u201356), which in the final step underwent cyclization to regioisomeric ..45\u201347) wb;4,5-b\u2019]-dithiophenes (57). In this approach, 2-bromo-3-methylsulfinylbenzothiophene (58) underwent the Stille coupling reaction with tin derivatives (59) providing teraryls (60), which were next cyclized in the presence of the Eaton\u2019s reagent (7.7 wt% P2O5 in CH3SO3H) and finally aromatized with pyridine to afford the desired products (57) (57) had suitable HOMO energy levels to be applied in organic transistors as p-channel organic semiconductors. Thin-film transistor characteristics showed that all derivatives displayed a high device reproducibility and nearly no dependence on substrates temperature.Similar synthetic methodology was used by Li and coworkers for the synthesis of thieno. Fu. Fub;4,5b:3,4-b\u2019:5,6-b\u2019\u2019]-tri (61) starting from symmetrical benzo-trithiophene (62). Bromination of (62) followed by coupling with boronic acid (52) afforded the trisulfide (63). Oxidation of the latter in the next step and cyclization in the presence of triflic acid (TfOH) provided polycyclic heteroacene system (61) in 45% yield containing dibenzothiophene moieties. In this synthesis, the palladium catalyzed polycondensation of cyclic diboronic acid diesters (65) with 2,4-dibromo-1,5-di-n-dodecylthiobenzene (66) followed by oxidation of the sulfide to sulfoxide function with hydrogen peroxide provided polyphenylene (67), which was cyclized to the corresponding dibenzothiophene polymer (64) under strong acidic conditions via sulfonium derivative (68) (Nishide and coworkers synthesized poly(thiaheterohelicene) (ive (68) 26]..64) cont69) by the cyclization reaction of bithienyls or terthienyls (70) to sulfonium derivatives (71) followed by aromatization with pyridine to give fused thieno-systems (69) (Tuschida and coworkers synthesized a new type of polythiophene oligomers (ems (69) 27]..69) by t72, 73) in the presence of triflic acid (TfOH) provided polymers possessing ionic character , the corresponding dithianhtrene , polyphenothiazine, as well as phenoxantine systems with imine, ether, and thioether bridges, respectively, were obtained in good to excellent yields in addition to sulfur. Starting from precursors and (81) were synthesized from mono- and dibrominated BODIPY precursors (82) and (83). In this synthesis, the Pd-catalyzed Suzuki\u2013Miyaura cross-coupling reactions of the latter with 2-(methylthio)-phenylboronic acid (50) afforded, after oxidation with hydrogen peroxide, intermediate 2-(methylsulfinyl) phenyl-substituted BODIPY derivatives (84) and (85). The intramolecular cyclization of the mono-sulfoxide (84) with H2SO4 (neat), led to the cyclic intermediate product without boron, which then was borylated with BF3\u00b7OEt2 to give BT-BODIPY (80). However, the reaction of the bis-sulfoxide (85) with H2SO4 (neat) led to the mono-cyclization product only, in 84% yield. This product was complexed with BF3\u00b7OEt2 and again submitted to strong acidic conditions H2SO4 (neat), which made cyclization of the second sulfoxide moiety effective in 51% yield. The resulting intermediate which lost boron was complexed with BF3\u00b7OEt2 to form the desired benzothieno[b]-fused BODIPYs (81). Finally, it was found that both BT-BODIPY (80) and BBT-BODIPY (81) displayed red shifted absorption, increased molar absorptivity, and fluorescence efficiency were obtained in a moderate yield by the Suzuki cross-coupling reaction of thienothiophenes with boronic acids and subsequent oxidation of sulfur atoms in the corresponding sulfides to sulfoxides using 30% aqueous hydrogen peroxide. Cyclization of the latter derivatives delivered the target compounds in 75% yield. Measurements of charge mobilities (0.15 for (86) and 0.047 cm2/V s) for (87)) revealed that the linear C2-symmetrical isomer (86) was a better candidate for fabrication of organic field-effect transistors than the kinked one (87) (Two tetrathienoacenes (one (87) 38]..86, 87) 93\u201395) based on benzodithiophene (BDT) skeleton were synthesized and characterized as p-type semiconductors with wide band gaps. The synthetic strategy, which delivered derivatives (93\u201395), included two key steps: the cross-coupling of bis(dimethylsulfinyl) benzene with derivatives (98\u2013101) and the multi-ring closing reaction of polysulfinyl benzothiophene derivatives (102\u2013104) catalyzed by the trifluoroacetic acid (TFA)/P2O5 reagent system (93\u201395) showed high emission and quantum yields. Moreover, they were found to be good two-photon absorbers, exhibiting high two-photon absorption coefficients ..119) uti124) with derivatives (98) or (125) in different ratios provided sulfoxide derivatives (126\u2013128). Cyclization of the latter by a ring-closing reaction followed by lithiation and stannylation generated monomers (129\u2013131) which can be applied to the synthesis of oligo-heteroacenes with a varied number of fused rings benzene (ed rings 43]. . 124) wi132\u2013134), measured according to the space charge limited current (SCLC) model, were in the of range 5.02 \u00d7 10\u22124\u20135.56 \u00d7 10\u22126 cm2/(V s). Photovoltaic properties of these polymers were investigated in a device of the following structure: ITO/PEDOTS:PSS/polymer:PC71BM /Ca/Al. Polymers (132\u2013134) revealed a photoconversion efficiency in the range of 0.014\u20137.6% and light intensity within 0.28-14.5 mA/cm2. The hole mobilities of polymers (135) was achieved by an acid-mediated ring closure of the biphenyl (136) having a sulfoxide substituent at the ortho-position. The latter was synthesized in the Suzuki coupling reaction of boronic acids with substituted halobenzenes followed by oxidation with hydrogen peroxide was141) and 2-substituted methylthiobenzene (142) produced after oxidation of sulfur atom with hydrogen peroxide the methyl sulfoxide derivative (143) in 80% yield. The acid-induced condensation of the latter and subsequent demethylation in the presence of water/pyridine afforded unsymmetrical, fused compounds (144). The di-n-hexyl substituted derivative (144) exhibited intense fluorescence in solution with the highest quantum yield of up to 91%. Moreover, the solution-processed, green phosphorescent, organic light-emitting diodes with this derivative as the host material exhibited a maximum brightness of 14,185 cdm\u22122 and a luminescence efficiency of 12 cdA\u22121 and145) was realized in the four-step methodology including: the Suzuki cross-coupling reaction of 9,10-dibromoanthracene (146) and 2-methylthiobenzene boronic acid (52), oxidation of the resulting anthracene derivative with hydrogen peroxide to the precursor 9,10-bis(2-methylsulfinyl-phenyl)anthracene (147), cyclization of (147) in the presence of triflic acid (TfOH) acid, and finally demethylation in a water\u2013pyridine mixture. The electroluminescent device employing (145) as the emitting layer exhibited stable red emission and current efficiency up to 4.4 cd A\u22121 (The synthesis of benzobisthioxanthene (4 cd A\u22121 45]..145) was3) yielded triphenylphosphine sulfide upon reaction with benzene and excess aluminum chloride. Olah and coworkers developed this method for preparation of triphenylphosphine sulfide in 71% yield from benzene and sulfur, phosphorus trichloride, and aluminum chloride .,49.3-catb 48,49]b]phosphole derivatives (150) via the Rh(III)-catalyzed C-H alkenylation of arylthiophosphinamides (151) with alkynes (152) followed by the formal phospha-Friedel\u2212Crafts-Bradsher cyclization, catalyzed by TfOH and subsequent oxidation of the intermediate (153) with hydrogen peroxide (Miura and coworkers developed a regioselective synthetic sequence leading to benzo[peroxide 50]. . b]phosp154) with the epoxide (155) proceeded smoothly under rhodium (III) catalysis and involved hydroarylation followed by dehydrative aromatization to form biarylphosphine derivatives (156), which were next transformed to fused dibenzophosphole derivatives (157) through the TfOH-mediated intramolecular cyclization in a one-pot manner (Direct coupling of arylphosphine oxides and sulfides (t manner 51]..154) wit158\u2013160) starting from 1,3-dichlorobenzene (161). The synthesis involved 1) lithiation at the 2 position in (161), 2) subsequent Cl/Ar replacement with Grignard aryl reagents and 3) iodination to deliver teraryls (162), and 4) the iodine/lithium replacement in (162) followed by phosphinylation with phosphorus trichloride to give the substrate (163) for the electrophilic tandem ring-closure in the presence of AlCl3/S8/NEt(i-Pr)2 to afford phosphaperylenes . Other phosphaperylenes were obtained by desulfurization of the latter with triethylphosphine. The corresponding phosphine oxides were synthesized by treatment of the corresponding phosphine sulfides and phosphine selenides with H2O2 , (159c), and (160c) exhibited strong blue and cyan fluorescence with maxima (\u03bbem) at 418, 415, and 468 nm, respectively. The quantum yield of (159c) (\u03a6f = 0.83) was higher than that of (158c) (\u03a6f = 0.68).The obtained phosphaperylenes were thermally stable, and none of the derivatives decomposed below 600 K. Phosphine oxides (164). In this synthesis, hexabromobenzene (165) was treated with Grignard aryl reagents followed by quenching with elemental iodine to give 2,3,5,6-tetraaryl-1,4-diiodobenzene (166). The halogen\u2013lithium exchange in the diiodo derivatives (166) and subsequent condensation of the resulting aryllithiums with bis chlorophosphine, gave 2,3,5,6-tetraaryl-1,4-bisphosphine (167). Finally, sulfurization and tandem intramolecular phospha-Friedel-Crafts-Bradsher reaction of (167) with AlCl3 yielded the helicene (164) (The same research group described a synthesis of P-fused double helicene (ne (164) 53]. . 164). I164) with triethylphosphine Et3P afforded the corresponding bis(phosphine) helicene (168) and a selective oxidation of the latter with m-chloroperoxybenzoic acid (MCPBA) delivered the corresponding bisphosphine oxide helicene (169). Due to the non-planarity of the central ring in (164), its aromaticity was reduced but decomposition was not observed even at 600 K under air atmosphere.Desulfurization of (170) through the reaction with n-butyllithium and PCl3 gave diarylaminodichlorophosphine, which after sulfurization with elemental sulfur and the subsequent tandem phospha-Friedel-Crafts-Bradsher reaction in the presence AlCl3 afforded azaphosphadibenzochrysene (171) in 61% yield (Phosphination of diarylamine (1% yield 5]..170) thr172\u2013176) by the direct ortho-lithiation of 1,3-diphenoxybenzene (177) with n-butyllithium and subsequent trapping of the resulting carboanion with PCl3 followed by the standard sulfurization of the intermediate phosphine with S8 to give arylthiophosphonic acid dichloride (178). In the presence of excess of AlCl3 and H\u00fcnig\u2019s base (NEtiPr2), the dichloride (178) underwent a tandem phospha-Friedel-Crafts-Bradsher reaction at elevated temperature to give 5,9-dioxa-13b-thiophosphanaphthoanthracene (172) in 56% yield. This polycyclic phosphine sulfide was oxidized with m-chloroperbenzoic acid (MCPBA) to afford appropriate phosphine oxide, i.e., 5,9-dioxa-13b-oxaphosphanaphthoanthracene (DOPNA) (173), or was reduced to the free phosphine (174) by Et3P (The Hatakeyama group reported a synthesis of a novel group of cyclic triarylphosphine derivatives ( by Et3P 54]. . 172\u2013176de]anthracene (6-Ph-DOPNA) (176) was synthesized from (172) by electrophilic bromination of the latter using N-bromosuccinimide (NBS) in N,N-dimethylformamide (DMF) followed by Suzuki\u2013Miyaura coupling with phenylboronic acid in the presence of dichlorobis(p-dimethylaminophenylditert-butylphosphine)palladium(II) ((AMPHOS)2PdCl2) and Na2CO3. The direct substrate (172) was obtained by the reaction sequence involving 2-lithiathion of 1,3-diphenoxybenzene and then the reaction of the resulting lithium derivative with phosphorus trichloride, followed by sulfurization of the dichlorophosphine obtained with elemental sulfur. The DOPNA phosphine derivative (174) was synthesized via trans-sulfurization with triethylphosphine (179) starting from 2-(2-bromo-3-phenoxy-phenoxy)-biphenyl (180) by lithium\u2013bromine exchange in (180) with n-BuLi and by trapping the obtained aryllithium with bischlorophosphine (ClP(NEt2)2). Then, sulfurization with S8 of the intermediate phosphine amide formed at 70 \u00b0C afforded N,N,N\u2019,N\u2019-tetraethyl-P-arylphosphonothioic diamide (181) in 82% yield. The double phospha-Friedel-Crafts-Bradsher reaction of (181) in the presence of Lewis acid (AlCl3) in ortho-dichlorobenzene (ODCD) at 150 \u00b0C gave the corresponding 4-phenyl-5,9-dioxa-13b-thiophosphanaphtho-anthracene (182) in 57% yield. Oxidation of the resulting phosphine sulfide by m-chloroperbenzoic acid (MCPB) at room temperature afforded (179) in 52% yield values of DOPNA (2.87 eV), 6-Ph-DOPNA (2.53 eV), and 4-Ph-DOPNA (2.49 eV) were higher than those of Ir(ppy)3 (2.45 eV) and BPhen (2.35 eV), which are representative phosphorescence and electron transport materials for phosphorescent organic light-emitting diodes (PHOLEDs). Spectroscopic measurements revealed that triplet energy ETo demonstrate the potential of DOPNA derivatives as OLED materials, the authors fabricated phosphorescent organic light-emitting diodes (PHOLED) using these compounds as hole/exciton blocking layer (HBL) components. The addition of 4-Ph-DOPNA and 6-Ph-DOPNA substantially improved the OLED lifetime.b]phosphole derivatives (183) and (184) through a one-pot multicomponent coupling reaction. The starting materials were the arylzinc reagent (185) prepared from arylmagnesium bromide and ZnCl2 in the presence of TMEDA and alkyne (186). The sequential coupling procedure involved a [CoCl2(xantphos)]-catalyzed reaction of (185) with (186) (step 1), the addition of CuCN\u20222LiCl, and trapping the resulting ortho-alkenylarylzinc species with PhPCl2 to give aryl phenyl chlorophosphine (187) (step 2). The subsequent ring closure in the presence of Lewis acid (ZnX2) afforded the final benzo[b]phosphole ring system (183) (step 3). Oxidation of (183) with hydrogen peroxide provided phosphine oxide (188a), and sulfurization led to phosphine sulfide (188b). Alternatively, in step 2, phosphorus trichloride was used to give the intermediate (189) followed by addition of the Grignard reagent RMgBr to substitute one P\u2013Cl bond by aryl and ring closure in one step to afford (187) (step 3). Oxidation with H2O2 or sulfurization with S8 gave phosphine oxides or phosphine sulfides (190a) or (190b), respectively to activate the P\u2013Cl bond; however, this phospha-cyclization proceeds in THF under relatively mild conditions in the presence of weak Lewis acid (ZnX2). Usually, intramolecular 191). The presence of electron withdrawing substituents on the aryl group at the phosphole phosphorus in the benzophosphole (191a) also had a notable effect. Compounds with 4-fluorophenyl and 4-trifluoromethylphenyl (192) groups exhibited intense blue emission at 420 and 422 nm, respectively. They also revealed high fluorescence quantum yields of 0.86 and 0.93, respectively. The 2-phenyl and 2,3-diphenyl analogues (193) and (194) showed \u03bbabs and \u03bbem red-shifts due to extended conjugation at the 2 and 3 positions.Most of the obtained benzophosphole derivatives, especially oxides, were fluorescent in solution. High fluorescence quantum yields (0.57\u20130.94) were obtained in the case of benzophosphole oxides bearing phenyl, amino, and carbazolyl substituents in the presence of NiCl2 as a catalyst were added to triple bond of alkynes (196) to form the magnesium intermediates (197) followed by trapping the resulting cis-\u03b2-styrylmagnesium species with dichlorophosphine (RPCl2) in the presence of CuCN\u20222LiCl to afford (198). A weak Lewis acid (MgX2) formed during the reaction, spontaneously catalyzed the phospha-Friedel-Crafts-Bradsher cyclization, leading to the benzo[b]phosphole ring system (199). Oxidation of the latter by hydrogen peroxide afforded the relevant phosphine oxides (200) .201) usually proceeds via the phospha-Friedel-Craft-Bradsher cyclization of the phosphorus dichloride (202) in the presence of Lewis acid at very high temperature. The P\u2013Cl bond in (201) was next hydrolyzed to H-phospinate (203). In this approach, the substrate (205) was obtained from condensation of 2-hydroxybiphenyl (204) with phosphorus trichloride. Later, Pastor et al. and Holmes et al. carried out the same reaction without a solvent using a weaker Lewis acid (ZnCl2) at 200 \u00b0C . . 2O-medi211\u2013213) through triple phospha-Friedel-Crafts-Bradsher cyclization [213) was synthesized in five steps starting from tri-p-tolylamine (214), which was brominated with N-bromosuccinimide (NBS) to give the corresponding tribromide (215). Triaryllithium, generated from (215) by n-butyllithium, was trapped with excess of bischlorophosphine (ClP(NEt2)2) and submitted to sulfurization with elemental sulfur to afford the intermediate tris(thioamide) (216). The triple cyclization of (216) with H\u00fcnig\u2019s base in the presence of AlCl3, at elevated temperature, afforded triphosphaazatriangulene (211) and (213). The Hatakeyama group reported synthesis of triphosphaazatriangulenes (lization . The trine (211) . Oxidati213) indicated that its complex with copper (213)\u2022Cu2(OH)4) could be a highly proton-conducting material. The triangulene was subjected to AC impedance spectroscopy under conditions of controlled humidity. The proton conductivity was found to be 5.9 \u00d7 10\u22128 S cm\u22121 at 25 \u00b0C and 55% relative humidity (RH). Nyquist plots, under a variety of humidity conditions (from 55% to 95% RH) at 25 \u00b0C, showed that conductivity increased with increasing RH.The presence of a phosphinic acid group (P(O)(OH)) in the triangulene . The review demonstrates the progress made in both types of reactions, leading to construction of a variety of benzo- and thieno-fused, carbo- and heterocyclic frameworks which gained applications, mainly as semiconducting and light emitting materials in organic diodes, transistors, and photovoltaic devices. Extensive literature and a variety of examples show that this type of reaction has become an important synthetic tool in modern organic chemistry for introduction of ring phosphorus and sulfur into molecular structures. We believe that this review will serve as a useful reference for chemists interested in developing libraries of new thia- and phospha-derivatives and in extending their applications over emerging areas. This review should also stimulate the development of the chemistry of arsenic and selenium, the two heavier neighbors of sulfur and phosphorus in the periodic table, based on electrophilic aromatic substitution reaction.These two heteroatoms have been introduced into carbon backbones by harnessing the classical Friedel-Crafts and Bradsher reactions in new heteroatomic versions ("} +{"text": "CDKN2A gene.About 25\u2009years ago, the acquired chromosome abnormality dicentric dic was seen described as a non-random aberration in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet, about 200 cases were reported. However, dicentric dic is a subtle abnormality which easily may be mixed up with monosomy 20 and/or del(9p). The dicentric dic can be found as a sole chromosomal abnormality or can be masked within complex rearrangements; also, a dicentric dic is often associated with mono- or biallelic loss of CDKN2A. After successful chemotherapeutic treatment the patient experienced a relapse with a secondary ALL without complex karyotype but a deletion del(19)(p13). Unfortunately, the patient died after 17\u2009months of the initial diagnosis.Here we report a case of 16-year-old male diagnosed with a de novo pre-B-ALL. Molecular approaches (array-based multicolor banding (aMCB) and array comparative genomic hybridization (aCGH)) were applied, and a unique complex karyotype involving six chromosomes was identified. It included three previously unreported chromosomal aberrations: dicentric dic, deletion del(7)(p22.2p15.2) and dicentric dic. The dicentric dic also led to monoallelic loss of tumor suppressor gene To the best of our knowledge, a comparable childhood ALL associated with such complex karyotype and deletion del(19)(p13) in secondary ALL was not previously reported. Thus, the complex karyotype with dicentrc dic seems to indicate for a poor prognosis. The stable chromosome abnormality dicentric dic9;20) was first reported as a non-random aberration in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) in 1995 /46,XY[3].Genomic DNA was extracted from BM cells prior to chemotherapy treatment and aCGH was performed using the Agilent Sure Print G3 Human Genome Microarray 180\u2009K as previously described .7p22.3 to 7p15.2 at positions 109,626 to 26,260,755 including five COSMIC census cancer genes;7p14.2 to 7p11.2 at positions 35,292,065 to 56,174,888 including 3 COSMIC census cancer genes;9p24.3 to 9p13.2 at positions 207,437 to 37,270,400 including 10 COSMIC census cancer genes, and13q12.3 to 13q24 at positions 32,035,219 to 115, 059,020 including 10 COSMIC census cancer genes.Array-CGH revealed four losses of copy numbers in:whole chromosome 8, including 34 COSMIC census cancer genes;20p13 to p11.1 at positions 60,747 to 25,713,574 including 2 COSMIC census cancer genes;20q11.2 to 20q11.2 at positions 29,467,937 to 29,948,374 (no COSMIC census cancer gene identified), and20q13.13 to 20q13.13 at positions 46,828,431 to 48,880,347 (no COSMIC census cancer gene identified) was positive for CD45After chemotherapy and relapse GTG-banding revealed a karyotype of 46,XY18],46,XY,del(19)(p13)[2] has been reported in 199 ALL cases listed in Mitelman database . DicentrThe dicentric dic9;20) contains centromeres of both chromosomes 9 and 20, resulting in loss of 9p and 20q material , 2, 4, 50 containThe dicentric dic can be found as a sole chromosomal aberration (~\u200940% of the ALL cases) or with additional chromosomal aberrations (ACAs) (60% of the ALL cases) . StreffoCDKN2A gene in 31% of all cases analyzed by FISH CDKN2A and subsequent deletion del(19p13) without all the previously observed changes in the secondary ALL were seen. Overall, such complex chromosomal changes seem to have adverse prognosis in pre-B-ALL.In conclusion, we report the first pre-B-ALL case obtained complex karyotype with a new acquired stable variant of a dicentric dic resulting from masked partial trisomy 20. In addition, monoallelic deletion of tumor suppressor gene"} +{"text": "As in-hospital sepsis mortality has decreased, more \u201csepsis survivors\u201d are progressing into poorly characterized long-term outcomes. The purpose of this study was to describe the current epidemiology of sepsis in older adults compared to middle-aged and young adults. Design: Prospective longitudinal study with patients categorized into young (\u2264 45 years), middle-aged (46-64 years) and older (\u2265 65 years) patient groups. 328 sepsis patients were characterized by a) baseline demographics and predisposition factors, b) septic event, c) hospital outcomes and discharge disposition, d) 12-month mortality and e) Zubrod Performance status, physical function and cognitive function at three, six and 12-month follow-up. Follow-up visits were not completed due to death (in 68) and withdrawal of consent (in 32). Compared to young and middle-aged patients, older patients had: 1) significantly more comorbidities at presentation , intra-abdominal infections (14% vs 25% vs 37%), septic shock (12% vs 25% vs 36%) and organ dysfunctions, 2) higher 30 day mortality (6% vs 4% vs 17%) and fewer ICU free days (median 25 vs 23 vs 20), 3) more progression into CCI with higher poor disposition discharge to non-home destinations (19% vs 40% vs 62%), 4) worse 12-month mortality (11% vs 14 % vs 33%) and, 5) poorer Zubrod Performance status and objectively-measured physical and cognitive functions with slight improvement over 12 month follow-up. Conclusion: Compared to younger patients, older sepsis survivors suffer with both a higher persistent disability burden and 12-month mortality."} +{"text": "Background: Neuroendocrine neoplasms (NENs) are a heterogeneous group of neoplasms that span from well-differentiated neuroendocrine tumors (NETs) to highly aggressive neoplasms classified as neuroendocrine carcinomas (NECs). The genomic landscape of NENs has not been well studied. The aim of this study is to confirm the feasibility of next generation sequencing (NGS) testing circulating tumor DNA (ctDNA) in patients with NENs and characterize common alterations in the genomic landscape.Results: Of the 320 NEN patients, 182 (57%) were male with a median age of 63 years (range: 8-93) years. Tumor type included pancreatic NET , gastrointestinal NEC , large cell lung NEC , nasopharyngeal NEC and NEC/NET not otherwise specified . ctDNA NGS testing was performed on 338 plasma samples; 14 patients had testing performed twice and 2 patients had testing performed three times. Genomic alterations were defined in 280 (87.5%) samples with a total of 1,012 alterations identified after excluding variants of uncertain significance (VUSs) and synonymous mutations. Of the 280 samples with alterations, TP53 associated genes were most commonly altered , followed by KRAS , EGFR , PIK3CA , BRAF , MYC , CCNE1 , CDK6 , RB1 , NF1 , MET , FGFR1 , APC , ERBB2 and PTEN .Conclusions: Evaluation of ctDNA was feasible among individuals with NEN. Liquid biopsies are non-invasive methods that can provide personalized options for targeted therapies in NEN patients.Patients and Methods: Molecular alterations in 338 plasma samples from 320 patients with NEN were evaluated using clinical-grade NGS of ctDNA (Guardant360\u00ae) across multiple institutions. The test detects single nucleotide variants in 54-73 genes, copy number amplifications, fusions, and indels in selected genes. NETs are a rare and diverse group of tumors with variable survival outcomes and behaviors , defined\u00ae NGS from patients with a diagnosis of NEN across various histologies is evaluated. The aim was to confirm the feasibility of NGS using ctDNA in NEN and characterize common alterations in the genomic profile. Furthermore, we aimed to identify whether the molecular alterations lead to the identification of potential actionable targets.With the complexity of the classification, novel biomarkers are required to assist in clinical decision making and ultimately improve patient outcomes . Identif\u00ae testing using clinical-grade NGS of ctDNA across multiple institutions, and 280 (87.5%) patients had at least one sample with alterations. The median age was 63 years (range: 8-93), with a male preponderance (57%). Tumor type included pancreatic NET , NEC/NET not otherwise specified (NOS) , gastrointestinal NEC , large cell lung NEC and nasopharyngeal NEC . ctDNA N 16, 5%) . The seqTP53 associated genes were most commonly altered , followed by KRAS , EGFR , PIK3CA , BRAF , MYC , CCNE1 , CDK6 , RB1 , NF1 , MET , FGFR1 , APC , ERBB2 and PTEN , followed by KRAS (N = 63), APC (N = 49), NF1 (N = 46), EGFR (N = 43), MET (N = 42), BRCA1 (N = 32), MYC (N = 30), BRCA2 (N = 29), CDK6 (N = 25), ERBB2 (N = 22), BRAF (N = 20), CCNE1 (N = 19), PIK3CA (N = 17), MTOR (N = 15), FGFR1 (N = 14), RB1 (N = 13) and PTEN (N = 11). For gastrointestinal NEC patients, TP53 associated genes were most commonly altered (N = 54), followed by APC (N = 28), EGFR (N = 18), ERBB2 (N = 11), NF1 (N = 11), KRAS (N = 10), CCNE1 (N = 10), BRCA2 (N = 10), BRCA1 (N = 9), PIK3CA (N = 9), RB1 (N = 8), MYC (N = 7), BRAF (N = 7), CDK6 (N = 5), MTOR (N = 4), MET (N = 3), and FGFR1 (N = 3). For large cell lung NEC patients, TP53 mutation was most commonly altered (N = 48), followed by BRAF (N = 11), PIK3CA (N = 10), APC (N = 10), MET (N = 9), FGFR1 (N = 9), EGFR (N = 8), KRAS (N = 8), MYC (N = 7), BRCA2 (N = 5), ERBB2 (N = 5), CCNE1 (N = 5), RB1 (N = 5), CDK6 (N = 4), NF1 (N = 3), MTOR (N = 2), BRCA1 (N = 1) and PTEN (N = 1). Genomic alterations stratified by tumor type are shown in In the total cohort of NEN patients, 14, 5%) . AlteratKRAS mutations occurred more commonly among males (66%) with a mean age of 59.3 years. Prevalence of BRAF mutations occurred more frequently in males (60%) with a mean age of 61.5 years. Seven ATM mutations were detected and occurred more frequently in males (57%) with a mean age of 67.1 years. In this study, BRCA1 and BRCA2 mutations were seen in males more frequently (82% and 65%) with a mean age of 54.7 years and 58.9 years, respectively. MTOR mutations occurred more commonly in females (56%) with a mean age of 63.4 years and 47 PIK3CA mutations were detected, of which 51% were male and mean age was 58.4 years [With current technology the genome of a tumor can be analyzed by studying the tumor tissue as well as the DNA shed by the tumor (ctDNA). A significant challenge for the use of ctDNA in the NEN field is the relative lack of recurrent mutations in comparison with other tumors. Requirements for accurate ctDNA analysis include adequate tumor DNA being shed into the blood stream and a PCR primer based assay that detects the mutations of interest . Unfortuf cases) . Pancreamodeling . Interesutations . The mututations . Howeverutations . This di (DAXX)] , while B (DAXX)] .ALK translocation revealed by ctDNA analysis in a patient with metastatic atypical carcinoid tumor of the lung [ALK translocation was the driver mutation. In another case report, a patient with high-grade, large cell neuroendocrine cervical carcinoma was successfully treated with nivolumab combined with stereotactic body radiation therapy, based on blood ctDNA results targetting alterations suspicious for high tumor burden [The analysis of ctDNA may be useful for multiple purposes including early detection of residual or recurrent disease, monitoring tumor burden, assessing molecular heterogeneity targeted treatments, prognostic and predictive implications . Recentlthe lung . The patr burden .EGFR , PIK3CA , BRAF , CDK6 , MET , FGFR1 , ERBB2 , and BRCA1/2 . Repeat sampling is a unique advantage of liquid biopsies over tissue based assays. In this series, 16 patients had serial profiling of ctDNA. Analysis showed gain and loss of mutations with time. Some of the gained mutations are targetable including FGFR2, ATM and BRCA1.The present analysis is the first and largest population-based study exploring the genetic mutations in patients with NEN utilizing ctDNA derived from liquid biopsy. Some of the alterations reported here are in clinical development as potential targets. In our population of NEN patients, alterations were identified with therapeutic implications that could potentially be targeted by drugs approved for other cancers. Examples of these mutations with their respective frequency of alterations include with possible drug examples: MEN1, ATRX or DAXX, which are clinically important in pancreatic NET guidelines.This is a retrospective review evaluating the molecular alterations in 338 ctDNA samples from 320 patients who had a diagnosis of NEN and underwent Guardant360\u00ae), a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory. The Guardant360\u00ae assay detects single-nucleotide variants (SNV), indels, fusions, and copy number alterations in 73 genes, including the most prevalent tumor suppressor genes in human cancers, with a reportable range of \u2265 0.04%, \u2265 0.02%, \u2265 0.04%, and \u2265 2.12 copies, respectively, as well as microsatellite instability. It does not report tumor mutation burden (TMB). This is a highly analytically/clinically sensitive and specific test, able to detect single molecules of tumor DNA in 10 mL blood samples with an analytic specificity of > 99.9999% [NGS of plasma cfDNA (liquid biopsy) was done by Guardant Health . Hybrid-capture sequencing libraries were prepared from up to 30ng cfDNA and labeled with nonrandom oligonucleotide barcodes , followed by library preparation, hybrid capture enrichment , and sequencing at 15,000 \u00d7 read depth of the critical exons in the targeted panel by paired-end synthesis . Bioinformatics analysis and variant detection were performed as previously described . NGS dat"} +{"text": "So far, the production of natural lactones with flavor and fragrance properties from fatty acids by non-genetically modified organisms (non-GMO) involves whole cells of bacteria catalyzing the hydration of unsaturated fatty acids as well as yeast strains responsible for further \u03b2-oxidation processes. Development of a non-GMO process, involving a sole strain possessing both enzymatic activities, significantly lowers the costs of the process and constitutes a better method from the customers\u2019 point of view regarding biosafety issues. Twenty bacteria from the genus of Bacillus, Comamonas, Dietzia, Gordonia, Micrococcus, Pseudomonas, Rhodococcus and Streptomyces were screened for oxidative functionalization of oleic acid (1). Micrococcus luteus PCM525 was selected as the sole strain catalyzing the one-pot transformation of oleic acid (1) into natural valuable peach and strawberry-flavored \u03b3-dodecalactone (6) used in the food, beverage, cosmetics and pharmaceutical industries. Based on the identified products formed during the process of biotransformation, we clearly established a pathway showing that oleic acid (1) is hydrated to 10-hydroxystearic acid (2), then oxidized to 10-ketostearic acid (3), giving 4-ketolauric acid (4) after three cycles of \u03b2-oxidation, which is subsequently reduced and cyclized to \u03b3-dodecalactone (6) (Scheme 1). Moreover, three other strains , with high concomitant activities of oleate hydratase and alcohol dehydrogenase, were identified as efficient producers of 10-ketostearic acid (3), which can be used in lubricant and detergent formulations. Considering the prevalence of \u03b3-dodecalactone (6) and 10-ketostearic acid (3) applications and the economic benefits of sustainable management, microbial bioconversion of oleic acid (1) is an undeniably attractive approach.Microbial conversion of oleic acid ( It is a natural aroma compound characterized by an intense peach flavor with a creamy note and it occurs in fruits such as apricot, peach, strawberry, pineapple, mango, plum and acerola (7), 264 (49), 235 (6), 222 (30), 180 (19), 166 (10), 152 (12), 137 (17), 123 (26), 110 (32), 97 (62), 83 (68), 69 (79), 55 (100).GC\u2013MS (EI): Rt 19.24 minLinoleic acid methyl ester m/z (%) = 294 [M+] (18), 263 (15), 234 (1), 220 (4), 178 (6), 164 (10), 150 (16), 135 (15), 123 (18), 109 (36), 95 (70), 81 (93), 67 (100), 55 (56).GC\u2013MS (EI): Rt 19.29 minLinolenic acid methyl ester m/z (%) = 292 [M+] (7), 261 (4), 249 (2), 236 (5), 191 (3), 173 (5), 149 (13), 135 (15), 121(20), 108 (34), 95 (56), 79 (100), 67 (66), 55 (43).GC\u2013MS (EI): 2) Rt 21.58 minMethyl 10-acetoxystearate (m/z (%) = 313 [M+-MeCO] (6), 296 [M+-AcOH] (3), 281 (17), 264 (31), 243 (11), 222 (9), 201 (100), 169 (64), 157 (16), 125 (21), 97 (18), 83 (19), 69 (21), 55 (27).GC\u2013MS (EI): 3) Rt 21.30 minMethyl 10-ketostearate (m/z (%) = 312 [M+] (2), 281 (23), 239 (5), 227 (5), 214 (52), 199 (40), 182 (11), 156 (100), 141 (67), 125 (86), 97 (60), 81 (31), 71 (90), 55 (89).GC\u2013MS (EI): 4) Rt 14.90 minMethyl 4-ketolaurate (m/z (%) = 228 (1), 197 (10), 141 (21), 130 (88), 115 (57), 98 (100), 87 (13), 81 (8), 71 (31), 55 (40), 43 (21).GC\u2013MS (EI): 6) Rt 15.08 min \u03b3-Dodecalactone (m/z (%) = 180 (1), 162 (1), 141 (3), 128 (12), 114 (4), 100 (6), 85 (100), 69 (9), 55 (14), 41 (13).GC\u2013MS (EI): Micrococcus luteus PCM525, R. erythropolis DSM44534, R. ruber PCM2166 and Dietzia sp. DSM44016 effectively converted oleic acid (1) to 10-ketostearic acid (3), showing high concomitant oleate hydratase and alcohol dehydrogenase activities. M. luteus PCM525 was selected to catalyze the one-pot transformation of oleic acid (1) directly into the natural industrially valuable flavor, \u03b3-dodecalactone (6). This is the first example of bacteria possessing such activity. Based on the analyzed products, the biotransformation pathway was established. Moreover, the presented study allows the drawing of relevant remarks. We observed that several factors have a negligible influence on \u03b3-dodecalactone (6) synthesis, whereas the type and phase of growth considerably influenced the biotransformation process. Biotransformation performed in PCM medium with the concentration of 0.25% oleic acid (1) added to the culture of M. luteus PCM525 in the stationary phase was characterized by complete conversion and afforded, after five days , a mixture of \u03b3-dodecalactone (6) (37%) and 4-ketolauric acid (4) (63%). We demonstrated that M. luteus PCM525 is tolerant to a high concentration of oleic acid (1); although, with increasing substrate concentration, instead of exclusive production of lactone 6, a mixture of 10-ketostearic acid (3), 4-ketolauric acid (4), \u03b3-dodecalactone (6) was observed. Besides, the presence of glucose is mandatory for M. luteus PCM525 growth and \u03b3-dodecalactone (6) production; however, its supplementation during biotransformation is inadvisable due to the inhibition of \u03b2-oxidation of 10-ketostearic acid (3). Overall, considering the relevance of \u03b3-dodecalactone (6) and 10-ketostearic acid (3) applications and the economic benefits of sustainable management of side-stream feedstocks, industrial transformation of oleic acid (1) catalyzed by M. luteus PCM525 should be further investigated.Among the studied bacteria, originating from different genus,"} +{"text": "T-box Transcription Factor 1 (TBX1) and DiGeorge Critical Region 8 (DGCR8) in the clinical phenotypes. However, the haploinsufficiency of these genes alone cannot account for the tremendous variation in the severity and penetrance of the clinical complications among those affected. Recent RNA and DNA sequencing approaches are uncovering novel genetic and epigenetic differences among 22q11.2del patients that can influence disease severity. In this review, the role of coding and non-coding genes, including microRNAs (miRNA) and long noncoding RNAs (lncRNAs), will be discussed in relation to their bearing on 22q11.2del with an emphasis on TBX1.Chromosome 22q11.2 deletion syndrome (22q11.2del) is a complex, multi-organ disorder noted for its varying severity and penetrance among those affected. The clinical problems comprise congenital malformations; cardiac problems including outflow tract defects, hypoplasia of the thymus, hypoparathyroidism, and/or dysmorphic facial features. Additional clinical issues that can appear over time are autoimmunity, renal insufficiency, developmental delay, malignancy and neurological manifestations such as schizophrenia. The majority of individuals with 22q11.2del have a 3 Mb deletion of DNA on chromosome 22, leading to a haploinsufficiency of ~106 genes, which comprise coding RNAs, noncoding RNAs, and pseudogenes. The consequent haploinsufficiency of many of the coding genes are well described, including the key roles of Screeniin utero . The disin utero . Hypoplain utero . Those iin utero . DiGeorgin utero Table 1 in utero . Low TREin utero . The hetin utero . Impactethyroids . Over tithyroids . Males athyroids . The leathyroids . Not surthyroids . Mid-agethyroids . With suthyroids . Yet, hethyroids .via the translocation breakpoint sequences. The most frequent deletion in 22q11.2del patients spans LCR A-D (3 Mb), with a less frequent deletion between LCR A-B (1.5 Mb) . A rare (1.5 Mb) . Even mo(1.5 Mb) .T-Box 1 Transcription Factor (TBX1), DiGeorge Syndrome Critical Region 8 (DGCR8), Crk-like Adaptor Protein L (CRKL), Proline Dehydrogenase (PRODH), Reticulon 4 Receptor (RTN4R), Zinc-finger DHHC-type Containing 8 (ZDHHC8), Catechol-O-Methyl Transferase (COMT), Guanine Nucleotide Binding Protein b-polypeptide 1-Like (GNB1L), Septin 5 (SEP5) and Glycoprotein Ib Platelet Subunit Beta (GP1BB). Yet, the haploinsufficiency of these genes is clearly unable to explain the heterogeneous penetrance and severity of clinical phenotypes that differ from patient to patient. This is even noted among family members with the same mutation in TBX1 and with genetically identical in-bred strains of mice used as models of 22q11.2del syndrome. In this review, we present recent findings revealing how variations in the expression of TBX1, the functions of DGCR8, and the miRNAs and long noncoding RNAs within and outside the 22q11.2 locus can influence the severity of the clinical manifestations of 22q11.2del -family , a gene also encoded on the frequently deleted segment of chromosome 22q11.2. DGCR6 down-regulates TBX1, impacting neural crest migration within the pharyngeal region -family . The KMT)-family Figure 2)-family . The TBX)-family . These tl region . As neurpatients . Some inpatients . Such drprinting . Noteword to CHD . These fth SMAD1 . This inth SMAD1 . As Bmp4th SMAD1 . Bmp4 alth SMAD1 . TBX1 inth SMAD1 . In summTBX1 levels in relation to the severity of the congenital malformations in humans is further supported by comparisons with the diverse 22q11.2del mouse models. Multiple mouse lines were originally created with deletions of varying length on chromosome 16 (orthologous to human chromosome 22q11.2) to identify causal genes in the disorder can increase the methylation levels of H3K4 and partially rescue the cardiovascular anomalies in the Tbx1-mutant embryos , a metabolite of vitamin A that functions as a natural morphogen involved in the patterning of the 3rd, 4th, and 6th pharyngeal arch arteries and 3rd PP , an enzyme required for RA synthesis. +/-Rald2 embryos produce less RA, increasing the levels of Tbx1. In the setting of a Tbx1 haploinsufficiency, the severity of the heart defects was reduced in the Rald2+/- background (Monocytic Leukemia Zinc Finger (MOZ/Myst3/Kat6a), a histone acetyltransferase. MOZ, in turn, positively regulates TBX1 levels, with Moz-knock-out mice and those with loss-of-function mutations having less Tbx1, along with Tbx2, Tbx5, and Tbx9 , in the caudal region (tailbud) of developing embryos is another key gene whose haploinsufficiency in 22q11.2del patients can influence the severity of their clinical problems. It is a nuclear miRNA binding protein required for the biogenesis of microRNAs (miRNAs) . MiRNAs (miRNAs) . DGCR8 b(miRNAs) . These p(miRNAs) . Thus, acontrols . This dycontrols . The disDgcr8 causes a 30-50% reduction in the overall expression of miRNAs screened in neurons , Bruton\u2019s Tyrosine Kinase (Btk), Calmodulin Kinase 4 (Camk4), 2+-ATPaseSarco/endoplasmic Reticulum Ca (Serca2), and Nuclear Factor of Activated T cells 3c (Nfat3c) , a target of miR-185 , affecting epithelial to mesenchymal transitions and TGF beta-receptor 2, which is involved in the TGF-beta-SMAD4 signaling process , Glucose Transporter 3 , and Ras Responsive Element Binding protein 1 (RREB1) (In addition to 7 miRNAs Table 2. samples . It is e(Nfat3c) . A commoectively . Moreoveectively . MiR-185al cells . In B ce miR-185 . Notablyectively . MiR-130 process . Other hl cortex . MiR-649 pathway . Several (RREB1) . Several (RREB1) .TBX1. One is miR-96, mutations in which cause a non-syndromic hearing loss in humans embedded in the frequently deleted segment of chromosome 22q11.2 Table 2.Along with the miRNAs and lncRNAs encoded on chromosome 22q11.2 are two small nucleolar RNAs (snoRNAs), SNORA15, and SNORA77 Table 2.Taken together, it is clear that the haploinsufficiency of diverse noncoding RNAs and the extensive dysregulation of the miRNAs within this group will impact both developmental processes during embryogenesis and post-natal cardiac, immune, and neurological functions. Identifying the pathways affected by these diverse noncoding RNAs may better guide clinical management of the 22q11.2del patients.TBX1 often have overlapping congenital problems that still vary in severity , MYC Induced Nuclear Antigen (MINA), and Lysine-Specific Demethylase (KDM7A). This once again reveals an epigenetic component to 22q11.2del. SNPs have also been reported in Ras Responsive Element Binding protein 1 (RREB1) and SEC24 family member C (SEC24C) selectively in the 22q11.2del with CHD.Patients with both deletions and duplications of chromosome 22q11.2 and those with loss- or gain- of-function mutations in severity . Moreoveenotypes . These fenotypes . This isenotypes . Identifenotypes . This scGLUT3 , located on chromosome 12p13.3 (KANSL1 (chromosome 17q21.31), contributing to an increased odds ratio for CHD (OR = 2.75) . KANSL1 = 2.75) . How thedividual .Vascular endothelial growth factor (Vegf), Fibroblast growth factor 8 (Fgf8), and Platelet derived growth factor receptor (Pdgfr) (Vegf recapitulate the cardiac defects of 22q11.2del (Tbx1 and Fgf8 (Tbx1+/\u2212Fgf8+/\u2212) have a higher penetrance of aortic arch artery defects, with Tbx1 regulating Fgf8 expression Table 3 (Pdgfr) . In miceq11.2del . Mice hapression . These rq11.2del . In one q11.2del . Anotherl region . Its tarl region . Interes aplasia . Other c aplasia . In summth pharyngeal arch artery is either missing and/or poorly developed in nearly 100% of the murine 22q11.2 del embryos when assessed at embryonic e10.5 . However week 7) . This inBRUNOL3 (GATA3 (Zinc Finger Protein 717 (ZNF717) are affected by this deletion, resulting in DiGeorge-like syndrome and renal insufficiency. Given the clinical overlap among these different microdeletions, it is anticipated that several may affect TBX1 expression and/or modulate histone modifications among cells differentiating within the pharyngeal region.In an analysis of >1400 22q11.2del patients, 1% were found to have secondary mutations at other loci . These s2, ETR3) . HDR is ) (GATA3 . Chromos) (GATA3 . A 371-k) , Beecherl funds from the Department of Immunology at UT Southwestern Medical Center (NO), and the Jeffrey Modell Foundation (MM).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Nature Communications 10.1038/s41467-020-18723-y, published online 1 October 2020.Correction to: The original version of this Article contained an error on page 5 of the Results section, which incorrectly read \u2018They are characterized by craniofacial dysmorphisms (9/10), thin vermillion border and lips (4/7), and feeding difficulties (6/11), and exhibit neonatal hypotonia (10/7)\u2019. The correct version states \u2018They are characterized by craniofacial dysmorphisms (9/10), thin vermillion border and lips (4/7), and feeding difficulties (6/11), and exhibit neonatal hypotonia (7/10)\u2019."} +{"text": "We examined caregiving relationships for individuals with vision impairment (VI) and dementia, using 2011 National Health and Aging Trends Study (NHATS) data, a survey of Medicare beneficiaries, linked to the National Study of Caregiving, a survey of family/unpaid helpers to NHATS participants. VI was defined as self-reported blindness or difficulty recognizing someone across the street, watching television or reading newspaper print. Dementia was defined as probable dementia based on survey-report or AD8 criteria. Caregiving outcomes included: (1) hours of care provided in the last month and (2) number of valued activities affected by caregiving. Among 1,196 caregivers, 617 assisted older adults without dementia or VI (D-/VI-), 298 with dementia but without VI (D+/VI-), 143 without dementia but with VI (D-/VI+), and 138 with dementia and VI (D+/VI+). In fully-adjusted regression models, caregivers of older adults D+/VI+ spent twice as many hours providing care than caregivers of older adults D-/VI-; however, caregivers of adults D+/VI- and those providing to older adults D-/VI+ spent 1.5-times more hours . Additionally, caregivers of older adults D+/VI+ reported 4 times as many valued activities were affected (95%CI=2.8-5.6) then caregivers of those D-/VI-, while caregivers of those D+/VI- reported 1.9-times (95% CI=1.3-2.8) and D-/VI+ 1.6-times (95% CI=1.1-2.3) more activities were affected. Our results suggest that caring for older adults with VI has similar demands as caring for older adults with dementia, but that these implications may be magnified when caring for older adults with both dementia and VI."} +{"text": "Staphylococcus aureus (MRSA) infections necessitates the use of validated methods for the identification and typing of this bacterium. This study aimed to determine the distribution of main molecular types of MRSA strain circulating among hospitalized patients in teaching hospitals in Isfahan and Kashan.The global spread of methicillin-resistant Staphylococcus aureus strains were isolated from patients in four teaching hospitals in Isfahan and Kashan during June 2017 to September 2018. The antimicrobial resistance patterns of Staphylococcus aureus strains were performed by disc diffusion method. The MRSA strains were identified phenotypically and confirmed by PCR assay. The prevalence of microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) genes among MRSA strains was evaluated by multiplex PCR. The genotypes of MRSA strains were determined by multilocus sequence typing and SCCmec typing.A total of 146\u2009Staphylococcus aureus isolates, 24 (16.4%) isolates were identified as MRSA strains. According to antimicrobial susceptibility testing the highest resistance rates were seen for tetracycline, erythromycin, ciprofloxacin and gentamicin. All of Staphylococcus aureus isolates were susceptible to vancomycin whereas 3 (2.1%) isolates were resistant to linezolid. Three different SCCmec types were obtained among MRSA strains including 16 (66.7%) SCCmec type V, 3 (12.5%) SCCmec type III and 5 (20.8%) SCCmec type II. Of 24 MRSA isolates 20 (83.3%) carried MSCRAMMs genes including eno (70.8%), fib (54.1%), cna (25.0%), fnbB (16.6%), ebps 5 (20.8%), and the fnbA, bbp and clfA genes were not detected in any MRSA isolate. MLST analysis revealed 11 sequence types among MRSA isolates as follows: ST239, ST291, ST22, ST861, ST889, ST8, ST59, ST343, ST772, ST6 and ST1465. Also seven MLST-based clonal complexes (CCs) were identified among MRSA strains including: CC8, CC7, CC398, CC59, CC22, CC1 and CC5.Of 146\u2009A relatively high diversity was found in MRSA genotypes in Kashan and Isfahan hospitals, and seven clonal complexes were identified. Pandemic MRSA clones including CC8 and CC22 were the most prevalent clones and the novel ST types including ST1465, ST861, ST 889 and ST772 are reported for the first time in Iran in the present study. In addition the high prevalence of MSCRAMMs genes in MRSA isolates demonstrates the high potential of these strains for pathogenicity. Staphylococcus aureus (S. aureus) is one of the most important human pathogen that causes a wide range of infections collected from teaching hospitals in Isfahan and Kashan . Clinical samples were collected of burn wound 56 (38.4%), eye infection 49 (33.6%), respiratory infections 11 (7.5%), trauma 6 (4.1%), diabetic wound 5 (3.4%), brain abscess 5 (3.4%), blood 3(2%), urine 9(6.2), and other infections 2 (1.4%). There was no significant difference between MRSA and MSSA isolates in terms of age groups, gender and clinical specimens (mecA gene showed among 146 studied S. aureus isolates 24 (16.4%) isolates identified as MRSA strains.The results of PCR amplification of S. aureus isolates were sensitive to vancomycin (MIC <\u20092\u2009\u03bcg/mL) (Table\u00a0P\u2009<\u20090.05), and there was a significant correlation between multiple-drug resistance and MRSA isolation (P\u2009=\u20090.001).According to results obtained from antibiotic susceptibility testing, resistance rates to tetracycline 19 79.2%), erythromycin 17 (70.8%), ciprofloxacin 16 (66.7%), and gentamicin 15 (62.5%) was high among MRSA strains and all %, erythrmec types were obtained among MRSA strains including 16 (66.7%) SCCmec type V, 3 (12.5%) SCCmec type III and, 5 (20.8%) SCCmec type II , 13 (54.1%), 6 (25.0%), 4 (16.6%) and 5 (20.8%), respectively. Six, 2, and 4 isolates carried 4, 3 and 2 bands related to MSCRAMMs determinants respectively and the fnbA, bbp and clfA genes were not detected in any MRSA isolate carried MSCRAMMs genes and in 4 (16.6%) of which, none of the MSCRAMMs genes studied were isolated. The prevalence of .3% carrieno, cna and fib genes, (P\u2009<\u20090.001). In statistical analyses a significant correlation was obtained between MRSA and MSSA strains regarding eno, cna and fib genes (P\u2009<\u20090.001).In statistical analyses a significant correlation was obtained between MRSA strains and mec type III (2 isolates), ST239-SCCmec type II (2 isolates), ST291-SCCmec type V (2 isolates), ST291-SCCmec type II (1 isolates), ST22-SCCmec type II (1 isolate), ST22-SCCmec type V (4 isolates), ST861-SCCmec type III (1 isolate), ST 889-SCCmec type II (1 isolate), ST8-SCCmec type V (1 isolate), ST59-SCCmec type V (3 isolates), ST343-SCCmec type V (1 isolate), ST772-SCCmec type V (1 isolate), ST6-SCCmec type V (1 isolate) and ST1465-SCCmec type V (3 isolates). Also seven MLST- based clonal complexes (CCs) were identified among MRSA strains including: CC8 (41.7%), CC7 (4.2%), CC398 (12.5%), CC59 (12.5%), CC22 (20.7%), CC1 (4.2%) and CC5 (4.2%) phenotype. In a study conducted by Goudarzi et al. [mec IV in comparison to our MRSA ST22 which was ST22-SCCmec V. These findings highlight the importance of using several typing methods simultaneously to achieve better analysis. In previous studies of MRSA and MSSA strains in the cities of Isfahan and Tehran the majority of MRSA isolates belonged to ST239 [mec types II and III, with similar antimicrobial resistance and virulence patterns [mec V, ST291-SCCmec V and ST1465-SCCmec V. The association of ST291 with HA- MRSA has been reported from Iran [mec V has been documented as the predominant CA- MRSA strains in Asia [S. aureus strains have been documented to be highly clonal and the most of the strains belong to a limited number of closely related genotypes. Literature have shown that CC8 , CC5 and CC22 (epidemic MRSA-15) belong to epidemic MRSA (EMRSA) clones with global distribution in hospitals [eno, fib) and none of these genes were found in one strain with ST1465. However, further studied is needed to give a precise information about the virulence of these strains. In addition the MRSA- ST861 strain was one of the most virulent strains studied, carrying four MSCRAMMs determinants including eno, cna, fib, fnbB. Since all of these strains had a MDR phenotype, they should be carefully considered. Finally, the MRSA-ST772 strain belonged to CC1, and found to carry eno, cna, ebp, and fib genes.Nowadays, different clones of antibiotic-resistant strains, such as the MRSA strains, are spreading between healthcare centers and the community . This isectively . In the ectively , 25 Alsoectively in Belgito ST239 . In accorom Iran , and ST5 in Asia . Howeverospitals . In accoospitals . Also geospitals . ST22 stospitals . Furtherospitals . The inceno and fib genes encoding binding proteins was high. The high prevalence of adhesive protein genes in MRSA isolates indicates the persistence of these strains after colonization and subsequent infection. From the point of view of MSCRAMMs genes and correlation with ST groups, the most virulent strains of our MRSA isolates were belonged to CC8, CC1, and CC398. The eno and fib genes were present in all seven identified clonal complexes, whereas the cna was detected in the CC1, CC7, CC8, CC59, and the ebp gene identified in the CC1, CC5, CC8, and CC398. The fnbB gene, encoding fibronectin binding protein B was detected in only two clonal complexes including CC8 and CC398. However, all isolates that carried the fnbB gene were identified as the most virulent strains with multiple resistance phenotypes and isolated from various hospitals and important clinical samples including blood and brain abscess. In other studies, all of the S. aureus isolates from the bloodstream have been showed to carry the fnb gene [Our results confirmed that majority 83.3%) of the MRSA isolates harbored genes of binding factors and the prevalence of .3% of thmec typing results, a relatively high diversity was found in MRSA genotypes in the hospitals of Kashan and Isfahan, and seven clonal complexes were identified. However, it should be considered that only a limited number of isolates were genotyped during current study. Pandemic MRSA clones including CC8 and CC22 were the most prevalent clones and the novel ST types including ST1465, ST861, ST 889 and ST772 are reported in the present study for the first time in Iran. Furthermore, presence of momentous sequence types including ST22-SCCmec type II, ST239-SCCmec types II and III and ST291-SCCmec type II among important clinical samples such as burn wound and blood due to the risk of further spread of these global multi-antibiotic resistant strains is noteworthy. In addition the high prevalence of MSCRAMMs genes in MRSA isolates demonstrates the high potential of these strains for pathogenicity.According to MLST and SCC"} +{"text": "I542N/Y549H, has become an epidemic in fur-bearing animals in China since 2012. To well understand the genomic and replicated characteristics of the CDV variants, we determined the viral growth kinetics and completed the genome sequences of two CDV strains, namely SDZC(17)M2 and LNDL(17)M4, isolated from CDV-infected minks from Shandong and Liaoning province in China, in 2017. SDZC(17)M2 showed higher viral titers and extensive syncytia in BHK-minkSLAM (BMS) cells than LNDL(17)M4. Although both two strains belong to the Asia-1 genotype and clustered an independent clade in the phylogenetic tree, SDZC(17)M2, harboring I542N/Y549H substitutions in the H protein, shared high identity (99.3\u201399.6% nt) with the other variant strains, whereas LNDL(17)M4, with the only Y549H substitution, shared a lower identity (97.7%\u201397.9% nt) with the other variant strains. Furthermore, a novel R223K substitution was identified in the conserved cleavage site (RRQRR \u2192 RRQKR) of the F protein in the SDZC(17)M2 strain. However, it which did not significantly affect the cell to cell fusion activity when combined with the CDV H/minkSLAM in BHK-21 cells. The key variations in the genome contributed to the virulence and the evolutionary trend need to be determined in the future.Canine distemper (CD), caused by the CDV variant strain with H Morbillivirus within the family Paramyxoviridae. CDV particles are pleomorphic, frequently spherical, with a diameter ranging between 150 nm and 300 nm. Its genome comprises 15,690 nucleotides (nt) and encodes six structural and two non-structural proteins. The genomic RNA, tightly encapsulated by the nucleocapsid protein (N), is used as a template for transcription and replication, forming the ribonucleoprotein (RNP) together with the large protein (L) and phosphoprotein (P) (Canine distemper (CD) is a highly contagious, often fatal, multisystemic disease caused by canine distemper virus (CDV) in a wide range of mammalian hosts, with clinical symptoms including conjunctivitis, anorexia, diarrhea, lymphopenia, and encephalitis . CDV is tein (P) . The RNPtein (P) . The P gtein (P) , 8. The tein (P) , 8. The tein (P) . The 3\u2032-tein (P) . CDV enttein (P) , 13.RR \u2192 RRQKR) of F protein was identified in SDZC(17)M2. To further evaluate whether this substitution affects the interaction between CDV-H/F and mink Signaling Lymphocytic Activation Molecule (SLAM) we have constructed amino acids mutation expression plasmids, and conducted a cell to cell fusion assay. Our results could provide important clues to better understand variations of CDV strains and to further insights into the virus evolution.Since the outbreak in 2012, a number of fur-bearing animals have been infected with CDV variants, particularly with the I542N/Y549H substitutions of the H protein of CDV strains isolated in Shandong province in China, resulting in increased mortality and significant economic loss to the fur-bearing animal industry , 15. HowVeroDogSLAMtag (VDS) cells expressing dog SLAM were cultured in Dulbecco's modified essential medium supplemented with 5% heat-inactivated fetal bovine serum . BHK-minkSLAM (BMS) cells expressing minkSLAM were established by our laboratory and wereKC427278) was isolated using Vero cells from a CDV-infected mink from Hebei in China in the year 2008 and maintained in our laboratory. The SD (14)7 strain (GenBank accession no. KP765763) and SD(14)11 strain (GenBank accession no. KP738610) were isolated using VDS cells from a CDV-infected fox and raccoon dog, respectively from Shandong in China in the year 2014, and maintained in our laboratory , ill minks had been tested positive for CDV antigens. Finally, those minks in these farms had succumbed to CD despite receiving attenuated vaccines. Viral particles from these mink tissues (lung and spleen) were isolated using VeroDogSLAMtag (VDS) cells and identified using an indirect immunofluorescence assay (IFA) . In addiboratory .50 using Reed-Muench method. The assay was repeated 3 times and the mean value was obtained.BMS cells were plated in 6-well plates and infected with SDZC(17)M2, SD(14)7, SD(14)11 LNDL(17)M4, and Hebei strain at a multiplicity of infection (MOI) of 0.1 for 1 hour, and the inocula were replaced with DMEM. The cell-associated progeny virus was harvested daily for 6 days and the number of syncytia was counted under an inverted microscope. Virus titers were determined in VDS cells and expressed as TCIDTotal RNA was extracted from VDS cells infected with CDV SDZC(17)M2 and LNDL(17)M4 using a viral RNA extraction kit . Viral RNA was transcribed to cDNA using the PrimeScriptTMII 1st Strand cDNA Synthesis Kit according to the manufacturer's instructions and the cDNAs were used for amplification of the full-length CDV genome using overlapping primers . PCR ampThe complete genome sequences of SDZC(17)M2 and LNDL(17)M4 were assembled after sequencing. The two isolated CDV strains were aligned by ClustalW along with CDV reference strains from the GenBank database. Phylogenetic trees were constructed with MrBayes version 3.2 using the maximum likelihood method. Each Bayesian tree was run for 5 million generations with a sample frequency of 1,000 generations. Tracer version 1.6 was used to determine whether the runs had reached stationarity and that a 25% burn was appropriate Ronquist. The tree was visualized using FigTree v.1.4.0.To further explore the genetic characterization of SDZC(17)M2 and LNDL(17)M4 strains with seven CDV reference strains from Chinese fur-bearing animals, the complete nucleotide sequences of 5'UTR, 3'UTR, untranslated regions and structural proteins were analyzed. Among these representative CDV isolates, SY/raccoon dog/Jilin/2012/KJ466106, LN (10)1/fox/Liaoning/2010/KP765764, HLJ1-06/fox/Heilongjiang/2006/JX681125, and Hebei/mink/Hebei/2008/KC427278 were typical strains from four provinces, whereas SD(14)7/fox/2014/KP765763, SD(14)11/raccoon dog/2014/KP738610, and SD16F/fox/2016/MH337872 were identified as belonging to CDV H I542N/Y549H variant strains from Shandong province.CpoI, purified, and cloned into the mammalian expression vector pCI , respectively named as pCI-SDZC(17)M2 Fwt and pCI-LNDL(17)M4 Fwt. Next, two single-site mutations of pCI-SDZC(17)M2 Fwt-K223R and pCI-LNDL(17)M4 Fwt-R223K were obtained using the QuikChange site-directed mutagenesis kit with the relevant primers (PCR amplification of SDZC(17)M2 and LNDL(17)M4 F genes were performed using the appropriate primers . The PCR primers . All expTo compare the differences in cell to cell fusion between different strains, a quantitative fusion assay was performed. Briefly, BHK-21 cells plated in 6-well plates were co-transfected with various expression plasmids: 0.5 \u03bcg of pCI-F, 1 \u03bcg pCI-H, and 0.5 \u03bcg pDisplay-minkSLAM using the X-tremeGENE HP DNA Transfection Reagent according to the manufacturer's protocol. At 24 h post-transfection, the syncytia formation were observed using a microscope (10\u00d7).2 for 5 hours. The cells were lysed using the Dual-Luciferase Assay System Lysis buffer for 20 min at 4\u00b0C. To quantify fusion, the relative fusion activity represented by the ratio of firefly luciferase activity to renilla luciferase activity was calculated. The luciferase or renilla activity were measured using a Dual-luciferase reporter Assay System .To confirm the functional importance of CDV F protein, a quantitative fusion assay was performed as described previously , with slP < 0.05, P < 0.01 and P < 0.001 were considered to indicate levels of statistical significance. The data were expressed as the mean \u00b1 S.E.M. from three independent experiments.Statistical analyses were performed using the SPSS 17.0 package and GraphPad Prism\u00ae 5 for Windows\u00ae . Significance was tested using one-way analysis of variance followed by Tukey's multiple comparisons test. No animal and human studies are presented in this manuscript and no potentially identifiable human images or data are shown.P < 0.01), SD(14)7 (P < 0.001), and SD(14)11 (P < 0.01), while the number of syncytia of SDZC(17)M2-infected cells was significantly higher than that of Hebei (P < 0.001) and LNDL(17)M4 (P < 0.01) and Hebei M4, SDZC(17)M2, SD(14)7, and SD(14)11) were performed in BMS cells and the respective single step growth curves were determined. After 48 h post-infection, viruses induced syncytia, while their fusion-inducing capabilities varied . LNDL17. The num < 0.01) . Moreove < 0.01) . The tit < 0.01) . The syn < 0.01) . No sign < 0.01) .MK408454 and MK408453, respectively. Sequence analysis revealed that the SDZC(17)M2 genome shared the highest nucleotide identity (99.6%) with SD(14)7/fox/2014/KP765763 and SD(14)11/raccoon dog/2014/KP738610, and the lowest nucleotide identity (97.4%) with HLJ1-06/fox/Heilongjiang/2006/JX681125. In contrast, the LNDL(17)M4 genome shared the highest identity (99.1%) with SY/raccoon dog/Jilin/2012/KJ466106 and the lowest identity (97.7%) with the SDZC(17)M2 strain (To further explore the molecular characteristics of SDZC(17)M2 and LNDL(17)M4, the genomes of both CDV strains were amplified and sequenced. The complete genome sequences of CDV SDZC(17)M2 and LNDL(17)M4 strains were deposited in the GenBank database of NCBI with the accession number 2 strain . FurtherTo further examine the genomic variations between CDV variant and typical strains, their complete amino acid sequences and genome UTRs were analyzed in detail. A total of 16 amino acid substitutions and 11 nucleotide sites were identified between the translated region and UTR, respectively . These sTo determine the genetic relationship between the SDZC(17)M2 and LNDL(17)M4 strains, the two CDV strains, along with 21 reference strains, were phylogenetically analyzed using the maximum likelihood method in MrBayes version 3.2. Based on the phylogenetic tree generated, 23 whole genome CDV isolates were divided into 6 genotypes: Asia-1, Asia-2, Europe, America-2, America-1, and Arctic . The twoN-glycosylation sites in the H amino acid sequences of LNDL(17)M4. However, SDZC(17)M2 had 10 N-glycosylation sites in its H amino acid sequences, which at position 542NRT, is different from the LNDL(17)M4 and LN(10)1, and Hebei strains isolated from the Liaoning and Hebei province, respectively. The novel N-glycosylation site at position 542-544 was reported in SDZC(17)M2, and was also found in other CDV strains (SD(12)3, SD(13)5, and SD(14)7) (N-glycosylation site in the CDV H protein (manuscript in preparation).The H amino acid sequences of the SDZC(17)M2 or LNDL(17)M4 isolates and other reference isolates were compared and analyzed . The isoN-glycosylation sites in the F protein and found 6 sites in the LNDL(17)M4 and SDZC(17)M2 strains, of which four were conserved in all CDV and in the F region (RRQRR) were highly conserved in all the CDV strains analyzed. However, the cleavage site (RRQKR) of SDZC(17)M2 showed an amino acid difference compared with other CDV stains, including the Asia-2 and vaccines strains. Interestingly, the cleavage site (RRQKR) substitution was also observed in the amino acid sequences of other CDV variant strains . We then all CDV . We alsoP < 0.01, To elucidate whether the R223K substitution of F protein affects the fusion activity, the pCI-SDZC(17)M2 and pCI-LNDL(17)M4 Fwt or their mutation-expressing plasmids were co-transfected with LNDL(17)M4H/minkSLAM or SDZC(17)M2H/minkSLAM in BHK-21 cells. The results showed that the CDV F R223K substitution resulted in cell fusion when combined with LNDL(17)M4H or SDZC(17)M2H . To precin vitro. These strains induced syncytia formation with comparable sizes. Compared with the LNDL(17)M4 strain, the SDZC(17)M2 together with its similar SD(14)11 and SD(14)7 variant strains had higher virus titers and syncytia numbers in BMS cells M2-infected minks displayed higher virulence index with 80% mortality than the LNDL(17)M4-infected minks (Manuscript in preparation). The SDZC(17)M2 variant strain had significant replication and spread capacity on cell lines expressing minkSLAM, whereas the adaptability of viruses in different species expressing SLAM/Nectin4 warrants further investigation.In this study, we have compared the growth characteristics of LNDL(17)M4 and SDZC(17)M2 isolates with their respective similar strains MS cells . These rM. mulatta, and Canis lupus familiaris. Based on the F, H, and the CDV complete genome sequences, our results showed that the SDZC(17)M2 together with similar variant strains were more closely related to each other than to other CDV strains, which was consistent with the findings of Zhao et al. can be found in the article/No animal and human studies are presented in this manuscript. No potentially identifiable human images or data is presented in this study.QL and JZ conceived the study. RT, JC, TZ, CG, HP, RA, XL, SS, QL, and JZ were involved in all other aspects of the study, data collection, data analysis, and drafting and editing the paper. All authors have read and agreed to the published version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "In early 2020, Japan repatriated 566 nationals from China. Universal laboratory testing and 14-day monitoring of returnees detected 12 cases of severe acute respiratory syndrome coronavirus 2 infection; initial screening results were negative for 5. Common outcomes were remaining asymptomatic (n = 4) and pneumonia (n = 6). Overall, screening performed poorly. With the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, several countries, including Japan, repatriated their nationals .We conducted day 1 entry screening by testing oropharyngeal swab samples collected from all 566 returnees at the hospitals to which they were initially transported for SARS-CoV-2 were positive by PCR ; test reFor the 503 asymptomatic/subclinical passengers, entry-screening PCR results were positive for 5 (1.0%) ; 3 remaiAmong the 566 returnees, 12 cases of SARS-CoV-2 infection were detected; 540/541 facility-quarantined persons were confirmed negative by PCR performed on days 1 and 14 . Entry screening detected 7 infections, for an infection point prevalence of 1.2%; infection period prevalence was 2.2% (12/552 returnees with complete follow-up). Despite universal testing, entry screening captured only 7/12 cases (58.3% sensitivity). Although screening symptomatic passengers (3.2%) was more efficient than screening all passengers (1.2%), screening only symptomatic passengers missed 5/7 prevalent infections at entry. Among symptomatic passengers, with 2 initially negative persons subsequently testing positive, entry-screening sensitivity was 2/4 (50%). Among asymptomatic passengers, with 3 initially negative persons subsequently testing positive, entry-screening sensitivity was 5/8 (62.5%).,Testing all returnees\u2014with follow-up for disease onset and course\u2014enabled us to evaluate the spectrum of severity for SARS-CoV-2 infections . From leOur findings have public health implications. As recently reported (,The potentially long incubation period of COVID-19 was consistent with that recently reported (,\u2013,,Testing and follow-up of all returnees provided valuable information about the spectrum of SARS-CoV-2 infection. Most reported data have been from medically attended patients, skewed toward symptomatic patients and more severe cases, limiting our knowledge of the clinical spectrum of infection (When confronted with an emerging pathogen, researchers can generate critical epidemiologic information by studying quarantine populations. As with the First Few X study ("} +{"text": "Post-COVID-19 syndrome (PCS) refers to debilitating physical and neuropsychiatric symptoms for at least \u2265 4 weeks following the recovery from COVID-19 infection. The goal of this study is to identify shared epidemiological and clinical features among patients with PCS to identify possible risk factors that can guide studies in the prevention of PCS.Chart reviews of patients referred to the post-COVID clinic of Northport VA Medical Center, NY between January 2021 to March 2023 were performed. 57 patients with mild COVID-19 infection without requiring hospitalization that met CDC definition of PCS were included. Cases were reviewed and demographics, comorbidities, treatment/vaccine status, common symptoms reported and baseline inflammatory markers were recorded and analyzed.The mean age was 56 years, and most patients were between the ages of 46-60 years old . More male patients reported symptoms of PCS compared to females . Common comorbidities included pre-existing psychiatric diagnoses (47.4%), obesity (40.4%), hypertension (40.4%), hyperlipidemia (43.9%), and chronic lung disease (36.9%), with an average Charlson comorbidity index of 1.9. Most patients (59.6%) reported only being infected with COVID-19 once (table 1). Most patients (75.4%) did not receive outpatient therapy against COVID-19 and most had only two vaccines against COVID-19 . Predominant symptoms included fatigue (56.1%), brain fog (56.1%), dyspnea on exertion/decreased exercise tolerance (42.1%), and cough (24.6%) (table 3). Of those with values measured, baseline ESR, CRP, ferritin values were normal and a small percentage had elevated D-dimer >150 ng/mL D-DU (table 4).Majority had comorbidities such as hypertension, hyperlipidemia, pre-existing mental health conditions and obesity. Most had only 2 doses of a COVID-19 vaccine and did not receive any outpatient treatment for COVID-19. This suggests that these features may serve as potential risk factors for PCS and further study is needed to elucidate the relationship between these attributes and PCS.All Authors: No reported disclosures"} +{"text": "Microbes play an important role in coastal and estuarine waters. We present 93 metagenomes and 677 metagenome-assembled genomes (MAGs) from Comau Fjord, Patagonia (42\u00b0S), to further understand the microbial dynamics and their response to anthropogenic disturbances. These data represent a spatially (35-km transect) and temporally (2016 to 2019) explicit data set. Coastal and estuarine waters not only receive carbon and nutrients from rivers and other freshwater sources but also are a hot spot of disturbances of anthropogenic origin \u20135. Comau\u20136\u2013https://doi.org/10.6084/m9.figshare.21960866.v3).We collected seawater over a period of 3\u2009years at depths of 5 and 20\u2009m, from the mouth to the end of the fjord . The water was prefiltered using a 50-\u03bcm nylon mesh (Sefar) to avoid macroscopic organisms and debris, followed by filtering with 3-\u03bcm polycarbonate filters to collect eukaryotes and particle-attached prokaryotes. Free-living prokaryotes were collected in 0.22-\u03bcm polyethersulfone (PES) Sterivex filters , and DNA from this fraction was obtained using phenol-chloroform extraction with the xanthogenate protocol \u201311. Sequ\u2013De novo metagenome coassembly was carried out on each of the four clusters using MEGAHIT v1.2.9 (\u2013min-contig-len 1500) (\u2013https://doi.org/10.6084/m9.figshare.21960866.v3) (https://github.com/wwood/CoverM).We used default software parameters unless otherwise stated. We removed adapters (\u2013detect_adapter_for_pe) and carried out filtering and trimming (-q 30 -l 100) using fastp 0.20.1 . We firsen 1500) \u201319. The Proteobacteria (49%), Bacteroidota (31%), Actinobacteriota (7%), Cyanobacteria (4%), Verrucomicrobiota (2%), Planctomycetota (1.4%), and Thermoplasmatota (1.2%). Likewise, at the family level, the most abundant MAGs belonged to Flavobacteriaceae (26%), Rhodobacteraceae (20%), Actinomarinaceae (5%), Cyanobiaceae (4%), Thioglobaceae (4%), D2472 (3.7%), Porticoccaceae (3.2%), Methylophilaceae (2.8%), Pseudohongiellaceae (2.3%), Schleiferiaceae (2.2%), Halieaceae (1.8%), HTCC2089 (1.4%), Akkermansiaceae (1.3%), TMED25 (1%), and SAR86 (1%).At the phylum level, the most abundant MAGs belonged to PRJNA729490. The version described in this paper is the first version.This whole-metagenome shotgun project has been deposited at GenBank under the BioProject accession no."} +{"text": "The prevalence of metabolic syndrome is increasing worldwide,and patients with metabolic syndrome have increased risk of developing cardiovascular disease and type 2 diabetes. Although specific criteriavary, the National Cholesterol Education Program Adult Treatment Panel III(NCEP/ATP III) criteria (2002) defined metabolic syndrome as the presence of 3 or more of the following 5 components: waist circumference more than 102 centimeters (cm) for men or more than 88 cm for women; triglycerides 150 milligrams per deciliter (mg per dL) or more; high-density lipoprotein cholesterol (HDL-C) less than 40 mg per dL for men or less than 50 mg perdL for women; blood pressure (BP) 130/85 millimeters mercury (mm Hg) ormore; and fasting blood glucose 110 mg per dL or more.To evaluate the effect of a pharmacist-physician collaborative practice compared with usual care in the management of patients withmetabolic syndrome as defined by the NCEP/ATP III criteria.A prospective, randomized controlled trial conducted in family medicine outpatient clinics in Jordan enrolled 199 patients who met theNCEP/ATP III criteria for metabolic syndrome during an enrollment period from March 15, 2009, through May 10, 2009. Patients were randomized into 2 groups, with 110 in the intervention group (pharmacist-physician collaborative practice) and 89 in usual care (physician only). The patients in the intervention group were provided with pharmacist recommendations and pharmaceutical care counseling. Outcome measures included metabolic syndrome status and changes in mean values for each metabolic syndrome component and for body weight. A contingency table with a Pearson chi-square test was used to assess by group differences in metabolic syndrome status after 6 months of followup.In difference-in-difference analyses, t-tests (Mann-Whitney U tests when appropriate) were used to assess by-group differences in changes in the individual metabolic syndrome components and body weight.From baseline to follow-up, 39.1% (n = 43) of intervention group patients versus 24.7% (n = 22) of usual care patients were successfully shifted from a status of metabolic syndrome to no metabolic syndrome(P = 0.032). Three of 7 outcome measures were improved more in the intervention group compared with the usual care group. Mean (SD) triglyceride(mg per dL) declined by 30.9 (54.4) from 189.3 (79.6) to 158.4 (77.3) inthe intervention group and by 14.5 (50.7) from 202.5 (88.0) to 188.5 (89.0)in the usual care group (P = 0.029). For the intervention and usual caregroups, mean baseline systolic BPs were 134.7 (16.2) mm Hg and 134.6(12.2) mm Hg, respectively, declining after 6 months follow-up by 12.1(20.1) mm Hg in the intervention group versus 6.9 (14.6) mm Hg in the usual care group (P = 0.018). Mean baseline diastolic BPs were 83.6 (10.7)mm Hg and 83.6 (7.9) mm Hg, respectively, declining by 7.2 (12.6) mm Hgin the intervention group versus 4.9 (8.1) mm Hg in the usual care group(P = 0.049).Compared with usual care provided by physicians only, pharmacist involvement in the clinical management of patients with metabolic syndrome increased the proportion of patients who no longer met criteria for the syndrome after 6 months follow-up and improved control of BP and triglycerides."} +{"text": "Children and adults have had different experiences during the COVID-19 pandemic, especially in the context of new SARS-CoV-2 variants and changing vaccine eligibility. We aimed to compare the changing epidemiology of SARS-CoV-2 testing, positivity, and variants in adults versus children over multiple pandemic waves in a multi-hospital health system in New York City.We analyzed SARS-CoV-2 RT-PCR testing data from 10/1/20 to 9/11/22 from children (0-21 years) and adults ( > 21 years) and compared positivity rates during 5 pandemic waves in New York City: Wave 2 (10/1/20-6/30/21), Wave 3 (7/1/21-12/1/21), Wave 4 (12/2/21-3/5/22), Wave 5 (3/6/22-6/12/22), and Wave 6 (6/13/22-9/11/22). The first test per patient per wave was included. If a patient had a positive test, the first positive test was included. Whole genome sequencing was performed on a subset of nasopharyngeal specimens with Ct values < 33 from 12/1/20 to 5/22/22.From 10/1/20 to 9/11/2022, 243,457 adults and 33,298 children were tested for SARS-CoV-2 with 15095 (6.2%) adults and 1961 (5.9%) children testing positive. Distribution of cases, positivity rates, and vaccine coverage over time are presented in Figure 1. Positivity rate was higher in adults compared to children in Wave 2 , similar in Wave 3 , higher in children in Wave 4 and similar in Wave 5 and Wave 6 . In Wave 4, the high positivity rate in children was driven by younger age groups, outpatient testing, and unvaccinated children . WGS of 1996 adult and 381 pediatric SARS-CoV-2 isolates demonstrated a mix of Alpha (13%), Iota (22%), and B lineages (61%) in Wave 2, predominance of Delta (87.4%) in Wave 3, predominance of Omicron (BA.1) (81%) in Wave 4, and predominance of BA.2 (84%) in Wave 5, with no difference in distribution between adults and pediatrics over time .Number of tested and positive cases presented as daily case counts. Positivity rates presented as 14-day rolling averages. Due to low testing numbers, rolling average of pediatric positivity rate was excluded in Waves 5 and 6. Vaccination rates indicate daily proportion of patients with 2 or more vaccines doses.Despite multiple wave-specific differences, SARS-CoV-2 variant distribution did not differ between adults and children over time. Additional work is indicated to understand if the difference in positivity rates is related to differences in immune response or exposure patterns between children and adults.Melissa Cushing, MD, Cerus Corporation: Advisor/Consultant|Haemonetics: Advisor/Consultant|Octapharma: Advisor/Consultant"} +{"text": "International guidelines recommend that prospective organ transplant patients receive a psychosocial assessment to optimise outcomes. There is limited consensus regarding the criteria for psychosocial evaluation. The Stanford Integrated Psychosocial Assessment for Transplantation (SIPAT) tool was developed to enhance the pre-transplant psychosocial workup. The Mater Hospital is the National Centre for heart and lung transplantation in Ireland. The consultation-liaison psychiatry (CLP) service provides screening of pre-transplant candidates using a biopsychosocial assessment, SIPAT and cognitive screening tools. Post-transplant patients are reviewed on a referral basis.To identify the psychosocial needs of heart and lung transplant recipients and CLP service input over a one year period.st and December 31st 2021 was conducted. The following data were recorded: demographics, pre-existing mental illness, SIPAT scores, and referral to the CLP service within six months of transplantation.A review of all heart and lung transplant recipients between January 1excellent candidates, 75% (15/20) were good candidates and 1 (1/20) was minimally acceptable. Pre-existing mental illness was associated with higher total SIPAT scores (p=0.013) and higher scores on the psychological stability subscale (p=0.032). Post-transplant, 50% (14/28) were referred for psychological support and 21.4% (6/28) were referred to the CLP service. A further 10.7% (n=3) were attending CLP prior to transplant. Referrals to CLP occurred (median) 13 days (range 1-275) post-transplant surgery. The reasons for attending CLP were anxiety (5/9), delirium (3/9) and mood (1/9).Twenty-eight individuals received a heart/lung transplant in 2021 . Prior to transplant 50% (14/28) had a pre-existing mental health diagnosis, 7% (2/28) had attended a psychiatrist, and 28.6% (8/28) were on psychotropic medication. SIPAT scores were available for 20 patients. The overall mean SIPAT score was 10.8 (SD 6.1). The subscales were as follows: Patient Readiness, mean 3.2 (SD 1.7); Social Support System, mean 2.1 (SD: 1.8); Psychological Stability & Psychopathology, mean 1.6 (SD 2.7); and Lifestyle & Substance Misuse, mean 3 (SD 1.5). Based on SIPAT scores, 20% (4/20) were SIPAT can be a valuable tool for use in the pre-transplant workup to help identify those that will require intensive psychosocial support post- transplant.None Declared"} +{"text": "Plasma cell-free metagenomic next-generation sequencing (cf-mNGS) offers potential for rapid, noninvasive diagnosis of complex infections, though clinical impact remains incompletely characterized. Here, we describe impacts on diagnosis and antimicrobial management among patients evaluated with plasma cf-mNGS.Patients evaluated with plasma cf-mNGS (Karius\u00ae) in the Mount Sinai Health System from January 1, 2019 to December 23, 2022 were included. Cases were each reviewed independently in the medical record by two investigators using a standardized data collection form with discrepancies adjudicated collectively. Data were analyzed descriptively.Plasma cf-mNGS was sent for 37 patients of whom 29 (78%) were immunocompromised. 26 (70%) had prior invasive diagnostics. Median time from admission to NGS was 15 days. NGS was positive in 24 cases (65%), with results reflecting 20 bacterial infections, 9 viral, and 4 fungal . Results were deemed clinically relevant in 18 cases (49%) including 12 positive and 6 negative tests. Testing led to antimicrobial changes in 11 cases (30%), discontinuation in 3 cases (8%), and no change in 23 cases (62%). After plasma cf-mNGS (compared with prior), fewer patients received 3 or 4 antimicrobials, while more received 0, 1, or 2 antimicrobials ; fewer patients received combined antibiotic/antifungal therapy, while more received no antimicrobials or antifungal therapy alone; there was no change in use of antibiotic therapy alone . Final diagnoses included 15 bacterial infections (41%), 9 fungal (24%), 0 viral, and 7 noninfectious conditions (19%). Final diagnoses were attributed to NGS in 6 cases (16%), other diagnostics in 9 cases (24%), and both NGS and other diagnostics in 6 cases (16%); in the latter group, NGS provided a diagnosis prior to another study in 3 cases by intervals of 13, 19, and 72 days, respectively.A. Changes in number of antimicrobials, B. Changes in classes of antimicrobialsPlasma cf-mNGS, as an adjunct to traditional methods, may provide unique or expedited diagnosis of bacterial or fungal infections, accelerate diagnosis of noninfectious conditions, or inform changes in broad-spectrum antimicrobial regimens. Continued study is warranted to delineate clinical impact and optimal use of plasma cf-mNGS.All Authors: No reported disclosures"} +{"text": "This study aimed to characterize the microbiology and clinical outcomes of SBP in our health system to determine the applicability of these guidelines.2021 SBP treatment guidelines recommend empiric therapy with spectra broader than 3Setting: 5-hospital academic health system with > 1500 beds. Design: retrospective, observational study. Adult pts from 2010-2022 with ICD 9/10 codes for SBP & liver dysfunction were screened. Pts with concomitant secondary peritonitis were excluded. Study included all pts with culture-positive (CX-pos) SBP and randomly screened pts with culture-negative (CX-neg) SBP to provide a total sample of 80 pts. Primary outcome was % of peritoneal fluid CX with organisms non-susceptible to ceftriaxone (CRO) in CX-pos pts. Secondary outcomes included mortality & effect of MDO risk factors on microbiological & clinical outcomes.49 pts with CX-pos and 31 pts with CX-neg SBP were included. Median age was 59; median MELD score was 25; 26 (33%) were admitted to the ICU. 67 of 80 (84%) total pts had \u2265 1 MDO risk factor; 40 of 49 (82%) in the CX-pos cohort. 8 (16%) isolates were CRO-non-susceptible, 7 in the 40 CX-pos pts with MDO risk factors (17.5%) vs. 1 in the 9 CX-pos pts without risk factors (11%) (p=NS). 49 (61%) pts received initial TGC therapy. Mortality at 30 days & 90 days was 29 (43%) & 40 (60%) and 3 (23%) & 6 (46%) for pts with and without MDO risk factors, respectively. Outcomes based on empiric therapy are summarized in Table 1.In our facilities, 16% of isolates in CX-pos SBP pts were not susceptible to CRO. There was no significant difference in the number of non-susceptible isolates in pts with and without MDO risk factors. Treatment with broader therapy was not associated with improved outcomes. Within our health system, giving all SBP pts with MDO risk factors broad empiric therapy may not be necessary. Evaluating local microbiologic data may help health systems assess the local applicability of national treatment guidelines.Tyler J. Stone, PharmD, ViiV Healthcare: Employee"} +{"text": "The use of coronavirus disease 2019 (COVID-19) monoclonal antibody (mAb) treatment in solid organ transplant (SOT) patients have been shown to reduce the rates of hospitalization, Emergency Department (ED) visits, and mortality in previous studies. However, most of these studies provide little or no data in minority patients, specifically Hispanic patients, a group that has been associated with worse outcomes with COVID-19. Our study describes the use of COVID-19 mAbs in the SOT recipients at our institution, where a majority of patients are of Hispanic ethnicity.We performed a retrospective chart review of all adult SOT patients who received COVID-19 mAbs from December 2020 to December 2022.We identified 54 patients who were SOT recipients. The mean age was 46.3 (IQR 33-59), and 30 (55.6%) were male. Of the 54 patients, 34 (63.0%) identified as Hispanic, 17 (31.5%) as White, 2 (3.7%) as Asian, and 1 (1.9%) as Black. There were 23 (42.6%) heart, 22 kidney (40.7%), 6 liver (11.1%), 2 (3.7%) combined kidney and liver, and 1 (1.9%) combined kidney and pancreas recipients. There were four mAbs available during the study period. Of the 54 SOT recipients, 16 (29.6%) received casirivimab/imdevimab, 5 (9.3%) received bamlanivimab, 19 (35.2%) received bebtelovimab, and 14 (25.9%) received sotrovimab. Average time from symptom onset to receipt of infusion was 4 (IQR 1-5) days. The 30-day hospitalization rate due to COVID-19 from time of diagnosis in our cohort was 5.6%. There were 3 (5.6%) patients who visited the ED due to COVID-19 within 30 days of diagnosis and there were no deaths due to COVID-19 within 30 days of diagnosis. When comparing between the Hispanic and non-Hispanic groups in our cohort, the 30-day hospitalization rate due to COVID-19 from time of diagnosis was not statistically significant . There was one patient who had an infusion reaction and 3 patients who developed allograft rejection within 90 days of mAb infusion.In our small cohort of SOT recipients, the majority of which are Hispanic, use of COVID-19 mAbs had low rate of poor outcomes and adverse events. There was no statistically significant difference in hospitalization rate following mAb infusions between the Hispanic and non-Hispanic SOT recipients in our group.All Authors: No reported disclosures"} +{"text": "Lyme disease is the most common vector-borne disease in the U.S. Incidence of Lyme disease is rising, partly due to climate change, and is likely underreported. We evaluated an automated method to analyze Lyme disease trends over two decades in the Veterans Health Administration (VHA).We included individuals receiving VHA outpatient and/or inpatient care during fiscal years (FY) 2000-2022 (10/1/1999 \u2013 9/30/2022). Automated case-finding was performed via ICD 9/10 Lyme Disease code plus a prescription for \u22657 days of appropriate antimicrobial treatment within 30 days of encounter AND/OR confirmatory lab testing (Table 1). Data was extracted from VHA Corporate Data Warehouse. We calculated FY incidence and prevalence per 10,000 individuals in VHA care and analyzed demographic trends. Positive Predictive Value (PPV) of case-finding methodology and clinical characteristics of identified cases was determined by review of 75 randomly selected case records.*Nelson, C.A., et al. Emerging Infectious Diseases. Vol. 21, No. 9, September 2015Automated methodology detected a total of 24,349 Lyme disease cases. Incidence rose steadily, peaking at 3.25 per 10,000 in FY 2017, with prevalence reaching 32.72/10,000 in FY 2022 . States with highest average incidence per 10,000 in care were RI (12.65), ME (10.61), VT (9.81), and WI (8.51). Distribution of Lyme disease incidence expanded nationally, particularly in the Northeast and Northern Midwest. Demographic groups with highest average incidence per 10,000 in care included individuals in rural/highly rural areas (2.41), non-Hispanic Whites (2.26), age groups 55-64, 65-74, and 25-34 , and males (1.95) . Overall PPV of automated case-finding was 85.3%, with ICD 9/10 code + appropriate antimicrobial treatment AND confirmatory lab testing being the most accurate method (PPV 100%) (Table 2).*CSTE case definition = the current surveillance definition used by the Centers for Disease Control and Prevention Lyme Disease (Borrelia burgdorferi) 2022 Case Definition | CDC, based on 2021 Council of State and Territorial Epidemiologists Position Statement 21-ID-05: \u201cModification of Lyme Disease Case Definition\u201d.Automated surveillance methodology for Lyme disease provided an efficient and reasonably accurate estimation of the epidemiology of Lyme disease in VHA. The VHA pattern of Lyme disease geographic expansion in recent years is consistent with CDC national reporting. Providers should be aware of Lyme disease as an emerging threat.All Authors: No reported disclosures"} +{"text": "High grade pleomorphic xanthoastrocytomas (HGPXAs) are very rare and their management and prognostic outcomes remain unclear. To better understand the disease, we aimed to evaluate the risk factors for progression-free survival (PFS) and overall survival (OS), and propose a treatment protocol based on cases from our institute and cases from the literature.The authors reviewed the clinical data of 26 patients with HGPXAs who underwent surgical treatment in Department of Neurosurgery of Beijing Tiantan Hospital between August 2014 and September 2021. We also searched the PubMed database using the keywords \u201canaplastic\u201d combined with \u201cpleomorphic xanthoastrocytoma(s)\u201d between January 1997 and October 2022. Risk factors for PFS and OS were evaluated in the pooled cases.The authors\u2019 cohort included 11 males and 15 females with a mean age of 36.7 \u00b1 20.3 years (range: 5.5-71 years). Gross-total resection (GTR) and non-GTR were achieved in 17 (65.4%) and 9 (34.6%) patients, respectively. Radiotherapy and chemotherapy were administered to 22 and 20 patients, respectively. After a mean follow-up of 20.5 \u00b1 21.2 months (range: 0.5-78.1 months), 7 patients suffered tumor recurrence and 6 patients died with a mean OS time of 19.4 \u00b1 10.8 months (range: 8-36 months). In the literature between January 1997 and October 2022, 56 cases of HGPXAs were identified in 29 males and 27 females with a mean age of 29.6 \u00b1 19.6 years . Among them, 24 (44.4%) patients achieved GTR. Radiotherapy and chemotherapy was administered to 31 (62%) patients and 23 (46%) patients, respectively. After a median follow-up of 31.4 \u00b1 35.3 months (range: 0.75-144 months), the mortality and recurrence rates were 32.5% (13/40) and 70% (28/40), respectively. Multivariate Cox regression model demonstrated that non-GTR , age\u226530 , no RT and no CT were negative prognostic factors for PFS. Non-GTR , secondary HGPXAs , age\u226530 and no RT were risk factors for OS.High grade pleomorphic xanthoastrocytomas are very rare brain tumors. Children and younger adults have better clinical outcome than elderly patients. Secondary HGPXAs had worse OS than primary HGPXAs. Complete surgical excision plus RT and CT is recommended for this entity. The frequency of BRAF mutations in HGPXAs is 47.5% (19/40) in this study, however, we do not find the connections between BRAF mutations and clinical outcomes. Future studies with larger cohorts are necessary to verify our findings. Pleomorphic xanthoastrocytomas (PXAs) are rare brain tumors which often occur in children and young adults \u20133. In 19We performed a retrospective analysis of 26 cases of high grade pleomorphic xanthoastrocytomas (HGPXAs). All the patients accepted surgery in Beijing Tiantan Hospital between August 2014 and September 2021. The following clinical data were included: age, sex, imaging characteristics, extent of tumor resection, histopathological results, treatment protocol and outcomes. Pre- and postoperative MRI images were performed to evaluate the extent of tumor excision, which was defined as gross total resection (GTR) and non-GTR. The follow-up was performed by telephone interview every six months. This research was approved by the Beijing Tiantan Hospital Research Ethics Committee. The pathological diagnosis of HGPXAs was confirmed by the Department of Neuropathology at Beijing Neurosurgical Institute according to the 2021 World Health Organization Classification of Tumors of the Central Nervous System. Histopathological examination showed malignant glial component with numerous mitoses. Eosinophilic granules and ribosome-lamellar complexes can be observed under the light microscope, which are characteristic features of PXA. All cases exhibiting increased mitotic activity, >5/10 HPF mitotic figures with or without accompanying necrosis. The mutation status of BRAF, IDH, and TERT promoter, the methylation status of the MGMT promoter, and the co-deletion status of 1p/19q were also assessed in some of our cases.For the pooled analysis of HGPXAs, we performed a search in the PubMed database between January 1997 and October 2022. The keyword used was \u201canaplastic\u201d combined with \u201cpleomorphic xanthoastrocytoma(s)\u201d and a total of 56 cases were included. All cases were pathologically diagnosed as \u201canaplastic pleomorphic xanthoastrocytoma\u201d, which were classified into WHO grade 3 PXAs.Cox regression models were used to evaluate variables and their association with PFS and OS. The Kaplan-Meier method was used to determine the OS and PFS differences with p-values calculated from the log-rank test. Analyses were performed using SPSS Statistical Package software with the significant set at p < 0.05.The author\u2019s cohort included 11 males and 15 females with an average age of 36.7 \u00b1 20.3 years (range: 5.5-71 years). Preoperative seizure was observed in 8 (30.8%) patients. 22 patients experienced primary HGPXAs, 4 patients suffered malignant transformation of previous PXAs. The lesion locations included temporal lobe (n=13), frontal lobe (n=3), occipital lobe (n=2), parietal lobe (n=2), frontal-parietal lobe (n=2), parietal-occipital (n=1), lateral ventricle (n=1), brainstem (n=1), cerebellopontine angle area (n=1). The morphology was classified as solid (n=16) and cystic-solid (n=10). MRI scans showed that peritumoral edema was significant in 21 (80.8%) patients and enhancement was observed in 25 (96.2%) patients. All patients accepted surgical treatment in our hospital. Gross-total resection (GTR) and non-GTR were achieved in 17 (65.4%) and 9 (34.6%) patients, respectively. Combined radiotherapy and chemotherapy was administered to 19 (73.1%) patients, radiotherapy alone was administered to 3 (11.5%) patients, chemotherapy alone was administered to 1 (3.9%) patient and 3 (11.5%) patients did not undergo any adjuvant therapy. After a median follow-up of 20.5 \u00b1 21.2 months (range: 0.5-78.1 months), 7 patients suffered tumor recurrence and 6 patients died with a mean OS time of 19.4 \u00b1 10.8 months (range: 8-36 months). Immunohistochemistry of this series showed a more or less consistent positivity for GFAP, S100, Olig-2 and CD34 with a significant Ki67 expression (ranged from 3.5% to 60%). In our study, 40% (6/15) of the patients exhibited the BRAF V600E mutation, while none of the available patients (13 patients) had IDH mutations. Additionally, we identified TERT promoter mutation in 3 out of the 13 cases examined. Testing the methylation status of the MGMT promoter in 13 patients revealed that 3 patients had MGMT promoter methylation. Furthermore, we examined the co-deletion status of 1p/19q in 15 patients, and none of them exhibited co-deletion of 1p/19q diagnosed of HGPXAs were included from January 1997 and October 2022. The mean age was 29.6 \u00b1 19.6 years (range: 4-74 years). Preoperative seizure was observed in 20 (38.5%) patients. 45 patients experienced primary HGPXAs, 9 patients suffered malignant transformation of previous PXAs. The lesion locations include temporal lobe (n=27), frontal lobe (n=9), frontal-parietal lobe (n=5), parietal lobe (n=3), parietal-occipital lobe (n=2), cerebellum (n=2), lateral ventricle (n=2), tectal region (n=2), occipital lobe (n=1), occipital-parietal lobe (n=1), posterior fossa (n=1), brainstem (n=1). The morphology was classified as solid (n=19) and cystic-solid (n=16). MRI scans showed that peritumoral edema was significant in 23 (67.6%) patients and enhancement was observed in 32 (97%) patients. GTR and non-GTR were performed in 24 (44.4%) and 30 (55.6%) patients, respectively. Combined radiotherapy and chemotherapy was administered to 19 (38%) patients, radiotherapy alone was administrated to 12 (24%) patients, chemotherapy alone was administrated to 4 (8%) and 15 patients (30%) accepted no adjuvant therapy. 14 patients harbored BRAF V600E mutation and no patients (9 patients were available) harbored IDH mutations. BRAF inhibitors, such as dabrafenib, trametinib, were used for 7 patients who suffered tumor recurrence and showed clinical stability and radiographic improvement. It is worth noting that 10 (20.4%) patients experienced spinal metastasis. After a median follow-up of 31.4 \u00b1 35.3 months (range: 0.75-144 months), the mortality and recurrence rates were 32.5% (13/40) and 70% (28/40), respectively , no CT , age>30 years years predicted a poor PFS. Multivariate cox regression analysis confirmed that non-GTR , age>30 years , no CT and no RT were significantly associated with poorer PFS (Pleomorphic xanthoastrocytoma (PXA) is a rare brain tumor, which was first reported in 1979 , 49. \u2018PXvia analyzing 167 cases and Rodrigues et\u00a0al. reported the median age of grade 2 PXA patients was 21 years via analyzing 346 cases in this study, however, we do not find the connections between BRAF mutations and clinical outcomes. Future studies with larger cohorts are necessary to verify our findings.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The studies involving human participants were reviewed and approved by human research ethics committee of Beijing Tiantan Hospital. The patients/participants provided their written informed consent to participate in this study.Writing, original draft, Conceptualization: PZ; Statistical analysis: TS, WW; Literature review: TL, YW; Follow up: MZ; Methodology, Resources: ZW, JZ; Review, editing, Supervision: LZ. All authors contributed to the article and approved the submitted version."} +{"text": "To know the frequency of modifiable cardiovascular risk factors in knee osteoarthritis patients.Cross sectional study was done at Department of Rheumatology Indus Medical College, Tando Mohammad Khan from March 25, 2022 to November 24, 2022. Total 246 Osteoarthritis of knee cases with (Kellgren-Lawrence grad-II and above) on x-ray, were selected after demographic details, blood pressure, body mass index and physical examination was done, 5ml of venous blood was drawn by phlebotomist, sent for fasting blood sugar, serum lipids analysis and Framingham 10years risk score was calculated afterward for each participant.In this study males (126) and females (120). Overall (78%) had risk factors, Patients having one CVD risk factor were (22.8%), two risk factors in (21.1%), three in (21.5%), four (9.8%) and five factors in (1.6%) while frequency of modifiable cardiovascular risk shows obesity (45.5%) hypertension (40.2%) intermediate to high risk of framingham score (40%) diabetes mellitus (25%), smoking (17%), high low density lipoproteins (8.1%). In males obesity(54.2%), hypertension (47.5% ) and (45.8%) were on medication, diabetes mellitus(31.7%), smoker(31%), high risk FRS(39.2%), K-L grade-IV(58.4%) and in females: obesity (42%), hypertension (43.7%) and (40.5%) were on medication, diabetes mellitus in (19%), smoking (4%), high risk FRS (13.5%), K-L Grade-4 (42%), significant association of diabetes mellitus, smoking, FRS and K-L grades with gender (p<0.05).In OA knee there is high prevalence of modifiable cardiovascular risk factors and together these imposes a major health risk for future cardiac events and disability. Worldwide prevalence is around 3.5%, occurs in old age and its increasing in developed and developing countries, very important public health problem.2Osteoarthritis (OA) is one of the most prevalent joint problems, affects weight bearing joints of body. It is the 6The prevalence ranges from 12.3% to 21.6% in France and USA ,more in women than men, common in developed than developing countries.4Australian national health survey 2017-2018) shows risk of cardio-vascular deaths is increased in (inflammatory and degenerative joint diseases), 1.5-2.0 fold rise in RA, 1.3 fold in systemic connective tissue disorders, 1.5 gout and twofold in OA, and these patients are at increased risk of having obesity, diabetes, hypertension, dyslipidemia specially in younger age.-2018 sho9Osteoarthritis could be potential major risk factor for cardiovascular problems, secondary to difficulty in walking and exercise ability; risks can be reduced with regular walk/exercise and proper management of osteoarthritis and vice versa. Our objective was to know the frequency of modifiable cardiovascular risk factors in knee osteoarthritis patients.th 2022.This cross sectional study was performed at Department of Rheumatology Indus Medical College from March 25, 2022 to November 24To know the frequency of modifiable cardiovascular risk factors in knee osteoarthritis patients. All those patients who had history of pain in both knee joints and fulfilling American college of rheumatology criteria osteoarthritis criteria and K-L Grade-2 and above were enrolled, autoimmune diseases, and those who had history of surgery to their knee joint due to any cause in last one year and currently using lipid lowering medicines were excluded.The study was approved by the Ethics Committee of the Hospital wih Ref.(IRB No: IRB/51/2022) Tando Mohammad Khan. Written and informed consents were taken from each participant.Demographic data like age, disease duration, smoking habits, history of blood pressure and diabetes mellitus with medications in use were asked , waist circumference, height and weight were noted for body mass index, blood pressure was measured after five minutes rest with best of two reading was noted, Radiologist did X-rays reporting on basis of Kellgreen-lawrence Grading : Grade-1: doubtful narrowing of joint space and possible osteophytes, Grade-2: definite osteophytes, definite narrowing of joint space, Grade-3: moderate multiple osteophytes, and definite narrowing of joints space, some sclerosis and possible deformity of bone contour, Grade-4: large osteophytes, marked narrowing of joint space, severe sclerosis and definite bony deformity of. Participants were instructed to come on next morning with 14 hours fasting state, 5 ml of blood was taken, samples were sent to laboratory for fasting blood sugar and if someone has level of >126mg/dl test was repeated on second day), Lipid analysis. Each individual\u2019s 10 years FRS risk was calculated, and categorized into<10%score=low,11-20% =intermediate. >20%= high.IBM-SPSS version 23.0 was used, Mean with standard deviation were reported on age (years), BMI, SBP, DBP, Cholesterol, TG, HDL, LDL (F), FRS and disease duration. Means of these variables were compared with respect to gender using independent sample t-test. Counts with percentages were reported on BMI level, hypertension, diabetes mellitus, smoking, FRS and K-L grades. Association of these variables with gender was tested using Pearson Chi Square test.Out of 246 patients, in 120 males,the mean of studied variables: age 51.9 (SD=\u00b18.4) years, BMI 29.5 (SD=\u00b14.8) kg/m2, SBP 128.6mmhg (SD=\u00b115.2), DBP 84.3mmhg (SD=\u00b19.9), Cholesterol 195 mg/dl (SD=\u00b140.2) ,TG 210.8 mg/dl (SD=\u00b191.9),HDL 45.4mg/dl (SD=\u00b16.6), LDL (F) 105.3mg/dl(SD=\u00b140.5),FRS 16.2 (SD=\u00b110.6) and disease duration 6.1 (SD=\u00b14.2) years. Females (126), mean age 49.7 (SD=\u00b18.6) years, BMI 28.8 (SD=\u00b15.2) kg/m2,SBP 126.8 (SD=\u00b113.4), DBP 82.9 (SD=\u00b18.9) , Cholesterol 181.8 (SD=\u00b133.9), TG 201.7 (SD=\u00b184),HDL 45.1 (SD=\u00b17.1), LDL (F) 96.4 (SD=\u00b134.1), FRS 8.2 (SD=\u00b18.4) and disease duration 5.0 (SD=\u00b14.2) years with significant mean differences for Age, cholesterol, and FRS scores to gender (p<0.05) .obesity (54.2%),hypertension (47.5%) and(45.8%) were on medication, diabetes mellitus(31.7%), smoker(31%), high risk FRS(39.2%), K-L Grade-4 (58.4%).In females: obesity (42%), hypertension (43.7%) and (40.5%) were on medication, diabetes mellitus(19%), smoker (4%), high risk FRS (13.5%), K-L Grade-4 (42%), significant association of Diabetes mellitus, smoking, FRS and K-L grades with gender (p<0.05).obesity (45.5%), hypertension (40.2%), intermediate to high risk of FRS (40%),diabetes mellitus (25%), smoking (17%), high LDL (8.1%). Bar chart-1. Out of 246 patients 189 (76.8%) samples were found with modifiable CVD risk factors. One CVD risk factor in (22.8%), two (21.1%), three (21.5%), four (9.8%) and five factors (1.6%). Pie chart-1On association of FRS and K-L Grade-4 (34%) were low risk FRS, 60% with intermediate risk FRS and 81.3% with high risk FRS, a significant association of FRS and K-L grades (p<0.05) The mechanisms between OA and increased cardiovascular events are not fully understandable; many factors play their role, first interplay between OA and most of cardiovascular risk factors, second commonly used medicines are non-steroidal anti-inflammatory drugs which enhance the risk, third physical inactivity due to severe pain and lastly, the hall mark features of CVD , leads to ischemia and impairs bone and cartilage nutrition causing several bone infarcts, a feature of advance OA.11This study shows higher prevalence of hypertension (45.5%), diabetes mellitus (25.5%) and high framingham risk score in comparison to western world with less mean age 49-51 years. A Systematic review and meta-analysis study revealed that OA was related to a 31% increased risk of myocardial infarction.14In our cohort Obesity (45%) was also more prevalent than other risk factors, which makes someone more vulnerable to OA and future cardiovascular events. Amsterdam Osteoarthritis cohort showed knee or hip OA patient had more activity limitations in association with CVD and its risk factors and poorly performed on get up-go and stair-climb test.19In Korean nationwide health survey, OA patients had more hypertension, diabetes mellitus, lipid problems, angina and myocardial infarction than healthy population.21Kluzek et al. reported that OA was not only associated with increased risk of cardiovascular disease, but increased the risk of all-cause and cardiovascular mortality.This is the first study which has extensively focused on modifiable CVD risk factors in local setup with Knee OA, although sample size is small and results are not true representation of entire population, but helps in understanding the implicit role of these two disorders with each other.In chronic bone and joint diseases like OA knee there is very high chances of having cardiovascular events due to hidden risk factors, commonly prescribed medicines and physical inactivity due to disease itself. As such it will be highly helpful to investigate and treat them accordingly and encourage patients to adopt healthy life style and daily exercise within their limitations is highly helpful.AAW: Design, drafting, data acquisition data analysis, data interpretation, accuracy, final approval. He is also responsible for the integrity and accuracy of the study.PS AQ AA: Data analysis and interpretation, Critical Review and final approval of the manuscript."} +{"text": "Cardiomyopathies are a clinically heterogeneous group of cardiac diseases characterized by heart muscle damage, resulting in myocardium disorders, diminished cardiac function, heart failure, and even sudden cardiac death. The molecular mechanisms underlying the damage to cardiomyocytes remain unclear. Emerging studies have demonstrated that ferroptosis, an iron-dependent non-apoptotic regulated form of cell death characterized by iron dyshomeostasis and lipid peroxidation, contributes to the development of ischemic cardiomyopathy, diabetic cardiomyopathy, doxorubicin-induced cardiomyopathy, and septic cardiomyopathy. Numerous compounds have exerted potential therapeutic effects on cardiomyopathies by inhibiting ferroptosis. In this review, we summarize the core mechanism by which ferroptosis leads to the development of these cardiomyopathies. We emphasize the emerging types of therapeutic compounds that can inhibit ferroptosis and delineate their beneficial effects in treating cardiomyopathies. This review suggests that inhibiting ferroptosis pharmacologically may be a potential therapeutic strategy for cardiomyopathy treatment. Cardiomyopathies are a clinically heterogeneous group of cardiac diseases characterized by heart muscle damage, causing cardiac muscle or myocardium disorders, diminished cardiac function, heart failure, and even sudden cardiac death . Cardiomin vivo. Thereafter, several studies have revealed that ferroptosis plays a vital role in the pathogenesis of cardiomyopathy mechanism, has been rapidly acquiring attention in cardiomyopathies. Novel studies have explored the role of ferroptosis in DICM and ICM in murine models of cardiomyopathy , which dmyopathy . MeanwhiIn this review, we summarize the core mechanism by which ferroptosis leads to the genesis of cardiomyopathies. We focus on the emerging variety of therapeutic compounds that can inhibit ferroptosis and delineate their beneficial effects for treating cardiomyopathies. This review indicates that inhibiting ferroptosis pharmacologically may be a promising therapeutic strategy for treating cardiomyopathies.pLs to generate PUFA-PLs, which includes AA-phosphatidylethanolamine or AdA-phosphatidylethanolamine . Other m-PL-OOH) . LPO and-PL-OOH) . FerroptIschemic cardiomyopathy (ICM) principally results from long-term ischemia/hypoxia within coronary atherosclerosis; it impairs the systolic or diastolic function of the heart. ICM represents the leading cause of heart failure (HF) worldwide . Furthera major contributor to the global disease burden and constitutes the leading cause of global mortality worldwide. Acute myocardial infarction (AMI) resulting from reduced oxygen supply causes initial damage to the cardiac tissues, thus making it the primary cause of disability and mortality. Myocardial reperfusion strategies and reoxygenation are effective and the preferred treatment for AMI; non-etheless, reperfusion inevitably triggers the cell death of cardiomyocytes, increases the infarct size, and worsens the condition, which is referred to as myocardial ischemia-reperfusion injury (MIRI) . MIRI lein vivo correlation between ferroptosis and cardiac cell death (A novel study reported on the role of ferroptosis in ischemia/reperfusion (I/R)-induced cardiomyopathy in murine models , which ell death . Thereafll death . Numerou2+, and MDA levels, along with decreased levels of GPX4 receptor (TfR1), and divalent metal transporter (DMT1) .Iron enters the cardiomyocytes principally through TfR1 as TF or through LTCC as non-TF-bound iron, TTCC, and DMT1. During MIRI, the intracellular iron-storing protein, the degraded ferritin to release iron and perform iron-mediated Fenton reaction, resulting in oxidative damage to cardiomyocytes and loss of cardiac function. Studies have demonstrated excessive iron accumulation in the myocardial scar in mice MIRI models , therebyNuclear receptor coactivator 4 (NCOA4)-mediated autophagy, i.e., ferritinophagy, causes I/R-induced ferroptosis. The activation of ferritinophagy degrades ferritin and increases the availability of iron in the cells . FTH1 biDeferoxamine therapy decreases myocardial injury by inhibiting ferroptosis in I/R-induced rat hearts. The specific redox reactions of PUFA-PLs in ischemia-induced cardiomyocytes initiate oxidative damage in the reperfusion phase. ALOX15 induction by ischemia/hypoxia initiates the oxidation of PUFA-PLs (particularly PUFA-PE) and results in cardiomyocyte ferroptosis. Further, ALOX15 ablation in mice confers resistance to PUFA-dependent ischemia-induced cardiac injury . The ove2+, and MDA, along with decreased GPX4 levels, are observed in the myocardium after MIRI prevents DM-evoked and oxidative stress. Ferroptosis inhibitors preserve the cardiomyocyte function and inhibit LPO induced by the high glucose/high fat (HGHF) challenge roptosis . FUN14 droptosis . Furtherroptosis . In summAnthracyclines are the most widely used anticancer chemotherapeutic agents. However, doxorubicin (DOX) causes cardiotoxicity, resulting in DICM, thereby limiting its clinical efficacy . FerroptSepsis is a life-threatening organ dysfunction resulting from dysregulated immune response to an infection. Seventy percent of patients with sepsis develop septic cardiomyopathy (SCM), which is the leading cause of sepsis-related morbidity and mortality . FerroptSpecific regulators play a role in modulating ferroptosis and SCM. The transmembrane protein 43 (TMEM43), a transmembrane protein related to cardiomyopathy, protects against SCM by inhibiting ferroptosis in LPS-induced mice . The knoin vitro or in vivo. We try to sort these ferroptosis-inhibiting small molecules by mode of action. These categories maybe include activator of system Xc\u2212, ferroptosis-inhibiting Nrf2 activators, GPX4 activator (direct or indirect), ferroptosis inhibitors through combined mechanisms, or ferroptosis inhibitors through unknown mechanisms. However, it is hard to clearly classify the ferroptosis-inhibiting small molecules into a specific categories.Ferroptosis was first described in 2012; the studies on its role in cardiomyopathy are still in their infancy. However, existing evidence suggests a strong correlation between ferroptosis and cardiomyopathy. Thus, the inhibition of ferroptosis may be a promising target for treating cardiomyopathy. Ferroptosis reportedly plays a pathogenic role in cardiomyopathy; thus, scientists have begun identifying a targeted antiferroptosis approach for cardiomyopathy treatment. Numerous drugs have been recognized to exert a therapeutic impact on cardiomyopathy treatment by inhibiting ferroptosis. Several experimental compounds and clinical drugs inhibit ferroptosis to achieve therapeutic purposes in cardiomyopathies. The pharmacological inhibition of ferroptosis is becoming a cardioprotective strategy for cardiomyopathy prevention (1) ((2) ((3) ((4) ((5) ((6) ((7) ((8) ((9) ((10) ((12) ((13) ((14) ((15) ((16) (Icariin (1) , xanthoh(1) ((2) , britani2) ((3) , etomida) ((4) ,GAA(5) (4) ((5) ,dexmedet(5) ((6) , sulfora(6) ((7) , naringe(7) ((8) , C3G (9)(8) ((9) , resvera) ((10) ,5-aza-CdCdR (11) , ferulic1) ((12) , PDA NPs2) ((13) , atorvas) ((14) , baicali ((15) , and pon ((16) alleviat ((16) .(1), a natural flavonoid compound, is the main component of the Chinese herb Epimedium that has the functions of anti-aging, anti-inflammation, antioxidation, anti-osteoporosis, and ameliorating fibrosis (1 is a potent inducer of Nrf2 (1 inhibit hypoxia/reoxygenation (H/R)-induced ferroptosis by increasing GPX4 and decreasing ACSL4 and content of Fe2+ in cardiomyocytes through activating the Nrf2/HO-1 signaling pathway and icaritin (ICT) have garnered great interest in drug development. 1 possesses a variety of beneficial effects in regulating cardiovascular inflammation and other biological activities. In China, YinYangHuo and its compound have been used in the treatment of numerous diseases, like AD, stroke, and depression. ICA and its metabolites, which contain flavonoids, polysaccharides, vitamin C, and other active compounds, have been proven to have cardio-cerebrovascular protective benefits to ICA can result in a vast increase in its water solubility, consequently achieving considerably better bioavailability (in vivo promotes ICA absorption (Icariin fibrosis .1 is a p of Nrf2 . 1 inhib pathway . Owing tbenefits . 1 can wlability . The degsorption .(2) is a principal prenylated chalcone isolated from hops with its anti-inflammatory, anti-oxidative, and cancer-preventive properties is a potent inducer of Nrf2 is an ultrashort-acting, non-barbiturate hypnotic intravenous anesthetic agent. 4 mitigated IR-induced ICM through inhibiting ferroptosis by upregulating GPX4 expression, and decreasing the levels of MDA and iron and ACSL4. Nrf2 inhibitors ML385 eliminated the inhibition of 4 on ferroptosis induced by IR, suggesting that 4 attenuated the myocardial injury by inhibiting IR-induced ferroptosis via Nrf2(5), a natural product taken from the seeds of cotton plants, attenuates ICM through inhibiting ferroptosis by chelating iron content, and downregulating mRNA levels of Ptgs2 in RSL3, and Fe-SP-induced H9c2, inhibiting LPO in oxygen-glucose deprivation/reperfusion (OGD/R)-induced H9c2.5 attenuates IR-induced ICM through inhibiting ferroptosis by decreasing the production of LPO, increasing the Nrf2 and GPX4 protein, while decreasing the mRNA levels of Ptgs2 and Acsl4, and the protein levels of ACSL4 ((6), a highly selective alpha2-adrenoceptor agonist with sedative, analgesic, sympatholytic, and hemodynamic-stabilizing properties, posess the protective effect against I/R (6 attenuates ICM through inhibiting ferroptosis by activating AMPK/GSK-3\u03b2-dependant Nrf2/SLC7A11/GPX4 (Xanthohumol operties .2 protecof ACSL4 . The poolization . Britanir of Nrf2. 3 exerting GPX4 . Etomida via Nrf2. Gossypoof ACSL4 . Dexmedeinst I/R and H/R inst I/R induced A11/GPX4 .(7) is a naturally occurring dietary phytochemical extracted from cruciferous vegetables ameliorates myocardial injury and cardiac dysfunction ((10) ((11) ((12) (13) cyanins) , resveras) ((10) , 5-aza-C0) ((11) , ferulic1) ((12) , and pol12) (13) alleviat13 ((14) ((15)[76], and baicalin (16) is a potent, orally available inhibitor of hepatic 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, the major rate-limiting enzyme in cholesterol synthesis.14 reversed erastin or H/R-induced cell injury in H9C2 cells through inhibiting ferroptosis by decreasing Fe2+ via upregulating expression of FPN1 and hypertrophic cardiomyopathy were completed ongoing. However, there is no clinical trials to study the effect of 14 on ICM, remaining an open conundrum for future investigate on.15, an iron chelators can block ferroptosis. The combination of ponatinib with 15 exerted synergistic effect on reducing H/R injury, showing simultaneous suppression of ferroptosis[76].13 ,atorvast13 ((14) ,ponatinilin (16) are claslin (16) .13 functse model . Atorvasn of FPN1. 14 incrC2 cells .14 protechanisms . Two cli(17) ((18) ((19) ((20) ((7) ((21) alleviates DCM through inhibiting ferroptosis in prediabetic rats ((21) alleviates DCM through inhibiting ferroptosis through by down-regulating ferritinophagy ((7) also works as an activators of System Xc\u2212 to alleviates DCM(6- Gingerol (17) , curcumi7) ((18) , canagli8) ((19) , L6H21 (9) ((20) , sulfora20) ((7) , and SR97) ((21) attenuat7) ((21) . The maje effect . 17 allerf2/GPX4 . 18, a ny injury .18 allevtment DCM. 19 is abenefits . 19 alleeostasis . Myeloidtic rats . As a Reinophagy . Sulforaiates DCM.(22) ((23) ((24) ((25) ((10) ((26) ((27) ((28) ((29) ((30) ((31) , a naturally occurring polyphenol that is frequently present in a variety of fruits and vegetables, exert cardioprotective effect against cardiomyopathy , a glucoside of the phenylpropanoid tyrosol isolated from Rhodiola rosea L, is a natural bioactive compound with anti-oxidative, anti-inflammatory, and neuroprotective properties ((27) ((28) , LCZ696 2) ((23) , fisetin3) ((24) , salidro4) ((25) , resvera5) ((10) , dexazox0) ((26) , melaton6) ((27) , EGCG(287) ((28) , 16d and8) ((29) , ethoxyq9) ((30) , and 7j 0) ((31) inhibit 0) ((31) . 22 is aactivity .22 atten of GPX4 . 23 is aroptosis . 23 sign pathway . Fisetinmyopathy .24 atten pathway . 24 incrtivation . Salidrooperties . 25 has myopathy . 25 atteting LPO . AMPK inpathways . Dexazoxys ((26) , melaton6) ((27) , and EGC7) ((28) also wor(29) ((30) ((10) is a new class of ferroptosis inhibitors, maintaining high ferroptosis inhibitory activity (EC50 = 0.001\u00a0\u00b5M on the erastin-induced HT1080 cell ferroptosis model) , ethoxyq9) ((30) , and res0) ((10) functionotential . Ethoxyqeroxides . 30 amelacrolein . 10 workroptosis . The 2-vs model) . 31 actereat DICM.(32) ((33) ((34) (2S (NaHS) (35) ((6) ((10) can suppress LPS-induced oxidative stress and LPO that lead to ferroptosis in vivo and in vitro through activating Nrf2. 32 can regulate the expression of iron regulatory proteins, maintaining intracellular iron homeostasis ((33), a ferroptosis inhibitor, improves SCM through inhibiting ferroptosis and ferritin heavy chain (FTH1), while upregulating GPX4 and ferroportin ((34) is an isoflavone compound derived from Pueraria lobata in traditional Chinese medicine with cardiovascular benefits against cardiomyopathy , ferrost2) ((33) , puerari3) ((34) , H2S (NaHS) (35) , dexmede35) ((6) , resvera6) ((10) , and att6) ((10) .10 allevroptosis . This obprove SCM. Vitamineostasis . Ferrostroptosis .33 allevSLC40A1) . Compounmyopathy . 34 inhi content .The pathophysiology of cardiomyopathies is complex and still undergoing extensive investigation. In this review, we appraised articles that emphasized research progress in the pathological roles of ferroptosis in ICM, DCM, DICM, and SCM and ferroptosis inhibitors to mitigate cardiomyopathies. Meanwhile, researchers have identified novel targeted treatments for these cardiomyopathies through the pharmacological inhibition of ferroptosis. The pharmacological inhibition of ferroptosis is a potential therapeutic target for these cardiomyopathies, with potential novel drug targets and strategies for these diseases. However, the current research on the role of ferroptosis in cardiomyopathies is still in the infancy, and is still poorly understood. And more studies are required to clarify its role and functional mechanisms. Furthermore, most data reported in the literature are derived from experimental studies that do not directly report clinical applications and implications. Although a phase III clinical trial is underway to determine if resveratrol exert the potential heart benefits of resveratrol in patients with non-ischemic cardiomyopathy . In addition, a multi-center, randomized, placebo-controlled phase II clinical trial is also being conducted to investigate the LCZ696 in adult patients with non-obstructive hypertrophic cardiomyopathy (nHCM) . However, there is still lacking the study directly targeting ferroptosis to treat ICM, DCM, DICM, and SCM using bioactive compounds. Therefore, more clinical studies need to be conducted to inform practical treatment and management strategies. Despite these considerations, the current evidence strongly indicates that inhibiting ferroptosis marks a significant new direction for treating cardiomyopathies."} +{"text": "Accurate diagnosis of fungal infection is a challenge & mortality remains high(2) as expertise and dedicated mycology services are lacking globally. Our centre provides one of the UK\u2019s first complex fungal infection clinics, established in 2019. We sought to describe the patients attending this clinic, as a step towards understanding the landscape of clinical mycology in the UK.The WHO recently set out priority fungal pathogens of global importance which were previously neglected in terms of awareness & funding(3)Electronic health record systems were searched for all patients attending our clinic over 4 years from 01/04/19-01/04/23. Patients referred for consideration of a fungal diagnosis were included in the analysis. Invasive fungal infections (IFIs) were classified as per EORTC/MSGERC guidance.Aspergillus, 8 by Cryptococcus & 2 each by Coccidiodes, Candida & Histoplasma. The IFIs mainly affected the upper & lower respiratory tract (17/28). 20/80 (25%) were immunosuppressed . On average (median), patients visited clinic 4 times (IQR 2-7) & received 2 different antifungal drugs (IQR 1-3). The most common side-effects prompting a change in therapy were visual changes, rash & diarrhoea.80/407 patients attending our clinic were referred for consideration of a fungal diagnosis. 31 (39%) were male. Median age was 53 (IQR 38-62). Most referrals were received from within our institution. 41 (51%) had a fungal diagnosis confirmed prior to review. 28 were treated for invasive fungal infections (IFIs), 9 for chronic mycoses (including 5 chronic pulmonary aspergillosis & 2 mycetoma), 28 for superficial mycoses (20 recurrent mucocutaneous infections & 8 onychomycoses) & 15 had no evidence of fungal infection. Of the IFI: 16 were proven; 8 probable; 2 possible IFI & 2 did not meet diagnostic criteria. 7 IFI were caused by (4) Establishing centralised complex fungal infection clinics helps to build diagnostic & clinical capacity in mycology.Our data illustrate the need for dedicated follow-up for patients with complex fungal infections. With several new antifungal drugs currently undergoing clinical trials, complexity in therapeutic decision-making will only increase.Hamish Houston, BA MBBCh, Gilead Sciences: Grant/Research Support Neil RH Stone, MD PhD, Gilead: Advisor/Consultant|Gilead: Grant/Research Support|Gilead: Honoraria|Pfizer: Honoraria|Shionogi: Honoraria"} +{"text": "Serum samples from HCWs were tested for TAbs using the Elecsys Anti-SARS-CoV-2 S reagent, while NAbs against wild type SARS-CoV-2 and Omicron variant in non-infected HCWs were measured using the blocking ELISA cPass SARS-CoV-2 neutralization antibody detection kit.We prospectively measured total (TAbs) and neutralizing (NAbs) antibodies against the receptor binding domain of SARS-CoV-2 spike protein in healthcare workers (HCWs) 4 and 8 months after the 2nd dose breakthrough infection happened in 8/486 (1.6%) [median time 3 (IQR:0.75) months] and 11/486 (2.3%) [median time 6 (IQR:6)], respectively. One and 8 months after the 3rd dose breakthrough infection happened in 35/486 (7.2%) [median time 1 (IQR:0) month] and 188/486 (38.7%) [median time 4 (IQR:2) months], respectively. No significant differences in vaccinated HCWs 1 month after the 3rd dose were detected among those who got infected or did not have a breakthrough infection during the next 7 month regarding TAbs and NAbs , respectively. After infection, HCWs had significantly increased TAbs levels in all time points compared to non-infected vaccinated HCWs (Table 1). In non-infected HCWs, a negative association of TAbs and NAbs levels with age was detected after the 2nd and 3rd vaccine dose (p< 0.05). No association was found in 8 months after the 3rd dose between antibody levels and demographic and clinical parameters.A cohort of 486 vaccinated HCWs with BNT162b2 vaccine with median age (IQR): 49 years (38-56) and 377 (77.6%) females were included in the study. A significant increase in breakthrough infections were observed over time. Specifically, 4 and 8 months after the 2Median values of total antibodies and neutralizing antibodies SARS-CoV-2 spike antibodies after 4 months and 8 months from the 2nd dose, 1 month and 8 months from the 3rd dose of BNT162b2 vaccine. Values refer to median \u00b1 interquartile range, P-value1 of Mann-Whitney U test or Kruskall-Wallis H test, P-value2 of two-way analysis of variance (ANOVA). Statistically significant values are marked in bold.Findings of the present study indicate that levels of TAbs and NAbs after 3 doses of the BNT162b2 vaccine are not directly associated with the possibility of a breakthrough infection.All Authors: No reported disclosures"} +{"text": "In the current era novel immunosuppressive therapies and improved health status of immunocompromised patients (ICPs), international travel has become more accessible for this group, putting them at risk of travel-related infections. As hepatitis A (hepA) is a common vaccine-preventable disease in travellers, guidelines recommend immunization of all travellers to endemic areas. HepA vaccination is highly immunogenic in healthy individuals, however there is uncertainty about the immunogenicity in ICPs.Figure 1). The primary outcome measure was the seroconversion rate 2 months after the last hepA vaccination, defined as the proportion of vaccinated participants with an antibody level \u2265 20 mIU/mL.This prospective cohort study assessed the immunogenicity of hepA vaccination among patients living with HIV (PLWH), patients on immunosuppressive monotherapy, patients on immunosuppressive combination therapy, and controls not on immunosuppressive therapy. Participants received two hepA vaccine doses at months 0 and 6-12, or three combined vaccine hepA/B doses at months 0, 1 and 6-12. Quantitative antibody responses were measured at the first and last vaccination, 2 months after the first, and 2 and 6 months after the last vaccination (Table 1). Among PLWH, patients on monotherapy, combination therapy and controls, respectively 18/32 (56%), 19/35 (54%), 11/32 (34%) and 23/25 (92%) subjects seroconverted after the first hepA vaccination and 25/26 (96%), 31/32 (97%), 23/28 (82%), 21/21 (100%) after the last hepA vaccination. Six months after the last hepA vaccination seroconversion rates were 26/26 (100%), 26/30 (87%), 21/30 (70%), 21/22 (96%), respectively .We included 129 participants (Impaired immune responses were observed in PLWH and patients on immunosuppressive therapy after a single hepA vaccine dose, and in patients on immunosuppressive therapy 2-6 months after the last hepA vaccine dose. The implication of this finding is that serological testing in these ICPs is required before travel to endemic areas, to assess seroprotection. However, serological testing may not be necessary in virologically suppressed PLWH on cART who completed a full 2 dose hepA vaccination series.All Authors: No reported disclosures"} +{"text": "Fagopyrum tataricum Gaertn.) is an important pseudocereal crop with excellent edible, nutritional and medicinal values. However, the yield of Tartary buckwheat (TB) is very low due to old-fashioned cultivation techniques, particularly unreasonable application of nitrogen fertilizer. To improve the understanding on the theories of nitrogen use in TB, the effects of nitrogen application on growth, as well as chemical properties and microbial community of rhizosphere soil were investigated in this study. Nitrogen application could promote the plant height, stem diameter, nitrogen accumulation and yield of TB. The relative abundance and diversity of bacteria and fungi in the rhizosphere soil of TB were improved by nitrogen fertilizer. Nitrogen application increased the abundance of beneficial bacteria such as Lysobacter and Sphingomonas in rhizosphere soil, and decreased the abundance of pathogenic fungi such as Fusarium and Plectosphaerella. The results indicated that nitrogen application changed the distribution of microbial communities in TB rhizosphere soil. Furthermore, the specific enriched or depleted microorganisms in the rhizosphere soil of four TB varieties were analyzed at OTU level. 87 specific nitrogen-responsive genes with sequence variation were identified in four varieties by integrating genomic re-sequencing and transcriptome analysis, and these genes may involve in the recruitment of specific rhizosphere microorganisms in different TB varieties. This study provided new insights into the effects of nitrogen application on TB growth and rhizosphere microbial community, and improved the understanding on the mechanisms of TB root\u2013microbe interactions.Tartary buckwheat ( Fagopyrum tataricum Gaertn.) is a dicotyledonous plant belonging to the Polygonaceae family and Fagopyrum genus, which is one of the main cultivated varieties of buckwheat (Fagopyrum spp.) . Tartaryum spp.) . TB is aum spp.) . Howevert demand . The lowOryza sativa L.), wheat (Triticum aestivum L.), sorghum (Sorghum bicolor L.) and other crops (Sesamum indicum L.) . In addiicum L.) . Thus, dindica and japonica rice recruit distinct root microbiota, which is depending on the variation of a rice nitrate transporter gene (NRT1.1B) by integrating plant metagenomic sequencing and 16S ribosomal RNA gene analysis. Another study showed that rice histone methylation plays a key role in regulating the assembly of root microbiota . In addition, association studies of GWAS and metagenomics can identify key drivers that affect the assembly of plant-associated microbiota, and individual microbial taxa and genes can also be linked to plant physiology and traits related to plant fitness , Fagopyrum tataricum cv. Yunqiao No. 2 (YQ2), Fagopyrum tataricum cv. Xiqiao No. 2 (XQ2) and Fagopyrum tataricum cv. Fenghuang (FH), were used in this study. The nitrogen fertilizer (urea contained \u2265 46.0% nitrogen) was purchased from Sichuan Meifeng Chemical Co., Ltd.This study was carried out from March to June 2022 in an experimental field at Chengdu city in Sichuan province, China . The climate of this station is mid-subtropical humid. The mean annual temperature is 17.5\u00b0C, and precipitation is 774.1 mm. Four TB varieties, 2 (N0), 45 kg/hm2 (N45), 90 kg/hm2 (N90), and 135 kg/hm2 (N135). The subplots were assigned to four TB varieties. The area of each plot was 5 m2 . The sowing density was set as 1,500,000 plants/hm2. Each treatment was repeated three times. The application of phosphate fertilizer (P2O5) and potassium fertilizer (K2O) were 120 kg/hm2 and 40 kg/hm2, respectively, which were applied as base fertilizer at one time. Nitrogen fertilizer was applied according to base fertilizer: topdressing = 1: 1, and topdressing urea was applied at the flowering stage of TB plants. Disease, insect pests and weed infestation were controlled regularly and timely.The experiments were conducted using a split plot design, and a total of 48 subplots were given. The main plots were assigned to four nitrogen fertilizer concentrations: 0 kg/hmAt the mature stage of TB plants, ten plants were randomly selected in each plot. And then, the plant height, stem diameter, effective branch number, main stem node number, seed number and seed weight of TB were measured and recorded. The SPAD value and nitrogen content of TB leaf were measured by using a plant nutrition analyzer .The rhizosphere soil of TB plants that were cultivated in the N0 and N90 conditions was collected. All the roots of TB plants were carefully dug out, the soil on the surface and large soil lumps at the roots were removed. And then, the soil on the root surface was brushed into a sterilized centrifuge tube by using a sterilized brush . FinallyThe measuring methods of all the chemical properties of soil are as described in a previous reported book . The glaFor the pretreated samples , nucleic acid was extracted by OMEGA Soil DNA Kit (D5635-02) kit. The quality of DNA was detected by 0.8% agarose gel electrophoresis, and the DNA was quantified by Nanodrop .2O (8.75 \u03bcL). The reaction procedure was as follows: pre-denatured 5 min at 98\u00b0C, 25 cycles , finally, keep 5 min at 72\u00b0C.Using 20 ng/\u03bcL of the DNA extracted from the rhizosphere soil of YQ1, YQ2, XQ2 and FH as PCR template. The bacterial 16s rRNA V3-V4 region specific primers were used for PCR amplification . The reaPRJNA980195).The TruSeq Nano DNA LT Library Prep Kit of Illumina Company was used to build the database. And then, the quality of library was checked by using Agilent High Sensitivity DNA Kit on the Agilent Bioanalyzer 2100 system. Finally, for the qualified library, NovaSeq 6000 SP Reagent Kit (500 cycles) was used for carrying out 2 \u00d7 250 bp double-terminal sequencing on the Illumina NovaSeq machine. The raw data was submitted to NCBI Short Read Archive database was compared. Alpha diversity index and beta diversity (PCoA) analysis were carried out by using QIIME2 software.A total of 20 ng/\u03bcL of DNA extracted from YQ1, YQ2, XQ2 and FH rhizosphere soil was also used as template for PCR amplification of fungal ITS sequence. The fungal ITS1 region primers were selected for amplification and sequencing . The PCRPRJNA980190).Library quality inspection and sequencing, as well as high-throughput sequenced data processing were the same as the above 16S rDNA high-throughput sequencing. The raw data was submitted to NCBI Short Read Archive database (accession number: PRJNA980146). The genome-wide genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletions (InDels), copy number variations (CNVs) and structure variations (SVs), were examined by comparing the genomes of YQ1 and YQ2 with reference genome sequence of TB,1 and the genes with genome sequence variation were finally generated , 100 (N2), 1,000 (N3) and 10,000 (N4) \u03bcM KNOus study . In addiThe data of agronomic characters, yield factors and physical and chemical properties of rhizosphere soil of TB were processed by Microsoft Excel 2019, the significant differences were analyzed by SPSS 25.0 software with Duncan multiple-range test, and the basic graphics were made by GraphPad prism 9.2 to 90 kg/hm2, the height and stem diameter had increased significantly. TB plants showed no significant change of plant height and stem diameter under nitrogen fertilization ranging from 90 kg/hm2 to 135 kg/hm2 . Nitrogen application can significantly increase the content of alkali nitrogen in the rhizosphere soil of four TB varieties except YQ1 gradually increased with the increase of sequencing reads, and the rarefaction curves flattened when the sequencing reads exceeded 15,000 . It is iFor fungi, an average of 49,453 raw reads per sample was obtained, and an average of 41,101 clean reads per sample was obtained after removing chimeras, low-quality and short sequences. As showed in Chao 1 and Shannon indices were used to calculate the alpha diversity index of rhizosphere soil samples to explain the abundance and diversity of bacterial communities. In terms of abundance indicator, Chao1, nitrogen application increased the bacterial abundance of FH, XQ2, and YQ2 rhizosphere soil, but decreased that of YQ1 . BesidesP < 0.05) . In term < 0.05) . Thus, nActinobacteria (average 36.1%) was the most abundant phylum in all samples, followed by Proteobacteria (average 26.8%), Acidobacteria (average 14.2%) Gemmatimonadetes (average 5.8%), Chloroflexi (average 4.7%) (Actinobacteria in FH and XQ2 but increased that in YQ1 (P < 0.05). Compared with N0, nitrogen application decreased the abundance of Acidobacteria in YQ1 and YQ2, and increased the abundance of Acidobacteria in FH and XQ2 (P < 0.05).Based on species annotation and statistical analysis, a total of 25 bacterial phyla, 70 bacterial classes, 215 bacterial families and 323 bacterial genera were detected in all samples, and the variations in abundance of the top 10 bacteria at phylum, class, family and genus levels were listed in the ge 4.7%) . The appSubgroup 6 (average 9.3%) was the most abundant genus in all samples (Nocardioides (average 3.2%), Streptomyces (average 3.1%) and Amycolatopsis (average 2.7%). Nitrogen application reduced the relative abundance of Subgroup 6, Nocardioides, Streptomyces and Amycolatopsis in rhizosphere samples of YQ1 and YQ2 (P < 0.05), the abundance of Amycolatopsis and Nocardioides in FH and XQ2 samples was also reduced (P < 0.05). However, applying nitrogen fertilizer increased the relative abundance of Subgroup 6 in FH and XQ2 samples (P < 0.05).At the genus level, samples , followeAscomycota (average 93.4%) was the highest average abundance (Basidiomycota (average 2.6%) and Mortierellomycota (average 0.4%). Nitrogen fertilizer application reduced the abundance of Mortierellomycota in the rhizosphere soil of all TB varieties (P < 0.05). For Ascomycota, nitrogen application reduced its relative abundance in the rhizosphere soil of FH and YQ2, and increased the relative abundance of Ascomycota in the samples of XQ2 and YQ1 (P < 0.05). Nitrogen application decreased the relative abundance of Basidiomycota in FH, XQ2 and YQ1 samples, while the abundance of Basidiomycota in YQ2 samples increased (P < 0.05).The variations in abundance of the top 10 fungi at phylum, class, family and genus levels were analyzed . At the bundance . FolloweFusarium (average 21.3%), Penicillium (average 15.8%), Mycosphaerella (average 6.7%) and Monilinia (average 2.9%) were the most abundant genus in all samples . The relative abundance of Fusarium in XQ2 and YQ2 under N90 was lower than that under N0, while the abundance of Mycosphaerella was higher under N90 than that under N0 (P < 0.05). For Penicillium, nitrogen application increased its abundance in XQ2 and decreased its abundance in YQ1 and YQ2 rhizosphere soil (P < 0.05). In addition, the abundance of Monilinia was decreased in XQ2, but that in YQ2 was increased by applying nitrogen fertilizer (P < 0.05).At the genus level, samples . ApplyinIn this study, unique and shared OTUs between different samples were analyzed. As seen from P < 0.05), which indicating that nitrogen application had a significant impact on the distribution of FH, XQ2, and YQ1 rhizosphere bacterial communities. For fungi (P < 0.05), which indicating that nitrogen application significantly affected the distribution of fungal communities in the rhizosphere soil of XQ2, YQ1, and YQ2.Based on PCoA analysis , FH and or fungi . The samLysobacter, Gemmatimonas, bacteriap25, Nitrospira, MND1, and Steroidobacter in the rhizosphere soils of FH, XQ2, and YQ2, but decreased the abundance of these bacteria in YQ1. Meanwhile, nitrogen application increased the abundance of Gaiella, 67-14 and Solirubrobacter in YQ1, but decreased the abundance of these bacteria in the rhizosphere soil of FH, XQ2, and YQ2.We further illustrated the effect of nitrogen fertilization on rhizobacteria . NitrogeMycosphaerella and Acrocalymma, in TB rhizosphere soil. Also, nitrogen application could increase the abundance of Talaromyces, Chaetomium, Humicola, and Staphylotrichum in FH rhizosphere soil and decrease the abundance of these fungi in XQ2, YQ1 and YQ2. The abundance of Fusarium in TB rhizosphere soil in N90 area was lower than that in N0 area.As showed in 67-14 was the largest (12 OTUs), followed by Nocardioides (10 OTUs), Solirubrobacter (10 OTUs), Gaiella (6 OTUs) and bacteriap25 (4 OTUs), while those specifically depleted genera were Subgroup_6 (19 OTUs), Sphingomonas (5 OTUs) and 67-14 (3 OTUs) (Streptomyces (4 OTUs), Iamia (3 OTUs) and Subgroup_6 (3 OTUs) were specifically enriched in YQ2, while Subgroup_6 (12 OTUs), Rokubacteriales (4 OTUs), 67-14 (3 OTUs) and RB41 (3 OTUs) were specifically depleted in YQ2 (Subgroup_6 (17 OTUs), Rokubacteriales (6 OTUs) and Sphingomonas (6 OTUs) were specifically enriched in XQ2, and 67-14 (16 OTUs), Gaiella (9 OTUs), Conexibacter (4 OTUs) and JG30-KF-CM45 (4 OTUs) were specifically depleted (Subgroup_6 (13 OTUs), bacteriap25 (4 OTUs), Longimicrobiaceae (4 OTUs) and Gemmatimonas (3 OTUs) were specifically enriched in FH, while Subgroup_6 (15 OTUs), 67-14 (6 OTUs), bacteriap25 (6 OTUs), Gaiella (6 OTUs), Nocardioides (6 OTUs) and Solirubrobacter (6 OTUs) were specifically depleted . Streptod in YQ2 . Subgroudepleted . Subgroudepleted .Mycosphaerella (3 OTUs), Penicillium (2 OTUs), Immersiella and Fusariella; while Fusarium (4 OTUs), Acremonium (3 OTUs), Aspergillus (3 OTUs), Aspergillus (3 OTUs) and Papiliotrema (2 OTUs) were specifically depleted (Acremonium (2 OTUs), Sarocladium (2 OTUs), Vishniacozyma (2 OTUs) and Monosporascus were found in YQ2, while Chaetomium (2 OTUs), Schizothecium (2 OTUs) and Hannaella (2 OTUs) were specifically depleted (Aspergillus (2 OTUs), Clonostachys (2 OTUs), Preussia (2 OTUs) and Talaromyces (2 OTUs) were specifically enriched in XQ2, while Coprinellus (4 OTUs), Hannaella (2 OTUs), Nigrospora (2 OTUs), Psathyrella (2 OTUs) and Sarocladium (2 OTUs) were specifically depleted (Cyphellophora (5 OTUs), Aspergillus (2 OTUs), Penicillium (2 OTUs) and Torula (2 OTUs) were specifically enriched in FH, while Acremonium (2 OTUs), Coprinopsis (2 OTUs), Cladosporium and Conocybe were specifically depleted , respectively . In this3 treatments with different concentrations were analyzed based on the transcriptome data that was reported in our previous study , cysteine-rich repeat secretory protein (FtCRRSP1), receptor-like protein kinases (FtpLRR-RLK and FtLECRK2) and cell number regulator (FtCNR11) encoding genes (FtWAKL2 and FtLECRK41), transcription factor (FtWRKY41 and FtCOL2), protein phosphatase 2C (FtPP2C40), cysteine-rich repeat secretory protein (FtCRRSP55-1 and FtCRRSP55-2) and alpha-L-arabinofuranosidase (FtASD1) encoding genes (FtKCS12), beta-1, 6-galactosyltransferase (FtGALT29A), metal transporter Nramp5 (FtNRAMP5), bidirectional sugar transporter (FtSWEET14), delta-1-pyrroline-5-carboxylate synthase (FtP5CS), 7-deoxyloganetin glucosyltransferase (FtUGT85A23) and peroxidase (FtPER71) encoding genes , ABC transporter , receptor-like protein kinases , 9-cis-epoxycarotenoid dioxygenase (FtNCED3), calcium-binding protein (FtCML25), expansin (FtEXPA30), galactinol synthase (FtGOLS1), bidirectional sugar transporter (FtSWEET15) and glyceraldehyde-3-phosphate dehydrogenase (FtGAPC2) encoding genes rhizosphere environment and shape the structure of rhizosphere microbial community can be found in the article/CL, HL, and QQ designed the experiments and provided financial support. QQ, DX, QL, HW, YW, QW, XY, LJ, YF, BL, YL, and HL performed data processing. CL, HL, and QQ wrote the manuscript. All authors read and approved the final manuscript."} +{"text": "Multidrug-resistant gram-negative bacteremia (MDR-GNB) is a growing threat worldwide as it is associated with increased morbidity and mortality. We sought to describe the clinical features of MDR-GNB and outcomes in cancer and non-cancer Pts.We performed a retrospective study of adult patients with MDR-GNB at the Ochsner LSU Health Shreveport between January 2018 and July 2022. We collected patients' demographics, medical comorbidities, cancer diagnosis, causative bacteria (MDROs), source of bacteremia, antibiotics therapy, and clinical outcomes.p-value=0.4). Mean length of hospital stay was comparable, 34 d in cancer vs 31 d in non-cancer. 9 Pts were admitted to ICU in cancer group (27%) vs 39 Pts (49%). Mortality rate was 39% in cancer (8 pts went to hospice) vs 16.4% in non-cancer.We identified 112 Pts with MDR-GNB. Pts were divided into 2 groups: cancer group and non-cancer group . In the cancer group, the majority of Pts had solid tumors vs liquid tumors . Mean age was 69 y in cancer compared to 57 y in the non-cancer group. Enterobacteriaceae were isolated in 28 cancer Pts (85%) including ESBL E. coli in 20 Pts (61%), Klebsiella s.p (CRE/ESBL) in 5 Pts (15%), and ESBL P. mirabilis in 3 Pts (9%). Pseudomonas aeruginosa CRO in 3 Pts (9%) and A. baumannii in 2 Pts (6%). In non-cancer Pts, Enterobacteriaceae were isolated in 65 Pts (82%) including ESBL E. coli in 40 Pts (51%), Klebsiella s.p (CRE/ESBL) in 18 Pts (23%) and ESBL P. mirabilis in 6 Pts (8%). P. aeruginosa CRO found in 6 Pts (8%) and A. baumannii in 8 Pts (10%). The sources of bacteremia in cancer group were UTI in 14 Pts (42.4%), osteoarticular infection (OAI) in 5 Pts (15%), pneumonia in 3 Pts (9%), CLABSI in 2 Pts (6%), endovascular in 1 Pt (3%) and unknown in 8 Pts (24%), whereas in non-cancer group, UTI was reported in 40 Pts (68%), pneumonia in 9 (27%), OAI in 1 (1.3%), endocarditis in 1 Pt (1.3%), and unknown in 20 Pts (25.3%). Mean duration of targeted antibiotics was 9 days in cancer vs 13.3 days in non-cancer group (Our data showed that the common source of MDR-GNB remains urinary tract infection in both groups and the bacterial epidemiology is comparable between the two groups. Further studies are warranted to assess the impact of resistant organisms on cancer Pts.All Authors: No reported disclosures"} +{"text": "Research findings show that during the COVID-19 pandemic, healthcare workers (HCWs) have been subject to increased workload while also exposed to many psychosocial stressors.The aim of this study was to investigate Covid\u2019s impact on healthcare professionals\u2019 mental health and their coping strategiesThe study population consisted of 144 health professionals from health care facilities in Patras. An internet based questionnaire was distributed,which included demographic survey questions and the following three scales: (1) The Psychological Consequences Questionnaire (PCQ) scale, (2) The Kessler Psychological Distress scale (k6) and (3) Toulouse\u2019s scale for coping strategies (E.T.C.).144 health care workers participated in the survey, who were basically women (72.2%) and nurses (60%) In terms of psychological consequences, participants felt pressured, stressed (3.12), and sad/depressed (2.78). The most frequently used coping strategies were acceptance (3.44), active focus (3.38), cognitive focus (3.31), cognitive control and planning (3.30), emotional control (3.17), social informational support (3.16) and cooperation (3.15). In contrast, the strategies used to a lesser extent are substance addiction (1.91), emotional focus ( 2.13), denial (2.27) and alexithymia (2.49). Generally, positive strategies (3.11) were chosen to a greater extent than negative ones ( 2.38).It is very important for hospital administrations to design specific psychological support programs and encourage health professionals to participate in them in order to manage their fear, anxiety and stress experienced.None Declared"} +{"text": "The emergence of SARS-CoV-2 in early 2020 with subsequent implementation of public health and social measures influenced the epidemiology of respiratory viruses worldwide. This study describes circulation of respiratory viruses during two winter seasons and inter-seasonal periods in Georgia.We aggregated data obtained from Influenza like illness (ILI) and Severe Acute Respiratory Infection (SARI) cases during 2020/21 and 2021/22 (weeks 40-20) and inter-seasonal (weeks 21-39) periods in Georgia. All specimens from patients were screened on 22 respiratory viruses by real time RT-PCR.During 2020/21 season 50% (868/1729) specimens tested positive on at least one virus. No influenza virus and few RSV detections were observed in Georgia. Mostly identified virus was Rhino (44.8%) circulating almost all season; followed by Coronavirus OC43 (23.7%), primarily seen in weeks 12-18 and SARS-Cov-2 (15%) with highest detection rates during weeks 48-52. In 2021 inter-season 54% (825/1513) of specimens were positive. A gradual increase in RSV detections was observed in summer. Most seen viruses were Rhino (30%), HMPV (22%) and Parainfluenza virus 3 (21%) circulating mainly in June and July. During 2021/22 season 44% (2012/4545) of specimens screened positive, out of which RSV (25.7%) with earlier circulation in weeks 40-2 and Rhino (25.7%) with most detections in the beginning and at the end of the season. Unusually influenza A/H3 (17%) peaked in late spring (weeks 12-18). SARS-Cov-2, Parainfluenza viruses 3 and 4, Adenoviruses, Human bocavirus, enteroviruses were actively co-circulating too. In 2022 inter-season 54% (1320/2456) of samples tested positive. Influenza A/H3 circulation continued until July. SARS-Cov-2 (27.7%), Rhino (22%), HMPV (14.5%), Parainfluenza virus 3 (12.7%), RSV (10.8%) were mostly seen viruses predominantly in June.Wider range respiratory viruses with higher positivity rates were detected among ILI and SARI cases in 2021/22 season compared to 2020/21 presumably due to mitigation of public health and social measures. Low detection rates of SARS-CoV-2 at sentinel sites could be explained by referral of COVID-19 patients to dedicated clinics. RSV and Influenza circulations were unusual in summer months in Georgia.All Authors: No reported disclosures"} +{"text": "Objectives: The highly transmissible SARS-CoV-2 has swept across the globe, causing large swaths of COVID-19, displacing medical resources and attention from patients with other life-threatening illnesses, and overwhelming healthcare institutions. Shifting toward endemicity, the Singapore Ministry of Health ceased issuing quarantine orders to close contacts of infected cases on October 11, 2021. However, contact tracing and exposure management within SGH continued with the same risk criteria.\u00a0We have examined COVID-19 exposures in different hospital locations to determine the effectiveness of surveillance in breaking the chain of transmission. Methods: Contact tracing of COVID-19 exposures among Singapore General Hospital (SGH) staff and patients has been conducted since the first COVID-19 diagnosis in January 2020. The information collected is used to identify those at higher risk of infection for enhanced surveillance or isolation. The data analyzed in this study were collected during later periods of the SARS-CoV-2 \u03b4 (delta) pandemic wave between August 1, 2021, and December 31, 2021. Results: During the 4-month study period, there were 1,686 SARS-CoV-2 exposures in SGH. Among these 1,686 exposures, 1,157 (69%) were contacts with an infected patient. Among these infected source patients, 915 were emergency department patients, 210 were ward inpatients, and 32 were clinic outpatients. The remaining 524 exposure events (31%) were contacts with infected staff, of whom 441 were SGH employees and 83 were employees from other SingHealth institutions. The remaining 5 index cases were visitors to SGH. Of the 1,686 exposure events, 330 had associated at-risk contacts requiring exposure management. Among 330 patient index cases, 213 (64.5%) resulted in 699 exposed contacts (patients vs staff), whereas 117 staff index cases resulted in 435 exposed contacts (patients vs staff).\u00a0For 434 exposed contacts who were staff, 204 (47%) of their exposures occurred in inpatient ward settings, followed by 153 (35.3%) that occurred in outpatient clinics, 36 (8%) that occurred common lounging areas, 16 (3.6%) that occurred in office sites, 15 (3.4%) that occurred in the community, 8 (1.8%) that occurred in occupation therapy, and 2 (0.5%) that occurred in the emergency department. For 688 exposed contacts who were patients, 579 (84.1%) exposures occurred in inpatient wards, 70 (10.2%) occurred in DEM, 19 (2.7%) occurred in other SingHealth institutions, 16 (2.3%) were exposures to roving porters, and 3 (0.4%) occurred in the community.\u00a0During the study period, 3 hospital clusters were identified and investigated, one of which included secondary cases. Conclusions: Most SARS-CoV-2 exposures in SGH occurred in inpatient settings where patients were index cases. Despite intensive contact tracing and stringent surveillance and isolation measures, inpatient clusters could not be prevented."} +{"text": "Extracorporeal membrane oxygenation (ECMO) is a well-known type of advanced life support used in critically ill patients with serious heart and/or lung problems. ECMO treatment is associated with multiple life-threatening complications. The objectives of this study were to identify the prevalence of surgical site infections (SSI) and bloodstream infections (BSI) along with the associated risk factors and outcomes in patients on ECMO.In this retrospective study, clinical charts of patients were reviewed from January 2012 to April 2023. All admitted pediatric patients 14 years or less who received ECMO treatment were enrolled. Mann-Whitney and Fisher exact tests were used to assess mortality-related risk factors.A total of 165 patients were included in the study, 79 (47.88%) females and 86 (52.12%) males, with a median age of 4 [IQR 0.8-24] months. BSI were found in 33 (20%) of them, 10 (30.30%) were gram-positive, 25 (75.75%) were gram-negative, and 6 (18.18%) were fungi. Furthermore, 33 (20%) developed SSI. The overall mortality rate in this study is (50.30%) with a median duration from ECMO procedure initiation to death being 11 [IQR: 5-26] days. Most of mortalities (78.31%) were noticed in infants aged \u226424 months. Compared with patient with neither SSI nor BSI, patients with SSI and BSI had a higher mortality rates of 19 (22.89%) and 16 (19.28%) respectively.Additionally, other noted complications were mediastinitis 4 (2.42%), sternal osteomyelitis 2 (1.21%), infective endocarditis 4 (2.42%).Younger age and thrombocytopenia were found to be a mortality related risk factors .Our study found a high rate of bacteremia and SSI in pediatric patients receiving ECMO. Younger age, thrombocytopenia were the potential risk factors associated with higher mortality rates in this group.All Authors: No reported disclosures"} +{"text": "Migraine often leads to reduction of social power and prestige of the patients, hence leading further emotions of shame.Exploring the role of external and internal shame in people with migraines.The sample consisted of 180 people, more specifically 140 people from the general population and 40 people who have been diagnosed with migraine and receiving treatment for migraine, who completed the following questionnaires voluntarily and anonymously: a) Migraine Experience Questionnaire and Headache Impact Test-6 (HIT-6), b) the Other As Shamer scale (OAS) c) the Experience of Shame Scale (ESS), and socio-demographic and self-reported questionnaire.Patients scored higher level external Shame (OAS) rates (31.28 \u00b1 6.98) than people from the general population who scored lower external Shame (OAS) rates (16.89 \u00b1 10.00) with a statistically significant difference between them (p = 0.000). Also, patients scored lower-level internal shame (ESS) rates (45.58 \u00b1 6.91) than people from the general population who scored higher internal shame (ESS) rates (53.36 \u00b1 15.62) with a statistically significant difference between them (p = 0.003).Patients with symptoms of migraine show statistically higher level of external shame and lower level of internal shame and further study is considered necessary.None Declared"} +{"text": "Taenia solium infection. There is limited evidence to guide clinical management of these patients.Subarachnoid (racemose) neurocysticercosis (SANCC) is an uncommon but severe form of We performed a multicenter retrospective chart review of 15 U.S. sites. A total of 69 subjects with racemose disease were entered.The most common region of exposure was Mexico (67%) followed by Central America (24%). Median age was 43 years (range 15-76) and 71% were male. Common symptoms at the time of index admission were headache (80%), nausea/vomiting (46%), dizziness (44%), and blurry vision (33%). Cysts were intracranial in 64 (93%) subjects and exclusively intraspinal in 4. One patient had meningitis without visible cystic lesions. Incident admission magnetic resonance imaging (MRI) demonstrated ventriculomegaly in 41 (59%) and focal findings in 9 (13%) including ischemic infarct, subarachnoid hemorrhage, and/or arterial aneurysm. For 55 (80%), SANCC was first diagnosed during the index admission. Of these, 23 (42%) had prior medical visits and substantial delay in diagnosis . Of the 69 subjects, 54% underwent a neurosurgical procedure during index admission . At the time of discharge, 6 (8.6%) patients were not given albendazole and/or praziquantel due to cost or availability. Six months following discharge, < 10% of follow up MRIs demonstrated cyst resolution. Planned treatment course of < 4 weeks at discharge compared to >4 weeks was associated with increased risk for new cyst development on follow up imaging at a median of 3.8 years following discharge (range 2.6 months-8 years). Those with a delayed diagnosis received a significantly longer duration of corticosteroids (median 8 weeks) than those without a delay .The diagnosis of SANCC is often missed, and most patients require neurosurgical intervention. Antiparasitic therapy is suboptimal, especially with regimens developed for parenchymal NCC.Jeffrey D. Jenks, MD, MPH, Astellas: Grant/Research Support|F2G: Grant/Research Support|Pfizer: Grant/Research Support"} +{"text": "Molnupiravir is being widely used as a treatment for coronavirus disease 2019 (COVID-19); however, its acceptability and safety in older patients aged \u2265 80 years in real-world clinical practice is not well understood.We conducted a single-centre retrospective study and assessed the outcome of patients with COVID-19 treated with molnupiravir according to the following criteria: (A) discontinuation rate of molnupiravir; (B) type, frequency, and severity of adverse events; (C) all-cause mortality within 30 days of the diagnosis of COVID-19.Forty-seven patients (46.1%) were aged \u2265 80 years (older patients) and 55 (53.9%) were aged < 80 years (younger patients). There were no significant differences in coexisting diseases and history of vaccination for COVID-19 between older and younger patients. Older patients were significantly more likely to have moderate disease (moderate 1 and 2) according to the Japanese Ministry of Health, Labour and Welfare classification than younger patients. During treatment, 8.5% of older patients and 1.8% of younger patients stopped taking molnupiravir, but the difference was not significant. Adverse events were observed in 39/102 (38.2%) patients. The most common adverse events were diarrhoea (9.8%), exacerbation of coexisting diseases (6.9%), bone marrow suppression (6.9%), liver dysfunction (5.9%), and loss of appetite (4.9%). Most adverse events were minor, ranging from grades 1 to 3. The all-cause mortality rate was 10.8%, and no molnupiravir-related deaths were observed.Molnupiravir treatment is acceptable and safe in older patients with COVID-19 aged \u2265 80 years.All Authors: No reported disclosures"} +{"text": "Hepatocellular carcinoma (HCC) is one of the most frequent and life-threatening human cancers worldwide. Despite curative resection surgery, the high recurrence rate of HCC leads to poor patient survival. Chronic hepatitis B virus (HBV) infection is a major etiological factor for HCC. HBV pre-S2 gene deletion mutation leads to the expression of an important oncoprotein called a pre-S2 mutant. It represents an independent prognostic biomarker for HCC recurrence. This study aimed to identify other independent prognostic biomarkers from clinicopathological characteristics of 75 HBV-related HCC patients receiving resection surgery and to validate their potential to be combined with pre-S2 gene deletion mutation as a combination biomarker for HCC recurrence. Patients with both the presence of pre-S2 gene deletion mutation and tumor-node-metastasis (TNM) stage IIIA\u2013IIIC had a higher HCC recurrence risk than patients with either one or none of these two factors. Moreover, the combination of pre-S2 gene deletion mutation and TNM stage exhibited better performance than either of these two factors alone in discriminating patients from patients without HCC recurrence. Collectively, this study proposed that the TNM stage held significance as a combination biomarker with pre-S2 gene deletion mutation with a greater performance in predicting HCC recurrence after curative surgical resection. As the most common histological type of liver cancer, hepatocellular carcinoma (HCC) ranks as the sixth most prevalent human cancer and the third leading cause of cancer-related death worldwide, leading to over 800,000 new cases and 800,000 new deaths every year ,2. AlthoChronic infection with the hepatitis B virus (HBV) is one of the most significant risk factors for HCC. It is responsible for as high as 50% of total HCC cases worldwide ,10. The In this study, many different clinicopathological characteristics obtained from a cohort of 75 HBV-related HCC patients who received curative surgical resection were analyzed to assess their association with HCC recurrence after surgery. The clinicopathological characteristics, which were significantly and independently associated with HCC recurrence, were identified, and were further combined with HBV pre-S2 gene deletion mutation to evaluate the performance of their combination in predicting HBV-related HCC recurrence.The plasma samples were retrospectively collected from 75 HBV-related HCC patients who received curative surgical resection as monotherapy at the China Medical University Hospital from March 2004 to September 2016 under the approval of the China Medical University & Hospital Research Ethics Committee (protocol no. CMUH107-REC1-080) and were stored at \u221280 \u00b0C until use. All patients included in this study were HBV-infected without concurrent HCV or HDV infection and did not experience virological failure after anti-viral treatment. The clinicopathological data were retrieved from the patient medical records of CMUH. All experiments were performed ethically according to the guidelines of the 1975 Declaration of Helsinki and written informed consent was obtained from all enrolled patients.The pre-S2 gene deletion mutation was detected using an approach based on next-generation sequencing (NGS) analysis from the plasma samples of patients with HBV-related HCC as previously described . BrieflyThe chi-square test was performed to assess the association between clinicopathological characteristics and HCC recurrence in patients. The Cox proportional-hazards regression model was conducted for the univariate and multivariate analyses of recurrence-free survival (RFS) of patients. The Kaplan-Meier method and the log-rank test were carried out to construct and compare the RFS curves of patients, respectively. The receiver operating characteristic (ROC) curves were plotted to compare the performance of clinicopathological characteristics in differentiating patients with HCC recurrence from patients without HCC recurrence and the Hanley-McNeil test was applied to determine the area under the ROC curve (AUC).4 (21.5 to 1.5 \u00d7 108) copies/mL. All 65 (100%) patients with available data were HBV surface antigen (HBsAg)-positive and 62 of 71 (87%) patients with available data were HBV e antigen (HBeAg)-negative in serum. The median tumor size (range) in all patients was 4.5 (1.1 to 19.5) cm. There were 40 (53%) patients with American Joint Committee on Cancer (AJCC) tumor-node-metastasis (TNM) stage I, 20 (27%) patients with TNM stage II, 7 (9%) patients with TNM stage IIIA, 5 (7%) patients with TNM stage IIIB, and 3 (4%) patients with TNM stage IIIC; however, there were no patients with TNM stage IVA or IVB. Moreover, by the NGS-based analysis, the presence of HBV pre-S2 gene deletion mutation in plasma was detected in 31 of 75 (41%) patients but not in the other 44 (59%) patients. After curative surgical resection, 52 of 75 (69%) patients suffered HCC recurrence but the other 23 (31%) patients did not; the median RFS (range) of all patients was 26.2 (1.5 to 158.9) months at a maximum follow-up of 158.9 months. In addition, the overall survival (OS) rate of patients after surgery was 79% with the median OS (range) of 61.5 (2.5 to 171.1) months at a maximum follow-up of 171.1 months.As shown in p-value = 0.0248). Among the other clinicopathological characteristics analyzed, AJCC TNM stage was the only factor which exhibited a significant association with HCC recurrence; patients with HCC recurrence had a significantly higher proportion of AJCC TNM stage IIIA-IIIC (14 of 52 (27%) patients) than patients without HCC recurrence did (1 of 23 (4%) patients) . Moreover, based on the analysis of Kaplan-Meier RFS curves, patients with the presence of pre-S2 gene deletion mutation or AJCC TNM stage IIIA-IIIC displayed significantly poorer RFS than patients with the absence of pre-S2 gene deletion mutation or AJCC TNM stage I\u2013II did (median RFS (range), 15.1 (1.6 to 158.9) vs. 32.6 (1.5 to 158.1) months, p value = 0.0283; 5.1 (1.9 to 141.3) vs. 33.1 (1.5 to 158.9) months, p value < 0.0001, respectively) , p value < 0.0001; 2.189 (1.195 to 4.013), p value = 0.0112; 0.515 (0.288 to 0.923), p value = 0.0258, respectively); however, in the multivariate analysis of RFS, only the presence of pre-S2 gene deletion mutation and AJCC TNM stage IIIA-IIIC were validated as the independent prognostic factors which showed a significantly negative impact on RFS of patients (HR (95% CI), 1.910 (1.065 to 3.425), p value = 0.0300; 3.822 (1.920 to 7.607), p value = 0.0001, respectively) A,B. In tctively) .p value = 0.0008; 4.8 (1.9 to 15.1) vs. 36.8 (1.5 to 158.1) months, p value < 0.0001, respectively) ; however, in the multivariate analysis of RFS, the Group 2, Group 3, and Group 4 combinations of pre-S2 gene deletion mutation and AJCC TNM stage displayed a significantly independent negative impact on RFS of patients (HR (95% CI), 4.522 (1.803 to 11.344), p value = 0.0013; 2.078 (1.068 to 4.043), p value = 0.0312; 6.660 (2.535 to 17.496), p value = 0.0001, respectively) ; Group 2, absence of pre-S2 gene deletion mutation but AJCC TNM stage IIIA\u2013IIIC (8 patients); Group 3, presence of pre-S2 gene deletion mutation but AJCC TNM stage I\u2013II (24 patients); and Group 4, presence of pre-S2 gene deletion mutation and AJCC TNM stage IIIA\u2013IIIC (7 patients). As shown by the Kaplan-Meier RFS analysis, the Group 2 and Group 4 patients, rather than the Group 3 patients, had significantly shorter RFS than the Group 1 patient did (median RFS (range), 5.1 (2.0 to 141.3) vs. 36.8 (1.5 to 158.1) months, ctively) C. In thectively) . Moreovectively) .Although curative resection surgery has been available for the treatment of HCC patients, an extremely high rate of HBV-related HCC recurrence after treatment is still a big challenge and leads to poor patient survival ,31. The The prognostic value of the TNM stage combined with other clinicopathological factors in the prediction of HCC recurrence after curative surgical resection has been validated in several studies. Sonohara et al. showed that the established scoring system combining TNM stage and albumin-bilirubin grade (ALBI-T scoring) exhibited an independent prognostic performance for HCC recurrence . Zhang e2+)/reactive oxygen species (ROS)), chromosome instability , genomic instability (importin \u03b11/Nijmegen breakage syndrome 1 (NBS1)), cell proliferation -A/VEGF receptor-2/protein kinase B (Akt)/mammalian target of the rapamycin (mTOR)), cell cycle progression (Jun activation domain-binding protein 1 (JAB1)/p27/cyclin-dependent kinase (Cdk2)/retinoblastoma protein (Rb)), cell growth (nuclear factor-\u03baB (NF-\u03baB)/p38 mitogen-activated protein kinase (p38 MAPK)/cyclooxygenase-2 (COX-2)), cell survival (B cell lymphoma-2 (Bcl-2)), aerobic glycolysis (Yin Yang 1 (YY1)/Myc/solute carrier family 2 (facilitated glucose transporter) member 1 (SLC2A1)), and lipid biosynthesis (sterol regulatory element-binding transcription factor 1 (SREBF1)/adenosine triphosphate citrate lyase (ACLY)/fatty acid desaturase 2 (FADS2)) [As an important HBV oncoprotein, pre-S2 mutant has been shown to predominantly accumulate in the endoplasmic reticulum (ER) of HBV-infected hepatocytes to induce ER stress and activate many ER stress-dependent or -independent oncogenic signaling pathways in promoting hepatocyte malignant transformation and eventually HCC development, including the signaling pathways related on oxidative DNA damage ) ,28,39. H(FADS2)) ,18,19, t(FADS2)) , furtherThis study proposed a combination of the HBV viral factor, pre-S2 gene deletion mutation, and the clinicopathological factor, AJCC TNM stage, as a novel combination biomarker with an improved performance in predicting HCC recurrence in HBV-related HCC patients after curative surgical resection."} +{"text": "Patients with left ventricular assist devices (LVAD) infected with SARS-CoV-2 may be at increased risk of complications and mortality. The purpose of the study was to analyze the characteristics and outcomes of LVAD patients with SARS-CoV-2 infection at our center.A retrospective review of LVAD patients diagnosed with COVID-19 via PCR between March 1st, 2020, and March 1st, 2023, was conducted. Patient demographics, clinical, laboratory, and imaging data were collected. We performed descriptive statistical analysis on the data obtained.During the study period, we were actively following 130 LVAD patients, 34 (26.2%) developed COVID-19. Our cohort consisted of 27 males (79.4%) with a median age of 63.5 years and median BMI of 27.6 (Table 1). Eighteen and 12 self-identified as African American (52.9%) and Hispanic (35.3%), respectively. The common comorbidities included hypertension (94.1%), hyperlipidemia (79.4%), atrial fibrillation (67.4%), and chronic kidney disease (61.8%). The most common presenting symptoms were shortness of breath (41.2%), cough (35.3%), and fever (29.4%). Nine (26.5%) patients were asymptomatic. Twenty-eight (82.4%) and 16 (57.1%) were admitted to the hospital and ICU, respectively (Table 2). Ten (35.7%) and 2 (7.1%) patients required supplemental oxygen via nasal canula, and mechanical ventilation, respectively. Most of the hospitalized patients were managed with Remdesivir (71.4%) and systemic corticosteroids (42.9%). No complications of pump hemolysis or thrombosis, or systemic embolisms were noted. Two deaths were reported: one patient (2.9%) died while in the hospital from COVID-19, and another patient died 16 months later secondary to acute respiratory failure in the setting of post-COVID pulmonary fibrosis.This is the largest single center study analyzing outcomes of COVID-19 in LVAD patients to date. Our cohort experienced a lower mortality rate from COVID-19 infection compared to prior studies. Larger studies are needed to guide management strategies and determine optimal timing for heart transplant after COVID-19.All Authors: No reported disclosures"} +{"text": "NT5C2 or PMS2 gene related to thiopurine-dose response. In addition, 60% (3/5) of these cases were preceded by an initial hit in the epigenetic regulator, KMT2D. Mutations in common relapse-enriched genes comprised 33% of the very early relapses, 50% of the early and 40% of the late relapses. Overall, 14/46 (30%) of the samples showed the hypermutation phenotype, of which the majority (50%) had a TA pattern of relapse. Conclusions: Our study highlights the high frequency of early relapses driven by TA clones, demonstrating the need to identify their early rise during chemotherapy by digital PCR.Methods: Forty pediatric (0\u201312 years) B-ALL DNA samples (20 paired Diagnosis-Relapse) and an additional six B-ALL DNA samples (without relapse at 3 years post treatment), as the non-relapse arm, were retrieved from the biobank for advanced genomic analysis. Deep sequencing was performed using a custom NGS panel of 74 genes incorporating unique molecular barcodes. Results: A total 47 major clones (>25% VAF) and 188 minor clones were noted in 40 cases after bioinformatic data filtering. Of the forty-seven major clones, eight (17%) were diagnosis-specific, seventeen (36%) were relapse-specific and 11 (23%) were shared. In the control arm, no pathogenic major clone was noted in any of the six samples. The most common clonal evolution pattern observed was therapy-acquired (TA), with 9/20 (45%), followed by M-M, with 5/20 (25%), m-M, with 4/20 (20%) and unclassified (UNC) 2/20 (10%). The TA clonal pattern was predominant in early relapses 7/12 (58%), with 71% (5/7) having major clonal mutations in the The relapse of B-cell acute lymphoblastic leukemia (B-ALL), comprising 10\u201315% of cases, continues to be one of the foremost causes of cancer death in the pediatric population and, despite the application of high-throughput genomics to unravel the biology of the relapse of the disease, gaps exist in evolution trajectories and the nature of relapses due to leukaemic clone heterogeneity and differences between chemotherapy doses in different treatment protocols being used world-wide ,14,15,16CREBBP, WHSC1, NT5C2, PRPS1, PRPS2, MSH2, MSH6, PMS2, NR3C1, NR3C2, Tp53 and FPGS). Such therapy-acquired somatic mutations in chemotherapy-dose-response genes drive >20% of early and late relapses [Multi-agent chemotherapy is known to induce variable stress on leukaemic clones, leading to clonal evolution and the development of drug-resistant mutations in the genes related to chemotherapy-dose response from 20 pediatric (0\u201312 years) B-ALL cases (20 paired diagnosis (D)\u2013relapse (R)) who experienced very early (<9 months from diagnosis), early (9\u201336 months) or late relapse (>36 months) and an additional cohort of 6 non-relapsed B-ALL cases (without relapse >5 years post treatment), as control arm, were retrieved and enrolled for analysis after due approval of institute ethics committee. For excluding germline variants, DNA was obtained from remission sample (post-induction bone marrow) slides. All cases had or were receiving uniform treatment as per ICiCLe protocol with a curative intent . Cases wInformed written consent was taken from patients\u2019 parents/legal guardians before enrolment in the study. Biobanked DNA and RNA were extracted from peripheral blood mononuclear cells (PBMCs) using Qiagen DNA and RNA blood mini kit , according to manufacturer\u2019s protocol. The quality and quantity of DNA and RNA were checked prior to storage and after retrieval using both Nanoquant and Qubit fluorometer. One \u00b5g of total RNA was transcribed into cDNA by superscript cDNA vilo synthesis kit and the quality of cDNA was checked by running a 1.5% agarose gel for PCR product of GAPDH housekeeping gene.ETV6-RUNX1, KMT2A, BCR-ABL1) FISH panel and DNA ploidy index (FxCycle violet on BD FACS), as per routine testing. Cases negative for above translocations and or ploidy abnormalities were evaluated for Ph-like gene expression followed by targeted next generation sequencing (NGS) RNA fusion panel analysis. The Ph-like gene expression was assessed by RQ-PCR TaqMan-based array method using a set of pre-validated 15 genes, as reported by Roberts et al. [Ph-like expression. The NGS-based targeted RNA fusion panel was designed on Ampliseq studio (hg19) and covered 109 translocations, including isoforms/fusion partners, along with 12 internal control genes with 100% coverage , 98 \u00b0C for 15 s, 60 \u00b0C for 4 min (27 cycles), holding at 10 \u00b0C followed by amplicon digestion, adaptor ligation and library amplification. Library quantification was performed on Qubit fluorometer, followed by sequencing on Ion Torrent S5 Studio. Fusions were reported as per Ion Reporter software default parameters of >10,000 reads for internal control genes and >25 junctional reads for true translocation call.Primary genetic events in B-ALL were classified by standard triple probe and copy-number variations (CNVs), were evaluated using a custom DNA NGS panel of 74 genes based on ArcherDx proprietary chemistry incorporating unique molecular barcodes for error correction refer . The panThe variants noted were classified as diagnosis (D)-specific, relapse specific (R) or shared. Clonal mutations were classified as major (>25% VAF) and minor/sub-clonal (<25% VAF), based on assumption that those with VAF >25% have a dominant in clonal composition. The changes in the variant allele frequency (VAF) of somatic SNVs were examined to determine the clonal evolution pattern from diagnosis to relapse. Clonal evolution patterns from diagnosis to relapse were classified into following groups: (i) TA (therapy acquired) for genetically distinct clones at relapse with the major relapse clonal mutation not present in diagnostic sample even at ultra-deep (>3000\u00d7) sequencing analysis of the data; (ii) m-M (minor to Major) for clones with minor sub-clones at diagnosis to major sub-clones at relapse (iii) M-M (major to major) for cases in which major clones at diagnosis were the only major clones at relapse ; and (iv) UNC (unclassifiable), in which no major clones could be identified at diagnosis or relapse. The somatic SNVs were clustered based on their VAFs at diagnosis and relapse and plots were designed using CanvasXpress. The input included the clonal fraction of each tumor cell population, representation of descent in the form of parental relationship and the time points at which the samples were obtained. Hypermutation phenotype in samples (>1.5 mutations per MB) was defined as per definition and criteria proposed by Waanders et al. using Co9/L. The day-35 marrow was M1 (100%); however, seven (35%) had positive MRD (>0.01%) post induction. The final risk stratification post induction was: standard risk 25%, intermediate risk 25% and high risk (50%). The time to relapse ranged from 8\u201340 months (median 26) with predominant early relapses , 25% (5/20) late relapses and 15% (3/20) very early relapses.The baseline clinical and hematological characteristics of the paired-sample cohort are presented in The site of relapse was predominantly medullary in 55% (11/20), combined medullary with/out CNS and/or testes in 30% (6/20) and CNS and testicular alone in 10% (2/10) and 5% (1/20), respectively.ETV6:RUNX1 (4), BCR:ABL1 (4), TCF3:PBX1 (1) and hypodiploidy (1) on standard FISH and DNA ploidy analysis and P2Y8:CRLF2, MEF2D:BCL9, TAF15:ZNF384, EBF1:PDGFRB and KMT2A:MLLT1 in one case each on targeted NGS-based RNA fusion analysis. The remaining negative cases after NGS testing were categorized as B-cell other. Overall, Ph-like B-ALL genomic lesions were noted in 2/20 (10%) cases. The pie chart in TCF3:PBX1 cases and one AF4:MLL case.A definitive primary genetic abnormality could be defined in 15/20 (75%) cases, both on diagnosis and in paired samples at relapse. These included p-0.765). After a second data filtration (based on the criteria defined in p-0.316); CDKN2A/2B deletion noted in 65% (13/20) and IKZF1 deletion noted in 25% (5/20). Two or more CNVs were noted in 30% (6/20) of the cases only. The recurrently mutated genes (five or more samples) included TENM3 (11), MSH6 (11), NOTCH1 (10) and MSH2 (10), with minor clones in all the cases , followed by KMT2D (9), KRAS (9), NRAS (7), PMS2 (7) and EP300 (6), with both major and minor clones driving the relapse, while only two cases had diagnosis-specific major clones. Mutations in the relapse-enriched genes comprised 33% (1/3) of the very early relapses, 50% (6/12) of the early and 40% (2/5) of the late relapses. Multiclonal mutations were noted in nine genes in fifteen cases (75%), with minor clonal TENM3 or NOTCH1 being most common . On other hand, KRAS, KMT2D, Flt3 and FPGS had both major and minor clones, either on diagnosis or on relapse were minor. In total, nine out of twenty (45%) had major clones in one of these twelve genes , originating in minor RAS clones. The late relapses had an equal frequency of M\u2013M and TA-type patterns, with Tp53 clones persisting at diagnosis and relapses in two M\u2013M cases, which is characteristic of Tp53 clones, since they are known to enter a quasi-dormant state under chemotherapy and later lead to late relapses , in 9/20 (45%), followed by M\u2013M 5/20 (25%), m\u2013M 4/20 (20%) and UNC 2/20 (10%). The TA clonal pattern was most predominant in the early relapses, with 7/12 (58%), followed by 2/5 (40%) in late relapses. In addition, two cases with the m\u2013M pattern in very early and early relapse each had a late therapy-acquired clonal gene mutation in the relapses . Two latOverall, 14/46 (30%) samples showed a hypermutation phenotype based on the criteria suggested by Waanders et al. in their study Table 1Table 1. BCR:ABL and ETV6:RUNX1 comprised the majority of the cases , but if we combine these primary abnormalities into standard prognostic groups, nine (60%) were at lower risk and all of them had either very early or early relapse, while six (40%) were at high-to-intermediate risk and had early-to-late relapses.This is one of the first genomic studies in pediatric B-ALL from our sub-continent to address relapse biology and define clonal evolution patterns and therapy-acquired mutations. The study is relatively novel in terms of the error-read correction technology used and the integrated SNV/INDELs and CNV detection performed using a targeted deep sequencing NGS approach. The study cohort of 20 paired diagnosis\u2013relapse B-ALL cases had a heterogenous distribution of primary genetic abnormalities, which was defined in 75% (15/20) of the cases. The RAS pathway genes, respectively. Moreover, the RAS gene mutants showed heterogenous clonal evolution consistent with their dual nature as sensitive to vincristine and resistant to methotrexate, thereby driving the balance in either direction in individual cases [No significant difference in the mutational burden of secondary abnormalities of SNVs/INDELs and/or CNVs in the diagnostic and relapse samples was observed a, which al cases ,28,29. Ial cases , around ETV6:RUNX1-positive cases, the relapse was driven by a major clone in the epigenetic gene, UHRF1. Mutations in UHRF1 make cells more sensitive to chemotherapy by reducing FANC-associated repair, but they also lead to global hypomethylation, pre-disposing patients to porto-oncogene activation, as was evident in the late KRAS mutation in one of our cases. However, the role of UHRF1 as a surrogate marker of early relapse in ETV6:RUNX1 cases needs to be prospectively studied.Mutations in relapse-enriched genes comprised 33% (1/3) of the very early relapses, 50% (6/12) of the early and 40% (2/5) of the late relapses, which is quite comparable to the prevalence rates of 17%, 65% and 32% respectively, described by Li et al. [NT5C2 or PMS2 genes related to thiopurine-dose response. In addition, in 60% (3/5) of these cases, the NT5C2/PMS2 clones were preceded by an initial hit in the epigenetic regulator, KMT2D, making it an important screening gene to predict early relapses during treatment. The NT5C2 relapse-specific clonal mutations, R363L and R367Q, noted in two of our samples were already been shown by Li et al. to be functionally resistant to 6-mercaptopurine [PMS2, have also been linked with thiopurine response in different studies [PMS2 noted at relapse were either nonsense or frameshift mutations, with one clone showing a high VAF, of 79%, later noted as having a loss of heterozygosity at Chr. 7p. However, none of the PMS2-driven relapse cases had evidence of underlying congenital mismatch repair-deficiency syndrome. Very early relapses were primarily m\u2013M originating from a minor RAS clone, which was consistent with previous evidence [Tp53 clones, which enter a quasi-dormant state under chemotherapy and result in late relapses and showing persistence as minor clones at relapse. On the other hand, KRAS, KMT2D, Flt3 and FPGS had both major and minor clones, either at diagnosis or relapse. Ma et al. noted multiclonal mutations in six genes in 50% (10/20) of their cases and only three of their genes overlapped with our data [The TA clonal pattern was predominant in 7/12 (58%) of the early relapses, with 71% (5/7) of these having major clonal mutations in the topurine . Loss-of studies ,20,21. Aevidence ,31,32. Trelapses . Overallrelapses . The hyprelapses . Multiclour data .CDKN2A/2B deletions were the most commonly encountered CNVs, seen in 13/20 (65%) cases. However, only 46% of these (6/13) were either shared or present only at diagnosis, while 54% (7/13) were seen exclusively at relapse. Furthermore, IKZF1 CNVs were seen in 25% of the cases (5/20) and 60% of these (3/5) were shared, which was similar to the findings of Kuiper et al. [IKZF1 CNVs in 23.5% of their cohort, of which 79% were shared.The r et al. , who notKRAS, NRAS, TP53, UHRF1 and CREBBP genes, followed by prospective testing of sequential samples (3-monthly) with a panel with additional NT5C2, PMS2, KMT2D, ETV6 and PAX5 genes will likely help to identify a significant proportion of cases with impending relapse, although this strategy might require dynamic modification based on prospective data emerging from the relapse biology in our setting.To conclude, our study highlights a high frequency of early relapses driven by TA clones, suggesting the need for the development of an active surveillance strategy to identify their clonal rise. Ultra-deep sequencing (>3000x) in all the newly diagnosed B-ALL cases using a custom NGS panel for the"} +{"text": "International Classification of Diseases, Tenth Revision (ICD-10) encounter coding is used to identify sub-optimal outpatient antibiotic use, but the utility of a popular billing data based metric, antibiotic prescribing rate (APR), for diagnoses which antibiotics are situationally indicated remain unexplored. We assessed the impact of different ICD-10 groupings on outpatient sinusitis APR to characterize its use.We included all adult telemedicine and office encounters from January 2021 to March 2022 with an acute or chronic sinusitis ICD-10 from two academic urgent care and eight academic primary care clinics. We calculated an APR by sinusitis ICD10 code, ICD10 group (acute vs. chronic) and clinic type (Table 1). We then reviewed 100 urgent and 182 randomly selected primary care sinusitis encounters conducted in 2021 to assess symptom documentation and guideline adherence (Table 2). This quality improvement project was deemed non-human subjects research.We included 987 sinusitis encounters of 821 unique patients with an overall APR of 56.5% (Table 3). The APR for acute sinusitis encounters was higher than chronic (72.7% vs 22.0%), with a larger difference in primary care (65.5% vs 10.4%) compared to urgent care (76.9% vs 54.2%). Upon chart review, 42.3% (77/182) of primary care sinusitis encounters had no active symptoms (60/77) or did not address sinusitis (17/77); the majority used chronic sinusitis ICD-10s (66/77) (Table 4). Antibiotic prescriptions were guideline adherent for 32.8% of primary care (23/70) compared to 58.0% (40/69) of urgent care encounters .Combining acute and chronic sinusitis ICD10 codes yielded lower APR than acute sinusitis ICD10s alone, predominately in primary care, suggesting a dilution effect. Compared to urgent care, lack of documentation of active symptoms for chronic sinusitis encounters was common in primary care, hindering the assessment of antibiotic appropriateness. Until there is improved ICD10 utilization with methods to control for \u2018carryover\u2019 ICD-10s in primary care, acute and chronic sinusitis ICD-10 categories should likely be analyzed separately to increase the usefulness of sinusitis APR as a metric.All Authors: No reported disclosures"} +{"text": "Acinetobacter baumannii (AB) is a significant human pathogen that is frequently antibiotic resistant and has been associated with post-COVID-19 infections.In this study, we performed whole-genome sequencing on AB isolates collected at an academic medical center in Dallas, TX between January 2020 and June 2021. We extracted clinical and laboratory data and analyzed both outcomes and molecular epidemiology of AB isolates in patients with and without COVID-19.Nineteen isolates collected from 17 AB-infected patients were included in this study. Most isolates were cultured from the respiratory tract (58%), followed by urine (16%), blood (10.5%), wound (10.5%), and catheter tips (5%). 4/17 patients were COVID-19 positive. The average Charlson Comorbidity Index at admission was lower for patients with COVID-19 (2.75) compared to counterparts (4.46). Using Fisher\u2019s exact test, no statistical significance was observed in hospital events: ICU Admission (0.08), Ventilation (1.0), and Sepsis (0.23). The mortality rate during admission was 50% for COVID-19 patients and 23% for patients without COVID-19 . All 19 isolates were carbapenem-resistant (CRAB) and multi-drug resistant (MDR) per definitions established by Magiarkos et al. 67% of isolates from COVID-19 patients were extensively-drug resistant (XDR) compared to 33% of isolates from non-COVID-19 patients. MIC data for cefiderocol was available for 9/19 isolates. Values ranged from 0.5 \u2013 16 \u03bcM with 4/9 isolates being < 4 \u03bcM. Meropenem MIC values for all isolates were \u2265 64 \u03bcM. Many isolates contained at least one carbapenemase: OXA-72 (15/19), OXA-23 (3/19), OXA-95 (3/19), OXA-24 (1/19). MLST analysis revealed ST2 as the most common in all patients (15/19), followed by ST499 (3/19) and ST406 (1/19).COVID-19 patients infected with AB trended towards a significant difference in mortality compared to AB patients without documented COVID-19 during the same period. All AB isolates were CRAB, and isolates from COVID-19 patients were more likely to be XDR.David E. Greenberg, MD, University of Texas Southwestern Medical Center: Dr. Greenberg has numerous patents on PPMOs"} +{"text": "The gastrointestinal tract (GIT) is a reservoir of antibiotic resistant organisms (ARO). ARO colonisation precedes infections which are more challenging to treat than if drug susceptible, with excess morbidity and mortality. Presently, no effective GI decolonisation strategy exists. Faecal microbiota transplant (FMT) has emerged as a potential therapeutic. However, there is uncertainty about feasibility, safety and effectiveness.Population: Patients with history of invasive infection with extended spectrum beta-lactamase (ESBL) or carbapenemase producing Enterobacterales (CPE) and evidence of persistent GIT ARO carriage (assessed by culture)3 doses of encapsulated lyophilised FMT each manufactured from 80g raw stool given on consecutive daysMatched placebo capsulesPrimary outcome - participant consent rate (as proportion of those approached screened for GIT carriage of ESBL-E/CPE). Secondary outcomes \u2013 safety and efficacy metrics including adverse event (AE) rates and GIT ARO carriage rates at 1 week, 1, 3 and 6 months. Exploratory outcomes \u2013 metagenomic and metabolomic stool analyses.Of 460 approached individuals, 124 (27%) consented. 53/124 participants (43%) fulfilled eligibility criteria. 44/53 (83%) randomised and 41/44 (93%) received investigational medicinal product (IMP): 20 FMT and 21 placebo. 39/41 (95%) completed dosing, 18/20 (90%) FMT (1 investigator and 1 participant discontinuation) and 21/21 (100%) placebo. Overall, GIT AE including reflux, bloating, change in bowel habit, were more common in FMT arm. 6 serious AE in 5 participants occurred in FMT arm, compared to 1 in placebo ; none were deemed attributable to FMT. No unanticipated harms from FMT administration were realised. GIT ARO carriage rate assessed in 38/41 (93%) IMP recipients providing stool for analysis at 1-month was lower in FMT compared to placebo - FMT: 13/18 (72%) vs. placebo: 17/20 (85%), p=0.34.FERARO trial consort diagramESBL/CPE detection rateDetected by culture over timeBased on a priori assessment, a substantive trial would be feasible with protocol modifications. Encapsulated FMT appears safe intervention for eradication of GIT ARO carriage. Our feasibility trial informs design, and provides evidence to conduct future efficacy randomised controlled trials.David Moyes, PhD, MSc, BSc, Pfizer: Grant/Research Support Simon D. Goldenberg, FRCPath, MD (Res), PGDipID, DipHIC, MSc, EnteroBiotix: Honoraria|Tillotts Pharma UK: Honoraria"} +{"text": "GATA1 mutations and has a favorable prognosis. In contrast, AMKL in children without DS is often associated with recurrent and mutually exclusive chimeric fusion genes and has an unfavorable prognosis. This review mainly summarizes the unique features of pediatric non-DS AMKL and highlights the development of novel therapies for high-risk patients. Due to the rarity of pediatric AMKL, large-scale multi-center studies are needed to progress molecular characterization of this disease. Better disease models are also required to test leukemogenic mechanisms and emerging therapies.Acute megakaryoblastic leukemia (AMKL) is a rare subtype of acute myeloid leukemia (AML) in which leukemic blasts have megakaryocytic features. AMKL makes up 4%\u201315% of newly diagnosed pediatric AML, typically affecting young children (less than 2\u00a0years old). AMKL associated with Down syndrome (DS) shows KMT2A (lysine methyltransferase 2A) and NUP98 (nucleoporin 98) rearrangements now form independent subgroups of AML with defining genetic abnormalities , and cases with CBFA2T3 ::GLIS2 (GLIS family zinc finger 2) and RBM15 (RNA binding motif protein 15)::MKL1 (megakaryoblastic leukemia 1) fusions belong to a subgroup of AML with other defined genetic alterations. Other cases of AMKL lacking defined genetic alterations remain defined by differentiation, which requires blasts to express at least one of the platelet glycoproteins: CD41 (glycoprotein IIb), CD61 (glycoprotein IIIa), or CD42b (glycoprotein Ib). Myeloid proliferations associated with DS form a subtype of myeloid neoplasms associated with germline predisposition (Acute megakaryoblastic leukemia (AMKL) is a rare but life-threatening hematological malignancy characterized by clonal megakaryoblastic proliferation and impaired differentiation of these cells. AMKL was first described in 1931 and included in the French-American-British (FAB) classification as acute myeloid leukemia (AML) the M7 subtype . In the position .GATA1 (GATA Binding Protein 1) mutations, and a range of other somatic mutations, in particular those affecting cohesin molecules, signaling pathways, epigenetic regulators, and hematopoietic transcription factors , RBM15::MKL1, and HOX (homeobox) gene rearrangements , KMT2A rearrangements (KMT2Ar) (7%\u201317%), NUP98::KDM5A (11%\u201312%), RBM15::MKL1 (10%\u201311%), and HOX rearrangements (HOXr) (14%\u201315%) ::FLI1 (friend leukemia integration 1 transcription factor), BCR (breakpoint cluster region protein):ABL1 , and MAP2K2 (mitogen-activated protein kinase 2)::MLLT10 (myeloid/lymphoid or mixed-lineage leukemia translocated to 10) is a highly molecularly heterogeneous disease characterized by recurrent and mutually exclusive genetic aberrations, including 14%\u201315%) (de Rooi14%\u201315%) . A furthd to 10) . Moleculcurrence . Thus, icurrence . In contotherapy . This reotherapy , 2. OngoCBFA2T3::GLIS2 fusion) is the most frequently, but not exclusively detected in 18%\u201327% of pediatric non-DS AMKL (CBFA2T3::GLIS2 is not specific to AMKL and occurs in diverse morphologic subtypes of de novo AML (except for acute promyelocytic leukemia (APL) and leukemia with erythroid differentiation), overall found in approximately 8.4% of cytogenetically normal AML cases :RHEBL1 (Ras homologue enriched in brain like 1) fusion tend to be younger (median age of onset \u223c1.5 years) and display distinct clinical and laboratory features, including stronger expression of CD56 and a more frequent extramedullary involvement compared to other AML , CD38, and CD45 referred to as the RAM immunophenotype (p13.3q24.3) (generating the -DS AMKL (de Rooi-DS AMKL . A newer-DS AMKL . CBFA2T3ML cases . The inv cohorts . CBFA2T314%\u201340%) . Among C) fusion . The co-S2 alone . Childrether AML . Standarhenotype . The somubgroups . Howeverubgroups . CBFA2T3diploidy .CBFA2T3::GLIS2 fuses the 5\u2032 portion of CBFA2T3 in frame with the 3\u2019 region of GLIS2. The majority of chimeric CBFA2T3::GLIS2 fusions (80%) are between exon 11 of CBFA2T3 and exon 3 of GLIS2. Other rare fusion transcripts have also been reported, including between exons 9, 10 or 12 of CBFA2T3 and exons 2 or 3 of GLIS2 complex. CBFA2T3 belongs to the eight-twenty-one (ETO) family of chromatin-associated proteins, functioning as a master transcriptional coregulator and a Wnt (wingless/integrated) and Notch (neurogenic locus notch homolog protein) signaling suppressor in normal and malignant hematopoiesis . CBFA2T3turation ; whilst ntiation .GLIS2 in murine LSK (Lin-SCA1+c-KIT+) cells reduces HSC repopulation, suggesting GLIS2 could regulate HSC engraftment and hematopoietic reconstitution (GLIS2 overexpression in MOZ (monocytic leukemia zinc finger protein):TIF2 leukemic cells promotes their differentiation into mature myeloid cells and delays AML development in mice, indicating that GLIS2 inhibits AML initiation by inducing LSC differentiation upregulation, and activation of super enhancer elements may impair megakaryocytic differentiation and increase abnormal self-renewal of leukemic cells in AMKL associated with CBFA2T3::GLIS2 involved in leukemic progression , GABRE (gamma-aminobutyric acid type A receptor subunit epsilon), miR-224 and miR-452 may be responsible for the reduction in expression of apoptotic and tumor suppressor genes, and simultaneous downregulation of tumor suppressive miRNAs (CBFA2T3::GLIS2 is not well defined. Overexpression of miR-181b-5p downregulates apoptotic genes CASP1 (caspase 1) and TRAIL-R2 (TNF-related apoptosis-inducing ligand receptor 2), and the circadian rhythm gene PER2 (period circadian regulator 2), while loss of miR-196b is associated with ITGA2 and DNMT3B (DNA methyltransferase 3 beta) overexpression and signaling pathways , bone morphogenetic proteins (BMP), JAK/STAT and Hedgehog) (CBFA2T3::GLIS2 leukemia.Although the molecular bases for AMKL transformation by ustrated . CBFA2T3 pattern . GATA1 d3::GLIS2 . Super e3::GLIS2 . Ectopicgression . CBFA2T3 miR-452 . Both mi-199a/b) . The rolpression . When his in AML . CBFA2T3edgehog) . OverallCBFA2T3::GLIS2, this fusion probably is the primary genomic alteration. However, the evidence is mixed on whether CBFA2T3::GLIS2 alone is sufficient for leukemic transformation. On the one hand, the introduction of CBFA2T3::GLIS2 into murine bone marrow is insufficient to induce overt leukemia in mice and leads to highly aggressive leukemia in mice . Despite the use of intensive chemotherapy and HSCT, the outcomes of CBFA2T3::GLIS2 leukemia are poor. The mechanism of leukemogenesis associated with CBFA2T3::GLIS2 remains incompletely understood. Therefore, further mechanistic studies are required to inform the development of novel therapies.In summary, cytogenetically cryptic KMT2A gene located at 11q23.3 are found in both acute lymphoblastic leukemia (ALL) and AML, making up \u223c10% of all leukemia cases in all age groups (KMT2A rearrangements (KMT2Ar) are one of the most common recurrent genetic aberrations found in 15%\u201325% of all newly diagnosed cases of pediatric AML and are much less common in other subtypes , AFF1 , MLLT3 , MLLT6, MLLT9, MLLT10 , and SEPT9 (septin 9) (generating KMT2A::MLLT3 fusion) and t (generating KMT2A::MLLT10 fusion) and is more common in males, although these differences were not statistically significant in the study by de Rooij et al. , KRAS , PTPN11 (tyrosine-protein phosphatase non-receptor type 11), NF1 (neurofibromatosis type 1), EPOR (erythropoietin receptor), MPL (thrombopoietin receptor), JAK1/2/3, PIK3C2A , KIT, cohesin and epigenetic regulators, e.g., STAG3 , SETD2 , IDH1 (isocitrate dehydrogenase 1), CREBBP (cyclic adenosine monophosphate response element binding protein binding protein), transcription factors, e.g., GATA1, RNA splicing and regulatory proteins, e.g., U2AF1 and DDX3X (DEAD-Box helicase 3 X-linked) . Numeroueptin 9) . The two fusion) . Translo fusion) . In the fusion) . The prosurvival . KMT2Ar j et al. . Pediatrtype AML . However-linked) . KMT2Ar rognosis . Severalaryotype . The cliKMT2Ar predominantly consists of the N-terminal DNA-interacting domains of KMT2A (residues 1\u2013\u223c1400) fused in frame with one of over 100 fusion partners , SIX1 (SIX homeobox 1) and SIX4 (SIX homeobox 4), highlighting that the transforming capacity of KMT2A fusion may not be limited to HOXA/MEIS1 genes methyltransferase that serves as a master controller for the transcription of critical genes implicated in normal embryonic development and hematopoiesis . KMT2A ipartners was initially identified in pediatric AMKL in 2006 (NUP98::KDM5A fuses NUP98 located on chromosome 11p15 with KDM5A located on the telomeric end of chromosome 12p13.3 (NUP98::KDM5A AML patients have a median age at diagnosis of 3.2 years (ranging from 3 weeks to 18.5\u00a0years) (resulting in in 2006 . NUP98:: 12p13.3 . The fus 12p13.3 . NUP98::5\u00a0years) . NUP98::se cases . The med2 years) . NUP98:: relapse . Additioaryotype .NUP98 has many different partner genes (over 30) to produce a series of abnormal fusion proteins in several hematopoietic malignancies (KDM5A is the most common fusion partner of NUP98 in AML and AMKL (NSD1 (nuclear receptor) is the second most common locus frequently associates with NUP98::KDM5A , and GATA1 mutations were present in 2 of 9 NUP98::KDM5A patients with the RB1 loss , and HOXB genes compared with RBM::MKL1 and CBFA2T3::GLIS2 fusions ::NUP214 (nucleoporin 214), and NPM1 (nucleophosmin 1) mutated cases, suggesting HOXA and HOXB overexpression is a common alteration in leukemia development (NUP98::KDM5A and NUP98::NSD1 AML show upregulation of targets of E2F (E2F transcription factor 1) and FLT3, and downregulation of targets of TP53 and HDAC . KDM5A iand AMKL , and NSDt common . NUP98::t common . NUP98::ower WCC . Additio8::KDM5A . In contRB1 loss . Leukemi fusions . Intriguelopment . Additioand HDAC . The uprD1 cases .NUP98::KDM5A is undetectable with conventional karyotyping, whereas newly developed next-generation sequencing (NGS) technologies can detect it into and out of the nucleus . NUP98 aKDM5A overexpression in leukemia associates with a poor prognosis , and epigenetic activation of the HOXA gene cluster , MPIG6B (megakaryocyte and platelet inhibitory receptor G6b), and NEO1 (neogenin) as novel disease biomarkers gene, also named as OTT (one twenty-two) located on chromosome 1p13 to the MKL1 (megakaryoblastic leukemia-1) gene, also named as MAL (megakaryocytic acute leukemia) or MRTFA (myocardin-related transcription factor A) located on chromosome 22q13 results in a fusion of the me 22q13 . Althougme 22q13 , it is ame 22q13 . The t, has two isoforms consisting of two or three N-terminal RPEL-repeats, basic regions, a glutamine-rich domain, a SAP domain , a leucine zipper-like domain, and a TAD domain Scharen. MKL1 reryocytes . The abiy of SRF .RBM15::MKL1 causes abnormal megakaryopoiesis during embryonic and adult development but rarely generates AMKL and ITGB1, and several components of Notch signaling with AMKL. RBM15::MKL1 possesses the function of both RBM15 and MKL1 proteins, including constitutive activation of RBPJ, MKL1-and SRF- dependent target genes. By itself, RBM15::MKL1 appears insufficient to drive AMKL. However, with a MPL mutation, RBM15::MKL1 causes rapid transformation to AMKL. It remains to be determined how RBM15::MKL1 alters megakaryopoiesis and the mechanism through which cooperating mutations drive leukemogenesis.In summary, HOX rearrangements (HOXr) are seen in 14.9% of pediatric non-DS AMKL and associate with better outcomes than the aforementioned molecular subgroups ::HOXA9, NIPBL::HOXB9, GATA2::HOXA10, EWSR1 (Ewing Sarcoma breakpoint region 1)::HOXB8, PLEK (pleckstrin)::HOXA11AS (HOXA11 antisense RNA), BMP2K (BMP-2-inducible protein kinase)::HOXD10, EP300::HOXA7, C8orf76 ::HOXA11AS, HOXA11::BZW2 (basic leucine zipper and W2 domains 2), HOXA9::ANGPT1 (angiopoietin 1) and HOXA10AS::CD164 , STAG2, CTCF (CCCTC-binding factor), and other genes , ATM (ataxia-telangiesctasia mutated), SMARCA2 , NSD1, and TP53) . The med5::MKL1) . There atein 24) (de Rooitein 24) . HOXr caOX genes . As high-DS AMKL . Multiplnd TP53) . HOXr AM n = 12) . Murine nd STAT5 . Additioaryotype . Given tHOX genes are found, situated in clusters on four chromosomes drives AML by deregulating expression of MEIS1, HOXA9, and PBX3, arresting differentiation and inducing long-term proliferation of human HSCs . HOX genand HOXD . Except and HOXD . For exaand HOXD . HOXA9 ioutcomes . A recurman HSCs . Neverth in mice . Both fu in mice . HOXr ar-DS AMKL . HoweverMN1::FLI1, GRB10 (growth factor receptor bound protein 10)::SDK1 (sidekick cell adhesion molecule 1), BCR::ABL1 and MAP2K2::AF10 and STAG2::LINCO1285) are detected in 3.5% of non-DS AMKL, and all are predicted to induce a truncated STAG2 protein act as critical players in megakaryopoiesis have inferior outcomes, mostly because of the primary refractoriness to chemotherapy and/or early relapse and primary leukemic cells from patients are more sensitive to GANT61 than fusion-negative cells . NeverthHOX gene cluster, including the leukemogenic HOXA9 and its co-factor MEIS1 in myeloid stem and progenitor cells . Leukemicluster) . VTP5046ed cells . These ftigation . For exa . The dru trials) . It was trials) .CBFA2T3::GLIS2 is associated with higher expression of CD56 and FOLR1, and activation of super enhancers, which provides highly plausible therapeutic targets and the myeloid cell lymphoma-1 (MCL1) protein (using S63845) inhibits the proliferation of CBFA2T3::GLIS2 cells in vitro and abrogates leukemia progression in mouse xenografts and JAK inhibitors (ruxolitinib and tofacitinib) (KMT2Ar (In egulated . Studiescitinib) . A combi inhibitors (selumetinib and MEK162) have been proposed as potential options for utations . RAS mut2Ar AMKL ; thus in2Ar AMKL . Foretinrrations .KMT2Ar AML are considered an intermediate risk, except for DS-like AMKL that has an excellent prognosis. Different subgroups of AMKL share similarities and differences in gene and transcript changes, which offer new therapeutic targets. Novel drugs that interfere with driver fusions, downstream molecules, and cooperating alterations are being developed for these patients.Pediatric non-DS AMKL is a rare, heterogeneous entity characterized by mostly poor outcomes, in contrast to excellent outcomes seen in ML-DS. Assisted by advanced genomic characterization, pediatric non-DS AMKL has been divided into distinct molecular subtypes. In the latest 2022 WHO and ICC classifications, cases with Progress in understanding AMKL pathogenesis has been immense in the last decade, but many challenges persist. We still need to improve our knowledge of this disease\u2019s genetic and molecular landscape. Leukemogenic drivers are unknown in approximately 15% of non-DS AMKL, and the role of many known genetic alterations and cooperating events is unclear. Further progress in these areas will be critical to enable better insights into AMKL pathogenesis and improve patient outcomes."} +{"text": "Sexual health clinics, vital to the 2022 mpox outbreak response, were challenged by high patient volumes and delayed access to vaccines and tecovirimat. We describe the Public Health - Seattle King County Sexual Health Clinic (SHC) response, including vaccine and tecovirimat distribution, from 5/23/22 (first case in King County) to 10/14/22.SHC began vaccinations in clinic on 7/4/22 and implemented a mass vaccination clinic on 7/25/22. Tecovirimat prescriptions initially required positive test results; by 7/29/22 SHC offered same-day presumptive treatment based on clinical suspicion. We calculated vaccines administered per week, proportion of visits related to mpox evaluation, and collected and summarized demographic and clinical data for diagnosed mpox cases. We assessed temporal trends in treatment type (presumptive vs results-based) using Kruskal-Wallis testing and differences in treatment receipt by race/ethnicity using chi-square testing (p< 0.05).From 5/23/22 to 10/14/22, SHC provided \u22651 vaccine dose to 9,753 people; the highest number within a week were provided the week of 8/1/22 . Of 4,845 clinic visits, 486 (10%) patients were evaluated and tested for mpox; 174 (36%) were positive, comprising 36% of cases in King County at the time. 94% were cisgender men; 57% were White. 74 (43%) had severe symptoms including proctitis, hematochezia, or need for adjunctive pain control. Of 172 patients with complete clinical data, 154 (90%) received tecovirimat, including 83 (54%) treated presumptively. Provision of presumptive treatment increased significantly over time (P< 0.001) . Treatment receipt did not differ significantly by race/ethnicity (P=0.4).The SHC substantially expanded vaccine access, served over 1/3 of patients with mpox in King County, and expedited mpox treatment through presumptive therapy, while continuing general sexual health services for patients within the county.Chase Cannon, MD MPH, Roche Diagnostics: Advisor/Consultant Julia C. Dombrowski, MD, MPH, Hologic: Grant/Research Support|Mayne Pharmaceuticals: Grant/Research Support"} +{"text": "Correction: Cellular and Molecular Life Sciences (2023) 80:214 10.1007/s00018-023-04851-3In the original published article, the ESM files was missed during acceptance and was unnoticed in the subsequent stages. The ESM as follows.Supplementary file1 (DOCX 3459 kb)Supplementary file2 (MP4 1635 kb)Supplementary file3 (MP4 1570 kb)Supplementary file4 (MP4 1549 kb)Supplementary file5 (MP4 1662 kb)Below is the link to the electronic supplementary material."} +{"text": "Early detection and appropriate treatment of newborn sepsis reduce mortality and morbidity. A rapid, inexpensive laboratory approach is needed to assess newborn sepsis, even though blood culture is the gold standard for diagnosis. To compare serial CRP andTotal Leukocyte Count (WBC) with blood culture, this study aimed to evaluate the role of newborn sepsis. A total 148 neonates with clinical symptoms of sepsis were included .CRP was measured by quantitative immuno turbidimetric method andotal leukocyte count(WBC) was measured by automated cell counter. CRP1 and WBC1 were measured within 6 hours of clinical symptoms. CRP2 and WBC2 were measured after 48 hours of clinical symptoms. Sensitivity, specificity, PPV, NPV of CRP1 and CRP2,WBC 1and WBC 2 were compared withculture positive and negative sepsis.CRP 2 showed high sensitivity 96% and high NPV95% with significant p value <0.0001. WBC2 has high sensitivity (90.57%) and NPV (91%) with significant p value <0.0001. CRP 1 has sensitivity 83%and NPV 82.3%, with p value< 0.001.WBC1 has lowest sensitivity (62.2%) and NPV (71.4%) compared to all other parameters. Serial CRP and WBC measurements are useful in the diagnosis of neonatal sepsis. Measurement of CRP and Total Leukocyte Count (WBC) after 48 hours of clinicalsymptoms were considered promptly for diagnose neonatal sepsis. Within the first four weeks of life, newborns can develop neonatal sepsis, a systemic infection . The leaThis cross-sectional study was carried out at the Government Stanley Medical College and Hospital, Neonatal Intensive Care Unit (NICU), Department of Pediatrics, Department of Biochemistry and RSRM. The institutional ethical committee's clearance wasobtained. The study involved 148 newborns admitted to the NICU with sepsis-related clinical signs. The neonates were included in the study after parents or guardians gave informed consent based on the inclusion and exclusion criteria listed below. All newbornsadmitted to the NICU with a clinical suspicion of neonatal sepsis in accordance with WHO integrated criteria were included Culture-proven sepsis is defined as sepsis with culture-positive results and sepsis-related clinical signs.[2] Sepsis with culture-negative results and clinical signs of the disease (probable sepsis)Sensitivity, specificity, PPV, NPV of CRP 1&2 and WBC 1&2 compared with gold standard test (blood culture)This study examined 148 newborns who had sepsis-related clinical signs. In all infants exhibiting clinical signs of sepsis, CRP 1, CRP 2, Total Leukocyte count 1 (WBC1), Total Leukocyte count 2 (WBC2), and blood culture were conducted. The total leukocytecount, WBC (1&2), blood culture, and CRP (1&2) findings were entered into excel sheets, and SPSS 16 software was used to conduct the statistical analysis. The Chi-square test is one of the statistical tests used for comparison. A p-value of 0.05 wasconsidered significant. In addition to CRP1, CRP2, and WBC1 & WBC2, sensitivity, specificity, PPV, and NPV calculations were made.Out of 148 neonates with clinical symptoms of sepsis, 97 (65.54%) neonates had CRP 1 that was positive (>5mg/L), while 51 (34.45%) of those same neonates had negative CRP (5mg/L). Fifty-three positive blood cultures were found. Out of 95 infants withnegative blood cultures, 44 (83%) had positive CRP1, and 53 (55.7%) had positive CRP1. As a result, the correlation between CRP1 and the blood culture results was statistically significant .Out of 148 newborns with clinical signs of sepsis, 108 (72.9%) had positive CRP 2 results (>5mg/L), while 40 (27.0%) had negative CRP 2 results (5mg/L). One hundred forty-eight neonates had sepsis-related clinical signs. CRP 2 was positive in 51 (96.2%)of the 53 infants with positive blood cultures and 57 (60%) of the 95 neonates with negative blood cultures. As a result, the relationship between CRP2 and the blood culture results was statistically significant .Out of 148 infants with clinical signs of sepsis, total leukocyte count 1 (WBC1) was positive (5000/L or >15000 L) in 78 (52.7%) neonates and normal (5000-15000 L) in 70 (47.3%) neonates. WBC1 was positive in 33 (62%) of the 53 neonates with sepsis withpositive blood cultures. WBC was positive in 45 (47%) of the 95 newborns with sepsis who had negative blood cultures. With a p-value of 0.1, the test result was not statistically significant. Out of 148 neonates with clinical signs of sepsis, 89 (or 60%) had WBC2 that was positive (5000\u201315000 L), and 59 (or 40%) had it normal? WBC2 was positive in 48 (90 percent) of the 53 newborns with positive blood cultures for sepsis. Out of 95 neonates with negative blood cultures, 41 (43%) had positive WBC2 results. With ap-value of 0.0001, this test result was statistically significant.Table 1(see PDF) displays the baseline characteristics of the study population. It shows 148 neonates with clinical signs & symptoms of sepsis were included in this study, out of 148 neonates with clinical signs & symptoms of sepsis 90(60.8%) were male and 58(39.2%) were female. 85 (57.44%)were delivered through assisted deliveries, and 63(42.5%) were delivered through vaginal route. Based on maturity 81(54.7%) were pre term babies, 67 (45.2%) were term babies. Regarding birth weight 76(51.3%) were Low birth weight(LBW), 72 (48.6%) were normal weight.53 (35.8%) were blood culture positive, 95 (64.1%) was negative on blood culture.Table 2(see PDF) explains percentage of male neonates preterm babies LBW babies were high in culture proven sepsis compared with culturenegative sepsis which was statistically significant p vale <0.05. Table 3(see PDF) describes percentage of microorganism found in blood culture Acinetobacter was the most common organism isolated followed by Klebsiella and Coagulus negative Staphylococcusaureus, Staphlococcus aureus and Enterobacter, Pseudomonas, E. coli and Citrobacter were less commonly present. Table 4(see PDF) shows comparison of CRP1,CRP2 ,TOTAL LEUCOCYTE COUNT (WBC) 1&2 with Gold standard blood culture. Table 5(see PDF) shows CRP2 has highestsensitivity 96% and NPV 95%, next toCRP2, Total Leukocyte Count 2(wbc2) has high sensitivity 90.57%, NPV 91% .CRP1 has83% sensitivity and NPV 82.3%. WBC1 has lowest sensitivity 62.2%, NPV 71.4%.The current study included 148 neonates brought to the neonatal critical care unit with clinical signs of sepsis. Ninety newborns (60.8 percent) were male, and 58 (39.2 percent) were female of the 148 neonates. Ninety-five neonates 65.18%) and 53 (35.18%)neonates, respectively, have sepsis that has been confirmed by culture. Fifty-three neonates with positive blood cultures were divided into 45 (84 percent) males and 8 (16 percent) females. It might be because males have an X-linked immune-regulatory genecomponent that makes them more susceptible to infections . 33 . Serial measurement of CRP and Total leukocyte count (WBC) neonates with clinicalsymptoms can be considered promptly for diagnosis of neonatal sepsis would be rather than single measurement."} +{"text": "Staphylococcus aureus causes staphylococcal food poisoning and several difficult-to-treat infections. The occurrence and dissemination of methicillin-resistance S. aureus (MRSA) in Nigeria is crucial and well documented in hospitals. However, findings on MRSA from meat in the country are yet to be adequately reported. The current study determined the prevalence, virulence profile and antibiogram characteristics of MRSA from a raw chicken product from retail outlets within Edo.A total of 368 poultry meat samples were assessed for MRSA using a standard culture-based approach and characterized further using a molecular method. The antimicrobial susceptibility profile of the isolates was determined using the disc diffusion method. The biofilm profile of the isolates was assayed via the crystal violet microtitre-plate method. Virulence and antimicrobial resistance genes were screened using polymerase chain reaction via specific primers.mecA), tetracycline resistance genes , erythromycin resistance genes , trimethoprim resistance gene (dfrK). All the staphylococcal cassette chromosome mec (SCCmec) IVa and SCCmec V positive isolates harboured the Panton-Valentine Leukocidin Gene (PVL).Of the samples tested, 110 (29.9%) were positive for MRSA. All the isolates were positive for deoxyribonuclease (DNase), coagulase and beta-hemolysis production. Biofilm profile revealed 27 (24.55%) weak biofilm formers, 18 (16.36%) moderate biofilm formers, and 39 (35.45%) strong biofilm formers. The isolates harboured 2 and \u226417 virulence genes. Enterotoxin gene profiling revealed that 100 (90.9%) isolates harboured one or more genes. Resistance against the tested antibiotics followed the order: tetracycline 64(58.2%), ciprofloxacin 71(64.6%), trimethoprim 71(64.6%) and rifampin 103(93.6%). A total of 89 isolates were multidrug-resistant, while 3 isolates were resistant to all 22 antibiotics tested. The isolates harboured antimicrobial-resistant determinants such as methicillin-resistant gene (S. aureus was resistant to commonly used antibiotics; a concern to public health concerning the transmission of these pathogens after consuming these highlight the significance of antimicrobial and enterotoxigenic monitoring of S. aureus in food chains.In conclusion, Differences exist in the SCCmec types of S aureus strains, which may increase by independently acquiring the mec gene. Furthermore, HA-MRSA, livestock-associated MRSA (LA-MRSA), and CA-MRSA can contaminate human foods, causing cases of staphylococcal food poisoning (SFP) . S. aurerecently .S. aureus, which may persist in foodstuffs after heat decimation of the bacteria, thus causing SFP is associated with emetic activity, sepsis-related infections, pneumonia, and toxic shock syndrome (TSS) . Upon cosing SFP . Staphylsing SFP . The SE- factors .S. aureus strains at high cell densities under optimal temperatures and environmental conditions operon-encoded polysaccharide adhesion molecules ; P = prevalence expected based on previous studies , New Benin (n=32) , Oba (n=32) , Santana (n=30) , Aduwawa (n=32) , Uselu (n=31) , Ileha (n=30) , Ekiosa (n=31) , Oka (n=30) , Egor (n=30) , Oregbeni (n=30) , and Ugbor (n=30) markets. The sampling was conducted from June 2018 to April 2019. Seasonal durations in Nigeria include a wet season characterized by heavy rainfall with a temperature reaching 35 \u00b1 2\u00b0C (March to September) and a dry season characterized by low to no rainfall with a temperature reaching 39 \u00b1 2\u00b0C (November to February). A total of 368 frozen fresh chicken meat samples were collected. In all cases, 50\u00a0g of samples were collected into a plastic tube from retail outlets within Benin City and transported on ice to the laboratory .N = Number of expected samples; Zes , chloramphenicol , erythromycins , tetracyclines and beta-lactamase (BlaZ); and virulence genes such as intercellular adhesion protein , toxic shock syndrome toxin 1 (tsst-1), exfoliative toxin , enterotoxins (sea to seu), haemolysins , Panton-Valentine Leucocidin (PVL), staphylococci protein A (spa), and coagulase (coa) were amplified as described previously (mec I to V and subtype SCCmec (IVa to d) of the MRSA isolates was carried out using PCR as described previously (The genomic DNA of the MRSA isolates and positive primers by targeeviously . SCCmec eviously using sp2.5The antibiogram profiling of the MRSA isolates was conducted using the Kirby-Bauer disc diffusion procedure. Antibiotics used includes Penicillin G (10 units), ceftaroline (30\u00b5g), gentamicin (10\u00b5g), amikacin (30\u00b5g), kanamycin (30\u00b5g), azithromycin (15\u00b5g), clarithromycin (15\u00b5g), erythromycin (15\u00b5g), doxycycline (30\u00b5g), minocycline (30\u00b5g), tetracycline (30\u00b5g), ciprofloxacin (5\u00b5g), levofloxacin (5\u00b5g), moxifloxacin (5\u00b5g), nitrofurantoin (300\u00b5g), clindamycin (2\u00b5g), trimethoprim-sulfamethoxazole (1.25/23.75\u00b5g), trimethoprim (5\u00b5g), chloramphenicol (30\u00b5g), sulfonamides (300\u00b5g), linezolid (30\u00b5g) and rifampin (5\u00b5g). The interpretation of the zone of inhibitions of the isolates as resistance, intermediate, or susceptibility was based on the Clinical and Laboratory Standard Institute\u2019s interpretative chart to deter2.6S. aureus ATCC 12600, respectively. Each assay was done in independent biological triplicate. Biofilm-producing ability of the isolates was defined as non-producing/negative (ODi< ODc), weak/poor-producing (ODc< ODi<0.1), moderate/intermediate-producing (ODi \u00bc 0.1< 0.12), or strong producer (ODi>0.12) as described somewhere else (Biofilm formation assay was carried out by suspending pure MRSA colonies in 4.5 mL tryptone soy broth (TSB) and incubating for 18\u00a0h at 37\u00b0C. After that, the cells were harvested at 12,000 rpm for 2\u00a0min., washed, re-suspended in phosphate-buffered solution at pH 7.2), and adjusted to 0.5 McFarland standards. A 20 mL of the suspended cell inoculant and 80 mL TSB were introduced into sterile 96-welled polystyrene microtitre plates to assess Staphylococci adherence onto a solid matrix/medium well-contained as described previously . The negere else .33.1via resistance (\u2264 21\u00a0mm zone diameter) to the cefoxitin disc test. As such, representative isolates from the 110 samples were carefully screened using the S. aureus specific primer (nuc gene), where a total of 110 isolates were detected were positive for MRSA detected Table\u00a01.3.2All MRSA isolates from this study were 100% positive for DNase, coagulase, and beta-hemolysis production Table\u00a01.3.3coa 110(100%), spa 98(89.1%), hla 110(100%), pvl 50(45.5%), hlb 23(20.95), sea 27(24.6%), seb 16(14.6%), sec 19(17.3%), sed 14(12.7%), see 13(11.8%), seg 39(35.5%), seh 13(11.8%), sei 11(10%), sej 32(29.1%), sek 4(3.6%), sel 4(3.6%), sep 20(18.2%), ser 13(11.8%), tsst 16(14.6%), etb 17(15.5%), eta 17(15.5%), icaA 45(40.9%), icaB 44(40%) formed biofilms phenotypically. All the isolates that possessed the hla and hlb genes were \u03b2-hemolytic phenotypically on blood agar. All the isolates in the study were coagulase positive via biochemical process and possessed the coa determinant. Enterotoxin gene (18 sea-seu genes) profiling of the isolates revealed that 90.9% (100/110) of the isolates were enterotoxigenic, harboring either one or more genes of the 13 genes that were positive. The chain of enterotoxin gene occurrence was seg>sej>sea>sep>sec>seb>sed> see,she,ser>sei>sek,sel. All the ica gene-carrying isolates were biofilm formers (hla+hlb 23(20.9%), eta+etb 17(15.5%), icaA+IcaB 37(33.6%), pvl+hla+hlb 23(20.9%), pvl+tsst-1 16(14.5%) (The occurrence of virulence genes screened in this study is as follows: 44(40%) Table\u00a01.3.4S. aureus in The resistance profile of the R+CPTR+GENR+AMIR+KANR+AZMR+CLRR+ERYR+DOXR+MINR+ TETR+CIPR+LVXR+MXFR+NITR+CLIR+SXTR+SSSR+TMPR+CHLR+LNZR+RIFR with a MAR index of 0.81.\u00a0A total of 57 resistance phenotypic patterns were observed amongst all the isolates studied isolates were multidrug resistant been resistant to \u22651 antibiotic in \u22653 antimicrobial classes. A total of 3 isolates were resistant to 22/27(81.5%) antibiotics used in this study. All isolates were resistant to \u2265 1 antibiotic, while 89(80.9%) isolates were resistant to \u2265 3 antibiotics Table\u00a02.mecA 91/110(82.7%), blaZ 91/110(82.7%), tetK 64/110(58.2%), tetL 23/110(20.9%), ermA 55/110(50%), ermB 9/110(8.2%), ermC 21/110(19.1%), aac(6\u00b4)-Ie-aph(2\u00b4\u00b4)-Ia 37/110(33.6%), ant(4\u00b4)-Ia 28/110(25.5%), aph(3\u00b4)-IIIa 26/110(23.6%), cat::pC194 20/110(18.2%), cat::pC221 12/110(10.9%), cat::pC223 12/110(10.9%), dfrD 64/110(58.2%), dfrK 22/110(20%), dfrG 38/110(34.5%) , tetK+tetL 23(20.9%), ermA+ermB 9(8.2%), ermA+ermB+ermC 3(2.7%), aac(6\u00b4)+ ant(4\u00b4)+aph(3\u00b4) 25(22.7%), aac(6\u00b4)+ant(4\u00b4) 30(27.3%), cat::pC194+cat::pC221+ cat::pC223 7(6.4%), cat::pC194+ cat::pC221 12(10.9%), dfrD+dfrK+dfrG 17(15.5%), dfrD+dfrK 22(20%), dfrD+dfrG 37(33.6%) (The antibiotic-resistant genes detected includes: 0(34.5%) Table\u00a03.SCCmec is as follows: SCCmec III 18(16.4%), SCCmec IVa 33(30%) and SCCmec V 17(15.5%) were not detected (SCCmec and pvl genes includes SCCmec IVa+pvl 33(30%) and SCCmec V+pvl 17(15.5%). All the SCCmec IVa and SCCmec V isolates also harbored the PVL gene, while all the SCCmec III isolates didn\u2019t harbor the PVL gene (The distribution of 7(15.5%) Table\u00a03.4S. aureus from poultry meat poses a public health risk that can transmit to humans via the handling or consumption of contaminated poultry meat. Lower prevalence rates than those of our study (ranging from 0 \u2013 27%) have been reported previously in North and South America, Europe, and Asia . Biofilm occurrence meant that the MRSA isolates have adhesive potentials to the host\u2019s extracellular matrix; these likely favor zoonotic potential, persistence, and colonization. Nigeria, where a significant proportion of the population is non-vegetarian, suggests that a large population is t risk of meat-borne hazards. icaA gene have been demonstrated previously were found by sea - seu) which aligns with other studies (etb and tsst-1 genes which were similar to our findings. tsst-1 gene detection (3.70%) compared to ours (14.6%). None of the MRSA isolates from previous studies , bacteriophages (sea), or pathogenicity islands (sec) , which eds (sec) . The occ origins .S. aureus strains from previous studies (S. aureus may become a virulent/pathogenic strain pathogen under favorable conditions (mecA gene from our study. Lower mecA gene occurrence (5.5%) of examined samples has been reported previously with phenotypic MRSA-positive isolates in Egypt (mecA gene occurrence (100%) from cefoxitin-resistant MRSA-positive isolates has been documented in Poland, Oklahoma, and China (mecA or mecC genes but were oxacillin-resistant (S. aureus isolates (5.07%) phenotypically resistant to oxacillin from India but genotypically lacking mecA gene carry virulence traits that encode and etb) . Therefonditions . A totalin Egypt . Higher nd China . Some isesistant . There hecA gene . Such a affinity .blaZ) was found among MRSA isolates in the current study in addition to mecA. Phenotypic resistance to gentamicin, tetracycline, and erythromycin was supported by detecting tetK, aphA3 and ermA/ermB/ermC. blaZ, mecA, aacA-aphD, ermB, ermC, tetK, tetL, and tetM) similar to the findings of our study. All the tested MRSA by dfrG gene (which confers resistance to trimethoprim) compared to our research. blaZ, mecA, tetK, linA, tetM, ermA, ermB, and aacA-D which was much higher than the 82.7% of the isolates from our study. The presence of the tetK and tetM genes similar to our finding explained the tetracycline resistance phenotype observed by A significant proportion of the \u03b2-lactamase-encoding gene (SCCmec typing from our study showed that few belonged to the human-associated (HA) clones\u2019 type SCCmec III, with the majority belonging to the CA-MRSA SCCmec IVa, similar to a previous study (SCCmecV also harbored the pvl gene identical to the SCCmecV+pvl variants by SCCmecV+pvl as the commonest MRSA isolate from meat samples (SCCmec elements of types IV and V are the commonly found SCCmec types in CA-MRSA (SCCmec types IVa and V have been documented in HA-MRSA in Nigeria (The us study . All MRS samples . SCCmec CA-MRSA . SCCmec Nigeria .5The MRSA recovered demonstrated MDR potential while harboring potent enterotoxin determinants and other virulence traits that could be detrimental to human health. The MRSA isolates also showed biofilm-forming capacity, which could make them more prone to antimicrobial resistance and persist on biotic and abiotic surfaces. The findings highlight the significance of surveillance studies and the need to continuously monitor the food chain for foods of animal origin for the occurrence and spread of MRSA superbugs. Our findings have revealed that raw chicken meat from Nigeria is the reservoir of MRSA. This study has also raised concerns about MRSA transmission after consuming contaminated chicken products. These findings could proactively assist industries and governments in Nigeria to improve food safety measures and enhance antimicrobial stewardship to curb the spread of critical antimicrobial-resistant pathogens.The original contributions presented in the study are included in the article/EI and AB, conceptualization. EI, AB, II, AGO, and TE, formal analysis. EI and AIO, funding acquisition. EI, AB, II, AGO, TE, and AIO, investigation. EI, AB, II, and AGO, methodology. EI, AB, II, and AIO, project administration. EI and AIO, resources. EI and AIO, supervision. EI, AB, and II, roles/writing - original draft. EI, AB, II, AGO, TE, and AIO, writing - review and editing. All authors have approved the final version of the manuscript for submission. All authors agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved."} +{"text": "Acinetobacter is a gram-negative bacterium that can cause several infections, particularly in hospitalized and immunocompromised patients. Invasive Acinetobacter infection in pediatrics can lead to significant morbidity and mortality. This study aims to investigate Acinetobacter bacteremia clinical characteristics and outcome in pediatric patients.Acinetobacter species from January 2015 to December 2022. Medical charts were reviewed for demographics, clinical data, and outcomes. IRB approval number (2231132).This is a retrospective study conducted in a tertiary-care center in Riyadh, Saudi Arabia, including pediatric patients (0-14 years) with a confirmed blood culture of one of the Acinetobacter bacteremia were identified. The median age was 10.5 [interquartile range (IQR): 2-48] months, and 25 (59.52%) were males. Over half of the episodes were hospital-acquired infections 26 (61.90%). The most reported subspecies were Acinetobacter calcoaceticus\u2013Acinetobacter baumannii complex 34 (81.13%), then Acinetobacter lwoffii 4 (9.52%). Polymicrobial infection was found in 15 patients (35.71%), most commonly Enterococcus faecalis 4 (26.67). The antimicrobial susceptibility showed that all isolates were susceptible to Colistin, and (68%) to Cefepime and Meropenem. Most of the patients were previously hospitalized 32 (76.19%), exposed to antimicrobial therapy 26 (61.90%), and underwent invasive procedures 23 (54.76%) one month prior to the bacteremia episode. The median duration of treatment was 15 days [IQR: 12-21]. Two patients (4.76%) had relapse (while on treatment), and two (4.76%) had recurrent infection. The overall 14-day crude mortality rate was (11.90%). Interestingly, non-survivors were significantly younger than survivors (median age: 2 [IQR: 1-2] vs. 18 [IQR: 3-48] months respectively.Forty-two pediatric patients with Acinetobacter spp. are important emerging nosocomial pathogens. Most of the mortalities were associated with younger age. Previous hospitalization, prior antimicrobial therapy, and invasive procedures were common features for mortality in this study. Further multi-centers studies might be needed to investigate the mortality related risk factors.All Authors: No reported disclosures"} +{"text": "The US Coast Guard Academy began adenovirus vaccination of incoming cadets in 2022. Of 294 vaccine recipients, 15%\u201320% had mild respiratory or systemic symptoms within 10 days postvaccination but no serious adverse events after 90 days. Our findings support the continued use of adenovirus vaccines in congregate military settings. Adenovirus infection results in considerable illness among congregate military populations , 293 (97.3%) of 301 first-year cadets received the adenovirus vaccine; 4 (1.3%) cadets were unable to swallow the vaccine. Of 4 cadets isolated for COVID-19 during the initial vaccination period, only 1 subsequently received the vaccine. Of 294 vaccinated cadets, a total of 159 (54.1%) received 1 other vaccine and 53 (18.0%) received >1 vaccine surveillance sign or symptom. Commonly reported signs and symptoms were cough (20.1%), sore throat (17.0%), headache (16.0%), fatigue (16.0%), nasal congestion (15.3%), and shortness of breath (11.6%) cadets reported (11.6%) . Frequen (11.6%) . During >1 enhanced surveillance sign or symptom, 8 (12.3%) also tested positive for COVID-19.During the enhanced postimmunization monitoring period, a concomitant COVID-19 outbreak affected \u224820% of first-year cadets. Of the 65 students who sought care at the CGA clinic and had The live adenovirus vaccine was well-tolerated; only 4 vaccination failures occurred, the cadets who could not swallow the medication. Of 294 vaccinated CGA cadets, <25% reported signs or symptoms during the monitoring period. Phase 1 adenovirus vaccine trial data (Shortness of breath in 11.6% of cadets did not clearly correspond to signs and symptoms identified in phase 1 or phase 3 trial safety data. Given that >25% of nonhospitalized adults with COVID-19 report shortness of breath (In conclusion, enhanced passive monitoring established after introducing adenovirus vaccination for incoming first-year CGA cadets did not identify any serious adverse events. Even with the receipt of multiple vaccines and an intercurrent COVID-19 outbreak, the signs and symptoms profile among cadets who had sick calls during the 10-day postvaccination period appears consistent with profiles reported in previous adenovirus vaccine trials. A positive COVID-19 test was observed for 12.3% of cadets who completed the surveillance questionnaire during their sick call, which might explain the 11.6% of cadets who reported shortness of breath. Our favorable real-world findings support continuing adenovirus vaccination of incoming CGA cadet classes and wider use of the vaccine in congregate military settings.Additional information for enhanced adenovirus vaccine safety surveillance in military setting, United States."} +{"text": "At St. George\u2019s Hospital, neonates with central-line access are administered vancomycin by continuous infusion. A protocol instructs a 1-hour 15 mg/kg-loading dose, followed by a creatinine clearance- (CLCR)/weight\u2013based maintenance dose. Due to vancomycin\u2019s narrow therapeutic margin, daily therapeutic drug monitoring (TDM) of serum concentrations is necessary to obtain safe/effective therapy. Concentrations between 15 and 25 A locally approved service evaluation retrospectively analysed 78 courses of vancomycin from 46 patient\u2019s electronic prescribing and medicine administration (ePMA) records (July 2021\u2013March 2022). Data on vancomycin administration/TDM were analysed using descriptive statistics.Individual loading and maintenance doses were calculated correctly in 83% (65/78) and 97% (75/77) of records. 72% (33/46) of patients received both correctly calculated loading/maintenance doses. A gap greater than 1 hour between loading and maintenance doses was recorded in 32% (24/75) of courses. 61% (41/67) of courses had appropriately taken serum concentrations within 22\u201326 hours of treatment initiation. In correctly dosed patients, therapeutic vancomycin courses increased from 43% (23/54) to 53% (19/36) and 55% (17/31) between 24\u201348\u201372-hour timepoints. In pre-term neonates\u200a<\u200a28 weeks gestational age (GA), subtherapeutic courses were consistent between 38% (15/40)\u201342% (11/26)\u201336% (8/22) at 24\u201348\u201372-hour timepoints. Supra-therapeutic courses decreased from 20% (8/40)\u20130% (0/26)\u20135% (1/22), respectively. In term neonates\u200a>\u200a37 weeks GA, subtherapeutic courses increased from 33% (3/9)\u201343% (3/7)\u201350% (3/6) between 24\u201348\u201372-hour timepoints. As did respective supra-therapeutic courses from 11% (1/9)\u201314% (1/7)\u201317% (1/6). Insufficient course data (5) were available for neonates between 28\u201332/32\u201337 weeks GA.1 A quality improvement project addressing protocol ePMA interface issues and implementing a dose-amendment nomogram may improve dose calculation/monitoring. Delays between manually input loading/maintenance dose administration times onto the ePMA system require investigation before dosing revisions. Aspects of protocol compliance require improvement. Therapeutic target attainment was erratic, but reflective of the literature.1 Optimized dosing is required for specific neonatal subgroups.Non-therapeutic treatment worsened over 72 hours for neonates\u200a>\u200a37 weeks GA, whereas toxic concentrations decreased over time despite consistent subtherapeutic concentrations in neonates\u200a<\u200a28 weeks. Neonatal pharmacokinetic (PK) variability due to evolving renal function/distribution volume/non-blood protein-bound vancomycin concentrations, likely contributed to non-therapeutic concentrations. As did limitations of sample size/non-capture of dosing amendment impact. Population PK\u2013derived dosing based on covariates explaining vancomycin PK variability could be used to improve neonatal target attainment. Whereas, neonatal area under the vancomycin concentration time curve targets supported by clinical data are needed to benchmark the therapeutic target. This will provide insight into if lower concentrations adequately treat common infections with coagulase-negative organisms."} +{"text": "Trimethoprim/sulfamethoxazole (TMP/SMX) is the recommended first-line treatment for human immunodeficiency virus (HIV)-infected patients with Pneumocystis jirovecii pneumonia (PJP).However, in June 2010, the lone manufacturer of intravenous (IV) TMP/SMX in the United States stopped production of this medication.To (a) evaluate the impact of the national IV TMP/SMX shortage on PJP treatment outcomes between 2 groups of HIV-infected patients\u2014those treated before the shortage and those after the shortage\u2014and (b) compare the length of hospital stay (LOS) and PJP treatment used before and after the shortage.A retrospective, quasi-experimental study examining 2 groups of HIV-infected adult patients with PJP was performed at an academic medical center from September 1, 2008, to June 30, 2012. Patients treated when IV TMP/SMX was available, or preshortage (PRE), were compared with patients treated when IV TMP/SMX was not available, or postshortage (POST).PRE included patients treated between September 1, 2008, and May 30, 2010, and POST included patients treated between June 1, 2010, and June 30, 2012.Thirty-six patients were included in the study, 18 in each group. Treatment failure, the primary outcome, included mortality or worsening clinical status (WCS) after at least 5 days of therapy. Three patients in PRE (16.7%) and 6 patients in POST (33.3%) experienced treatment failure (P\u2009=\u20090.248). No patients in PRE and 3 patients in POST (16.7%) experienced WCS (P\u2009=\u20090.035). Three patients in each group expired.In POST, 5 of the 6 treatment failures (83.3%) occurred during the first 6 months of the shortage. Median (interquartile range) LOS was 11 days (7-17) in PRE and 14 days (5-22) in POST (P\u2009=\u20090.800).In PRE, 7 patients (38.9%) were initiated on oral PJP treatment compared with 13 (72.2%) in POST (P\u2009=\u20090.042).The national shortage of IV TMP/SMX may have led to an immediate but temporary negative impact on treatment outcomes among HIV-infected patients with PJP at an academic medical center.Pharmacist collaboration with physicians may have helped mitigate the impact of this drug shortage on patient outcomes."} +{"text": "Pediatric population was generally less affected clinically by SARS-CoV-2 infection. Few pediatric cases of COVID-19 have been reported compared to those reported in infected adults. However, a rapid increase in the hospitalization rate of SARS-CoV-2 infected pediatric patients was observed during Omicron variant dominated COVID-19 outbreak. In this study, we analyzed the B.1.1.529 (Omicron) genome sequences collected from pediatric patients by whole viral genome amplicon sequencing using Illumina next generation sequencing platform, followed by phylogenetic analysis. The demographic, epidemiologic and clinical data of these pediatric patients are also reported in this study. Fever, cough, running nose, sore throat and vomiting were the more commonly reported symptoms in children infected by Omicron variant. A novel frameshift mutation was found in the ORF1b region (NSP12) of the genome of Omicron variant. Seven mutations were identified in the target regions of the WHO listed SARS-CoV-2 primers and probes. On protein level, eighty-three amino acid substitutions and fifteen amino acid deletions were identified. Our results indicate that asymptomatic infection and transmission among children infected by Omicron subvariants BA.2.2 and BA.2.10.1 are not common. Omicron may have different pathogenesis in pediatric population. Coronavirus disease 2019 (COVID-19) is a viral respiratory disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ; the difHowever, during the fifth COVID-19 outbreak in Hong Kong which was dominated by Omicron variant (B.1.1.529) between January 2022 and May 2022, there was a rapid increase in the hospitalization rate in SARS-CoV-2 infected pediatric patients . Four deSARS-CoV-2 infection may cause mild signs and symptoms but can also affect multiple organs simultaneously as organs and cells harboring ACE-2 receptors are the primary targets of SARS-CoV-2. Recent studies have highlighted the effects of COVID-19 on multiple organs and systems, including respiratory, cardiovascular, gastrointestinal, urinary, nervous, endocrine, reproductive, immune and integumentary systems [\u00ae Liat\u00ae SARS-CoV-2 & Influenza A/B assay and cepheid\u00ae Xpress SARS-CoV-2 assay as described in our previous study [Nasopharyngeal swab (NPS), combined nasal and throat swab (CNTS) and posterior oropharyngeal saliva (POS) were collected from sixty-eight RT-PCR confirmed SARS-CoV-2 infected pediatric patients aged between 0 and 17 years old between January 2022 and March 2022 at Hong Kong Adventist Hospital in Hong Kong. All SARS-CoV-2 RT-PCR results were confirmed using both cobasus study . NPS andus study . This st\u00ae Viral RNA Mini Kit according to manufacturer\u2019s instruction.Viral RNA was extracted from NPS, CNTS and POS specimens using QIAampTM SARS-CoV-2 Primer Panel , which contain primer sequences defined by the ARTIC network (ARTIC v4.1). The resulting ~400bp amplicons were fragmented, end repaired, and A-tailed using COVIDSeqTM Library Prep Kit according to manufacturer\u2019s instruction. Unique dual indexes were added to the samples using the 10 base pair index i7 and i5 adapters of COVIDSeqTM according to manufacturer\u2019s instruction. The size distributions of the sequencing libraries were checked using Tapestation 4150 . KAPA Pure Beads were used to perform double size selection of the libraries and equimolar pooling of libraries was performed by quantifying the samples using Qubit 4 fluorometer . Libraries were sequenced using NextSeq2000 P2 2 x 100bp kit with at least 10M reads per sample.Extracted RNA was first reverse transcribed to cDNA and subjected to whole-genome targeted amplification of SARS-CoV-2 sequences using COVIDSeqSequencing data was analyzed using DRAGEN COVID Lineage and method as described previously ,12. In b\u00ae Liat\u00ae SARS-CoV-2 & Influenza A/B assay) . Among these cases, ten cases (14.7%) were in children aged below 1 year old, twenty-one cases (30.9%) were in children aged between 1 and 2 years old, fifteen cases (22.1%) were in children aged between 3 and 5 years old, ninteen cases (27.9%) were in children aged between 6 and 12 years old and three cases (4.4%) were in children aged between 13 and 17 years of age (Table 1).A total of sixty-eight laboratory-confirmed SARS-CoV-2 infected children aged between 0 and 17 years old were studied . Children in this cohort infected by Omicron subvariants BA.2.2 and BA.2.10.1 showed similar signs and symptoms of infections. There was no evidence to show that children infected by Omicron subvariant BA.2.10.1 would result in worse and more severe clinical outcomes than children infected by BA.2.2. No sexual dimorphism was observed . Among all the 68 pediatric cases of SARS-CoV-2 infection, none of them displayed any underlying conditions.Results of this study suggest a milder course of disease in children infected by Omicron subvariants BA.2.2 and BA.2.10.1. However, no asymptomatic case was identified. Fifty-one children (75%) presented more than one sign or symptom while seventeen children (25%) presented one sign or symptom only. No case of co-infection was found. The most common symptoms reported were fever (94.1%), cough (33.8%), running nose (33.8%), sore throat (32.4%) and vomiting (23.5%). Two children (2.9%) had diarrhea and one child (1.5%) had shortness of breath (In nine cases (13.2%), cohabiting family members were reported to have similar symptoms as the infected children. Two cases (2.9%) were reported to have a contact history with suspected or confirmed COVID-19 cases in the past 21 days. None of the cases had travel history outside Hong Kong in the past 21 days. This indicates that all the sixty-eight pediatric COVID-19 cases were local infections.Fig 4).Two distinctive groups were identified. The first group consisted of four genome sequences that belong to subvariant BA.2.10.1 whereas the second group consisted of sixty-one genome sequences that belong to subvariant BA.2.2 (Table 2).Compared to the reference genome of Wuhan-Hu-1 strain, a total of one nucleotide insertion, one frameshift mutation, one hundred and eighteen nucleotide substitutions, four nucleotide deletions and seven PCR primers and probes changes were identified. On protein level, eighty-three amino acid substitutions and fifteen amino acid deletions were identified in the B.1.1.529 Omicron variant (One nucleotide insertion (14760T) was found in nine sequenced subjects at the non-structural protein 12 (NSP12) of the open reading frame 1b (ORF1b), leading to a novel frameshift mutation.Table 3). Forty (33.9%) of them were found in ORF1a ; fourteen (11.9%) were found in ORF1b ; thirty-six (30.5%) were found in spike (S) gene ; three (2.5%) were found in ORF3a ; one (0.8%) was found in envelope (E) gene (C26270T); five (4.2%) were found in membrane (M) gene ; four (3.4%) were found in ORF6 ; one (0.8%) was found in ORF7a (C27741T); one (0.8%) was found in ORF7b (C27807T); one (0.8%) was found in ORF9b (G28436T) and twelve (10.2%) were found in nucleocapsid (N) gene . Of these changes, eighty-three (70.3%) of them resulted in nonsynonymous mutations, while thirty-five (29.7%) of them resulted in synonymous mutations.A total of one hundred and eighteen nucleotide substitutions were identified in this cohort (100%), ORF1b (between positions 21633 and 21641) (100%), ORF9b (between positions 28362 and 28370) (100%) and N gene (between positions 29734 and 29759) (93.8%).Table 3). One (1.2%) of the substitutions was found in E protein (T9I), three (3.6%) were found in M protein , eight (9.6%) were found in N protein , twenty-one (25.3%) were found in ORF1a , thirteen (15.7%) were found in ORF1b , two (2.4%) was found in ORF3a , one (1.2%) was found in ORF6 (D61L), one (1.2%) was found in ORF9b (P10S) and thirty-three (39.8%) were found in S protein .A total of eighty-three amino acid substitutions were identified in this cohort of these deletions were found in N protein , four (26.7%) in ORF1a , two (13.3%) in ORF1b (P403- and G404-), three (20%) in ORF9b , three (20%) in S protein .Table 4). Of the seven changes, five (71.4%) were located in N gene. C28770T was located within the N gene probe of Charit\u00e9, G28881A, G28882A and G28883C were located within the N gene forward primer of China CDC, whereas C28311T was located within the N1 gene probe of US CDC. One change (14.3%) was located in RdRp gene. T15521A was located within the RdRp gene reverse primer of Charit\u00e9. One (14.3%) was located in E gene. On the other hand, C26270T was located within the E gene forward primer of Charit\u00e9.A total of seven polymerase chain reaction (PCR) primers and probes changes in WHO listed SARS-CoV-2 primers and probes were found in Omicron subvariants BA.2.2 and BA.2.10.1 presented more than one sign or symptom while seventeen children (25%) presented one sign or symptom only. No asymptomatic cases were identified. The cycle threshold (Ct) values in the sixty-eight pediatric cases were low , showing that the viral load was high in these cases and these infected children were infectious to others. The data suggests that asymptomatic infection and transmission among children infected by Omicron subvariants BA.2.2 and BA.2.10.1 are not common. In Hong Kong, only children aged above 3 were recommended to receive COVID-19 vaccination. In this cohort, thirty-one children 45.6%) were aged below 3. Of the other thirty-seven children (54.4%) aged above 3, six 16.2%) of them have received COVID-19 vaccination. The pediatric population was generally less affected clinically by SARS-CoV-2 infection in the past few waves of COVID-19 outbreaks caused by variants other than Omicron. This discrepancy in clinical responses between adults and pediatric population may have been due to the differences in various immune responses and physiological differences such as lower ACE2 expression in children relative to adults [5.6% were% present.2% of thIn a recent study that compared the antibody specificity in COVID-19 pediatric population to that in adults, the antibodies response against the structural protein E and accessory protein ORF8 was found to be significantly elevated in SARS-CoV-2 infected pediatric population, compared to adults . In contIn this study, a novel frameshift mutation caused by insertion (14760T) was found at the NSP12 of the ORF1b region. NSP12 is a 932-amino acid long protein. It is an essential RNA-dependent RNA polymerase (RdRp) of the replication transcription complex (RTC) responsible for making copies of genomic and subgenomic RNAs and polymerizing antisense RNA during viral replication of SARS-CoV-2 . During From this study, we also found that fever (94.1%), cough (33.8%), running nose (33.8%), sore throat (32.4%) and vomiting (23.5%) were the more commonly reported symptoms in children infected by Omicron variant. For adults who were infected by Omicron variant, headache (76.5%), running nose (74.9%), sneezing (69.3%) and sore throat (68.4%) were the more commonly reported symptoms. Only 39.2% and 18.7% of the infected adults presented fever and diarrhoea respectively . There iIn conclusion, asymptomatic infection and transmission among children infected by Omicron subvariants BA.2.2 and BA.2.10.1 are not common. A novel frameshift mutation was found in the ORF1b region (NSP12) of the genome of Omicron variant in this study. There was also no significant difference between the genomes of the SARS-CoV-2 Omicron variant infecting the pediatric population, and those infecting the adults. However, Omicron variant may have different pathogenesis in pediatric population, when compared to adults."} +{"text": "S. enterica) is a commensal organism or pathogen causing diseases in animals and humans, as well as widespread in the environment. Antimicrobial resistance (AMR) has increasingly affected both animal and human health and continues to raise public health concerns. A decade ago, it was estimated that the increased use of whole genome sequencing (WGS) combined with sharing of public data would drastically change and improve the surveillance and understanding of Salmonella epidemiology and AMR. This study aimed to evaluate the current usefulness of public WGS data for Salmonella surveillance and to investigate the associations between serovars, antibiotic resistance genes (ARGs), and metadata. Out of 191,306 Salmonella genomes deposited in European Nucleotide Archive and NCBI databases, 47,452 WGS with sufficient minimum metadata of S. enterica were retrieved from 116 countries and isolated between 1905 and 2020. For in silico analysis of the WGS data, KmerFinder, SISTR, and ResFinder were used for species, serovars, and AMR identification, respectively. The results showed that the five common isolation sources of S. enterica are human (29.10%), avian (22.50%), environment (11.89%), water (9.33%), and swine (6.62%). The most common ARG profiles for each class of antimicrobials are \u03b2-lactam , fluoroquinolone , folate pathway antagonist , macrolide , phenicol , polymyxin B , and tetracycline . Our study reports the first overview of ARG profiles in publicly available Salmonella genomes from online databases. All data sets from this study can be searched at Microreact.( Salmonella enterica can be found as a commensal organism in a wide range of hosts, especially in food animals, and is also a leading pathogen in animals and humans has been increasingly used to characterize bacterial isolates, for research, outbreak detection, and surveillance. A large part of these data are shared publicly and could potentially provide novel insights into the global distribution, diversity, and transmission of Salmonella surveillance.However, despite being used for comparison with local surveillance initiatives, there has to the best of our knowledge never been any studies evaluating the usefulness of the publicly shared data for Salmonella, the distribution overview of serovars, AMR, and the most common antibiotic resistance gene (ARG) profiles.This study aimed to investigate the current usefulness of these publicly available data for surveillance of Salmonella WGS data and metadata were downloaded from European Nucleotide Archive (ENA) . The metadata from the NCBI Pathogen Detection project was also downloaded and merged with the ENA metadata . Combined data that did not have information on either geographical location (country), isolation source (source), or year were excluded. Duplicate data from the same source or outbreak were also excluded. We did genome quality checking with FoodQCPipeline . The sources of isolates were clustered into 11 clusters . The isolates represented common serovars that were 70% of all identified serovars. The duration of isolation was 1905\u20132020. The data obtained from single countries might not reflect the epidemiological situation of Salmonella in the country because the reason for submitting the data to NCBI or ENA was not considered and remains unknown. All data sets can be searched at https://microreact.org/project/tptbR3fX8fa7p5zGV5VRbu-publicly-available-salmonella.Low-quality genomes or non-https://jgi.doe.gov/data-and-tools/bbtools) according to the following: (1) length of read higher or equal to 50 base pairs (bp), (2) phred score per base higher or equal to 20, and (3) adapters filtered away based on an internal database with Illumina adapters. The pipeline uses FastQC10 version 0.11.5 for fastq quality checking before and after trimming . For identification of ARGs, ResFinder v.4.1 was used with the default setting, at least 60% minimum length and 90% identity, for both chromosomal point mutation and acquired ARGs . The proportion of ARGs was calculated by the number of positive-predicted ARGs divided by the total number of isolates in each continent, source, or serovar. The figures in this study were visualized in Microreact , whereas those isolates with missing country or source were 9.7% and 3.7%, respectively. The missing data were in isolates from humans in North America.S. enterica isolates. The data were classified into 11 sources and 22 serovars. The genomes were mainly from 2011 to 2020 (87.12%), followed by 2001\u20132010 (10.74%). Salmonella genomes were isolated from human (29.10%), followed by avian (22.50%), environment (11.89%), water (9.33%), swine (6.62%), bovine (6.49%), food (4.54%), plant (1.40%), feed (1.22%), nut/bean (0.33%), and others (5.72%).The final data set consisted of WGS data and metadata of 47,452 Salmonella Enteritidis (13.84%), Salmonella Typhimurium (12.04%), Salmonella Newport (5.73%), Salmonella Infantis (5.50%), Salmonella Kentucky (4.55%), Salmonella Muenchen (3.04%), Salmonella Heidelberg (2.66%), Salmonella Javiana (2.41%), Salmonella Montevideo (2.38%), and Salmonella Anatum (2.35%) (The top 10 common serovars were (2.35%) .S. enterica isolates from South America was almost exclusively recovered from environment, water, or avian, whereas isolates from Europe, Africa, Asia, and especially Oceania were predominantly isolated from humans. The isolates from North America were mainly isolated from human and avian samples, whereas those from the Middle East were mainly recovered from human and food samples , Salmonella Typhimurium (4.50%), and Salmonella Newport (2.00%). In avian samples, the most common serovars were Salmonella Kentucky (3.70%), Salmonella Enteritidis (3.16%), and Salmonella Infantis (2.76%). From environmental samples, the most common serovars were Salmonella Enteritidis (1.37%), Salmonella Newport (0.96%), and Salmonella Typhimurium (0.92%) (The distribution of (0.92%) .Salmonella Newport (1.09%), Salmonella Typhimurium (0.78%), and Salmonella Muenchen (0.45%). From swine samples, the most common serovars were Salmonella Typhimurium (1.93%), Salmonella Derby (0.66%), and Salmonella Anatum (0.59%). From bovine samples, the most common serovars were Salmonella Dublin (1.03%), Salmonella Typhimurium (0.76%), and Salmonella Montevideo (0.68%) .S. enterica. The results showed the percentage of AMR for aminoglycoside (98.39%), tetracycline (23.85%), folate pathway antagonist (18.63%), \u03b2-lactam (15.78%), phenicol (7.94%), fluoroquinolone (3.36%), polymyxin (1.18%) and macrolide (0.51%) .aac(6\u2032)-Iaa (92.22%) was commonly found in S. enterica genomes. The gene was also detected together with other aminoglycoside genes as aac(3)-IV, aac(6\u2032)-Iaa resistance gene profile (2.55%), and aac(3)-VIa, aac(6\u2032)-Iaa resistance gene profile (1.11%). The aac(3)-IV, aac(6\u2032)-Iaa profile was predominantly harbored by Salmonella Infantis. The aac(3)-VIa, aac(6\u2032)-Iaa profile was predominantly harbored by Salmonella Heidelberg (The gene idelberg .blaTEM-1B (6.78%), blaCMY-2 (2.82%), and blaCTX-M-65 (1.68%). The blaTEM-1B was predominantly harbored by Salmonella Heidelberg, Salmonella Typhimurium, and Salmonella Saintpaul. The blaCMY-2 was the second most common resistance profile and was predominantly harbored by Salmonella Heidelberg and Salmonella Dublin. Furthermore, blaCTX-M-65 was predominantly driven by Salmonella Infantis. In addition, there were other \u03b2-lactam resistance gene profiles, blaCARB-2 (1.03%) and blaCMY-2, blaTEM1-B, blaTEM-206 profile (0.54%). The blaCARB-2 was predominantly carried by Salmonella Typhimurium. Whereas the blaCMY-2, blaTEM1-B, blaTEM-206 profile was driven by Salmonella Dublin ; aac(6\u2032)-Ib-cr, parC[T57S] profile (0.54%); and qnrB19 profile (0.43%). The parC[T57S], qnrB19 profile was predominantly harbored by Salmonella Heidelberg. The aac(6\u2032)-Ib-cr, parC[T57S] profile was predominantly carried by Salmonella Heidelberg. The qnrB19 was driven by several serovars (Common fluoroquinolone resistance gene profiles were serovars .sul2 (8.35%); sul1 (4.23%); and dfrA14, sul1 profile (1.56%). The sul2 was predominantly harbored in Salmonella Reading, Salmonella Typhimurium, and Salmonella Dublin. The sul1 was predominantly carried by Salmonella Heidelberg, Salmonella Infantis, and Salmonella Derby. The dfrA14, sul1 profile was predominantly driven by Salmonella Infantis (Common folate pathway antagonist resistance gene profiles were Infantis .mph(A) (0.39%), mef(B) (0.07%), and msr(E) (0.03%). The mph(A) and mef(B) profiles were found in several serovars. The msr(E) profile was predominantly harbored by Salmonella Agona and Salmonella Typhimurium (Common macrolide resistance gene profiles were himurium .floR (5.94%), catA1 (0.51%), and cmlA1 (0.45%). The floR profile was predominantly carried by Salmonella Infantis and Salmonella Dublin. The catA1 profile was predominantly harbored in Dublin. The cmlA1 profile was prominently driven by several serovars (Common phenicol resistance gene profiles were serovars .mcr-1.1 (0.09%), mcr-5.1 (0.04%), and mcr-3.1 (0.02%). The mcr-1.1 profile was driven by several serovars. The mcr-5.1 profile was predominantly carried by Salmonella Typhimurium and Salmonella 1,4,[5],12:i:- (12.95%), tet(B) (8.00%), and tet(G) (0.88%). The tet(A) profile was the most common tetracycline resistance profile predominantly harbored by Salmonella Derby, Salmonella Infantis, and Salmonella Dublin. The tet(B) profile was predominantly carried by Salmonella Kentucky. The tet(G) profile was predominantly harbored by Salmonella Typhimurium (Common tetracycline resistance gene profiles were himurium .aac(3)-IV, aac(6\u2032)-Iaa profile (2.06%) and aac(3)-VIa, aac(6\u2032)-Iaa profile (1.33%). Common \u03b2-lactam resistance gene profiles were blaTEM-1B (4.33%), blaCMY-2 (3.36%), and blaCTX-M-65 (1.24%). Common fluoroquinolone resistance gene profiles were parC[T57S], qnrB19 profile (0.83%); aac(6\u2032)-Ib-cr, parC[T57S] profile (0.69%); and qnrB19 (0.38%).We found the same resistance gene profiles in the United States as in other countries. Common aminoglycoside resistance gene profiles were sul2 (7.68%); sul1 (4.22%); and dfrA14, sul1 profile (1.15%). Common macrolide resistance gene profiles were mph(A) (0.21%), mef(B) (0.04%), and msr(E) (0.03%). The most common phenicol resistance gene profile was floR (5.58%). Common polymyxin resistance gene profile was mcr-1.1 (0.003%). Common tetracycline gene resistance profiles were tet(A) (12.47%) and tet(B) (7.85%).Common folate pathway antagonist resistance gene profiles were Salmonella. It is also useful for global surveillance and AMR tracking -Iaa gene. This was consistent with the study by Srednik et al. in the United States recovered from cattle carried aac(6\u2032)-Iaa gene detected using ResFinder. Consistently, S. enterica isolated from duck, chicken, and pig farms and retail markets in Eastern China harbored aac(6\u2032)-Iaa gene by 95.00% -Id and aph(3\u2033)-Ib in human infections and plasmid-mediated quinolone resistance -Ib-cr, parC[T57S] profile; qnrB19 profile; parC[T57S], qnrS1 profile; and qnrS1 profile are the resistance profiles that could confer low-level resistance to fluoroquinolone , mef(B), and msr(E). These profiles composed of 0.49% of the 0.51% macrolide resistance. The mph(A) was predominantly carried by Salmonella Newport. The Resistome Tracker similarly showed that mph(A) was the most common macrolide resistance gene and (2) plasmid-mediated colistin resistance mechanism . The most common mcr gene in our study was mcr-1.1 corresponding to 0.09% of 1.18% of the overall polymyxin resistance genes. Whereas mcr-9 (0.99%) was not associated with colistin resistance in Salmonella and Escherichia coli alteration of polymyxin resistance gene and tet(B). Both profiles consisted of 20.95% of the 23.85% tetracycline resistance. The Resistome Tracker also showed that tet(A) and tet(B) were common tetracycline resistance genes was highly frequent among analyzed WGS data , folate pathway antagonist (18.63%), and \u03b2-lactam (15.78%). The most common ARG profiles in S. enterica were \u03b2-lactam (blaTEM-1B), fluoroquinolone , folate pathway antagonist (sul2), macrolide [mph(A)], phenicol (floR), polymyxin B (mcr-1.1), and tetracycline [tet(A)]. This study showed that updating and sharing data are one of the key points for better surveillance of Salmonella.Common AMR in"} +{"text": "Throughout the COVID-19 pandemic, students were vulnerable to mental health issues and dentistry students were no exception. All Iraqi universities were transitioning back to face-to-face learning in the last year. Acclimatization with all pandemic regulations that schools apply might increase the vulnerability to depression.The current study aims to assess the levels of depression among Iraqi dentistry students after transitioning from online to onsite learning during the pandemic period.A cross-sectional study was conducted online after transitioning from online to the onsite learning method during the pandemic period. Sociodemographic data and Patient Health Questionnaire-8 (PHQ-8) were included in the questionnaire.A total of 307 respondents, 216 (70.4%) female and 91 (29.6%) male, 276 (90%) live with family, 20 (6.5%) live with friends and 11 (3.5%) live alone, 268 (87.3%) of student claimed that post-COVID-19 regulations face to face learning is more stressful while 39 (12.7%) answered no difference. 39 (12.7%) of dentistry student with normal level of depression, 199 (38.8%) have mild depression 101 (32.9%) moderate depression, 32 (10.4%) moderately severe, 16 (5.2%) severe. Depression level and students\u2019 perception of teaching mode transition showed a significant association (p<0.05).However, there are no significant associations between gender, living conditions, or dentistry stages with depression levels (p>0.05).A high prevalence of depression symptoms among Iraqi dentistry students was found during onsite learning, along with all educational institutions\u2019 pandemic rules and regulations. Psychological supporting preventive programs are needed to apply for supporting students\u2019 mental health.None Declared"} +{"text": "The COVID-19 pandemic, resulting from the rapidly evolving SARS-CoV-2 virus, has drastically impacted health systems and economies worldwide. Genomic sequencing is critical for the surveillance of SARS-CoV-2 to monitor the rapidly evolving virus and identify new strains.583 isolates from Henry Ford Health were retrospectively profiled across 3 years . DNA was extracted using Kingfisher viral isolation kit; RT-PCR screening was used to identify isolates with cycle threshold < 32 for whole genome sequencing (WGS). Libraries were generated using QIAseq DIRECT SARS-CoV-2 Kit, followed by Illumina sequencing . Lineage analysis of the SARS-CoV-2 consensus genome sequences generated from samtools variant analysis pipeline was determined using Nextclade and Pangolin software.Sequences were classified into 11 unique clades across 108 lineages by Nextclade and Pangolin, respectively. Almost three-fourths of the sequenced isolates were from 2022. 117 (20%) genomes were from the early pandemic (2020) and were clustered into 8 clades: 19A, 19B, 20A, 20B, 20C, 21 J (Delta) and 21L (Omicron). Most of the 2022 genomes (72%) were in clade 20C from lineage B.1, identified during the outbreak in Europe. 15 (13%) genomes had clade 19A (lineage B) and 1 had 19B (lineage A.3), identified early in the pandemic in Wuhan, China. Of the 39 (7%) genomes from 2021, the majority (82%) clustered into clade Delta 21J that originated in India. Only 2 (5%) of the genomes from 2021 had Alpha variant of concern (21I) from the lineage B1.1.7, which were suspected to be more transmissible. Of the 427 (73%) genomes from 2022, 393 (92%) had variants within Omicron variant of concern (21L), with 79 different lineages; 1 was Omicron variant 21K from the lineage BA1.1. Other clades observed in the 2022 batch were 19A (6%), 20A (0.2%), 20B (0.2%), 20C (0.2%) and 21M (1%).Our genomic surveillance data suggest that SARS-CoV-2 infections at the local level mirrored global outbreaks. This underscores the importance of robust genomic surveillance efforts to inform public health planning and practice.Marcus Zervos, MD, Contrafect: Advisor/Consultant|GSK: Grant/Research Support|Johnson and Johnson: Grant/Research Support|Pfizer: Grant/Research Support"} +{"text": "MYO6 gene), DFNA8/12 (TECTA gene), DFNA20/26 (ACTG1 gene), DFNA6/14/38 (WFS1 gene), DFNA15 (POU4F3 gene), DFNA2A (KCNQ4 gene), and DFNA10 (EYA4 gene) are some of the most common forms of autosomal dominant non-syndromic HL. The characteristics of autosomal dominant non-syndromic HL are heterogenous. However, in most cases, HL tends to be bilateral, post-lingual in onset (childhood to early adulthood), high-frequency (sloping audiometric configuration), progressive, and variable in severity (mild to profound degree). DFNA1 (DIAPH1 gene) and DFNA6/14/38 (WFS1 gene) are the most common forms of autosomal dominant non-syndromic HL affecting low frequencies, while DFNA16 (unknown gene) is characterized by fluctuating HL. A long audiological follow-up is of paramount importance to identify hearing threshold deteriorations early and ensure prompt treatment with hearing aids or cochlear implants.Autosomal dominant non-syndromic hearing loss (HL) typically occurs when only one dominant allele within the disease gene is sufficient to express the phenotype. Therefore, most patients diagnosed with autosomal dominant non-syndromic HL have a hearing-impaired parent, although de novo mutations should be considered in all cases of negative family history. To date, more than 50 genes and 80 loci have been identified for autosomal dominant non-syndromic HL. DFNA22 ( The World Health Organization (WHO) estimates that approximately 34 million children worldwide have disabling hearing loss (HL), defined as HL greater than 35 dB in the better ear . HL can Particularly, congenital CMV infection is considered the leading nongenetic cause of sensorineural HL in the developed world . The chaWFS1 and ACTG1) cause both syndromic and non-syndromic HL [Autosomal dominant inheritance occurs when only one dominant allele within the disease gene is sufficient to express the phenotype . Thereforomic HL .To date, more than 50 genes and 80 loci have been identified for autosomal dominant non-syndromic HL , and areGJB2 gene), autosomal dominant non-syndromic HL does not have a single identifiable gene responsible for the majority of cases worldwide [Unlike autosomal recessive non-syndromic HL (in which the majority of cases are caused by mutations in the orldwide .MYO6 gene) and DFNA8/12 (TECTA gene), accounting for 21% and 18% of all cases, respectively [ACTG1 gene), DFNA6/14/38 (WFS1 gene), and DFNA15 (POU4F3 gene), accounting for 9%, 9%, and 6.5% of all cases, respectively [KCNQ4 (DFNA2A) and EYA4 (DFNA10) genes contribute 2.5% each, while the remaining genes are residually represented [GJB2 (DFNA3A) [ACTG1 (DFNA20/26) [TECTA (DFNA8/12) [MYH14 (DFNA4A) [CEACAM16 (DFNA4B) [ATP2B2 (DFNA82) [WFS1 (DFNA6/14/38) [In Europe, the most common forms of autosomal dominant non-syndromic HL are DFNA22 (ectively . Other fectively . KCNQ4 (resented . De novo(DFNA3A) ,128, ACTNA20/26) ,130, TECFNA8/12) , MYH14 ((DFNA4A) , CEACAM1(DFNA4B) , ATP2B2 (DFNA82) , and WFS6/14/38) .MYO6 gene can cause either autosomal dominant non-syndromic HL (DFNA22) or autosomal recessive non-syndromic HL (DFNB37) [MYO6) on chromosome 6q14 [MYO6 mutations was reported in large Italian [Mutations in the (DFNB37) . DFNA22 ome 6q14 . Myosin ome 6q14 . Autosom Italian , Danish Italian , Belgian Italian ,137, Dut Italian , German Italian , and Aus Italian families Italian ,142,143, Italian ,145, the Italian , and Bra Italian . HL is t Italian ,148. Vol Italian .TECTA gene on chromosome 11q23 [TECTA cause DFNA8/12, while nonsense mutations cause autosomal recessive non-syndromic HL (DFNB21) [TECTA gene encodes alpha-tectorin, one of the major non-collagenous components of the tectorial membrane of the inner ear that bridges the stereocilia bundles of the sensory hair cells [TECTA missense mutations was reported in families from different European countries, including Belgium [zona pellucida domain lead to mid-frequency sensorineural HL (\u201cU-shaped\u201d or \u201ccookie bite\u201d audiometric configuration), while missense mutations in the zonadhesin region cause high-frequency sensorineural HL (\u201csloping\u201d audiometric configuration). HL is progressive if cysteine residues are affected [Autosomal dominant non-syndromic sensorineural deafness 8/12 (DFNA8/12) is caused by heterozygous mutations in the ir cells . HL asso Belgium ,150, Aus Belgium ,152, Fra Belgium , Sweden Belgium , Spain [ Belgium , and The Belgium ,158,159. Belgium ,162,163, Belgium , America Belgium ,165, Kor Belgium ,167, Bra Belgium , Chinese Belgium ,169,170, Belgium , and Alg Belgium familiesaffected .ACTG1 gene on chromosome 17q25 [ACTG1 gene can be associated with autosomal dominant non-syndromic HL (DFNA20/26) and Baraitser\u2013Winter syndrome [ACTG1 gene encodes gamma actin, which is a major actin protein in the cytoskeleton of auditory hair cells and is essential for the maintenance of stereocilia [ACTG1 gene were also frequently described in American [Autosomal dominant non-syndromic sensorineural deafness 20/26 (DFNA20/26) is caused by heterozygous mutations in the me 17q25 . Mutatioability) ,173. Thereocilia ,174,175,reocilia , Spanishreocilia , and ItaAmerican ,179,180,American ,183,184,American ,186,187,American ,189,190 American .WFS1 gene on chromosome 4p16 [WFS1) [WSF1 gene can be responsible for both autosomal dominant non-syndromic HL (DFNA6/14/38) and Wolfram syndrome [WFS1 gene encodes \u201cWolframin\u201d, a transmembrane protein located in the endoplasmic reticulum and ubiquitously expressed [Autosomal dominant non-syndromic sensorineural deafness 6/14/38 (DFNA6/14/38) is caused by heterozygous mutations in the ome 4p16 . The DFN6 [WFS1) . Mutatioural HL) ,191. Thexpressed ,196,197,xpressed ,202,203,xpressed ,209,210.xpressed ,212,213,xpressed , Danish xpressed , Hungarixpressed , Finnishxpressed , and Gerxpressed familiesxpressed , the Repxpressed ,221, Iraxpressed , and Indxpressed . HL is gxpressed . InteresPOU4F3 gene on chromosome 5q32 [POU4F3 gene encodes a transcription factor which plays a key role in the maintenance of inner ear hair cells [Autosomal dominant non-syndromic sensorineural deafness 15 (DFNA15) is caused by heterozygous mutations in the ome 5q32 . The POUir cells . DFNA15 ir cells ,226,227 ir cells ,231,232.ir cells ,235,236.ir cells ,237,238,ir cells ,240, Japir cells ,241, andir cells . HL is pir cells . It is cir cells . HL may ir cells .KCNQ4 gene on chromosome 1p34.2 [Autosomal dominant non-syndromic sensorineural deafness 2A (DFNA2A) is caused by a heterozygous mutation in the e 1p34.2 .KCNQ4 gene forms a potassium channel that plays a key role in the regulation of neuronal excitability, particularly in the sensory cells of the cochlea [KCNQ4 mutations was reported in Indonesian [The protein encoded by the cochlea . Autosomdonesian , Americadonesian ,249,250,donesian ,253,254,donesian ,256,257,donesian , Brazilidonesian , Pakistadonesian , Iraniandonesian , Chinesedonesian ,263,264,donesian ,267,268 donesian ,269, Dutdonesian ,273,274,donesian ,271, anddonesian familiesdonesian . Most paEYA4 gene on chromosome 6q23 [EYA4 gene encodes a member of the eyes absent (EYA) family of proteins, which is a transcriptional activator required for proper eye development as well as for the maturation and maintenance of the organ of Corti. Mutations in EYA4 can also cause a syndromic variant characterized by HL and dilated cardiomyopathy [EYA4 gene were reported in Belgian [Autosomal dominant non-syndromic sensorineural deafness 10 (DFNA10) is caused by heterozygous mutations in the ome 6q23 . The EYAmyopathy . DFNA10 myopathy ,280,281,myopathy , Indian myopathy , Korean myopathy ,283,284,myopathy ,289,290,myopathy , and Japmyopathy ,291 fami Belgian ,293, Nor Belgian , Hungari Belgian , Swedish Belgian , Dutch [ Belgian , Italian Belgian , Slovaki Belgian , and Spa Belgian families Belgian . The aud Belgian . DFNA10 Belgian .GJB2 gene), DFNA3B (GJB6 gene), DFNA6/14/38 (WFS1 gene), DFNA7 (LMX1A gene), DFNA8/12 (TECTA gene), DFNA13 (COL11A2 gene), DFNA19 (unknown gene), DFNA23 (SIX1 gene), DFNA24 (unknown gene), DFNA27 (REST gene), DFNA30 (unknown gene), DFNA37 (COL11A1 gene), DFNA40 (CRYM gene), DFNA59 (unknown gene), DFNA66 (CD164 gene), DFNA69 (KITLG gene), DFNA71 (DMXL2 gene), DFNA78 (SLC12A2 gene), DFNA80 (GREB1L gene), DFNA84 (ATP11A gene), DFNA87 (PI4KB gene), and DNA89 (ATOH1 gene) (TECTA gene), DFNA13 (COL11A2 gene), DFNA19 (unknown gene), DFNA23 (SIX1 gene), DFNA24 (unknown gene), DFNA40 (CRYM gene), DFNA59 (unknown gene), DFNA66 (CD164 gene), DFNA69 (KITLG gene), DFNA76 (PLS1 gene), DFNA78 (SLC12A2 gene), and DFNA80 (GREB1L gene), which tend to be stable (DIAPH1 gene), DFNA6/14/38 (WFS1 gene), DFNA44 (CCDC50 gene), DFNA49 (unknown gene), DFNA54 (unknown gene), DFNA56 (TNC gene), DFNA57 (unknown gene), and sometimes DFNA11 (MYO7A gene), and DFNA69 (KITLG gene) . The dege stable . Interese stable . HoweverLG gene) .DIAPH1 gene on chromosome 5q31 and causes progressive low-frequency HL, resulting in a profound degree by the fourth decade of life [WFS1 gene on chromosome 4p16 and does not progress to profound HL [TECTA gene), DFNA13 (COL11A2 gene), DFNA31 (unknown gene), DFNA37 (COL11A1 gene), DFNA66 (CD164 gene), and DFNA72 (SLC44A4 gene) . AlthougA4 gene) .All children diagnosed with sensorineural HL should be screened early for genetic mutations to ensure timely appropriate treatments , personalized rehabilitation programs , prognosis , and family planning . The teaGJB2, COCH, MYO7A, ACTG1, or MYO6 genes. Conversely, cochlear implants are generally less effective if genetic mutations affect auditory nerve function [Cochlear implantation has a high probability of being effective if the mutated lesion is located in the hair cells or afferent synapses between hair cells and the auditory nerve, such as in patients with pathogenic variants in function ,302,303.As a matter of fact, better knowledge regarding genotype\u2013phenotype correlation and cochlear implant outcome may provide effective auditory rehabilitation and would reduce unnecessary procedures, thereby limiting both surgical risks and healthcare costs .The genetics of non-syndromic HL are constantly evolving, and there are currently many limitations of knowledge in this field. The etiology of some patients with evident familial HL still remains unknown. Indeed, intra-familial variability in sensorineural HL is common not only from parent to child in dominant cases but also between siblings . Many paCurrently, many children with mild or progressive forms of HL remain undiagnosed during their critical period of speech development and neuroplasticity. Therefore, it appears to be a priority to develop a new cost-effective method of universal genetic screening that ensures early diagnosis of genetic HL in order to identify potential comorbid conditions and guide treatments .In recent years, there have been major advances in the development of gene therapy vectors to treat sensorineural HL in animal models, representing a promising approach to prevent or slow down genetic HL. Interestingly, gene therapy is not limited to the addition of a healthy copy of the defective gene but may also involve gene silencing or editing through nucleic acid-based strategies, including antisense oligonucleotides, siRNA, microRNA, or nuclease-based gene editing . HoweverPatients diagnosed with autosomal dominant non-syndromic HL typically have a parent affected by HL, although de novo mutations should be considered in the case of negative family history. Overall, autosomal dominant non-syndromic HL tends to be bilateral, post-lingual in onset, high-frequency, progressive, and variable in severity. However, congenital, low-frequency, and stable forms of HL are also possible. A long and accurate audiological follow-up is of paramount importance to early identify hearing threshold deterioration and ensure prompt treatment with hearing aids or cochlear implants according to the degree of HL.Despite the importance of the major findings, the study has many limitations, including that it does not show the mutations described in each gene and whether there are \u201chot spots\u201d mutations or domains in which these mutations are localized."} +{"text": "A global outbreak of mpox occurred in 2022; we evaluated characteristics of mpox patients in Minnesota.Cases of mpox are reportable to the MN Department of Health (MDH). Cases are interviewed to collect demographic, exposure and clinical information; medical records from hospitalized patients (HP) are reviewed to collect data on clinical course, testing and treatment.> 14 days prior to symptoms; no HP received vaccine. Unstable housing and substance use were reported in 5 and 7 HP respectively. HP, if PWH were 4.1 times more likely to have CD4< 200 or detectable virus (p=0.035). Reasons for hospitalization included oropharyngeal pain/airway compromise (4), painful proctitis (1), isolation (2), epididymitis/orchitis (1), and preseptal cellulitis (1). The median length of initial stay was 4.5 days (range 1-10). A case with concomitant GAS pharyngitis (not PWH) required intubation and prolonged stay. Other longer length of stay occurred for isolation (2 PWH) and for PWH who had non-suppressed HIV and severe mpox disease.Between June 25 and November 5, 2022, 234 lab-confirmed cases of mpox, including 10 HP and 0 deaths were reported; 85% cases were interviewed. Overall median age was 34 years (IQR 29-43), 59% White, 92.3% male and 34% persons living with HIV (PWH). One outpatient received JYNNEOS vaccine Among HP, mean orthopox testing occurred 6.1 days (range 0-14) and mean tecovirimat initiation 8.6 days (range 3-18), following symptom onset; similar to outpatient cases. Three HP received no mpox therapies (including 1 PWH). Of 5 HP and PWH, 3 had CD4 < 100; all received tecovirimat. One PWH (with CD4 36) required 3 hospitalizations totaling 69 days and multiple courses of po (108 days) and IV (26 days) tecovirimat, VIGIV (6), brincidofivir (4), cidofovir (7), and topical and intralesional cidofovir.Approximately 4% of reported mpox were HP; reasons varied including unstable housing and need for isolation. Very severe courses occurred in a patient with GAS superinfection and 1 of 3 PWH with low CD4. Attention to potential superinfection, HIV infection and suppression are important. Efforts must be strengthened to reach at risk populations, including those with less access to care, for education and mpox vaccination.All Authors: No reported disclosures"} +{"text": "It is crucial to note that comorbidities may significantly increase the risk of mortality among COVID-19 patients. That's why it's vital for individuals with multiple comorbidities to make getting fully vaccinated a top priority, in order to safeguard their own health and the health of those around them. This study describes prevalence of comorbidities and COVID-19 vaccination among patients who died of COVID-19.This was a retrospective study that assessed 220 inpatients at the UNC Medical Center who died with COVID-19 per discharge diagnosis from 7/11/21-4/3/23. Data included demographics, COVID-19 vaccination status and preexisting comorbidities. Comorbidities were classified based on CDC designated risk factors for severe COVID-19 .> 65 years, 60% were male, and 90% of patients had comorbidities ranging from 1 to > 3. The top 6 comorbidities among all genders and ages were hypertension (48%), heart conditions (42%), diabetes (35%), chronic kidney disease (29%), immunocompromised (29%), and obesity (25%), respectively. The proportion vaccinated was 38%; among those vaccinated, doses received were 1 (11%), 2 (40%), 3 (32%), 4 (10%), and 5 (7%). Among those who died and were vaccinated, they were 1.13 times more likely to have comorbidities (97%) compared to those not vaccinated (86%) (Risk ratio (RR) 1.13, 95% CI 1.05-1.22, P=0.004) (Table).Of 220 patients who died, 45% were Prevalence of comorbidities and vaccination among COVID-19 deaths> 65 years with comorbidities, most often with multiple comorbidities. Hypertension, heart conditions, diabetes, chronic kidney disease, immunocompromised, and obesity emerged as the most common comorbidities. More than half of the patients had not received COVID-19 vaccination. This highlights the importance of getting fully vaccinated, especially for those with pre-existing conditions.In this cohort study of COVID-19 deaths, the majority of patients dying with COVID-19 were White, non-Hispanic, males David J. Weber, MD, MPH, BD: Advisor/Consultant|Germitic: Advisor/Consultant|GSK: DSMB|PDI: Advisor/Consultant|Pfizer: Advisor/Consultant|Wellair: Advisor/Consultant"} +{"text": "Nature Communications 10.1038/s41467-020-18859-x, published online 12 November 2020Correction to: The original Article contained errors in text in the Methods section, and in Equations (2), (4), (6), (11), and (15). All calculations were performed with the correct equations, so none of the reported results or conclusions are affected.In the section \u201cSingle-molecule fluorescence spectroscopy\u201d of the Methods section, the second sentence incorrectly read \u2018After passing through a 100-mm pinhole, \u2026\u2019. The correct version states \u2018100-\u03bcm pinhole\u2019 instead of \u2018100-mm pinhole\u2019.Equation (2) incorrectly readThe correct form of Equation (2) isEquation (4) incorrectly readThe correct form of Equation (4) isEquation (6) incorrectly readThe correct form of Equation (6) isEquation (11) incorrectly readThe correct form of Equation (11) isEquation (15) incorrectly readThe correct form of Equation (15) isThis has been corrected in both the PDF and HTML versions of the Article."} +{"text": "Studying post-vaccination side effects and identifying the reasons behind low vaccine uptake are pivotal for overcoming the pandemic.This cross-sectional study was distributed through social media platforms and face-to-face interviews. Data from vaccinated and unvaccinated participants were collected and analyzed using the chi-square test, multivariable logistic regression to detect factors associated with side effects and severe side effects.Of the 3509 participants included, 1672(47.6%) were vaccinated. The most common reason for not taking the vaccine was concerns about the vaccine\u2019s side effects 815(44.4). The majority of symptoms were mild 788(47.1%), followed by moderate 374(22.3%), and severe 144(8.6%). The most common symptoms were tiredness 1028(61.5%), pain at the injection site 933(55.8%), and low-grade fever 684(40.9%). Multivariable logistic regression analysis revealed that <40\u2009years , females , did not receive influenza shot last year , AstraZeneca , co-morbidities , and diabetes mellitus were associated with severe post-vaccine side effects. Serious side effects reported were blood clots 5(0.3%), thrombocytopenia 2(0.1%), anaphylaxis 1(0.1%), seizures 1(0.1%), and cardiac infarction 1(0.1%).Our study revealed that most side effects reported were mild in severity and self-limiting. Increasing the public\u2019s awareness of the nature of the vaccine\u2019s side effects would reduce the misinformation and improve the public\u2019s trust in vaccines. Larger studies to evaluate rare and serious adverse events and long-term side effects are needed, so people can have sufficient information and understanding before making an informed consent which is essential for vaccination. Age < 40 years, females, not receiving influenza shot, AstraZeneca vaccine, co-morbidities, and diabetes mellitus were factors significantly associated with severe post-vaccination side effects.Although most of the reported vaccine side effects were mild in severity and well-tolerated, larger prospective studies to understand the causes of rare serious adverse events and long-term side effects are needed to overcome vaccine hesitancy among people and enable them to have sufficient information and understanding before making an informed consent which is essential for vaccination. On 11 March 2020, the novel Coronavirus disease of 2019 (Covid-19) was announced a pandemic by the World Health Organization (WHO), only four months after the first known case of Covid-19, reported in China [The vigilance around personal protective measures including wearing face masks, maintaining interpersonal 2-meter distance, avoiding mass gatherings, washing hands, and quarantine have slowly eased off. Although such measures might have mitigated the spread and thus saved lives, sustaining these measures in the long term must be balanced against the various health, social, and economic aspects , as leadToday 2.7 billion people have yet to receive their first vaccine dose against Covid-19 . Most ofAlthough the efficacy and safety of the approved vaccines have been shown to be promising by many prestigious organizations ,10, infoOur study aims to assess Covid-19 vaccine uptake, self-reported vaccine side effects and the reasons for not taking the vaccine among Syrians more than a year after the introduction of vaccines in Syria. The objectives of this study are to identify factors associated with Covid-19 vaccine side effects and severe side effects.https://www.surveysystem.com/sscalc.htm) was used to calculate the sample size of 2401 participants based on a confidence interval of 2%, and a confidence level of 95%, for a population of 18284423.A cross-sectional study was carried out between 13 April 28 and May 2022, using convenience sampling strategy. A literature review was conducted to find related research on the topic of the study using relevant keywords . After an extensive review, the survey was created by the authors according to the information published by the Centres for Disease Control and Prevention (CDC) . The secvia Google Forms and were analyzed by entering the data in the statistical package for the social sciences (SPSS) software version 25. Descriptive statistics were used to express the socio-demographic features of the study sample. Pearson Chi-Square test was performed to evaluate the association between categorical variables. All p-values < 0.05 were considered statistically significant. A multivariable logistic regression model was carried out to detect factors associated with side effects (vs. no side effects), the selected factors included age (<40 vs \u226540), gender , smoking history (smoker vs non-smoker), occupation , seasonal influenza shot (received it vs did not receive it), vaccine brand , history of Covid-19 infection (positive history vs no history of Covid-19 infection before vaccination), and co-morbidities (yes vs no). These selected factors entered into the model concurrently. The second multivariable logistic regression model was developed to identify factors associated with severe adverse effects . the selected factors included age (<40 vs \u226540), gender , smoking history (smoker vs non-smoker), occupation , seasonal influenza shot (received it vs did not receive it), vaccine brand , history of Covid-19 infection (positive history vs no history of Covid-19 infection before vaccination), co-morbidities (yes vs no), diabetes mellitus (vs no diabetes mellitus), and hypertension (vs no hypertension).The data was collected p-value < .001). Regarding residency, people who live in rural areas were lower in the vaccinated 341 (20.4%) compared with the unvaccinated group 552 (30.0%) . In contrast, Syrians who live in cities or who took the vaccine outside Syria were higher in the vaccinated group 1160 (69.4%) and 171 (10.2%) compared with the unvaccinated group 1244 (67.7%) and 41 (2.2%) respectively. Further data about participants residing outside Syria are available in the Supplementary Table 1. There were higher proportions of healthcare workers in the vaccinated group 660 (39.5%) compared with the unvaccinated group 380 (20.7%) . Participants with a history of known allergy, chronic co-morbidity, and smoking were lower in the vaccinated group 208 (12.4%), 369 (22.1%), and 727 (43.5%) compared with the unvaccinated group 288 (15.7%), 459 (25.0), and 902 (49.1%) respectively. Participants who received an influenza shot last year were higher in the vaccinated group 406 (24.3%) compared with the unvaccinated group 87 (4.7%) . Of 3509 participants enrolled in the study, 1672 (47.6%) received at least one dose of the Covid-19 vaccine while 1837 (52.3%) remain unvaccinated. Of 1672 participants with at least one dose of Covid-19, 316 (18.9%) were partially vaccinated and 1356 (81.1%) were fully vaccinated. Males represented 1662 (47.4%) and females represented 1847 (52.6%) of the sample. The age group 20 to 29\u2009years represented a majority in the sample 1380 (39.3%). Participants in the age category 30 to 59\u2009years were lower in the vaccinated group 689 (41.2%) compared with the unvaccinated group 819 (44.6%) (The 1837 unvaccinated participants reported the following reasons for not taking the vaccine: concern about the vaccines side effects 815 (44.4%), unconvinced of the vaccine benefits 762 (41.5%), will not contract Covid-19 as previously contracted the virus 400 (21.8%), medical exemption 94 (5.1%), and vaccine unavailability 84 (4.6%).p-value < .001). Reported severe side effects was higher among participants in the age categories 16\u201320\u2009years 16 (11.0%), 20\u201329\u2009years 60 (8.3%), 30\u201339\u2009years 29 (9.5%), and 40\u201349\u2009years 34 (15.0%) compared with the age categories 50\u201359\u2009years 4 (2.6%) and 60\u2264 years 1 (0.9%) had mild side effects, 374 (22.3%) had moderate side effects, 366 (21.9%) had no side effects, and 144 (8.6%) had severe side effects. Regarding gender, a higher proportion of females suffered from severe side effects 104 (72.2%) compared with males 214 (58.5%) ( < .001) .p-value < .001). Of the co-morbidities reported, diabetes mellitus was associated with higher numbers of mild side effects 27 (32.1%) compared with no side effects 21 (25.0%) , while allergies, respiratory disease, and hematological disease were associated with higher numbers of severe side effects 60 (28.8%), 13 (23.2%), and 4 (36.4%) compared with no side effects 31 (14.9%), 10 (17.9%), and (0.0%) , , and , respectively (Participants with chronic co-morbidities reported higher numbers of mild side effects 156 (42.3%) compared with no side effects 78 (21.1%) . A history of Covid-19 infection was associated with higher numbers of vaccine side effects 583 (82.6%) compared with no side effects 123 (17.4%) . Participants who received an influenza vaccine (flu jab) reported higher numbers of mild side effects 192 (47.3%) and no side effects 133 (32.8%) compared with moderate side effects 60 (14.8%) and severe side effects 21 (5.2%) (The majority 591 (81.3%) of smokers reported post-vaccine side effects compared with no side effects 136 (18.7%) ( < .001) .p-value = 0.001) (Vaccine brands available in Syria at the time of the study were AstraZeneca-Oxford 552 (33.0%), Sputnik light 294 (17.5%), Pfizer-BioNTech 280 (16.7%), Sputix v 203 (12.1%), Sinophram 140 (8.4%), Sinovac 93 (5.6%), Johnson & Johnson 58 (3.5%), and Moderna 52 (3.1%). The majority of symptoms started within 12 to 24\u2009h 614 (47.0%) while the minority started after 48\u2009h 36 (2.8%) (= 0.001) .p-value < .001). Headache was more common among Moderna 27 (51.9%) compared with Sinovac 23 (24.7%) . Low grade fever (<39) was more common among Johnson & Johnson 32 (55.2%) compared with Sinovac 26 (28.0%) . High grade fever was more common among AstraZeneca 90 (16.3%) compared with Pfizer-BioNTech 14 (5.0%) . Chills were higher among AstraZeneca 157 (28.4%) compared with Sinovac 5 (5.4%) . Pain at the injection site was more common among Sputnik light 190 (64.6%) compared with Sinovac 31 (33.3%) . Swelling, redness, and/or temperature at the injection site were more common among Moderna 15 (28.8%) compared with Sinovac 5 (5.4%) . Joint pain was more common among Johnson & Johnson 25 (43.1%) compared with Pfizer-BioNTech 65 (23.2%) . Myalgia was more common among AstraZeneca 261 (47.3%) compared with Sinopharm 30 (21.4%) . Diarrhoea was more common among Johnson & Johnson 7 (12.1%) compared with Sputnick light 2 (0.7%) . Blurred vision was higher among AstraZeneca 22 (4.0%) compared with Johnson & Johnson 0 (0.0%) . Sweating was more common among Johnson & Johnson 19 (32.8%) compared with Sinopharm 18 (12.9%) and Sinovac 12 (12.9%) . Cough was more common among Moderna 14 (26.9%) compared with Sputnick light 20 (6.8%) . Nasal congestion was more common among AstraZeneca 97 (17.6%) compared with Sputnick light 21 (7.1%) . Runny nose was more common among Johnson & Johnson 8 (13.8%) compared with Sputnick light 10 (3.4%). Sore throat was more common among AstraZeneca 76 (13.8%) compared with Sinopharm 9 (6.4%) . Laziness was more common among AstraZeneca 247 (44.7%) compared with Sinovac 18 (19.4%) . Insomnia was more common among Sputnick light 87 (29.6%) compared with Sinopharm 24 (17.1%) . Dysrhythmia was more common among AstraZeneca 64 (11.6%) compared with Sinopharm 2 (1.4%). Hypotension or hypertension was more common among Moderna 5 (9.6%) compared with Johnson & Johnson 0 (0.0%) . Chest pain was more common among Johnson & Johnson 5 (8.6%) compared with Moderna 1 (1.4%) . Dyspnoea was more common among AstraZeneca 57 (10.3%) compared with Sinopharm 5 (3.6%) . Anxiety was more common among Johnson & Johnson 8 (13.8%) compared with Sinopharm 0 (0.0%) (The most common reported side effects were tiredness and fatigue 1028 (61.5%), pain at the injection site 933 (55.8%), low-grade fever 684 (40.9%), headache 648 (38.8%), and muscle pain 615 (36. 8%). Tiredness and fatigue were higher among AstraZeneca-Oxford 377 (68.3%) and Sputnick light 200 (68.0%) compared with Sinophram 67 (47.9%) and Sinivac 39(41.9%) ( < .001) .p-value < .001), while most of the mild side effects were associated with Sputnik light 168 (57.1%) compared with AstraZeneca 215 (38.9%) . Moderate side effects were most reported among participants who received Johnson & Johnson 21 (36.2%) compared with Sinovac 8 (8.6%) . Severe side effects were most associated with AstraZeneca 83 (15.0%) compared with Sinopharm 5 (3.6%) compared with Johnson & Johnson 7 (12.1%) ( < .001) . Post-va < .001) . Shockin < .001) , and L.p-value = 0.011) , 12-24\u2009h 508 (38.9%), 1-2\u2009days 380 (29.1%), 3\u2009days to 1\u2009week 105 (8.0%), 1-2\u2009weeks 23 (1.8%), and >2\u2009weeks 28 (2.1%) (= 0.011) . ParticiThe proportion of participants who took painkillers for their symptoms were higher among AstraZeneca 377 (68.3%), Johnson & Johnson 39 (67.2%), Sputnik Light 182 (61.9%), Sputnik v 122 (60.1%), and Moderna 31 (59.6%) compared with Pfizer-BioNTech 139 (49.6%), Sinopharm 69 (49.3%), and Sinovac 42 (45.2%). The highest number of required hospitalization post-vaccination was among AstraZeneca 34 (6.2%) .Serious medical complications, such as blood clots and low platelet counts were reported by 5 (0.3%) and 2 (0.1%) respectively. Anaphylaxis shock 1 (0.1%), seizures 1 (0.1%), and cardiac infarction 1 (0.1%) were only reported among those who took the AstraZeneca vaccine .p-value < .001). The highest Covid-19 reinfection rate after the first dose was among Sinovac 12 (12.9%), whereas after the second dose was among Sinopharm 21 (15.0%) and after taking two doses 117 (7.0%) ( < .001) .p-value < .001). Viral- vector vaccines were also associated with higher percentage of severe side effects and use of painkillers 111 (10.0%) and 720 (65.0%) respectively compared to other types of formation . The highest reported Covid-19 reinfection rate after the first dose and the second dose were among inactivated vaccines 23 (9.9%) and 26 (11.2%) retrospectively , showed that viral-vector vaccines were associated with a higher percentage of side effects 905 (81.8%) compared with m-RNA vaccines 250 (75.3%) and inactivated vaccines which were associated with lowest post vaccination side effects 151(64.8%) (= 0.013) .p-value < .001), females , current smoker , did not receive Influenza shot last year , AstraZeneca vaccine , history of Covid-19 infection pre-vaccination , and co-morbidities were significantly associated with post-vaccination side effects , females , did not receive influenza shot last year , AstraZeneca , co-morbidities , and diabetes mellitus were significantly associated with severe post-vaccination side effects (A multivariate logistic regression analysis was performed to identify the variables including age, sex, smoking, occupation, influenza vaccine, vaccine brand, history of Covid-19 infection, co-morbidities, hypertension, and diabetes mellitus and their association with the development of severe side effects versus no, mild, and moderate side effects post-vaccination. The logistic regression model was statistically significant for the following factors, age <40 (vs. \u226540; OR: 2.113, effects .Multiple vaccines have been developed during the past two years; these vaccines must be available, safe, and effective , with thRegarding vaccinated participants, 78.1% were symptomatic after receiving a Covid-19 vaccine. The most common symptoms according to our results were tiredness and fatigue, pain at the injection site, low-grade fever, headache, and muscle pain. This was consistent with previous studies conducted in Saudi Arabia, Iraq, and the Czech Republic . The symIn this study, people with a history of previous Covid-19 infection had greater odds of post-vaccine side effects. This finding was similar to previous studies conducted in the United Kingdom and Italy ,47. PartPain at the injection site was the most frequent symptom, and the reason behind this might be due to delayed-onset injection site reactions ,50, or wSyrian vaccination rates are extremely low by global standards , but theThe cross -vaccine comparison of our study showed that viral vector-based vaccines were associated with the more frequent side effects. Our results are consistent with the findings of a German cross-sectional study . A studyThe data deduced may not be generalized to the wider Syrian population. Credible published national data on the socio-demographic distribution of the population are unavailable to assess the representativeness of the study\u2019s sample. The authors used a convenience sampling strategy involving various social media platforms and convenient location interviews. Syrians of an older age group represented a minority due to limited internet access. The elderly, the most vulnerable population, require vaccine protection; therefore, a study must be conducted to assess the vaccine uptake among this age group. As such, reaching out to these vulnerable populations must be prioritized. Additionally, as this study is a self-reported survey, the responses may be subject to recall bias.Most of the reported vaccine side effects were mild in severity and well-tolerated. However, age < 40\u2009years, females, not receiving influenza shot, AstraZeneca vaccine, co-morbidities, and diabetes mellitus were factors significantly associated with severe post-vaccination side effects. Viral vector-based vaccines were associated with the more frequent side effects. Inactivated virus vaccines were associated with lower adverse effects and higher reinfection rates following vaccination. Larger prospective studies to understand the causes of rare serious adverse events are needed to overcome vaccine hesitancy among people. The long-term adverse effects of vaccines will become more important in the future. However, these adverse effects may not be known unless the medical environment is favourable and access to medical care is easy.Click here for additional data file."} +{"text": "Background and objectives: Since the introduction of the COVID-19 vaccine through the National COVID-19 Immunization Program in Malaysia in February 2021, the number of cases of severe COVID-19 and mortality have progressively decreased. We explored the association between vaccination status, type of vaccine, and the highest COVID-19 clinical category. Methods: Patients were recruited via the electronic medical record (EMR) at University Malaya Medical Centre (UMMC) from July 2021 onward. Included patients were aged \u226518 years old with positive SARS-CoV-2 RT-PCR results from respiratory samples . Patient demographic data, COVID-19 clinical category, vaccination status, and type of vaccine received were recorded. Results: In total, 1,391 positive SARS-CoV-2 PCR results were reviewed; 1,188 patients (85%) with complete data were analyzed. These patients\u2019 median age was 50 years. The proportions of patients COVID-19 clinical categories were as follows: category 1 (4.04%), category 2 (28.37%), category 3 (10.7%), category 4 (30.6%), and category 5 (2.6%). The mortality rate was 21.5%. As of July 2021, only 16.8% of patients were fully vaccinated, 30.3% were vaccinated, 31.5% unvaccinated, and 21.5% had unknown vaccination status. In total 364 patients with category 4 COVID-19 were fully vaccinated and no patients who were fully vaccinated had category 5 COVID-19 (P = .011). Furthermore, 40.8% of patients who died had unknown vaccination status (P < .01); 28.1% of patients who died were unvaccinated (P = .015); 25.3% of patients who died were partially vaccinated (P = .036); and 0.4% of patients who died were fully vaccinated (P < .001). For category 4 and 5 illness and death, there were no significant differences between the type of vaccine received and severe COVID-19. Conclusions: The completion of 2 doses of government-approved COVID-19 vaccination is paramount in preventing severe COVID-19 disease and death. Rapid rollout and equitable distribution of vaccination should be initiated. Vaccine hesitancy should be promptly addressed to ensure vaccination uptake."} +{"text": "Bartonella henselae infection causes Cat Scratch Disease (CSD). Lymphadenopathy is the most common symptom and a small percentage of patients have systemic impairment. CSD can mimic malignancy and manifest atypically, therefore reliable serological testing has clinical importance. CSD is diagnosed if two of the following criteria are met: 1) the presence of clinical symptoms consistent with CSD; 2) the existence of antibodies against B. henselae IgM and/or IgG (1:256) . We aim to assess the accuracy and diagnostic utility of IgM and IgG in pediatric patients with suspected CSD.A retrospective, observational and analytical study was carried out from April 2022 through April 2023. Medical and laboratory records of patients with follow-up in the Infectious Diseases Department of a Children's Hospital in Buenos Aires (Argentina) were evaluated.We included 244 serum samples from patients with clinical suspicion of CSD using Immunofluorescent assay (IFA).Median age: 84 (IQR 48-132) months, 137 were female, 95% (233/244) had cat interaction.Twenty eight percent (70/244) were diagnosed with CSD based on serological evidence: 83,9% (58/70) had IgM +/IgG + (group 1); 10% (7/70), IgM-/IgG+ >1/64 (group 2) and 7,15% (5/70), IgM+/IgG \u2013 (group 3). The average time of symptom onset was 22,8 (6-90) days for group 1, 29,4 (11-90) days for group 2, and 11,4 (5-15) days for group 3.Lymphadenopathy was found in 87,1% (61/70) with or without systemic involvement and 6 % (4/70) had systemic involvement without lymphadenopathy.IgM had Sensitivity: 89%, Specificity: 97%, Positive Predictive Value (PPV): 92% and Negative Predictive Value (NPV) : 96%.Between 5-15 days after the onset of symptoms, IgM allowed us to diagnose 5 patients with CSD. The identification of IgM antibodies in CSD patients with systemic impairment has a great diagnostic performance. IgM remained positive after 90 days . We were able to diagnose CSD in 7 patients between 11 and 28 days following the onset of symptoms due to the presence of IgG 1:256 or higher. Combination of different methods and a correct time of sampling, greater than 5 days, should be considered for rapid and accurate CSD diagnosis.All Authors: No reported disclosures"} +{"text": "Correction: European Radiology Experimental 7, 54 (2023)https://doi.org/10.1186/s41747-023-00369-2The original article containsIn the row \"Elective delivery, n (%)\", the respective cells state '30 (75)' and '7 (100)'.They should instead respectively state '13 (72.0)' and '17 (73.0)'\u00a0as shown in Table"} +{"text": "Acute coronary syndrome includes life-threatening clinical conditions ranging from unstable angina to non-Q-wave myocardial infarction and Q-wave myocardial infarction that are a major cause of emergency medical care and hospitalization in the United States. The American College of Cardiology/American Heart Association (ACC/AHA) guidelines on the management of patients with unstable angina and non-ST-segment elevation myocardial infarction (2002-2004) recommend (1) angiotensinconverting enzyme (ACE) inhibitors or angiotensin II receptor blockers (ARBs) for ACE inhibitor intolerance, (2) beta-blockers, and (3) statins for long-term treatment of patients after an acute coronary event.To examine rates of use of 3 key evidence-based drug therapies after hospital discharge for patients with acute coronary syndromes (ACS).The study cohort was identified using medical claims from commercial health plans within a managed care organization located in the Mid-Atlantic states, with approximately 3.4 million members with medical benefits of whom 1.2 million members (35.3%) had pharmacy benefits. Members were included if they were (1) aged e 18 years, (2) continuously enrolled with the same commercial plan from January 1, 2003, through December 31, 2005, (3) had any medical claims for hospitalization for ACS defined by International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes 410.xx or 411.1 (intermediate coronary syndrome) during the sample identification period from July 1, 2003 through June 30, 2004, and (4) had no medical claims for ACS hospitalizations from January 1, 2003, through June 30, 2003, in any of 10 diagnosis fields on an inpatient hospital claim. Pharmacy claims for ACE inhibitors, ARBs, beta-blockers, and statins were obtained for 18 months following each index date, defined as the earliest ACS diagnosis date during the identification period. Utilization was defined as the member having at least 1 pharmacy claim within each class from index date to 3 months post-index date. Five time periods were examined to assess therapy: - 180 to 0 days (6 months prior), 0 to 90 days (3 months), 0 to 180 days (6 months), 0 to 365 days (12 months), and 0 to 548 days (18 months) following the index date. ACE inhibitors and ARBs were considered together . Logistic regression analyses were used to predict use of the 3 drug classes for patients with different clinical (diagnosis and prior use) and demographic (sex and age) characteristics.The study cohort included 1,135 patients with ACS as defined by ICD-9-CM codes in medical claims from July 1, 2003, to June 30, 2004. Nearly 65% of the sample patients were men (n = 734 men and n = 401 women), with a mean (standard deviation [SD]) age of 63.8 (SD 13.1) years. Of the 1,135 members with ACS, 588 (51.8%) had at least 1 pharmacy claim for an ACE inhibitor or ARB, 725 (63.9%) for a beta-blocker, and 710 (62.6%) for a statin during the 3-month follow-up period; receipt of at least 1 prescription in all 3 classes was found in 339 (29.9%) of patients. Patients who were aged less than 45 years, 65-79 years, and e 80 years were significantly less likely than patients aged 45-64 years to receive statins (P less than 0.05). In addition, patients who were aged e 80 years were significantly less likely to receive ACE inhibitors/ARBs (P = 0.003), beta-blockers (P less than 0.001), or all 3 classes (P = 0.002). Women were less likely than men to receive statins (P = 0.004) and all 3 drug classes (P = 0.012). Patients with intermediate coronary syndrome were significantly less likely than those with acute myocardial infarction to receive any of the study drugs (P less than 0.001). Those patients who had used ACE inhibitors/ARBs, beta-blockers, statins, and all 3 drug classes during the 6 months prior to the index diagnosis of ACS were more likely than those without prior use to have these medications continued after ACS diagnosis.At 3 months following the index ACS hospitalization, the majority of the patients were not receiving the 3 guideline medication therapies. ACS patients with intermediate coronary syndrome and those aged 80 years or older were less likely to be receiving any of the 3 therapies, and women were less likely than men to receive statin therapy."} +{"text": "BACKGROUND: The National Quality Forum recently endorsed the proportion of days covered (PDC)\u2014a measure of medication adherence\u2014as an indicator of quality in drug therapy management.To inform initial efforts to improve the quality of drug therapy management, we compared PDC and persistence among new users of 6 commonly used chronic medication categories.A retrospective analysis of pharmacy claims in a database of more than 64 million members enrolled in 100 health plans assessed persistence and adherence to drug therapy in 6 chronic conditions. Patients were included in the analysis if they initiated a prescription drug of interest in any of 6 drug classes\u2014prostaglandin analogs, statins, bisphosphonates,oral antidiabetics, angiotensin II receptor blockers (ARBs), and overactive bladder (OAB) medications\u2014between January 1 and December 31, 2005.The first claim for a drug of interest during this period was considered a patient\u2019s index date. Patients were required to have a minimum of 12months of continuous enrollment both preceding and following their index date. New users of a treatment were identified by excluding patients who filled a prescription for any drug in the same class during the previous 12months and were followed for a minimum of 12 months. Nonpersistence was defined as discontinuation of the therapy class following an allowed gap between refills\u201430-, 60-, and 90-day refill gaps were used. Adherence was defined as a continuous measure of the proportion of days covered (PDC) during the 12-month post-index period. Logistic regression analyses predicted (a) nonpersistence during the 12-month post-index period and (b) adherence (PDC) of at least 80%, with drug class as the predictor variable of interest, controlling for demographic variables, insurance and plan type, history of hospitalization, Charlson comorbidity score,copayment for index medication, and number of medications at index.A total of 167,907 patients were identified across 6 cohorts.Using the 60-day gap, 6-month persistence rates were prostagl and in analogs 47%, statins 56%, bisphosphonates 56%, oral antidiabetics 66%,ARBs 63%, and OAB medications 28%. After the first 90 days of therapy,relative persistence was stable across cohorts, and rates declined consistently from 6 months post-index to study end. Logistic regression models showed that oral antidiabetic users had a 59%, 36%, 37%, and 79% decreased risk of nonpersistence in a 12-month follow-up period compared with patients taking prostaglandin analogs, statins, bisphosphonates, orOAB medications, respectively. Risk of nonpersistence decreased with increasing age. Mean (SD) 12-month adherence rates were: prostagl and in analogs 37% (26%), statins 61% (33%), bisphosphonates 60% (34%), oral antidiabetics 72% (32%), ARBs 66% (32%), and OAB medications 35%(32%). Logistic regression indicated that oral antidiabetic use was a significantpredictor of adherence (PDC) of at least 80% compared with other therapy classes. Adjusted odds ratios for oral antidiabetics were 17.60 versus prostaglandin analogs,2.06 (95% CI=1.99-2.12) versus statins, 1.92 (95% CI=1.83-2.02) versus bisphosphonates, 1.29 (95% CI=1.24-1.34) versus ARBs, and 5.77 (95%CI=5.38-6.19) versus OAB medications."} +{"text": "This cohort study examined the incidence, characteristics, and long-term outcomes of chronic immune-related adverse events from adjuvant anti\u2013programmable cell death-1 for advanced and metastatic melanoma at 6 institutions in the US and Australia. What are the incidence and spectrum of long-term outcomes of chronic immune-related adverse events (irAEs) from adjuvant anti\u2013programmable cell death-1 (anti\u2013PD-1) therapy?In this cohort study of 318 patients treated with adjuvant anti\u2013PD-1 therapy for advanced and metastatic melanoma, 63.3% of patients with chronic irAEs experienced persistent irAEs with prolonged follow up.These findings suggest that chronic irAEs are common and often persistent, emphasizing the importance of careful risk-benefit analysis and prolonged monitoring and management when considering adjuvant anti\u2013PD-1 therapy. Anti\u2013programmable cell death-1 (anti\u2013PD-1) improves relapse-free survival when used as adjuvant therapy for high-risk resected melanoma. However, it can lead to immune-related adverse events (irAEs), which become chronic in approximately 40% of patients with high-risk melanoma treated with adjuvant anti\u2013PD-1.To determine the incidence, characteristics, and long-term outcomes of chronic irAEs from adjuvant anti\u2013PD-1 therapy.This retrospective multicenter cohort study analyzed patients treated with adjuvant anti\u2013PD-1 therapy for advanced and metastatic melanoma between 2015 and 2022 from 6 institutions in the US and Australia with at least 18 months of evaluable follow-up after treatment cessation .Incidence, spectrum, and ultimate resolution vs persistence of chronic irAEs (defined as those persisting at least 3 months after therapy cessation). Descriptive statistics were used to analyze categorical and continuous variables. Kaplan-Meier curves assessed survival, and Wilson score intervals were used to calculate CIs for proportions.Among 318 patients, 190 (59.7%) were male , 270 (84.9%) had a cutaneous primary, and 237 (74.5%) were stage IIIB or IIIC at presentation. Additionally, 226 patients (63.7%) developed acute irAEs arising during treatment, including 44 (13.8%) with grade 3 to 5 irAEs. Chronic irAEs, persisting at least 3 months after therapy cessation, developed in 147 patients , of which 74 (50.3%) were grade 2 or more, 6 (4.1%) were grade 3 to 5, and 100 (68.0%) were symptomatic. With long-term follow-up , 54 patients (36.7%) experienced resolution of chronic irAEs (median [IQR] time to resolution of 19.7 [14.4-31.5] months from anti\u2013PD-1 start and 11.2 [8.1-20.7] months from anti\u2013PD-1 cessation). Among patients with persistent irAEs present at last follow-up ; 55 (59.1%) were grade 2 or more; 41 (44.1%) were symptomatic; 24 (25.8%) were using therapeutic systemic steroids (16 [67%] of whom were on replacement steroids for hypophysitis (8 [50.0%]) and adrenal insufficiency (8 [50.0%]), and 42 (45.2%) were using other management. Among the 54 patients, the most common persistent chronic irAEs were hypothyroid (38 [70.4%]), arthritis (18 [33.3%]), dermatitis (9 [16.7%]), and adrenal insufficiency (8 [14.8%]). Furthermore, 54 [17.0%] patients experienced persistent endocrinopathies, 48 (15.1%) experienced nonendocrinopathies, and 9 (2.8%) experienced both. Of 37 patients with chronic irAEs who received additional immunotherapy, 25 (67.6%) experienced no effect on chronic irAEs whereas 12 (32.4%) experienced a flare in their chronic toxicity. Twenty patients (54.1%) experienced a distinct irAE.In this cohort study of 318 patients who received adjuvant anti\u2013PD-1, chronic irAEs were common, affected diverse organ systems, and often persisted with long-term follow-up requiring steroids and additional management. These findings highlight the likelihood of persistent toxic effects when considering adjuvant therapies and need for long-term monitoring and management. While most severe irAEs are acute and resolve with glucocorticoids, we recently reported that up to 43% of irAEs persist for at least 12 weeks following therapy cessation in patients with melanoma treated with adjuvant anti\u2013PD-1.7Immune checkpoint inhibitors (ICIs) have become the preferred first-line treatment for advanced melanoma and produce durable antitumor responses in approximately 50% of patients.Given the expanding use of anti\u2013PD-1 across various tumor types, it is imperative to further assess its long-term effects, which have not been well defined. To address this gap, we conducted a large, multicenter cohort study with extended follow-up in patients with chronic irAEs from adjuvant anti\u2013PD-1 therapy. This study aimed to determine the incidence, characteristics, and long-term outcomes, including resolution vs persistence, of chronic irAEs from adjuvant anti\u2013PD-1.STROBE) reporting guideline. Institional review board or ethics committee approval was obtained from each institution, and informed consent was waived because patient data were deidentified.This cohort study followed the Strengthening the Reporting of Observational Studies in Epidemiology , treatment details , and disease recurrence details were collected from the electronic medical record from each institution. Type, grade, duration, treatment, and resolution details of acute, delayed, and chronic irAEs were noted.essation . In totaDescriptive statistics were used to analyze categorical and continuous variables. The IQR was calculated by subtracting the first quartile, the RFS or OS value below which 25% of the data fell, from the third quartile, the RFS or OS value above which 25% of the data fell. The start time for RFS and OS was the date of anti\u2013PD-1 initiation. Kaplan-Meier curves assessed survival using GraphPad version 9.5.1 (GraphPad Prism). Wilson score intervals were used to calculate CIs for proportions.Of the 318 patients included in this study, the median (IQR) age was 64 (52.3-72.0) years and 190 (59.7%) were male experienced acute irAEs and 53 (17.0%) experienced delayed toxic effects . Most acWe assessed how often acute irAEs, including delayed irAEs, became chronic. Adrenal insufficiency (8 of 10 patients [80.0%]), hypophysitis (8 of 8 patients [100.0%]), thyroiditis/hypothyroid (48 of 56 patients [85.7%]), neuropathy (6 of 7 patients [85.7%]), and nephritis (4 of 5 patients [80%]) appeared particularly likely to evolve into chronic irAEs, similar to our prior report . ColitisAmong all 318 patients, 147 patients developed chronic toxic effects, 74 (50.3%) of those patients (or 23.3% of the full cohort) had at least grade 2, and 6 (4.1%) of those patients (or 1.9% of the full cohort) were grade 3 to 5 . Of all Among 75 patients with acute endocrine irAEs, 64 (85.3%) became chronic, 11 of which also had nonendocrine irAEs. Among chronic endocrine irAEs, 20 (31.3%) were symptomatic, 55 (85.9%) were grade 2 or more, and 1 (1.6%) was grade 3 (hypophysitis). Additionally, 94 of 244 (38.5%) patients with acute nonendocrine irAEs developed chronic irAEs, of which 86 (91.5%) were symptomatic, 26 (27.7%) were grade 2 or more, and 6 (6.4%) were grade 3 to 5.With prolonged follow-up , 54 of 147 patients (36.7%) experienced resolution of chronic irAEs at last follow-up, while 93 of 147 patients with chronic toxic effects were ongoing . The medAmong the 93 patients with persistent toxic effects present at last follow-up, 55 were grade 2 or above and 41 remained symptomatic (eTable 4 in Compared with 77 patients without chronic irAEs (45.0%), 48 patients with chronic irAE (32.7%) developed disease recurrence, 18 (12.2%) had regional recurrence, and 30 (20.4%) had metastatic recurrence , increased from our previous study showing that 14.4% of chronic toxic effects resolved with at least 6 months follow-up. While endocrine toxic effects were more likely to become chronic and persist at last follow-up than nonendocrine toxic effects, other more symptomatic irAEs persisted at low rates individually, including cutaneous, rheumatologic, oral, and ocular events.9 The resolution of some chronic irAEs, as well as the flares occurring with retreatment (32.4%) suggest some patients have ongoing inflammation. The persistent nature of irAEs, particularly endocrinopathies, suggests that permanent damage may occur in some patients. For this population, rechallenge with a lower risk of irAEs may be possible .10 Further research should aim to identify patients that are predisposed to persistent toxic effects.We and others have previously speculated whether chronic irAEs represent smoldering autoimmunity vs a burnout phenotype, where all the relevant cells have been destroyed or damaged, leading to continued symptoms.This study had limitations. Review of toxic effects and adverse events using clinical data and notes may lack the fidelity of formal clinical trial adverse event reporting. Documentation may not mention every toxicity in every note, thus lowering the fidelity of the resolution date for individual patients. While most patients overlap with our prior study, the departure of 1 investigator from their prior institution resulted in slightly distinct patient populations from our previous study. RFS analysis between patients with and without chronic irAEs is highly likely to suffer from time-dependent bias.Insights into the long-term impact of adjuvant anti\u2013PD-1 therapy are crucial to optimize patient outcomes as these agents are used across different tumor types. The high prevalence of chronic irAEs suggests the importance of considering the risk-benefit ratio when initiating adjuvant therapy and the need for prolonged monitoring and proactive management of irAEs."} +{"text": "Over 1 million people traveled to Qatar and surrounding countries during the World Cup 2022 soccer tournament, a mass gathering that could enhance transmission of SARS-CoV-2 variants. Minimal information about circulating variants in World Health Organization (WHO) Eastern-Mediterranean region (EMRO) which includes Qatar, United Arab Emirates, and Saudi Arabia were available from global data bases (GISAID). The Traveler-based Genomic Surveillance (TGS) program samples arriving international travelers to detect new variants and fill surveillance gaps. Monitoring of flights from EMRO was increased during the tournament.Travelers at six US airports volunteered to provide nasal swabs that were pooled by flight origin and sent to laboratories for SARS-CoV-2 reverse transcription polymerase chain reaction. Positives underwent whole genome sequencing. Pool positivity and variant frequencies were compared for travelers from EMRO vs. other regions. Chi-square tests were used to determine statistical significance.During November 20, 2022\u2013January 2, 2023, 2050 sample pools from 16,595 travelers were collected. Of these, 100 pools (703 travelers) were from EMRO and 1950 pools were from other regions. Pool positivity from EMRO was 28% (28/100) vs. 25% (489/1950) in other regions (p=0.51). Regionally detected variant proportions were: EMRO (n=25) XBB (40%), BQ.1 (20%), BQ.1.1 (20%); Europe (n=166) BQ.1.1 (48%), BQ.1 (20%), XBB (9%); Western Pacific (n=51) BA.5 (24%), BN.1 (22%), XBB (18%); South-East Asia (n=21) BQ.1.1 (33%), XBB (29%), BA.2 (10%), BA.5 (10%), XBB.1.5 (10%); and Africa (n=15) BQ.1.1 (53%), BA.5 (27%), XBB (20%). The proportion of XBB in EMRO was significantly higher than Europe and Western Pacific regions (p< 0.05).During World Cup 2022, SARS-CoV-2 positivity was similar for travelers from EMRO compared to all other regions. Variant proportions differed among regions, with EMRO having the highest proportion of XBB, a recombinant lineage associated with higher transmissibility. TGS fills gaps in SARS-CoV-2 surveillance and can be surged during mass gathering events.Benjamin Rome, MBA, Ginkgo Bioworks, Inc.: Employee|Ginkgo Bioworks, Inc.: Stocks/Bonds Robert C. Morfino, MBA, Ginkgo Bioworks Inc.: I am an employee|Ginkgo Bioworks Inc.: Stocks/Bonds"} +{"text": "In loco nursing practice inspection costs in a Brazilian setting\u201d, with DOI code number https://doi.org/10.1590/1980-220X-REEUSP-2021-0382, published at Revista da Escola de Enfermagem da USP [online], v.56: e20210382, on the page 3:In the article \u201cWhere it was written:\u201cThe calculation of the weighted average of the monthly wages (144 hours/month) of the inspectors corresponded to BRL 23,167.30/144 from which the average cost per hour (BRL 115.84) and per minute (BRL 1.93) was obtained.\u201dShould read:\u201cThe calculation of the weighted average of the monthly wages (200 hours/month) of the inspectors corresponded to BRL 23,167.30/200 from which the average cost per hour (BRL 115.84) and per minute (BRL 1.93) was obtained.\u201d"} +{"text": "Most childhood meningitis nowadays is caused by viruses in countries with widespread use of conjugate vaccines. There is limited knowledge about outcomes following childhood viral meningitis, necessary to inform clinical guidelines.Children aged 19-42 months in Canterbury New Zealand, who had enterovirus (EV) or human parechovirus (HPEV) meningitis as infants were included. Clinical data was collected. Comprehensive neurodevelopmental assessments were completed using the Bayley Scale for Infant Development (BSID) Third Edition. Mean composite and scaled scores, and proportion below cutoff were assessed in each domain. Normative mean composite scores for any domain is 100. Expected scaled score range is 8-12. Mean scores between EV and HPEV meningitis were compared by t-tests, with P< 0.05 considered significant.BSID assessments were completed for 33 children of mean age 31 months, from 2019-22, including 23 with EV and 10 with HPEV meningitis. There were 24 children of NZ European, 4 M\u0101ori, 4 Asian, and 1 Middle Eastern ethnicity. Mean age at diagnosis was 43 days, and mean length of admission was 2.79 days (CI 1.74-3.15). Of 33 children, 32 (97%) received intravenous or intramuscular antibiotics, 6 (18%) received a fluid bolus on arrival at hospital, and 9 (27%) required high dependency or intensive care. Following viral meningitis, parents reported developmental speech concerns in 6 children, and delayed motor milestones in 1 child. There was no reported sensorineural hearing loss. BSID mean composite scores were in expected range for cognition 102 (CI 98-106), language 96 (93-100) and motor 102 (98-106) domains. Mean scaled scores were in expected range for receptive language 9 (9-10), expressive language 9 (9-10), fine motor 11 (11-12) and gross motor 9 (9-10) domains. Overall, 12/33 (36%) children had below expected scores in one area of development including cognition , receptive language , expressive language , and gross motor . There were no significant differences between BSID scores in EV and HPEV meningitis.Following viral meningitis, 36% percent of preschool children had findings below expected in at least one developmental domain, suggesting targeted follow-up should be considered.Manish Sadarangani, BM BCh, FRCPC, DPhil, GlaxoSmithKline: Grant/Research Support|Merck: Grant/Research Support|Moderna: Grant/Research Support|Pfizer: Grant/Research Support|Sanofi Pasteur: Grant/Research Support|Seqirus: Grant/Research Support|Symvivo: Grant/Research Support|VBI Vaccines: Grant/Research Support"} +{"text": "Mycobacterium-avium complex infection (DMAC) remains a concerning issue given its high mortality and diagnostic challenges. Therefore, we aimed to describe the clinical and microbiological characteristics and outcomes of PWH with DMAC in a tertiary care center in Mexico City over a period of 23 years.Despite universal access to combined antiretroviral therapy (ART) in Mexico since 2005, people with HIV (PWH) still present with late-stage complications due to delayed diagnosis and/or entry into care. Among these complications, disseminated In this retrospective study, we reviewed all records of PWH attending our hospital from 1999-2022. We included adult PWH with any positive extra-pulmonary MAC-culture. We developed a standardized case report form and recorded sociodemographic, clinical, and microbiological characteristics. We followed patients until microbiological cure or death.We included 37 PWH diagnosed with DMAC infection, of whom 34 (92%) were men. Overall, 4 (11%) were diagnosed with DMAC before 2005 and 33 (89%) after 2005. The median age was 34 years (IQR 27-36 years). Following HIV diagnosis, mean time to diagnosis of DMAC was 14.2 months (IQR 1.6-11.3 months). At DMAC diagnosis, 12 (32%) patients were on ART and 25 (68%) were ART na\u00efve. Fever was the most common presenting symptom, affecting 32 patients (86%). Mean time to microbiological diagnosis was 34 days. The most common sites for culture isolation were blood (76%) and bone marrow (70%). Anemia occurred in 34 patients (92%), followed by leukopenia in 23 (62%) and pancytopenia in 9 (24%). All patients required hospitalization, with 32 (86%) receiving DMAC-specific treatment and 5 (14%) dying before treatment initiation. Thirty-four patients (92%) received a clarithromycin-based regimen, 15 (41%) of patients developed IRIS. Overall mortality during follow-up was 51%, with 79% deaths occurring within the first year after DMAC diagnosis.Despite universal ART access, DMAC remains a high-mortality AIDS-defining illness in Mexico City. Efforts must be made to promote HIV testing, early diagnosis, and entry into care.All Authors: No reported disclosures"} +{"text": "Salmonella infection. However, clinical information of infectious complications in this patient population remains scarce.Adult-onset immunodeficiency (AOI) with anti-interferon (IFN)-\u03b3 autoantibodies is an acquired immunodeficiency syndrome increasingly recognized in East and Southeast Asia. Antibody against IFN- \u03b3 or its receptor is the main pathophysiology leading to opportunistic infections especially mycobacterial, dimorphic fungal or A retrospective study was conducted in Buddhachinaraj hospital, Phitsanuloke, Thailand. We collected data on demographic, infectious complications, treatment and outcomes in patients with AOI with anti-IFN-\u03b3 autoantibodies who presented to our center between March 2013 and February 2023. All patients were diagnosed by elevation of anti-IFN- \u03b3 antibody level in serum more than 1.0.A total of 35 patients. 54.3% were men with a median age of 58 years (IQR 14-63). Lymphadenopathy was the most common initial presentation (57%), followed by prolonged fever (40%), cough (11%) and skin lesions (11%). Lymph node involvement was found in 80% while 31% and 11% had intra-abdominal abscess and osteomyelitis.Mycobacterium abscessus (43%). Six patients (28%) had evidence of mycobacterial infection but were unable to specified. Histoplasma capsulatum was found in 2 patients (9%). Another 14 patients (40%) were presumptive treated as non-tuberculous mycobacterium (NTM) infection without retrieving specific organism.Organisms were identified in 21 patients (60%). Mycobacterial infections were found in 19 patients (90%) which the main etiologic agent was All patients were treated with antimicrobial agents according to identified causative organism. Fourteen patients with presumptive NTM infection were empirically treated with combination antibiotics. Median time of treatment was 24 months (IQR 12-35). Seven patients (20%) experienced relapse after antimicrobial discontinuation requiring retreatment. Three patients (6%) had died at median duration of 4 months from diagnosis.AOI with (IFN)-\u03b3 autoantibodies should be considered in patient whom suspected mycobacterium or fungal infection among non-HIV patients. Diagnosis and treatment are challenge and recurrent infection is common.All Authors: No reported disclosures"} +{"text": "Streptococcus pneumoniae. In October 2021, the Advisory Committee on Immunization Practices updated pneumococcal vaccine guidelines in all adults >65 years and for adults 19-64 years with certain medical conditions or risk factors. Pneumococcal vaccination among patients >65 years is a national VHA performance measure. We reviewed vaccine status in patients >65 years with pneumococcal infection since guidelines changed.Pneumococcal infection is a vaccine-preventable illness caused by >65 years with pneumococcus were evaluated and compared to VHA\u2019s electronic quality measurement (eQM) for national pneumococcal vaccination rates.Demographics, pneumococcal vaccination in relation to time of infection and laboratory testing during 11/1/2021-4/11/2023 were retrieved from VHA data sources. Patients aged >65 years had at least 1 pneumococcal vaccine. VHA\u2019s national pneumococcal vaccination of patients >65 years for fiscal years 2022-23 was 65.3%-65.9% per eQM. Of cases not vaccinated, 22.1% were non-Hispanic Black patients. Median time of vaccination before infection was 4.7 years (IQR 2.8-6.5). Most recent vaccination prior to infection for the overall cohort and those with recurrent infections was 23-valent pneumococcal polysaccharide vaccine (PPSV23) (56.5% and 57.9% respectively). In addition, 108/1,128 (9.6%) cases were vaccinated after their pneumococcal infection (17/108 were not previously vaccinated). 71/108 (65.7%) vaccines given after illness were 20-valent pneumococcal conjugate vaccine (PCV) (PCV20).1,128 cases were identified (Table 1). 20 patients had recurrent infections. Median age was 74 years (IQR 69-77) with non-Hispanic Blacks (14.1%) slightly overrepresented compared to VHA\u2019s Black population (12.7%); primary infection sites were pulmonary (68.4%) and blood (23.5%). 1,006/1,128 (89.2%) of cases in patients >65 years with pneumococcal infection, nearly 90% had had at least 1 pneumococcal vaccine which was mainly PPSV23 and given on average almost 5 years before infection. VHA could target non-Hispanic Black patients with pneumococcal vaccination efforts and ensure providers are utilizing PCV20 or PCV15+PPSV23 vaccines.In VHA patients All Authors: No reported disclosures"} +{"text": "COVID-19 vaccination is one of the most important public health tools to prevent severe COVID-19.COVID-19 vaccine (Pfizer-BioNTech) first received the U.S. Food and Drug Administration (FDA) Emergency use authorization (EUA) for individuals 16 years of age and older on 12/11/2020 and for 12-15 years of age on 5/10/2021. We evaluated clinical and epidemiologic characteristics of critically ill adolescents with COVID-19 admitted to the intensive care unit (ICU) at our tertiary-care centers in Northwestern Iowa (encompassing Sioux City and Sergeant Bluff locations) during the 1-year post-vaccination approval period from June 1, 2021- May 31, 2022. Adolescence was defined as age-group 12-21 years per WHO definition.Twenty-one adolescents were admitted to the ICU with a median age of 16 years (IQR 12-20 years) and male: female ratio of 1:1.3. The majority (77%) were admitted with COVID-19 related pneumonia and 10 developed hypoxemic respiratory failure; 19 of 21 (90%) adolescent patients admitted to the ICU during this period were unvaccinated and all adolescents developing respiratory failure were unvaccinated. Majority of patients with respiratory failure (70%) required mechanical ventilation (MV). Seventy % of patients with respiratory failure were obese (BMI of >30); 40% of patients had two or more pre-existing comorbidities; those with BMI >40 were 4.3 times more likely to develop respiratory failure (p< 0.0001). Inflammatory markers were 5-20 times higher among patients with respiratory failure (p< 0.05); 60% of those with respiratory failure developed complications including ARDS, acute renal injury and cerebral anoxic encephalopathy. All with respiratory failure required parenteral steroids. Mean duration of ICU stay was significantly longer for patients with respiratory failure . None of the patients died. After hospital discharge, 30% patients reported post COVID-19 fatigue at 3-month follow up.Our results showed that all of the critically ill adolescent patients with COVID-19 associated hypoxemic respiratory failure were unvaccinated and majority developed complications. These results further emphasize importance of COVID-19 vaccination efforts for adolescents.All Authors: No reported disclosures"} +{"text": "According to the CDC, STI including syphilis infections in adults have recently increased in the upper Midwest. Studies evaluating epidemiology of Congenital syphilis (CS) are needed to facilitate prompt recognition to prevent sequelae.We retrospectively studied epidemiologic, clinical characteristics and outcomes of neonates with CS at our tertiary care center which is the largest maternal/neonatal center in NW Iowa during 1/1/2021-12/31/2022 (labeled P2). Epidemiologic characteristics during P2 were compared with the period from 1/1/2019-12/31/2020 (labeled P1). Diagnosis and treatment for CS were in accordance with CDC/American Academy of Pediatrics Committee on Infectious Diseases Red Book guidelines.During P2, a total of 42 newborns were diagnosed with CS compared to 0 during P1 (p< 0.05); 64% of infected newborns were White followed by Native American (21%), Hispanic (11%) and Black (2%). All (100%) neonates with CS were born to mothers infected during or after second trimester of pregnancy with negative first trimester RPR (Rapid Plasma Reagin) testing. Maternal RPR titers ranged from 1:1-1:256. Majority (62%) of newborns were diagnosed with proven/possible CS with RPR-titers > 4-fold mother's titers /untreated or inadequately treated maternal infection and required 10 days of intravenous Aqueous crystalline penicillin G treatment and NICU care; 2 newborns had meningitis and 3 developed sensorineural hearing loss. Thirty-eight% received 1 dose of intramuscular Benzathine penicillin G. Need for cerebrospinal fluid syphilis testing and 10 days of intravenous penicillin treatment increased by > 600% from P1 to P2 (p=0.02). CS evaluation/treatment in infected Native American neonates increased by > 1000% in P2 (p< 0.001). Mean hospitalization duration was 9.5 (\u00b11.6) days. No infant died. Only 33% of infants followed up at 2 months for repeat testing. None of the Native American/Hispanic/Black neonates compared to 52% White neonates had follow-up testing (p< 0.05).Our results show an alarming increase in CS in NW Iowa and underline the need for urgent preventive measures including STI prevention education, adequate maternal/ neonatal testing and follow-up, especially among marginalized populations.All Authors: No reported disclosures"} +{"text": "Long term maintenance with NRTI-sparing regimens may be preferable for patients with NRTI toxicities, and may offer potential cost savings. Dual ART with once daily darunavir/r and etravirine may be preferable to previous PI/r/NNRTI combinations due to its theoretical higher genetic barrier to resistance and good PK profile. We looked at the use of this regimen within our HIV cohort.Patients prescribed dual ART with darunavir/ritonavir 800mg/100mg QD with etravirine 400mg/day (DRV/r/ETR) until January 2010 were identified by our virtual clinic database. Reason for switch, HIV resistance, viral outcomes were identified.21 patients were switched to DRV/r/ETR with median time on regimen of 51.5 weeks (IQR 33-69 wks). 85% (18/21) where given ETR 400mg QD. 62% (13/21) switched from dual PI/r regimens, 10 combined with efavirenz or nevirapine. 28% (6/21) switched from conventional cART (2 NRTI + PI/r or NNRTI). Patients had a median exposure to 9 ARV drugs prior to switch (IQR 4-11), with 90% (19/21) having previous NNRTI exposure, 7 of which had CNS toxicity with efavirenz. At switch, 57% (12/21) had no previous resistance, 19% (4/21) NRTI mutations only, and 19% (4/21) had NNRTI mutations (K103N (2), Y181C combined with NRTI K65R, M184V mutations (1), prior NNRTI failure (2)). 90% (19/21) had VL<50cps/ml at switch, with 95% (20/21) achieving/maintaining VL<50cps/ml on regimen. Four patients discontinued the regimen, 2 switching to darunavir/r monotherapy, one switching to kivexa/darunavir/r due to non-adherence, and one switching back to previous regimen after 4 weeks. One patient was lost to follow up. Median virological follow of patients remaining on therapy was up 40.8 wks (IQR 32-58 wks). Median CD4 change for the 17/21 who remained on therapy was +101 cells/mm3 (IQR -50-138) with median 39 wks follow up (IQR 31-58 wks). Indications for switch were desire for simplification (9) , and need for NRTI-sparing regimen (12), including previous renal toxicity with tenofovir (4), lipoatrophy (7), peripheral neuropathy (1) and lactic acidosis (2).For patients with VL<50cps/ml, simplification to dual therapy with darunavir/r 800/100mg QD plus etravirine 400mg QD maintains viral suppression and immune reconstitution."} +{"text": "To our knowledge, the antiviral activity of pegylated interferon alfa plus HAART has not been studied in patients with human immunodeficiency virus type 1 (HIV-1) coinfected with chronic hepatitis B virus (HBV).To evaluate the effectiveness of pegylated interferon alfa plus HAART in HIV/HBV treatment-na\u00efve coinfected patients.We performed a prospective cohort study in HIV/HBV treatment-na\u00efve coinfected patients taking care at \"La Raza\" National Medical Center, Mexico City. Patients were treated with Efavirenz or Lopinavir-ritonavir, each with tenofovir/emtricitabine plus pegylated interferon alfa-2b (1.5 \u00b5g/kg/week) or pegylated interferon alfa-2a (180 \u00b5g/week) during 48 weeks. HBV genetic analysis was obtained. The study had a primary measure of effectiveness assessed at 24 and 48 weeks of treatment: suppression of HIV RNA to levels below 50 IU/ml. Secondary endpoints were increased in CD4+ cells count, HBV DNA to levels below 60 IU/ml, HBeAg seroconversion (defined by the loss of HBeAg and the presence of anti-HBe antibody) and HBsAg seroconversion (defined by the loss of HBsAg and the presence of anti-HBs antibody). Cumulative incidence with 95% confidence interval (95%CI) were calculated.We enrolled 18 subjects, 1 patient discontinued treatment because adverse events related to PEG-IFN. The mean (\u00b1 SD) age was 30.3 \u00b1 6.9 years old, all patients were men. The median (interquartile range) basal CD4+ cells count was 112 (61 to 300), RNA HIV 163,000 copies/ml , DNA HBV 20,200,000 IU/ml . All patients had positive HBeAg and were negative to HDV serology. HBV genotype distribution was H 9 (52%), G 6 (35%), A 1 (6%) and F 1 (6%). Primary endpoint (RNA HIV < 50 copies/ml) was present in 100% of our patient at 24 and 48 weeks; the median increased in CD4+ cells count was 231 cells/ml at 24 weeks and 322 cells/ml at 48 weeks; cumulative incidence of secondary endpoints were: DNA HBV < 60 UI/ml was present in 8 patients [47% CI95% 26-69%)] at 24 weeks and 17 patients (100 %) at 48 weeks; HBeAg seroconversion was in 8 patients [47% CI95% 26-69%)] at 24 weeks and 16 patients [94% CI95% 73-98%)] at 48 weeks, HBsAg seroconversion was in 0 patients (0%) at 24 weeks and 6 patients [35% CI95% 17-58%)] at 48 weeks.Pegylated interferon alfa plus HAART were well tolerated and exhibited high viral effectiveness in HIV/HBV treatment-na\u00efve coinfected patients."} +{"text": "Health care-associated infections (HCAI) result essentially from cross-transmission of pathogenic microorganisms by the hands of healthcare workers (HCW). Their care represents a universal challenge in practice.Our study aimed to measure HCW compliance with hand hygiene.We conducted a direct observance of hand hygiene compliance of HCW over a period of three months, based on the WHO\u2019s \u201cfive indications of the hand hygiene\u201d approach.For a total of 338 opportunities, the rate of global observance of hand hygiene was 36.1% with 80.3% of handrubbing realized. According to the department, this rate of observance was variable: Pneumology (42.3%), Thoracic Surgery and Cardiovascular (58.6%), Neurology (20%), Neurosurgery (24%), Emergency (25%), Laboratories (30%), Infectious diseases (39%), Psychiatry (33.3%), ORL (25%), Oral department (44.4%). According to the professional category, the observance was the following one: doctors (50.6%), nurses (34%) auxiliaries (29.1%) other nursing staffs (43.8%). The level of use of Alcohol-based handrub (ABHR) during hand hygiene was: auxiliaries (93%), doctors (82.1%), nurses (75.8%), others (14.3%). The observance of ABHR according to \"five indications\" was 87.7% before patient contact, of 83.3% before aseptic procedure, 44.4% after a risk of body fluid exposure, of 78% after patient contact and of 100% to the immediate surroundings of patient.Observance of hand hygiene with ABHR is still low in the structure. A training program coupled with a sharing experience of outcomes of the survey should allow to improve it.None declared"} +{"text": "To the Editor: WU polyomavirus (WUPyV) is a human polyomavirus first detected in respiratory samples in 2007 were 6 months\u20131 year, 7 (25%) were 1\u20132 years, and 1 (4%) was 2\u20135 years of age. The age distribution was similar to that of the original cohort. We found WUPyV-positive samples in most months, except for March 2008. Highest proportion of WUPyV-positive samples occurred in December 2008 (27%), followed by April 2008 (25%), November 2008 (22%), and February 2009 (19%).Of the 174 nasopharyngeal aspirate specimens tested, 28 (16%) had WUPyV VP2 gene\u2013positive fragments; 24 had LTAg gene\u2013positive fragments. Four VP2-positive but LTAg-negative fragments were sequenced; nucleotide sequences were identical to WUPyV strains in GenBank. Mean age of WUPyV-infected patients was 11.7 months (range 12 days\u201339 months); 10 patients (36%) were We detected WUPyV VP2 fragment\u2013positive specimens by multi-PCR using the Seeplex RV Detection kit-1 for other respiratory viruses, including adenovirus, parainfluenza viruses 1, 2, 3 , influenza viruses A and B, rhinovirus (rhinovirus V), human metapneumovirus, respiratory syncytial virus A and B , and coronaviruses OC43/HKU1 and 229E/NL63, according to the manufacturers\u2019 instructions. First strands of cDNA were produced by using the RevertAid First Strand cDNA Synthesis Kit . Human bocavirus (HBoV) was tested as described previously (Twenty (71%) case-patients were co-infected with other respiratory viruses, most commonly RSV B , followed by HBoV , rhinovirus V and PIV3 , human metapneumovirus , adenovirus and influenza A , and 229E . Of 20 patients with co-infections, 14 (50%) were infected with 2 viruses; 2 (7%) with 3 viruses ; 3 (11%), with 4 viruses ; and 1 (4%), with 5 viruses .Three (4%) of 68 throat swabs from outpatients with URTIs were WUPyV positive, substantially lower than from inpatients with LRTIs. Among 3 WUPyV-positive case-patients, 2 were 2 years of age and 1 was 3. No WUPyV was detected in 43 control samples.The prevalence of WUPyV in hospitalized children with acute respiratory tract infections in Tianjin was 16.1%, higher than 7.1% found in a study in the United States (Most WUPyV infection has been detected during later winter and early spring (Frequency of WUPyV co-infection with other pathogens varied from 42.1% to 79.7% ("} +{"text": "Sudden cardiac arrest (SCA) results from malignant ventricular arrhythmias that may be due to myocardial ischemia, infarct, edema, fibrosis or infiltration. The underlying cause is often unknown. Cardiac magnetic resonance (CMR) may provide structural and functional data and identify myocardial ischemia, inflammation and fibrofatty infiltration.This study determines the diagnostic ability of CMR in SCA of unknown cause.Seventy-six patients with SCA of unknown cause underwent CMR. The results were adjudicated into either non-diagnostic (no convincing cause identified) or diagnostic CMR.Of the 76 CMR studies, 41 (52%) demonstrated potentially causative pathology for SCA. Of these 41 patients- 11 (14%) had recent ischemia or major LV wall motion defects, 7 (9%) had myocarditis, 6 (7%) had arrhythmogenic right ventricular dysplasia (ARVD) per modified task-force criteria, 5 (6%) had LV intramyocardial fibrosis, 7 (9%) had severe cardiomyopathy (LVEF of <40%), and 5 (6%) had abundant RV fat. No potential cause for SCA was identified in 35 (46%) patients.CMR can identify otherwise undetected possible etiologies of SCA in more than half of resuscitated patients.No Disclosure"} +{"text": "Tuberculosis (TB) is one of the most common opportunistic infections in HIV-infected patients, with severe evolutive potential.We evaluated the prevalence and the clinical aspects of TB in HIV-infected persons in order to identify factors associated with unfavorable evolution of TB.Mycobacterium tuberculosis, immunovirological evaluation) for patients who presented at least 2 times per year at the regional center.We performed an observational, retrospective study (01 January 2009 \u2013 31 December 2011) on 387 HIV-infected patients in evidence at the HIV/AIDS Craiova Regional Center. We analyzed the epidemiological, clinical and paraclinical data (smears and cultures for 10. TB was: pulmonary: 46 cases (77.9%), extrapulmonary 8 (13.6%), multiple locations 5 (8.5%). 19 cases (32.2%) were bacteriologically confirmed (positive smears and/or positive cultures). 53 patients (89.8%) were under antiretroviral treatment, with a very good adherence in 19 patients (32.2%). Other opportunistic infections apart from TB were recorded in 28 patients (47.4%). 29 patients (49.2%) had favorable outcome, complication or relapse occurred in 10 cases (16.9%) and 20 patients (33.9%) died. Factors associated with unfavorable evolution were: delay in the introduction of anti-TB treatment more than 30 days from the first symptom (p=0.001); the presence of other opportunistic infections apart from TB (p=0.0001), low adherence to treatment (p=0.0001). Death was associated with extrapulmonary/multiple location of TB (p=0.005) and average CD4<100 cells/cmm (p=0.002).During the studied period 59 patients (15.3%) presented TB (9 cases simultaneously diagnosed with HIV and TB). General data on the study group: average age at the moment of TB diagnosis: 25.5\u00b17.4 years; equal gender distribution: male/female 30/29; rural/urban 40/19 (67.8/32.2%); average CD4 count 3 months before TB diagnosis: 179\u00b1204 cells/cmm; average viral load: 5.09\u00b15.3 logTuberculosis is common in patients infected with HIV, the unfavorable evolution being associated with severe immunosuppression, extrapulmonary TB location, poor adherence and delay in the introduction of anti-TB treatment."} +{"text": "Epigenetics& Chromatin, 2013 6(Suppl 1):O25 should read: 'Abstract notsubmitted for online publication'.In volume 6 Supplement 1, Epigenetics and Chromatin: Interactions and processes,abstract O25 was published erroneously. The published record for"} +{"text": "Caregivers have been shown to be at increased risk of emotional stress, depression, medical illness, and death. Studies of Mindfulness Based Stress Reduction (MBSR) have established its efficacy in reducing stress and physical and psychological concomitants of stress in multiple patient populations. The purpose of this study is to determine the effectiveness of MBSR in reducing caregiver stress, as measured by psychological and biological markers.20 participants in Mindfulness for Caregivers classes completed before and after psychological assessments as well as gave blood samples to assess biological markers.16/20 demonstrated increased mindfulness, mean increase in FFMQ (score range 22-110) in responders 12.7(range 1-26); 15/20 improved CSAQ (range 0-16), mean responder decrease 5.1 (range 1-10); 15/20 improved CESD (range 0-30), mean responder decrease 8.9 (range 1-22); 16/20 improved PSS10 (range 0-40), mean responder decrease 10.2 (range 0.5\u201321); 16/20 improved RSCB (range 0-28), mean responder decrease 6.8 (range 2-16); 15/20 improved ITGPL (range 0-76), mean responder decrease 7.7 (range 1-22). All psychological outcome parameters showed significant correlation with CSAQ, in which improvement was linearly correlated with increase in mindfulness as measured by the FFMQ. Proteomic analysis identified significant changes in several plasma chemokines and cytokines in good psychological responders vs. poor psychological responders. Microarray gene expression profile analysis identified 124 genes that are differentially regulated in good responders vs. poor responders.MBSR is an effective intervention for reducing caregiver stress. Preliminary data suggest that MBSR may benefit caregiver health by modulating inflammatory responses. Results of microarray gene expression profile analysis may suggest a \u201cpersonalized medicine\u201d approach for identifying likely responders to mindfulness training."} +{"text": "Corticosteroid injection to the Temporo-Mandibular (TMJ) joint in children with Juvenile Idiopathic Arthritis (JIA) has been shown to be effective, but debate continues whether radiological guidance for needle placement produces better outcomes.To review clinical outcomes following TMJ injection without radiological guidance.All patients having TMJ injections (Triamcinolone Acetonide or Hexacetonide) in 2003-2009 were identified. Injections were performed under general anaesthesia. Notes were retrospectively reviewed looking at: symptoms, response to treatment, and examination findings .47 patients had a total of 71 joints injected. Pain and reduced jaw opening were the most common preceding symptoms. Mean age at JIA diagnosis was 9.3 years, and at time of TMJ injection was 12.8. Mean time between JIA diagnosis and first TMJ injection ranged from 0.9-14.5years. JIA subtypes were: oligoarticular (18.6%), extended-oligoarticular (16.5%), polyarticular (37.2%), enthesitis-related (9.3%), and psoriatic (18.6%). At the time of TMJ injection 18 patients were receiving methotrexate, 4 prednisolone, 1 etanercept and 1 leflunomide.3 months after TMJ injection, 51% had complete resolution of symptoms, 44% had improved and 5% had no response. 36 patients had follow-up data at a mean of 2.5 years, showing complete resolution of symptoms in 29/36 (80.5%), improvement in 3/36 (8.3%) and no improvement in 4/36 (11.2%). No cases of micrognathia, Cushing\u2019s syndrome, or subcutaneous atrophy were documented.In this retrospective series corticosteroid injection of the TMJ without radiologically-guided needle placement, was a safe and effective treatment with no adverse side-effects documented."} +{"text": "The incidence of food allegy in children seems to be approximantely 6 to 8% in developed countries.The diagnosis of food allergy has to be confirmed by skin test, by performing specific IgE and by food challange.The aim of this study was to assess the correlations between results obtained with skin prick tests (SPT) using commercial extracts and prick-prick test (PPT) with fresh food, and the correlations between these results and those obtained with specific IgE.We performed a retrospective review of 249 children reffered to the University Children's Hospital of Belgrade for assessment of food allergy between 2008 and 2010. Children underwent cutaneous , serologic (Specific IgE) diagnostic and provocative test with commercially aviable allergen reagens and extracts.132 (53%) SPT were assessed as being positive: 33 (47.8%) for CMP, 29 (51.7%) for egg white, 25 (44.6%) for egg yolk, 21 (47.7%) for peanuts, 11 (39.2%) for wheat, 9 (33.4%) for soybeans, 4 (16%) for kiwi. 211(85%) PPT were assessed as being positive: 50 (72.5%) for CMP, 41 (73.2%) for egg white, 37(66.07%) for egg yolk, 27 (61.4%) for peanuts, 21 (75%) for wheat, 16 (59.25%) for soybeans, 19 (76%) for kiwi. Specific IgE levels were being pozitive in 228 (91.5%) children. The conformable between a positive SPT and serum measurement specific IgE was 57.8% and the conformable between positive PPT and serum measurement specific IgE was 92.5%.Fresh food extracts are more effective in detecting sensitization. We obtained better conformable between fresh food tests and specific IgE, than with commercial extracts and measurement specific IgE."} +{"text": "This study aims to assess the performance of DRV in clinical practice, as part of salvage therapy strategies.We did retrospective assessment of HIV+ patients who received DRV at our institution, prescribed as part of a salvage regimen since 2006. Liver, metabolic and renal profile were assessed at baseline, after 1 month and every 3 months. 52 HIV1+ patients have been enrolled; mean age was 48 (IQR 44-54) years, male 82%, IDUs 29%, MSM 37%, heterosexuals 33%; 15 patients were HCV or HBV co-infected. All but one were subtype B. Median CD4 nadir was 82 (IQR 27-234). Thirty-one patients had AIDS history. Mean time on ARVs was 15 (IQR14-17) years; major mutations were: 8 for NRTI, 2 for NNRTI and 5 for PI.Median follow-up was 104 weeks (IQR 60\u2014139). Two patients died: one following a car accident, the other one due to disseminated Kaposi's sarcoma. Four patients stopped DRV: one lost to follow-up, one developed decompensated diabetes, one rash, one virological failure. Companion drugs with DRV were NRTI (71%), etravirine (14%), maraviroc (33%), raltegravir (RAL) (33%), enfuvirtide (ENF) (33%). Seventeen patients had changes in therapy during follow up, four patients stopped NRTIs, among 13 patients who stopped ENF, 5 replaced with RAL. Mean CD4 and HIV-RNA values at baseline were 251 cells/mm3 and 4.3 log10 copies/ml, respectively; CD4 median monthly increase was 9 (IQR 5.1-14.5) cells/mm3. After 1 month, 49 % had HIV-RNA <50 copies/ml; after 12, 24 and 33 months 91% of patients were still undetectable. No statistically significant modification were seen in transaminases, creatinine, glucose, triglycerides values.Darunavir was highly effective and well tolerated in most of patients and showed good metabolic, renal and liver profile in our cohort where the rate of co-infected patients was high."} +{"text": "Objective was to evaluate the postoperative results after different sternal resections for malignances.A total of 32 patients were operated on during a 7 years period in two institutions. There were 16 sarcomas , 1 recurrent desmoid tumor, 3 local breast cancer recurrences, 1 plasmocytoma, and 11 metastatic tumors . Four-five cm free margins on each side were achieved in all patients with total sternectomy (13), subtotal sternal resection (17), and partial resection (2). Concurrent en bloc resections included anterior ribs (7), clavicle (6), pericardium (2), brachiocephalic vein (2), and diaphragm (1). The chest was reconstructed with Gore-tex (5) or Marlex mesh (22) and myocutaneous flap in 18 (56.25%) patients or omentum in 6 (18.75%) patients. Only double layer Marlex mesh with breast mobilization was performed in 5 women (15.62%). Combination of prostetic material and metal bars or wires was needed in 6 patients after total sternectomy (18.75%). Multimodality treatment pre- or postoperatively was administered in most of the patients.There was no 30-day operative mortality. Mechanical ventilation for 5 days was needed in a 78 years old female after total sternectomy. Local suppuration was found in 3 patients. The mean in-hospital stay was 12.7 days. After a median follow-up of 56 months the overall 5-year survival was 58%, with a median survival of 61 months. Local recurrence occurred in 3 patients, who underwent a repeat total resection. Metastases developed in 2 patients.Wide sternal resection (4-5 cm free margins) is a safe and effective treatment of sternal malignances. The chest wall reconstruction depends on the size and site of the resection, and should be planned with plastic surgeons."} +{"text": "Infections with opportunistic pathogens in stable chronic haematological patients are well known. Recent reports suggest that these patients admitted to intensive care (ICU) tend to do as well as or better than those without infection . We sougData on infections were retrospectively collected for haematology patients consecutively admitted to our unit for the period of January 2005 to December 2008. Readmissions (9/106) were excluded. Bacteria, mycobacteria and fungi were identified by culture and viruses detected by DNA PCR. Coagulase-negative staphylococcus was excluded from the analysis, as they most probably represented contaminants. Data were analysed with SPSS software.Pseudomonas aeruginosa (15.4%) and Enterococcus faecalis (11.3%); viruses were cytomegalovirus (CMV) (17.5%) and respiratory syncytial virus (RSV) (17.5%); and fungi were Candida species (6.2%). Known or clinically suspected infection at admission, identifying an organism, presence of infection with multiple organisms, and infection type were not associated with increased ICU or hospital mortality (P > 0.05), but resulted in significantly longer ICU and hospital LOS. Increased ICU LOS (days) (mean (SD)) was associated with identifying an organism (7 (8) vs. 16 (6); P < 0.001), number of organisms per patient (7 (7), 13 (13), 16 (8), 41 (29); P = 0.006), infection type (7 (8), 15 (19), 16 (12), 17 (9), 26 (24); P < 0.001)), viral infection (11 (15), 16 (11); P = 0.005), CMV viraemia (11 (14), 18 (12); P = 0.002), while increased hospital LOS (days) (mean (SD)) was associated with identifying an organism (37 (34) vs. 61 (60); P = 0.004) and infection type (37 (34), 47 (34), 52 (41), 67 (77), 69 (36); P = 0.025).Ninety-seven patients were admitted during the study period, 71% with known or clinically suspected infection. The most commonly identified bacteria were Most patients with haematological diagnoses admitted to our ICU had a clinically suspected or documented infectious cause. Although infection characteristics are not associated with overall mortality, they are associated with prolonged ICU and hospital LOS."} +{"text": "Purpose. To review the postoperative seizure outcomes of patients that underwent surgery for epilepsy at King Faisal Specialist Hospital & Research Centre (KFSHRC). Methods. A descriptive retrospective study for 502 patients operated on for medically intractable epilepsy between 1998 and 2012. The surgical outcome was measured using the ILAE criteria. Results. The epilepsy surgery outcome for temporal lobe epilepsy surgery at 12, 36, and 60 months is 79.6%, 74.2%, and 67%, respectively. The favorable 12- and 36-month outcomes for frontal lobe epilepsy surgery are 62% and 52%, respectively. For both parietal and occipital epilepsy lobe surgeries the 12- and 36-month outcomes are 67%. For multilobar epilepsy surgery, the 12- and 36-month outcomes are 65% and 50%, respectively. The 12- and 36-month outcomes for functional hemispherectomy epilepsy surgery are 64.2% and 63%, respectively. According to histopathology diagnosis, mesiotemporal sclerosis (MTS) and benign CNS tumors had the best favorable outcome after surgery at 1 year and 3 years . The least favorable seizure-free outcome after 3 years occurred in cases with dual pathology (66.6%). Thirty-four epilepsy patients with normal magnetic resonance imaging (MRI) brain scans were surgically treated. The first- and third-year epilepsy surgery outcome of 17 temporal lobe surgeries were (53%) and (47%) seizure-free, respectively. The first- and third-year epilepsy surgery outcomes of 15 extratemporal epilepsy surgeries were (47%) and (33%) seizure-free. Conclusion. The best outcomes are achieved with temporal epilepsy surgery, mesial temporal sclerosis, and benign CNS tumor. The worst outcomes are from multilobar surgery, dual pathology, and normal MRI. The incidence of epilepsy in developed countries is currently estimated to be 57 people per 100,000 inhabitants \u20134. The rSeventy to 80% of epilepsy patients can be satisfactorily managed with anticonvulsive medication while 20Epilepsy: a comprehensive textbook (chapter 296). This study, however, was an early systematic review of epilepsy surgery outcomes and related variables in the comprehensive epilepsy program at a single center (KFSH&RC) in Saudi Arabia. The focus of this current study is to review the postoperative seizure outcomes of patients that underwent epilepsy surgery at our centre over the 14-year period from 1998 to 2012. The clinical semiology, preoperative investigations, histopathological diagnoses, and surgical procedures were identified in the determination of outcomes.Epilepsy surgery procedures were initiated in Saudi Arabia in 1998. Our first evaluation of these procedures was published in A descriptive retrospective study was conducted using data from the epilepsy registry database of our epilepsy program. The study analyzed all patients operated on between 1998 and 2012. The inclusion criteria for surgical evaluation were as follows: (1) recurrent partial seizures with or without secondary generalized seizures and (2) failure of at least two first-line antiepileptic drugs to control the seizures .vide supra), the selection criteria for epilepsy surgery includes (1) a confirmed diagnosis of epilepsy, (2) the presence of medically intractable or disabling seizures, (3) a concordance of the localization data to a respectable focus, (4) the presence of a nonprogressive underlying disease , and (5) high probability that seizure control will significantly improve the patient's quality of life.The preoperative evaluation includes a neurological examination, MRI video-EEG recording with electrodes placed according to the International 10\u201320 system, invasive video-EEG recording, a neuropsychological evaluation, a sodium amobarbital test, and nuclear brain-scan studies. Once the evaluation is completed, the data are usually discussed in a multidisciplinary patient management conference, which includes epileptologists, neurosurgeons, a neuroradiologist, and a neuropsychologist. A standard epilepsy MRI protocol was used to study all patients : sagittal T1 sequences (5\u2009mm slice thickness), coronal FLAIR (5\u2009mm), T2 (3\u2009mm), axial T1, T2, and T2* (5\u2009mm), 3D T1 sequences, and diffusion of 1.6\u2009mm slice thickness. Video-EEG monitoring with intracranial electrode implants was also used prior to surgery. Interictal FDG-PET scan was used to evaluate surgical cases. Neuropsychological evaluation was done using a comprehensive test battery and following clinical diagnostic requirements. In contrast to the inclusion criteria for surgical evaluation (The epilepsy procedures were classified as follows: (1) temporal lobe surgery , (2) frontal lobe surgery, (3) parietal lobe surgery, (4) occipital lobe surgery, (5) functional hemispherectomy, (6) multilobar surgery , (7) anterior 2/3 callostomy, and (8) multiple subpial transaction.Epilepsy surgery outcomes were measured according to the ILAE classification. Seizure-free patients with or without auras and patients with 1\u20133 seizures per year were considered to have favorable outcomes while more than 3 seizures per year were considered unfavorable . EpilepsRasmussen encephalitis), gliosis, dual pathology , non specific and normal.The histopathology results were classified into one of the following nine categories: mesial temporal sclerosis (MTS), cerebral dysgenesis , primary CNS tumor, vascular malformation, chronic inflammation underwent surgery for their refractory epilepsy between 1998 and 2012. Out of those 502 patients, 65.3% were adults, and 34.7% were pediatric. The epilepsy surgical procedures included 295 temporal lobe surgeries, 53 frontal lobe surgeries, 16 parietal and occipital lobe surgeries, 64 functional hemispherectomies, 26 multilobar surgeries, 10 corpus callosotomies, and 3 multiple subpial transections and one hypothalamic hamartoma resection. The surgical outcome assessments of 468 patients that completed at least 3 years after surgery were evaluated. The invasive EEG was used in 141 patients (28%). The invasive EEG procedure was performed in patients with intractable epilepsy in whom the clinical analysis, scalp EEG, MRI, PET scan, and neuropsychology failed to lateralize seizure origin confidently.porencephalic cysts, 15 vascular malformations, 11 tuberous scleroses, and 7 others. A PET scan was conducted on 398 patients, which showed 358 with hypometabolism, 21 with hypermetabolism, and 19 as normal.MRI brain scans revealed 202 MTS cases, 78 primary CNS tumors, 66 cerebral cortical dysgenesis, 35 normal MRI, 66 focal atrophy and encephalomalacia, 22 arachnoid and The histopathology results showed 11 patients were normal, 203 had MTS, 142 had a cortical dysplasia/heterotopia, 96 had CNS tumors, 11 had encephalomulacia, 11 had chronic inflammations, 12 had vascular malformations, and other 16 . Thirty-eight of the histopathology results disclosed a dual pathology, each of which might have contributed to, or been responsible for, the epilepsy.According to the ILAE, the favorable first-year epilepsy surgery outcome for patients following temporal lobe surgery is 79.6%; in our study, 172 patients 58.3%) were seizure-free without auras, 17 (5.7%) were seizure-free with auras, and 46 (15.5%) had 1\u20133 seizures per year. The favorable outcome for the third year following temporal lobe surgery, according to ILAE criteria, is 74.2%. At this point, our study found 105 patients (53.8%) were seizure-free without auras, 13 patients (6.6%) were seizure-free with auras, and 27 patients (13.8%) had 1\u20133 seizures per year. According to ILAE, the favorable outcome for the fifth year following temporal lobe surgery was 67%; in our series, 47 patients (47%) were seizure-free without auras, 9 (9%) were seizure-free with auras, and 11 (11.0%) had 1\u20133 seizures per year were seizure-free without auras, 2 patients (4.3%) were seizure-free with auras, and 3 patients (6.4%) suffered from 1\u20133 seizures per year. According to the ILAE, the favorable outcome for the third year following frontal lobe surgery is 52%; in our series, 10 patients (40.0%) were seizure-free without auras, 2 (8%) were seizure-free with auras, and 1 (4.0%) with 1\u20133 seizures per year were seizure-free without auras and 3 patients 25.5%) had 1\u20133 seizures per year. The favorable outcome in the third year following parietal and occipital surgery is 66.6%; our cases showed 4 patients (44.4%) were seizure-free without auras, 1 (11.1%) was seizure-free with auras, and 1 (11.1%) had 1\u20133 seizures per year were seizure-free without auras, 1 (5%) was seizure-free with auras, and 4 20%) had 1\u20133 seizures per year. According to ILAE, the favorable outcome for the third year following multilobar surgery, according to the ILAE, is 50%; in our cases, we had 5 patients (41.7%) that were seizure-free without auras, and 1 (8.3%) had 1\u20133 seizures per year were seizure-free without auras, 2 (3.8%) were seizure-free with auras, and 2 (3.8%) had 1\u20133 seizures per year. The favorable outcome for the third year following a hemispherectomy, according to the ILAE, is 63%. Our study found 14 patients (46.7%) were seizure-free without auras, 1 (3.3%) was seizure-free with auras, and 4 (13.3%) had 1\u20133 seizures per year , and 2 of Sturge Weber disease. Forty-one of the patients were children .146 children with refractory epilepsy underwent epilepsy surgery. The favorable first-year epilepsy surgery outcome for temporal lobe surgery according to ILAE criteria is 88.4%, (48 (69.6%) were seizure-free without aura, 2 (2.8%) seizure-free with aura, and 11 (16%) 1\u20133 seizures per year). The favorable third year for temporal lobe surgery (ILAE) is 72%; (25 (58%) seizure-free without aura, 4 (9%) seizure-free with aura, and 2 (5%) with 1\u20133 seizures per year). The favorable fifth year for temporal lobe surgery (ILAE) is 71%; (12 (57%) seizure-free without aura, 3 (14%) seizure-free with aura).The favorable first year epilepsy surgery outcome for frontal lobe surgery according to ILAE criteria is 70% (11 (55%) were seizure-free without aura, 1 (5%) seizure-free with aura, and 2 (10%) 1\u20133 seizures per year). The favorable third year for frontal lobe surgery (ILAE) is 70% (6 (60%) seizure-free without aura and 1 (10%) seizure-free with aura).The favorable first-year epilepsy surgery outcome for parietal and occipital lobes surgery according to ILAE criteria is 50% (2 (50%) were seizure-free without aura). Only one case completed three years after surgery and the outcome was seizure-free without aura.The favorable first-year epilepsy surgery outcome for multilobar surgery according to ILAE criteria is 80%, (3 (60%) were seizure-free without aura and 1 (20%) with 1\u20133 seizures per year).The favorable first-year epilepsy surgery outcome for functional hemispherectomy according to ILAE criteria is 60% (22 (55%) were seizure-free without aura, 1 (2.5%) seizure-free with aura, and 1 (2.5%) 1\u20133 seizures per year). The favorable third-year epilepsy surgery outcome for functional hemispherectomy (ILAE) is 58%; (10 (53%) seizure-free without aura and 1 (5%) 1\u20133 seizures per year).According to the ILAE, the favorable outcome for patients with a histopathology diagnosis of mesial temporal sclerosis in the first year following epilepsy surgery is 77.27%. In our cases, 109 patients 58.9%) were seizure-free without auras, 5 (2.7%) were seizure-free with auras, and 29 15.6%) had 1\u20133 seizures per year. The favorable outcome for patients in the third year following epilepsy surgery with a histopathology diagnosis of mesial temporal sclerosis, according to the ILAE, is 76%. In our cases, we found 68 patients (57%) were seizure-free without auras, 3 (2.0%) were seizure-free with auras, and 20 (17%) had 1\u20133 seizures per year. The favorable outcome for patients with a histopathology diagnosis of mesial temporal sclerosis in the fifth year following epilepsy surgery, according to ILAE criteria, is 58%. Our series found 21 patients (42%) were seizure-free without auras, 1 (2%) was seizure-free with auras, and 7 (24%) had 1\u20133 seizures per year were seizure-free without auras, 6 (4.8%) were seizure-free with auras, and 18 (14.4%) had 1\u20133 seizures per year. According to ILAE criteria, the favorable outcome for patients in the third year following epilepsy surgery is 65.48%. In our series, 40 patients (47.6%) were seizure-free without auras, 6 (7.14%) were seizure-free with auras, and 9 (10.7%) suffered from 1\u20133 seizures per year. According to the ILAE criteria, the favorable outcome for patients in the fifth year following epilepsy surgery is 61.2%. Our study showed 23 patients (47%) were seizure-free without auras, 5 (10.2%) were seizure-free with auras, and 2 (4%) had 1\u20133 seizures per year were seizure-free without auras, 7 (8.43%) were seizure-free with auras, and 9 (10.9%) had 1\u20133 seizures per year. The favorable outcome for patients in the third year following epilepsy surgery, according to the ILAE, is 75%. In our series, we found 27 patients (51.9%) were seizure-free without auras, 8 (15.4%) were seizure-free with auras, and 4 (7.7%) suffered from 1\u20133 seizures per year. According to the ILAE, the favorable outcome for patients in the fifth year following epilepsy surgery is 66.5%. Our research found 12 patients (44.5%) were seizure-free without auras, 3 (11%) were seizure-free with auras, and 3 (11%) had 1\u20133 seizures per year were seizure-free without auras, 1 (2.6%) was seizure-free with auras, and 7 (18.4%) had 1\u20133 seizures per year. According to the ILAE, the favorable outcome for patients in the third year following epilepsy surgery is 66.6%. In our study, we found 11 patients (40.7%) were seizure-free without auras, 3 (11.1%) were seizure-free with auras, and 4 (14.8%) suffered from 1\u20133 seizures per year and (47%) seizure-free, respectively. The first- and third-year epilepsy surgery outcomes of 15 extratemporal epilepsy surgeries were (47%) and (33%) seizure-free. The histopathology results were 12 focal cortical dysplasia and heterotopias, 12 sclerosis and gliosis, 2 nonspecific, 5 had normal histopathology results and no histopathology tissues were obtained for 2 corpus callosotomies and 1 frontal multiple subpial transaction.This study of the Saudi epilepsy surgery series demonstrated that the epilepsy surgery outcomes in our epilepsy center compare well to those from other countries . In thisThe study included the patients that underwent resective surgery in the epilepsy program of Riyadh's KFSHRC between 1998 and 2012. The postoperative outcome was assessed according to a classification adapted from the ILAE. Seizure-free patients without auras, seizure-free patients with postoperative auras, and patients with fewer than three seizures per year were considered to be favorable outcomes based on the recommendations of the ILAE commission report , 18.The literature showed a significant improvement in seizures with temporal and extratemporal epilepsy surgery in children and adults \u201324. SignVarious studies have examined the rates and predictors of seizure-freedom after resection for frontal lobe epilepsy. There is significant variability in their results due to patient diversity. Across 1,199 patients in 21 studies, the overall rate of postoperative seizure-freedom for at least 48 months (Engel Class I outcome) was 45.1% , 29. In Surgery on the parietal and occipital lobes depends largely on the underlying pathology. Previous studies suggest 20% of nonlesional and 75% of lesional parietal lobe cases may be rendered seizure-free by resective surgery . One of Rasmussen encephalitis, 25 were hemimegalencephaly and cerebral cortical dysgenesis, and 15 were encephalomalacia. Forty-one of the 53 patients were children. ILAE class 1\u20133 surgical outcomes for the first- and third-year followup are 64% and 63%, respectively. The atypical variable in our series is the high ratio (47%) of the hemimegalencephaly and cortical dysgenesis.A total of 53 functional hemispherectomies were performed in our series. Of the 53 procedures, 11 cases were Hemimegalencephaly was first described by Sims in 1835 [hemimegalencephaly that underwent a functional hemispherectomy were described. Engel class (1a\u2013c) was achieved in 10 out of 15 cases [with Rasmussen encephalitis underwent surgery [ in 1835 . 15 case15 cases . Another15 cases . MoreoveWe did analyze the surgical outcome based on the histopathology diagnosis. CNS and MTS patients had a better outcome than those with cortical dysplasia (CD) or dual pathology at 1 and 3 years after surgery. In the Irish epilepsy surgery experience, MTS patients had a significantly better outcome than those with CD, a CNS tumor, and other pathology groups at 1, 2, and 5 years after surgery . Dual paIn our series, 34 cases of refractory nonlesional focal epilepsy cases have been operated upon with encouraging results, although the number is too small to allow indisputable analysis; however, our results match with some of the reported similar literature. Jayakar et al. studied 102 patients with nonlesional intractable partial epilepsy that underwent excisional surgery. At the 2-year followup, 44 out of 101 patients were seizure-free, and 15 experienced greater than 90% reduction .In conclusion, the epilepsy surgery outcome in our comprehensive epilepsy program is comparable to the international standard. In our series, the most favorable outcomes are achieved with temporal epilepsy surgery procedure, histopathological diagnosis of mesial temporal sclerosis, benign CNS tumor, and cortical dysplasia, while the least favorable outcomes occurred with multilobar surgery procedure, dual pathology, and normal MRI brain patients."} +{"text": "An error occurred in Figure 1A, in the first panel of flowcytometry plots depicting change in the expression of CD21/35 versus FSC in resting B cells upon concomitant signaling. The correct values for these plots should read as 1022+21 (unstimulated); 1065+31(Pam2CSK4); 1035+33 (anti-CD86 Ab) and 1277+27(anti-CD86 Ab+Pam2CSK4). http://plosone.org/corrections/pone.0054392.g001.cn.tifPlease view the correct version of Figure 1 here:"} +{"text": "To investigate the potential of a commonly used botanical supplement, Echinacea purpurea, to interact with the boosted protease inhibitor darunavir/ritonavir.Open-label, fixed-sequence study in 15 HIV-infected patients receiving antiretroviral therapy including darunavir/ritonavir (600/100 mg twice daily) for at least 4 weeks. Echinacea purpurea root extract-containing capsules were added to the antiretroviral treatment (500 mg every 6 hours) from days 1 to 14. Darunavir concentrations in plasma were determined by using HPLC immediately before and 1, 2, 4, 6, 8, 10 and 12 hours after a morning dose of darunavir/ritonavir on days 0 (darunavir/ritonavir) and 14 (darunavir/ritonavir + echinacea). Individual darunavir pharmacokinetic parameters were calculated by using non-compartmental analysis, and were compared between days 0 and 14 by using the geometric mean ratio (GMR) and its 95% confidence interval (95% CI).2. Echinacea was well tolerated and all participants completed the study. Relative to administration of darunavir/ritonavir alone, its coadministration with Echinacea purpurea resulted in little change in darunavir pharmacokinetic parameters. Table Median (range) age was 49 (43-67) years, and body mass index was 24.2 18.7-27.5) kg/m8.7-27.5 coadministration of Echinacea purpurea with darunavir/ritonavir was safe and well tolerated in HIV-infected patients; data suggest that no dose adjustment for darunavir/ritonavir is necessary."} +{"text": "The growing prevalence of infectious diseases among patients, including HIV infection, increases the risk of transmission of an infection during endoscopic procedures. In 2009 the first 3 cases of HIV transmission through colonoscopy were reported in the USA.Studying of infectious danger of colonoscopes, processed in the manual and automated way.Microbiology .Swab samples taken from instrumental channels of colonoscopes immediately after the procedure (sample 1), after mechanical brushing of channels (sample 2), and after completing high-level disinfection (HLD) or a complete reprocessing cyclein the Automatic Endoscope Reprocessor (AER) ASP Johnson & Johnson (sample 3). Swabs taken from 48 colonoscopes were studied.Bacterial contamination of instrumental channels in 17 colonoscopes after their use, brushing, and processing in AER was 8.7 (8-10), 4.74 (3.32-6.3), and 0 lgCFU/ml, respectively. Bacterial contamination (samples 1 and 3) of 16 colonoscopes processed in AER only was 8.87 (8-9.7) and 3.8 (2.7-4.85) lgCFU/ml, respectively. Bacterial contamination of 15 colonoscopes cleaned manually was 8.99 (8-10.4), 5.2 (3-6.7), and 2.9 (2.7-4.1) lgCFU/ml, respectively.Processing of colonoscopes in the AER, after preliminary brushing of channels, is the most reliable and effective. In 2008, we have proved that the endoscopes after use on HIV - infected patients represent essential infectious danger. HIV was isolated in the MT-4 human T-lymphoblastoid cells in 33 of 35 (94.3%) samples taken from instrumental channels of endoscopes directly after use and in three samples (8.6%) after completing HLD. All cases of ineffective cleaning were associated with violations of national standards.None declared."} +{"text": "To investigate the outdoor aeroallergens at two different, a fully developed (FD) and a less developed (LD), sites in Riyadh, capital city of Saudi Arabia.Two Burkard Volumetric 7-day Recording Spore Traps were employed at both locations. Exposed slides were read at 12 bi-hourly traverses, with a total of 60 fields per 24 hours (0-24hours). The study was initiated in January 2012.Phoenix dactylifera (31%), grass pollen (14%), Atriplex nummularia (12%), Amaranthus viridus (10%), Artemisia monosperma (7%), Plantago sp. (6%) and Populus sp. (4%). The minor species (<1%) were Casuarina sp., Chenopodium murale, Eschscholtzia sp., Eucalyptus sp., Lilium sp., Prosopis juliflora, Salix sp. and Salsola imbricata. At the LD site, the major species included Phoenix dactylifera (36%), grass pollen (15%), Salix sp (8%), Artemisia monosperma (6%), Atriplex nummularia (6%), Plantago sp. (3%), Populus sp. (3%), Amaranthus viridus (2%) and Ambrosia sp. (2%). The minor species included Daucus carota, Eucalyptus sp. and Salsola imbricata. The fungal spores recorded at both sites displayed only quantitative variations. The major components of these spores at FD site included Arthrinium (14%), Ulocladium (14%), Cladosporium (13%), Alternaria (10%), ascospore septate (10%), smut spores (9%), Basidiospore (7%), ascospore non septate (6%), Bipolaris (3%), Myxomycete (3%), Periconia (3%), Aspergillus/Penicillium (2%), Stemphyllium (2%) and Curvularia (1%). The minor components (<1%) were Drechslera, Melanospora, Peranospora, Pithomyces and Torula. The major fungal spores at LD site were Ulocladium (13%), Cladosporium (12%), Aspergillus/Penicillium (11%), smut spores (11%), Alternaria (9%), ascospore septate (9%), Basidiospore (9%), Arthrinium (8%), Stemphyllium (5%), ascospore non septate (4%), Periconia (3%) and Bipolaris (2%), while the minor spores included Curvularia, Drechslera, Melanospora, Myxomycete, Peranospora, Pithomyces and Torula.The data analyzed so far revealed the presence of different pollen and fungal species at both sites. The ratio between the pollen and fungal spores was 1:5. The airborne pollen grains showed quantitative and qualitative differences between the two sites. At FD site, the major pollen grains included The results indicate that developed and less developed sites have no impact on the qualitative and quantitative diversity of fungal spores but such diversities were recorded in airborne pollen species."} +{"text": "The clinical relevance of X-ray findings may not justify routine postoperative radiographic controls at 0, 3, 6, 12, and 24 months in adolescent idiopathic scoliosis (AIS) patients undergoing instrumented fusion with third-generation implants.Full-spine X-rays and clinical records from the first 2 years\u2019 postoperative follow-up in all AIS patients who underwent instrumented fusion in our center between 2005 and 2008 were independently analyzed by 2 investigators (consensus for discrepancies). The reviewers sought any clinical feature justifying X-ray control and any relevant radiologic finding .Records from 43 patients were evaluated. A total of 414 full-spine X-rays (9.6/patient) were performed during the first 2 postoperative years: 392 were available for analysis, and 391 had an associated clinical note. Excluding the 89 immediate postoperative films, only 48 of 325 (14.8%) were clinically justified: pain in 17 (34%) patients, clinical progression of deformity in 4 (8%) and previous X-ray finding in 29 (58%). All patients with clinical progression had a relevant X-ray finding. Pain was associated with a relevant finding in 23.5% of cases ; 7.4% of films with no clinical justification showed a relevant finding . Only 4.3% of films led to a therapy change. Lower Risser sign increased the risk of having a relevant radiographic finding (p<0.05).Routine 3, 6, 12, and 24-month postoperative X-rays are not justified in AIS and should be avoided in mature, uncomplicated cases."} +{"text": "To analyse the demographics, types and mechanisms of injury, management and outcomes of all cardiothoracic trauma during the first year of a South London Major Trauma Centre in comparison to national standards.A retrospective analysis of a trauma database in conjunction with electronic patient records and paper notes for the 12 month period April 2010 to March 2011.Of 1556 trauma patients, 254 had cardiothoracic trauma. 90% (228/254) were male and 10% (26/254) were female. Median age of all patients was 26 (range 1-91). 57% (145) were penetrating injuries mainly knife wounds (128) and gunshots (10). 43% (109) were blunt injuries (90 high and 19 low velocity). The actual injuries are detailed with rib fractures (35%) and pneumothorax (30%) the commonest and cardiac (5%) and diaphragm (3%) injuries the least common. 48% (121) of all cases had isolated thoracic injury, with 52% (133) being multiply injured. Of those multiply injured 36% (48) had head injuries, 65% (87) had orthopaedic injuries and 32% (43) had abdominal injuries. Operative and non-operative management is described in detail. Of the 15 patients requiring cardiothoracic surgery, 6 had a clamshell incision, 5 posterolateral thoracotomy, 2 median sternotomy and 1 thoracoscopy. Overall mortality was 3.5% (9/254). Operative mortality was 13% (2/15). Median length of stay was 4 days.Despite a higher incidence of violent penetrating trauma compared to the national average of 2% of all thoracic trauma, the pre hospital care and in hospital multi-disclipinary approach with resident cardiothoracic care results in a favourably low mortality."} +{"text": "Streptococcus (GAS) causes human diseases ranging in severity from uncomplicated pharyngitis to life-threatening necrotizing fasciitis and shows high rates of macrolide resistance in several countries. Our goal is to identify antimicrobial resistance in Spanish GAS isolates collected between 1994 and 2006 and to determine the molecular epidemiology (emm/T typing and PFGE) and resistance mechanisms of those resistant to erythromycin and tetracycline.Group A emm4T4, emm75T25, and emm28T28, accounting the 67.1% of the 21 emm/T types. Spread of emm4T4, emm75T25 and emm28T28 resistant clones caused high rates of macrolide resistance. The distribution of the phenotypes was M (76.9%), cMLSB (20.3%), iMLSB (2.7%) with the involvement of the erythromycin resistance genes mef(A) (89.5%), msr(D) (81.7%), erm(B) (37.3%) and erm(A) (35.9%).Two hundred ninety-five out of 898 isolates (32.8%) were erythromycin resistant, with the predominance of emm77T28 among 20 emm/T types. To note, the combination of tet(M) and tet(O) tetracycline resistance genes were similar to tet(M) alone reaching values close to 40%. Resistance to both antibiotics was detected in 19 isolates of 7 emm/T types, being emm11T11 and the cMLSB phenotype the most frequent ones. erm(B) and tet(M) were present in almost all the strains, while erm(A), mef(A), msr(D) and tet(O) appeared in less than half of them.Sixty-one isolates were tetracycline resistant, with the main representation of the emm/T type was noticed. Clonal spread of emm4T4, emm75T25 and emm28T28 was the main responsable for macrolide resistance where as that emm77T28 clones were it to tetraclycline resistance. A wide variety of macrolide resistance genes were responsible for three macrolide resistance phenotypes.Spanish GAS were highly resistant to macrolides meanwhile showed minor resistance rate to tetracycline. A remarkable correlation between antimicrobial resistance and Streptococcus (GAS) causes a broad spectrum of illness in humans, ranging from pharyngitis to severe systemic diseases. A resurgence in serious GAS infections, such as rheumatic fever, and invasive diseases, such as bacteraemia, necrotising fasciitis, septic arthritis, sepsis, pneumonia and streptococcal toxic shock syndrome, has been observed since the mid 1980s. Indeed, these have become an important cause of morbidity and mortality all over the world [Group A Penicillin is the first choice treatment. Macrolides and tetracyclines are the most common alternative antibiotics used with penicillin-allergic patients or when first line therapy fails. Increases in macrolide resistance have been reported from many countries, being in Europe, very common in the Mediterranean countries ,3.B phenotype). The MLSB phenotype may be expressed constitutively (cMLSB) or inducibly (iMLSB). These methylases are encoded by erm (erythromycin ribosome methylation) genes, with the erm(B) and erm(A) the most common [14 and C15 macrolides out of the cell (M phenotype). The M phenotype is associated with the presence of the mef(A) and msr(D) genes, which code for the transmembrane and ATP-binding domains of this pump respectively [Streptococci have two main mechanisms of macrolide resistance: target site modification and macrolide efflux systems. The first is achieved through a family of enzymes (rRNA methylases) that methylate an adenine residue (A2058) of the 23S rRNA V domain. This leads to a conformational change that reduces the binding of macrolides, lincosamide and streptogramin B to ribosomes, conferring co-resistance to these antibiotics (the MLStet(M) and tet(O) and by efflux pumps encoded by the tet(K) or tet(L) genes, although these last genes are relatively rare [Less information is available on the characteristics of tetracycline resistance mechanisms. In streptococci, resistance to tetracycline is conferred by ribosome protection genes such as ely rare .emm types. The aim of the present study was to identify antimicrobial resistance in Spanish group A Streptococcus (GAS) isolates and to determine the molecular epidemiology (emm/T typing and PFGE) and resistance mechanisms of those resistant to erythromycin and tetracycline. This study is focused on Spanish GAS population collected from a wide spectrum of clinical backgrounds and not only from carriers as occurs for other studies. The long term studied period (13\u2009years) and the different geographical origin may allow us to obtain an approach more real to susceptibility, phenotypes, genotypes, emm-types and PFGE profiles distribution in Spain.The prevalence of antimicrobial resistance is due to several circulating clones associated with certain All 898 Spanish GAS isolates showed susceptibility to penicillin and vancomycin. In addition, a 32.8% (295 isolates) rate of resistance to erythromycin was seen, along with 6.5% (59) resistance to clindamycin, 6.8% (61) resistance to tetracycline, and 0.3% (3) resistance to rifampin.B and iMLSB phenotypes (Table\u2009B phenotype showed high-level resistance to erythromycin and clindamycin (MIC90 \u2265256\u2009mg/L), whereas those with the iMLSB and M phenotypes showed lower erythromycin resistance values and susceptibility to clindamycin erythromycin resistant isolates were detected among the 898 GAS isolates gathered over the 13-year collection period. The M phenotype was clearly predominant , followed by the cMLSmef(A) (89.5%) and msr(D) (81.7%) genes were the most prevalent macrolide resistance determinants. erm(B) and erm(A) were observed in just 37.3% and 35.9% of isolates respectively (Table\u2009msr(D)/mef(A) (38%) and msr(D)/mef(A)/erm(A)(19.7%) the two most common combination. Both genotypes were associated with the M phenotype.In the present work, the msr(D) 8.7% genesly Table\u2009, with ms50 16\u2009mg/L, MIC90 32\u2009mg/L) with a genotype distribution of tet(M)/tet(O) (42.6%), tet(M) (39.3%) and tet(O) (18.0%).Tetracycline-resistant phenotype was observed in 61 isolates (6.8%), showed MICs ranging from 8 to 64\u2009mg/L (MICerm(B) (94.7%), erm(A) (42.1%), mef(A) (47.4%), msr(D) (36.8%), tet(M) (100.0%) and tet(O) (36.8%), with tet(M) the only tetracycline resistance determinant in 13 isolates, while in 6 it was simultaneously detected with tet(O) (Table\u2009Co-resistance was detected in 19 isolates (2.1%). The erythromycin MIC was >256\u2009mg/L for 18 isolates and just 32\u2009mg/L for one isolate. The clindamycin MICs were also high at >256\u2009mg/L for 14 of the 19 isolates. All isolates except one (iMLSB) had the cMLSB macrolide resistance phenotype. The resistance genes detected were emm/T types were observed in the erythromycin-resistant population (295) (Table\u2009emm4T4 (39.3%), emm75T25 (14.6%), emm28T28 (13.2%), emm6T6 (9.8%), emm12T12 (6.8%) and emm11T11 (4.1%) which represented 87.8% of the erythromycin-resistant isolates. High macrolide resistance rates were associated with the above emm/T types: emm75T25 (93.5%), emm4T4 (84.7%), emm11T11 (50%), emm28T28 (50%), emm6T6 (43.3%) and emm12T12 (29.4%).Twenty one 5) Table\u2009, the 6 memm/T types were identified (Table\u2009emm77T28 (37.3%) was the main emm/T type associated with tetracycline resistance; all emm77T28 isolates detected over the 13\u2009years of the study were resistant to this antibiotic.In the present tetracycline-resistant population (61), 20 different ed Table\u2009. emm77T2emm/T types were observed, the majority being emm11T11 (57.8%) were co-resistant.In the erythromycin- and tetracycline-resistant population population (19), 7 %) Table\u2009; indeed,emm/T types and macrolide resistance genotypes is shown in Table\u2009mef(A)/msr(D) gene complex was the most common in almost all emm/T types, either alone or in combination with other genes. The mef(A)/msr(D) genotype was the most common in the emm1T1 (6/10), emm4T4 (62/116), emm6T6 (26/29) and emm12T12 (10/20) types. The msr(D)/mef(A)/erm(A)(36/116) was the most common genotype among the emm4T4 (36/116) and emm75T25 (17/43) types.The correlation between the different SmaI-restricted and 216 (73.2%) SmaI-non-restricted isolates were identified. SmaI-restricted isolates generated 30 pulsotypes with a similarity range of 38.8% to 94.7% and iMLSB (6).In the erythromycin-resistant population (295 isolates), 79 (26.8%) SmaI-non-restricted isolates and iMLSB (2) phenotypes. In addition, 11 different emm/T types were detected isolates were SmaI-restricted.In the case of tetracycline-resistant isolates, all were Several reports show that GAS resistance to macrolides and tetracyclines are high some countries such Spain and continue to increase; indeed, they have become clinically problematic.In Europe, the most northerly countries (with the exception of Finland) have reported low levels of resistance (<4%) while stIn our study, 32.8% of isolates showed resistance to macrolides. Efflux pumps (M phenotype) are one of the major mechanisms conferring resistance to macrolide antibiotics, and streptococci making use of this system have been commonly reported from European countries, Argentina, the USA and Canada ,13-15. TB phenotype, another common phenotype reported in Europe [B phenotype was the second most commonly encountered (20.3%) like SAUCE project carried out in 2006\u20132007 [B phenotype from 14% in 2001\u20132002 to 35.5% in 2006\u20132007 [cMLSn Europe , was disn Europe ,19. In o006\u20132007 . In this006\u20132007 .B phenotype was minority (2.7%) in contrast to Norway (75%) (1993\u20132002) or Bulgaria (57.7%) (1993 \u2013 2002) where it was reported the most prevalent phenotype [Among Spanish isolates of this work, iMLS Norway 7% (1993\u20132mef(A) and erm(B) were predominant in isolates with the M and cMLSB phenotype respectively, whereas all isolates with the iMLSB phenotype harboured the erm(A) gene.A gene-phenotype correlation previously described was also noticed ,9. mef(Amef(A) gene responsible for the M phenotype was detected in all but three of the present Spanish isolates with that phenotype. One of these three isolates showed none of the genes studied. In the remaining two, msr(D) was observed alone or in combination with erm(A). In these last two cases, the msr(D) gene might be only one of the determinants responsible for the M phenotype. msr(D) and mef(A) have been placed in the same genetic element [msr(D)-encoded pump can function independently of the mef-encoded protein [The element ,20, suggerm(B) gene responsible for the cMLSB phenotype was identified in all but three of the present isolates with this phenotype. None of genes tested could be amplified in two isolates, indicating that other resistance genes must be involved. The remaining isolate harboured erm(A) and mef(A). In this case, erm(A) may be responsible for the cMLSB phenotype since alterations in the regulatory region of the gene have been identified that induce constitutive expression [The pression .erm(B)/msr(D)/mef(A) genotype showed M and MLSB phenotypes in 25 and 8 isolates respectively, while the erm(B)/erm(TR)/msr(D)/mef(A) genotype showed all three macrolide resistance phenotypes. Nowadays, this correlation between genotype and phenotype is not well understood.An ample macrolide resistance genes combination was identified, specifically fourteen genotypes. Interestingly, single genotypes could show one or several phenotypes, a phenomenon reported by other authors ,10. One emm/types: emm4T4 (39.3%), emm75T25 (14.6%), emm28T28 (13.2%), emm6T6 (9.8%), emm12T12 (6.8%) and emm11T11 (4.1%) have been previously associated with macrolide resistance in numerous reports [emm28 and emm4 have been reported the most common in Europe (2003\u20132004) [emm12 is the main resistant emm type in Germany, Greece, Italy, Portugal, Israel [emm75 [In our erythromycin-resistant population (295), the 6 most common reports ,12,14. e03\u20132004) , and to , Israel ,12,13 anSma-non-restricted (73.2%) due to the presence prophage-like elements that confer the M phenotype and harbour the mef(A) and msr(D) genes. These genetic elements encode a DNA-modifying methyltransferase that acts on the SmaI recognition sequence and renders DNA refractory to cleavage by SmaI [SmaI non-restricted isolates were susceptible to tetracycline and had an M phenotype. This suggests that these isolates carry mef(A) and msr(D) contained within a Tn1207.1 transposon inserted into a larger genetic element such as the Tn1207.3 or 58.8\u2009kb chimeric element, flanked by the comEC gene from the Tn1207.3/\u03a610394.4 family [emm4T4 and all emm75T25 erythromycin-resistant isolates but one were SmaI non-restricted and had the M phenotype; together these accounted for 53.9% of the Spanish macrolide-resistant isolates. Several resistant clones previously described in Spain were identified [emm4T4 Sfi1 (79) clone resembles to clone B described in 1999 [emm4T4 Sfi4 and emm4T4 Sfi5.Most of erythromycin-resistant isolates were by SmaI . All but4 family . In our in 1999 . Clone C in 1999 was not emm75T25 Sfi12(41) was similar to clone D described by Perez-Trallero et al. [emm6T6 Sfi17 and emm84T25 Sfi22 clones might be associated with resistance since they were only observed in isolates resistant to erythromycin.The major macrolide-resistant clone o et al. . The emmRegarding tetracycline resistance, we detected values of 6.8% between 1994 and 2006, indicating there to be no trend towards increased tetracycline in Spain. However, higher rates have been found in other countries such as Israel (23.6%), Denmark (33.7%), Portugal (38.7%) or Iran (42%) -12.tet(M) and tet(O) (42.6%) was observed. But no Spanish reports citing the predominance of both genes appears to exist, tet(M) alone is usually the most common resistance determinant followed by tet(O) [In this study, a predominance of genotype with both genes y tet(O) .emm77T28 was the main emm/T type. emm77 has been previously associated with resistance to tetracycline in Israel and Europe [emm77 clone has been reported that is characterised by its carrying tet(O) linked to erm(A)and being associated with the iMLSB phenotype [emm77T28 isolates showed genotypes different to those described by Palmieri et al. [In the present tetracycline-population, d Europe . In ItalB macrolide resistance phenotype such as Greece (Athens) and Norway [B isolates showing co-resistance have reached rates of 93% [With regard to co-resistance, we found that all isolates 19) except one had the cMLSd Norway ,15. In c except os of 93% , but thitet(M)/erm(B) as their only resistance genes, suggesting they may carry conjugative transposons of the Tn916 family in which erm(B) and tet(M) are linked [tet(M)/erm(B) associated with other resistance genes. In the remaining isolate, the erm(B), mef(A), tet(M) and tet(O) genes were all detected. mef(A) and tet(O) linkage has been previously reported in co-resistant isolates [mef(A) appeared associated with other macrolide resistance genes and linked to tet(M) (1 isolate) or to tet(M)/tet(O) (5). The main emm/T type detected in coresistant isolates was emm11T11 (57.8%). This emm/T type has previously been associated with co-resistance [erm(B)/tet(M) clone prevalent among Spanish MLSB isolates [Of the 19 co-resistant isolates, five carried e linked ,whereas isolates ,25. In temm4T4, emm75T25, both associated with M phenotype and SmaI non-restricted, and emm28T28. Whereas tetracycline resistance and coresistance is due to clonal spread of emm77T28 and emm11T11, respectively, all SmaI restricted.In summary, the resistance against erythromycin, single or together to tetracycline, is due to a wide combination of resistance genes in Spanish GAS. Erythromycin resistance is mainly consequence of clonal spread of Between 1994 and 2006, 898 GAS isolates were submitted for their characterisation to the Streptococcal Reference Laboratory from 75 Hospitals and Public Health Laboratories in 32 Spanish provinces. GAS identification was confirmed by colony morphology, \u03b2-haemolysis on blood agar, a latex agglutination assay , and by using the rapid ID 32 STREP kit . The erythromycin- and tetracycline-resistant isolates were selected as the study population . This population (337 isolates) was collected from a wide spectrum of clinical backgrounds, including necrotising fasciitis (3), cellulitis and other skin infections (67), streptococcal toxic shock syndrome (13), sepsis and meningitis (17), respiratory infection (5), bone infection and rheumatic fever (4), genital infection (20), otitis (12),conjunctivitis (1), scarlet fever (70) and pharyngotonsillitis (80), as well as from asymptomatic carriers (45). For the latter status, the GAS isolates were recovered from oropharyngeal swabs. A limitation of the study was due to the voluntary nature of the submission of these strains, producing a bias in the annual number.Streptococcus pneumoniae ATCC 49619 was used as control.The minimum inhibitory concentrations (MICs) of penicillin, vancomycin, erythromycin, clindamycin, tetracycline and rifampin were determined using the E-test following the standard method . SusceptB (constitutive erythromycin and clindamycin resistant), and iMLSB (erythromycin resistant and clindamycin inducible). Blunting of the clindamycin inhibition zone near to the erythromycin disk indicated an iMLSB phenotype, whereas susceptibility to clindamycin with no blunting indicated the M phenotype.Erythromycin-resistant isolates were classified on the basis of their susceptibility patterns as shown by double-disk tests involving erythromycin (15\u2009\u03bcg) and clindamycin (2\u2009\u03bcg ) disks . Three perm(B) [erm(A) [mef(A) [msr(D) [tet(M) and tet(O) [All erythromycin-resistant isolates were screened by PCR for the erythromycin resistance genes erm(B) , erm(A) [erm(A) , mef(A) [mef(A) , and msr [msr(D) . Tetracyd tet(O) . PCR assemm sequencing was performed according to the protocol of the CDC International Streptococcal Reference Laboratory (http://www.cdc.gov/ncidod/biotech/strep/protocols.htlm).The T-serotype was determined by slide agglutination using type-specific antisera . SmaI (40U) restriction enzyme for 4\u2009h at 30\u00b0C and the electrophoresis conditions were 22\u2009h with an 0.5 to 40s switch time ramp at a 120\u00b0 angle and 6\u2009V/cm. SmaI non-restricted isolates were typed by PFGE using the SfiI restriction enzyme under previously described conditions [Sma- and Sfi-profiles were number-coded. For closely related Sma-types (1\u20132 bands of difference) a letter was added.PFGE was performed as previously described with slinditions . The PFGThis research was funded by an intramural predoctoral fellowship from the Carlos III Health Institute (grant number 05/0030) and the Spanish Ministry of Science and Innovation.The authors declare that they have no competing interests.PV, MJM, SV, JA and VR participated in the molecular data collection and analysis. DA, CS and VR conducted the microbiological methods and analysed data. SV, JA and VR interpreted data, and drafted the manuscript. SV and JA were involved in critically revising the manuscript. All authors read and approved the final manuscript."} +{"text": "Malperfusion is a factor associated with higher risk of death and complications in patients with acute type A aortic syndrome (AAAS). Our objective is to determine the incidence and characteristics of this disease in our population and to verify the relevance in morbidity and in-hospital mortality.A historical cohort study that includes all patients with AAAS admitted to the ICU after surgical management in a single institution from January 2000 to July 2010. Anatomical, clinical, biochemical, electrocardiographic and echocardiographic signs of ischemia were considered. The events of interest were death or major complication , acute lung injury (ALI), postoperative hemorrhage) during hospitalization.P = 0.03), neurological complication , MOF (16.6% vs. 25%. P = 0.07) and ALI were found.A total of 65 patients were identified . Thirty-three (50.8%) presented branch compromise, affecting coronary arteries in 12 patients (18.4%) (symptomatic (S) seven (10.5%), asymptomatic (A) five (7.7%)), nine (13.8%) carotid (S five (7.7%), A four (6.1%)), 28 (43%) brachiocephalic or subclavian (S 17 (26.1%), A 11 (16.9%)), 15 (22.8%) mesenteric (S seven (10.5%), A eight (12.3%)), 13 (20%) renal (S nine (13.8%), A four (6.1%)), and 31 (47.7%) iliac (S 16 (24.6%), A 15 (23%)). Twenty-eight (43.1%) showed clinical ischemia of at least one system and 54 (83%) clinical signs of global hypoperfusion. Comparing patients with and without data of hypoperfusion, differences in incidence of death (45.5% vs. 18.8%, More than 80% of the patients with AAAS suffered malper-fusion in our series. They had a higher risk of death and neurological complication during hospitalization."} +{"text": "Prevalence of temporomandibular arthritis in JIA varies widely, reported rates ranging from 17- 87%. Untreated inflammation with joint destruction can lead to asymmetrical mandibular growth with jaw deviation, dental malocclusion and micrognathia. Intra-articular steroid injection for TMJ arthritis has been found to be effective. There are limited reports on the efficacy of ultrasound guided steroid injections of the TMJ\u2019s in JIA.To assess the safety and efficacy of ultrasound guided corticosteroid injection, done by a paediatric rheumatologist, into the temporomandibular joints in children with JIA.Children with JIA presenting to rheumatology clinic assessed for TMJ arthritis. Triamcinolone hexacetonide injected in those with active arthritis assessed by MRI, using ultrasound guidance under general anaesthesia by a single paediatric rheumatologist trained in procedure. Efficacy and safety was assessed post-injection by patient guided symptoms and physical examination.38 children (34 girls) with TMJ injection between Jan 2009\u2013Jan 2011 studied. Mean age: 12.25\u00b13.55years(range=5-18 years). Mean disease duration: 4.54\u00b12.73 years (1.5-11.1years). Symptoms pre-injection: pain:17/38(44.7%), jaw deviation:14/38(36.8%), restricted jaw movement:13/38(34.2%), chewing dysfunction:7/38(18.4%), micrognathia:5(12.5%). Total 63 joints injected. Injection efficacious:58/63(92.06%) joints(Table Ultrasound guided corticosteroid injection into the temporomandibular joint done by a paediatric rheumatologist trained in the procedure safe with a high rate of success."} +{"text": "Persons with KS and uncontrolled HIV infection have HHV-8 DNA detected more frequently at mucosal sites and plasma , but it Participants collected daily oral swabs and weekly plasma samples over 4 weeks to quantify HHV-8 DNA by polymerase chain reaction.297 participants collected a total of 8,045 oral swabs and 1,392 plasma samples. HHV-8 DNA was detected in 1,561 (19%) oral swabs and 419 (30%) plasma samples. The frequency of detecting any HHV-8 differed by KS status. HHV-8 was detected in the oropharynx of 70% (64/92) persons with KS vs. 27% (52/194) without KS (p<0.001), and in the plasma of 96% (88/92) persons with KS vs. 20% (38/194) without KS (p<0.001). The median amount of HHV-8 DNA detected in oral swabs was significantly lower in persons with KS (3.2 log copies/ml) than those without KS (Figure Increased quantities of HHV-8 DNA were detected in the oropharynx of persons without KS and those with poor dentition. The latter observation may be explained if higher CD4 counts allow for increased inflammation in the oropharynx, in turn leading to greater HHV-8 replication. Quantities of HHV-8 are higher in the plasma of persons with either HIV infection or KS, perhaps representing the propensity of HHV-8 to disseminate systemically in the absence of effective immune control or from foci of replication in KS tumors."} +{"text": "To determine the influence of ethnicity and sociodemographic factors on disease presentation, manifestations, disease activity, and disease outcomes, using baseline data from the pediatric arm of the 1000 Canadian Faces of Lupus Study, a multicenter, prospective study of the Canadian Lupus population.th birthday) patients at four pediatric centers . Collected data included sociodemographics, disease manifestations, current/past medications, laboratory measures and multiple disease measures. The Child Health Questionnaire (CHQ), measuring multiple domains of health status was administered. For analysis, patients were categorized by their primary self-selected ethnic category.Childhood-onset SLE , Vancouver 54 (25%), Montreal 17 (8%), and Halifax 8 (4%). There were 176 (83%) females, mean age at diagnosis was 12.5 \u00b1 0.3 years, mean disease duration was 2.5 \u00b1 2.7 years, and 175 patients (82%) were born in Canada. Demographic data were similar across the geographic sites, except for a longer disease duration in Vancouver . Primary self-reported race/ethnicity data was available for 191 patients: White (31%), Asian (30%), South Asian (15%), Black (10%), Latino/Hispanic (4%), Aboriginal (4%) and Arab/Middle Eastern (3%). Because of low numbers, the Latino/Hispanic and Arab/Middle Eastern groups were excluded from the analysis. Ethnic distribution across the centers differed (p<.001), reflecting known differences in the urban populations. The distribution of household income, and prescription drug plan coverage did not differ across ethnicities, however, fewer Asians (64%) had dental insurance coverage as compared to White (88%) and Aboriginal (100%) patients (p<.01). Missed school days did not differ by ethnicity, although 26% of the entire cohort reported missing on average 6 days per month. CHQ scores were lower in 7 of 10 domains in white patients vs. non-white ethnicities (p<.05 for each). Autoantibodies and SLE classification criteria present at any time that differed by ethnicity are listed in table Medications were prescribed equally across ethnicities; most patients were taking prednisone (75%), hydroxychloroquine (84%), and 56% required additional immunosuppression . Disease measures were similar across ethnicities, overall SLEDAI was 3.1 \u00b1 4.2, SLAM 3.4 \u00b1 3.7; SDI median 0.3 (range 0-5), and physician global VAS was 15 \u00b1 23 (range 0-99).Canadian cSLE patients reflect our multi-ethnic population, with observed differences in disease manifestations, antibody profiles and health status by ethnicity.Deborah M. Levy: None; Earl D. Silverman: None; Lori B. Tucker: None; Gaelle Ch\u00e9deville: None; Adam Huber: None; Janet E. Pope: None; Christine A. Peschken: None; CaNIOS Investigators: None."} +{"text": "We evaluated a high (6%) cholera case-fatality rate in Haiti. Of 39 community decedents, only 23% consumed oral rehydration salts at home, and 59% did not seek care, whereas 54% of 48 health facility decedents died after overnight admission. Early in the cholera epidemic, care was inadequate or nonexistent. Epidemic cholera remains a public health problem in developing countries. In 2009, a total of 45 countries reported 221,226 cases and 4,946 deaths; for both, >98% occurred in sub-Saharan Africa should remain <1% . To dete>5 years of age ), ORS (27 [56%]), both (20 [42%]), or neither (3 [9%]).Household members of 33 (69%) health facility decedents and 30 (81%) community decedents reported receiving information about cholera after the outbreak started. The most common information sources for families of health facility and community decedents, respectively, were radio (26 [79%] vs. 26 [89%]), friend (6 [18%] vs. 8 [27%]), cellular telephone text message from MSPP (4 [12%] vs. 4 [13%]), community meeting (2 [6%] vs. 2 [7%]), and CHWs (1 [3%] vs. 3 [10%]). Fewer than half of family members of health facility (23 [48%]) and community (19 [49%]) decedents believed cholera was treatable. Of these, 16 (70%) health facility decedents and 17 (90%) community decedents knew to seek care at a health facility.Our findings suggest that, early in the cholera epidemic in Haiti, death occurred rapidly, and care was either inadequate or nonexistent. We found several possible explanations for this situation.First, early in the outbreak, the population knew little about cholera. Many decedents did not know to seek care immediately. Knowledge, availability, and use of ORS were inadequate. Although many families acknowledged receiving cholera messages, their understanding was incomplete. Few reported receiving cholera messaging or ORS from CHWs. Global deficiencies in the distribution and use of ORS in recent years have impeded the ability of CHWs to initiate treatment .In response to the epidemic, training and supplies have been provided to health workers in all 10 departments of Haiti. By April 2011, the cholera CFR had declined to <1% ("} +{"text": "Non-contrast-enhanced MR angiography (MRA) of the aorta is a robust alternative to using contrast-enhanced (CE) angiography in the imaging of thoracic aortic diseases. What is the cost impact of not using intravenous contrast routinely in thoracic aorta MRA?Free-breathing, ECG-triggered, navigator-gated 3D segmented steady state free precession (SSFP) MRA is a promising MR technique for imaging the thoracic aorta. We wanted to establish the economic impact of using non-contrast enhanced angiography (non-CEMRA) in our unit compared to the same time period last year when only CEMRA was used.Over a 3 month period, 22% of referrals to our cardiac MRI unit were for diseases of the aorta. These patients were divided into 5 subsets: 1) familial screening , 2) dilatation, 3) follow-up aortic dissection, 4) congenital aortic and valve disease & 5) vasculitis. 80 data sets for patients referred for evaluation of their aorta were examined. These were compared with 80 data sets in patients with aortic disease imaged in a similar period when only CEMRA was available. Clinical evaluation included recording the patients' serum creatinine, correlation with aortic measurements from previous imaging studies and subjective assessment of image quality. Cost analysis included costs of contrast agent, power injector sets and routine consumable costs associated with intravenous access.The unit price for consumables for thoracic aortic CEMRA was estimated at $140CAD*/patient ($110CAD for Gadolinium and $30CAD for other disposables). Vasculitis patients (group 5) were excluded from both data sets as intravenous contrast was needed for delayed enhancement imaging. No patient was excluded from CE-angiography due to a high serum creatinine . No patient undergoing non-CEMRA required an additional CEMRA for a non-diagnostic study. We examined 75 data sets in the 'pre-navigator' group and 72 in the 'post-navigator' group. In the pre-navigator group, 50 patients (67%) underwent CEMRA as part of their examination: 9/12 (75%) group 1, 12/28 (43%) group 2, 2/3 (67%) group 3 and 27/32 (84%) group 4. In the post-navigator group, 14 patients (19%) underwent CEMRA: 5/18 (28%) group 1 (268% reduction), 6/31 (19%) group 2 (266% reduction), 1/5 (20%) group 3 (335% reduction) and 5/18 (28%) group 4 (300% reduction). Costs associated directly with CEMRA in the pre-navigator group were $7000CAD (50 x $140CAD) and in the post-navigator group were $1960CAD (14 x $140CAD), a saving of $5040.*CAD = Canadian dollars.We conclude that using a free-breathing, ECG-triggered, navigator-gated 3D segmented steady state free precession (SSFP) sequence is a cost-effective way of imaging disease of the aorta without compromising imaging quality.Not applicable."} +{"text": "The autoinflammatory syndromes (AIS) include monogenic and polygenic disorders characterized by primary dysfunction of the innate immune system.To describe the spectrum of AIS in a Pediatric Rheumatology reference center.Medical records of AIS patients followed until November 2010 were studied.Fifty six patients were included: 17 CAPS, 4 TRAPS, 5 HIDS, 18 FMF, 6 CRMO, 2 SAPHO and 4 Behcet. The median follow-up period was 2 years (0-14 years). The male/female ratio was 20/36. The median age was 2.5 years at disease onset and 4 years at diagnosis. Family history was positive in 34% of patients. Clinical manifestations included fever (79%), mucocutaneous (61%), musculoskeletal (77%), ocular (34%), cardiorespiratory (12%), gastrointestinal (62%), neurological (41%) and genitourinary (2%) findings, lymphadenopathy with/or hepatosplenomegaly (16%) and growth impairment (27%). Seven patients presented severe manifestations: neonatal peritonitis (1 CAPS), pancreatitis (1 TRAPS), acute glomerulonephritis (1 FMF), complicated Henoch-Sch\u00f6nlein purpura (1 FMF), peritoneal adhesions with intestinal occlusion (1 FMF), periorbital pain (1 CRMO), and cerebral thrombosis (1 Behcet). One mutation was found in 93% of CAPS, and in all TRAPS patients. Two mutations were present in 11% of FMF, and in all HIDS patients. 43% of patients received colchicine, 23% steroids, and 54% biologics . 57% of patients were in complete and 41% in partial remission.AIS in children are associated with a broad spectrum of symptoms. A detailed history, thorough review of clinical symptoms and molecular testing of specific causative genes can provide early and accurate diagnosis."} +{"text": "First line HAART with tenofovir DF (TDF) and emtricitabine (FTC) in pivotal trials has been associated with high efficacy and good tolerability. However, real-life clinical practice often differs from clinical trials due to co-morbidities, co-infections, and less intensive clinical monitoring.+ antiretroviral na\u00efve patients (pts) from 50 German centres enrolled in this non-interventional cohort. All patients were to be followed for three years every three months to monitor and document efficacy , renal safety, tolerability, regimen changes and resistance profile. All patients received TDF+FTC as a single tablet fixed-combination mostly in combination with either NNRTI or PI/r as their first regimen.Between July 2005 and August 2006, 534 HIV3. TVD was combined with NNRTI (efavirenz (EFV)27%, nevirapine 16%), PI/r (54%) or other (3%). In an as treated analysis after 36 months, 91% of pts achieved VL<50 copies/mL . Median CD4 cell count increased to 472 cells/mm3 (IQR: 341-631). Regimen with TVD showed a good safety profile and 36 pts were switched to a single tablet regimen with EFV/TDF/FTC (Atripla); 113 adverse events (AEs) of any grade were reported in 73/534 pts (13.7%); 15 of these were rated serious. 21 (3.9%) pts discontinued the TVD regimen due to AEs. Most of them (n=13) discontinued within the first six months. Renal abnormalities of any grade were reported in 10 pts . Median creatinine clearance was 109.0 mL/min (n=444) at baseline and 103.3 mL/min (n=287) after 36 months. Virological failure as a reason for discontinuation was documented in 12 pts; in 11 failing pts genotyping was performed and detected M184V (n=2) or K65R (n=2) among other NRTI, PI or NNRTI mutations. One failing patient had shown M184V at baseline.As of April 2010, three years of therapy have been documented for 330/534 (61.8%) pts; 81% male; median age was 39 years. Clinical AIDS diagnosis was documented in 22% pts; 46% pts started therapy with median 211 (IQR: 111-297) CD4 cells/mmDuring three years of follow-up, overall safety of TVD was good. Virological failure was rare (12 pts) and K65R was detected in only 2 failing patients. First line HAART with Truvada (TDF/FTC) plus an NNRTI or PI/r in clinical practice showed comparable efficacy to that observed in controlled clinical trials."} +{"text": "AbstractKarnyothrips cyathomorphussp. n. (Phlaeothripidae: Phlaeothripinae) is described as a new apterous species in the genus Karnyothrips Watson 1923, and it represents the fourth species of the genus to be recorded from China. A key to the Chinese species is given. PageBreakKarnyothrips, belonging to the Haplothrips lineage in Phlaeothripinae, was established by Watson for the species Karynia weigeli, a synonym of Karnyothrips flavipes (Jones). Currently 47 species have been described in the genus is distributed in tropics and subtropics, and Karnyothrips robustus Okajima has been found only in Japan and Taiwan of China.The genus he genus , of whiche genus . KarnyotKarnyothrips species usually live on live plant leaves, branches and dead forest litter, where they feed on micro-invertebrates or fungi. Recently, a distinct new species of Karnyothrips has been found while studying the litter thrips fauna in subtropical and tropical China. Specimens were mounted into Canada balsam and deposited in the Insect Collection, Department of Entomology, South China Agricultural University (SCAU).The The diagnosis of the genus includes the following features : head lohttp://zoobank.org/1ED76766-7E7B-4CEC-8045-3037DD74D9A9http://species-id.net/wiki/Karnyothrips_cyathomorphusHolotype: female. CHINA: Guangdong Province, Guangzhou, Botanical Garden of South China Agricultural University , from leaf-litter, 15.xii.2004, leg. Jun Wang. Paratypes: 2 females and 3 males, same data as holotype; 1 female and 4 males, same locality, habitat and collector, 20.xi.2004; 1 male; Longdong , from leaf-litter of Acacia mangium plantations, 5.xii.2007, leg. Jun Wang.PageBreakFemale apterous . Body coHead: dorsum ; eyes length 48, diameter of ocelli 5; distance of posterior ocelli 34; pronotum median length 119, width 231; tube length 89, tube maximum width 56, apex width 35. Antennal segments I\u2013VIII length (width) as follows: 25(29); 33(26); 26(21); 40(25); 35(21); 31(19); 38(15); 23(11). Postocular setae 34; antennal terminal setae 20; pronotum anteroangular setae 31, midlateral setae 31, posteroangular setae 31, epimeral setae 39; tergum IX SApterous male: Color and structure similar to apterous female. Major setae on head, pronotum and abdomen capitate except that setae S2 on tergite IX are short and pointed, and S3 finely acute (ly acute . Fore fely acute . AbdominPageBreakPageBreak26(21); 39(25); 34(21); 29(19); 38(14); 24(11). Postocular setae 29; antennal terminal setae 16; pronotum anteroangular setae 28, midlateral setae 28, posteroangular setae 28, epimeral setae 35; tergum IX S1 setae 60, S2 setae 26.Total body length 1263; head L/W (144/138); eyes length 48, diameter of ocelli 4; distance of posterior oceelli 34; pronotum median length 110, width 213; tube length 85, tube maximum width 56, apex width 38. Antennal segments I\u2013VIII length (width) as follows: 19(28); 29(25); The specific epithet is a combination of Latin words cyatho and morphus, referring to the shape of antennal segment III.China (Guangdong).Karnyothrips cyathomorphus sp. n. resembles Karnyothrips inflatus Okajima in having a sub-basal ring-like swelling on antennal segment III, but it can be distinguished from the latter by the following features: (1) no wing; (2) antennal segment IV with 4 sense cones, antennal segment VII shorter than segment IV; (3) pelta semicircle-shaped and smooth medially and posteriorly. The new species is also similar in appearance to Priesneria kellyana Bagnall which is apterous and antennal segment III with a sub-basal ring-like swelling, but Priesneria kellyana has only one sensorium on antennal segment III and two sensoria on segment IV, and a glandular area on abdominal sternite IX (rnite IX which ca"} +{"text": "The aim of this study is to analyze the incidence of difficult intubation, and likewise characteristics, complications and mortality of urgent orotracheal intubation (OTI) in critically ill patients.2 saturation with pulsioximetry, before and after OTI, indications, type of technique, medication administrated, place where the technique was performed, and complications were collected.An observational, descriptive and prospective study. We analyze the impact of difficult OTI, morbidity and mortality in urgent OTI, in the noncoronary ICU of a third-level university hospital in Madrid. We collected all OTIs during the period of 1 year. Demographic data, blood pressure and OPatients: 277. OTIs: 305. Average attempts: 1.15 (SD: 0.41). Sex: male (M): 197 (64.6%), female (F): 108 (35.4%). Age: 56 years (15 to 87). Indications for OTI: low level of consciousness: 103 (34%), excessive work of breathing: 88 (29%), airway protection: 58 (19%), poor secretion management: 44 (14.4%), endotracheal tube change: 29 (9.5%), combative patient: 27 (8.8%), autoextubation: 6 (2.1%), glottis or laryngeal edema: 5 (1.7%), others: 6 (2%). Two or more indications agreed in 36%. Place technique was performed: ICU: 172 (56.4%), Emergency Department (ED): 85(27.9%), hospital ward: 29 (9.5%), burn unit: 16 (5.2%), others: 3 (1%). Complications: 113 (37%): hemodynamic deterioration: 72 (23.6%), hypoxemia: 22 (7.2%), esophageal intubation: 5 (1.6%), selective bronchial intubation: 4 (1.3%), bronchoaspiration: 4 (1.3%), impossible OTI: 3 (0.9%), others: 3 (0.9%). Difficult and impossible OTI: 7 (2.3%): difficult OTI: 4 (1.3%), impossible OTI: 3 (0.98%). Average age: 52 years (38 to 81). Sex: M: 3 (42.8%), F: 4 (57.2%). Place technique was performed: ICU: 3 (42.9%), ED: 2 (28.5%), hospitalization ward: 1 (14.3%), burn unit: 1 (14.3%). Average attempts: 4.5 (SD 0.5). Total mortality of the study: 3 (0.98%).In our study, difficult intubation rates were lower than those reported in other series, so it is remarkable the low mortality of the series, less than 1%, which was determined by hemodynamic deterioration after the technique and not associated with the procedure. In view of the results it is advisable to carry out predictive tests, taking into account the characteristics of the critical patients who require urgent intubation, to provide technical difficulties in carrying out the process and anticipate the preparation of necessary materials before starting sequence intubation; likewise, new systems have access to the airway for risk."} +{"text": "TLRs 2, 4 and 9 have been implicated in murine models and human patients of arthritis, but the other TLRs are not well-investigated. Thus, we studied TLR expression and signaling and effect of TLR ligand stimulation in peripheral blood (PB) and synovial fluid (SF) monocytes (MC) of ERA patients.Levels of TLR2, TLR4 and TLR9 were measured by flow cytometry in ERA PBMC (n = 26), paired SFMC (n = 13) and healthy PBMC (n = 19) Real time PCR was done for TLRs 1-9 and their adaptors IRAK1, IRAK4, TRIF, TRAF3, TRAF6. PBMC and SFMC were stimulated with ligands for TLR1 (pam3-cys), 2 (peptidoglycan), 3 (polyI:C), 4 (LPS), 5 (flagellin) and 6 (zymosan). Levels of IL-6, IL-8 and MMP3 (ng/ml) were measured in the culture supernatants.ERA PBMC had higher MFI of TLR2 and TLR4 compared to controls. Intracellular TLR9 expression showed no significant difference between both groups. In paired samples, SFMC had higher MFI of both TLR2 and TLR4 compared to PBMC. Difference in TLR9 expression was not significant [-598 vs 1Increased TLR expression and signaling on PBMC and SFMC from JIA-ERA patients may exacerbate disease by upregulating IL-6, IL-8 and MMP-3 in response to microbial/ endogenous ligands. TLR pathway is a potential therapeutic target in these patients."} +{"text": "Treatment of chronic hepatitis C virus (HCV) infection in HIV-1 co-infected individuals remains challenging due to numerous factors including drug-drug interactions. The aim of this study was to assess the safety and pharmacokinetic (PK) profile of raltegravir, a recently licensed antiretroviral agent, and ribavirin, when dosed separately and together.phase 1). Following a wash-out period, subjects received raltegravir (400 mg twice daily) on days 15-19 (phase 2) and single dose ribavirin (800 mg) with raltegravir (400 mg) on day 20 (phase 3). Intensive PK sampling was undertaken on days 1, 19 and 20 and differences in geometric mean ratios (GMR) for PK parameters between study periods assessed.Fourteen healthy volunteers (mean (standard deviation) age 35 (10) years, 71% male) entered this phase I PK study and received single dose ribavirin (800 mg) on day 1 and increase in time to maximum plasma concentration (Tmax) was observed for ribavirin in phase 3 compared to phase 1 (GMR (95% CI) 0.79 (0.62 - 1.00) and 1.39 (1.08 - 1.78), respectively; Table No statistically significant differences in PK parameters were observed for raltegravir between The PK profile of ribavirin is altered when administered with raltegravir (reduced Cmax and increased Tmax). This is unlikely to be of clinical significance or have an impact on the antiviral effects of ribavirin in HIV-1 and HCV co-infected subjects."} +{"text": "Daily short intravenous infusions of Interleukin-2 (IL-2) have been developed to decrease toxicity while maintaining anticancer activity of this agent against kidney cancer. Such IL-2 schedules have previously been shown to increase Lymphokine Activated Killer cell (LAK) numbers (Quan) and LAK activity (Mitchell). Famotidine may increase LAK activity by increasing Interleukin-2 internalization by the IL-2 receptor on lymphocytes (Tsunoda). We treated 15 patients with metastatic clear cell kidney cancer using IL-2 18 Million IU/M2 intravenously over 15-30 minutes preceded by famotidine 20 mg IV daily for 3 days for 6 consecutive weeks on an outpatient basis. Cycles were repeated every 8 weeks until disease progression. Patient characteristics: 7 males/8 females, median age-59 (range: 28-70), median ECOG performance status-1; common metastatic sites: lungs (14), lymph nodes (9), liver (4), bone (4), and pancreas (4). Prior systemic therapy: oral TKI (8), Interleukin-2 (6), mTor inhibitor (2), no prior (3). Prior nephrectomy (9). Most common toxicities were rigors (13), arthralgia/myalgia (12), nausea/emesis (11), fever (11), hypotension (11), and constipation (8). All episodes of hypotension were transient and alleviated with outpatient intravenous fluid. No patients have required hospitalization due to toxicity of therapy. There have been no treatment-related deaths. One complete response (7%) (in lungs lasting 13 months) and four partial responses (26%) have been seen . Responses have occurred in lungs, liver, lymph nodes, and bone. Median response duration = 5 months (2-13). Median survival = 13.75 months (3-41 months). Two patients are alive at 35.7+ and 35.2+ months. Dose-dense outpatient intravenous Interleukin-2 preceded by famotidine has activity in metastatic clear cell kidney cancer."} +{"text": "Functional and structural lung evaluations are part of the follow-up of patients with primary ciliary dyskinesia (PCD). We aimed to evaluate transversal and longitudinal relationships between lung function tests (LFT) and chest computed tomography (CT) in children with PCD, in stable clinical condition.Data from children followed in the French National Center were retrospectively collected. Inclusion criteria were (i) definitive diagnosis of PCD, (ii) age less than 15 years at the beginning of follow-up, (iii) at least 8 years of follow-up and (iv) at least 2 couples of concurrent CT and LFT performed in stable clinical condition. Twenty children were included. Concurrent LFT (blood gas and spirometry) and CT (score) results were recorded.LFT indices (PaO2 (n=210), FVC, FEV1, FEF2575% (n=195)) significantly decreased with age, and the mean annual decrease (z-score (% predicted)) was -0.17 (-0.49%), -0.09 (-0.50%), -0.10 (-0.89%), and -0.07 (-1.73%), respectively. First CT (median age 8.7 years) revealed bronchiectasis (70%), mucous plugging (70%), peribronchial thickening (90%), parenchymal abnormalities (65%) and hyperinflation (50%). CT-scores (n=74) significantly increased with age, and was negatively correlated to PaO2, FVC, FEV1 and FEF2575% longitudinal changes.In stable clinical condition, functional and structural progressive impairments significantly correlated in children with PCD. Further prospective studies, including large populations with various levels of disease severity, are needed to confirm whether LFT follow-up can be used to adjust CT frequency and help at minimizing the radiation burden in children with a good life expectancy."} +{"text": "The autoinflammatory diseases (AID) include monogenic and polygenic disorders characterized by primary dysfunction of the innate immune system.To describe the clinical spectrum, genetic background and therapy in a cohort of AID patients followed in a reference Pediatric Rheumatology center.Medical records of AID patients followed between May 2007 and November 2010 and entered in the Eurofever Registry were studied.Fifty six patients were included: 17 Cryopyrin-Associated Periodic Syndromes (CAPS), 4 TNF-Receptor-Associated Periodic fever Syndrome (TRAPS), 5 Hyperimmunoglobulinaemia D with periodic fever Syndrome (HIDS), 18 Familial Mediterranean Fever (FMF), 6 Chronic Recurrent Multifocal Osteomyelitis (CRMO), 2 Synovitis, Acne, Pustulosis, Hyperostosis, Osteitis (SAPHO) syndrome and 4 Beh\u00e7et\u2019s Disease (BD). The median follow-up was 2 years (0-14). The male/female ratio was 20/36. The median age was 2.5 years at disease onset and 4 at diagnosis. Family history was positive in 34% of patients. Clinical manifestations included fever (79%), musculoskeletal (77%), gastrointestinal (63%), mucocutaneous (61%), neurological (41%), ocular (34%), cardiorespiratory (13%), and genitourinary (2%) findings, lymphadenopathy with/or hepatosplenomegaly (16%) and growth impairment (25%). Complications/sequelae developed in 45% of patients. Six patients presented with unusual manifestations: neonatal peritonitis (1 CAPS), pancreatitis (1 TRAPS), acute glomerulonephritis (1 FMF), complicated Henoch -Sch\u00f6nlein purpura (1 FMF), peritoneal adhesions with intestinal occlusion (1 FMF), periorbital pain (1 CRMO) and cerebral thrombosis (1 BD). AID was associated with other diseases in 2 patients (FMF/Henoch-Sch\u00f6nlein purpura and CRMO/enthesitis-related arthritis). One mutant allele was found in 16/17 CAPS, 4/4 TRAPS and 4/18 FMF patients. Two mutant alleles were present in 5/5 HIDS and 11/18 FMF patients. The most used therapeutic agents were biologics (54%) , NSAIDs (48%), colchicine (45%) and corticosteroids (29%). Anti-interleukin-1 therapy and colchicine proved efficacy in CAPS and FMF patients, respectively. In addition, favorable responses demonstrated anti-interleukin-1 therapy in TRAPS, HIDS and colchicine-resistant FMF patients, as well as Etanercept in TRAPS, HIDS and CRMO patients non-responsive to NSAIDs. 57% and 41% of patients were in complete and partial remission, respectively, at last visit.AID in children are associated with a broad spectrum of manifestations. Early diagnosis and referral are essential as efficient therapy can be proposed in most cases.None Declared."} +{"text": "Multiple sexual partnerships and HIV sero-discordant relationships are among the most at-risk for HIV transmission. Polygamy is a common form of multiple-partnered relationships in Eastern Uganda. We investigated the association between HIV risk patterns and polygamy among HIV sero-discordant couples at The AIDS Support Organization in Jinja, Uganda Methods Participants were enrollees in a prospective cohort of HIV sero-discordant couples, the Highly Active Antiretroviral therapy as Prevention (HAARP) Study at TASO Jinja. Descriptive and bivariate analyses to compare sexual risk patterns among HIV sero-discordant men; in polygamous as compared to single-spouse relationship.Polygamous Vs Single-spouse couples \u22652 wives 1 wife P value N = 241 56 185 Male HIV+ve 38 (68%) 99 (54%) 0.065 Male-controlled sexual decision making 34 (61%) 66 (36%) 0.001 Male-controlled condom use 33 (59%) 51 (28%) <0.001 Condom last time had sex 45 (80%) 128 (69%) 0.086 Financial support 45 (80%) 152 (82%) 1.00 HIV positive partner on ART 24 (37%) 88 (48%) 0.143 Median age (IQR) 44 (39\u2013 50) 43 (37\u2013 50) 0.451.This study demonstrates continued gendered risks for women in HIV sero-discordant relationships in sub-Saharan Africa. In particular, men with 2 or more wives are more likely to make decisions about when to have sex or when to use a condom. However, we found no differences in condom use at last sex by polygamy status."} +{"text": "Terebratalia transversa.Larval features such as the apical organ, apical ciliary tuft, and ciliated bands often complicate the evaluation of hypotheses regarding the origin of the adult bilaterian nervous system. Understanding how neurogenic domains form within the bilaterian head and larval apical organ requires expression data from animals that exhibit aspects of both centralized and diffuse nervous systems at different life history stages. Here, we describe the expression of eight neural-related genes during the larval development of the brachiopod, Tt-Six3/6 and Tt-hbn in the animal cap ectoderm. Tt-NK2.1 and Tt-otp are restricted to a central subset of these cells, and Tt-fez and Tt-FoxQ2 expression domains are already asymmetric at this stage. As gastrulation proceeds, the spatial expression of these genes is split between two anterior ectodermal domains, a more dorsal region comprised of Tt-Six3/6, Tt-fez, Tt-FoxQ2, and Tt-otp expression domains, and an anterior ventral domain demarcated by Tt-hbn and Tt-NK2.1 expression. More posteriorly, the latter domains are bordered by Tt-FoxG expression in the region of the transverse ciliated band. Tt-synaptotagmin 1 is expressed throughout the anterior neural ectoderm. All genes are expressed late into larval development. The basiepithelial larval nervous system includes three neurogenic domains comprised of the more dorsal apical organ and a ventral cell cluster in the apical lobe as well as a mid-ventral band of neurons in the mantle lobe. Tt-otp is the only gene expressed in numerous flask-shaped cells of the apical organ and in a subset of neurons in the mantle lobe.Radially symmetric gastrulae broadly express Tt-Six3/6, Tt-FoxQ2, and Tt-otp confirm some aspects of bilaterian-wide conservation of spatial partitioning within anterior neurogenic domains and also suggest a common origin for central otp-positive cell types within the larval apical organs of spiralians. However, the field of sensory neurons within the larval apical organ of Terebratalia is broader and composed of more cells relative to those of other spiralian larvae. These cellular differences are mirrored in the broader spatial and temporal expression patterns of Tt-FoxQ2 and Tt-otp. Corresponding differences in the expression of Tt-hbn, Tt-NK2.1, and Tt-FoxG are also observed relative to their respective domains within the cerebral ganglia of spiralians. Based on these data we argue that the anterior region of the bilaterian stem species included Six3/6, NK2.1, otp, hbn, fez, and FoxQ2 expression domains that were subsequently modified within larval and adult neural tissues of protostome and deuterostome animals.Our expression data for Several hypotheses exist concerning the putative homology of various parts of larval and adult nervous systems found among bilaterian animals. Based on similar expression patterns of evolutionarily conserved transcription factors, some authors have concluded that the structure of the adult nervous system of the last common ancestor of the Bilateria included an anterior brain with three divisions and a distinct longitudinal ventral nerve cord -3, with homeobrain, rx, and orthopedia) are only expressed within oral ectoderm of cnidarians [Confounding issues regarding the origin of the adult bilaterian nervous system pertain to its spatial proximity and integration with components of a larval nervous system, particularly, the development of ciliated apical tuft cells, which numerous larval forms exhibit, and their relationship to the larval apical (sensory) organ where many neuronal cell bodies of larval forms are concentrated. Despite some shared developmental and structural features there is no uniform consensus regarding the homology of the larval aboral organs of cnidarian planulae with the larval apical organs of various bilaterians -15. One idarians . How theidarians -19). Theidarians ,21, testThe larval apical organs of phoronids and brachiopods are relevant to the evolutionary reconstruction of bilaterian brains. Although the evolutionary relationships within phoronids and brachiopods ,23 as weSix3/6, homeobrain, and NK2.1 [Considering all of these structural and biochemical differences among bilaterian larval apical organs, evaluating the homology of cell types and the complex neuronal centers they make up becomes problematic as there are no universally agreed upon criteria for discriminating homologous neuronal cell types (but see ). Some snd NK2.1 -45. EvenNK2.1; [Terebratalia transversa, by analyzing the expression patterns of eight genes known to have roles in specification and differentiation of anterior neural tissues in other bilaterian animals.Evaluating alternative viewpoints regarding either the wide-scale homology or independent origin of larval apical organs requires more developmental data focused on the molecular specification of various neurogenic tissue domains from additional bilaterian animals with structurally diverse larval nervous systems. Recent reports on the development and structure of the sensory cells and larval nervous system in brachiopods ,46 suggeNK2.1; ) differsNK2.1; ). HoweveTerebratalia Erebratalia transversa orthologs of the transcription factors forebrain zinc-finger (fez), Forkhead G (FoxG), Forkhead Q2 (FoxQ2), homeobrain (hbn), NK2.1, orthopedia (otp), and Six3/6, and the synaptic vesicle-localized transmembrane protein synaptotagmin 1, were isolated by rapid amplification of cDNA ends (RACE). Orthology of each gene to representatives from other metazoan taxa was confirmed by Bayesian analysis of phylogenetics of centrally located flask-shaped cells near the apical tuft region expand in an equatorial ring around the middle of the apical lobe that correlates with the position of the developing transverse ciliated band and some rows of cells anterior to it , as well as another neurogenic domain within the mid-ventral portion of the mantle lobe. Neuronal cells within the anterior dorsal domain include the broad sensory and supportive histaminergic epithelium of the apical organ [Tt-synaptotagmin 1 expression is more pronounced in early and late trilobed larval stages consistent with this gene's role in late neuronal differentiation [Tt-synaptotagmin 1 expression is mainly found in anterior neural tissues and the basiepithelial nerve rings of the transverse ciliated band.Despite the broad expression domains exhibited by genes such as al organ , the cilal organ , and theal organ . Tt-synantiation . Tt-synaTt-hbn and Tt-NK2.1, both of which overlap with and are bordered laterally by Tt-fez in the anterior dorsal portion of the apical lobe. On the ventral surface of the apical lobe, both Tt-hbn and Tt-NK2.1 are bordered posteriorly by the expression of Tt-FoxG within the region of the transverse ciliated band was also observed in similar larval cells of Patella vulgata [otp-positive cells are present throughout much of the dorsal neurogenic domain and are likely beyond the limits of the Tt-FoxQ2 domain, overlapping with Tt-fez neurogenic domain and the ventral nerve cord of annelids are conserved [Terebratalia larvae is not centralized, then aspects of both anterior-posterior patterning and centralization of neurogenic domains may be different between Platynereis and Terebratalia. Collectively, however, these gene expression and immunohistochemical domains in T. transversa larvae are still reminiscent of anterior and ventral neurogenic domains in spiralian larval forms , albeit complicated by the basiepithelial nature of the larval nervous system in T. transversa. To evaluate the putative homology of these neurogenic domains we review the known expression patterns for genes we have isolated in T. transversa in several larval forms among protostome and deuterostome animals in the following sections.Of the eight genes considered here, only e Figure . Althougonserved . HoweverTerebratalia to orthologous genes in similar developmental stages of various bilaterian animals in Figure Species-specific tissue types, differences in developmental stages, and derived anatomical features of particular larval types complicate comparisons of gene expression patterns among disparate animals. In terms of the developing nervous system, discerning discrete larval versus juvenile expression domains can be difficult in more gradually developing animals such as annelids and mollusks, as opposed to echinoderms in which dramatic distinctions between larval and adult structures can be made -59. Howeotp and NK2.1. In the trochophore larva of the limpet, Patella vulgata, Pv-otp is expressed in a 'U'-shaped field of ectodermal cells that surrounds the apical tuft region in proximity to the expression of Pd-NK2.1 and especially within the structures that Tomer et al. [Homeobrain-like expression is known for another polychaete annelid, Capitella teleta, where Ct-hbn is expressed in a subset of cells in the developing cerebral ganglia and the histaminergic cells within the ventral cluster in the apical lobe of the larva are homologous to the cerebral ganglion of spiralians.Expression data for these genes from molluscan trochophores are not well characterized, except for n Figure . These ctectable . The troal organ . Anterioe domain , but Pd-n Figure mainly weceptors . It is nr et al. called mSix3/6 dependent neurogenic domain [NK2.1, homeobrain, and FoxQ2 [otp is a marker for specific neuronal cell types in deuterostomes, trochozoans, and ecdysozoans [FoxG is expressed throughout the oral ectoderm in the blastula, but is restricted to the developing ciliated bands during gastrulation [Hemicentrotus pulcherrimus, suggests that Hp-fez is positively regulated by Hp-FoxQ2, and that the fez protein serves to maintain the size of the neurogenic animal ectoderm by modulating the inhibitory effects of BMP2/4 [Tt-fez are consistent with these observations as Tt-fez expression generally borders the Tt-FoxQ2 domain. Six3/6 also demarcates the anterior ectoderm in the development of the direct-developing hemichordate worm, Saccoglossus kowalevskii is found in the developing apical organ, the anterior lip of the mouth, and within select neuronal cells of the neotroch are progressively separated into dorsal and ventral domains during the gastrulation of true spiralians and other related taxa with trochozoan larval features such as T. transversa. Since Cl-otp is also expressed in a subset of ventral neural cells similar to Tt-otp, and these expression patterns are spatially similar to what is observed in the mesosome of the hemichordate worm, Saccoglossus kowalevskii [NK2.1 expression in the neural tube of the tunicate, C. intestinalis [NK-class genes in the ventral nerve cord of spiralians [Insight into the complexity and degree of centralization of the adult nervous system of the ancestor of protostomes and deuterostomes may be gained from studying the development of acoelomorph 'flatworms' , dependi 'brain' ,6. Withithin it , none of which originate from the larval ciliary bands [The cellular morphology of the bilaterian anterior larval nervous systems may include an apical organ consisting of a single group or bilateral masses of numerous (thirty of more) bipolar serotonergic neurons, some of which are sensory, as found in the larvae of particular classes of echinoderms and hemichordates -77. Spirry bands -81. AlthTt-otp within a subset of cells of the developing apical organ of late gastrula stage Terebratalia show striking similarities to the morphology of the central (serotonergic) flask cells of larval entoprocts, annelids, and some mollusks [Terebratalia coincides with late differentiation of neuronal and other ciliated cell types . This interpretation is supported by numerous flask-shaped cells that express Tt-otp in the apical organ of the trilobed larval stage and also correlates with the widening of the Tt-FoxQ2 domain at this stage. Expression of Tt-Six3/6, Tt-fez, Tt-FoxQ2, and Tt-otp in the dorsal neural ectoderm that gives rise to the apical organ continues into the late larval stage. These expression patterns are also reflected in the numerous sensory neurons and other supportive cells labeled by anti-acetylated \u03b1-tubulin and anti-histamine only at the late larval stage.Our results of the expression of mollusks -81, suppmollusks . Howevermollusks , as indimollusks . Larval FoxQ2, COE, and FGFa1 are expressed within the region of the aboral ciliary tuft in planula larvae of the hydrozoan, Clytia hemisphaerica, and the anthozoan, Nematostella vectensis [Nematostella planulae, the oral-aboral axis of cnidarians is believed to be homologous to the anterior-posterior axis in bilaterians, and the bilaterian dorsal-ventral axis is homologous to the cnidarian directive axis [NK2.1, homeobrain, noggin1, and otp expression domains and several other bilaterian anterior-related genes [Six 3/6 that is present in the aboral region of the larva homeobrain, otp, and NK2.1 expression. How these separate expression domains became coupled at the animal pole of bilaterian embryos, the adult head, and the bilaterian larval apical organ remains unclear where i were dredged from the waters adjacent to San Juan Island, Washington, USA during the early spring of 2005 and the winter of 2008. Adults were maintained in a free-flowing seawater table (8 to 10\u00b0C) at Friday Harbor Laboratories until needed. Gametes were gathered and larval cultures were created using the methods of Reed [Adults of of Reed . BrieflyTt-fez, Tt-FoxG, FoxQ2, Tt-homeobrain, Tt-NK2.1 and Tt-otp, were identified from Expressed Sequence Tags (ESTs) clones sequenced for a previous phylogenomic analysis [http://www.ncbi.nlm.nih.gov/projects/dbEST/). Fragments of Tt-synaptotagmin 1 and Tt-Six3/6 were amplified by degenerate PCR using cDNA generated from mRNA isolated from mixed embryological stages. Nested primer sets for Tt-Six3/6 were Six3/6 F1 FLSWSLP 5' TTYYTNTGGWSNYTNCC 3', Six3/6 R1 QRDRAA 5'GCNGCNCKRTCNCKYTG 3', Six3/6 R2 NWFKNRRQ 5'TGNCKNCKRTTYTTRAACCARTT 3', Six3/6 F2 GPVDKYRV 5'GGNCCNGTNGAYAARTAYMGNGT 3'. Nested primer sets for Tt-synaptotagmin were Syn F1: 5' TYAAYCCNGTNTTYAAYGA 3', Syn F2: 5' TAYGAYTTYGAYMG/ideoxyI/TT 3', Syn R1: 5' TCRTTRTARTANGGRTT 3', Syn R2: 5' SWRAARCADATRTC/ideoxyI/CC 3'. Full-length cDNAs were obtained by rapid amplification of cDNA ends using the SMART RACE kit using sequence specific primers.analysis publiclyTerebratalia forebrain embryonic zinc-finger, Forkhead G, orthopedia, otx, NK2.1, homeobrain, synaptotagmin 1, and Six3/6 along with those for representative related proteins from other taxa, retrieved from NCBI and Joint Genome Institute , were aligned with MUSCLE [The deduced amino acid sequences for h MUSCLE or MacVeh MUSCLE ,97, withIn situ hybridizations were conducted using an established protocol [protocol . Probes = 7.4) or filtered seawater. Larvae were removed from this solution and larval tissues were permeablized with 0.1 M S\u00f8renson's phosphate buffer and 0.1% to 0.3% Triton-X detergent (PTA solution) for 24 hours at 4\u00b0C before proceeding with the staining protocol. All further steps were carried out on a rotary shaker table. Nonspecific sites were blocked with 4% normal goat serum in PTA solution (GS-PTA) for 24 hours at 4\u00b0C. The primary antibody or anti-histamine was diluted 1:500 with 4% GS-PTA and incubated with the larvae for 48 hours at 4\u00b0C. Specimens were washed (three times) in PTA for a total of 24 hours. Larvae were exposed to the secondary antibody, goat anti-mouse or rabbit AlexaFluor 488 or 568 immunoglobin , at a dilution of 1:50 or 1:100 for 24 hours. Deleting the primary antibody from the protocol produced negative controls. Some specimens were then stained for either fibrous actin or nucleic acids. Nucleic acids were stained with a 1:1,000 dilution of sytox green for 10 minutes or a 1:500 dilution of propidium iodide for 10 to 15 minutes. Specimens were adhered to clean glass slides coated with a poly-L-lysine solution and put through an alcohol dehydration series using 2-propanol within four minutes. Finally, specimens were cleared in a solution of benzyl benzoate and benzyl alcohol (2:1) for two minutes and mounted in the same solution. Slides were kept in the dark at 4\u00b0C until viewed with a BioRad Radiance 2100 laser confocal system and a Nikon E800 microscope or a Zeiss 710 Confocal Laser Scanning Microscope . Confocal z-series were gathered as 1 \u03bcm sections. Z-projections and volume renderings of embryos and larvae were created using OsiriX or FIJI.Fixation and immunohistochemical procedures of embryos and larvae followed Santagata . BrieflyBranchiostoma Fez (ADK13096.1); Caenorhabditis Y38H8A.5 (NP_502594.2); Capitella fez (18104); Capitella Gfi (45287); Drosophila earmuff (NP_608631.1); Daphnia fez (EFX89329.1); Homo fez1 (NP_001019784.2); Homo fez2 (NP_060478.3); Homo Gfi-1b (NP_004179.3); Homo ZF430 (AAP30885.1); Homo ZF85 ; Lottia Gfi1 (129344); Lottia Gfi2 (83709); Mus fez1 (NP_082738.1); Mus fez2 (NP_536681.2); Nematostella 12000017 (228271); Nematostella 265000001 (230810); Nematostella 30000108 (201757); Nematostella e_gw.3.372.1 (80425); Nematostella Gfi (182742); Saccoglossus fez (NP_001158457.1); Schmidtea fez (XP_002575460.1); Schmidtea Gfi (XP_002580588.1); Trichoplax fez (7089); Trichoplax Gfi (63664); Terebratalia fez (JQ88195)Clytia FoxQa (ABG21224.1); Clytia FoxQb (ABG21225.1); Capitella FoxA (169665); Capitella FoxAB (131123); Capitella FoxB (225366); Capitella FoxC (199610); Capitella FoxD (126386); Capitella FoxF (50240); Capitella FoxG (139421); Capitella FoxGa (182306); Capitella FoxI (154409); Capitella FoxJ1 (222987); Capitella FoxJ2/3 (137131); Capitella FoxK (23732); Capitella FoxL1 (49410); Capitella FoxL2 (88179); Capitella FoxM (115253); Capitella FoxN1/4 (129521); Capitella FoxN2/3 (102038); Capitella FoxO (91312); Capitella FoxP (173180); Capitella FoxQ1 (175391); Capitella FoxQ2a (111555); Capitella FoxQ2b (148596); Nematostella (110212); Nematostella (118122); Nematostella (120142); Nematostella (121754); Nematostella (123903); Nematostella (125256); Nematostella (132285); Nematostella (138488); Nematostella (150900); Nematostella (161006); Nematostella (165261); Nematostella (165603); Nematostella (18324); Nematostella (187332); Nematostella (192525); Nematostella (19405); Nematostella (200222); Nematostella (200356); Nematostella (201028); Nematostella (213966); Nematostella (218419); Nematostella (228732); Nematostella (38679); Nematostella (39596); Nematostella (39632); Nematostella (5001); Nematostella (58039); Nematostella (59063); Nematostella (65438); Nematostella (67043); Nematostella (67209); Nematostella (88569); Nematostella (93177); Nematostella (96685); Lottia FoxA (183845); Lottia FoxAB (99760); Lottia FoxB (186344); Lottia FoxC (117369); Lottia FoxD (137594); Lottia FoxF (117350); Lottia FoxG (59807); Lottia FoxH (134143); Lottia FoxJ1 (69660); Lottia FoxJ1 (59864); Lottia FoxJ2/3 (98413); Lottia FoxK (183124); Lottia FoxL1 (178394); Lottia FoxL2 (89841); Lottia FoxN2/3 (138633); Lottia FoxP (54435); Lottia FoxQ2 (79770); Mus FoxA1 (NP_032285.2); Mus FoxA2 (NP_034576.2); Mus FoxB1 (NP_071773.2); Mus FoxB2 (NP_032049.1); Mus FoxC1 (NP_032618.2); Mus FoxC2 (NP_038547.2); Mus FoxD2 (NP_032619.1); Mus FoxD3 (NP_034555.3); Mus FoxD4 (NP_032048.1); Mus FoxE1 (NP_899121.1); Mus FoxE3 (NP_056573.1); Mus FoxF1 (NP_034556.1); Mus FoxF2 (NP_034355.2); Mus FoxG1 (NP_032267.1); Mus FoxH1 (NP_032015.1); Mus FoxI1 (NP_076396.3); Mus FoxI2 (NP_899016.1); Mus FoxJ1 (NP_032266.3); Mus FoxJ2 (NP_068699.1); Mus FoxJ3 (NP_766287.1); Mus FoxK1 (NP_951031.2); Mus FoxK2 (NP_001074401.2); Mus FoxM1 (NP_032047.4); Mus FoxN1 (NP_032264.1); Mus FoxN2 (NP_851305.2); Mus FoxN4 (NP_683737.2); Mus FoxO1 (NP_062713.2); Mus FoxO3 (NP_062714.1); Mus FoxO6 (NP_918949.1); Mus FoxP1 (NP_444432.1); Mus FoxP2 (NP_997600.1); Mus FoxP3 (NP_473380.1); Mus FoxP4 (NP_083043.2); Mus FoxQ1 (NP_032265.3); Mus FoxS1 (NP_034356.1); Platynereis FoxG (ADG26725.1); Ptychodera FoxQ2 (ADZ61650.1); Rattus FoxR1 (XP_243815.4); Rattus FoxR2 (XP_228808.3); Strongylocentrotus FoxI (ABB89485.1); Strongylocentrotus Fox_L1 (ABB89488.1); Strongylocentrotus FoxA (ABE68834.1); Strongylocentrotus FoxAB-like (ABB89474.1); Strongylocentrotus FoxB (NP_999797.1); Strongylocentrotus FoxC (ABB89478.1); Strongylocentrotus FoxD (ABB89476.1); Strongylocentrotus FoxF (ABB89479.1); Strongylocentrotus FoxG (ABB89477.1); Strongylocentrotus FoxJ1 (ABB89480.1); Strongylocentrotus FoxK (ABB89486.1); Strongylocentrotus FoxL2 (ABB89483.1); Strongylocentrotus FoxM (ABB89490.1); Strongylocentrotus FoxN1/4 (ABB89491.1); Strongylocentrotus FoxN2/3 (ABB89482.1); Strongylocentrotus FoxO (ABB89484.1); Strongylocentrotus FoxP (ABB89487.1); Strongylocentrotus FoxQ1 (ABB89489.1); Strongylocentrotus FoxQ2 (ABB89473.1); Terebratalia FoxG (JQ88193); Terebratalia FoxQ2 (JQ88200)Capitella Lbx (ACI26672.1); Capitella NK-like-1a (ACH70609.1); Capitella NK-like-1b (ACI26669.1); Capitella NK-like-2.1a (ACH89430.1); Capitella NK-like-2.1b (ACH89431.1); Capitella NK-like-2.2a (ACH89432.1); Capitella NK-like-2.2b (ACH89433.1); Capitella NK-like-3 (ACI26670.1); Capitella NK-like-4a (ACH89434.1); Capitella NK-like-4b (ACH89435.1); Capitella NK-like-5 (ACH89437.1); Capitella NK-like-5b (ACH88440.1); Capitella NK-like-6 (ACI26668.1); Capitella NK-like-7_ACI26671.1); Capitella Tlx (ACH89436.1); Drosophila bap (NP_732637.1); Drosophila C15 (NP_476873.2); Drosophila dll (NP_726486.1); Drosophila drop (NP_477324.1); Drosophila H6 (NP_732244.3); Drosophila lbe (NP_524435.2); Drosophila lbl (NP_524434.2); Drosophila scro (NP_001015473.1); Drosophila slou (NP_476657.1); Drosophila tinman (NP_524433.1); Drosophila vnd (NP_001036253.1); Mus Dlx1 (NP_034183.1); Mus Dlx2 (NP_034184.1); Mus Dlx3 (NP_034185.1); Mus Dlx4 (NP_031893.3); Mus Dlx5 (NP_034186.2); Mus Dlx6 (NP_034187.1); Mus HMX1 (NP_034575.1); Mus HMX2 (NP_666110.1); Mus HMX3 (NP_032283.3); Mus Lbx1 (NP_034821.2); Mus Lbx2 (NP_034822.1); Mus Msx1 (NP_034965.2); Mus Msx2 (NP_038629.2); Mus Msx3 (NP_034966.1); Mus Nk2.5 (NP_032726.1); Mus Nk3.2 (NP_031550.2); Mus Nkx-3.1 (NP_035051.1); Mus Nkx-6.1 (NP_659204.1); Mus Nkx-6.2 (NP_899071.2); Mus Nkx-6.3 (NP_083278.1); Mus Nkx1.1 (XP_001473685.1); Mus Nkx1.2 (NP_033149.1); Mus Nkx2.1 (NP_033411.3); Mus Nkx2.2 (NP_035049.1); Mus Nkx2.3 (NP_032725.1); Mus Nkx2.4 (NP_075993.1); Mus Nkx2.6 (NP_035050.2); Mus Nkx2.8 (NP_032727.2); Mus Tlx1 (NP_068701.1); Mus Tlx2 (NP_033418.1); Mus Tlx3 (NP_064300.2); Platynereis Dlx (CAJ38799.1); Platynereis Lbx (ABQ10642.1); Platynereis Msx (CAJ38810.1); Platynereis Nk1 (CAJ38797.1); Platynereis NK2.1 (CAJ38809.1); Platynereis NK2.2 (ABO93209.1); Platynereis NK3 (ABQ10641.1); Platynereis NK4 (ABQ10640.1); Platynereis NK5 (ABQ10644.1); Platynereis Tlx (ABQ10643.1); Terebratalia NK2.1 (JQ88197)Crepidula Pitx (ADI48168); Ciona Prop (XP (002119699); Ciona otp (NP (001072023); Ciona otx (NP (001027662); Capitella EBX (ABC58683); Capitella Gsx (AAZ23124); Capitella Pax3-7 (ABC68267); Capitella Xlox (AAZ95509); Capitella cdx (AAZ95508); Drosophila Pitx (NP (733410); Drosophila Vsx1 (NP (572232); Drosophila Vsx2 (NP (001033832); Drosophila aristaless (NP (722629); Drosophila dll (NP (523857); Drosophila gsc (NP (476949); Drosophila homeobrain (NP (788420); Drosophila otd (P22810); Drosophila otp (P56672); Drosophila repo (NP (477026); Drosophila rx (NP (726006); Hydroides otx (ABK76302); Platynereis Arx (ADG26723); Platynereis Cdx (ACH87546); Platynereis Gsx (ACH87540); Platynereis Pax6 (CAJ40659); Platynereis Xlox (ACH87551); Platynereis dlx (CAJ38799); Platynereis dlx (CAJ387991); Platynereis gsc (CAC19336); Platynereis otp (ABR68849); Platynereis otx (CAC19028); Platynereis rx (AAU20320); Patella gsc (CAD45551); Patella otp (AAM33145); Patella otx (AAM33144); Saccoglossus Prop (NP (001161635); Saccoglossus hbn (XP (002731203); Saccoglossus otd (NP (001158360); Saccoglossus otp (NP (001158374); Strongylocentrotus hbn (XP (781057); Strongylocentrotus otp (XP (784599); Strongylocentrotus otx (NP (999753); Terebratalia Pax6 (ADZ24784); Terebratalia homeobrain (JQ88198); Terebratalia otp(JQ88194); Terebratalia otx (ADZ24785)Capitella 180297 (180297); Capitella 180301 (180301); Capitella 180303 (180303); Capitella 226834 (226834); Capitella 227938 (227938); Drosophila optix (NP_524695.2); Drosophila sine-oculis (NP_476733.1); Drosophila Six4_NP_649256.10; Lottia 115798 (115798); Lottia 129577 (129577); Lottia 179424 (179424); Mus Six1 (NP_033215.2); Mus Six2 (NP_035510.1); Mus Six3 (NP_035511.2); Mus Six4 (NP_035512.1); Mus Six5 (NP_035513.1); Mus Six6 (NP_035514.1); Nematostella 126214 (126214); Nematostella 130873 (130873); Nematostella 138693 (138693); Platynereis Six2 (CAC86663.1); Platynereis Six3 (CAR66435.1); Saccoglossus Six1 (XP_002735213.1); Saccoglossus Six3 (NP_001158378.1); Saccoglossus Six4 (XP_002735606.1); Strongylocentrotus Six1 (XP_001181583.1); Strongylocentrotus Six3 (XP_781696.1); Strongylocentrotus Six4 (XP_001181543.1); Terebratalia Six3/6 (JQ88196)Capitella_Dblc2 (195440); Capitella_Esyt2 (160561); Capitella_Rph (238583); Capitella_Syt12 (238576); Capitella_Syt15 (238580); Capitella_Syt16 (238581); Capitella_Syt17 (238578); Capitella_Syt1var1 (183139); Capitella_Syt1var2 (183138); Capitella_Syt4 (238579); Capitella_Syt44 (238582); Capitella_Syt7 (175638); Capitella_Syt9 (181126); Capitella_Sytalpha (238577); Lottia_Dblc2 (236949); Lottia_Esyt2var1 (249373); Lottia_Esyt2var2 (249374); Lottia_Rph (249375); Lottia_Syt12 (249365); Lottia_Syt15a (249370); Lottia_Syt15b (249367); Lottia_Syt16 (249369); Lottia_Syt17 (249364); Lottia_Syt18 (249372); Lottia_Syt1var1 (249360); Lottia_Syt1var2 (249359); Lottia_Syt21 (249371); Lottia_Syt4 (249363); Lottia_Syt47 (249366); Lottia_Syt7 (249362); Lottia_Syt9 (249361); Lottia_Sytalpha (249358); Mus_Dblc2 (NP_034199.1); Mus_Rph (NP_035416.1); Mus_Syt1 (NP_033332.1); Mus_Syt1 (NP_061274.2); Mus_Syt10 (NP_061273.1); Mus_Syt12 (NP_598925.1); Mus_Syt13 (NP_109650.1); Mus_Syt14 (NP_853524.1); Mus_Syt15 (NP_852682.1); Mus_Syt16 (NP_766392.2); Mus_Syt17 (NP_619590.1); Mus_Syt2 (NP_033333.2); Mus_Syt3 (NP_057872.2); Mus_Syt4 (NP_033334.2); Mus_Syt5 (NP_058604.1); Mus_Syt6 (NP_061270.2); Mus_Syt7 (NP_061271.1); Mus_Syt8 (NP_061272.2); Mus_Syt9 (NP_068689.2); Terebratalia_Syt1 (JQ88199)2; NCBI: National Center for Biotechnology Information; NBT: nitroblue tetrazolium chloride; PCR: polymerase chain reaction.BCIP: 5-bromo-4-chloro-3-indolyl phosphate; ESTs: Expressed Sequence Tags; FMRFamide: Phenylalanine-Methionine-Arginine-Phenylalanine-NHThe authors declare that they have no competing interests.SS designed the study, conducted the immunohistochemistry and microscopic imaging, contributed to the gene expression protocols, and drafted the paper. CR participated in molecular cloning, gene expression protocols, microscopic imaging, and assisted in drafting the manuscript. AH participated in molecular cloning, gene expression protocols, microscopic imaging, and assisted in drafting the manuscript. MQM assisted in drafting the manuscript. YJP conducted the molecular cloning and gene expression protocols, participated in microscopic imaging, and assisted in the drafting of the paper. All authors read and approved the final manuscript.Tt-hbn and Tt-otpPhylogenetic analysis of . Phylogram of Tt-hbn, Tt-otp, and related paired-class homeodomain proteins, supporting the orthology assignments of Tt-hbn and Tt-otp. Posterior probability for the homeobrain clade, including Tt-hbn, is 95 percent. Posterior probability for the otp clade, including Tt-otp, is 99 percent. The phylogram is a consensus of the last 2,000,000 generations from a Bayesian likelihood analysis with four independent runs of 10,000,000 generations each.Click here for fileTt-Six3/6Phylogenetic analysis of . Phylogram of Tt-Six3/6 and related Six-class homeodomain proteins, supporting the orthology assignment of Tt-Six3/6. Posterior probability for the Six3/6 clade, including Tt-Six3/6, is 100 percent. The phylogram is a consensus of the last 2,000,000 generations from a Bayesian likelihood analysis with four independent runs of 10,000,000 generations each.Click here for fileTt-fezPhylogenetic analysis of . Phylogram of Tt-fez and related zinc-finger proteins, supporting the orthology assignment of Tt-fez. Posterior probability for the Fez clade, including Tt-fez, is 100 percent. The phylogram is a consensus of the last 2,000,000 generations from a Bayesian likelihood analysis with four independent runs of 10,000,000 generations each.Click here for fileTt-NK2.1Phylogenetic analysis of . Phylogram of Tt-NK2.1 and related NK-class homeodomain proteins, supporting the orthology assignment of Tt-NK2.1. Posterior probability for the NK2.1 clade, including Tt-NK2.1, is 70 percent. The phylogram is a consensus of the last 2,000,000 generations from a Bayesian likelihood analysis with four independent runs of 10,000,000 generations each.Click here for fileTt-FoxG and Tt-FoxQ2Phylogenetic analysis of . Phylogram of Tt-FoxG, Tt-FoxQ2, and related Forkead box proteins, supporting the orthology assignments of Tt-FoxG and Tt-FoxQ2. Posterior probability for the FoxG clade, including Tt-FoxG, is 100 percent. Posterior probability for the FoxQ2 clade, including Tt-FoxQ2, is 94 percent. The phylogram is a consensus of the last 2,000,000 generations from a Bayesian likelihood analysis with four independent runs of 20,000,000 generations each.Click here for fileTt-synaptotagmin 1Phylogenetic analysis of . Phylogram of Tt-synaptotagmin 1 and related synaptotagmin proteins, supporting the orthology assignment of Tt-synaptotagmin 1. Posterior probability for the synaptotagmin 1 clade, including Tt-synaptotagmin 1, is 100 percent . The phylogram is a consensus of the last 2,000,000 generations from a Bayesian likelihood analysis with four independent runs of 10,000,000 generations each.Click here for file"} +{"text": "With increasing applications of cardiac magnetic resonance (CMR) for definitive diagnosis of congenital heart disease (CHD) in infants, safety of this technology is of particular interest in this age group. We report our ten-year experience with CMR in neonates and small infants with particular focus on the safety profile and incidence of adverse events.Clinical, anesthesia and nursing records of all patients (pts)<120 days of age who underwent CMR were reviewed. Variables including cardiac diagnosis, study duration, anesthesia type and agents used, prostaglandin E1 (PGE1) dependence and gadolinium (Gd) use were recorded. Serially recorded temperature, systemic saturation, and cardiac rhythm were analyzed. Primary outcome measure was any adverse event (AE) during or <24 hours after the procedure, including minor AE such as hypothermia (axillary temperature \u226495 F), desaturation (SpO2 drop \u2265 10% below baseline) and bradycardia (heart rate \u2264100/ min). Secondary outcome measure was unplanned overnight hospitalization of out-pts.Pts had a median age of 7 days (1-117), and 98 were \u226430 days at the time of CMR. The median weight was 3.4 kg (1.4-6) and body surface area 0.22 m2 (0.13-0.32). There were 118 (83%) in-pts (108 receiving intensive care) and 25 (17%) out-pts. Indications were assessment of aortic arch (n=57), complex CHD (n=41), pulmonary veins (n=15), vascular ring (n=8), intracardiac mass (n=8), pulmonary artery (n=7), ventricular volume (n=4), and systemic veins (n=3). CMR was performed using a 1.5-T scanner (Philips), and a commercially available coil. CMR utilized general anesthesia (GA) in 86 pts, deep sedation in 50 and no sedation in 7. Gd angiography was performed in 136 pts. Fifty-nine pts were PGE1 dependent and 39 had a univentricular circulation. Among pts on PGE1, 43 (74%) received GA and 10 (26%) had deep sedation. Twelve pts (8%) had AE, 1 major and 11 minor. Nine of the12 pts had GA, and 3 had deep sedation. The single major AE was respiratory arrest after chloral hydrate sedation in a neonate (resuscitated without sequelae). Minor AE included desaturations (n=2), hypothermia (n=5), bradycardia (n=2), and bradycardia with hypoxemia (n=2). Incidence of minor AE was 9% for in-pts (vs. 4% for out-pts), and 8% for neonates (vs. 9% in pts \u2265 30 days). Incidence of minor AE was similar between PGE1 dependent infants and non-PGE1 group. There were no AE related to Gd angiography. Of 25 out-pts, 5 (20%) were admitted for overnight observation due to desaturations.CMR imaging can be accomplished safely in neonates and infants \u2264 120 days for a wide range of pre surgical cardiac indications. Incidence of AE was unrelated to pt age, complexity of heart disease, type of anesthesia and PGE1 dependence.None."} +{"text": "Unfractionated heparin is preferred over LMWH in ICU patients but LMWH is used more frequently in many European ICUs. Thromboprophylaxis with standard doses of nadroparin and enoxaparin has been shown to result in significantly lower anti-Xa in ICU patients when compared with medical patients ,2.n = 44; pressors n = 32) received 7,500 IU or 5,000 IU dalteparin s.c. . Twenty-nine medical patients receiving 5,000 IU dalteparin served as controls (Group 3).ICU patients were delayed (tmax-anti-Xa) in Group 2 compared with Groups 1 and 3 (Table Group 2 had significantly lower areas under the Xa curve (AUC) compared with Groups 1 and 3 (Table In ICU patients a s.c. dose of 5,000 IU dalteparin results in significantly lower Xa activities when compared with normal ward patients. A s.c. dose of 7,500 IU dalteparin in ICU patients resulted in kinetics and peak anti-Xa activities comparable with medical patients receiving 5,000 IU dalteparin."} +{"text": "Reassortment of influenza A virus genes enables antigenic shift resulting in the emergence of pandemic viruses with novel hemagglutinins (HA) acquired from avian strains. Here, we investigated whether historic and contemporary avian strains with different replication capacity in human cells can donate their hemagglutinin to a pandemic human virus. We performed double-infections with two avian H3 strains as HA donors and a human acceptor strain, and determined gene compositions and replication of HA reassortants in mammalian cells. To enforce selection for the avian virus HA, we generated a strictly elastase-dependent HA cleavage site mutant from A/Hong Kong/1/68 (H3N2) (Hk68-Ela). This mutant was used for co-infections of human cells with A/Duck/Ukraine/1/63 (H3N8) (DkUkr63) or the more recent A/Mallard/Germany/Wv64-67/05 (H3N2) in the absence of elastase but presence of trypsin. Among 21 plaques analyzed from each assay, we found 12 HA reassortants with DkUkr63 (4 genotypes) and 14 with MallGer05 (10 genotypes) that replicated in human cells comparable to the parental human virus. Although DkUkr63 replicated in mammalian cells at a reduced level compared to MallGer05 and Hk68, it transmitted its HA to the human virus, indicating that lower replication efficiency of an avian virus in a mammalian host may not constrain the emergence of viable HA reassortants. The finding that HA and HA/NA reassortants replicated efficiently like the human virus suggests that further HA adaptation remains a relevant barrier for emergence of novel HA reassortants. Several influenza pandemics in the last century were caused by influenza A viruses carrying a hemagglutinin (HA) serotype novel to the global human population. Repeated emergence of those heterologous strains was facilitated by the segmentation of the viral genome into eight genes. Such a genome organization allows the exchange of entire gene segments during co-infection by two different strains, designated as reassortment To enforce selection of the avian virus HA during co-infection in the absence of elastase, we generated an elastase-dependent HA cleavage site mutant (HK68-Ela) from the human influenza strain Hk68 To select reassortants carrying the HA of an avian strain, we performed co-infection experiments on human A549 cells in the absence of elastase using Hk68-Ela as acceptor strain and either DkUkr63 (H3N8) or the more recent MallGer05 (H3N2) as HA donor. After co-infection, we harvested supernatants from infected cells after 8 and 24 hours and performed plaque assays. From each co-infection experiment, we isolated 21 plaques of different sizes and passaged them on A549 cells in the presence or absence of trypsin. If no HA titer was detectable in the supernatant, we added an egg passage. From those propagated virus stocks, we determined partial sequences of each segment for assigning the parental origin. For the DkUkr63 co-infection, genotyping revealed that 16 of 21 (D1\u2013D21) single plaque isolates were reassortants carrying the avian HA either alone or in combination with other DkUkr63 genes . NA co-sThe second co-infection experiment with the more recent avian strain MallGer05 yielded 18 HA reassortants of the 21 genotyped plaque isolates (M1\u2013M21) . NA co-sThe plaque morphology of parental and reassortant viruses on MDCK cells differs considerably. Whereas Hk68 and Hk68-Ela yielded pinpoint plaques, DkUkr63 and MallGer05 formed large, clear plaques of approximately 4.0 mm and 2.5 mm in diameter, respectively. Reassortants carrying the N2 from Hk68 displayed tiny, hardly visible plaques like the human parent. In contrast, reassortants carrying the N8 from DkUkr63 or the N2 from MallGer05 formed large plaques comparable to those of their respective avian parental virus . Taken t10(pfu/ml) after 48 h. The elastase cleavage site mutant Hk68-Ela replicated with a delay and reached a titer of 5.4 log10(pfu/ml) at 48 h in the presence of elastase. DkUkr63 replicated as efficiently as Hk68 during the first 24 hours but reached a lower titer of 5.2 log10(pfu/ml) after 48 h (10(pfu/ml) (10(pfu/ml)). (3) Four reassortants carrying HA and NA from DkUkr63 also replicated more efficiently than DkUkr63 reaching 48 h titers between 6.2 and 7.0 log10(pfu/ml) (10(pfu/ml), slightly higher than that of Hk68 (6.9 log10(pfu/ml)). Similar titers were observed for D1 and D15 carrying DkUkr63 HA, NA and NP (7.2 and 6.7 log10(pfu/ml)). In contrast, reassortant D13 carrying the DkUkr63 M gene in combination with DkUkr63 HA and NA genes, exhibited significantly reduced replication with a 48 h titer of 4.6 log10(pfu/ml) that is even below that of the parent virus DkUkr63 ) (10(pfu/ml), and reassortant D18 with DkUkr63 HA, NA, PB1, and NS showed the strongest, significant growth impairment with a 48 h titer of 3.8 log10(pfu/ml) Fiv(pfu/ml) correspo(pfu/ml) . (4) Foupfu/ml)) . (5) Two(pfu/ml) .Taken together, most DkUkr63 HA reassortants reached titers in A549 cells higher than the parent virus DkUkr63. The titers of all HA or HA/NA reassortants deviated only up to one magnitude from that of Hk68 demonstrating that donation of DkUkr63 HA and NA genes to a human strain resulted in reassortants with robust replication competence in A549 cells. Highest replication efficiency was observed with reassortants D1 and D15 containing the DkUkr63 HA, NA and NP, and in particular with reassortant D7 carrying the DkUkr63 HA, NA and PB1 and, thus, specifying a similar gene constellation as that of the 1957 pandemic strain.10(pfu/ml) in A549 cells which was close to that of Hk68 with 6.9 log10(pfu/ml) (10(pfu/ml) similar to Hk68 with 6.9 log10(pfu/ml) (10(pfu/ml), M6 7.1 log10(pfu/ml), and M9 6.9 log10(pfu/ml) (10(pfu/ml) equivalent to Hk68. M7 and M35 and M10 replicated to 48 h titers comparable to MallGer05. M3 exhibited a 48h titer of 4.8 log10(pfu/ml) which was approximately 100-fold below Hk68 (10(pfu/ml). Remarkably, M8 (only PB2 and PB1 from Hk68) and M4 (only M from Hk68) reached final titers of only 4.2 and 4.0 log10(pfu/ml), respectively, demonstrating severely impaired, significant replication . Accordi(pfu/ml) . (2) Fou(pfu/ml) . (3) Thr(pfu/ml) . (4) Fivlow Hk68 . (5) Sixlication .In sharp contrast to the DkUkr63 M gene, the MallGer05 M gene did not restrict host range since the HA/NA/M (M36), PB1/HA/NA/M/NS (M6), and HA/NA/M/NS (M9) reassortants replicated better than Hk68. Most notably, all HA/NA reassortants (4 of 18) reached 48 h titers very close to that of Hk68 indicating the ability of MallGer05 to donate its HA and NA genes efficiently to a human strain.In the past century, several pandemics were caused by influenza A strains that had reassorted their HA genes. This enormous genetic plasticity results from the segmentation of their viral genomes enabling reassortment. Replacement of the HA gene segment in a seasonal human strain by that from an avian strain has led to the emergence of pandemic strains with novel HA serotypes in 1957 and 1968 7 possible unique combinations of viral genes minus those of the two homologous parent viruses) are to be expected at equal frequencies among sufficiently high numbers of isolated plaques in case of the absence of any restriction against the other seven virus genes. Among 21 investigated plaques for each co-infection, we found with DkUkr63 16 and with MallGer05 18 reassortants. We anticipated the occurrence of approximately 15 different genotypes (i.e. unique gene combinations) for DkUkr63 and 17 different genotypes for MallGer05 according to a martingale-based exact formula of the coupon collection problem To reveal whether some gene constellations of reassortants were restricted, we assumed the absence of any restriction and considered the distribution of genotypes in relation to the number of isolated plaques to be a coupon collector problem Pinpoint plaques similar to those formed by Hk68 parental virus were observed for reassortants carrying an Hk68 NA as for D12 or M7 which had acquired only the avian virus HA. In contrast, the DkUkr63 and MallGer05 HA/NA double reassortants, as D9 and M26, yielded plaque sizes comparable to those of the respective avian parent virus. Thus, irrespective of the origin of the HA and the presence of any other avian virus genes, the plaque size was determined by the NA corresponding to previous findings Efficiently replicating reassortants with heterologous polymerase complexes containing the DkUkr63 PB2 or PA were not isolated. In case of the MallGer05 reassortants, all six PA reassortants exhibiteIn contrast to the PB2 and PA genes, the PB1 gene was found in several reassortants with different replication efficiencies. One DkUkr63 reassortant with exchanged PB1, HA, and NA achieved highest titers (D7), whereas a PB1/HA reassortant displayed impaired growth (D14). One MallGer05 reassortant carrying the PB1, HA, NA plus the M and NS genes replicated efficiently in the human cells. This finding is consistent with the acquisition of the PB1 gene of the 1957 and 1968 pandemic viruses from an unknown avian strain The M gene was shown to segregate with the HA in two HPAIV For virus entry, human strains use surface glycans with \u03b1-linked sialic acids as receptors, whereas avian strains prefer \u03b1-linked sialic acids Taken together, at least three conceivable constraints on reassortment acting on different levels are conceivable: (I) putative strain-specific differences in vRNP packaging signals especially in the PB2, PA, NP, and M segments th egg passage) and A/Mallard/Germany/Wv64-67/2005 (H3N2) (at 2nd egg passage) were propagated in embryonated chicken eggs. The comparison of the Hk68 amino acid sequences to published sequences (accession numbers AF348170 (PB2), AF348172 (PB1), AF348174 (PA), AF348176 (HA), AF348180 (NP), AF348184 (NA), AF348188 (M), and AF348198 (NS)) yielded the following results: PB2 I584V, PB1 100% identity, PA N142T and K673R, HA 100% identity, NP Q311H, NA N339D, M1 100% identity, M2 100% identity, NS1 I81M, and NS2 100% identity.Human lung epithelium (A549), Madin-Darby kidney (MDCK) and human embryonic kidney (HEK293T) cells were maintained in minimal essential medium containing 10% fetal bovine serum. The human strain A/Hong Kong/1/68 (H3N2) (Hk68) and the avian strains A/Duck/Ukraine/1/63 (H3N8) (DkUkr63) , cloned into plasmid pHWSccdB \u22122) in the absence of elastase, and either with (1.0 \u00b5g/ml) or without N-tosyl-L-phenylalanine chloromethyl ketone (TPCK)-treated trypsin (Sigma). After eight and 24 hours, we harvested the supernatants plaque-titrated them on MDCK cells in the presence of 2.0 \u00b5g/ml TPCK-treated trypsin. For each co-infection experiment, we picked 21 plaques and propagated them on A549 cells in the presence of 1.0 \u00b5g/ml trypsin. If no hemagglutination titer was detectable in the supernatants, we propagated the virus in 11-day-old embryonated chicken eggs.A549 cells were co-infected with Hk68-Ela at a multiplicity of infection (MOI) of 1 and either DkUkr63 or MallGer05 . The viral RNA was then reverse-transcribed into cDNA using the Onestep Kit (Qiagen) together with a primer pair universal for NP, NA, M and NS genes Figure S1Strict elastase dependency of Hk68-Ela. The plaque assay was performed on MDCK cells in the presence of elastase or trypsin or in the absence of an exogenous protease.(TIF)Click here for additional data file.Figure S2Plaque morphology of parental viruses and reassortants. The plaque assays were performed on MDCK cells in the presence of trypsin except Hk68-Ela requiring elastase.(TIF)Click here for additional data file.Table S1(DOC)Click here for additional data file.Table S2(DOC)Click here for additional data file.Table S3(DOC)Click here for additional data file."} +{"text": "Right ventricular (RV) function predicts prognosis in pulmonary hypertension (PH) patients (pts) and right ventricular (RV) failure. Prior studies evaluating of 3D RV ejection fraction (EF) have yielded inconsistent prognostic information. Here we explore the prognostic value of contrast enhanced Cardiac MRI (CMR) in PH (WHO group 1-5) pts.We hypothesize that CMR-Late Gadolinium Enhancement (LGE), a marker for myocardial fibrosis when present in RV or RV insertion points (RVIP), is a predictor of adverse prognosis in PH pts and remains more so when a quantitative analysis is incorporated.A retrospective chart review of PH pts (n=42) who underwent clinically indicated CMR were analyzed. Demographic data: mean age 61 yrs; 26% male; WHO group 1 (55%) group 2 (21%), group 3 (5%) group 4 (14%) group 5 (5%). RV volumetric data were indexed to BSA, and along with RV LGE information were correlated with MACE including hospitalization, death, referral/need for lung transplantation and addition/increase in inotropic therapy.LGE was positive (+) in 18 pts (43%) and negative (-) in the remaining 24 pts (57%). The predominant MACE events occur in the LGE+ group (78%). Specifically, in LGE+ group, 7 pts (39%) had MACE while 11 pts (61%) did not have MACE. In comparison, the LGE- group had only 2 pts (8%) who had MACE and 22 pts (92%)who did not have MACE, <0.03 for all). The results were similar when WHO group 1 were sub analyzed. In WHO 1 subgroup, 11 pts (48%) were LGE+ and 12 pts (52%) were LGE-. In the LGE+ group 4 pts (36%) had MACE while 7 pts . Fisher's exact test was used for group comparisons. Univariate analysis revealed only RVESVI, RVEF, RVEDVI and MRI LGE predicts MACE. However, via multivariable logistic regression analysis only RVESVI and MRI LGE predict MACE.. In a subset of those +LGE pts who had none-zero fibrosis after threshold quantitiation, no additive value was demonstrable.RV-LGE is >seven-fold stronger predictor of MACE than standard CMR metrics in PHTN pts. LGE's role as an independent adverse prognosticator may define the pathophysiologic hallmark in PH pts directly reflecting underlying RV failure due to progressive myocardial fibrosis. However, in limited fashion, quantitation appeared not to add clincal value over visual assessment.Internal"} +{"text": "To determine the contribution of transmission clusters on transmitted drug resistance (TDR) in newly diagnosed antiretroviral naive patients in Northern Greece, during 2000 -2007.Viral reverse transcriptase and protease genes from 369 individuals with newly diagnosed HIV-1 infection were sequenced at baseline. A maximum-likelihood phylogenetic analysis method was employed to examine for linkage between viral isolates. Clinical data were retrieved from the database and cross-referenced with the patients' medical files. Transmitted drug resistance was defined in accordance with the Surveillance Drug Resistance Mutation (SDRM) 2009 list.The study population characteristics were as follows: 82.8% male, 89.7% of Greek nationality, mean age 38, median CD4 cell count at diagnosis 295 cells/\u00b5l and mean HIV-1 RNA 4.94 log10 copies/ml. The most prevalent risk exposure category was men who have sex with men 59.1% (n=218) followed by heterosexual transmission 21.4% (n=79) and intravenous drug use 7.6% (n=28). Subtype B viruses were most prevalent (53.1%), followed by subtype A (32.5%). At least one drug resistance mutation was identified in 46/369 patients (12.4%). Twenty-eight patients (7.6%) harbored resistance mutations to nucleoside/nucleotide RT inhibitors, 20 patients (5.4%) to non-nucleoside RT inhibitors and 12 patients (3.3%) to protease inhibitors (PIs). Dual-class resistance mutations were identified in 14 patients (3.8%). The median CD4 cell count in patients with TDR was not significantly different compared to patients without (p=0.072). Phylogenetic analyses, supported by bootstrapping >90% and genetic distance <0.015, revealed three transmission clusters involving drug resistant strains, including one cluster of 11 patients infected with a strain carrying RT mutations Y181C and T215 variants conferring NRTI and NNRTI resistance.The overall prevalence of TDR in our study population was 12.4%. Phylogenetic analyses of viral sequences from these new diagnoses demonstrated the impact of transmission clusters on the primary drug resistance. The outbreak of dual-class TDR, coupled with late HIV diagnosis in this population may require improved public health interventions."} +{"text": "Children represent a population at higher risk of HIV-1 infection and AIDS-related death. Tuberculosis is a common cause of severe lung disease and death in children infected with HIV, particularly those living in areas of high tuberculosis prevalence. We investigated the causes of death in HIV-infected paediatric patients.A retrospective survey conducted in 29 ART centres in Karnataka, India. Medical records of all deaths that occurred between January and September 2011 amongst paediatric patients were reviewed. Immediate and underlying causes of death were described.Ninety-seven deaths occurred between January-September 2011. 55% of the deceased were males. The mean duration of survival on antiretroviral therapy was 36 weeks. Median age at time of death was 10 years (range 1-19) median CD4 count was 210 cells/\u00b5l (7-2500); 57% had CD4 cell count <250 cells/\u00b5l. In all, 64 causes of death were reported. In 44% (28/64), the causes were WHO clinical stage IV AIDS-defining illness, 36% (23/64) and 2% (1/64) were stage III and stage II conditions, respectively. Adverse effects to anti retrovirals were noted in 6% (4/64) of patients. Multiple causes were also reported in 6% (4/64). Other immediate causes of death were cardio respiratory arrest (2), suicide (1) and intra-cerebral haemorrhage (1). Infections were noted in 22% (14/64) patients. 43% (23/64) patients had tuberculosis at the time of death. Patients dying from AIDS-related events were more often men (17 out of 31).Although antiretroviral therapy has substantially and dramatically decreased AIDS-related opportunistic infections (OIs) and deaths, prevention and management of OIs remain critical components of care for HIV-infected children."} +{"text": "Multiple sclerosis (MS) is a common immune-mediated inflammatory disease of the central nervous system that causes severe neurological disability . TreatmeOur aim was to assess the prevalence and type of cutaneous adverse events associated with long-term use of DMT.A cross-sectional study was conducted in 2010-2011 among 15 clinics in the Netherlands. Eligible for inclusion were MS patients who were treated with their first DMT for at least 2 years. All consecutive eligible patients willing to participate were enrolled, irrespective of the presence of skin reactions. Skin reactions were assessed from digital photographs of the injection-sites by dermatologists, who were blinded for the DMT.A total of 146 patients were enrolled. The median age was 47 years (interquartile range [IQR] 41-54 years) and most patients (76%) were female. The median duration of DMT treatment was 4 years (IQR 3-8). Forty-four (30%) patients were treated with intramuscular (IM) IFN beta-1a, 43 (29%) with subcutaneous (SC) IFN beta-1a, 38 (26%) with IFN beta-1b, and 21 (14%) with GA. The proportion of patients with cutaneous adverse events was 40%, 77%, 63%, and 81% among patients receiving IM IFN beta-1a, SC IFN beta-1a, SC IFN beta-1b, and GA, respectively. Skin reactions were local injection-site reactions (61%), lipoatrophy (24%), healed skin ulcers (7%), postinflammatory hyperpigmentation (4%), urticaria (3%), and skin necrosis (1%).The prevalence of cutaneous adverse events associated with DMT treatment was high. The most common skin reactions were local injection-site reactions and lipoatrophy related to panniculitis."} +{"text": "Neuron-specific enolase (NSE) values >33 \u03bcg/ml and low In this nonblinded prospective study, we observed all CA patients from February 2011 until September 2012 surviving at least 24 hours. NSE was measured between 24 and 72 hours after CA. From October 2011 onward, we recorded BIS and suppression ratio (SR) values as soon as possible after arrival in the ICU. Patients treated with therapeutic hypothermia (TH) (33\u00b0C for 24 hours) received cisatracurium. Cerebral Performance Category (CPC) [NSE >45 occurred in 24/68 patients (35.3%) and invariably correlates with bad outcome. The positive predictive value (PPV) NSE >45 for bad outcome is 100%. No patient in this group ever had a GCS \u226512. NSE >33 and <45 occurred in 16/68 patients (23.5%). Thirteen out of 16 patients (81.2%) had bad outcome. However, 7/16 patients (43.8%) woke up at some time (GCS \u226512). NSE <33 occurred in 28/68 patients (41.2%), 17/28 patients (60.7%) had good outcome and 23/28 patients (88.4%) had GCS \u226512 at some time. The PPV NSE <33 for good outcome is 60.7%. The BIS and SR were measured in only 28 patients. Initial BIS \u226410 occurred in 13/28 patients (46.4%) and correlates with bad outcome in 12/13 patients (92.3%). BIS >30 occurred in nine patients, 6/9 (66.7%) had good outcome. Initial SR \u226575 occurred in 11/28 patients (39.3%) and invariably correlates with bad outcome. NSE >25 and SR >60 occurred in 15/28 patients (53.6%) and invariably correlates with bad outcome.NSE >45 uniformly correlates with bad outcome after CA. However, we urge caution for the use of intermediate values (33 to 45). In preliminary data, we report that SR >75 might correlate with bad outcome and that combining NSE and SR might improve the predictive value. Also, low NSE and good initial BIS values correlate with preserved cerebral potential and should encourage the clinician."} +{"text": "Juvenile dermatomyositis (JDM) is a rare, chronic inflammatory disease. Anti-TNF-\u03b1 agents are increasingly being used to treat disease that is refractory to other treatments. There is a lack of literature regarding the effectiveness of anti-TNF-\u03b1 agents in JDM.To assess the response of refractory JDM patients to anti-TNF-\u03b1 agents.The Juvenile Dermatomyositis National (UK and Ireland) Cohort Biomarker Study and Repository for Idiopathic Inflammatory Myopathies database was searched for patients treated with anti-TNF-\u03b1 agents.INFLIXIMAB: 28/30(93%) patients had data available. Indicators for starting infliximab were: muscle weakness (70%), non-ulcerative skin disease (57%), calcinosis (33%), and nail fold changes (30%). All patients with a low CMAS (n=18) improved. Physician VAS improved in 20/26(77%), CHAQ score in 11/16(69%), skin disease in 19/23(83%), calcinosis in 6/13(46%) and muscle enzymes in 6/10(60%). Prednisolone dose decreased in 17/21(81%).ADALIMUMAB: 10/11(91%) had previously been treated with infliximab. 6/10(60%) were changed to improve disease control: 4 had persistent skin disease, 2 improved; 3 had progressive calcinosis, 1 improved, 2 remained stable. 8/9(89%) maintained previous gains or made further improvement in other parameters other than skin and calcinosis.ETANERCEPT: 4/7(57%) patients had data available. 2 improved, 2 were switched to infliximab, one for increasing calcinosis, one for compliance issues.Infliximab provides clinical benefit to patients with JDM refractory to other treatments; particularly muscle weakness. Switching to adalimumab benefited some patients; gains made on infliximab were maintained in most cases."} +{"text": "E coli clonal lineage ST131 has emerged explosively, causing predominantly community-onset antimicrobial resistant infections. E coli ST131 has been shown to harbor a number of virulence and resistance genes and is now recognized for its ability to cause potentially severe infections in many parts of the developing world, implying public health measures in attempt to control infection.During the past years an E coli isolates from patients with blood stream infections (BSI) were screened by a ST131-clone allele-specific PCR for the pabB gene and analyzed for genes encoding ESBL by PCR and sequencing. Integrons were detected by PCR targeting the integrase gene. Gene cassette PCR was conducted on all class 1 integrase-positive isolates. BSI were classified according to the setting of infection: community acquired (CA), healthcare-associated (HCA), and hospital acquired (HA).Eighty-five drug-resistant E coli BSI, were: urinary in 50 (59%), gastrointestinal in 9 (11%), respiratory in 4 (5%), other (including skin and soft tissue) in 3 (3%), unknown in 19 (22%) patients. By pabB PCR, we identified 22 (26%) E coli isolates belonging to the O25b-ST131 clonal lineage. Among 22 ST131 E coli isolates, 6 (27%) were from CA, 11 (50%) were from HCA, and 5 (23%) were from HA infections, while among 61 non-ST 131 E coli isolates, 30 (49%) were from CA, 14 (23%) were from HCA, and 17 (28%) from HA infections (p=0.053). ESBL genes were found in 20 (91%) ST131 and 13 (21%) non-ST131 E coli isolates . The ST131 isolates carried blaCTX-M in 18 (82%), blaTEM-1 in 6 (27%) and blaOXA-1 in 18 (82%). Class I integrons were identified in 11 (50%) ST131-producing E coli strains and 36 (57%) non-ST131 E coli strains . Resistance to trimethoprim/sulfamethoxazole was found in 11 (50%) ST131 E coli isolates and in 32 (59%) non-ST131 E coli strains (p=0.610), while resistance to both fluoroquinolones and aminoglycosides was identified in 18 (82%) ST131 E coli isolates compared to 10 (16%) non-ST131 E coli strains (p<0.001). Among patients with BSI caused by resistant E coli, the in-hospital mortality was similar in patients infected with strains carrying the ST131 clonal lineage versus non ST131 (p=0.921).The sources of E coli ST131 were most likely to be hospital rather than community associated. We found more ESBL genes in ST131 E coli isolates, while class I integrons were present in both groups in similar rates.In our study group, BSI caused by"} +{"text": "S/GSK1349572(572) showed potent activity in Phase 2 studies in INI-naive HIV-infected subjects and limited cross-resistance to raltegravir (RAL) and elvitegravir in vitro. VIKING is an ongoing 24-week Phase 2b pilot study assessing 572 in subjects with RAL-resistant HIV. A good antiviral response during the functional monotherapy phase (through Day 11) of this pilot study was observed with a strong correlation between baseline susceptibility to 572 and response.27 RAL-experienced, adult subjects, with screening plasma HIV-1 RNA \u22651000c/mL and genotypic resistance to RAL and \u2265 2 other ART classes, received 572 50mg QD in Cohort I while continuing their failing regimen (without RAL). At Day 11 the background regimen was optimised, where feasible, and 572 continued. The antiviral activity (primary end-point at Day 11), tolerability, safety and virology data through Week 24 of Cohort I are presented. A higher dose is being assessed.3 and 4.47 log10c/mL , respectively. Median number (range) of prior ART drugs was 18 . Twenty one (78%) subjects achieved plasma HIV-1 RNA<400 c/mL (n=11) or \u2265 0.7 log10 c/mL decline (n=10) at Day 11 (primary end-point). Post Day 11, the optimised background regimen (OBR) phenotypic susceptibility score (PSS) was 0, 1 and \u2265 2 for 12 (44%), 7 (26%) and 8 (30%) subjects, respectively. 17 subjects continued therapy through Week 24 when 14/27 (52%) and 11/27 (41%) subjects achieved < 400 c/mL and < 50 c/mL, respectively by TLOVR. Response correlated with OBR PSS: 2/12 (17%) subjects with PSS =0, 4/7 (57%) with PSS=1 and 8/8 (100%) with PSS \u22652 achieved <400 c/mL at Week 24. Drug related AEs (any grade) were observed in 6 (22%) subjects. Two subjects with advanced AIDS died after withdrawal from study for SAEs unrelated to 572.At Baseline, subjects harboured viruses displaying high level resistance to RAL and low median FC to 572 . Median (IQR) Baseline CD4+ and plasma HIV-1 RNA were 110 cells/mmDespite high level baseline resistance to RAL and the limited activity of the OBR co-administered with 572, the majority of subjects achieved < 400 c/mL at Week 24 with improved response rates in those receiving at least one active background ART. S/GSK1349572 was generally well tolerated in this advanced population."} +{"text": "Prolonged mechanical ventilation and length of stay (LOS) in the ICU is associated with long-term impaired functional capacity. However, little is known about functional dependency in the direct post-ICU phase. Therefore the timing and location for optimal post-ICU rehabilitation programs remain to be established.P < 0.05 was considered significant.In this single-centre observational study we aimed to quantify functional dependency at three different time points: discharge from ICU (DI), discharge from hospital (DH) and discharge from nursing home rehabilitation unit (DR). To this end we retrospectively assed Barthel scores (BS) for individual patients , with a P < 0.001), indicating severe dependency, and finally to 16 (11 to 18) at DR, indicating independency with some disabilities (P < 0.001). The absolute increase in BS was significantly greater during the stay in the rehabilitation unit, as compared to the general hospital ward (P < 0.001).Thirty-four patients were included. Baseline characteristics: APACHE II score 20 (17 to 25), age 68 (55 to 73) years, LOS ICU 22 (8 to 36) days, mechanical ventilation 8 (2 to 17) days, LOS hospital 21 (14 to 30) days, LOS rehabilitation unit 53 (31 to 85) days. Median BS at DI was 2 (1 to 3), indicating total functional dependency. In comparison to baseline, BS increased to 8 (2 to 12) at DH (ICU patients with prolonged mechanical ventilation remain severely functionally dependent after ICU discharge, but dependency reduces significantly during rehabilitation in hospital and in a nursing home rehabilitation unit."} +{"text": "A multi-ethnic background with high rates of consanguinity characterizes the population living in Qatar. Understanding the uniqueness of clinical presentation of autoinflammatory disorders (AID) in this population will enhance our knowledge in regards to the spectrum of clinical phenotype and prevalence of mutations in our region.To report the clinical and genetic profile of children with AID from the only childhood rheumatology center in Qatar over the past 5 years.A retrospective review of medical records.MEFV mutant alleles (17 probands), only 25 were identified while 9 were unidentified. Of the 25 MEFV mutations M694V (12), E148Q (5), E167D/F479L (2), V726A (2), M694I (2), N599D (1), and M680I (1).Familial Mediterranean Fever: 30 symptomatic children, 9 asymptomatic carriers, and 21 adult relatives were included. Among symptomatic children, the male to female ratio was 1:1, 19 were Arabic, 8 were Persian, and 3 were Turkish/Arabic. Median age at first symptoms was 5 years (range 1 \u2013 16 years). Most common manifestations included recurrent abdominal pain and fever (n=25), arthralgia (15), chest pain (4), arthritis (3), oral aphthouses (3), erysipelas (1), and recurrent pyogenic arthritis (1). Other features include anemia (4), hypothyroidism or hyperthyroidism (2), and renal failure due to membranoproliferative glomerulonephritis (1). Response to colchicine was good (23) or partial (2); 4 others are not yet started and 1 was lost follow-up. A 23 member four-generation family of Persian ethnicity was followed showing variable severity of clinical manifestations, severe pustulosis and psoriasis. Out of the expected 34 MVK mutation. Two symptomatic siblings are homozygote for V377I MVK mutation. All members have complex MEFV mutations. Detailed clinical and genotype characteristics are reported separately due to exceptionality of such combination.Hyper-IgD syndrome group includes one Arabic family: parents and 3 siblings are carriers of V377I/- PSTPIP1. He responded well to courses of prednisone.One boy with Pyogenic Arthritis, Pyoderma Gangrenosum and Acne syndrome presented at 6 months of age and diagnosed at 4.5 years. He had recurrent pyogenic arthritis and skin abscesses and had a de novo and novel D246N mutation of LPIN2 mutations but one had Q219H/- PSTPIP1 variant. Treatments include naproxen (5), infliximab (3), pamidronate (2), and canakinumab (1).Chronic Recurrent Multifocal Osteomyelitis (CRMO) group inlcuded 5 Arabic patients with a median age of disease onset of 7 years presenting with recurrent arthralgia (5), arthritis (3), abnormal gait (4) and back pain (2). One had compression fractures of the spine with kyphosis within 6 months of presentation. Other features included anemia (5) and psoriasis (1). All had elevated acute phase reactants, a diagnostic bone biopsy (3), bone scans (5), and MRI studies (5). Genetic testing results are pending in 2 whereas 2 had no We report an expanding cohort of children with AID in Qatar. Clinical manifestations were variable for similar mutations even among the same family. Concomitant mutations in different AID genes can be present. Clinical phenotype of CRMO in our cohort was more severe then typically reported in the literature.B. Aladbe: None declared, A. Aly: None declared, R. Taha: None declared, H. Elshanti: None declared, T. Moussa: None declared, F. AlAmry: None declared, B. Fathalla Grant / Research Support from: Medical Reserach Committee/ Hamad General Hospital"} +{"text": "HIV associated BL remains of concern for toxicity of dose-intensive regimens used in HIV negative patients (pts). Less intensive regimens have a high relapse rate. We modified CODOX-M/IVAC hoping to preserve efficacy while improving tolerability, particularly treatment related mortality (TRM). Primary object: improving 1 year overall survival (OS) from the historical 65 to 85%.Modifications of the US NCI regimen include rituximab (R), cyclophosphamide reduction [800 mg/m2 x 2 days], vincristine 2 mg cap, methotrexate (mtx) 3000 mg/m2, dual chemotherapy lumbar punctures and IVAC infusion (high risk pts). Antibiotic prophylaxis & growth factor support specified, 100% grade IV hematopoietic toxicities in the original regimen. HAART therapy at the discretion of the local MD. Pathology review included CD20, CD10, BCL2, BCL6, p53, Ki67, BLIMP1, IRF4/MUM1 and EBV EBER. (Table 5 (27%); HIV viral load 1819 . Median follow up (fu) is 9 mos for surviving pt. Number of pts with gr3/4 toxicity: any 20 (61%), 13 (39%) hematologic, 16 (48%) infection including 7 febrile neutropenia, 6 metabolic with 1 tumor lysis syndrome, 4 neurologic, 2 thrombotic and 1 each coagulation, GI or pain. Only 2 gr 1/2 stomatitis/mucositis; 0 had gr 3/4. Six deaths: encephalopathy with hepatic failure, hepatitis B and pneumonia (1), disease progression (3) including 1 in the CNS; fungal infection (1); HIV. Median 1 year OS (n=34) was 81.7% with a 35 mo median survival. OS by non-BL defining proteins: EBER +/- (8/16) and p53 +/- (10/10) were not predictive. IRF4/MUM1 +/- (8/15) highly predictive in overall pts, but not in the confirmed Burkitt +/- (6/14) with only 1 IRF4/MUM1 neg pt dying of BL.Accrual of 33 planned pts by April 2010. Baseline: Classical Burkitt, 97%; Low/High Risk, 9/91%; Median (range) Age 42 (19 \u2013 55); CD4 count 195 (0 - 721), CD4 <100, AMC 048 with a median fu of 9 mos has a 1 yr OS of 82% in BL. Relapses after 1 year are rare. TRM was zero. R did not appear to increase toxicity. Only 5 pts withdrew due to AEs. Grade 3/4 toxicities were markedly reduced. Results compare favorably with 2 studies of HIV neg pts. Magrath (1995) reported 100% grade 4 hematologic and 20% grade 4 mucositis in 39 adults, 33 children (92% 2 yr EFS). MRC/NCRI LY10 trial (Mead 2008) reduced mtx (3gr/m2), but reported 9% TRM (64% 2 yr OS). IRF4/MUM1 deserves further study in BL."} +{"text": "Our hospital is a reference centre located in one of the South-South states, which has a HIV sero prevalence of 8% and one non AIDS defining malignancy (squamous cell carcinoma of the conjunctiva), also commonly diagnosed in these patients. Records of the patients which are histologically confirmed and diagnosed between 1A total of 4123 histologically confirmed biopsies were received, 852 (21%) were cancers, 24 (2.8%) were Kaposi sarcoma (KS), 8 (33%) KS occurred in females, range 21-60 years (y), 16 (67%) in males, range 19-60 y and 17 (71%) of KS were AIDS associated, 6 (35%) females and 11 (65%) males. Thirty five 35 (4.1%) of cancers were Non Hodgkin lymphomas including Burkitt\u2019s lymphomas, 8 (23%) in females, range 6-60 y and males 27 (77%), range 6-71 y. Two 2 (5.7%) were AIDS associated 2 (100%) were males on long standing antiretroviral treatment. Cervical cancers accounted for 84 (9.9%) all cancers and 14 (17%) occurred in HIV positive patients age range. Conjunctival squamous cell carcinomas were 13 (1.5%) of all cancers, 6 (46%) females 7 (54%) males. Two 2 (15%) occurred in HIV positive patients.AIDS associated malignancies appear to be very common in this environment and perhaps non AIDS associated malignancies may be on the increase. Under-reporting and lack of capacity may account for the fewer numbers reported in this environment."} +{"text": "Intensive insulin therapy (IIT) has been shown to reduce mortality in intensive care patients ,2. A larThree hospitals developed and implemented an evidence-based guideline for IIT; we collected all BGL measurements and patient demographics for the 2 years after implementation. We captured all patients with SH, and randomly selected the same number of patients without SH as controls. To evaluate long-term outcome, we used the following scores: Glasgow Outcome Scale (GOS), Short-Form (SF)-12 for health-related quality of life (HRQOL) expressed as physical (PCS-12) and mental component score (MCS-12), Informant Questionnaire on Cognitive Decline in the Elderly (IQ-CODE) and the Modified Blessed Dementia Rating Scale (MBDRS) by proxies.P < 0.001). Median BGL was lower in patients with SH, 101 (97 to 106) versus 113 (102 to 123) mg/dl (P < 0.001). Outcome indicators were similar between patients with at least one episode of SH and control patients: GOS; 1 (1 to 1) versus 1 (1 to 2) (P = 0.173); PCS-12; 44 (33 to 50) versus 42 (34 to 52) (P = 1.000); MCS-12; 49 (38 to 56) versus 45 (35 to 52) (P = 0.093), IQ-CODE; 3.0 (3.0 to 3.3) versus 3.0 (3.0 to 3.1) (P = 0.116) and MBDRS 1; (0.5 to 1.5) versus 0.5 .Our analysis included 93 patients, 43 patients with at least one episode of SH, and 50 control patients. Median length of an SH episode, assuming linear changes of glucose values between measurements, was 20 (10 to 50) minutes. Patient demographics were similar. Median length of ICU stay was longer in patients with SH, 12 (6 to 20) versus 4 (8 to 23) days (Neither long-term functional and cognitive outcome, nor HRQOL of patients who encountered IIT-associated SH differed from patients who never had SH. However, it should be noted that the analyzed groups are small. Our data suggest IIT-associated SH not being harmful."} +{"text": "Detection of psychological characteristics of the children with JIA of different age groups.155 patients with JIA aged 4-17 years. Group 1 \u2013 aged 4-7 years (15 people), Group 2 \u2013 aged 8-12 years (40 people), Group 3 \u2013 aged 13-17 years (100 people).Family pattern (Karen Mahover) , House-Tree-Person (John N. Buck) (Group 1), Scale of Tailor by Spilberg-Hanin (Group 3), the L\u00fcscher color test , Junior\u2013Senior High School Personality Questionnaire by Cattell (HSPQ \u2013 teenager version) (Group 3), Picture of a non-existent animal (M.Z. Dukarevich) , Cattell\u2019s methods for junior personality psychology study (Group 2).fears (73%), communicative disorders (67%), high level of anxiety (40%), aggression (20%), low level of social adaptation (13%).high level of anxiety (65%), communicative disorders (55%), fears (42%), increased level of psychoemotional stress (35%), aggression (25%), tendency toward depression (25%), low level of social adaptation (12%) and appearance complexes (12%).communicative disorders (69%), high level of anxiety (58%), psychoemotional stress (37%), fears (34%), low level of social adaptation (24%), tendency toward depression (24%), appearance complexes (22%), aggression (20%).The studied groups showed the same levels of communicative disorders and aggression. Age increase was followed by the decrease in number of patients with fear; and by increase in number of patients with low level of social adaptation, the percentage of appearance complexes and psychoemotional stress appeared and was increasing. The defined characteristics should be considered during the individual work with the patients."} +{"text": "Several cardioplegic solutions have been previously studied in patients undergoing CABG. However data on elderly high risk surgical patients is lacking. The main objective is to determined differences on mortality and clinical outcomes regarding the type of cardioplegic solution.Consecutive high risk patients with a recient acute coronary syndrome(ACS) undergoing CABG on CPB inducing cardiac arrest were enrolled prospectively. A Comparison between those who received plegisol\u00ae(HCS) vs. Custodiol\u00ae(HTK) was performed. Statistical analysis of preoperative, operative and postoperative variables were done utilizing spss version 19.0.During 36 months, 721 patients underwent CABG. Only patients older that 70 years-old with an acute coronary syndrome were included. High risk was defined as Euroscore I greater than 7. Exclusion criterias were Chronic Renal Failure, off-pump surgery and additional procedures. 85(12%) patients were selected for analysis. Mean Age was 75(70-87). 56(65.9%) were male and 29(34.1%) were female. Mean Euroscore I was 10(8-20). Mean EF was 46%(+/-11). Left-main coronary obstruction was present in 13(15%). Cardioplegic solution was administered randomly. HCS was administered to 40(47%) and HTK to 45(53%) patients. 30 days-Mortality occurred in 7(8.2%), 4 in HCS and 3 in HTK (p:0.551). Mean CPB time was 84min(42-110) and Cross-clamp time was 50min(24-65) with no difference between groups. Number of grafts performed were 3(1-5) Perioperative infarction occurred in 11(12%) patients, 5(7.9%) in HTK and 6(5.9%) in HCS (p:0.4), postoperative atrial fibrilation was present in 15(17.5%), 8 in HCS and 7 in HTK(p:0.4), Mean ICU time was 3days (1-5) for HTK and 5 for HCS (2-7). LOS was 4 for HTK and 6 days for HCS(p:0.2).CABG outcomes in high risk patients with an acute coronary syndrome was not affected by the type of cardioplegia."} +{"text": "The expression of CD19 on chronic lymphocytic leukemia (CLL) cells offers a novel therapy for relapsed CLL patients (pts) previously treated with rituximab. MEDI-551 is an affinity-optimized anti-CD19 Ab with enhanced Ab-dependent cellular cytotoxicity (ADCC) effector function.Response and toxicity of single-agent MEDI-551 in multiply relapsed CLL pts with prior rituximab therapy was assessed in a phase 1/2 (ph 1/2), open-label, dose-escalation and expansion study. Combination therapy was assessed in an ongoing phase 2 (ph 2) study comparing MEDI-551 or rituximab+bendamustine in relapsed/refractory CLL pts. For the ph 1/2 study, B cell depletion was assessed with flow cytometry and BAFF biomarker analysis; response was assessed using the 2008 IWG criteria.In the ph 1/2 study, 26 CLL pts received \u22651 dose of MEDI-551. In the ph 2 study, 44 pts received study drug as of 20Mar2013. Loss of CD19 detection due to depletion and/or occupancy with MEDI-551 was rapid and apparent after cycle 1. B cell depletion occurred 1 day after dose 1 and was associated with increased serum BAFF concentrations. In the ph 1/2 study, of 21 MEDI-551-treated CLL pts evaluable for response, 5 achieved partial remission and 13 had stable disease. Commonly reported adverse events (AEs) in MEDI-551 pts were infusion-related reactions , nausea (23%), pyrexia (23%), and neutropenia (23%) in the 26 ph 1/2 pts; in the 29 ph 2 pts, they were nausea (62%), IRRs (31%), pyrexia (28%), chills (28%), and fatigue (28%). 11 pts had \u2265 grade 3 AEs in the ph 1/2 study and 16 in the ph 2. Common treatment-related AEs: IRRs (58%) and nausea (12%) in the ph 1/2; nausea (52%), IRRs (28%), chills (24%), and fatigue (24%) in the ph 2. Three treatment-unrelated AEs of general health deterioration (ph 1/2), subarachnoid hemorrhage (ph 1/2), and sepsis (ph 2), resulted in death.MEDI-551 as a single agent demonstrated B-cell depletion, increased serum BAFF levels, clinical activity, and an acceptable risk-benefit profile in relapsed/refractory CLL pts. Preliminary results of the ongoing ph 2 study of MEDI-551+bendamustine demonstrated an acceptable safety profile."} +{"text": "To evaluate safety and efficacy in young adults with JIA treated by TNF and non anti-TNF inhibitors.36 patients with JIA treated with anti-TNF followed at Transition Clinic of Florence from January 2008 to December 2010 were enrolled in a observational, single-centre, retrospective study. 12 pts failed to respond or did not tolerate the first therapy and switched to a second one. Moreover, 9 patients has received non anti-TNF drug . In all, 53 treatments were performed. Safety assessments were based on adverse events (AEs) report, divided in moderate AES (if infective events or injection site reactions have been occurred) and severe AES (including infusion reactions). Efficacy was assessed using the PedACR30/50/70 criteria.Of the 36 patients treated with TNF-blockers, Ped ACR30/50/70 response was reached by 78%/67%/58% after 24 weeks, 72%/68%/60% after 48 weeks and 87%/87%/73% after 96 weeks of treatment. Of the 9 patients treated with abatacept or tocilizumab, PedACR30/50/70 response was reached by 89%/78%/67% after 24 weeks, 80%/80%/80% after 48 weeks and 75%/75%/75% after 96 weeks. 108 AEs (both moderate and serious) occurred in 26 patients (59%) treated with anti-TNF. Among non anti-TNF agents, 36 AEs occurred in 7 patients (78%), no one was serious and any patient leaved the biological treatment due to AEs.In our study, anti-TNF agents were well tolerated and provided clinically significant efficacy in young adults with JIA. In the refractory systemic form of JIA, tocilizumab seemed to be effective and safe."} +{"text": "Early access to critical care interventions may improve outcomes for severely ill and injured patients. A Cochrane review in 2009 We performed a retrospective observational study of paramedic RSI performed by a national ambulance service, between 12/12/2009 and 12/12/2011. RSI was defined as the administration of Suxamethonium, with or without an induction agent. RSI was performed according to a standard operating procedure following telephonic physician approval. Effectiveness was defined as self-reported successful tracheal intubation. Safety was defined as the absence of an adverse event (AE) (hypoxia or hypotension at handover or reported complications) as a result of the RSI procedure.Eighty-six RSI\u2019s were performed during the study period. No failed intubations were reported. Nineteen patients (22%) had an adverse event (AE). Complications included: haemodynamic instability (11.6%), tension pneumothorax (3.5%), difficult intubation (2.3%), low ETCO2 (2.3%), high ETCO2 (1.2%), and bronchospasm (1.2%). 4 of these patients were hypotensive (4.7%) and 2 hypoxic (2.3%) at handover to hospital or helicopter staff. Female gender, helicopter transport and age (<18 years) were significantly associated with an AE on univariate analysis. Female gender (Odds ratio 18.3 (3.46-99.38); p = 0.001) and helicopter transport (Odds ratio 7.24 (1.44-36.32); p = 0.016) remained independently associated with AEs after adjustment for confounders.In South African Pre-hospital Care, RSI performed by specially trained paramedics is effective in terms of self-reported success. However, the 1 in 5 AE rate highlights safety concerns. The importance of a robust clinical governance programme to identify problems, refine practice and improve the quality of care is underscored."} +{"text": "The association of hepatic enzymes and blunt hepatic trauma has been widely researched and a general consensus exists on the role of non-operative management of these injuries. PenetratA retrospective cohort study of all penetrating and blunt liver injuries at a Level 1 Major Trauma Centre was undertaken. Cases were defined by having radiological evidence of liver trauma following injury. Initial aspartate transanimase (AST) levels were documented along with intervention (non-operative or operative) and outcome.35 cases of penetrating trauma over a 48 month period were identified. ISS mean 14.77 (4-36), Length of Stay (LOS) mean 13.97 days (3-54), age mean 26.25yrs (17-52), 97.14% male. 28.57% (n=10) had abnormally elevated AST levels (51 to 188IU/L) at time of presentation to the ED. Of those with elevated initial AST levels, 70% (n=7/10) had an emergency laparotomy compared with 28% (n=7/25) of cases of penetrating trauma with a normal AST level. Initial raised AST was therefore more likely associated with need for operative management (p=0.022). Of interest, of the three cases with raised AST without laparotomy, one developed a bile leak requiring CBD stent and another developed a pseudoaneurysm and self-discharged prior to further evaluation. In contrast, 28 cases of blunt trauma over a 29 month period were identified with an ISS mean of 26.32 (4-66), LOS mean 24.27 (1-114), mean age of 33.34yrs (1-58.1). 89% (n=25) of these blunt liver injuries had elevated AST levels (69 to 3913IU/L) and only 2 cases proceeded to laparotomy which was for associated injuries and not liver trauma.There study suggests that raised (AST) is associated with having a laparotomy rather than conservative management in penetrating hepatic injuries and justifies further research into the diagnostic value of hepatic enzymes in the stable patient with penetrating injury."} +{"text": "According to the new classification community-onset bacteremias (COB) are divided in healthcare-associated (HCAB) and community-acquired (CAB). The objective of this study was to apply this classification to a cross-sectional study of patients with COB and to determine differences between the two groups in terms of epidemiology, treatment and outcome.The study was conducted at the University Hospital of Heraklion, Greece, from March 2010 to November 2011. Patients were classified as HCAB or CABusing pre-defined selection criteria. Epidemiological, clinical and therapeutic characteristics, antimicrobial resistance and outcome were compared in both groups. The statistical analysis was performed using SPSS 19.0.Escherichia coli was the mostcommon causative agent but the prevalence of Klebsiella pneumoniae in HCAB was significantly higher than CAB (19.3% vs. 4.8%). Patients with HCAB had higher Charlson score and higher Pitt bacteremia score, less frequent administration of appropriate empirical antibiotic treatment and higher probability of death than patients with CAB.\u0391mong 145 patients with gram-negative COB, 83 (57.2%) had HCAB and 62 (42.8%) had CAB. The frequency of malignant tumors, renal insufficiency and dementia was higher in patients with HCAB than with CAB. In both groups The antimicrobial resistance in HCAB \u03ba\u03b1\u03b9 CAB patients respectively, was found 27/83 (32.5%) vs. 4/62 (6.5%) (P<.001) to third-generation cephalosporins (3GC), 22/83 (26.5%) vs. 7/62 (11.3%) (P=.021) to aminoglycosides, 29/83 (34.9%) vs. 9/62 (14.5%) (P=.005) to quinolones. Bacteria that produced ESBL were 16/76 (21.1%) vs. 2/59 (3.4%) (P=.003), and carbapenem-resistant were 10/83 (12.0%) vs. 2/62 (3.2%) (P=.056) in HCAB \u03ba\u03b1\u03b9 CAB patients respectivelyThere are significant differences in the severity of underlying diseases, causative pathogens, antibiotic resistance, outcome and treatment between the two groups. In our region 3GC, aminoglycosides or fluoroquinolones are proposed as appropriate empirical treatment for patients with CAB, whereas in patients with HCAB carbapenems should be the initial therapyNone declared"} +{"text": "Lm) bioengineered to secrete a HPV-16-E7 fusion protein targeting HPV transformed cells. The Lm vector serves as its own adjuvant and infects antigen presenting cells (APC) where it cross presents, stimulating MHC class I and II pathways resulting in specific T-cell immunity to tumors. Here we describe final 12 month overall survival data associated with ADXS11-001 administration in Lm-LLO-E7-015, a randomized P2 study conducted in India in 110 patients with recurrent cervical cancer; previously treated with chemotherapy, radiotherapy or both. Patients were randomized to either 1 cycle (3 doses) of ADXS11-001 at 1 x 109 cfu or 4 doses of ADXS11-001 at 1 x 109 cfu with cisplatin chemotherapy. Naprosyn and oral promethazine were given as premedications and a course of ampicillin was given 72 hours after infusion. Patients received CT scans at baseline and 3, 6, 9, 12 and 18 months. The primary endpoint is overall survival. As of May 17, 2013, the trial has completed enrollment and 110 patients received 264 doses of ADXS11-001. The percentage of patients at 12 months is 36% (39/110) and currently the 18 month survival is 22% (16/73). The response rate was 11% (6 CRs and 6 PR/110) with tumor responses observed in both treatment arms. 33 additional patients had stable disease > 3 months, for a disease control rate of 41% (45/110). Activity was observed against all high risk HPV strains detected. Two Grade 3 serious adverse events and 104 mild-moderate adverse events possibly related/related to ADXS11-001 treatment have been reported in 41% (45/110) of patients. The non-serious adverse events consisted predominately of transient, non-cumulative flu-like symptoms associated with infusion that either self-resolved or responded to symptomatic treatment. ADXS11-001 can be safely administered to patients with advanced cancer alone and in combination with chemotherapy. ADXS11-001 is well tolerated and presents a predictable and manageable safety profile. The addition of cisplatin to ADXS11-001 in this study did not significantly improve tumor responses or overall survival. Objective tumor responses included CR\u2019s and apparent prolonged survival with minimal adverse experiences. Average duration of response in both treatment groups was 10.5 months. The 36% 12 month survival and 11% response rate observed in this recurrent disease setting is encouraging and suggests that ADXS11-001 is an active agent in recurrent cervical cancer. Final 18 month overall survival will be presented at the meeting.ADXS11-001 immunotherapy is a live attenuated Listeria monocytogenes ("} +{"text": "Myeloid derived suppressor cells (MDSC) are detected at elevated levels in the peripheral blood mononuclear cells (PBMC) of human renal cell carcinoma (RCC) patients and have been shown to mediate tumor growth by promoting angiogenesis and immune suppression . Granulocytic-MDSCs (G-MDSCs), the dominant population in RCC patients, have been shown to suppress T-cell function in RCC patients . However, less is known regarding the role of neutrophils in promoting tumor growth in RCC patients and their relationship to G-MDSC. In this study we compared the suppressive and angiogenic profile of neutrophils from RCC patients to those of normal donors and the impact that RCC conditioned media has in altering neutrophils normal function. We showed that IFN\u03b3 production of T-cells stimulated with anti-CD3/antiCD28 antibodies (n=4) was suppressed by neutrophils pretreated with SK-RC-26b tumor supernatant (TCM) when compared to neutrophils not exposed to TCM. Further experiments showed that neutrophils from RCC patients had increased expression compared to normal healthy donor neutrophils of genes Vegfa (15.28 fold increase), Vegfb (10.84 fold increase), Tgfb1 (3.31 fold increase), IL10 (23.45 fold increase), IDO1 (4.60 fold increase), Nox1 (9.33 fold increase), and Prokr2 (4.14 fold increase) utilizing custom pro-angiogenic and immunosuppressive RT-PCR arrays (n=4). Furthermore, human angiogenesis Proteome Profile Arrays (n=2) were performed comparing RCC patient and normal healthy donor neutrophils and exhibited an increased level of Activin A (94.5% increase), Angiogenin (70% increase), Angiostatin/ plasminogen (56% increase), IGFBP-1 (188% increase), IGFBP-2 (263% increase),TGF-B1 (157.5% increase), Pentraxin 3 (140% increase), PD-ECGF (184.5% increase), Serpin E1 (196% increase), and Serpin F1 (114.5% increase) in RCC patient neutrophils. Normal neutrophils cultured with ACHN tumor supernatant for 18 hours (n=2) had up-regulation of proteins CXCL16 (111% increase), FDF-7 (82% increase), Serpin E1 (470.5% increase), and uPA (198.5% increase) when compared to normal healthy donor\u2019s neutrophils cultured 18 hours in media. In summary, we observed up-regulation of several pro-angiogenic/ immunosuppressive genes in RCC patient neutrophils, suggesting RCC patient neutrophils may promote tumor escape. In addition, the normal healthy donor neutrophils cultured with ACHN tumor supernatant produces several angiogenic proteins suggesting the tumor microenvironment could be providing factors to mediate these angiogenic functions in RCC patient\u2019s neutrophils."} +{"text": "Seasonal influenza (SI) is usually a benign self-limited disease. However, it can present a serious health threat.We describe influenza cases admitted to a 34-bed adult intensive care unit (ICU) in a Swiss university hospital during winter season 2012/2013.From 28/11/2012 to 11/03/2013, among 268 hospitalized cases of SI confirmed through nasopharyngeal samples using real-time PCR, 34 were admitted to the ICU. Droplet precautions were applied to all patients (pts) at ICU admission without single room isolation.S. pneumonia (n=5), S. pyogenes (n=2), methicillin-sensitive S. aureus (n=1) and Coronavirus (n=1). 27 pts (79%) were treated with oseltamivir, with a median delay after onset of symptoms of 5 d (IQR: 3-7). 27 pts (79%) needed ventilatory support: invasive ventilation (n=17 [50%] for a median duration of 6 d [IQR: 2-13]) or non-invasive ventilation (n=15 [44%] for a median duration of 2 d [IQR: 2-3]). The median length of ICU and hospital stay were 5 (IQR: 3-9) and 11 d (IQR: 7-23), respectively. 5 pts (19%) died of influenza-related complications, including 1 case of nosocomial superinfection.23 pts (68%) were positive for influenza A and 11 (32%) for influenza B. 18 pts (53%) were male; median age was 63 years (interquartiles range [IQR]: 47-74]); 29 pts (85%) presented a least one co-morbidity and 19 (56%) had risk factors for SI: chronic respiratory disease (n=12), diabetes (n=7), obesity (n=4), chronic cardiac disease (n=4), immunosuppression (n=3) and pregnancy (n=1). Only 5 pts had received influenza vaccination. 29 cases were community-acquired (85%) while 5 were hospital-acquired (15%) (symptoms occurring >3 days [d] after admission). No ICU-acquired influenza was detected. 9 pts (26%) had a documented co-infection with: Winter season 2012/2013 was characterized by a massive burden of cases in the ICU, with no co-morbidity for 15% of the patients. Despite increased workload, use of face mask ventilation and no isolated rooms, it is remarkable that no clinical case of transmission was recognized or microbiologically documented inside the ICU during this period.None declared"} +{"text": "With combination antiretroviral therapy (cART), HIV-associated mortality rates have declined substantially in the UK. However HIV-infected adults are living longer to develop co-morbidities, including low bone mineral density (BMD). This study investigates fractures in a UK cohort of HIV-infected adults.A cross-sectional survey of 1050 HIV-infected adults from routine HIV clinics was conducted. Subjects completed a questionnaire about demography, lifestyle factors, fracture history and management, exposure to glucocorticoids and other drugs influencing bone metabolism. HIV details were recorded.There were 859 useable replies (response rate 82%) from 775 men and 84 women: mean age 43 years (range 19-77 years) and 87% Caucasian. Mean duration of HIV infection was 8 years (range 0-23 years). Co-infection with hepatitis B occurred in 16 subjects and hepatitis C in 11. Overall, 125 (15%) subjects reported 200 fractures: 119 (15%) men and 6 (7%) women. Common fracture sites were forearm (n=65), tibia/fibula (n=29), hand/foot (n=22) and digit (n=19). Hip fractures occurred in 6 subjects and 2 had clinical vertebral fractures. A bimodal distribution of fracture was seen: 114 (57%) fractures occurred in subjects <25 years (peak age 7-12 years) and 33 (17%) fractures in those >40 years, with 8 (24%) in subjects >50 years. Among subjects >40 years with fractures , common fracture sites were forearm and tibia/fibula ; there was 1 hip fracture (age 46 years). 15% of these subjects reported oral glucocorticoid exposure (vs. 9% without fractures (p=ns)) and 79% had ever smoked (vs. 72% without fractures (p=ns)).This is the first epidemiological study of fractures in HIV-infected adults in the UK. There were 2 peaks of fracture incidence: <25 years and 40-60 years. Forearm fractures were the commonest but fractures at other 'typical' osteoporotic sites were seen. The second peak occurred at a younger age than those reported in HIV-negative subjects. This is consistent with data showing accelerated immune senescence in HIV. Although the clinical importance of low BMD is yet to be fully evaluated, if fracture rates are increased, routine assessment of low BMD and fracture risk may be warranted in this relatively young population."} +{"text": "Polymorphisms at cleavage sites (CS) can influence Gag and Pol proteins processing by the viral protease (PR), restore viral fitness and influence the virological outcome of specific antiretroviral drugs. However, data of HIV-1 variant-associated CS variability is scarce.gag and 3,906 pol HIV-1 sequences deposited in GenBank, focusing on the 110 residues (10 per site) involved at 11 CS: P17/P24, P24/P2, P2/P7, P7/P1, P1/P6gag, NC/TFP, TFP/P6pol, P6pol/PR, PR/RTp51, RTp51/RTp66 and RTp66/IN. CS consensus amino acid sequences across HIV-1 groups , group M 9 subtypes and 51 circulating recombinant forms (CRF) were inferred from our alignments and compared to the HIV-1 consensus-of-consensuses sequence provided by GenBank.In this descriptive research, we examine the effect of HIV-1 variants on CS conservation using all 9,028 p51, RTp51/RTp66, P24/P2 and RTp66/IN and the least P2/P7 and P6pol/PR. Conservation was significantly lower in subtypes vs. recombinants in P2/P7 and TFP/P6pol and higher in P17/P24. We found a significantly higher conservation rate among Group M vs. non-M Groups HIV-1. The late processing sites at Gag (P7/P1) and GagPol precursors (PR/RTp51) presented a significantly higher conservation vs. the first CS (P2/P7) in the 4 HIV-1 groups. Here we show 52 highly conserved residues across HIV-1 variants in 11 CS and the amino acid consensus sequence in each HIV-1 group and HIV-1 group M variant for each 11 CS.In all HIV-1 variants, the most conserved CS were PR/RTThis is the first study to describe the CS conservation level across all HIV-1 variants and 11 sites in one of the largest available sequence HIV-1 dataset. These results could help other researchers for the future design of both novel antiretroviral agents acting as maturation inhibitors as well as for vaccine targeting CS. They coordinate viral trafficking, membrane binding, assembly, cofactor packaging, budding, and viral modulation. Gag proteins are generated through viral maturation, essential in the viral life cycle by enabling the generation of mature infectious viral particles through the proteolytic process in specific cleavage sites (CS) of Gag precursor -designated by a number and the genetic subtypes present in their genome- and multiple unique recombinant forms (URF), widely spread throughout the world and with different recombination breakpoints from those found in CRFs. At least 20% of the 34 million infected humans have an inter-subtype URF or CRF Whether or not the processing regulation is different across HIV-1 variants remains unclear. It is well known that HIV-1 shows a high genetic diversity due to its high replication rate, the error-prone RT and the recombination events between HIV-1 variants occurring during the viral replication after co-infection and/or superinfection events Despite the high biological relevance of CS during HIV-1 maturation and the importance of the knowledge of CS conservation for the design of both novel antiretroviral agents acting as maturation inhibitors as well as for vaccine targeting CS in future, scarce data of HIV-1 variant-associated CS variability is available. Previous reports only analyzed a limited number of HIV-1 variants and site sequences gag/pol sequences were retrieved from GenBank, (http://www.ncbi.nlm.nih.gov/). The 12,934 gag/pol sequences comprised 2,844 nucleotides, located from 790 to 2,292 in gag and from 2,253 to 5,096 in pol encoding the proteins shown in gag/pol nucleotides sequences were retrieved in FASTA format, including the subtype B HXB2 reference sequence. The MEGA program version 5.05 (http://www.megasoftware.net/) All the available HIV-1 gag, P7/TFP, TFP/P6pol, P6pol/PR, PR/RTp51, RTp51/RTp66 and RTp66/IN according to HXB2 sequence.After performing the alignments, we determined the residues and their location in Gag and Pol proteins Table 1,http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html). The HIV-1 Group M variants with inferred consensus sequences in GenBank are indicated in http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html#consensus. Using our amino acid alignment, composed of 12,934 sequences, we determined new consensus sequences for each HIV-1 group and each Group M subtype, CRF and URF in the 11 CS . Significance was set at p<0.05.A total of 9,028 Gag and 3,906 Pol HIV-1 sequences were downloaded from GenBank database. They included 43/43 Gag/Pol sequences from 3 HIV-1 Groups and 8,985/3,863 Gag/Pol sequences from Group M. gag and 15.4% pol sequences. Among subtypes, sequences from subtype B were the most represented in both gag/pol (43%/74.3%) coding regions, followed by sequences ascribed to subtype C (27.4%/16.7%), sub-subtype A1 (21.6%/4.3%) and subtype D (5.6%/1.9%). There were no gag sequences from sub-subtype F2 and subtypes J and K available in our dataset. Within the recombinants, family 01 (69.7%/44.4%) was the most represented, followed by families BC (7.2%), AG (5.9%), cpx (5.6%) and BF (4.5%) in gag and by families AG (16.8%), cpx (12.5%), BF , and BG (4.3%) in pol, among others. URF sequences represented less than 0.3% of downloaded sequences (12 gag and 11 pol sequences).In order to simplify the analysis, we grouped all the sequences from the 51 CRFs in 12 different CRF families according to a similar recombination pattern Figure 2gag and pol available in GenBank, which carries the most frequent residue, either nucleotide or amino acid, at each position in a multiple sequence alignment. gag/24 pol individual consensus sequences, corresponding to 8/7 subtypes among 9 in Group M and to 11/10 CRF within the 58 described .Since and p51 presented the highest number of highly conserved residues (9/10), followed by RTp51/RTp66 and P24/P2 (7/10), RTp66/IN (6/10), P7/P1 and P7/TFP (5/10), P1/P6gag and P6pol/PR (4/10), P17/P24 (3/10) and TFP/P6pol and P2/P7 (1/10).Interestingly, we identified 52/110 (47.3%) amino acids conserved in more than 99% of the 9,028 Gag and 3,906 Pol HIV-1 sequences with respect to the consensus-of-consensuses sequence and these are marked in black in We evaluated the percentage of conserved residues in the retrieved sequences for each HIV-1 variant and site with respect to the GenBank consensus-of-consensuses amino acid sequence, as explained in Methods. We established a color code to indicate the different levels of conservation, and the exact amino acid conservation rate in each CS and variant Figure 5p51, 99%), CS10 , CS2 , CS11 , CS1 , CS4 and CS6 . The least conserved CS across HIV-1 groups, Group M subtypes and recombinants were CS3 , CS8 , CS7 and CS5 . CS8 and CS3 showed different lengths across variants (data not shown). We observed a significantly higher conservation at the last processing sites in Gag and GagPol precursors compared to the first processing site in the 4 HIV-1 groups showed more than 90% of conserved residues regarding consensus-of-consensuses amino acid sequence in the 4 HIV-1 groups. Comparing M and non-M Groups, we observed higher conservation in CS9 and in CS10 . However, CS7 (TFP/P6pol) presented the poorest conservation rate across non-M Groups (41%), followed by CS5 , CS3 , CS8 and CS1 . Group O showed the lowest conservation in 6 of the 11 CS , Group N in CS1 and CS7 and Group P in CS3, CS5, CS9 and CS10 , probably due to the use of group M consensus for comparison.We observed differences in the CS conservation rate across HIV-1 groups and sites Figure 5gag) in sub-subtype A1 (76%) and recombinant family AU (73%); CS6 (P7/TFP) in subtype G (84%) and recombinant family BG (88%); CS7 (TFP/P6pol) in subtype B (77%) and recombinant families AB and BC (both 75%); CS8 (P6pol/PR) in sub-subtype A2 and subtype C (both 68%) and recombinant family BG (67%); CS9 (PR/RTp51) sub-subtype A2 (90%) and recombinant family A1 (95%); CS10 (RTp51/RTp66) in clades H (88%) and G (89%) and recombinant family A1 (90%); and CS11 (RTp66/IN) in sub-subtype F1 (90%) and recombinant family BF (91%). Thus, subtype G showed the highest variability in CS3, CS4 and CS6 and subtype B in CS7 compared to other Group M subtypes.Seven sites were well conserved within the total HIV-1 Group M subtypes and recombinants, showing more than 90% conservation Figure 5vs. recombinants in CS3 and in CS7 and higher in CS1 .The recombinant families DF, BG, A1 and BF showed the highest variability in CS3 Figure 5vs. 98%, p<0.001), in CS3 and in CS9 , significantly higher conservation in CS5 and the conservation was of great significance in CS11 . Sub-subtype F2 showed superior conservation compared to sub-subtype F1 in CS11 , although the number of available F2 sequences was very low with respect to the rest of groups (43/43 gag/pol sequences) or certain subtypes , sub-subtypes (F2) or CRF, available data permitted the establishment of a comparison among conservation rates at CS and we were able to define specific-variant differences at each CS consensus sequence for each HIV-1 group, subtype, CRF and URF would suggest a higher requirement of structural constrains in the last steps of viral processing. Although the aim of our study is purely descriptive, we strongly believe that it can serve as a working tool for research into the better understanding of the CS structure required for a correct cleavage efficacy across HIV-1 variants and for the design of maturation inhibitors and vaccines targeting CS. Understanding HIV-1 gag and pol co-evolution Our study reveals which can be the most important CS amino acid sequence for maintaining viral processing by PR and the level of tolerance to amino acid change in each HIV-1 variant. Moreover, the significantly higher conservation observed comparing the late gag in antiretroviral resistance and in the development of future maturation inhibitors It has been suggested that sequences around the CS in Gag are equally conserved as functional motives and sequences targeted by RT inhibitors and are more conserved than non-functional motives gag structure-function relationships, among others. Our descriptive research could help other researchers in the design of both novel antiretroviral agents acting as maturation inhibitors and for vaccine targeting CS. The biological significance of HIV-1 variant-associated variability found in each processing site in our study needs further future investigation.This descriptive study firstly determines the CS conservation degree across most HIV-1 variants and sites in a large dataset composed of 12,934 sequences, inferring the consensus sequences at amino acid level in 11 CS in all Group M subtypes and most CRF and URF, as well as in Groups O, N and P. Our results provide new findings that can help for a better understanding of viral evolution, Gag and GagPol precursors\u2019 processing and Table S1HIV-1 variants showing differences with the CS consensus-of-consensuses sequence inferred by GenBank.(DOC)Click here for additional data file."} +{"text": "Heart transplantation is the therapy of choice for advance heart failure. Our group developed two transplant programs at Instituto Nacional del Torax and Clinica Davila. We report our clinical experience based with generic immunosuppression with may have lower costs and may allow more patients to be transplanted.Fifty-three consecutive patients were transplanted between November 2008 and April 2013, representing 51% of all Chilean cases.Ischemic or dilated cardiomyopathy were the main indications (23(43%) each), age 48+13 years and 48(91%) were male. Transplant listing Status: IA 14(26%)(VAD or 2 inotropes), IB 14(26%)(1 inotrope) and II 25 (47%) (no inotrope). Mean waiting time 70+83 days. Twelve (24%) were transplanted during VAD support (median support: 36 days). Operative technique: orthotopic bicaval transplant with ischemia time: 175+54 min. Operative mortality: 3 (6%), all due to right ventricular failure. Re-exploration for bleeding 2 (4%), stroke 3(6%), mediastinitis 0(0%), pneumonia 4(8%), and transient dialysis 6 (11%). Mean follow-up was 21+14 months. Three-year survival was 86+6%. One patient died of Pneumocystis Jirovecii pneumonia and the other died suddenly (non-compliance). Freedom from rejection requiring specific therapy was 80+7% at 3 years of follow-up. Four hundred eighty four endomyocardial biopsies were done: 11(2.3%) had 2R rejection. All survivors are in NYHA (New York Heart Association) functional class I and all but one has normal biventricular function.Mid-term results are similar to those reported by the registry of the International Society for Heart and Lung Transplantation. Rejection rates are low in spite of generic immunosuppression."} +{"text": "The present study is conducted to find the prevalence of Allergic Rhinitis (AR) and its associated co-morbidity in school going children in urban area of Jaipur City, Rajasthan.A questionnaire based survey was conducted during November-December 2011 in 2300 school children (4-18 yr). Modified ARIA questionnaire translated in Hindi language containing 20 questions was used. Questions 1-4 were AR defining symptoms, question 5 related to classification (intermittent Vs persistent), questions 6 related to allergens and conditions inducing or aggravating symptoms and question 7-20 were related to co morbidities and family history. We screened questionnaires and those who answered yes to any AR defining symptoms were shortlisted. Children having two or more rhinitis symptoms in association with minimum 2 identifiable triggers were considered to have allergic rhinitis. Detailed history and physical examination was done by team consisting a pediatrician and ENT specialist in cases wherever diagnosis was in doubt.Out of 2300 questionnaire forms distributed, 1693 were returned (response rate 73.60%) and 1572 forms were adequately filled (92.85%). Prevalence of AR in different age groups was as follows: 4-8 years 33.87% (167/493), 8-12years 34.87% (143/410) and in 12-18 years 32.43 % (217/669) with an overall prevalence 33.52% (527/1572). Male: Female of the cohort was 1.9:1. Nasal obstruction was the most frequent symptom followed by running nose , sneezing and nasal itching . Of these 527 children with AR 35.67% (188/527) children had intermittent symptoms while 64.33% (339/527) had persistent rhinitis. Majority of the children with AR had one or more co-morbidity while 116 (22.01%) had 2 or more co \u2013morbidities and only 221 children (41.93%) children had AR without any co morbidity. The prevalence of different co morbidities was as follows: Adenoids 119 (22.5%), asthma 101 (19.16%), recurrent or chronic otitis media 125 (23.71%), sleep disturbances in 48 (9.1%), conjunctivitis 41 (7.78%) and laryngitis in 06 (1.13%).A high prevalence of AR and its co morbidities was observed in school children as compared to previous reports from this area."} +{"text": "Chest wall tumors are a heterogenous group of lesions that provide an interactive therapeutic and reconstructive challenge for surgeons.To show our experience in chest wall surgery today which calls for complete resection of chest wall tumor, reconstruction of the thoracic defect with semirigid wire and covered by soft tissue.Retrospective study from 1986 to 2012 (26 years) at The Division of Thoracic and Cardiovascular Surgery Dr. Soetomo Hospital Hospital Surabaya, reporting 101 cases of chest wall tumor excision and chest wall reconstruction using Tahalele\u2019s method.64 patients with primary neoplasm (63.37 %) and 37 patients with secondary tumor (36.63%). There were 30 patients (29.70%) with benign tumor and 71 patients (70.29%) with malignant tumor. Primary tumor consist of chondroma , osteoma , benign toratoma , chondro sarcoma , osteo sarcoma , soft tissue sarcoma , Ewing sarcoma , rhabdomyosarcoma . Metastatic tumor consist of metastatic breast cancer in 22 patients (21.78%), metastatic malignant teratoma in 2 patients (1.98%), matastatic thyroid cancer in 13 patients (12.87%). In the follow-up four years after the operation, no operative mortality. Hospital mortality in 2 patient (1.98%). Local recurrence in 4 patient (3.96%). Five patients with partial flap necrosis (4.95%). No flail chest complication (0 %). Infection rate after operation 3 patient (2.97%). Average LOS after the operation 7-21 days. Loss of follow-up were 58 patients (57.43%), and 52 patients survive (51.48%).All the patients were satisfied with this method, complete resection of chest wall tumor, reconstruction of chest wall defect with semirigid wire and covered by soft tissue Chest physiotherapy before operation play a significant rule."} +{"text": "Eosinophilic oesophagitis has been described in patients from all ethnic backgrounds in studies originating in all continents apart from Africa.A cohort of 8 patients identified at Red Cross Hospital during 2009-2010 is described. Average age 7 years (1yr 11 months to 15 years 10 months). Ethnicity 2 caucasian, 5 mixed, 1 Black African. Age of onset: mean 3 years, median 1 year 4 months. Age of diagnosis mean 6years 3 months, median 3 years 9 months.Time to diagnosis: mean 3 years 3 months, median 6 months, IQ range 5 months to 6 years.Presenting symptoms in order of prevalence are reflux (7/8), long time to eat (6/8), difficult swallowing (6/8), growth failure (5/8), food refusal (5/8) and painful swallowing (4/8).Associated atopic diseases comprised immediate food allergy (6/8), eczema (6/8), rhinitis (6/8), asthma (3/8) and urticaria (2/8).Total of 26 biopsy specimens, mean 3.25 per patient. Only 4/8 confirmed peak eosinophil count >15/hpf, 7/8 had minor features present.Food skin prick tests 152 (19 per patient). Positive skin tests >=1mm 57 (13 per patient). The most commonly identified foods are peas, wheat, milk, egg white, banana and egg yolk.Skin tests >=3mm 32 (7 per patient). Most commonly identified foods by SPT >3mm are egg yolk, egg white, peas, soya, rye, rice, carrot and green beans.Patch tests 167 (21 per patient). 30 positive, average of 4.3 per patient. Most commonly identified foods are beef, peanut, lamb, chicken, soy and ham.All commenced on initiation of short course of oral steroids. All put on targeted elimination diet. All had clinical improvement. 3 controlled and acceptable symptoms, 2 some symptoms and difficulties, 2 very symptomatic with poor control, 1 defaulted."} +{"text": "Childhood osteoporosis can be treated with intravenous bisphosphonates in order to improve bone mass and density. The aims of this study were to evaluatethe safety and efficacy of six-monthly zoledronic acid (ZA) in children with osteoporosis.A retrospective cohort study of 27 patients weretreated with six-monthly ZA (0.05mg/kg/dose) for a minimum of one year.17 patients were immobile, 4 had steroid-induced osteoporosis, 2 had osteogenesis imperfecta and 4 had other diagnoses. 16/27 (59%) had long bone fractures and 12/27 (44.4%) had vertebral wedging at baseline. Mineral homeostasis, bone mineral density by DXA and vertebral morphometry were evaluated at baseline and 1year.The median age at commencement of treatment was 12.3 years (range 8-15.8). Following the first infusion, 2/27 (7%) and 1/27 (4%) developed asymptomatic hypocalcemia at 48 hours and 72 hours, respectively.A fever above 38\u00b0C developed in 14/27 (52%), generalised aches/pains in 13/27 (48%) and nausea in 6/27 (22%).At 1year there was a significant reduction in bone turnover and improvement in bone mineral density (BMD) (see Table Six monthly ZA was associated with an acute phase reaction to the first dose and improvement in BMD, reduction in bone turnover and improved vertebral shape at 1 year."} +{"text": "Hyperplastic polyposis syndrome (HPS) is a colorectal cancer (CRC) predisposition of unknown genetic aetiology that is characterised by the presence of multiple serrated polyps throughout the colon, and an increased risk of having a first-degree relative with CRC -3. ThougKRAS codon 12 and 13 and BRAF V600E somatic mutations.A total of 151 patients diagnosed with at least 5 serrated polyps outside the rectum were recruited from high-risk genetics clinics. Polyp counts were extracted from colonoscopy reports. Polyps, including contiguous polyps, and CRCs underwent pathology review and testing for BRAF V600E mutation. Somatic KRAS mutations were less frequent at 9/48 (19%). Contiguous polyp was seen in 16/53 (30%) evaluable CRCs, and of these 4 (25%) were tubular adenomas, 5 (31%) were tubulo-villous adenomas and 1 (6%) was a villous adenoma. Overall 10/16 (63%) showed conventional adenomatous morphology whereas 6/16 (37%) had serrated morphology. BRAF mutation was present in 5/16 (31%). CRC was present in more than one-third of clinic-based individuals who presented with multiple serrated polyps.CRC was identified in 56 patients (37%) with 31/56 (55%) being females. The mean polyp count in patients with CRC was 58, and their mean age was 52 years. A total of 65 CRCs were available for analysis. Where site was known, most CRCs 43/61 (71%) arose in the proximal colon; however, only 19/58 (33%) of CRCs demonstrated a BRAF V600E mutation, the molecular hallmark of the serrated neoplasia pathway, suggesting that though multiple serrated polyps act as a marker of an abnormal mucosa, the majority of CRC in these patients may arise through other mechanisms.Despite a high serrated polyp count, only one-third of these CRCs demonstrated a"} +{"text": "Breast phyllodes tumors are rare neoplasms which present challenges for histological classification. Microscopic features are not always predictive of clinical behavior, and scarce data exist on the prognostic role of biological markers. Our study evaluated a series of 145 phyllodes tumors diagnosed at the Department of Pathology, Singapore General Hospital between 2006 and 2009, incorporating 91 (62.8%) benign, 40 (27.6%) borderline, and 14 (9.7%) malignant phyllodes tumors.Antibodies to keratin 15 (KRT15), transcobalamin I (TCN1), and homeobox gene Hox-B13 (HOXB13) were applied to sections cut from tissue microarray blocks. KRT15 and TCN1 positivity was defined when there was reactivity of 1% or more stromal cells, while HOXB13 positivity was defined using a H-score of 100 and above.Positive immunohistochemical expression for KRT15, TCN1, and HOXB13 was seen in 21 (14.5%), 96 (66.2%), and 66 (45.5%) of tumors, respectively. Stromal expression of KRT15, TCN1, and HOXB13 was significantly correlated with tumor grade , stromal hypercellularity , mitotic activity (P<0.001), and microscopic borders .Co-expression of TCN1 and HOXB13 was seen in 21 of 91 (23.1%) benign, 18 of 40 (45.0%) borderline, and 11 of 14 (78.6%) malignant tumors, suggesting that the dual-marker panels of TCN1 and HOXB13 might be helpful in classifying borderline and malignant tumors. Although expression of TCN1 alone was present in all malignant and 34 of 40 (85.0%) borderline tumors, a combined panel with HOXB13 excluded some benign cases and was a better discriminant for a significant proportion of borderline and malignant tumors."} +{"text": "The purpose of the study was to record the incidence, the etiology and management of acute desaturation (AD) in intubated critically ill ICU patients.2 (> 3%) in combination with clinical signs of respiratory distress requiring medical intervention. Etiology of AD was investigated by clinical evaluation, ABG analysis and chest X-ray. Numerical data are presented as mean (SEM) or median.We collected demographics of the patients developing AD defined as a documented fall in SaO2 was 5%, in PaO2 44 mmHg and in PaO2/FiO2 113. Eight episodes developed while on T-piece due to atelectasis/secretion retension (6) or respiratory muscle fatigue (2). The remaining episodes developed in patients under sedation: atelectasis/secretion retention (10), pulmonary edema (6), fever/SIRS (5), occlusion/displacement of endotracheal tube (5), patient-ventilator asychrony (4), bronchospasm (2), patient transfer (1) and pneumothorax (1). Management included FiO2 increase (53.5%), physiotherapy/bronchial toilet/patient poisoning (39.5%), change in ventilator mode (23.3%), PEEP increase (23.3%), drugs , change in respiratory rate (11.6%), use of Ambu bag (4.6%), reintubation (2.3%), insertion of chest tube (2.3%) and other measures (11.6%). Most patients required at least two interventions. Patients developing AD had significantly higher (P < 0.05) SAPS II (median 54 vs. 42), SOFA (9 vs. 6) scores and ICU stay (41 vs. 8). None of the episodes had fatal outcome. Most common hours for developing AD were 07.00, 14.00 and 23.00.We included 57 patients (37 men) admitted to our ICU within 6 months of mean age 54.4 (2.7) and mean ICU stay of 25.9 (5.7) days. We recorded 42 episodes of AD in 19 patients (33%). Mean age was 51.4 (3.8), mean ICU stay 51.1 (15.3) days and illness severity APACHE II 20.8 (1.6), SAPS II 52.2 (3.3) and SOFA 9.2 (0.8). The incidence was one episode per 30 ventilator-days or one every 4.3 days, corresponding to 2.3 (1.1) episodes per patient. Mean fall in SaOAD is a common medical emergency condition requiring prompt interventions. One over three patients developed at least two episodes of AD corresponding to one episode per 4.3 days. The most common etiology is atelectasis and secretion retention."} +{"text": "The goal of this study was to identify mutations in 25 known causative genes in 47 unrelated Chinese families with cone-rod dystrophy (CORD).Forty-seven probands from unrelated families with CORD were recruited. Genomic DNA prepared from leukocytes was analyzed by whole exome sequencing. Variants in the 25 genes were selected and then validated by Sanger sequencing.CNGB3 (three families), PDE6C (two families), ABCA4 (one family), RPGRIP1 (one family), RPGR (two families), and CACNA1F (one family).Fourteen potential pathogenic mutations, including nine novel and five known, were identified in 10 of the 47 families (21.28%). Homozygous, compound heterozygous, and hemizygous mutations were detected in three, four, or three families, respectively. The 14 mutations in the 10 families were distributed among This study provides a brief view on mutation spectrum of the 25 genes in a Chinese cohort with CORD. Identification of novel mutations enriched our understanding of variations in these genes and their associated phenotypes. To our knowledge, this is the first systemic exome-sequencing analysis of all of the 25 CORD-associated genes. Cone-rod dystrophy (CORD) refers to a series of hereditary retinal disorders with a predominantly cone involvement AIPL1) CRX) ; guanylate cyclase activator 1A (GUCA1A) ; guanylate cyclase 2D (GUCY2D) ; PITPNM family member 3 (PITPNM3) ; prominin 1 (PROM1) ; peripherin 2 (PRPH2) ; regulating synaptic membrane exocytosis 1 (RIMS1) ; sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A (SEMA4A) ; unc-119 homolog (UNC119) ABCA4) ; ADAM metallopeptidase domain 9 (ADAM9) ; chromosome 8 open-reading frame 37 (C8ORF37) ; calcium channel voltage-dependent alpha 2/delta subunit 4 (CACNA2D4) ; cadherin-related family member 1 (CDHR1) ; ceramide kinase-like (CERKL) ; cyclic nucleotide gated channel beta 3 (CNGB3) ; cyclin M4 (CNNM4) KCNV2) ; phosphodiesterase 6C, cGMP-specific, cone, alpha prime (PDE6C) ; retina and anterior neural fold homeobox 2 (RAX2) ; retinol dehydrogenase 5 (RDH5) ; retinitis pigmentosa GTPase regulator interacting protein 1 (RPGRIP1) CACNA1F) ; and retinitis pigmentosa GTPase regulator (RPGR) https://sph.uth.edu/Retnet/). Of the 25 genes, mutations in the first 10 genes are responsible for adCORD, the next 13 for arCORD, and the last two for xlCORD. The associated genomic information of the 25 genes is listed in CORD may be transmitted as an autosomal dominant (adCORD), autosomal recessive (arCORD), or X-linked trait (xlCORD). To date, mutations in at least 25 genes have been reported to be associated with different forms of CORD, including the following: aryl hydrocarbon receptor interacting protein-like 1 as well as of all exons harboring reported mutations in other 17 CORD-associated genes In our previous study on CORD, mutations were only detected in 7 of 130 (5.38%) Chinese families with CORD by using cycle sequencing of all coding exons of five genes by the Ministry of Public Health of China. This study was approved by the Institute Review Board of the Zhongshan Ophthalmic Center. Genomic DNA was prepared from the blood leukocytes as previous described http://www.genomics.cn/index.php). The exome sequencing, genotype calling, and SNP calling were in the same way as the methods reported before http://www.ncbi.nlm.nih.gov/biosample: accession number SAMN01997562 to SAMN01997571).Exome sequencing was completed by using a commercial service from BGI Shenzhen (http://frodo.wi.mit.edu/primer3/) http://www.hgvs.org/mutnomen/). The conservation of a variation was evaluated by Phastcons_score (http://varianttools.sourceforge.net/Annotation/PhastCons) http://sift.jcvi.org/) and Polyphen-2 http://genetics.bwh.harvard.edu/pph2/) online tools, and the effect of splicing site changes was predicted by Berkeley Drosophila Genome Project (BDGP) http://www.fruitfly.org/).Sanger sequencing was used to validate variants in the 25 genes that resulted from exome sequencing, including heterozygous variants in the adCORD genes, homozygous or compound heterozygous variants in the arCORD genes, or hemizygous variants in the xlCORD genes. Primers used to Considering that CORD-causing mutations are rare and the presence of the normal carriers of arCORD gene mutations, we assumed that the affected individuals were likely homozygous or compound heterozygous, so variants absent in the dbSNP134, 1000Genome or with allelic frequencies \u22640.006 were considered to be potentially pathogenic of the 13 genes associated with arCORD, and three hemizygous mutations in the two genes (RPGR and CACNA1F) associated with xlCORD. Of the 14 mutations, nine were novel. The 14 mutations in the 10 families involved six of the 25 CORD-associated genes, including CNGB3 (three families), PDE4C (two families), RPGR (two families), ABCA4 (one family), RPGRIP1 (one family), and CACNA1F (one family) families with CORD , includi family) , respect family) . Segrega family) . No poteClinical data of the 10 probands with potential pathogenic mutations are listed in CNGB3 (6.38%), PDE6C (4.26%), RPGR (4.26%), ABCA4 (2.13%), RPGRIP1 (2.13%), and CACNA1F (2.13%).Based on an initial screening of exome sequencing and the subsequent confirmation of Sanger sequencing, potential pathogenic mutations were identified in 10 of the 47 (21.28%) families with CORD, involving 14 mutations in six of the 25 CORD-associated genes. For the 47 families in this study, the contributions of causative mutations in individual genes are as follows: The frequency of mutations detected in this study is significantly higher than in our previous study, in which mutations were only detected in seven of 130 (5.38%) Chinese families with CORD through the process of sequencing the coding exons of five genes and all exons with reported mutations in 17 other genes GUCY2D (24%), PRPH2 (12%), GUCA1A (8%), CRX (4%), and PROM1 (2%) CRX are responsible for a 4.76% proportion of CORD GUCY2D for 11.11% of CORD in a Japanese population GUCA1A for 16.67% of CORD in a German one PRPH2 for 11% of CORD in another German population AIPL1 for 1.82% of CORD in an American sample PROM1 for 0.93% of CORD in a Dutch population SEMA4A for 8.00% of CORD in a Pakistani group UNC119 for 5.00% of CORD in another American population Previously studies on an individual gene or a set of genes have revealed a different frequency of mutation in CORD-associated genes in different populations. Sanger sequencing of 10 adCORD-associated genes identified mutations in 25 of 52 (48%) German families with adCORD, and mutations were found in PDE6CPRGRIP1RAX2 in 0.62% of CORD CERKL in 1.85% of Canadian CORD ADAM9RDH5CDHR1C8ORF37For genes known to be associated with arCORD, their mutations might be responsible for nearly 40% of arCORD Figure S1Sequence chromatography. Forteen sequence changes detected in the probands with CORD are shown (left column) compared with corresponding normal sequences (right column). Some known mutations were not verified in the normal controls, so the normal sequences are absent.(TIF)Click here for additional data file.Table S1Genomic information of the 25 genes referred in this study. This table listed the accession numbers of the genomic DNA, mRNA, and protein for each of the 25 genes. The information is based on human genome reference GRCh37.p10.(XLS)Click here for additional data file.Table S2Sequences of primers used in this study. This table listed 52 primers used to amplify the genomic fragments with variants detected by exome sequencing.(XLS)Click here for additional data file."} +{"text": "Assays that detect anti-citrullinated peptides antibodies (ACPA) are considered to be more specific than rheumatoid factor in the diagnosis of rheumatoid arthritis (RA). Several tests have been developed using different antigens: first, second and third-generation cyclic-ACPA and modified citrullinated vimentin (MCV).To investigate anti-CCP3 in a group of patients positive citrullinated vimentin antibodies (MCVA).A total of 259 patients positive for IgG MCVA+ attending the outpatient rheumatology clinic of a single general hospital (HUGTiP) were tested for anti-CCP3 (by ELISA). From the total, 182 (70.3%) of them had a rheumatic disease (RD): RA in 121 (66.5%) and other RDs in 61 (33.5%). 77 (29.7%) patients with other conditions positive for MCVA were also tested for anti-CCP3.From the 121 RA patients, 106 (87.6%) were positive for anti-CCP3. In contrast, only 15 (24.6%) of the 61 patients without RA and only 4 (5.2%) of the 77 MCVA+ patients with no RD associated were CCP3 positive. Interestingly, within the group no RA, of the 13 patients with anti-CCP3 values >60 U/ml, 6 (46.2%) were cases of palindromic rheumatism and two of them had developed RA. Specificity of anti-CCP3 for RA as compared to other RDs was 76.7%, that raised to 86.9% when comparing RA versus to non-RA (with or without another RDs). Positive and negative predictive values of anti-CCP3 for RA were 85.5% and 88.8%, respectively whereas PPV for anti-MCV was 39.1%.Anti-CCP3 antibodies show a higher specificity for RA when compared to MCVA with a better PPV, a crucial feature for a test in use for clinical practice."} +{"text": "Post exposure prophylaxis (PEP) with antiretroviral therapy (ART) aids in preventing HIV infection from accidental or occupational exposure. Hospital staff should be vaccinated against HBV to protect them in the event of accidental exposure to blood and body fluids.To ascertain adherence and completion of PEP among staff at a regional referral hospital in W. Kenya.We reviewed staff PEP registers at a Regional Referral hospital in Western Kenya between January 2011 and December 2012. National PEP guidelines recommend ART initiation within 72 hours of exposure, use of ART for28 days post-exposure and HIV re-testing at1.5, 3 and 6 months following ART initiation. A high-risk exposure occurs when a source is HIV-positive with injury on a mucosal membrane by needleprick, cut or splash. The risk of HBV infection increases if the exposed is not HBV-vaccinated and source of exposure is HBV-positive. Chi Square statistics were used to determine factors associated with PEP completion.Of 52 hospital staff who initiated PEP; 33 were health workers (63%), 3 support staff (6%), 14 students (27%), and 2 unknown cadres (4%). Half were female (n=27); 29 from in-patient units (56%) and 30 had high-risk exposures (58%).Of the staff with documented timing of both HIV exposure and ART initiation (n=47), ART was initiated within the recommended time. Half of all staff (n=27) completed PEP. Reasons for non-completion were side effects (n=2), referral (n=1) and unknown (n=23). PEP completion did not vary by gender (p=0.78), exposure-type (p=1.0) or exposure-unit (p=0.75).At 1.5, 3, and 6 months after ART initiation, HIV re-testing rates were 96%, 25%, 17%and negativity rates were 100%, 100%,75%, respectively.Only17% (n=9) of staff were HBV-vaccinated;94%(n=49) of sources had unknown HBV status. No intervention was documented HBV prevention.Despite timely PEP initiation, low rates of completion negate its intended benefits. Universal precaution-practices and PEP completion should be enforced; so should HBV staff-vaccination and testing for both staff and sources of exposure to tackle the low rates of HBV testing and vaccination.None declared"} +{"text": "Adenovirus serotype 5 (Ad5) utilizes coxsackievirus and adenovirus receptor (CAR) as its primary cellular receptor. However, the cellular receptor utilized by Ad26 and the inflammatory responses elicited following Ad26 vaccination remain unclear.11 viral particles (vp) of replication-competent Ad5 and Ad26 (N=6) or saline (N=6) at weeks -8 and -4, and were vaccinated intramuscularly with 3\u00d71010 vp replication-incompetent Ad26-Gag/Pol/Env vectors. At week 2, monkeys were sacrificed to assess immunologic and inflammatory responses at mucosal surfaces.Receptor usage was assessed using CD46 transgenic mouse cells, as well as by CAR- and CD46-specific mAb blocking studies using human PBMC. Twelve adult rhesus monkeys were inoculated with of 10+ T cell responses in both PBMC and colorectal biopsies. Inflammatory cell infiltrates in colorectal and foreskin mucosa were comparable in baseline and vaccinated animals regardless of baseline Ad5/Ad26 immunity.Transduction by Ad26 and Ad35 vectors was markedly enhanced in CD46 transgenic mouse cells compared with wild type mouse cells. Moreover, transduction of human PBMC by Ad26 and Ad35 vectors was efficiently blocked by the anti-CD46 mAbs 13/42, M177 and MEM-258, but not by the anti-CAR mAbs RmcB and E1-1. Monkeys with and without baseline Ad5/Ad26 immunity exhibited similar magnitude and only transient activation (1-2 weeks) of vector-specific CD4+ T lymphocytes in baseline Ad5/Ad26-seropositive monkeys as compared with baseline seronegative monkeys following Ad26 vaccination. These data contribute to our understanding of the biology of Ad26 as a candidate vaccine vector.Ad26 utilizes CD46 and not CAR as a primary cellular receptor for infection. We also observed no increased mucosal cellular activation or vector-specific CD4"} +{"text": "To determine the etiology of precocious puberty at tertiary care hospital and to compare the clinical and laboratory parameters of central and peripheral precocious puberty.Cross sectional study.Endocrine clinic at National Institute of child health, Karachi, Pakistan from January 2009 to December 2011.Children who fulfilled the criteria of precocious puberty were included. Precocious puberty defined as the development of secondary sexual characteristics before the age of 8 years in girls and 9 years in boys. All patients evaluated clinically and on laboratory investigations. Data was entered and analyzed using SPSS version 17.0. Independent sample t-test/ Mann-Whitney U-test were applied.Total numbers of patients registered during this period were 84.The conditions causing precocious puberty were central precocious puberty (36.5%), peripheral precocious puberty (38.8%), premature pubarche (10.6%) and premature thelarche (14.1%). In central precocious puberty 26 were female and 5 were male. The causes identified in them were idiopathic (67.74%), hypothalamic hamartoma (12.90%), craniopharagioma (9.67%), arachnoid cyst (3.22%), hypothalamic astrocytoma (3.2%), hydrocephalus (3.2%). In peripheral precocious puberty21 were male and 12 were female. Congenital adrenal hyperplasia (81.8%), adenocarcinoma (9.1%), ovarian teratoma (6.1%) and Mc Cune Albright syndrome (3%) were diagnosed in them. There was difference in the age of onset of puberty of central precocious puberty 3(2-6) versus peripheral precocious puberty 5.25(3.62-7.0). Central precocious puberty children showed higher height SDS, weight SDS, FSH, LH than peripheral precocious puberty.Peripheral precocious puberty is more common than central precocious puberty. Height SDS, weight SDS, FSH, LH was higher in central precocious puberty versus peripheral precocious puberty."} +{"text": "SLC25A13 gene encoding a mitochondrial aspartate/glutamate carrier isoform 2 (AGC2), can lead to AGC2 deficiency, resulting in NICCD and an adult-onset fatal disease namely citrullinemia type II (CTLN2). To study the prevalence of NICCD and SLC25A13 mutations in Thai infants, and to compare manifestations of NICCD and non-NICCD, infants with idiopathic cholestatic jaundice or INH were enrolled. Clinical and biochemical data were reviewed. Urine organic acid and plasma amino acids profiles were analyzed. PCR-sequencing of all 18 exons of SLC25A13 and gap PCR for the mutations IVS16ins3kb and Ex16+74_IVS17-32del516 were performed. mRNA were analyzed in selected cases with possible splicing error.The most common causes of cholestatic jaundice are biliary atresia and idiopathic neonatal hepatitis (INH). Specific disorders underlying INH, such as various infectious and metabolic causes, including neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) especially, in East Asian populations are increasingly being identified. Since most NICCD infants recovered from liver disease by 1 year of age, they often are misdiagnosed with INH, leading to difficulty in determining the true prevalence of NICCD. Mutation(s) of human p< 0.05). NICCD patients showed higher citrulline level and threonine/serine ratio than non-NICCD infants (p< 0.05). Fatty liver was found in 2 NICCD patients. Jaundice resolved in all NICCD and in 87.5% of non-NICCD infants at the median age of 9.5 and 4.0 months, respectively.Five out of 39 (12.8%) unrelated infants enrolled in the study were found to have NICCD, of which three had homozygous 851del4 (GTATdel) and two compound heterozygous 851del4/IVS16ins3kb and 851del4/1638ins23, respectively. Two missense mutations (p.M1? and p.R605Q) of unknown functional significance were identified. At the initial presentation, NICCD patients had higher levels of alkaline phosphatase (ALP) and alpha-fetoprotein (AFP) and lower level of alanine aminotransferase (ALT) than those in non-NICCD patients (NICCD should be considered in infants with idiopathic cholestasis. The preliminary estimated prevalence of NICCD was calculated to be 1/48,228 with carrier rate of 1/110 among Thai infants. However, this number may be underestimated and required further analysis with mutation screening in larger control population to establish the true prevalence of NICCD and AGC2 deficiency. Cholestatic jaundice affects approximately 1 in every 2,500 infants world-wide . INH couSLC25A13 gene (7q21.3) ) in Patients 1, 2, and 5, 851del4/IVS16ins3kb (or mutation [XIX]) in Patient 3 restriction digestion in the p.M1? allele . The p.M1? was present in only heterozygous state in 3 controls . None of the controls were found to have 851del4, IVS16ins3kb, 1638ins23, and the p.R605Q variant (creating a p<0.05) (Table The major presentations of five definite NICCD patients (Patients 1-5) were cholestatic jaundice and hepatomegaly. Median age at onset of cholestatic jaundice was 0.5 months (range 0.1-4.0) in NICCD patients and 1.0 month (range 0.5-5.0) in non-NICCD patients (Patients 8-39). Splenomegaly was initially found in 2 NICCD (40%) and 11 non-NICCD patients (34.4%). At presentation, NICCD patients had significantly higher alkaline phosphatase (ALP), lower ALT and higher alpha-fetoprotein (AFP) than in non-NICCD infants (Table Liver histology was available in 3 NICCD and 15 non-NICCD infants. Cholestasis and fatty changes were found in two NICCD patients (Patients 3 and 4). In addition, histologic features of cirrhosis were demonstrated in Patient-4. Patient-2 had marked cellular swelling, disarray of hepatic cords, cholestasis, multinucleated giant cell transformation, and decreased interlobular bile ducts. The major histological findings in non-NICCD infants were multinucleated giant cell transformation and features compatible with INH (n=9), paucity of interlobular bile duct (n=4), fatty changes and severe periportal fibrosis (n=1). The liver histologic findings of the 2 suspected NICCD patients were compatible with INH.The management of all the patients was directed toward treating the consequence of cholestasis, consisting of non-lactose and medium chain triglycerides formula and supplementation with fat-soluble vitamins. Jaundice resolved in all NICCD patients at the median age of 6.6 months (range 5-11) and liver biochemistry became normal in 4/5 NICCD patients (except patient 4) at the median age of 9.5 months (range 5-10). Patient 4 had the most severe manifestation in the NICCD group in this study. He had jaundice started at 1 month old, developmental delay due to unrecognized hypoglycemia till the age of 8 months when he was referred to our department. After 4 months of treatment, jaundice and hypoglycemia resolved and liver chemistry became near normal. At the time of this report, he is 38 month-old with appropriate growth and psychomotor development.Jaundice resolved in the two suspected NICCD cases, at the age of 5 and 9 months, respectively. Among the non-NICCD infants, 87.5% (28/32) had jaundice resolved at median age of 4 months (range 2-24). The remainder had progressive jaundice leading to cirrhosis; one patient underwent liver transplantation and has been well, and another patient died of complications of end-staged liver disease.SLC25A13 mutation-carrier among Thai infants calculated from the incidence of NICCD is predicted to be 1 in 110 . This number is lower than the frequency of SLC25A13 mutations carrier among Chinese (1/63), Japanese (1/65), and Korean (1/108) populations, respectively or Ex16+74_IVS17-32del516), gap PCR was performed by using long-range PCR and primers Ex16F and Ex18-3\u2032R, as previously described [SLC25A13 variants is assigned following the guidelines of the Human Genome Variation Society (http://www.hgvs.org/mutnomen) [PCR-sequencing of all 18 exons of the escribed . Positivutnomen) .SLC25A13 mutation(s) identified on both alleles were considered definite case of NICCD while those with pathogenic/unclear significant mutation identified on only one allele were considered suspected NICCD, and those known as nonpathogenic/silent or unidentifiable mutation were considered non-NICCD cases.Infants with pathogenic U test and Fisher's Exact test were used to compare continuous variables and dichotomous variables, respectively. A P-value of <0.05 was considered statistically significant.Data were analyzed using SPSS . Mann\u2013Whitney The authors declare that they have no competing interest.ST, SJ, PP, collected and analyzed clinical data, and wrote/edited the manuscript. DW, PS, SJ designed laboratory work and wrote/edited the manuscript. PK and DC performed laboratory work and edited the manuscript. KK advised the study design and editing the manuscript. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-230X/12/141/prepubPrimer sequence and molecular method.Click here for file"} +{"text": "Central nervous system infections in neurosurgical patients (pts) are a seriuos complication with high morbidity and mortality. We describe characteristics of patients and episodes, microorganisms and evolution of neurosurgical pts with meningitis (M) or ventriculitis (V) in one ICU in Uruguay.Retrospective analysis of neurosurgical pts with M or V in a ten year period (2000-2010). M and V was defined based in cerebrospinal fluid findings , lactate > 4 mM/L) and culture (definitive episodes). V required intraventricular procedure or device implantation.69 pts developed 77 episodes . Neurosurgical diseases were trauma (39%), meningeal hemorrhage (20%), intracerebral hemorrhage (17%), intracranial tumor (12%). Cerebrospinal fluid leakage was present in 25%, ventriculostomy in 35% (catheter permanence 6.2 days), subdural catheter in 30% (catheter permanence 4.2 days). Microorganisms were mainly Gram negative bacilli , Klebsiella sp , Ps aeruginosa , Proteus sp , Enterobacter sp , S aureus , S coagulase negative , Enterococcus sp , Candida sp ). Crude mortality was 29% (20/69).In a selected group of seriously ill and high risk neurosurgical patients M and V were mainly caused for Gram negative bacilli and had high mortality.None declared."} +{"text": "Partial liver grafting predisposes recipients to a unique set of potential technical and anatomic complications that are not prevalent in whole deceased donor grafts. We aimed to assess the preoperative Model for End-stage Liver Disease (MELD) score, postoperative 30-day clinical and laboratory follow-up, and detection of the value of MELD score in predicting 30-day postoperative outcome of LDLT recipients.A prospective multicenter registry involving 142 patients who underwent LDLT from October 2004 to December 2010. Preoperative MELD score was calculated: (0.378\u00d7log (bilirubin) (mg/dl) + 1.120\u00d7log (INR) + 0.957\u00d7log (creatinine) (mg/dl) + 0.643)\u00d710 then rounded to the nearest integer. Postoperative daily recording of all the clinical and laboratory data was done for a period of 30 days.The survival rate recorded in our study was 86.62%. The most frequent complications were renal complications (86.6%), pulmonary complications (73.9%), neurological complications (14%), cardiovascular complications (12.6%), infectious complications (13.3%), intra-abdominal infections (10.5%) and immunosuppressant toxicity (7.7%). MELD score proved to be a good predictor of perioperative outcome, patients with MELD score (>12) was associated with less favorable outcome, accuracy was (80.3%).MELD score >12 was associated with less favorable outcome with an accuracy of 80.3%."} +{"text": "Signaling did not increase in response to MIP-1\u03b2, suggesting that the Thr2.56(82) mutants were fully stabilized in active conformations. The Thr2.56(82)Lys mutation severely decreased cell surface CCR5 expression. Combining the Thr2.56(82)Lys mutation with an Arg6.32(225)Gln mutation partially reversed the decrease in expression. Mutants with Thr2.56(82)Lys substitutions were poor mediators of HIV envelope-directed membrane fusion, but mutants with the Thr2.65(82)Pro substitution exhibited full co-receptor function. Our results suggest that the Thr2.65(82)Lys and Thr2.65(82)Pro mutations stabilize distinct constitutively active CCR5 conformations. Lys in position 2.65(82) stabilizes activated receptor conformations that appear to be constitutively internalized and do not induce envelope-dependent membrane fusion, whereas Pro stabilizes activated conformations that are not constitutively internalized and fully mediate envelope-directed membrane fusion.The CCR5 chemokine receptor is a rhodopsin-like G protein-coupled receptor that mediates the effects of pro-inflammatory \u03b2-chemokines. CCR5 is also the major co-receptor for entry of human immunodeficiency virus (HIV) into human cells. G protein-coupled receptors exist in ensembles of active and inactive conformations. Active receptor conformations can be stabilized by mutations. Although binding of the HIV envelope protein to CCR5 stimulates cellular signaling, the CCR5 conformation that induces fusion of the viral membrane with cellular membranes is not known. We mutated conserved amino acids to generate constitutively active CCR5 receptors, which are stabilized in active conformations, and tested the ability of constitutively active CCR5 receptors to mediate HIV envelope-directed membrane fusion. Mutation of the Asp The CCR5 chemokine receptor is a G protein-coupled receptor (GPCR) that mediates leukocyte chemotaxis and recruitment to sites of inflammation in response to pro-inflammatory \u03b2-chemokines, including macrophage inflammatory protein 1\u03b2 GPCR proteins exist in ensembles of inactive conformations, which are stabilized by inverse agonists and do not support intracellular signaling, and active receptor conformations, which are stabilized by agonists and activate corresponding ensembles of cellular signaling pathways. Ligands may selectively stabilize ensembles of receptor conformations that activate subsets of cellular signaling pathways The structures of a small number of GPCR proteins have been determined in inverse agonist-bound inactive conformations 3.49 and Arg3.50 residues of the conserved DRY (Asp-Arg-Tyr) motif, in transmembrane segment (TMS) 3, stabilizes mutant receptors in activated conformations, which stimulate cellular signaling in the absence of agonist 2.56(82) and Pro2.58(84) residues of the conserved TxP motif, stabilized CCR5 mutants in inactive 6.32(225)Gln mutation causes partial constitutive activity in CCR5 Supporting the switch hypothesis, mutation of the AspThe CCR5 conformation(s) that induce the fusogenic changes in Env are not known. Binding of the gp120 subunit of Env to CCR5 stimulates intracellular signaling 3.49(125) and Arg6.32(225) did not increase constitutive activity. CCR5 mutants with Pro or Lys substituted for Thr2.56(82) showed high basal cellular signaling, which was not increased by stimulation with MIP-1\u03b2. The Thr2.56(82)Lys mutation decreased cell surface CCR5 protein, whereas the Thr2.56(82)Pro mutation did not. Constitutively active CCR5 receptors differed in their ability to mediate Env-directed membrane fusion. Our results suggest that Pro and Lys substitutions in position 2.56(82) stabilize distinct activated CCR5 conformations that differ in their localization at the cell surface and in their ability to induce HIV Env-dependent membrane fusion.We have investigated the ability of activated conformations of CCR5 to mediate Env-directed membrane fusion by mutating conserved \u201cswitch\u201d residues of the human CCR5 chemokine receptor. Mutation of Aspenv construct pTHr.gp150CT env, Du151 gp150, was subcloned into the pcDNA3.1(+) expression vector (Invitrogen). The HIV-1 tat (GenBank Accession number X07861) cloned into pcDNA3.1, HIV-1 rev (GenBank Accession No. M34378) cloned into pcDNA3.1/Hygro (Invitrogen) and the pHIV-1LTR-Luc reporter construct The chimeric G protein construct, G\u03b1qi, which allows receptors that usually activate the Gi/o family of G proteins to stimulate inositol phosphate (IP) signaling 125 residue in the conserved DRY motif of the CCR5 receptor is designated Asp3.49(125), because it immediately precedes the most conserved residue in TMS3, Arg3.50(126). Asp3.49(125) was mutated to Ala (Asp3.49(125)Ala) and Asn (Asp3.49(125)Asn), whereas the Thr2.56(82) residue in TMS2 of CCR5 was mutated to Pro (Thr2.56(82)Pro), Lys (Thr2.56(82)Lys) and Arg (Thr2.56(82)Arg) and Arg6.32(225), in the third intracellular loop, was mutated to Gln, Ala, Asp and Glu. The Arg6.32(225)Gln construct was used as the template for the double mutants, Thr2.56(82)Lys/Arg6.32(225)Gln and Thr2.56(82)Pro/Arg6.32(225)Gln. Mutant constructs were sequenced and subcloned into the pcDNA3.1(+) and pcDNA3.1/Hygro(+) expression vectors.Mutant CCR5 receptor constructs were generated by PCR using Deep Vent high fidelity DNA polymerase and the wild type human CCR5 chemokine receptor cDNA, cloned into the pcDNA3.1(+) expression vector , as template. The Ballesteros and Weinstein amino acid numbering system 2. HEK-Gqi cells were maintained in DMEM supplemented with FBS (10%) and G418 (200 \u00b5g/ml). HOS-CD4.pBABE-puro and HOS-CD4-CCR5 cells were maintained in DMEM supplemented with FBS (10%) and puromycin (1 \u00b5g/ml), whereas the same cell lines stably transfected with pHIV-1LTR-Luc to generate the cell lines, HOS-CD4-Luc and HOS-CD4-CCR5-Luc, were maintained with FBS, puromycin (1 \u00b5g/ml) and G418 (400 \u00b5g/ml).HEK 293 cells (ATCC) were maintained in Dulbecco\u2019s Modified Eagle\u2019s Medium containing fetal bovine serum and cultured at 37\u00b0C with 10% CO2 dishes in a final volume of 10 ml DMEM with FBS (10%) 24 h before transfection. DNA constructs (6 \u00b5g) were incubated with FuGene HD in serum-free DMEM and added directly to the 10 ml medium in the 10 cm dishes. Cells were incubated overnight . For stable transfections, selection antibiotics were added two days later and individual colonies of antibiotic-resistant cells were harvested and propagated. Attempts to stably transfect CCR5 constructs into HOS-CD4-Luc cells were unsuccessful. HOS-CD4-Luc cells transiently transfected with wild type and mutant CCR5 constructs were cultured in the presence of hygromycin B (200 \u00b5g/ml) for two days to increase the proportion of receptor-expressing cells and thus compensate for low transfection efficiency.Cells were plated into 10 cm6 per 10 cm dish), transfected with wild type or mutant CCR5 receptor constructs, were distributed into 12-well plates , incubated overnight and then incubated with 3[H]myo-inositol . The resulting radio-labeled cells were pre-incubated with buffer I and then incubated in duplicate with buffer I containing various concentrations of MIP-1\u03b2 , after which the medium was replaced with pre-cooled formic acid . The resulting cell lysates were applied to ion exchange columns and [3H]IP was eluted into vials containing scintillation fluid and counted. MIP-1\u03b2 concentrations that stimulated half-maximal IP production were calculated using GraphPad Prism software . Data are presented as means \u00b1 SEM and statistical significance was assessed using unpaired T-tests (GraphPad Prism).Basal and MIP-1\u03b2-stimulation of IP second messenger production was assessed as previously described 6/10 cm dish), transiently transfected with wild type or mutant CCR5 receptor constructs were detached , re-suspended (3\u00d7105 cells/tube) in binding buffer and incubated, in triplicate, with [125I]-MIP-1\u03b2 and increasing concentrations of unlabelled MIP-1\u03b2 (0 to 10\u22127 M) in a total volume of 0.2 ml , as previously described 2, 5 mM MgCl2 and 0.5 M NaCl) and radioactivity was counted in a \u03b3-counter. Total binding (B0) of [125I]-MIP-1\u03b2 to the receptor was determined in the absence of unlabeled ligand, whereas non-specific binding (NSB) was determined as the amount of radio-labeled ligand bound in the presence of 10\u22127 M unlabeled MIP-1\u03b2 or bound to untransfected cells. Specific binding of [125I]-MIP-1\u03b2 was calculated as the difference between B0 and NSB. Concentrations of MIP-1\u03b2 that displaced 50% of total specific [125I]-MIP-1\u03b2 binding were calculated using GraphPad Prism and nonlinear regression for one-site competition curves. Data are presented as means \u00b1 SEM and statistical analysis of pIC50 values was performed using unpaired two-tailed T-tests.MIP-1\u03b2 was radio-iodinated using the chloramine T method as previously described 2 dishes, suspended in 10 ml of phosphate-buffered saline containing BSA and centrifuged . The cell pellet was re-suspended in PBS-BSA (0.5 ml) and re-suspended cells (20 \u00b5l) were incubated with phycoerythrin-labeled 2D7 mouse anti-hCCR5 antibody in the dark. Samples were centrifuged , washed in PBS-BSA (1.5 ml) and re-suspended in PBS-BSA (500 \u00b5l) for FACS analysis using a FACScalibur flow cytometer . Untransfected HEK 293 cells stained with PE-2D7 were used as a negative control to set the gating threshold and the mean fluorescence of gated cells transfected with the wild type construct was defined as 100% for each experiment.HEK 293 or HOS-CD4-Luc cells transfected with wild type or mutant CCR5 constructs were detached from the 10 cmA cell fusion assay that models the interaction of the host cell receptors with the Env protein expressed on the membrane of the HIV-1 virion envrev and tat 24 h after transfection of HOS-CD4-Luc cells were layered at increasing densities (30 cells/well \u201348 000 cells/well in triplicate) onto transfected HOS-CD4-Luc cells and co-cultured overnight to allow cell fusion. Luciferase activity was determined using the luciferase assay system according to the manufacturer\u2019s instructions and a Veritas luminometer (Promega).HOS-CD4-Luc cells were transiently transfected with wild type or mutant CCR5 receptor cDNA cloned into the hygromycin resistant vector, pcDNA3.1/Hygro(+) (Invitrogen), cultured overnight and then cultured (48 h) in DMEM supplemented with FCS (10%), G418 (400 \u00b5g/ml) and hygromycin to select for transfected cells. Expression of CCR5 was assessed by FACS analysis and HOS-CD4-Luc cells expressing wild type or mutant CCR5 constructs were seeded into 96-well plates . HEK 293 cells transfected with Du151 gp150 \u22127 M, 2.56(82) residue displayed enhanced basal IP production compared with the wild type receptor (3.49(125)Ala and Asp3.49(125)Asn, displayed basal IP production that was similar to wild type levels, but displayed decreased IP production in response to MIP-1\u03b2 (6.32(225)Ala, Arg6.32(225)Asp and Arg6.32(225)Glu, displayed basal IP production that was comparable with wild type IP production and decreased MIP-1\u03b2-stimulated IP production and showed enhanced IP production in response to MIP-1\u03b2 10\u22127 M, , Table 1receptor , Table 1receptor , Table 1receptor and 2A, o MIP-1\u03b2 , Table 1oduction , Table 12.56(82)Pro mutant, which showed the highest basal IP production, exhibited mean fluorescence comparable with that of the wild type receptor (2.56(82)Lys mutant receptor, which also showed increased basal IP production, was poorly expressed, exhibiting low mean fluorescence Lys mutant receptor is highly constitutively active. The Thr2.56(82)Arg mutant receptor showed intermediate expression levels (3.49(125) to Ala decreased receptor expression, whereas mutation of Asp3.49(125) to Asn or mutation of Arg6.32(225) (Arg6.32(225)Asp, Arg6.32(225)Ala or Arg6.32(225)Glu) had less marked effects on expression of receptor protein Gln mutation, which previously yielded partial constitutive activity without decreasing receptor expression 2.56(82)Lys/Arg6.32(225)Gln double-mutant receptor produced basal IP levels 7.7-fold higher than the wild type receptor and the Thr2.56(82)Pro/Arg6.32(225)Gln mutant receptor displayed basal IP production 9.3-fold higher than that of the wild type receptor (2.56(82)Lys/Arg6.32(225)Gln double-mutant receptor was increased compared with the Thr2.56(82)Lys receptor Lys receptor showed specific binding that was too low for calculation of an IC50 value, consistent with poor expression of this mutant. In contrast, the double mutant, Thr2.56(82)Lys/Arg6.32(225)Gln, displayed total binding comparable to the wild type receptor with an IC50 value of 20.67\u00b14 nM (2.56(82)Pro and Thr2.56(82)Pro/Arg6.32(225)Gln, displayed total binding and affinity comparable to the wild type receptor with IC50 values of 31.9\u00b17.4 nM and 30.6\u00b113 nM respectively Lys and Thr2.56(82)Lys/Arg6.32(225)Gln, both mediated very low levels of Env-directed fusion (2.56(82)Pro and Thr2.56(82)Pro/Arg6.32(225)Gln, displayed high levels of Env-directed fusion that were comparable with that mediated by the wild type receptor Pro mutant was similar to wild type Pro/Arg6.32(225)Gln double mutant was lower Pro and Thr2.56(82)Pro/Arg6.32(225)Gln, showed high maximum fusion coefficients of 16.5\u00b14.1 and 18.8\u00b15.6 respectively (2.56(82)Lys and Thr2.56(82)Lys/Arg6.32(225)Gln, both showed very low maximum fusion coefficients Pro and Thr2.56(82)Pro/Arg6.32(225)Gln mutants, which were expressed at levels similar to the wild type receptor in HEK 293 cells, the Thr2.56(82)Lys mutant, which was poorly expressed, and the double mutant, Thr2.56(82)Lys/Arg6.32(225)Gln, which showed enhanced expression relative to the Thr2.56(82)Lys mutant. Constitutively active mutants with Lys in position 82 showed very low fusion efficiency, but mutants with Pro in position 82 showed good fusion efficiency that was comparable to the wild type receptor.In summary, we generated four CCR5 mutants that constitutively activate IP signaling. The Thr3.49(125) in the DRY motif and substitutions of the naturally occurring Arg6.32(225)Gln mutation of CCR5 did not increase constitutive activation of IP signaling. However, substitution of the Thr2.56(82) residue of the TxP motif caused high levels of ligand-independent cellular signaling. The Thr2.56(82)Lys mutation also decreased cell surface CCR5 protein. Severely decreased expression of mutants with Lys, but not Pro, in position 82 suggests that the conformations of the constitutively active mutant receptors differ. Mutant CCR5 receptors with Lys in position 82, which constitutively activated IP signaling, were poor mediators of Env-directed membrane fusion, suggesting that HIV might not enter cells via the activated receptor conformation. However, constitutively active receptors with Pro substituted into the TxP motif mediated Env-directed membrane fusion very efficiently. The differential effects on receptor expression and membrane fusion suggest that Lys and Pro substitutions in position 82 stabilize distinct activated conformations of CCR5 that vary in their ability to mediate Env-dependent membrane fusion.We have investigated the ability of activated CCR5 conformations to mediate HIV Env-directed membrane fusion by generating constitutively active mutant CCR5 receptors. Charge-neutralizing substitutions for AspConstitutively active GPCR mutants are defined by increased ligand-independent signaling activity. The increased signaling results from an increased population of activated receptor conformations by mutant receptors. Many constitutively active mutants exhibit decreased cell surface expression, which may result from constitutive internalization of the activated receptor, or from increased flexibility of activated receptor conformations that results in protein instability Inactive and agonist-stabilized activated conformations of CCR5 are likely to be broadly similar to those of other family A GPCRs for which crystal structures are known, including the closely related CXCR4 chemokine receptor 3.50 interacts simultaneously with the adjacent acidic Asp3.49 (Glu3.49 in rhodopsin) and with Glu6.30 at the cytosolic end of TMS6, forming an \u201cionic lock\u201d that stabilizes inactive receptor conformations. In activated receptors the ionic lock is broken and the guanidino group of Arg3.50 moves to interact with Tyr5.58 in TMS5 3.49 or Arg3.50, which cause constitutive activity in many GPCRs 3.49(125) did not cause constitutive activation of IP signaling in CCR5. Decreased expression of the mutant receptors suggests that substitution of Asp3.49(125) decreases receptor protein stability or increases receptor internalization and down-regulation, as has been described for the Arg3.50(126)Asn CCR5 mutant The \u201cDRY\u201d motif, at the cytosolic end of TMS3, is one of the most conserved sequences among class A GPCRs. According to the \u201cconsensus\u201d view of its function, the basic side-chain of Arg6.30 residue in intracellular loop 3 forms part of the ionic lock in rhodopsin, but many GPCRs, including CCR5, have basic residues in position 6.30 3.50 and Arg6.306.32(225)Gln CCR5 mutant is partially constitutively active and we hypothesized that Arg6.32(225), which is two residues away from Arg6.30(223), might form alternative interactions that stabilize the inactive CCR5 conformation. Other mutations of Arg6.32(225) did not increase constitutive activity. Decreased expression of these mutants is consistent with the role of basic amino acids in stabilizing membrane-spanning helices 6.32(225)Gln mutation did not decrease receptor expression 2.56(82)Lys and Thr2.56(82)Pro mutations with the Arg6.32(225)Gln mutation increased expression of constitutively active mutant CCR5 receptors. The Arg6.32(225)Gln mutation may stabilize a receptor conformation that is less susceptible to internalization or to degradation. The Arg6.32(225)Gln double mutation enhanced expression of constitutively active receptors more effectively in HEK 293 cells than in HOS-CD4-Luc cells. This may result from different receptor trafficking in the two cell lines or it may reflect the generally lower transfection efficiency and receptor expression in HOS-CD4-Luc cells.The Glu2.56(82)Lys and Thr2.56(82)Pro CCR5 mutants that we tested displayed increased basal IP production and could not be further stimulated by MIP-1\u03b2. The same mutants were constitutively active and showed no further response to chemokine treatment in a yeast reporter system 2.56(82)Lys and Thr2.56(82)Pro mutations do not fully stabilize the CCR5 conformation that activates the cognate G\u03b1i protein. The double mutants, Thr2.56(82)Lys/Arg6.32(225)Gln and Thr2.56(82)Pro/Arg6.32(225)Gln, both showed basal IP production that was similar to the maximum MIP-1\u03b2-stimulated IP production mediated by wild type CCR5, suggesting that they are fully stabilized in activated conformations. However, it is not known whether the CCR5 conformations that activate native G\u03b1i signaling pathways are fully stabilized in the double mutant receptors. Mutant receptors with Lys substituted for Thr2.56(82) showed decreased cell surface protein, which may result from decreased receptor stability or stabilization of receptor conformations that constitutively expose cytosolic Ser residues to G protein-coupled receptor kinases, leading to constitutive internalization 2.56(82)Pro mutation may stabilize receptor conformations that are not recognized by receptor kinases or are less flexible. The differential expression suggests that constitutively active CCR5 mutants with Pro or Lys in position 2.56(82) may be stabilized in distinct conformations that are differentially sensitive to internalization and/or degradation. Distinct receptor conformations of the Thr2.56(82)Lys and Thr2.56(82)Pro CCR5 mutants is supported by the report that CHO cells expressing the Thr2.56(82)Pro CCR5 mutant exhibited a wild type-like chemotactic response to the chemokine ligand, RANTES, whereas cells expressing the Thr2.56(82)Lys mutant showed no chemotactic response A proposal that the TxP motif acts as a switch that activates CCR5 was supported by mutations that uncoupled the CCR5 receptor from cellular signaling 50 values for MIP-1\u03b2 binding to constitutively active CCR5 mutants. Arias et al reported similar results for MIP-1\u03b2 binding, but found that the Thr2.56(82)Lys mutation decreased affinity for the agonist chemokines, MIP-1\u03b1 and RANTES, whereas the Thr2.56(82)Pro mutation had less effect 2.56(82)Lys mutation may selectively destabilize the ensembles of CCR5 conformations that preferentially bind MIP-1\u03b1 and RANTES.The extended ternary complex model of receptor activation predicts that constitutively active receptors have increased agonist binding affinity, even in the absence of G protein The gp120 subunit of HIV Env is a CCR5 receptor agonist 2.56(82)Lys/Arg6.32(225)Gln double mutation did not fully recover expression in the HOS-CD4-Luc cells used for the fusion assay. Fusion remained lower than that mediated by wild type CCR5 after correction for receptor expression, but we cannot exclude threshold effects of receptor protein levels. In contrast, constitutively active CCR5 receptors with Pro in position 82 mediated membrane fusion similar to that mediated by wild type CCR5. Our results suggest that CCR5 receptors that constitutively activate IP signaling exist in at least two distinct conformations. One conformation, stabilized by Pro in position 82, supports Env-directed membrane fusion, whereas the other conformation, stabilized by Lys in position 82, does not.Consistent with our hypothesis, both of the constitutively active mutants with Lys in position 82 showed low Env-directed membrane fusion efficiency. The decreased fusion may result from decreased expression, as the Thr2.56(82) to Lys, may stabilize an ensemble of CCR5 conformations that includes the micro-conformations that activate G proteins and receptor internalization, but not the micro-conformations that induce Env-directed membrane fusion. In contrast, mutation of Thr2.56(82) to Pro appears to stabilize an ensemble of receptor conformations that activate G protein and mediate the co-receptor functions of CCR5, but do not activate internalization residue of the DRY motif do not result in constitutive activity of CCR5, confirming that the CCR5 receptor does not conform to the consensus mechanism of receptor activation. We have confirmed that Lys or Pro substitutions for the Thr2.56(82) residue of the TxP motif cause constitutive activity of CCR5, but we have shown that mutants have distinct properties. Constitutively active mutants with Lys in position 82 show decreased cell surface expression and decreased HIV co-receptor function, whereas mutants with Pro in position 82 were well expressed and fully functional as HIV co-receptors. These distinct properties suggest that the mutations stabilize ensembles of receptor conformations that differ in their ability to induce the fusogenic HIV Env conformation. Our results suggest that drugs that stimulate internalization of CCR5 may effectively inhibit HIV infection, both by decreasing cell surface expression of CCR5 and by stabilizing receptor conformations that inhibit fusion of virus that binds to drug-occupied receptor.In conclusion, we have shown that charge-neutralizing mutations of the Asp"} +{"text": "Sir,The spectrum of disease due to dengue infection ranges from a subclinical or mild illness to a severe form of haemorrhagic fever which may prove fatalThe study included consecutive adult patients aged > 18 yr) who were admitted to Sri Ramachandra Medical College and Research Institute, a tertiary care centre in Chennai between August 2007 and February 2009 (two consecutive monsoon seasons). Patients were required to fulfill the 1997 World Health Organization (WHO) case definitions for DHF on admission or during hospital stay8 yr who etc., were done on clinical suspicion. Informed written consent was obtained from all stable patients and from the closest relative of patients who were critically ill. The ethics committee of Sri Ramachandra University approved the study protocol.Patients were interviewed and examined with an objective of identifying the symptoms and signs associated with current febrile illness, associated co-morbidities and other baseline characteristics. This was followed up with basic blood tests , urine analysis, chest X-ray and ultrasound abdomen. IgM and IgG antibodies against dengue was detected using a commercial enzyme-linked immunoassay kit . Additional tests like IgM antibodies for leptospirosis , smear for malaria, blood culture, urine culture, d-dimer, partial thromboplastin time, endoscopy, P<0.05 was considered to be statistically significant.Continuous variables were expressed as mean \u00b1 SD and categorical variables were expressed as number (%). Association between patient factors and mortality was studied using chi-square test or Fisher exact test for categorical variables and Mann-Whitney U test for continuous variables. A total of 128 patients were admitted with features of DHF during the study period; 109 (85%) were admitted during monsoon seasons. The mean age was 33 \u00b1 15 yr; 15 (11.7%) were older than 60 yr. Overall, the proportion of male and female were equal (1:1). A small proportion of patients had co-morbidities like diabetes 5 (3.9%), hypertension 5 (3.9%) or chronic obstructive pulmonary disease (COPD) 2 (1.5%) and none of them had pre-existing chronic kidney disease. Mean duration of fever was 4 days (range 2-6 days). The most frequent symptom was fever 128 (100%) followed by myalgia 88 (68%), gingival bleed 81 (63%), headache 73 (57%), fatigue 54 (42%) and arthralgia 26 (20%). Fifty nine patients (46%) had petechiae or purpura making it the most frequent clinical sign in our study population followed by altered sensorium 24 (19%), sub-conjuctival bleed 15 (12%), ecchymosis 14 (11%), rash 13 (10%), malena 12 (9%) and menorrhagia 11 (8%) : 28 (22%) had hepatomegaly and 6 (5%) had splenomegaly. Also, 47 (37%) had hypotension defined as systolic blood pressure less than 90 mm Hg.The mean duration between onset of fever and sampling for initial investigation was 5 days (range 3-9 days). Seventy three (57%) had leucopenia defined as total count (TC) < 4000 per \u00b5l; 23 (18%) had a platelet count of less than 20, 000 per \u00b5l and none had a platelet count of less than 10,000 per \u00b5l. Evidence of hepatitis defined as transaminase elevation \u2265 400 IU/l was seen in 35 (27.3%) . Of themSix of 11 patients who had symptoms of upper gastrointestinal bleed underwent endoscopy which showed fundal erosions (n=3), duodenal ulcer (n=1) and duodenitis (n=2). Ten patients required ventilatory support within the first 48 h of admission due to impaired mentation of whom five continued to receive mechanical ventilator support till death. Ventilator associated pneumonia occurred in two and acute respiratory distress syndrome (ARDS) complicated the course in one of them. Disseminated intravascular coagulation (DIC) was present in 4 patients. Platelet concentrates were administered to 68 (53%). 34 (26%) received fresh frozen plasma. 66 (51%) received antibiotics and 20 (15.6%) received antibiotics along with artesunate. Refractory shock was present in 16 (12.5%) and progressive renal failure occurred in 15 (12%). The mortality rate was 14 per cent (18 of 128).P< 0.001), progressive renal failure (P< 0.001), refractory shock (P< 0.001), dual infection (P< 0.001), admission platelet count < 20000 per \u00b5l (P=0.009) and admission INR>2 (P=0.02) were associated with mortality. While age, sex, presence of gastrointestinal bleeding, presence of co-morbidities, higher PCV at admission and serum albumin at admission <2.5 mg/dl, were not associated with mortality.Level of creatinine on admission of 2 mg/dl or higher and the proportion of patients having a platelet count of less than 20000/\u00b5l (18%) was lesser compared to previous reports, the frequency of bleeding tendencies was comparable69The mean alanine transaminase (344 IU/l) observed in our study was markedly higher compared to the range of mean alanine transaminase (75 to 143 IU/l) reported in previous studies6Mortality rate due to DHF in adults ranges from 1-8 per cent681114In conclusion, the DHF is spreading across all age groups in Chennai, south India. Given the high complexity of the nature of the disease and failure of containment strategies, more scientific inputs are required to decrease the morbidity and mortality in these patients."} +{"text": "Vitamin D defficiency has been reported to have negative association with clinical manifestation and disease activity of SLE ,2. Vit D55 female patients with SLE were recruited from Clinic of Rheumato-Immunology, Saiful Anwar Hospital, Malang, Indonesia. Mean age of the patients 31.12 years (12-64 yo) with duration of illness 18,4 months (2-54 mo). Serum vitamin (25 (OH)D3 level was assayed using ELISA method . Anti ds-DNA and Anti Cardiolipin antibodies were assayed using ELISA method . Disease activity assessed by SLE disease activity index (SLEDAI) and BMD was assessed by bone densitometry using DEXA. Association between variables were analyzed using Spearman correlation.+ 10.46. Serum vitamin D levels were inversely correlated with SLEDAI . Normal BMD at lumbal spine found in 21 (38.2%) patients. 26 patients (47.3%) were osteopenia, and 8 (14.5%) patients were osteoporosis. At femoral neck, 25 (45.5%) patients had normal BMD, 23(41.8%) patients were osteopenia, 7 (12.7%) patients were osteoporosis. There were no significant correlation between vitamin D level and BMD at lumbal spine and at femoral neck .The mean of serum 25(OH)D3 level was 22.80 \u00b1 16,23 ng/mL.14 patients (25.5%) had vitamin D deficiency (<10 ng/mL), 34 patients (61.8%) had vitamin D insufficiency (10-30 ng/mL), and 7 patients (14.7%) had normal vitamin D levels. There were significant difference level of anti-dsDNA antibodies and IgM ACA in patients with vitamin D insufficiency and vitamin D defisiency. Serum level of 25(OH)D3 were negatively related with level of anti-dsDNA and IgM ACA . The mean of SLEDAI was 15,0 A large proportion of SLE patients had low vitamin D levels. There were positive association between vit D level and autoantibodies expression in SLE and negative association between serum vitamin D levels with SLEDAI. No association was found between serum vit D level and BMD."} +{"text": "Escherichia coli resistant to quinolones are not haemolytic. The objective of this study was to determine the phylogroup, clonal relationship, mechanism of quinolone resistance and virulence factors in 70 haemolytic E. coli resistant to nalidixic acid. Sixty-six isolates contained the hlyA gene, belonged to phylogroup B2, and 61 of them presented low-level resistance to fluoroquinolones. Four isolates presented high-level resistance to fluoroquinolones, contained the clyA gene and were included in phylogroup D. One single isolate contained both cytotoxins.Most The online version of this article (doi:10.1186/2193-1801-2-71) contains supplementary material, which is available to authorized users. Escherichia coli strains causing extraintestinal infections (ExPEC) express different virulence factors (VF), including \u03b1-haemolysin (HlyA) and cytolysin A , both of which can induce osmotic lysis of erythrocytes . Seventy were haemolytic and resistant to nalidixic acid. Organisms were cultured from urine (63 isolates), blood (2), soft tissue abscess (1), abdominal abscess (1), wound (1), tracheal aspirate (1) or skin ulcer (1). Bacteria were identified with the Microscan WalkAway 96 system . MICs of nalidixic acid , ciprofloxacin (Sigma-Aldrich), norfloxacin (Sigma-Aldrich) and levofloxacin were determined by broth microdilution, according to CLSI guidelines . This resulted in the recognition of 13 REP-PCR pattterns, 14 PFGE patterns and 11 sequence types (ST), which combined allowed to define 15 distinct organisms. The quinolone resistance-determining regions (QRDRs) of gyrA and parC were amplified -Ib-cr) was investigated by multiplex PCR were analyzed in the previously indicated 15 isolates associated to a mutation in parC and five (7.2%) isolates corresponded to phylogroups B2 and D. Most isolates of phylogroup B2 belonged to ST73, ST12, ST372 or ST131, while the majority of the isolates of the group D belonged to ST350 isolates contained the clyA gene and one (1.4%) single isolate contained both hlyA and clyA. In a previous study by Ker\u00e9nyi et al. on 540 extraintestinal E. coli strains, the clyA gene was identified in 241 isolates and hlyA in 198 isolates . It would be possible that this relationship is related to the phylogenetic background of the isolates, as hlyA was linked to phylogroup B2, while clyA was linked to phylogroup D. Additional studies are in progress to evaluate this observation in a large collection of E. coli consecutively isolated from bacteremic episodes. This analysis would also provide more data on the presence of hlyA in strains with just low-level resistance to fluoroquinolones.Sixty-five (92.9%) isolates contained the fimH (100%), cnf1 (87%), traT (80%), fyuA (80%) and papC (80%). None of the isolates presented kpsMTIII. Other genes such as PAI (73%), iroN (73%), K5 (67%), kpsMTIII (67%), ibeA (53%), iutA (46.7%), sfaS (33.3%), focG (26.6%), afa/dra (20%), sat (13.3%), bmaE (6.6%), K1 (6.6%) and gafD (6.6%) were less frequently detected. Isolates with clyA also contained more frequently iutA and ibeA. Previous studies have shown that the fimH and traT genes are more frequently found in E. coli isolates (irrespective of their susceptibility to quinolones) than other virulence genes such cnf1 or hlyA than for those of phylogroup D (7.6). In the 15 isolates studied in detail, the most frequent virulence-associated genes are shadowed in dark and pale grey, respectively. (PDF 25 KB)Additional file 1: Table 1: Distribution of absolute (and cumulative) MICs (\u03bcg/ml) of four quinolones against 70 haemolytic"} +{"text": "To describe presentation and course of paediatric systemic lupus erythematosus (pSLE), associated with Parvovirus B19(PB19) primo-infection.Retrospective monocentric study of patients with pSLE, defined according to ARA criteria, diagnosed before 16 years old, and associated with PB19 primo-infection, defined by the presence of PB19 IgM antibodies and PB19 DNA detected by PCR in blood and/or in tissue.3 girls aged from 8 years to 15 years 8 months have been included. PB19 infection was present at diagnosis in all patients. Maternal history of autoimmune diseases was noted in a consanguineous family. Clinical manifestations at diagnosis were fever(3), arthritis/arthralgia (3), skin rash (1), grade IV glomerulonephritis (1), interstitial pneumonia (1), cerebral vasculitis (1), pericarditis/pleurisy (1), adenopathy (2), hepatomegaly/splenomegaly (1). Aregenerative anaemia requiring packed red blood cell transfusion was present in all patients. AAN (3), anti \u2013DNA (3), anti-SSa (1), anti-SSb (1), anti-phospholipid (1), anti-platelet (2), rheumatoid factor (2), pANCA (1), anti-actin (1) antibodies were found. PB19 PCR was positive in blood (3), bone marrow (2) and kidney (1). Corticosteroids have been initiated for the 3 patients, in association with one or more immunosuppressive therapies. A sustained remission has been observed in 2 patients after a follow-up of 4 years and 1 year 8 months off-therapy respectively. A severe course with joint damages, recurrent pericarditis and gradeIV glomerulonephritis, associated with persistent infection by PB19, has been observed in the third case (family autoimmunity history).PB19 infection-associated-pSLE may evolve either to a persistent remission off-therapy or to a severe pSLE. It should be considered in patient with pSLE associated with a severe aregenerative anemia."} +{"text": "Nelumbo nucifera Gaertn. cv. Rosa-plena (Nelumbonaceae), commonly known as lotus, is a perennial aquatic plant grown and consumed throughout Asia. All parts of N. nucifera have been used for various medicinal purposes in oriental medicine. From the leaves of Nelumbo nucifera Gaertn. cv. Rosa-plena (an aquatic plant), liriodenine (1), lysicamine (2), (\u2212)-anonaine (3), (-)-asimilobine (4), (-)-caaverine (5), (-)-N-methylasimilobine (6), (-)-nuciferine (7), (-)-nornuciferine (8), (-)-roemerine (9), 7-hydroxydehydronuciferine (10) and cepharadione B (11) were isolated and identification and anthelmintic activities of aporphine was evaluated against Anisakis simplex and Hymenolepis nana. This study found that the above constituents killed H. nana or reduced their spontaneous movements . However, the above constituents at various concentrations demonstrated no larvicidal effect or ability to halt spontaneous parasite movement for 72 h against A. simplex, respectively. In addition, according to an assay of cestocidal activity against H. nana and nematocidal activity against A. simplex, we found that the above compounds showed greater lethal efficacy on H. nana than against A. simplex. Further investigation showed that these above constituents have effects against peroxyl radicals under cestocidal effect. Together, these findings suggest that these constituents of Nelumbo nucifera Gaertn. cv. Rosa-plena might be used as anthelmintic agents against H. nana. Rosa-plena is a perennial aquatic crop grown and widely distributed throughout Asia, and long used for food and medicine. All segments of N. nucifera have been used for various medicinal purposes in traditional oriental medicine. The matured leaf is fibrous and usually used as a health food in Asia. The leaves are famous for their astringent properties and use as diuretics, and are also used to treat sweating, fever, strangury and as a styptic + (1) as in , yellow 275 [M]+ .Lysicamine (2) as in + (2) as in , yellow 291 [M]+ .(-)-Anonaine (3) as in + (3) as in , pale ye265 [M]+ .(-)-Asimilobine (4) as in + (4) as in , brown p267 [M]+ .(-)-Caaverine (5) as in + (5) as in , brown p267 [M]+ .(-)-N-methylasimilobine (6) as in + (6) as in , white n281 [M]+ .(-)-Nuciferine (7) as in + (7) as in , brown p295 [M]+ .(-)-Nornuciferine (8) as in + (8) as in , brown p281 [M]+ .(-)-Roemerine (9) as in + (9) as in , pale br279 [M]+ .7-Hydroxydehydronuciferine (10) as in + (0) as in , brown p309 [M]+ .Cepharadione B (11) as in + (1) as in , orange 321 [M]+ .2.2.1), lysicamine (2), (-)-anonaine (3), (-)-asimilobine (4), (-)-caaverine (5), (-)-N-methylasimilobine (6), (-)-nuciferine (7), (-)-nornuciferine (8), (-)-roemerine (9), 7-hydroxydehydronuciferine (10) and cepharadione B (11) treatment of 2, 4, 6 and 12 h. In oscillation activity assay, vehicle control (0.1% dimethyl sulphoxide (DMSO)) was decreased by 16% from 12 h cultivation (H. nana was more sensitive than oscillation via treatment of vehicle. Treatment with 100 \u03bcM liriodenine (1), lysicamine (2), (-)-anonaine (3), (-)-asimilobine (4), (-)-caaverine (5), (-)-N-methylasimilobine (6), (-)-nuciferine (7), (-)-nornuciferine (8), (-)-roemerine (9), 7-hydroxy dehydronuciferine (10) and cepharadione B (11) has a greater effect of peristalsis than on oscillation for 2, 4, 6 and 12 h.tivation . Howevertivation . The cha1), lysicamine (2), (-)-anonaine (3), (-)-asimilobine (4), (-)-caaverine (5), (-)-N-methylasimilobine (6), (-)-nuciferine (7), (-)-nornuciferine (8), (-)-roemerine (9), 7-hydroxydehydronuciferine (10) and cepharadione B (11) treatment of 24, 48 and 72 h. In oscillation and peristalsis activity assay, vehicle control (0.1% DMSO) was decreased to 70% and 20%, respectively from 24 to 72 h cultivation -caaverine, lysicamine, (-)-nornuciferine, (-)-nuciferine and (-)-roemerine for 72 h cause the maximum cestocidal effect of H. nana without any peristalsis activity. This cestocidal effect on peristalsis is stronger than on oscillation activity. Peristalsis activity disappeared before oscillation activity was lost when H. nana died. This demonstrates that (-)-nornuciferine have maximum cestocidal effect than above compounds. The order of the cestocidal effect of the compounds was: (-)-nornuciferine > (-)-nuciferine > lysicamine > (-)-asimilobine \u2265 (-)-caaverine > liriodenine \u2265 (-)-anonaine > (-)-roemerine. However, 7-hydroxydehydronuciferine, (-)-N-methylasimilobine and cepharadione B have no cestocidal effect against H. nana.In the oscillation activity assay , exposurty assay , exposur2.3.1), lysicamine (2), (-)-anonaine (3), (-)-asimilobine (4), (-)-caaverine (5), (-)-N-methylasimilobine (6), (-)-nuciferine (7), (-)-nornuciferine (8), (-)-roemerine (9), 7-hydroxydehydronuciferine (10) and cepharadione B (11) to alter survival of AsL3. In the time-dependent course shown above compounds have no nematocidal activity against A. simplex (AsL3). Additionally, the loss of spontaneous movement of AsL3 did not occur at a concentration of 100 \u03bcM of liriodenine (1), lysicamine (2), (-)-anonaine (3), (-)-asimilobine (4), (-)-caaverine (5), (-)-N-methylasimilobine (6), (-)-nuciferine (7), (-)-nornuciferine (8), (-)-roemerine (9), 7-hydroxydehydronuciferine (10) and cepharadione B (11). However, according assay of cestocidal activity against H. nana and nematocidal activity against A. simplex, we found above compounds shown more lethal efficacy of H. nana than against A. simplex.In the first series of experiments, the larvicidal effects were used to study the ability of liriodenine (2.4.1), lysicamine (2), (-)-anonaine (3), (-)-asimilobine (4), (-)-caaverine (5), (-)-N-methylasimilobine (6), (-)-nuciferine (7), (-)-nornuciferine (8), (-)-roemerine (9), 7-hydroxydehydronuciferine (10) and cepharadione B (11) as determined by oxygen radical absorbance capacity (ORAC) fluorescein assay are shown in The peroxyl radical absorbing abilities of Trolox, ascorbic acid, liriodenine (1), lysicamine (2), (-)-anonaine (3), (-)-asimilobine (4), (-)-caaverine (5), (-)-N-methylasimilobine (6), (-)-nuciferine (7), (-)-nornuciferine (8), (-)-roemerine (9), 7-hydroxydehydronuciferine (10) and cepharadione B (11) for relative Trolox equivalents (TE) ORAC were determined to be 1.00, 0.20, 1.73, 0.67, 2.62, 5.23, 0.89, 1.89, 0.63, 1.43, 1.14, 1.54 and 1.59, respectively (N-methylasimilobine > liriodenine > cepharadione B \u2265 7-hydroxydehydronuciferine > (-)-nornuciferine > (-)-roemerine > Trolox > (-)-caaverine > lysicamine \u2265 (-)-nuciferine > ascorbic acid.When the test compounds were added, the relative fluorescence intensity decreased. Fluorescein was exposed to excitation light at 495 nm in the absence of AAPH over a 60-min period. There were no significant changes in fluorescence intensity over 60 min, suggesting that 0.06 \u03bcM fluorescein is photostable under such conditions. As shown in ectively . The ordH. nana. In ORAC fluorescein assay, (-)-asimilobine, (-)-anonaine, liriodenine, (-)-nornuciferine and (-)-roemerine were evaluated as radical scavengers compared to ascorbic acid and Trolox. A previous study demonstrated that not only is scavenging activity not involved in larvicide activity for A. simplex, but also that free radicals could harm the A. simplex; in this case, the scavenging of these free radicals allows for larvae survival and gave liriodenine (1) (4 mg)The leaves of 3.3.H. nana adult worms were obtained from each part of the intestines of wild type mice, purchased from Lin\u2019s farm in Fengshan, Kaohsiung, Taiwan. These parts of the duodenum, jejunum, ileum, colon and rectum were used. The H. nana adult worms ranged in length from 5\u201350 mm, and were collected using a needle with a blunt tip, before being placed in Petri dishes with 0.9% NaCl and gentamycin (10 mg/mL). They were then washed several times. The adult worms were individually observed under an inverted microscope and those that exhibited any kind of internal or external damage were discarded. The adult worms were then identified by their morphological features, divided into groups and placed in 24-well plates contained cultivated media RPMI-1640 (Gibco BRL Life Technologies) plus 20% FBS, pH 7.4, in an atmosphere of 95% O2/5% CO2, 37 \u00b0C. These culture conditions have been shown to maximize the development and survival of H. nana and aporphines have not only cestocidal activity for H. nana but also radical scavenging activity against peroxyl radical, respectively. So those compounds have radical scavenging activity that did not reduce their cestocidal activity against H. nana. Further investigations of the mode of Nelumbo nucifera Gaertn. cv. Rosa-plena constituents\u2019s actions and/or mechanisms for its cestocidal effects between free radical scavenging activity are necessary. In addition, we found dehydroaporphines [7-hydroxydehydronuciferine (10) and cepharadione B (11)] have antioxidant capacity but no cestocidal and nematocidal effect against H. nana and A. simplex, respectively. These results might be useful in the search for more selective and efficient naturally anthelmintic compounds.This study is the first to determine the anthelmintic activities of"} +{"text": "Juvenile idiopathic arthritis (JIA) is a heterogeneous disease, and it\u2019s associated with an increased use of various biological agents in recent years.Evaluate clinical response to current biological agent in JIA patients.This is a retrospective study of 109 JIA patients from a tertiary centre (see poster 1). Variables included were: current biological treatment and duration of treatment (years with a new agent or since reintroduction of an agent used before) plus physician visual analogue scale (ph-VAS), erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) at baseline and at the end of the study. Concomitant therapy with methotrexate (MTX) was also recorded.Duration of treatment with the current biological agent was 1.2 \u00b1 1 (0.1- 4.9) median 0.8 years. This agent was etanercept (ETA) in 58 cases, adalimumab (ADA) in 16, tocilizumab (TCZ) in 11, anakinra (AK) in 9 and infliximab (IFX) in 2. Thirteen patients were off treatment with biological agents, 12 due to inactive disease and one because of inefficacy.Concomitant treatment with MTX was observed in 8/58 14%) patients with ETA, 4/16 (25%) with ADA, 5/11 (46%) with TCZ, 1/2 (50%) with IFX and none with AK. Table 4% patienThe results indicate that reintroduction of a previously effective biological agent may be successful; besides, switching to a second, third or even fourth biological agent in those patients whose disease remains active, can be effective as well."} +{"text": "Inflammatory myopathies (IM) in children comprise a heterogeneous group of disorders, the most common being juvenile dermatomyositis and to a lesser degree juvenile polymyositis.To assess the clinical characteristics and treatment response of a cohort of IM patients.Clinical chart review of clinical, laboratory and treatment related parameters of IM patients treated at 2 referral centers for the last 12 years.Outcome measures included disease remission and muscular function.17 IM patients ) were followed for a mean of 6,3years (1-12years): 3 were labeled as polymyositis and 14 as juvenile dermatomyositis.Positive diagnostic criteria: typical skin lesions-14/17, proximal muscle weakness-15/17, elevated muscle enzymes-16/17, EMG-10/10, muscle biopsy-9/9.Frequent presenting symptoms included: proximal muscle weakness-16/17, skin lesions-11/17, lethargy-8/17, fever-7/17. During follow-up, patients presented with: muscle weakness (17/17), skin lesions (14/17), lipodystrophy (2/17), arthralgia (6/17), arthritis(4/17), vasculitis (4/17), gastro-intestinal vasculitis (1/17), restrictive pulmonary disease (1/17), calcinosis (4/17).Laboratory: ESR was raised in 6/17, muscle enzymes in 17/17 ; Positive auto-antibodies: ANA-11/17, SSA(Ro-52)-2/17; 10/17 underwent muscle biopsy and 9/17 EMG.Therapeutic regimens included more commonly steroids, methotrexate (17/17) and CyclosporinA (16/17).Regarding disease activity, 9/17 patients have inactive disease, 6 of which are in remission without treatment; 6/17 have permanent loss of muscular function.IM are potentially severe, incapacitating diseases. All patients with polymyositis in this series have loss of muscular function, contrasting with 3/14 of JDM patients.About half of this cohort is asymptomatic and it should be stressed that early diagnosis and aggressive treatment are important prognostic factors."} +{"text": "A prospective study was performed for evaluating the amino acid losses during continuous venovenous hemodiafiltration (CVVHDF).Serum, 24-hour urine and dialysate/ultrafiltrate solutions of CVVHDF were obtained on days 1, 3, and 5 from 11 critically ill patients ) in the surgical ICU. We analyzed 40 kinds of amino acid concentrations in serum (34 samples), urine (15 samples) and dialysate/ultrafiltrate solutions (30 samples) by high-performance liquid chromatography analysis. The mean dialysate amount was 918.2 ml , mean replacement fluid amount 1,136.4 ml and mean blood flow rate 175 ml (100 to 200 ml), respectively. Nutritional support for CVVHDF patients was guided as protein intake at 1.2 to 1.5 g/kg/day, caloric intake at 30 kcal/kg/day.P = 0.000). The mean amount of total amino acid loss on day 5 of CVVHDF was 2.8 times that of day 1 and 1.7 times that of day 3. The increase of amino acid loss according to CVVHDF progression was most prominent in glutamic acid (8.9 times from day 1 to day 5).Among the analyzed 40 amino acids, the five highest mean concentration levels of 24-hour dialysate/ultrafiltrate solutions were glutamine ), alanine , glycine , proline , lysine ; of serum were glutamine (694.4), alanine (438.1), glycine (349.7), lysine (275.7), proline (262.4); and of 24-hour urine were glycine , histidine (957.5), alanine (920.7), glutamine (904.6), lysine (699.1), respectively. Amino acid concentrations of 24-hour dialysate/ultrafiltrate solutions showed significant correlation with amino acid concentrations of serum (The highest concentration level of 24-hour dialysate/ultrafiltrate solution was glutamine. The amount of amino acid loss after CVVHDF was correlated with the serum amino acid amount and increased according to CVVHDF progression."} +{"text": "Dear Editor,LPP is one of the main causes of primary cicatricial alopecias. This study was performed for review of histopathological characteristics of LPP, and for the first time the density of hair follicles in vertical scalp biopsies was compared with healthy scalp biopsies. Vertically sectioned scalp 5mm punch biopsies of 44 cases of LPP were examined(H & E and Alcian blue) according to NAHRS criteria . Also weCharacteristic findings of LPP were: markedly reduced hair density (63.6 %), absence of vellus hair (59.1 %), and follicular lichenoid changes (61.40 %). We found mucinous fibroplasias (50.0 %) and presence of interfollicular mucin 2.3 %). The only significant epidermal change was spongiosis (40.9 %). The most prominent pattern of follicular involvement was lichenoid (58.69%).Other changes included mild to moderate lymphocytic, primarily perifollicular (77.3 %) and perivascular (97.7 %) inflammation, Periinfundibular hypergranolosis (77.3 %), foreign body granuloma (13.6 %),demodex(25.0 %) , max-Josef cleft(38.6 %),epidermal(65.90 %) and follicular civatte bodies(45.45%). Vertical sections are useful in LPP in which the findings are focally confined to dermo-epidermal junction (DEJ) and superficial dermis [.3 %. TheCommon findings in LPP are as follows: lichenoid lymphocyte infiltration in follicular DEJ 4]5], w[5], w4], wIn LPP, lichenoid changes are seen more than vacuolar degeneration . In our Epidermal and follicular cytoid bodies were seen in 66% and 45% of our patients. Mehrgan has reported the cytoid body prevalence to be 53% . In LPP,"} +{"text": "Congenital hypothyroidism (CH), is caused by inadequate production of thyroid, represent one of the most common preventable causes of mental retardation. Undetected near birth, CH clinically manifests as mental retardation, coarse facial features, poor growth, deafness and neurological abnormalities.To describe characteristics of patient with congenital hypothyroidism diagnosed in Pediatric Department of Hasan Sadikin General Hospital, Bandung, IndonesiaWe reviewed 26 children with congenital hypothyroidism confirmed by thyroid scintigraphy from October 2010 to June 2012 who came to Dr.Hasan Sadikin General Hospital Bandung, Indonesia.Twenty six subjects were diagnosed with congenital hypothyroidism, consisted of 15 (57.7%) girls and 11 (42.3%) boys, mean age 11.42 \u00b110.35 month. The youngest age when the diagnosis (CH) was established was 2 months and the oldest was 46 months. Thirteen subjects (50%) were referred by primary care pediatrician, 5 subjects (19.2%) by general practitioners, 4 subjects by neuropediatrician and 4 subjects by growth and development clinic. The main presenting complaints in CH were global delayed development , constipation (50%), prolonged icteric (15.4%) and growth retardation (13.5%). The most common of clinical appearance were hypotonia (69.2%), coarse faces (46.2%), mottled (34.6%), large fontanel (34.6%), umbilical hernia (23.1%) and macroglossia (26.9%). We found 25 subjects were diagnosed as primary CH and only 1 case with secondary CH. The most common etiology of CH was thyroid agenesis (53.8%), thyroid ectopic (19.2%), thyroid hypoplasia (11.5%) and dyshormonogenesis (11.5%). Decreased fT4 value were found in all subjects (mean 0.553\u00b10.35 ng/dl) and mean TSHs value at presentation was 31.02\u00b120.71 mIU/L. Of the 26 late diagnosed CH cases, 46.% had mental and motor development delay, 23.1% short stature and mental retardation, and 15.4% mental retardation and neurological sequel as complications.Late diagnosis of congenital hypothyroidism in children result varied clinical manifestation and had mental retardation, gross motor delay, short stature and neurological abnormalities as complications."} +{"text": "We already reported good virological and immunological responses after 1 to 4 years in cohorts of patients on 1st line and more recently, among an Esther cohort of 70 patients after 2 years on LPVr-based 2nd line regimen. However, emergence of LPV resistant associated mutations is becoming a major concern in low and middle income countries.By the end of 2009, the number of HIV-1 infected patients on RTI-based 1nd line regimen in Cambodia.This study aimed to describe the resistance pattern of both the protease (PR) and integrase (IN) coding regions in HIV-1 CRF01-AE infected patients failing LPV-based 2nd line regimen in Cambodia.Analysis of the Protease and Integrase drug resistance genotyping of 95 HIV-1 strains infected patients presenting detectable viral load on LPV/r-based 210 copies/ml [IQR: 2.8-3.4]). The 77 other CRF01_AE strains, harbored polymorphism mutation in position M36, H69 and L89 conferring possibly resistance to TPV/r. Forty-nine (median VL: 5Log10 copies/ml [IQR: 4 - 5.5]) did not present any other PI associated resistance mutation. In contrast, 28 patients showed multiple resistances to PI. The median duration on LPV/r regimen was 34.5 months [IQR: 23.5 \u2013 53.3] and the median VL was 5Log10 copies/ml [IQR: 4.3-5.6]. Twenty-five patients were resistant to LPV/r (7 possibly resistant). Twenty-seven were resistant to IDV, 21 and 19 to ATV/r and FPV/r, respectively. Twenty-five were resistant to NFV (10 possibly), 22 resistant to SQV/r (9 possibly). Seven showed resistance to DRV/r (5 possibly). Finally, excluding possible resistance, 21/28 (75%) was resistant for at least 3 PIs. Clinical investigation revealed that most of these 28 patients starting several RTIs and PIs early around 2000. All of them were sensitive to raltegravir, elvitegravir (integrase inhibitors), and etravirine (Non-Nucleoside reverse transcriptase inhibitorse).Lack of amplification in PR gene was observed for 18/95 presenting low viral load of Cambodian patients presenting detectable viral load on LPV/r\u2013based 2"} +{"text": "Patients on ADA (24 mg/mSubjects in the 4-12-year-old subgroup (n=41) were 73% female and 98% white, with a mean age of 9 years. At baseline, mean PhyGA was 58.1, mean PaGA was 47.9, AJC was 18.6, and DI-CHAQ was 1.0. ACR Pedi 30/50/70/90 responses at wk 106 (Table) were comparable to completer patients (n=62) in the overall population who reached ~240 wks in the OL extension FD phase (95%/90%/82%/69%). Improvements in core disease activity/severity variables were maintained throughout the study (Table ADA was efficacious and well tolerated in a BSA-dosed JIA subpopulation aged 4-12 years. ACR Pedi 30/50/70/90 responses were maintained through 106 weeks. Overall, efficacy was comparable to the entire study population, in whom maintenance of response was observed throughout the entire study with ADA for up to 6 years."} +{"text": "Early aggressive therapy has been shown to result in superior outcomes in adults with RA, but evidence for a similar benefit has not been demonstrated in children with JIA. The objective was to determine if aggressive treatment initiated within the first 12 mos after onset of extended oligoarticular (e-oligo), or RF + or (-) polyarticular JIA (poly JIA) can induce inactive disease (ID) within 6 mos (primary endpoint) and clinical remission on medication within 1 yr of starting therapy.TREAT was designed as a multi-centered, prospective, double blind, randomized, placebo controlled clinical trial in children aged 2 to 16 yrs with e-oligo or poly JIA of \u2264 12 mos duration. Participants were randomized 1:1 into 1 of 2 aggressive treatment arms: (Arm 1) MTX 0.5 mg/kg/wk SQ (40 mg max), plus etanercept 0.8 mg/kg/wk (50 mg max), plus prednisone 0.5 mg/kg/d (60 mg max) tapered to 0 by 17 wks or; (Arm 2) MTX (same dose as Arm 1) plus etanercept placebo, plus prednisolone placebo, then followed on protocol for up to 12 mos. After 4 mos on therapy participants who failed to achieve at least an ACR Pediatric 70 received open label etanercept, MTX, and prednisolone in the same doses as Arm 1. At 6 mos the participants who achieved ACR Pediatric 70 but failed to achieve ID received open label medication as in Arm 1. Efficacy analyses focused on the intent-to-treat approach. Safety data were recorded for all participants who received at least one dose of medication.15 centers enrolled 85 participants with a median age of 11.1 yrs and disease duration of 4.1 mos. 70% were ANA+, 33% RF+, and 33% anti-CCP+. At baseline the median physician\u2019s global assessment of disease activity and parent global assessment of overall well-being were 7 and 5 respectively. There were no significant inter-Arm differences in any of these variables. At baseline, Arm 2 had a statistically higher mean ESR (45 vs. 29 mm/hr) and active joint count (25.5 vs. 18.9) compared to Arm 1. By 4 mos, 30 of 42 (71%) participants in Arm 1 and 19 of 43 (44%) in Arm 2 achieved an ACR Pediatric 70 . By 6 mos, 17 of 42 (40%) of participants in Arm 1 achieved ID, compared to 10 of 43 (23%) in Arm 2 . Although all 6 ACR pediatric core set variables showed highly significant improvement from baseline by 6 mos in both Arms (p < .001), 5 of 6 core set variables showed statistically greater improvement in Arm 1 vs. Arm 2. By 12 mos, 12 (14%) participants achieved CRM; 9 (21%) had remained in Arm 1, and 3 (6%) had remained in Arm 2 throughout the study (p = 0.0534). There were no significant inter-arm differences in the incidence of Grade 3 or higher adverse events, including infections requiring systemic therapy. There were 3 SAEs: pneumonia (Arm 1), psychosis (open label), and bacteremia with septic arthritis (open label). All resolved without sequelae.Although this trial did not reach its primary endpoint, early aggressive therapy in this cohort of children with severe JIA and a high rate of RF positivity resulted in substantial proportions of participants achieving an ACR Pediatric 70 by 4 mos, ID by 6 mos, and CRM within 12 mos of treatment initiation.Carol A. Wallace: Amgen Inc., 2; Edward H. Giannini: None; Steven J. Spalding: None; Philip J. Hashkes: None; Kathleen M. O\u2019Neil: None; Andrew S. Zeft: None; Ilona S. Szer: None; Sarah M. Ringold: None; Hermine Brunner: None; Laura E. Schanberg: None; Robert P. Sundel: None; Diana Milojevic: None; Marilynn G. Punaro: None; Peter Chira: None; Beth S. Gottlieb: Pfizer Inc, 5; Gloria C. Higgins: None; Norman T. Ilowite: None; Yukiko Kimura: None; Bin Huang: Amgen Inc., 2; Daniel J. Lovell: Abbott Laboratories, 9, Amgen Inc., 5, Bristol-Myers Squibb, 9, Centocor, Inc., 9, Hoffmann-La Roche, Inc., 9, Novartis Pharmaceuticals Corporation, 9, Regeneron Pharmaceuticals, Inc., 9, UBC, 9."} +{"text": "A wide range of hepatotoxicity rates associated with antiretroviral drugs (ARV) has been reported in different studies. Reasons for this include diverse populations, with different prevalence of viral hepatitis coinfection, exposure to diverse ARV and variable criteria to define liver toxicity across studies. The liver safety of regimens including efavirenz (EFV), nevirapine (NVP) or boosted-protease inhibitors (PI/r) has not been compared in a single large cohort of HIV/HCV-coinfected patients with a uniform definition of hepatotoxicity. Because of this, we evaluated the incidence and risk factors for grade 3 or 4 ALT or AST elevations (TE) and grade 4 total bilirubin elevations (TBE) among ARV-na\u00efve HIV/HCV-coinfected patients with an initial regimen including two nucleoside analogs (NRTIs) plus EFV, NVP or a PI/r.Retrospective multicenter cohort (January 2000-June 2006) of 745 HIV/HCV-coinfected patients starting their first ARV treatment consisting of two NRTIs plus either EFV, NVP or PI/r. Patients were included if they were exposed to ARV for one week or more and had evaluations within the first three months of follow-up. Definition of grade 3 or 4 TE: 1) Normal baseline ALT or AST levels: ALT or AST elevations \u22655 times above the upper limit of normal (ULN); 2) Baseline ALT or AST levels above the ULN: ALT or AST elevations \u22653.5 times the baseline values Definition of grade 4 TBE: Increases of total bilirubin \u22655 mg/dl.323 (43%) patients received EFV, 126 (17%) NVP and 296 (40%) PI/r. Grade 3 or 4 TE were observed in 19 (5.9%) individuals on EFV, 14 (11%) on NVP and 31 (10.5%) on PI/r . Grade 4 TBE were identified in 7 (2.2%) patients on EFV, 1 (0.8%) on NVP and 11 (3.7%) on PI/r (p=0.19). Severe TBE was detected in 5 (12%) and 15 (2%) patients with and without cirrhosis, respectively (p=0.003). Discontinuations due to hepatotoxicity were: 13 (4%) patients on EFV, 16 (13%) on NVP and 17 (6%) on PI/r .Liver tolerability of regimens including EFV, NVP or PI/r is generally good in ARV-na\u00efve HIV/HCV-coinfected patients. Severe TE are less commonly seen with EFV than with NVP or PI/r. Discontinuations due to hepatotoxicity were less frequent for patients receiving EFV than for those treated with NVP."} +{"text": "A cohort of patients participating in a multicentric, multinational phase III trial to assess the efficacy and safety of abatacept in juvenile idiopathic arthritis (JIA) were discontinued from the study due to administrative reasons.To assess long term efficacy and monitor clinical follow up after the sudden removal of abatacept.Patients in the open arm of the trial, receiving 10mg/kg monthly infusions of abatacept were followed for 4 years after its suspension. Outcome measures included clinical remission and disease control without biologics.Eight patients (7M/1F) with mean age of 16.5 years (range 13-19years) and disease duration of 8,6years were followed. All patients had polyarticular involvement only partially responsive to methotrexate (extended oligoarticular (OE)-3, polyarticular Rheumatoid factor IgM negative (Poly)-2, systemic onset (SoJIA)-3). Concurrent therapies, maintained after the abatacept trial included NSAIDS, Methotrexate (8/8) and low dose steroids (3/8).All patients met the ACRpedi30 criteria, 5 of which (OE and Poly) were either in remission (2/8) or had marked improvement (1or 2 active joints). After 12 months of follow-up, all OE patients had inactive disease, as well as one Poly (4/8). Subsequently, 1of the OE and the other Poly flared, with etanercept being introduced at 27 and 29months of follow-up, respectively; 3 patients currently remain in full remission after 4 years .SoJIA patients maintained active disease, requiring biologic therapy (mean 18months).Although it\u2019s a small cohort, this study suggests that abatacept may induce long term remission in polyarticular JIA patients, especially EO and Poly subtypes. Similar results were not observed in SoJIA patients."} +{"text": "Pseudomonas aeruginosa (PA) pneumonia (PN) represents a serious complication of long-term hospitalization [lization . The aimAll patients admitted to the 18-bed ICU of our university hospital between 1 January 2009 and 30 June 2010, affected by PAPN, were retrospectively enrolled in a cohort study.P < 0.01), with a longer length of ICU stay (P < 0.01), more frequently admitted for a traumatic reason (P = 0.02) and presented less severe SAPS II (P < 0.05). The independent risk factors associated with ICU mortality are listed in Table Over the study period 1,109 patients were admitted and 322 bacterial PN were diagnosed. Sixty-five PAPN occurred: 52 ICU-acquired (ICUa) and 13 non-ICU-acquired (nICUa). Patients were mainly admitted because of a medical condition (71%), with a median length of ICU stay of 29.2 \u00b1 27.6 days. The median SAPS II and SOFA scores were 40 \u00b1 13.5 and 6.2 \u00b1 3. A total of 35.4% of PA isolated were multidrug-resistant (MDR), 49.2% of patients with PAPN received a >24 hour delayed adequate antimicrobial treatment (DAAT >24 hours) and 57% received an anti-pseudomonas combination therapy; 25 patients (38.5%) died in the ICU. Comparing patients with ICUaPN with those with nICUaPN, the former group were younger , PA (MDR) and physicians' (DAAT >24 hours) related factors can influence the outcome of PN. The knowledge of local bacterial epidemiology and the prompt use of an anti-pseudomonas empiric treatment in patients with recognized PA risk factors could improve the outcome of severe MDR PAPN."} +{"text": "Etanercept has been approved in polyarticular juvenile idiopathic arthritis (JIA) patients refractory or intolerant to methotrexate. The objectives of the study were to evaluate safety and efficacy of Etanercept and Methotrexate combination therapy versus Etanercept mono therapy in JIA using a matched pair analysis.A cohort of 1190 JIA patients enrolled in the German JIA Enbrel registry has been used for screening. Matching criteria included JIA subtype, gender, disease duration, use of corticosteroids, oligo- versus polyarthritis at therapy start and the sedimentation rate. Efficacy was determined using the PedACR 30/ 50 and 70 response criteria. Safety assessments were based on adverse events reports. The matched data at month 1, 3, 6, 12, 18 and 24 on treatment have been analyzed using the McNemar\u2019s test.87 JIA matching pairs with a total of 658 visits have been identified. No difference in PedACR 30/50/70 treatment response between mono and combination therapy has been found: month 1: 73%/61%/33% vs. 70%/61%/33%, month 3: 73%/69%/51% vs. 65%/59%/41%; month 6: 82%/77%/59% vs. 83%/72%/59%; month 12: 85%/78%/63% vs. 89%/80%/67%; month 18: 77%/73%/69% vs. 89%/81%/77%; month 24: 63%/56%/50% vs. 56%/34%/34%. In the mono therapy group 18 patients (21%) experienced 28 adverse events. Five of them have been reported as serious. In the combination group 19 patients (22%) experienced 30 adverse events. Seven of them have been reported as serious. No infectious serious adverse events occurred in the mono therapy group compared to 3 in the combination group. Two malignancies have been observed in the combination group, none in the monotherapy group. Treatment has been discontinued in 29 patients on mono therapy compared to 51 patients in the combination group .In contrast to the wide spread belief, combination treatment with Etanercept and Methotrexate did not offer a better outcome than treatment with Etanercept alone in JIA patients who previously have been treated ineffectively with methotrexate. However the rate of serious adverse events, especially serious infections was slightly increased.Heinrike Schmeling: None; Gerd Horneff: Abbott Immunology Pharmaceuticals, 2, 5, Bristol-Myers Squibb, 5, Chugai, 5, Nycomed, 5, Pfizer Inc, 2, 5, Sandoz, 5."} +{"text": "MVC is the first-in-class CCR5 antagonist approved for use in treatment of CCR5-tropic (R5) HIV-1 infection; however, there is limited experience with MVC in regimens containing newer PIs and other new agents. This open-label 96-week multi-center study evaluates MVC in a variety of regimens to obtain additional safety and efficacy data in TE patients with limited options due to intolerance or resistance in Brazil.Adult TE patients with R5 HIV-1 only (HIV-1 RNA >1000 cp/mL) received MVC 150-600mg (based on concomitant ARV) twice daily, combined with optimized background therapy (OBT). Every 12 weeks, safety parameters (primary endpoint), HIV RNA, and CD4 counts were assessed; we report data at 48 weeks.10 copies/mL and 185 cells/mm3, respectively. OBT comprised PI+NRTI (67%), PI+NRTI+NNRTI (7.8%), PI+NRTI+other (14.6%), or other regimens (10.2%). The most frequently used NRTIs were TDF (82%), 3TC (76%) and AZT (23%); the most common PIs (most boosted with RTV) were DRV (45%), LPV (41%) and ATV (15%); 16% received RAL. OBTs contained \u22641 drug (1% of patients), 2 drugs (7.3%), 3 drugs (24.3%), 4 drugs (35.4%), 5 drugs (23.8%), or \u22656 drugs (8.2%). Sixty-five patients (31.6%) discontinued; reasons included death (6 patients), adverse events (5), insufficient clinical response (36), lost to follow-up (4), or other (14). There were 238 treatment-related adverse events in 103 patients; 16 treatment-related serious adverse events in 9 subjects; 10 category C events, none treatment-related; and 2 of the 4 malignancies were considered treatment-related. The most common grade 3/4 lab test abnormalities were GGT elevation (11% of patients), hyperbilirubinemia (11%) and serum amylase elevation (6%). Median CD4 count increased persistently through week 48 , with similar responses comparing quartiles of baseline CD4; the median increase from baseline at week 48 was 164.5 cells/mm3. HIV-1 RNA decreases were maintained regardless of baseline viral load; overall 41.1% of patients had HIV-1 RNA <400 copies/mL at week 48.Of treated 206 patients, 70% were male (mean age 43 yrs) and 80% Caucasian; 2.9% and 5.8% were seropositive for HBV or HCV infection, respectively. Median baseline HIV-1 RNA and CD4 counts were 4.9 logIn highly TE patients, regimens combining MVC with different agents from multiple classes were well tolerated and provided marked antiviral and immunologic responses."} +{"text": "Tailoring of antiretroviral therapy (ART) in HIV-2 remains unclear, therefore therapeutic experience in this population is presented.Retrospective analysis of HIV-2 infected patients (pts) on ART followed at a single Portuguese center, between 1988 and 2010.3 [3-586] and mean TCD4+ count prior to ART initiation was 205 cells/mm3. The main reason for starting ART was immunological deterioration followed by pregnancy . Ten pts (27%) had an AIDS defining illness prior to ART initiation and 4 (11%) developed it while on ART. The mean value of the last TCD4+ count was 305/mm3. Overall the median number of regimens received per patient (pt) was 3 [1-7]; 12 (32%) pts took just one regimen. Mean length of ART was 61 months [1-228] and mean duration of the last prescribed regimen was 23 months [0.25-125]. Viral load (\"in house\" assay) was always undetectable in 19 (51%) pts. Switch of ART occurred in 21 (57%) pts with 1.4 reasons/pt. The main cause for switching was GI intolerance , followed by failure , toxicity and simplification .37 pts were included; 19 (51%) female and 28 (76%) Caucasian. Mean ages were: 46 years [18-77] at HIV-2 diagnosis and 48 years [20-81] at the beginning of ART. The majority was probably infected in West Africa through heterosexual intercourse . The average T CD4+ nadir was 137 cells/mmThe last prescribed regimens were as follows:a) 73% (27): 2 NRTIs + 1 PI ;b) 19% (7): 2NRTIs (FTC/TDF) + 1 PI (DRV/r) + 1 INSTIs (RAL);c) 8% (3): dual/triple NRTIs.3 [3-239]. Currently: 21 (57%) pts are kept on follow up, 19 (90%) of whom on ART; 9 (24%)pts died (4 with AIDS related deaths) and 7 (19%)were lost to follow-up.Only one pt on RAL was ART na\u00efve. After a median follow-up of 11 months [4-24] on RAL based regimens, 3 pts had undetectable viral load (the remaining had it from the beginning). Median length of previous ART was 77 months with an average of 2.4 regimens/pt. The median gain of T CD4+ with RAL regimen was +94 cells/mmThis population had a fairly good T CD4 cell recovery while on therapy which is the best approach to assess treatment response together with clinical improvement. NRTIs/PI/INSTI containing regimens appears to be effective, although longer term outcomes are needed."} +{"text": "Vacuum-assisted core biopsy (VACB) of the breast is a minimally invasive technique, used increasingly for the assessment of mammographically and ultrasound detected, nonpalpable breast lesions. The effectiveness of VACB has been demonstrated on lesions both with and without microcalcifications. VACB allows the operator to obtain a sufficient specimen with a single insertion to provide for a more accurate diagnosis.n = 157) were identified. Of these, 133 were stereotaxis guided, the remaining 24 ultrasound guided. The overall lesion workload was as follows: asymmetrical densities = 6 (4%); mass = 31(20%); parenchymal distortion = 32(20%); and calcification = 88(56%).The aim of this study was to audit the use and effectiveness of ultrasound and stereotaxis guided VACB at a single centre over a 3-year period. We retrospectively identified patients from the Leicestershire Breast Screening Service and Radiology Information Systems records. A total of 152 patients undergoing 157 VACB of the total VACBs performed. Of these patients, 136 (88.9%) had a prior 14G core biopsy, 16 (10.5%) had VACB as a first-line procedure. Outcomes for VACB were then compared against 14G biopsies for individual histological grade, presented as follows - grade on 14G needle (definitive diagnosis percentage on VACB): B1 (83%); B2 (67%); B3 (62%); B4 (76%); and B5c (100%). Overall, 51 (33.6%) patients avoided surgery for benign breast disease (95% CI = 26.1 to 41.1%), and 33 patients (21.7%) had single definitive surgery thereby avoiding multiple procedures (95% CI = 15.2 to 28.3%).VACB is a safe, well-tolerated and extremely useful sampling modality which can, in selective cases, accurately determine onward surgical management and avoid unnecessary surgery for benign breast disease."} +{"text": "Novel reassortant swine H1N2 influenza viruses were isolated from pigs in a commercial slaughterhouse in the Republic of Korea. Genome sequence analyses revealed that these isolates contain segments from Eurasian avian-like swine (hemagglutinin [HA]), Korean swine H1N2 (neuraminidase [NA]), and North American H3N2pM-like (remaining genes) viruses. Further characterization is needed to gauge the potential threats of these viruses to public health. Swine influenza viruses (SIVs) of the H1N1, H1N2, and H3N2 subtypes remain endemic in major swine populations worldwide and reasIn April 2013, 12 H1N2 SIVs were isolated from monolayers of Madin-Darby canine kidney cells infected with supernatants of homogenized swine lung tissue collected in a commercial slaughterhouse located in Chungcheongbuk-do, Republic of Korea, which caters to various swine farms in the Chungcheong provinces. The whole-genome sequences were characterized and generated by reverse transcription PCR using influenza-specific primers as previously described , followeGenetic analysis revealed that all isolates are highly identical to each other (99 to 100% homology), suggesting that they came from the same farm. The viral genome, represented by A/swine/Korea/CY0423-12/2013(H1N2), consists of 8 single-stranded RNA segments: polymerase basic 2 (PB2), PB1, polymerase (PA), hemagglutinin (HA), nucleoprotein (NP), neuraminidase (NA), matrix (M), and nonstructural protein (NS), with corresponding nucleotide lengths of 2,341, 2,341, 2,233, 1,778, 1,565, 1,466, 1,027, and 890. Encoded viral proteins and amino acid lengths include PB2 (759), PB1 (757), PB1-F2 (90), PA (716), PA-X (232), HA (566), NP (498), NA (469), M1 (252), M2 (97), NS1 (219), and NS2 (121). Phylogenetic analyses revealed that the HA and NA genes belong to Eurasian avian-like H1 SIVs circulating in Hong Kong and preexisting Korean H1N2 SIVs, respectively. The internal segments clustered together with contemporary North American triple-reassortant H3N2pM-like SIVs, including the Korean isolates in 2012 (KF142492 to KF142499.The genome sequence of A/swine/Korea/CY0423-12/2013(H1N2) has been deposited in GenBank under accession no."} +{"text": "Neisseria meningitidis. The isolates were assigned to 3 clonal complexes (cc): cc11, cc32, and cc103. These hyperinvasive disease lineages were associated with endemic disease, outbreaks, and high case-fatality rates.During 2003\u20132012, 8 clusters of meningococcal disease were identified in Rio de Janeiro State, Brazil, all caused by serogroup C Neisseria meningitidis serogroup C meningococcal disease in Rio de Janeiro State, Brazil, occurred in 1994. It was caused by C:2b:P1.10 isolates that belonged to cluster A4 . Chemoprophylaxis with rifampin is currently recommended for close contacts of persons with confirmed or suspected cases of meningococcal disease.Public health surveillance of meningococcal disease in Rio de Janeiro State is conducted by the Meningitis Advisory Committee of the State Department of Health, which uses data obtained from 2 surveillance sources: mandatory reports of meningococcal disease cases and reports of laboratory-confirmed N. meningitidis of the same serogroup recovered from either a normally sterile site or detected by PCR. Reports of invasive meningococcal disease during 2000\u20132012 were obtained from the Meningitis Advisory Committee and analyzed by using EpiInfo . This study was approved by the Ethical Committee of the Evandro Chagas Research Institute of the Oswaldo Cruz Foundation.A cluster was defined as \u22653 cases of meningococcal disease with a clear epidemiologic link and with N. meningitidis or serogroup-specific PCR directly from cerebrospinal fluid samples or directly detected in cerebrospinal fluid samples (n = 24) was determined by multilocus sequence typing (MLST), and the antigenic profile was determined by sequencing antigen-encoding genes: porB, porA (variable regions 1 and 2), and fetA variable region (N. meningitidis MLST database (www.mlst.net).The genetic lineage of Serogroup C disease increased from 121 (26%) of 463 cases during 2000\u20132003, to 174 (44%) of 394 cases during 2004\u20132007, and to 499 (84%) of 594 cases during 2008\u20132012 (p<0.01). The case-fatality rate of serogroup C disease also increased during the same periods: 12%, 14%, and 19% (p = 0.03), respectively. These serogroup C isolates were mainly represented by 4 serologic phenotypes: C:23:P1.14\u20136 (60%), C:4,7:P1.7,1 (15%), C2a:P1.5,2 (12%), and C:4,7:P1.19,15 (6%).New cases associated with serogroup C meningococcal disease clusters occurred within an average of 15 days (range 1\u201330 days), and those infected had proximity to each other . The average age of patients was 13 years (range 10 months\u201351 years). The clinical signs and symptoms recorded when the person sought medical treatment were fever (98%), vomiting (80%), hemorrhagic rash (67%), headache (65%), neck stiffness (50%), impaired consciousness (41%), diarrhea (15%), abdominal pain (15%), convulsions (13%), sore throat (9%), and myalgia (6%). The overall case-fatality rate was 28% (13/46), ranging from 17% (cc103) to 44% (cc11) .Isolates assigned to clonal complex (cc) 11, cc32, and cc103 were associated with the clusters of meningococcal disease Technical; all werN. meningitidis infections in several countries during the 1990s clone from 2009 was found to express a serogroup W capsule , clusters of meningococcal disease marked a change in the epidemiology of N. meningitidis associated with invasive disease.Chemoprophylaxis to control clusters has been ineffective in preventing new cases, possibly because transmission might have been occurring among social networks that did not receive chemoprophylaxis. In addition, it is not known whether chemoprophylaxis reduces risk in educational institutions (Table showing characteristics of patients from clusters of serogroup C meningococcal disease, Rio de Janeiro State, Brazil, 2003\u20132012"} +{"text": "Conventional techniques for repairing interrupted aortic arch (IAA) using deep hypothermic circulatory arrest (DHCA) is known to be associated with the risk of postoperative neurological injury. We have used alternative technique with direct innominate artery cannulation for continuous cerebral perfusion, without DHCA, during repair of IAA in neonates regardless of patient\u2019s weight.Between September 1999 and July 2011, 32 consecutive children with IAA underwent repair using continuous, hypothermic (18 \u00b0C) low flow CPB without circulatory arrest. Associated cardiac lesions were Truncus Arteriosus (4), VSD (22), DORV (2), aortopulmonary window (4). Associated cardiac lesions were corrected in all except the DORV which were banded.Age at time of surgery was 7 days (4-120 days) and weight 3.1 kg (2.1 to 5.8 kg). Selective cerebral perfusion was maintained in all patients throughout aortic reconstruction. During the period of selective cerebral perfusion, pump flow rate was maintained at 30 mls/kg/min. Aortic cross clamp time, low-flow, and total CPB time were 66 (42-114), 29 (18-41) and 109 (83-217) minutes, respectively. There were no deaths or neurological injury in this series. Postoperative ventilation time, and length of ICU and hospital stay were 3 (2-14), 5 (3-21), and 13 (6-27) days, respectively. Follow-up, complete at 48 months (21-156), revealed no late neurologic sequelae nor innominate artery complications. There were three late re-stenosis of the aortic arch requiring balloon dilatation in 2 and surgical repair in 1.Direct innominate arterial cannulation with continuous selective cerebral perfusion can be safely applied during repair of IAA even with low birth weight neonates. It is technical simple and associated with excellent clinical outcomes."} +{"text": "Autoimmune hepatitis (AIH) is a progressive inflammatory fribrosing disease of the liver of unknown etiology, which in its normal progress leads to cirrhosis. It is characterized by the increase in aminotranferases and hypergammaglobulinemia, and the presence of non-organ and specific liver autoantibodies in serum, which allow for its classification. Two subtypes are differentiated: Type I AIH with anti-smooth muscle antibodies (SMA) and/or antinuclear antibodies (ANA); and Type II AIH with antimichondrial antibodies (LKM).AIH can be associated with other autoimmune illnesses such as thyroiditis, Type I diabetes, thrombocytopenia, hemolytic anaemia and ulcerative colitis. Likewise, the association to connective tissue diseases (CTD) has been communicated, such as Systemic Lupus Erythematosus, Sj\u00f6gren\u2019s Syndrome, Undifferentiated Connective Tissue Disease, Mixed Connective Tissue Disease, Localized Sclerodermia and Juvenile Idiopathic Arthritis.We aim to research defined or probable clinical and laboratory manifestations of CTD in patients with AIH diagnosis in pediatric age.20 records of patients with AIH diagnosis under care in the Hepatology Unit and Rheumatology Unit were analyzed retrospectively since 1995 until May 2008.In the group of 20 patients, 6 were male (30%) and 14 were female (70%). Their average AIH diagnosis age was 9.6 yrs (Min 1.4 yrs-Max 15.2 yrs). Type I AIH diagnosis occurred in 18/20 patients (90%), 5 males (27.8%) and 13 females (72.2%), their average diagnosis age being 9.8 yrs (Min 1.4 yrs-Max 15.2 yrs), and Type II AIH diagnosis occurred in 2/20 patients (10%), 1 male and 1 female. Their average AIH diagnosis age was 7.5 yrs (Min 4.2 yrs-Max 10.9 yrs). Average follow-up period of the patients until the end of the study was 41.4 months in average.8/20 patients with defined AIH (40%) showed some manifestations of CTD in their progress; 6/18 patients with Type I AIH (33.3%), 2 males and 6 females, and 2/2 patients with Type II AIH (100%). Most common manifestations were: arthralgia/arthritis, vasculitis, AHA with positive Coombs\u2019 Test results, oral ulcers, hypocomplementemia, leukopenia/lymphopenia and positive ANA results. CTD defined diagnosis were: SLE, vasculitis, Sj\u00f6rgren\u2019s Syndrome and Overlap Syndrome. In the remaining 4 patients diagnosis was probable. In one patient manifestations of CTD were simultaneous with AIH diagnosis. In 3/8 patients manifestations were before (25 months average) and in 4/8 were afterwards (29 months average).In 8 out of 20 patients AIH was associated with defined or probable CTD. Three of the 8 patients developed AIH after CTD diagnosis.This association should be investigated in all patients with AIH and CTD diagnosis."} +{"text": "We aimed to highlight the incidence, clinical course and therapeutic aspects of acute viral myositis in the epidemiological context of respiratory virus diseases in 2013.We performed a retrospective study on the clinical, biochemical, therapeutic and prognostic of patients diagnosed with viral myositis in the Clinic of Infectious Diseases I T\u00e2rgu-Mures between 01 January 2013 \u2013 30 April 2013.There were 578 clinically diagnosed cases of respiratory virus spread by age: 0-3 years: 40 cases (6.92%); 4-7 years: 81 cases (14.01%); 8-14 years old: 107 cases (18.51%); 15-20 years 38 patients (6.57%); over 20 years in 312 cases (53.97%); acute viral myositis was observed in a total of 22 patients (3.80%). Calendar distribution was as follows: in March, 14 cases (63.63%) compared to 6 cases (27.27%) in February, 1 case (4.54%) in January and 1 case (4.54%) in April 2013. The area of origin was urban in 18 cases (81.81%) and rural in 4 cases (18.19%). Mild clinical forms were common in 20 cases (90.9%), severe forms were determined by the prolonged evolution of the disease and association of neurological complications (polyradiculoneuritis) in 2 cases (9.1%). Positive diagnosis was clinical and laboratory confirmed (muscle enzymes). Evolution was favorable in all cases under treatment: corticosteroids and neurotrophic. Two patients received virological diagnosis, but in one of them we isolated influenza type B; this viral strain was isolated in most cases investigated virologically and confirmed with influenza viruses in patients with respiratory virus.Acute viral myositis was a complication of respiratory virus diseases of winter-spring season 2013, net prevailed at preschool age groups. The severity of the disease was low or moderate in the majority of cases, severe forms being determined by neurological damage. Therapeutic response to corticosteroid therapy was favorable."} +{"text": "Hereditary nonpolyposis colorectal cancer (HNPCC) is hallmarked by microsatellite instability. The prognosis of HNPCC-related colon cancer is well characterized, but little is known about rectal cancers. The aim of this study was to report the long-term outcomes of HNPCC-related rectal cancer where current-era multimodality therapy was utilized.Patients referred to our institution for either primary or recurrent rectal cancer between 1992-2010 were identified based on following inclusion criteria: 1) pathogenic germline mutation in DNA mismatch repair genes ; 2) germline variants of uncertain significance but tumor studies suggestive of MMR (n=6); 3) suggestive tumor studies but negative germline testing (n=5); and 4) suggestive tumor studies but no germline testing (n=4). Patients were reviewed for clinical characteristics and treatments, and followed to death or last contact.Among the 34 patients, 21 (62%) were female. The median age at diagnosis of rectal cancer was 40 (range: 20-72). In 28 patients (82%), this was the index cancer leading to the diagnosis of HNPCC, and in 22 patients (65%), this was their first malignancy. Only a minority satisfied Amsterdam I (21%) or Amsterdam II (21%) criteria, while nearly all (94%) met the revised Bethesda criteria. Pathogenic mutations included MLH1 (15%), MSH2 (32%) and MSH6 (9%). The majority (67%) presented with locally advanced or metastatic disease (n=3), and 50% received neoadjuvant radiation with 5-FU based chemotherapy. Final pathologic stages are as outlined below. Patients underwent proctectomy (65%), total/near total coloproctectomy (21%), transanal excision (9%), and chemoradiation only (3%). Multivisceral resection was required in 9 patients (28%) and adjuvant therapy was given in 24 (71%). After a median followup of 4.1 years, 94% were alive. Six patients developed local-regional (n=3) or distant (n=3) disease recurrence, and 5 underwent successful surgical salvage. Metachronous CRC was found in 4 patients (12%) after a median of 8 years (range: 3.2-17), and all were amenable to surgical resection. The estimated 5-year freedom from recurrent or metachronous CRC was 76%. The 5-year overall survival was 93%, which was preserved at 10-years. Table Rectal cancer may present as the index cancer for HNPCC over a wide age range. Despite advanced stages at presentation, excellent long-term prognosis can be expected with aggressive multimodality therapy. Vigilant surveillance for recurrent or metachronous CRC should be carried out over a prolonged time period to allow for repeat surgical salvage and preserved long-term survival."} +{"text": "Acute ascending aortic dissection is life-threatening condition that requires emergency surgery. When left untreated, about 33% of patients die within the first 24 hours, and 50% die within 48 hours. The aim of our study was to evaluate the clinical characteristics, management, and outcomes of patients with acute type A aortic dissection during the 5 years period.From January 2008 to December 2012, 227 patients aged 12 to 84 years (mean 58) underwent emergency operation for type A aortic dissection. Mean admission-to-table time was 2.3 (1-19) hours. Cannulation was accomplished in 211(92.9%) patients through the femoral artery. Supracommissural replacement of the ascending aorta was applied to 146 (64.3%) patients. In 52 patients (22.9%), the aortic valve was replaced either independently or by means of a composite graft . \u201cOpen distal anastomosis\u201d strategy was applied in 63 patients (27.8%) with isolated replacement of the ascending aorta, 47 pts (20.7%) with transverse arch, and 10 pts (4.4%) with total arch replacement, 3 (1.3%) of whom had an \u201celephant trunk\u201dgraft extension.Overall early mortality was 23.3% (53 pts): operative 7.5% (17 pts) and hospital 15.9% (36 pts). The early major postoperative complications were: low cardiac output syndrome 28 pts (12.3%), hemorrhage 24 pts (10.5%), focal neurological deficit 26 pts (11.4%), coma 16 pts (7.0%) and acute renal failure 12 pts (5.3%).During this period of time, we have adopted a strategy of \"the earliest possible surgery\", reducing preoperative diagnostic algorithm on carefully clinical examination and the least possible number of imaging tools. The more successful tactics of aortic dissection treatment should focus on: earlier clinical suspicion and diagnosis decrease in \"onset-to-admission\" time, improvements in surgical strategy/ technique and establishment of National aortic dissection registry."} +{"text": "In Table 1, the numbers of US medical schools should have been 130 (circa 1970), 173 (circa 2010), and 43 (change), instead of 126, 174, and 21 respectively. Please see the corrected Table 1 here: ."} +{"text": "To estimate peculiarities of diagnosis and clinical course of generalized TB in HIV patients with AIDS who received treatment in TB Hospital #7, Moscow in 2006-2009.94 cases of generalized TB have been analyzed. Most of them are men , the mean age of the patients being 31,2\u00b17,02. The average period from HIV detection to TB diagnosis is 5,7\u00b12,96 years.3. M. tuberculosis was found in 52 cases : in the sputum analyses of 26 patients and in 26 more analyses of other biological materials . Among 29 patients tested for TB drug resistance 13 proved to be multidrug-resistant TB cases. The chest X-ray examination showed intrathoracic lymphoadenopathy in 68,1% cases, interstitial dissemination in 29,7% cases and only 7,5% cases revealed disintegration of tissue. 77 patients underwent different surgical interventions for the purpose of diagnosis or treatment, namely: diagnostic laparoscopy (16 cases), curative laparotomy (22), mediastinoscopy with intrathoracic lymph node biopsy (4), pleura biopsy (9), debridement of a peripheral lymph node (17), pericardial microdrainage (6), pleural cavity drainage (2), orchectomy (1). While examining the received diagnostic material morphological markers of TB inflammation were found in 56 cases . Among most often discovered extrapulmonary localizations are abdominal involvement , nodal involvement , meningoencephalitis , pericarditis . Involvement of more than 3 systems was diagnosed in 25 patients . Specific TB treatment included 4 to 6 drugs, the follow-up period for complete treatment was 6 months. Treatment results: cured - 36 cases , defaulters - 34 cases , died - 24 cases .In 62 cases (66%) the clinical TB symptomatology developed quite fast, in 2,2\u00b11,9 months on average. An acute beginning was seen in 32 cases (34%). 44 patients had both TB and other secondary diseases. The CD4 lymphocyte mean level was 91 cells/mm3 before treatment increases significantly the probability of an unfavorable outcome of generalized TB.Thus, providing treatment and diagnosis to patients with multiple-localization TB is complicated and requires an interdisciplinary approach including different surgical methods of diagnosis and treatment. The CD4 lymphocyte level lower than 100 cells/mm"} +{"text": "Rapid expansion of smartphones use in the clinical setting has been reported. Purpose of this review is to summarize the smartphone applications (apps) useful for thoracic surgeons.We\u2019ve searched the online stores of the most popular smartphone for specific thoracic surgery apps. Search terms were: thoracic surgery, lung cancer, esophageal, chest, surgery; data were then stored and analyzed.We\u2019ve found a total of 159 apps; we\u2019ve excluded from our study 85 apps, related to patient education and basic medical knowledge, and 22 apps designed for students. Fifty-two apps were elegible for our study, all of them reporting a medical involvement or a bibliographic support. The topics were online version of journals (10 apps), TNM staging tools (6), risk assessment (5), radiology tools (9), pulmonary function test evaluation (3), past cardiothoracic annual meetings (6), guidelines/online resources (9), self-evaluation quiz (4). Three apps (6%) were released in 2010, 9 (17%) in 2011, 28 (54%) in 2012 and 12 (23%) in 2013. Forty-six apps (88%) were free of charge. Six (12%) had a price ranging from 0.89 to 17.99 \u20ac (average 5.39 \u20ac). Only three (6%) had customer satisfaction rating (5-16 rates), with an average vote of 4.3 out of 5 (range 3-5).Smartphone apps can improve education, diagnostic and therapeutic skills of thoracic surgeons. Initial data from this study can be useful for thoracic surgeons to try and rate smartphone apps in their daily practice, guiding developers to release updated and high-quality apps."} +{"text": "Although occurrence of seizures is common in the course of viral encephalitis, its influence on outcome is less known .The frequency and type of seizures in 229 patients with viral encephalitis were studied. We compared frequency of loss of consciousness, mental disorders, respiratory failure, need for intubation, mechanical ventilation and hospitalization in the ICU, duration of hospitalization and degree of disability at discharge from the hospital according to the Glasgow Outcome Scale (GOS).P < 0.001), loss of consciousness in 28 (90.32%) versus 16 (8%) patients (P < 0.001) and need for intubation, mechanical ventilation and hospitalization in the ICU . The mean total time of hospitalization was substantially longer in patients with seizures in comparison with the group without them . Patients presenting seizures were prognosticated worse in the scope of good recovery as well as every degree of disability in comparison with a group of patients without attacks (P = 0.001). Outcome after viral encephalitis according to GOS in patients with seizures (31) and without them (198) was as follows: GOS 5 (good recovery) - 19 (61.2%) versus 180 (90.9), GOS 4 (moderate disability) - 7 (22.5%) versus 12 (6%), GOS 3 (severe disability) - 4 (12.9%) versus 5 (2.5%), GOS 1 (death) - 1 (3.2%) versus 1 (0.5%).Patients with seizures (31), significantly more frequent in comparison with patients without attacks (198), presented: mental disorders in 17 (54.83%) versus 62 (31.31%) patients (The occurrence of single generalized seizures, epilepsy and particularly status epilepticus had substantial influence on a course of viral encephalitis and worsened the outcome. Appearance of every type of seizure attack, independent of other clinical symptoms, was a good indicator of the disease severity."} +{"text": "Healthcare worker hand hygiene is thought to be one of the most important strategies to prevent healthcare-associated infections, but compliance is generally poor. Hand hygiene improvement interventions must include audits of compliance , which are most often done by direct observation - a method that is expensive, subjective, and prone to bias. New technologies, including electronic and video hand hygiene monitoring systems, have the potential to provide continuous and objective monitoring of hand hygiene, regular feedback, and for some systems, real-time reminders. We propose a systematic review of the evidence supporting the effectiveness of these systems. The primary objective is to determine whether hand hygiene monitoring systems yield sustainable improvements in hand hygiene compliance when compared to usual care.MEDLINE, EMBASE, CINAHL, and other relevant databases will be searched for randomized control studies and quasi-experimental studies evaluating a video or electronic hand hygiene monitoring system. A standard data collection form will be used to abstract relevant information from included studies. Bias will be assessed using the Cochrane Effective Practice and Organization of Care Group Risk of Bias Assessment Tool. Studies will be reviewed independently by two reviewers, with disputes resolved by a third reviewer. The primary outcome is directly observed hand hygiene compliance. Secondary outcomes include healthcare-associated infection incidence and improvements in hand hygiene compliance as measured by alternative metrics. Results will be qualitatively summarized with comparisons made between study quality, the measured outcome, and study-specific factors that may be expected to affect outcome . Meta-analysis will be performed if there is more than one study of similar systems with comparable outcome definitions.Electronic and video monitoring systems have the potential to improve hand hygiene compliance and prevent healthcare-associated infection, but are expensive, difficult to install and maintain, and may not be accepted by all healthcare workers. This review will assess the current evidence of effectiveness of these systems before their widespread adoption.CRD42013004519PROSPERO registration number: Healthcare-associated infections (HAIs) lead to significant morbidity, mortality, and excess hospital costs. In 2002, it was estimated that HAIs affected 1.7 million patients in the US, resulted in 99,000 deaths, and were associated with excess healthcare costs of\u2009>\u2009USD 5 billion (998131)14 exp anti infective agents/ (1244944)15 exp Decontamination/ (3345)16 disinfect$.mp. (30342)17 or/12-16 (2181031)18 12 and 17 (76024)19 exp hand hygiene/ [includes the MeSH Hand Disinfection] (4492)20 (hand adj2 wash$).mp. (1782)21 (hand adj2 hygiene$).mp. (1971)22 (hand adj2 clean$).mp. (218)23 (hand adj2 sanitiz$).mp. (162)24 (hand adj2 disinfect$).mp. (4688)25 or/19-24 (6625)26 18 or 25 (76904)27 exp population surveillance/ (50191)28 exp population surveillance/ (50191)29 surveillance.mp. (136275)30 monitor$.mp. (606051)31 feedback.mp. (95605)32 alarm.mp. (6107)33 or/27-32 (819570)34 26 and 33 (7684)35 exp automation/ [includes MeSH robotics] (25847)36 automated system.mp. (2316)37 automatic$.mp. (76950)38 sensor$.mp. (242568)39 RFID.mp. (423)40 exp Radio Frequency Identification Device/ (220)41 exp Electronics/ (25648)42 exp Video-Audio Media/ (5502)43 (monitor adj2 computer$).mp. (656)44 (monitor adj2 video$).mp. (481)45 (monitor adj2 electr$).mp. (812)46 (system$ adj2 computer$).mp. (38430)47 (system$ adj2 video$).mp. (2522)48 (system$ adj2 electr$).mp. (16530)49 exp tape recording/ [includes Videotape Recording] (14287)50 computer.ti,ab. [title or abstract] (158475)51 video.ti,ab. [title or abstract] (47539)52 exp computer systems/ (136153)53 or/35-48 (409583)54 34 and 53 (268)55 remove duplicates from 55 (252)The authors report no financial or non-financial conflicts of interest.JAS and MPM contributed to the conception and design of the review. JAS wrote the draft protocol and registered the protocol with the PROSPERO database. JAS, DL, MG, and MPM will be involved in data acquisition. JAS, GF, MG, and MPM will synthesize and interpret results. All authors were involved in the editing of this protocol and have given their approval for publication."} +{"text": "A large RCT of our research group demonstrated that targeting age-adjusted normal fasting blood glucose concentrations with insulin infusion improves outcome in critically ill infants, children and adults -3. TightWe performed a retrospective data analysis on all pediatric patients admitted to the Leuven PICU over a 12-month period, from 1 January 2009 to 31 December 2009.One hundred and forty-two of the 333 PICU admissions (43%) were infants (<1 year) and 191 of 333 (57%) were children (1 to 16 years). We obtained a total of 12,208 blood samples in the infant group. The mean blood glucose level per infant was 98 mg/dl, the median was 86 mg/dl (interquartile range 67 to 111 mg/dl). Forty-six infants (32%) experienced at least one hypoglycemic period. Hypoglycemia (<40 mg/dl) was noted in 168 (1.4%) of the samples, and 37 samples (0.3%) were extreme hypoglycemic (\u226430 mg/dl). A total of 8,008 blood samples were taken in the children's group. The mean blood glucose level per child was 116 mg/dl, the median was 103 mg/dl (interquartile range 88 to 125 mg/dl). Sixteen (8%) children experienced at least one hypoglycemic period. Twenty-two samples (0.3%) were hypoglycemic (<40 mg/dl) and three samples (0.04%) were extreme hypoglycemic (\u226430 mg/dl).Even outside the setting of a RCT, the blood glucose control achieved in clinical practice mimicked that during the study on tight glycemic control in critically ill infants and children . The ris"} +{"text": "Darunavir/Ritonavir (DRV/r) dosed 600/100 mg bid has shown good efficacy and tolerability in treatment-experienced patients in clinical trials . To assess whether these results can be transferred to clinical practice and a more diverse patient population this prospective non-interventional Janssen-sponsored cohort study was established.Between August 2007 and March 2009, 340 HIV-1 infected antiretroviral-experienced patients from 62 German centers enrolled in this non-interventional cohort. All patients received DRV/r 600/100 mg bid as part of their HAART. Virological and immunological response was monitored every 3 months. Patients were followed for up to 48 weeks.10 copies/mL (SD 5.44) with a mean CD4 count of 392 cells/mm3 (SD 251); 213 (63%) patients started therapy with CD4 < 200 cells/mm3. Patients had been pretreated with NRTIs (94%), PIs (88%), NNRTIs (63%), FI (11%), INI (5%) and/or CCR5 (3%). No data is available for 17 patients. At baseline, only 138 patients received DRV/r in combination with 2 NRTIs; the majority (202/340) of patients received DRV/r in different combinations based on the individual pretreatment situation. Of note, 116 patients received a combination containing DRV/r, RAL + other antiretrovirals. ETR and DRV/r plus other ARVs were used in 23 patients. 51 patients received an NRTI-sparing regimen. At the time of this analysis, 32 patients had discontinued prematurely and 251/340 patients had reached week 48. VL and CD4 measurements at week 48 are available for 186 patients, 80.6 % patients achieved a VL < 50 copies/ml (VL < 400 copies/ml: 94.6 %), mean CD4 count in these patients (n=185) increased from 402 at baseline to 476 cells/ mm3 . 10 patients (2.9%) discontinued DRV/r due to adverse events. Virological failure (VL >50 copies/mL at 2 visits) was documented in 10 patients (2.9%). 3 patients were genotyped; primary PI mutations were detected in all 3 patients, DRV-RAMs in none of them.296/340 (87%) patients were male with a mean age of 47 years (SD 9.9); median time since HIV diagnosis was 12 years. At baseline, mean viral load (VL) was 4.7 logOverall, Darunavir/r, dosed at 600/100 mg bid in combination with other antiretrovirals, showed good efficacy and safety in treatment-experienced patients in clinical practice."} +{"text": "To the Editor: Four species of human bocavirus (HBoV1\u20134) have been identified since 2005 detected in respiratory samples. Nasopharyngeal aspirates were collected from 1,238 children (784 boys and 454 girls) with acute lower respiratory tract infections hospitalized in Beijing Children\u2019s Hospital from March 2008 through July 2010. Patients\u2019 ages ranged from 1 month to 9 years .Viral nucleic acid was extracted from nasopharyngeal aspirates by using the NucliSens easyMAG system . We screened for HBoV1\u20134 by nested PCR with touch-down procedure using primers targeting the viral proteins (VP) 1/2 region . Additio<5 years old was 124/131 (94.7%), 4/5 (80%), and 4/5 (80%), respectively. Additional respiratory viruses were co-detected in 120/141 (85.1%) HBoV-positive patients (9 copies/mL) and 2/5 positive samples for HBoV3 . In contrast, we detected viral loads of 8.35 \u00d7 104 to 1.28 \u00d7 109 copies/mL in 5 randomly selected HBoV-1\u2013positive samples.We found 141 positive samples for HBoVs (11.4%) from patients ranging in age from 1 to 132 months (GenBank accession nos. HQ871520\u2013HQ871650 and HQ871664\u2013HQ871673). Among these samples, 131 were positive for HBoV1, 5 for HBoV2, and 5 for HBoV3 on the basis of sequence alignment and phylogenetic analysis of PCR amplicons. No specimens were positive for HBoV4. The number of samples positive for HBoV1, -2, and -3 in children patients . An unanThe clinical diagnoses of patients providing HBoV-positive samples included pneumonia (63.1%), bronchitis (14.9%), bronchopneumonia (12.8%), and acute asthmatic bronchopneumonia (9.2%). No clinically significant differences were found between the signs and symptoms of patients with HBoV1, -2, and -3 . For patients positive for HBoV3, the major diagnoses were pneumonia (2/5), bronchopneumonia (2/5), and acute asthmatic bronchopneumonia (1/5). Main signs and symptoms included cough (5/5), wheezing (4/5), sputum production (3/5), fever (3/5), runny nose (1/5), and diarrhea (1/5). For patients positive for HBoV2, the diagnoses were pneumonia (4/5) and bronchopneumonia (1/5), and main signs and symptoms included cough (5/5), sputum production (4/5), wheezing (3/5), fever (3/5), and runny nose (2/5) .HBoV2 and HBoV3 were detected sporadically during the study. HBoV3 was detected in samples collected in July and October 2008, December 2009, and March and April 2010, whereas HBoV2 was detected in May, June, and October 2008, March 2009, and January 2010. The prevalence of HBoV1, which was responsible for 92.9% of the HBoV cases, was highest in January 2009 and April 2010.Multiple-alignment analysis of sequences obtained in this study and reference sequences from GenBank by using MEGA 4.0 (In summary, we report detection of genomic DNA of HBoV1, -2, and -3 in children with lower respiratory tract infections in China. The predominant HBoV species identified in our study was HBoV1. HBoV2 and HBoV3 appear to be present in much fewer positively identified cases and their viral load seems very low. For these latter viruses, however, low level mucosal contamination from the gastrointestinal tract cannot be entirely excluded in all cases. Further investigations are needed to confirm potential associations of HBoV2 and HBoV3 with acute lower respiratory tract infections, to determine their replication in the respiratory tract, and the viruses\u2019 role in human disease.Real-time PCR for Human Bocavirus."} +{"text": "Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are two major forms of primary liver cancer. The aim of this study was to investigate CD79\u03b1 (HM47/A9) antibody expression patterns in normal liver, HCC and ICC samples. HM47/A9 expression was examined in tissues surrounding liver cancer in adults, 8-week embryos and 20-week embryos. In total, 82 cases of HCC, 31 cases of ICC and 11 cases of combined HCC and cholangiocarcinoma (cHCC-CC) were reviewed. HM47/A9 expression was observed as early as 8-week embryo liver tissue and exhibited focal granular cytoplasmic positivity, which was maintained throughout life. All 82 HCC cases demonstrated cytoplasmic granular positivity for HM47/A9, while no ICC cases were immunostained with HM47/A9. No CC components in cHCC-CC expressed the HM47/A9 antibody. A high number of HCC components in cHCC-CC showed positive staining for HM47/A9 [10/11 (90.9%)]. Our results suggest that HM47/A9 may be employed effectively to differentiate HCC from ICC. Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) constitute two major forms of primary liver cancer. The two malignancies have different clinical and pathological features and prognosis, but in some cases histopathological overlap exists. Immunochemistry is thus required to facilitate differential diagnosis between HCC and ICC. To date, several antibodies, such as cytokeratin 19 (CK19), CD10, Hep Par 1, AFP, CA19-9, MOC31, glypican-3 and CEA, have been used to differentiate between the two malignant tumor types , including 82 cases of HCC, 31 cases of ICC and 11 cases of combined HCC and cholangiocarcinoma (cHCC-CC), which were subjected to resection or puncture. All specimens were fixed in 10% neutral-buffered formalin, dehydrated in graded alcohol solutions, embedded in paraffin and cut into 4-\u03bcm-thick sections for hematoxylin and eosin staining, followed by visualization using light microscopy.Immunohistochemical staining was performed on formalin-fixed, paraffin-embedded tissue sections using the EnVision method. The primary antibodies employed included CD79\u03b1 (HM47/A9), AFP (ZSA06), CK19 (A53-B/A2.26), MOC31 (MOC31), CA19-9 (TA888), CEA (Col-1) and Hepatocyte (OCH1E5). All antibodies were purchased from Maxin-Bio Co. . Slides were counterstained with hematoxylin. To observe mallory hyaline bodies and globular hyaline bodies, slides were counterstained with eosin after immunostaining for CD79\u03b1.The 82 HCC patients included 48 males and 34 females with a median age of 46 years . The 31 ICC patients included 16 males and 15 females with a median age of 51 years . The 11 cases of cHCC-CC occurred in 6 males and 5 females with a median age of 48 years .Normal hepatocytes exhibiteIn the 8-week embryo liver , \u223c20% ofHCC cells resembled hepatocytes . Some tuICC cells were round or oval, and some were pleomorphic . Nuclei Each of the CC parts in cHCC-CC [11/11 (100%)] did not express HM47/A9. The majority of HCC components in cHCC-CC [10/11 (90.9%)] exhibited positive staining for HM47/A9. The excluded case was in a 26-year-old female. These tumor cells demonstrated a similar histology to hepatocytes, with abundant eosinophilic or vacuolated cytoplasm and a centronucleus. Prominent nucleoli were observed in the nucleus. Tumor cells grew as entities and invaded the inter-lobular bile duct wall . SignifiPale bodies, mallory hyaline bodies, fatty degeneration and globular hyaline bodies were negative for HM47/A9 .CD79\u03b1, also known as Ig\u03b1, is encoded by mouse B cell-specific gene 1 (mb-1) . The genCD79\u03b1 expression precedes immunoglobulin heavy-chain gene rearrangement and CD20 expression, and disappears later than CD20 in the plasma cell . In our We additionally compared HM47/A9 expression in hepatocytes from normal and diseased livers. As mentioned previously, HM47/A9 was expressed in hepatocytes, but not in the bile canaliculus or interlobular bile duct. In view of these findings, we hypothesized that HM47/A9 expression patterns differ among HCC, ICC and hepatic metastatic carcinoma. In this study, we observed that 82/82 HCC cases expressed HM47/A9, while no cases of ICC were positive for HM47/A9 (0/31). These results strongly support the utility of the HM47/A9 antibody in distinguishing HCC from ICC.None of the 11 CC areas in cHCC-CC expressed HM47/A9. A majority of HCC components (10/11) in cHCC-CC showed positive staining for HM47/A9. The excluded case was a notable case of cHCC-CC, a rare subtype of primary liver carcinoma \u201314. HoweWe additionally examined HM47/A9 expression in pale bodies, fatty degeneration, clear cell change, mallory hyaline bodies, intranuclear inclusion and glycogen. Notably, HM47/A9 granular expression was observed around pale bodies, fatty degeneration, clear cell change and mallory bodies, indicating that HM47/A9 is not a component of intermediate filaments, endoplasmic reticulum, glycogen and fat \u201320.In conclusion, our results strongly suggest that HM47/A9 is an important protein component in hepatocytes that may be effectively employed to differentiate HCC from ICC. HCC with bile duct differentiation had poor prognosis, which may be related to the loss of HM47/A9."} +{"text": "Circulatory support is usually not available in developing countries due to cost restrictions. Long-term devices are almost always not affordable for our health system and Thoratec Centrimag\u00ae may be an alternative. We report our experience in the treatment of cardiogenic shock with this intermediate-term device.Thoratec Centrimag\u00ae was used in 22 cardiogenic shock patients. All were INTERMACS class I and all but one had multiorgan failure. Seventeen (77%) were male, mean age 41+13 years. Etiology was ischemic in 11(50%), dilated in 4(22%), and other etiology in 7(32%). Nine (41%) had previous cardiac arrest with a mean arrest time of 18+16 min. Circulatory support was biventricular in 18(82%), univentricular 4(18%), and in 6(27%) an oxygenator was interposed within the outflow line until respiratory recovery. Patients with veno-arterial ECMO configurations were excluded.Bridge-to-transplant or recovery was obtained in 14 out of 22 (64%). Mean support time 44 days, range 1-292 days. Eight patients (36%) were supported for more than 4 weeks. Thirty-day post-implant survival was 73% (16 patients). Post-implant complications were re-exploration for bleeding 7(32%), neurologic dysfunction 3(14%), pneumonia 8(36%), and renal failure with dialysis in (32%). Eleven (50%) patients are in NYHA class I after a mean follow-up time of 32+6 months. Kaplan Meier one-year survival was 56+11%. Eleven out of 12 (92%) bridged-to-transplant are in NYHA functional class I with normal biventricular function. One patient died 3 days post-transplant due to inflammatory response. Two patients were bridged-to-recovery. One is in NYHA class I and the other died due to non-compliance.Thoratec Centrimag\u00ae is useful to provide intermediate-term circulatory support for cardiogenic shock and multiorgan failure in a developing country. Support time longer than 4 weeks is feasible. A multidisciplinary approach is needed since morbidity is common."} +{"text": "Many families seek natural therapies for children. We describe what families want when they seek consultation for natural therapies for children with ADHD.For new patients seen in an integrative pediatric clinic between 1/2010 and 6/2011, we reviewed intake forms, physician reports, and laboratory studies.Of the 75 new patients, 23 (31%) families had concerns about ADHD. Of these, 70% were male; the average age was 11.2 \u00b1 3.1 years; and 80% also received care from specialists. Eleven patients (48%) were taking a prescription medication, but only 3 (13%) were taking medicine for ADHD; dietary supplements were taken by 12 patients (52%). Most families were interested in health promotion information about diet (87%), exercise (78%), stress management (74%), and sleep (74%). Of 11 patients tested, 82% had low ferritin. Recommendations focused on health promotion (100%), dietary supplements such as multivitamins/minerals (71%) and omega-3 fatty acids (82%), and specialist referrals (30%).Families seeking natural therapies for children with ADHD have needs for health promotion and care coordination that are well addressed using tools and skills already present in the medical home."} +{"text": "Post-traumatic stress disorder (PTSD) comprises a collection of symptoms following exposure to injury-causing accidents of life. It is estimated that the prevalence of PTSD in children with malignancy and their parents is between 10-30% and even several years after treatment of malignancy this disorderremain in 20-20% of these patients.This study investigated the prevalence of post-traumatic stress disorder in parents of children with cancer.In this analytic-descriptive study, 256parents of children with cancer (mean age: 30.06 \u00b1 14.6 years-old) that their children treated in pediatric hematology ward of Ali ebn-e Abitaleb (AS) teaching hospital of Zahedan city (south east of Iran) at 2009-2010 were evaluated. The demographic data and symptoms of PTSD were collected by standard questionnaire (based on DSM-IV). After data analysis was performed using statistical software SPSS (version 18).All parents who were studied had PTSD. The severity of PTSD in 111 of parents was mild, in 103 (40.2%) moderate and in 42 (16.4%) parents was severe. Furthermore, there were a significant correlation between the severity of PTSD with number of children, age of parents, gender, literacy, religion and economic state (P = 0.001).Our results showed that factors such as age, sex, number of children, educational state and religion of parents with economic state of the family can effect on the severity of PTSD. As for role of parents of children with chronic disease especially malignancy diseases on decline of psycho-social disorders with mental and physical supports of their children should be given the necessary recommendations and educations regarding PTSD. Basicaldulthood . It is edulthood . It is BThe aim of this study was to evaluate post-traumatic stress disorder (PTSD) and related factors in parents of children with cancer in south east of Iran at 2009-2010.In this cross-sectional observational descriptive-analytical study, 256 parents of children with cancer (mean age: 30.06 \u00b1 14.6 years-old) that their children were treated in pediatric hematology ward of Ali ebn-e Abitaleb (AS) teaching hospital of Zahedan city (south east of Iran) at August 2009- April 2010 were studied. The selection of samples was performed by simple random method and information was collected during 9 months. then the description of the necessary information regarding PTSD to interviews, early demographic information of studied persons including of: sex, age and literacy of parents, sex and age of their patient child, number of child, number of hospitalization of child, religion, family history of malignancy, family income was registered in the informational forms. Inclusion criteria for selection of parents were included:1. At least 4 weeks had elapsed from diagnosis of malignant disease in their child.2. In course of remedy patient child had owned no relapse period.et al in Iran) was used (2) test was used to determine the correlation between quantitative variables (demographic data of studied persons in PTSD severity subgroups). Also Fisher Exact test was used as needed (for definition ofcorrelation between quantitative variables), by using a significant level of P < 0.05.It should be mentioned that parents of the children with the following conditions had been excluded from our study while: death of child in duration of study, disinclination of parents for continuance of their child treatment. For survey of PTSD, was used the PTSD standard questionnaire according TO DSM-IV-TR that its validity had been confirmed by Mohammadi was used . The queIn this study, of 256 parents of children with malignancy, 128 persons (50%) were male. The average age of studied parents was 30 \u00b1 14.6 years-old (Age range: 29-75 years), the mean age in males was 32.6 \u00b1 14.7 years-olds (Age range: 31-75 years); and among females was 27.2 \u00b1 14.1 years-old (Age range: 29-70 years) that there was no correlation between genders (P = 0.056).It should be noted that 129 persons of studied parents (50.3%) had age lower 35 years, 111 persons (43.5%) aged 35-50 years and 16 persons (6.2%) had upper 50 years-old. Of 130 pediatric patients with malignancy, 87 patients (66.9%) were males and 43 patients (33.1%) female. In addition, 48 children (36.9%) lower 5 years, 47 children (36.1%) 5-10 years and 35 children (27%) had upper 10 years respectively. In studied patients children, 64 children (49.2%) leukemia, 28 children (21.6%) lymphoma, 38 children (29.2%) had solid tumor . Of 64 children with leukemia, 34 children (53.1%) in the standard risk (SR), and 30 children (46.9%) were (46.9%) in the High risk (HR).Also, of 28 children with lymphoma, 8 children (28.6%) were in stage II of disease, 7 children (60.7%) in stage III and 3 children (10.7%) in stage IV. Among 38 children with solid tumor, 17 children (44.7%) were in stage II, 14 children (36.9%) in stage III and 3 children (10.7%) in stage IV disease. 85 parents (33.2%) were illiterate and in educational level, 75 persons (29.3%) were elementary school, 44 cases (17.2%) guide school, 49 cases (19.1%) high school/graduate and 7 persons (1.2%) were upper than graduate. Of 256 surveyed parents, 90 persons (35.1%) had 1-3 children, 84 persons (32.8%) 4-6 children and 90 persons (35.1%) had more than 6 children. The Number time of hospitalization of the patients children, in 125 parents (48.8%) was 2-5 times, 75 parents (29.3%) 6-10 times, 36 parents (14%) 11-15 times and 20 parents (7.9%) was Upper than 15 times. Only 21 studied persons (8.2%) had positive family history for malignancy. The levels of family income in 37.1% of studied persons were low income , and 46.4% moderate income and 16.5% had high income . All surveyed parents (100%) were Muslim, and for Islamic religion 109 persons (42.5%) Shiite and 147 persons (57.5%) were Sonnat. In our study, all assessed parents had some degree of PTSD, that the severity of PTSD in 111 cases (43.4%) was mild, 103 persons (40.2%) moderate and 42 persons (16.4%) severe. In 127 studied parents of patient child with leukemia, 56 persons (44.1%) had mild PTSD, 51 persons (40.2%) moderate PTSD and 20 persons (15.7%) severe PTSD. Also, in 56 studied parents of patient child with lymphoma, 24 persons (42.9%) had mild PTSD, 26 persons (46.4%) moderate PTSD and 6 persons (10.7%) severe PTSD. Of studied parents that had patient child with leukemia (73 persons), 31 persons (42.5%) had mild PTSD, 26 persons (35.6%) moderate PTSD and 16 persons (21.9%) severe PTSD (P = 0.486). in parents of children with stage II Solid Tumor/ Lymphoma, 25 persons (49%) had mild PTSD, 42 persons (43.2%) moderate PTSD and 4 persons (7.8%) severe PTSD; and among parents of children with stage III Solid Tumor/ Lymphoma, 24 persons (40%) had mild PTSD, 26 persons (43.3%) moderate PTSD and 10 persons (16.7%) severe PTSD. Also among parents of children with stage IV Solid Tumor/ Lymphoma, 7 persons (35%) had mild PTSD, 5 persons (25%) moderate PTSD and 8 persons (40%) severe PTSD. It Should be mentioned that among 65 studied parents of patient child with standard risk (SR) leukemia, 29 persons (44.6%) had mild PTSD, 28 persons (43.1%) moderate PTSD and 8 persons (12.3%) severe PTSD; while in 60 studied parents of patient child with high risk (HR) leukemia, 26 persons (43.3%) mild PTSD, 22 persons (36.7%) moderate PTSD and 12 persons (20%) had severe PTSD (P = 0.119). The distribution of PTSD severity in parents of child with malignancy based on the type and stage of malignancy in child has been shown, respectively in Furthermore, the distribution of PTSD severity in parents of child with malignancy based on the sex, age and literacy of parents, sex and age of child, number of child, number of hospitalization of child, Islamic religion, family history of malignancy and family income has been displayed in PTSD prevalence have been reported 10-35% in previous studies , 9. In o"} +{"text": "Sudden cardiac arrest (CA) is one of the leading causes of death in adults in many parts of the world . Every yAim of the study was to determine cause and outcome of CA in patients with liver cirrhosis after CPR.Out of a cohort of 1068 consecutive patients who were successfully resuscitated and treated at the Medical University of Vienna, 47 (4%) patients with liver cirrhosis could be identified. Patient characteristics, admission diagnosis, severity of disease, course of the disease and 28d mortality were assessed.Overall 47 patients with liver cirrhosis and CA with successful CPR were assessed. 17 patients had Child-Pugh A, 17 Child-Pugh B and 13 Child-Pugh C. SOFA-Score on admission was 11 \u00b1 5, MELD-Score was 18 \u00b1 8 on admission. Cause of liver cirrhosis was alcohol in 35 patients, viral hepatitis in 6 patients and other causes in 6 patients.Cardiac events leading to CA were observed in 21 (44%) patients. Initial rhythm was VF/VT in 10 (21%) patients, asystole in 11 (24%) patients, PEA in 24 (51%) patients and unknown in 2 (4%) patients. 31 (66%) patients suffered CA out-of-hospital. Time to ROSC was 17 \u00b1 15 minutes.28d-survival was overall 28%. 37 (78%) patients were dead after 1 month or had bad neurological outcome (CPC III/IV). None of the patients with Child-Pugh C cirrhosis survived 1 month with good neurologic outcome.Cause of CA in patients with liver cirrhosis is rarely cardiac. About one quarter of patients with liver cirrhosis survived more than 28d after successful CPR. No patient with Child-Pugh C cirrhosis survived longer than 28d after successful CPR with good neurological outcome."} +{"text": "Remifentanil target-controlled infusion (TCI), widely used in the operating room owing to its reliability, is poorly assessed in the ICU, while several procedures may induce pain and discomfort. Only one series of 14 patients focused on Remifentanil-TCI use for performing fiberoptic bronchoscopy (FB) in the ICU and number (percentage), respectively.From November 2014 to March 2015, 40 patients were included. FB was performed in patients receiving nasal oxygen (85%), high-flow humidified oxygen (12.5%) or non-invasive ventilation (2.5%), and a broncho-alveolar lavage was done in 7 patients (17.5%). Total infusion duration was 22 minutes [15-29], TCI concentration goal was 4 ng/mL [3.5-5.5] and total drug dose infused wad 279 \u00b5g [196-377].FB was performed completely without any additional drugs in 38 patients (95%), whereas propofol was used in 2 (5%). Three patients presented side effects comprising bradypnea (n = 1) and hypotension that occurred during the procedure and were completely reversible with TCI goal decrease. Thus, FB was performed entirely without additional anesthesia or complication in 35 patients (87.5%).Comfort was assessed in 28 patients (70%): 22 (79%) stated that they experienced a bearable pain or no pain at all, 6 (21%) had a moderate pain, and none felt severe pain. Among the 26 patients who were asked, 20 (77%) would agree to have a FB in the same conditions.Our findings suggest that TCI of Remifentanil may be useful and safe, for performing FB in the ICU, with acceptable patients' comfort and tolerance, even in those with respiratory failure. The study completion should strengthen these preliminary results."} +{"text": "This study examines weight gain and assesses complications associated with refeeding adolescent inpatients admitted with a restrictive eating disorder (ED) who were provided with caloric intakes above current recommendations.Patients admitted to an adolescent ED program for >48 hours were included in a 3-year retrospective chart review. The structured \u2018rapid\u2019 refeeding program mostly utilised initial nasogastric feeding, with routine phosphate prescription.The mean (SD) age of the 184 adolescents was 16.7 years (0.9). Mean (SD) admission BMI was 16.9kg/m2 (2.3) and discharge BMI was 19.5kg/m2 (1.5). The mean (SD) starting caloric intake was 2523.6kcal/day (383.5) equating to 56kcal/kg (12). Most patients (87.5%) were treated with nasogastric tube feeding. Mean (SD) length of stay was 3.5 weeks (1.9) with a weekly weight gain of 2.1kg (0.9). No patients developed cardiac signs of refeeding syndrome or delirium; complications included peripheral oedema (3.8%), hypophosphatemia (1.1%), hypomagnesaemia (6%), and hypokalaemia (1.6%). Caloric prescription on admission was not associated with developing hypophosphatemia (p=0.15), hypokalaemia (p=0.40) and hypomagnesaemia (p=0.96).Results demonstrated the efficacy of treating adolescent inpatients with restrictive EDs safely with higher initial caloric intakes, resulting in rapid weight restoration without major refeeding complications; which challenges current conservative calorie prescriptions advocated in clinical guidelines."} +{"text": "Focal myocardial injury is an important diagnostic feature of myocarditis and is typically assessed by cardiovascular magnetic resonance (CMR) on late gadolinium enhancement (LGE) images. T1 mapping, T2 mapping, and extracellular volume (ECV) imaging are novel techniques which potentially improve the diagnostic value of CMR in myocarditis. This study evaluated the potential of T1 and T2 mapping CMR to assess focal myocardial lesions in myocarditis.We included 20 patients with myocarditis who had typical focal myocardial lesions on LGE images as reference method. Native T1, T2, and ECV maps were acquired in addition to a conventional CMR protocol at 1.5 Tesla. Myocardial lesions were quantified on LGE images by a standard threshold technique using a region of interest in normal appearing myocardium as reference tissue. Furthermore, myocardial lesions were quantified using normal values for native myocardial T1, T2, and ECV obtained from a group of 20 matched healthy controls as reference tissue. Injured myocardium was defined by a signal-intensity, native myocardial T1, T2 and ECV \u2265 2 standard deviations above reference values and expressed in percent of LV myocardium.Median lesion size was 14% (9-20%) on LGE images. Areas with normal appearing myocardium on LGE images had significantly increased median native myocardial T1 and ECV values compared to myocardium of healthy volunteers (1085ms (1048-1120ms) vs. 1051ms (1021-1064ms); p<0.01 and 32% (30-35%) vs. 26% . Consequently, median lesion sizes were larger on native T1 maps (48% (32-56%); p<0.01) and ECV maps (58% (50-66%); p<0.01) compared to the median lesion size on LGE images. Median T2 values did not differ significantly between normal appearing myocardium of patients with myocarditis and myocardium of healthy volunteers (56 ms (54-60 ms) vs. 58 ms (53-62 ms); p=0.47). No significant difference in lesion size was found between T2 maps and LGE images (18% (9-38%); p=0.06).Native T1 and ECV maps reveal hidden myocardial injury in patients with myocarditis using myocardium of healthy controls as reference tissue.Dr. Marija Orlovic Foundation."} +{"text": "Identification of the causative food in food allergy patients is crucial. However, offending allergens can vary with a country\u2019s food choices and preparation methods. In this study, we analyzed the sensitization rate to specific food allergens in Korean adult food allergy patients.This study enrolled 134 adult patients who visited the allergy clinic of Severance Hospital due to their allergic symptoms related to food ingestion. Patients underwent skin prick test (SPT) with 55 allergens. Our food SPT panel included hairtail, yellow corvina, common eel, skate, squid, mackerel, anchovy, saury, octopus, chrysalis, sunflower seed, and pollock allergens prepared at our Institute of Allergy and reflecting the daily eating habits of Korean people.p = 0.008).Of the 134 patients, 73 (54.5%) were sensitized to one or more food allergens. The sensitization rate of men (69.2%) was higher than that of women (45.1%) , shrimp (11.9%), almond (11.1%), sunflower seed (8.2%), mackerel (5.2%), pollack (5.2%), halibut (4.5%), anchovy (4.4%), squid (3.7%), saury (3.0%), common eel (3.0%), yellow corvina (3.0%), hairtail (2.2%), octopus (2.2%), and skate (0.7%).Food sensitization patterns in Korean food allergy patients are different from those in other countries. Chrysalis showed the highest sensitization rate in Korean patients (25.4%). Interestingly, mackerel, pollack, halibut, anchovy and yellow corvina which are popular food ingredients in Korea were also highly sensitized. Therefore skin prick test panel is need to reflect the preferred food choices of a region."} +{"text": "Atypical haemolytic uraemic syndrome (aHUS) is a rare, life-threatening disease in which patients experience uncontrolled complement activation leading to systemic thrombotic microangiopathy (TMA). We report on the effect of eculizumab (Ecu), a terminal complement inhibitor approved for the treatment of aHUS, in the largest prospective clinical trial in aHUS.9/l and LDH \u22651.5 ULN were recruited into a 26-week single-arm, phase 2 study evaluating Ecu treatment. Patients with STEC-HUS (Shiga toxin and E. coli) and severe ADAMTS13 deficiency (activity <5%) were excluded. Identification of complement mutation was not required for enrolment. The primary endpoint was complete TMA response and <25% increase in serum creatinine from baseline (BL)). Other efficacy evaluations measured platelet counts and eGFR improvement (by MDRD).Adult aHUS patients (\u226518 years) with platelets <150 \u00d7 109/l and 17.3 (12.1) ml/minute/1.73 m2, respectively. Thirty-eight (93%) patients received Ecu for 26 weeks. Table Forty-one patients were enrolled (mean (SD) age 40.3 15.3) years; 28 (68%) females), 30 (73%) of whom with first presentation of aHUS (median 2 weeks before Ecu). BL mean (SD) platelets and eGFR were 119 (66.1) x105.3 yearsResults from this large prospective clinical trial in adult patients with aHUS confirm prior trials with Ecu to inhibit complement- mediated TMA, improve renal and haematological outcomes and show the benefit of early diagnosis and treatment. There were no unexpected safety concerns. The trial is ongoing."} +{"text": "Hyperlactatemia (plasma lactate > 2 mmol/l or >18 mg/dl) can occur in the setting of inadequate tissue perfusion or hypoxia or have non hypoxic origin like impaired buffering systems or metabolic disorders. Numerous studies have proven lactate concentration to be a good marker of disease severity for ICU patients. A single centre study recently have demonstrated it's predictive value following cardiac surgery.The aim of our study was to establish the prevalence of hyperlactatemia following normothermic and mild-hypothermic cardiopulmonary bypass (CPB) and to determine whether normal lactate levels (NL), moderate hyperlactatemia (MHL) or severe hyper lactatemia (SHL) at ICU admission was associated with a different postoperative outcomes.Retrospective analysis of consecutive normothermic and mild-hypothermic CPB cases performed in Vilnius University Hospital Stanatriskiu Clinics during the 4-month period in 2014. Based on previous publication we defined groups according to post-operative lactate levels - NL group < 1.6 mmol/l, MHL group 1,6-4,4 mmol/l and SHL group \u2265 4.4 mmol/l. We analysed the impact of hyperlactatemia on the length of post-operative ICU and hospital stay and also on the incidence of infectious and non-infectious complications. STS derived 30-day morbidity endpoints were used: permanent stroke, renal dysfunction or renal failure requiring dialysis, any cardiac re-operation and lung ventilation for more than 48 hours.Statistical analysis was performed using MS Office Excel and GraphPad Prism 6 software.Data of 271 consecutive patients was analysed. Medium age of the cohort was 65 \u00b1 10,36 years, 180 (66%) of patients were male, 91(33%) - female. Normal lactate levels postoperativelly were detected in 127 patients, moderate hyperlactatemia in - 105 , and severe elevation of lactates in - 39 patients.The overall incidence of postoperative infectious complications was 12(9%) in NL group, 20(19%) in MHL and 12(31%) in SHL accordingly . Sternal would infection was significantly more frequent in MHL group (7(6%) vs. 9(9%) vs. 0(0%), p < 0,0001). The distribution of non infectious complications amongst three groups was 47(37%), 41(39%) and 24(62%) p = 0,0391. There was no significant difference between groups regarding development of single postoperative non-infectious complications. The longest post-operative ICU stay of 7 \u00b1 8,62 days, was observed in SHL group . Overall post-operative in hospital stay was 14 \u00b1 15,47 days in NL group, 16 \u00b1 13,84 days in MHL and 18 \u00b1 13,01 days in SHL group . There was a significant difference in mortality rates between groups 1(1%) v 1(1%) v 2(5%), p = 0,0018.Post-operative lactate level higher than 4,4 mmol/l was a significant predictor of worse post-operative outcomes (longer ICU and in-hospital stay, greater incidence of postoperative complications and increased mortality rates."} +{"text": "To provide extensive genotype-phenotype correlations for Joubert syndrome (JS), a ciliopathy characterized by a distinctive hindbrain malformation (\"the molar tooth sign\"), ataxia and cognitive dysfunction.Phenotypic data was collected from the University of Washington JS cohort and all known JS genes were sequenced in 429 individuals (364 families) using the MIPS capture technique and next-generation sequencing.C5ORF42, CEP290, CC2D2A, AHI1, TMEM67). Bi-allelic causal mutations in B9D2 and C2CD3 were identified in 2 families each. Bi-allelic mutations in 2 different genes were identified in 4 families and heterozygous mutations were present in 62 individuals. Significant (p<0.0001) genotype-phenotype correlations were observed: CEP290 with renal disease and retinal dystrophy; TMEM67 with liver fibrosis and coloboma.Core JS diagnostic features were present in >80% of individuals, while abnormal breathing pattern was reported in 60%. Frequently associated features included retinal dystrophy (31.4%), renal disease (20.9%), coloboma (17.7%), polydactyly (15.3%), liver fibrosis (15.2%) and encephalocele (8%). Liver fibrosis and coloboma were strongly associated with each other , while retinal dystrophy and renal disease were weakly associated . Additional clinical features included other brain abnormalities (n = 73), seizures (n = 49), cleft palate (n = 16), hearing loss (n = 14) and psychiatric problems (n = 45). The genetic cause was identified in 60% of families, with 5 genes accounting for the majority of patients (This study provides a comprehensive description of the phenotypic spectrum, genetic makeup and genotype-phenotype correlations of a large JS cohort."} +{"text": "Elevated inflammatory mediators in alcoholism may influence brain function leading to increased impulsiveness and/or phobia. The novel association between RANTES and GRO and impulsivity phenotype in alcoholism should be further investigated in alcoholism and psychiatric conditions with core impulsivity and anxiety phenotypes lending support for therapeutic intervention.Chronic alcohol use alters adaptive immunity and cytokine activity influencing immunological and hormone responses, inflammation, and wound healing. Brain cytokine disturbances may impact neurological function, mood, cognition and traits related to alcoholism including impulsiveness. We examined the relationship between plasma cytokine levels and self-rated psychiatric symptoms in 40 adult males with current alcohol dependence and 30 control males with no history of alcoholism using multiplex sandwich immunoassays with the Luminex magnetic-bead based platform. Log-transformed cytokine levels were analyzed for their relationship with the Symptom Checklist-90R (SCL-90R), Barratt Impulsivity Scales (BIS) and Alcoholism Severity Scale (ASS). Inflammatory cytokines (interferon \u03b3-induced protein-10 (IP-10); monocyte chemoattractant protein-1 (MCP1); regulated on activation, normal T cell expressed and secreted (RANTES)) were significantly elevated in alcoholism compared to controls while bone marrow-derived hematopoietic cytokines and chemokines (granulocyte-colony stimulating factor (GCSF); soluble CD40 ligand (sCD40L); growth-related oncogene (GRO)) were significantly reduced. GRO and RANTES levels were positively correlated with BIS scales; and macrophage-derived chemokine (MDC) levels were positively correlated with SCL-90R scale scores ( Alcoholism is a complex, multifactorial behavioral disorder characterized by the loss of control over alcohol consumption often involving other drug abuse with a relapsing and remitting course leading to clinically significant impairment . Direct + T helper (Th) cells guide adaptive immune responses to specific antigens through rapid initiation of gene transcription and production of cytokines [Innate immune responses involve non-specific cellular recruitment and activation of leukocytes and phagocytic cells such as macrophages, neutrophils and dendritic cells for the identification and elimination of harmful pathogens . Immunolytokines ,15. Incrytokines .et al. (2014) [Acute and chronic alcohol exposure interferes with cellular immune responses leading to dysregulation and functional impairment ,15,17. B. 2014) found ac. (2014) . Alcohol found a. (2014) . Circula. (2014) ,22. Incr. (2014) ,24.Up-regulation of cellular inflammatory mediators exacerbates alcohol-related biochemical disturbances and accelerates the associated degenerative processes impacting long term outcomes. Inflammatory mediators in alcoholism precipitate organ failure leading to increased morbidity and mortality ,5. ActivF = 4.53, NumDF = 23, DenDF = 44, p < 0.0001) on cytokine level with significance group differences in sCD40 L , IP-10 , MCP1 , RANTES , and GCSF levels.Twenty-three of the 41 (56%) cytokines tested were within a detectable and analyzable range meeting criteria for inclusion of our analyses. Plasma levels of 14 hematopoietin-derived cytokines (interleukin 1\u03b1 (IL1\u03b1); interleukin 1\u03b2 (IL1\u03b2); interleukin 1 receptor antagonist (IL1Ra); interleukin 2 (IL2); interleukin 3 (IL3); interleukin 4 (IL4); interleukin 5 (IL5); interleukin 6 (IL6); interleukin 9 (IL9); interleukin 10 (IL10); interleukin 13 (IL13); interleukin 15 (IL15); interleukin 12 subunit p40 (IL12(p40)); Fit3Ligand), 2 inflammatory cytokines (macrophage inflammatory protein 1 \u03b1 (MIP1\u03b1); transforming growth factor \u03b1 (TGF\u03b1)) and TNF\u03b2 fell below detection limits in >2/3 of subjects and were then excluded from primary analysis of cytokine levels. In addition, plasma platelet-derived growth factor subunit AB/BB (PDGFAB/BB) levels were excluded for exceeding the maximum detection limits (2191 pg/mL) in >2/3 of subjects. As expected, hematopoietic cytokines, granulocyte-colony stimulating factor (GCSF) and sCD40 L, and chemokine, growth-related oncogene (GRO), were significantly reduced in the alcohol dependent cohort . Conversr = \u22120.34, p < 0.03; Fractalkine, r = \u22120.31, p < 0.05) and chemokine (monocyte chemoattractant protein 3 (MCP3), r = \u22120.31, p < 0.05; interleukin 12 subunit p70 (IL12p70), r = \u22120.39, p < 0.01) families were significantly negatively correlated with Alcoholism Severity in our sample of alcohol dependent men , dent men .r = 0.31, p < 0.05) and vascular endothelial growth factor (VEGF) levels were negatively associated with Perseverance but these relationships were not significant after controlled regression analysis. Cytokine levels were not broadly correlated with SCL-90R scores, however, macrophage-derived chemokine ) levels were positively correlated with Interpersonal Sensitivity and Phobia subscales. The relationship between MDC levels and Phobia remained significant after adjusting for the effects of ASS and Symptom Checklist-90R (SCL-90R) psychometric assessments. As shown in s of ASS .r = 0.42, p < 0.01); obsessive symptoms ); interpersonal sensitivity ; depression ; anxiety ; phobia ; GSI . MCP3 levels were also inversely correlated with OCD scores .Mean IP-10 levels for alcohol dependent participants was 231.3 \u00b1 365 pg/mL (50\u20132014 pg/mL) which was within a concentration range considered to be normal but significantly higher than control levels of 161.5 \u00b1 455 pg/mL (64\u20132570 pg/mL). IP-10 is a known biomarker for viral infections, particularly hepatitis and HIV, which are increased in alcoholism. Participants with alcoholism did not report a history of hepatitis or HIV infection, but their status was not confirmed through analytical testing. To control for possible influences of active hepatitis or HIV infection on study outcomes, data were re-analyzed excluding three participants exhibiting high IP-10 levels (>800 pg/mL), which could have been attributable to active viral infection. The results of these analyses were comparable to those obtained in the initial case vs control comparisons and correlations with BIS outcomes (RANTES and GRO were significantly associated with impulsiveness). However, correlations between cytokine level and ASS were weakened and no longer considered significant for Fractalkine, IL17 and MCP3. Interestingly, correlational analysis of MDC levels showed enhanced association and positive correlations with multiple SCL-90R subscales including: somatization is found in platelets and is a biomarker of platelet activation and the coagulation cascade. GRO is produced by macrophages, neutrophils and epithelial cells and has been shown to impact the migration of oligodendrocyte precursors in spinal cord development and angiogenesis ,31,32. TInflammatory mediators MCP1 (CCL2), RANTES (CCL5) and IP-10 were found to be elevated in alcoholism, which has been reported previously in association with alcoholism-related viral infection, alcoholic liver and pulmonary disease ,34,35. TIn our study, plasma concentrations of RANTES were significantly elevated in alcoholism and positively correlated with empirical measures of impulsiveness. RANTES promotes inflammation through the recruitment of T cells, eosinophils, basophils and the activation of natural-killer cells. RANTES activation has been previously implicated in pathological processes for several inflammatory and behavioral disorders including atherosclerosis, autoimmune disorders , depression, traumatic brain injury, schizophrenia and obesity ,38. To oCCL22) is also homologous to the RANTES gene (CCL5) [The chemokine, GRO, was reduced in alcoholism but positively correlated with impulsivity measures in our subjects. Cytotoxic effects of GRO activation in childhood or adolescence may influence neurodevelopmental processes leading to impulsiveness and hence increased vulnerability to the development of alcoholism. Inter-correlation between inflammatory mediators and impulsiveness may represent novel biomarkers of value for the prediction of alcoholism vulnerability, course and responsiveness to recovery. Cytokine levels were not broadly correlated with psychiatric symptomatology as assessed by the SCL-90R instruments. However, MDC was positively correlated with several measures of anxiety and phobia, which may be evidence of specific neurodegenerative or inflammatory processes. MDC, RANTES, and MIP-1\u03b1/\u03b2 all target the CCR4 receptor which activates phosphatidylinositol-calcium second messenger and Akt signaling pathways in endothelial cells mediating angiogenesis or angiostasis with activity in the CNS. Alterations in vascular growth, maintenance and density may also influence frontal-temporal development and function impacting mood, cognition and impulsiveness. The MDC gene (e (CCL5) , but didThe multiplex immunoassay methodology utilized did not detect very low circulating levels of many cytokines, particularly those in the interleukin family, limiting our assessments of several important targets including previously associated with psychiatric symptomatology and alcoholism ,15,25,29Forty adult male African-American participants who met DSM-IV-TR criteria for alcohol use disorder were enrolled for a clinical trial on alcoholism with oversight of Kansas University Medical Center (KUMC) Human Subjects Research Committee ,41. The A comprehensive interview was completed on each participant by a trained research nurse to determine final eligibility based upon DSM-IV-TR diagnostic criteria for an alcohol use disorder as previously reported ,41. The Plasma cytokine levels were determined using multiplex sandwich immunoassays with the Milliplex Human 41 Cytokine/Chemokine Premixed Kit according to manufacturer\u2019s protocol. The 41 cytokines included in the kit belong to four families: hematopoietins, chemokines, growth factors and interferons and included: hematopoietin ; chemokines ; platelet derived growth factors (PDGFAA and PDGFAB/BB); tumor necrosis factors (TNF\u03b1 and TNF\u03b2) and interferons (IFN\u03b12 and IFN\u03b3).Blood plasma (25 \u00b5L) and a concentration standard, or a Milliplex quality control standard were combined with pre-mixed antibody-coupled fluorescent beads and assay buffer followed by overnight incubation at 4 \u00b0C. All incubation steps were carried out on a micro-titer plate shaker at 300 rpm. The following day, the samples were washed, followed by incubation with secondary detection antibodies for 1 h at room temperature (RT). The samples were then put through another series of washes followed by addition of the Streptavidin-Phycoerythrin detection solution. This mixture was incubated for 30 min at RT. Each sample was run in duplicate. Following incubation, sheath fluid was added to each sample well and the plate was read on the Luminex 200TM instrument based on fluorescent-bead technology. The following cytokines/chemokines were analyzed using the Luminex 200TM v2.3 software with the indicated minimum detectable concentration levels given in pg/mL values: IL1\u03b1 (0.4), IL1\u03b2 (0.4), IL1Ra (0.4), IL2 (0.4), IL3 (0.4), IL4 (0.9), IL5 (0.4), IL6 (0.4), IL7 (1.1), IL9 (0.4), IL10 (0.4), IL12p40 (2.9), IL12p70 (2.0), IL13 (1.5), IL15 (1.6), IL17 (0.1), CD40L (5.1), Flt3 ligand (2.8), GCSF (1.0), GMCSF (1.1), EGF (2.8), Eotaxin (2.2), FGF2 (6.0), Fractalkine (5.0), RANTES (1.2); GRO (9.9), IL8 (0.4), IP-10 (8.6), MCP1 (1.9), MCP3 (1.3), MDC (3.6), MIP1\u03b1 (1.4), MIP1\u03b2 (1.4), TGF\u03b1 (0.4), VEGF (0.3), TNF\u03b1 (0.4), TNF\u03b2 (2.7), IFN\u03b12 (3.1), IFN\u03b3 (0.9), PDGFAA (0.4) and PDGFAB/BB (2.2). Plasma cytokine concentraptions were calculated using a standard curve derived from the reference cytokine concentration standards supplied by the manufacturer. The inter-assay coefficient of variation for the cytokines ranged from 3.7% to 17.2% while the intra-assay coefficient of variation ranged from 4.5% to 13.8%. Plasma samples were analyzed using numbers and blinded to alcoholism status during each assay run.p-values of <0.05 were considered significant. All analyses were carried out using SAS version 9.2 .The final analyses considered data that fell within the detections limits of the Luminex assay. Data falling below the detection limit were replaced with values one half of the minimum detection level for that cytokine as reported in previous studies ,48,49. CCytokine biology in chronic severe alcoholism is complex with many interacting influences related to race and sex, the general health of the individual and lifetime severity of alcoholism. Up-regulation of cellular inflammatory mediators may exacerbate alcohol-related biochemical disturbances, disrupt frontal cortical angiogenesis and neurodevelopment or accelerate neurodegenerative processes impacting behavior either through direct cytotoxic effects of cytokine mediators or secondary to other biochemical disturbances impacting cellular functioning or energy production. Further studies are needed to confirm these relationships and characterize the biochemical mechanisms involved. Inter-correlations between inflammatory mediators and psychometric measures of distress and impulsiveness may represent novel biomarkers of value for consideration in future studies of alcoholism course and responsiveness to recovery. The role of RANTES, GRO and MDC should be further investigated in alcoholism and other psychiatric conditions with core impulsivity and anxiety phenotypes and address therapeutic interventions when needed."} +{"text": "We resequenced the genome of equid herpesvirus 2 (EHV2) strain 86/67 and sequenced the genomes of EHV2 strain G9/92 and equid herpesvirus 5 (EHV5) strain 2-141/67. The most prominent genetic differences are the dissimilar locations of the interleukin-10 (IL-10)-like genes and the presence of an OX-2-like gene in EHV5 only. Percavirus, subfamily Gammaherpesvirinae, family Herpesviridae (Equid herpesviruses 2 and 5 (EHV2 and EHV5) belong to genus sviridae , 2. Evidsviridae , except sviridae . The gensviridae has beensviridae . We resesviridae and EHV5sviridae .http://www.bioinformatics.cvr.ac.uk/Tanoti/index.php), and by viewing them using Tablet aligned (using Tanoti) with the sequences at coverage values of 1,812, 8,776, and 3,085 reads per nucleotide, respectively. The genome sizes are 184,439, 186,110, and 182,380\u00a0bp, respectively, including an unmatched complementary nucleotide at the 3\u2032 end of each DNA strand. The slightly larger size of the EHV5 2-141/67 genome from that estimated by restriction site analysis (179 kbp) is due tThe number of functional open reading frames (ORFs) was conservatively estimated to be 78 in EHV2 (one duplicated in TR) and 79 in EHV5. Six ORFs exhibit <80% amino acid sequence identity between the EHV2 strains. The diversity in EHV2 has been studied by restriction site analysis and in tKM924294 and KM924295, respectively.The EHV2 G9/92 and EHV5 2-141/67 genome sequences have been deposited in GenBank under the accession nos."} +{"text": "Juvenile dermatomyositis (JDM) are potentially life-threatening.We report 11 cases of severe JDM admitted in intensive care unit (ICU) to determine their early severity signs and outcomes.We performed a retrospective study of cases of JDM admitted in ICU in 2 pediatric rheumatology centers from 2005 to 2013, and compared them to the JDM patients who did not require ICU.9/L )(7). The patients were treated by corticosteroids , intravenous immunoglobulins (7), plasmapheresis (7), Rituximab (4) and cyclophosphamide (2). One patient died in ICU from pneumocystosis ; 5 are currently in complete remission and 5 in partial remission with a mean follow-up duration of 4,7 years.11/116 DMJ (9.3%) were admitted in ICU for digestive involvement (2 with digestive perforation after pulse corticosteroids) (4 patients), bradycardia (1 patient), cardiac arrest (1 patient), hypoxemic pneumonia (1 patient), PRES syndrome due to cyclosporine (1 patient), thrombotic microangiopathy (TMA) (2 patients) and anaphylactic shock due to Rituximab (1 patient). The incidence of some clinical and biological manifestations differed from severe patients to patients with mild JDM: hyponatremia (9), hypoalbuminemia (9), generalized edema (6), anemia (8), abdominal pain (7), thrombocytopenia , thrombocytopenia (with TMA), hyponatremia and hypoalbuminemia seem to be early warning signs of severe DMJ and should be identify to improve prognosis. Our study suggests that severe DMJ should early benefit from plasmapheresis \u00b1 Rituximab, whereas pulse corticosteroids might contribute to digestive perforation in patients presenting with digestive involvement.None declared."} +{"text": "The juvenile spondyloarthropathies (JSpA) are a group of related seronegative rheumatic diseases characterized by involvement of the axial joints, peripheral large joints and entheses. JSpA and adult SpA are probably parts of the same disease continuum. JSpA are represented by enthesitis related arthritis (ERA). juvenile psoriatic arthritis (JPsA) and probably undifferentiated arthritis (UA) in the ILAR criteria. Sets of classification criteria have been developed in adult patients with SpA. The ASAS classification criteria for axial and peripheral SpA have not been validated in pediatric populations.To assess the sensibility and specificity of the ASAS criteria for identification of patients with JSpA among the different Juvenile idiopathic arthritis (JIA) categories. To compare the performance of the ASAS criteria with that of ESSG classification criteria in JIA patients. To identify associations between criteria fulfillment and disease features.Consecutive patients with JSpA followed in our center with complete records were included. Clinical charts and databases were retrospectively reviewed. Randomly selected patients with oligoarthritis, polyarthritis RF negative and systemic arthritis from our cohort served as controls. Demographic and clinical characteristics as well as disease duration at first visit and follow up time were recorded. Items corresponding to the ASAS, ESSG, Amor, seronegative enthesopathy and arthropathy (SEA) syndrome and Modified New York (NY) criteria were obtained from first visit and during disease course. Descriptive , summary statistics and Wilcoxon Rank sum test were used.106 patients with JSpA were included (M:92), age at onset: 10 (1-15) years, disease duration at first visit 10 (1-15) months, follow-up time 4 (1-12) years. Controls: 65 patients with other JIA (M: 27). At first visit cases showed: 103 (97%) arthritis, 87 (82%) asymetrical oligoarthritis, 67 (63%) elevated CRP, 52 (49%) limitation of lumbar spine motion, 51 (48%) HLA-B27, 45 (42%) enthesitis, 39 (37%) low back pain, 32 (30%) good response to NSAIDS, 26 (25%) positive family history, 20 (19%) radiographic bilateral sacroiliitis grade 2-4, 13 (12%) dactylitis, 8 (8%) uveitis, 7 (7%) unilateral sacroiliitis grade 3-4, 7 (7%) diarrhea, 5 (5%) previous infectious disease, 2 (2%) urethritis, 2 (2%) inflammatory bowel disease, 2 (2%) buttock pain, 1 (1%) psoriasis. At first visit (106 patients): 79 (75%) patients fulfilled ASAS criteria, 78 (74%) peripheral ASAS, 78 (74%) ESSG, 69 (65%) Amor , 32 (30%) SEA, 25 (24%) NY , 24 (23%) axial ASAS. During disease course (102 patients): 100 (98%) patients fulfilled ESSG criteria, 97 (95%) ASAS, 97 (95%) peripheral ASAS, 94 (92%) Amor , 75 (74%) NY , 42 (41%) SEA, 41 (40%) axial ASAS. ASAS sen 95%, sp 83%, PPV 90%, NPV92%. ESSG sen 98% sp 89% PPV 93%, NPV 97%. Unilateral and bilateral sacroiliitis were associated only with axial ASAS .In our cohort ASAS criteria performed similarly to ESSG criteria in the classification of JSpA. Both sets of criteria allow the inclusion of JSpA patients under one unified category to facilitate research and communication. Peripheral ASAS criteria allow the classification of all patients with JSpA who meet axial ASAS criteria.None declared."} +{"text": "Leptospirosis is one of the most common zoonoses in the world, with a wide range of manifestations that can vary from mild to severe with acute hepatic and renal failure, pneumonia or meningitis. Between 2005-2011 in Romania, according to ECDC, 1740 cases have been reported. Objective: To describe clinical and laboratory characteristics of confirmed cases of leptospirosis.Retrospective study, between January 2004-June 2014, in one infectious diseases hospital in Bucharest. We included patients with leptospirosis diagnosis at discharge and/or positive serology for leptospirosis. Serological diagnosis of acute leptospirosis was made by microscopic agglutination test using a battery of 17 antigens from international reference strains in one national reference laboratory and/or positive IgM-enzyme-linked immunosorbent assay (ELISA). Statistical analysis was performed with SPSS v19.0; continuous variables were described with medians and ranges; categorical variables were described with numbers and percentages.Of 132 patients with leptospirosis diagnosis at discharge, 105 (80%) had positive serology for leptospirosis. The median age was 37 (IQR 29-53) and 94 (90%) were male. 71 (68%) patients were diagnosed between May and September, 54 (51%) lived in urban areas and 8 (8%) patients had professional exposure. Leptospirosis serotype has been identified in 75 (71%) patients. 9 (9%) patients had meningeal involvement, 12 (12%) patients respiratory manifestations, 66 (63%) patients renal impairment and 38 (36%) patients coagulation impairment. The median level of alanin aminotransferase, gamma-glutamyl transpeptidase and total bilirubin were 88 IU/mL (IQR 50-158), 162 IU/mL (IQR 86-279) and 4.7 mg/dL (IQR 1.2-14.7), respectively. Leukocytosis (WBC >10.000/\u00b5L) was present in 55 (52%) patients, severe thrombocytopenia (PLT <50.000/\u00b5L) in 25 (24%) patients and 87 (83%) patients had inflammatory syndrome. In-hospital mortality was 4% (4/105).Liver and renal failure were the most common manifestations in leptospirosis. Increased awareness should be maintained in order to diagnose and initiate early adequate treatment to reduce mortality and morbidity."} +{"text": "In DUET, etravirine (ETR) 200 mg bid had durable efficacy and a favourable safety profile versus placebo, both arms with an optimised background regimen (BR) including darunavir/ritonavir (DRV/r). TMC125IFD3002 investigated ETR plus ARVs other than DRV/r.This was a 48 week, Phase IV, open-label, single-arm, multicentre study. HIV-1-infected treatment-experienced adult patients on=8 weeks ARV therapy prior to screening, switching either for virologic failure (VF) or regimen simplification/AEs (RS/AE) (VL<50 c/mL), received active ETR 200 mg bid with an investigator-selected BR of =1 active ARVs, but excluding DRV/r or NRTIs only. The primary objective was to evaluate safety, tolerability and pharmacokinetics (PK).10 c/mL and CD4+ count 238 versus 410.5 cells/mm3. Overall, 96% previously used <2 NNRTIs and 99% used=5 PIs; median number of BL NNRTI RAMs was 2, PI RAMs 5 and NRTI RAMs 1. Overall, most common BR ARVs were PIs (83%), mostly lopinavir/r (62%) and mostly used alone (20%) or with 1 or 2 NRTIs (61%). Raltegravir was used in 9% of patients. Most frequent AEs (any cause/grade) were diarrhoea (17%) and URTI (8%). Incidence of grade 3\u20134 AEs was 13%, serious AEs 5% , AEs leading to discontinuation 4%, AEs possibly related to ETR 23% and AEs of interest: rash (any type) 4%, hepatic 6% and neuropsychiatric 3%. At week 48, VF and RS/AE virologic responses were: 48% (74/155) and 75% (42/56), respectively. VF rates were 42% and 13%; 10% and 13% had no VL data in the week 48 window. The percentage of patients adherent to treatment (assessed based on PK sampling plus ETR pill count) was 47% (69/148) and 57% (30/53), in VF and RS/AE, respectively. Median CD4+ count (NC=F) increases were 0.0 and 24.0 cells/mm3. In 29/49 of VFs with genotypic data at failure, ETR RAMs emerging in =5 patients were Y181C, E138A and M230L. The geometric mean ETR AUC12h was 4877 ng.h/mL and C0h 293 ng/mL (N=199).Of 211 treated patients, 55% were female, 61% black/African American. 155 patients (73%) had baseline (BL) VL=50 c/mL versus 56 (27%) with BL VL<50 c/mL. Between these two latter subgroups, median BL VL was 4.42 versus 1.28 logResults of this study were consistent with those for ETR in other similar populations and support the use of ETR 200 mg bid with a non-DRV/r based BR."} +{"text": "Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a Cenozoic origin. Dung beetles of the subfamily Scarabaeinae are a well-known group of insects thanks to their exploitation of animal feces, a behavioral trait with a global impact on Earth\u2019s ecosystems. With more than 6200 species in 267 genera and with an estimated 30\u201350% of the species still undescribed , dung beetles exhibit diversity comparable to the Aves (ca. 9.800 species ), as welOnthophagus, one of the most species-rich genera in animal kingdom, in which horns exhibit fascinating phenotypic diversity, has emerged as a model system in evolutionary developmental biology and ecological development 1) and itsense of is well 1, recovered in the present study, and comprising the majority of Australasian genera, one African genus Pedaria, and a subclade formed of New Zealand and New Caledonia genera [Prionocephale deplanate Lin, 1980 is described from the Upper Cretaceous of China. The original description of that fossil does not list any unambiguous characters for placing it within Scarabaeinae, which indicates that there are no reliable evidence to consider it a member of the subfamily. The latest study [Dung beetle origin is a controversial issue whose main dilemma lies in a Cenozoic versus Mesozoic age of origin , 60. TheSiberia) . The desSiberia) as premast study dating tst study .Besides the abovementioned fossils, there is an ichnofossil from the Nearctic Cretaceous representing a herbivorous dinosaur coprolite and associated dung filled tunnels . HoweverThe lack of a reliable dated phylogeny does not allow testing a Cenozoic and Mesozoic hypotheses; however, the present tree, if assumed correct, can be used to assess these competing evolutionary scenarios. Here, we discuss the potential implications for this debate, which derived from the biogeographical pattern of the present phylogeny. We consider long-distance dispersal, dispersal via land bridges, and vicariance as main processes that potentially could shape present distribution of Scarabaeinae. Undoubtedly, such approach is speculative as it is not based on a robust biogeographical analyses but currently, due to the lack of other data, it is the only way to get an insight into dung beetle evolutionary history.1 and L (consisting of Old World and New World taxa) can only be explained by long-distance intercontinental dispersal events occurring between Africa and Australia as well as between Africa and S. America. We can rule out the dispersal via land bridges scenario as we lack evidence for it. Some members of Scarabaeinae, as Onthophagini, indeed, owe their cosmopolitan distribution to land bridge dispersal from Old World to New World and Australia through Asia as supported by phylogeny indicating that monophyletic Australasian and American clades derive from Asian ancestors which potentially could host Scarabaeinae if they were able to reach them, lack any traces of native dung beetle species. The longest recorded dispersal refers to the presence of two endemic Scarabaeinae genera on volcanic island of Mauritius, which seemingly happened from Madagascar (distance between two is ca. 900 km). This fact suggests that even medium-distance dispersal is a rare event in dung beetles, and assigns a very low probability to intercontinental dispersal requiring a few thousand kilometers to cross.First, suppose, dung beetles evolved during the Cenozoic after the Gondwana breakup, then biogeographical composition of such clades as e.g., Auscestors would fit well the vicariance hypothesis if they were correspondingly aligned with fragmentation of Gondwana. This alignment would imply minimal age for clades Aus1, B and dung beetle origin coinciding with the separation of Africa from Gondwana in Late Jurassic (160 MYA). Clades consisting of New World and Old World taxa would be constrained to minimal age of the separation of Africa from South America, which remained connected until mid-Cretaceous (110\u201395 MYA). In addition, vicariance pattern can also explain the nested position of the clade composed of New Zealand + New Caledonia taxa within Aus1. This phylogenetic pattern is consistent with breakup of a land mass, comprising New Caledonia and New Zealand, from Gondwana at 80 MYA, and its subsequent split separating New Zealand and New Caledonia taxa at 40\u201330 MYA. Although the current phylogeny supports a vicariant pattern, such a scenario poses quite old minimal ages for the origin of dung beetles and diversification of their main lineages. This strict vicariance can be relaxed assuming that dung beetles originated in Mesozoic after Gondwana breakup, and then dispersed among fragments of Gondwana when they were not too far away from each other. For example, the African south margin broke from Antarctica, the part of Gondwana, at 160 MYA and started drifting slowly northward, remained separated from Antarctica by the Indian opening of 300\u20131000 km over Early Cretaceous. This assumption can reduce minimal ages for the origin of the dung beetles and their lineages to early\u2014mid Cretaceous and at the same time, it still reserves a key role for Gondwana and its fragments in shaping current distribution of Scarabaeinae.However, if we assume a Mesozoic origin for the dung beetles it could explain their present biogeographic pattern by Gondwana vicariance. The nested position of African Although, the conclusion about Mesozoic origin is preliminary, since we lack comprehensive dated phylogeny of dung beetles, the present tree has higher likelihood of fitting this hypothesis. At the same time, we cannot, by far, rule out, the hypotheses of Cenozoic origin.Detailed examination of morphology coupled with parsimony and Bayesian analyses using ontology for matrix partitioning has shed new light on the evolution of dung beetles. Many clades in the present phylogeny are congruent with those in other existing molecular and morphological phylogenies while some clades suggest novel relationships that have not been hypothesized before. We can, to a certain extent, consider congruent clades among previous phylogenies as well-supported but the number of such clades is low and does not allow for the selection of any specific phylogeny as more reliable over the others. Our results are consistent with the results from different studies and provide further resolution for Deltochilini and Dichotomiini as well as the remaining Scarabaeinae tribes whose placement has been contentious. Therefore, the present study provides an integrative pattern of phylogenetic relationships in Scarabaeinae, many parts of which are backed up by previous works. The consistency of the current phylogeny with biogeography likely suggests a Mesozoic rather than Cenozoic age of the origin of dung beetles. However, this conclusion is speculative and has to be confirmed by future total evidence studies integrating morphological, molecular and fossil data to date the dung beetle tree of life. The resulting phylogeny demonstrates that the present classification of Scarabaeinae has to be substantially revised. The mapped synapomorphies can be used to define the new (sub)tribes and groups of genera; however, nomenclatural changes, at present, would be premature and more data, primarily molecular, are required to corroborate the findings presented here.The photo-based illustrations of endophallic sclerites in Figs. The aedeagus lies on its lateral side inside the abdomen , which cThe notes for the illustrations of the somatic characters Figs. \u201347 are pPhallobase, basal area dorsally: (0) with one tubercle on each side : (0) cylindrical; symmetrical or sometimes feebly subsymmetrical ventral portion reduced presenting large phallobase opening starting at apical margin and continually enlarging toward base; sclerotization of ventral portion subtle, translucent vennslucent .Phallobase, rectangular notch of basal margin, presence (rear view): (0) absent; (1) present absent; (1) present absent; both parameres symmetrical pral Figs. , 21 e, fParameres, relatively wide, rounded apically (Macroderes\u2014Xinidium groundplan): (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present absent; (1) present.Parameres, short, rounded apically : (0) absent; (1) present : (0) absent; (1) present.Parameres shortened, basolateral plate projected: (0) absent; (1) present.Parameres long, beak-shaped : (0) absent; (1) present.Parameres extremely reduced: (0) absent; (1) present absent; (1) present : (0) absent; (1) present absent; (1) present.Axial sclerite presence: (0) absent; (1) present : (0) axial sclerite processed in several lobes and occupying basal part of aedeagal sac; basal part of aedeagal sac possess either solely A or A and BSc sclerites : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present absent; (1) present : (0) absent; (1) present : (0) absent; (1) present absent; (1) present absent; (1) present : (0) absent; (1) present absent prent Figs. , 24 k, lNote. See note for character 22.SA sclerite tightly wrapped within axial sclerite; almost inseparable but recognizable : (0) absent ; (1) present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present absent; (1) present (0) absent; (1) present .FLP*, presence: (0) absent; (1) present absent; (1) present absent; (1) present absent absent ; (1) present : (0) absent; (1) present that also cannot be unequivocally scored with either state of present character. Due to this ambiguity, we score this character in Heliocopris with question mark.SRP sclerite represents flat lamella located along right side of aedeagal sack; SRP bears small ring structure apically (Epirinus\u2014Neosisyphus ground plan): (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present absent or very weakly sclerotized; (1) distinctly present : (0) absent; (1) present : (0) absent; (1) present : (0) absent; (1) present.FLP sclerite(s), presence: (0) absent . To avoid incorrect homology assumption, this character is coded with question mark in Gymnopleurus and Paragymnopleurus.FLP sclerite, small c-shaped, superior apical portion indistinctly sclerotized (Dichotomius groundplan): (0) absent; (1) present absent; (1) present.FLP sclerite, big, long, comprising 2\u20133 distinct lobes located in the same plane: (0) absent; (1) presentBSc sclerite, semicircularly shaped, presence: (0) absent; (1) present absent; (1) present absent; (1) present.IAS2sclerite, presence : (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present ( present .Elytron with 10 distinctly visible striae: (0) absent; (1) present absent; (1) present ( present .Elytron with 8 stria and/or traces of striation 8: (0) absent; (1) present absent; (1) present ( present .Elytron with 10 stria and/or traces of striation: (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present one twone e.g., , 37e.Elytron, 8thstria largely reduced (Anomiopus\u2014Scatonomus): (0) absent; (1) present absent; (1) present absent; (1) present : (0) absent; (1) present visible only preapically: (0) absent; (1) present relatively narrow; (1) large (1) large .Elytron, 7thand 8thstriae largely reduced and visible only preapically: (0) absent; (1) present absent; (1) present absent; (1) present distinctly depressed: (0) absent; (1) present absent; (1) present , inner one extends from apex to median portion of elytra, and closely located to (merged with) outer one extending from apex to base: (0) absent; (1) present absent; (1) present absent; (1) present.Wing, RA4significantly longer than RP1; RP1arcuate, not parallel to RA4: (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present : (0) absent; (1) present : (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present.Wing, MPa vein presence: (0) either absent or very weakly developed diseveloped .Galea, dorsal part covered with big spurs: (0) absent; (1) present absent; (1) present absent absent .Galea and lacinia, galea strongly sclerotized, hook-like: (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent absent ; (1) pre) absent .Glossal flap thick; internal margin usually densely haired: (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present ( present .Epipharynx with triangular deep notch anteriorly: (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present mandibles with largely extended membranous incisor lobes memor lobes .Right mandible, molar lobe enlarged, with big denticles: (0) absent; (1) present absent; (1) present absent; (1) present.Gula, emarginated anteriorly; emargination shagreened and/or haired: (0) absent; (1) present gular ridges invaginated only posteriorly, forming longitudinal lamella (ntorium) ; (1) gulntorium) .Eye, degree of development: (0) well-developed; (1) significantly reducedClypeus, ventral anterior area with ridges forming rectangular pattern that medially divided into two parts: (0) absent; (1) present absent; (1) present absent; (1) present.Clypeus, apical emargination with medial pit: (0) absent; (1) present ; eyes not exposed dorsally: (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present : (0) absent; (1) present.Prothorax, basisternal furca: (0) absent; (1) present absent; (1) present present.Prosternum, coxal depressions widened, closely approaching lateral margin of pronotum: (0) absent; (1) present absent; (1) present absent; (1) present absent/invisible; (1) present/visible.Protarsus in male: (0) absent; (1) present.Protarsus in female:(0) absent; (1) present.Protarsus, last tarsomere triangularly processed apically: (0) absent; (1) present.Protarsus, claws: (0) absent; (1) present.Protarsus, claws big, bifurcate preapically: (0) absent; (1) present absent; (1) present.Pro-, meso-, and metatarsus and apex of meso- and metatibia, ventral surface, with short dense hairs: (0) absent; (1) present absent; (1) present.Meso- and metatarsus with one fixed claw: (0) absent; (1) present.Metatarsus and mesotarsus with thick tarsomere and big claws: (0) absent; (1) present.Meso- and metatarsus, last tarsomere triangularly projected apically: (0) absent; (1) present no visible spurs; (1) one; (2) two.Mesotibia, number of apical spurs: (0) no visible spurs; (1) one; (2) two.Metepisternum, apex of lateral surface modified, convex and/or depressed (sometimes with unclear keel): (0) absent; (1) present cut into elytron by notching it: (0) absent; (1) present more or less rectangular with apical part rounded: (0) absent; (1) present absent; (1) present only one lateral process; (1) with two processes\u2014lateral, and rear directed backward absent; (1) present absMetasternum, frontal part raised and projected forward: (0) absent; (1) present absent; (1) present.Metascutellum, small, truncate, with bunch of hairs apically: (0) absent; (1) present abdomen soft; sternites separated from each other by membrane; 1st sternite well developed laterally abdaterally .Abdomen, 7thsternite largely expanded and crowding out remain sternites along midline; remain sternites visible only laterally: (0) absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present absent; (1) present ( present .Pygidium distinctly swollen: (0) absent; (1) present ( present .Pygidium with grooved line(s) and/or ring: (0) absent; (1) present absent; (1) present ( present .S1 Document(TXT)Click here for additional data file.S1 Fig(PDF)Click here for additional data file.S2 Fig(PDF)Click here for additional data file.S3 Fig(PDF)Click here for additional data file.S4 Fig(PDF)Click here for additional data file.S5 FigValues above branches indicate posterior probabilities.(PDF)Click here for additional data file.S6 FigValues above branches indicate posterior probabilities.(PDF)Click here for additional data file.S7 FigValues above branches indicate posterior probabilities.(PDF)Click here for additional data file.S1 Matrix(NEX)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file."} +{"text": "An increasing number of treatment-experienced perinatally HIV-infected adolescents (PHA) are being transitioned from paediatric centres to adult HIV-care . Most ofwww.hiv-druginteractions.org) [Descriptive pilot cross-sectional study (March to June 2014). PHA under ARVs at the time of the study were assessed for concomitant medication. CSDDIs were screened and categorized using the University of Liverpool Drug Interactions Program age: 20 years (18\u201322). CDC-stage C was observed in 27 (79%); 50% had \u22651 comorbidities including 3 with HCV co-infection. Drug abuse was observed in 6 (13%). The median of prior ARV regimens was 3 (3\u20135). Current ARV regimen included: PI: 87%, NNRTI: 27%, INSTI: 20%, enfuvirtide: 7% and CCR5 inhibitor: 4%. Median CD4 T-cell count: 568 cells/mL (279\u2013771). Viral load <50 copies/mL: 80%. Sixty percent (27/45) had \u22651 co-medications (median 1). The most frequent co-medications were NSAIDs (40%), hormonal therapy (19%) and antimicrobials (19%). Use of herbal supplements was observed in 10 (22%). Overall, 23 (51%) had \u2265 1 CSDDIs: 19/27 (70%) with co-medication (orange flag=18 and red flag=1); and 2/10 (20%) with herbal supplements. ARV\u2013ARV interactions were observed in 4/45 (9%): unboosted atazanavir+tenofovir (n=2), unboosted atazanavir+efavirenz (n=1) and lopinavir/ritonavir+efavirenz (n=1) . Considering patients with CSDDIs, 6 (26%) had a CSDDI that could reduce ARV levels.In this pilot study, a high prevalence of comorbidities, co-medications and CSDDIs was observed in PHA. A considerable proportion of patients had CSDDIs with a potential to cause sub-therapeutic ARV levels, what could be a concern in patients harbouring drug-resistance viruses. Therefore, clinicians should be aware of comorbid conditions pharmacologic management in order to avoid CSDDIs with ARVs agents."} +{"text": "Identifying molecular biomarkers in melanoma may provide useful diagnostic and therapeutic tools. Melanoma delivers immune suppressive stimuli through the pathway PDL-1/PD-1. Recent data suggest tumour-cell expression of PD-L1 in melanoma may be driven by constitutive oncogenic pathways. FK506 binding protein 51 (FKBP51), is an immunophilin that is highly expressed in melanoma and in tumour infiltrating lymphocytes (TIL). It is capable of immune suppression and has a relevant role in the progression of this tumour. We explored the expression of a variant generated by alternative splicing of FKBP51(FKBP51s) on TIL and its potential relation to PDL-1 in metastatic melanoma patients during Ipilimumab therapy (IPI).We collected melanoma samples (12 primaries and 64 metastases) and peripheral blood mononuclear cells (PBMC) of 76 metastatic melanoma patients at week 0,1,4,7,10 and 12 of IPI.We measured expression levels of FKBP51s on TIL and PDL-1 on tumour, by quantitative polymerase chain reaction (QPCR) and by immunohistochemical assay with a cutoff of 5%, respectively.Expression of PDL-1 was found in 16% (2/12) and 40% (26/64) of primary and metastatic melanomas, respectively.In melanoma negative for PDL-1, a low/no expression of FKBP51s was observed in TILs. In PDL-1 expressing melanomas, FKBP51s stained >80% of TILs. In addition, in melanoma negative for PDL-1, but with numerous PDL-1+ infiltrating macrophages, 10-15% of FKBP51s+ TILs was measured.We found 29% of patients (22/76) had increased levels of FKBP51s (high FKBP51s) and PDL-1 positive, while 69% (53/76) had low levels (low FKBP51s) and PDL-1 negative at baseline (week 0). Indeed 11/22 (50%) of high FKBP51s responded to IPI and only 12/53 (23%) of low FKBP51s were responders (p < 0.01).Furthermore, in responders patients we observed a decrease of the levels of FKBP51s during IPI therapy.We identified a spliced isoform of FKBP51 as a molecule associated to PDL-1, whose expression is increased in PBMCs of melanoma patients. High expression and reduction during IPI therapy may provide a potential predictive biomarker of response. These findings need more exploration.Written informed consent was obtained from the patient for publication of this abstract and any accompanying images. A copy of the written consent is available for review by the Editor of this journal."} +{"text": "Adequate monitoring of the patient on mechanical ventilation (IMV) reduces complications and improves safety. In order to know more about this important issue in Brazil, we performed an electronic survey.An open web-based electronic survey with questions about mechanical ventilation became available for intensive care practitioners in Brazil (DATAVENT) from 17 November 2013 to 31 August 2014 regarding the following questions: 1. Which of these predictive indexes or maneuvers do you (or someone in your ICU staff) routinely apply during the IMV withdrawal process? 2. Check what of these parameters are measured or calculated in your ICU daily practice? 3. How do you obtain the driving pressure value? 4. How do you obtain the resistive pressure value? 5. Check what are the imaging resources available in your hospital for the patient under IMV? 6. What is the value of tidal volume (ml/kg of predicted body weight (PBW)) that you use in patients under IMV without lung disease, including immediate postoperative period?2 as an index in withdrawal process. Two hundred and seventy-four (65.55 %) use the rapid shallow breathing index. One hundred and five (25.12 %) use the maximal inspiratory pressure (PiMax) and 32 (7.66 %) use the integrative weaning index (IWI). In total, 336 (80.38 %) measure plateau pressure, 295 (70.57 %) measure intrinsic PEEP, 243 (58.13 %) measure static compliance, 99 (23.68 %) measure driving pressure and 98 (23.44 %) measure resistive pressure as routine. Thirty-eight (9.09 %) have access to monitor work of breath (WOB). A total of 216 (51.67 %) does not know how to obtain the driving pressure. A total of 241 (57.65 %) answered correctly how to obtain resistive pressure. A total of 329 (78.71 %) has access to conventional computerized tomography in their hospitals. A total of 245 (58.61 %) has ultrasound and 223 (53.35 %) have echocardiography available. A total of 246 (58.85 %) perform chest radiography on a daily basis. A total of 183 (43.77 %) keeps the tidal volume of a patient under IMV without lung diseases (including postoperative patients) in 8 ml/kg/PBW. In total, 139 (33.25 %) use 6 ml/kg/PBW, 68 (16.26 %) use 7 ml/kg/PBW, 14 (3.35 %) use 9-10 ml/kg/PBW and 14 (3.35 %) use less than 6 ml/kg/PBW.There were 418 responders. Two hundred and ninety-seven of the intensive care practitioners (71.05 %) use SpOMonitoring of the patient under IMV is realized, focusing on the withdrawing process and basic mechanical parameters. Practitioners need to know more about obtaining the driving pressure and its important safety value, aiming to improve its use in their daily practice. Image resources availability on the ICU can be improved, mainly echography resources. The use of a tidal volume of 6 ml/kg/PBW in patients without lung disease should be encouraged."} +{"text": "This is biochemically equivalent to mediator activity because it depends on the C-terminal Rad51-binding region of yRad52 and on functional Rad52-RPA interaction. It has been reported that the N-terminal two thirds of both yRad52 and hRAD52 is essential for binding to and annealing ssDNA. Although a second DNA binding region has been found in the C-terminal region of yRad52, its role in ssDNA annealing is not clear. In this paper, we also show that the C-terminal region of yRad52, but not of hRAD52, is involved in ssDNA annealing. This suggests that the second DNA binding site is required for the efficient ssDNA annealing by yRad52. We propose an updated model of Rad52-mediated ssDNA annealing.Yeast Rad52 (yRad52) has two important functions at homologous DNA recombination (HR); annealing complementary single-strand DNA (ssDNA) molecules and recruiting Rad51 recombinase onto ssDNA (recombination mediator activity). Its human homolog (hRAD52) has a lesser role in HR, and apparently lacks mediator activity. Here we show that yRad52 can load human Rad51 (hRAD51) onto ssDNA complexed with yeast RPA Saccharomyces cerevisiae, where Rad52 is required for DSB repair both in the high-fidelity homologous recombination (HR) pathway [In vitro studies have shown that Rad52 can associate with single-stranded DNA (ssDNA) that is complexed with the ssDNA binding protein RPA [Faithful repair of DNA double-strand breaks (DSBs) is crucial for genome stability. An unrepaired DSB may cause cell death and erroneous DSB repair may cause cancer \u20133. Rad52 pathway \u20139 and in pathway . In vitrtein RPA , 12, andtein RPA , 14. Thetein RPA . The rectein RPA .Rad52 is conserved from yeast to human, with homology mainly in the N-terminal two thirds of the protein . The conin vitro have been unsuccessful [in vitro. Consistent with the in vitro observations, the impact of the loss of RAD52 function in mammalian cells is less pronounced than in yeast. RAD52-/- mouse ES cells showed only moderate reduction in homology-dependent gene-targeting. RAD52-/- ES cells were not hypersensitive to X-ray or MMS. Furthermore, RAD52-knockout mice were viable, fertile, and had normal immune systems [The role of the C-terminal region of Rad52 seems to be considerably different in yeast and mammals. The C-terminal region (amino acids 327\u2013504) of yRad52 is involved in protein-protein interaction with yRad51, and is required for mediator activity , 25, 26. systems .in vitro. Then we analyzed the roles of the C-terminal regions of yRad52 and hRAD52 in mediator activity and ssDNA annealing. We also constructed Rad52-BRC repeat fusion proteins and explored whether the BRC repeat can substitute the C-terminal region of Rad52 and thereby stimulate the DNA strand exchange by hRAD51.BRCA2, not Rad52, seems to be a major mediator protein in mammalian cells , 30. hBR6) tag. pQE60-yRad52NM was constructed from pQE60-yRad52 by deleting a BamHI fragment that encoding C-terminal region RAD52 ORF. pET21-yRad52NM-BRC4 was constructed as follows. First, a double-strand DNA (dsDNA) encoding the BRC4 polypeptide (35 amino acids) was produced by hybridization of two synthetic DNA molecules (Pri-1 and 2) followed by PCR amplification. The dsDNA product was inserted at the BamHI site of pQE60-yRad52NM. The resulting plasmid was used as a template for PCR (with Pri-3 and 4) to amplify the yRad52NM-BRC4 ORF, and the PCR product was inserted between the NdeI and XhoI sites of pET21a. pET21-yRad52NM-BRC3-4 was constructed as follows. First, to create an XhoI site just after the BamHI site of yRad52NM encoding region, pQE60-yRad52NM was amplified by PCR (with Pri-5 and 6) and cloned between NdeI and XhoI sites of pET21a. The resulting plasmid was digested with BamHI and XhoI and ligated with two synthetic dsDNAs (BRC3 and BRC4a) that encode BRC3 (35 amino acids) and BRC4. pET21-yNM-BRC4X3 containing three BRC4 repeats was constructed by ligating three synthetic dsDNA (BRC4b) encoding BRC4 into the BamHI site of pQE60-yRad52NM, and the fused ORF was amplified by PCR (with Pri-7 and 8) and cloned between NdeI and XhoI sites of pET21a. Human RAD52 cDNA was obtained from PlasmID and amplified by PCR (with Pri-9 and 10) and cloned between NdeI and XhoI sites in pET21a to create pET21-hRAD52. Sequence alignment indicated that the region from the 1st to the 286th amino acid of hRAD52 corresponded to yRad52NM encoding the BRC4 peptide into the BamHI site in pET21-hRAD52NM. All newly constructed plasmids were confirmed by sequencing.The plasmids for overexpression of hRAD51 (phRad51.1), hRPA (p11d-tRPA), and yRad52 (pQE60-yRad52) were obtained from Patrick Sung , Mark Wold (University of Iowa), and Rodney Rothstein (Columbia University), respectively. Sequences of synthetic DNA that were used in this study are shown in 1-327th; . To crea6-tag fusion proteins. yRad52 was purified as previously published [E. coli BL21(DE3) harboring pQE60-yRad52NM, pET21-yRad52-BRC4, and pET21-yRad52-BRC3-4, respectively, and purified by the same protocol [All Rad52 derivatives were expressed as C-terminal Hisublished with modublished . yRad52Nprotocol . hRAD52,protocol except tX3 was overexpressed by IPTG in BL21(DE3) harboring pET21-yRad52NM-BRC4x3 and purified as follows. First, cells were suspended in lysis buffer (30 mM Tris-HCl (pH 7.5), 5% (v/v) glycerol and 500 mM NaCl) containing 10mM imidazole, 1 mM PMSF, and a protease inhibitor cocktail (Roche) and lysed using a Branson Sonifier 250. Insoluble cell debris was removed by centrifugation at 20,000 rpm for 30 min with a Beckman JA25.50 rotor. The cleared lysate was loaded on a nickel (Ni) Sepharose column . The yRad52NM-BRC4X3 protein did not bind to the resin. Thus the flow through (FT) was diluted with an equal volume of TDEG buffer (30 mM Tris-HCl (pH7.5), 1 mM dithiothreitol, 1 mM EDTA, 5% (v/v) glycerol) containing no NaCl and loaded onto a Heparin Sepharose column that was pre-equilibrated with TDEG buffer containing 100 mM NaCl. The column was washed with TDEG buffer containing 100 mM NaCl, and then subjected to a linear gradient from 100 mM to 1M NaCl in TDEG buffer. The fractions containing yRad52NM-BRC4X3 (eluted with approximately 800 mM NaCl) were pooled and dialyzed for 3 hours (2x) against TGEB buffer (30 mM Tris-HCl (pH7.5), 5 mM 2-mercaptoethanol, 1 mM EDTA, 5% (v/v) glycerol) containing 100 mM NaCl, and loaded on the Mono-Q column equilibrated with the TGEB buffer containing 100mM NaCl. The column was washed with the same buffer and subjected to a linear gradient from 100 mM to 1 M NaCl in the TGEB buffer. The fractions containing yRad52NM-BRC4X3 were pooled and loaded onto a 1 ml Ni-Sepharose column that was equilibrated with 50 mM Tris-Cl (pH7.5), 500 mM NaCl, 5% (v/v) glycerol, and 10 mM imidazole (I-10 buffer). The column was washed with I-10 buffer and subjected to a step gradient of 50 mM and 200 mM imidazole in I-10 buffer. The yRad52NM-BRC4X3 was eluted with 200 mM imidazole and concentrated with an Amicon ultra 30 (Millipore) to 20.4 \u03bcM, and stored at -80\u00b0C.yRad52NM-BRC4E. coli BLR(DE3) (pLysS) harboring phRAD51.1 as described [yRad51 was purified as described . hRAD51 escribed , and purThe yeast strain to overexpress yRPA was obtained from Richard Kolodner and yRPA was purified as described . hRPA wa32P using T4 polynucleotide kinase (NEB) and \u03b3-32P-ATP (Perkin Elmer). Rad52 or its derivatives was incubated with 100 nM of the labeled TSO252 at 37\u00b0C for 15 minutes in a 10 \u03bcl reaction mixture containing 30 mM TrisAc (pH7.5), 3 mM MgAc, and 20 mM NaCl. The sample was then mixed with 4 \u03bcl of TAE loading dye (50% (v/v) glycerol and 0.1% bromophenol blue in Tris-acetate EDTA buffer), loaded onto a 6% polyacrylamide gel (19 cm x 16 cm) in Tris-borate EDTA buffer, and separated by electrophoresis at 200 V. The gel was dried on DE81 chromatography paper (Whatman) and the labeled products were visualized using a BioRad Personal FX phosphor imager. Radioactive signals were quantified using Quantity One software (BioRad), and the percentage of the Rad52-ssDNA complex in reference to total radioactivity in each lane was determined.The 70-nt ssDNA TSO252, was labeXhoI. RPA and ssDNA were incubated for 2 minutes at 37\u00b0C in buffer containing 40 mM Tris-HCl (pH 7.5), 1 mM DTT, 2 mM ATP, 1 mM MgCl2, 8 mM creatine phosphate, and 28 \u03bcg/ml creatine phosphokinase. Then Rad52 or its derivatives was added to the reaction and incubation continued for 3 min. Then hRAD51 was added to start hRAD51-ssDNA filament formation. After 5 minutes, linear dsDNA, ammonium sulfate (to 100 mM), and spermidine (to 4 mM) were added to start DNA strand exchange. The volume of the reaction at this point was 15 \u03bcl, in which the final concentrations of RPA, hRAD51, ssDNA, and dsDNA were 2.65 \u03bcM, 7.5 \u03bcM, 15 \u03bcM (nt), and 15 \u03bcM (bp), respectively. After 90 minutes at 37\u00b0C, the reaction was stopped and deproteinized by adding 5 \u03bcl of stop buffer and incubating for another 15 minutes. The DNA products were separated by 1% agarose gel electrophoresis (20 x 26 cm) in TAE buffer at 35 V for 15 hours. The gel was stained with ethidium bromide (1 \u03bcg/ml) in TAE for 1 hour and destained in H2O for another 1 hour. DNA bands were visualized with BioRad ChemiDoc XRS+ imaging system and quantified using Image Lab software. DNA strand exchange was quantified as percentage of products (sum of the nicked circle dsDNA and the joint molecules) in total DNA each lane. Then, relative DNA strand exchange was expressed as a value relative to the control reactions carried out in the absence of the potential mediator. For better band visualization, black and white images of the gels were inverted in the figures.\u03a6X174 phage circular ssDNA and dsDNA were purchased from New England Biolabs and the dsDNA was linearized using A fluorescence-based annealing assay was performed in a 400 \u03bcl reaction essentially as described . First, 6-tagged yRad52 (40 pmoles) were incubated for 10 min at 37\u00b0C in 30 \u03bcl of buffer containing 30 mM Tris-acetate (pH7.5), 5 mM Mg-acetate, 0.03% Igepal, 2.5 mM ATP, and 10 \u03bcl (bed volume) of Ni-Sepharose beads. Reaction mixture was then centrifuged at 800 xg for 3 min, and beads fraction was washed with 400 \u03bcl of 30 mM Tris-acetate (pH 7.5), 10 mM imidazole, 50 mM NaCl, 5 mM Mg-acetate, 0,03% Igepal, and 1 mM ATP three times. Bound proteins were eluted in 20 \u03bcl of 1x SDS loading dye and analyzed by 10% SDS-PAGE. Gel was stained with Coomassie brilliant blue R-250.hRAD51 (100 pmoles) and Hisin vitro.Although yRad52 and hRAD52 share 34% amino acid similarity, attempts to detect recruitment of hRAD51 onto hRPA-ssDNA complex by hRAD52 (mediator activity) have been unsuccessful . To undein vitro via an equivalent mechanism to the mediator. Consistently, we observed direct interaction between hRAD51 and yRad52 in vitro . Although it was reported that the multi-copy BRC repeats further enhanced the mediator activity of BRCA2 [We also constructed yRad52NM-BRC4 fusion protein, Click here for additional data file.S1 Table(PDF)Click here for additional data file."} +{"text": "Migraine (M) is one of the most frequent diseases recognized as a cause of disability, with a relevant influence on the quality of life, particularly in women.Our study proposes to evaluate whether migraine affects reproductive choices and motherhood.We interviewed 399 women affected by M without (93.5%) and with (6.5%) aura, aged 17-79 years, using a semi-structured questionnaire. We collected data about intensity of attacks and frequency, fertility, pregnancies, abortion/miscarriage, number of children, influence on decisions about pregnancy and perceived ability in motherhood. A control group of 400 non migrainous women was interviewed for comparable items.Among the 399 women interviewed, 94 (23.6%) were post-menopausal, while 305 (76.4%) had their menses; 155 (38.8%) were nulliparous while 244 (61.2%) had had at least one pregnancy; 224 (56.1%) were mothers while 175 (43.9%) did not have children; 86/244 (35.2%) experienced miscarriage or chose abortion at least once. Two hundred and twenty-three (55.9%) had less than 5 attacks/month, 130 (32.6%) had 5 to 14 attacks/month, 46 (11.5%) had 15 or more attacks/month. Pain intensity was low (NRS 1 to 4) in 18 (4.5%), moderate (NRS 5 to 7) in 108 (27.1%), high (NRS 8 to 10) in 273 (68.4%). Among the 399 women we interviewed, of those who wanted another child , 60/184 (32.6%) considered their headache a problem for a pregnancy. Two patients interrupted a sought-pregnancy because of the headache. Among patients who did not want (further) pregnancies , 20/215 (9.3%) listed headache among the causes for this choice. Few patients considered headache the only reason for their choice. Two hundred and twenty-seven of 399 women (56.9%) reputed headache an impediment to their being mothers. However, few women asked their doctor for information on the relationship between pregnancy and migraine.Our results seem to show a negative influence of M on decision of facing a pregnancy and self-perception as mothers, may be contributing in perceived disability.Written informed consent to publication was obtained from the patient(s)."} +{"text": "Nowadays, only carbohydrate has shown to be an effective countermeasure to exercise-induced immune dysfunction while the effect of protein remains controversial. The purpose of this study was to investigate the acute effects of a commercially available multi-nutrient supplement on performance and salivary markers of humoral immunity, following a bout of circuit resistance training in young athletes.Twelve recreationally resistance-trained males volunteered to participate in the study completing 2 randomised controlled circuit resistance training sessions (CT). Participants ingested 2 doses of 500ml of water mixed 60g of a multi-ingredient (MTN) containing whey proteins, carbohydrate, creatine, HMB and sodium bicarbonate or maltodextrin (PL). Beverages were consumed (3 doses of ~166ml) during and after the workout (1 \u00d7 500ml). Both MTN and PL looks the same colour and flavour and provide a similar amount of calories (~230 per serving). CT involved three rounds of 7 resistance exercises followed by 1 min rest. Participants performed 12 repetitions at 70% 1RM in each of the exercises with no rest in between (only the time to change from one exercise to the next).Measurements included pre and post (30 min and 60 min) salivary markers of humoral immune response: Antimicrobial Peptide, Alpha Defensins (HNP 1-3). The total kg lifted per exercise and in the overall workout was considered as indicator of performance. ANOVA design and Cohen d effect sizes (ES) were used to analyse potential differences between times and treatment conditions.No significant differences were observed between the total weight (kg) lifted per exercise or for the entire session (p > 0.05). HNP 1-3 showed a strong trend (p = 0.06) with a moderate effect size (d = 0.53) at 30 min for the CHO condition [2.001 (1.95) vs 3.037 (2.49) ng/mL], nevertheless, no significant differences were observed at 60 min with respect to the values measured at both pre [3.825 (3.21) vs 2.001 (1.95) ng/mL] and 30 min [3.825 (3.21) vs 3.037 (2.49) ng/mL]. On the other side, HNP 1-3 did not increase at either 30 min [2.464 (3.31) vs 3.656 (3.22) ng/mL] or 60 min [2.464(3.31) vs 2.387 (2.46) ng/mL] post workout for the MTN treatment condition. No differences were observed between the two tested treatment conditions for the three analysed times points .Ingesting both MTN and CHO supplements during and after a circuit resistance-training workout, resulted in no impact on performance. However, even when both nutritional interventions were effective to attenuate the increase of antimicrobial peptide alpha-defensins, MTN showed a stronger effect to blunt exercise-induced immune-dysfunction. These results did not support the notion that only carbohydrate with no added proteins is the only effective nutritional countermeasure against the transient post exercise immunosuppression."} +{"text": "The management of septic shock due to gram negative infections is challenging due to the multidrug antibiotic resistance of some bacterial species.We investigated outcomes of critical care patients with septic shock due to gram negative bacteraimia susceptible only to phosphomycine.Data from septic shock cases hospitalized in a tertiary ICU, during 2014, were retrospectively collected if patients had received phosphomycine i.v. at least for seventy-two hours, as rescue therapy for septic shock bacteraemia due to multidrug resistant (including colistin resistance) bacteria. Main outcomes were compared with cases of septic shock due to multidrug resistant (but susceptible at least to colistin) gram negative bacteraemia (first ICU episode) who received appropriate antibiotic therapy for at least seventy-two hours (Controls).Twelve Cases and 14 Controls were included in the study. Median(IQR) age (years) were 56(45.5-69.2) and 62(57-65), APACHE II 21(20-31) and 18(14-24.5), ICU day of septic shock 63.5(39.5-129.7) and 10(5-16). Duration (days) of phosphomycine treatment was 12.5(9.7-15). Initial empirical antibiotic therapy was appropriate in 62.5% of Controls. Four (33%) Case and 9 (64%) Controls recovered from septic shock in both groups (p = 0.23). ICU duration in Cases and Controls were 73(41-152) and 25(16-33) (p = 0.02) while overall mortality was 75% and 67% respectively (p > 0.5).The use of phosphomycine as rescue therapy in septic shock due to multidrug resistant bacteraemia resulted in low recovery rates although not significantly different compared to patients with septic shock due to multidrug resistant (susceptible to more than two antibiotics including colistin) bacteria."} +{"text": "Nucleoside reverse transcriptase inhibitors (NRTI)-sparing regimens have been studied in antiretroviral therapy (ART)-na\u00efve patients but data with ART-experienced are scarce. NRTI-sparing regimens may be an option in patients with toxicities and for simplification reasons.Retrospective multicentre analysis including ART-experienced patients starting treatment with darunavir/ritonavir and etravirine (DRV/r 800 mg/100 mg QD or 600 mg/100 mg BID and ETV 400 mg QD or 200 mg BID) with at least six months of follow-up. Primary endpoint was proportion of patients with VL<50 copies/mL at 48 weeks with an ITT analysis . Secondary endpoints were safety, CD4 count and lipid changes over 48 weeks.Seventy-five patients were included of whom 44 (58.6%) had HIV RNA<50 copies/mL. Baseline characteristics: median age 50 years (IQR 34\u201365), 72% males, 93% Caucasians, 38.6% hepatitis C, and 45.4% with CDC C stage. Median HIV duration and time on ART were 20 (IQR 7\u201328) and 14 years (IQR 5\u201321) respectively. Reasons for switching were virologic failure in 27 (36%), simplification in 25 (33.3%), toxicity in 20 (26.6%) and other 3 (4.1%). Most of them received DRV/r and ETV QD. Thirty-nine patients had NNRTI resistance mutations and 29 patients had \u22651 primary PI mutations. Main analysis (ITT) showed that 67 (89.3%) had a VL undetectable at 24 weeks (95% CI 83.1\u201395.5) and 57 (76%) at 48 weeks (95% CI 68.4\u201383.6). On treatment analysis showed that 94.3% and 89% had a viral load<50 copies at 24 and 48 weeks, respectively. 11 (14.6%) patients discontinued the regimen . No significant changes in CD4+ count and lipid changes were observed at 48 weeks.Dual therapy with Darunavir/ritonavir and etravirine is an efficacious and safety option in ART-experienced HIV patients even in patients on virologic failure."} +{"text": "Current research suggests that graded introduction of cow's milk, starting with baked milk, may be used as a prognostic indicator for outgrowing Cow's Milk Allergy (CMA).This survey aimed to investigate the attitudes and practice of health professionals on the use of baked milk challenges and graded introduction of milk products in IgE and non-IgE mediated CMA in different regions of the world.The participants were identified by National and International Health Professional Associations and completed the survey online.Of 113 participants 51(45.1%) were dietitians, 31(27.4%) Paediatric Allergists and Paediatricians, 15(13.3%) Allergists/Clinical Immunologists, 2(1.9%) General Practitioners, and 14(12.4%) other health scientists. 14(12.7%) of participants reported that they use baked milk challenges to confirm the diagnosis in CMA and 82(73.2%) to determine tolerance to milk. 52(46%) perform baked milk challenges in IgE mediated CMA in hospital, 8(7.1%) suggest home and 33(29.2%) in both places. In non-IgE mediated CMA, 8(7.1%) conduct these challenges in hospital, 51(45.1%) at home and 27(23.9%) at both places. 17(15%) of responders stated that they use graded introduction of milk containing foods (Milk Ladder) to diagnose CMA and 80(70.8%) to determine tolerance. 19(16.8%) carry out the Milk Ladder in IgE CMA in hospital, 22(19.5%) use it at home and 27(23.9%) in both places. 3(2.7%) perform graded milk introduction in non-IgE mediated CMA in hospital, 56(49.6%) suggest home, and 18(15.9%) in both places.Data indicates that most of the health care professionals use baked milk challenges and graded introduction of baked milk foods to determine the development of tolerance to cow's milk in clinical practice."} +{"text": "Inversion of the CD4:CD8 ratio (<1) has been identified as a hallmark of immunosenescence and an independent predictor of mortality in the general population. We aimed to assess the association between the CD4:CD8 ratio and intima-media thickness (IMT) progression in treated HIV-infected patients as a marker of early atherosclerosis.A longitudinal study during three years was conducted in 120 HIV-infected patients receiving antiretroviral treatment (ART). We analyzed the associations between the CD4:CD8 ratio, cardiovascular risk factor and antiretroviral (ARV) treatment and progression of subclinical atherosclerosis assessed using carotid IMT at baseline and after three years.Finally, 96 patients completed the study. Seventy-six (79.1%) patients were male, aged 44\u00b110 years, 39 (40.6%) were on treatment with Protease inhibitors, 49 (51.04%) with non-nucleoside reverse transcriptase inhibitors (NNRTI), 6 (6.25%) with integrase inhibitors, 3 (3.12%) with maraviroc and 2 (2.08%) only with nucleoside reverse transcriptase inhibitors (NRTI). The mean of ARV exposition was 6.9\u00b15.9 years. Twenty six (27 %) patients had family history of ischemic heart disease, 51 (53.12%) were smokers, 12 (12.5%) hypertensive, 4 (4.16%) type 2 diabetes, 23 (23.9%) with dyslipidemia and 31 (32.3%) were infected with C hepatitis virus. Baseline IMT was significantly associated with age , basal glucemia , triglycerides , Framingham score , CD4:CD8 ratio and dyslipidemia . In multivariable analysis where cardiovascular risk factor and ARV were included, IMT progression was inversely associated with CD4:CD8 ratio and treatment with NNRTI .The inversion of CD4:CD8 ratio in treated HIV-infected patients is independently associated with IMT progression, a marker of age-associated disease. Therefore, it might be clinically useful as predictor of cardiovascular events. Surprisingly, there was a positive correlation between receiving NNRTI and progression of IMT."} +{"text": "To study the spectrum of accidental injuries in the Pediatric Emergency Department of a community hospital.Setting: Pediatric Emergency Department (ED) of a Community hospital with around 10500 ED visits annually. The hospital conducts DNB Pediatrics, MCEM and BSc Accident & Emergency Technology Courses.Participants: 784 Children with accidental injuries between 0 and 18 years of age who attended ED in a 10-month period from January 2013 to October 2013. Design: Retrospective observational study.Tools: The ED records of the study group were analysed retrospectively.Of a total of 8855 children seen in the ED during the study period, 784 (8.9%) presented with accidental injuries. The age distribution was 48 (6.1%), 345 (44%), 172 (21.93%), 131 (16.71%), 88 (11.2%), in <1 year, 1-5 years, 5-10 years, 10-15 years and 15-18 years age groups respectively. Falls accounted for 492 (62.8%), cut injuries 76 (9.7%), RTA 60 (7.7%), poisoning 48 (6.1%), sports related injuries 39 (4.97%), burns 32 (4.1%), crush injuries 15 (1.91%), foreign body 12 (1.53%), fight with peers 8 (1.02%), child abuse 2 (0.25%).In 495 (63.1%) males, falls accounted for 307 , cut injury 56 (73.7%), RTA 37 (61.7%), poisoning 25 (52.1%), sports related injuries 28 (71.8%) burns 18 (56.3%), crush injuries 7 (46.7%), foreign body 7 (58.3%), fight with peers 8 (100%), child abuse 2 (100%).Majority of accidents occurred in evening hours and at home . Of 552 falls and RTAs, 115 (20.8%) and 86 (15.6%) sustained head injury and extremity fracture respectively; 3 (2.6%) and 18 (21%) required immediate surgical intervention and open reduction respectively.232 (29.6%) cases required hospitalisation. There was one death (a 15-year old girl who fell from terrace). Falls were the major cause of injury irrespective of age and gender.A longer study period could have perhaps yielded a larger spectrum of injuries.Childhood accidental injuries can cause serious morbidity and mortality. Injuries peaked in the 1-5 years age group with falls being the leading cause of injury. Studying epidemiology of childhood injuries can help formulate effective preventive strategies and increase parental awareness."} +{"text": "In a previous interim 24-week virological safety analysis of the PROTEST study , initiatPROTEST was a phase 4, prospective, single-arm clinical trial (ID: NCT01378910) carried on in 24 HIV care centres in Spain. Maraviroc-na\u00efve HIV-1-positive adults with HIV-1 RNA (VL) <50 c/mL on stable ART during the previous 6 months, requiring an ART change due to toxicity, with no antiretroviral resistance to the ART started, and R5 HIV by proviral DNA genotypic tropism testing (defined as a G2P FPR >10% in a singleton), initiated MVC with 2 NRTIs and were followed for 48 weeks. Virological failure was defined as two consecutive VL>50 c/mL. Recent adherence was calculated as: (# pills taken/# pills prescribed during the previous week)*100.3 at screening, and median nadir CD4+ counts were 143 cells/mm3. Previous ART included PIs in 46 (62%) subjects, NNRTIs in 27 (36%) and integrase inhibitors (INIs) in 1 (2%). The main reasons for treatment change were dyslipidemia (42%), gastrointestinal symptoms (22%), and liver toxicity (15%). MVC was given alongside TDF/FTC in 40 (54%) subjects, ABC/3TC in 30 (40%), AZT/3TC in 2 (3%) and ABC/TDF in 2 (3%). Sixty-two (84%) subjects maintained VL<50 c/mL through week 48, whereas 12 (16%) discontinued treatment: two (3%) withdrew informed consent, one (1%) had a R5\u2192X4 shift in HIV tropism between the screening and baseline visits, one (1%) was lost to follow-up, one (1%) developed an ART-related adverse event (rash), two (3%) died due to non-study-related causes , and five (7%) developed protocol-defined virological failure, although two of them regained VL<50 c/mL with the same MVC regimen (Tropism results were available from 141/175 (80.6%) subjects screened: 87/141 (60%) were R5 and 74/87 (85%) were finally included in the study. Their median age was 48 years, 16% were women, 31% were MSM, 36% had CDC category C at study entry, 62% were HCV+ and 10% were HBV+. Median CD4+ counts were 616 cells/mm regimen . Initiation of MVC plus 2 NRTIs in aviremic subjects based on genotypic tropism testing of proviral HIV-1 DNA is associated with low rates of virological failure up to one year."} +{"text": "The Pathway Registry is an open label registry of SPG stimulation therapy for cluster headache treatment. In a previous randomized, double-blind, multi-center study (Pathway CH-1 study) 68% of patients experienced clinically significant improvements.The aim of this interim analysis is to evaluate acute and/or preventive therapeutic effectiveness at 6 months following insertion of an SPG neurostimulator.Therapeutic effectiveness (acute pain response following SPG stimulation and/or attack frequency reduction) was analyzed during the first six months following SPG neurostimulator insertion. Acute pain responders achieved relief from moderate or greater pain, or freedom from mild pain in \u226550% of analyzable attacks (with completed diary questions). Frequency responders achieved \u226550% attack frequency reduction at the six month study visit , versus the 4 week baseline period.49 patients have been enrolled, 18 completed follow-up through six months[RJ1] . Average baseline attack frequency was 28.4 attacks/week (range 0-70), and the average attack frequency at 6 months was 17.3 attacks/week (range 0-70), a 40% reduction. 67% (12/18) were responders. Of the 12 responders, 67% (N=8) were acute responders, treating 86% of their attacks effectively (N=546). 75% (N=9) were frequency responders; frequency reduced by 90% (from 22.3 at baseline to 2.1 (range 0-8) attacks/week). 5 patients were both acute and frequency responders.Interim data from a registry of cluster headache patients continues to demonstrate the effectiveness of SPG stimulation therapy."} +{"text": "Detailed information on organizational factors in ICUs located in emerging countries is scarce.To investigate the impact of organizational factors on patient outcomes and resource use in a large sample of Brazilian ICUs.n = 67 (86 %); medical-surgical; n = 62 (79 %)) during 2013. We retrieved demographic, clinical and outcome data from an electronic ICU quality registry (Epimed Monitor System). We surveyed ICUs using a standardized questionnaire regarding organizational aspects, staffing patterns and process of care. We used multilevel logistic regression analysis to identify factors associated with hospital mortality. Efficient resource use was assessed by estimating standardized mortality rates (SMR) and standardized resource use (SRU) adjusted for the SAPS 3 score.Retrospective cohort study of 59,483 patients ) admitted to 78 ICUs were associated with lower mortality. Estimated SMR and SRU were 0.97 (0.72-1.15) and 1.06 (0.89-1.37). There were 28 (36 %) \"most efficient\" (ICUs with both SMR and SRU median), 11(14 %) \"overachieving\" (ICUs with low SMR and high SRU) and 11 (14 %) \"underachieving\" (ICUs with high SMR and low SRU) ICUs. \"Most efficient\" ICUs were usually located in private hospitals, with step-down units and training programs in critical care. In univariate analyses comparing \"most efficient\" and \"least efficient\" ICUs, a graduated nurse-bed ratio >0.25 (OR = 4.40 (1.04-18.60)) was associated with efficient resource use. Daily checklists also tended to be associated with efficient resource use (OR = 2.89 (0.95-8.72), p = 0.057).Forty (51 %) ICUs had critical care training programs. The median nurse-bed ratio was 0.20 and board-certified intensivists were present 24/7 in 16 (21 %) of the ICUs. Routine clinical rounds occurred in 67 (86 %) and daily checklists were used in 36 (46 %) ICUs. The most frequently implemented protocols focused on sepsis management and VAP and CLABSI prevention. Median number of patients per center was 898 (585-1715). SAPS 3 score was 41 (33-52) points. ICU and hospital mortality rates were 9.6 % and 14.3 %. Adjusting for relevant patients' characteristics , case volume and type of ICU, clinical protocols jointly managed by different care providers , In emerging countries such as Brazil, organizational factors are potential targets to improve patient outcomes and efficient resources in ICUs."} +{"text": "Type 1 Diabetes Mellitus (DM)Male 22 years of age Figure Insulin dependent since 2003Visual acuity:OD: 0,10OS: Light PerceptionPreparing for surgical treatmentOperation rejected because of:Blood hypertension (230/110 mmHg)HBA1C: 10.7 %AnemiaRenal Insufficiency (not diagnosed)Hart ischemic changes, left ventricular hypertrophy (not diagnosed)DM is a major cause of avoidable blindness all over the world. Patients with diabetic retinopathy (DR) are 25 times more likely to become blind than non-diabetics. Prevalence of type 1 diabetes is 10-15% of the diabetic population. Prevalence of DR in Wisconsin Epidemiological Study of Diabetic Retinopathy was 50.1 and 54.2% in the diabetes control and complications trial in type 1 diabetes .WHO esti"} +{"text": "Exercise induced bronchoconstriction (EIB) is more prevalent in elite athletes compared to controls. It is however unclear how many young athletes suffer from EIB.2, 21% O2 and 74% N2) at a target rate of 85% of their maximal voluntary ventilation (MVV) per minute (assessed before the EVH test) for 6 minutes. Spirometry was performed at 1, 5, 10 and 15 min after the EVH challenge. EVH test was considered positive if the fall in FEV1 \u226510%. Allergy for house dust mite, grass pollen, tree pollen, weeds, dog and moulds was assessed by skin prick test (considered positive if at least one SPT was positive).Football players (n=24), basketball players (n=15), swimmers (n=12) were recruited at the elite sport high school (12-14 years old) in Leuven (Belgium). Age-matched controls (n=7) were recruited among children performing sports at a recreational level. Eucapnic voluntary hyperventilation test was used to assess EIB according to previous standards. Subjects breathed a gas mixture (5% CO1 \u226510% at EVH test) was diagnosed in 4 out of 12 swimmers, 3 out of 20 football players, 1 out of 11 basketball players and 1 out of 7 control individuals. Only 1 of these individuals (swimmer) had pre-existing asthma. Maximal fall in FEV1 (%) was significantly higher in swimmers (mean: -8.8%) compared to football players (mean: -6.1%), basketball players (mean: -1.0%) and controls (mean: -3.6%) (p=0.027). Allergy was equally distributed among four groups: 7 out of 24 football players, 1 out of 7 controls, 5 out of 11 basketball players, 3 out of 11 swimmers (p=0.94).FVC (L) was significantly higher in swimmers compared to controls (p<0.05). EIB and controls. This might explain why airway hyperreactivity is more common in swimmers compared to other athletes.Swimmers had highest prevalence of EIB. Maximal fall in FEV"} +{"text": "The prevalence of chronic daily headache (CDH) is 4-5% in general population. In headache clinics about 40% patients have CDH and 50-82% of them overuse acute drugs. Combining pharmacological and behavioural therapies can increase effectiveness of treatment, but predictive factors of treatment response are still discussed.To examine predictive factors of treatment response for patient with CDH35 patients with CDH in age from 23 to 78 years were included in the study. All patients were treated by pharmacological therapy and cognitive-behavioural therapy. Patients with medication-overuse headache (MOH) underwent withdrawal therapy. Prospective analysis of clinical-psychological characteristics was performed at the end of 1 and 3 months of treatment.40% (N=14) of patients were classified as having chronic migraine (CM), 25,7% (N=9) had chronic tension-type headache (CTTH), 31,4% (N=11) had CTTH and episodic migraine, 2,9% (N=1) had hemicrania continua. 62,9% (N=22) patients suffered from comorbid psychiatric conditions. Of those, 15,6% (N=5) had mood disorder, 17,1% (N=6) - anxiety disorder,14,3% (N=5) - personality disorder and 17,1% (N=6) suffered from somatization disorder. 60% (N=21) of participants experienced at least 50% reduction of headache frequency after 3 months of treatment. Predictive factors of poor treatment response were: 1) certain psychiatric disorders ; 2) duration of CDH is more than 5 years; 3) out of employment.Predictive factors of poor treatment response are mood disorder, somatization disorder, schizoid personality disorder, more than 5-years duration of CDH and out of employment.No conflict of interest."} +{"text": "The correct sentence is: To avoid aggregation/agglomeration of the nanoparticulate iron, the medium for cellular uptake consisted of a balanced salt solution (BSS) containing 130 mM NaCl, 10 mM KCl, 1 mM MgSO4, 5 mM Glucose and 1.8 mM CaCl"} +{"text": "Legionella pneumophila, was first recognized in 1976. Symptoms of LP include fatigue, myalgia, fever, headache, confusion, diarrhea, nausea, cough, hyponatremia and hypophosphatemia. LP accounts for 2-15% of all hospitalized community-acquired pneumonia (CAP) and carries a mortality rate of 15-25%.Legionella pneumonia (LP), caused by The objectives of this study are to1) describe hospitalized LP cases in the Niagara Region, Ontario, Canada in 2013, and2) to validate the Winthrop University Hospital (WUH) point score on our patient cohort.We conducted a retrospective cohort study on all hospitalized LP cases in the Niagara Region, Ontario, Canada in 2013. Local research ethics approval was obtained. Patient data was extracted from electronic and paper medical records.Public Health Ontario has confirmed 17 cases of Legionellosis from June to December of 2013. 14 cases were hospitalized with LP. 13 cases of LP were confirmed with urinary antigen test. 1 case was confirmed by polymerase chain reaction of bronchial washing. The median age was 57 years, 8 patients (57%) were men; 3 (21%) had a history of ischemic heart disease, 9 (64%) had hypertension, 5 (36%) had diabetes, 2 (14%) had chronic obstructive pulmonary disease, 4 (29%) had chronic renal insufficiency, 1 (7%) had malignancy and 3 (21%) were immunocompromised. 10 (71%) were cigarette smoker and 3 (21%) were cannabis users. The most common symptoms were fever , change of mental status (50%), productive cough (50%), and unproductive cough (36%). Contrary to the literatures, only a small proportion of patients reported diarrhea (29%), abdominal pain (29%), nausea and vomiting (21%), headache (14%), fatigue (29%), and myalgia (21%). Patients were more likely to present with unilateral airspace disease (64%) than bilateral airspace disease (36%) on chest xray. The median sodium, phosphate and creatine kinase were 133 mmol/L, 0.84 mmol/L, and 440 u/L respectively. The severity of illness was high in this cohort reflected by a median Pneumonia Severity Index of 119. 8 (57%) were considered likely whereas 6 (43%) were considered very likely to have LP based on the WUH point score. The median presenting WUH point score was 15. 4 (29%) had delayed antibiotics therapy (> 24 hours). 6 (43%) received fluoroquinolone, and 10 (71%) received macrolide. 9 (64%) required endotracheal intubation with a median length of ventilation of 10 days. 8 (57%) required vasopressive support and 5 (36%) required renal replacement therapy. 3 (21%) died. 11 (79%) required intensive care unit (ICU) admission with a median ICU length of stay (LOS) of 14 days. The median hospital LOS of all patients was 11 days.LP is a serious form of CAP that carries a high mortality rate despite appropriate antibiotic therapy. Symptoms of LP were not always consistent with the literatures but the WUH point score was helpful."} +{"text": "Background: Since PI3K/AKT/mTOR pathway activation diminishes the effects of hormone therapy, combining aromatase inhibitors (anatrozole) with mTOR inhibitors (everolimus) was investigated.Patients and Methods: We evaluated anastrozole and everolimus in 55 patients with metastatic estrogen (ER) and/or progesterone receptor (PR)-positive breast and gynecologic tumors. Endpoints were safety, antitumor activity and molecular correlates.Results: Full doses of anastrozole (1 mg PO daily) and everolimus (10 mg PO daily) were well tolerated. Twelve of 50 evaluable patients (24%) (median = 3 prior therapies) achieved stable disease (SD) \u2265 6 months/partial response (PR)/complete response (CR) (n = 5 (10%) with PR/CR): 9 of 32 (28%) with breast cancer (n=5 (16%) with PR/CR); 2 of 10 (20%), ovarian cancer; and 1 of 6 (17%), endometrial cancer. Six of 22 patients (27%) with molecular alterations in the PI3K/AKT/mTOR pathway achieved SD \u2265 6 months/PR/CR. Six of 8 patients (75%) with SD \u2265 6 months/PR/CR with molecular testing demonstrated at least one alteration in the PI3K/AKT/mTOR pathway: mutations in PIK3CA (n=3) and AKT1 (n=1) or PTEN loss (n=3). All three responders (CR (n = 1); PR (n=2)) who had next generation sequencing demonstrated additional alterations: amplifications in CCNE1, IRS2, MCL1, CCND1, FGFR1 and MYC and a rearrangement in PRKDC.Conclusions: Combination anastrozole and everolimus is well tolerated at full approved doses, and is active in heavily-pretreated patients with ER and/or PR-positive breast, ovarian and endometrial cancers. Responses were observed in patients with multiple molecular aberrations.Clinical Trails Included: NCT01197170 Estrogens regulate growth, differentiation and development in many tissues including the female reproductive tract, bone, central nervous system, immune and cardiovascular systems -3. The aneu-negative, advanced breast cancer who have progressed on anastrozole or letrozole. Other studies have evaluated the aromatase inhibitor letrozole in combination with everolimus and have demonstrated responses in patients with metastatic endometrial carcinoma 532-554 of exon 9 and c1011-1062 of exon 20 (kinase domain) [PIK3CA proto-oncogene by Sanger sequencing following amplification of 276 bp and 198 bp amplicons, respectively, utilizing primers designed at MD Anderson. For AKT1 and PTEN mutations, similar methods were used. Codons 17, 1173, and 179 were examined for AKT1 mutations, and for PTEN, the entire coding sequence of exons 1 through 9 were examined as previously described [Clinical Laboratory Improvement Amendment (CLIA) certified mutational and/or immunohistochemistry assays were performed, when tissue was available, for domain) , which iescribed . PTEN loescribed , 17.neu, estrogen and progesterone receptors. Estrogen and progesterone receptors were assessed using antibody 6F11 . Alternatively, fluorescence in situ hybridization (FISH) was used to measure the copy number of HER2/neu.Under CLIA conditions, immunohistochemistry was used to measure of HER2/Genomic libraries were captured for 3230 exons in 182 cancer-related genes plus 37 introns from 14 genes often rearranged in cancer and sequenced to average median depth of 734\u00d7 with 99% of bases covered >100\u00d7 .Descriptive statistics are provided for all endpoints using SPSS v.19 . Continuous measurements were summarized using mean, standard deviation, median, range, number of patients, and percentages. Time to treatment failure (TTF) and overall survival were calculated using the method of Kaplan and Meier , 19 in m"} +{"text": "Treating chronic HCV/HBV-infected patients with concomitant rheumatoid arthritis (RA) may be a challenge to the clinician. The liver disease limits to some degree the treatment for the rheumatic disease as the drugs used are hepatotoxic or at risk of infection reactivation. The aim of the study is to evaluate the particularities and the safety of RA treatment in patients with both conditions and to investigate the prevalence of HBV/ HCV-infections in RA patients.We performed a cross-sectional analysis of all HCV/HBV or co-infected patients with concomitant RA admitted between 2009-2014, assessing the clinical, laboratory, treatment data and verifying the statistic correlations.The study included 66 patients, with both chronic liver infection and RA, of which 35 (53%) patients had HCV, 24 (36.3%) had HBV and 7 (10.6%) were co-infected. The median age was 61\u00b111 years, sex ratio male/female 13/53. The HCV-infected patients had a very active rheumatic disease activity score (DAS28) (5.03\u00b11.43) while the HBV and co-infected patients had a moderate DAS (DAS28=4.06\u00b11.68), respectively DAS28 (3.05\u00b11.74) (p=0.015). Therapeutic options include disease-modifying anti-rheumatic drugs (DMARDs), classic or biologic as well as corticosteroids (CS). In our study, most patients, 25 (37.8%) received hydroxychloroquine, 9 (13.6%) patients received methotrexate and 7 (10.6%) patients sulphasalazine alone. Combinations included hydroxychloroquine + sulphasalazine in 5 (7.57%) patients and methotrexate + hydroxychloroquine in 4 (6%) patients.th cycle of therapy.In 1 (14.2%) patient out of 7 receiving biologic treatment 6 (85%) infliximab, 1 etanercept, 5 rituximab \u2013 current or prior treatment, reactivation of the HBV infection occurred, during the 6The rise in the liver enzymes, leading to discontinuation were seen in 14 (56%) patients receiving methotrexate, followed by 7 (10.6%) patients receiving sulfasalazine, and 1 (4.3%) in the hydroxychloroquine group. Significantly more patients in the HCV group 27 (80%), compared with the HBV group 24 (45.8%), had an active disease and were given low dose corticosteroids (p=0.028).The presence of the liver infection limits to some degree the therapy for RA. Classic DMARDs such as methotrexate should be closely monitored as they proved most hepatotoxic and led to frequent discontinuation. Hydroxychloroquine was best tolerated. HCV-patients with RA often require more aggressive therapy, including biologics, which also have to be used with caution. The prevalence of HCV infection was higher than HBV infection in the study RA group. Also HCV-infected patients had a more active rheumatic disease and used corticosteroids more frequently."} +{"text": "Juvenile systemic lupus erythematous (JSLE) is a multi-system autoimmune disorder of unknown origin. Involvement of the mucocutaneous ,musculoskeletal system and kidney disease are the most common manifestation of JSLE. This investigation was performed to define the demography and clinical manifestation of JSLE in Iran.Fifty nine patients with JSLE were enrolled in this retrospective study. All patients fulfilled the American College of Rheumatology revised criteria 1982 for the diagnosis of SLE and had shown clinical manifestations of the disease before the age of 16.A total of 59 patients, 49 (89%) were female and10 (16.9%) male. The female to male ratio was 4.9:1. The mean age of onset was 10.5 years (range 2-16). The mean duration of disease from diagnosis was 2 years (range7 months-5 years). The most common of constitutional sign was fatigue (76.3%) and the other signs were fever (32.2%), Nocturnal pain (20.3%), Mood disorder (20.03%), and Weight loss (22%). The most common manifestation of JSLE were as follows: 48 patients (81.35%) had mucocutaneous involvement, 46 patients (77.9%) had musculoskeletal involvement, 25 children (42.37%) suffered from renal disease, hematological abnormalities were detected in 19 patients (32.2%), 10 patients (16.94%) had cardiovascular disease, 33 patients (55.93%) presented nervous system involvement, 12 patients (20.33%) had pulmonary disease, and 13 patients (22.03) experienced infection complications. During the follow up period(3years) two patients died, one from renal failure, one from infections.A high index of suspicion must be preserved for the diagnosis of SLE in adolescent children, particularly girls. Juvenile systemic lupus erythematous (JSLE) is a critical multi-system organ disease. JSLE still has a significant mortality rate high, although it has a high remission rate with early diagnosis and treatment.None declared"} +{"text": "Some parts of world, including India observed a recrudescent wave of influenzaA/H1N1pdm09 in 2012. We undertook a study to examine the circulating influenzastrains, their clinical association and antigenic characteristics to understandthe recrudescent wave of A/H1N1pdm09 from November 26, 2012 to Feb 28, 2013 inKashmir, India. Of the 751 patients presenting with acute respiratory infection at a tertiary care hospital inSrinagar; 184 (24.5%) tested positive for influenza. Further type and subtypeanalysis revealed that 106 (58%) were influenza A and78 (42%) were influenza B. The influenza positive cases had a higher frequencyof chills, nasal discharge, sore throat, body aches and headache, compared toinfluenza negative cases. Of the 206 patients hospitalized for pneumonia/acuterespiratory distress syndrome or an exacerbation of an underlying lung disease,34 (16.5%) tested positive for influenza .All influenza-positive patients received oseltamivir and while most patientsresponded well to antiviral therapy and supportive care, 6 patients (4 withH1N1pdm09 and 2 with influenza B) patients died of progressive respiratoryfailure and multi-organ dysfunction. Following a period of minimal circulation,H1N1pdm09 re-emerged in Kashmir in 2012-2013, causing serious illness andfatalities. As such the healthcare administrators and policy planners need to bewary and monitor the situation closely. Clinical history and examination of the patients was recordedincluding any history of clustering for the entire study period. After clinicaldata recording, combined throat and nasal swabs were collected in viral transportmedium and tested by real-time RT-PCR for influenza viruses using the CDC protocol,The Kashmir province of the state of Jammu and Kashmir is one of the 3 majorprovinces of the northern Indian state that borders Pakistan, China and Afghanistan.The valley of Kashmir has a temperate climate with respiratory illnessesconstituting the bulk of hospital visits during the winter months, either in theform of acute respiratory illnesses or as exacerbations of underlying chronic lungdiseases. Sheri-Kashmir Institute of Medical Sciences (SKIMS) is a 650-bed facilityin the capital, Srinagar, and is the main tertiary referral centre for respiratorycases for the areaWe recruited a total of 751 patients meeting the case definitions of ILI (n=545) andSARI (n= 206) from November 26, 2012 to Feb 28, 2013 at SKIMS, Srinagar, India. Ofthe 751 patients, 184 (24.5%) tested positive for influenza. No major differenceswere noted in the demographic profile of the influenza positive and negativepatients (Table 1). However, influenza positivity was significantly higher in thoseaged >18yrs (27.1%) compared to those <18 yrs The clinicalfeatures among influenza positive cases revealed a significantly higher frequency(p<0.0001) of chills, nasal discharge, sore throat, body ache, and headache anddiarrhea in influenza positive patients (Table 1). Further type and subtype analysisof 184 influenza positives revealed that 106 (37.3 %) were influenza A and 78 (42.4%) were influenza B. Longitudinal analysis ofsurveillance data from January 2011 to February 28, 2013 revealed peaks of influenzacirculations during winter months (December-March) with discrete types over theyears. Among influenza A viruses, H1N1pdm09 were predominant circulating strains inwinter of 2010-2011 and 2012-2013, whereas A/H3N2 was predominant influenza A duringwinter of 2011-2012. Influenza B activity was observed during peaks of circulationthrough the entire study period . Taken together, these data suggest arecrudescent wave of A/H1N1pdm09 during the winter of 2012-2013 two year after thepandemic strain first emerged in Srinagar area.Phylogenetic analysis of a subset of A/H1N1pdm09 (n=6) isolated during 2012-2013revealed clustering with the original pandemic A/California/07/2009-like (H1N1)pdm09 Further antigenic analysis of randomly selected A/H1N1pdm09 virus(n=17) by the hemagglutination-inhibition (HI) test using a panel of post-infectionferret antisera revealed antigenic relatedness to A/California/07/2009 (H1N1)pdm09.Additionally, HAI analysis of influenza B (n=10) showed antigenic relatedness to theB/Yamagata lineage.We next examined the age distribution of the 751 patients studied during the2012-2013 season Influenza positivity was comparable in children (18%) and those>65 yrs (19%), but significantly higher in those aged >18-65 yrs (28%) (Table2).Of the 105 patients from whom A/H1N1pdm09 was recovered, 22.8% (n=24) were aged<18 years, 62% (n=65) were aged 18-60 years whereas 15% (n=16) were aged >60years.The positivity rate for A/H1N1pdm09 virus was 11.5% in patients aged 60 age group.Influenza positivity rates for both A/H1N1pdm09 and influenza B were generallyhigher among outpatients as compared to those hospitalized. However influenza A andInfluenza B was observed equally among the hospitalized patients.Further, we found no major differences in demographic or clinical features amongthose infected with influenza A/H1N1pdm09 vs influenza B (Table 3). A total of 206enrolled cases required hospital admission in winter of 2012-2013 and 34 (16.5%) ofthem tested positive for influenza . Mostof the influenza patients who required hospitalization had associatedco-morbidities, including chronic obstructive pulmonary disease ,hypertension (n=19), diabetes (n=8), coronary heart disease (n=4), hypothyroidism(n=3), heart failure (n=3), malignancy (n=3), chronic kidney disease (n=2), and oneeach with lupus erythematosus, cyanotic heart disease, chronic demyelinatingpolyneuropathy and panhypopitutarism. Hypoxia was seen in all of the admitted cases(paO2 from 24 to 81(mean 58.12 +13.32) and blood pH ranged from 7.25 to 7.53 (mean +SD 7.38+0.057). Laboratory features among the hospitalized patients includedneutrophilic leukocytosis (n=6), lymphopenia (n=9); azotemia (n=9) and elevated LDH(n=16). All except one hospitalized influenza positive patient had radiographicfeatures of pneumonia or ARDS (n=8). Extensive chest infiltrates were seen in 6 caseson CT imaging. Among the 34 influenza positive hospitalized patients in 2012-2013,all had severe symptoms suggestive of acute pneumonia, acute respiratory distresssyndrome or a respiratory failure. Of 34, 28 recovered with routinesymptomatic/supportive and antiviral therapy; however, 16 required admission to ahigh dependency unit (HDU) or an intensive care unit (ICU). Of the 16, 6 patientsdied with ARDS, progressive respiratory failure and multi-organ dysfunction; 2 hadbeen managed at a different facility for sepsis and were referred after onset ofrespiratory failure. Of the 6 who died, 4 hadA/H1N1pdm09; 2 (ages 62 and 75 yrs) had influenza B and died with severe pneumonia.The percent of hospitalized SARI patients who tested positive for influenzawas comparable in winters of 2010-2011 , 2011-2012, and 2012-2013 . However, nofatalities were recorded among the hospitalized SARI patients positive for influenzain the 2010-2011 or 2011-2013 seasons.,, but is not welldocumented in the tropics,,,,We report a recrudescent wave of A/H1N1pdm09 in the temperate region of Kashmir inwinter of 2012-2013 , more than 18 months after theprevious peak of influenza in the winter of 2010-2011Taken together, our data is suggestive of a recrudescent wave of A/H1N1pdm09 in atemperate climate area of northern India, almost two years after its firstappearance in the region"} +{"text": "KSHV ORF57 (MTA) promotes RNA stability of ORF59, a viral DNA polymerase processivity factor. Here, we show that the integrity of both ORF59 RNA ends is necessary for ORF57-mediated ORF59 expression and deletion of both 5\u2019 and 3\u2019 regions, or one end region with a central region, of ORF59 RNA prevents ORF57-mediated translation of ORF59. The ORF59 sequence between nt 96633 and 96559 resembles other known MTA-responsive elements (MREs). ORF57 specifically binds to a stem-loop region from nt 96596\u201396572 of the MRE, which also binds cellular RBM15. Internal deletion of the MRE from ORF59 led to poor export, but accumulation of nuclear ORF59 RNA in the presence of ORF57 or RBM15. Despite of being translatable in the presence of ORF57, this deletion mutant exhibits translational defect in the presence of RBM15. Together, our results provide novel insight into the roles of ORF57 and RBM15 in ORF59 RNA accumulation and protein translation. Following primary infection, KSHV establishes a lifelong latency in which the KSHV episome is replicated by the host cell replication machinery. Upon reactivation to lytic cycle, the replication of KSHV genome depends on several viral proteins, including DNA polymerase Pol-8, ORF9), processivity factor of DNA polymerase PF-8, ORF59), helicase HEL, ORF44), primase PRI, ORF56), primase-associated factor ORF40/41), single-strand DNA binding protein , replication and transcription activator (ORF50 or RTA), and replication-associated protein , single-,3. ORF594, primas9, helica, primase, ORF9, poriLyt) . RTA alsoriLyt) . Lytic roriLyt) , but prooriLyt) . ORF57 poriLyt) ,14,15,16oriLyt) . ORF57 boriLyt) ,19,20. WoriLyt) ,18 and ppVM7 for FLAG-tagged ORF57, pVM68 for 3 \u00d7 FLAG-tagged ORF57, pVM18 for FLAG-tagged ORF59 and RBM15-FLAG were described in previous reports ,21,22. T5/well) plated in a six-well plate. Twenty four hrs after seeding the cells were co-transfected with 1 \u00b5g of individual ORF59 expression vector together with 0.2 \u00b5g of ORF57 (pVM7 or pVM68) or RBM15 vectors. The cells cotransfected with an empty pFLAG-CMV-5.1 vector were used as a negative control. All transfections were carried out with Lipofectamine 2000 as recommended. Protein samples were obtained by direct cell lysis with 0.5 mL of 2\u00d7 SDS protein loading solution supplemented with 5% 2-mercaptoethanol and analyzed by Western blotting with following antibodies: rabbit polyclonal anti-ORF57 antibody [32P-labeled antisense oligo probes: oVM11 for ORF57, oVM158 and oJM65 for ORF59, oZMZ270 for GAPDH and oST197 for U6 small nuclear RNA . All co-transfection assays were carried out in HEK293 cells (5 \u00d7 10antibody (1:3000)antibody . The exp6 of TREx BCBL1\u2013RTA or \u2013vector cells in RIPA buffer as described [KSHV-infected, engineered BCBL1 cells, TREx BCBL1-vector and TREx BCBL1-RTA cells , were cuescribed . RNA-proescribed ,26 usingescribed . The proORF59 RNA decay was analyzed in HEK293 cells transiently transfected with an ORF59 expression vector in the presence or absence of ORF57 as described previously ,19. The In an attempt to delineate ORF59 sequences responsible for regulation by ORF57, we constructed a series of progressive 5\u2019 to 3\u2019 and 3\u2019 to 5\u2019 truncations of ORF59 A and evaIt has previously been shown that ORF57 is capable of enhancing translation of viral mRNAs by recruiting PYM, a cellular protein capable of facilitating the assembly of the 48S pre-initiation complex onto viral intronless mRNAs . As all Previous anti-ORF57 CLIP assays identifivs. V in Our previous studies have shown that ORF57 affects ORF59 accumulation by interacting with RBM15, an RNA binding export cofactor . TherefoTo evaluate the relevance and functionality of the ORF59 5\u2019 MRE sequence, we analyzed the MRE truncation mutants pJM22 and pJM23 A furtherKSHV ORF57 interacts with RNA export factor Aly/REF and NXF1 ,30 and cWe also analyzed RBM15's ability to accumulate RNA from other progressive 3\u2019- and 5\u2019-truncation mutants of ORF59. All of the mutants analyzed showed higher levels of ORF59 RNA expression in the presence of RBM15 A. In agrIn summary, this study has demonstrated that KSHV ORF59 contains multiple regions or motifs responsible for viral ORF57 and cellular RBM15. ORF57 promotes protein translation from ORF59 RNA and requires two terminal regions or one terminal region plus a central region of ORF59 for this function. The MRE identified by anti-ORF57 CLIP binds ORF57 protein and RBM15 and appears to be important for RNA export and stability of ORF59. However, this MRE motif is also important for RBM15-mediated protein translation of ORF59. Together, these studies provide further insight into how ORF57 promotes ORF59 expression by balanced interplay with RBM15."} +{"text": "To study the awareness and execution of road safety practices among school children.Design: Questionnaire based studySetting & Participants: Children studying in 9th & 10th grades of city schools in Chennai, Tamilnadu, India.Questionnaires were completed by 234 (93.6%) of 250 children who were approached. The mean age of the children was 14.3 (range 13-15 years). 70 (29%) were girls and 141 (60%) were boys; 23 (9.8%) did not fill in the personal details. 12 girls had driven a car or bike, of which 6 always, 4 sometimes and 2 never had driven without a helmet/seat-belt. 66 boys had driven a car or bike of which 32 has always, 22 sometimes and 12 had never driven without a helmet/seat-belt.33 (47%) girls and 90 (63.8%) boys had ridden as pillion, of which only 5 boys and no girls wore a helmet. 17 (6.8%) children did not answer this question. 31 (21.9%) boys and 14 (2%) girls had had a road traffic accident (RTA); 4 boys and no girls sustained fractures. None of the children had a license. 34 (24%) boys and 17 (24%) girls used seat-belts in the passenger seat of cars. 10 boys and no girls had used mobile phones when driving. 10 (7%) boys and 11 (15%) girls admitted to disregarding traffic signals. 58 (41%) boys and 28 (40%) girls had friends who had an RTA. 22 (15%) boys and 2 (2%) girls had involved in racing while driving. None had consumed alcohol while driving.116 (82%) boys and 49 (70%) girls rode bicycles on the road, 2 (4%) girls and 5 (4.3%) boys used helmets. 48 mothers and 115 fathers of these children used helmets while driving two wheelers: 60 mothers and 107 fathers used seat-belts while driving cars. 122 (86%) boys and 59 (84.2%) girls believed that helmets and seat-belts prevent serious injury.Doing a cluster sampling of all the city schools would have yielded a more holistic picture.The non-use of seat-belts, helmets, unlicensed driving of vehicles and scant regard to traffic rules are rampant in school-going children. The law regarding this has to be enforced and punishment maximised to improve road safety practices."} +{"text": "We have previously reported a more advanced radiological presentation in HIV+/HCV+ than HIV-/HCV+ patients (pts). The aim of our study was to define prognostic factors of death in HIV+/HCV+ pts with HCC.Cases of HCC in HIV+/HCV+ pts were obtained from the 3 ANRS Prethevic, HepaVih and CirVir cohorts. Imaging was reviewed according to EASL criteria.Fifty HIV+/HCV+ coinfected pts (n=44 men (88%), median age 50 years [40-74], median CD4 cell count 334/mm3 [58-1621], n=28 Child A cirrhosis (60%)) developed HCC. Thirty-one (63%) pts presented cirrhosis decompensation before HCC diagnosis. At HCC diagnosis, median serum aFP was 20.4 ng/ml, 38 (76%) pts had a nodular tumor (median main diameter 23.5 [11-70] cm) and 12 (24%) pts an infiltrating form (62.5 [10-130] cm), p=0.007. Tumor portal thrombosis was diagnosed in 14 (28%) pts. A curative or a palliative procedure was further performed in 22 (44%) pts and 20 (40%) pts, respectively. The 2-years and 4-years overall survival rates were 51% and 28%, respectively. Age (p=0.0005), infiltrating or nodular tumor (p= 0.0009) and tumor portal thrombosis (p=0.004) were associated to survival. In a Cox model, two prognostic factors of deaths were found: prior episode of cirrhosis decompensation and tumor portal thrombosis , adjusted on age, CD4 cell count and the therapeutic strategy for HCC.Cirrhosis decompensation and tumor portal thrombosis significantly impact the survival of HIV+/HCV+ pts with HCC. Our results suggest new rules of screening HCC in HIV+/HCV+ pts with advanced liver disorders."} +{"text": "HER2-positive breast cancers are more likely to achieve a pathological complete response . We review our data to see what happens to HER2-positive DCIS associated with HER2-positive invasive cancer treated with NACT.There are few data regarding the effect of neoadjuvant chemotherapy (NACT) and trastuzumab on any ductal carcinoma All cases that were HER2-positive from our local NACT database were identified from 2010 to 2012. The imaging features, core biopsy and final histology were documentedA total 41 of 150 patients that received NACT (anthracycline and taxane based) were HER2-positive and treated with trastuzumab. In total, 40/41 cases had surgery following neoadjuvant treatment, 24/41 (59%) cases had calcifications on mammography, and 21/41 (51%) obtained a pCR. Of the 24 cases with calcification, 14 (44%) had a pCR with 9/14 (29%) having residual DCIS. Seven of 24 cases had a WLE in which the calcifications on mammography were unchanged in extent or appearance. A total 17/41 were without calcification, seven (57%) had a pCR with 2/7 (62%) having residual DCIS that was noncalcified.pCR is higher in the HER2-positive group compared with the HER2-negative group (51% vs. 20%). In total, 48% achieved a pCR with no residual DCIS but 52% still had residual DCIS, suggesting that trastuzumab may be less effective in treating HER2-positive DCIS."} +{"text": "Immunosuppression (IS) has been described as a factor associated with mortality in intensive care unit (ICU) and with increased susceptibility to infection by multidrug-resistant pathogens (MDR). Variables that increase these risks have not been completely determined.Characterization of the population under immunosuppressive therapy (IST) admitted in ICU with infection, and description of risk factors for infection by a MDR pathogen and hospital mortality.Retrospective cohort study of all patients under IST admitted with infection at a 11-bed mixed ICU, in a tertiary care, university-affiliated hospital, between January 2011 and December 2014. Patients who started IS in the same episode were excluded. MDR pathogen was defined as a pathogen resistant to at least three antibiotics from different groups recommended for its treatment. Heavy IST was defined as prednisolone> 20 mg/day and/or multiple IS and/or chemotherapy. The association of several variables with infection by MDR pathogen and with hospital mortality was studied through logistic regression.During the study period 91 patients under IST were admitted in the ICU, of those 61 were hospitalized for infection (67%). The mean \u00b1 SD age was 59 \u00b1 15 years, 54% were male, and the mean \u00b1 SD SAPS II was 52 \u00b1 22 and SOFA 9 \u00b1 4. The underlying diseases identified were: autoimmune diseases (31%), solid tumors (21%), transplanted patients (25%), hematologic diseases (16%) and others (7%); 46 (75%) patients were under heavy IST. The most prevalent foci infection were respiratory (61%) and abdominal (13%). Microbiological documentation of infection was possible in38 patients (62%): 16 (44%) gram negative, 7 (18%) gram positive, 2 (5%) fungus, 2 (5%) other and 11(29%) polimicrobial. MDR pathogens were identified in 8 (21%). Diabetes was significantly associated with infection by a MDR pathogen . Empiric antibiotherapy was adequate in only 34% of the patients. Those infected with MDR pathogen had a significantly higher rate of inadequate antibiotic therapy . Hospital mortality rate was 54%. Variables associated with increased hospital mortality were: male gender [OR(95%CI) = 4.14(1.42-12.09)], chemotherapy [OR(95%CI) = 4.33(1.33-14.14)], duration of treatment < 1 month [OR(95%CI) = 0.19(0.05-0.77)], acute hematological dysfunction [OR(95%CI) = 9.2(2.75-30.79)], acute renal dysfunction [OR(95%CI) = 3.09(1.08-8.82)], total SOFA score [OR per point (95%CI) = 1.169(1.008-1.356)] and SAPS II score [OR per point (95%CI) = 1.030(1.003-1.057)].Infection was the most common cause of ICU admission in IS patients. Diabetic had higher prevalence of infection by MDR pathogens. Surprisingly, infections by MDR pathogens or inadequate initial antibiotic therapy were not among the risk factors associated with increased hospital mortality."} +{"text": "Mallotus japonicas, a Japanese edible herb historically used for the treatment of stomach ulcers. The mammalian target of rapamycin (mTOR) has been shown to regulate rates of muscle protein synthesis and a mechanical stimulus (resistance exercise) has been shown to activate mTOR with PA playing a key role. Supplementation with soy-derived PA significantly increases responses in skeletal muscle hypertrophy, lean body mass, and maximal strength to resistance exercise. PA accounts for less than 0.1% of the total glycerophospholipid concentration of 201 mg/dl in the human plasma. 15 of the more than 600 distinct molecular lipid species quantified in human plasma are PA, 6 are lysophosphatidic acid (LPA). Orally administered PA can be metabolized to LPA and glycerophosphate by pancreatic phospholipases A1 and A2, which hydrolyze the fatty acid at the sn-1 position and the sn-2 position, respectively. Lysophospholipids are absorbed by the mucosal cells of the gastrointestinal tract and are rapidly re-acylated with fatty acids of the body pool resulting in a newly-formed phospholipid-molecule whose fatty acid composition is determined by the physiological and nutritional status and not by its source. This study sought to assess the effect of soy-derived PA supplementation on concentrations LPA and PA molecular species in human plasma.The glycerophospholipid Phosphatidic acid (PA) has been identified as a potential nutritional treatment for gastrointestinal disorders. Dietary food sources rich in PA include cabbage and radish leaves as well as After a 12 hour overnight fast one subject was assigned to receive 1.5 grams of soy-derived PA . Blood draws were taken immediately prior to, and at 30 min, 1, 2, 3, and 7 hours following supplementation. The samples were analyzed by an ultra-performance liquid chromatograph with triple quadrupole mass spectrometry (LC/MS/MS) using 17:1-LPA and 37:4-PA as internal standards to determine the concentration of LPA and PA molecular species in human plasma.At baseline, 19 PA (highest concentrations: C34:2 (15%), C40:4 (11%), and C36:4 (10%)) and 5 LPA (16:0 (45%), 18:2 (19%), 20:4 (17%), 14:0 (11%) and 18:1 (8%)) molecular species could be quantified with total concentrations of PA of 2.66 nmol/ml, and LPA of 0.11 nmol/ml. Plasma concentrations of PA peaked at 3 hours (+32%) after ingestion and stayed elevated even after 7 hours (+18%). LPA showed a bimodal absorption kinetic with peaks after 1 hour (+500%) and 3 hours (+264%), after almost dropping back to baseline levels after 2 hours. On an individual fatty acid level, most prominent was a 23-fold increase in 20:4-LPA after 1 hour compared to baseline. The increase in 20:4-LPA does not result from the administration of PA, since soy-derived PA does not contain any arachidonic acid (fatty acids distribution of soy-PA: 18:2 (66.1%), 18:1 (12.6%), 16:0 (11.7%), 18:3 (6.1%) and 18:0 (3.4%)). Absorption of soy-derived PA must yield glycerophosphate which is re-acylated with arachidonic acid.LPA and PA can be molecularly identified and measured. LPA, PA and LPA+PA plasma levels increase 30 min after ingestions, plateau at 1-3 hours and remain above baseline levels after 7 hours. This is the first case study showing that orally administered PA is bioavailable. Future research should repeat this case study with a larger n-size and include the analysis of omega 3 fatty acid-LPA molecular species."} +{"text": "Atopic dermatitis (eczema) is a highly pruritic chronic inflammatory skin disease. Food allergy has been strongly correlated with the development of persistence of atopic dermatitis.To investigate the association of food allergy in Greek children with atopic dermatitis.Eighty-eight (88) children with eczema (59 boys and 29 girls) aged between 12 months and 6 years were studied. All the children underwent allergological investigation with assignment of specific IgE antibodies (Elisa Method) to the following food allergens: \u03b1- lactalbumin, \u03b2-lactoglobulin, casein, milk proteins, egg white, egg yolk, beef, soy, wheat, and cod.Food sensitization occurred in 39 out of 88 children . The frequency distributions for elevated specific IgE antibodies to various food allergens in children with eczema are shown in the following Table Table .Food sensitization has a high prevalence of almost 44% among children with eczema.Milk proteins are the most common food allergens implicated in children with eczema (27.25%), followed by egg white (22.21%), a-lactalbumin (21.2%), egg yolk (12.11%), \u03b2-lactalbumin (10.9%) and wheat (8.7%).Beef, soy and cod fish are less common food allergens in children with eczema."} +{"text": "This retrospective study aimed to investigate that if switch of combination antiretroviral therapy (cART) would result in viral suppression (<40 copies/mL) at 48 weeks for patients with persistent low-level viremia after having received cART for six months or more at two hospitals designated for HIV care in Taiwan.Between January 2001 and January 2013, patients were enrolled if plasma HIV RNA load (PVL) were >20 to <1000 copies/mL detected for six months or more [In this study, 165 patients were enrolled, 119 patients (72.1%) did not switch (Group 1), and 46 patients (27.9%) switched previous regimens to ARV of different mechanism (Group 2). The two groups differed significantly in the proportion of injecting drug users (IDU) and median PVL (67 vs 159 copies/mL), and the proportion of PVL<200 copies/mL (84.0% vs 58.7%) when low-level viremia was first detected. In Group 1, 39 (32.8%) continued two nucleoside reverse-transcriptase inhibitors (NRTIs) plus nNRTI; 29 (24.4%) 2 NRTIs plus PI, 47 (39.5%) 2 NRTIs plus boosted PI, and 4 (3.3%) 2 NRTIs plus integrase inhibitor (II). In Group 2, two (4.3%) switched to 2 NRTIs plus PI, 38 (82.6%) 2 NRTIs plus boosted PI, three (6.5%) 2 NRTIs plus II and three (6.5%) boosted PI plus II. In multivariate analysis, IDUs and PVL of 200\u2013999 copies/mL at enrollment were more likely to be switched. At 48 weeks, patients in Group 2 were more likely to achieve PVL<40 copies/mL than Group 1 , while no difference was observed in achieving PVL <200 copies/mL between the two groups . According to the clinical guidelines of BHIVA, patients with low-level viremia who switched to cART consisting of 2 NRTIs plus boosted PI or newer mechanisms were more likely to re-establish viral suppression to <40 copies/mL at week 48."} +{"text": "Macrophage activation syndrome (MAS) is a life-threatening complication of chronic rheumatic disease in childhood.We aim to eveluate MAS findings and outcomes that differ according to disease in childhood.We obtain 11 rheumatic patients followed in two different pediatric rheumatology units (Erciyes University and Ege University) who presented with MAS. We report their clinical and laboratory findings, therapies and outcomes.The primary diagnoses of the patients included in the study, respectively; systemic juvenil idiopathic arthritis (n=5), Systemic Lupus Erythematosus (n=2), juvenile dermatomyositis (n=2), a neonatale onset multisystem inflammatory disease (NOMID) and a microscopic polyartritis nodosa. The mean age of the patients was 9.9 years old (1-14), and male to female ratio was 3:8. The mean duration of underlying disease was 6 months (1-24 months) at the diagnosis of MAS. We found MAS due to infection in four patients ,while used medicine in a patient. MAS were developed spontaneously in 6 patients. The clinical manifestations of MAS included fever 7 (63.6%),mucosal bleading 6 (54.5%), neurologic involvement 4 (36.4%) and hepatomegaly 6 (54.5%).We found thrombocytopenia in 9 (81.8%), leucopenia in 5 (45.5 %), increased AST in 7 (63.6%), hypofibrinogenemia in 6 (54.5%), increased ferritin in 11 (100%), decreased ESH in 4 (36.4%) and increased triglyceride in 10 (90.9%) patients. We investigated bone marrow in all patients, and hemophagocytosis were determinated in 8 (72.7%). The medications were pulse methylprednisolone 6 (54.5%), intravenous immunoglobulin 8 (72.7%), plasma exchange 5 (45.5%), cyclosporine 6 (54.5%), dexamethasone 1 (9.1%), etoposide 1 (9.1%). The prognosis of patients were recovery 8 (72.7%), and exitus 3 (27.3%).In conclusion, MAS can be developed in various pediatric rheumatologic disease and fatal. Prompt recognition and timely treatment can result good outcomes.None declared."} +{"text": "Determine the prevalence of positivity to different groups of battery contact tests performed in a specialized Service.300 patients were evaluated at 36 months, with a diagnosis of contact dermatitis. All of them underwent delayed skin test reading (patch test), with Brazilian Standard Battery of 30 substances. The test steps (placing two readings and grading of positive responses) were performed according to the standards established by the Brazilian Study Group of Contact Dermatitis (BSGCD) and the International Contact Dermatitis Research Group (ICDRG).Of the 300 tests, positivity was observed in 194 (65%). 106 (35%) tests were negative and characterized contact dermatitis by primary irritant. There was a predominance of females (76%) compared to males (24%). The most affected locations were hands , feet (back and plants - 41%), arms (31%) and face (26%). Positive results were obtained by groups of substances: Anthraquinone (0.5%), Balsam of Peru (5.1%), PPD mix (7.7%), Hydroquinone (2%), Potassium bichromate (19%) Propylene glycol (1.5%), p-tertiary Butyl Phenol (1%), Neomycin (4.1%), Irgasan (1.5%), Kathon CG (10.8%), Cobalt chloride (9.2 %), Lanolin (1.5%), Thiuram mix (3.6%), Ethylenediamine (3.6%) Perfume mix (6.7%), Mercaptobenzothiazole (mix) (2%), Benzocaine (3.6%) Quaternium 15 (1.5%), Quinoline mix (6.7%), Nitrofurazone (4.6%) Paraben mix (6.1%), Epoxy-resin (1.5%), Thimerosal (24. 2%) Turpentine (2%), Carba mix (7.2%), Promethazine (7.7%), Nickel sulfate (45.8%), Colophony (5.1%), Paraphenylenediamine (12.3%), Formaldehyde (6.7%).Although positivity was observed in all groups, there was a predominance of Nickel sulfate, followed by Thimerosal and Potassium bichromate. This highlighted the importance of these substances in cases of allergic contact dermatitis admitted in our Service."} +{"text": "Medical mentoring is becoming increasingly complex with the evolving needs of trainees and the complexities of their personal and social lives. The Internet is an enabling technology, which increasingly facilitates interaction with multiple people at a distance. Web 2.0 and 3.0 technology shows promise in furthering this facilitation.The objective of our study was to establish opinions among doctors in postgraduate surgical training regarding mentoring and whether these doctors would readily accept virtual mentoring following a brief experience.On the 12th of February 2012, an introductory teaching class was arranged by The London Postgraduate School of Surgery for doctors in training. Participants were introduced to a novel virtual mentoring system and asked to complete a questionnaire regarding their opinions before and after the demonstration.P<.001). Prior to using MentorSL, regarding usefulness of voice communication for virtual mentoring, 11/35 (31%) agreed or strongly agreed and 18/35 (51%) were unsure. Following 20 minutes using MentorSL, 19/35 (54%) agreed or strongly agreed and 10/35 (29%) were unsure of usefulness. Regarding ease of use of navigation, search mentor, meeting scheduling, and voice communication features, 17/35 (49%), 13/35 (37%), 15/35 (43%), and 16/35 (46%) participants agreed or strongly agreed, respectively. Regarding usefulness of telementoring, 24/35 (69%) agreed or strongly agreed, increasing to 28/35 (80%) following the introduction. For usefulness of multiple mentors, initially 24/35 (69%) agreed or strongly agreed increasing to 29/35 (83%). For overall satisfaction, 30/35 (86%) reported good or adequate and 19/35 (54%) agreed or strongly agreed with using the system again.A total of 57 junior doctors attended. Among them, 35 completed questionnaires pre- and postdemonstration. Regarding usefulness of a 3D virtual environment for mentoring, 6/35 (17%) agreed or strongly agreed and 20/35 (57%) were unsure prior to the session. Following 20 minutes using MentorSL, this significantly increased to 14/35 (40%) agreeing or strongly agreeing with 11/35 (31%) unsure (These data suggest that a short introduction on how to use virtual systems may result in significant participation and use of virtual mentoring systems. Doctors in postgraduate surgical training often require guidance to overcome hurdles associated with modern-day surgical training. Good mentoring delivered in a timely fashion is a way in which surgical trainees may be helped through these difficulties in a manner compatible with the principles of adult learning.The Standing Conference on Postgraduate Medical and Dental Education (SCOPME) in the United Kingdom, describes mentoring as:The process whereby an experienced, highly regarded, empathic person (the mentor) guides another individual (the mentee) in the development and re-examination of their own ideas, learning, and personal and professional development. The mentor, who may or may not work in the same organization or field as the mentee, achieves this by listening and talking in confidence to the mentee The mentors have many roles that have previously been reviewed . BrieflyIt has been previously reported that trainees often do not have mentors or are unaware of the role of the mentor and therefore do not have beneficial meetings with them ,3. The mThe latest digital technologies may be a key enabler to support these requirements. The Department of Health in the United Kingdom has recently published a \u201cFramework for Technology Enhanced Learning\u201d that advocates the use of e-learning and simulation to enhance learning where there is a clear benefit to patient care . InterneVirtual worlds including Second Life (SL) by Linden Laboratories and OlivFor the purposes of exploring new methods to support mentoring, a 3D virtual system, MentorSL, was developed . AvatarsDoctors in postgraduate surgical training in the London Postgraduate School of Surgery see were invThe London Postgraduate School of Surgery is the largest surgical training organization in the world. It is responsible for managing more than 900 trainees. The school offers programs at prestigious teaching centers across the capital city. Doctors in postgraduate training spend an initial 2 years in generic foundation training; this is followed by a further 2 years in core surgical training. Successful competitive progression results in spending an additional 6 years in specialty surgical training (ST3 to ST8) toward award of completion of training.Doctors in postgraduate surgical training were invited to attend a \u201ctaster\u201d session introducing virtual mentoring via the online virtual world SL at the London Postgraduate School of Surgery, UK. This session was a subsection of a wider training meeting being held. The trainees were within the first four years of postgraduate training. All participants had previously experience of mentoring as a component of \u201cFoundation Training\u201d which includes appointing of an \u201cAssigned Educational Supervisor\u201d by the training program. A 10-minute presentation on SL and specifically on MentorSL including an \u201cin-world\u201d walk through was given via a large screen projector. SL as a virtual world facilitating interaction of virtual people or avatars was explained. Methods used to navigating and communicate in SL were explained to participants. MentorSL was introduced as a tool to facilitate mentoring in the virtual world of SL. The search mentor facilities in MentorSL and the facilities to arrange and hold meeting within the MentorSL framework were explained and demonstrated. Following a short questions and answers session, participants were able to sit in groups at computer stations running Second Life fitted with multiple headsets. Facilitators in the real world as well as SL were available to help and guide participants.Participants were invited to fill in an anonymous questionnaire regarding their perceptions both prior to and after the session. The questionnaire consisted of 7 domains: (A) demographic data, (B) perceptions regarding mentoring, (C) perceptions regarding the 3D Web, (D) perceptions regarding the practicalities of MentorSL, (E) perceptions regarding tele- and multiple mentoring, (F) perceptions regarding further enhancements in virtual mentoring, and (G) perceptions regarding future use of MentorSL . Data were presented as ratios and percentages. The chi-square test was used for significance testing.There were 57 participants in total, median age was 28.1 years (range 24-43). There were 32 females and 25 males .Of the total participants, 1/57 (2%) qualified in 2004, 3/57 (5%) qualified in 2007, 23/57 (40%) qualified in 2008, 13/57 (23%) qualified in 2009, and 17/57 (30%) qualified in 2011. Of the total participants, 20/57 (35%) were in foundation year 1 (FY1), 22/57 (39%) were in core surgical training 1 (CT1), and 15/57 (26%) were in core training 2 (CT2).Of the 57 participants, 40/57 (70%) participants reported that they had firm plans for which specialty they would like to enter, 3/57 (5%) had no plans as yet, and 14/57 (25%) were unsure of their choice. The response rate for the questionnaire was 35/57 (61%).In terms of previous experience with the 3D virtual environments, 6/57 (11%) had had previous experience and 51/57 (89%) had no experience or were unsure. Mentee perceptions are described below and summarized in P<.001; chi-square test). Of 35 participants, 11/35 (31%) strongly agreed, 20/35 (57%) agreed, 3/35 (9%) were unsure, and 1/35 (3%) disagreed.With regards to having understood of the roles of a mentor, prior to the experience, 3/35 (9%) said they strongly agreed, 19/35 (54%) said they agreed, 12/35 (34%) were unsure, and 1/35 (3%) strongly disagreed. Following the experience, there was a statistically significant improvement toward agreement . Of 35 participants, 14/35 (40%) strongly agreed, 17/35 (49%) agreed, and 4/35 (11%) were unsure.With regards to whether mentoring was thought to be useful, 10/35 (29%) strongly agreed, 21/35 (60%) agreed, and 4/35 (11%) were unsure. Following the experience, there was a statistically significant improvement toward agreement . Of 35 participants, 3/35 (9%) strongly agreed, 11/35 (31%) agreed, 11/35 (31%) were unsure, 8/35 (23%) disagreed, and 2/35 (6%) strongly disagreed.When asked whether they thought whether a 3D virtual environment would be useful in mentoring prior to experiencing it, 2/35 (6%) strongly agreed, 4/35 (11%) agreed, 20/35 (57%) were unsure, and 9/35 (26%) disagreed. Following the experience, there was a statistically significant improvement toward agreement . Of 35 participants, 6/35 (17%) strongly agreed, 13/35 (37%) agreed, 10/35 (29%) were unsure, 5/35 (14%) disagreed, and 1/35 (3%) strongly disagreed.Prior to experiencing MentorSL, when asked whether voice communication would be useful in the mentoring relationship, 3/35 (9%) strongly agreed, 9/35 (26%) agreed, 18/35 (51%) were unsure, and 5/35 (14%) disagreed. Following experiencing MentorSL, there was a statistically significant improvement toward agreement strongly agreed, 11/35 (31%) agreed, 14/35 (40%) were undecided, 2/35 (6%) disagreed, and 2/35 (6%) strongly disagreed.When asked whether the search for mentor facility in MentorSL was sufficiently simple to use, 7/35 (20%) strongly agreed, 6/35 (17%) agreed, 19/35 (54%) were undecided, 2/35 (6%) disagreed, and 1/35(3%) strongly disagreed.When asked whether the meeting scheduling facility in MentorSL was sufficiently simple to use, 4/35 (11%) strongly agreed, 11/35 (31%) agreed, 18/35(51%) were undecided, and 2/35 (6%) disagreed.When asked regarding ease of using voice communication in SL, 6/35 (17%) strongly agreed, 10/35 (29%) agreed, and 19/35 (54%) were undecided.Regarding overall satisfaction with MentorSL, 6/35 (17%) reported very good, 24/35 (69%) reported adequate, 4/35 (11%) reported slightly disappointing, and 1/35 (3%) reported very poor.P<.001; chi-square test). Of 35 participants, 13/35 (37%) strongly agreed, 15/35 (43%) agreed, 6/35 (17%) were unsure, and 1/35 (3%) disagreed.Regarding the usefulness of a specialist mentor who may be geographically remote, prior to the experience, 6/35 (19%) strongly agreed, 18/35 (51%) agreed, and 11/35 (31%) were unsure. Following the experience, there was a statistically significant improvement toward agreement . Of the participants, 12/35 (34%) strongly agreed, 17/35 (49%) agreed, and 6/35 (19%) were unsure.When asked regarding the perceived benefits of having multiple mentors available for specific mentoring needs, prior to the experience, 8/35 (23%) strongly agreed, 16/35 (46%) agreed, 10/35 (29%) were unsure, and 1/35 (3%) disagreed. Following the experience, there was a statistically significant improvement toward agreement strongly agreed, 13/35 (37%) agreed, 13/35 (37%) were undecided, and 7/35 (20%) disagreed.When asked whether hand gesture recognition and animation of avatar would be useful, 2/35 (6%) strongly agreed, 12/35 (34%) agreed, 14/35 (40%) were undecided, and 7/35 (20%) disagreed.When asked whether participants would use MentorSL in the future, 4/35 (11%) strongly agreed, 15/35 (43%) agreed, 10/35 (29%) were undecided, 4/35 (11%) disagreed, and 2/35 (6%) strongly disagreed.This study demonstrates that doctors in postgraduate surgical training are willing to \u201cbuy-in\u201d to a virtual mentoring system in SL. The most well-received facilities were those of tele- and multiple mentoring and that of voice communication. The implication of these findings is that this mentoring system may be able to deliver mentoring to this group of doctors in a manner commensurate with their needs.The response rate of 61% (35/57) in this study, seemingly low and a limitation of the study, is commensurate with other studies in this population . We woulIt the context of team training for triage of mass casualties, it has been demonstrated that trainees quickly adapt to a virtual environment and find it an experience that is beneficial to their professional development .Despite the all-pervasive nature of the Internet in today\u2019s society, 89% (51/57) of participants had no significant previous experience of 3D Web 3.0 technology. Despite this, we found that only 17% (6/35) of participants disagreed or strongly disagreed, following a short introduction, with using the system in the future.Central to the provision of a virtual \u201cjust-in-time\u201d mentoring system is the mentee perceiving the need for being mentored. At outset, only 21/35 (60%) participants agreed or strongly agreed that they understood the concept of mentoring; this improved to 31/35 (89%). In addition, the initial high agreement with the usefulness of mentoring was maintained following the introduction (31 predemonstration vs 32 postdemonstration).The specific use of the 3D virtual world for mentoring is perhaps the most contentious issue to be assessed in the confines of a short introduction. More formed decisions will most likely require the on-going usage of the system by mentees. This seems to be reflected in that 14/35 (40%) were positive regarding the system, and 11/35 (31%) were unsure.Importantly, the more immediate and apparent facilitatory benefits of the system seemed to be well received by the participants. This was reflected by the strong performance in the voice communication, tele-, and multiple-mentoring domains. Indeed, the voice communication domain showed a large increase in agreement from 4/35 (11%) to 16/35 (46%). The user-friendliness of the voice communication was found to have a major impact in acceptance of a SL training program for nurses .There may be barriers to the adoption of these new technologies for medical mentoring. Hansen et al recalled Roger\u2019s diffusion of innovation theory in explaining attributes of a new technology affecting an individual\u2019s decision to adopt . These aWith regards to future developments in the MentorSL, equivalent numbers were positive regarding animation of the avatars facial features and hand gestures to improve the experience.We have demonstrated that the MentorSL system has the potential to be well accepted by mentees. This may be a reflection of the rapidly acquired understanding of the role of a mentor and the feeling of need for mentoring. Junior surgical trainees are able to rapidly familiarize with this novel communication modality and seem interested in further expansion of the virtual mentoring experience using facial and gesture recognition and avatar animation technology. Further work is required to evaluate utilization of this virtual mentoring facility when made available to doctors in postgraduate surgical training and to establish benefit. We are currently establishing a pilot study to trial medical mentoring using MentorSL in a cohort of surgical trainees in the London Postgraduate School of Surgery."} +{"text": "Leishmania often relies on gene rearrangements to survive stressful environments. However, safeguarding a minimum level of genome integrity is important for cell survival. We hypothesized that maintenance of genomic integrity in Leishmania would imply a leading role of the MRE11 and RAD50 proteins considering their role in DNA repair, chromosomal organization and protection of chromosomes ends in other organisms. Attempts to generate RAD50 null mutants in a wild-type background failed and we provide evidence that this gene is essential. Remarkably, inactivation of RAD50 was possible in a MRE11 null mutant that we had previously generated, providing good evidence that RAD50 may be dispensable in the absence of MRE11. Inactivation of the MRE11 and RAD50 genes led to a decreased frequency of homologous recombination and analysis of the null mutants by whole genome sequencing revealed several chromosomal translocations. Sequencing of the junction between translocated chromosomes highlighted microhomology sequences at the level of breakpoint regions. Sequencing data also showed a decreased coverage at subtelomeric locations in many chromosomes in the MRE11-/-RAD50-/- parasites. This study demonstrates an MRE11-independent microhomology-mediated end-joining mechanism and a prominent role for MRE11 and RAD50 in the maintenance of genomic integrity. Moreover, we suggest the possible involvement of RAD50 in subtelomeric regions stability.The parasite Leishmania relies on gene rearrangements to survive stressful conditions. However, maintaining a minimum level of genomic integrity is crucial for cell survival. Studies in other organisms have provided evidence that the DNA repair proteins MRE11 and RAD50 are involved in chromosomes organization, protection of chromosomes ends and therefore in the maintenance of genomic integrity. In this manuscript, we present the conditional inactivation of the Leishmania infantum RAD50 gene that was only possible in MRE11 deficient cells and suggest the genetic background is crucial for RAD50 inactivation. We demonstrate the occurrence of chromosomal translocations in the MRE11 and RAD50 deficient cells and described a MRE11-independent microhomology-mediated end-joining mechanism at the level of translocation breakpoints. We also suggest a possible involvement of RAD50 in subtelomeric regions stability. Our results highlight that both MRE11 and RAD50 are important for the maintenance of genomic integrity in Leishmania.The parasite Leishmania with response to drug and oxidative stress . We. WeLeishs (PFGE) and hybrmplicons . Howevericon at 4 kb is prFR probe . Howeverfication we hybrimplicons . Howeverexposure , lane 0.pressure , lane + MRE11-/- and MRE11-/-RAD50-/- lines were subjected to Illumina next-generation paired-ends sequencing (NGS). Sequencing reads were first aligned to the genome of L. infantum JPCM5 using bwa-mem alignment dCTP-labeled DNA probes according to standard protocols . All prosp72-PT4 . Intact ribed in . Leishmaeviously . The ranLate log phase promastigotes (30ml) were pelleted at 3000 rpm for 5 minutes and pellets were washed once with 1X HEPES-NaCl, resuspended in suspension buffer , then lysed in 1% SDS and 50\u03bcg/ml proteinase K at 37\u00b0C for 2 hours. Genomic DNA was extracted with 1 volume phenol, precipitated with 2 volumes 99% ethanol, washed with 70% ethanol twice and dissolved in 1ml 1X TE buffer. RNAse A (Qiagen) was added at 20\u03bcg/ml and DNA was incubated at 37\u00b0C for 30 minutes, followed by the addition of 50\u03bcg/ml of proteinase K and 0.1% SDS at 37\u00b0C for 30 minutes. DNA was extracted with 1 volume of phenol, precipitated and washed in ethanol, and dissolved in DNase free-water (Millipore) at 37\u00b0C overnight. Sequencing libraries were produced with the Nextera DNA sample preparation kit (Illumina Inc) according to manufacturer\u2019s instructions.Leishmania infantum JPCM5 (TriTrypDB version 8.0) using Burrows-Wheeler Alignment (bwa-mem) ATP . Aliquots (5 \u03bcl) were removed, stopped by addition of EDTA, and the percentage of ATP hydrolyzed was determined by thin layer chromatography followed by quantification using a Fujifilm Phosphoimager.Reactions (10 \u03bcl) contained 40nM of ingly to ) in 50mMhttp://www.ebi.ac.uk/ena) under study accession number PRJEB11440 with sample accessions ERS934506, ERS934507 and ERS934508 for L. infantum MRE11-/-RAD50-/-, L. infantum MRE11-/- and L. infantum JPCM5, respectively. L. infantum 263 WT sequencing data is available under the study ERP001815 and sample accession number ERS179382.The data set supporting the results of this article is available at the EMBL-EBI European Nucleotide Archive Schematic representation of the RAD50 locus in L. infantum before and after integration of the inactivation cassettes blasticidin-S deaminase (5\u2019-BLAST-3\u2019), puromycin acetyltransferase (5\u2019-PURO-3\u2019). S, SacI restriction sites. (B) Southern blot analysis with genomic DNAs digested with SacI were hybridized with probes covering the 5\u2019 flanking region of RAD50. Lanes: 1, L.infantum WT; 2, PURO RAD50-/+; 3, BLAST RAD50-/+; 4, PURO/BLAST/WT RAD50-/-/+. (C)RAD50 mRNA levels were analyzed by quantitative real-time RT-PCR. The RAD50 RNA expression ratios were normalized to GAPDH expression. 1, L.infantum WT; 2, PURO RAD50-/+; 3, BLAST RAD50-/+; 4, PURO/BLAST/WT RAD50-/-/+; 5, MRE11-/-; 6, MRE11-/-RAD50-/-.(TIF)Click here for additional data file.S2 Fig(A) Schematic representation of the RAD50 locus in L. infantum before and after integration of the inactivation cassettes blasticidin-S deaminase (5\u2019-BLAST-3\u2019), puromycin acetyltransferase (5\u2019-PURO-3\u2019) and transfection construct Psp-NEO-RAD50K42A. S, SacI restriction sites. Southern blot analysis with genomic DNAs digested with SacI were hybridized with probes covering either the 5\u2019 flanking region of RAD50(B) or the RAD50 ORF (C). Lanes: 1, L.infantum WT; 2, WT Psp-NEO-RAD50; 3, WT Psp-NEO-RAD50K42A; 4, RAD50-/- Psp-NEO-RAD50; 5, RAD50-/- Psp-NEO-RAD50K42A. (D) Purified LiRAD50 and LiRAD50K42A proteins (300 ng) were loaded on an 8% SDS-PAGE, run then stained with Coomassie blue (left panel). Percentage of ATP hydrolysis was measured for both LiRAD50 and LiRAD50K42A (40nM).(TIF)Click here for additional data file.S3 Fig(A) Schematic representation of the RAD50 locus in L. infantum before and after integration of the inactivation cassettes blasticidin-S deaminase (5\u2019-BLAST-3\u2019) and neomycin phosphotransferase (5\u2019-NEO-3\u2019). S, SacI restriction sites. Southern blot analysis with genomic DNAs digested with SacI were hybridized with probes covering either the 5\u2019 flanking region of RAD50(B) or the RAD50 ORF (C). Lanes: 1, L.infantum WT; 2, HYG/PUR-MRE11H210Y; 3, HYG/PUR-MRE11H210YBLAST/NEO/WT RAD50-/-/+.(TIF)Click here for additional data file.S4 Fig Growth retardation of promastigote MRE11 and RAD50 null mutants. Susceptibility to methyl methanesulfonate (MMS). L. infantum WT (\u25cb), RAD50-/- Psp-NEO-RAD50 (\u25cf), MRE11-/- (\u25a1), MRE11-/-RAD50-/- (\u25a0), WT Psp-RAD50 (\u25b2), MRE11-/- Psp-RAD50 (\u25bc). (E) Inactivation of LiMRE11 impairs gene targeting with a ZEO inactivation cassette.(TIF)Click here for additional data file.S5 FigL. infantum chromosomes were separated by pulse-field gel electrophoresis using a separation range between 150 kb and 1500 kb and incubated with ethidium bromide. No bands similar to linear amplicons could be observed.(TIF)Click here for additional data file.S6 Fig(A) Schematic representation of the fusion between chromosomes 27 telomeric and chromosome 02 subtelomeric regions. (B) DNA sequences obtained from direct sequencing of the junction 27\u201302. Insertion of 21 bp between sequences of chromosome 27 and chromosome 02 is indicated in bold.(TIF)Click here for additional data file.S7 Fig2-transformed normalized read counts for non-overlapping 5 kb genomic windows on chromosomes 18 (A) and 20 (B). Arrows indicate direction and breakpoints of the translocations. Asterik indicates internal duplications on chromosomes 18 and 20 present in T 18\u201320. Blue, L. infantum 263 WT; orange, LiMRE11-/- and green, LiMRE11-/-RAD50-/-.Log(TIF)Click here for additional data file.S8 Fig2-transformed normalized read counts on chromosomes 09, 15, 20, 23, 24, 31, 32 and 36.Log(TIF)Click here for additional data file.S9 FigMRE11-/- and MRE11-/-RAD50-/- cells were isolated, digested with Sau3aI/AluI/RsaI as described in [(A) and a PTR1 probe (B). Lanes: 1, L.infantum WT; 2, MRE11-/- and 3, MRE11-/-RAD50-/-.Genomic DNAs of WT, ribed in and hybr(TIF)Click here for additional data file.S1 Table(DOCX)Click here for additional data file."} +{"text": "Leber congenital amaurosis (LCA) is the earliest and most severe retinal dystrophy. It occurs as non-syndromic or syndromic. 26/37 LCA genes are important to ciliary function and account for < 1/3 of cases. These cases develop- or are at risk to develop- skeletal, renal and/or neurologic symptoms. Here, we assessed efficiency of ciliome resequencing (CR) as a tool for molecular diagnosis and patient care.The DNA of 60 unrelated young children with LCA was screened for mutations using a custom 5.3 Mb Agilent SureSelect Target Enrichment library which captures 32,146 exons of 1,666 genes selected form cilia databases. Segregation analysis of rare candidate variants was performed by Sanger sequencing.CEP290 (n = 4), CRB1 (n = 4), RPGRIP1 (n = 2), LCA5 (n = 1), IQCB1 (n = 2), IFT140 (n = 2), AHI1 (n = 1), ALMS1 (n = 1). In addition, 3/60 patients harbored biallelic mutations in three novel genes which screening in additional non syndromic and syndromic LCA cases allowed identifying additional mutations in 2/3 of them.Biallelic disease-causing mutations in known genes were identified in 17/60 patients (30 %): The identification of mutations in known and novel genes in 33 % of the cases, makes targeted sequencing an interesting alternative to exome resequencing. The identification of mutations in several genes responsible for syndromic LCA in young children with no overt extraocular expression demonstrates the importance of NGS-based molecular diagnosis to set-up a rational and efficient follow-up of patients."} +{"text": "Hemato-Oncology paediatric patients are more vulnerable to the development healthcare associated infections (HAI), due to the condition of immunosuppression, repeated hospitalizations, and long-term use of central venous catheters.The objective was to evaluate the clinical and epidemiological profile of catheter related bloodstream infection (CRBI) in children with haematological and oncological disorders, in patients hospitalized in paediatric haematology and oncology unit, at Hospital Pequeno Principe.Retrospective study from January 2008 to December 2012 was performed. Data from the Epidemiology and Infection Control Department and medical records, of hospitalized paediatric patients at Hemato-Oncology unit, consisting of 12 beds, were analysed. All hospitalized patients, in the period of the study and diagnosed with HAI were included. The diagnostic criteria of Centers for Disease Control and Prevention (CDC) were used.Coagulase Negative Staphylococcus (CONS), 16% (4/25) Enterococcus sp, 12% (2) Pseudomonas aeruginosa; 8% (2/25) Klebsiella oxytoca, 4.5% (1/25) Candida guillierrmondii; 4.5% (1/25) Candida albicans; 12% (3/25) others. Catheters used were: 42.85% (6/14) peripherally inserted central catheter, 35.71% (6/14) totally implantable venous access port devices; 21.42%(3/14) caheter not specified.In the period of five years, were admitted to the haematology-oncology unit 3107 patients, and diagnosed 44 episodes of HAI (1.77%) in 32 patients. (1.02%). The mean age of the patients was 5 years old, 47% female and 53% male. The mean hospital stay was 6.6 days. The most prevalent topographies of infection were: 56.81% (25) CRBI 13.63% (6) pneumonia; 20:45% (9) urinary tract Infection; 15% (4) others topography . The main underlying diseases were: 37.5% (12/32) malignant hematologic disease; 59.37% (19 / 32) solid tumours. Of the 25 episodes of CRBI the etiologic agent was identified in 84%: 28% (7/25) Children undergoing immunosuppressive treatments and catheters are at high risk for the development CRBI. The study of epidemiology is essential to establish preventive measures. In consensus with the literature, the most prevalent agent was CONS.None declared."} +{"text": "Breast cancer is the most frequent and most deadly cancer in females and incidence rates are increasing at an alarming rate in Saudi Arabia . StudiesWe performed transcriptomic profiling of 42 surgically-resected breast tumors using Affymetrix Gene 1.0 ST chip. Partek Genome Suit 6.4 and Ingenuity Pathway Analysis package were used for identification of differentially expressed genes, hierarchical clustering, gene ontology, pathway analysis and establishing clinical significance.We identified 30 differentially expressed genes, including 10 up and 20 down-regulated in lymph node involved breast cancer using cut off of p value <0.05 and fold change >2. Ceruloplasmin (CP), immunoglobulin J polypeptide (IJP), cellular retinoic acid binding protein 1 (CRABP1), keratin 23 (KRT23), paraoxonase 3 (PON3), and integrin beta 6 (ITGB6) genes were up-regulated whereas genes like AF4/FMR2 family member 3 (AFF3), v-erb-a erythroblastic leukemia viral oncogene homolog 4 (ERBB4), anterior gradient homolog 2 (AGR2), serpin peptidase inhibitor clade A (SERPINA5), and POTE ankyrin domain family member E (POTEE) were downregulated. Transcriptomic signatures showed significant disruption in signaling pathways associating genes of the B-Cell development, Hematopoiesis from Pluripotent Stem Cells, Primary Immunodeficiency Signaling, Fatty Acid Biosynthesis Initiation II and LXR/RXR Activation.In the present study, we identified transcriptomic signature in Saudi breast cancer patients that is associated with lymph node metastasis. Our analysis reveals appropriate biological relevance and a number of molecular pathways that may serve as targets for novel therapeutics.Authors would like to acknowledge the KACST, Riyadh, Saudi Arabia (Project ID: 10BIO1073-03 and 10-BIO1258-03) for funding the research."} +{"text": "Multiple drug hypersensitivity (MDH) has been defined as a hypersensitivity to two or more chemically unrelated drugs. This has been specially studied in IgE-mediated hypersensitivity reactions to antibiotics and more recently in T-cell-mediated reactions. However, studies focusing in MDH in large populations are lacking. The aim of our study was to describe a well-characterized group of patients diagnosed of MDH.We analyzed retrospectively all patients with a confirmed diagnosis of drug hypersensitivity evaluated in our allergy department between January 2005 and December 2010.A MDH was diagnosed in 48 (2.41%) of the 1989 patients evaluated, being 32 females, with a mean age of 50\u00b114,43 years. A total of 137 episodes were reported: 80 (58.39%) suggested an IgE-mediated reaction, 37 (27%) a non-immunologic mechanism (cross-reactive to NSAIDs) and 20 (14.55%) a T-cell mediated reaction. The percentage of MHD in patients with IgE-mediated reactions (9.78%) was higher compared to those with T-cell mediated reactions (5.23%) and non-immunologic reactions (1.91%) . The drugs most frequently involved were dypirone (13.6%), ciprofloxacin (12.1%), amoxicillin-clavulanic acid (11.4%), amoxicillin (10%), ASA (8.6%), ibuprofen (7.1%) and moxifloxacin (5.7%). Sensitivity to 2 chemically unrelated drugs was diagnosed in 44 patients and to 3 drugs in 4. The most frequent clinical entities were anaphylaxis/shock (42.85%) and urticaria (34.92%).Patients with IgE-mediated reactions have a higher risk for developing MHD. More studies are needed to confirm this finding."} +{"text": "Critical illness today is well recognized as being associated with new or worsening physical impairment, diminished mental health and cognitive dysfunction. We studied the scope of somatic complaints in ICU survivors 4 to 6 months after ICU treatment.Patients who were treated in our ICU from 1 January 2013 until 31 December 2013, for 5 or more days, were invited to visit our ICU aftercare clinic. Six weeks after ICU discharge a letter of invitation together with a health-related questionnaire, the Hospital Anxiety and Depression Scale questionnaire [Ninety-seven patients visited our aftercare program in 2013. Median time after ICU discharge and visit to our after care clinic was 165 days. Twenty-five patients died after ICU discharge. Fifty-four patients were excluded because of various reasons; that is, language barrier, psychiatric illness, mental handicap, hospital admittance elsewhere, great distance. Seventy patients (81.4%) had somatic complaints influencing daily performance and quality of life. Fatigue (74.4%), muscle weakness (48.8%), dyspnea (34.9%), impairment of daily activity (81.4%), pain (38.4%) and weight loss (33.3%) were the most frequently reported complaints. Pain was most reported in patients with subarachnoid hemorrhage (27.3%), multitrauma (15.2%) and pneumonia (12.1%). Pain was most localized in the head (15.6%), one or both legs (15.6%), back (10.9%), shoulder (9.3%), hip (9.3%) and thorax (6.3%). Muscle weakness, fatigue, dyspnea, impairment of daily activity, pain and hoarseness were associated significantly with PTSD and HAD. There was no significant difference in somatic complaints between men and women.Somatic complaints after ICU discharge are frequently reported in our post-ICU aftercare patients, influencing daily performance and quality of life. Patient-centered research and treatment focusing on somatic complaints is of great importance."} +{"text": "Left ventricle (LV) remodeling associated with lower LV ejection fraction after successfully treated ST-elevation myocardial infarction (STEMI) may occur in some patients. We investigated the prognostic value of intramyocardial hemorrhage (IMH) as assessed by T2* images beyond a comprehensive CMR assessment with late gadolinium enhancement (LGE) imaging including microvascular obstruction (MVO) evaluation.A total of 110 patients with STEMI were prospectively recruited and were examined with CMR at Day 4 \u00b1 2 and Month 6 after reperfusion for measurement of LV end-diastolic (EDV) and end-systolic (ESV) volumes, LV ejection fraction (LVEF) infarct size (IS) and presence and extent of MVO and IMH. Adverse remodeling was defined as dilated left ventricular end-systolic volume indexes (EDV) at 6 months CMR.All patients were analysed. 41 patients (45%) presented with Anterior AMI, 26 with Lateral (23%) and 29 with Inferior MI (32%). Mean age was 54 +/- 12 y.o . Mean delay for reperfusion therapy was 115 +/- 100 min. LV remodelling was observed in 39 patients (36%). Despite identical EDV, patients with LV remodelling had lower LVEF at baseline , a bigger IS and MVO extent (p < 0.01). By multivariate analysis, IMH (OR = 2.8[1.3-6.0]) and IS (OR = 3.2[1.8-12.5]) were identified as independent predictors of LV remodelling.Presence of IMH after STEMI assessed by T2* CMR predicts LV adverse remodeling.Research Grant from the french Society of cardiology (SFC)"} +{"text": "Enthestis related arthritis (era) represent an undifferentiated form of spondyloarthritis (spa), distinguishing it from other subtypes of JIA for optimum treatment and outcome, as well as for studies aimed at understanding genetic predisposition and pathogenesis. Majority of these studies focused on genome associations within MHC, only few searched for connections outside of this region and only some analyzed transcriptome of era patients. Our preliminary results of gene expression profiling in PBMC of 11 new onset and untreated patients diagnosed with era, identified 744 differentially expressed genes.To validate results of gene expression analysis in groups of patients diagnosed with era and other subtypes of JIA.Based on extensive and diligent statistical analysis, ten genes were selected for further RT-PCR analysis in four groups of patients selected according to ILAR criteria (N = 56): untreated era patients with obtained expression profile , untreated era patients , treated era patients and treated JIA patients (P4 = 11). All groups were compared to healthy controls (N = 12). For all era patients HLA typing was preformed.Statistically significant (p < 0.05) fold change (FC) was shown for CXCR4 (FC 1.89), TLR4 (FC 4.36), MAPKBP1 (FC -3.13) and PTPN12 (FC -3.70) in P1 group, CXCR4 (FC 1.87), NLRP3 (FC -5), PTPRN2 (FC -5.55), TLR4 (FC 3.91) and PTPN12 (FC -2.63) in P2 group, CXCR4 (FC 1.37), NLRP3 (FC -3.71), MAPKBP1 (FC -1.82), PTPN12 (FC -2.44) and TNFSF4 (FC -1.52) in P3 group and PTPN12 (FC -5) in P4 group.Majority of genes with significant FC had a role in NF-\u03bab and MAPK pathways, which are important for regulation of immune response. TLR-4 is known activator of inflammatory cascade that involves NLRP3, and is responsible for secretion of proinflammatory cytokines, while PTPN12 negatively regulates TLR-triggered innate response and lymphocyte activation. Hence, lower expression of PTPN12 can boost immune response. CXCR4 triggers MAPK signaling in response to LPS, and recruits inflammatory cells. CXCR4 showed higher expression in all groups of era patients, regardless of treatment, and PTPN12 showed lower expression even in group of other JIA patients, which could indicate an important role of these genes in pathogenesis of era and other JIA subtypes. TLR4 showed higher expression in untreated era patients, suggesting that standard treatment could influence this gene expression. Interestingly, NLRP3 showed lower expression in group of treated and untreated patients with era. Polymorphisms of NLRP3 that causes decreased gene expression and IL-1\u03b2 production were linked with increased susceptibility to Chron's disease, while polymorphisms of PTPN12 gene were identified in autoinflammatory diseases. Further on, oncology studies showed PTPN12 gene could be silenced by methylation. Precise mechanism responsible for lower expression of these genes in era and other JIA patients still needs to be clarified.None declared."} +{"text": "Surveillance of primary resistance to antiretroviral drugs is particularly important in pregnant population, in which infection by drug-resistant HIV has not only implications for maternal treatment, but could also jeopardize the efficacy of neonatal prophylaxis. We aim to describe the prevalence of resistance associated mutations (RAMs) in pregnant women with intrapartum HIV diagnosis in a public hospital of Buenos Aires, Argentina.Prospective pilot study (period from 2008 to October 2013). Plasma samples were tested for viral load by Versant HIV-1 RNA 3.0 (bDNA) and sequenced using HIV-1 TRUGENE\u2122Genotyping Kit (Siemens). The prevalence of RAMs was analyzed according to World Health Organization (WHO) criteria.Of 231 HIV-infected pregnant women assisted, 6% (n=14) had intrapartum diagnosis of HIV infection. 12 patients (85.7%) had previous pregnancies, 10 (71.4%) had inadequate prenatal care and 3 (23.1%) seroconverted during pregnancy. Maternal characteristics (expressed medians and ranges) were: age 25.5 (16\u201335) years; gestational age at birth: 39 (30\u201342) weeks; CD4 count: 500 (132\u2013925) cells/\u00b5L; viral load: 9418 (1800\u201355299) copies/mL. No one had hepatitis B virus (HBV) or hepatitis C virus (HCV) coinfection; four (33.3%) had syphilis. Eight patients (57.1%) had vaginal delivery and six emergency C-section (42.9%). In six cases (46.2%), membrane rupture was spontaneous; four patients (28.6%) failed to receive intrapartum zidovudine (ZDV) infusion. In 12 patients a genotypic resistance test was performed: two (16.7%) had WHO RAMs corresponding to K103N mutation in both cases, conferring high-level resistance to nevirapine (NVP) and efavirenz. Two newborns (14.3%) were preterm. All received neonatal prophylaxis: ZDV in 1 case and combined prophylaxis (ZDV/3TC/NVP) in the remaining 13 (92.9%). All newborns were formula-fed. Two (14.3%) had congenital syphilis, one of whom died. One newborn was HIV-infected .This pilot study suggests that levels of transmitted resistance in this high-risk population of pregnant women could be moderate to high. We preliminarily observed high-level resistance to NVP: if this finding is confirmed with a larger sample, it could potentially jeopardize the utility of this drug in the combined neonatal prophylaxis recommended in the absence of maternal antiretroviral therapy."} +{"text": "High pathogenicity avian influenza viruses (HPAIV) have caused fatal infections in mammals through consumption of infected bird carcasses or meat, but scarce information exists on the dose of virus required and the diversity of HPAIV subtypes involved. Ferrets were exposed to different HPAIV (H5 and H7 subtypes) through consumption of infected chicken meat. The dose of virus needed to infect ferrets through consumption was much higher than via respiratory exposure and varied with the virus strain. In addition, H5N1 HPAIV produced higher titers in the meat of infected chickens and more easily infected ferrets than the H7N3 or H7N7 HPAIV. Influenza virus infections in mammals are primarily respiratory centric with transmission via aerogenous droplets or contact with fomites . HoweverThe ferret model has been established for studying the pathogenicity and transmissibility of influenza viruses following respiratory and conjunctival routes of exposure . Some H550) and lethal (FLD50) doses of two H5N1 HPAIV through consumption of infected meat: A/Whooper swan/Mongolia/244/05 (Mong/05) and A/Vietnam/1203/04 (VN/04). Previously, these same viruses were shown to infect ferrets following consumption of meat containing high virus concentrations (109.5 EID50) [n\u2009=\u20093/group) representing a low, medium, or high exposure dose. Ferrets were fed breast meat collected from chickens 24\u00a0h after intranasal inoculation with Mong/05 or VN/04. Prior, for each virus three groups of meat were classified based on virus concentration, and each meat group was given to the corresponding ferret group. Therefore, 30\u00a0g of specific titred infected meat was offered to each ferret individually. The dose consumed per ferret was calculated taking into account the virus concentration in the meat and the amount of meat consumed. Each of three individual ferrets received 104.2 (low dose), 106.8 (medium dose) or 109.2 (high dose) mean egg infectious doses (EID50) of Mong/05, or 104.3 (low dose), 106.9 (medium dose) or 109.6 (high dose) EID50 of VN/04. Ferrets were monitored for clinical signs and mortality. Body weight measurements and nasal washes for virus isolation were taken at 0, 3, 7, and 14\u00a0days post-challenge (dpc). Necropsy was performed on dead animals and the following tissues were collected for histologic examination: nasal cavity, lung, pharyngeal tonsil, esophagus, duodenum, pancreas, cecum, rectum, liver, spleen, kidney, heart, and brain. At 14 dpc, the remaining ferrets were bled and euthanized.The objective of Experiment 1 was to determine the ferret mean infectious (FID5 EID50) . Ferrets5 EID50) . However50 was 104.9 EID50, while the lack of deaths made FLD50\u2009>\u2009109.2 EID50 (Table\u00a050 was 107.5 EID50 and the FLD50 was 108.9 EID50 (Table\u00a01.7 and 101.5 mean tissue culture infectious dose (TCID50)/mL), exhibited listlessness and ataxia, and had severe respiratory and systemic lesions including bronchial edema; severe multifocal encephalomalacia with accompanying gliosis, lymphohistiocytic perivascular cuffings and scattered vasculitis , A/Iraq/NAMRU3-207/06 (H5N1) (Iraq/06) (105.7 EID50), A/chicken/Canada/314514-2/04 (H7N3) (Canada/04) (107.1 EID50), and A/chicken/Netherlands/219/03 (H7N7) (Neth/03) (106.9 EID50). Despite differences in the inoculated doses, all birds died on 2 dpc with high concentrations of virus present in Egypt/07 (109.0\u20139.2 EID50/30\u00a0g) and Iraq/06 (1010.4 EID50/30\u00a0g) infected breast meat, and lower concentrations of virus present in Canada/04 (107.3\u20137.6 EID50/30\u00a0g) and Neth/03 (107.5\u20137.8 EID50/30\u00a0g) infected breast meat. Ferrets of 17\u201321 weeks-of-age were determined to be H5-and H7-seronegative by HI and VN. However, all animals possessed HI antibody titers to human H3N2 influenza A virus (A/Hiroshima/52/05). Four ferrets were fed 30\u00a0g of meat obtained from the infected chickens at doses listed above. Ferrets were monitored for clinical signs and mortality. Temperatures were recorded daily using subcutaneous probes. Body weight measurements, nasal washes, and rectal swabs were taken at 0, 1, 2, 4, 7, 10, and 14 dpc. At four and 14 dpc, two ferrets per virus were bled and euthanized, and tissues were collected for histologic examination.The objective of Experiment 2 was to determine if other H5N1 (North Africa and Middle East) and H7 HPAIV (Europe and North America) could produce similar infections and disease from consumption of infected meat. Chickens were intranasally inoculated with a lethal dose of one of four HPAIV: A/chicken/Egypt/9402-NAMRU3HK213/07 (H5N1) (Egypt/07) (101.75 TCID50/mL). Canada/04 exposed ferrets lacked mortality, but both ferrets euthanized at 14 dpc were infected based on seroconversion or fed infected meat (109.5 EID50) with Mong/05 lacked mortality but seroconverted [6 EID50) or oral consumption (109.5 EID50) of infected meat with VN/04 [1 to 104 TCID50[1 EID50[50 and FLD50 for infection via consumption of infected meat suggesting the dose of virus needed to infect and/or kill ferrets through consumption of infected meat is much higher than for the same virus via respiratory exposure.Previous studies have demonstrated infection in ferrets by H5N1 viruses via intranasal exposure or consumption of infected meat. Ferrets intranasally inoculated or even absence of infection (Neth/03) in ferrets. Whether a higher virus dose in meat would allow Neth/03 to infect through consumption warrants further study, although the inability to produce a high concentration of H7 HPAIV in meat may prevent testing the hypothesis. Supporting the infection efficiency hypothesis, both respiratory and ingestion exposures of Asian H5N1 HPAIV at 104 TCID50 produced systemic virus replication with severe necrosis and inflammation in cats [7 EID50, causing respiratory and neurological signs, and systemic lesions [In the current study, consumption of non-Asian H5N1 viruses caused primarily respiratory disease. However, the presence of mild meningoencephalitis without neurological signs or viral antigen detection in the brain of one Egypt/07 infected ferret suggests some extent of systemic spread with damage to the nervous system. Therefore, North African and Middle Eastern H5N1 HPAIV caused infection in ferrets through feeding meat containing high concentrations of HPAIV and produced primarily respiratory disease, being less lethal than Asian VN/04. Consumption of H7 HPAIV infected meat was less pathogenic or non-infectious for ferrets compared to H5N1 HPAIV, which may be explained by the difference in infection efficiency of H5 compared to H7 AIV. However, the 2\u20133 log in cats while in in cats . Also, N lesions . Collect lesions ,23, withIn conclusion, relatively high concentrations of H5N1 HPAIV are required to produce infection and death by consumption of infected meat in ferrets as compared to respiratory exposure. Ingestion of HPAIV-infected meat can produce infection that primarily involves the respiratory tract but can also spread systemically depending on both the virus strain and virus dose received. Although human infections by HPAIV through direct oral contact have been occasionally reported ,13, airbThe authors declare that they have no competing interests.KB analyzed the results and carried out the histopathological examinations. DES conceived the study and participated in its design, coordination, and implementation. KB and DES draft the manuscript. Both authors read and approved the final manuscript."} +{"text": "The NIH FACEBASE consortium was established in part to create a central resource for craniofacial researchers. One purpose is to provide a molecular anatomy of craniofacial development. To this end we have used a combination of laser capture microdissection and RNA-Seq to define the gene expression programs driving development of the murine palate. We focused on the E14.5 palate, soon after medial fusion of the two palatal shelves. The palate was divided into multiple compartments, including both medial and lateral, as well as oral and nasal, for both the anterior and posterior domains. A total of 25 RNA-Seq datasets were generated. The results provide a comprehensive view of the region specific expression of all transcription factors, growth factors and receptors. Paracrine interactions can be inferred from flanking compartment growth factor/receptor expression patterns. The results are validated primarily through very high concordance with extensive previously published gene expression data for the developing palate. In addition selected immunostain validations were carried out. In conclusion, this report provides an RNA-Seq based atlas of gene expression patterns driving palate development at microanatomic resolution. This FACEBASE resource is designed to promote discovery by the craniofacial research community. Failure of midline fusion resulting in cleft lip with/or without cleft palate is one of the most common birth defects \u20134. The pThe mouse provides a useful model for the study of palate development. The palate develops primarily from neural crest , but witGlobal expression studies, using microarrays or RNA-Seq, can provide an important discovery function, identifying previously overlooked pathways that might play important roles in craniofacial development. An early work used 6800 gene Mu11kB Affymetrix microarrays to examine gene expression in vertical, horizontal, and fused palatal shelves, providing a large scale genomics view of this developmental progression ,13. In aThe FACEBASE consortium was established in part to provide a resource center for craniofacial researchers > 2. This analysis compares all combined anterior versus all combined posterior compartments, identifying 163 genes with differential expression . A more Msx1 (19FC), and Shox2 (13FC) in the anterior domain, and Barx1 (25FC), Meox2 (12FC) and Tbx22 (8FC) in the posterior domain. Additional transcription factor genes with differential (FC > 3) AP expression included Pax3 (6FC), Tbx15 (3FC), Heyl (3FC), Gata2 (3FC), Dlx1 (12FC), Eya1 (5FC), Eya4 (3FC), Alx1 (59FC), Sim2 (32FC), and Sall3 (3FC). Growth factor genes with differential AP expression included Pdgfc (2FC), Bmp3 (3FC), Cxcl12 (2FC), Clec11a (3FC), Fgf18 (3FC), Inhba (2FC), Wnt5a (4FC) and Gdf10 (4FC). It is interesting to note that most of the gene expression differences with FC >3 along the AP axis are consistently differentially expressed across each of the sampled medial, lateral, oral and nasal compartments , Actg2 (23FC), Nmbr (14FC), Aldh1a2 (10FC) and Bmp3 (5FC) with higher expression in the lateral compartment, and Gal (54FC), Gsc (12FC), Tnn (12FC), Prph (11FC), Grem2 (6FC), and Sox9 (5FC) with higher expression in the medial compartment. Aldh1a2 synthesizes retinoic acid from retinaldehyde. Nmbr encodes the neuromedin B receptor. Gsc encodes a homeodomain transcription factor of known importance in craniofacial development. Gal encodes the galanin neuropeptide. Prph encodes a neuronal cytoskeletal protein. Sox9 is a key driver of chondrogenesis. Bmp3, also known as osteogenin, induces bone formation, while Grem2 encodes a BMP antagonist.We compared the gene expression patterns of the anterior lateral and medial compartments, screening for expression over 5 RPKM in at least three samples, moderated t-test P < 0.05, and FC > 2, finding 232 genes with differential expression . A more Ppbp (18FC), Pla2g7 (8FC), Pax3 (4FC), Fgf10 (8FC), Ltbp2 (46FC), Npnt (7FC), Egfr (5FC), Hes1 (4FC), Jag1 (3FC). Ltbp2 encodes a TGF-beta binding protein. Hes1 and Jag1 are involved in Notch signaling. Ppbp encodes a platelet derived growth factor and Npnt encodes nephronectin, an integrin binding protein that regulates expression of GDNF . Of interest, several of the differentially expressed genes play important roles in growth factor signaling.A comparison of the posterior lateral and medial compartments, using the same parameters described for the anterior lateral versus medial, identified 79 genes with FC > 2 . A modesNpnt (nephronectin), Thbs2 (Thrombospondin2), Egfr (EGF receptor), Wisp1 , and Ptprv .It is also interesting to note that there are relatively few genes in common between the anterior and posterior comparisons of medial and lateral compartments. Only ten genes are included in both lists of FC > 2, including Cxcl13 (23FC), Gsc (13FC), Dlx5 (11FC), Cbr2 (8FC), Tnn (7FC), Gata2 (6FC), Cma1 (6FC), Sema3e (4FC), Unc5d (4FC), and Runx2 (3FC). Genes with the most compelling elevated expression in the anterior oral compartment included Tsga13 (11FC), Nmbr (5FC), Klf14 (4FC), and Enpp (4FC).A comparison of the oral and nasal compartments, in the forming anterior palate, gave 123 genes with differential expression . IncreasCdh20 (17FC), and Cdh18 (4FC), the leucine rich repeat genes Lrrtm1 (9FC), Lrrc4c (9FC), Lrrtm3 (6FC), and Lrrc3b (6FC), the adenylate cyclase Adcy8 (10FC), Enpp1 (6FC), Ncam2 (6FC), the growth factors Fgf18 (5FC), Fgf10, (4FC), Sema5b (4FC), Pdfd (5FC), Bmp4 (3FC), as well as Bmp inhibitors Grem1 (5FC) and Grem2 (3FC), and transcription factors Osr1 (4FC), Osr2 (3FC), Foxd1 (3FC), Foxf2 (4FC), Npas3 (3FC) and many other genes of interest (Ibsp (83FC), Panx3 (40FC), Dlx3 (40FC), Hrc (18FC), Smpd3 (15FC), Slc8a3 (11FC), Sp7 (9FC), Sox6 (7FC), Tcf7 (5FC), Dlx5 (5FC), Bmp6 (5FC), Tnn (4FC), Pax3 (4FC) and Gdf10 (4FC).The comparison of the posterior oral and nasal compartments found 311 differentially expressed genes . Increasinterest . Genes wSirt1, Foxf2 Twist1, Runx2, Nfatc4, Myc, Tcf3, Tcf4, Tcf12, Tcf7l1, Shox2, Sox9, Sox11, Ezh2, Tcea1, Pax3, Lhx6, Lhx8, and Ski. Growth factor genes with strong expression include Nenf, Mdk, Hdgf, Ptn, Cxcl12, Igf1, Igf2, Inhba, Ogn, Bmp4, Gmfb and Vegfb.The dataset can also be screened to find genes with particularly strong expression, even though not necessarily compartment specific. Important functionality is not always related to differential expression. Transcription factor genes with RPKM expression levels over 50 in at least one compartment include Fgf10 has been reported expressed more in the lateral and oral compartments, compared to medial and nasal [Fgf10 up 4.2 fold in the posterior oral versus nasal, up 2.3 fold in anterior oral versus nasal, up 4.9 fold in anterior lateral versus medial, and up 8.6 fold in the posterior lateral versus medial. Similarly, Gli1 in situ hybridizations show stronger expression in oral/lateral compartments [Gli1 up 1.8 fold in posterior lateral versus medial, up 1.75 fold in anterior lateral versus medial, and up 3.2 fold in anterior oral versus nasal compartments. Conversely, Dlx5 is expressed more strongly in the nasal compartment compared to oral [Dlx5 in the posterior nasal versus oral compartments, and an even stronger 11 fold higher expression in the anterior nasal versus oral compartments. In situ hybridizations show Ctgf expression higher in the medial compartment [Ctgf four fold higher in the anterior medial versus lateral compartment, with much stronger expression in the anterior versus posterior palate. Previous in situ hybridizations show Osr1 with stronger expression in the lateral compartment [Runx2 expression has been shown elevated in the nasal versus oral compartment [Frzb elevated expression elevated 2.1 fold in the posterior lateral versus medial compartments, consistent with published expression data [Sox9 showed 5.2 fold elevated expression in the anterior medial versus lateral compartments [Tnn in the nasal compartment [The dataset described in this report provides a global view of the gene expression patterns of the multiple compartments of the developing palate. A comparison of this dataset with previously published expression patterns for specific genes provides a key measure of validation. For example, nd nasal . The RNAartments , and the to oral . Consistpartment , furtherpartment , again cpartment , agreeinion data . Once agartments . The RNApartment , with thpartment . In summWe further validated the RNA-seq dataset by carrying out selected immunostains. For Agtr2 we observed elevated expression in the lateral and oral compartments, as predicted by the RNA-seq . Similarhttps://gataca.cchmc.org/gataca/) identifies 91 human genes related to some degree with cleft palate. It should be noted that this is a broadly inclusive list, and not all of the cleft palate gene associations are strong. Of these 91 genes 20 showed no expression in the developing E14.5 murine plate. Of course these genes could still be functionally important and expressed at other critical stages of palate development. Nevertheless, they would represent weaker candidates. Another 14 genes, including Bmp4, Satb2, Runx2, Msx1, Sox9, Tfap2a, Fras1, Alx4, Tbx22, Sema3e, Ptch1, Irf6, Fgfr2 and Eya1 showed expression that varied among the E14.5 palate compartments. The predominant expression pattern observed, however, was uniform expression throughout the developing palate. In some cases this expression was at high levels (over 50 RPKM), for Yhae, Sumo1, Ubb, Twist1, Gpc3, Flna, Col11a1 and Fgfr1. For most of the cleft associated genes, however, gene expression was relatively uniform throughout all palate compartments and at moderate levels (5\u201350 RPKM). The subset of genes with the strongest cleft palate associations also showed multiple expression patterns. For example, Wnt3 and Vax1 showed no detectable expression, Msx1, Irf6 and Bmp4 showed expression that varied among compartments, and Bmpr1a showed uniform high expression. Therefore no simple formula for connecting the observed gene expression patterns to cleft palate causation emerged.One potential use of the gene expression data presented in this report is to aid in the screening of DNA sequencing data from patients for causative mutations associated with cleft palate. Genes with appropriate expression during palate formation would represent preferred candidates. To this end it is interesting to examine genes previously associated with cleft palate to determine the types of expression patterns represented. A search of the GATACA website was approved by the Institutional Animal Care and Use Committee (IACUC) of Cincinnati Children\u2019s Research Foundation. CD-1 strain mice were used. All efforts were taken to minimize pain experienced by the mice. Animals were sacrificed by carbon dioxide inhalation.Immunostains were carried out with TSKit #12, with HRP\u2014Goat Anti-Rabbit IgG and Alexa Fluor 488 Tyramide, T-20922, Life Technologies, stanard protocol for immunohistochemistry. Antibodies used were as follows. Crabp1: CRABP1 (D7F9T) Rabbit mAb #13163, Cell Signalling,1:400 dilution. Ibsp: Rabbit Anti-Bone Sialoprotein II Polyclonal Anitbody (bs-2668R), Bioss, 1:100 dilution. Agtr2: Anti-Angiotensin II Type 2 Receptor antibody (ab19134), Abcam, 1:75 dilution. App: Rabbit Anti-APP/Amyloid Precursor Protein Polyclonal Antibody (bs-0112R), Bioss, 1:50 dilution.Data analysis was carried out with GeneSpring 12.6.1, as previously described . RNA-SeqS1 Table(XLS)Click here for additional data file.S2 Table(XLS)Click here for additional data file.S3 Table(XLS)Click here for additional data file.S4 Table(XLS)Click here for additional data file.S5 Table(XLS)Click here for additional data file."} +{"text": "Among the 1660 isolates recovered from invasive pneumococcal disease (IPD) in adults (> = 18 yrs) in 2008\u20132011, a random sample of \u226550% of each serotype (n = 871) was chosen for MLST analysis and evaluation for the presence and type of pilus islands (PIs). The genetic diversity was high with 206 different sequence types (STs) detected, but it varied significantly between serotypes. The different STs represented 80 clonal complexes (CCs) according to goeBURST with the six more frequent accounting for more than half (50.6%) of the isolates\u2014CC156 , CC191 (serotype 7F), CC180 (serotype 3), CC306 (serotype 1), CC62 (serotypes 8 and 11A) and CC230 (serotype 19A). Most of the isolates were related to 29 Pneumococcal Molecular Epidemiology Network recognized clones. The overall proportion of isolates positive for any of the PIs was small (31.9%) and declined gradually during the study period (26.6% in 2011), mostly due to the significant decline of serotype 1 which is associated with PI-2. The changes in serotypes that occurred in adult IPD after the introduction of the seven-valent pneumococcal conjugate vaccine (PCV7) for children were mostly due to the expansion of previously circulating clones, while capsular switching was infrequent and not related to vaccine use. The reduction of IPD caused by PCV7 serotypes in the years following PCV7 implementation did not result in a decline of antimicrobial resistance in part due to the selection of resistant genotypes among serotypes 14 and 19A. The 7-valent conjugate vaccine (PCV7) was available for children through the private sector in Portugal from 2001 onwards until it was replaced in the beginning of 2010 by the 13-valent conjugate vaccine (PCV13). In 2012, PCV13 received approval for use also in adults > 50 years of age with an extension being made to all ages in 2013. Additionally, PCV13 entered the Portuguese National Immunization Program (NIP) in June 2015 for children born from January 2015 onwards. Two other vaccines, the 23-valent pneumococcal polysaccharide vaccine (PPV23) and the 10-valent conjugate vaccine (PCV10), have also been available in Portugal since 1996 and 2009, respectively, but with a low uptake [Among the more than 90 different pneumococcal serotypes identified, only a few cause the majority of IPD. While for some serotypes the capsular polysaccharide is the dominant determinant of invasiveness, for others distinct genotypes show important differences in invasiveness . AdditioWhile numerous studies have addressed the serotype distribution of IPD, information regarding the clonal composition of pneumococcal populations has been scarcer. In a previous study we defined the clonal composition of pneumococci causing IPD in both children and adults in the pre-PCV7 period . In a suThe isolates included in this study were recovered from adult patients \u226518 yrs) with invasive pneumococcal disease between 2008 and 2011 and were characterized in previous studies regarding serotype distribution and antimicrobial susceptibility 8 yrs wit. A case From a total of 1660 isolates recovered, a random sample of \u226550% of the isolates (n = 871) from each serotype and from each year was chosen to be characterized by MLST and tested for the presence of the pilus islands. Briefly, among the 1660 isolates, there were 52 different serotypes, with the 10 most frequent being serotypes 3 (13.0%), 7F (10.0%), 19A (9.8%), 1 (8.5%), 14 (8.1%), 8 (5.7%), 22F (3.9%), 4 (3.2%), 9N (2.8%) and 11A (2.8%). However, the 10 most frequent serotypes were different in each of the age groups. In the 18\u201349 yr olds (n = 472) these were serotypes 1 (14.0%), 7F (11%), 8 (9.1%), 14 (8.7%), 3 (7.6%), 19A (6.1%), 9N (4.2%), 4 (3.8%), 22F (3.2%), 11A (2.8%). In the 50\u201364 yr olds (n = 358) these were serotypes 3 12%), 19A (10.3%), 1 (9.5%), 7F (9.2%), 14 (6.1%), 4 (5.0%), 8 (4.5%), 11A (3.4%), 22F (3.4%), 9V (2.8%). In the \u226565 yr olds (n = 830) these were serotypes 3 (15.8%), 19A (11.6%), 7F (10.2%), 14 (8.7%), 1 (4.9%), 22F (4.6%), 8 (4.2%), 6C (3.0%), 11A (2.5%), 9N (2.3%). Overall, the proportions of PCV7, PCV13 and PPV23 serotypes were 18.4%, 61.9% and 79.4%, respectively. Non-susceptibility to penicillin, defined as either intermediate level penicillin resistance (MIC 0.12\u20131.0 \u03bcg/ml) or high level resistance (MIC\u22652.0 \u03bcg/ml) as discussed previously [%, 19A was evaluated by PCR. Briefly, for PI-1 in the absence of the pilus islet, a product of 1-3Kb was expected using primers PFL-up and P-dn flanking the islet . In stra of PI-2 .http://www.comparingpartitions.info. Differences were evaluated by the Fisher exact test with the false discovery rate (FDR) correction for multiple testing [Sample diversity was evaluated using the Simpson\u2019s index of diversity (SID) and the respective 95% confidence intervals (CI95%) . To comp testing and the The 871 isolates analyzed by MLST presented 206 different STs grouping into 80 CCs according to goeBURST analysis, when including all STs deposited in the database. The 14 most frequent STs, which accounted for more than half of the genotyped isolates (50.6%) were, in decreasing order, ST191 (9.9%), ST306 (7.0%), ST180 (6.9%), ST53 (4.5%), ST156 (4.0%), ST276 (3.6%), ST433 (3.2%), ST66 (2.8%), ST408 (1.7%), ST232 (1.7%), ST260 (1.5%), ST143 (1.4%), ST179 (1.3%) and ST289 (1.3%).aroE, 429, 636 and 637 for ddl, 294, 295, 428 and 430 for gdh, 437 and 438 for gki, 273 for recP and 588, 589, 590, 592, 593 and 605 for xpt.Twenty new allelic combinations and 19 new alleles were identified. The new allelic combinations were identified as STs: 6176, 6177, 6180, 6181, 6182, 6973, 8866, 9955, 9956, 9957, 9958, 9960, 9963, 9966, 9969, 9970, 9971, 9979, 9982 and 9986. The novel alleles identified were designated 200, 307 and 309 for There was a strong correlation between CC and the vaccine serotype groups , with the six most prevalent CCs being mainly composed of isolates presenting vaccine serotypes (95.5%). 7F-191 (n = 88), Spain9V-156 (n = 71), Netherlands3-180 (n = 68), Netherlands8-53 (n = 63), Sweden1-306 (n = 63), Denmark14-230 (n = 47), Tennessee14-67 (n = 24), Tennessee23F-37 (n = 24) and Netherlands15B-199 (n = 21) presented STs related to 29 of the 43 clones recognized by the Pneumococcal Molecular Epidemiology Network (PMEN) , sharing21) Figs . AdditioThe correlation between ST and serotype was high , but there were STs that presented more than one serotype Tables. When analyzing the evolution of STs between 2008 and 2011 we identified some fluctuations, although the majority reflected changes in serotype prevalence occurring in this period. However, while for ST306 (serotype 1) there was a decline, significant after correcting for multiple testing , for the other STs the changes were only significant before FDR correction. The STs for which there was a significant p-value in the Cochran-Armitage test for trends but unsupported after FDR correction were: ST53 (serotype 8), that increased from 3.3% to 6.5% (p = 0.043); ST289 (serotype 5), that accounted for 2.4% of IPD in 2008 and 0% in 2011 (p = 0.020); ST717 (serotypes 33A and 33F) that increased from 0% to 1.4% (p = 0.048); and STs 193 (serotype 19A) and 409 (serotype 14) that were only detected in 2008 . Regarding changes in CCs with time, these reflected the changes identified in STs, with only CC306 declining significantly after FDR correction .When grouping the isolates according to the three patient age groups\u2013 18\u201349 yrs, 50\u201364 yrs and > = 65 yrs\u2014only CC5902 showed a statistically significant association with age. The seven isolates belonging to this CC were all recovered from individuals with 18\u201349 yrs .A total of 278 isolates, representing 31.9% of the genotyped collection, carried at least one PI. Among these, 107 (38.5%) had only PI-1, 165 (59.4%) only PI-2 and 6 (2.2%) presented the two PIs simultaneously.While the proportion of PI-1 positive isolates remained stable between 2008 and 2011 , there was a significant decline of PI-2 carrying isolates . This also resulted in an overall increase in the proportion of isolates lacking any of the pilus islands, from 63.8% in 2008 to 72.6% in 2011 (p = 0.013).The presence and variants of the PIs were more strongly associated with ST than with serotype . The STs that were significantly associated with PI-1 and PI-2 are shown in Among the 105 isolates presenting only PI-1, 87.9% expressed PCV7 serotypes, namely serotypes 14 (n = 49), 4 (n = 15), 19F (n = 13), 9V (n = 11) and 6B (n = 6). The remaining isolates were from serotypes 19A (n = 9) and 7F, 24A and 35B . PI-2 positive isolates were from serotypes 7F (n = 85), 1 (n = 68), 11A (5), 19A (n = 2), 3, 7A and 31 and NT (n = 2). The isolates presenting simultaneously the two types of PIs were from serotypes 19A (n = 5) and 19F (n = 1).No associations between isolate source and type of PI were detected. Still, there was a low proportion of PI-2 positive isolates among isolates recovered from the CSF, with only 6 of the 73 CSF isolates presenting PI-2, and while 7 of the 15 isolates recovered from pleural fluid carried PI-2, none carried PI-1.Similarly to pilus islands, resistance to antimicrobials was more strongly associated with ST than with serotype. The AW for ST or serotype and penicillin susceptibility was, respectively, 0.785 (CI95%: 0.729\u20130.841) and 0.389 (CI95%: 0.326\u20130.452), while the AW for ST or serotype and erythromycin susceptibility was, respectively, 0.711 (CI95%: 0.598\u20130.824) and 0.315 (CI95%:0.217\u20130.413). The sequence types that were associated with penicillin non-susceptible pneumococci (PNSP) and erythromycin resistant pneumococci (ERP) are presented in 9V-156, Colombia23F-338 and Greece6B-273 [In spite of several years of PCV7 use in children, the most frequent CC was CC156 11.6%, , a lineace6B-273 .Overall, the clones recognized by the PMEN were strongly represented in our collection with up to 67.3% of the isolates being at most DLVs of one of the 29 different PMEN clones identified. Among the 22 major CCs occurring in the study period , only si3-180), 7F (Netherlands7F-191), 22F (ST433) and 9N (ST66) [14-230 while in the USA and Asia it was associated with the emergence of the PMEN clone Taiwan19F-236, as previously described [1-306 European clone [1-217 (STs 217 and 3081), which has been responsible for epidemics with high mortality in Africa [9V-156 and Netherlands8-53, respectively, similarly to Spain [4-205 and ST246 being common to the two collections of isolates [The eight more frequent CCs were maiN (ST66) \u201326,28\u201330N (ST66) . Among tN (ST66) , indicatan clone . Howevern Africa ,32. The When comparing our results with those from a recent carriage study in adults in Portugal in addit14-230 expressing the non-PCV13 serotype 24F (http://pubmlst.org/). In Portugal, in the pre-PCV7 period, serotype 24F was predominantly CC81 and mostly susceptible to antimicrobials. In 2008\u20132011, among the nine isolates genotyped, four represented CC81 and were mainly antimicrobial susceptible as before, while five represented CC230 and were EPNSP. The detection of this genotype expressing serotype 24F in Portugal is of concern since ST276, an SLV of ST230, was behind the expansion of serotype 19A as a cause of IPD in Portugal in the post-PCV7 era [After the introduction of PCV7, several studies documented a general decrease in IPD incidence. However, the benefits of vaccination were also partly overcome by increases in incidence of non-vaccine serotypes ,7,34,35.type 24F . This coPCV7 era ,39. HoweClonal expansion of previously less frequent lineages was a major contributor to the expansion of non-PCV7 serotypes, since the 22 most frequent CCs occurring in 2008\u20132011 were alrThe presence and type of the PIs was more strongly associated with genotype than with serotype, as previously reported . The gen14-230 Click here for additional data file.S2 Table(PDF)Click here for additional data file."} +{"text": "Legionella spp. infection and conducted a retrospective epidemiologic investigation. Of 1,805 patients tested, Legionella was detected in samples of 21 (1.2%); most were adults who had HIV or tuberculosis infections and were inappropriately treated for Legionella.During June 2012\u2013September 2014, we tested patients with severe respiratory illness for Legionella spp. bacteria that cause community-acquired pneumonia (CAP) in Africa (Legionella spp. infections in South Africa and describe epidemiologic characteristics of patients with Legionnaires\u2019 disease (LD).Data are limited regarding prevalence of Legionella spp. infections by using a real-time PCR assay, as previously described surveillance at 2 sites in South Africa: Klerksdorp-Tshepong Hospital Complex, Klerksdorp, North West Province; and Edendale Hospital, Pietermaritzburg, KwaZulu-Natal Province. A patient with SRI was defined as a person hospitalized with lower respiratory tract infection of any duration. We used a standardized questionnaire to collect demographic and clinical information. Nasopharyngeal specimens and induced sputum samples were tested for Legionella spp. detection, were collected from 1,805 (40%). Of 1,803 patients with sputum specimens for which data were available, 885 (49%) were male, and 324 (18%) were children <5 years of age. HIV prevalence was 64% , and prevalence of active tuberculosis (TB) infection was 24% . Of 1,720 patients with sputum specimens and known survival status, 142 (8%) patients died.During June 2012\u2013September 2014, a total of 4,525 SRI patients were enrolled; induced sputum specimens, the recommended specimen type for Legionella spp. by real-time PCR. For 1 patient from whom sputum could not be collected, Legionella spp. infection was detected in the nasopharyngeal specimen, so 22 patients with Legionella spp. infections were detected in total. Among the 21 patients whose sputum tested positive for Legionella spp. infections, median age was 40 years tested positive for Legionella spp. infection, so we were unable to perform strain typing to confirm whether the clusters were caused by related strains. The remaining 6 patients from Klerksdorp-Tshepong Hospital Complex appeared to have sporadic infections.A cluster of case-patients (15/21 [71%]) was observed during July\u2013December 2012 , includiLegionella patients resided in different areas or communities within the cities of Pietermaritzburg and Klerksdorp. Epidemiologic investigation revealed exposure to several potential sources of infection, such as waste management, air conditioners, plumbing, mining, and swimming pools; however, no common exposure could be identified, so environmental sampling and testing were not performed.Legionella patients with known HIV status were infected with HIV, and 9 (43%) of the 21 patients tested positive for TB at the admission during which Legionella infection was detected. HIV or TB infection, or both, was detected in 18 (90%) of 20 patients with known HIV and TB status. A history of active TB before the admission during which Legionella was detected was reported for 14 (82%) of 17 patients. For 17 Legionella spp.\u2013infected patients for whom information was available, additional LD-associated factors included regular alcohol consumption (10 [59%]), cigarette smoking (9 [53%]), asthma (2 [12%]), and heart disease (2 [12%]).Fifteen (75%) of 20 >43% had TB). Median duration of hospitalization for Legionella patients was 4 days (range 1\u201335 days), and 1 (9%) patient was admitted to intensive care and survived the illness; 4 (20%) patients died. Antimicrobial drug treatment was known for 21 patients and included amoxicillin/clavulanic acid (16 [76%]), anti-TB medications (15 [71%]), cotrimoxazole (7 [33%]), cefuroxime/ceftriaxone (5 [24%]), and erythromycin (5 [24%]).Eighteen (86%) of 21 patients had symptoms >7 days before hospital admission, a delay possibly occurring because many patients were chronically ill . Co-infecting pathogens were Mycobacterium tuberculosis (9 [43%]), rhinovirus (6 [29%]), respiratory syncytial virus (2 [10%]), adenovirus (2 [10%]), Bordetella pertussis (1 [5%]), and Streptococcus pneumoniae (1 [5%]).Legionella spp. detection rates in this study were similar to those described in other countries more than twice that for all SRI patients (8%) surveillance from June 2012\u2013September 2014 at 2 sites in South Africa: Klerksdorp-Tshepong Hospital Complex, Klerksdorp, North West Province; and Edendale Hospital, Pietermaritzburg, KwaZulu-Natal Province."} +{"text": "Predicting extubation failure in Intensive Care is vital to reduce mortality and lower costs due to increased length of Intensive Care Unit (ICU) and hospital stay. We look at predictors of extubation failure in patients passing a spontaneous breathing trial.To identify specific factors leading to increased risk of failed extubation.A retrospective study was conducted of patients who had been re-intubated within 72 hours of extubation at the Royal Sussex County ICU between Dec'02 and Nov'14. Only patients who were intubated intially within the unit were included as they could be identified by the set search criteria in the electronic system.Out of 680 intubations, 73(11%) patients [46 (63%) male] had failed extubations. Average age was 60(21-88)years. Average time to re-intubation was 22.1(1-72) hours, 45(62%) being re-intubated at\u226424 hours. Average time intubated was 2.2 days with 3 patients intubated for >7 days.Fifteen(21%) patients had had no sedation within 4 hours of extubation. All others had one or more of fentanyl, Remifentanil, propofol, midazolam, and morphine. Eighteen (25%) patients had a Glasgow Coma score(GCS)< 10, of which 16(89%) were on at least one sedative. Five patients did not have GCS recorded. Forty-four (60%) patients had mucoid secretions, the rest having thick, purulent or yellow secretions.Mean respiratory rate(RR) was 19/minute (range 9-39) with mean rapid shallow breathing index (RSBI) f/Vt 37.5 breaths/min/l (10.8 - 203.1). Eight (11%) patients had FiO2 >40% pre-extubation. Mean pre-extubation PEEP was 5.8cmH2O(5-10) with mean pressure support(PS) of 14cmH2O (range 5-27), with 57(78%) having PS >10.Fifty eight(80%) patients were hypercapnoeic(PaCO2 >45mmHg) pre-extubation, 2 patients had no arterial blood gas documented shortly prior to extubation, 1 with venous sample. Of these 58 patients, 5 (9%) were acidotic and 8 (14%) received NIV immediately post extubation. One patient self-extubated. Post extubation ABG showed 15/58 (26%) had respiratory acidosis , 3 of which received NIV immediately post extubation.Incidence of failed extubation was low at 11%. Failed extubation happened across all age groups and almost half(45%) the patients needed re-intubation within the first 24 hours. Low GCS may increase risk but may also be due to lack of sedation wean pre-extubation.RSBI was not a good indicator at predicting risk as only one patient scored >105.High PS mean 14cmH2O) pre-extubation very likely contributed towards extubation failure. Hypercapnoea pre-extubation is a risk factor for failed extubation and use of NIV post extubation was low at 14% in these patients. Use of NIV in this group possibly could have averted re-intubation [4cmH2O pr"} +{"text": "Objective: to describe clinical and laboratory characteristics; to assess predictors for death in HIV-infected patients with Kaposi sarcoma (KS).We performed a retrospective study of HIV-infected patients diagnosed with KS in one infectious diseases hospital in Romania, between January 2008-November 2013. KS diagnosis was established on physical examination, skin biopsy, and for visceral involvement upper gastrointestinal endoscopy, bronchoscopy and computed tomography. KS was staged according to the AIDS Clinical Trials Group (ACTG) [We identified 27 HIV-infected patients with KS. The median age was 42 years (IQR 34-52) and 18 (67%) were male. The median CD4 count at HIV diagnosis was 195 cells/cmm (IQR 55-313), while at KS diagnosis the median CD4 count was 101 cells/cmm (IQR 41-270). Eighteen (67%) patients had a CD4 count <200 cells/cmm. The median HIV viral load at the time of KS diagnosis was 120,000 copies/mL . HIV infection was diagnosed before KS in 19 patients (70%), with a median time between HIV and KS diagnosis of 7 months (IQR 0-58). The most frequent KS localization was the lower limb in 16 (59%) patients and 7 (26%) patients had disseminated KS. Oral, gastrointestinal and pulmonary involvements were seen in 10 (37%), 4 (15%) and 3 (11%) patients respectively. Concomitant opportunistic infections were diagnosed in 20 (74%), while other malignancies in 3 (12%) patients. According to the ACTG classification 16 (59%) patients had poor risk KS. Fifteen (56%), 6 (22%), 1 (4%) and 5 (18%) were in stage 1, 2, 3 and 4, respectively according to the Mitsuyasu classification. Six (22%) patients received specific KS treatment: three local radiotherapy and three systemic therapy . The overall mortality was 41% with a median duration between KS diagnosis and death of 6 months (IQR 2-15). Gastrointestinal involvement (p=0.019), poor-risk KS in ACTG classification (p<0.001) and stage IV Mitsuyasu (p=0.006) were associated with death in univariate analysis.The mortality rate in this study was high, due to poor immunological status, extended KS and high incidence of opportunistic infections, but also due to the lack of specific systemic treatment."} +{"text": "In transthyretin (TTR) cardiac amyloidosis, myocardial deposition of liver-derived TTR fibrils results in heart failure and death. Wild-type TTR (ATTRwt) amyloidosis is an acquired disease, whereas familial amyloidotic cardiomyopathy (FAC) is a hereditary form of the disease caused by mutations in the TTR gene resulting in the deposition of both mutant and wild-type TTR. Published data on disease progression in TTR cardiac amyloidosis is limited. To explore this further, we analyzed natural history data in ATTRwt amyloidosis patients to characterize disease progression in this population and compared this to our previously reported data in FAC.Demographic and overall survival (OS) data from patients with ATTRwt amyloidosis (ATTRwt OS cohort) was collected retrospectively from two centers. Six-minute walk distance (6MWD) data from patients with ATTRwt amyloidosis (ATTRwt 6MWD cohort) was collected prospectively from a single center. Data from ATTRwt amyloidosis patients was compared descriptively with our previously reported results from FAC patients collected at the same centers.The ATTRwt OS cohort had a median survival (95% CI) from time of first visit of 31.6 months . The ATTRwt 6MWD cohort , had a mean baseline 6MWD (+/- SEM) of 313m (10). In these ATTRwt amyloidosis patients, the mean change from baseline in 6MWD (+/- SEM) at 6 (N=125), 12 (N=88) and 18 (N=55) months was -30m (7), -59m (13) and -89m (16) respectively. In our previously reported data in FAC patients , median survival (95% CI) was 34.1 months . For a subset of FAC patients in whom 6MWD data was available , mean baseline 6MWD (+/- SEM) was 281m (20), and mean change from baseline in 6MWD (+/- SEM) was -36m (23), -106m (24) and -140m (39) at 6 (N=32), 12 (N=27) and 18 (N=16) months respectively.Survival is limited in both ATTRwt amyloidosis and FAC. Patients with both ATTRwt amyloidosis and FAC demonstrate a decline in functional status over an 18 month time period."} +{"text": "Temporomandibular joint (TMJ) arthritis in childhood is seen in a substantial percentage of children with Juvenile idiopathic arthritis (JIA) and may lead to reduced mouth opening, pain and craniomandibular growth disturbances.To assess the prevalence of TMJ involvement in a JIA cohort and the association between TMJ involvement and other disease variables such as cervical spine and upper limb involvement, and the impact of TMJ involvement on daily life.This descriptive study is based on data from a cross-sectional sample from 32 countries worldwide between 1998-2000, diagnosed with JIA, enrolled for validation of the Child Health Assessment Questionnaire (C-HAQ) and Child Health Questionnaire (CHQ), and also children enrolled in the PRINTO Methotrexate (MTX) trial. Disease activity and quality of life were assessed. Diagnosis of TMJ involvement was based on clinical assessment of the presence of swelling or limitation of motion (LOM) with pain and/or tenderness in at least one TMJ.Of the 3344 children included, 68.3% were female and 45.8% were diagnosed with persistent or extended oligoarthritis. The prevalence of TMJ involvement was 11.6%. TMJ involvement was strongly associated with poly-arthritis (odds ratio (OR) 9.8 6.1-15.8)), systemic (OR 7.4 (CI 4.5-12.3)) and extended oligo-arthritis (OR 6.7 (CI 4.0 - 11.1)) > 2 joints with LOM in upper limb > 2 (OR 9.8 (CI 7.5 - 12.7)) and cervical involvement (OR 7.8 (CI 6.2-9.8)) in univariate analysis. Finally, a multivariate logistic regression model with the disease activity measures, polyarticular JIA course, active joints >5, MTX use, female gender, age at visit, higher CHAQ scores, erythrocyte sedimentation rate (ESR), positive rheumatoid factor (RF) and other variables was performed; we underline the role of the following predictors in the association with the TMJ involvement: cervical spine involvement (3.0 (CI 2.2-4.0)), eating difficulties (1.2 (CI 1.0-1.4)) and superior limb involvement (1.1 (CI 1.0-1.1)).The prevalence of TMJ involvement was low in this large cohort compared with other studies probably due to a diagnosis based on clinical diagnostic criteria only. However, we found significant associations between TMJ involvement and cervical spine involvement, upper limb involvement, and eating difficulties. Further studies with both clinical and imaging diagnostic assessment of TMJ involvement in a longitudinal cohort study are warranted.None declared."} +{"text": "Warning symptoms or \u201cred flags\u201d are useful in targeting which patients with headache require investigation. Many red flags, even with normal neurological examination, are the cause of neuroimaging (CT or MRI) overutilization, in addition to patient reassurance. Optimizing headache neuroimaging practices should be a major priority. The aim of our study was to evaluate the investigation rate in patients referred for the first time in the period from 2011 to 2013 to our Headache Center (HC) conducted by a general practitioner particularly an expert in headache management, and to correlate the reasons of investigation with neuroradiological findings.A total of 118 (10.9%) of 1,078 new patients , 85% suffering from episodic or chronic migraine, were referred for neuroimaging: 107 MRI (20 MR angiography), 11 CT. Considering only the 676 subjects whom had never undergone neuroimaging, the percentage was 14.6. Sixteen out of 118 patients were investigated in the past .ab initio from 1-6 months), recent onset in patients over 40 years (19), abnormal neurological signs (12): alteration of Mingazzini or Romberg test, precipitated by exertion (8), atypical aura (8), first-degree relatives died from cerebral aneurism (4), memory deficit (4), migraine associated vertigo (7), paresthesia not typical of aura (7), nighttime onset (3), atypical cluster headache (1), trigeminal neuralgia first branch (1), recent thunderclap headache (1).The reasons for headache investigation were: recent change in characteristics (6), significant increased frequency from 1-12 months , recent (1-12 months) onset therefore concerned 87 patients aged 14-78 years, 53 of them with migraine without aura and 11 with migraine with aura.Insignificant abnormalities were found in 33 patients: paranasal sinus thickening (13), septum pellucidum cyst (2), pineal cyst (3), arachnoid cyst (3), circle of Willis variants (6), signs of chronic cerebral ischemia (5), doubtful small subependymoma (1). Significant abnormalities possibly related to headache were found in two patients (2.2%) with cavernous angioma and intracranial hypotension.The rate of headache patients investigated through neuroimaging was largely inferior to that previously reported in various clinical settings \u20133. We suWritten informed consent to publish was obtained from the patient(s)."} +{"text": "Clinical trials (CT) on triple therapy against HCV infection in HIV-infected patients including TVR plus pegylated interferon and ribavirin (PR) have reported considerably higher response rates than with PR alone. This study was aimed to evaluate the efficacy and safety of triple therapy including TVR in HIV/HCV-coinfected patients in real-life conditions.HIV/HCV genotype 1 patients seen at four Hospitals in Madrid who received therapy including TVR plus PR for at least two weeks were included. The response was evaluated during treatment, and sustained viral response (SVR) was evaluated 12 and 24 weeks after the end of the treatment.Fifty-eight patients have been included; 79% male, median age 48 y.o.; 38% were IL28B rs12979860 genotype CT or TT, 58.6% of patients presented cirrhosis and 24.1% presented fibrosis F3. Infection with genotype 1a was observed in 53.4% of patients. Median baseline HCV-RNA was 3,282,263 IU/mL . The most commonly used antiretroviral (ARV) drugs were tenofovir/emtricitabine [36 (62%) patients], etravirine [21 (36%) patients], abacavir/lamivudine [18 (31%) patients], boosted protease inhibitors [16 (27.5%) patients] and raltegravir [12 (20.6%) patients]. Of the 42 (72.4%) patients who had received previous HCV treatment, 13.7% were null responders, 25.8% were partial responders and 31% had relapsed. In an ITT approach, proportions of patients with undetectable HCV RNA were 67.8% (38/56) at TW4, 83.3% (40/48) at TW12, 80% (36/45) at TW24, 79.4% at TW36 (31/39) and 72% (26/36) at TW48. Fifteen (25.8%) patients discontinued HCV therapy . Rash associated with TVR (grade 1) was observed in two cases (3.4%) and all the patients showed anaemia at some point of treatment. In an analysis by ITT in the 31 patients who had a 60 week follow-up after starting therapy, SVR-12 was observed in 21 (67.7%) patients. And in the analysis by ITT in 28 patients who had a 72 week follow-up after starting therapy, SVR-24 was observed in 17 (60.7%) patients.Response to triple therapy with TVR plus PR in HIV/HCV-patients under real-life conditions, and therefore, including a high proportion of difficult to treat patients, is similar to that found in CT. The safety profile of TVR-based therapy is also comparable to that shown in CT, with only a rate of discontinuation of 8.6% of individuals related to toxicity."} +{"text": "Treatment adherence during adolescence is challenging. Limited data exist for the rate of medication adherence in adolescents.To evaluate medication adherence using two different methods (electronic monitoring system and tablet count) in adolescents with Type 1 Diabetes (T1D) participating in an RCT.Medication adherence was assessed in 54 T1D adolescents enrolled in a 1 year RCT to receive metformin or placebo [Adherence was assessed using tablet count and prospective electronic monitoring using Medication Event Monitoring System caps , which recorded episodes of bottle opening for each participant. These data were then compared to prescribed doses.Adequate adherence was defined as \u2265 80% of prescribed doses taken over a defined period. Adherence was assessed after allowing a 3-month run-in period to account for dose titration and minimise potential for reactivity associated with initial adherence monitoring. Data were reported from 3-6 months (short-term) and from 6-12 months (long-term).Adolescents had mean T1D duration 5.9\u00b14.2y, median HbA1c 8.5 (6.3-11.6)%. 26 used CSII.MEMS adherence data for short and long-term use was available for 53 and 48 participants respectively. Adequate adherence using MEMS was 47% (25/53) short-term and 35 (17/48) long-term. Median (IQR 25-75%) adherence was 79 (46.6-88.7%) short-term and 67 (43.4-86.8%) long-term.Tablet count adherence data for short and long-term use was available for 35 and 42 participants respectively. Adequate adherence using tablet count was 63% (22/35) short-term and 45% (19/42) long-term. Median (IQR 25-75%) was 84 (70.8-90.1%) short-term and 77 (61.7-86.8%) long-term.There was no statistically significant difference in adherence between the two methods used p=0.22 (short-term) and p=0.07 (long-term). Adolescents who were adherent in the short-term by MEMS were more likely to have a longer diabetes duration .Adolescent adherence to intervention in this clinical trial was suboptimal as shown by both electronic monitoring and tablet count. This finding reinforces the importance of parental involvement in treatment regimens in this population."} +{"text": "Abatacept (ABA) - a new generation biological DMARD. It was approved in Russia in 2009. ABA selectively modulates T-cell activation, which seems to play the key role in the pathogenesys of Juvenile Idiopathic Arthriris (JIA). Efficacy and safety of ABA was assessed in AWAIKEN trial in different types of patients who had polyarticular course of JIA at the enrollment.This prospective observation was aimed to assess effectiveness and safety of ABA in patients with different types and clinical variants of active JIA in real clinical practice.30 children with JIA were treated with ABA. 23 (77%) pts had polyarticular course of JIA and 7 (23%) - systemic JIA. 11 children were diagnosed with acute uveitis . 28 (93%) of pts were female. All patients had high degree (III) of disease activity. Mean disease duration was 6,1 \u00b1 3,2 yr. 29 patients previously had an inadequate response to 2 or more non-biological, one child with heavy course of systemic JIA was treated with infliximab during 1 year before starting ABA. Treatment effectiveness was assessed according to the ACR Pediatric criteria: ACR pedi 30, ACR pedi 50, acrpedi 70, and ACR pedi 90 after 6 and 12 months of abatacept therapy. All patients received ABA in dose 10 mg/kg at day 1, week 2 and 4 and every 4 weeks thereafter.In the group of pts with systemic JIA after 6 months of ABA treatment 6 of 7 patients (86%) achieved ACR Pedi 30 response, 5 (71%) - ACR Pedi 50, and 3 (43%) - ACR Pedi 70. 12 months data was available for 5 patients (others are still on treatment but less than 12 moths). Four of five pts (80%) achieved ACR pedi-30, 3(60%) - ACR Pedi 50 response, 2 (40%) ACR pedi 70, and 1 (20%) ACR pedi 90.rd infusion and ABA treatment was stopped. After 6 months 20 of 22 pts (91%) achieved ACR pedi 30 response, 17 (77%) - ACR pedi-50, 9 (41%) - ACR pedi-70, 2 (9%) - ACR pedi 90. 14 of 22 patients with polyarticular JIA have completed 12 months of ABA treatment. 12 of them (86%) achieved ACR pedi 30 response, 11 (78%) - ACR pedi 50, 8 (57%) - ACR pedi 70 and 2 (14%) - ACR pedi 90. Abatacept also showed efficacy in treatment of JIA associated uveitis. After 6 months of treatment the count of affected eyes was significantly reduced. In 72% of patients complete remission of uveitis was achieved.In the group of pts with poliarticular course of JIA treatment effectiveness was assessed in 22 pts. One girl had experienced an infusion-related reaction after 3Adverse events were observed in 2 patients : 1 case of infusion related reaction, 1 pts experienced common Herpes simplex infection (ABA treatment was stopped after 12 months).Abatacept have shown its effectiveness in the majority of patients with long standing JIA (systemic and polyarticular course) with high disease activity, and inadequate response to previous treatment with dmards. Better results were observed in patients with poliarticular JIA.None declared."} +{"text": "Pectus Excavatum is the most common congenital chest wall deformity (90%) and the documented incidence ranges between 0.1% - 0.3%. Patients with Pectus Excavatum can suffer with body image and psychological issues. Indications for surgical correction remains controversial although a decrease in exercise tolerance is frequently overlooked. A general consensus persists that Pectus Excavatum is a cosmetic defect with no physiological consequences.In this study we investigated the functional exercise capacity of patients with Pectus Excavatum (PE).Between Feb 2006 and March 2015: 44 patients presented to our institution with symptomatic PE. 29 patients underwent complete investigational study including Computed Tomography (CT) of the thorax Cardiopulmonary Exercise tolerance (CPEX) testing including measurement of Cardiovascular parameters: Maximal oxygen consumption (VO2 max) ; normal > 85% predicted. Anaerobic Threshold (AT)=: change from aerobic to anaerobic metabolism . O2 pulse . Respiratory parameters: Ventilatory reserve (VE BTPS) ; normal > 85% predicted. Peak exercise. End Tidal CO2 (PETCO2) ; normal 30 - 38 mmHg.Results Mean Age 22.4 years (13 - 33 years). All presented with symptoms of dyspnoea /fatigue /dysphagia. Mean VO2 max was 78% (51 - 102%). VO2 max was sub-normal in 19 (65%) indicating cardiac dysfunction. 15 (51%) patients had reduced AT. 15 patients had reduced VO2 /HR. 28 (96.5%) had marked increase/unused ventilatory reserve. 14 (48%) had a marked increase in PETCO2, inability to expire CO2.Pectus Excavatum is associated with significant compromise in cardiopulmonary physiology (65%).The aetiology of the defect is mainly cardiac or respiratory in nature with some having a mixed picture. We advocate the routine use CPEX testing in PE patients prior to corrective surgery. These results support the premise that most patients with severe anatomical PE defect also have an associated severe physiological defect."} +{"text": "Increasing number of studies is now devoted to immunotherapy of cancer. We evaluated the clinical benefit of hepcortespenlisimut\u2010L (V5) \u2013 an oral therapeutic vaccine designated by the US FDA as an orphan drug for treatment of hepatocellular carcinoma (HCC).Open-label Phase II trial (NCT02256514) is currently underway, which by now has enrolled 75 patients with advanced HCC, consisting of 29 (38.7%) females and 46 (61.3%) males with median age 60 years (Mean 61.6\u00b18.1). Out of these 32 (42.7%) had hepatitis B and 43 (57.3%) hepatitis C infections, including 8 (10.7%) with dual infection, 4 (5.3%) negative for both viruses and 5 (6.7%) without established viral diagnosis.After median 2 months of daily dose of V5 pill, 50 out 75 patients had experienced decline in serum levels of tumor marker, alphafetoprotein, . Baseline median AFP levels were 245.2 IU/ml and post-treatment values were 102.3 IU/ml . The decrease in AFP was correlated either with tumor clearance or regression on CT scans. The median overall survival time could not be established since 70 out 75 (93.3%) are still alive after median follow-up of 10 months . The first patient in this study received immunotherapy 57 months ago and is doing well without any trace of lesions. None of the patients experienced any adverse effects, contrary their liver function tests had improved.The results indicate that hepcortespenlisimut-L is safe, effective and fast-acting immunomodulatory intervention for HCC. The Phase III randomized, double-blind, placebo-controlled trial is now initiated to confirm these promising findings (NCT02232490).ClinicalTrials.gov identifier NCT02232490."} +{"text": "Autologous monocyte-derived mRNA electroporated dendritic cells (TriMixDC-MEL) are immunogenic and have anti-tumor activity in patients (pts) with pretreated advanced melanoma . Ipilimumab (Ipi) is a monoclonal antibody directed against the CTLA-4 receptor that counteracts physiologic suppression of T cell function and improves the overall survival of pts with advanced melanoma.The activity and safety of TriMixDC-MEL combined with Ipi (10 mg/kg q3wks x4), followed by Ipi maintenance therapy was investigated in pts with advanced pretreated melanoma according to a Simon two-stage Phase II study design. The primary endpoint was the 6-mths disease control rate (DCR) by irRC.39 pts initiated study treatment . Following DC-administration, gr2 skin injection site reactions were observed in all pts, post-infusion chills (< gr2) in 15 (38%), and transient flu-like symptoms (< gr2) in 33 pts (85%). Most frequent grade 3/4 adverse events of special interest were: dermatitis (2 pts [5%]); diarrhea/colitis (2 pts [5%]), hypophysitis/hypopituitarism (7 pts [18%]), hepatitis (5 pts [13%]), and pneumonitis (3 pts [8%]). Systemic corticotherapy was used to treat irAE in 18 pts (46%). Best overall tumor response by irRC: 8 CR, and 7 PR (BORR 38%), 6 SD and 18 PD. All CR, and 3 PR are ongoing after a median duration of 19 mths (range 3-29 mths). The 6-mths DCR by irRC is 50% (95% CI 34-66). Median PFS and OS are respectively 6,2 (95% CI 3-9), and 14,4 mths (95%CI 10-18).This Phase II trial of autologous mRNA electroporated dendritic cells in combination with Ipilimumab in patients with pretreated advanced melanoma achieved its primary endpoint and resulted in an encouraging rate of durable tumor responses. Further clinical investigation of autologous mRNA electroporated DC-therapy in combination with immune checkpoint modulators is warranted."} +{"text": "Tuberculosis lymphadenopathy is the most common form of extrapulmonary tuberculosis. The aim of the present study is to detect the duration of treatment required in patients with cervical lymphadenopathy.The patients attending the Department of Pulmonary Medicine OPD with cervical lymphadenopathy were screened. Detailed history, clinical examination, USG neck, FNAC, Mantoux test, biopsy, and chest X ray frontal view were performed and anti tuberculosis treatment initiated.Total patients examined: 117, in the age group 10-70 years (mean age 40). Females affected \u2013 89 (76.07%), Males - 28 (23.93%). Most common age group affected (M/F): 15-20 years: 37 (31.63%) patients. Biopsy was done in 73 patients (62.39%). Patients received Category-1ATT under RNTCP. After 6 months of therapy, 22 patients (18.81%) stopped treatment in view of non-palpable mass. Out of remaining 95 patients (81.19%), 14 patients\u2019 (11.96%) lymph node size increased with slow regression, 17 patients\u2019 (14.52%) liquefaction and repeated aspiration was done, 57 patients\u2019 (48.72%) lymph node size showed regression less than 50%, 7 patients (5.98%) came up with new group of lymph nodes with size gradually increased. For all 95 patients, therapy was extended (continuation phase) for 2-3 months. 7 patients received ATT for 12 months.Extrapulmonary tuberculosis like tuberculous lymphadenopathy is benefited with extension of anti tuberculosis treatment."} +{"text": "Dizziness is a common complaint in HAM/TSP and can occur due to vestibulospinal tract dysfunction. This tract can be assessed through Vestibular Evoked Myogenic Potential (VEMP). The aim was to correlate the result of VEMP generated by acoustic stimuli and dizziness in individuals with HTLV-1-asymptomatic infection and HAM/TSP. VEMP was recorded from sternocleidomastoid muscle of 60 HTLV-1-negative adults (56 \u00b1 5 years) and 60 individuals infected with HTLV-1, being 30 asymptomatic (56 \u00b1 8 years) and 30 with HAM/TSP (59 \u00b1 8 years). In all groups, 90% of the participants were women. The acoustic stimuli were short tone bursts , stimulation rate of 5 Hz and the analysis time for each response was 60 ms; 200 responses were averaged for each run. The electromyographic signals were amplified and band-pass filtered between 10 and 1.5 KHz. Of 60 HTLV-1-negative individuals, 14(23%) reported dizziness; VEMP was normal in all. In the HTLV-1-asymptomatic group, 11(37%) complained of dizziness (P=0.22); VEMP was altered in 4(40%) subjects with dizziness and in 1(5%) without dizziness (P=0.05). In the group with HAM/TSP, dizziness was reported by 17(57%) subjects (P=0.002); VEMP was altered in 11(64%) with dizziness and in 5(38%) without dizziness (P=0.15). Damage of vestibulospinal tract seems to occur in the early stages of HAM/TSP. VEMP was previously shown to be a useful test for the follow-up of asymptomatic carriers. Dizziness without an apparent cause in HTLV-1-asymptomatic carriers deserve investigation about a possible spinal cord involvement."} +{"text": "Apart from financial purposes (cost accounting), DRG as case - mix system are not used for obtaining competitive advantage. MDC can be useful to classify the SS; if so, it is possible to assign each focus of sepsis to a specific category, which is important from a socio-economic perspective.Identify which MDCs encompasses a greater or lesser number of CIPs con SS.Find out which MDC incorporating CIPs with SS carries a higher an average relative weight (RW).Type of Study: prospective, analytical, longitudinal, and observationalPeriod: January 1-2011 / June 30-2014 (42 months)Medical/Surgical ICUPopulation: 2559 CIPs admitted consecutively to the ICU; sample: 484 CIPs.Exclusi\u00f3n criteria: CIPs < 16 y., major burn CIPs, incomplete clinical documentation, and voluntary discharge.DRG AP-DRG 25.0 version (684 DRG are grouped into 25 MDC and 1 extra MDC).Depending on the focus of sepsis, SS related to MDC '0' (precategor\u00eda) are transferred to another MDC.MDC: 1 (neurology), 2 (eye), 3 , 4 (respiratory), 5 (circulatory), 6 , 8 , 9 (skin & breast), 10 (endocrine), 11 (urinary tract), 12 , 13 , 14 (pregnancy & childbirth), 15 (newborn), 16: , 17 (mMyeloproliferative), 18 (infectious), 19 , 20 , 21 (Injuries & poison), 22 (burns), 23 , 24 (HIV), 25 (PLT), 0 See Tables Excluded MDCs (< 8 DRG with SS): '2', '3', '4', '12','13', '14', '15', '16', '17', '19', '20', '21', '22', '23', '24' y '25'16 MDC do not identify SS (or less than 8 DRG).MDC '6', '4' and '7' carry more SS, that, it respectively, correspond to the septic focus abdominal, respiratory, and biliopancreatic.MDC '4' and '6' show the highest RW"} +{"text": "Streptococcus (GAS) infections, which suddenly start before puberty and display remitting/relapsing course.PANDAS includes neuropsychiatric symptoms, mainly obsessive-compulsive disorder (OCD) or tics, temporally associated with an immune-mediated response to group A \u03b2-hemolytic To describe clinical features of a cohort of 65 Italian pts with previous confirmed GAS infection and sudden occurrence of OCD and/or tics.Descriptive analysis of a cohort of Italian patients with PANDAS.Between may 2009 - may 2013 we observed 65 pts with OCD and/or tics starting before puberty, associated with a previous GAS infection. Demographic and familiar data, routine and specific laboratory data: thyroid function, autoimmunity tests were collected. 55/65 underwent brain MRI, all EEG, echocardiography and neuropsychiatric evaluation.nti-streptolysin O titer less than 250 lU, 20 (30.8%) between 250 and 550 IU, 29 (44.6%) over 500 IU. Anti-DNase titer was increased (650-1200 U) in 38 . All pts received benzathine benzylpenicillin. Sertraline or haloperidol were added in 10, and a psychotherapeutic help in 6. Seventy eight, 5% pts displayed complete or partial remission of initial symptoms.13/65 pts (20%) born from Caesarean section, 60/65 (92.3%) full-term, 32/65 had familiars with OCD/tics or other neurologic diseases, and 57/65 (87.7%) did sports. Acute and dramatic onset occurred at a mean age of 74.3 \u00b1 25.9 months (range 24-160). Out of 65 pts, 22 (33.8%) started with motor tics; 2 (3.1%) with OCD; 5 (7.7%) with motor/vocal tics; 28 with motor tics and OCD; 1 (1.5%) with vocal tics and compulsive behavior and 7 (10.8%) with motor/vocal tics and OCD. 41/65 patients (63.1%) had previously pharyngitis, otitis and/or upper airway infections, 1 impetigo. Brain MRI, EEG, thyroid tests, and coeliac disease screening were normal in all. Mean age to diagnosis 101.2 \u00b1 29.9 months. At onset and at our first clinical evaluation inflammatory parameters were negative in all. Five (7.7%) had aOur preliminary data show that PANDAS is mainly observed in males with familiar recurrence of different motor disturbances, clinical onset occurs at a mean age of 6 \u00b1 2 years with the coexistence of OCD and motor tics in most cases, and increased anti-DNase titer is found in 58.5% of patients. Benzathine benzylpenicillin has resulted effective in 78.5% of cases with complete/partial remission of symptoms. New studies on large prospective cohorts of patients of different age and the identification of reliable biomarkers indicating early diagnosis and outcome of PANDAS are needed.None declared."} +{"text": "HIV infection during pregnancy still raises controversial issues. Combined antiretroviral therapy (cART) has been successful in reducing mother-to-child transmission (MTCT). Routine screening in pregnancy and in pre-conception consultation proved to be one of the best methods able to get this treatment on time. We review our experience with pregnant patients with HIV infection.Retrospective and descriptive study. Data obtained from HIV-infected pregnant women from 1999 to 2012 with delivery and subsequent infectious diseases follow-up at our hospital.3. MTCT occurred in 3/147 cases (2%): in one mother HIV-1 infection was diagnosed three weeks before delivery, other immediately after delivery and the third woman started cART (2NRTI+1PI/r) in the second trimester of pregnancy, always adherent and without secondary effects, VL at delivery was 50 copies/mL and elective C-section was performed.We evaluated 136 patients (169 pregnancies), with a total of 147 living newborns (2 twin pregnancies) and 1 stillbirth. Median age at pregnancy was 30 (SD 5.7) years. Four patients were HIV-2 infected and one HIV-1+2 infected. 26 (19.1%) women were HCV co-infected and 6 (4.4%) HBV co-infected; 1 patient has HCV and HBV co-infection. Sexual risk for HIV acquisition was determined in 102 (75%) patients and 31 (22.8%) were intravenous drug users. 33/136 (24.2%) women were diagnosed on routine screening in pregnancy, 4 during delivery and 2 immediately after delivery. 36 (26.4%) patients had an AIDS-defining entity before pregnancy and no new opportunistic infections were diagnosed. ART was used in 157 (92.9%) pregnancies and 15 (9.5%) of them were treated only with NRTIs. At the time of delivery 86/144 (59.7%) patients had undetectable viral load (VL) (25 patients without VL determined), 91.7% of those on ART. 119 (70.4%) had a TCD4 cell count above 200 cells/mmThe fact that 24% of patients were diagnosed during pregnancy shows the importance of routine screening to all pregnant women. MTCT occurred in three children, but only one was administered cART for prevention."} +{"text": "We report the SVR12 final analysis of a phase 3 study of telaprevir in combination with peginterferon (P)/ribavirin (R) in HCV-genotype 1, treatment-na\u00efve and -experienced patients with HCV/HIV co-infection (INSIGHT).Patients receiving stable, suppressive HIV antiretroviral (ARV) therapy, containing atazanavir/ritonavir, efavirenz, darunavir/ritonavir, raltegravir, etravirine or rilpivirine, received telaprevir 750 mg q8h (1125 mg q8h if on efavirenz) plus P (180 \u00b5g once-weekly) and R (800 mg/day) for 12 weeks, followed by an additional 12 weeks or 36 weeks of PR alone. Analysis was performed when all patients had completed the follow-up visit of 12 weeks after last planned dose.3. Sixty four patients (40%) were HCV treatment-na\u00efve and 98 (60%) were treatment experienced . 64% were subtype 1a. 30% had bridging fibrosis (17%) or cirrhosis (13%). 19% of patients discontinued telaprevir, including 9% due to an adverse event (AE), 8% reaching a virologic endpoint and 2% for other reasons (non compliance or not defined). Treatment responses are shown in One hundred sixty-two patients were enrolled and treated . Mean age was 45 years, 78% were male, 92% were Caucasian; mean CD4 count was 687 cells/mmIn this phase 3 study of HIV-infected, HCV treatment-na\u00efve and -experienced patients, 49% achieved eRVR and 57% reached SVR12. In patients with an eRVR, SVR12 rates were >80%, irrespective of prior treatment history."} +{"text": "Detection rate for anterior prostate cancer (PCa) in men who underwent initial and repeat biopsy has been prospectively evaluated.From January 2013 to March 2014, 400 patients all of Caucasian origin (median age 63.5 years) underwent initial (285 cases) and repeat (115 cases) prostate biopsy; all the men had negative digital rectal examination and the indications to biopsy were: PSA values > 10 ng/mL, PSA between 4.1-10 or 2.6-4 ng/mL with free/total PSA\u226425% and \u226420%, respectively. A median of 22 and 31 cores (repeat biopsy) were transperineally performed including 4 cores of the anterior zone (AZ) and 4 cores of the AZ plus 2 cores of the transition zone (TZ), respectively.Median PSA was 7.9 ng/mL; overall, a PCa was found in 180 (45%) patients: in 135 (47.4%) and 45 (36%) of the men who underwent initial and repeat biopsy, respectively. An exclusive PCa of the anterior zone was found in the 8.9 vs 13.3% (repeat biopsy) of the men: a single microfocus of cancer was found in the 61.2% of the cases; moreover, in 7 out 18 AZ PCa the biopsy histology was predictive of significant cancer in 2 (28.5%) and 5 (71.5%) men who underwent initial and repeat biopsy, respectively.However AZ biopsies increased detection rate for PCa (10% of the cases), the majority of AZ PCa with histological findings predictive of clinically significant cancer were found at repeat biopsy (about 70% of the cases). Prostate cancer (PCa) has become the most common tumor in men , but in In our study, detection rate for PCa with a prostate biopsy scheme that included anterior zone cores in men who underwent initial and repeat procedure has been prospectively evaluated.From January 2013 to March 2014, 400 patients all of Caucasian origin and between the ages of 47 and 75 years (median 63.5 years) underwent initial (285 cases) and repeat 115 cases) prostate biopsy; all men had negative digital rectal examination and the indications to biopsy were : PSA val5 cases pMedian PSA was 7.9ng/mL (range: 2.858ng/mL): 50 12.5%) had PSA>10ng/mL, 330 (82.5%) between 4-10 and 20 (5%) between 2.6-4ng/mL, respectively. Overall, a cT1c stage PCa was found in 180/400 (45%) patients: in 135 (47.4%) and 45 (36%) of the men who underwent initial and repeat biopsy, respectively. In the remaining 220 patients an intraepithelial prostatic neoplasia (HGPIN), an atypical small acinar proliferation (ASAP), a chronic prostatitis and a normal parenchyma was found, in 18 (4.5%), 3 (0.7%), 29 (7.2%) 170 (42.5%) cases, respectively. Overall, clinical parameters and histological findings in the presence of PCa are listed in .5% had POverall, side effects following prostate biopsy occurred in 36.2% (140/400) of patients: 105 (26.2%) cases of hemospermia, 42 (10.5) of acute urine retention and 36 (9%) of hematuria; none needed hospital admission; moreover, all patients had a grade I of the Clavien-Dindo complications scale .Aggressive screening and prostate needle biopsy protocols have been successful in early detection of low-volume tumors increasing the incidence of anterior-predominant prostate cancers especially in patients submitted to repeat biopsy \u201321. AnteIn our series, overall detection rate for cancer located in the anterior zone was equal to 10% (18/180 cases) in initial (8.9% of the cases) vs repeat (13.4% of the cases) prostate biopsy (p=0.36). In detail, 11/18 (61.2%) AZ PCa were characterized by the presence of a single microfocus of PCa at risk for clinically indolent PCa; on the other hand, 7/18 clinically significant AZ PCa (GS\u22656 and GPC>50%) would have be missed through a standard biopsy scheme . In definitive, the AZ biopsies increased detection rate for PCa allowing to reduce the prostate biopsy false negative rate and to characterize the histological findings of the cancer; in addition, in case of repeat SPBx biopsy AZ cores found a statistically significantly higher percentage of significant PCa in comparison with TZ cores (13.4 vs 2% of the cases) (p=0.003).Regarding our results, some limitations should be reported. Firstly, the true incidence of AZ PCa should be evaluated in the entire specimen of the prostate; secondly, the clinical relevance of the AZ PCa remains unknown; finally, a greater number of cases should be evaluated.In conclusion, although AZ biopsies increased overall detection rate for PCa (10% of the cases) the majority of AZ cancers with histological findings predictive of clinically significant PCa were found in case of repeat procedures (about 70% of the cases)."} +{"text": "Listeria monocytogenes (Lm) bioengineered to secrete a tLLO-HPV-16-E7 fusion protein targeting HPV-transformed cells. The Lm vector serves as its own adjuvant and infects APC where it cross presents HPV-E7-tLLO fusion peptide, stimulating MHC class 1 and 2 pathways resulting in HPV-E7 specific T cell immunity. Lm-LLO-E7-015 , is a randomized Phase II study designed to evaluate the safety and efficacy of ADXS11-001 +/- Cisplatin in patients with recurrent cervical cancer in India.ADXS11-001 immunotherapy is a live attenuated 9 cfu or 4 doses of ADXS11-001 at 1 \u00d7 109 cfu with Cisplatin chemotherapy . Naproxen and oral Promethazine were given as premedications. Patients received CT scans at baseline and 3, 6, 9, 12 and 18 months. The primary endpoint was overall survival.110 patients were randomized to either 3 doses of ADXS11-001 at 1 \u00d7 10\u22653 months, for a disease control rate of 38% (42/109). Average duration of response in both treatment groups was 9.5 months. Long term survivors included patients with tumor shrinkage and patients with increased tumor burden as their best tumor response overall; 8% (2/24) of LTS failed at least two prior treatments; and 25% (3/11) of LTS were ECOG performance status 2 at baseline. Activity against different high-risk HPV strains was observed. The addition of Cisplatin to ADXS11-001 did not improve survival or tumor response over ADXS11-001 alone but contributed to toxcity. Baseline ECOG performance status, type of prior therapy, or aggressiveness of disease had no significant effect on survival or tumor response. ADXS11-001 was well tolerated as 62% (68/109) of patients reported no adverse events and 38% (41/109) of patients reported only mild transient adverse events (G1-2) that occurred on the day of infusion. The incidence of SAEs possibly related/ related to ADXS11-001 was 1% G3 (0% G4-5).Final 12-month survival was 32% (35/109), 18-month survival was 22% (24/109) and 24-month survival was 18% (16/91). The response rate was 11% (5 CRs and 6 PRs/109) with tumor responses observed in both treatment arms; 31 additional patients had stable disease ADXS11-001 appears to have significant clinical activity in patients with recurrent cervical cancer. The observed prolonged survival, objective tumor responses, and stabilization of recurrent disease compare favorably with more toxic chemotherapy treatment options and support ADXS11-001 as an active agent in the treatment of cervical cancer."} +{"text": "Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease in childhood and the polyarticular subtype is associated with persistent activity and a low rate of remission. The goal of an early and aggressive treatment is to achieve remission preventing irreversible joint destruction and long-term disabilities.1) To assess disease activity in patients with pJIA \u201cunder early therapy with MTX.\u201d.2) To determine predictors of ID in this cohortClinical charts of 174 pJIA pts (ILAR\u00b401), (1998 -2009) we reviewed. Inclusion criteria:-pJIA pts under \u201cearly\u201d MTX\u2013follow up \u201ca minimum of 12mo\u201d. Demographic, clinical, laboratory, and therapeutic variables were analyzed at disease onset, 12mo and last visit. Functional disability(CHAQ), damage (JADI Articular score) and Remission Criteria were properly assesed.Ninety eight patients were included , 85 girls, (86.7%) median age at onset 10 years ( IQR :6 -12) ,median disease duration 60 months ( IQR :36 -74 ) and follow-up 48 months ; 34 pts (34.6%) were RF Positive. All patients received MTX; 32 /98 (32.6%) reached ID at amedian follow up time of 12 mo with a CHAQ mean value 0,37 and a JADI mean value 1,3. Nineteen out these 32 pts (60%) sustained remission for at least 37 mo. ID was associated with a less time of disease evolution (p.05), a better function CHAQ (p .05) and less damage (p .04)A higher prevalence but not significantly RF titers (40 vs 25%); seronegative ANA titers (60 vs 53 ) and RX damage (47 vs 32 ) were observed in the group of non responders pts to MTX. On multivariate analysis a less time of disease evolution was the only predictive risk factor associated to inactive disease .In our series , only 32/98 (32.6%) pJIA pts reached ID , this clinical state was sustained in 60% of them longer than 2 years. A less interval between disease onset and Mtx start was the only variable predicting inactive disease.None declared."} +{"text": "Medical patients who arrive severely ill at the Emergency Department (ED) need to be diagnosed and treated immediately, as prognosis decreases rapidly with time spent before correct treatment is given for most of these patients.At Odense University Hospital, patients arriving at the ED with either a pulse rate >140, systolic blood pressure <80 mmHg, Glasgow Coma Scale <9, respiratory frequency >35 or <8 or a saturation <80% are met by the medical trigger team. Patients with suspected apoplexy, STEMI or orthopedic multitrauma are met by other specialized teams.To describe frequency, patient characteristics, and 7 day mortality for adult patients (>18 years) managed by medical trigger teams, thrombolysis, and orthopedic trauma teams.All patients who were met by a medical trigger team, a thrombolysis, or an orthopedic trauma team at arrival to the ED, Odense University Hospital between April 1st 2012 and May 31th 2013 were included.A total of 884 patients were met by the medical trigger team, 306 by the thrombolysis and 377 by the orthopedic multitrauma team. The median (range) number of team activations per day was 2 (0-9), 0(0-6), and 1 (0-6). Median age (25-75%) was 70 (56-80), 67 (54-76), and 42 years (26-59), 54% (95% CI 50%-57%), 53% (95% CI 48-59%), and 73% (95% CI 68-78%) were male, 7 day mortality was 18% (95% CI 16-21%), 9% (95% CI 6-13%) and 7% (95% CI 5-11%).Medical trigger teams were used median twice a day. Their patients have a higher mortality than patients met by the thrombolysis or orthopedic multitrauma teams."} +{"text": "A dried blood spot (DBS) on filter paper has been used for different tests globally and has gained popularities in resource limited settings especially during HIV/AIDS epidemic. We assessed the efficiency of molecular characterization of HIV-1 subtypes using DBS collected under field conditions in northern Tanzania.In 2011 and 2012, 60 DBS samples were collected under field conditions from exposed and newly diagnosed HIV-1 infected children from Kilimanjaro (n=20), Arusha (n=20), Tanga (n=10) and Manyara (n=10).Of 60 DBS analyzed at both Protease (PR) and Reverse Transcriptase (RT) regions, 45 (75%) were analyzed, including 17 (85%) from Kilimanjaro, 15 (75%) from Arusha, 8 (80%) from Tanga, and 5 (50%) from Manyara region. All 45 DBS characterized had viral load above 1000 copies/mL with mean log10 viral loads of 3.87 copies/mL (SD 0.995). The phylogenetic results indicated presence of subtype and circulating recombinant form (CRF). In which, 24 were subtype A1 (53.33%), 16 were subtype C (35.55%), 3 were subtype D (6.67%) and 2 were CRF10_CD (4.35%). All major mutations were detected in the RT region, none from protease (PR) region. The mutations detected were Y181C (n=8), K103 (n=4) and G190A (n=1), conferring resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs), and M184V (n=1), conferring resistance to lamivudine and emtricitabine.Our results indicate that DBS collected from field conditions in resource scarcity areas can be used to determine the phylogeny of the virus and drug resistance mutations in areas with diverse HIV-1 group M subtypes."} +{"text": "Background. To investigate the clinical significance of the perioperative CA19-9 change for predicting survival in intrahepatic cholangiocarcinoma (ICC) patients treated with surgical resection. Methods. We retrospectively reviewed the data from 74 ICC patients treated with surgical resection between April 2001 and July 2010. Perioperative CA19-9 levels were analyzed for patient distribution and survival. Results. Before surgery, there were 45 patients who had high preoperative CA19-9 levels (>37\u2009U/mL) and 29 who had normal levels (\u226437\u2009U/mL). Of 45 patients with high CA19-9 levels, 34 had normalized CA19-9 levels after resection and 11 had persistently high levels. Of 34 patients with normalized CA19-9 levels, 18 showed recurrence. Of 29 patients with normal preoperative levels, 15 showed recurrence. Multivariate analysis presented that old age , persistently high postoperative CA19-9 level , perineural invasion , narrow resection margin , and lymph node metastasis were significant independent risk factors for survival. Conclusions. Patients who have normalized CA19-9 levels postoperatively have longer survival outcomes. Therefore, normalized postoperative CA19-9 may be a useful clinical marker for ICC survival. Intrahepatic cholangiocarcinoma (ICC) is the second most common primary hepatic cancer besides hepatocellular carcinoma but remains an uncommon and enigmatic disease . ICC is 1 and high preoperative CA19-9 level is independent dismal prognostic factor [Carbohydrate antigen 19-9 (CA19-9) is one of the most frequently studied prognostic factors which have been evaluated for diagnosis, survival, and recurrence in ICC patients. Previous studies have reported that CA19-9 expression is also prevalent in ICCBetween April 2001 and July 2010, a total of 99 patients who underwent surgical resection of ICC with curative intent and had a confirmed pathological diagnosis were recruited from our database. Then, 74 patients with complete data of perioperative CA19-9 levels, including preoperative CA19-9 (preopCA19-9), postoperative lowest CA19-9 (postopCA19-9), and CA19-9 levels at recurrence (recurCA19-9), were included in the study. Of the 74 patients, 54 (72.9%) were men and 20 (27.1%) were women, and their median age was 65 years . Seventeen patients had viral hepatitis: 15 patients were positive for hepatitis B surface antigen and 2 for hepatitis C virus antibody. Hepatolithiasis was observed in 4 patients and liver cirrhosis in 15. PreopCA19-9 levels were increased above the normal value in 45 patients (60.8%) and were within the normal range in 29 patients (39.2%).Preoperative diagnosis was based on a combination of radiologic staging, tumor makers testing (CA19-9 and CEA), and routine medical assessment. We restricted patients without elevated bilirubin and/or no clinically evident cholangitis before and after surgery because insufficient control of the biliary obstruction could raise serum CA19-9 concentrations . RoutineAll 74 patients underwent liver resection with curative intent to obtain R0 resection. There were 6 trisectionectomies , 53 hemihepatectomies , 5 sectionectomies, and 10 segmentectomies. Combined resection of the extrahepatic bile duct was performed on 5 patients in whom the tumors invaded the extrahepatic bile duct. Lymph node dissection was performed on 51 patients (68.9%), and the policy of lymph node dissection in ICC surgery at our institute was previously described elsewhere [n = 29) and those with elevated CA19-9 before resection. After resection, we chose the postopCA19-9 level as the lowest level during follow-up period in order to allow adequate time for recovery from surgery or any adjuvant therapy. Forty-five patients with elevated preopCA19-9 were stratified into 2 groups based on the postopCA19-9 nadir.We also checked CA19-9 at tumor recurrence during the follow-up period. When disease progression was confirmed by repeated imaging studies, the date of the first detection of a suspicious radiologic finding was recorded as the date of the initial disease recurrence and radiologic evidence of tumor recurrence was accepted as a criterion of recurrence even if a patient did not undergo a biopsy. Twenty-seven of the 45 patients with elevated preopCA19-9 recurred, and 15 of the 29 patients with normal preoperative levels recurred.t-test for continuous variables and using contingency table analysis (chi-square test or Fisher exact test when appropriate) for categorical variables. All statistical analyses were performed using STATA, version 10.1 for Windows. Statistical test results were two-sided, and a p value of \u22640.05 was considered statistically significant.The data on survival was obtained from the medical records of the patients. Survival analysis was undertaken using the Kaplan-Meier method, with group comparisons using log-rank analysis. To identify the influencing factors related to survival, the clinicopathological factors, age, sex, hepatitis B virus status, preopCA19-9 (37\u2009U/mL), postopCA19-9 (37\u2009U/mL), tumor size (5\u2009cm), vascular invasion, perineural invasion, lymphatic invasion, intrahepatic metastasis, resection margin, lymph node metastasis, and adjuvant therapy, were analyzed by Cox's proportional hazard regression with forward stepwise technique. Demographics and clinicopathologic characteristics of the patients were compared between the groups using Student's The overall median survival time (MST) was 37.2 months and estimated rates of the overall survival at 1, 3, and 5 years were 72.2%, 51.5%, and 31.1%, respectively.p = 0.039) (p = 0.02) and had a tendency toward smaller tumors, less lymphatic invasion, less lymph node metastases, longer resection margins, and earlier T-stages, although statistically not significant . Table nificant .p < 0.001) (p = 0.034/p = 0.048) . Microva= 0.048) .p = 0.058) (p = 0.042) (p = 0.359).43 (58.1%) of the 74 patients recurred during follow-up period: 30 (69.8%) patients had intrahepatic recurrence, 4 (9.3%) had peritoneal dissemination, 3 (7%) had bone metastasis, 3 (7%) had lymph node metastasis, 2 (4.6%) had lung metastasis, and 1 (2.3%) had skin metastasis. Recurrence at resection site was observed in 11 of 30 patients with intrahepatic recurrence and rest of patients had hepatic recurrence at nonresection site. Of the 11 patients whose postopCA19-9 levels were still elevated, 9 recurred and died of the recurrence within 2 years . Of the 34 patients with normalized postopCA19-9 levels, 8 with elevated recurCA19-9 levels showed marginal survival difference from 10 patients with normal recurCA19-9 levels after resection . However= 0.462) . Perineu= 0.042) . Of the p < 0.01), persistently elevated postopCA19-9 levels , perineural invasion , narrow resection margin , and lymph node metastasis were significant independent risk factors for ICC survival . Although there is no consensus regarding the predictability of preopCA19-9 for patient prognosis, our study has shown that even slightly elevated levels (>37\u2009U/mL) appear to be associated with poorer outcomes. However, in our multivariate analysis, preopCA19-9 was not independent risk factor for survival. Furthermore, when we compared the clinicopathologic factors between patients with elevated and normal preopCA19-9 levels, patients with preopCA19-9 \u226437\u2009U/mL had a higher positivity of HBsAg (p = 0.017).Many authors have described the associations between elevated preopCA19-9 levels and poor outcomes, in biliary malignancy, using different value cutoffs. Jan et al. have reported that high preopCA19-9 levels >37\u2009ng/dL) significantly influence the overall survival of ICC patients after hepatic resection \u2009ng/dL si. In thisp < 0.001) [p = 0.002) [p < 0.001). Multivariate analysis also showed that persistently high postopCA19-9 was significant independent risk factors in ICC patient for overall survival. Therefore, postopCA19-9 may be more important factor in assessing the survival after resection, although preopCA19-9 concentration is important in the preoperative assessment of risk of survival. Moreover, high incidence of recurrence was observed in elevated postopCA19-9 compared with normalized postoperative levels. In group with persistently high postopCA19-9, 9 of 11 (81.1%) patients had recurrence after resection, while 18 of 34 (52.9%) patients with normalized postopCA19-9 had recurrence. Therefore, patients with high postopCA19-9 might be eligible for aggressive adjuvant chemotherapy and irradiation regardless of lymph node metastasis or resection margin status.We investigated changes in postopCA19-9 levels after surgery in patients with elevated preopCA19-9 levels. Although we assume that normalized postopCA19-9 would be favorable prognostic factor after curative resection of ICC, there is little information about changes in postopCA19-9 level for detecting ICC patients. On the contrary, some numerous studies on the relationship between pancreatic cancer and postopCA19-9 levels have been conducted to predict survival. Ferrone et al. reported that the strongest predictive levels of pre- and postopCA19-9 were 1,000 and 200\u2009U/mL, respectively [< 0.001) . Uenishi= 0.002) . In thisp = 0.058). Whereas half of patients with normal preopCA19-9 levels had recurrence, most of them still had normal CA19-9 levels. This indicates that a considerable number of ICC patients with normal preopCA19-9 have normal recurCA19-9 levels. Therefore, patients with normal preopCA19-9 levels should be closely followed up with other tumor marker tests as well as radiologic studies.We also investigated the relationships between recurCA19-9 levels and survival rates. In 34 patients with elevated preopCA19-9 and normalized postopCA19-9 levels, only 8 of the 18 recurrent patients had elevated recurCA19-9 levels. Normalized postopCA19-9 patients with normal recurCA19-9 levels had marginally better survival than those with elevated recurCA19-9 levels (MST = 14 versus 45, The results of this study are subjected to some limitations. This is a retrospective cohort review of patients undergoing radical resection. By design, our study was based on 10 years of experience with treatment of ICC. With advances in surgical techniques and chemotherapy, there may be an element of lead time bias; patients treated more recently may have better survival rates because of lessons learned from more experience, better adjuvant therapy, and better supportive care. Despite these potential weaknesses, perioperative CA19-9 change was significant, and thus we believe that these perioperative CA19-9 levels may be predictors for prognosis in ICC patients treated with surgical resection.Taken together, postoperative CA19-9 change is significant prognostic factors for predicting survival in ICC patients treated with surgical resection. Therefore, we suggest that this level should be measured in patients amenable to attempted curative resection. Moreover, postopCA19-9 level can be used to aid clinicians in the appropriate course of therapy. Because patients who do not have normalized CA19-9 levels postoperatively have shorter survival outcomes, accrual to clinical trials and continued or alternative therapy should be considered in such patients, even if radiographic evidence of disease is absent."} +{"text": "Rupture of SIA causes thunderclap headache but it remains unclear whether headache in general and migraine in particular is more prevalent in patients with unruptured SIA.In this case-control study we therefore estimate the prevalence of headaches in patients with SIA during 1 year before rupture.Prospectively 155 consecutive patients with SIA and 184 healthy blood donors received o purpose developed semistructured interview. Diagnosis were made according to the International Headache Society criteria. Aneurysms were diagnosed by conventional cerebral angiography.Headaches in patients with SIA before their diagnostics or rupture were revealed in 103 patients, therefore their 1-year prevalence was 61.6%. The mean duration of these headaches was 12.5 years, the mean age at the beginning of headaches was 30.2 years. These headaches included:migraine without aura(MO)-58(40.2%), migraine with aura(MA)-2(1%),tension type headache (TTH)-19(18.4%), cluster headache(CH)-2(1%), post-traumatic headaches(PH)-2(1%).1-year prevalence of headaches in controls was 32.5%(58 patients out of 184), they included:TTH-41(23.2%), MO-16(8.8%), PH-1(0.5%). Among this headaches in patients with SIA and controls only the prevalence of migraine was significantly (4.5times) higher in patients with SIA .This is the first study that convincingly shows a significant association between unruptured SIA and migraine.No conflict of interest."} +{"text": "HTLV-1 Associated Myelopathy/Tropical spastic paraparesis (HAM/TSP) is the classical neurological syndrome associated with this retrovirus, although other neurological complications are described. We collected data in the neurological and epidemiological databases related of the GIPH cohort, from 1997 and 2012, as well as in the records of the participants. Statistics involved a 95% confidence interval (CI). The main neurological outcomes presented by seropositive patients in the cohort were described and a comparison between groups of patients with and without HAM/TSP was performed with regard to other clinical manifestations. Among the 255 cohort participants examined by a neurologist, 233 (91%) were positive for HTLV-1 (CI 88-95%). From those, 12% had HAM/TSP (CI 8-16%), 20% had low back pain (CI 15-25%); 18% were diagnosed with depression, cramps and fatigue (CI 13-23%); 14% had myalgia (CI 10-18%); 13% had acute pain (CI 9-17%), 11% had urinary incontinence (CI 7-15%) and 10% had hearing loss (CI 6-14%). Comparing groups of patients with and without HAM/TSP, we found that symptomatic myelopathy patients had a greater chance of developing events such as urinary retention (RR= 9.8), gait abnormalities (RR= 7.3), constipation (RR= 6.7), urinary incontinence (RR= 5.0), sexual dysfunction (RR= 3.2), fatigue (RR= 2.9) and myalgia (RR= 2.7), when compared with asymptomatic to HAM/TSP (p<0.0001). In conclusion, 12% of patients developed HAM/TSP, which is a higher rate than that described in the literature. Furthermore, we found that patients with HAM/TSP had higher risk to develop other neurological outcomes related to this virus infection."} +{"text": "Sj\u00f6gren's syndrome is an autoimmune disease characterized by the presence of a lymphocytic infiltrate in the salivary and lacrimal glands, manifesting with xerostomia and xerophthalmia, which is more common in women between 30 and 50 years old, uncommon in children, with few cases reported in the literature.To describe the clinical and laboratory presentation of pediatric patients with Sj\u00f6gren's syndrome treated in primary Rheumatology Department of the Hospital Universitario Clementino Fraga Filho of the UniversidadeFederal of Rio de Janeiro, Brazil (HUCFF-UFRJ).26 child and adolescent patients were selected with diagnosis of primary Sj\u00f6gren's syndrome, treated in the Rheumatology Department of HUCFF-UFRJ. Patients were evaluated according to modified European criteria by the American-European Consensus .26 patients were included in the study: 20 girls (76%), 6 boys (24%), with mean age at diagnosis of 12.6 years (3-21 years). Patients were 16 years of age or younger at the onset of symptoms. Eight (30.7%) patients had parotid gland enlargement as the initial manifestation of the disease, with recurrent episodes in 2 (7.6%) patients. Ten (38%) had dry mouth complaint and 16 (62%) had ocular signs and symptoms, 18 patients (69%) had altered parotid ultrasonography, 19 patients (73%) had impaired salivary glandscintigraphy and 6 patients (23%) had abnormal parotid MRI. In 8 patients (30%) the minor salivary gland biopsy showed chronic sialadenitis compatible with Sj\u00f6gren syndrome. The analysis of serum autoantibodies, showed 8 patients (30%) positive for rheumatoid factor, 10 patients (38%) with Anti-Ro, 9 patients (34%) with Anti-La, 9 patients (34.6%) Anti-Ro and Anti-la and 18 patients (69%) with antinuclear antibody (ANA). 12 patients (46%) had arthritis. 7 patients (26%) had CNS involvement. 3 patients (11.5%) had vascular compromise. One patient (3.8%) showed tachyarrhythmia, leucopenia in 2 patients (7.6%), hypergammaglobulinemia in 8 patients (30%) and hypogammaglobulinemia in 1 patient (3.8%). With regard to treatment, 25 patients (96%) received hydroxychloroquine. Azathioprine was used in 4 patients (15.3%), methotrexate in 12 patients (46%), human immunoglobulin in 1 patient (3.8%), cyclophosphamide in 2 patients (7.6%), leflunomide in 1 patient (3.8%) and rituximab 2 patients (7.6%).This present study demonstrated the demographic, clinical, and therapeutic profile in a series of patients with Sj\u00f6gren's syndrome in children and adolescents, a relatively rare condition, presenting an overview of this population in our hospital.None declared."} +{"text": "CMR is increasingly used to diagnose myocarditis in adults but its use in pediatric-age pts is not well established. We sought to describe the clinical presentation, CMR imaging protocols, CMR findings, and outcomes in a multicenter cohort of children with myocarditis.A retrospective review was conducted among 12 institutions from 3 countries. All pts meeting the following criteria were included: 1) age < 21 years, 2) ultimate clinical diagnosis of myocarditis by the referring physicians, 3) CMR examination within 30 days of presentation, and 4) no congenital heart disease. Clinical data and test results, including CMR findings, were abstracted from the medical record.A total of 112 pts (median age 16 yrs (0-20)) met inclusion criteria. On echo at presentation, 22 pts (20%) had moderate or severe left ventricular (LV) dysfunction, and 20 (24%) had regional wall motion abnormalities. Endomyocardial biopsy was performed in 24 pts (21%), of which 12 were positive based on histology and 5 borderline. Percent of pts undergoing biopsy was similar across institutions (p = 0.32). Median time from presentation to CMR was 2 days (0-30), and 107 (96%) were inpatients. Sedation was used in 15 CMR studies (14%), and inotropic support in 16 (14%). Median LV ejection fraction (EF) was 56% (10-74) with 22% having EF < 45%. Median right ventricular EF was 55% (16-72) with 9% having EF < 40%. T2-weighted imaging (T2W) was performed in 71 studies (66%) and was abnormal in 49 (69%). First pass contrast perfusion (FPP) imaging was performed in 42 studies (45%) and was abnormal in 4 (10%). T1-weighted imaging for early gadolinium enhancement (EGE) was performed in 35 studies (37%) and was abnormal in 19 (51%). Late gadolinium enhancement (LGE) imaging was performed in all studies, and was abnormal in 93 (83%) with the following reported distributions: 89% subepicardial or midwall, 6% patchy, 3% sub-endocardial, 1% transmural, and 1% diffuse. The CMR study was interpreted as positive for myocarditis in 96 pts (87%), negative in 11 (10%), and equivocal in 4 (4%), yielding a sensitivity of 86% for an ultimate clinical diagnosis of myocarditis. There was significant practice variation in the use of T2W, FPP, and EGE imaging among the participating institutions (Figure This is the largest study to date describing the CMR findings in children with myocarditis. The CMR techniques used, from most to least common, were LGE, T2W, FPP, and EGE. Abnormalities were most often seen with LGE followed by T2W, EGE, and FPP. There was significant practice variation in the CMR protocol between institutions. The information from this study should be useful in planning a prospective study to evaluate the diagnostic and predictive performance of CMR in children with suspected myocarditis.None."} +{"text": "HCV Triple therapy opens new perspectives for HCV cure in HIV-HCV patients but data concerning the use of HVC DAA-PI in this patients in a real life setting are scarce. Our objective was to evaluate efficacy and safety of Telaprevir (TLV) and Boceprevir ( BOC) based- therapy in our cohort.We included HIV-HCV patients treated with Peg Interferon RIB (PR) plus TLV/BOC between 2011-2013 in a multicenter retrospective cohort. Demographic, clinical and imunologic characteristics were obtained, as well as adverse events and discontinuations. Treatment efficacy and safety data were collected at week (W) 4, 8, 12, 24 and 48 . Success if HCV-RNA became undetectable (PCRHVC-)72 weeks after the end of treatment (SVR). Failure if treatment was discontinued due to virologic failure (VF), adverse events (AE).31 patients were analyzed, 5 Naives and 26 re-treatments . All were Caucasian, 86% were male with a 49 years old\u2019s mean age. Mode of transmission of HIV& HCV was IUDV for 24 patients, MSM for1. Median CD4 counts 692. All were on HAART with undetectable Viral Load in 92%. Background HIV therapy contained in 51% raltegravir (RAL), 20% ritonavir-boosted atazanavir (ATV/r), 12% etravirine (ETV) 9% darunavir (DRV/r),6% lopinavir, efavirenz and rilpivirine. Tenofovir in 72%. Genotype 1a (n=20) or 1b (n=10) or 4 (n=1), METAVIR fibrosis stage was F3F4 in 55%, F2 in 32% and F0F1 in 13% of cases. HVC was treated with PR+ BOC (33%) or TLV (67%). 25 patients reached W72. PCRVHC- was observed in 54% of patients at W4, 67% at W12, 58% at W24 and 58% at W48. SVR was obtained for 58% and in 51% of cirrhotic patients. Six patients discontinued therapy for VF (n=1) or AE (n=5).Despite SVR increased with DAA-PI based therapy, treatment of HCV in HIV remains complex with multiple challenges, including high pill burden, higher rates of adverse events (AEs) and difficult drug-drug-interactions."} +{"text": "Juvenile dermatomyositis is a chronic inflammatory muscular disease that affects every year 1.5-3 children permillion and also produces systemic, skin, joint, digestive and respiratory manifestations.To describe the main epidemiological, clinical andanalytical aspects of Juvenile dermatomyositis diagnosed in La Fe Hospital .Patients diagnosed of Juvenile dermatomyositis in La Fe Hospital since June 1992 to March 2013. Dates are shown in median and interquartile range for non-parametric variables, and for parametric variables is given as mean and standard deviation. To assess response to treatment, we used Wilcoxon test for paired measures of non-parametric variables and t-student for parametric variables.We included 22 patients, 45.5% women, age at diagnosis 7.6 (3.7-10.8) years and evolution time 2.75 (1-5) months.The most frequent initial manifestation were muscle weakness (40%) and skin alterations (40%). Also constitutional symptoms (15%) and myalgia (5%). They presented muscle weakness (100%), heliotrope rash (100%), Gottron papules (90.9%), calcinosis (27.3%), other skin lesions such as telangiectasias, oral ulcers, livedo reticularis and purpura (55.5%), mialgia (55.5%), arthralgia (55.5%), arthritis (50%), constitutional symptoms (50%), esophageal involvement (31.8%), gastrointestinal (28.6%), Raynaud (18.2%), fever (27.3%), anasarca (18.2%), dysphonia (18.2%), and lung disease (18.2%).Patients were treated with corticosteroids, immunoglobulins and immunosuppressants such as methotrexate, tacrolimus, cyclosporine and antimalarial, alone or in combination, with significant improvement.CPK at diagnosis was 1114 UI/I (280-4952), and 73 (46-106) after 3 months, with significant improvement (p = 0.0010). Aldolase at diagnosis 15.45 U/L (12-37) and 6 (4-10)after 3 months (p = 0.0148). GOT at diagnosis 149 U/L (73-180) and 28 (25-38) after a year (p = 0.0005). GPT at diagnosis 102 U/L (44-187) and 23 (17-36) after a year (p = 0.0003). ESR at diagnosis 18 mm (16-36.5) and 13 (7-18) after a year (p = 0.0139). Strength at diagnosis was 2.5 \u00b1 1 and 4.25 \u00b1 0.87 after 3 months (p < 0.00001).Capilarocopy was realised in most of patients at diagnosis and showed pathological capillary patterns , with improvement in subsequent assessments.Dermatomyositis is a rare disease of childhood. Children we presented had muscle weakness and heliotrope erythema (100%) and in varying proportions Gottron's papules, calcinosis, Raynaud, artromialgias and general symptoms. We propose a comprehensive patient monitoring, assessing muscle strength and laboratory findings as CPK, aldolase, GOT, GPT and ESR but also by capillaroscopy. Capillaroscopy may be indicative of dermatomyositis outbreak, has diagnosis value and may observe an early improvement pattern when patients are in remission.None declared."} +{"text": "Health is defined by WHO as \u201ccomplete physical, mental and social well-being\u201d. Though the physical well-being is improved with antiretroviral therapy, it does not guarantee mental and social well-being. Hence we wanted to assess the Quality of Life (QOL) and to identify the factors that influences QOL in People Living with HIV/AIDS (PLHA)A cross sectional study of 141 adult PLHA attending the out patient department of a community care center in Chennai during the period from 1st January to 31st August 2011 were included in the study.QOL was evaluated using WHOQOL-HIV BREF questionnaire. Analysis: Mean Scores of QOL was calculated using SPSS syntax file developed by WHO, Geneva. The One way Analysis of Variance (ANOVA) was performed to find out significant difference between the socio-demographic variables and clinical categories on QOL domains.In study population 76 (53.9%) were males, 59 (41.8 %) were females and 6 (4.3 %) transgender. The overall QOL mean score on a scale of 0-20 was found to be 13.1. The mean scores of six domains of QOL in descending order were Spirituality/Religion/Personal beliefs (SRPB) (14.5); level of independence (LOI) (14.3); physical (13.3); environmental (12.5); psychological (12.3) and social relationships domain (11.7): . QOL in physical domain was high among transgenders (17.3) when compared with males (12.7), and females (13.7): (p=0.019). Social relationships domain scores between those who were single (11.5), married (12.8), and separated/widowed/divorced (10.9):(p=0.000). LOI domain was high among employed (14.5) than the unemployed (13.2): (p=0.028). Significantly better QOL scores in the LOI domain (15.2) (p=0.000) with respect to the CD4 count category. LOI domain better among patients without current history of tuberculosis (14.5) (p=0.008).In our study, QOL was associated with gender, marital status, employment status, CD4 counts of the patients and current history of tuberculosis."} +{"text": "In our unit, invasive breast cancer patients undergo axillary ultrasound and sometimes needle sampling with fine-needle aspiration or core biopsy for preoperative staging. Results triage patients to appropriate axillary surgery. We present a complete audit cycle. Between cycles 1 and 2, departmental guidelines were changed to include repeat preoperative biopsy in cases with suspicious ultrasound but negative biopsy result (LN4 and LN5 of an LN1 to LN5 node ultrasound grading system), and for patients with inconclusive biopsy results.The authors performed a retrospective analysis of multidisciplinary team meeting records of all invasive breast cancer patients operated upon from January 2010 to June 2010 (cycle 1), and from January 2012 to December 2013 (cycle 2). Descriptive statistics were performed.Initial audit (cycle 1): 125 female patients with 64% (921/33) overall combined sensitivity of ultrasound/needle biopsy and 100% (92/92) specificity. Re-audit (cycle 2): 676 female patients, axillary ultrasound performed in all cases. Needle sample performed in 52.8% (357/676) patients. Repeat needle sampling in 16% (57/357) patients: 77.2% (44/57) benign, 22.8% (13/57) malignant. Ultrasound sensitivity 79.1% (163/206), needle sampling sensitivity 76.1% (124/163). Overall combined sensitivity of ultrasound/needle sampling 59% (466/469). Overall combined specificity of ultrasound/needle sampling was 99.3% (466/469).The introduction of repeat preoperative lymph node biopsy guidelines did demonstrate node metastases that were not seen on initial node biopsy, increasing accuracy of triage to an appropriate axillary surgical procedure in those patients. Unfortunately this did not lead to an improvement in overall sensitivity of preoperative axillary staging between cycles."} +{"text": "About 10-20% of patients with familial Mediterranean fever (FMF) show an inadequate response to colchicine. Patients with colchicine-resistant FMF with or without AA-Amyloidosis can be treated with Interleukin-1 (IL-1)-inhibiting drugs.We report our experience in adult patients with colchicine-resistant FMF who were treated with anakinra or canakinumab.Demographic data, clinical and laboratory parameters, MEFV mutations, patient reported outcomes and physician global health were analyzed in 15 patients treated with anakinra or canakinumab.Within our cohort of 160 adult patients with FMF, we identified 15 patients who were treated with anakinra (n=13) or canakinumab (n=2). Twelve of 15 patients (80%) were of turkish-armenian ancestry. The median FMF severity score was 8 (range 5-14). Patients carrying two high-penetrance MEFV mutations (M694V or M680I) had a severity score of 9 (8/15=53%). Patients with a single high penetrance mutation had a severity score of 11 (3/15=20%). Four patients (4/15=27%) had no MEFV mutations and the FMF severity score was 7.5 (p=0.2). FMF-related AA amyloidosis was diagnosed in 6 patients (40%) and the median FMF severity score was 10 compared to a severity score of 7 in 9 patients without amyloidosis (60%) (p=0.3). Anakinra was used continuously in 13 patients and in 2 patients only during attacks. The number of FMF attacks was significantly reduced by anti-IL1 treatment (p=0.0024). The patient reported health and the physician reported global health were both improved significantly (pIL-1-blocking therapies are well tolerated and effective in patients with colchicine-resistant FMF. Blocking IL-1 reduced the number and severity of FMF attacks."} +{"text": "Light sedation is preferred for critical ill patients. We often use dexmedetomidine for light sedation, but sometimes additional sedative drugs(such as midazolam and propofol) is needed. Benzodiazepine is risk for delirium, but it is unclear benzodiazepine use combined with dexmedetomidine is risk for delirium.This prospective observational study was conducted in open ICU, urban hospital between February 2013 and March 2015. Adult patients intubated within 24 hours from ICU admission and underwent light sedation with dexmedetomidine was eligible. Exclusion criteria were: age < 18, stroke, cardiopulmonary arrest, neurosurgery, seizure, traumatic brain injury. We compared alternative sedative dug use with no additional drug. Primary outcome is delirium incidence.268 patients were eligible and 254 patients were analyzed. Median age (Q1-Q3) was 74 (66-81) years, 162 male(64%), median APACHE II score was 19 (15-23). 89 patients were administrated additional sedative drugs . Delirium was observed more frequently compared with dexmedetomidine alone, 41 (46%) vs. 51 (31%), p = 0.02. Additional sedative drugs were associated with prolong ICU stay (5 (3-8) days vs. 3 (2-4.5) days, p < 0.001) and decreased ventilator free days (25 (21-26) days vs. 26 (26-27) days, p < 0.001).Additional sedative drugs to light sedation with dexmedetomidine might be risk for delirium."} +{"text": "Anaemia is frequent in critically ill patients. Iron deficiency, secondary to blood losses or prior to admission, is in part responsible for this anaemia. Iron may thus be proposed to critically ill patients (CI). However, iron may promote oxidative stress, which is potentially deleterious. In a mouse model, we previously demonstrated that iron induces less oxidative stress in inflamed mice than in control ones , but no To compare the oxydative stress induced by an intravenous infusion of iron in CI and healthy volunteers (V).0-6) have been compared using a Wilcoxon test. Data are expressed as n(%), mean\u00b1SD or median[min-max].Adult critically ill patients (from 2 ICUs) and healthy Volunteers were included after informed consent. Blood samples were drawn before (T0) and 2, 6 and 24 hours after an intravenous infusion of 100 mg of iron sucrose (Venofer\u00a9) over 60 minutes. Markers of lipid oxidation -8\u03b1-Isoprostanes (8ISO)-, protein oxidation -Advanced Oxydized Protein Product (AOPP)- as well as glutathion reduced/oxidized (GSH/GSSG), Non-transferrin bound iron (NTBI) have been measured at these time points. Variations of area under the curves from T0 to T6 , but the \u0394AUC0-6h(8ISO) was not different . Only the \u0394AUC0-6h (GSH) was lower in V , arguing for a more important decrease in anti-oxidant defences. The table summarized all the results. Eight CI had a second set of dosages (after the 4th iron infusion) showing no difference in any markers compared to the first set of dosages.38 CI have been studied (25(66%) males, aged 67.9[19-85]yrs, 38(100%) ventilated, SAPSII 48.5[21-80], Hb 8.4[6.6-11.8] g/dl) and 39 V (18(46%) males, aged 42.1[21-78] yrs, Hb 13.9[11.9-17.2] g/dl). Iron treatment indications for CI were (many causes possible): 18(45%) elevated soluble transferrin receptor (sTfR), 14(35%) ferritin < 100 \u00b5g/l + TSat< 20%, 12(30%) blood loss > one blood mass, 9(22%) elevated sTfR/log Ferritin ratio. At TWe haven't seen any increase in lipid (8ISO) or protein (AOPP) oxidation in CI compared to V. On the contrary, V had a greater decrease in anti-oxidant (ie GSH), suggesting higher oxidative stress. Iron in the CI doesn't induce more oxidative stress than in V, but other studies are needed to confirm the absence of clinical toxicity."} +{"text": "Pain therapy settings often offer psychological interventions complementary to biomedical treatments . While aIn March 2015, we searched the Cochrane Central Register of Controlled Trials using the keywords \u201cpsychotherapy\u201d, \u201cchronic headache\u201d, \u201cneuropathic pain\u201d, and \u201cfibromyalgia\u201d. We excluded non-randomized studies and identified works involving psychotherapeutic approaches showing evidence of efficacy. We performed descriptive statistics over quantitative and qualitative data.Concerning neuropathic pain conditions, we found evidence for Cognitive-Behavioral Therapy (CBT) (2 studies), Psycho-education (PE) (2 studies) and Neuropsychological Rehabilitation 1 study). Regarding fibromyalgia, we found evidence for CBT (3 studies), PE (3 studies), Guided Imagery (GI) (3 studies), Strategic-Systems Therapy (Ericksonian) (2 studies), Brief Psychodynamic Therapy (1 study), Relaxation Training (RT) (1 study), Acceptance and Commitment Therapy (ACT) (1 study), Biofeedback (1 study), Mindfulness (1 study). We found evidence for CBT (4 studies), RT (3 studies), GI (2 studies), Biofeedback (1 study), ACT (1 study) in the treatment of chronic headache and psycho-physiological interventions integrated with psychotherapy models are useful in managing the considered forms of chronic pain."} +{"text": "Eosinophilic esophagitis (EoE) is a clinicopathologic entity defined by symptoms of esophageal dysfunction and histological eosinophil (eos) inflammation. Its patients (pts) commonly present concurrent reactivity to both food and aeroallergens, outlining the importance of an allergological evaluation.Clinical and sensitization profile description of the pediatric population with EoE diagnosis (EoEd) in our Immunoallergology Department.Retrospective study using the EoE database (Feb2009-Mar2014) of pts up to 18 years (yrs). Outcomes were characterization of demographic, symptomatic, laboratorial , endoscopic and histological features and sensitization profile (prick and patch tests).We included 24 pts [yrs)]; median age at EoEd: 7(1-14)yrs. Average between symptom onset and EoEd:19\u00b130 months. Average follow-up for 28 (5-60) months.Most frequent symptoms (%): dysphagia (54), impaction (50), GERD-like symptoms (42), abdominal and/or epigastric pain (42), vomiting (33). Most frequent onset symptom: dysphagia (46%). 96% of pts had prior history of atopy (p<0.001). Average peripheral Eos count 627cel/mL (170-1830) and total IgE 524kU/L (25-2798). At EoEd, the most common endoscopic finding were furrows(79.2%). Histologically 29% had>40eos/High Power Field and 33% had microabcesses (which were more frequent in patients with impactation [p<0.1]).After EoEd, 96% had confirmed allergy with 92% to aeroallergens (p<0.01) and 75% to food (P=0.023).The main allergens were(%): food ; mites (75); pollens (54.2).After a 12 month therapy, all had symptomatic improvement; with 8.3% achieving biopsy normalization.Of those with pre-EoEd allergenic testing, all had acquisition of new sensitizations after EoEd.The first and the most frequent symptom was dysphagia. The prevalence of allergic sensitization was >95%. The potential clinical severity of EoE justifies the multidisciplinary evaluation for clinical, diagnostic and therapeutic workup."} +{"text": "Environmental factors, such as atmospheric pollution, may trigger the inflammation in adult systemic lupus erythematosus (SLE) patients. However, the role of atmospheric pollution and disease activity in childhood-onset systemic lupus erythematosus (C-SLE) population was not reported at this moment.To investigate the association between changes in daily concentrations of air pollutants in S\u00e3o Paulo metropolitan region and disease activity in C-SLE patients.10), sulfur dioxide (SO2), nitrogen dioxide (NO2), ozone (O3) and carbon monoxide (CO). Meteorological variables, such as the minimum temperature and relative humidity, were obtained from the Institute of Astronomy and Geophysics of the University of S\u00e3o Paulo. Generalized estimation equation (GEE) model were used for binomial distribution to assess the impact of these measurements in the SLEDAI 2K score, considering the fixed effects for repetitive measurements, and adjusted for erythrocyte sedimentation rate, C-reactive protein, prednisone and/or immunosuppressant use, presence of infection 20 days before the medical appointment, minimum temperature and relative humidity. The results were expressed in relative risk (RR) and confidence interval (CI) of 95%.This was a longitudinal panel study including 410 consecutive medical visits in 22 C-SLE patients (ACR criteria). They were followed at the Pediatric Rheumatology Unit, Children's Institute, Faculdade de Medicina da Universidade de Sao Paulo, Brazil, between 2005 and 2010. Disease activity was evaluated according to Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2K), and the patients were divided arbitrarily in two groups: with disease activity (SLEDAI>8) and without disease activity (SLEDAI<8). The S\u00e3o Paulo State Environmental Agency (CETESB) provided daily concentrations of inhaled particulate matter (PM10 (25.2 \u03bcg/m3), CO (0.8 \u03bcg/m3), and NO2 (102 \u03bcg/m3) were associated with increases of 1.74 (CI of 95% 1.28-2.39), 1.37 (CI 95% 1.12-1.67) and 1.11 (CI 95% 1.02-1.21) in the risk of SLEDA-2K score score>8), respectively, 13 days after the exposure to these pollutants. The four days PM10 cumulative effect (from lag13 to lag16) increased the risk of outburst of SLE in 65% (CI 95% 1.06- 2.75). In contrast, ozone and SO2 did not show a significant effect on the SLEDAI-2K score.410 consecutive medical visits were evaluated in 22 C-SLE patients (20 girls), with a mean of 19 visits/patient (4-30). The mean current age at the time of evaluation was 15.3 years (10.8-19.0). The mean age at C-SLE diagnosis was 10.3 years (6-12) and the mean age at disease duration was 5.3 years (7 months-11 years). Interquartile range increases of PMVariations in air pollution may influence disease activity in C-SLE patients. Therefore, oxidative stress may be an important trigger of inflammation in this systemic autoimmune disease.None declared."} +{"text": "Kawasaki disease(KD) is an autoimmune disease and one of the most common vasculitis of childhood, it has many clinical manifestation but most serious effect is on the heart where it can cause severe coronary artery aneurysms in untreated childrento shade light on our experience on clinical Presentation, management and outcome of KD.Sitting: all medical department of Benghazi children hospital.)) Subject: all the patients who diagnosed as KD during study period(from Jan 2009-dec 201 2).Retrospective descriptive case series study.data collected by reviwing their admission files.There are 28 patient diagnosed as KD during study period.Male to female ratio 2.1:134% of the cases are atypical KD.. 79% below 5 years of age...Peak admissions in October, November, DecemberThe frequency of clinical criteria for diagnosis of KD:Fever in all the patients (mean duration of fever before admission 8 days), oropharyngeal changes 22 (78%), extremity changes 21 (75%) cervical lymphadenitis 20 (71%), skin rash 18(64%). conjunctivitis 16 (57%).Other associated symptoms and signs: vomiting 13(46%), diarrhea 11(40%), cough 8(29%), arthritis 2 (7%), hepatomegaly were present in 4(14%), splenomegaly 2 (7%), jaundice 2(7%) no case with meningitis.Echocardiogram done in 26 patients, 17 (69%) normal, 9 (31%) abnormal coronary arteries.Regarding treatment: 18 patients receive sandglobulin; aspirin received by 18 patients during admission. no patient receive steroids.7 patients diagnosed in late stage and 3 patients left LAMA.Antibiotics used for 17 patients.we have significant delay in diagnosis and high rate of coronary aneurysm.None declared."} +{"text": "Daily multidisciplinary clinical rounds involving physicians, nurses, respiratory therapists, nutritionists and clinical pharmacists improve the quality and outcomes of ICUs . HoweverTo address the characteristics and the main interventions proposed and made during multiprofessional clinical rounds performed in a clinical-surgical open ICU.This observational study was conducted in a 41-bed open clinical-surgical ICU of a tertiary-care, private hospital in S\u00e3o Paulo, Brazil. From February 20 through March 28 2013, demographic data, SAPS 3, the participants of the ICU clinical rounds, the number and type of the proposed interventions, and the number of performed interventions by the multidisciplinary team were recorded and analyzed.A total of 158 clinical rounds were included in this analysis. Fifty-four percent (85/158) of the patients were male with median (IQR) age of 73 (60-84) years and SAPS 3 score of 52 (44-65). The multidisciplinary team was composed of a senior physician (157/158 (99%)), nurses (157/158 (99%)), an on-call staff physician (150/158 (95%)), respiratory therapists (149/158 (94%)), a clinical pharmacist (89/158 (56%)) and nutritionists (62/158 (39.2%)). The median (IQR) number of interventions proposed during the multidisciplinary rounds was 1 (0-2) and the number of performed interventions was 1 (0-2) (Table 1). Interventions were more frequently proposed by senior physicians (82/158 (52%)) followed by respiratory physiotherapists (43/158 (27%)) and a clinical pharmacist (29/158 (18%)).In our open ICU model where decisions should be shared with assistant doctors, the implementation of daily clinical rounds was associated with an intense participation of the multidisciplinary team and with a high level of performance of the proposed interventions. These actions are probably associated with better care of the critically ill patients. However, further studies are needed to correlate such interventions with clinical outcomes."} +{"text": "IgE mediated allergy to fish is a cause of severe anaphylatic reactions. Parvalbumins are considered major fish allergens and also responsible for cross-reactivity.Evaluation of tolerance acquisition using the recombinant fish parvalbumin (Gad c 1) in a group of fish allergic patients (pts).\u00ae, Thermo-Fisher). Oral food challenge was performed to evaluate fish tolerance acquisition. Statistical analysis was performed using GraphPad Prisma version 5.0 . Two groups were compared using a paired t test Wilcoxon. P values<0.05 were considered significant.We selected 55 pts . All had fish allergy, characterized by positive clinical history, skin-prick tests and serum specific IgE to several fish and Gad c 1 (UniCapp=0.15. 38/55 (69%) pts were intolerant and 17/55 (31%) pts tolerated at least one fish species. Gad c 1 average values were significantly higher (21.6 KU/L) in the intolerant group than in the partially tolerant group (2.7 KU/L); p=0.009. 24/38 pts were followed for at least one year, on average 3.7 years. 14/24 pts developed fish tolerance to at least one fish species-Group I and 10/24 were intolerant-Group II . Group I showed lower average values (4.6 KU/L) of Gad c 1 than the Group II (25.1 KU/L); p=0.0001.The 55 fish allergic pts had clinical symptoms for more than one fish species: 43 (78%) pts had skin manifestations, 12 (22%) anaphylaxis, 8 (15%) respiratory and 9 (16%) gastrointestinal symptoms. Pts who suffered anaphylaxis had lower Gad c 1 average values (31 KU/L) than the others (76.7 KU/L); Lower Gad c 1 values seem to be an important predictive parameter in fish tolerance acquisition but not in predicting clinical symptoms\u2019 severity and might be considered a useful tool in the follow-up of fish allergic patients."} +{"text": "Escherichia coli is a commensal bacterium that is frequently associated with multidrug-resistant zoonotic and foodborne infections. Here, we report the 5.6-Mbp draft genome sequence of an E.\u00a0coli recovered from poultry, which encodes multiple acquired antibiotic resistance determinants, virulence factors, pathogenicity determinants, and mobile genetic elements. Escherichia coli is the most prevalent commensal microorganism of the human and animal gastrointestinal tract, remaining one of the most frequent causes of bacterial infections worldwide . Libraries were prepared from 1\u00a0ng of genomic DNA using the Nextera XT DNA sample preparation kit according to the manufacturer\u2019s instructions. Whole-genome sequencing (WGS) was performed using 150-bp paired-end reads on a MiSeq (Illumina). Sequence reads were then trimmed and filtered according to quality criteria and assembled de novo using CLC genomics workbench version 8.0 (Qiagen). The NCBI prokaryotic genome automatic annotation pipeline (PGAAP) was used for annotation. PathogenFinder 1.1, ResFinder 2.1, VirulenceFinder 1.4, SerotypeFinder 1.1, and MLST 1.8 were used to estimate pathogenicity determinants, antibiotic resistance genes, virulence factors, multilocus sequence type (MLST), and serotype of this isolate, respectively (5ctively 58.E.\u00a0coli INSLA289 was assembled de novo into 300 contigs (each >200\u00a0bp long), which together comprised 5,584,816\u00a0bp. Global results indicated a GC content of 50.6%, an average coverage of 175.2, and an N50 of 99.169\u00a0bp. The largest obtained contig was 444,397\u00a0bp, presenting a coverage of 131.7-fold. The obtained contigs were searched against the GenBank database nucleotide collection (nr/nt) using Megablast. Globally, a total of 70 contigs matched multiple plasmid sequences therein deposited.The draft genome of the blaCTX-M-1 (contig 77), blaSHV-12 (contig 179), blaTEM-116 (contig 193), aadA1y (contig 20), aph(3\u2032)-Ic (contig 172), strA and strB (contig 172), sul2 (contig 72), dfrA1 (contig 20), tetA (contig 188), tetB (contig 99), and sat2 (contig 20). This ST57 E.\u00a0coli isolate also carried an IS10-disrupted In2-4 class 2 integron, where dfrA1, sat2, and aadA1y were accommodated, resulting in the disruption of the attI2 integration site. Seven virulence factors were also detected, cma (contig 154), ireA (contig 98), prfB (contig 9), ioN (contig 89), tsh (contig 86), iss (contig 89), and iha (contig 20). Moreover, the isolate expressed serotype O86:H25 and displayed a prediction of 91.4% for being a human pathogen.ResFinder 2.1 (90% identity and 40% minimum length) enabled the detection of 12 antibiotic resistance genes, E.\u00a0coli isolates.This draft genome sequence constitutes a valuable resource for international genomic comparison studies and may be helpful for identifying genomic traits associated with the zoonotic potential of multidrug-resistant LHAT00000000. The version described in this paper is version LHAT01000000.This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number"} +{"text": "Rapid and sustained efficacy of canakinumab (CAN) were previously demonstrated in patients with systemic juvenile idiopathic arthritis (SJIA) . HoweverTo evaluate the long-term efficacy and safety profile of CAN-na\u00efve SJIA patients with and without SJIA-associated fever.patients aged 2-20 years with SJIA with and without SJIA associated fever at enrollment received open-label CAN 4mg/kg s.c. every 4 wks. Every 3 months, response to CAN was measured by adapted JIA ACR response criteria (aACR/JIA); juvenile arthritis disease activity score (JADAS); clinical inactive disease; clinical remission on medication . Safety was assessed monthly.Data on 122/267 patients, 53 (43%) with and 69 (57%) without SJIA associated fever, were available for analysis with a median 94 wk study duration. At Wk4, ~75% of both subgroups had responded (\u2265 aACR/JIA30), increasing to 90% at Wk12. At Wk2, ~21% of both subgroups had inactive disease; 44% at Wk8; 60% at Wk20 and then 60-70% for the remainder of the trial. CRM was achieved in about 29% of patients in both subgroups with ~22% maintaining it for \u226512 consecutive months. At baseline, the median JADAS score was 21.5 with 8 (7.5%) and 99 (92.5%) patients meeting the criteria for moderate (JADAS >3.8 and \u226410.5) and high disease activity (JADAS >10.5), respectively. At Day 15, the median JADAS was 6.8 and 1.5 at the last assessment. At the last assessment, 53 (48%) patients had inactive disease (JADAS \u2264 1); 10 (9%) with low active disease activity (JADAS >1 and \u22643.8); while 14 (13%) had moderate and 31 (28%) with high disease activity. Infection (0.56 infections/100 patient-days), typically involving upper respiratory tract was the most common type of adverse event. Fifteen patients discontinued due to an AE and 40 had >1 SAE , or flare-associated) and no deaths. Eight cases of MAS (0.013 events/100 patient-days) were reported.Canakinumab provides similar efficacy in SJIA patients with and without SJIA-associated fever at treatment onset. The long-term safety profile was acceptable and similar to the pivotal program in SJIA children with fever at enrollment."} +{"text": "Late Gadolinium enhancement represents a widely employed method for detecting myocardial scarring e.g. after myocardial infarction or for myocardial Inflammation. A frequent finding is slight basal septal enhancement as well as intramyocardial enhancement, mostly referred as myocardial fibrosis. Less is known about the impact on myocardial conduction and a possible correlation to ECG findings such as atrioventricular node conduction delay and bundle branch blockations.For 81 consecutive patients referred for magnetic resonance cardiac (MRI) including a late gadolinium enhancement study scans were anonymized and correlated to an ECG performed within one week before or after the MRI. A 1.5T Siemens Sonata with TIM upgrade was used. Scanning protocol comprised short- and long axis cine mode and a perfusion study with Gd-DOTA and/or T1 and T2 TSE as well as 2d and 3d IR short axis sequences for late enhancement. The latter was analysed visually for the study by two experienced operators and subdived as (1) normal, (2) intramyocardial fibrosis, (3) subendocardial or transmural ischemic scar and (4) bright acute inflammation or postmyocardial subepicardial enhancement pattern. The ECGs had been re-evaluated by an experienced cardiologist.The baseline data between the 4 groups was similar :group 1 : 30 patients (37%), LVEF 62% (17-79%), EDVI 73ml (40-222ml), ventricular septum thickness (IVS) 11mm, age 57yrs;group 2 (fibrosis): 30 patients (37%), LVEF 58% (20-76%), EDVI 72ml (45-142ml), IVS 13mm, age 68yrs;group 3 (ischemic scar): 15 patients (19%), LVEF 51% (30-76%), EDVI 82ml (36-152ml), IVS 11mm, age 69yrs;group 4 (myocarditis): 6 patients (7%), LVEF 55% (42-71%), EDVI 82ml (57-122ml), IVS 10mm, age 44yrs.Atrial fibrillation was present in 10%, 20%, 27%, and 0% respectively.ECG findings are presented in Table Abnormal ECG findings such as AV conduction delay and bundle branch blockation are significantly correlated to myocardial scarring or fibrosis in late enhancment studies.None."} +{"text": "Beh\u00e7et's disease (BD) is rare in childhood and remains challenging in diagnosis and lack of evidence-based data for its treatment. Hence there is an urgent need to understand the scope of the disease in children.The aim of this study is to describe the clinical spectrum and the therapies used to treat children with Beh\u00e7et's disease (BD) in children.P = 0.044). The majority of children were treated with colchicine (74%) and corticosteroid (41%). Anti TNF-a treatment was reserved for severe and/or refractory cases (15%). There was a median of 2 (range 0-12) episodes of oral ulceration per year after the treatment. Interestingly only 10 patients fulfilled The International Study Group (ISG) BD diagnostic criteria.46 patients were identified with a positive family history of BD in 6 cases. Age of onset was 4.87 (0.04-15.71) years with a time to diagnosis of 3.74 (0.25-13.48) years. The main clinical features at presentation were: recurrent oral ulceration (87%), genital ulceration (20%), cutaneous symptoms (11%), fever (30%), gastrointestinal symptoms (26%), musculoskeletal (22%). uveitis (2%). Recurrent genital ulceration was significantly more common in female patients (P = 0.044). The majority of children were treated with colchicine (74%) and corticosteroid (41%). Anti TNF-a treatment was reserved for severe and/or refractory cases (15%). There was a median of 2 (range 0-12) episodes of oral ulceration per year after the treatment. Interestingly only 10 patients fulfilled The International Study Group (ISG) BD diagnostic criteria.46 patients were identified with a positive family history of BD in 6 cases. Age of onset was 4.87 (0.04-15.71) years with a time to diagnosis of 3.74 (0.25-13.48) years. The main clinical features at presentation were: recurrent oral ulceration (87%), genital ulceration (20%), cutaneous symptoms (11%), fever (30%), gastrointestinal symptoms (26%), musculoskeletal (22%). uveitis (2%). Recurrent genital ulceration was significantly more common in female patients (Although most cases were diagnosed in late childhood the first presentation was as early as 1 month old. Delay in diagnosis due to incomplete presentation in certain cases. Oral ulceration was the most common presenting symptom. Uveitis was less frequent than previous series. A range of drugs was used including biologic therapy for severe cases.None declared."} +{"text": "Pulmonary contusion (PC) is common after blunt chest trauma, leads to inhomogeneous lung injury and can result in acute respiratory distress syndrome (ARDS) . StrategTo study the effects of the ARDSnetwork lower PEEP (ARDSnet) 2O, 10 breaths), respiratory rate 80/min, I/E 2:1, TV< 6 ml/kgBW, positive inspiratory pressure (PIP) \u226430 cmH2O. Total PEEP of approx. 19 cmH2O resulted from development of intrinsic PEEP on top of external PEEP of 10 cmH2O. Cardiorespiratory, gas exchange and extra-vascular lung water parameters were measured. Electrical impedance tomography was used to assess changes in lung ventilation (Vent). Vent was calculated as the number of pixels showing an impedance change of >15% of the global impedance change and expressed as % of baseline. Data are given as median and interquartile (25th-75th) range. Mann-Whitney-tests and General Linear Model statistics were used.Pigs (n=16) were anesthetized, tracheotomized and received MV. Catheters were placed aseptically. Cefuroxime 750mg was given IV q6h. Unilateral PC was induced by a 10 kg weight dropped from 1.85 m height on a predefined location of the right chest. Chest tubes were inserted on both sides. Conditions comparable to an ICU were established. At 90 min after PC (post-PC) pigs were randomized to 24 hours of MV using ARDSnet (n=8) or OLC (n=8). Pressure controlled MV in the OLC group involved: an initial recruitment maneuver (50 cmH2O) vs. OLC 19 (17-21) cmH2O). PaO2/FIO2 (477 (296-514) vs. 87 (72-118) mmHg) and static compliance were significantly higher in OLC (Tab.1). Intrapulmonary shunt (28 (27-36) vs. 11 (8-18) %), PaCO2 (46 (43-63) vs. 43 (33-45) mmHg), TV (7 (7-7) vs. 5 (5-6) ml/kg BW), driving pressure (deltaP) and EVLW were all significantly higher in ARDSnet after 24 hours, whereas Vent was significantly lower (Table 2O vs. ARDSnet 34 (29-38) cmH2O) was not statistically significant.Cardiorespiratory conditions were stable without significant between-group differences at pre-PC and post-PC. At 24 hours after randomization PEEP was significantly lower in ARDSnet (8 5-10) cmH0 cmH2O) OLC ventilation better fulfilled common criteria for lung protection, because it facilitated MV with lower TV, deltaP, less edema (EVLW) and better lung function. It also prevented progressive derecruitment (decrease in Vent) during lung protective ventilation."} +{"text": "Continuous near-infrared spectroscopy (NIRS) has been used to assess adequacy of cerebral oxygenation following stroke, traumatic brain injury and subarachnoid haemorrhage [15O PET within healthy volunteers.The gold standard technique for imaging cerebral blood flow (CBF) and metabolism is 15O PET with arterial sampling was performed to measure CBF, cerebral metabolic rate of oxygen (CMRO2), oxygen extraction ratio (OEF) and cerebral blood volume (CBV) [2 and an assumed arterial/venous blood volume ratio of 30/70 [Fifteen healthy subjects were recruited ; PET precluded females of reproductive age. Steady-state 15O PET CBF, CMRO2, OEF and CBV were mean (SD) 44.9 (10) ml/100 ml/minute, 158.7 (24.7) \u03bcmol/100 ml/minute, 45.8 (7.3)%, and 2.8 (0.8) ml respectively, and there was no relationship between NIRS and 15O PET (Figure The frontal region 15O PET. Further studies should assess the dynamic response of NIRS to a measured change in physiology in patients. Further confines of NIRS include its limited and focal brain coverage.We found no relationship between NIRS and baseline physiology as determined by"} +{"text": "Systemic lupus erythematosus (SLE) is a multisystem disease of autoimmune etiology, which carries a high morbidity and mortality.To describe clinical and immunoserological features at the time of diagnosis within a cohort of pediatric patients attending the service of rheumatology of a Colombian pediatric hospital.Cross-sectional study. 89 patients with diagnosis SLE (1986 ACR criteria) from a rheumatology center at a pediatric hospital were evaluated. Medical records were reviewed registering the following variables: sex, mean age, score SLEDAI, organ involvement, current pharmacological treatment and autoimmune profile. Descriptive analysis was done for qualitative and categorical variables (percentages and averages) using STATA11.76 patients (85.4%) were female and 13 (14.6%) were men. Mean age 11.3 y/o (min 2 max 16). Median score SLEDAI at onset was 23 (min 4 max 61). Organ involvement: Renal 75 patients , hematologic 75 , skin 60 , neurolupus 26 , serositis 17 , arthritis 50 , Raynaud 8 , photosensitivity 34 . Current pharmacological treatment: antimalarials 80 (93%), Azathioprine 57 (64%), Cyclophosphamide 33 , Mycophenolate Mofetil 8 , Rituximab 4 , Cyclosporine 1 . Autoimune profile: Antinuclear antibodies (ANAs) reactivity 74 , Anti-DNA antibodies 56 , Antiphospholipid antibodies (aPL) 25 .The demographic characteristics and laboratory tests of this cohort are according to previously reported in worldwide and latin American literature. The score SLEDAI at the diagnosis was found in median activity. The most common medications prescribed were antimalarials followed by azathioprine and cyclophosphamide.None declared."} +{"text": "Although hepatotoxicity related to antiretroviral treatment (ART) has become less frequent, hepatotoxic events, such as transaminase elevations (TE), are still a matter of concern. RPV/FTC/TDF (EPA) is a new single tablet regimen which is widely used in real life practice. Clinical trials showed an adequate profile of liver safety in the sub-population of HIV/HCV-coinfected patients receiving rilpivirine. However, the number of individuals included in these analyses is low . The aimThis is a retrospective analysis of HIV/HCV-coinfected subjects who started EPA at the infectious diseases units of 14 centres throughout Spain, included as cases. Subjects who started an ART different to EPA during the study period at the same hospitals were selected as controls. The primary outcome variables were grade 3 or 4 TE and grade 4 TBE.Of the 191 patients included, 31 (16.2%) subjects were na\u00efve to ART. Eighty-seven individuals started EPA and the remaining ones were controls. The most common NRTI backbone among the controls was TDF/FTC [59 (56.7%) patients] followed by NRTI-sparing regimens [24 (23.1%) individuals] and ABC/3TC [17 (16.3%) subjects]. Among controls, 67 (64.4%) started a ritonavir-boosted protease inhibitor, mainly DRV/r [41 (39.4%) patients] followed by ATV/r [16 (15.4%) subjects]. EFV, ETV and RAL were started in 16 (15.4%), 12 (11.5%) and 13 (12.5%) subjects, respectively. The median (Q1\u2013Q3) follow-up was 5.79 (3.65\u20138.61) months for the cases and 11.44 (5.8\u201312.88) months for the controls. TE was observed in two (2.3%) cases versus five (4.8%) controls (p=0.358), accounting for a density of incidence of 4.32/100 person-years versus 5.51/100 person-years . All TE were grade 3 and no patient discontinued ART due to TE. None of the cases developed TBE versus four (3.8%) controls, all of them receiving ATV/r.The frequency of grade 3\u20134 TE associated with EPA in HIV/HCV-coinfected patients under real life conditions is very low. In addition, TE in HIV/HCV-coinfected patients treated with EPA are usually mild and do not lead to treatment discontinuation. TBE was not seen in patients taking EPA. All these data confirm that EPA is safe in this particular subpopulation."} +{"text": "N = 1) and 2) aspartate aminotransferase (AST) \u2265 1,000 IU/L . Of 143 patients, 118 (82.5%) had \u2265 1 warning sign : mucosal bleeding 66/143 (46.1%), soft tissue edema 54/143 (37.7%), and ultrasound detected plasma leakage 30/129 (23.25%). 138 (96.5%) patients received intravenous (IV) fluids: 3 L (IQR: 0.5\u20138.5 L). Most patients had non-severe dengue with warning signs. High rates of edema and plasma leakage may be explained partly by liberal use of IV fluids. Studies are needed on optimizing fluid management in non-severe adult dengue.Knowledge of adult dengue virus (DENV) infection from Hanoi, Vietnam, is limited. In 2008, we prospectively studied 143 confirmed adult dengue patients of median age 23.5 (range 16\u201372) years. They were admitted to the National Hospital for Tropical Diseases, Hanoi, on median illness day (D) 5 (range 1\u20138). By D8, 141 (98.6%) were afebrile. Platelet counts and hematocrit nadired and peaked on D5 and D4, respectively: 40,000/\u03bcL , 43.4% (34.9\u201349.7%). Four (2.8%) patients had severe dengue: 1) D10 shock ( Aedes mosquito. Most dengue infections are asymptomatic,7Serotypes 1\u20134 of the dengue flavivirus cause dengue, a predominantly tropical infection transmitted to humans by the In 2009, updated World Health Organization (WHO) guidelines classified dengue as severe or non-severe to reflect its changing clinical epidemiology better.12Box 1Common dengue-induced laboratory changes include thrombocytopenia, leukopenia, atypical lymphocytes, immature neutrophils, raised hematocrit (Hct) and liver enzymes, mild increases in prothrombin time (PT) and activated partial thromboplastin time (aPTT), and increased fibrinolysis.17In Vietnam, all four dengue serotypes are transmitted.24Given the importance of adult dengue in Hanoi and the lack of data describing its clinical and laboratory features, we conducted the observational study reported herein, classifying patients according to the 2009 WHO criteria.8The study took place from September to November 2008 at the National Hospital for Tropical Diseases (NHTD), in Hanoi, an adult tertiary referral hospital. Admission numbers for clinically suspected dengue have varied from < 100/year to up to 5,000 in 2009 (NHTD data). In an earlier analysis, our patients had DENV serotypes 1 (32%) and 2 (30%), and serological findings were consistent with primary and secondary infections in 34% and 61% patients, respectively.19Patients were enrolled into the study if they gave signed, informed consent and had clinically suspected dengue,Patients were managed by their attending physicians in the general infection ward. Enrolled patients underwent 1) history, 2) daily physical examinations, 3) 8 hourly pulse, blood pressure (BP), and axillary temperature (fluid input\u2013output measurements were not done routinely), 4) a tourniquet test in patients without bleeding signs , 5) daily full blood count, 6) routine biochemistry , 7) aPTT , 8) PT (NR: 70\u2013140%), 9) fibrinogen (NR: 1.75\u20134 g/L), 10) dengue viral load and serotype by polymerase chain reaction (PCR), as previously reported,Treatment included encouraging oral intake, intravenous (IV) fluids and platelet transfusions. National guidelines suggest platelet transfusions if either the platelet count is < 50,000/\u03bcL with significant bleeding or the platelet count is < 5,000/\u03bcL. Patients were discharged and asked to return for follow-up for convalescent clinical and laboratory assessments.Serological samples were positive for IgM or IgG if the optical density (OD) units were \u2265 6 times higher than the negative control sera ; all other results were classed as negative including \u201cindeterminate\u201d ratios of 8\u2013< 12.Confirmed DENV29Highly suggestive/probable dengue infection was diagnosed if consistent clinical features were present and if paired serological tests showed one of the following: 1) static IgM titers, 2) an increase of IgM titers < 20%, 3) declining IgM titers when the convalescent sample was taken before illness D14, and 4) paired IgG titers showing a < 4 fold rise in titer. A single IgM positive serological sample was considered unclassifiable.See Introduction and 2 or Fisher's exact test, continuous data by student's t test or Mann\u2013Whitney U (skewed data) test, as appropriate.Data were recorded onto a case record form (CRF), double entered into Microsoft Access 2003 , and analyzed with Access and Stata v9 . Trends in clinical and laboratory data are shown by illness day; D1 is the first day of reported fever. Proportional data were analyzed by two-sided \u03c7Of the 206 patients screened, 158 were enrolled: 1) 143 were dengue confirmed, 2) 5 had highly suggestive/probable dengue, and 3) 10 did not have dengue. The NS1 antigen test was positive in 96/158 (60.7%) patients and DENV PCR was positive in 81/158 (51.3%), together accounting for 110/143 (76.9%) confirmed dengue diagnoses. The IgM and IgG antibody responses varied and were similar between the NS1 and PCR positive and negative groups . In the The majority of patients came from Hanoi and their median age was 23.5 years; just over half were males. Patients were admitted to hospital on illness day D1\u20138 (median 5) and remained in hospital for a median of 5 days; 13 (9.1%) patients were hospitalized for > 1 week.P = 1).Prior to admission, 107/118 (90.7%) patients had received a variety of drugs, usually paracetamol, vitamins, and antibiotics and 70/115 (60.9%) had received IV fluids; 32/127 (25.2%) had been transferred from another hospital. Admission symptoms and signs are detailed in Supplemental Table 1.The number of patients in the study by illness day is shown in N = 90) versus no warning signs (N = 17): 38,000 versus 67,000/\u03bcL (P = 0.0046) and 2) mucosal bleeding (N = 49) versus no mucosal bleeding (N = 58): 37,000 versus 47,500/\u03bcL (P = 0.037).Nadir or peak median values of hematologic and biochemical parameters occurred generally between D4 and D6 , Table 2The highest median Hcts were recorded on D4, 43.4% (IQR: 34.9\u201349.7%), D5, 43.3% (IQR: 35\u201350.9%), and D6, 43.1% (IQR: 33.8\u201349.8%); in individual patients, peak Hcts were on D5 (IQR: 4\u20137). Most aPTTs and PTs were within normal limits but median times trended upward, peaking on D5 and D7, respectively . Median The median total white cell count showed leukopenia for the first 5 days. Absolute lymphopenia was detected at least once in 76/143 (53.1%) patients, most frequently during the first 5 illness days . AbsolutAST and ALT values varied widely . The higN = 42/143 [29.4%]); persistent vomiting ; edema of face, hands, or feet ; mucosal bleeding (N = 66 (46.2%): nose/mouth (N = 35), subconjunctival (N = 35), vagina (N = 16); lethargy ; and a palpable liver . Ultrasounds, performed in 129 patients, detected 30 (23.3%) with ascites alone (N = 9), a pleural effusion alone (N = 14), or both (N = 7) from D4 to D14, median 7 (IQR: 5\u201311). The risk of developing ultrasound detected plasma leakage was 3.5-fold higher in those who received preadmission IV fluids (22/70 [31.4%]) versus those who had not (4/45 [8.9%]), but the median IV fluid volumes administered during admission were similar (P = 0.31) in patients with and without plasma leakage: 3 and 3.2 L, respectively. Patients with concurrent rising Hcts and declining platelet counts numbered 17 (11.9%).Of the 143 patients, 122 had at least one dengue warning sign: abdominal pain or tenderness (N = 1), lethargy (N = 1), and a pleural effusion (N = 1). No patients had severe bleeding, reduced consciousness, or clinical evidence of other end-organ damage, and none died.Four patients (2.8% [95% CI: 0.77\u20137.01]) developed severe dengue: 1) one [0.69 (0\u20133.8)%] developed shock (systolic BP 70 mmHg) on D10 and 2) three had AST > 1,000 IU/L but no clinical features of acute liver failure. All had prior warning signs. The shocked patient had facial swelling, abdominal pain, and ascites; the other three had mucosal bleeding (N = 44) showed significantly higher median admission versus convalescent values for 1) right ventricular myocardial performance index (RVMPI) 0.27 (range: 0.16\u20130.52) versus 0.23 , 2) RV diameter 1.97 (1.6\u20132.5) versus 1.88 (1.6\u20132.2) cm (P = 0.001), and 3) left ventricular diameter 4.8 (3.9\u20135.7) versus 4.71 (4\u20135.4) cm (P = 0.04).Echocardiograms (138/143 (96.5%) patients, received IV fluids during their hospitalization. The most frequently prescribed fluid was Ringer's lactate , followed by normal saline and gelofusine/colloid . Total fluid volumes ranged from 0.5 to 13.5 L, median 3 L (IQR: 0.5\u20138.5 L) and were given for a median of 3 days , starting on D5 (IQR: 2\u20139) and finishing on D8 (IQR: 4\u201315). On \u2265 D10, 3/134 (2.2%) started IV fluids and 24/134 (17.9%) were still on IV fluids. Platelets were administered to 47 (32.9%) patients whose median nadir platelet count was 17,500/\u03bcL . No blood transfusions were given.In this prospective dengue study in adults from metropolitan Hanoi, almost all patients had non-severe dengue, many had received preadmission IV fluids, most had dengue warning signs, and four (~3%) developed severe dengue, manifest as shock, and AST values exceeding 1,000 IU/L.Our low rate of decompensated shock is consistent with adult data from Trung and others.About 60% of our patients had received IV fluids prior to admission and almost all received IV fluids during admission. The majority finished IV fluids by the end of the critical period but a small proportion started IV fluids late in their illness and almost 20% continued on IV fluids to D10 and beyond. On admission, ~20% of patients had soft tissue edema and ~3% ascites/pleural effusions (A/PE), rising during admission to 38% and 23%, respectively.The echocardiographic findings of impaired RV function and biventricular enlargement were consistent with fluid overload, and contrast the findings of normal RV function and smaller ventricular dimensions on admission versus discharge reported by Yacoub and others from southern Vietnam.Adopting a proactive policy of IV fluids almost certainly resulted in some of our patients receiving IV fluids unnecessarily. Trung and others gave IV fluids to only 30% patients with mild dengue in the infection ward. Identifying non-severe dengue patients who could be managed adequately with oral fluids requires randomized trials of IV versus oral fluids. Such data would be helpful for clinics and general wards where detailed patient monitoring is too challenging.Mucosal bleeding occurred in 45% of our patients, similar to the rate reported by Trung and others in their series.31Our study took place during the dengue season when the prior probability of dengue was high. The antibody responses were essentially the same between NS1 antigen\u2014PCR positive and negative groups. In the latter, we followed the 2009 WHO guidelines but also included patients with declining IgM titers when the convalescent sample was taken after D14, the mean time to peak IgM titers. If validated by others, this criterion could be incorporated into future WHO dengue guidelines.Our study had limitations. It was conducted in an adult referral hospital, and the relatively small number of patients came mostly from Hanoi, a city with good medical facilities. These biases limit the applicability of our results. Ultrasound data were not collected systematically to monitor the changes in plasma leakage, and the severity of mucosal bleeding was not classified.To conclude, non-severe dengue dominated the clinical picture in our setting and a significant proportion of patients developed evidence of fluid overload. More research is needed in community and hospital settings to optimize the fluid management, broaden our knowledge of dengue epidemiology, and assess their epidemic preparedness.Supplemental Table."} +{"text": "Chronic nonbacterial osteomyelitis (CNO) is the most common autoinflammatory bone disorder in childhood (1). Diagnostic information is provided by TC-99 bone scintigraphy (BS) and/or whole body MRI. Non-steroidal anti-inflammatory drugs (NSAIDs), glucocorticoids, bisphosphonates and tumour necrosis factor inhibitors have been used until now with variable response (2).To describe clinical, biological and radiological response to treatment with anakinra in patients with CNO refractory to NSAIDs and bisphosphonates.Seven patients with refractory CNO were treated with anakinra for at least 6 months in our institution. Response to treatment was evaluated assessing clinical manifestations , laboratory findings (C-reactive protein (CRP)), erythrocyte sedimentation rate (ESR)) and serum amyloid A level (SAA))) and number of bone lesions on TC-99 BS at the start of treatment and at 6 months.The median age at diagnosis and before starting anakinra was 9.7 years (IQR 7.8-14.7) and 13.3 years (IQR 8.0-15.9) respectively. All were treated with NSAIDs and bisphosphonates as first-line therapy. Glucocorticoid therapy was required in one patients with concomitant recurrent fever and pleural effusion. These patients did not respond satisfactorily and anakinra (2 mg/kg/day) was started. At the start of treatment 7/7 patients (100%) had pain, 3/7 (43%) local swelling and 5/7 (71%) functional impairment; at 6 months of follow up 6/7 patients (86%) were completely asymptomatic, with one patient complaining of arthralgia. Before starting anakinra the median CRP, ESR and SAA were 2.7 mg/dl (IQR 1.7-4.9) 26 mm/h (IQR 12-46) and 53 mg/dl (IQR 27-112); at 6 months 5/7 patients (71%) normalized CRP, ESR and SAA; 2/7 had a decrease in inflammatory markers. Before anakinra 59 bone lesions were detected on TC-99 BS. After 6 months of therapy 24/59 lesions (40%) had completely resolved, 1/59 lesions (2%) had partially improved and 29/59 lesions (49%) remained stable. In two patients with persistent high biological inflammatory markers, new lesions (14) developed during treatment.Our data suggest that anakinra appears effective in CNO in controlling symptoms and laboratory findings; subclinical bone inflammation was still detectable by BS after 6 months of treatment. Long-term follow-up studies with a larger number of patients are needed."} +{"text": "Data regarding the safety and efficacy of treatment regimens for juvenile dermatomyositis (JDM) tends to be from anecdotal, small, uncontrolled, non-randomized case series.To find out the treatment regimen associated with the lowest occurrence of flare and the lowest drug related toxicity in juvenile dermatomyositis (JDM).Children with newly diagnosed JDM were randomized in an open fashion to receive: prednisone (PDN) versus PDN plus methotrexate (MTX) versus PDN plus Cyclosporine A (CASA). Primary outcome measures after 6 months of treatment: response rate according to the Paediatric Rheumatology International Trials Organisation (PRINTO) provisional definition of improvement. Primary outcome measures after 24 months of treatment: a) time to inactive disease; b) time to major therapeutic changes because of inefficacy/flare/adverse events; time to flare.4.4-10.6) and a median disease duration of 2.8 months (1.3-5.3). Frequency of response at 6 months was for 24/47 (51%) for PDN, 32/46 (70%) for PDN+CSA and 32/46 (70%) for PDN+MTX (p 0.032).139 randomized patients were included in the efficacy dataset. There were 82 females (59%) with a median age at onset of 7.4 years versus group 2 (PDN +CSA) and 1 (PDN) combined and in the time to major therapeutic change (defined as the addition of CSA or MTX or any other disease-modifying anti-rheumatic drug) between group 1 (PDN) versus group 2 (PDN+CSA) and 3 (PDN+MTX) combined (p = 0.009). No statistical significant differences in time to flare . The safety analysis showed that group 2 (PDN+CSA) had greater number of adverse events (AE) when compared to group 1 (PDN) and 3 (PDN+MTX) (p = 0.005). Similarly there was a statistically significant increase in the frequency of AE in group 2 (PDN+CSA) when compared to Group 1 (PDN) and 3 (PDN+MTX) in several systems and others . There were no statistically significant differences in serious AE among the 3 groups (p 0.17). There were no deaths.Combined therapy with PDN and either CSA or MTX was more effective than with PDN alone. However the safety profile favors the combination with MTX with respect to CSA.None declared."} +{"text": "AbstractCyperaceae (109 species), Rubiaceae (129), Solanaceae (131), Poaceae (155), Melastomataceae (157), Myrtaceae (257), Orchidaceae (288), Fabaceae (323), and Asteraceae (426), between angiosperms. Among the ferns and lycophytes are: Hymenophyllaceae (30), Thelypteridaceae (31), Aspleniaceae (32), Dryopteridaceae (43), Pteridaceae (54) and Polypodiaceae (60). There are five type specimens among them: one holotype, one isotype and three paratypes. To date, the FURB herbarium has donated 19,521 herbarium duplicates for identification or expansion of other herbaria.The premise of this study is to present the collection of the FURB herbarium, its collection area and type specimens, as well as its projects and contributions to the flora of the Subtropical Atlantic Forest. The FURB herbarium currently has nearly 41,000 records of vascular plants and has the largest collection of lycophytes and ferns in Southern Brazil, with more than 8,000 records. More than 4,500 scanned images of 4,436 species are available online, and it is expected that the whole collection will be scanned in less than one year. There are 198 families of angiosperms, 33 of ferns, three of lycophytes and six of gymnosperms. All collections of the Floristic and Forest Inventory of Santa Catarina project are recorded in FURB, which represents almost 35,000 herbarium specimens. The families with the largest number of species are: The Dr. Roberto Miguel Klein Herbarium (FURB) was founded in 1990 by Lucia Sevegnani, PhD. Roberto Miguel Klein (1923-1992) was an important botanist and ecologist. In 1949, together with Father Raulino Reitz, he founded the Sellowia Journal, which published contributions of researchers linked to Herb\u00e1rio Barbosa Rodrigues (HBR). In addition to HBR, the Sellowia papers are considered Klein\u2019s major works, among those that treated the relation between malaria outbreaks and the local flora and addrKleinodendron L.B.Sm. & Downs, besides 75 specific epithets, from 37 families . The aim of the herbarium is to study the plant diversity of the local vegetation, especially that of the Serra do Itaja\u00ed National Park, Itaja\u00ed Valley, and Santa Catarina State. Initially the collection was established by professors for didactic purposes, but with the advent of new projects, such as the Floristic and Forest Inventory of Santa Catarina , SpeciesLink (http://splink.cria.org.br/), and Reflora (http://reflora.jbrj.gov.br). The software (Herbaria 3.1), an Access-based software, has been developed by EPAGRI (http://www.epagri.sc.gov.br) in partnership with the herbarium staff . There are 4,556 images of 4,436 species.The herbarium has 41,325 specimens , but the first specimen for the FURB herbarium was collected on September 7, 1991, of a Pliniarivularis (Cambess.) Rotman. (Myrtaceae). The distribution of collected specimens by year can be seen in Figure The earliest specimen is dated March 1, 1937, a Most of the plant samples are from Southern Brazil, Santa Catarina State Figure being thPageBreakPageBreakAfter being dried in ovens at 65 to 70 degrees Celsius, the specimens are incorporated into the database. All data such as scientific name, location, city, coordinates, altitude, and general descriptions of the plant are recorded. The registration number is generated automatically by the software. Afterwards, the plants are glued with hot glue onto A2 sheets, packed in plastic bags in order to avoid being contaminated by insects or fungi and to prevent loss of material during handling, and subsequently frozen for five days at -20 degrees Celsius. Next, the plants are stored in specific cans that are sealed and stored separately in groups: lycophytes and ferns, gymnosperms and angiosperms. Among the groups, the cans are alphabetized according to family and gender.http://splink.cria.org.br/dc/index?criaLANG=pt&colecao=FURB), which checks the coordinates, toponymy, scientific names, and their authors. The \u201cdoubtful\u201d records are reviewed by the curator. The names are checked using the List of Species of All databases are reviewed by a DataClean tool, from CRIA shows that the FURB herbarium possesses 0.0725 records per sq km of the Southern region. Although seemingly small, it is a high number compared to other featured herbaria in Santa Catarina; FLOR, JOI and CRI have 0.0677, 0.0150, and 0.0119 records per sq km, respectively. Among these herbaria, FURB also has the largest number of herbarium specimens with photographs available online , and the goal is to start photographing all specimens before the end of 2014. It also deserves to be mentioned that the collection has 1,417 unique names not found in other herbaria. This is quite a high number despite the fact that, due to the impracticability of this analysis, possible synonyms were not excluded.The database SpeciesLink , 4,771 specimens being collected in other Conservation Units , Bromeliaceae (542), Aspleniaceae (612), Piperaceae (769), Orchidaceae (848), Myrtaceae (854), Melastomataceae , Rubiaceae , Polypodiaceae , Fabaceae , Asteraceae , and Lauraceae . Likewise, 3,794 herbarium specimens have already been loaned to perform theses, dissertations, and other taxonomic studies.With the implementation of an exchange program and the aim of supporting other collections, the FURB herbarium has donated 19,521 herbarium specimens. The families with more than 500 duplicates donated are: Vriesearubens J.G.Silva & A.F.Costa (Bromeliaceae), isotypus of Crotonpygmaeus L.R.Lima (Euphorbiaceae), paratypus of Calystegiabrummittii P.P.A.Ferreira & Sim.-Bianch (Convovulaceae), paratypus of Pleurostachysarcuate W.W. Thomas, M. Alves & R. Trevis (Cyperaceae), and paratypus of Sarcoglottiscatharinensis Mancinelli & E.C.Smidt (Orchidaceae).It is worth mentioning that there are five types in the collection: Holotypus of Kingdom: ChlorobiontaSubclass:Lycopodiidae (lycophytes), Equisetidae, Marattiidae, Ophioglossidae, Polypodiidae, Psilotidae (ferns), Ginkgoidae, Cycadidae, Pinidae, Gnetidae (gymnosperms), and Magnoliidae (angiosperms)Lycophyte families: Isoetaceae (1 specimen/1 species); Lycopodiaceae (326/21) and Selaginellaceae (129/11).Fern families: Anemiaceae (261 specimens/6 families); Aspleniaceae (833/32); Athyriaceae (234/13); Blechnaceae (542/18); Culcitaceae (1/1); Cyatheaceae (425/10); Cystopteridaceae (2/1); Davalliaceae (2/1); Dennstaedtiaceae (70/9); Dicksoniaceae (69/2); Dryopteridaceae (954/43); Equisetaceae (13/3); Gleicheniaceae (99/9); Hemidictyaceae (1/1); Hymenophyllaceae (578/30); Lindsaeaceae (185/8); Lomariopsidaceae (40/6); Lygodiaceae (32/1); Marattiaceae (104/5); Marsileaceae (3/3); Ophioglossaceae (25/4); Osmundaceae (12/2); Parkeriaceae (3/1); Plagiogyriaceae (2/1); Polypodiaceae (2163/60); Psilotaceae (5/1); Pteridaceae (760/54); Saccolomataceae (44/2); Salviniaceae (16/6); Schizaeaceae (25/2); Tectariaceae (68/4); and Thelypteridaceae (330/31).Gymnosperm families: Araucariaceae (17 specimens/3 species); Cupressaceae (59/10); Cycadaceae (6/3); Ginkgoaceae (2/1); Pinaceae (26/8); and Podocarpaceae (40/4).Magnoliidae families: Acanthaceae (384 specimens/35 species); Achatocarpaceae (2/2); Actinidiaceae (1/1); Adoxaceae (15/3); Aizoaceae (3/2); Alismataceae (14/4); Alstroemeriaceae (23/4); Amaranthaceae (185), 23); Amaryllidaceae (51/13); Anacardiaceae (135/13); Annonaceae (271/23); Apiaceae (84/22); Apocynaceae (339/70); Aquifoliaceae (196/8); Araceae (547/35); Araliaceae (123/21); Arecaceae (154/14); PageBreakAristolochiaceae (13/6); Asparagaceae (15/6); Asteraceae (2839/426); Balanophoraceae (10/2); Balsaminaceae (7/1); Basellaceae (10/1); Begoniaceae (325/24); Berberidaceae (16/3); Bignoniaceae (271/53); Bixaceae (8/2); Boraginaceae (172/23); Brassicaceae (23/8); Bromeliaceae (1676/85); Burmanniaceae (11/1); Burseraceae (12/1); Cabombaceae (1/1); Cactaceae (356/28); Calceolariaceae (4/3); Calyceraceae (12/2); Campanulaceae (81/19); Canellaceae (17/2); Cannabaceae (65/4); Cannaceae (25/2); Capparaceae (18/3); Caprifoliaceae (32/7); Cardiopteridaceae (13/3); Caricaceae (11/3); Caryocaraceae (4/1); Caryophyllaceae (31/12); Casuarinaceae (8/1); Celastraceae (116/18); Ceratophyllaceae (1/1); Chloranthaceae (37/1); Chrysobalanaceae (44/13); Cleomaceae (5/2); Clethraceae (65/2); Clusiaceae (140/9); Combretaceae (46/14); Commelinaceae (176/19); Connaraceae (11/3); Convolvulaceae (133/33); Costaceae (15/4); Crassulaceae (3/1); Cucurbitaceae (124/26); Cunoniaceae (52/5); Cyclanthaceae (26/1); Cyperaceae (656/109); Dilleniaceae (60/7); Dioscoreaceae (36/10); Droseraceae (2/1); Ebenaceae (11/4); Elaegnaceae (1/1); Elaeocarpaceae (43/5); Ericaceae (69/11); Eriocaulaceae (48/15); Erythroxylaceae (74/14); Escalloniaceae (27/5); Euphorbiaceae (594/83); Fabaceae (1611/323); Fagaceae (8/6); Gentianaceae (29/7); Geraniaceae (3/2); Gesneriaceae (364/25); Goodeniaceae (4/1); Griseliniaceae (18/1); Gunneraceae (8/1); Heliconiaceae (64/3); Hernandiaceae (1/1); Humiriaceae (8/2); Hydrangeaceae (1/1); Hydrocharitaceae (3/1); Hydroleaceae (5/1); Hypericaceae (35/5); Hypoxidaceae (7/1); Icacinaceae (3/1); Iridaceae (97/17); Juglandaceae (2/1); Juncaceae (59/9); Juncaginaceae (1/1); Krameriaceae (3/1); Lacistemataceae (5/3); Lamiaceae (448/70); Lauraceae (921/66); Lecythidaceae (4/2); Lentibulariaceae (15/5); Liliaceae (13/2); Linaceae (1/1); Linderniaceae (3/3); Loasaceae (4/2); Loganiaceae (69/8); Loranthaceae (56/5); Lythraceae (120/21); Magnoliaceae (26/3); Malpighiaceae (255/43); Malvaceae (388/66); Marantaceae (97/10); Marcgraviaceae (33/3); Melastomataceae (1811/157); Meliaceae (368/18); Menispermaceae (41/6); Menyanthaceae (5/1); Molluginaceae (3/1); Monimiaceae (297/12); Moraceae (259/24); Musaceae (5/3); Myristicaceae (16/4); Myrtaceae (1899/257); Nyctaginaceae (132/11); Nymphaeaceae (3/1); Ochnaceae (152/8); Olacaceae (25/2); Oleaceae (15/4); Onagraceae (166/18); Opiliaceae (2/1); Orchidaceae (2611/288); Orobanchaceae (22/6); Oxalidaceae (53/10); Papaveraceae (3/2); Passifloraceae (116/23); Paulowniaceae (7/1); Pentaphylacaceae (9/2); Peraceae (54/2); Phrymaceae (2/1); Phyllanthaceae (72/11); Phytolaccaceae (92/12); Picramniaceae (21/4); Piperaceae (1528/89); Pittosporaceae (1/1); Plantaginaceae (90/18); Platanaceae (2/1); Plumbaginaceae (3/2); Poaceae (641/155); Podostemaceae (3/1); Polygalaceae (93/11); Polygonaceae (110/21); Pontederiaceae (24/9); Portulacaceae (7/6); Primulaceae (427/21); Proteaceae (36/7); Quillajaceae (9/1); Ranunculaceae (25/6); Rapateaceae (3/2); Rhamnaceae (58/11); Rhizophoraceae (7/1); Rosaceae (178/17); Rubiaceae (1779/129); Rutaceae (256/23); Sabiaceae (32/1); Salicaceae (195/21); Santalaceae (59/10); Sapindaceae (435/40); Sapotaceae (100/15); Saxifragaceae (1/1); Schlegeliaceae (7/1); Schoepfiaceae (4/2); Scrophulariaceae (32/3); Simaroubaceae (14/4); Siparunaceae (5/1); Smilacaceae (68/4); Solanaceae (1218/131); Styracaceae (53/4); Symplocaceae (84/15); Talinaceae (15/1); Tamaricaceae (1/1); Theaceae (18/2); Thymelaeaceae (37/3); TrigoniaceaePageBreak(19/1); Tropaeolaceae (2/1); Typhaceae (8/2); Urticaceae (208/25); Velloziaceae (6/5); Verbenaceae (286/38); Violaceae (47/8); Viscaceae (3/0); Vitaceae (53/8); Vivianiaceae (12/1); Vochysiaceae (28/15); Winteraceae (103/2); Xanthorrhoeaceae (2/1); Xyridaceae (27/11); and Zingiberaceae (27/8).Herbarium collections have a fundamental importance in biodiversity conservation, exhibiting aspects such as reducing the distribution of a particular species or accumulating information in regard to rare or endangered species e.g. , and theDicksoniasellowiana Hook. (Dicksoniaceae), a threatened species, have been described by Gasper et al. (2011) in a study that was also based on the FURB collection. Finally, the collection has enabled studies on secondary succession and the assessment of the conservation status of the sampled forests , most have fewer than 50,000 records (80% according to Of the 170 active herbaria listed in the Catalogue of the Brazilian Herbaria (PageBreakums (In addition to the novelties promoted by the e-taxonomy, the availability of data online, including the recently added images, allows for the rapid updating of herbariums , as wellums .fungi collection. This may result from the second cycle IFFSC, with the collection of macrofungi, which requires special care (Finally, one of the novelties of the FURB herbarium is the expansion of its ial care . The col"} +{"text": "Hereditary angioedema (HAE) with normal C1 esterase inhibitor (C1INH) was described for the first time in 2000. It was characterized by subcutaneous, gastrointestinal and laryngeal edema with familial history. Triggering factors are: stress, hormonal factors, trauma and infections. The authors evaluate response to therapy in patients with HAE without C1-INH deficiency.It was analized therapeutical response to hereditary angioedema without deficiency of C1INH. Patients with clinical symptoms compatible with HAE have been included after normal quantitative and functional C1INH levels and positive family history for HAE, independent of factor XII mutation.Nineteen patients have been identified . The following therapies were oriented: combined contraceptive substitution for progestagen (10/19); treatment with progestagen (2/19); tranexamic acid (15/19): 1250mg (2), 1000mg (1), 750 (5), 500 mg (4), 250 mg (1); oxandrolon (5/19) (0.5 mg-5mg/day), danazol 200mg/day (1/19) and combined therapy woth oxandrolon and tranexamic acid in two patients. Icatibant was used in seven patients with clinical improvement. One of them reported increasing frequency of attacks after repeated use of this drug. Two patients received fresh frozen plasma during attacks with clinical improvement.HAE without C1-INH deficiency has no established treatment. Clinical improvement was evident with the exclusion of combined contraceptives. The majority of the patients presented clinical response to tranexamic acid in variable doses. Icatibant was adequate for the therapy of attacks."} +{"text": "Targeted viral load (VL) strategy is followed in the ART programme of India. Patients failing antiretroviral therapy, undergo VL testing and switched to 2ndline ART if VL is >5000 copies/ml.Data of patients referred to School of Tropical Medicine, Kolkata for suspected treatment failure (TF) was analyzed for the period of December2008 to November2013 to ascertain the positive predictive value (PPV) of immunologic and/or clinical parameter for confirming virologic failure (VF) and to observe the short term outcome of secondline treatment. Paired t- test was used for data analysis.3 at suspected TF. Number of patients failing by immunologic, clinical and clinicoimmunologic criteria was 414(74%), 11(2%) & 135(24%) respectively with corresponding PPV of 48%, 46% & 63% respectively. PPV of CD4 falling below baseline, >50% drop from on-treatment peak value and failure to reach 100 cells/mm3 after 12 months of ART was 37%, 55% and 25% respectively. Among 216 patients with minimum 6 months follow-up, the median CD4 & VL changed significantly following 6 months of secondline ART . Undetectable VL was achieved in 164(76%). Out of 284 patients starting secondline ART, 25 (8.8%) died within 6 months.VF was noted in 287(51.3%) of 560 patients ; median CD4 109 cells/mmImmunoclinical criteria have low PPV in diagnosing VF. Despite late switch, majority (76%) could achieve undetectable VL at 6 months but the high early mortality (8.8%) is a concern."} +{"text": "Metabolic bone disease (MBD) of prematurity is an increasingly well-recognized complication of pre-term birth. Despite this, there is limited evidence for the optimum method for assessing and monitoring bone health and appropriate supplementation.This study assesses the effectiveness of the MBD protocol at Monash Health nurseries in infants born under 32 weeks\u2019 gestation between November 2012 and January 2014.Preliminary data of 93 infants 29 weeks (24-32.3weeks), birth weight (BW) 1279.4g (553-2512g)) were assessed. Risk factors assessed include 8.8% IUGR infants (n=56), 12.9% maternal pre-eclampsia, 7.5% necrotising enterocolitis (NEC) episodes and exposure to medications as follows:caffeine , diuretics and steroids (2.2%). Preterm infants received 14.3 days of total parenteral nutrition (TPN) on average, with the majority on fortified expressed breast milk once enteral feeding was established.Initial MBD screen was performed for 80.6% infants (mean age 36.6 days) with only 24.7% having repeated monitoring (mean age 67.9 days). 6.5% had Alkaline phophosphatase (ALP) levels >500U/I initially (range 143-827U/l), reducing to 1.1% (range 173-573U/I). Average Tubular Resorption of Phosphate (TRP) was 79.7% (n=71). The majority of infants were on Vitamin D 400units/day. 23.6%(n=22) commenced phosphate supplements (mean duration 41 days) and 15.1%(n=14) commenced calcium supplements (mean duration 53.2 days).thcentile) with evidence of slowing growth velocity (mean follow up length 49cm (<3rdcentile) at mean age 79.9 days). Five infants were identified with fractures however two were from birth trauma and two suspected non-accidental injury. One patient had an incidental finding of fractured femur with multiple risk factors for MBD including very low birth weight (700g), NEC episodes requiring prolonged antibiotic therapy (69 days), TPN (48 days), caffeine (88 days) and diuretic use (22 days).Average birth length was 38cm (10-50Significant difference (p<0.001) is noted between phosphate-treatment and untreated groups for both GA and BW: Median 27weeks and 929g for treated subjects versus 29.6weeks and 1343g if untreated. In the phosphate-treatment group, ALP levels improved and difference in phosphate levels were also significant with p=0.003. Between phosphate-treatment group versus untreated group, differences were insignificant for ALP (p=0.05) and phosphate levels (p=0.09), though this may reflect insufficient subsequent MBD screens .Further evaluation is anticipated to help improve MBD understanding in this high-risk cohort particularly given morbidity associated with MBD occult fractures. In addition, secondary outcomes would include cost efficiency of MBD surveillance and identifying optimal supplemental therapy."} +{"text": "TTR-FAP is progressive, disabling, irreversible and life-threatening neuropathy due to a point mutation of TTR gene with autosomal dominant transmission. France is a non endemic European country. To study the impact of labeling French reference center for FAP (NNERF) and building of a national network CORNAMYL.In 1986-2014 period, 482 FAP patients were registered in NNERF's database. All carried amyloidogenic TTR gene mutations and Congo positive amyloid deposit (CPAD). To report genotypic and phenotypic varieties of FAP in France in 2008-2014 period and the sensitivity of the tools for diagnosis.In 2008-2014 period: 180 new TTR-FAP cases were identified, in 14 additionnal geographical departments , with 9 further TTR gene mutations .Mean age was 60 (22-89), a late onset (> or = 50 y) in 69%. Sex ratio: 2.16. Positive family history of FAP 55%. Portuguese origin 18.3%. Diagnosis of FAP was delayed by 2.93y (0.2-13.5) after first symptoms; 69% had walking difficulties including 39% requiring aid.Five phenotypes were identified: Small Fiber Polyneuropathy (PNP) (43%), All-Fiber SensoryMotor-PNP (25%), Upper Limbs neuropathy (NP) (17%), Ataxic NP (14%), Motor NP (2%). CPAD after nerve biopsy in 19/26pts (73%), Labial Salivary Gland Biopsy (LSGB) in 91/128 pts (71%); 76% required multiple biopsies.The French network for TTR-FAP allows to identify new TTR-FAP cases in most of geographical departments with varied phenotypes. The larger use of TTR gene analysis in idiopathic aggressive polyneuropathy cases will help to accelerate diagnosis of TTR-FAP."} +{"text": "Where available, antiretrovirals (ARVs) and antenatal HIV testing and care have significantly reduced mother to child transmission (MTCT). Higher maternal viral load (VL) is linked with higher risk of MTCT, increasing risk of MTCT for women starting ARVs during pregnancy compared to those already suppressed.A single-centre, retrospective cohort of women starting ARVs during pregnancy from 2004 till 2013. Demographic, obstetric and virological data, and neonatal outcomes were collected where available.60 pregnancies were recorded (in 56 women) in which ARVs were started or restarted from a total of 129 recorded pregnancies. 48% (27/56) were new antenatal HIV diagnoses and in these median gestational age (GA) at diagnosis was 16.1 weeks (range 5.3-37.6). Median GA at ARV commencement was 22.4 weeks (range 8-37.7) with 63% (35/56) starting before 24 weeks and 91% (51/56) before 28 weeks. HIV diagnosis during pregnancy was associated with a later commencement of ARVs . The ARV regimen was available for 58 pregnancies. Treatment was with two NRTIs plus NNRTI (3), or PI (54) or raltegravir (1). Raltegravir was added as a forth agent in 7 patients.87% (52/60) had resistance genotyping before (14) or during (38) pregnancy, 81% (22/27) for new diagnoses in pregnancy. The rate of any ARV resistance was 12% (6/52): 4 patients had NNRTI and 2 NRTI resistance mutations, 4 were treatment-na\u00efve. This was not associated with treatment failure.HIV VL at delivery was available in 57 pregnancies with detectable VL in 16% (9/57). Pre-treatment VL >100,000 copies/mL during pregnancy was associated with higher risk of detectable VL at delivery (p=0.016). 69% babies were delivered by Caesarean section, 32% as an emergency. There was one late miscarriage at 17 weeks. Median GA at birth was 38 weeks (range 17-42) with 21% born at <37 weeks (10/48). There was one HIV MTCT in a woman who was poorly adherent with ARVs throughout pregnancy with a VL of 216 copies/mL at delivery following a period of directly observed therapy.Over 10 years of integrated HIV and antenatal care, there was only one case of MTCT. Initiating ART for prevention of MTCT is complex, requires a multi-disciplinary approach and importantly patient engagement. Antenatal practices and guidelines have changed over the period of this dataset, allowing normalisation of pregnancy when HIV is diagnosed and treated early."} +{"text": "Transthyretin Familial Amyloid Polyneuropathy (TTR-FAP) is a worldwide autosomal dominant disease due to point mutation of TTR gene. The main endemic area is Portugal, associated with V30M variant and an early onset (EO) (mean age 30 yo). Phenotype is a progressive length dependent small fiber polyneuropathy with autonomic dysfunction and cardiac conduction disorders; the median survival is 12 years. France is a prototypic non endemic country, characterized by sporadic cases in 50%, a late onset (LO>50 yo) in 75%, a genetic heterogeneity . Liver transplantation (LT) is the gold standard treatment allows to stop progression of the neuropathy in EO V30M patients and to prolonge significantly the survival. Tafamidis, a TTR kinetic stabilizer, received marketing authorization in Europe for stage 1 FAP allowing to slow progression of the neuropathy. Aims of the study was to assess the place of tafamidis in the management of TTR-FAP.In a population of 131 patients diagnosed during period (2008-2012). Mean age : 59.3 yo SD 15.9. Stage 1 (60%) stage 2 (36%) stage 3 (4%). Mutation : V30M: 59%, non V30M variants n=18, Late onset (LO): 73.3%. mean NIS : 40.65 SD 28.6. In Stage 1 mean NIS=27.32 SD 20. Locomotion (PND score) : 71% with Walking difficulties. Patients were followed periodically (every 6 months) in consultation assessing by a questionnaire : new manifestations , erectile dysfunction)). And on examination looking for orthostatic dysfunction.Among the 78 patients of stage 1, 56 accessed to tafamidis (73% V30MTTR), 16 underwent LT, 6 were lost of follow-up. The follow-up ranged from 0.5-4.5 years. Fourteen patients (25%) remained stable for > 2 years under tafamidis (max 4.5 years) including 8/15 with NIS<10, 80% V30MTTR; 7/15 EO. Twenty three/56 pts (41%) worsened with increased or onset walking disability (n=14); daily diarrhea (5) with anal incontinence (3); extensive painful and sensory neuropathy (n=2), hand weakness (n=1), onset of erectile dysfunction (n=1). Worsening occurred during the first year in 65%, between 1 to 2.5 years in 35%. Most of them had a NIS \u226510 (87%), 69% V30MTTR; 48% LO. Among the 23 patients who worsened, 12 were enrolled in clinical trials with TTR gene silencing ; 11 underwent LT.Treatment of stage 1 TTR-FAP by tafamidis requires a close and long term monitoring of patients including a detailed questionnaire on walking disability, autonomic dysfunction, extension of pain and sensory loss. In case of significant progression in these items, a switch to clinical trials or LT should be done."} +{"text": "Identify the prevalence and impact of foot problems, assess the access to foot care services and describe the care received, in a sample of patients with RA.Foot problems in rheumatoid arthritis (RA) derive from a combination of the disease process and altered foot mechanics. Guidelines recommend regular review of patients\u2019 feet but the extent to which the general population of RA patients report foot problems and access foot care has not been established.All RA patients under hospital care in a defined geographical area were identified. A random sample was sent a postal survey (reminder after 3 weeks) about presence of foot problems, disability ), patient characteristics , and foot care received (if any), including podiatry, orthotics and orthopaedics. Measures of impact ) with additional questions related to importance, severity, coping and ability to work derived from a previous study. Socio-economic status was established by IMD scores from postcodesOf 739 patients sent the survey, 413 (56%) replied. Responders and non responders were similar for age (63.5 vs.62.6 years), gender (74%F vs. 75%F) and socio-economic status (IMD highest deprivation quintiles 13% vs.15%). Responders\u2019 median (inter-quartile range) disease duration was 10 (5-20) years and HAQ score 1.5 (0.75-2.0). Most responders were taking arthritis medication and 273 (66%) reported additional medical conditions (including 28 (7%) with diabetes). Almost all reported current or previous foot problems .Current problems included: articular features 74%; extra articular features 43%; cutaneous lesions 66%; structural deformity 58%; infection 7.5%. Median (IQR) FISIF score 10/21 (6-14); and FISAP score 16/30 (7-23). Median (IQR): importance 6 (3-8); severity 6 (3-8); and coping 5 (3-7). Overall, 38% reported foot problems that affected their ability to work.Self-care strategies adopted by responders were: aids 188 (46%), cutaneous treatments 268 (65%); CAMs 96 (23%); and devices 275 (67%). A total of 278 (67%) had accessed foot care: podiatry 204 (73%) [Private sector n=149 (54%)]; orthotics 192 (69%); and orthopaedics 92 (32%). Care received included: insoles 190 (66%); prescribed footwear 73 (25%); treatment cutaneous lesions 99 (49%); and foot surgery 72 (35%). Podiatry was the most frequently requested additional service Relevance/impact: Foot problems are common in patients with RA and impact on many aspects of patients\u2019 lives.Unlike previous studies this was representative of all hospital patients with RA and almost all reported foot symptoms. Although FIS scores were slightly lower than in previous studies, substantial impact was reported including affecting ability to work. In spite of this, 30% had never accessed foot care.Many patients reported current foot problems. Further research is required to compare self-report of foot problems with clinical observations and explore the reasons why patients do and do not access foot care. Also as many patients who had accessed care still reported foot problems, the quality of foot care requires further exploration."} +{"text": "KRAS (28%), TP53 (18%), ARID1A (12%), IDH1/2 (9%), PBRM1 (9%), BAP1 (7%), and PIK3CA (7%). IDH1/2 (p=0.0005) and BAP1 (p=0.0097) mutations were characteristic of ICC, while KRAS (p=0.0019) and TP53 (p=0.0019) were more frequent in ECC and GBC. Multivariate analysis identified tumour stage and TP53 mutations as independent predictors of survival. Alterations in chromatin remodeling genes were seen in 31% of cases. Potentially actionable mutations were seen in 104/153 (68%) cancers: i) KRAS/NRAS/BRAF mutations were found in 34% of cancers; ii) mTOR pathway activation was documented by immunohistochemistry in 51% of cases and by mutations in mTOR pathway genes in 19% of cancers; iii) TGF-\u00df/Smad signaling was altered in 10.5% cancers; iv) mutations in tyrosine kinase receptors were found in 9% cases. Our study identified molecular subgroups of cholangiocarcinomas that can be explored for specific drug targeting in clinical trials.One-hundred-fifty-three biliary cancers, including 70 intrahepatic cholangiocarcinomas (ICC), 57 extrahepatic cholangiocarcinomas (ECC) and 26 gallbladder carcinomas (GBC) were assessed for mutations in 56 genes using multigene next-generation sequencing. Expression of EGFR and mTOR pathway genes was investigated by immunohistochemistry. At least one mutated gene was observed in 118/153 (77%) cancers. The genes most frequently involved were Cholangiocarcinoma is a phenotypical and clinical heterogeneous collection of biliary tract malignancies, classified according to the World Health Organization (WHO) as intrahepatic (ICC) or extrahepatic cholangiocarcinomas (ECC) , 2. The KRAS, TP53, CDKN2A and SMAD4) [PIK3CA, PTEN, AKT1, IDH1 and IDH2 have been reported in this class of tumours [BAP1, ARID1A and PBRM1 in the development of these tumours [Previous studies on molecular alterations in biliary tract cancers have focused on selected genes, including those altered in pancreatic adenocarcinoma (d SMAD4) . Mutatio tumours -20. Howe tumours , 21.The validation of whole exome studies by sequencing analysis of hotspot mutations in larger and characterized series has been a fruitful approach in identifying potential targets for personalized therapy for several malignancies . Next-geIn the present study, we assayed the mutational status of 56 cancer-related genes in 153 biliary tract cancers, using a targeted next-generation sequencing methodology, with the aim of identifying molecular subgroups driving the development of personalized therapy approaches for patients affected by these neoplasms.p=9.77 E\u221212). Synchronous multinodular lesions were found in 31 cases (20.3%). Tumour grading was G1 in 20, G2 in 94, and G3 in 38 cases, while the remaining case was undifferentiated.Patients' demographic and clinico-pathological data are summarized in Table p=0.0002). Vascular and perineural invasion were present in 107 (69.9%) and 93 (60.8%) cases, respectively. Perineural invasion showed a significantly lower prevalence in ICC than ECC and GBC . Hepatitis virus infection (HBV and/or HCV) and cirrhosis prevalence were significantly higher in ICC patients .Biliary intraepithelial neoplasia (BilIN) was present in 49/153 cases (32.0%), and its prevalence was significantly higher in ECC and GBC compared to ICC .The pathologic stage of the 153 neoplasms was Stage I in 20, II in 51, III in 43, and IV in 39. ICC presented with more advanced stages at surgery compared to ECC and GBC , TP53 (18.3%), ARID1A (11.8%), IDH1/IDH2 (9.2%), PBRM1 (9.2%), BAP1 (7.2%), and PIK3CA (7.2%). Mutations in BRAF, KRAS, and TP53 were all confirmed at Sanger sequencing samples were restricted to ICC and BAP1 mutations were all found in ICC (p=0.0097) with the exception of one GBC, while KRAS (p=0.0019) and TP53 (p=0.0019) were more represented in ECC and GBC, respectively (Table Mutations were differently distributed across the different tumour subtypes: IDH1/IDH2 mutations (20.0%) and the significant involvement of chromatin remodeling genes PBRM1 (14.3%), BAP1 (14.3%) and ARID1A (11.4%) . Eleven (15.7%) ICC had mutations in at least one of mTOR pathway genes: AKT1 (2.8%), PIK3CA (5.7%), PIK3C2A (7.1%), PIK3C2G (4.3%), and PTEN (1.4%). Mutations in tyrosine kinase receptors were uncommon, with the exception of TGFRB2 (4.3%). Of interest, most NRAS (5 of 6) and all BRAF (3 of 3) mutations clustered in ICC tumour subtype and were mutually exclusive with KRAS (15.7%). TP53 was mutated in 6 cases (8.6%). Low prevalence mutations were found in APC, CDKN2A, ERBB4, FBXW7, FGFR3, KDR/VEGFR2, SMAD4, and STK11.ICC were characterized by a high prevalence of PBRM1 14.%, BAP1 (KRAS was the most commonly mutated gene (47.4%), with codons 12, 13, 61 and 146 affected; one mutation was observed in NRAS, and none in BRAF. TP53 was the second most mutated gene (17.5%). Excluding ARID1A (12.3%), chromatin-remodeling genes were occasionally involved (PBRM1: 3.5%), whereas 24.6% of ECCs showed mTOR pathway gene mutations, including PIK3CA (8.7%), PIK3C2A (7.0%), PIK3C2G (8.7%), and PTEN (3.5%). SMAD4 mutations were observed in 6 cases (10.5%) and were mutually exclusive to TGFBR2 mutations that were found in 3 cases (5.3%). Low prevalence mutations were found in CTNNB1, FBXW7, and KDR/VEGFR2. The EGFR T790M mutation was observed in one case [In ECC, one case .TP53 mutations , and in 6 cases TP53 mutation was the only alteration detected. KRAS was mutated in 19.2% of cases. Chromatin remodeling genes were mutated in 30.8% of cases: ARID1A, 11.5%; BAP1, 3.8%; PBRM1, 7.7%; SMARCB1, 7.7%. MTOR pathway genes were mutated in 11.5% of cases: PIK3CA (7.7%) and PTEN (3.8%).GBC showed a high prevalence of EGFR gene copy number was analyzed by FISH.The results of immunohistochemistry are summarized in Table p=0.05 and p=0.00012, respectively). Pten was significantly down-regulated in the whole series, particularly in ECC of common bile duct and in GBC: a weak cytoplasmic/nuclear immunolabeling was observed in most cases.A significant over-expression of the activated forms of mTOR and its effectors p70S6K and 4EBP1 was seen in most cancers with no significant differences among subtypes, but for p70S6K Table . Of inteEGFR amplification labeled for Egfr with sharp membranous pattern and signals ranging from very strong to moderate . Median survival was 31 months and 79 (63.2%) subjects were followed to their deaths from disease.p=0.0001), TP53 (p=0.0043) and KRAS (p=0.0162) mutations . ICC showed a better outcome than ECC (p=0.018). No correlation emerged for any of the other clinicopathologic variables considered: sex, age, grade, vascular/perineural invasion.At univariate analysis, the most significant predictors of cancer outcome were tumour stage , Stage IV , and TP53 mutations as being significantly associated with cancer-related death the vast majority (77.1%) of cancers harbours a driver-gene mutation; ii) the diverse sites of origin in the biliary tree have significantly different molecular profiles, and each site of origin also shows molecular heterogeneity; iii) targetable pathway alterations are present in 68% (104/153) of cancers, defining molecular cancer subclasses; iv) specific alterations are eligible for the investigational development of prognostic and non-invasive follow-up markers.KRAS was the most frequently mutated gene (28.1%), followed by TP53 (18.3%), as reported in prior studies [ARID1A, PBRM1 and BAP1 [KRAS mutations were associated to a worse patients' prognosis confirming the univariate analysis previously described by Andersen [TP53 gene mutations as independent predictors of poor survival.The vast majority of cancers harboured at least one driver-gene mutation, and 39.2% (60/153 cases) showed concurrent mutations in two or more genes. studies , 35-38. and BAP1 was alsoAndersen . MultivaIDH1/IDH2 mutations were restricted to ICC (p=0.0005) and, with the exception of one GBC, BAP1 mutations were all found in ICC (p=0.0097). ECC and GBC were characterized by a high prevalence of KRAS (p=0.0019) and TP53 (p=0.0019) mutations, respectively.The different sites of origin showed significantly diverse molecular characteristics. The standard of care of biliary tract cancer is based on the combination of cisplatin and gemcitabine . To dateALK, EGFR, ERBB2, ERBB4, FGFR3, MET, KIT, KDR/VEGFR2) potentially amenable to target therapies were found in 9.2% of cases, with a higher prevalence in GBC than in ICC and ECC . In spite of a relatively high prevalence of Egfr overexpression detected by immunohistochemistry (35.4% of cases with 2+ or 3+), only two cases had EGFR mutations and three had gene amplification, confirming the low prevalence reported in the literature in cholangiocarcinomas unassociated with chronic liver disease [Mutations in tyrosine kinase receptors were observed in 34% of the whole series. In particular KRAS was the most frequently mutated gene in the 153 tumours (28.1%). KRAS mutations have been described in most of prior studies [KRAS/NRAS/BRAF mutations were mutually exclusive, and the highest mutation prevalence in RAS pathway was observed in ECC (49.1%) vs. ICC (27.1%) and GBC (19.2%). Of note, RAS mutations sensitize tumours to MEK inhibitors, highlighting the importance of these mutations in the use of targeted therapies [Mutations in components of the studies , 35-38. herapies , 40.AKT, FBXW7, PIK3CA, PIK3C2A, PIK3C2G, PTEN). This suggests that mTOR inhibitors might play a role in this molecular subgroup of patients.MTOR pathway relevance in biliary tract cancers is suggested by our immunohistochemical detection of activated forms of mTor and its downstream effectors in 51.3% of the cancers. The molecular basis of this activation in a proportion of cases is the mutation in one of the genes involved in this pathway , 9 of which were ECC . Our finding supports previous studies demonstrating the involvement of this pathway in cholangiocarcinomas, 46. OurARID1A, BAP1, IDH1, IDH2, PBRM1, SMARCB1) were found in 30.7% (47/153) of cancers in our series, confirming recent reports on the significant involvement of these genes in cholangiocarcinoma [IDH1 and IDH2 (p=0.0005), or cluster within this cancer type as is the case for ARID1A, BAP1, and PBRM1 that were found in 34.3% (24/70) of ICC. The open challenge is now to translate knowledge of the targeting of these genes to improved patient care through either the development of new disease specific markers or of therapy targets. Of interest, IDH1/2 mutated cancers accumulate 2-hydroxyglutarate in tumour tissue and release the molecule in blood, and the measurement of 2-hydroxyglutarate might be used as both a surrogate biomarker for IDH1/2 mutational status and a non-invasive test for the assessment of tumour burden in ICC [Alterations in chromatin remodeling genes showed no alterations in the 56 genes assayed, including 50 genes from a commercial panel and a custom panel exploring 6 recently discovered cholangiocarcinoma genes % showed . MechaniIn conclusion, we demonstrate that specific molecular alterations are associated to different cholangiocarcinomas categories and that potentially drug actionable pathways are evident in 68% of cases. These data further support the pathological and molecular heterogeneity characterizing biliary tree carcinomas. In currently designed clinical trials, cholangiocarcinomas are grouped together irrespective of their intrahepatic or extrahepatic site of origin. Our study shows that ICC and ECC should be considered separately, since they have different molecular characteristics. However, in the advent of molecular designed clinical trials, it would be appropriate to consider them together but only for the proportion of ICC and ECC sharing common molecular alterations.We also show that a high-throughput next-generation sequencing analysis can be successfully applied using low amounts of DNA from routinely processed paraffin tissues. Such a time- and cost-effective analysis is the basis to significantly improve the development of personalized treatments for cholangiocarcinoma patients, and their early access to innovative drugs.A retrospective series 1990-2011) of 153 surgically-resected primary biliary cancers were retrieved from the FFPE archives of the ARC-Net Biobank at Verona University Hospital under the local ethics committee approval (n. prog. 1959). All cases were re-classified according to WHO 2010 990-2011 . MatchedIn 113 cases , sufficient material for the construction of 1-mm cores tissue microarrays (TMAs) was available. Eighteen non-neoplastic controls were included in the TMAs. Three tissue cores per case were analyzed.DNA was prepared after enrichment for neoplastic cellularity to at least 70% using manual microdissection of 10 consecutive 4-\u03bcm FFPE sections, purified using the QIAamp DNA FFPE Tissue Kit (Qiagen), and qualified as reported elsewhere , 27.http://www.lifetechnologies.com. The custom panel targets 6 genes selected upon the results of published ICC exome sequencing: ARID1A, BAP1, PBRM1, PIK3C2A, PIK3C2G, TGFBR2[Two multigene panels were used: the 50-gene Ion AmpliSeq Cancer Hotspot panel v2 (Life Technologies) and an AmpliSeq custom panel targeting 6 genes not included in the commercial panel. The first explores selected regions of 50 cancer- genes: ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAS, GNAQ, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR/VEGFR2, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL. Details on target regions of the commercial panel are at G, TGFBR2. DetailsTwenty nanograms of DNA were used for each multiplex PCR amplification. Emulsion PCR was performed with the OneTouch2 system (Life Technologies). The quality of the obtained libraries was evaluated by the Agilent 2100 Bioanalyzer on-chip electrophoresis (Agilent Technologies). Sequencing was run on the Ion Torrent Personal Genome Machine loaded with 316 (50-gene panel) or 318 chips (6-gene panel). Data analysis, including alignment to the hg19 human reference genome and variant calling, was done using the Torrent Suite Software v.3.6 (Life Technologies). Filtered variants were annotated using the SnpEff software v.3.1. Alignments were visually verified with the Integrative Genomics Viewer; IGV v.2.2, Broad Institute.To validate the mutations detected by deep sequencing, BRAF (exon 11), KRAS (exon 2), and TP53 were analyzed by Sanger sequencing .The immunohistochemical expression of Egfr (Dako), Pten (Abnova Corporation), and of the phosphorylated forms of mTOR and its downstream effectors 4EBP1 and p70S6K was examined on consecutive 4-\u03bcm FFPE TMA sections. Appropriate positive and negative controls were run concurrently.Egfr expression was scored according to the EGFR pharmDx protocol (Dako): 0, no staining or membrane staining in \u226410% cancer cells; 1+, faint and partial membrane staining in >10% cancer cells; 2+, moderate and complete membrane staining in >10% cancer cells; 3+, strong and complete membrane staining in >10% cancer cells. Cases were then classified in two groups Egfr-positive (2+ and 3+) or Egfr-negative (0 and 1+).Pten expression was considered positive if more than 50% of neoplastic cells showed a moderate/strong nuclear and cytoplasmic immunoreaction.Staining for phosphorylated markers was considered positive when tumour cells showed cytoplasmic and/or nuclear staining with equal to stronger intensity compared with that of endothelial cells .The EGFR gene copy number status was assessed applying the Vysis EGFR/CEP7 Probe Kit (Vysis/Abbott Molecular). At least 50 representative nuclei per specimen were scored and EGFR-amplification was defined as described .Kruskal-Wallis test, Chi-squared test with Monte Carlo simulation, and Fisher's exact test corrected for multiple comparisons were used as appropriate. For comparison of Kaplan-Meier survival curves, Mantel-Cox log-rank test was used; for multivariate survival analysis, stepwise Cox proportional hazards regression was used; selection of the best model was performed using the \u201cbackward elimination\u201d algorithm. For all the analyses a p-value below 0.05 was considered significant. Graphs and univariate analyses were performed using GraphPad Prism\u00ae version 5.00 for Mac , multivariate Cox regression was done with R v. 3.0.2, using survival library v.2.37-4."} +{"text": "The degree of aortic insufficiency (AI) after transcatheter aortic valve replacement (TAVR) has been identified as a predictor of increased mortality. Since even mild AI is associated with increased mortality in some studies, accurate quantification of post-TAVR AI is critical. Assessment of AI by echocardiography is typically performed by visual inspection and semi-quantitative methods. Most post-TAVR AI is paravalvular, however echocardiography has limited ability to quantify multiple eccentric paravalvular jets. Using flow quantification methods, cardiac MRI (CMR) may more accurately quantify AI severity post-TAVR and therefore more accurately assess risk in this population.Twenty-three patients who underwent TAVR with a SAPIEN prosthesis were studied. All patients underwent an intraoperative transesophageal echocardiogram (TEE), as well as a post-procedure transthoracic echocardiogram (TTE) and CMR. Paravalvular AI by TTE and TEE was graded using color Doppler by quantifying the circumferential extent of AI as a percentage of the aortic annulus following recommendations from the Valve Academic Research Consortium. AI severity by CMR was quantified as the regurgitant fraction of forward aortic flow based on previously published recommendations .The mean age was 79 +/- 10 years; 52% were men. TTE and CMR were performed at 1 [1-1] and 4 [1-4] days post-TAVR respectively (median [IQR]). The left ventricular ejection fraction (LVEF) by CMR was 65 +/- 10%. AI severity by TTE was none in 9 (39.1%), trace in 11 (47.8%), and mild in 3 (13%) patients. TEE identified trace central AI in 6 patients (26%). Paravalvular AI by TEE was none in 4 (17.4%), trace in 14 (60.9%), and mild in 5 (21.7%) patients. AI by CMR was none in 2 (8.7%), trace in 5 (21.7%), mild in 13 (56.5%), and moderate in 3 (13%) patients; whether echocardiography alone underestimates the risk of adverse outcomes related to post-TAVR AI, and 2) whether similar degrees of post-TAVR AI by CMR also translate into adverse outcomes.None."} +{"text": "Describe the clinic-epidemiological characteristics of elderly patients (\u00b380 years) admitted to ICU for medical reasons, analyze the impact of orotracheal intubation (IOT), acute renal failure (RF) and shock at the mortality adjusted for habitual scales .Retrospective cohort study from January-2003 to May-2011. In this study we included patients (\u00b3 80 years) admitted to the ICU for medical causes, except ischemic heart disease or arrhythmias. Logistic regressions were used to calculate the OR of different variables as predictors of mortality (dependent variable). The ability to predict mortality of different \"scores\" adjusted for IOT, RF and Shock was performed using multivariate logistic regressions.They were analyzed 95 patients, 58% male; median age was 81 years (IQR 80-83 years). 52 patients died (54.7%), withdrawing life-sustaining therapy in 22 patients (23.2%). They were readmitted to ICU 3.3%. The median number of days in the ICU and hospital were 4 (IQR: 1.4 to 11) and 12 days (IQR: 6-25) respectively. The median APACHE II, SAPS II and SOFA were 23 (IQR 18-29), 7 (IQR: 4-10) and 49 (IQR: 40-65). 63% was intubated (60/95) for a median of 4 days (IQR: 1-13.75), died 73.3% (44/60). 65.3% presented shock (62/95), 66.1% died (41/62). 61% renal failure (58/95) and 60.3% died (35/58).Mortality was associated in univariate analysis with IOT , Shock ), but not with FR or age (p = 0.65); for every one point increase in score of APACHE II, SAPS II and SOFA, the increased in mortality was 16%, 32% and 13% respectively . In a conditional stepwise multivariate analysis, adjusting for FR, IOT, shock, age, sex and different \"scores\", only the SAPS II and IOT were independent predictors of mortality.In our series, the overall mortality of elderly patients (\u00b3 80 years) admitted to the ICU was very high (54.7%). The orotracheal intubation and SAPS II are independent variables associated to mortality patients admitted to ICU for medical cause with at least 80 years."} +{"text": "All patients had baseline pretreatment The study included 70 eligible LANPC patients. The 4-year OS and DFS rates were 86.7% and 78.6%, respectively. The median OS and DFS intervals were not reached. On a univariate analysis, the 4-years DFS was significantly higher in patients with pretreatment SUVmax <8 compared versus \u2265 8 . Furthermore, DFS was significantly correlated with pretreatment T stage (P=0.01), N stage (P=0.02), treatment response (P<0.001) and treatment breaks (P<0.001). On a multivariate analysis, the SUVmax category was the only factor correlated with 4-year DFS but not OS (P=0.085).There is no actual or potential conflict of interest with the production and publication of this work. No author has a direct or indirect commercial financial incentive associated with the publication of this article.18F-FDG-PET-CT SUVmax is a potential independent prognostic predictor of clinical outcomes in patients with LANC treated definitively with TPF induction chemotherapy followed by CRT. Further controlled clinical trials are worthwhile.This study shows that the pretreatment primary tumor Concurrent Chemoradiation (CRT) has been established as the standard treatment of locally advanced nasopharyngeal carcinoma (LANPC) based on the results of randomized clinical trials and a recent meta-analysis, which demonstrate a clear benefit of chemotherapy and radiotherapy in comparison to radiotherapy alone -7.The Intergroup-0099 study demonstrated statistically significant overall survival (OS), disease free survival (DFS), and local-regional control (LRC) rate favoring CRT followed by adjuvant chemotherapy versus radiation therapy (RT) only. The study showed poor patient\u2019s compliance in the CRT group with only 55% undergoing adjuvant treatment and notably high local-regional failure and distant metastases rates . Therefo18F-FDG positron emission tomography with computed tomography (PET-CT) has been investigated as a potential tool to predict treatment outcomes in patients with head and neck cancers, the diverse tumor sites, and inconsistent results limit those studies . To minimize partial volume effects, the maximum-pixel SUV within a region of interest encompassing the tumor was used for further calculations. The median pretreatment primary tumor and lymph nodes SUVmax were 10.3 (range 3.2 to 24.3), and 8.5 (range 2.8 to 18.3) respectively.All patients had pretreatment Sixty-three patients (90%) received 3 cycles of induction chemotherapy, and seven patients received 2 cycles of induction chemotherapy due to Grade 3 nausea and vomiting in 4 patients and febrile neutropenia in three patients.2) treatment. Seven patients of them (35%) completed 3 cycles of tri-weekly cisplatin with 25% dose reduction in 3 patients due to grade 3 mucositis, dermatitis and neutropenia, while 10 patients (50%) tolerated 2 cycles and only three patients (15%) had 1 cycle. The other 50 patients (71.4%) received concomitant cisplatin (40 mg/m2) on weekly basis. Of these patients, three patients (6%) received 3 weeks of weekly cisplatin, six patients (12%) had 4 weeks, 18 patients (36%) had 5 weeks, and 23 patients (46%) had 6 weeks. Of the patients who received 6 weeks of concurrent weekly cisplatin, 20% dose reduction was applied on 5 patients due to development of grade 3 adverse events. After induction chemotherapy, nine patients (12.8%) achieved complete response, 54 patients (77.1%) had partial response, and 7 patients (10%) had stable disease.Twenty patients (28.5%) received standard tri-weekly concomitant cisplatin (100 mg/mNineteen patients ( 27%) received IMRT utilizing SIB technique, while 51 patients (72.8%) were treated using 3D-RT. Total cumulative RT dose delivered ranged from 66 to 70 Gy (median 70 Gy).All patients were assessed 6-8 weeks after definitive concurrent chemoradiation with radiologic imaging (CT and/or MRI). Sixty patients (85.7%) achieved CR and 10 patients (14.3%) had PR after treatment completion. On multiple linear regression analysis, the response achieved at the end of definitive CRT was significantly associated with tumor stage (P<0.001), nodal stage (P=0.002), treatment breaks (P<0.001) and the pretreatment PET-CT SUVmax (P=0.041). At a mean follow up time of 39.7 months, 13 patients (18.5%) relapsed. Three patients had local relapse only, five patients had distant metastases and five patients had both local and distant metastases. The 4-year OS and DFS rates were 86.7% and 78.6%, respectively and 2. TReceiver Operating Characteristic (ROC) curve was used to depict the ability of SUVmax to predict prognosis. Area under the curve was 0.564, and the best cut-off value was 8.0 . On a unInduction chemotherapy was well tolerated, seven patients (10%) received only 2 induction cycles because of grade 3 toxicities, three (4%) of them developed grade 3 neutropenia and four (6%) patients had G3 nausea and vomiting. The most frequent acute toxicity encountered during chemoradiation was mucositis as 37 patients (53%) developed Grade 3 while only 4 patients (6%) suffered from Grade 4 mucositis, which necessitated hospitalization and discontinuation of treatment for 7-10 days.Fourteen patients (20%) developed Grade 3 weight loss (10-19.9 Kg) while three patients (4.3%) had Grade 4 weight loss \u2265 20 kg during CRT . NotablyThe role of induction chemotherapy followed by concurrent chemoradiotherapy (CRT) is a matter of outstanding interest in LANPC because of the relatively high incidence of locoregional or distant metastasis of more than 40% due to the poor patient tolerance and limited penetration of adjuvant chemotherapy after CRT ,20. MoreThis study demonstrated that 3 cycles of TPF induction chemotherapy followed by CRT is a tolerable treatment modality with acceptable toxicity profile. The objective response rates (RR) were 89.6% (complete response (CR) was 12.5% and partial response (PR) was 77.1%) after induction TPF and 100% (CR in 85.7% and PR in 14.3%) after treatment completion. These results compare favorably with previous reports on induction chemotherapy. Bae et al. reported objective RR of 97% after induction chemotherapy (CR in 15.2% and PR in 81.8%) and 97% (CR in 69.7% and PR in 27%) after CRT (18). Similarly, Ekenel et al. reported objective RR of 87% and CR of 12% after induction and 100% objective RR with 95% CR after CRT .In our study, the 4-year OS and PFS rates were 86.7% and 78.6%, respectively .The median DFS and OS intervals were not attained. Comparable survival rates have been reported. Bae et al. treated 32 LANC patients with TPF followed by CRT, PFS and OS rates were 75% and 86% respectively . HelleniKong et al. reported the results of phase II trial on induction TPF followed by CRT using weekly cisplatin, the overall RR after RT was 90.2% and the 1-year OS was 100% .18F-18F 18F FDG-PET-CT-CT-CT, in addition to being used for the diagnostic work-up of patients with LANPC, 18F-FDG-PET-CT uptake, as measured by maximal SUV, showed a statistically significant association with DFS rate in NPC patients treated with CCRT [The pretreatment ith CCRT . In agreith CCRT . On a muith CCRT . Howeverith CCRT . Our stuith CCRT . A possiThe most commonly encountered acute toxicities during induction chemotherapy were Grade 3 neutropenia, nausea and vomiting in 4% and 6% of patients respectively, which were uncomplicated and manageable. The most frequent acute toxicity encountered during CRT was mucositis as 37patients (53%). Moreover, fourteen patients (20%) developed Grade 3 weight loss 10-19.9 Kg) while three patients (4.3%) had Grade 4 weight loss \u2265 20 kg during the CRT phase. Similarly, Bae et al. reported that febrile neutropenia (9.1%), and nausea (9.1%) as the most notable grade 3 and 4 toxicities during induction chemotherapy phase, while mucositis (39.4%), fatigue (15.2%), and nausea (9.1%) were the most common grade 3 and 4 toxicities during CRT . Additio.9 Kg whi18F-FDG uptake (SUVmax \u2265 8) may indicate poor outcome in such patients.The pretreatment primary tumor PET-CT SUVmax is a potential independent prognostic predictor of clinical outcomes in patients with LANPC treated with TPF induction chemotherapy followed by CRT. A high"} +{"text": "A multinational collaborative effort aimed to develop a new set of criteria for macrophage activation syndrome (MAS) complicating systemic juvenile idiopathic arthritis (sjia) is ongoing. The data-collection phase of the project has been recently completedTo describe the demographic, clinical, laboratory, and histopathologic features, therapeutic interventionsand outcome of 362 children with MAS collected in the studyPatient data were collected retrospectively in a web-based database, developed and handled at the coordinating centre 362 patients with sjia-associated MAS were entered in the study website by 95 investigators from 33 countries. 208 patients (57.5%) were females. Median age at onset of sjia was 5.3 years (IQR 2.7-10.1 years) and median disease duration at onset of MAS was 3.5 months (IQR 0.1-2.6 years); MAS occurred at onset of sjia in 77 patients (22.2%). The most frequently observed clinical features were fever (96%), liver enlargement (70%) and spleen enlargement (58%); CNS involvement was reported in 122 patients (35%) and haemorrhagic manifestations in 71 patients (20%). The main laboratory abnormalities were: hyperferritinemia, increased D-dimer and liver enzymes, falling platelet count, hypertriglyceridemia and increased LDH. The most frequently reported trigger of MAS was sjia flare (53.8%), followed by infections (37.8%) and medication toxicity (4.3%). Hyperferritinemia, increased liver enzymes, LDH, triglycerides and D-dimer and falling platelet count were the sole laboratory parameters that showed a percentage change greater than 50% between pre-MAS visit and onset of MAS. Hemophagocytosis was seen in 2/3 of patients who underwent bone marrow aspirate. Therapeutic interventions included corticosteroids (97.7%), cyclosporine (61.2%), Iv Ig (36.3%), biologic medications (15.2%), etoposide (11.8%), other immunosuppressants (7.1%) and plasma exchange (4.1%). ICU admission was required in 34.9% of patients; the mortality rate was 8.1%Fever and hepatosplenomegaly were the most frequently reported clinical features. Hyperferritinemia, increased liver enzymes, LDH, triglycerides and D-dimer and falling platelet count were the most frequently observed laboratory abnormalities. These laboratory parameters also showed the greatest change between pre-MAS visit and onset of MAS. Bone marrow aspirate exhibited hemophagocytosis in 2/3 of instances. Corticosteroids and cyclosporine were the most frequently used medications.None declared."} +{"text": "Significant mitochondrial function impairment is known to result from cardiac ischemia reperfusion injury (IR) precipitated by cardiopulmonary bypass during heart surgery.We sought to determine the effect of different ischemia time spans in cardiac IR on mitochondrial respiratory chain (RC) function, inner membrane polarization and Ca2+homeostasis.Wistar rat hearts were harvested and divided into 4 groups of stop-flow induced warm global IR: 0, 15, 30 and 40 min of ischemia followed by 30 min of reperfusion, respectively. Myocardial contractility was determined from left ventricular pressure records . Subsarcolemmal mitochondria (SSM) were isolated and analyzed regarding electron transport chain (ETC) coupling using a Clark-type electrode (polarography), membrane polarization (JC1 fluorescence) and Ca2+-handling in terms of Ca2+induced swelling and Ca2+-uptake and release (Ca2+-sensitive electrode).IR in general depressed LV contractility irrespective of ischemia duration. In contrast, increasing length of ischemia time highly significantly promoted ETC uncoupling at complex I-V and II-IV in state 3 respiration, respectively. Membrane potential showed a distinct hyperpolarization in IR30/30 and IR40/30 compared to the other groups (p < 0.0001), continuously wearing off after CCCP-induced uncoupling. Regarding Ca2+-induced swelling, light transmission of IR40/30 SSMs started to differ significantly (p < 0.04) from IR0/30 after 6.5 min of Ca2+-addition, swiftly followed by IR15/30 (8.5 min) and 30/30 (16.5 min). All effects were delayed by app. 3.6 min by pyruvate addition in parallel assays also halving recorded swellings. Ca2+-uptake revealed slower rates and greater spans in IR15/30 and IR30/30 (p < 0.005) whereas Ca2+-release was delayed for ischemia an duration \u226430 min (p < 0.0001).Longer ischemia duration in IR injury gradually impairs SSMs in terms of respiratory chain function and Ca2+-homeostasis. Membrane hyperpolarization appears to be responsible for impaired Ca2+-cycling and ETC function. Therefore, ischemia time should be considered an important factor influencing IR experiment-derived conclusions."} +{"text": "One of the aims of lung recruitment is to improve oxygenation , but it 0) PEEP was increased by 5 cmH2O (t1). Recruitment maneuver was applied for 40 seconds with 40 cmH2O PS. Measurements were taken immediately after recruitment (t2) then 15 minutes (t3) and 30 minutes later (t4).In a prospective, observational study, 30 patients with a Lung Injury Score \u22652 were recruited. Following baseline measurements , low responders and high responders . In the NR-group, PaO2/FiO2 decreased significantly: median (interquartile), PaO2/FiO2 = 178 (159 to 240) versus 165 (118 to 210) mmHg; in the LR-group and in the HR-group there was significant improvement: 119 (98 to 164) versus 161 (123 to 182) mmHg and 141 (130 to 183) versus 239 (224 to 369) mmHg, P < 0.05, respectively. Dynamic compliance (Cdyn) significantly dropped at t as compared with t in the NR-group, Cdyn = 62 (48 to 87) versus 53 (43 to 78) ml/cmH2O, while there was no significant change in the LR- and HR-groups, P < 0.05. At the same time points the dead space to tidal volume ratio (Vds/Vte) significantly increased in the NR-group, Vds/Vte = 30 (23 to 37) versus 37 (26 to 42)%, but not in the LR- and HR-groups, P < 0.05.According to the difference of PaO2/FiO2 in the majority of patients (73%) without affecting Cdyn or Vds/Vte; therefore it may be a safe approach to improve oxygenation in patients ventilated in CPAP/PS mode.Recruitment maneuvers improved PaO"} +{"text": "Chromosomal imbalances are implicated in the etiology of Developmental Delay (DD)/Intellectual Disability (ID)/Congenital Malformations. However, most of these cases may not be diagnosed by conventional cytogenetic techniques. We aimed to establish a-CGH technique and assess its potential as a diagnostic tool for chromosomal imbalances and to detect known and novel chromosomal aberrations in patients with DD/ congenital malformations.Microin-situ hybridization techniques (FISH), besides we applied (array-CGH) high resolution Agilent scanner with 1X244 K array format in 25 samples and 2X400 K format in 50 samples.A total of 75 patients presented with DD/ congenital malformations with or without ID were referred to the CEGMR for cytogenetic analyses. We used both conventional cytogenetic G-banding and Fluorescent Chromosomal aberrations were detected in 10/72 (13.8%) patients by G-banding technique and 4/50 (8%) by FISH technique, however, 17/72 (23.6%) were diagnosed by a-CGH technique. All micro-deletion syndromes and partial duplications were detected by the chromosomal microarray technique: (Del 15 (q11.2); Del 15 (q13-14); Del 22 (q11.2); Del 7 (q11.23); Del 18 (q21 q23); Del 1 (p36); del 21q21-q23, del 13q21-q31.3, del 11q24.2-q25, and duplications in: dup 18p (p11.21); dup 15 (q11 q23); dup 18 (q23). However, one patient with unbalanced translocation could not be detected by this technique. The increase in the CNVs number detected by a-CGH needs further investigation for contribution to phenotypes.Our results indicate the strength of high resolution genomic arrays in diagnosing cases of unknown etiology and in detection of contiguous genomic alterations in the wide spectrum of cases with DD/ID/congenital malformations."} +{"text": "Cardiovascular disease (CVD) is a significant cause of non-AIDS-related morbidity and mortality in HIV-positive individuals . ManagemDescribe the clinic caseload; record clinic interventions and outcomes; recommend service development.We conducted a retrospective notes review of patients attending the co-morbidity clinic from January 2012 to May 2014. Data collected: demographic, HIV, CVD, CV risk, investigations and clinical interventions.From a cohort of approximately 960 patients (70% African), 60 (6%) were seen in the co-morbidity clinic over the specified time period. Median age was 53 (range 24-80). Although 60% of our cohort is female, 43% (26/60) of the CVD clinic were female. 42 (70%) were African. The mean CD4 was 560 (range 48-1339). All patients were on ART and 6 (10%) had a detectable viral load > 400 copies/mL. Clinic caseload: i) CVD: 9 had a prior CV event (ACS or CVA); 5 had CCF; new diagnoses included LVH (2), cardiac dysfunction (6); AF (2); atrial thrombus (1). ii) Co-morbidities: 48(80%) had hypertension \u2013 10 (16.6%) were on quadruple therapy; 17 (28%) had diabetes; 35 (58%) were on a statin. Three had their smoking status clearly documented. Seventeen (28%) were referred to the dietician. Investigations included echo, 24-hour BP/ tape, CT angio, cardiac MR.The joint clinic facilitated real-time decision making on clinical interventions. Patient access to cardiac investigations was expedited. Patients attended fewer outpatient appointments. Both cardiology and HIV clinicians preferred the benefits of joint working. Clinical outcomes were difficult to assess and will need further definition. Recommendations for development include: improved CV risk assessment, improved outcome measures, links to smoking cessation services."} +{"text": "The coronavirus disease 2019 (COVID-19) pandemic has had a profound worldwide impact on health. Acute Confusional Syndrome (ACS) is the most common neuropsychiatric complication in COVID-19 infection.Describe the characteristics of the admited patients attended by the liaison psychiatry service for acute confusional syndrome during the COVID 19 pandemic. Sociodemographical and clinical variables were descrived.We conducted an observational, descriptive study. All patients attended by the liaison psychiatry service of Hospital del Mar, between February and April 2020, with ACS diagnosis were included.We included 62 patients with acute confusional syndrom; 35 were men (56.5%), and mean age was 71.71 years (standard deviation [SD]:11.345). The mean duration of admision stay was 41.19 days [SD: 38.039]. The mean number of consultations carried out was 6.5 [SD: 5.422]. 52.5% of our sample of our sample had confusional symptoms for 8 days. 50 patients presented complications during admission (80.6%), of which 43 patients developed infectious complications (69.4%). 59 patients had a history of chronic diseases (95.2%). 54 patiens (88.5%) had potencial risk factors associated with acute confusional syndrome including: isolation in 24 (39.3%), active infection in 46 (74.2%), hypoxemia in 25 (40.3%), previous cognitive impairment in 15 (24.6%)Acute Confusional Syndrome mainly affects people with risk factors such as isolation, active infection and hypoxemia (which in turn are symptoms of Covid-19).No significant relationships."} +{"text": "Forty-nine (80.33%) E. coli strains were isolated from 61 samples from a pig farm and were screened for the presence of tet(X). Among them, six (12.24%) strains were positive for tet(X4) and exhibited resistance to tigecycline (MIC \u2265 16 mg/L). They were further sequenced by Illumina Hiseq. Six tet(X4)-positive strains belonged to ST761 with identical resistance genes, resistance profiles, plasmid replicons, and cgMLST type except that additional ColE10 plasmid was present in isolate SH21PTE35. Isolate SH21PTE31, as a representative ST761 E. coli strain, was further sequenced using Nanopore MinION. The tet(X4) in SH21PTE31 was located on IncFIA18/IncFIB(K)/IncX1 hybrid plasmid pYUSHP31-1, highly similar to other tet(X4)-carrying IncFIA18/IncFIB(K)/IncX1 plasmids from ST761 E. coli and other E. coli lineages in China. These IncFIA18/IncFIB(K)/IncX1 plasmids shared closely related multidrug resistance regions, and could reorganize, acquire or lose resistance modules mediated by mobile elements such as ISCR2 and IS26. Phylogenetic analysis were performed including all tet(X4)-positive isolates obtained in this pig farm combined with 43 tet(X4)-positive E. coli from pigs, cow, pork, wastewater, and patients with the same ST from NCBI. The 50 tet(X4)-carrying E. coli ST761 isolates from different areas in China shared a close phylogenetic relationship (0-49 SNPs). In conclusion, clonal transmission of tet(X4)-positive E. coli ST761 has occurred in this swine farm. E. coli ST761 has the potential to become a high-risk clone for tet(X4) dissemination in China.This study aimed to investigate the prevalence and characterization of Enterobacteriaceae (tet(X3) in Acinetobacter baumannii and tet(X4) in Escherichia coli from animals in China significantly impairs the clinical efficacy of tigecycline (tet(X) and its variants [tet(X1)\u223ctet(X47)] have been identified in Gram-negative pathogens and encode flavin-dependent monooxygenase that modify tigecycline (tet(X4) gene has been increasingly identified in E. coli from various sources including food-producing animals, wild birds, food products, humans, and the environment, mainly in China (tet(X4) has subsequently detected in various Enterobacteriaceae species, such as Proteus, A. baumannii, Aeromonas caviae, Citrobacter freundii, Enterobacter cloacae, E. hormaechei, Klebsiella pneumoniae, and Shewanella xiamenensis gene and tigecycline resistance are frequently described in E. coli from food-producing animals (mainly pigs) in China (tet(X) in livestock (tet(X4) in Enterobacteriaceae (tet(X4) in E. coli isolates from one pig farm in Shanghai, China, to provide insights into the spread of tet(X4) in this swine farm.Although tigecycline is not applied in livestock, the in China . The heaivestock . In addieriaceae . In thisn = 41) and pig feed (n = 20) were collected from a pig farm in Shanghai, China. Samples were incubated in LB broth for 18\u223c24 h and then cultured on the MacConkey agar with and without 2 mg/L tigecycline. One E. coli isolate per plate was selected and identified by 16S rRNA gene sequencing (tet(X) were detected by PCR and sequencing 1. The tet(X4)-positive isolates were further tested susceptibility to other 13 antimicrobial agents including ampicillin, cefotaxime, meropenem, gentamicin, amikacin, streptomycin, tetracycline, chloramphenicol, florfenicol, nalidixic acid, ciprofloxacin, colistin, and sulfamethoazole/trimethoprim by using the broth microdilution method. The results were interpreted according to Clinical Laboratory Standards Institute (CLSI) M100, 30th edition. Florfenicol (> 16 mg/L) and streptomycin (> 16 mg/L) were interpreted according to the epidemiological cut-off values for E. coli set by EUCAST (see Text Footnote 1). The E. coli strain ATCC 25922 was used for quality control.The MICs of tigecycline were determined in all E. coli C600 (streptomycin-resistant) as the recipient strain. Transconjugants were selected on MacConkey agar plates supplemented with 2 mg/L tigecycline and 3,000 mg/L streptomycin.Conjugation experiments were conducted according to a previously described protocol using E.tet(X4)-positive E. coli strains were sequenced on the Illumina Hiseq platform, and the quality-trimmed raw sequence data were assembled into contigs using SPAdes v.3.8.2 with -careful and -cov cut-off auto options. One representative E. coli isolate SH21PTE31 was sequenced using Nanopore MinION, assembling with Unicycler version 0.4.9. The genome sequences of them were analyzed multilocus sequence typing (MLST), resistance genes, and plasmid replicons by using the Center for Genomic Epidemiology (CGE) pipeline2. The tet(X4)-carrying plasmid pYUSHP31-1 in strain SH21PTE31 was analyzed by ISfinder3, BLAST4 and the Gene Construction Kit 4.5 . pYUSHP31-1 was compared with other similar plasmids using BLASTn and BRIG.The tet(X4)-positive ST761 E. coli strains in the NCBI database were downloaded (tet(X4)-carrying ST761 E. coli strains obtained from this pig farm and NCBI was constructed using Parsnp5 and visualized by iTOL6. Core genome MLST (cgMLST) profiles based on 2,513 alleles were analyzed using cgMLSTFinder 1.27.The genome sequences of 43 h, 2022) . The phytet(X4)-positive E. coli isolates have been deposited in the GenBank under accession number PRJNA836295.The whole genome sequences of E. coli strains were obtained from 61 samples. Among them, six strains (12.24%) from different fecal samples were positive for tet(X4), including five strains isolated under selection with tigecycline and one strain isolate without selection. The tet(X4)-positive isolates exhibited resistance to tigecycline (MIC \u2265 16 mg/L), and the remaining isolates showed susceptibility to tigecycline with MICs of 0.125 to 0.5 mg/L. These tet(X4)-positive isolates were also resistant to ampicillin, tetracycline, chloramphenicol, florfenicol, and sulfamethoazole/trimethoprim, but susceptible to cefotaxime, meropenem, gentamicin, amikacin, streptomycin, colistin, nalidixic acid, and ciprofloxacin (tet(X4) to E. coli C600 via conjugation.A total of 49 floxacin . Howevertet(X4)-positive E. coli strains were obtained by Illumina (tet(X4)-positive E. coli strains belonged to ST761 with identical resistance genes and plasmid replicons , except that additional ColE10 plasmid was present in isolate SH21PTE35 and four plasmids (tet(X4) and another eight resistance genes were co-located on the largest plasmid, designated as pYUSHP31-1. This plasmid had a size of 104,163 bp, and belonged to the hybrid IncFIA18/IncFIB(K)/IncX1 plasmid. It was highly similar to our previously reported plasmid pYUSHP6-tetX (GenBank accession no. MW423609) from ST761 E. coli isolate SH19PTE6 collected from the same pig farm in 2019 (tet(X4)-carrying IncFIA18/IncFIB(K)/IncX1 plasmids from ST761 E. coli strains in China, such as pNT1W22-tetX4 , pRF108-2_97k_tetX , pSTB20-1T , p54-tetX , pYPE12-101k-tetX4 , and pYPE3-92k-tetX4 (tet(X4) were also present among other E. coli lineages obtained from a pig farm in Jiangsu province, China (tet(X4) dissemination between different bacteria.The complete sequences of isolate SH21PTE31, as a representative ST761 plasmids . Among t in 2019 , and alsP041453) . Similare, China , e.g., pe, China , highlig26 and IS1, respectively. The pYUSHP31-1 MRR contained nine resistance genes and consisted of five regions bounded by IS26 or ISCR2 /IncX1 plasmids, but differed by 46-bp shorter (limited to pNT1N25-tetX4) or 126-bp longer Tn2 except pYUSHP6-tetX ; deletion of a 5,198-bp structure (IS26-\u0394Tn2-\u0394Tn21) in pNT1F31-tetX4 (The second part (\u223c14.8 kb) contained three resistance genes 31-tetX4 .tet(X4) structure [\u0394ISCR2-orf1-abh-tet(X4)-ISCR2-orf2-orf3-orf4-\u0394ISCR2] and downstream floR-\u0394ISCR2 module, as observed in other IncFIA18/IncFIB(K)/IncX1 plasmids with one to four copies of tet(X4) structure (tet(X4) structure [\u0394ISCR2-orf1-abh-tet(X4)-ISCR2] with varied copies was identified in plasmids pNT1F10-tetX4, pRF108-2_97k_tetX, pSTB20-1T, pRF148-2_101k_tetX, and NT1N25-tetX4 (1 was inserted into orf1 within the tet(X4) structure with 9-bp direct repeats in plasmids pNT1F10-tetX4 and pNT1N31-tetX4, and the latter plasmid carried the tet(X4) fragment in the opposite orientation and additional two copies of IS26 upstream of floR-\u0394ISCR2 module (CR2 is associated with tet(X4) transmission by forming an rolling-cycle transposable unit, thus generating tandem copies of tet(X4)-harboring structures in different IncFIA18/IncFIB(K)/IncX1 plasmids.The third region corresponded to the core tructure . Compare25-tetX4 ; one cop2 module . As prev2 module , ISCR2 i26, an incomplete Tn1721 carrying tetracycline resistance gene tet(A) and an intact Tn2 (tnpA-tnpR-blaTEM\u20131b), followed by 5,391-bp module [\u0394intI4-IS440 tnpA-tet(M)-\u0394IS26] and qnrS1 structure (IS26-qnrS1-\u0394ISKpn19). This region was also found in other IncFIA18/IncFIB(K)/IncX1 plasmids with the same \u0394ISKpn19/IS26 boundary except pYPE3-92k-tetX4 (26-mediated homologous recombination could explain the loss or acquisition of this region.The fourth segment (\u223c18.4 kb) included one copy of IS2k-tetX4 . IS26-me26-\u0394IS1294-gshB-IS1) was identical to segments in other plasmids except p54-tetX -carrying IncFIA18/IncFIB(K)/IncX1 plasmids may evolve from the same ancestor, and form variable but related MRRs by insertions, deletions, or rearrangements of different resistance modules mediated by mobile elements such as IS26 and ISCR2.These Escherichia coli ST761 has been increasingly reported in different sources associated with tet(X4) in China, particularly from pigs (tet(X4)-positive E. coli isolates of the same ST, we performed a phylogenomic analysis based on cgSNP. The results revealed a relatively close genetic relationship (0-49 SNPs) among 50 tet(X4)-positive ST761 E. coli isolates (n = 44) was the most prevalent type, and it contained two isolates from patients, two from wastewater, three from pork, and 37 from pigs including six strains obtained in this study and SH19PTE6 from the same pig farm (tet(X4) were present in all isolates, and the core resistance genes within tet(X4)-carrying IncFIA/IncFIB(K)/IncX1 plasmid pYUSHP31-1 were shared by 45 strains is the main mechanism for tet(X4) transmission (tet(X4)-carrying strains, such as E. coli ST877, ST10, and ST48 clones is also responsible for tet(X4) dissemination between animals and humans (E. hormaechei co-harboring tet(X4) and blaNDM could also clonally spread from the slaughterhouse to the retail market (E. coli ST761 isolates carrying tet(X4) has been detected in pigs, cow, pork, wastewater, and patients in different areas from China sharing a close phylogenetic relationship, suggesting that the ST761 lineage has the potential to be a successful clone to transfer tet(X4) and other resistance genes as well in China.Although horizontal transfer mediated by plasmids and insertion sequences -positive ST761 E. coli was the main reason for spread and persistence of tet(X4) in this pig farm. Importantly, E. coli ST761 has the potential to become a high-risk clone for tet(X4) dissemination in China. On the other hand, the tet(X4)-carrying IncFIA18/IncFIB(K)/IncX1 hybrid plasmids within ST761 E. coli lineage could reorganize, acquire or lose resistance modules mediated by mobile elements such as ISCR2 and IS26. The horizontal transfer of similar IncFIA18/IncFIB(K)/IncX1 plasmids further facilitates the tet(X4) dissemination in distinct lineages.Our findings suggest that The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/XJ and JW conceived the study. M-JL, HW, Z-YW, and YJ carried out the experiments. JW, Z-YW, and YJ analyzed the data. JW wrote the manuscript. Z-MP and XJ revised the manuscript. All authors read and approved the final manuscript."} +{"text": "Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique ; (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification. When considering the biodiversity on Earth, Fungi are the third most diverse group of eukaryotic organisms, with approximately 140,000 known species, although the estimates can be as low as 700,000 and as high as 12 million ,4. FungiMolecular markers are the portions of DNA sequences dispersed along the genome used to identify a given organism . As the In this work, a systematic revision of the literature was performed to identify the most commonly used molecular markers and their use in Kingdom Fungi. Between March and June 2022, the online Google Scholar database was searched using the keywords \u201cRestriction Fragment Length Polymorphism; fungi\u201d, \u201cRandom Amplification of Polymorphic DNA; fungi\u201d, \u201cAmplified Fragment Length Polymorphism; fungi\u201d, \u201cInter-Simple Sequence Repeats; fungi\u201d, \u201cMinisatellites; fungi\u201d, \u201cMicrosatellites; fungi\u201d, \u201cSingle-nucleotide polymorphisms; fungi\u201d, \u201cInDels; fungi\u201d, \u201cDNA barcoding; fungi\u201d, \u201cMetabarcoding; fungi\u201d, and \u201c; \u201cWhole Sequencing Genome; fungi\u201d limited to the period between 2012 and 2022 and the resulting articles were ordered by relevance. More than 4400 articles were initially selected. After an exhaustive manual curation was performed on this list, all the selected articles were read and analyzed. A total of 1332 papers were considered for the preparation of this study.Restriction Fragment Length Polymorphism (RFLP) was developed by Alec Jeffreys in 1984. In this technique, DNA samples are digested with specific endonucleases resulting in a profile of fragments of different lengths which is characteristic of each species. RFLPs have the advantage of resulting in medium polymorphic variability and do not require prior knowledge of the genome sequence analyzed. However, as disadvantages, these markers have high development and running costs and require high quality and quantity of DNA .Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is based on Polymerase Chain Reaction (PCR) amplification of a target region containing polymorphic sites followed by digestion with restriction enzymes and fragment separation by electrophoresis. Primers are designed to flank the polymorphic sites and positioned to create unequally sized fragments upon restriction endonuclease cleavage of the PCR products .Terminal-RFLP (T-RFLP), the automated version of RFLP, involves an intermediate restriction digest after PCR and before the separation of the fragments. The procedure can be applied to rRNA genes and nuclear ribosomal internal transcribed spacer (ITS) region, with amplified fragments subjected to digestion with one or more restriction enzymes and the fragments separated by gel electrophoresis. T-RFLP develops this by separating fragments using an automated sequencer that detects fluorescently labeled (using fluorescently labeled primers during PCR) amplicons. In T-RFLP analysis, the fragments are determined by the peak height and intensity (relative fluorescence). Each set of restriction fragments creates specific pattern fingerprints .The Multiplex PCR-terminal restriction fragment length polymorphism (MT-RFLP) was developed to simultaneously analyze a significant number of samples in a single reaction, reducing the cost and time of the study. Multiplexing allows performing one common reaction for various groups of microorganisms in a condition when the parameters of the reaction will be appropriate for each tested element. The multiplexing might be applied to PCR, and each subsequent step is performed with a mixture of multiplex PCR products. Alternatively, single reactions (PCR and restriction) can be carried out and followed by multiplex fragment analysis of pooled samples .Candida spp. (48.4%), the etiological agent of diseases such as candidiasis and candidemia, Trichophyton spp. (15.6%), responsible for dermatomycosis and onychomycosis, and Aspergillus spp. (10.2%), associated with superficial and invasive infections. In the soil, aspects such as the effects of geographical distance (12.5%), plant composition (12.5%), and application of fertilizers (9.4%) on microbial composition were studied. The most studied plant pathogens were Colletotrichum spp. (20.8%), Fusarium spp. (12.5%), and Penicillium spp. (8.3%) , the study of soil microorganisms (28.7%), and plant health (11.9%). In human health, the most frequently studied fungi were . (8.3%) .Random Amplification of Polymorphic DNA (RAPD) was simultaneously developed by the teams of Welsh and McClelland and WillThis technique uses high polymorphic molecular markers and requires a medium quantity of DNA, and presents intermediate technical development and running costs. Among the disadvantages is the low reproducibility of the results .Fusarium\u201419.0%; Aspergillus\u20149.5%; Rhizoctonia\u20147.1%). These studies include vegetative compatibility, fingerprinting of toxigenic and non-toxigenic strains, and antifungal susceptibility. Among the plant pathogens, Fusarium spp. (26.9%) was associated with wilts in different crops and pokkah boeng disease in sugarcane; Alternaria spp. (7.7%), associated with diseases such as brown spot, leaf spot, and black rot or being endophytic fungi; and Phaeoacremonium spp. (7.7%), responsible for grapevine diseases such as esca. In the case of the identification of food products, the main species identified were the edible mushrooms Pleurotus (30.8%) and Agaricus (3.8%), while the main species concerning food contamination and spoilage were Aspergillus spp. (17.3%) and Penicillium (7.7%) , the study of diverse plant pathogens (29.0%), and the authentication or safety verification of products such as food and drinks (15.9%). Genetic diversity in fungi was the focus of studies related to diseases in plants and humans .Amplified Fragment Length Polymorphism (AFLP) was developed by KeyGene in 1990 .These markers are highly polymorphic and abundant in the genome. The main limitations of this technique are the high development and running costs, high quality and quantity of DNA requirements, prior knowledge of the DNA sequence, and show intermediate reproducibility and low automation capacity ,22.Coniophora species-complex, Fusarium spp., Macrophomina phaseolina, Nigrospora oryzae, and Sclerotinia sclerotiorum; rusts (11.9%) induced by Veronaea botryose, Puccinia striiformis, Hemileia vastatrix, and Phakopsora pachyrhizi; and anthracnose (9.5%) caused by species belonging to the Colletotrichum genus; rice blast (8.1%) caused by Magnoporthe spp.. In the case of fungal genomic diversity were studied aspect as the difference among strains among the same species (41.2%), differential gene expression (17.6%), phylogeny (11.8%), or population structure (11.8%) , fungal genetic variability (12.6%), and food and beverage products (10.7%). Concerning phytopathogens, the most frequently studied crop diseases were rots (14.3%) caused by fungal species such as (11.8%) .Inter-Simple Sequence Repeats (ISSR) was developed by Ztetikiewicz and colleagues in 1994 . This teThe microsatellite markers present several advantages over the above-mentioned markers: high polymorphism level and low development and running costs, and requirements for low quality and quantity of DNA .Fusarium spp. (15.5%) as the etiological agent of the yellowing disease, wilt, and storage rot in different cultures, Colletotrichum (13.8%), causing bitter rot and anthracnose, and Alternaria (5.2%), responsible for symptoms of brown leaf spot and blight. In terms genomic diversity, the most common fungi studied were Fusarium (14.7%), Aspergillus (11.8%), and Sclerotium (8.8%) comprehending aspects such as genetic diversity (65%), virulence (10%), and vegetative compatibility (5%). Finally, in the field of the identification of food and beverage products, the most frequently studied fungal species were Pleurotus (21.9%), Agaricus (9.4%), and Aspergillus (9.4%) and fungal genetic diversity (25.0%), and to identify food and beverage products (17.2%). Amongst the 51 fungal species studied, the most representative ones were s (9.4%) .Variable Number of Tandem Repeats (VNTR) includes minisatellites and microsatellites. Minisatellites, first described by Alec Jeffreys and his team in 1990, are repeat motifs mostly about 9 to 30 bp long ,26. MicrMicrosatellites are generally abundant and polymorphic in non-transcribed genomic regions, the reason why this marker is considered selectively neutral. Nevertheless, SSR loci can also occur in genomic regions involved in transcription, translation, chromatin organization, or recombination . Due to Furthermore, the rapid mutation rates of SSRs may also be a confounding signal of population structuring and divergence. For instance, frequent forward and backward mutations can create identical alleles in unrelated or genetically isolated populations. This undesirable effect can be compensated by increasing the number of polymorphic SSR loci used, but populations\u2019 level of genetic differentiation that diverged a long time ago could still be underestimated .Minisatellites and microsatellites show a high level of polymorphism and genomic abundance, low requirements in terms of both DNA quality and quantity, and high reproducibility.Puccinia (7.4%), the etiological agent of rust; Colletotrichum (6.4%) causing anthracnose; Fusarium (6.4%), responsible for diseases such as blight, rot, and wilt; Alternaria (3.2%), the etiological agent of blight and rot, Diaporthe (3.2%) as endophytic fungi; Ustilago (3.2%), inducing smut; and Rhizoctonia (3.2%), causing aggregate sheath spot and blight. The human pathogens most frequently studied were Candida spp. (40.0%), the etiological agent of candidiasis and candidemia; Aspergillus spp. (17.1%), inducing invasive infections; Cryptococcus spp. (14.3%), causing cryptococcosis. As for fungal genetic diversity, the most studied species were Aspergillus (13.5%), Fusarium (13.5%), and Epichlo\u00eb (8.1%), comprehending topics such as genetic diversity (43.6%), mating-type (20.5%), and population structure (12.8%) and human health (15.0%), fungal diversity (15.0%), and food and beverage (8.4%). The most commonly plant pathogens studied were (12.8%) .Single-nucleotide polymorphisms (SNP), developed by Lander in 1996, result from changes in a single nucleotide position in the DNA sequence . These mSingle-nucleotide polymorphisms are co-dominant markers with high level of polymorphism and very high genomic abundance. The analyses of these markers require a low quantity of DNA, allowing a high automation capacity resulting in very reliable and reproducible data.Fusarium spp. (15.3%) and Monilinia spp. (5.1%), being the most prevalent diseases rusts (11.5%) and blight (7.7%). The most common studied crop was wheat (20.0%). In the case of plant pathogens, Aspergillus spp. (19.4%) and Exophiala spp. (16.1%) were frequently studied. The most studied diseases were aspergillosis (33.3%) and candidiasis (26.7%). Genomic diversity studies were conducted in Glomeromycota (50.0%) and Fusarium spp., covering aspects such as species genetic diversity (36.4%), population structure (27.3%), and toxin production (18.2%) and human health (16.0%), and genomic variability (10.1%). Concerning plant pathogens, the most frequently studied fungal pathogens were (18.2%) .The molecular markers Insertions or Deletions are fragments of different sizes (ranging from 1 to 1000 bp) inserted or lost at a given location in the genome. Given its nature and the unlikeliness of recurrence or back mutation, these markers are very stable within the genome and can, therefore, be relevant for population studies .These markers are co-dominant, with high polymorphism and very abundant, presenting both high reliability and reproducibility.Fusarium spp. (16.7%), Botrytis spp. (10.0%), and Puccinia spp. (10%). The majority of the published papers cover aspects such as genetic diversity (23.7%), the distinction between the species of the complex (7.9%), resistance to fungicides (7.9%), in crops wheat (21.4%), oilseed rape (14.3%), and soybean (14.3%). The most frequently studied human pathogens were Cryptococcus spp. (19.2%), Aspergillus spp. (11.5%), and Trichophyton spp. (11.5%). This marker was used to elucidate aspects such as genetic diversity (40.0%), recombination (15.0%), and virulence factors (15.0%). The diseases included were aspergillosis (25.0%), diarrhea (16.7%), and other enteric diseases (16.7%) and human health (17.0%), and food and beverage (17.0%). The most commonly studied plant pathogens were (16.7%) .Theoretically, DNA barcoding relies on using a single universal marker\u2014the DNA barcode sequence\u2014for rapid and accurate species identification and classification, mainly by non-taxonomist . \u201cDNA baAspergillus spp., Penicillium spp.), plant, human or animal pathogens or other fungi . As such, it is common to resort to secondary barcoding markers, such as the intergenic spacer (IGS), \u03b2-tubulin II (TUB2), DNA-directed RNA polymerase II largest (RPB1) and second largest (RPB2) subunits, translational elongation factor 1\u03b1 (TEF-1\u03b1), DNA topoisomerase I (TOP1), phosphoglycerate kinase (PGK), and cytochrome c oxidase subunit I (COX1) and subunit II (COX2), 28S nrDNA (LSU), and 18S nrDNA (SSU) [For animals, the universal standard barcode is cytochrome c oxidase 1 (COI). Many strategies have been suggested for plants, some based on a single chloroplast genomic region or a combination of different regions . For phyNA (SSU) ,46.These markers are co-dominant and present high genomic abundance, being their analysis highly reliable and reproducible. A disadvantage is that the same marker cannot be universally used for all fungal species, and prior knowledge of the DNA sequence is required .Fusarium spp. (11.6%), Alternaria spp. (2.9%), Curvularia spp. (2.9%), Diaporthe spp. (2.9%), Exserohilum spp. (2.9%), Mycosphaerella spp. (2.9%), and Neofusicoccum spp. (2.9%) fungal species collected from several crops . The aims of such studies were diagnosis (15.8%), identification of leaf spot pathogens (15.8%), and quarantine species (10.5%). In human health, the most common barcode genes were ITS (33.3%), \u03b2-TUB (18.5%), and TEF-1\u03b1 (14.8%). The human pathogens included were Scedosporium spp. (9.7%), Aspergillus spp. (6.5%), Cunninghamella spp. (6.5%), and Fusarium spp. (6.5%); whereas, the major diseases were invasive fungal infections (28.6%), keratitis (21.4%), and opportunistic fungi (14.3%). In the category of food and beverage production and spoilage, the barcodes were mainly ITS (43.3%), LSU (20.0%), and \u03b2-TUB (10.0%), applied to the study of Lactarius spp. (2.7%), Penicillium spp. (2.7%), and Pleurotus spp. (2.7%) associated either with edible mushrooms (53.3%) or dairy products (20.0%) and human health (13.4%), and food and beverage (12.5%). Regarding plant health, the most used barcode genes were ITS (36.2%), TEF-1\u03b1 (13.8%), and LSU (12.1%), applied to (20.0%) .The developments of massive parallel sequencing (MPS) techniques allow a more profound knowledge of the microorganisms, either unraveling the entire microbial composition retrieved from a given environment both in terms of identification and quantification (relative abundance) or deterThe advantages of MPS include the high-throughput capacity; a single protocol can be applied for all microorganisms for identification and genotyping purposes; no need for DNA cloning (only require libraries preparation); no need for an a priori knowledge about the sequence of a particular gene/genome (MPS can read the DNA templates randomly distributed throughout the entire genome); no need for isolation and culture of the microorganism to be studied (many strains are unable to grow in culture media); and reduced costs (less than US $1000 per genome) and the turnaround time (only a few hours) ,51. On tMetabarcoding corresponds to the automated identification of various organisms present in a single bulk sample or from an environmental sample with degraded DNA using a species-specific genetic marker (DNA meta-barcode) .As previously referred to, ITS can be indicated as the universal marker for fungi due to its high interspecific variability and conserved primer sites. However, due to length limits intrinsic to the existing sequencing platforms, only one of the two subunits (ITS1 or ITS2) can be analyzed in DNA metabarcoding . The regNowadays, several sequencing platforms and bioinformatics pipelines are available for the MPS of the fungal community. The 454 pyrosequencing from Roche Life Sciences was the most used platform until 2013 when Illumina took the lead ,58, a siHigh-throughput DNA sequencing data rely on a bioinformatics pipeline\u2019s efficient and accurate use . GeneralFrom 2012 to 2022, Metabarcoding studies included plant health (14.9%), food and beverage (14.4%), and soil (10.9%). In plant health studies, the most frequently used metabarcodes were ITS2 (31.0%) and ITS1 (27.6%) either isolated or in a combination of both (13.8%). The selected works included studies on fungal community (30.8%), endophytes (26.9%), trunk disease (11.5%) applied to forest trees (27.3%), cereals (22.7%), and fruit trees (13.6%). As for food and beverage, although in different proportions, the same metabarcodes were used . Sequencing was used for the identification of species involved in beverage fermentation (26.9%), food contamination (19.2%), and the production of dairy products (15.4%). In the soil\u2019s fungal diversity studies, the three usual metabarcodes were used . The selected soils were forests (21.1%), agro-environment (15.8%), and public gardens (15.8%) .Whole genome sequencing includes two different techniques: de novo genome assembly, when the species to be studied has not been previously sequenced and assembled; or re-sequencing, which identifies genome-wide variants comparing an existing reference assembly with a sequenced isolate through the alignment of sequence reads against the reference . These vFusarium spp. (12.1%), Trichoderma spp. (6.1%), and Venturia spp. (6.1%); while the major diseases analyzed were rot (27.8%), blight (19.4%), and cancer (8.3%). The most common studied cultures were soybean (13.6%), grapevine (9.1%), sugarcane (9.1%), and wheat (9.1%). Concerning human health, the most common fungal species were Candida spp. (42.1%), the etiological agent of candidiasis and candidemia (42.1%), and Aspergillus spp. (15.8%) causing aspergillosis (10.5%) and other infections (5.3%). In the identification of food and beverages, species such as Agaricus bisporus (4.8%), Auricularia spp. (4.8%), Flammulina spp. (4.8%), among others, were studied for their interest as edible mushroom (55.0%); while Aspergillus spp. (23.8%) and Penicillium spp. (19.0%) were studied for their role in food spoilage (45.0%) and human health (13.4%), and food and beverage (12.8%). Regarding plant health, the main fungal phytopathogens studied were (45.0%) .Identification of fungal species is a crucial aspect of many fields in science. Although whole genome sequencing techniques are now available at an amenable cost, this was not true thirty or twenty years ago. The scientific community has developed several molecular techniques to obtain information on these species. Nowadays, these markers range from non-PCR, PCR-based techniques to more advanced MPS-based techniques.Fusarium spp. (14.9%), Colletotrichum spp. (6.2%), Alternaria spp. (3.7%), and Puccinia spp. (3.7%). Diseases such as rots (27.8%), rust (11.1%), wilts (11.1%), and cankers (10.2%) were included. The most frequent human pathogens studied over the last 10 years were Candida spp. (32.2%), Aspergillus spp. (12.2%), Trichophyton spp. (12.2%), and Cryptococcus spp. (4.2%). The most commonly studied diseases were aspergillosis (14.7%), candidiasis (11.6%), dermatophytosis (20.0%), and mucormycosis (8.4%). Genomic studies included Aspergillus spp. (13.0%), Fusarium spp. (12.4%), Colletotrichum spp. (2.5%), Ganoderma lucidum (2.5%), and Lentinus spp. (2.5%), covering aspects such as molecular diversity (59.7%), recombination (8.3%), antifungal resistance (5.0%), population structure (4.4%), and virulence (4.4%).Over the past ten years, these molecular markers have been mainly used to study aspects related to plant (31.8%) and human health (13.7%), and genomic diversity (12.0%). Regarding plant health, the most commonly studied fungal phytopathogens were Soon, the most dated techniques (non-PCR and PCR-based techniques) will be surpassed by MPS-based techniques. However, some breakthroughs associated with increasing storage data availability, bioinformatic analysis, and standardization of protocols are required."} +{"text": "This database gathers 10,721 specimens, belonging to 2,578 species from the Chilean vascular flora deposited in the Herbarium of the Pontificia Universidad Cat\u00f3lica de Valpara\u00edso (PUCV) in Chile. The PUCV botanical collection was started by the renowned botanist Otto Z\u00f6llner and represents a major natural historical legacy for central Chile, with decades of information represented through preserved specimens. This collection is currently deposited in the Curauma campus of the PUCV. This digitisation effort is part of the PUCV's endeavour to mobilise its biological collections and make them freely available through GBIF, encouraging national and international researchers to generate new knowledge, based on this invaluable heritage, which is a silent witness of the vast plant diversity that once existed in Chile and that is now vanishing due to anthropogenic drivers.legitimavit and determinavit of specimens, general observations). The database serves as a repository containing records from past decades on the diversity and distribution of plant species, mainly from the Chilean Mediterranean biodiversity hotspot.The database provides occurrence records from 10,721 specimens of vascular flora held in the PUCV Herbarium, representing 2,578 species, 914 genera and 177 families. Each record includes data on taxonomy, geographic distribution, elevation and collection information (e.g. date of collection, Those collections are the silent witness of the country biodiversity and allow us to reconstruct past species distribution, assess local extinctions and track the spread of invasive species . Thus, the database presented here was developed taking the FAIR principles in mind . The nexThe main aim is to mobilise the PUCV biological collections, making them freely available while encouraging researchers to generate new knowledge, based on this invaluable heritage.Vascular flora from the PUCV Herbarium.Chile, South America.This database contains the specimens of vascular flora recorded in the Herbarium collection held at the Pontificia Universidad Catolica de Valpara\u00edso, indexed on Index Herbariorum as PUCV. The collection results from almost a century of work initiated by Prof. Otto Z\u00f6llner and continued by many professors and students.legitimavit and determinavit and observations. Finally, a unique identifier is provided for each specimen, which is then integrated into the herbarium collection.Specimen processing follows standard procedures for fresh material collection and dried material mounting and conservation . Specimewww.theplantlist.org) and the Taxon Match Tool (https://www.gbif.org/tools/species-lookup). Since the taxonomy of many groups has changed during the last decades, sometimes tricky to track, we also revised the Catalog of Chilean vascular plants ; Adiantaceae (30/3); Aextoxicaceae (9/1); Aizoaceae (22/9); Alstroemeriaceae (2/2); Altingiaceae (1/1); Amaranthaceae (125/48); Amaryllidaceae (27/11); Anacardiaceae (88/12); Annonaceae (4/2); Apiaceae (340/85); Apocynaceae (88/14); Aquifoliaceae (4/1); Araliaceae (6/3); Araucariaceae (10/3); Asparagaceae (8/3); Asphodelaceae (1/1); Aspleniaceae (141/8); Asteraceae (1889/540); Atherospermataceae (4/2); Begoniaceae (1/1); Berberidaceae (61/11); Betulaceae (7/3); Bignoniaceae (26/9); Blechnaceae (142/13); Boraginaceae (53/19); Brassicaceae (216/69); Cactaceae (10/9); Calceolariaceae (176/41); Campanulaceae (2/2); Cannabaceae (7/5); Caprifoliaceae (74/26); Cardiopteridaceae (20/1); Caryophyllaceae (120/30); Casuarinaceae (15/2); Celastraceae (32/5); Cephalotaxaceae (3/2); Ceratophyllaceae (1/1); Cervantesiaceae (1/1); Columelliaceae (4/1); Combretaceae (3/2); Convolvulaceae (77/22); Coriariaceae (5/1); Cornaceae (1/1); Crassulaceae (6/3); Cucurbitaceae (13/7); Cunoniaceae (32/4); Cupressaceae (94/24); Cyatheaceae (3/1); Cyperaceae (2/2); Cystopteridaceae (42/1); Dennstaedtiaceae (42/3); Dicksoniaceae (35/2); Dioscoreaceae (3/3); Dryopteridaceae (113/13); Ehretiaceae (9/5); Elaeagnaceae (3/2); Elaeocarpaceae (38/3); Ephedraceae (39/6); Equisetaceae (37/2); Ericaceae (54/17); Erythroxylaceae (2/2); Escalloniaceae (92/16); Euphorbiaceae (162/36); Fabaceae (812/241); Fagaceae (29/7); Francoaceae (12/2); Frankeniaceae (23/4); Gentianaceae (22/7); Geraniaceae (79/19); Gesneriaceae (13/3); Ginkgoaceae (3/1); Gleicheniaceae (128/4); Gomortegaceae (1/1); Goodeniaceae (10/1); Griseliniaceae (5/2); Grossulariaceae (37/10); Gunneraceae (8/2); Haloragaceae (36/1); Hydrangeaceae (9/3); Hydroleaceae (2/1); Hydrophyllaceae (47/7); Hymenophyllaceae (259/15); Hypericaceae (4/2); Iridaceae (3/3); Isoetaceae (2/1); Juglandaceae (2/1); Juncaceae (3/3); Krameriaceae (11/2); Lamiaceae (172/39); Lardizabalaceae (6/2); Lauraceae (59/9); Lentibulariaceae (4/1); Linaceae (30/4); Lindsaeaceae (12/1); Loasaceae (86/24); Loranthaceae (49/7); Lycopodiaceae (22/1); Lythraceae (35/11); Magnoliaceae (5/3); Malesherbiaceae (48/14); Malpighiaceae (18/5); Malvaceae (141/67); Marantaceae (1/1); Meliaceae (9/5); Misodendraceae (31/3); Molluginaceae (2/1); Monimiaceae (15/1); Montiaceae (74/24); Moraceae (13/7); Muntingiaceae (1/1); Myrtaceae (192/45); Nanodeaceae (1/1); Nephrolepidaceae (2/1); Nothofagaceae (111/9); Nyctaginaceae (30/9); Oleaceae (17/13); Onagraceae (91/21); Ophioglossaceae (3/1); Orchidaceae (27/7); Orobanchaceae (41/16); Oxalidaceae (120/29); Papaveraceae (77/12); Passifloraceae (11/7); Phrymaceae (42/8); Phytolaccaceae (30/6); Pinaceae (33/19); Piperaceae (7/4); Pittosporaceae (1/1); Plantaginaceae (132/37); Platanaceae (7/2); Plumbaginaceae (34/5); Poaceae (26/26); Podocarpaceae (43/7); Polemoniaceae (44/14); Polygalaceae (48/12); Polygonaceae (156/38); Polypodiaceae (87/7); Primulaceae (30/10); Proteaceae (69/7); Pteridaceae (371/23); Quillajaceae (15/1); Ranunculaceae (73/27); Rhamnaceae (109/21); Rosaceae (166/47); Rubiaceae (108/38); Rutaceae (23/11); Salicaceae (88/18); Salviniaceae (14/2); Santalaceae (7/1); Sapindaceae (50/10); Sapotaceae (14/4); Saxifragaceae (5/5); Schizaeaceae (3/1); Schoepfiaceae (58/6); Scrophulariaceae (37/9); Selaginellaceae (12/1); Simaroubaceae (2/1); Smilacaceae (1/1); Solanaceae (445/109); Strelitziaceae (1/1); Stylidiaceae (1/1); Tamaricaceae (2/1); Tectariaceae (4/1); Thelypteridaceae (21/2); Thymelaeaceae (7/1); Tropaeolaceae (67/8); Ulmaceae (4/3); Urticaceae (38/16); Verbenaceae (182/43); Violaceae (54/26); Viscaceae (1/1); Vitaceae (9/1); Vivianiaceae (71/8); Winteraceae (13/1); Woodsiaceae (2/1); Zygophyllaceae (60/7). The general taxonomic distribution of occurrences, including higher taxonomic categories, is presented in Fig. izoaceae 2/9; AlstAlthough the founding year of the PUCV Herbarium is unknown, it is presumed to have been in 1931 since the institution was founded in 1924 and the first specimen was deposited seven years later by the botanist Gualterio Looser. However, the Herbarium contains a few earlier records from 1900, probably integrated from the personal collection of the professors Otto Z\u00f6llner and Beatriz Palma. During the following years, few specimens were deposited until 1955, when the additions increased and were regularised Vascular flora from the PUCV Herbariumhttps://www.gbif.org/dataset/0f99f0f9-e32a-4deb-ad51-4e729dc9f2741Vascular flora from the PUCV Herbariumhttps://www.gbif.org/dataset/0f99f0f9-e32a-4deb-ad51-4e729dc9f274This database includes 10,721 specimens from vascular flora deposited in the Herbarium of the Pontificia Universidad Cat\u00f3lica de Valpara\u00edso (PUCV) in Chile. This botanical collection was started by the renowned botanist Otto Z\u00f6llner and represents a major natural historical legacy for central Chile, with decades of information represented through preserved specimens. This collection is currently deposited in the Curauma campus of the PUCV. This digitisation process is part of the PUCV effort to mobilise its biological collections and make them freely available through GBIF, encouraging national and international researchers to generate new knowledge, based on this invaluable heritage, which is a silent witness of the vast plant diversity that once existed in Chile and that is now vanishing due to anthropogenic drivers."} +{"text": "Actinomyces species are Gram-positive anaerobic bacilli colonizing the human oropharynx, gastrointestinal tract, and urogenital tract asso\u00adciated with a wide range of infections. The isolation of Actinomyces spp. from sterile clinical samples is regarded as significant. We reviewed the risk factors, clinical features, and outcomes in patients with Actinomyces bacteremia.Actinomyces bacteremia from two tertiary care centers from 1/1/06 -9 /26/19 . Data were collected on demographic and clinical characteristics, co-morbidities, primary source of infection, treatment received and duration of therapy and outcomes. True bacteremia was defined as Actinomyces bacteremia with systemic manifestations of infection.We conducted a retrospective study of all inpatients with A.meyeri 8 (30%), A.odontolyticus 7 (26%), A.israelli 7 (26%), A.turicensis 4 (15%) and A.neuii 1 (4%). The infectious diseases service was consulted in 20 cases of true bacteremia. Duration of antibiotics ranged between 0-84 days (17.6 \u00b120.7). All-cause mortality during hospitalization was 24% (8).A total of 82 cases of positive blood cultures were identified of which 33 were true bacteremia, based on clinical criteria among 19 females and 14 males ranging from 19-93 years (63.8 \u00b119.5). Majority of patients were blacks (70%). Clinical risk factors predominantly were diabetes mellitus (21%), chronic renal failure (18%) and active malignancy (12%). Majority of blood cultures were positive within 48 hrs. of admission 84.8%. Skin and soft tissue (27%) was the most common source followed by respiratory (15%), intrabdominal (15%), osteomyelitis (12%), odontogenic (6%), endovascular (6%) genitourinary (3%) and unknown source (16%). In 27 (81%) cases, bacteremia was isolated to species level: Actinomyces bacteremia may be relevant and can represent transient bacteremia. Better awareness and involvement of infectious disease service is recommended in understanding of the clinical significance, to ensure appropriate therapy for patients thereby implementing antibiotic stewardship to improve antibiotic use and, patient safety and improve outcomes. Further research will help to identify the true significance of these isolates.Not all All Authors: No reported disclosures."} +{"text": "Bradyrhizobium sp. strain Ce-3, which produced exopolysaccharide (EPS) and oxidized methanol in the presence of Ce3+. The genome for strain Ce-3 was estimated at 7,608,996\u2009bp and showed that the strain is closely related to Bradyrhizobium erythrophlei MT12 and Bradyrhizobium sp. strain C9.We present the draft genome sequence of Bradyrhizobium sp. strain Ce-3 (= MAFF 211645) shows unique phenotypes depending on the presence of Ce3+, such as production of exopolysaccharide (EPS) (2Bradyrhizobium sp. strain Ce-3. = MAFF 21645 showe (EPS) 24. In thiBradyrhizobium elkanii USDA 61) were assembled using SPAdes v3.15.2 , Bradyrhizobium pachyrhizi PAC 48 (GenBank accession number LFIQ01000091), Bradyrhizobium tropiciagri SEMIA 6148 (GenBank accession number LFLZ01000084), Bradyrhizobium brasilense UFLA 03-321 (GenBank accession number MPVQ01000039), and Bradyrhizobium ripae WR4 (GenBank accession number MF593081), the 16S rRNA genes of which are identical to that of Ce-3. The taxonomy of strain Ce-3 based on the Genome Taxonomy Database (release 202) determined by GTBD-Tk v1.7.0 (Bradyrhizobium in the phylum Proteobacteria. The strains that were closely related to strain Ce-3 were Bradyrhizobium sp. strain C9 (GenBank accession number GCF_002532045.1) and Bradyrhizobium erythrophlei MT12 (GenBank accession number GCF_900105845.1), with average nucleotide identities of 91.86 and 91.79%, respectively.The comparison of 16S rRNA gene sequences was performed by EzBioCloud . The 16SBradyrhizobium genus.Information from the genome of strain Ce-3 may help to elucidate new mechanisms for the Ln-dependent phenotypes of the Bradyrhizobium sp. strain Ce-3 was deposited in DDBJ/ENA/GenBank under the accession number BQUV00000000.1. The draft genome project data were submitted under BioProject accession number PRJDB12974, DRA accession number DRA013545, and Sequence Read Archive (SRA) accession number DRX336804.The draft genome sequence of"} +{"text": "In the version of this article initially published, there were errors resulting from merged authors\u2019 names. The following sentences highlight the errors and the corrected details:1 Abayomi Fadeyi, 2 Adekunle Olatayo Adeoti, 3 Muhammed Akanbi Nurudeen Adeboye, 4 Joseph Abioye Awosanya, 5 Ibironke Omowumi Oluwadiya, 6* Kehinde Sunday Oluwadiya.Should read:1Fadeyi Abayomi, 2 Adeoti Adekunle Olatayo, 3Adeboye Muhammed Akanbi Nurudeen, 4Awosanya Joseph Abioye, 5Oluwadiya Ibironke Omowumi, 6*Oluwadiya Kehinde Sunday."} +{"text": "Intravenous (IV) amphotericin B is the gold standard treatment of severe mycoses. A new orally absorbed, less-toxic formulation of amphotericin has been developed (Matinas Biopharma). We evaluated the efficacy of this novel anti-fungal agent amongst adults with cryptococcal meningitis.We conducted a phase II randomized clinical trial testing oral encochleated amphotericin B (cAMB) versus IV amphotericin B for first episode cryptococcal meningitis in Kampala, Uganda from December 2020 to August 2021. Participants were HIV-positive, CSF cryptococcal antigen (CrAg) positive, and had the capacity to consent and take oral medications (GCS=15). Participants in the experimental arm received two loading doses of either IV deoxycholate amphotericin B 1.0 mg/kg/day or liposomal amphotericin 3 mg/kg/day, followed by 1.8g oral cAMB daily in 6 divided doses through 2 weeks with flucytosine (5FC) at 100mg/kg/day, and thereafter cAMB at 1.2g daily in 4 divided doses through 6 weeks. Participants in the control arm received 7 days of IV amphotericin B with 5FC, then 7 days of fluconazole 1200mg/day. After 14 days, all participants received fluconazole 800mg/day through 10 weeks and thereafter a maintenance dose of 200mg/day.We randomized 40 participants to oral cAMB + 5FC and 30 control participants to IV amphotericin + 5FC. With cAMB the 30-day survival was 97.5% (39/40) and 18-week survival was 90% (36/40) compared with 87% (26/30) 18-week survival in IV amphotericin controls.10Cryptococcus CFU/mL/day; 95%CI, 0.29 to 0.54) versus IV amphotericin . Among those CSF culture positive at baseline, CSF sterility was achieved by 2 weeks in 65% (24/37) of cAMB participants and 68% (17/25) of controls.The CSF Early Fungicidal Activity (EFA) was lower with oral cAMB (mean EFA = 0.42 logGrade >=3 laboratory adverse events were more common with IV amphotericin. Grade 3\u20134 anaemia occurred in 10% (n=4) with cAMB versus 37% (n=11) with IV amphotericin. Grade 3 hypokalaemia (< 3mEq/L) occurred in 5% (n=2) with cAMB versus 27% (n=8) with IV amphotericin.Novel oral cAMB appears to be a safe agent with promising efficacy for HIV-related cryptococcal meningitis.All Authors: No reported disclosures."} +{"text": "Suicide is the second most common cause of adolescent mortality worldwide.To study the characteristics of a sample of adolescents (<18years of age) who died by suicide in Greece.We investigated all suicides that took place within the area of the Piraeus Department of Forensic Medicine for the period 1992-2016, based on the victims\u2019 forensic records.During the 25-year period, 16 adolescents (and 1162 adults) died by suicide. They were mostly males (11/68.75%) and of Greek Nationality (14/87.5%). The mean age was 15.56 years . Two (12.5%) were under psychiatric medication ; none was receiving a benzodiazepine or a mood-stabilizing antiepileptic. None had used amphetamine, cannabis, cocaine or heroin. Two (12.5%) -one girl one boy- had consumed alcohol. The suicides took place primarily at home (12/75%), followed by outdoors (3/18.75%); one (6.25%) took place in a correctional facility. Hanging was the most prevalent method (6/37.5), followed by jumping (5/31.25%), shooting by a firearm (2/12.5%), drowning (1/6.25%), medication overdose (1/6.25% -amitriptyline poisoning) and a case of suffocating death (1/6.25%). Most suicides happened in September (5/31.25%) and April (3/18.75%). No significant differences were noted with the adult sample.The methods chosen by the adolescents who died by suicide in our sample differ strikingly from those of usual suicide attempts at that age (medication overdose/self-cutting). The periods when the suicides took place may imply a role for school stress. Our study was retrospective and focused primarily on a large urban area."} +{"text": "Using conventional criteria, the respective response rates for spleen and \u201ctransfusion-dependent anemia\u201d were 47%, 32%, 83%, 62% and 51%, 30%, 10%, 44%, respectively, favoring momelotinib for anemia response (p\u2009=\u20090.02) and fedratinib for spleen response (p\u2009<\u20090.01). All study patients were followed to death or 2022, during which time 177 (97%) drug discontinuations, 27 (15%) leukemic transformations, and 22 (12%) allogeneic stem cell transplants (ASCT) were recorded. 5/10-year survival rate for all 183 patients was 41%/16% and not significantly different across the four drug cohorts (p\u2009=\u20090.33). Multivariable analysis of pre-treatment variables identified age >65 years (HR 3.5), absence of type 1/like CALR mutation (HR 2.8), baseline transfusion need (HR 2.1), and presence of ASXL1/SRSF2 mutation (HR 1.6) as risk factors for overall survival; subsequent HR-based modeling segregated three risk categories with 5/10-year survival rates of 84%/60%, 44%/14%, and 21%/5% (p\u2009<\u20090.01). In addition, spleen (p\u2009<\u20090.01) and anemia (p\u2009=\u20090.01) responses were independently associated with improved short-term survival while long-term survival was secured only by ASCT . The current retrospective study suggests the value of specific pre-treatment variables in identifying long-lived MF patients receiving JAKi and also confirms recent observations on the favorable impact of treatment response on short-term and of ASCT on long-term survival.Between October 2007 and July 2013, 183 Mayo Clinic patients with high/intermediate risk myelofibrosis (MF) were enrolled in consecutive phase 1/2 JAK2 inhibitor (JAKi) clinical trials with momelotinib ( Moreover, spleen response was comparable with momelotinib and ruxolitinib therapy (26.5% vs 29%) [Currently, ruxolitinib, fedratinib and pacritinib are three FDA-approved JAK2 inhibitors (JAKi) for treatment of myelofibrosis (MF) . In addiplacebo) , and COMtherapy) , studiestherapy) . Howevertherapy) , 4. On ttherapy) , 6. Thestherapy) (momelot studies (momelot vs 29%) . Similar vs 29%) , in MF. vs 29%) .The favorable impact of JAKi on splenomegaly and constitutional symptoms, and of momelotinib on anemia in patients with MF is well-established, but whether achievement of response following JAKi therapy positively influences long-term survival is unclear. Accordingly, in the current study, which includes MF patients treated on JAKi clinical trials at the Mayo Clinic, our primary objective was to i) retrospectively compare long-term treatment outcomes in momelotinib, ruxolitinib, fedratinib, and BMS-911543 treated patients with MF, ii) identify clinical and molecular predictors of response, overall and leukemia-free survival, and iii) examine the impact of treatment response on survival.JAK2, MPL, CALR, ASXL1, SRSF2, IDH1/2, and U2AF1 mutations and dynamic international scoring system (DIPSS)-plus risk stratification and unfavorable karyotype categorization were as previously described [The current study includes JAKi na\u00efve patients with primary myelofibrosis (PMF), post-polycythemia vera and post-essential thrombocythemia MF enrolled in consecutive phase-1/2 momelotinib NCT00935987), ruxolitinib (NCT00509899), fedratinib , and BMS-911543 NCT01236352) clinical trials between October 2007 and July 2013. The latter clinical trial was terminated by the sponsor in November 2015. Study patients were retrospectively recruited after institutional review board approval with follow-up updated in July 2022. Patient eligibility, study design, drug doses and schedule have previously been published 987, ruxo. Diagnos36352 clin\u2009=\u200979, 43%, median dose, 300\u2009mg daily), ruxolitinib , fedratinib , and BMS-911543 at a median of 27 months following diagnosis. Driver mutation profile included JAK2 in 80%, CALR in 11% (type 1/like CALR in 9%), MPL in 5%, triple negative in 4%; other mutations included ASXL1 in 58/124 (47%), SRSF2 in 16/84 (19%), U2AF1 in 3/47 (6%) and IDH1/2 in 2/74 (3%) of evaluable patients. Karyotype was abnormal in 97 (53%); among the latter, 53% were unfavorable. DIPSS-plus risk distribution was intermediate-1 (15%), intermediate-2 (46%), and high (39%). At the time of study drug initiation, 166 (91%), 66 (36%), and 136 (74%) of patients demonstrated palpable splenomegaly, transfusion-dependent anemia, and constitutional symptoms, respectively. Table p\u2009<\u20090.01), transfusion-dependent (p\u2009=\u20090.01), harbor type 1/like CALR mutations (p\u2009=\u20090.09) and belong to DIPSS-plus high-risk category (p\u2009<\u20090.01), and less likely to be affected by constitutional symptoms (p\u2009<\u20090.01), compared to patients not receiving momelotinib. On the other hand, patients receiving ruxolitinib were more likely to be younger (p\u2009=\u20090.02), males (p\u2009=\u20090.01), JAK2 mutated (p\u2009=\u20090.04), belong to DIPSS-plus intermediate risk group (p\u2009<\u20090.01), and less likely to present with transfusion-dependent anemia (p\u2009<\u20090.01). Fedratinib treated patients were more likely to present with leukocytosis (p\u2009=\u20090.02) and thrombocytosis (p\u2009=\u20090.02) while patients receiving BMS-911543 were more likely to be females (p\u2009=\u20090.04) and affected by constitutional symptoms (p\u2009<\u20090.01). However, ASXL1/SRSF2 mutation distribution and median time from diagnosis to initiation of therapy was similar for each treatment group (p\u2009>\u20090.1).A total of 183 JAKi na\u00efve patients with MF received momelotinib (p\u2009<\u20090.01). Reasons for drug discontinuation included suboptimal response or progressive disease (61%), toxicity (19%), study discontinuation by sponsor (9%), leukemic transformation (4%), death (3%) or secondary malignancy (2%). 108 (59%) of patients received subsequent therapy following discontinuation of study drug, which included JAKi therapy in 61(33%), hydrea in 16 (9%), imetelstat clinical trial in 11 (6%), thalidomide/lenalidomide/pomalidomide in 8 (4%), cladribine in 4 (2%), hypomethylating agent in 4 (2%), alisertib clinical trial in 3 (2%) and SL-401 clinical trial in 1 (1%). Overall, treatment-related grade 3 or 4 hematologic and non-hematologic adverse events were reported in 88 (48%) and 34 (19%) of patients, respectively.At a median follow up of 3.7 years (0.1\u201314.4 years), 178 (97%) patients have discontinued therapy. 3 and 5-year discontinuation rates were 77 and 92%, respectively with median treatment duration of 17 months for all patients. Notably, patients receiving momelotinib remained on therapy longer than patients on ruxolitinib , and in the absence of ASXL1/SRSF2 mutations . Multivariable analysis confirmed superior spleen response with fedratinib and absence of ASXL1/SRSF2 mutations and in the absence of thrombocytopenia < 100\u2009\u00d7\u2009109/l . In addition, symptom response was documented in 83 of 136 (60%) of patients with constitutional symptoms at baseline, response rates were 48, 57, 65, and 85% in patients receiving momelotinib, ruxolitinib, fedratinib, and BMS-911543, respectively.Spleen response was achieved in 83 of 166 (50%) evaluable patients with median response duration of 22 months (2\u2013132 months) and was more likely with fedratinib (83% p\u2009=\u20090.33) , absence of type 1/like CALR mutation (p\u2009<\u20090.01), baseline transfusion need (p\u2009<\u20090.01), unfavorable karyotype (p\u2009=\u20090.02), and presence of ASXL/SRSF2 mutations (p\u2009=\u20090.01) predicted inferior survival , absence of type 1/like CALR mutation , baseline transfusion need , and presence of ASXL1/SRSF2 mutations as risk factors for inferior survival , intermediate risk (3 points) and high risk (>3 points) with 5/10-year survival rates of 84%/60%, 44%/14%, and 21%/5%, respectively (p\u2009<\u20090.01) and anemia response were independently associated with improved short-term survival (Table p\u2009=\u20090.33).All study patients were followed to death or 2022, during which time 149 (81%) deaths, 27 (15%) leukemic transformations, and 22 (12%) allogeneic stem cell transplants (ASCT) were recorded. Median overall survival was 3.7 years with 3/5/10-year survival rates of 60, 41 and 16%, respectively. Survival was similar with momelotinib, ruxolitinib, fedratinib and BMS-911543 Fig. . but was9%) Fig. . In univ01) Fig. . In addival Fig. , c. On tASXL1/SRSF2 mutations. Previous studies on the impact of mutations on spleen response in JAKi treated patients with MF have yielded conflicting results. In an analysis of MF patients treated with ruxolitinib in the COMFORT-2 study, spleen response was not influenced by mutational profile [ASXL1/EZH2/IDH1/2 mutations in ruxolitinib treated patients [ASXL1 mutations in momelotinib treated patients with MF [We pioneered early clinical development of momelotinib, ruxolitinib, fedratinib and BMS-911543 JAKi for the treatment of MF, therefore the current study is uniquely poised to provide comparative data on long-term outcomes for patients treated with each JAKi , 9, 10. profile , while apatients . On the with MF , 20.Additional noteworthy observations include high treatment discontinuation rates, with less than 5% of study patients remaining on long-term therapy (>10 years). Importantly, two-thirds of patients discontinued therapy due to suboptimal response or disease progression, while death or leukemic transformation on-study was documented in a minority (<5%) of patients. In our series, the high discontinuation rates secondary to toxicity was likely a result of exposure to higher drug dosage in the phase-1 studies. The high treatment discontinuation rates attest to the transient benefit from JAKi therapy and although short-term survival was superior in spleen and anemia responders, long-term survival was not impacted by neither achievement of spleen nor anemia response with 10-year survival rates of <25%. Moreover, we have recently shown that the short-term survival benefit associated with anemia response in momelotinib treated MF patients might be limited to those with unfavorable genetic profile . It is tCALR mutation, presence of ASXL1/SRSF2 mutations, and transfusion dependence [The subject of whether MF patients derive long-term survival benefit from JAKi therapy remains contentious. A pooled analysis of the COMFORT-1 and 2 studies and a recently published prospective real-world series suggested prolonged survival in ruxolitinib-treated patients , 23. In pendence , 25. Baschecklist"} +{"text": "Correction: World J Surg Oncol 20, 176 (2022)https://doi.org/10.1186/s12957-022-02627-wFollowing the publication of the original article , the aut2 /m2 for males and 3.92 cm2 /m2 for females) that defined the low muscle mass of 541 Japanese living donor liver transplant donors in previous studies .\u201d\u201cThese values approximate the cut-of values (6.36 cmThe original article has been updated."} +{"text": "FLc originates from both coelomic epithelium and notch-active Nestin-positive perivascular cells located at the gonad\u2013mesonephros borders, and get specified as Nr5a1 (previously known as Ad4BP/SF-1) expressing cells by embryonic age (E) 12.5 days in fetal mouse testes. These cells produce androstenedione and play critical a role in initial virilization and patterning of the male external genitalia. However, in neonatal testis, FLc undergoes massive regression/dedifferentiation and gradually gets replaced by T-producing ALc. Very recent studies suggest a small fraction (5-20%) of FLc still persists in adult testis. Both Nestin-positive perivascular cells and FLc are considered to be the progenitor populations for ALc. This minireview article summarizes the current understanding of Lc development in fetal and adult testes highlighting their common or diverse cellular (progenitor/stem) origins with respective functional significance in both rodents and primates. (227 words)Leydig cells (Lc) reside in the interstitial compartment of the testis and are the target of Luteinising hormone (LH) for Testosterone (T) production, thus critically regulates male fertility. Classical histological studies have identified two morphologically different populations of Lc during testicular development [fetal (FLc) and adult (ALc)]. Recent progress in Historiin utero life, peaking during birth, gradually declines and subsequently disappears during neonatal/pre-pubertal life E 9.5-10.5 days . The tra1.5 days , 13 or i1.5 days and WT1 1.5 days etc.2.2Sf-1 and Daz1 show a complete loss of FLc suggesting a synergistic effect of these two factors on FLc differentiation (via respective receptors e.g.- Patched (Ptch) 1 and PDGF-\u03b1 expressed by interstitial stem/progenitor cells (Dhh-null mouse (showing reduced numbers of FLc) (Gli 1 (Gli- Kru\u00a8ppel family of transcription factor1) (via antagonizing SF1 (Hes1) being a negative regulator of FLc differentiation or over-factor1) and Smo factor1) (showingfactor1) or by rezing SF1 . Howeverntiation . Notablyntiation . Firstlyntiation . Secondl-renewal .2.3Cyp11\u03b21) & 21-hydroxylase (Cyp21) however lack 17\u03b2-hydroxysteroid dehydrogenase type 3 (Hsd17\u03b23). Therefore, although they can respond to ACTH signals but fail to convert androstenedione to T . Null mutations in either Insl3 or Rxfp2 result in cryptorchidism and tubule-vesicular mitochondria, etc. . Moreove3.3via an autocrine fashion and fertility . ALc exp fashion . Althoug fashion , 52, bot fashion and LH-R fashion null mic fashion , the est fashion , progres fashion .4Rodent and primate Lc differ in structure, development and function . There aFirstly, FLc of both the species are independent of fetal LH action, despite being responsive towards LH signal . Mouse Fvia the canonical pathway which gets converted toT in Sc).However, dihydrotestosterone (5\u03b1-DHT) is a more potent/bioactive androgen recently reported to be critical for the virilization of human male external genitalia (Srd5a2 gene) and men with inactive Srd5a2 mutations have ambiguous genitalia (Akrc2 and Akrc4) . The criutations , 66. Intnedione) .Finally, unlike mice and rats, primate Lc development is triphasic , 69. In 5Progressive decline in T production is manifested with testicular aging \u201374. Stud6In summary, both traditional histological studies and modern high-throughput multi-omics approaches using genetically manipulated mice models have revealed the diverse origin of Lc during testicular development , 12, 13.Recent advancements in targeted reprogramming [like selective ablation of Wt1 in Ctnnb1 (cadherin-associated protein \u03b21) over-expressing Sc results into Lc cell-like tumor development , manipulIB conceived the idea and designed the initial draft. IB prepared the text and figure and generated the final form with active support from SD. SD revised the manuscript. All authors contributed to the article and approved the submitted version."} +{"text": "Escherichia coli is a foodborne pathogen commonly associated with human disease characterized by mild or bloody diarrhea hemorrhagic colitis and hemolytic uremic syndrome. This study investigated the occurrence of STEC in fecal samples of 289 goats in South Africa using microbiological culture and PCR. Furthermore, 628 goat STEC isolates were characterized by serotype (O:H) and major virulence factors by PCR. STEC was found in 80.2% (232/289) of goat fecal samples. Serotyping of 628 STEC isolates revealed 63 distinct serotypes including four of the major top seven STEC serogroups which were detected in 12.1% (35/289) of goats: O157:H7, 2.7% (8/289); O157:H8, 0.3%, (1/289); O157:H29, 0.3% (1/289); O103:H8, 7.6% (22/289); O103:H56, 0.3% (1/289); O26:H2, 0.3% (1/289); O111:H8, 0.3% (1/289) and 59 non-O157 STEC serotypes. Twenty-four of the sixty-three serotypes were previously associated with human disease. Virulence genes were distributed as follows: stx1, 60.6% (381/628); stx2, 72.7% (457/628); eaeA, 22.1% (139/628) and hlyA, 78.0% (490/628). Both stx1 and stx2 were found in 33.4% (210/628) of isolates. In conclusion, goats in South Africa are a reservoir and potential source of diverse STEC serotypes that are potentially virulent for humans. Further molecular characterization will be needed to fully assess the virulence potential of goat STEC isolates and their capacity to cause disease in humans.Shiga-toxin-producing E. coli (STEC) is a foodborne pathogen commonly associated with enteric disease in humans characterized by mild watery or bloody diarrhea hemorrhagic colitis (HC) and the hemolytic uremic syndrome (HUS) as a complication in 5\u201310% of humans. According to the Foodborne Disease Burden Epidemiology Reference Group (FERG), STEC was responsible for around 2.5 million of new cases of human disease, of which 1.2 million may have been foodborne, with 3330 HUS cases and 269 deaths, which corresponded to 27,000 disability-adjusted life years (DALYs) in 2010 [Shiga-toxin-producing Domestic ruminants including cattle, sheep, and goats are the main reservoirs of STEC ,3,4,5. IEscherichia coli (STEC) have been described in humans, animals and the environment [More than 1000 different serotypes of Shiga-toxin-producing ironment ,12. STECironment . Howeverironment ,12,14,15ironment .stx1 and stx2) and a number of stx subtypes are considered the major STEC virulence factors [stx1 and stx2) [stx2 are more frequently associated with severe disease including HUS in comparison to strains that possess stx2 alone or both stx1 and stx2 concomitantly [Bacteriophage-encoded Shiga toxins ,19,20. Smitantly ,23,24,25eaeA) is an additional important STEC virulence factor [E. coli O157:H7 termed the locus of enterocyte effacement (LEE) [hlyA) and additional virulence-associated genes which are located on pathogenicity-islands [Intimin ,29. Intint (LEE) . Further-islands ,33,34,35stx1, stx2, eaeA, and hlyA). The overall goal is to contribute to STEC monitoring and surveillance in South Africa. Current reports on the occurrence and characteristics of STEC in animals and humans in South Africa are scanty. Furthermore, the few studies that have reported on the occurrence of STEC in South Africa have largely investigated the presence of STEC in cattle populations ,37,38 whA total of 289 fecal samples were collected from four goat herds on communal rangeland in the Gauteng province of South Africa and screened for STEC. PCR revealed that 80.2% (232/289) of goat fecal samples were positive for STEC. STEC was detected in 75.3% (116/154) of goats in herd A; 90.6% (39/43) in herd B; 78.8% (41/52) in herd C and 90% (36/40) in herd D . At least 99% (622/628) of isolates were O:H serotypeable by PCR. PCR serogrouping revealed 34 O groups and 17 H types with a total of 63 O:H distinct serotypes. Six isolates were O-untypable (ONT) and threAmong the 34 O serogroups, 18 were associated with a single H type , and 16 O groups were associated with more than one H type . The folAmong the 63 O:H distinct serotypes, 55.5%, (35/63) were each represented by a single isolate while the remaining 44.4% (28/63) were represented by more than one isolate . O:H serThe six most frequent goat STEC serotypes were: O3:H21, 7.9% (23/289); O103:H8, 7.6% (22/289); O43:H2, 6.5% (19/289); O76:H19, 5.8% (17/289); O75:H8, 3.1%, (9/289); O157:H7, 2.7% (8/289). Big seven STEC serotypes were recovered from 11.0% (32/289) of goats. Big seven STEC serotypes were distributed as follows among goats: O157:H7, 2.7% (8/289); O103:H8, 7.6% (22/289); O26:H2, 0.3% (1/289); O111:H8, 0.3% (1/289); O103:H56, 0.3% (1/289); O157:H8, 0.3% (1/289); O157:H29, 0.3% (1/289).stx1, 60.6% (381/628); stx2, 72.7% (457/628); eaeA, 22.1% (139/628); hlyA, 78.0% (490/628). Both stx1 and stx2 were found concomitantly in 33.4% (210/628) of isolates ; stx2 eaeA hlyA 20.3%, (128/628) and stx1 hlyA 20.0%, (126/628). STEC characteristics are depicted in The distribution of four STEC virulence genes among the 628 STEC isolates was as follows: isolates . The foleaeA gene was observed in 22.1%, (139/628) of isolates which corresponded to 12.8% (37/289) of goats which were eaeA positive. Of the 139 isolates that were eaeA positive, 131 belonged to five of the major seven serogroups including O157:H7 , O157:H8 , O103:H8 , O26:H2 and O111:H8 . In addition, eight isolates (1.2%) which were non-Big seven STEC serotypes possessed eaeA: O71:H14 , O108:H25 , O163:H8 were also eaeA-positive . Most of the eaeA positive isolates, 92.0% (128/139) had the stx2eaeA genotype while the remaining 7.9% (11/139) isolates were stx1eaeA positive. The Previous reports from different countries have shown that goats are a reservoir of STEC ,40,41,42The within-herd occurrence of STEC ranged from 75.3% 116/154) to 90.6% (39/43) which was significantly higher in comparison to similar studies in Brazil (46.7\u201373.3%) and Viet to 90.6%E. coli isolates that carry genes encoding O:H antigens but cannot be expressed. In this study, we were able to validate the Iguchi et al. [E. coli PCR serotyping (O:H) protocols which were highly discriminatory and unambiguously serotyped the large number of goats STEC isolates tested in this study [In the present study, 99.0% of goat STEC isolates were serotypeable by PCR. A total of 63 serotypes (34 O and 17 H groups) were recovered from goats. The number of serotypes detected in this study was very high compared to previous studies ,40,45. Ti et al. ,59 and Bi et al. E. coli is study ,58,59. TAmong the 63 serotypes, only 4 serotypes belonged to the major 7 STEC serogroups. STEC O103:H8 (15.6%) was the most frequent Big seven STEC among goats, followed by STEC O157:H7 (4.7%), O111:H8 and STEC O26:H2. Overall, the major seven STEC serotypes accounted for 21.3% of all isolates which were serotyped, in contrast to most similar studies which never recovered major seven STEC from goats ,45,60,61Previously, STEC O157:H7 has been incriminated in foodborne disease after consumption of raw goat milk and home-made cheese made from raw milk ,62,63. FThe remaining 59 serotypes were non-O157, of which 24 have been previously incriminated in mild to severe human disease worldwide including South Africa, Europe, North America and Asia ,12,16,67Highly diverse and farm specific STEC serotypes were observed in individual goat herds except for STEC O76:H19 which was the serotype shared among the four goat herds surveyed while STEC O146:H21 and OgX18:H2 were recorded in three herds. Overall, the highly diverse and farm specific serotypes are most likely a reflection of the fact that the four herds were situated in geographically separate and distant areas from each other to allow isolate interchange between herds. stx2 was more frequent that stx1 among goat STEC in contrast to similar studies which have shown that stx1 is predominant among goat STEC isolates [stx2 was more prevalent in goat STEC isolates. Reports on clinical STEC have suggested that stx2-positive isolates are more virulent and frequently incriminated in severe human disease including hemorrhagic colitis and hemolytic uremic syndrome in comparison to STEC isolates carrying stx1 or both stx1 and stx2 [Regarding the virulence characteristics of the STEC isolates under study, isolates ,69,70,71isolates which reand stx2 ,23,24,25hlyA gene was present in 78.0% (490/628) of goat STEC isolates, consistent with previous reports which have shown similar rates in goat STEC elsewhere [hlyA ranging from 35\u201360.9% have also been reported [hlyA gene encodes a pore-forming hemolysin which lyses human erythrocytes with subsequent release of iron from heme, a chemical needed for STEC growth and survival in the intestine. Previously, the presence and expression of hlyA has been associated with severe STEC disease in humans including HC and HUS [hlyA-negative have also been incriminated in severe disease including bloody diarrhea, HC and HUS, thereby suggesting that the pathogenic role of hlyA in STEC remains uncertain [The lsewhere ,42,44. Hreported ,41,45. Tncertain . eaeA-negative except for the top seven STECs (22.1%) including O157:H7, O26:H2, O111:H8 and O103:H8 and a few (0.7%) non-O157/non-top seven isolates: O71:H14, O108:H25 and O163:H8, in agreement with previous studies which have shown that eaeA is not common among goat STEC [eaeA in goat top seven STEC isolates is of clinical significance as eaeA is considered an important STEC adhesin and marker of high virulence and potential to cause severe disease (HC and HUS) in humans [stx2 [eaeA-negative serotypes (O91:H21 and O113:H21) STEC have also been associated with severe disease thereby suggesting that other virulence or unknown host factors may influence disease severity [eaeA may indicate that goat STEC are less virulent and may also explain why goat STEC are rarely incriminated in human disease worldwide. Of particular interest were eaeA-positive goat isolates which belonged to serotypes O103:H8, O71:H14, O108:H25 and O163:H8 but have never been associated with human disease or outbreaks. These isolates will be worth monitoring closely as possession of eaeA may be indicative of higher virulence potential and likelihood to cause severe disease in humans. Most of the goat STEC were oat STEC ,42,45. Tn humans , especians [stx2 . Howeverseverity ,73,74. THistorically, studies on the presence of STEC in goats are very few compared to cattle which are considered the main STEC reservoir. This study is the first report on the presence of STEC in goats in South Africa. The findings of this study show that goats carry a diverse range of STEC serotypes, some of which have been previously incriminated in mild to severe enteric disease in humans. Collectively, these findings suggest that goats grazing on communal rangeland in South Africa are a reservoir and potential source of STEC for humans in South Africa. Further molecular characterization of goat STEC isolates will be needed in the future to fully assess the virulence potential of goat STEC and capacity to cause disease in humans. In addition, studies that compare STEC isolates from goats and humans will be necessary to fully understand the role played by goats as a source of STEC human disease in South Africa. Data from this study will be useful for understanding the epidemiology of STEC in animals and formulating policies aimed at preventing and controlling zoonotic or foodborne diseases along the food chain. n = 154), herd B (n = 43), herd C (n = 52) and herd D (n = 40). Each herd was visited once. Refer to Goat fecal samples (N = 289) were obtained from four goat herds. The goat herds were located on different communal rangelands in Gauteng province, South Africa. The herds were designated using alphabetical letters: herd A . Each fecal sample (5 g) was enriched at a 1:10 ratio in EC broth supplemented with Novobiocin at 37 \u00b0C for 18\u201324 h. A 100 \u00b5L aliquot of the overnight enrichment was spread on Drigalski Lactose agar and CHROMagar STEC base ST162(B) containing supplement ST162(S) , 1 U of Taq DNA Polymerase and 5 \u03bcL of DNA template. The DNA from Escherichia coli O157:H7 strain EDL933 (ATCC 43895) and sterile water were used as positive and negative PCR controls, respectively. All PCR reagents were purchased from New England BioLabs except for the primers which were supplied by Inqaba Biotec .All Drigalski Lactose and CHROMagar STEC agar Petri dishes showing bacterial growth were screened for STEC by PCR . Briefly primers . Brieflystx1 and/or stx2 on PCR and streaked onto Drigalski Lactose agar and CHROMagar STEC to obtain single colonies. Five single colonies were purified from each plate and multiplied individually on Luria Bertani agar . Once again, DNA was extracted from purified colonies by the boiling method [stx1, stx2, eaeA and hlyA by PCR [stx1 and/or stx2 were preserved at \u221280 \u00b0C in a bacterial freezing mixture [For STEC isolation and identification, colony sweeps were collected from Drigalski Lactose agar and CHROMagar plates which were positive for g method . DNA froA by PCR to verif mixture for furtEscherichia coli (LREC), Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain and a number of E. coli O:H types in our collection (unpublished) were also used as positive controls in PCR serotyping assays. Furthermore, the following STEC isolates which were provided by the European Union Reference Laboratory for Escherichia coli, Istituto Superiore di Sanit\u00e0, Rome Italy, were used as positive controls for serotyping the major seven STEC serogroups: STEC-C210-03 (O157), STEC-ED476 (STEC O111), STEC-C1178-04 (STEC O145), STEC-C125-06 (STEC O103) and STEC-ED745 (O26).All confirmed STEC pure single colonies were serotyped (O:H) by PCR using previously described primers and cycling conditions ,58,59. S"} +{"text": "A recent meta-analysis of 48 studies, showed an equal prevalence of AP (16%) among the following etiologies; systemic disease, alcohol, medication, genetics, gallstones and infection in North American hospitalized and ambulatory pediatric patients. However, data on the epidemiology of severe pediatric acute pancreatitis (AP) in Canada are lacking.We aim to evaluate the clinical presentation, etiologies, comorbidities and outcome of pediatric patients with AP admitted to a tertiary hospital in Quebec, Canada.A retrospective observational cohort study (January 2014-December 2021) was performed at the CHU Sainte-Justine. Descriptive analyses were performed with SAS statistical softwarAmong the 214 patients included (110 (51%) males), 58 (27.1%) were already hospitalized at time of AP diagnosis (AP as secondary diagnosis) while 156 (72.9%) were admitted from the emergency room mainly with a presentation of abdominal pain (AP as primary diagnosis). Thirty-two patients (15.0%) were transferred to the ICU due to hemodynamic instability or respiratory failure. Comorbidities included cancer (38 patients (17.7%)), obesity (17 (7.9%)) and inflammatory bowel disease (15 (7.0%)). The three most commonly identified etiologies were medication (19.6%), biliary disease (16.3%) and infection . Despite extensive investigations, 26.2% of cases were idiopathic. The main complications were, ascites (48 patients (22.4%)), necrotic pancreatitis (10 (4.6%)) and pancreatic pseudocyst (10 (4.6%)). The median duration of hospitalization for AP as a primary diagnosis was 4 days (interquartile range (IQR) 2-7) as compared to 22 (11-37) for AP as a secondary diagnosis.Approximately one third of hospitalized patients had an underlying condition requiring treatments that could cause AP, which explains the high prevalence of drug-induced AP in this report. The longest hospitalizations were associated with AP as secondary diagnosis. Ongoing work will identify factors associated with disease severity and outcome in particular in primary AP.NoneNone Declared"} +{"text": "There is a limited literature available showing mental health burden among adolescents following cyberbullying.Aim is to evaluate the association of low mood and suicidality amongst cyberbullied adolescents.A study on CDC National Youth Risk Behavior Surveillance (YRBS) (1991-2017). Responses from adolescence related to cyberbullying and suicidality were evaluated. Chi-square and mix-effect multivariable logistic regression analysis was performed to find out the association of cyberbullying with sadness/hopelessness, suicide consideration, plan, and attempts.A total of 10,463 adolescents, 14.8% of adolescents faced cyberbullying a past year. There was a higher prevalence of cyberbullying in youths aged 15-17 years (25 vs 26 vs 23%), which included more females to males (68 vs 32%).(p<0.0001) Caucasians (53%) had the highest number of responses to being cyberbullied compared to Hispanics (24%), African Americans (11%).(p<0.0001) There was an increased prevalence of cyberbullied youths with feelings of sadness/hopelessness (59.6 vs 25.8%), higher numbers considering suicide (40.4 vs 13.2%), suicide plan (33.2 vs 10.8%), and multiple suicidal attempts in comparison to non-cyberbullied.(p<0.0001) On regression analysis, cyberbullied adolescence had a 155% higher chance of feeling sad and hopeless , considered suicide [1.52 (1.39-1.66)], and suicide plan [1.24 (1.13-1.36)].In our study, cyberbullying was associated with negative mental health outcomes. Further research is warranted to examine the impact and outcomes of cyberbullying amongst adolescents and guiding the policies to mitigate the consequences.No significant relationships."} +{"text": "Being the parent of a child followed for a chronic pathology can require different resources and coping skills.to determine the adaptation strategies of the parents of children monitored for adrenal insufficiency in the face of their children\u2019s pathologyWe conducted a descriptive cross-sectional study carried out with parents of children with Adrenal Insufficiency followed at the pediatric outpatient clinic in Taher Sfar Mahdia University Hospital between February 2019 and April 2020. We used a pre-established questionnaire collecting sociodemographic data and the strategies of coping using the Brief-COPE Board.A total of 38 parents of children with adrenal insufficiency and 38 control parents participated in the study. The Brief-Cope board\u2019s study of Coping strategies revealed that the strategies most used by parents of children with Adrenal insufficiency were, in descending order: religion (92.1%), support emotional (73.7%), distraction (63.9%), behavioral disengagement and acceptance (57.9%), instrumental support (52.6%), expression of feelings (50%), positive reinterpretation (39.5%), blame (38.9%), denial and humor (36.8%), active coping and planning (36.1%). On the other hand, those used by the control population were in descending order: religion (94.4%), distraction (84.2%), blame (78.9%), acceptance (72.2%) %), emotional support (69.4%), humor (63.9%), behavioral disengagement (61.1%), active coping (47.2%), expression of feelings , planning (41.7%), instrumental support (30.6%), positive reinterpretation (22%), denial (19.4%).Psychological support for the parents of children with chronic illnesses would be necessary to prevent parental burnout and improve their ability to adapt to their experiencesNo significant relationships."} +{"text": "Escherichia Coli (E coli) is a gram-negative rod that can cause devastating periprosthetic joint infections (PJIs) in patients with total hip and knee replacements (THA/TKA). Minimal literature exists on outcomes of E coli PJIs.Retrospective review of our institution\u2019s electronic medical record from 2009-2020 identified 21 patients that met MusculoSkeletal Infection Society criteria for E coli hip or knee PJI. Primary outcome was 1-year infection clearance - eradication of infection off antibiotics with no further surgeries for 1 year after completion of standard postoperative antibiotics. Minimum followup was 1 year.>1 E coli urine culture <1 mo pre-PJI (14.3%). Surgical treatments included DAIR (66.7%), 2-stage revision (14.3%), Girdlestone/Resection Arthroplasty , and fusion (4.8%), with 7.1%, 100%, 66.7%, and 100% 1-year infection clearance, respectively, and 33.3% 1-year infection clearance overall (p=.001). Common reasons for treatment failure were reinfection requiring surgery (57.1%) and chronic antibiotics (38.1%). Patients clear at 1 year had a longer mean time from most recent surgery to index PJI surgery and more AH than acute or chronic infections . Patients who were not clear at 1 year had more acute infections . The E coli PJI persisted in 23.8% of patients. Outcomes at final followup included G/RA (28.6%), original prosthetic (28.6%), new prosthetic (19%), above knee amputation (9.5%), destination spacer (9.5%), and arthrodesis (4.8%).We analyzed 21 patients . There were 11 acute, 8 acute hematogenous (AH), and 2 chronic PJIs. Several patients had recent gastrointestinal/urinary tract surgery (14.3%), recurrent urinary tract infections (9.5%), or E coli PJI 1-year infection clearance is poor, with DAIR being the most common yet least effective surgical treatment. Most E coli PJIs occurred postoperatively as opposed to hematogenously, as is sometimes assumed. This serves as a foundation for future studies evaluating E coli treatment outcomes.William A. Jiranek, MD, Biomech Holdings LLC: Stocks/Bonds|DePuy, A Johnson & Johnson Company: IP royalties Thorsten M. Seyler, MD, PhD, Heraeus: Paid consultant|Pattern Health: IP royalties|Restor3d: IP royalties|Smith & Nephew: Paid consultant|Total Joint Orthopedics: Paid consultant|Zimmer: research."} +{"text": "Pyroptosis is a proinflammatory form of programmed cell death in response to inflammation. It involves in the pathogenesis and outcomes of atherosclerosis characterized by NLRP3 inflammasome assembly, membrane pore formation, cell swelling, pro-inflammatory mediator and cytokine release. There are known pyroptosis molecular pathways including the caspase-1 depended canonical signaling pathway and the caspase-4/5/11 determined non-canonical signaling pathway. It is essential to explore the connection among NLRP3 inflammasome, pyroptosis and atherosclerosis, which may shed light on the potential therapeutic strategies that target pyroptosis in atherosclerotic treatment. Activatthe body 13]14][[14][+) e[[14]17][[17][16][[[17][16]Figure 1). Activated NLRP3 recruits ASC and pro-caspase-1 through a homotypic interaction of PYD-PYD and CARD-CARD, respectively.NLRP3 inflammasome is one of the best known inflammasomes, which is consisted of NLRP3 sensor, ASC adaptor, and caspase-1 effector . NLRP3 cFigure 2). Extracellular ATP, particulate matter, crystals, and pore-forming toxins are common up-regulators of NLRP3 inflammasome activation 41].[41].40][.[41].40]ase-1/11 47]48].[48].\u2013/\u2013 .[48].\u2013/\u20131 or not , which iale mice . Moreoveale mice . Taken t+ efflux (reduction of intracellular K+), Ca2+ influx (increase in intracellular Ca2+), cathepsin leakage by lysosomal destabilization, ER stress, and mtROS/mtDNA 53].[53].+ ef.[53].+ eigure 2) 39]54].[54].+ ef.[54].+ eigure 2) 56]57].[57].+ ef.[57].+ eigure 2) . Additioigure 2) 60]61][[61][+ ef[[61][+ eigure 2) . Extrace lesions 64]65].[65].+ ef.[65].+ e lesions 67]68].[68].+ ef.[68].+ e lesions 70]71].[71].+ ef.[71].+ eFigure 3) 74].[74].Figu.[74].Figigure 3) 76]77][[77][Figu[[77][Figigure 3) 79]. The. TheFiguigure 3) .The pathogenesis of atherosclerosis is characterized by recruitment of monocytes and lymphocytes, dysfunction of ECs, formation of foam cells (FCs), proliferation of smooth muscle cells (SMCs), secretion of proinflammatory cytokines, accumulation and oxidation of LDL, adherence of platelets, and death of abundant cells 81]. Pre. Pre81].-/-/caspase-1-/- mice were lower than those in ApoE-/- mice [105[105104]107][108[108107]. Many in, etc 112][112], et[112], et, etc . Additio, etc . Generalin vivo studies and clinical trials that could provide a solid foundation for developing pyroptosis-inducing drugs. Future studies should concentrate on the molecular mechanisms of NLRP3-mediated pyroptosis in atherosclerosis and other pyroptosis-related chronic diseases.As a proinflammatory form, pyroptosis plays a crucial role in the pathogenesis and complications of atherosclerosis that mainly targets ECs, macrophages, and SMCs. Pyroptosis in atherosclerotic lesions mainly depends on the NLRP3 inflammasome activation, and the signaling pathways involved provide some potential targets for novel therapeutic interventions in atherosclerosis. There still lacks Xiang Zeng: Writing \u2013 Original draft, Conceptualization, Supervision, Funding acquisition. Dongling Liu: Writing \u2013 review & editing, Conceptualization, Validation, Funding acquisition. Xia Huo: Writing \u2013 review & editing, Validation. Yue Wu: Writing \u2013 review & editing, Validation. Cuiqing Liu: Writing \u2013 review & editing, Validation, Funding acquisition. Qinghua Sun: Writing \u2013 review & editing, Validation, Supervision. All authors have read and approved the final manuscript."} +{"text": "Callyspongia is a sponge genus found in the seas, making it easily available. In this review, the pharmacological activity and mechanism of action of the secondary metabolites of Callyspongia spp. are addressed, which may lead to the development of new drugs and targeted therapeutic approaches. Several scientific databases, such as Google Scholar, PubMed, ResearchGate, Science Direct, Springer Link, and Wiley Online Library, were mined to obtain relevant information. In the 41 articles reviewed, Callyspongia spp. was reported to possess pharmacological activities such as cytotoxicity against cancer cell lines (36%), antifungal (10%), anti-inflammatory (10%), immunomodulatory (10%), antidiabetic and antiobesity (6%), antimicrobial (8%), antioxidant (4%), antineurodegenerative (4%), antihypercholesterolemic (2%), antihypertensive (2%), antiparasitic (2%), antiallergic (2%), antiviral (2%), antiosteoporotic (2%), and antituberculosis (2%) activities. Of these, the antioxidant, antituberculosis, and anti-inflammatory activities of Callyspongia extract were weaker compared with that of the control drugs; however, other activities, particularly cytotoxicity, show promise, and the compounds responsible may be developed into new drugs.One of the most widespread biotas in the sea is the sponge. The ocean, which covers 71% of the earth\u2019s surface, regulates our climate and contains abundant resources .One of the most ubiquitous sea organisms is the sponge. Sponges are often abundant in shallow water habitats, making them a unique biodiversity component . They arCallyspongia belongs to the family Callyspongidae. More than 60 species are widely distributed in the tropical sea +, was able to permeate the blood\u2013brain barrier, making it a suitable candidate for developing central nervous system drugs [Kinase inhibitorSelectively inhibiting \u03b2-secretase 1 in specific subcellular compartments is an effective strategy to reduce the accumulation of neurotoxic amyloid plaques . The metem drugs .Kinase Callyspongia sp. (CMB-01152), inhibits casein kinase 1, cyclin-dependent kinase 5, and GSK3\u03b2 with IC50 values of 0.03 \u03bcg/mL, 0.16 \u03bcg/mL, and 0.07 \u03bcg/mL, respectively. They abnormal hyperphosphorylate highly soluble microtubule-associated proteins to produce neurofibrillary tangles [Kinases have a role in neurodevelopmental and central nervous system physiology. Activation of the glycogen synthase kinase 3\u03b2 (GSK3\u03b2) results in tau phosphorylation, amyloid-\u03b2 accumulation, microglia activation, neurogenesis, and memory abnormalities . This su tangles .Callyspongia siphonella. These compounds possess antiosteoporotic activity by inhibiting receptor activator of nuclear factor-kB ligand (Rankl) with IC50 values of 32.8 \u03bcM and 12.8 \u03bcM (quercetin as positive control: 25 \u03bcg/mL) [Neviotine A and D are isolated triterpene-type compounds from 5 \u03bcg/mL) . The int5 \u03bcg/mL) . Nevioti5 \u03bcg/mL) ,119.Callyspongia spp. is reported to possess include cytotoxic against cancer cell line (36%), antifungal (10%), anti-inflammatory (10%), immunomodulatory (10%), antidiabetic and antiobesity (6%), antimicrobial (8%), antioxidant (4%), antineurodegenerative (4%), antihypercholesterolemic (2%), antihypertensive (2%), antiparasitic (2%), antiallergic (2%), antiviral (2%), antiosteoporotic (2%), and antituberculosis (2%) activities (Callyspongia sp. predicted from in silico results or the antioxidant, antituberculosis, and anti-inflammatory activities of Callyspongia extract were weaker compared with those of the control drugs. Although many promising compounds with a high potential to become drugs remain to be comprehensively evaluated in vivo, Callyspongia with its known mechanisms of action, such as antidiabetic and cytotoxic effects, may be further developed for targeted therapy.In the 41 articles we reviewed, the pharmacological activities that tivities . The mos"} +{"text": "C auris is an emerging often multidrug resistant pathogen capable of causing severe morbidity and mortality. C auris has been increasingly isolated from patients in skilled nursing facilities and hospitals, and has been associated with facility outbreaks. A resilient pathogen, C. auris survives harsh disinfectants, desiccation and readily colonizes the environment posing an especially great risk to immunocompromised patients with large open wounds and long lengths of stay.C auris in clinical cultures from the Burn ICU (BICU). A multidisciplinary team involving infection prevention, nursing/medical directors, health and safety, engineering, environmental services, and hospital leadership investigated the cluster as a potential outbreak. Mitigation measures involved a multi-modal response of C auris admission screening, weekly point prevalence testing of all BICU patients, environmental surface cultures, enhanced room cleaning, staff education, hand hygiene and personal protective equipment usage audits.From 7/1/21 - 8/30/21 we noted a cluster of 4 patients with C auris were identified on our BICU from 7/1/21 - 2/28/22. 5 (45.5%) cases from clinical isolates, 1 (9.1%) from a BICU point prevalence screen on 12/15/21, 5 (45.5%) as a part of weekly point prevalence screens started on 1/1/22. 6 (54.5%) patients were admitted for burn related injuries, 2 (18.2%) for Steven Johnson Syndrome, 2 (18.2%) for necrotizing wounds, and 1 (9.1%) for COVID-19 pneumonia. Cases occurred in 6/10 rooms in the Burn ICU. One (9.1%) patient expired during this outbreak (not deemed to be from C auris infection).11 cases of C auris pose a risk of nosocomial transmission and potential high morbidity and mortality to burn patients with impaired immune defense and large open wounds. A multidisciplinary team using targeted interventions including screening, education, enhanced cleaning eradicated the outbreak in our BICU. As of 5/1/22, we went 13 + weeks without identifying a new case. The last patient with C auris was discharged 3/16/22. To prevent future outbreaks, we created a standardized response plan and instituted a universal screening protocol for C auris targeting all patient admissions from skilled nursing facilities and admissions to all ICUs.Resilient infections like Jorge Paiva Parada, MD MPH, Shionogi: Honoraria."} +{"text": "The scope of the clinical problem of anorexia or appetite loss (AL) in older populations is potentially under-appreciated. A systematic literature review (SLR) was conducted following PRISMA guidelines to summarize associations of anorexia/AL in older adults with a range of clinical outcomes. Searches were run January/1/2011\u2013July/31/2021 in PubMed, Embase\u00ae, and Cochrane databases to identify English-language studies of adults (aged \u226565 years) with anorexia/AL. Two independent reviewers screened titles/abstracts and full text against pre-defined inclusion/exclusion criteria. In all, 146 studies underwent full-text review; 58 met eligibility criteria. Most were from Europe (34/58 [58.6%]) or Asia (16/58 [27.6%]); only 3 (5.2%) were from the United States (US). Although mortality (n=18) and malnutrition (n=15) were the most reported outcomes, no US study reported on these outcomes. Other commonly reported outcomes included sarcopenia (n=7), functional status (n=6), need for increased care (n=6), and hospitalization (n=4). Significant associations of anorexia/AL were most consistently observed with mortality (17/18 studies), malnutrition (15/15 studies), and functional status (5/6 studies). Although the overall number of studies is small, associations have emerged with falls (2/3 studies), health related quality of life (2/3 studies), depression (2/2 studies), and cognition (2/2 studies). However, associations with hospitalization (1/4 studies), sarcopenia as assessed by muscle strength (2/4 studies) or by muscle mass (1/3 studies), and need for increased care (3/6 studies) were less consistent. Together, these studies highlight the breadth of adverse outcomes associated with anorexia/AL in older populations and a need for more US-based research into this common clinical problem."} +{"text": "Studies from the beginning of 2020 show that symptoms of depression and anxiety are increasing among health care workers. It is important to assess the dynamics of health care workers mental health.To assess the dynamic of symptoms of depression and anxiety among health care workers over a 3-month period during the COVID-19 pandemia in Latvia.A longitudinal cohort study of symptoms of depression and anxiety in the population of physicians, physician assistants and nurses in Latvia during the COVID-19 pandemia. Symptoms of depression were assessed using the Patient Health Questionnaire-9 (PHQ-9) scale, symptoms of anxiety were assessed using the General Anxiety Disorder (GAD-7) scale, cut-off score for both scales was 10. Initial data was collected on April-May 2020 with a 3 month follow-up.. Data was analyzed using SPSS- Related-Samples McNemar test.348 physicians were initially included and 376 physicians assistants and nurses . After the 3-month follow up 189 physicians and 141 physicians assistants and nurses were left . During the 3 months symptoms of depression among physicians rose from 26,80% (n=94) to 27,5% (n=52), symptoms of anxiety from 17,70% (n=62) to 20,6% (n=39). Depression symptoms among physician assistants and nurses dropped from 25,50% (n=96) to 23,9% (n=34), symptoms of anxiety stayed almost the same 18,20% (n=68) to 18,30% (n=26). Symptoms of depression among physicians changed from 26,80% (n=94) to 27,5% (n=52), symptoms of anxiety from 17,70% (n=62) to 20,6% (n=39), changes were not statistically significant . Symptoms of depression among physician assistants and nurses changed from 25,50% (n=96) to 23,9% (n=34), symptoms of anxiety from 18,20% (n=68) to 18,30% (n=26), changes were not statistically significant .No change in the dynamics of symptoms of depression and anxiety among health care workers over a 3-month period during the COVID-19 pandemia in Latvia was observed."} +{"text": "Pneumothorax (PTX) and pneumomediastinum (PM) have been reported among hospitalized patients with COVID-19. It can occur among patients breathing spontaneously or as a result of barotrauma from invasive positive-pressure ventilation or from medical procedures. We aim to study the clinical features and outcomes of pneumothorax and pneumomediastinum within 48 hours of hospitalization among COVID-19 patients.We conducted a multicenter retrospective study among the hospitalized adults with COVID-19 who had pneumothorax and pneumomediastinum within 48 hrs. of admission between November 2020 and December 2021. Cases were identified using ICD 10 codes. Electronic medical records were reviewed after Institutional Board approval.We identified a total of 21 patients, 12 (57%) only had PTX, 6 (28%) only had PM, and 3(14%) had both. Mean age for the cohort was 57 yrs, 13 (62%) were females, and 14 (67%) were whites. Chronic lung and end-stage renal diseases were noted among 9 (43%) patients followed by obesity in 9 (43%) and diabetes in 4 (19%). A total of 12 (57%) patients have smoked tobacco. At the time of hospitalization, 12 (57%) patients had oxygen saturation \u226494% and 9 (43%) had \u226490%. PTX and PM on admission chest x-ray were noted in 12(57%) and 4 (19%) respectively. 3 (14%) developed them after intubating and/ or after BiPAP. Patients were treated with steroids (90%), remdesivir (62%), interleukin-6 inhibitors (24%), and convalescent plasma (9%). Chest tube was placed in 7 (33%) patients and thoravent in 1 (5%) patient. Complications were septic shock (14%) and deep venous thrombosis (10%). There were 4(19%) deaths.Spontaneous PTX can be a presenting sign for COVID-19. We noted higher complications and mortality among the COVID-19 patients with PTX and PM than reported in literature. Clinicians should be aware of this potential occurrence, requiring close monitoring and aggressive management. Larger studies can further validate the findings of our study.All Authors: No reported disclosures."} +{"text": "Non-alcoholic fatty liver disease (NAFLD) is the leading cause of liver disease worldwide with an increasing prevalence of 25-40%. Although the prevalence increases to 57.5-74% in obese patients, lean individuals also develop NAFLD. Patients are commonly asymptomatic and the diagnosis is often incidental or when progressed to cirrhosis. Once fibrosis has developed, the risk of cardiovascular and liver-related death increases exponentially. The increasing prevalence of NAFLD presents significant healthcare and economic consequences.The severity of NAFLD and its risk factors have been studied in various countries, which guide decisions on screening and management. Similar studies have not been performed in Canada.Purpose: To determine the severity of NAFLD in a tertiary care centre and associated risk factors.Retrospective review of patients with NAFLD diagnosed on ultrasound, or fibroscan from January 1, 2019 to December 31, 2021. Patients were 18 years or older and were excluded if they had co-existent liver disease, significant alcohol use or CAP <238. CAP and fibrosis scores were determined using transient elastography. Chi-square and multivariate analysis were performed for statistical analysis.Result(s): A total of 583 patients were included in the study; 312 (53.5%) were male and the mean age was 54.04 years. The majority of cases, 317 (56.8%), were diagnosed by ultrasound or CT scan and only 30 (5%) patients had a known family history of NAFLD. Lean-NAFLD (L-NAFLD) was present in 83 (15.2%) patients, overweight NAFLD (OW-NAFLD) 220 (40.2%), obese-NAFLD (OB-NAFLD) 206 (37.7%) and morbidly obese-NAFLD (MB-NAFLD) 38 (6.9%).The prevalence of T2DM was 28.6%, dyslipidemia 37.4%, hypertension 35.5%, coronary artery disease 6.2% and obstructive sleep apnea 6.7%. Risk factors for Stage 3 steatosis (CAP>290) included BMI>30 (2.84) and type 2 diabetes (OR 2.45), but not dyslipidemia, hypertension, age or gender. Type 2 diabetes, dyslipidemia, hypertension, BMI, gender and age were not significantly predictive of moderate steatosis (CAP 260-289).The proportion of patients with transient elastography scores of F2, F3, and F4 were 16.0%, 7.7%, and 11.0%, respectively. F2 and F3 scores were associated with T2DM (OR 1.94), BMI > 30 and age >60 , but not dyslipidemia or hypertension. F4 scores were significantly associated with age > 60 (OR 1.89), T2DM (OR 2.60), dyslipidemia (OR 1.79), hypertension (OR 1.86) and BMI>30 (OR 2.54).Diabetes and BMI were associated with severe steatosis and fibrosis. Dyslipidemia and hypertension were only associated with advanced fibrosis. Our study demonstrates challenges in identification of early NAFLD given that metabolic syndrome factors were not associated with mild to moderate steatosis.NoneNone Declared"} +{"text": "In 2019, 65.8 million U.S. adults reported past-month binge drinking and 35.8 million reported illicit drug use or prescription pain reliever misuse during the past month; 20.4 million met diagnostic criteria for a substance use disorder during the past year , non-Hispanic White persons (65.8%), had a high school education or less (65.4%), and were assessed in metropolitan areas (66.6%) and in the South U.S. Census Bureau region (62.2%) .Alcohol was the substance most commonly reported (35.8%), followed by cannabis (24.9%), prescription opioid misuse (18.5%), illicit stimulants (14.0%), heroin (10.2%), misuse of prescription sedatives or tranquilizers (8.5%), cocaine (7.4%), illicit fentanyl (4.9%), and prescription stimulant misuse (1.8%). Compared with men, women reported higher use of all substances except alcohol. Comparing the prevalence of past 30-day substance use reported in each of the four U.S. Census Bureau regions, the prevalence of heroin, cocaine, illicit fentanyl, and prescription sedative use was highest at Northeast treatment sites, whereas the prevalence of illicit stimulant use was highest at Midwest treatment sites. Among all adults assessed, 32.6% reported use of two or more substances during the past 30 days; the most common polysubstance combinations were alcohol and cannabis (17.2%), followed by cannabis and illicit stimulants (3.7%), and alcohol and prescription opioids (3.4%) .Among the biopsychosocial domain problems measured, 45.4% of adults assessed reported more severe problems with drugs, followed by psychiatric (35.2%), legal (28.8%), medical (27.4%), employment (25.0%), alcohol (24.2%), and family problems (22.8%) . CompareThis study found that among adults assessed for substance use at 399 treatment centers during 2019, alcohol was the most commonly reported substance used during the past 30 days, followed by cannabis, prescription opioid misuse, and illicit stimulants. Nearly one third of all assessments involved polysubstance use, and co-occurring severe problems across multiple biopsychosocial domains were common. Consistent with previous research on substance use patterns in the general population and multiple substances (32.6%) were most commonly reported, along with severe problems across multiple biopsychosocial domains.Actions to enhance comprehensive substance use programs that incorporate polysubstance use and co-occurring mental health problems into strategies for prevention, treatment, and response are needed, as is expanded linkage to services."} +{"text": "The physicochemical properties of (PANI-HCl)/Al(NO3)3 complex composite films were studied for various Al(NO3)3 concentrations . The refractive index of the (PANI-HCl)/Al(NO3)3 complex composite films increased continuously as Al(NO3)3 concentrations increased. The electrical conductivity values increased from 5.10 \u00b5S/cm to 10.00 \u00b5S/cm as Al(NO3)3 concentration increased to 32 wt.%. The sensitivity of the SPR sensing device was investigated using a theoretical approach and experimental measurements. The theoretical system of SPR measurement confirmed that increasing Al(NO3)3 in (PANI-HCl)/Al(NO3)3 complex composite films enhanced the sensitivity from about 114.5 [Deg/RIU] for Au-layer to 159.0 [Deg/RIU] for Au-((PANI-HCl)/Al(NO3)3 (32 wt.%)). In addition, the signal-to-noise ratio for Au-layer was 3.95, which increased after coating by (PANI-HCl)/Al(NO3)3 (32 wt.%) complex composite layer to 8.82. Finally, we conclude that coating Au-layer by (PANI-HCl)/Al(NO3)3 complex composite films enhances the sensitivity of the SPR sensing device.Complex composite films based on polyaniline (PANI) doped hydrochloric acid (HCl) incorporated with aluminum nitrate (Al(NO Light photons interact with the conduction electrons at the metal/dielectric interface, which generates longitudinal surface waves called surface plasmons . Recentl3+) ions enhances the electrical conductivity and tuning of the optical properties and \u0394n was refractive index change [refractive index unit: RIU]. The linear fit of the SPR angle shift as a function of refractive index changes represented the sensitivity of the SPR sensor (3)3 in the PANI-HCL films enhanced the SPR sensitivity from 114.5 [Deg/RIU] for pare Au-layer to 159.0 [Deg/RIU] for Au-((PANI-HCl)/Al(NO3)3) layers for 32 wt.% of Al(NO3)3 (3)3 concentrations decreased in the PANI-HCl.software . The incectivity . The senR sensor b. InclusAl(NO3)3 c. In add3)3) layers with Al(NO3)3 concentration of 32 wt.% were studied experimentally. After recording images using a CMOS camera, ImageJ software for Au-layer to 159.0 [Deg/RIU] for Au-((PANI-HCl)/Al(NO3)3 (32 wt.%)). In addition, the signal-to-noise ratio for Au-layer was 6.22, which reached 9.97 after coating by (PANI-HCl)/Al(NO3)3 (32 wt.%) complex composite layer. In addition, the FOM of the bare Au layer was 79.51 RIU\u22121, which decreased as Al(NO3)3 concentrations increased in the PANI-HCl to 7.23 RIU\u22121. The LOD value for the bare Au layer was 0.12 RIU, which decreased to 0.08 RIU after coating with (PANI-HCl)/Al(NO3)3 with a concentration of 32 wt.%. This means that coating the Au layer with (PANI-HCl)/Al(NO3)3 can detect fewer concentrations than the bare Au layer.Synthesized (PANI-HCl)/Al(NO"} +{"text": "In Jaiswaled et al.,The authors apologize for this error.Results the symptoms recorded read \u201cThe major symptoms were rash (100%), fever (96%), and other important symptoms were upper respiratory symptoms (97%), headache (95%), vomiting (95%), oral ulcers (96%), conjunctivitis (96%), and lymphadenopathy (85%).\u201dIn They should have read: \u201cThe major symptoms were rash (100%), fever (99%), and other important symptoms were upper respiratory symptoms (55%), lymphadenopathy (85%), headache (78%), vomiting (25%), oral ulcers (56%), and conjunctivitis (21%).\u201dParagraph 3.3 the reported symptoms read \u201cThe major and most significant symptoms were rash 1078/1078 (100%), fever 1037/1075 (96%). Other important symptoms were upper respiratory symptoms 1026/1060 (97%), headache 1015/1068 (95%), vomiting 1011/1059 (95%), oral ulcers 1018/1057 (96%), conjunctivitis 1017/1058 (96%), and lymphadenopathy 905/1070 (85%).\u201dIn They should have read: \u201cThe major and most significant symptoms were rash 1078/1078 (100%), fever 1037/1047 (99%). Other important symptoms were upper respiratory symptoms 563/1027 (55%), headache 797/1021 (78%), vomiting 251/1012 (25%), oral ulcers 570/1018 (56%), conjunctivitis 211/1017 (21%), and lymphadenopathy 886/1047 (85%).\u201dParagraph 4.3 the clinical features read \u201cOverwhelmingly, the clinical features of monkeypox are like those of smallpox. More than 90% patients of monkeypox clinically present with a fever, rash, headache, and upper respiratory symptoms and more than 80% patients have lymphadenopathy, oral ulcers, conjunctivitis, vomiting, and diarrhea as noted by this review.\u201dIn They should have read \u201cOverwhelmingly, the clinical features of monkeypox are like those of smallpox. Patients with monkeypox clinically present with a fever, rash, headache, lymphadenopathy, and upper respiratory symptoms and other less common symptoms which include oral ulcers, conjunctivitis, vomiting, and diarrhea as noted by this review.\u201dIn Supporting Information:\u00a0Table 1, affected values have been corrected and uploaded online.Table"} +{"text": "The phase II TALAPRO-1 study (NCT03148795) demonstrated durable antitumor activity in men with heavily pretreated metastatic castration-resistant prostate cancer (mCRPC). Here, we detail the safety profile of talazoparib.Men received talazoparib 1 mg/day orally until radiographic progression, unacceptable toxicity, investigator decision, consent withdrawal, or death. Adverse events (AEs) were evaluated: incidence, severity, timing, duration, potential overlap of selected AEs, dose modifications/discontinuations due to AEs, and new clinically significant changes in laboratory values and vital signs.N = 127; median age 69.0 years), 95.3% (121/127) experienced all-cause treatment-emergent adverse events (TEAEs). Most common were anemia (48.8% [62/127]), nausea (33.1% [42/127]), decreased appetite (28.3% [36/127]), and asthenia (23.6% [30/127]). Nonhematologic TEAEs were generally grades 1 and 2. No grade 5 TEAEs or deaths were treatment-related. Hematologic TEAEs typically occurred during the first 4-5 months of treatment. The median duration of grade 3-4 anemia, neutropenia, and thrombocytopenia was limited to 7-12 days. No grade 4 events of anemia or neutropenia occurred. Neither BRCA status nor alteration origin significantly impacted the safety profile. The median (range) treatment duration was 6.1 (0.4-24.9) months; treatment duration did not impact the incidence of anemia. Only 3 of the 15 (11.8% [15/127]) permanent treatment discontinuations were due to hematologic TEAEs .In the safety population (Common TEAEs associated with talazoparib could be managed through dose modifications/supportive care. Demonstrated efficacy and a manageable safety profile support continued evaluation of talazoparib in mCRPC.NCT03148795 To aid clinicians in the management of adverse events and to inform clinical trials investigating the use of talazoparib in combination with other anticancer treatments, this article provides an in-depth analysis of the safety profile of talazoparib in men with metastatic castration-resistant prostate cancer. In the TALAPRO-1 phase II trial, nonhematologic treatment-emergent adverse events were generally mild/moderate. Hematologic treatment-emergent adverse events were common but manageable through dose modifications and supportive care. The median duration of grade 3-4 anemia, neutropenia, and thrombocytopenia was limited to 7-12 days. No grade 4 events of anemia or neutropenia occurred. Permanent discontinuations due to adverse events occurred in slightly more than 1 in 10 patients (11.8%); 3 patients discontinued due to hematologic adverse events. Durable antitumor efficacy, coupled with the generally manageable safety profile, supports the further evaluation of talazoparib for men with metastatic castration-resistant prostate cancer.2 With improved detection and life expectancies, the global incidence of prostate cancer is expected to increase to 2.43 million cases in 2040.4 While androgen-deprivation therapy (ADT) induces remission for approximately 90% of patients with metastatic castration-sensitive prostate cancer (mCSPC), virtually all patients progress over time (median 24-36 months) and develop metastatic castration-resistant prostate cancer (mCRPC).5-7 The median survival time for patients with mCRPC is approximately 2-3 years.9 Despite declining mortality rates in most western countries, possibly due to early detection and treatment, the need for novel therapeutic strategies remains.11Prostate cancer is the second most common cancer in men worldwide, with approximately 1.4 million new cases and 375\u2009000 deaths in 2020.12-15 While these alterations are associated with worse clinical outcomes,16-18 they may sensitize patients to targeted therapies, such as poly(ADP-ribose) polymerase (PARP) inhibitors.19 Talazoparib inhibits PARP1 and PARP2, two key factors involved in DDR, and effectively traps PARP on single-stranded DNA breaks, causing an accumulation of double-stranded DNA breaks that cannot be effectively repaired in cancer cells with alterations in DDR-HRR genes such as BRCA1 and BRCA2.19-23Germline or somatic alterations in cellular DNA damage response (DDR) genes, involved directly or indirectly with homologous recombination repair (HRR), have been identified in 23%-27% of men with mCRPC.25 PARP inhibitors are known to cause hematologic toxicities in patients with different tumor types.26 The phase III EMBRACA and phase II ABRAZO trials established the safety profile of talazoparib in female and male patients with advanced breast cancer.27-30 The most common hematologic toxicities were anemia, neutropenia, and thrombocytopenia.28-31Preclinical studies have also demonstrated that PARP2 plays a protective role against replicative stress in hematopoietic stem/progenitor cells, and depletion of PARP2 leads to anemia.33 The study demonstrated durable antitumor activity, with an objective response rate (ORR) of 29.8% observed for the primary cohort of patients with measurable disease. The highest efficacy was observed in men with BRCA1/2 alterations (ORR = 45.9% [28/61]), although objective responses were observed in men with alterations in PALB2 alone (ORR = 25.0% [1/4]) or ATM (ORR = 11.8 [2/17]). Adverse events observed in older men with mCRPC appeared similar to the established safety profile of talazoparib in younger women and men with breast cancer and included anemia, gastrointestinal events, and asthenia.33 Here, we provide an in-depth analysis of the specific safety profile of talazoparib in men with mCRPC that may aid clinicians in the management of AEs and inform clinical trials investigating the use of talazoparib in combination with other anticancer treatments.TALAPRO-1 is the first international phase II trial to evaluate the efficacy and tolerability of talazoparib monotherapy in heavily pretreated men with mCRPC and DDR-HRR alterations.33 but in summary, male patients (aged \u226518 years) with mCRPC were enrolled at 43 sites from within Australia, Brazil, Europe, South Korea, and the US. The safety population included patients with DDR-HRR core gene alterations that may sensitize to PARP inhibition . Patients were previously treated with at least 1 taxane-based chemotherapy regimen for metastatic prostate cancer (castration-sensitive or -resistant) and progressed on at least 1 novel hormonal therapy given in the mCRPC setting.TALAPRO-1 is an ongoing, multinational, open-label phase II trial. Detailed study information has been previously published2 provided by the central laboratory. Appropriate dose modifications were allowed; dosage could be reduced in increments of 0.25 mg/day, and supportive care could be provided following grade 2, 3, or 4 events. For grade 3-4 hematologic AEs , talazoparib was paused and the patient was monitored weekly. Upon resolution of the event , talazoparib was resumed at the next lowest dose level . If the event persisted for >4 weeks without recovery, despite supportive care, talazoparib was permanently discontinued. Detailed protocol requirements following additional AEs have been previously published.33 Clinical laboratory tests and safety assessments were performed at screening and at each scheduled visit while taking talazoparib .All men received oral talazoparib 1 mg/day and continued treatment until radiographic progression, unacceptable toxicity, investigator decision, withdrawal of consent, or death. Moderate renal impairment was defined as an estimated glomerular filtration rate of 30-59 mL/minute/1.73 mTALAPRO-1 followed good clinical practice standards, the Declaration of Helsinki, and the International Conference on Harmonization. The Institutional Review Board or Ethics Committee at each study site approved the protocol. All patients provided signed informed consent.33 The primary endpoint was confirmed ORR by blinded independent central review (BICR). Secondary and exploratory endpoints included time to objective response, duration of objective response, prostate-specific antigen (PSA) decline \u226550% from baseline, time to PSA progression, circulating tumor cell (CTC) conversion rate, radiographic progression-free survival per BICR and investigator assessment, overall survival, safety, and potential biomarkers of response. Patient-reported outcomes have been reported previously.34 The pharmacokinetic data will also be reported separately.Outcomes and assessments have been previously published.Safety analyses comprised the incidence of serious and nonserious AEs , severity of AEs, timing and duration of AEs, and incidence of dose modifications and of permanent treatment discontinuation due to AEs. All AEs were evaluated using the National Cancer Institute-Common Terminology Criteria for Adverse Events, version 4.03, and coded using the Medical Dictionary for Regulatory Activities, version 23.0. Adverse events of special interest (AESI) included acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), venous thrombotic events, pneumonitis, and second primary nonhematologic malignancies. The treatment-emergent period was defined as starting from the first dose of talazoparib and continuing until 28 days after the last dose, or before new systemic antineoplastic therapy or investigational drug, whichever occurred first. AEs were considered treatment-emergent AEs (TEAEs) if they occurred during the treatment-emergent period. For concurrent events, TEAEs were considered overlapping if the patient experienced both the AEs for at least 1 day. For analyses of anemia followed by fatigue, thrombocytopenia followed by bleeding event, and neutropenia followed by infections, the second AE had to start the same day or later after the first AE , but the start date of the second AE was before the end date of the first AE.33 Most statistical analyses of the safety endpoints presented here are descriptive, although time-to-event endpoints are summarized using the Kaplan-Meier method and 95% CIs for medians are based on the Brookmeyer-Crowley method.The full statistical methodology has been previously reported.\u00ae CDx; Foundation Medicine, Cambridge, MA) including genes likely to sensitize to PARP inhibition.Data cutoff (at the primary completion date) was September 4, 2020. All safety analyses were performed on the safety population, which was defined as all men who received \u22651 dose of talazoparib, including a subset of men with nonmeasurable disease enrolled under an early version of the protocol and DDR-HRR gene alterations assessed using an expanded DDR-HRR gene panel of men, followed by alterations in ATM (15.7% [20]), CHEK2 (9.4% [12]), PALB2 (5.5% [7]), and BRCA1 and MLH1 (each 4.7% [6]). Five (3.9%) men had alterations detected in MSH2; 4 (3.1%) in NBN; 3 (2.4%) each in FANCA and RAD51C; 2 (1.6%) each in ATR, FANCD2, MUTYH, and RAD50; and 1 (0.8%) each in ERCC4, FANCE, MRE11A, MSH6, POLD1, RAD51B, and TP53BP1.The safety population comprised 127 men (median age 69.0 years) with at least one DDR-HRR alteration enrolled between July 4, 2017, and March 20, 2020, from an initial population that included 1425 screened men with mCRPC . Of the BRCA1/2 alterations.Within the safety population, there were 37 (29.1%) men who received talazoparib for between \u22656 months and <12 months and 28 (22.0%) men who received talazoparib for \u226512 months. The median (range) treatment duration of talazoparib was 6.1 (0.4-24.9) months for all men and 8.3 (0.9-22.2) months for men with In the safety population, 95.3% (121/127) of all men experienced all-cause TEAEs . The mosNone of the grade 5 TEAEs (7.9% [10/127]) were related to the study drug, and they included death due to disease progression (4.7% [6/127]), general physical health deterioration (0.8% [1/127]), pulmonary embolism (0.8% [1/127]), subdural hematoma (0.8% [1/127]), and cardio-respiratory arrest (0.8% [1/127]).All-cause serious TEAEs were reported in 43 (33.9%) men . The mos35The median time (range) from the first dose of talazoparib to the onset of the first episode of grade 3 or higher anemia, neutropenia, and thrombocytopenia was 56.0 (13.0-198.0), 48.5 (15.0-263.0), and 17.0 (13.0-116.0) days, respectively. The median (range) duration of grade 3 anemia, grade 3 neutropenia, grade 3 thrombocytopenia, and grade 4 thrombocytopenia was 7 (1-38), 12 (7-18), 8 (5-28), and 11 (8-17) days, respectively . No gradThe cumulative risk by week for the most common hematologic TEAEs is shown in TEAEs were managed by dose modifications and supportive care. In the safety population, 34.6% (44/127) of men received \u22651 concomitant blood transfusion product and 29.9% (38/127) received a packed red blood cell transfusion ; of thosBRCA status nor DDR-HRR gene alteration origin significantly impacted the development of grade 3-4 anemia. The baseline characteristics, prior treatments, germline or somatic DDR-HRR alteration status, and duration of treatment within the overall safety population, patients with grade 3-4 anemia, and patients with grade 3-4 neutropenia are shown in BRCA1/2 alterations and 72.7% (16/22) of these men had a duration of treatment 6 months or longer versus 56.4% (22/39) of men in the overall population with grade 3-4 anemia.Neither P < .0001). Men with 4 or more prior anticancer regimens experienced a higher incidence of treatment-emergent grade 3-4 anemia (35.6% [26/73]) than men with 1-3 prior anticancer regimens (24.5% [13/53]), although the difference was not significant (p =.24). Duration of treatment was not significantly associated with the incidence of treatment-emergent grade 3-4 anemia: 27.4% (17/62) who received treatment for less than 6 months developed treatment-emergent grade 3-4 anemia versus 33.8% (22/65) who received treatment for no less than 6 months. The incidence of any grade anemia was similar between men with normal renal function (48.5% [32/66]) and mild renal impairment (43.6% [17/39]), and the incidence was higher in men with moderate renal impairment (59.1% [13/22]).The impact of various baseline characteristics on the development of treatment-emergent grade 3-4 anemia or neutropenia was examined. Men with low baseline hemoglobin (<100 g/L) were more likely to experience treatment-emergent grade 3-4 anemia (75% [15/20]) than those with baseline hemoglobin within normal limits . For men with at least 10 bone metastases at baseline, the incidence was 62.5% ([35/56] for developing any grade of anemia and 42.9% [24/56]) for developing grade \u22653 anemia .Dose interruptions or reductions due to TEAEs occurred in 47 (37.0%) and 33 (26.0%) men, respectively. The most common TEAEs leading to dose interruptions (>2 men) were anemia (18.9% [24/127]), thrombocytopenia (11.0% [14/127]), neutropenia (7.9% [10/127]), and decreased appetite (4.7% [6/127]). The most common TEAEs leading to dose reductions (>1 patient) were anemia (22.0% [28/127]), thrombocytopenia (4.7% [6/127]), neutropenia (3.1% [4/127]), and lymphopenia ([2.4% [3/127]) . Of the Permanent treatment discontinuations due to all-causality TEAEs occurred in 15 men (11.8%); median (range) duration of treatment was 1.97 (0.43-7.92) months. The majority of permanent discontinuations were due to nonhematologic AEs, including back pain (1.6% [2 men]), and cancer pain, cardio-respiratory arrest, and disease progression (0.8% [1 man] each). Two (1.6%) men discontinued due to decreased platelet count and 1 (0.8%) man discontinued due to a decreased white blood cell count .BRCA1/2 alterations.33 The TALAPRO-1 patient population can be difficult to treat.36-38 Although the populations are distinct (patients with breast cancer were on average younger than patients with prostate cancer), the TEAEs were consistent with the established safety profile for talazoparib in female and male patients with germline BRCA (gBRCA)-altered advanced breast cancer.39 Here, we detail the safety profile of talazoparib in heavily pretreated men with mCRPC and somatic or germline DDR-HRR alterations to inform dosing in future clinical trials and provide clinicians with a thorough understanding of the incidence and management of TEAEs associated with talazoparib treatment.The TALAPRO-1 trial demonstrated talazoparib to be effective in the treatment of mCRPC, particularly in men with 27-30 In the EMBRACA trial, which led to the approval of talazoparib for the treatment of adult female and male patients with gBRCA1/2-altered human epidermal growth factor receptor 2-negative metastatic or locally advanced breast cancer, the most common hematologic toxicities were anemia, neutropenia, and thrombocytopenia.31 The most common nonhematologic AEs were fatigue, nausea, headache, alopecia, and vomiting.29 In the ABRAZO trial, patients with advanced breast cancer and gBRCA1/2 alterations, who had previously received either platinum or platinum-free cytotoxic regimens, demonstrated a similar safety profile. The most common AEs reported were anemia, fatigue, and nausea.30 In the EMBRACA and ABRAZO trials, the median (range) age of patients was 45 (27-84) years and 50 (31-75) years, respectively,30 versus 69.0 (interquartile range [IQR] 63.0-74.0) years in the TALAPRO-1 trial.33 All men in the TALAPRO-1 trial had received 1 or 2 prior chemotherapy regimens, including 1 or more taxane-based regimen in the metastatic setting. In contrast, in the EMBRACA trial, 76% of patients had received \u22641 prior cytotoxic regimen for advanced breast cancer.29 The ABRAZO population was more heavily pretreated: a median (range) of 3 (1-10) prior cytotoxic therapies for advanced disease.30The phase III EMBRACA and phase II ABRAZO trials established the safety profile of talazoparib in female and male patients with advanced breast cancer.gBRCA-altered advanced breast cancer treated with talazoparib in the EMBRACA trial and ABRAZO trial .30 In TALAPRO-1, hematologic TEAEs were generally well-managed through dose modifications and supportive care. Of the 62 men who experienced anemia, 72.6% (45/62) received \u22651 supportive treatment and anemia was the most common TEAE leading to dose interruptions or reductions. With supportive care, the median duration of the most common grade 3 hematologic events was limited to 7-12 days. In the EMBRACA and ABRAZO trials, anemia was also the most common cause leading to a dose reduction or temporary interruption.30 However, there were no permanent discontinuations due to anemia in the TALAPRO-1 study. In the PROfound trial, 21.5% (55/256) of men (median [range] age 69 [47-91] years) treated with olaparib for mCRPC experienced grade \u22653 anemia.40 In the GALAHAD trial, 33% (95/289) of men (median [IQR] age 69.0 [64.0-74.0] years) with mCRPC treated with niraparib experienced grade \u22653 anemia.41PARP inhibitors are known to cause hematologic toxicities, and anemia (48.8%) was the most common any grade hematologic toxicity in the TALAPRO-1 population. This finding is consistent with the incidence of anemia reported in patients with BRCA status or germline versus somatic alteration origin were observed. Ledermann et al also reported no significant difference in the proportion (or incidence) of patients with anemia between the overall patient population and those with BRCA1/2 alterations in patients with ovarian cancer treated with olaparib.42 However, in the TRITON2 trial, which examined rucaparib in men with mCRPC, anemia was found to be more common in men with BRCA1/2 alterations than men with deleterious non-BRCA DDR alterations .44 In the TRITON2 trial, the median age (range) of patients with BRCA alterations was 72.0 (50-88), median number (range) of prior therapies for CRPC was 2 (1-8), and the proportion of patients who had \u226510 bone metastases was 47.0% (54/115).44 The median age (IQR) for patients with ATM, CDK12, CHEK2, and other alterations in the TRITON2 trial was 73.0 (68.0-77.0), 64.0 (56.0-72.0), 71.5 (64.5-75.0), and 66.5 (61.0-72.0) years, respectively, and the median number of prior CRPC treatments for non-BRCA patients ranged between 2 and 3 (IQR 2-4).43No significant differences in the safety profile based on BRCA alterations and advanced breast cancer. Any grade alopecia and vomiting occurred in 25.2% (72/286) and 24.8% (71/286) of patients.28 However, in TALAPRO-1, the incidence of alopecia was lower than the \u226510% cutoff (4.7% [6/127]) and 13.4% (17/127) of men experienced vomiting.In TALAPRO-1, the most common any grade nonhematologic TEAEs were nausea (33.1% [42/127]), decreased appetite (28.3% [36/127]), asthenia (23.6% [30/127]), and fatigue (19.7% [25/127]); most events were grade 1 or 2 in severity. Serious AEs due to nonhematologic TEAEs were less common. In the EMBRACA trial, the most common nonhematologic TEAEs associated with talazoparib were fatigue (62.2% [178/286]) and nausea (48.5% [139/286]) in women with g27 In TALAPRO-1, dose reductions due to an AE were common (26.0%); while permanent discontinuations due to an AE occurred in 11.8% of patients, only 2.4% of discontinuations were due to hematologic AEs. This finding is consistent with the trend observed in the EMBRACA trial .29Higher talazoparib exposure is associated with a higher incidence of hematologic AEs and dose interruptions, and reductions are an effective management strategy.45 TALAPRO-3 (NCT04821622) is enrolling men with mCSPC and DDR-HRR alterations receiving either 0.5 mg talazoparib plus 160 mg enzalutamide, or enzalutamide monotherapy.A thorough understanding of the safety profile for treatment with talazoparib monotherapy and management of AEs in men with metastatic prostate cancer is essential in making treatment decisions and in future studies where there may be drug-drug interactions to consider. There are currently two ongoing phase III trials that compare talazoparib plus enzalutamide with enzalutamide monotherapy in men with metastatic prostate cancer: TALAPRO-2 and TALAPRO-3. TALAPRO-2 (NCT03395197) is studying men with mCRPC, with and without DDR-HRR alterations in a first-line setting. Following the conclusion of Part 1 of the TALAPRO-2 trial, the recommended dose of talazoparib was 0.5 mg/day due to drug-drug interactions when combined with enzalutamide (160 mg/day).In the ongoing TALAPRO-1 phase II study, no new safety signals were observed with talazoparib monotherapy in men with heavily pretreated mCRPC with DDR-HRR alterations. The most common any-grade TEAEs were anemia, nausea, decreased appetite, and asthenia. TEAEs were not associated with germline compared with somatic alterations. TEAEs were well managed through dose modifications and supportive care, with grade 3 hematologic AEs having a median duration of 7-12 days for the 3 most common hematologic AEs. The manageable safety profile and observed antitumor activity support further evaluation of talazoparib in advanced prostate cancer.oyac172_suppl_Supplementary_Figure_1Click here for additional data file.oyac172_suppl_Supplementary_Figure_2Click here for additional data file.oyac172_suppl_Supplementary_Figure_3Click here for additional data file.oyac172_suppl_Supplementary_Figure_4Click here for additional data file.oyac172_suppl_Supplementary_Figure_5Click here for additional data file.oyac172_suppl_Supplementary_FiguresClick here for additional data file.oyac172_suppl_Supplemental_Tables_1_6_finalClick here for additional data file."} +{"text": "We noted an increase in infective endocarditis (IE) cases in recent years. The purpose of the study was to examine the changes in incidence, risk factors, microbiology, complications and outcome of IE in our patient population.Records of children < 18 yrs with discharge diagnosis of IE during 2002-2020 at Children\u2019s Hospital of Michigan, Detroit were reviewed. Modified Duke criteria were used to determine \u201cdefinite\u201d and \u201cpossible\u201d IE cases.p = 0.0059). Cardiac surgery had been performed in 28/51 (55%) prior to IE diagnosis. CVC related infections were more frequent in the early period than the late period , (p = 0.0005). Overall, 16 (15.8) cases were culture negative. In culture-positive IE, S. aureus was most common followed by streptococci (17), S. epidermidis (10), Gram negative bacilli (8), Enterococci (7), fungi (5) and HACEK group (4). Causative organisms were similar in both periods except for fungal organisms (5) and B. henselae (1) in the late period only. Valve replacement or valvuloplasty were performed in 19 (18.8%) patients. Complications included acute kidney injury (9) and emboli to brain (10) and to lungs (7). Mortality occurred in 15 (14.8%): 8 had CHD, 5 had CVC and 1 had fulminant MRSA infection.101 patients with IE were identified, representing annual incidence of 4.9/10,000 admissions. During 2002-2011 (early period), the incidence was 2.8/10,000 (33 cases). However, during 2012-2020 (late period), the incidence was 7.0/10,000 (68 cases): a 2.5-fold increase. Males were 53.4%. The age range was 1 mo \u2013 17 yrs (median 6 yrs). Of 101 patients, 37 (36.6%) met criteria for definitive and 64 (63.4%) for possible IE. The most common predisposing conditions included congenital heart disease (CHD) (50.5%), central venous catheter (CVC) (25.7%), and immunosuppression (13.9%). CHD was more frequent in the late period compared to early period (. S. aureus was the predominant pathogen followed by streptococci. Mortality rate in our patients was 14.8%.Most of our IE patients had underlying medical conditions. The higher incidence of IE during the late period is likely due to an increase in the number of patients with complex cardiac conditions who underwent surgery at our institutionAll Authors: No reported disclosures."} +{"text": "Several psychiatric adverse events can occur after vaccination. Passive surveillance reporting systems can support the identification of rare adverse events and contribute to hypothesis generation for potential causal associations.To describe the psychiatric adverse reactions associated with various COVID-19 vaccines reported in the WHO database (VigiBase\u00ae)We for individual case reports (ICSRs) for \u201cPsychiatric disorders\u201d linked to COVID-19 vaccines authorized in the EU, the US and the UK. Reporting rates were calculated using the number of administered doses as a denominator. Disproportional reporting was investigated through frequentist and Bayesian approaches by the calculation the information component (IC) for adverse psychiatric adverse not included in the vaccine label.63322 ICSRs including 76,163 psychiatric adverse events were identified, 21878 (34.6 %) were serious events. Mean age in the reports was 48.8 years old (SD: 17.8) and involved 44441 (70.2%) female and 17975 (28.4%) women; sex was not specified in 906 (1.4%) reports. Rate of reported psychiatric adverse events per million administered doses were 52.0, 110.3, 164.8 and 170.8 for Tozinameran/Cominarty (Pfizer-BioNTech), Elasomeran (Moderna), Vaxzevria (AstraZeneca) and Ad26.COV2-S (Janssen) vaccines respectively. UK recorded the highest rates. The most frequently reported events were insomnia (21.6%), confusional state (13.6%) and anxiety (13.5%). Disproportionality was found for: habit cough (IC:3.6), clinomania (IC: 2.2), exploding head syndrome (IC: 2.2) and autoscopy (IC: 2.1).Rates of reported psychiatric adverse events are very low. Doctors and patients should be aware of these potential adverse reactions. Continuing monitoring of emerging potential safety signals is advised.No significant relationships."} +{"text": "Placement of ventriculoperitoneal (VP) shunt is an important treatment for pediatric hydrocephalus. Although prolonged perioperative antibiotic prophylaxis has theoretically no benefit in reducing device-associated infections, duration of antibiotic prophylaxis for VP shunt placement in pediatrics is not well established. As a part of antimicrobial stewardship program (ASP), our ASP team recommended to stop perioperative antibiotic prophylaxis for sterile medical placement within 48 hours following surgery in April 2017.Our aim of this study was to evaluate rate of VP shunt-associated infections following shunt placement between children received < 48 hours and \u2267 48 hours of perioperative antibiotic prophylaxis.Children aged 15 years old or younger who underwent VP shunt insertion between April 2014 and November 2021 were enrolled at Tokyo Metropolitan Children's Medical Center. Children with co-existing infection at time of surgery were excluded. Rates of VP shunt-associated infections following 1 month and 6 months of post-surgical periods were compared between children who received < 48 hours and \u2267 48 hours of perioperative antibiotic prophylaxis.A total of 110 children were identified. Among them, 11 cases with VP shunt-associated meningitis and 15 cases with other infections were excluded. Girl ratio was 44%. Median age was 4.5 months old (IQR 8-40). Numbers of children with cefazolin and vancomycin-contained regimen were 83 (98.8%) and 1 (1.2%), respectively. Numbers of children who received perioperative antibiotic prophylaxis for < 48 hours and \u2267 48 hours were 43 (51.2%) and 41 (48.8%), respectively. Incidence of VP shunt-associated infections for 1 month of post-surgical period in < 48 hours and \u2267 48 hours antibiotic prophylaxis groups were 4.65% (2/43) and 12.2% (5/41), respectively. (P=0.211)\u3000Incidence of VP shunt-associated infections for 6 months of post-surgical period in < 48 hours and \u2267 48 hours antibiotic prophylaxis groups were 11.6% (5/43) and 12.2% (5/41), respectively. (P=0.936).Shorter duration of < 48 hours of perioperative antibiotic prophylaxis did not increase rates of VP shunt-associated infections among children in short and long terms.All Authors: No reported disclosures."} +{"text": "To summarize the anesthetic management of patients undergoing mediastinal mass operation.Electronic databases were searched to identify all case reports of patients undergoing mediastinal mass operation. Information such as clinical characteristics, perioperative management and patients\u2019 outcomes were abstracted and analyzed.n\u2009=\u200948), superior (n\u2009=\u200915), middle (n\u2009=\u20099) and posterior (n\u2009=\u20099) mediastinum, respectively. Clinical manifestations included dyspnea (n\u2009=\u200945), cough (n\u2009=\u200929), chest or radiating pain (n\u2009=\u200912), swelling (n\u2009=\u20098), fever (n\u2009=\u20097) and chest distress (n\u2009=\u20094). Most patients (n\u2009=\u200975) had signs of compression or invasion of vital structures. General anesthesia (n\u2009=\u200976) was the most commonly used method of anesthesia. Muscle relaxants were administered in 35 patients during anesthesia induction and spontaneous respiration was maintained in 37 patients. Mediastinal mass syndrome (MMS) occurred in 39 cases. Extracorporeal circulation was utilized in 20 patients intraoperatively. Three patients experienced cardiac arrest after ventilation failure and two patients died intraoperatively and one postoperatively.Seventy-seven case reports with 85 patients aging from 34 days to 81 years were included. Mediastinal masses were located in anterior (Peri-operative management of patients undergoing mediastinal mass operation could be challenging. Pre-operative multi-disciplinary discussion, well-planned anesthetic management and pre-determined protocols for emergency situations are all vital to patient safety. Peri-operative management of patients undergoing mediastinal mass operation could be challenging. Mediastinal mass syndrome (MMS), initially described by Bittar in the 1970\u2005s, is caused by a mediastinal mass, which can quickly deteriorate to acute respiratory and hemodynamic decompensation and is associated with increased morbidity and mortality . TherefoRelevant case reports were identified through computerized searches of PubMed, Embase and Ovid databases until May 15th, 2020, using different combinations of search terms \u201cmediastinal mass\u201d, \u201canesthesia\u201d and \u201ccase\u201d . ChineseThe following data from the included case reports were abstracted to a data collection form by two authors (J.C.T. and P.S.L.) independently: (1) literature information (author and year of publication); (2) patients characteristics ; (3) mediastinal mass features and clinical manifestations ; (4) perioperative management and (5) patients' outcomes. Disagreements were resolved by discussion among all authors during the process of data abstraction.As depicted in the flow chart , the datThe 85 patients aged between 34 days and 81 years, of whom 42 were males and 39 females (4 cases did not describe sex). Forty-eight (59.3%) cases of masses were located in anterior mediastinum, 15 (28.5%) in superior mediastinum, 9 (11.1%) in middle mediastinum and 9 (11.1%) in posterior mediastinum. The mass sizes ranged from 35mm\u2009\u00d7\u200944mm\u2009\u00d7\u200942\u2005mm to 200mm\u2009\u00d7\u2009200mm\u2009\u00d7\u2009180\u2005mm. Anterior mediastinum masses were usually bigger than those of other origins. Lymphoma was the most common pathological type, followed by teratoma or seminoma . Of the 85 patients, 45 (59.2%) presented with dyspnea, 29 (38.1%) with cough, 12 (15.8%) with chest or radiating pain, 8 (10.5%) with swelling, 7 (9.2%) with fever, 4 (5.2%) with chest distress and 6 (7.8%) patients were asymptomatic. Seventy-five cases had signs of compression or invasion of trachea , bronchia , superior vena cava and heart . Examination such as Computed tomography (CT), transthoracic echocardiogram (TTE), pulmonary function testing (PFT) and magnetic resonance imaging (MRI) were performed in 84 (97.4%), 24 (28.2%), 10 (11.8%), and 5 (5.9%) patients, respectively. Fifty-one (60.0%) patients underwent open thoracotomy, 28 (32.9%) patients underwent video-assisted thoracoscopic surgery (VATS) and 6 (7.1%) patients underwent other surgery. Fifty-seven (67.1%) patients had mass resection, 27(31.8%) patients received mass biopsy and 1(1.1%) case did not report surgical procedure.n\u2009=\u200923), midazolam (n\u2009=\u200921), propofol (n\u2009=\u200919), ketamine (n\u2009=\u200915) and sevoflurane (n\u2009=\u200912) were most frequently used agents, followed by dexmedetomidine (n\u2009=\u20096), halothane (n\u2009=\u20095), remifentanil (n\u2009=\u20094), etomidate (n\u2009=\u20093), nitrous oxide (n\u2009=\u20093), diazepam (n\u2009=\u20092) and isoflurane (n\u2009=\u20092). Muscle relaxants were reported to be administered in 35 of the 85 included patients during anesthesia induction and in 5 patients after sternotomy, respectively. Succinylcholine was the most commonly used muscle relaxant before endotracheal intubation. As for airway management, 66 (77.6%) patients were intubated with single lumen tube (SLT) including 1 with bronchial blocker (BB), 5 (5.9%) with double lumen tube (DLT), 4 (4.7%) with laryngeal mask airway (LMA) and 9 (10.6%) patients were tubeless. Spontaneous respiration was maintained in 32 (37.6%) patients, including 23 with spontaneous ventilation (SV) and 9 with assisted ventilation (AV).Seventy-six (89.4%) patients were operated under general anesthesia (GA), 8 (9.4%) patients under sedation and 1 (1.2%) patient under local anesthesia. Fentanyl (Thirty-nine (45.9%) included patients developed MMS, 2 (2.4%) cases occurred before anesthetic induction, 13 (15.3%) cases after non-paralytic (without muscle relaxant) endotracheal intubation, 3 (3.5%) cases after muscle relaxant administration, 10 (11.8%) cases during position change, 10 (11.8%) cases during mass dissection, 3 (3.5%) cases during post-anesthesia recovery, respectively. Extracorporeal circulation (ECC) technique was applied in 20 (23.5%) patients: 2 initiated before anesthesia induction and 18 just with ECC standby. Three patients underwent ECC support due to severe intraoperative cardiopulmonary collapse. One patient experienced severe oxygen desaturation as the airway collapsed after endotracheal intubation without muscle relaxant and the operation was finally cancelled . Three pAnesthetic management of mediastinal mass operation could be complicated by MMS characterized by acute respiratory and hemodynamic decompensation, which is caused by mechanical compression of mediastinal structures . HoweverComprehensive preoperative assessment is crucial in the management of patients with mediastinal mass , 39. Som2 . The extent of postoperative monitoring for patients in the uncertain risk category should be decided depending on preoperative findings and intraoperative course . It is wTo sum up, pre-operative multi-disciplinary discussion, well-planned anesthetic management and pre-determined protocols for emergency situations are all vital to patient safety."} +{"text": "C. difficile infection (CDI) as community onset (CO) versus hospital onset (HO) is based upon the timing of the laboratory testing. Any lab diagnosis made after day 3 of hospitalization is classified as HO-CDI, even if there is clinical evidence that the patient had CDI before lab testing was sent on day 4 or later. Capturing CDI infection early in hospitalization is essential to proper diagnosis and management of CDI.Identification of This is a single center retrospective study of all HO-CDI cases identified from January 2018 through January 2022. All cases were reviewed to determine if patients had loose stools during days 1-3 which were not tested, as these may have been missed opportunities to diagnose CO-CDI. We used nursing flowsheet determine if the patient had soft, loose, watery, liquid or pasty stool bowel movements (BM).We identified 302 unique patients diagnosed with HO-CDI during the 4 year study period. 181 (60%) were men. The mean age 57 (range 3-98 years), with increasing case numbers with increasing age groups: age 0-18 (19/6.3%), 19-39 (39/12.9%), 40-59 (73/24.2%), \u2265 60 (171/56.6%). Mean time of HO-CDI diagnosis was 12.4 days (range 4-122 days) with a skew towards early onset HO-CDI diagnosis as 86/302 (28.5%) testing positive on days 4-6. Overall, 119/302 (39.0%) of patients had identified missed opportunities for testing stools during days 1-3 of hospitalization. 38/86 (44.2%) of patients with HO-CDI diagnosed on days 4-6 had missed opportunities for testing. 40/302 (13.2%) patients expired during the index hospitalization.Better tracking of patients' symptoms, number and consistency of BMs could improve recognition of patients presenting with CO-CDI. In turn, this would help to institute earlier isolation and treatment of these patients, as well as decreasing HO-CDI resulting from late recognition of CO-CDI which may falsely inflate HO-CDI case numbers, and/or lead to secondary hospital transmission from delayed isolation of patients with CDI. Our findings likely represent a significant under estimation of the magnitude of the errors of omission of missing opportunities for early diagnosis of CDI since it based on review of nursing flowsheets which often miss the number and consistency of patients' BMs.Jorge Paiva Parada, MD MPH, Shionogi: Honoraria."} +{"text": "TP53 (64%), followed by ARID1A (62%), KMT2C (60%) and KMT2D (58%). In cfDNA samples, the most commonly mutated genes were FAT4 (19%) and MACF1 (19%), followed by KMT2D (18%), ARID1A (14%) and LRP1B (14%). The concordance of mutation patterns in these 29 genes was 42.0% between cfDNA and tumor DNA. A specificity of 100% was found when using the mutation status of cfDNA to predict mutations in tumor samples. The sensitivity of the mutation status of cfDNA to predict mutation in tumor samples was highest in FAT4 (88.9%), followed by MACF1 (80%), CDH1 (75%) and PLB1 (75%). For cfDNA with PLB1 mutations, patients were more likely to develop distant lymphatic metastasis than peritoneal metastasis. Patients with multiple-site metastases had significantly more mutated spots than patients with single-site metastasis. Due to the high sensitivity and specificity of some genes in the prediction of mutation in tumor samples, monitoring the mutation pattern of cfDNA may be useful in the stage IV GC treatment.Compared to stage I\u2013III gastric cancer (GC), the level of cell-free DNA (cfDNA) was significantly higher in stage IV GC. The mutation patterns of different metastatic patterns between cfDNA and tumor DNA in stage IV GC have not yet been reported. We used next-generation sequencing (NGS) to analyze cfDNA and tumor DNA in 56 stage IV GC patients. Tumor DNA and cfDNA were analyzed using a 29-gene NGS panel. In tumor samples, the most commonly mutated gene was Gastric cancer (GC) is the sixth most common cancer and the second most common cause of cancer-related death worldwide . RadicalCirculating cell-free DNA (cfDNA) can serve as a liquid biopsy and noninvasive method for cancer monitoring and management \u20134. cfDNANext-generation sequencing (NGS) has been used to investigate the concordance of genetic mutations between tumor tissue DNA and cfDNA . AlthougIn the current study, we used NGS and evaluated the concordance of genetic mutations between tumor DNA and cfDNA in stage IV GC patients. The relationship between the genetic mutations and metastatic patterns was analyzed.The clinicopathological features of the 56 stage IV GC patients are shown in Among the 56 stage IV GC patients, genetic mutations were observed in both tumor DNA and cfDNA in 54 (96.4%) patients. Two patients had no genetic mutations detected in either tumor DNA or cfDNA.KMT2D (45%), followed by TP53 (42%), KMT2C (42%), ARID1A (39%), MACF1 (27%), LRP1B (24%), FAT4 (21%), CDH1 (21%), APC (18%), and ABCA10 (18%). In LRP1B (67%) and KMT2C (67%), followed by TP53 (33%), PREX2 (33%), MACF1 (33%), KRAS (33%), KMT2D (33%), FAT4 (33%), CTNNB1 (33%), CREBBP (33%), CDH1 (33%), BNC2 (33%), BCOR (33%), and ARID1A (33%). In TP53 (46%), followed by FAT4 (38%), ARID1A (38%), KMT2C (35%), PLB1 (31%), MACF1 (23%), LRP1B (23%), MUC6 (23%), CREBBP (15%), CDH1 (15%), BCOR (15%), ERBB3 (15%), and BNC2 (15%). The most common mutated spot in both peritoneal and distant lymphatic metastases was KMT2C c.8390delA.We analyzed the genetic mutation according to the metastatic sites. As shown in CDH1, MACF1, TP53, PLB1, ARID1A, KMT2C, FAT4, and KMT2D. As shown in CDH1 mutations were associated with significantly more negative expression of the correlated E-cadherin protein (P = 0.021), which was also observed in tumors with mutations in MACF1 (P < 0.001), TP53 (P < 0.001), PLB1 (P < 0.001), ARID1A (P < 0.001), KMT2C (P < 0.001), FAT4 (P < 0.001), and KMT2D (P < 0.001).We further analyzed the immunohistochemical (IHC) stain for some common mutated genes in the tumor samples, including MACF1 (19.3%), followed by KMT2D (17.0%), FAT4 (13.6%), KMT2C (13.6%), LRP1B (12.5%) and PLB1 (11.4%). The median number of mutated genes in the 56 GC cfDNA samples was 1 (range 0\u20135). Among them, twenty-six (46.4%) patients had more than one mutated gene.As shown in As shown in PLB1 mutations was significantly higher in patients with distant lymphatic metastasis than in those with peritoneal metastasis .As shown in FAT4 (88.9%), followed by MACF1 (80%), CDH1 (75%), PLB1 (75%), KMT2D (72.7%), LRP1B (71.4%), KMT2C (40%), ARID1A (25%), and TP53 (13.6%).The specificity of all genetic mutations in cfDNA was 100% in predicting mutations in tumor DNA. As shown in In total, 621 mutation spots among these 29 genes were found in tumor samples. Among these 56 patients, 360 mutation spots in tumor samples in 45 patients could not be detected in cfDNA. The concordance of mutation spots in these 29 genes was 42.0% (261/621) between cfDNA and tumor samples. Among the 56 stage IV GC patients, one patient had both peritoneal and hematogenous metastases. The patient had ten mutated genes in the tumor DNA and a total of 60 mutated spots, and only one mutated gene, MACF1, was detected in both tumor DNA and cfDNA.CDH1 and MUC6), five mutated genes in two patients , and ten mutated genes in two patients . Regarding cfDNA, three patients had one mutated gene (including MUC6 mutation in one patient and FAT4 mutation in two patients), and two patients had two mutated genes .Among the 56 stage IV GC patients, five patients had both peritoneal and distant lymphatic metastases. All of them had at least two mutated genes in tumor DNA and at least one mutated gene in cfDNA. Regarding tumor DNA, there were two mutated genes in one patient (P = 0.273) was not significantly different between single-site and multiple-site metastases, while patients with multiple-site metastases had significantly more mutated spots than patients with single-site metastases . Regarding cfDNA, the number of mutated genes and mutated spots were not significantly different between single-site and multiple-site metastases.We further compared the number of mutated genes and mutated spots between single-site and multiple-site metastases in tumor DNA and cfDNA. Regarding tumor DNA, the number of mutated genes , indicating that cfDNA can serve as a predictor of treatment response and PFS for GC . Jin et anced GC . It was therapy . ConsequTP53, KMT2C, KMT2D and ARID1A, which were also among the top high-frequency mutations for GC reported by the Catalogue of Somatic Mutations in Cancer (COSMIC) database [TP53 mutation was associated with lymph node metastasis and distant metastasis in GC, especially in the Asian population [ARID1A mutation was reported to be associated with distant metastasis in GC [ARID1A mutation could serve as a biomarker for immunotherapy in GI tract cancer [KMT2D and KMT2C mutations in GC were associated with the DNA repair process, and these two genetic mutations were considered targets for cancer treatment using poly ADP-ribose polymerase (PARP) inhibitors [PARP inhibitors for mutations of the KMT2 family and immunotherapy for ARID1A mutations.We also analyzed the correlation between metastatic pattern and genetic mutation pattern in tumor DNA and cfDNA in stage IV GC, which has not yet been reported. The four most commonly mutated genes among the three metastatic patterns were database . All foudatabase \u201323. TP53pulation , which wis in GC , and ARIhibitors , 24. AccMACF1 mutations were associated with upregulation of the mTOR signaling pathway and had a worse prognosis in breast cancer [PLB1 mutation was reported to be associated with poor survival in non-small cell lung cancer and glioblastoma multiform [CDH1, ARID1A, FAT4, KMT2C, TP53, KMT2D, MACF1, and PLB1) were associated with the down regulation of the associated protein function, which may be involved in the up-regulation or down-regulation in the mechanism of cancer developing. In addition, our results showed that PLB1 mutation was more common in the cfDNA of GC patients with single distant lymphatic metastasis than in patients with peritoneal metastasis, which has not yet been reported yet. According to our results, PLB1 mutation in cfDNA may serve as a risk factor for distant lymphatic metastasis in GC.Low expression of E-cadherin (CDH1), ARID1A, FAT4, and KMT2C were associated with a poor prognosis in GC \u201328, whilt cancer . PLB1 . The pathological staging of GC was performed according to the 8th American Joint Committee on Cancer (AJCC)/Union for International Cancer Control (UICC) TNM classification system . The metWhole blood (4~8 ml) was drawn from each clinical patient using disposable venous blood lancet and stored directly in cfDNA Blood Collection Tube (Streck). Blood samples were stored at room temperature and used for plasma separation extraction within three days. In plasma separation, tube containing whole blood was centrifuged at 3,000 \u00d7 g for 10 minutes at room temperature, then the upper layer was transferred to the 1.5 ml micro-centrifuge tube. The transferred tubes were processed for the second centrifuge at 11,000 \u00d7 g for 10 minutes, and finally transfer the supernatant to new sample tubes for cfDNA extraction. cfDNA was extracted from 1,000 \u03bcl of plasma by using the QIAamp MinElute ccfDNA Kits (Qiagen), and tumor DNA was extracted from tissue specimens by using a QIAamp DNA Tissue Kit . After DNA extraction, DNA quantity was measured by using the Qubit dsDNA High-Sensitivity assay (Thermo Fisher Scientific).ABCA10, APC, ARID1A, BCOR, BNC2, CDH1, CNGA4, CREBBP, CTNNB1, ERBB3, EYA4, FAM46D, FAT4, KMT2C, KMT2D, KRAS, LRP1B, MACF1, MUC6, PIK3CA, PLB1, PREX2, RASA1, RHOA, RNF43, SMAD2, SMAD4, SOHLH2 and TP53) was enriched using probe-based methods. The probes were synthesized by Integrated DNA Technologies (USA) according to our previously designed probe sequences, and the capture procedure was performed following the IDT guidelines. After probe-based enrichment, libraries of each pool were amplified with 14 cycles. The amplified libraries were quantified using an LC480 qPCR system (Roche) and pooled into a new 1.5-ml tube as a 10-nM pooled DNA library. The final pool was used for sequencing . The raw output of each tumor tissue was >1.5 Gb, and the average depth of target regions was >250X. The raw output of each cfDNA was >15 Gb, and the average depth of target regions was >2000X. We used the Illumina Basespace Dragen somatic mutation pipeline (https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/edico-genome-inc-dragen-somatic-pipeline.html) to perform variant calling and annotated all variants by using Illumina variant interpreter (https://variantinterpreter.informatics.illumina.com/home). In this study, although adjacent-normal parts or white blood cells were not collected for genotyping and identifying germline variants of each case, single-nucleotide polymorphisms, defined as the minor allele frequency >1%, of the primary variants of tumor and cfDNA were filtered out based on the databases of Taiwan biobank, 1,000 Genome and GnomAD East Asian populations. Variants with >5% and >1% frequencies were retained for the following in tissue and cfDNA, respectively. Although some variants were found to have high confidences in variant calling with more than 2,000 depth, however, only >1% variants were considered in this study, which might reduce the sensitivity in this study.A total of 250 ng DNA from each tumor tissue was used to construct an NGS library using an IDT Lotus Library Preparation Kit . Each DNA sample was fragmented and then used to prepare a DNA library by performing end repair, a-overhang addition, adaptor ligation and size selection (250~350 bp). Fifteen microliters of each cfDNA sample was used to construct a library by using the xGen Prism DNA Library Prep Kit (IDT). Target DNA of exonic regions of 29 frequently-mutated genes in GC , MACF1, p53, PLB1, ARID1A, KMT2C, FAT4, and KMT2D. Antibodies utilized were: E-cadherin (Genemed #61-0192), MACF1 (Proteintech #13058-1-AP), p53 (Leica #P53-D07-L-CE), PLB1 (Invitrogen #PA5-119343), ARID1A (Sigma #HPA005456), KMT2C (Invitrogen #PA5-68419), FAT4 (Invitrogen #PA5-72970), KMT2D (Invitrogen #PA5-57490).Immunoreactivity E-cadherin was localized in membranes; MACF1 and PLB1 were localized in the cytoplasm and membranes; p53 and ARID1A were localized in the nucleus; KMT2C and FAT4 were localized in the cytoplasm; KMT2D was localized in the cytoplasm and nucleus, and mainly in nucleus . Immunor2 test with Yates correction or Fisher\u2019s exact test was used to compare the categorical data. The frequency of the specific gene mutation was calculated using the number of patients carrying the specific gene mutation divided by the total number of the patients and was presented as a percentage. A P value < 0.05 was defined as statistically significant.IBM SPSS Statistics 25.0 was used for statistical analyses. A \u03c7Due to the high sensitivity and specificity of some genes in the prediction of mutation in tumor samples, monitoring the mutation pattern of cfDNA may be a substitute for tumor biopsy and may be applicable in the treatment of stage IV GC."} +{"text": "Cryptococcus neoformans is the etiologic agent of cryptococcosis, a lethal worldwide disease. Synthetic biology could contribute to its better understanding through engineering genetic networks. However, its major challenge is the requirement of accessible genetic parts. The database presented here provides 23 biological parts for this organism in Synthetic Biology Open Language. Cryptococcus neoformans is a facultative intracellular basidiomycete fungus, which became an important human pathogen after the HIV/AIDS pandemic, mostly affecting immunocompromised patients . The promoters were acquired from genes encoding actin (ACT1) , galacton (ACT1) , galacton (ACT1) , 19, UDPn (ACT1) , glyceran (ACT1) , U6 (CnUn (ACT1) , and elon (ACT1) , Cas9 (9n (ACT1) , the flun (ACT1) , green fn (ACT1) , URA5 (2n (ACT1) , hygromyn (ACT1) , 25, neon (ACT1) , 26, andn (ACT1) , 27 resin (ACT1) , HOG1 (Hn (ACT1) , TEF1 (9n (ACT1) . In concCryptococcus neoformans database can be found at https://doi.org/10.6084/m9.figshare.19990838.v2 and in Synthetic Biology Open Language, which is available and can be accessed in SynBioHub by the following link: https://synbiohub.org/public/CnDatabase/CnDatabase_collection/1.Detailed information on the"} +{"text": "The study aims to summarize and analyze the clinical and CT findings of severe COVID-19 patients. From February 11 to March 31, 2020, 61 COVID-19 patients in intensive care in the E1-3 ward of Tongji Hospital were analyzed retrospectively. The main clinical manifestations were cough, expectoration in 56 cases (91.8%), shortness of breath, chest tightness in 48 cases (78.7%), fever in 61 cases (100%), muscle ache and weakness in 40 cases (65.6%), diarrhea or vomiting in 8 cases (13.1%), and headache in 4 cases (6.6%). After admission, the leukocyte count was normal in 40 cases (57.7%), higher in 9 cases (15.4%), and lower in 12 cases (26.9%). The lymphocyte count decreased in 53 cases (86.9%). CRP was increased in 29 cases (47.5%); PCT was increased in 15 cases (24.6%); ESR was increased in 38 cases (62.3%); D-dimer increased in 39 cases (63.9%); ALT/AST increased in 40 cases (65.6%); CK/CK-MB increased in 8 cases (13.1%); troponin I increased in 6 cases (9.8%); NT-proBNP increased in 35 cases (57.4%); IL-1 increased in 5 cases (8.2%); IL-2 receptor increased in 28 cases (45.9%); IL-6 increased in 23 cases (37.7%); IL-8 increased in 15 cases (24.6%); IL-10 increased in 12 cases (19.7%); and NTF increased in 22 cases (36.1%). The chest CT images showed that 38 cases (65.5%) of right lung lesions were more extensive than those of left lung lesions, 20 cases (34.5%) of left lung lesions were more extensive than those of right lung lesions, 42 cases (72.5%) of lower lobe lesions were more extensive than those of upper lobe lesions, 6 cases (10.3%) of upper lobe lesions were more extensive than those of lower lobe lesions, and 10 cases (17.2%) of upper and lower part lesions were roughly the same. Ground-glass opacity (GGO) was found in 12 cases (20.7%); GGO with focal consolidation in 38 cases (65.5%); small patchy edge fuzzy density increased in 24 cases (41.4%); large consolidation in 20 cases (34.5%); reticular or fibrous cord in 54 cases (93.1%); and air bronchogram in 8 cases (13.8%). COVID-19 patients in intensive care have no specific clinical manifestation and CT findings. However, analysis and summary of relevant data can help us assess the severity of the disease, decide the timing of treatment, and predict prognosis. As of April 14, 2020, coronavirus disease 2019 (COVID-19) has spread across 185 countries/regions, infected more than 1.9 million people, and killed 120 thousands of people. To this day, COVID-19, which is \u201cnot very impressive,\u201d can cause such a great \u201clethality\u201d in the progress of science and technology and the highly developed medical science. The reason is that we do not know enough about the \u201clittle virus\u201d or have enough imagination about its impact. All we can do now is to know as much as we can about it. COVID-19 is a new type of severe pneumonia. We have collected clinical manifestations and CT imaging findings of 61 COVID-19 cases in intensive care.From February 11, 2020 to March 31, 2020, 61 adult patients in intensive care were admitted to the ward E1-3 of Tongji Hospital. Forty-five patients were selected from community isolation clinic and hospital fever clinic on February 11, 2020, and the rest 16 cases were transferred from the designated hospital. Sixty-one patients were confirmed by diagnostic criteria of China COVID-19 treatment . Detection novel coronavirus nucleic acid positive by RT-PCR in specimens , and/or COVID-19 specific anti-IgM and anti-IgG were positive in serum samples. At the same time, all patients at the time of admission have any of the following conditions: (1) shortness of breath and respiratory rate (RR)\u2009\u2265\u200930 times/min; (2) at rest, refers to oxygen saturation \u226493%; and (3) arterial blood oxygen partial pressure (PaO2)/oxygen concentration (FiO2)\u2009\u2264\u2009300\u2009mmHg, which are the COVID-19 cases in intensive care unit. Among them, 6 patients had one of the following conditions during hospitalization: (1) respiratory failure, and mechanical ventilation was required; (2) shock occurred; and (3) combining other organ failures required ICU monitoring treatment, and the diagnosis was severe COVID-19. Of the 61 patients included in the study, male 32 and female 29, aged 24\u201383, mean age (58.52\u2009\u00b1\u20091.67), 18 patients with hypertension, 11 patients with diabetes or stress hyperglycemia, and chronic heart disease 9 cases, COPD 3 cases, gout 3 cases, chronic kidney disease 2 cases, and hematological malignancy 1 case.\u03b1-interferon in combination with daily nebulized inhalation, ribavirin 500\u2009mg, and intravenous infusion twice daily. The duration of antiviral treatment is 10 days. Third, based on the patient's respiratory symptoms and changes in CT imaging, we decide whether to use glucocorticoids. If the patient has shortness of breath and the respiratory rate is greater than 30 breaths per minute, when the CT imaging shows that the exudation is the main change, you can optionally use methylprednisolone 40\u201380\u2009mg intravenous drip and evaluate it again after 5 days. It should either be used or stopped directly. Fourth, based on the treatment of the patient's symptoms, acetaminophen is administered when the body temperature is \u2265102.2\u00b0C, bronchial spasm relief drugs and acetylcysteine tablets 0.6\u2009g orally, 2 times a day, and when the cough and sputum are obvious 0.3\u2009g of acetylcysteine solution is used for inhalation or 3 times a day. Fifth, nutrition support is strengthened to ensure that the daily calorie intake of the patient is greater than 35\u2009Kcal/kg and infusion of 20% human serum albumin solution makes the patient's serum albumin level greater than 30\u2009g/L. Sixth, the possibility of secondary bacterial or fungal infections is assessed.Treatment mainly covers six aspects: First, choose the appropriate oxygen therapy according to the degree of dyspnea of the patient. Most patients use a dual-cavity nasal catheter to inhale oxygen. The oxygen flow is 3\u20135\u2009L/min. The target refers to oxygen saturation \u226593%, and a noninvasive ventilator is immediately used when unable to meet the needs. Second, the antiviral treatment plan is determined and Abidor 200\u2009mg, 3 times a day or lopinavir/ritonavir 200\u2009mg/50\u2009mg/capsule, 2 capsules each time, 2 times a day. Two critically ill patients used 5 million units of Onset time, primary symptoms, epidemic history, nucleic acid testing (NAT) results, CT imaging results, and medicine treatment were taken into account before admission. Blood routine, CRP, PCT, ESR, liver enzyme, myocardial enzyme spectrum and troponin I, NT-proBNP, D-dimer, inflammatory factors, and chest CT imaging were detected irregularly.Of the 61 patients, 3 died after tracheal intubation and treated with a ventilator and 1 patient with acute hematological malignancies died of secondary multidrug resistant bacteria (CRE) bloodstream infection The symptoms of the remaining patients disappeared or were significantly alleviated. The chest CT scan showed obvious absorption of the lesion, and the patient was discharged after retesting negative NAT.Sixty-one patients were local Wuhan personnel, and most of them had a clear history of epidemiological contact (77%), with 61 cases of fever (100%) as the first symptom, 56 cases of cough and expectoration (91.8%), 48 cases of shortness of breath and chest tightness (78.7%), muscle soreness and fatigue in 40 cases (65.6%), diarrhea or vomiting in 8 cases (13.1%), and headache in 4 cases (6.6%). At admission, 15 patients had a course of \u22647\u2009d, 23 patients from 8\u201314\u2009d, and 23 patients >14\u2009d. Before admission, all patients underwent different degrees of medicine treatment, including 3 cases of Abidor, 8 cases of ribavirin, 15 cases of oseltamivir, 10 cases of glucocorticoids, 28 cases of antibiotics, 57 cases of antipyretics and, 61 cases of Chinese herbal medicine preparation.After admission, 40 cases of normal white blood cell count (57.7%) were checked, 9 cases (15.4%) were higher than normal, and 12 cases (26.9%) were lower than normal. The lymphocyte count decreased in 53 cases (38.5%). CRP increased in 29 cases (57.7%); PCT increased in 15 cases (24.6%); the erythrocyte sedimentation rate increased in 38 cases (62.3%); the D-dimer test increased in 39 cases (63.9%); ALT/AST increased in 40 cases (65.6%); CK/CK-MB increased in 8 cases (13.1%); troponin I increased in 6 cases (9.8%); NT-proBNP increased in 35 cases (57.4%); IL-1 increased in 5 cases (8.2%); IL-2 increased in 28 cases (45.9%); IL-6 increased in 23 cases (37.7%); IL-8 increased in 15 cases (24.6%); IL-10 increased in 12 cases (19.7%); and NTF increased in 22 cases (36.1%), which are shown in Of 61 COVID-19 patients, 3 patients were in critical condition after admission, unable to complete chest CT examination, and died after being transferred to ICU. The remaining 58 patients completed chest CT examination. There were 38 cases (65.5%) with a wider range of right lung lesions than left lung lesions and 20 cases (34.5%) with a wider range of left lung lesions than right lung lesions. There were 42 cases (72.5%) with lower lobe lesions than upper lobe lesions, and 6 cases (10.3%) with upper lobe lesions than lower lobe lesions are shown in From the picture, 58 COVID-19 patients showed one or more of the following signs: ground-glass opacity (GGO) was found in 12 cases, with subpleural distribution Figures ; GGO merCOVID-19 is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) \u20136. At thThe total number of peripheral blood leukocytes in patients with COVID-19 is normal or reduced, and the lymphocyte count is reduced. In some patients, ALT/AST, CRP, ESR, D-dimer, NT-proBNP, IL-1, IL-2 receptor, IL- 6. IL-8, IL-10, and NTF increased. In critically ill patients, troponin, IL-2 receptors, IL-6, and NTF will increase significantly, which means the advent of inflammatory storm. This is an important time point for us to start some special treatments, including the use of glucocorticoids, infusion recovery period plasma, and CRRT. White blood cell count, CRP, and PCT of patients with severe new coronary pneumonia can increase simultaneously as one of the basis for judging secondary bacterial infection.We must recognize that chest CT imaging plays an important role in the diagnosis, treatment, and follow-up of COVID-19. Imaging examination revealed that most patients showed bilateral GGO on CT scans , 14. CT In summary, the clinical manifestations of patients with severe COVID-19 are not specific to the chest CT manifestations. The assessment of the disease requires a comprehensive analysis of relevant symptoms, signs, and laboratory data so as to help us judge the severity of the disease and decide timing of treatment and assess the prognosis."} +{"text": "Little is known how COVID-19 is affecting children. Autopsies help gain an understanding of the pathophysiology of new and developing diseases. Numerous post-mortem studies had been conducted in adults with COVID-19, but few in children. Thereby, this systematic review aims to investigate the autopsy findings from pediatric COVID-19 patients.There were a total of 15 patients from eight studies. COVID-19 mainly affects the heart and lungs. Pathology findings from the heart of COVID-19 pediatric patients include diffuse inflammatory infiltrate, myocarditis, cardiomyocyte necrosis, pericarditis, and interstitial edema. Histopathology abnormalities observed in the lungs are diffuse alveolar damage, cytopathic changes, thrombi in arterioles and septal capillaries, lung congestion, focal acute hemorrhage and edema, focal exudative changes, and mild pneumocyte hyperplasia. In addition, pathological findings from other organs, such as the liver, kidney, brain, bone marrow, lymph node, skin, spleen, muscle, colon, parotid gland, and adrenal of COVID-19 pediatric patients are also included in this review.Cardiomyocyte necrosis, interstitial edema, lung congestion, and diffuse alveolar damage are the most significant pathologic findings of the heart and lung in pediatric COVID-19 patients. More studies are needed to elucidate the pathophysiology of SARS-CoV-2 in autopsy findings and to determine the exact cause of death since it could be related to COVID-19 or other comorbidities. At the start of the pandemic, little is known how COVID-19 is affecting children. It seems that children are somewhat protected from COVID-19 due to lower exposure to the outside world, reduced number of angiotension converting enzyme 2 (ACE2) receptors in children, and the fact that children have a strong innate immune response due to trained immunity caused by SARS coronavirus 1 (SARS-CoV-1) in 2002 and Middle East Respiratory Syndrome (MERS) caused by MERS-related coronavirus (MERS-CoV) in 2012, revealed insights into their pathophysiology and helped improve patient management 2020 was followed COVID-19 patients, a multisystem inflammatory syndrome in children (MIS-C), and pediatric inflammatory multisystem syndrome-temporally associated with SARS-COV-2 (PIMS-TS) will be included in this review. Exclusion criteria comprised no autopsy related, molecular study, not SARS-COV-2-related, no pathology data, and animal studies. Abstracts, letters to the editor, and reviews were screened for references to ensure literature saturation before they were excluded.2), partial pressure of oxygen (PaO2), central venous oxygen saturation (ScvO2), lactate, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), total protein, albumin, total bilirubin, aspartate aminotransferase (AST), alanine aminotransferase (ALT), and gamma-glutamyl transferase (GGT). Postmortem examination would also be tabulated, including the heart, lung, nasopharyngeal polymerase chain reaction (PCR) test, cerebrospinal fluid (CSF) culture, and immune deficiency test. Data of post-mortem toxicology such as blood culture and vitreous examination are tabulated in this review. A separate email will be sent to the corresponding research author if the reviewer found some data missing from this systematic review.The literature search started on 25 July 2021 and ended on 27 July 2021. The authors utilized eight databases, including PubMed, Science Direct, MEDLINE, Scielo, Medrxiv, Research Square, and Biorxiv, without restrictions on the language. Table Four independent reviewers conducted the initial search and maintained each study\u2019s quality assessment. The studies were conducted and selected using the Rayyan software appraisal checklist to measure the general consistency of case series and case reports (Institute JB All data within this review were combined using pooled descriptive tests. The data presented in median and range (or interquartile range) and the percentile were converted into mean and standard deviation , increased ferritin, increased interleukin-6, decreased bicarbonate, decreased lactate, increased CRP, increased (ESR), decreased albumin, increased total bilirubin and direct bilirubin, elevated (AST) and alanine aminotransferase (ALT), and increased gamma-glutamyltransferase (GGT) Table .Pathology findings from the heart of COVID-19 pediatric patients include diffuse inflammatory infiltrate (2/8), myocarditis (3/8), cardiomyocyte necrosis (4/8), pericarditis (1/8), and interstitial edema (4/8). In one patient, more than one findings are observed, including the results presented in this paragraph and the following ones. Histopathology abnormalities were observed in the lungs of eight patients. These include diffuse alveolar damage (5/8), cytopathic changes (5/8), thrombi in arterioles and septal capillaries (4/8), lung congestion (6/8), focal acute hemorrhage and edema (5/8), focal exudative changes, and mild pneumocyte hyperplasia (1/8). The liver findings of COVID-19 pediatric patients were hepatic congestion (5/6), centrilobular necrosis (4/6), arterial thrombi with ischaemic necrosis (1/6), cholestasis (1/6), sinusoids thrombi (1/6), steatosis (1/6), syncytial metaplasia of hepatocytes (1/6), hemophagocytosis (1/6), portal infiltrate (1/6), and hepatocyte binucleation (1/6).Histopathological examination of the kidney showed acute tubular necrosis (6/7), congestion (5/7), thrombi in capillaries (2/7), tubular apoptosis (1/7), hyaline and granular casts (1/7), nephrocalcinosis (1/7), and mesangial hyperplasia (1/7). The pathology findings of the brain revealed reactive microglia in all patients (6/6), neuronal ischemia (5/6), congestion, edema (2/6), capillary fibrin thrombi (1/6), and Alzheimer type II glial cells (1/6). The gross neuropathological findings in COVID-19 autopsies were reactive microglia (6/6), neuronal ischemia (5/6), cerebral oedema (5/6), cerebral congestion (1/6), Alzheimer type II glial cells (1/6), and formation of capillary fibrin thrombin (1/6). One patient\u2019s post-mortem bone marrow finding showed hypercellular, emperipolesis and mild nuclear atypia of megakaryocytes Table .In COVID-19 patients, the lymph nodes showed lymphoid depletion and signs of hemophagocytosis (2/6), lymphoid hypoplasia in pulmonary lymph nodes (1/6), and normal lymph nodes (1/6). The skin biopsy revealed normal histology (1/3), superficial perivascular mononuclear infiltrate (3/3), and periadnexal mononuclear infiltrate (1/3). Pathological findings of the spleen were splenitis (5/5), hemorrhage (5/5), lymphoid hypoplasia with reactive cells (5/5), hemophagocytosis (2/5), and sinusoidal fibrin thrombi (1/5). In a muscle biopsy, myolysis (5/5) and necrotic fibres (4/5). Histopathological findings of the colon showed edema, mild inflammation, colitis, arteriolar microthrombi, and appendicitis with peritonitis. Parotiditis (2/5) and adrenal carcinoma with intense necrosis were also found in biopsies of COVID-19 patients.Postmortem COVID-19 testing was done with a positive nasopharyngeal test (7/9) and a positive antibody test (1/1). The onset of the first symptoms among patients was ten days (2-27). Among all patients, five patients had comorbidities. The reported comorbid diseases were Edwards syndrome (1), diabetes (1), hypertension (1), and obesity (2). One patient was found to have an congenital immunodefficiency error of immunity. In the performed blood culture, the content of the blood was sterile (1/3), naloxone (1/3), and caffeine positive (1/3). Vitreous examinations were positive for glucose (1) and acetone (1). We found that the weight of the right and left lungs of COVID-19 patients were 955 g (880\u20131030 g) and 835 g (770\u2013900 grams), respectively. One autopsied patient had a heart weighing 500 g with 80 mL pericardial fluid Table .Table 4POur study includes eight studies and describes the histopathology or autopsy findings from pediatric COVID-19 patients. Some of the COVID-19 pediatric patients experience prolonged illness duration. A similar result is found in other studies that state the pediatric patient\u2019s median illness duration was 6 days, with 4.4% of the children having an illness duration of at least 28 days are the most common histopathological manifestation in severe COVID-19 patients. DAD consists of permanent damage to the alveoli epithelial cells and capillary endothelial cells due to phenotypic expression from different proteins transcription modulated by COVID-19 infection in severe COVID-19 patients satisfied the British Association of Pediatric Nephrology\u2019s criteria for acute kidney injury (AKI) levels were observed in several COVID-19 patients\u2019 post-mortem renal histopathology analyses in China, presumably indicating myolysis (Su et al. There are several limitations in our review. Firstly, our systematic review has a low sample, with most of the studies being case reports which reflect the rarity of pediatric post-mortem findings with COVID-19 infections. Secondly, not all corresponding authors provide the data required in this review (de Almeida Monteiro et al. This systematic review describes the histopathology or autopsy findings from pediatric COVID-19 patients. Cardiomyocyte necrosis and interstitial edema are the most significant pathologic findings of the heart. Histopathological examinations of the lungs show lung congestion and diffuse alveolar damage. The autopsy analysis also found pathology findings from other organs such as the liver, kidney, brain, bone marrow, lymph node, skin, spleen, muscle, colon, parotid gland, and adrenal of COVID-19 pediatric patients. Further studies are required to elucidate the pathophysiology of these findings."} +{"text": "Developments in investigational agents and novel regimens in acute myeloid leukemia (AML) were reported in the 2022 American Society of Hematology (ASH) annual meeting. Encouraging efficacy data were presented from first-in-human studies of two investigational menin inhibitors, SNDX-5613 and KO-539, in relapsed and refractory (R/R) acute myeloid leukemia (AML) with KMT2A rearrangement or mutant NPM1, with overall response rates (ORR) of 53% (32/60) and 40% (8/20), respectively. The addition of the novel drug pivekimab sunirine, a first-in-class antibody\u2013drug conjugate targeting CD123, to azacitidine and venetoclax in R/R AML resulted in an ORR of 45% (41/91), which rose to 53% in those who were venetoclax na\u00efve. Additional novel triplet treatment combinations included the addition of magrolimab, an anti-CD47 antibody, to azacitidine and venetoclax, with an ORR of 81% (35/43) in newly diagnosed AML, including an ORR of 74% (20/27) in TP53 mutated AML. The addition of the FLT3 inhibitor gilteritinib to azacitidine/venetoclax was also featured, with an ORR of 100% (27/27) in newly diagnosed AML and an ORR of 70% (14/20) in R/R AML. To the editorEach year, exciting new developments and innovations in hematology are presented at the American Society of Hematology (ASH) meeting. In this article, we review some of the most impressive developments in investigational agents and novel regimens in acute myeloid leukemia (AML) from ASH 2022.Several presentations featured exciting activity from the novel class of menin inhibitors, which target the interaction of menin with the epigenetic regulators of KMT2A in AML. This inhibits leukemogenesis in AML cases featuring KMT2A rearrangement (KMT2Ar) or mutant NPM1 (mNPM1), two previously untargeted genetic alterations that represent 3\u201311% and 30% of newly diagnosed AML patients, respectively [An alternative menin inhibitor KO-539 (ziftomenib) was featured in Dr. Erba\u2019s presentation of preliminary results from the KOMET-001 first-in-human Phase 1/2 trial of ziftomenib in adults with R/R AML. Preliminary efficacy data showed that in a similarly heavily pretreated population, the 600\u00a0mg dose had meaningful efficacy, with an ORR of 40% (8/20) and CRc in 35% (7/20) in mNPM1 AML, although outcomes were worse with KMT2Ar AML . Differentiation syndrome (DS) was a notable adverse event, with at least grade 3 severity occurring in 27% (8/29) of KMT2Ar patients including 1 death, although no grade 3 DS occurred in mNPM1 patients. However, DS was associated with improved response (75% of mNPM1 patients), and DS severity decreased with improved protocol guidance [Pivekimab sunirine is a first-in-class antibody\u2013drug conjugate (ADC) targeting CD123, which is expressed on most AML blasts, with a novel indolinobenzodiazepine pseudodimer (IGN) payload that alkylates DNA. In this phase 1b/2 study of the triplet regimen of PVEK, azacitidine (AZA), and venetoclax (VEN) presented by Dr. Daver, there was an ORR of 45% (41/91) with CRc of 25% (23/91), with higher responses (ORR 53% and CRc 38%) in the 47 patients who were VEN-na\u00efve. The drug was well tolerated, with infusion reactions occurring in 22% (20/91) of patients, and only 5% discontinued treatment due to PVEK-related adverse events [Dr. Daver also presented data from the phase 1/2 study of the novel triplet regimen of magrolimab, an anti-CD47 antibody that blocks the \u201cdon\u2019t eat me\u201d signal on leukemia cells, with AZA and VEN in older/unfit or high risk AML. The ORR in newly diagnosed AML was similar to prior reported responses with AZA/VEN, with ORR 81% (35/43) including an ORR of 74% (20/27) with TP53 mutations. Median OS (mOS) was not reached in newly diagnosed non-secondary AML patients, with mOS 7.6\u00a0months in untreated secondary AML with TP53 mutation. Responses in R/R AML were more modest, with prior VEN exposed patients faring poorly (ORR 11%), resulting in closure of this study arm. Grade 3 anemia occurred in 23% (18/79), and median hemoglobin drop was 1.2\u00a0g/dL after magrolimab infusion [Another exciting novel triplet regimen was the addition of gilteritinib, an oral FLT3 inhibitor, to AZA/VEN in FLT3-mutated AML. The ORR in this phase I/II study presented by Dr. Short was 100% 27/27) with 92% CR in newly diagnosed patients, with median OS not yet reached and 1-year OS 85%. The ORR was 70% (14/20) in R/R patients, with 20% (4/20) achieving CR, and a median OS of 5.8\u00a0months. Outcomes were better in those who had not received prior VEN or gilteritinib, with mOS 10.5\u00a0months [/27 with Overall, the ASH 2022 annual meeting showcased several notable advances in the field of investigational therapies in AML, as summarized in Tables"} +{"text": "Adenoviridae, genus Mastadenovirus) (HAdV) species B, C and E cause acute respiratory illnesses (ARI). In particular, respiratory HAdV types 3, 4, 7, 11, 14, 21 and 55 were associated with ARI outbreaks in the US and in other countries. The risk of outbreaks can be effectively controlled by implementation of the live HAdV types 4 and 7 vaccines or mitigated by screening and preventive measures.Human adenoviruses received 24,300 specimens from its surveillance network. In total, 322 (1.3%) respiratory specimens were positive for HAdV in molecular assays. HAdV samples that produced positive cytopathic effects (CPE) in subsequent viral cultivation were subjected to next-gen sequencing (NGS) for genome sequence assembly, HAdV genome typing, whole genome phylogeny, and sequence comparative analyses to identify sequence insertions, deletions and amino acid mutations.Out of 166 viral culture samples available for NGS, whole genome sequences were obtained for 161 isolates. A variety types of HAdV were identified, including HAdV-1 (N = 15), HAdV-2 (N = 26), HAdV-3 (N = 60), HAdV-4 (N = 13), HAdV-5 (N = 6), HAdV-6 (N = 3), HAdV-7 (N = 12), HAdV-14 (N = 10), HAdV-55 (N = 1), and HAdV-56 (N = 1). HAdV types 4, 7 and 14, which were reported causing ARI outbreaks in the US military and other congregate settings, were found in clustered cases in several US states. Comparative sequence analyses of these isolates revealed the emergence of novel genetic mutations despite the stability of adenovirus genomes.Routine clinical respiratory pathogen diagnostics or molecular surveillance of respiratory diseases detect adenovirus without determination of HAdV type. Human adenoviruses are genetically diverse and can infect a number of tissues with severities varied from mild to fatal. Enhanced genomic surveillance of HAdV in the US and worldwide will shed light on prevalence, genetic divergence, and viral evolution of human adenoviruses and inform timely risk assessment and countermeasures.All Authors: No reported disclosures."} +{"text": "Scientific Reports 10.1038/s41598-022-18145-4, published online 02 September 2022Correction to: r\" in Equations 22, 29 and 30 was wrongly presented as \"r\".The original version of this Article contained errors in Equations 22, 29, and 30 where extra brackets were incorrectly added to Equations 22 and 29, and the brackets in Equation 30 were captured in the wrong font size. Additionally, value \"Equation 22now reads:Equation 29now reads:Equation 30now reads:The original Article has been corrected."} +{"text": "In 2012, pneumococcal conjugate vaccine (PCV13) and pneumococcal polysaccharide vaccine (PPSV23) were recommended for immunocompromised adults \u226519 years, but pneumococcal vaccination (PV) in these patients (pts) remains suboptimal. With a new PV (PCV20) allowing for simplified PV, we study rates of PV in pts on infliximab (INX) 1 year post-initiation of a pt and provider education-based quality improvement project aiming to increase PV in pts on Tumor Necrosis Factor-alpha inhibitors (TNF-\u03b1I).Starting in 11/2020, pamphlets detailing PV indications were distributed to the Walter Reed National Military Medical Center infusion center and pharmacies to be given to pts prescribed/administered TNF-\u03b1I. Provider educational materials and pt pamphlets were given to services prescribing TNF-\u03b1I. Provider education was also offered to these services. Up to date (UTD) on PV was defined as receipt of PCV13 and PPSV23 . Ongoing INX (o-INX) was defined as INX initiation before 10/1/2020. Newly initiated INX (new-INX) was 10/1/2020-10/1/2021. One-year post implementation, we reviewed the PCV13 and PPSV23 immunization records of pts \u226519 years of age on INX from 1/1/21-12/31/21. This project was approved by the IRB under a non-research determination.111 pts prescribed INX between 1/1/21-12/31/21 met inclusion criteria (87 o-INX and 24 new-INX). Prior to the intervention, of 87 o-INX pts, 45 (52%), 45 (52%), and 18 (21%) pts had received PCV13, \u22651 PPSV23 dose, and were UTD on PV respectfully. Between 1/1/21-12/31/21, 14 o-INX pts had PV , with 7 newly UTD (10% of the 69 previously not UTD), totaling 25 (29%) o-INX pts UTD on PV (figure 1). Of 24 new-INX pts, only 12 (48%), 9 (36%), and 6 (24%) had had PCV13, PPSV23, and were UTD on PV as of 12/31/21. No services prescribing TNF-\u03b1I requested the offered PV educational talks.Despite frequent healthcare in a system where vaccination has no out of pocket expense, guideline-concordant PV was low in this cohort. With new, simplified PV, next steps include updated pt and targeted provider education. However, with prior small gains using multidisciplinary education, additional efforts to remove PV barriers may be needed.Benjamin L. Custer, MD, Beam Therapeutics: Stocks/Bonds|CRISPR Therapeutics: Stocks/Bonds|glaxo-smith-kline: Stocks/Bonds|Hologic: Stocks/Bonds|Moderna: Stocks/Bonds|Pfizer: Stocks/Bonds|Regeneron: Stocks/Bonds|sanofi: Stocks/Bonds|Vertex Pharmaceuticals: Stocks/Bonds."} +{"text": "Plagiochila porelloides harvested in Corsica were investigated by chromatographic and spectroscopic methods. In addition to already reported constituents, three new compounds were isolated by preparative chromatography and their structures were elucidated by mass spectrometry (MS) and NMR experiments. Hence, an atypic aliphatic compound, named 1,2-dihydro-4,5-dehydronerolidol and two isomers, (E) and (Z), possessing an unusual humbertiane skeleton are newly reported and fully characterized in this work. The in vitro antiprotozoal activity of essential oil and extract of P. porelloides against Trypanosoma brucei brucei and Leishmania mexicana mexicana and cytotoxicity were determined. Essential oil and Et2O extract showed a moderate activity against T. brucei with IC50 values: 2.03 and 5.18 \u03bcg/mL, respectively. It is noteworthy that only the essential oil showed a high selectivity (SI = 11.7). Diethyl oxide extract exhibited moderate anticancer (cancerous macrophage-like murine cells) activity and also cytotoxicity with IC50 values: 1.25 and 2.96 \u03bcg/mL, respectively.Volatiles metabolites from the liverwort Bryophytes are largely located in various ecosystems characterized by humid climates, such as lakes, rivers, swings, etc., where the water, an essential element for their development and sexual reproduction, is abundantly present. Considered as the oldest green plants, they are the first vegetables that adapted to terrestrial life 500 million years ago . FurtherIn particular, Corsica has more than 500 species of bryophytes spread over all the vegetation levels of the island . Most ofPlagiochila species is the largest genus in the Marchantiophyta, with at least 1600 varieties -8-ol for 42. Contrary, the double bond brought by the 42b side chain was found as Z stereochemistry; these was assigned according to correlations between H3 \u2192 H13, and H11 \u2192 H15, respectively a of F27 . An Atta4.16 ppm . Two-dim4.16 ppm confirmeble bond . The isoh isomer . Concernectively .42a and 42b possess a humbertiane skeleton, a relatively rare sesquiterpene pattern. To our knowledge, only four isomeric isohumbertiols, structurally related to the alcohols 42a and 42b, were identified from the wood of Humbertia madagascariensis Lam (4), 107 (100), 41 (80), 135 (73), 69 (62), 91 (53), 93 (53), 105 (49), 43 (46), 79 (40), 204 (30), 119 (30), 161 (29), 77 (28), 55 (26). HRMS: detected ion m/z 245.1879 [MNa+] .1,2-dihydro-4,5-dehydronerolidol data see ; MS ; RI apolar 1528, RI polar 1917; for 1H and 13C NMR data (see m/z (rel. Int): 222 [M+] (1), 107 (100), 59 (31), 161 (31), 91 (31), 41 (28), 175 (26), 105 (25), 135 (23), 79 (23), 119 (22), 93 (21), 108 (19), 43 (16), 77 (16). HRMS: detected ion m/z 245.1878 [MNa+] .data see ; MS bloodstream forms were cultured in vitro in HMI9 medium containing 10% heat-inactivated fetal bovine serum -8-ol, could be fully characterized using combined analytical approach. Moreover, an atypic aliphatic compound, named 1,2-dihydro-4,5-dehydronerolidol is also newly reported and fully characterized in this work. The in-vitro antiprotozoal activity of essential oil and extract of P. porelloides against Trypanosoma brucei brucei and Leishmania mexicana mexicana and cytotoxicity were assessed. Essential oil and diethyl oxide extract showed a moderate activity against T. brucei . It is noteworthy that only the essential oil sample has shown a high selectivity (SI = 11.7), whereas the diethyl oxide extract exhibited moderate anticancer (cancerous macrophage-like murine cells) activity and cytotoxicity with IC50 values: 1.25 and 2.96 \u03bcg/mL, respectively.Three new phytochemicals were isolated and identified from Corsican"} +{"text": "Since the onset of the pandemic, the unCoVer network has been identifying real-world data from EMR of hospitalised patients with COVID-19 across countries. These heterogeneous data are integrated into a multi-user data repository operated through Opal/DataSHIELD, an interoperable open-source server application, providing privacy-preserving access to individual-level information for federated data analyses.unCoVer\u2019s federated data platform provided access to EMR collected between 02/2020 - 04/2022 from 6 hospitals in Bosnia and Herzegovina (1), Romania (2), Spain (2), and Turkey (1) for a total of 14,236 patients. Demographics, and co-morbidities at admission, length of hospital stay and intensive care (ICU) needs, are presented according to the patients\u2019 status at discharge.A total of 11,248 (79.0%) of all patients reviewed recovered from COVID-19 after an average 11.5 (SD 10.8) days hospitalised, with only 4.09% of patients needing ICU. A smaller proportion of patients were transferred (5.93%), and 2143 (15.1%) were considered in-hospital deaths after an average 11.6 (SD 10.5) days in the hospital where most (81.2%) needed ICU. Recovered patients had a mean age of 57.7 (SD 16.3) years old, and gender neutral (51.2% men), in contrast to deceased patients that were 74.2 (SD 12.4) years old (59.7% men). Current smoking was infrequent for both recovered or deceased patients . Cardiometabolic conditions were less commonly reported among later recovered patients in comparison with deceased patients: obesity (10.7% vs 12.1%), diabetes (15.9% vs 27.4%), hypertension (23.2% vs 42.7%), and CVD (9.33% vs 44.9%). Chronic pulmonary disease was also more frequent among deceased patients (10.3% vs 18.1%).Characteristics of hospitalised COVID-19 patients differ according to outcomes at discharge with more in-hospital death reported among older, chronic patients across 6 hospitals in 4 countries.\u2022\u2002Federated analyses provide unique opportunities for robust results by privacy-preserving accessing individual-level data from heterogeneous data sources.\u2022\u2002The unCoVer network aims to demonstrate the usability of the infrastructure to address research questions related to the COVID-19 while extending the concept to other clinical areas."} +{"text": "The severely Immunocompromised are at an increased risk of fatal infection caused by invasive molds. Amphotericin B and triazole agents with anti-mold activity are commonly used in treating invasive mold infections. There is some data from in-vitro experiments to suggest an enhanced killing of some molds when terbinafine is used in combination with certain azoles or amphotericin B. At our center, terbinafine is occasionally used in combination with other systemic anti-fungal agents in treating severely immunocompromised patients with invasive mold infections.The study was a retrospective review of electronic medical records. Sixty-four patients treated for culture confirmed infection with mold isolates at the Moffitt Cancer Center from 1/1/2015 to 6/1/2021 were included in this study. There were 2 treatment groups: Group A comprised of those treated with a terbinafine containing regimen and Group B comprised of patients that were not treated with a terbinafine containing regimen.Treatment group A: Comprised of 14 patients. Twenty-nine percent (4/14) had skin/soft tissue infections, 21% (3/14) had rhinosinusitis, 21% (3/14) had pulmonary infections and 4 patients (29%) had disseminated infection. Thirty-six percent (5/14) were discharged with treatment response, 57% (8/14) did not respond to treatment or died due to the invasive mold infection and 7% (1/14) died as a result of malignancy.Treatment group B: Had 50 patients. thirty-eight percent (19/50) had pulmonary infections, 28% (14/50) with skin/soft tissue infections, 16% (8/50) had rhinosinusitis, 2% (1/50) were diagnosed with central nervous system infection, 2% (1/50) had gastrointestinal infection, 14% (7/50) had an unclear source of infection. Forty-eight percent (24/50) were discharged with treatment response, 42% (21/50) had treatment failure or died due to the invasive mold infection and 10% (5/50) died as a result of malignancy.There was no statistically significant improvement in outcome observed in this study when terbinafine was used in addition to other systemic anti-fungal medications as treatment of invasive mold infections. There is a need for larger studies to determine if terbinafine has a role in the treatment of invasive mold infections.All Authors: No reported disclosures."} +{"text": "Background: Medical University of South Carolina Health began vaccinating care team members December 15, 2020, with the Pfizer-BioNTech SARS-CoV-2 mRNA vaccine. We report surveillance data for cases diagnosed following vaccination. Methods: Care team members (CTMs) diagnosed with COVID-19 following SARS-CoV-2 vaccination were self-identified during online electronic contact-tracing surveys. Demographic data, symptoms, and dates of symptoms were recorded. CTMs testing positive at MUSC were linked to viral burden data from nasopharyngeal swabs tested on Abbott PCR platforms. Results: As of January 31, 2021, 111 CTMs tested positive for SARS-CoV-2 following vaccination: 99 and 12 after 1 and 2 doses, respectively, at medians of 10 days and 5 days , respectively, from vaccination to testing. Of 2 cases that tested positive >14 days from dose 2, CTMs had symptom onset at 4 and 12 days from dose 2. Among CTMs reporting symptoms, 104 did so after a median of 7 days from vaccination to symptom onset, with 8 reporting symptoms before vaccination, 9 on the day of vaccination, and 3 CTMs at 1 day after vaccination, 6 CTMs at 2 days after vaccination, and 11 CTMs at 3 days after vaccination. Overall, 86 (78%) of 111 were female and 95 (86%) of 111 were white. The median age was 44 years . Clinical job roles were most frequently nurses , physicians or physician extenders , and CTMs with no patient contact . Assessment by the contact-tracing team assigned sources as household clusters , local transmission , occupational acquisition from coworkers , travel related , and unknown . Only 32 (32%) CTMs were compliant with physical distancing. Among 104 CTMs reporting symptoms, cough (75%), headache (71%), rhinorrhea (63%), myalgia (60%), sore throat (48%), anosmia (44%), and subjective fever (40%) were the most commonly reported symptoms. Among 54 symptomatic CTMs with available viral-load data, the median and mean cycle numbers (Cn) were 19.98 and 21.91, respectively, for samples tested a median 3 days from symptom onset. Asymptomatic and symptomatic CTMs had a median Cn of 30.1 vs 20.9, respectively (p <0.001) and overall 50% of vaccinated CTMs had Cn >20, with no significant effect seen by vaccine dose (Figure Conclusions: Most COVID-19 cases following vaccination occurred in CTMs with infection incubating prior to vaccination. No significant attenuation of viral load is apparent among vaccinated CTMs with COVID-19, but asymptomatic CTMs diagnosed with COVID-19 following vaccination appear to have resolved infections. Our data reinforce the need to adhere to public health measures by people who have been vaccinated.Funding: NoDisclosures: None"} +{"text": "Reports showing high rates of antibiotic use (AU) in patients with coronavirus disease 2019 (COVID-19) despite low rates of secondary bacterial infection have emerged from various countries across the globe. We evaluated the impact of the COVID-19 pandemic on AU in healthcare facilities (HCFs) in Argentina, Brazil, and Chile.We conducted an ecologic evaluation of AU in inpatient adult acute care wards (excluding maternity wards) in 6 HCFs in Argentina, Brazil, and Chile; 2 HCFs per country. AU data for intravenously administered antibiotics commonly used to treat respiratory infections were collected from pharmacy dispensing records and aggregated to monthly defined daily dose (DDD)/1000 patient days. Graphs were created to depict AU and COVID-19 discharges over time throughout the 36-month study period (03/2018\u201302/2021). Relative changes in AU for all antibiotics combined and specific classes were calculated by comparing median AU for the 24-month pre-pandemic period (3/2018\u20132/2020) with the 12-month pandemic period (3/2020\u20132/2021). Only statistically significant differences (P< 0.05) determined by the Wilcoxon signed-rank test are reported.Pseudomonas aeruginosa increased in 3/6 HCFs (31.3\u201382.5%) and decreased in 1/6 HCFs (-18.9%). Vancomycin and linezolid use increased in 3/6 HCFs (36.9\u201377.1%).Compared to the pre-pandemic period, the use of all included antibiotics combined increased in 4/6 HCFs (6.7\u201335.1%). In the 4 HCFs that experienced increases in AU, Figure\u00a01 shows that use was high during months when COVID-19 patient surges occurred. In 3/4 of these HCFs, AU remained high despite significant decreases in COVID-19 discharges. Ceftriaxone use increased in 2/6 HCFs (27.1\u201351.6%). Use of \u03b2-lactam antibiotics with activity against Increases in AU among hospitalized adults were observed in 4 of 6 South American HCFs included in this study. The high rates of broad-spectrum antibiotic use in the HCFs may impact further emergence of antibiotic resistance. Understanding how this increase in antibiotic use compares to rates of bacterial infections during this time period is critical.Jose M. Munita, MD, BioMerieux: Grant/Research Support|MSD: Grant/Research Support|Pfizer: Grant/Research Support Matias Salomao, MD, Cepheid: Lecture."} +{"text": "Eculizumab, an inhibitor of terminal complement activation, has been utilized in pre-transplant desensitization, treatment of antibody-mediated rejection and thrombotic microangiopathy in solid organ transplant recipients (SOTR). Eculizumab is associated with meningococcal disease, leading to guidelines for vaccination against serogroups ACWY (menACWY) and B (menB) at least 2 weeks prior to eculizumab therapy. In persons requiring emergent use of eculizumab, prophylaxis for at least 2 weeks is recommended. SOTRs respond suboptimally to vaccination, raising consideration for pre-transplant vaccination and prolonged prophylaxis in those undergoing eculizumab therapy. We sought to describe meningococcal vaccination and prophylaxis practices among SOTRs receiving eculizumab.We performed a retrospective chart review of meningococcal vaccination, including number and timing pre- or post-transplant, along with prophylaxis prescribing and duration in SOTRs receiving eculizumab across 3 distinct Mayo Clinic Enterprise sites .200 SOTRs receiving at least one dose of eculizumab between 1/1/2008 and 9/16/2021 were reviewed. Eculizumab indications included antibody mediated rejection (38%), desensitization (26%), and thrombotic microangiopathy (19%). 83% (166/200) of SOTRs received eculizumab for an unanticipated post-transplant complication. Vaccination rates were 82% (164/200) and 35.5% (71/200) for menACWY dose 1 and 2, respectively, and 54% (108/200) and 28.5% (57/200) for menB dose 1 and 2, respectively. The majority received their first vaccination post-transplant: menACWY 66.5% (133/200) and menB 2.5% (185/200). Among those without vaccination pre-eculizumab, 22.3% (41/184) were not prescribed prophylaxis. The median duration of prophylaxis was 62 (range 4-2651) days.Most SOTRs underwent meningococcal vaccinations near the time of eculizumab administration post-transplant for an unanticipated complication. One-fifth of those meeting criteria were not provided meningococcal prophylaxis. These findings may support pre-transplant administration of meningococcal vaccinations and heightened awareness for meningococcal prophylaxis in SOTRs receiving eculizumab.All Authors: No reported disclosures."} +{"text": "Anti-retroviral therapy (ART) has been associated with significant weight gain and metabolic derangements in persons with HIV (PWH), and many PWH on ART experience comorbid obesity. GLP-1 receptor agonists (GLP-1RA) are used to treat type-2 diabetes and obesity in people without HIV infection, but data on the use of these agents in PWH on ART are limited.We extracted data from electronic medical records of PWH on ART receiving care at a clinic in New Orleans, LA who had been started on GLP-1RA therapy. We tracked weight and changes in hemoglobin A1c (Hba1c) over time from initiation of GLP-1RA to April 2022. A control group of PWH on metformin only will be compared to those on GLP-1RA at a later stage of analysis.Of 35 PWH on GLP-1RA, the mean age was 55.2 (standard deviation [SD] 10.0); 29 (83%) were Black/African American, 14 (40%) were assigned female at birth, 21 (60%) were assigned male at birth, and 2 were non-binary. Average BMI was 35.7 (SD 9.8) and average HbA1c was 9.5 (SD 2.6) at baseline. Integrase inhibitors were prescribed for 31 (89%) and metformin was prescribed for 20 (57%). Other baseline characteristics are shown in Figure\u00a01. Mean duration of GLP-1RA therapy was 20.6 months (SD 14.0), and 20 (57%) had greater than 12 months of follow-up. Most on GLP-1RA lost weight, 3 (9%) had a stable weight, and 9 (26%) gained weight. Five percent or more of body weight was lost by 11 (31%) of the total cohort (those with any amount of time on GLP-1RA) and by 9/20 (45%) of those on GLP-1RA for more than 12 months.Our data show moderate weight loss among PWH on GLP-1RA. This study is limited by small sample size and limited follow-up time. Further research is needed to determine whether GLP-1RAs are an effective treatment option for obesity in PWH.Meredith E. Clement, MD, Gilead Sciences: Grant/Research Support|Roche: Advisor/Consultant|Viiv Healthcare: Advisor/Consultant|Viiv Healthcare: Grant/Research Support."} +{"text": "Within a large multi-institutional genomic database, do tumors from patients with Merkel cell carcinoma stratified by tumor mutation burden (TMB) harbor actionable alterations?In this cross-sectional analysis of 324 tumor samples from 313 patients, 82 patients (26.2%) had a high TMB (\u226510 mutations per megabase). Actionable alterations were more common among high TMB cases, with 37 of 82 patients (45.1%) harboring level 3 alterations compared with only 18 of 231 patients (7.8%) with low TMB.These findings support the continued clinical investigation of targeted therapies as single agent or in combination with immunotherapy or cytotoxic chemotherapy in Merkel cell carcinoma. This cross-sectional study analyzes genomic data to examine the presence of actionable alterations in Merkel cell carcinoma in association with tumor mutation burden. Merkel cell carcinoma (MCC) is a rare and highly aggressive cutaneous neuroendocrine carcinoma with increasing incidence. Cytotoxic chemotherapy and checkpoint inhibitors provide treatment options in the metastatic setting; however, there are no approved or standard of care targeted therapy treatment options.To identify actionable alterations annotated by the OncoKB database therapeutic evidence level in association with tumor mutation burden (TMB).This is a retrospective, cross-sectional study using data from the American Association for Cancer Research Genomics Evidence Neoplasia Information Exchange, a multicenter international cancer consortium database. Patients with MCC were enrolled in participating institutions between 2017 and 2022. Data from version 11.0 of the database were released in January 2022 and analyzed from April to June 2022.The main outcome was the percentage of patients with high TMB and OncoKB level 3B and 4 alterations.PIK3CA (12 patients [3.8%]), BRCA1/2 (13 patients [4.2%]), ATM (7 patients [2.2%]), HRAS (5 patients [1.6%]), and TSC1/2 (6 patients [1.9%]). The most common level 4 variants include PTEN (13 patients [4.1%]), ARID1A (9 patients [2.9%]), NF1 (7 patients [2.2%]), and CDKN2A (7 patients [2.2%]). Copy number alterations and fusions were infrequent. In 61.0% of cases (191 cases), a PanCancer pathway was altered, and 39.9% (125 cases) had alterations in multiple pathways. Commonly altered pathways were RTK-RAS (119 patients [38.0%]), TP53 (103 patients [32.9%]), cell cycle (104 patients [33.2%]), PI3K (99 patients [31.6%]), and NOTCH (93 patients [29.7%]). In addition, oncogenic DNA mismatch repair gene alterations were present in 8.0% of cases (25 patients).A total of 324 tumor samples from 313 patients with MCC were cataloged in the database. The median (range) number of alterations was 4.0 (0.0-178.0), with a mean (SD) of 13.6 (21.2) alterations. Oncogenic alterations represented 20.2% of all alterations . Tissue originated from primary tumor in 55.0% of patients (172 patients) vs metastasis in 39.6% (124 patients). TMB-high (\u226510 mutations per megabase) was present in 26.2% of cases (82 patients). Next-generation sequencing identified 55 patients (17.6%) with a level 3B variation for a Food and Drug Administration\u2013approved drug for use in a biomarker-approved indication or approved drug in another indication. An additional 8.6% of patients (27 patients) had a level 4 variation. Actionable alterations were more common among high TMB cases, with 37 of 82 patients (45.1%) harboring level 3 alterations compared with only 18 of 231 patients (7.8%) with low TMB. The most common level 3B gene variants included In this cross-sectional retrospective study of alterations and TMB in MCC, a minority of patients had potentially actionable alterations. These findings support the investigation of targeted therapies as single agent or in combination with immunotherapy or cytotoxic chemotherapy in selected MCC populations. We surveyed the presence of targetable alterations in MCC from the American Association for Cancer Research (AACR) Genomics Evidence Neoplasia Information Exchange (GENIE).10 Patient data were accessed from GENIE version 11.0, which was publicly released in January 2022 via cBioPortal, and were analyzed in May 2022. The present study analyzed publicly available deidentified data and was determined to be exempt from institutional review board review and the need for informed consent, in accordance with 45 CFR \u00a746. This report follows the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guideline for retrospective cross-sectional studies.The AACR Project GENIE database is a large, publicly accessible, international cancer registry that contains clinical data from 19 different participating cancer centers worldwide.11 Demographic data collected for each patient included patient age at sequencing, sex, and race as recorded by the submitting institution. Race was analyzed in this study given the large variation in cancer incidence between races and the potential for differential variant factors by race. Recorded tumor characteristics included sample site (primary tumor vs metastases), total number of variants, number of oncogenic variants, number and type of structural variants, and number and type of copy number alterations (CNAs).Variables of interest extracted from the database included demographic data, genomic alterations with their OncoKB annotations for therapeutic evidence level, presence of The Cancer Genome Atlas PanCancer pathway alterations, and estimation of TMB.12 Variants were considered potentially actionable if they had an FDA-approved drug for use in a biomarker-approved indication or approved drug in another indication (levels 1-3). Level 4 evidence indicates potential targetability based on biological evidence.OncKB level of evidence . Categorical variables are presented as percentages and compared with \u03c7Of 136\u2009096 samples present in AACR GENIE version 11.0, 1025 were nonmelanoma skin cancer samples that contained 324 MCC samples from 313 patients (107 women [34.2%]). Reported race was 91.7% White (287 patients), 2.2% Black (7 patients), and 0.6% Asian (2 patients). Full demographic data are presented in the PIK3CA (12 cases [3.8%]), BRCA1/2 (13 cases [4.2%]), ATM (7 cases [2.2%]), HRAS (5 cases [1.6%]), and TSC1/2 (6 cases [1.9%]). The most common level 4 variants include PTEN (13 cases [4.1%]), ARID1A (9 cases [2.9%]), NF1 (7 cases [2.2%]), and CDKN2A (7 cases [2.2%]). The median (range) number of alterations was 4.0 (0.0-178.0), and the mean (SD) was 13.6 (21.1) alterations. Oncogenic alterations represented 20.2% (862 of 4259 variants) of all variants. Tissue originated from primary tumor in 172 cases (55.0%) vs metastasis in 124 cases (39.6%). There are no FDA-approved targeted therapies for MCC; therefore, there are no level 1 or 2 alterations. Genomic sequencing identified 55 patients (17.6%) with an FDA-approved drug for use in a biomarker-approved indication or approved drug in another indication (level 3 variation). An additional 8.6% (27 patients) had a level 4 variation. The most common level 3B gene variants include ATM-CDK12 and intragenic TSC2 and a level 4 intragenic PTEN. CNAs were identified in a small subset of patients. Level 3B CNAs included ATM (1 patient), CHEK1 (1 patient), BARD1 (1 patient), BRCA2 (1 patient), RAD51B (1 patient), and RAD51D (1 patient). Level 4 CNAs identified included CDKN2A (4 patients) and PTEN (1 patient).Only 3 fusions were identified: level 3B PIK3CA (10 cases [12.2%]), SMARCA4 (6 cases [7.3%]), NF1 (4 cases [4.9%]), BRCA1 (3 cases [3.7%]), and TSC1/2 (3 cases [3.7%]); the most common level 4 alterations were PTEN (7 cases [8.5%]), CDKN2A (6 cases [7.3%]), ARID1A (6 cases [5.3%]), and ATM (4 cases [4.9%]). Among TMB-L cases, the most common level 3B gene alterations were BRCA1/2 (3 cases [1.3%]), HRAS (4 cases [1.7%]), ARID1A (2 cases [0.9%]), and TSC1/2 (3 cases [1.3%]); the most common level 4 alterations were PTEN (6 cases [2.6%]) and NF1 (2 cases [0.9%]). Actionable alterations were more common among TMB-H cases, with 37 of 82 patients (45.1%) harboring level 3 alterations compared with only 18 of 231 patients (7.8%) with TMB-L.Cases were separated into TMB cohorts of TMB high and TMB-low . Within each cohort, 231 cases (73.8%) were TMB-L, whereas 82 cases (26.2%) were TMB-H. Among TMB-H cases, the most common level 3B alterations were RTK-RAS (119 cases [38.0%]), TP53 (103 cases [32.9%]), cell cycle (104 cases [33.2%]), PI3K (99 cases [31.6%]), and NOTCH (93 cases [29.7%]) (In 61.0% of cases (191 cases), a PanCancer pathway was altered, and 125 cases (39.9%) had alterations in multiple pathways. Commonly altered pathways were [29.7%]) . In addiIn this cross-sectional analysis of 324 samples from 313 patients, to our knowledge, we present the largest genomic analysis of MCC patient samples to date. We found 20.2% of alterations identified to be oncogenic. Variants that were potentially targetable with an FDA-approved drug were present in 17.6% of patients (55 patients), and 61.0% of cases had a PanCancer pathway altered.PIK3CA/PTEN, CDKN2A, BRCA1/2, NF1, ATM, and TSC1/2), suggesting that many variants may be passenger rather than driver alterations in the setting of highly altered tumors. However, there remains a minority of patients with TMB-L and TMB-H tumors who have actionable and potentially actionable alterations.Many of the most frequent actionable alterations within TMB-H tumors were within tumor suppressor pathways , TP53, and PIK3CA. In a small set of tumors, Harms et al14 showed that MCPyV-negative tumors were TMB-H and had an ultraviolet signature with additional oncogenic alterations in HRAS, PRUNE2, and NOTCH family genes, whereas MCPyV-positive tumors were TMB-L and had no ultraviolet signature. Similarly, Wong and colleagues15 analyzed 34 patients with a 619-gene panel and found that all virus-negative tumors harbored RB1 or TP53 variants with an increased frequency of NOTCH1 and FAT1 variants. MAPK and PI3K pathway alterations were also common. In a single-institution study of 17 patients by Cohen et al,20 there was a high frequency of variants in the TP53 gene (12 of 17 cases [71%]); cell cycle pathway ; PI3K, AKT, and mTOR pathway (9 of 17 cases [53%]); and DNA repair genes (5 of 17 cases [29%]). Although the small sample size limited generalizability, they found frequencies of variants similar to those we observed.Previously, single institution and small case series have described smaller sets of genomic analysis from patients with MCC.21 Using known genomic sequences of MCPyV, the authors were able to separate MCPyV-positive vs MCPyV-negative tumors and TMB-H vs TMB-L status.21 The most common variants in that cohort were TP53, RB1, NOTCH1, KMT2D, and FAT1, with an incidence of more than 25% among TMB-H MCCs.21 The most frequent mutations in TMB-L MCCs were the same, but no variation had an incidence greater than 10%.21 Notably, that study did not report the actionability of variants.21The only study of comparable size to ours is from a single next-generation sequencing platform analysis of 317 tumors.22 These results reveal that targeted therapies may be effective in select patients with variants in commonly altered pathways, including the TP53, cell cycle, PI3KA, and RTK-RAS pathways. Ongoing and reported clinical trials using targeted therapies are shown in eTable 2 in Although targeted therapy and immunotherapy combinations have been successful in other cancer types, MCC has been infrequently included within targeted therapy basket trials.This analysis is limited by database constraints, and bias may exist in terms of which samples are submitted for including by participating institutions. Variables not captured by the database included cancer stage, systemic and surgical treatments and outcomes, and the presence of MCPyV. Nonuniform next-generation sequencing testing panels lead to variation in tested genes and reporting of zygosity, copy numbers, and allele fraction.This cross-sectional study found that most patients with MCC had an oncogenic alteration in a cancer pathway and identified a subset of patients with targetable variants in MCC. However, the majority of targetable variants occurred in TMB-H tumors. These findings may support the investigation of small molecule inhibitors as single agent or in combination with immunotherapy or cytotoxic chemotherapy in MCC."} +{"text": "Tea plant necrotic ring blotch virus (TPNRBV-J). The predicted TPNRBV-J genes have the same organization as those of a Chinese isolate, and the 5\u2032 termini of the segments have conserved nucleotide sequences.We report the complete genome sequence of a Japanese isolate of Tea plant necrotic ring blotch virus (TPNRBV) is a member of the genus Blunervirus, in the family Kitaviridae (Camellia sinensis [L.] O. Kuntze) with discoloration and necrotic ring blotches on the leaves . A partial fragment each from TPNRBV RNA1 to -4 was amplified by reverse transcription-PCR (RT-PCR) using TPNRBV-specific primer pairs showed thttps://www.ncbi.nlm.nih.gov/orffinder/) was used to predict each ORF using default parameters. Putative protein functions were manually annotated using the NCBI conserved domain database (v. 3.19) using default parameters (AATTACGA-3\u2032) was found at the 5\u2032 termini of RNA1 to -3, while RNA4 had a slightly different one (5\u2032-TTAACGAA-3\u2032). The sequence identity with the reported isolate was calculated using the MUSCLE algorithm tails at the 3\u2032 ends were 5,912 (42.2% GC content), 4,118 (41.4% GC content), 2,684 (42.0% GC content), and 2,232 (44.7% GC content) nucleotides (nt) long, respectively. The National Center for Biotechnology Information (NCBI) open reading frame (ORF) finder (lgorithm . The amiLC566237 (RNA1), LC566238 (RNA2), LC566239 (RNA3), and LC566240 (RNA4).The genome sequence of TPNRBV-J has been deposited in the DDBJ under accession numbers"} +{"text": "Vaccination is essential to control SARS-CoV-2 transmission and complications. The study aimed to estimate the number of SARS-CoV-2 infections, COVID-19 hospitalizations and deaths averted by booster vaccination in Portuguese population aged 80 or more years old.We developed an ecological study for the period of the Omicron variant of concern predominance . Data on vaccine coverage and effectiveness, and number of events of different severity reported to the national COVID-19 surveillance system were used to estimate the number of averted events, prevented fraction and number needed to vaccinate. Uncertainty intervals (UI) were obtained using Monte Carlo simulations.By week 2 2022, vaccination coverage in the target population reached 91.2%. Booster vaccine effectiveness was 4.1% (CI95%: -0.1 to 9.0), 87.5% (CI95%: 84.9 to 89.7) and 83.2 (CI95%: 80.3 to 85.7) against infection, hospitalization and death, respectively. During the study period, 70862 SARS-CoV-2 infections, 2697 COVID-19 hospitalizations and 2106 deaths were reported. Booster vaccination averted 2731 (UI95%: -298 to 5838) infections, 10629 (UI95%: 9173 to 12127) hospitalizations and 6608 (UI95%: 5725 to 7546) COVID-19 related deaths among individuals aged 80 years or more resident in Portugal. Prevented fractions were 3.7% (UI95%: 0 to 7.6%), 79.7% (UI95%: 77.3 to 81.7%) and 75.8% (UI95%: 73.2 to 78.1%), respectively. It would require to vaccinate 59 individuals (UI95%: 52 to 69) to prevent one hospitalization and 94 individuals (UI95%: 82 to 109) to prevent one death in the target population.The booster vaccination strategy had considerable impact on preventing severe outcomes in the Portuguese population aged 80 and more years old.\u2022\u2002High vaccine coverage combined with high vaccine effectiveness resulted in considerable reduction of severe COVID-19 outcomes.\u2022\u2002Information on number of outcomes of different severity levels averted by COVID-19 booster vaccination allows to strength public health communication."} +{"text": "Background: Whether working on COVID-19 designated units put healthcare workers (HCWs) at higher risk of acquiring COVID-19 is not fully understood. We report trends of COVID-19 incidence among nonphysician HCWs and the association between the risk of acquiring COVID-19 and work location in the hospital. Methods: The University of Iowa Hospitals & Clinics (UIHC) is an 811-bed, academic medical center serving as a referral center for Iowa. We retrospectively collected COVID-19\u2013associated data for nonphysician HCWs from Employee Health Clinic between June 1st 2020 and July 31th 2021. The data we abstracted included age, sex, job title, working location, history of COVID-19, and date of positive COVID-19 test if they had a history of COVID-19. We excluded HCWs who did not have a designated working location and those who worked on multiple units during the same shift to assess the association between COVID-19 infections and working location. Job titles were divided into the following 5 categories: (1) nurse, (2) medical assistant (MA), (3) technician, (4) clerk, and (5) others . Working locations were divided into the following 6 categories: (1) emergency department (ED), (2) COVID-19 unit, (3) non\u2013COVID-19 unit, (4) Clinic, (5) perioperative units, and (6) remote work. Results: We identified 6,971 HCWs with work locations recorded. During the study period, 758 HCWs (10.8%) reported being diagnosed with COVID-19. Of these 758 COVID-19 cases, 658 (86.8%) were diagnosed before vaccines became available. The location with the highest COVID-19 incidence was the ED (17%), followed by both COVID-19 and non\u2013COVID-19 units (12.7%), clinics (11.0%), perioperative units (9.4%) and remote work stations (6.6%, p Conclusions: Strict and special infection control strategies may be needed for HCWs in the ED, especially where vaccine uptake is low. The administrative control of HCWs working remotely may be associated with a lower incidence of COVID-19. Given that the difference in COVID-19 incidence among HCWs by location was lower and comparable after the availability of COVID-19 vaccines, facilities should make COVID-19 vaccination mandatory as a condition of employment for all HCWs, especially in areas where the COVID-19 incidence is high.Funding: NoneDisclosures: None"} +{"text": "Despite the rapid increase in the needs for home- and community-based services (HCBS), including home health care which is the most commonly used HCBS, workforce shortage has become a critical challenge to home health agencies in providing quality care to meet the needs of millions of homebound Americans. This study aimed to examine the availability of home health care workforce and its variations by neighborhood characteristics. We linked several national datasets from 2019 and included information from 11,005 HHC agencies in 1,849 counties. The unit for analysis is county. We found that on average county had fulltime equivalent (FTE) 83 (SD=351) home health care nurses, 120 (SD=411) FTE skilled home health providers and 37 (SD=411) FTE aides. For every 1,000 persons, on average counties had 0.7 (SD=4.6) FTE nurses, 0.9 (SD=4.7) FTE skilled providers, and 0.2 (SD=0.8)) FTE aides. For every 1,000 older adults (>=65), on average counties had 3.6 (SD=23.9)) FTE nurses, 4.8 (SD=24.6) FTE skilled providers and 1.2 (SD=4.4) FTE aides. We also found that counties with moderate (2nd tertile) proportion of Black and Hispanic Americans; counties with highest (3rd title) proportion of Black and Hispanic Americans had the lowest number of FTE home health care aides per every 1,000 persons. Our findings highlight the staff shortage facing home health care and suggest the existence of disparities in availability of home health care workforce."} +{"text": "In addition, olive leaf extract was previously reported in several in vivo studies for its anti-inflammatory, analgesic, antipyretic, immunomodulatory, and antithrombotic activities which are of great benefit in the control of associated inflammatory cytokine storm and disseminated intravascular coagulation in COVID-19 patients. In conclusion, the described biological activities of olive leaves alongside their biosafety, availability, and low price make them a potential candidate drug or supplement to control COVID-19 infection and are recommended for clinical investigation.Beginning from December 2019, widespread COVID-19 has caused huge financial misfortunes and exceptional wellbeing emergencies across the globe. Discovering an effective and safe drug candidate for the treatment of COVID-19 and its associated symptoms became an urgent global demand, especially due to restricted information that has been discharged with respect to vaccine efficacy and safety in humans. Reviewing the recent research, olive leaves were selected as a potential co-therapy supplement for the treatment and improvement of clinical manifestations in COVID-19 patients. Olive leaves were reported to be rich in phenolic compounds such as oleuropein, hydroxytyrosol, verbascoside, apigenin-7- Although several vaccine candidates are now available, only few data have been released regarding the efficacy and safety of vaccines in humans, not to mention that the long-term adequacy of those vaccines still remain as an open address. Nowadays, there is a global trend toward the invention of drug leads that act against COVID-19 infection through different techniques such as in silico, in vitro, in vivo, and clinical studies of the drug candidates. However, until now, only one drug (Paxlovid\u00ae) has been approved recently, in December 2022, by the FDA for the treatment and prevention of COVID-19 infection , Americas (23%), Southeast Asia (8%), Western Pacific (7%), Eastern Mediterranean (4%), and then Africa (1%) . AdditioOlea europaea L., family Oleaceae) is a small tree native to Asia, whose cultivation spreads to all the Mediterranean countries, Europe, Iran, and northern Africa has been reported from the methanolic and aqueous extracts of leaves of Olea europaea (2) (3), oleuricine B (4) (5) (E-p-coumaroyl-secologanoside (comselogoside) (6) (O--secologanoside (7) (8) (9), elenolic acid methyl ester (10), hydroxytyrosol-elenolate (11) (12) and hydroxytyrosol acetate (14), were reported in high amount in olive leaves (Oleuropein (europaea . Oleuroppaea (2) , oleuricne B (4) , oleuros (4) (5) , secologide) (6) , 6\u2032-O-[(side (7) , oleosid (7) (8) , secologate (11) , and 3,411) (12) were isoe leaves Figure has beenO. europaea leaves resulted in the isolation of different steroids and triterpenoids such as \u03b2-sitosterol (15) (16) (\u03b2-amyrin (17) (18) (19) (20) (21) (22) (23) (The ethyl acetate fraction of rol (15) , betulin15) (16) , \u03b2-amyririn (17) , erythro17) (18) , uvaol (18) (19) , ursolic19) (20) , maslini20) (21) , oleanol21) (22) , and cor22) (23) (23) .Olea europaea leaves. Different types of flavone and flavonols such as aglycones and glycosides were reported in olive leaves such as kaempferol (24) (25) (26) (27) (O-glucoside (28) (O-rutinoside (29) (30) (O-glucoside (31) (O-glucoside (32) (O-diglucoside (33) (34) , quercet24) (25) , luteoli25) (26) , diosmet26) (27) , apigeniide (28) , apigeniide (29) , rutin (29) (30) , luteoliide (31) , luteoliide (32) , luteoliide (33) , and que33) (34) (34) .Olea europaea leaves, such as caffeic acid (35), gallic acid (36), chlorogenic acid (37), ellagic acid (38), and verbascoside (39) .Olea europaea leaves such as 4\u2032-O-\u03b2-D-glucosyl-9-O-(6\u2033-deoxysaccharosyl) olivil (40) (41) (42) (Other miscellaneous compounds were reported from the vil (40) , 1,5 anh40) (41) , and epi41) (42) (42) .Olea europaea leaves, including hydrocarbons, tocopherols, triglycerides, waxes, esters, esterols, terpenic alcohols, terpenic dialcohols, and lineal to undergo further in silico computational studies. Several viral targets were tested, such as viral proteases , TLRs, ACE2, RBD, NSP15, HSPA5 SBD\u03b2, TMPRSS2, S protein, and furin showed virucidal activity against SARS-CoV-2 through structural changes in SARS-CoV-2, which is attributed to changing the molecular weight of the spike proteins and disrupting the viral genome . In addiectively .A spray containing 3.80% hydroxytyrosol was proven for its activity as protection against SARS-CoV-2 infection in 50 volunteers, and it showed decrease in the viral load and cure in six patients within ten\u00a0days .in vivo of asthma induced by exposure to interleukin IL-4, ovalbumin (OVA), or cigarette smoke (CS). The mechanism of action of oleuropein was by reducing the influx of eosinophils and lymphocytes in the airway and diminishing IL-4 secretion in the lung, suppressing the infiltration of macrophages and neutrophils by blocking the induction of intercellular adhesion molecule 1 (ICAM-1), F4/80, CD68, and CD11b in airways \u2013stimulated human coronary artery endothelial cells (HCAECs) and reduced matrix metalloproteinase (MMP2) levels in unstimulated cells Table 2Table 2. airways .\u03b2, IL-6, IL-8, TNF-\u03b1, and iNOS) that also resulted in its anti-inflammatory effects reduced the expression of pro-inflammatory mediators such as IL-1\u03b2, IL-6, IL-8, TNF-\u03b1, and iNOS and improved the integrity of the epithelial barrier and restored the expression of ZO-1, MUC-2, and TFF-3 . Maslinic acid suppressed the chronic inflammation and exhibited antimodulatory activity comparable with that of dexamethasone through the development and sustainability of intestinal adenomatous polyps in ApcMin/+ production .Maslinic acid was reported to regulate platelet aggregation and exhibited antithrombotic activity by different mechanisms. It inhibited protein kinase C (PKC) activation by activating the phosphorylation of myristoylated alanine-rich C kinase substrate (MARCKS), which is a phosphorylated substrate of PKC. Maslinic acid inhibited the enzymatic activity of coagulation factor Xa (FXa) and platelet aggregation induced by adenosine diphosphate (ADP) and a thromboxane A2 (TXA2) analog .in silico, in vitro, or in vivo antiviral activities against SARS-CoV-2.Olive leaves are rich in bioactive secondary metabolites. The major secoiridoid (oleuropein and its metabolite hydroxytyrosol), triterpenes , and flavonoids (luteolin and kaempferol) exhibited Apart from the antiviral properties, these bioactive compounds significantly modulated several signaling pathways and demonstrated various activities such as anti-inflammatory, antipyretic, analgesic, immunomodulatory, and antithrombotic properties. These compounds provide a potential natural source to control the cytokine storms observed during COVID-19 infection, manage the symptoms, and protect against complications.The potential antiviral activity of olive leaves and their other described benefits such as biosafety, availability, and low cost, along with the absence of an effective treatment for COVID-19 infection, makes olive leaves a potential natural remedy for the treatment and control of COVID-19. Clinical studies should be conducted with this plant and its metabolites to prove its efficacy in the treatment of COVID-19 infection."} +{"text": "NF2-wildtype meningiomas account for about a third of all meningiomas [NF2-mutated cases, SMO, POLR2A, PIK3CA, AKT1, and KLF4 mutations, the latter both regularly with TRAF7 mutations, have been described [AKT1/TRAF7 mutations are associated with meningothelial histology and basal localization, while KLF4/TRAF7 mutations are highly specific for secretory meningioma without any predominant localization. Also, AKT1 and KLF4 have clear hotspots, with all mutations occurring at AKT1E17K or KLF4K409Q. In contrast, TRAF7 mutations can occur throughout the WD40 domain of the protein . The order of mutational acquisition, whether alterations in TRAF7 or in AKT1/KLF4 occurs first, remains elusive.Most meningiomas carry mutations in the tumor suppressor neurofibromatosis gene 2 (NF2) on chromosome 22q, while ingiomas , 7. In nescribed . TRAF7, escribed . The comTRAF7 mutation N520S, but separate AKT1 and KLF4 hotspot mutation and KLF4mut /TRAF7mut (n\u2009=\u200915) from our database we compared the variant allele frequencies (VAFs) for possible indications of heterogeneity and temporal sequence. 27/28 of the co-mutated samples were classified as WHO grade I meningiomas. 12/15 tumors of the KLF4mut/TRAF7mut cohort were expectedly of the secretory subtype, one tumor was of transitional subtype (subtyping and grading based on the WHO classification 2016) and 2/15 were not assigned in records (no slides available for review). In line, 11/13 tumors of the TRAF7mut/AKT1mut cohort were of the meningothelial subtype, while 2/13 were of transitional subtype. AKT1 and KLF4 mutations displayed clear hotspots, all occurring at AKT1E17K or KLF4K409Q. In contrast, a broad variety of TRAF7 mutations appeared, the two most frequent locations being N520S/H/T (8/28) and K615E/T (5/28) .In an additional 28 cases of AKT1mut/TRAF7mut: p\u2009=\u20090.75; KLF4mut/TRAF7mut: p\u2009=\u20090.62) suggested no major gap between the time points of mutational acquisition or only AKT1 (n\u2009=\u200912) mutant.Looking at mutational co-occurrence in bulk data, mutations assigned with higher VAFs, unless explained by copy number changes, are typically thought to be acquired earlier than those with lower VAFs. Our bulk-measured variant allele frequencies, being similar for both mutations . A total of 875,000 cells were prepared resulting in a median throughput of 2315 cells per sample (interquartile range (IQR): 1622\u20132953) and a median coverage of 105X (IQR: 88X-122X) using the droplet-based technology of Mission Bio (Tapestri). For more details on sequencing metrics see Supplementary Table 3, online resource.Single-cell sequencing technologies allow more insight into the clonal architecture and complexity of thousands of individual cells. We; thus, performed amplicon-based single-cell DNA sequencing on 7 samples of quencing . The panGenotype clustering analysis was performed using the Tapestri bioinformatics pipeline v2. In short, single cells were initially classified into clonal populations based on the variants known from bulk sequencing data. Only cells genotyped for both of the variants were included.TRAF7 without any mutation in KLF4 or AKT1 (detected for 6/7 samples) and another clone harboring the co-mutations in TRAF7 and KLF4 or AKT1 , another clone carrying a mutation in TRAF7 mutation is typically acquired first, but in line with bulk data also supports that the co-mutation of TRAF7 is still either not indispensably needed in every KLF4 or AKT1 mutant meningioma, or that some TRAF7-modifying events are not captured with the current approaches.Although single-cell DNA sequencing in particular is associated with technical challenges such as false positive variant calling and allelic dropouts, high numbers of recovered cells as well as high sequencing metrics allow conclusive information on cellular zygosity and a robust analysis of mutational acquisition. In our cohort, the single-cell data suggest, in this small series, that Supplementary file 1 (DOCX 53 KB)Supplementary file 2 (TIFF 782 KB)Supplementary file 3 (TIFF 598 KB)Supplementary file 4 (XLSX 20 KB)Supplementary file 5 (XLSX 69 KB)Supplementary file 6 (XLSX 12 KB)Supplementary file 7 (XLSX 10 KB)Below is the link to the electronic supplementary material."} +{"text": "Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease in childhood and is usually treated with non-steroidal anti-inflammatory drugs or disease-modifying anti-rheumatic drugs. The outcome in patients with JIA has markedly improved with the advent of biologic drugs.The aim of this study was to describe treatments prescribed for children with JIA in Batna, Algeria.A multicentre retrospective and descriptive study was conducted in Batna health centers (public and private sectors), over a seven-year period from January 2013 to December 2019, based on (JIA patient\u2019s data collection). As public sector source, we referred to the department of pediatrics of the university hospital center (CHU Benflis Touhami Batna), and as private sector source, we referred to private adult rheumatologists based in Batna.The study included a total of 69 cases of JIA that were being followed in Batna health centers over the study period. Treatment modalities used for these patients included non-steroidal anti-inflammatory drugs (NSAIDs) in 54 patients (79.4%), steroids (prednisolone) in 37 patients (54.4%), conventional disease-modifying anti-rheumatic drug (c-DMARDs) in 51 patients (72.5%), biologic agents in 11 (15.9%) and intra articular injections in 17 patients (24.6%). The most frequently used c-DMARDs was methotrexate 42 (63.7%). The mean maximal dose reached was 7.5 mg (range 2.5\u201315). It was associated to other c-DMARDs in 2 cases. Sulfasalazine was used in 8 cases, Leflunomide in 1 case, and Hydroxychloroquine in 1 case. Biologics were used in 11 cases (15.9%).n = 2), Tocilizumab (n = 1), Anakinra (n = 1), Etanercept (n = 1) and Infliximab (n = 1). The was 4.8 \u00b1 5.4 years (range 0.5\u20138 years). At the time of enrolment, 31 patients (44.9%) were in remission: 20 patients (29%) were under treatment and 11 patients (15.9%) were not, while 12 patients (17.4%) had active disease.RF-positive polyarthritis 4(50%), RF-negative polyarthritis 3 (33.3), systemic arthritis 2 (33.3) were the groups that most commonly needed a biological therapy. Biologics included Rituximab (A high proportion of children presenting with JIA received cDMARDs. Biologics were needed in a few cases.None declared"} +{"text": "The SARS-CoV-2 pandemic resulted in an unprecedented number of severe cases among pregnant women , 2. To dWe here present a case series of 14 pregnant and peripartum women with severe acute respiratory distress syndrome (ARDS) due to Covid-19 treated at our institution between January 2020 and December 2021.2/FiO2 (PF ratio) on admission was 74\u00a0mmHg (60\u201393).Figure\u00a010/14 (71.4%) women required invasive mechanical ventilation, 6/14 (42.8%) with additional extracorporeal membrane oxygenation (ECMO). 4/14 (28.5%) patients could be managed with non-invasive support, 3/14 (21.4%) with high flow nasal cannula (HFNC) and 1/14 (7.1%) with non-invasive ventilation (NIV). Prone positioning was used in 5/14 (35.7%) patients. Specific Covid-19 therapies included Remdesivir in 3/14 (21.4%), Tocilizumab in 5/14 (35.7%) and Glucocorticoids in 12/14 (85.7%).7/14 (50%) women had isolated ARDS in pregnancy and another 7/14 (50%) had multi organ failure (MOF), defined by additional non-pulmonary organ specific sub-SOFA scores\u2009\u2265\u20092 points. In 3/14 (21.4%) MOF developed after delivery of women with previously isolated ARDS.Considering all MOF together, the second most common organ failure besides ARDS was circulatory failure in 10/14 (71%) women. Kidney failure was present in 5/14 (36%) women. In 4/14 (29%) there was maternal cardiac failure, 3/14 (21.4%) with predominant left heart and one right heart failure, and 2/14 (14.2%) required additional arterial ECMO cannulation for circulatory support.None of the 7/14 (50%) patients with isolated ARDS during pregnancy died. In 3/14 (21.4%) women, caesarean section was performed while on the ICU between gestational weeks 33 and 38 due to progressive respiratory failure. These women and their offspring survived but all 3 women developed MOF after delivery. All maternal and fetal deaths occurred in patients with MOF who required high-dose catecholamine support: 2/14 (14.2%) of the women and 4/14 (28.5%) of the unborn died. Two intrauterine fetal deaths (IUFD) occurred in the setting of maternal MOF at 21 and 28\u00a0weeks\u2019 gestation, respectively. One stillbirth occurred at gestational week 17 after maternal recovery from MOF, and one patient requested abortion at 30\u00a0weeks\u2019 gestation after she had already left ICU because her child displayed severe ischemic brain damage presumably resulting from maternal MOF and profound shock.All 7/14 (50%) women with MOF were before 28\u00a0weeks\u2019 gestation, 3/14 (21.4%) were before gestational week 24, before viability, thus delivery was not a reasonable option. The other 4/14 (28.5%) patients with MOF were between gestational week 26 and 28. In these patients, emergency caesarean section was discussed on a daily basis within a multidisciplinary team consisting of critical care and obstetric professionals.In summary, the management of pregnant patients with severe Covid 19 is complex and requires a multidisciplinary approach. Despite the relatively small sample size, our data suggest that patients with severe Covid-19-related ARDS can be successfully carried through pregnancy with invasive ventilation and ECMO, if needed, as long as they suffer from isolated lung failure. However, the risk of maternal and fetal death increases substantially once MOF develops. Additional circulatory failure requiring high-dose catecholamine support seems to be the major determinant of adverse maternal and fetal outcome in pregnant women with severe Covid-19 associated ARDS.The decision regarding delivery in women with severe Covid-19 associated ARDS needs to balance multiple risks and benefits, including the risk of prematurity to the fetus, the potential to improve or worsen maternal respiratory status with delivery, and the risks accompanying major surgery such as cesarean section, particularly in patients requiring ECMO support. These preliminary observations need to be tested in larger multicenter studies."} +{"text": "Background: To evaluate the accuracy of 68Ga-prostate specific membrane antigen (PSMA) PET/CT in the diagnosis of clinically significant prostate cancer (csPCa) (Grade Group > 2) in men enrolled in Active Surveillance (AS) protocol. Methods: From May 2013 to May 2021, 173 men with very low-risk PCa were enrolled in an AS protocol study. During the follow-up, 38/173 (22%) men were upgraded and 8/173 (4.6%) decided to leave the AS protocol. After four years from confirmatory biopsy (range: 48\u201352 months), 30/127 (23.6%) consecutive patients were submitted to mpMRI and 68Ga-PSMA PET/CT scan before scheduled repeated biopsy. All the mpMRI (PI-RADS > 3) and 68Ga-PET/TC standardised uptake value (SUVmax) > 5 g/mL index lesions underwent targeted cores (mpMRI-TPBx and PSMA-TPBx) combined with transperineal saturation prostate biopsy (SPBx: median 20 cores). Results: mpMRI and 68Ga-PSMA PET/CT showed 14/30 (46.6%) and 6/30 (20%) lesions suspicious for PCa. In 2/30 (6.6%) men, a csPCa was found; 68Ga-PSMA-TPBx vs. mpMRI-TPBx vs. SPBx diagnosed 1/2 (50%) vs. 1/2 (50%) vs. 2/2 (100%) csPCa, respectively. In detail, mpMRI and 68Ga-PSMA PET/TC demonstrated 13/30 (43.3%) vs. 5/30 (16.7%) false positive and 1 (50%) vs. 1 (50%) false negative results. Conclusion: 68Ga-PSMA PET/CT did not improve the detection for csPCa of SPBx but would have spared 24/30 (80%) scheduled biopsies showing a lower false positive rate in comparison with mpMRI (20% vs. 43.3%) and a negative predictive value of 85.7% vs. 57.1%, respectively. In the last decade, active surveillance (AS) has become an alternative to radical treatment of low-/very low-risk prostate cancer (PCa), focusing on prevention of overtreatment (50% of the cases in screening studies) ,2,3. MulRecently, prostate-specific membrane antigen (PSMA) inhibitors conjugated with the radionuclides 68Ga and 18F-fluoride have been well-explored and successfully translated for the clinical diagnosis of PCa ,8. MoreoThe aim of this study was to prospectively evaluate the diagnostic accuracy of 68Ga-PSMA PET/CT and mpMRI in the diagnosis of csPCa (Grade Group > 2) in men eFrom May 2013 to May 2021, 173 men aged between 52 and 73 (median age 63) with very low-risk PCa were enrolled in an AS protocol study. After institutional review board and ethical committee approval were granted, informed consents were obtained from all participants included in the study. Presence of the following criteria defined eligibility: life expectancy greater than 10 years, clinical stage T1C, PSA below 10 ng/mL, PSA density (PSA-D) < 0.20, <2 unilateral positive biopsy cores, Gleason score 6/International Society of Urologic Pathology (ISUP) Grade Groups (GG) 1 and maxiAll mpMRI examinations were performed using a 3.0 Tesla scanner equipped with 16 surface channel phased-array coils placed around the pelvic area with the patient in the supine position; multi-planar turbo spin-echo T2-weighted (T2W), axial diffusion weighted imaging (DWI) and axial dynamic contrast enhanced (DCE) were performed for each patient. The mpMRI lesions characterised by Prostate Imaging Reporting and Data System (PI-RADS) version 2 (4) scores > 3 were considered suspicious for cancer; two radiologists blinded to pre-imaging clinical parameters evaluated the mpMRI data separately and independently; moreover, one urologist with more than 25 years of experience performed the biopsy procedure .PET/CT imaging was performed using a CT-integrated PET scanner . 68Ga-PSMA was prepared with a fully automated radiopharmaceutical synthesis device based on a modular concept . 68Ga-PSMA-11 was given to patients via an intravenous bolus , and the PET acquisition was started at a mean of 58 \u00b1 12 min afterward. Scans were acquired in 3-dimensional mode with an acquisition time of 3 min per bed position. Emission data were corrected for randoms, dead time, scatter and attenuation and were reconstructed iteratively using ordered-subsets expectation maximisation followed by a post-reconstruction smoothing Gaussian filter . For attenuation correction, a low-dose unenhanced CT scan was performed from the skull base to the middle of the thigh. Images were processed to obtain PET, CT, and PET-CT fusion sections in the axial, coronal, and sagittal planes with a thickness of approximately 0.5 cm by two experienced nuclear medicine specialists, who were blinded to the clinical data. The location of focal uptake on 68Ga-PSMA PET/CT , three-dAll the mpMRI (PI-RADS score > 3) and 68Ga-PET/TC index lesions (SUVmax > 5 g/mL) underwenThe clinical parameters of the 30 men enrolled in the active surveillance protocol are listed in Multiparametric MRI and 68Ga-PSMA showed 14/30 (46.6%) and 6/30 (20%) lesions suspicious for PCa those were submitted to targeted cores combined with SPBx. In detail, mpMRI PI-RADS score resulted < 2 vs. 3 vs. 4 in 16 (53.3%) vs. 12 (40%) vs. 2 (6.7%) men. The average intraprostatic SUVmax and tumor dimension was 4.8 g/mL (range: 3.2\u201319.8) and 7.3 mm (range 4\u201312 mm), respectively; only 6/30 (20%) men had a SUVmax > 5 g/mL (range: 5.1\u201319.8 g/mL), moreover, 68Ga-PSMA PET/TC showed two suspicious areas in correspondence of iliac ala and spinal cord; were shown to be negative for metastases in targeted MRI for bone evaluation. In 2/30 (6.6%) men, a csPCa (GG2) was found: both patients had a GPC equal to 20% with a number of positive cores equal to 3 and 4, respectively. PSA density was 0.15 and 0.11.68Ga-PSMA-TPBx vs. mpMRI-TPBx vs. SPBx diagnosed 1/2 (50%) vs. 1/2 (50%) vs. 2/2 (100%) csPCa, respectively. In detail, PET/CT PSMA and mpMRI missed the diagnosis of csPCa in two different patients: one patient had a PI-RADS score of 2 and SUVmax of 6.8 g/mL; the man not detected by PSMA PET had a PI-RADS of score 3 at moMRI and SUVmax equal to 4.5 g/mL at 68Ga-PET/TC. In detail, mpMRI and 68Ga-PSMA PET/TC demonstrated 13/30 (43.3%) vs. 5/30 (16.7%) false positive and 1 (50%) vs. 1 (50%) false negative results. In addition, mpMRI and 68Ga-PSMA PET/TC showed a negative predictive value (NPV) in the diagnosis of csPCa equal to 57.1 and 85.7%, respectively.The estimated risk-free treatment at 5, 10 and 15 years in men enrolled in AS with GG1 PCa is equal to 76, 64 and 58% . In thisRecently, 68Ga-PSMA-PET/CT has been suggested to improve the clinical stadiation of high-risk PCa and disease recurrence ; at the To our knowledge, this is the first study that prospectively evaluated the role of 68Ga- PSMA PET/CT in men enrolled in prostate cancer AS protocols . In our Diagnostic imaging should not replace scheduled prostate biopsy but is mandatory to detect targeted lesions suspicious for csPCa. Several biochemical parameters, such as thymidine kinase I, mindin or PHI, could be helpful in decrease the ratio of scheduled biopsy. We have no data about these parameters; however, we evaluated our patients according to PSA density, as suggested by latest EAU guidelines.Among our results, some considerations should be made. First, the number of patients evaluated was low; secondly, the results should be evaluated in the entire prostate specimen and not in biopsy histology. A more detailed histological evaluation of patients who underwent biopsy upstaging would be of interest, for example by adding supplementary staining for PSMA on the biopsy samples. However, this type of staining is not routinely performed at our institution. Third, the low rate of reclassification (6.6% of the cases) could be explained because the patients previously underwent SPBx plus mpMRI evaluation before confirmatory biopsy. Four, 68Ga-PSMA PET/TC evaluation could be proposed in men with negative mpMRI or in the presence of claustrophobia or cardiac pacemaker. Finally, a 68Ga-PSMA PET/TC fusion platform would have increased the accuracy of targeted prostate biopsy.In conclusion, 68PSMA PET/CT did not improve the detection for csPCa of SPBx ; at the same time, 68Ga-PSMA PET/CT would have spared 24/30 (80%) scheduled biopsies showing a lower false positive rate in comparison with mpMRI (20% vs. 43.3%) and a better NPV (85.7 vs. 57.1%)."} +{"text": "Crataegus monogyna, Cydonia oblonga, Malus sylvestris, Matricaria chamomilla, Morus alba, Morus nigra, Rosa canina, Sambucus nigra, Tilia cordata, and Vaccinium myrtillus) were separated and then identified using GC-MS, whereas GC-FID is employed for the quantitative analysis. Experimental data revealed different patterns of volatile constituents depending on plant species. Monoterpenes, sesquiterpenes, diterpenes, and norisoprenoids were the most abundant volatile constituents. Principal component analysis (PCA) was deployed for data analysis and resulted in grouping these ten species in four principal clusters. The combination of various volatile constituents present in specific plant species may play an important role in the specific aroma and taste sensation of these species used as recreational teas.The study evaluates the chemical composition of the volatile constituents of ten plant species traditionally used as herbal tea in the Sharri Mountain regions (Kosovo and North Macedonia). Volatile constituents responsible for the flavour and fragrance of selected species ( Crataegus monogyna Jacq., Cydonia oblonga Mill., Malus sylvestris (L.) Mill., and Rosa canina L.), Adoxaceae (Sambucus nigra L.), Ericaceae (Vaccinium myrtillus L.), Moraceae , Malvaceae (Tilia cordata Mill.), and Asteraceae (Matricaria chamomilla L.).The Sharri Mountain lies in the southern part of Kosovo and northwest part of North Macedonia. The region is rich in terms of biological diversity, and in recognition of its biodiversity richness, a part of Sharri Mountain in Kosovo and that in North Macedonia (2021) were declared as a National Park . The regThe plant material was collected from July to October 2018 in Sharri Mountains (Kosovo and North Macedonia). Only plant species used as hot aromatic beverages (water infusion) for recreational consumption were selected. They were selected based on the reviewed data from previously published ethnobotanical studies, unpublished ethnobotanical data, and interviews carried out during the fieldwork. Plant material was either collected from wild populations in Sharri Mountains, purchased in the local markets (in 2018), or provided by local residents that were wildcrafted or cultivated for family use. The plant species were identified according to the Flora Europaea , while t\u22121 using a Clevenger apparatus for 3 hours. Their volatiles were collected in 1\u2009mL n-hexane, and the extracts were stored at \u221218\u00b0C in the freezer until further analysis.Plant material was dried, cut into small pieces (>0.3\u2009cm), and then extracted by hydrodistillation at a distillation rate of 3\u2009ml.min\u03bcL of the sample was injected with a split ratio of 50\u2009:\u20091. The initial GC oven temperature was 60\u00b0C (5\u2009min), increased from 60\u00b0C to 280\u00b0C at a rate of 5\u00b0C/min. GC-FID analyses were performed with the same column and temperature program as the analytical GC/MS.The volatile constituents were separated using a HP-5ms column in a gas chromatograph (Agilent 7890A). The identification was made using a mass spectrometry detector (Agilent 5975C MSD). The mass spectrometer ionization energy was 70\u2009eV, with a mass range of 40\u2013400\u2009m/z. Helium was used as a carrier gas at an initial flow rate of 0.6\u2009mL/min (50\u2009psi), and 1.0\u2009Each constituent was identified by comparing the Kovats retention indices with those reported in the literature . The retPrincipal component analysis (PCA) was used for data analyses. Only chemical constituents with concentrations higher than 5% were selected for statistical analysis. The XLStat program (version 2021.2.2) was used for the PCA.Rosa was represented with four species and the genus Morus was represented with two species, while all other genera were represented with only one species.Eighteen plant species were identified for making recreational herbal teas in the Sharri Mountain area. The chemical composition of eight plant species of the Lamiaceae family was reported previously , while iCrataegus monogyna Jacq.). Oxygenated sesquiterpenes (36.35%) were the most prominent constituents, followed by oxygenated monoterpenes (31.22%), sesquiterpenes (18.32%), hydrocarbons (5.74%), fatty acids and derivatives (2.23%), and monoterpenes (1.15%). The principal constituents were spathulenol (22.76%), cis-pinocamphone (19.86%), E-caryophyllene (6.87%), 1.8-cineole (4.52%), caryophyllene oxide (4.17%), and isomenthone (3.17%). In hawthorn leaf and flower samples collected in Turkey, the principal volatile components were aldehydes, benzaldehyde (82.54%), butyraldehyde (38.27%), and (E) 2-hexenal (21.67%), while linoleic (64.23%), oleic (39.36%), and palmitic (8.16%) acids were the principal constituents of seeds [The volatile composition of the analyzed species is presented in of seeds .Cydonia oblonga Mill.), forty-six compounds were identified. Hydrocarbons (34.44%) and oxygenated sesquiterpenes (23.29%) were the most prominent classes of identified compounds, followed by fatty acids and their derivatives (21.34%) and other compounds (10.61%), whereas sesquiterpenes (5.08%), diterpenes, oxygenated diterpenes (3.55%), and oxygenated monoterpenes were present in smaller amount (0.36%). E-\u03b2-ionone (7.73%) was the most prominent compound followed by n-eicosane (5.94%), 14-oxy-\u03b1-muurolene (5.38%), n-tricosane (4.86%), dodecanoic acid (4.55), 3Z-hexenyl salicylate (4.18%), hexacosane (4.02%), \u03b4-cadinol (3.95%), n-docosane (3.88%), n-hexadecanoic acid (3.67%), \u03b1-bisabolone oxide (3.62), linoleic acid (3.36%), and 3E-cembrene (3.14%). The principal volatile constituents in quince leaves collected in Turkey during the flowering period were benzaldehyde (12.8%), followed by the fatty acid, hexadecanoic acid (7.2%), oxygenated monoterpene, linalool (5.7%), and E-\u03b2-ionone (5.1%), while during the fruiting period, the main constituents are sesquiterpenes, germacrene D (8.6%), and benzaldehyde (4.9%) [\u03b2-ionone (C13-norisoprenoid) (7.73%) in our samples was higher, whereas the percentage of hexadecanoic acid (3.67%) was lower than in Turkish samples. On the other hand, the most prominent constituents of essential oils obtained from Serbian samples were ethyl 2-methylbutanoate, -\u03b1-farnesene, ethyl--decadienoate, pentadecanol, \u03b2-acoradienol, ethyl decanoate, ethyl octanoate, (E)-nerolidol, and ethyl dodecanoate [In the extract of the quince leaves . Mill) represent a complex mixture of constituents composed of thirty-seven compounds. The main classes of chemical constituents were sesquiterpenes and oxygenated sesquiterpenes, with 44.87% and 20.11%, respectively (\u03b2-farnesene (12.86%), \u03b1-cadinol (16.6%), E-spiroether (9.7%), \u03b1-bisabolone oxide (5.9%), \u03b1-bisabolol oxide A (5.46%), 2E-dodecanal (4.6%), hexacosane (3.51%), and caryophyllene oxide. GC-FID and/or GC-MS analysis of dichloromethane extracts of European wild apple fruit distillates originating from Serbia revealed complex volatile profiles of the main detected components to be alcohols, shikimate metabolites, esters, terpenes, aldehydes and acetyls, fatty acids, and carotenoid-derived compounds [The volatile constituents obtained from European crab apple and revealed in the identification of forty-six compounds. Fatty acids and their derivatives (28.56%), hydrocarbons (27.46%), and other compounds, mostly tetrahydrofurans (15.34%), were the principal components in oils, followed by oxygenated monoterpenes (11.59%), sesquiterpenes (6.22%), monoterpenes (4.29%), and oxygenated sesquiterpenes (4.07%). The principal constituents were the fatty alcohol, n-tetradecanol (13.51%), followed by a C13 spiroether vitispirane (11.47%), fatty aldehyde, n-nonanal (5.12%), oxygenated monoterpene, \u03b1-terpineol (5.09%), 14-oxy-\u03b1-muurolene (4.07%), n-hexanol (3.86), 1-octadecene (3.69%), (E)-\u03b2-ocimene (3.55%), heptacosane (3.45%), n-octane (3.08%), and n-heneicosane (3.01%). In fresh and dried rosehip samples collected in Serbia, diverse compounds were detected, including ketones, n-nonanal (5.12%), esters, phenols, sitosterol, and alcohols. Monoterpenes and aromatic acids were present in fresh fruits, while aldehydes, monoterpenes, and aromatic acids were absent in dried rosehip fruits [Among the abovementioned species of the family Rosaceae, the volatile constituents were analyzed in the extracts of the dog rose fruits , followed by hydrocarbons (22.09%), oxygenated sesquiterpenes (18.87%), and diterpenes and oxygenated diterpenes (16.35%). Other compounds (6.23%), oxygenated monoterpenes (4.87%), and fatty acids and derivatives (1.96%) were present in a smaller amount. On the other hand, the main classes of constituents for M. nigra are oxygenated diterpenes (32.07%), sesquiterpenes (22.27%), and oxygenated sesquiterpenes (17.2%), followed by hydrocarbons (14.71%), oxygenated monoterpenes (7.07%), and fatty acids and derivatives (2.93%). The principal constituents in M. alba oils were trans-phytol (15.71%), germacrene D (6.37%), E-caryophyllene (6.26%), n-pentacosane (4.90%), \u03b3-eudesmol (4.04%), caryophyllene oxide (3.86%), octacosane (3.76%), squalene (3.44), and \u03b2-bisabolene (3.2%), while the main constituents in M. nigra were trans-phytol (31.78%), germacrene D (6.40%), zierone (4.61%), E-caryophyllene (4.14%), \u03b1-humulene (3.62%), n-pentacosane (3.91%), methyl citronellate (3.31%), octacosane (3.43%), and \u03b3-eudesmol (3.39%). In samples collected in Serbia, the principal compound was trans-phytol . Other classes of prominent compounds were alkanes, carotenoid-derived compounds, and fatty acid-related constituents [M. alba leaves collected in Hungary [GC/MS analysis revealed that fifty-six and fifty-one volatile compounds could be identified in the leaves of Morus alba and Morus nigra, respectively . The maiterpenes .35%. Othterpenes .2%, follMatricaria chamomilla L.), forty-nine compounds were identified. Oxygenated sesquiterpenes (38.13%) and sesquiterpenes (29.02%) were the principal constituents, followed by other compounds including spiroketals (14.32%), fatty acids and derivatives (5.94%), hydrocarbons (5.64%), diterpenes/oxygenated diterpenes (3.28%), and oxygenated monoterpenes (2.12%). The most abundant characteristic constituents were E-\u03b2-farnesene (21.17%), \u03b1-bisabolol oxide A (14.83%), E-spiroether (8.97%), bisabolone oxide (7.53%), epi-\u03b1-cadinol (4.58%), 2E-dodecenal (4.49%), chamazulene (3.32%), and trans-phytol (3.28%). Our findings are in line with previously published data for the most abundant classes of compounds and specific constituents. In samples collected in Serbia and Bosnia and Herzegovina, E-\u03b2-farnesene, \u03b1-bisabolol and its oxide, chamazulene, germacrene D, and spiroether were present in high concentrations [In the essential oil of the chamomile flowers , followed by fatty acids and their derivatives (21.31%), oxygenated monoterpenes (14.91%), and sesquiterpenes (7.52%) and oxygenated sesquiterpenes. Hydrocarbons, nonadecane (17.72%), n-tricosane (10.31%), n-eicosane (5.73%), n-heneicosane (4.08%), n-pentacosane (5.19%), and n-docosane (3.79%) were the most prominent compounds, followed by fatty acids and their derivatives, n-hexadecanoic acid (9.94%), linoleic acid (6.28%), and linalool (3.27%). Carvacrol (1.95%), citronellol (1.9%), and methyl citronellate (1.90%) were the most prominent oxygenated monoterpenes, while trans-\u03b1-bergamotene (1.01%) and germacrene D (1.08%) were the principal sesquiterpenes. Our results were in agreement with previously published results of elderberry flower volatile constituents originated from Turkey, dominated by heneicosane (18.8%), tricosane (17.3%), nonadecane (13%), and pentacosane (10.3%) [The hydrocarbons (49.46%) were the most abundant classes of the volatile compounds in the extracts of elderberry flowers ( (10.3%) . On the ivatives .31%, oxyVaccinium myrtillus L.) fruit extracts. Oxygenated monoterpenes (59.65%) were the most prominent constituents, followed by fatty acids and their derivatives (17.38%), sesquiterpenes (11.79%), and oxygenated sesquiterpenes (4.28%). Oxygenated diterpenes and hydrocarbons were present in smaller concentrations. Oxygenated monoterpenes, neral (31.24%) and geranial (22.31%), were the most prominent compounds, followed by sesquiterpene E-caryophyllene (10.73%) and its oxygenated derivative, and caryophyllene oxide (3.85%). Peak areas of hexadecanoic acid, 3Z-hexenyl salicylate, dodecanoic (lauric) acid, and linoleic acid were 9.06%, 2.98%, 2.40%, and 2.12%, respectively. To the best of our knowledge, only a few papers reported data on the chemical composition of the volatile constituents obtained from the fruits of the European blueberry. In the study reported by Jens et al. [Twenty-four volatile compounds were identified in European blueberry , seventy compounds were identified, predominantly belonging to chemical classes of hydrocarbons (44.36%), fatty acids and their derivatives (22.99%), oxygenated monoterpenes (7.5%), oxygenated sesquiterpenes (5.41%), and sesquiterpenes (3.18%). The most prominent class of compounds was hydrocarbons: n-pentacosane (11.66%), squalene (4.61%), n-nonacosane (2.78%), n-heneicosane (11.49%), and n-tricosane (4.72%), followed by fatty acids and their derivatives, including n-nonanal (7.15%), hexadecanol (2.93%), and dodecanoic acid (2.24%). The concentration of allylbenzene derivative, eugenol and terpenoid ketone, and Z-jasmone, was 6.78% and 3.08%, respectively. In accordance with our data, the study of essential oil from the flowers, bracts, and leaves of Tilia sp. originated from Turkey showed high percentages of hydrocarbons and fatty acids and their derivatives (47.5\u201366.5% in comparison with 49.46% in our sample). Likewise, the high content of aliphatic acids was found in samples from Turkey (28.3\u201337.1%) [In the leaf extracts of small-leaved lime (3\u201337.1%) .Tilia cordata, Sambucus nigra, and Vaccinium myrtillus clustered in the first group, Morus alba, Morus nigra, and Crataegus monogyna clustered in the second group, and Matricaria chamomilla and Malus sylvestris clustered in the third group, whereas the fourth group included Cydonia oblonga and Rosa canina, with greater similarities concerning their chemical composition has been used to group the analyzed plant species based on their chemical composition . PCA demposition .Matricaria chamomilla, Tilia cordata, and Rosa canina are still frequently used in this region, and Vaccinium myrtillus is occasionally used to prepare tea. The species Malus sylvestris and Sambucus nigra are rarely used nowadays, while Morus alba, Morus nigra, Crataegus monogyna, and Cydonia oblonga are not used anymore for this purpose.Some of the plant species analyzed in this study still have importance in use as herbal in the culture of the Sharri Region. Thus, Eighteen plant species were identified to be used as recreational herbal teas in the Sharri Mountain area. The chemical composition of eight plant species (Lamiaceae family) was reported previously, while in this article, the volatile constituents of the species belonging to the families of Adoxaceae, Asteraceae, Ericaceae, Malvaceae, Moraceae, and Rosaceae are reported. Experimental data revealed different patterns of volatile constituents depending on plant species. The variety of volatile constituents present in plant species suggests that their combination may play an important role in the specific aroma and taste sensation of recreational teas, and these factors are important for consumers' preferences. On the other hand, besides phytochemical characteristics, evaluating the pharmacological and nutritional properties of plants used for the tea preparation is needed to warrant their safe and appropriate use, especially for those teas consumed regularly."} +{"text": "UNRS measures BU severity in the past 24 hours from 0 (no urgency) to 10 (worst possible urgency). Psychometric evaluation of the UNRS showed Clinically Meaningful Improvement (CMI) is This analysis evaluated the proportions of patients in LUCENT studies achieving BU CMI and BU remission.The modified intent-to-treat (mITT) population (patients receiving \u22651 dose of miri or placebo (PBO); N= 1281) was randomized at induction study baseline in a 3:1 ratio to IV doses of 300mg miri or PBO every 4 weeks (Q4W) during induction . Patients achieving Clinical Response, measured by Modified Mayo Score (MMS), to miri during induction were re-randomized at W0 of the maintenance study in a 2:1 ratio to subcutaneous (SC) 200mg miri or PBO Q4W through W40 (52 weeks of treatment). Patients recorded their UNRS score daily in an e-diary. Mean weekly UNRS scores were calculated from diary data if \u22654 days of data were available. Rates of BU CMI and BU remission in the miri v PBO groups were compared at W12 (induction) in the mITT population with a baseline UNRS score \u22653, and W52 (maintenance) among miri clinical responders at W12 with a baseline UNRS score \u22653. Cochran-Mantel-Haenszel tests with non-responder imputation for missing values were used for all treatment comparisons.Patient population: mean age 43 years, 60% male, disease duration 7 years; 63.0% left-sided colitis; 36.3% pancolitis; 46.7% moderate disease (MMS 4-6); 53.2% severe disease (MMS 7-9). Significantly higher proportions of miri versus PBO patients achieved BU CMI (48.7% v 32.2%) and BU remission (22.1% v 12.3%) at W12 in the induction study. Similarly, at W40 of maintenance, significantly greater proportion of miri patients achieved BU CMI (65.2% v 41.9%) and BU remission (42.9% v 25.0%) compared to PBO among miri induction responders .Miri had a highly significant and clinically meaningful benefit on reducing bowel urgency, one of the most disruptive UC symptoms. The Urgency Numeric Rating Scale usefully quantified the baseline level and change in bowel urgency after treatment across a spectrum of severity.OtherEli Lilly and CompanyNone Declared"} +{"text": "Background: The feasibility and value of pericardial effusion as a liquid biopsy sample for actionable alteration detection in patients with non-small cell lung cancer (NSCLC) has not been adequately investigated. Here, we aim to reveal genomic alterations between pericardial effusion and paired tumor tissue, plasma (plasma cfDNA), and pleural effusion supernatant (PE-cfDNA) based on second-generation sequencing technology.Material and methods: A total of 26 advanced NSCLC patients were retrospectively studied. The following samples were collected and sequenced using two targeted next-generation sequencing panels: pericardial effusion (n = 26), matched tumor tissue (n = 6), plasma (n = 16), and pleural effusion supernatant (n = 5).Results: A total of 10 actionable alterations were identified in pericardial effusion of the NSCLC patients, including MET amplification, EGFR L858R, EGFR T790M, EGFR exon 19 deletion, EGFR L861Q, KRAS G12C, EML4-ALK (exon 18: exon 20) fusion, EML4-ALK (exon 20: exon 20) fusion, EML4-ALK (exon 6: exon 20) fusion, and ERBB2 exon 20 insertion. All these actionable alterations harbored multiple drug-sensitive targets as well as several drug-resistant targets, such as EGFR T790M. Compared to plasma cfDNA of 16 patients, paired pericardial effusion had higher number of actionable alterations (p = 0.08) as well as higher percentage of the population with actionable alterations (p = 0.16). Moreover, 8 out of 10 actionable alterations with single nucleotide variations (SNVs) or insertions/deletions (indels) had a higher variant allele frequency (VAF) in pericardial effusion than plasma cfDNA. In addition, we identified two actionable alterations in paired pericardial effusion, which were absence in PE-cfDNA. Clearly, 2 out of 3 actionable alterations with SNVs/indels in pericardial effusion had a higher VAF than those in PE-cfDNA. Our finding suggested the importance of pericardial effusion in the optimal selection of patients for targeted therapy.Conclusion: Among liquid biopsy specimens from the advanced NSCLC patients, pericardial effusion may be a better candidate for genomic profiling than plasma cfDNA, while it could serve as a supplement to PE-cfDNA in detecting actionable alterations. Therefore, pericardial effusion might provide a new alternative for selection of patients for better treatment management. Lung cancer is the second most common cancer as well as the leading cause of cancer death worldwide . NumerouWhile tissue specimens are typically considered optimal for molecular testing , plasma https://www.oncokb.org/) , pericardial effusion cell sediment , tumor tissue, plasma cfDNA, and PE-cfDNA in 26 advanced NSCLC patients. The actionable alterations were identified by interrogating the OncoKB database (kb.org/) . The preThis study recruited a total of 26 advanced NSCLC patients from in-patient department of the First Hospital of Jilin University between January 2016 and December 2020, including 20 cases with lung adenocarcinomas and 6 cases with lung squamous carcinoma. The diagnosis was made according to the Guidelines for the Diagnosis and Treatment Standardization of Lung Cancer (2011 Edition). All the patients were staged based on the tumor node metastasis (TNM) staging system as presented in the 2012 National Comprehensive Cancer Network (NCCN) Clinical Practice Guidelines. They were pathologically classified using the 2015 edition of the World Health Organization\u2019s Lung Cancer Histology Classification . The medn = 26), peripheral blood (n = 26), PE (n = 5), and tumor tissue (n = 6) from the NSCLC patients. 26 pericardial effusion specimens and 5 pleural effusion samples were subjected to centrifugation, and the cell pellets and supernatants were collected separately. In the meantime, 26 peripheral blood samples were centrifuged, and the plasmas and white blood cells were collected separately. NGS was performed to simultaneously detect gene alterations on pericardial effusion-cfDNA, pericardial effusion-sDNA, PE-cfDNA, plasma cfDNA, genomic DNA of white blood cells, and genomic DNA of formalin fixed paraffin-embedded (FFPE) tissue from NSCLC patients. Genomic DNA from the white blood cells of those 26 NSCLC patients was extraction as the germline controls for variant calling of other paired sample types. Plasma of 10 patients was excluded because of hemolysis in peripheral blood, insufficient plasma cfDNA extraction or failed quality control of sequencing data and centrifuged at 4000xg for 15\u00a0min at 4\u00b0C. Afterwards, 4\u00a0ml supernatant of pericardial effusion, 4\u00a0ml supernatant of PE and 4\u00a0ml plasma of peripheral blood were collected respectively for cfDNA extraction. The cell pellets of pericardial effusion were lysed with Proteinase K. The lysed cell pellets and white blood cells were used for genomic DNA extraction.CfDNA was extracted from supernatant of pericardial effusion, supernatant of PE and plasma of peripheral blood using MagMAX Cell-Free DNA isolation kit and KingFisher\u2122 Flex Magnetic Particle Processor 24DW according to the user guide. Genomic DNA was extracted from the cell pellets of pericardial effusion and white blood cells with TIANamp Genomic DNA Kit . The blackPREP FFPE DNA Kit was used to extract genomic DNA from FFPE tumor tissue samples.Genomic DNA from FFPE tumor tissue, white blood cells or cell pellets of pericardial effusion was sheared into 150 to 20\u00a0bp fragments using covaris M220 according to the recommended settings. CfDNA and fragmented DNA were input for library construction. Indexed Illumina NGS libraries were prepared using KAPA hyper preparation kit according to the manufacturer\u2019s instructions. Ligated fragments were amplified for 9 PCR cycles using indexed primers depending on the DNA mass of pre-PCR. DNA was purified with Agencourt AMPure XP beads , and dual size selection was performed during the library preparation. All the libraries were quantified with Qubit DNA dsDNA assay kit , and the fragment length was determined on Agilent bioanalyzer 2,100 using the DNA 1000 kit .Targeted region selection was performed using NimbleGen SeqCap Hybridization and Wash kit . 1 ug of mixed library DNA from 8-12 indexed Illumina libraries was captured with a hybridization probe. The probe library was designed through the NimbleDesign portal (Version 02) using genome build hg19 NCBI Build 37.1/GRCh37. DNA libraries were captured with two designed Genescope panels including a total of 467 shared tumor-related genes. The captured products were quantified with Qubit dsDNA assay kit, subjected to determination of fragment length by Agilent 2,100 bioanalyzer with the DNA 1000 kit, and then sequenced using 150-bp paired-end runs on the Illumina Novaseq 6,000.Data quality control, reference mapping and duplication masking were performed by Trimmomatic (version 0.36), BWA aligner (version 0.7.17) and Picard (version 2.23.0), respectively . ThereafSingle nucleotide variations (SNVs) and insertions/deletions (indels) were identified using VarDict (version 1.5.1) and FreeBayes (version 1.2.0) programs, and functional annotation of genetic variants was performed by ANNOVAR assay. To identify somatic SNVs and indels, matched white blood cell from each patients was used to filter the germline variants, sequencing artifacts and clonal hematopoiesis. Somatic genetic alterations including SNVs and indels were selected with the following filters: 1) those located in intergenic regions or intronic regions; 2) synonymous SNVs; 3) those with a minor allele frequency of >= 0.002 in database Exome Aggregation Consortum (ExAC) and genomad; 4) those with a variant allele frequency (VAF) of <0.003 in tumor tissue, plasma, pericardial effusion supernatant, pericardial effusion cell sediment, and PE supernatant; 5) strand bias for genetic alterations in the reads; 6) the number of supporting reads for a variation was <2; and 7) depth was <30x . The cnvp values <0.05 were regarded as statistically significant unless otherwise specified.The coincidence rate of altered genes between the two groups of samples was defined as / * 100%. Statistical analyses were performed using R (version 3.6.3) or scipy. stats (version 1.3.1), statsmodels (version 0.10.1) and scikit_posthocs (version 0.6.7) packages in python (version 3.7.4). Fisher\u2019s exact test was performed to evaluate differences between the proportions. Differences between multiple groups were compared using the Kruskal\u2013Wallis test, and a comparison of two matched groups was made by post-hoc analyses using the Dunn\u2019s test. Paired wilcoxon test was used to compare difference between paired samples of two groups. All the tests were two-sided, and We compared the genetic alteration profiles among tumor tissue, plasma cfDNA, pericardial effusion-cfDNA, pericardial effusion-sDNA, and PE-cfDNA from 26 advanced NSCLC patients. As shown in EGFR (54%), TP53 (50%), MLH1 (35%), KRAS (23%), MTOR (15%), MSH6 (15%), MSH2 (15%), IDH1 (15%), DICER1 (15%), CTNNB1 (15%), ATM (15%), FLT3 (12%), ARID1A (12%), EP300 (12%), CDKN2A (12%), PIK3C2G (12%), PTEN (12%), and AMER1 (12%). Among them, 4 genes including TP53, CTNNB1, ARID1A, and AMER1 were altered simultaneously in paired pericardial effusion-cfDNA and pericardial effusion-sDNA. In addition, the coincidence rate of altered genes EGFR, DICER1, FLT3, CDKN2A, PIK3C2G, KRAS, IDH1 and ATM between pericardial effusion-cfDNA and pericardial effusion-sDNA ranged from 50% (50% included) to 100%. Notably, genetic alterations of MLH1 and MSH2 were detected exclusively in pericardial effusion-cfDNA or pericardial effusion-sDNA.We further analyzed the consistence and difference of altered genes between pericardial effusion-sDNA and pericardial effusion-cfDNA. As illustrated in MET amplification (27%), EGFR L858R (19%), EGFR T790M (15%), EGFR E746_A750delELREA , EGFR L861Q (8%), KRAS G12C (8%), EML4-ALK (exon 18: exon 20) fusion (4%), EML4-ALK (exon 20: exon 20) fusion (4%), EML4-ALK (exon 6: exon 20) fusion (4%), and ERBB2 Y772_A755dupYVMA (4%). Among them, EGFR T790M, EGFR E746_A750delELREA, EGFR L861Q, KRAS G12C, EML4-ALK (exon 18: exon 20) fusion, EML4-ALK (exon 20: exon 20) fusion, and ERBB2 Y772_A755dupYVMA were detected in both pericardial effusion-cfDNA and pericardial effusion-sDNA. Meanwhile, EGFR L858R and MET amplification remained a modest consistence (40\u201380%) between paired pericardial effusion-cfDNA and pericardial effusion-sDNA. On the contrary, EML4-ALK (exon 6: exon 20) were found only in pericardial effusion-sDNA. All these data indicated that pericardial effusion-cfDNA and pericardial effusion-sDNA are complementary for detecting altered genes and actionable alterations in the advanced NSCLC patients.As depicted in Given the difference and overlap of detected genetic alterations between pericardial effusion-cfDNA and pericardial effusion-sDNA, we combined the variations of pericardial effusion-cfDNA and the corresponding sDNA in subsequent comparisons with other sample types.IDH1, TP53, CDK4, EP300, EPHA3, MAP3K1, PRDM1, and RBM10 displayed a 100% coincidence rate of genetic alteration between pericardial effusion and paired tumor tissue, while KRAS, CDK8, DOT1L, and EGFR had a coincidence rate of 50% or more. In addition, NF1 was found to have a coincidence rate of 33%. Notably, 16 genes were differentially altered in the tumor tissue and pericardial effusion. As illustrated in MET amplification (33 vs. 0%), EGFR C797S (17 vs. 0%), EGFR E746_A750delELREA (17 vs. 17%), EGFR T790M (17 vs. 17%), EML4-ALK (exon 20: exon 20) fusion (17 vs. 17%), and KRAS G12C (17 vs. 17%). Among the actionable alterations, MET amplification exhibited the highest population frequency, while EGFR E746_A750delELREA, EGFR T790M, EML4-ALK (exon 20: exon 20) fusion, and KRAS G12C displayed a 100% consistency between the tumor tissue and pericardial effusions. Besides, MET amplification and EGFR C797S were detected only in the tumor tissues. The patient (pt26) carrying the EGFR C797S alteration had both EGFR 19del and EGFR T790M alterations detected, consistent with the patient\u2019s history of treatment with icotinib and osimertinib.Among the 26 advanced NSCLC patients with pericardial effusion, 6 had paired primary tumor tissues. As shown in p = 0.016) of altered genes and the genetic alteration rate (p = 0.043) were significantly increased in pericardial effusion compared with plasma cfDNA. We next examined actionable alterations from paired plasma cfDNA and pericardial effusion. As illustrated in EGFR E746_A750delELREA (12 vs. 12%), EGFR T790M (12 vs. 19%), EML4-ALK (exon 18: exon 20) fusion (6 vs. 6%), EML4-ALK (exon 6: exon 20) fusion (6 vs. 6%), KRAS G12C (6 vs. 12%), MET amplification (6 vs. 19%), EGFR L858R (0 vs. 6%), and ERBB2 Y772_A755dupYVMA (0 vs. 6%). Clearly, pericardial effusion harbored a higher number of actionable alterations than the corresponding plasma cfDNA with a certain trend toward significance (p = 0.08) (p = 0.16) . Moreove = 0.16) . Besides = 0.16) . TogetheEML4-ALK (exon 20: exon 20) fusion (20 vs. 20%), ERBB2 Y772_A755dupYVMA (20 vs. 20%), KRAS G12C (20 vs. 20%), VCL-NTRK2 (exon 14: exon 17) fusion (20 vs. 0%), EGFR L861Q (0 vs. 20%), and MET amplification (0 vs. 20%). Among the 6 actionable alterations, EML4-ALK (exon 20: exon 20) fusion, ERBB2 Y772_A755dupYVMA and KRAS G12C showed a consistency of 100% between PE-cfDNA and pericardial effusion. Moreover, we identified EGFR L861Q and MET amplification as two unique actionable alterations in pericardial effusion, suggesting that NGS sequencing on pericardial effusion could lead to identification of advanced NSCLC patients who are qualified for TKI based therapy. Notably, 3 out of the 6 actionable alterations were found to harbor SNVs/indels, including EGFR L861Q, ERBB2 Y772_A755dupYVMA and KRAS G12C. Among the 3 actionable alterations with SNVs/indels, 2 (66.7%) (EGFR L861Q and KRAS G12C) had a higher VAF in pericardial effusion compared with PE-cfDNA is a better source of tissue-derived gene alterations than plasma cfDNA . Paired PE-cfDNA .As a non-invasive method, liquid biopsy has been used in clinical practice for monitoring the tumor treatment efficacy and occurrence of drug resistance . Plasma-Pericardial effusion is among liquid biopsy specimens for detection of genetic variants. In this study, we compared the genetic alteration profiles between tumor tissue and pericardial effusion from the NSCLC patients and found that both shared and unique altered genes were detected in each specimen. This finding indicates that pericardial effusion harbors unique altered genes that were absent in matched tumor tissues, suggesting that pericardial effusion is representative of the tumor heterogeneity in NSCLC. Moreover, we observed a 57.1% (4/7) coincidence rate of actionable alterations between pericardial effusion and tumor tissue, indicating that pericardial effusion could be an alternative source of tumor-derived DNAs for genetic alteration profiling and for guiding targeted therapy as well as a fluid biopsy sample.The present study showed that compared with plasma, pericardial effusion had a greater capability for detecting altered genes and actionable alterations. Although plasma can be used to guide targeted therapy in NSCLC patients whose tumor tissue is not accessible for biopsy, plasma cfDNA accounts for only approximately 0.01% of tumor cfDNA . In thisMultiple studies have shown that PE-cfDNA is superior to plasma as a liquid biopsy specimen. In these cases, a more comprehensive genetic alteration profile was detected in PE-cfDNA as compared to plasma samples . MoreoveThere were still several limitations in this study. First, the sample size needs to be increased to obtain results with a high confidence. Second, lack of detailed treatment history and follow up of patients prevented us from evaluating and comparing therapeutic outcomes among the different treatment options based on pericardial effusion, plasma cfDNA or PE-cfDNA.Among liquid biopsy specimens from the advanced NSCLC patients, pericardial effusion could be a better candidate for genomic profiling than plasma cfDNA, while it may serve as a complement to PE-cfDNA in detecting actionable alterations."} +{"text": "To determine the epidemiology of human parainfluenza virus in homeless shelters during the COVID-19 pandemic, we analyzed data and sequences from respiratory specimens collected in 23 shelters in Washington, USA, during 2019\u20132021. Two clusters in children were genetically similar by shelter of origin. Shelter-specific interventions are needed to reduce these infections. Human parainfluenza virus (HPIV) contributes to acute respiratory tract infection burden in young children . We analyzed the data descriptively by using SAS software version 9.4 (https://www.sas.com).We tested samples by using a TaqMan reverse transcription PCR platform that included influenza virus , respiratory syncytial virus, HPIV , and sub>1 chronic condition) Figure 1ndition) Table 2.Six of 32 encounters involved viral co-infections with HPIV . Participants with HPIV infection reported symptoms at 25 (78%) encounters. Commonly reported symptoms included rhinorrhea (95%), cough (74%), sore throat (53%), and subjective fevers (47%) Table 3.Of 32 HPIV-positive specimens, we identified 3 of the 4 HPIV serotypes: 10 HPIV-1, 11 HPIV-3, and 5 HPIV-4. Six specimens were untypeable. Sequencing of 16 specimens generated 11 sequences from 6 shelters . HPIV-1 Respiratory viruses are increasingly appreciated as major pathogens in homeless shelters (The pediatric HPIV-3 cases illustrate the need for mitigation guidance to reduce intrashelter HPIV transmission, particularly because younger children have higher upper respiratory tract viral levels than older persons (Additional information on human parainfluenza virus in homeless shelters before and during the COVID-19 pandemic, Washington, USA."} +{"text": "In US nursing homes, 2% of residents have documentation of suicidal ideation (SI). Whether older residents\u2019 health profiles differ by SI is unknown. Using the 9th Patient Health Questionnaire-9 (PHQ-9) item on Minimum Data Set 3.0, we identified 15,277 older residents with and 562,184 without SI. Latent class analysis using frailty, cognitive impairment, palliative care index, pain, and remaining PHQ-9 items as indicators identified health profiles by at-admission SI and estimated the association between profiles and SI at 90 days. In residents with at-admission SI, four profiles emerged: (1) frail, intact/moderate cognitive impairment, all depressive symptoms ; (2) frail, moderate/severe pain, depressed mood, sleep problems, fatigue (32.2%); (3) frail, severe cognitive impairment, depressed mood, fatigue, feelings of worthlessness (22.9%); (4) pre-frail, moderate/severe cognitive impairment, depressed mood (22.0%). Compared to the residents in profile 4, those in profile 1 and those in profile 2 were more likely to continue reporting SI at 90 days. In residents without at-admission SI, three profiles emerged: (1) frail, depressed mood, fatigue (33.9%); (2) frail, severe cognitive impairment (38.1%); (3) prefrail/frail (28.0%). Residents in profile 1 were more while those in profile 2 were less likely profile 1 residents to report SI at 90 days. Findings indicate substantial heterogeneity in the health profiles between and within older residents with and without self-reported SI."} +{"text": "Ten GWAS-important for KOA SNPs of eight candidate genes were studied. To assess the link between SNPs and KOA susceptibility, logistic regression (to establish independent SNP effects) and MB-MDR (to identify SNP\u2013SNP interactions) were used. As a result of this genetic analysis, the associations of individual SNPs with KOA have not been proven. Eight loci out of ten tested SNPs interacted with each other (within twelve genetic models) and determined susceptibility to KOA. The greatest contribution to the disease development were made by three polymorphisms/genes such as rs6976 (C>T) GLT8D1, rs56116847 (G>A) SBNO1, rs6499244 (T>A) NFAT5 (each was included in 2/3 [8 out 12] KOA-responsible genetic interaction models). A two-locus epistatic interaction of rs56116847 (G >A) SBNO1 \u00d7 rs6499244 (T>A) NFAT5 determined the maximum percentage (0.86%) of KOA entropy. KOA-associated SNPs are regulatory polymorphisms that affect the expression/splicing level, epigenetic modification of 72 genes in KOA-pathogenetically significant organs such as skeletal muscles, tibial arteries/nerves, thyroid, adipose tissue, etc. These putative KOA-effector genes are mainly involved in the organization/activity of the exoribonuclease complex and antigen processing/presentation pathways. In conclusion, KOA susceptibility among Europeans of Russia is mediated by intergenic interactions (but not the main effects) of GWAS-important SNPs.This study was conducted to examine the associations between genome-wide association studies (GWAS)-important single nucleotide polymorphisms (SNPs) and knee osteoarthritis (KOA) among Europeans of Russia. The present replicative study (\u201cpatient-control\u201d design has been used) was carried out on 1000 DNA samples from KOA ( Osteoarthritis (OA) is a common chronic degenerative joint disease , resultip < 5 \u00d7 10\u22128) KOA-responsible genetic interaction models). The highest Wald index was in a four\u2013level genetic model: rs6499244 (T>A) NFAT5 \u00d7 rs56116847 (G>A) SBNO1 \u00d7 rs6976 (C>T) GLT8D1 \u00d7 rs2820443 (T>C) LYPLAL1 was found for some SNPs genotypic combinations such as TT(rs6499244)NFAT5 \u00d7 AG(rs56116847)SBNO1 \u00d7 CT(rs6976)GLT8D1, TT(rs6499244)NFAT5 x AG(rs56116847)SBNO1 \u00d7 AG(rs11177)GNL3, TT(rs6499244)NFAT5 \u00d7 AG(rs56116847)SBNO1 \u00d7 CT(rs6976)GLT8D1 xTT(rs2820443)LYPLAL1, TT(rs6499244)NFAT5 \u00d7 AG(rs56116847)SBNO1 \u00d7 AG(rs11177)GNL3 \u00d7 TT(rs2820443)LYPLAL1, TT(rs6499244)NFAT5 \u00d7 AG(rs56116847)SBNO1 \u00d7 AG(rs11177)GNL3 \u00d7 CT(rs6976)GLT8D1 factors . The gre LYPLAL1 . Very im6)GLT8D1 .SBNO1 and rs6499244 (T>A) NFAT5 possessed a strong KOA effect (registering the maximum KOA entropy percentage-0.86%).Five of the investigated 315 SNPs were missense loci leading to amino acid substitutions in the GNL3 , SPCS1 , NEC4 and SBNO1 proteins. The above changes were predicted to be tolerated (SIFT tools information) and benign , and only Pro>Ala replacement at position 225 in NEC4 protein (rs1029871) was possibly damaging ) . Epigenetic modification of DNA regions near eighteen genes can be caused by eight KOA-involved SNPs and 292 loci out of 309 in LD SNPs (94.50%) due to the regulation of the activity of enhancers and promoters , communication of specific DNA sites with protein-regulators and factors that promote the transcription process by changing the structure of chromatin . LYPLAL1 (rs2820436 and rs2820443), GNL3 (rs11177), GLT8D1 (rs6976), WWP2 (rs34195470) and NFAT5 (rs6499244) were localized in the enhancer DNA regions at chondrocyte cell culture (E049(Epigenome ID)/STRM.CHON.MRW.DR.MSC(Mnemonic)), primary osteoblast cells (E129(Epigenome ID)/BONE.OSTEO(Mnemonic)); loci of LYPLAL1 (rs2820443), GNL3 (rs11177) and GLT8D1 (rs6976) genes have been positioned in the adipocytes promoter sites (E023(Epigenome ID)/FAT.MSC.DR.ADIP(Mnemonic)); specific nucleotide changes of GNL3 (rs11177), GLT8D1 (rs6976) and SBNO1 (rs56116847) genes were situated in the enhancer positions of peripheral blood T helper cells (E043(Epigenome ID)/BLD.CD4.CD25M.TPC(Mnemonic)).It is important to underline that almost all KOA-associated polymorphic variants (with the exception of rs1060105) and a majority of strongly-linked loci exhibit their outstanding epigenetic effects in KOA-impact cell cultures and tissues such as primary osteoblast cells, chondrocytes, adipocytes, etc. For example, SNPs of genes such as SBNO1, rs11177 GNL3, rs6499244 NFAT5, rs6976 GLT8D1) .The four KOA-associated loci (rs1060105 GLT8D1) and 70 h GLT8D1) were modABCB9, ALAS1, ARL6IP4, C12orf65, CCDC62, CDK2AP1, CLEC18A, CLEC18C, COG4, DNAH1, EXOSC6, GLT8D1, GLYCTK, GLYCTK-AS1, GNL3, IL34, ITIH1, ITIH4, KMT5A, LYPLAL1-AS1, MPHOSPH9, MUSTN1, NEK4, NFAT5, NOB1, NPIPB14P, NQO1, NT5DC2, OGFOD2, PBRM1, PDXDC2P, PITPNM2, POC1A, PPM1M, PRKCD, RFT1, RILPL2, RIMKLBP2, RP11-168J18.6, RP11-282O18.3, RP11-296I10.3, RP11-392O17.1, RP11-394B2.1, RP11-394B2.5, RP11-546D6.3, RP11-894J14.2, RP11-972P1.11, RP5-1157M23.2, RP5-966M1.5, RP5-966M1.7, SBNO1, SERBP1P3, SFMBT1, SLC30A10, SMG1P7, SMIM4, SPCS1, TMEM110, WDR82, WWP2, ZC3H11B) (Changes in the gene quantitative traits (transcription and splicing) in different organs due to the allele-specific effects of the eight studied SNPs and high-LD loci (283 out 309 SNPs [91.59%]) have been detected as potential predictors of KOA. In total, the 61 genes transcription (ZC3H11B) and 24 g0, WWP2) may be cSTIMATE-MUSTN1, STIMATE\u2013TMEM110, STIMATE\u2013MUSTN1, MRC1\u2013STAB1, ARID2\u2013PBRM1, NQO2\u2013NQO1 (indicators of weight were 0.71\u20130.86) .GNL3, rs1060105 SBNO1, rs2820436 and rs2820443 LYPLAL1, rs56116847 SBNO1, rs6976 GLT8D1, rs6499244 NFAT5 and rs34195470 WWP2). The greatest contribution to the KOA susceptibility was made by the three polymorphisms/genes rs6499244 (T>A) NFAT5, rs6976 (C>T) GLT8D1, and rs56116847 (G>A) SBNO1 (each was included in 2/3 [8 out 12] KOA-responsible genetic interaction models). The associations between individual SNPs and KOA predisposition have not been supported. The present \u201cpatient-control\u201d study demonstrated that KOA susceptibility among Europeans of Russia can be caused by intergenic interactions of eight GWAS-important SNPs (rs11177 NFAT5. For rs6499244 NFAT5 (located on chromosome 16q22.1), in silico data indicated its pronounced functional actions by influences on enhancer sequences in chondrocytes (E049(Epigenome ID)/STRM.CHON.MRW.DR.MSC(Mnemonic)), primary osteoblast cells (E129(Epigenome ID)/BONE.OSTEO(Mnemonic)), primary T-regulatory and T-helper cells of peripheral blood (E044(Epigenome ID)/BLD.CD4.CD25.CD127M.TREGPC(Mnemonic) and E043(Epigenome ID)/BLD.CD4.CD25M.TPC(Mnemonic), respectively), fat nuclei (E063(Epigenome ID)/FAT.ADIP.NUC(Mnemonic)), promoter sites in fat nuclei (E063(Epigenome ID)/FAT.ADIP.NUC(Mnemonic)), transcriptional levels of 10 genes , and transcript alternative splicing of four genes in the skeletal muscles, fatty tissue, thyroid gland, and other KOA-related organs. In a previous GWAS, the causal link between rs6499244 (T>A) NFAT5 and KOA risk was shown [NFAT5 (r2 = 0.91), with an increased level of DNA methylation in the WWP2 gene in patients with OA [PDXDC2P, CLEC18A, NOB1, NFAT5, IL34 [nuclear factor gene of activated T cells 5 (NFAT5) encodes a transcription factor that manages the quantitative expression traits of genes implicated in the regulation of osmoprotective and inflammatory reactions [NFAT5 in the formation of innate immunity by activating gene expression in macrophages during TLR (Toll-like receptor) ligation [NFAT5 also plays an important role in the proliferation of synoviocytes themselves [NFAT5 expression was found in the synovial membrane [NFAT5 indirectly affects the migration of myoblasts during skeletal muscle myogenesis via the CYR61-dependent pathway [The outcome of this work demonstrated involvement in the KOA genetic architecture of rs6499244 (T>A) as shown . The potas shown ,72,73. Reactions ,75,76,77ligation ,79. TLR2ligation . NFAT5 aemselves . A highemembrane . NFAT5 i pathway . Transcr pathway ,84,85.SBNO1 as a KOA risk locus were first established by Tachmazidou et al. in GWAS on samples of European origin from UK Biobank and Arthritis Research UK Osteoarthritis Genetics (arcOGEN) [NFAT5, makes the greatest contribution to KOA susceptibility (0.86% of the disease entropy) among Europeans of Russia. The literature data indicate a serious epigenetic potential (relationship with the level of methylation in cartilage) of the locus rs56116847 (G>A) SBNO1 [ABCB9, ARL6IP4, C12orf65, CDK2AP1, KMT5A, MPHOSPH9, OGFOD2 and RILPL2) and sQTL of four genes in fibroblasts cell culture, tibial nerve, skeletal muscles, whole blood, etc. The KMT5A gene is closely related to the regulation of various biological processes such as DNA replication, chromosome condensation and activation of DNA replication checkpoints, cell proliferation, etc. [KMT5A regulates the transcription of Ras, p53 and Wnt genes [Wnt is well known for its participation in osteogenesis due to activation of the signaling pathways such as Wnt/calcium, Wnt/cyclic adenosine monophosphate (cAMP), Wnt/c-Jun NH(2)-terminal protein kinase (JNK) and Wnt/\u03b2-catenin [ERa plays responsible role in cartilage degradation [KMT5A in the proliferation and metastasis of osteosarcoma cells through the transmission of \u03b2-catenin signals is also known [The data for rs56116847 (G>A) arcOGEN) . AccordiA) SBNO1 . The infnt genes ,88,89. F-catenin . ERa plaso known .GLT8D1 locus in the KOA-important intergenic interactions among Europeans of Russia. The rs6976 GLT8D1 association with OA was shown in three previously-published GWAS in Europeans [GLT8D1 with KOA in Europeans [GLT8D1 and one of the statistical models of the shape of the proximal femur in patients with hip OA of European origin was shown [GLT8D1 is functionally significant when associated with active enhancers in chondrocyte cell culture (E049(Epigenome ID)/STRM.CHON.MRW.DR.MSC(Mnemonic)), primary osteoblast cells (E129(Epigenome ID)/BONE.OSTEO(Mnemonic)), in skeletal muscle microtubule cells (E121(Epigenome ID)/MUS.HSMMT(Mnemonic)), and active promoters in adipocytes (E023(Epigenome ID)/FAT.MSC.DR.ADIP(Mnemonic)) and chondrocytes (E049(Epigenome ID)/STRM.CHON.MRW.DR.MSC(Mnemonic)). The rs6976 (C>T) GLT8D1 locus is linked to four non-synonymous SNPs , which determine amino acid modification in three proteins such as GNL3 , SPCS1 (Pro41Ala) and NEC4 (Pro225Ala). The SNP rs6976 studied by us is associated with the expression/splicing parameters of 28 genes in the tibial artery/nerve, skeletal muscles, thyroid gland, adipose tissue, etc. The data about rs6976 as a functional-impact locus were previously presented in other sources [GLT8D1 was found to be associated with a lower level of methylation in the STAB1 gene in the cartilage of OA patients [SPCS1 (rs6617) and GNL3 (rs11177), which are strongly coupled with rs6976 GLT8D1, with a significant imbalance of gene expression in cartilage and other joint tissues such as ligaments, meniscus, adipose tissue, synovial membrane, were shown [GNL3 with the OA risk in both European and Asian populations [p \u2264 5 \u00d7 10\u22128) [We have identified the most substantial contribution of the rs6976 (C>T) uropeans ,32,35. Huropeans ,92 and ouropeans of signiuropeans , Africanuropeans and Euroas shown . In accoas shown ,96. Accoulations ,32,99, i \u00d7 10\u22128) ,32.GLT8D1 gene, located in the 3p21.1 region, encodes a protein from the glycosyltransferase family. Glycosyltransferases are a family of enzymes that catalyze the biosynthesis of oligosaccharides, polysaccharides and glycoconjugates [GLT8D1 gene and its corresponding protein. The GNL3 gene encodes a guanine-nucleotide-binding protein (nucleostemin), which plays an important role in many processes occurring in the cell, including participation in stem cell proliferation, regulation of the cell cycle, maintenance of telomerase activity [GNL3 is expressed in mesenchymal stem cells, from which chondrocytes originate [GNL3 gene expression in synovial tissue/fluid samples was significantly higher in the group of patients with primary OA compared with the control cohort [The njugates . To dateactivity ,102,103.riginate , shows ariginate . In a stl cohort . The nucl cohort .This study has certain limitations, which include the following: (a) only ten SNP of KOA candidate genes have been studied in the work and the inclusion of more loci in the analysis may cause a \u201cshift\u201d in the estimates of the intergenic interactions role of the examined loci in the formation of KOA; (b) the results of this work were not replicated on another sample from the same population or samples of another ethnic group; (c) this study did not take into account all possible risk factors for KOA and, accordingly, their effects as covariates were not taken into account when evaluating associations; and (d) much broader experimental evidence of the functional effects of SNPs determining susceptibility to KOA is required (only in silico data were used in this work).In the current study it has been revealed that the KOA susceptibility among Europeans of Russia is mediated by intergenic interactions (but not the independent effects) of GWAS-important SNPs."} +{"text": "There is little published research analysing the relationship between \u03b2-lactams with differing bacterial PBP targets and how they can be manipulated in combinations with respect to clinical or microbiological (e.g. resistance) outcomes and E. coli strains of variable resistance in vitro. This included fully susceptible isolates, ESBL producers and carbapenemase producers (CPEs). For each of 10 antibiotics, the MIC was determined individually, and subsequently in combination with 9 further antibiotics, using the MTS\u2122 \u2018cross\u2019 synergy method .We systematically explored the relationship between double \u03b2-lactam therapy combinations against seven Overall, 86/630 (13.6%) of all combinations tested showed synergy and 408/630 (64.8%) were additive; 136/630 (21.6%) combinations showed indifference. Of the 86 \u2018bug\u2013drug\u2019 combinations that showed synergy, 42/86 (49%) included ceftazidime/avibactam, representing 42/126 (33%) of all ceftazidime/avibactam-based combinations tested, and 56/86 (65%) of synergistic combinations covered PBP2. Synergy was most commonly detected in ESBL producers and less frequently seen in CPEs and fully susceptible isolates . Additive effects were seen in 92/180 (51%) combinations versus ESBLs, compared with 18/90 (20%) in CPEs, versus 154/180 (86%) in fully susceptible isolates. No antagonism was identified with any antibiotic combination.In the combinations tested, synergy or additive effects were common (78%); similar to our previous work with fosfomycin/\u03b2-lactam combinations (89%), but higher than we found with fosfomycin/non-\u03b2-lactam combinations (28%). Many of the synergistic bug\u2013drug combinations identified contained a \u03b2-lactam inhibitor as a partner and/or provided PBP2 activity. This provisionally suggests a role for PBP2 in synergy, although the presence of a \u03b2-lactamase inhibitor may also be important. Confirmation using an alternative method and mechanistic elucidation is required. The clinical/microbiological importance of such effects remains unclear."} +{"text": "Since sinonasal intestinal-type adenocarcinomas (ITAC) show resemblance to colorectal adenocarcinomas, we aimed to investigate novel prognostic factors of outcome, with particular focus on the role of tumor budding (TB). Retrospective clinico-pathological single-institution study on consecutive ITAC patients between 1996 and 2020. Histopathological parameters including conventional subtypes and TB features were evaluated with the aid of pancytokeratin (AE1/AE3) immunohistochemical staining. Parameters were correlated to clinical data and outcome. A total of 31 ITAC patients were included. Overall, 19/31 patients (61.3%) presented with stage III/IV disease. Presence of lymph node or distant metastases was rare . Treatment protocols consisted of tumor resection in 30/31 patients (96.8%) and primary radiochemotherapy in 1/31 patient (3.2%). Adjuvant radiation therapy was conducted in 20/30 surgically treated patients (66.7%). The 3- and 5-year overall survival (OS) was 83.9% and 78.3% and the 3- and 5-years disease-specific survival (DSS) 83.7% % and 78.5%, respectively. The presence of intermediate/high TB (defined as\u2009\u2265\u20095 buds) was associated with both, worse DSS (log rank p\u2009=\u20090.03) and OS (log rank p\u2009=\u20090.006). No patient with low TB revealed progressive disease or died of the disease. No association between TB and tumor stage or conventional tumor subtype was found. Tumor budding seems to be an independent prognostic factor of worse outcome in ITAC. Intestinal-type sinonasal adenocarcinoma (ITAC) is a rare epithelial sinonasal tract malignancy and accounts for approximately 8\u201325% of all sinonasal cancers . TherebyWhile ITACs most frequently involve the nasoethmoidal complex including the posterior ethmoidal cells, the middle turbinate, the posterior-superior septum, the ethmoidal roof and the cribriform plate, involvement of the maxillary sinus is rare . More prRecently, tumor budding (TB), a known risk factor in particular for colorectal carcinoma (CRC), but also certain head and neck cancer subtypes , 15\u201320, This study received ethical approval from the Ethical Committee of the Canton of Zurich, Switzerland . We retrospectively reviewed a consecutive cohort of treatment-na\u00efve ITAC patients, treated at the department of otorhinolaryngology/head and neck surgery at the University Hospital of Zurich (Switzerland), between January 1996 and July 2020. Patients with documented denial to contribute personal health-related data were not included. Included patients from 01/2016 signed a written consent for the use of their material and data. Tumors were staged according to the eight edition of American Joint Committee on Cancer staging system. As described earlier, all patients underwent endoscopic biopsy and exploration of the tumor under general anesthesia . TreatmeThe following patient data and tumor data were collected: age, gender, exposition to occupational carcinogens , initial clinical classification , tumor stage (stage I\u2013IV) based on clinical and radiological assessment. Treatment protocols consisted of either (1) surgical tumor resection\u2009\u00b1\u2009postoperative radiation therapy (RT) in intensity-modulated technique (IMRT) or (2) primary radiochemotherapy. Surgical procedures were classified as (1) transnasal endoscopic resection, (2) cranioendoscopic resection (combination of endoscopic and open approach) or (3) open craniofacial resection . Surgica2) using a three-tiered-system as low (0\u20134 buds), intermediate (5\u20139 buds) and high (\u2265\u200910 buds) , DAKO A/S; Cytokeratin 7, 1:100 [monoclonal] OV-TL 12/30, DAKO A/S; Cytokeratin 20, Prediluted [monoclonal] SP33, Ventana-Roche; CDX2 Protein, prediluted [monoclonal] EPR2764Y, Ventana-Roche; Mouse monoclonal anti-SATB homeobox 2, 1:100 [monoclonal] EP281, BIO-SCIENCE Products AG (Biochemica\u2009+\u2009Diagnostica); MutL homolog 1, 1:40 [mono-clonal] Es05, Novocastra Laboratories Ltd; Mouse anti-human PMS2, 1:100 [monoclonal], A16-4 PharMingen (Becton Dickinson), MSH2 1:100 [monoclonal] G219-1129, Cell Marque Lifescreen Ltd; MSH6 (SP93), 1:30 [monoclonal] SP93, Cell Marque Lifescreen Ltd.The normality of distribution was checked using the Kolmogorov\u2013Smirnov test. Data are either presented as median and interquartile range (IQR) or as mean\u2009\u00b1\u2009standard deviation (SD), depending on the distribution of data. Differences among the low TB and intermediate/high TB group regarding the distribution of achievement of CR, tumor stage and Barnes subtype were calculated using contingency tables and Fisher\u2019s exact test. For time-to-event-analysis only patients treated in curative intention were included. Regarding the presence of TB, patients were stratified in low-TB (0\u20134 buds) vs. intermediate/high TB (\u2265\u20095 buds). Disease free survival (DFS) was defined as time from completed primary treatment until relapse any site or death from all causes and included only patients, who achieved CR after initial treatment. Overall survival (OS) was defined from initial diagnosis until death from any cause or last follow-up, while disease specific survival (DSS) was defined from initial diagnosis until death of disease or last follow-up (patients with death of other causes were excluded). Kaplan-Meyer estimates with calculation of log rank statistics were performed to present OS, DSS and DFS and to compare between sub-groups. The end of follow-up was March 2021. A p-value less than 0.05 indicated significance. Statistics used SPSS version 22 .In total, 31 ITAC patients were included . Mean age at initial diagnosis was 66\u00a0years (\u00b1\u200913). In 20/31 patients (64.5%), the past medical history revealed an exposition to wood dust, while in 1/31 patient (3.2%) an exposition to leather dust was observed. Table Primary treatment protocols consisted of either surgical tumor resection in 30/31 patients (96.8%) or primary radiochemotherapy in 1/31 patient (3.2%). The surgical approach was transnasal endoscopic in 24/30 patients , cranioendoscopic in 2/30 patients (6.7%) and craniofacial in 4/30 patients (13.3%). Surgical margins, based on the histopathological workup and intraoperative assessment of the surgeon, were documented as follows: R0 18/30 patients (60%), R1 3/30 patients (10%), R2 4/30 patients (13.3%), not determinable according to surgeon in 5/30 patients (16.7%). Of all 30 surgically treated patients, 20/30 patients (66.7%) underwent adjuvant radiation therapy.Overall, CR after primary treatment protocols was achieved in 26/31 patients (83.9%), while 5/31 patients (16.1%) showed progressive/persistent disease. Among all 26 patients with CR, a total of 7 recurrences were observed during the follow-up period. This translates into a recurrence rate of 26.9%, with isolated local recurrence in 6/7 patients and combined loco-regional recurrence with synchronous distant metastases (DM) in 1/7 patient.Among all patients who achieved CR, median DFS was 39\u00a0months . The 3- and 5-year OS was 83.9% and 78.3% and the 3- and 5-years DSS 83.7% % and 78.5%, respectively. The 3- and 5-year DFS was 77.9% and 69.9%.The median follow-up duration was 39\u00a0months . At last follow-up, 18/31 patients (58.1%) were alive without disease, 2/31 patients (6.5%) were alive with disease, 6/31 patients (19.4%) died of the disease and 5/31 patients (16.1%) died of other causes.Barnes subtypes of our cohort was rated as solid in 3/31 patients (9.7%), colonic in 11/31 patients (35.5%), mucinous in 7/31 patients 22.6%), papillary in 6/31 patients (19.4%) and mixed in 4/31 patients (12.8%) . Unequivocal bone invasion was seen in 16/31 patients (51.6%). Signet ring cells were present in 9/31 patients (29%). Based on Kaplan Meyer estimates, no significant difference with regard to OS or DSS for presence of (1) signet ring cells, (2) presence of stromal infiltration (yes vs. no) or (3) presence of bone invasion (yes vs. no) was observed.Determination of TB was applicable in 22/31 patients (71.0%). Thereof, 12/22 patients (54.5%) revealed a low TB (0\u20134 buds), 6/22 patients (27.2%) intermediate TB (5\u20139 buds) and 4/22 (18.2%) patients high TB (\u2265\u200910 buds) evaluated for Cytokeratin 7, 7/16 patients (43.8%) showed either negative or positive staining, while 2/16 patients (12.5%) revealed only focal positivity. However, all the tested 16 patients were consistently positive for Cytokeratin 20. Overall, 20/31 patients (64.5%) were stained for CDX2, all with a positive result. Furthermore, SATB2 was performed on 9/31 patients (29.05), of which 7/9 patients (77.8%) showed a diffuse positive result, while one patient was negative (11.1%) and another presented with focal positivity (11.1%). In total, 9/31 patients (29.0%) were tested for DNA MMR proteins and showed no sign of loss of any of the markers MLH1, PMS2, MSH2 or MSH6, indicating no evidence of microsatellite instability.In this retrospective clinico-pathological study on ITAC patients at a tertiary referral center, we found the presence of intermediate/high TB to be a strong prognostic factor of poor outcome in terms of both, DSS and OS. In contrast to intermediate/high TB, all patients with low TB reached CR after primary treatment protocols and no patient died of disease. However, DFS was not different between low TB and intermediate/high TB patients, indicating that also low TB does not prevent from recurrence. Similar to previous findings and in accordance with CRC, no association between TB and tumor stage or tumor subtype (indicative of grading) was observed.In our study we confirmed ITAC to mainly originate from the nasoethmoidal complex with a strong predominance for the male gender and incidence peaking in the seventh decade , 5, 31. As it was shown previously, ITAC and adenocarcinomas of the intestinal tract show to a great extent morphological similarities, as well as overlapping immunohistochemical expression profile, including typically positive staining for CK20, CDX2, villin, MUC2 and SATB2 , 40, 41.To the best of our knowledge this is only the second study on the role of TB in ITAC patients . SimilarTumor budding seems to be an independent prognostic factor of worse outcome independent of tumor stage and conventional subtype/grading. In order to promote the implementation into daily clinical practice, additional studies need to corroborate these encouraging data."} +{"text": "A. To investigate the nature of liaison psychiatry consultations for COVID-19 patients in a tertiary care hospital in India B. To assess pattern and prevalence of mental health disorders and management, in COVID-19 patients in a tertiary care hospital in India.Retrospective chart-based studyData from medical records of 1600 confirmed COVID-19 patients was studied and charts of 368 patients among that who, during their in-patient stay for COVID-19 treatment in Lourdes Hospital, Kochi (September 2020 - December 2021), received liaison psychiatry consultation was selected for retrospective analysisPsychiatric consultations were sought for 23%(368) patients with COVID-19 (1600) during the study period. The most common symptoms of mental health problems for referral were sleep disturbance (74.9%), agitation/restlessness, increased tension (50.3%), depressive symptoms like low mood, loss of interest (11.1%) and psychotic symptoms like talking to self, hearing voices, suspiciousness (8%). Liaison psychiatry consultation was most sought-after for critically ill patients (69.2%), with disturbed behaviour as the most common presenting complaint. Psychiatric diagnoses included in the spectrum of delirium (39.3%), sleep disorders (33.3%), anxiety (15.5%), depression (7.1%) and psychosis (4.8%). In terms of psychiatric treatments, 95.9% of patients who received psychiatric consultation were treated with psychotropic medications, including non-benzodiazepine sedative-hypnotic agents (54.8%), anti-psychotic (26.2%), benzodiazepines (22.6%) and antidepressant (10.7%). The symptoms of 61% of patients had improved and they were prescribed medications to continue the treatment on discharge.A significant proportion of hospitalized COVID-19 patients experienced mental health problems, especially patients in intensive care unit. Data that emerged from this study regarding pattern of mental illness and management options will serve as a template for psychiatrists to liaise with medical teams to treat future patients."} +{"text": "Brucella canis discospondylitis (BDS).To describe the clinical and imaging findings of 33 dogs with B. canis test and spinal diagnostic imaging.33 client owned dogs from four veterinary specialty hospitals within Colorado and Arizona with at least one positive B. canis serology, and diagnostic imaging of 33 dogs with BDS. All imaging was reviewed by a board-certified veterinary neurologist. Radiographs were reviewed by a board-certified veterinary radiologist blinded to MRI and CT findings.Retrospective review of signalment, physical and neurological examination findings, laboratory results, 31/33 (94%) dogs were <5 years old . 21/29 (72%) dogs had signs of nonspecific pain, spinal pain, or lameness for >3 months . Fever was seen in only 4/28 (14%) dogs. Multifocal lesions were evident on radiographs in 21/29 (72%) dogs and MRI in 12/18 (67%) dogs. Smooth, round, central end-plate lysis, defined as \u201chole punch\u201d lesions, were identified radiographically in 25/29 (86%) dogs. Vertebral physitis or spondylitis without discitis was evident on MRI in 7/18 (39%) dogs.B. canis.Dogs with BDS typically present at a young age with a long duration of clinical signs. Identification of radiographic \u201chole punch\u201d lesions and MRI evidence of vertebral physitis, spondylitis, and paravertebral inflammation without discitis should increase suspicion for BDS. BDS may be increasing in frequency in the southwestern United States, and dogs with signs of chronic spinal pain and/or lameness should be screened for Staphylococcus spp being the most frequently isolated organism (Brucella canis (B. canis), a gram-negative coccobacillus, is the primary cause of canine brucellosis and can result in DS (B. canis has a worldwide distribution and within the United States is reported most frequently in the southeastern and midwestern states (Discospondylitis (DS) is defined as infection of the intervertebral disc and adjacent endplate, which contains a cartilaginous layer that fuses with the intervertebral disc and a bony endplate that attaches to the vertebrae. Discospondylitis is most commonly bacterial, with organism \u20135. Brucelt in DS , 7. Bruclt in DS \u201314. B. cn states \u201311, 15.Risk for DS increases with age, with the greatest risk in dogs >10 years old , 16\u201318. B. canis isolation rate of 8.9\u201310% in dogs with DS , 23. TraBrucella canis alone was cultured from urine or blood and/or a positive result was obtained on 2ME-RSAT and/or cytoplasmic antigen AGID which have a reported 100% specificity , Arizona (n = 6), New Mexico (n = 4), Colorado (n = 2), Mexico (n = 2), Nebraska (n = 1), and a Native American reservation of an unknown location (n = 1). Two BDS littermates originating from Texas were from the same litter (adopted by different families). Nine dogs lived in Arizona and 24 dogs lived in Colorado at the time of diagnosis.Data describing signalment, origin of adoption, and duration of clinical signs are listed in The duration of clinical signs prior to presentation ranged from 5 days to 4 years , and 21/29 (72%) dogs had chronic signs of 3 months or longer. Three dogs that had clinical signs for 1\u20132 weeks (and documented as such in the duration of signs) had previous episodes of spinal pain in the previous year. Fifteen dogs showed signs of nonspecific pain, spinal pain, or lameness since being adopted as puppies.The BDS population included 22 (67%) males and 11 (33%) females. All dogs were neutered except for one 9-month-old intact female. Breeds included 8 purebred or mixed German Shepherd Dogs, 5 purebred or mixed Laborador Retrievers, 2 purebred or mixed Australian Shepherds, 2 Border Collie mixes, 2 Chow Chow mixes, 1 Bernese Mountain Dog, 1 Siberian Husky mix, 1 Staffordshire Terrier Mix, and 1 Australian Cattle Dog mix. There were 10 other mixed breed dogs of unspecified breed.Size distribution included 1 (3%) small breed dog, 11 (33%) medium breed dogs, 18 (55%) large breed dogs, and 3 (9%) giant breed dogs . The majority of dogs were young with 30/33 (91%) less than 5 years of age and 23/33 (70%) 3 years of age or less .n = 9), thoracolumbar (n = 1), lumbosacral (n = 3) or multifocal (n = 7). Non-specific pain (n = 6) and coxofemoral pain (n = 2) were also noted. Lameness was described as unilateral thoracic limb (n = 3), bilateral thoracic limb (n = 2), unilateral pelvic limb (n = 1) or bilateral pelvic limb (n = 2). Signs of potential systemic infection included uveitis in 1 dog, and generalized lymphadenopathy in 1 dog. No other physical or neurological examination abnormalities were reported.Complete physical, orthopedic, and neurological exams were performed on all dogs. Body temperatures were available for 28 dogs at the time of diagnosis ; only 4/28 (14%) dogs were febrile (T > 102.5 F/39.2 C). Spinal pain was the most common clinical sign and was recorded as cervical . Other mild changes included elevated ALP (n = 2), elevated lipase (n = 1), hyperbilirubinemia (n = 1), and hyperphosphatemia (n = 1).CBC was abnormal in 4/18 (22%) dogs and included a mild neutrophilia in 2 dogs, mild monocytopenia in 1 dog, mild lymphopenia in one dog, and mild thrombocytopenia in 1 dog . The 2 dBrucella canis on a single test in 9 dogs, two tests in 13 dogs, three tests in 10 dogs, and four tests in 1 dog. Urine culture was positive for Brucella canis in 1/16 (6%) dog and negative for all bacteria in 15/16 (94%) dogs. Blood culture was positive for Brucella canis in 13/18 (72%) dogs and negative for Brucella canis in 5/18 (28%) dogs. Culture of the L7-S1 intervertebral disc was acquired intraoperatively in one dog and showed no growth. Brucella 2ME-RSAT (Zoetis D-Tec\u2122 CB) was positive in 6/7 (86%) dogs and inconclusive in 1 dog (with positive AGID), and 2ME-RSAT (Cornell) was positive in 15/15 (100%) dogs. Brucella canis IFA was positive in 13/14 dogs (93%) and negative in 1 dog (with positive 2ME-RSAT and Brucella canis blood culture). AGID was positive in 19/21 (90%) dogs, suspicious in 1 dog (with positive 2-ME RSAT), and negative in 1 dog (with positive 2-ME RSAT and Brucella canis blood culture).Brucellosis diagnostic findings are listed in Aspergillosis antigen (Miravista) was negative in 5/5 dogs. Coccidiodies antibody (Miravista) was negative in 8/8 dogs.Imaging included radiographs alone in 15 dogs, radiographs and MRI in 13 dogs, MRI alone in 4 dogs, and radiographs, MRI, and CT in 1 dog. There were 109 lesions identified on radiographs, 74 lesions on MRI, and 8 lesions on CT.Spinal radiographs were reviewed in 29 dogs and included 18 partial spine studies and 11 complete spine studies. Seven (24%) dogs had a single visible radiographic abnormality, 21 (72%) dogs had multiple (\u22652) radiographic changes, and one dog had no visible radiographic abnormalities. A total of 109 radiographic abnormalities were identified on spinal radiographs. Many were characterized by a round, well-defined, central lucency that affected both vertebral endplates and were termed \u201chole punch\u201d lesions, which were apparent in 25/29 (86%) dogs . More diLocation of radiographic changes included 18/109 (17%) cervical, 1/109 (0.9%) cervicothoracic junction, 26/109 (24%) thoracic, 13/109 (12%) thoracolumbar junction, 41/109 (38%) lumbar, and 10/109 (9%) lumbosacral junction. The most common locations noted radiographically included L1-2 in 14/29 (48%) dogs, T13-L1 in 13/29 (45%) dogs, L2-3 in 12/29 (41%) dogs, T12-13 in 10/29 (34%) dogs, and L7-S1 in 10/29 (34%) dogs. Radiographic changes correlated with the location of spinal pain in all dogs. All dogs with multifocal or nonspecific pain had radiographic abnormalities at multiple sites.MRI was available in 18 dogs and included 11 partial spine studies and 7 complete spine studies. Eighteen dogs had STIR sequences, 14 dogs had T2W sequences, 7 dogs had T1W pre-contrast and 14 dogs had T1W post-contrast imaging. A single lesion was noted in 6/18 (33%) dogs and multiple lesions were noted in 12/18 (67%) dogs. Abnormalities were noted at 74 locations and included 16 (22%) cervical, 25 (34%) thoracic, 8 (11%) thoracolumbar junction, 17 (23%) lumbar, and 8 (11%) lumbo-sacral junction. The most common MRI lesion locations were T13-L1 in 8/18 (44%) dogs, L7-S1 in 8/18 (44%) dogs, L1-2 in 6/18 (33%) dogs and L2-3 6/18 (33%) dogs.The majority of lesions involved the intervertebral disc and vertebral endplates. Focal, well-defined, round lesions affecting the central region of the intervertebral disc and endplate similar to the \u201chole-punch\u201d lesions noted on radiographs were identified in 7/18 (39%) dogs and comprised 27/74 (36%) lesions .Brucella IFA.Several lesions affecting only the bony endplate or vertebral body, determined to represent vertebral physitis or spondylitis without discitis, were apparent in 6/18 (33%) dogs \u2013D. AbnorSTIR, T2W, and T1W-post imaging were available for 18 lesions. Changes to the intervertebral disc space, endplates or vertebral bodies suggestive of DS were most evident on STIR imaging 18/18 (100%) compared to T2W and T1W-post imaging.A total of 8 lesions were identified in the single patient with a CT study; these lesions were also seen on the patient's MRI. Lesions were characterized by disc space narrowing , irregular end-plate lysis , and end-plate sclerosis .In fifteen patients with radiographs and MRI, 21 of 57 (37%) lesions visible on MRI were not identified on blinded radiograph review by a board-certified radiologist. Six of 21 (29%) unidentified lesions were from a single dog with paravertebral inflammatory changes only, making radiographs alone insufficient to diagnose DS. Of the remaining lesions, 10/21 (48%) affected the vertebral body or osseous endplate with minimal change to the intervertebral disc and 2/21 (10%) were subtle hole-punch lesions on MRI. B. canis is not commonly reported had a chronic presentation with a mean duration of clinical signs of 10.1 months compared to previously reported mean durations of 4 months at the longest with DS % had a c, 17. B. to years , 31, 36.to years , blood cto years .n = 2), and 9 months suggesting no correlation between presence of fever and duration of clinical signs.The predominant clinical signs of spinal pain, nonspecific pain, and lameness in dogs with BDS in this study are consistent with other reports of DS , 4. ThreCBC and biochemistry panels are often normal in dogs with DS, and laboratory abnormalities suggestive of systemic inflammation were also uncommon in this group . HyperglB. canis infection. Blood culture is considered gold standard . Addition of 2ME gives a 100% specificity , Brucella PCR, and Brucella canis serology should be considered in young dogs presenting with chronic spinal pain even without radiographic evidence of DS. Advanced imaging, in particular STIR MRI imaging, should be pursued in dogs with suspicion of BDS even when spinal radiographs are normal.This study has the limitations of a retrospective multi-institutional study where information was not documented in all dogs for all data points. Different The original contributions presented in the study are included in the article/CL and EB: house officers and manuscript preparation and review. RW: overseeing clinician, study design, manuscript preparation and review, and corresponding author. CC: a board certified radiologist responsible for imaging review. LS, RP, JS, SE, and KK: board certified neurologists who provided cases and assisted with manuscript review. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Enterococci are the third most common hospital-acquired infection responsible for high morbidity and mortality, and are associated with high-grade vascular infections like infective endocarditis (IE). Our objective of the study is to discuss the outcomes of IE among patients with Enterococcus Bacteremia (EB) using ICD-10 CM codes from the national database.We conducted a retrospective cohort study using the publicly accessible National Inpatient Sample (NIS) database from October 2015 to December 2017. Adult patients ( >/=18), who developed EB were included in the study. SAS 9.4 was used for univariate and multivariate logistic regression analyses.There were a total of 75,465 patients included in the study who developed EB, among them 5440 (7.21%) patients with IE. In this cohort, 3,620 were males and 1,820 females, among them 3,955 (68.2%) were Caucasians, 620 (11.7%) were African Americans, 6,445 (8.80%) were Hispanic, 100 (1.9%) were Asian and 285 (5.4 %) were native Americans with IE. The majority of them were suffering from congestive heart failure (39.0%), valvular disease (22.0%), peripheral vascular disease (14.8%), chronic lung disease (16%) neurological complications (9.2%), diabetes mellitus with complications (13%) renal failure (32%), obesity (11.0%), and/or drug abuse (8%). In-hospital mortality was 13.7% (p< 0.0001), which was most likely due to the underlying co-morbidities, with an average length of stay of 15.8 (7-18) days and an economic burden of 48,850.3 USD in comparison to patients without IE, who had in-hospital mortality 10.9%, average length of stay 13.6 (5-15) days, and economic burden 49,638 (11009-36665) USD. Age-adjusted mortality among the patients with Infective Endocarditis was 1.2 (1.07-1.28).Based on the results from our study, we found that patients with enterococcus bacteremia in appropriate settings should be screened for infective endocarditis to decrease the in-hospital mortality, length of stay, and economic burden.All Authors: No reported disclosures."} +{"text": "Management of pancreaticobiliary malignancy is complex and multi-disciplinary. Decompression of malignant biliary obstruction (MBO) is preferentially achieved with endoscopic retrograde cholangiopancreatography (ERCP) and biliary stent placement. This may improve the quality of life for patients with unresectable disease and improve outcomes in resectable/borderline-resectable disease.To assess quality outcomes in patients undergoing biliary stenting for MBO.This is a retrospective chart audit of patients referred to the University of Alberta Hospital (UAH) for suspected or confirmed MBO. The primary outcome was clinical success (reduction in bilirubin of >50% at 30 days). Secondary outcomes were technical success, type of stent used, need for re-intervention, adverse events (AEs), time from stent placement to surgery or cancer centre assessment, and survival.Between January 2020 and June 2022, 222 patients with a mean age of 70\u00b11 years (range 34-93 years) underwent 290 ERCPs. The cause of MBO was pancreatic cancer in 130 (59%), cholangiocarcinoma in 32 (14%), ampullary cancer in 9 (4%), and others in 51 (23%).Technical success for stent insertion on first ERCP was achieved in 180/222 patients (81%) with only brushings performed in 2. Of the 40 patients (18%) with unsuccessful ERCP, further success was achieved by repeat ERCP (8), percutaneous transhepatic drainage , PTC with rendezvous ERCP (1), surgical decompression (3), and endoscopic ultrasound-guided biliary drainage (1). No biliary drainage was performed in 12 patients. Overall, ERCP with stent insertion was technically successful in 188/222 patients (85%).2 17.4 p<0.05).A total of 233 biliary stents were inserted . Clinical success was achieved in 20/38 patients (53%) with plastic stents and 151/181 patients (83%) with metal stents (\u03a72 20.1 p<0.001).Adverse events were encountered in 33 patients (11%) with stent migration occurring in 8 (3%), cholangitis in 7 (2%), post-ERCP pancreatitis in 7 (2%), post-sphincterotomy bleeding in 4 (1%), and death in 2 (1%). Re-intervention was required in 36 patients (20%) after initial ERCP with successful stent placement. The re-intervention rate was significantly higher with plastic stents than with metal stents after initial ERCP for patients with plastic stents and 248\u00b1 16 days (1-959) for those with metal stents. Survival was significantly worse in patients with unresectable disease vs resectable/borderline-resectable disease , Figure 1.In MBO, metal stents appear to provide significantly better biliary drainage, with less need for re-intervention, but do not appear to be associated with any survival benefit over plastic stents. We hope that this quality assurance project will help in the development of a regional management pathway for optimizing the care of patients presenting with MBO.NoneNone Declared"} +{"text": "Klebsiella pneumoniae (CRKP) is widespread throughout the world, and the mechanisms for the transmission and evolution of major serotypes, ST11-KL47 and ST11-KL64, were analyzed to investigate the global distribution and evolutionary characteristics of ST11 CRKP; (2) Methods: The Pathosystems Resource Integration Center (PATRIC) database was downloaded and all K. pneumoniae from 2011 to 2020 were screened to obtain ST11 CRKP genome assemblies with basic information. The relationship of serotype evolution between KL47 and KL64 was then investigated using statistical and bioinformatic analysis; (3) Results: In total, 386 ST11 CRKP isolates were included for analysis. Blood , respiratory tract , and feces were the major sources of samples. China was the leading country where ST11 CRKP was isolated. KL47 and KL64 were found to be the most prevalent serotypes. ST11-KL64 CRKP [median 78(P25~P75: 72~79.25)] had remarkably more virulence genes than the KL47 [median 63(P25~P75: 63~69)], and the distinction was statistically significant (p < 0.001). A differential comparison of virulence genes between KL47 and KL64 revealed 35 differential virulence genes, including rmpA/rmpA2, iucABCD, iutA, etc. The comparison of the recombination of serotype-determining regions between the two serotypes revealed that KL64 CRKP carried more nucleotide sequences in the CD1-VR2-CD2 region than KL47 CRKP. More nucleotide sequences added approximately 303 base pairs (bp) with higher GC content (58.14%), which might facilitate the evolution of the serotype toward KL64; (4) Conclusions: KL47 and KL64 have become the predominant serotypes of ST11 CRKP. KL64 CRKP carries more virulence genes than KL47 and has increased by approximately 303 bp through recombinant mutations, thus facilitating the evolution of KL47 to KL64. Stricter infection prevention and control measures should be developed to deal with the epidemic transmission of ST11-KL64 CRKP.(1) Objective: ST11 carbapenem-resistant Klebsiella pneumoniae can cause a variety of healthcare-associated infections, including pneumonia, bloodstream infections, and wound or surgical site infections. The frequent use of antibiotics has made it easier for K. pneumoniae to undergo chromosomal changes and develop antibiotic resistance . However, the ST11-KL64 CRKP [median 78(P25~P75: 72~79.25)] had remarkably more virulence genes than the ST11-KL47 CRKP strains [median 63(P25~P75: 63~69)] (p < 0.001). In comparison to ST11-KL64 CRKP [median 3(P25~P75: 3~4)], ST11-KL47 CRKP carried more plasmids [median 4(P25~P75: 3~4)] (p < 0.003) .p < 0.05) of the ST11-KL64 strains carry this gene. More ST11-KL64 strains carry the glf and gnd genes. The entF gene is a cytoplasmic enzyme for making siderophore enterobactin. The glf gene is a capsule biosynthesis gene that is essential for capsule biosynthesis. The gnd gene is a gluconate dehydrogenase gene and has a highly variable nucleotide sequence that plays a facilitating role in virulence evolution. The carriage of gnd and glf in ST11-KL64 strains might play an important role in the evolution of virulence.To determine the differences in virulence genes carried by KL47 and KL64, we examined the 134 virulence genes carried by both ST11-KL47 and ST11-KL64 in the VFDB database. As a result, the proportions of 35 virulence genes were significantly different between the KL47 and KL64 strains ( < 0.05) . The wbbiucABCD and iutA are primarily enriched. Clb is an ICEKp-associated pathogenicity locus that is enriched in three pathways, including transferase activity, transferring acyl groups, phosphopantetheine binding, and ligase activity. The iro, iuc, rmpA, and rmpA2 are loci associated with pathogenic plasmids, and KL64 CRKP strains carry more genes, including Clb, iro, iuc, rmpA, and rmpA2 genes, the difference being statistically significant. It is hypothesized that ST11-KL64 CRKP contains more virulence genes than KL47 due to iron carrier-associated chemical reactions that promote bacterial growth, reproduction, and virulence spread, as well as the pathogenicity locus gene Clb, which plays an important role in virulence evolution. Some studies have confirmed that these genes in ST11-KL64 strains arose during recombination due to the gain or loss of gene clusters involved in heavy metal resistance and mobile genetic elements, as a manifestation of the evolution of ST11-KL47 to ST11-KL64 after a recombination event than KL47 [median 63 (P25~P75: 63~69)]. A comparison of the two serotypes regarding the number of 134 virulence genes carried revealed 35 virulence genes with statistically significant differences, including rmpA/rmpA2, iucABCD, iutA genes, etc., confirming that these virulence genes were differential genes between the two serotypes ST11-KL64 and ST11-KL47, consistent with previous studies [It was found that ST11-KL64 CRKP carried more virulence genes [median 78 than KL47 CRKP, which facilitated the evolution of the serotype toward KL64. The discovery that mobile genetic elements play a role in the evolution of recombination provides a new basis for exploring the evolutionary process of the ST11-KL64 CRKP [In summary, we found that KL47 and KL64 were the main serotypes of ST11 L64 CRKP ."} +{"text": "Leishmania as one of the 17 \u201cneglected diseases\u201d that burden tropical and sub-tropical climate regions with over half a million diagnosed cases each year. Despite this, currently available anti-leishmania drugs have high toxicity and the potential to be made obsolete by parasite drug resistance. We chose to analyze organoselenides for leishmanicidal potential given the reduced toxicity inherent to selenium and the displayed biological activity of organoselenides against Leishmania. Thus, the biological activities of 77 selenoesters and their N-aryl-propanamide derivatives were predicted using robust in silico models of Leishmania infantum, Leishmania amazonensis, Leishmania major, and Leishmania (Viannia) braziliensis. The models identified 28 compounds with >60% probability of demonstrating leishmanicidal activity against L. infantum, and likewise, 26 for L. amazonesis, 25 for L. braziliensis, and 23 for L. major. The in silico prediction of ADMET properties suggests high rates of oral absorption and good bioavailability for these compounds. In the in silico toxicity evaluation, only seven compounds showed signs of toxicity in up to one or two parameters. The methodology was corroborated with the ensuing experimental validation, which evaluated the inhibition of the Promastigote form of the Leishmania species under study. The activity of the molecules was determined by the IC50 value (\u00b5M); IC50 values < 20 \u00b5M indicated better inhibition profiles. Sixteen compounds were synthesized and tested for their activity. Eight molecules presented IC50 values < 20 \u00b5M for at least one of the Leishmania species under study, with compound NC34 presenting the strongest parasite inhibition profile. Furthermore, the methodology used was effective, as many of the compounds with the highest probability of activity were confirmed by the in vitro tests performed.The World Health Organization classifies Leishmania as one of the 17 \u201cneglected diseases\u201d that, burden primarily tropical and sub-tropical climate regions as (2016) (1\u201329). L. amazonensis, L. infantum, L. braziliensis and L. major.Eight classification models were developed to perform the ligand-based virtual screening. The models used Random Forest (FR) algorithms as well as Dragon 7 and VolSThe RF models were evaluated for their predictive capabilities using specificity, sensitivity, positive predictive value (PPV) and negative predictive value (NPV). The performance and robustness of the models were evaluated using the Receiver Operating Characteristic Curve (ROC) and the Mathews Correlation Coefficient (MCC). For both of the descriptors, the cross-validation confirmed the excellent model performance, with a precision higher than 71% in all models developed. The ROC values for the depicted models were no lower than 0.8, and in consideration with the other statistics, the models were considered robust and predictive.N-aryl-propanamide intermediates were then screened to select compounds that are predicted to be active against L. amazonensis, L. infantum, L. major and L. braziliensis.Given these results, the bank of selenium compounds and Consensus analysis was run on the generated models to increase the reliability of the independent model predictions ,52. AfteVNa = Model\u2019s true negative rate a;VNb = Model\u2019s true negative rate b;Pa = Probability of model positive compounds a;Pb = Probability of model positive compounds b.Leishmania amazonensisL. amazonensis was able to predict all but two compounds within the applicability domain (NC63 and NC75). Furthermore, the model classified 39 molecules with a probability of activity above 50%. Selene-ethylenelactamide derivatives NC36 (p = 84%), NC34 (p = 81%), NC53 (p = 81%), NC58 (p = 77%) and NC30 (p = 77%) were selected for leishmanicidal behavior, as well as NC31(p = 77%), NC40 (p = 76%), NC51 (p = 66%), and NC41 (p = 61%).The model built on VolSurf descriptors for p = 73%), NC58 (p = 72%), NC38 (p = 68%), NC37 (p = 68%) and NC42 (p = 63%). NC34, NC40, NC41, NC53, NC36, and NC30 were all above 53% and were also selected for testing due to their ease of availability.The model using Dragon 7.0 descriptors classified 33 molecules with a probability of activity above 50% and featured two molecules above 70%. Outside of these, 17 compounds fell outside the AD. The compounds with the highest activity prediction were NC67 and halogens in the structures.p = 74%), NC34 (p = 72%), NC76 (p = 71%), NC36 (p = 70%) e NC53 (p = 70%). Additionally, NC40, NC30, NC51, NC41, and NC31 showed > 61% probability upon consensus analysis. It is worth noting that molecules with electron-withdrawing groups (EWGs) in the benzene ring closest to the selenium atom (such as molecule NC58) have greater probabilities of activity so long as it did not also have an EWG in the farthest ring. We hypothesize this is due to the lower contribution of aromatic amides in the presence of EWGs.The consensus of these models resulted in 38 molecules with activity above 50%. The strongest candidates within the tested applicability domain were NC58 (Leishmania infantump = 81%), NC77 (p = 77%), NC76 (p = 77%), NC58 (p = 76%) and NC69 (p = 76%). Additionally, NC40 (p = 75%), NC51 (p = 71%), NC53 (p = 71%), NC36 (p = 65%), NC08 (p = 62%), NC19 (p = 61%), as well as NC02, NC01, NC09, NC31, NC07, NC34, and NC30 (55% < p < 59%), were included in the following investigation, due to the ease of obtaining these substances.The model utilizing VolSurf descriptors selected 57 molecules with a probability of activity > 50%, one of which displayed an activity probability above 80%. NC38, NC50, NC63 and NC75 were not within the applicability domain. The most likely molecules were NC66 (p = 82%), NC08 (p = 79%), NC06 (73%), NC05 (p = 72%) and NC03 (71%). In addition to these compounds, high probabilities were recorded for NC07 (59%), NC13 (58%), NC53 (55%), and NC41 (50%).The Dragon 7.0 based models classified 42 molecules as potentially active, with two molecules registering between 80 and 84%. Twenty-two compounds were outside the applicability domain. The most likely compounds comprised, respectively, NC01 (p = 81%), a selenium compound with bulky , more electronegative groups in its structure. The Dragon 7 descriptors, on the other hand, showed greater activity in the compounds of the N-aryl propanamides series, where the compound with the highest probability was NC01 (p = 82%).The two descriptors showed a different classification pattern in this species of Leishmania, and it was observed that for the VolSurf descriptors the molecule with the highest probability was NC66 (p = 74%), NC53 (p = 71%), NC66 (p = 69%), NC31 (p = 68%) e NC51 (p = 68%). Other compounds of interest that were selected to move forward include NC36 (p = 68%), NC34 (p = 67%), NC19 (p = 60%), NCO2 (p = 59%), NC41 (p = 59%), and NC13 (p = 52%). Of the molecules that showed greater probability, all had a group that offered an inductive effect, except NC53, which presented a bromine atom in the ring farthest from the selenium. In this compound, the inductive effect is likely lower due to the high atomic radius of the bromine atom. Electronegative groups in the para position also reduced these inductive effects, and therefore decreased activity (NC51). Except for NC66 (whose inductive effect is decreased by two ortho electron donating groups), it also appears that activity probability increases when the benzene ring closest to the selenium was not substituted.In the consensus model, 55 molecules exceeded 50% probability. The strongest candidates are NC40 . The molecules with the strongest prediction were selene-ethylenelactamide derivatives NC65 (p = 77%), NC28 (p = 75%), NC76 (p = 71%), NC74 (p = 69%) and NC70 (p = 68%), as well as NC51 (p = 58%).For the promastigote form of p = 79%), NC66 (p = 76%), NC49 (p = 75%), NC28 (p = 72%), NC54 (p = 70%)), while 27 compounds were not within the AD. Other compounds selected for testing include NC35 (p = 67%), NC34 (p = 67%), NC40 (p = 67%), NC36 (p = 66%), NC41 (p = 64%), NC51 (p = 64%), NC53 (p = 63%), NC31(p = 63%), and NC30 (p = 62%).The Dragon 7.0 model selected 40 molecules with a probability of activity above 50%. The five highest scoring compounds showed probability above 70% , NC28 (p = 73%), NC66 9 (p = 72%), NC54 (p = 65%) and NC49 (p = 63%). Compounds NC51, NC40, NC53, NC41, and NC13 delivered activity probabilities between 52% and 61% and were therefore also selected for testing.From the consensus model, 25 molecules exceeded 50% activity probability. The molecules with the highest probability were: NC65 (Leishmania majorp = 81%), NC60 (p = 79%), NC63 (p = 78%), NC67 (p = 77%) and NC52 (p = 73%). NC53, NC40, NC36, NC30, and NC31 displayed activity probabilities between 62 and 68%.The model developed using VolSurf descriptors resulted in 24 molecules with an activity probability > 50% and two molecules being excluded due to the AD. The most likely molecules were NC50 (p = 63%), NC62 (p = 63%), NC50 (62%), NC53 (p = 60%), and NC39 (60%) were the compounds with the highest activity. In addition to these compounds, high probabilities were recorded for NC36 (54%), NC30 and NC40 (54%), NC51 (53%), NC31 (52%), as well as NC41 and NC34 (50%). Therefore, these compounds were also selected for synthesis and testing.Using the Dragon7 descriptors, the model classified 37 molecules as potentially active, with five molecules having a probability in the range of 60-63% and the remaining 32 molecules having activity probability above 50%. Seven compounds did not show reliability within the applicability domain. NC52 (p = 81%) presents a bis-benzyl substitution, which refers to the influence of globularity descriptors. With the Dragon 7.0 descriptors, the influence of acid groups with carboxylic acids and amine groups is noticeable, since the compound NC52 (p = 63%) was the most likely in this descriptor set, and delivers values above 60% in VolSurf descriptors.After observing the classification patterns of the models, we noticed the importance of bulky groups in the VolSurf descriptors, since the NC50 molecule (p = 70%), NC52 (p = 67%), NC67 (p = 66%), NC53 (p = 64%) and NC58 (p = 63%). NC40, NC36, NC30, and NC31 (56% < p < 60%) were also included in testing due to their easy obtainment.In the consensus model, a total of 23 molecules showed activity percentages above 50%. The molecules with the highest probability within the applicability domain were: NC50 calculates the weight of descriptor blocks and can provide insight into the most influential descriptors. The LOGS (solubility descriptors), OH2 (descriptors of hydrophilic regions), and SIZE/SHAPE (topology descriptors) were most prominent in this test set.The PCA analysis determined that NC63, NC75, NC15, and NC27 presented structural differences compared to others in the study. The PCA corroborates the data from the CPCA, in which three groups of descriptors from the OH2 block largely explain the variability in the data through the polarity of the analyzed molecules. The most influential descriptors were identified as hydrophilic volume descriptors W1-W8, hydrophilic interaction descriptors IW1-IW4, and hydrophilic capacity descriptors CW1-CW8. Again, further analysis of these results suggests the best-performing molecules have hydrophilic regions and H-bond acceptors.Toxicity is understood to be the inherent ability of a substance to produce harmful effects in a living organism or ecosystem. The toxic risk then, is the probability that the harmful effect, or toxic effect, occurs under the conditions of use of the substance ,54.Compounds with activity probabilities above 60% were evaluated for toxicity in the OSIRIS program. Parameters evaluated included mutagenicity, skin irritability and reproductive toxicity. The results are shown in In addition to evaluating the risk of toxicity, we evaluated the rate of oral absorption and violations of Lipinski\u2019s rule, as shown in \u22121, no more than five hydrogen bond donors or 10 hydrogen bond acceptors, and an Octanol/water partition coefficient (LogP) less than 5 sel50) . This suLeishmania species under study, molecular dynamics simulations were performed with the test compound NC34 to assess the flexibility of the enzyme and the stability of interactions in the presence factors such as solvent, ions, pressure, and temperature. This information is important because it complements the results of docking and the biological tests, in addition to allowing the evaluation of the compounds that remained strongly bound to the studied enzymes in the presence of factors that are found in the host organism. For this, the following enzymes were chosen for analysis: CYP-51 from Leishmania infantum (PDB: 3L4D) (A) and Dihydroorotate Dehydrogenase from Leishmania amazonensis (B). NC34 showed a greater affinity for these proteins, corroborating the previous in silico and in vitro results of a greater inhibition for these two species. Then, the RMSD was calculated for the C\u03b1 atoms of the complexed enzyme and the structures of each ligand, separately.After analyzing the activity potential of the test compound NC34 against the four important For the CYP-51 target (PDB: 3L4D), the analysis of the RMSD metric of the protein A showed L. amazonensis A, it wasTo understand the flexibility of residues and amino acids that contribute to the conformational change in CYP-51 (PDB: 3L4D) A and DihSixteen selene-ethylenelactamides derivatives with the highest probability of antileishmanial activity were prioritized in silico. In addition to elucidating potential binding mechanisms, multiple physicochemical properties were calculated. The screened compounds were predicted to have high oral absorption (>60%), and were largely in accord Lipinski\u2019s rule of five, indicating good bioavailability; only seven compounds showed indications of toxicity in one or even two parameters.N-arylpropanamide derivatives and eight selene-ethylenelactamide compounds), were screened in vitro and all were found to be active against at least one of the four tested forms of Leishmania: Leishmania infantum, Leishmania amazonensis, Leishmania major, and Leishmania (Viannia) braziliensis.Compounds NC01, NC02, NC07, NC08, NC09, NC13, NC18, NC19, NC30, NC31, NC34, NC36, NC40, NC41, NC51, and NC53 through the INOVA/UFPB agency, having been accepted on December 22, 2021 under case number: BR 10 2021 026090 4 and petition: 870210119497."} +{"text": "Correction to: Pediatr Rheumatol 19, 46 (2021)https://doi.org/10.1186/s12969-021-00514-4Results section in Abstract should read as follows: All 35 RCTs reported efficacy while 34/35 provided safety outcomes and 16/35 provided pharmacokinetic data.Table\u00a04 should have IL-1 inhibitor canakinumab 4mg/kg single doseResults section text should be as follows: In march 2020, the FDA has approved all 23 reviewed drugs, including bDMARDs and JAK inhibitors for adult rheumatology, whereas the EMA has approved 22 (Table 6).Following publication of the original article , the aut"} +{"text": "Novel coronavirus disease 2019 (COVID-19) was discovered in December 2019 and has infected more than 80 million people worldwide, and more than 50 million people have achieved a clinical cure. In this study, the pulmonary function results of patients after clinical medicine for three months were reported. To investigate the effect of COVID-19 on lung function in patients. A retrospective analysis was performed on 56 COVID-19-infected patients who were cured after the clinical treatment at Taizhou Public Health Medical Center in Zhejiang Province from January 31, 2020, to March 10, 2020. At discharge and three months after discharge, lung function was measured, including inspiratory vital capacity (IVC), forced vital capacity (FVC), forced expiratory volume in first second (FEV1), forced expiratory volume in first second to inspiratory vital capacity (FEV1/IVC), maximum mid-expiratory flow rate (MEF), peak expiratory flow rate (PEF), and carbon monoxide dispersion (DLCO). P\u2009<\u20090.05). There were 41 patients of normal type (73.2%) and 15 patients of severe type (26.8%). Among the 15 severe patients, 8 patients (53.3%) had ventilation dysfunction at discharge, 9 patients (60%) had small airway dysfunction, 4 patients (26.7%) still had ventilation dysfunction 3\u2009months after discharge, 7 patients (46.7%) had small airway dysfunction, and 10 patients (66.7%) had diffuse dysfunction. Among the 41 common type patients, 14 patients (34.1%) had ventilation dysfunction at discharge, 22 patients (53.7%) had small airway dysfunction, 6 patients (14.6%) still had ventilation dysfunction 3\u2009months after discharge, 17 patients (41.5%) had small airway dysfunction, and 19 patients (46.3%) had diffuse dysfunction. Patients with severe COVID-19 had more pulmonary impairment and improved pulmonary function than normal patients. At discharge, there were 37 patients (66.1%) with pulmonary dysfunction, 22 patients (39.3%) with ventilation dysfunction, 31 cases (55.4%) with small airway dysfunction, and 16 cases (28.6%) with restricted ventilation dysfunction combined with small airway dysfunction. At 3 months after discharge, 24 of the 56 patients still had pulmonary dysfunction and all of them had small airway dysfunction, of which 10 patients (17.9%) were restricted ventilation dysfunction combined with small airway dysfunction. DLCO was measured three months after discharge. Twenty-nine patients (51.8%) had mild to moderate diffuse dysfunction. All pulmonary function indexes of 56 patients recovered gradually after 3 months after release, except FEV1/IVC, and the difference was statistically significant ( COVID-19 infection can cause lung function impairment, manifested as restricted ventilation dysfunction, small airway dysfunction, and diffuse dysfunction. The pulmonary function of most patients was improved 3\u2009months after clinical cure and discharge, and some patients remained with mild to moderate diffuse dysfunction and small airway dysfunction. Since December 2019, COVID-19, first discovered in Wuhan, has rapidly spread to many countries and regions worldwide, and is now a pandemic with high morbidity and mortality that has occurred all over the world , 4. ThisThere have been several recent literature reports \u20138, whichAt present, there are few reports on the recovery of lung function in COVID-19 patients after recovery. So will the infection of COVID-19 patients lead to impaired lung function or even left pulmonary fibrosis? Our study aims at elucidating the effect of novel COVID-19 infection on the lung function of patients and providing clues for the later pulmonary rehabilitation therapy of clinically cured patients with COVID-19.2/FiO2)\u2009\u2264\u2009300; and (3) chest imaging lesion progression [This study retrospectively collected 56 patients with COVID-19 who met the clinical cure criteria after hospitalization in Taizhou Public Health Center of Zhejiang Province from January 31, 2020, to March 10, 2020 ; that isgression within 2All patients were examined for pulmonary function after reaching clinical cure. The detection indexes included inspiratory vital capacity (IVC), forced vital capacity (FVC), forced expiratory volume in 1s (FEV1), and the ratio of forced expiratory volume in the first second to inhaled vital volume FEV1/IVC. The maximum expiratory flow at 25% of vital capacity is denoted by MEF 25, maximum expiratory flow at 50% of vital capacity is denoted by MEF 50, maximum expiratory flow at 75% of vital capacity is denoted by MEF 75, peak expiratory flow is denoted as PEF, and diffusion capacity for carbon monoxide is denoted as DLCO. All of the patients tested for lung function were seated comfortably in separate and enclosed rooms, and were tested for lung function three times, with the highest FEV1 value. Except FEV1/IVC and FEV1/FVC, other pulmonary function indexes were expressed as the percentage of measured values to predicted values. The lung function tester used in this study was Powercube Body BF lung function tester produced by Ganshorn Medizin Ectronic (Germany). All lung function tests were performed by the same technician. All practices are performed and assessed in accordance with the new standards issued by the European Respiratory Society/American Thoracic Society (ERS/ATS) in 2017 , 15. PulAll statistical analyses were carried out using SPSS (v20.0). Categorical variables were described as frequency rates and percentages, and continuous variables were described using mean and median.The median age of 56 patients was 44.13\u2009\u00b1\u200910.15 years , and 50 percent of them were male; 4 patients (7.14%) had a history of smoking; and 2 patients (3.57%) had a history of COPD (chronic obstructive pulmonary disease). There were 41 patients of normal type (73.2%) and 15 patients of severe type (26.8%) .P\u2009<\u20090.05) of the 56 COVID-19 patients had pulmonary dysfunction: 22 (39.3%) showed ventilation dysfunction, including 15 (26.8%) with mild and 7 (12.5%) with moderate, 1 (1.8%) with obstructive ventilation dysfunction, and 21 (37.5%) with restrictive ventilation dysfunction. Thirty-one patients (55.4%) presented small airway dysfunction, of which 16 patients (28.6%) were restricted ventilation dysfunction combined with small airway dysfunction. Three months after discharge, 24 patients (42.9%) remained with pulmonary dysfunction, all of which were presented as small airway dysfunction, and 10 patients (17.9%) were restricted ventilation dysfunction combined with small airway dysfunction. Fifty-six patients with COVID-19 were tested by DLCO 3 months after cure and discharge, 29 patients (51.8%) had diffuse dysfunction, 10 patients (17.9%) had restricted ventilation dysfunction and small airway dysfunction, of which 23 patients (41.1%) had mild diffuse dysfunction, and 6 patients (10.7%) had moderate diffuse dysfunction . Lung fuPulmonary function in mild and severe COVID-19 patients: Among the 15 severe patients, 8 patients (53.3%) had ventilation dysfunction at discharge, 9 patients (60%) had small airway dysfunction, 4 patients (26.7%) still had ventilation dysfunction 3 months after discharge, 7 patients (46.7%) had small airway dysfunction, and 10 patients (66.7%) had diffuse dysfunction. Among the 41 common type patients, 14 patients (34.1%) had ventilation dysfunction at discharge, 22 patients (53.7%) had small airway dysfunction, 6 patients (14.6%) still had ventilation dysfunction 3 months after discharge, 17 patients (41.5%) had small airway dysfunction, and 19 patients (46.3%) had diffuse dysfunction . Lung fuNovel coronavirus has spread around the world and seriously threatened people's safety and health. The pandemic of COVID-19 has posed a significant challenge to the global health service system. The coronavirus is high transmissible with strong pathogenicity, transmitted by respiratory droplets or close contact. With the invasion of the coronavirus in the respiratory tract, the patient could have lung tissue injured directly or get an acute respiratory distress syndrome incurred by the inflammatory immune response, which has a high fatality rate , 18. EveThe sequela of some SARS patients is pulmonary fibrosis . Recent Our research shows that reaction ventilation dysfunction and pulmonary function index of small airway dysfunction IVC, FEV1 and FVC, MEF 25, and MEF 50 recover gradually over time. The lung function of 57% patients recovers well at three months after cured and discharge, which is consistent with a recent study about the lung injury recovery status of the the SARS patients after 15 years . TherefoBecause the detection of lung function is safe, noninvasive, and easy to be accepted by patients, it can be used as an objective indicator for clinical monitoring and evaluation of the pulmonary outcome of COVID-19 patients during recovery. This study shows that COVID-19 patients have pulmonary function impairment after clinical cure and discharge, mainly in dispersion dysfunction and small airway dysfunction. The pulmonary function could be improved gradually over time, and early pulmonary rehabilitation intervention might be helpful to the recovery of pulmonary function."} +{"text": "Pyogenic spondylodiscitis is an infection of the intervertebral disc(s) and/or adjacent vertebrae. It might be associated with epidural involvement. We aimed to study clinical, laboratory and evolutionary features of epidural involvement complicating pyogenic spondylodiscitis.We conducted a retrospective study including patients hospitalized for spondylodiscitis with epidural involvement in the infectious diseases department between 2007 and 2019.Staphylococcus aureus (31.8%). Elevated C-reactive protein levels (81.8%) and accelerated erythrocyte sedimentation rate (63.6%) were noted. Imaging features showed vertebral body osteolysis (81.8%), inflammation of adjacent soft tissue (81.8%), spinal cord compression (40.9%) and psoas abscess (13.6%). Along with medical treatment, immobilisation (72.7%), abscess drainage (13.6%) and surgery (9.1%) were indicated. The disease evolution was favourable in 20 cases (90.9%). Two patients were dead (9.1%). Sequelae were noted in 9 cases (40.9%) represented by back pain (31.8%) and spinal deformity (9.1%).We included 22 patients among whom 16 were males (72.7%). The mean age was 64\u00b111 years. Eleven patients had diabetes mellitus (50%). The onset of the disease was acute in 18 cases (81.8%) and sub-acute in 4 cases (18.2%). The median delay to diagnosis was 4 [2-13] weeks. The revealing symptoms were back pain (95.5%), fever (68.2%) and asthenia (54.5%). Motor deficit was noted in 9 cases (40.9%), sensory deficit in 4 cases (18.2%) and sphincter dysfunction in one case (4.5%). Physical examination revealed spinal tenderness (77.3%), paravertebral tenderness (22.7%) and spinal stiffness (18.2%). Blood cultures were positive in 13 cases (59.1%) represented by Spondylodiscitis complicated with epidural involvement might lead to complications and sequelae if not promptly diagnosed and treated. All Authors: No reported disclosures"} +{"text": "As remdesivir (GS-5734) has become a leading treatment for COVID-19, we sought to assess remdesivir utilization patterns, including utilization of concomitant and supportive therapies, and heterogeneity in treatment approaches.Our retrospective cohort study included hospitalized Veterans with positive COVID-19 PCR tests treated with remdesivir, from 03/2020 through 4/2021. Using exposure mapping of barcode medication administration records and medication dispensings, we assessed other medications received by each patient on each day of remdesivir treatment. Heterogeneity was defined as patterns of treatment (drug & duration) not shared by any other patient.Our study included 13,665 patients with COVID-19 receiving remdesivir. The median time to remdesivir initiation from either positive test or hospital admission was 1 day . The median duration of remdesivir treatment was 5 days (IQR 4-5 days). Median length of hospital stay was 7 days (IQR 4-13). Inpatient mortality was 13.9% and an additional 6.2% of patients died within 90 days of discharge. The most common concomitant and supportive therapies were anticoagulants/antiplatelets , corticosteroids , statins , antibiotics , angiotensin receptor blockers (11.9%) and angiotensin-converting enzyme inhibitors (20.4%), melatonin (29.7%), and aspirin (35.6%). Concomitant utilization of Janus kinase inhibitors (0.5%), interleukin-6 inhibitors (2.4%), and hydroxychloroquine (0.5%) was low. Heterogeneity in concomitant and supportive therapies during remdesivir treatment was 84.6% (68.3% when assessed as drug class/category). Among hospitalized patients with COVID-19 in the national VA Healthcare system receiving remdesivir, remdesivir was initiated early in the admission and substantial heterogeneity was observed in concomitant and supportive therapies during remdesivir treatment.Aisling Caffrey, PhD, Merck (Research Grant or Support)Pfizer (Research Grant or Support)Shionogi, Inc (Research Grant or Support)"} +{"text": "Osteoarticular tuberculosis remains a common disease among which the spine is the most affected site. Less frequently, sacroiliac joint is involved. Its diagnosis is often delayed due to misleading and varied symptoms. The aim of this work was to study the clinical features and the contribution of imaging results in the diagnosis of tuberculous sacroiliitis.We conducted a retrospective study including all patients hospitalized in the infectious disease department for tuberculous sacroiliitis. The diagnosis was based on clinical, laboratory and radiological features.In total, we encountered 12 women with a median age of 51 [39-63] years. Three patients had a family history of tuberculosis (25%). The median diagnostic delay was 155 [48-331] days. The revealing symptoms were lower back pain (75%) and hip pain (25%) associated with fever (83.3%) and weight loss (75%). Reduced mobility was noted in 3 cases (25%). Pulmonary tuberculosis and tuberculous spondylodiscitis were associated with tuberculous sacroiliitis in 5 cases (41.7%) and 4 cases (33.3%), respectively. Tuberculin skin test was positive in 6 cases (50%). Laboratory investigations revealed elevated C-reactive protein levels in 11 cases (91.6%) and accelerated erythrocyte sedimentation rates in 9 cases (75%). Needle biopsy of the sacroiliac joint (41.7%) and soft tissues abscess puncture (16.6%) were performed. Computed tomography scan revealed joint space widening (83.3%), peripheral joint erosions (83.3%) and osteolysis (58.3%). Soft tissue abscesses were noted in 66.7% of the cases. Magnetic resonance imaging was performed in 4 cases (33.3%). Sacroiliac joint was hypointense in T1-weighted images (75%), hyperintense in T2 weighted images (50%) and in STIR images (50%). Bone scintigraphy, performed in 5 cases, revealed hyperfixation of the sacroiliac area (100%). All patients received antitubercular therapy. Percutaneous abscess drainage was indicated in 4 cases (33.3%).Because of its deep localization, the diagnosis of tuberculous sacroiliitis is mainly based on imaging results associated with epidemiological, clinical and laboratory features. Antitubercular therapy initiated promptly leads to recovery.All Authors: No reported disclosures"} +{"text": "In 12 patients (5 COVID-19 and 7 non-COVID-19), AHRF evolved to pediatric acute respiratory distress syndrome (PARDS). All non-COVID-19 patients had severe PARDS, while 3 out of 5 patients in the COVID-19 group had mild or moderate PARDS. Overall Pediatric Intensive Care Medicine (PICU) mortality was 14.3%. Conclusions: Children with AHRF due to SARS-CoV2 infection had fewer comorbidities and better oxygenation than patients with non-COVID-19 AHRF. In this study, progression to severe PARDS was rarely observed in children with COVID-19.Study design: This is a prospective, multicenter, and observational study with the aim of describing physiological characteristics, respiratory management, and outcomes of children with acute hypoxemic respiratory failure (AHRF) from different etiologies receiving invasive mechanical ventilation (IMV) compared with those affected by SARS-CoV-2. Methods and Main Results: Twenty-eight patients met the inclusion criteria: 9 patients with coronavirus disease 2019 (COVID-19) and 19 patients without COVID-19. Non-COVID-19 patients had more pre-existing comorbidities (78.9% vs. 44.4%) than COVID-19 patients. At AHRF onset, non-COVID-19 patients had worse oxygenation (PaO The novel coronavirus disease 2019 (COVID-19) has affected the population around the globe. The first pneumonia cases were reported in Wuhan in December 2019 . Early rAdults with COVID-19 developed acute hypoxemic respiratory failure (AHRF) with an associated high mortality requiring intubation and invasive mechanical ventilation (IMV) ,14,15. HThe present study includes an analysis of children admitted with AHRF and receiving IMV in a Spanish network of Pediatric Intensive Care Units (PICUs) during the first wave (March/April 2020) of the COVID-19 outbreak. As one of the three hardest hit countries in the world with an overwhelming pressure on its health care system, Spain has a population of 47,351,567 inhabitants , and offThis study was approved by the Ethics Committees at Cruces Hospital (PI201935) and Ni\u00f1o Jes\u00fas Hospital (R-0026/19), the coordinating centers, and was adopted by all participating centers as required by Spanish regulations. This study followed the \u201cStrengthening the Reporting of Observational Studies in Epidemiology (STROBE)\u201d guidelines for observational cohort studies Electron2/FiO2 \u2264 300 mmHg (or SpO2/FiO2 \u2264 264 if PaO2 was unavailable and provided that SpO2 \u2264 97%) that remained higher at 48 h [56 mm Hg (43\u201359) vs. 43 (39.5\u201346), p = 0.03) (n = 12), non-COVID-19 patients had greater severity according to PALICC criteria (p = 0.04).Median age was 26 months (P = 0.03) . In pati25\u2013P75 6.1\u20139), median PEEP was 8 cmH2O (P25\u2013P75 6\u20139), and median Pplat and driving pressure were 25.5 (P25\u2013P75 21\u201329) cmH2O and 16 cmH2O (P25\u2013P75 13\u201320.5), respectively were managed with non-invasive ventilation and 28.6% (8/28) received high-flow nasal oxygen. Neuromuscular blockade (NMB) was used in two-thirds of patients within 24 h of enrolment, and two out of three patients received corticosteroids . Other a25\u2013P75 5.5\u201324) with no significant differences between groups (25\u2013P75 12\u201326) and 23.5 (19\u201341) days, respectively. Overall PICU mortality was 14.3% (4/28) and in-hospital mortality was 17.9% (5/28). Probability of survival at 60 days is shown in p = 0.75). Multiple system organ failure was the cause of death in two patients (one COVID-19 patient) and refractory hypoxemia in two patients (one COVID-19 patient); brain death was declared in one patient.Pneumothorax developed in two patients (10.7%), two of them with a VT >8 mL/kg PBW, without differences between groups. Mean ventilator-free days were 19 days , patients with AHRF due to a cause other than COVID-19 were younger and had more comorbidities than COVID-19 patients. However, three patients less than 1 year old in the COVID-19 cohort had severe respiratory compromise. This is consistent with several studies describing the seriousness of COVID-19 in some children. Severe respiratory impairment associated with SARS-CoV-2 infection has been described as more frequent in younger children ,31 similWe found that patients with AHRF caused by non-COVID-19 diseases had worse oxygenation at AHRF onset. We observed confirmed more abnormal ventilatory data, which were maintained throughout the course of mechanical ventilation , which may be explained by the inclusion of two immunocompromised patients with severe ARDS, a comorbidity associated with greater mortality. Overall PICU mortality was 14.3%, but was higher at 25% in patients with PARDS, and was 33% in patients with severe PARDS. These results parallel those reported in other series of pediatric ARDS [Most patients received protective mechanical ventilation strategies with low VT, plateau and driving pressures. We found no significant group differences in relation to outcomes. However, PICU deaths were two-fold higher in the COVID-19 cohort (22% vs. 10.5%, although this difference did not reach significance, ric ARDS . AlthougOur study has limitations that may affect comparisons and generalizability. The major limitation is that our overall patient population is small, despite the fact that the population of Spain is in excess of 47 million people. However, our data are representative of the scenario in Spain, and most likely, in western Europe, during the first couple of months of the pandemic, since 64.3% of children intubated for COVID-19 in Spain during tIn conclusion, in this multicenter prospective study, children with AHRF due to SARS-CoV-2 infection had fewer comorbidities and better oxygenation than patients with non-COVID-19 AHRF. Unlike the adult population, progression to severe ARDS is uncommon."} +{"text": "Correction to: BMC Cancer 21, 1179 (2021)https://doi.org/10.1186/s12885-021-08701-yA small number of references were not inserted in-text correctly. As a result, some in-text citations are not correct for specific statements in our results section on pages 4-5. The corrected version should read as follows:\u201cThere were 58 (54%) studies conducted among adults diagnosed with solid tumours , 25 (23%) studies in haematological cancers and 24 (22%) studies including patients with mixed cancer diagnoses . For the studies in solid tumours, exercise interventions were delivered during cancer treatment in 20 (34%) studies [34-53], during and after treatment in 12 (21%) studies , and entirely after treatment in 26 (45%) studies [65-90]. The most common solid tumour groups investigated were cancers of the colon or rectum , lung , and head and neck . For studies in haematological cancers, 13 (52%) delivered exercise interventions during treatment [91-103], specifically stem-cell transplant or chemotherapy, four (16%) during and after treatment , and eight (32%) after treatment [107-114]. In studies that enrolled adults with mixed cancer diagnoses, seven (29%) of these studies delivered interventions during cancer treatment , six (25%) during and after treatment [121-126], and 11 (46%) after treatment [127-137].\u201dThis in-text error affects downstream citation numbering, including citations in Table One of the studies in Table Following publication of the original article , the autPlease see below for the corrected Table These corrections were typesetting errors and do not influence the results of this article. The publishers apologise for this error. The original article has been"} +{"text": "Antimicrobials used for the treatment and prevention of bacterial infections are mainly released nonmetabolized into the aquatic environment via wastewater. Sometimes, unused therapeutic drugs are released down the drains that could act as selective pressure for the development of resistance. The aim of this study was to assess the bacteriological profile of wastewater in health facilities and determine antibiotic susceptibility patterns of bacterial isolates. A cross-sectional study was conducted from October 1 to December 26, 2020, in health facility wastewater. A total of 128 samples were collected from health facilities for bacteriological analysis and antimicrobial susceptibility testing. S. aureus (16/81 (19.8%)) followed by Klebsiella spp. (15/81 (18.5%)), E. coli (13/81 (16%)), P. aeruginosa (10/81 (12.3%)), Enterobacter spp. (8/81 (9.9%)), Citrobacter spp. (7/81 (8.6%)), coagulase-negative Staphylococcus (5/81 (6.2%)), Salmonella spp. (5/81 (6.2%)), and Shigella spp. (2/81 (2.5%)). A majority of isolates were resistant to ampicillin (62/81 (76.5%)). Only few isolates were resistant to ciprofloxacin (11/81 (13.6%)), chloramphenicol (13/81 (16%)), and kanamycin (8/54 (14.8%)). A majority of bacterial isolates (57/81 (70.4%)) were multidrug resistant (MDR). A total of 128 samples were processed, and 81 bacterial isolates were recovered. The most common bacterial isolates were Wastewater from the health facilities contains antibiotic-resistant including multidrug-resistant bacteria. Therefore, health facility wastewater should be treated by appropriate wastewater treatment before being released into the environment. Medical waste is categorized into pathological waste\u2014body fluids from surgery, infectious waste from laboratories, pharmaceutical waste\u2014out-of-date pharmaceutical products, and chemical wastes\u2014used solvents, disinfectants, pesticides, and diagnostic chemicals, aerosol containers and gas, and open sources used in in vitro diagnosis or nuclear medical therapy . Sewage The amount of antibiotics present in hospitals discharge into effluent results, a selection pressure on bacteria . In addiThe impact of polluted sewage on the surface and groundwater is widely regarded as a serious threat to human health and environment in many developing countries of the world . In EthiA facility-based cross-sectional study was conducted from October to December 2021 at health facilities in Arba Minch, Ethiopia, namely, Arba Minch Hospital, Sikella Health Center, and Secha Health Center.Each sample was collected four times a day from all sites in 250\u2009mL cleaned and sterile microbiological glass bottles containing 0.2\u2009mL of 3% w/v sodium thiosulphate . The samWastewater samples were collected from the septic tank before being released to the open field according to guidelines of wastewater sampling technique . A totalth and 8th (10\u22127and 10\u22128) dilutions of health facility wastewater. Duplicate samples were plated onto MacConkey (MAC) agar, Mannitol Salt Agar (MSA), Pseudomonas agar, and Selenite F Broth and then incubated at 37\u00b0C for 24\u201348 hours. After incubation, based on colony morphology, representative colonies were picked and subcultured on different selective and differential media such as blood agar (BA), MacConkey (MAC) agar, Mannitol Salt agar (MSA), Xylose Lysine Deoxycholate (XLD) agar, and Pseudomonas agar. After obtaining pure colonies and recording important features, isolated organisms were further identified at the species level by biochemical tests [The sample was thoroughly shaken to get a homogeneous mixture before a portion was taken for culture. Serial 10-fold dilutions of wastewater samples were prepared in 0.85% NaCl . Serial dilution was done in order to get pure colonies. The bacteria were cultivated by plating 0.5\u2009ml of each of the desired serial dilutions of the bacterial suspensions, 7al tests .\u03bcg), ciprofloxacin (5\u2009\u03bcg), ampicillin (10\u2009\u03bcg), amoxicillin (25\u2009\u03bcg), doxycycline (30\u2009\u03bcg), gentamycin (10\u2009\u03bcg), erythromycin (15\u2009\u03bcg), tetracycline (30\u2009\u03bcg), chloramphenicol (30\u2009\u03bcg), kanamycin (30\u2009\u03bcg), and ceftazidime (30\u2009\u03bcg). The zones of inhibition were measured, and interpretation was made using the National Committee for Clinical and Laboratory Standards Institute guidelines [The standard Kirby\u2013Bauer disk diffusion method was used to determine the antimicrobial susceptibility profiles of the isolates . Bacteriidelines .Pseudomonas aeruginosa (ATCC 27853), Escherichia coli (ATCC 25922), and Staphylococcus aureus (ATCC 25923) were used.Reagents, culture media, and antimicrobial disks were checked for expiry date, damage, and storage problems. Culture media preparation was made based on the respective manufacturer's instructions. Five percent of media per batch was incubated at 37\u00b0C overnight and observed for bacterial growth. Those media which showed growth were discarded. Control strains T-test, and paired T-test were used to compare means of some parameters. A critical value of 0.05 was used for the inferential statistics.Data were entered, cleaned, and analyzed by using Statistical Package for Social Sciences (SPSS) software version 20.0. One-way ANOVAs, independent Students' S. aureus (16/81 (19.8%)) ) were from Arba Minch Hospital followed by 9/81 (11.1%) bacterial isolates from Sikella Health Center and 6/81 (7.5%) bacterial isolates from Secha Health Center. The most common bacterial isolate was (19.8%)) .A majority of isolates were resistant to ampicillin (62/81 (76.5%)). Only few isolates were resistant to ciprofloxacin (11/81 (13.6%)), chloramphenicol (13/81 (16%)), and kanamycin (8/54 (14.8%)).S. aureus isolates showed resistance to ampicillin (11/16 (68.8%)) and tetracycline (8/16 (50%)), but only few isolates were resistant to ciprofloxacin (3/16 (18.8%)), chloramphenicol (2/16 (12.5%)), ceftazidime (3/16 (18.8%)), and erythromycin (4/16 (25%)). A majority of Klebsiella species showed resistance to ampicillin (13/15 (86.7%)), but only few isolates were resistant to chloramphenicol (2/15 (13.3%)), ciprofloxacin (3/15 (20%)), gentamycin (3/15 (20%)), and kanamycin (3/15(20%)). A majority of E. coli isolates showed resistance to ampicillin (10/13 (76.9%)), but only few isolates were resistant to gentamycin (1/13 (7.7%)), kanamycin (1/13 (7.7%)), and ciprofloxacin (2/13 (15.4%)). A majority of Pseudomonas species showed resistance for ampicillin (8/10 (80%)), but only few isolates were resistant to ciprofloxacin (2/10 (20%)), ceftriaxone (2/10 (20%)), and gentamycin (2/10 (20%)) (see Tables 2A majority of ne (8/16 0%), but A majority of bacterial isolates from Arba Minch Hospital influent wastewater were resistant to ampicillin (33/40 (82.5%)) and tetracycline (16/35 (46%)) see .Salmonella species were 100% resistant to ampicillin, coagulase-negative Staphylococci were found to be 100% resistant to ceftriaxone, and Salmonella species were 50% resistant to ceftriaxone ). Among bacteria isolates from Sikella Health Center effluent wastewater, picillin .Klebsiella species and E. coli were 100% resistant to ampicillin ). Among bacteria isolates from Secha Health Center effluent wastewater, picillin .A majority of bacterial isolates (57/81 (70.4%)) were multidrug resistant (MDR).Staphylococcus aureus were isolated in high number among wastewater samples from the health facilities continuously released to the receiving environment. Detection of E. coli from all sites may be due to the fact that E. coli is one of the commensal organisms commonly available in the gastrointestinal tract of humans and animals. Direct and indirect fecal contamination of wastewater from hospital and health centers can easily contaminate the receiving water bodies with potential pathogenic E. coli as well as multidrug-resistant strains which can horizontally disseminate to other organisms. The same result was observed in Ethiopia as E. coli was detected in high concentration from the effluents of wastewater [S. aureus and P. aeruginosa were recovered from wastewater [Pseudomonas aeruginosa, E. coli, Staphylococcus aureus, and Salmonella species were the predominant bacteria isolated from health facility wastewater. This may be due to inefficient removal of pathogenic bacteria by oxidation pond or admission of a large number of cases with these bacterial infections [In our study, stewater , 15. Anostewater . Similarstewater , Nigeriastewater , 19, Tunstewater , and EthHigh numbers of bacteria were isolated from health facility wastewater samples. This is an indication of poor and inefficient management of wastewater in community health facilities. The absence of health facility wastewater treatment before releasing wastewater into the sewage system may contribute to the dissemination of such multidrug-resistant bacteria from the health facilities to the environment by draining those bacteria into the city sewage pool or directly into the water bodies such as lakes and rivers. The persistence of large amounts of antibiotics in the environment poses a serious threat to the ecosystem as these could enhance resistance in microbes, which may result in an increase in disease burden along with the change in the structure of the microbial community.In our study, a majority of bacterial isolates (70.4%) were multidrug resistant (MDR). A similar study conducted in India showed simultaneous resistance of isolates for ampicillin, combination of ampicillin with clavulanic acid, cotrimoxazole, tetracycline, and cephalosporins first, second, and third generation in the final effluent of the wastewater treatment plant . Health The present study showed that most bacterial isolates from hospital wastewater show a higher rate of resistance than bacterial isolates from health center wastewater. However, other studies reported that a higher rate of resistance in bacterial isolates from the final effluent of the wastewater treatment plant was found , 26. A sAlthough the filter paper is important to filter the microorganisms from the liquid, it helps to easily diagnose the organisms; this study failed to filter the sample due to the lack of the pore membrane.High numbers of drug-resistant including multidrug-resistant bacteria were isolated from health facility wastewater samples. Therefore, health facility wastewater should be treated by an appropriate wastewater treatment plant before being released into the environment to minimize dissemination of pathogenic and potentially pathogenic bacteria to the receiving environment."} +{"text": "New substituted azomethines of benzanthrone with heterocyclic substituents were synthesized by condensation reaction of 3-aminobenzo[de]anthracen-7-one with appropriate aromatic aldehydes. The resulting imines were reduced with sodium borohydride to the corresponding amines, the luminescence of which is more pronounced in comparison with the initial azomethines. The novel benzanthrone derivatives were characterized by NMR, IR, MS, UV/Vis, and fluorescence spectroscopy. The structure of three dyes was studied by the X-ray single crystal structure analysis. The solvent effect on photophysical behaviors of synthesized imines and amines was investigated. The obtained compounds absorb at 420\u2013525 nm, have relatively large Stokes shifts (up to 150 nm in ethanol), and emit at 500\u2013660 nm. The results testify that emission of the studied compounds is sensitive to the solvent polarity, exhibiting negative fluorosolvatochromism for the synthesized azomethines and positive fluorosolvatochromism for the obtained amines. The results obtained indicate that the synthesized compounds are promising as luminescent dyes. Azomethines, imines, anils, or Schiff bases are useful intermediates in the synthesis of important pharmaceutical and biochemical substances due to multifunctional transformations via reductions, condensations, additions, etc. . These sMany heterocyclic Schiff bases show promising physical, chemical, and biological properties. An interest in the exploration of novel heteroaromatic azomethines has undoubtedly been growing due to their proven usefulness as attractive lead structures for the development of catalysts, intermediates in organic synthesis, dyes , pigmentA variety of azomethine derivatives bearing heterocyclic ring have been known to show a wide range of biological activities including antioxidant , antibacToday, luminescent benzanthrone derivatives are used in various fields, such as synthetic and natural fiber dyes, photoconductors, luminophores, fluorescent labels, and probes . The firDespite the previously discovered interesting properties of 3-iminobenzantrone, only a few benzaldehyde derivatives have been synthesized and described in the literature. Benzanthrone azomethines with heterocyclic substituents are not described in the literature at all, but may have interesting physical and chemical properties.In our previous investigations, it was demonstrated that various nitrogen-containing derivatives of benzanthrone have various optical properties with emission in the spectral region from green to red ,26,27,28Since imines are of great interest for the development of new materials, and on the other hand, Schiff bases are relatively rarely used as fluorescent dyes, we decided to prepare such benzanthrone derivatives. Considering our experience in the synthesis of amino, amido, amidino, and azo derivatives of benzanthrone and the good optical properties of them, it was of interest to synthesize new Schiff bases by introducing an azomethine group into the benzanthrone molecule, expanding the system of conjugated double bonds and, thus, increasing the chromophore length. As a result, substances with new photophysical properties can be obtained.2a\u2013f) investigated in the present study have been synthesized by condensation of amine 1 with corresponding heterocyclic aldehydes , C=C (1512\u20131574 cm\u22121), as well as fluctuations of the C\u2013H bond (2924\u20133073 cm\u22121).The identification of prepared substances was realized using IR and NMR spectra. The obtained spectroscopic data fully confirm the structures of the synthesized imines. The infrared spectra of the obtained compounds have characteristic absorption bands: 1592\u20131647 cm1H NMR spectra clearly show a typical multiplet signal of aromatic protons at 6.20\u20139.00 ppm (see 2a) demonstrates singlet signal in a weak field at 12.01 ppm.The ppm see . This mu13C NMR spectra carbonyl group demonstrates typical signal about 182\u2013190 ppm, but aromatic carbon atoms show multiple signals at 110\u2013150 ppm.In 2d) and furan (2e) residues, where the molecular ion was not detected, probably due to low stability of these derivatives. The first peak was identified as 3-aminobenzanthrone ion (m/z 245) in the spectra of these compounds.In the mass spectra of the derivatives obtained, the molecular ion and in some cases ions with M+1 and/or M\u22121 were detected, except for the spectra of derivatives with quinoline (m/z 256), and then the isonitrile ion with further fragmentation to 1-phenylnaphthalene (M = 201) ion, which is usual for benzanthrone derivatives losing C=O and side chains anthracen-7-one (2a), 3-[N-(thiophen-2-ylmethylidene)amino]benzo[de]anthracen-7-one (2e) and 3-[N-(1H-pyrrol-2-ylmethyl)amino]benzo[de]anthracen-7-one (3a) were also confirmed by X-ray diffraction analysis. The studied single crystals were grown in benzene. The data obtained fully confirm that the aromatic part of the benzanthrone molecule is flat.The structures of 3-[N-(1H-pyrrol-2-ylmethylidene)amino]benzobenzo[de]anthracen-7-one (2a).3-+ (89), 321 (100), 292 (14), 265 (8), 239 (6), 227 (12), 201 (18), 200 (22), 161 (14), 147 (16).de]anthracen-7-one (2b).3-[N-(Pyridin-4-ylmethylidene)amino]benzo+ (100), 256 (16), 202 (12), 201 (27), 200 (25).de]anthracen-7-one (2c).3-[N-(Pyridin-2-ylmethylidene)amino]benzo+ (100), 333 (57), 306 (15), 278 (10), 256 (24), 201 (22), 200 (27), 167 (12), 79 (16).de]anthracen-7-one (2d).3-[N-(Quinolin-2-ylmethylidene)amino]benzobenzde]anthracen-7-one (2e).o+ (100), 338 (28), 310 (12), 201 (20), 200 (21).3-[N-(Furan-2-ylmethylidene)amino]benzde]anthracen-7-one (2f).o+ (100), 294 (25), 200 (23), 161 (12).3a\u2013f: Dissolve 0.5 mmol of the corresponding azomethine 2a\u2013f in 15\u201320 mL of dimethylformamide and add 0.5 mmol of NaBH4 in small portions over 15 min. Add 2\u20133 mL of methanol dropwise to the solution prepared at room temperature. Stir the reaction mixture at room temperature in an ultrasonic bath for 5\u20136 h, monitoring the reaction by thin layer chromatography in benzene: acetonitrile 3: 1. The product obtained is precipitated with water, filtered, dried, and recrystallized from chloroform.General Procedure for synthesis of amines H-Pyrrol-2-ylmethyl)amino]benz3-[N-(1de]anthracen-7-one (3a).o+ (22), 322 (100), 321 (95), 201 (24), 200 (23), 161 (12), 146 (12).de]anthracen-7-one (3b).3-[N-(Pyridin-4-ylmethyl)amino]benzo+ (28), 334 (100), 201 (24), 200 (25), 133 (26).de]anthracen-7-one (3b).3-[N-(Pyridin-2-ylmethyl)amino]benzo+ (100), 258 (19), 244 (29), 217 (29), 189 (12).3-[N-(Quinolin-2-ylmethyl)amino]benzde]anthracen-7-one (3d).oanthracen-7-one (3e).3-[N-(Thiophen-2-ylmethyl)amino]benzo+ (40), 244 (10), 217 (12), 97 (100).3-[N-(Furan-2-ylmethyl)amino]benzde]anthracen-7-one (3f).o+ (25), 323 (100), 322 (16), 321 (95), 294 (30), 201 (19), 200 (26), 161 (19).6H6), chloroform (CHCl3), ethyl acetate (EtOAc), acetone, ethanol (EtOH), dimethyl sulfoxide (DMSO), and dimethylformamide (DMF) with concentrations of 10\u22125 M at an ambient temperature in 10 mm quartz cuvettes. All solvents were of p.a. or analytical grade. The absorption spectra were obtained using the UV-visible spectrophotometer SPECORD\u00ae 80 . The fluorescence emission spectra were recorded on a FLSP920 spectrofluorometer in the visible range 450\u2013800 nm. The quantum yields were measured relative to rhodamine 101 as standard.The spectral properties of the investigated compound were measured in benzene , and emit at 500\u2013660 nm. The achieved results testify that emission of the aimed dyes is sensitive to the solvent polarity showing negative fluorosolvatochromism for azomethines and positive fluorosolvatochromism for prepared amines. Fluorescence in the red region of the spectrum provides a high analytical sensitivity of the method, which further expands the possibilities of practical application of the synthesized amines."} +{"text": "Heterogeneous catalysis plays a crucial role in many chemical processes, including advanced organic preparations and the design and synthesis of new organic moieties. Efficient and sustainable catalysts are vital to ecological and fiscal viability. This is why green multicomponent reaction (MCR) approaches have gained prominence. Owing to a broad range of pharmacological applications, pyranopyrazole syntheses have received immense attention. This review aimed to emphasise recent developments in synthesising nitrogen-based fused heterocyclic ring frameworks, exploring diverse recyclable catalysts. The article focused on the synthetic protocols used between 2010 and 2020 using different single, bi- and tri-metallic materials and nanocomposites as reusable catalysts. This review designated the catalysts\u2019 efficacy and activity in product yields, reaction time, and reusability. The MCR green methodologies proved eco-friendly and ideal, with a broad scope that could feasibly lead to advancements in organic synthesis. The strategy of using sustainable green methodologies to synthesise various heterocycles utilising heterogeneous catalysts is a continuously expanding area of interest for researchers and industries ,2,3,4. OOn the other hand, multicomponent reactions (MCRs) have steadily gained significance in synthetic organic chemistry ,17,18,19Heterocycles are important components of many natural materials and are extremely valuable in organic and medicinal chemistry ,43,44,45c]-pyrazoles 1, pyrano-pyrazoles 2, pyrano-pyrazoles 3 and pyrano-pyrazoles 4 single metal-containing, (ii) two-metal containing, (iii) three-metal containing and (iv) with miscellaneous materials and composites as recyclable catalysts.This review focused on the protocols used for synthesis of different 4Several single metal-based as catalysts have been developed as catalysts for carbon-carbon or carbon-heteroatom-making conversions. The cost-effective and eco-friendly supports associated with these metals further enhance their candidacy as one of the most-desired catalysts for medicinal and chemical productions. The appeal of transitioning to metal-catalysed reactions is due to the robust activity and selectivity achievable. Another advantage of MCRs is their potential to utilise mono metal oxide catalysts and composites entirely.These mono metal oxide catalysts are pigeon-holed with the higher surface-to-volume percentages of the active metal species, improving the material\u2019s efficacy. Moreover, highly distributed metal oxide particles are presumed to perform as additional energetic and choosy catalysts more than most materials. Additionally, owing to their extraordinary surface energies, minor particles tend to cumulate easily.c]-pyrazole derivatives (5) from the reaction of different aldehydes\u2014(1) substituted hydrazine (2), malononitrile (3), and 3-oxoproponoate (4)\u2014catalysed by nanosized magnesium oxide (MgO). A total of 50 mg of nanocatalyst performed well in an aqueous medium for 20 min reaction time at room temperature (RT) and afforded 88\u201397% yields of the desired products in the presence of SiO2 supported n-propyl-4-aza-1-azoniabicyclo-[2.2.2]-octane chloride (SB-DABCO). The multicomponent reaction was conducted using various substituted aldehydes (6), different active methylene compounds (7) and 3-methyl-pyrazolone (8) in ethanol as solvent medium (2 kg\u22121). Their protocol offered several benefits including simple handling, greater stability, and an easy workup, and was recyclable up to five runs without loss of catalytic activity. This protocol offered high yields with all three active methylene compounds .Hasaninejada et al. synthesit medium . Excellec]-pyrazoles (13) through a one-step process. The condensation was carried under solvent-free conditions at RT by reacting the substituted aldehydes (10), malononitrile (3), hydrazine hydrate (11) and ethyl acetoacetate (12). Additionally, 0.25 mmol of nano-titania showed excellent product yields (81\u201396%) (Shaterian and co-workers develope(81\u201396%) . The pro2/H14[NaP5W30O110])\u2014as a catalyst by sol-gel approach. The catalyst\u2019s structure was characterised and confirmed by BET and TEM analysis. TEM analysis confirmed nanoparticles with an average size (15\u201350 nm) and BET-specific surface area (175 m2g\u22121). The nano TiO2/H14[NaP5W30O110] material quickly catalysed the three-component reaction of malononitrile (3), aromatic aldehydes (14), 3-methyl-pyrazolinone (8) and 25 mg catalyst, along with ultrasound irradiation at 40 \u00b0C in ethanol solvent medium (c]pyrazoles (15) were synthesised by good-to-excellent yields due to the higher surface area of catalyst particles.Azarifar et al. developet medium . The tarc] pyrazole derivatives (20) and spiro-pyranopyrazoles (21) using uncapped SnO2 quantum dots (QDs). The catalyst was synthesised by solvothermal technique, and the resultant catalyst was confirmed by XRD, TEM and SEM spectroscopy analysis. The XRD, SEM, and TEM analyses revealed that the SnO2 QDs (with an average size of 3.9 nm) had an equally uniform nanoflower spherical shape size (with 100 nm), corresponding to the lattice plane (110). The four-component condensation reaction involved malononitrile (3), substituted hydrazine (16), dialkyl acetylenedicarboxylates (17) and aldehydes (18) or substituted isatins (19) in the aqueous medium. The high Lewis acidic character and surface area of the Sn+4 catalyst (8 mol%) performed well and provided the anticipated target molecules at room temperature for 2.5 h reaction time with excellent yields (89\u201398%) . The catc]-pyrazoles (23). P-XRD, TEM, SEM and BET microscopic spectroscopic analysis validated the structure of the subsequent ZnS nanoparticles. The prepared ZnS nanoparticle\u2019s P-XRD pattern displayed a single-phase hexagonal arrangement with crystallite size (20 nm) and was confirmed with TEM and SEM analysis. Furthermore, the BET spectrum revealed that the nanoparticle specific surface area was (84.71 m2.g\u22121), the pore volume was (0.0865 cc g\u22121) and diameter was (31.11 \u212b). The four-component reaction between aromatic aldehydes (22), hydrazine hydrate (11), ethyl acetoacetate (12), and malononitrile (3) under solvent-free and grinding conditions was efficiently accelerated by ZnS nanoparticles, affording excellent yields (87\u201397%) in 12 min . The composite material and solvent influenced the optimised conditions. The spectroscopic analysis of the prepared [SnS-NPs@AC] specified that the nanoparticles had a homogeneously spherical morphology and were in the range of (40\u201390 nm) and (30\u201370 nm), respectively, which was in agreement with the PXRD (64 nm) outcomes. The multicomponent reaction of 3-methyl-pyrazolinone (8), various aldehydes (24), malononitrile (3) and catalyst in ethanol solvent led to the target compounds at 80 \u00b0C for 25 min reaction time with excellent yields (85\u201391%) . The nanc]-pyrazole derivatives (28) in the presence of amino-functionalised SBA-15 (SBA-Pr-NH2) catalyst. The multicomponent reaction was performed using arylmethlidenemalononitrile (26), phenylhydrazine (27) and ethyl acetoacetate (12) in ethanol at RT for 8 min with excellent yields (80\u201395%) . The pos32) using N-methyl-morpholine N-oxide-doped silver oxide (NMO-Ag2O) catalyst. The condensation reaction was progressed using benzyl halide (29), active methylene compound (30), dialkylacetylenedicarboxylate (31) and hydrazine hydrate (11) in ethanol solvent medium under reflux condition for 1 h reaction time (33) in the presence of a catalyst. It proceeded with Knoevenagel condensation (34). The obtained pyrazolone (35) involved Michael\u2019s addition (36) and was followed by cyclisation (37) to afford target compounds.Beerappa and his colleagues investigion time . The repc]-pyrazoles (39) by applying a recyclable nano-SiO2 catalyst. The nano-silica catalyst was synthesised from the agriculture waste of wheat straw via the sol-gel process. The results indicated that the prepared catalyst comprised a spherical shape with uniform distribution and crystallite size range of 100\u2013200 nm. The BET analysis showed the surface area (215.6 m2 g\u22121), pore volume (0.269 cm3 g\u22121) and pore diameter (7.1 nm) for the catalyst. The multicomponent reaction involved hydrazine hydrate (11), malononitrile (3), aromatic aldehydes (38) and ethyl acetoacetate (12) in water. Additionally, 10 mol% of nanocatalyst showed the best performance and offered 87\u201394% yields for 40 min reaction time at 80 \u00b0C and spiro-pyrano-pyrazoles (44) using a nano SiO2-supported 1,4-diazabicyclo-[2.2.2]-octane (nano SiO2/DABCO) catalyst. The SEM-EDX showed that the synthesised SiO2/DABCO nanomaterial contained C, Cl, N, O and Si elements. The catalyst activity was investigated on the multicomponent reaction of the beta-keto ester (12), substituted hydrazine (40), malononitrile (3) and aldehyde (41) or isatin (42) in the absence of solvent at RT via the grinding method using Fe3O4@L-arginine as a heterogeneous catalyst via one-pot manner. The structure of the prepared nanocatalyst was analysed by P-XRD, FT-IR, SEM and VSM spectroscopy methods. SEM investigation indicated that the catalyst particles were made in circular shapes with an average size of (10\u201315 nm). TEM study confirmed that the morphology and nanoparticle average size (10\u201320 nm) was established by P-XRD analysis. The four-component condensation carried out between the substituted hydrazines (45), \u03b2-keto esters (46), various functional groups substituted isatin (47) and active methylene compound (48) under solvent-free conditions. The use of 8 mol% of nanocatalyst offered excellent yields (86\u201397%) of the target products at room temperature after a 60 min reaction time in the presence of cobalt nanoparticles (CoNPs) as heterogeneous catalyst. The cobalt nanoparticles were prepared from the aqueous extract of zingiber. SEM analysis showed that the morphology and homogeneous nanoparticles had an average size (20\u201350 nm). The EDS investigation affirmed the existence of elements in the prepared catalyst. The condensation reaction was carried out between the hydrazine hydrate (11), malononitrile (3), diethyl acetylenedicarboxylate (50) and substituted aldehydes (51) in an aqueous ethanol medium. The use of 0.005 g of nanocatalyst performed well and afforded excellent yields (83\u201397%) of desired products after a 1 h reaction time at room temperature (Mianai and co-workers reportedperature . Mild rec]-pyrazoles (55), applying ZnO@PEG as a nanocatalyst. Various aromatic aldehydes having electron-donating/electron-withdrawing substituents (54) were reacted with ethyl acetoacetate (12), hydrazine hydrate (11), and 4-nitro phenyl acetonitrile (53) in ethanol under ultrasound-assisted conditions, affording excellent 87\u201397% yields in 15 min . The magnetic catalyst was evaluated for the synthesis of pyrano-pyrazoles (57) through the one-step, multicomponent reaction of 3-methyl-pyrazolone (8), malononitrile (3) and substituted aldehyde (56) in green solvent ethanol at RT. The nanocatalyst performed significantly and afforded excellent product yields (90\u201398%) with less reaction time (30 min) . Heteroa3O4@THAM-SO3H material as a reusable heterogeneous catalyst for the one-pot synthesis of pyrano-pyrazole derivatives (59). The resultant nanocatalyst, Fe3O4@THAM-SO3H, was characterised by spectroscopy systems like FT-IR, P-XRD, TGA, DTA, VSM, FE-SEM, EDS, and TEM analyses. The FESEM and TEM analyses proved that the nanocomposite was spherical and uniform, with good dispersity and average size (14 nm). The multicomponent reaction was carried out between the malononitrile (3), hydrazine hydrate (11), ethyl acetoacetate (12), various aldehydes (58) and 10 mg catalyst in an equal amount of aqueous ethanol solvent media which was prepared via the wet impregnation method. The spherical morphology and the crystallite size (12\u201323 nm) of the catalyst material was established by SEM and TEM investigation. Additionally, N2 adsorption-desorption studies showed the catalyst surface area (194.56 m2/g) and pore volume (0.563 cc/g). The Mn/ZrO2 catalyst was applied for the novel synthesis of two series of pyrano-pyrazoles (62 and 63) from a one-pot, multicomponent reaction of ethyl acetoacetate (12)/dimethylacetylenedicarboxylate (61), malononitrile (3), hydrazine hydrate (11), aryl aldehydes (60) and ethanol (5 mL) solvent under ultrasound irradiation at 80 \u00b0C. Excellent product yields (88\u201398%) were obtained in 10 min reaction time using Mn/ZrO2 catalyst (30 mg) . This rec] pyrazole scaffolds (65) using Preyssler-type hetero polyacid (H14[NaP5W30O110]) as a recyclable catalyst via a one-pot reaction. A multicomponent reaction employed malononitrile (3), a variety of aldehydes (64) and 3-methyl-pyrazolone (8) at refluxing conditions for 60 min. Additionally, 1 mol% of catalyst effectively performed under ethanol or water media, affording excellent yields (85\u201394%) of the target molecules (66), Michael addition (67) and was followed by intramolecular cyclisation (69) to yield the desired product. The catalyst was reused five times with sustainable activity. Excellent yields, reusability, simple workup procedure and green solvents were the primary merits of this protocol.Heravi et al. reportedolecules . Authors2O4), using the simple citric acid complex method. Attributable to its Lewis acidic sites, the catalyst worked efficiently for the synthesis of pyrano-pyrazoles (74 and 75) from the four-component reaction of alkyl nitrile derivatives (70), various hydrazine derivatives (71), dialkyl acetylenedicarboxylate (72 and 73) and ethyl acetoacetate (12) (2O4 gave excellent yields (85\u201397%) in water at 60 \u00b0C for 4 h reaction time. The reaction mechanism proposed that first, a Knoevenagel condensation occurred between hydrazine and ethyl acetoacetate. In the second step, a Michael reaction occurred between malononitrile and diethyl acetylenedicarboxylate, possibly due to Cu2+ active sites. The above two intermediates cyclised together via intramolecular action, facilitated by the Fe3+ Lewis acidic sites and Cu2+ active sites. Unsatisfactory yields (12\u201343%) of the desired products were obtained by the replacement of the ethyl acetoacetate (36) to the dialkyl acetylenedicarboxylate (46). This protocol offered several benefits, such as the simple workup, highly functional group tolerance, avoidance of harmful solvents, eco-friendly conditions, and significant yields.Pradhan et al. synthesiate (12) . Additio3O4@SiO2@(CH2)3-Imidazole-SO3HCl as a magnetic catalyst. Using FT-IR, DTA, TGA, SEM, SEM-EDX, TEM, BET, P-XRD, and ICP analysis, the authors established the prepared catalyst structure. TGA and DTA analyses showed a 2% weight loss and thermal decomposition at 550 \u00b0C in three stages. The presence of nanocatalyst-expected elements, C, Cl, Fe, N, O, S and Si, was confirmed by EDX analysis. The nanocatalyst P-XRD pattern exhibited crystallite size (40 nm), in good agreement with TEM and SEM analysis (12.42\u201357.12 nm). The BET spectrum of nanoparticles showed the specific surface area (129 m2 g\u22121), pore volume (0.281 cc g\u22121) and diameter (8.77 \u212b). The activity of the nanocatalyst was assessed on the three-component reaction of varieties of aldehydes (76), malononitrile (3), and 3-methyl-pyrazolineone (8) to synthesise dihydropyranopyrazole derivatives (77). Remarkably, 85\u201398% of the target yields were obtained under solvent-free conditions with 0.0007 g of catalyst at RT for <90 min as a heterogeneous catalyst and prepared it by the wet impregnation method. The CeO2/ZrO2 catalyst was performed by the synthesis of novel pyranopyrazoles (79) with excellent yields (88\u201398%) in 15 min at RT (3), hydrazine hydrate (11), ethyl acetoacetate (12) and substituted aldehydes (78) in ethanol (5 mL)\u2014was effectively catalysed by 50 mg catalyst. The catalyst was recovered by filtration and recycled for six cycles with sustained efficiency. The protocol offered high atom economy, avoided the use of a column and hazardous chemicals, and boasted a simple workup procedure and swift reaction time.Maddila et al. developein at RT . The fou2, as a recyclable catalyst for the preparation of pyrano-pyrazoles (81) from the four-component reaction between ethyl acetoacetate (12), malononitrile (3), structurally substituted aldehydes (80) and hydrazine hydrate (11). The nanocatalyst performed well with various aldehydes to give 26 dihydropyrano--pyrazole derivatives with excellent yields (78\u201393%) at 70 \u00b0C for 55 min using aqueous ethanol mesoporous catalyst (Fe3O4@FSM-16-SO3H) for the preparation of novel dihydropyrano--pyrazole scaffolds (83). FESEM study showed that the nanoparticles had a spherical morphology with size < 100 nm. The target molecules were prepared by a multicomponent reaction between malononitrile (3), 3-methyl-pyrazolone (8) and aldehydes (82) in the presence of Fe3O4@FSM-16-SO3H (30 mg) in a water-ethanol system in high yields (79\u201389%) for 80 min at reflux condition , 3-methyl-pyrazolinone (8), and aromatic aldehydes (84) leading to pyranopyrazole derivatives (85) progressed well under a solvent-free condition in 120 min at 80 \u00b0C with the aid of a low catalytic amount (0.003 g) of Fe3O4@TiO2@(CH2)3OWO3H via one-pot manner , 387) with nanomagnetic iron material [CoFe2O4] as a reusable catalyst in aqueous solvent was described by Mishra and co-workers -pyrazole analogues (91). The catalyst complex\u2019s core shell was assessed using TGA, FT-IR, SEM-EDX, VSM, and P-XRD analysis. The TEM and SEM analysis revealed a spherical particle distribution and core-shell morphology with average size (80 nm) for the prepared catalyst. Furthermore, the EDX study showed C, Fe, Mo, N, O and Si elements, all of which were homogeneously dispersed in the complex. The one-pot reaction of malononitrile (3), ethyl acetoacetate (12), hydrazine hydrate (11), and substituted aldehydes (90) was successfully catalysed by core-shell catalyst in water for reaction time (20 min) at RT at RT . The mag3PW12O40-loaded, aminated magnetic (Fe3O4@SiO2-EP-NH-HPA) nanocatalyst for the novel preparation of pyrano-pyrazole scaffolds (93) -pyrazole scaffolds (21) under ultrasound irradiation conditions from the reaction between malononitrile (5), different aromatic aldehydes (20) and 3-methyl-pyrazolinone (7) in ethanol medium and tetrahydrobenzo-pyrans (100) using an effective silica-coated magnetic catalyst as a heterogeneous acidic catalyst. FTIR analysis confirmed the presence of NFS-PWA peaks at 807, 888 and 984 cm\u22121, signifiying the effective hold of the PWA on NFS\u2019s surface. Furthermore, TEM and SEM morphology showed that catalyst particles were a regular spherical shape and narrowly dispersed, with sizes ranging from 28 to 97 nm. The nanocatalyst revealed high efficacy in the three-component reaction of 3-methyl-pyrazolineone (8), active methylene compound (96), and various functional groups substituted aldehydes (97) under ethanol solvent conditions. Use of 0.02 g of the nanocatalyst gave superior results (76\u201394%) within a 10 min reaction time at reflux conditions (98) to the 3-methyl-pyrazolineone (8) resulted in the significant yields (80\u201395%) of tetrahydrobenzopyrans (100) with similar reaction conditions after 15 min. The catalyst material showed matching activity for five runs and offered excellent yields of both the tetrahydrobenzopyran and pyranopyrazole derivatives within a short reaction time.Maleki1 et al. demonstrnditions . Further\u03b3-Fe2O3@Cu3Al-LDH-TUD material which showed superior catalytic activity in the synthesis of new dihydropyranopyrazoles (103) from the corresponding 3-methylphenylpyrazolinone (8), malononitrile (3), and substituted aldehyde (101) at 100 \u00b0C for 45 min under solvent-free conditions. SEM, XRD, EDX and FT-IR spectroscopic techniques characterised the configuration of the \u03b3-Fe2O3@Cu3Al-LDH-TUD catalyst. The P-XRD analysis indicated that diffraction peaks at 9\u00b0, 30\u00b0, 35\u00b0, 43\u00b0, 57\u00b0 and 63\u00b0 agreed with \u03b3-Fe2O3@Cu3Al-LDH-TUD catalyst. Further, SEM analysis showed spherical morphology and average particle size (22 nm). Similarly, this protocol proved good with 4-hydroxy coumarin (102) for the preparation of dihydropyrano-chromenes (104) with significant yields (75\u201393%) . The mul108) and spiro-pyrazole] derivatives (109) using meglumine as a biodegradable catalyst. The four-component reaction, comprising malononitrile (3), hydrazine hydrate (11), \u03b2-keto ester (12) and carbonyl compound (106) or isatin (107) in EtOH-H2O solvent in the presence of 10 mol% meglumine at RT, gave excellent yields (85\u201395%) (114), enolate formation (112) in the presence of meglumine from ethyl acetoacetate and hydrazine, Michael type addition (115), intramolecular cyclisation (116) and tautomerisation (117) was suggested, in order to deliver the desired pyranopyrazoles.Guo et al. develope(85\u201395%) . The catc]-pyrazoles (120 and 121) in the presence of Aspergillus niger Lipase (ANL) catalyst. Lipase effectively catalysed the four-component condensation of hydrazine hydrate (11), malononitrile (3), ethyl acetoacetate (12) and aldehyde (118) or ketone (119) in ethanol medium. Use of 20 mg of ANL catalyst resulted in excellent yields (70\u201398%) at 30 \u00b0C for 1 h reaction time (Bora and his research group describeion time . The bioc]-pyrazole derivatives (123). The catalytic performance of BSA was assessed by the four-component reaction between hydrazine hydrate (11), malononitrile (3), ethyl acetoacetate (12) and a wide range of carbonyl compounds (122) in an ethanol system at 45 \u00b0C for 45 min reaction time, obtaining excellent yields (84\u201395%) (H-pyrazol-5(4H)-one as other intermediates via Knoevenagel condensation. Further, Michael addition of 3-methyl-1H-pyrazol-5(4H)-one and olefin facilitated by BSA generated the intermediate. Lastly, the new intermediate was cyclised via intramolecular cyclisation, followed by tautomerisation to afford the target compounds. Recycling investigations showed that the recovered BSA could be reused for up to five runs with similar efficiency.Xingtian and his co-workers effectiv(84\u201395%) . Initialc]-pyrazole scaffolds (125) through the one-pot approach. The multicomponent condensation reaction, involving malononitrile (3), 3-methyl-pyrazolone (8), and varied substituted aldehydes (124) under ethanol medium at reflux conditions, afforded excellent yields (85\u201398%) of the target molecules within a short reaction time (<25 min), employing 10 mol% [Amb]L-prolinate as the catalyst via a one-pot reaction of malononitrile (3), \u03b2-keto ester (12), hydrazine derivatives (127), and carbonyl compounds (126). The reaction in the absence of solvent at 90 \u00b0C for 15 min time afforded excellent (83\u201395%) yields nanocatalyst was synthesised by Safari and co-workers via the silane condensation process . The MMT) yields . All the131) in the presence of sodium dodecyl sulfate (SDS) as a micelle catalyst. The three-component condensation was carried out between the isatin (129), malononitrile (3) and 3-methyl-pyrazol-one (130) under an aqueous medium. A 2.5 mol% of SDS catalyst offered excellent (80\u201391%) yields at RT for 60 min (132) and Michael addition (133), and was followed by cyclisation (134).Devi and her research group reportedr 60 min . The mic4 catalyst for the one-pot synthesis of pyrano-pyrazoles with higher yields (85\u201395%) (137) in a short reaction time (20 min) at 90 \u00b0C (136), ethyl acetoacetate (12), aromatic aldehyde (135), hydrazine hydrate (11) and [DMBSI]HSO4 (0.18 mmol) under solvent-free conditions. The plausible mechanism then proceeded to the resulting tandem reactions\u2014Knoevenagel condensation, Michael addition and cyclisation in sequence\u2014to obtain the target molecules.Farokhian and co-workers developeat 90 \u00b0C . The fouc]-pyrazoles (140) and pyrazolyl-4H-chromene (141) derivatives via the four-component reactions of malononitrile (3), hydrazine hydrate (11), ethyl acetoacetate (12), various aldehydes (138) and water as a medium, at room temperature for 30 min (H-chromenes (141), with excellent yields (86\u201394%) from different salicylaldehydes (139) after 15 min. The catalyst was stable for up to 5 runs with little loss in its activity.Shinde and his research group designedr 30 min . The proc]-pyrazoles (133). The EDX study revealed the catalyst material\u2019s elemental composition as Al, Cd, Cr, Fe, K, Na, S, Si, and Mg. The BET analysis of the K09 catalyst showed the specific surface as 13.8 m2.g\u22121. The one-pot reaction between malononitrile (5), hydrazine hydrate (22), ethyl acetoacetate (36) and aryl aldehydes (132) in ethanol medium gave excellent results (90\u201398% yield) using 0.05 g of K09 catalyst at RT in 20 min catalyst was synthesised by Ali et al. for the creation of novel pyrano-pyrazole derivatives with good-to-excellent yields (78\u201390%) (145) [12), malononitrile (3), hydrazine hydrate (11) and various substituted aldehydes (144) in ethanol at 60 \u00b0C via a one-pot approach (145) . The catapproach . The rea2+ doped Ni-Zn nano ferrite composite (Ni0.5Cu0.3Zn0.2Fe2O4), was designed by Mandle et al. via the sol-gel approach [147) from malononitrile (3), hydrazine hydrate (11), ethyl acetoacetate (12), and various substituted benzaldehydes (146) was catalysed by 20 mg of Ni0.5Cu0.3Zn0.2Fe2O4 catalyst in the presence of ethanol under reflux condition by applying nitrogen-doped graphene oxide (NGO) as a recyclable catalyst. The prepared NGO catalyst\u2019s SEM analysis showed unsystematically-aggregated, narrowly-connected tinny sheets with various morphologies. Further, TEM displayed a well-ordered and distinct sheet and a silk-like morphology. Additionally, HR-XPS analysis strongly demonstrated the presence of multiple types of nitrogens in the NGO catalyst. The condensation reaction involved malononitrile (3), ethyl acetoacetate (12), hydrazine hydrate (11), and various functional groups of substituted aldehydes (148) under solvent-free conditions. Excellent results (80\u201399%) were obtained using 10 mg of NGO catalyst in 2 min through the grinding approach (Ganesan and his co-workers reportedapproach . It is nThis review outlined the increased available selection of recyclable catalyst materials, which are ideal for organic synthesis in general and pyranopyrazoles in particular and are expanding the scope and utility of heterogeneous catalysts. Simultaneously, the assessment of the implementation of multicomponent reactions under green techniques offers good compatibility with sustainable organic syntheses. With many green chemistry principles, the intrinsic features of the MCR approach becomes the foremost device in the synthetic chemist\u2019s toolbox. Nitrogen-based pyranopyrazole compounds are constituents of several natural products with numerous pharmaceutical applications. Thus, these emerging innovative and versatile approaches for synthesising these heterocyclic skeletons have always been challenging and rewarding. This review compiled recent literature, detailing the scope and broader choice of heterogeneous metal-based catalysts available to create the prized fused heterocycles, pyranopyrazoles. In this perspective, we emphasised the efficiency of MCRs as the ideal process for green synthesis. In most of the protocols, the employed catalysts were easily recyclable for successive runs with consistent performance. We sincerely hope this article will help synthetic chemists to develop novel heterogeneous materials and synthetic routes with greater efficiency and sustainability."} +{"text": "We conducted a multi-institutional study in Taiwan and a systematic review of the literature for reports of Guillain-\u200bBarr\u00e9 syndrome after coronavirus disease vaccination. This condition, mostly the classic form and the acute inflammatory demyelinating polyneuropathy subtype, has been reported in 39 cases and has occurred within 2 weeks of vaccine administration. Guillain-Barr\u00e9 syndrome (GBS), an immune-mediated polyradiculoneuropathy with a \u22485% mortality rate, has an incidence worldwide of 0.81\u20131.91 cases/100,000 person-years (https://www.astrazeneca.com) starting March 22, 2021. We included healthcare workers vaccinated during March 22\u2013May 31 and followed them for 30 days after vaccination. We identified GBS cases on the basis of code G610 from the International Classification of Disease, 10th Revision, Clinical Modification, or spontaneous adverse drug reaction reporting systems within the hospitals. Two authors (C.H.W. and S.C.L.) confirmed diagnosis and classification of GBS cases through chart reviews .To summarize clinical features of published cases from literature, we searched PubMed and Embase for reports posted through August 17, 2021, using relevant key terms such as \u201cCOVID-19,\u201d \u201cGuillain-\u200bBarr\u00e9 syndrome,\u201d and \u201cvaccine\u201d with suitable MeSH terms. Two independent reviewers performed the study selection and data extraction; a third-reviewer (S.C.L.) settled any differences between them. We excluded cases with coexisting COVID-19 or preexisting GBS. We included only publications with reports of clinical features related to GBS. We described basic characteristics, laboratory data, pathologic reports, treatment patterns, and prognosis of GBS cases associated with COVID-19 vaccination. The study protocol of this systematic review is published on PROSPERO who received ChAdOx1-S vaccine during the study period. After these 18,257 first-dose and 544 second-dose vaccinations, we identified 1 GBS case after a first dose of ChAdOx1-S vaccine in 1 of the hospitals participating in the study.https://www.pfizer.com), Ad26.COV2.S (1/39) , and CoronaVac (1/39) . The GBS rate after COVID-19 vaccination ranged from 1.8 to 53.2 cases/1 million doses. The initial symptoms of GBS included myalgia (12/39), paraparesis (5/39), quadriparesis (22/39), paresthesia (28/39), and facial palsy (23/39), and symptoms of dysautonomia also were observed during hospitalizations (3/39). The average time from vaccination to symptom onset was 11.3 days. A total of 34 case-patients received lumbar puncture; 30 had manifestations of albuminocytologic dissociation in the cerebrospinal fluid.After a systematic review of published literature , we incl>4 during follow-up or after discharge.On the basis of the clinical diagnostic classification of GBS, we found that most case-patients had the classic form (22/39), followed by bilateral facial palsy with paresthesia (12/39), the paraparetic form (4/39), and GBS\u2013Miller Fisher syndrome overlap variant (1/39). We defined all classic and paraparetic forms of GBS (26/26) as level 1 or 2 on the basis of the Brighton criteria and the acute inflammatory demyelinating polyneuropathy subtype (based on electrodiagnostic features) within 2 weeks of infection or vaccination of COVID-19 vaccination far outweighing the potentially severe adverse events after infection (Additional information about Guillain-\u200bBarr\u00e9 syndrome associated with COVID-19 vaccination."} +{"text": "Several risk factors are known to increase the severity of coronavirus disease 2019 (COVID-19) illness in adults, including age and obesity. Specific comorbidities affecting COVID-19 outcomes in children are less well defined. We performed a retrospective cohort study of overweight and obese (OW) children compared to underweight and normal weight (NW) children with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Children between 2 and 18 years of age who were admitted to Texas Children\u2019s Hospital from April through December of 2020 with a positive SARS-CoV-2 polymerase chain reaction test were included. Asymptomatic patients undergoing surveillance testing for SARS-CoV-2 were excluded. Body mass index (BMI) was calculated using the Centers for Disease Control definition. Demographic and clinical information was obtained from the electronic medical record. Statistical analyses were performed using SAS 9.0. P=0.17). OW children were more likely to have pneumonia than NW children [relative risk1.6 (CI 1.40-2.45)]. An elevated BMI was also associated with an increased risk of requiring oxygen [relative risk 1.4 (CI 1.03-1.96)]. The median length of hospitalization was 4 days for NW versus 5 days for OW children (P=0.6). Admission to the Intensive Care Unit (ICU) was similar between the groups (P=0.7). There was no significant difference in treatments administered to children in the two groups, although there was a trend towards increased steroid (29 (53%) vs 59 (67%), P=0.13) and remdesivir (12 (22%) vs 30 (33%), P=0.14) use in the OW children. Four children in each group died. We identified 145 total children who met inclusion criteria. Fifty-five (38%) children were NW and 90 (62%) children were OW. Demographics and characteristics are shown . Underlying asthma or chronic lung disease was present in 13 (24%) vs 31 (34%) in the NW and OW groups respectively or tracheostomy and home MV(4).For children admitted with symptomatic COVID-19, being overweight or obese was significantly associated with having pneumonia and with requiring oxygen. A difference in ICU admission, length of hospitalization, and mortality was not observed. Obesity prevention along with vaccination efforts may prevent COVID-19 related morbidity in this group. All Authors: No reported disclosures"} +{"text": "Chiral cyclic molecules are some of the most important compounds in nature, and are widely used in the fields of drugs, materials, synthesis, etc. Enantioselective photocatalysis has become a powerful tool for organic synthesis of chiral cyclic molecules. Herein, this review summarized the research progress in the synthesis of chiral cyclic compounds by photocatalytic cycloaddition reaction in the past 5 years, and expounded the reaction conditions, characters, and corresponding proposed mechanism, hoping to guide and promote the development of this field. In recent years, enantioselective photocatalysis has been successfully applied to extensive practical work of organic synthesis ,2,3, proThis review mainly discusses the research progress of enantioselective photocatalysis for constructing chiral cyclic compounds by photo-induced asymmetric cycloaddition reaction in the past 5 years, though some comprehensive contents regarding this topic were reported by the pioneers ,5,6,7,8.1) underwent a triplet sensitized di-\u03c0-methane rearrangement reaction to form 3-cyclopropylquinolones (3) in the presence of a chiral hydrogen bonding sensitizer thioxanthone (2) (1) was associated with a chiral hydrogen bonding sensitizer (2) to form the 1,3-diradical intermediate (1a), which further closed the ring to form the complex (ent-4) or complex (4). Owing to the geometric constraints in complex (1a), generating (ent-4) is expected to decay preferentially. In other words, this process favours formation of (4) while the latter process shows a preference for ent-3a (higher association constant Ka than [3a]), thus reducing the enantioselectivity of the deracemization process. Finally, the major enantiomer 3-cyclopropyl-quinolones (3) were obtained.A ternary ring is a kind of tension ring. It is a very challenging process to construct chiral ternary ring molecules via photocatalysis. There are very few reports on the construction of 3-membered ring by enantioselective photocatalysis in the past five years. In 2019, Bach et al. reported a simple, efficient, and enantioselective route to obtain the cyclopropyl substituted quinolone compounds . Under thone (2) . The rea5) irradiated by blue LED light with Ir(III) photosensitizer (6) to synthesize products (7) in good yields and enantioselectivitiy . Chloro-8) could couple with styrenes (9) to construct diarylcyclobutanes (10) in the presence of Sc(OTf)3, t-BuPybox, and Ru(bpy)32+ upon the irradiation of 23 W CFL (8) initially cooperated with Lewis acid to form the Lewis-acid-bound substrates (11), which could be transform into (11*) via triplet energy transfer by Ru(bpy)32+ under the irradiation of 23 W CFL, then styrenes (9) captured with 1,4-diradical intermediates (12) to produce diarylcyclobutanes (10).Earlier, Yoon et al. developed a new strategy to achieve enantioselective [2+2] photocycloaddition of 2\u2032-hydroxychalcones via Lewis acid-catalyzed triplet energy transfer . Subsequ23 W CFL . The tra13) to synthesize the photocycloaddition products (14) from benzofurans (15) and styrenes (16) upon the irradiation of bule light in good yields and excellent enantioselectivity -\u03b2-methylstyrene and (E)-\u03b2-alkylstyrene. Moreover, the methodology could be applied to prepare benzothiophene as well. The proposed mechanism was conducted as follows. The first step was the cooperation of (15) with the chiral rhodium catalyst to form complex (17), then the complex (17) transformed into (17a) upon the irradiation of blue light, which subsequently underwent intersystem crossing to generate (17b). The intermediates (17b) further combined with alkenes (16) to give the 1,4-biradical intermediates (17c), which closed the ring to furnish the desirable photocycloaddition products (14).In 2018, a new visible-light-activated [2+2] photocycloaddition to asymmetric dearomatization of benzofurans was reported by Meggers et al., using the chiral rhodium Lewis acid catalyst ( 99% ee) 14]. Th. Th13) t18) to synthesize cyclobutanes (19) in good yields and enantioselectivity with olefins (20) induced by visible light (\u03bb = 366 nm) (3 Lewis complex (21) was used as the photocatalyst. 1,1-Disubstituted olefins were well tolerated. A variety of substituents at \u03b2-position of cyclic enones could also participate the reaction with high enantioselectivity. The proposed mechanism was conducted as follows. Initially, (18) cooperated with (21) to form the intermediates (22) which could be transformed into (22a), then (22a) reacted with olefins 20 to give relatively 1,4-diradical intermediates (22b), which released (21) to produce cyclization products (19).In 2018, Bach et al. found an enantioselective [2+2] photocycloaddition reaction of cyclic enones ( 366 nm) 15]. A . A 18) t23) catalyzed photocycloaddition was reported by Bach et al. for the cooperation of olefins (24) with phenanthrene-9-carboxaldehydes (25) in 2018 (26) were afforded with good enantioselectivity upon the irradiation of visible light (\u03bb = 457 nm). Substituents at 3- and 6-positions of phenanthrene-9-carboxaldehydes were well tolerated, but the substituents at 2- and 5-positions could decrease the enantioselectivity somehow. A similar mechanism has been mentioned before cd before .27) to form photocyclization products (28) by utilizing a chiral oxazaborolidine Lewis acid catalyst (29) upon the irradiation of visible light (\u03bb = 366 nm). The photocyclization products were produced well in yields and enantioselectivity 17]. Al. Al27) t30) and styrenes (31) to synthesize the cyclobutane derivatives (32) upon the irradiation of blue LED light, using a new dual catalytic system by merging chiral oxazaborolidine Lewis acid (33) with Ir(III) photocatalyst in 2019 a in 2019 .34) catalyzed carbonyl-olefin [2+2] photocycloaddition of carbonyl substrates (36) and olefins (37) to produce 4-membered ring products (35) with 100 W Hg lamp in good yields and excellent enantioselectivity (36) to form the corresponding complex (38) with TpCu (34), which could be excited to generate (38a). Subsequently, (38a) reacted with olefins (37) to generate oxetanes (35).In 2019, Schmidt et al. disclosed a Cu(I) (>95% ee) [19]. Al39) from \u03b1,\u03b2-unsaturated ketones (40) and olefins (41) via a diamine catalyst (42) upon the diffraction of blue LED light (456 nm) in good yields and enantioselectivity with diamine catalyst (42) to form iminium ion intermediates (43), then the iminium ion intermediates transformed into (43a) upon the irradiation with blue LED light, which underwent photocycloaddition with (41) to form 1,4-biradical intermediates (43b). (43b) closed the ring and gave cyclobutyl iminium ions (43c) which could further release the desirable products (39) and finish a catalytic cycle.In 2020, Alem\u00e1n et al. reported a novel enantioselective catalytic [2+2] cycloaddition to generate cyclobutanes (\u201391% er) [20]. TF3(PF6)2) and a chiral secondary amine catalyst (44) to synthesize cyclobutanecarbaldehydes (45) from \u03b1,\u03b2-unsaturated aldehydes (46) and olefins (47) upon the irradiation of visible light (\u03bb = 458 nm) in moderate to good yields and enantioselectivity (46) reacted with chiral amine catalyst to form eniminium ions (48), which could transform into the triplet intermediates (48a) through energy transfer from ruthenium catalyst at assistance of light. Subsequently, the addition of intermediates (48a) to olefins (47) generated 1,4-diradical intermediates (48b), which underwent intersystem crossing and hydrolysis to give the desired products (45) from (48c).Bach et al. found a co-catalytic system with ruthenium catalyst (Ru(bpz)\u201396% er) 21]. A . A 3(PF649). 3-Hydroxyquinolones (50) reacted with maleimide (51) to generate cycloaddition products (52) under the irradiation of blue LED light in excellent yields and enantioselectivity (50) partially combined with the pyrazole of the iridium complex to afford complex (53), which was then transformed into an excited state (53a) under the irradiation of blue LED light. The excited state (53a) reacted with maleimide (51) by bimolecular energy transfer to obtain the complex (53b) and provided cycloaddition products (52) from (53c).Yoon et al. reported a highly enantioselective intermolecular [2+2] photocycloaddition reaction catalyzed by chiral hydrogen bond ion iridium photosensitizer ( 99% ee) 22]. Th. Th49). 54). Under the irradiation of visible light (\u03bb = 420 nm), intramolecular cyclization of 3-alkylquinolones (55) with 4-O-tethered alkenes or allenes occurred to form cycloaddition products (56) in good yields and enantioselectivity (55c) could react with thioxanthraquinones (54) to deliver the complex (57) which gave the quinolone triplet (57a) by energy transfer, then the internal carbon atom of olefin was added to form 1,4-diradical (57b), which underwent intersystem crossing (ISC) to produce (57c) and further gave desired product (56c).Recently, Bach et al. reported an enantioselective photoaddition reaction catalyzed by chiral thioxone (\u201399% ee) 23]. Th. Th54). 58) could be synthesized, using thioxanthone (59) as a chiral catalyst. Under the irradiation of visible light (\u03bb = 420 nm), 3-substituted quinoxalin-2 (1H)-ones (60) and olefins (61), could occur an intermolecular aza Patern\u00f3\u2013B\u00fcchi reaction in good yields and enantioselectivity 24]. Th. Th58) cechanism .62). When phosphoric acid (63) was used as a photocatalyst, cycloaddition products (64) were obtained with good yields and enantioselectivity under the irradiation of visible light (\u03bb > 290 nm) (65) formed by substrate (62b) and phosphoric acid (63) through dual hydrogen bonding, then the olefin moiety on the complex reacted with the enone moiety to form cycloadduct (64b) via photocycloaddition.In 2020, Takagi et al. reported an enantioselective intramolecular [2+2] photocycloaddition of 4-bishomoally-2-quinolones ( 290 nm) 25]. Me. Me62). 66). Under the irradiation of visible light (\u03bb = 459 nm), the reaction could combine N,O-acetals (67) with olefins (68) to form cyclobutanecarbaldehydes (69) in good yields and enantioselectivity , which were combined by the substrates (67) and the catalyst (66).Very recently, Bach et al. reported another enantioselective [2+2] photocycloaddition catalyzed by chiral phosphoric acid (\u201398% ee) 26]. Th. Th66). 71) containing cyclobutane (72) which could easily convert into iminium ions. Under the irradiation of blue light (\u03bb = 459 nm), the modified salicylaldehydes (73) could be successfully obtained in good yields and enantioselectivity photocycloaddition to give the cyclobutyl iminium ions (74c). Finally, the cyclobutyl iminium ions (74c) produced the desired product, (71a).In 2021, Alem\u00e1n et al. reported an intramolecular [2+2] photocycloaddition for the synthesis of polycyclic ethers (lobutane . The rea\u201391% er) . The ena75) to obtain cyclobutane products (76) by asymmetric [2+2] photocycloaddition from \u03b1,\u03b2-unsaturated carbonyl compounds (77) and alkenes (78) in good yields and enantioselectivity 28]. Th. Th75) t79) via a co-catalytic system , iridium photocatalyst (81) and HAT catalyst (82)) to obtain five-membered, six-membered, or seven-membered cyclic aldehydes (83) under the irradiation of blue LED light in good yields and enantioselectivity (79) combined with amine catalyst (80) to afford enamines (84). At the same time, under the irradiation of visible light, enamines (84) formed electrophilic radical (84a) through SET initiated by iridium photocatalyst, which was added to olefins to produce nucleophilic radical (84b). Nucleophilic radical (84b) underwent HAT to generate iminium ions (84c); finally desired products (83) were obtained by releasing amine catalyst (80) from iminium ions (84c).In nature, 5-Membered ring compounds exist widely, and some five-membered heterocyclic compounds, such as furan, pyrrole, and thiophene, are widely used in organic synthesis and have a variety of physiological activities as drugs. In 2017, MacMillan et al. reported an intramolecular \u03b1-alkylation of aldehydes ( 95% ee) 29]. Th. Th79) v85) which was used for enantioselective anti-Markovnikov hydroetherification of alkenols (86) to synthesize five-membered oxygen-containing heterocyclic adducts (87) under the irradiation of bule LED light (\u03bb = 450 nm) in good yields and enantioselectivity . The chiral ion-pair is composed of chiral BINOL-based sodium phosphate and 9-mesityl-10-methylacridinium tetrafluoroborate (86) into radical intermediates (88), radical intermediates (88) combine with chiral phosphate anion to form complex (89), and complex (89) undergo cyclization to yield cyclic adducts (90), which through chiral phosphate anion mediated hydrogen transfer to give desired products (87).In 2017, Luo et al. reported a chiral ion-pair photoredox organocatalyst (roborate 30]. Th. Th85) w91) to cis-2,3,4a,9b-tetrahydro-1H-dibenzofuran-4-ones (92) in moderate yields and enantioselectivity (4)2\u00b76H2O and bisoxazoline ligand (93), the reaction could be carried out under the irradiation of visible light (\u03bb = 368 nm), or under the irradiation of visible light (\u03bb = 418 nm) with the addition of 50 mol% of thioxanthone. The electron-donating groups on the aryl para-position have no effect, while the electron-withdrawing groups lead to the decrease in enantioselectivity. Studies have shown that the substrate (91a) could form the complex (94) with chiral copper-bisoxazoline complex so that the \u03b2-carbon atoms of ketene could be attacked to generate cyclic adducts (92a).In 2017, Bach et al. reported an enantioselective photocyclization reaction which converted 2-aryloxy-cyclohex-2-enones ( 60% ee) 31]. In. In91) t95) from tryptamine substrates (96) under the irradiation of blue LED light in good yields and enantioselectivity (3 and 8H-TRIP BINOL phosphate (97) were used as catalysts. Some substituents on the indole core were well tolerated, such as Br-, Cl-, Methoxy-, and alkyl-substituents. Moreover, the reaction could also be applied to the synthesis of alkaloid natural products. The proposed mechanism was conducted as follows. Chiral phosphates could first form hydrogen-bonded adducts (98) with substrates (96). Under the irradiation of visible light, electron transfer occurred and reacted with stable nitroxyl TEMPO\u00b7 to produce closed-shell intermediates (99); iminium ions underwent nucleophilic addition with pendant amine to obtain alkoxyaminesubstituted pyrroloindoline products (95).In 2018, Knowles et al. reported a photocatalytic reaction to synthesize pyrroloindolines (\u201392% ee) 32]. Ir. Ir95) f100). Under the irradiation of bule LED light, cyclopropanes (101) reacted with alkenes (102) or alkynes (103) to deliver chiral cyclopentanes (104) or cyclopentenes (105) in good yields and enantioselectivity (101) and rhodium complex RhS (100) to generate intermediates (106), which were excited to intermediates (106a) under the irradiation of visible light. Intermediates (106a) as a strong oxidant were reduced to intermediates (106b) by tertiary amine. Intermediates (106b) were converted into radical intermediates (106c), which were added to alkenes (102) to generate ketyl radical (106d). Then ketyl radical (106d) released cycloaddition products (105) to complete catalytic cycle.In 2018, Meggers et al. reported a [3+2] photocycloaddition catalyzed by chiral-at-metal rhodium complex (>99% ee) 33]. Al. Al100).107) to five-, six-, seven-, and eight-membered lactams (108) under the irradiation of 50 W cyan light (\u03bb = 497 nm) in good yields and enantioselectivity , GluER-T36A (109) is used as the main chiral catalyst (108) could combine with catalyst (109) to yield complex (110), which underwent electron transfer to obtain radical intermediates (111). Intermediates (111) formed exocyclic radical (111a) via cyclization, which gave desired products (108) through hydrogen atom transfer.In 2019, Hyster et al. reported a photoexcitation catalyzed by flavin-dependent \u201cene\u201d-reductase. The methodology could convert chloroacetamides 112). Under the irradiation of blue LED light, substituted indolines (113) could react with N-hydroxycarbamates (114) to form cyclic adducts (115) in good yields and enantioselectivity went through first SET oxidation to form radical cation intermediate (116) under the irradiation of visible light, which cooperated with chiral phosphate anion (112) to generate complex (117); then, complex (117) converted to complex (117a) through CPA-mediated cyclization. Complex (117a) underwent second SET oxidation to produce tertiary pyrroloindoline carbocation intermediate (117b). Finally, tertiary pyrroloindoline carbocation intermediate (117b) reacted with N-hydroxycarbamate (114) to obtain desired product (115d).In 2019, You et al. reported an asymmetric dearomatization catalyzed by an iridium photocatalyst and a chiral phosphoric acid ( 96% er) 35]. Ma. Ma112).118) catalyzed by an iridium photocatalyst and a chiral phosphate (119). Pyrrolidines (120) were successfully obtained under the irradiation of blue LED light in good yields and enantioselectivity 36]. In. In118) 121) [122)-catalyzed [3+2] photocycloaddition of cyclopropylurea (123) with \u03b1-substituted acrylates (124). Under the irradiation of bule light (\u03bb = 470 nm), the reaction showed good yields and enantioselectivity , which r 97% ee) . Various125) from 2-(2-iodophenoxy) propane-1,3-diol analogues (126) under the irradiation of blue LED light in good yields and enantioselectivity (2\u00b7glyme and Ir(dFCF3ppy)2(dtbbpy)PF6 were selected as catalysts, and axially chiral 2,2\u2032-bipyridine (127) was used as ligand. Halidecontained substrates were well tolerated, this reaction could also be used to synthesize 1,4-benzodioxane containing oxa-quaternary stereocenters. The mechanism proposed by the authors was conducted as follows. Substrates (126) could undergo oxidative addition with chiral Ni(0) complex (128) to form Ni(II) aryl complex (129), which could give Ni(II) aryl alkoxides (129a) under the action of chiral 2,2\u2032-bipyridine ligand. Ni(II) aryl alkoxides (129a) formed critical Ni(III) aryl alkoxides (129b) through iridium(III) photocatalyst mediated SET process. Finally, critical Ni(III) aryl alkoxides (129b) underwent reductive elimination to release desired products (125) and chiral Ni(I) complex (130).Six-membered ring compounds are also a kind of very important organic compounds, especially six-membered heterocyclic compounds which play a significant role in the field of drug synthesis. In 2018, Xiao et al. reported a dual photoredox and nickel catalyzed desymmetric C\u2013O coupling reaction to synthesize enantioselective 1,4-benzodioxanes ( 88% er) 38]. Ni. Ni125) N-aryl \u03b1-amino acids (131) into chiral 4-amino-2methyl THQs (132) under the irradiation of blue LED light in good yields and enantioselectivity for the first time (133) and a chiral phosphate (134) were utilized as co-catalysts. In the study of the reaction range, the benzene ring of substrates substituted by some groups, such as Br-, Me-, and MeO-, were well tolerated.In 2018, Jiang et al. reported a photoredox dual-catalysis, which converted rst time 39]. Di. DiN-aryN-aryl amino acids (136) react with 3-methyleneisoindolin-1-ones (137) to form chiral isoindolin-1-ones (138) in good yields and enantioselectivity in the presence of a chiral phosphoric acid (135) and DPZ as catalysts (N-aryl amino acids (136), oxidized by a photoredox catalyst, underwent proton transfer and decarboxylation to form a-aminoalkyl radical (139); \u03b1-aminoalkyl radical (139) transferred an electron to HO2\u00b7 to furnish N-aryl imines (140), which reacted with 3-methyleneisoindolin-1-ones (137) to produce chiral isoindolin-1-ones (138) via chiral Br\u00f8nsted acid-mediated Povarov reaction.Later, Jiang et al. reported a kind of cooperative photoredox and chiral Br\u00f8nsted acid catalysis. Under the irradiation of bule LED light, atalysts 40]. A . A N-ary141) organic photoredox catalyzed [4+2] cycloaddition to form tetrahydrocyclopenta[b]chromenes (142) from ortho-quinone methides (143) and fulvenes (144) under the irradiation of green light in good yields and enantioselectivity to form radical cations (145). At the same time, the photoredox catalyst converted O2 to O2\u00b7\u2212 through single electron transfer, radical cations (145) underwent [4+2] cycloaddition with fulvenes (144) to obtain radical cations (146). Finally, radical cations (146) produced cycloadducts (142) under the reaction of superoxide radical (O2\u00b7\u2212).In 2020, Honda et al. reported a thioxanthylium (.6:1 ee) 41]. In. In141) A) from substituted 2-methylbenzaldehydes (147) and dienophiles (148) via a chiral titanium (149)-mediated enantioselective photoenolization/Diels\u2013Alder reaction cycloaddition, merging a chiral ligand ( 96% er) 44]. Va. Va153) 160) and \u03b1-diazoketones (161) to synthesize 7-membered lactones (162) upon the diffraction of blue LED light in good yields and enantioselectivity (2(dba)3\u00b7CHCl3 and a chiral ligand (163) acted as catalysts. Notably, substitutions the alkyl chain of lactones by some functional groups, such as alkenyl, alkynyl, and OTBS, were well tolerated in this reaction.In 2020, Xiao et al. found a new asymmetric [5+2] dipolar cycloadditions of vinylcyclopropanes ( 99% er) 45]. Pd. Pd160) 164) and Pd2(dba)3\u00b7CHCl3, vinyl carbamates (165) could react with photogenerated ketenes (166) to deliver 10-membered cycloadducts (167) upon the diffraction of blue LED light in excellent yields and enantioselectivity 46]. A . A 164) 168) to synthesize cycloaddition products with bicyclic structure (169) from trienes (170) upon the diffraction of blue LED light (\u03bb = 470 nm) in good yields and enantioselectivity (170) underwent the one-electron oxidation by photoredox catalyst upon the diffraction of blue LED light to transform into radical intermediates (171), which gave radical intermediates (171a) via cyclization. One-electron reduction of intermediates (171a) furnished bicyclic products (169).Compared with traditional synthesis methods, photocatalytic synthesis of chiral polycyclic compounds is new and effective. In 2018, Nicewicz et al. reported an asymmetric cation radical intramolecular Diels\u2013Alder reaction, utilizing an oxidizing pyrilium salt bearing a chiral N-triflyl phosphoramide anion ( 75% er) 47]. Mo. Mo168) 172) as a photo-organocatalyst, and \u03b1,\u03b2-unsaturated aldehydes (173) reacted with allenes (174) to provide bicyclic lactones (175) upon the irradiation of single high-power (HP) LED light (\u03bb = 420 nm) in good yields and enantioselectivity (172) and a \u03b1,\u03b2-unsaturated aldehydes (173) to form chiral iminium ions (176), which was excited to give strong oxidants (176a). Allenes (174) underwent SET activation with (176a) to generate the chiral 5\u03c0-electron intermediates (176b) and the allene cation radicals (177), then a polar-radical-crossover addition of allene radical cations (177) could afford the tertiary radicals (179), which reacted with chiral 5\u03c0-electron intermediates (176b) to intermediates (179). An aldol-type cyclisation could occur in intermediates (179) to provide adducts (179a), which finally furnished bicyclic lactones (175) through acyl migration step and complete catalytic cycle.In 2019, Melchiorre et al. reported an enantioselective photocatalysis which utilized chiral amine ( 88% ee) 48]. Al. Al172) 180) to synthesize benzo[d]cyclopropa[b]pyranones (181) from 3-(2-formylphenyl)-1-pyrazol-1-yl-propenones (182) upon the irradiation of visible light (\u03bb = 450 nm) in good yields and enantioselectivity (up to 93% yield and up to >99% ee) (182) initially could combine with a rhodium catalyst to form complex (183), complex (183) could transform into photoexcited complex (183a) in the presence of visible light, which underwent HAT to generate diradical intermediates (183b). Next, singlet-state ketenes (183c) went through intersystem crossing and hetero-Diels\u2013Alder reaction to produce rhodium bound cyclopropanes (183d) which finally released desired products (181).In 2019, Meggers et al. used a bis-cyclometalated rhodium catalyst (>99% ee) 49]. Di. Di180) 184) from 2,4-cyclohexadienones (185) upon the irritation of visible light (\u03bb = 437 nm) in good yields and high enantioselectivity with a chiral Lewis acid (186) as a catalyst 187), with a chiral bisphosphine (188) as ligand. In the presence of bule light (\u03bb = 448 nm), enediynes (189) could produce tricyclic cyclohexadienes bearing a quaternary bridgehead carbon (190) in good yields and enantioselectivity underwent the yne-yne coupling with Co0 catalyst to generate cobaltacyclopentadiene intermediate (191), which could give intermediate (191a) via photoinduced oxidation. Finally, intermediate (191a) were reduced to furnish product (190c) and the CoI species, CoI through photocatalyst-mediated reduction to restore Co0 and compete catalytic cycle.In 2021, Yamamoto et al. found an enantioselective [2+2+2] cycloaddition via dual cobalt and photoredox catalysis (>99% er) 51]. A . A 187),In the past 5 years, enantioselective visible light catalysis has become an important strategy for the synthesis of chrial organic molecules. In this review, we have mainly summarized the new methods for the construction of chiral cyclic compounds via photo-induced transformation. The substrate applicability and mechanism of various methods are briefly described. It is worth noting that these photochemical synthesis methods provide a good supplement for the construction of polychiral and polycyclic compounds which are difficult, or even impossible, to synthesize with the previous methods. It can be predicted that photocatalysis will become a greener and more environmentally friendly synthesis method and will play an important role in the synthesis of a variety of corresponding chiral compounds, providing new ideas for the total synthesis of natural products and drugs."} +{"text": "Burn Intensive Care Units (BICU)s are resource-heavy and labor-intensive units with very sick patients. The removal of burns as a requirement from the surgical curriculum has decreased the number of rotating surgical trainees, but did not impact patient care needs. Our unit adopted an Advanced Practice Provider (APP) service model in fiscal year 2018 to provide consistent standardized clinical care, with surgical trainees rotating monthly, to mitigate the loss of residents over time. We aimed to critically evaluate the impact of an APP run BICU on mortality and quality improvement initiatives.Patients were identified using Institutional Burn Center registry, and linked to the clinical and administrative data. All patients admitted to the BICU between July 1, 2016 and June 30, 2020 were eligible for inclusion. All central line associated blood stream infections (CLABSI), catheter associated urinary tract infections (CAUTI), ventilator associated pneumonias (VAP) and mortality rates were compared. Demographics, length of stay (LOS), co-morbid conditions and mortality were evaluated. Statistical analysis was performed with Students\u2019 t-test, and chi-squared tests. Significance was accepted as p< 0.05.There were no significant differences in admission rates over the study period. The number of CLABSIs significantly decreased each year (15 (2017), 6 (2018), 5 (2019), 3 (2020)). The number of CAUTIs significantly decreased ((13 (2017), 6 (2018), 1 (2019), 3 (2020)). The number of VAPs significantly decreased ((15(2017), 12 (2018), 7 (2019), 3 (2020)). Mortality was unchanged from 2017-2019 but significantly decreased in 2020 ((2.2% (2017), 2.4% (2018), 2.5% (2019), 0.9% (2020)).There were no significant differences in admission rates over the study period. The number of CLABSIs significantly decreased each year (15 (2017), 6 (2018), 5 (2019), 3 (2020)). The number of CAUTIs significantly decreased ((13 (2017), 6 (2018), 1 (2019), 3 (2020)). The number of VAPs significantly decreased ((15(2017), 12 (2018), 7 (2019), 3 (2020)). Mortality was unchanged from 2017-2019 but significantly decreased in 2020 ((2.2% (2017), 2.4% (2018), 2.5% (2019), 0.9% (2020))."} +{"text": "Rapid detection of intrinsic vancomycin resistance and acquired resistance genes (n=101) received standard of care (SOC) culture and antimicrobial susceptibility testing (AST). Additionally, samples were evaluated with the BCID-GP panel but only SOC results were reported in the EMR and available to inform clinical decisions. Patients were excluded if the sample was a subsequent culture in a persistent episode of bacteremia (n=17) or if the assay failed (n=4). Chart review was performed to evaluate the expected impact of the BCID-GP panel on the time to organism identification, AST results, and optimization of antimicrobial therapy. S. epidermidis was the most common bacteria identified, followed by S. aureus, and other coagulase-negative staphylococci. Thirty-nine patients with staphylococci (48.8%) had the mecA gene detected and 2 patients with E. faecium had the vanA gene detected. The BCID-GP panel saved a mean of 24.4 hours (h) to identification and 48.3h to susceptibility testing compared to standard methods across all patients. In 38 patients (47.5%), the BCID-GP panel result could have enabled an earlier change in antibiotic therapy. Table 2 highlights opportunities to optimize antimicrobial therapy 53.4h earlier for 16 (20%) patients with organisms expressing AMR genes, 29.2h earlier for 8 (10%) patients infected with organisms, such as streptococci, with very low resistance rates, and to stop antimicrobial therapy 42.9h earlier for 14 (17.5%) patients with contaminated blood cultures.A total of 80 patients were included in the final analysis (Table 1). The BCID-GP panel could have enabled earlier optimization or stopping of antibiotics in many patients with significant time savings compared to standard laboratory methods. Todd P. McCarty, MD, Cidara (Grant/Research Support)GenMark T2 Biosystems (Consultant) Sixto M. Leal, Jr., MD, PhD, Abnova (Grant/Research Support)AltImmune (Grant/Research Support)Amplyx Pharmaceuticals (Grant/Research Support)Astellas Pharmaceuticals (Grant/Research Support)CNINE Dx (Grant/Research Support)GenMark Diagnostics IHMA (Grant/Research Support)IMMY Dx (Grant/Research Support)JMI/Sentry (Grant/Research Support)mFluiDx Dx (Grant/Research Support)SpeeDx Dx (Grant/Research Support)Tetraphase Pharmaceuticals (Grant/Research Support)"} +{"text": "Density functional theory (DFT) calculations were also employed to calculate quantum chemical descriptors of the compounds. Molecular docking studies against human alpha amylase were also conducted. The results were compared with the control drugs, metformin and acarbose. The drug-likeness prediction results showed that all flavonoids, except myricetin, were found to obey Lipinski\u2019s rule of five for their drug like molecular nature. Pharmacokinetically, chrysin, wogonin, genistein, baicalein, and apigenin showed best absorption profile with human intestinal absorption (HIA) value of \u2265 30%, compared to the other flavonoids. Baicalein, butein, ellagic acid, eriodyctiol, Fisetin and quercetin were predicted to show carcinogenicity. The flavonoid derivatives considered in this study are predicted to be suitable molecules for CYP3A probes, except eriodyctiol which interacts with P-glycoprotein (p-gp). The toxicological endpoints prediction analysis showed that the median lethal dose (LD50) values range from 159\u20133919 mg/Kg, of which baicalein and quercetin are found to be mutagenic whereas butein is found to be the only immunotoxin. Molecular docking studies showed that the significant interaction of the studied molecules in the binding pocket of the \u03b1-amylase protein relative to the control metformin with the crucial amino acids Asp 197, Glu 233, Asp 197, Glu 233, Trp 59, Tyr 62, His 101, Leu 162, Arg 195, His 299 and Leu 165. Chrysin was predicted to be a ligand with high absorption and lipophilicity with 84.6% absorption compared to metformin (78.3%). Moreover, quantum chemical, ADMET, drug-likeness and molecular docking profiles predicted that chrysin is a good bidentate ligand.Computer aided toxicity and pharmacokinetic prediction studies attracted the attention of pharmaceutical industries as an alternative means to predict potential drug candidates. In the present study, Computational pharmacology is a fast-growing research field focusing on the development of techniques for employing software and databases to generate and analyze molecular, biological and medical data from diverse sources , 2. The Diabetes mellitus (DM) is a group of metabolic conditions in which high blood sugar levels transpire over an extended period \u201317. ModeMetal based organic compounds that are synthesized using phytochemicals as ligands are serving as metalo-therapeutics, and they are emerging strategies to treat type II diabetes mellitus. They are known to significantly improve hyperglycemia, glucose intolerance, insulin resistance, and decrease level of serum triglyceride and plasma glucose , 27. Prein-silico pharmacokinetic (ADME) properties, drug-likeness, toxicity profiles and toxicological endpoints of sixteen antidiabetic flavonoids that have ideal bidentate chelating sites for metal ion coordination were examined using SwissADME, Pro Tox II, vNN and ADMETlab web tools, Molecular docking and DFT calculations.In the present study, 9, having a bidentate coordination cite and showed antidiabetic activity in-vitro, were retrieved from literature [The overall procedures followed for the ligand screening process is shown in terature , 42. Theterature web toolterature .The molecular docking study of the target flavonoids was made by following the reported method. The 3D structure of human pancreatic \u03b1-amylase was obtained from Protein Data Bank (PDB ID:O/w), pharmacokinetics properties ) which are critical parameters for prediction of the absorption and distribution of drugs within the body [Absorption: CaCO3 Permeability (CaCO2), P-gp inhibitor/substrate (P-gp), Human Intestinal Absorption (HIA), 20% bioavailability (F20%), and 30% bioavailability (F30%)); Distribution: Plasma Protein Binding (PPB), Blood Brain Barrier (BBB) and Volume Distribution (VD) and Excretion: Half Life (T1/2) and Clearance (CI). The properties of CaCO2, VD, PPB, CI, T1/2 were expressed numerically, whereas the rest of the pharmacokinetic parameters were expressed categorically [Pharmaceutically significant descriptors and physically relevant properties of the target flavonoids were predicted , 46. Thethe body , and druthe body . The perthe body . The ADMorically . Besidesorically , which aorically .50, mg/Kg) of the studied flavonoids were determined using ProTox-II server [A total of 19 parameters were predicted to study the toxicity profile of the sixteen flavonoids and the two controls. The toxicological endpoints and the level of toxicity , electronegativity (\u03c7 = -\u00bd (EHOMO + ELUMO)), electronic chemical potential (\u03bc = \u00bd (EHOMO + ELUMO) = -\u03c7), global chemical hardness (\u03b7 = \u00bd (ELUMO\u2014EHOMO)), global softness (\u03c3 = 1/2\u03b7), global electrophilicity index (\u03c9 = \u03bc2/2\u03b7), and nucleophilicity index (Nu = 1/\u03c9), and dipole moment were also calculated and analyzed at the same level of theory [Geometry optimizations and frequency calculations were performed using the Gaussian 09 program f theory , 58.16) holding six NHBDs (> 5). It is important to note that Lipinski\u2019s rule of five is essential for rational drug design and it has been suggested that the low permeability or poor absorption for a given compounds results when it violates one of Lipinski\u2019s rule of five [1) and Baicalein (2); Fisetin (7) and Kaempferol (8); Isorhamnetin (11), Luteolin (12), and Naringenin (14)) showed similarities in TPSA, %Abs and MR , while those with a TPSA 60 \u00c52 would be well absorbed (> 90%) [1), baicalein (3), chrysin (4), genistein (10), and wogonin (15) with better and comparable percent absorption to the control metformin (18). It is found that the %Abn and TPSA values follow the order chrysin (4) > wogonin (15) > metformin (18) > genistein (10) = apigenin (1) = baicalein (2).Out of the sixteen flavonoids listed in of five . Moleculs and MR . The mol4) have the highest percent absorption (84.6%) than all the other flavonoids and the two controls, whereas metformin (18) displayed better percent absorption (78.3%) than acarbose. These results are in good agreement with a previous report on pharmacokinetic properties of apigenin (1), eriodyctiol (6), fisetin (7), kaempferol (8) and quercetin (9) via molinspiration and pkCSM servers [The results also showed an inverse relationship between TPSA and %Abs, and direct relationship between %Abs and MR. The analysis of the %Abs of the sixteen studied flavonoids and the two controls for their percent absorption showed t servers .4) (-3.709) is the least soluble molecule and ellagic acid (5) (-3.076) has the highest solubility. The relatively high solubility of ellagic acid (5) is due to the presence of four hydroxyl and two ketone pharmacophores [7.4) of the flavonoids (17) has moderate solubility, moderate permeability and low metabolism with logD7.4 value of 2.543 and very low lipophilicity of -8.565.The calculated result of LogS showed that chrysin (cophores relativeavonoids showed t17) and metformin (18), are less than zero, -1.034 and -8.565, respectively, suggesting that the two compounds have poor membrane permeability. The logP of apigenin (1) (3.07) and chrysin (4) (3.44) were found to be greater than three as predicted in ALOGPS (The distribution coefficients (logP) of the flavonoids Tables and 2 ran ALOGPS which mi5) has high solubility (0.823 mg/mL), whereas chrysin (4) is found to have low solubility (0.105 mg/mL). These results are in agreement with those predicted using ADMETlab as well as with the experimental findings suggesting that chrysin (4) has low aqueous solubility and high absorption or absorption enhancer role [The water solubility (mg/mL) of some of the flavonoids considered in this work was retrieved from the drug bank (predicted using ALOGPS) and tabulated in cer role .Ka results range from 5.54 to 7.91 indicating that the studied flavonoids fall under the category of neutral organic acids, in good agreement with experimental pKa of apigenin (1), ellagic acid (5) and quercetin (9) . The relatively high pKa of naringenin (14) (7.91), apigenin (1) (6.63), chrysin (4) (6.58), luteolin (12) (6.57) and genistein (10) (6.55) may cause difficulty of deprotonation, suggesting that the ligands have stronger coordination ability with metals [The ph metals .o/w) study showed that wogonin (15) (2.880), chrysin (4) (2.871), genistein (10) (2.557), apigenin (1) and 2 (2.577) are highly lipophilic than the other molecules, whereas quercetin (9) and morin (13) (1.988) were found to be less lipophilic ligands next to ellagic acid (5) (1.313) (15) makes it more lipophilic than chrysin (4). It has also been found that the structural resemblance in benzoyl or cinnamoyl part of the flavonoid derivatives play a role in their physicochemical properties. The calculated LogPo/w of the flavonoid derivatives considered in this work is found to range between 1.313 and 2.880. Our predicted results are in good agreement with the previously reported Po/w values of 1.92, 2.27, 3.11 and 1.82 for apigenin (1), eriodyctiol (6), fisetin (7) and kaempferol (8), respectively [On the other hand, the lipophilicity (LogP 1.313) . The pre13 . The 20), and 30% bioavailability (F30) as presented (16) (-6.63 cm/s), morin (13) (-6.206 cm/s), kaempferol (8) (-6.163 cm/s) and ellagic acid (5) (-6.001 cm/s) is mainly due to the presence of large number of NHBDs and NHBAs in their structures which have the potential to rendere their permeability. The two controls, acarbose (17) and metformin (18) are predicted to have Caco-2 permeability values of -5.803 cm/s and -7.128 cm/s, respectively. The predicted HIA data of the sixteen flavonoids and the two control drugs are represented categorically as 0 and 1 (1), chrysin (4), fisetin (7), genistein (10), wogonin (15), and metformin (18) have high HIA (\u2265 30%) whereas acarbose (17) and the rest six flavonoids are predicted to have HIA below 30% ((2), chrysin (4), genistein (10), wogonin (15) and the control, metformin (18) predicted to show bioavailability greater than 30%, whereas the rest of the flavonoids are predicted to show bioavailability between 20 to 30%. Acarbose (17) is known for its extremely low bioavailability and less than 2% of absorption as active drug [To evaluate the absorption property of the flavonoids, we predicted Caco-2-Permeability (Papp), P-glycoprotein (P-gp), substrate or inhibitor (P-gpinh/P-gpsub), Human intestinal absorption (HIA), 20% bioavailability (Fresented . It is f 0 and 1 which shelow 30% . Flavonoive drug . We pred1), eriodyctiol (5), fisetin (7), kaempferol (8) and quercetin (9) are predicted to be above 90% to bind to common blood proteins significantly, indicating that the pharmacologic effect of these compounds is low. The control drugs, acarbose (17) and metformin (18) weakly bind to common blood proteins. This could be one of the reasons that make acarbose as a working drug, while it has very low percent absorption (-1.8%).Plasma Protein Binding (PPB), Blood Brain Barrier (BBB) permeability, and Volume of distribution (VD) were parameters considered to study the distribution of drug candidates . The PPB2), chrysin (4), ellagic acid (5), eriodyctiol (6), wogonin (15) and metformin (18) were predicted to permeate BBB using ADMETlab. However, our prediction using SwissADME webtool showed that only chrysin (4) can permeate BBB. On contrary to previous report on ellagic acid (5) studied using pkCSM server [5) to permeate BBB.Baicalein and chrysin (4)\u2014relative to the other flavonoids -showed the consistency of absorption and distribution parameters.The volume of distribution (VD) in L/Kg were predicted to be all negative, indicating higher distribution of the flavonoid derivatives and the two control drugs in plasma than in tissues, confined to plasma proteins. The hydrophilic character of the flavonoids contributed to low values of VD. The more negative value of VD for quercetin (-1.56) and less negative value for wogonin (-0.32) followed by chrysin (-0.35) among flavonoids were also presented in 6) is the only flavonoid to act as drug transporter of P-glycoprotein substrate from target flavonoids considered (6) to be excluded from the list of bidentate ligands for metal complexation. Except ellagic acid (5), the rest of the flavonoid derivatives considered in this study are predicted to interact with CYP3A, making them very suitable molecules as CYP3A4 probes (2), chrysin (4), fisetin (7), kaempferol (8), quercetin (9), genistein (10), isorhamnetin (11), luteolin (12), morin (15), naringenin (14) and wogonin (15) are predicted as D6 inhibitors. Previous study by May & Schindler, [5) were found to inhibit CYP3A4. These results suggest that the flavonoids studied in this work potentially have antidiabetic effect in agreement with previous reports [3) and wogonin (15) are predicted to interact with 2C9. Previous report indicated that the inhibition and induction of the CYP enzymes are probably the common causes for most drug interactions [The skin permeability, Kp, values obtained for all the flavonoid derivatives considered in this study are in the range of -7.4 to -5.35 cm/s inferrinnsidered . This mansidered . Its int4 probes . CYP3A ehindler, showed thindler, . In the reports , 68. In ractions . Hence, 5) and acarbose (17) were predicted to be inactive for MMP. Apigenin (1) was active for HLM prediction, and could be metabolized rapidly by the liver that will reduce its effective therapeutic concentration in the body [The human liver microsomal (HLM) stability and mitochondrial membrane potential (MMP) parameters of the flavonoid derivatives predicted via the vNN method showed t2), myricetin (16), luteolin (12) and quercetin (9) and butein (3) show two toxicological endpoints; carcinogenicity and mutagenicity, and carcinogenicity and immunotoxicity, respectively. On the other hand, ellagic acid (5), eriodyctiol (6), fisetin (7) and morin (15) show one toxicological endpoint (carcinogenicity). Apigenin (1), chrysin (4), kaempferol (8), wogonin (15), naringenin (14), isorhamnetin (11), and genistein (10) are free from any of the predicted toxicological endpoints. Acute toxicity predictions indicate that the flavonoids considered are not fetal; however, they can be categorized as harmful toxic classes.Absence of toxicity is one of the major factors for selecting a compound as a therapeutic candidate . Herein,50) values were found to be in the range from 159\u20133919 mg/Kg (9), fisetin (7), and myricetin (16) are predicted as toxic (Class III), whereas apigenin (1), butein (3), elagic acid (5) and eriodyctiol (6) are harmful (Class IV) and the rest were categorized as \u201cmay be harmful\u201d (Class V) toxicity classes. The results show that most of the drug-like compounds have the tendency to have carcinogenic activities than any toxicological endpoints.The median lethal dose (LD19 mg/Kg . Accordi1), baicalein (2) and genistein (10), the rest of the flavonoid derivatives and the two control drugs were not predicted to be human ether-a-go-go related gene (hERG) blockers. However, most of them were predicted to show H-HT and mutagenicity , human hepatotoxicity (H-HT), Ames Mutagenicity (AMES), Skin sensitization (SkinSen) were used to predict the toxicity of the flavonoid derivatives and the two controls. The results are presented in genicity .1) and acarbose (17) were predicted with inactive and active, respectively, to induce liver injury. The results also indicate the tendency of acarbose (17) to cause DILI (17) [The vNN predicted drug induced liver injury (DILI) and cytotoxicity results showed tuse DILI , which iILI (17) and the ILI (17) .\u03c7), electronic chemical potential (\u03bc), globalchemical hardness (\u03b7), global softness (\u03c3), global electrophilicity index (\u03c9) and nucleophilicity index (Nu) were derived from the energy gap (Eg = ELUMO\u2014EHOMO), are presented in HOMO and ELUMO play an important role in predicting the energy gap of molecules and determining the anti-oxidant, reactivity, hardness and softness of molecules [4)) to 7.982eV (genistein (10)), whereas metformin (18) has the largest band gap. The high HOMO energy (-4.734 eV), the small energy gap (2.428 eV), small chemical hardness (0.045 eV), and large softness (11.207 eV) calculated for chrysin (4) molecule makes the molecule a good candidate as a chelating agent. On the other hand, the high dipole moment (8.293 Debyee) value found for chrysin (4) makes the molecule a preferred ligand for biological activity . Among the 16 flavonoid derivatives, the highest HOMO-LUMO energy gap, hardness, and high nucleophilicity were predicted for genistein (10) was performed to predict the reactivity of the flavonoid derivatives. DFT chemical descriptors: electronegativity .10) has the highest chemical hardness (0.147 eV) and the lowest electrophilicity (0.013 eV). Whereas the highest electrophilicity (0.309 eV) and the lowest chemical hardness (0.052 eV), next to chrysin (4) (0.045 eV), was predicted for the chalcone family, butein (3). The electrophilicity, electronegativity and softness quantum chemical descriptors for apigenin (1)/genistein (10) were found to be 0.077/0.147 eV, 6.494/3.409 eV and 0.156/0.013 eV, respectively, indicating good chelating nature of apigenin (1) over genistein (10).Based on the quantum chemical reactivity descriptors, the isoflavone class of flavonoids, genistein (1)-, chrysin (4)- and the control metformin (18)-protein interactions are given from Figs 18) (anti-diabetic drug) were summarized in 18), the flavonoid compounds shown significant interaction within the active site of the protein with the key amino acids Asp 197, Glu 233, Asp 197, Glu 233, Trp 59, Tyr 62, His 101, Leu 162, Arg 195, His 299 and Leu 165.\u03b1-Amylase has been a pivotal target in anti-diabetic drug development. In the present work, we studied the interactions between the Human \u03b1-amylase (PDB ID: 4w93) protein against the flavonoids and compared the results against the clinical drug metformin. The 2D and 3D representations of apigenin (18) with -4.5 kcal/mol. The top seven flavonoids with low binding energies were apigenin (1), baicalein (2), chrysin (4), ellagic acid (5), kaempferol (8), quercetin (9), and luteolin (12). A previous work reported that compound quercetin (9) has low binding energy against \u03b1-glucosidase [in-silico docking analysis indicated that apigenin (1) that interacts with the \u03b1-amylase residues of Tyr 62, Trp 58, His 299, Asp 300, Asn 298, Arg 195 and Ile 235 with binding energy -8.3 kcal/mol, chrysin (4) that interacts with the \u03b1-amylase residues of Trp 58, Trp 59, Tyr 62, His 299 and Gln 63 with binding energy -8.1 kcal/mol, kaempferol (8) that interacts with the \u03b1-amylase residues of Trp 58, Trp 59, Tyr 62, His 299, Glu 233, Asp 197, Arg 195, Ala 198, and Leu 165 with binding energy -8.1 kcal/mol, quercetin (9) , and luteolin (12) that interacts with the \u03b1-amylase residues of Trp 59, Tyr 62, Arg 195, Trp 58, His 299, Glu 233, Ala 198, and Leu 165\u20138.3 kcal/mol are better anti-diabetic agents compared to other compounds reported in this study.The tested flavonoids showed a binding energy ranging from -7.5 to -8.3 kcal/mol. All the investigated compounds showed strong binding score compared to the clinical drug metformin , chrysin (4), kaempferol (8), quercetin (9), luteolin (12) relative to the control metformin (18) also indicated that they fit well in the binding pocket of the human \u03b1-amylase forming a stable inhibitor-protein complex.The lower binding energies predicted for compounds apigenin (18) and acarbose (17)). The results show appropriate logP, LogS, and high HIA values for chrysin (4), wogonin (15), baicalein (2), genistein (10) and apigenin (1), suggesting better absorption and less toxicity. This has an implication that the flavonoids can be used as bidentate metal complexing agents, of which chrysin (4) was found to be more ideal for metal complexation with high absorption and lipophilicity with 84.6% absorption compared to metformin (18) (78.3%). The tendency of chrysin (4) to cross BBB and act on CNS was also predicted using SwissADME and ADMETlab predictions. Baicalein (2), butein (3), ellagic acid (5), eriodyctiol (6), fisetin (7) and quercetin (9) were predicted to show carcinogenicity. Most of the molecules are predicted as CYP3A probes, except eriodyctiol (6) which interacts with p-gp. Toxicological endpoints prediction analysis indicated median lethal dose (LD50) values ranging from 159\u20133919 mg/Kg, of which baicalein (2) and quercetin (9) were found to be mutagenic, whereas butein (3) and morin (15) were found to be immunotoxin among the studied flavonoid derivatives. Based on the findings from the predicted drug-likeness, toxicity, pharmacokinetic properties together with quantum chemical descriptors and molecular docking, chrysin (4) is found to be a molecule of potential chelating agent to synthesize coordination compounds for further in vitro and in vivo studies. Moreover, the findings from the DFT calculated quantum chemical reactivity descriptors indicated that chrysin (4) is most likely to interact with metal ions to form stable coordination compounds than the other flavonoids. Overall, the results obtained in this study showed better pharmacokinetics and drug likeness profiles for chrysin (4), wogonin (15), genistein (10), baicalein (2) and apigenin (1), and showed toxicity alerts to the toxicological endpoints (above class three toxicity). However, further detailed experimental study is required to confirm the findings reported in this work.In this study we presented the pharmacokinetic, drug-likeness, and toxicity profile of sixteen flavonoid derivatives and two control drugs (metformin (S1 File(DOCX)Click here for additional data file.S2 File(XYZ)Click here for additional data file."} +{"text": "Determine predictive factors for long-term remission of acromegaly after transsphenoidal resection of growth hormone (GH)-secreting pituitary adenomas.We identified 94 patients who had undergone transsphenoidal resection of GH-secreting pituitary adenomas for treatment of acromegaly at the USC Pituitary Center from 1999-2019 to determine the predictive value of postoperative endocrine lab values.Patients underwent direct endoscopic endonasal (60%), microscopic transsphenoidal (38%), and extended endoscopic approaches (2%). The cohort was 63% female and 37% male, with average age of 48.9 years. Patients presented with acral enlargement , macroglossia , excessive sweating , prognathism and frontal bossing . Seventy-five (80%) were macroadenomas and 19 (20%) were microadenomas. Cavernous sinus invasion was present in 45%. Available immunohistochemical data demonstrated GH staining in 88 (94%) and prolactin in 44 (47%). Available postoperative MRI demonstrated gross total resection in 63% of patients and subtotal resection in 37%. Most patients (66%) exhibited hormonal remission at 12 weeks postoperatively. Receiver operating characteristic (ROC) curves demonstrated postoperative day 1 (POD1) GH levels \u22651.55ng/mL predicted failure to remit from surgical resection alone . A second ROC curve showed decrease in corrected insulin-like growth factor-1 (IGF-1) levels of at least 37% prognosticated biochemical control .POD1 GH and short-term postoperative IGF-1 levels can be used to successfully predict immediate and long-term hormonal remission respectively. A POD1 GH cutoff can identify patients likely to require adjuvant therapy to emphasize clinical follow-up. Acromegaly is a disease of excess growth hormone (GH) and insulin-like growth factor-1 (IGF-1) levels, with GH-secreting pituitary adenomas causing 98% of cases . PatientSurgical resection alone has shown to be effective in controlling disease in up to 80% of patients with microadenomas and 50% of patients with macroadenomas, with long-term disease control occurring in up to 65% of cases , 2. In cWe retrospectively reviewed our USC Pituitary Center RedCap database of operations performed by two neurosurgeons (GZ and MW) at Los Angeles County + University of Southern California (LAC + USC) Medical Center and Keck Hospital of USC between June 1999 and December 2019. We identified 101 patients with acromegaly who underwent either microscopic or endoscopic endonasal transsphenoidal resection of GH-secreting pituitary adenomas. Seven patients without follow-up IGF-1 levels were excluded, leaving 94 patients included for final analysis. For each surgery, the pathology, type of exposure, presence of intraoperative CSF leak and complications were recorded. Based on Schroeder et\u00a0al.\u2019s conclusion that a small percentage of tumors from clinically acromegalic patients do not stain positive for GH on immunohistochemistry (IHC), one patient without a pathologically confirmed GH-secreting tumor but with significantly elevated preoperative IGF-1 levels and acromegalic signs and symptoms was included . The insAll patients underwent preoperative MRI to assess tumor size, presence of cavernous sinus invasion, infrasellar invasion, suprasellar extension, sphenoid anatomy, carotid anatomy, anatomy of normal pituitary gland, and position of the optic chiasm and nerves. Patients underwent MRI at 3 months postoperatively to assess extent of resection (EOR), and then annually to monitor tumor progression or recurrence. EOR was defined as either gross total resection (GTR) if no tumor was visible on postoperative MRI or subtotal resection (STR) in cases of observed residual disease. Tumor size was defined by maximal diameter in either the anteroposterior, lateral, or craniocaudal dimension. Parasellar extension into the cavernous sinus(es) was assessed according to the Knosp classification, consisting of 4 grades based on proximity to the ICA . Knosp svia the RIA technique. Postoperative assessment of pituitary function was performed to assess for hormone deficit recovery or new hypopituitarism.Preoperative IGF-1 levels were obtained in all patients to confirm the diagnosis of acromegaly. GH levels were not routinely obtained preoperatively due to its low clinical utility because of its pulsatile secretion. Patients additionally underwent full preoperative endocrine panels to screen for other endocrinopathies. Cabergoline, bromocriptine, and SRL medications were discontinued when decision for surgery was made, on average 4-6 weeks preoperatively. Postoperative GH levels were obtained on POD1, and follow-up IGF-1 levels were obtained at 6 and 12 weeks postoperatively to assess for remission. Hormonal remission was defined as normalization of age- and sex-normalized IGF-1 levels at 12 weeks postoperatively, though IGF-1 levels obtained prior to this were used as indicators of future remission. OGTT and GH levels were used to assess for remission only in patients with postoperative IGF-1 reduction that did not continue to fall within normal limits or that subsequently rose in the setting of symptom resolution. OGTT was performed after 12 weeks postoperatively. For the purposes of between-subject comparison, when available, IGF-1 levels were corrected using the age- and sex-specific upper limit of normal (ULN) and expressed as a percentage of ULN (IGF-1 level/IGF-1 ULN*100). Biochemical control was defined as normalization of IGF-1 with the use of adjuvant therapy in the postoperative period. GH and IGF-1 assays were all sent to Quest Diagnostics laboratories, where assay techniques have changed during the study period according to Quest\u2019s practices. GH assays were performed Patients underwent either microscopic endonasal transsphenoidal, endoscopic endonasal (direct) transsphenoidal, or rarely endoscopic endonasal extended approaches for tumor resection.p-value <0.05 was considered significant.Continuous variables were assessed for normality of distribution using the Kolmogorov-Smirnov test and are displayed as the means and standard deviation (SD), or medians with interquartile ranges (IQR). Categorical variables are displayed as frequencies. Pearson\u2019s chi-squared analysis was used to compare categorical variables. Correlations were determined using Spearman\u2019s rank-order correlation. Means were assessed using independent samples t-test or Mann-Whitney U test based on distribution. Medians were compared using nonparametric statistical analyses. Multivariate regression was performed to analyze the utility of POD1 GH and IGF-1 as independent predictors of remission to account for both preoperative maximal tumor diameter and postoperative extent of resection (EOR). Receiver operator curves (ROC) were generated to determine predictive cut-off points. Statistical analysis was performed using SPSS 25.0 statistical software and a 2-tailed th percentile for height.Of the 94 patients included in this study, 59 (63%) were female and 35 (37%) were male. Mean age at surgery was 48.9 years (SD 13.7). Seventeen patients (18%) underwent surgery at LAC + USC Medical Center and the other 77 (82%) were operated on at Keck Hospital. Thirty-eight patients (40%) presented with headache, 22 (23%) with fatigue, 15 (16%) with visual changes, 11 (12%) with decreased libido, 13 (14%) with amenorrhea/oligomenorrhea, and 5 (5%) with galactorrhea. Four patients (4%) had incidentally discovered pituitary adenomas with subsequent diagnosis of acromegaly. All patients except one presented with typical signs and symptoms of acromegaly including acral enlargement in 72 patients (77%) and facial changes in 60 patients (64%). The most common facial changes included macroglossia , prognathism , frontal bossing , and teeth gaps . Thirty-nine patients (42%) reported excessive sweating, 31 (33%) had skin tags, 24 (26%) reported snoring, 22 (23%) had oily/thickened skin, and 18 (19%) had arthralgias. The patient who did not present with typical signs or symptoms of acromegaly was 13 years old when the pituitary adenoma was discovered on CT scan as part of sinusitis workup, but he had always been above the 90On preoperative neurological exam, 5 patients (5%) had visual acuity loss, 5 (5%) had visual field cuts, and 1 (1%) had cranial nerve IV palsy. The majority had no focal neurological deficits. Twelve patients (13%) were treated with medications preoperatively for disease control, including bromocriptine in 2 (2%), cabergoline in 4 (4%), and somatostatin receptor ligands (SRL) in 7 (7%) Table\u00a01.All patients met clinical criteria for acromegaly and presented with elevated IGF-1 levels. Other preoperative endocrinopathies are presented in Corrected preoperative IGF-1 levels were available for 63 of the 94 included patients (67%), with a median value of 238ng/mL (IQR 165-302). Elevated preoperative IGF-1 levels were available for 82 patients (87%) with a median value of 714ng/mL (IQR 510-877). The other 12 patients (13%) had reports of elevated preoperative IGF-1 levels that were unable to be accessed as they were performed at outside laboratories. For the 82 patients with preoperative IGF-1 levels available, there was a significant correlation between preoperative IGF-1 levels and tumor size (p=0.001) Table\u00a01.Preoperative tumor size was available for 77 patients (82%) with a mean maximal diameter of 1.8 cm (SD 1). The majority were macroadenomas and 19 (20%) were microadenomas. Five (5%) were giant pituitary adenomas (>4cm). Suprasellar invasion was observed in 27 patients (29%), cavernous sinus invasion in 42 patients (45%), and infrasellar extension in 28 patients (30%). Knosp scoring was available for 60 patients (64%) with a score of 0 in 21 (22%), a score of 1 in 21 (22%), a score of 2 in 9 (10%), a score of 3 in 6 (6%) and a score of 4 in 3 (3%). Purely intrasellar tumors were found in 24 patients (26%) Table\u00a02.p = 0.137) or hormonal remission outcomes (p=0.257) and surgical technique.The majority of patients underwent EETS, 36 patients (38%) underwent microscopic transsphenoidal surgery, and 2 (2%) underwent an extended endoscopic approach. Intraoperative CSF leak occurred in 28 cases (30%) and were repaired with fat , fascia , dural substitute , dural sealant , pedicled naso-septal flap , and lumbar drain . No significant difference was found between POD1 GH levels . Nine patients (10%) were diagnosed with mammosomatotroph adenomas, one of whom did not present with hyperprolactinemia, and 1 patient (1%) was diagnosed with a non-functional adenoma based on immunohistochemistry but was considered to have acromegaly based on preoperatively elevated IGF-1 that decreased postoperatively, combined with acromegalic features. In 1 patient (1%) pathology was not available, but elevated preoperative IGF-1 levels consistent with acromegaly decreased postoperatively to within normal limits. In patients with available immunohistochemical (IHC) staining, 88 (94%) stained positive for GH, 44 (47%) also stained positive for prolactin, 19 (20%) also stained positive for TSH, 6 (6%) also stained positive for LH, 6 (6%) also stained positive for FSH, 5 (5%) also stained positive for ACTH, and 1 (1%) also was the null-cell adenoma referred to above. CAM5.2 staining was performed in 25 tumors, with positive staining in 24 (96%).The mean hospital stay was 2.6 days (SD 2). Within the 30-day postoperative period, 12 patients (13%) had hyponatremia, 6 (6%) had epistaxis, 5 (5%) experienced postoperative CSF leaks, 3 (3%) had transient diabetes insipidus (DI), 2 (2%) became septic, 1 (1%) had permanent DI, 1 (1%) experienced meningitis, and 1 (1%) experienced sinusitis. No patients included in this series died.Early readmission within a 30-day postoperative period occurred in 7 patients (7%), all for hyponatremia. One patient (1%) underwent early reoperation for CSF leak repair. CSF leak self-resolved without intervention in the other 4 patients.p<0.001). Furthermore, patients who underwent GTR were significantly more likely to achieve postoperative remission (p=0.02).Postoperative MRI was available for 67 patients (71%) and demonstrated gross total resection (GTR) in 42 (63%) and subtotal resection (STR) in 25 (37%). Median imaging follow-up time was 16 months (IQR 4.8-38). Disease recurrence after GTR occurred in 3 patients (3%) with a mean time of 16 months (SD 14). Progression of residual disease occurred in 2 patients (2%) at a mean time of 20 months (SD 15). EOR was significantly correlated with POD1 GH levels, with lower levels being observed in patients who underwent GTR . All patients were followed in clinic postoperatively with a median clinical follow-up time of 17 months (IQR 4.6-41). The majority experienced hormonal remission at a median time of 3 months (IQR 1-5). Twenty-four patients (26%) received additional treatment, 15 of which (16%) ended up achieving biochemical control. Eight patients (9%) did not receive additional treatment and did not achieve hormonal remission before being lost to follow-up at a mean of 3 months (SD 2). Follow-up IGF-1 levels were available for all patients except 1 in which there was no follow-up IGF-1 but GH suppression was observed during OGTT. At most recent clinical follow-up, the median IGF-1 level was 190ng/mL (IQR 138.5-274) and apex level (as defined by highest recorded postoperative IGF-1) was 238ng/mL (IQR 175-370.5). Corrected IGF-1 scores were available for 71 patients (76%) with a median of 62.8 (IQR 45-80) for most recent levels and 80.4 (IQR 64-114) for apex levels.p=0.011). Specifically, the mean POD1 GH level in patients who achieved hormonal remission was 1.60ng/mL versus 9.51ng/mL in patients who did not remit. A ROC curve predicted hormonal non-remission with a sensitivity of 75% and a specificity of 59% in patients whose POD1 GH levels were greater than 1.55ng/mL (p=0.001).POD1 GH levels were significantly associated with hormonal remission Figure\u00a01p=0.575). All patients on preoperative SRL medications were excluded from POD1 GH analyses due to their potential influence on GH levels. Pre-treatment IGF-1 levels were used for analysis of delta IGF-1 levels.A ROC curve demonstrated that a 37% or greater decrease in IGF-1 from preoperative levels as measured at 6-12 weeks postoperatively prognosticated hormonal remission with a sensitivity of 90% and specificity of 80% Figure\u00a02Of the 24 patients who underwent additional treatment, 8 (9%) underwent adjuvant stereotactic radiosurgery, 2 (2%) received external radiation therapy, and 1 (1%) underwent additional surgical resection. Twenty-one patients (22%) received adjuvant medical therapy with bromocriptine , cabergoline , SRL , and pegvisomant . Of patients who received additional treatment, 15 (16%) exhibited biochemical control after treatment and 9 (10%) had refractory disease. Seven of those who did not achieve biochemical control (7%) were lost to follow-up. The other 2 (2%) have known residual disease that has been deemed unresectable and continue to be in non-remission despite treatment with SRL in both and adjuvant radiotherapy in one.p<0.001).In order to predict the need for additional treatment in this patient population, an additional analysis was performed after eliminating the 9 previously mentioned patients who did not undergo hormonal remission but were lost to follow-up without initiation of adjuvant therapy. Mean POD1 GH levels were 5.9ng/mL (SD 8) in patients who received additional treatment, compared to 1.5ng/mL in patients who did not , and smaller mean maximal tumor diameter . However, no significant differences were noted in patient demographics, prior treatment, preoperative IGF-1 levels, or tumor invasion characteristics. Patients who underwent GTR were more likely to have POD1 GH levels less than 1.55ng/mL . Patients with POD1 GH levels less than 1.55ng/mL were additionally more likely to undergo hormonal remission , and less likely to receive additional treatment, specifically adjuvant medical therapy .In order to better understand the value of the proposed POD1 GH cutoff of 1.55ng/mL and its relationship with pre- and postoperative characteristics, patients were divided into two groups according to POD1 GH level 4. PatieIn this study, we analyzed patient data from 94 surgical cases with long term follow-up treated at a tertiary pituitary center in order to investigate the utility of endocrine lab values in predicting postoperative hormonal remission in acromegaly. All patients underwent pituitary adenoma resection, either\u00a0by microscopic, endoscopic, or extended endoscopic transsphenoidal surgery. The two main predictors assessed in this study were POD1 GH levels and degree of change in IGF-1 levels. GH half-life of 20-30 minutes suggests that GH levels within 24 hours postoperatively may reliably predict the success of surgical resection . Indeed,vs. between 6-12 weeks). While IGF-1 levels have been found to fluctuate up to 3 months following resection . Written informed consent for participation was not required for this study in accordance with the national legislation and the institutional requirements.TC: Formal analysis, investigation, data curation, writing \u2013 original draft, and writing \u2013 revisions. CC: writing \u2013 original draft. MiW: formal analysis, writing \u2013 revisions. PS: resources and writing \u2013 revisions. MaW: resources and writing \u2013 revisions. GZ: resources, conceptualization, methodology, resources, supervision, project administration, and writing \u2013 revisions. JC: resources, conceptualization, methodology, resources, supervision, project administration, and writing \u2013 revisions. All authors contributed to the article and approved the submitted version.JC: Recordati: Honoraria, advisory board Chiasma Principal investigator Crinetics Principal investigator.The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Pentacalia herzogii (Asteraceae) growing wild in the High Valley region of the department of Cochabamba was determined by a combination of GC and GC-MS measurements. \u03b1-Pinene was the main constituent of this essential oil (34%), accompanied by limonene (22%) and germacrene D (7.5%) as well as an important fraction of methoxylated monoterpenoids. They were mainly isomers of thymol methyl ether, accounting for 13% of the chromatogram. A new quantitatively important compound (9%) was identified through NMR and chemical synthesis as 4-isopropyl-6-methylbenzo[d]dioxole, and designated herzogole, alongside the minor related compound 1-isopropyl-2,3-dimethoxy-5-methylbenzene. The monoterpene benzodioxole featured a distinctive green-phenolic aroma which could raise interest for fragrance use. Since these compounds were not known naturally, a biosynthetic mechanism of their formation was proposed and put in perspective to illustrate the metabolic originality of P. herzogii.Over 15 years, with the support of a Canadian funding agency, the Universidad Mayor de San Sim\u00f3n, in Bolivia, undertook a large survey of aromatic plants of the South American country. More than a hundred species were studied under various aspects, including the production and characterization of essential oils. As part of this survey, the chemical composition of an essential oil sample obtained from In the late 1980s until the early 2000s, several research groups of the Universidad Mayor de San Sim\u00f3n, Cochabamba, Bolivia, have driven a large survey of the Bolivian flora. This effort was conducted with the support of the International Development Research Centre (IDRC) in Canada. In this regard, agronomists, biochemists, phytochemists, engineers and chemists joined efforts to gather knowledge about national plant species. One of the objectives of this multidisciplinary endeavor was to identify potential crops and vegetable resources that could in part replace the traditional coca plantations in Bolivia and provide revenue to local populations.Clinopodium axillare, for which ensuing disambiguation dioxole : Crude essential oil (1.49 g) was deposited on a chromatographic column comprising 200 g of silica gel 60 previously wetted with n-hexane. The sample was eluted with pure n-hexane, then 9:1 and 8:2 mixtures of n-hexane and dichloromethane to afford compound 1 as a green-phenolic-scented light-yellow liquid (27 mg), alongside more fractions of 1 contaminated with thymol and isothymol methyl ethers. Compound 1 was also prepared by suspending 5-methyl-3-(propan-2-yl)benzene-1,2-diol in 3 mL dry dimethylformamide under argon atmosphere, then adding Cs2CO3 and diiodomethane . The solution was heated to 110 \u00b0C for one hour, cooled down, then quenched with saturated aqueous NH4Cl. The reaction product was extracted with 3 \u00d7 5 mL ethyl acetate, and the combined organic phases were dried over sodium sulfate and evaporated under reduced pressure. The dried residue was purified by flash chromatography over 4 g silica, eluting with 15 mL pure n-hexane then n-hexane/dichloromethane (7:3) until the product was obtained as a green-phenolic-scented clear liquid .4-Isopropyl-6-methylbenzo+ (84), 163 (100), 150 (1), 145 (7), 133 (21), 119 (3), 105 (45), 91 (10), 79 (9), 77 (16).RI (DB-5/ Wax): 1330/1749; Rf = 0.54 (Hex/DCM 5:1); 2): The compound, of 95% purity, was purchased from Enamine LLC as a custom synthesis product, batch # 2017-0154152. The certificate of analysis is provided in the 5-Methyl-3-(propan-2-yl)benzene-1,2-diol (m/z 166 [M]+ (50), 151 (100), 133 (13), 123 (3), 105 (22), 103 (4), 91 (3), 79 (5), 77 (7).RI (DB-5/ Wax): 1487/2728; EI-MS (70 eV) 10): To a solution of diol 2 in acetone (5 mL) was added potassium carbonate and dimethyl sulfate . The mixture was stirred at room temperature for 18 h. The mixture was then cooled to 0 \u00b0C, quenched with an aqueous solution of sodium hydroxide and stirred at room temperature for 3 h. It was then extracted with dichloromethane (3 \u00d7 10 mL), washed with a saturated aqueous solution of ammonium chloride (2 \u00d7 10 mL), water (2 \u00d7 10 mL) and brine (10 mL). The organic layer was dried over anhydrous sodium sulfate, filtered and the solvent was rotary evaporated. Comparison of the NMR data of the crude residue with the literature description + (95), 179 (100), 164 (67), 147 (17), 119 (25), 91 (19), 77 (11).RI (DB-5/ Wax): 1386/1776; Rf = 0.35 (Hex/AcOEt 19:1); EI-MS (70 eV)"} +{"text": "Invasive fungal infections (IFI) are emergent complications in SARS-CoV-2 infection. We aimed to describe the epidemiology, characteristics and outcome of IFI during the pandemic.Between March 2020 and April 2021, patients admitted to the Intensive Care Unit (ICU) in a COVID-19 center in Mexico City who developed IFI were included. COVID-19 associated pulmonary aspergillosis (CAPA) was defined according to the ECMM/ISHAM criteria. Demographic and clinical data were obtained from the electronic medical record. Descriptive analysis was made. The study was approved by the Institutional Review Board.C. parapsilosis, 11 (46%) C. albicans and 2 C. glabrata. Twenty-two received antifungal treatment, 20 with echinocandins and 2 fluconazole. Among 37 CAPA, 8 (22%) were probable and 29 (78%) possible. Serum galactomannan was positive in 8 (22%), 33 respiratory cultures grew Aspergillus . Aspergillus fumigatus was the most frequent isolate in 18/33 (55%). Chest CT showed ground glass opacities in 21 (57%). Most received voriconazole . The median time from ICU admission to IFI was 9.5 (IQR 3-14) days. The median ICU and hospital stay length were 30 days (IQR 16-41) and 40 days (IQR 23-49), respectively. In-hospital mortality was 48%. The incidence rate of IC was higher early in the pandemic, due to Infection Control breaches, while higher CAPA incidence may have occurred later due to ventilation system gaps . Sixty-seven patients with COVID-19 developed IFI during ICU stay, of which 37 (55%) had CAPA, 24 (36%) had Invasive Candidiasis (IC), 3 Cryptococcosis and 3 pulmonary Mucormycosis. The median age was 57.5 (IQR 48-68) and 46 (69%) were male. Thirty-six (54%) had obesity and 20 (30%) type 2 diabetes. Sixty-two received COVID-19 directed therapy: 48/67 (72%) steroids, 4/67 (6%) tocilizumab and 8/67 (12%) were included in clinical trials. Among 24 patients with IC, 13 (54%) were fluconazole-resistant Bi-monthly Invasive Fungal Infection incidence rate/100 ICU admissions.C. parapsilosis was found.We found 9% incidence of IFIs in critically-ill COVID-19 patients with high mortality. The majority received steroids, had obesity and had a prolonged hospital stay. Most had possible CAPA. An outbreak of fluconazole-resistant All Authors: No reported disclosures"} +{"text": "There is a paucity of data of bloodstream infections (BSI) before and during the COVID-19 pandemic. The aim of our study was to compare the incidence and characteristics of blood stream infections (BSI) in hospitalized patients before and during the surge of COVID-19 pandemic in a community hospital in South Bronx. This is a retrospective observational comparative study of adult hospitalized patients with BSI admitted before and during COVID-19 surge . The incidence of BSI, patient demographics, clinical and microbiological characteristics of infections including treatment and outcomes were compared. Enterococcus (20.2%), E.coli (13.2%), and MSSA (12.3%) were predominant microbes causing BSI during COVID vs. MRSA (15.5%), Streptococci (15.5%), and S. pneumoniae (14.1%) before COVID . In multivariate logistic regression, Enterococcal coinfection was associated with COVID positivity , mechanical ventilation , and presence of COPD/Asthma .Of the 155 patients with BSI, 64 were before COVID and 91 were during the COVID surge (Table 1). Incidence of BSI was 5.84 before COVID and 6.57 during surge (p = 0.004). Majority of patients during COVID period had ARDS (39.6%), required mechanical ventilation (57%), inotropic support (46.2%), therapeutic anticoagulation (24.2%), proning (22%), rectal tube (28.6%), Tocilizumab (9.9%), and steroids (30.8%) in comparison to pre-COVID (Table 2). Days of antibiotic therapy prior to BSI was 5 days before COVID and 7 during COVID. Mortality was higher among patients with BSI admitted during COVID surge (41.8% vs. 14.1% p < 0.0001). Of 185 BSI events, 71 were Pre-COVID and 114 during surge. Primary BSI were predominant (72%) before COVID contrary to secondary BSI (46%) (CLABSI) during COVID. Time from admission to positive culture was 2.5 days during COVID compared to 0.9 pre-COVID. Majority of BSI during COVID period were monomicrobial (93%) and hospital acquired (50%) (p=0.001). Comparison of Microorganisms Isolated in the BSIX-axis represents the total number of BSI events whereas the number at the end of each bar represents the percentageEnterococcus spp. was observed during the surge of COVID-19 infection in the South Bronx. Breakdown of infection control measures during the COVID-19 pandemic could have been contributory. Higher incidence of secondary BSI (CLABSI) due to All Authors: No reported disclosures"} +{"text": "The most common underlying medical condition among children \u2265 5 years of age with invasive pneumococcal disease is asthma. How asthma affects pneumococcal colonization is not fully understood. Our objective was to compare pneumococcal colonization rates in children with persistent asthma vs. without asthma.lytA primers (positive Ct \u2264 35). Positive samples were further tested with multiplex serotype-specific PCR assays to determine pneumococcal serotype. This is a single center retrospective cohort study. We used salvage mid-turbinate samples testing negative for influenza per routine care from 5-18 year-olds with upper respiratory symptoms or febrile illness during 2017-18 and 2018-19 northern hemisphere respiratory seasons (November to April). Analyzed groups were those with persistent asthma or those without asthma. Samples were evaluated for pneumococcal colonization by real-time PCR using CDC Of 363 children (120 with persistent asthma and 243 without asthma), 87.6% were 5-10 years old; and 49.9% were male. Fifty percent of samples were from January-February. Pneumococcal colonization rate was lower in children with persistent asthma (10%) vs. without asthma (18.9%) (p=0.03). The odds of colonization were lower in children with persistent asthma (OR 0.4 [95%CI 0.2-0.9]) after adjusting for age, sex, clinic site, smoking exposure, and number of pneumococcal vaccine doses. Colonized patients without asthma were younger than the other groups (Table 1). Pneumococcal serotype/serogroup was assigned in 45 (77.6%) positive samples; 16 (36%) samples corresponded to PCV13 serotypes and 29 (64%) samples to non-PCV13 serotypes. The most common serotypes were: 19F (n=7), 3 (n=6), 6C/6D (n=5), 23B (n=4), 33F/33A/37 (n=4), 35B (n=3), 22F/22A (n=3), 23A (n=3).Table 1Patients with persistent asthma had lower rates of pneumococcal colonization than patients without asthma during respiratory season. Liset Olarte, MD, MSc, GSK (Research Grant or Support)Merck (Research Grant or Support)Pfizer (Research Grant or Support)Sanofi (Research Grant or Support) Douglas S. Swanson, MD, Merck (Research Grant or Support)Pfizer (Research Grant or Support)Sanofi (Research Grant or Support) Brian R. Lee, PhD, MPH , Merck (Grant/Research Support)Pfizer (Grant/Research Support) Christopher J. Harrison, MD, GSK (Grant/Research Support)Merck (Grant/Research Support)Pfizer"} +{"text": "Clostridioides difficile infection (CDI) is an urgent public threat and carries a 25% chance of recurrence (rCDI). Data on safety and efficacy of oral vancomycin prophylaxis (OVP) in reducing rCDI is limited. We implemented a best practice advisory (BPA) to alert the prescriber and antibiotic stewardship (ASP) team for patients with CDI in the previous 60 days being initiated on systemic antimicrobials. The alert states \u201cDon\u2019t use antibiotics in patients with recent CDI without convincing evidence of need. Antibiotics pose a high risk of recurrence\u201d. ASP team would recommended OVP if antibiotics are continued. This study evaluated the impact of the BPA alert on OVP prescribing and patient outcomes.Enterococcus spp (VRE) in clinical culture post-OVP and 1-year mortality. IRB approved, retrospective, observational cohort study comparing patients who received OVP to no OVP. Inclusion: adults with history of laboratory confirmed CDI, \u2265 14 days post-CDI treatment completion, BPA from 3/7/19 \u2013 3/31/20, receiving non-CDI systemic antimicrobials, and without history of bezlotoxumab infusion. Data were reported using descriptive statistics and bivariate analysis. Primary endpoint: rCDI within 2-8 weeks post-OVP completion. Secondary endpoints: vancomycin-resistant P = 0.654). Mortality: 10 (31%) no-OVP and 16 (42%) OVP (P = 0.458). 70 patients included: 32 (46%) no-OVP and 38 (54%) OVP. Baseline characteristics, previous CDI treatment, and outcomes were similar (Table 1). Index CDI was severe in the OVP group . Median Charlson comorbidity index: 7 (3 \u2013 9) no-OVP and 7 (5 \u2013 9) OVP. OVP regimens, 125 mg by mouth: once daily 4 (10%), twice daily 22 (58%), and every 6 hours 12 (32%). Median prophylaxis duration: 10 days (6 \u2013 13). rCDI occurred in 3 (9%) no-OVP and 2 (5%) OVP Susan L. Davis, PharmD, Nothing to disclose"} +{"text": "Streptococcus pneumoniae are a major health concern globally. In children, currently licensed pneumococcal conjugate vaccines (PCVs) provide protection against PD from vaccine serotypes, but other non-vaccine serotypes have emerged and contribute to most residual disease. V114 is a 15-valent investigational PCV containing serotypes 22F and 33F in addition to the 13 serotypes shared by Prevnar 13TM (PCV13). This phase 3 study evaluated safety and immunogenicity of mixed PCV13/V114 regimens when changing from PCV13 to V114 at doses 2, 3, or 4.Pneumococcal diseases (PD) caused by In this double-blind trial, 900 infants were randomized in equal ratios to five treatment groups using a 3 + 1 immunization schedule (3-dose infant primary series followed by one toddler dose). Groups 2, 3, and 4 started with PCV13 and switched to V114 at doses 4, 3, and 2, respectively. Groups 1 and 5 received four doses of PCV13 and V114, respectively. Immunoglobulin G (IgG) responses to the 15 pneumococcal serotypes in V114 were measured at 30 days post-dose 3, prior to dose 4, and 30 days post-dose 4 (PD4). Primary immunogenicity analysis was based on 13 shared serotype responses at PD4. Safety was evaluated as the proportion of participants with adverse events (AEs). At 30 days PD4, IgG geometric mean concentrations (GMCs) for the 13 shared serotypes were generally comparable between V114/PCV13 mixed regimens (Groups 2-4) and participants that received the 4-dose PCV13 regimen (Group 1). Additionally, IgG GMCs for the 13 shared serotypes were generally comparable for participants that received the 4-dose V114 regimen (Group 5) and participants that received the 4-dose PCV13 regimen (Group 1). Infants given at least one dose of V114 mounted immune responses to two unique serotypes in V114 (22F and 33F). Frequency of injection-site and systemic AEs among study participants were generally comparable across all study groups. V114 was well tolerated with a generally comparable safety profile to PCV13. For the 13 shared serotypes, both mixed-dose and 4-dose regimens of V114 induced generally comparable antibody responses to a PCV13 4-dose regimen. Study results support interchangeability of V114 with PCV13 in infants.Adroniki Bili, MD, Merck & Co., Inc. Ron Dagan, MD, Medimmune/AstraZeneca MSD Pfizer Marissa B. Wilck, MD, Merck & Co., Inc. Waldimir Vallejos, MD, Merck & Co., Inc. Christine Nunn, MS, Merck & Co., Inc. Richard McFetridge, B.S., Merck & Co., Inc (Employee) Rong Fu, PhD, MSD China Robert Lupinacci, M.S, Merck & Co., Inc Luwy Musey, MD, Merck & Co., Inc. (Employee) Kara Bickham, MD, Merck Sharp and Dohme"} +{"text": "New types of artificial intelligence products are gradually transferring to voice interaction modes with the demand for intelligent products expanding from communication to recognizing users' emotions and instantaneous feedback. At present, affective acoustic models are constructed through deep learning and abstracted into a mathematical model, making computers learn from data and equipping them with prediction abilities. Although this method can result in accurate predictions, it has a limitation in that it lacks explanatory capability; there is an urgent need for an empirical study of the connection between acoustic features and psychology as the theoretical basis for the adjustment of model parameters. Accordingly, this study focuses on exploring the differences between seven major \u201cacoustic features\u201d and their physical characteristics during voice interaction with the recognition and expression of \u201cgender\u201d and \u201cemotional states of the pleasure-arousal-dominance (PAD) model.\u201d In this study, 31 females and 31 males aged between 21 and 60 were invited using the stratified random sampling method for the audio recording of different emotions. Subsequently, parameter values of acoustic features were extracted using Praat voice software. Finally, parameter values were analyzed using a Two-way ANOVA, mixed-design analysis in SPSS software. Results show that gender and emotional states of the PAD model vary among seven major acoustic features. Moreover, their difference values and rankings also vary. The research conclusions lay a theoretical foundation for AI emotional voice interaction and solve deep learning's current dilemma in emotional recognition and parameter optimization of the emotional synthesis model due to the lack of explanatory power. Nowadays, the core technologies of artificial intelligence (AI) are becoming increasingly mature. People face a new bottleneck in giving the \u201cemotional temperature of humans\u201d to a cold, intelligent device Yonck, . The conAffective computing is crucial to implementing man\u2013machine emotional interactions through intelligent products Picard, . In the As a result of these shortcomings, an empirical study on the correlation between information enabling the emotional evaluation of acoustic features concerning emotional voice state and psychology is required in AI emotional voice interaction using a PAD model, which is the theoretical basis for adjustment of model parameters . The scale of this objective physical quantity corresponds to the fundamental frequency (Fo) of the vocal cord vibrations. Pitch is a subjective psychological quantity of sound, its value determined by the frequency of the acoustic waves (unit: Mel) . Loudness is the scale of a subjective psychological index of intensity and results from a subjective judgment of a pure tone (unit: phon) Sueur, . General) Sueur, . Higher ) Sueur, ; relativ) Sueur, . Additio) Sueur, .spectrum, referring to the energy distribution of signals in the frequency domain; it is expressed in graphs by analyzing perturbations of acoustic waves or periodic features . Because it is easy to induce and simulate emotional recordings that can express real and natural emotions to some extent, PPT was used to provide films as the emotional stimuli to induce and guide recording of the participant , and N is the quantity of all pitch periods. Jitterabsolute calculates the absolute mean of differences between any two adjacent pitch periods. The mean period is calculated usingThe jitter percentage is calculated usingjitterabsolute is divided by the meanPeriod, deriving the ratio between perturbation of fundamental frequency and mean during the pronunciation.The Shimmer percentage reflects changes of amplitude among different periods and is calculated usingshimmerabsolute. The Shimmer% is the ratio between the mean variation of amplitudes and the average value.The mean of amplitude changes between two adjacent periods is calculated from HNR refers to the ratio of the periodic and noise parts in speech signals, and it primarily reflects the hoarse degree of voices. The calculation used to determine HNR is explained below.r(x)) of the voice delay signal x is defined asThe autocorrelation function (s(t) is the stable time signal, and the function achieves the global maximum when x = 0. If the function has global maximum points at other moments in addition to x = 0, a period of T0is assumed. For any positive integer (n), thenwhere to x = 0 are detected, then other local maximum points may exist, whereIf no other global maximum points in addition s(t) is defined as the periodic signal with a period of T0, and N(t) is a noise signal. At x = 0, the voice signal is r(0) = TH(0) + TN(0). As r(0) = rH(0) + rN(0), the following equations can be applied:The function has a global maximum when \u03c4 = 0, where x(t) is a steady time signal and a global maximum when \u03c4 = 0.The extracted seven-feature data of different emotions of different genders were analyzed using SPSS V.26 to conduct a two-way ANOVA, mixed design. Gender was used as the independent variable, and emotional state was used as the dependent variable to understand the variation in seven acoustic features of different genders under different emotions.A total of 62 respondents, including 31 males and 31 females, were recruited. These participants can be grouped according to age: 21\u201330 years old: nine females and eight males; 31\u201340 years old: eight females and eight males; 41\u201350 years old: eight females and eight males; and 51\u201360 years old: six females and seven males.To show significant differences in acoustic features under different emotions and gender, the same respondents were repeatedly measured, testing the seven acoustic features of emotions. Results of the correlation analyses are shown below.Velocity: relevant data of seconds per word are listed in SS = 0.01; Df = 2.53; MS = 0.00; F = 0.25; P > 0.05) did not yield any significant results, i.e., participants' velocity in expressing the nine different emotions was not significantly correlated to gender.The interaction tests for gender and emotional state . The velocity (M = 0.33) of female respondents under different emotional states is significantly lower than that of males (M = 0.29).State main effect: Velocity under different emotional states varies significantly for the overall factor, gender . According to the multiple comparison, the state anxious (M = 0.23) shows the highest velocity, followed by exuberant and hostile (M = 0.26), disdainful (M = 0.27), neutral (M = 0.28), docile (M = 0.31), relaxed (M = 0.32), dependent (M = 0.37), and bored (M = 0.5), successively.Fo (Hz): The interaction test showed significant results for both gender and emotional state , i.e., participants' Fo (Hz) varied across gender and emotional state. Relevant data abstracts of mean pitch are listed in Gender simple main effect: Females show significantly different effects of Fo on emotional states , according to the results of post hoc comparisons: (1) > (4); (2) > (1)\u2013(6), (9); (3) > (5); (4) > (5); (6) > (1), (3) (5); (7) > (1), (3)\u2013(6), (9); (8)> (1), (3)\u2013(6), (9); (9) > (1), (3)\u2013(5). Males also show differences, according to results of post hoc comparisons: (1) > (4); (2) > (1)\u2013(6), (8), (9); (3) > (4); (5) > (1), (3), (4); (6) > (1), (3)\u2013(5), (8)\u2013(9); (7) > (1), (3)\u2013(9); (8) > (1). (3)\u2013(5), (9); (9) > (1). (3)\u2013(5). These results demonstrate that ranks of emotional states are different between males and females.State simple main effect: With respect to influences of Fo (Hz) on gender under different emotional states, F-values of neutral, exuberant, bored, dependent, relaxed, disdainful, anxious, docile, and hostile states are 198.83, 113.02, 147.32, 324.47, 49.67, 51.28, 43.98, 66.71, and 207.12, respectively (p < 0.05). According to the results of post hoc comparisons, females have a significantly higher Fo than males.Fo SD: The interaction test was significant across gender and emotional state , i.e., participants' Fo SD varied across gender and emotional state. Relevant data abstracts of pitch variability are listed in Gender simple main effect: Females show significantly different effects of Fo SD on emotional states , according to the results of post hoc comparisons: (1) > (4)\u2013(6); (2) > (1), (4)\u2013(8); (3) > (1), (4)\u2013(8); (6) > (4); (7) > (1), (5); (8) > (4)\u2013(6); (9) > (1), (4)\u2013(8). Males show no significant differences.State simple main effect: Concerning influences of Fo SD on gender under different emotional states, F values of exuberant, bored, dependent, and hostile states are 47.88, 92.90, and 9.52, respectively (p < 0.05). According to the results of post hoc comparisons, females give significantly higher values than males; however, males > females with respect to the dependent variable.Intensity (dB): The interaction test was significant across gender and emotional state , i.e., participants' intensity varied across gender and emotional state. Relevant data abstracts of mean-sones intensity are listed in Gender simple main effect: Both males and females show significantly different effects of intensity (dB) on emotional states: Females and males . According to post hoc comparisons, results of females are (1) > (3)\u2013(4), (7)\u2013(8); (2) > (1)\u2013(8); (4) > (3); (5) > (1), (3)\u2013(4), (7)\u2013(8); (6) > (1), (3)\u2013(4), (7)\u2013(8); (7) > (3); (8) > (3); (9) > (1), (2)\u2013(8). Results of males are (1) > (3)\u2013(4), (7); (2) > (1), (3)\u2013(9); (3) > (7); (4) > (7); (5) > (1), (3), (4), (7); (6) > (1), (4)-(8); (8) > (3), (4), (7); (9) > (3), (4), (5), (7), (8). The results demonstrate that ranks of emotional states are different between males and females.State simple main effect: Concerning influences of intensity (dB) on gender under different emotional states, F-values of bored, dependent, and docile are 17.46, 8.23 and 9.88, respectively (p < 0.05). According to the results of post hoc comparisons, males give significantly higher results than females.Jitter%: The interaction test resulted in significant outcomes considering gender and emotional state , i.e., participants' Jitter% varied across gender and emotional state. Relevant data abstracts of the ratio between the fundamental frequency changes and the mean are listed in Gender simple main effect: With respect to Jitter% of males and females under different emotional states, females and males both have significant effects. According to post hoc comparisons, females show (1) > (2), (8); (3) > (2), (8); (4) > (2), (8); (5) > (2), (8)-(9); (6) > (1)\u2013(5), (7)\u2013(9); (7) > (1)\u2013(5), (8)\u2013(9). Males show (1) > (2)\u2013(6), (9); (2) > (5)\u2013(6), (9); (4) > (3)\u2013(6), (9); (7) > (1)\u2013(6), (8)\u2013(9); (8) > (2)\u2013(6), (9). These results demonstrate that ranks of emotional states are different between males and females.State simple main effect: Concerning influences of Jitter% on gender under different emotional states, F-values of neutral, exuberant, bored, dependent, relaxed, anxious, and docile are 82.90, 63.04, 8.11, 14.52, 23.77, 35.51, and 65.22, respectively (p < 0.05). According to the results of post hoc comparisons, females > males for relaxed and males > females for the remaining six emotional states.Shimmer%: The interaction test yielded significant results considering gender and emotional state , i.e., participants' Shimmer % varied across gender and emotional state. Relevant data abstracts of intensity perturbations are listed in Gender simple main effect: With respect to Shimmer% of males and females under different emotional states, females and males both have significant effects. According to post hoc comparisons, females show (1) > (2), (4), (8)\u2013(9); (2) > (8)-(9); (3) > (2), (4), (8)-(9); (4) > (8)\u2013(9); (5) > (1)\u2013(4), (8)\u2013(9); (6) > (1)\u2013(4), (8)\u2013(9); (7) > (1)\u2013(4), (8)\u2013(9); (8) > (9). Males show (1) > (2)\u2013(9); (2) > (8)\u2013(9); (3) > (2), (8)\u2013(9); (4) > (2)\u2013(3), (6), (8)\u2013(9); (5) > (2), (6), (8)\u2013(9); (6) > (8)\u2013(9); (7) > (2)\u2013(9); (8) > (9). These results demonstrate that ranks of emotional states are different between males and females.State simple main effect: Concerning influences of Shimmer% on gender under different emotional states, F-values of neutral, exuberant, bored, dependent, disdainful, relaxed, anxious, docile, and hostile are 82.90, 63.04, 8.11, 14.52, 19.99, 23.77, 35.51, 65.22, and 7.58, respectively (p < 0.05). According to post hoc comparison results, females are significantly higher than males concerning disdainful and relaxed, which is the opposite of the remaining emotional states.HNR: The interaction test yielded significant results considering gender and emotional state , i.e., participants' HNR varied across gender and emotional state. Relative data abstracts of the ratio of periodic part and noise in signals are listed in Gender simple main effect: With respect to HNR of males and females under different emotional states, females and males both show a significant effect. According to post hoc comparisons, females show (1) > (3), (5)\u2013(7); (2) > (1), (3)\u2013(7); (3) > (6)\u2013(7); (4) > (3), (5)\u2013(7); (5) > (6)\u2013(7); (8) > (1)\u2013(7); (9) > (1), (3)\u2013(7). Males show (2) > (1), (7); (3) > (1)\u2013(2), (4)\u2013(5), (7)\u2013(9); (4) > (1); (5) > (1), (7); (6) > (1)\u2013(2), (4), (7)\u2013(9); (8) > (1)\u2013(2), (7); (9) > (1)\u2013(2), (7). These results demonstrate that ranks of emotional states are different between males and females.State simple main effect: With respect to influences of HNR on gender under different emotional states, F-values of neutral, exuberant, bored, dependent, relaxed, docile, and hostile are 62.35, 40.59, 8.50, 18.12, 49.74, 22.60, and 15.43, respectively (p < 0.05). According to the results of post hoc comparisons, males give significantly higher values than females in terms of bored and relaxed although the opposite phenomenon is observed for the remaining five emotional states.SD, intensity (dB), Jitter%, Shimmer%, and HNR have interactions, and velocity displays no interaction. (2) There are significant gender differences in terms of velocity of eight emotional states in PAD. Moreover, males show significantly higher velocity (M = 0.29) compared to females (M = 0.33). (3) Males show no significant differences in six of the acoustic features, except Fo SD. Looking at the gender simple main effect, there are significant gender differences in terms of degree and ranking of emotional states. Looking at the state simple main effect, Fo (Hz) shows significant differences among different emotional states. Fo SD is significantly different in terms of exuberant, bored, dependent, and hostile states. Intensity (dB) is significantly different with respect to bored, dependent, and docile states. There are significant differences in Jitter% in neutral, exuberant, bored, dependent, relaxed, anxious, and docile states. Shimmer% has significant differences. HNR presents significant differences in neutral, exuberant, bored, dependent, relaxed, docile, and hostile states. The above analyses found physical quantities of relevant parameters and rankings as shown in the results. Specifically, the voice-affective interaction of intelligent products was used as the preset scene. Therefore, the PAD model is different in terms of emotional classification from the emotional classification found in the literature review With respect to gender and emotional states, Fo (Hz), Fo We comprehensively explored the influence of eight emotional states of the PAD model and gender on affective recognition and expression of acoustic features in a systematic method. In terms of theoretical implications, the PAD model of intelligent products provides an emotional model that is different from previously used models. In emotional computing, the PAD model is conducive to understanding the influences of gender and emotional states on the connection between acoustic features and psychology in AI affective-voice interaction, including physical variables and their differences. This aids in understanding the acoustic features of affective recognition and expression. In terms of practical applications, in view of the development trends of intelligent products on the market, man\u2013machine interaction will be popularized in intelligent-home life, travel, leisure, entertainment, education, and medicine in the future. This study will help to improve the affective-voice interaction scenes of intelligent products and connections between the emotional states and acoustic features of the speaker. The analysis of acoustic features under different emotions and genders provides an empirical foundation for adjusting the parameters of the affective-voice interaction mathematical models and offsets limitations of current deep learning acoustic models' \u201cexplanatory\u201d power. The research results can provide a reference for the adjustment of model parameters during optimization of affective recognition and affective expression.This study was designed for theoretical and practical application; however, the recorded voices only used Chinese materials. There may be some differences with different languages, which deserves particular attention for generalization of the results. Subsequent studies can further investigate correlations between emotional classification of PAD and voice rhythm of different genders in the PAD model to provide a theoretical basis and supplement shortages of deep learning. This study aims to strengthen emotional integration during man\u2013machine interaction, allowing users and products to generate the empathy effect and, thus, expand the human\u2013computer relationship and highlighting the value of products.The original contributions presented in the study are included in the article/Ethical review and approval was not required for the study on human participants in accordance with the local legislation and institutional requirements. Written informed consent for participation was not required for this study in accordance with the national legislation and the institutional requirements.K-LH: conceptualization and writing. K-LH and S-FD: methodology and formal analysis. K-LH and XL: investigation. S-FD and XL: resources. K-LH: organized the database and analyzed and interpreted the data.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Childhood Primary Angiitis of Central Nervous System (cPACNS) is rare, but can cause significant damage and result in disability or even death. Because of its rarity, the sometimes acute and variable presentation, limited awareness, and the absence of widely accepted diagnostic and therapeutic standards, cPACNS is a diagnostic and therapeutic challenge. Three subcategories of cPACNS exist, including angiography-positive non-progressive p-cPACNS, angiography-positive progressive p-cPACNS which both affects the medium to large vessels, and angiography-negative small vessel sv-cPACNS. Diagnosis and treatment of cPACNS relies on personal experience, expert opinion and case reports/case series. To collect information on diagnostic and therapeutic approaches to transient and progressive cPACNS, a survey was shared among international clinicians . Results from this survey will be used to define statements toward a consensus process allowing harmonization of diagnostic and therapeutic approaches and the generation of evidence in a rare condition. Childhood Primary Angiitis of Central Nervous System (cPACNS) is a rare, severe and potentially life threatening disease . While tDue to the rarity of the condition and, variable clinical symptoms, cPACNS can be difficult to diagnose and manage. Presentation and prognosis are dependent on the size and location of affected vessels, and the severity and extent of the inflammatory response induced. The presence of (sometimes) age-specific differential diagnoses, including primary seizures, migraines, tumors, infections, etc., represent additional diagnostic challenges .Though case definitions have been proposed, they vary between neurological and rheumatological/immunological literature, and no uniformly recognized guidelines for diagnosis and treatment exist , 4. CalaThough helpful in some cases, criteria leave cPACNS a diagnosis of exclusion, and time to diagnosis and treatment are largely dependent on the awareness and experience of the treating team.Arteria cerebri anterior or media. While causing variable degree of damage during inflammatory activity, non-progressive p-cPACNS is self-limited within 3 months. Transient disease can be discriminated from progressive p-cPACNS that can affect either short or longer segments of one or more medium to large sized cerebral arteriae, including posterior vessels can be a tool in rare conditions where clinical trials are currently not available or realistic, such as p-cPACNS. They allow prospective data collection on therapy and associated outcomes. As a first step, real-life standard of care requires to be documented to develop statements e.g., through Delphi surveys that can then be used toward an expert consensus conference for CTP development , 12.We describe a survey undertaken with international experts in which we sought information on diagnostic and therapeutic strategies in transient and progressive p-cPACNS.A survey was designed to collect information on diagnostic and therapeutic approaches in p-cPACNS by experts in the field. It consisted of introductory questions addressing demographics and experience of participants, and 2 case scenarios accompanied by multiple choice questions. One case (case 1) represented a patient with progressive p-cPACNS, the second (case 2) had two alternative outcomes: transient p-cPACNS likely not related to VZV, and transient p-cPACNS likely related to VZV. Survey details can be accessed in www.surveymonkey.com). A link to the survey was sent to addressees in August 2019 and the survey was open for 2 months. A reminder e-mails was sent out at both 4 and 6 weeks after the initial survey link was shared. The survey was distributed among colleagues from Europe, North America, and globally with experience in the diagnosis and treatment of p-cPACNS. This was achieved through member email lists of the German Society for Pediatric Rheumatology (GKJR) , the Pediatric Rheumatology European Society (PRES) , members of the German speaking \u201cNetwork Pediatric Stroke\u201d with members in Germany, Austria and Switzerland , and subscribers to the American College of Rheumatology/CARRA Pediatric Rheumatology Bulletin Board (ped-rhe-list-bounces@mcmaster.ca) .The survey was conducted online using the web-based tool Survey Monkey .N = 92 responses). N = 85 responses).The survey was answered by a total of 92 clinicians, with the majority of colleagues specializing in Pediatric Rheumatology , followed by 11 Pediatric Neurologists (11.9%), 4 General Pediatricians (4.3%), one Adult Rheumatologist, Pediatric Intensive Care Clinician, Pediatric Hematologist and Adult Neurologist each (Q1). The number of responses varied slightly between individual questions; the number of responses to each question are indicated throughout this manuscript. Experience of responders in their subspecialty varied, as did number of cases of cPACNS treated , and among 34 respondents who specified, most suggested testing for deficiency of adenosine deaminase 2 . Further conditions mentioned included Ehlers-Danlos and Marfan syndromes (2.9% each), systemic and organ-specific inflammatory disorders, such as granulomatosis , hemophagocytic lymphohistiocytosis (HLH), Systemic lupus erythematosus (SLE), Sj\u00f6gren's syndrome, collagen tissue disease, and Moya Moya disease.When asked whether genetic testing should be considered, 50/87 respondents (57.5%) felt that genetic testing should indeed be performed and new acute-onset symptoms of aphasia, ataxia, headaches, and progressive vertigo for the past 24 h. He has no personal of family history of clotting disorders, strokes or autoimmune/inflammatory disease. He has had no infections in the past year and no travel history (other than a \u201csore throat or sniffles here and there\u201d), no pets, and no other symptoms.N = 74 responses), respondents ranked emergency MRI of the brain including angio-MRI (90.5%) and blood tests including full blood counts, inflammatory markers and clotting tests (90.5%) as most important. These were followed by lumbar puncture to analyze the CSF (82.4%), and brain CT scan including CT angiography (23.0%). Of the respondents who considered blood tests essential , 98.6% would order full blood count including complete white cell count, 97.3% would order clotting tests including PTT, INR, fibrinogen and D dimers, and 94.6% would order immunology tests including ANA, ENA, complement factors, cardiolipin antibodies and ANCA. When asked which blood immunology tests they would order, 97.3% answered anti-phospholipid antibody testing, followed by antinuclear antibody testing (93.2%), requested anti-neutrophil cytoplasmic antibodies (89.2%), anti-dsDNA antibodies (87.8%), complement factors and activation of the complement cascade (83.8%), and anti-NMDA (N-methyl-D-aspartate) receptor and aquaporin antibodies (67.6%) . Of 74 respondents who considered performing a lumbar puncture , most (98.6%) would request cell counts, differentiation and protein quantification, followed by microbial culture (93.2%), glucose levels (90.5%), oligoclonal bands (89.1%), CSF opening pressure (86.5%), lactate (74.3%) and anti-NDMA and aquaporin antibodies (68.9%). When asked about helpful MRI techniques , 87.3% of responders requested MRI angiography, followed by fluid-attenuated inversion recovery , diffusion-weighted MRI sequences , T1 with fat saturation , T1FS with contrast medium , T2FS , Turbo inversion recovery magnitude (TIRM)/Short tau inversion recovery . Detailed results are summarized in When asked about diagnostic approaches to this specific case and CRP (4mg/L). Approximately 30 h after the onset of ataxia and aphasia, Magnetic Resonance Imaging (MRI) shows alterations in proton diffusion capacity in the Cerebellum and a significant and long ranging stenosis of the distal Basilar artery in MRI angiography .N = 73 responses). Most respondents selected progressive p-cPACNS (80.8%), followed by transient p-cPACNS (69.9%), ischaemic stoke (64.4%), congenital anatomical deformity (39.7%) and infections (38.4%). Asking indicators of likely progressive p-cPACNS , the majority of respondents suggested imaging results (87.7%), followed by clinical course with disease progression over 3 months or more (69.9%), laboratory findings suggesting systemic inflammation (46.6%), acute presentation with \u201csystemic signs\u201d (43.8%), and response to immune modulation (41.1%). Detailed results are summarized in Based on new information provided, respondents were asked to select 5 most likely differential diagnoses progressive p-cPACNS is made.N = 73 responses). Sixty-eight of 73 respondents would start treatment with intravenous Methylprednisolone (IVMP) over 5 days, followed by oral prednisolone (93.2%), 47/73 (64.3%) consider treatment with intravenous Cyclophosphamide every month for 4\u20136 months, 9/73 (12.3%) would start treatment with mycophenolate mofetil (MMF), and 3/73 (4.1%) would treat with oral prednisolone. None of the respondents chose oral cyclophosphamide or azathioprine for induction treatment.Participants were asked to decide which medication they consider for the induction of remission , most responders agreed on administering IV heparin initially (65.7%), followed by acetyl salicylic acid (ASA), and a combination of ASA and clopidogrel. Considering post-acute phase thrombosis prophylaxis , the majority of respondents would prescribe aspirin (47.1%), followed by subcutaneous heparin (22.9%), a combination of ASA and clopidogrel (14.3%), warfarin (11.4%), clopidogrel alone (5.7%), or DOACs (2.9%). Opinions on when to discontinue anticoagulation treatments were divided and ranged between 3 and 36 months. One respondent would not administer anticoagulation treatment (1.4%) .N = 73 responses), the majority of respondents (72.6%) would prescribe MMF, followed by azathioprine (20.5%), oral prednisolone (17.8%), intravenous cyclophosphamide (13.7%), rituximab (9.6%), methotrexate (5.5%), oral cyclophosphamide (following Fauci scheme) or TNF inhibitors (1.4% each). Opinions on the required duration of treatment were divided and ranged between 3 and 36 months. When asked how long to include oral corticosteroid treatment in the regimen, including slow taper , respondents responded: 3 months (20.8%), 6 months (41.7%), 12 months (15.3%), 18 months (4.2%), 24 months (5.6%), 36 months (1.4%), and 1.4% indicated no corticosteroid treatment , 56/72 (77.8%) respondents suggested to repeat MRI after 3 months, 36/72 after 6 months (50.0%), 25/72 after 12 months (34.7%), 11/72 after 18 months (15.3%), 21/72 after 24 months (29.1%), and 10/72 after 36 months (13.9%) and 11/72 answered other (15.3%). When asked when to schedule clinical follow up , 59/73 respondents indicated within 3 months (80.8%), 23/73 after 6 months (31.5%), 22/73 after 12 months (30.1%), 19/73 after 18 months (26.0%), 21/73 after 24 months (28.8%) and 15/73 after 36 months (20.6%).Monitoring disease activity and damage using MRI . She has a past medical history of a clinically diagnosed Varicella Zoster Virus (VZV) infection 6 months ago. There's no history of strokes or clotting disorders in her personal or family history.N = 70 responses), the majority of respondents suggested that initial investigations should include blood test (94.3%), emergency MRI of the brain including an MRI angiography (92.9%), lumbar puncture and CSF analysis (88.6%), and brain CT scan including CT angiography (31.4%). Of the participants who considered blood tests essential , 98.6% would request full blood count including complete white cell count; 97.1% clotting tests including PTT, INR, fibrinogen and D dimers, and 90.0% would order immunology tests including ANA, ENA, complement factors, cardiolipin antibodies and ANCA; 42.9% suggested blood tests for adenosine deaminase 2 activity (ADA2) and 41.4% for interferon gamma release assay (IGRA) to exclude tuberculosis , 94.3% considered anti-phospholipid antibodies as required, followed by antinuclear antibodies, ANCA, anti-dsDNA antibodies, complement factors and activation of the complement cascade, and anti-NMDA and aquaporin antibodies. Of the 70 participants requesting a lumbar puncture , 98.6% considered cell counts and differentiation, followed by protein (95.7%), glucose (92.9%), microbial cultures (90.0%), opening pressure (84.3%), oligoclonal bands (81.4%), lactate (78.5%), and anti-NMDA and aquaporin antibodies (54.3%). Of 68 participants who considered emergency MRI , 88.2% requested MRI angiography, followed by FLAIR (73.5%), diffusion-weighted sequences (73.5%), T1FS with contrast medium (54.4%), T2FS (50.0%), T1 with FS (41.2%), and TIRM/STIR (39.7%) .Next, the participants were informed that autoantibodies in CSF and blood come back negative, there's no evidence for clotting disorders or infection . Blood and CSF inflammatory markers remain within normal limits. DWI sequences unveiled altered diffusion capacity in the left hemisphere; Time of flight MR Angiography (TOF-MRA-)sequences demonstrate narrow caliber of left distal internal carotid artery and proximal anterior and medial cerebral artery. Post-gadolinium MRI sequences reveal contrast enhancement of the thickened vascular wall in the affected segments. Conventional angiography showed incomplete occlusion of the left A. cerebri media .N = 70 responses). Most respondents (81.4%) considered p-cPACNS, likely transient related to VZV, followed by ischaemic stroke (70.0%), transient p-cPACNS not related to VZV (62.9%), CNS tuberculosis (61.4%) and infections e.g., meningitis (32.9%) .N = 69 responses), 53/69 (76.8%) respondents suggested IVMP over 5 days, followed by 18/69 who considered intravenous Cyclophosphamide every month for 4\u20136 months (26.1%), 12/69 MMF (17.4%), 9/69 (13.0%) oral Prednisolone, and 2/69 Azathioprine (2.9%). None of the participants chose oral Cyclophosphamide for induction treatment. Respondents were asked how long to continue oral corticosteroid treatment including slow taper for , they answered: 3 months , 6 months , 12 months , 18 months , 24 months and 36 months . Five of 66 respondents answered no to prescribing oral corticosteroid treatment (7.6%).When asked which medication to administer for induction treatment , most responders agreed on administering IV Heparin initially as anticoagulation treatment (52.2%) in the acute phase, followed by ASA (29.9%), a combination of ASA and clopidogrel (6.0%) and warfarin (4.5%). Considering post-acute phase prophylaxis , a majority of responders would prescribe Aspirin (53.0%), followed by subcutaneous Heparin (18.2%), a combination of Aspirin and Clopidogrel (9.1%), warfarin (7.6%), clopidogrel or DOACs (4.6% each). Regarding discontinuation of anticoagulation treatments , respondents answered after 3 months (11.1%), 6 months (17.5%), 12 months (20.6%), 18 months (3.2%), 24 months (12.7%) and 35 months (6.4%). Five of 63 respondents answered they would not administer anticoagulation treatment (7.9%) .N = 69 responses) was suggested after 3 months by 60/69 (87.0%) respondents, after 6 months by 32/69 (46.4%) and after 12 months by 25/69 (36.2%). Eight of 69 respondents would repeat MRI after 18 months (11.6%), 17/69 after 24 months (24.6%) and 6/69 after 36 months (8.7%). Clinical follow up was considered reasonable at 3 months by 58/70 respondents (82.9%), at 6 months by 24/70 (34.3%), 12 months by 24/70 (34.3%), 18 months by 16/70 (22.9%), 24 months by 18/70 (25.7%), and after 36 months by 14/70 (20.0%).Monitoring of disease activity and damage using MRI , the majority of the respondents indicated they would treat the patients with IV Acyclovir treatment over 14 days , 32/68 (47.1%) of responders indicated initially treating with IVMP over 5 days followed by oral Prednisolone. Less common answers indicated by participants were induction with oral Prednisolone, followed by oral Prednisolone taper , IV Cyclophosphamide , MMF induction treatment , Azathioprine . None of the participants indicated they would treat the patient with oral Cyclophosphamide (Fauci scheme).As a result of positive testing for VZV . Answers suggested multi-professional approaches in both clinical scenarios.For both cases, participants were asked to indicate which specialties should be involved in the patient's care (N = 91 responses). As responses varied significantly, especially among answers not within the top 3, only the top three most commonly selected answers for diagnosis and treatment methods were used. Responses related to case 1 were associated with years of experience associated with variable approaches to diagnosis and treatment , which may have been caused by limited experience with the condition across medical specialties and countries. Indeed, only 19.6% of responders had <5 years' clinical experience as a specialist suggesting that mostly more senior colleagues with personal experience in diagnosing and treating PACNS patients responded. Only 74.7% of participants had personal experience in the care of patients with cPACNS. This survey represents opinions from a relatively small number of pediatric rheumatologists, neurologists and other experts involved in the management of this rare condition. It will remain to be determined, e.g., through Delphi questionnaires and subsequent expert consensus meetings, whether responses are indeed widely representative for standard-of-care.Diagnostic approaches for both forms of cPACNS queried here (progressive vs. transient p-cPACNS) did not vary between forms. Overall, 75.3% agreed that MRI is essential for diagnosing p-cPACNS, 26.8% favor lumbar puncture and CSF analyses, 20.2% would perform CT scans as an alternative to MRI. Interestingly, when confronted with the two case scenarios, responses were slightly different. MRI and blood laboratory tests were considered the most important and therefore likely most helpful tools with agreement between 90.5 and 94.3%, followed by CSF analyses (82.4 vs. 88.6%), and CT scans (23.0 vs. 31.4%).Agreement regarding appropriate MRI strategies between respondents and cases was strong. Most participants would request MRI angiography (87.3 vs. 88.2%), followed by FLAIR (77.5 vs. 73.5%), diffusion weighted imaging (74.7 vs. 73.5%), T1 FS with contrast application (53.5 vs. 54.4), T2 FS (52.1 vs. 50.0%), T1 FS (42.3 vs. 41.2%), and lastly TIRM or STIR (39.4 vs. 39.7%). Based on published reports, MRI angiography is a strong tool to assess local perfusion and (to some extent) vessel obstruction , FLAIR sWhile patients with transient pPACNS can exhibit mild clinical symptoms indicative of focal neurological deficits, patients with progressive pPACNS usually present with symptoms of both focal and diffuse neurological deficits, including cognitive impairment, headaches and in some cases seizures , 22, 23.Based on participants' responses, most important blood tests include blood cell counts and differentiation (99% both), clotting tests (97% both), immunology profiling . Additional tests frequently requested included ADA2 levels for the exclusion of DADA2, and IGRA to exclude TBC, as both conditions have been reported to cause neuroinflammation/vasculitis , 25. LumTherapeutic approaches varied between participants and (not surprisingly) progressive vs. transient disease. In progressive p-cPACNS (case 1), most participants would have chosen an induction treatment regimen with IVMP 93.2%), followed by CPM 64.3%), MMF (12.3%) and oral prednisolone (4.1%), while in transient p-cPACNS (case 2), CPM was less frequently chosen 26.1%), while oral prednisolone appears to play a bigger role (13.0%). Provided potential side-effects and the transient nature of the disease, the use of CPM in transient p-cPACNS appears surprising, but prospective trials are lacking , followed by azathioprine (21%), prednisolone (18%), CPM , rituximab (10%), methotrexate (5%) and TNF inhibitors (1%). Responses reflect few available published reports in which aforementioned regimens had been chosen. However, data is limited to relatively small and retrospective case collections, and evidence from prospective trials is lacking.Duration of corticosteroid treatment was recorded in progressive and transient p-cPACNS, and was largely comparable. Most colleagues would treat patients with transient disease for 3 (37.9%) or 6 months (34.9%), while slightly more would treat for 6 (41.7%) than 3 (20.8%) months in progressive p-cPACNS.Antithrombotic prophylaxis was considered essential by a majority of participants in the acute and post-acute phase in both progressive and transient p-cPACNS. Heparin i.v., in the acute phase was deemed important in progressive (65.7%) and transient (52.2%) disease, followed by aspirin (27.1 vs. 29.9%), and the combination of aspirin and clopidogrel (7.1 vs. 6.0%). For post-acute phase prophylaxis, colleagues consider aspirin (47.1 vs. 53.0%), heparin s.c. (22.9 vs. 18.2%), aspirin and clopidogrel in combination (14.3 vs. 7.6%), clopidogrel (6 vs. 4.6%), DOACs (vs. 4.6% each). As many as 12.1% of colleagues would not prescribe post-acute phase thromboembolism prophylaxis in patients with transient p-cPACNS. Suggested duration of anticoagulant treatment did not vary dramatically, most colleagues suggested 12 months (18.6% in progressive and 20.6% in transient p-cPACNS), followed by 24 months (18.6 vs. 12.7%). Interestingly, few colleagues preferred 18 months treatment (4.3 vs. 3.2%). However, this reflects the absence of evidence and the urgent need for data collection and generation of consensus.Proposed monitoring of disease activity and damage was comparable between both progressive and transient p-cPACNS, and, based on participants' responses, should include MRI imaging and clinical examinations every 3 months. However, agreement significantly reduced over time, and at 18 months only 15 vs. 12% found MRI and 26 vs. 23% clinical examinations to be of importance. This is special interest, as a majority of 73% would continue immune modulating treatment for up to 24 months, and flares appear more likely with or after treatment discontinuation.Consensus on a multi-professional approach to diagnosis and treatment was strong for both transient and progressive p-cPACNS.In the absence of widely accepted and prospectively evaluated diagnostic criteria and evidence-based therapeutic strategies for p-cPACNS, clinical management varies between centers. Diagnostic and therapeutic strategies vary considerably, especially in regards to therapeutics used and treatment duration. Based on data from this survey, Delphi questionnaires will be developed to define statements to be used toward expert consensus meetings. This process will aim at the development of diagnostic and treatment plans for patients with p-cPACNS following agreed consensus-based protocols.The original contributions presented in the study are included in the article/All authors were involved in study planning and manuscript preparation, AQ and CH lead on data analysis and preparation of the first written draft, all authors read and agreed on the final version of this manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Correction to: Trop Med Health 49, 56 (2021)https://doi.org/10.1186/s41182-021-00349-59,10, Shoaib Ahmad10,11 and Mohammad Yasir Essar11,12 to Oumaima Outani10, Shoaib Ahmad11 and Mohammad Yasir Essar12.Following publication of the original article , the affThe author affiliation list has been updated above and the original article has been"} +{"text": "Odonata from Santiago Dominguillo, Oaxaca is presented here. A total of 1601 specimens from six families, 26 genera and 50 species were obtained through monthly samplings of five days each. Libellulidae was the most diverse family (21 species), followed by Coenagrionidae (19), Gomphidae (4) and Calopterygidae (3). The Lestidae, Platystictidae and Aeshnidae families were the less diverse, with only one species each. Argia was the most speciose genus with 11 species, followed by Enallagma, Hetaerina, Erythrodiplax and Macrothemis with three species each and Phyllogomphoides, Brechmorhoga, Dythemis, Erythemis and Orthemis with two species each. The remaining 17 genera had one species each. Argiapipila Calvert, 1907 and Leptobasisvacillans Hagen in Selys, 1877 were recorded for the first time for the state of Oaxaca. We also analysed the temporal patterns of taxonomic and phylogenetic divergence for the Santiago Dominguillo Odonata assemblage: the Shannon diversity value throughout the year was 21.07 effective species, while the Simpson diversity was 13.17. In general, the monthly phylogenetic divergence was higher than expected for taxonomic distinctness, and lesser for average taxonomic distinctness. Monthly diversity, evenness and taxonomic divergence showed significant positive correlations (from moderate to strong) with monthly precipitation values. The analysis of our results, however, indicates that an increase in rainfall not only influences the temporal diversity of species, but also the identity of supraspecific taxa that constitute those temporal assemblages, i.e. there is an increase in temporal phylogenetic divergence.A study on the patterns of richness, diversity and abundance of the Tropical forests are the most important reservoirs of terrestrial biodiversity around the world. Despite there being many studies in these ecosystems,most of them focus on tropical wet forests (TWF), with less attention to the tropical dry forests . TropicaSeasonal fluctuations of richness and abundance of insects inhabiting tropical forests has been documented elsewhere e.g. . In MexiNoguera et al. 2017Odonata was included in that project as a \u201ctest group\u201d, with the aim of comparing if their local assemblages vary in a similar way as those exhibited by other insect groups that are more directly associated with plants . Dragonflies are predaceous insects that do not depend directly on plants from a trophic point of view, but forests can provide certain requirements for the adults, such as optimal microclimates for effective thermoregulation, conditions for an optimal foraging and a provision for nocturnal roosting or daytime shelter from both inclement weather and predators , south of the Tehuacan-Cuicatlan Biosphere Reserve. The area belongs to what is known as the Floristic Province of the Tehuacan-Cuicatlan Valley, which is considered part of the xerophytic Mexican region (The study area was the vicinity of the town of Santiago Dominguillo (referred to herein as Dominguillo), in the north-eastern part of the State of Oaxaca (n region .Lysilomadivaricatum (Jacq.), Burseraaptera Ram\u00edrez, B.morelensis Ram\u00edrez, B.schlechtendalii Engl, Cyrtocarpaprocera Kunth, Pachycereusweberi (J.M. Coult.) Backeb, Escontriachiotilla (F.A.C.Weber ex K.Schum.) Rose and Ceibaparvifolia Rose and other minor tributaries around the Cuicatlan-Dominguillo vicinity, including the towns of Santiago Dominguillo and San Pedrito Chicozapote , with an occasional collection also in Rio Grande, Presa Derivadora Matambo . Fieldwork was carried out monthly from November 1997 to October 1998. Samplings were done for five days every month, from 09:00 to 15:00 h (10:00 to 16:00 h during daylight savings time).Diversity analysis. We analysed the diversity of the Odonata assemblage of Santiago Dominguillo and its temporal pattern. The assemblage structure was analysed through the abundance , richness , Shannon diversity and Simpson diversity Jost 2006ity e.g. and we uor nats) .1D and 2D using the estimators proposed by Magurran , based on the monthly information occurrence of collected odonates. Additionally, we evaluated the monthly phylogenetic divergence using the taxonomic distinctness (\u0394*) and average taxonomic distinctness (\u0394+) indices based on the abundance and incidence of the species, respectively , the monthly phylogenetic diversity and the average rainfall and temperature recorded in Dominguillo during the sampling time. All the analyses were done using Past software , UNAM, Mexico City.Odonata species registered from Santiago Dominguillo, Oaxaca, Mexico, including phenology data and number of individuals collected (in parenthesis). Additional information in Suppl. materials List of LestidaeArchilestesgrandis . Jun (1). , Jul (2), Aug (6).CalopterygidaeHetaerinaamericana . Nov (41), Jan (23), Mar (30), Apr (11), May (23), Jun (6), Jul (7), Aug (3), Sep (24), Oct (4). .Hetaerinacruentata . Jan (2), Mar (11), Apr (7), May (1), Jun (2), Jul (6), Aug (7), Sep (7), Oct (5).CoenagrionidaeApanisagrionlais . Jul (1).Acanthagrionquadratum Selys, 1876. Jan (1), Apr (4), May (9), Jun (6), Jul (2), Sep (2).Argiaanceps Garrison, 1996. Nov (8), Jan (9), Mar (14), Apr (7), May (17), Jun (4), Jul (7), Aug (8), Sep (19), Oct (6).Argiaextranea . Nov (2), Jan (2), Mar (10), Apr (2), May (6), Jun (4), Jul (4), Aug (3), Sep (21), Oct (4).Argiafuncki . May (1), Jun (1), Jul (2), Aug (1).Argiaharknessi Calvert, 1899. Jan (1), Mar (5), Apr (1), May (1), Jun (3), Jul (2), Aug (2), Sep (4).Argiaimmunda . Nov (31), Jan (6), Feb (3), Mar (19), Apr (7), May (7), Jun (2), Jul (4), Aug (2), Sep (2), Oct (4).Argiaoculata Hagen in Selys, 1865. Jan (3), Mar (1), Apr (8), May (7), Jun (1), Jul (5), Aug (2), Sep (14), Oct (3). , Jan (6), Feb (3), Mar (14), Apr (25), May (28), Jun (6), Jul (4), Aug (4), Sep (7), Oct (6).Argiapallens Calvert, 1902. Nov (6), Jan (8), Mar (8), May (2), Jun (2), Jul (1), Aug (1), Oct (4).Argiapipila Calvert, 1907. Aug (1).Argiapulla Hagen in Selys, 1865. Nov (42), Jan (21), Feb (5), Mar (45), Apr (54), May (85), Jun (19), Jul (9), Aug (6), Sep (20), Oct (5). , Jan (8), Feb (7), Mar (29), Apr (15), May (28), Jun (9), Jul (1), Aug (2), Sep (5), Oct (2).Enallagmanovaehispaniae Calvert, 1907. Nov (2), Jan (1), Mar (4), Jun (5).Enallagmapraevarum . Nov (6), Jan (11), Feb (2), Mar (5).Enallagmasemicirculare Selys, 1876. Mar (1).Ischnuradenticollis . Jan (1).Leptobasisvacillans Hagen in Selys, 1877. Apr (1)Telebasissalva Hagen in Selys, 1877. Nov (4), Jan (4), Feb (1), Mar (6), Apr (3), May (3), Jun (4), Aug (7).AeshnidaeAnaxwalsinghami McLachlan, 1883. Nov (1).GomphidaeErpetogomphuselaps Selys, 1858. Nov (4), Jun (4), Jul (8), Aug (6), Sep (8), Oct (7).Phyllogomphoidesdanieli Gonz\u00e1lez & Novelo, 1990. Jun (3), Jul (9), Aug (2).Phyllogompoidessuasus . Aug (3), Oct (2).Progomphusclendoni Calvert, 1905. Jun (1), Jul (4).LibellulidaeBrechmorhogamendax . Nov (1).Brechmorhogapraecox . Nov (2), Mar (2), May (5), Jun (8), Jul (9), Aug (7), Sep (4), Oct (1).Dythemisnigrescens Calvert, 1899. Mar (1), Jun (4), Jul (4), Aug (2).Dythemissterilis Hagen, 1861. Nov (7), Jan (5), Mar (8), Apr (2), May (6), Jun (15), Jul (7), Aug (1), Sep (2), Oct (1). Erythemisplebeja . Jun (1).Erythemisvesiculosa . May (2), Jun (1).Erythrodiplaxfunerea . Apr (1), May (2), Jun (2).Erythrodiplaxfusca . Nov (12), Jan (4), Feb (3), Mar (8), Apr (4), May (5), Jun (8), Jul (2), Aug (6).Erythrodiplaxumbrata . Apr (1). , Apr (1), Jun (4), Jul (7), Aug (5), Sep (1), Oct (3).Macrothemishemichlora . Nov (1), Apr (2), May (5), Jun (7), Aug (3), Sep (1).Macrothemisinacuta Calvert, 1898. Jun (6), Jul (3).Macrothemispseudimitans Calvert, 1898. Nov (4), Jan (5), Feb (1), Mar (6), May (1), Jun (9), Jul (6), Aug (3), Oct (3). . Jun (3).Orthemisdiscolor . Jan (1), Mar (2), May (2), Jul (1), Sep (4), Oct (2).Orthemisferruginea . Nov (5), Jan (2), Apr (1), Jun (1), Oct (3).Paltothemislineatipes Karsch, 1890. Nov (1), May (1), Jul (3), Aug (1), Oct (1).Pantalaflavescens . Nov (1), Aug (1), Oct (1).Perithemismooma Kirby, 1889. Mar (1), Jul (3), Aug (2).Pseudoleonsuperbus . Nov (1), Mar (1), May (1), Jun (2), Jul (2), Aug (3), Oct (1). .Libellulidae and Coenagrionidae were the families with the highest number of species, 21 and 17, respectively, followed by Gomphidae with four, Calopterygidae with three and Lestidae, Platystictidae and Aeshnidae with only one species each , followed by Hetaerinaamericana Fabricius, 1798 (172), Argiaoenea Hagen in Selys, 1865 (124), Argiatezpi Calvert, 1902 (112) and Argiaanceps Garrison, 1996 (99). Those five species represented 51% of the total abundance of the assemblage and Argia, in particular, contributed the highest number of individuals (646). No anisopteran had more than 100 individuals, with Dythemissterilis Hagen, 1861 being the most abundant, with 54 individuals. In contrast, 11 species were represented by only one individual, contributing only 0.68% of the total abundance and 64.5% (77.48 species) versus the richness of 50 observed species, calculated through the interpolation-extrapolation method and the Chao1-Our estimations indicated that more sampling efforts in Dominguillo are necessary in order to obtain more species, although, based on the collector experience of one of us (EGS), we suggest that the more probable scenario to be expected might be the one calculated through the interpolation-extrapolation method.1D) throughout the year was 21.07 effective species and 13.17 for the Simpson diversity or evenness (2D), while the estimated values of effective species for those same metrics were 21.64 and 13.27, respectively , Hetaerinaamericana and A.tezpi made up 45% of all the individuals registered in that month; 25 species were recorded in May, of which Argiapulla , A.tezpi, A.oenea and H.americana made up 66% of the individuals collected that month. In fact, the monthly pattern of high dominance \u2014 with just a few species being highly abundant and most species being very scarce \u2014 was more evident in the dry season than in the rainy season, as was shown through 2D was recorded early in the rainy season, during June, July and August , but in September \u2014 still during the rainy season \u2014 a low species richness was also recorded and the highest from June (25.38) to August (23.79), coinciding with the rainy season and the highest in July (21.85) for each month was less than that expected in all cases were recorded flying from 8 to 10 months and opposite to that, 13 species were rare and flew only during one month. The species that flew all year long belong to the Seasonally, 33 species were active in both the rainy and the dry seasons, nine only during the rainy season and eigth only during the dry season. Regarding abundance, 537 individuals were collected in the rainy season and 1066 during the dry season.r = 0.721, P = 0.012), the Simpson diversity , the taxonomic distinctness and the average taxonomic distinctness were significant and positively correlated with the average monthly precipitation. In other words, as rainfall begins to increase, the diversity and evenness also increase, as well as the phylogenetic divergence (taxonomic relationship between species) of the taxonomic monthly structure within the odonate assemblage. No significant relationship was found between temperature and diversity or phylogenetic divergence.In our study, the Pearson\u2019s correlation showed that only the Shannon diversity , was greater than reports from Aguililla, Michoacan (40) (can (40) and simican (40) and Pinocan (40) . Howevercan (40) and fromcan (40) , which iThe number of species that Dominguillo shares with these localities is variable, but the values are relatively close. Dominguillo shares 29 species (58%) with Aguililla and San Javier each, 32 species (64%) with Huautla and Pinolapa each and 28 species (56%) with Chamela.Dominguillo is located in the north-eastern part of the State of Oaxaca, in what is known as the Ca\u00f1ada Region. It is part of the Tehuacan-Cuicatlan Biosphere Reserve, an interesting xerophytic area with a large proportion of endemic animal and plant species, but with poor knowledge on its odonate fauna.Aeshnidae with only one species) also denotes this. In Dominguillo, the Rio de las Vueltas is an exposed rocky stream with a permanent water flow and few zones of lentic backwaters. In contrast, the presence of a dam in the vicinity of sampling sites in Huautla and the occurrence of remnant pools downstream from the dam during the dry season, facilitate the presence of more species associated with lentic habitats, which, in turn, contributes to the increase in the richness of the site and Hymenoptera (e.g. Encyrtidae at some sites), the highest number of species coincides with the beginning or the middle of the rainy season that constitute those temporal assemblages. When precipitation increases during the rainy season, the taxonomic distances amongst species also increase. During the wet season, high rainfall probably increases the availability of niches and resources (biotic and abiotic), which brings forth not only a higher number of taxa, but also allows the co-existence of taxa with more diverse ecological requirements. Taxonomic distinctness has been proven to be a highly useful index to evaluate the taxonomic structure of communities and assemblages in other odonates studies .Archilestesgrandis Rambur, 1842, Palaemnemadomina Calvert, 1903, Phyllogomphoidesdanieli Gonz\u00e1lez & Novelo, 1990, P.suasus Selys, 1859 and Progomphusclendoni Calvert, 1905 are species that were observed only during the wet season. This sub-group alone results in the addition of four genera, three families and four subfamilies that were not recorded during the dry season. Additionally, Apanisagrionlais Brauer in Selys, 1876 (Coenagrionidae) and Miathyriamarcella Selys in Sagra, 1857 (Libellulidae) are two species belonging to unique genera within the study area that were recorded only during the wet season. All species of the \u201clate spring/summer\u201d group contributed significantly to an increase in the observed phylogenetic diversity during the wet season.A close examination of the Dominguillo assemblage Fig. reveals Coenagrionidae and Calopterygidae (Hetaerina) are active as adults throughout most of the year in Dominguillo, Huautla and San Javier. On the other hand, species of the Gomphidae family and the Platystictidae family (at some sites) occurred as adults only during the wet season and available through the IBdata Portal developed by that institute at: File: oo_467310.xlsxhttps://binary.pensoft.net/file/467310Enrique Gonz\u00e1lez-Soriano and Ubaldo Melo-Samper2513B0DF-942A-53BC-B0CD-9C9536A839F410.3897/BDJ.9.e60980.suppl2Supplementary material 2Dictionary of database fieldsData typeExcel sheetBrief descriptionOdonata database, following the DarwinCore standard.This file contains the description of the fields used in the File: oo_467312.xlsxhttps://binary.pensoft.net/file/467312Enrique Gonz\u00e1lez-Soriano and Ubaldo Melo-Samper"} +{"text": "Osteoarticular tuberculosis (TB) represents 1% to 3% of all TB cases, among which spondylodiscitis is the most common presentation of the disease. Non-axial TB is less frequent. We aimed to study the clinical, therapeutic and evolutionary features of non-axial osteoarticular TB.We conducted a retrospective study including all patients hospitalized in the infectious diseases department for non-axial osteoarticular TB between 1999 and 2019.We encountered 51 cases, among which 26 cases were males (51%). The mean age was 41\u00b120years. Ten patients were previously treated for TB (19.6%). The revealing symptoms were fever (70.5%), asthenia (68.6%), weight loss (60.7%) and night sweets (43.1%). Arthritis was noted in 20 cases (39.2%) represented by TB of the hip (10 cases), knee (4 cases), shoulder (4 cases) and elbow (2 cases). There were 12 cases of sacroiliac osteoarthritis (23.5%) and 6 cases of femur osteomyelitis (11.7%). Other affected sites included sternum (7.8%), toe (5.9%), tibia (5.9%), mandible (2%), clavicle (2%) and mastoid bone (2%). Multifocal TB was noted in 12 cases (23.5%). Pulmonary TB was associated to osteoarticular TB in 13.7% of cases. The mean duration of antitubercular therapy was 10\u00b15months. Fixed dose combinations were prescribed in 17.6% of the cases. The disease evolution was favorable in 47 cases (92.1%). Relapse was noted in 3 cases (5.8%) and death in one case (2%).Non-axial osteoarticular TB was not a rare disease. Multiple sites might be involved which facilitate the diagnosis confirmation. Prolonged antitubercular therapy might be required. All Authors: No reported disclosures"} +{"text": "To describe antibiotic prescribing and early bacterial and fungal coinfection in patients admitted to two London hospitals with COVID-19.A retrospective review of adults with PCR-confirmed SARS-CoV-2 infection admitted between 9 February and 10 May 2020. Demographics, critical care unit (CCU) admission, antibiotic prescribing and microbiology results within 10 days of COVID-19 diagnosis were analysed.Escherichia coli 9.5% (7), Klebsiella pneumoniae 4.0% (3), and MSSA 2.7% (2). Organisms isolated from lower respiratory tract samples included Candida albicans 44.4% (12), Staphylococcus aureus 22.2% (6), Klebsiella species 11.0% (3), Pseudomonas aeruginosa 11.0% (3) and Citrobacter species 11% (3). Legionella and pneumococcal urinary antigen tests were positive in 0/117 and 2/71 episodes, respectively. Patients admitted to CCU during their inpatient stay were more likely to have positive microbiology compared with patients managed outside CCU . Ninety-one percent (1051) of all patients received antibiotics. Clarithromycin and amoxicillin (21%) were most frequently used, followed by piperacillin/tazobactam (12.6%), gentamicin (10.6%), co-amoxiclav (9.3%) and meropenem (3.2%). Patients given piperacillin/tazobactam or meropenem had a higher length of stay and mortality.In total, 1155 patients were identified; 32.9% (380) died during admission and 12.4% (143) had positive microbiology. After excluding likely contaminants, 6.9% (80) had evidence of coinfection. The most common organisms isolated from blood cultures were Bacterial coinfection in COVID-19 is uncommon, but more frequent in patients requiring CCU admission. Antibiotic use was widespread, despite lack of microbiological evidence of coinfection. When present, infection was more likely due to Gram-negative bacteria. Future local clinical and antimicrobial guidelines should reflect these findings."} +{"text": "Correction to: Mol Cancer (2018) 17:119https://doi.org/10.1186/s12943-018-0870-5Following publication of the original article , the autFigure 3BFigure 4AFigure 4DFigure 7DThe corrected figures are given below. The corrections do not have any effect on the final conclusions of the paper."} +{"text": "The novel coronavirus SARS-CoV2 is the causative agent for COVID-19 responsible for the ongoing global pandemic. The spike protein on its surface binds to the angiotensin-converting enzyme 2 receptor helps to enter human cells. Neutralizing antibodies to this protein can be protective and helpful in alleviating symptoms. Monoclonal antibodies (mAb) have been utilized in the U.S. under an emergency use authorization by the FDA, including bamlanivimab (BAM) and casirivimab-imdevimab (CAR/IMD). We report our experience of using COVID mAb.We conducted a retrospective chart review of patients that received CAR/IMD or BAM between December 1st, 2020, and May 15th, 2021. Medical records were reviewed to determine demographic and clinical information as well as tolerability and effectiveness of mAb.463 patients with mild to moderate symptoms of SARS-CoV2 received mAb: 355(176 Men) BAM, 108(53 Men) CAR/IMD. The median BMI was 31 (17.4 to 62.5), 85% Caucasian, 4% Asian, 3% African American, 4% Hispanic, 4% others. The average duration of symptoms was 3.4 days and included cough (74%), malaise (71%), Headache (28%), dyspnea (28%), rhinorrhea (25%), fever (20%), diarrhea (18%), and anosmia (14%). Risk factors included hypertension (65%), diabetes mellitus (32%), coronary artery disease (22%), asthma (16%), COPD (9%), CHF (9%), CKD (8%), active malignancy (6%), and immunocompromised state (7%). Those who received BAM were older (p=0.000) and have underlying dementia and congestive heart failure . 27 patients got admitted to the hospital due to worsening of their respiratory status and were treated for COVID-19. 4 patients in the BAM group and 0 in the CAR/IMD group died. 2 patients developed a mild allergic reaction to CAR/IMD, no other side effects were reported in both groups. 37 patients received mRNA COVID vaccine prior. Overall mortality rate was 0.8%. There was no significant difference between BAM and CAR/IMR in terms of hospitalization (p= 0.104) or mortality (p=0.268).Treatment with BAM versus CAR/IMR was well tolerated and resulted in similar outcomes in terms of hospitalization or mortality.All Authors: No reported disclosures"} +{"text": "To identify factors causing diagnostic and therapeutic delay in patients with rheumatoid arthritis, and to evaluate relationship of diagnostic and therapeutic delay with disease outcome.This cross-sectional study was conducted in Rheumatology Department, Fatima Memorial Hospital, Lahore, Pakistan, from May 2018 to July 2018. In this study 102 patients fulfilling ACR/EULAR criteria 2010 were enrolled. Lag times were calculated in months: lag-1 ; lag-2 (delay in consulting rheumatologists); lag-3 (diagnostic delay); lag-4 (therapeutic delay). Disease activity and functional outcome were measured by DAS28, HAQ-DI respectively. Association of lag-3 and lag-4 with HAQ-DI and DAS28 was calculated by Pearson correlation.Median (IQR) disease duration of study group was 6(2-10) years. Initial consultations were with; orthopedic surgeon 40(39.2%), general practitioner 27(26.5%), rheumatologist 13(12.7%), medical specialists 14(13.7%). Median (IQR) lag times in months: lag-1 : 2(0-5), lag-2 (delay in consulting rheumatologist): 30(7.7-72), lag-3 (diagnostic delay): 12(3-48), lag-4 (therapeutic delay):18(5.7-72). Factors attributed to lag-3 (diagnostic delay) and lag-4 (therapeutic delay) (p<0.05): older Age (r= 0.2), education level(r= - 0.2), initial consultation (non-rheumatologist) (r=0.2), lag-2(r=0.8), >three doctors visited before diagnosis(r=0.6). Positive anti-CCP antibodies(r=0.2) and lag-1 (r=1) were associated with lag-3 (diagnostic delay) only; no association was found with positive RA factor. Significant correlation (p=<0.05) of lag-3 (diagnostic delay) was found with both DAS28(r=0.2) & HAQ-DI(r=0.2). Similarly lag-4 (therapeutic delay) also correlated with both & DAS28(r=0.2) & HAQ-DI(r=0.3) (p=<0.05).Diagnostic and therapeutic delay were associated with older age, lower education and delayed consultation with rheumatologist but not with positive RA factor. Positive anti-CCP antibodies were associated with diagnostic delay only. Diagnostic and therapeutic delay led to high disease activity and poor functional outcome in RA patients. Rheumatoid arthritis (RA) is an autoimmune, systemic, chronic inflammatory disorder with articular and extra-articular manifestations.42229.99 ($34)/month.8Damage is irreversible once erosions develop on radiograph leading to deformities within one to two years.Initiating treatment within 12 weeks of symptoms onset (therapeutic window of opportunity)12Main objective of this study was to identify factors contributing to diagnostic and therapeutic delay in RA patients and to evaluate relationship of diagnostic and therapeutic delay with disease outcome, previously never studied in Pakistan. Considering the data available on disease burden and disability(annex-1) classification criteria 2010, with age \u226518 years, and disease duration of \u22653 months were included using 95% Confidence level (SD=1.96), 10% margin of error (SE=0.1), keeping 31% patients (P=0.31) assessed within 12 weeks, showed less joint destruction and higher chances of remission,This cross-sectional study was conducted in Rheumatology department, Fatima Memorial Hospital, Lahore, Pakistan, from May 2018 to July 2018. After receiving approval from Hospital Ethical Committee , total one hundred and two patients, both male and female with RA fulfilling ACR/EULARRA overlapping other connective tissue diseases.Comorbidity/medical illness leading to functional impairment.Pregnancy.Diagnostic and treatment delay was defined as delay in establishing RA diagnosis and initiating treatment after 12 weeks (therapeutic window of opportunity)13Lag-1: delay in initial consultation from symptoms onset.Lag-2: delay in consulting rheumatologist from symptoms onset.Lag-3 (diagnostic delay): delay in diagnosis from symptoms onset.Lag-4 (therapeutic delay): delay in initiating 1st DMARD from symptoms onset.(annex2) and HAQ-DI respectively. Threshold of disease activity with DAS28 was interpreted as follow: Remission <2.6, low activity >2.6-<3.2, moderate activity \u22653.2-\u22645.1, high activity >5.1.15Impact on disease outcome was measured by calculating disease activity and functional disability; DAS28 Data was analyzed by SPSS version 17 and quantitative study variables like age were presented as mean and standard deviation. Qualitative variables like gender and factors were presented as frequency and percentages. Lag time1-4 and disease duration were calculated in median and interquartile range (IQR). All patients were divided into three groups according to diagnostic and therapeutic delay (lag-3 & lag-4) of \u22641 year, >1-\u22645 years and >5 years. Mean DAS28 & HAQ-DI values were calculated for each group and were compared among them by applying ANNOVA. Lag-3 and lag-4 were correlated with both DAS28 and HAQ -DI by using Pearson correlation. Spearman correlation was used to correlate all factors with both lag3 and lag4. P<0.05 was taken as significant.st DMARDS in 78(76.5%) and non-rheumatologists in 24(23.5%) patients.Initial consultations were with; orthopaedic surgeon 40 (39.2%), general practitioner 27 (26.5%), rheumatologist 13(12.7%), medical specialists 14 (13.7%), hakeem 7(6.9%), homeopathic 1 (1%). Lack of awareness (50.5% of patients) and lack of referral (49.55% of patients) were causes of delay in consulting rheumatologists. At initial consultation RA was diagnosed in only 49 (48%) patients. Rheumatologists diagnosed RA in 48(47.1%) patients, orthopaedic surgeons in 30(29.4%), medical consultants in 15(14.7%) and GP in 9(8.9%) patients. Rheumatologists started 1Median (IQR) lag times were calculated in months.Lag-1: 2(0-5).Lag-2: 30(7.7-72).Lag-3: 12(3-48).Lag-4: 18(5.7-72).Patients having diagnostic and therapeutic delay of one year or less were found to have lower disease activity and better functional outcome. .In our study group, lag-1 was two (0-5) months, shorter than that (3.1(0-5.7) months) observed in developed countries like Canada, USA, UK.This study showed that median lag-3 (diagnostic delay) was one year while median lag-4 (therapeutic delay) was one and half years but initial consultations were done within \u201cwindow period of opportunity\u201d. On average >three physicians were consulted before RA diagnosis was reached . Median Median (IQR) time in months for lag-2: 30(7.7-72); lag-3: 12(3-48) & lag-4: 18(5.7-72) were greater than those observed in developed countries like Canada, USA, UK where measured median (IQR) lag-2 was 2.13(0.5-6.6) months, lag-3 was 2.91(0-5) months, lag-4 was 2.14(0-2.2) months.Initial consultation with rheumatologists was done by 12.7% patients only. Major causes of delay in seeking initial consultation with rheumatologist were lack of awareness and lack of referral. One study conducted in Rawalpindi reported that even in diagnosed RA patients only 1.5% patients had knowledge on disease.16Gender and geographical region , presence of initial symptoms were not found to be associated with lag-3 and lag-4. Delay in initial consultation led to diagnostic delay . Older age was associated with lag-3 and lag-4 r=0.21, p=0.03) . Hussain, p=0.03 +/anti-CCP+ led to delay in seeking medical care which in turn led to diagnostic delay. Diagnostic and therapeutic delay in RA factor-/anti-CCP- patients occurred in secondary care.We did not find any association of RA factor+/- with diagnostic and therapeutic delay. Positive anti-CCP antibodies were associated with diagnostic delay but not with therapeutic delay . Pratt eSignificant statistical correlation of lag-3 was found with both DAS28 , and HAQ-DI & 1b. CoThis single concise study gives true insight into the lag times along with different factors causing diagnostic and therapeutic delay in RA patients and their impact on disease outcome in Pakistan. This study is first of its kind ever done in Pakistan.All patients in this study belonged to lower socioeconomic status. Other factors e.g. myths and fears of patients regarding disease and treatment, adherence to treatment, and reason of delay in patient with better socioeconomic status were not evaluated in this study. This study needs to be repeated after few years in same population to evaluate any decline in lag times and improvement in disease outcome.Older age, lower education and delayed consultation with rheumatologist were the factors associated with both diagnostic and therapeutic delay. Positive RA factor did not impact on diagnostic and therapeutic delay. Positive anti-CCP antibodies were associated with diagnostic delay only. Diagnostic and therapeutic delay ultimately led to high disease activity and poor functional outcome in RA patients. It is essential to address these factors to minimise diagnostic and therapeutic delay in RA patients to improve their physical wellbeing and to decrease burden of disease, disability and economic burden in our patients.FN and SEAK conceived and designed manuscript.FN collected data, did statistical analysis, wrote & edited manuscript, she is also responsible for integrity and accuracy of research work.MAS and SF reviewed, gave final approval of manuscript."} +{"text": "Identifying infectious etiology is often challenging, yet essential for patient management, including antibiotic use. Studies have shown that a host signature comprising TNF-related apoptosis induced ligand (TRAIL), interferon gamma induced protein-10 (IP-10) and C-reactive protein (CRP) accurately differentiates bacterial from viral infection with negative predictive value >98%. Performance data was lacking in chronic obstructive pulmonary disease (COPD) patients with suspected lower respiratory tract infection (LRTI).Adults aged >18 years with suspected LRTI were prospectively recruited at 3 medical centers . Reference standard infection etiology was adjudicated by 3 independent experts based on clinical, laboratory, microbiological, radiological and follow-up data. Host signature generates a bacterial likelihood score (0-100), providing three results: viral (0-35), equivocal (35-65) and bacterial (65-100). Experts were blinded to the signature result.Out of 583 adults recruited with suspected LRTI, 422 met infectious criteria, of whom 48 had a recorded history of COPD. 19 cases were adjudicated by the experts as bacterial, 14 as viral and 15 were indeterminate . The mean age was 68.2 years (standard deviation 12.3); 33 (68.8%) presented after two or more days of symptoms and 38 (79.2%) were hospitalized for a median of 6 days. 15 (31.2%) were female. For the patients adjudicated bacterial or viral labels (n=33), the discharge diagnoses were: COPD exacerbation, 12 cases (36.4%); pneumonia, 12 cases (36.4%) (3.0%); acute bronchitis, 2 cases (6.1%); upper RTI ,1 case; unspecified viral infection 1 case (3.0%); or other, 5 cases (15.2%). Host signature correctly classified all 19 bacterial cases and 8 of the viral cases, providing accurate etiology labels for 27/33 COPD patients with reference standard labels (81.8%). The remaining 6 viral cases received equivocal scores (18.2%).COPD patient enrollment and etiology labels in the Observer studyHost signature accurately differentiates between bacterial and viral infections in patients with COPD history, supporting potential to improve management among these patients frequently admitted for RTIs.Michal Stein, MeMed (Employee) Meital Paz, MD, MeMed (Employee) Tanya Gottlieb, PhD, MeMed Eran Barash, MA, MeMed (Employee) Roy Navon, MSc, MeMed Einat Moscoviz, BSc+ MBA, MeMed (Employee) Tahel Ilan Ber, MD, MeMed Liran Shani, MD, MeMed (Employee) Olga Boico, PhD, MeMed (Employee) Einav Simon, PhD, MeMed Noa Avni, PhD, MeMed (Employee) Kfir Oved, MD, PhD, MeMed Eran Eden, PhD, MeMed"} +{"text": "Smoking has been observed to associate with an elevated severity of disease and risk of mortality among people with COVID-19. Additionally, African American smokers have higher rates of mortality from lung cancer than other racial/ethnic groups. Low dose computed tomography (LDCT) screening can detect lung cancer early to decrease lung cancer-specific mortality for current smokers but remains under-utilized among these population. However, we know little about the effect of COVID-19 pandemic on smoking behavior changes among African American smokers who qualify for LDCT screening. This study recruited 60 African American daily smokers seen in primary care clinics, who qualified to receive LDCT screening in a New Orleans, LA hospital. A total of 22 participants (36.7%) completed anonymous cross-sectional survey that collected demographic, disease history, tobacco use, and smoking cessation behaviors during the period of COVID-19 pandemic via phone interview. The majority were older (61.2 [SD=4.7]), female (77.3%), earned annual income less than $20,000 (100.0%), had Medicaid (63.6%), overweight/obesity (72.7%), planned to quit smoking within 6 months (52.4%), and would consider taking LDCT screening after COIVD-19 pandemic (95.2%). Half of smokers reported they have been diagnosed hypertension (47.6%), diabetes (52.4%), and arthritis (57.1%). Regarding health behavior changes, 42.9% smokers reported they smoked more, felt more stress (42.9%) and anxiety (33.4%) after COVID-19 outbreak. Smoking cessation programs may focus on this high-risk minority population in the post COVID-19 pandemic to help them decrease cigarette smoking and enhance their motivation to quit smoking."} +{"text": "The introduction of primary HPV screening has doubled the number of colposcopy referrals because of the direct referral of HPV-positive women with a borderline or mild dyskaryosis (BMD) cytology (ASC-US/LSIL) triage test. Further risk-stratification is warranted to improve the efficiency of HPV-based screening.FAM19A4/miR124-2 methylation, HPV16/18 genotyping and HPV16/18/31/33/45 genotyping in HPV-positive women with BMD (n\u2009=\u2009294) in two Dutch screening\u00a0trials. Absolute CIN3+ risks and colposcopy referrals within one screening round were calculated.This study evaluated the discriminative power of FAM19A4/miR124-2 methylation, HPV16/18 and HPV16/18/31/33/45 genotyping, respectively. The CIN3+ risk after a negative result could be lowered to 2.8% by combining methylation and extended genotyping, at the expense of a higher referral percentage of 75.5%.Methylation analysis discriminated well, yielding a CIN3+ risk of 33.1% after a positive result and a CIN3+ risk of 9.8% after a negative result. HPV16/18 and HPV16/18/31/33/45 genotyping resulted in a 27.6% and 24.6% CIN3+ risk after a positive result, and a 13.2% and 9.1% CIN3+ risk after a negative result. Colposcopy referral percentages were 41.2%, 43.2%, and 66.3% for FAM19A4/miR124-2 methylation and/or HPV genotyping in HPV-positive women with BMD can lead to a substantial reduction in the number of direct colposcopy referrals.The use of Human papillomavirus (HPV)-based cervical screening has an increased sensitivity for the detection of high-grade cervical intraepithelial neoplasia (CIN) and cervical cancer compared with cytology-based screening, but has a suboptimal specificity , 2 and tThe Netherlands was the first country that implemented primary HPV screening with cytology triage in the national cervical screening programme in 2017 . HPV-posFAM19A4/miR124-2 methylation analysis has shown a high sensitivity for cervical cancer and advanced high-grade CIN in HPV-positive women [HPV16/18 genotyping or HPV16/18/31/33/45 genotyping (extended genotyping) has been considered for triaging HPV-positive women with BMD cytology, because CIN3+ risks vary between individual high-risk HPV genotypes \u201315. An ave women , 23.FAM19A4/miR124-2 methylation, HPV16/18 genotyping, HPV16/18/31/33/45 genotyping and combinations thereof in HPV-positive women with BMD cytology in two large Dutch population-based screening cohorts.In this study, we evaluate the performance of n\u2009=\u2009167 and POBASCAM n\u2009=\u2009192) were selected. Fifty-two samples were excluded due to insufficient leftover material for methylation analysis (VUSA-Screen n\u2009=\u200941 and POBASCAM n\u2009=\u200911).This study is a post hoc analysis within the VUSA-Screen trial and POBASCAM trial. HPV-positive women with borderline or mild dyskaryosis (BMD) and registered in the trial register . The study was designed to evaluate the effectiveness of combined HPV and cytology testing in the Dutch national screening programme. A detailed description of the VUSA-Screen trial has been published before . CervicaThe POBASCAM trial is a population-based cervical screening study within the Dutch screening programme with enrolment between January 1999 and September 2002. The POBASCAM trial was approved by the Medical Ethics Committee of the VU University Medical Center (no 96/103A) and by the Ministry of Public Health VWS no 328 650) and registered in the trial register . The study was designed to evaluate the effectiveness for CIN2/3 detection of combined HPV and cytology testing in the intervention group compared with sole cytology testing and blinded HPV testing in the control group. A detailed description of the POBASCAM trial has been published before , 27. Cer 650 and In both studies, histology results were classified as no dysplasia, CIN grade 1, 2, 3, or cervical cancer. Adenocarcinoma in situ was classified as CIN3. Histopathologic follow-up data were collected through the nationwide network and registry of histopathology and cytopathology (PALGA) .HC2-positive samples from the VUSA-Screen trial were tested with GP5+/6+ PCR-EIA. All EIA-positive samples from both trials were typed by reverse line blot (RLB) assay for identification of 14 high-risk HPV types . SamplesFAM19A4/miR124-2 methylation analysis was performed as described previously [FAM19A4/miR124-2 methylation result (VUSA-Screen n\u2009=\u20093 and POBASCAM n\u2009=\u200910) and were excluded from further analysis. Methylation status was labelled positive if the QIAsure Methylation Test\u00ae result exceeded the preset \u0394\u0394Ct value threshold for methylation positivity according to the manufacturer\u2019s instructions.eviously , 31, bliFAM19A4/miR124-2 methylation, HPV16/18 genotyping and HPV16/18/31/33/45 genotyping. The performance of five triage strategies was evaluated: (I) FAM19A4/miR124-2 methylation, (II) HPV16/18 genotyping, (III) HPV16/18/31/33/45 genotyping, (IV) HPV16/18 genotyping combined with FAM19A4/miR124-2 methylation and (V) HPV16/18/31/33/45 genotyping combined with FAM19A4/miR124-2 methylation. Strategy (I) was labelled positive if the methylation result was positive. Strategy (II) was labelled positive if HPV 16 and/or 18 was present. Strategy (III) was labelled positive if HPV 16, 18, 31, 33, and/or 45 was present. Strategy (IV) was labelled positive if HPV 16 and/or 18 was present or if the methylation result was positive. Strategy (V) was labelled positive if HPV 16, 18, 31, 33, and/or 45 was present or if the methylation result was positive. Sensitivity and specificity were estimated with Wald 95% confidence intervals (95% CI). Direct referral percentage was calculated as the percentage of positives from each screening strategy and the number of referrals needed to detect one CIN3+ was calculated by dividing the number of screen positives by the number of true positives. We constructed 95% confidence intervals (95% CI) for the risk differences in STATA . If the 95% CI did not contain the value 0, the difference was considered significant. All other statistical analysis were performed with SPSS Statistics .Data of the VUSA-Screen trial and POBASCAM trial were pooled and absolute CIN3+ risks were calculated. All CIN3+ detected within one screening round were included. Separate estimates were retrieved for single and combined triage strategies using FAM19A4/miR124-2 methylation analysis , in whom 56 CIN3 and 1 cervical carcinoma were detected. The median age of women included was 35.0 years (range: 29\u201360 years) and median time to CIN3+ detection was 0.7 years (IQR: 0.2\u20131.3 years). In total, 121/294 women (41.2%) tested methylation positive, 127/294 women (43.2%) tested HPV16/18 positive and 195/294 women (66.3%) tested HPV16/18/31/33/45 positive.The final study population consisted of 294 HPV-positive women with BMD and valid results for HPV genotyping and FAM19A4/miR-124 methylation, HPV16/18 genotyping, HPV16/18/31/33/45 genotyping or combinations thereof. Fig.\u00a0FAM19A4/miR124-2 methylation, HPV16/18 or HPV16/18/31/33/45 had a CIN3+ risk of >9%. Combinations of HPV genotyping and methylation lowered the CIN3+ risk among test-negatives with a CIN3+ risk of 6.5% (95% CI: 1.8\u201311.1%) among women who were both HPV16/18-negative and FAM19A4/miR124-2 methylation-negative and a CIN3+ risk of 2.8% (95% CI: 0\u20136.6%) among women who were both HPV16/18/31/33/45-negative and FAM19A4/miR124-2 methylation-negative. Supplementary Table\u00a0Table\u00a0Table\u00a0FAM19A4/miR124-2 methylation, HPV16/18 genotyping and HPV16/18/31/33/45 genotyping (extended genotyping) for additional risk-stratification of HPV-positive women with BMD cytology to reduce direct colposcopy referral rates, while maintaining high sensitivity for CIN3+ detection. The choice of additional triage tests depends on the CIN3+ risk, the number of repeat tests and the number of colposcopy referrals that are deemed acceptable.We evaluated FAM19A4/miR124-2 methylation resulted in the highest CIN3+ risk of 33.1% and the largest risk-difference between test-positives and test-negatives (23.2%). Recently Bonde et al. also showed in a large multicentre cohort that FAM19A4/miR124-2 methylation detected the very large majority of CIN3 in HPV-positive women with ASC-US/LSIL [FAM19A4/miR124-2 methylation led to a referral percentage of 41.2% and a sensitivity of 70.2%. Still, the CIN3+ risk after a negative test for any of the single strategies was >9%. Combined strategies lowered the CIN3+ risk among test-negatives substantially with the lowest CIN3+ risk of 2.8% among women who were both HPV16/18/31/33/45-negative and FAM19A4/miR124-2 methylation-negative. Despite a high referral percentage of 75.5%, a benefit of this combined strategy is that the CIN3+ risk among triage-negative women seems sufficiently low to recommend return to the regular cervical screening programme.Of the single triage strategies, -US/LSIL . In our FAM19A4/miR124-2 methylation has shown a very high sensitivity for cervical cancer [FAM19A4/miR124-2 methylation test is associated with high spontaneous regression [FAM19A4/miR124-2 methylation has also prognostic value for development of cervical cancer in the long term. De Strooper et al. found a significantly lower 14-year cervical cancer risk among HPV-positive, FAM19A4/miR124-2 methylation-negative women compared with HPV-positive, cytology-negative women. Collectively, these data indicate that FAM19A4/miR124-2 methylation-negative CIN2/3 have high regression rates and low cervical cancer progression risks. As a consequence, methylation analysis may be considered when deciding whether women can be returned to routine screening.l cancer and adval cancer . Hence, l cancer . Furthergression (Kremer,FAM19A4/miR124-2 methylation on the number of referrals and detection of CIN3+ will be considerable. Surely, the high colposcopy referral rates and low CIN3+ risk in the national screening programme makes the need for additional triaging of HPV-positive women with BMD even larger than anticipated based on our studies. For the implementation of methylation analysis, applicability and reproducibility of the test among different sample types and DNA extraction methods is essential. Floore et al. evaluated the intra- and inter-laboratory agreement of the FAM19A4/miR124-2 methylation test with the use of several cervical scrape collection media and several DNA extraction methods and showed a good to excellent intra- and inter-laboratory agreement on the assay and the full workflow [In the new HPV-based screening programme in the Netherlands, the proportion of HPV-positive women who were directly referred for colposcopy because of BMD cytology was 70.3% in year 2019 . The cumworkflow .A strength of our study is that we used data of two large population-based HPV DNA screening trials within the Dutch screening programme. As shown in Supplementary Table\u00a0FAM19A4/miR124-2 methylation could reduce direct colposcopy referral rate with 60%, while retaining high CIN3+ sensitivity. The combination of FAM19A4/miR124-2 methylation with HPV16/18/31/33/45 genotyping would reduce colposcopy referrals with only 25%, but the low residual CIN3+ risk would obviate the need of short-term follow-up testing.To conclude, the implementation of primary HPV screening with cytology triage in the Netherlands has led to a two-fold increase in direct colposcopy referrals and \u2264CIN1 diagnosis, mainly because of the direct referral of women with BMD. Additional risk-stratification of HPV-positive women with BMD by Supplementary Table 1"} +{"text": "However, the dissemination pattern of plasmid-borne tet(X) genes remains unclear. We here recovered tet(X)-positive Acinetobacter isolates from 684 fecal and environmental samples collected at six livestock farms. Fifteen tet(X)-positive Acinetobacter isolates were identified, mainly including 9 tet(X3)- and 5 tet(X6)-positive Acinetobacter towneri isolates. A clonal dissemination of tet(X3)-positive A. towneri was detected in a swine farm, while the tet(X6)-positive A. towneri isolates mainly disseminated sporadically in the same farm. A tet(X3)-carrying plasmid (pAT181) was self-transmissible from a tigecycline-susceptible A. towneri strain to Acinetobacter baumannii strain ATCC 17978, causing 64- to 512-fold increases in the MIC values of tetracyclines (including tigecycline). Worrisomely, pAT181 was stably maintained and increased the growth rate of strain ATCC 17978. Further identification of tet(X) genes in 10,680 Acinetobacter genomes retrieved from GenBank revealed that tet(X3) (n\u2009=\u2009249), tet(X5)-like (n\u2009=\u200961), and tet(X6) (n\u2009=\u200953) were the prevalent alleles mainly carried by four species, and most of them were livestock associated. Phylogenetic analysis showed that most of the tet(X3)- and tet(X6)-positive isolates disseminated sporadically. The structures of the tet(X3), and tet(X6) plasmidomes were highly diverse, and no epidemic plasmids were detected. However, cross-species and cross-region transmissions of tet(X3) might have been mediated by several plasmids in a small proportion of strains. Our study implies that horizontal plasmid transfer may be insignificant for the current dissemination of tet(X3) and tet(X6) in Acinetobacter strains. Continuous surveillance for tet(X) genes in the context of One Health is necessary to prevent them from transmitting to humans.The emergence of high-level tigecycline resistance mediated by plasmid-borne IMPORTANCE Recently identified plasmid-borne tet(X) genes have greatly challenged the efficiency of tigecycline, a last-resort antibiotic for severe infection, while the dissemination pattern of the plasmid-borne tet(X) genes remains unclear. In this study, we identified a clonal dissemination of tet(X3)-positive A. towneri isolates on a swine farm, while the tet(X6)-positive A. towneri strains mainly disseminated sporadically on the same farm. Of more concern, a tet(X3)-carrying plasmid was found to be self-transmissible, resulting in enhanced tigecycline resistance and growth rate of the recipient. Further exploration of a global data set of tet(X)-positive Acinetobacter genomes retrieved from GenBank revealed that most of the tet(X3)- and tet(X6)-positive isolates shared a highly distant relationship, and the structures of tet(X3) and tet(X6) plasmidomes exhibited high mosaicism. Notably, some of the isolates belong to Acinetobacter species that are opportunistic pathogens and have been identified as sources of nosocomial infections, raising concerns about transmission to humans in the future. Our study evidenced the sporadic dissemination of tet(X3) and tet(X6) in Acinetobacter strains and the necessity of continuous surveillance for tet(X) genes in the context of One Health. With the global dissemination of carbapenemases and mobilized colistin resistance , was identified in Tn4351 and Tn4400 on the chromosome of Bacteroides fragilis in 1990 (tet(X) genes, tet(X1) to tet(X14), have been reported in various species originating from animals, humans, and the environment (\u2013tet(X3) and tet(X4) genes were found in livestock-associated Acinetobacter baumannii and Escherichia coli strains, respectively, in 2019 (tet(X) alleles have been reported to be plasmid borne, including tet(X5) and tet(X6) and their variants. Epidemiological studies reveal that these novel tet(X) orthologs have mainly circulated in animals in China due to the heavy use of tetracyclines in husbandry genes, through circular intermediates (\u2013tet(X) genes remains obscure.The first flavin-dependent monooxygenase gene, named ironment \u201312. Thesronment \u2013. The fir in 2019 , raisingusbandry . In some) to tetX, have beediates \u2013. Howevertet(X) genes have been detected in over 16 bacterial species, and Acinetobacter spp. were among the major hosts (17\u2013tet(X)-positive Acinetobacter species isolates have been associated with livestock, and very few have been found in humans (Acinetobacter species strains were tet(X) positive -positive isolates from pig farms, migratory birds, and samples from human (tet(X3) and tet(X6) were prevalent in livestock-associated Acinetobacter species isolates, and tet(X5) has so far only been detected in an A. baumannii strain from humans -positive Acinetobacter species isolates recovered from livestock and their surrounding environmental sources was performed at six livestock farms located in Zhejiang Province in 2019. The epidemiological and genetic characterizations of tet(X)-positive isolates and tet(X)-harboring plasmids were dissected. We further investigated the population structure and distribution of tet(X)-positive Acinetobacter strains identified in a public database, as well as the plasmidomes of tet(X3) and tet(X6).In this study, surveillance of Acinetobacter spp. and 77 isolates belonging to other species. Twenty-three tet(X)-positive isolates were identified , including 15 Acinetobacter species isolates , 5 Empedobacter stercoris isolates, and 3 Myroides odoratimimus isolates (tet(X)-positive isolates were exclusively isolated from swine farms. The Acinetobacter spp. and E. stercoris isolates were all recovered from the fecal samples of swine farm 1, and the 3 M. odoratimimus isolates were from the soil samples of swine farm 2.Two hundred ninety-two isolates were recovered from 534 stool samples and 150 environmental samples collected from 2 swine farms, 2 dairy farms, and 2 sheep farms, including 215 isolates of isolates . The 23 tet(X)-positive Acinetobacter species isolates were assigned by average nucleotide identity (ANI) analysis to Acinetobacter towneri (n\u2009=\u200914) and an unclassified species (n\u2009=\u20091), and the other 8 tet(X)-positive isolates were E. stercoris (n\u2009=\u20095) and M. odoratimimus (n\u2009=\u20093) (tet(X) genes were identified in the 23 tet(X)-positive isolates (tet(X2) was exclusively detected in the 8 non-Acinetobacter isolates, and tet(X3) was in 9 A. towneri isolates and 1 unclassified species isolate (ZJ199). tet(X6) and tet(X14) were found in 5 A. towneri and 2 E. stercoris isolates, respectively. Notably, two copies of tet(X6) were carried by an A. towneri isolate (AT185). Eight of the tet(X3)-positive Acinetobacter species isolates clustered together, with 3 to 36 single-nucleotide polymorphisms (SNPs) (tet(X6)-positive isolates were also clonally related (1 SNP). The remaining five isolates showed distant relationships , indicating sporadic dissemination of these strains.The 15 (n\u2009=\u20093) . Four diisolates . tet(X2)s (SNPs) , suggesttet(X)-positive isolates (34.78%) were resistant to tigecycline, with MIC values at 1 to 2\u2009mg/liter, encompassing 4 tet(X3)-positive A. towneri isolates, 1 tet(X6)-positive A. towneri isolate, 2 tet(X2)- and tet(X14)-positive E. stercoris isolates, and 1 tet(X2)-positive M. odoratimimus isolate (A. towneri isolates and 2 E. stercoris isolates) additionally exhibited resistance to the newly FDA-approved eravacycline, with MIC values at 1 to 4\u2009mg/liter. Except for the isolate carrying 2 copies of tet(X6), the other 14 Acinetobacter species isolates were resistant to tetracycline with MIC values of \u226516\u2009mg/liter -positive Acinetobacter species isolates were susceptible to colistin and carbapenems. The M. odoratimimus isolates were resistant to colistin and carbapenems due to intrinsic resistance (Eight of the 23 isolate . Five timg/liter . Strain mg/liter . Four anectively . All of sistance .tet(X)-positive isolates were subjected to whole-genome sequencing (WGS) . All of the A. towneri strains were multidrug resistant (MDR), and more antibiotic resistance genes (ARGs) were detected in the tet(X6)-carrying clone than in the tet(X3)-carrying clone , albeit the difference was not significant (P\u2009>\u20090.05) (tet(X3)-carrying clone shared an identical resistome , further supporting the aforementioned clonal dissemination (tet(X6)-carrying strains were highly diverse, with genes that included the following: aacC4, ant(3\u2033)-Ia, and aph(4)-Ia, encoding resistance to aminoglycosides; blaOXA-58, encoding resistance to beta-lactams; floR, encoding resistance to phenicols; dfrA1, encoding resistance to trimethoprim; erm(B), mph(E), and msr(E), encoding resistance to macrolides; and tet(X6) and tet(Y), encoding resistance to tetracyclines (sul2 and tet(X3)]. The resistomes of E. stercoris and M. odoratimimus were different from those of Acinetobacter spp. (Table S2).The 23 \u2009>\u20090.05) . The 8 smination , while tcyclines . Only twtet(X) genes, i.e., tet(X3) and tet(X6), five representative strains were additionally chosen for long-read sequencing based on their antimicrobial resistance profiles and the genetic environments of their tet(X) genes (Table S1). The hybrid assembly confirmed that tet(X3) and tet(X6) were plasmid borne in the four A. towneri isolates, and a chromosome-carried tet(X3) was detected in ZJ199.To understand the vectors of the two prevalent tet(X3)-carrying plasmids detected in AT181 (pAT181) and AT184 (pAT184) were circularized (confirmed by PCR) and identical, with a size of 75,969 bp. These two plasmids were untypeable, with an average GC content of 42.5%. Multiple ARGs were carried by the two plasmids, including aph(3\u2032)-Ia, aph(3\u2033)-Ib, aph(6)-Id, sul2, and tet(X3). BLAST analysis of the nucleotide sequence of pAT181 in GenBank showed that the best match was a transferable tet(X3)-harboring plasmid, p10FS3-1-3 (accession number CP039146) (100% identity and 97% coverage) carried by a novel species of Acinetobacter (tet(X5)-harboring plasmid, pAB17H194-1 , carried by an A. pittii strain and a tet(X3)-harboring plasmid, p18TQ-X3 , carried by an A. indicus strain. These data suggested that pAT181-like plasmids have disseminated among various species of Acinetobacter.The tobacter . Others tet(X3)-carrying plasmids carried by the 8 clonal isolates were all homologous to pAT181, with >90% coverage and nucleotide identity , and the tet(X3)-carrying plasmid carried by AT200 was different from pAT181, with <50% coverage and >90% identity . The best match for pAT200 in GenBank was p10FS3-1-3, with 58.77% coverage and 70% identity.In accordance with the phylogeny, the tet(X6)-harboring circularized plasmids pAT232 and pAT235 shared as little as 38% coverage and 99.95% identity; however, the sequences of their rep genes were identical, indicating that they might originate from a common ancestor. pAT232 was 186,508-bp in length, with a GC content of 41.03%. A BLAST search against GenBank showed that the best matches for pAT232 were a tet(X6)-carrying plasmid, pAT205 (accession number CP048015) (76% coverage and 99.99% identity), carried by A. towneri strain AT205 isolated on the same swine farm (tet(X)-negative plasmid, p19110F47-2 (accession number CP046044) (70% coverage and 99.99% identity), carried by an A. towneri strain isolated from pigs. pAT235 was 124,466 bp in length, with a GC content of 41.16%. The best matches for pAT235 were pAT205 (49% coverage and 100% identity) and a tet(X3)-harboring plasmid, pGX7 (accession number CP071772) (44% coverage and 99.95% identity), detected in an A. towneri strain isolated from pigs in China. These data suggest that pAT232 and pAT235 might originate from A. towneri strains associated with pigs.The two ine farm , and a ttet(X6) in the other tet(X6)-positive isolates collected here, AT208 showed the highest similarity to pAT232 (77.84% coverage and 99.16% identity) . When pAT235 was used as a reference, AT185 shared 100% coverage and 94.51% identity , suggesting that a pAT235-like tet(X6)-encoding plasmid was harbored in AT185. Of note, AT185 was genetically distant from AT235, with 30,097 SNPs (tet(X6)-harboring plasmid was detected in AT208 when pAT205 was used as a reference (100% coverage and 96.48% identity) . These results reveal that horizontal transfers of tet(X6)-carrying plasmids might have occurred sporadically.When pAT232 was used as a reference to identify the plasmids bearing 097 SNPs . A pAT20tet(X3) [\u0394ISCR2-xerD-tet(X3)-res-ISCR2] detected in 8 of 9 A. towneri strains were identical and highly similar to that of the prototype detected in A. baumannii strain 34AB (tet(X3)-carrying Acinetobacter strains, we used BLAST to compare it to 249 tet(X3)-carrying Acinetobacter genomes retrieved from GenBank (see below). The fragment \u0394ISCR2-xerD-tet(X3)-res-ISCR2 was detected on a single contig of 21.3% (53/249) of genomes with >90% coverage and identity. The proportion increased to 86.35% (215/249) when matches on different contigs were counted together, implying a major structure encoding tet(X3) in Acinetobacter spp. A different tet(X3) genetic environment [IS4-IS4-tet(X3)-res-\u0394ISCR2] was detected on the chromosome of strain ZJ199 (The genetic environments of plasmid-borne ain 34AB 7). To . To tet(in ZJ199 .tet(X6) were much more diverse than those of tet(X3) detected in our collection (CR2-IS30-tet(X6)-abh-guaA-ISCR2] was detected in pAT232, which is similar to the prototype [\u0394ISCR2-tet(X6)-abh-guaA-ISCR2] identified in pAT205 and a Proteus genomospecies 6 strain (30. The tet(X6) located within a 6,885-bp region [ISCR2-fabF-tet(X6)-abh-glmM-sul2] in pAT235 (A. indicus strain Q186-3_T (100% coverage and 99.58% identity) and on pABF9692, carried by an A. baumannii strain (accession number CP048828) (100% coverage and 98.70% identity). In strain AT185, the genetic context of one copy of tet(X6) was identical to that detected in pAT235, and a truncated structure was found for the other copy (CR2-fabF-tet(X6)-abh fragment was also found on the chromosomes of A. indicus strain LYS68A (CP070997) and A. baumannii strain 31FS3-2 (CP0445177), indicating that this structure might mediate the mobilization of tet(X6) between plasmids and chromosomes in Acinetobacter spp.The genetic environments of llection . A 7,2706 strain , 27, excn pAT235 was almoher copy . The ISCtet(X)-encoding plasmids. We only obtained tigecycline-resistant A. baumannii transconjugants from A. towneri strain AT181, with frequencies of 1.85\u2009\u00d7\u200910\u22126 per recipient cell. Multiple attempts at plasmid transfers failed when E. coli strain EC600 was used as a recipient. Compared with those of the recipient strain ATCC 17978, the MIC values of tigecycline and the other tetracyclines against the transconjugant ATCC 17978-pAT181 increased by 128-fold and \u223c64- to 512-fold, respectively (Table S3). WGS was performed for ATCC 17978-pAT181 and ATCC 17978 to detect the transferable structure of tet(X3). A unique plasmid, pAT181, was detected in the transconjugant ATCC 17978-pAT181, demonstrating that the transmission of tigecycline resistance was mediated by pAT181 . This is different from another self-transmissible tet(X3)-harboring plasmid p10FS3-1-3 in that the transfer of p10FS3-1-3 into Acinetobacter baylyi strain ADP1 did not bring a significant additive effect to the resistance to tetracyclines (tet(X3)-carrying plasmid conferring tetracycline resistance to the recipient.A conjugation assay was performed to test the transferability of cyclines . To the tet(X3) was stable in the recipient strain ATCC 17978 without antibiotic stress during 10 days of passage, with a 100% retention rate. Compared with that of ATCC 17978, the doubling time of ATCC 17978-pAT181 was shortened from 4.59\u00a0h to 2.91\u00a0h (tet(X3) among Acinetobacter spp. strains.o 2.91\u00a0h . These rtet(X) genes among Acinetobacter spp., a BLAST comparison of the nucleotide sequences of 15 known tet(X) alleles and their variants to 10,680 Acinetobacter genomes retrieved from GenBank was performed. tet(X3) was found in 249 genomes, tet(X4) in 9 genomes, tet(X5) (n\u2009=\u20092), tet(X5.2) (n\u2009=\u200953), and tet(X5.3) (n\u2009=\u20096) in 61 genomes, tet(X6) in 53 genomes, and tet(X13), a 1-residue variant of tet(X6), in 4 genomes. These data reveal that tet(X3), tet(X5.2), and tet(X6) are the prevalent tet(X) genes among Acinetobacter spp.To fully understand the distribution of Acinetobacter species carrying tet(X3), i.e., A. indicus , Acinetobacter sp002018365 (an unclassified species with Acinetobacter sp. ANC 4845 as the reference), and A. towneri (Table S4). Except for A. variabilis , A. indicus , Acinetobacter sp002018365 , and A. towneri are also the predominant species carrying tet(X6). The distribution of tet(X5.2)-harboring species was similar to that of species carrying tet(X6), including A. indicus , Acinetobacter sp002018365 , A. towneri , A. variabilis , and A. lwoffii . These results indicate that A. indicus and Acinetobacter sp002018365 are the most prevalent species carrying tigecycline-resistant tet(X) genes.Species identification by ANI analysis showed three predominant tet(X3) and tet(X6) among Acinetobacter populations, we performed phylogenomic analysis for tet(X3)-/tet(X6)-positive isolates carried by four major species as representatives, i.e., A. indicus, Acinetobacter sp002018365, A. towneri, and A. variabilis was detected for 4 isolates (1 to 44 SNPs) of Acinetobacter sp002018365 (tet(X3) and tet(X6) mainly disseminated sporadically among Acinetobacter populations.To further evaluate the patterns of dissemination of riabilis ; Fig. S302018365 . The dattet(X3) and tet(X6) in Acinetobacter spp., we here intended to dissect the genetic relatedness of tet(X3)- and tet(X6)-harboring plasmids. Four circularized tet(X3)-/tet(X6)-harboring plasmids were obtained in this study, and all finished tet(X3)-/tet(X6)-harboring plasmids deposited in GenBank were analyzed first. Twenty-five of the 30 publicly available plasmids were carried by Acinetobacter spp. Most of the 26 tet(X3)-harboring plasmids [including the 6 tet(X3)-tet(X6)-harboring plasmids] shared a coverage lower than 65%, indicating a highly diverse structure for the plasmidome of tet(X3) (tet(X3)-tet(X6)-positive plasmids shared high similarity (>89.8% coverage and >85% identity), suggesting that they were derived from an ancestor. The four plasmids were hosted in A. schindleri and A. indicus strains isolated from goose and soil samples collected in different provinces of China (tet(X3)-encoding plasmids carried by A. towneri and a novel species of Acinetobacter as mentioned above (To explore the role of plasmids in the dissemination of tet(X3) . Four ofof China , indicated above .tet(X6)-harboring plasmids carried by Acinetobacter and an unknown species share low similarities, except for pAT232 and pAT205, as mentioned above (tet(X6)-harboring plasmids carried by Proteus species and from the 6 tet(X3)-tet(X6)-harboring plasmids (tet(X3)-tet(X6)-harboring plasmids might have resulted from the capture of tet(X6) by tet(X3)-harboring plasmids.The 5 ed above . They arplasmids . Hence, tet(X3)-harboring plasmids among Acinetobacter spp., we selected 17 plasmids out of 26 tet(X3)-harboring plasmids as references according to their similarities (<80% coverage and identity). The 17 plasmids were compared to the 243 tet(X3)-positive genomes [6 genomes with chromosome-carried tet(X3) were excluded] by using BLAST, and no epidemic plasmids were found (tet(X3) plasmid structures were highly diverse among isolates (mean plasmid coverage range of 12.09% to 55.05%). Using a cutoff range of >80% coverage and >90% identity, we found that pGX5-like plasmids were hosted in 36 strains belonging to different species , and p34AB-like, p94-2-tetX3-like, pXM9F202-2-tetX-90k-like, and p10FS3-1-3-like plasmids were found in 17, 9, 8, and 7 strains belonging to different species, respectively (tet(X3) in Acinetobacter is mainly mediated by various plasmids and that cross-species transmissions mediated by a few of them might have occurred in a small proportion of cases.To further estimate the distribution of re found . We furtre found , and thiectively . These dtet(X) genes causing the horizontal transfer of tigecycline resistance have significantly compromised the treatment effectiveness of tigecycline and, thus, have aroused considerable concern. A set of surveillance studies revealed the wide range of ecosystems in which tet(X) genes can be found, including soil, sewage, animals, hospitals, livestock farms, and the human gut (\u2013tet(X)-positive isolates are especially prevalent in livestock and poultry, such as pigs, cows, and chickens, and less so in shrimp, migratory birds, and waterfowl (28\u2013tet(X) genes in the context of One Health is imperative to efficiently control their further dissemination. In this study, we isolated tet(X)-positive Acinetobacter spp. from livestock and their surrounding environmental sources and comprehensively investigated their population structures and genetic characterizations.Recently identified plasmid-borne uman gut \u201316, 19. aterfowl , 28\u201330. tet(X)-positive isolates were recovered from 2 different swine farms but not from dairy farms or sheep farms. A. towneri was the most prevalent species carrying tet(X) genes in Acinetobacter spp., with tet(X3) and tet(X6) being the prevalent alleles (tet(X3)-positive Acinetobacter species isolates were exclusively detected in intensive pig farms in China has been reported recently (tet(X) genes to humans from pigs could be much higher than the risk of dissemination from other kinds of livestock.According to our surveillance data, 23 alleles . A similrecently . These rAcinetobacter spp. are ubiquitous in the natural environment, and some of them, e.g., A. baumannii, A. indicus, and A. lwoffii, have become important opportunistic pathogens in clinical settings. Our and other studies showed that Acinetobacter spp. was the major reservoir of tigecycline-resistant tet(X) genes (tet(X) genes in GenBank, we found that A. indicus, Acinetobacter sp002018365, and A. towneri were the prevalent species carrying tet(X3) and tet(X6). Likewise, a national surveillance of tet(X)-positive Acinetobacter isolates from humans, animals, and their surrounding environments conducted between 2015 and 2018 showed that, after a novel species of Acinetobacter, A. towneri and A. indicus were the major hosts of tet(X3), tet(X4), and tet(X5) (tet(X)-positive Acinetobacter isolates were livestock associated, raising concerns that the tigecycline-resistant tet(X) genes could be transmitted to humans from livestock via opportunistic pathogens of Acinetobacter. Our analysis showed that most of the tet(X)-positive Acinetobacter isolates disseminated sporadically; however, few interregional transmission events were detected here, highlighting the need for controlling the dissemination of tet(X3)- and tet(X6)-positive Acinetobacter species isolates.X) genes , 20, 22.tet(X) genes have been continuously identified either on chromosomes or on plasmids in various bacterial species, the major vectors of tigecycline-resistant tet(X) genes remain unclear. Pioneering studies have shown the importance of the ISCR2-mediated tet(X) transposition structure (tpnF-tet(X3)-hp-hp-ISCR2 cassette clone, and inverse PCR assays identified ISCR2-xerD-tet(X3)-res-ORF1 and ISCR2-ORF2-abh-tet(X4) minicircles in different studies (CR2 was found upstream or downstream from tet(X3) and tet(X6) genes. Albeit we did not test the transferability of the ISCR2-mediated tet(X) transposition structure, the genetic contexts of tet(X3) carried by 249 genomes of Acinetobacter species were comprehensively compared. The proportion of the structure ISCR2-xerD-tet(X3)-res-ISCR2 might be up to 86.35% (215/249), implying a critical role of ISCR2 in the dissemination of tet(X3).Although numerous tructure , 17. The studies . In our tet(X3)-encoding plasmid, pAT181, was self-transmissible from A. towneri to A. baumannii and conferred tetracycline resistance to the recipient. Currently, very few studies have identified self-transmissible plasmids carrying tet(X) genes. Chen et al. reported the conjugability of a tet(X3)- and tet(X5.3)-harboring plasmid, pYH12207-2, from Acinetobacter piscicola to A. baylyi strain ADP1 and the conjugability of a tet(X3)-harboring plasmid, p10FS3-1-3, from a novel Acinetobacter species to A. baylyi ADP1. However, these two plasmids did not enhance the resistance to tetracyclines in the recipient strain (\u22126), did not impose a fitness cost but increased the growth rate of the recipient. It is suggested that successful dissemination of resistance plasmids largely depends on the fitness cost imposed on hosts (tet(X3) gene in the future. Additionally, although no epidemic plasmids carrying tet(X3) have been detected currently, several plasmids were found to be circulating in a small proportion of strains. These plasmids could become epidemic after transmitting to other hosts in the future.Of note, we found that a on hosts . No fitntet(X) alleles, tet(X3) and tet(X6), disseminate sporadically in Acinetobacter populations. Currently, the dissemination of tet(X3) and tet(X6) is mainly limited to livestock-associated sites. Continuous surveillance for tet(X) genes in the context of One Health is necessary to prevent them from transmitting to humans.Our study provides evidence that the predominant n\u2009=\u200972) and water (n\u2009=\u200978) surrounding the farms. All the samples were initially enriched in LB medium for 6\u2009h and spread on CHROMagar Acinetobacter medium plates to recover Acinetobacter species isolates. PCR screens of tet(X) alleles were performed as previously described -positive isolates were determined using the broth microdilution method according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI) . The tes to CLSI . The breCAST V10 . E. colitet(X)-positive isolates were extracted using the Puregene yeast/bact. kit B according to the instructions of the manufacturer and were sequenced by using the HiSeq 4000 system . The isolates were taxonomically assigned using GTDB-Tk (version 1.3.0) with the Genome Taxonomy Database (release 95) (tet(X)-harboring plasmids were analyzed using BRIG version 0.95 (tet(X) genes were selected to be further sequenced using the PromethION platform . Hybrid assembly of short-read and long-read sequencing data was performed using Unicycler version 0.4.8 (Genomic DNAs of the ease 95) . The seqion 0.95 . Represeon 0.4.8 .https://card.mcmaster.ca/) with a threshold of nucleotide identity of >90% and coverage of >90%. Synteny analysis was performed using Easyfig deposited in GenBank (as of 31 May 2021) were downloaded to search for tet(X) genes. The 15 tet(X) alleles were queried in these genomes by BLAST comparison to their nucleotide sequences, using 99% identity and 100% coverage as the cutoff (All assembled genomes of e cutoff .https://github.com/katholt/RedDog) was used to simulate 100-bp reads from tet(X3)-carrying genomes. To calculate the coverage of each representative plasmid in each genome, those 100-bp reads were mapped against representative tet(X3)-harboring plasmids by using Bowtie2 version 2.2.9 (tet(X3)-carrying genomes containing annotated genes of each reference plasmid was calculated according to the gene presence/absence table reported by RedDog (at least five reads covering \u226595% of the length of the gene was defined as presence), and the results were plotted as circular heatmaps using ggplot2 in R (geom_tile for heatmap grid and coord_polar for circularization).Conservation of reference plasmid genes was calculated as previously described . Brieflyon 2.2.9 . The prohttps://www.r-project.org/).Pairwise sequence comparison of circularized plasmids was performed as previously described . Brieflytet(X3) and tet(X6) was evaluated by a conjugation assay. Briefly, a donor tet(X)-carrying Acinetobacter isolate (AT181) was mixed with the rifampicin-resistant A. baumannii strain ATCC 17978 or rifampicin-resistant E. coli strain EC600 as a recipient strain at a ratio of 1:1 by conjugational mating at 37\u00b0C without shaking overnight. The transconjugants were selected on LB agar plates containing rifampicin (600\u2009mg/liter) and tigecycline (2\u2009mg/liter). The species of all putative transconjugants were verified by using matrix-assisted laser desorption ionization\u2013time of flight (MALDI-TOF) mass spectrometry . PCR verifications of tet(X) genes were performed for the putative transconjugants for which the species was confirmed as A. baumannii or E. coli. Transfer frequency was calculated as the number of transconjugants obtained per donor. The growth of the donor strain and transconjugants was measured by determining the optical density at 600\u2009nm (OD600) every 30\u2009min. The assay was in triplicate.The transmissibility of tet(X)-specific PCRs to determine the proportion of tet(X)-positive bacteria in each population. Plasmids were considered stable when the retention rates were still over 80% at the end of the experiment. The plasmid stability was evaluated in triplicate.Plasmid stability was estimated according to the method of a previous study with minor modifications . Transcot test was performed to compare the number of ARGs in the tet(X6)-carrying clone and the tet(X3)-carrying clone, and statistical significance was taken as a P value of <0.05.The unpaired tet(X)-positive strains have been submitted to GenBank under BioProject accession number PRJNA631342, and the accession number of each genome is listed in The genome sequences of"} +{"text": "This study examined the molecular characterization of a prenatal case with true fetal mosaicism of small supernumerary marker chromosome 16 (sSMC(16)). A 41-year-old female underwent amniocentesis at 19 weeks of gestation due to advanced maternal age. Chromosomal analysis for cultured amniocytes revealed a karyotype of 47,XY,+mar[4]/46,XY[16]. Spectral karyotyping and metaphase fluorescence in situ hybridization (FISH) demonstrated that the sSMC was derived from chromosome 16 (D16Z1+)[13/20]). Confined placental mosaicism was initially suspected because the prenatal ultrasound revealed a normal structure and the pregnancy was uneventful. However, interphase FISH of cord blood performed at 28 weeks of gestation showed 20% mosaicism of trisomy chromosome 16 (nuc ish(D16Z2\u00d73)[40/200]). Chromosome microarray analysis further demonstrated 55% mosaicism of an 8.02 Mb segmental duplication at the subcentromeric region of 16p12.1p11.1 (arr[GRCh37] 16p12.1p11.1(27021975_35045499)\u00d73[0.55]). The results demonstrated a true fetal mosaicism of sSMC(16) involving chromosome16p12.1p11.1 that is associated with chromosome 16p11.2 duplication syndrome (OMIM #614671). After non-directive genetic counseling, the couple opted for late termination of pregnancy. This case illustrated the use of multiple molecular cytogenetic tools to elucidate the origin and structure of sSMC, which is crucial for prenatal counseling, decision making, and clinical management. Small supernumerary marker chromosome (sSMC), which is defined as additional centric chromosome fragments too small to be identified or characterized by banding cytogenetics alone , occurs de novo origin of the sSMC(16). The prenatal ultrasound showed unremarkable results, including fetal anatomy, biometry, and target neurosonography. A diagnosis of fetal mosaicism was questionable because of the normal ultrasound findings. The pregnant woman initially denied follow-up genetic analyses. Until 28 weeks of gestation, she opted for cordocentesis because of the increased feeling of anxiety. Interphase FISH of cord blood confirmed a true fetal mosaicism of trisomy chromosome 16 (nuc ish(D16Z2\u00d73)[40/200]). Chromosome microarray analysis revealed a mosaic duplication in chromosome 16p12.1p11.1, comprising the breakpoint 1\u20135 (BP1-BP5) of chromosome 16p11.2. The chromosomal 16p11.2 BP1-BP5 duplication is associated with chromosome 16p11.2 duplication syndrome with features of autism spectrum disorders (ASD) and other neurodevelopmental disorders /46,XY[16]. Spectral karyotyping (SKY) and metaphase fluorescence in situ hybridization (FISH) revealed the sSMC was derived from chromosome 16 (sSMC(16)). Karyotypes of both parents were normal, indicating a isorders . After nConventional cytogenetic G-banding analysis with Wright\u2019s dye staining at the 550 bands of resolution was performed on cultured amniocytes according to the standard cytogenetic protocol. SKY using 24-color SKY probes and metaphase FISH using Satellite Enumeration probes were further carried out to determine the origin of the sSMC detected in the cytogenetic analysis of cultured amniocytes.\u00ae gene chip (ID 040427) was further used to determine the entity of sSMC following the standard protocol . Scanned CMA images were analyzed by Feature Extraction 9.5.3 software , and the extracted data were processed using the Agilent Genomic Workbench 7.0 program . The CMA findings were described based on the reference genome version of GRCh37, following the latest guideline of An International System for Human Cytogenomic Nomenclature (ISCN2020). The clinical significance of copy number variations/sSMCs was according to the Genomic Variation Database (http://dgv.tcag.ca/dgv/app/home) (accessed on 12 July 2021), DECIPHER (https://www.deciphergenomics.org/) (accessed on 12 July 2021), and ChromosOmics-Database (http://cs-tl.de/DB/CA/sSMC/0-Start.html) (accessed on 12 July 2021).Interphase FISH analysis of uncultured specimen of cord blood was performed to confirm the existence and proportion of sSMC using chromosome 16 Satellite Enumeration probe encompassing the locus D16Z2 (16p11.1-q11.1) , based on the molecular cytogenetic findings in cultured amniocytes. Chromosome microarray analysis (CMA) using an Agilent customer design oligonucleotide 8 \u00d7 60 K CytoScan2 ratio = 0.35), indicating a 8.02 Mb segmental duplication at the subcentromeric region of 16p12.1p11.1 encompassing 139 genes and covering the BP1-BP5 region of chromosome 16p11.2 with 55% mosaicism for genomic imbalance is the most frequent autosomal anomaly seen in early spontaneous abortions, accounting for 12.7\u201315% of first-trimester pregnancy losses ,15. FullQPRT (OMIM#606248), PRRT2 (OMIM#614386), KCTD13 (OMIM#608947), and DOC2A (OMIM#604567). Levels of QPRT, involved in the catabolism of quinolinic acid, in the human brain have been postulated to be involved in the pathogenesis of neurodegenerative disorders. It was suggested that QPRT may play an important role in the pathogenesis of ASD in 16p11.2 deletion carriers [PRRT2 encoded a protein involved in synaptic transmission in central nerve system and associated with autosomal dominant familial infantile convulsions with paroxysmal choreoathetosis (OMIM # 602066), benign familial infantile seizures type 2 (OMIM # 605751), and episodic kinesigenic dyskinesia type 1 (OMIM: 128200). KCTD13 has been suggested to drive the mirror microcephaly/macrocephaly phenotypes in a zebrafish study [KCTD13 in mice showed reduced synaptic transmission, supporting a role of KCTD13 in the regulation of neuronal function relevant to neuropsychiatric disorders [DOC2A encodes a calcium sensor which most probably regulates the fusion of vesicles with membranes. DOC2A can regulate spontaneous synaptic transmission and has been implicated in Ca2+-dependent neurotransmitter release. The abnormal protein expression of DOC2A in epileptic brain tissue may play an important role in epilepsy [Several genes in the BP4-BP5 region of chromosome 16p may play roles in NDD, including carriers . PRRT2 esh study . Additioisorders . DOC2A e OMIM#6068, PRRT2 This report presented the prenatal diagnosis of a true fetal mosaicism of sSMC(16) involving chromosome 16q12.1q11.1, related to chromosome 16p11.2 duplication syndrome. By using different molecular cytogenetic tools, including SKY, FISH, and CMA, the origin and structure of the abnormal chromosome were determined that provides crucial information for prenatal counseling and clinical management."} +{"text": "Team-based care is necessary to provide better healthcare outcomes for the complex needs of older adults. Shared clinical learning experiences prepare practitioners to work in collaborative partnership to achieve optimal outcomes. To promote collaborative partnership, we established interprofessional community based clinical experiences with older adults at home, in assisted living and in skilled nursing facilities. One nurse practitioner faculty member was paired with 2 students for each clinical experience day. Initially these were face-to-face encounters, however, with the onset of COVID-19, all high-risk encounters were converted to a virtual modality. The clinical encounters focused on the Age Friendly Model (4M). Post clinical discussions and recommendations focused on interprofessional treatment plans. A REDCap(TM) survey was completed by all student participants for program evaluation. Of the 14 surveys sent, 11 were completed; 10 (77%) females; 3 (23%) males; 7 (50%) family practitioner students; 7 (50%) adult-gerontology nurse practitioner students. Four had previous home health experience (14%), and 10 had none (86%). 4M Likert scale (1-5) means were \u201cwhat matters\u201d = 4.27, medications = 4.18, mentation = 4.09, and mobility = 4.09. Students found the overall experience valuable (mean = 4.27). Of 11 students, 3 (27%) were involved telehealth experiences. Students found real community based clinical experiences to be very enlightening, offering a different perspective, and altering their appreciation for the everyday life of the older adult. Future plans include adding social work and physical therapy students to these clinical experiences to enhance interprofessional education."} +{"text": "Bloodstream infections (BSI) cause significant morbidity and mortality after hematopoietic cell transplant recipients (HCT). Surveillance blood cultures (SBC) are commonly used to decrease the risk of developing BSI but prior data suggest limited clinical utility. At our center, SBC monitoring was discontinued on 12/1/2019. This is a single center study evaluating the impact and safety of discontinuing routine SBC monitoring.Retrospective review of allogeneic hematopoietic cell transplant recipients (HCTR) seen before (12/1/2017 \u2013 11/30/2019) and after (12/1/2019 - 12/1/2020) discontinuation of SBC. We evaluated utility of SBC and the impact of discontinuation of SBC on admissions, mortality, and other variables.Staphylococcus aureus or fungi. Fifty-one (63%) of the positive SBC resulted in an admission; median (range) length of stay (LOS) was 3 days (1-11). Following discontinuation of SBC, median monthly blood culture-related admissions decreased from 3 (0-6) to 1 (0-3) shown in Figure 1. In the pre-intervention period, there were 2 BSI-related deaths, and 0 following cessation of SBCs. One hundred thirty-six and 133 HCTR were followed before and after discontinuation of SBC, respectively. Median (range) ages were 58 (22-73) and 56 (19-73); 60 (44%) and 59 (44%) were female, respectively. The most common cancer was acute myelogenous leukemia (71 (52%) and 61 (46%)); 87 (64%) and 77 (58%) had graft-versus-host disease respectively. Pre-intervention, 1946 SBCs were drawn; 81/1946 (4.2%) were positive. Post-intervention, 29 SBC were drawn; 1/29 (3.4%) were positive. Of the 82 positive SBCs, 63 (77%) were skin flora, and 9 (11%) were gram negative rods. No cultures grew Figure 1. Monthly Hospital Admissions for Positive Outpatient Blood CulturesSBCs were infrequently positive and often resulted in unnecessary antibiotic use, admission, and clinical interventions. After SBC monitoring was discontinued, there was a decrease in hospital admissions and health care utilization for positive blood cultures drawn in the outpatient setting. This intervention did not negatively impact clinical outcomes, including BSI-related mortality. Discontinuation of SBC appears to be safe and results in a reduction in healthcare utilization. Centers performing SBC should consider eliminating this practice.Ghady Haidar, MD, Karuys (Grant/Research Support)"} +{"text": "Accurate diagnosis in patients with suspected coronavirus disease 2019 (COVID-19) is essential to guide treatment and limit spread of the virus. The combined nasal and throat swab is used widely, but its diagnostic performance is uncertain.In a prospective, multi-centre, cohort study conducted in secondary and tertiary care hospitals in Scotland, we evaluated the combined nasal and throat swab with reverse transcriptase-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in consecutive patients admitted to hospital with suspected COVID-19. Diagnostic performance of the index and serial tests was evaluated for a primary outcome of confirmed or probable COVID-19, and a secondary outcome of confirmed COVID-19 on serial testing. The diagnosis was adjudicated by a panel, who recorded clinical, laboratory and radiological features blinded to the test results.We enrolled 1368 consecutive patients who underwent a total of 3822 tests (median 2 [IQR 1\u20133] tests per patient). The primary outcome occurred in 36% (496/1368), of whom 65% (323/496) and 35% (173/496) had confirmed and probable COVID-19, respectively. The index test was positive in 255/496 (51%) patients with the primary outcome, giving a sensitivity and specificity of 51.4% and 99.5% (95% CI 99.0 to 99.8%). Sensitivity increased in those undergoing 2, 3 or 4 tests to 60.1% (95% CI 56.7 to 63.4%), 68.3% (95% CI 64.0 to 72.3%) and 77.6% (95% CI 72.7 to 81.9%), respectively. The sensitivity of the index test was 78.9% (95% CI 74.4 to 83.2%) for the secondary outcome of confirmed COVID-19 on serial testing.In patients admitted to hospital, a single combined nasal and throat swab with RT-PCR for SARS-CoV-2 has excellent specificity, but limited diagnostic sensitivity for COVID-19. Diagnostic performance is significantly improved by repeated testing.The online version contains supplementary material available at 10.1186/s12879-021-05976-1. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a novel coronavirus, which is responsible for the global pandemic of coronavirus disease 2019 (COVID-19) tests per patient) for symptoms of suspected COVID-19 .Patients with confirmed or probable COVID-19 were older than those with an alternative diagnosis (median age of 71 [57\u201382] versus 67 [53\u201380] years), and were less likely to be from an area of deprivation (13% [65/496] versus 20% [174/872]). However, they had similar comorbidities and were as likely to be receiving angiotensin converting enzyme inhibitors, corticosteroids or immunosuppressants at presentation 9/L versus 1.44\u2009\u00d7\u2009109/L and 5.8\u2009\u00d7\u2009109/L versus 6.4\u2009\u00d7\u2009109/L, respectively), but a higher C-reactive protein concentration (52\u2009mg/dL versus 22\u2009mg/dL) at presentation patients with the primary outcome eTable\u00a0a. The neThe majority of patients underwent serial testing 59.6%, 815/1368) with 22.7% (310/1368) undergoing 4 or more serial tests or negative (blue). eFigure 2. Heat map of RT-PCR testing in patients with confirmed COVID-19 stratified according to whether the index test was negative (a) or positive (b). eFigure 3. Sensitivity of serial testing using the combined nasal and throat swab for the primary (confirmed and probable COVID-19) and secondary (confirmed COVID-19) outcome in patients who were tested at least four times. eFigure 4. Negative predictive value of serial testing using the combined nasal and throat swab for the primary (confirmed and probable COVID-19) and secondary (confirmed COVID-19) outcome in patients who were tested at least four times. eFigure 5. Forest plot of the (a) sensitivity and (b) negative predictive value of the index combined nasal and throat swab for a diagnosis of confirmed COVID-19 stratified by subgroups."} +{"text": "Coronavirus disease (COVID-19) caused by SARS-COV2 represents global public health concern, with varied severity of illness in different ages and racial groups. This study aims to describe clinical presentation and outcomes in children aged 0-21 years in a community hospital setting in New Jersey.This is a retrospective medical record review of pediatric patients (0-21 years) admitted to Saint Barnabas Medical Center between March 2020- December 2020 with confirmed diagnosis of COVID-19 infection. Diagnosis of COVID-19 infection is based on ICD-10 diagnosis code. Data was extracted from electronic medical records, including demographics, pre-existing conditions, presenting symptoms, treatments used and outcomes. We identified 48 cases of pediatric COVID-19 patients at Saint Barnabas Medical Center during period of 03/20-12/20. Review of demographic data showed 29 patients (60%) were female, and 19 (40%) were male. Race distribution was 38% black, 17% white, 4 % Asian Indian, and 41% others/unknown. Age distribution was as follows: 40% >15 yrs, 15% 11-15 yrs, 15% 0-1 yrs, 13% 6-10 yrs, 13% 1-5 yrs, and 6% newborn. Fever (65%) was the most frequent symptom identified, followed by cough (31%), nausea/vomiting (29%), abdominal pain (19%), shortness of breath (17%), rash (15%), diarrhea (10%), headache (10%), myalgia/body-aches (8%), chest pain (6%), red eyes (6%), and loss of taste/smell (2%). Of 48 patients, 10 (21%) had positive chest X-ray findings of lung infiltrates or opacities, 4 (8%) had abnormal echocardiogram findings, and 1 (2%) had abnormal CT chest. 21 of 48 patients had underlying comorbid conditions, with Diabetes and Asthma being the most common. No deaths were reported. 8 of 48 COVID-19 patients were diagnosed with MIS-C. Of these MIS-C patients, 5 (63%) were male and 3 (38%) were female. 6 of 8 affected patients were black (75%). 50% of MIS-C patients were between 6-10 years. 3 of 8 patients (38%) had abnormal echocardiogram findings. This review supports clinical findings from other studies and also suggests certain racial ethnicities may be disproportionately impacted, which warrants further exploration to determine genetics vs environmental factors that lead to increased predisposition to severe illness.All Authors: No reported disclosures"} +{"text": "Patients with severe coronavirus disease (COVID-19) may have COVID-19\u2013associated invasive mold infection (CAIMI) develop. We report 16 cases of CAIMI among 146 nonimmunocompromised patients with severe COVID-19 at an academic hospital in Santiago, Chile. These rates correspond to a CAIMI incidence of 11%; the mortality rate for these patients was 31.2%. Invasive mold infection is a serious complication described in patients with severe viral pneumonia (We retrospectively identified adults admitted to the intensive care unit (ICU) at Hospital Cl\u00ednico of UC-CHRISTUS Health Network in Santiago, Chile, during May 18\u2013July 18, 2020 for COVID-19\u2013associated invasive mold infection (CAIMI). We diagnosed CAIMI on the basis of respiratory failure, refractory fever, lung infiltrates, positive mold culture, positive galactomannan from serum, bronchoalveolar lavage (BAL), or a combination of these. The study was approved by the hospital\u2019s institutional review board .We recorded clinical and microbiological data, imaging reports, treatments, and survival outcome. A thoracic radiologist (A.H.) reviewed chest radiographs and computed tomography (CT) scans, and we calculated a chest radiograph severity score (2/FiO2 for each patient was 124 (range 57\u2013476). Fourteen patients (87.5%) required invasive mechanical ventilation. In 12 cases (75%), prone position was applied for an average of 5 (range 2\u201319) days. All patients received antimicrobial drug therapy, 15 (93.8%) received corticosteroids, and 3 (18.8%) received tocilizumab.Of the 856 COVID-19 patients admitted, 146 (17.1%) were hospitalized in the ICU and 16 (11%) received a diagnosis of CAIMI Table. MAspergillus spp. , 2 (16.7%) Rhizopus spp. , and 1 (8.3%) Scedosporium spp. In relation to positive galactomannan, 6 cases (37.5%) were obtained from serum (index 1.29 [0.75\u20133.61]) and 2 (12.5%) from BAL (index 4.63 [3.65\u20135.6]).We diagnosed CAIMI a mean of 18.5 (range 1\u201347) days after a positive COVID-19 test, at 14.5 (range 0\u201328) days after ICU admission, and at 12.5 (range 0\u201328) days after invasive mechanical ventilation was initiated. We performed BAL in 4 cases (25%); during bronchoscopy, we observed no ulcerative lesions in tracheobronchial mucosa. We diagnosed bacterial infection in 7 patients (43.8%). We obtained mold mycological evidence by fungal culture in 9 cases (56.3%) and galactomannan in 8 cases (50%); cultures came from tracheal aspirate in 7 cases and BAL in 2 had CT. The mean radiologic score Table.Aspergillus identification cases, the CAPA criteria do not apply. Case 14 was in a previously healthy person who had Aspergillus and mucorales co-infection without other fungal foci. Case 15 was a proven disseminated mucorales infection, according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group criteria . Thirteen (81.3%) patients received antifungal therapy at standard doses: 10 (76.9%) received voriconazole, 2 (15.4%) liposomal amphotericin B, and 1 (7.7%) isavuconazole. We obtained therapeutic drug monitoring in 9 patients receiving voriconazole therapy . Eleven (68.8%) patients survived.Applying CAPA diagnostic criteria (The 6.8% CAPA rate shown in our series is below the lower range reported previously (Diagnoses beyond aspergillosis, such as mucormycosis and scedosporiosis, add to a previously reported pulmonary fusariosis in an immunocompetent patient (The classic predisposing underlying conditions associated with mold disease were absent in our cases. In fact, all patients were apparently immunocompetent, and the most relevant underlying conditions were the frequent conditions described in severe COVID-19 cases (As previously reported (The certainty of CAIMI diagnosis is one of the main challenges in the COVID-19 scenario. Serum galactomannan is included in the CAPA diagnostic criteria (Aspergillus mold infections. In conclusion, we highlight the need for clinicians to have a high level of suspicion of mold infection in the list of possible superinfections among patients with severe COVID-19. In addition, CAIMI diagnostic criteria should include non-Additional information on the characteristics of patients with COVID-19\u2013associated mold infection, Chile."} +{"text": "Background: Aromatase inhibitors (AIs) are associated with musculoskeletal pain in one third (20\u201347%) of breast cancer patients. Recently, CDK4/6 inhibitors have emerged as a new therapeutic approach in hormone receptor (HR)-positive breast cancer. While hematological and gastrointestinal toxicities are frequently reported during treatment with CDK4/6 inhibitors, musculoskeletal symptoms are less commonly encountered. Methods: Herein, we present a retrospective study of 47 breast cancer patients who received CDK4/6 inhibitors along with endocrine therapy in our department between 01/01/2018 and 01/09/2020. Results: Median age at diagnosis was 58 years (29\u201381). Median duration of treatment was 8.76 months . Median PFS was 24.33 months . Overall, toxicity was reported in 61.7% of the cases (29/47). Arthralgia was reported in 6.4% (3/47) of the patients. Hematological toxicity was reported in 51.1% (24/47) of the patients. Neutropenia was the main hematological toxicity observed along with anemia , thrombocytopenia , and leukopenia . Conclusions: Though our data reflect a small sample size, we report a reduced arthralgia rate (6.4%) during treatment with CDK4/6 inhibitors compared with that reported in studies of AIs (20\u201347%). Aromatase inhibitor-induced musculoskeletal syndrome (AIMSS) is a syndrome commonly encountered by breast cancer patients treated with aromatase inhibitors (AIs). Even though third generation AIs have been widely implemented in clinical practice, musculoskeletal symptoms often lead to treatment discontinuation. Approximately one third of breast cancer patients receiving AIs 20\u201347%) report AI-induced joint symptoms, most commonly arthralgia and myalgia. The prevalence of musculoskeletal symptoms varies within different studies according to the type of aromatase inhibitor administered, previous chemotherapy treatment, prior treatment with tamoxifen, and body mass index ,2. Event0\u201347% repp < 0.00001) and OS compared with endocrine therapy alone in HR-positive, HER2-negative advanced breast cancer [Today, cyclin-dependent kinase 4/6 (CDK4/6) inhibitors have emerged as new treatment options in the management of advanced or metastatic breast cancer. In February 2015, the Food and Drug Administration (FDA) granted accelerated approval to CDK4/6 inhibitor Palbociclib for the treatment of metastatic HR-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancer based on results of the PALOMA-1 Phase II study . Ribocict cancer . CollectThe toxicity profile of CDK4/6 inhibitors is well-defined based on Phase III trials. Hematologic toxicities are the most common adverse events for palbociclib or ribociclib. Approximately 85% and 76% of breast cancer patients treated with palbociclib or ribociclib, respectively, experience neutropenia of any grade . Grade 3Interestingly, arthralgia of any grade was observed in 18%, 29%, and 14% of patients treated with palbociclib, ribociclib, or abemaciclib, respectively . In addiThis is a single-institute, retrospective study, which was carried out in the Oncology Unit of Clinical Therapeutics Department of University of Athens in Alexandra General Hospital. The study was performed in accordance with the 1964 Helsinki Declaration and was approved by the institutional ethics committee on November 30, 2020 (Ethic Code: 56941). Medical records of patients who were treated with CDK4/6 inhibitors in the adjuvant or metastatic setting between 01/01/2018 and 01/09/2020 were retrospectively reviewed. All subjects gave written informed consent. Data were collected through a single institution database that consists of clinicopathological, treatment-related, and survival data. Breast cancer patients that received CDK4/6 inhibitors in the adjuvant setting were also included.Descriptive statistics were used to assess the clinicopathological parameters of the patients. Disease progression was defined as the time between the initiation of treatment with CDK4/6 inhibitors and the date of local or distant disease recurrence. Progression free survival (PFS) was calculated from the initiation of treatment with CDK 4/6 inhibitors until disease progression (PD) or last follow-up in metastatic breast cancer patients. The distribution of PFS was estimated using the Kaplan\u2013Meier method. Statistical analysis was performed with SPSS 24.0 statistical software.Between January 2018 and September 2020, 47 women received treatment with CDK4/6 inhibitors in our department. Median age at diagnosis was 58 years (29\u201381). There were 21.3% (10/47) premenopausal, 66% (31/47) postmenopausal, and 12.8% (6/47) perimenopausal women. Overall, 53.2% (25/47) of women were diagnosed with early breast cancer, while 46.8% (22/47) of women were presented with de novo metastatic disease. The tumor was estrogen receptor (ER)-positive in 95.7% (45/47) of the cases and progesterone receptor (PR)-positive in 91.5% (43/47) of the cases. Breast cancer was hormone-receptor positive (ER- or/and PR-positive) in all cases (100%) and human epidermal growth factor receptor 2 (HER2)-negative in all cases. Most breast tumors were grade II , while 38.3% (18/47) were grade III. Adjuvant chemotherapy was administered in 92% (23/25) of women with early-stage breast cancer, while 80% (20/25) of women with early disease received adjuvant hormone therapy. In this population, 76% (19/25) of women had progressive disease and received CDK4/6 inhibitors, while the rest of them received CDK4/6 inhibitors in the adjuvant setting. Overall, CDK4/6 inhibitors were administered as adjuvant treatment in 12.8% (6/47) of the cases, as 1st line in 53.2% (25/47) of the cases and as 2nd line treatment in 29.8% (14/47) of the cases.Overall, 12.8% (6/47) of women received abemaciclib, 63.8% (30/47) received palbociclib, and 23.4% (11/47) of women received ribociclib. CDK4/6 inhibitors were administered in combination with fulvestrant (34%), letrozole (59.6%), or tamoxifen (6.4%). Overall, 34% (16/47) experienced progressive disease while on treatment with CDK4/6 inhibitors. In addition, 38.3% (18/47) of patients discontinued treatment with CDK4/6 inhibitors. Reasons of discontinuation were disease progression (88.9%), hematological toxicity in two cases (11.1%), and hyperkalemia in one case (5.6%). Median duration of treatment was 8.76 months . Overall, median PFS was 12.6 months for patients treated with CDK4/6 inhibitors for metastatic disease. The Kaplan\u2013Meier curve for PFS is depicted in Overall, toxicity was reported in 61.7% of the cases (29/47) . ArthralWe evaluated treatment-associated musculoskeletal symptoms in patients treated with CDK4/6 inhibitors in our department. The incidence of arthralgia reported was 6.4%, which is lower than the incidence reported in Phase III trials. Two of the patients that experienced arthralgia received CDK4/6 inhibitors in combination with aromatase inhibitors and one with fulvestrant. Interestingly, none of the patients experiencing joint pain discontinued treatment.Arthralgia has been more frequently reported in patients treated with palbociclib compared with the other two approved CDK4/6 inhibitors . A meta-In our study, arthralgia incidence was 6.4% in patients treated with CDK4/6 inhibitors either in the adjuvant or in the metastatic setting. This incidence is lower than the one described in Phase III trials ,15,16. FMultiple mechanisms of AI-induced arthralgia have been reported. The main mechanism proposed is via estrogen deprivation . AromataCDK4/6 inhibitors regulate the passage of cells in the S phase by maintaining the repressive effect of RB protein on the E2F family of transcription factors . During Regardless of the mechanism, CDK4/6 inhibitors have been shown to exert an anti-inflammatory mechanism in the joint microenvironment. CDK4/6 inhibitor palbociclib inhibited the proliferative phase of rheumatoid arthritis in an animal model, especially when combined with TNF-a or IL-6 blockers . PalbociCollectively, there is evidence that CDK4/6 inhibitors possess a protective role in treatment-related arthritis. Here, we here report a reduced rate of treatment-related arthralgia (6.4%) in patients receiving CDK4/6 inhibitors compared with hormone monotherapy treatment 20\u201347%) ,2,5.0\u201347% ,2,"} +{"text": "ERBB2 amplification, mutations in PIK3CA, AKT1, and ESR1, and tumor mutational burden (TMB), have become important biomarkers for treatment selection in breast cancer (BC). This study aimed to investigate the mutational features of Chinese early-stage BC patients.Various genomic alterations and genomic signatures, including Tumors and matched blood samples collected from 589 Chinese patients with early-stage BC were sequenced using a commercial gene panel consisting of 520 cancer-related genes to analyze all types of genomic alterations and estimate the TMB status.P<0.05) or amplified (P<0.05) in stage T3\u20134 tumors as compared with T1\u20132 tumors. A total of 18 genes were found to be differentially mutated (P<0.05) or amplified (P<0.05) in patients with lymph node metastasis than those without lymph node metastasis. Younger patients (\u226435 years) were more frequently identified with mutations or gene amplifications in eleven genes (P<0.05). TMB >10mutations/Mb were found in 5.7% of our cohort. Although the TMB was similar for various molecular subtypes between our cohort and the BC cohort of The Cancer Genome Atlas (TCGA) study, the TMB were statistically different for HR+/HER-, HR+/HER2+, and triple-negative subtypes between our cohort and African Americans in the TCGA study. As compared to the TCGA BC cohort, our cohort had a much earlier median age of diagnosis , and had significantly lower frequency of triple-negative subtype and invasive lobular BC . Further subgroup analyses revealed that mutation rates in various genes including TP53, ERBB2, and PIK3CA were distinct for patients who were younger (\u226435 years), had triple-negative or invasive lobular BC in our cohort than in the TCGA cohort.A total of 18 genes were found to be more frequently mutated (This study revealed distinct mutational features of various molecular subtypes of early-stage BC among Chinese patients. Moreover, we provide new insights into the differences in early-stage BC between the East and West. TP53 and PIK3CA, have been implicated in the development of breast cancer and human epidermal growth factor receptor 2 (HER2) status were defined according to the guidelines of the American Society of Clinical Oncology (ASCO) and CAP.Chinese patients diagnosed with various histology of early-stage (stage I-III) breast cancer in Guangdong Provincial People's Hospital (GDPH) who submitted paired breast tissue samples and blood samples for targeted sequencing to Burning Rock Biotech, a clinical laboratory accredited by the College of American Pathologist (CAP) and certified by the Clinical Laboratory Improvement Amendments (CLIA), were included in this retrospective study. Hormone receptor (HR) and multiple hypothesis testing was performed according to the Benjamin-Hochberg program.The clinical and pathological characteristics of the 589 patients included in our study are shown in TP53 (47.0%), PIK3CA (45.0%), and ERBB2 (30.0%) were the most frequently mutated genes in our cohort. Other genes that were mutated in \u226510% of the patients included CDK12 (18.0%), GATA3 (15.0%), CCND1 (12.0%), FGF19 (11.0%), and FGFR1 (10.0%).Targeted sequencing was performed on tissue samples of all 589 patients. A total of 5,592 somatic mutations in 418 genes were identified from 577 patients, resulting in a mutation detection rate of 98.0% (577/589). Various mutation types were detected including 2,109 CN amplification, 1,780 missense mutations, 389 frameshift mutations, 214 nonsense mutations, 183 splice-site variants, 81 indels, 78 fusions, and 24 CN deletions. LPR1B, EGFR, POLE, PTPRT, KAT6A, HIST1H3C, LATS1, SDHA, and SRC . Younger patients (\u226435 years) with breast cancer had more mutations in EZH2 but fewer mutations in PIK3CA and MAP3K1 , lymph node status (N), and age at diagnosis. As compared to T1\u20132 tumors, T3\u20134 tumors had significantly more mutations in nine genes including ERBB2 aberrations were detected in 175 of the 589 breast cancer cases, revealing an ERBB2 mutation rate of 29.7%. Various mutation types detected from our cohort included CN amplification (n=166), missense mutations (n=14), fusion (n=12), synonymous mutations (n=7), splice-site mutations (n=3), and intronic mutations (n=3). ERBB2 amplifications were detected in 28.2% (166/589) of the cohort; of them, eight patients had HER2-negative subtype and may be candidates for targeted HER2 therapy. We also found that ERBB2 aberrations were more likely to co-occur with CDK12 (Odds ratio (OR)=10), RAPA (OR=10), and SPOP (OR=7.4). Moreover, mutual exclusivity were found between ERBB2 aberrations and GATA3 (OR=0.5), KMT2C (OR=0.3), PTEN (OR=0.2), AKT1 (OR=0.2), CBFB (OR=0.2), or MAP2K4 (OR=0.1). In addition, 12 novel ERBB2 gene fusion partners were detected in seven patients from our cohort, including KSR1-ERBB2, KRTAP1-4-ERBB2, PIP4K2B-ERBB2, MED1-ERBB2, METRNL-ERBB2, SRCIN1-ERBB2, GLRA3-ERBB2, LOC100288778-ERBB2, IKZF3-ERBB2, ABCA9-ERBB2, PPP1R1B-ERBB2, and ABCA6-ERBB2.In addition to the mutational landscape of the cohort, we also analyzed the genetic features of our cohort in specific genes. A total of 205 ESR1 mutations, including six CN amplifications, six missense mutations, two frameshift mutations, one splice-site mutation, and one synonymous mutation. A majority of the ESR1 mutation were detected from stage III breast cancer. Interestingly, 25.0% (4/16) of the ESR1 mutation-positive patients were hormone receptor-negative. Moreover, all breast cancers with ESR1 mutations were invasive ductal carcinomas, with a majority of luminal B subtype and the remaining four patients had HER2-enriched (n=2) and triple-negative (n=2) subtypes.A total of 2.7% (16/589) of patients were detected with ERBB2 and ESR1, we also analyzed the mutation frequency of other oncogenic drivers, including KRAS, ROS1, ALK, MET, NTRK, and EGFR, to identify potentially actionable targets. KRAS mutations were detected in 2.7% (16/589) of the cohort, most of which were CN amplification . ROS1 mutations were detected in 4.1% (24/589) of the cohort; of which, two (8.33%) patients were detected with novel ROS1 gene fusions including CNTN3-ROS1, HACE1-ROS1, and NUS1-ROS1. ALK mutations were detected in 2.0% (12/589) of the cohort; of which, three patients were detected with ALK gene fusions including ADGRL3-AS1-ALK, EML4-ALK, and STRN-ALK. Gene mutations in NTRK1/2/3 were detected in 4.9% (29/589) of patients, with a majority of CN amplifications. No patient was detected with NTRK gene fusion in our cohort. Gene mutations in MET were detected in 4.9% (28/589) of the cohort; of which, three patients were detected with novel MET gene fusions including AGBL3-MET, MMD-MET, LVCAT5-MET, and XKR6-MET.In addition to CD274/PD-L1 were detected in 1.4% (8/589) of the cohort, six of which were CN amplification. Among these eight cases, only one case was triple-negative subtype, six patients had luminal B, and one patient had HER2-enriched subtype. BRAF alterations were detected in 1.5% (9/589) of the cohort, including four missense mutations, three CN amplifications, and two intronic mutations. The mutation frequencies of POLE and POLD genes were 3.4% (20/589) and 2.2% (13/589), respectively. Mutations in both genes had been reported by previous studies to predict the efficacy of immunotherapy.In addition to gene mutations related to targeted therapy, we also investigated gene mutations and TMB status that are associated with immunotherapy response. Gene alterations in The median TMB of our cohort was four mutations/Mb. Only 5.7% of the cohort had TMB greater than 10 mutations/Mb.). We then conducted further subgroup analysis based on ethnicity and found that the TMB of HR+/HER-, HR+/HER2+, and triple-negative subtypes in our cohort were statistically different from those of the African Americans (black) from the TCGA study . However, no statistical difference was observed in TMB between our cohort and the Caucasians , PTEN (7.5%), and AKT1 (5.9%). Among the cell cycle pathway-related genes, the most commonly mutated were CCND1 (45%), MYC (11%), and CDKN1B (3.0%). Among the genes involved in the FGFR pathway, FGF19 and FGFR1 were the most frequently mutated, with an incidence of 11% and 10%, respectively. The other FGFR pathway-related genes detected from our cohort were FGF4 (n=48), FGF3 (n=48), FGFR2 (n=18), FGFR4 (n=11), FGFR3 (n=5), FGF14 (n=7), FGF12 (n=2), and FGF7 (n=1).We further analyzed the pathways most commonly mutated in our cohort. Among the genes involved in the PI3K-AKT pathway, the most commonly mutated were CDK12 (18.2%) was the most frequently mutated, followed by PTEN (7.5%), NBN (6.3%), BRIP1 (4.3%), RAD51C (4.8%), BRCA1 (2.7%), FANCD2 (2.7%), PALB2 (2.4%), BRCA2 (2.2%), ATM (2.2%), POLD1 (2.0%), and FANCI (2.0%) (Among the homologous recombination repair (HRR) pathway-related genes, BRCA2 (n=19), BRCA1 (n=15), ATM (n=4), BARD1 (n=1), BRIP1 (n=2), CDH1 (n=3), CHEK1 (n=1), FANCA (n=3), FANCL (n=1), MUTYH (n=4), PALB2 (n=6), PMS2 (n=1), PTEN (n=1), RAD51C (n=2), SDHA (n=1), and TP53 (n=2). Germline BRCA1/2 mutations were detected in 34 patients (5.8%). Other germline mutations in genes related to the HRR pathway were detected in 21 patients (3.6%). According to molecular subtypes, P/LP germline mutations were detected in 39 patients with HR+/HER2\u2212, 10 patients with HR+/HER2+, six patients with HR-/HER2+, and 10 patients with triple-negative subtype. BRCA1 mutations were detected in 15 patients; of which, six patients had HR +/HER2\u2212, one had HR+/HER2+, three had HR-/HER2+, and five had triple-negative subtypes. BRCA2 mutations were detected in 19 patients; of which, 15 patients had HR+/HER2\u2212, two had HR+/HER2+, one had HR-/HER2+, and one had unknown subtype. No germline BRCA2 P/LP mutation was detected in triple-negative subtype.We further explored the pathogenic/likely pathogenic (P/LP) germline mutations in our cohort. P/LP germline mutations were detected from 11.2% (66/589) of our cohort. P/LP germline mutations were detected in genes including TP53 mutations were more likely to have a mutually exclusive relationship with mutations in GATA3 (OR=0.1), AKT1 (OR=0.3), and CBFB (OR=0.2). PIK3CA mutations were more likely to have a mutually exclusive relationship with mutations in ADGRA2 (OR=0.4) and AKT1 (OR=0.1). ERBB2 mutations were more likely to co-exist with mutations in CDK12 (OR=10), RAPA (OR=10), and SPOP (OR=7.4), but were mutually exclusive with mutations in GATA3 (OR=0.5), PTEN (OR=0.3), AKT1 (OR=0.2), CBFB (OR=0.2), and MAP2K4 (OR=0.1). Being located in the same chromosome (chromosome 11q13), CCND1 amplifications were more likely to be co-amplified with FGF3 (OR=10), FGF4 (OR=10), FGF19 (OR=10), EMSY (OR=10), and PAK1 (OR=10). GATA3 mutations were more likely to co-occur with mutations in BRIP1 (OR=5.7), CBFB (OR=10), and CD79B (OR=10).To understand the relationship between genomic aberrations, we further analyzed which somatic gene mutations were likely to exist together or in mutual exclusivity in the whole cohort (P<0.001), and had significantly lower frequency of triple-negative breast cancer and invasive lobular breast cancer . These results indicate the distinct clinicopathological characteristics of breast cancer between Chinese and Western breast cancer.To understand the distinct clinical characteristics of breast cancer among Chinese patients, we compared our data with the breast cancer cohort of the TCGA study. Compared to the TCGA breast cancer cohort, our cohort had a much younger median age of diagnosis , breast cancer histological subtype (i.e. invasive lobular breast cancer), and molecular subtype (i.e. triple-negative subtype).We then performed subgroup analysis of the mutation profile of patients in our cohort and those in the TCGA cohort with similar clinical characteristics, particularly in age (TP53 (51% vs. 30%) and ERBB2 (34% vs. 24%), and lower mutation rates in PIK3CA (25% vs. 30%) and GATA3 (15% vs. 24%). Meanwhile, the TCGA cohort had more mutations in RPTOR, PRKAR1A, and RAD51C than our cohort in our cohort had higher mutation rates in PIK3CA (25% vs 14%) and lower mutation rate in TP53 (79% vs 90%) and PTEN (12% vs 22%) than the TCGA cohort. KRAS gene mutations were detected in 9% of our cohort but were relatively rare (5.4%) in the TCGA cohort and PIK3CA (79% vs 37%) than in the TCGA cohort. However, the TCGA cohort had more frequent mutations in genes including CCND1 (19%), FGF19 (19%), FGF4 (19%), FGF3 (18%), IKBKE (14%), AKT3 (13%), FH (12%), PTEN (12%), CDC73 (12%), ABL2 (12%), NOTCH2 (11%), ERBB2 (11%), NTRK1 (10%), DDR2 (10%), and FGFR1 (10%) than our cohort , PIK3CA (45%), and ERBB2 (30%) were mutated in more than 30% of the cohort. These three genes were also differentially mutated across molecular subtypes wherein PIK3CA mutations (48%) were mostly identified among HR+/HER2\u2212 tumors, TP53 mutations (79%) were mostly identified among triple-negative subtype, and ERBB2 mutations (88% in HR+/HER2+ and 92% in HR+/HER2\u2212) were mostly identified among the HER2-positive subtype. In addition, we have discovered a number of candidate markers that have generally low incidence in breast cancer but have potential therapeutic value, including genetic aberrations in KRAS, ROS1, ALK, MET, NTRK, and EGFR. Certain mutations in these genes are associated with response to targeted therapy in other cancer types, but their therapeutic value in breast cancer requires further evaluation. These observations also suggest that comprehensive genomic analysis of breast cancer is required to facilitate the identification of the subset of patients who may benefit from targeted therapy.The main purpose of precision cancer medicine is to develop management strategies based on specific molecular events related to tumor progression. The use of targeted NGS sequencing increases the possibility of the application of targeted therapies for breast cancer patients by enabling the detection of clinically-relevant genomic changes. In our cohort, 98.0% (577/589) of the samples showed at least one mutation across 520 cancer-related genes. ERBB2 amplification is a predictive biomarker of response for HER2 targeted therapy in breast cancer. Conventional methods including immunohistochemistry and fluorescence in situ hybridization are still routinely used as clinical testing methods for HER2 overexpression and amplification; while the clinical value of panel-based NGS in breast cancer remains unclear. Through the use of NGS, we found that in addition to ERBB2/HER2 amplification, genomic aberrations in ERBB2 also exist as point mutations and gene fusions, albeit in much lower frequency than CN amplifications. In our cohort, we found that the common hotspot mutations in ERBB2 were L755S, D769Y, and V777L, which are all located in the ERBB2 kinase domain and were shown to be activating mutations in various solid cancers of the patients harboring ESR1 mutation had stage III breast cancer. cancers . These tsistance . Since t therapy . In our Furthermore, the subgroup comparative analysis revealed the distinct mutation landscape between our cohort and the TCGA cohort, particularly among younger patients, triple-negative breast cancer, and invasive lobular breast cancer, which may provide new insights into the differences between Chinese and Western breast cancers and may shed light on novel therapeutic targets.TP53, ERBB2, and CCND1 and lower mutation rates in PIK3CA and GATA3 in our cohort than the TCGA cohort. As a tumor suppressor gene, mutations in TP53 are closely related to the proliferation, invasion, and angiogenesis of cancer cells. TP53 mutations were also implicated in the poor prognosis of breast cancer patients is frequently mutated in a variety of human cancers and is considered to be essential in the development of many cancers can be found below: National Omics Data Encyclopedia (NODE), accession number OEP001295,\u00a0The studies involving human participants were reviewed and approved by The Institutional Review Board of GDPH. The patients/participants provided their written informed consent to participate in this study.Conceptualization: NL and WX. Data curation: WX, GZ, and BC. Formal analysis: WX, GZ, and BC. Funding acquisition: NL. Investigation: all authors. Methodology: WX, GZ, BC, ML, HL, JLiu, and HH-Z. Project administration: NL and WK. Resources: WX, GZ, and BC. Software: WX and ML. Supervision: NL and WX. EAR validation: WX, GZ, ML, and BC. Visualization: WX, GZ, ML, and BC. Roles/writing\u2014original draft: WX, GZ, and BC. Writing\u2014review and editing: all authors. All authors contributed to the article and approved the submitted version.This work was supported by funds from the National Natural Science Foundation of China (grant number: 82003066), Guangdong Provincial People\u2019s Hospital Science and Technology Special Fund (Ph.D. Startup Project), and Guangdong Medical Science and Technology Research Fund (grant number: A2021080).ML, HL, JLiu, HH-Z, and AL are employees of Burning Rock Biotech.The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "By scoring BATF3 expression (BATF3-score) we observed constitutively high BATF3-scores in cHL and ALCL and low to moderate BATF3-scores in all other entities examined. Western blot analysis confirmed BATF3 protein expression in cell lysates from cHL cell lines (n = 7). Thus, BATF3 can be considered a useful IHC marker for the diagnosis of cHL as it is highly sensitive and sufficiently specific when analyzed by BATF3-scoring.It is well recognized that the AP-1 transcription factor BATF3 is constitutively expressed in Hodgkin/Reed-Sternberg (HRS) cells, but its potential as a diagnostic marker for classical Hodgkin lymphoma (cHL) has not yet been addressed. In this study, we performed immunohistochemistry and analyzed the BATF3 expression in lymphoma cells on 218 lymphoma samples belonging to 14 different lymphoma entities. We observed varying degrees of BATF3 expression in nearly half of the cases ( Classical Hodgkin lymphoma (cHL) is one of the most common lymphomas . The corThere is no specific immunohistochemical (IHC) marker for cHL. The immunophenotype of HRS cells is characterized by a substantial loss of B-cell associated antigens ,5,6,7,8 Published studies indicate that BATF3 expression is a distinctive feature of HRS cells ,22,23,24Since BATF3 is constitutively expressed in HRS cells, we hypothesized that BATF3 could be an ancillary IHC marker for the diagnosis of cHL. To test this, we performed BATF3 immunohistochemistry and compared the BATF3 expression in cHL to that in NLPHL and NHL.Specimens were drawn from our archive of formalin fixed paraffin embedded (FFPE) tissue. Hematoxylin-eosin stained sections and available immunohistochemical and molecular material were checked and, if necessary, completed by newly performed staining. A total of 218 samples were selected. FFPE material was pseudonymized to comply with the German law for correct usage of archival tissue for clinical research . The samBATF3 staining was performed on 2-3 \u00b5m thick sections of FFPE tissue on DAKO Autostainer PLUS . Antigen retrieval was performed by microwave heating in citrate buffer, pH6, for 20 min. After peroxidase blocking, sections were incubated for 1 hour with a polyclonal sheep anti-BATF3 antibody (AB) at a dilution of 1:200. Polink-2 HRP Plus Sheep IgG DAB Detection System was used for signal amplification. BATF3 expression was scored in analogy to the H-score method (BATF3-score) by multiplying the percentage of stained tumor cells by the staining intensity . The ran\u00ae PREMIUM Chemiluminescent substrate using the C-DiGit\u00ae Blot Scanner (LI-COR) and Image StudioTM Lite Version 5.2 software (LI-COR).Proteins were separated by 10% SDS-PAGE and transferred to a 0.2 mm nitrocellulose membrane . Western blotting was performed using sheep anti-BATF3 AB (R&D Systems) and mouse anti-\u03b2-actin AB at a dilution of 1:1000. Signal development was performed using HRP\u2013conjugated secondary AB at a dilution of 1:10.000: anti-sheep HRP (Sigma-Aldrich) and anti-mouse HRP (Sigma-Aldrich). Protein bands were visualized by WesternSureMicrosoft Excel Version 16.16.27 and GraphPad Prism Version 9.1.0. were used for statistical analyses and constructing figures. n = 100/218) lymphoma samples distributed across 11 of the 14 (n = 11/14) entities examined. Strong BATF3 expression was a constitutive feature in cHL (n = 53/53) and in ALCL (n = 3/3). Varying degrees of BATF3 expression were observed in primary mediastinal large B-cell lymphoma (PMBL) (n = 14/15), diffuse large B-cell lymphoma (DLBCL) (n = 7/22), T-cell/histiocyte-rich large B-cell lymphoma (THRLBL) (n = 3/3), follicular lymphoma (FL) (n = 5/22), chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL) (n =1/15), plasma cell neoplasm (PCN) (n = 1/15), peripheral T-cell lymphoma (PTCL) (n = 6/12), intestinal T-cell lymphoma (ITCL) (n = 2/2) and NLPHL (n = 7/16) (We observed BATF3-expressing tumor cells in 100 of the 218 ( = 7/16) . BATF3-scoring was used to evaluate the BATF3 expression semi-quantitatively and to highlight the differences in the BATF3 expression between the individual lymphoma entities. BATF3-scores were constitutively high in cHL and ALCL and constitutively low in CLL, FL, MCL, MZL, PCN and BL. An apparent threshold of 205 separated cHL and ALCL from the other lymphoma entities. DLBCL, PMBL, THRLBL, PTCL, ITCL and NLPHL showed low to moderate BATF3-scores . Western blot analysis confirmed BATF3 protein expression in cHL. Anti-BATF3 AB labeled the 17-kDa BATF3 protein in cell lysates from cHL and T-LBL/ALL (Jurkat), while cell lysates from BL (Ramos) were not reactive . n = 53/53). This study addresses the usefulness of BATF3 as an ancillary IHC marker for the diagnosis of cHL. We performed immunohistochemistry and analyzed the BATF3 protein expression in lymphoma cells on 218 lymphoma samples belonging to 14 different lymphoma entities. BATF3 expression was a constitutive feature of cHL and observed in all samples investigated (n = 8/8)) or in the majority and Vrzalikova et al. (n = 36/52)) of the analyzed cHL samples [n = 7/7). The cHL cell lines examined showed variable amounts of BATF3 protein showed increased BATF3 expression. Even so, by evaluating the BATF3 expression in analogy to the H-score method , we wereWe consider BATF3 to be a useful IHC marker for the diagnosis of cHL. BATF3 expression is a constitutive feature of cHL and can be reliably demonstrated by IHC staining. BATF3-positivity can confirm the diagnosis of cHL in cases where HRS cells display an atypical immunophenotype or the specimen's properties limit the use of other IHC markers. Moreover BATF3-scoring can help to differentiate cHL from DLBCL, PMBL, THRLBL, PTCL and NLPHL."} +{"text": "Conclusions: Given the fact that considering themselves informed regarding vaccination is the most important factor in order to be immunized against SARS-CoV-2, effective information campaigns would substantially increase willingness.Background: During the COVID-19 pandemic, patients with immune diseases are a vulnerable population. We aimed to evaluate their access to medical care, as well as their awareness and willingness to obtain the vaccine after a year of the SARS-CoV-2 pandemic. Methods: A cross-sectional, multicenter study was conducted on a questionnaire basis, handled both online as well as in person. Results: 651 patients with autoimmune or immune mediated diseases were enrolled. More than half (339/641 [53%]) reported difficulties in obtaining medical care throughout the pandemic and 135/651 ([21%]) of them were confirmed with COVID-19; 442/651, ([68%]) expressed their willingness to be vaccinated against SARS-CoV-2. The factors associated with an increased probability of vaccination were the male gender (OR = 2.01, CI95% 1.2\u20133.7, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in December 2019 in China\u2019s Hubei Province and soon spread around the world, causing a pandemic with significant impact on the medical system.Until now, with 4.5 million deaths, COVID-19 ranks eighth in history\u2019s most deadly pandemics ) were non-health care professionals, while the rest were also either health care workers (doctors 43/651 [6%] or nurses 29/651 [5%]) or had connection with the medical system (68/651 [10%]).Common pathologies identified were autoimmune thyroid disease (140 [22%]), rheumatoid arthritis (104 [16%]), systemic lupus erythematosus (SLE) (99 [15%]) Sj\u00f6gren\u2019s syndrome (80 [12%]), ankylosing spondylitis (69 [11%]), psoriatic arthritis (55 [8%]), inflammatory bowel disease (IBD) (44 [7%]), systemic sclerosis (SSc)/limited scleroderma (31 [5%]), myasthenia Gravis (30 [5%]), antiphospholipid syndrome (AFLS) (26 [4%]), multiple sclerosis (25 [4%]), hepatic autoimmunity (21 [3%]), systemic vasculitis (20 [3%]), celiac disease (20 [3%]), dermatomyositis/polymyositis (12 [2%]), as well as other immune mediated disorders listed in Except for a minority of the patients (29/651 [4%]) who associated three or more autoimmunities, the rest reported one (513/651 [79%]) or two (109/651 [17%]) immune diseases.In addition to conventional synthetic DMARDs (disease-modifying anti-rheumatic drugs), such as hydroxychloroquine (HCQ) (137 [21%]), methotrexate (72 [11%]), sulfasalazine (50 [8%]) and leflunomide (21 [3%]), the patients were also taking glucocorticoids (144 [22%]), biologic DMARDs (133 [21%]) as well as other immunosuppressive drugs such as azathioprine (46 [7%]), mycophenolate mofetil (18 [3%]) and cyclophosphamide (2 [0.3%]).More than half of the responders (442/637 [69%]) had a diagnosis of autoimmune/immune- mediated disease for more than five years, while 4% (27/637) of them were diagnosed in the past year a. When asked to mention \u201cthe last date of their disease aggravation (flare)\u201d, only 75% (481/651) of them were able to answer the question. More than half of the patients (280/481 [58%]) reported having a flare since the beginning of 2020, and 9% (26/280) of them reported the flare after COVID-19 disease. bAs presented in A.Access to medical care during the pandemicMore than half of the responders (339/641 [53%]) reported difficulties in obtaining medical care throughout the pandemic, mostly because their regular hospital became a COVID-19 support facility (126/339 [37%]), were afraid of contracting the virus (120/339 [35%]), or considered the appointments difficult to obtain (41/339 [12%]).The rest of the patients [47%], stated that they either did not require medical care (123/641 [19%]) or were successfully assessed by their attending physician at its private practice and using telemedicine (141/641 [22%]), while 6% (41/641) of them were addressed to primary care physicians for treatment continuance and monitoring.In addition, only a small part of the subjects responded that their hospital continued its regular activity (80/641 [12%]), while (24/641 [4%]) of them were forced to change their doctor.B.SARS-CoV-2 infection in subjects with autoimmune and immune-mediated diseasesAlthough only 26% (167/651) of the responders had symptoms resembling COVID-19, half (331/651 [51%]) of them were tested at least once of their own free will. Four percent (23/651 [4%]) avoided testing despite having symptoms as they were afraid of mandatory hospital admission.A total of 135 subjects (135/651 [21%]), 114 females and 21 males, median age 47 , were confirmed with the infection using RT-PCR (96/135), rapid antigen test (27/135) or both (12/135).Almost a quarter (33/135 [24%]) of the positive patients denied having contact with infected individuals.Autoimmune thyroiditis (24 [13%]), SLE (22 [12%]), rheumatoid arthritis (16 [9%]), Sjogren syndrome (16 [9%]), psoriasis (14 [8%]), IBD (14 [8%]), spondylo arthritis (13 [7%]), SSc/limited scleroderma (8 [4%]), myasthenia gravis (7 [4%]) and AFLS (6 [3%]) were the most frequent autoimmune disease entities from this group. .Twenty-eight percent of the patients (38/135 [28%]) were not receiving treatment for their autoimmune disease, and they did not require treatment during the SARS-CoV-2 infection, either.The rest were receiving corticosteroids (26 [19%]), conventional synthetic DMARDs, such as HCQ (29 [21%]), methotrexate (13 [10%]), leflunomide (9 [6%]), sulfasalazine (8 [6%]), as well as azathioprine (12 [9%]), mycophenolate mofetil (5 [4%]) and biologic DMARDs (31 [23%]).Most of the patients enrolled had mild COVID-19 and the top symptoms reported were anosmia (79/135), dry cough (76/135), general weakness (74/135), ageusia (65/135), fever (60/135), headache (56/135), myalgia (55/135), chills (50/135), sore throat (40/135), diarrhea (31/135), nausea/vomiting (34/135), dyspnea only at exertion (25/135) or at rest (19/135), rhinorrhea (18/135), fatigue (17/135), productive cough (14/135), arthralgia (5/135), sweating (3/135), loss of appetite (2/135) as well as memory disorders (1/135) and dizziness (1/135).Only 19% (26/135) of the patients were admitted to the hospital. During their stay in the hospital 11/26 received oxigenotherapy, of whom four were managed in the intensive care unit, while 6/26 considered that hospitalisation was not required at all. The rest were monitored by their treating physician or general practitioner as outpatients (62/135 [46%]), or handled COVID-19 on their own (47/135 [35%]).When asked about the pulmonary involvement secondary to SARS-CoV-2 infection, only 26 patients from 127 responders acknowledged having a documented viral pneumonia, most of them mild (17/26) or moderate (6/26).Frequently, they were prescribed antibiotics (50/135), anticoagulants (38/135), symptomatic treatment (38/135) or vitamins (35/135), while tocilizumab (3/135), anakinra (3/135), remdesivir (8/135), lopinavir/ritonavir (7/135), favipiravir (5/135), umifenovir (1/135) and convalescent plasma (1/135) were administered in a smaller number of subjects. Corticosteroids and HCQ were prescribed exclusively for COVID-19 in 22 and 7 patients, respectively.Regular background treatment was administered without changes in 64% (62/97) of the patients, adjusted in 10% (10/97) and discontinued in 26% (25/97) of them.C.Perspective, basic knowledge and willingness to be immunized against SARS-CoV-2Eighty five percent of the participants (546/640) considered themselves informed regarding the national program of immunization.The most common sources of information were the media (71%), treating physician (34%), general practitioner (23%) and patient associations (10%). Information obtained from a friend/colleague/work environment (6%), medical literature (3%), family (2%), vaccination platform (2%) or another patient (1%) were less mentioned.p < 0.001) and were more likely to decide to be vaccinated compared with those enrolled during face-to-face evaluations.Most of the responders expressed their willingness to be vaccinated against SARS-CoV-2. A total of 250 (60.7%) patients received the first dose of the COVID-19 vaccine before enrolment. The patients enrolled online had an increased willingness of vaccination , lack of confidence in the promoted effect (21/203), doctor\u2019s contraindication (18/203) as well as the history of COVID-19 (18/203), lack of contact with infected subjects (15/203) or insufficient studies involving patients with immune pathologies (3/203). Only a few of them (21/645) were undecided as to whether to be vaccinated or not.p = 0.015), while subjects who completed the survey during face-to-face evaluations were less inclined to be vaccinated . Although there was a significant difference regarding gender between the patients who completed the questionnaire online or face-to-face\u2014males completed the survey mostly during hospital evaluations , there were no differences regarding age (p = 0.09), or Charlson index (p = 0.066).Males were more inclined to be vaccinated , the patient\u2019s opinion that she/he was well informed , physician\u2019s advice , and flu vaccination in the past , while those associated with a decreased probability of vaccination were completing the survey during face-to-face evaluations , having COVID-19 disease in their past medical history , or the opinion that patients with autoimmune diseases are at increased risk for adverse reactions .In logistic regression, the factors associated with an increased probability of vaccination were the male gender of the responders considered themselves informed and the most mentioned source of information was the media (284/635), followed by medical articles (121/635), their treating physician (83/635) and general practitioner (52/635). The rest of the patients, either did not associate the vaccine with potential side effects (39/635) or were not interested in being informed (32/635) or denied access to information sources (40/635).When asked if they considered themselves to be at greater risk of developing post immunization adverse reactions due to their immunological pattern, 51% (320/631) of them gave a positive response, while the rest either denied (144/631 [23%]) having additional risk compared to the general population or were unable to evaluate their risk (167/631 [26%]).However, more than half (184/320 [58%]) of those who considered that the vaccine might have an impact on their disease activity, were willing to take the risk.More than half of the responders (450/635 [71%]) approached their treating physician for vaccine-related medical advice, while the rest did not consider it necessary to discuss this topic (116/635 [18%]) or could not reach their doctor (69/635 [11%]). Of those seeking medical guidance, it was recommended to 63% (282/450) to receive the vaccination and only 6% (26/450) were advised to avoid immunization due to their autoimmune status.Regarding influenza vaccination of the 624 responders, 59% (366/624) had never been vaccinated, 15% (93/624) had the vaccine annually, 14% (84/624) usually were vaccinated but not every year, while 5% of them (31/624) were vaccinated frequently. In addition, 42 patients decided to do it this year, regardless of their previous hesitancy.In an attempt to limit COVID-19 transmission, face-to-face evaluations for chronic patients were reserved for severe cases only. The rest were assessed by telemedicine, a satisfactory option on both sides at least in patients with mild forms of the disease ,9,10.Since the first months of the pandemic, Romanian health policy imposed the conversion of various hospitals exclusively into COVID-19 facilities, destined only for the care of SARS-CoV-2 infected patients, including asymptomatic ones, explaining the difficult access to medical care among the responders. In addition, this decision led treating physicians to feel that \u201cchronic rheumatic patients were left aside, while caring mostly for COVID-19 patients\u201d .In addition to limited access to health care, the use of anti-malarials worldwide as primary prophylaxis and initially as treatment for SARS-CoV-2 infection caused shortages of hydroxychloroquine provoking distress especially among patients with SLE, in whom treatment efficacy has been already established in studies . Regardlp = 0.0001), the risk of death is similar ) and a Charlson Comorbidity Index lower or equal to 2 (102/135 [76%]). In addition, pre-existing pulmonary damage did not predispose to a severe form of COVID-19.The national vaccination program was launched in Romania on 27 December 2020, using the BNT162b2 mRNA Covid-19 Vaccine . The immunization campaign was planned in three consecutive rounds\u2014vaccine was first available for health care workers, followed by chronic disease patients and individuals aged over 65 in the second round and the general population in the third round. Vaccination centers were set up within medical units and public institutions in local communities. mRNA-1273 vaccine was available since 4 February, AZD1222/ChAdOx1 since 15 February and JNJ-78436735 since 4 May 2021. Patients with autoimmune diseases were eligible for vaccination in the second round of the vaccination campaign, which overlapped with the third wave of COVID-19 in Romania and with social restrictions and lockdown measures in place [The VAXICOV study, a worldwide online questionnaire, conducted in 56 countries, mostly France, United Kingdom, Chile, United States of America, Venezuela, Spain, Mexico and Argentina, which collected data from 265 healthcare professionals and 1266 patients with autoimmune and rheumatic diseases, showed that patients with autoimmune diseases were more afraid of being infected compared to healthcare professionals, but their willingness to get vaccinated against SARS-CoV-2 remained moderate . HoweverGiven the fact that one of the most important causes of vaccine hesitancy in patients with autoimmune diseases is their concern towards adverse reactions and the increase in their autoimmune disease activity , we advoAs such, besides consulting with their treating physician, which increased vaccination willingness up to 20% , anotherHowever, on the verge of the fourth wave, achieving the target level of herd immunity via vaccination remains unlikely in Romania, as until 11 September 2021 only 27% of the general population was fully vaccinated against COVID-19 .Given the fact that the survey was designed for patients with rare disorders, a strength of the study is the large sample size we were able to gather.Also it is the first study to highlight features regarding SARS-CoV-2 infection in this category of patients. The number of COVID-19 patients enrolled is similar to what Romania reported in the EULAR\u2014COVID-19 and SECUThe patients recruited during face-to-face evaluations were less willing to be vaccinated, even after adjusting for gender, which was different between the sources of recruitment (a significantly higher proportion of women recruited online), which means that there were also other differences between these groups of patients .The main weakness of this study is the fact that it was a convenience sample, and probably not very representative for all of this group. Excepting the patients recruited in the clinics, the other patients were patients with internet access, and/or members of patient\u2019s associations, and therefore patients with a certain level of education.Another limitation of our study might be the selection bias given the fact that most of the responders enrolled were already considering vaccination. Therefore, our findings might not apply to the entire population of patients with autoimmune /immune-mediated diseases.A substantial limitation of the study concerns SARS-CoV-2 infection. Even if based on our results it might appear appropriate to assume that their course of the disease was a mild one, only the patients who survived could have completed the questionnaire, therefore we cannot conclude concerning the survival. We did not have access to population registries in order to accurately evaluate the death rate among COVID-19 patients with autoimmune diseases/immune-mediated diseases. In addition, studies published in Romania until now listed among the most common comorbidities associated with COVID-19 deaths diabetes, chronic renal disease, hypertension and obesity ,29, but Even though access to health care was obstructed during the pandemic, most of the patients with autoimmune /immune-mediated pathologies managed to find a suitable way to monitor their disease. Also, it appears that while contracting the virus their course of the disease was mostly a mild one. Factors that contributed to their decision to obtain the COVID vaccine were considering themselves informed regarding vaccination, doctor\u2019s advice, and the habit of getting the flu shot. We advocate that effective information campaigns would substantially increase their willingness to be immunized against SARS-CoV-2."} +{"text": "A review of literature revealed no analgesia or opioid sparing treatment guidelines for > 10% TBSA pediatric burns. Clinicians may benefit from an analgesia support guidance tool for the management of critically ill PICU and non-PICU inpatient pediatric burn patients with > 10% TBSA.A multi-disciplinary team of experts created a pediatric analgesia support guidance tool for clinicians managing non-procedural pain in critically ill pediatric burn patients in the PICU and non-PICU inpatient setting. Agent selection was at the discretion of the clinician based on FLACC scoring. We performed a retrospective chart review, Jan 2019 to Jun 2021, of pediatric patients age 1 month to 14 years of age admitted to the Pediatric Burn Trauma service with > 10%TBSA. Analgesia was categorized as Yes/No for acetaminophen, ibuprofen, opioids , gabapentin, alpha 2-agonists .16 pediatric burn patients age 2 months to 14 years. 75% male, 4 (25%) PICU, 3 (19%) mechanically ventilated. Average LOS 7.19 days, range 1 to 25 days. 9 (56%) received standing acetaminophen, 1(6%) ibuprofen, 12 (75%) opioids, 4 (25%) gabapentin, 3 (19%) alpha-2 agonists.Y, years; M, months; TBSA Total Body Surface Area; MOI mechanism of injury; LOS length of stay; vent ventilator; PICU pediatric intensive care unit;We found 75% of our pediatric patients received opioids, and only 56% received standing acetaminophen. 7 patients (43.8%) received either gabapentin and/or alpha-2 agonists. Our pediatric analgesia support guidance tool influenced clinician pain management practice for the pediatric burn patient. With continued use, we will determine if this multimodal approach can reduce an over reliance on opioid analgesia regimens."} +{"text": "ABSTRACT IMPACT: The potential to use vaginal pH as a low cost, non-invasive diagnostic test at the point of CIN2 diagnosis to predict worsening of cervical disease. OBJECTIVES/GOALS: We previously reported that persistence/progression of cervical intraepithelial neoplasia-2 (CIN2) was uncommon in women living with HIV (WLH) from the Women\u2019s Interagency HIV Study . Here we examined additional factors that may influence CIN2 natural history. METHODS/STUDY POPULATION: A total of 337 samples from 94 WLH with a confirmed CIN2 diagnosis were obtained from the MWCCS. 42 cervicovaginal HPV types and 34 cervicovaginal cytokines/chemokines were measured at CIN2 diagnosis (94 samples) and 6-12 months prior to CIN2 diagnosis (79 samples). Covariates, including CD4 count and vaginal pH, were abstracted from core MWCCS visits. Logistic regression models were used to explore CIN2 regression vs. persistence/progression . Log rank tests, Kaplan Meier method, and Cox regression modeling were used to determine CIN2 regression rates. RESULTS/ANTICIPATED RESULTS: The most prevalent HPV types were HPV54 (21.6%) and 53 (21.3%). 33 women (35.1%) had a subsequent CIN2/CIN3 diagnosis (median 12.5 years follow-up). Each additional hr-HPV type detected at the pre-CIN2 visit associated with increased odds of CIN2 persistence/progression . Higher vaginal pH and bacterial vaginosis at the CIN2 diagnosis visit associated with higher odds of CIN2 persistence/progression. Vaginal pH >4.5 at CIN2 diagnosis also associated with unadjusted time to CIN2 persistence/progression (log rank p=0.002) and a higher rate of CIN2 persistence/progression . Cervicovaginal cytokine/chemokine levels were not associated with CIN2 persistence/progression. DISCUSSION/SIGNIFICANCE OF FINDINGS: We found relatively low prevalence of HPV16/18 in this cohort. Elevated vaginal pH at the time of CIN2 diagnosis may be a useful indicator of CIN2 persistence/progression and the rate of persistence/progression."} +{"text": "Worldwide SARS-CoV-2 infections increase every day. Despite the infection is less severe in children, it can be severe and associated with complications. However, local data remain scarce. We sought to describe epidemiological and clinical characteristics of COVID-19 infection in this population across different age groups. Observational, multicenter study across 23 Colombian hospitals from 22 different territories. We included all patients from 0 months to 17 years with confirmed SARS-CoV-2 infection by either antigen or RT-PCR testing. From March 1, 2020, to October 31, 2021, we identified 1,186 patients: neonates (88), 1 to 3 months (130), 4 to 23 months (306), 2 to 4 years (169), 5 to 11 years (229) and 12 to 18 years (226) with confirmed COVID-19 infection. Of those,77(6.2%) were asymptomatic, 631(53.2%) hospitalized, 132(11.2%) required PICU. 58 cases met WHO definition of MIS-C. Patients less than 24 months of age were characterized by fever (74%) and more respiratory distress (30.1%) compared to other groups. Patients >5yo seemed to have a more severe presentation. They had more gastrointestinal (GI) symptoms (31% vs 37.8%), had more need for ICU care given presentation with shock increased with age . Lab markers including thrombocytopenia and Lymphopenia were more common on this age group. Antibiotic treatment was common (%%) especially in neonates (40.9%), despite bacterial coinfection was rare (8.7%), length of hospitalization was longer in older than 2-year-old groups. 23(1.9%) patients died, similar across different age groups. Heat map by age groupCOVID-19 infection in Colombian children presented differently across different age groups. Children older than 5 years had a more severe clinical course and prolonged hospital stays. Clinical findings according to age groups could help clinicians in characterizing and identifying COVID 19 infections in Children.Ivan Felipe Guti\u00e9rrez Tobar, n/a, Pfizer and MSD Pfizer and MSD Juan P. Rojas -Hernandez, Candidate for doctorate in Public Health, Pfizer Eduardo L\u00f3pez Medina, n/a, Pfizer"} +{"text": "Refractory or resistant (R/R) cytomegalovirus (CMV) infection after hematopoietic cell transplant (HCT) and solid organ transplant (SOT) cause serious, potentially fatal complications; therapeutic options are limited. In a Phase 3 study (NCT02931539), maribavir (MBV) was superior to investigator-assigned therapy for CMV clearance (Wk 8) and clearance plus symptom control (Wk 8 through Wk 16) in HCT/SOT recipients with R/R CMV infections. Here we present further study results on efficacy and safety of MBV in the rescue arm.Patients (pts) were stratified and randomized 2:1 to MBV (400 mg/bid) or IAT for 8-wk treatment then 12-wk follow-up. After minimum 3 wks\u2019 treatment, pts in the IAT group meeting criteria (worsening/lack of improvement of CMV infection or failure to achieve viremia clearance plus IAT intolerance) could enter a MBV rescue arm . In the rescue arm, efficacy was evaluated by confirmed CMV viremia clearance (plasma CMV DNA < 137 IU/mL in 2 consecutive tests \u2265 5 days apart) at end of Wk 8 and confirmed clearance with symptom control at Wk 8 through Wk 16. Safety was assessed.Table 1). At Wk 8 of rescue therapy, 11 (50.0%) pts achieved confirmed CMV viremia clearance; 6 (27.3%) pts had CMV clearance with symptom control at Wk 8 maintained through Wk 16 (Table 2). All 22 pts reported treatment-emergent adverse events ; most common TEAEs of special interest were nausea, vomiting, and diarrhea (54.5%), and taste disturbance (50.0%). Neutropenia and acute kidney injury TEAEs were reported by 0 and 3 pts in the rescue arm, respectively.A total of 352 pts were randomized . Confirmed CMV viremia clearance at Wk 8 was achieved in 131 (55.7%) and 28 (23.9%) pts, respectively, in the randomized set. Having met criteria, 22 (18.8%) pts entered the MBV rescue arm; at entry, 6 (27.3%) pts had developed neutropenia and 9 (40.9%) had increased serum creatinine (Table 1. Summary of patients from IAT-randomized group meeting criteria for entry into MBV rescue arm*Table 2. Patients achieving confirmed CMV viremia clearance at end of Wk 8 (end of treatment) or achieving confirmed CMV viremia clearance and symptom control at end of Wk 8 maintained through Wk 16Table 3. Treatment-emergent adverse events during the on-rescue observation periodRescue arm data show MBV was efficacious for R/R CMV infection in HCT/SOT recipients inadequately responding to IAT with/without intolerance and had a similar safety profile to that reported for pts in the randomized MBV group.Marcus Pereira, MD, Hologic (Scientific Research Study Investigator)Merck (Scientific Research Study Investigator)Takeda Carlos Cervera, MD, PhD, Avir Pharma Lilly Merck Sunovion Takeda Veritas Pharma Camille Kotton, MD, Shire/Takeda (Advisor or Review Panel member) Camille Kotton, MD, UpToDate Involved: Self): I write chapters on zoonoses for UpToDate., Independent Contractor Joseph Sasadeusz, MBBS, PhD, Abbvie Gilead Merck Takeda (Grant/Research Support) Jingyang Wu, MS, Shire Human Genetic Therapies, Inc., a Takeda company Martha Fournier, MD, Shire Human Genetic Therapies, Inc., a Takeda company Shire ViroPharma, a Takeda company"} +{"text": "Best Practice Caregiving (BPC) is a free online database providing comprehensive information on research and implementation characteristics for 44 evidence-based dementia caregiving programs. Programs eligible for BPC have research-tested positive outcomes for family/friend caregivers and demonstrated feasibility in community implementations. This symposium presents results from analyses of the BPC database that includes surveys of 44 program developers and 324 healthcare or community delivery-organizations, and content analysis of 231 published studies. Findings show the most common of 19 types of assistance provided by programs were: Supporting Caregiver/Individual-with-Dementia (IWD) Communication, Encouraging Positive Caregiver-IWD Activities, and Strengthening Coping (93.2%). Least common were: Getting a Dementia Diagnosis (29.5%) and Monitoring Service Benefits (20.5%). Methods of delivering the types of assistance were: information/referral (M=11.1), skills training (M=7.5), and direct provision of care (M=3.8). The most common types of organizations that delivered programs were healthcare organizations (23.8%) and Area Agencies on Aging (23.8%). The greatest delivery-challenges were program marketing (69.8%) and caregiver engagement (66.3%). Most organizations \u2018strongly agreed\u2019 that programs had positive impacts on caregivers (59.5%) but were less certain about IWD benefits (25.1% \u2018strongly agreed\u2019). Published research studies found the most improved caregiver outcomes were: 1) Strain and/or burden (84.1%), 2) Depressive symptomology (79.5%), and 3) Caregiving efficacy (63.6%). Least common improved outcomes were 1) Access to support information/Community service use (9.1%); 2) Unmet needs (6.8%); and 3) Respite/break from care (2.3%). Overall, results highlight strengths of evidence-based dementia caregiving programs, along with gaps and challenges to be addressed by existing and new developing programs."} +{"text": "Correction to: BMC Microbiol 19, 236 (2019)https://doi.org/10.1186/s12866-019-1616-2Following the publication of the original article , we wereThe corrected Additional files can be found below:Additional file 1: Supplementary Table 1. Significant genera from PERMANOVA analysisAdditional file 2: Supplementary Table 2. Genera correlated with aging with Spearman correlationAdditional file 3: Supplementary Table 3. Critical genera revealed by SPDAdditional file 4: Supplementary Figure 1. The relative abundance of all the 35 critical genera across different age groups."} +{"text": "Correction to: BMC Pediatr 22, 12 (2022)https://doi.org/10.1186/s12887-021-03047-7The legends of figures 4 and 5 should be:Following the publication of the original article , the aut2.Additional file Additional file 2: Supplemental figure 1. Number of packages and NIHDI expenditure per 1000 inhabitants by month (2019). Supplemental figure 2. Number of packages (A) NIHDI expenditure (B) by region per 1000 inhabitants per year (2010-2019). Supplemental figure 3. Number of packages (A) and NIHDI expenditure (B) by rurality category per 1000 inhabitants per year (2010-2019)."} +{"text": "Knockdown of PMCA4 in human umbilical vein endothelial cells (HUVECs) leads to an increase in tubule formation and upregulation of regulator of Calcineurin 1 (RCAN1.4) signaling, a downstream effector of the calcineurin/nuclear factor of T-cells (NFAT) pathway i i which ha [Ca2+]i . Recentl [Ca2+]i . HoweverATP2B1 (si-PMCA1), ATP2B4 (si-PMCA4), or non-targeting (si-NT) scrambled control (Dharmacon) in HUVECs (TCS Cellworks) was achieved using published methods and The 10.13039/501100000770University of Manchester.This work was supported by the None."} +{"text": "Comparative data on bloodstream infections (BSI) in hospitalized patients with and without SARS-CoV2 positive test is lacking.A retrospective observational study comparing (BSI) with and without COVID-19 infection was performed was performed from Jan1- May 1, 2020. Patient demographics, clinical microbiological characteristics of infections, therapeutic interventions and outcomes was compared between the two groups. Enterococcus spp (28%), Candida spp(12%), MRSA (10%) and E.coli (10%) were predominant microbes in P compared to Streptococcus grp (16%), MSSA (14%), MRSA (13%) and E.coli (12%) in N (figure 1). Mortality from BSI was associated with COVID-19 infection , DM , Charlson comorbidity index >3 , and mechanical ventilation on multivariate analysis. Of 155 patients with BSI, 104 were SARS-CoV2 PCR negative (N) while 51 were positive (Table 1). Majority of SARS-CoV2 positives (P) had ARDS (58.8%), required mechanical ventilation (73%), inotropic support (55%), therapeutic anticoagulation (28%), proning (35%), Rectal tube (43%), Tocilizumab (18%), and steroids (43%) (Table 2). BSI was higher in N with HIV (16.3% vs 3.9% p=0.027). Duration of antibiotic therapy (DOT) prior to BSI was significantly longer in P (table 2). In-hospital mortality was significantly higher among P with BSI (49% vs. 21% p < 0.0001). 185 BSI events were observed during the study period with 117 in N patients and 68 in P. Primary BSI was predominant (76%) in N while secondary BSI (65%) was common in P of which 50% were CLABSI. Median time from admission to positive culture was 0.86 days in N compared to 12.4 in P (p = 0.001). Majority of BSI in P were monomicrobial (88%) and hospital acquired (71%) when compared to N (p< 0.001). Comparison of Microorganisms isolated in the BSIX-axis represents the number of BSI events whereas the number at the end of each bar represents the percentagenterococcus was observed in adult P compared to N. These patients were critically ill, developed BSI in the second week of hospitalization, had longer DOT prior to positive cultures and worse outcomes. Breakdown of infection control measures and inappropriate antimicrobial use during the surge could be contributory. Increased events of hospital acquired, secondary BSI (CLABSI) due to EAll Authors: No reported disclosures"} +{"text": "Prior population-based elder mistreatment (EM) risk factor research has focused on problem prevalence using cross-sectional designs, which cannot make causal inferences between proposed risk factors and EM or discern existing cases from new cases entering the population. This study sought to estimate the incidence of EM and identify risk factors for new cases. It is a ten-year prospective, population-based cohort study with data collected between 2009 (Wave 1) and 2019 (Wave 2). Based on Wave 1 random, stratified sampling to recruit English/Spanish-speaking, cognitively intact, community-dwelling older adults (age \u2265 60) across New York State, this study conducted computer assisted telephone interviews (CATI) with 628 respondents participating in both Wave 1 and Wave 2 interviews (response rate=60.7%). Ten-year EM incidence was regressed on factors related to physical vulnerability, living arrangement, and socio-cultural characteristics using logistic regression. Ten-year incidence rates included overall EM (11.4%), financial abuse (8.5%), emotional abuse (4.1%), physical abuse (2.3%), and neglect (1.0%). Poor self-rated health at Wave 1 significantly predicted increased risk of new Wave 2 overall EM (odds ratio [OR]=2.8), emotional abuse (OR=3.67), physical abuse (OR=4.21), and financial abuse (OR=2.8). Black older adults were at significantly heightened risk of overall EM (OR=2.61), specifically financial abuse (OR=2.8). Change from co-residence (Wave 1) toward living alone (Wave 2) significantly predicted financial abuse (OR=2.74). Healthcare visits represent important opportunities to detect at-risk older adults. Race is highlighted as an important social determinant for EM requiring urgent attention. This study represents the first longitudinal, population-based EM incidence study."} +{"text": "Rickettsiosis, a re-emerging disease, is characterized with a myriad clinical symptoms and various manifestations. Ocular involvement is often misdiagnosed since it\u2019s rarely symptomatic. It especially involves the posterior segment. We aimed to study the clinical, laboratory and therapeutic features of ocular involvement associated with rickettsial infection.Rickettsia in skin biopsy.We encountered a retrospective study including all patients hospitalized for rickettsial infection with ocular involvement in the infectious disease department between 2007 and 2020. The diagnosis was confirmed based on serology (seroconversion) and/or positive polymerase chain reaction for A total of 24 patients were included with a mean age of 40\u00b112 years. There were 13 women (54.2%). Sixteen patients sought medical care during the warm months, from June to October (66.6%). The revealing clinical signs were febrile maculopapular skin rash (79.2%), cephalalgia (54.2%) and arthralgia (33.3%). Five patients had visual loss (20.8%). Physical examination revealed conjunctival hyperemia (37.5%) and pathognomonic eschar (29.1%). Laboratory investigations revealed elevated liver enzymes (79.1%), thrombocytopenia (75%) and cholestasis (58.3%). Ocular involvement was unilateral in 14 cases (58.3%). Retinitis was the most common manifestation (70.8%), followed by anterior uveitis (20.8%). Retinal fluorescein angiography, performed in ten cases (41.6%), confirmed retinitis in 8 cases (80%). Both retinal vasculitis and papillary hyperfluorescence were noted in two cases (20%). Patients received doxycycline in 21 cases (87.5%) and fluoroquinolones in three cases (12.5%). The median duration of treatment was 7[6-15] days. The disease evolution was favourable in all cases (100%). No ocular sequelae were noted. Complications were noted in two cases (8.2%) represented by thrombophlebitis (one case) and recurrent seizures (one case). Systematic fundus examination should be performed in front of suspected rickettsiosis, even in the absence of ocular symptoms and signs. It provides clinical clues to promptly diagnose and treat rickettsiosis.All Authors: No reported disclosures"} +{"text": "In vitro determination of severe acute respiratory syndrome coronavirus 2 neutralizing antibodies induced in serum samples from recipients of the CoronaVac vaccine showed a short protection period against the original virus strain and limited protection against variants of concern. These data provide support for vaccine boosters, especially variants of concern circulate. Clinical studies show CoronaVac efficacy against symptomatic COVID-19 ranging from 51% (Brazil) to 65.9% (Chile) and 100% against severe illness and illness requiring hospitalization ((TCTR20210325003). Investigators adhered to U.S. Department of Defense AR 70\u201325 policies for protection of human subjects.Circulation of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants capable of evading vaccine-derived protection is challenging the efficacy of coronavirus disease (COVID-19) vaccines (https://www.genscript.com) ; all had received their first dose during February 22\u2013March 12, 2021. Median age was 39 (interquartile range 30\u201351) years of age; 103 (49.6%) were men. Among study participants, 58 (28%) provided blood samples only at baseline (when the first dose was administered), 93 (44.0%) both at baseline and 2\u20133 weeks after the second dose, and 56 (27.0%) at baseline and at 2\u20133 weeks and 10\u201312 weeks after the second dose. Using an in vitro system (Appendix), we evaluated the ability of the serum of CoronaVac recipients to neutralize SARS-CoV-2. We measured circulating serum neutralizing antibodies to the original wild-type strain by using a cPass receptor binding domain antigen-based surrogate virus neutralization test (sVNT) ELISA of participants were seropositive against the Wild-type strain, 35.6% (53/149) against Alpha variant, 3.4% (5/149) against Beta, and 8.7% (13/149) against Delta . Mean ne4,5). Our findings support administering vaccine boosters, especially where these variants circulate. Comparing sVNT ELISA results between the 2 time points, Wild-type strain antibodies appear to have a half-life of 83.4 days (95% CI 76.6\u201390.3 days). However, when the MNA was used, neutralizing antibodies waned in a time- and variant-dependent manner. The half-life of neutralizing antibodies was as low as 47.2 days (95% CI 37.5\u201356.9 days) for Wild-type strain, 38.6 days (95% CI 31.2\u201345.9 days) for Alpha variant, 6.9 days (95% CI 3.2\u201310.6 days) for Beta, and 12.3 days (95% CI 6.8\u201317.8 days) for Delta . These dAdditional information about neutralizing titers in serum of coronavirus vaccine recipients."} +{"text": "CDC\u2019s May 25 MMWR report of 10,262 vaccine breakthrough infections in the U.S. is likely an underestimate. Herein, we report Veterans Health Administration (VHA) breakthrough cases, focusing on hospitalizations and deaths.A COVID-19 vaccine breakthrough infection is defined as SARS-CoV-2 RNA or antigen detected We extracted COVID-19 vaccine breakthrough infections tested between 1/19/2021 and 4/30/2021 from the VHA Corporate Data Warehouse (including screening tests). We reviewed medical records of cases who died and/or were hospitalized within 14 days of SARS-CoV-2 positive test for clinician documentation of conditions deemed high risk for COVID-19 and to confirm hospitalization or death was related to COVID-19. SARS-CoV-2 whole genome sequencing (Clear Labs platform) and antigen testing (Abbott BinaxNOW) from available patient samples were performed and Pangolin lineage determined.1,142 COVID-19 vaccine breakthrough infections were identified. 357/1,142 (31.3%) were hospitalized and/or died. 1,085 (95%) were male (Table 1), and median age was 72.5 years . COVID-19 infection contributed to hospitalization and/or death in 139 (38.9%) cases. The remaining 218 (61.1%) were hospitalized or died of causes apparently unrelated to COVID-19. Smoking and heart conditions were seen most frequently among hospitalized/deceased breakthrough cases (Table 2). Variant B.1.1.7 was predominant, present in 17/27 (63%) total samples sequenced, and 13/21 (61.9%) hospitalized/deceased. (Table 3). Of 21 sequenced hospitalized/deceased cases, SARS-CoV-2 antigen positivity was present in 11 (52.4%).Compared to CDC reported breakthrough infections, VHA cases were more male, older, and hospitalized/died at higher frequency. Further study is needed to determine the contribution of specific underlying conditions, COVID-19 vaccine formulations and variants on hospitalization and death among COVID-19 vaccine breakthrough infections. Sequencing efforts for breakthrough cases should be intensified, particularly for those presenting with more severe infections.All Authors: No reported disclosures"} +{"text": "Patients were excluded if they were on third-line ART < 6 months or received RAL and/or ETV and/or DTG before starting third-line ART. A retrospective evaluation of adults \u226518 years old on third-line ART regimens at UTH between January 2012 to June 30, 2020 was conducted. Patients were referred for second-line virologic failure defined as HIV RNA VL > 1000 copies/mL on two consecutive measurements after 6 months on second-line ART.10 3.60 and 3.33, respectively. The immunologic response revealed 49 (56.3%) had CD4 increase with mean increase of 61.1 cells/mm3. (See Table 1.)A total of 539 patients were included; 231 males (42.9%) and 308 (57.1%) females. The mean age of third-line initiation was 29.8 years; mean time from ART initiation to third-line initiation was 9.9 years. Out of 25 combination 349 (64.7%) received DTG, 272 (50.5%) DRV/r, 85(15.8%) ETR, and 49 (9.1%) RAL. There were 215 (39.9%) genotypes; common mutations were to zidovudine (80%), non-nucleoside reverse transcriptase inhibitors (NNRTIs) (78%), and protease inhibitors (PIs) (41%). Patients with at least one viral load and CD4 upon third-line initiation was 296 (54.9%) and 350 (64.9%), respectively. Among patients with sufficient data , VL suppression increased from 44 (38%) patients at baseline to 53 (46%) at next available follow-up; with mean baseline VL and follow-up VL of logWe found moderate improvements in VL suppression and immunologic response. Nearly all third-line patients had genotypic resistance to first-line NNRTI and nearly half to second-line PI regimens. Quality improvement measures are needed to improve viral load timing following ART changes to better assess regimen efficacy.All Authors: No reported disclosures"} +{"text": "The ePlex BCID Gram-Positive (GP) panel utilizes electrowetting technology to detect the most common causes of GP bacteremia (20 targets) and 4 antimicrobial resistance genes in positive blood culture bottles. Rapid detection of intrinsic vancomycin resistance and acquired resistance genes Time of Flight mass spectrometry. Samples submitted for standard of care testing in Biomerieux BacT/Alert resin FA/FN blood culture bottles on the BacT/Alert VIRTUO automated blood culture system with GP bacteria on direct exam (n=100) were included. Bacillus, 1 Corynebacterium) were identified, and 7/7 coinfections with Gram negative (GN) bacteria were detected by the Pan GN target and identified by the BCID-GN panel. Discordant analyses revealed a positive percent agreement (PPA) of 96/97 (99%) with 1 false negative CNS and a negative percent agreement (NPA) of 92/97 (94.8%) with 5 false positives for either S. epidermidis or Corynebacterium. Detection of vanA yielded a PPA of 4/4 and NPA of 9/9. mecA gene detection exhibited a PPA of 14/14 and NPA of 14/14 for S. aureus and a PPA of 31/32 (97%) and NPA of 16/16 for coagulase negative staphylococci with 1 false negative methicillin resistant S. epidermidis. All GP bacteria were represented on the BCID-GP panel, most tests 97/100 (97%) yielded valid results, 53 common skin contaminants (50 coagulase negative staphylococci (CNS), 2 mecA gene detection in Staphylococcus species (n=30) represent opportunities for early optimization of antimicrobial therapy in 34/100 (34%) of samples. The BCID-GP panel provides rapid accurate detection of resistant isolates and common contaminants enabling high quality data driven optimization of antimicrobial therapy. Detection of acquired vancomycin resistance (n=4) and absence of Todd P. McCarty, MD, Cidara (Grant/Research Support)GenMark T2 Biosystems (Consultant) Sixto M. Leal, Jr., MD, PhD, Abnova (Grant/Research Support)AltImmune (Grant/Research Support)Amplyx Pharmaceuticals (Grant/Research Support)Astellas Pharmaceuticals (Grant/Research Support)CNINE Dx (Grant/Research Support)GenMark Diagnostics IHMA (Grant/Research Support)IMMY Dx (Grant/Research Support)JMI/Sentry (Grant/Research Support)mFluiDx Dx (Grant/Research Support)SpeeDx Dx (Grant/Research Support)Tetraphase Pharmaceuticals (Grant/Research Support)"} +{"text": "HIV outpatient in-person (IN-P) visits were limited during the COVID-19 pandemic, and most patients (pts) were cared for remotely through telehealth (TELE). We sought to evaluate the impact of TELE on HIV infected pts during the pandemic compared to the pre-pandemic IN-P care.Retrospective chart review of pts in an outpatient HIV clinic, study period 03/30/2019 to 03/29/2021. Two periods were defined: pre-COVID (Pre-CO) 3/30/2019 to 3/29/2020 and COVID (CO) 3/30/2020 to 3/29/2021. Data was collected on demographics, HIV risk, type of encounter, number of encounters, CD4, HIV Viral loads (VL) at first, and last visit, treatment regimen information. HIV VL < 200 copies/ml was considered as undetectable.A total of 607 pts were evaluated. Mean age 51years; (Range-20-84). Male 306 (50.4%), African American 545(90%), Hispanic 50 (8.2%), white 9 (1.5%), Asian 3(0.5%). HIV risk: heterosexual 437(72%), male sex with male 118(19.4%), intravenous drug use 8 (1.3%). In the Pre-CO period, 530 pts were seen as IN-P; in the CO period 606 pts were encountered of which 304 (50.2%) were TELE visits, 89(14.7%) IN-P, 213(35%) had both TELE and IN-P encounters. Mean number of encounters were 2.59 in the Pre-CO and 2.46 during CO. The number of new pts in the Pre-CO were 36 (7%) vs. 52(8.6%) in the CO (p=0.26). During the pre-CO, 373 pts had CD4 measured at first and last visits, 353(95%) at the first visit and 352 (94.3%) at the last visit had CD4 counts \u2265 200/uL (p=.87); 373 pts had a VL done at first and last visits, 330 (88.5%) at the first visit and 337(90.3%) at last visit were undetectable (p=0.41). During CO, 445 pts had CD4 measured at first and last visits, 402 (90.3%) at the first visit and 445(94.2%) at the last visit had CD4 count \u2265200/uL (p=0.03); 448 pts had VL measured at first and last encounters, 389(87%) at the first visit and 417(93%) in the last visit were undetectable (p=0.002). Antiretroviral changes occurred in 29% in the Pre-Co compared to 19% in the CO (p=0 .32).In our clinic, more pts were cared for during the CO period compared to the Pre-CO period. Significantly, more pts had undetectable HIV VL during CO period. At least one TELE visit was utilized by over \u00be of the pts. TELE has a potentially important role in future HIV care without compromising patient outcomes. All Authors: No reported disclosures"} +{"text": "Pulmonary nodules in asymptomatic patients could represent latent pulmonary infections. Intestinal transplant (ITx) recipients with preexisting pulmonary nodules might be at higher risk for pulmonary infections. However, data is lacking. Aspergillus, Cryptococcus and latent tuberculosis infection (LTBI) performed within 12 months prior ITx was obtained. We assessed for worsening pulmonary nodules, and fungal and mycobacterial infections during the 1st year post-transplant. Survival at one year post-transplant was also assessed. This retrospective study included adult patients that underwent intestinal transplantation (ITx) from 5/2016 to 5/2020. Chest computed tomography (CT) scans performed within 12 months prior of ITx were obtained to evaluate for preexisting pulmonary nodules. Screening for endemic mycoses, Coccidioides antibody (Ab) was done in 15 (50%) patients, Blastomyces Ab and Histoplasma Ab in 7 (23%) each, Histoplasma urine antigen (Ag) and Aspergillus serum galactomannan in 3 (10%) each, and Cryptococcus serum Ag in 10 (33%) patients]. QuantiFERON-TB (QFT) was negative in 35 (81%) patients, positive in 2 (5%) and indeterminate in 6 patients (14%). QFT-Gold In-Tube was replaced to QFT-Plus in 3/2019. Post-transplant worsening of pulmonary nodules was noted in 12 (40%) patients and bronchoscopy was performed in six of them. Note that only 1 (3%) of the patients that had pre-existing pulmonary nodules developed a pulmonary infection (invasive pulmonary aspergillosis diagnosed 33 days after ITx). Our cohort survival at one year post-transplant was 79%. Forty-three patients underwent ITx. Twenty-three (53%) were Female. Median age was 46 years (range: 18-67). Chest CT scans were performed in 36(84%) patients prior to ITx. Preexisting pulmonary nodules were found in 30 (83%) of the patients. All were asymptomatic. Nodules were not calcified in 10 (33%) patients, calcified in 4 (13%), some calcified and some not calcified in 4 (13%) and unclear in 12 (40%). All the patients screened negative for fungi [Preexisting pulmonary nodules was common in our ITx cohort. However, only one case of pulmonary infection was noted among those who had preexisting pulmonary nodules. Clinical monitoring is essential. All Authors: No reported disclosures"} +{"text": "Proteasome inhibitors (PIs), including carfilzomib, potentiate the activity of selinexor, a novel, first-in-class, oral selective inhibitor of nuclear export (SINE) compound, in preclinical models of multiple myeloma (MM).2)\u2009+\u2009dexamethasone (40\u2009mg) (XKd) once weekly (QW) was evaluated in patients with relapsed refractory MM (RRMM) not refractory to carfilzomib.The safety, efficacy, maximum-tolerated dose (MTD) and recommended phase 2 dose (RP2D) of selinexor (80 or 100\u2009mg)\u2009+\u2009carfilzomib \u2009\u2265\u2009very good partial responses. Median progression-free survival was 15 months.Thirty-two patients, median prior therapies 4 , were enrolled. MM was triple-class refractory in 38% of patients and 53% of patients had high-risk cytogenetics del(17p), t, t and/or gain 1q. Common treatment-related adverse events were thrombocytopenia 72%/47% (G3 and G4), nausea 72%/6%, anaemia 53%/19% and fatigue 53%/9%, all expected and manageable with supportive care and dose modifications. MTD and RP2D were identified as selinexor 80\u2009mg, carfilzomib 56\u2009mg/mWeekly XKd is highly effective and well-tolerated. These data support further investigation of XKd in patients with MM. Exportin 1 (XPO1) is a critical nuclear exporter for tumour suppressor proteins , 4, 5. XSelinexor is a novel, first-in-class oral selective inhibitor of nuclear export (SINE) compound that blocks XPO1, forcing the nuclear retention and activation of TSPs, ultimately causing cancer cell death , 10. Cononce weekly (QW) selinexor, bortezomib and dexamethasone (XVd) showed superior median progression-free survival and ORR (76.4 vs. 62.3%), reduced peripheral neuropathy and a trend to reduced mortality, as compared with standard twice weekly bortezomib and dexamethasone (Vd), despite XVd using 40% less bortezomib and 25% less dexamethasone than standard Vd at initial diagnosis or screening did not compromise the efficacy of XKd: In the 17 patients with high-risk cytogenetics, the ORR was 82.4% (14/17), the median PFS was 15.0 months , the median DOR was 22.7 months and the mOS was not reached .XKd induced responses in patients with triple-class refractory MM , with an ORR of 78.1% including 2 (6.3%) sCR, 3 (9.4%) CR, 9 VGPR (28.1%) and 11 PR (34.4%). Moreover, XKd induced long-lasting responses with median DOR of 22.7 months, median PFS of 15.0 months and median OS not reached (median follow-up 15.1 months). No clinically significant and unexpected cumulative toxicities have been observed. Importantly, efficacy was preserved in genetically high-risk disease; ORR was 82.4%, median PFS 15.0 months, median DOR 22.7 months and median OS not reached. Similar results were observed in triple-class refractory MM where ORR was 66.7%, median PFS 23.7 months, median DOR 22.7 months and median OS 20.4 months. Anti-MM activity was not affected by any specific prior therapy consistent with the lack of cross-reactivity of selinexor with other anti-MM agents.The high efficacy demonstrated here by XKd is on par with the efficacy demonstrated by currently recommended triplet combinations utilising carfilzomib and dexamethasone to treat RRMM. In RRMM patients treated with a median of 2 prior therapies (range 1\u20134), none of whom had previous treatment with daratumumab or had triple-class refractory MM, daratumumab, carfilzomib and dexamethasone (DKd) induced an ORR of 84% . At a me2 carfilzomib and 80\u2009mg selinexor with 70\u2009mg/m2 carfilzomib, both with 40\u2009mg dexamethasone QW, were found to be intolerable in our patient cohort. However, the next lower level, 80\u2009mg selinexor with 56\u2009mg/m2 carfilzomib and 40\u2009mg dexamethasone all QW, was identified as MTD and determined to be the RP2D. Additional dose levels including 60\u2009mg selinexor with 70\u2009mg/m2 carfilzomib and 80/100\u2009mg selinexor with carfilzomib 70/56\u2009mg/m2, both only on days 1, 8 and 15 of the 28-day cycles, are being evaluated in eight patients.Two dose levels tested, 100\u2009mg selinexor with 56\u2009mg/mMechanistically, the notable potency of the XKd regimen is well supported by preclinical studies , 14\u201317: The XKd safety profile was similar to that observed previously for each of the components , 18, wit2 provided deep and durable responses in patients with heavily pretreated RRMM, of whom 37.5% had triple-class refractory MM and 53.1% had high-risk cytogenetics. Based on the preliminary results presented in this study in a more heavily pretreated population than those previously reported with carfilzomib-based triplets, QW XKd has compelling, durable activity, including in high-risk and triple-class refractory MM, and additional studies in both previously treated, as well as newly diagnosed MM, are warranted.In conclusion, the QW combination of oral selinexor 80\u2009mg, dexamethasone 40\u2009mg and IV carfilzomib 56\u2009mg/m2 carfilzomib cohort experienced a DLT (Grade 3 thrombocytopenia and Grade 3 vomiting) (Table\u00a02 carfilzomib cohort experienced a DLT (Grade 4 thrombocytopenia\u2009\u00b1\u2009pneumonia) , the most common (\u226550%) non-haematologic TRAEs were nausea , fatigue and decreased appetite , were mostly Grade 1/2 and manageable by dose modification and/or supportive care. Nausea was the only Grade \u22653 non-haematological TRAEs that occurred in at least two patients . Most common haematologic TRAEs were thrombocytopenia and anaemia . Grade 4 thrombocytopenia occurred in three patients (16.7%) and again was not accompanied by bleeding in any patient.Among patients at the RP2D (No patient had nausea or vomiting leading to discontinuation of any study drug. All patients received at least one prophylactic anti-nausea agent. Twenty-four (75%) received a 5-HT3 antagonist, and of those, 19 (79.2%) received at least one additional antiemetic medication. Ten patients (31.3%) received two or more additional antiemetic medications. Four (12.5%) patients received an additional appetite stimulant and 11 (34.4%) patients received potassium chloride tablets. Six (18.8%) patients received transfusions (either red blood cell or platelet transfusions). Six (18.8%) patients received the thrombopoietin receptor agonists eltrombopag or romiplostim, one (3.1%) patient received filgrastim and two patients (6.3%) received an erythropoietin-stimulating agent.Pneumocystis jirovecii pneumonia (Grade 3), 1 viral pneumonia (Grade 3), 1 pulmonary embolism (Grade 3), and 1 thrombocytopenia .Six patients had at least one serious AE) attributed to any of the study drugs: 2 pneumonia , 1 anaemia (Grade 3), 1 coronavirus disease 2019 (Grade 3), 1 cardiac failure (Grade 1), 1 fatigue (Grade 3), 1 influenza (Grade 3), 1 left ventricular failure (Grade 3), 1 encephalopathy (Grade 3), 1 XKd Manuscript Supplemental"} +{"text": "Septic arthritis is considered the most important differential diagnosis in suspected Lyme arthritis. The present study sheds light on the most frequent misdiagnoses in Lyme arthritis cases and clues for differentiation from Staphylococcal and Streptococcal septic arthritis.Staphylococcus aureus (SA) and streptococci and Lyme polymerase chain reaction (PCR) positive joint fluid in 9 hospitals in Eastern Pennsylvania and 1 in Warren county, New Jersey over a 3 year period.We studied patients with positive joint fluid cultures with One hundred and thirty four out of 7000 SA and 21 out of 1321 streptococcal isolates were from joint fluid. Twenty nine had Lyme arthritis, ages 5-74 . Twelve out of 29 were ages 10-18 with 20/29 under age 40. Predominant joint affected was a single knee 27/29. All had pain with or without swelling and little erythema. Two had fever. One reported a tick bite. None had other manifestations of Lyme disease. The diagnosis at the initial visit was sprain or sports injury in 5, osteoarthritis in 5, inflammatory arthritis or gout in 2 each, i septic arthritis, 1 viral syndrome and 1 ruptured Baker's cyst. Joint fluid count range was 3500-77,360 with only 3 over 50,000. White blood cell count (wbc) range was 3200-14,580. SA arthritis involved knee in 66 (49.3%), hip 31(23.9%), elbow 19 (14.2%), shoulder 14 (10.4%) with 2 wrist, 1 ankle and 1 sterno-clavicular joint. Fifty seven had a history of joint surgery. Eighty six were male and 48 female. age range 14-95 with a median age 65. Synovial fluid cell count was 335-470,000 and wbc 5,200-28,410 . Streptococcal septic arthritis involved the knee in 17/21 with one each of hip, elbow, shoulder. The ages were 36-86 with 15/21 over age 60. Synovial fluid count was15,242-641,425 . Wbc count 11,140-25,080 .Nine out 21 had prior joint surgery.Lyme arthritis patients were younger, mostly involving 1 knee, majority male without other manifestations of Lyme disease. Highest synovial fluid count was 77,360 and highest wbc count 14,580. Most frequent misdiagnoses were sports injury/sprain or osteoarthritis. SA and Streptococcal arthritis were mostly in elderly, with higher joint fluid cell and wbc counts. Only 1/29 Lyme arthritis was initially misdiagnosed septic arthritis.All Authors: No reported disclosures"} +{"text": "Little is known about how social determinants, comorbidity, and disability status are associated with functional recovery after an acute illness. A prospective cohort study was conducted between 2019-2020 at a university hospital in Korea, to investigate functional recovery after hospitalization for pneumonia in older adults with different degrees of social deprivation, disabilities, and comorbidities. K-means cluster analysis was used to identify groups of patients based on social deprivation score, activities of daily living, instrumental activities of daily living, physical limitation score, and Gagne comorbidity index. Four groups were identified: Group A: non-disabled group with limited social support (n=61 [30.3%]); Group B: multimorbid but non-disabled group with social support (n=45 [22.4%]); Group C: multimorbid and disabled group with social support (n=38 [18.9%]); Group D: multimorbid and disabled group with limited social support (n=57 [28.4%]). Functional status, defined as ability to perform 21 activities and physical tasks independently, was measured via telephone interviews at 1, 3, and 6 months after discharge. Group-based trajectory model identified four functional status trajectories: excellent (n=29 [14.4%]), good (n=51 [25.4%]), fair (n=58 [28.9%]) and poor (n=63 [31.3%]). The most common functional trajectory by four groups was good trajectory (59%) in Group A, excellent trajectory (48.9%) in Group B, fair (50%) and poor trajectory (50%) in Group C, and poor trajectory (77.2%) in Group D. Our results suggest that most patients without disability recover functional status after pneumonia, despite multimorbidity or limited social support. Social support seems to be more important for those with multimorbidity and disability."} +{"text": "Currently, the Best Practice Caregiving website provides information on 231 published studies from 44 dementia caregiving evidence-based programs that have demonstrated beneficial outcomes for dementia caregivers within health care and community-based settings. Across all programs, a total of 34 biopsychosocial outcomes were identified. Supported by the commonly used stress-related frameworks for which the programs were developed, the most frequently utilized program outcomes included: 1) Caregiver stress, strain, and/or burden (84.1%); 2) Caregiver depressive symptomology (79.5%); and 3) Caregiving efficacy, skills, and/or confidence (63.6%). The least common programmatic outcomes included: 1) Access to support information/Community service use (9.1%); 2) Unmet needs (6.8%); and 3) Respite/break from care (2.3%). The lesser utilized outcomes provide critical insight into current evidence-based programmatic priorities and ways in which professionals can seek to fill gaps in dementia caregiving interventions. Discussion will also focus on future directions of caregiver-related outcome assessments."} +{"text": "Nothopassalora personata in groundnut is responsible for up to 50% yield loss. To dissect the complex nature of LLS resistance, comparative transcriptome analysis was performed using resistant (GPBD 4), susceptible (TAG 24) and a resistant introgression line (ICGV 13208) and identified a total of 12,164 and 9954 DEGs respectively in A- and B-subgenomes of tetraploid groundnut. There were 135 and 136 unique pathways triggered in A- and B-subgenomes, respectively, upon N. personata infection. Highly upregulated putative disease resistance genes, an RPP-13 like (Aradu.P20JR) and a NBS-LRR (Aradu.Z87JB) were identified on chromosome A02 and A03, respectively, for LLS resistance. Mildew resistance Locus (MLOs)-like proteins, heavy metal transport proteins, and ubiquitin protein ligase showed trend of upregulation in susceptible genotypes, while tetratricopeptide repeats (TPR), pentatricopeptide repeat (PPR), chitinases, glutathione S-transferases, purple acid phosphatases showed upregulation in resistant genotypes. However, the highly expressed ethylene responsive factor (ERF) and ethylene responsive nuclear protein (ERF2), and early responsive dehydration gene (ERD) might be related to the possible causes of defoliation in susceptible genotypes. The identified disease resistance genes can be deployed in genomics-assisted breeding for development of LLS resistant cultivars to reduce the yield loss in groundnut.Late leaf spot (LLS) caused by fungus Arachis hypogaea L.) is a self-pollinated tetraploid oilseed legume crop and is cultivated on 34.1 million hectares (Mha) with an annual production of 66.3 million tons with productivity of 2.17 tons/ha during 2019 of these 48 samples generated a total of 1459.5 million pair reads. After rigorous filters, such as the reads with adapter sequences, short reads and reads with too many ambiguous (N) bases during quality analysis, 1308.6 million paired reads were retained for global gene expression profile and differential gene expression studies. On an average, 78.2% reads were mapped on both subgenomes but the highest percentage of mapping was achieved for B-subgenome (A resistant genotype (GPBD 4), a susceptible genotype (TAG 24) and an introgression line (ICGV 13208) carrying LLS resistant QTL, derived from the marker-assisted backcrossing between TAG 24 (recurrent parent) \u00d7 GPBD 4 (donor parent) were used for transcriptome analysis under control (non-inoculated) and inoculated condition in all the samples were filtered out and not used for further analysis. With this criterion, a total of 22,670 genes in A-subgenome and 24,349 genes in B-subgenome were found to be expressed with FPKM value \u2265 1. The fold-change (log2 fold) of each gene was calculated across combinations of resistant and susceptible genotypes at disease development and symptom development stages and the gene was said to be differentially expressed when the log2 fold-change value was \u22652 (induced) or \u2265\u22122 (repressed). With these criteria, a total of 12,164 DEGs in A-subgenome and 9954 DEGs in B-subgenome were found to be differentially expressed across combinations. Highest number of DEGs (1605) were mapped on chromosome B03 followed by A03 (1603 DEGs) which indicated that highest number of DEGs were mapped on homologous chromosomes (A03/B03) followed by A06/B06 of both subgenomes a.A core set of 1093 DEGs showed similar expression patterns in all three genotypes. Some DEGs were also detected which commonly expressed between combination of any two genotypes such as 642 DEGs in GPBD 4 vs. ICGV 13208; 762 DEGs in ICGV 13208 vs. TAG 24; 686 DEGs in GPBD 4 vs. TAG 24. A total of 439 DEGs showed similar expression pattern in GPBD 4 and introgression line ICGV 13208 b.In GPBD 4 control vs. GPBD 4 stressed samples, total 5056 DEGs were transcriptionally active across stages. The expression trend of up and downregulation was high at 50DPI with 1764 DEGs . The trend of upregulation was more intense from 1DPI to 35 DPI. A total of 284 DEGs were expressed at 1DPI (253 upregulated and 34 downregulated) . In ICGVIn case of ICGV 13208 control vs. ICGV 13208 stressed samples, the highest number of DEGs (3856) were expressed at 2DPI. The total number of DEGs were decreased with increasing DPI in ICGV 13208 and therefore, only 306 DEGs were expressed . In TAG A day-wise overlap between resistant and susceptible samples at all stages was also analyzed. Largest fraction of DEGs were unique at 50DPI for TAG 24 stressed vs. GPBD 4 stressed (400 DEGs) followed by 35DPI (246 DEGs), 7DPI (150 DEGs), 1DPI (100 DEGs), and 2DPI (150 DEGs) a. In TAGN. personata infection. The highest number of DEGs (4019) across stages were expressed between TAG 24 stressed vs. GPBD 4 stressed (1678 upregulated and 2341 downregulated). The expression trend of upregulation was high at 50 DPI where total 702 DEGs were upregulated and 581 DEGs were downregulated. At 1DPI (333 downregulated), 7DPI (491 downregulated), and 35DPI (609 downregulated) (The expression levels of DEGs between resistant and susceptible genotypes were compared to identify the upregulated and downregulated DEGs upon gulated) d. In TAGgulated) e. In GPBgulated) f.Plants respond to pathogen attack by establishing a highly coordinated series of molecular, cellular and tissue-based defense barriers as ample transcript reprogramming occurs in response to a pathogen. We identified important disease resistant genes expressed under stressed condition in resistant and susceptible genotypes when compared with their respective controls. Four different clusters of DEGs identified in three combinations of ICGV 13208 controls vs. ICGV 13208 stressed, GPBD 4 control vs. GPBD 4 stressed and TAG 24 control vs. TAG 24 stressed. In cluster I, large fraction of DEGs was downregulated in susceptible genotype and upregulated in resistant genotypes.Araip.5N6GI), aldo-keto reductase family oxidoreductase (Aradu.L3IQI) and fatty acyl-co-A reductase (Aradu.90BJM) were downregulated in TAG 24 and upregulated in GPBD 4 and ICGV 13208. Disease resistance response proteins (Aradu.0X3DX) and ethylene responsive transcription factor (Araip.BUP6F) were downregulated in susceptible genotype and upregulated in resistant genotypes. Important disease resistant proteins (TIR-NBS-LRR) (Aradu.R3HWW), MLO-like proteins (Aradu.SSV2N), kunitz trypsin inhibitor (Aradu.GS29Q), growth regulating factor (Araip.489C1), also anthocyanin pigment producing gene anthocyanin 5-aromatic acyltransferase (Araip.XH0KD) were downregulated in susceptible genotype. Pathogenesis related proteins (Aradu.C87QN), and purple acid phosphatase (Aradu.5K7BE) were found upregulated in resistant genotypes. In cluster II, DEGs were highly upregulated in resistant as well as susceptible genotypes. Included MADS-box (Aradu.8KH6E) family proteins and NAC domain containing protein (Araip.8NR3H) were highly upregulated in resistant as well as susceptible genotypes. In cluster III, DEGs upregulated in susceptible genotypes including stress upregulated Nod 19 protein (Aradu.T4WFS), and wound responsive family protein (Araip.707XL). In cluster IV, a large fraction of DEGs was downregulated in TAG 24 and ICGV 13208. Included are zinc finger protein (Araip.3ZN37), tryptophan synthase (Araip.CM5I1), chalcone synthase (Araip.62EH4), sugar transporters SWEET genes (Aradu.HBL25), and secondary metabolites producing genes such as jasmonic acid carboxyl methyltransferase (Aradu.12ETV) and terpene synthase (Araip.E734B) (DEGs included LL-diaminopimilate aminotransferease (p.E734B) .Aradu.P20JR), ZIP transport family proteins (AraipV9JLA), F-box proteins (Aradu.EQ6UY), WRKY TFs (Aradu.KG41H), NAC domains (Araip.DL86S), nematode resistance proteins (Araip.0D8F4), jasmonates-zim-domain (Araip.64KG6), ubiquitin-conjugating-enzyme (Araip.8IP1M). However, cluster II showed induced expression of DEGs in all combinations, comprising the genes such purple acid phosphatase (Aradu.ASA64), pathogenesis related proteins (Araip.4B6XP), defensins (Aradu.CK6H7), MADS box (Araip.F0RXE), terpene synthases (Araip.E734B), disease resistance proteins (TIR-NBS-LRR) (Aradu.Z87JB), indole 3-acetic acid (Araip.179L2), kunitz trypsin inhibitor (Araip.31ZB6), MYB transcription factor (Aradu.A9JEU), chitinases (Aradu.1BC5C), desiccation related proteins (Aradu.I3E1J). DEGs in cluster III showed upregulation in GPBD 4 vs. ICGV 13208 and TAG 24 vs. GPBD 4 combinations. The genes in this cluster included zeaxanthin epoxidase (Aradu.E3EHQ), stress upregulated Nod 19 (Aradu.T4WFS), gibberellin regulated family protein (Araip.TG4Z7), peroxidase superfamily protein (Aradu.X9PNA), zinc-finger protein (Araip.JJU0M). In cluster IV, three DEGs were downregulated in all three combinations. In cluster V, the expression trend showed downregulation in TAG 24 vs. ICGV 13208 and TAG 24 vs. GPBD 4. The genes in this cluster consisted cysteine proteinases (Araip.D3HLX), serine threonine protein kinases (Araip.Q80VR), copper/zinc superoxide dismutase (Araip.0J9BI), disease resistance response protein (Araip.CHQ37), The expression trend in cluster VI was upregulated in combinations of GPBD 4 vs. ICGV 13208 and TAG 24 vs. ICGV 13208. The fraction of DEGs in this cluster included MLP-like proteins (Aradu.2V7UE), chalcone synthase (Araip.JD11C), lipid transfer protein (Aradu.B20QU), pathogenesis related protein (Aradu.D14Q2) (Expression trends during disease development (DD) and symptom development (SD) stages identified six different clusters in both stages. In cluster I, 12 DEGs showed downregulation in GPBD 4 vs. ICGV 13208 combination at DD stage, however, were found upregulated in TAG 24 vs. ICGV 13208 and TAG 24 vs. GPBD 4 combinations. The genes of this cluster included putative disease resistance RPP13 (u.D14Q2) a.Araip.NFP9Z), beta galactosidase (Aradu.DB6JJ), cytochrome b5-like heme/steroid binding domain (Aradu.JR9IZ), ZIP transport proteins (Aradu.1P1D6), ATP synthase beta subunit (Araip.CH5RM), auxin responsive protein (Aradu.B5GNC), eukaryotic aspartyl protease (Aradu.A3AX6), inorganic pyrophosphate (Araip.JP12S). Cluster II comprised the DEGs upregulated across three combinations. Cluster II included defensins (Aradu.CK6H7), disease resistance protein (TIR-NBS-LRR) (Aradu.J4Y5T), pathogenesis related (PR) proteins (Aradu.9G825), acyl-CoA-synthase (Aradu.V73WK), leucine rich receptor (Aradu.3S3UE), proline reach protein (Aradu.DZ5Y1) and MADS box (Aradu.Y02KH). While, in cluster III, the DEGs were upregulated in GPBD 4 vs. ICGV 13208 and TAG 24 vs. GPBD 4 combinations. This cluster consisted of WRKY transcription factor (Aradu.XE5AY), disease resistance protein , auxin transporters (Aradu.B5GNC), MLO-like protein (Aradu.SSV2N), calcium binding protein (Aradu.F99CN), isoflavone reductase homolog (Aradu.Q7212) and heat shock transcription factors (Aradu.E740H). However, in cluster IV, four DEGs were upregulated in TAG 24 vs. GPBD 4 and GPBD 4 vs. ICGV 13208. The genes in this cluster included chalcone synthase (Aradu.YC5B5), jasmonic acid carboxyl methyltransferase (Aradu.12ETV) and ripening related protein family (Aradu.T873S). The genes in cluster V were downregulated across combinations. The fraction of DEGs in cluster VI were upregulated in GPBD 4 vs. ICGV 13208 combination. The genes in this cluster included myb transcription factor (Araip.VH6HT), serine protease inhibitor (Aradu.8CV4T), caffeoyl-CoA-3-O-methytransferase (Aradu.M62BY) and stress upregulated Nod 19 protein (Aradu.T4WFS) b.The pattern of gene expression was studied for the genes reported in the previously identified QTL regions conferring resistance to LLS mapped on chromosome A02 and A03 10 transformed FPKM values were used for visualization of expression pattern of DEGs on heatmap. Of these 13 genes, 5 DEGs, including tetratricopeptide repeat (TPR) superfamily proteins , putative disease resistance RPP-like proteins , pentatricopeptide repeat (PPR) , chitinases A (Aradu.1BC5C), NADP dependent alkenal double bond reductase (Aradu.JZB0C) were upregulated in GPBD 4 and ICGV 13208. The putative disease resistance RPP13-like protein (Aradu.P20JR) was consistently upregulated (with log2 fold change > 3) in disease development stage and symptom development stage in resistant genotypes and downregulated in susceptible TAG 24. A fraction of eight DEGs from this QTL region were upregulated in ICGV 13208 and TAG 24. Zinc finger proteins and AN1 domain stress associated proteins (Aradu.PH3JT), calmodulin binding heat shock proteins (Aradu.MS73B), late embryogenesis abundant protein (Aradu.KAB2Z), heavy metal transport/detoxification proteins (Aradu.S0307), MLO-like proteins (Aradu.5Y217), CAAX prenyl proteases (Aradu.F2ZNU), ubiquitin protein ligase (Aradu.P4SDG) and calcium binding EF family protein (Aradu.4GK35).In total, 13 DEGs were differentially expressed in a region of 1.4 Mb (0.04 Mb\u20131.47 Mb) on chromosome A02 . Log10 tThe MLOs are expressed in both disease development and symptom development stage with upregulation trend in TAG 24 and ICGV 13208 and downregulation in GPBD 4. However, late embryogenesis abundant protein was upregulated in all genotypes along with zinc finger stress associated protein a.Aradu.2RW34), glutathione S-transferase (Aradu.V4NFM), ATP binding ABC transporter (Aradu.2BI4W), disease resistance protein (TIR-NBS-LRR) (Aradu.Z87JB) and xyloglucan endotransglucosylase (Aradu.4I7WA).In the QTL region on chromosome A03, 11 DEGs were transcriptionally active in a genomic region of 2.7 Mb (131.67 Mb\u2013134.65 Mb) identified for LLS resistance [Aradu.Z87JB; Arahy.R8KUIR) was consistently upregulated in resistant genotypes and downregulated in susceptible genotypes during disease and symptom development stages. A fraction of DEGs including tetratricopeptide repeat (TPR) protein , purple acid phosphatase and acyl-transferase family protein were upregulated in GPBD 4 and ICGV 13208 as compared to TAG 24. In both genomic regions (chromosome A02 and A03), the disease resistance proteins were consistently upregulated in GPBD 4 and ICGV 13208 (The disease resistance protein (TIR-NBS-LRR) .N. personata infection in all 48 samples of TAG 24, ICGV 13208 and GPBD 4 genotypes at disease development and symptom development stages. The information on primer sequences of forward and reverse primers of each gene is provided in Aradu.L3677, Aradu.T5FHF and Araip.E30MW showed induced expression under stress at symptom development stage in resistant genotypes. Among these genes Aradu.L3677 encoding for GDSL-like lipase/acylhydrolase was shown upregulation in resistant genotypes GPBD 4 and ICGV 13208 at 50DPI when compared with the susceptible it showed upregulation in TAG 24 at 7DPI when compared with control. Similarly, Aradu.T5FHF encoding beta-fructofurosidase showed highly induced expression in GPBD 4 and ICGV 13208 at 21DPI under N. personata infection. Highly induced expression was observed for Araip.E30MW encoding for cell wall protein at 35DPI in GPBD 4 however downregulation in TAG 24 and ICGV 13208 at all stages. The gene Araip.I9KX3 encoding for disease resistance response protein was differentially expressed in all genotypes at all stages. During disease development stages 1DPI and 7DPI, it was highly upregulated in GPBD 4. However, at 2DPI it was upregulated in ICGV 13208 (3.7-fold) and 50 DPI it was upregulated (3-fold) in TAG 24. Chitinases (Araip.DN5WT) showed upregulation in ICGV 13208 at 2DPI (~90-fold) when compared with control. Protein kinase superfamily proteins (Araip.BHU8R) showed induced expression at 2DPI in GPBD 4 and ICGV 13208 and at 50DPI in TAG 24 (5.7-fold). O-methyltransferase (Araip.94GCY) showed induced expression at 21DPI, 35DPI and 5DPI when compared with control. 5-methylthioadenosine/S-adenosylhomocysteine deaminase (Araip.8ZP6J) sowed induced expression at 2DPI (12.3-fold) in GPBD 4, at 21DPI (10.4-fold) in TAG 24 and at 50DPI (6.5-fold) in ICGV 13208. Polyphenol oxidase (Araip.36N6E) showed induced expression (22.3-fold) at 2DPI in susceptible TAG 24 and resistant GPBD 4 (7.6-fold). UDP-glucuronic acid decarboxylase (Aradu.42MBK) was upregulated at 1DPI and 2 DPI in GPBD 4 and induced expression at 3DPI and 50DPI (2.9- and 3.0-folds) in TAG 24. Lipid-transfer protein/seed storage protein (Aradu.25DKA) showed induced expression at 1DPI and 2DPI (32.5- and 19.2-folds) in TAG 24, at 35DPI (15.2-fold) in GPBD 4. The results of qRT-PCR showed similar expression patterns with high-throughput RNA-seq data upon LLS infection , late leaf spot (LLS) and rust often occur together leading to 50\u201370% yield loss in groundnut. The circular dark spots of the fungus nfection ,31. Durinfection ,20,32. Tnfection ,9. High-nfection ,34 and tN. personata infection. The transcriptome analysis unraveled the substantial transcriptome changes in resistant genotypes, GPBD 4 and ICGV 13208, and susceptible genotypes TAG 24 under N. personata infection at seven stages in 48 samples. Of the seven stages, four stages belong to disease development and three stages as symptom development. Recently, an attempt was made for transcriptome analysis discovered DEGs for rust caused by Cercospora arachidicola [Puccinia arachidis [C. arachidicola while rust study generated 86.3 million reads for resistant GPBD 4 and susceptible JL 24 at 24 h post inoculation of P. arachidis. We have selected more stages and genotypes and generated more data for LLS transcriptome analysis than the previous transcriptome studies for foliar fungal diseases.The objective of this study was to identify the DEGs from the QTL region which was transferred using marker-assisted backcrossing in introgression line (ICGV 13208) using the LLS resistance donor (GPBD 4) and the differential expression pattern of the genes among resistant and susceptible genotypes under hidicola and earlrachidis while noAradu.P20JR) showed upregulation (34 folds) in GPBD 4 as compared to TAG 24. However, the expression of Aradu.P20JR showed downregulation in ICGV 13208 (by 34 folds) when compared with resistant GPBD 4. In QTL region on chromosome A03, the expression of disease resistance protein (TIR-NBS-LRR) (Aradu.Z87JB) (133776795-133780539) was increased periodically with increasing days post inoculation. Where, the Aradu.Z87JB showed upregulation (25.5-fold) more during disease development stage and more (56.7-fold) during symptom development stage in GPBD 4 and ICGV 13208 as compared with TAG 24. It is important to note that the disease resistant NBS-LRR genes were also reported upregulated in ELS resistant GPBD 4 (4.3-fold) when compared with susceptible JL 24 for ELS disease under C. arachidicola infection [P. arachidis infection the NBR-LRR class showed upregulation (3.3-fold) in rust resistant GPBD 4 when compare with susceptible JL 24 [We targeted the discovery of differentially expressed candidate resistance genes from reported QTL genomic regions on chromosomes, A02 and A03 for LLS resistance. In QTL region on chromosome A02, the expression of putative disease resistance RPP13-like protein have significant role in plant recognition and infection of N. personata. Mitogen activated protein kinase (MAPK) is the signaling cascade widely triggered in response to pathogen infection [N. personata, needs JA-mediated signal transduction and SA-dependent pathways and thus monitor crosstalk between JA- and SA-regulated disease response pathways [Pseudomonas syringe through SA signaling in Arabidopsis [HvWRKY1, imparting resistance to powdery mildew in Hordeum vulgare [N. personata activates the ethylene signaling pathway in which ERF1 encodes a transcription factor of the ethylene-responsive element-binding protein (EREBP) family. ERF1 upregulated the GDSL-like lipase (GLIP) and released into the cell wall. The signaling cascade of GLIP occurs through phloem to systemic tissues and causes the reactivation of ERF1 and the breakdown of EIN3, rising SID2 and SA levels in systemic tissues leads to the launching of systemic acquired resistance (SAR) [Pseudomonas syringae pv. tabaci and empowered the expression of defense related genes after salicylic acid treatment [2+ dependent interaction with calmodulin. The PEN2 and PEN3 act separately in different pathways contributing resistance against pathogen penetration [Botrytis cinerea. The downregulation of pathogenesis-related thaumatin superfamily protein (TLP) could not act on invading fungi by means of hydrolysis of \u03b2-1, 3-glucans in susceptible cultivar [N. personata infection in the groundnut. Ref. [N. personata infection. These datasets would be useful genomic resources in understanding the late leaf spot resistance mechanism in groundnut ,47. Jasmce (SAR) . The uprce (SAR) . The glyce (SAR) . The uprreatment . The MLOetration ,53. In petration . PAP5, wetration . The Bcletration demonstrcultivar . The PR ut. Ref. identifiroundnut .N. personata infection. Ethylene responsive factors were identified which are highly expressed in susceptible genotypes at symptom development causing defoliation in susceptible genotypes at maturity.In summary, the comparative transcriptome analysis in groundnut identified important differentially expressed genes at disease development and symptom development stages including defoliation. Important disease resistance genes such as RPP13-like protein and NBS-LRR genes in previously reported QTL regions were identified for LLS resistance. The tetraploid gene IDs for a few important DEGs are provided in result section. However, the tetraploid gene IDs for the rest of the genes can be retrieved from peanutbase. Pathway analysis identified important pathways such as antibiotic biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis which were triggered in both subgenomes under 2F6 LLS resistant introgression line with genomic regions imparting resistance to LLS introgressed from donor parent GPBD 4 in the background of recurring parent TAG 24 [N. personata at 40 days after sowing (DAS).Three groundnut genotypes were used in this study, namely TAG 24, GPBD 4 and ICGV 13208. TAG 24 is an elite groundnut cultivar that is highly susceptible to LLS. GPBD 4 is an elite cultivar that is a well-adapted LLS and rust resistant variety in India, used as a donor parent during marker-assisted backcrossing. ICGV 13208 is the BCt TAG 24 . In totaN. personata were collected from the highly susceptible groundnut cultivar TMV 2 in rainy season of year 2016. The brown spot with mass of spores with velvety appearance were usually found on the underside of the leaf. These spores were collected by gentle brushing and the concentrations of the spore suspensions were optimized to 20,000 spores mL\u22121 using a hemocytometer by adding sterile distilled water with few drops of Tween-80 (polyoxyethylene sorbitan mono-oleate) for proper adhesion. Inoculation was done with an atomizer sprayer on the leaves of each plant at 40 DAS in one set and the control plants were not inoculated. For proper disease development, the plants were covered with polythene sheets and were sprayed with distilled water once in every two hours so that humidity of >95% is maintained. The conducive conditions for disease development were maintained for seven days by monitoring the relative humidity and temperature (25\u201330 \u00b0C).The spores of The leaf tissues were harvested for RNA isolation both from control and inoculated treatments and flash frozen in liquid nitrogen and stored at \u221280 \u00b0C. The samples were collected just before inoculation on 40 DAS, then one day post inoculation (1 DPI) (41 DAS), 2DPI (42 DAS), 3 DPI (43 DAS) and 7 DPI (47 DAS) for studying the disease development in all three genotypes GPBD 4, TAG 24 and ICGV 13208. In order to study the symptom development stages, the samples were collected on 21 days post inoculation (DPI) (61 DAS), 35 DPI (75 DAS) and 50 DPI (95 DAS). In total, 48 samples (8 stages \u00d7 three genotypes \u00d7 2 treatments) were used for RNA isolation and sequencing .\u00ae RNA Plant\u201d kit following user\u2019s manual. RNA quality and quantity was determined using Nanodrop 1000 spectrophotometer and Bioanalyzer RNA Nano chip . The RNA samples with 260/280 ratio of 1.8 to 2.1, 260/230 ratio of 2.0 to 2.3 and RNA integrity number (RIN) more than 7.0, were used for mRNA sequencing. The cDNA library was prepared using mRNA-Seq Sample Prep kit following manufacturer\u2019s instructions. Poly (A)-containing mRNA was isolated using magnetic beads with oligo (dT) and fragmented into short pieces. These short fragments were used as templates to synthesize first-strand cDNA using reverse transcriptase and random hexamer-primers. The second-strand cDNA was then synthesized using DNA polymerase, dNTPs and RNase H. After completing purification and end repair process, the cDNA fragments were ligated to sequencing adapters. The fragments were then purified and amplified by PCR to obtain the final library followed by purification. Paired-end sequencing was carried out on Illumina HiSeq 2500 platform and raw reads of 100nt were generated. Filtered reads were obtained after running the quality control (QC) using NGS-QC box [Total RNA was isolated from the groundnut leaves using \u201cNucleoSpinS-QC box .A. duranensis) and B-subgenome (A. ipaensis) of cultivated groundnut (A. hypogaea) [p-value \u2264 0.05 after Benjamini\u2013Hochberg correction for multiple-testing [Genome assemblies of both the progenitor subgenomes A-subgenome (ypogaea) was usedypogaea) . Read coypogaea) . Transcrypogaea) . Genes w-testing with sigN. personata infection load at different time points. The pairwise correlation matrix was further used for cluster analysis using R package \u2018pheatmap\u2019 version 1.0.12 [Transcripts with abundance > 1 FPKM were used for calculation of pairwise correlation between each sample pair. The function \u2018corrl\u2019 implemented in Microsoft office excel 2013 was used to calculate pairwise correlation matrix between 48 samples including 24 control and 24 under n 1.0.12 . Furthern 1.0.12 . Differehttp://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi). The alcohol dehydrogenase (Adh) gene was used as an internal reference as Adh shows highly stable expression across all groundnut tissues as compare to other housekeeping genes such as 14-3-3 [To validate the expression analysis of key candidate genes, primers were designed using Primer 3 plus tool (s 14-3-3 . The cDNs 14-3-3 ."} +{"text": "During March 1, 2020\u2013October 26, 2021, approximately 2,500,000 COVID-19 cases and 58,000 COVID-19\u2013associated deaths occurred in the state of New York.COVID-19 vaccines have been shown to be effective against symptomatic infection and hospitalization in New York, including during the period when the B.1.617.2 (Delta) and B.1.1.529 (Omicron) variants of SARS-CoV-2, the virus that causes COVID-19, predominated COVID-19 vaccine or 2 doses of the BNT162b2 (Pfizer BioNTech) or mRNA-1273 (Moderna) COVID-19 vaccines \u226514 days before October 24, 2021; only the first of a 2-dose series vaccine (Pfizer-BioNTech or Moderna); or having no matching vaccine record.**Among 101,205 PLWDH included in the analysis,Receipt of either a single dose of Janssen vaccine or 2 doses of Pfizer-BioNTech or Moderna vaccine increased with age, including 71.4% of PLWDH aged \u226565 years and 54.3% of those aged 18\u201349 years. Coverage was higher among men (64.8%) than women (60.5%), and among persons who identified as nonbinary or nonconforming (58.1%). Among racial/ethnic groups, coverage was highest among non-Hispanic White PLWDH (70.8%), and lowest among non-Hispanic Black (58.6%) and American Indian or Alaska Native persons (58.4%). Coverage was substantially lower among PLWDH who were not virally suppressedThis study found that COVID-19 vaccination coverage among PLWDH overall (63.5%) was lower than that in the general adult New York population (75.0%).Members of non-Hispanic Black and Hispanic communities are more likely to acquire SARS-CoV-2 and experience severe COVID-19\u2013related outcomes than are those of other non-Hispanic and White communities (In addition to primary vaccination coverage, ensuring that PLWDH receive booster doses is critically important moving forward."} +{"text": "The majority of adults and children with meningitis and encephalitis have unknown etiologies fostering universal admission, prolonged length of stay, empirical antibiotic and antiviral therapies. A qualitative multiplexed nucleic acid-based in vitro diagnostic test (FilmArray) is helping clinicians identify organisms and improve clinical outcomes.CSF) with WBC >5 cells/mm3, and leftover CSF were available for testing. All CSF specimens underwent testing with the Biofire\u00ae Film Array Meningitis Encephalitis (FAME) panel. This multiplex PCR tool utilizes 0.2 ml CSF sample to identify the presence of 14 viral, bacterial and fungal pathogens in 1 hour.Patients presenting between July 5, 2018, to April 26, 2021, with meningitis or encephalitis, cerebrospinal fluid (Haemophilus influenzae (8.3%), HHV6 (8.3%), Streptococcus pneumoniae (8.3%) and HSV1 (4.1%)]. The addition of the FAME panel to the standard of care evaluation increased the known etiologies from 119 (41.7%) to 197 pathogens (69.1%), (p< 0.05). 52 patients (18.2%) underwent a repeat LP . Empirical antibiotic and antiviral therapy were given to 89% and 63% of patients, respectively.Of 5291 CSF specimens screened, 285 (5.3%) met the criteria for meningitis or encephalitis and underwent FAME testing. The majority were adults , male , White , immunocompetent and had meningitis presentation. Median age was 41 years (0 mo-100 yrs) and were admitted to the hospital. Median duration between CSF collection and viral PCR result as 13 hrs for Enterovirus, 31 hrs for HSV, and 57 hrs for VZV. The FAME panel detected a pathogen in 103 patients (36.1%) of whom 76 (73.7%) had a viral etiology. 166 (58.2%) patients were discharged with unknown etiology of whom FAME was positive in 24 (14.4%) [VZV (37.5%), HSV2 (16.6%), Enterovirus (16.6%), A rapid multiplex PCR decreases the proportion of unknown etiologies and has the potential to decrease length of stay and the use of empirical antibiotic and antiviral therapies. Testing with the FA ME panel resulted in pathogen detections not previously recognized and for which treatment is recommended.Rodrigo Hasbun, MD, MPH, Biofire (Speaker\u2019s Bureau) Rodrigo Hasbun, MD, MPH, Biofire Involved: Self): Consultant, Research Grant or Support"} +{"text": "Throughout the SARS-CoV-2 pandemic, there have been many questions about how COVID-19 affects patients living with HIV (PLWH). We examined the clinical courses of 45 PLWH who required hospitalization with SARS-CoV-2 infection.This is a retrospective cohort study in which ICD-10 codes were used to identify PLWH who were admitted to three large hospital systems in Memphis, TN with COVID-19. We included all patients \u2265 18 years of age with HIV and a documented positive SARS-CoV-2 PCR test. After manual abstraction from the electronic health records, chi-squared and T-tests were performed to evaluate associations between patient-level factors and outcomes.A total of 45 patients with HIV who tested positive for SARS-CoV-2 were admitted to Memphis, TN area hospitals between March 2020 and October 2020. 18 (40%) were female, 43 (95.6%) were Black, and the average age was 50.3 years (SD 12.6). The average BMI was 30.2 (SD 8.6). 40 (88.9%) patients admitted had at least one comorbidity with the most common being hypertension and diabetes . 24 (46.7%) patients had a Charlson Comorbidity Index > 3. 15/43 (48.4%) patients had a CD4 count < 200, and 35 (77.8%) were on ART. 30 (66.7%) patients met SIRS criteria within 24 hours of admission, and 27 (60%) required some form of oxygen supplementation during hospitalization, including 4 (8.9%) who required intubation. The average length of stay was 10.4 days (SD 12.5). 9 (20%) patients required an ICU stay, and 3 (6.7%) died. BMI > 30, CD4 count < 200, and viral load > 1000 were not associated with worse outcomes. Both a Charlson Comorbidity Index > 3 and the absence of ART were associated with need for ICU-level care.Viral load, CD4 count, and BMI were not correlated with differences in mortality or oxygen use in our study. Patients with higher Charlson Comorbidity Indices and patients who were not on ART at presentation were significantly more likely to require the ICU. Further study is needed to definitively determine factors affecting the outcomes of PLWH with SARS-CoV-2 infection.All Authors: No reported disclosures"} +{"text": "Highly substituted vinylidenecyclopentanes were obtained with good yields, complete selectivity, and excellent functional group tolerance. A plausible mechanism, supported by DFT calculations, involves the oxidative addition of bromoarene to Pd(0), followed by cyclization and reductive elimination. The excellent regio- and stereoselectivity arises from the Cyclization of alkynes and alkenes bearing a tethered nucleophilic group constitutes a direct and effective strategy for the construction of a range of carbo- and heterocyclic scaffolds ,7,8,9,105-exo-dig cycloisomerization and cyclization/coupling processes catalyzed by carbophilic Lewis acids is the low reactivity of substrates derived from internal alkynes. As the challenge arises from steric interactions of metal catalyst with a substituent at the alkyne terminus, shorter homologues cyclizing through a 5-endo-dig manifold, and thus lacking such constrains, undergo facile cyclization , 256(27), 230(24), 229(97), 228(59), 197(23), 170(24), 169(100), 168(27), 141(27), 128(16), 115(17), 105(7), 91(27), 77(10), 59(11); HRMS (EI): m/z calcd for C17H20O4 288.1362; found 288.1364."} +{"text": "Cytomegalovirus (CMV) infections continue to be associated with increased morbidity and mortality in Hematopoietic Cell Transplant (HCT) recipients. Treatment of high risk patients with low level viremia may reduce overall duration of therapy and reduce complications. CMV T Cell Immunity Panel (TCIP) may help identify patients at high risk of CMV reactivation prior to developing clinically significant CMV infection (CS-CMVi). Our study aims to identify HCT recipients with low level CMV viremia who are at high risk of CMV reactivation with the use of CMV-TCIP while on or off letermovir for prophylaxis. We enrolled in a prospective cohort study allogeneic HCT recipients (excluding cord blood transplantation) with low level of CMV viremia on no therapy, starting October 2019. CMV TCIP assay was performed at enrollment, weeks 1, 2, 3, 4, 6 and 8. CMV TCIP results were interpreted as negative or positive based on percentage of interferon gamma producing CD4+ or CD8+ CMV specific T cells. The primary endpoint was progression to a CS-CMVi. We are presenting the results of the first 30 patients with data up to 4 weeks from enrollment.P >0.05) .Among the 30 patients, 73% were on letermovir for CMV prophylaxis. Majority of the patients were \u2265 40 years old (77%), male (63%), received transplant for AML (40%), were in complete remission at time of transplant (23%) and received cyclophosphamide (90%). The median time from transplant to enrollment was 77 days (IQR 37-172) (table 1). At enrollment, 10 (33%) patients had a positive CMV TCIP, 10 (33%) had a negative CMV TCIP, and 10 (33%) had an uninterpretable CMV TCIP result due to inability to quantify T cells (table 1). Four (13%) patients developed CS-CMVi; 3 of these patients had a negative TCIP and 1 had unquantifiable CMV TCIP . The mean percentage of CMV specific CD4+ and CD8+ interferon producing cells was 1.76% (SD 2.24) and 9.37% (SD 11.35) for those on letermovir and 2.09% (SD 2.05) and 3.97% (SD 5.24) off letermovir respectively marked.Abbreviations: CMV: CytomegalovirusTable 1. Baseline characteristics of patients enrolledAbbreviations: CMV: Cytomegalovirus; TCIP: T cell immunity panel; IQR: Interquartile rangeOur results demonstrate the value of the CMV TCIP in identifying high risk HCT recipients prior to developing CS-CMV infection. Fareed Khawaja, MBBS, Eurofins Viracor (Research Grant or Support) Ella Ariza Heredia, MD, Merck (Grant/Research Support) Michelle Altrich, PhD, HCLD, Eurofins Viracor (Employee) Roy F. Chemaly, MD, MPH, FACP, FIDSA, AiCuris (Grant/Research Support)Ansun Biopharma Chimerix Clinigen (Consultant)Genentech Janssen Karius (Grant/Research Support)Merck Molecular Partners Novartis (Grant/Research Support)Oxford Immunotec Partner Therapeutics (Consultant)Pulmotec Shire/Takeda Viracor (Grant/Research Support)Xenex (Grant/Research Support)"} +{"text": "Solid organ transplant (SOT) is a growing option for patients with end-stage organ diseases. Immunosuppressive therapy (IT) is utilized in this population to minimize risk of allograft rejection, which increases infection risk particularly of atypical pathogens that can complicate the infection-related diagnostic journey. The purpose of this analysis was to evaluate baseline clinical characteristics and microbiological testing utilization patterns among a cohort of patients with a history of SOT and IT.st observation of SOT status and IT. Subsequent inpatient admissions for suspected infection were analyzed.This retrospective cohort study utilized a US hospital-based, service-level database. Patients were selected from a subsample of database facilities utilizing plasma microbial cell-free DNA diagnostic assays. The study period was 1/1/2017-3/21/2020. Eligible patients were identified by 1st 48 hours of presentation (4 [1-7] vs. 2 [1-5]). We identified 749 patients with SOT history and use of IT, 56.4% were male, and the mean age was 52.8 (18.7) years. Kidney was the most prevalent transplant category (49.1%), followed by liver (14.1%), lung (10.9%), and heart (10.3%), and 9.7% were multi-organ. Patients experiencing multiple transplants had the most chronic conditions with a mean Elixhauser comorbidity score of 26.3 (14.7). The median length of stay was 4 [3-7] days. The median number of tests per encounter was 6 [IQR=3-11]. Culture was the most utilized test category (2 [1-4]). Blood culture was the highest utilized culture and overall test at 13.5% of all tests observed, while CMV PCR (7.8%) and multi-panel EIA (2.7%) were the most frequent molecular and antigen tests, respectively. Lung transplant recipients had the greatest utilization of tests overall (9 [3.5-17]) versus other transplant categories (6 [3-10]), consistent with the observed test rate in the 1This analysis suggests that the infection-related diagnostic journey among patients with a history of SOT involves high utilization of microbiological testing, with greater utilization among lung transplant recipients versus other SOT recipients. Variation in clinical characteristics and microbiological testing patterns were observed across SOT categories. T Matthew Hill, PharmD, PhD, Karius, Inc Erick R. Scott, MD, MHS, Karius, Inc Sivan Bercovici, PhD, Karius (Employee)"} +{"text": "Although cigarette smoking has declined over the past several decades, a diverse landscape of combustible and noncombustible tobacco products has emerged in the United States differences in current cigarette smoking by urban-rural designation among each racial and ethnic group, changes in prevalence of tobacco product use during 2019 and 2020, and changes in average number of cigarettes smoked per day during 2005\u20132020. SAS-callable SUDAAN software was used to conduct all analyses. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.Among U.S. adults in 2020, 19.0% (estimated 47.1 million) currently used any tobacco product, 15.2% (37.5 million) used any combustible tobacco product, and 3.3% (8.1 million) used two or more tobacco products. Cigarettes were the most commonly used tobacco product . Prevalence of use and estimated number of users of other tobacco products in 2020 was as follows: e-cigarettes , cigars , smokeless tobacco , and pipes . Among pCurrent cigarette smoking prevalence was higher among persons who resided in rural areas than among those who resided in urban areas among non-Hispanic Black (38% higher), Hispanic (38% higher) and non-Hispanic White (62% higher) adults; in contrast, prevalence among non-Hispanic Asian adults was 32% higher among those in urban areas (p<0.05) . Among aThe prevalence of any current tobacco product use was higher among 1) men (24.5%) than among women (13.9%); 2) persons aged 25\u201344 years (22.9%), 45\u201364 years (20.4%), or 18\u201324 years (17.6%) than among those aged \u226565 years (11.8%); 3) non-Hispanic AI/AN (34.9%), non-Hispanic Other (29.1%), non-Hispanic White (21.1%), and non-Hispanic Black (19.4%) adults than among Hispanic (11.7%) and non-Hispanic Asian (11.5%) adults; 4) persons living in the Midwest (22.0%) or the South (21.1%) than among those living in the Northeast (16.6%) or West (15.0%); 5) persons from rural areas (27.3%) than among those from urban areas (17.7%); and 6) persons with a GED (40.5%) than among those with other levels of education . The preFrom 2019 to 2020 the prevalence of any commercial tobacco product use and use of certain commercial tobacco products decreased, yet nearly one in five adults (47.1 million) continued to use commercial tobacco products. Approximately three quarters of adults who used tobacco products used combustible products, with 30.8 million adults currently smoking cigarettes. Among all tobacco products, cigarettes and other combustible tobacco products are the predominant cause of tobacco-related morbidity and mortality could further aid in reducing disparities in tobacco use used any tobacco product. Cigarettes were the most commonly used tobacco product (12.5%), followed by e-cigarettes (3.7%). From 2019 to 2020, the prevalence of overall tobacco product use, combustible tobacco product use, cigarettes, e-cigarettes, and use of two or more tobacco products decreased.Continued monitoring of tobacco product use and tailored strategies and policies that reduce the effects of inequitable conditions could aid in reducing disparities in tobacco use."} +{"text": "Between 1972 and 1982, 60 patients with histologically proven duct carcinoma in situ (DCIS) without evidence of invasive disease were treated by surgery alone. Treatment was not randomised and was total mastectomy (19), subcutaneous mastectomy (6) or local excision (35). Follow-up was by clinical examination and mammography with a median follow-up of 9 years (range 4-16 years). Twenty-six patients (43%) have recurred locally. The estimated proportion recurrence free at 7 years is 59% (95% CI 46-72%). Local recurrence on the chest wall occurred in one patient having total mastectomy and in the chest wall or nipple in three patients having subcutaneous mastectomy. Twenty-two patients recurred locally in the breast after conservative surgery. The 7-year recurrence-free rates were 94%, 44% and 45% respectively in the three groups. Of those patients who recurred locally 14/26 (54%) did so with invasive disease. Of the 34 who did not develop local recurrence, two developed metastases. The only factor which correlated with local recurrence and invasive local recurrence on multivariate analysis was conservative surgery (hazard ratio 4.71 (1.59-14.0), P = 0.001, and 4.05 (1.00-18.7), P = 0.03, respectively). DCIS can be an aggressive local disease and local excision may be inadequate treatment."} +{"text": "The pNR-2/pS2 protein is regulated by oestrogens in breast cancer cell lines. This report describes a systematic survey of pNR-2/pS2 expression in a number of common epithelial tumours. Expression was evaluated immunohistochemically in an archival series using antisera raised against the C-terminus of the pNR-2/pS2 protein. Expression of pNR-2/pS2 by malignant epithelial tumours was widespread. Intense immunohistochemical staining was found in tumour cells in a proportion of pancreatic (6/8), large intestinal (7/12), gastric (9/16) and endometrial (4/12) carcinomas. Positive staining for the pNR-2/pS2 protein was also found in both benign and malignant ovarian epithelial tumours and was very significantly associated with mucinous differentiation (P less than 0.00001). Small numbers of carcinomas of bladder (2/10) and prostate (2/7) showed less intense staining and single examples of cervical carcinoma (1/7) and lung carcinoma (1/19) stained positively. None of the renal carcinomas (0/16) examined stained positively. Positive staining showed no correlation with gender. Although there are reports of oestrogen receptor expression in most of the tumour types considered, the possibility of other regulatory influences must also be considered. The pNR-2/pS2 protein may well have a more general role in human epithelial neoplasia than hitherto realised."} +{"text": "Phospholipid metabolism of human breast cancer was studied by 31P magnetic resonance spectroscopy (MRS). In vivo localised 31P MR spectra were obtained from the tumour alone using phase modulated rotating frame imaging. For 31 tumours, median (range) phosphomonoester (PME) to ATP ratio was 1.48 (0.57-3.78) and phosphodiester (PDE) to ATP ratio was 1.65 (0.44-3.89). DNA index and S phase fraction (SPF) were measured by flow cytometry of paraffin embedded tissue. Twelve (39%) tumours were diploid and 19 aneuploid. Median (range) SPF for 29 assessable tumours was 5.3% (0.6-28%), with significantly greater median SPF for aneuploid tumours (9.3%) than diploid . There was a significant association between PME/ATP and SPF (P = 0.03) due to a significant correlation for aneuploid tumours (P = 0.01). High resolution 31P MRS of extracts from 18 tumours (including seven studied in vivo) demonstrated that the PME peak consists predominantly of phosphoethanolamine (PE) with a smaller contribution from phosphocholine (PC) (median (range) PE/PC: 3.02 (1.13-5.09)). Changes in PME/ATP were observed for two tumours where tamoxifen stablized disease and may be consistent with the cytostatic effects of this drug."} +{"text": "Lonidamine (LND) is a new anti-cancer drug which interferes with the energy-yielding processes of tumour cells without affecting DNA replication. A total of 69 previously untreated patients with non-small cell lung cancer (NSCLC) entered this study. LND was given orally as a single agent at doses ranging from 450 to 900 mg day-1 until tumour progression . Partial responses (PR) occurred in 7/69 patients (10.1%); 4/25, 1/27 and 2/9 for epidermoid, adenocarcinoma and large cell cancer respectively. PR by stage was 4/10, 1/3, 1/20 and 1/28 for stages I, II, III and IV, respectively. The median duration of response was 303 days . The median survival for the whole group was 261 days. Toxicity was assessed in all patients. No myelosuppression occurred. The main side-effects were myalgia (68%), loss of appetite (23%), asthenia (20%) and testicular pain (13%). Doses above 450 mg day-1 produced more severe side-effects without any improvement in therapeutic activity."} +{"text": "Objective: The aim of this study was investigate the impact of vaginal flora and vaginal inflammation onconception and early pregnancy loss following in-vitro fertilization (IVF).Methods: We enrolled 91 women who were undergoing IVF. At embryo transfer (ET), all of the women hadquantitative vaginal culture, ET catheter-tip culture, and vaginal Gram stain scored for bacterial vaginosis andquantitated for polymorphonuclear leukocytes (PMNs). Conception and early pregnancy loss were comparedwith culture and Gram stain results. Statistical analyses included the Chi-square test, Fisher's exact test andthe Mann\u2013Whitney U-test.Results: The overall live birth rate (LBR) was 30% (27/91), and the rate of early pregnancy loss was 34% (14/41). Inwomen with bacterial vaginosis, intermediate flora and normal flora, the conception rates were 30% (3/10), 39%(12/31) and 52% (26/50), respectively (p = 0.06 for trend). Early pregnancy loss occurred in 33% (1/3), 42%(5/12) and 31% (8/26) of women, respectively . The vaginallog concentration of hydrogen peroxide-producing lactobacilli was 7.3 \u00b1 1.7 in women with a live birth (n = 27)and 4.9 \u00b1 2.5 in those with early pregnancy loss (n = 14) (p = 0.1).Conclusions: IVF patients with bacterial vaginosis and with a decreased vaginal log concentration of hydrogenperoxide-producing lactobacilli may have decreased conception rates and increased rates of early pregnancy loss.A larger prospective treatment trial designed to evaluate the impact on IVF outcomes of optimizing the vaginalflora prior to IVF may be warranted."} +{"text": "Promising clinical results have been obtained with radiolabeled antibodies in lymphoma patients. The higher uptake by lymphomas of 67Gallium (67Ga) compared with monoclonal antibodies makes selective radiotherapy by the widely available 67Ga appealing. However, the gamma radiation of 67Ga used in scintigraphy is considered to be almost non-toxic to lymphoma cells. However, in addition to photon radiation 67Ga emits low energy Auger electrons and 80-90 keV conversion electrons which could be cytotoxic. The objective of the present study was the assessment of radiotoxicity of 67Ga on a lymphoid cell line: U937. Proliferation (MTT-assay) and clonogenic capacity (CFU-assay) were measured after 3 and 6 days incubation with 10, 20 and 40 microCi ml-1 67Ga. Growth inhibition was 36% after 3 days incubation and 63% after 6 days incubation with 40 microCi 67Ga ml-1. Clonogenic capacity was reduced by 51% after 3 days and 72% after 6 days incubation with 40 microCi ml-1 67Ga. A survival curve showed an initial shoulder and became steeper beyond 200-250 pCi cell-1 (low linear energy transfer type). Iso-effect doses of 67Ga and 90Yttrium (90Y) were determined. The iso-effect dose of 40 microCi 67Ga ml-1 (cumulative dose of conversion electrons 306 cGy) was 2.5 microCi 90Y ml-1 (cumulative dose 494 cGy) and the iso-effect dose of 80 microCi 67Ga ml-1 was 5.0 microCi 90Y/ml. The main cytotoxic effect of 67Ga seems to be induced by the 80 keV conversion electrons. We conclude that the conversion electrons of 67Ga have a cytotoxic effect on U937 cells and that in our experiments a 16-fold higher microCi-dose of 67Ga than of 90Y was needed for the same cytotoxic effect. We believe that 67Ga holds promise for therapeutic use."} +{"text": "From November 1977 to July 1983, 82 children with T leukaemia/lymphoma entered a randomised trial of combination chemotherapy and radiotherapy. Twenty-five were designated T lymphoma and 57 T leukaemia, 28 having greater than 100 x 10(9)1(-1) blasts in peripheral blood at diagnosis. Twenty-seven patients with mediastinal primaries who were treated on the companion non-Hodgkin lymphoma (NHL) trial were comparable in all respects to the T lymphoma patients and the results of treatment were therefore combined and analysed together. Overall 4-year survival (48-53%) and failure-free survival (FFS) (37-40%) were similar in all groups except the 28 with T leukaemia and WCC greater than 100 X 10(9)1(-1) (20% and 13%). There was a significant advantage in FFS for patients randomised to receive low dose mediastinal radiation, and this was most marked in patients with T lymphoma ."} +{"text": "Since compensatory hyperplasia promotes experimental carcinogenesis in the gut, we tested the ability of two surgical models of pancreatic growth to promote pancreatic carcinogenesis. Male Wistar rats (n = 60) weighing 250-300 g underwent pancreatobiliary diversion (PBD), 90% small bowel resection (PSBR) or triple transection and reanastomosis of the small intestine (controls). Postoperatively, each group received azaserine (20 mg kg-1 wk-1 i.p.) for 6 weeks. Surviving rats were killed at 6 months, pancreatic wet weight was measured and histological sections were examined for atypical acinar cell foci (AACF), the putative precursor of carcinoma. Median relative pancreatic weight (mg pancreas/g body weight) was 2.20 for controls (n = 18), 4.08 for PSBR (n = 11) (P less than 0.001) and 6.86 for PBD (n = 16) (P less than 0.001). PSBR did not affect the development of acidophilic AACF, but PBD produced an enormous increase in their number per cm3 and a 7-fold increase in their volume (P less than 0.001). Both operations cause pancreatic growth, but only PBD promotes carcinogenesis, possibly because of its unique hormonal effect."} +{"text": "Interstrand cross-linking, repair and lethal effects of (-)-(R)-2-aminomethylpyrrolidine platinum(II) (DWA2114R) were studied in normal human. Fanconi's anaemia (FA) and xeroderma pigmentosum group A (XPA) cells. Interstrand crosslinking by DWA2114R was slower than that by cisplatin (CDDP), since DWA2114R produced mainly Pt(II)-monoadducts after 1 h treatment, followed by progressive interstrand crosslinking to a maximum 5 h post-incubation, while CDDP induced rapidly interstrand crosslinks in approximately 70% DNA during the 1 h treatment, followed by a approximately 30% residual increase. At the maximum rate, DWA2114R was 18 times less interstrand-crosslinking than CDDP on the 1 mM basis. FA cells were specifically defective in the first half-excision of DWA2114R and CDDP-induced Pt(II) interstrand crosslinks, but XPA cells were as proficient as normal cells (t1/2 = 5-7 h). On the contrary, XPA cells were deficient in excision repair of intrastrand crosslinks, but FA cells were normal. In clonogenic survival curves of all types of cells, mean lethal doses (Do) of DWA2114R were an order of magnitude greater than those of CDDP. FA cells were most (3.5 times) sensitive (Do = 25.1 +/- 0.96 microM) and XPA cells were 1.9 times more sensitive (Do = 47.1 +/- 0.17 microM) to DWA2114R than normal cells (Do = 87.6 +/- 5.65 microM). DWA2114R and carboplatin with a cyclobutanedicarboxylato group exhibited almost similar lethal effects on each of normal, FA and XPA strains. FA (Do = 3.44 +/- 0.44 microM) and XPA cells (Do = 3.84 +/- 0.17 microM) were similarly 3-fold more sensitive to CDDP than normal (Do = 9.97 +/- 0.15 microM). On the basis of a single lethal hit (Do), thus DWA2114R and carboplatin effectively killed more FA cells defective in interstrand crosslink repair than XPA cells defective in intrastrand crosslink repair."} +{"text": "The serum levels of CA 19-9 and carcinoembryonic antigen (CEA) were determined in 37 patients with benign colorectal diseases and in 111 patients with newly discovered colorectal carcinomas or clinically verified relapses. In cancer patients, the CA 19-9 level ranged from normal (0-37 U ml-1) to 77,500 U ml-1 whereas all samples but one from patients with benign colorectal diseases had a normal value. CA 19-9 was increased in 46% and 45% of patients with an advanced (Dukes C or D) carcinoma or a verified recidive, respectively. Only one out of 26 patients (4%) with a localized (Dukes A or B) carcinoma displayed an elevated CA 19-9 level (greater than 37 U ml-1). No clear correlation was found between the CA 19-9 and CEA levels. The sensitivity of the CA 19-9 test (36%) was poorer than that of the CEA assay (69%), but the new test was markedly more specific (97% vs 70%) than the CEA assay."} +{"text": "HLA associations were observed in unrelated Malay patients with nasopharyngeal carcinoma (NPC). HLA-B18 was observed in 18/45 (40%) Malay NPC patients compared to 22/167 (13%) Malay normals . The frequency of HLA-B17, one of the antigens associated with Chinese NPC, was also increased among Malay NPC (13/45 29%) compared to controls . Similar to the findings among Chinese NPC, the frequency of B17 was higher in early onset Malay NPC resulting in a higher relative risk (RR = 5.0)."} +{"text": "A novel mechanism of aggregation-induced emission defined as the restriction of the ligand dissociation\u2013aggregation process in the nanocluster range is proposed. 29(BDT)12(TPP)4 NC as a model. By the addition of TPP into an N,N-dimethylformamide solution of Ag29(BDT)12(TPP)4, the PL intensity of the Ag29(BDT)12(TPP)4 NC could be significantly enhanced due to the restricted TPP dissociation\u2013aggregation process. This novel mechanism is further validated by a low-temperature PL study. Different from the significant PL enhancement of the Ag29(BDT)12(TPP)4 NC, the non-dissociative Pt1Ag28(S-Adm)18(TPP)4 NC (S-Adm: 1-adamantanethiol) exhibits a maintained PL intensity under the same TPP-addition conditions. Overall, this work presents a new mechanism for largely enhancing the PL of NCs via modulating the dissociation of ligands on the NC surface, which is totally different from the previously reported AIE phenomena in the NC field.The strategy of aggregation-induced emission (AIE) has been widely used to enhance the photo-luminescence (PL) in the nanocluster (NC) research field. Most of the previous reports on aggregation-induced enhancement of fluorescence in NCs are induced by the restriction of intramolecular motion (RIM). In this work, a novel mechanism involving the restriction of the \u201cdissociation\u2013aggregation pattern\u201d of ligands is presented using a Ag The PL intensity of the Ag29(BDT)12(TPP)4 NC in the solid or crystal state is significantly higher than that in the solution state. Considering the particularly close packing of Ag29(BDT)12(TPP)4 as well as the existence of \u03c0\u00b7\u00b7\u00b7\u03c0 and C\u2013H\u00b7\u00b7\u00b7\u03c0 interactions between the ligands, the AIE process is unlikely caused by the RIM completely in the case of the Ag29(BDT)12(TPP)4 NC. Furthermore, electrospray ionization mass spectrometry (ESI-MS) and 31P nuclear magnetic resonance (31P NMR) analyses are performed on the Ag29(BDT)12(TPP)4 NC, and they reveal several dissociated ligands from Ag29(BDT)12(TPP)4; that is, the mechanism of AIE in Ag29(BDT)12(TPP)4 could be the restriction of the TPP dissociation\u2013aggregation process. To prove the mechanism, different concentrations of TPP molecules are added to the dissociative Ag29(BDT)12(TPP)4 and non-dissociative Pt1Ag28(S-Adm)18(TPP)4 NC solution. Resultantly, the PL intensity of Ag29(BDT)12(TPP)4 is significantly enhanced by the addition of TPP owing to the restriction of the TPP dissociation\u2013aggregation process 12(TPP)x NCs, summarized in 1Ag28(S-Adm)18(TPP)4 shows nearly the same intensity of PL after the addition of TPP. In addition, the temperature-dependent PL of the Ag29(BDT)12(TPP)4 NC shows two segments of rising curves, which represent both the restriction of the TPP dissociation\u2013aggregation process (the QY varies from 0.9% to 22.5%) and the quenched thermal vibration process (the QY varies from 22.5% to about 100%). However, the non-dissociative Pt1Ag28(S-Adm)18(TPP)4 only exhibits a quenched thermal vibration process (the QY varies from 9.3% to \u223c100%).Herein, a novel AIE pattern (the restriction of the ligand dissociation\u2013aggregation process) is discovered using a Ag23, 99%, metal basis), hexachloroplatinic(iv) acid , triphenylphosphine , benzene-1,3-dithiol , 2,4-dimethylbenzenethiol , 1-adamantanethiol , sodium borohydride , methylene chloride , acetic ether , methanol , ethanol and N,N-dimethylformamide were purchased from Sigma-Aldrich and used without further purification. Pure water was purchased from Wahaha Co. Ltd. All glassware was thoroughly cleaned with aqua regia (HCl\u2009:\u2009HNO3 = 3\u2009:\u20091 v/v), rinsed with copious amounts of pure water, and then dried in an oven prior to use.All chemicals including silver nitrate (AgNO29(BDT)12(TPP)4 NC was performed following a method reported by Bakr and coworkers.27The synthesis of the Ag1Ag28(S-Adm)18(TPP)4 NC was performed according to our previous work.43The synthesis of the Pt1Ag28(BDT)12(TPP)4 NC was performed following a method previously reported by Bakr and coworkers.44The synthesis of the Pt29(BDT)12(TPP)4 (or Pt1Ag28(S-Adm)18(TPP)4 or Pt1Ag28(BDT)12(TPP)4) NC was dissolved in 10 mL of DMF. Then the TPP ligand was added to the DMF solution with the molar ratio of TPP/NC ranging from 0.1 to 10. The PL spectra were then measured for these mixed solutions.10 mg of Ag29(BDT)12(TPP)4 (or Pt1Ag28(S-Adm)18(TPP)4) NC was dissolved in 10 mL of DMF. Then the solutions were cooled to different temperatures and the PL spectra were measured.10 mg of AgAll UV-vis absorption spectra of NCs dissolved in DMF were recorded using an Agilent 8453 diode array spectrometer, with the background corrected by using a DMF blank. Solid samples were dissolved in DMF to make a dilute solution, which was transferred to a 1 cm path length quartz cuvette for spectral measurements.\u20131.PL spectra were measured on an FL-4500 spectrofluorometer with the same optical density (OD) of \u223c0.05. In these experiments, the NC solutions were prepared in DMF at a concentration of less than 1 mg mLAbsolute quantum yields (QYs) were measured with dilute solutions of NCs (0.05 OD absorption at 445 nm) on a HORIBA FluoroMax-4P.31P NMR spectra were acquired using a Bruker 600 Avance III spectrometer equipped with a Bruker BBO multinuclear probe . To achieve a sufficient signal-to-noise ratio, the 31P NMR spectra were recorded by collecting 1k scans with a recycle delay time of 5 s.Electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS) measurements were performed on a MicrOTOF-QIII high-resolution mass spectrometer.329(BDT)12(TPP)4 NC was prepared following a method previously published by Bakr and coworkers.29(BDT)12(TPP)4.29(BDT)12(TPP)4 is composed of a three-layer configuration: the icosahedral Ag13 kernel is enclosed by four Ag3S6 motifs to form a Ag25(BDT)12 architecture (it should be noted that the four Ag3S6 motifs are united by the BDT ligands); the Ag25(BDT)12 architecture is further capped by four Ag\u2013TPP units. 29(BDT)12(TPP)4, which exhibits broad, multiband optical absorption bands centred at 345, 360, 445, and 510 nm. Furthermore, Ag29(BDT)12(TPP)4 possesses an emission band centred at 642 nm 12(TPP)4 is only 0.9%, which is too weak to be perceived by the naked eye (29(BDT)12(TPP)4 NC exhibits enhanced fluorescence in the solid or crystal state (29(BDT)12(TPP)4. Previously, the RIM pattern was believed to be the primary cause either in the solvent- or ion-induced AIE process.It is noteworthy that the PL QY of Agaked eye .27,28 Inal state . These o29(BDT)12(TPP)4 NC is analyzed in order to gain insight into the aforementioned solvent evaporation-induced AIE. In the solution state, the energy dissipation of photo-excited Ag29(BDT)12(TPP)4 includes two pathways: (i) non-radiative transitions (mainly affected by intra-molecular vibrations), and (ii) radiative transitions (through luminescence). 29(BDT)12(TPP)4 NC, which comprise rota-vibrations and swing-vibrations. However, the considerable close-packing of the structural configuration 12(TPP)4 NC in solution is not thermal vibration, because the architecture of the Ag29(BDT)12(TPP)4 NC exhibits strong rigidity. Consequently, the AIE of the Ag29(BDT)12(TPP)4 NC is unlikely induced by the RIM pattern completely.The crystal structure of the Agin total . In addi29(BDT)12(TPP)4 NC? From the ESI-MS spectrum of Ag29(BDT)12(TPP)4 (29(BDT)12(TPP)x (x = 0\u20133) and the dissociated TPP ligands. For instance, the highest signal in the ESI-MS spectrum is the peak of Ag29(BDT)12(TPP)2, which is generated by dissociating two TPP ligands of the intact NC. To further validate the TPP dissociation process of Ag29(BDT)12(TPP)4 in the solution state, ESI-MS measurements were also performed on the mixture of Ag29(BDT)12(TPP)4 NC with extra TPP. The spectrum (29(BDT)12(TPP)4 NC compared with the case of the Ag29(BDT)12(TPP)4 NC only (29(BDT)12(TPP)x signals in the sample mixture). Therefore, based on the ESI-MS results, the reversible reaction of the Ag29(BDT)12(TPP)4 NC in solution could be determined to be Ag29(BDT)12(TPP)4 \u2194 Ag29(BDT)12(TPP)3 + Ag29(BDT)12(TPP)2 + Ag29(BDT)12(TPP)1 + Ag29(BDT)12 + TPP (shown in 29(BDT)12(TPP)4 NC are in dynamic dissociation/aggregation. It is suggested that the breaking of coordination bonds would consume energy,29(BDT)12(TPP)4 NC in the solution state. Thus, we speculate that the significantly enhanced PL of the Ag29(BDT)12(TPP)4 NC in the solid or crystal state should arise from the restriction of the TPP dissociation\u2013aggregation process\u2014which inhibits the non-radiative pathways, and thus enhances the radiative pathway (PL). Therefore, the AIE of the Ag29(BDT)12(TPP)4 NC could be induced by the restriction of the ligand dissociation\u2013aggregation process.The above discussion raises an interesting question: what is the essential role of the AIE in the Agshown in . Accordi29(BDT)12(TPP)4 increases the PL intensity rapidly in the beginning, and then it levels off, with the highest PL QY being 11.7%, which is in striking contrast to the weakly luminescent Ag29(BDT)12(TPP)4 NC with no TPP addition (QY = 0.9%). A quantitative test was performed to obtain the relationship between the PL intensity and the amount of TPP added (versus NC) to the DMF solution of Ag29(BDT)12(TPP)4 NC, the PL intensity increases by almost 3 times compared with the initial state. Furthermore, by the further addition of TPP, the QY enhancement gradually becomes steady. Finally, a 13-fold enhancement compared to the initial state is achieved when the amount of added TPP is greater than 2 (molar ratio). The PL intensity at 642 nm is compared . To sum up, the redundant TPP ligands will prevent the TPP dissociation\u2013aggregation process on the nanocluster surface, and then enhance the PL intensity of the Ag29(BDT)12(TPP)4 NC.Considering that the TPP dissociation\u2013aggregation process is a reversible reaction, we are motivated to control the reversible process to control the intensity of PL. As shown in 1Ag28(S-Adm)18(TPP)4 NC 18(TPP)4).1Ag28(S-Adm)18(TPP)4 NC shows a distinct peak at 3637.63 Da (29(BDT)12(TPP)4 NC, the PL intensity of the Pt1Ag28(S-Adm)18(TPP)4 NC maintains a QY of 9.3% no matter how high the TPP amount added to the solution is (1Ag28(S-Adm)18(TPP)4 in CH2Cl2 is 4.9%,1Ag28(S-Adm)18(TPP)4. The PL intensity of the Pt1Ag28(S-Adm)18(TPP)4 NC monitored at 672 nm by fluorescence spectroscopy also indicates the unchanged fluorescence (1Ag28(S-Adm)18(TPP)4 NC does not display any equilibrium dissociation\u2013aggregation process, and thus the addition of TPP would not alter the PL intensity in the solution state. The sharp contrast between the PL variation trends of the Ag29(BDT)12(TPP)4 and Pt1Ag28(S-Adm)18(TPP)4 NCs indicates that the restriction of the ligand dissociation\u2013aggregation process should be the major underlying mechanism of AIE in the Ag29(BDT)12(TPP)4 NC.For comparison, the same TPP-addition experiment was performed on the Pt37.63 Da . Importaution is , top. No1Ag28(S-Adm)18(TPP)4 NC, the TPP-addition experiment was performed on a Pt centrally doped Ag29(BDT)12(TPP)4 NC 12(TPP)4 NC).1Ag28(BDT)12(TPP)4 also exhibits significant enhancement by the addition of TPP (the maximum PL QY was 18.9%), which is similar to the case of Ag29(BDT)12(TPP)4; hence, Pt doping is not the critical factor for PL enhancement with TPP addition. Specifically, the fluorescence intensity (centered at 720 nm) rises rapidly during the initial TPP addition and then levels off once the molar ratio (TPP to Pt1Ag28(BDT)12(TPP)4 NC) is greater than 1.5. A 7-fold enhancement is finally obtained by the addition of TPP to the Pt1Ag28(BDT)12(TPP)4 NC. Considering the same PL enhancement phenomenon of the Pt1Ag28(BDT)12(TPP)4 and Ag29(BDT)12(TPP)4 NCs with the addition of TPP ligands, the difference in the metallic composition is unlikely to be the primary cause for being dissociative or not of these NCs. The major different between the dissociative Ag29(BDT)12(TPP)4 and non-dissociative Pt1Ag28(S-Adm)18(TPP)4 nanoclusters is the outer ligands (BDT vs. S-Adm). The difference of these two ligands largely affects the structure of the metallic kernel and outer complex shell, which is a critical factor in the dissociative/non-dissociative phenomenon 12(TPP)4 as well as the Pt1Ag28(S-Adm)18(TPP)4).Additionally, in order to structurally and compositionally match the Pt31P NMR was performed to validate the TPP dynamic dissociation\u2013aggregation state of the Ag29(BDT)12(TPP)4 and Pt1Ag28(S-Adm)18(TPP)4 NCs. As shown in Fig. S7 and S8,31P NMR spectrum of the Ag29(BDT)12(TPP)4 NC (without the addition of TPP) exhibits a broad peak , which narrows down continuously with the addition of more TPP 12(TPP)4 solution). The notable decrease in the peak width illustrates that the state of P is uniformalized; that is, the TPP dynamic dissociation\u2013aggregation extent of the Ag29(BDT)12(TPP)4 NC in solution is remarkably suppressed with the addition of excess TPP. Furthermore, the maintained width of the 31P NMR peak 18(TPP)4 with or without TPP addition demonstrates the TPP non-dissociated state of the Pt1Ag28(S-Adm)18(TPP)4 NC.29(BDT)12(TPP)4 and Pt1Ag28(S-Adm)18(TPP)4 NCs was monitored. As shown in 29(BDT)12(TPP)4 NC shows two stages: (1) when the temperature is reduced from 293 K to 251 K, the fluorescence shows a 25-fold enhancement , and (2) the fluorescence intensity is increased significantly (a 280-fold boost comparing the 107 K data with the 293 K data) when the temperature is reduced to 107 K, and the UV-vis absorption presents a 2.5-fold enhancement 12(TPP)4 NC appeared to be extremely bright at 107 K, which is in striking contrast to the nearly invisible fluorescence at room temperature (1Ag28(S-Adm)18(TPP)4 NC exhibits only one stage during the same temperature lowering process (1Ag28(S-Adm)18(TPP)4 NC in the final stage is also nearly 100%. Furthermore, it should be noted that the single stage of Pt1Ag28(S-Adm)18(TPP)4 is similar to stage 2 of the Ag29(BDT)12(TPP)4 NC. Therefore, the PL boost in stage 2 of the Ag29(BDT)12(TPP)4 NC as well as in Pt1Ag28(S-Adm)18(TPP)4 should be completely induced by the suppression of thermal energy dissipation (or by the RIM pattern). Additionally, because the TPP dissociation process is much more sensitive to the temperature, the PL enhancement in stage 1 of the Ag29(BDT)12(TPP)4 NC should be mainly caused by the restriction of the TPP dissociation\u2013aggregation process. Because this restriction process is easily influenced by the temperature variation, stage 1 is observed in the relatively high-temperature region (compared with stage 2 in the lower temperature region). To sum up, decreasing the temperature (from r.t. to 251 K) is effective in restricting the TPP dissociation\u2013aggregation process which will lead to a significant enhancement in the fluorescence of the Ag29(BDT)12(TPP)4 NC in the solution state.It is well known that the temperature would significantly influence the dissociation\u2013aggregation dynamic equilibrium process. Thus, to further verify the above-mentioned AIE mechanism, the temperature\u2013PL intensity correlation of the Ag Fig. S11. Accordiperature , insets. process and S12\u202029(BDT)12(TPP)4 NC in the TPP addition process and temperature reduction process is different . In the TPP addition process, we find that the half-peak width (in the 31P NMR spectrum) of the Ag29(BDT)12(TPP)4 NC shows a continual decrease with the addition of TPP; however, the half-peak width in the final state is also wider than that in the Pt1Ag28(S-Adm)18(TPP)4 NC (0.17 versus 0.02 ppm). This suggests that the TPP dissociation\u2013aggregation dynamic equilibrium in the Ag29(BDT)12(TPP)4 NC is not completely prohibited, but is just limited to a certain extent. In other words, the non-radiative pathways caused by the TPP dissociation\u2013aggregation process still exist, even with the excess dose of TPP, which makes it difficult to reach the highest PL (with the non-dissociated state) of the Ag29(BDT)12(TPP)4 NC. By contrast, the non-dissociated state could be easily achieved in the temperature reduction process, and apparently, the Ag29(BDT)12(TPP)4 NC in the non-dissociated state (at 251 K) exhibits a higher PL QY than the final state in the TPP addition process (22.5% versus 11.7%).It should be noted that the PL enhancement of the Ag429(BDT)12(TPP)4 can be significantly enhanced via promoting the aggregation of TPP onto the easy-to-dissociate nanocluster surface. Furthermore, the TPP dissociation\u2013aggregation dynamic equilibrium process of Ag29(BDT)12(TPP)4 is also restrained by reducing the temperature, which results in enhanced photoluminescence intensity (25-fold) in Ag29(BDT)12(TPP)4. In contrast, the same experiments performed on the non-dissociative Pt1Ag28(S-Adm)18(TPP)4 nanocluster do not show any PL enhancement. These different results are not caused by the presence of the Pt dopant, but by the different thiolate ligands (BDT versus S-Adm). The retained PL intensity in the case of Pt1Ag28(S-Adm)18(TPP)4 validates the aforementioned mechanism for the Ag29(BDT)12(TPP)4 nanocluster. Overall, this work presents a new mechanism of aggregation-induced emission in nanoclusters. In addition to previous studies on the enhancement of nanocluster photo-luminescence, this work will hopefully draw greater attention of optical and theoretical chemists to fully understand the photo-luminescence properties of metal nanoclusters. Future work will focus on extending this new AIE mechanism to other fluorescent nanoclusters.In summary, a novel mechanism of aggregation-induced emission is discovered in nanoclusters, which involves the restriction of the ligand dissociation\u2013aggregation process. The fluorescence intensity of AgThere are no conflicts to declare.Supplementary informationClick here for additional data file."} +{"text": "Mutations involving TET2 (4q24) have widely been reported in the context of age-related clonal hematopoiesis (~10% >80 years of age)2, and hematological malignancies such as myelodysplastic syndromes (MDS 5\u201320%), myeloproliferative neoplasms (MPN~15%), chronic myelomonocytic leukemia (CMML ~60%), acute myeloid leukemia (AML 8\u201330%), and T and B cell lymphoproliferative disorders5. In CMML, thus far, clonal TET2 mutations in the absence of clonal ASXL1 mutations (ASXL1wt/TET2mt) have been associated with favorable outcomes6. Conversely, mutations in TET1 (10q21.3) and TET3 (2p13.1) are extremely infrequent with a large study of 408 MPN, CMML, and AML patients demonstrating no identifiable mutations in these genes3. In a recent study, whole exome sequencing was performed in 49 CMML patients resulting in the detection of two loss-of-function, subclonal, TET3 mutations (R148H and S1708fs), both in patients with co-existing TET2 mutations7. ASXL2 mutations were recently described in adult and pediatric patients with t/core binding factor AML (RUNX1\u2013RUNX1T1) (~20%) and were associated with a higher cumulative incidence of relapse8. In MDS/MPN overlap syndromes including CMML, thus far, the frequency and prognostic impact of ASXL2 mutations remain unknown. We carried out this study to estimate the frequency and clinical correlates of TET1, TET3, and ASXL2 mutations in patients with MDS/MPN overlap syndromes.Ten Eleven Translocation (TET) proteins are a family of dioxygenases that catalyze the oxidation of 5-methyl-cytosine (5mC) to 5-hydroxymehylcytosine (5hmC), 5-formlycytosine (5fC), and 5-carboxylcytosine (5caC)n\u2009=\u200930) and MDS/MPN-Unclassifiable were included in the study9. The median age was 73 years and 66% were male. All patients had bone marrow (BM) biopsies and cytogenetic studies performed at diagnosis. Target capture-based next generation sequencing (NGS) was carried out on diagnostic BM DNA from all 83 patients for the complete coding regions of the following 42 genes: TET1, TET2,TET3, DNMT3A, IDH1, IDH2, ASXL1, ASXL2, ATM, EED, EZH2, JARID2, SUZ12, BCOR, BCORL1, STAG2, GATA2, TERC, TERT, SRSF2, SF3B1, ZRSR2, U2AF1, PTPN11,PHF6, Tp53, SH2B3, RUNX1, CBL, NRAS, KRAS, JAK2, CSF3R, FLT3, KIT, CALR, MPL, NPM1, CEBPA, IKZF1, ETNK1, and SETBP1 by previously described methods6. Paired-end indexed libraries were prepared from individual patient DNA using the NEBNext Ultra Library prep protocol on the Agilent Bravo liquid handler. Capture libraries were assembled according to Nimblegen standard library protocol. Base-calling was performed using Illumina\u2019s RTA version 1.17.21.3. Genome_GPS v4.0.1 (formerly named as TREAT) was employed to analyze the data10. Specific variants were included if they were cited by the Catalog of Somatic Mutations in Cancer database and/or if they were found at less than 0.1% by the Exome Aggregation Consortium and not associated with a COSMIC identifier. Previously annotated single-nucleotide polymorphisms (http//www.hapmap.org) in these genes were excluded. For ASXL1, only frameshift and nonsense mutations were considered pathogenic11.Eighty three patients meeting the 2016 World Health Organization (WHO) criteria for CMML who had presented with monocytosis and thrombocytopenia11. BM NGS analysis revealed a TET3K1760del , with an additional PHF6F172Lfs*46 (88%) mutation. He is being treated with 5-azacitidine and at last follow up (15.5 months) remains in a morphological complete remission (CR) after 10 cycles of therapy. Patient two was an 80-year-old female with CMML-0 and normal cytogenetics (MMM\u2014high risk), who had presented with monocytosis and circulating immature myeloid cells. BM NGS at diagnosis identified TET3Y473* (43%) with a coexisting TET1Q683 (46%) mutation (previously cited as pathogenic shown in Table ASXL1G646Wfs*12 (26%) and PTPN11N308D (14%). She received supportive care and died within a month of diagnosis without evidence for leukemic transformation.Overall, we observed seven patients (5 CMML 17%] and 2 MDS/MPN-U [4%]) with mutations and/or VUS involving 7% and 2 ASXL2 mutations or VUS in four patients (3 MDS/MPN-U [6%] and 1 CMML [3%]). Of these, two patients with MDN/MPN-U harbored loss-of-function ASXL2 mutations. Patient one was a 67-year-old male with trisomy 21 who had presented with transfusion-dependent anemia and thrombocytopenia. BM NGS at diagnosis identified ASXL2S634* (20%) and SRSF2R94dup (39%). He was treated with 5-azacitdine and had no response after four cycles. He died shortly thereafter with no evidence for leukemic transformation. Patient two was a 75-year-old female with MDS/MPN-U and trisomy 8 and trisomy 9, who had presented with transfusion-dependent anemia. BM NGS at diagnosis identified ASXL2P969Cfs*10 (22%), RUNX1R237K (38%), and SRSF2P95_R102del (15%). She was treated with transfusional supportive care and was lost to follow-up.We identified TET1, TET3, and ASXL2 mutations can be seen in patients with MDS/MPN overlap syndromes. TET1 and TET3 mutations were seen exclusively in CMML, were found to coexist with each other (TET1 and TET3), and occurred independent of TET2 mutations. ASXL2 mutations were seen in MDS/MPN-U, were associated with numerical chromosomal aberrations, and occurred independent of ASXL1 mutations. The current study was limited by a small number of informative cases to opine on clinical correlates and survival outcomes. Studies exploring the functional redundancy of TET1 and TET3 mutations with TET2 activity, the impact of TET1, TET3, and ASXL2 mutations on global and sequence-specific 5-mC and 5-hmC levels and post-translational histone modifications (H3K27me3), and the impact of these mutations on survival are currently being planned.Our study reveals that although uncommon, loss-of-function"} +{"text": "S1 Movie3D-SIM of NMJ12 boutons from third instar larvae labeled for Brp (green), pMad (red), and Neto (blue).(MOV)Click here for additional data file.S2 Movie(MOV)Click here for additional data file.S3 Movie(MOV)Click here for additional data file.S4 Movie3D-SIM of NMJ12 bouton from third instar larvae labeled for Brp (green), pMad (red), and Neto (blue).(MOV)Click here for additional data file.S5 MovieScale bars: 100 nm.(MOV)Click here for additional data file."} +{"text": "The study reported an acceptable safety and tolerability profile and an overall response rate of 83% (5/6).2 ELOQUENT-2 (NCT01239797) is a phase 3, international, randomized clinical trial that investigated the efficacy and safety of ELd compared with lenalidomide/dexamethasone (Ld) in patients with RRMM who had received one to three previous therapies.3 Patients were randomized 1:1 to ELd (n=321) or Ld (n=325). Asian patients comprised 10% (64/646) of the overall population, of which 94% (60/64) were enrolled from Japan.Elotuzumab is a humanized immunoglobulin G1 immunostimulatory monoclonal antibody targeted against signaling lymphocytic activation molecule F7 (SLAMF7).n=12; Ld, n=5). The most common reason for discontinuation was disease progression. Eighty-four percent (26/31) of ELd patients tolerated \u2a7e90% of the planned elotuzumab dose. The median ) progression-free survival was 22.2 (17.5\u2013not estimated (NE)) months in the ELd group and 18.5 (11.1\u201321.2) months in the Ld group. The hazard ratio (HR) was 0.51 (95% CI: 0.25\u20131.06), representing a 49% reduction in the risk of disease progression or death in patients treated with ELd. The rate (95% CI) of progression-free survival in the ELd and Ld groups, respectively, was 74% (55\u201386%) and 66% (45\u201380%) at 1 year, and 48% (29\u201365%) and 18% (7\u201334%) at 2 years , with follow-up of 3 years, 40% (24/60) of patients had died: 39% (12/31) in the ELd group and 41% (12/29) in the Ld group. Median overall survival was not reached. The interim HR (95% CI) for overall survival was 0.81 (0.35\u20131.87). One-year survival rates (95% CI) among ELd and Ld patients, respectively, were 100% (NE\u2013NE) and 97% (78\u2013100%), 2-year survival rates were 90% (73\u201397%) and 86% (67\u201394%), and 3-year survival rates were 68% (48\u201381%) and 64% (44\u201379%).2 Drug-related adverse events (AEs) of any grade were reported in 97% (30/31) of patients in the ELd group and 97% (28/29) in the Ld group (7 Four patients (13%) in the ELd group reported infusion reactions, which were pyrexia (four patients), asthenia (one patient), chills (one patient) and headache (one patient). All were grade 1 and none led to discontinuation of study medication.Although there are some limitations to this subpopulation analysis\u2014the small sample and patient demographics, including the greater number of patients with high-risk cytogenetic profiles del(17p) and t in the Ld group\u2014ELd demonstrated efficacy in the Japanese cohort of ELOQUENT-2, similar to the high response rates and durable responses observed in the Japanese phase 1 study.Ld group . There wLd group . SeriousLd group . AEs leaInfections occurred in 81% (25/31) of the ELd group and 79% (23/29) of the Ld group . There w3 AEs were manageable and the safety profile was similar to the global study. Although median overall survival has not been reached, preliminary evaluation suggests a benefit with elotuzumab. These results suggest that elotuzumab is a feasible new treatment option in Japanese patients with RRMM, with potential to provide durable responses.In conclusion, Japanese patients treated with ELd experienced prolonged progression-free survival, consistent with the international ELOQUENT-2 population, with a similar overall response rate to the international ELd treatment group."} +{"text": "Scientific Reports7: Article number: 4425410.1038/srep44254; published online: 03142017; updated: 05022017This Article contains errors in Figures 3, 4 and 5 where the graphs were labelled incorrectly. The correct Figures 3, 4 and 5 appear below as"} +{"text": "Bioinformatics (2015) 31(21):3460\u20133467.Author, Sayoni Das, would like to report a typographical error in Equation (2) in the above article.Equation (2), on page 3462, should read as follows:"} +{"text": "Knowing local spectrum and sensitivity for bacterial isolates causing febrile neutropenia is important as starting an appropriate empirical antibiotic therapy is considered a medical emergency in these high-risk patients.A retrospective study of a total of 106 microbiologically febrile episodes in hospitalized adult neutropenic cancer patients, who were admitted from May 2009 to May 2013, at King Fahad Specialist Hospital, Dammam, Saudi Arabia, was conducted.Escherichia coli 30.43 (42/138), Klebsiella pneumonia 14.49% (20/138), Staphylococcus aureus 13.04% (18/138), Sptreptococcus spp. 7.25% (10/138), Pseudomonas spp. 7.25% (10/138), Enterococcus spp. 5.80% (8/138), Staphylococcus spp. 4.35% (6/138), Corynebacterium spp. 3.62% (5/138), Enterobacter spp. 3.62% (5/138), Acinobacter spp. 2.90% (4/138), Serratia marcescens 2.17% (3/138), Proteus mirabilis 1.45% (2). Aeromonas hydrophylia, Citrobacter freundii, Providencia stuartii, Sphingomonas paucimobilis and Stenotropomonas multipholia contributed to 0.72% with one isolate each. For gram-negative Escherichia coli and Klebsiella pneumonia, the extended-spectrum beta-lactamases producers (ESBLs) rates were 38% and 22.22% respectively. For Pseudomonas aerugenosa imipenem-cilastatin resistance rate was 18.84%. For gram-positive bacteria, methicillin-resistant Staphylococcus aureus (MRSA) rate was 28.62%. The vancomycin-resistant Enterococci (VRE) rate was 1.18%.Among 106 microbiologically documented febrile neutropenic episodes, the majority of malignancies were solid tumors accounting for 53.8% (57/106) and hematological malignancies accounted for 46.23% (49/106). The most common malignancies were non-Hodgkin\u2019s lymphoma 19.81% (21/106) followed by acute myeloid leukemia 15.09% (16/106), then colorectal cancer 13.21% (14/106), pancreatic cancer and acute lymphoblastic leukemia accounting for 5.66% (6/106) each, multiple myeloma 4.72% (5/106), gall bladder cancer 3.77% (4/106), and lung cancer 2.83% (3/106). A total of 138 bacterial isolates were identified. The overall prevalence of gram-negative bacteria was 65.94% (91/138) and for gram-positive bacteria was 34.06% (47/138). The most common bacterial isolation sites were blood 33.32% (46 isolates), urine 29.71% (41 isolates), wound 19.55% (27 isolates), body fluids 9.41% (13 isolates) and sputum 7.96% (11 isolates). The most predominant pathogens were Escherichia coli and Klebsiella pneumonia with high ESBLs rates being the most common pathogens. Blood stream infections followed by urinary tract infections were the most common sites of infection. The use of initial antibiotic therapy in febrile neutropenic episodes should be based on local bacterial spectrum and susceptibility/sensitivity patterns to prevent treatment failure with increased morbidity and mortality.Gram-negative bacteria were more prevalent as a cause of infection in adult cancer patients with febrile neutropenia at our institution, with Fever may be the only manifestation of underlying infections following chemotherapy treatment in cancer patients [Febrile neutropenia is an adverse effect and serious complications of cytotoxic chemotherapy treatment in cancer patients. Oral temperature \u2265 38.3 \u00b0C or \u2265 38 \u00b0C for more than 1 h, when absolute neutrophill count < 500 cells/mmpatients . SpecifiInfection remains the principal complication in netropenic cancer patients. During 1960s and 1970s, 80% of mortality in hematological malignancies was due to infection . NowadayIn the 1970s gram-negative pathogens were prevailing later in 1980s and 1990s the gram-positive bacteria were emerging . The IntRecently the etiology of infecting pathogens changed again. Several studies from United States and Europe reported the re-emergence of gram-negative bacteria in neutropenic cancer patients , 11.The antimicrobial therapy must be initiated as soon as the infection is suspected in febrile neutropenic patients . Older rOver the past two decades, the antibiotic resistance patterns have changed in both gram-positive and gram-negative pathogens that cause infections in febrile neutropenic patients . The emeIn our literature review, we found limited numbers of studies addressing bacterial spectrum, isolation sites and susceptibility patterns in febrile neutropenic patients in Saudi Arabia, and our study is the first comprehensive report to address these issues , 15.3 or predicted decrease below 500 cells/mm3 during the next 48 h; 3) having a single oral temperature measurement of \u2265 38.3 \u00b0C (101 \u00b0F) or a temperature of \u2265 38.0 \u00b0C (100.4 \u00b0F) sustained over 1 h period; 4) having known malignancies; 5) patients with presumed infectious cause of fever were included as high risk. The definition of fever neutropenia was based on the Infectious Diseases Society of America (IDSA) and National Comprehensive Cancer Network (NCCN) clinical guidelines in neutropenic fever in cancer patients. All the data were collected from electronic hospital information system, MedicaPlus. All microbiology reports were as per Clinical and Laboratory Standard Institute (CLSI) guidelines.A retrospective study was conducted on the bacterial spectrum, isolation sites and susceptibility patterns of pathogens in adult febrile neutropenic patients hospitalized between May 2009 and May 2013 at the King Fahad Specialist Hospital, a referral hospital providing tertiary care for the Eastern province of Saudi Arabia, with Oncology and Transplant as core competencies. The study was approved by the hospital IRB committee. The patients were included if they met the following inclusion criteria: 1) male and female over the age of 18 years; 2) presence of neutropenia of the infections were in patients with solid tumours and 46.23% (49/106) were in patients with hematological malignancies. The distribution of malignancies showed that non-Hodgkin\u2019s lymphoma 19.81% (21/106) was the commonest, followed by acute myeloid leukemia 15.09% (16/106), colorectal cancer 13.21% (14/106), breast cancer 12.26% (13/106) and acute lymphoblastic lymphoma and pancreatic cancer 5.66 (6/106) each , 2.Overall 138 organisms were isolated. In solid tumors, gram-negative organisms accounted for 71.05% (54/76) of the total infections, while gram-positive organisms accounted for 28.95% (22/76) where as in hematological malignancies, gram-negative organisms accounted for 59.68% (37/62), and gram-positive organisms accounted for 40.32% (25/62) .The most common source of bacterial isolation sites was blood stream infections 33.33% (46/138) followed by urine 29.71% (41/138), wound 19.56% (27/138), body fluids 9.42% (13/138) and sputum 7.97% (11/138) , Fig. 3.Gram-negative organisms attributed to 16.7% (23/138) of blood stream infections and 25.36% (35/138) of urinary tract infections while gram-positive organisms accounted for 16.66% (23/138) of the blood stream infections and 10.86% (15/138) of wound infections , Fig. 3.Escherichia coli was the most predominant isolate overall accounting for 30.43% (42/138), Klebsiella pneumonia accounted for 14.49% (20/138), Pseudomonas species 7.25% (10/138), Streptococcus species 7.25% (10/138), Enterococcus species 5.8% (8/138) and Staphylococcus aureus 4.35% (6/138) ( (6/138) .In our study, the majority of pathogens were gram-negative organisms accounting for 65.94% (91/138) of total isolates, while gram-positive organisms accounted for 34.06% (47/138) .Escherichia coli showed the following susceptibility patterns: imipenem-cilastatin (99.86%), amikacin (91.6%), piperacillin-tazobactam (83.15%) and ceftriaxone (62.06%); ESBLs rate was 38%. While Klebsiella pneumonia showed the following susceptibility patterns: imipenem-cilastatin (98.96%), amikacin (95.24%), ciprofloxacin (75.42%) and ceftriaxone (77.78%); ESBLs rate was 22.22%. The Pseudomonas aeruginosa isolates showed the following susceptibility patterns: amikacin (88.92%), ciprofloxacin (82.62%), piperacillin-tazobactam (82.28%) and imipenem-cilastatin (81.16%). Acinobacter baumanii showed high resistance to ciprofloxacin (65.5%) and imipenem-cilastatin (56.65%).We examined the susceptibility patterns of the predominant gram-negative and gram-positive pathogens. Among gram-negative pathogens, Staphylococcus aureus (MRSA) rate was (28.62%). Enterococcus showed vancomycin-resistant rate in 1.2% of isolates. For gram-positive organisms, methicillin-resistant Infection is a most common complication of chemotherapy, and it causes morbidity and mortality in neutropenic cancer patients. Fever may be the only indication of infection in febrile neutropenia. Bacterial infections are common in this population. In order to treat effectively, the knowledge of likely pathogens and local bacterial spectrum is very important .Pseudomonas aerugenosa are more predominant in warmer climates [In the past two decades, there was a shift in the etiology of bacterial infections in febrile neutropenic patients towards gram-positive organisms accounting for as much as 70% in various reports , 7, 10. climates .Recently, the bacterial etiology has changed again from gram-positive to gram-negative organisms. Many studies from different parts of the world showed this change of trend , 20-22 aIn our study of the etiology of bacterial infections in febrile neutropenic patients, gram-negative pathogens (65.94%) accounted for almost two-thirds of bacterial infections whereas gram-positive organisms were identified in 34.06%. Our findings are similar to other studies in our geographical region, pointing to the importance of covering gram-negative organisms empirically according to the most likely pathogens, and local sensitivity data in this high-risk group of patients , 18.Our data provide a greater emphasis on the importance of local data in managing patients as described in the literature and a combination of an antipseudomonal beta-lactam agent and an aminogylcoside empirical regimen was adapted in our hospital according to our data; vancomycin was added for patients with MRSA risk factors.There are many studies showing the importance of geographical location in bacterial isolation sites , 21, 23.Our study showed similar trends of site of isolation as discussed in the above studies. The most predominant isolation sites were blood stream 33.32%, urine 29.71%, wounds 19.55%, body fluids 7.96%, and from sputum 7.96%.Acinobacter and Pseudomonas aerugenosa, which makes treatment of these infections more difficult [Extended-spectrum \u03b2-lactamase (ESBL)-producing bacteria have become a serious problem in many different geographical regions. Carbapenems are the corner stone of treatment for these organisms, and because of its increase usage for empirical therapy, the risk of selecting resistant organisms is increasing (carbapenem-producing organisms). Many centers are also reporting increased rates of multidrug-resistant gram-negative bacteria such as ifficult . Studiesifficult .Escherichia coli (38%) and Klebsiella pneumonia (22.22%) and increased imipenem-cilastatin resistance among Pseudomonas aerugenosa (18.84%); MRSA rate was 28.72%. This higher than reported rate of ESBLs in our hospital compared to the published rates in the region is probably due to the nature of our high-risk cancer patients, recurrent hospitalizations, and prior use of antimicrobials and the increased use of antibiotics for prophylaxis especially flouroquinolones [In our study we found high rates of ESBLs among inolones .In conclusion, our study shows similar results with international studies in overall prevalence of gram-negative organisms and their isolation sites but different trends in bacterial etiology and susceptibility patterns. Local data for bacteria causing infections in febrile neutropenic patients are needed to help in selecting appropriate empirical antimicrobial therapy."} +{"text": "Streptococcus pneumoniae, several new serotypes were identified since the introduction of pneumococcal conjugate vaccines (PCVs). A decrease of the 6B-2 variant among invasive pneumococcal disease (IPD), but not 6B-1, was noted post conjugate vaccine introduction, underpinned by a decrease of CC273 isolates. Serotype 6C was associated with adult IPD and increased in this age group representing two lineages (CC315 and CC395), while the same lineages expressed other serogroup 6 serotypes in children. Taken together, these findings suggest a potential cross-protection of PCVs against serotype 6C IPD among vaccinated children but not among adults. Serotype 6A became the most important serogroup 6 serotype in children but it decreased in adult IPD. No other serogroup 6 serotypes were detected, so available phenotypic or simple genotypic assays remain adequate for distinguishing serotypes within serogroup 6 isolates.Although serogroup 6 was among the first to be recognized among An adThe 7-valent PCV (PCV7), which includes serotype 6B, was introduced in Portugal in 2001. However, PCV7 was not included in the National Immunization Plan so its uptake increased slowly. Previous work from our laboratory identified a period when no PCV7 attributable changes in serotypes causing invasive pneumococcal disease (IPD) occurred , early-PCV7 2003\u20132006) and late-PCV7 (2007\u20132009) periods \u20132006 and. By mid-wciN and wciP.In 1999\u20132012, n = 4812 isolates causing IPD (n = 985 in children <18 yrs and n = 3847 in adults \u226518 yrs) were identified and characterized regarding serotype and antimicrobial susceptibility [http://pubmlst.org/spneumoniae) to identify the alleles and respective sequence types (STs). PHYLOViZ [MLST was performed as previously described . BrieflyPHYLOViZ was usedEtest strips were used to determine the minimal inhibitory concentration (MIC) for penicillin, cefotaxime and levofloxacin. Susceptibility to erythromycin, clindamycin, vancomycin, linezolid, trimethoprim-sulfamethoxazole, tetracycline and chloramphenicol was tested by the Kirby-Bauer disk diffusion technique according to CLSI procedures. Unless otherwise stated, the interpretative criteria prior to 2008 were use95%) [Genetic diversity was evaluated using Simpson\u2019s index of diversity (SID) and respective 95% confidence intervals (CI95%) . The Coc95%) was usedThe serotypes identified were 6A (n = 80), 6B (n = 79) and 6C (n = 83). All class 2 loci were identified among serotype 6B isolates . No representatives of serotypes 6D, 6F, 6G and 6H were found, confirming their rarity in Europe ,17. The 6B315, n = 47), CC395 , CC65 (n = 35), CC176 (n = 26), CC273 , CC1876 (n = 22) and CC1150 (n = 17) (All isolates were characterized by multilocus sequence typing (MLST) to complement the information already available and PHYL(n = 17) Tables. (n = 17) . The 6B-The genetic diversity of serogroup 6 isolates recovered from both children and adults was similar when considering both STs and CCs, with all seven major lineages present in both age groups Tables. wciN and wciP identified 5 and 14 alleles, respectively Click here for additional data file.S1 Table(PDF)Click here for additional data file.S2 Table(PDF)Click here for additional data file.S3 Table(PDF)Click here for additional data file.S4 Table(PDF)Click here for additional data file.S5 Table(PDF)Click here for additional data file."} +{"text": "Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer with poor prognosis and is enriched in cancer stem cells (CSCs). However, it is not completely understood how the CSCs were maintained in TNBC. In this study, by analyzing The Cancer Genome Atlas (TCGA) provisional datasets and several small-size breast datasets, we found that cadherins (CDHs) 2, 4, 6, and 17 were frequently amplified/overexpressed in 47% of TNBC while E-cadherin (CDH1) was downregulated/mutated at 10%. The alterations of CDH2/4/6/17 were strongly associated with the elevated levels of several stem cell-related transcription factors (SC-TFs) including FOXM1, MCM2, WWTR1, SNAI1, and SOX9. CDH2/4/6/17-enriched genes including FOXM1 and MCM2 were also clustered and regulated by NFY (nuclear transcription factor Y) and/or EVI1/MECOM. Meanwhile, these SC-TFs including NFYA were upregulated in TNBC cells, but they were downregulated in luminal type of cells. Furthermore, small compounds might be predicted via the Connectivity Map analysis to target TNBC with the alterations of CDH2/4/6/17 and SC-TFs. Together with the important role of these SC-TFs in the stem cell regulation, our data provide novel insights into the maintenance of CSCs in TNBC and the discovery of these SC-TFs associated with the alterations of CDH2/4/6/17 has an implication in targeted therapy of TNBC. Breast cancer can be classified depending on the status of estrogen receptor (ER) and/or progesterone receptor (PGR) and epidermal growth factor receptor 2 (ERBB2/HER2) in clinic . When alCadherins (CDHs) are a family of adhesion proteins consisting of more than 20 subtypes. These CDHs play important roles in cell-cell or cell-matrix junctions and regulate multiple aspects of fundamental cellular events such as cell polarity, motility, embryonic stem cell self-renewal and differentiation . Among thttp://cancergenome.nih.gov/), which include the complete tumors group (n = 960) and triple-negative group (n = 116) from the Breast Invasive Carcinoma . TCGA datasets, as of December 15, 2016, contained the experimental data including gene mutations, copy number alterations (CNA), mRNA and protein expression and clinical data, and were retrieved from cBioPortal for Cancer Genomics [https://www.oncomine.org/). Breast cancer cell lines datasets (GEO GSE36139 and ArrayExpress E-MTAB-181) [http://www.broadinstitute.org/ccle) or UCSC Cancer Genomics Browser (http://xena.ucsc.edu/).Breast cancer sample data used in this study were in whole or part based upon data generated by the TCGA Research Network . Other bal.org/) and Eurooup n = 1 from theTAB-181) were rethttps://www.oncomine.org/). Gene set enrichment analysis data (including mRNA level or RPPA [reverse phase protein assay]-based protein level) and survival data were also retrieved from cBioPortal with default parameters unless otherwise indicated. Gene Ontology (GO)/KEGG (Kyoto Encyclopedia of Genes and Genomes) or Reactome pathway analysis and transcription factor discovery were performed through the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources 6.8 (https://david-d.ncifcrf.gov/). Heatmap was created from GenePattern according to the instructions (https://genepattern.broadinstitute.org/). Expression levels of stem cell-related transcription factors (SC-TFs) and several CDHs were retrieved from UCSC Cancer Browser with default parameters.Alterations of interested genes including amplifications, deletions, mutations, and up- or downregulation were retrieved from TCGA datasets with cBioPortal or from n = 27) screened in this study include CDH1 (E-cadherin), CDH2 (N-cadherin), CDH3 (P-cadherin), CDH4 (R-cadherin), CDH5 (VE-cadherin), CDH6 (K-cadherin), CDH7 (cadherin 7), CDH8 (cadherin 8), CDH9 (T1-cadherin), CDH10 (T2-cadherin), CDH11 (OB-cadherin), CDH12 (N-cadherin 2), CDH13 (H-cadherin), CDH15 (M-cadherin), CDH16 (KSP-cadherin), CDH17 (LI-cadherin), CDH18 (cadherin 18), CDH20 (cadherin 20), PCDHGA12 (CDH21), CDH22 CDH23 CDH24 DCHS1 , CDH26 DCHS2 (CDH27), CDHR3 (CDH28), and CDHR4 (CDH29).All CDH genes (\u03b2-catenin), FOXM1, FOXO3, GLI2, HIF1A, HMGA1B, KLF4, MAF (c-MAF), MCM2, NANOG, POU5F1 (Oct-3/4), PRDM14, SNAI1 (Snail), SOX2, SOX9, STAT3, WWTR1, TBX3, TWIST1, ZEB1, LIN28A, LIN28B, and MYC (c-Myc) [SC-TFs used here include CTNNB1 ( (c-Myc) \u201330.\u2212/lowCD44+/high. Fluorochrome-conjugated monoclonal antibodies against CD24 and CD44 were purchased from BD Biosciences . Fluorescent staining of CD24 and CD44 was performed as described elsewhere [Stem cell population of triple-negative (or claudin-low) breast cancer cells MDA-MB231 and luminal cells SKBR3 was determined by flow cytometry with stem cell marker CD24http://www.broadinstitute.org/cmap/) [CDH2/4/6/17-enriched gene signature identified in this study, which included 101 genes with 12 downregulated and 89 upregulated, was used as a query for the CMap analysis according to the instructions (g/cmap/) , 33. CMahttps://doi.org/10.1155/2017/5091541). In TNBC, CDH1, CDH2, CDH4, CDH6, CDH17, and CDH26 also exhibited marked alterations were mainly grouped into a cluster that can be regulated by Nuclear Transcription Factor Y (NFY) and/or MECOM (EVI1) , both of\u2212/lowCD44+/high was simultaneously higher in TNBC cell lines than other subtypes of breast cancer cell lines . We found that two SC-TFs such as FOXM1, MYC exhibited modest negative correlation with ESR1/PGR or HER2 status (Supplementary Table\u2009\u2009S4). To further investigate the status of SC-TFs in TNBC, we analyzed the levels of CDH2/4/6/17-associated SC-TFs in the samples and cell lines of TNBC. All 7 SC-TFs were found to be amplified and/or upregulated in TCGA TNBC samples; the rates of their alterations were much higher than those in TCGA total breast samples . Conversll lines . For ins (0.21%) , as repo++, PI3K/mTOR [To evaluate whether TNBC cells with the alterations of CDH2/4/6/17-SC-TFs axis can be targeted, we adopted a web-based resource CMap. The CMap utilizes a pattern-matching algorithm to link the compounds (perturbagens) with physiological or pathological phenotypes by measuring similarities in gene expression, and therefore can be used to predict the affected pathways through the perturbagens affiliated with known molecular targets and signaling pathways, and discover potential pharmaceutical treatment based on the query signatures . A CMap I3K/mTOR , it provI3K/mTOR , 54. ThuIn this study, we evaluated the status of CDHs in TCGA breast cancer samples, especially in TNBC by using informatics and experimental analyses, and demonstrated that CDH2/4/6/17 themselves and their associated SC-TFs including WWTR1, NFYA, and FOXM1 might be involved in the enrichment of CSCs in TNBC.CDH1 is an original cadherin and plays a pivotal role in epithelial structure remodeling and maintaining the stemness of stem cells in breast epithelial and cancer cells \u20137, 38\u201340Our study here demonstrated that SC-TFs such as WWTR1, FOXM1, NFYA, and SOX9 might be involved in the enrichment of CSCs in TNBC . ConsistAlthough CDH1 is key for the maintenance of epithelial stem cells , 7, 80, In this study, we demonstrated that CDH2/4/6/17 were amplified/overexpressed in TNBC, where the expression of CDH2/4/6/17-enriched SC-TFs was also increased. In parallel, these SC-TFs were strongly associated with the accumulation of CSCs in TNBC cells. Thus, we concluded that one mechanism through which the stemness is maintained in TNBC when E-cadherin is downregulated or lost is by way of upregulating the expression of other CDH family members such as CDH2/4/6/17 along with increased expression of SC-TFs. Moreover, we demonstrated that small compounds might be used to target TNBC based on alterations of CDH2/4/6/17 and SC-TFs. Although further studies have to be conducted on the mechanisms for regulation of SC-TFs by CDH2/4/6/17, all these observations highlight the potential functions of CDH2/4/6/17 on the reservoir of CSCs in TNBC with low expression or mutation of CDH1 and provide evidence with implications in targeted therapy in TNBC.Supplementary information contains 5 supplementary figures and 4 supplementary tables (Table S1 to S4). Figure S1 and S2 show the alterations of all 27 CDHs in all breast cancer samples and TNBC samples from TCGA respectively. Figure S3 shows alteration of top 24 genes while Figure S4 demonstrates alterations of 7 stem cell-related transcription factors in breast cancer samples used for analysis. FigureS5 shows representative data of Figure 3C. Table S1 and S2 demonstrate the correlation of altered CDH1 and expressions of ESR1, PGR and HER2 or stem cell-related transcription factors respectively. Table S3 lists genes enriched with altered CDHs in breast cancer samples. Table S4 describes correlation between stem cell-related transcription factors and ESR1, PGR and HER2 status in breast cancer using RPPA dataset."} +{"text": "Scientific Reports6: Article number: 2524710.1038/srep25247; published online: 05052016; updated: 04072017This Article contains errors in Tables 1, 2, 3 and 4 where references 29, 30 and 31 are incorrectly given as references 21, 22 and 30 respectively."} +{"text": "AbstractAsprothrips with a bicoloured body, A.atermaculosussp. n., is described and illustrated from China. This is characterised by considerable intra-population variation in the number and size of brown markings on the abdominal tergites. Asprothripsfuscipennis Kud\u00f4, previously described from Japan, is newly recorded in China.The second species of the genus Asprothrips Crawford, a small genus of the subfamily Dendrothripinae, currently comprises seven described species .The thrips were collected by beating vegetation over a white plastic tray using a stick, and then sorted and preserved in 90 % alcohol. Examined specimens were mounted Taxon classificationAnimaliaORDOFAMILIAhttp://zoobank.org/AEA30996-615F-4E7E-A000-21E3EC4AA61FHolotype female (in SCAU): CHINA, Hunan province, Chaling County, Yunyangshan National Forest Park , collected from leaves of Lophatherumgracile (Poaceae), 8.viii.2017, leg. Zhaohong Wang.Paratypes (in SCAU): 20 females, 25 males, taken with holotype. Fujian province, Sanming City, Sanyuan National Forest Park , 21 females and 31 males from leaves of Lophatherumgracile (Poaceae), 24.viii.2017, leg. Zhaohong Wang. Hunan province, Hengyang City, Mt. Hengshan , 2 females, collected from L.gracile (Poaceae), 6.viii.2017, leg. Zhaohong Wang.Female body bicoloured, head, pronotum and antennal segments I\u2013II brown; abdomen white except for the intra-population variation in the number and size of brown markings on the abdominal tergites I\u2013VIII; fore wing white with two dark brown bands and the surface uniformly covered with microtrichia. Male body is similar to female in structure and colour pattern, but antennae white or yellowish white and the paired brown markings exist only in abdominal tergites I\u2013II and VI; abdominal sternites III\u2013VIII each with a small and oval pore plates.Female (macropterous) Fig. . Body biHead on abdominal tergites II to VII small, the distance between their basal pores much greater than their length; paired campaniform sensilla between setae S1 and S2, much closer to S2 on tergites II\u2013VII . Total distended body length 960. Head length (width) 63 (122); eye length (width) 47 (32). Pronotum length (width) 79 (147). Length of antenna 182; length (width) of antennal segments I 15 (20), II 22 (24), III 30 (14), IV 30 (13), V 26 (13), VI 36 (12), VII 10 (4) and VIII 13 (3). Fore wing length 1250.Male (macropterous) Fig. . Similarus) Fig. ; fore wius) Fig. ; the paius) Fig. , 15; abdus) Fig. .Measurements . Total distended body length 840. Head length (width) 60 (110); eye length (width) 50 (32). Pronotum length (width) 76 (130). Length of antenna 173; length (width) of antennal segments I 15 (19), II 22 (22), III 30 (12), IV 30 (11), V 26 (12), VI 31 (11), VII 9 (4) and VIII 10 (3). Fore wing length 1090.ater\u201d meaning black, and \u201cmaculosus\u201d meaning spotted or markings, in reference to the abdominal tergites with many dark brown markings.The species name is an arbitrary combination of two Latin adjective, \u201cChina .Asprothrips by the variable number and size of brown markings on the abdominal tergites had been given 18 different names , the Western flower thrips, has been reported to exist in three colour morphs, with light, dark, and bicoloured forms from different populations or seasons, resulting in at least 16 described species being placed as synonyms of F.occidentalis and Sanming (Fujian province) respectively, these two localities are approximately 400 km apart. In \u201cChaling\u201d population, there are eight colour patterns of brown markings on tergites III\u2013V in female , 12 females collected from leaves of Ilexcrenata (Aquifoliaceae), 9.xi.2015, leg. Xiaoli Tong.Female full winged and body brown except for all tarsi yellow Fig. . AntennaJapan and China (Jiangxi).Asprothripsfuscipennis Kud\u00f4 is newly recorded from China in this study. Although A.bucerus. These two species are very similar in colouration and structure, but fuscipennis can be distinguished from bucerus by (1) antennal segment II with a sub-basal dorsal seta (this seta absent in bucerus); (2) antennal segment IV shorter than VI (segment IV longer than VI in bucerus); (3) posterior margin of tergite IX with a pair of long and fine setae medially , and (4) abdominal tergite X with complete longitudinal dorsal split ."} +{"text": "Scientific Data 4:170003 doi: 10.1038/sdata.2017.3 (2018); Published 14 March 2017; Updated 8 May 2018The affiliation of Cathrine Lund Myhre was incorrectly stated in the original publication. It is: 19 NILU -Norwegian Institute for Air Research, Instituttveien 18, Kjeller 2007, Norway."} +{"text": "TP53, CDKN2A, KRAS, PTEN, PI3KCA, RB1, APC, ERBB2, MYC, EGFR, CDKN2B, ARID1A, SMAD4, FGFR1, MDM2, BRAF, ATM, CCNE1, FGFR3 and FRS2. One hundred fifty-nine patients (28%) were included in early phase trials. The treatment was matched with a tumour profile in 86 cases (15%). The two main reasons for non-inclusion were non-progressive disease (31.5%) and general status deterioration (25%). Twenty-eight percent of patients presented with a growth modulation index >1.3.Previous precision medicine studies have investigated conventional molecular techniques and/or limited sets of gene alterations. The aim of this study was to describe the impact of the next-generation sequencing of the largest panel of genes used to date in tumour tissue and blood in the context of institutional molecular screening programmes. DNA analysis was performed by next-generation sequencing using a panel of 426 cancer-related genes and by comparative genomic hybridization from formalin-fixed and paraffin-embedded archived tumour samples when available or from fresh tumour samples. Five hundred sixty-eight patients were enrolled. The median number of prior lines of treatment was 2 (range 0\u20139). The most common primary tumour types were lung (16.9%), colorectal (14.4%), breast (10.6%), ovarian (10.2%) and sarcoma (10.2%). The median patient age was 63\u00a0years (range 19\u201388). A total of 292 patients (51.4%) presented with at least one actionable genetic alteration. The 20 genes most frequently altered were Extensive molecular profiling using high-throughput techniques allows for the identification of actionable mutations in the majority of cases and is associated with substantial clinical benefit in up to one in four patients.The online version of this article (doi:10.1186/s13045-017-0411-5) contains supplementary material, which is available to authorized users. Previous precision medicine studies have investigated conventional molecular techniques and/or limited sets of gene alterations \u20133. We deBetween January 1, 2014, and June 30, 2015, 568 patients were enrolled in the study. Their characteristics are summarized in Additional file TP53, CDKN2A, KRAS, PTEN, PI3KCA, RB1, APC, ERBB2, MYC, EGFR, CDKN2B, ARID1A, SMAD4, FGFR1, MDM2, BRAF, ATM, CCNE1, FGFR3 and FRS2 , molecular analysis failed mainly because of insufficient tissue quantity or quality. The median time from first referral to reporting was 9\u00a0weeks (range 1\u201336\u00a0weeks). The 20 genes found most frequently altered were Two hundred ninety-two 51.4%) patients had at least one genetic alteration that was considered actionable by the molecular tumour board. Molecular profiles by tumour type are presented in Additional file 1.4% patiOne hundred fifty-nine 28%) patients were randomized in an early phase clinical trial (EPCT) after the screening results. The main reasons for non-inclusion were non-progressive disease on current treatment regimen 31.5%), general status deterioration (25%), death (16.5%), clinical trial not available (10.5%), screening failure (6.5%), loss to follow-up (7%) and patient refusal (3%). The drug used in the EPCT was genotype-matched (GM) in 86 (15.1%) patients and non-matched (NM) in 73 (12.9%) patients was 47.7% .Fifty-nine patients were evaluable for the growth modulatin index (GMI) calculation. The median GMI was 0.63Thirty-nine patients with coupled primary and metastatic tumours were analysed to evaluate the correlation between the molecular screening results of the two samples. Twenty-six patients (67%) had at least one mutation considered targetable. In this population, 9 cases had a discordant mutational status between the primary and metastatic sites. This discordance was related to an actionable mutation in only four cases for a final concordance rate in terms of targetable alterations of 85% (22/26 patients).Seventy-five patients underwent also a tumour molecular profile-based circulating-free DNA (cfDNA) analysis. Their characteristics are shown in Additional file Our extensive molecular screening program allowed the identification of at least one actionable genetic alteration in 51.4% of cases and was associated with a significant clinical benefit since 27.8% of the patients in the GM group experienced a GMI\u2009>\u20091.3 (Additional file Overall, this study demonstrates the feasibility and potentially positive clinical impact of using comprehensive molecular profiling to improve the outcomes of cancer patients."} +{"text": "Both TTO and Ag+ have broad spectrum antimicrobial activity and act on multiple target sites, hence reducing the likelihood of developing resistance. Combining such agents with responsive, controlled release delivery systems such as hydrogels may enhance microbiocidal activity and promote wound healing. The advantages of using chitosan to formulate the hydrogels include its biocompatible, mucoadhesive and controlled release properties. In this study, hydrogels loaded with TTO and Ag+ exhibited antimicrobial activity against P. aeruginosa, S. aureus and C. albicans. Combining TTO and Ag+ into the hydrogel further improved antimicrobial activity by lowering the effective concentrations required, respectively. This has obvious advantages for reducing the potential toxic effects on the healthy tissues surrounding the wound. These studies highlight the feasibility of delivering lower effective concentrations of antimicrobial agents such as TTO and Ag+ in ionically crosslinked chitosan hydrogels to treat common wound-infecting pathogens.The emerging problems posed by antibiotic resistance complicate the treatment regime required for wound infections and are driving the need to develop more effective methods of wound management. There is growing interest in the use of alternative, broad spectrum, pre-antibiotic antimicrobial agents such as essential oils and metal ions (e.g., silver, Ag The increasing occurrence of antibiotic-resistant strains and reports of hospital cross-infection further complicate current practices in wound management. Statistics show that acute and chronic wounds affect approximately 2% of the population, with treatment costs taking up to 4% of the overall health care budget . In EuroAcute and chronic wounds require relatively lengthy treatment with antibiotics which carry the attendant risk of developing drug resistance. Additionally, hypersensitivity reactions to antibiotics and the lack of access to new treatments within the health care industry make the care of such patients difficult . This seManagement of acute and chronic wounds such as varicose insufficiency ulcers, diabetic foot ulcers and burns aims to minimise infection, speed up wound healing and minimise scarring . ColonisStaphylococcus aureus, (MRSA)) and Vancomycin-resistant enterococci) and Gram-negative bacteria [The problems posed by increasing antibiotic resistance in Gram-positive ,9 have ruginosa) ,11.\u00ae is a commercial hydrogel dressing impregnated with TTO for the treatment of burns [The essential oil tea tree oil (TTO) contains >100 different components which contribute to its broad spectrum antibacterial, antifungal, antiviral, antimycoplasmal, antiprotozoal and anti-inflammatory activity . Commercof burns . The topof burns . The useof burns .+) have regained popularity as an antimicrobial agent due to their broad spectrum antibacterial, antiviral, antiprotozoal and antifungal activity [+ are classified as highly reactive moieties, which readily bind anions formed by electron donor groups containing sulphur (thiols), oxygen and nitrogen [+ to affect multi-target sites is beneficial to reduce the potential development of resistant strains [+ has been reported to enhance wound healing directly by modulating the inflammatory response [+ are of interest in the development of improved wound management products. Formulations containing silver are commonly used to treat a variety of Gram-positive and Gram-negative bacteria, as well as common highly-antibiotic-resistant microorganisms such as P. aeruginosa [\u00ae, Smith and Nephew Healthcare Limited, Hull, UK), have been successfully used for the treatment of burn wound infections. In addition, controlled release delivery systems have also incorporated Ag+ to reduce infection and improve the wound healing process. Some current examples of silver-containing wound dressings include DuoDERM\u00ae , Aquacel\u00ae Ag , TegadermTM , VaselineTM , Sorbsan\u00ae , Lyofoam\u00ae C and Nu-GelTM [+ can trigger unwelcome side effects. Long-term topical exposure to high concentrations of Ag+ leads to a build-up of metallic silver (Ag0) in the dermis, causing an irreversible blue-grey discolouration of the skin (argyria). This is particularly pronounced in areas exposed to sunlight which accelerates the photo-reduction and deposition of Ag0 [Silver ions ,24. As in of Ag0 ,26,27. Sn of Ag0 . Other mvia pores in the polymer network [d-glucopyranose and 2-amino-2-deoxy-d-glyco-pyranose monomers [Hydrogels are three-dimensional crosslinked polymer networks which can imbibe large amounts of water or biological fluids ,29. Thes network . When ap network ,32. The monomers ,34,35. Cmonomers .The useful properties of alternative antimicrobial agents, together with advances in drug delivery technologies, may be able to enhance and expand the medical applications of these agents. Combining these alternative antimicrobial agents with advanced drug delivery systems aims to: (1) promote bioavailability of the agent at microbiocidal concentrations; (2) reduce drug concentration to enhance safety and practicality of application; (3) minimise scarring and promote wound healing processes; (4) reduce discomfort and pain in consideration of the patients\u2019 psychological needs; and (5) decrease the frequency of dressing changes . These ain vitro antimicrobial efficacy of hydrogels incorporating TTO alone and in combination with Ag+ against representative wound-infecting organisms, namely P. aeruginosa, S. aureus and C. albicans. We report here on the characterisation and optimisation of both preparation and formulation techniques of a hydrogel-based delivery system for controlled release of antimicrobially active Ag+ and TTO.Therefore, the aims of this investigation were to examine the P. aeruginosa (NCIB 8295) was prepared by aseptically inoculating 50 mL of sterile TSB and incubating overnight in an orbital shaker at 37 \u00b0C. Similarly, overnight cultures of S. aureus (NCIB 6571) in TSB and C. albicans (NCYC 854) in MEB were also similarly prepared.Sterile tryptone soy broth (TSB), tryptone soy agar (TSA), malt extract broth (MEB) and malt extract agar (MEA) were obtained from Lab M, Lancashire, UK, and prepared according to manufacturer\u2019s recommendations. Overnight culture of w/v) were prepared in sterile distilled water. Medium- or low-viscosity chitosan solutions (1.25% and 2.5% w/v) were prepared in 1.0% v/v glacial acetic acid . Phosphate buffer saline (PBS) was prepared according to manufacturer\u2019s recommendation and autoclaved prior to use.Sodium phosphate , Na-P solutions (25% and 50% w/v), Na-P (25% or 50% w/v) and 10% w/v poly (PVA) 13\u201323 kDa, PVA13-23, or 31-50kDa, PVA31-50, solutions. After mixing for 2 min the gelling mixtures were passed through 0.45 \u03bcm sterile syringes, transferred into sterile Petri dishes, covered and allowed to set for a minimum of 2 h.Ionically crosslinked chitosan hydrogels were prepared by vigorous magnetic stirring of various ratios of chitosan were cut and placed in a clean Petri dish with 20 mL of distilled water. Hydrogel formulation discs that maintained their shape, could easily be cut out and handled, as well as remaining stable after incubation in water were chosen for further study.w/v PVA (35:65 v/v ratio) for 1 min. TTO:PVA-loaded hydrogels were prepared by substituting or adding sufficient emulsified TTO as part of the PVA component in the formulations to produce hydrogels with final TTO concentration of 5% or 7% v/v.TTO:PVA emulsions were prepared by probe sonicating TTO and 10% TTO-encapsulated hydrogel discs (8 mm diameter) were incubated in 20 mL PBS at room temperature. At time zero and at every hour up to 6 h, 6 mL of PBS was sampled, and replaced by 6 mL of fresh PBS. Further samples were taken after 7.5 and 24 h. Subsequently the amount of TTO and chitosan released from the hydrogels was quantified using the monoterpene and ninhydrin quantification assays, respectively.w/v vanillin in concentrated sulphuric acid was adapted from Doneva-\u0160apceska et al., 2006 [A colorimetric method for determining the total monoterpene content using 2.5% l., 2006 . Vanilliet al., 2004 [Quantification of chitosan was performed using a colorimetric ninhydrin assay adapted from Leane l., 2004 . Lithiuml., 2004 to deduc30-70v/v, Ag+ and TTO:Ag+:PVA30-70 were produced. It was found that the Ag+ solutions used in the formulations also acted as the crosslinker for the hydrogels; hence, in the formulations containing Ag+, Na-P was substituted with 1% or 2% w/v AgNO3. The emulsion of TTO:Ag+:PVA30-70 was prepared by dissolving sufficient AgNO3 in 10% w/v PVA30-70, adding sufficient TTO and sonicating the mixture for 3 min. The concentration of TTO:Ag+:PVA30-70 used were as follows:340% TTO: 0.5% AgNO320% TTO: 1.0% AgNOFollowing the initial trial formulations confirming the feasibility of hydrogels to deliver TTO, another batch of hydrogels containing 35% TTO: 65% PVA+, which were used for antimicrobial studies.P. aeruginosa and S. aureus were adjusted accordingly to the following absorbance reading at 500 nm based on the British Society for Antimicrobial Chemotherapy (BSAC) disc diffusion method guidelines [P. aeruginosa \u2212> 0.1\u22120.3S. aureus \u2212> 0.3\u22120.6The antimicrobial effect of the agents encapsulated into hydrogels was tested using a standard well diffusion method. Overnight cultures of idelines :P. aeruC. albicans were used without dilution in the disc diffusion experiments, as they contained sufficient number of cells for the experiments. The adjusted cultures were swabbed on the surface of the agar plates in triplicate according to the BSAC disc diffusion method recommendations. A well (12 mm diameter) was aseptically bored in the middle of the agar plate using a sterile metal borer. The hydrogel was aseptically placed in the well and incubated overnight at 37 \u00b0C, prior to measuring the diameter of the zone of inhibition. Control experiments were prepared by substituting the hydrogels with those formulated without TTO:PVA and AgNO3.Overnight cultures of Data from the preliminary studies showed that stable, uniform hydrogels were formed using the composition ratios as detailed in w/v) emulsion. The release profiles of chitosan from formulations containing 50% TTO: 50% PVA (10% w/v) are shown in The release mechanism of chitosan and monoterpene (TTO) from hydrogels was investigated as a function of hydrogel degradation. \u22122 to 3.99 \u00d7 10\u22121 %/mL at 24 h post-incubation eroded at a higher rate (more chitosan released). The hydrogels formulated with PVA13-23 and chitosanL1.25 released 3.99 \u00d7 10\u22121 %/mL compared to 2.07 \u00d7 10\u22121 %/mL in gel formulated using chitosanL2.5. Similarly, in hydrogels formulated with PVA31-50, stability was also improved in gels formulated with chitosanL2.5, resulting in 9.72 \u00d7 10\u22122 %/mL chitosan release compared to 2.99 \u00d7 10\u22121 %/mL in the gel formulated using chitosanL1.25.Low-viscosity chitosan formulations showed chitosan release was between 9.72 \u00d7 10cubation A. Compar0\u22121 %/mL A. ResultM1.25 formulations gradually released both chitosan and monoterpene over time. The formulation having a higher volume of 25% w/v Na-P (formulation CM1.25PVA13-23) displayed better stability properties, i.e., low chitosan release (low erosion) with slow release of monoterpene. In contrast, formulations with chitosanM2.5 showed a steep increase in chitosan release between 5 and 7.5 h post-incubation, resulting in the higher final amount released. Although the gels formulated with chitosanM2.5 are considered to be more stable, those formulated with PVA13-23 (formulation CM2.5PVA13-23) may be more prone to erosion due to the lower chitosan:Na-P ratio, resulting in weaker crosslinking. Similarly, the stability of the gels may also be compromised by the chitosan-PVA chain entanglement interaction. Hence, despite the higher chitosan:Na-P ratio, the gels formulated with PVA31-50 (formulation CM2.5PVA31-50) appear to be less stable (greater chitosan erosion) due to the dissociation of the chitosan-PVA interaction. Consequently, this also resulted in higher monoterpene release, despite the more viscous properties of these formulations within the group.The trend of chitosan and monoterpene release from hydrogels formulated with medium-viscosity chitosan differs from the low-viscosity hydrogels. Results in v/v, there were observable changes in the chitosan and monoterpene release profiles was between 7.65 \u00d7 10\u22122 and 1.19 \u00d7 10\u22121 %/mL. When monoterpene release for hydrogel formulations was analysed with zero order, first order, Higuchi and Korsmeyer-Peppas equations [M1.25PVA13-23, follows the zero order release with a correlation coefficient of R > 0.97, i.e., release of monoterpene was constant over time [M1.25PVA13-23 fits the Higuichi equation (R2 > 0.97); hence, the monoterpene was released via a diffusional process according to Fick\u2019s law [Similar to the other formulations, increasing crosslinking along with increased viscosity improves hydrogel stability. These gels [i.e., C. albicans > S. aureus \u2265 P. aeruginosa Na-P25(17)TTO35(8)-CL2.5(7)Na-P25(9)TTO35(5) vary with increasing viscosity and amount of crosslinker which can improve gel stability. This resulted in more stable TTO hydrogels which can entrap more of the essential oil; the improved antimicrobial activity is observed by an increased ZOI for microorganisms with higher TTO sensitivity, e.g., C. albicans. Despite increased formulation stability (CL1.25(17)Na-P25(17)TTO35(8)-CL2.5(7)Na-P25(9)TTO35(5)), the ZOI for less sensitive microorganisms, e.g., P. aeruginosa and S. aureus, has not been significantly affected (p > 0.05). This may be due to the slower rate of TTO release (from more stable hydrogels) which limits the availability of the agent at microbiocidal concentrations, and thus the ZOI for less sensitive microorganisms are not affected. Conversely, formulation CL2.5(10)Na-P50(7)TTO35(4) had the lowest chitosan: Na-P ratio which makes it less stable and more prone to faster erosion and drug release, resulting in a burst release of TTO which leads to a higher ZOI after 24 h incubation. Such immediate burst release with concomitant rapid hydrogel erosion is not particularly useful when treating wounds with heavy microbial loads. Formulations therefore need to be optimised to reduce the rate of erosion and degradation of the hydrogel whilst maintaining prolonged delivery of agents at microbiocidal concentrations.The effect of TTO-hydrogel (low viscosity) formulations follows an order of sensitivity similar to that of the minimum lethal concentration (MLC) reported in Low . (2011) for freeruginosa A. ResultM2.5(11.75)Na-P25(4.25)TTO35(5)-CM1.25(12)Na-P50(5)TTO35(4)) against P. aeruginosa. The ZOI in hydrogels CM2.5(12.5)Na-P50(2.5)TTO35(4) and CM1.25(12)Na-P50(5)TTO35(4) follows the MLC sensitivity trend of C. albicans > S. aureus > P. aeruginosa. However, the extent of antimicrobial activity, especially against the more sensitive C. albicans, is lower than those formulated with low-viscosity chitosan (CL2.5(10)Na-P50(7)TTO35(4)-CL2.5(7)Na-P25(9)TTO35(5)). This reduce in antimicrobial activity is probably due to the overall increase in chitosan chain length (moving from low to medium viscosity), which potentially increases inter-chain entanglement, hence retarding the ability of TTO diffusion and thereby reducing the amount released from the hydrogel structure. Within this group, formulation CM2.5(12.5)Na-P50(2.5)TTO35(4) (lowest chitosan:Na-P ratio) forms a less stable hydrogel with a higher rate of erosion; the reduced crosslinking also contributes to a less stable gel network to maximise TTO:PVA encapsulation by allowing chain entanglement interactions between PVA and chitosan. As a result, TTO escape from the hydrogel may again follow a burst release profile and increase the ZOI for C. albicans and S. aureus. However, the concentration was insufficient to show a clear ZOI for P. aeruginosa, although there was an observed zone of restricted growth with an average diameter of 30.33 mm. Formulations CM2.5(12)Na-P25(5)TTO35(4) and CM1.25(12)Na-P50(5)TTO35(4) are more stable due to their increased viscosity (there is more chitosan in the formulation which is not diluted by the addition of aqueous Na-P). Despite having the same chitosan:Na-P ratio, the antimicrobial performance of CM2.5(12)Na-P25(5)TTO35(4) and CM1.25(12)Na-P50(5)TTO35(4) was different. This may be due to the variations in Na-P concentration, which can alter crosslinking and viscosity of hydrogels (CM2.5(12)Na-P25(5)TTO35(4) formulated using 25% w/v Na-P, CM1.25(12)Na-P50(5)TTO35(4) formulated using 50% Na-P). Such properties include both the viscosity of the various chitosan solutions and the ability of oppositely charged crosslinking phosphate anions to diffuse into the solution and form an electrostatically crosslinked semi-solid structure. The order of sensitivity in formulation CM2.5(11.75)Na-P25(4.25)TTO35(5) was altered to S. aureus > C. albicans > P. aeruginosa, which could have resulted from the higher concentration of TTO present in the hydrogels.Results from C. albicans increased with increasing viscosity. The ZOI against S. aureus remained fairly consistent, possibly due to the increased gel stability and higher encapsulation of TTO and its components, which are subsequently available for release. Formulation CH2.5(10)Na-P50(1)TTO35(4)PVA10(6)-CH2.5(22)Na-P50(7)TTO35(8)PVA10(5) showed no clear ZOI against P. aeruginosa; however, similar to formulation CM1.25(12)Na-P50(5)TTO35(4), there was an insufficient concentration of TTO to result in a clear ZOI and zones of restricted growth with average diameters of 13.5 mm (CH2.5(10)Na-P50(1)TTO35(4)PVA10(6)), 33.0 mm (CH1.25(13)Na-P50(4)TTO35(4)) and 30.667 mm (CH2.5(22)Na-P50(7)TTO35(8)PVA10(5)) were observed. Formulation CH1.25(10)Na-P25(7)TTO35(4) was shown to have a ZOI against P. aeruginosa. The results in + hydrogels will be discussed based on the viscosity of chitosan and concentration of AgNO3 because it has electrostatic crosslinking properties that affect the stability of the resultant hydrogels as well as their antimicrobial activity. In Ag+ hydrogels, the order of sensitivity also follows the MLC order of Ag+ reported in Low et al., 2011 [i.e., C. albicans > P. aeruginosa \u2265 S. aureus Ag2(7)PVA10(7), CL2.5(10.5)Ag0.75(7)PVA10(3.5), CM2.5(10)Ag1(5)PVA10(6), CM2.5(7)Ag1(7)PVA10(7) and CH2.5(14)Ag2(2)PVA10(5)), the order changes to P. aeruginosa > S. aureus \u2265 C. albicans. Experimental results also showed that as Ag+ diffuses into the MEA, a precipitate is formed in the agar. This can reduce the bioavailability of Ag+ against C. albicans, resulting in a shift in the order of sensitivity. Despite its role as a crosslinker, the antimicrobial activity of Ag+ is not affected if there are sufficient metal ions available for release from the hydrogel matrix Ag2(12)-CL1.25(8)Ag2(13)) all showed a ZOI against C. albicans, unlike formulations CL2.5(28)Ag2(7)PVA10(7) and CL2.5(10.5)Ag0.75(7)PVA10(3.5). The observed ZOI was not influenced by the small increase in Ag+ concentration from 0.635% to 0.786% w/v. All formulations showed a ZOI against P. aeruginosa and S. aureus. The increase in Ag+ from CL1.25(9)Ag2(12) to CL1.25(8)Ag2(13) showed a gradual increase in ZOI, although this increase was not significant (p > 0.05). This may be due to the higher free Ag+ MLC of P. aeruginosa (1.59 \u00d7 10\u22123 % w/v) and S. aureus (5.08 \u00d7 10\u22123 % w/v) compared to C. albicans (6.35 \u00d7 10\u22124 % w/v) [+ (CL2.5(28)Ag2(7)PVA10(7) and CM2.5(10)Ag1(5)PVA10(6); CL2.5(10.5)Ag0.75(7)PVA10(3.5) and CM2.5(7)Ag1(7)PVA10(7)). Formulations CM1.25(22)Ag2(20) and CM1.25(10.5)Ag2(10.5) also showed a similar order of sensitivity as observed in CL1.25(9)Ag2(12). The increased viscosity in CM1.25(22)Ag2(20) and CM1.25(10.5)Ag2(10.5) may increase entrapment of Ag+ within the hydrogel, leading to a slight increase in the ZOI against P. aeruginosa and S. aureus. However, this is not observed in C. albicans, as the slower release lowered the availability of Ag+, making it difficult to overcome the reaction with MEA and to express antimicrobial activity.In 4 % w/v) . Medium-H1.25(14)Ag2(10.5) in P. aeruginosa being most sensitive, followed by C. albicans and S. aureus. Disregarding C. albicans, this trend of sensitivity showed similarities to the results obtained from the MLC of free Ag+ [+ and MEA makes it more difficult to monitor the actual extent of antimicrobial activity against C. albicans.A similar trend applies when hydrogels formulated with high-viscosity chitosan were used, e.g., formulation Cfree Ag+ . In addiet al., 2011 [i.e., C. albicans > P. aeruginosa > S. aureus, for low- and medium-viscosity but not high-viscosity chitosan hydrogels. Formulation CL1.25(12)TTO-Ag20-0.5(3)Na-P25(1)PVA10(5)-CL1.25(9.5)TTO-Ag20-1(11.5) TTO-Ag20-0.5(3)Na-P25(1)PVA10(5)-CL1.25(9.5)TTO-Ag20-1(11.5), except CL1.25(12)TTO-Ag20-0.5(3)Na-P25(1)PVA10(5) against C. albicans). The lower Ag+ content in CL1.25(12)TTO-Ag20-0.5(3)Na-P25(1)PVA10(5) may reduce crosslinking to enable a faster release of TTO. Thus, the observed higher ZOI may be due to C. albicans having higher sensitivity to TTO. Similarly, this was also observed in the ZOI of formulations CM2.5(11)TTO-Ag20-1(6)PVA10(4), CM2.5(7)TTO-Ag20-1(7)PVA10(7) and CM1.25(10)TTO-Ag20-1(11) TTO-Ag20-1(7)PVA10(7) (0.1058% w/v Ag+ and 13.333% v/v TTO) resulted in the higher C. albicans ZOI compared to a relatively similar counterpart, formulation CM2.5(11)TTO-Ag20-1(6)PVA10(4) (0.1814% w/v Ag+ and 5.7143% v/v TTO). The ZOI of S. aureus and P. aeruginosa remained fairly consistent between formulations CM1.25(12)TTO-Ag20-0.5(3)Na-P25(0.75)PVA10(5.25)- CM1.25(10)TTO-Ag20-1(11).According to l., 2011 , i.e., C-1(11.5) A shows t20-1(11) B againstP. aeruginosa \u2265 C. albicans > S. aureus. Similar to all the other formulations, the overall viscosity of the system, the crosslinking capacity of Ag+ and the amount of TTO affect the antimicrobial activity of the formulations.High-viscosity chitosan hydrogels C showed + managed to maintain their antimicrobial activity despite having agent concentrations lower than those in TTO or Ag+ hydrogels. For example, formulation CH2.5(21.5)TTO-Ag20-1(3.5)PVA10(14), containing 0.0570% w/v Ag+ and 1.795% v/v TTO, maintained antimicrobial activity when compared to similar formulations Ag2(2)PVA10(5) containing 0.0605% w/v Ag+, and CH2.5(10)Na-P50(1)TTO35(4)PVA10(6) containing 6.6667% v/v TTO). At low concentrations of Ag+, formulation CH2.5(14)Ag2(2)PVA10(5) did not show a clear ZOI against C. albicans, while formulation CH2.5(10)Na-P50(1)TTO35(4)PVA10(6) did not show a clear ZOI against P. aeruginosa, despite having higher TTO content. The ZOI observed for S. aureus remained fairly consistent when comparing the hydrogels formulated with varying chitosan viscosity. The maintenance of activity when using both agents at lower concentrations demonstrates the feasibility of using combined agents at lower effective concentrations.Nevertheless, hydrogels containing both TTO and Ag+ into chitosan hydrogels demonstrated the possibility of maintaining antimicrobial activity when using a delivery system. The capacity and performance of antimicrobial agents varies depending on the type of dressing and wound. For the treatment of moist wounds, e.g., ulcers, the absorptive properties of hydrogels make them a better option compared to non-absorptive dressings such as gauzes. Research indicated that there is no single dressing that can produce the optimum microenvironment for all wounds [Incorporation of TTO and/or Agl wounds , thus th3) and the amount of available antimicrobial agent (Ag+ or TTO), may result in the observed varying order of sensitivity between formulations. Low-, medium- and high-viscosity chitosans derive their rheological properties from the increasing chain length of the polymer. Within each of these groups the concentration of chitosan and the degree of crosslinking also influence viscosity. In addition, increasing the amount of Na-P improves crosslinking and increases hydrogel stability. Factors such as the differences in physicochemical properties of the hydrogels, including chitosan viscosity, concentration of the crosslinker (Na-P or AgNO+ varies according to the concentration required for crosslinking (AgNO3 donates the anionic crosslinking nitrate group) and the release of Ag+ from the hydrogel. Changes in TTO composition in the hydrogels may occur due to the loss of volatile TTO components during the gel setting period. The availability of Ag+) into hydrogel-based formulations may be a feasible option to enhance biodistribution and biological activity of the agents. Despite the effectiveness of combined treatments, the toxicity of individual agents towards human host cells should also be carefully considered. Although toxicity or irritancy are less likely to occur, various reports of toxicity associated with the misuse/overuse of TTO [+ and silver-containing products have been discussed [+ concentrations to avoid toxicity issues whilst maintaining antimicrobial properties. In this investigation, PVA was used to emulsify TTO to form an oil-in-water emulsion. This will allow more efficient encapsulation into the hydrogels, reducing loss and degradation of volatile components which may affect the oil\u2019s therapeutic activity [Encapsulation of broad spectrum antimicrobial agents against a wide range of different microorganisms due to their multiple target sites might be used to improve the current treatment strategies for various chronic wound infections. Combining agents with different intra- and extracellular target sites has two advantages. One is to limit the development of resistance towards these antimicrobial compounds by extending the range of target sites. The activity of microbial agents with a single site of action can much more readily be overcome, thus making it easier for resistance to develop. Another advantage is to reduce the likelihood of toxic effects. + in combination. As a whole, the results from this investigation have provided the basis to develop hydrogel formulations for the delivery of an essential oil (TTO) and metal ion (Ag+) as antimicrobial agents for the treatment of acute wounds. The relationship between the variables in the hydrogel formulations and antimicrobial activity requires further work. Consequently, the characteristics of the hydrogel formulations, including the encapsulated agent concentration, can be modified to enhance their potential as a smart delivery system.This study showed the feasibility of developing hydrogels as a controlled release system for the delivery of TTO and Ag"} +{"text": "AbstractThis paper provides a quantitative and general description of the Rio de Janeiro Botanical Garden herbarium (RB) dataset. Created over a century ago, the RB currently comprises ca. 750,000 mounted specimens, with a strong representation of Brazilian flora, mainly from the Atlantic and Amazon forests. Nearly 100% of these specimens have been entered into the database and imaged and, at present, about 17% have been geo-referenced. This data paper is focused exclusively on RB's exsiccatae collection of land plants and algae, which is currently increasing by about twenty to thirty thousand specimens per year thanks to fieldwork, exchange and donations. Since 2005, many national and international projects have been implemented, improving the quality and accessibility of the collection. The most important facilitating factor in this process was the creation of the institutional system for plants collection and management, named JABOT. Since the RB is continuously growing, the dataset is updated weekly on SiBBr and GBIF portals.The most represented environments are the Atlantic and Amazon forests, a biodiversity hotspot and the world's largest rain forest, respectively. The dataset described in this article contains the data and metadata of plants and algae specimens in the RB collection and the link to access the respective images. Currently, the RB data is publicly available online at several biodiversity portals, such as our institutional database JABOT, the Reflora Virtual Herbarium, the SiBBr and the GBIF portal. However, a description of the RB dataset as a whole is not available in the literature. Created in 1890, the RB herbarium of the Rio de Janeiro Botanical Garden (JBRJ) is composed of seven botanical collections consisting of: mounted specimens , wood , fruits , DNA bank , spirit , seed bank and ethnobotany (RBetno \u2013 ca. 200 specimens). For further details about the history and structure of the herbarium see . This daSamples are organised alphabetically across two floors in the herbarium building: the dicots families of angiosperms from A to N are stored on the first floor; the remaining families of dicots, monocots, gymnosperms, ferns, lycophytes, bryophytes, algae, fungi, lichens and the other collections on the second floor.Regarding the adopted taxonomic classification system, due to its large size and the efforts involved in rearranging so many specimens, currently the angiosperms are organised according to Fabaceae , Asteraceae , Rubiaceae and Melastomataceae . Non-angiosperm groups are represented as follows: Gymnosperms - Podocarpaceae (187), Gnetaceae (112), Pinaceae (73) and Araucariaceae (59); Ferns - Polypodiaceae , Pteridaceae , Dryopteridaceae and Aspleniaceae ; Bryophyte - Lejeuneaceae , Sphagnaceae (707), Leucobryaceae (622) and Metzgeriaceae (613); Algae - Rhodomelaceae , Cladophoraceae (835), Dictyotaceae (620) and Corallinaceae (487).Fig. JABOT system (GBIF) and the ) (GBIF) . Current) (GBIF) .The RB herbarium was created by the naturalist Jo\u00e3o Barbosa Rodrigues in 1890. The first specimens came from a private collection of about 25,000 specimens donated by Emperor Dom Pedro II . Aiming The herbarium specimen collection combines specimens from institutional projects, undergraduate and post-graduate research and exchanges or donations from other herbaria. In addition, from 1970 onwards, relevant national projects of flora documentation sent specimens to RB, such as RADAMBRASIL Project (1970-1985) and the Flora Program CNPq . Furthermore, as the official custodian for the Ministry of Environment, RB also receives many specimens from private companies with activities related to environmental impact studies and phytochemical products and most of these specimens are donated in exchange for identification. The institution includes 53 associate researchers and hosts around 550 visiting taxonomists every year, standing out as the most visited herbarium in Brazil.The RB uses the institutional system JABOT to perform all functions regarding herbarium management . The JABOT is a PostgreSQL database management system with 117 tables specifically created for botanical collections. The data insertion can be made directly into the JABOT interface or via uploading spreadsheets, with controlled and free text fields .Plant processing proceduresAlgae can also be mounted on acid-free paper with gummed cloth tape or stored in plastic boxes in the case of calcareous algae.The herbarium follows the usual procedures for processing specimens . Fresh mCollection digitisation historyProjeto de Informatiza\u00e7\u00e3o\u201d funded by Petrobras, which lasted until 2007. After this, between 2008 and 2010, without a project specifically directed towards data inclusion into the system, this task was performed only for new specimens of previously digitised families, by a smaller team, part of institutional projects and core herbarium staff. At the end of 2010, the Reflora project started, boosting data entry into the system and was completed during 2014. The GFJP and GUA herbaria were incorporated into RB in 2016 and 2017, respectively, which substantially increased the number of specimens entered into the system, as can be seen in Fig. Once JABOT was created in 2005, data entry for the herbarium started with the \u201cThe majority of specimens were collected in Brazil (ca. 90%) and the country\u2019s most widely represented region is the Southeast, where the herbarium is based . The south-eastern states of Rio de Janeiro and Minas Gerais are represented by the largest number of specimens and 28,000 (ca. 4%), respectively Fig. . One of -34.1618 and 5.5285 Latitude; -34.4531 and -74.1796 Longitude.Taxonomic ranksGroup: SpermatophytaFamily: ACANTHACEAE (6603 specimens/773 names); ACERACEAE (52/43); ACHARIACEAE (96/19); ACHATOCARPACEAE (27/4); ACORACEAE (3/6); ACTINIDIACEAE (33/19); ADOXACEAE (14/3); AGAVACEAE (82/43); AIZOACEAE (84/20); ALISMATACEAE (504/64); ALSTROEMERIACEAE (489/47); AMARANTHACEAE (2664/273); AMARYLLIDACEAE (727/220); ANACARDIACEAE (2918/227); ANISOPHYLLEACEAE (20/6); ANNONACEAE (6334/548); ANTHERICACEAE (18/10); APIACEAE (923/144); APOCYNACEAE (10292/1144); APODANTHACEAE (12/5); APONOGETONACEAE (2/2); AQUIFOLIACEAE (1382/168); ARACEAE (7726/1102); ARALIACEAE (1957/499); ARAUCARIACEAE (59/17); ARECACEAE (2235/546); ARISTOLOCHIACEAE (693/166); ASCLEPIADACEAE (3520/543); ASPARAGACEAE (272/115); ASPHODELACEAE (6/6); ASTERACEAE (45873/5672); ASTERANTHACEAE (5/1); AVICENNIACEAE (129/12); BALANOPHORACEAE (230/22); BALSAMINACEAE (61/13); BARRINGTONIACEAE (9/7); BASELLACEAE (64/8); BATACEAE (5/1); BEGONIACEAE (3434/251); BERBERIDACEAE (149/42); BETULACEAE (86/52); BIGNONIACEAE (9683/968); BIXACEAE (250/14); BOMBACACEAE (1465/187); BONNETIACEAE (142/17); BORAGINACEAE (5052/419); BRASSICACEAE (159/97); BROMELIACEAE (12391/1641); BURMANNIACEAE (224/49); BURSERACEAE (2006/171); BUTOMACEAE (7/2); BUXACEAE (13/6); CABOMBACEAE (59/10); CACTACEAE (3026/351); CALCEOLARIACEAE (6/3); CALLITRICHACEAE (15/7); CALOPHYLLACEAE (55/7); CALYCANTHACEAE (3/2); CALYCERACEAE (107/16); CAMPANULACEAE (1410/184); CANELLACEAE (51/12); CANNABACEAE (266/17); CANNACEAE (245/18); CAPPARACEAE (975/91); CAPRIFOLIACEAE (258/89); CARDIOPTERIDACEAE (22/7); CARICACEAE (160/22); CARYOCARACEAE (312/26); CARYOPHYLLACEAE (1156/468); CASUARINACEAE (41/12); CECROPIACEAE (110/22); CELASTRACEAE (2542/209); CENTROLEPIDACEAE (4/3); CERATOPHYLLACEAE (14/5); CHENOPODIACEAE (309/118); CHLORANTHACEAE (235/22); CHRYSOBALANACEAE (3841/339); CISTACEAE (60/32); CLEOMACEAE (513/56); CLETHRACEAE (346/19); CLUSIACEAE (2439/264); COCHLOSPERMACEAE (131/9); COLCHICACEAE (20/13); COMBRETACEAE (2715/180); COMMELINACEAE (2492/146); CONNARACEAE (1035/115); CONVALLARIACEAE (44/23); CONVOLVULACEAE (5549/504); CORIARIACEAE (11/6); CORNACEAE (121/41); CORYNOCARPACEAE (4/1); COSTACEAE (591/38); CRASSULACEAE (151/38); CRUCIFERAE (778/360); CUCURBITACEAE (2175/247); CUNONIACEAE (473/36); CUPRESSACEAE (169/84); CUSCUTACEAE (105/23); CYCADACEAE (6/10); CYCLANTHACEAE (256/30); CYMODOCEACEAE (3/3); CYPERACEAE (9590/1154); CYRILLACEAE (33/6); DIALYPETALANTHACEAE (25/2); DICHAPETALACEAE (293/44); DICLIDANTHERACEAE (22/7); DILLENIACEAE (2238/108); DIOSCOREACEAE (2179/150); DIPSACACEAE (45/28); DIPTEROCARPACEAE (12/33); DRACAENACEAE (29/12); DROSERACEAE (256/47); DUCKEODENDRACEAE (9/2); EBENACEAE (742/86); ELAEAGNACEAE (18/8); ELAEOCARPACEAE (991/98); ELATINACEAE (6/5); EMPETRACEAE (5/2); EPACRIDACEAE (28/22); EPHEDRACEAE (32/16); ERICACEAE (2111/298); ERIOCAULACEAE (2816/464); ERYTHROXYLACEAE (3067/163); ESCALLONIACEAE (77/8); EUPHORBIACEAE (16907/1973); EUPHRONIACEAE (4/3); FABACEAE (57/14); FAGACEAE (176/134); FLACOURTIACEAE (4123/204); GELSEMIACEAE (16/5); GENTIANACEAE (2239/250); GERANIACEAE (207/91); GESNERIACEAE (2849/284); GINKGOACEAE (2/1); GNETACEAE (112/13); GOODENIACEAE (56/19); GOUPIACEAE (9/3); GRISELINIACEAE (14/2); GUNNERACEAE (18/7); GUTTIFERAE (3053/379); HAEMODORACEAE (57/12); HALORAGACEAE (62/18); HAMAMELIDACEAE (17/14); HELICONIACEAE (1420/100); HEMEROCALLIDACEAE (18/10); HERNANDIACEAE (140/18); HIPPOCASTANACEAE (10/9); HIPPOCRATEACEAE (1133/113); HIPPURIDACEAE (2/1); HUMIRIACEAE (1237/82); HYACINTHACEAE (29/20); HYDNORACEAE (1/1); HYDROCHARITACEAE (108/27); HYDROLEACEAE (24/5); HYDROPHYLLACEAE (103/38); HYPERICACEAE (505/61); HYPOXIDACEAE (106/10); ICACINACEAE (688/64); ILLECEBRACEAE (5/4); IRIDACEAE (1336/243); IXONANTHACEAE (3/2); JUGLANDACEAE (24/31); JUNCACEAE (386/110); JUNCAGINACEAE (19/5); KRAMERIACEAE (165/10); LACISTEMATACEAE (625/17); LAMIACEAE (6952/907); LARDIZABALACEAE (2/2); LAURACEAE (12630/753); LECYTHIDACEAE (2281/214); LEGUMINOSAE (78391/7103); LENTIBULARIACEAE (889/91); LEPIDOBOTRYACEAE (2/2); LILIACEAE (164/75); LINACEAE (206/50); LINDERNIACEAE (9/5); LISSOCARPACEAE (8/2); LOASACEAE (166/46); LOBELIACEAE (8/3); LOGANIACEAE (1495/152); LOMANDRACEAE (2/2); LORANTHACEAE (5629/455); LYTHRACEAE (2867/300); MAESACEAE (11/2); MAGNOLIACEAE (173/66); MALESHERBIACEAE (4/4); MALPIGHIACEAE (11646/706); MALVACEAE (7095/846); MARANTACEAE (3594/275); MARCGRAVIACEAE (707/45); MARTYNIACEAE (13/9); MAYACACEAE (109/8); MELANTHIACEAE (29/14); MELASTOMATACEAE (30923/2316); MELIACEAE (4466/272); MENISPERMACEAE (1316/130); MENYANTHACEAE (113/10); MOLLUGINACEAE (205/12); MONIMIACEAE (4887/158); MONTIACEAE (2/1); MORACEAE (8940/799); MORINGACEAE (11/5); MUNTINGIACEAE (19/2); MUSACEAE (38/23); MYOPORACEAE (26/15); MYRICACEAE (33/17); MYRISTICACEAE (1545/119); MYRTACEAE (25903/1808); NARTHECIACEAE (1/1); NELUMBONACEAE (1/2); NEPENTHACEAE (32/31); NYCTAGINACEAE (3302/127); NYMPHAEACEAE (227/46); OCHNACEAE (3076/252); OLACACEAE (1331/127); OLEACEAE (334/121); ONAGRACEAE (1854/201); OPILIACEAE (229/13); ORCHIDACEAE (13096/2258); OROBANCHACEAE (239/57); OXALIDACEAE (1366/159); PANDANACEAE (16/16); PAPAVERACEAE (233/99); PASSIFLORACEAE (2958/203); PEDALIACEAE (15/9); PELLICIERACEAE (2/2); PENTAPHYLACACEAE (42/12); PERACEAE (94/15); PERIDISCACEAE (7/2); PHILESIACEAE (4/3); PHYLLANTHACEAE (231/54); PHYTOLACCACEAE (992/54); PICRAMNIACEAE (137/19); PICRODENDRACEAE (3/1); PINACEAE (73/100); PIPERACEAE (18265/631); PITTOSPORACEAE (57/22); PLANTAGINACEAE (451/106); PLATANACEAE (15/8); PLUMBAGINACEAE (218/55); POACEAE (18370/2588); PODOCARPACEAE (187/29); PODOSTEMACEAE (114/43); POLEMONIACEAE (128/68); POLYGALACEAE (6825/458); POLYGONACEAE (2373/256); PONTEDERIACEAE (461/38); PORTULACACEAE (556/41); POTAMOGETONACEAE (93/46); PRIMULACEAE (4897/332); PROTEACEAE (945/146); PUNICACEAE (21/3); PUTRANJIVACEAE (80/12); PYROLACEAE (24/13); QUIINACEAE (374/51); QUILLAJACEAE (2/1); RAFFLESIACEAE (65/9); RANUNCULACEAE (1031/376); RAPATEACEAE (312/60); RESEDACEAE (9/4); RESTIONACEAE (9/9); RHABDODENDRACEAE (4/5); RHAMNACEAE (1643/176); RHIZOPHORACEAE (185/26); ROSACEAE (1930/596); RUBIACEAE (31966/3124); RUPPIACEAE (35/6); RUSCACEAE (13/7); RUTACEAE (3974/476); SABIACEAE (110/21); SACCIFOLIACEAE (2/1); SALICACEAE (1272/188); SALVADORACEAE (2/2); SANTALACEAE (260/67); SAPINDACEAE (8942/519); SAPOTACEAE (4937/524); SARRACENIACEAE (17/14); SAURURACEAE (5/4); SAXIFRAGACEAE (388/133); SCHEUZERIACEAE (2/2); SCHISANDRACEAE (2/2); SCHLEGELIACEAE (41/12); SCHOEPFIACEAE (18/3); SCROPHULARIACEAE (2936/605); SIMAROUBACEAE (961/103); SIPARUNACEAE (232/20); SMILACACEAE (3730/79); SOLANACEAE (14488/1256); SONNERATIACEAE (2/3); SPHENOCLEACEAE (3/1); STACHYURACEAE (4/1); STAPHYLEACEAE (29/11); STEMONURACEAE (17/2); STERCULIACEAE (2398/268); STILBACEAE (2/2); STRELITZIACEAE (12/7); STYRACACEAE (630/52); SURIANACEAE (6/1); SYMPLOCACEAE (757/66); TACCACEAE (11/7); TAMARICACEAE (28/14); TAXACEAE (13/8); TEPUIANTHACEAE (8/5); THEACEAE (646/66); THURNIACEAE (10/2); THYMELAEACEAE (562/100); TILIACEAE (1518/146); TOFIELDIACEAE (10/5); TRAPACEAE (4/2); TRIGONIACEAE (961/45); TRIURIDACEAE (32/13); TROPAEOLACEAE (60/17); TURNERACEAE (1120/155); TYPHACEAE (111/14); ULMACEAE (1009/88); URTICACEAE (2916/232); VALERIANACEAE (237/193); VELLOZIACEAE (1471/206); VERBENACEAE (5550/541); VIOLACEAE (2500/256); VITACEAE (1266/123); VIVIANIACEAE (23/11); VOCHYSIACEAE (3971/237); WINTERACEAE (242/17); XANTHORRHOEACEAE (35/26); XYRIDACEAE (1135/181); ZAMIACEAE (19/15); ZANNICHELLIACEAE (8/2); ZINGIBERACEAE (532/63); ZOSTERACEAE (3/2); ZYGOPHYLLACEAE (92/46).Group: Ferns & LycophytesFamily: ANEMIACEAE (607 specimens/58 names); ASPLENIACEAE (2532/183); ATHYRIACEAE (716/109); BLECHNACEAE (1340/99); CULCITACEAE (17/4); CYATHEACEAE (1329/162); CYSTOPTERIDACEAE (48/14); DAVALLIACEAE (56/32); DENNSTAEDTIACEAE (502/100); DESMOPHLEBIACEAE (2/1); DICKSONIACEAE (145/27); DIPTERIDACEAE (4/2); DRYOPTERIDACEAE (3708/578); EQUISETACEAE (142/20); GLEICHENIACEAE (664/59); HEMIDICTYACEAE (28/1); HYMENOPHYLLACEAE (2099/170); ISOETACEAE (39/16); LINDSAEACEAE (539/74); LOMARIOPSIDACEAE (377/46); LYCOPODIACEAE (1620/167); LYGODIACEAE (375/15); MARATTIACEAE (198/24); MARSILEACEAE (57/17); MATONIACEAE (3/1); METAXYACEAE (62/4); OLEANDRACEAE (50/12); ONOCLEACEAE (8/3); OPHIOGLOSSACEAE (83/17); OSMUNDACEAE (115/19); PLAGIOGYRIACEAE (27/4); POLYPODIACEAE (5733/589); PSILOTACEAE (33/3); PTERIDACEAE (5280/577); SACCOLOMATACEAE (110/8); SALVINIACEAE (233/18); SCHIZAEACEAE (1524/69); SELAGINELLACEAE (1294/133); TECTARIACEAE (262/23); THELYPTERIDACEAE (1529/237); WOODSIACEAE (51/16).Group: BryophytesFamily: ACROBOLBACEAE (3 specimens/3 names); ADELANTHACEAE (7/5); ADELOTHECIACEAE (7/1); AMBLYSTEGIACEAE (87/25); ANDREAEACEAE (43/13); ANEURACEAE (255/19); ANOMODONTACEAE (11/8); ANTHOCEROTACEAE (45/8); ARNELLIACEAE (25/1); AULACOMNIACEAE (8/3); AYTONIACEAE (11/4); BALANTIOPSIDACEAE (142/12); BARTRAMIACEAE (202/61); BRACHYTHECIACEAE (386/68); BRUCHIACEAE (12/4); BRYACEAE (318/60); CALLIERGONACEAE (5/4); CALYMPERACEAE (475/46); CALYPOGEIACEAE (53/12); CATAGONIACEAE (6/2); CEPHALOZIACEAE (45/18); CEPHALOZIELLACEAE (57/15); CHONECOLEACEAE (12/3); CORSINIACEAE (3/3); CRYPHAEACEAE (15/10); DALTONIACEAE (8/5); DENDROCEROTACEAE (23/4); DICRANACEAE (357/88); DITRICHACEAE (40/26); DUMORTIERACEAE (85/2); ENTODONTACEAE (37/12); EPHEMERACEAE (1/1); ERPODIACEAE (40/6); EUSTICHIACEAE (7/5); FABRONIACEAE (24/9); FISSIDENTACEAE (270/59); FONTINALACEAE (18/10); FOSSOMBRONIACEAE (24/5); FRULLANIACEAE (635/43); FUNARIACEAE (50/19); GEOCALYCACEAE (48/15); GRIMMIACEAE (73/47); GYMNOMITRIACEAE (15/7); HEDWIGIACEAE (31/9); HELICOPHYLLACEAE (21/1); HERBERTACEAE (73/14); HOOKERIACEAE (54/28); HYDROPOGONACEAE (3/1); HYLOCOMIACEAE (19/8); HYPNACEAE (2/64); HYPNACEAE (327/64); HYPOPTERYGIACEAE (85/12); JAMESONIELLACEAE (121/13); JUNGERMANNIACEAE (75/32); LEJEUNEACEAE (1/255); LEJEUNEACEAE (2439/255); LEMBOPHYLLACEAE (153/25); LEPICOLEACEAE (6/2); LEPIDOZIACEAE (361/58); LEPYRODONTACEAE (7/1); LESKEACEAE (25/12); LEUCOBRYACEAE (622/89); LEUCODONTACEAE (17/8); LEUCOMIACEAE (8/3); LOPHOCOLEACEAE (202/29); LUNULARIACEAE (10/1); MARCHANTIACEAE (134/7); METEORIACEAE (131/37); METZGERIACEAE (613/53); MNIACEAE (96/32); MONOCLEACEAE (48/2); MYRINIACEAE (2/2); NECKERACEAE (250/48); NOTOTHYLADACEAE (15/4); ORTHODONTIACEAE (11/3); ORTHOTRICHACEAE (351/83); PALLAVICINIACEAE (259/13); PELLIACEAE (40/5); PHYLLODREPANIACEAE (1/1); PHYLLOGONIACEAE (98/6); PHYMATOCEROTACEAE (1/1); PILOTRICHACEAE (444/70); PLAGIOCHILACEAE (615/65); PLAGIOTHECIACEAE (15/6); PLEUROZIACEAE (1/1); POLYTRICHACEAE (1/46); POLYTRICHACEAE (346/46); PORELLACEAE (45/9); POTTIACEAE (471/167); PRIONODONTACEAE (33/7); PTERIGYNANDRACEAE (2/2); PTEROBRYACEAE (65/16); PTYCHOMITRIACEAE (25/7); PTYCHOMNIACEAE (1/1); PYLAISIADELPHACEAE (96/16); RACOPILACEAE (63/3); RADULACEAE (243/28); RHABDOWEISIACEAE (63/16); RHACHITHECIACEAE (3/3); RHACOCARPACEAE (64/5); RHIZOGONIACEAE (141/11); RICCIACEAE (52/22); RIGODIACEAE (21/2); RUTENBERGIACEAE (2/1); SCAPANIACEAE (56/22); SELIGERIACEAE (2/2); SEMATOPHYLLACEAE (427/52); SPHAGNACEAE (1/114); SPHAGNACEAE (707/114); SPLACHNACEAE (5/4); STEREOPHYLLACEAE (57/7); SYMPHYODONTACEAE (2/1); THUIDIACEAE (172/35); TRICHOCOLEACEAE (43/8).Group: AlgaeFamily: ACINETOSPORACEAE (40 specimens/10 names); ANADYOMENACEAE (33/6); ARESCHOUGIACEAE (3/3); BANGIACEAE (99/28); BONNEMAISONIACEAE (39/8); BOODLEACEAE (20/2); BRYOPSIDACEAE (159/32); CALLITHAMNIACEAE (187/71); CAULERPACEAE (295/34); CERAMIACEAE (516/104); CHAMPIACEAE (101/22); CHARACEAE (103/44); CHLAMYDOMONADACEAE (28/21); CHNOOSPORACEAE (5/1); CHORDARIACEAE (199/76); CLADOPHORACEAE (835/163); CLOSTERIACEAE (64/31); CODIACEAE (259/17); CORALLINACEAE (3/65); CORALLINACEAE (484/65); CYSTOCLONIACEAE (279/22); DASYACEAE (163/40); DASYCLADACEAE (9/4); DELESSERIACEAE (186/62); DERBESIACEAE (20/3); DESMIDIACEAE (273/193); DICTYOTACEAE (620/85); DUMONTIACEAE (11/9); ECTOCARPACEAE (75/35); ERYTHROTRICHIACEAE (3/2); GALAXAURACEAE (97/12); GELIDIACEAE (204/31); GELIDIELLACEAE (43/7); GIGARTINACEAE (174/32); GRACILARIACEAE (296/30); HALIMEDACEAE (41/8); HALYMENIACEAE (216/31); HILDENBRANDIACEAE (5/3); HYPNEACEAE (74/5); KALLYMENIACEAE (27/9); KORNMANNIACEAE (6/2); LAMINARIACEAE (57/18); LIAGORACEAE (22/14); LOMENTARIACEAE (79/18); NEMASTOMATACEAE (4/3); PALMOPHYLLACEAE (3/1); PEYSSONNELIACEAE (18/7); PHYLLOPHORACEAE (113/14); PLOCAMIACEAE (74/9); POLYPHYSACEAE (49/7); PTEROCLADIACEAE (169/5); PYLAIELLACEAE (18/3); RHIZOPHYLLIDACEAE (15/2); RHODOMELACEAE (1334/278); RHODYMENIACEAE (146/38); SARGASSACEAE (411/58); SCENEDESMACEAE (16/11); SCHIZYMENIACEAE (3/3); SCINAIACEAE (5/3); SCYTOSIPHONACEAE (71/17); SEBDENIACEAE (5/1); SIPHONOCLADACEAE (45/9); SOLIERIACEAE (66/17); SPHACELARIACEAE (38/17); SPOROCHNACEAE (27/13); SPYRIDIACEAE (44/16); UDOTEACEAE (39/15); ULVACEAE (1/58); ULVACEAE (587/58); VALONIACEAE (15/10); WRANGELIACEAE (118/42); ZYGNEMATACEAE (199/110).Herb\u00e1rio Dimitri Sucre BenjaminRBDried and pressedOtherCreative Commons Attribution 4.0 International License.This work is licensed under a RB - Rio de Janeiro Botanical Garden Herbarium Collectionhttp://www.gbif.org/dataset/4300f8d5-1ae5-49e5-a101-63894b0058681RB - Rio de Janeiro Botanical Garden Herbarium CollectionDarwin Core Archive (DwC-A)46http://ipt.jbrj.gov.br/jbrj/archive.do?r=jbrj_rb&v=84.131Version 84.131, published in 2017-11-22) or via JABOT system (http://www.jbrj.gov.br/jabot). For the integration of Web-based applications, the JABOT Web service is available at http://servicos.jbrj.gov.br/jabot.The RB herbarium has 750,000 mounted specimens, making it the largest herbarium in Brazil . The fulProject title: \u201cInformatiza\u00e7\u00e3o do Herb\u00e1rio do Jardim Bot\u00e2nico do Rio de Janeiro\u201d .Project description: The digitisation of specimens started with the creation of an institutional system, known as JABOT. Constant upgrades were made during the last decade, including the construction of a digitisation module and improvements to the public interface.Funding: Petrobras (Petr\u00f3leo Brasileiro S.A.)Duration: 2005-2007Project title: Global Plants InitiativeProject description: The project focused on constructing a database and producing high-resolution images (600 dpi) of all type specimens deposited at RB. The image capture workflow involved inverted scanners developed by the Royal Botanic Gardens, Kew, called HerbScan.Funding: The Andrew W. Mellon FoundationDuration: 2007-2011Project title: \u201cPlantas do Brasil: Resgate Hist\u00f3rico e Herb\u00e1rio Virtual para o conhecimento e conserva\u00e7\u00e3o da flora brasileira \u2013 REFLORA\u201d Project description: This project, coordinated by the JBRJ, developed a virtual herbarium for public access, including samples collected in the Brazilian territory, during the 18th, 19th and 20th centuries, deposited at European herbaria. Concomitantly with the repatriation process, this project also financed the imaging of the RB specimens, which were also published on the Reflora Virtual Herbarium.Funding: Brazilian National Council for Scientific and Technological Development (CNPq); Research Support Foundation of the State of Rio de Janeiro (FAPERJ); Minas Gerais State Agency for Research and Development (FAPEMIG); Vale Foundation, Natura Cosmetics and Newton Fund.Duration: 2010-2016Project title: \u201cConhecimento e conserva\u00e7\u00e3o da flora brasileira: futuros desafios das cole\u00e7\u00f5es biol\u00f3gicas do Jardim Bot\u00e2nico do Rio de Janeiro\u201d .Project description: The project, aimed to capture data and images of RB specimens previously unavailable in the JABOT system, especially those in the fungi, bryophyte, algae, fruits and wood collections. It also facilitated visits by taxonomists, improving the quality of identifications, particularly for those groups for which there are no specialists at the RB.Funding: The Brazilian Science, Technology and Innovation Ministry (MCTI), CNPq and The Brazilian Biodiversity Information System (SiBBr).Duration: 2012-2015Project title: \u201cContribui\u00e7\u00f5es do Jardim Bot\u00e2nico do Rio de Janeiro \u00e0 implementa\u00e7\u00e3o do SiBBr\u201d .Project description: The Brazilian Biodiversity Information System (SiBBr), is an initiative that intends to ensure the proper use of Brazilian biodiversity and ecosystem data, integrating information and facilitating processes of decision-making and public policy development. It also assists national herbaria in the digitisation of their specimens and in the repatriation of images of specimens from European and North American herbaria. The RB contributes to this initiative by making available its collections' data and those of Reflora Virtual Herbarium and the Brazilian Flora 2020, projects coordinated by this institution. This initiative currently supports daily data and image capture of new specimens incorporated into RB herbarium.Funding: MCTI, SiBBr, CNPqDuration: 2014-2017Project title: \u201cInvent\u00e1rio Florestal Nacional\u201d Project description: The National Forestry Inventory (IFN) is coordinated by the Brazilian Forest Service (SFB) and aims to collect socio-economic and ecological information about the country's forest resources. It supports the formulation, implementation and execution of public policies for the development, use and conservation of these resources. In the state of Rio de Janeiro, the process for identification of botanical material has been carried out by taxonomist consultants hired by the IFN in the RB. In addition, all the fertile specimens collected by the project in the other Brazilian states are also sent to the RB. This project financed the acquisition of imaging equipment for all participant herbaria, contributing to collections digitisation. Also, at RB, due to its size, three technicians were hired to help with day-to-day herbarium activities.Funding: Brazilian Forest ServiceDuration: 2013-currentThe costs related to the maintenance and curation of a herbarium are significant and curators are always under pressure to gain financial support . There iThe first phases of the project of digitisation and publishing the contents of the RB herbarium occurred between 2005 and 2007, with an investment of around US$254,000 for the incorporation of metadata of 291,630 specimens and digitisation of 10,646 specimens . From 20Regarding infrastructure, the dataset associated with the RB collection represents 2 5.6% of all institutional digital storage space, 6.8% of processing power (CPUs) and 9.7% of memory. The associated costs of power consumption, especially of climate control in the tropics, are also significant.Despite the fact that literature cites a number of initiatives of online open-access biodiversity databases that failed due to lack of funding, after the initial push for resources , there hThus, it is considered that the trade-off for committing a substantial portion of theinstitutional budget, as well as technical and scientific staff time, to digitisation of and publication about the collections, has been very positive for the institutional relevance, as well as for its visibility and image and this is associated with a resulting gain in funding opportunities."} +{"text": "The subfamily Syntermitinae comprises a group of Neotropical termites with 18 genera and 101 species described. It has been considered a natural group, but relationships among the genera within the subfamily remain uncertain, and some genera appear to be non-monophyletic. Here, we provide a comprehensive phylogeny including six Neotropical species of Termitinae as outgroup, 42 Syntermitinae species as ingroup, 92 morphological characters and 117 molecular sequences (109 obtained for this study and 8 from GenBank) of 4 gene regions . Morphological and molecular data were analyzed in combination, with the Bayesian inference method, and the important aspects of termite biology, defense and feeding habits are discussed based on the resulting tree. Although useful for providing diagnostic characters, the morphology of the soldier caste reveals several cases of convergence; whereas the feeding habit shows indications of evolutionary significance. Cahuallitermes) to northern Argentina , with the richest generic and specific diversity in the Brazilian Cerrado biome. Fifteen syntermitine genera occur in the Cerrado, where several species of Cornitermes, Silvestritermes and Syntermes construct conspicuous epigeal nests that characterize this savanna-like landscape. Cornitermes cumulans can reach a nest density of 55/ha, and is considered a keystone species in the Cerrado [The subfamily Syntermitinae comprises a group of Neotropical termites that ranges from southern Mexico absent ; (1) pre02. Shape of hyaline tip: (0) flat ; (1) fin03. Silhouette in dorsal view: (0) cuspidate ; (1) lan04. Cuspidate margins: (0) slender ; (1) cle05. Postmentum lateral margins: (0) angled ; (1) sin06. Postmentum length: (0) elongated ; (1) sho07. Shape of head in dorsal view: (0) rectangular, elongated; (1) rectangular, sort; (2) rounded.08. Number of antennal articles: (0) 20; (1) 19; (2) 18; (3) 17; (4) 16; (5) 15; (6) 14; (7); 13; (8); 12 (9) 11.09. Head capsule microsculpture: (0) absent; (1) present (character 7 of ).10. Visibility of frontal pore aperture: (0) indistinct ; (1) dis11. Frontal pore shape: (0) retracted and narrow ; (1) pro12. Membranous tissue at frontal pore aperture: (0) absent ; (1) pre13. Frontal projection: (0) absent ; (1) pre14. Length of frontal tube: (0) reaching clypeus ; (1) sur15. Row of stout bristles on outer margins of forecoxae: (0) absent; (1) present (character 29 of ).Labiotermes [16. Stout bristles along femur: (0) absent; (1) present (as described for iotermes ).17. Ornaments on internal face of tibia: (0) flat; (1) row of 20 spines.18. Tibial spurs formula: (0) 3:2:2; (1) 2:2:219. Shape of outer margin of forecoxae: (0) nearly straight ; (1) wit20. Outer margin of forecoxae, distal portion: (0) round ; (1) kee21. Spine on proximal portion of coxae: (0) absent ; (1) pre22. Lateral lobes of pronotum: (0) not projected ; (1) sli23. Lateral margins of lobes (pronotum): (0) rounded ; (1) ang24. Lateral margins of lobes (mesonotum): (0) rounded ; (1) ang25. Lateral margins of lobes (metanotum): (0) rounded ; (1) ang26. Outer margin of pronotum: (0) smooth ; (1) ser27. Outline of margins of metanotum and mesonotum: (0) smooth ; (1) ser28. Molar region: (0) indistinct ; (1) dis29. When distinct, relative size of molar region: (0) reduced ; (1) dev30. First marginal tooth of left mandible: (0) absent; (1) present31. Second marginal tooth of left mandible: (0) absent; (1) present.32. Shape between first and second marginal teeth of left mandible: (0) \u201cV\u201d concavity; (1) cutting edge33. Shape of cutting edge between first and second marginal teeth of left mandible: (0) smooth; (1) serrated.34. First marginal tooth of right mandible: (0) absent; (1) present35. Second marginal tooth of right mandible: (0) absent; (1) present.36. Position of second marginal tooth: (0) in proximal portion; (1) in middle.37. Shape of apical tooth: (0) slender; (1) strong; (2) sinuous.38. Apical tooth curvature: (0) strongly arched; (1) slightly arched.39. Internal outline of apical tooth: (0) concave ; (1) sin40. Subapical tooth: (0) present; (1) absent.41. Gizzard: Ornamentation of first-order pulvilli: (0) without notable ornaments ; (1) wit42. Insertion of stomodeal valve in mesenteron: (0) apical ; (1) sub43. Mesenteric tongue: (0) absent; (1) present.44. Mesenteric tongue, proximal portion: (0) robust ; (1) con45. Alignment of mesenteric tongue: (0) continuous with external face of the mesenteric arch ; (1) wit46. Secondary mesenteric tongue: (0) absent; (1) present.47. Malpighian tubules attachment: (0) in two pairs; (1) four united.48. Large ampulla at insertions of Malpighian tubules: (0) absent; (1) present.49. Position of Malpighian tubules: (0) internal to mesenteric arch; (1) external to mesenteric arch.The P1 internal ornaments were described by Rocha and Constantini , and the50. Ornaments: (0) absent; (1) present.51. Type of spines covering central area (0) Small spines in rows; (1) aciculiform; (2) robust spines; (3) as thin setae; (4) trifurcated spines.52. Degree of sclerotization of spines: (0) slightly sclerotized; (1) strongly sclerotized.53. Pattern of spine coverage in central area: (0) transverse; (1) longitudinal; (2) spaced.54. Position of spines of central area, relative to mesenteric tongue: (0) after mesenteric tongue; (1) lateral to mesenteric tongue.55. Central ridges: (0) absent; (1) present.56. Spines around mesenteric tongue: (0) absent; (1) present.57. Type of spines around mesenteric tongue: (0) single; (1) in small rows.58. Coverage in distal area: (0) absent; (1) present.59. Pattern of coverage in distal area: (0) sparse; (1) grouped in three areas.60. When grouped in three areas: (0) complete columns; (1) incomplete columns; (2) rounded areas.61. Shape of P1: (0) tubular; (1) dilated.62. Length of P1 relative to abdomen: (0) nearly the same (relatively outstretched in the abdomen); (1) longer (relatively coiled inside the abdomen).63. Shape of dilated portion: (0) fusiform; (1) globose.64. Transition from tubular portion to dilated portion of P1, see arrows: (0) distally constricted ; (1) gra65. P1 orientation in relation to body axis: (0) parallel ; (1) dia66. Shape of P1 final portion: (0) tubular ; (1) con67. Shape of tubular P1 final portion: (0) arched; (1) straight.68. Position of P2 insertion relative to abdomen length: (0) distally ; (1) at 69. Position of P2 insertion in dorsal view: (0) on left side of body; (1) on right side of body.70. Symmetry of enteric valve armature: (0) hexa-radial; (1) tri-radial; (2) asymmetric.71. Category of ridges: (0) large pads ; (1) sim72. Type of finger-like ridge: (0) protruded ; (1) obl73. Type of lobate ridge: (0) slightly lobed ; (1) aur74. Proportions of lobate ridge: (0) equal; (1) unequal.75. When slightly dilated at apex, length: (0) elongated; (1) short.76. Ornaments: (0) absent; (1) present.77. Ornament coverage: (0) triangular; (1) aciculiform.78. Initial portion of P3: (0) directly connected ; (1) bot79. Smooth diverticulum of P3a: (0) absent; (1) present.80. P3b shape in dorsal view: (0) globose ; (1) arc81. Direction of P3b when arched: (0) turned forward ; (1) tur82. Insertion of isthmus: (0) apical ; (1) sub83. Size proportion of head to thorax: (0) head much larger than thorax ; (1) hea84. Body in profile: (0) slender ; (1) wai85. Mandibles: Relative size of left apical tooth: (0) smaller than M1 ; (1) equ86. Edge of apical tooth: (0) straight ; (1) con87. M3 tooth on left mandible: (0) present, conspicuous ; (1) pre88. M2 tooth on right mandible: (0) present, conspicuous ; (1) pre89. Relative position of right M2 tooth: (0) near middle of M1 and molar plate ; (1) nea90. Right M2 posterior margin: (0) straight; (1) concave.91. Molar plate notch: (0) absent; (1) present, 90 degrees , arrow; 92. Molar region: (0) with ridges; (1) with reduced ridges; (2) without ridges.We chose four regions of the mitochondrial genome, Cytochrome Oxidase I and II , Cytochrome b (Cyt B ~340 bp) and 16S rDNA (~430 bp). The DNA was extracted preferentially from the head and thorax of a single soldier individual preserved in 95% ethanol , with thThe saturation of the molecular data was assessed with DAMBE v.6.0.48 using thTo evaluate the most useful data set, we made several tests combining different sets of sequences , with and without the morphological data, and with the protein-coding sequences partitioned either by genes or by the codon position. The results are summarized in the The models for each DNA data partition were determined using the JModel Test 2 and PartAncestral character states were reconstructed with the help of Mesquite v.3.04 , by the From the total of 48 species used in our analyses, we obtained DNA data from three or four different gene for 25 species, two different sequences for 16 species and only one sequence for 4 species . Two taxAmong the trees obtained, three of them present informative topology (with few polytomies) and high posterior probabilities ; 1)The result of an analysis with Morphology + COII + 16S rDNA, partitioned by genes represented in Acangaobitermes krishnai, Cahuallitermes intermedius, Macuxitermes triceratops and Noirotitermes noiroti represented by only one sequence and Armitermes armiger and Ibitermes tellustris, with no sequences, remains stable in the three more consistent trees , not resolved in tree A and positioned in trees B and C as a sister group of the yellow branch, composed of Rhynchotermes (indicated by the acronym \u201cRH\u201d), Procornitermes (PR), Cahuallitermes (CA) and Cornitermes (CO). The relationships among the taxa are indicated by dark-green branches; Genuotermes (GESP), Curvitermes (CUOD), Embiratermes (EM), Paracurvitermes (PAMA), Cyrilliotermes (CYAN) and Silvestritermes (SI); possible paraphyletic in trees A and B, and recovered as a monophyletic group in tree C.The more notable differences among the selected trees are: The position of the genus Although these results do not contradict each other, for prudence we opted to reconstruct and discuss the ancestral character states using tree A, which is less resolved but more conservative.Armitermes (possibly), Procornitermes (possibly), Embiratermes, and Ibitermes.The sample of species is sufficiently comprehensive to allow a discussion that previous studies did not attempt. Four genera appeared as paraphyletic in our analysis: Armitermes into a single genus, since the node that it is grouping the five taxa has a high posterior probability. Nevertheless, considering we only obtain one sequences for Macuxitermes, and also the support for the three more internal nodes are low, we think more studies are necessary to infer consistently the relationship among the taxa before introducing nomenclatural changes; for Procornitermes, resurrecting it from Triacitermes Emerson, now including Procornitermes triacifer and P. araujoi is a admissible solution, however the paraphyly of the genus is not a consensus among the results. More detailed studies for these cases are necessary before formal proposals for nomenclatural changes can be made.The cases of Embiratermes and Ibitermes within other members of the subfamily, since their named species used herein as terminals are spread all over the tree.A revisionary work is necessary in the next future to reassess generic and specific limits as well as the intergeneric relationships of Genuotermes, deeply inserted in our tree. Although the association with Syntermitinae is unintuitive, some unique characteristics are shared with Syntermitinae. The soldier frontal-gland aperture is at the tip of a large projection located in the frontal region of the head; the soldier mandibles have a clearly recognizable molar plate and prominence, as in Silvestritermes [Cyrilliotermes [Curvitermes [A surprising result is the position of ritermes , Cyrilliiotermes , and Curvitermes ; and thevitermes . ConsideTwo aspects stand out in termite research: defense and feeding habits. The first aspect relates to the soldier caste in Isoptera, which comprises a very particular case for evolutionary biology. Soldiers are a \u201cburden\u201d on the colony maintenance, since they need to be fed by the workers, and the effective contribution of a very specialized caste for the colony defense is not clear. The proportion of soldiers and workers varies widely among species and nearOrthognathotermes sp. is formally classified as \u201cSlashing/Snapping\u201d, but this is not relevant to the present discussion; the result is represented in For the reconstruction of the defense behavior, each taxon was classified according to the categories of primary individual defense mechanisms summarized in . Three cRhynchotermes nasutissimus Click here for additional data file.S1 FigThe two firsts plots correspond to each run and the low to the combined result.(TIF)Click here for additional data file.S2 FigThe two first plots correspond to each run and the low to the combined result.(TIF)Click here for additional data file.S3 FigThe two first plots correspond to each run and the low to the combined result.(TIF)Click here for additional data file.S4 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S5 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S6 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S7 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S8 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S9 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S10 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S11 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S12 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S13 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S14 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S15 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S16 FigThe respective posterior probability is indicated above each node, the branch color represents the posterior probability.(TIF)Click here for additional data file.S1 File(DOCX)Click here for additional data file."} +{"text": "Kashala (2005) [25]Cluver (2006) [26]Kashala (2006) [27]Cluver (2007) [28]Menon (2007) [29]Okello (2007) [30]Cluver (2008) [31]Cluver (2009) [77]Doku (2009) [34]Elhamid (2009) [32]Menon (2009) [35]Bakare (2010) [36]Doku (2010) [37]Mueller (2011) [38]Puffer (2012) [39]Abbo (2013) [40]Atilola (2013) [41]Cortina (2013) [42]Kinyanda (2013) [43]Marais (2013) [44]Bhana (2014) [45]Devries (2014) [46]Escueta (2014) [47]Lachman (2014) [48]Marais (2014) [49]Skeen (2014) [51]Sharp (2014) [50]Waller (2014) [52]Asante (2015) [53]Casale (2015) [33]Chirwa-Mwanza (2015) [62]Collishaw (2015) [54]Hermenau (2015) [55]Mazzucato (2015) [56]Okewole (2015) [78]Pappin (2015) [57]Profe (2015) [58]Abdulmalik (2016) [59]Bella-Awusah (2016) [60]Bhana (2016) [61]Cortina (2016) [63]Dow (2016) [64]Doku (2016) [65]Hecker (2016) [66]Hensels (2016) [67]Lentoor (2016) [68]Levetan (2016) [69]Okewole (2016) [71]Puffer (2016) [72]Skeen (2016) [73]Sherr (2016) [74]Thumann (2016) [75]Tucker (2016) [76]Mazzucato (2017) [70]After publication of the article , it has This has now been corrected in the original article."} +{"text": "After the publication of this work it was nAdditional file 1: Table S1.List of reporter genes and pathways. (XLSX 398 kb)Additional file 2: Table S2.AmpliSeq identifiers and primer pairs of reporter genes. (XLSX 84 kb)Additional file 3:Heatmap of pathway activity as in Figure 2B, with pathway names. (PNG 294 kb)"} +{"text": "TP53 deficiency remains a major adverse event in Multiple Myeloma (MM) despite therapeutic progresses. As it is not possible to target TP53 deficiency with pharmacological agents, we explored the possibility of activating another p53 family member, p73, which has not been well studied in myeloma. (2) Methods: Using human myeloma cell lines (HMCLs) with normal or abnormal TP53 status, we assessed TP73 methylation and expression. (3) Results: Using microarray data, we reported that TP73 is weakly expressed in 47 HMCLs and mostly in TP53 wild type (wtTP53) HMCLs (p = 0.0029). Q-RT-PCR assays showed that TP73 was expressed in 57% of wtTP53 HMCLs (4 out of 7) and 11% of TP53 abnormal (abnTP53) HMCLs (2 out of 18) (p = 0.0463). We showed that TP73 is silenced by methylation in abnTP53 HMCLs and that decitabine increased its expression, which, however, remained insufficient for significant protein expression. Alkylating drugs increased expression of TP73 only in wtTP53 HMCLs but failed to synergize with decitabine in abnTP53 HMCLs. (4) Conclusions: Decitabine and melphalan does not appear as a promising combination for inducing p73 and bypassing p53 deficiency in myeloma cells.(1) Background: TP53 [TP53 were exclusively found in myeloma cells displaying a hemi-deletion of the short arm of chromosome 17 (del17p) [TP53 mutations, which is low at diagnosis (around 3%), increases with relapses and is high in plasma cell leukemia and human myeloma cell lines , these latter mostly deriving from extramedullary MM and mainly from PCL [Met, which were selected for their ability to induce cell death in p53 mutated cells were shown to bind to p53 protein [TP53 status and p53 expression [TP53 mutations, which are irreversible, are an adverse event whatever the treatment regimen, alternative treatments that bypass or circumvent p53 are needed. For instance, the p53 family member p73 could be of interest as p73 is also able to transactivate pro-apoptotic genes [TP73 is rarely mutated but frequently silenced by CpG methylation in hematological malignancies and in multiple myeloma (MM) [TP73 expression might thus be reactivated by drugs preventing CpG methylation after DNA replication such as decitabine. To assess the interest in activating p73 in myeloma cells, we studied p73 expression and regulation, TP73 methylation and TP73 sequencing in a large panel of human myeloma cell lines HMCLs with a normal or abnormal TP53 status [Multiple Myeloma (MM) is characterized by an important biological heterogeneity related to recurrent chromosomal abnormalities, which occurs early in the disease development at the MGUS stage . The recTP53 . Mutatiofrom PCL ,5,6,7,8. protein . Howeverpression ,11. Becaic genes ,13. Moreoma (MM) ,15,16,173 status .TP73 mRNA in 47 HMCLs using Affymetrix microarray data [TP53 status (wtTP53) appeared to significantly express higher level of TP73 mRNA than abnTP53 HMCLs or an abnormal TP53 status and 15 TP53 mutated (mutTP53) HMCLs) , in one out of three delTP53 HMCLs (JJN3) and in one out of fifteen mutTP53 HMCLs (XG11), p = 0.0463, Mann\u2013Whitney test, HMCLs) [7,11,18ey test, B. p73 exey test, C. Whole radation .TP73 promoter, we performed nested methyl-specific PCR (MS-PCR) targeting the CpG island upstream of the gene and could thus not detect \u0394Np73, we performed three RT-PCRs to assess the total TP73 expression (exons 7\u201310), the full-length TAp73 (exons 2\u20136) and the \u0394Np73 (exons 3\u2032\u20136) isoforms, respectively. The TAp73 isoform was increased in the three mutTP53 HMCLs, although in KMS12PE the \u0394Np73 isoform was the main increased isoform JJN3 HMCL . TP73 gene also harbors an intrinsic CpG island that governs \u0394Np73 isoform transcription. Thus, TP73 gene appears particularly methylated in MM cells and demethylation might equally induce expression of TAp73 and \u0394Np73 isoforms, the latter being an inhibitory isoform [TP73 expression suggesting a stabilization/lack of degradation of the protein that might be related to the presence of the mutation in the transactivation inhibitory domain, which is involved in degradation [TP73 and p73 expression: this regulation seemed to be restricted to wtTP53 HMCLs as it did not occur in the delTP53 JJN3 HMCL. This finding is consistent with the possible regulation of TP73 expression via p53/p21/E2F1, which can only occur in wtTP53 HMCLs [mutTP53 HMCLs that displayed a TP73 expression after decitabine treatment. Moreover, MDM2, which stabilizes p73 instead of inducing its degradation [wtTP53 HMCLs [TP73 expression was shown to be regulated by HDAC: indeed, the HDAC inhibitor sodium butyrate increased the \u201cfree\u201d E2F1 pool and therefore TP73 transactivation independently from p53 [In myeloma, regulation of p73 expression has not been deeply investigated yet. For instance, ll death ,21. Howehylation . Indeed,g to DNA . In KMS1 isoform . We founradation . In threwt HMCLs . Indeed,radation , could twt HMCLs . Neverthfrom p53 . We did HMCLs were previously described ,11. UnmeDNAs were treated with bisulfite as indicated by the supplier. Methylation specific PCRs and quantifying PCR (PCR-Q) were performed after a first amplification (PCR1). PCR1, M-PCR, U-PCR and PCR Q were run with 25, 17, 20 and 19 cycles, respectively. The following primers were used: PCR-1 GTTTTGGGTTTTGGGAGTTGAGAG and ACCACCCACTTCTCCTATAAAA ; U-PCR GGGTTATTATGGGTAGAGGATATT and ACATACTAAACAAATTCCAAACAACTCTC 112 bp); and PCR Q TAAATAGTGGGTGAGTTATGAAGATGT and TACACCAAACCCTAACTAAAAAACC (285 bp). Extracted RNAs were reversed transcripted and amplified as previously described [ bp; and TP73 RT-PCR assays, the following primers were used: TAp73 ex2-6 CACCACGTTTGAGCACCTCT and AGATTATTGCCTTCCACGCG (630 bp); TP73 ex7-10 GACGGAATTCACCACCATCCT and CCAGGCTCTCTTTCAGCTTC (389 bp); and \u0394Np73 ex3\u2032-6 CCATGCTGTACGTCGGTGAC and CCAAATCCTTCTCCCTATCC (519 bp). For TP73 Q-PCR assays, the TP73 (Hs01056230_m1) and RPL37A (Hs01102345_m1) probes were used.For Expression of p53 and p73 was determined by Western blotting as previously described . A minim"} +{"text": "In 2011, the 46 World Health Organization (WHO) African Region (AFR) member states established a goal of measles eliminationWHO and the United Nations Children\u2019s Fund (UNICEF) estimate vaccination coverage using annual government-reported administrative data and data from independent surveys. During 2013\u20132015, the estimated MCV1 coverage in AFR increased from 71% to 74%, while the number of AFR countries with \u226595% MCV1 coverage decreased from eight (17%) to seven (15%) . In 2015Countries performing measles case-based surveillance electronically report surveillance dataOverall, 176,785 confirmed measles cases were reported in AFR through case-based surveillance during 2013\u20132016 . The numAlthough measles incidence decreased 63% in AFR during 2013\u20132016, the region did not meet vaccination coverage, surveillance, and disease incidence targets needed to achieve measles elimination by 2020. During 2013\u20132015, estimated MCV1 coverage increased only 3%, and in 2015 was <95% in 87% of AFR countries. Among the estimated 8.9 million infants in AFR who did not receive MCV1 in 2015, approximately 4.8 million (54%) resided in Nigeria (3 million), Ethiopia (0.7 million), the Democratic Republic of the Congo (DRC) (0.6 million), and Angola (0.5 million) countries achieved the target of <1 case per 1 million population in 2016. However, most confirmed cases detected during 2013\u20132016 were among children aged 9\u201359 months who were unvaccinated or had unknown vaccination status. In addition, 84% of cases were reported from the same four countries that accounted for half of children who missed MCV1: Nigeria (44%), Ethiopia (22%), Angola (10%), and DRC (8%). The recent WHO Measles and Rubella Global Strategic Plan Midterm Review emphasized the limits of MCV coverage data as an indicator and recommended, with SAGE endorsement, using measles disease incidence as another indicator to guide elimination efforts and United Nations Children\u2019s Fund (UNICEF) estimated first dose of measles-containing vaccine (MCV1) coverage in countries of the WHO African Region (AFR) to be 73% and >90% in 13 (28%) of 46 AFR countries. Among 35 measles supplementary immunization activities (SIAs) conducted during 2011\u20132012, 23 (66%) had >95% administrative coverage. Nineteen (44%) countries met the two key surveillance performance indicator targets. In 2012, only 16 (37%) countries met the incidence target of <5 cases per 1 million population.In 2015, WHO-UNICEF estimated MCV1 coverage in AFR to be 74%; seven (15%) countries reported \u226595% MCV1 coverage. Among 52 measles SIAs conducted during 2013\u20132016, 41 (79%) reported \u226595% administrative coverage. In 2016, 19 (40%) countries met both surveillance performance indicator targets. In 2016, only 15 (32%) countries met the target of <1 case per 1 million population.To eliminate measles by 2020, AFR countries need to achieve high (95%) 2-dose measles vaccination coverage, through introduction of a second MCV dose into routine immunization programs, increasing routine immunization coverage, improving SIA quality, fully implementing elimination-standard surveillance, conducting annual district-level risk assessments, and establishing national verification committees and a regional commission for the verification of measles elimination."} +{"text": "Bph14, QBph3, QBph4, Bph17, Bph15, Bph20, Bph24, Bph6, Bph3, Bph9, Bph10, Bph18 and Bph21) into cultivar 9311 by marker assisted backcross breeding (MABB). Through positive and negative selection we narrowed the segments from donors containing Bph14, Bph15, Bph6 and Bph9 to 100\u2013400\u2009kb. Whole-genome background selection based on a high resolution SNP array was performed to maximize reconstitution of the recurrent parent genome (RPG 99.2\u201399.9%). All genes reduced BPH growth and development and showed antibiotic responses in seedlings. Based on genetic effects and amino acid sequences of genes in three clusters we inferred that Bph10 and Bph21 might be identical to Bph26, whereas Bph9 and Bph18 were different. Bph15 might be same with Bph17, but QBph4, Bph20 and Bph24 might be different. We believe that these NILs will be useful in rice BPH resistance research and breeding.Brown planthopper (BPH) is the most destructive pest of rice in Asia. To date 29 BPH resistance genes have been identified, but only a few genes are being used in breeding due to inefficient markers for marker-assisted selection (MAS) and little knowledge of the real effects of the genes. In this study we individually transferred 13 genes or QTLs ( Nilaparvata lugens St\u00e5l), a monophagous sucking insect, is the most damaging insect pest of rice in Asia14Brown planthopper encode coiled-coil, nucleotide-binding, leucine-rich repeat (CC-NB-LRR) proteins, whereas Bph17 consists of three clustered genes encoding lectin-receptor kinases, and Bph29 encodes a B3 DNA-binding domain8111213At least 29 resistance genes have been identified in Bph3 and Wxa alleles was successfully broken by negative selection allowing development of ILs with broad-spectrum resistance to BPH and good qualityBph18 in positive selection, and 260 SSR markers for background selection a group of ILs carrying Bph18 were developedMolecular marker-assisted backcross breeding (MABB) has greatly improved the efficiency and effectiveness of rice breeding. There are three aspects of MABB, namely, positive selection for the target gene using linked markers, negative selection of alleles from the donor parent surrounding the target gene, and background selection for the maximum recovery of the recurrent parent genome using polymorphic markers covering the whole genome151617Bph3 and Bph17), B5 (Bph14 and Bph15), IR54751-1-2-44 (QBph3 and QBph4), IR65482-4-136 (Bph10), IR71033-121 (Bph20 and Bph21), IR65482-7-216 (Bph18), Swarnalata (Bph6), Pokkali (Bph9) and BR96 (Bph24)]1121222325262728Bph14, Bph17 and Bph26, respectively.In our study, 13 BPH resistance genes from nine donors were obtained from IRRI, Wuhan University and Guangxi Academy of Agricultural Sciences. Hua 2613S (H2613S) is an improved two-line thermo-sensitive genic male sterile line with blast resistance gene R6 added by molecular marker assisted selection to the genetic background of Guangzhan 63S (data not shown). Both cv. 9311 and Guangzhan 63S are leading male and female parents for a number of commonly used two line hybrids in China, including Yangliangyou 6, the most widely cultivated hybrid in central and southern China during the last five years.Nine donor parents (DPs) were used to develop a set of monogenic NILs carrying genes for BPH resistance in the genetic background of cultivar (cv.) 9311. The DPs , 10\u2009\u03bcl ddH2O, and 20\u2009\u03bcl mineral oil. The cycling regime was: 94\u2009\u00b0C for 4\u2009min, followed by 32 cycles of 94\u2009\u00b0C/30\u2009s, 55\u2009\u00b0C/30\u2009s, and 72\u2009\u00b0C/40\u2009s, and a final extension at 72\u2009\u00b0C for 7\u2009min. PCR products were separated on 4% non-denaturing polyacrylamide gels and detected by silver staining. SSR sequences were identified in Gramene (www.gramene.org), and Indel markers were designed based on sequence alignments of the Nipponbare and 9311 reference genomes in Rice Var Map (http://ricevarmap.ncpgr.cn/) (Genomic DNA was extracted from fresh seedling leaves by the CTAB methodpgr.cn/) . For genBph17, Bph3, QBph3, QBph4, Bph6, Bph9, Bph10, Bph14, Bph15, Bph18, Bph20, Bph21 and Bph24 was conducted using gene-linked marker pairs XC4-9/IN15-6, RM586/RM589, C3-14/IN76-2, XY4-17/XC4-27, Y37/RM17008, J18-7/HJ12, XC12-2/HJ12, C3-14/IN76-2, RM261/HJ16, HJ12/J18-7, XY4-17/HJ28, HJ12/HJ9, XC12-2/HJ12 and HJ22/RM16717, respectively. Flanking marker pairs for negative selection were J64/J6-7/6-10 (Bph6), RM570/J14-8/J14-12 (Bph14), IN15-6/J23/MS5 (Bph15) and J18-15/RM3331/HJ9 (Bph9) (Positive selection for the presence of genes 9 (Bph9) .The 26 NILs and hybrids containing the BPH resistance genes were planted in a randomized complete block design at Wuhan in the summer of 2015. Plots of each line consisted of two rows with 10 plants per row at a planting density of 17\u2009cm between plants in a row and 27\u2009cm between rows. The central eight plants from each plot, were used to measure agronomic traits including plant height (PH), days to heading (DTH), panicle number (PN), number of grains (NG), number of grains per panicle (NPG), spikelet fertility (SF), 1,000 grain weight (GW), and yield per plant (YD). There were three replications for each NIL and hybrid combination.et al.et al.The BPH bioassay was performed as a modified bulk seedling test in the greenhouse, following the method of Pathak et al.Determination of areas of honeydew deposition followed the method of Du et al.Survival rates were calculated following the method of Du Mean phenotypic values of plants were compared using one-way ANOVA. Duncan\u2019s multiple range and t tests were used for multiple mean comparisons. All statistical analyses were conducted using SPSS 7 for Windows version 16.0 .How to cite this article: Xiao, C. et al. Development and evaluation of near-isogenic lines for brown planthopper resistance in rice cv. 9311. Sci. Rep.6, 38159; doi: 10.1038/srep38159 (2016).Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations."} +{"text": "Escherichia coli BLR(DE3) is a commercially available recA-deficient derivative of BL21(DE3), one of the most widely used strains for recombinant protein expression. Here, we present the full-genome sequence of BLR(DE3) and highlight additional differences with its parent strain BL21(DE3) which were previously unreported but may affect its physiology. Escherichia coli is widely used for the production of recombinant polypeptides, including therapeutic proteins -inducible T7 RNA polymerase cascade system, in which expression of the gene of interest is controlled by a T7 RNA polymerase promoter in a strain carrying the T7 RNA polymerase gene under control of an IPTG-inducible promoter (E.\u00a0coli B strain BL21(DE3) (recA-deficient derivative of BL21(DE3) that helps stabilize plasmids containing repetitive sequences (recA [\u0394(srl-recA)306::Tn10], which was initially obtained in an E.\u00a0coli K-12 background (proteins . The mosstrains) . The genequences . Accordickground and lateckground , 6.de novo hybrid assembly from PacBio sequencing and Illumina HiSeq 2000 sequencing for closing gaps and correcting PacBio sequencing errors. A total of 4,306 coding sequences (CDSs), 230 pseudogenes, 85 tRNA genes, 22 rRNA genes (8 operons), and 64 noncoding RNA genes were annotated.We sequenced the BLR(DE3) strain obtained from Novagen in order to verify whether additional differences are present in BLR(DE3) compared to BL21(DE3). We performed cro-Rz), 1.8 kb (A-B), and 11.1 kb (Fi-J), suggesting the prophage is nonfunctional. As expected, the second divergent region is the recA locus. A 6.9-kb region from recA to srlR is replaced with Tn10 in BLR(DE3). Besides recA and the srl operon, BLR(DE3) thus also lacks pncC . Downstream of Tn10, a large region diverges significantly from BL21(DE3), with 577 nucleotide substitutions (1 to 3\u00a0bp), short insertions/deletions (1\u00a0bp), and the replacement of an IS186 element with a full clustered regularly interspaced short palindromic repeat (CRISPR) locus, as found in E. coli MG1655. We infer that the entire ~85-kb region from recA to queE was transferred from the original K-12 background bearing the \u0394(srl-recA)306::Tn10 mutation. This region contains several genes involved in metabolism and other key processes, such as DNA mismatch repair (mutS) or stress response (rpoS). Importantly, rpoS carries a nonsense mutation at codon 33, which has been shown to reduce \u03c3S activity and BL21(DE3) contain fewer than 20 differences. Of note, these include a previously identified mutation in ilvA, a gene responsible for isoleucine auxotrophy (A comparison with BL21(DE3) indicates larger differences than expected, with two main divergent regions. First, the DE3 prophage contains three large deletions of 4.9 kb (de cycle ) and mtlrecA-deficient BL21(DE3) strain. The newly identified differences might contribute to a differential physiology of BLR(DE3), besides its reported impaired homologous recombination.Globally, the genome sequence of BLR(DE3) indicates that it cannot be merely considered a Escherichia coli BLR(DE3) has been deposited at GenBank under accession number CP020368.The complete genome sequence of"} +{"text": "Unfortunately this article publisheAdditional file 1:Participating sites. (DOCX 13 kb)Additional file 2: Table S7.Baseline characteristics and outcomes in vasopressin and norepinephrine-treated patients, grouped by serum troponin levels. (DOCX 17 kb)Additional file 3: Table S8.Specific ECG diagnoses and patient outcomes. (DOCX 14 kb)Additional file 4: Table S9.Outcomes related to ECG ischemia for all patients and for patients with troponin elevation. (DOCX 15 kb)Additional file 5: Figure S1.Comparison of mean arterial pressure and heart rate in the norepinephrine group and vasopressin group. (DOCX 122 kb)Additional file 6: Figure S2.Rates of total norepinephrine infusion (open-label and study drug) in the vasopressin treated group and the norepinephrine treated group. (DOCX 60 kb)Additional file 7: Figure S3.Serum creatinine in the vasopressin treated group and the norepinephrine treated group. (DOCX 64 kb)"} +{"text": "Currently, clinical data for primary HPV screening alone are lacking in China. Here, we evaluate cervical cancer screening with primary HPV genotyping, as well as possible future screening strategy. Overall, high-risk HPV (hrHPV) prevalence was 18.2% among hospital-based population in Taizhou area. For cervical intraepithelial neoplasia 2 or worse (CIN2+), the sensitivity of primary hrHPV genotyping strategy and current cervical cancer screening strategy were 93.5%, and 71.1%, respectively; whereas the specificity was 17.5%, and 62.4%, respectively. Current cervical screening strategy had slightly higher positive predictive values (28.4%) for CIN2+ than hrHPV genotyping strategy (21.9%), whereas primary hrHPV genotyping strategy demonstrated higher negative predictive values (94.7%) than current cervical screening strategy (91.1%). Compared to HPV35/39/45/51/56/59/66/68 genotypes, the odds ratios (OR) for CIN2+ in HPV16/18/31/33/52/58 infection women were 3.2 . Primary hrHPV genotyping strategy provides a better predictive value than HPV16/18 genotyping alone in guiding the clinical management of the current cervical cancer screening. HPV testing without adjunctive cytology may be sufficiently sensitive for primary cervical cancer screening. Worldwide, cervical cancer is the second most common female malignancy. Approximately 500,000 new cases of cervical cancer are diagnosed and 275,000 deaths from cervical cancer occur annually. Persistent infection of high-risk human papillomavirus (hrHPV) is necessary for the development of high-grade intraepithelial neoplasia (CIN2/3) and cervical cancer . More thPublic health screening programmes have successfully decreased cervical cancer incidence and mortality, including cervical cancer screenings and HPV vaccinations. Current guidelines for cervical cancer screening which cosponsored by the American Cancer Society (ACS), the American Society for Colposcopy and Cervical Pathology (ASCCP), and the American Society for Clinical Pathology (ASCP) in 2012, were recommendations address age-appropriate screening strategies, including the use of cytology and hrHPV testing (co-testing) , 4. ReceWith the aim to establish a foundation for primary HPV screening in a certain area, and to support the local vaccination program in Taizhou region. This population-based, prospective observational study was designed to analyze the distribution of individual hrHPV genotypes across the complete spectrum of cervical disease; we have performed the primary HPV screening in detecting precancerous high-grade cervical lesions and cervical cancer.The Taizhou Area HPV study is a population-based, prospective observational study. We used HPV genotyping for primary cervical screening strategy, women with screen results of hrHPV positive referred directly to colposcopy biopsy. Moreover, the current cervical screening strategy with cytology and hrHPV testing (co-testing), the management of screen results stratified follow by: 1) atypical squamous cells of undetermined significance (ASCUS) or worse, referred directly to colposcopy biopsy; 2) cytology normal and HPV16/18 positive, referred directly to colposcopy biopsy , 7.Between December 2012 and April 2015, a total of 19207 consecutive women underwent cervical cancer screening in gynecological clinic at Taizhou Hospital of Zhejiang Province. The flowchart of study population was shown on Figure TM analyzer.HPV genotyping was performed using the GP5+/bioGP6+-PCR/MPG assay, which was approved by the China Food and Drug Administration (CFDA Certified NO. (2014): 3400847). DNA was extracted from 200\u03bcl of each sample and collected in 50\u03bcl elution buffer according to the manufacturer's instructions. 5\u03bcl of extracted DNA was amplified by the GP5+/bioGP6+ broad-spectrum primer set with a final volume of 20\u03bcl. Reactions were heated for 5min at 95\u00b0C, followed by 35 repeated cycles of 94\u00b0C for 30s, 55\u00b0C for 30s, 72\u00b0C for 30s, and a final extension step at 72\u00b0C for 10min. Following the PCR amplification, 3\u03bcl of biotin-labeled PCR products and 22\u03bcl of hybridization solution containing 27 types of coupled beads of each set were transferred to 96-well plates. Hybridization was performed at 95\u00b0C for 5min followed by 48\u00b0C for 30min. Subsequently, streptavidin-phycoerythrin was added to each well at 48\u00b0C for 15min. The biotin-labeled PCR products were captured by HPV type-specific probes attached to color-coded beads, streptavidin-phycoerythrin was used as the reporter bound to the target, and the HPV genotypes were analyzed using the Luminex200In short, it comprises the GP5+/bioGP6+-PCR, which using sets of biotinylated amplimers and a multiplex human papillomavirus genotyping (MPG) methods with bead-based Luminex suspension array technology , 9, whicin situ (AIS), and adenocarcinoma.Cytological results, which blinded to the outcomes of HPV testing, were reported according to the 2001 Bethesda system. Cytological results were grouped as negative for intraepithelial lesion or malignancy (NILM), ASCUS, atypical squamous cells and cannot exclude high-grade squamous intraepithelial lesions (ASC-H), low-grade squamous intraepithelial lesions (LSIL), high-grade squamous intraepithelial lesions (HSIL), squamous cell carcinoma, atypical glandular cells (AGC), endocervical adenocarcinoma Histopathologic diagnoses were adjudicated by pathologists and classified as normal, CIN grade 1, 2, 3 or invasive cervical cancer, according to international criteria. The suffix \u201c+\u201d means the indicated histology or more severe. Disease end points were histopathologically confirmed CIN2+ or CIN3+.in situ, and ICC) were determined using standard statistical tests. The chi-squared and Fisher's exact tests were used to evaluate relative CIN2+ risk associate with HPV genotypes, odds ratios (ORs) and relative 95% confidence interval (CI). All statistical analyses were performed using SPSS version 15.0 . P values were two-sided, and statistical significance was accepted if the P value was 0.05 or less.Performance characteristics of hrHPV test for identification of CIN2+ . According our recommended hrHPV genotyping for primary cervical screening strategy, 1399 women underwent colposcopy biopsy. According the current cervical screening strategy, 567 women underwent colposcopy biopsy.As shown in Table The overall prevalence of HPV was 22.2% (95% CI 21.6-22.8%), hrHPV and lrHPV infection rates were 18.2% (95% CI 17.6-18.7%) and 4.0% (95% CI 3.7-4.3%), respectively. Overall, HPV52 was the most prevalent genotype (4.9%), either alone or in combination with other types, followed by 16 (3.1%), 58 (2.7%), 39 (1.6%), 18 (1.5%), 56 (1.5%) .To assess the clinical predictive value for different hrHPV types, we further evaluated our data on the prevalence of individual hrHPV infection rates for cervical pathology status Table . For theIn this study, we recommended hrHPV genotyping for primary cervical screening strategy, when women with screen results of hrHPV positive referred directly to biopsy. According to this guideline, 3210 women need biopsy, irrespective of women age. In fact, 1399 (43.6%) women with hrHPV infection accepted biopsy, including 885 women with cervicitis, 195 with CIN1, 117 with CIN2, 169 with CIN3, and 33 with ICC, respectively. According this screening strategy, the sensitivity and specificity for detecting CIN2+ were 93.5 % and 17.5%, respectively. The positive predictive value and negative predictive value were 22.8% and 91.2%, respectively.According to the current cervical screening strategy, 1217 women need biopsy, irrespective of women age. In fact, 567 (46.6%) women with ASCUS+ or HPV16/18 positive accepted biopsy, including 309 women with cervicitis, 95 with CIN1, 60 with CIN2, 81 with CIN3, and 22 with ICC, respectively. The sensitivity and specificity for detecting CIN2+ were 71.1% and 62.4%, respectively. The positive predictive value and negative predictive value were 28.4% and 91.1%, respectively. Compared to the current cervical screening, primary hrHPV genotyping test had higher sensitivity and lower specificity (Table We further examined whether hrHPV positive women for HPV16/18 (2 types), or HPV16/18/31/33/52/58 (the 6 major carcinogenic types) can serve as a triage tool to discriminate women who need biopsy immediately. Compared to 12 other hrHPV infection women, the ORs for CIN2+ in HPV16/18 (2 types) infection women was 2.7 (95%CI 2.1-3.4). Notably, the relative CIN2+ risk (ORs) was 3.2(95%CI 2.3-4.1) for women with HPV16/18/31/33/52/58 (6 types) infection compared to women with HPV35/39/45/51/56/59/66/68 infection. For detecting CIN2+, the sensitivity and specificity were 86.5% and 43.5%, respectively. The positive predictive value and negative predictive value were 28.5% and 92.5%, respectively. Therefore, when women with HPV16/18/31/33/52/58 infection can be recommended colposcopy biopsy immediately.Women who are HPV35/39/45/51/56/59/66/68 positive should be detected with cervical cytological testing. Among women with ASCUS cytology, HPV35/39/45/51/56/59/66/68 infection rate was 32.4%. Women with ASCUS+ can be recommended colposcopy biopsy immediately. The accuracy values of different triage strategies for the detection of CIN2+/CIN3+ were shown in In recent years, hrHPV testing for triaging ASCUS and co-testing with cervical cytology have been implemented in clinical practice , 10. HowThe prevalence of hrHPV (18.2%) obtained in this present study were similar to that in Hangzhou 19.9%) and Nanchang (18.4%) which also region in southeast of China . Consist.9% and NIn our population, we found that HPV16, 31, 33, and 58 increased the risk for CIN1 lesions progress to CIN2 or worse 10-18 years after enrollment compared with hrHPV-negative women. The 18-year cumulative incidence rates (CIRs) of CIN2+ among hrHPV-positive and hrHPV-negative women were 23.2% and 1.5%, respectively. [Compared with current cervical cancer screening strategy, we recommended screening strategy had higher sensitivity (93.5%) and higher negative predictive values 91.2%). In the present study, the current cervical screening strategy had been missing the majority of women with hrHPV infections who progress to high-grade cervical lesions (CIN2+) and poor positive predictive value (22.8%) for the determination of CIN2+ in the current study would be limits the use of our recommended screening strategy. In our study, women with HPV16/18/31/33/52/58 (the 6 major carcinogenic types) infections rate were 71.1% (2282/3210) of overall hrHPV-positive women. In order to reduce the number of biopsy, we suggested when women with HPV16/18/31/33/52/58 infection can be recommended colposcopy biopsy immediately. For detecting CIN2+, the specificity and positive predictive value were 43.5% and 28.5%, respectively. In order to improve the CIN2+ detection rate, our data suggested that reflex cytology for women with HPV35/39/45/51/56/59/66/68 infection will be clinically useful as a triage test tool for immediate biopsy for women with ASCUS or worse.In summary, hrHPV genotyping provide a better predictive value than HPV16/18 genotyping alone in guiding the clinical management of the current cervical cancer screening. HPV testing without adjunctive cytology may be sufficiently sensitive for primary cervical cancer screening."} +{"text": "Significant variations have been observed for the differentiation efficiency of various human ESC lines. The precise underpinning molecular mechanisms are still unclear. In this work, we compared transcriptome variations of four hESC lines H7, HUES1, HUES8 and HUES9. We found that hESC lines have different gene expression profiles, and these differentially expressed genes (DEGs) are significantly enriched in developmental processes, such as ectodermal, mesodermal and endodermal development. The enrichment difference between hESC lines was consistent with its lineage bias. Among these DEGs, some pluripotency factors and genes involved in signaling transduction showed great variations as well. The pleiotropic functions of these genes in controlling hESC identity and early lineage specification, implicated that different hESC lines may utilize distinct balance mechanisms to maintain pluripotent state. When the balance is broken in a certain environment, gene expression variation between them could impact on their different lineage specification behavior.Human embryonic stem cells (hESCs) have the potential to form any cell type in the body, making them attractive cell sources in drug screening, regenerative medicine, disease and developmental processes modeling. However, not all hESC lines have the equal potency to generate desired cell types Filtered cells fixed with 1% (vol/vol) paraformaldehyde for 10 min and permeabilized with 70% methanol for 10 min at room temperature. For NPCs, cells were stained using 1: 200 rabbit polyclonal IgG PAX6 as primary antibody for 1 hour and 1: 1,000 Alexa Fluor 488 goat anti-rabbit IgG H&L as secondary antibody for 30 min at room temperature. Rabbit polyclonal IgG were employed as an isotype control. For cardiomyocyte, cells were stained with PE mouse anti-cardiac Troponin T type 2 for 1 hour at room temperature and PE mouse IgG1 kappa was used as isotype control. All samples were run on BD FACSJazz.Many factors influence genes expression, such as feeder cells, culture media, additives and passage methods . In ordeNext, we analyzed highly expressed and lineage-specific genes across the four cell lines. Normally, most highly expressed genes regulating pluripotency and self-renewal should be common in all hESC lines while lineage-specific genes should be expressed at a much lower level. Here, we used transcripts per million (TPM) to normaMeanwhile, we also did GO-slim enrichment analyses on those highly expressed genes not shared among the hESC lines to see their functional enrichment. Interestingly, these genes were significantly enriched in developmental processes, especially in ectoderm development . Among tGenes with more than 2-fold change (maximum CPM divide by minimum CPM among the four cell lines for each gene) and FDR less than 0.01 were assigned as DEGs. Overall, we identified 3571 DEGs, accounting for 18.38% of the total expressed genes . To inveIn order to inspect how expression variations associated with differentiation bias, we performed two-two comparison analysis . Resultsin vitro.To verify our results, we downloaded public available hESC lines H1 and HUES64 RNA-Seq data to carry out differential expression analysis . Markedl2.0 [Transcription factors play key role in genes expression regulation and several master transcription factors can control cell fate decision, such as combination of transcription factors POU5F1, SOX2, KLF4, and C-MYC or OCT4, SOX2, NANOG and LIN28 have been used to transform human fibroblasts into induced pluripotent stem cells (iPSCs) , 18. In 2.0 and their related functions in all the TFs set, 335 DETFs were identified using the same selecting method mentioned above, accounting for 26.07% of the total expressed TFs . NotablyThere are several key signaling pathways required for maintaining pluripotent state while suppressing differentiation in hESCs, including insulin-like growth factor /phosphatidylinositol-3 kinase (IGF/PI3K), fibroblast growth factor (FGF)/Mitogen- activated protein kinase (MAPK), TGF-\u03b2and Wnt pathway , 70\u201375. in vitro [Previous studies have confirmed that physiological and functional variability exists among hESC lines, although they have the common properties in the ability to differentiate into any cell type of the body and self-renew indefinitely in vitro , 38. Onein vitro , 21. Thein vitro . Howeverin vitro , 38. Thuin vitro by RNA-seq analysis. We compared expression profiles of four hESC lines H7, HUES1, HUES8 and HUES9, and totally identified 19, 429 expressed genes, among which 4, 302 (22.14%) genes, including 362 (1.86%) transcription factors, were differentially expressed at least in two cell lines. Functional annotation demonstrated that these DEGs were significantly enriched in developmental processes, such as ectoderm development, mesoderm development Click here for additional data file.S2 Fig(A) GO-slim biological process enrichment analysis of DEGs between H7 and HUES1. (B) GO-slim biological process enrichment analysis of DEGs between H7 and HUES8. (C) GO-slim biological process enrichment analysis of DEGs between H7 and HUES9. (D) GO-slim biological process enrichment analysis of DEGs between H1 and HUES64 downloaded from public available RNA-seq data.(TIF)Click here for additional data file.S3 Fig(A) H7 compared to HUES1, HUES8 and HUES9. (B) HUES1 compared to H7, HUES8 and HUES9. (C) HUES8 compared to H7, HUES1 and HUES9. (D) HUES9 compared to H7, HUES1 and HUES8. Upregulated: logFC > 1 and FDR < 0.01, downregulated: logFC <_ -1 and FDR < 0.01.(TIF)Click here for additional data file.S4 Fig(A) Expression variations of genes in Wnt signaling pathway upstream component between hESC lines HUES1 and H1. (B) Expression variations of genes in Wnt signaling pathway downstream component between hESC lines HUES1 and H1.(TIF)Click here for additional data file.S5 Fig+ cells derived from H7, HUES1, HUES8 and HUES9. (C) Example of flow cytometry analysis for PAX6+ cells derived from H7, HUES1, HUES8 and HUES9.(A) Fold change of PAX6 and Nestin expression in spontaneously differentiating embryoid bodies derived from H7, HUES1, HUES8 and HUES9 at day 28. (B) Percentage of PAX6(TIF)Click here for additional data file.S6 Fig+ cells derived from H7, HUES1, HUES8 and HUES9. (C) Example of flow cytometry analysis for TNNT2+ cells derived from H7, HUES1, HUES8 and HUES9.(A) Example of cardiomyocytes morphology in culture derived from H7, HUES1, HUES8 and HUES9. (B) Percentage of TNNT2(TIF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.S6 Table(XLSX)Click here for additional data file.S7 Table(XLSX)Click here for additional data file.S1 Video(MP4)Click here for additional data file.S2 Video(MP4)Click here for additional data file.S3 Video(MP4)Click here for additional data file.S4 Video(MP4)Click here for additional data file."} +{"text": "After publication of the original article the authWhile the legends are correctly cited, the figures themselves are incorrect.The correct order of additional files follows below:A full list of the correct corresponding files and their legends are included with this Correction.The publisher apologises for this error.Additional file 1:Table S1. Oligonucleotides used as adaptors and PCR primers. (DOCX 15 kb)Additional file 2:Table S2. Barcodes on Barcoded Tn5 adaptors for labeling different cell samples. (DOCX 14 kb)Additional file 3:Figure S1. Validation of SALP method. (DOCX 309 kb)Additional file 4:Cloning sequencing. (DOCX 21 kb)Additional file 5:Figure S2. The structure of SALP library. (DOCX 68 kb)Additional file 6:Figure S3. Verification of the ligation efficiency of SSA adaptors. (DOCX 187 kb)Additional file 7:Table S3. Reads from a lane of Illumina Hiseq X Ten sequencing. (DOCX 15 kb)Additional file 8:Figure S4. Comparison of fold enrichment of two types of GM12878 SALP-seq peaks. (DOCX 45 kb)Additional file 9:Figure S5. Construction of NGS library of gDNAs sheared by sonication and restriction endonuclease digestion with SALP method. (DOCX 295 kb)Additional file 10:Figure S6. Comparison of the distribution of Hind III digestion library reads density and Hind III restriction sites through the whole genome. (DOCX 444 kb)Additional file 11:Figure S7. Reads distribution of sonication library. (DOCX 395 kb)"} +{"text": "Bovine respiratory disease (BRD) is a significant and costly illness in feedlot cattle. Metagenomic analysis was performed on bronchoalveolar lavage samples obtained from 18 feedlot cattle that died of BRD. Bovine respiratory disease (BRD) is the most frequent cause of morbidity and mortality in feedlot cattle, resulting in significant economic losses in the North American beef cattle industry . It is aThe BAL samples were filtered to remove bovine cells, and microbial cells were then pelleted via centrifugation. Metagenomic DNA was extracted from each BAL sample as described by Beukers et al. , with thMannheimia haemolytica (18.8%), Bacteroides pyogenes (14.3%), Pseudomonas taetrolens (5.7%), Anaplasma phagocytophilum (5.0%), Clostridium perfringens (3.8%), Mycoplasma bovis (3.2%), Psychrobacter sp. SHUES1 (2.7%), Histophilus somni (2.5%), and Streptococcus pneumoniae (2.1%). The most frequently detected antibiotic resistance genes were aadA, floR, tet(40), tet(H), tet(Q), tet(W), and sul2. The metagenomes obtained in this study represent the first characterization of the lower respiratory tract in BRD-related mortalities.The most abundant bacterial species among the BAL samples were SRR5877067 to SRR5877084.The metagenomic sequences have been deposited in the NCBI Sequence Read Archive under accession numbers"} +{"text": "To observe the impact of acute renal morbidities with obstetrical emergencies on maternal health.In this study pregnant women between 28-40 weeks gestational period and delivered women in their puerperal period up to 42 days after delivery having acute renal problems associated with obstetrical emergencies were included. Pregnant and delivered women with obstetrical emergencies and associated other morbidities were excluded. These women were registered on the predesigned proforma after taking written informed consent and taking approval from institutional ethic research committee. The data was collected and analyzed on SPSS version 21.Out of these 196 total registered women, majority of these women 81(41.32%) were between 21-30 years of age and multiparous women with parity four and above were 83(42.34%). Commonest presenting symptoms were generalized oedema 123(62.75%) and oligouria 92(46.93%). Frequent obstetrical emergencies observed were pre-eclampsia 53(27.04%), post partum haemorrhage 48(24.48%) and ante partum haemorrhage 36(18.36%) women. The complete recovery was observed in 86(43.87%) women, while mortality was seen in 56(28.57%) women.Renal morbidities were more frequently observed in obstetrical emergencies leading to high morbidity and mortality rate. Acute renal failure is a clinical syndrome characterized by an abrupt decrease in the glomular filtration rate, rising in plasma urea and creatinine levels, and urine out put less than 300 ml in 24 hours. The obstetrical acute renal morbidities, a serious maternal health issue mainly concerned with the life of mother.4In recent years the rates are increased in both Canada and the United States.8Invasive hemodynamic monitoring and mechanical ventilation may be indicated in the event of acute hemorrhage requiring massive fluid resuscitation. Disseminated intravascular coagulopathy, acute kidney injury, and lung injury can result from hemorrhage and protracted hypovolemia.st September 2013 to 31st August 2016. This was an observational study on 196 pregnant and delivered women with obstetrical emergencies and renal morbidities.This study was carried out at the Department of Obstetrics and Gynaecology of Liaquat University of Medical and Health Sciences Jamshoro from 12> (pq)/e2. Confidence interval 95%. Sampling technique is Non \u2013Probability Purposive. These women were registered on the predesigned proforma after taking written informed consent and approval from Institutional ethic research committee. The study variables were the age of women, gestational period, in delivered women postnatal period, symptomatology, general, obstetrical examination finding. Investigations complete blood count, renal functions tests, ultrasonographic record. All these women were managed with institutional management protocol and where ever required with multidisciplinary approach. The management out come was recoded in terms of complete recovery when renal functions were with in normal limit, partial recovery when there was improvement in renal functions but was not with in normal limit and mortality.The renal morbidities were diagnosed on the basis of history of sudden oliguria (urine out put <300 ml/ 24 hours), or with anuria and increase in the level of renal function tests, while the pregnant and delivered women with liver disorders, cardiac and respiratory problems were excluded. Sample size was estimated by formula (N= (Z)The data was collected and analyzed on SPSS version 21 . Categorical variables were analyzed with frequency and percentage; means with standard deviation were calculated for age. Qualitative type of analyses was done with statistical Chi-Square test P-Value < 0.05 was considered significant.st 24 hours of delivery 91(66.42%) ., their gestational period varied between 28-40 weeks, while delivered women were 137(69.89%), their postnatal period varied between day one to 42 days. Majority of these women were between 21-30 years of age 80(40.81%). Mean age\u00b1SD was 26.52\u00b15.993. The most affected group was grand multiparous women, para four and above 83(42.34%) . Pregnant women presented commonly during 33-37 weeks gestational period 32(54.23%) , while delivered women were frequently presented within 1e 0.235)..On general examination anaemia was found in 139(70.91%) while generalized oedema was seen in 123 (62.75%). The common clinical presentation was in the form of oligouria 92 (46.93%), anuria 68(34.69%), status of shock 59(30.10%) , and fits 38(19.38%). Investigation report showed highest blood urea level more than 151mg/dl in 78 (39.79%) women, serum creatinine level above 7mg/dl in 63(32.14%) women, creatinine clearance level above 251ml/min in 39 (19.89%) women, serum uric acid level 12mg/dl in 40 (20.40%) women. Ultrasound examination report showed severe degree of renal parenchymal changes in 45(22.95%) women ..Most frequent obstetrical emergencies were Pre eclampsia 53(27.04%), Post partum Haemorrhage 48(24.48%), Ante partum haemorrhage 36(18.36%), Ruptured uterus 22(11.22%), Eclampsia 19(9.69%), Puerperal sepsis 12(6.12%), andoperative morbidities were 6(3.06%). Complete recovery was observed in women commonly with eclampsia 29(14.79%), ante partum haemorrhage 17(8.67%), ruptured uterus 12(6.12%), post partum haemorrhage 11(5.61%), eclampsia 10(5.10%). Mortality rate was highest with post partum haemorrhage 19(9.69%), ante partum haemorrhage 13(6.63%), puerperal sepsis 8(4.08%), eclampsia 7(3.57%), ruptured uterus 6(3.06%)..Obstetrical acute renal failure is a rare entity in developed world. In the early days of dialysis, obstetric renal failure was a major part of the work of a renal unit. Acute renal failure was estimated to occur in one in 1400 to one in 5000 pregnancies in the UK; over the next 20-30 years medical complications of pregnancy remained a regular and frightening reason for acute renal referrals. Hammersmith Hospital in West London had a special interest in acute renal failure from the 1940s, and attracted many referrals. In their 1965 report by Smith K et al studyIn this study acute renal morbidities with obstetrical emergencies were observed mostly in younger women having mean age\u00b1SD:26.52\u00b15.993, grandmultiparous women (Para 4 and above)83(42.34%), mostly these referred women were delivered 137(69.89%), while pregnant women were 59(30.10%), these women were in their late pregnancy and with obstetrical emergencies. This is inconsistent with Nigerian study.The general condition of these women was poor, majority of these women presented with oedema 123(62.75%), oliguria92(46.93%), anuria68(34.69%), status of shock 59(30.10%). On investigation highly raised blood urea level above 151mg/dl was reported in 78(39.79%), serum creatinine level above 7mg/dl in 6332.14%). Ultrasound examination report showed severe degree renal parenchymal changes in 45(22.95%) women, same is reported by Piccoli GB et al study.%. UltrasIn this study complete recovery rate was 86 (43.87%), this is inconsistent with Gurrier C et al studyRenal morbidity and related consequences are the major events with obstetrical emergencies. Most common obstetrical emergencies leading to renal morbidities and associated mortalities were pregnancy induced hypertensive disorders, antepartum and postpartum haemorrhage, ruptured uterus, puerperal sepsis. Appropriate preventive measures such as early identification of at risk women, proper referral for providing multidisciplinary services at the tertiary level, optimization of fluid balance, identification and treatment of cause, delivery at appropriate gestational period, and timely initiation of renal replacement therapy may reduce mortality.Meharunnissa Khaskheli: Concept, designed the study and is accountable for all the work.Shahla Baloch: Contributed in drafting the manuscript.Aneela Sheeba: Critically revised for important intellectual content.Sarmad Baloch: Helped in data analyses.Fahd Khan: Helped in acquisition and interpretation of data.M. Rafique Ansari: Approval of the final version to be published."} +{"text": "Half of the ~250 intramolecular interactions in GPCRs differ between inactive and active structures. Conformation-specific interhelical contacts depend on amino acids changing partners during activation. Conserved inactive conformation-specific contacts prevent receptor activation by stabilizing proximity of TM helices 3 and 6 and a closed G protein-binding site. Mutations of GnRH receptor residues involved in these interactions, such as Arg3.50(139) of the DRY/S motif or Tyr7.53(323) of the N/DPxxY motif, increase or decrease receptor expression and efficiency of receptor coupling to G protein signaling, consistent with the native residues stabilizing the inactive GnRH receptor structure. Active conformation-specific interhelical contacts stabilize an open G protein-binding site. Progress in defining the GnRH-binding site has recently slowed, with evidence that Tyr6.58(290) contacts Tyr5 of GnRH, whereas other residues affect recognition of Trp3 and Gly10NH2. The surprisingly consistent observations that GnRH receptor mutations that disrupt GnRH binding have less effect on \u201cconformationally constrained\u201d GnRH peptides may now be explained by crystal structures of agonist-bound peptide receptors. Analysis of GPCR structures provides insight into GnRH receptor function.Gonadotropin-releasing hormone (GnRH) regulates reproduction. The human GnRH receptor lacks a cytoplasmic carboxy-terminal tail but has amino acid sequence motifs characteristic of rhodopsin-like, class A, G protein-coupled receptors (GPCRs). This review will consider how recent descriptions of X-ray crystallographic structures of GPCRs in inactive and active conformations may contribute to understanding GnRH receptor structure, mechanism of activation and ligand binding. The structures confirmed that ligands bind to variable extracellular surfaces, whereas the seven membrane-spanning \u03b1-helices convey the activation signal to the cytoplasmic receptor surface, which binds and activates heterotrimeric G proteins. Forty non-covalent interactions that bridge topologically equivalent residues in different transmembrane (TM) helices are conserved in class A GPCR structures, regardless of activation state. Conformation-independent interhelical contacts account for a conserved receptor protein structure and their importance in the GnRH receptor structure is supported by decreased expression of receptors with mutations of residues in the network. Many of the GnRH receptor mutations associated with congenital hypogonadotropic hypogonadism, including the Glu Activated GTP-bound G\u03b1q/11 subunits activate phospholipase C\u03b2, which catalyzes production of the second messengers diacylglycerol and inositol trisphosphate, which initiate the cellular signaling pathways that culminate in gonadotropin synthesis and secretion regulates reproduction by binding and activating GnRH receptors on pituitary gonadotrope cells, which synthesize and secrete the gonadotropins, LH, and FSH. The gonadotropins act on the gonads to stimulate gametogenesis, gonadal cell proliferation, and production of the gonadal steroids. GnRH secretion is suppressed during childhood and increases at puberty, when increased production of gonadotropins and gonadal steroids initiate sexual development. Disruption of GnRH receptor function disrupts reproduction and mutations of the GnRH receptor gene disrupt or delay pubertal development, resulting in congenital hypogonadotropic hypogonadism (cHH) , 2. Thisecretion , 6, 7. Aell line , 8, 9 anll lines \u201312 and iproteins , suggest2+), small molecule neurotransmitters and immune modulators to peptide and protein hormones, cytokines and even light, which changes the 11-cis-retinal prosthetic group of rhodopsin from a covalently bound inverse agonist (an antagonist that actively stabilizes inactive receptor conformations) to an agonist. In spite of their diverse physiological functions and ligands, all GPCRs share a common molecular function, which consists of transducing an extracellular signal across a biological membrane via a change in receptor protein conformation (The GnRH receptor belongs to the G protein-coupled receptor (GPCR) family, which constitutes the largest family of membrane proteins in the human genome , 15. Theormation \u201318. Thisormation , 19, 20.ormation with emp319 of the human GnRH receptor is designated Asp7.49(319), because it immediately precedes the most conserved residue in TM7, Pro7.50(320). The equivalent residue of the mouse receptor is Asp7.49(318).Based on conserved amino acid sequence features Table , the GnRThis review will focus on the mammalian type 1 GnRH receptor, which is characterized by absence of a cytoplasmic carboxy-terminal tail , 40 that2.50 in TM2, which is substituted with uncharged Asn (Table 2.50(87) to the normal Asp disrupted GnRH receptor expression (7.49-Pro7.50-x-x-Tyr7.53 where x represents any amino acid) is changed to DPxxY (Asp7.49-Pro7.50-Leu7.51-Ile7.52-Tyr7.53). Mutation of Asp7.49 to Asn reversed the disruption of GnRH receptor expression caused by mutation of Asn2.50 to Asp, suggesting these resides might be close to each other in the three-dimensional structures of class A GPCRs residue in TM2, which has risen to prominence because a cHH-associated Glu2.53(90)Lys mutation disrupts membrane expression of the receptor, but treatment with a pharmacoperone nic mice , 47, 48.nic mice and is Ieceptors , 43, sug5.58 residue was revealed by crystal structures of active rhodopsin residue, which is also present in type 2 GnRH receptors.The functional importance of the highly conserved Tyrhodopsin , 50. Typ Tyr5.58 , 40, 43.e triad\u201d or \u201ctrane triad\u201d , 31, 32,Ligands interact with the variable extracellular half of GPCR molecules. The membrane-spanning domain conveys the ligand-binding signal to the cytosolic surface of the receptor, which interacts with the G protein . In ordeCurrent theories of receptor activation posit that GPCRs exist in an equilibrium of inactive \u201cR\u201d and activated \u201cR*\u201d conformations, with the equilibrium balanced toward the R conformations in the absence of ligand. The R conformations cannot activate G proteins, are stabilized by binding of inverse agonist (antagonist) ligands and have low affinity for agonist ligands. In contrast, R* conformations bind and activate G proteins, have high affinity for agonist ligands and are stabilized by binding of agonists and/or G proteins , 52\u201354. 5.50, Pro6.50, and Pro7.50 residues in TM5, TM6, and TM7 cause bends in the \u03b1-helices that are not classical proline kinks Arg mutation of the GnRH receptor completely disrupts receptor function, which cannot be recovered by pharmacoperone treatment (6.47(279)Tyr mutant GnRH receptor and a laboratory-produced Cys6.47(279)Ala mutant showed no measurable GnRH binding and severely decreased cellular responses to GnRH stimulation that were recovered after pharmacoperone treatment of cells transfected with the mutant receptor (6.47(279) mutations disrupt receptor folding during biosynthesis, but the rescue shows that its effect is less destructive than mutating the Pro6.50(282). A Tyr6.51(283)His GnRH receptor mutation causes cHH and results in no measurable function in vitro is stabilized by ~200\u2013260 non-covalent intramolecular contacts and by a network of hydrogen-bonded water molecules in the interior of the TM domain. Depending on methodology, 24\u201340 interhelical contacts between topologically equivalent loci (positions) are present in all active and inactive class A GPCR structures , 19, 20.Gonadotropin-releasing hormone receptor residues topologically equivalent to the residues in conserved conformation-independent interhelical contacts are listed in Table S1 in Supplementary Material, with the predicted interhelical contacts and effects of previously reported mutations of the residues on GnRH receptor expression and function. Many mutations result in undetectable receptor function, consistent with disruption of cell surface GnRH receptor expression or severe misfolding of the receptor protein. The disruption of functional receptor expression confirms the importance of the residues for GnRH receptor structure and indicates that the conserved interhelical contacts constitute part of the GnRH receptor structure, similar to their roles in other GPCRs.2.50(87) in TM2 was substituted with Ala or Asp supports a role for the Asn2.50(87) residue in stabilizing GnRH receptor structure. However, GPCR crystal structures show that Asp2.50 makes conserved contacts with residues in TM1 and TM7, but it is only connected to Asn7.49via the water-mediated hydrogen bond network (2.50(87) of the GnRH receptor contacts Asn1.50(53) and Pro7.46(316), whereas Asp7.49(319) does not form any conserved conformation-independent contacts .The complete disruption of GnRH receptor expression when Asn network , 58. Bas2.53(90)Lys, Glu2.53(90)Asp, Ala4.57(171)Thr, Cys6.47(279)Tyr, Tyr6.51(283)His, Tyr6.52(284)Cys, Pro7.50(320)Arg, and Tyr7.53(323)Cys mutations. Most cHH-associated mutant receptors are poorly expressed in vitro , consistent with the mutations disrupting the structural scaffold of the receptor. Disruption of interhelical contacts would destabilize receptor protein folding, resulting in fewer correctly folded receptor molecules being transported to the cell membrane or decreased residence time of less stable receptor proteins once they get to the cell membrane. Pharmacoperones act as templates for folding of nascent receptor proteins, stabilizing biosynthesis, and increasing protein expression side chain of the GnRH receptor forms a interhelical salt-bridge with Lys3.32(121) in TM3 and that the cHH-associated Glu2.53(90)Lys mutation disrupted receptor biogenesis and folding by breaking this salt bridge (2.53(90) is conserved in type 1 GnRH receptors, type 2 GnRH receptors and other class A GPCRs have large hydrophobic residues at position 2.53 (2.53(90) may not be necessary for type 1 GnRH receptor structure and that the effect of the Glu2.53(90)Lys mutation may result from disruptive effects of introducing Lys, rather than lack of Glu. This is supported by a mutation of Glu2.53(90) to uncharged Gln, which had no effect on receptor function (2.53(90)Asp, which is associated with cHH . A Glu2.53(90)Ala mutation resulted in undetectable GnRH receptor function (2.53(90)Asp mutation, which would formally test the salt bridge hypothesis.The late Michael Conn\u2019s laboratory and others proposed that the Glut bridge \u201369. Althion 2.53 , 49, 57.function and a cofunction , but we 2.53(90) interacts with Ser3.35(124) . Interaction of Glu2.53(90) with Ser3.35(124) is supported by an automated (unbiased) structural homology model of the GnRH receptor (2.53(90) close to Ser3.35(124), whereas Lys3.32(121) points away, toward Asp2.61(98) Asp mutation resulted in undetectable binding, suggesting that the mutation caused receptor instability by introducing close apposition of two carboxyl side chains (2.53(90)Lys mutation disrupts GnRH receptor expression by disrupting the conserved interhelical contact with the 3.35 locus, rather than disrupting a salt-bridge with Lys3.32(121).The conserved interhelical contacts in GPCR structures predict that Glureceptor , which sh Ser3.3524 His, also showed undetectable function in vitro His mutation may disrupt receptor structure by disrupting an interhelical contact of Tyr6.51(283) with Phe7.39(309) in TM7 of the GnRH receptor .Another cHH-associated GnRH receptor mutant, Tyrin vitro . Since T6.48(280) residue in the CWxPY motif was proposed to directly contact the Trp3 residue of the GnRH peptide (6.48(280) to Ala, His, Ser, Gln, and Met disrupted GnRH receptor expression, as did mutation of Trp6.48(279) of the rat GnRH receptor to Arg or Ser (6.48(280) does not directly contact GnRH, but is important for GnRH receptor structure. Trp6.48(280) likely forms conserved interhelical contacts with Met3.36(125) and Ala7.42(312) of the GnRH receptor , which would be disrupted by the mutations.The Trp peptide , 73. Sysg or Ser . Howeverg or Ser , 38, 73.About half of the intramolecular interactions differ between the inactive and active GPCR structures. The GnRH receptor residues equivalent to the residues that form conserved conformation-specific interhelical contacts are listed in Table 3.50 of the D/ERY motif at the cytoplasmic end of TM3, and Glu6.30 at the cytosolic end of TM6 , which clearly cannot form a salt bridge with Arg3.50(139). Nevertheless, mutations show that both Arg residues are important for GnRH receptor structure and function. The cHH-associated Arg6.30(262)Gln mutation decreased ligand binding and cellular signaling (6.30(262) side chain forms an intramolecular interaction that stabilizes folding of the unoccupied GnRH receptor. Since GPCRs are biosynthesized in cellular compartments that are inaccessible to endogenous ligands, receptors are likely synthesized in inactive conformations. Inactive conformation-specific interhelical contacts may thus stabilize receptor biosynthesis, so mutations that disrupt these contacts may also disrupt expression.The inactive rhodopsin structure showed a salt bridge between Argd of TM6 , 82. Thid of TM6 , 83, 84.ignaling , which wh Arg3.5039. Neverignaling , suggest3.50(139) in the DRY/S motif to other basic amino acids, His or Lys, resulted in no measurable receptor function, consistent with disruption of a structurally important interaction. An Arg3.50(139)Gln mutation increased GnRH receptor expression and decreased activation of cellular signaling (3.50(139) that stabilizes receptor folding and stabilizes the inactive receptor conformation. The importance of the Arg3.50(139) side chain for GnRH receptor structure is also supported by cHH-associated Arg3.50(139)His and Arg3.50(139)Cys mutations, which are poorly expressed (3.50(139) cannot form an ionic lock in the GnRH receptor, it must form a different contact. GPCR structures show a conserved inactive conformation-specific interhelical contact of Arg3.50 with the 6.37 locus (3.50(139) side chain may stabilize the inactive GnRH receptor conformation by forming an interhelical hydrogen bond with Thr6.37(269) (Table 3.50(139)Gln mutant receptor.Mutation of Argignaling . This suxpressed , 78, butxpressed suggesti37 locus . Thus, th Thr6.3769 (Table3.43(132), conserved as a large hydrophobic residue in most GPCRs, is likely to stabilize the inactive GnRH receptor conformation by interacting with Phe6.40(272) and Ala6.41(273) in TM6 (Table 3.43(132) and four mutations of Phe6.40(272) decreased GnRH receptor expression, suggesting that they disrupt receptor biogenesis. In contrast, the Phe6.40(272)Leu mutation increased receptor expression (Table 6.40(272)Leu mutation enhances the TM3-TM6 interhelical contact with Met3.43(132) and so enhances expression of the inactive GnRH receptor.Many conserved inactive conformation-specific interhelical contacts involve residues in TM3 and TM6 , suggest3.4313, conserv3.4313, conservon Table , 81, sug3.46(135) and Thr6.37(269) (Table 3.46(135) to Ala and Val both completely ablated GnRH receptor function (3.46(135) with Leu, which has a large branched aliphatic side chain, partially preserved GnRH receptor expression and increased coupling efficiency (3.46(135)Leu mutation may destabilize the inactive conformation of the GnRH receptor by weakening the Ile3.46(135)\u2013Thr6.37(269) interhelical contact and favoring formation of the R* active conformation. A cHH-associated Thr6.37(269)Met mutation resulted in no measurable function in several assay systems (6.37(269) in GnRH receptor structure, but provides no information about its function in receptor conformation.A more recent study, using five pairs of GPCR structures found that only one TM3\u2013TM6 inactive conformation-specific contact is conserved . This ind Thr6.3769 in TM1 and Tyr7.53(323) in the N/DPxxY motif in TM7 and Asp7.49(319) (of the N/DPxxY motif) residues may provide negative charges that enhance cation binding, as suggested for the PAR1 receptor in type 1 GnRH receptors) and Tyr7.53 side chains toward the interior of the TM bundle and opening of a cytoplasmic surface cleft that allows G protein access and binding inwards. It also changes the position of TM3, rotating it and moving it slightly toward the extracellular of side the TM domain residue in TM3 of the GnRH receptor decreased binding of GnRH agonists but not antagonists (3.32(121) initiates activation. Although mutagenesis experiments do not support a role for Trp6.48(280) in ligand binding or activation of the GnRH receptor (6.58(290) at the extracellular end of TM6 (6.51(283) of the CWxPY affects ligand-binding affinity , Asp7.49(318) and Tyr7.53(322) residues decreases GnRH receptor coupling efficiency , which is smaller than Tyr. The NTSR1 neurotensin receptor also has Asn5.58 and an \u201cactive-like\u201d NTSR1 structure shows a hydrogen bond between Asn5.58(257) and Arg3.50(167) (5.58(231) stabilizes the open ionic lock in the GnRH receptor.Rotation of TM6 and opening of the hydrophobic barrier break the inactive conformation-specific interhelical contacts and form new active conformation-specific interhelical contacts. The ionic lock opens and the Argion 6.40 , 22, 28..50(167) , which s3.43 breaks its inactive conformation-specific interhelical contact with the residues in positions 6.40 and 6.41. The release of the hydrophobic side chain in position 6.41 allows it to contact the hydrophobic residue in position 5.55, forming one of two key active conformation-specific interhelical contacts (5.55(228) and Ala6.41(273) , Thr6.37(269) and Tyr7.53(323) (Table 3.46(135) to Leu increased GnRH receptor coupling efficiency (7.53(323) over interaction with Thr6.37(269), thus favoring the active conformation. A role for Tyr7.53(323) in stabilizing the active GnRH receptor conformation is supported by the Tyr7.53(323)Ala mutant, which did not activate cellular signaling residue (3.32(121), to Gln or Ala decreased GnRH affinity and signaling, but had minimal effect on binding of a peptide antagonist, which had modified amino-terminal residues. This led to a conclusion that Lys3.32(121) may form a hydrogen bond with the aromatic rings of His2 or Trp3 of GnRH (3.32(121) contacts pGlu1 or His2 (3.32(121) directly contacts GnRH or initiates receptor activation.The endothelin-1 peptide penetrates the TM core of the ET Gln3.32 . The sma residue . Mutatio of GnRH , 99. Sub or His2 , 110\u20131136.48 of the CWxPY motif of the GnRH receptor interacts with Trp3 of the GnRH peptide (6.48(280) had minimal effects on GnRH affinity or cellular signaling Phe mutation in the GnRH receptor and mutations of Phe7.39(309) to Leu or Gln decreased GnRH-binding affinity (7.39(309) may contact Trp3 of GnRH , Tyr6.51(283), and Phe7.39(309), but not Trp6.48(280). It remains uncertain whether GnRH binds to a largely extracellular surface of the receptor like NTS8\u201313 in the amino terminus of the GnRH receptor is close to the carboxy-terminal Pro9-Gly10NH2 of GnRH. Mutations of Arg1.35(38) decreased GnRH-binding affinity, but had lesser effects on binding of [Pro9-NHEt]-GnRH, which lacks Gly10NH2 (1.35(38) and Gly10NH2, but show that both the geometry and charge of the Arg1.35(38) side chain are important for additional inter- or intramolecular interactions. Asn2.65(102) in TM2 has similar functions in distinguishing Gly10NH2 of GnRH (1.35(38) and Asn2.65(102) . Systematic mutagenesis of Asp2.61(98) of the GnRH receptor, combined with ligand modification, showed that the Asp2.61(98) side chain determines receptor recognition of His2 of the GnRH peptide, via a hydrogen bond, whereas the charge of the Asp2.61(98) side chain may configure the surface of the ligand-binding pocket by forming an interhelical salt bridge with Lys3.32(121) , 116. Th6.58(290), two helical turns toward the extracellular end of TM6 from the CWxPY motif, with the Tyr5 side chain of the GnRH peptide. Systematic mutagenesis showed that both the hydroxyl group and the aromatic ring of the Tyr6.58(290) side chain contribute to high affinity binding of GnRH, but had less effect on binding of [Ala5]-GnRH, consistent with the hydroxyl group of Tyr6.58(290) interacting with the aromatic ring of Tyr5 of the peptide. The receptor mutations also decreased GnRH potency in signaling assays more than they decreased binding affinity, showing that the Tyr6.58(290) side chain has an additional role in coupling agonist binding to receptor activation (6.58(290)\u2013Tyr5 interaction may initiate movement and rotation of TM6 in the GnRH receptor.Molecular models of the GnRH receptor showed contact of Tyrtivation . The Tyr7.36(305) at the extracellular end of TM7 in the mouse GnRH receptor to non-polar amino acids decreased GnRH-binding affinity, suggesting loss of a hydrogen bond interaction. Ligand modification suggested a His7.36(305)-Trp3 hydrogen bond contact. However, mutation of His7.36(305) to polar amino acids had no effect on ligand-binding affinity, making a direct interaction with the ligand unlikely. Molecular modeling showed that His7.36(305) made only intramolecular contacts with the amino terminus of the receptor, whereas Trp3 of GnRH was oriented near the consensus ligand-binding residue, Phe7.39(308). This suggests that His7.36(305) forms an interhelical contact that positions Phe7.39(308) to form \u03c0\u2013\u03c0 contact with Trp3 of the peptide interhelical contacts and may disrupt the interhelical contact.Mutation of His peptide . The cHHaffinity , is imme8 residue, which is important for binding to type 1 GnRH receptors. Mutation of the acidic Asp7.32(302) residue to uncharged Asn decreased binding affinity of GnRH, but had no effect on binding of peptides with uncharged Gln8. This suggests that Asp7.32(302) forms a salt bridge contact with Arg8 of the peptide. However, \u201cconformationally constrained\u201d GnRH peptides, in which the high affinity \u03b2-turn was stabilized by a d-amino acid in position 6, retained high affinity binding in the absence of Asp7.32(302) or Arg8 or both. Since the Arg8 side chain also contributes to stabilizing the \u03b2-turn in the native GnRH peptide, it was concluded that the interaction of Asp7.32(302) with Arg8 induces the high-affinity peptide conformation -Arg8 interaction induced the high affinity conformation of GnRH on binding to the receptor, mutation of many different GnRH receptor residues causes a similar large decrease in binding affinity of native GnRH, but much smaller decreases in affinity for conformationally constrained GnRH peptides (7.32(302)-Arg8 interaction. In the active GPCR conformations that have increased agonist-binding affinity, a \u201ccap\u201d forms over the extracellular surface of the ligand-binding pocket and increases agonist affinity by hindering dissociation of the ligand and trapping it in the binding pocket (B-endothelin receptor structures with and without endothelin-1 showed that the peptide induces inward movement of the extracellular ends of the TM helices \u201ctightening\u201d the ligand pocket (via multiple contacts with the ligand-binding pocket. The tightening would overcome mutation-induced loss of individual contacts.Although it was hypothesized that the Asppeptides , 115. Sog pocket . In peptg pocket . Comparid pocket . ExtrapoAlthough only direct determination will confirm the GnRH receptor structure, growing numbers of other GPCR structures provide insight into common features likely to be shared by the GnRH receptor. GPCR structures can be used to hypothesize mechanisms by which agonist binding is coupled to G protein activation, which must be tested by dynamic methods, such as site-directed mutagenesis and functional analysis, regardless of availability of directly determined structures. Identification of the conformation-independent interhelical contact network has provided explanations for decreased expression of many cHH-associated mutant GnRH receptors, whereas the conserved conformation-specific interhelical contacts begin to explain how conserved residues mediate receptor activation. In spite of the diversity of ligand-binding surfaces, recent agonist-bound peptide-binding GPCRs suggest that ligand contacts in TM3 may trigger receptor activation and they may explain the high affinity of conformationally constrained GnRH peptides.CF conceived the project and wrote the manuscript. AM wrote a preliminary review as part of her MSc dissertation, which was partly used in the current project.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "The shortest genes are the ones coding for micro (MIR3143) or small nuclear (U7) RNAs at 63bp each. There is only partial information regarding the chromatin state of each variant. However, from the information gathered in the analysis we observed 14 transcription start sites and 245 enhancers (Supplementary Table 8).Applying HaploReg v4.1 analysis to the 536 variants resulted in 9 categories (Supplementary Table 8): miscRNA (1 variant); snoRNA (2 variants); microRNA (4 variants); snRNA (9 variants); pseudogenes (14 variants); sequencing in progress (43 variants); LINC RNA (86 variants); and 372 variants within protein coding genes. In addition, some variants annotate to the same gene resulting in a total of 139 genes (protein-coding or non-coding). Of those genes, 6 are exceptionally long, containing over a million base-pairs, the longest of which is Corrected: The corrected text is provided below.PTPRT coded by1117219bp. The shortest genes are the ones coding for micro (MIR3143) or small nuclear (U7) RNAs at 63bp each. There is only partial information regarding the chromatin state of each variant. However, from the information gathered in the analysis we observed 14 transcription start sites and 245 enhancers (Supplementary Table 8).Applying HaploReg v4.1 analysis to the 536 variants resulted in 9 categories (Supplementary Table 8): miscRNA (1 variant); snoRNA (2 variants); microRNA (4 variants); snRNA (9 variants); pseudogenes (14 variants); sequencing in progress (43 variants); LINC RNA (86 variants); and 372 variants within protein coding genes. In addition, some variants annotate to the same gene resulting in a total of 139 genes (protein-coding or non-coding). Of those genes, 6 are exceptionally long, containing over a million base-pairs, the longest of which is The authors sincerely apologize for this error."} +{"text": "AbstractHelionothripslushanensissp. n. is described from China. The new species is characterised by the head entirely dark brown, antennal segments I\u2013VIII almost uniformly yellowish brown and III\u2013IV strongly vasiform, metascutellum without produced posterior margins, and male has no pore plate on the abdominal sternites. Helionothrips Bagnall, 1932, is one of the most species rich taxa in the subfamily Panchaetothripinae, currently comprises 28 described species in the world which is reported from South America. Of the described species, the majority of species (more than 80%) in the genus are known from the Asian region (PageBreakPanchaetothripinae species from China is available (he world . The spen region . The revvailable . In the SCAU).The thrips were collected by beating vegetation over a white plastic tray using a stick, and then sorted and preserved in 90% alcohol. Examined specimens were mounted in Canada balsam using the method outlined by Taxon classificationAnimaliaThysanopteraThripidaehttp://zoobank.org/7481BEA8-A3C4-4C92-A378-B723D6C04AF7Holotype female (in SCAU): CHINA, Jiangxi province, Jiujiang City, Mt. Lushan , collected from older leaves of Ligustrumsinense (Oleaceae), 9.xi.2015, leg. Xiaoli Tong.Ligustrumsinense (Oleaceae), 4 males from older leaves of Viburnum sp. (Caprifoliaceae), 1 female from older leaves of Rhododendronsimiarum (Ericaceae), all taken with holotype. Hunan province, Liuyang City, Daweishan National Forest Park , 1 male from older leaves of Rhododendronlatoucheae (Ericaceae), 15.viii.2016, leg. Zhaohong Wang.2 males from older leaves of Both sexes macropterous; body dark brown; head entirely dark brown; antennal segments I\u2013VIII yellowish brown; fore wing brown with two pale bands. Head entirely reticulate without internal wrinkles within the reticules; antennae 8-segmented, segments III and IV strongly vasiform with forked sensoria, that on IV reach near the apex of V. Pronotum, meso- and metanotum completely reticulate, all lacking internal wrinkles within the reticles. Antecostal line on abdominal tergites III\u2013VIII divided into broad arched sculpture with heavy anterior margin; tergite VIII with complete comb of microtrichia on posterior margin. Male similar to female in structure and colour but smaller; abdominal sternites without pore plates.Female (macropterous): Body dark brown . Distended body length 1870. Head length (width) 100 (210); eye length (width) 70 (50). Pronotum length (width) 175 (250). Fore wing length 1040. Antennal segments I\u2013VIII length (width) as follows: 26(25), 40(33), 65(29), 53(33), 40(25), 31(21), 10(9), 30(6).Male (macropterous) Fig. . Similarus) Fig. , tergiteus) Fig. . AbdominMeasurements . Distended body length 1570. Head length (width) 100 (175); eye length (width) 60 (40). Pronotum length (width) 140 (200). Fore wing length 840. Antennal segments I\u2013VIII length (width) as follows: 20(22), 35(29), 58(27), 48(33), 33(24), 28(20), 8(9), 30(5).The specific epithet is named after the type locality, Mt. Lushan, Jiujiang City, Jiangxi province, China.China .H.errans (Williams) in colour and structure, particularly in the pronotum lacking internal wrinkles within the reticules and abdominal tergite VIII having a complete comb on its posterior margin, but it can be distinguished from the latter by (1) head entirely dark brown (head anterior of fore ocellus yellow in H.errans); (2) antennal segments I\u2013VIII almost uniformly yellowish brown ; (3) antennal segments stouter, especially III and IV strongly vasiform, segment IV approximately 1.6 times as long as wide ; (4) metascutellum normal, lacking produced posterior margins (metascutellum with posterior margins produced in H.errans) and (5) male has no pore plate on the abdominal sternites .The new species is most similar to"} +{"text": "On the basis of our personal experience in 70 cases observedduring the period January 1984- January 1996 we are here illustrating and discussingthe diagnostic role of thoracoscopy in malignant pleural mesothelioma.\t\tA histological diagnosis was achieved in 94.2% of cases. The endoscopic appearancewas clearly neoplastic in 53 patients (75.7%) and simply inflammatoryin 17 pachypleuritis in 13 (18.6%) and of diffuse hyperemia in 3 (5.7%). In allcases fluid cytology (diagnostic yield: 18.5%) and needle biopsy (diagnostic yield17.1%) were performed.\t\tThe extension of pleural involvement (endoscopic staging according to Boutin) wasalso determined. In 16 patients (22.8%) a parietal and diaphragmatic involvement(stage Ia) was found. In 40 patients (57.2%) an associated visceral invasion (stage Ib).In 14 cases (20%) a diffuse parietal, visceral and mediastinal extension (stage II).The exam has always been well tolerated with few immediate complications: subcutaneousemphysema (4 cases) and some negligeable parietal bleeding (2 cases)."} +{"text": "The use of photodynamic therapy (PDT) as an adjunct to curative tumour resection was investigated in a tumour recurrence model, using rat mammary adenocarcinoma BN472. Tumours were inoculated subcutaneously in 60 animals and resected after 21 days of growth. Immediately after removal, the operation site was exposed to 320-450 nm light of 0.1 W cm-2 and 60 J cm-2 after photosensitisation with either Photofrin (5 mg kg-1 i.v. 48 h before illumination) or 5-aminolaevulinic acid (ALA) (2 mg ml-1 in drinking water for 9 days). Porphyrin concentrations were measured in tissue samples. After 28 days, animals treated with adjunctive PDT had a significantly longer tumour-free interval than controls (P < 0.01); median 25 days (Photofrin), 18 days (ALA), 14 days (controls). Moreover, in the PDT groups significantly fewer rats had lymph node metastasis. A prophyrin concentration ratio between tumour and mammary tissue of 2:1 was found after Photofrin and 4:1 after ALA. The results indicate that adjuvant intraoperative PDT may be a safe and effective method of destroying residual tumour, thereby preventing locoregional tumour recurrence."} +{"text": "Clinical features and molecular characterization of 109 group B streptococci causing neonatal invasive infections were determined over an 18-month period in France. Sixty-four percent of the strains were from late-onset infections, and 75% were capsular type III. The hypervirulent clone ST-17 was recovered in 80% of meningitis cases. Streptococcus (GBS) is the leading cause of infectious illness among newborns. Invasive infections in neonates can result in pneumonia, sepsis, or meningitis. Early-onset disease (EOD) occurs within the first week. Late-onset disease (LOD) occurs after the first week and accounts for most meningitis cases and deaths . Antimicrobial drug\u2013resistance genes were detected by using the multiplex PCR as described and 64% (n = 70) were responsible for EOD and LOD, respectively . Eighty LOD had a male:female ratio of 1.15, and 82.6% of cases occurred during the first 8 weeks of life, with a peak (63%) at 4\u20138 weeks (data not shown). Sepsis occurred in 27.1% of LOD cases and meningitis in 65.7%. In 5 cases of LOD, less frequent manifestations were observed: sepsis was associated with parotitis (2 cases), osteomyelitis (1), spondylodiscitis (1), and orchitis (1). Three cases (4.5%) of recurrent invasive infections were reported. For 2 of these 3 cases, the first episode was early meningitis with a relapse of meningitis 2\u20133 weeks later, despite correct antimicrobial drug treatment. The third case was a late-onset sepsis that relapsed as a sepsis after the infant had received 3 weeks of amoxicillin. None of these infants was fed breast milk, which ruled out the possibility of contamination by this route. The death rate for LOD was 14.5%; 90% of deaths were associated with meningitis. Capsular type distribution of GBS LOD isolates was as follows: type III was largely predominant (83%) compared with types Ia (7.4%), Ib (4.5%), and V (1.5%) . Among s90 0.016 mg/L), amoxicillin (MIC90 0.016 mg/L), cefotaxim (MIC90 0.016 \u03bcg/mL), imipenem (MIC90 0.032 \u03bcg/mL), rifampin (MIC90 0.032 \u03bcg/mL), vancomycin (MIC90 0.75 \u03bcg/mL), and displayed low-level resistance to gentamicin (MIC90 8 \u03bcg/mL). Also, 95.5% were resistant to tetracycline because of the presence of tet(M) associated with tet(O) or tet(L) in 3 and 1 strains, respectively. Resistance to erythromycin was detected in 13.8% of the isolates and was not correlated with the capsular type or the onset of disease. Erythromycin resistance was caused by the presence of mef(A) (46.6%), erm(A) (26.6%), or erm(B) (20%).All 109 GBS strains tested were susceptible to penicillin , whereas LOD was more frequently responsible for meningitis (65.7%) (p<0.01). Deaths, all associated with meningitis, were higher in LOD (14.5%) than in EOD cases (2.5%).The predominance of capsular type III among infants with meningitis is well-known ("} +{"text": "P< 0.001). All of the 13 patients relapsing with normal markers remain alive, having been primarily treated surgically. Overall these results indicate an improving outlook for relapsed NSGCT. \u00a9 2000 Cancer Research CampaignBetween 1991\u201396, 41 patients were treated in this unit for relapsed non-seminomatous germ cell tumours (NSGCT). Twenty-eight patients had raised markers at relapse: 17 required salvage chemotherapy and post-chemotherapy surgery, 11 only chemotherapy. In addition 9 patients received high dose chemotherapy. Overall 16/28 patients (57%) requiring chemotherapy remain alive, 14 (50%) disease free. Of the 17 patients treated with chemotherapy and surgery: 12 remain alive, 10 (59%) with no evaluable disease. Only 4/11 (36%) patients treated with chemotherapy alone remain alive, all in complete remission (CR). For relapse with raised markers, univariate analysis suggests that less than CR to induction therapy, resulting in the presence of residual disease is the most important predictor of poor outcome ("} +{"text": "Of 47 consecutive patients aged 15-60 years with acute non-myelogenous leukaemia (ANML) (40 acute lymphoblastic leukaemia (ALL); 5 acute Burkitt-like leukaemia (ABLL), 2 acute undifferentiated leukaemia (AUL) treated with a standard chemotherapy protocol (OPAL), 31 achieved complete remission (28/40(70%) of patients with ALL). CNS leukaemia occurred in 4/16 non-remitters, and in 6 patients who achieved complete remission (CR). CNS leukaemia occurred in all 5 patients with acute Burkitt-like leukaemia. 4/28 patients with ALL achieving CR had evidence of CSF involvement on cytocentrifuge examination shortly after CR. The apparent risk of early CNS disease suggests that prophylactic CNS therapy should be given early in the treatment of acute non-myelogenous leukaemia."} +{"text": "In ovarian cancer patients a 6 kDa polypeptide, the tumour-associated trypsin inhibitor (TATI), can occur at elevated concentrations in both urine and serum. In this study pretreatment serum levels of TATI (cut-off point 21 ng ml-1) and CA 125 (cut-off points 35 U ml-1 and 65 U ml-1) were determined in 152 patients with epithelial ovarian cancer (115 primary and 37 recurrent) and in 267 women with benign pelvic diseases. The data obtained were correlated with the tumor stage, histological type and tumour grade. Overall, TATI showed a sensitivity of 64% and a specificity of 75%. The sensitivity and specificity of CA 125 > 35 U ml-1 were both 80%. Corresponding values for CA 125 > 65 U ml-1 were 70% and 87%. The combination of the two markers increased the sensitivity to 91% (CA 125 > 35 U ml-1) and 86% (CA 125 > 65 U ml-1), while the specificity dropped to 61% and 68% respectively. TATI was clearly superior in mucinous carcinomas of the ovary, the rate of true-positive findings in these neoplasms was 67% vs 42% for CA 125 > 35 U ml-1 and 33% for CA 125 > 65 U ml-1. Unlike CA 125, TATI correlated well with tumour grade. The combination of the two markers had a higher negative predictive value, i.e. 93% (CA 125 > 35 U ml-1) and 90% (CA 125 > 65 U ml-1) respectively. It is concluded that, while TATI cannot replace CA 125 in the diagnosis of malignant epithelial carcinomas of the ovaries, it is a valuable additional marker in cases of mucinous carcinomas and in combination with CA 125."} +{"text": "A phase II trial was performed to evaluate the efficacy and tolerance of vinorelbine (VNB), mitomycin C (MMC), and recombinant human granulocyte colony-stimulating factor (G-CSF) in advanced breast cancer. Between October 1992 and July 1994, 55 patients entered this trial. Nine patients had locally advanced disease and 46 had distant metastases, including 14 who had received previous palliative chemotherapy with (n = 9) or without anthracyclines (n = 5). Therapy consisted of VNB 40-50 mg m(-2) diluted in 250 ml saline infused over 30 min every 3 weeks, and MMC 15 mg m(-2) administered by intravenous bolus injection every 6 weeks. G-CSF was given at 5 microg kg(-1) day(-1) subcutaneously from days 2 to 7 following each cytotoxic drug administration. Treatment was continued in case of response or stable disease for a total of six courses. The overall response rate was 73% for all 55 patients , including 12 (22%) complete response (CR) and 28 (51%) partial response (PR); 13 patients (24%) had stable disease (SD), and only two (4%) progressed. All nine patients with locally advanced disease were rated responsive and underwent surgery with curative intent. Eight out of nine remain disease free after a median observation period of 18 months . Among the 32 previously untreated patients with metastatic disease, nine (28%) achieved CR, 15 PR (47%), seven SD (22%) and one PD (3%). Second-line chemotherapy with this regimen resulted in 7/14 (50%) objective remissions , six had SD and one PD. The median time to progression was 12 months in previously untreated patients with disseminated disease, and 6.0 months in those who had failed prior chemotherapy. After a median follow-up time of 20 months, 24 patients with distant metastases are still alive with disease; median survival has not been reached yet. The dose-limiting toxicity was myelosuppression: six (11%) and ten patients (18%) had World Health Organization grade 3, and eight (14%) and nine patients (16%) had grade 4 leucopenia and granulocytopenia respectively. Severe (WHO grade 3) non-haematological toxicities included nausea/vomiting in 7%, constipation in 9%, peripheral neuropathy in 5%, infectious episodes in 7%, phlebitis due to drug extravasation in 5%, alopecia in 9%, and acute reversible pulmonary toxicity in 11%. Our data suggest that vinorelbine, mitomycin C plus G-CSF has an excellent anti-tumour activity in advanced breast cancer, probably superior to most other available combination chemotherapy regimens. This combination does not seem to present significant cross-resistance with previous CMF or anthracycline regimens. Apart from reversible, acute pulmonary toxicity, a rare adverse reaction that had previously been described for VNB, as well as the combination of natural vinca alkaloids with mitomycin C, and few episodes of grade 3 neurotoxicity VNB dose level), the tolerance of this regimen seems acceptable and justifies further evaluation in front-line and salvage therapy of advanced breast cancer."} +{"text": "Thirty-seven eligible patients, median age 59 years (range 37-72) and median performance status 1 (0-2), with advanced, untreated, measurable gastric carcinoma were given docetaxel, 100 mg m-2 i.v. over 60 min without premedication, once every 3 weeks. Metastatic sites included the liver in 12 patients and retroperitoneal lymph nodes in 16. Eight of the 33 evaluable patients (24%) achieved a partial remission for a median of 7.5 months (3-11+). An additional 11 patients had stabilisation of disease. The patients received a median of four cycles of docetaxel (range 1-8) for a total of 156 courses. Dose reduction was necessary in 30 cycles; 14 cycles were delayed a mean of 3 days. Haematological toxicity consisted mainly of non-cumulative neutropenia, with a median nadir count of 0.35 x 10(9) l-1 (0.04-1.64) and eight episodes (5%) of leucopenic fever; non-haematological toxicities included alopecia, mild nausea and vomiting and allergic manifestations such as skin rash and pruritus. There were no drug-related deaths. Our data indicate that docetaxel is an active agent in advanced gastric cancer; further clinical investigations seem warranted."} +{"text": "The distal half of chromosome 1p was analysed with 15 polymorphic microsatellite markers in 683 human solid tumours at different locations. Loss of heterozygosity (LOH) was observed at least at one site in 369 cases or 54% of the tumours. LOHs detected ranged from 30\u201364%, depending on tumour location. The major results regarding LOH at different tumour locations were as follows: stomach, 20/38 (53%); colon and rectum, 60/109 (55%); lung, 38/63 (60%); breast, 145/238 (61%); endometrium, 18/25 (72%); ovary, 17/31 (55%); testis, 11/30 (37%); kidney, 22/73 (30%); thyroid, 4/14 (29%); and sarcomas, 9/14 (64%). High percentages of LOH were seen in the 1p36.3, 1p36.1, 1p35\u2013p34.3, 1p32 and 1p31 regions, suggesting the presence of tumour-suppressor genes. All these regions on chromosome 1p show high LOH in more than one tumour type. However, distinct patterns of LOH were detected at different tumour locations. There was a significant separation of survival curves, with and without LOH at chromosome 1p, in the breast cancer patients. Multivariate analysis showed that LOH at 1p in breast tumours is a better indicator for prognosis than the other variables tested in our model, including nodal metastasis. \u00a9 1999 Cancer Research Campaign"} +{"text": "Subjects consisted of 5483 general population aged 40\u201374 years, who received initial CT scans in 1996, followed by repeat annual scans for most subjects in 1997 and 1998, with a total of 13 786 scans taken during 1996\u20131998. Work-up examinations for patients with suspicious lesions were conducted using diagnostic CTs. The initial screening in 1996 detected suspicious nodules in 279 (5.1%) of 5483 subjects, and 22 (8%) were confirmed surgically to have lung cancer. Corresponding figures in 1997 and 1998 screening studies were 173 (3.9%) of 4425 and 25 (14%) of 173, and 136 (3.5%) of 3878 and 9 (7%) of 136, respectively. The sensitivity and specificity of detecting surgically confirmed lung cancer were 55% (22/40) and 95% (4960/5199) in 1996 and 83% (25/30) and 97% (4113/4252) in 1997 screening, respectively. 88% (55/60) of lung cancers identified on screening and surgically confirmed were AJCC stage IA. Our trial allowed detection of nearly 11 times the expected annual number of early lung cancers. Repeat CT allowed the detection of more aggressive, rapidly growing lung cancers, compared to those in the initial screening. \u00a9 2001 Cancer Research Campaign"} +{"text": "Fine needle aspirates from 82 patients with breast carcinoma were fixed in methacarn, double embedded in agar or gelatin, and then in paraffin wax. Sequential sections were stained with monoclonal antibodies to the oestrogen receptor-related protein P29 (antibody D5), carcinoembryonic antigen (CEA), epithelial membrane antigen (EMA) and cytokeratin (CAM 5.2). Sixty-one of 82 (74%) aspirates provided sections suitable for immunostaining. Twenty-six (43%) were D5 positive, 23 (38%) CEA positive, 59 (97%) EMA positive, and 54 (89%) CAM 5.2 positive. Twenty-six of these patients were treated with some form of endocrine therapy. Twelve (46%) showed positive staining for D5. Eleven (92%) of the 12 D5-positive patients responded or had static disease, and 8% progressed. Of the 14 D5-negative tumours 43% responded or remained static, and 57% progressed. The difference in response between the D5-positive and the D5-negative tumours was significant . There was no correlation between staining for CEA, EMA or cytokeratin and response to endocrine therapy."} +{"text": "The purpose of this study was to evaluate in a randomized phase II trial the efficacy and toxicity of combination biochemotherapy compared with chemotherapy alone in patients with metastatic melanoma. Sixty-five patients with metastatic melanoma (ECOG performance status 0 or 1) were randomized to receive intravenous BCNU 100 mg m(-2) , cisplatin 25 mg m(-2) (days 1-3), DTIC 220 mg m(-2) (days 1-3) and oral tamoxifen 40 mg (BCDT regimen) with (n = 35) or without (n = 30) subcutaneous interleukin 2 (IL-2) 18 x 10(6) iu t.d.s. (day - 2), 9 x 10(6) iu b.d. (day - 1 and 0) and interferon 2 alpha 9 MU (days 1-3). Evidence for immune activation was determined by flow cytometric analysis of peripheral blood lymphocytes. Treatment was repeated every 4 weeks up to six courses depending on response. The overall response rate of BCDT with IL-2/IFN-alpha was 23% [95% confidence interval (CI) 10-40%] with one complete response (CR) and seven partial responses (PR), and for BCDT alone 27% (95% CI 12-46%) with eight PRs; the median durations of response were 2.8 months and 2.5 months respectively. Sites of response were similar in both groups. There was no difference between the two groups in progression-free survival or overall survival . Although 3 days of subcutaneous IL-2 resulted in significant lymphopenia, evidence of immune activation was indicated by a significant rise in the percentage of CD56- (NK cells) and CD3/HLA-DR-positive (activated T cells) subsets, without any change in the percentage of CD4 or CD4 T-cell subsets. Toxicity assessment revealed a significantly higher incidence of severe thrombocytopenia in patients treated with combination chemotherapy than with chemotherapy alone and a higher incidence of grade 3/4 flu-like symptoms (20% vs 10%) and fatigue (26% vs 13%). The addition of subcutaneous IL-2 and IFNalpha to BCDT chemotherapy in a randomized phase II trial resulted in immune activation but did not improve response rates in patients with metastatic melanoma, and indeed may increase some treatment-related toxicity."} +{"text": "In a multicentre study, 83 patients with advanced and previously uniformly treated multiple myeloma (MM) were randomised between cyclophosphamide (600 mg m-2) and epirubicin (70 mg m-2), administered every 3 weeks for three courses and both associated with prednisone and interferon-alpha2b. Both regimens were administered on an outpatient basis and had low haematological toxicity. Clinical results were similar. Overall response rate (43%) and median response and survival (5.9 and 14.1 months respectively) compare well with those obtained with more aggressive chemotherapy schedules."} +{"text": "We studied the incidence of intracranial tumours in Lothian Region in south-east Scotland in 1989-90. Among 106 patients resident in the Region, 60 (57%) were of working age (15-64 years). All but two cases (97%) were histologically confirmed. The average annual incidence of cerebral glioma in this age range was 5.9 (95% CI 3.8-8.0) per 100,000 per year. Cerebral glioma will affect approximately 2100 people of working age in the UK every year."} +{"text": "To prospectively evaluate the prevalence of hepatitis B virus (HBV) positivity and study the evolution of HBV profile during cancer chemotherapy, serum HBV markers and liver biochemistry were determined in 1008 of 1402 (72%) cancer patients admitted in our Unit and in all 920 (91%) who received chemotherapy. We found that 54 (5.3%) were HBsAg carriers while 443 (44%) had at least one HBV marker positive. Of the latter, 405 (91%) were HBcAb+ve, 321 (72%) HBsAb+ve and 212 (48%) HBeAb+ve. No patient was HBeAg+ve. Among 920 chemotherapy receivers, 374 (41%) were HBcAb+ve, 280 (30%) HBsAb+ve and 178 (19%) HBeAb+ve. Fifty (5.4%) were HBsAg carriers (versus 0.6% in Greek blood donors). All 50 were systematically screened for HBsAg and HBsAb status throughout chemotherapy, during follow-up or until their death, and liver biochemistry was performed before each chemotherapy course. Stable antigenaemia was observed in 43/50 (86%) while 7/50 (14%) developed clinical and/or biochemical hepatitis. Six of these seven developed serum anti-HBs antibodies with an associated decrease of serum HBsAg titres. We conclude that reactivation of HBV infection during chemotherapy is not rare (14%), while disappearance of HBs antigenaemia is neither a frequent nor usually a permanent phenomenon. \u00a9 1999 Cancer Research Campaign"} +{"text": "Comparative genomic hybridization was applied to detect and map changes in DNA copy number in 24 well or moderately differentiated epithelial ovarian carcinomas . Twenty-three of the 24 tumours showed changes in DNA copy number in one or several regions . Gains were more frequent than losses (ratio 1.6:1.0). The most frequent gains occurred in chromosomes 1q (38%), 2p (29%), 7q (25%), 8q(38%) and 17q (38%), and the most common losses were located in chromosomes 8p (21%), 9p (25%) and 13q (21%). High-level amplifications were detected in seven tumours at 1q22-32, 2p15-22, 3qcen-23, 6p21-22 and 8q. In the three histological subtypes the copy number karyotypes showed substantial differences. Gains at 1q were observed in endometrioid (five cases) and serous tumours (four cases). Increased copy number at 10q was seen in endometrioid tumours only (four cases), whereas gains at 11q occurred mostly in serous tumours (four cases). In mucinous tumours, the most common copy number change was a gain at 17q (six cases). The results show that, in epithelial ovarian carcinoma, changes in DNA copy number are a rule rather than an exception, chromosomes 1, 2, 7, 8, 9, 13 and 17 being the most frequently affected. The diverging pattern of genetic changes seen in epithelial ovarian carcinomas with different histological phenotypes suggests that various pathways may lead to tumorigenesis and/or progression in these subgroups."} +{"text": "JM216 (bis-acetato ammine dichloro cyclohexylamine Pt IV) is an oral platinum complex presently undergoing phase II clinical trials. Previous studies have identified some of its biotransformation products in clinical materials. This study evaluated the nature of JM216 biotransformation products intracellularly in two different human ovarian carcinoma cell lines, one relatively sensitive to platinum agents (CH1: JM216 4 h IC50 of 5.8 microM) and the other relatively resistant (SKOV3: JM216 4 h IC50 of 60.7 microM). Metabolic profiles were also evaluated at different growth status and in cells pretreated with buthionine sulphoximine (BSO), an agent known to decrease intracellular glutathione levels. Results showed that JM216 enters the cells and that the nature and percentage of biotransformation products was dependent upon glutathione levels. Furthermore, results support the view that the previously reported peak A biotransformation product contains a glutathione adduct. In exponentially growing SKOV3 cells which contain higher glutathione levels than CH1, (82.5 vs 37.8 nmol mg-1 protein), peak A represented 89% of total platinum 4 h after JM216 exposure compared with only 24% in CH1. Moreover, 60-70% depletion of glutathione achieved by 24 h pretreatment of cells with BSO resulted in a significant decrease in peak A in both cell lines and increased the cytotoxicity of JM216 in both CH1 and SKOV3 by approximately 2-fold. Following a 4 h exposure of exponentially growing SKOV3 cells to JM216, only peak A (89%) and JM216 (11%) could be detected whereas in CH1 cells, peak A (24%), JM216 (73%) and JM118 [cis-ammine dichloro (cyclohexylamine) platinum II] (3%) were detected. However, in CH1 cells at confluence, where glutathione is lower (8 nmol mg-1 protein) four metabolites (plus JM216 itself) were detected following exposure to 50 microM JM216; peak A, JM118, JM383 (bis-acetato ammine (cyclohexylamine) dihydroxy platinum IV) and an unidentified metabolite (D), also observed in patient's plasma ultrafiltrate. In confluent SKOV3 cells exposed to 50 microM JM216, peak A, JM216 and JM118 were detected. A further unidentified metabolite observed in patients receiving JM216 (metabolite F) was not formed inside these tumour cells. Overall, these data suggest that glutathione conjugation represents a major deactivation pathway for JM216."} +{"text": "SummaryExpression of apoptosis-related proteins, bcl-2, Bax, Fas and Fas ligand (L), in ovarian epithelial neoplasms together with its clinical relevance was examined by immunohistochemistry. They included 36 cases with adenoma, 33 with low potential malignancy (LPM) and 63 with carcinomas. bcl-2 expression was observed in 14 of 36 cases (39%) with adenoma, five of 33 (15%) with LPM (P< 0.05) and 12 of 63 (19%) with carcinoma (P< 0.05). Cases with bcl-2 expression showed more favourable prognosis than those without, but the difference was not statistically significant. There was no difference in frequency of Bax and Fas expression between each histologic category. Fas L expression was observed in one of 36 cases (3%) with adenoma, but in 12 of 33 (36%) with LPM (P< 0.001) and 42 of 63 (67%) with carcinoma (P< 0.0001). In carcinomas, cases expressing Fas L showed a less favourable prognosis than those without (P= 0.02). Density of CD8+ lymphocytes, possibly cytotoxic T-cells, was higher in serous carcinoma with negative Fas L expression than those with positive Fas L expression. These findings suggest that Fas L expressing carcinomas induce apoptosis in infiltrating CTL with Fas expression, and escape from immune surveillance. \u00a9 2000 Cancer Research Campaign"} +{"text": "Pharmacokinetically guided dosing was performed in nine paediatric patients receiving etoposide. Doses on day 2 of a 2- or 3-day schedule were adapted on the basis of the day-1 area under the plasma etoposide concentration vs time curve (AUC). The day-1 AUC was estimated using a limited sampling model and the day-2 target AUC defined by the etoposide dose-AUC relationship observed in 33 children. Target AUC values (4.6-8.2 mg ml(-1) x min) were achieved with a high degree of precision and with little bias (mean error 11% and root mean squared error 15% respectively). Pharmacokinetic parameters were similar to those reported previously in children, although interpatient pharmacokinetic variability was less than that observed previously: plasma clearance, 23 (18-26) ml min(-1) m(-2); volume of distribution at steady state (Vdss), 6.0 (3.9-8.9) l m(-2); t(1/2) 254 (127-550) min (median and range). This study has demonstrated that pharmacokinetically guided dosing with etoposide is feasible. However, pharmacokinetically guided dosing is likely to be of most benefit in patients with abnormalities of renal or hepatic function, or in children with prior exposure to cisplatin."} +{"text": "Thirty patients with symptomatic colorectal carcinoma were commenced on treatment with 5-fluorouracil (2.5 g week-1) administered by continuous intravenous infusion and alpha 2b interferon (3 x 10(6) U s.c. three times a week). Six out of 30 patients (20%) achieved a partial response. Three patients (10%) had stable disease and 21 patients (70%) progressed on treatment. Twenty patients (67%) completed ten or more weeks of treatment. In nine patients, treatment was withdrawn after 2-9 weeks because of disease progression or death. One patient's treatment was interrupted by emergency surgery. The median survival for all patients was 210 days (7 months). The principal side-effects were oral mucositis (12/30 patients), nausea (8/30 patients) and transient diarrhoea (4/30 patients), and initial constitutional symptoms due to alpha 2b interferon. The combination of low-dose continuous infusional 5-fluorouracil and low-dose alpha 2b interferon is well tolerated but has no obvious advantage over alternative infusional regimens using 5-fluorouracil as a single agent."} +{"text": "Thalidomide based regimen is an effective and well tolerated therapy in multiple myeloma (MM) patients, however, there were a small number of studies written about the results of thalidomide therapy in non-transplant MM patients. We therefore conducted a retrospective study of 42 consecutive patients with newly diagnosed and relapsed/refractory MM treated with thalidomide- based induction regimens followed by thalidomide maintenance therapy.Induction regimens with thalidomide and dexamethasone, and the oral combination of melphalan, prednisolone and thalidomide were administrated in 22 and 16 patients, respectively. The remaining 4 patients received other thalidomide- containing regimens. Twenty-nine patients received thalidomide as a salvage regimen. Twenty-three out of 26 patients achieving complete remission (CR) and very good partial remission (VGPR) received thalidomide maintenance. Of the 41 evaluable patients, median time of treatment was 21 months (3- 45 months), ORR was 92.7% with a 63.4% CR/VGPR. With a median follow up of 23 months, 3-year- PFS and 3-year-OS were 58.6 and 72.6%, respectively. Median time to progression was 42 months. While 3-year-PFS and 3-year-OS in non-transplant patients receiving thalidomide maintenance therapy were 67 and 80%, respectively.Prolonged thalidomide therapy enhanced survival rate and less frequently developed serious toxicity in non-transplant multiple myeloma patients. To the editor:2/day (d1-7), prednisolone 40 mg/m2/day (d1-7) and thalidomide 100 mg/day every 4 weeks, 3 patients received thalidomide 200-400 mg/day and the remaining 1 patient received thalidomide 100 mg/day, pegylated liposomal doxorubicin i.v. 40 mg/m2/day (d1) and oral dexamethasone 40 mg/day every 4 weeks. Eighty-eight percents (23/26 patients) achieving CR/VGPR received thalidomide maintenance therapy (100-200 mg/day). Aspirin 65- 325 mg/day or warfarin 1.5 mg/day was given to all patients for deep vein thrombosis prophylaxis. Of the 41 evaluable patients, median treatment period was 21 months (3- 45 m). The ORR was 92.7%, with a 63.4% CR/VGPR. Median number of courses to achieve PR and CR/VGPR were 4 and 6 courses , respectively. There was no difference in ORR and CR between frontline and salvage therapy groups (92.3% vs 93%) and (39% vs 23%), respectively. The ORR and CR rate for those treated with thal/dex were slightly higher than those treated with MPT (95.2% vs 87.5% and 38% vs 25%). Median follow up was 23 months, 3-year-OS and 3-year-PFS were 72.6 and 58.6%, respectively. Median TTP was 42 months, non- VGPR/CR patients had significant poorer PFS by multivariate analysis (p = 0.01) and non-responders had significant shorter OS (p = 0.01). In maintenance group, median treatment duration was 14 months (4-37 m). Three-year-PFS and 3-year-OS were 67 and 80%, respectively. Toxicities were constipation (81%), neuropathy (67%), muscle weakness in the legs (5%), infection (7%) and thrombosis (5%). New agents for treatment of MM with no planned ASCT show the CR/VGPR rates of 50- 80% with a PFS of 2 years [Thalidomide based therapy for multiple myeloma (MM) improves the response and the complete remission (CR) rates in previously untreated and relapsed/refractory MM . In this"} +{"text": "We examined 159 consecutive cases of non-small-cell lung cancer (NSCLC) for a mutation at codon 12 of the K-ras gene and for a mutation of the p53 gene occurring in exons 5-8. Eleven (6.9%) had mutations of the K-ras (ras+) and 57 (35.8%) had mutations of the p53 (p53+). There were 95 cases (59.7%) with ras- p53-, seven cases (4.4%) with ras+/p53-, 53 cases (33.3%) with ras-/p53+ and four cases (2.5%) with ras+/p53+. The ras+ group had a worse prognosis than the ras group in all cases and in 107 early-stage cases . The p53+ group had a worse prognosis in 107 early-stage cases (P<0.01), but there was no statistically significant difference when 52 advanced-stage cases (stage III-IV) or all patients were considered. Both ras and p53 mutations were unfavourable prognostic factors in 94 cases with adenocarcinoma, but there was no statistical significance in 57 cases with squamous cell carcinoma. According to Cox's model, the pathological stage, ras mutation and p53 mutation were found to be independent prognostic factors. Our results suggest that ras and p53 mutations were independent unfavourable prognostic markers especially in the early stage of NSCLC or in adenocarcinoma."} +{"text": "This study was undertaken to investigate the intracellular induction of reactive oxygen species (ROS) by cis-dichlorodiammineplatinum (CDDP) and the augmentation of their cytotoxicity in bladder cancer cells (KU7) by enhancement of ROS generation by the glutathione (GSH) depletors buthionine sulphoximine (BSO) and diethylmaleate (DEM). CDDP-induced cytotoxicity in KU7 cells and its modulation by GSH depletors were determined using spectrophotometric measurement with crystal violet staining. The effects of GSH depletors on intracellular GSH levels were confirmed using the GSH reductase-DTNB recycling method. Intracellular ROS generation induced by CDDP with or without GSH depletors was estimated from the amount of intracellular dichlorofluorescein (DCF), an oxidized product of dichlorofluorescein (DCFH), which was measured with an anchored cell analysis and sorting system. The cytotoxic effects of CDDP (IC50 15.0 +/- 2.5 microM) were significantly enhanced by BSO and DEM . BSO and DEM produced a significant depletion in intracellular GSH levels (9.6 +/- 0.4 nmol 10(-6) cells, 17.9 +/- 1.0 nmol 10(-6) cells) compared with the controls (30.5 +/- 0.6 nmol 10(-6) cells). Intracellular DCF production in KU7 cells treated with CDDP (1.35 +/- 0.33 microM) was significantly enhanced by the addition of BSO (4.43 +/- 0.33 microM) or DEM (3.12 +/- 0.22 microM) at 150 min. These results suggest that ROS may play a substantial role in CDDP-induced cytotoxicity and that GSH depletors augment its cytotoxicity through an enhancement of ROS generation in bladder cancer cells."} +{"text": "Purpose. This study investigates the efficacy and toxicity of daily oral etoposide inchemotherapy for non-heavily pretreated advanced and metastatic soft tissue sarcoma (STS). Subjects. Twenty-seven patients with progressive and measurable disease were treated. Median age was 53 years(range 20\u201371 years) and performance status WHO 0 or 1. Histologies included mainly leiomyosarcoma (8),malignant fibrous histiocytoma (4), rhabdomyosarcoma (4), liposarcoma (2) and synovial sarcoma (2). Fifteenpatients had received prior radiotherapy, of whom three included sites with haematopoiesis. All patients had receivedprior chemotherapy, including adjuvant therapy (7) and mostly consisted of one two-drug schedule (ifosfamide anddoxorubicin) or two single-drug regimens. Methods. Chemotherapy consisted of etoposide (VP16-213), 50 mg m-2 day-1 \u00d7 21 q 4 weeks. Blood cell countswere done weekly. Dose reductions and a maximum delay of 2 weeks was allowed depending on cell counts duringtreatment and at the start of a new 4-week treatment cycle. Results. No objective response was observed. Progressive disease was observed after two treatment cycles in 17/27patients (68%) and after three cycles in 22/27 patients (81%). The other patients received three to five cycles.Twenty-four patients went off study due to progressive disease. Grade 3 and 4 neutropenia was observed in eightand one patients, respectively. Thrombocytopenia grade 3 was seen in two patients. Non-haematological toxicitygrade 3 was observed in three patients, and grade 4 in three patients. Discussion. No objective response was obtained. Oral etoposide at a dose of 50 mg m-2day-1 \u00d7 21 q 4 weeks isinactive in chemotherapy of pretreated STS. Disease progression occurred within three cycles in the majority (81%)of patients. Toxicity of this regimen in non-heavily pretreated patients is low."} +{"text": "Cyclophosphamide was administered every 28 days while 5-FU/LV every 14 days. In an intention-to-treat analysis, complete response (CR) was achieved in 2 (4.9%) patients and partial response (PR) in 9 (22%) . Stable disease (SD) and progressive disease (PD) were observed in 9 (22%) and 21 (51%) patients, respectively. The overall response rate was 6% and 40% in patients with primary and secondary resistance to anthracyclines/taxanes, respectively (P = 0.047). The median duration of response and the median time to disease progression was 8 and 9.5 months, respectively. The median overall survival was 13 months and the probability for 1-year survival 51%. Grade 3/4 neutropenia occurred in 9 (22%) patients and 4 (9%) patients developed grade 3/4 thrombocytopenia. Non-haematological toxicity was mild. There were no cases of febrile neutropenia, toxic deaths or treatment-related hospital admissions due to toxicity. The combination of high-dose 5-FU/LV with conventional doses of cyclophosphamide is a well tolerated and effective salvage regimen in patients with MBC heavily pretreated with both anthracyclines and taxanes. \u00a9 2001 Cancer Research Campaignhttp://www.bjcancer.comhttp://www.bjcancer.comThe purpose of this study was to evaluate the activity and tolerance of high-dose leucovorin (LV) and infusional 5-fluorouracil (5-FU) in combination with conventional doses of cyclophosphamide (CPM) as salvage chemotherapy in patients with metastatic breast cancer (MBC) pretreated with anthracyclines and taxanes. 41 patients (median age 59 years) with MBC refractory or resistant to anthracyclines and taxanes were enrolled. The patients' performance status (WHO) was 0 in 10 patients (24%), 1 in 22 (54%), and 2 in 9 (22%). 30 (73%) patients had received 2 or more prior chemotherapy regimens. Cyclophosphamide (600\u2008mg\u2008m"} +{"text": "Seventy-seven men with histologically proven and newly diagnosed prostate cancer we investigated for the presence of bcl-2 protein overexpression and p53 protein accumulation 1 immunohistochemistry. Forty-five men had evidence of locally advanced and metastatic disease and we treated by means of hormone manipulation. Twenty-eight patients either failed to respond to initial hormone manipulation or relapsed within 37 months from diagnosis (median 20 months). Of the 77 cancers, 37 (48% showed bcl-2 overexpression at diagnosis. Twenty-seven of those were treated with androgen ablation and 2 (74%) had hormone-refractory disease (P = 0.0128). Twenty-three of 77 men (29.8%) had nuclear staining for p53 protein. Twenty-one of those were treated with hormone manipulation and 14 (66.6%) showed hormone resistance (P = 0.0012). Seventeen patients had both bcl-2 overexpression and p53 protein accumulation, 16 of whom were hormonally treated, with 13 (81.2%) having hormone-refractory disease (P < 0.0001). These findings suggest that the combined detection of p53 protein accumulation and bcl-2 overexpression may be useful in predicting hormone resistance in prostate cancer. By deregulating programmed cell death, alteration in these genes may prevent patients from responding to androgen ablation, or allow them to escape hormonal control of the disease."} +{"text": "The folates present in liver, gut and tumour tissue were examined before and after autolysis. Before autolysis 10-formylfolate tetraglutamate (10-CHOFA(glu)4), 5-methyltetrahydrofolate triglutamate (5-CH3THF(glu)3) and possibly tetrahydrofolate polyglutamate(s) (THF(glu)n) were detected. Liver contained all 3 species whereas no 5-CH3THF(glu)3 was present in the tumours; gut showed an intermediate situation. After autolysis the predominant monoglutamates formed were 5-CH3THF in the liver, 10-formylfolates in the gut and possibly tetrahydrofolate (THF) in the tumour extracts. These differences illustrate changes in tissue folates with the proliferation rate of the tissue and suggest an explanation for the methionine auxotrophy of Walker 256 carcinosarcoma cells."} +{"text": "A phase I trial of the combination of irinotecan (CPT-11) with cisplatin in advanced non-small cell lung cancer (NSCLC) showed a very promising response rate of 54% in previously untreated NSCLC patients. This study was conducted to confirm the activity and toxicities of CPT-11 and cisplatin combination for previously untreated NSCLC in a multi-institutional phase II study. Seventy patients with stage IIIB or IV NSCLC received CPT-11 60 mg m(-2) intravenously (i.v.) on days 1, 8 and 15, and cisplatin 80 mg m(-2) (i.v.) on day 1 every 4 weeks. Assessments were made of response, survival and toxicities. Sixty-nine were eligible, and evaluable for toxicities and survival, and 64 patients evaluable for response. Thirty-three patients achieved an objective response, with one complete response (2%) and 32 partial responses (50%). The median duration of response was 19 weeks and the overall median survival time was 44 weeks. The 1-year survival rate was 33%. The major toxic effects were leucopenia and diarrhoea. Grade 3 or 4 leucopenia, neutropenia, and diarrhoea occurred in 32 patients (46%), 53 patients (80%), and 13 patients (19%) respectively. A combination of CPT-11 and cisplatin is very effective against non-small-cell lung cancer with acceptable toxicities."} +{"text": "A late phase II clinical trial of RP56976 (docetaxel), derived from Taxus baccata was performed to evaluate anti-tumour activity, time to progression and clinical toxicity in patients with advanced or recurrent breast cancer. The patients, between 15 and 80 years old with performance status (PS) of 0-2, received at least two cycles of docetaxel 60 mg m-2 intravenously at 3-4 week intervals. Of the 81 patients enrolled, the 72 eligible for the study were given a total of 327 cycles, with a median of four cycles each. Five patients obtained a complete response (CR) and 27 a partial response (PR); the response rate (RR) was 44.4% . A relatively high RR of 9/28 (32.1%) was observed in patients who had received prior chemotherapy involving anthracyclines. The dose-limiting toxicity was grade 3-4 leucocytopenia or neutropenia, found in 78.9% and 85.9% patients respectively. Other severe (grade > 3) toxicities included alopecia (38%), anorexia (18.3%), nausea/vomiting (11.3%), and fatigue (9.9%). Hypersensitivity reactions, oedema and skin toxicity were not severe and were reversible. One therapy-related death occurred 10 days after the initial dose was given. These findings indicate that docetaxel has potent activity against metastatic breast cancer, and that the dose of 60 mg m-2 is safe."} +{"text": "Upstream open reading frames (uORFs) can mediate translational control over the largest, or major ORF (mORF) in response to starvation, polyamine concentrations, and sucrose concentrations. One plant uORF with conserved peptide sequences has been shown to exert this control in an amino acid sequence-dependent manner but generally it is not clear what kinds of genes are regulated, or how extensively this mechanism is invoked in a given genome.Ka/Ks analysis showed that purifying selection had acted on nearly all conserved peptide uORFs and their associated mORFs. Functions of predicted mORF proteins could be inferred for 16 homology groups and many of these proteins appear to have a regulatory function, including 6 transcription factors, 5 signal transduction factors, 3 developmental signal molecules, a homolog of translation initiation factor eIF5, and a RING finger protein. Transcription factors are clearly overrepresented in this data set when compared to the frequency calculated for the entire genome (p = 1.2 \u00d7 10-7). Duplicate gene pairs arising from a whole genome duplication (ohnologs) with a conserved uORF are much more likely to have been retained in Arabidopsis than are ohnologs of other genes . Two uORF groups were found in animals, indicating an ancient origin of these putative regulatory elements.By comparing full-length cDNA sequences from Arabidopsis and rice we identified 26 distinct homology groups of conserved peptide uORFs, only three of which have been reported previously. Pairwise Conservation of uORF amino acid sequence, association with homologous mORFs over long evolutionary time periods, preferential retention after whole genome duplications, and preferential association with mORFs coding for transcription factors suggest that the conserved peptide uORFs identified in this study are strong candidates for translational controllers of regulatory genes. Upstream open reading frames (uORFs) are small open reading frames found in the 5' UTR of a mature mRNA, and can mediate translational regulation of the largest, or major, ORF (mORF). Regulation by uORFs has been studied in several individual transcripts demonstrating the importance of uORFs in such processes as polyamine production , amino aCPA1 [SAMDC1/AdoMetDC1 [The majority of characterized uORFs appear to act in an amino acid sequence-independent manner, regulating mORF translation by the uORF start codon nucleotide context, by the uORF length, or by the distance between the uORF stop codon and the mORF start codon, rather than by uORF-encoded peptides -11. SomeCPA1 and SAMDdoMetDC1 , have dedoMetDC1 ,20. In tdoMetDC1 and overdoMetDC1 ,22.S. cerevisiae by analyzing genomic sequence upstream of predicted mORF start sites [Aspergillus nidulans genome, comparison to A. fumigatus and A. oryzae has identified 38 uORFs with putatively conserved start and stop codon positions relative to the mORF, 14 of which are conserved in one of Neurospora crassa, Fusarium graminaerum, or Magnaporthe grisea [In general, it has been difficult to carry out genome-wide surveys of conserved peptide uORFs due to poor annotation of 5' UTRs. The availability of expressed sequence tags (ESTs) has improved exon and intron annotation of the genomic sequence, but they are relatively short and often do not predict the entire mRNA molecule, even when several ESTs overlap the same genomic region and can be assembled to predict one transcript. As there are very few introns in yeast transcripts, prediction of uORF conservation has been attempted in rt sites , but it Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis) full-length cDNA sequence collections to estimate the incidence of conserved peptide uORFs in the rice and Arabidopsis genomes, to determine the prevalence of uORFs within regulatory genes, and to compare evolutionary rates for uORFs versus mORFs. By examining more distantly related sequences, we posit an ancient origin for select uORFs and we provide evidence for one mechanism by which uORFs can arise within genes.With the emergence of large plant full-length cDNA sequence collections -26, it iTo identify conserved peptide uORFs, we developed \"uORF-Finder\", a Perl program that first compares the mORF amino acid sequence of each cDNA from one collection with the mORF sequences of another species' collection to identify putative mORF homologs, and then compares the uORFs in the 5' UTRs of the two paired sequences to identify uORFs with conserved amino acid sequences (see Methods). Comparison by uORF-Finder of a corrected set of 34000 full-length cDNA sequences from Arabidopsis with a similar set from rice resulted in the identification of conserved peptide uORFs in 44 Arabidopsis genes and 36 rice genes, which together comprise 19 homology groups based on uORF amino acid similarity Tables , 3, 4, 5Ks value) of 0.7 is similar to the median Ks of recent duplicate pairs (0.8) and is within their Ks range (0.4\u20131.6) [Conserved uORFs that are not sufficiently well conserved to be detected in a rice-Arabidopsis comparison could conceivably be detected in ohnologs, homologous genes arising by whole-genome duplication (WGD) , and in 0.4\u20131.6) . The cor pairs 0. and is wKa/Ks tests for selection on amino acid sequences were applied to each uORF homology group and their associated mORFs to determine whether uORF amino acid sequences are under selective constraints similar to their associated mORFs. Both an approximate method (Yn00) and a maximum likelihood method (codeml) were used to calculate mean pairwise Ka/Ks ratios for each group. A Ka/Ks ratio less than 1 implies that negative, or purifying, selection has acted on the sequence, a ratio equal to 1 suggests drift, and a ratio greater than 1 indicates that positive selection has acted on an amino acid sequence. It is also true that conservation at the nucleotide level, not the amino acid level, can drive the Ka/Ks ratio to one. Analysis of all 26 homology groups showed that generally both uORFs and mORFs have been under mild to strong purifying selection since the divergence of each gene pair was identified between the N-terminal and central region of the uORF and the central and C-terminal region of the mORF found at locus At5g03190 (group 17). Classification of this putative uORF is shown in Table One possible explanation for low 0 group 1. ClassifThe lengths of uORFs vary to differing degrees within and among homology groups, but in amino acid sequence alignments nearly all groups exhibit considerable conservation of the position of the N-terminus and/or the C-terminus, i.e., length variation is usually due to a variable region in the middle or at one end of the uORF Table , 6, 7, 8-7) among conserved peptide uORF loci. In each case, GO terms were validated by manual annotation of protein functions using domain predictions from NCBI Conserved Domain and InterProScan Database searches [A total of 31% of mORFs encoded by conserved peptide uORF loci in Arabidopsis were predicted to be a transcription factor, as determined by GO molecular function terms Tables and 4, wsearches ,36. A vaBiological functions could be inferred for 16 of the 26 uORF homology groups , but thiAdiantum); group 3 was found as far from angiosperms as the green algae (Ulva); group 13 was found in an animal ; and group 8 uORF sequence was found in primitive plants, animals, fungi, and a slime mold from the Genbank non-redundant database was identified belonging to group 3 (Genbank: AJ841703). The group 13 uORF homolog found in a X. tropicalis EST was also found in a genomic contig sequence [Xenopus genome rather than being an EST library contaminant.To determine whether any of the 19 uORF homology groups conserved between rice and Arabidopsis might also be present in other eukaryotes, we searched for uORF sequences in all Genbank eukaryotic ESTs. Amino acid sequences similar to four homology groups were detected in non-angiosperms. Group 15 was found only as distantly as a fern mORF sequences while the mORFs downstream of the group 8 uORF homologs in nematodes and arthropods code for an unknown protein and a putative mannosyl transferase, respectively Figure . AvailabHaemonchus (nematode), to 74 amino acids in humans, and length is even more highly conserved within each of the land plant, arthropod, nematode, fungal, and vertebrate lineages . Four cysteine residues consistently align in all eukaryotes, with nine amino acids separating the first and second cysteine residues, as well as the third and fourth cysteine residues, whereas 11\u201315 residues separate the second and third cysteines. Two intron positions are perfectly conserved among the land plants, vertebrates, and at least one member of the fungal lineage. The first intron lies between the third and fourth amino acids following the first conserved cysteine position, and the second intron lies between the fourth and fifth amino acids following the fourth conserved cysteine position , is also similar to the group 8 uORF, as determined by BLAST similarity searches.The four cysteines are part of a putative coiled coil-helix, coiled coil-helix (CHCH) domain (Pfam accession number PF06747), also found in three small yeast proteins, Cox17p, Cox19p, and Mrp10p. Cox17p and Cox19p are required for assembly of functional cytochrome oxidase and Mrp10p is homologous to a nuclear-encoded mitochondrial ribosomal protein. A hypothetical human gene, CHCH domain 7 , Debaryomyces group 8-like (Genbank: NC_006045), and Dictyostelium Cox19p-like (Genbank: XM_631387) sequences were more divergent than other sequences, causing long branch attraction [Fungal, animal, and plant representatives of each CHCH-containing ORF were identified using a BLAST search, and their evolutionary relationships were inferred using a Bayesian phylogenetic analysis Figure . Animal Branchiostoma sequences with weak branch support (0.53). Dictyostelium, sea urchin (Strongylocentrotus), and one further Branchiostoma sequence do not group with any of these with weak support (0.53). Sea squirt, Branchiostoma, and sea urchin sequences should be more similar to other deuterastomes (includes the vertebrate lineage) than other organisms, but the short group 8-like sequence alignment could prevent resolution of correct evolutionary relationships of some groups with strong branch support (0.85\u20131.00) in all but the fungal lineage suggest that there has been a duplication event within this lineage, there is no evidence for maintenance of ancient group 8-like gene duplications occurring within the plant, vertebrate, nematode, arthropod, or fungal lineages. In Arabidopsis both the recent and ancient duplicates from two WGD events have been lost from the genome. Only the Mesostigma genome contains two group 8-like transcripts. Their short branch lengths indicate that this duplication occurred relatively recently and it is possible that insufficient time has passed for loss of the second copy.Although two Comparative analysis by uORF-Finder of 5' UTRs in full-length cDNAs from two distantly related plant species, rice and Arabidopsis, identified conserved peptide uORFs in 58 Arabidopsis loci that comprised 26 uORF homology groups and in 36 rice loci that comprised 19 homology groups, increasing the number of known conserved uORF homology groups from two to 26 and providing useful, new information for investigations of regulatory biology. Because full-length cDNAs derived from both Arabidopsis and rice only represent a fraction of all nuclear genes, not all conserved uORFs are expected to be detected by this approach. Extrapolation to the whole Arabidopsis genome suggests that it possesses approximately 61 to 102 genes with conserved peptide uORFs that are also conserved in the rice genome . An additional 24 conserved peptide uORF genes are predicted among Arabidopsis loci with retained duplicates from the most recent WGD event. In all, there are likely to be approximately 99\u2013140 genes, or 0.38\u20130.53% of all protein-coding genes, with conserved peptide uORFs in the Arabidopsis genome. Because short conserved uORFs (<20 amino acids) would not have been detected by uORF-Finder, this is a conservative estimate.To find additional conserved uORFs, more extensive collections of full-length cDNA sequences will need to be developed and/or 5' UTRs predicted from genomic sequence will be required. As full-length cDNA sequence resources become available for other plant species, such as maize and poplBased on the study of a few hundred genes, it has been suggested that uORFs are usually associated with mORFs that encode proteins that regulate cell growth ,46, but Certain eukaryotic conserved peptide uORFs are known to control translation of a downstream mORF in response to a metabolic product such as arginine or polyamines ,14,47. IN-methyltransferase (PEAMT/NMT), the key enzyme in phosphocholine (PCho) biosynthesis. Recently, NMT1 has been shown to contain a uORF that differentially affects translation of the mORF in response to exogenously added choline [PEAMT/NMT transcripts. The fact that the group 13 uORF peptide was also found in Xenopus suggests that its regulatory role is widespread in eukaryotes.Our analysis identified not only these previously known examples of genes involved in pathways exhibiting small molecule feedback in a uORF sequence-dependent manner, but several additional genes that might also act via this mechanism. One is the conserved group 13 uORFs, which are present in genes that encode phosphoethanolamine choline . This ef choline . The preAnother example is homology group 11, whose mORFs are predicted to encode trehalose-6-phosphate phosphatase (TPPase); trehalose-6-phosphate is postulated to regulate sugar metabolism in plants . In summAs mentioned, six conserved uORF families specify transcription factors, one of which is regulated by the small signaling molecule sucrose. In plants, transcription factors often act quantitatively to control target gene expression proportionate to transcription factor concentration . TherefoIf conserved uORF peptides can regulate mORF levels in response to small molecules, they are clearly analogous to RNA sensors and riboswitches that sense small molecules and regulate transcript translation accordingly ,54. It iIt is perhaps interesting to note also that the uORFs of 9 homology groups are rich in serine, threonine, and/or tyrosine. These amino acids are potential targets for phosphorylation that conceivably could promote or inhibit ribosome stalling or initiation at downstream mORFs. As mentioned above, lysine/arginine-rich motifs could function in RNA binding .UPF1 ortholog, which is required for NMD.Because uORFs create a premature termination codon (PTC), the nonsense-mediated decay (NMD) system might target uORF transcripts for degradation. Yoine et al carried upf1 mutant as in wild type Arabidopsis, we found representatives of seven uORF homology groups , suggesting that these uORF transcripts are susceptible to nonsense-mediated decay. The uORFs in these groups might work in a manner analogous to the uORF arginine attenuator protein (AAP) in the fungal CPA1 transcript. The CPA1 transcript exclusively exhibits increased levels of degradation via NMD when the AAP inhibits translation termination in response to high levels of arginine, ultimately decreasing translation using a two-pronged approach [Among 75 genes that Yoine et al identified that accumulate transcripts at more than twice the level in the approach . SimilarVery little is known about how uORFs arise. In the extant rice and Arabidopsis genomes, sequences homologous to uORFs identified by uORF-Finder were observed only in 5' UTRs and never as part of another mORF, within 3' UTRs, within introns, or in non-transcribed regions. Possible origins of 5' UTR ORFs include (a) fragmentation of mORF sequences, (b) creation of an AUG or alternate start codon by random mutation within the 5' UTR and subsequent selection for the peptide sequence, and (c) relocation of other ORF sequences within the genome to the 5' UTR or upstream region of a given gene and subsequent transcriptional fusion of the two ORFs.de novo creation, will require further analysis of closely related organisms.Transcriptional fusions occur in an estimated 2% of adjacently transcribed mRNAs in the human genome . The evoin trans when the cis uORF is intact [trans acting factor in the cell.uORFs can regulate specific mORF protein expression s intact ,60 but is intact ,62. Potetrans factor.Group 13 uORFs contain peptides similar to RS motifs found in SR proteins. SR proteins are a family of proteins required for alternative and constitutive pre-mRNA splicing ,64. A suSimilarly, some uORFs in mammalian genomes might adopt these dual roles and further characterization of conserved mammalian uORFs could reKa/Ks analyses suggest that conserved peptide uORFs are under mild to strong negative selection and might therefore be useful for resolving orthology and paralogy of specific gene pairs. For example, phylogenetic studies have sometimes failed to identify all members within a uORF homology group when only considering the mORF sequence (e.g. homology group 2). Although the bHLH transcription factor domain occurs in the mORF of all three group 2 members, none were identified in the original studies, and only two of the three members have been included in the latest description of Arabidopsis bHLH family members [ members -69.Further characterization of conserved peptide uORFs and their functional mechanisms might also provide useful tools for creating inducible or repressible expression vectors in plants. AdoMetDC1, bZIP11, and PEAMT/NMT1 protein levels are regulated by conserved uORFs in a metabolite-dependent manner and other conserved uORFs might also regulate mORF translation in response to cellular compounds, such as TPPases. If this is the case, further functional characterization of conserved peptide uORFs could provide the tools necessary to build constructs that are quickly inducible or repressible at the translational level under various conditions.Arabidopsis thaliana ecotype Columbia and NIAS, FAIS and RIKEN Oryza sativa spp. japonica cv Nipponbare full-length cDNA collections were used for all analysis [Corrected RIKEN and Genoscope analysis . A cDNA'analysis . Arabidoanalysis ,73 to fianalysis . The recMedicago truncatula and Lotus corniculatus genomic sequences.All pairs with scores >50 were kept and examined manually against existing Arabidopsis transcript annotations (TAIR and TIGR) and existing ESTs to determine whether aligned peptides fall within a probable 5' UTR. To validate the putative uORFs, the first 100 amino acids of the Arabidopsis mORF were aligned to Genbank plant ESTs using tBLASTn , and all retrieved plant uORF sequences were aligned to rice and Arabidopsis uORFs using ClustalW , manuallTo test whether uORFs appear upstream of non-homologous genes, Arabidopsis uORF sequences were aligned to the entire Arabidopsis genome (version 5) using tBNMT3 (AGI locus identifier At1g73600). The annotated mORF for NMT3 [NMT3 by comparison with its paralog, NMT1 (At3g18000) [NMT3 possesses sequences similar to the NMT1 uORF, as well as sequences similar to the NMT1 mORF, but the TAIR annotation fuses these into a single ORF. However, NMT3 possesses potential splice sites that would produce transcripts with uORF and mORF sequences similar to those in NMT1. The NMT3 uORF predicted by one alternative splice model is the same length as, and is 72% identical to, the NMT1 uORF amino acid sequence . NMT3 poThe TAIR website was used to assign locus numbers for each Arabidopsis transcript and the TIGR website for rice locus numbers. The Arabidopsis locus numbers were then used to search for retained duplicates from the recent and ancient whole genome duplications as defined on the Arabidopsis Paralogon website .Ka/Ks values for homologous rice and Arabidopsis mORFs and uORFs were determined using pairwise_kaks.PLS (version 1.7) [Ka/Ks values resulting from a Ka or Ks value >10 was excluded from the analysis, as these values result in inaccurate predictions of Ka/Ks [Ka/Ks values for homology groups 20\u201326 were determined with the same approach using Arabidopsis sequences only.For homology groups 1\u201319, ion 1.7) . Both thof Ka/Ks ,81. The P-value [GO molecular function terms were retP-value .Conserved uORFs were found in Arabidopsis duplicates in much the same way as conserved uORFs were found between rice and Arabidopsis. uORFs and mORFs were defined in the same way, and mORF sequences were aligned to the entire Arabidopsis full-length cDNA collection using BLASTp to detect transcripts deriving from a duplicated locus. mORFs aligning with \u2265 99% identity were discarded, and uORFs of all remaining pairs were aligned using needle and validated as above.Sequences similar to Cox17p, Cox19p, Mrp10, CHCHD7, and uORF homology group 8 were aligned using Muscle , trimmedSequences similar to uORF homology group 8 were aligned, edited, and analyzed in the same manner with one exception, ngen = 3000000.There is an average of 2.23 full-length cDNAs per uORF locus identified , which suggests that 15200 Arabidopsis genes are represented in the cDNA collections (34000 cDNAs/2.23 cDNAs per locus), representing approximately 60% of all Arabidopsis genes (assuming 26000 genes) . In addiA total of 60% of Arabidopsis genes are represented in the full-length cDNA collections used for this study. Therefore, the probability of selecting two loci that have conserved peptide uORFs from the pool of known sequences is 0.6*0.6 = 0.36. This translates to a total of 38 loci that have conserved uORFs using an Arabidopsis-Arabidopsis comparison (14 identified (36%), and 24 unidentified).We therefore predict that there are between 99 and 140 loci in the Arabidopsis genome that contain conserved peptide uORFs, 41\u201358% of which have been identified.Acyrthosiphon pisum; Adica, Adiantum capillus-veneris; Ajeca, Ajellomyces capsulatus; Allce, Allium cepa; Anoga, Anopheles gambiae; Apime, Apis mellifera; Arath, Arabidopsis thaliana; Ascsu, Ascaris suum; Aspof, Asparagus officinalis; Betvu, Beta vulgaris; Bosta, Bos taurus; Brafl, Branchiostoma floridae; Brana, Brassica napus; Brugy, Bruguiera gymnorhiza; Caeel, Caenorhabditis elegans; Cicli, Cicindela litorea; Ciosa, Ciona savignyi; Citja, Citrus jambhiri; Citpa, Citrus paradisi; Citsi, Citrus sinensis; Chlre, Chlamydomonas reinhardtii; Cocpo, Coccidioides posadasii; Cryne, Cryptococcus neoformans; Cycru, Cycas rumphii; Danre, Danio rerio; Debha, Debaryomyces hansenii; Dicdi, Dictyostelium discoidium; Drome, Drosophila melanogaster; Drops, Drosophila pseudoobscura; Erate, Eragrostis tef; Escca, Eschscholzia californica; Eupes, Euphorbia esula; Eupti, Euphorbia tirucalli; Galga, Gallus gallus; Gibze, Gibberella zeae; Glomo, Glossina morsitans; Glyma, Glycine max; Glyso, Glycine soja; Gosar, Gossypium arboreum; Goshi, Gossypium hirsutum; Gosra, Gossypium raimondii; Haeco, Haemonchus contortus; Helan, Helianthus annuus; Hetgl, Heterodera glycines; Hevbr, Hevea brasiliensis; Homsa, Homo sapiens Horvu, Hordeum vulgare; Iponi, Ipomoea nil; Jugre, Juglans regia; Lacsa, Lactuca sativa; Lacse, Lactuca serriola; Linus, Linum usitatissimum; Locmi, Locusta migratoria; Lyces, Lycopersicon esculentum; Maldo, Malus domestica; Medtr, Medicago truncatula; Mescr, Mesembryanthemum crystallinum; Mesvi, Mesostigma viride; Molte, Molgula tectiformis; Musmu, Mus musculus; Neucr, Neurospora crassa; Nicbe, Nicotiana benthamiana; Oncmy, Oncorhynchus mykiss; Oryla, Oryzias latipes; Orysa, Oryza sativa; Parbr, Paracoccidioides brasiliensis; Pethy, Petunia hybrida; Phaac, Phaseolus acutifolius; Phaco, Phaseolus coccineus; Phypa, Physcomitrella patens; Pontr, Poncirus trifoliata; Popde, Populus deltoides; Popca, Populus canadensis; Popeu, Populus euphratica; Poptd, Populus trichocarpa \u00d7 Populus deltoides; Poptt, Populus tremula \u00d7 Populus tremuloides; Prupe, Prunus persica; Sacce, Saccharomyces cerevisiae; Sachc, Saccharum hybrid cultivar; Sacof, Saccharum officinarum; Schma, Schistosoma mansoni; Schpo, Schizosaccharomyces pombe; Selmo, Selaginella moellendorffii; Soltu, Solanum tuberosum; Sorbi, Sorghum bicolor; Strpu, Strongylocentrotus purpuratus; Strra, Strongyloides ratti; Styhu, Stylosanthes humilis; Tetni, Tetraodon nigroviridis; Theha, Thelungiella halophila; Torru, Tortula ruralis; Triae, Triticum aestivum; Trisp, Trichinella spiralis; Ulvli, Ulva linza; Ustma, Ustilago maydis; Vitsh, Vitis shuttleworthii; Vitvi, Vitis vinifera; Welma, Welwitschia mirabilis; Xenla, Xenopus laevis; Xentr, Xenopus tropicalis; Yarli, Yarrowia lipolytica; Zeama, Zea mays.Acypi, Group 1: Arath1 (CNS0ABWH); Arath2 (CNS09Y87); Arath3 (CNS0A364); Arath4 (CNS0A728); Arath5 (RAFL11-10-D10); Orysa1 (AK070887); Orysa2 (AK065180); Orysa3 (AK064903); Orysa4 (AK109929); Orysa5 (LOC_Os12g37410).Group2: Arath1 (At2g31280); Arath2 (At1g06150); Arath3 (RAFL04-15-e03); Lacsa (BQ869454); Lyces (AW621910); Medtr, (BF643643); Orysa (AK074015.1).Group3: Arath1 (CNS0A7A6); Arath2 (RAFL04-16-A04); Arath3 (RAFL09-22-L13); Cycru (CB092297); Orysa1 (AK072162); Orysa2 (AK100397); Orysa3 (AK070259); Selmo (DN838497); Torru (CN201012); Ulvli (AJ892634).Group4: Arath1 (RAFL09-11-P17); Arath2 (RAFL09-63-H05); Arath3 (RAFL06-76-P19); Brana (CD823274); Goshi (AI730427); Gosra (CO113165); Medtr (AW689516); Orysa (AK060830); Poptt (BU896557); Prupe (BU045695).Group 5: Arath1 (RAFL05-05-C03); Arath2 (CNS0A9PN); Gosra (CO130855); Hevbr (CB376393); Lacse (BU011020); Orysa (AK103103); Phaac (BU791117); Triae (BJ233459).Group 6: Arath1 (RAFL05-17-I08); Arath2 (CNS0A6ZP); Aspof (CV291431); Glyma (BM143067); Gosar (BG442153); Orysa (AK064902); Pontr (CD576165); Triae (CK161649); Vitvi (CB980452).Group 7: Arath (RAFL09-25-N17); Brana (CD836460); Mescr (BM301482); Nicbe (CK290710); Orysa1 (AK067685); Orysa2 (LOC_Os06g48350); Triae (CV066319).Group 8: Arath (RAFL07-08-P17); Chlre (BE121764); Mesvi1 (DN255332); Mesvi2 (DN261354); Orysa (AK072620); Phypa (BJ174896); Popca (CX178804); Popeu (AJ776458); Sachc (CF573523); Triae (CA499582).Group 9: Allce (CF443194); (Arath1 (RAFL07-09-G06); Arath2 (RAFL09-23-F23); Arath3 (At1g64140); Gosra (CO081490); Orysa1 (AK101398); Orysa2 (AK105763); Orysa3 (AK068099); Orysa4 (AK099577).Group 10: Arath1 (RAFL07-11-O11); Arath2 (RAFL09-17-I10); Brana (CN732239); Orysa1 (AK069526); Orysa2 (AK100056); Poptt (BI131713); Sorbi (CN139168); Theha (BE758596).Group 11: Arath1 (RAFL07-14-D12); Arath2 (CNS0A404); Glyma (CA783255); Jugre (CV197923); Medtr (AW691064); Orysa1 (AK103391); Orysa2 (AK069361); Soltu (BQ113418).Group 12: Arath1 (RAFL07-18-F03); Arath2 (CNS0AB39); Brana (CD812479); Citse (CN185367); Jugre (CV196770); Orysa (AK060405); Popde (CK319714); Triae (BQ752938); Zeama (CD433782).Group 13: Arath1 (RAFL08-10-M03); Arath2 (At1g48600.2); Arath3 (At1g73600); Cycru (CB093136); Gosra (CO080661); Iponi (BJ562806); Linus (CA483285); Medtr (AW587372); Orysa1 (LOC_Os05g47540); Orysa2 (AK102037); Phypa (BJ204269); Xenla (CA792398); Xentr (CX412233); Zeama (AY103779).Group14: Allce (CF450799); Arath (RAFL09-10-M04); Medtr (AW267817); Nicbe (CK295530); Orysa (AK101569); Soltu (CK258175); Zeama (CO519993). Group 15: Adica (BP914226); Arath1 (CNS0ADY7); Arath2 (RAFL08-17-G21); Arath3 (RAFL04-17-N21); Arath4 (RAFL16-69-M04); Citpa (DN959636); Gosra (CO125506); Maldo (CV082382); Medtr (CX528608); Orysa1 (AK102703); Orysa2 (AK101749); Orysa3 (AK071582); Orysa4 (AK065674); Sacof (CA154823); Vitvi (CB001711); Welma (DT579937).Group 15: Adica (BP914226); Arath1 (CNS0ADY7); Arath2 (RAFL08-17-G21); Arath3 (RAFL04-17-N21); Arath4 (RAFL16-69-M04); Citpa (DN959636); Gosra (CO125506); Maldo (CV082382); Medtr (CX528608); Orysa1 (AK102703); Orysa2 (AK101749); Orysa3 (AK071582); Orysa4 (AK065674); Sacof (CA154823); Vitvi (CB001711); Welma (DT579937).Group 16: Arath (CNS0A4RC); Medtr (AW693231); Orysa1 (AK071885); Orysa2 (AK067447).Group 17: Arath1 (RAFL09-25-E19); Arath2 (At5g03190); Arath3 (RAFL19-67-G09); Arath4 (At5g01710); Gosra (CO108440); Lyces (AW738430); Medtr1 (BQ149694); Medtr2 (AC144517); Orysa1 (AK69088); Orysa2 (AK070250); Sacof (CA191644).Group 18: Arath (RAFL08-18-B11); Gosra (CO115325); Nicbe (CK286574); Orysa (AK061433).Group 19: Arath (CNS09ZXM); Eupes (DV113097); Helan (AJ541596); Medtr (BI309364); Orysa (AK068270); Triae (CD927685); Vitvi (CB918939); Zeama (DV166198).Group 20: Arath1 (RAFL04-17-G13); Arath2 (CNS0A8YX); Brana (CD835762); Brugy (BP941533); Gosar (BF274209); Maldo (CN940921); Medtr (BE316669); Styhu (L36823).Group 21: Allce (CF450138); Arath1 (RAFL07-08-G04); Arath2 (RAFL21-49-G19); Betvu (BQ594525); Brana (CD835573); Erate (DN481483); Escca (CD481239); Eupti (BP958766); Gosra (CO074819); Glyma (BU761432); Horvu (AV834976); Lacse (BQ998418); Maldo (CV881926); Medtr (CA991201); Orysa (AK100575); Popca (CX182168).Group 22: Arath1 (RAFL07-11-D20); Arath2 (RAFL11-03-J07); Brana (CD836422); Horvu (CA023398); Orysa (CK041713); Sacof (CA242575); Triae (BJ247925); Zeama (CO458204).Group 23: Arath1 (RAFL07-11-L03); Arath2 (RAFL09-07-L11); Citsi (CV720092); Glyma (BI892512).Group 24: Arath1 (RAFL07-14-J09); Arath2 (CNS0A44P); Brana (CD828343); Glyma (BI471587); Horvu (BQ471053); Orysa (AK119634); Sacof (CA118382); Sorbi (CB928687); Triae (CA483985); Zeama (CO520078).Group 25: Arath1 (RAFL09-94-P19); Arath2 (CNS0A6N0); Brana (CD835519); Citsi (CN191447); Escca (CD481312); Glyma (BE805986); Phaco (CA913939); Soltu (DN940765); Vitsh (CV098492).Group 26: Arath1 (CNS0A7NI); Arath2 (CNS0A1F5); Citja (CO912573); Pethy (CV298852); Poptd (CN521002); Prupe (BU045483).Arath (RAFL07-08-P17); Caeel (U10402); Ciosa (BW577210); Danre (CO350578); Dicdi (AU072562); Drome (AI297387); Homsa (BU541024); Mesvi (DN255332); Neucr (BX284746); Orysa, (AK072620); Phypa (BJ174896); Strpu (CX079489); Ustma (CF644197).Arath1 (RAFL08-10-M03); Arath2 (At1g48600.2); Arath3 (At1g73600); Cycru (CB093136); Gosra (CO080661); Iponi (BJ562806); Linus (CA483285); Medtr (AW587372); Orysa1 (LOC_Os05g47540); Orysa2 (AK102037); Phypa (BJ204269); Xenla (CA792398); Xentr (CX412233); Zeama (AY103779).Acypi (CV847404); Ajeca (CV605785); Anoga1 (BX617953), Anoga2 (XM_552406); Apime (NW_622706); Arath1 (BP562704), Arath2 (AY065264), Arath3 (RAFL07-08-P17), Arath4 (NM_179521), Arath5 (NM_112400); Ascsu (BM964977); Bosta (CO877216); Brafl1 (BW786058), Brafl2 (BW840607); Caeel (U10402); Chlre1 (BE121764), Chlre2 (AF280543); Cicli (CV156944); Ciosa (BW577210); Cocpo (CO006101); Cryne (XM_572394); Danre (CO350578); Debha (NC_006045); Dicdi1 (AU072562), Dicdi2 (XM_631387); Drome1 (AI297387), Drome2 (AY102691); Drops (DR121964), Erate (DN481021); Galga1 (BX935835), Galga2 (CR407540); Gibze (BI750032); Glomo (BX557417); Glyso (BG045953); Haeco (CA956938); Hetgl (CB299856); Homsa1 (DR155443), Homsa2 (CR607136), Homsa3 (BU541024), Homsa4 (AY957566), Homsa5 (NM_005694); Hordvu (BF628344); Locmi1 (CO854527), Locmi2 (CO825844); Mesvi1 (DN255332), Mesvi2 (DN261354); Molte (CJ368011); Musmu1 (BC030366), Musmu2 (AK010111); Neucr (BX284746); Oncmy (BX081024); Oryla (BJ737531); Orysa1 (XM_482456), Orysa2 (AK072620), Orysa3 (AK120143), Orysa4 (XM_468245); Parbr (CA581923); Phypa1 (BJ966696), Phypa2 (BJ174896); Popca (CX178804); Popeu (AJ776458); Sacce1 (NC_001136), Sacce2 (AY692601), Sacce3 (NC_001144), Sacce4 (NC_001144); Sachc (CF573523); Schma (CD081475); Schpo1 (NM_001019463), Schpo2 (NM_001022867), Schpo3 (NM_001022571); Sorbi (CD423660); Strpu (CX079489); Strra (BI323578); Tetni1 (CR709012), Tetni2 (CNS0G27U); Triae (CA499582); Trisp (BQ693345); Ustma1 (CF644197), Ustma2 (XM_754796); Xenla1 (BI477811), Xenla2 (BC084847); Xentr1 (BC075310), Xentr2 (CN119217); Yarli (XM_500713).Acypi (CV847404); Ajeca (CV605785); Anoga (BX617953); Apime (NW_622706); Arath (RAFL07-08-P17); Ascsu (BM964977); Bosta (CO877216); Brafl1 (BW840607), Brafl2 (BW786058); Caeel (U10402); Chlre (BE121764); Cicli (CV156944); Ciosa (BW577210); Danre (CO350578); Debha (NC_006045); Dicdi (AU072562); Drome (AI297387); Drops (DR121964); Galga (CR407540); Gibze (BI750032); Glomo (BX557417); Haeco (CA956938); Hetgl (CB299856); Homsa (BU541024); Locmi (CO825844); Mesvi1 (DN255332), Mesvi2 (DN261354); Molte (CJ368011); Musmu (AK010111); Neucr (BX284746); Oncmy (BX081024); Oryla (BJ737531); Orysa (AK072620); Phypa (BJ174896); Popca (CX178804); Popeu (AJ776458); Sachc (CF573523); Schma (CD081475); Sorbi (CD423660); Strpu (CX079489); Strra (BI323578); Tetni (CR709012); Triae (CA499582); Trisp1 (BQ693345), Trisp2 (BQ692350); Ustma (CF644197); Xenla (BI477811); Xentr (CN119217).Both CAH and RAJ designed and implemented the analyses for the present study. CAH drafted the manuscript and RAJ provided critical comments. Both authors have read and approved the final manuscript.Alignment used to generate Figure 12Click here for fileAlignment used to generate Figure 13Click here for file"} +{"text": "Twenty-seven patients with disseminated malignant melanoma were treated monthly with cisplatin (CDDP) 120 mg m-2 on day 1, vindesine (VDS) 3 mg m-2 on day 2 and dacarbazine (DTIC) 250 mg m-2 on days 2-6. None of them had received prior chemotherapy. All patients are evaluable for response and toxicity. There were five (19%) complete (CR) and seven (26%) partial (PR) responses for a total response rate of 45%. We conclude that the combination of DTIC, VDS and CDDP is capable of producing a relatively high rate of response in patients with advanced metastatic malignant melanoma, but responses are short."} +{"text": "The anti-tumour antibody-dependent cell-mediated cytotoxicity (ADCC) capacity of the conventional antibody m17-1A was compared with its chimerised analogue c17-1A and a newer chimeric antibody, cSF25, specific for colonic adenocarcinoma. The results show that mononuclear cells from patients with adenocarcinoma mediate ADCC as efficiently as those from controls for m17-1A (143 +/- 14 vs 153 +/- 14), c17-1A (174 +/- 16 vs 189 +/- 14) cSF25 (215 +/- 18 vs 237 +/- 13) and effectors and targets alone (57 +/- 9 vs 51 +/- 8). Both chimeric antibodies mediated ADCC more effectively than m17-1A with cSF25 consistently producing the highest lysis. Furthermore, more efficient ADCC was found to correspond with monocyte activation examined flow cytometrically. The results (mean channel fluorescence) show that HLA-DR expression is increased with c17-1A (1436 +/- 200) and cSF25 (2252 +/- 298) above that observed when effectors and targets were incubated alone (1157 +/- 168) or with m17-1A (1286 +/- 170). Similarly, interleukin 2 receptor (IL-2R) expression (percentage of positive cells) was augmented in the presence of m17-1A (15 +/- 3), c17-1A (14 +/- 3) and cSF25 (25 +/- 3) when compared with no antibody (9 +/- 2). We discuss the possibility that the superior ADCC activity of chimeric antibodies, especially cSF25, may be due to increased monocyte activation."} +{"text": "In this report two hundred and twenty six patients with hydatid disease were admitted to the SurgicalDepartment of Erciyes University (Kayseri) and \u015ei\u015fli Etfal Hospital (Istanbul) between 1978 and 1990and reviewed retrospectively. One hundred and two patients (45.1%) were male and 124 (54.9%)female. In the patients with hydatid cysts the most frequent symptom was right upper abdominal pain(66%). The most frequent signs were hepatomegaly (43.8%) and palpable mass (39%). One hundredand sixty seven patients (73.9%) were examined with ultrasonography which has a diagnostic value of94%. Preoperative complications were infection of cyst (7%), intrabiliary rupture (3.5%) and anaphylacticshock (0.4%). All patients were operated on by using various surgical techniques; omentoplasty(101), external drainage of residual cavity (64), marsupialization (25), capitonnage (15), introflexion(10), pericystectomy (6), and hepatic resection (5).\t\tThe main postoperative complications were wound infection (12%) and biliary fistula (2.6%). Thetotal mortality rate was 1.8% in this series."} +{"text": "GSTM1 (adjusted odds ratio (AOR) 1.14), GSTT1 (AOR: 1.19) and CYP1A1 (AOR: 1.08) polymorphisms and pancreatic cancer susceptibility. Smoking and drinking status did not affect results. These polymorphisms do not appear to be important gene modifiers in pancreatic cancer. \u00a9 2000 Cancer Research CampaignA prospective study of 149 unselected incident cases of pancreatic adenocarcinoma and 146 ethnically-matched controls found no associations between"} +{"text": "In the present study the putative chemopreventive effect of dietary fish oil (MaxEPA) on azaserine-induced pancreatic carcinogenesis in rats was investigated. Groups of rats were maintained on a semipurified low-fat diet or on semipurified high-fat diets containing 5 wt% linoleic acid (LA) and including 0.0, 1.2, 2.4, 4.7, 7.1 or 9.4 wt% MaxEPA. Animals fed a HF diet developed significantly higher mean numbers of atypical acinar cell nodules (AACNs), adenomas and carcinomas than animals fed a LF diet. Dietary MaxEPA caused a significant (P < 0.01) dose-related increase in mean number of AACNs (0.5 < phi < 3.0 mm). The mean number of adenomas and carcinomas remained similar among the groups. Cell proliferation was significantly lower in AACNs from animals fed HF containing 9.4% MaxEPA in comparison with HF without MaxEPA and with LF. LA levels had increased and arachidonic acid (AA) levels had decreased in blood plasma and pancreas with increasing dietary MaxEPA. Feeding MaxEPA resulted in significant decreases in 6-keto-prostaglandin (PG) F1 alpha (P < 0.05) and PGF2 alpha (P < 0.01) in non-tumorous pancreas, whereas PGE2, PGF2 alpha and thromboxane B2 (TXB2) levels were significantly (P < 0.001) higher in pancreatic tumour tissue than in non-tumorous pancreatic tissue. It is concluded that (i) dietary MaxEPA enhances dose-relatively growth of putative preneoplastic AACNs in the pancreas of azaserine-treated rats; (ii) dietary MaxEPA inhibits the conversion of LA to AA, as well as the conversion of AA to TXB2 or PGF2 alpha in non-tumorous pancreatic tissue; (iii) the high levels of PGE2, PGF2 alpha and TXB2 in pancreatic adenocarcinomas indicate a possible role for these eicosanoids in modulation of tumour growth."} +{"text": "Between June 1, 1976 and June 30, 1989 The Regional Trauma Unit at Sunnybrook Medical Centre inToronto, Ontario, Canada received 3730 patients. Of these 335 (9%) sustained a liver injury, 95% beingdue to blunt trauma. Open peritoneal lavage was performed on 80% of liver trauma patients (267/335),99% being true positive.\t\tA laparotomy was performed on 97% of patients (324/335). Major surgical treatment was required in132 patients (41%) and minor treatment in 192 patients (59%). The remaining 11 patients were treatedconservatively (n = 3) or died during resuscitation (n = 8).\t\tMorbidity directly related to the liver injury was seen in 29 of 249 surviving patients (11%) althoughoverall morbidity was 27% (67/249). Reoperation was required in 6% (14/249) with abscess orhematoma accounting for 11 of 14 operations.\t\tThe overall mortality rate was 26% (86/335). Eighty two percent of patients (n = 276) had a grade I, IIor III liver trauma according to Moore\u2019s classification with a mortality of 12% (n = 32). The remaining18% of patients (n = 59) had a grade IV or V liver trauma with a mortality of 44% (n = 26). Of the 86deaths, head injury accounted for 48 (56% of deaths); liver hemorrhage for 17 (20%), liver sepsis for(1%) and other causes for 20 deaths (23%). Thus death due to the liver injury itself (hemorrhage andsepsis) occurred in 18 out of 335 patients . Head injury accounted for the death of 48 out of335 patients .\t\tOver the past 13 years a trend has occurred at our institution whereby we are seeing less liver traumain our population of multiply injured patients from 12% (1976\u20131983) down to 7% (1985\u20131989); with agradual decline in overall mortality from 32% (1976\u20131983) to 19% (1985\u20131989), whereas the precentageof deaths due to head injuries and liver injury have increased."} +{"text": "Male DBA2 mice were given 10(6) P-388 leukaemic cells i.p. and cimetidine (CMT) at 100 mg/kg 1 day for 10 days, or as a single 100 mg/kg injection 30 min before cyclophosphamide (CTX). CMT significantly prolonged the survival of groups of mice receiving 50, 100 and 200 mg/kg of CTX 3 days after tumour inoculation. Median survival increased by 5.5 days (P less than 0.05), 10 days (P less than 0.05) and 13 days (P less than 0.05) respectively. The addition of CMT had the effect of roughly doubling the CTX dose, without increasing the lethality. CMT produced the only long-term survival seen in the study (1-2/10) CMT alone had no apparent antitumour activity. CMT significantly prolonged mean pentobarbital sleep to 28.6-60 min vs only 10 min for phenobarbital treated mice. Both CMT regimens increased the plasma concentration time products for CTX-induced metabolites (NBP) by about 1.3 fold . On average the single-dose CMT regimen produced the greatest effect on survival, on pentobarbital sleep duration and on total NBP reactive species. Probable mechanisms for the CMT-CTX interaction include competitive microsomal enzyme inhibition and/or acutely depressed hepatic blood flow. Caution should be used in combining CMT with full doses of CTX and any other highly metabolized antineoplastic agents in man."} +{"text": "Wistar rats were sensitized to rat embryonic tissue by immunization with irradiated (5000 rad) rat embryo cells (2 X 10(6) s.c. + 1 X 10(6) i.p.) derived from embryos aged 14-15 days, or by implantation of irradiated (5000 rad) tissue grafts from these embryos. Three to five immunizations were given at weekly intervals, and the rats were then challenged subcutaneously 7-10 days after the final inoculum with minimal tumour-producing tumour cell doses. Immunization with irradiated rat embryo cells failed to influence the growth and development of tumour cells prepared from hepatoma D23 and D30, sarcoma Mc57, mammary carcinoma AAF57 or cells prepared from spontaneously arising mammary carcinomata Sp4 and Sp15. Using adoptive transfer techniques, lymphoid cells from embryo-sensitized rats, when used in a 3000 : 1 ratio (lymphoid cells : tumour cells), were shown effectively to retard the growth of hepatoma D23 in 3 out of 7 experiments performed. Similar adoptive transfer procedures proved ineffective in preventing the growth of mammary carcinoma AAF57. Using in vitro cytotoxicity tests, lymph node cells and spleen cells from embryo-immunized rats were shown to be cytotoxic for several rat tumour cell targets : hepatoma D23 (7/10 tests), sarcoma Mc7 (8/12 tests), mammary carcinoma AAF57 (2/2 tests) and Sp4 (3/4 tests), and for 14-15-day-old rat embryo cells (5/10 tests). In comparative tests lymphoid cells were relatively non-cytotoxic for 20-day-old rat embryo cells (1/6 tests) or cells prepared from adult rat lung or kidney (1/10 tests). The role of embryonic antigen(s) in tumour rejection is discussed."} +{"text": "Of 119/235 (51%) cases reviewed, primary liver cancer was confirmed in 66 (55%) with 21 (18%) definite secondary cancers. The proportions of true primaries ranging between 55% and 82% (i.e. excluding secondary cancers) give revised estimates of between 0.53 and 0.78 excess cases per 10"} +{"text": "Identification of the key genetic alterations leading to ovarian cancer is in its infancy. Polymerase chain reaction (PCR)-based analysis of loss of heterozygosity (LOH) is a powerful method for detecting regions of altered tumour-suppressor genes. Focusing on chromosome 12, we examined 23 ovarian cancer samples for LOH using 31 highly polymorphic microsatellite markers and found the chromosomal localization of two putative tumour-suppressor genes. Two commonly deleted regions were 12p12.3-13.1 in 6/23 (26%) and 12q23-ter in 7/23 (30%) samples. LOH on chromosome 12 was more common in late-stage ovarian carcinomas. The region of LOH at 12p12.3-13.1 includes the genes that code for the ETS-family transcriptional factor, known as TEL, and the cyclin-dependent kinase inhibitor, known as p27Kip1. Mutational analysis of both TEL and p27Kip1 using single-strand conformation polymorphism (SSCP) showed no abnormalities, suggesting that the altered gene in this region is neither of these genes. Taken together, our data suggest that new tumour-suppressor genes in the region of chromosomes 12p12.3-13.1 and 12q23-ter may be involved in the development of ovarian cancer."} +{"text": "The tolerability and efficacy of four courses of paclitaxel and ifosfamide plus cisplatin every 3 weeks was evaluated in patients with residual or refractory ovarian cancer. Additionally, supportive haematological effects of recombinant human interleukin 3 (rhIL-3) and recombinant human granulocyte colony-stimulating factor (G-CSF) were studied. Paclitaxel starting dose was 135 mg m(-2) (day 1), with ifosfamide dose 1.2 g m(-2) day(-1) (days 2-4) and cisplatin dose 30 mg m(-2) day(-1) (days 2-4). All 16 patients received 5.0 microg kg(-1) day(-1) G-CSF (days 7-16) and, in addition, eight patients were randomized to receive 10 microg kg(-1) day(-1) rhIL-3 (days 5-9). Paclitaxel and ifosfamide doses were reduced when grade IV haematological toxicity occurred. In the absence of grade IV haematological toxicity and normal recovery of haematopoiesis, paclitaxel dose was escalated. Toxicity was evaluable in 56 courses, with haematological effects in 52. Despite antiemetic treatment, nausea and vomiting (> or = grade I) occurred in 50 courses. Five patients had persisting peripheral neuropathy. Renal and liver function were not affected. Grade IV neutropenia occurred in 12 out of 52 courses, with neutropenic fever in two patients, both of whom died from fatal septicaemia. Grade IV thrombocytopenia without bleeding was observed in 15 courses. Grade IV haematological toxicity was associated with hepatic metastases and concurrent increases in alkaline phosphatase (P <0.001) and gamma-glutamyltransferase (P=0.007). No relation was found between haematological toxicity and pharmacokinetic parameters of paclitaxel. Patients treated with rhIL-3 showed a tendency to a faster platelet recovery (not affecting platelet nadir), and the cisplatin dose intensity was higher (P=0.025). Six of the nine evaluable patients had a tumour response. The overall median progression-free survival was 7 months and the overall mean survival was 13 months. In conclusion, this potentially interesting combination as second-line treatment showed a low tolerability with unexpected mortality, while rhIL-3 administration tended to induce a more rapid platelet recovery."} +{"text": "Patients with invasive cancer of the breast were assigned to pretreatment based on oestrogen receptor (ER) status; patients with ER-negative tumours received chemotherapy for 3 months, patients with ER-positive tumours underwent endocrine therapy [luteinising hormone releasing hormone (LHRH) agonist goserelin or 4-hydroxyandrostenedione ] for 3 months. Of the first 100 patients assessed at 3 months, 47 with ER-positive tumours had a 40.4% response and 53 with ER-negative tumours had a 60% response . Patients with early breast cancer (T1/T2) had a complete clinical resolution in 41% (16/39) of cases after MMM and in 20% (7/35) of cases following endocrine therapy compared with 14% (2/14) advanced tumours (T3/T4) following MMM and (0/12) following endocrine therapy. However, in those patients achieving a complete clinical response, subsequent appropriate surgery showed that 16 of 19 patients (84%) had evidence of residual viable tumour on histological examination."} +{"text": "After 49 hours, DEN was no more detectable in the milk.Mothers of 5-day old rats were given diethylnitrosamine (DEN) (130 mg/kg body weight) by stomach tube. The milk removed from the stomachs of the suckling young contained 5, 16 and 36 parts/10"} +{"text": "A phase II trial was performed to investigate the efficacy and tolerance of vinorelbine (VNB), 5-fluorouracil (5-FU), l-leucovorin (LLV) and recombinant human granulocyte colony-stimulating factor (G-CSF) in advanced breast cancer. Between August 1994 and October 1996, 53 patients entered this trial. Thirty-seven patients were previously untreated and 16 patients had failed previous palliative chemotherapy with (n = 12) or without anthracyclines (n = 4). Therapy consisted of VNB 40 mg m(-2) diluted in 250 ml of saline infused over 30 min on days 1 and 14 and LLV 100 mg m(-2) administered by intravenous bolus injection and 5-FU 400 mg m(-2) diluted in 500 ml of saline infused over 2 h, both given on days 1-5 every 4 weeks. G-CSF was administered at 5 microg kg(-1) day(-1) subcutaneously on days 6-10 during each cycle. Treatment was continued in cases of response or stable disease until a total of six courses were completed. The overall response rate was 59% for chemotherapeutically naive patients , including five complete responses and 17 partial responses ; ten patients (27%) had stable disease (SD) and only five (14%) progressed (PD). Second-line chemotherapy with this regimen resulted in 3/16 (19%) objective remissions, but nine patients had SD and four had PD. The median time to progression was 10.5 months (range 2-23) in previously untreated patients and 7.0 months (range 2-19) in those who had failed prior chemotherapy. After a median follow-up time of 14 months, 29 patients (55%) are still alive with metastatic disease; median survival has not been reached yet. The dose-limiting toxicity was myelosuppression: WHO grade III and IV neutropenia occurred in 15 (28%) and four patients (8%), and was complicated by septicaemia in two; grade III anaemia and thrombocytopenia were noted in four (8%) and three (6%) patients respectively. Severe (WHO grade 3) non-haematological toxicities included stomatitis in 6% and nausea/vomiting and alopecia in 2% each. Our data suggest that the combination of vinorelbine, 5-fluorouracil and l-leucovorin plus G-CSF is an effective first line regimen for treatment of advanced breast cancer. Overall toxicity was modest, with myelosuppression being the dose-limiting side-effect. Other severe adverse reactions were uncommon."} +{"text": "The activity and toxicity of single-agent standard-dose doxorubicin were compared with that of two schedules of high-dose epirubicin. A total of 334 chemonaive patients with histologically confirmed advanced soft-tissue sarcomas received (A) doxorubicin 75 mg m(-2) on day 1 (112 patients), (B) epirubicin 150 mg m(-2) on day 1 (111 patients) or (C) epirubicin 50 mg m(-2) day(-1) on days 1, 2 and 3 (111 patients); all given as bolus injection at 3-week intervals. A median of four treatment cycles was given. Median age was 52 years (19-70 years) and performance score 1 (0-2). Of 314 evaluable patients, 45 (14%) had an objective tumour response . There were no differences among the three groups. Median time to progression for groups A, B and C was 16, 14 and 12 weeks, and median survival 45, 47 and 45 weeks respectively. Neither progression-free (P = 0.93) nor overall survival (P = 0.89) differed among the three groups. After the first cycle of therapy, two patients died of infection and one owing to cardiovascular disease, all on epirubicin. Both dose schedules of epirubicin were more myelotoxic than doxorubicin. Cardiotoxicity (> or = grade 3) occurred in 1%, 0% and 2% respectively. Regardless of the schedule, high-dose epirubicin is not a preferred alternative to standard-dose doxorubicin in the treatment of patients with advanced soft-tissue sarcomas."} +{"text": "MVP chemotherapy (mitomycin C 8 mg m(-2), courses 1, 2, 4 and 6, vinblastine 6 mg m(-2), cisplatin 50 mg m(-2)) is an active low-toxicity regimen in non-small-cell lung cancer (NSCLC). Based on the single-agent activity of these agents in SCLC, we have conducted a phase II trial of MVP in SCLC. Fifty chemo-naive patients with SCLC were entered in this trial. There were 33 men and 17 women with median age 66 years (range 46-83 years); 18 patients had limited disease (LD) and 32 extensive disease (ED). WHO performance status (PS) was: three patients PS 0, 33 patients PS 1, ten patients PS 2, four patients PS 3. A maximum of six cycles was given in responding patients. On completion of chemotherapy, patients with LD obtaining complete response (CR)/good partial response (PR) received thoracic irradiation and those obtaining CR were offered entry into the ongoing MRC Prophylactic Cranial Irradiation Trial. The overall response was 79% with 17% CR and 62% PR. For LD patients, 38% obtained CR but for ED only one patient achieved CR. Median response duration for LD patients was 8 months and for ED patients 5 months. Median survival was 10 months for LD patients and 6 months for ED patients. There was complete resolution of symptoms in 24%, partial improvement in 68%, no change in 2% and progressive symptoms in 6%. As regards toxicity, 24% developed WHO grade 3/4 neutropenia, 16% grade 3/4 thrombocytopenia and 6% significant hair loss. Two patients died during the first week of treatment with neutropenic infection. Quality of life using the EORTC questionnaire (QLC-C30) with lung cancer module demonstrated significant improvements from baseline levels in emotional and cognitive functioning, global QOL, of pain, dyspnoea and cough. MVP, an effective palliative regimen for NSCLC, is also active against SCLC with low toxicity and merits comparison with more toxic conventional schedules."} +{"text": "Deletions of tumour-suppressor genes can be detected by loss of heterozygosity (LOH) studies, which were performed on 23 cases of adenocarcinoma of the oesophagus, using 120 microsatellite primers covering all non-acrocentric autosomal chromosome arms. The chromosomal arms most frequently demonstrating LOH were 3p (64% of tumours), 5q (45%), 9p (52%), 11p (61%), 13q (50%), 17p (96%), 17q (55%) and 18q (70%). LOH on 3p, 9p, 13q, 17p and 18q occurred mainly within the loci of the VHL, CDKN2, Rb, TP53 and DCC tumour-suppressor genes respectively. LOH on 5q occurred at the sites of the MSH3 mismatch repair gene and the APC tumour-suppressor gene. 11p15.5 and 17q25-qter represented areas of greatest LOH on chromosomes 11p and 17q, and are putative sites of novel tumour-suppressor genes. LOH on 9p was significantly associated with LOH on 5q, and tumours demonstrating LOH at both the CDKN2 (9p21) and MSH3 (5q11-q12) genes had a significantly higher fractional allele loss than those retaining heterozygosity at these sites. Six of nine carcinomas displaying microsatellite alterations also demonstrated LOH at CDKN2, which may be associated with widespread genomic instability. Overall, there are nine sites of LOH associated with oesophageal adenocarcinoma."} +{"text": "Subtype IIb originates from recombination with porcine transmissible gastroenteritis virus. Coronaviruses of potential recombinant origin with porcine transmissible gastroenteritis virus (TGEV), referred to as a new subtype (IIb) of canine coronavirus (CCoV), were recently identified in dogs in Europe. To assess the distribution of the TGEV-like CCoV subtype, during 2001\u20132008 we tested fecal samples from dogs with gastroenteritis. Of 1,172 samples, 493 (42.06%) were positive for CCoV. CCoV-II was found in 218 samples, and CCoV-I and CCoV-II genotypes were found in 182. Approximately 20% of the samples with CCoV-II had the TGEV-like subtype; detection rates varied according to geographic origin. The highest and lowest rates of prevalence for CCoV-II infection were found in samples from Hungary and Greece . Sequence and phylogenetic analyses showed that the CCoV-IIb strains were related to prototype TGEV-like strains in the 5\u2032 and the 3\u2032 ends of the spike protein gene. Coronaviridae) are exceptionally prone to genetic evolution through accumulation of point mutations in genes encoding for structural and nonstructural proteins and homologous recombination among members of the same antigenic group (Coronaviruses (CoVs) assay. In addition, we evaluated the genetic relationship among the identified strains by using sequence and phylogenetic analyses.During 2001\u20132008, a total of 1,172 fecal samples were collected from dogs with acute enteritis in 14 European countries: Italy (n = 760), United Kingdom (n = 199), Greece (n = 81), Hungary (n = 41), Portugal (n = 33), Spain (n = 32), Belgium (n = 7), Romania (n = 6), Bulgaria (n = 3), Germany (n = 3), Sweden (n = 3), Slovakia (n = 2), Poland (n = 1), and Slovenia (n = 1). Some samples were retrieved from previous studies ; according to the manufacturer\u2019s protocol, RNA templates were stored at \u201370\u00b0C until use.Specimens were homogenized (10% wt/vol) in Dulbecco modified Eagle medium and subsequently clarified by centrifuging at 2,500 \u00d7 10 dilutions of standard RNA and TGEV-like (subtype IIb) CCoVs, specific CCoV-IIa and CCoV-IIb gel-based RT-PCRs were developed. Primer 20179 binds a conserved region at the 3\u2032 end of ORF1b and was recruited from a previous study and European Molecular Biology Laboratory (www.ebi.ac.uk) analysis tools. Phylogenetic and molecular evolutionary analyses were conducted by using Mega 4.1, beta . The sequences were manually edited and analyzed by using BioEdit software , United Kingdom 54/199 (27.13%), Greece 45/81 (55.5%), Hungary 32/42 (78.05%), Portugal 12/33 (36.36%), Spain 2/32 (6.25%), Belgium 4/7 (57.14), Romania 4/6 (66.66%), Bulgaria 1/3 (33.33%), Germany 3/3 (100%), Sweden 3/3 (100%), Slovakia 1/2 (50%), Poland 1/1 (100%), and Slovenia 1/1 (100%) (CCoV RNA was detected in 493 (42.06%) of 1,172 fecal samples from dogs with diarrhea. Viral RNA titers ranged from 1.25 \u00d7 101 (100%) .The geographic distribution of the CCoV types and subtypes is reported in By using the developed TGEV-like RT-PCR, we found that 78 (19.50%) of 400 samples containing CCoV-II strains, alone or in combination with CCoV-I, were positive for CCoV-IIb. The remaining 322 CCoV-II strains were positive for subtype IIa, whereas mixed infections caused by both CCoV-II subtypes were not detected in any samples. Almost all CCoV\u2013IIb-positive samples were from Italy , the United Kingdom , and Hungary . Single CCoV-IIb strains were detected in samples from Greece , Romania , and Sweden , whereas no samples from the other countries had TGEV-like CCoVs.After RT-PCR with primer pair N3SN/R3AS, CCoV and FCoV reference strains yielded an amplicon >1,000 bp, with the exception of TGEV-like CCoV 341/05, which gave a 929-bp product as a consequence of a 154-nt deletion in ORF7b .We selected the following TGEV-like strains for sequence analysis of the 5\u2032 and 3\u2032 ends of the spike protein gene: 12 strains from Italy, 8 from the United Kingdom, and 5 from Hungary, plus the single strains from Greece, Romania, and Sweden. All RT-PCR products were sequenced except those obtained from the samples from Greece and Sweden, which yielded weak bands despite the considerable viral RNA titers in the original fecal samples strains, against the emerging TGEV-like (CCoV-IIb) viruses. Only vaccination trials and subsequent challenges by TGEV-like strains might assess whether the poor cross-reactivity between CCoV-IIa and CCoV-IIb observed in a previous study ("} +{"text": "Staphylococcus aureus (CA-MRSA) is a global healthcare problem. The purpose of this study was to characterize CA-MRSA clones and their distribution in Kuwait hospitals.Community-associated methicillin-resistant tst).In total, 135 CA-MRSA isolates, carrying the SCCmec IV or V genetic elements, isolated in eight hospitals were characterized using antibiogram, pulsed-field gel electrophoresis, multilocus sequence typing, and carriage of genes for Panton-Valentine Leukocidin (PVL), capsular polysaccharides types (cap) 5 and 8, accessory genes regulators (agr), Staphylococcal enterotoxins (SE) and toxic shock syndrome toxin 1 (tst while 103 isolates were positive for SE genes with sei (63.0%), seg (41.5%) and sed (29.6%) as the common SE genes.They were susceptible to vancomycin, teicoplanin and linezolid but resistant to kanamycin (62%), fusidic acid (42.2%), tetracycline (39.3%), erythromycin and clindamycin (21.5%), gentamicin (5.9%), streptomycin (6.7%), trimethoprim (5.9%), mupirocin (6.6%) and cadmium acetate (82.2%). They consisted of 10 pulsotypes with the majority belonging to PFGE type I (51.1%), type II (22.2%), type IV (13.3%) and type III (3.7%). They belonged to 10 sequence types (ST) comprising ST80 (51.1%), ST30 (22.2%), ST5 (14.1%), ST1 (4.45), ST6 (3.7%), ST88 (1.5%), ST834 (1.5%), ST8 (0.7%), ST46 (0.7%) and ST950 (0.7%). Genes for PVL, cap 8, cap 5 and agr III, agr I and agr II were detected in 61.5%, 77.3%, 20.7% and 62.2%, 17% and 8.1% of the isolates respectively. Nine (6.7%) isolates contained mecIV was the most common CA-MRSA clone in Kuwait hospitals presenting new challenges for infection control.ST80-SCC S. aureus (CA-MRSA) has now been reported in many countries and has become a global public health problem [mec) types IV and V whereas the larger SCCmec types I, II and III are present in MRSA traditionally associated with infections in healthcare facilities [Following their initial reports from patients in remote communities with no access to healthcare facilities -3, Commu problem ,5. CA-MRcilities ,5. Initicilities ,4,5. Howcilities -9.The transmission of CA-MRSA was restricted to particular populations with distinctive risk factors such as injections drug users and aboriginal communities ,4,5. Howmec typing, PFGE and multi-locus sequence typing to ascertain their clonal composition and prevalence.CA-MRSA was first isolated in small numbers in Kuwait hospitals in 2001 when it mec IV or V genetic elements and urease production. The 135 isolates originated from 131 patients located in eight hospitals. The isolates were collected from Mubarak , Amiri , Al-Sabah , Farwania , Ibn Sina , Al-Razi , Jahra and the Maternity hospital . from wound swabs (37 isolates), abscesses (18 isolates), nasal swabs (18 isolates), ear swabs (9 isolates), blood samples (5 isolates), groin (5 isolates), throat swabs (5 isolates), urine samples (4 isolates), skin swabs (3 isolates), tracheal aspirates (3 isolates), high vaginal swabs (2 isolates), sputum (2 isolates) and eye swab (1 isolate). The source for 20 isolates was not provided. The four isolates from the same patient were obtained from four different sites and were all resistant to mupirocin [mec typing and urease production. Pure cultures were preserved in 40% (v/v) glycerol in brain heart infusion broth (BHIB) at -20\u00b0C. Isolates were recovered in BHIB, incubated at 37 \u00b0C, and sub-cultured on brain heart infusion agar plates before testing.From January 2005 to December 2006, the MRSA Reference Laboratory, located at the Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, received 889 MRSA for typing. One hundred and thirty five of these isolates were classified as CA-MRSA based on their carriage of SCCS. aureus strain ATCC25923 was used as quality control strain for susceptibility testing. Methicillin resistance was confirmed by detecting PBP 2a using a rapid latex agglutination kit according to the manufacturer's instructions.Susceptibility testing to antibacterial agents was performed by the disk diffusion method using oxUrease production was detected on Christensen's urea agar slope after incubation at 35\u00b0C for 48 hours.mec (SCCmec) typing and subtyping were performed as described previously [mec type 1, ccr 2); XU642 ; WBG525 , and K1814 (SCCmec type IV) and WBG 8318(SCCmec type V) as controls.Staphylococcal cassette chromosome eviously . The caseviously . Strain Sma I- for 4 hr at 25\u00b0C. Counter-clamped homogenous electric field (CHEF) electrophoresis of digested chromosomal DNA was performed in 1.2% agarose at 6 V/cm for 21 h at 14\u00b0C, with pulse times of 5 s-40 s using a CHEF-DRIII system (BioRad). Sma I digested chromosomal DNA of S. aureus strain NCTC8325 was used as a molecular size marker. After electrophoresis, the gel was stained with ethidium bromide 0.5 \u03bcg/ml and photographed under ultraviolet illumination. The chromosomal patterns were examined visually and similarities of the PFGE patterns were assigned using criteria published previously [Genomic DNA was prepared in agarose plugs as described previously . DNA waseviously .arc, aroE, glpF, gmk, pta, tpi and yqiL) were compared to existing sequences in the MLST database http://www.mlst.net for assignment of allelic numbers. Sequence types (ST) were assigned according to their allelic profiles.Multilocus sequence typing (MLST) was performed by following previously published protocols . The seqS. aureus for PCR following a protocol described previously [sea, seb, see, sed, sei, seh and toxic shock syndrome gene, tst were amplified in multiplex PCR as described previously [DNA was extracted from eviously . PCR asseviously . The Lukeviously . The ampeviously . Genes feviously . All PCReviously .Differences in the distribution of CA-MRSA clones were assessed by Chi square test. A P-value of \u2264 0.05 was considered significant.mec type IV or type V. Urease positivity was used to differentiate CA-MRSA carrying the SCCmec IV genetic element from the healthcare-associated epidemic MRSA-15 (EMRSA-15) which also carries the SCCmec-IV genotype but does not produce urease [mec type IV, 11 (8.1%) carried SCCmec type IVa, 10 (7.4%) carried SCCmec type IVc and 12 (8.9%) the SCCmec type V genetic element. A total of 123 (91.1%) isolates consisting of the SCCmec type IV, SCCmec IVa and SCCmec IVc isolates belonged to ccr type 2 while the 12 SCCmec type V isolates belonged to ccr type 5.The 135 MRSA isolates included in this study produced urease and belonged to SCCe urease . In totaAll isolates were susceptible to vancomycin MIC: \u2264 2 \u03bcg/ml), teicoplanin MIC: \u2264 2 \u03bcg/ml), rifampicin and linezolid but were resistant to oxacillin (MIC 8- > 256 \u03bcg/ml) and the antibacterial agents summarized in Figure Figure tpi). Based on the distribution of sequence types according to their PFGE patterns, 69 (51.1%) of the 135 isolates were ST80. This was followed by ST30 (22.2%), ST5 (14.1%), ST1 (4.4%), ST6 (3.7%), ST88 (1.5%), ST834 (1.5%), ST8 (0.7%), ST46 (0.7%) and ST950 (0.7%). As shown in Table P = 0.29), while the proportion of ST30 isolates decreased from 30.8% in 2001-2003 to 23.7% (P = 0.45)MLST was performed on 28 isolates representing each of the PFGE subtypes to determine their sequence types (ST). MLST results showed extensive agreement with PFGE except for ST5 that was detected in PFGE types IV and IX. The isolate belonging to PFGE type IX was ST5 while the isolate belonging to subtype IXa was ST950 , agr I (17%), agr II (8.1%), capsular polysaccharides types 8 (77.3%) and type 5 (20.7%). Three (2.2%) isolates yielded negative result for both sea (10.4%), seb (3.7%), sec (4.4%), sed (29.6%), seg (41.5%), seh (1.5%), sei (63.0%) and tst (6.7%). None of the isolates was positive for see. Twenty-seven (26.2%), 52 (50.5%), 17 (16.5%) and seven (6.8%), of the 103 isolates were positive for single, two, three and four SE genes respectively. Twenty-three isolates contained seg and sei while 20 isolates contained sed and sei.In total, 103 (76.3%) isolates yielded positive results for Table mec-IV isolates . Of these 23 isolates, 15 expressed additional resistance to one or more of ciprofloxacin, gentamicin, erythromycin, trimethoprim, mupirocin and chloramphenicol. Furthermore, some of the isolates were susceptible to kanamycin, tetracycline and fusidic acid that usually characterize ST80-SCCmec-IV isolates. Ten isolates were resistant to cadmium acetate but were susceptible to all of the non beta-lactam agents tested. Forty one (59.4%) of the 69 isolates were multiresistant (resistance to more than three antibiotic classes).The ST80 isolates expressed low oxacillin MIC (MIC 8-64 \u03bcg/ml). They also expressed diverse resistance phenotypes. In total, 23 of the 69 isolates were resistant to kanamycin, tetracycline and fusidic acid, that are traditionally associated with ST80-SCCsei (77.6%) and seg (36.7%). Nineteen (27.9%) isolates were positive for sed and sei, and ten (14.7%) were positive for seg and sei. Two isolates were positive for tst.All ST80 isolates carried genes for capsular polysaccharide types 8 and agr III but varied in the carriage of other virulence-associated genes. As presented in Table This study characterized ten different CA-MRSA clones in Kuwait hospitals with ST80 (51.1%) and ST30 (22.2%) as the major CA-MRSA clones similar to the composition of CA-MRSA isolates circulating in Kuwait hospitals in 2001-2003 . HoweverThere was a high prevalence of resistance to cadmium acetate, kanamycin, fusidic acid, tetracycline, erythromycin, clindamycin and ciprofloxacin with 50.4% of the isolates being multiresistant to non-beta lactam antibiotics. Multiresistant-CA-MRSA isolates have also been reported among CA-MRSA clones isolated in Brazil , Japan and USA sei (63%) was the most common SE gene among our CA-MRSA isolates, seg was the most abundant SE gene in MRSA obtained in Ireland [seg and sei in our isolates which has also been reported in CAMRSA studied in USA [see. However, in contrast to the low prevalence of tst (6.7%) in this study, Rossney et al., [tst in 24% of CA-MRSA isolates in Ireland.We detected genes for PVL in 61.5% of the CA-MRSA isolates distributed among different sequence types as has also been reported in other countries ,12,30,31d in USA . Furtherd in USA , none ofmec-IV clone has been the dominant CA-MRSA clone in European countries for some time [sed, sei, seg, seb, seh and sea, singly or in combinations. In contrast, studies from the Netherlands [seh in their ST80 isolates. The detection of genes for different SEs in this study suggests that ST80 isolates may be acquiring genes for different SEs probably due to the acquisition of toxin-carrying bacteriophages [The ST80-SCCome time ,16. Withome time ,16, the iophages . In addiiophages . It is uThe dominance of the ST80 and ST30 CA-MRSA clones in Kuwait hospitals in 2001-2003 was attributed to their importation into the country by returning patients who sought medical care abroad, or expatriate staff from countries where these clones are prevalent . Their pmec-IV clone was the most common CA-MRSA clone in Kuwait hospitals in 2005-2006. However, other sequence types such as ST5 and ST6 also appeared. Most of the isolates were multi-resistant to antibacterial agents and harbored genes for different virulence factors. The successful expansion of CA-MRSA clones in Kuwait hospitals calls for novel approaches in infection control measures to control their spread.This study has shown that the ST80-SCCThe authors declare that they have no competing interests.EEU designed the study, procured funding, guided the experimental work and wrote the first draft of the paper. ES contributed to the study design, performed experimental work and contributed to writing the manuscript. Both authors read and approved the final manuscript."} +{"text": "In this report, 226 patients with hydatid disease admitted to the Surgical Department of ErciyesUniversity (Kayseri) and \u015ei\u015fli Etfal Hospital (Istanbul) in Turkey between 1978 and 1990 werereviewed retrospectively. 102 patients (45.1%) were male and 124 (54.9%) female. The mostfrequent symptom was right upper abdominal pain (66%). The most frequent signs werehepatomegaly (43.8%) and palpable mass (39%). 167 patients (73.9%) were examined withultrasonography which has a diagnostic value of 94%. Preoperative complications wereinfection of cyst (7%), intrabiliary rupture (3.5%) and anaphylactic shock (0.4%). Patients wereoperated on by various techniques; omentoplasty (101), external drainage of residual cavity (64),marsupialization (25), capitonnage (15), introflexion (10), pericystectomy (6), and hepatic resection(5). Main postoperative complications were wound infection (12%) and biliary fistula(2.6%). Total mortality rate was 1.8% in this series."} +{"text": "We investigated p21 immunoreactivity in normal breast and in 91 breast carcinomas with long-term follow-up (median = 58 months). Seven additional breast carcinomas with known p53 gene mutations were investigated. In normal breast p21 expression was seen in the nuclei of rare luminal cells of acinar structures, and in occasional myoepithelial cells. Poorly differentiated DCIS showed high p21 expression, whereas well-differentiated DCIS tumours showed few p21-reactive cells. p21 was seen in 82 (90%) infiltrating tumours; staining was heterogeneous; the percentage of reactive nuclei ranged from 1% to 35%. High p21 expression (more than 10% of reactive cells) was seen in 24 (26%) cases, and was associated with high tumour grade (P = 0.032); no associations were seen with tumour size, metastases, oestrogen receptor status, MIB1 expression and p53 expression. p21 expression in cases with p53 gene mutations was low in six cases and high in one. High p21 expression was associated with short relapse-free survival (P = 0.003)."} +{"text": "As well, intraoperative blood loss (p=O.01)number of intraoperativeblood units used (p=0.002), and postoperative length of stay (p=O.O09) have been significantly reducedby USD. IOUS was used on 64 patients. Not only has it improved the sensitivity (99%) and specificity(98%) for detection of hepatic neoplasms, it has also helped increase the precision and accuracy ofanatomical tumour localization. As a result, 11/64 patients (17.2%) had their preoperative planschanged: 8 were abandoned and 3 were revised. In summary, USD has significantly reducedintraoperative blood loss and hence reduced the number of intraoperative transfusions, incidence ofpostoperative complications and postoperative length of stay. IOUS should be routinely employed inpatients undergoing liver resection since it provides critical information that could obviate oncologicallyuseless resections.Ultrasonic dissetion (USD) and intraoperative ultrasonography (IOUS) have shown encouraging resultsin a retrospective analysis of 109 patients with benign or malignant liver disease. Of 109 patients assessedbetween 1980 and 1993, 84 were resected: 27 by finger fracture technique (FFT) and 57 by USD. Hospitalmortality was 4.8% (4/84) and 30-day mortality was 6.0% (5/84). Overall morbidity was 48.8% (41/84)and liver related morbidity was 34.5% (29/84); of the 29 patients,5 required re-operation. Liver complications occurred in 12/27 (44.4%) in the FFT group as opposed to17/57 (29.8%) in the USD group. The incidence of postoperative hepatic bleeding was significantly lessby USD than by FFT("} +{"text": "Patients with refractory metastatic renal cell carcinoma (RCC) were enrolled in a phase II study with teniposide (VM26) and cyclosporin A (CSA) to investigate (1) the effect of CSA on the response rate to VM26; and (2) the effect of CSA on the pharmacokinetics and pharmacodynamics of VM26. Sixteen patients initially received VM26 alone (200 mg m(-2) day(-1) i.v.). No objective responses were observed and all patients crossed over to receive at least an additional two courses (range 2-5) of VM26 plus CSA (5 mg kg(-1) 2h(-1) followed by 30 mg kg(-1) 48h(-1) i.v.). At the end of the 2-h loading dose of CSA, whole-blood CSA levels ranged from 2250 to 3830 ng ml(-1), whereas at the end of the 48-h CSA infusion, CSA ranged from 1830 to 4501 ng ml(-1). CSA significantly (P<0.01) increased the area under the curve (AUC) of VM26. The variation in the paired AUC of VM26 was 50%. Terminal half-life of VM26 was significantly (P<0.01) increased (1.72-fold) after CSA administration, whereas the systemic clearance of VM26 was decreased by 1.4-fold (P<0.01). The nadir neutrophil count after VM26 plus CSA (median 700 microl(-1), range <100 to 2860 microl(-1)) was lower than after VM26 alone (median 1900 microl(-1), range 200 to 6000 microl(-1)). Increased haematological toxicity after CSA could be explained by the increase in the VM26 AUC and by inhibition of P-glycoprotein (P-gp) activity in haematopoietic precursor cells. Bilirubin concentrations in the serum were increased after VM26 plus CSA compared with VM26 alone (P<0.01). Among the 15 patients evaluable for response, one had a minor response, eight had stable disease, and six had progressive disease. In conclusion, the dose of CSA we used achieved plasma concentrations within the effective range for P-gp inhibition. CSA affected both the pharmacokinetics and pharmacodynamics of VM26 in the patients, principally by increasing the plasma concentrations of the antineoplastic drug and VM26 haemopoietic toxicity."} +{"text": "Serum samples from 22 hantavirus pulmonary syndrome (HPS) patients were tested for Sin Nombre virus (SNV)-reactive antibodies. In the acute phase of HPS, 100% and 67% of the samples tested positive for SNV-specific immunoglobulin (Ig) M and IgA, respectively. Among the virus-specific IgG antibodies, the most prevalent were IgG3 (in 97% of samples), followed by IgG1 (70%), IgG2 (30%), and IgG4 (3%)."} +{"text": "A phase I study to determine the maximum tolerated dose and toxicity of gemcitabine when given as a 24 h infusion to patients with inoperable non-small-cell lung cancer (NSCLC). A total of 24 patients with unresectable stage IIIa-IV NSCLC were entered into the study. Gemcitabine was administered as a 24 h infusion on days 0, 7 and 14. Courses of therapy were repeated every 28 days. There were 16 males and 8 females with a median age of 51 years (range 40-73 years). The WHO performance score was 1 (21 patients) or 2 (3 patients). The TNM stage was IIIa (6), IIIb (10) and IV (8). Three patients were entered at each dose level with six at the maximum tolerated dose (MTD). Dose levels were 10, 20, 40, 80, 120, 180 and 210 mg m-2. The MTD was 180 mg m-2 and dose-limiting toxicity was neutropenia and lethargy. Partial response was observed in five (21%) patients (95% CI 7-42%) lasting 10, 14, 18, 47 and 51 + weeks. The maximum tolerated dose of gemcitabine given as a 24 h infusion was 180 mg m-2."} +{"text": "Infection by an animal-like strain of rotavirus (PA260/97) was diagnosed in a child with gastroenteritis in Palermo, Italy, in 1997. Sequence analysis of VP7, VP4, VP6, and NSP4 genes showed resemblance to a G3P[3] canine strain identified in Italy in 1996. Dogs are a potential source of human viral pathogens. Group A rotaviruses are enteric pathogens of humans and animals. Rotaviruses usually exhibit host species restriction, although interspecies transmission or reassortment between animals and humans viruses can occur in a 2-year-old child hospitalized with severe acute diarrhea at the \u201cG. Di Cristina\u201d Children\u2019s Hospital of Palermo. The virus, PA260/97, exhibited a long e-type and was recognized by an SG-specific monoclonal antibody (MAb) and by a VP7-specific MAb as SGI and G3 (The sequences of human strains PA260/97 and PAH101/97 and of canine strains RV198/95 and RV52/96 have been deposited in GenBank. The accession numbers are as follows: EF442738 (VP6), EF442733 (VP7), EF442735 (VP8*), and EF442741 (NSP4) for strain PA260/97; EF534715 (VP6), EF442734 (VP7), and EF534716 (NSP4) for strain PAH101/97; EF442737 (VP6), EF442736 (VP8*), and EF442739 (NSP4) for strain RV198/95; EF442742 (VP6), EF442740 (VP8*), and EF442743 (NSP4) for strain RV52/96.The VP8* of strain PA260/97 displayed the highest amino acid (aa) identity (98%) to the canine strain RV52/96, G3P[3], isolated in Italy in 1996 . SimilarA close genetic relationship between human strain PA260/97 and canine strain RV52/96 was also observed by comparing the genes that encode VP6 and NSP4. On the basis of MAb reactivity, strain PA260/97 was characterized as SGI and strain PAH101/97 was characterized as SGII. Sequencing of an informative fragment of the VP6 gene display G3 and P[3] specificities (Canine rotavirus infection is considered a minor disease in young dogs (pups) because it is usually mild or unapparent; however, serologic investigations have shown a high prevalence of antibodies to rotavirus in adult dogs ("} +{"text": "From June 1990 to February 1996, 35 patients with B-cell acute lymphoblastic leukaemia (B-ALL) 13 of whom had CNS disease and 28 patients with stage IV B-cell non-Hodgkin's lymphoma (B-NHL) 22 of whom had CNS involvement were treated with a short, intensive multiagent chemotherapy regimen (UKCCSG 9003 protocol) based on the French LMB 86 regimen. Fifty-five were boys. The age range was 11 months to 16.5 years (median 8.4 years). Chemotherapy included cyclophosphamide, vincristine, daunorubicin, high-dose methotrexate (COPADM) and etoposide/high-dose cytarabine (CYVE) with frequent intrathecal (i.t.) triple therapy . Cranial irradiation (24 Gy in 15 fractions) was recommended in patients with overt CNS disease. One patient with Wiskott-Aldrich syndrome was withdrawn after entry and has been excluded from the analysis. Ten patients (16%) have relapsed 4-11 months after diagnosis and two patients never achieved complete remission (CR). All have died. In seven of the patients who relapsed, treatment had been modified or delayed because of poor clinical condition. Seven patients (11%) died of toxicity 11 days to 4 months after diagnosis. The cause of death was sepsis (n = 5) or sepsis with renal failure (n = 2). With a median follow-up of 3.1 years from diagnosis (range 9 months to 6.3 years), 43 patients (69%) survive in CR. This study confirms the effectiveness of this regimen with regard to the relapse rate (16%), although the rate of toxic death is of concern."} +{"text": "To the Editor: Twenty-three countries have reported >1 case of extensively drug-resistant tuberculosis (XDR TB) and Germany and reviewed original clinical records. Drug susceptibility testing for first- and second-line anti-TB drugs was performed according to World Health Organization (WHO) recommendations by quality-assured laboratories and retested at WHO Supranational Reference Laboratories , Student t test (admission days), and Kaplan-Maier curve , where appropriate.XDR TB was defined as resistance to at least rifampin and isoniazid (MDR TB definition) in addition to any fluoroquinolone and Of 2,888 culture-positive TB cases analyzed , 126 (4.4%) were MDR and 11 (0.4%) were XDR . We estimate that the TB cases analyzed represent 24% of culture-positive cases reported in Italy (69.7% of MDR) and 4.2% of those reported in Germany (12.6% of MDR). XDR TB was diagnosed in each year of the study. All 11 XDR TB patients were receiving retreatment, and of the 126 MDR TB patients, 74 (58.7%) were receiving retreatment. All XDR TB patients were HIV seronegative; and of 109 MDR TB patients tested for HIV, 10 (9.2%) were HIV seropositive. Details about previous treatment regimens, drug resistance, and duration of treatment of XDR TB patients are summarized in the In Germany, nonnationals accounted for 95.3% (41/43) of MDR-TB cases and 100% (3 of 3) of XDR TB cases ; in Italy, they accounted for 72.3% (60/83) and 50% (4/8), respectively (p<0.001). Of 126 patients with MDR, 8 (6.3%) died, 45 (35.7%) were treated successfully, 67 (53.2%) were still receiving treatment and 6 defaulted (4.8%). Of 11 patients with XDR, 4 (36.4%) died and 7 (63.6%) were still receiving treatment. Compared with MDR TB patients, XDR TB patients had a 5-fold higher risk for death and required longer hospitalization and longer treatment durations . Smear and culture conversions were observed for 4 XDR TB patients compared with 102 MDR TB patients ; time to smear and culture conversion significantly differed between the 2 groups (p<0.01). A higher percentage of XDR TB than MDR-TB patients had received previous anti-TB treatment and were >45 years of age . Radiologic patterns of the thorax did not differ between XDR TB and MDR TB patients. In the overall sample, the only variable significantly associated with death (other than XDR TB status) was immigrant status (p<0.01). The association between XDR TB status and risk for death remained significant after stratification by immigrant status (p<0.05).Our findings suggest that mismanagement of TB cases plays a major role in emergence of the problem in Europe (XDR TB patient characteristics, Italy and Germany, 2003-2006*"} +{"text": "In a prospective trial of 75 Chinese patients with histologically proven inoperable hepatocellular carcinoma (HCC), 25 patients were randomised to receive doxorubicin 60-75 mg m-2 intravenously once every 3 weeks, 25 to receive recombinant alpha 2 interferon (rIFN) (Roferon) 9-18 x 10(6) IU m-2 intramuscularly (i.m.) daily and 25 to receive rIFN 25-50 x 10(6) IU m-2 i.m. three times weekly. Patients were switched to the other drug if: (a) there was progressive disease after 12 weeks, (b) unacceptable toxicity developed and (c) they had received a total of 500 mg m-2 of doxorubicin. Six patients had switching over of therapy, three on doxorubicin and three on rIFN. In the remaining 69 patients on single drug therapy, the median survival rate of patients on doxorubicin and rIFN was 4.8 and 8.3 weeks respectively (P = ns.). rIFN induced tumour regression of 25-50% in 12% of patients and of over 50% in 10% of patients. When compared with doxorubicin, rIFN was associated with more tumour regression (P = 0.00199) and less progressive tumours (P = 0.00017). It caused less prolonged and less severe marrow suppression (P = 0.01217), and had significantly less fatal complications than doxorubicin (P = 0.01383). Doxorubicin caused fatal complications due to cardiotoxicity and neutropenia in 25% of patients. rIFN was associated with fatal complications due to dementia and renal failure in 3.8% of patients. In the treatment of inoperable HCC, rIFN is superior to doxorubicin in causing more tumour regression, less serious marrow suppression and less fatal complications."} +{"text": "Between July 1979 and December 1981, 43 patients with metastatic germ-cell tumours (36 testicular non-seminomas and 7 testicular seminomas) were treated with 2-6 cycles of bleomycin, etoposide and cis-platin (BEP). Forty (93%) are alive, 37 (86%) with no evidence of disease. Of 36 men with testicular non-seminoma 30 (83.3%) are alive and disease-free at 8-38 months (median 17.0 months). In the latter group 25/28 (89.3%) who had had no prior irradiation are alive and disease-free. Fourteen non-seminoma patients had small volume metastases and 13 are in complete remission, as are 12/14 patients with bulky disease. All 7 patients with advanced seminoma are alive and disease-free. It is concluded that BEP is a well tolerated and effective first line treatment for patients with metastatic germ-cell tumours."} +{"text": "In a multicentre trial of the EORTC-Early Clinical Trials Group (ECTG) we treated 31 chemotherapy-naive patients with advanced non-small-cell lung cancer (NSCLC) with rhizoxin, a novel tubulin-binding agent. The drug was given as an i.v. bolus injection at 2 mg m-2 once every 3 weeks in an outpatient setting. Prophylactic antiemetics were not routinely given. Of the 29 eligible patients, nine had been treated surgically and three had received radiotherapy. The main toxic effects observed were stomatitis (34% of cycles) and neutropenia (41% of cycles). Neutropenic fever was rare (3% of cycles). Twenty-seven patients were evaluable for response. There were four partial responses (15%), while 13 patients (48%) showed stabilisation of their disease. The median duration of response was 7 months (range 6.0-10.7 months) and median survival from the start of rhizoxin treatment was 6 months (range 2-14.7 months). Rhizoxin as single agent shows activity in patients with advanced NSCLC."} +{"text": "Following publication of this work we foundAt time 1, boys were less frequent than girls in the PSU group (13/30 vs. 17/30) and the controls (271/563 vs. 292/563) (McNemar p < .001) whereas males were more frequent among the adolescents at time 2 in the PSU group (79/155 vs. 76/155) and less frequent in the control group (205/437 vs. 233/437) (McNemar p < .001). At time 3 there were no significant gender effects.The correct text should read as follows:At time 1 and 2, there were no significant gender effects in the PSU groups and among the controls . In contrast, at time 3 there were more males than females in the PSU group (160/290 vs. 130/290) and less males than females in the control group (124/303 vs. 179/303) ."} +{"text": "Two faecal occult blood tests (FOBTs), Hemoccult II (guaiac based) and Hemeselect were compared in a population screening for colorectal cancer on 24 282 subjects aged 40-70. Hemeselect was interpreted according to a lower (+ and +/-) and a higher (+) positivity threshold. A total of 8008 compliers were enrolled in the study. Positivity rates: Hemoccult = 6.0%, Hemeselect (+ and +/) = 8.2%, Hemeselect (+) = 3.1%. Among FOBT-positive subject complying with the diagnostic work-up, 22 had colorectal cancer (17 Hemeselect-positive (+), four Hemeselect-borderline (+/-), 15 Hemoccult-positive) and 166 subjects had adenomas (62 Hemeselect(+), 56 Hemeselect-borderline (+/-), 79 Hemoccult-positive) were detected. The positive predictive values (PPVs) for cancer were as follows: Hemoccult = 3.7%, Hemeselect (+ and +/-) = 3.8%, Hemeselect (+) = 8.4%. The PPVs for adenoma(s) were: Hemoccult = 19.7%, Hemeselect (+ and +/-) = 21.4%, Hemeselect (+) = 30.5%. The specificity for cancer was: Hemoccult = 94.1%, Hemeselect (+ +/-) = 92%, Hemeselect (+) = 97.1%. Ratios between detection rates of each test and expected incidence of colorectal cancer suggest that Hemoccult anticipates cancer diagnosis by approximately 2 years on average whereas the mean diagnostic anticipation of Hemeselect ranges between 2.5 and 3.2 years. Hemeselect is superior to Hemoccult as it is at least as effective but more efficient and acceptable than guaiac testing. Further evaluation of Hemeselect cost-effectiveness and sensitivity is needed in order to assess the optimal threshold of positivity and screening frequency."} +{"text": "Toxicity associated with high-dose recombinant interleukin 2 (rIL-2) therapy simulates a sepsis syndrome, but the mechanism remains unclear. We hypothesised that translocated gut-origin bacteria may be important. Fifty-one male rats were randomised to receive rIL-2 by intraperitoneal injection at doses (IU) of 10(5) (n = 15), 10(4) (n = 8), 10(3) (n = 8) or 10(2) (n = 8) twice daily, or a saline bolus (n = 12). After 5 days, ileal histomorphology was assessed and the mesenteric lymph node complex cultured. Results showed that colonisation of mesenteric lymph nodes with Escherichia coli occurred in all rats treated with 10(5) IU of rIL-2, and in 62%, 37% and 12% of rats treated with decreasing doses of rIL-2. No translocation was observed in control animals. An increase in submucosal lymphatics and occasional mucosal disruption was seen only in the group receiving 10(5) IU. These data show that rIL-2 promotes bacterial translocation and suggests a mechanism that may fuel high-dose rIL-2 toxicity in man."} +{"text": "Lasiocarpine, a pyrrolizidine alkaloid, was fed at a dietary concentration of 50/10(6) for 55 weeks, to 20 male F-344 rats. Malignant tumours developed in 17/20 animals between 48 and 59 weeks. Forty-five percent (9/20) developed angiosarcomas of the liver and 35% (7/20) had hepatocellular carcinomas. Other tumours included malignant adnexas tumour of the skin (1 rat) and lympohoma (1 rat). Lung metastases were observed in 4 animals with angiosarcoma of the liver and one animal with hepatocellular carcinoma. From one animal, angiosarcoma was successfully transplanted through 4 generations."} +{"text": "P< 0.00001), respectively the pT (P< 0.01) and pN (P< 0.00001) categories and the multiple molecular marker parameter (P< 0.01) were of significant prognostic importance. This study demonstrates that testing 3 molecular markers improves estimation of prognosis compared to single marker testing and appears to define low and high risk groups for treatment failure in potentially curative (RO) resected NSCLC. \u00a9 2000 Cancer Research CampaignA prospective study was performed in patients with non-small cell lung cancer (NSCLC) to evaluate the prognostic importance of multiple molecular marker testing. 103 patients with potentially curative resections (RO resection) for NSCLC in histopathological stages I\u2013IIIA were included. SSCP analysis and DNA sequencing for p53 and c-Ki-ras genes were performed on paired tumour and normal lung tissue samples and immunohistochemistry (c-erbB-2) was done on frozen tissue sections with a specific anti-c-erbB-2 monoclonal antibody. 46/103 (44.6%) NSCLC showed p53 mutations and 17/103 (16.5%) c-Ki-ras mutations including 12/37 (32.4%) adenocarcinomas. Overexpression of c-erbB-2 (p185) was detected in 56/103 (54.4%) tumours. 24/103 (23.3%) NSCLC were negative for alterations in all 3 parameters whereas 79/103 (76.7%) were positive for at least one of the 3 parameters. In a regression model including a multiple molecular marker parameter , histopathological stage ("} +{"text": "Somatic allelic loss is regarded as a hallmark of tumour-suppressor gene (TSG) inactivation. Thirty-one human bladder transitional cell carcinomas (TCCs) were examined for allelic loss at five chromosome 18q loci, including the DCC gene and at chromosome 11p15 in a restriction fragment length polymorphism analysis. Allelic loss was observed at one or more 18q loci in 9/26 (35%) samples, associated with muscle-invasive disease (P < 0.02). Allelic loss was observed at DCC in 8/24 (33%) samples, associated with muscle-invasive disease (P = 0.05). Three out of the five evaluable recurrent TCCs exhibited allelic loss at DCC, two of which were superficial. No allelic losses were detected at other 18q loci in tumours which retained both DCC alleles. Allelic loss was observed at 11p15 in 5/20 (25%) tumours. These data suggest the presence of a late-acting TSG located on 18q in TCC bladder cancer. DCC is a candidate gene since it lies within the region of most common deletion (18q21.3-qter)."} +{"text": "A Rift Valley fever outbreak occurred in Mauritania in 1998. Seroepidemiologic and virologic investigation showed active circulation of the Rift Valley fever virus, with 13 strains isolated, and 16% (range 1.5%-38%) immunoglobulin (Ig) M-positivity in sera from 90 humans and 343 animals . One human case was fatal."} +{"text": "We examined the prevalence of tuberculosis (TB), rate of multidrug-resistant (MDR) TB, and characteristics of TB on a female general medicine ward in Peru. Of 250 patients, 40 (16%) were positive by sputum culture and 27 (11%) by smear, and 8 (3%) had MDRTB. Thirteen (33%) of 40 culture-positive patients had not been suspected of having TB on admission. Six (46%) of 13 patients whose TB was unsuspected on admission had MDRTB, compared with 2 (7%) of 27 suspected cases (p = 0.009). Five (63%) of 8 MDRTB patients were smear positive and therefore highly infective. In developing countries, hospital control, a simple method of reducing the spread of MDRTB, is neglected."} +{"text": "Haemophilus influenzae (NTHi) is an important bacterial pathogen that causes otitis media and exacerbations of chronic obstructive pulmonary disease (COPD). Here, we report the complete genome sequences of NTHi strains 10P129H1 and 84P36H1, isolated from COPD patients, which contain the phase-variable epigenetic regulators ModA15 and ModA18, respectively.Nontypeable Haemophilus influenzae (NTHi) is an important bacterial pathogen that causes otitis media and exacerbations of chronic obstructive pulmonary disease (COPD). Here, we report the complete genome sequences of NTHi strains 10P129H1 and 84P36H1, isolated from COPD patients, which contain the phase-variable epigenetic regulators ModA15 and ModA18, respectively.Nontypeable Haemophilus influenzae (NTHi) is responsible for human respiratory tract infections (6-adenine DNA methyltransferases (ModA) are involved in epigenetic regulation and virulence (\u2013phase-variable regulon (phasevarion) in their central target recognition domain (TRD), which dictates specificity , 8. modAcificity . Differecificity . We havemodA allele , for genome sequencing and methylome analysis. DNA was sequenced at the Yale Center for Genome Analysis (YCGA) using a PacBio RS II platform with P6-C4 chemistry and a library size of 10\u2009kb, with one strain per single-molecule real-time (SMRT) cell, and assembled de novo using the Hierarchical Genome Assembly Process (HGAP) . PreassemodA15, containing 5\u2032-AGCC(16) repeats in its ORF. NTHi strain 84P36H1 resolved into a genome of 2,025,527\u2009bp with a G+C content of 38.4% and containing 2,115 ORFs. Strain 84P36H1 encodes the modA18 allele, containing 5\u2032-AGCC(19) repeats in its ORF. modA in both strains is expressed (on) with the strains\u2019 respective numbers of AGCC(n) repeats. The pregenome on/off status of modA15 and modA18 was verified using our fragment analysis approach as detailed previously . Strain 10P129H1 encodes eviously . We alsoeviously .Haemophilus influenzae biogroup aegyptius ((n) repeat in their upstream region and CP029621 (84P36H1).The complete genome sequences of the"} +{"text": "Since the fall of Saigon, over 1.3 million Vietnamese immigrated to the U.S. making Vietnamese the 4th largest Asian ethnic but most vulnerable group to disparities. There is a paucity of knowledge on the health of elders and their caregivers. The Vietnamese Aging and Care Survey (VACS) was developed, and health data on 67 caregivers were collected in Houston, Texas. Adult-child caregivers (n=44) were on average, 45.3 years old, married (64%), working (91%), female (61%) in good/excellent health (90%). Spousal caregivers (n=23) were 70.6 years-old, retired (57%), female (78%) in fair/good health (73%). Adult-child received more help (43%) than spousal caregivers (29%), however, felt more caregiver burden (p=0.01) and perceived stress (p=0.05). Living in a multi-generation household, sharing caregiving, and working may alleviate their financial burden and provide psychological support. Findings suggest healthcare professionals to encourage caregivers to utilize available culturally-relevant social services to further ease their caregiving experiences."} +{"text": "PhytoMolecularTaste database (PhytoMolecularTasteDB) described in the present work is related to the article \u201cMain phytocompunds\u05f3 tastes: a better predictor for the ethnopharmacological activities of medicinal plant than the phytochemical class?\u201d [1]. It includes a comprehensive list of plant derived tastants, as well as details on the \u201cphyto-molecular taste\u201d (PMT) . To collect the data, we searched publications in various databases and journals by using relevant keywords. Wherever necessary, manual search of lacking information was also performed in several books. We then extracted the reported phytoconstituents and PMT of all the ayurvedic medicinal plants included in DB. Data were compiled in Excel. In total, PhytoMolecularTasteDB includes 431 ayurvedic medicinal plants, 94 EPAs, 223 phytochemical classes, and 438 plant-derived tastants. Specifications tableValue of the data\u2022First database on plant-derived tastants and \u201cmolecular taste\u201d of ayurvedic medicinal plants\u2022Data scattered in various publications, databases, gathered in one place.\u2022PhytoMolecularTasteDB will facilitate future research on the patterns that shape the traditional medical knowledge.\u2022PhytoMolecularTasteDB can be used in cross-cultural comparative studies on medicinal plants and phyto-molecular taste.\u2022PhytoMolecularTasteDB can inform pharmacologists about new therapeutic agents from ethnomedicine and potential biological activities of plant-derived tastants.1PhytoMolecularTasteDB presents an inventory of plant-derived tastants and \u201cphyto-molecular taste\u201d (PMT) of ayurvedic medicinal plants. In total, PhytoMolecularTaste DB includes 431 ayurvedic medicinal plants with their Sanskrit and Latin name, 94 EPAs, 223 phytochemical classes, and 438 plant-derived tastants. Data are analysed in a related article 2We have build, for the first time to our knowledge, a mixed database (PhytoMolecularTasteDB) on ayurvedic medicinal plants, by integrating modern data with traditional data . We elaborated PhytoMolecularTasteDB in three steps.2.1karman) was available.We have included in our analysis all the plants described (in dedicated monographs) in one recognized text of ayurvedic medicine (Pandey\u05f3s \u201cDravyaguna vijnana\u201d) Here is the distribution among the various botanical families of medicinal plants included in our database (the number of plants in each family is indicated in the paranthesis):Acanthaceae (5), Agaricaceae (1), Alangiaceae (1), Amaranthaceae (5), Amaryllidaceae (2), Anacardiaceae (8), Annonaceae (2), Apiaceae (12), Apocynaceae (8), Araceae (5), Arecaceae (6), Aristolochiaceae (2), Asclepiadaceae (6), Asparagaceae (2), Asphodelaceae (1), Asteraceae (19), Basellaceae (1), Berberidaceae (1), Betulaceae (1), Bignoniaceae (3), Bixaceae (1), Boraginaceae (4), Brassicaceae (7), Bromeliaceae (1), Burseraceae (3), Caesalpiniaceae (2), Calophyllaceae (3), Cannabinaceae (1), Capparaceae (2), Capparidaceae (2), Caricaceae (1), Celastraceae (2), Ceratophyllaceae (1), Cleomaceae (1), Clusiaceae (2), Colchicaceae (1), Combretaceae (5), Convolvulaceae (5), Crassulaceae (1), Cucurbitaceae (16), Cupressaceae (1), Cyperaceae (2), Dilleniaceae (1), Dioscoreaceae (1), Dipterocarpaceae (3), Ebenaceae (1), Elaeocarpaceae (1), Ephedraceae (1), Euphorbiaceae (7), Fabaceae (49), Fagaceae (1), Flacourtiaceae (1), Gentianaceae (3), Iridaceae (2), Juglandaceae (1), Lamiaceae (8), Lauraceae (3), Lecythidaceae (2), Liliaceae (5), Linaceae (1), Loganiaceae (1), Loranthaceae (1), Lythraceae (2), Magnoliaceae (1), Malvaceae (18), Marsileaceae (1), Meliaceae (4), Menispermaceae (5), Moraceae (10), Moringaceae (1), Musaceae (1), Myricaceae (1), Myristicaceae (1), Myrsinaceae (1), Myrtaceae (3), Nyctaginaceae (2), Nymphaeaceae (2), Oleaceae (5), Orchidaceae (1), Oxalidaceae (2), Paeoniaceae (1), Pandanaceae (1), Papaveraceae (3), Parmeliaceae (1), Pedaliaceae (1), Pinaceae (3), Piperaceae (5), Plantaginaceae (1), Plumbaginaceae (1), Poaceae (14), Polygonaceae (1), Portulacaceae (1), Pteridaceae (2), Punicaceae (1), Putranjivaceae (1), Ranunculaceae (7), Rhamnaceae (2), Rosaceae (6), Rubiaceae (7), Rutaceae (7), Salicaceae (4), Santalaceae (1), Sapindaceae (3), Sapotaceae (3), Saxifragaceae (1), Scrophulariaceae (3), Simarubaceae (2), Smilacaceae (1), Solanaceae (9), Sterculiaceae (2), Styracaceae (1), Symplocaceae (1), Trapaceae (1), Ulmaceae (1), Valerianaceae (2), Verbenaceae (7), Violaceae (1), Vitaceae (2), Zingiberaceae (10), Zygophyllace (2).2.21)phytocompounds mentioned in Ayurveda/Indian Materia Medica or Pharmacopoeia to the herbal chemical composition;2)phytocompounds to which one of the following terms \u201cmain\u201d, \u201cprincipal\u201d, \u201cmajor\u201d were attributed, as revealed by the 1077 scientific references see ;3)phytocompounds to which one of the scientifically recognized pharmacodynamic actions of that plant is currently attributed, as revealed by the 1077 scientific references see .We collected the information about the main chemical constituents of the plants from several acknowledged books on ayurvedic/Indian medicinal plants In order to increase the reliability of information included in our database, we introduced the double checking criterion: only the phytochemicals with at least two references have been included.These sources provided useful information for most, but not all the ayurvedic herbs in Pandey\u05f3s \u201cDravyaguna vijnana\u201d 2.3rasa) of various phytochemicals were: 1) BitterDB, a database on bitter compounds http://foodb.ca/) rasas or orosensation transducers . Phytochemicals were included in the PhytoMolecularTasteDB only if they were reported as having a certain taste or if they displayed experimentally activatory potential on at least one taste receptor or orosensation transducer. Supplementary information was also obtained by manual search in various books For only 394 plants were we able to define a taste based on the chemical constituents (see"} +{"text": "The increased prevalence of carbapenem-resistant Gram-negative isolates caused by Metallo-\u03b2-lactamase (MBL) is worrisome in clinical settings worldwide. The mortality rate associated with infections caused by MBLs producing organisms ranging from 18 to 67%.This study aimed to determine the prevalence of Metallo-\u03b2-lactamase genes among some Gram-negative clinical isolates (Carbapenems susceptible and resistant).blaVIM, blaIMP and blaNDM) by multiplex PCR mixture reaction among 200 Gram-negative clinical isolates . Khartoum hospitals during 2015 to 2016.This paper describes a descriptive cross-sectional study carried out to detect MBL genes such as .The prevalence of MBL genes by multiplex PCR assays among 200 Gram-negative clinical isolates was 72(36.1%). MBL positive genes among 100 carbapenems sensitive and 100 resistant isolates were 27(27%) and 45(45%) respectively. There was a statistically, significant association between the antimicrobial susceptibility and the presences of MBL genes (E.coli was the predominant species possessing MBL genes 26(36.1%), with 22(30.7%) species having a combination of MBL genes.Verona integron Metallo beta-lactamase (VIM) was the most frequent genes 28(38.9%) out of 72 MBL detected genes, followed by imipenemase (IMP) was 19(26.4%), and consequently, New Delhi Metallo beta lactamase was 3(4.2%).This study revealed a high prevalence of MBL genes in some Gram-negative isolates from Khartoum State Hospitals which were not previously established in these hospitals.The online version of this article (10.1186/s12879-018-3581-z) contains supplementary material, which is available to authorized users. The production of hydrolytic \u03b2-lactamase enzymes is the most prevalent resistance mechanism towards \u03b2-lactam antibiotics , 2. MetaIMP , , and [70(33%) and 20(9%)] respectively. However, our findings were disagrees with that found in Iraq by Anoar et al, (4) they reported IMP was the most frequently detected gene 33(18.6%), VIM 19(10.7%), and NDM 2(1.12%) isolates.Our results agree with studies done in Uganda, Tanzania, Egypt and Iran by Okoche et al, Mushi [5, and Agha, , they reE.coli was the most isolate harbours MBL genes 26(36.1%), followed by Pseudomonas aeruginosa 23(31.9%). Moreover, 22 isolates have harboured a combination of MBL genes. These findings disagree with Okoche et al, study, where K.pneumoniae was the most frequent MBL genes harbour 35(52.2%), and then 19(28.4%) E.coli, and 8 isolates of MBL genes positive harboured a combination of MBL genes similar to our findings [findings .blaVIM, blaIMP and blaNDM) were detected in the study samples.This study revealed a high prevalence of MBL genes in some Gram-negative isolates from Khartoum State Hospitals, all the three genes assayed MBL genes in Gram-negative strains in Khartoum State, Sudan.This is the first report of the prevalence of"} +{"text": "Petunia axillaris subsp. parodii, which produces various volatiles in its corolla limbs and emits metabolites to attract pollinators. RNA-sequencing from leaves, buds, and limbs identified 53,243 unigenes. Analysis of differentially expressed genes, combined with gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, showed that many biological processes were highly enriched in limbs. These included catabolic processes and signaling pathways of hormones, such as gibberellins, and metabolic pathways, including phenylpropanoids and fatty acids. Moreover, we identified five transporter genes that showed high expression in limbs, and we performed spatiotemporal expression analyses and homology searches to infer their putative functions. Our systematic analysis provides comprehensive transcriptomic information regarding morphological differentiation and metabolite transport in the Petunia flower and lays the foundation for establishing the specific mechanisms that control secondary metabolite biosynthesis in plants.The biosynthesis of plant secondary metabolites is associated with morphological and metabolic differentiation. As a consequence, gene expression profiles can change drastically, and primary and secondary metabolites, including intermediate and end-products, move dynamically within and between cells. However, little is known about the molecular mechanisms underlying differentiation and transport mechanisms. In this study, we performed a transcriptome analysis of Plants produce various secondary metabolites to adapt to their environments. Most of these metabolites are produced only in specific organs, tissues, and cells, where biosynthetic enzymes are expressed. Therefore, the proper timing and regulation of these enzymes is associated with morphological and metabolic differentiation of plant organs .Petunia, floral phenotype and pollinators have coevolved [Petunia integrifolia flowers have short and wide corolla tubes, which are suitable for bee pollination, but the long and narrow tubes of P. axillaris flowers are associated with hawkmoth pollination. At the metabolite level, the color (anthocyanin and other metabolites) and scent (benzenoids and phenylpropanoids) differ between these species and are implicated in pollinator attraction. Several studies of volatile composition and biosynthesis of Petunia species have been performed [Flowers are specialized organs that are morphologically and metabolically differentiated. Most flowers have sepals, petals, and reproductive organs (pistils and stamens). In the petals, pigments are produced and accumulate, whereas volatiles are produced and emitted. In some plants, morphology and secondary metabolites play important roles in reproductive success. For example, in the South American genus oevolved . Petuniaerformed \u20135. For eerformed . During + symporter. Therefore, the plasma membrane-type SUT/SUC uptakes sucrose from the apoplast [Arabidopsis URGT1 ~6 are localized in the Golgi and transports UDP-Rha or UDP-Gal into the Golgi lumen [Most metabolites are transported across the membrane via membrane transporters. Recent analyses have identified various transporter families \u201311. For apoplast . By contapoplast , 13, 14.gi lumen . Since tgi lumen , this tr+/substrate co-transporters [Plant hormones also are transported among cells. Some transporter families, including the ABC (ATP-binding cassette), MATE (multidrug and toxic compound extrusion), NPF (Nitrate transporter 1/Peptide transporter family), PIN (PIN-FORMED proteins), and AUX/LAX (AUXIN1-RESISTANT1 (AUX1)/LIKE AUX1), are involved in hormone transport . ABC prosporters . Their ssporters . PIN andsporters .Petunia species, previous studies reported transcriptome changes of P. hybrida flowers in response to pollination or ethylene [P. axillaris. In this paper, we performed RNA-seq (RNA-sequencing) from flower cells of P. axillaris subsp. parodii, which emits a mixture of several benzenoids and phenylpropenes, and some enzymatic genes were characterized [Despite these progresses, a comprehensive understanding of morphological differentiation and metabolite transport during flower development and volatile production is still lacking. In ethylene , 19, howcterized , 20. AnaP. axillaris flower, we performed transcriptome analysis (RNA-seq) to compare transcript levels in corolla limbs to those of leaves and flower buds (stage2 of flower development). After de novo assembly, 53,243 unigene sequences were obtained with an average length of 1,199 bp and N50 of 1,572 bp. The obtained unigene sequences were annotated based on a homology search performed using BLASTX [To investigate the genetics of morphological differentiation and metabolite transport during flower development of g BLASTX . In totaO-methyltransferase activity (GO:0042409), xyloglucan:xyloglucosyl transferase activity (GO:0016762), cytokinin dehydrogenase activity (GO:0019139), and nitrate transmembrane transporter activity (GO:0015112). In addition, we also identified biological pathways enriched in limbs by KEGG analysis , and limbs, and found that 2,576 unigenes were expressed highly in limbs . The enzymes and transcription factors responsible for the biosynthesis of VBPs have been studied and characterized from other Petunia species, especially P. hybrida [P. axillalis subsp. parodii, we successfully identified 37 unigenes encoding these proteins. The expression profiles of these are shown as a heat map . The amino acid sequences of unigene00003171 and 00031991 showed relatively high amino acid identity with AtSWEET1 (At1g21460) (67%) and AtSWEET15 (At5g13170) (46%) (46%) . TherefoET15 At5g170 (46%) pistils . Its mRN pistils . Since A pistils . Its exp pistils . AtSWEETET1 At1g260 (67%) Panpf3.1. Its mRNA was expressed at high levels in limbs, and slightly higher in tubes, sepals, and stamens P. hybridhaliania . In addiArabidopsis URGT and related NSTs , which encodes a putative polypeptide 338 amino acids long. Its predicted structure has eight TMDs . This geted NSTs . This geted NSTs . Across ted NSTs . AtURGT4ted NSTs , and gala flower . TherefoP. axillaris limbs, buds, and leaves identified 53,243 unigenes, with 2,576 unigenes highly expressed in limbs. GO and KEGG analyses of DEG clarified that genes involved in hormone response, drought tolerance, and phenylpropanoid biosynthesis were enriched and implicated in morphological and metabolic differentiation in the flower. Several candidate genes for VBP transcription factors and biosynthetic enzymes were identified, which would be useful for characterization of VBP biosynthesis in P. axillaris. In addition, five transporter genes highly expressed in limbs were identified. Spatiotemporal expression analysis revealed their distinct expression profiles, with a possible involvement of these transporters in morphological differentiation and metabolite transport. PaNPF3.1 might be involved in flower opening and volatile production through its gibberellin transport. PaSWEET1 would supply sugars as energy for flowering and volatile biosynthesis. PaSWEET15 might play an important role in volatile production and seed production through its sucrose transport. PaABCG1 would function in the formation of apoplastic diffusion barrier like cutin and suberin by transport of lipidic compounds. PaURGT4 would transport galactose into Golgi lumen, which leads to cell wall biosynthesis. These findings provide a foundation to further the comprehensive identification of the genes involved in organ development and metabolite production, and they further elucidate the dynamics of metabolite transport in plant cells producing secondary metabolites.Transcriptome analysis from Petunia axillaris subsp. parodii were sown on soil and grown for 3 months in a culture room under 14 h of light and 10 h of dark at 25\u00b0C. The leaves, stems, tubes, sepals, limbs, pistils, and stamens were collected from three independent plants (at two months old). Flower stages were defined previously [Seeds of eviously and sampP. axillaris using an RNeasy Plant Mini Kit . RNA quality was evaluated using the BioAnalyzer 2100 . A 10 \u03bcg aliquot of total RNA was used to construct a cDNA library using the Illumina TruSeq Prep Kit v2, according to the manufacturer\u2019s protocol . The resulting cDNA library was sequenced using the HiSeq 1500 (Illumina) in high output mode with 100 bp paired-end reads. Reads were assembled using the CLC Genomics Workbench version 5.5.2 with the following parameters: minimum contig length of 400 bp, and scaffolding after adaptor sequences and low quality reads were removed. For each sample, the reads were aligned to obtain Reads Per Kilobase of exon per Million mapped reads (RPKM). All raw read sequences are available on the NCBI sequence read archive under accession number, DRA006635.RNA-seq was performed as described previously with minArabidopsis thaliana TAIR10 (https://www.arabidopsis.org/) and NCBI refseq protein databases, with an e-value cutoff of 1e-15. Unigenes satisfying the following: RPKM of Limb \u2265 1; RPKM of Limb > 4 x RPKM of Stage2; RPKM of Limb > 4 x RPKM of Leaf, were considered to be up-regulated unigenes. Unigenes satisfying the following: RPKM of Stage2 \u2265 1; RPKM of Limb < 1/4 x RPKM of Stage2; RPKM of Leaf \u2265 1; RPKM of Limb < 1/4 x RPKM of Leaf, were considered to be down-regulated unigenes. These DEGs were classified based on their GO (http://www.geneontology.org/) or KEGG metabolic pathway (http://www.genome.jp/kegg/) of the most similar proteins from Arabidopsis thaliana . The GO and pathway enrichment analyses were performed using Fisher\u2019s exact test [Obtained unigene sequences were annotated based on results of a homology search performed using BLASTX against act test relativeact test .http://www.cbs.dtu.dk/services/TMHMM/).We searched for unigenes annotated as transporters from among the 500 top RPKM unigenes in limbs. From those unigenes, we also selected five unigenes that displayed RPKM values in limbs greater than those in leaves and stage2. For unigenes 00005960 and 00019148, we performed Rapid amplification of cDNA ends using a GeneRacer kit to obtain the missing 5\u2019 or 3\u2019 cDNA sequence. PCR was performed using high-fidelity KOD-plus Neo DNA polymerase . PCR products were cloned into pT7Blue T-vector and their sequences were confirmed. The full-length cDNA sequences were deposited to the DDBJ database (Japan). The transmembrane regions of each transporter were predicted using the web program .To obtain the genomic structure of each unigene, genomic DNA was extracted from a frozen stem using the BioMasher II . Primers were designed to amplify each gene, PCR was performed using KOD-plus Neo DNA polymerase , and their sequences were analyzed. Genome sequences were confirmed against the reference sequence of the s genome and Sol Total RNA was prepared from seven tissues , and seven developmental stages of flowers. Reverse transcription was conducted using the ReverTra Ace qPCR RT Master Mix with gDNA Remover , according to manufacturer\u2019s instructions. Primers were designed to amplify each gene separately. UBQ (Accession no. SGN-U207515) and RAN1 (Accession no. SGN-U207968) were used as an endogenous control, according to Mallona et al. . Data weS1 Fig(EPS)Click here for additional data file.S2 FigIntrons are in black, exons are in pink, and UTRs are in blue.(TIFF)Click here for additional data file.S3 Figran1 was used to normalize the expression values.Expression analysis in different organs (A) and during flower development (B). Le, leaves; St, stems; Tu, tubes; Sp, sepals; Lm, limbs; Ps, pistils; Sm, stamens; S2, stage2; S4, stage4; S5, stage5; D0, day0; D1, day1; D2, day2; Sn, senescence. Relative expression levels are shown as fold change values. Results are mean \u00b1 SD of triplicates. The reference gene (EPS)Click here for additional data file.S4 Fighttp://www.cbs.dtu.dk/services/TMHMM/).The membrane-spanning domains of transporters were predicted using the TMHMM program ((EPS)Click here for additional data file.S5 FigPaSWEET1 (LC375808), PaSWEET15 (LC375809), AtSWEET1 (At1g21460), AtSWEET2 (At3g14770), AtSWEET3 (At5g53190), AtSWEET4 (At3g28007), AtSWEET5 (At5g62850), AtSWEET6 (At1g66770), AtSWEET7 (At4g10850), AtSWEET8 (At5g40260), AtSWEET9 (At2g39060), AtSWEET10 (At5g50790), AtSWEET11 (At3g48740), AtSWEET12 (At5g23660), AtSWEET13 (At5g50800), AtSWEET14 (At4g25010), AtSWEET15 (At5g13170), AtSWEET16 (At3g16690), AtSWEET17 (At4g15920).Phylogenetic analyses were conducted in MEGA7 software ) using maximum likelihood and 1000 bootstrap resampling events. Bootstrap values (maximum 100) are shown at branching points. The scale bar shows the number of amino acid substitutions per site.(EPS)Click here for additional data file.S6 FigPaNPF3.1 (LC375810), AtNPF1.2 (At1g52190), AtNPF2.7 (At3g45650.1), AtNPF2.9 (At1g18880.1), AtNPF2.10 (At3g47960.1), AtNPF2.11 (At5g62680.1), AtNPF2.12 (At1g27080.1), AtNPF2.13 (At1g69870.1), AtNPF3.1 (At1g68570.1), AtNPF4.1 (At3g25260.1), AtNPF4.2 (At3g25280.1), AtNPF4.3 (At1g59740.1), AtNPF4.4 (At1g33440.1), AtNPF4.5 (At1g27040.1), AtNPF4.6 (At1g69850.1), AtNPF5.2 (At5g46050.1), AtNPF5.13 (At1g72125.1), AtNPF5.14 (At1g72120.1), AtNPF6.2 (At2g26690.1), AtNPF6.3 (At1g12110.1), AtNPF6.4 (At3g21670.1), AtNPF7.2 (At4g21680.1), AtNPF7.3 (At1g32450.1), AtNPF8.1 (At3g54140.1), AtNPF8.2 (At5g01180.1), AtNPF8.3 (At2g02040.1), AtNPF8.4 (At2g02020.1), AtNPF8.5 (At1g62200.1), OsNPF2.2 (Os12g44100.1), OsNPF4.1 (Os11g12740.1), OsNPF5.5 (Os10g33210.1), OsNPF7.1 (Os07g41250.1), OsNPF7.3 (Os04g50950.1), OsNPF7.4 (Os04g50940.1), OsNPF8.1 (Os01g04950.1), OsNPF8.2 (Os07g01070.1), OsNPF8.5 (Os03g51050.1), OsNPF8.9 (Os03g13274.2), OsNPF8.20 (Os06g49250.1), CsNPF3.2 (Z69370.2), MtNPF1.7 (Medtr1g009200.1), MtNPF6.8 (Medtr5g085850.1).A. thaliana, Cs: Cucumis sativus, Mt: Medicago truncatula, Os: Oryza sativa, Pa: Petunia axillarisAt: Phylogenetic analyses were conducted in MEGA7 software ) using maximum likelihood and 1000 bootstrap resampling events. Bootstrap values (maximum 100) are shown at branching points. The scale bar shows the number of amino acid substitutions per site.(EPS)Click here for additional data file.S7 FigPaABCG1 (LC375811), AtABCG1 (At2g39350), AtABCG2 (At2g37360), AtABCG3 (At2g28070), AtABCG4 (At4g25750), AtABCG5 (At2g13610), AtABCG6 (At5g13580), AtABCG7.1 (At2g01320.1), AtABCG7.2 (At2g01320.2), AtABCG7.3 (At2g01320.3), AtABCG7.4 (At2g01320.4), AtABCG8 (At5g52860), AtABCG9 (At4g27420), AtABCG10 (At1g53270), AtABCG11 (At1g17840), AtABCG12 (At1g51500), AtABCG13 (At1g51460), AtABCG14 (At1g31770), AtABCG15 (At3g21090), AtABCG16 (At3g55090), AtABCG17 (At3g55100), AtABCG18 (At3g55110), AtABCG19 (At3g55130), AtABCG20 (At3g53510), AtABCG21.1 (At3g25620.1), AtABCG21.2 (At3g25620.2), AtABCG22.1 (At5g06530.1), AtABCG22.2 (At5g06530.2), AtABCG22.3 (At5g06530.3), AtABCG23 (At5g19410), AtABCG24 (At1g53390), AtABCG25 (At1g71960), AtABCG26 (At3g13220), AtABCG27 (At3g52310), AtABCG28 (At5g60740), PpABCG7 (XP001775949.1), StABCG1 (XP006345915.1), NtWBC1 (AAR06252), SbWBC11 (Sb06g023280), PhABCG1 (JQ088099), OsABCG5 (Q8H8V7), OsABCG15 (Os06g40550), OsABCG26 (Os10g0494300), OsSTR1 (JN608807), OsSTR2 (JN608806).A. thaliana, Nt: Nicotiana tabacum, Os: Oryza sativa, Pa: Petunia axillaris, Ph: Petunia hybrida, Pp: Physcomitrella patens, Sb: Sorghum bicolor St: Solanum tuberosumAt: Phylogenetic analyses were conducted in MEGA7 software ) using maximum likelihood and 1000 bootstrap resampling events. Bootstrap values (maximum 100) are shown at branching points. The scale bar shows the number of amino acid substitutions per site.(EPS)Click here for additional data file.S8 FigPaURGT4 (LC375812), AtURGT1 (At1g76670), AtURGT2 (At1g21070), AtURGT3 (At5g42420), AtURGT4 (At4g39390), AtURGT5 (At4g09810), AtURGT6 (At1g34020), AtUXT1 (At2g28315), AtUXT2 (At2g30460), AtUXT3 (At1g06890).Phylogenetic analyses were conducted in MEGA7 software ) using maximum likelihood and 1000 bootstrap resampling events. Bootstrap values (maximum 100) are shown at branching points. The scale bar shows the number of amino acid substitutions per site.(EPS)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file."} +{"text": "The purpose of this study was to investigate relationships among peak exercise parameters on 6-minute walk (6MWT) and shuttle walk tests (SWT), and laboratory-based cardiopulmonary exercise testing (CPET). These relationships have been established in cardiopulmonary patient populations, but not in community-dwelling older adults with mild-moderate Alzheimer\u2019s dementia (AD). This study is a cross-sectional analysis of the baseline data of 6MWT, SWT, and CPET from the FIT-AD Trial . Peak values for each test included heart rate (HR), systolic blood pressure (SBP), and rating of perceived exertion (RPE). Peak oxygen assumption (VO2) was measured in the CPET. Peak walking distance (PWD) was measured for the 6MWT and SWT. CPET produced significantly higher peak HR (118.7 [17.5] vs. 106 [22.8] vs. 106 [18.8] bpm), RPE (16 [2.1] vs. 12 [2.3] vs. 11 [2.1]) and SBP (182 [23.7] vs. 156 [18.9] vs. 150 [16.9] mmHg) compared to the SWT and 6MWT respectively. PWD on SWT (240.4 [128.1] m) and 6MWT (364.3 [108.5] m) significantly correlated with peak VO2 (17.0 [4.3]ml/kg/min) on CPET (r=.44 and r=.43) respectively. Correlations of peak VO2 and PWD on SWT in persons with AD are considerably lower than what is seen for persons with cardiopulmonary diseases. This lower correlation seen in our sample may be due to shorter PWD on walking tests. Future research should focus how mobility affects correlation of peak values on these tests."} +{"text": "This article has been corrected: The correct author name and author contributed information is given below:1,*, Giuseppina Rosaria Rita Ricciardi2,*, Antonio Ieni3, Tindara Franchina2, Carmine Fazzari4, Maria Vita San\u00f25, Giuseppe Angelico6, Michele Caruso5, Giovanni Tuccari3 and Vincenzo Adamo2Barbara Adamo* These authors have contributed equally to this work76974-76986. https://doi.org/10.18632/oncotarget.20293Original article: Oncotarget. 2017; 8:"} +{"text": "Using predictive analytic modelling, the Veterans Affairs has identified Veterans considered to be High Need High Risk (HNHR) requiring increased support. This pilot study sent needs assessment questionnaires to 1112 HNHR Veterans to better understand gaps regarding technology use, access, physical function, and mobility. There were 341(30.7%) respondents: 270(80.4%) Non-Hispanic, 64(18.8%) Hispanic/Latino; 210(61.6%) White, 119(34.9%) Black/African Americans; and 310(90.4%) had \u2265high school education. Average Barthel(ADL) score was 81.5\u00b122.8 and Lawton(IADL) score was 5.8\u00b12.2. Younger Veterans (age<70) were more likely able to use Internet ((117(65%) vs 74(46%)),(p\u22640.01) and email (106(58.9%) vs 67(41.6%),( p\u22640.01). They were also more likely enrolled in MyHealtheVet (87(48.3%) vs 58(36%),(p=0.043). Secure messaging was used by 62(34.3%) younger and 37(23%) older Veterans,(p=0.026). More higher functioning Veterans (140(55.1%)) used email than lower functioning (33(37.9%)),(p=0.018). Among higher functioning Veterans, 148(58.3%) were willing to use videoconference for care coordination and 116(45.7%) owned a smartphone or computer with camera for this; more than lower functioning Veterans (33(37.9%) and 28(32.2%)), (p\u22640.01 for both). Less dependent Veterans preferred to be contacted via cellphone (88(62.4%)) or Internet (10(7.1%)) compared to the more dependent (96(48%) and 6(3%)) respectively (p=0.01). Only 71(44.1%) of older Veterans were willing to use videoconference (p\u22640.01) and 54(33.5%) owned a smartphone or computer with camera,(p\u22640.01). There are significant variations in technology use by age and ethnicity. However, although there are differences by functional ability, a significant number of disabled veterans are willing and able to use technology, and this may provide a way to address access barriers in this population."} +{"text": "TRAF molecules available from The Cancer Genome Atlas (TCGA) and the Catalog of Somatic Mutations in Cancer (COSMIC) as well as the published literature, including copy number variations and mutation landscape of TRAFs in various human cancers. Such analyses reveal that both gain- and loss-of-function genetic alterations of different TRAF proteins are commonly present in a number of human cancers. These include pancreatic cancer, meningioma, breast cancer, prostate cancer, lung cancer, liver cancer, head and neck cancer, stomach cancer, colon cancer, bladder cancer, uterine cancer, melanoma, sarcoma, and B cell malignancies, among others. Furthermore, we summarize the key in vivo and in vitro evidence that demonstrates the causal roles of genetic alterations of TRAF proteins in tumorigenesis within different cell types and organs. Taken together, the information presented in this review provides a rationale for the development of therapeutic strategies to manipulate TRAF proteins or TRAF-dependent signaling pathways in different human cancers by precision medicine.The tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of cytoplasmic adaptor proteins regulate the signal transduction pathways of a variety of receptors, including the TNF-R superfamily, Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs), and cytokine receptors. TRAF-dependent signaling pathways participate in a diverse array of important cellular processes, including the survival, proliferation, differentiation, and activation of different cell types. Many of these TRAF-dependent signaling pathways have been implicated in cancer pathogenesis. Here we analyze the current evidence of genetic alterations of The tumor necrosis factor receptor (TNF-R)-associated factor TRAF 1\u20137) family of cytoplasmic adaptor proteins regulates the signal transduction pathways of a variety of receptors, including the TNF-R superfamily, Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs), and cytokine receptors \u20137 family. TRAF prTRAF molecules available from the Cancer Genome Atlas (TCGA) analyses of cancers at the post-genome era, it has become increasingly clear that genetic alterations of TRAF proteins are commonly present in various human cancers. Here we analyze the current evidence of genetic alterations of s (TCGA) and the s (TCGA) as well TRAF1 is generally <4% in human cancers (TRAF1 are gene amplification (copy gain) and mutation. Deep deletion (copy loss) is less common but also detected in several types of human cancers , skr (3.7%) , sarcomar (3.7%) , ovarianTRAF1 gene detected in human cancers, comprising 80% (111/139) mutations that alter the protein sequence of TRAF1 and 20% (28/139) coding silent mutations of the coding-altering mutations of TRAF1 are recurrent and have been detected in at least two patients with various cancers. Almost all the recurrent mutations of TRAF1 are missense mutations except one nonsense mutation (truncation) and one fusion , including its kinase domain (ALK and NF-\u03baB pathways as demonstrated by the elevated levels of phosphorylated ALK (pALK) and STAT3 (pSTAT3) as well as nuclear p50 NF-\u03baB1 and p52 NF-\u03baB2 in ALCL cells results in significant inhibition on lymphoma growth but could not eradicate lymphoma cells (There is only one fusion of the a (ALCL) \u201319. All e domain \u201319. InteCL cells . SimilarCL cells , suggestma cells . Thus, cTRAF1 genetic alteration in human cancers. TRAF1 expression is ubiquitously elevated in skin squamous cell carcinoma (SSCC), non-small cell lung cancer (NSCLC), Hodgkin lymphomas (HLs) and non-Hodgkin lymphomas (NHLs) cells from patients with refractory disease, suggesting a role for TRAF1 in the progression of this disease and in the development of chemoresistance -NF-\u03baB1 signaling pathways, respectively \u201325. Notafication . In thisof NF-\u03baB , 26, 27.sistance . Furtherk of CLL . Thus, hon (UVR) , 29. Mecon (UVR) . TRAF1\u2212/urethane . In thisurethane . Consist T cells , while Tectively \u201334. In lTRAF1-dependent oncogenic pathways that have been verified in both human cancers and in vivo mouse models, several oncogenic pathways involving TRAF1 have been suggested by studies using patient samples, cultured human cancer cells or xenograft models. These include: (1) CD30-TRAF1 in HL and ALCL tumors L tumors ; (3) WntL tumors , 94; andL tumors \u201397. FurtTRAF2 is generally <6% in human cancers , ovarianr (5.5%) . Notably 10/165) , 101 and 10/165) 102). I. ITRAF2 s Figure 103). T. TTRAF2 TRAF2 detected in human cancers, comprising 86% (205/237) mutations that change the protein sequence of TRAF2 and 14% (32/237) coding silent mutations , but also frameshifts , truncations , in frame deletions and fusion is found in 16 patients with colon cancer, colorectal cancer (CRC), uterine cancer, stomach cancer, and sarcoma, and an additional missense mutation at P9 (P9S) is also detected in a CRC patient (TCGA) (*76) or insertion (G10fs*70) or missense mutation (G10D) in five patients with colon cancer, CRC, gallbladder cancer, and glioblastoma (TCGA) (*), a frameshift insertion (Q457fs*277), and missense mutations (Q457K or L) in six patients of HNSCC, oral squamous cell carcinoma (OSCC), stomach cancer, melanoma, and breast cancer (TRAF2. Missense mutations at R372 and the complex mutations at Q457 of the TRAF-C domain of TRAF2 are predicted to result in inactivation of the TRAF2 protein (There are 237 different mutations of t (TCGA) , 104\u2013108a (TCGA) , 109. Mi COSMIC) \u2013113. Ano COSMIC) . Framesh protein \u2013102.TRAF2 gene detected in human cancers, including TRAF2-CCDC183 in breast and bladder cancers, TRAF2-CACNA1B in bladder cancer, TMEM141-TRAF2 in breast cancer (TCGA), TRAF2-NOTCH1 in ovarian cancer (NTRK2-TRAF2 in melanoma (TRAF2-CCDC183 fusion is recurrently detected in two patients with breast cancer and bladder cancer (TCGA). Functional contribution of these TRAF2 fusions to cancer pathogenesis is currently unclear.There are five different fusions of the n cancer and NTRKmelanoma . Among tTRAF2 are frequently detected in human MCL and DLBCL, resulting in elevated activation of NF-\u03baB1 and NF-\u03baB2 in malignant B cells mice exhibit expanded B cell compartment in lymphoid organs due to constitutive NF-\u03baB2 activation and survival advantage independent of the B cell survival factor BAFF , inhibition of TRAF2 also leads to splenomegaly and lymphadenopathy due to constitutive NF-\u03baB2 activation and increased numbers of B cells leads to spontaneous development of hepatocellular carcinoma, which results from extensive hepatocyte apoptosis due to hyperactivation of caspase-8 but impaired NF-\u03baB activation induced by TNF\u03b1 . In humarognosis . In lineF\u03b1 Table . Interesly Table . TherefoTRAF2 are detected in 3\u20134% of human HNSCC and melanoma of human colon cancers . In cultured primary human colon cancer cells, TRAF2 mediates the apoptosis by acting in the AMPK-ASK1-TRAF2-JNK-p53 axis in response to chemotherapies of human sarcomas (TCGA) and TRAF2\u2212/\u2212 mice display decreased viability of skeletal muscle tissue because of defective TNF\u03b1-induced NF-\u03baB activation in myotubes IRE1\u03b1-TRAF2-ASK1-JNK in the apoptosis of melanoma, lung cancer and OSCC cells induced by chemotherapies or ER stress R stress , 128; , T, TTRAF2 e cancer , pancreae cancer , lung cae cancer , stomache cancer , colon ce cancer , glioblae cancer than in c cancer , stomachc cancer , and glic cancer . Importae cancer and inhie cancer . Thus, TA variety of TRAF2-dependent oncogenic pathways have been reported based on studies of patient samples, cultured human cancer cells or xenograft models. Examples include: (1) TRAF2-NEMO-p65-NF-\u03baB1-Bcl2/XIAP/Survivin/TNF\u03b1/IL-1/IL-8/HIF-1\u03b1 in the migration, invasion, metastasis, or drug resistance of breast, stomach and pancreatic cancer cells as well as DLBCL , 138\u2013140TRAF3 is generally <6% in human cancers , lung caC (5.4%) , ovarians Figure 113). N. NTRAF3 gnancies , includignancies , multiplgnancies , 156, HLgnancies , DLBCL . TogetheTRAF3 detected in human cancers, comprising 90% (253/280) mutations that change the protein sequence of TRAF3 and 10% (27/280) coding silent mutations and truncations . TRAF3 recurrent mutations also include 69% (75/108) missense mutations, 1% (1/108) in frame deletion, 1% splice mutation, and 1% fusion identified in 10 patients with HNSCC (COSMIC) and the frameshift deletion (N16fs*3) detected in a patient with splenic MZL (*38), frameshift insertion (N285fs*13) and missense mutation (N285S) identified in 8 patients with HNSCC, MZL, NPC, CRC, stomach cancer and uterine cancer (*7 or fs*11) and truncation (K286*) detected in six patients with B cell malignancies, including MM, CLL and WM (*) as detected in 8 patients with DLBCL, MM, HNSCC, cervical cancer and uterine cancer (TCGA) , 165. SiL and WM , 167. A r (TCGA) , 168. Mir (TCGA) , 169. Mar (TCGA) , 170. ThTRAF3 detected in human cancers, including TRAF3-WDR20 in stomach and uterine cancers, four fusions of TRAF3-MYO16, TRAF3-RCOR1, TRAF3-KLC1, and EVL-TRAF3 in breast cancer, TRAF3-SFXN1 in cervical cancer, UBR5-TRAF3 in HNSCC, two fusions of TRAF3-ZNF839 and TRAF3-MARK3 in kidney cancer, two fusions of TRAF3-BMP3 and SLC22A23-TRAF3 in lung cancer, TRAF3-IFNL1 in ovarian cancer, TRAF3-ITPK1 in pheochromocytoma and TRAF3-SIVA1 in stomach cancer (TCGA). Among the 14 fusions, only the TRAF3-WDR20 fusion is recurrently detected in two patients with stomach cancer and uterine cancer . However, the functional significance of these TRAF3 fusions is currently unknown.There are 14 different fusions of TRAF2 and also consistent with the frequent deletions and inactivating mutations of TRAF3 identified in human B cell malignancies mice also exhibit severe peripheral B cell hyperplasia due to prolonged survival of mature B cells independent of BAFF, which results from constitutive NF-\u03baB2 activation leads to spontaneous development of histiocytic sarcomas derived from TRAF3ing mice , 174. Throphages , 174. Twsarcomas , 176. DOsarcomas . Similar pathway . TRAF3 itic data , 179, po\u2212/\u2212 (M-TRAF3\u2212/\u2212) mice spontaneously develop chronic inflammation and other cancers that often affect multiple organs including the gastrointestinal tract of human colon cancers . Furthermore, miR-32-TRAF3-mediated inhibition of the NIK-NF-\u03baB2 pathway protects human colorectal epithelium against colorectal cancer in response to a diet of non-digestible carbohydrates mouse model suggest an oncogenic role for TRAF3 in T cells. Despite their constitutive NF-\u03baB2 activation, TRAF3\u2212/\u2212 T cells exhibit impaired proliferation and activation in response to TCR and CD28 co-stimulation TRAF3-mediated inhibition of the oncogenic RelB-SMAD4 association that represses TGF\u03b2-SMAD target gene expression to promote the tumorigenesis of lung cancer, in which TRAF3 is targeted by RAS-NDP52-mediated autophagic degradation via the NDP52-TRAF3 interaction LIGeraction ; (3) memeraction \u2013187; anderaction . Taken tTRAF4 is generally <11% in human cancers , bladder (10.1%) , breast (10.1%) , uterine (10.1%) , melanom (10.1%) , and ova0.1% , blTRAF4 detected in human cancers, comprising 85% (105/123) mutations that cause changes in the amino acid sequence of TRAF4 and 15% (18/123) coding silent mutations , 3 truncations, 1 frameshift deletion, and 1 in frame deletion are identified in 4 patients with prostate cancer, uterine cancer, HNSCC, and OSCC , with currently unknown functional significance.There is only one fusion of TRAF4 genetic alteration in cancers and that TRAF4 expression is ubiquitously elevated in many human cancers , TRAF4 is also required for ontogenic processes and TRAF4\u2212/\u2212 mice show defects in embryonic development and neurulation (\u2212/\u2212 dendritic cells (DCs) derived from the null mice exhibit reduced in vivo and in vitro migration TRAF4-Akt/NF-\u03baB-Glut1/HK2/RSK4/Slug in the proliferation and metastasis of lung and breast cancer cells as well as the migration and epithelial-mesenchymal transition (EMT) of hepatocellular carcinoma cells (HCC) , 206; (2ls (HCC) , 207; (3ls (HCC) ; (4) NGFls (HCC) ; (5) TNFls (HCC) ; (6) TRAls (HCC) , 211; (7ls (HCC) ; and (8)ls (HCC) . It woulTRAF5 genetic alterations is similar to that of TRAF4. The frequency of genetic alterations of TRAF5 is generally <13% in human cancers , liver c (12.2%) . As descn Figure . Deep deTRAF5 detected in human cancers, comprising 85% (160/188) mutations that alter the amino acid sequence of TRAF5 and 15% (28/188) coding silent mutations , but also some truncations , frameshift deletions , and an in frame deletion (Table *) and missense mutations (R164Q or L), are detected in six patients with uterine, colon and bile duct cancers and DLBCL (TCGA) (TRAF5 mutations await further investigation.There are 188 different mutations of and 15% 8/188 cod7) Table . Mutatio7) Table . ComplexL (TCGA) , 215. AnL (TCGA) . MissensL (TCGA) . The funTRAF5 mutations are detected in 5% (5/101) of human DLBCL . Us. UsTRAF5on Table , Kraus e of LMP1 . TRAF5 des Table 73). To. ToTRAF5in vivo evidence indicates the importance of TRAF5 in the survival, proliferation and differentiation of different T cell subsets as detailed in Table TRAF5 alterations in human T cell lymphomas/leukemias is still lacking.Additionally, available in vivo studies of TRAF5\u2212/\u2212 mice, a number of TRAF5-dependent signaling pathways have been proposed based on the studies of patient samples, cultured human cancer cells or their xenografts in immunodeficient mice. These include: (1) CD30-TRAF2/TRAF5-NIK-IKK\u03b1-NF-\u03baB-IL-13 in the survival of Hodgkin-Reed-Sternberg (H-RS) cells of HL LIGls of HL ; (3) uprls of HL ; (4) TRAls of HL ; and (5)ls of HL . The aboTRAF6 is generally <7% in human cancers , uteriner (6.9%) , HNSCC (r (6.9%) , lung car (6.9%) , bladderr (6.9%) , sarcoma 24/261) and OSCC 24/261) . Consistmelanoma \u2013233. TRA cancers , 232. Ton Figure . Deep deTRAF6 detected in human cancers, comprising 85% (152/178) mutations that alter the protein sequence of TRAF6 and 15% (26/178) coding silent mutations except 2 truncations and 1 frameshift insertion (Table *) and missense mutation (R335Q) at R335 within the coiled-coil domain of TRAF6 are detected in five patients with colon and uterine cancers (TCGA) , 234. Mis (TCGA) , 235. FuTRAF6 knockout or transgenic mice yet. However, available in vivo evidence supports potential contributions of TRAF6 dysregulation in tumorigenesis. Consistent with the genetic alterations (mainly amplification and mutation) and frequent overexpression of TRAF6 detected in human epithelial cancers such as breast cancer and uterine cancer self-renewal and loss of hematopoietic stem/progenitor cells (HSPCs) in the bone marrow (BM) (Table TRAF6 mutations have been detected in 2.1% human DLBCL (TCGA) and 2.4% human cutaneous T cell lymphoma (CTCL) (\u2212/\u2212 mice have reduced numbers of immature B cells in the BM and B cells from the null mice show defects in CD40 and LPS-induced proliferation and NF-\u03baB activation (Table \u2212/\u2212 mice (B-TRAF6\u2212/\u2212) mice also exhibit reduced numbers of mature B cells in the BM and spleen as well as defective B1 B cell development (Table \u2212/\u2212 mice (T-TRAF6\u2212/\u2212) mice show multiorgan inflammation due to hyperactivation of the PI3K-Akt pathway in T cells Table 81). Kn. KnTRAF6M) Table . In the a (CTCL) . TRAF6\u2212/on Table , 75. B cnt Table . Knockdont Table , 244. Inls Table . T-TRAF6ignaling , but havignaling . In addils Table . In supp in mice . Further in mice . Collectin vivo evidence also indicates the functional importance of TRAF6 in the brain and muscle the TRAF6-p53 crosstalk, in which TRAF6 promotes K63-linked ubiquitination of p53 and limits the tumor suppressive function of p53 in cancer development and resistance to chemotherapy and radiotherapy theotherapy , 251; otherapy , 257; otherapy ; (8) nutotherapy ; (9) pVHotherapy ; (10) ADotherapy ; (11) TRotherapy ; and TRAF6-p62-mediated inhibition of the HK2 glycolytic activity and the growth of liver cancer, in which TRAF6 catalyzes the K63-linked ubiquitination of HK2 and targets HK2 for p62-mediated autophagic degradation ; (2) TRATRAF7 are breast cancer (6%) of malignant mesothelioma patients' malignant cells in pleural fluids , prostatcer (6%) , stomach, 31/31) , secreto, 31/31) , intrane, 31/31) , and men, 31/31) . In part studies \u2013288, andingiomas , 289\u2013291l fluids . The mosTRAF family, TRAF7 has the highest counts of total and recurrent mutations. There are 376 different mutations of TRAF7 detected in human cancers, including 87% (326/376) coding-altering mutations and 13% (50/376) coding silent mutations . Small percentages of other recurrent mutations include 5 frameshifts, 3 truncations, 2 in frame deletions, 2 splice mutations, and 1 fusion (TRAF7-LRRC1 fusion is recurrently detected in two patients with lung cancer (TCGA). However, all the TRAF7 gene fusions have not been verified at the protein level and their functional consequence is unknown.There are six different fusions of r (TCGA) . Among t\u2212/\u2212 or TRAF7-tg mouse model has been published yet. Importantly however, Tokita et al. recently reported that de novo missense mutations in TRAF7 cause developmental abnormalities and other clinical symptoms in seven unrelated patients, including developmental delay (5/5), congenital heart defects (6/7), limb and digital anomalies (7/7), and dysmorphic facial features (7/7) . TRAF7 mnd T601A . Interesnd T601A . Both K3nd T601A , 303. Th patient . Both T6s Figure , 305. Toignaling . Consist defects . These hTRAF7 mutants of patients with developmental defects, the following TRAF7 signaling pathways have been proposed based on in vitro studies. (1) Transfection of tumor-derived TRAF7 mutants but not WT TRAF7 in 293T cells causes increased phosphorylation of RelA and expression of the NF-\u03baB target gene L1CAM, which is also elevated in adenomatoid tumors Oveof MEKK3 , 303. (3of MEKK3 . (4) TRAof MEKK3 . Paradoxof MEKK3 . (5) TRAof MEKK3 . (6) TRAof MEKK3 . (7) TRAt cancer . In summTRAF gene in human cancers individually, we next examined the combined genetic alterations of all TRAFs in the same type of human cancer using the TCGA tool. Although the frequency of the genetic alterations of each TRAF is generally low , their combined rate is substantially increased to 10\u201335% in many types of human cancers . s Figure , 314. Ths Figure , 19% is a major cause of gastric cancer. H. pylori infection induces TRAF1 overexpression and the expression of the transcription factor Cdx2 in both human gastric epithelial cells and mice, which are mainly driven by NF-\u03baB activation. TRAF1 overexpression plays an antiapoptotic role in H. pylori-infected gastric cells , Kaposi's sarcoma-associated herpesvirus (KSHV), human cytomegalovirus (HCMV) and human papilloma virus (HPV), cause NPC, B lymphomas, breast cancer, glioma, cervical cancer, and HNSCC in the host , 336. RNin vivo, display a unique hyperproliferative feature driven by the Pu.1-TRAF6-NF-\u03baB axis are common for TRAF1, TRAF4, TRAF5, and TRAF6 in human cancers, and are also identified for TRAF2 in epithelial cancers. Corroborating human evidence, direct causal roles of TRAF genetic alterations (except TRAF7) in tumorigenesis have been demonstrated in vivo with genetically engineered mouse models that have each TRAF gene deleted or overexpressed in specific cell types. Importantly, however, the functional significance of most TRAF point mutations identified in human cancers remains to be assessed in future studies. A number of interesting TRAF-dependent oncogenic and tumor suppressive pathways have been elucidated from both in vivo and in vitro studies, although current understanding is still far from complete and further investigation is required. The significance of TRAFs in cancer pathogenesis is reinforced by the evidence that TRAF proteins also participate in pathogen-induced carcinogenesis, including bacteria and viruses. Furthermore, emerging evidence indicates that TRAF proteins can indirectly contribute to tumorigenesis and metastasis by affecting tumor immunity, chronic inflammation, bone resorption, and the tumor microenvironment. In conclusion, the information presented in this article provides a rationale for the development of novel immunotherapies and other strategies to manipulate TRAF proteins or TRAF-dependent signaling pathways in human cancers by precision medicine, which represents the next primary challenge in the field.In this article, we have analyzed the current evidence of genetic alterations of the PX and SZ have taken the leading roles in designing and writing this manuscript, and all co-authors have also made significant contributions to writing this manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "We characterized exposures and demographics of Middle East respiratory syndrome coronavirus cases reported to the Saudi Arabia Ministry of Health during July 1\u2013October 31, 2017, and June 1\u2013September 16, 2018. Molecular characterization of available specimens showed that circulating viruses during these periods continued to cluster within lineage 5. Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) epidemiology in Saudi Arabia is characterized by healthcare-associated outbreaks reported during July 1\u2013October 31, 2017, we conducted telephone interviews using a standardized questionnaire addressing demographics and activities during the 14 days before symptom onset (exposure period). For deceased or unavailable patients, we interviewed proxies. We did not conduct interviews for cases reported during June 1\u2013September 16, 2018; this period was selected because of specimen availability. Cases were confirmed by testing respiratory specimens with MERS-CoV real-time reverse transcription PCR assays years; 43 (70%) were male, and 23 (38%) died. Nine (15%) cases were associated with a hospital outbreak, 10 (16%) were household contacts of known cases, and 42 (69%) were classified as sporadic and further investigated. During November 2017, we interviewed 35 (83%) sporadic case-patients, 9 directly and 26 by proxy; 7 were unavailable. Among the 42 sporadic case-patients, median age was 57 (range 25\u201389) years; 35 (83%) were male, and 33 (79%) reported underlying conditions, most commonly diabetes (n = 24) and hypertension (n = 23). All were symptomatic and hospitalized; 22 (52%) died. During the exposure period, 21 (50%) sporadic case-patients reported camel contact: 12 had direct contact (touching), 5 indirect contact (visiting a setting with camels or exposure to others with direct camel contact), and 4 contact that could not be further classified. Among patients with camel contact, 6 also reported visiting a healthcare facility without a known MERS-CoV outbreak for a reason unrelated to their subsequent MERS illness. Of the 21 sporadic case-patients without camel contact, 8 (38%) visited a healthcare facility without a known MERS-CoV outbreak, 5 (24%) denied high-risk exposures, 1 (2%) was reclassified after interview as a contact of a previously identified case-patient, and 7 (17%) had insufficient exposure data to further characterize.We analyzed MERS-CoV whole-genome sequences from 4 sporadic cases from 2017 . All seqDuring June 1\u2013September 16, 2018, a total of 32 MERS cases were reported from 10 administrative regions (In conclusion, dromedary contact was common for recent case-patients with sporadic MERS-CoV in Saudi Arabia, indicating continued zoonotic transmission to humans. MERS-CoV infection continues to be reported periodically among those without known high-risk exposures, warranting further investigation. Recently circulating viruses remain in lineage 5, the predominant circulating strain in Saudi Arabia since 2015. Sporadic unique ORF sequence deletions continue to be observed, highlighting the importance of ongoing molecular virology surveillance."} +{"text": "The results of GenoType MTBDR plus were recorded and analysed using SPSS version 22. For all analyses, a p value <0.05 was considered statistically significant.A total of 256 sputum samples from Pulmonary TB patients suspected of MDR-TB were tested by GenoType MTBDR rpoB, katG and inhA genes respectively. Unknown mutations were found in 50.77% (33/65), 3.66% (3/82) and 26.83% (22/82) isolates for rpoB, katG and inhA genes respectively. Hetero-resistance in MDR, rifampicin monoresistant and isoniazid monoresistant isolates was found to be 26% (13/50), 20% (3/15) and 34.37% (11/32) respectively.Fifty (19.53%) isolates were found MDR, 32 (12.50%) isolates were found mono-resistant to isoniazid and 15 (5.86%) isolates were found mono-resistant to rifampicin. Eleven isolates (4.3%) were found NTM. Mutation in codon S531L, S315T1 and C15T were most common in Mutation in codon S531L, S315T1 and C15T were most common mutations associated with MDR-TB. Further high number of isolates showed mutations in unknown regions and hetero-resistance thus more elaborate studies based on sequencing are desirable in this region. Mycobacterium tuberculosis has complicated the situation of Global TB control program. In 2015, World Health organization (WHO) estimated 5, 80,000 new cases of drug resistant TB globally, 480,000 among them were mutli drug resistant tuberculosis (MDRTB) i.e. resistance to both isoniazid and rifampicin which are the most potent drugs in management of tuberculosis has shown promises to be an ideal rapid tool for early detection of MDR-TB and thus endorsed by WHO for detection of isoniazid and rifampicin resistance (plus is a line probe assay based on multiplexed polymerase chain reaction coupled with reverse hybridization on a nitrocellulose membrane targeting common mutations in rpoB gene (coding for \u03b2-subunit of RNA polymerase) for rifampicin resistance, katG gene and inhA gene (coding for NADH enoyl ACP reductase) for high and low level isoniazid resistance respectively remained a global concern with an annual incidence of 10.4 million new cases and accounting for 1.8 million deaths were analyzed by GenoType MTBDR For all sputum samples AFB smears were prepared and were stained with Auramine O and counter stained with potassium permanganate and then were evaluated as per Revised National Tuberculosis Control Program (RNTCP) guidelines .plus assay as per manufacturer\u2019s instructions using M. tuberculosis H37Rv strain as internal quality control whereas all smear negative samples were cultured in liquid medium and were processed after obtaining growth.All samples were decontamination by N-acetyl-L-cysteine and sodium hydroxide (NALC-NaOH) method . All smeplus assays and patients demographic details were recorded and analysed using SPSS version 22 . Data were compared using Chi square test. For all analyses, a p value <0.05 was considered statistically significant.The result of GenoType MTBDR A total of 256 TB patients comprising of 34 (13.28%) treatment defaulters, 39 (15.23%) relapse cases, 7 (2.73%) treatment failure cases, 34 (13.28%) cases with history of TB, 112 (43.75%) cases on ATT treatment and 30 (11.72%) new cases with doubtful history. Average age of the patient was 43.38 years . Two hundred thirty one samples (90.23%) were smear positive and 25 (9.77%) were smear negative. Fifty five (21.48%) patients were diabetic and 13 (5.09%) were co-infected with HIV.plus analysis 148 (57.81%) isolates were found sensitive to both isoniazid and rifampicin. Fifty (19.53%) isolates were found MDR i.e. resistant to both isoniazid and rifampicin; Thirty two (12.50%) isolates were found mono-resistant to isoniazid and 15 (5.86%) isolates were found mono-resistant to rifampicin. Further in 11 (4.3%) smear positive isolates TUB band was absent thus were considered as Non Tuberculous Mycobacteria (NTM).On GenoType MTBDR rpoBMUT3 band conferring mutation in S531L codon was present in 30 isolates . Difference of rpoB S531L mutations in MDR-isolates compared with rifampicin mono-resistant strains was found statistically significant (p = 0.02). Mutation in codon H526D was found in 3 isolates each was found with mutation in codon D516V and codon H526Y in rifampicin mono-resistant isolates. On considering all isoniazid resistant isolates katG mutation was found in 46 isolates whereas inhA mutation was found in 41 isolates . katGMUT1 (S315T1) mutation was found in 40 isolates and mutation in katGMUT2 (S315T2) was found in 3 isolates on comparing difference between MDR and isoniazid monoresistant isolates no statistically significant difference was seen for these two mutations. InhAMUT1 (C15T) mutation was found in 22 isolates ; inhAMUT1 difference in MDR isolates and isoniazid monoresistant isolates was statistically significant (p = 0.0010). Further mutation in inhAMUT3A was found in 1 (1.23%) MDR isolate. The detailed description of band patterns of drug resistant Myco-bacterium tuberculosis isolates by Genotype MTBDR plus assay is given in Among 65 rifampicin resistant isolates plus assay offers an additional advantage of detection of isoniazid mono-resistant which cannot be detected by the GeneXpert MTB/RIF. Further studies in recent past which was in concordance to previous studies , rpoB codon H526Y and rpoB codon H526D were seen in rifampicin monoresistant strains only whereas rpoB codon H526D mutation was found in only 1 (1.52%) MDR isolate. Isolates with unknown mutations (missing Wild Type probe without any mutation bands) has been variably reported in earlier studies (katG mutation in high burden countries (katG mutation in codon S315T1 was found in 48.78% isolates (12/32 in isoniazid mono resistant and 28/50 in MDR isolates.) whereas mutation in codon S315T2 was found in 3.65% isolates (1/32 in isoniazid monoresistant and 2/50 in MDR isolates), further inhA mutation in codon C15T was found in 26.83% isolates (15/32 in isoniazid mono-resistant and 7/50 in MDR isolates); mutation in codon C15T was more common in isoniazid monoresistant isolates as compared to MDR isolates (p= 0.0010), further one MDR isolate (1.22%) showed mutation in codon T8C. On considering unknown mutations (due to missing wild type) in inhA and katG gene, katG mutation was observed in 3.66% (3/82) isolate whereas inhA mutation was observed in 26.83% (22/82) isolates. Further previous studies have reported high prevalence of katG mutation than inhA gene mutation but we didn\u2019t observe any significant difference between the two clinical isolates were found resistant to one or more drug which is almost comparable to our earlier study from this region where 33.5% isolates were found resistant to one or more drug , a studypoB gene . In the studies , 21, 22 studies , 24. Othountries . In presplus assay over smear based diagnosis. One of the limitations of this study was inability to perform sequencing which might have provided better insight of hetero-resistant isolates.Hetero-resistance in MDR, rifampicin monoresistant and isoniazid monoresistant isolates was found to be 26% (13/50), 20% (3/15) and 34.37% (11/32) respectively. Authors in the past have also reported higher percentage of hetero-resistant isolates in their studies , 28. Eleplus assay offers rapid detection of Rif and INH resistance, routine use of this assay for the diagnosis of pulmonary Tuberculosis can substantially reduce burden of tuberculosis by early detection of MDR-TB providing better management of patient. In the present study mutation in S531L codon in rpoB gene among rifampicin resistant isolates and mutation in codonS315T1 in katG gene and codon C15T in inhA gene among isoniazid resistant isolates were found most commonly associated with drug resistance. Further mutations in unknown regions and hetero-resistance was seen in very high number of MDR isolates thus; future studies based on sequencing are desirable in this region to fully explore the mutations associated with MDR-TB.GenoType MTBDR"} +{"text": "Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group.Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000\u00a0Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats.Here we report the sequencing and manual annotation of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders.Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the The online version of this article (10.1186/s12864-018-5163-2) contains supplementary material, which is available to authorized users. The semi-aquatic bugs (Gerromorpha) are a monophyletic group of predatory heteropteran insects characterized by their ability to live at the water-air interface \u20134. Over This shift in habitat exposed the Gerromorpha to new selective pressures compared to their terrestrial ancestors. The Gerromorpha face two primary challenges unique among insects: how to remain afloat and how to generate efficient thrust on the fluid substrate for locomotion , 3, 12. G. buenoi, the first sequenced member of the infraorder Gerromorpha. G. buenoi is part of the family Gerridae, and has been previously used as a model to study sexual selection and developmental genetics [G. buenoi can easily breed in laboratory conditions and is closely related to several other Gerris species used as models for the study of water-walking hydrodynamics, salinity tolerance, and sexual conflict. With a particular focus on manual annotation and analyses of processes involved in phenotypic adaptations to life on water, our analysis of the G. buenoi genome suggests that the genomic basis of water surface invasion might be, at least in part, underpinned by clustered gene family expansions and tandem gene duplications.While we are starting to uncover the developmental genetic and evolutionary processes underlying the adaptation of water striders to the requirements of water surface locomotion, predator-prey, and sexual interactions , 15\u201319, genetics \u201322. MoreG. buenoi genome comprises 1,000,194,699\u00a0bp (GC content: 32.46%) in 20,268 scaffolds and 304,909 contigs . The assembly recovers ~\u200987% of the genome size estimated at ~\u20091.15\u00a0GB based on k-mer analysis. The G.buenoi genome is organized into 18 autosomal chromosomes with a XX/X0 sex determination system [Limnoporus dissortis (PRJNA289202) [Cimex lectularius genome [Oncopeltus fasciatus [G. buenoi official gene set (OGS) 1.0 includes 1,277 manually annotated genes, including 1,378 mRNAs and 15 pseudogenes, representing development, growth, immunity, cuticle formation as well as olfaction and detoxification pathways genes, amongst others , as wells genome and the G. buenoi, we were able to find and annotate gene models for all ten Hox genes occur in opposite transcriptional orientations . Inversion of the divergent zen locus is not new in the Insecta [C. lectularius, in which the complete Hox cluster was fully assembled [labial is present but split across scaffolds, while only partial gene models could be created for Ultrabithorax and Abdominal-B. Furthermore, while there are clear single-copy orthologues of members of the small Iroquois complex, iroquois and mirror, they are not linked in the current assembly gene clusters as indicators of draft genome quality and as an opportunity to assess synteny among species. The Hox cluster is conserved across the Bilateria , and the Insecta , but wasssembled . Future tularius and 403 asciatus ). LastlyG. buenoi genome we were able to annotate 90 out of 120 genes known to be involved in bristle development [Beadex (Bx). A similar duplication found in C. lectularius and H. halys suggest that the Bx duplication may have predated the separation of these lineages and the radiation of Gerromorpha, although a broader phylogenetic sampling is needed to strengthen this conclusion. In Drosophila, Bx is involved in neural development by controlling the activation of achaete-scute complex genes [Bx have extra sensory organs [Beadex might have been exploited by water striders and subsequently linked to changes in bristle pattern and density. This possibility opens up new research avenues to further understand the adaptation of water striders to living on the water surface.One of the most important morphological adaptations that enabled water striders to conquer water surfaces is the change in shape, density, and arrangement of the bristles that span the contact surface between their legs and the fluid substrate. These bristles, by trapping air, act as non-wetting structures, forming a cushion between the legs and the water surface Fig. 2, 3, 1, 13. QTLelopment , 35 whether the third copy in Gerromorpha and Blattodea share a common ancestor, we performed a phylogenetic reconstruction that included the sequences of eight Gerromorpha (three InR copies), four Blattodea (three InR copies), Daphnia (four copies) and an additional sample of 126 Arthropoda, all of which possess either one or two InR copies and Sternorrhyncha (Pachypsylla venusta) Fig. . Based oG. buenoi LWS opsin 3 as a high confidence candidate for a blue-shifted paralog, followed by G. buenoi LWS opsin 1 and 2. Moreover, the G. buenoi LWS opsin 4 paralog matches all of the butterfly green-sensitive amino acid residue states, thus favoring this paralog as green-sensitive and Drosophila are the single OrCo and fructose receptors, the IR family has single orthologs in each species. This is not restricted to only the highly conserved co-receptors but also includes receptors implicated in sensing amino acids, temperature, and humidity . As is common in other insects the amine-sensing IR41a lineage is expanded to four genes, while the acid-sensing IR75 lineage is highly expanded to 24 genes, and like the other heteropterans there are nine more highly divergent IRs proteins play a role in metabolic detoxification of xenobiotics including insecticides , 87. The insects . UGTs ca insects , 93.O. fasciatus (58 CYPs), R. prolixus (88 CYPs) and N. lugens (68 CYPs) [D. melanogaster (85), A. mellifera (45), and B. mori (86) . CYP genes fall into one of the four distinct subfamilies: Clan 2 (6 genes), Clan mito (62 genes), Clan 3 (25 genes) and Clan 4 (10 genes) [C. lectularius (7) [D. melanogaster (11), A. mellifera (6) and B. mori (14) [T. castaneum (28) [We annotated and analyzed a total of 103 CYP genes , 94, 95,atus (1) , C. lect, Clan 3 genes anori (14) , and ideeum (28) .Fig. 5PhG. buenoi CYPs, the Clan 2 and Clan mito have undergone relatively little gene expansion might have been generated by tandem gene duplications . The 180 and 500\u00a0bp paired-end libraries as well as the 3\u00a0kb mate-pair library were made from eight adult males. The 8\u00a0kb mate-pair library was made from eight adult females. Total RNA was isolated from 39 embryos, three first instar nymphs, one second instar nymph, one third instar nymph, one fourth instar nymph, one fifth instar nymph, one adult male and one adult female. RNA was extracted using a Trizol protocol (Invitrogen).Genomic DNA was sequenced using HiSeq2500 Illumina technology. 180 and 500\u00a0bp paired-end and 3 and 10\u00a0kb mate-pair libraries were constructed and 100\u00a0bp reads were sequenced. Estimated coverage was 28.6\u00d7, 7.3\u00d7, 21\u00d7, 17\u00d7, 72.9\u00d7 respectively for each library. Sequenced reads were assembled in draft assembly using ALLPATHS-LG and autoG. buenoi automatic annotation. These curators selected genes or gene families based on their own research interests and manually curated MAKER-predicted gene set GBUE_v0.5.3 at the i5k Workspace@NAL [International groups within the i5k initiative have collaborated on manual curation of pace@NAL resultinpace@NAL .G. buenoi predicted genes.Genome assembly completeness was assessed using BUSCO . The Arthttp://orthodb.org/) was used to find orthologues of G. buenoi (OGS 1.0) on 76 arthropod species. Proteins on each species were categorised using custom Perl scripts according to the number of hits on other eight arthropod species: Drosophila melanogaster, Danaus plexippus, Tribolium castaneum, Apis mellifera, Acyrthosiphon pisum, Cimex lectularius, Pediculus humanus and Daphnia pulex.OrthoDB8 . Each r et al. as well al Omega \u2013109 and al Omega , Acyrthosiphon pisum (2), Aedes aegypti (1), Aedes albopictus (1), Aethina tumida (2), Agrilus planipennis (2), Amyelois transitella (1), Anopheles darlingi (1), Anopheles gambiae (1), Anopheles sinensis (1), Anoplophora glabripennis (2), Aphis citricidus (2), Apis cerana (2), Apis dorsata (2), Apis florea (1), Apis mellifera (2), Aquarius paludum (3), Athalia rosae (2), Atta cephalotes (2), Atta colombica (2), Bactrocera dorsalis (1), Bactrocera latifrons (1), Bactrocera oleae (1), Bemisia tabaci (2), Blattella germanica (3), Bombus impatiens (2), Bombus terrestris (2), Bombyx mori (1), Caenorhabditis elegans (1), Camponotus floridanus (2), Cephus cinctus (2), Ceratina calcarata (2), Ceratitis capitata (1), Ceratosolen solmsi marchali (1), Cimex lectularius (2), Clunio marinus (1), Copidosoma floridanum (1), Cryptotermes secundus (3), Cyphomyrmex costatus (2), Danaus plexippus (1), Daphnia pulex (4), Dendroctonus ponderosae (1), Diachasma alloeum (2), Diaphorina citri (1), Dinoponera quadriceps (2), Diuraphis noxia (2), Drosophila ananassae (1), Drosophila arizonae (1), Drosophila biarmipes (1), Drosophila bipectinata (1), Drosophila busckii (1), Drosophila elegans (1), Drosophila erecta (1), Drosophila eugracilis (1), Drosophila ficusphila (1), Drosophila grimshawi (1), Drosophila kikkawai (1), Drosophila melanogaster (1), Drosophila miranda (1), Drosophila mojavensis (1), Drosophila obscura (1), Drosophila persimilis (1), Drosophila pseudoobscura (1), Drosophila rhopaloa (1), Drosophila sechellia (1), Drosophila serrata (1), Drosophila simulans (1), Drosophila suzukii (1), Drosophila takahashii (1), Drosophila virilis (1), Drosophila willistoni (1), Drosophila yakuba (1), Dufourea novaeangliae (2), Ephemera danica (2), Eufriesea mexicana (2), Fopius arisanus (2), Gerris buenoi (3), Glossina morsitans morsitans (1), Habropoda laboriosa (2), Halyomorpha halys (2), Harpegnathos saltator (2), Hebrus sp (3), Helicoverpa armigera (1), Heliothis virescens (1), Hydrometra cumata (3), Lasius niger (2), Leptinotarsa decemlineata (2), Limnoporus dissortis (3), Linepithema humile (2), Locusta migratoria (2), Macrotermes natalensis (3), Manduca sexta (1), Maruca vitrata (1), Megachile rotundata (2), Melipona quadrifasciata (1), Mesovelia furcata (3), Microplitis demolitor (2), Microvelia longipes (3), Monochamus alternatus (1), Monomorium pharaonis (2), Musca domestica (1), Myzus persicae (2), Nasonia vitripennis (1), Neodiprion lecontei (2), Nicrophorus vespilloides (2), Nilaparvata lugens (2), Oncopeltus fasciatus (2), Onthophagus nigriventris (1), Onthophagus taurus (2), Ooceraea biroi (2), Orussus abietinus (2), Oryctes borbonicus (1), Papilio machaon (2), Papilio polytes (1), Papilio xuthus (1), Parasteatoda tepidariorum (2), Pediculus humanus corporis (1), Pieris rapae (1), Plutella xylostella (1), Pogonomyrmex barbatus (2), Polistes canadensis (2), Polistes dominula (2), Pseudomyrmex gracilis (2), Rhagoletis zephyria (1), Rhagovelia antilleana (3), Rhodnius prolixus (2), Solenopsis invicta (2), Spodoptera litura (1), Stomoxys calcitrans (1), Strigamia maritima (1), Trachymyrmex cornetzi (2), Trachymyrmex septentrionalis (2), Trachymyrmex zeteki (2), Tribolium castaneum (2), Trichogramma pretiosum (1), Trichomalopsis sarcophagae (1), Vollenhovia emeryi (2), Wasmannia auropunctata (2), Zeugodacus cucurbitae (1), and Zootermopsis nevadensis (3).Gerris buenoi (Gb), Rhodnius prolixus (Rp), Nilaparvata lugens (Nl), Bombyx mori (Bm) and Tribolium castaneum (Tc). All nodes have significant bootstrap support based on 1000 replicates.CYPs phylogenetic analysis was performed using Maximum-Likelihood method and the trees were generated by MEGA 6. The phylogenetic trees were generated by MEGA 6 with Maximum-Likelihood method using the amino acid sequences from Additional file 1:Supplementary Online Information. Additional files Additional file 2:Gerris buenoi. (XLSX 12 kb)List of annotated autophagy genes in Additional file 3:Accession number and gene name of 225 arthropod genes used to reconstruct Insulin receptors phylogeny (highlighted). (XLSX 91 kb)Additional file 4:Gerris buenoi, Aquarius paludum, Limnoporus dissortis, Rhagovelia antilleana, Microvelia longipes, Mesovelia furcata, Hydrometra cumata and Hebrus sp). (DOCX 40kb)\u00a0Nucleotide sequences of Insulin receptors genes annotated in Gerromorpha Additional file 6:Gerris buenoi including gene names and closest identity. (XLSX 58 kb)List of annotated aquaporin genes in Additional file 7:Gerris buenoi including gene names and closest identity. (XLSX 15 kb)List of annotated aquaporin genes in Additional file 8:Gerris buenoi : 155 Or, 135 Gr and 45 IR genes. (DOCX 83 kb)Protein sequences of annotated chemoreceptors in Additional file 9:Gerris buenoi genome.\u00a0(XLSX 14 kb)List of cytochrome P450 (CYP) genes annotated from the Additional file 10:Gerris buenoi serosins nucleotide and protein sequences. (DOCX 12 kb)Additional file 11:Gerris buenoi genome. (XLSX 13 kb)List of antioxidant enzyme genes identified in the"} +{"text": "Staphylococcus aureus bacteremia (SAB) is associated with high morbidity and mortality, which varies depending on the source of infection. Nevertheless, the global molecular epidemiology of SAB and its possible association with specific virulence factors remains unclear. Using DNA microarrays, a total of 833 S. aureus strains (785 SAB and 48 colonizing strains) collected in Spain over a period of 15 years (2002\u20132017) were characterized to determine clonal complex (CC), agr type and repertoire of resistance and virulence genes in order to provide an epidemiological overview of CCs causing bloodstream infection, and to analyze possible associations between virulence genes and the most common sources of bacteremia. The results were also analyzed by acquisition , methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) strains, and patient age (adults vs. children). Our results revealed high clonal diversity among SAB strains with up to 28 different CCs. The most prevalent CCs were CC5 (30.8%), CC30 (20.3%), CC45 (8.3%), CC8 (8.4%), CC15 (7.5%), and CC22 (5.9%), which together accounted for 80% of all cases. A higher proportion of CC5 was found among HA strains than CA strains . CC5 was associated with methicillin resistance , whereas CC30, CC45, and CC15 were correlated with MSSA strains (p < 0.001). Pathogen-related molecular markers significantly associated with a specific source of bacteremia included the presence of sea, undisrupted hlb and isaB genes with catheter-related bacteremia; sed, splE, and fib genes with endocarditis; undisrupted hlb with skin and soft tissue infections; and finally, CC5, msrA resistance gene and hla gene with osteoarticular source. Our study suggests an association between S. aureus genotype and place of acquisition, methicillin resistance and sources of bloodstream infection, and provides a valuable starting point for further research insights into intrinsic pathogenic mechanisms involved in the development of SAB. Staphylococcus aureus is an opportunistic pathogen that can potentially cause a wide range of infections. It is a leading cause of bacteremia and represents a significant global health problem is often associated with severe metastatic infections, such as infective endocarditis, septic arthritis and osteomyelitis and complications, such as sepsis and septic shock, which lead to adverse outcomes that are challenging to manage , catheter-related bacteremia (CRB) (N = 212), skin and soft tissue infections (SSTI) (N = 66), and bone and joint infections (N = 100). Eight of these collections corresponded to SAB infections in adults, and two in children (< 15 years of age). The percentage of MRSA strains included in each collection varied. The studies were approved by the ethics committee of the University Hospital 12 de Octubre . It was not considered necessary to obtain written informed consent because the participants were anonymized (IRH-ANT-2013-01).A total of 785 strains causing bacteremia with different source and 48 colonization strains collected over a period of 15 years 2002\u20132017) were analyzed. These strains were obtained from different sources in hospitals geographically distant from each other spread across the territory of Spain or community-acquired (CA). HA included both nosocomial cases with a positive blood culture obtained from patients who had been hospitalized for 48 h or longer . Automatic microdilution techniques were used for identification and susceptibility testing of isolates. Bacterial DNA was extracted using commercial extraction kits according to the manufacturer's recommendations. DNA microarrays .Categorical variables were compared using the chi-squared or Fisher's exact test, as appropriate. Significance levels of DNA microarray results were corrected using the Bonferroni correction for multiple tests. Pairwise comparisons of the main CCs, S. aureus strains causing bacteremia and 48 S. aureus colonizing strains were characterized in this study with the DNA microarray. Of a total of 187 genes included in the array, 67 genes were excluded from further analysis. Twenty one genes because they were found in almost all of the strains (>95%): sarA(99.5%), saeS(98.4%), vraS(99.7%), lukF(96.7%), hl(97.5%), hld(99.3%), sspA(99.8%), sspB(100%), sspP(99.8%), icaA(99.6%), icaC(98.4%), icaD(99.5%), clfA(99.6%), clfB(99.4%), ebpS(99.4%), eno(99.5%), fnbA(98.1%), map(97.6%), sdrC(99.3%) and isdA(99.6%); and 47 genes because they were absent from almost all of the strains (< 5%): ermA(4.7%), ermB(0.3%), lnuA(0.7%), mefA(0%), vatA(0%), vatB(0%), vgaA(2.6%), vgaB(0%), aacA-aphD(3.9%), dfrS1(2.5%), fusB(0%), fusC(0.8%), tetK(2.2%), tetM(2.1%), cat(0.8%), cfr(0.1%), fexA(0.2%), qacA(0.2%), qacC(2.2%), vanA(0%), vanB(0%), vanZ(0%), seb(3.6%), see(0%), seh(4.6%), sej(3.6%), sek(3.4%), seq(3.1%), ser(3.4%), pvl(1.8%), etA(2.5%), etB(0.8%), etD(3.1%), edinA(0.6%), edinB(3.3%), edinC(0.7%), ACME cluster(0.5%), arcA-SCC(0.2%), arcB-SCC(0.1%), arc-SCC(0.1%), arcD-SCC(3.6%), cap1(0.7%), and bap(0.1%). Nine additional genes were discarded due to an unacceptable number of missing values (>30%): mecC(55%), mecR(56.2%), merA(53.3%), merB(39.5%), fosBplasmid(62.8%), lukM(52.8%), lukY(51.3%), setC-selX(52.3%), setB3(51.5%), setB2(51.7%), setB1(52.6%), fnbB(51.3%), and sdrD(51.6%).A total of 785 agrII type was the most common (41.7%), followed by agrI (33.7%) and agrIII (22.2%).The main CCs detected in this study were: CC5 (30.8%), CC30 20.3%), CC45 (8.3%), CC8 (8.4%), CC15 (7.5%) and CC22 (5.9%). In addition, up to 22 minor CCs were also detected: CC398 (2.4%), CC121 (2.4%), CC25 (2.2%), CC9 (1.7%), CC97 (1.6%), CC6 (1.3%), CC1 (1.1%), CC7 (1.1%), CC188 (1.0%), CC101, CC10, CC49, CC59, CC509, CC20, CC12, CC75, CC96, CC395, CC522, CC707 and CC1021 compared to CA strains, which accounted for 31.6%. Healthcare-associated strains were assigned to 26 different CCs, with CC5 (35.6%) being the most common, followed by CC30 (18.6%). The CC diversity was slightly lower among CA strains, which were assigned to 23 CCs, with CC30 (23.4%) and CC5 (20.2%) being the ones most commonly found , agrII was associated with HA acquisition, .The distribution of N = 28) and showed a higher clonal diversity than MRSA strains. The major clones detected among MSSA strains were CC30 (26.5%), CC5 (14.5%), CC45 (10.5%) and CC15 (10.0%). A comparison of the two groups revealed that only CC5 was associated with methicillin resistance , whereas CC30, CC45 and CC15 were correlated with MSSA strains . By contrast, among the MSSA strains, all the CCs detected in our collection were represented , whereas, agrI was associated with MSSA strains , CC30 was significantly related to strains from the child population , while agrIII was associated with the child population .The distribution of S. aureus strains from healthy carriers was also added to the analysis in order to evaluate potential differences between colonizing and bacteremic strains.The main objective was to explore the distribution of CCs and virulence genes according to source of bacteremia. A collection of agrII predominated in SAB from osteoarticular infections . In addition, the undisrupted hlb gene mostly presented in CRB strains , there was significant detection of fib genes in SSTI sources. Finally, the isaB gene was more commonly found among CRB strains and in the SSTI bacteremia group adjusted for different sources of bacteremia and colonization was the majority clone among adults and CC30 (agrIII) among children.Several studies have suggested that while the S. aureus virulence genes, and various clinical syndromes which was significantly related to sources, such as CRB and SSTI. Different studies have demonstrated its contribution to SSTI inserts into the hlb gene sak-chip-scn and 87% (scn). Interestingly, the absence of the intact hlb gene was significantly associated with an osteoarticular source. This intriguing association should be investigated further since other studies have reported the association between these phage-integrated genes and less severe staphylococcal infections have reported up to 12 different variants of hla. In our study, the hla gene was detected in 92.2% of strains. We think that the low frequency of this gene observed in our collection may have been due to the DNA microarray technology, which may underestimate the presence of certain minority hla variants due to lack of sensitivity. Whole genome sequencing may be a more effective genotypic characterization approach for detecting different genetic variants that may not be detected by hybridization procedures, although previous studies have shown good agreement between the genotypic results obtained using a DNA array-based methodology and those using high-throughput sequencing precluded us from adjusting for these variables in multivariate analysis. Moreover, the proportion of colonization strains was small in comparison with the number of SAB strains. The results therefore should be interpreted with caution. At the same time, our study includes a large number of S. aureus genotype and acquisition, methicillin resistance and bloodstream infection sources. The results of this study reinforce the view that SAB continues to represent a major clinical challenge. Thus, a better understanding of S. aureus epidemiology and pathogenesis is crucial to the detection of prognostic biomarkers as well as to the development of potential therapeutic targets aimed at improving patient outcomes.In conclusion, the current study suggests a potential association between DP-M, EV, and FC conceived and designed the experiments. EV, CG-G, ERG, NL, NF-H, RS, and IM-G collected the isolates. Funding was obtained by FC and BA. Experiments were performed by EV, CG-G, and IM-G. The data were analyzed by EV and DP-M. EV and DP-M prepared the manuscript draft. All authors agreed to be accountable for all aspects of the work. EV, DP-M, and FC contributed in giving final approval of the version to be published. All authors reviewed and approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "The structure of compound 3-110-22 depicted in Figs S2 Fig(TIF)Click here for additional data file.S8 Fig(TIF)Click here for additional data file.S9 Fig(TIF)Click here for additional data file."} +{"text": "Flavonoids have been reported to exert antihyperglycemic effects and have potential to enhance the current therapy options against type 2 diabetes mellitus. However, the structure activity relationships (SAR) studies of flavonoids against this disease have not been thoroughly comprehended. Hence, in the present study, 14 structurally related flavonoids viz. wogonin, techtochrysin, norwogonin, isoscutellarein, hypolaetin, kaempferol, quercetin, methyl ether of wogonin, acetate of wogonin, acetate of norwogonin, 8-hydroxy-7-methoxyflavone, chrysin, (+)-catechin and (-)-epicatechin were taken into account for in vitro antidiabetic evaluation. Cell viability of RIN-5F pancreatic cells and 3T3-L1 pre-adipocyte cells was initially tested, then an insulin secretion assay of RIN-5F as well as adipogenesis and glucose uptake measurements of adipocyte were investigated. Subsequently, protein expressions study through adipokines measurement via enzyme-linked immunosorbent assay (ELISA) kit, Western blotting analysis against GLUT4 and C/EBP-\u03b1 as well as molecular docking against GLUT1 were analyzed. The results from cell culture antidiabetic assays , protein expressions and molecular docking pointed that the methoxy group at position C-8 is responsible for antidiabetic property of selected flavonoids via glucose uptake mechanism indicated by up regulation of GLUT4 and C/EBP-\u03b1 expressions. The mechanism could be enhanced by the addition of an acetate group at C-5 and C-7 of the flavone skeleton. Type 2 diabetes mellitus (T2DM) is a common disease responsible for significant morbidity and mortality around the world. According to the American Diabetes Association, this disease is one of the major metabolic disorders that continue to present a significant health problem worldwide and mostly associated with chronic disturbances in protein, carbohydrate and lipid metabolisms. It is a serious debilitating disease that has now reached an epidemic proportion and is on the rise at an alarming rate .Flavonoids are a class of plant secondary metabolites that have well categorized structure function relationships. They are abundantly found in vegetables, fruits, herbs, tea, cocoa, soy, red wine and other plant food and beverage products. Flavonoids are well reputed as antioxidants in nature, however, they also can act as an antihyperglycemic agent as has been demonstrated by several researchers ,7,8,9,10Although there are only a few studies on the structure activity relationship (SAR) analysis of flavonoids isolated from different medicinal plants as far as their antidiabetic potential is concerned ,9,14,16,\u00ae polyvinylidene difluoride (PVDF), non-fat dried milk were purchased from Bio-Rad, Santa Rosa, CA, USA. Primary antibodies were bought from ElabScience, Wuhan, China. Secondary antibody HRP-conjugated goat anti-rabbit immunoglobulin (Ig) was purchased from GeneTex, Irvine, CA, USA. Chemiluminescence, Chemi-Lumi One L and Tween-20 were bought from Nacalai-tesque, Kyoto, Japan.8-hydroxy-7-methoxyflavone, (+)-catechin, (-)-epicatechin, quercetin (control), ascorbic acid, trolox, ABTS+ radical, potassium persulphate, xanthine, xanthine oxidase, anhydrous potassium carbonate, anhydrous sodium sulphate, acetic anhydride, pyridine, 2,2-diphenyl-1-picrylhydrazyl (DPPH) were purchased from Sigma Aldrich (Singapore). 2,4,6-Tris (2-pyridyl)-s-triazine , iron (III) chloride hexahydrate and sodium acetate were purchased from Sigma-Aldrich . Rin-5F pancreatic cell line and 3T3-L1 preadipocyte cells were bought from ATCC, Manassas, VA, USA. 96 well plates, 24 well plates and RPMI-1640 media were bought from Gibco, . ELISA kits were bought from Cusabio Biotech Co., Ltd., Houston, TX, USA. An insulin secretion enzyme-linked immunosorbent assay (ELISA) kit was purchased from Elabscience, Wuhan, China. For Western blotting, 10% SDS TGX stain free\u2122 FastCast acrylamide gel kits, Immun-BlotTetracera indica using the method described by Alhassan et al. uptake in a dose-dependent manner, whereas, isoscutellarein (MN9), hypolaetin (MN10), kaempferol (MN11), quercetin (MN12), (+)-catechin (MN13), and (-)-epicatechin (MN14) did not follow the same trend of glucose uptake. This consistent trend has further validated the lipid droplet formation (adipogenesis) result.p < 0.05). However, (-)-epicatechin (MN14) showed the lowest reduction similar to positive control, rosiglitazone (10 \u03bcM), followed by techtochrysin (MN4), isoscutellarein (MN9), quercetin (M12), (+)-catechin (MN13), wogonin (MN1), 8-hydroxy-7-methoxyflavone (MN5), norwogonin (MN7), chrysin (MN6), hypolaetin (MN10), kaempferol (MN11), acetate of wogonin (MN3), acetate of norwogonin (MN8), and methyl ether of wogonin (MN2), respectively.p < 0.05). Hypolaetin (MN10), showed the highest concentration, followed by isoscutellarein (MN9), norwogonin (MN7), (-)-epicatechin (MN14), methyl ether of wogonin (MN2), wogonin (MN1), (+)-catechin (MN13), techtochrysin (MN4), quercetin (MN12), 8-hydroxy-7-methoxyflavone (MN5), acetate of wogonin (MN3) and chrysin (MN6), respectively.For adiponectin measurement, at 12 \u03bcg/mL, except for acetate of norwogonin (MN8) and kaempferol (MN11), result of the tested flavonoids showed statistically increased in adiponectin concentration (ng/mL) as compared to the non-treated group (p < 0.05). Quercetin (MN12) showed the lowest concentration of TNF-\u03b1, followed by (-)-epicatechin (MN14), norwogonin (MN7), kaempferol (MN11), (+)-catechin (MN13), wogonin (MN1), techtochrysin (MN4), chrysin (MN6), methyl ether of wogonin (MN2) and the least concentration was shown by the acetate of wogonin (MN3), respectively.For tumor necrosis factor, i.e., \u03b1 (TNF-\u03b1), at 12 \u03bcg/mL, except for acetate of norwogonin (MN8), the result of the tested flavonoids displayed statistically decreased in TNF-\u03b1 concentration (ng/mL) as compared to the non-treated group (p < 0.05). (-)-epicatechin (MN14) showed the lowest concentration, followed by kaempferol (MN11), hypolaetin (MN10), norwogonin (MN7), 8-hydroxy-7-methoxyflavone (MN5), methyl ether of wogonin (MN2), wogonin (MN1), isoscutellarein (MN9), chrysin (MN6), acetate of norwogonin (MN3), acetate of norwogonin (MN8), quercetin (MN12), and the least concentration was displayed by (+)-catechin (MN13), respectively.Subsequently, for retinol binding protein IV (RBP-IV), at 12 \u03bcg/mL, except for techtochrysin (MN4), result of the tested flavonoids exhibited statistically reduced in RBP-IV concentration (ng/mL) as compared to the non-treated group (p < 0.05). Techtochrysin (MN4) and 8-hydroxy-7-methoxyflavone (MN5) showed no significant difference with non-treated group, while the rest of the flavonoids showed slightly upregulation expression, however, these results were not significant as compared to non-treated group (p > 0.05). For the expression of C/EBP-\u03b1, 8-hydroxy-7-methoxyflavone (MN5) showed the highest expression, followed by norwogonin (MN7), acetate of norwogonin (MN8), methyl ether of wogonin (MN2), techtochrysin (MN4), wogonin (MN1), and chrysin (MN6) (p < 0.05). The rest of the flavonoids showed downregulation of C/EBP-\u03b1 expression (p > 0.05).Acetate of norwogonin (MN8) exhibiteGlucose is the most potent stimulator of insulin secretion and can achieve acute and long-term regulation of insulin . Neverthp < 0.05). Groups mentioned above exhibited increased in lipid droplet formation in a dose-dependent manner. On the other hand, it can be observed that isoscutellarein (MN9), hypolaetin (MN10), kaempferol (MN11), quercetin (MN12), (+)-catechin (MN13) and (-)-epicatechin (MN14) showed average lipid droplet formation, however not in a dose-dependent manner, as compared to other flavonoids groups. Adipocytes are involved in the development of insulin resistance, resulting from the dysfunction of insulin signalling pathway . Thus, iN-amino]-2-deoxyglucose (2-NDBG) is transported using the same glucose transporter (GLUT) as d-glucose uptake in a dose-dependent manner, whereas, isoscutellarein (MN9), hypolaetin (MN10), kaempferol (MN11), quercetin (MN12), (+)-catechin (MN13), and (-)-epicatechin (MN14) did not follow the same trend of glucose uptake. This consistent trend has further validated the lipid droplet formation (adipogenesis) result. Johnstan et al. [According to Shang et al. , glucose-glucose are influenced by the flow of uptake and release from the cells. Hence, the present study investigated the adipokines measurement upon the treatment of flavonoids to find the association between glucose uptake and adipokines secretion . For leptin measurement, at 12.5 \u03bcg/mL, the result of all groups of tested flavonoids showed statistically reduced leptin concentration (pg/mL) as compared to the non-treated group (p < 0.05). However, (-)-epicatechin (MN14) showed the lowest reduction similar to positive control, rosiglitazone (10 \u03bcM) that indicated that ketonic functional group at position C-4 in a flavonoid molecule is not essential in order to reduce the leptin concentration. This result was further followed by techtochrysin (MN4), isoscutellarein (MN9), quercetin (M12), (+)-catechin (MN13), wogonin (MN1), 8-hydroxy-7-methoxyflavone (MN5), norwogonin (MN7), chrysin (MN6), hypolaetin (MN10), kaempferol (MN11), acetate of wogonin (MN3), acetate of norwogonin (MN8), and methyl ether of wogonin (MN2), respectively, which indicated that the presence of acetate and methoxy groups slightly helped to reduce the leptin concentration.According to Dunmore and Brown , insulinp < 0.05) which suggested that acetate group is responsible for the inhibition of adiponectin secretion. Hypolaetin (MN10) showed the highest adiponection concentration, followed by isoscutellarein (MN9), norwogonin (MN7), (-)-epicatechin (MN14) that highlighted the role of hydroxyl groups especially in the B ring (catechol) of flavonoids. Methyl ether of wogonin (MN2), wogonin (MN1), (+)-catechin (MN13), techtochrysin (MN4), quercetin (MN12), 8-hydroxy-7-methoxyflavone (MN5), acetate of wogonin (MN3) and chrysin (MN6) showed moderate secretion of adiponectin.Adiponectin is an adipocyte-derived hormone that reverses insulin resistance associated with both lipoatrophy and obesity . For adip < 0.05) which revealed that the acetate group did not help the cells to suppress, whereas the hydroxyl group was able to contain TNF-\u03b1 production. Quercetin (MN12) showed the lowest concentration of TNF-\u03b1, followed by (-)-epicatechin (MN14), norwogonin (MN7), kaempferol (MN11), (+)-catechin (MN13) which revealed that the total number of hydroxyl groups and configuration are essential in suppressing TNF-\u03b1 in the molecules of flavonoids. Wogonin (MN1), techtochrysin (MN4), chrysin (MN6), methyl ether of wogonin (MN2) and acetate of wogonin (MN3) showed moderate TNF-\u03b1 suppression which clearly indicated that the methoxy group does not possess strong impact in order to facilitate the cell to go against this marker. Tumor necrosis factor \u03b1 (TNF-\u03b1) is a well-known marker associated with induction of obesity related to insulin resistance and dyslipidemia . Accordip < 0.05) except for techtochrysin (MN4). (-)-epicatechin (MN14) showed the lowest RBP-4 concentration, followed by kaempferol (MN11), hypolaetin (MN10), norwogonin (MN7), 8-hydroxy-7-methoxyflavone (MN5), methyl ether of wogonin (MN2), wogonin (MN1), isoscutellarein (MN9), chrysin (MN6), acetate of wogonin (MN3), acetate of norwogonin (MN8), quercetin (MN12), and the least concentration was displayed by (+)-catechin (MN13), respectively. These results further highlighted the essential features of the total number and configuration of hydroxyl groups in the flavonoids skeleton. Meanwhile, methoxy and acetate groups in the flavonoids molecules were also found to increase the effect of flavonoids against this adipokine.The liver and adipocytes secrete retinol-binding protein-4 (RBP-4) which affects systemic insulin sensitivity and glucose homeostasis . Studiesp < 0.05) which emphasized the importance of the methoxy group at C-8 and the acetate group at C-7 attached to the flavones that helped to trigger the GLUT4 expression. Techtochrysin (MN4) and 8-hydroxy-7-methoxyflavone (MN5) showed no significant difference with the non-treated group, while the rest of the flavonoids showed insignificant upregulated expression as compared to the non-treated group (p > 0.05). For the expression of C/EBP-\u03b1, 8-hydroxy-7-methoxyflavone (MN5) showed the highest expression, followed by norwogonin (MN7), acetate of norwogonin (MN8), methyl ether of wogonin (MN2), techtochrysin (MN4), wogonin (MN1), and chrysin (MN6) (p < 0.05). The rest of the flavonoids showed downregulation of C/EBP-\u03b1 expression (p > 0.05). The loss of synergism between GLUT 4 and C/EBP\u03b1 was observed and it can be suggested that GLUT4 and C/EBP-\u03b1 have a weak interaction between each other.Decrease in the translocation of GLUT-4 protein of the plasma membrane has been found to be the main cause of the insulin resistance . MoreoveGlucose transporter 1 (GLUT1) belongs to a family of homologous sugar transporters or cotransporters found in both prokaryotes and eukaryotes. It is a uniporter that transports glucose from the extra cellular membrane into cells . GLUT1 iMethyl ether of wogonin (MN2), acetate of wogonin (MN3) and techtochrysin (MN4) displayed binding interactions with the residues that interact with glucose in the active site, viz., Asn415, Trp412 and Trp418. Wogonin (MN1) displayed additional interaction with Gln288 and Gln 282 while flavone-5,7,8-triacetate showed hydrogen bonding with Gln288 and Gln 282, Pro385 and Glu380. The interactions of these flavonoid derivatives with Trp412 and Trp388 which was not observed in the case of glucose might have accounted for the agonist effect of these molecules towards the GLUT1 protein. Moreover, acetate of norwogonin (MN8) exhibited binding interactions similar to that of acetate of wogonin (MN3). Hydrogen bonding interactions with Asn411, Asn288, Trp388, Asn317, Pro385 and Glu380 were exhibited by acetate of norwogonin (MN8), whereas, norwogonin (MN7) formed hydrogen bonding interactions with fewer amino acids which include Asn288, Gln283, trp415 and Trp388. For kaempferol (MN11) ligand, hydrogen bonding interactions with Asn288, Gln282, Gln283, Asn411 and Gly408 were exhibited, however, for (-)-epicatechin (MN14), hydrogen bonding interactions with Asn288, Gln282, Asn411, Asn288, Gly408 and Ser30 were observed. Both compounds displayed hydrophobic interactions with Trp412. Both compounds also showed fewer similarities of bonding interaction with the co-crystallized ligand as compared with the bonding interactions of the other which explained the weak free-binding energy against the receptor. The flavonoids bind to the inner polar region of the active site. Unlike the inhibitors of GLUT1 such as cytochalasin B, which are bulky molecules that occupy the larger portion of the GLUT1 active site to exert their inhibitory effect, flavonoids are smaller molecules. This perhaps could indubitably explain why these flavonoids activated the glucose transport protein instead of exerting an inhibitory effect.criterion is a fundamental for the bioactivity of these polyphenolic compounds as shown in From SAR perspectives, results of cell culture, molecular and in silico assays have shown that the chemical Flavonoids are one of the most important groups of bioactive compounds among secondary metabolites. We have reported antidiabetic activities of some selected flavonoids from in vitro and in silico perspectives. The present study concludes that tested flavonoids have shown in vitro antidiabetic activities through improved insulin secretion, upregulatory activity of glucose uptake, regulating adipokines secretion, and activation of glucose transporter (GLUT4). The results of this study have further enabled us to understand the key pharmacophores of flavonoids via a SAR study and should be encouraged for further studies, which could ultimately lead to the development of nutritional products and semi-synthetic analogs that retain substantial antidiabetic capacities with minimal adverse effects."} +{"text": "Nilaparvata lugens St\u00e5l.) is a major pest of rice, Oryza sativa, in Asia. Host plant resistance has tremendous potential to reduce the damage caused to rice by the planthopper. However, the effectiveness of resistance genes varies spatially and temporally according to BPH virulence. Understanding patterns in BPH virulence against resistance genes is necessary to efficiently and sustainably deploy resistant rice varieties. To survey BPH virulence patterns, seven near-isogenic lines (NILs), each with a single BPH resistance gene and fifteen pyramided lines (PYLs) carrying multiple resistance genes were developed with the genetic background of the japonica rice variety, Taichung 65 (T65), and assessed for resistance levels against two BPH populations . Many of the NILs and PYLs were resistant against the Hadano-66 population but were less effective against the Koshi-2013 population. Among PYLs, BPH20+BPH32-PYL and BPH2+BPH3+BPH17-PYL granted relatively high BPH resistance against Koshi-2013. The NILs and PYLs developed in this research will be useful to monitor BPH virulence prior to deploying resistant rice varieties and improve rice\u2019s resistance to BPH in the context of regionally increasing levels of virulence.The brown planthopper (BPH: Nilaparvata lugens St\u00e5l.) is a major pest of rice (Oryza sativa L.) in tropical and subtropical Asia [The brown planthopper and six quantitative trait loci (QTLs) for BPH resistance have been identified on chromosome 4S [QBph4 (6.7\u20136.9 Mbp) from IR02W101 and QBph4.2 (6.6\u20136.9 Mbp) from IR65482-17 were identified at similar locations based on physical distance; QBPH4.1 (5.8\u20137.8 Mbp) and QBPH4.2 (15.2\u201317.2 Mbp) were identified from Rathu Heenati; qBph4.3 (0.2\u20130.7 Mbp) and qBph4.4 (0.7\u201313.1 Mbp) were detected in Salkathi. On chromosome 4L, five genes for BPH resistance\u2014BPH6, BPH12(t) from GSK185-2, BPH18(t) from BPH2183, BPH27 from GX2183 and BPH27(t) from Balamawee have been identified [BPH3, BPH4, BPH25, BPH32, Qbph6 and qBPH6(t) [BPH1, BPH2, BPH7, BPH9, BPH10 and BPH18 from IR65482-7-216-1-2, and BPH21 and BPH26 [BPH1, BPH10, BPH18 and BPH21; type 2\u2014BPH2 and BPH26; type 3\u2014BPH7; and type 4\u2014BPH9 [Oryza minuta carrying BPH20, BPH21 and qBPH6(t) [BPH3, BPH17, QBPH4.1 and QBPH4.2 [BPH2 and BPH32 [To date, more than 34 BPH resistance genes have been identified from rice cultivars and wild rice species. Seven genes: e levels ,11,12. Fe levels . Four geosome 4S ,20. Amonentified ,23,24,25qBPH6(t) ,29,30. End BPH26 ,36,37,38qBPH6(t) ; Rathu Hh4.4 0.7\u2013.1 Mbp wend BPH32 ,41.BPH1 and/or BPH2 genes after these were widely deployed in rice varieties across Asia [BPH1, BPH2, BPH5, BPH7, BPH8, BPH9, BPH10 and BPH18 genes [BPH1, BPH2, BPH3, BPH8, BPH9, BPH10 and BPH32 [Monogenic resistance is vulnerable to rapid adaptation by BPH populations. Research indicates that BPH populations have sufficient genetic variability to enable them to overcome specific resistance genes when selected on a resistant host over multiple generations ,42,43. Ioss Asia . A recen18 genes . Under lnd BPH32 ,47,48,49nd BPH32 . TherefoBPH3, BPH4, BPH6, BPH9, BPH10, BPH12, BPH14, BPH15, BPH17, BPH18, BPH20, BPH21, BPH25, BPH26, BPH30 and BPH32) have been developed on the genetic backgrounds of several indica and japonica-susceptible varieties. These NILs have been evaluated against different BPH populations from China, the Philippines and Japan [To prevent further adaptation by BPH populations to available resistance genes, a strategy for deploying resistance based on insect virulence is necessary . Howevernd Japan ,56,57,58BPH14 and BPH15 enhanced resistance against BPH from China compared to monogenic NILs with either BPH14 or BPH15 alone [BPH6 + BPH12 PYL and BPH3 + BPH27 PYL exhibited greater resistance levels in bulk seedling tests than monogenic lines with each of the genes present alone [BPH17 + BPH21 PYL had greater resistance against BPH in the Philippines than lines with either gene alone [BPH25 and BPH26 genes into a single rice line was reported to have positive epistatic effects against BPH populations collected in Vietnam, the Philippines and Japan [Because the resistance of rice varieties carrying single genes is weaker and less durable to BPH than varieties with multiple resistance genes, several researchers have proposed the pyramiding of two or more genes to enhance resistance levels and thereby avoid pest adaptation . Combina15 alone . Similarnt alone , and BPHne alone . Pyramidnd Japan ,61. TherBPH2, BPH3, BPH17, BPH20, BPH21, BPH32 and BPH17-ptb) and a japonica rice genetic background were developed to evaluate the effects of different resistance genes on BPH populations. Based on the NILs developed, 15 pyramided lines (PYLs) carrying two or three resistance genes were developed to enhance levels of resistance against BPH. Additionally, using the NILs and PYLs we developed, the study compared resistance against two BPH populations collected in Japan: the first was collected in 1966 (before resistant varieties were widely released) and the second was collected in 2013 (recently migrated from China to Japan). Comparisons of the reactions by BPH from each population to the NILs and PYLs indicates the utility of resistance genes and their different combinations (some with epistatic effects) against modern BPH populations. In this study, seven NILs with BPH resistance genes markers that were equally distributed across the whole genome . One substituted segment with a size of 21.3\u201325.4 Mbp encompassing BPH2 was detected between RM247 and RM5479 on chromosome 12. The other three segments were detected between RM5426 and RM248 on chromosome 7 with a size of 3.4\u20134.2 Mbp, between RM5688 and RM444 on chromosome 9 with a size of 4.2\u20139.2 Mbp and between RM7492 and RM216 on chromosome 10 with a size of 5.0\u201316.2 Mbp. Seven NILs with BPH resistance genes from three donor parents on the genetic background of Taichung 65 (T65) were developed through marker-assisted selection (MAS) and backcrossing . For thr Heenati . Thus, we genome . The genBPH3-NIL was confirmed using 195 polymorphic SSR markers, and the ratio of substituted segment from Rathu Heenati was 1.0\u20133.0% . One segment with a size of 1.6\u20131.8 Mbp including BPH3 was detected between MSSR1 and RM1369 on the short arm of chromosome 6. The other substituted segments were detected between RM1359 and RM1155 on chromosome 4 with a size of 0.5\u20134.2 Mbp and between RM1345 and RM3155 on chromosome 8 with a size of 1.8\u20134.9 Mbp. The genetic background of BPH17-NIL was surveyed using 173 polymorphic SSR markers. The ratio of substituted segments was 1.0\u20134.8% containing one segment located between RM8213 and B40 on chromosome 4, including the BPH17 region. The genetic background of BPH17-ptb-NIL was analyzed using 229 polymorphic SSR markers, and the ratio of substituted segments from PTB33 on BPH17-ptb-NIL was 2.8\u20137.6% . One substituted segment with 5.8\u201313.1 Mbp encompassing BPH17-ptb was detected between C61009 and B40 on chromosome 4. Two other substituted segments were detected at RM3126 on chromosome 3 and between RM7048 and RM6971 on chromosome 9 (4.7\u201311.5 Mbp). The genetic background of BPH20-NIL was confirmed using 237 polymorphic SSR markers and the ratio of substituted segments of IR71033-121-15 was 5.6\u20139.6% . One segment with a size of 13.8\u201319.9 Mb containing BPH20 was detected between RM335 and RM5900 on chromosome 4. Two other substituted segments were detected between RM224 and RM5926 on chromosome 11 (1.5\u20137.7 Mbp) and between RM7315 and RM3103 on chromosome 12 (5.3\u20137.9 Mbp). The genetic background of BPH21-NIL was surveyed using 229 polymorphic SSR markers, and the ratio of substituted segments from IR71033-121-15 was 7.1\u201311.6% . One segment with a size of 22.6\u201323.7 Mbp, including BPH21, was detected between RM1880 and RM28493 on chromosome 12. Three other segments were detected between RM6841 and RM3348 on chromosome 5 (2.3\u20137.2 Mbp), around RM1328 on chromosome 9 and between RM224 and RM5926 on chromosome 11 (1.5\u20137.7 Mbp). The genetic background of BPH32-NIL was confirmed using 233 polymorphic SSR markers. The ratio of substituted segments of PTB33 on BPH32-NIL was 1.9\u20134.1% . One segment with a size of 1.6\u20133.2 Mbp containing BPH32 was detected between RM6775 and RM190 on chromosome 6. Three other segments from the donor parent were detected between RM5755 and RM3280 on chromosome 3 with a size of 4.9\u20138.1 Mbp, between RM1306 and RM248 on chromosome 7 with a size of 0.4\u20133.2 Mbp and between RM5349 and RM5961 on chromosome 11 with a size of 0.2\u20130.6 Mbp. The genetic background of 4F3 equivalent generation, except BPH3 + BPH17-PYL from the BC4F4 equivalent generation, BPH20+BPH21-PYL from the BC3F8 generation and BPH32 + BPH17-ptb-PYL from the BC3F8 generation.Twelve PYLs carrying two BPH resistance genes and three PYLs containing three BPH resistance genes were developed using NILs and PYLs with BPH resistance gene(s) . The PYLBPH2-NIL (DS: 3.0) and BPH17-NIL (3.2) showed the highest resistance levels. The other NILs BPH3-NIL (6.0), BPH20-NIL (6.0), BPH21-NIL (6.5), BPH25-NIL (6.7), BPH26-NIL (4.8), BPH32-NIL (6.7) and BPH17-ptb-NIL (5.7), had lower DSs than T65\u2019s but were not significantly different from the T65. Damage scores across the 15 PYLs ranged from 2.3 to 6.0. Among PYLs, the DSs of 10 PYLs\u2014BPH2 + BPH17-PYL (2.7), BPH2 + BPH25-PYL (2.5), BPH2 + BPH32-PYL (3.0), BPH2 + BPH17-ptb-PYL (3.0), BPH17 + BPH21-PYL (2.3), BPH20 + BPH21-PYL (2.3), BPH21 + BPH25-PYL (3.3), BPH21 + BPH17-ptb-PYL (2.7), BPH2 + BPH3 + BPH17-PYL (3.0) and BPH20 + BPH21 + BPH32-PYL (2.3), were equal to or less than 3.3, while the DSs of five PYLs\u2014BPH3 + BPH17-PYL (5.0), BPH20 + BPH32-PYL (5.3), BPH25 + BPH17-ptb-PYL (6.0), BPH32 + BPH17-ptb (5.0) and BPH2 + BPH32 + BPH17-ptb-PYL (4.3), were more than 4.3. Although the DSs between NILs and PYLs were not significantly different, the resistance levels of the PYLs tended to be higher than those of the NILs.T65 was highly damaged (damage score (DS) = 8.2) by the Hadano-66 population A. The DSBPH17-NIL (58.7%) had the lowest FBRR and was significantly different from T65. The other NILs, BPH2-NIL (68.6%), BPH3-NIL (82.4%), BPH20-NIL (77.3%), BPH21-NIL (84.3%), BPH25-NIL (85.3%), BPH26-NIL (73.8%), BPH32-NIL (86.7%) and BPH17-ptb-NIL (77.6%), had lower FBRRs than T65; however, the differences were not significant. The FBRRs of four PYLs\u2014BPH2 + BPH32-PYL (59.1%), BPH2 + BPH17-ptb-PYL (56.7%), BPH21 + BPH17-ptb-PYL (50.1%) and BPH2 + BPH3 + BPH17-PYL (57.6%), were less than 60%. The FBRRs of five PYLs\u2014BPH2 + BPH17-PYL (64.5%), BPH2 + BPH25-PYL (68.4%), BPH20 + BPH21-PYL (62.3%), BPH2 + BPH32 + BPH17-ptb-PYL (64.0%) and BPH20 + BPH21 + BPH32-PYL (63.2%), ranged from 60% to 70%; and the FBRRs of six PYLs\u2014BPH3 + BPH17-PYL (79.3%), BPH17 + BPH21-PYL (70.9%), BPH20 + BPH32-PYL (71.6%), BPH21 + BPH25-PYL (70.3%), BPH25 + BPH17-ptb-PYL (78.9%) and BPH32 + BPH17-ptb-PYL (74.4%), ranged from 70% to 80%. Additionally, DSs and FBRRs were positively correlated . Additionally, fresh biomass reduction rates (FBRRs) of the NILs and PYLs were calculated as an indicator of resistance B. T65 haBPH2-NIL and BPH17-NIL had the highest ADM rates, 68.9% and 59.0%, respectively. The ADM rates of other NILs were not significantly different from that of T65. The PYLs carrying the BPH2\u2014BPH2 + BPH17-PYL (75.0%), BPH2 + BPH25-PYL (87.5%), BPH2 + BPH32-PYL (84.0%) and BPH2 + BPH17-ptb-PYL (84.0%), showed the highest ADM rates among PYLs with two genes and were higher than any of the corresponding NILs. The ADM rates of seven PYLs\u2014BPH3 + BPH17-PYL, BPH17 + BPH21-PYL, BPH20 + BPH32-PYL, BPH21 + BPH25-PYL, BPH21 + BPH17-ptb-PYL, BPH25 + BPH17-ptb-PYL and BPH32 + BPH17-ptb-PYL, ranged from 50.0% to 68.0%, while the ADM of BPH20 + BPH21-PYL was 33.3%. The ADM rates of PYLs for three genes\u2014BPH2 + BPH3 + BPH17-PYL (96.0%), BPH2 + BPH32 + BPH17-ptb-PYL (95.8%) and BPH20 + BPH21 + BPH32-PYL (92.0%), were higher than those of the corresponding NILs and PYLs for two genes, and were similar to the ADM rates of the donor parents (100%). Furthermore, the ADM rates were negatively correlated with the DSs and FBRRs .Levels of adult mortality (ADM) of the donor parents IR71033-121-15, PTB33 and Rathu Heenati (100%) were significantly higher than that of T65 (17.6%) . Among tBPH2 + BPH17-PYL (32.0%), BPH20 + BPH32-PYL (36.0%) and BPH2 + BPH3 + BPH17-PYL (36.0%) were highest. The ADM rates of the six PYLs, BPH3 + BPH17-PYL, BPH20 + BPH21-PYL, BPH21 + BPH25-PYL, BPH32 + BPH17-ptb-PYL, BPH2 + BPH32 + BPH17-ptb-PYL and BPH20 + BPH21 + BPH32-PYL ranged from 20% to 28%. The ADM rates of the other PYLs, BPH2 + BPH32-PYL, BPH2 + BPH17-ptb-PYL, BPH17 + BPH21-PYL, BPH25 + BPH17-ptb-PYL, BPH2 + BPH25-PYL and BPH21 + BPH17-ptb-PYL ranged from 8.0% to 16.0%.T65 was susceptible to the Koshi-2013 population with an ADM of 5.0%. Rathu Heenati had the highest ADM among entries (84.0%), which was significantly higher than T65. The ADM rates of the other donor parents, IR71033-121-15 (44.0%) and PTB33 (36.0%), were lower than that of Rathu Heenati. The ADM rates of the NILs were less than or equal to 20.0%. Among the PYLs, the ADM rates of BPH2-NIL had longer culms, BPH25-NIL had shorter panicles and BPH3-NIL had wider flag leaves. The PLs, CLs, LLs and LWs were not significantly different between the PYLs and T65, except that BPH2 + BPH17-PYL, BPH2 + BPH25-PYL, BPH2 + BPH32-PYL, BPH2 + BPH17-ptb-PYL, BPH21 + BPH25-PYL and BPH2 + BPH3 + BPH17-PYL had longer culms; BPH21 + BPH25-PYL had longer flag leaves; BPH2 + BPH32-PYL, BPH17 + BPH21-PYL and BPH20 + BPH32-PYL had narrower flag leaves; and BPH3 + BPH17-PYL had wider flag leaves. Six agronomic traits\u2014days to heading (DTH), panicle length (PL), culm length (CL), flag leaf length (LL), flag leaf width (LW) and panicle number per plant (PN) of the NILs and PYLs are presented in BPH17-NIL, BPH20-NIL and BPH17-ptb-NIL), on the short arm of chromosome 6 (BPH3-NIL and BPH32-NIL) and on the long arm of chromosome 12 (BPH2-NIL and BPH21-NIL). One of the resistance genes on chromosome 12, BPH2, was originally identified from ASD7 which was used as a donor parent for many modern resistant varieties [BPH2 from ASD7 is identical to BPH26 in DNA sequence and resistance level [BPH2 from ASD7 was resistant against the Hatano-66 population (synonym of Hadano-66) but susceptible to Nishigoshi-05, a BPH population collected in Koshi, Kumamoto Prefecture in 2005 [BPH2 and BPH3 using conventional genetic analysis [BPH2 from PTB33. In our study, BPH2-NIL had similar resistance patterns to BPH2 in ASD7: BPH2-NIL was highly resistant (ADM of 68.9%) against the Hadano-66 population but less effective (ADM of 4.0%) against the recently collected population, Koshi-2013. Moreover, BPH2-NIL (PTB33) and BPH26-NIL had similar resistance levels against both Hadano-66 and Koshi-2013, suggesting that PTB33, ADR52 and ASD7 might harbor the same resistance gene. Further sequence analysis for BPH2 from PTB33 is necessary to understand its genetic basis. Another gene on chromosome 12, BPH21, was originally identified from IR71033-121-15, an introgression line derived from O. minuta and estimated to be located between two markers, S12094A and B122, on the long arm of chromosome 12 [BPH21 has been reported to be allelic to BPH26 [BPH18 [BPH18 and BPH26 were isolated and located at 22.9 Mbp on chromosome 12 [BPH21 was around 22.9 Mbp on chromosome 12, and the region carrying BPH21 from IR71033-121-15 was selected using RM1246 (19.2 Mbp) and RM28493 (23.3 Mbp) in this study.The seven NILs we developed carried BPH resistance genes on the short arm of chromosome 4 (d so on) ,67. BPH2ce level . BPH2 fr in 2005 . PTB33 w in 2005 that weranalysis . Howevert ADM of .9% againBPH17 locus on chromosome 4S from Rathu Heenati has been reported by Sun et al. (2005) [BPH17 was mapped between two markers, RHD9 (6.2 Mbp) and RHC10 (7.0 Mbp), on chromosome 4S and isolated by Liu et al. (2014) [BPH17 from Rathu Heenati were the same as those of BPH17-ptb from PTB33 [BPH17-NIL and BPH17-ptb-NIL against the Hadano-66 population differed; however, both NILs had similar effects on the Koshi-2013 population. The different resistant levels might be because the loci were derived from different accessions or varieties of rice. Therefore, the amino acid sequences of PTB33 and Rathu Heenati used in this study on the BPH17 locus should be determined for future research. Additionally, BPH20 was detected between two markers, B42 (8.7 Mbp) and B44 (8.9 Mbp) on chromosome 4 [BPH17 and BPH20 on the genetic background of 9311 varieties developed by Xiao et al (2016) [BPH17 and BPH20 were different in both MSST and antibiosis tests against the Hadano-66 population and against the Koshi-2013 population, which corresponds well with previous research by Xiao et al. (2016) [BPH17, BPH17-ptb and BPH20.The . (2005) . BPH17 w. (2014) . The amiom PTB33 . In thisl (2016) showed dl (2016) . In our . (2016) . TherefoO. sativa and its wild relatives [BPH3 and BPH32 have been widely introduced to elite rice cultivars to improve BPH resistance and were related to durable and broad-spectrum resistance in PTB33 and Rathu Heenati [BPH3 was mapped onto chromosome 6 between two markers, RM19291 (1.2 Mbp) and RM8072 (1.4 Mbp) [BPH32 from PTB33 was identified at the same location as BPH3 from Rathu Heenati, but the amino acid sequence of BPH3 was not identical to that of BPH32 [BPH3-NIL were slightly different from those of the BPH32-NIL, suggesting that BPH3 might be different from BPH32. A comparison of amino acid sequences between BPH3 and BPH32 would be necessary to confirm whether these resistance genes are different.Among six genes/QTLs that have been identified on the short arm of chromosome 6 of elatives ,12, BPH3 Heenati ,69. In pBPH3-NIL, BPH17-NIL, BPH17-ptb-NIL and BPH32-NIL had around 97.0% of their chromosomal segments from the recurrent parent. This proportion coincides with the theoretical ratio for substituting chromosomal segments from recurrent parents by backcrossing four times. The other NILs had fewer chromosomal segments from T65 than the theoretical rate. The substituted chromosomal segments from the donor parents might be related to undesirable traits such as the suppression of the associated BPH resistance gene. Additionally, due to the low density of available polymorphic SSR markers between T65 and donor DNA around the target genes, the BPH resistance genes on the NILs were selected using two flanking markers that were relatively far apart. Furthermore, BPH17, BPH20 and BPH17-ptb on the NILs were selected by flanking markers with longer intervals because of the low density of polymorphic markers between donor parents and T65 around the chromosome 4S region. The intervals between each of the flanking marker pairs for BPH17 and BPH17-ptb were 3.7 Mbp, and that for BPH20 was 5.7 Mbp. Similarly, the interval for each of the two flanking markers for BPH2 and BPH21 on chromosome 12 was 4.1 Mbp because the exact locations of genes had not been identified before we started to develop the NILs by MAS. Therefore, many of the NILs had relatively long chromosome segments derived from the donor parents and there is a possibility that the remaining chromosomal segments from donor DNA around the target genes included linkage drag associated with susceptibility. In further research, ensuring that flanking markers are tightly linked to target genes will avoid linkage drag from donors through MAS and backcrossing.Among the developed NILs, the BPH2 + BPH32-PYL (84.0%) and BPH2 + BPH32 + BPH17-ptb-PYL (95.8%) had higher resistance levels than those of the BPH2-NIL (68.9%), BPH32-PYL (14.0%) and BPH17-ptb-PYL (22.0%) in antibiosis tests against the Hadano-66 population. The ADM rates of BPH2 + BPH17-PYL (32.0%) and BPH2 + BPH3 + BPH17-PYL (36.0%) were higher than those of BPH2-NIL (4.0%), BPH3-NIL (0%) and BPH17-NIL (20.0%) against the Koshi-2013 population. Additionally, the FBRR of BPH2 + BPH17 (42.3%) was lower than for BPH2-NIL (67.6%) and BPH17-NIL (58.8%). However, the effectiveness of the PYLs was not consistently higher than that of the corresponding NILs. The effect of PYLs was influenced by specific interactions between gene loci, the specific BPH populations and the screening methods. For example, the resistance levels of BPH3 + BPH17-PYL (50.0%) and BPH17 + BPH21-PYL (58.3%) were not higher than that of BPH17-NIL (59.0%) in antibiosis tests (or ADM rates) against the Hadano-66 population. BPH2 + BPH25-PYL (87.5%) showed higher ADM against the Hadano-66 population in comparison to BPH2-NIL (68.9%) and BPH25-NIL (16.0%), while the ADM rate of BPH2 + BPH25-PYL (12.0%) was lower than that of BPH25-NIL (16.0%) against the Koshi-2013 population. A similar tendency has been reported for gene combinations between BPH1 and BPH2 [BPH18 and BPH32; BPH20 and BPH32; and BPH2, BPH18 and BPH32 [An improvement of rice resistance levels against BPH is necessary since many genes have become less effective against BPH across Asia . In thisand BPH2 ; BPH18 and BPH32 . That thBPH1), ASD7 (BPH2), Rathu Heenai (BPH3 and BPH17), Babawee (BPH4), Chin Saba (BPH8), Balamawee (BPH9) and two NILs, BPH25-NIL and BPH26-NIL [BPH20 + BPH32-PYL and BPH2 + BPH3 + BPH17-PYL, had relatively high resistance, suggesting that PYLs with combinations of these genes are likely to provide good resistance against the current BPH populations that arrive to Japan (Koshi-2013). Finding new sources of resistance genes will be necessary to further improve resistance against contemporary BPH populations as they gain virulence.In a previous study, virulence of a BPH population collected during 2005 in Japan had increased compared with the virulence of a population collected in 1966 . ThroughPH26-NIL ,71. In tQBPH4.1 (5.8-7.8 Mbp) and QBPH4.2 (15.2-17.2 Mbp) on chromosome 4S rather than BPH3 and BPH17 [QBPH4.1 and QBPH4.2 should be developed and evaluated in further analyses. On the other hand, the lower resistance levels of the NILs and PYLs might be related to the relatively high ratio of substituted chromosomal segments from donors in the NILs (from 3.8 to 55.0 Mbp) and PYLs. There is a possibility that the retained donor chromosomal segments in the genetic background of the NILs and PYLs might be linked to the suppression of BPH resistance. To gain further knowledge of BPH resistance controlled by multiple genes, it will be essential to reduce the donor parent chromosomal segments on the NILs and PYLs by further backcrossing and MAS.In comparison to the corresponding NILs and PYLs, the resistance levels of PTB33, Rathu Heenati and IR71033-121-15 were higher. This suggests that PTB33, Rathu Heenati and IR71033-121-15 might also contain other BPH resistance gene(s). The other genetic factor(s) for BPH resistance can be revealed by analyzing the segregating populations derived from crosses between the developed PYLs and their donor parents in future studies. Additionally, Rathu Heenati had nd BPH17 . Therefojaponica rice variety, T65, that is susceptible to BPH, was used as a recurrent parent, and three rice varieties resistant to BPH were donor parents. The donor lines were IR71033-121-15, PTB33 and Rathu Heenati. IR71033-121-15 contains two BPH resistance genes, BPH20 and BPH21, from the wild rice species O. minuta (Accession number: IRGC101141) [BPH2, BPH17-ptb and BPH32. Rathu Heenati (Acc. no. IRGC 11730), that originated from Sri Lanka, carries BPH3 and BPH17 [1 plants were backcrossed four times with T65 to generate BC4F1 plants . PTB33 , 0.25 \u03bcM of primer and 4 \u03bcL of 20 times-diluted DNA. Each PCR amplification included one cycle at 96 \u00b0C for 5 min, 35 cycles at 96 \u00b0C for 30 s, 55 \u00b0C for 30 s and 72 \u00b0C for 30 s, followed by one extension cycle at 25 \u00b0C for 1 min. PCR products were analyzed by electrophoresis at 200 V using 4% agarose gel with 0.5 \u03bcg/mL ethidium bromide in 0.5X TBE buffer for 1 h and photographed under ultraviolet light. During MAS for resistance genes on chromosome 4S, the plants with BPH17 and BPH17-ptb, were selected using two markers, RM8213 and MS10, and the plants with BPH20 were selected using MS10 and RM5900 using GGT software version 2.0 [In the genetic background survey of the NILs, the bulk DNA from five plants was used. A total of 384 SSR markers distributed on 12 rice chromosomes were used during polymorphism tests with T65 and the donor parents . Among tsion 2.0 .japonica rice variety, Reiho, at 25 \u00b0C with 16 h/8 h of light/dark at Kyushu Okinawa Agricultural Research Center of the National Agriculture and Food Research Organization in Japan. Two BPH populations from Japan (Hadano-66 and Koshi-2013) were used to evaluate the NILs and PYLs for their resistance. Hadano-66 was collected in Hadano City, Kanagawa Prefecture, Japan in 1966 , and KosTo evaluate resistance, an adaptation of the modified seedbox screening test (MSST) ,74 was aAntibiosis tests were conducted at 25 \u00b0C following the method described by Myint et al. (2009) . Five plThe NILs and PYLs were grown in a paddy field at Saga University in 2018 and characterized for their agronomic traits compared to those of T65. Seedlings were transplanted at 28 DAS as one plant per hill, with 20 cm between hills and 25 cm between rows. Each entry was planted as at least three rows (12 plants per a row). Six agronomic traits: DTH, CL, PL, LL, LW and PN were measured for five plants in the same row. DTH was the days from sowing until 50% of panicles flowered. CL was measured from the soil surface to the panicle neck. PL is the length from tip to panicle neck of the longest panicle. The flag leaf width and length were measured from the largest and longest flag leaf of each sampled plant. Panicle number is the number of reproductive panicles of each plant at maturity.Mean values of BPH resistance for the NILs and PYLs and agronomic traits were compared using one-way ANOVA. Dunnett\u2019s test and Tukey Kramer\u2019s test were conducted for multiple comparisons of BPH resistance and agronomic traits, respectively, using R software version 3.5.2."} +{"text": "The Risky Family Model postulates that adverse childhood experiences (ACE) are likely to be encountered across generations within custodial grandfamilies which, in turn, may adversely impact their overall well-being. The present study is a pioneering attempt to examine the patterns of ACEs self-reported by custodial grandmothers (CGM) and adolescent grandchildren (AGC) from the same families, and how their total ACE scores correlate with key physical and mental health outcomes. A total of 129 CGM-ACG dyads recruited for a nationwide RCT study completed separately at baseline the 10-item ACE-CDC and 4 items from the ACE-IQ, as well as various standardized measures of physical and emotional well-being. The most frequent ACEs reported by AGC were loss of a parent (60.5%), verbal abuse (58.1%), bullying by peers (46.5%), and living with someone jailed (45.0%). The predominant ACEs for CGM were bullying by peers (48.8%), verbal abuse (48.1%), living with a mentally ill person (34.1%), being touched sexually (29.5%), and loss of parent (29.5%). Only 10.1% of ACG and 15.5% of CGM reported 0 ACEs, whereas 65.1 % of ACG and 59% of CGM reported > 3 ACEs. For ACG, total ACE scores correlated significantly with externalizing (r=.32) and internalizing (r=.30) difficulties, self-esteem (r= -.28), loneliness (r=.27), school problems (r=.24), and physical health (r= -.26). For CGMs, anxiety (r=.23) and depression (r=.19) only were correlated significantly with total ACEs. We conclude that although both CGM and ACG reported alarmingly high levels of ACEs, different patterns and correlates exist between the generations. [Funded by R01AG054571]"} +{"text": "Staphylococcus aureus (MRSA) is reported as one of the important bacterial causes of burn wound infections. This study was carried out to investigate molecular characterization of community-associated MRSA (CA-MRSA) isolated from Iranian burn patients. Methicillin-resistant S. aureus were collected from the Motahari Burns Hospital in 2016. All isolates were collected from outpatients and inpatients within 48 hours of admission. The mecA, pvl, tsst-1, hla-\u03b1, and psm\u03b1 genes detecting, SCCmec, agr and PFGE typing were done.A total of 31 isolates of mecA-positive, which were considered as MRSA. The SCCmec typing MRSA strains revealed type II in 1 (7.7%), type III in 9 (69.2%), and other types in 3 isolates (23.7%) cases. The agr typing of all 31 isolates showed that 14 (45.2%), 1 (3.2%), 6 (19.4%), and 10 (32.3%) strains belonged to agr groups 1, 3, 4, and unknown type, respectively. The pvl, tsst-1, hla-\u03b1, and psm\u03b1 genes were positive in 3 (9.7%), 4 (12.9%), 21 (67.7%), and 31 (100%) isolates, respectively. Considering the cut-off values of \u226550%, 3 groups of related isolates in PFGE study were observed.A total of 13 (41.9%) isolates were cefoxitin-resistant and The MRSA strains of this study were initially isolated as Community-associated S. aureus (CA-MRSA); however molecular characterization showed that a significant proportion of them had hospital-associated MRSA (HA-MRSA) features. Therefore, it is likely that the HA-MRSA strains are spread among the community. Due to the skin damaged and weakened innate immunity, burn patients become susceptible to various infections , 2, amonStaphylococcus aureus is one of the most common bacteria isolated from burn infections (S. aureus (MRSA) including hospital-associated MRSA (HA-MRSA) (fections . MethiciHA-MRSA) , 6 and cHA-MRSA) are repoHA-MRSA) -10.mecA regulatory system and is used for screening MRSA strains (mec (SCCmec) element of MRSA strains carry mecA gene that mediates resistance to methicillin system, panton-valentine leukocidin (pvl), toxic shock syndrome toxin (tsst), \u03b1-hemolysin (hla), and alpha-type phenol soluble modulins (psm\u03b1). These virulence factors can make extensive infection and severe damage in the time period of May to October 2016. All isolates were collected from outpatients and inpatients within 48 hours of admission. Bacterial morphology study and biochemical tests including catalase, tube and slide coagulase, DNase, and mannitol-fermenting were done to identify S. aureus. After identification, all strains were preserved in trypticase soy broth medium containing 15% glycerol at -70\u00b0C.A total of 31 isolates of Antimicrobial Susceptibility TestingS. aureus ATCC 25923 was used as a control strain.Antimicrobial susceptibility testing was done by disk diffusion method according to the clinical and laboratory standards institute (CLSI) 2015 guidelines. Antibiotic discs containing cefoxitin (30 \u03bcg), gentamicin (10 \u03bcg), erythromycin (15 \u03bcg), tetracycline (30 \u03bcg), rifampin (5 \u03bcg), clindamycin (2 \u03bcg), ciprofloxacin (5 \u03bcg), trimethoprim-sulfamethoxazole (1.25/23.75 \u03bcg), and linezolid (30 \u03bcg) (MAST UK) were used. Molecular Detection and TypingDNA ExtractionFour to five fresh colonies of bacteria were suspended in 400 \u03bcL of lysis solution buffer containing lysostaphin (200\u03bcg/mL) . Then, DNA was extracted by phenol/chloroform /isoamyl alcohol (Merck Co).PCR AmplificationmecA was used as target gene for the detection of MRSA strains , buffer , deionized distilled water, and DNA template were used for PCR amplification. The PCR amplification performed in thermo cycler (BIO RAD T100) by following annealing temperatures: mecA; 55\u00b0C, SCCmec typing; 60\u00b0C, agr typing; 50\u00b0C, and virulence genes typing; 50\u00b0C for pvl and hla-\u03b1, and 51\u00b0C for tsst-1 genes. The final volume of 25 mL PCR reaction mixture containing reverse and forward primer (10 pmol) , DNA taq polymerase enzyme (1.5 units), dNTPs (0.02 mM), MgClPulsed-field Gel Electrophoresis (PFGE)SmaI restriction enzyme (Takara) digestion was carried out using the PulseNet standard protocol on 13 SCCmec-positive S. aureus strains . After optimizing conditions, PFGE was run on CHEF MAPPERXA (BIO RAD) device as follows: initial switch 5 s, final switch 40 s, run time 21 h, voltage 200 (6v/cm). 1% agarose gel (intron biotechnology) in TBE 0.5 X was used for electrophoresis. According to the PulseNet protocol, Salmonella enterica serotype Braenderup (H9812) was used as a control. After gel staining with ethidium bromide (10 mg/mL), imaging was performed by UV light gel documentation system . GelCompar II version 6.6.11 software was used for drawing dendrogram graph and interpretation of results. Cut-off values of \u226550% were considered to define clusters.PFGE analysis based on PatientsS. aureus isolates were investigated in this study. All isolates were collected from burn patients within 48 hours of admission. 20 (64.5%) of these patients were inpatients and 11 (35.5%) outpatients.A total of 31 non-duplicate Antimicrobial Susceptibility TestingAntibiotic susceptibility test results revealed that a total of 13 (41.9%) isolates were resistant to cefoxitin, which were considered as MRSA. All isolates were susceptible to Linezolid. The resistance rates of other antibiotics were as follows: erythromycin 15 (48.4%), tetracycline 11 (35.5%), ciprofloxacin 11 (35.5%), gentamicin 10 (32.3%), clindamycin 9 (29.0%), rifampin 6 (19.4%), and trimethoprim-sulfamethoxazole 4 (12.9%) . Molecular Detection and TypingmecA-positive , type III in 9 (69.2%), and other types in 3 isolates (23.1%) (Molecular studies showed that 13 (41.9%) isolates were positive . The SCC (23.1%) . agr typing of all 31 isolates showed that 14 (45.1%), 1 (3.2%), 6 (19.4%), and 10 (32.3%) strains belonged to agr groups 1, 3, 4, and unknown type, respectively , 4 (12.9%), 21 (67.7%), and 31 (100%), respectively.The All 13 MRSA isolates were studied by PFGE. Considering the cut-off values of \u226550%, 3 groups of isolates were observed in this study: cluster A1; 3 pulse types, cluster B1; 3 pulse types and cluster C1; 2 pulse types .S. aureus is one of the common causes of burn wound infections compared to 58.2% , and 90.mec typing of 13 MRSA strains showed that 9 (69.2%) strains belonged to SCCmec III, that's almost is consistent with some studies in Iran; 56.8% of MRSA strains in this study and 75.5% in Goudarzi\u2019s study compared to 84.9% in Iran (agr type 3 (3.2%) compared to 15.1% in Iran (The in Iran and 96.5 in Iran . In thistsst-1 gene detection showed that 12.9% of the isolates in this study belonged to MSSA strains, but this gene was not seen in MRSA strains. In contrast to this study, in a different study in Iran 18.9% of MRSA isolates were tsst-positive which were distributed among SCCmec type III (The type III .hla-positive compared to another study in Iran which reported 51.8% (In the present study, 67.7% strains were ed 51.8% . Data anOur results showed that 41.9% of isolates were MRSA, which indicates the presence of antibiotic resistance elements in a significant number of strains and necessity of performing antibiogram before starting treatment. Furthermore, the MRSA strains of this study were initially isolated as CA-MRSA, however molecular characterization showed that a significant proportion of them had HA-MRSA features. Therefore, it is likely that the HA-MRSA strains are spread among the community. Finally, the investigation of virulence factors in this study showed the presence of various toxin genes in isolates that can enhance their ecological niche ability and also make treatment more complicated, especially in burn patients."} +{"text": "Simple and mild reaction conditions, the use of a cheap catalyst and easy workup and isolation are notable features of this method. MS (EI) m/z (relative intensity) 374 , 359 (100), 319 (23), 263 (7)."} +{"text": "Bioscience Reports (2019) 39(4), BSR20182266; https://doi.org/10.1042/BSR20182266The authors of the published article have made an error in"} +{"text": "Mycobacterium tuberculosis complex strains in Serbia (2008\u20132014) revealed an outbreak of TUR genotype strains in a psychiatric hospital starting around 1990. Drug unavailability, poor infection control, and schizophrenia likely fueled acquisition of additional resistance and bacterial fitness\u2013related mutations over 2 decades.A retrospective population-based molecular epidemiologic study of multidrug-resistant We retrMost patients were male and born in Serbia ; mean age was 49.5 years (range 15\u201383). We observed concurrent conditions for 55 patients; schizophrenia was the most prevalent . Of the 110 patients, 61 (55.5%) had previously experienced TB. Susceptibility testing results showed that 19/110 (17.3%) MDR MTBC isolates were resistant to all first-line drugs, and 11/110 (10.0%) were classified as XDR Table 1.We considered 6,512 single-nucleotide polymorphisms (SNPs) differentiating all isolates to analyze their phylogenetic relationships. The MDR MTBC strain population comprised 37/103 (35.9%) isolates classified as lineage 4.2.2.1 (TUR genotype), 20/103 (19.4%) isolates of lineage 4.1.2 (Haarlem genotype), 17/103 (16.5%) isolates of lineage 2.2.1 (Beijing genotype), 15/103 (14.6%) isolates of lineage 4.8 (H37Rv-like strains), 8/103 (7.8%) isolates of lineage 4.4.1.1 (S-type), 2/103 (1.9%) isolates of lineage 4.2.1 (URAL genotype), 1 isolate of lineage 4.1 (Ghana), and 1 nonclassified lineage 4 isolate. Among lineage 2.2.1 Beijing isolates, the previously described Europe/Russia W148 MDR outbreak isolates .Seeking to identify recent chains of transmission, we defined molecular clusters as surrogate markers for epidemiologically linked cases . OverallkatG S315T), streptomycin (rpsL K43R), and ethambutol (embB Q497R); we therefore classified them as TUR-outbreak isolates. TUR-outbreak isolates further differentiated into 2 individual transmission chains characterized by 2 distinct rifampin resistance\u2013mediating mutations: rpoB S450W in 1998 (95% highest posterior density [HPD] 1993\u20132001) and rpoB S450L in 2003 (95% HPD 2000\u20132005) , which have been proposed to enhance the in vitro growth rate of rifampin-resistant strains , thus indicating their ability to restore fitness of rpoB mutants, increase transmission success, or both.Our main finding was that 35/37 (94.6%) TUR isolates shared identical mutations that confer drug resistance to isoniazid (00\u20132005) Figure 2Of the 35 TUR-outbreak isolates, 26 (74.3%) were from patients hospitalized in Bela Crkva (BC) Hospital, the national center for treatment of all psychiatric patients with concomitant respiratory illnesses. Of note, 22 (84.6%) of these 26 patients had been transferred from 7 different psychiatric hospitals to BC Hospital for pulmonary diagnosis and treatment; 5 were admitted at BC Hospital with either confirmed or suspected TB diagnosis . ScreeniTo determine the geographic origin of the 3-fold resistant TUR ancestor and to test for the putative independent introduction of 2 different rifampin-resistant cases to the BC Hospital from other hospitals, we extended our Bayesian approach with a discrete trait model introducing the likely place of infection for each patient. We used 2 assumptions: first, a fast disease progression assumed infection and diagnosis of MDR TB within the first 2 years after admission to BC Hospital; and second, a slow disease progression in which patients who received a diagnosis within 2 years after admission were identified as latent MDR TB cases, meaning they had contracted the infection in their hometown or a previous hospital.rpoB S540W node, 95% for rpoB S540L node, and <15% for other location probabilities). Individual transmission events occurred to remote cities but also within Belgrade indeed coexisted over 2 decades , panel Aocations Figure 3 decades Figure 4In a retrospective approach using WGS-based molecular epidemiology, Bayesian statistics, and detailed epidemiologic investigations, we show that MDR TB in Serbia is associated with nosocomial transmission at BC Hospital, likely accompanied by a fast progression to disease within 2 years. Drug unavailability in the 1990s (Detection of the extensive transmission network in BC Hospital led to the development and implementation of an appropriate TB infection control program featuring the use of rapid laboratory tests for prompt detection of new cases, completion of appropriate second-line treatment regimens, and markedly expanded contact tracing activities. Since 2015, only 1 new case of MDR TB has been recorded in BC Hospital. However, MDR TB transmission in the general population must continue to be carefully monitored.Additional methods and information about a longitudinal study of MDR TB in a hospital setting, Serbia. Additional data for longitudinal study of MDR TB in a hospital setting, Serbia."} +{"text": "Rice blast disease is a major restriction in rice production. That is usually managed using chemical pesticides, which are expensive in terms of cost and environment hazards. Use of blast-resistance genes to develop resistant varieties may therefore be a more economical and environmentally friendly method for effective control.Pi37, Pit, Pid3, Pigm, Pi36, Pi5, Pi54, Pikm and Pb1. Through molecular marker-assisted selection and backcross breeding, 31 single-gene derived lines and 20 double-gene combination lines were obtained. When infected naturally, single-gene lines with Pigm or Pid3 showed significantly enhanced resistance during whole growth period relative to their recurrent parent. Single-gene lines with Pi37, Pi5, Pit, Pi36, Pi54 or Pikm showed significantly enhanced resistance in some of the four backgrounds. No obviously enhanced resistance was observed in single-gene line with Pb1 for the whole growth period. Compared with recurrent parents, most of the double-gene lines showed improved resistance. Among these double-gene lines, lines with Pi37/Pid3, Pi5/Pi54, Pi54/Pid3 or Pigm/Pi37, exhibited significantly enhanced resistance and observable additive effects.In this study, we improved the blast resistance of four sterile lines, Y58S, GuangZhan63S (GZ63), C815S and HD9802S, by introgression of 9 cloned broad-spectrum blast resistance genes Pigm and Pid3, showed significantly enhanced resistance for the whole rice growth period, and six blast resistance genes Pi37, Pi5, Pit, Pi36, Pi54 or Pikm showed significantly enhanced resistance for some of the four backgrounds. Double-gene lines with Pi37/Pid3, Pi5/Pi54, Pi54/Pid3 and Pigm/Pi37 exhibited significantly enhanced resistance and observable additive effects. These lines could be used in rice hybrid and production.Two blast resistance genes, The online version of this article (10.1186/s12284-019-0292-z) contains supplementary material, which is available to authorized users. Oryza sativa) is a staple food crop for more than 50% of the world\u2019s population. Rice blast disease is a major restriction on rice production in both tropical and temperate countries, and it is also a major obstacle to hybrid rice production in China due to the relatively narrow genetic base of hybrid rice and the increased use of nitrogen fertilizer protein on rice chromosome 1 markers TRS26, TRS33 and a functional marker Pi54-MAS have been identified were introduced into rice variety Jin23B is a highly efficient breeding approach that could offer an opportunity to select the targeted gene rapidly and precisely , K59 (Pit), Digu (Pid3), Gumei4 (Pigm), Q61 (Pi36), RIL260 (Pi5), Tsuyuake (Pikm), Tetep (Pi54) and Modan (Pb1), were used as donors of the cloned resistance genes , K59 (Pit), Digu (Pid3), Gumei4 (Pigm), Q61 (Pi36), RIL260 (Pi5), Tsuyuake (Pikm), Tetep (Pi54) and Modan (Pb1) were crossed separately with Y58S, GZ63S, C815S and HD9802S, and their F1 hybrids were backcrossed with Y58S, GZ63S, C815S and HD9802S to obtain the BC1F1 populations , dominant effect (D) and phenotypic variation explained (PVE) of the resistance genes were analyzed in a segregated population between different genotypes at P\u2009=\u20090.05 and 0.01 significance. The analyses of these statistical parameters were carried out using the statistical software SPSS 20.0.The data obtained from the experiments were statistically analyzed using analysis of variance (ANOVA) of respective experimental designs. Phenotypic and genotypic data were collected for each individual plant in the BCPi37, Pit, Pid3, Pigm, Pi36, Pi5, Pi54, were introgressed into Y58S, GZ63S, C815S and HD9802S separately following a recurrent backcrossing procedure, combined with MAS as described in Fig. Pikm for blast resistance was introgressed into C815S and HD9802S, and Pb1 for blast resistance was introgressed into GZ63S, using the marker-assisted backcross breeding method , Y58S (Pi5/Pi37), Y58S (Pi5/Pigm), Y58S (Pigm/Pi54), Y58S (Pi37/Pid3), Y58S (Pi37/Pigm) in Y58S background, GZ63S (Pit/Pigm), GZ63S (Pit/Pb1), GZ63S (Pi5/Pit), GZ63S (Pi5/Pi37), GZ63S (Pi36/Pb1), GZ63S (Pi5/Pigm), GZ63S (Pi36/Pid3), GZ63S (Pb1/Pigm), GZ63S (Pi5/Pi54), GZ63S (Pid3/Pi54) in GZ63S background, C815S (Pit/Pigm), C815S (Pi5/Pit), C815S (Pi5/Pigm) and C815S (Pi37/Pigm) in C815S background were introduced into four recurrent parents Y58S, GZ63S, C815S and HD9802S, one blast resistance gene (Pikm) was introduced into C815S and HD9802S, and one blast resistance gene (Pb1) was introduced into GZ63S. The resistance to leaf blast and neck blast of single gene introduced lines was tested in 2014 and 2015 in Xianfeng. Pid3 showed greater resistance to leaf blast and neck blast in the background of Y58S, GZ63S, C815S and HD9802S than the control in 2014 and 2015 , 4.00 for Y58S (Pi5/Pi37), 1.75 for Y58S (Pi5/Pigm), 2.00 for Y58S (Pigm/Pi54), 1.60 for Y58S (Pi37/Pid3), and 2.50 for Y58S (Pi37/Pigm), while the percentage of infection for neck blast was 3.88%, 32.34%, 2.08%, 10.00%, 6.80% and 3.05%, respectively , GZ63S (Pit/Pb1), GZ63S (Pi5/Pit), GZ63S (Pi5/Pi37), GZ63S (Pi36/Pb1), GZ63S (Pi5/Pigm), GZ63S (Pi36/Pid3), GZ63S (Pb1/Pigm), GZ63S (Pi5/Pi54), GZ63S (Pid3/Pi54) were 5.42, 5.84, 6.00, 4.58, 6.33, 6.00, 5.18, 5.50, 2.80 and 2.25, respectively. At maturation, the percentage of infection for neck blast was 55.02%, 50.29%, 47.30%, 11.40%, 23.83%, 15.20%, 16.69%, 16.34%, 12.67% and 0%, respectively for the 10 pyramiding lines in GZ63S background , C815S (Pi5/Pit), C815S (Pi5/Pigm), C815S (Pi37/Pigm) were 3.50, 4.50, 3.62 and 2.29, respectively, for leaf blast and 4.76%, 22.50%, 22.50% and 0%, respectively, for neck blast , Digu (Pid3), Tetep (Pi54) and Q1333 (Pi37)\u2014have high resistance to leaf and neck blast, four donor parents K59 (Pit), Tsuyuake (Pikm), Modan (Pb1) and RIL260 (Pi5) have medium or high resistance to leaf blast and susceptible to neck blast, while Q61 (Pi36) was susceptible to leaf and neck blast. From the results, we can see that the resistance of donor parents could differ even under the same infection conditions.In our study, the blast resistance of 9 donor parents was evaluated under natural infection conditions in 2014, 2015 and 2016. Four donor parents\u2014Gumei4 , GZ63S (Pi5/Pi54), GZ63S (Pi54/Pid3) and C815S (Pigm/Pid37) that were highly resistant to leaf and neck blast under natural infection conditions, and the phenotypes showed that the effect on neck blast was better than on leaf blast in the Y58S, GZ63S and C815S backgrounds.Broad spectrum and durable resistance are the major objectives of rice blast resistance breeding. Most efforts in breeding for blast resistance have been directed towards incorporating single genes. Rice varieties containing only one major resistance gene have a tendency to break down as unpredictable changes occur in the composition of pathogen populations, so pyramiding more blast resistance genes in a rice cultivar may solve this problem"} +{"text": "Escherichia coli (STEC) isolates (N = 38) that were incriminated in human disease from 2006 to 2013 in South Africa were characterized by serotype, virulence-associated genes, antimicrobial resistance and pulsed-field gel electrophoresis (PFGE). The isolates belonged to 11 O:H serotypes. STEC O26:H11 (24%) was the most frequent serotype associated with human disease, followed by O111:H8 (16%), O157:H7 (13%) and O117:H7 (13%). The majority of isolates were positive for key virulence-associated genes including stx1 (84%), eaeA (61%), ehxA (68.4%) and espP (55%), but lacked stx2 (29%), katP (42%), etpD (16%), saa (16%) and subA (3%). stx2 positive isolates carried stx2c (26%) and/or stx2d (26%) subtypes. All pathogenicity island encoded virulence marker genes were detected in all (100%) isolates except nleA (47%), nleC (84%) and nleD (76%). Multidrug resistance was observed in 89% of isolates. PFGE revealed 34 profiles with eight distinct clusters that shared \u226580% intra-serotype similarity, regardless of the year of isolation. In conclusion, STEC isolates that were implicated in human disease between 2006 and 2013 in South Africa were mainly non-O157 strains which possessed virulence genes and markers commonly associated with STEC strains that have been incriminated in mild to severe human disease worldwide. Improved STEC monitoring and surveillance programs are needed in South Africa to control and prevent STEC disease in humans.Shiga toxin-producing Escherichia coli (STEC) is a zoonotic foodborne and waterborne pathogen associated with enteric disease in humans characterized by abdominal cramps, mild to severe diarrhea, hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS) [Shiga toxin-producing me (HUS) . Majowicme (HUS) have estme (HUS) ,4,5.More than 600 STEC serotypes have been recovered from animals, humans, the environment and various foods around the world ,8. STEC stx1 and stx2) are the main virulence factors of STEC. At least 15 Shiga toxin subtypes have been identified (http://old.iss.it/binary/vtec/cont/STEC_2018_Wrap_up.pdf), including stx1a, stx1c, stx1d, stx1e, stx2c, stx2d, stx2e, stx2f, stx2g, stx2h, stx2i, stx2j, stx2k and stxl [E. coli attachment and effacement gene (eae) which encodes intimin (eaeA) [eaeA) is encoded on the locus of the enterocyte effacement (LEE) pathogenicity island [eaeA positive E. coli, including STEC [Shiga toxins ,17. Intiy island and is ring STEC ,17.hlyA or ehxA) [katP) [espP) [etpD) [saa) and subtilase cytotoxin (subA) are also recognized as key plasmid-encoded virulence factors in eaeA negative STEC strains [saa) of enterocytes, cytotoxicity (subA), reduction of oxidative stress (katP), exoprotein secretion (etpD), suppression of the host\u2019s immune system and cleavage of coagulation factor V (espP) and lysis of human erythrocytes with subsequent mucosal hemorrhage in the host (hlyA) [STEC produce plasmid-encoded virulence-associated proteins, including hemolysin (or ehxA) , catalas) [katP) , extrace) [espP) and a ty) [etpD) . STEC au strains ,23. Plast (hlyA) ,23,24,25pagC, which encodes a protein sharing 46% homology with the phoP-activated gene C product in Salmonella enterica serovar Typhimurium. PagC enables survival in macrophages. Another OI-122\u2013encoded gene is sen, which encodes a protein that is 38.2% homologous to Shigella flexneri enterotoxin 2 [efa1 and efa2 (enterohemorrhagic E. coli factor for adherence), which have been associated with epithelial cell adhesion and inhibition of bovine peripheral blood lymphocyte proliferation [iha (iron-regulated gene A), which encodes an adhesin [ureC [terC [nleA (OI-71), nleB/Z4328 (OI-122), nleB2, nleC (OI-36), nleD (OI-57), nleE/Z4329 (OI-122), nleG (OI-71), nleG2-1 (OI-71), nleG2-3 (OI-57), nleG6-2 (OI-57), nleG9 (OI-71), nleH1-2 (OI-171) [ent/espL2 (OI-122). These genes are mainly found in high risk (HUS) STEC strains and are associated with colonization and survival in the host, and may interfere with signaling pathways during inflammation [Several genes that are encoded on pathogenicity islands (O-islands-OIs) other than the LEE are also considered STEC virulence markers . Particuotoxin 2 ,27, as wferation ,28. OI-1feration . In addi adhesin and ureCin [ureC ,31 and tammation . Non-LEEammation ,35.E. coli, which are then converted into antimicrobial resistant strains. Therefore, E. coli, including STEC, as commensal bacteria in the intestinal tracts of animals and humans are considered reliable indicators of antimicrobial resistance, and have been used for monitoring and surveillance of antimicrobial resistance in livestock, humans and along the food chain.The emergence of antimicrobial resistant bacteria as a consequence of the indiscriminate use and abuse of antimicrobials in animals and humans has become a public health concern ,37,38,39Although the first case and largest outbreak of human STEC disease in South Africa occurred in 1990 and 1992, respectively ,42, ten Serotyping (O:H) assigned the 38 STEC isolates to 11 O:H serotypes, including 11 O serogroups and 6 H types. The isolates belonged to the following serotypes: O5:HNT (2), O8:H19 (1), O22:H16 (1), O26:H11 (9), O107:H7 (3), O111:H8 (6), O113:H21 (1), O117:H7 (5), O118:H16 (1), O156:H7 (2), O157:H7 (5), ONT:H8 (1) and ONT:H21 (1) . Overallstx1, 29% (11/38) carried stx2, 26% (10/38) carried stx2c and 26% (10/38) carried stx2d (stx1 and stx2 were detected concurrently in 13% (5/38) of isolates while both stx1 and stx2c were detected in 0.5% (2/38) of isolates. stx1 alone or stx2 alone were detected in 66% (25/38) and 16% (6/38) of isolates, respectively. The following stx subtypes were not detected: stx1c and stx1d, stx2e, stx2f and stx2g. Additional genotypes were also observed: stx1 + stx2c in 8% (3/38), stx1 + stx2 + stx2d in 8% (3/38), stx2 + stx2c + stx2d in 13% (5/38) and stx1 + stx2 + stx2c + stx2d in 5% (2/38) of isolates. Both stx2c + stx2d were detected concurrently in 18% (7/38) of isolates which belonged to the following serotypes: STEC O157:H7 (5), STEC O8:H19 (1) and STEC O113:H2 (1). The eaeA gene was detected in 60.5% (23/38) of isolates which belonged to the following serotypes: STEC O5:HNT, O26:H11, O111:H8, O118:H16, O157:H7 and ONT:H8. The frequencies of virulence genes are depicted in ed stx2d . Both stehxA, 68.4% (21/38); katP, 42% (16/38); espP, 55% (21/38); etpD, 16% (6/38) and saa, 16% (6/38) was detected in STEC O157:H7 isolates only while O26:H11 isolates possessed all plasmid marker genes except etpD. The following OI marker genes were present in 100% of isolates: OI-122 markers: pagC, sen, efa1 and efa2 except ent/espL2, which was detected in 89.4% of isolates; OI-43/48 markers: terC, ureC and iha were present in 100% of isolates. Most nle effector genes, including nleB, nleB2, nleF, nleE, nleG, nleG2-1, nleG2-3, nleG5-2, nleG6-2, nleG9, nleH1-1 and nleH1-2, were present in 100% of isolates, while nleA was found in 47% (18/38), nleC in 84% (32/38), and nleD in 76% (29/38).Plasmid-encoded genes were distributed as follows: % (6/38) . Only onOverall, the STEC isolates carried 50\u201374% (20\u201328 out of 34) genes. STEC O157:H7 carried 28/34 genes, STEC O118:H16 had 27/34 genes, STEC O26:H11 had 26\u201327/34 genes, STEC O5:HNT had 25\u201326/34 genes, STEC O8:H19 had 25/34 genes and two STEC O111:H8 isolates had 25/34 genes. The remaining serotypes, including STEC O111:H8, O113:H21, O107:H7, O117:H7, O22:H16, O156:H7, ONT:H21 and ONT:H8, carried 21\u201324/34 genes. The distribution of antimicrobial resistance patterns is depicted in PFGE was performed to investigate genetic relationships among isolates. The 38 STEC isolates were all typeable by PFGE. The isolates were classified into 33 PFGE profiles. Based on a Dice similarity index \u226580%, the 33 PFGE profiles were grouped into seven distinct clusters comprising mainly three to nine isolates/per cluster . STEC thSerotyping, virulence characterization, antimicrobial resistance and PFGE genotyping of STEC isolates that are recovered from infected humans are used in high income countries with robust STEC monitoring and surveillance programs for risk assessment purposes. While current data on the molecular epidemiology of STEC are readily available in high income countries, information on the occurrence and characteristics of STEC isolates from infected humans in low income countries, such as South Africa and most middle income economies, is scarce. Currently, STEC surveillance in South Africa remains passive and STEC disease in South Africa may be underestimated due to lack of active surveillance and/or underreporting. In addition, with cattle being an important STEC reservoir , the appOverall, the STEC isolates belonged to 11 O:H serotypes including O5:HNT, O8:H19, O22:H16, O26:H11, O107:H7, O111:H8, O113:H21, O117:H7, O118:H16, O156:H7, O157:H7, ONT:H8 and ONT:H21. Apart from STEC O107:H7, all the isolates belonged to serotypes which have been previously incriminated in mild to severe human STEC disease in various countries worldwide . Altogetstx1 positive (84%), while only a low number (29%) possessed stx2. No stx1 subtypes were detected in this study. The stx1 + eaeA genotype was mostly observed among STEC O26:H11 and O111:H8 strains. STEC that carry stx1 alone or both stx1 + eaeA are considered low risk and are commonly associated with mild diarrhea or non-HUS infections in humans [stx1 + eaeA positive STEC have been involved in severe disease and outbreaks, suggesting that some stx1 + eaeA positive STEC strains may have yet unidentified virulence factors that make them highly virulent [The vast majority of STEC isolates were n humans ,47. Howevirulent . stx2 positive isolates carried both stx2c and stx2d subtypes concurrently. STEC isolates that possessed stx2 exhibited stx2 + stx2c + stx2d + eaeA or stx2 + stx2c + stx2d gene combinations. stx1 + stx2 + stx2c + stx2d + eaeA or stx2 + stx2c + stx2d + eaeA were observed in STEC O157:H7 isolates only while the stx2 + stx2c + stx2d genotype was detected in STEC O113:H21. The stx1 + stx2 + stx2d genotype was detected in STEC O107:H7 isolates, while the stx1 + stx2 + stxc + stx2d genotype was observed in one STEC O8:H19 isolate. STEC that possess stx2 alone or stx2 + eaeA have been significantly associated with severe disease in humans, including HC and HUS, in comparison to STEC that possess stx1 alone or stx1 + stx2 concurrently [stx2c and stx2d concurrently was higher compared to the results of two studies, which previously reported single strains that possess both subtypes [stx2c and/or stx2d subtypes in a STEC isolate has been associated with human disease, varying from mild to bloody diarrhea and HUS [Almost all urrently ,47. The subtypes ,49. The and HUS ,51,52.eaeA gene was detected in the majority of isolates (60.5%). The eaeA gene was observed in the following serotypes: STEC O5:HNT, O26:H11, O111:H8, O118:H16, O157:H7 and ONT:H8. The high frequency of eaeA in these human STEC isolates is in sharp contrast with the very low rates of eaeA found in STEC isolates from cattle in South Africa [eaeA positive with a high capacity of being easily transmitted to humans may be involved in human disease in South Africa.The h Africa , which aehxA, katP and espP but lacked etpD, saa and subA. A complete plasmid (pO157) was observed in O157:H7 isolates only, while O26:H11 isolates possessed ehxA, katP, espP and etpD but lacked etpD, which was only found in all STEC O157:H7 and O5:HNT strains. The plasmid-encoded genes katP, espP and etpD are more frequent in STEC isolates that are recovered from human disease outbreaks and cases of HUS, particularly [saa gene was present in only a small number of eaeA-negative STEC isolates [The majority of STEC isolates carried plasmid-encoded virulence markers icularly . As previsolates ,54 whichsmid pO15 , in agreement with Ju et al. [stx2, eaeA and a complete plasmid is a hallmark of highly virulent STEC strains that are frequently associated with outbreaks and severe disease such as HC and HUS [Most of the isolates carried the full complement of OI-122 and OI-43/48 marker genes and all non-LEE encoded effector genes, except u et al. . Possess and HUS ,56,57, w and HUS ,32,57,58eaeA. While the presence of a high number of virulence genes in STEC O157:H7, O26:H11, O111:H8 and O113:H21 isolates that are commonly implicated in severe foodborne STEC disease outbreaks around the world may not be surprising [Interestingly, STEC O157:H7, O26:H11, O111:H8, O113:H21, O118:H16, O5:HNT and O8:H19 harbored the highest number of virulence genes (24\u201328 genes). Possession of the highest number of virulence-associated genes significantly correlated with the presence of All of the 38 STEC isolates were resistant to one or more antimicrobials. Most (>50%) of the isolates were resistant to cephalothin, streptomycin and ampicillin, while moderate resistance rates (40\u201350% of isolates) were observed for cefotaxin and kanamycin, and lower resistance levels (< 25%) were observed for sulfonamides, sulfa-trimethoprim and colistin. The levels of resistance recorded in this study were very high compared to rates that have been reported elsewhere ,60,61. IPulsed-field gel electrophoresis was used to classify the 38 STEC isolates into 33 profiles which were assigned to eight distinct clusters. Among the eight clusters, four distinct clusters grouped STEC O26:H11, five of the six STEC O111:H8 and all STEC O107:H7 and O157:H7. The four clusters were serotype specific with very high intra-cluster similarity (>80%), regardless of the year of isolation. The high intra-serotype similarity among STEC O26:H11, O111:H8, O107:H7 and O156:H7 strains regardless of their year of isolation suggests that the STEC isolates which were implicated in disease in South Africa from 2006 to 2013 are clonally related STEC strains which may have a high capacity for survival and persistence in their respective reservoir or sources.stx1 + eaeA positive, fewer isolates carried stx2 only or concurrently with stx2c and stx2d and a smaller number was positive for both stx1 and stx2. Most isolates carried all or most pathogenicity island encoded virulence-associated genes. PFGE revealed high intra-serotype similarity among STEC. The majority of isolates were resistant to two or more antimicrobials that are commonly used in clinical medicine for treatment of various bacterial diseases. To the best of our knowledge, this is the first detailed characterization of human STEC isolates from South Africa. Further molecular epidemiology studies that compare STEC isolates of human, animal and food origin are needed to fully understand the epidemiology of STEC and identify reservoirs and sources of human disease in South Africa.In summary, the majority of STEC infections which occurred in South Africa from 2006 and 2013 were caused by serotypes O26:H11, O111:H8 and O157:H7 that belong to \u201cbig 7\u201d serogroups, in agreement with global trends. Virulotyping revealed that most of the isolates were A total of 38 STEC isolates which were previously recovered from humans showing foodborne disease symptoms, including mild to severe diarrhea, between 2006 and 2013 were characterized in this study. These isolates were obtained from the culture collection of the Centre for Enteric Diseases, National Institute of Communicable Diseases, South Africa (CED-NICD). Because the isolates were obtained through passive surveillance, detailed clinical information on patients from which the STEC isolates were recovered was unavailable. The 38 STEC isolates belonged to the following serogroups: O5 (2), O8 (1), O107 (3), O22 (1), O26 (9), O111 (6), O113 (1), O117 (5), O118 (1), O156 (2), O157 (5) and ONT (1). This study was approved by the University of Pretoria Research Ethics Committee (REC005-18).E. coli colony sweeps from Luria Bertani Agar plates. A loop-full of colony sweeps was suspended in a 1.5 mL Eppendorf tube containing 1 mL of FA Buffer . Bacterial suspensions were mixed and washed by vortexing, followed by centrifugation for 5 min. After the first wash and centrifugation cycle, the supernatant was discarded and the bacterial pellet was re-suspended in FA buffer . After two additional washes and centrifugation cycles, the pellet was suspended in 500 \u00b5L of sterile water and thoroughly vortexed. The homogeneous cell suspension was boiled [The isolates were resuscitated on Luria Bertani Agar after incubation at 37 \u00b0C overnight. DNA was extracted from bacterial cells by the boiling method, as described previously . Brieflys boiled to 100 \u00b0Escherichia coli flagellar genes (fliC) that are commonly found in STEC [STEC isolates were further serotyped for flagellar antigens (H antigens) only, as STEC serogrouping (O antigen typing) had been carried out previously by the tube agglutination test . H typing was carried out by three multiplex PCR assays that targeted 14 genes encoding in STEC . stx1, stx2, eaeA, and ehxA [stx2 subtypes was carried out according to Scheutz et al. [katP [espP [etpD [saa [subA [iha, ureC and terC [pagC (Z4321), sen (Z4326), efa1 (Z4332) and efa2 (Z4333) [nleA (OI-71), nleB (OI-122), nleC (OI-36), nleD (OI-57), nleE (OI-122), nleG (OI-71), nleG2-1 (OI-71), nleG2-3 (OI-57), nleG6-2 (OI-57), nleG9 (OI-71) and nleH1-2 (OI-171). STEC O157:H7 strain EDL 933 (E. coli O157:H7) was used as a positive control. Virulotyping was performed using previously described primers and PCR cycling conditions to amplify 34 genes that encode various STEC virulence factors and markers. A multiplex PCR was used for the detection of and ehxA . Detectiz et al. . Single l. [katP , espP [2tP [espP , etpD [2pP [etpD , saa [64aa [subA . Previouand terC ,30,31 an (Z4333) . The PCR [pagC Z41, sen . The panhttp://www.cdc.gov/pulsenet/pdf/ecoli-shigella-salmonella-pfge-protocol508.pdf). Salmonella serotype Braenderup was used as the marker for all PFGE gels. Briefly, DNA was extracted and digested with XbaI. XbaI PFGE patterns were analyzed for similarity, and a dendrogram was generated by the Bionumerics software, version 6.5 with Dice similarity indices and the unweighted-pair group method with arithmetic means. In this study, a cluster was defined as STEC isolates that grouped together in the dendrogram with a Dice similarity index equal or above 80%.PFGE was carried out according to the CDC/PulseNet protocol to determine relationships among STEC, particularly STEC belonging to the same serotype . A"} +{"text": "ALK fusion gene. Application of liquid biopsy, i.e., detection and quantitation of the fusion product in plasma cell-free DNA (cfDNA), could improve clinical practice. To detect ALK fusions, because fusion breakpoints occur somewhere in intron 19 of the ALK gene, sequencing of the entire intron is required to locate breakpoints.Tyrosine kinase inhibitors targeted to anaplastic lymphoma kinase (ALK) have been demonstrated to be effective for lung cancer patients with an ALK intron 19. This system can amplify fragments, including breakpoints, regardless of fusion partners. The data analysis pipeline firstly detected fusions by alignment to selected target sequences, and then quantitated the fusion alleles aligning to the identified breakpoint sequences. Performance was validated using 20 cfDNA samples from ALK-positive non-small cell lung cancer patients and samples from 10 healthy volunteers. Sensitivity and specificity were 50 and 100%, respectively.We constructed a target sequencing system using an adapter and a set of primers that cover the entire ALK fusions in cfDNA from lung cancer patients. The system offers an alternative to existing approaches based on hybridization capture.We demonstrated that PCR-based target sequencing using a tiling primer set and two-step mapping/alignment quantitatively detected ALK) gene fusions are found in 3\u20137% of non-small cell lung cancer (NSCLC) patients . Al. Al14]. mer mixO , and 1 umer mixO , the purALK fusions recorded in COSMIC v86 and targeted exons/introns with inferred breakpoints. They were as follows, ATIC exon/intron 7, C2orf44 exon 4, CARS exon/intron 17, CLTC exons/introns 30, 31, DCTN1 exons/introns 16, 26, EML4 exons/introns 2, 6, 13, 14, 15, 17, 18, 20, FN1 exon/intron 23, HIP1 exons/introns 21, 28, 30, KIF5B exons/introns 15, 17, 24, KLC1 exon/intron 10, MSN exon/intron 11, NPM1 exon/intron 5, PPFIBP1 exons/introns 8, 12, RANBP2 exon/intron 18, SEC31A exon/intron 20, SQSTM1 exon/intron 5, STRN exon/intron 3, TFG exons/introns 4, 5, 6, TPM3 exon/intron 7, TPM4 exon/intron 7, and VCL exon/intron 16. Details regarding nucleotide positions are shown in We extracted partner genes of ALK intron 19 and parts of exon 19 and 20 (chr2:29446370\u201329448369 on GRCh37/hg19) using the BWA-MEM mapping program [ALK intron 19 sequence. Then, reads mapped/aligned on both ALK intron 19 and candidate partner sequences were collected and grouped using information of individual index sequences and breakpoint positions. These processes were performed using in-house Perl scripts. Fusion allele fractions were calculated as follows; counts of reads with fusion alleles/sequencing depth of ALK intron 19 at the breakpoint \u00d7 100 (%). When the fusion allele fraction was over 0.2%, we aligned reads against the 20 bp breakpoint sequence using BLAST and corrected quantitation of fusion alleles. The 20 bp breakpoint sequences were prepared by combining 10 bp of the ALK side and 10 bp of the partner side around detected breakpoints. We also prepared counterpart sequences for ALK wild-type. After raw sequencing reads assorted using individual indexes were aligned against the 20 bp sequences, we collected alignments with \u226517 bp matches and calculated fusion allele fraction as follows; number of alignments of fusions/ \u00d7 100 (%).Sequencing reads in FASTQ files were analyzed in accordance with the flowchart presented in program . Reads w program . At the 0 value), the fusion allele fraction (%) was calculated as follows, N0 of amplicon for fusion/(N0 of amplicon for fusion + N0 of amplicon for wild-type) \u00d7 100.Primer sequences are listed in S1 FigEML4-ALK fusions were detected above 0.1%.Allele fraction of the detected false fusions was below 0.05%. (PDF)Click here for additional data file.S2 FigALK-positive NSCLC patients. (b) Healthy volunteers.X-axis represents the sequence position on chr2. Y-axis denotes the sequencing depth. (a) (PDF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file."} +{"text": "Structural characterization reveals that the Ag NPs are uniformly immobilized in the Fe3O4 microsphere-based supports. Moreover, Ag NPs are more stable in the hybrid structure than in the naked state and show high catalytic activity for the reduction of nitro compounds and hydration of nitriles to amides in water. The Fe3O4 microspheres were recycled several times using an external magnet.As hybrid nanostructures have become more important in many fields of chemistry, Ag nanoparticles (NPs) are being increasingly immobilized onto Fe In recent years, numerous attempts have been made toward designing and synthesizing hybrid nanostructures, which combine or even improve the physical and chemical properties of the constituent parts . Many st3O4 has gained significance owing to its nanostructure and cutting-edge technological applications, including its usage as a magnetic storage medium were mixed and sonicated for 30 s at room temperature. Then, 1.0 mL of 2.22 M NaBH4 (300 equiv. to per equiv. of substrate) solution was added to the mixture. The reaction progress was monitored by UV/vis spectrometer.As a representative example, 7.50 \u00d7 103O4 catalyst (3.0 mol%), water (3.0 mL), and the corresponding nitrile (1.0 mmol) were introduced into a stainless steel reactor. After the reaction, the catalysts were separated from the solution by external magnet. The reaction products were analyzed by mass spectra on GC-MS. (Ag/Fen GC-MS. .3O4 19.0 mg (0.03 mmol) and H2O (3 mL). The mixture was heated at 150 \u00b0C for 6 h. After cooling to room temperature, the solution was extracted with ethylacetae (20 mL). MS (EI) m/z: 28(100), 32(34), 51(30), 77(74), 105(75), 121(60).Benzamide , entry 5m/z: 75(33), 111(52), 139(100), 155(51).4-Chlorobenzamide , entry 1m/z: 28(27), 50(48), 139(100), 155(51), 183(100), 199(51).4-Bromobenzamide , entry 2m/z: 28(100), 118(28), 150(78), 166(55).4-nitrobenzamide , entry 3m/z: 28(100), 32(33), 65(29), 92(31), 120(75), 136(55).4-aminobenzamide , entry 4m/z: 28(85), 32(28), 65(25), 91(72), 119(100), 135(62).4-Methylbenzamide , entry 5m/z: 65(26), 91(83), 119(100), 135(71).3-methylbenzamide , entry 6m/z: 65(33), 91(100), 119(87), 135(84 ).2-methylbenzamide , entry 7m/z: 28(100), 32(32), 44(77), 59(89).Acetamide , entry 8m/z: 27(75), 28(73), 32(17), 43(31), 74(83), 55(64), 71(100).Acrylamide , entry 93O4 microspheres in situ by substituting sodium cations with Ag ions. The Ag NPs were uniformly immobilized in the Fe3O4 support while preserving their particle size and crystallinity, as well as the structural integrity of the Fe3O4 support. The Ag/Fe3O4 catalyzed the reduction of nitro compounds and hydration of nitriles to amides in water with high conversion. Furthermore, the Ag/Fe3O4 catalyst was readily separated using an external magnet and could be reused at least three times with benzonitrile under the optimized reaction conditions without any loss of catalytic activity. The magnetic separability eliminated the requirement of catalyst filtration after the completion of the reaction.Ag NPs were immobilized onto Fe"} +{"text": "PIM1, MYD88, CD79B, DST, IRF4, ERBB3, MYH11, DCC, and KMT2D. Furthermore, somatic mutations of MYH11 were related to poor prognoses in PCNSL patients. Copy number variations were also duplicated and/or deleted from deep-sequencing in segmental genomic islands. In addition to these prognostic marker candidates, analysis of RTK-RAS-MAPK signaling and the PTEN-PI3K-AKT proapoptotic pathway showed that somatic activations and aberrations, respectively, may be involved in a promising central oncopathway harboring mTOR, c-Myc, FOXO1, and p53. This study provides a foundation for molecular targeted therapies based on genome diagnostics and prognosis in PCNSL.Exome-sequencing for somatic mutation detection and copy number variation analysis are effective and valid methods for evaluating human cancers in current molecular medicine. We conducted target amplicon exome-sequencing analyses using PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Twenty-seven primary central nervous system lymphoma (PCNSL) specimens and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverages of the entire coding regions of 409 cancer-related genes. The average of the total numbers of somatic mutations including single-nucleotide variations and insertion/deletion mutations in each specimen was 13.3. Of these, the average of the ratios of nonsynonymous substitutions in each specimen was 74.8%. The most frequent mutations in 27 specimens were in Primary central nervous system lymphoma (PCNSL) is a rare subgroup of diffuse large B-cell lymphoma (DLBCL) arising in the brain, meninges, spinal cord, and eyes , 2 and ide novo methods for targeted therapies [BCL6 overexpression and aberrant somatic hypermutation of many genes, coupled with surface localization of IgM, suggest that the tumors are arrested at the terminal B-cell differentiation stage [CD79B, MYD88, TBL1XR1, and ODZ4 genes are most frequently mutated [PRDM1 and CARD11 [High-resolution genomic arrays and whole genome sequencing have been shown to be efficient approaches for inclusive analyses of chromosome imbalances and gene mutations in solid cancers and hematologic malignancies, including DLBCL \u20138. The mherapies . In PCNSon stage . Studies mutated , 20, 21,d CARD11 , 23.in situ hybridization and sequencing of candidate genes identified as recurrently translocated genes such as BCL6 [MYD88 and CD79B [Additionally, recent studies have indicated that molecular changes stimulate NF-\u03baB signaling and sustain the high-breakpoint cluster region , 25, as as BCL6 \u201330 and rnd CD79B , 32.MYH11) associated with poor prognosis. Furthermore, CNVs of the 12 prognostic marker candidates and genes related to RTK-RAS-MAPK signaling and the PTEN-PI3K-AKT proapoptotic pathway were examined, and their biological significance was confirmed by survival analysis of patients with PCNSL.These results demonstrated that gene mutations including an aberrant somatic hypermutation and specified CNVs influence the malignancies of PCNSL cells. However, few retrospective studies have examined the detailed molecular network and cell signaling based on diagnosis with gene mutations and CNVs or the prognosis of patients with PCNSL. Thus, in this study, we conducted target amplicon exome-sequencing analyses using PCR target enrichment and next-generation sequencing to obtain targeted coverage of the entire coding regions of 409 cancer-related genes in the genomic landscape by using tumor specimens and matched normal control tissues derived from 27 patients with PCNSL. We identified significant single-nucleotide variations (SNVs) in myosin heavy chain 11 were identified by tumor-normal analyses in which germline variants can be eliminated from the tumor variants. The sequencing results derived from 27 PCNSL specimens were compared with the results from 17 paired normal control tissues and control sequence data within Ion Reporter software (see Methods). All SNVs and INDELs identified were confirmed by visual inspection with the Integrative Genomics Viewer (IGV). In total, 361 somatic mutations in 136 genes were identified. Averages of nonsynonymous and synonymous mutations were 13.37 (range: 6\u201319) and 4.77 (0\u201310), respectively, per specimen Figure . The ratPIM1) (N = 71), myeloid differentiation primary response 88 (MYD88) (N=22), cluster of differentiation 79B (CD79B) (N = 21), and interferon regulatory factor 4 (IRF4) (N = 13) were most frequent, followed by ERBB3 (N = 8), KMT2D (N = 8), MYH11 (N = 7), DST (N = 7), CSMD3 (N = 6), DCC (N = 6), FOXO1 (N = 5), PAX5 (N = 5), and USP9X (N = 5) (PIM1 (85.1%), MYD88 (81.4%), CD79B (59.2%), IRF4 (29.6%), MYH11 (25.9%), KMT2D (25.9%), PAX5 (22.2%), DCC (22.2%), and ERBB3 (22.2%) , PIM1 (11.1%), and patched-1 (PTCH1) (7.4%) . A total (N = 5) . The gen) Figure . Splice ) Figure . These rFOXO1 (18.5%) in apoptosis, FOXP4 (7.4%) and MYC (7.4%) in cell proliferation, and RAF1 (3.7%) in MAP-kinase and BCL10 (25.9%) in NF-\u0138B signaling, CD79B (59.2%), PAX5 (22.2%), and BCR (7.4%) in B-cell development, and MYH11 (25.9%), RUNX1 (7.4%), and TET2 (7.4%) in leukemia were observed and MARK1 (7.4%) in Ser/Thr-kinases, ERBB3 (22.2%), FLT4 (11.1%), PDGFRA (7.4%), and PDGFRB (7.4%) in receptor tyrosine kinases (RTKs), and EPHA7 (11.1%) and EPHA3 (7.4%) in non-RTKs were found in kinase genes and using the Kaplan-Meier method . The medKMT2A , AR , MYC , NSD1 , EPHA3 , MYH11 , MARK1 , NTRK1 , FOXO1 , PAX5 , RUNX1 , and UBR5 were detected in KMT2A, 845C>G (18.5%) in MYH11, 4165T>C (7.4%) in NSD1, and 2303C>T (7.4%) in NTRK1 were detected (-8) in detected . Signifited (-8) . Interesectively . These rWe next examined copy number variations (CNVs) in the 27 PCNSL specimens were mapped to human chromosomes by copy number gains and losses Figure . AdditioNTRK1, MARK1, MYC, PAX5, KMT2A, and RUNX1 were increased (gain > 70%). In contrast, copy number losses in EPHA3, NSD1, UBR5, FOXO1, and MYH11 were also found (loss > 30%) Figure . The CNVR Figure . Second,R Figure . Kaplan-R Figure . Especia) Figure . Using mERBB3 , ERBB2 (3.7% and 22.2%), MYC (7.4% and 11.1%), RAF1 (7.4% and 33.3%), TP53 (3.7% and 29.6%), NRAS (3.7% and 11.1%), MAP2K2 (3.7% and 7.4%), and MYCN (3.7% and 7.4%) , CD79B (30%), PIM1 (22%), and TBL1XR1 (19%) [ETV6 (16%), IRF4 (14%), IRF2BP2 (11%), and EBF1 (11%). However, a recent exome-sequencing analysis revealed somatic hypermutations in PIM1 (100%), BTG2 (92.7%), and MYD88 (79-85.4%), as well as focal deletions and somatic mutations in the HLA genes which were linked to poor prognoses in PCNSL [PIM1 (85.1%), MYD88 (81.4%), CD79B (59.2%) contained somatic mutations . In addiin PCNSL , 37. Ours Figure . Thus, tnd PTPRD . In this) Figure but did MYD88 %, CD79B On the other hand, some of somatic mutations were detected by low frequencies , which should be validated to be the reliable mutations. Then, we performed PolyPhen-2 and SIFT analyses for the mutational significances in the representative genes including EPHA3, ADAMTS20, and TRRAP . The resEPHA3, KMT2A, PAX5, and RUNX1 clearly divided the Kaplan-Meier curves of the two subgroups with or without CNVs in cases with poor prognosis corresponding to the HLA locus, 6q16.3 (37%), 6q21.1-q25 (34%), and 6q14.1-q16.3 27%) on chromosome 6, and 12q12-q22 (27%), 7q21.11-q21.12 (20%), and 9p21 regions in PCNSL % on chro. In conts Figure . Our datMYD88 and BCL10 in NF-\u03baB signaling, CD79B, PAX5, and BCR in B-cell development, and MYH11, RUNX1, and TET2 in leukemia and MYH11 were associated with short survival, while PAX5 mutations were associated with long survival . Additionally, CNVs in regions including EPHA3 (3p11.1) and MYH11 (16p13.11) were relatively decreased , whereas that of PAX5 (9p13.2) was relatively increased (83.3%) /Toll-like receptor (TLR)-NF-\u0138B pathways are altered in >90% of PCNSL . Mutatioa Figure . Additio) Figure . Furthers Figure .ERBB2/3/4, MYC, RAF1, TP53, PIK3CD, NRAS, and MAP2K2 , which mediates growth factors and RAS-MAPK signaling, governs MEK1/2 activities downstream at MAP-kinase in DLBCL-type PCNSL . We also) Figure . Thus, rTwenty-seven patients with PCNSL were diagnosed and treated at Chiba University, Toyama Prefectural Central Hospital, Wakayama Medical University School of Medicine, and Yamaguchi University. Clinical characteristics are shown in DNA was extracted from the frozen and formalin-fixed paraffin-embedded (FFPE) tissues and peripheral blood using a QIAamp DNA Mini Kit and QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer's instructions. The TaqMan RNase P Detection Reagents Kit was used to quantify the purified DNAs. Semiconductor-based next-generation sequencing was performed as described previously . DNA washttp://www.broadinstitute.org/igv) was used to filter out possible strand-specific errors, such as a mutation that was only detected in the forward or reverse DNA strand but not in both strands.Genome Reference Consortium Human Build 37 (GRCh37/hg19) was used as a reference. Alignment to the GRCh37/hg19 genome and sequencing read counting were performed in Torrent Suite version 5.0 (Thermo Fisher Scientific). Somatic mutations including SNVs and INDELs were detected using statistics in tumor and matched normal control samples from the Ion Reporter software 5.0 tumor-normal workflow (Thermo Fisher Scientific) or the provided control sequence data (Thermo Fisher Scientific), as described previously . The 20\u00d7CNVs were detected by Ion Reporter software (Thermo Fisher Scientific) using an algorithm based on a hidden Markov model. Recurrent genomic regions with CNVs were identified by copy numbers \u22653 (gain) and <2 (loss). CNVs were analyzed for somatic mutations, signaling pathways, and patient's prognoses.https://genome.ucsc.edu/). Sanger sequencing is performed according to standard protocols. In brief, target DNAs were amplified from total DNAs with primers (Target sequences were surveyed by UCSC Genome Browser on Human GRCh37/hg19 Assembly ( primers by polymhttp://gostat.wehi.edu.au/) and The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8 (https://david.ncifcrf.gov/) as described [Functional gene annotation was performed using GOstat as described .The Kaplan-Meier method was used to estimate survival distributions for each group with the log-rank test among subgroups using JMP built-in modules (SAS Institute Inc.) . Hazard Statistical analyses were performed using JMP v10 (SAS Institute Inc.). Statistical significance was assessed using a log-rank test. P < 0.05 was considered statistically significant."} +{"text": "The Nurses Improving Care for Health System Elders (NICHE) program aims to improve geriatric care competencies for improved care quality. A quantitative descriptive design utilizing secondary data analysis was done to evaluate geriatric workforce enhancement efforts in one acute healthcare system. Data were collected using the Geriatric Institutional Assessment Profile (GIAP) from 2008 and 2013. The GIAP measures perceived professional issues on a Likert scale from best=0 to poor=10. Staff perception of the Geriatric Care Environment was scored by the GIAP as: age sensitive care delivery (0-40), institutional values (0-28), resource availability (0-32) and capacity for collaboration (0-12). Higher scores on the Geriatric Care Environment reflected improvements. Independent sample t-tests examined changes in baseline scores. Post-NICHE implementation, compared to peer hospitals by teaching status and bed size in 3 hospitals there were significantly (p<0.05) improved scores for: access to geriatric services (2.79-3.21), burden of behavioral problems (2.40-3.15), aging sensitivity care delivery (26.05-29.53), institutional values (18.85-19.59) and resource availability (19.51-19.97). Peer hospitals had significantly (p<0.05) better scores for: disagreements among staff about treatment of older adults (1.63-1.94) and capacity for collaboration (7.72-7.99). Findings indicate improvement in perceived professional issues and need for improvement in the geriatric care environment and care redesign to progress to becoming an Age-Friendly health system. This was an initial step in a health system to improve care quality through health workforce development."} +{"text": "PRPF3 expression is potentially associated with carcinogenesis. However, the biological role of PRPF3 in hepatocellular carcinoma (HCC) remains to be determined. We analyzed PRPF3 expression via multiple gene expression databases and identified its genetic alterations and functional networks using cBioPortal. Co-expressed genes with PRPF3 and its regulators were identified using LinkedOmics. The correlations between PRPF3 and cancer immune infiltrates were investigated via Tumor Immune Estimation Resource (TIMER). PRPF3 was found up-regulated with amplification in tumor tissues in multiple HCC cohorts. High PRPF3 expression was associated with poorer overall survival (OS) and disease-free survival (DFS). Functional network analysis suggested that PRPF3 regulates spliceosome, DNA replication, and cell cycle signaling via pathways involving several cancer-related kinases and E2F family. Notably, PRPF3 expression was positively correlated with infiltrating levels of CD4+ T and CD8+ T cells, macrophages, neutrophils, and dendritic cells. PRPF3 expression showed strong correlations with diverse immune marker sets in HCC. These findings suggest that PRPF3 is correlated with prognosis and immune infiltrating in HCC, laying a foundation for further study of the immune regulatory role of PRPF3 in HCC.pre-mRNA processing factor 3 (PRPF3) is an RNA binding protein in a core component of the exon junction complex. Abnormal Hepatocellular carcinoma (HCC) is the most common form of liver cancers , which hPRPF3), a component of the U4/U6 di-snRNP, is required for U4/U6\u2022U5 tri-snRNP formation and recruitment to active spliceosomes, which is essential for efficient pre-mRNA splicing . Th. Th15]. ng liver . POU2F1 pathway . Suppres hypoxia .PRPF3 AMP involves in the immune response and inflammatory response.Whether for the liver-specific PPI network or the TF-miRNA coregulatory network, the function annotation implied that PRPF3 expression was correlated with immune infiltration levels in HCC from TIMER database. The results show that PRPF3 expression has significant correlations with tumor purity and significant correlations with the dominant immune cells infiltration levels and 1.36 times higher risks on DFS (p = 0.0259) .PRPF3 co-occurrence genes with Log Ratio > 10 also showed the significant correlations with tumor purity and varying degree with immune cells , immune inhibitory or stimulatory genes (including immune checkpoint gene sets), cytokine-related genes, cancer-testis antigen genes, and major histocompatibility complex (MHC) genes genes .PRPF3 expression level was significantly correlated with most immune marker sets of various immune cells in LIHC. PRPF3 and marker genes of activated T cells. In activated CD8 T cells, PRPF3 is highly correlated with Myelin Protein Zero Like 1 (MPZL1). Indeed, AMP of MPZL1 promotes tumor cell migration through Src-mediated phosphorylation of cortactin in HCC [PRPF3 is significantly correlated with NUF2 Component Of NDC80 Kinetochore Complex (NUF2), which was suggested as a valuable prognostic biomarker to predict early recurrence of HCC [TTK), Kinesin Family Member 2C (KIF2C), Centrosomal Protein 55 (CEP55), Sperm Flagellar 2 (SPEF2), Opa Interacting Protein 5 (OIP5), and Tubulin Polymerization Promoting Protein Family Member 2 (TPPP2), etc., were also shown significant correlations with PRPF3 expression.After the correlation adjustment by tumor purity, the results revealed the n in HCC . For acte of HCC . DendritPRPF3 and marker genes of Treg and myeloid-derived suppressor cell (MDSC), such as Methyltransferase Like 7A (METTL7A), Adenosine Deaminase TRNA Specific 2 (ADAT2), LDL Receptor Related Protein 1 (LRP1), Lysosomal Protein Transmembrane 4 Beta (LAPTM4B), Nuclear Factor Erythroid 2-Related Factor 3 (NFE2L3), Leucine Rich Repeat Containing 42 (LRRC42), CD14, Suppressor Of Cytokine Signaling 2 (SOCS2), Hydroxysteroid Dehydrogenase Like 2 (HSDL2), and Ankyrin Repeat Domain 10 (ANKRD10). Interestingly, LAPTM4B decreases Transforming Growth Factor Beta 1 (TGF-\u03b21) production in human Treg cells [+HLA-DR\u2212/low phenotype that suppresses the proliferation of T cells [+HLA-DR\u2212/low MDSCs was significantly higher in HCC patients [We also found significant correlations between eg cells . A recen T cells . The frepatients .CTLA4) and Programmed Cell Death 1 (PD-1), and Programmed Cell Death 1 Ligand 2 (PD-L2) have positive or negative correlations with PRPF3 expression, respectively, while TNF Superfamily Member 4 (TNFSF4), Inducible T Cell Costimulator Ligand (ICOSLG), TNF Superfamily Member 9 (TNFSF9), etc., have correlations with PRPF3 expression in immunostimulator genes. Specifically, we showed chemokine (C-C motif) ligand (CCL)-16, CCL14, Interleukin 12A (IL12A), CCL20, CCL26, C-X3-C Motif Chemokine Ligand 1 (CX3CL1), CCL27, and CD19 Molecule (CD19) were significantly correlated with PRPF3 expression (p < 0.0001). Overexpression of the cancer-testis (CT) antigens represents the advanced disease of cancer. High PRPF3 expression relates to high induction of cancer-testis antigen genes in LIHC, such as the significant positive correlation between PRPF3 and NUF2, TTK, KIF2C, CEP55, SPEF2, and OIP5, etc.In immunoinhibitory genes, results showed the expression levels of Cytotoxic T-Lymphocyte Associated Protein 4 (PRPF3 were Interleukin Enhancer Binding Factor 2 (ILF2), CREB Regulated Transcription Coactivator 2 (CRTC2), NUF2, Exonuclease 1 (EXO1), and TTK. And the top 5 markers negatively correlated with PRPF3 were Transmembrane BAX Inhibitor Motif Containing 6 (TMBIM6), METTL7A, Tubulin Polymerization Promoting Protein Family Member 2 (TPPP2), HIG1 Hypoxia Inducible Domain Family Member 1A (HIGD1A), and Aldo-Keto Reductase Family 7 Member A3 (AKR7A3). Survival map analysis clearly demonstrated the high risk of PRPF3 positively correlated marker genes and the low risk of PRPF3 negatively correlated marker genes . Oncomine is a cancer microarray database and web-based data-mining platform. The threshold was determined according to the following values: p-value of 0.05, fold change of 1.5, and gene ranking of all.The expression level of the http://ualcan.path.uab.edu) uses TCGA level 3 RNA-seq and clinical data from 31 cancer types [UALCAN (http://gepia.cancer-pku.cn/) is an interactive web that includes 9,736 tumors and 8,587 normal samples from TCGA and the GTEx projects [The Gene Expression Profiling Interactive Analysis (GEPIA) database has multidimensional cancer genomics data sets [PRPF3.The cBio Cancer Genomics Portal (ata sets . Mutatiohttp://www.linkedomics. org/login.php) is a web-based platform for analyzing 32 TCGA cancer-associated multi-dimensional datasets [PRPF3 co-expression was analyzed statistically using Pearson\u2019s correlation coefficient, presenting in volcano plots, heat maps, or scatter plots. Function module of LinkedOmics performs analysis of Gene Ontology biological process (GO_BP), KEGG pathways, kinase-target enrichment, miRNA-target enrichment and transcription factor-target enrichment by the gene set enrichment analysis (GSEA). The rank criterion was FDR < 0.05 and 1000 simulations were performed.The LinkedOmics database [Network interpreting gene expression was used by NetworkAnalyst 3.0 tool (yst.ca/) , which iyst.ca/) .https://cistrome.shinyapps.io/timer/), which includes 10,897 samples across 32 cancer types [PRPF3 expression in LIHC and the correlation of PRPF3 expression with the abundance of immune infiltrates, including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells, as well as the tumor purity.TIMER is a comprehensive resource for systematic analysis of immune infiltrates across diverse cancer types from TCGA , Natural killer T cell (NKT), Activated dendritic cell, Plasmacytoid dendritic cell, Immature dendritic cell, Macrophage, Eosinophil, Mast cell, Monocyte, Neutrophil, Tumor-associated macrophage (TAM), M1 Macrophage, and M2 Macrophage, as well as markers from multiple types of oncoimmunology containing genes associated with immunomodulators and chemokines, were referenced in prior studies [Further, gene signatures of 28 tumor-infiltrating lymphocytes (TILs) , compris studies .t-test p < 0.05 was utilized to determine the statistical significance between groups with different expression level of PRPF3. We compared the survival and recurrence-free survival (RFS)) of HCC patients separated by the median expression level of specific genes. Kaplan-Meier curves were used to compare the survival time differences. The log-rank test p < 0.05 indicates the significance of survival time differences. The survival analyses were performed by R programming of \u201csurvival\u201d and \u201csurvminer\u201d package.The PRPF3 and immune signature score or gene expression levels using the Spearman or partial Spearman method. Tumor purity-corrected partial Spearman\u2019s correlation calculated the correlation between PRPF3 expression and immune genes while controlling for tumor purity, which was explored using ppcor package [p < 0.05 indicates the significance of correlation.We calculated the correlation between package . The thrSupplementary FiguresSupplementary Table 1Supplementary Table 2Supplementary Table 3Supplementary Table 4Supplementary Table 5Supplementary Table 6Supplementary Table 7Supplementary Table 8Supplementary Table 9"} +{"text": "Physical activity is an established intervention for the management of arthritis. This study evaluated the effect of 3 months of participation in Gerofit on physical function by arthritis status. Participants, 519 Veterans aged \u2265 65 years self-reported either no arthritis (NA) (49%), upper body arthritis (UB) (8.2%), lower body arthritis (LB) (12.7%), or both upper and lower body arthritis (UB&LB) (30.4%) upon enrollment. Physical function measures were assessed at baseline and follow-up. Mean differences between time points were calculated. At baseline, compared to NA, LB and UB&LB had slower GS (1.10 and 1.06 vs 1.13) and shorter SMW distance (468.8 and 448.8 vs 490.7). All groups tended to increase physical function, with greatest improvement among LB . Participation in Gerofit is associated with functional gains, regardless of burden of disease."} +{"text": "M1, M2, M4, M7, and M8) were designed and synthesized, and their respective chemical structures were deduced using various spectral tools . The compounds were synthesized via Schiff's condensation reaction and their anti-inflammatory activity was investigated applying the Carrageenan-induced paw edema model against Diclofenac as positive control. Percentage inhibition of edema indicated that all compounds were exhibiting a comparable anti-inflammatory activity as Diclofenac. Moreover, the anti-inflammatory activity was supported via virtual screening using molecular docking study. Interestingly compound M2 showed the highest in vivo activity (61.32% inhibition) when compared to standard Diclofenac (51.36% inhibition) as well as the best binding energy score (-10.765) and the virtual screening docking score (-12.142).The design, synthesis, and development of novel non-steroidal anti-inflammatory drugs (NSAIDs) with better activity and lower side effects are respectable area of research. Novel Diclofenac Schiff's bases ( Diclofenac is a phenyl acetic acid derivative and belongs to the non-steroidal anti-inflammatory drugs (NSAIDs) family .Despite the huge prescription of NSAIDs, most of them exhibit shared set of adverse effects including gastrointestinal complications \u20136 that aAmide modification of carboxylic acid group of the existing NSAIDs such as Indomethacin, Meclofenamic acid, and Ketoprofen conferred the compounds greater selectivity for COX-2 over the COX-1 enzyme resulting in GI sparing effect .Diclofenac is potent cyclooxygenase enzyme inhibitor with complete absorption and extensive metabolism . Isatin In light of the above, regarding the biological importance of Diclofenac and Isatins as well as increasing COX-2 selectivity via extension of ligand size, we aim to design and synthesize novel Diclofenac derivatives with lower side effects, potent activity, and selective cyclooxygenase COX-2 enzyme inhibition. After synthesis, we aimed to evaluate the anti-inflammatory activity via in vivo method and molecular docking study. Many methods are used for the evaluation of anti-inflammatory activity including Carrageenan edema method, which is selected in this essence, as it gives constant results with most of anti-inflammatory drugs besides being rapid and simple in vivo method .Molecular docking is valuable tool for studying the binding affinities and ligand-target interaction ; hence wThe 1H Isatin and 5-bromo Isatin were purchased from Sigma-Aldrich, USA, while Diclofenac was obtained as gift sample from Unamid pharmaceuticals, Sudan.All solvents and reagents are of analytical grade and used without further purification. Precoated silica gel TLC plates were used to monitor reaction progress; UV lamp (254 nm) was used to visualize the spots. The purity of synthesized compounds was checked by TLC using ethyl acetate and n-hexane (1:1) as a mobile phase. For each compound, a single spot was detected in the TLC plate reflecting the purity of the corresponding compound. Melting points were determined on Electrothermal Karl kolb and were uncorrected.\u03cd (cm-1). NMR spectra were determined in acetone and recorded on Bruker Avance 111 NMR Spectrophotometer operating at 400 MHz for 1H and at 100 MHz for 13C NMR at the research center, College of Pharmacy, Ain Shams University, Egypt. The chemical shifts are expressed as \u03b4 values (ppm) relative to TMS as internal standard. Signals are indicated by the following abbreviations: s = singlet, bs = broad singlet, d = doublet, dd = doublet of doublet, t = triplet, q = quartet, and m = multiplet. The J constant was given in Hz.Infrared (IR) spectra were recorded as KBr disk using SHIMADZU FT\u2013IRapparatus, Japan. The data is given in Mass spectra were taken on Single ISQLT Quadrapole\u2013MS spectrometer at the research center, College of Pharmacy, Azhar University, Egypt. Mass spectral data were given as m/z (intensity %). I was weighed and placed in 50 ml round bottom flask and dissolved in 40 ml methanol and few drops of concentrated sulfuric acid were added. The reaction mixture was refluxed for 6 hours and allowed to cool to room temperature. The reaction was monitored by TLC using ethyl acetate and n-hexane (1:1) as mobile phase and the product was obtained by addition of 3 ml of sodium carbonate solution. The product was purified by recrystallization from methanol.The esterification reaction was carried out using Fischer esterification procedure in acidi III with Isatin nucleus a1 for 6 hours in Schiff's condensation reaction carried out in the presence of catalytic amount of glacial acetic acid. Preparation of Diclofenac hydrazide III involved synthesis of Diclofenac ester II from Diclofenac acid I via Fischer esterification reaction. The ester II is then reacted with hydrazine hydrate to afford the hydrazide III. Modification to Isatin nucleus a1 is carried out either by hydroxy methylation reaction with 37% formalin and refluxing for 5 hours to give intermediate IV or through N-Alkylation to afford intermediate V.The core reaction is achieved by refluxing equimolar quantities of Diclofenac hydrazideII) was placed in 50 ml round bottom flask and dissolved in 20 ml absolute ethanol, and 30 ml of hydrazine hydrate 80% was added or N-Alkylation reaction (V). For intermediate IV, 0.5 grams of appropriate Isatin was initially weighed and refluxed with 20 ml of formalin (37 % v/v) for 5 hours. After evaporation of solvent, the resultant solid was purified by recrystallization from ethanol.The synthesis of both intermediates is based on N-modification of Isatin V, a weight equivalent to 0.03 moles of appropriate Isatin was properly placed in 50 ml round bottom flask containing 20 ml of dimethyl formamide (DMF). An amount equal to 1.5 moles of potassium carbonate was added. This mixture was stirred for 30 minutes; after the specified time, a volume equivalent to 1.5 moles of an alkyl halide was added and the reaction mixture was stirred at 80\u00b0C for 24 hours. The reaction was monitored for completion by TLC and final compounds were precipitated by addition of 20 ml of distilled water and then purified by recrystallization from ethanol.For intermediate a1 and Diclofenac hydrazide III were dissolved in 20 ml of ethanol and refluxed for 6 hours in the presence of 5 drops of glacial acetic acid. Final compounds were obtained and recrystallized from suitable solvent.Equimolar quantities (0.03 moles) of appropriate IsatinThe result of yield percent, physiochemical properties, and spectroscopic data are presented in the Results section.The synthesized Diclofenac Schiff's bases were investigated for anti-inflammatory activity via Carrageenan-induced paw edema model. These compounds were tested in a single dose molecularly equivalent to 20mg/Kg of Diclofenac acid and compared to Diclofenac as standard , 19.Wistar albino rats of either sex weighing 90-120 grams were obtained from the animal house of Khartoum University, Khartoum, Sudan. All the animals were housed under standard environmental conditions of temperature (24\u00b12\u00b0C) and relative humidity of 30-70 %. All the animals were fasted overnight prior to the experiment with free access to water. All the experimental procedures and protocols used were reviewed and approved by the Institutional Animal Ethical Committee (IAEC) of Faculty of Pharmacy, Omdurman Islamic University, constituted in accordance with the guidelines of the Committee for the Purpose of Control and Supervision of Experiment on Animals (CPCSEA).Carrageenan, carboxymethyl cellulose (CMC), and all the chemicals were of analytical grade.This investigation was performed following procedure of Winter et al. . AnimalsOne hour after administration of tested compounds, each rat received a subplanter injection of 0.1 ml of a freshly prepared Carrageenan solution (1.0% w/v) in its right hind paw.The swelling volume of the paw was measured before (time 0) and at 1, 2, 3, and 4 hours after the carrageen injection.The measurements of the hind paw volumes were given in millimeters (mm) using vernier caliper and the percentage decrease in the paw volume (% inhibition of edema) was calculated from the normal paw volume using the following equation: of rats .Data was expressed as % inhibition \u00b1 S.E.M. and analyzed by one-way ANOVA to determine the significance of the difference between the control group and rats treated with the test compounds. The difference in results was considered significant when P < 0.05. All statistical calculations were carried out using Graph Pad\u00ae Prism 5.0 (USA) statistical software .In an attempt to deduce whether lipophilicity affected observed activity of tested compounds, the predicted LogP values of compounds were related to percentage inhibition of oedema as expression of activity. Despite variation in ClogP values, there is no clear relationship between lipophilicity and observed activity as shown in Mus musculus COX-2 (PDBID 1PXX). For the docking process, the targets were prepared and minimized via Cresset Flare software (100%); 278(15%); 250(16%); 242(11%); 217(13%); 214(60%); 154(30%); 136(23%); 91(12%); 69(17%); 55(20%); 43(19%); 41(15%). (III). 2-phenyl)acetohydrazideWhitish yellow, odorless crystals; Yield%: 81; m.p: 159 - 161\u00b0C (30%); 307(15%); 278(45%); 214(25%); 154(100%); 136(68%); 107(20%); 89(25%); 77(20%); 55(18%); 43(14%); 41(14%). - 161\u00b0C ; IR \u03cd cm (IV). 1-(Hydroxymethyl) indoline-2,3-dionePale orange, odorless powder; Yield%: 75; m.p: 230-233\u00b0C; IR \u03cd cm\u22121 (KBr): 3446 sharp and medium (-OH stretch); 2983(ArH stretches); 2920(Aliphatic \u2013CH stretches); 1733 sharp & strong(C=O stretches); 1610(Aromatic C=C stretches); 1095(C-O stretch). 1H NMR-Acetone: \u03b4 ppm 5.19; 7.07; 7.08; 7.45; 7.58. 13C NMR-Acetone: \u03b4 ppm 72.4 (N-CH2); 111.64, 117.6, 123.6, 124.3, 138.2, 150.7 (Ar-C); 157.53(N-C=O); 183.6 (C=O). EI-MS, Rel. Int (%): 177 ([M+] (30%); 130(12%); 128(12%);105(14%); 104(25%); 136 (68%); 103(18%); 84(14%); 76(12%); 76(30%); 70(12%); 6 (18%); 65(24%); 64 (14%); 59(12%); 58(52%); 56(24%); 55(48%); 53(30%); 49(30%); 44(72%); 43 (78%); 42(100%). (V). 1-Decylindoline-2,3-dioneReddish, odorless powder; Yield%: 68; m.p: 73-75\u00b0C; IR \u03cd cm\u22121 (KBr): 3095(ArH stretches); 2918, 2848(Aliphatic \u2013CH stretches); 1957 (Aromatic overtone); 1737 sharp & strong (C=O stretches); 1608, 1465(Aromatic C=C stretches). 1H NMR-Acetone: \u03b4 ppm 0.73; 1.13-1.24; 1.56-1.59; 3.62; 7-7.06; 7.43; 7.55 . 13C NMR-Acetone: \u03b4 ppm 13.45 (Aliphatic CH3); 22.40, 26.60, 27.06, 31.69, 39.71 (Aliphatic CH2); 61.01(N-CH2-CH2); 72.50(N-CH2); 110.57, 117.72, 123.16, 124.36, 138.21, 151.34 (Ar-C); 157.96 (NH2-C=O); 183.73(C=O). EI-MS, Rel. Int (%): 287 ([M+] (2%); 242(12%); 236(10%); 214(20%); 146(12%); 132(12%);130(10%); 117(12%); 111(15%); 109(18%); 98(25%); 97(38%); 95 (30%); 84(38%); 83(55%); 81(42%);73(25%); 71(64%); 69(88%); 67(40%); 60 (18%); 57(100%); 55(92%); 54(15%); 45(22%). M1. 2-phenyl)-N\u2032-(2-oxoindolin-3-ylidene)acetohydrazidePale yellow, odorless powder; Yield%: 62; m.p: above 240\u00b0C; IR \u03cd cm\u22121 (KBr): 3272(NH stretches); 3087, 3072(ArH stretches); 2881, 3823(Aliphatic \u2013CH stretch); 1720 sharp & strong (Ar-NH-C=O stretch); 1666 sharp and strong (-NHN-C=O stretch); 1606(C=N stretch); 1504, 1456 (Aromatic C=C stretches). EI-MS, Rel. Int (%): 439 [M+] (6%); 307(30%); 289(15%); 154(100%); 136(92%); 107(20%); 89(23%); 77(20%). M2. N\u2032-(5-Bromo-2-oxoindolin-3-ylidene)-2-phenyl) acetohydrazidePale orange, odorless powder; Yield%: 66; m.p: above 240\u00b0C; IR \u03cd cm\u22121 (KBr): 3363(NH stretches); 3143, 3107(ArH stretches); 2846, 2792(Aliphatic \u2013CH stretch); 1915(Aromatic overtone); 1733 sharp & strong (Ar-NH-C=O stretch); 1685 sharp and strong (-NHN-C=O stretch); 1606(C=N stretch); 1494, 1467, 1446 (Aromatic C=C stretches). 1H NMR-Acetone: \u03b4 ppm 3.53; 6.42; 6.92; 7.18; 7.46-7.48 ; 8.03. EI-MS, Rel. Int (%): 518 ([M+] (22%); 516(12%); 281(20%); 280(34%); 279(78%); 276(100%); 244(20%); 242(70%); 241(42%); 239(38%); 215(15%); 214(44%); 181 (20%); 179(28%); 151(22%); 132(12%); 88(12%); 77(12%). M4. 2-phenyl)-N\u2032-(1-(hydroxymethyl)-2-oxoindolin-3-ylidene)acetohydrazidePale red, odorless powder; Yield%: 64; m.p: above 240\u00b0C; IR \u03cd cm\u22121 (KBr): 3267 Broad (OH stretch); 3033(ArH stretches); 2972(Aliphatic CH2 stretch); 1911(Aromatic overtone); 1787 sharp & strong (Ar-NH-C=O stretch); 1622 sharp and strong (-NHN-C=O stretch); 1612(C=N stretch); 1583, 1504, 1452 (Aromatic C=C stretch). 1H NMR-Acetone: \u03b4 ppm 3.62; 4.14; 6.45; 6.87-6.88; 7.11-7.13; 7.30; 7.43-7.46.13C NMR-Acetone:\u03b4 ppm 61.04(ArCH2-C=O); 72.4(N-CH2-OH); 116.4, 117, 121.22, 121.29, 123.61, 123.78, 124.39, 124.60, 125.39, 127.34, 127.48, 129.02, 129.05, 129.51, 129.56, 129.61(Ar-C); 158(-C=O-NH); 170.44 (C=O).EI-MS, Rel. Int (%): 469 ([M+] (2%); 410(22%); 408(70%); 406(100%); 392 (18%); 381(20%); 380(50%); 378(75%); 366(20%); 364(30%); 363(15%); 344 (20%); 343(20%); 333(50%); 291(32%); 289(50%); 256(38%); 254(28%); 217 (25%); 216(28%); 213(90%); 117(10%); 107(55%); 106(20%); 95(12%); 83 (12%); 71(15%). M7. N\u2032-(1-Decyl-2-oxoindolin-3-ylidene)-2-phenyl)acetohydrazidePale yellow, odorless powder; Yield%: 67; m.p: above 240\u00b0C; IR \u03cd cm\u22121 (KBr): 3288(NH stretches); 3066(Ar-H stretches); 1722 sharp & strong (Ar-NH-C=O stretch); 1664 sharp and strong (-NHN-C=O stretch); 1610(C=N stretch); 1510, 1458(Aromatic C=C stretches). 1H NMR-Acetone: \u03b4 ppm 0.71; 1.21-1.58; 2.81; 3.47; 3.68; 4.236; 6.33; 6.77; 6.99-7.03; 7.26-7.33; 7.64.13C NMR-Acetone:\u03b4 ppm 13.48(AliphaticCH3); 29.01(AliphaticCH2); 29.8(AliphaticCH2); 39.39(N-CH2-CH2); 62(C=O-CH2); 72.51(N-CH2); 117.07, 119.71, 120.66, 121.47, 123.07, 124.89, 127.66, 128.98, 129.05, 129.85, 129.91, 131.38, 131.54, 134.18, 137.69(Ar-C); 160.99(NH-C=O);173.98(N-C=O).EI-MS, Rel. Int (%): 579 ([M+] (1%); 302(40%); 301(100%); 285(40%); 278(30%); 277(18%); 225(15%); 224(62%); 214(20%); 130(15%); 128(18%); 105(15%); 103 (48%); 102(25%); 89(10%); 77(25%); 75(50%); 74(20%); 69(18%); 57(14%). M8. N\u2032-(1-Benzyl-2-oxoindolin-3-ylidene)-2-phenyl)acetohydrazidePale yellow, odorless powder; Yield%: 67; m.p: above 240\u00b0C; IR \u03cd cm\u22121 (KBr): 3288(NH stretches); 3199 (Ar-H stretches); 2966, 2920(Aliphatic CH2 stretches); 1726 sharp & strong (Ar-NH-C=O stretch); 1664 sharp and strong (-NHN-C=O stretch); 1606(C=N stretch); 1508, 1460(Aromatic C=C stretches). 1H NMR-Acetone: \u03b4 ppm 3.60; 3.98; 6.3-7.35; 7.53; 8.20.See 1See The development of new anti-inflammatory drugs via hybridization techniques through linking of new entities or mutual prodrugs has been used extensively in literature to obtain new compounds with better actions . It is r\u22121) and appearance of a band in the range of 1585-1620 cm\u22121 which denotes stretching of the newly formed imine functional group (C=N). Furthermore, the spectra bear two major sharp and strong absorption bands between 1720-1780 cm\u22121 and 1660-1690 cm\u22121 characterizing stretches of two carbonyl functional groups (C=O lactam) and (C=O hydrazide), respectively. For 1H NMR, the most observable trend is related to aromatic protons that were always equal to the sum of aromatic protons of target compounds. The compounds also shared a common absorption signal around 3.55 ppm, characterizing the Diclofenac aliphatic methylene group (Ar-CH2-). The 13C NMR spectra of M4 and M7 are generally featured by increase in aromatic carbons compared to corresponding starting materials indicating the success of the reaction. Similarly, the spectra showed a signal around 72 ppm recognizing the (N-CH2-) moiety and two carbonyl absorptions at around 160 ppm and 170 ppm relating to the cyclic carbonyl group (N-C=O) and the acyclic carbonyl group (Ar-CH2-C=O), respectively. Although the molecular ion peak [M+] varied in intensity, it was evidenced for all analyzed Schiff's bases. A special peak at m/z = 215 seemed to form a common fragment among the compounds.Spectral characterization tools were applied to confirm the proposed structures of synthetic compounds, alongside physical data such as TLC analysis and melting point. The IR spectra of Diclofenac Schiff's bases were clearly differentiated from their respective intermediates, evidenced by absence of ketone stretching 1. M1 and M2 onset of action seems to be earlier than other synthesized compounds that start at the first hour and maximize in the second hour, indicating that M1 and M2 act on the late responses to inflammation. The pattern of activity of compound M4 is rather different from other candidates; the compound showed activity (43.13% and 50.39%) at two different time intervals . In contrast, in M7 and M8, the maximum inhibition was achieved at the fourth hour, suggesting that they have a delayed action. This delay in onset of action might be explained by the high lipophilicity that leads to distribution out of blood, or as they are prodrugs that metabolized via N-Dealkylation into the active forms (M1). In Carrageenan model, the development of edema in the rat hind paw following the injection of Carrageenan is a biphasic response, including the initial phase of edema (0-1 hour) that is not inhibited by NSAIDs, as well as the second phase of swelling (1-6 hours) that involve production of prostaglandins from the inducible cyclooxygenase (COX-2) enzyme . Within In order to validate this hypothesis, we used XenoSite server to predi M2 and M4 were the best and this finding is in consistence with the in vivo results.The pharmacological activity of NSAIDs is linked to the suppression of prostaglandin biosynthesis from arachidonic acid through inhibiting the enzyme cyclooxygenases . In orde M2, it showed the best binding energy score (Dg-score) and the virtual screening docking score, but due to the 2 violations of Lipinski rule-of-five (Rof5) it showed a decreased Rank score. On the contrary, M4 has no violations in Lipinski rule-of-five (Rof5); consequently it showed the highest Rank score are better than the control compounds . Regardink score . M2 forms hydrogen bonds with Tyr385 and Ser530. Additionally, the binding conformation of M2 is identical to Diclofenac, meaning that M2 will be promising cyclooxygenase (COX) enzyme inhibitor with irreversible action; consequently M2 is proven to be the best of synthesized compounds (The most important amino acids in active site of cyclooxygenase (COX) enzymes are Tyrosine (Tyr385) that is responsible for the activity via hydrogen abstraction and radical formation as well as Serine (Ser530); hence formation of hydrogen bond between NSAIDs and Tyr385 will inhibit the activity of cyclooxygenase (COX) enzymes and the formation of hydrogen bond with Ser530 will lead to irreversible inhibition . Accordiompounds . M2, it is the hydrogen of secondary amino group in amide bond). Moreover, we noticed that the aromatic system in Diclofenac is important for the hydrophobic interaction with the hydrophobic amino acids in the active site; hence it is important for stabilization of binding conformation. Furthermore, the neutral amide bond between Diclofenac and Isatin moiety masked the acidic functional group of Diclofenac that serve in reduction of gastrointestinal side effects. In addition, electron withdrawing groups at para position of phenyl ring in Isatin moiety (as in M2) prevent the interaction of Isatin's phenyl group (as in M1) that alter the optimum binding conformation leading to reduction in activity (M2 is better than M1) , we noticed that the hydrogen bond acceptors are essential for binding with the oxygen atom of hydroxyl group in amino acid Tyr385 and henthan M1) . On the M1, M2, M4, M7, and M8) were designed and their chemical structures were spectrally confirmed. The compounds were evaluated in vivo and in silico for their possible anti-inflammatory activity. The 5-bromo substituted compound (M2) showed the maximum in vivo activity and scored the best binding energy and virtual screening docking scores, arriving at the fact that it could be a good candidate for anti-inflammatory drug of higher activity, COX-2 enzyme selectivity, and lower gastrointestinal side effects. It is suggested that compounds M7 and M8 are prodrugs evidenced by their delayed onset of action and their susceptibility to N-Dealkylation by Cytochrome 2C9 enzyme.Five Diclofenac Schiff's bases ("} +{"text": "STAT4 rs7574865 polymorphism has been evidently associated with susceptibility to Rheumatoid Arthritis (RA) in European and Eastern Asian populations, whereas studies in other countries reported otherwise.STAT4 rs7574865 polymorphism in a group of Syrian RA patients.We investigated the distribution of STAT4 rs7574865 was genotyped by direct sequencing. RA patients were stratified according to Anti-Citrullinated Protein Antibodies (ACPA) status for analysis.Eighty-one RA patients and forty healthy controls were enrolled and STAT4 rs7574865 allele/genotype frequencies were found between ACPA-positive RA patients, ACPA-negative RA patients, and healthy controls (P>0.05).Minor T allele frequencies were 30.4%, 16.7%, and 23.8% in ACPA-positive RA patients, ACPA-negative RA patients, and healthy controls, respectively. No significant differences in STAT4 rs7574865 TT genotype showed a potential impact on ACPA positivity in Syrian RA patients. However, STAT4 rs7574865 effect on RA onset and severity is minor compared to other genetic factors such as HLA-DRB1 shared epitope alleles. It givetibility . Their itibility . Beyond y [STAT4 , 7, havey [STAT4 .STAT4) gene encodes for a transcription factor that lies in the signaling pathway of IL-12 and IL-23 leading to the production of IFN\u03b3 and differentiation of CD4+ T-cells into Th1 and Th17 [1/Th17 mediated inflammatory response [STAT4 gene in synovial macrophages [STAT4 gene and tagged by the T allele of rs7574865 has been shown to have a significant association with RA [STAT4 rs7574865 polymorphism for the first time among a group of Syrian RA patients adding to the data that have only been scarcely collected in the Middle East.Signal Transducer and Activator of Transcription 4 1987 revised criteria . PatientHLA-DRB1 genotype has been analyzed previously [Forty healthy unrelated controls matched for age and ethnicity were also enrolled in the study. Neither controls nor any of their first degree relatives had RA or any other autoimmune disease. An informed consent was obtained from both patients and healthy individuals whose eviously . This stSTAT4 rs7574865 by direct DNA sequencing. A 182 bp-fragment was amplified using a forward primer 5'-GGT GTG GAT GGA GGT AAG GA-3' and a reverse primer 5'-ATC CCC TGA AAT TCC ACT GA-3' [\u00ae Pro S . Thermal cycling was initiated at 94\u00b0C for 2 min, followed by 45 cycles of denaturation at 94\u00b0C for 2 min, annealing at 55\u00b0C for 30 sec and extension at 72\u00b0C for 2 min, and a final extension at 72\u00b0C for 7 min. Agarose gel electrophoresis (2.5%) was used for DNA visualization.DNAs extracted from whole blood samples were genotyped for CT GA-3' manufact\u00ae Terminator v3.1 Cycle Sequencing Kit on the ABI PRISM\u00ae 3100-TMAvant Genetic Analyzer according to the manufacturers' instructions. STAT4 rs7574865 genotypes GG, GT and TT were considered as wild-type, heterozygote mutant, and homozygote mutant, respectively.PCR products were purified using a High Pure PCR Product Purification Kit and sequenced using the forward primer and a BigDyeSTAT4 rs7574865 and HLA-DRB1 among study groups were analyzed using Kruskal-Wallis H and Mann-Whitney U tests. Whenever a significant difference was inferred, Kendall's tau-b correlation coefficient and Odds Ratio (OR) were calculated to test the strength and direction of the association between relevant variables. Statistical analyses were performed using IBM SPSS Statistics 19.0 software and MedCalc for Windows, version 17.7.1 and P-value <0.05 was considered significant.Samples were analyzed for Hardy-Weinberg Equilibrium (HWE) using a chi-square goodness-of-fit test of SNPStats . Differe3Our study included 65 (80.25%) females and 16 (19.75%) males aged 41.4\u00b110.6 years, and whose RA disease lasted for 11.3\u00b16.3 years with ESR and CRP values of 56.7\u00b129.7 mm/hr and 31.1\u00b138.4 mg/L, respectively. In addition, 55 of 81 (67.90%) RA patients were positive for RF and 51 of 81 (62.96%) RA patients were positive for ACPA with values of 160.7\u00b192.4 RU/mL. On the other hand, healthy controls included 26 (65%) females and 14 (35%) males aged 39.42 \u00b110.90 years.HLA-DRB1 alleles were 59 of 102 (57.8%), 20 of 60 (33.3%), and 16 of 80 (20%), while the frequencies of presumably protective (P) HLA-DRB1 alleles (DRB*11 and *13) were 17 of 102 (16.7%), 16 of 60 (26.7%), and 34 of 80 (42.5%) in ACPA-positive RA patients, ACPA-negative RA patients, and healthy controls, respectively Table 1.The frequencies of presumably Risky (R) STAT4 rs7574865 G allele were 71 of 102 (69.6%), 50 of 60 (83.3%), and 61 of 80 (76.3%), while the frequencies of STAT4 rs7574865 T allele were 31 of 102 (30.4%), 10 of 60 (16.7%), and 19 of 80 (23.8%) in ACPA-positive RA patients, ACPA-negative RA patients, and healthy controls, respectively Table 2.The frequencies of STAT4 rs7574865 GG genotype (wild-type) were 26 of 51 (51%), 20 of 30 (66.7%), and 25 of 40 (62.5%), the frequencies of STAT4 rs7574865 GT genotype (heterozygote mutant) were 19 of 51 (37.3%), 10 of 30 (33.3%), and 11 of 40 (27.5%), and the frequencies of STAT4 rs7574865 TT genotype (homozygote mutant) were 6 of 51 (11.8%), 0 of 30 (0%), and 4 of 40 (10%) in ACPA-positive RA patients, ACPA-negative RA patients, and healthy controls, respectively Table 2.The frequencies of HLA-DRB1 allele/genotype frequencies were significantly different between ACPA-positive RA patients, ACPA-negative RA patients, and healthy controls (P=0.00), where R allele was weakly correlated with ACPA positivity and P allele was weakly correlated with healthy status . Moreover, ACPA positivity was 6.8 and 4.7 times more likely to occur in patients with R allele compared with healthy controls and ACPA-negative patients , respectively. In addition, healthy status was 4.5 and 7.2 times more likely to be maintained in individuals with P allele compared with ACPA-negative patients and ACPA-positive patients , respectively. When compared in pairs in terms of HLA-DRB1 alleles, R alleles were not significantly different between ACPA-negative RA patients and healthy controls (P=0.21) and P alleles were not significantly different between ACPA-positive RA patients and ACPA-negative RA patients (P=0.24) Table 1.No deviation from Hardy-Weinberg equilibrium was found in the control group (P=0.18). STAT4 rs7574865 allele/genotype frequencies were found between ACPA-positive RA patients, ACPA-negative RA patients, and healthy controls (P>0.05). When compared in pairs in terms of STAT4 rs7574865 genotype, homozygote mutant and wild-type genotypes were solely significantly different between ACPA-positive RA patients and ACPA-negative RA patients (P=0.041), where ACPA-positivity was not necessarily associated with TT genotype albeit weakly correlated Table 2. However, no significant correlation was found between STAT4 rs7574865 and HLA-DRB1 alleles/genotypes in ACPA-positive RA patients, ACPA-negative RA patients, and healthy controls (P>0.05).No significant differences in 4STAT4 rs7574865 among RA patients in Syria (25.3%) seems consistent with Tunisians (25%) [STAT4 rs7574865 has only been reported in Egypt. Albeit diverse among both RA patients (8% and 37%) and healthy controls (5% and 17%), Egyptian MAFs were inconsistent with those of our study [The Minor Allele Frequency (MAF) of ns (25%) and Eurons (25%) , 27, 28 ns (25%) and lowens (25%) , Easternns (25%) , 16, 19,ns (25%) . On the ns (25%) and Eurons (25%) , 27, 28 ns (25%) and lowens (25%) , Easternns (25%) , 16, 19,ns (25%) . Regardiur study , 31.While the MAFs among ACPA-positive patients were perceptibly higher versus ACPA-negative patients in Syria and Iran , respectSTAT4 rs7574865 was not associated with RA in Syria (p>.05) as well as in Turkish [In discord with more than twenty studies conducted in Europe , 27, 28, Turkish , Iranian Turkish , and Afr Turkish populatiOn the other hand, the reports on the effect of TT genotype showed vast disparity. While no effect was evidenced in seven studies , 29, 30 STAT4 gene, rs7574865 SNP biological impact is still debated. Whereas it does not disrupt any transcription factor binding site [STAT4 gene upregulation was established [STAT4 rs7574865 SNP regarding both RA onset and severity. The remarkable discrepancies among different populations in terms of minor T allele frequency, TT genotype frequency, presence/absence of association with RA status, and strength of association denote the higher impact of other genetic and environmental factors. HLA-DRB1 alleles/genotypes, for instance, were weakly-to-moderately correlated with RA onset and ACPA status. In addition, the odds of having RA with positive ACPA was as high as 7 times in the presence of an HLA-DRB1 shared epitope allele .Being located in the third intron of ing site , alternaablished . CollectThe reported average onset of RA usually ranges between the ages of 30 and 60; hence case-control studies with young adult healthy controls might get biased. Furthermore, the larger the sample size the higher the statistical power. However, the presence/absence of an association between minor T allele and RA does not seem relevant to the sample size and age as much as the ethnicity of subjects enrolled in the published studies , 29-31. STAT4 rs7574865 TT genotype on ACPA positivity and a more significant impact of HLA-DRB1 shared epitope alleles on RA onset and ACPA status. However, we failed to pinpoint an association between STAT4 rs7574865 minor T allele and RA susceptibility. More studies are recommended to be conducted repeatedly in different ethnic groups so that the debate on such an association might be resolved. Being involved in the RA-associated inflammatory response, STAT4 gene might exhibit other variations to be investigated alike in future studies.Our preliminary study points to a potential impact of"} +{"text": "Bohaiornis-like enantiornithine species\u2014and numerous specimens\u2014have been recognized from the celebrated Jehol Biota of northwestern China. In this paper, we describe the anatomy of another \u201cbohaiornithid\u201d species from the 125 million-year-old Yixian Formation of Liaoning Province, China. The new taxon differs from previously recognized \u201cbohaiornithids\u201d on a number of characters from the forelimb and shoulder girdle. We also provide a new phylogenetic framework for enantiornithine birds, which questions the monophyly of the previously recognized bohaiornithid clade and highlights ongoing challenges for resolving enantiornithine interrelationships. Additionally, we offer the first assessment of the flight properties of Bohaiornis-like enantiornithines. Our results indicate that while \u201cbohaiornithids\u201d were morphologically suited for flying through continuous flapping, they would have been unable to sustain prolonged flights. Such findings expand the flight strategies previously known for enantiornithines and other early birds.During the last decade, several During the last three decades, the celebrated Early Cretaceous Jehol Biota of north-eastern China has yielded a rich fauna of enantiornithines , a diverBohaiornis guoi was erected by B. guoi and several other mid-sized enantiornithes from the early Cretaceous of China, and coined the term Bohaiornithidae to name a seemingly monophyletic clade of enantiornithines. Nowadays, as most commonly accepted, Bohaiornithidae is seen as including at least six species of medium-sized birds (Lapwing to Magpie size): Shenqiornis mengi (Sulcavis geeorum (Zhouornis hani (Longusunguis kurochkini (Parabohaiornis martini (Fortunguavis xiaotaizicus (Bohaiornis-like taxon (based on BMNH Ph 829) from the 125 million-year-old Yixian Formation was selected as the root. The data matrix was analyzed using both maximum parsimony and Bayesian inference analyses. The maximum parsimony analysis was conducted using PAUP version 4.0 B10; sequences were added at random and the analysis was set to 100 repetitions. The support of the clades was assessed through a bootstrap analysis, also run in PAUP and using 200 bootstrap replicates. The Bayesian analysis was conducted using the software MrBayes v3.1.2, and it was run for 1,000,000 generations after which the standard deviation of split frequencies was 0.02 .The character list and dataset used in the phylogenetic analyses was based on http://life.bio.sunysb.edu/morph/). Body mass (bM) estimates were obtained using multivariate equations derived from modern flying birds and described by B) were also calculated using multiple regressions (LS) were obtained from a new multiple regression derived specifically for \u201cbohaiornithids,\u201d following the procedure of bM and B for a range of velocities (tV) as the summation of the induced power (Pind = 2k(b gM)2/tV\u03c0B2\u03c1, where k is the induced power factor, g is the gravity acceleration, and \u03c1 is the air density), the parasite power , and the profile power (Ppro = (2k(b gM)2/Vmp\u03c0B2\u03c1 + \u03c1Vmp3bCSDb/2)Cpro/(B2/LS), where Vmp is the minimum power speed and Cpro is the profile power constant). Models assume an elliptical lift distribution across the wingspan; k (set at k = 1.2) accounts for any deviations from this distribution. Cpro was fixed at 8.4 to make Ppro proportional to wing area. Body frontal area was calculated as bS = 0.00813bM0.666 , was calculated as the tangent to the power curve intersects with the origin of the speed\u2013power plot (Pav) was calculated from the oxygen consumption rate , by considering that one ml of O2 generates 20.1 J each second , and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix Aves Linnaeus, 1758Pygostylia Chiappe, 2002Ornithothoraces Chiappe, 1995Enantiornithes Walker, 1981Gretcheniao sinensis gen. et sp. nov.Holotype. BMNH Ph 829 ; Table 1Etymology.Gretcheniao in recognition of Mrs. Gretchen Augustyn and her support to the Dinosaur Institute of the Natural History Museum of Los Angeles County, and the Chinese character (ni\u0103o), meaning \u201cbird\u201d; sinensis from \u201csino,\u201d a term generally used in reference to China.Geographic and Stratigraphic Provenance. BMNH Ph 829 . The transverse processes define broad, U-shaped depressed areas, which gradually disappear caudally . The transverse processes of the last two synsacral vertebrae are very long; the last one is strongly angled caudolaterally, as is typical of many enantiornithines . The medial margin is concave, and the lateral margin is generally straight, lacking the strongly convex condition characterizing most other enantiornithines including the Bohaiornis-like taxa. Its sternal margin is slightly arched. Above the midshaft, medially, there is a long, slit-like opening for the passage of the supracoracoid nerve (observable on the left element) . The rigelement) . The omaelement) . Proxima surface ; a similForelimb. Both humeri are exposed cranially. They have a slightly sigmoid overall shape. The humeral head is proximally flat, lacking the \u201cdouble humped\u201d morphology of some other enantiornithines . Poorly preserved proximal carpals are visible on both wings. The ulnare is heart-shaped as in some other enantiornithines and the alular metacarpal from its contact with major metacarpal (left wing) (M. extensor carpi ulnaris (see visible . The dis visible . The two visible . The fle visible . The venft wing) . The semft wing) , which ift wing) , the disft wing) ; this tuft wing) and the aris see . In contBohaiornis-like enantiornithines, the distal extension of the alular digit approaches the end of the major metacarpal. The major digit contains two non-ungual phalanges (preserved on the left side); the proximal one is almost twice the length of the intermediate one, and much thicker. As in other enantiornithines, the proximal phalanx of the major digit is not expanded craniocaudally. A faint impression of the claw of this digit is visible on the left manus just distal to the end of the intermediate phalanx; based on this impression, the claw of the major digit is assumed to have been smaller than its counterpart on the alular digit. There is only a single phalanx of the minor digit; it is about half the length of the proximal phalanx of major digit and much thinner.The partially overlapped, proximal phalanx of the right alular digit and the impressions of the two phalanges of its left counterpart show that the proximal phalanx of this digit was shorter than the proximal phalanx of the major digit, but longer than that of the minor digit. As in other Pelvic girdle. The pelvic elements are unfused to one another . These taxa were previously included in Bohaiornithidae , which shares an overall morphology, and perhaps ecological niche, but do not constitute a monophyletic taxon. As such, the species typically considered as \u201cbohaiornithids\u201d appear to be relatively basal taxa closely related to Eoenantiornis buhleri and leading to the more derived forms such as Cathayornis yandica and Gobipteryx minuta. Otherwise, the relationships within Enantiornithes are for the most part unresolved , wing span (B), lift surface (LS), AR, and WL of BMNH Ph 829 and other five \u201cbohaiornithid\u201d specimens (bM (130\u2013236 g) and B (327\u2013566 cm) estimated for these birds, the Magpie-sized BMNH Ph 829 was the largest . These estimates indicate that Bohaiornis-like enantiornithines had short wings with respect to their body masses; a configuration observed in most modern birds that use strict flapping as their main flight modality and the Watercock . Although there is some overlap, strict flapping birds tend to have wings significantly shorter than those birds with facultative flap-gliding flight , and continuous flapping\u2014among the latter, there are those that can fly for long distances and others that spend little time flying (brief fliers such as divers and land fowl). The values of AR (6.1\u20136.6) and WL (3.78\u20135.13 Kg/m2) estimated for \u201cbohaiornithids\u201d (see Gretcheniao sinensis and its \u201cbohaiornithid\u201d counterparts score in a region of the AR\u2013WL morphospace where brief flyers and prolonged flyers overlap (Gretcheniao sinensis approach those of the Common Quail (Coturnix coturnix) and Coconut Lorikeet (Trichoglossus haematodus). Note that Longusunguis kurochkini and Sulcavis geeorum are also close to bounding flyers. The low AR shown by \u201cbohaiornithids\u201d could have allowed rapid take-offs as this type of wing maximizes the thrust during slow flight and the mechanical power output required for flapping (Pmec) or bounding , our analysis indicates that Pav was insufficient to cover the energetic requirements for flapping flight . By assung birds , Gretcheg flight . This ne-gliding , 2019, GBohaiornis-like enantiornithines (\u201cbohaiornithids\u201d) by providing morphological details previously unknown for these birds. The unique combination of skeletal traits of BMNH Ph 829 supports the recognition of a new species, Gretcheniao sinensis, which appears to represent an early divergence among these birds. Nonetheless, our extensive cladistic analyses show that despite the discovery of many well-preserved enantiornithines from the Jehol Biota (F. xiaotaizicus) have been interpreted as highly specialized .Gretcheniao sinensis and other \u201cbohaiornithids\u201d were morphologically suited for flying through continuous flapping, although not able to perform prolonged flights. Our aerodynamic results thus expand the previously known aerial repertoire of the Cretaceous enantiornithines.Our study also provides the first assessment of the flight properties of \u201cbohaiornithid\u201d enantiornithines. Key flight parameters inferred for these birds suggest ineffectiveness for performing intermittent flight (either flap-gliding or bounding) that was inferred for other enantiornithines , 2018. IPremaxillae in adults: unfused (0); fused only rostrally (1); completely fused (2). (ORDERED)Maxillary process of premaxilla: restricted to rostral portion (0); subequal or longer than facial contribution of maxilla (1).Frontal process of premaxilla: short (0); relatively long, approaching rostral border of antorbital fenestra (1); very long, approaching the lacrimals (2). (ORDERED)Premaxillary teeth: present throughout (0); present but rostral tip edentulous (1); present but restricted to rostral portion (2); absent (3).Caudal margin of naris: far anterior than rostral border of antorbital fossa (0); nearly reaching or overlapping rostral border of antorbital fossa (1).Naris longitudinal axis: considerably shorter than long axis of antorbital fossa (0); subequal or longer (1).Maxillary teeth: present (0); absent (1).Dorsal (ascending) ramus of maxilla: present with two fenestra (the promaxilllary and maxillary fenestra) (0); present with one fenestra (1); unfenestrated (2); ramus absent (3). (ORDERED)Caudal margin of choana: located rostrally, not overlapping orbital region (0); displaced caudally, at same level or overlapping rostral margin of orbit (1).Contact between palatine and maxilla/premaxilla: palatine contact maxilla only (0); contacts premaxilla and maxilla (1).Jugal process of palatine: present (0); absent (1).Ectopterygoid: present (0); absent (1).Postorbital: present (0); absent (1).Contact between postorbital and jugal: present (0); absent (1).Quadratojugal: sutured to quadrate (0); joined through ligamentary articulation (1).Lateral, round cotyla on mandibular process of quadrate : absent (0); present (1).Squamosal incorporated into the braincase, forming a zygomatic process: absent (0); present (1).Squamosal, zygomatic process: variably elongate, dorsally enclosing otic process of the quadrate and extending cranioventrally along shaft of this bone, dorsal head of quadrate not visible in lateral view (0); short, head of quadrate exposed in lateral view (1).Frontal/parietal suture in adults: open (0); close, bones fully fused to one another (1).Quadrate orbital process (pterygoid ramus): broad (0); sharp and pointed (1).Quadrate pneumaticity: absent (0); present (1).Quadrate: articulating only with squamosal (0); articulating with both prootic and squamosal (1).Otic articulation of the quadrate: articulates with a single facet (0); articulates with two distinct facets (1); articulates with two distinct facets and quadrate differentiated into two heads (2). (ORDERED)Quadrate distal end: with two transversely aligned condyles (0); with a triangular, condylar pattern, usually composed of three distinct condyles (1).Eustachian tubes: paired, lateral, and well-separated from each other (0); paired, close to each other and to cranial midline or forming a single cranial opening (1).Dentary teeth: present (0); absent (1).Robustness of teeth relative to dentary: anteroposterior width of largest tooth crowns (measured at thickest portion of crown\u2019s base) far less than half of dentary dorsoventral depth (0); close to half (or more) of dentary depth, i.e., 45%, or more (1). Taxa near the cutoff point are coded 0/1.Dentary tooth implantation: teeth in individual sockets (0); teeth in a communal groove (1).Symphysial portion of dentaries: unfused (0); fused (1).Deeply notched rostral end of mandibular symphysis: absent (0); present (1).Small ossification present at rostral tip of mandibular symphysis : absent (0); present (1).Caudal margin of dentary: unforked, or with weakly developed dorsal ramus (0); strongly forked with dorsal and ventral rami approximately equal in caudal extent (1).Meckel\u2019s groove of mandible : not completely covered by splenial (0); covered by splenial, not exposed medially (1).Rostral mandibular fenestra: absent (0); present (1).Caudal mandibular fenestra: present (0); absent (1).Articular pneumaticity: absent (0); present (1).Atlantal hemiarches in adults: unfused (0); fused, forming a single arch (1).One or more pneumatic foramina piercing centra of mid-cranial cervicals, caudal to level of parapophysis-diapophysis: present (0); absent (1).Cervical vertebrae: variably dorsoventrally compressed, amphicoelous (\u201cbiconcave\u201d: flat to concave articular surfaces) (0); cranial articular surface heterocoelous , caudal articular surface flat or slightly concave (1); heterocoelous cranial and caudal articular surfaces (2). (ORDERED)Prominent carotid processes in intermediate cervicals: absent (0); present (1).Postaxial cervical epipophyses: prominent, projecting further back from postzygapophyses (0); weak, not projecting further back from postzygapophyses, or absent (1).Keel-like ventral surface of cervical centra: absent (0); present (1).Prominent ventral processes of cervicothoracic vertebrae: absent (0); present (1).Thoracic vertebral count: 13\u201314 (0); 11\u201312 (1); fewer than 11 (2). The transition between cervical and thoracic vertebrae is often difficult to identify, which makes counting these vertebrae problematic; we identify the first vertebra in articulation with a long costal rib as the first thoracic vertebra (ORDERED)Thoracic vertebrae: at least part of series with subround, central articular surfaces that lack the dorsoventral compression seen in heterocoelous vertebrae (0); series completely heterocoelous (1).Thoracic vertebrae, lateral side of centra: weakly or not excavated (0); deeply excavated by a groove (1); excavated by a broad fossa (2).Cranial thoracic vertebrae, parapophyses: located in cranial part (0) or central part (1) of centra.Sacral vertebrae, number ankylosed centra (synsacrum): less than 7 (0); 7 (1); 8 (2); 9 (3); 10 (4); more than 10 (5). (ORDERED)Synsacrum, procoelous articulation with last thoracic centrum (deeply concave facet of synsacrum receives convex articulation of last thoracic centrum): absent (0); present (1).Cranial vertebral articulation of first sacral vertebra: approximately equal in height and width (0); wider than high (1).Degree of fusion of distal caudal vertebrae: fusion absent (0); few vertebrae partially ankylosed (intervening elements are well-discernable) (1); vertebrae completely fused into a pygostyle (2). (ORDERED)Distal caudal vertebra prezygapophyses: elongate, exceeding the length of centrum by more than 25% (0); shorter (1); absent (2). (ORDERED)Pygostyle: longer than or equal to the combined length of free caudals (0); shorter (1).Cranial end of pygostyle dorsally forked: absent (0); present (1).Cranial end of pygostyle with a pair of laminar, ventrally projected processes: absent (0); present (1).Distal constriction of pygostyle: absent (0); present (1).Ossified uncinate processes in adults: absent (0); present and free (1); present and fused (2).Gastralia: present (0); absent (1).Coracoid shape: rectangular to trapezoidal in profile (0); strutlike (1).Coracoid-scapula articulation: \u201cball and socket\u201d articulation (0); scapular articular surface of coracoid convex (1); flat (2).Scapula: articulated at omal end of coracoid (0); well below it (1).Coracoid, humeral articular facet (glenoid): dorsal to acrocoracoid process (\u201cbiceps tubercle\u201d) (0); ventral to acrocoracoid process (1).Humeral articular facets of coracoid and scapula: placed in same plane (0); forming a sharp angle (1).Coracoid, acrocoracoid: straight (0); hooked medially (1).Coracoid, laterally compressed omal end with nearly aligned acrocoracoid process, humeral articular surface, and scapular facet, in dorsal view: absent (0); present (1).Coracoid, procoracoid process: absent (0); present (1).Coracoid, broad, deep fossa on dorsal surface : absent (0); present (1).Coracoid, supracoracoidal nerve foramen: centrally located (0); displaced toward (often as an incisure) medial margin (1); absent (2). (ORDERED).Coracoid, medial surface, strongly depressed elongate furrow : absent (0); present (1).Coracoid, width of the sternal end relative to the length along the shaft: approximately half or greater (0); between half to 1/3 (1); less than 1/3 (2).Coracoid, sternal margin: convex (0); nearly straight (1); concave (2)Coracoid, supracoracoid nerve foramen, location relative to dorsal coracoidal fossa: above fossa (0); inside fossa (1).Coracoid, sternolateral corner: unexpanded (0); expanded (1); well developed squared-off lateral process (2); present and with distinct omal projection (hooked) (3).(244) Scapula and coracoid: fused (0); unfused (1).Scapula, blade: straight (0); sagittally curved (1).Scapula, length: shorter than humerus (0); as long as or longer than humerus (1).(245) Scapula, acromion process length relative to length of humeral articular facet: less than half (0); nearly equivalent (1); longer but less than two times (2); more than two times longer (3). (ORDERED)Scapula, acromion process: in lateral or costal view, strongly projecting craniodorsally, forming a large angle with proximal shaft (0); nearly parallel to shaft (1).Scapula, costal surface of blade with prominent longitudinal furrow: absent (0); present (1).Scapula, caudal end: blunt (may or may not be expanded) (0); sharply tapered (1).Furcula: boomerang-shaped (0); V to Y-shaped (1); U-shaped (2).Furcula, interclavicular angle: approximately 90\u00b0 (0); less than 70\u00b0 (1). The interclavicular angle is measured as the angle formed between three points: the omal ends of the rami and the center of the clavicular symphysis.Furcula, dorsal and ventral margins: subequal in width (0); ventral margin distinctly wider than dorsal margin so that furcular ramus appears concave laterally (1).Furcula, hypocleideum: absent (0); present as a tubercle or short process (1); present as elongate process approximately 30\u201350% the length of rami (2); hypertrophied, exceeding 50% the length of rami (3). (ORDERED)Sternum: unossified (0); partially ossified, coracoidal facets cartilaginous (1); fully ossified (2).Sternum, ossification: two flat bony plates (0); single, more or less flat element (1); single element, with slightly raised midline ridge (2); single element, with strongly projected carina (3).Sternum, carina: near to, or projecting rostrally from, cranial border (0); not reaching cranial border (1).Sternum, caudal margin, number of paired caudal trabeculae: none (0); one (1); two (2).Sternum, outermost trabeculae: tips terminate cranial to caudal end of sternum (0); tips terminate at or approaching caudal end of sternum (1); tips extend caudally past the end of sternal midline (2).Sternum, distal expansion of outermost trabecula: absent (0); present, simple bulb-like (1); fan-shaped (2); triangular\u2013shaped with acute medial angle (3); branched (4).Sternum, rostral margin broad and rounded: absent (0); present (1).Eoalulavis in which the preserved sternum does not bear actual sulci, the placement of the coracoids can be used to infer their position relative to the sternum.Sternum, coracoidal sulci spacing on cranial edge: widely separated mediolaterally (0); adjacent (1); crossed on midline (2). In taxa such as Sternum, costal facets: absent (0); present (1).Sternum, caudal half, paired enclosed fenestra: absent (0); present (1).Sternum, dorsal surface, pneumatic foramen (or foramina): absent (0); present (1).(243) Sternum, outermost trabecula: mainly parallel to long axis of sternum (0); clearly directed caudo-laterally (1).Humerus, proximal and distal ends: twisted (0); nearly co-planar (1)Humerus, head: concave cranially and convex caudally (0); globe shaped, craniocaudally convex (1).Humerus, proximal margin of head is concave in its central portion, rising ventrally and dorsally: absent (0); present (1).Humerus, proximocranial surface, well-developed circular fossa on midline: absent (0); present (1).Humerus, transverse ligamental groove: absent (0); present (1).Humerus, ventral tubercle projected caudally, separated from humeral head by deep capital incision: absent (0); present (1).Humerus, pneumatic fossa in caudoventral corner of proximal end: absent or rudimentary (0); well developed (1).Humerus, deltopectoral crest: projected dorsally (0); projected cranially (1).Humerus, deltopectoral crest width: less than shaft width (0); approximately same width (1); prominent and subquadrangular (2).Humerus, deltopectoral crest, distal end recedes abruptly with the humeral shaft: present (0); absent (1)Humerus, deltopectoral crest: imperforated (0); perforated by a fenestra (1).Humerus, bicipital crest: little to no cranial projection (0); developed as cranial projection relative to shaft surface in ventral view (1); hypertrophied, rounded tumescence (2).Humerus, distal end of bicipital crest, pit-shaped fossa for muscular attachment: absent (0); craniodistal on bicipital crest (1); directly ventrodistal at tip of bicipital crest (2); caudodistal, variably developed as a fossa (3).Humerus, demarcation of muscle origins on the dorsal edge of the distal humerus: no indication (0); a pit or a tubercle (1); a variably projected scar-bearing tubercle (2).Humerus, well-developed brachial depression on cranial face of distal end: absent (0); present (1).Humerus, well-developed olecranon fossa on caudal face of distal end: absent (0); present (1).Humerus, groove for passage of m. scapulotriceps: absent (0); present (1).Humerus, m. humerotricipitalis groove: absent (0); present as a well-developed ventral depression contiguous with the olecranon fossa (1).Humerus, distal margin: approximately perpendicular to long axis of shaft (0); strongly angled ventrally .Humeral distal condyles: mainly located on distal aspect (0); on cranial aspect (1).Humerus, long axis of dorsal condyle: at low angle to humeral axis, proximodistally oriented (0); at high angle to humeral axis, almost transversely oriented (1).Humerus, distal condyles: subround, bulbous (0); weakly defined, \u201cstraplike\u201d (1).Humerus, ventral condyle: length of long axis less than the same measure in dorsal condyle (0); same or greater (1).Ulna: shorter than humerus (0); nearly equivalent to or longer than humerus (1).Ulna: mid-shaft relative width: radial-shaft/ulnar-shaft ratio larger than 0.70 (0); smaller than 0.70 (1).Ulna, cotylae: dorsoventrally adjacent (0); widely separated by deep groove (1).Ulna, dorsal cotyla strongly convex: absent (0); present (1).Ulna, bicipital scar: absent (0); developed as slightly raised scar (1); developed as conspicuous tubercle (2).Ulna, proximal end with well-defined area for insertion of m. brachialis anticus: absent (0); present (1).Ulna, semilunate ridge on dorsal condyle: absent (0); present (1).Radius, long longitudinal groove on ventrocaudal surface of shaft: absent (0); present (1).Ulnare: heart-shaped with little differentiation into short rami (0); U-shaped to V-shaped, well-developed rami (1).Semilunate carpal and proximal ends of metacarpals in adults: unfused (0); semilunate fused to the alular (I) metacarpal (1); semilunate fused to the major (II) and minor (III) metacarpals (2); fusion of semilunate and all metacarpals (3). Juvenile specimens are scored as \u201c?\u201d to account for the possibility of ontogenetic change.Semilunate carpal, position relative to alular metacarpal (I): over entire proximal surface (0); over less than one-half proximal surface or no contact present (1).Carpometacarpus, proximal ventral surface: flat (0); raised ventral projection contiguous with minor metacarpal (1); pisiform process forming a distinct peg-like projection (2).Carpometacarpus, proximoventral surface, supratrochlear fossa deeply excavating proximal surface of pisiform process: absent (0); present (1).Alular metacarpal (I), round-shaped: absent (0); present (1).Alular metacarpal (I), extensor process: absent (0); tip barely (1) or conspicuously (2) surpasses cranial margin of distal articular facet. (ORDERED)Alular metacarpal (I), distal articulation with proximal phalanx: ginglymoid (0); shelf (1); ball-like (2).Minor metacarpal (III), craniocaudal diameter as percentage of same dimension of major metacarpal (II): approximately equal or greater than 50% (0); less than 50% (1).Alular digit (I), proximal phalanx: longer than proximal phalanx of major digit (II) (0); shorter than or equivalent to proximal phalanx of major digit (II) (1).Intermetacarpal process (or tubercle) on major metacarpal (II): absent (0); present (1).Intermetacarpal space: absent or very narrow (0); at least as wide as maximum width of minor metacarpal (III) shaft (1).Intermetacarpal space: reaches proximally as far as distal end of alular metacarpal (I) (0); terminates distal to end of alular metacarpal (I) (1).Distal end of metacarpals: unfused (0); partially or completely fused (1).Minor metacarpal (III) projecting distally more than major metacarpal (II): absent (0); present (1).Alular digit (I), proximal phalanx, distal extension relative to major metacarpal (II): beyond distal end of major metacarpal (II) (0); approximately equal in distal extension (1); shorter than distal end but beyond half of major metacarpal (II) (2); terminating less than half of major metacarpal (II) (3). (ORDERED)Proximal phalanx of major digit (II): round-shaped cross section (0); flat and craniocaudally expanded (1).Intermediate phalanx of major digit (II): longer than proximal phalanx (0); shorter than or equivalent to proximal phalanx (1).Ungual phalanx of major digit (II): present (0); absent (1).Ungual phalanx of major digit (II): larger or subequal to other manual unguals (0); smaller than alular ungual but larger than ungula phalanx of minor (III) digit (1); smaller than unguals of alular and minor digits (2).Ungual phalanx of minor digit (III): present (0); absent (1).Manus, relative length: length of semilunate carpal + major metacarpal and digit longer than humerus (0); subequal (1); shorter (2). (ORDERED)Intermembral index = (length of humerus + ulna)/(length of femur + tibiotarsus): less than 0.7 (0); between 0.7 and 0.9 (1); between 0.9 and 1.1 (2); greater than 1.1 (3).Pelvis, bone fusion at level of acetabulum: unfused or partial fusion (0); completely fused (1). Juvenile specimens with unfused pelvis are scored \u201c?\u201d to allow for ontogenetic fusion.Ilium/ischium, distal co-ossification to completely enclose ilioischiadic fenestra: absent (0); present (1).Ilium, midline proximity of preacetabular wings: separated (may exist cartilaginous connection) (0); co-ossified, dorsal closure of \u201ciliosynsacral canals\u201d (1).Preacetabular pectineal process (preacetabular tubercle of Baumel): absent (0); present (1).Pelvis, acetabulum proportions: large acetabulum, acetabulum/ilium length ratio greater than 0.11 (0); small acetabulum, same proportion equal or smaller than 0.11 (1).Prominent antitrochanter: caudally directed (0); caudodorsally directed (1).Ilium, postacetabular process: deep (0), more than 50% of depth of preacetabular wing at level of acetabulum; shallow (1), less than 50%.Ilium, brevis fossa: present (0); absent (1).Ischium, relative length: two-thirds or less the length of pubis (0); more than two-thirds the length of pubis (1).Ischium, obturator process: prominent (0); reduced or absent (1).Ischium, proximodorsal process: absent (0); present (1).Pubis, orientation of proximal portion: cranially to subvertically oriented (0); retroverted, separated from main synsacral axis by a 45\u201365\u00b0 angle (1); more or less parallel to ilium and ischium (2). (ORDERED)Ilium, pubic pedicel very compressed laterally and hook-like: absent (0), present (1).Pubis, shaft laterally compressed throughout its length: absent (0); present (1).Pubis, pubic apron: present (0); absent (absence of symphysis) (1).Pubis, distal foot: flaring into simple round shape (0); triangular shape with pointed caudal tip and caudoventally directed with respect to distal pubic shaft (1); caudal tip recurved caudodorsally with respect to distal pubic shaft (2); absent (3).Femur, distinct fossa for capital ligament: absent (0); present (1).Femur, neck: present (0); absent (1).Femur, anterior trochanter: separated from greater trochanter (0); fused to it, forming a trochanteric crest with laterally curved edge (1); fused to it, forming a trochanteric crest with flattened edge (2).Femur, trochanteric crest: projects proximally beyond femoral head (0); equal in proximal projection (1); does not project beyond femoral head (2).Femur, posterior trochanter: present, developed as slightly projected tubercle or flange (0); hypertrophied, \u201cshelf-like\u201d conformation (1); absent (2).Femur, prominent patellar groove: absent (0); present as continuous extension onto distal shaft (1); present and separated from shaft by slight ridge, giving it a pocketed appearance (2).Femur, lateral distal end: ectocondylar tubercle and lateral condyle separated by deep notch (0); ectocondylar tubercle and lateral condyle contiguous but without developing a tibiofibular crest (1); tibiofibular crest present, defining laterally a fibular trochlea (2). (ORDERED)Femur, popliteal fossa distally bounded by a complete transverse ridge: absent (0); present (1).Tibia, calcaneum, and astragalus: unfused or poorly co-ossified (sutures still visible) (0); complete fusion of tibia, calcaneum, and astragalus (1).Tibia, round proximal articular surface: absent (0); present (1).Tibia, proximal articular surface: flat (0); angled so that medial margin is elevated with respect to lateral margin (1).Tibiotarsus, proportions: tibiotarsus length/tarsometatarsus length equals 2 or more (0); between 2 and 1.6 (1); smaller than 1.6 (2). When distal tarsals are not fused with metatarsals, metatarsal III length is used.Tibiotarsus, cnemial crests: absent (0); present, one (1); present, two (2).Tibia, caudal extension of articular surface for tarsals/tarsometatarsus: absent, articular surface restricted to distalmost edge of caudal surface (0); well-developed caudal extension, sulcus cartilaginis tibialis , distincTibiotarsus, extensor canal: absent (0); present as emarginate groove (1); groove bridged by ossified supratendinal bridge (2). (ORDERED)Tibibiotarsus, condyles, cranial projection: medial condyle projecting farther cranially than lateral condyle (0); equal in cranial projection (1).Tibiotarsus, condyles, relative mediolateral width: medial condyle wider (0); approximately equal (1); lateral condyle wider (2). (ORDERED).Tibiotarsus, condyles, intercondylar groove: mediolaterally broad, approximately 1/3 with of anterior surface (0); less than 1/3 width of anterior surface (1).Tibiotarsus, condyles: gradual sloping of condyles towards tibiotarsal midline of tibiotarsus (0); no tapering of either condyle (1).Fibula, proximal end: prominently excavated by medial fossa (0); nearly flat (1).Fibula, tubercle for m. iliofibularis: craniolaterally directed (0); laterally directed (1); caudolaterally or caudally directed (2). (ORDERED)Fibula, distal end reaching proximal tarsals: present (0); absent (1).Distal tarsals in adults: free (0); completely fused to the metatarsals (1). Juvenile specimens are scored as \u201c?\u201d in order to account for the possibility of ontogenetic change.Metatarsals II\u2013IV, intermetatarsal fusion: absent or minimal co-ossification (0); partial fusion, sutural contacts easily discernible (1); completely or nearly completely fused, sutural contacts absent or poorly demarcated (2). (ORDERED)Metatarsal V: present (0); absent (1).Metatarsal III, proximal end: co-planar with metatarsals II and IV (0); plantarly displaced with respect to metatarsals II and IV (1).Tarsometatarsus, proximal vascular foramen and/or foramina between metatarsals III and IV: absent (0); one (1); two (2).Tarsometatarsus, intercotylar eminence: absent (0); present, low and rounded (1); present, high and peaked (2).Tarsometatarsus, projected surface and/or grooves on proximocaudal surface : absent (0); developed as caudal projection with flat caudal surface (1); at least one groove enclosed by bone caudally (2). (ORDERED)Tarsometatarsus, plantar surface: flat (0); excavated (1).Tarsometatarsus, distal vascular foramen completely enclosed by metatarsals III and IV: absent (0); present (1).Metatarsal I: straight (0); J-shaped, with short projection extending medially (1); J-shaped; articulation of hallux extending caudally (2); distal half of metatarsal I is laterally deflected so that laterodistal surface is concave (3).m. tibialis cranialis): absent (0); present, approximately centered on proximodorsal surface of metatarsal II (1); present, developed on lateral surface of metatarsal II, at contact with metatarsal III or on lateral edge of metatarsal III (2).Metatarsal II tubercle ; shallow notch (1); conspicuous ovoid fossa (2). (ORDERED)Relative position of metatarsal trochleae: trochlea III more distal than trochleae II and IV (0); trochlea III at same level as trochlea IV, both more distal than trochlea II (1); trochlea III at same level as trochleae II and IV (2); distal extent of trochlea III intermediate to trochlea IV and II where trochlea IV projects furthest distally (3).Metatarsal II, distal extent of metatarsal II relative to metatarsal IV: approximately equal in distal extent (0); metatarsal II shorter than metatarsal IV but reaching distally farther than base of metatarsal IV trochlea (1); metatarsal II shorter than metatarsal IV, reaching distally only as far as base of metatarsal IV trochlea (2).Tarsometatarsus, trochlea in distal view: aligned in a single plane (0); metatarsal II slightly displaced plantarly with respect to III and IV (1); metatarsal II strongly displaced plantarly in respect to III and IV, such that there is little or no overlap in medial view (2).Metatarsal II, trochlea of metatarsal II broader than trochlea of metatarsal III: absent (0); present (1).Metatarsal III, trochlea in plantar view, proximal extent of lateral and medial edges of trochlea: trochlear edges approximately equal in proximal extent (0); medial edge extends farther (1).Distal end of metatarsal II strongly curved medially: absent (0); present (1).Phalanx in digit IV; second and third phalanges reduced and significantly shorter than fourth phalanx: absent (0), present (1), present, but with proximal phalanx reduced to be nearly equal in length with second and third phalanx (2).Digit IV phalanges in distal view, medial trochlear rim enlarged with respect to lateral trochlear rim: absent (0); present, lateral trochlea reduced to a rounded peg (1).Pes, proximal phalanx of hallux is the longest non-ungual phalanx: absent (0); present (1).Size of claw of hallux relative to other pedal claws: shorter, weaker, and smaller (0); similar in size (1); longer, more robust, and larger (2).Alula: absent (0); present (1).Fan-shaped feathered tail composed of more than two elongate retrices: absent (0); present (1).10.7717/peerj.7846/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj.7846/supp-2Supplemental Information 2Specimens were measured directly from the Burke Museum of the University of Washington, Seattle (UWBM), and the Beaty Biodiversity Museum of the University of British Columbia, Vancouver (UBCBBM). Other specimens were taken from references: (BR) Bruderer et al. (2010); (FS) Flight software\u2019s dataset from Click here for additional data file.10.7717/peerj.7846/supp-3Supplemental Information 3Blue and yellow areas show deviation in the proportions of the carpometacarpus with respect to that of Bohaiornis guoi. Note the proportionally much longer carpometacarpus of Gretcheniao sinensis.Click here for additional data file."} +{"text": "Scientific Data 4:170104 doi: 10.1038/sdata.2017.104 (2017), Published 12 September 2017; Updated 24 July 2018VLIZ instead of EMODnet Bathymetry.In the HTML version of this Data Descriptor, Data Citation 8 incorrectly listed the repository as"} +{"text": "The fact that these diseases were historically not considered priorities for pharmaceutical companies made the available treatments options obsolete, precarious, outdated, and in some cases nonexistent. The use of plants for medicinal, religious, and cosmetic purposes has a history dating back to the emergence of humanity. One of the principal fractions of chemical substances found in plants are essential oils (EOs). EOs consist of a mixture of volatile and hydrophobic secondary metabolites with marked odors, composed primarily of terpenes and phenylpropanoids. They have great commercial value and were widely used in traditional medicine, by phytotherapy practitioners, and in public health services for the treatment of several conditions, including neglected diseases. In addition to the recognized cytoprotective and antioxidative activities of many of these compounds, larvicidal, insecticidal, and antiparasitic activities have been associated with the induction of oxidative stress in parasites, increasing levels of nitric oxide in the infected host, reducing parasite resistance to reactive oxygen species, and increasing lipid peroxidation, ultimately leading to serious damage to cell membranes. The hydrophobicity of these compounds also allows them to cross the membranes of parasites as well as the blood-brain barrier, collaborating in combat at the second stage of several of these infections. Based on these considerations, the aim of this review was to present an update of the potential of EOs, their fractions, and their chemical constituents, against some neglected diseases, including American and African trypanosomiasis, leishmaniasis, and arboviruses, specially dengue.The term Neglected diseases (ND) are a group of infections caused by various classes of infectious and parasitic pathogens, including protozoa, viruses, bacteria, and helminths. They most often affect low-income populations, with higher prevalence in tropical and subtropical countries. According to the World Health Organization (WHO), they are a set of 17 diseases, including leishmaniasis, African and American trypanosomiasis, leprosy, tuberculosis, leptospirosis, onchocerciasis, and schistosomiasis, affecting more than one billion people around the world and considered a threat to public health in 149 countries .The fact that these diseases are not considered priorities by large medical and pharmaceutical companies results in low investment in research and development of new drugs, causing the few available treatment options to become obsolete, precarious, outdated, and even in some cases nonexistent .These diseases are known for the lack of attention paid to them by political, social, and health entities. The worsening of social and health conditions in a great part of the world's population has accelerated in recent years according to studies providing data regarding current social policies \u20136.According to some studies in Latin American countries, Brazil has the highest rate of neglected diseases, and a large part of the Brazilian population both above and below the poverty line suffers from some of these diseases \u20139.Aedes aegypti that may transmit dengue, Zika, and chikungunya.Several neglected diseases are arboviruses, that is, viral diseases transmitted through the saliva of contaminated arthropods . Thus, tAccording to some authors , 14, 80%The use of plants for medicinal, religious, and cosmetic purposes dates back to the emergence of humanity. This historical interest promoted the development of several areas of inquiry invested in understanding and unraveling the potential of substances produced by plants as a result of their adaptive evolution , 16.One of the principal fractions of chemical substances found in plants are essential oils (EOs). EOs consist primarily of a mixture of volatile hydrophobic secondary metabolites with marked odors and great commercial value; EOs may be thought of as fingerprints of the plants where they are found , 18. TheThe main chemical compounds found in EOs are terpenoids and phenylpropanoids , 22 thatDespite the recognized cytoprotective and antioxidative activities of these compounds, in many cases larvicidal, insecticidal, and antiparasitic activities are associated with the induction of oxidative stress in the parasite, increasing the level of nitric oxide production by the infected host, reducing parasite resistance to reactive oxygen species, and generating high levels of free radicals and increasing lipid peroxidation, ultimately leading to serious damage to cell membranes and the killing of parasites \u201340.Based on these considerations, in this review an update of the potential of EOs, their fractions, and their components that are active against some neglected diseases, including American and African trypanosomiasis, leishmaniasis, and arboviruses, specially dengue is presented.To compose the database, the authors did a systematical search in the following databases: PubMed, Web of Science, Medline, SciELO, Cochrane Library, and NAPRALERT. The following search terms were combined and screened: essential oils, name of the neglected disease, and/or the parasite name. No language restrictions were applied. The period considered was the last 10 years, without however disregarding some articles of revision, and some classical literatures were considered important.Trypanosoma cruzi , 67Latan25) derivatives, with IC50 values between <20\u2009\u03bcM and >\u2009150\u2009\u03bcM ; 12-hydroxy-11,14-diketo-6,8,12-abietatrien-19,20-olide (26) isolated from Salvia cuspidate with IC50 value of 5\u2009\u03bcg/mL ; 5-epi-icetexone (27) used for 5 days, capable of reversing infection in Swiss mice ; and aphidicolin (28) derivatives obtained by semisynthesis exhibited high potency and selectivity against parasitic amastigote forms . Two of these derivatives gave IC50 values of 0.6\u2009\u03bcM (28 A) and 0.78\u2009\u03bcM (28 B), with selectivity index > 100 for both dPiper malacophylum (Piperaceae) presented two alkenyphenol derivatives as primary compounds: gibbilimbols A (29) and B (30), evaluated against promastigote/amastigote forms of Leishmania infantum and trypomastigote/amastigote forms of T. cruzi. Gibbilimbol B (30) showed better trypanocidal activity and lower toxicity to mammalian cells. These results encouraged researchers to prepare several quite simple synthetic analogues. Among these, the compound n-octyl-4-hydrozybenzylamine (LINS03003) (31) was the most potent, with IC50 values of 5.5\u2009\u03bcM against amastigote forms of T. cruzi, with a higher activity than that of the natural prototype of rototype 70]..Piper maP. malacophylum EO \u2014 compound 5-[(3E)-oct-3-en-1-il]-1,3-benzodioxole (32) . The synthetic compounds possessed promising antiparasitic activity; however, the compounds were considered to be cytotoxic. Compound LINS03011 (33) , but with better selectivity index (SI = 24.5) and less toxicity ..in vitroPiper aduncum EO (PaEO) and its main constituents against various forms of T. cruzi. GC-MS identified nerolidol and linalool (3) as the major PaEO components. PaEO showed IC50/24\u2009h = 12.1\u2009\u03bcg/mL against metacyclic trypomastigotes and IC50/24\u2009h values of 9\u2009\u03bcg/mL against amastigotes forms. Among the two main constituents isolated and identified, linalool (3) was the 06\u2009ng/mL .Syzygium aromaticum (SaEO) administrated orally, alone, and in combination with benznidazole (BZ) in mice infected with T. cruzi IV strain. GC-MS analysis identified eugenol (2) (82.2%) and \u03b3-caryophyllene (36) (13.0%) , BZ showed 25.0% (1/4), and BZ\u2009+\u2009SaEO showed 37.5% (3/8), considered a very interesting result hept-2-ene (94) (10.27%), benzene (95) (6.23%), and cyclohexene (96) (4.92%) in E. camaldulensis; 6-octenal (97) (77.11%) and 6-octen-1-ol (98) (14.09%) in E. citriodora; and citral (63) (38.32%) and 2,6-octadienal (99) (35.05%) and 2,6-octadien-1-ol (100) (26.63%) in C. citratus . EOs from E. citriodora and E. camaldulensis killed parasites in 4 minutes, and C. sinensis EO killed parasites in 5\u2009min. In smaller doses, the time of death increased to 6\u2009min (0.2\u2009g/mL) and 15\u2009min (0.1\u2009g/mL) for C. sinensis, 8\u2009min (0.2\u2009g/mL) and 17\u2009min (0.1\u2009g/mL) for E. camaldulensis, 8\u2009min (0.2\u2009g/mL) and 22\u2009min (0.1\u2009g/mL) for E. citriodora, and 4\u2009min (0.2\u2009g/mL) and 11\u2009min (0.1\u2009g/mL) for C. citratus. Thus, their activities appeared to be dose-dependent and the four EOs demonstrated powerful activity, causing the death of protozoa in short periods of time, compared with that of the reference drug (diminaveto) that promoted the death of the parasites in equivalent times.The death of the parasites was observed after the use of 0.4\u2009g/mL of the EOs. The EO most capable of killing parasites quickly was the Piper genus, a well-known source of bioactive compounds [Piper ossanum (leaves) was collected in two locations in Cuba (Bauta and Ceiba). Chromatograms of the EOs demonstrated the presence of 43 components for the Bauta species (PoB) and 39 for the Ceiba species (PoC). In both, the primary components were piperitone (57), camphene (15), camphor (14), and viridiflorol (101) . Some quantitative differences were observed in PoB and PoC EO constituents: camphor (14) (13.87% for PoB and 9.41% for PoC), viridiflorol (101) (12.97% for PoB and 18.80% for PoC), and camphene (15) (7.41% for PoB and 5.39% for PoC). PoB has as minor components p-cymene (11), sylvestrene (102), (Z)- and (E)-\u03b2-ocimene (89), terpinen-4-ol (103), cubebol (104), and humulene epoxide (105); PoC possessed small quantities of \u03b2-phellandrene (106), \u03b3-muurolene (107), spathulenol (108), and globulol (109) , suggesting that the various compositions of their constituents were not decisive for a differentiation of their potential, classified as weak when compared to the standard drug suramin (IC50 = 0.05\u2009\u03bcg/mL). Both EOs demonstrated low toxicity in a human fetal lung fibroblast cell line (MRC-5) (4.2\u2009\u03bcg/mL for PoB and 0.95\u2009\u03bc/mL for PoC). Evaluation of the T. brucei activity of the main compounds of each EO is necessary in order to identify more promising compounds.Guti\u00e9rrez et al. evaluateompounds . Piper ool (101) , with Pool (109) . The valStrychnos spinosa leaves are widely utilized in African trypanosomiasis treatment [T. brucei brucei activity of SsEO leaves and 16 of their components. SsEO leaves contained more than 100 constituents, including palmitic acid (71) (34.3%), linalool (3) (16%), (E)-phytol (82) (6.7%), and (E)-geraniol (6) (4%). SsEO showed moderately activity (IC50 = 13.5\u2009\u03bcg/mL) and weak selectivity index (SI = 4.4). Of the pure components tested, the prominent compounds were (E)-nerolidol (110) , linalool (3) , (E)-geranylacetone (85) , \u03b2-ionone (87) , (E)-phytol (82) , and \u03b1-terpineol (111) . Among these, only linalool (3) and (E)-phytol (82) were found in abundance in SsEO, leading to the conclusion that interaction with other compounds decreased the activity of the EO. In addition, the presence in minimal quantities of the more active compounds (identified as minority components) prevented the EOs from exerting their potential effects. Palmitic acid (71), the primary component for this species, was inactive and highly toxic (SI = 0.6).reatment . Hoet etreatment studied ol (110) (IC50 = ol (111) (IC50 = S. spinosa (IC50 = 1.5\u2009\u03bcg/mL), causing us to speculate that there are active components that are not EO constituents that should be evaluated more intensively. The better results observed with linalool (3) and (E)-nerolidol (110) reflect the need for further studies of these substances and for investigation of the potential of other oxygenated terpenes to identify alternatives for human African trypanosomiasis treatment.Preliminary results demonstrKadsura longipedunculata EO that had 50 identified components. The EO fraction was composed of 75% sesquiterpenes and 22.63% monoterpenes, including \u03b4-cadinene (34) (21.79%), camphene (15) (7.27%), borneol (112) (6.05%) (55) (5.12%), and \u03b4-cadinol (56) (5.11%). KlEO and camphene (15) were evaluated against bloodstream forms of T. brucei brucei and human hepatocellular liver carcinoma (HepG2); however, the results were not encouraging. KlEO had an IC50 of 50.52\u2009\u00b1\u20090.029\u2009\u03bcg/mL and an IC50 of 136.96\u2009\u03bcg/mL. The IC50 of the pure compounds were 80.66\u2009\u00b1\u20090.87\u2009\u03bcg/mL for camphene (15) and 70.00\u2009\u00b1\u20091.28\u2009\u03bcg/mL for borneol (112), both unfavorable cytotoxicity profiles. These results indicate that the active substances of K. longepedunculata useful against human African trypanosomiasis treatment were not part of their EO constituents.Mulyaningsih et al. investig (6.05%) , cubenolCitrus sp., C. jambhiri and C. pyriformis. For both species, 94 compounds were identified, with limonene (8) the major compound (92.48% for C. jambhiri and 75.56% for C. pyriformis). Both EOs had poor activity against bloodstream forms of T. b. brucei, with IC50 values of 72.47%\u2009\u00b1\u20090.87\u2009\u03bcg/mL for C. jambhiri and of 71.29\u2009\u00b1\u20090.38\u2009\u03bcg/mL for C. pyriformis, much less active than the standard drug diminazene aceturate (IC50 = 0.0832 \u00b1 0.0003\u2009\u03bcg/mL).Hamdan and coworkers evaluateEugenia uniflora EO from leaves and identified 87 compounds (spathulenol (108) \u2013 15.8%, \u03b1-copaene (113) \u2013 10.96%, muurola-4,10-dien-1\u03b2-ol (114) \u2013 9.3%, caryophyllene oxide (38) \u2013 8.93%, allo-aromadendrene (115) \u2013 5.5%, and nootkatone (116) \u2013 5.17%) with a weak selectivity index (SI = 6.82). The reference drug suramin had an IC50 of 0.16\u2009\u00b1\u20090.03\u2009\u03bcg/mL.Cruz et al. evaluate\u2013 5.17%) . The oxyErigeron floribundus aerial parts, containing 85 constituents. The primary class of constituents was sesquiterpenes (60.4% - being 38.5% oxygenated and 21.9% hydrocarbons). The main components were caryophyllene oxide (38) (12.4%), spathulenol (108) (12.2%), (E)-\u03b2-farnesene (117) (E)-caryophyllene (22) (4.2%), in addition to limonene (8) (8.8%). EfEO was evaluated for its antitrypanosomal activity against T. brucei and cytotoxicity in a human breast adenocarcinoma cell line (A375). There was moderate activity (IC50 = 33.5 \u00b1 2.7\u2009\u03bcg/mL) with a low selectivity index value (SI \u2265 5.97). Their main constituent, caryophyllene oxide (38), was also assayed and showed up inactive, reflecting the low antitrypanosomal activity of the EO. However, the evaluation of another potential major component, limonene (8), demonstrated promising activity (IC50 = 5.6 \u00b1 1.6\u2009\u03bcg/mL and SI \u2265 17.85), being the main contributor to the expression of EO potentiality. The authors concluded that this difference of activity in favor of limonene (8) could be attributed to the degree of its unsaturation, in addition to its exocyclic methylene group. The occurrence of a possible binding site with SH groups of proteins may be an indicator of their mechanism of action. However, this speculation requires more detailed investigation.Petrelli et al. investigne (117) (5.5%), Cymbopogon citratus L. (leaves), Distichoselinum tenuifolium , Juniperus oxycedrus (leaves and berries), Lavandula luisieri (influorescences), Lavandula viridis , Lippia graveolens , Mentha cervina (leaves), Mentha x piperita (leaves), Origanum virens (leaves), Rosmarinus officinalis (leaves), Seseli tortuosum , Syzygium aromaticum , Thymbra capitata , Thymus capitellatus , Thymus mastichina (leaves), and Thymus zygis sylvestris (leaves).EOs from aerial parts of a variety of plant species were analyzed by Costa et al. , includi6) (45.7%), neral (7) (32.5%), and \u03b2-myrcene (61) (11.5%) for C. citratus; \u03b2-myrcene (61) (84.6%) and limonene (8) (2.2%) for D. tenuifolium; \u03b1-pinene (118) (54.7%), germacrene D (24) (10.4%), and \u03b2-myrcene (61) (17.8%) for the berries of J. oxycedrus; \u03b1-pinene (118) (65.5%), \u0394-3-carene (119) (5.7%), \u03b2-phellandrene (106) (3.2%), and \u03b2-myrcene (61) (2.7%) for leaves of J. oxycedrus; 1,1,2,3-tetramethyl-4-hidroxymethyl-2-cyclopentene (120) (2.4%), 2,3,4,4-tetramethyl-5-methylene-cyclopent-2-enone (121) (5.2%), trans-\u03b1-necrodyl acetate (122) (16.0%), lyratyl acetate (123) (3.5%), 1,8-cineole (124) (18.9%), lavandulyl acetate (125) (7.2%), linalool (3) (3.1%), and \u03b1-pinene (118) (2.3%) for L. luisieri; 1,8-cineole (124) (29.7%), camphor (14) (10.0%), \u03b1-pinene (118) (9.2%), linalool (3) (9.0%), selina-3,7(11)-diene (126) (6.6%), Z-\u03b1-bisabolene (127) (6.3%), borneol (112) (2.7%), and camphene (15) (2.7%) for L. viridis; thymol (1) (19.8%), \u03c1-cymene (11) (16.9%), 1,8-cineole (124) (6.6%), caryophyllene oxide (38) (5.7%), linalool (3) (5.4%), \u0394-3-carene (119) (4.3%), \u03b1-terpineol (111) (3.6%), myrcene (61) (3.4%), E-caryophyllene (22) (2.4%), and trans-sabinene hydrate (17) (2.3%) for L. graveolens; pulegone (128) (74.8%), isomenthone (129) (10.6%), and limonene (8) (5.4%) for M. cervina; menthol (130) (44.0%), menthofuran (131) (10.9%), menthone (132) (9.8%), menthyl acetate (133) (7.8%), 1,8-cineole (124) (5.8%), neo-menthol (134) (4.0%), neo-isomenthol (135) (2.9%), and pulegone (128) (2.4%) for M. x piperita; carvacrol (10) (68.2%), \u03b3-terpinene (64) (7.9%), p-cymene (11) (7.4%), \u03b2-myrcene (61) (2.4%), and thymol (1) (2.1%) for O. virens; \u03b2-myrcene (61) (32.0%), 1,8-cineole (124) (13.7%), camphor (14) (11.9%), \u03b1-pinene (118) (11.1%), limonene (8) (6.6%), \u03c1-cymene (11) (3.8%), camphene (15) (3.4%), and linalool (3) (2.1%) for R. officinalis; \u03b1-pinene (118) (27.4%), \u03b2-pinene (39) (16.0%), limonene (8) (10.0%), \u03b3-terpinene (64) (9.3%), (Z)-\u03b2-ocimene (89) (8.0%), \u03b2-myrcene (61) (3.0%), camphene (15) (2.1%), and sabinene (17) (2.0%) for S. tortuosum; eugenol (2) (85.3%) and humulene (136) (6.8%) for S. aromaticum; carvacrol (10) (74.6%), p-cymene (11) (5.5%), E-caryophyllene (22) (3.9%), \u03b3-terpinene (64) (3.6%), and linalool (3) (2.8%) for T. capitata; 1,8-cineole (124) (58.6%), borneol (112) (10.0%), camphene (15) (6.5%), \u03b1-pinene (118) (4.5%), sabinene (17) (3.0%), and \u03b2-pinene (39) (2.0%) for T. capitellatus; 1,8-cineole (124) (67.4%), linalool (3) (4.3%), \u03b2-pinene (39) (4.0%), \u03b1-terpineol (111) (3.5%), \u03b1-pinene (118) (3.0%), and sabinene (17) (2.4%) for T. mastichina; and geranyl acetate (41) (44.5%), geraniol (6) (33.1%), and camphor (14) (3.9%) for T. zygis sylvestris , CcEO (IC50 = 3.2\u2009\u03bcg/mL and SI = 9.0), and LlEO (IC50 = 5.7\u2009\u03bcg/mL and SI = 11.9). Some pure compounds were also evaluated, and the best IC50 values were obtained with \u03b1-pinene (118) (IC50 = 2.9\u2009\u03bcg/mL) and citral (63) (IC50 = 18.9\u2009\u03bcg/mL). \u03b1-Pinene (118) is the main component of the most active EO (Juniperus oxycedrus), contributing to its high anti-T. brucei activity. Because the same result was not observed with JoEO leaves, the authors speculated that the synergistic effects on the most promising species potentiated their effects, suggesting that their interactions with germacrene D (24) and \u03b2-myrcene (61) should be further investigated [Of all these EOs, noteworthy findings were as follows: stigated .Aframomum sceptrum rizhomes. AsEO consists of 75 compounds, including \u03b2-pinene (39) (12.71%), caryophyllene oxide (38) (10.03%), cyperene (137) (5.99%), 3,4-dimethylcyclohex-3-ene-1-carbaldehyde (138) (3.40%), \u03b1-pinene (118) (2.78%), \u03b2-caryophyllene (22) (2.33%), \u03b1-terpineol (111) (2.12%), D-limonene (8) (1.89%), 1,8-cineole (124) (1.84%), and \u03b1-caryophyllene (or humulene) (136) (1.1%) (T. brucei brucei was determined for the EO (MLC = 1.47\u2009mg/mL) and for some pure compounds, \u03b2-pinene (39) (MLC > 0.1\u2009mg/mL) and caryophyllene oxide (38) (MLC = 0.1\u2009mg/mL). When compared to the reference drug pentamidine (MLC = 7.4\u2009\u03bcg/mL), this EO and their components showed very good anti-T. brucei brucei activities.Cheikh-Ali et al. evaluate) (1.1%) . The minCarlina acaulis root EO and identified carlina oxide (139) (T. b. brucei demonstrated promising results (IC50 = 1.0\u2009\u03bcg/mL), with great selectivity index values (SI = 446.0). In addition to the pure compound (main component of the C. acaulis EO), the authors analyzed the hexane, dichloromethane, and methanol extracts, and the two former (with considerable amount of carlina oxide (139)) were more active (IC50 = 3.7\u2009\u03bcg/mL (SI = 465.5) and 4.5\u2009\u03bcg/mL (SI = 443.3), respectively) than was the latter . When compared to the reference drug suramin (IC50 = 4.7\u2009\u03bcg/mL and SI = 280.2), carlina oxide (139) showed greater activity and better selectivity index. The authors suggested that the mechanism of action of carlina oxide (139) occurred through trypanothione reductase inhibition. The presence of the furan ring and the triple bond were considered by the authors to be important structural features for the activity and should be considered for the design of new drugs.Herrmann et al. obtainedde (139) as its mSiler montanum Crantz subsp. siculum \u2013 flowering aerial parts, Sison amomum L. \u2013 flowering aerial parts, Echinophora spinosa L. \u2013 roots and flowering aerial parts, Kundmannia sicula (L.) DC. \u2013 inflorescences, Crithmum maritimum L. \u2013 flowering aerial parts, Helosciadium nodiflorum (L.) Koch \u2013 whole, Pimpinella anisum L. \u2013 seeds, Heracleum sphondylium subsp. ternatum (Velen.) Brummit \u2013 seeds, and Trachyspermum ammi (L.) Sprague \u2013 seeds). The EOs from five of these plants were potent inhibitors of T. brucei , and some of their main components were evaluated in isolation. The great potentiality of these EOs was attributed to the presence of the main constituents, considering as well the great importance of synergistic effects with minority constituents. For SaEO, the main constituents were sabinene (17) (54.4%), \u03b2-phellandrene (106) (16.6%), and germacrene D (24) (6.7%). For EsEO roots, they were myristicin (41.3%) (140), terpinolene (141) (22.2%), and (Z)-falcarinol (142) (23.3%); for EsEO aerial parts, they were \u03b1-phellandrene (143) (47.2%), p-cymene (11) (25.6%), \u03b2-phellandrene (106) (8.3%), E,E-2,6-dimethyl-1,3,5,7-octatetraene (144) (6.3%), and \u03b1-pinene (118) (5.5%) (38.4%), \u03b3-terpinene (64) (19.9%), and sabinene (17) (12.4%); and for HnEO, they were myristicin (140) (49.1%), (Z)-\u03b2-ocimene (89) (19%), limonene (8) (7.8%), terpinolene (141) (7.1%), and germacrene D (24) (6.0%). With the exception of CmEO, all other active EOs showed significant selectivities against T. brucei, as well as good selectivity index values. For example, in their cytotoxicity evaluation performed in Balb3T3 rat fibroblasts, they found SI = 13 for S. amomum, 2.1 and 3.7 for E. spinosa roots and aerial parts, respectively, and >9.1 for H. nodiflorum.Kamte et al. investig) (5.5%) ; for CmET. brucei were terpinolene (141) , \u03b1-pinene (118) , \u03b2-ocimene (89) , p-cymene (11) , limonene (8) , sabinene (17) , \u03b1-phellandrene (143) , and myristicin (140) . As observed for the previous values, the high anti-T. brucei potentiality of terpinolene (141) should be responsible for the great EC50 value found in EsEO roots, containing these compounds as its primary constituents.The isolated components from the EOs were also evaluated by Kamte et al. . Some of141) with other structurally similar compounds (\u03b3-terpinene (64), \u03b1-phellandrene (143), limonene (8), and p-cymene (11)) highlighted the great importance of the presence of a double endocyclic and a double exocyclic bound, the latter linking the cyclohexene ring to a dimethylated carbon for the inhibition of T. brucei growth. This can be used as scaffold for drug design of new anti-T. brucei agents.Comparison of the chemical structure of terpinolene , known to be rich in furan ring-containing sesquiterpenes as the main constituents. CG-MS analysis identified a domain of oxygenated sesquiterpenes (68.2% - 74.5%), followed by monoterpene hydrocarbons (13.2\u201322.2%) and sesquiterpene hydrocarbons (3.1-14.1%). The EO from the fruits resulted in the identification of 66 constituents, including \u03b2-acetoxyfuranoeudesm-4(15)-ene (145) (31.2%), curzerene (146) (23.8%), isofuranodiene (147) (6.6%), \u03b2-phellandrene (106) (6.2%), and \u03b1-pinene (118) (5.4%). Among the flower EOs, they found 47 compounds, including curzerene (146) (30.5%), myrcene (61) (18.2%), furanoeremophil-1-one (148) (12.1%), germacrone (149) (10.4%), and isofuranodiene (147) (9.8%) (146) (39.7%), furanoeremophil-1-one (148) (24.4%), \u03b2-phellandrene (106) (14.4%), and isofuranodiene (147) (5.8%). The EO from leaves produced 43 constituents, including furanoeremophil-1-one (148) (30.0%), curzerene (146) (24.1%), germacrone (149) (9.7%), \u03b2-pinene (39) (9.5%), and isofuranodiene (147) (4.8%).Petrelli et al. evaluate) (9.8%) . They idSoEOs showed effectiveness against T. brucei brucei with satisfactory SIs. The most powerful EO was obtained from fruits , followed by the EO from flowers and from leaves , and at least active was the EO from roots . Some pure compounds were also tested, including isofuranodiene (147) , \u03b2-acetoxyfuranoeudesm-4(15)-ene (145) , and germacrone (149) (IC50 > 100\u2009\u03bcg/mL) which had the best profiles. Taking into account that curzerene (146) is a thermal degradation product of isofuranodiene (147) [147) is the major component of all SoEO and is therefore responsible for their antitrypanosomal activities. The SoEO from fruit had as its principal component \u03b2-acetoxyfuranoeudesm-4(15)-ene (145), also contributing to its superior potential over the other components.These ne (147) , 137, an149), as opposed to isofuranodiene (147) and \u03b2-acetoxyfuranoeudesm-4(15)-ene (145) structures (147) was already known for its inhibitory activity against dihydrofolate reductase, an important enzyme in purine biosynthesis and therefore in DNA synthesis. This may be the mechanism of action for its inhibition of T. brucei brucei growth [Structurally, the absence of the furan ring in germacrone EO and fractions, using pentamidine as the standard drug. CG-MS revealed that the majority of the constituents of CnEO were oxygenated monoterpenes (79%), sesquiterpenes (12.3%), oxygenated sesquiterpenes (2.6%), and monoterpene hydrocarbons (1.9%), including citronellal (62) (35.5%), geraniol (6) (28%), and citronellol (51) (11%). In the biological evaluation, C. nardus EO exhibited strong antitrypanosomal activity and high SI .Muhd Haffiz and colleagues evaluateT. b. brucei growth with low cytotoxicity. The most active fractions were as follows: subfraction 4\u2032 , subfraction 6\u2032 , subfraction 7\u2032 , and subfraction 8\u2032 . The major constituents were \u03b3-eudesmol (150) (\u03b1-cadinol (53) for subfractions 4\u2032 and 6\u2032 and elemol (52) for subfractions 7\u2032 and 8\u2032.These EOs were fractionated into 7 fractions, then combined, and then refracted into 8 subfractions, and finally their activities were determined. In the great majority of cases, the fractions and subfractions showed great potential for inhibition of ol (150) and \u03b1-caT. brucei potential of the EOs and constituents from Azadirachta indica (leaves), Aframomum melegueta (seeds), Aframomum daniellii (leaves), Clausena anisata (leaves), Dichrostachys cinerea (seeds), and Echinops giganteus (roots).Essential oils from aromatic and medicinal plants from Cameroon with known antitrypanosomal properties were evaluated by Kamte et al. . The autAiEO, 13 compounds were identified, with abundance of sesquiterpene hydrocarbons (97.4%), especially germacrene B (151) (74.0%) and \u03b3-elemene (152) (18.3%) , of which 1,8-cineole (124) (58.5%), \u03b1-terpineol (111) (19.4%), and \u03b2-pinene (39) (7.1%) were the main constituents; for AdEO, 57 compounds were identified, with greater abundance of monoterpene hydrocarbons (59.8%), where sabinene (17) (43.9%), (E)-caryophyllene (22) (16.6%), and \u03b2-pinene (39) (5.8%) were the most abundant; for CaEO, 47 compounds were identified, with abundance of phenylpropanoids (84.0%), where (E)-anethole (153) (64.6%) and (E)-methyl isoeugenol (2) (16.1%) , where silphiperfol-6-ene (154) (23.0%), presilphiperfolan-8-ol (155) (22.7%), presilphiperol-7-ene (156) (7.8%), cameroonan-7-\u03b1-ol (157) (7.1%), and caryophyllene (22) (6.3%) were the most abundant was the primary, and geraniol (6) (18.2%), terpinen-4-ol (103) (7.5%), linalool (3) (4.0%), and umbellulone (158) (3.8%) were the most representative constituents. Representative amounts of other classes of compounds were also observed, especially ligustrazin (159) (5.1%), elemicin (160) (3.0%), and decanoic acid (161) (2.8%) (For (18.3%) ; for AmE (16.1%) were theabundant ; and for) (2.8%) .in vitro evaluation of these EOs demonstrated inactivity of DcEO, AmEO, and CaEO (IC50 > 100\u2009\u03bcg/mL), and moderate activity of AdEO (IC50 = 7.65 \u00b1 1.1\u2009\u03bcg/mL), EgEO (IC50 = 10.50 \u00b1 1.7\u2009\u03bcg/mL), and AiEO (IC50 = 15.21 \u00b1 0.97\u2009\u03bcg/mL), when compared to standard drug suramin (IC50 = 0.0286 \u00b1 0.0008\u2009\u03bcg/mL). The SIs of the three more active EOs were also evaluated and were >13.1, >9.52, and >6.57, respectively [The ectively .A. melegueta and A. daniellii EOs were also evaluated. 1,8-Cineole (124) and terpinen-4-ol (103) (main compounds of AmEO) were inactive (IC50 > 100\u2009\u03bcg/mL), while sabinene (17) (IC50 = 5.96 \u00b1 1.3\u2009\u03bcg/mL), (E)-caryophyllene (22) (IC50 = 8.25 \u00b1 1.3\u2009\u03bcg/mL), and \u03b2-pinene (39) (IC50 = 11.4 \u00b1 2.6\u2009\u03bcg/mL), main components of AdEO, showed moderate to good anti-T. brucei activities [Some of the main constituents of tivities .Leishmania). It is estimated that at least 12 million people in more than 100 countries are infected, and at least another 350 million people are at risk in endemic areas [Leishmaniasis is a group of noncontagious infectious diseases caused by at least 20 parasitic protozoa belonging to the family Trypanosomatidae . More recently, for the treatment of refractory and resistant cases, pentamidine, miltefosine, amphotericin B, and paromomycin are used .In the same way as observed for the trypanosomiases described above, the scarcity of drugs for leishmaniasis necessitated the use of plants, and parts of plants, as therapeutic alternatives in several parts of the world.Leishmania species and forms .Between 2000 and 2018, the literature reported the use of EOs from 142 plant species (30 families) and 44 isolated compounds that were evaluated against various 50 values less than or equal to 10\u2009\u03bcg/mL against at least one species of Leishmania (promastigote or amastigote forms) and were considered active based on hit selection criteria for visceral leishmaniasis [50 values), selectivity index (SI), and morphological and ultrastructure alterations in the parasite, as well as for their mechanism of action. For inactive extracts and chemical entities (IC50 > 50\u2009\u03bcg/mL), and for those in which only the parasite was sensitive , see supplementary material and 13 isolated compounds showed ICmaniasis . In addimaterial .Leishmania, showed antileishmanial activities against L. major and L. infantum promastigote forms. In general, for all tested extracts, L. infantum species were more sensitive than were L. major, and only two EOs were more effective against the parasites than were murine macrophagic cells. EOs from Thymus hirtus sp. Algeriensis, rich in oxygen-containing monoterpenes, especially linalool (3) (17.62%) and camphor (14) (13.82%), and from Ruta chalepensis, rich in 2-undecanone (162) . On the other hand, for these two EOs, SI values ranging from 0.19 to 1.57 showed inadequate antileishmanial activity by hit selection [T. articulata and Lavandula multifida) were inactive against L. major promastigotes, and for the remaining six EOs, IC50 values ranged from 0.30 to 2.23\u2009\u03bcg/mL, but with high levels of cytotoxicity (SI < 1) [EOs from 10 plants issued from the Sned region of Tunisia, an endemic region for various forms of ne (162) (84.28%)ectively . In addielection . Two oth(SI < 1) .L. amazonensis promastigote forms after 24\u2009h of exposure [50 values. For the four most effective EOs , the IC50 values ranged from 48.55 to 64.75\u2009\u03bcg/mL and were considered moderately active or inactive. Furthermore, for all EOs tested, SI were not satisfactory (0.99 < SI > 3.94). From the chemical composition of the evaluated EOs and the IC50 and SI values, the authors compared these leishmanicidal activities and cytotoxicities with those of EOs from other plant species. Literature reports that EOs from Matricaria chamomilla showed no leishmanicidal activity against L. donovani specie. Another EO from Lantana camara, with similar major constituents (farnesene (117) derivatives as major constituents), showed significant leishmanicidal activity against L. amazonensis (IC50/72\u2009h = 0.25\u2009\u03bcg/mL), but with high cytotoxicity [Bulnesia sarmientoi, with 48.29% of guaiol (163) (L. amazonensis (IC50 = 85.56\u2009\u03bcg/mL). However, EO from Endlicheria bracteolate, with 72.12% of guaiol (163), had an IC50 of 7.93\u2009\u03bcg/mL against the same Leishmania species and a similar value of SI (1.91) [3) in the EO from Salvia sclarea was insufficient to promote leishmanicidal activity for this EO, since Ku\u017ama et al. demonstrated that linalool-rich EO from the leaves of Croton cajucara promoted morphological changes in L. amazonensis promastigotes treated at concentrations of 15\u2009ng/mL [EOs from sixteen plant species belonging to various families, purchased from QUINARI Cosmetic and Fragances Inc. or collected in Lavras, MG (Brazil), were evaluated for their biological potential against exposure . None oftoxicity , 146. Inol (163) as its mI (1.91) . Finally15\u2009ng/mL .L. amazonensis [50 values ranging between 5.0 and 22.0\u2009\u03bcg/mL. The most active EO demonstrated effects against axenic and intracellular amastigote forms, with IC50 values of 15.0 and 20\u2009\u03bcg/mL, respectively. With respect to cytotoxicity, this same EO showed a tolerable value of SI (8.0) to promastigote forms and an inadequate value (2.5) to axenic amastigote forms. Nevertheless, studies revealed that copaiba oil from Copaifera reticulata did not alter the viability of peritoneal macrophages at a concentration of 500\u2009\u03bcg/mL, and the treatment at 500\u2009mg/kg with EOs from Copaifera reticulata and Copaifera multijuga did not induce behavioral alterations, lesions, or bleeding in the stomachs of mice [In order to explore ethnopharmacological data of copaiba oils obtained from Peru, Maranh\u00e3o, and Amazonas (states in Brazil) and French Guiana which are used in folk medicine to treat leishmaniasis \u2013152, Sanzonensis . All cop of mice , 155.in vivo antileishmanial activity against L. amazonensis of an EO from Copaifera martii, also using electron microscopy, biochemical analysis, and flow cytometry [2) treatments reduced the average lesion size in relation to the control group ; however, no significant difference was observed when compared to the reference drug glucantime (79.5% reduction). Nevertheless, topical and subcutaneous (100\u2009mg/kg/day) treatments did not show significant reduction in average lesion size, and the subcutaneous treatment caused injuries to the animal.These results involving copaiba EOs from various species led the same authors to investigate the ytometry . InfecteL. amazonensis treated with concentrations of 14\u2009\u03bcg/mL (IC50) and 70\u2009\u03bcg/mL (IC90) showed ultrastructural changes and swollen mitochondria, and (ii) an increase in plasma membrane permeability and depolarization of the mitochondrial membrane potential were observed in axenic amastigotes treated with 100 and 200\u2009\u03bcg/mL promastigote forms of 00\u2009\u03bcg/mL . These rCopaifera reticulata and Copaifera martii species against L. amazonensis led another research group to investigate the biological potential of four commercial oils from Copaifera ssp. C1-C4, \u03b2-caryophyllene-, sesquiterpene- and diterpene-rich fractions were obtained from distillation [L. amazonensis promastigotes. Sesquiterpene-rich EOs C1 and C4 were more potent against intracellular amastigotes, with IC50 of 2.9 and 2.3\u2009\u03bcg/mL, respectively. In comparison with the same activity of EO from Copaifera reticulata [\u03b2-caryophyllene (22) as their major constituent, the good IC50 value (1.3\u2009\u03bcg/mL or 6.4\u2009\u03bcM) demonstrated by the isolated sesquiterpene suggested that this compound may directly influence the antileishmanial activity of the EOs assayed. In addition, SI values of 29.3, 40.1, and 48.9 for C1, C4, and \u03b2-caryophyllene (22), respectively, demonstrated a better ratio of efficacy to toxicity. Finally, the C4 sesquiterpene-rich fraction showed a similar antileishmanial activity against amastigote forms, probably due to the same concentration of \u03b2-caryophyllene (22) in both the EO and the fraction, and C4 diterpene-rich fraction was not active in low concentrations [The antileishmanial effects of copaiba EOs from illation . Diterpeticulata , C1 and trations .Artemisia absinthium L., Artemisia abyssinica, Echinops kebericho MESFIN, and Satureja punctata, were tested against promastigote and axenic amastigote forms of L. donovani and L. aethiopica. The results demonstrated that two EOs from Artemisia absinthium L. and Echinops kebericho MESFIN possessed strong antileishmanicidal activity against promastigote (IC50 ranging from 0.24 to 42.00\u2009\u03bcg/mL) and axenic amastigote forms (IC50 ranging from 0.0097 to 0.15\u2009\u03bcg/mL) of both Leishmania species. In relation to the other two species tested, Artemisia abyssinica was inactive against the two forms of parasite, and Satureja punctata showed high cytotoxicity. Unfortunately, the great number of constituents that appeared to have no specific cellular targets could explain the inadequate SI values for the most active oils [EOs from four plant species reported in traditional medicine in Ethiopia, ive oils , 159.Ocimum canum Sims. that is commonly used as an infusion or syrup for the treatment of a number of diseases. The biological results revealed that OcEO was rich in monoterpenes such as thymol (1) (42.15%), p-cymene (11) (21.17%), and \u03b3-terpinene (64) (19.81%), demonstrating moderate activity against promastigote and intracellular amastigote forms of L. amazonensis, with IC50 values of 17.4 and 13.1\u2009\u03bcg/mL, respectively. These values were more potent than those of the reference drug pentamidine, with satisfactory SI values [OcEO was associated with several ultrastructural alterations in promastigote forms of the parasite, including autophagosome-like structures that were multivesicular and had lipid bodies that could result in cell death, discontinuity of the nucleus membrane, and exocytic activity by the flagellar pocket [In a recent study, Silva and colleagues evaluated the antileishmanial activity of the EO from leaves of ctively) . Electror pocket .Achillea millefolium, species used as antihelmintic and trypanocidals, was evaluated in vitro against L. amazonensis. Significant activity was observed against promastigote and intracellular amastigote forms, with IC50 values of 7.8 and 6.5\u2009\u03bcg/mL and acceptable SI values of 9.2 and 11.0, respectively [AmEO were not determined. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analysis of the treated promastigote forms revealed morphological alterations in the shape and size of the parasite as well as ultrastructural alterations, including changes in the flagellar membrane, abnormal membrane structures, rupture of the plasma membrane, atypical vacuoles, myelin-like figures, and vesicles that resembled autophagic vacuoles. The mechanism of action remains unclear; however, the morphological changes observed in the parasite may be related to inhibition of two parasite enzymes: serine-protease and squalene synthase (BPQ-OH) [EO from leaves and flowers of ectively . Unfortu(BPQ-OH) .Croton cajucara and purified linalool (3) [3) showed potent antileishmanial activity, with IC50 values of 8.3 and 4.3\u2009ng/mL against promastigote forms and values of 22.0 and 15.5\u2009ng/mL against the amastigote form of the parasite, respectively. SI values were not determined, but for both, the concentration of 15.0\u2009ng/mL presented no cytotoxic effects against mammalian cells. Mitochondrial swelling and important alterations in the organization of the nuclear and kinetoplast chromatins decrease in the association between macrophages and parasites, and increases in nitric oxide levels in infected macrophages could explain the extreme toxicity of the CcEO for L. amazonensis [Rosa et al. investigated the leishmanicidal effects of linalool-rich EO from leaves of lool (3) . Both EOzonensis .3) (oxygenated monoterpene) and eugenol (2) (phenolic compound), chemical constituents in many EOs from various plant species, as well as eugenol- and linalool-rich EOs, were fatal for several species of Leishmania [L. infantum chagasi promastigotes and axenic amastigote forms at baseline and during the infection of peritoneal mouse macrophages [50 values for eugenol (2) and linalool (3) against axenic amastigotes forms were 220 and 550\u2009\u03bcg/mL, respectively. The IC50 value for eugenol (2) against promastigote forms was 500\u2009\u03bcg/mL, and for linalool (3), the IC50 value for the last parasite form was not determined. For both compounds, some of the mechanisms associated with leishmanicidal activity were confirmed: the two derivatives were able to enhance the activities of protein kinases PKC and PKA, linalool (3) decreased parasite oxygen consumption, and eugenol (2) reduced the parasite resistance to reactive oxygen species [Some studies reported that linalool , against L. amazonensis. The EO showed good activity against promastigote and amastigote forms, with IC50 values of 1.7 and 3.2\u2009\u03bcg/mL, respectively, a good SI value (14.7) for promastigotes and a tolerable value IC50 of 8.7\u2009\u03bcg/mL against promastigote forms, with a tolerable SI of 6.3. SEM and TEM analysis revealed aberrant morphologies of the amastigote forms exposed to the EO, including disintegration of the parasite, mitochondrial swelling, exocytic projections in the flagellar pocket, swollen mitochondria, and rupture of the plasma membrane, characterized by the presence of extracellular materials [Santim et al. (2009) evaluated the effect of EO from aterials .Eugenia uniflora L. and Syzygium cumini (L.) Skeels, and \u03b1-pinene (118), major constituents of EuEO. \u03b1-Pinene (118) was more effective than was the EO from the plant, without desirable potency (IC50 \u2265 38.1\u2009\u03bcg/mL against various forms of the parasite). The isolated compound showed moderate IC50 values and low cytotoxicity (SI > 21.5). The mechanism of action for monoterpene was mediated by immunomodulatory activity and elevated NO levels. However, EO from E. uniflora showed significant antileishmanial activity, with IC50 values of 3.04 and 1.92\u2009\u03bcg/mL against promastigote and amastigote forms, respectively, and good SI values of 14.9 and 23.9, respectively. In relation to the mechanism of action, this EO activity was not mediated by nitric oxide production, suggesting that macrophage activation may be involved in the biological activity, as demonstrated by increases in both phagocytic capacity and lysosomal activity [Rodrigues and colleagues , 169 evaactivity , 169.Piper angustifolium. PaEO rich in sesquiterpenes such as spathulenol (108) (23.78%) and caryophyllene oxide (38) (13.06%) reduced the number of intracellular amastigotes of L. infantum with an IC50 value of 1.43\u2009\u03bcg/mL. It was more toxic to NIH/3T3 fibroblasts and murine macrophage J774.A1, with good SI values of 33.72 and 22.5, respectively. For PpEO, the mechanism of action may be associated with increased NO release after treatment at low concentrations [Bosquiroli et al. evaluated the antileishmanial activity of EO from trations .Leishmania species [Lavandula stoechas, with fenchone (166) (31.81%), camphor (14) (29.60%), and terpineol (111) (13.1%) as major constituents, exhibited strong leishmanicidal effects against two Leishmania species, whereas L. major was the most sensitive strain with an IC50 of 0.9\u2009\u03bcg/mL, followed by L. infantum (IC50 = 7.0\u2009\u03bcg/mL) and L. tropica (IC50 > 10\u2009\u03bcg/mL). For the EO from Origanum compactum, three phenological stages of the plant were analyzed, and the oxygenated monoterpenes were the major constituents at the three phenological stages . In lower quantities, other chemical classes such as sesquiterpene hydrocarbons, oxygenated sesquiterpenes, alcohols, ketones, and acids were also identified. At low concentrations, these EOs showed significant cytotoxicity against three Leishmania species, while the cytotoxic effects are not significantly variable with increasing concentrations. The L. infantum species was the most sensitive strain, with IC50 values ranging from 0.02 to 0.12\u2009\u03bcg/mL at the three phenological stages. The other two EOs from Mentha pulegium and Rosmarinus officinalis were studied by the same authors, and both monoterpene-rich EOs were potent against L. major, L. infantum, and L. tropica species, showing IC50 values ranging from 0.36 to 2.6\u2009\u03bcg/mL. Unfortunately, for all EOs studied, the SI values were not determined, and the relationship between efficacy and toxicity could not be measured [EOs obtained from the aerial parts of four Moroccan plant species (Lamiaceae) were screened against various species \u2013173. Themeasured \u2013173.Ferula communis, Teucrium polium, and Pelargonium graveolens species displayed strong inhibitory activities against the promastigote forms ofL. major and L. infantum, showing IC50 values ranging from 0.05 to 0.28\u2009\u03bcg/mL. The second group contained five EOs belonging to Thymus hirtus, Artemisia campestris, Myrtus communis, Artemisia herba-alba, and Alvia officinalis, exhibiting good leishmanicidal activities with IC50 values ranging from 1 to 10\u2009\u03bcg/mL against the same species of the parasite, but with lower activity when compared with amphotericin B. In the third group, EOs from Nigella sativa, Laurus nobilis, Rosmarinus officinalis, and Eucalyptus globulus showed IC50 values up to 10\u2009\u03bcg/mL. Purified \u03b2-caryophyllene (22), camphor (14), and carvacrol (10) were screened against the same parasite species and showed less activity when compared with the most active EOs classified as the first group. In addition, the most active EOs and purified compounds showed low cytotoxicity to macrophage cells, presenting ideal values of SI (SI > 10) [Essid et al. evaluated the antileishmanial activity of EOs from twelve medicinal plants from Northern Tunisia. The first group of EOs isolated from SI > 10) .in vivo study was performed with the EO extracted from the leaves of Artemisia annua, which has camphor (14) (52.06%), \u03b2-caryophyllene (22) (10.95%), and 1,8-cineole (124) (5.57%) as major constituents. AaEO presented an IC50 value of 7.3\u2009\u03bcg/mL against amastigote forms of L. donovani, but no cytotoxic effects against mammalian macrophages even at 200\u2009\u03bcg/mL. In addition, intraperitoneal administration of the AaEO (200\u2009mg/kg/b.w.) to infected BALB/c mice reduced the parasite burden by almost 90% in the liver and spleen, with significant reduction in weight. There was no hepatic or renal toxicity, as demonstrated by normal levels of serum enzymes [An enzymes .Tetradenia riparia against L. amazonensis species. They found that TrEO induced 50% death of amastigote forms of the parasite after 24\u2009h incubation at a concentration of 30\u2009\u03bcg/mL. In addition, the oil did not present cytotoxicity in murine macrophages at the same concentration, with cell viability >95%. They evaluated the modulatory effects of TrEO on cytokine levels in peritoneal fluid cells that were infected with L. amazonensis. They observed inhibition of some of the most critical cytokines for parasite growth and the establishment of infection, including granulocyte-macrophage colony-stimulating factor, interleukin-4 (IL-4), IL-10, and tumor necrosis factor (TNF). The parasite inhibited interferon-\u03b3 and IL-12, and the EO blocked this inhibition, indicating that these cytokines were critical for activating mechanisms associated with the death and elimination of the parasite [Drmachi et al. (2016) evaluated the immunomodulatory effects of EO from parasite .Chenopodium ambrosioides, containing carvacrol (10) (62.36%) and ascaridole (37) (22.54%) as major constituents, was investigated against L. amazonensis. CaEO showed EC50 values of 3.7 and 4.6\u2009\u03bcg/mL against promastigote and amastigote forms, respectively, and cytotoxicity was approximately 15-fold higher for peritoneal macrophages than for both parasite forms [L. donovani, with EC50 values of 4.45 and 5.1\u2009\u03bcg/mL, respectively [in vivo study demonstrated significant reduction in the size of the lesions in animals treated with the EO during the first 15 days of treatment. They also observedsignificant suppression of the number of parasites in the infected footpads, as compared with the burden in the footpads of the other treated mice, and oral administration at a dose of 30\u2009mg/kg slowed the infection in an experimental model [EO from te forms . For thete forms , and othectively . An in val model .C. ambrosioides compared with untreated animals at doses of 30 and 150\u2009mg/kg by intralesional and oral routes. This activity was superior to that of the reference drugs glucantime, amphotericin B, and pentamidine, or the two major constituents carvacrol (10) and ascaridole (37) [Bixa orellana, at dose of 30\u2009mg/kg over 14 days [CaEO caused a breakdown of mitochondrial membrane potential and a modification of redox indexes [10), ascaridole (37), and caryophyllene oxide (38) mediated their leishmanicidal activity via various mitochondrial targets, including the electron transport chain, thiol depletion, and production of superoxide radical, causing significant impairment of mitochondrial coupling [In a subsequent study, the authors observed a significant reduction in lesion size in BALB/c mice treated with the EO from ole (37) , 180. Th 14 days . Finally indexes , and thecoupling .Vanillosmopsis arborea Baker showed that \u03b1-bisabolol (165) was its main constituent (97.9%). Both VaEO and \u03b1-bisabolol (165) efficiently inhibited the growth of L. amazonensis promastigotes, with IC50 values of 7.35 and 4.95\u2009\u03bcg/mL, respectively [\u03b1-bisabolol (165) was more effective against promastigotes and intracellular amastigotes, and the cytotoxic assay against intracellular amastigotes showed that the pure compound (SI = 9.38) was less toxic than was VaEO (SI = 11.52). These results suggested that both \u03b1-bisabolol (165) and VaEO increased cell permeability to exogenous compounds, since some sesquiterpenes can induce changes in membranes, allowing microorganisms to enter the cells, thus augmenting the microbial permeability to antimicrobial agents. The ultrastructural analysis of the parasite showed an elongated cell body and the presence of a well-defined kinetoplast and nucleus. The promastigotes treated with \u03b1-bisabolol (165) for 24 hours at 30\u2009\u03bcg/mL showed severe cell damage with loss of parasite morphology, discontinuity of the nuclear membrane, increased mitochondrial volume and kinetoplast, and presence of vesicles with an electrondense display with lipid inclusion in the plasma membrane. However, in the same conditions of analysis for VaEO, they observed increased volumes of flagellar pockets with consequent breakage, increased volumes and changes in mitochondrial kinetoplasts, abnormal condensation of chromatin in the nucleus, discontinuity of the nuclear membrane, lipid inclusions in the presence of electrondense vesicles, and visualization of the inclusion of a lipid envelope within the plasma membrane, with the consequent loss of parasite morphology [The chemical analysis of EO from ectively . In addirphology .\u03b1-bisabolol (165) against promastigote forms of L. infantum. In general, this sesquiterpene showed a very similar percentage of inhibition of the parasite when compared with the reference drug pentamidine -\u03b1-bisabolol (165) to treat leishmaniasis caused by L. infantum [Another group evaluated the effect of (\u2212)-tamidine . The valinfantum , 185.2), thymol (1), and carvacrol (10), by molecular hybridation with nitrated Morita-Baylis-Hillman adducts (MBHAs) [50 values of the most potent hybrid compounds against L. amazonensis promastigote forms are shown in 180, 181, and 182 exhibited the best antileishmanial activity, with IC50 values ranging from 4.71 to 8.75\u2009\u03bcg/mL, and SI > 45 . In addition, the compounds substituted with nitro groups at the ortho position were more bioactive than the meta and para nitroaryl isomers. Experimental and in silico studies indicated that the mechanism of action was connected to nitro group reduction that generated RNO\u2212\u2022 [Xavier et al. explored the leishmanicidal properties of synthesized compounds derived from the oxygenated monoterpenes eugenol ( (MBHAs) . The gened RNO\u2212\u2022 .L. amazonensis [10) and thymol (1) that presented a phenolic moiety were the most active compounds, showing moderate antiparasitic activity, with IC50 values of 25.4 and 26.8\u2009\u03bcg/mL, respectively. This result suggests that the position of the hydroxyl group in the aromatic ring did not influence the antileishmanial activity. For eugenol (2), a hydrogen bond between hydroxyl and o-methoxyl groups reduced the release of protons by the OH group, and the acidity of this group may play an important role in the potency of the compounds. In addition, for this series of compounds, the absence of aromatic hydroxyls caused compounds to be less potent, as observed for p-cymene (11) and menthol (130) with IC50 values of up to 198.9\u2009\u03bcg/mL.Ten chemical constituents of EOs, including nine monoterpenes and one phenylpropanoid, were investigated as antileishmanial agents against promastigote forms of zonensis . Among t50 value found for carvacrol (10) was different from values reported in the literature for L. chagasi and L. amazonensis promastigotes and thymol (1) compounds showed low cytotoxicity at concentrations of 50 and 100\u2009\u03bcg/mL, where the percentage of viability on L929 fibroblasts ranged from 46.1 to 64.5%.In the same study, the IC50 = 2.3 and 28.050 = 2.3 , and 15.3 [\u03bcg/mL , respectishmania , 189. BoAedes aegypti, which every year transmits diseases to more than 700 million people worldwide. According to the World Health Organization, it causes more death than any other arboviral disease, killing about 2.5% of all affected children [Arboviruses (arthopod-borne viruses) are viral diseases transmitted to humans by arthropods (insect and arachnid). Among the vectors, one that stands out is the mosquito children .Aedys aegypti is a carrier of various diseases, including dengue fever, dengue haemorrhagic fever, chikungunya, yellow fever, and even Zika virus [ka virus . Yellow ka virus , while dka virus .In recent decades, the spread of dengue has increased worldwide, and in 2012 it was considered the most important viral disease in the world, with more than 100 countries and more than 2.5 billion people (about 40% of the world population) at risk of infection by some mosquito-borne disease. Of this total population, approximately 50-100 million are infected annually, of which 500 thousand cases are considered of greater severity , 205The mosquito transmits arboviruses through the blood meals of the female. The life cycle consists of egg, larva, pulp, and adult. Eggs are deposited on the walls of any reservoirs containing water, and the ideal temperature range for hatching is 28-33\u00b0C; larval and pupal stages take place in the water. The transition phase from larval to pupa lasts 24 hours, and the pupal phase lasts 48 hours until the adult mosquito appears. When adults appear, it takes a few seconds for the stiffening of chitin that allows them to fly .Treatment of dengue, chikungunya, and Zika virus are symptomatic, and vaccines are not yet available. Currently, the only effective way to control these diseases is by breaking the disease transmission cycle, controlling the mosquito population through the use of biological and/or synthetic insecticides and repellents.A. aegypti), causing serious environmental impact [In several public health programs, various larvicides and insecticides currently used are effective in eliminating mosquitoes and larvae, including the organophosphates temephos and pyrel impact .Currently, in Brazil temephos 1% and Bti (an efficient bioinsecticide) are both used. Bti does not present the same environmental impact as does temephos; however, its high cost makes its general use impossible .In this scenario, it is necessary to identify new larvicides with various modes of action to reduce the development of mechanisms of resistance to pesticides, thereby bolstering public health system efforts .The use of biological agents such as EOs is an alternative to synthetic insecticides, with good selectivity to the target and low toxicity to other organisms and the environment , 212.The use of biological agents has been gaining great prominence, reaching the point of a single review article compiling the larvicidal activity of 361 EOs from 269 plant species. Among these, more than 60% were considered active, with LCs < 100\u2009mg/L .Aedes aegypti in the larval phase than in the adult phase [Knowing that it is easier to interfere with the proliferation of lt phase , severallt phase , more pllt phase , less tolt phase , and biolt phase . In theslt phase .Aedes aegypti adults and larvae. A summary of these studies is presented in In this context, several authors reported activity of EOs and their phytoconstituents in the control of Most of the studies, while identifying the constituents of the EO, restricted the experiments of biological activity to the oil itself, with few studies evaluating the activity of each individual substance. In some cases, only the activity of the compounds with the highest concentration was evaluated. This is primarily due to the high cost of these compounds, when they are available for purchase .n = 49) of the compounds shown in 119) (LC50 = 10.7 and 25.3\u2009\u03bcg/mL), \u03b1-terpinene (182) (LC50 = 14.7\u2009\u03bcg/mL), and limonene (8) (LC50 = 18.1\u2009\u03bcg/mL), among others.The monoterpenes were the most tested compounds, especially oxygenated monoterpenes, corresponding to 38% , which identifies characteristics related to the structure of the compound that describe the biological activity, making possible the design of new promising compounds.2O) of thymol (1) and carvacrol (10) derivatives that were important to explain the activities of the compounds against larva of Aedes aegypti [2O) for the activity of these compounds against the larva of Aedes aegypti; however, steric characteristics were also important to explain this activity, indicating that these characteristics were crucial to the activity of these substances, based on the evaluated compounds [One study conducted a consensus principal component analysis (CPCA) and principal component analysis (PCA), identifying characteristics related to hydrophobicity and linalool (3) showed similar activity when compared with benznidazole and quantified activity in nanomolar concentrations, respectively. In addition, semisynthetic aphidicolin (28) derivatives (diterpenes) exhibited high potency and selectivity against the same parasite.As examples for isolated active compounds against T. brucei activity, the isolated compounds rotundifolone (88) and (\u2212)-perillyl aldehyde (92) were slightly less active than the reference drug suramin, and carvacrol (10), ascaridole (37), and caryophyllene oxides (38) showed strong potential to growth inhibition of the parasite, with activity comparable to the same standard drug. In addition, some EOs and isolated compounds demonstrated promising antitrypanosomal activity and high selectivity index values, specially the compounds carlina oxide (139) (isolated from Carlina acaulis roots), linalool (3) , and C. nardus EO (rich in oxygenated monoterpenes), which demonstrated IC50 values ranged from 0.31 to 2.5\u2009\u03bcg/mL and high selectivity index (>40).For EOs with anti-50 \u2264 10\u2009\u03bcg/mL). Some of them promoted morphological alterations in the parasite, but few showed a great ratio of efficacy to toxicity. Linalool-rich EO (from Croton cajucara) and purified linalool (3) showed potent antileishmanial activity at nanomolar concentration, promoting morphological changes in the parasite, as well as decreased parasite oxygen consumption and enhances the activities of the protein kinases and increases in nitric oxide levels in infected macrophages, confirming some of the mechanisms associated with leishmanicidal activity. Another isolated compound identified as \u03b1-bisabolol (165) (main constituent of EO from Vanillosmopsis arborea) efficiently inhibited the growth of promastigotes and amastigotes forms of the same parasite, inducing several ultrastructural alterations and severe cell damage in the parasite, where the very similar percentage of inhibition (compared with pentamidine) and very low toxicity in vivo supported their therapeutic use to treat leishmaniasis.For antileishmanial activity, several EOs or isolated compounds were active against the parasite (IC108) and caryophyllene oxide (38) (from Piper angustifolium) and citral (63) (from Cymbopogon citratus) showed potential activity against promastigote and amastigote forms of the parasite and good SI values.Other EOs rich in spathulenol , \u03b1-terpinene (182), and limonene (8), exhibited the best activity.For control of In this sense, knowledge of the chemical structures of these phytochemicals may allow them to serve as scaffolds for rational drug design, suggesting chemical modifications to increase activity, bioavailability, and toxicity, among other characteristics, allowing the design of new and more active compounds."} +{"text": "Lesotho, a small mountainous country surrounded by South Africa, has a population of approximately 2 million persons and an estimated annual income of $1,210 per capita; 73% of the population resides in rural areas (Measures to achieve the Joint United Nations Programme on HIV and AIDS (UNAIDS) targets of 90% of all persons with HIV infection knowing their HIV status, 90% of all persons with diagnosed HIV infection receiving sustained ART, and 90% of all persons receiving ART achieving viral suppression (90\u201390\u201390) (The President\u2019s Emergency Plan for AIDS Relief (PEPFAR) supports HIV testing services in 121 health care facilities in five of Lesotho\u2019s 10 districts. The five PEPFAR-supported districts account for approximately 75% of all HIV-positive persons in the country who had previously tested HIV-positive and 189,864 (45.8%) who had tested negative within the preceding 3 months, leaving 160,506 (38.7%) persons eligible for HIV testing. Among these persons, 135,563 (84.5%) consented to testing, which identified 6,759 (5.0%) persons with newly diagnosed HIV infection. Thus, 389,964 (94.0%) persons attending these outpatient departments knew their HIV status before leaving the facility.Similarly, among 5,927 persons admitted to the eight PEPFAR-supported hospitals during this period, 1,029 (17.4%) patients had previously tested positive for HIV, including 133 (7.9%) of 1,687 children aged <15 years and 896 (21.1%) of 4,240 persons aged \u226515 years. In addition, 3,534 (59.6%) admitted patients had tested negative for HIV during the previous 3 months, resulting in 1,364 hospitalized patients being eligible for testing during their admission. Among these, 1,298 (95.2%) consented; 120 (9.2%) persons tested positive, including 21 (4.0%) of 526 children aged <15 years and 99 (12.8%) of 772 persons aged \u226515 years. Hospital-based HIV testing resulted in 5,861 (98.9%) hospitalized patients knowing their HIV status before discharge, with 1,149 (19.6%) being positive. Positivity rates ranged from 9.2% among children aged <15 years to 23.8% among persons aged \u226515 years.Lesotho has achieved close to 100% HIV testing coverage among hospitalized patients at PEPFAR-supported facilities and is approaching this level among patients seen in selected outpatient departments. In both facility-based testing and community-based testing , testing is being expanded to reach family members and intimate contacts of HIV-positive persons and to promote self-testing ("} +{"text": "In recent years, fish nucleated red blood cells (RBCs) have been implicated in the response against viral infections. We have demonstrated that rainbow trout RBCs can express the antigen encoded by a DNA vaccine against viral hemorrhagic septicemia virus (VHSV) and mount an immune response to the antigen in vitro. In this manuscript, we show, for the first time, the role of RBCs in the immune response triggered by DNA immunization of rainbow trout with glycoprotein G of VHSV (GVHSV). Transcriptomic and proteomic profiles of RBCs revealed genes and proteins involved in antigen processing and presentation of exogenous peptide antigen via MHC class I, the Fc receptor signaling pathway, the autophagy pathway, and the activation of the innate immune response, among others. On the other hand, GVHSV-transfected RBCs induce specific antibodies against VHSV in the serum of rainbow trout which shows that RBCs expressing a DNA vaccine are able to elicit a humoral response. These results open a new direction in the research of vaccination strategies for fish since rainbow trout RBCs actively participate in the innate and adaptive immune response in DNA vaccination. Based on our findings, we suggest the use of RBCs as target cells or carriers for the future design of novel vaccine strategies. Novirhabdovirus, a viral genus responsible for high economic losses in aquaculture [Aquaculture is one of the fastest growing food production sectors and the aculture , only glaculture ,6. Howevaculture ,8.RBCs have been involved in the fish immune response by expressing cytokines ,12,13,14Regarding RBCs, in recent decades, mammalian RBCs, which are not nucleated, have been proposed as possible drug and vaccine carriers ,16,17,18Taking everything into account, including the fact that the role of nucleated RBCs in the immune response has gained interest recently, our aim was to explore the currently unknown role of rainbow trout RBCs in the context of in vivo DNA vaccination. In this study, we show for the first time the role of rainbow trout RBCs in the global host immune response to a DNA vaccine. Our results show that rainbow trout RBCs can modulate their transcriptome and proteome in response to a DNA vaccine encoding GVHSV. In addition, these RBCs can act as cell mediators of the immune response to activate antigen presentation, blood and head kidney immune cell signaling, and hematopoiesis. RBCs transfected in vitro with GVHSV can boost leukocyte proliferation, increasing the number of cells and leukocyte-specific markers. Moreover, reinfusion of autologous GVHSV-transfected RBCs in vitro induced VHSV-specific antibodies in vivo.Oncorhynchus mykiss) of approximately 7\u201310 cm (for transcriptomic and proteomic assays) and 20\u201325 cm (for RBC reinfusion assays) were obtained from a VHSV-free commercial farm . Fish were maintained at the University Miguel Hernandez (UMH) facilities at 14 \u00b0C and fed daily with a commercial diet . Prior to experiments, the fish were acclimatized to laboratory conditions for 2 weeks.Rainbow trout , encoding the teal fluorescent protein 1 (mTFP1) , used asgvhsv gene transcripts expression monitorization in blood and head kidney (data not shown) and in the bibliography [For transcriptomic and proteomic analyses, juvenile rainbow trout (7\u201310 cm) were anesthetized with tricaine (40 mg/L) and injected intramuscularly (im) with 10 \u00b5g of TFP1 plasmid, or GVHSV plasmid in 50 \u00b5L of phosphate buffered saline (PBS) using insulin syringes . At 14 days post-injection (dpi), fish were sacrificed by overexposure to tricaine 0.3 g/L), and peripheral blood and head kidney were recovered. The sample collection time point was selected based on previous g/L, andiography .6 cells) that were GVHSV-transfected in vitro as previously described [6 cells using the Neon\u2122 Transfection System . Fish were immunized with im or iv injection of 4 \u03bcg GVHSV for immunization controls. At 30 dpi, blood was drawn from the caudal vein and left overnight at 4\u00b0C to separate the serum from the cell pellet.For the GVHSV-transfected RBC reinfusion assay, adult rainbow trout (20\u201325 cm) were anesthetized with 40 mg/L tricaine and reinfused intravenously (iv) with previously extracted autologous peripheral blood RBCs (PB-RBCs) supplemented with 10% fetal bovine serum (FBS) gamma irradiated , 1 mM pyruvate (Gibco), 2 mM L-glutamine (Gibco), 50 \u00b5g/mL gentamicin (Gibco), 2 \u00b5g/mL fungizone (Gibco), 100 U/mL penicillin (Sigma-Aldrich), and 100 \u03bcg/mL streptomycin (Sigma-Aldrich). Head kidney tissue was disaggregated with a Pasteur pipette and passed through a 40 \u03bcm Falcon nylon cell strainer using a plunger of a 1 mL syringe. Then, cells from head kidney and peripheral blood were stained with 500 nM SYTO RNA Select for 20 min at room temperature as recommended by the manufacturer. Head kidney RBCs (HK-RBCs) and peripheral blood RBCs (PB-RBCs) were FACS single-cell sorted using a BD FACSJazz\u2122 cell sorter using SYTO RNA Select staining, which stains RNA and allows to sort populations based on cell RNA quantity. RBCs population for sorting was selected based on SYTO RNA select staining (FITC) and side scatter light (SSC), as indicated in 2 HK-RBCs and 106 PB-RBCs of each individual were sorted as described in the previous section.Thirty-two individuals (16 for TFP1 injection and 16 for GVHSV injection) were immunized as described above. At 14 dpi, approximately 10Each sample was resuspended in lysis buffer and RNase Inhibitor as indicated in Reference and then7 cells per individual) were pelletized by centrifugation , the supernatant was removed, and the cell pellet was washed 3 times with PBS. The pellet was then digested, cleaned-up/desalted, and pooled into 2 pools of 8 individuals for each condition (TFP1 or GVHSV) were immunized as described above. Peripheral blood was extracted at 14 dpi, and PB-RBCs were purified by 2 density gradient centrifugations as previously described . The 99.r GVHSV) . Samplesp-value \u2264 0.05 and a p-value \u2264 0.5, respectively, and Kappa score of 0.4 as threshold values. The STRING v11 (http://string.embl.de/) [Homo sapiens model organism was used for ClueGO and STRING analyses. Genes and proteins were identified by sequence homology with Homo sapiens using Blast2GO version 4.1.9 [Pathway enrichment analysis of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were performed using the Cytoscape version 3.6.1 with Clumbl.de/) software, Spain) as previ, Spain) .RNA was isolated using E.Z.N.A. Total RNA Kit following the manufacturer\u2019s instructions together with DNAse and quantified with a NanoDrop Spectrophotometer . cDNA synthesis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) were performed using the ABI PRISM 7300 System as previously described . Specifi5 RBCs/105 WBCs per well. WBCs (cocultured with untransfected RBCs) treated with phytohemagglutinin-L (Sigma-Aldrich) (PHA-L) were used as a positive control of lymphocyte proliferation because PHA-L is a well-known lymphocyte proliferation compound [Ficoll-purified RBCs from peripheral blood were transfected with TFP1 or GVHSV plasmid as indicated previously . Transfecompound ,47,48. Acompound . WBC proSerum was collected from immunized or reinfused individuals at 30 dpi as indicated above. After centrifugation for 15 min at 3500 rpm, the serum was stored at \u221220 \u00b0C until used. Negative serum was collected from unimmunized individuals and positive serum was collected from VHSV-challenged survivors. VHSV-specific IgM antibodies were measured by ELISA as previously described with minwww.graphpad.com) was used for statistical analysis.The GraphPad Prism 6 software and by the competent authority of the Regional Ministry of Presidency and Agriculture, Fisheries, Food and Water supply . All methods were carried out in accordance with the Spanish Royal Decree RD 53/2013 and EU Directive 2010/63/EU for the protection of animals used for research experimentation and other scientific purposes.gvhsv gene transcripts were detected, but not significantly (FDR > 0.05), in HK-RBCs from GVHSV-immunized individuals.Transcriptome profiling of HK-RBCs that were FACS single-cell sorted from GVHSV-immunized individuals identificxcr4) (log2 fold change (FC) = 13.01), C\u2014C motif chemokine receptor 9 (ccr9) (log2 FC = 13.07), C\u2014C motif chemokine ligand 25 (ccl25) (log2 FC = 8.63), and C\u2014C motif chemokine ligand 13 (ccl13) (log2 FC = 8.97), all of which are involved in leukocyte chemotaxis.Functional pathway enrichment analysis of DEGs in HK-RBCs from GVHSV-immunized individuals using the GO Biological Process Database revealed overrepresentation of the following categories: organic substance biosynthetic process, cellular response to chemical stimulus, protein localization, vesicle-mediated transport, and cellular response to stress A Supple. Among tfcgr1a) (log2 FC = 10.79) and hematopoietic cell kinase (hck) (log2 FC = 5.97), which are implicated in the Fc receptor signaling pathway; TNF superfamily member 11 (tnfsf11) (log2 FC = 8.43), which is involved in the regulation of myeloid leukocyte differentiation; and C-C motif chemokine receptor 7 (ccr7) (log2 FC = 9.67), which is involved in the T cell receptor signaling pathway , in PB-RBCs from GVHSV-immunized individuals.The transcriptome profile of FACS single-cell sorted PB-RBCs from GVHSV-immunized individuals identifiwipi1) (log2 FC = 6.69), GABA type A receptor-associated protein (gabarap) (log2 FC = 5.12), and unc-51 like autophagy activating kinase 1 (ulk1) (log2 FC = 6.63), which are involved in the autophagy pathway; BCL2-like 1 (bcl2l1) (log2 FC = 3.93), BCL2-associated athanogene 3 (bag3) (log2 FC = 5.97), BCL2-associated athanogene 5 (bag5) (log2 FC = 5.25), BCL2-interacting protein 3 (bnip3) (log2 FC = 4.78), superoxide dismutase 1 (sod1) (log2 FC = 5.37), and superoxide dismutase 2 (sod2) (log2 FC = 6.22), which are involved in the apoptosis signaling pathway and, specifically, the negative regulation of apoptosis and the antioxidant response; TNF superfamily member 11 (tnfsf11) (log2 FC = 7.16), cytokine receptor-like factor 1 (crlf1) (log2 FC = 7.08), suppressor of cytokine signaling 3 (socs3) (log2 FC = 6.95), lymphocyte cytosolic protein 1 (lcp1) (log2 FC = 5.58), TNF receptor-associated protein 1 (trap1) (log2 FC = 4.31), and TNF receptor-associated factor 2 (traf2) (log2 FC = 6.78), which are involved in intracellular signal transduction; and interferon regulatory factor 8 (irf8) (log2 FC = 6.83) and the suppressor of cytokine signaling 5 (socs5) (log2 FC = 6.81), which participate in hematopoietic or lymphoid organ development (log2 FC = 7.37), calnexin (canx) (log2 FC = 4.42), TAP binding protein-like (tapbpl) (log2 FC =13.99), and genes related to the proteasome, such as proteasome subunit alpha 3 (psma3) (log2 FC = 7.17) and proteasome subunit alpha 7 (psma7) (log2 FC = 6.28) . Moreove = 6.28) B.The proteome profile of Ficoll-purified PB-RBCs from GVHSV-immunized individuals identified 848 DEPs (FDR < 0.05); 573 proteins were upregulated and 275 proteins were downregulated compared to PB-RBCs from TFP1-injected individuals . The GVH2 FC = 5.44), nucleoporin 155 (NUP155) (log2 FC = 3.64), nucleoporin 43 (NUP43) (log2 FC = 1.65), nucleoporin 133 (NUP133) (log2 FC = 1.72), nucleoporin 85 (NUP85) (log2 FC = 4.00), and nucleoporin 88 (NUP88) (log2 FC = 3.34). We found particularly interesting the identification of NLR family CARD domain-containing 3 (NLRC3) (log2 FC = 3.77), which is involved in the regulation of cellular component organization and in the regulation of response to stress and TAP binding protein (TAPBP) (log2 FC = 2.11) for antigen processing and presentation of exogenous peptide antigen via MHCI, TAP-dependent, as well as dynamin 2 (DNM2) (log2 FC = 1.59), dynein cytoplasmic 1 heavy chain 1 (DYNC1H1) (log2 FC = 3.48), and SEC13 homolog, nuclear pore and COPII coat complex component (SEC13) (log2 FC = 2.85) for antigen processing and presentation of exogenous peptide antigen via MHCII (2 FC = 4.98), interleukin 12 receptor subunit beta 2 (IL12RB2) (log2 FC = 3.56), tripartite motif-containing 25 (TRIM25) (log2 FC = 3.58), tripartite motif-containing 35 (TRIM35) (log2 FC = 2.65), interferon-induced protein 35 (IFI35) (log2 FC = 2.05), interferon-induced protein 44-like (IFI44L) (log2 FC = 3.71), and novel immune-type receptor 9 nitr9 (log2 FC = 4.09) , TAP-dependent, or via MHC class II (MHCII) and regulation of hematopoiesis C,F Supp. Within ia MHCII . Further = 4.09) . The PPI = 4.09) C.hck gene expression level, which was upregulated, although without statistical significance (mhcI), major histocompatibility complex II (mhcII), dnm2, and cluster of differentiation 83 (cd83) genes were upregulated, although without statistical significance genes were upregulated, but without statistical significance. For the interferon response pathway, interferon regulatory factor 8 (irf8), interferon-induced protein with tetratricopeptide repeats 5 (ifit5), dsRNA-activated protein kinase R (pkr), and interferon-inducible Mx (mx) gene expression levels were upregulated, but again without statistical significance (gvhsv gene transcripts were hardly detected (over 35 of 40 Cts) in PB-RBCs from GVHSV immunized individuals.Overrepresented pathways in PB-RBCs and HK-RBCs from GVHSV-immunized individuals were validated via RT-qPCR of Ficoll-purified PB-RBCs at 14 dpi. For the Fc receptor signaling pathway (overrepresented in the transcriptome profile of HK-RBC), we measured the ificance . For theificance . For theificance . For theificance . SeparatGVHSV-transfected RBCs cocultured with autologous WBCs from peripheral blood resulted in the proliferation of WBCs compared to WBCs cocultured with TFP1-transfected RBCs, as observed by the enumeration of cell nuclei A. As a pcd8) and T-cell receptor (tcr)) and B cells (paired box gene 5 (pax5) and IgM membrane (igm)) was upregulated in WBCs cocultured with GVHSV-transfected RBCs compared to WBCs cocultured with TFP1-transfected RBCs -challenged Atlantic salmon . In the emotaxis ,55,56. T T cells . In teled kidney ,59. The d kidney . In addi+ T lymphocytes for their clearance [Functional pathway analysis of the HK-RBC transcriptome profile from GVHSV-immunized fish using the GO Immune System Process Database revealed the overrepresentation of the antigen processing and presentation of exogenous peptide antigen via the MHCI, TAP-dependent pathway. This pathway was also overrepresented in the transcriptomic and proteomic PB-RBC profile from GVHSV-immunized fish. Commonly, MHCI is characterized by endogenous antigen presentation from the degradation of intracellular pathogens and presentation to CD8learance . MHCI pllearance . Transcrlearance revealedlearance revealedlearance ,63,64,65learance ,67,68. Rlearance . Antigenlearance ,70.Antigen presentation of exogenous peptide via MHCII was also overrepresented in the functional pathway analysis of the PB-RBC proteome from GVHSV-immunized fish. Genes and proteins related to the proteosomal cleavage of exogenous antigen and antigen presentation of exogenous peptides have been reported to be upregulated in GVHSV-transfected RBCs, indicating that RBCs could have the capacity to present DNA vaccine antigens via MHCI or MHCII . Additiohck gene expression [Another remarkable pathway overrepresented in the HK-RBC transcriptomic profile was the Fc receptor signaling pathway. The molecular signaling triggered by the union of the immunoglobulin Fc regions with Fc receptors mediates cellular responses that are fundamental in the immune response . HCK, whpression .ifn1 and mx gene expression and protected against VHSV infection in RTG-2 cells, in addition to inducing differentiation markers in the rainbow trout monocyte/macrophage-like cell line RTS11 [Lymphocyte signaling is an important issue to consider in DNA vaccination strategies to improve efficacy . Pathwayne RTS11 . The preFunctional pathway analysis using the GO Biological Process Database revealed overrepresentation of the autophagy pathway in the PB-RBC transcriptome from GVHSV-immunized fish. Autophagy is a natural, conserved, and self-digestive catabolic process that can be critical for cell survival under stressful conditions, such as viral infection ,79. In fThe reinfusion/immunization of fish with RBCs transfected in vitro with the GVHSV DNA vaccine revealed the presence of specific antibodies against VHSV in the serum, reaching the same levels of specific antibodies induced by the conventional intramuscular GVHSV DNA vaccination. The idea of RBCs as vaccine carriers has been previously explored in non-nucleated RBCs ,16,17,18+T cells [The use of cytokine genes as vaccine adjuvants has been shown to improve IgM titer, lymphocyte proliferation, and virus protection in glycoprotein G DNA vaccination of rainbow trout . The use+T cells . Nucleat+T cells ,12,13,14+T cells [+T cells, crosstalk with other leukocyte populations, respond by synthesizing cytokines, and link the innate and adaptive immune response, among other functions [The concept of atypical or no professional APCs has been previously explored in mammals. Some cells, such as mast cells, basophils, eosinophils, innate lymphoid cells , and neu+T cells . Studiesunctions . Nucleatunctions . In the unctions ,14. Thusunctions . As suchThe transcriptomic and proteomic prolife of RBCs after im DNA immunization of rainbow trout revealed the overrepresentation of immune system-related processes, such as the presentation of exogenous peptides. It is noteworthy to highlight that some of the immune response mechanisms that we found overrepresented in the present work have been previously identified in rainbow trout RBCs transfected with GVHSV in vitro. In addition, apart from corroborating previous results, this is the first time that these processes are found in vivo, after im DNA immunization, a scenario where RBCs are not the direct target of the DNA vaccine. This results led us to suggest that RBCs could act as mediator cells of the immune processes triggered by DNA immunization. Moreover, RBCs carrying a DNA vaccine were able to induce a humoral response in fish and stimulate proliferation in leukocytes. All of this would lead us to suggest the RBCs of fish as APC-like cells."} diff --git a/PMC_clustering_788.jsonl b/PMC_clustering_788.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..d7c820ee085b98ef8e09c47957bec0bec9ce74c0 --- /dev/null +++ b/PMC_clustering_788.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:670d88583a4f6c38b1af7207b60628c2645f0084e284fc2da29939a061594f9d +size 99174751 diff --git a/PMC_clustering_789.jsonl b/PMC_clustering_789.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..3f55e1814310f77ef306735544401b58925e68e4 --- /dev/null +++ b/PMC_clustering_789.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9686290ab306e3194e6510d21120fe8e124bd7b8b8f3cba55cd5ac26f54fcf72 +size 63791956 diff --git a/PMC_clustering_790.jsonl b/PMC_clustering_790.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..91d287a0c12e0fe99a890902fbe88a73455742fc --- /dev/null +++ b/PMC_clustering_790.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cf6669e5a6f15bc660e7fa948b3feb9afba8d679129c0f72a114b6f4230cd090 +size 80336596 diff --git a/PMC_clustering_791.jsonl b/PMC_clustering_791.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..3aaa4c158b9b950d31da7bda2181a49058486242 --- /dev/null +++ b/PMC_clustering_791.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c4b2236af023fb5cd2d7aae076455d775ae55b7d4004962a335d1078c097cc0a +size 44546387 diff --git a/PMC_clustering_792.jsonl b/PMC_clustering_792.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..0b0dac45ee65d11846d36fffa9a2ef9b70fd5419 --- /dev/null +++ b/PMC_clustering_792.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8b8917476c2d2eb268fffba1bf572febf6239bc873c8a51f3801814a98c7c938 +size 90986063 diff --git a/PMC_clustering_793.jsonl b/PMC_clustering_793.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..d590b3d7d12fdd32a1fa87fb953d3e1f354fb309 --- /dev/null +++ b/PMC_clustering_793.jsonl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:66b9e37599feb43586d2d0bb5cbb62368480711700f6d737ffb76c04f6300834 +size 81020931 diff --git a/PMC_clustering_794.jsonl b/PMC_clustering_794.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..65b3f7fecc0bf34b2662ca95d44db3ecc6565690 --- /dev/null +++ b/PMC_clustering_794.jsonl @@ -0,0 +1,1500 @@ +{"text": "Partially thrombosed giant aneurysms at the basilar apex (BA) artery are challenging lesions with a poor prognosis if left untreated. Here we describe a rare case of extensive brain edema after growth of a surgically treated and thrombosed giant basilar apex aneurysm.We performed a proximal surgical basilar artery occlusion on a 64-year-old female with a partially thrombosed giant BA aneurysm. MRI showed no ischemic lesions but showed marked edema adjacent to the aneurysm. She had a good recovery, but 3 months after surgical occlusion, her gait deteriorated together with urinary incontinence and worsening right hemiparesis. MRI showed that the aneurysm had grown and developed intramural hemorrhage, which caused extensive brain edema and obstructive hydrocephalus. She was treated by a ventriculoperitoneal shunt placement. Follow-up MRI showed progressive brain edema resolution, complete thrombosis of the lumen and shrinkage of the aneurysm. At 5\u2009years follow-up the patient had an excellent functional outcome.Delayed growth of a surgically treated and thrombosed giant aneurysm from wall dissection demonstrates that discontinuity with the initial parent artery does not always prevent progressive enlargement. The development of transmural vascular connections between the intraluminal thrombus and adventitial neovascularization by the vasa vasorum on the apex of the BA seems to be a key event in delayed aneurysm growth. Extensive brain edema might translate an inflammatory edematous reaction to an abrupt enlargement of the aneurysm. Partially thrombosed giant basilar artery (BA) aneurysms are uncommon vascular lesions with an extremely poor natural history . Among sBA obliteration proximal to the SCA, which is known as hunterian occlusion, has been performed for such unclippable giant BA aneurysms , 8, 9. IHere, we report the long-term outcome of a complex BA aneurysm treated by means of surgical occlusion of the proximal BA. Importantly, several weeks after hunterian occlusion, the patient presented at the emergency department (ED). Magnetic resonance imaging (MRI) depicted growth of the partially thrombosed giant basilar artery aneurysm by intramural hemorrhage, which caused brain compression and edema, leading to clinical deterioration.A 64-year-old female presented with cephalea, left ptosis and diplopia. Neurological examination detected left oculomotor nerve palsy. Computed tomography (CT) revealed a partially thrombosed giant aneurysm at the tip of the BA Fig.\u00a0. The aneThe patient underwent BA surgical occlusion. The BA was accessed using a pterional craniotomy and a transsylvian approach. The clip placement was selected on visual inspection after identifying a perforator-free zone of the BA between the origins of the anterior inferior cerebellar arteries (AICAs) and SCAs. Electrophysiological monitoring of evoked potentials (EPs) showed no decrease of motor evoked potentials (MEPs) or somatosensory evoked potentials (SSEPs). Post-surgery angiography demonstrated stagnant flow in the dome of the aneurysm, now filling from the PCoAs Fig. . AntiplaThree months after BA occlusion, she was referred to our institution because of progressive gait instability, urinary incontinence, worsening right hemiparesis, binge eating behaviour and memory difficulties. Plain CT scan demonstrated ventricular dilatation Fig.\u00a0. MRI shoLong-term follow-up has extended for 5 years. The patient has made an excellent recovery and the hemiparesis has almost resolved. Left oculomotor palsy was completely recovered. Follow-up MR imaging demonstrated a marked reduction in the size of the giant aneurysm with no filling of the aneurysm sac, and filling of the upper BA via the PCoAs and a new MRI obtained on readmission to the hospital after temporary symptom relief. A-C: Sagittal nonenhanced T1-weighted images (T1WI) exhibited a newer clot, expressed as a sickle-shaped high signal intensity area, on the outer surface of the intraluminal old thrombus. D-I: Fluid-attenuated inversion recovery (FLAIR) MRI depicted a thrombosed giant aneurysm severely compressing the brainstem in the backward direction. In addition, we observed marked edema surrounding the basilar apex (BA) aneurysm and involving the midbrain, thalamus and left internal capsule. The sickle-shaped high signal intensity structure was also observed on FLAIR images. J: Axial maximum intensity projection (MIP) reconstructions of magnetic resonance angiography (MRA) showed a decrease of the aneurysm blood lumen. K: Axial MIP reconstructions of contrast enhanced 3-dimensional time of flight (3D-TOF). A marked gadolinium enhancement is noted around the aneurysm, representing the new intraluminal thrombus. L-N: Sagittal nonenhanced T1WI exhibited a high signal in the posterior portion of the aneurysm, suggestive of a fresh intraluminal thrombus as well as new intramural hematoma, which caused a significant mass effect on the brainstem and third ventricle. O-T: Axial FLAIR images showed a marked increase in brain edema in comparison with the previous MRI study. Intraluminal and intramural hematomas evolution were also detected on FLAIR images. U: Axial MIP reconstructions of MRA confirmed reduced contrast filling of the blood lumen of the giant basilar apex aneurysm. V: Axial MIP reconstructions of 3D-TOF showed gadolinium enhancement around the aneurysm, representing the intraluminal and intamural thrombus."} +{"text": "Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr evolution to test the predictability of divergence in the most variable northern freshwater fish, the Arctic charr. Using a hierarchy of replication\u2014from individuals to divergent phylogeographic lineages\u2014we detect parallel evolution of foraging-related traits despite variation in genomic backgrounds and evolutionary histories. The level of phenotypic parallelism can be explained by the complex interplay of environment, shared genetic variation, and variability in gene expression. While phenotypic divergence may be determined and/or constraint by genetic and molecular divergence, the direction of change is largely determined by molecular parallelism and shared adaptive genetic variation. These are in turn associated with environmental similarity, reflected as ecosystem size. We suggest that gene expression facilitates parallel ecotype evolution, but that the extent of parallelism is further influenced by the level of shared genetic variation and ecological opportunity. The degree to which the pathways of evolution are predictable, particularly under complex natural conditions, remains one of the greatest questions in evolutionary biology ,2. Numerde novo mutation, recruitment of shared standing genetic variation, or introgression in all pairwise SNP comparisons for the four bimodal Scottish lakes. Right: LD decay with increasing distance from Fst outlier SNPs in the Atlantic lineage. (B) Left: LD decay in all pairwise SNP comparisons in the Siberian lineaege. The dataset is split into four plots to make the plots legible. Right: LD decay with increasing distance from Fst outlier SNPs in the Siberian lineage. LD decay could not be estimated for outlier SNPs in Tokko and Kudushkit due to the low number of SNPs.((TIFF)Click here for additional data file.S13 FigA) Distribution of z-scores along RDA1 across all SNPs estimated using a redundancy analysis for the Atlantic lineage. SNPs with z-scores above and below 2 or -2 (dashed lines) are considered significantly associated with ecotype across lakes. (B) Distribution of z-scores along RDA1 and RDA2 across all SNPs.((TIFF)Click here for additional data file.S14 FigA) Principal component (PCA) plots based on gene expression data for PC3 vs PC4 and PC5 vs PC6. Individuals are shown by individual points shaped by ecotype and coloured by lake of origin. Centroids for each ecotype are shown including standard error and coloured by ecotype . Centroids of sympatric ecotypes are connected by a line. (B) Linear model term effect sizes for PC1 to PC4 from the gene expression PCA. (C) Boxplots showing the normalised expression of different haemoglobin paralogs across ecotypes and lakes. (D) Expression of two genes (ABCC8 and ALDOA) that are significantly differentially expressed in 5 out of 7 ecotype pair comparisons. The boxplots show the normalized expression for each ecotype by lake and ecotypes are colour coded. (E) Distribution of explained variances for each transcript by model term for the linear mixed-effects model of gene expression. (F) Correlation between expression of WGCNA module eigengenes and lake (population of origin) and ecotype. Each row represents a module of co-expressed genes (identified by colour). Spearman\u2019s correlation coefficients for the module expression-variable correlations are given in each cell. The corresponding corrected p-values are given in parenthesis. Significant correlations are highlighted in bold. Cells are coloured based on their correlation, with orange cells being correlated with up-regulation of gene expression in benthivorous ecotypes and blue being associated with up-regulation in planktivorous ecotypes. (G) Distribution of gene expression trajectory angles and differences in trajectory lengths for within and between ecotype comparisons. Distributions are coloured by comparisons between replicated ecotype-pairs and between non-replicated ecotype pairs . The mean for each dataset is shown by the solid lines. Means do not differ between the comparisons (P > 0.05).((TIFF)Click here for additional data file.S15 FigA) Comparison of neutral genetic differentiation between sympatric ecotypes diverged post-LGM under ongoing gene flow or pre-LGM with secondary contact. P-value for Wilcoxon-test is shown in the plot. Distribution of (B) neutral allele frequency trajectory angles and differences in trajectory lengths and (C) adaptive allele frequency trajectory angles and lengths for within and between ecotype comparisons. Comparisons are coloured by comparisons between replicated ecotype-pairs (red) and between non-replicated ecotype pairs (blue). The mean for each dataset is shown by the solid lines and the P-value for Wilcoxon-tests is shown in the plot. (D) Correlation between mean trait variance across all sympatric ecotypes and ecosystem size (PC1) across all populations. Larger ecosystems harbor populations with a larger mean trait variance (results of linear model shown in plot).((TIFF)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table\u03b8, lower part) below the diagonal and p-values are above the diagonal.Differences in trajectory lengths or angles ((DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.S6 Table(DOCX)Click here for additional data file.S7 TableShown are the four best fitting models for each population/comparison and the respective \u0394AIC between them.(DOCX)Click here for additional data file.S8 Table(DOCX)Click here for additional data file.S9 Table(DOCX)Click here for additional data file.S10 TableGene co-expression modules in network generated from 1,512 ecotype associated genes.(DOCX)Click here for additional data file.S11 Tablecis-eQTL.Ecotype-associated expressed genes that are associated with (DOCX)Click here for additional data file."} +{"text": "Plant-based nutrition consisting of vegetarian/vegan dietary patterns are positively associated with metabolic fitness and inversely associated with risk of cardiovascular disease, diabetes and all-cause mortality. The nutritional and molecular basis of such benefits remains unclear. Here we considered the potential contribution of protein quality (amino acid profiles) and quantity to plant-based nutritional benefits. To this end, we investigated whether individuals adhering to plant-based diets consume a different AA profile, and used isocaloric diets in controlled rodent studies with modulation of both AA composition and total protein amount using crystalline AA vs. naturally-sourced protein ingredients. We found surprisingly few differences between AA profiles of vegans vs. omnivores, but large effects of total protein independent of source in rodent studies, strongly suggesting a major effect of total protein rather than AA composition in health benefits of plant-based diets. Mechanistically, we discuss the role of reduced protein intake on glucose and lipid homeostasis."} +{"text": "Adsorbent regeneration was demonstrated over multiple adsorption-desorption cycles with good uptake efficiency. CS-Ac-An has a strong fluorescence emission that undergoes prominent quenching at part per billion levels in aqueous solution. The quenching process displays a linear response over variable Cu(II) concentration (0.05\u20135 mM) that affords reliable detection of low level Cu(II) levels by an in situ \u201cturn-off\u201d process. The tweezer-like chelation properties of CS-Ac-An with Cu(II) was characterized by complementary spectroscopic methods: IR, NMR, X-ray photoelectron (XPS), and scanning electron microscopy (SEM). The role of synergistic effects are inferred among two types of active adsorption sites: electron rich arene rings and amine groups of chitosan with Cu(II) species to afford a tweezer-like binding modality.The detection and removal of heavy metal species in aquatic environments is of continued interest to address ongoing efforts in water security. This study was focused on the preparation and characterization of aniline grafted chitosan (CS-Ac-An), and evaluation of its adsorption properties with Cu(II) under variable conditions. Materials characterization provides support for the grafting of aniline onto chitosan, where the kinetic and thermodynamic adsorption properties reveal a notably greater uptake (>20-fold) of Cu(II) relative to chitosan, where the adsorption capacity ( Th. Thex-det 420 nm a. Analys0 nm cation which reduces the electron density in the HOMO of the arene moieties. In the other words, Cu(II) as the guest species bind to the fluorophore and quenches its fluorescence emission to yield a chelation enhanced fluorescence quenching (CHEQ) sensor . \u22121. This concentration is considerably lower than the maximum allowable level of copper in drinking water [molecular-tweezers can be deployed as a responsive adsorbent with utility for in situ detection of Cu(II) with high sensitivity. As noted in ng water . Thus, C1H-NMR spectroscopy. The adsorption properties of CS-Ac-An in the presence of Cu(II) were studied in aqueous solution at ambient pH (6.5\u20137) and temperature. The Sips isotherm model accounts for the equilibrium adsorption properties, where a relatively high adsorption capacity (106.6 mg g\u22121) was noted (>20-fold) relative to chitosan. The kinetic uptake profiles are well-described by the PSO model; the intra-particle diffusion model was applied to reveal the rate limiting step of the process. Temperature dependent adsorption studies reveal that the process is entropy-driven, according to changes in hydration of Cu(II) upon adsorption. The adsorption process reveals that the pendant aromatic rings and amine groups serve as the active adsorption sites that contribute synergistically due to the combined effect of weak (cation-\u03c0) and strong (dative) interactions, respectively. These metal-ligand bonding processes are the prominent metal-adsorbent interactions, as supported by the spectral results herein. SEM images clearly reveal porous surface features of the adsorbent before adsorption and copper aggregates after uptake, where the surface morphology changed during the adsorption process. EDX analyses reveal that Cu(II) ions are adsorbed mainly by active sites of the adsorbent and not as copper sulfate. Five cycles of adsorption-desorption show CS-Ac-An can be used repeatedly as an adsorbent without a significant loss of its adsorption capacity (<10%), in line with the chemisorption nature of the process. In aqueous media, the adsorbent exhibits fluorescence emission that undergoes quenching in the presence of low levels of Cu(II), where a linear response over a nominal range allows for practical in situ detection of Cu(II) that is relevant to drinking water guidelines. The dual properties of CS-Ac-An allow for its utility as a responsive material for the detection of Cu(II), along with its unique solid phase extraction properties and relatively high adsorption capacity.A grafted form of chitosan (CS-Ac-An) was fabricated and structurally characterized by FT-IR and"} +{"text": "Tyrosine kinase inhibitors (TKIs) therapy targets at epidermal growth factor receptor (EGFR) gene mutations in non-small-cell lung cancer (NSCLC). We aimed to compare the EGFR mutation-guided target therapy versus empirical chemotherapy for first-line treatment of advanced NSCLC in the public healthcare setting of Hong Kong.A Markov model was designed to simulate outcomes of a hypothetical cohort of advanced (stage IIIB/IV) NSCLC adult patients with un-tested EGFR-sensitizing mutation status. Four treatment strategies were evaluated: Empirical first-line chemotherapy with cisplatin-pemetrexed , and EGFR mutation-guided use of a TKI . Model outcome measures were direct medical cost, progression-free survival, overall survival, and quality-adjusted life-years (QALYs). Incremental cost per QALY gained (ICER) was estimated. Sensitivity analyses were performed to examine robustness of model results.Empirical chemotherapy and EGFR mutation-guided gefitinib gained lower QALYs at higher costs than the erlotinib group. Comparing with EGFR mutation-guided erlotinib, the afatinib strategy gained additional QALYs with ICER . In 10,000 Monte Carlo simulations for probabilistic sensitivity analysis, EGFR mutation-guided afatinib, erlotinib, gefitinib and empirical chemotherapy were preferred strategy in 0%, 98%, 0% and 2% of time at willingness-to-pay (WTP) 47,812 USD/QALY (1x gross domestic product (GDP) per capita), and in 30%, 68%, 2% and 0% of time at WTP 143,436 USD/QALY (3x GDP per capita), respectively.EGFR mutation-guided erlotinib appears to be the cost-effective strategy from the perspective of Hong Kong public healthcare provider over a broad range of WTP. Lung cancer is the second most common cancer, with highest mortality among the top 10 cancers in Hong Kong [Epidermal growth factor receptor (EGFR) gene mutations are actionable targets in NSCLC . These mFig 1). Markov model is an analytical framework in which the hypothetical patients proceed to mutually exclusive health states in the next model cycle according to transition probabilities, with costs and health outcomes aggregated over successive cycles. Four treatment strategies were evaluated in the present model: Empirical first-line chemotherapy with cisplatin-pemetrexed for all patients, and EGFR mutation-guided use of afatinib, erlotinib, and gefitinib. The model time horizon was 10 years (with monthly cycle) to allow adequate time for estimation of the lifelong outcome measures, including direct medical cost, progression-free survival, life-years and QALYs gained by each treatment strategy.A Markov model was designed to simulate outcomes of a hypothetical cohort of advanced (stage IIIB/IV) NSCLC adult patients with untested EGFR-sensitizing mutation status reports in English language; (2) adult patients with stage IIIB/IV NSCLC; and (3) progression-free survival, overall survival or adverse event rates were reported. Preferred studies were meta-analyses or randomized controlled trials. When multiple randomized trials were available for the same model input, the weighted average was used as the base-case value and the high/low values formed as the upper/lower limits for sensitivity analysis.All model inputs are listed in t with cisplatin-pemetrexed treatment was estimated by the following formula [The prevalence of EGFR mutation-positive in advanced NSCLC Hong Kong patients was approximated from 5-year pathological data 2013\u20132017) of the Queen Elizabeth Hospital, largest public hospital of the Hospital Authority. The probabilities of progression-free survival and overall survival among patients treated with cisplatin-pemetrexed were estimated from the Kaplan-Meier survival curves of progression-free survival and overall survival, respectively. Data were first extracted from the corresponding Kaplan-Meier survival curves of cisplatin-pemetrexed treatment group in prospective clinical trials on EGFR mutation-positive NSCLC treatment \u20132017 of . Weibull formula :P(t)=1\u2212A network meta-analysis, including 16 phase III randomized trials with 2,962 advanced NSCLC patients, integrated the treatment outcomes of gefitinib, erlotinib, afatinib and first-line chemotherapy [Table 1. The QALYs expected by each subject was estimated from cumulative subject-time spent in a heath state and the health state-specific utility value. The health states included progression-free survival, disease progression and death. The utility of the progression-free survival was further adjusted with disutility of treatment-related serious adverse events (SAEs) (\u2265Grade 3). The utility and disutility values were retrieved from literature on advanced NSCLC-related quality of life and health economic analysis [The utility inputs were shown in analysis , 18. Theanalysis \u20137, 13. TThe health economic analysis was conducted on direct medical costs from the perspective of Hong Kong public healthcare provider. Direct costs included biopsy-based EGFR mutation testing (for TKI arms), cost per month in progression-free survival state, cost per month for palliative care in disease progression state, and cost of managing SAEs. The healthcare resource utilization during progression-free survival and disease progression were estimated retrospectively at the Hospital Authority of Hong Kong. The Hospital Authority is the sole public healthcare provider in Hong Kong. Medical record review was conducted for patients aged \u226518 years with diagnosis of advanced (stage IIIB/IV) NSCLC who were treated with first-line chemotherapy or TKI in 2013 to 2017 at two general hospitals of the Hospital Authority . The study protocol was approved by the Research Ethics Committee for Kowloon Central / Kowloon East cluster. Healthcare resource utilization were collected to estimate monthly direct medical costs for progression-free survival state and disease progression state, and management cost per episode of treatment-related SAEs, using unit cost of 2020. The costs accumulated over the 10-year model timeframe were discounted with an annual rate of 3%.Cost-effectiveness and sensitivity analyses were conducted by TreeAge Pro 2020 and Microsoft Excel 2016 . Base-case analysis compared the expected direct medical cost and QALYs of each EGFR mutation-guided TKI therapy with the empirical chemotherapy, assuming 100% TKI compliance as indicated by mutation test results. A treatment strategy was dominated when it gained lower QALYs at higher cost than another option, and the dominated option was eliminated from further cost-effectiveness analysis. If a treatment strategy gained more QALYs at higher cost than another alternative, incremental cost per QALY gained (ICER) of the more effective strategy was calculated: \u0394cost/\u0394QALYs. The World Health Organization (WHO) recommended that ICER less than 1\u00d7 gross domestic product (GDP) per capita to be highly cost-effective and less than 3\u00d7 GDP per capita to be cost-effective . The GDPTable 1. The probability of each strategy to be accepted as cost-effective was determined over a range of WTP from 0\u2013200,000 USD/QALY in the acceptability curves. The incremental costs and incremental QALYs of EGFR mutation-guided TKI versus chemotherapy comparator were presented in scatter plots.Sensitivity analyses were performed by one-way sensitivity analysis on all model inputs to identify threshold values of influential factors. The probabilistic sensitivity analysis was performed using Monte Carlo simulation. The direct cost and QALYs of each study arm were recalculated 10,000 times by randomly drawing each of the model input from the probability distribution specified in Table 2. In the base-case analysis of incremental costs and QALYs (Table 3), EGFR mutation-guided use of all three TKIs gained higher QALYs than empirical chemotherapy with cisplatin-pemetrexed. When comparing to empirical chemotherapy (as common comparator), EGFR mutation-guided erlotinib gained higher QALYs with cost-saving and the ICER of afatinib was lower than WTP threshold . Both strategies of EGFR mutation-guided erlotinib and afatinib were accepted as cost-effective versus empirical chemotherapy. EGFR-guided gefitinib gained higher QALY than empirical chemotherapy at an ICER exceeding WTP, and was therefore not accepted as cost-effective.Expected direct medical costs, progression-free survival months, overall-survival months, and quality-adjusted life-years (QALYs) are shown in Two strategies gained lower QALYs at higher costs than the erlotinib group, and were therefore dominated by the erlotinib strategy (and the dominated arms were eliminated). Comparing with EGFR mutation-guided erlotinib (as the-less-costly strategy), the afatinib strategy gained additional QALYs at higher cost by an ICER of 540,633 USD/QALY (>WTP threshold), and was not accepted to be cost-effective. EGFR mutation-guided erlotinib was the only cost-effective strategy versus both the common comparator and the next-less-costly strategy in the base-case analysis.One-way sensitivity analysis found that the base-case results were robust to the variation of all model inputs and no threshold value was identified. The EGFR mutation-guided afatinib strategy gained the highest QALYs with the ICER (versus EGFR mutation-guided erlotinib) exceeding the WTP threshold. The monthly cost of afatinib therapy was further examined in an extended one-way sensitivity analysis from the base-case value (USD1870) to lower limit (USD200), for identification of a threshold value. The ICER of EGFR mutation-guided afatinib became lower than the WTP threshold (and accepted as cost-effective) when the monthly cost of afatinib therapy was lower than USD818. The compliance to use TKI among EGFR mutation-positive patients was also added to one-way sensitivity analysis, and no threshold value was identified.Figs 4 showed the scatter plots of the increment cost and QALYs gained by each EGFR mutation-guided TKI versus empirical chemotherapy. EGFR mutation-guided afatinib, erlotinib and gefitinib were accepted as cost-effective (with QALY gains and ICER\u200985% of the laboratories. Except for rods and rings, the cytoplasmic competent patterns were reported by\u2009>\u200972% of laboratories.Cytoplasmic IIF staining was considered ANA positive by 55% of clinicians and 62% of laboratory professionals, with geographical and expertise-related differences.Quantification of fluorescence intensity was considered clinically relevant for nuclear patterns, but less so for cytoplasmic and mitotic patterns. Combining IIF with specific extractable nuclear antigens (ENA)/dsDNA antibody testing was considered most informative.Of the nuclear competent patterns, the centromere and homogeneous pattern obtained the highest scores for clinical relevance and the DFS pattern the lowest. Of the cytoplasmic patterns, the reticular/mitochondria-like pattern obtained the highest scores for clinical relevance and the polar/Golgi-like and rods and rings patterns the lowest.This survey confirms that the major nuclear and cytoplasmic ANA IIF patterns are considered clinically important. There is no unanimity on classifying DFS, rods and rings and polar/Golgi-like as a competent pattern and on reporting cytoplasmic patterns as ANA IIF positive. We report on an international survey on Antinuclear Antibody (ANA) indirect immunofluorescence (IIF) pattern reporting.Both clinicians and laboratory professionals consider the major nuclear and cytoplasmic\u00a0IIF\u00a0patterns as clinically important.There is no unanimity on reporting cytoplasmic patterns as ANA IIF positive.Indirect immunofluorescence (IIF) on HEp-2 cells is commonly used to screen for antinuclear antibodies (ANA). ANA are helpful for the diagnosis of ANA-associated rheumatic diseases (AARD) , 2. In twww.anapatterns.org and [The International Consensus on ANA Patterns (ICAP), a working group of the Autoantibody Standardization Committee (ASC) , has rec.org and ). ICAP d.org and . Accordi.org and .In order to evaluate to which extent clinical laboratories and clinicians adhere to the ICAP recommendations and appreciate the clinical value of the IIF patterns, a survey on ANA IIF pattern reporting and interpretation was organized. The results of such surveys should guide further harmonization.The Belgian European Autoimmunity Standardization Initiative (EASI) working group prepared two structured survey forms, one addressed to laboratory professionals, reporting ANA IIF test results, and one to clinicians, requesting ANA IIF tests and interpreting the ANA IIF result report. Both survey forms closed survey Globally, the surveys forms were distributed in the following formats:p value\u2009<\u20090.05 was considered as statistically significant.Statistical analysis (chi-squared test relative proportion) was performed in MEDCALC . A Four hundred thirty-eight laboratory professionals and 248 clinicians from 67 different countries worldwide responded to the surveys, of whom 358 (82%) and 84 (34%), respectively, completed the whole survey. Since the survey was also distributed through an open, web-based format we were unable to accurately estimate the response rate. Table Table For each question, the results per pattern, are presented as percentages of the total laboratory (competent and expert reported separately) and clinician respondents. The competent patterns are highlighted in bold. The reported range represents the minimum and maximum number of responders to the specific questions posed.The competent-level patterns centromere (AC-3), homogeneous (AC-1), speckled AC-2,4,5) and nucleolar patterns were used in ANA IIF test result reporting by\u2009>\u200990% of competent-level and expert-level laboratories , speckled AC-18,19,20), reticular/ mitochondria-like (AC-21), polar/Golgi-like (AC-22), rods and rings (AC-23), the rods and rings pattern (AC-23) was the pattern that was least used (63% of the laboratories) and rods and rings pattern AC-23) were significantly (p\u2009<\u20090.0001) more used by expert-level laboratories than by competent-level laboratories (76% versus 48% for DFS and 73% versus 53% for rods and rings). Moreover, the DFS pattern was less reported by laboratories in North-America (44%) and Europe (57%) than by laboratories in the other continents between the ICAP classification and the provided responses, except for the DFS pattern. Only 50% of the respondents would classify this pattern as competent Table . Of inteFor the cytoplasmic patterns considered competent-level by ICAP, 71%\u201474% of the respondents consider the fibrillary, speckled and reticular/mitochondria-like pattern a competent pattern, 65% considered the polar/Golgi-like pattern a competent pattern and 57% considered the rods and rings pattern a competent pattern Table .Sixty-one percent of the clinicians (n\u2009=\u2009105) and 54% of the laboratory professionals (n\u2009=\u2009346) considered cytoplasmic HEp-2 cell IIF staining as ANA IIF positive. There were more expert-level laboratory professionals (61%) than competent-level laboratory professionals (46%) that considered cytoplasmic patterns as ANA positive (p\u2009=\u20090.0062). The fraction of laboratory professionals that considered cytoplasmic ANA patterns as ANA positive was higher in non-European countries (63%) than in European countries (48%) (p\u2009=\u20090.0075) nucleolar patterns into homogeneous, clumpy and speckled (respectively 45% and 34%), (ii) cytoplasmic fibrillary patterns into linear, filamentous and segmental (respectively 28% and 42%) and (iii) cytoplasmic speckled patterns into discrete dots, dense fine speckled and fine speckled (respectively 42% and 53%). Seventy-one percent of the clinicians and 86% of the laboratory professionals found it important to report the reticular/mitochondria-like cytoplasmic pattern (AC-21). Sixty-two percent of the laboratory professionals distinguished multiple nuclear dots from few nuclear dots (data not shown).p\u2009<\u20090.0001 for all sub-patterns). However, clinicians are not aware of such ANA IIF sub-specification and do not consider them clinically relevant (Table The most used sub-specifications in ANA IIF result reports are nuclear fine speckled AC-4 (63%), nuclear coarse speckled AC-5 (65%), multiple nuclear dots AC-6 (74%) and few nuclear dots AC-7 (69%). These sub-specifications are significantly more reported by expert-level than by competent-level laboratories (nt Table .There was no difference between competent-level and expert-level laboratories regarding follow-up testing for antibodies to extractable nuclear antigens (ENA) and to dsDNA in case of a positive ANA IIF test. A geographical difference, however, was observed and expert laboratories review their ANA IIF results after ENA/dsDNA confirmation testing, but only a minority would change the results (respectively 8% and 10%) or add a comment if clinically relevant (respectively 36 and 46%).Both clinicians and laboratory professionals considered the combination of an ANA IIF test result with a corresponding specific anti-ENA or anti-dsDNA test result as the most clinically relevant information.The quantification of the nuclear ANA IIF fluorescence intensity was found clinically relevant by 79% of laboratory professionals and by 74% of clinicians reported that they would take medical decisions based on ANA IIF titer, whereas 87% of the clinicians reported that they would take medical decision based on results of specific testing for anti-ENA or anti-dsDNA.Clinicians and laboratory professionals were also interrogated on how they appraise the clinical relevance of the various ANA patterns. Overall, clinicians scored the clinical relevance of the various patterns lower than laboratory professionals Table . The higOf the cytoplasmic patterns, the reticular/mitochondria-like pattern (AC-21) obtained the highest score for clinical relevance by laboratory professionals. The other competent cytoplasmic patterns received lower scores, with the lowest scores for polar/Golgi-like (AC-22) and rods and rings (AC-23).The mitotic patterns obtained low scores for clinical relevance overall with\u2009\u2264\u200930% of the clinicians and laboratory professionals scoring these patterns as clinically relevant.In the current paper, we present the results of a recent international survey on the reporting and interpretation of ANA IIF results in current daily practice. The results revealed concordances but also discordances with the recommendations posed by ICAP .The survey confirmed that there is no consensus on whether anti-cytoplasmic antibodies should be considered ANA IIF positive or negative , 22. EveThe familiarity with ANA IIF patterns is mainly clear for the nuclear competent patterns (with the exception of DFS) and the cytoplasmic reticular/mitochondria-like antibody (AC-21) pattern, findings which are in concordance to the results of a similar recent survey performed by the American association of Medical Laboratory Immunologists . CliniciThe survey shows that not all laboratories report the DFS pattern and the rods and ring pattern and that not all expert-level laboratory professionals are convinced that these two patterns should be classified as competent.www.autoab.org) should help laboratories across the world to improve the ability in recognizing the DFS (AC-2) pattern [The DFS pattern (AC-2) can vary depending on the manufacturer of the HEp-2 cell substrates , 28 and pattern .www.anapatterns.org), the AC-23 ANA IIF pattern is only detectable in selected HEp-2 cell slides. Thus, depending on the slide source (i.e. manufacturer) used, labs will be able or unable to report this pattern. This likely explains in part the relatively low recognition rate of this pattern even in expert laboratories.In contrast to the DFS pattern, the rods and rings (AC-23) pattern is easily recognizable and there is a defined clinical association (Hepatitis C virus infection under treatment with \u03b1-interferon and ribavirin) . HoweverOverall, the patterns that are most frequently reported are the patterns that are considered to have the highest clinical relevance, with some exceptions such as the centrosome, Golgi and spindle fiber patterns, which are reported by circa 80% of the laboratories despite not having peculiar clinical associations. In addition, the DFS pattern is reported in less than 50% of laboratories. Considering that this pattern includes the staining of the metaphase plate, the DFS pattern can be misclassified as nuclear homogeneous pattern (AC-1), which has completely different immunological and clinical implications.In daily routine practice, sub-specifying nucleolar patterns, cytoplasmic fibrillar patterns and cytoplasmic speckled patterns is infrequently performed, even among experts. However, clinicians do not consider such sub-classification clinically relevant Table .The highest scores for clinical relevance were obtained for the centromere (AC-3) and homogeneous (AC-1) pattern, followed by the nuclear speckled and cytoplasmic reticular (AC-21) patterns. Especially the centromere pattern is associated with a specific disease . It is tThe clinical significance of the cytoplasmic patterns as a whole was considered lower compared to nuclear patterns. Even cytoplasmic patterns such as the (dense) fine speckled patterns that are associated with clinically relevant antibodies such as the anti-synthetase antibodies, anti-SRP and anti-Rib-P are not widely recognized as clinically relevant patterns. This perception clearly indicates the need for implementing education programs in order to increase the awareness of such associations and improve the interpretation and optimal use of the ANA IIF test. The polar/Golgi-like pattern is considered a competent pattern. It is easily recognizable but its clinical association with a disease is limited , 35\u201337.The quantification of the ANA IIF fluorescence intensity was found clinically relevant for the nuclear ANA IIF patterns by a substantial fraction of clinicians (74%) and laboratory experts (79%). The importance of the autoantibody titer (level) is recognized by guidelines and recommendations , 11, 12.Clinicians are aware of the differences between laboratories for both ANA IIF and specific ENA/dsDNA testing. A low percentage of clinicians take medical decisions based on the ANA IIF titer (54%).Clinicians and laboratory professionals considered that combined information on HEp-2 ANA and specific tests for anti-ENA and anti-dsDNA antibodies is most informative. This is in line with recent studies that showed that combining an immunoassay with ANA IIF adds value if the results of both tests are correctly judged in the context of the clinical manifestations of the patient , 43. FurIn conclusion, this international survey confirms that the major nuclear and cytoplasmic (reticular) patterns are considered clinically important. It also supports the ICAP classification in competent and expert patterns for the majority of the competent patterns, but there is no unanimity on classifying DFS, rods and rings and polar/Golgi-like as a competent pattern. Compared to nuclear patterns, cytoplasmic patterns are less reported and their clinical relevance is considered lower than the clinical relevance of nuclear patterns. Combining IIF with testing for specific antibodies is considered to be most informative. There is no unanimity among the respondents regarding the question whether a cytoplasmic pattern is ANA IIF positive.Additional file 1. International EASI questionnaire ANA IIF patterns for Clinicians.Additional file 2. International EASI questionnaire ANA IIF patterns for laboratory professionals.Additional file 3.Table S5. Demographic differences in confirming ANA IIF results with specific tests for anti-ENA and anti-dsDNA.Additional file 4.Table S6. Overview of the fraction of respondents that considered it important to report the fluorescence intensity of nuclear, cytoplasmic or mitotic ANA IIF patterns."} +{"text": "Circulating glycemic traits (GTs) have been considered a risk factor for breast cancer, but studies using GT-associated genetic variants as an instrumental variable are limited and inconclusive.Our Mendelian Randomization analysis used the most recent genome-wide datasets focusing on European women.Of 44 single-nucleotide polymorphisms (SNPs) with GTs, 38 fasting-glucose and 6 fasting-insulin SNPs showed heterogeneous associations with breast cancer, without significant directional pleiotropy observed.Our findings indicate a null association between genetically determined GTs and breast cancer risk among European women. Our findings may contribute to more complete characterizing of metabolic pathways in GTs and breast cancer. Previous studies for circulating glycemic traits (GTs), including fasting glucose (FG) and insulin (FI) concentrations, have shown inconsistent associations with breast cancer development . This is1. Detailed rationale and design of the studies have been described elsewhere (2): (i) OncoArray; the Atlas of GWAS Summary Statistics (ATLAS3): (ii) CGEMS Breast Cancer GWAS, (iii) GEE adjusted for age, and (iv) GEE for age and body mass index. Study participants from each dataset provided written informed consent. Genetic instruments for each dataset were single-nucleotide polymorphisms (SNPs) associated with the trait at the genome-wide level (p < 5E-08).For the GT instrumental variables, we used the recently updated publicly available data in 2019 from genome-wide association studies (GWASs) of the Meta-Analysis of Glucose and Insulin-related traits Consortium (MAGIC) in non-diabetic European womenlsewhere . For brek mean change in the risk factor per additional variant allele with standard error \u03c3Xk and an observed Yk changes in the log-odds or the log-probability of an outcome per allele with standard error \u03c3Yk. The inverse-variance weighted estimates combine the ratio estimates from each variant in a fixed-effect meta-analysis model:We performed MR analysis using the inverse-variance weighted method which quThe approximate standard error of the estimate is:The results were reported as risk ratios and 95% confidence intervals for the change in breast cancer risk per unit increase in FG (mmol/L) or natural log-transformed FI (pmol/L). To determine the extent of pleiotropic signal, we applied Cochran\u2019s Q test and the MR-Egger analysis. Given obesity and diabetes\u2019s established role for breast cancer, we excluded those relevant SNPs from the analysis. R3.6.1 was used. The Institutional Review Board of the University of California, Los Angeles, approved this study.r2 < 0.1) were matched to either BCAC or ATLAS datasets and unmeasured confounding factors that could have introduced bias. MR analysis might also be subject to non-linearity between exposure and outcome, but potential violation of the linearity assumption tends to bias MR estimates toward the null, rather than generating a spurious association . MoreoveOur findings indicate a null association between genetically determined GTs and breast cancer risk among European women. Our study may contribute to more complete characterizing of molecular pathways in GTs and breast cancer. It also highlights the need to conduct a more comprehensive and individual-level analysis using more detailed trait information, including risk causing confusion in this field of research.The datasets generated for this study are available on request to the corresponding author.SJ, NM, SH, and Z-FZ designed the study. SJ and SH performed the genomic data QC and statistical analysis and interpreted the data. NM and Z-FZ supervised the genomic data QC and analysis and participated in the study coordination and interpreted the data. SJ secured funding for this project. All authors participated in the manuscript writing and editing, read and approved the submission of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Accumulation of DNA damage and myeloid-skewed differentiation characterize aging of the hematopoietic system, yet underlying mechanisms remain incompletely understood. Here, we show that aging hematopoietic progenitor cells particularly of the myeloid branch exhibit enhanced resistance to bulky DNA lesions\u2014a relevant type of DNA damage induced by toxins such as cancer drugs or endogenous aldehydes. We identified aging-associated activation of the Hedgehog (Hh) pathway to be connected to this phenotype. Inhibition of Hh signaling reverts DNA damage tolerance and DNA damage-resistant proliferation in aged hematopoietic progenitors. Vice versa, elevating Hh activity in young hematopoietic progenitors is sufficient to impair DNA damage responses. Altogether, these findings provide experimental evidence for aging-associated increases in Hh activity driving DNA damage tolerance in myeloid progenitors and myeloid-skewed differentiation. Modulation of Hh activity could thus be explored as a therapeutic strategy to prevent DNA damage tolerance, myeloid skewing, and disease development in the aging hematopoietic system. Given the pivotal role of stem cells in tissue maintenance and cancer formation, the protection of stem cells from DNA damage appears to be of utmost importance for the evolution of long-lived vertebrate species. One measure of stem cell protection from environmental factors inducing DNA damage certainly is the sheltering in niches . KeepingAging-associated accumulation of DNA breaks in hematopoietic stem cells (HSCs) as well as progenitor cells may contribute to the emergence of mutant, clonal hematopoiesis of indeterminate potential (CHIP) . CHIP caMechanistically, the causes for increases in DNA damage in aging HCSs and progenitors remain incompletely understood, but could be explained by defects in checkpoint responses. Recently, it has been shown that activation of ATM and apoptosis-priming is reduced in aged HSCs in the context of different types of DNA damage, especially DNA double-strand breaks (DSBs) . These dEvc and Evc2 specifically in myeloid progenitors and myeloid-biased HSCs, what coincided with elevated Hedgehog (Hh) signaling activity in such cells. Manipulation of Hh signaling activity using pharmacological as well as short-hairpin RNA (shRNA)-based approaches showed that Hh signaling by itself is sufficient to drive DNA damage-resistant proliferation of progenitors from young mice, whereas Hh inhibition restores DDRs and abrogates elevated rates of DNA damage-resistant proliferation of hematopoietic progenitors from old mice. Altogether, these data suggest that age-related elevation of Hh activity and DNA damage-resistant proliferation of myeloid-progenitor cells contributes to the development of myeloid-skewed hematopoiesis in aged mice.Here, we show that aging renders murine hematopoietic progenitors more resistant to DNA damage, in particular bulky DNA adducts. Transcriptome analysis revealed upregulation of The goal of this study was to analyze the intrinsic capability of aged hematopoietic cells to cope with bulky DNA lesions. We therefore freshly extracted and isolated different types of hematopoietic cells from C57Bl/6J wild-type mice of different age and both sexes. Young mice had an age of 12\u201314 weeks, while aged mice were at least 22 months old. The freshly isolated cells were then subjected to different treatments to induce bulky DNA lesions. Different experimental approaches were then applied such as colony formation assays, Western blotting, or analysis of DNA repair activities to obtain insight how treated cells react to bulky DNA lesions. Please find detailed information about experimental procedures in the supplement.Defects in nucleotide excision repair (NER) have been shown to induce HSC failure and segmental progeria of the hematopoietic system , 5. More2) and compared their ability to form colonies to control-treated cells. Irradiation suppressed colony formation of Lin- cells from both young and old mice compared to mock-treated cells ; for gating strategy see Supplemental Fig.\u00a0We exposed Lin- cells from young and old mice to a low dose of UVC , was reduced in UV-irradiated Lin- cells from old compared to young mice in UV-irradiated Lin- cells from young and old mice Fig.\u00a0. Similarice Fig.\u00a0. The anated Fig.\u00a0. Altoget+, Sca-1\u2212, CD34+, Fc\u03b3Rlow) and determined the transcriptome of CMPs extracted from young and old mice ). Strikingly, the genes showing second and sixth highest age-associated upregulation (of 654 at least 1.5-fold significantly upregulated genes) encode proteins that together form a heterodimeric complex, Ellis van Crefeld gene syndrom (Evc) and Ellis van Crefeld gene syndrom 2 (Evc2) . The complex of the Evc and Evc2 proteins positively regulates activity of the Hedgehog (Hh) signaling pathway and mutations in either factor triggers phenotypes that typically are observed in patients showing aberrant Hh signaling capacity [smoothend (SMO), the central activating component of the Hh pathway to the correct cellular localization [Evc and Evc2 in freshly isolated Lin- cells from old vs young mice . The analysis of CMPs and common lymphoid progenitors revealed that the age-related increase in the expression of these genes was predominantly observed in CMPs . Furthermore, immunofluorescence staining of Evc2 protein on freshly isolated myeloid- and lymphoid-biased HSCs revealed an age-related increase of expression in myeloid-biased HSCs, but not in lymphoid-biased HSCs . Altogether, Evc/Evc2 expression is upregulated in the myeloid branch of the aging hematopoietic system.We next wished to identify candidate pathways causing aging-related impairments of UV-induced DDRs in myeloid-progenitor cells. In order to obtain sufficient material for an analysis, we turned to common myeloid-progenitor cells containing the promoters of both genes . Histone modifications in this circumscribed region enhance expression of both genes in various types of human leukemia [+, c-Kit+) revealed a simultaneous decrease of methylated CpGs in both promoters . Altogether, these data suggest that the loss of epigenetic silencing marks contributes to the aging-associated induction of the expression of Evc and Evc2 in hematopoietic progenitors.Since there is increasing evidence that aging-associated alterations in the epigenome contribute to increases in self-renewal of HSCs during aging , 31, it leukemia . ChromatPtch1 [Mycn [Bcl2 [Ptch1 and Mycn) or maintained (Bcl2) Hh-target gene expression in myeloid-biased HSCs, while expression of these genes was rather reduced in aging lymphoid-biased HSCs .It has previously been shown that Hh pathway activity has the potential to overrule DNA damage checkpoints in cancerous and non-transformed cells \u201345. We t in ref. ) . Both sHence, we hypothesized that manipulation of Hh signaling potentially alters DDRs in HSCs in a similar fashion. Therefore, we promoted Hh pathway activity by knock down of Ptch1 in freshly isolated HSCs (CD34- LSK) from young adult mice followed by induction of bulky DNA adducts via UVC irradiation. Interestingly, HSCs carrying the shRNA against Ptch1 showed a reduced induction of p21 in response to UV-irradiation compared to non-infected cells from the same culture dish Fig.\u00a0.Fig. 4TrFrom our results so far we concluded that Lin- cells from aged mice are deficient in DNA damage checkpoint induction, which entails uncontrolled colony formation in response to bulky DNA lesion induction Figs.\u00a0 and 2. THere, we report that aging triggers elevated Hh signaling activity in the hematopoietic system, particularly in myeloid-biased HSCs and myeloid progenitors. Functionally, this suppresses adequate DDRs after induction of bulky DNA adducts and promotes DNA-damage-resistant proliferation, leading to increased colony formation of cells of the myeloid branch.Hh signaling is well known for its roles in embryonic development and carcinogenesis (reviewed in ref. ). Basal Aberrantly high Hh signaling has previously been shown to attenuate DDRs \u201345. One Aging seems to differently affect the way HSCs and hematopoietic progenitors handle different classes of DNA damage. The ability to repair DSBs was reported to be unaffected . In contSupplement"} +{"text": "The U.S. Gulf Coast hurricanes of 2004-08 led to research and policy reports highlighting the need for more emergency preparation among nursing homes (NH). In 2016, the federal government issued final rules requiring Medicaid and Medicare providers to develop comprehensive preparedness plans. The state of Florida previously imposed its own long-term care (LTC) preparedness requirements. Hurricane Irma tested the readiness of LTC facilities that care for disabled and vulnerable residents. This research examined the experiences of NHs (N=30) affected by the hurricane through qualitative interviews with administrative staff. Research team members analyzed the transcripts, identified codes, and met to reach consensus on themes. Three major themes emerged, 1) managing the unexpected, including last-minute evacuation orders, 2) caring for vulnerable residents amid the crisis, and 3) the struggle of maintaining staff. Results suggest LTC preparation has increased but long-standing problems continue, including conflicts with emergency management priorities."} +{"text": "Connections between the coronary sinus (CS) and ventricle have been reported previously, ablation of which can be successful only within the CS.A 15-year-old male patient was referred to our hospital for radiofrequency catheter ablation of a supraventricular tachycardia. His 12-lead electrocardiogram suggested left-sided Wolff-Parkinson-White syndrome. The earliest atrial activation site (EAAS) during ventricular pacing recorded by an ultra-high-density mapping system was 6 o\u2019clock on the mitral annulus A\u2013D, whicThe previous mapping systems make a point-to-point annotation of the earliest potential for the 3-dimensional activation maps. Considering that functional limitation, those systems could annotate only atrial or ventricular potentials and are not able to distinguish between atrial and ventricular potentials during the same mapping. The Rhythmia system has an intelligent annotation technology and annotates the largest bipolar potential, which enables distinguishing the atrial and ventricular potentials all at once and can construct an atrioventricular dual-chamber map without a manual reannotation.Posteroseptal APs have been recognized as the most frequent epicardial APs, and successful ablation from inside the CS has been reported."} +{"text": "Twenty-five Multi-Ethnic (ME) and 21 Exclusively Chinese (EC) care home staff participated in an education intervention focused on helping staff assist residents/families with goals of care conversations and other aspects of ACP in a culturally sensitive way. Surveys were completed at baseline and 6-8 week follow-up. Staff reported that the education session increased their ACP knowledge and provided strategies to help them initiate relevant ACP conversations. Registered staff demonstrated significantly higher levels of confidence to participate in and assist residents/families with goals of care conversations after compared to before training."} +{"text": "Design and development of an effective compound to combat COVID-19 is clearly critical in the current circumstances. Therefore, it is of interest to document the molecular dockinganalysis data of the cellular receptor Glucose regulated protein 78 (GRP78) with Withaferin A from Withania somnifera in the context of COVID-19 pandemic for further consideration.Here, we report the optimal interaction features of withaferin A, artemisinin, curcumin and andrographolide with the GRP78 receptor having low binding energies in this report. In order to gain additional insights, the interaction pattern of compounds with SARS-CoV-2 main protease (Mpro) was studied. Novel coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared by the World Health Organization (WHO) as aglobal pandemic [Development of therapeutic interventions to combat with COVID-19 pandemic depends largely on the understanding of coronavirus spike protein interaction with cell-surface receptors.SARS-CoV-2 invades the human cell via Angiotensin converting enzyme-2 (ACE-2) receptors .In additCoronavirus main protease (Mpro/3CLpro) is another crucial molecular target in anti-CoV drug discovery research due to its indispensable requirement for viral replication and infection. HCoV MpSeveral pharmacologically active principles from medicinal plants have been reported to exert antiviral activities ,12,13. The crystal structures of GRP78 bound to ATP (PDB ID: 5E84) and COVID-19 3CLpro/Mpro (PDB ID: 6LU7) were downloaded in .pdb format from PDB database (http://www.rcsb.org/). Chain Aof the respective proteins was used for macromolecule preparation.The coordinates of PDB structures were prepared for molecular docking by removing the water ions and ligands using Python molecule viewer. The druggability pocket prediction wasperformed for the proteins using PockDrug-server ,15.We have used the potent pharmacologically active phytochemicals such as withaferin A, artemisinin, curcumin, and andrographolide in this study. The 3D structures of these compoundswere obtained from Pubchem . The druThe active site residues in the substrate-binding domain (SBD) of GRP78 were retrieved from the literature . The actIn this study we have screened 25 natural compounds of plant origin for potential interaction with the possible therapeutic targets of SARS-CoV-2 infection. We could observe that fewof them have shown appreciable binding affinities with GRP78 and COVID-19 Mpro. Hence, we have presented here the detailed molecular docking analysis of four promising candidates.We have determined the interactive pattern of test compounds with the SBD of GRP78 using molecular docking analysis. Interestingly, we found appreciable interactions between the activesite residues of GRP78 and withanolide A with binding energy of -8.7 kcal/mol at its top-binding pose. Among the tested compounds withaferin A demonstrated strong interaction (Ki = 421nM) with the binding site . The molIn this study we have used the molecular docking tool to understand the interactions of natural products with plausible targets of SARS-CoV-2 infection such as host cell receptor GRP78and COVID-19 Mpro. The ability of protein active sites to bind to drug-like molecules with extreme affinity is a major phase of target identification in drug discovery .Our preWe have reported the optimal interaction features of withaferin A with the GRP78 receptor and SARS-CoV-2 Mpro in this study. Further research is required to validate the antiviralproperties of withaferin A against COVID-19."} +{"text": "Escherichia coli and purified by nickel-affinity column and size exclusion chromatography. Sequencing data indicated that the N genes of CCoV-BJ70 and CRCoV-BJ202 belonging to two distinctly different groups were relatively conserved within each subgroup. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) results showed that rNPs of CCoV and CRCoV were expressed efficiently and isolated with a final purity of over 95%. Western blot analysis revealed the rNP from CRCoV could cross-react with mice antisera against human coronavirus , while rNP of CCoV had cross-reactivity with only anti-sera against viruses belonging to the same group (HCoV-229E and NL63). In summary, CCoV and CRCoV rNPs were successfully expressed in E. coli and showed antigenic cross-reactivity with antisera raised against human coronaviruses. These findings indicate that further serologic studies on coronavirus infections at the animal-human interface are needed.To characterize the antigenicity of nucleocapsid proteins (NP) derived from canine coronavirus (CCoV) and canine respiratory coronavirus (CRCoV) in China, the N genes of CCoV (CCoV-BJ70) and CRCoV (CRCoV-BJ202) were cloned from swabs obtained from diseased pet dogs in Beijing and then sequenced. The recombinant NPs (rNPs) were expressed in"} +{"text": "John L Cooper J Urol. 2020 Nov;204(5):976-981.The ureteral access sheath (UAS) is a commonly used disposable device in flexible ureteroscopy (fURS) . Use of This retrospective study investigated the association of UAS use during 1332 ureteroscopic procedures with abnormal post-URS imaging. UAS (12/14F in 95.7%) was used in 78% of the cases. Upper tract imaging with KUB, ultrasound or CT scan was obtained at eight-week follow-up visit after URS. No significant association was seem between use of UAS and abnormal post-URS imaging. Incidence of hydronephrosis was 12% and the ureteral stricture rate was only 0.66%.Besides the main finding of no significant association between the use of UAS and development of abnormal post-URS imaging, this study brings light on the value of routine follow-up imaging following URS. There is no specific recommendation coming from guidelines about modality or timing of imaging after fURS. Follow-up imaging after ureteroscopy is essential due to irreversible renal function impairment caused by silent ureteral stones and to check for complications , 5. Non-"} +{"text": "Papilio xuthus (Lepidoptera: Papilionidae) was determined in this study. The mitochondrial genome is a circular molecule of 15\u2009359 and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The nucleotide composition of the A. chinensis mitogenome is strongly biased toward A\u2009+\u2009T nucleotides (80.45%). Nine protein-coding genes and 14 tRNA genes are encoded on the H strand, and the other four protein-coding genes and eight tRNA genes are encoded on the L strand. The gene order and the orientation of their mitogenomes were similar to all know Papilionidae species. Finally, the phylogenetic relationships of 11 Papilionidae species were reconstructed based on complete mitochondrial genome using the Bayesian inference (BI) and the maximum-likelihood (ML) method. These molecular-based phylogenies support the traditional morphologically based view of relationships within the Papilionidae.The complete mitochondrial genome of Popilio xuthus mainly distributed in East Asia , two rRNA genes, eight tRNA genes tRNA and ValtRNA) and A\u2009+\u2009T-rich region. The remaining 23 genes are encoded on the H strand. The arrangement of genes is similar to all know Papilionidae species.The mitochondrial genome is a circular molecule of 15\u2009359\u2009bp (accession no. KU356933) and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. Among these, 14 genes were encoded on the L-strand, including four PCGs , Graphium (Graphium chironides and Graphium timur), Troides (Troides aeacus). The subfamily Zerynthiinae (Sericinus montela and Luehdorfia taibai) forms the second clade and is sister to subfamily Papilioninae. These molecular-based phylogenies support the traditional morphologically based view of relationships within the Papilionidae and maximum-likelihood (ML) methods, using P. xuthus can provide a useful database for analyzing the classification and status in Papilionidae. In addition, it is useful to construct molecular identification of this species.Our study of"} +{"text": "The inequity in cessation resources is at the forefront of the recently enacted US smoking ban in public housing facilities. This pre-post, non-randomized pilot study assessed the feasibility of a smoking cessation program targeting smokers in Baltimore City public housing. The study implemented a four-phased, 10-week, community-based cessation program using a joint academic\u2013housing partnership that provided on-site cessation pharmacotherapy, behavioral counseling, and psychosocial/legal services. The community-led strategy involved: (1) two-week smoking cessation training for lay health workers; (2) screening and recruitment of smokers by housing authority residential leadership; (3) four-week resident-led cessation using evidenced-based strategies along with wraparound support services; (4) formative evaluation of the intervention\u2019s acceptability and implementation. Thirty participants were recruited of which greater than one-half attended the majority of weekly cessation events. Thirty percent were able to achieve biomarker-proven cessation, as measured by a reduction in exhaled CO levels\u2014a percentage comparable to the reported state quitline 30-day cessation rate. Despite weekly joint community\u2013academic led-education of nicotine replacement therapy (NRT) therapies, only two participants regularly and properly used NRT transdermal patches; <20% of participants used NRT gum correctly at their first follow-up visit. Less than one-half utilized psychosocial and legal services by our community-based organization partners. Post-intervention interviews with participants noted broad approval of the ease in accessibility of the cessation intervention, but more diversification in the timing and personalization of offerings of services would have assisted in greater adoptability and participant retention. Though a reduction in smoking behaviors was not broadly observed, we elucidated modifiable social, educational, and physical features that could enhance the likelihood of smoking cessation among public housing residents. As of July 2018, the U.S. Department of Housing and Urban Development (HUD) had instituted a smoking ban inside and within 25 feet of public housing agencies (PHAs) . UnderstThe major modality for promoting the smoking ban policy has been through evidence-based tobacco harm education, cessation pharmacotherapy, and tobacco-centered behavioral counseling ,6. HowevBaltimore City is an ideal testing ground for a novel, practical tobacco cessation intervention since it ranks 5th in most public housing units in the USA . The majOur non-randomized, pre-post pilot utilizes three community-centric core elements: (a) durable and jointly linked community/academic infrastructure systems, (b) recognition and referral to local community-based organizations to address acute psychosocial stressors contributing to smoking behaviors, (c) strong on-site (public housing) residential leadership commitment to cessation improvement. We engaged resident, on-site leaders to be the public face of the intervention since traditional academic staff are unable to promote an intervention with equal potency among residents who identify at geographically granular levels. The resident leaders assisted in the design, implementation, and evaluation of the intervention. This is the first of at least three pilots seeking to refine the development of a public housing-centered smoking cessation program. We hypothesize that the 30-day quit rate will be higher in our joint academic\u2013community led cessation program compared to the Maryland Quitline (the US state-based telephone/online tobacco cessation service in which the study occurred). The state quitline\u2019s 30-day quit rate is reported at 27.9%. However, it must be recognized that this frequently referenced marker is based on a self-report . This 30Study design: We conducted a pre-post, non-randomized 10-week pilot study (16 January 2019\u201327 March 2019) to determine the feasibility of a multi-component cessation program targeting residents in one Baltimore City public housing site. The protocol was approved by the institutional review board at The Johns Hopkins University School of Medicine (IRB00064875).Study population: Two resident leaders of the housing complex were selected and functioned as research staff. Resident leaders were identified by long-standing, on-site employees of the Office of Resident Services . The employees were familiar with both chosen individuals and were strongly recommended for inclusion in the project based on their past involvement in community-based projects. To ensure their position, perception, and relatability to the participants, the two selected adult African American female resident leaders self-identified as being former cigarette smokers and were confirmed by fellow residents as being leaders within the community. Forty participants were screened and enrolled in a week-long recruitment period within the housing community center. We selected participants based on: (a) age \u226518 years; (b) verbally expressing willingness to undertake cessation; (c) primary residence within the public housing site; (d) active smoking status confirmed by exhaled carbon monoxide (CO) > 4 ppm . ParticiStudy protocol: The intervention was divided into 4 phases . ResidenBehavioral counseling received the largest amount of teaching time in the curriculum. Resident leaders and academic research staff were educated on the application of brief motivation interviewing for tobacco cessation. Time was kept brief for this component based on resident leadership advice that individuals will only wish to spend maximum of 20\u201330 min on-site for each weekly event. Brief behavioral motivational interviewing applied a modified 5 A\u2019s model: Ask, Advise, Assess, Connect (A3C) ,23,24. T\u00ae BreathCO\u2122 (Station 3). Weekly supply of nicotine replacement therapy (NRT) in the form of transdermal patches and oral gum/lozenges were disseminated by academic staff, with oversight by a tobacco cessation-specialized pharmacist (Station 4). Over-the-counter NRTs were purchased using non-reimbursed, non-payor mechanisms through grant funding. Selection and general/absolute contraindications of NRTs were reviewed on recruitment and reinforced weekly using questionnaires. Side-effects on therapy were monitored using a 24-h accessible phone line manned by academically trained tobacco cessation specialists. Comprehensive psychosocial service screening and referrals to our Catholic Charities\u2019 Our Daily Bread Employment Center (ODBEC) was undertaken (Station 5). Screening for needs assessment involved application of CDC Community Needs Assessment Training Workbook prioritization grid [Recruitment involved a two-fold strategy using on-site promotion by housing authority-affiliated personnel and direct recruitment efforts by resident leaders. Implementation of the 4-week pilot was undertaken in the housing site\u2019s community center. The individual components of the intervention were delivered weekly using physical stations that were geographically delineated using tables manned by study staff/resident leaders . After uion grid . If partion grid ,24. RefrOutcome measures: The primary study endpoint was weekly exhaled CO levels. We relied primarily on exhaled CO since it serves as a more objective and reliable biomarker of smoking activity, as opposed to self-report ,25. Eval\u00ae, College Station, TX, USA). Descriptive statistics were generated for medication side effects, weekly follow-up retention, and requested CBO services. Stakeholder interviews were reviewed with study team investigators to identify recurring patterns of beliefs, interactions, behaviors and needs across stakeholder groups. Interview responses were reviewed through an iterative process using principles of qualitative description [Statistical analysis: The primary outcome was an adjusted comparison of the 4-week mean change in exhaled CO . Individn = 12) of individuals utilizing the offerings of our community partner organizations. Twelve participants did avail of on-site Maryland Legal Aid services for which all but one addressed criminal expungement issues.Tobacco-centered behavioral counseling was not utilized by every participant at each weekly event. Surveys of the most frequently reported psychosocial needs revealed, in order: employment, housing security, substance usage treatment, mental health and neighborhood crime . GreaterPost-intervention interviews of participants noted that most preferred the accessibility of the cessation intervention . They alThe pilot study demonstrated the strengths and weaknesses of a community-centered, joint academic-residential smoking cessation program targeting low-income public housing residents. The program was constructed and marketed during recruitment as a means to address the recent US public housing smoking ban. Despite the interest and general positive resident feedback towards the program, we were unable to reduce exhaled CO levels. We were able to approximate the success rates reported by the state quitline 30-day cessation benchmark of 27.9% ,20. VastSeveral limitations existed in the multi-phased feasibility study. Our hypothesis was based on exceeding the 30-day quit rate of our state quitline 27.9%), but that benchmark is based on self-report which may be prone to reporting bias ,20. We r.9%, but This project represents our first of multiple planned pilot trials to enhance smoking cessation among public housing residents. The next planned iteration is based on the analyses and feedback derived from this initial pilot. Features that are being prioritized include more repetitive and personalized education of NRT products, along with diversification of tobacco pharmacotherapies, with continued oversight by tobacco-treatment pharmacist. Purchasing of tobacco pharmacotherapy for on-site dissemination using insurance-based modalities is being investigated given the high-cost, potentially unsustainable approach of using grant funding for NRT products. Moreover, the concern for inadequate numbers of research staff to assist in the efficiency of the program implementation will be addressed by recruiting more residential leaders as research staff. The next iteration will use a more personalized marketing of psychosocial/legal services by advertising individually relevant services that each community-based organization offers. Along with promotion, future work will benefit from inclusion of a transport system to enhance access to off-site partners.Our feasibility study shows the general positive receptivity, as well as significant limitations in our public housing-centered smoking cessation intervention. The observed weaknesses are surmountable and, if successfully addressed, a highly needed program can be provided to address the disproportionate usage of smoking and subsequent health inequities in low-income residential settings. Ultimately, the work serves as the foundation to build and further improve health equity promoting projects in a susceptible and receptive population of residents in US public housing."} +{"text": "Existing tabular formats ambiguously or incompletely store information about genetic variants and associations, lack essential metadata and are typically not indexed yielding poor query performance and increasing the possibility of errors in data interpretation and post-GWAS analyses. To address these issues, we adapted the variant call format to store GWAS summary statistics (GWAS-VCF) and developed open-source tools to use this format in downstream analyses. We provide open access to over 10,000 complete GWAS summary datasets converted to this format (The online version contains supplementary material available at 10.1186/s13059-020-02248-0. P value) has enabled a range of important secondary research applications including causal gene and functional variant prioritisation [The GWAS is a powerful tool for identifying genetic loci associated with any trait, including diseases and clinical biomarkers, as well as non-clinical and molecular phenotypes such as height and gene expression (eQTLs).tisation , causal tisation , pathwaytisation , causal tisation , risk prtisation , genetictisation and heritisation . HoweverP value), imprecision is introduced reducing subsequent test power. Varying field names are easily addressed in principle, but the process can be cumbersome and error-prone. Third, data are frequently distributed with no or insufficient metadata describing the study, traits and variants which can lead to errors, impede the integration of results from different studies and hamper reproducibility. Fourth, querying unindexed text files is slow and memory inefficient, making some potential applications computationally infeasible .Historic lack of a common standard has resulted in GWAS analysis tools outputting summary statistics in different tabular formats developed a tab-separated values (TSV) text format with a minimal set of required columns along with standardised headings [Some proposals for a standard tabular format have been made. The NHGRI-EBI GWAS Catalog and a file body containing variant-level and sample-level (one sample per column) information. We adapted this format to include GWAS-specific metadata and utilise the sample column to store variant-trait association data the specification version number, (2) information about the reference genome assembly and contigs and (3) information about the fields used to describe variants and samples (or variant-trait associations in the case of GWAS-VCF) in the file body. We take advantage of the VCF file header to store additional information about the GWAS including (1) source and date of summary statistics, (2) study IDs and (3) description of the traits studied as well as the source and version of trait IDs .Unlike VCF where a row can contain information about multiple alternative alleles observed at the same site/locus (and thus may store more than one variant), the GWAS-VCF specification requires that each variant is stored in a separate row of the file body. Each row contains eight mandatory fields: chromosome name (CHROM), base-pair position (POS), unique variant identifier (ID), reference/non-effect allele (REF), alternative/effect allele (ALT), quality (QUAL), filter (FILTER) and variant information (INFO). The ID, QUAL and FILTER fields can contain a null value represented by a dot. Importantly, the ID value (unless null) should not be present in more than one row. The FILTER field may be used to flag poor-quality variants for exclusion in downstream analyses. The INFO column is a flexible data store for additional variant-level key-value pairs (fields) and may be used to store for example population frequency (AF), genomic annotations and variant functional effects. We also use the INFO field to store the dbSNP locus idP value was faster using TSV . However, when the number of variants stored in the GWAS-VCF was 0.5 million, uncompressed text was faster for single position and rsid lookups but not interval queries and encourage other centres to deploy their own instance . Further, the gwasglue R package provides convenient programming functions to automate the preparation of genetic association data for a range of downstream analyses to highlight records below prespecified thresholds if the exact value is unimportant. For example, all variants below genome-wide significance (P\u2009<\u20095e\u22128) or a more relaxed threshold (e.g. P\u2009<\u20095e\u22125).Our simulation studies demonstrated the GWAS-VCF was substantially quicker when the GWAS was densely imputed (8\u201344\u00d7) than TSV using standard UNIX tools for extracting records by genomic position. Although the GWAS-VCF was slower for extracting records by association A limitation of the current summary statistics formats, including GWAS-VCF, is the lack of a widely adopted and stable representation of sequence variants that can be used as a universal unique identifier for the said variants. Published summary statistics often use rsids to identAnother potential limitation is the use of multiple ontologies to describe the GWAS trait which might make inter-study comparisons difficult. However, we feel enforcing a specific trait identifier system could prevent the new ontologies and non-human data which would provide a barrier to adoption.Here, we present an adaptation of the VCF specification for GWAS summary statistics storage that is amenable to high-throughput analyses and robust data sharing and integration. We implement open-source tools to convert existing summary statistics formats to GWAS-VCF, and libraries for reading or querying this format and integrating with existing analysis tools. Finally, we provide complete GWAS summary statistics for over 10,000 traits in GWAS-VCF. These resources enable convenient and efficient secondary analyses of GWAS summary statistics and support future tool development.The specification was developed through the experience of collecting and harmonising GWAS summary data across two research centres at scale and perfP value or 1-Mb genomic interval. Tests were undertaken with 100 repetitions using BGZIP [Densely imputed summary statistics for GWAS of body mass index using data from the UK Biobank were obtained from Neale et al. . The datng BGZIP GWAS-VCFAdditional file 1: Figure S1. VCF format adapted to store GWAS summary statistics (GWAS-VCF). Example GWAS-VCF with individual sections labelled. Table S1. Data fields in the GWAS-VCF. Required and optional GWAS-VCF fields with descriptions as defined in the file specification. Table S2. Open-source tools for working with GWAS-VCF. Description of open-source software for working with GWAS-VCF and download links. Table S3. Possible variant identifier schemes for the ID column of GWAS-VCF. Example unique variant identifier schemes and their advantages/disadvantages.Additional file 2. Review history."} +{"text": "Epithelial ovarian cancer is a disease that encompasses a number of histologically and molecularly distinct entities; the most prevalent subtype being high-grade serous (HGS) carcinoma. Standard first-line treatment of advanced HGS carcinoma includes cytoreductive surgery plus intravenous paclitaxel/platinum-based chemotherapy. Despite excellent responses to initial treatment, the majority of patients develop recurrent disease within 3\u00a0years. The introduction of the vascular endothelial growth factor (VEGF) inhibitor, bevacizumab, and poly(ADP-ribose) polymerase (PARP) inhibitors into first-line management has changed the outlook for this lethal disease. In this review, we summarise the most recent clinical trials that determine current primary therapy of advanced HGS carcinoma and the ongoing trials that aim to change management in the future.Recent phase III clinical trials have shown that delayed primary surgery after completing neo-adjuvant chemotherapy is non-inferior to immediate primary surgery, but could provide a survival benefit in FIGO stage IV disease. The use of weekly intravenous chemotherapy regimens has not been proven to be more effective than standard 3-weekly regimens in Western patient populations, and the use of intraperitoneal chemotherapy remains controversial in the first-line setting. In contrast, newer systemic anti-cancer therapies targeting angiogenesis and/or HR-deficient tumours have been successfully incorporated into front-line therapeutic regimens to treat HGS carcinoma. Recent results from randomised trials investigating the use of PARP inhibitors as monotherapy and in combination with the anti-angiogenic agent, bevacizumab, have demonstrated highly impressive efficacy when combined with traditional first-line multi-modality therapy.Management of HGS carcinoma is evolving, but further work is still required to optimise and integrate tumour and plasma biomarkers to exploit the potential of these highly efficacious targeted agents. Ovarian cancer is the 8th commonest cancer diagnosed in women and the 8th commonest cause of female cancer-related death worldwide . ApproxiFirst-line treatment for advanced stage HGS carcinoma provides the only realistic opportunity for cure, with a 5-year survival of 27% in patients with FIGO stage III disease . In womep\u2009=\u20090.048) if they were treated with NACT followed by DPS . \u2022\u2022. BRCA Results from phase III trials combining immune checkpoint inhibitors with VEGF or PARP inhibitors in first-line management of EOC are eagerly awaited Table . The ratThe first-line treatment of HGS carcinoma now builds on the well-established backbone of surgery and paclitaxel/platinum-based chemotherapy. Surgery can be carried out upon diagnosis or after NACT. The role of IP chemotherapy and HIPEC remains undefined.Maintenance monotherapies with bevacizumab and PARP inhibitors have demonstrated progression-free survival benefits in certain clinically and molecularly defined subgroups. Key questions remain over the benefits of combination regimens and whether molecularly targeted biomarkers can optimise patient stratification. Nevertheless, 70% of patients are likely to develop recurrent disease and require further treatment. Bevacizumab has proven effective in the re-use setting but triaRecent phase III trials highlight the future need for randomised trials on the re-use of maintenance therapies, the upfront testing of BRCA and HRD status and the ongoing development of biomarkers for use of VEGFi."} +{"text": "Objective: We report the case of a young woman with postinfectious onset of myasthenia gravis after COVID-19 with mild respiratory symptoms and anosmia/ageusia 1 month before admission to our neurological department.Methods: Patient data were derived from medical records of Hannover Medical School, Germany. Written informed consent was obtained from the patient.Results: The 21-year-old female patient presented with subacute, vertically shifted double vision evoked by right sided partial oculomotor paresis and ptosis. About 4 weeks earlier she had suffered from mild respiratory symptoms, aching limbs and head without fever, accompanied by anosmia/ageusia. During the persistence of the latter symptoms for around 10 days the patient had already noticed \u201ctired eyes\u201d and fluctuating double vision. Clinical assessment including a positive test with edrophonium chloride and increased acetylcholine receptor antibodies related the ocular manifestation etiologically to myasthenia gravis. Antibodies (IgA/IgG) against SARS-CoV-2 using three different serological tests were detected in serum suggesting this specific coronavirus as previously infectious agent in our patient. The myasthenic syndrome was treated successfully with intravenous immunoglobulins and oral pyridostigmine.Conclusion: This is the first case presentation of postinfectious myasthenia gravis as neurological complication in a COVID-19 patient. Besides respiratory symptoms of COVID-19, frequent neurological manifestations including prolonged anosmia/ageusia during the acute SARS-CoV-2 infection have been described and MillWe present the first case of myasthenia gravis as neurological complication after SARS-CoV-2 infection.Euroimmun provided SARS-CoV-2 ELISA IgA/IgG and PCR. Two additional ELISA IgG tests from Abbott and DiaSorin were used to validate serological results.Written informed consents were obtained from the patient (consent for publication and consent to disclose photographs/video).A 21-year-old woman was admitted via the emergency room at Hanover Medical School in mid-April 2020 because of double vision and right-sided ptosis which had progressively worsened for 5 days. The patient stated that by end of March she and her family members had suffered from mild respiratory symptoms without fever, moderate fatigue with aching limbs and head, dry eyes and nasal mucosa as well as anosmia/ageusia. Until April all affected family members recovered without having been tested for SARS-CoV-2 using PCR or antibody assays.The patient's medical history had been been unremarkable so far. While there is no family history of neuromuscular disorders at all, there are cases of Hashimoto's thyreoiditis, Addison's disease and pernicious anemia in her family. However, the three siblings of the patient are healthy, she has no children.Most of the patient's COVID-19 related symptoms had regressed within 3 weeks when ocular symptoms evolved post-infectiously . The patNeuro-ophthalmological examination in mid-April showed a right eyed elevation deficit as cause of vertical double images and ptosis. An MRI scan with contrast enhancement displayed regular anatomical structures of brain and orbit. An oropharyngeal swab taken about 4 weeks after onset of respiratory symptoms was tested negative by PCR indicating no acute SARS-CoV-2 infection .Two days later, neurological examination revealed increasing oculomotor impairment due to right eyed elevation deficit and ptosis with positive Cogan lid twitch test (Besinger score 7). During investigation the patient described vertically offset double vision in all directions with reduced double images when looking to the left. The remaining neurological status was normal.Electrophysiological examinations showed inconspicuous motor and sensory neurographies without increment. In repetitive stimulations no decrement (3 Hz) of the orbicularis oculi or trapezius muscles could be detected. The Simpson test showed a significant worsening of ptosis and double vision during forced upward gaze after 20 s. An ice on eyes test was negative, whereas a test with intravenous edrophonium chloride (9 mg cumulative dose) was clearly positive . Further blood investigations including other myasthenia-associated antibodies and screening parameters for immunological diseases including ganglioside IgM/IgG remained unremarkable. SARS-CoV-2 IgA and IgG ELISA (Euroimmun) were positive in serum underlining the typical history of COVID-19 in our patient. Two additional IgG ELISA tests were performed to validate the positive SARS-CoV-2 serological results, an IgM test was not available. The microscopical CSF cell count, protein and lactate were normal, oligoclonal bands positive (type 2a). The PCR and IgG/IgA ELISA for SARS-CoV-2 in the CSF were negative . Further examinations of serum and CSF on herpes infection, borreliosis and lues showed no indication for acute infection.In the absence of dysphagia and dyspnea, standardized lung function tests remained inconspicuous. Electroencephalographical findings were unremarkable. Further examinations with thoracic X-ray and MRI did not show a thymoma. Lung parenchyma displayed no (post)inflammatory changes.) resulting in regression of ocular symptoms (Besinger score 3) before discharge. After gradual increase of oral pyridostigmine up to 3 \u00d7 120 mg/d during the next weeks further improvement was noted at a follow up in mid-May (Besinger score 0).Due to acute clinical exacerbation over the last days, the patient was treated with intravenous immunoglobulins . Anosmia/ageusia are commonly reported neurological symptoms of SARS-CoV-2 infections . Most COhttps://www.uniprot.org/blast).Myasthenia gravis is an autoimmune, neuromuscular disease that is mostly caused by antibodies against postsynaptic acetylcholine receptors. Generally, there are only few recent reports about post-infectious myasthenia gravis [after varicella-infections , 10/viraIn our patient's serum, IgA and IgG antibodies directed against SARS-CoV-2 were detected in calendar week 17, presumably 4 weeks after initial respiratory symptoms. We used a semiquantitative ELISA IgA/IgG test which detects the S1 domain reaching a specificity of 98.5% (for IgG)/92.5% . Validation of serological results was performed using two different ELISA IgG tests with a specificity of 98.5% (DiaSorin) and 99.45% (Abbott) applied >14 days after infection. However, cross-reactions to cytomegalovirus IgG (Abbott), hepatitis B and influenza A (DiaSorin) or other coronaviruses, especially SARS-CoV-1 (Euroimmun), are known to manufacturers. Due to typical COVID-19 symptoms in our patient's history and the multiple positive serological test results for SARS-CoV-2 we highly assume a preceding infection with this new coronavirus triggering post-infectious ocular manifestation of myasthenia gravis as neurological complication.On the other hand a COVID-19 patient might incidentally suffer from overlapping onset of myasthenia gravis. In our opinion this issue cannot be clarified completely even by retrospective comparison of disease occurrence rates. Despite the occurrence rate of SARS-CoV-2 infections in our area at the end of March 2020 was moderately high and myasthenia gravis is considered a rare disease we cannot rule out that myasthenia gravis might have been induced independently from the SARS-CoV-2 infection.Although our patient does not have any preexisting illnesses and particularly no neuromuscular disorders, the family history is positive for autoimmune diseases. This suggests that COVID-19 patients with a similar history may be prone to suffer from post-infectious neuroimmunological complications due to SARS-CoV-2.We present the first case of post-infectious myasthenia gravis associated with SARS-CoV-2. An increasing number of patients with various neurological symptoms during acute infection or post-infectious complications have been reported but the full clinical spectrum and incidence of COVID-19 related neurological manifestations is still unknown. Future studies should address if there is an association higher than expected by chance.All datasets generated for this study are included in the article/Ethical review and approval was not required for the study on human participants in accordance with the local legislation and institutional requirements. The patients/participants provided their written informed consent to participate in this study. Written informed consent was obtained from the individual(s) for the publication of any potentially identifiable images or data included in this article.MH and FW: conception, organization and execution of the research project, writing of the first draft, and the review and critique of the manuscript. SR, WP, CF, GH, and KH: conception, organization and execution of the research project, review and critique of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "This session presents findings from a STEADI process evaluation that was conducted within a primary care setting in New York State. This process evaluation used mixed methods including quantitative analysis of surveys with clinic staff as well as qualitative methods such as intercept interviews with healthcare providers and clinic staff, and structured interviews with key stakeholders. The RE-AIM framework guided development of the process evaluation tools. The process evaluation was conducted over a 2-month period approximately 18 months post-implementation. Facilitators included: (a) Adoption - physician champion and administrative support; (b) Implementation - wellness coordinators, preparation and training, and organizational quality measures; (c) Maintenance - feedback from patients, local and national recognition, and impact on fall-related outcomes. Barriers included: (a) Adoption \u2013 organizational priorities and complexity of electronic health records; (b) Implementation \u2013 resistance to change and competing patient care demands; (c) Maintenance - staff turnover and follow through of referrals."} +{"text": "Sexual minority (SM) health disparities constitute a serious public health concern, and disparities in mental health are among the most striking. Among a nationally-representative sample (NESARC-III) of US adults (aged 18-66), we used time-varying effects models (TVEM) to estimate the age-varying prevalences of past year major depressive episode (pyMDE) and generalized anxiety disorder (pyGAD) by SM status and biological sex. pyMDE and pyGAD were most common among SM women, followed by SM men, heterosexual women, and heterosexual men. pyMDE was highest among SM women and SM men in early adulthood with a second peak in the mid-50s (women)and around age 40 (men). pyGAD was highest among SM women aged 54-60 and among SM men aged 30-33. Our findings reveal that older adulthood may be a time of increased risk for pyMDE and pyGAD among SM women. Future work should explore factors that contribute to this increased risk."} +{"text": "Resistance becomes major clinical issue in cancer treatment, which strongly limits patients to benefit from oncotherapy. Growing evidences have been indicative of the critical role of fibroblast growth factor (FGF)/receptor (FGFR) signaling played in resistance to oncotherapy. In this review we discussed the underlying mechanisms of FGF/FGFR signaling mediated resistance to chemotherapy, radiotherapy and target therapy in various cancers. Meanwhile, we summarized the reported mechanism of FGF/FGFR inhibitors resistance in cancers. Fibroblast growth factor (FGF) family being part of the receptor tyrosine kinase (RTK) families are comprised of 18 ligands, exerting their functions through four highly conserved tyrosine kinase receptors The underlying mechanism of FGF/FGFR signaling pathway involved in resistance to oncotherapy can be generally divided into over-expression of ligands or receptors, epithelial-mesenchymal transformation (EMT), angiogenesis, nuclear translocation, downregulation of negative regulator and activation of other survival signaling Table .Lung cancer, including two subclasses, non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC), is the first leading cause of malignant tumor death around the world SCLC, accounting for 20% of lung cancer, could develop rapidly to chemo-resistance, harbouring a poor overall survival Estrogen receptor (ER) expresses in approximately 60% of breast cancer (BC). These ER positive BC patients initially respond well to antiestrogens like tamoxifen or Fulvestrant, while they gradually become resistant. Growth of FGF1 or FGF4 transfected ER positive BC cells is not inhibited by treatment of antiestrogen Anti-vascular endothelial growth factor (VEGF) therapy has been a promising therapeutic option for cancers, while it failed to improve survival in BC patients Data from 172 rectal carcinoma specimens who underwent neoadjuvant concurrent chemoradiotherapy (CCRT) indicated that high-level expression of FGFR2 is positively associated with advanced stage tumor, poor treatment response and poor prognosis Imatinib, selectively targeting KIT or PDGFRA, has observably improved prognosis in advanced gastrointestinal stromal tumors (GISTs) Increase of released FGF2 has been reported in the squamous cell carcinoma (SCC) cell lines after irradiation Previous study on 352 osteosarcoma patients, who received neo-adjuvant chemotherapy, indicated that amplification of FGFR1 gene was found exclusively in the poor response group and represented approximately 18.5% of patients in the group FGF8 upregulated the expression of EGFR in hepatocellular carcinoma (HCC) via increasing the expression of yes-associated protein 1 (YAP1), which then facilitated the resistance to EGFR inhibitors Antiangiogenic therapy could trigger upregulation of other pro-angiogenic factors in pancreatic tumors. FGF/FGFR signaling made great contribution to escaping anti-angiogenic targeting of VEGF signaling in pancreatic islet tumors and pancreatic neuroendocrine tumors in vivo, because hepatic stellate cells (HSCs) secreted FGF2 to promote the resistance to BET inhibitors 6-methylguanine-DNA-methyltransferase (MGMT) promoter decreased the expression of its associated protein O6 -alkylguanine-DNA-alkyltransferase (AGT) Bromodomain and extraterminal (BET) inhibitors could increase the expression of FGFR in uveal melanoma (UM) cells Overexpression of FGFR3 in myeloma confers resistance to dexamethasone, partly via upregulating of Bcl-xL FGF/MAPK signaling detours a requirement for androgens and the androgen receptor in promoting growth of prostate cancer The contribution of abnormal FGF/FGFR signaling pathway to oncogenesis has given rise to the advancement of a great number of therapies targeting the FGF/FGFR pathways. Though there has been no FGF/FGFR targeted therapies approved good clinical therapeutic effects in cancer treatment yet, the results from plenty of early-phase clinical trials have verified the momentous significance on targeting FGF/FGFR in the clinic. The problem of acquired resistance to targeted tyrosine kinase inhibitors gradually emerges in the clinic, and it may also restrict the clinical application of FGF/FGFR inhibitors. Several researches have indicated this phenomenon of resistance to FGF/FGFR inhibitors in cancers and expounded the possible underlying mechanism Figure .V561M and FGFR1N546K have been reported to be closely associated with the resistance of to FGFR inhibitors N546K mutant showed drug resistance by increasing its affinity for ATP, whereas FGFR1V561M mutant showed resistance against PD173074 by reducing its affinity for the drug V555M gatekeeper mutation is associated with resistance to FGFR inhibitors, AZD4547 and PD173074 V564F confers resistance to BGJ398 by causing a steric clash with BGJ398 in its FGFR2 binding pocket Mutation at the gatekeeper residue of FGFR is the first important mechanism of resistance to FGF/ FGFR inhibitors in kinds of cancer types Table . The gatFeedback activation of survival loop caused by FGFR inhibition is another important mechanism for the resistance to FGFR inhibitors Table . High-thAberrant activation of ligand dependent or independent FGF/FGFR signaling pathway makes a substantial contribution to oncotherapy resistance via promoting proliferation, survival, angiogenesis or EMT. Other non-canonical signaling mediated by FGF/FGFR, such as nuclear transition of FGFR and FGF"} +{"text": "Since the publishing of our meta-analysis evaluating the effects of randomized exercise trials on cognitive function of Older Adults with Cognitive Impairments (OAwCIs) , several meta-analysis reviews were published addressing similar question. We currently appraised this evidence and preliminary synthesis of twelve, well-designed meta-analysis reports resulted in 193 RCTs and 15,614 participants over the age of 65 years old diagnosed with MCI or Alzheimer\u2019s disease (AD). Exercise prescription paradigms averaged 156 minutes per week for 20-week. The combined cognitive function outcome mean effect size was medium; 0.67 (0.06-1.34 95% CI). Grounded in this unique umbrella study results, sustained and prolonged exercise training might provide an effective intervention for the maintenance or enhancement of cognitive function for MCI and AD. This comprehensive meta-analysis umbrella offers valuable and strong exercise recommendations for OAwCIs. This study results will be of great significance to professionals involved in the care of OAwCIs."} +{"text": "Access to primary healthcare during lockdown measures for COVID-19 in rural South Africa: an interrupted time series analysis. BMJ Open 2020;10:e043763. doi: 10.1136/bmjopen-2020-043763Siedner MJ, Kraemer JD, Meyer MJ, This article was previously published with an error in the x-axis of Figure 1. The correct figure is below:Figure 1 Ambulatory clinic visitation before and after the nationwide lockdown in South Africa at 11 outpatient clinics in rural uMkhanyakude District, KwaZulu-Natal South Africa. Scatter plots represent mean clinic visitation at each clinic on weekdays during the observation period. The black fit line represents the mean visitation across all clinics estimated by postregression margins from a linear regression model, with a regression discontinuity coefficient at the date of the lockdown . Grey bars represent 95% CIs. The dotted blue line represents the geometic mean of the number of visits across all clinics on each day."} +{"text": "Rationale: Biliary tract injury remains the most dreaded complication during laparoscopic cholecystectomy. New intraoperative guidance technologies, including near-infrared (NIR) fluorescence cholangiography with indocyanine green (ICG), are under comprehensive evaluation. Previous studies had shown the limitations of traditional NIR light in visualizing the biliary tract structures in specific clinical situations. The aim of this study was to evaluate the feasibility of performing the extrahepatic cholangiography in the second NIR window and compare it to the conventional NIR-I imaging.Methods: The absorption and emission spectra, as well as fluorescence intensity and photostability of ICG-bile solution in the NIR-II window were recorded and measured. In vitro intralipid\u00ae phantom imaging was performed to evaluate tissue penetrating depth in NIR-I and NIR-II window. Different clinical scenarios were modeled by broadening the penetration distance or generating bile duct injuries, and bile duct visualization and lesion site diagnosis in the NIR-II window were evaluated and compared with NIR-I imaging.Results: The fluorescence spectrum of ICG-bile solution extends well into the NIR-II region, exhibiting intense emission value and excellent photostability sufficient for NIR-II biliary tract imaging. Extrahepatic cholangiography using ICG in the NIR-II window obviously reduced background signal and enhanced penetration depth, providing more structural information and improved visualization of the bile duct or lesion location in simulated clinical scenarios, outperforming the NIR-I window imaging.Conclusions: The conventional clinically approved agent ICG is an excellent fluorophore for NIR-II bile duct imaging. Fluorescence cholangiography with ICG in the NIR-II window could provide adequate visualization of the biliary tract structures with increased resolution and penetration depth and might be a valid option to increase the safety of cholecystectomy in difficult cases. Iatrogenic biliary tract injuries remain the primary concern of general surgeons performing cholecystectomies, with an incidence ranging from 0.08% to 0.4% There are mainly two intraoperative techniques to consider, one is the conventional X-ray based intraoperative cholangiography (IOC), and secondly the emerging fluorescence-based NIR extrahepatic cholangiography. Although IOC reduces the rate of bile duct injuries However, conventional fluorescent cholangiography also has some inherent deficiencies. The limited tissue penetration capability of NIR-I light and high autofluorescence background in this window could result in the inability to visualize the extrahepatic duct under special clinical conditions, such as obesity and cholecystitis Recent studies in fluorescence imaging in the NIR-II window have shown significant advantages over NIR-I imaging In vitro evaluation of tissue penetrating capability in the NIR-II window was carried out by imaging capillary tubes submerged in 1% Intralipid\u00ae solution. Established rat or mouse models were used to perform in vivo comparison of the outcomes of NIR-I and NIR-II cholangiography. Also, measurement of the NIR-II emission properties and in vitro fluorescence intensity analysis were also performed in ICG-human bile solution to assess the clinical translation potentiality. The primary objective of the present study was to evaluate the validity and feasibility of applying the NIR-II imaging technique in extrahepatic cholangiography using a clinically approved fluorescence agent and demonstrate its strong potential for translation into clinical applications.Here, we applied the clinically approved agent ICG as a fluorophore for NIR-II extrahepatic cholangiography. The emission properties of ICG-bile solution in the NIR-II window were measured and compared to those of its aqueous solution. \u00ae was purchased from Baxter Healthcare Corporation (USA). Coomassie Brilliant Blue Fast Staining solution was purchased from Solaribo Life Sciences Company . Pierce\u2122 BCA Protein Assay Kit was acquired from Thermo Scientific Corporation . Deionized (DI) water with the resistivity of 18.2 M\u03a9/cm was used in all experiments.The fluorophore ICG was purchased from DanDong Pharmaceutical Factory and used without any further modification. Phosphate buffered saline (PBS) was obtained from Sinopharm Chemical Reagent Company and 20% intralipidMeasurement of absorption spectra of ICG dilutions in bile and water were obtained from 550-900 nm utilizing a Shimadzu UV-2550 UV-vis-NIR scanning spectrophotometer. The fluorescence emission spectra of ICG dilutions in bile and water in the NIR-II window were collected by a lab-built system based on a PG2000 spectrometer (Ideaoptics Instruments) and a 2000C spectrometer (Everuping Optics Corporation).The fluorescence quantum yield of ICG dilutions in water and bile were measured by Quantaurus-QY Plus , using an 808-nm laser as an excitation source. The samples to be measured were diluted and adjusted to proper concentration, the final optical density value of which ranged between 0.2-0.5 at 808-nm. The quantum yield of the sample was calculated by the following equation:2. During imaging, two 800-nm long-pass filters were used to filter away 793 nm excitation. The various long-pass filters were utilized to extract different NIR-II fluorescence signals as required. For instance, a 1000-nm long-pass filter was placed in front of the camera lens restricting wavelength below as well as allowing wavelength above 1000 nm to pass through the camera lens.As shown in 2.Images in the NIR-I window were captured using a silicon camera equipped with a prime lens , which was fitted with two 800-nm long-pass filters and a 900-nm short pass filter to extract NIR-I fluorescence signal. A 793-nm laser beam was coupled to a collimator and expanded by a lens to provide uniform illumination on the field. The facular power density was adjusted to 10-20 mW/cm2). NIR-I and NIR-II imaging were performed to visualize the extrahepatic bile duct structure. Then a piece of abdominal tissue was removed integrally from an anesthetized ICR mouse and instantly placed on the observing field of interest without any fold. NIR-I and NIR-II imaging were further performed to visualize the biliary structure through the covered tissue.After anesthetization, the rat was secured to a platform in the supine position, then laparotomy was performed, and the surgical field of interest was fully exposed. 0.5 mg/kg of ICG was intravenously injected through tail vein, using a 793-nm excitation for further comparison between the imaging performed in the NIR-I and NIR-II windows.2. The rat was then placed in a supine position under the NIR-I or NIR-II camera to visualize the extrahepatic bile duct and detect the ligation point. An intact piece of abdominal tissue (approximate 1.2 mm thickness) was removed from an anesthetized ICR mouse and instantly placed superficially on the surgical field of interest without any fold. Subsequently, NIR-I and NIR-II imaging were performed as previously described to detect the precise bile duct lesion location through the covered tissue.An acute bile duct stricture model was established by common bile duct ligation in the rat. In brief, after laparotomy, the common bile duct was partially separated and occluded by using a 5-0 suture, imitating intraoperative accident of bile duct ligation. ICG at a concentration of 0.5 mg/kg was intravenously injected through tail vein instantly after ligation, and the facular power density was adjusted to 10 mW/cmAn acute biliary perforation model (n = 6) was established as previously reported An acute complete common bile duct transection model (n = 6) was established by transecting the rat common bile duct with electrotome , both proximal and distal end of which would be occluded. Then NIR-I and NIR-II imaging were performed to detect the transection site. Moreover, a piece of fresh abdominal tissue was placed superficially on the surgical field of interest and NIR-I and NIR-II imaging were further performed to detect the precise lesion location through the covering tissue.All animal experiments in this study were conducted strictly in compliance with the requirements and guidelines of the Institutional Ethical Committee of Animal Experimentation of Zhejiang University. All procedures performed in studies involving human participants were in accordance with the ethical standards of the Clinical Research Ethics Committee of Sir Run-Run Shaw Hospital of Zhejiang University.The detailed experimental materials and methods are listed in Quantitative analysis of each fluorescent image was performed based on the measurement of mean signal intensity in the manually selected regions of interest, using Image J software . Graphs were generated using Origin Pro software . The data were presented as mean \u00b1 standard deviation (SD). Statistical analysis was performed using Student's t-test. * denotes a statistical significance between the experimental data of two groups.The emission spectrum of the ICG-rat bile solution was recorded on a system sensitive to both NIR-I and NIR-II light (detected by the PG2000 spectrometer and 2000C spectrometer respectively), showing that the ICG's fluorescence emission extended well into the NIR-II region Figure A-B. FurtThe fluorescence emission spectra of ICG-rat bile and ICG-water solutions were determined and compared over 900 to 1600 nm wavelength range. In aqueous solution, ICG exhibited a relatively low fluorescence emission value, whereas after being excreted into rat bile, the fluorescence intensity in different NIR-II spectral ranges was much greater than that of ICG in aqueous solution Figure A-F.At each equivalent concentration, the ICG-rat bile solution emitted a more intense fluorescence signal compared to its aqueous solution Figure A-B. The 2 for 160 minutes, the ICG-rat bile solution could still emit strong fluorescence signal at short integration time (5ms), exhibiting better photostability compared to that of aqueous solution . The distribution of the proteins in rat bile varied. As shown in \u00ae mimicking the optical characteristics of biological tissues was performed to compare the penetration depth of ICG-rat bile solution between the NIR-I and NIR-II windows. When the 1% Intralipid\u00ae solution was not added, sharp images could be formed in both NIR-I and NIR-II windows. However, the scattering effect became significantly pronounced with the increasing depth in the NIR-I window as a potentially novel investigation of biliary dyskinesia The high background signal hinders the visualization of fine anatomical structures. Here, by extending into the deep NIR-II window, the interfering background around extrahepatic biliary tract significantly reduced, enabling visualization of the fine anatomic structure where the common bile duct joins into duodenum. Interestingly, while using a 1500-nm long-pass emission filter, the strong background due to the rapid accumulation of ICG in the liver was significantly filtered out, yet the fluorescence intensity of extrahepatic biliary tract remained intense enough to be recognized. Since the strong background in liver has always been a problem for the surgeons during cholangiography surgery in vivo imaging in different animal models to highlight advantages of NIR-II imaging over conventional NIR-I imaging in deeper penetrating ability. In this study, we chose wavelength range above 1000-nm as the NIR-II emission collection region during in vivo imaging which allowed both considerable fluorescence signal and deep tissue penetration capability. We excised an intact abdominal tissue from a mouse to simulate the real penetration depth, and with similar tissue components, the mimics could be more reasonable and convincing. NIR-II imaging with the longer wavelength allowed larger penetration depth, making it possible to visualize biliary tract structures in deeper fields.We also performed Bile duct injuries are also common during biliary tract surgical procedures which could lead to serious complications The commercially available and clinically approved agent ICG exhibits remarkable NIR-II emission when excreted into bile and could be an excellent fluorophore for real-time NIR-II bile duct imaging. Fluorescence cholangiography in the NIR-II window allows adequate visualization of biliary tract structures with increased penetration depth and high resolution, and might be considered as a valid option for safe cholecystectomy in case of inflammation or obesity, surpassing the performance of the NIR-I window. By switching the detection of traditional silicon-based cameras to emerging indium gallium arsenide-based cameras could promisingly improve the fluorescence surgical navigation system and ensure safe biliary operation, accelerating the clinical translation of NIR-II imaging technology."} +{"text": "The COVID-19 pandemic (caused by SARS-CoV-2) has introduced significant challenges for accurate prediction of population morbidity and mortality by traditional variable-based methods of estimation. Challenges to modelling include inadequate viral physiology comprehension and fluctuating definitions of positivity between national-to-international data. This paper proposes that accurate forecasting of COVID-19 caseload may be best preformed non-parametrically, by vector autoregression (VAR) of verifiable data regionally.A non-linear VAR model across 7 major demographically representative New York City (NYC) metropolitan region counties was constructed using verifiable daily COVID-19 caseload data March 12\u2013July 23, 2020. Through association of observed case trends with a series of (county-specific) data-driven dynamic interdependencies , a systematically non-assumptive approximation of VAR representation for COVID-19 patterns to-date and prospective upcoming trends was produced.2 range: 0.9221\u20130.9751, all p < 0.001). Predictively, VAR regression of daily caseload results at a county-wide level demonstrates considerable short-term forecasting fidelity (p < 0.001 at one-step ahead) with concurrent capacity for longer-term (tested 11-week period) inferences of consistent, reasonable upcoming patterns from latest (model data update) disease epidemiology.Modified VAR regression of NYC area COVID-19 caseload trends proves highly significant modelling capacity of observed patterns in longitudinal disease incidence (county RIn contrast to macroscopic variable-assumption projections, regionally-founded VAR modelling may substantially improve projection of short-term community disease burden, reduce potential for biostatistical error, as well as better model epidemiological effects resultant from intervention. Predictive VAR extrapolation of existing public health data at an interdependent regional scale may improve accuracy of current pandemic burden prognoses. To date, it has affected at least 217 countries and territories, leading to more than 100 million positive cases and 2.2 million deaths as of January 2021 Many contemporary infectious disease models rely on the S-I-R population transmission-based framework. However, this approach, which utilizes a multitude of assumed variables and draws data from highly divergent sources, has received prominent criticism over predictive inaccuracies skewing both positive and negative in trend 2.y, dependent), rather than necessitating fundamental independent (x) assumptions, as might be appreciated in S-I-R projections. Reliable county level COVID-19 morbidity data was derived from governmental sources in the New York metropolitan area comprising of seven designated major counties within New York State (NYS) of noted COVID-19 burden and exported to classification on a daily continuum. Per protocol vector autoregression (VAR) of the filtered dataset was then conducted, sequentially in seven repetitions utilizing each individual county progression as the dependent (y) variable. Subsequently, one through three day lagged values were used as the independent variable matrix inside the encompassing VAR framework.Herein a modified vector autoregression (VAR) model based upon daily U.S. county-level public health agency test-positivity rate and mortality data in COVID-19 for the NYC metropolitan area is developed with prediction of upcoming regional disease patterns given late July 2020 disease control status as well comprehensive data encompassing past local caseload patterns . VAR modelling attempts to quantify interrelationships wherein two or more time-dependent series are collectively impactful upon observable trends, wherein all referenced variables are treated as being endogenous methodology. AIC represents an estimator of out-of-sample prediction error that quantifies the amount of information lost by using the model to approximate an underlying series (the true daily COVID-19 new caseload). That is, it signifies juxtaposition of the error created by using a specific model against the actual data. The lesser the degree of information loss therefore, the better a trialed model is valued. AIC was used in this manner to sort through and quality-control the entirety of possible county-specific VAR models, relative to each of all alternative models under logical consideration. This process was done in the R project software, using the “olsrr: Tools for Building OLS Regression Models\u201d package for procedures. As per the cited backward regression methodology, model analysis started with the full matrix of all lagged variables and then an AIC value was calculated for each variable. Variables that did not meet AIC criteria were iteratively dropped, until a final set of perceived best-representative regression variables, that all met AIC criterion, for county-wide COVID-19 caseload projections resulted. As reference, the initial equation for New York County is shown below.The equation in general form :wherein:\u03b1 = Intercept\u03b21, \u03b22, \u03b23, \u03b24, \u03b25, \u03b26, \u03b27 = Regression coeffientsB = Bronx County COVID casesK = Kings County COVID casesN = Nassau County COVID casesNY = New York County COVID casesQ = Queens County COVID casesR = Rockland County COVID casesW = Westchester County COVID cases\u03b5t = Regression error termt = Time subscriptj, l, m, n, p, s, u = individual counting subscripts for lagsA representative implementation of output model selection for New York County follows:t > represents the expected value operator for new COVID cases in the county of reference (here New York county) at time t.wherein variables are as defined previously, and < xThe described AIC analysis sequence was stopped when the backward process indicated that an optimal solution (model) had been reached, in that the latest attained AIC value (minimization of regression variance) exists less than all other possible candidate values. Translationally, the determined endpoint therefore indicates statistically that remaining independent variables correspond to the best predictors of disease progression for the input county data per the criterion. Modelling was performed by log of cases rather than raw caseloads, followed by translation into raw daily future caseload projections. This decision derives from the fact that in tracking available COVID-19 data historically, the distribution of new cases generally followed a lognormal distribution more closely than it did a normal distribution. All resultant equations were utilized to forecast predicted disease progression in the 7 counties . County one-day and multi-day ahead forecasts of daily caseloads were generated from best-fit VAR models.Statistical determination of strength of prediction and association between VAR model projected values to observed quantities was the primary outcome of analysis in the present study. A one-step ahead projection was first examined to quantify goodness-of-fit for the VAR model to represent existing COVID trends. To establish longer-term prediction power for this model, an approximately 11-week simulation was performed following for all 7 incorporated study counties , indicative of a high degree of model accountability for the multifactorial influences which have moderated COVID-19 caseload changes from the onset of pandemic spread (and data availability) to present. By assessment therefore of both past caseload and present disease status representation, the AIC-driven modified VAR model described presently was deemed appropriately representative of disease evolutions to-date and by extension thusly appropriate for extrapolation of future COVID-19 potentiality.Having established model fidelity , wider prediction of caseloads beyond one-step ahead assessment was performed, likewise independently for each county dataset. Herein estimates on daily new COVID+ case incidence was generalized to 11 weeks into the future , again utilizing the latest modified VAR regression per-county based on July 23, 2020 input figures. Examination of this model's expectations for disease progression across a 10 to 11 week for the greater NYC region revealed relatively consistent, gradual increases in COVID-19 prevalence across all seven counties of interest. Average percentage of predicted daily case growth from July 23 to October 9, 2020 ranged from approximately 75% to 135% between counties, a significant although less distinct acceleration as compared to numerous locales nationally or periods of rapid disease transmission in the same NYC metro region during preceding months of 2020. Demonstration of county-specific projected versus observed COVID caseloads for Nassau County and New York county (Manhattan) are demonstrated in As depicted in Similar projective extrapolation as modelled by the VAR function upon 7/23/2020 caseload data for New York county is demonstrated in Of note, wherein the sampled NYC region data over the period of VAR analysis has relatively reliably progressed within relatively small magnitudes of caseload variation, the capacity for this VAR model's \u201cshock\u201d-predicting capacity relative to exponential real-time case increases as in Florida or Texas, could not be efficaciously evaluated. A new case data outlier recorded on April 14, 2020 (1737 cases) resulting from inclusion of previously uncounted presumed COVID positives provides only a very limited amount of insight towards this consideration given the limited sample size (including one-day duration) and extenuating data spike circumstances . With wider available data and empirical course of COVID-19 community transmission however, the strong expectation persists that adapted VAR impulse-response evolution estimates may well concurrently provide a moderately accurate accommodation of periods of either rapid growth or decay in regional COVID-19 new identifications incidence. Empirical quantification of VAR model adjustment from extreme trends of epidemiological data alteration therefore requires further investigation and follow-up.4.This paper proposes that COVID-19 community containment and modeling may be best represented at a local or regional level, given persistent uncertainties regarding data quality and reliability at national and global scale. Furthermore, the study develops a modified VAR-based predictive representation based on New York City metropolitan area (7 NYS counties) disease data from July-through-October at the county level, in order to demonstrate prospective near- and medium-term epidemiological trends for COVID-19 cases. Note that the presently proposed model has been built with a minimum of distributional assumptions (inferences on either variable interrelationships or resultant caseload outcomes), allowing any results to closely mirror observable empiric trends A modified VAR model carries marked regression capacity of representing observed caseload patterns alongside generally significant predictive value for estimation of new COVID-19 cases as shown by an analysis of NYC metropolitan county data from the period of July 23 (latest date of data entry and by association model adjustment) to October 9, 2020. This functionality and efficacy denotes a significant improvement upon both prospective and retrospective accuracy reached by numerous mainstream state- and national-level models founded upon variations of S-I-R epidemiologic interactions Furthermore, given literature which has noted that a major challenge to accurate prediction of pandemic modeling at a macroscopic level derives at least partially from inherent differences between diverse populations 4.1.S-I-R models are fundamentally parametric and so implicitly assume an S-shaped curve for the life of an outbreak. As shown by previous data from representative NYC metropolitan counties however, observed daily infection counts did not in fact follow a logarithmic or logistic sigmoid regression. Instead, new infections started slowly and grew exponentially but consequent infection quantities declined significantly less precipitously and in a more linear fashion than would be projected by many transmission-variable derived models 0), test availability, asymptomatic transmission and population susceptibility status or degree of social contact over time. It is the position of this paper therefore, that a VAR-based modelling of regional disease patterns carries highly translatable advantages in COVID-19 modelling derived from this described allowance for multiple evolving variables. Unlike S-I-R or univariate mechanisms, VAR is not critically driven by assumptions or awareness of the underlying forces that impact variable behavior or patterns. VAR as mentioned represents a nonparametric model, indicating that there is no pre-existing shape assumption made about the disease-progression curve; instead, any visualized curve shape is generated solely based on trends in pre-existing data. This contrasts with the parametric S-I-R model that assumes an S-shaped curve. All predictions are based only specific to the ongoing development of COVID-19 community disease spreads, this quality is critical given that all derivative predictions by VAR are extrapolated from existing variable trends (derived from daily case rate) rather than theorized structural statistical relationships.The largely non-parametric COVID projection model discussed in this study is founded upon practices inherent to traditional vector autoregression (VAR) modelling within the field of econometrics. VAR models have been well validated in economic studies wherein intertemporal relationships between variables are hypothesized, a characteristic which implies considerable utility in medicine. In the setting of novel infectious diseases, adaptation of VAR allows for the simultaneous evolution of multiple interconnected yet singularly unquantifiable disease-modifying variables such as disease basic reproduction number can be preliminarily observed through the model for Rockland County , whereinPrognostic modelling involving mortality projections, a similar measure of interest across pandemic progressions, prove more difficult to quantitatively predict given an even greater quantity of uncertainties than is seen in caseload forecasts. Numerous mainstream S-I-R based models have come under heavy criticism for significant temporal adjustments to expected COVID-19 death toll from over the course of the pandemic progression 4.3.Future directions of development from the currently constructed model may center about using VAR to examine possible delivery mechanism between geographic areas at a wider , possibly allowing for a more concise predictability regarding warning indicators or at-risk medico-societal practices influencing disease distribution. By example, we might feasibly gain insight towards a potential returned period of caseload maximization in New York City through VAR analysis of lagged-indicators between hypothesized influential demographics (i.e. community socio-ethnic status) or bridging of the urban-rural divide in ongoing hotspots (i.e. metropolitan areas within Florida or Texas as of July 2020). A vigilant, regionally-based monitoring program could therefore quickly identify and potential concerns for community COVID-19 exacerbation or recurrence. Further study of VAR translational value for COVID-19 disease modelling thusly persists in need of model predictive power evaluation between the regional geographic scale illustrated herein, and more macroscopic VAR projections in example at the national level. The upcoming question of public health utility should center on if given robust historical case data, whether VAR-type epidemiologic models will be able to accurately predict population disease progression patterns across larger and more diverse patient or dataset characterizations.Mathematically, one-to-three days lags of the model variables (relatively short) were chosen with intent to most accurately represent regional disease propagation patterns on a short-term basis, due to a continued state of incomplete understanding regarding COVID-19 and its epidemiologic behaviors. Considering the strong capacity of VAR-founded modelling to account for NYC metro region COVID-19 caseload trends, an appropriate next step may involve trialing of longer lag times (i.e. 1\u20132 weeks) in order to more efficaciously evaluate extended-period (multiple months) predictive power of this VAR model. In contrast to S-I-R projections wherein predictive uncertainty rises exponentially with increasingly long-term projection, a validated VAR forecast might reasonably be expected to minimize degree of probable variability given that constituent long-term outlooks are based on similarly extended lag-values (extensive past COVID-19 case patterns) rather than parametric extrapolation of static variables made at a singular timepoint.5.According to extensively updated reviews, a significant proportion of previous and ongoing modeling efforts related to COVID-19 are significantly constrained by poor input data quality and inflexible guiding parameters. The current study develops a county-based VAR model derivative from infection data reported in the greater NYC metropolitan area, which demonstrates significantly improved correlation between projected and observed new cases, with promising predictive value at the short (days-to-weeks) to intermediate-term (months) regional level. Furthermore, as described previously the data-driven VAR approach as adapted in this framework remains of greater statistical reliability than assumed dynamics in S-I-R projections, given that all derived inferences built upon the significant quantity of COVID-19 progression data at a local level to-date; this functionality allows for greater tailoring to alternative projections in counterpart geographies or disease settings whilst minimizing quantity of necessary assumptions as long as there exists a robust source of input raw COVID-19 caseload measurements. In example, wherein major increases for New York and comparable U.S. metropolitan areas were separated by significant temporal distribution (March and April versus current June and July respectively), significant similarities in affected population It has been well reported in literature that models founded upon estimations of population status relative to disease require significant extrapolation of disease behaviors and epidemiological statistics which may not be appropriate for poorly understood emergent pandemics. Via construction of an adapted VAR extrapolative model which accounts for past patterns of COVID-19 disease trends instead of theoretical representations of pandemic spreading, this paper proposes that existing data-driven estimations of viral dissemination carry significant utility for the real-time projection of regional disease futures. Relative to the ongoing escalation of COVID-19 caseload in many U.S. states, this model was able to predict the gradual increase in COVID cases in the NYC metropolitan region with relative accuracy for a projective period of up to 11-weeks, a highly practical utility especially for information of healthcare infrastructure readiness as well as local public policy related to continued disease containment goals.Click here for additional data file."} +{"text": "Coronavirus disease 2019 (COVID-19) is caused by the virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several case series from Italy and China have highlighted the lung ultrasound findings of this disease process and may demonstrate its clinical utility during the current pandemic.We present a case of a COVID-19 patient who presented to the emergency department twice within a 24-hour period with rapidly progressing illness. A multi-organ point-of-care ultrasound (POCUS) evaluation was used on the return visit and assisted clinical decision-making.A multi-organ POCUS exam allows for quick assessment of acute dyspnea in the emergency department. As the lung involvement of COVID-19 is primarily a peripheral process it is readily identifiable via lung ultrasound. We believe that when applied efficiently and safely a POCUS exam can reduce clinical uncertainty and potentially limit the use of other imaging modalities when treating patients with COVID-19.This case highlights the utility of an early multiorgan point-of-care assessment for patients presenting with moderate respiratory distress during the severe SARS-CoV-2 pandemic. Point-of-care ultrasound (POCUS) examinations of patients with acute respiratory distress have been demonstrated to be useful for patients with acute unexplained dyspnea in the emergency department (ED).Early reports from China detailed the utility of computed tomography (CT) in demonstrating the classic multifocal, ground-glass opacities that are commonly present in patients with pulmonary manifestations of the rapidly progressing viral pandemic.Recent studies out of China have detailed ultrasound findings associated with coronavirus disease 2019 (COVID-19).A 56-year-old female with a past medical history of asthma and dyslipidemia presented to a community ED with one week of fever, non-productive cough, dyspnea, headache, nausea and vomiting. She denied smoking history or drug use. Travel history was significant for returning home from an amusement park in Los Angeles one week prior to onset of symptoms. Vital signs at triage were temperature 38.6\u00b0 Celsius; heart rate 117 beats per minute; respiratory rate 20 breaths per minute; and pulse oximetry 93% on room air.Significant laboratory results were as follows: rapid influenza diagnostic test was negative; white blood cells 11.7 10*3 per microliter (mcL) (reference range 4.5\u201311.5 10*3/mcL), neutrophils relative 92% (reference 50\u201370%), lymphocyte absolute 0.55 10*3/mcL (reference 0.8\u20134.80 10*3 /mcL), and lactic acid was 1.0 millimoles per L (reference 0.5\u20132.2 mmol). A two-view chest radiograph (CXR) was interpreted by the radiologist as pneumonia of the left lower lobe with interstitial changes . After sWhat do we already know about this clinical entity?The virus severe acute respiratory syndrome coronavirus 2 can cause severe pulmonary infection and inflammatory response in patients presenting during the coronavirus disease 2019 (COVID-19) pandemic.What makes this presentation of disease reportable?This case highlights the rapid progression of COVID-19 pneumonia and the utility of point-of-care-ultrasound (POCUS) in excluding alternative causes of dyspnea.What is the major learning point?Multiorgan-POCUS is useful for ED evaluation of dyspnea during the COVID-19 pandemic due to the peripheral nature of lung involvement.How might this improve emergency medicine practice?Multiorgan-POCUS has the potential to reduce diagnostic uncertainty in dyspneic patients and help limit use of other imaging modalities.Approximately 12 hours after discharge the patient returned to the same ED with worsening dyspnea. Upon arrival she was noted to be ill appearing, tachypneic and with moderate respiratory distress despite similar triage vital signs as the initial ED visit. Her lung exam was significant for poor inspiratory effort and rhonchi at the bases. A multi-organ POCUS exam was performed to determine the cause of the patient\u2019s dyspnea.A cardiac parasternal long-axis view demonstrated normal systolic ejection fraction and no pericardial effusion . The IVCBased on the POCUS multi-organ findings, the patient was resuscitated with an intravenous bolus normal saline and treated with broad-spectrum antibiotics (levofloxacin). SARS-CoV-2 oropharyngeal and nasopharyngeal swabs were sent from the ED for testing. The infectious disease consultant agreed with a plan for admission and continuation of droplet, airborne, and contact precautions given the progression of symptoms and worsening respiratory status. She was admitted to a negative pressure room on the medical floor for continued therapy and monitoring of respiratory status. An eventual non-contrast CT of the chest demonstrated diffuse multifocal infiltrates .As an inpatient, the patient\u2019s antibiotic regimen was adjusted to doxycycline and cefepime. She was under observation and isolation for six days at the hospital of presentation. At this point the SARS-CoV-2 testing had not yet resulted, but her clinical course had improved. She was discharged home with instructions to self-quarantine at home or return to the ED if symptoms worsened. SARS-CoV-2 testing resulted the day after discharge as positive for SARS-CoV-2 ribonucleic acid.During the current SARS-CoV-2 pandemic, prompt evaluation of patients in the ED presenting with acute dyspnea is imperative. Diagnostic testing of SARS-CoV-2 has been limited to date, and in our setting will not result during a typical ED visit. Likewise, serum laboratory markers for both SARS-CoV-2 associated pneumonia and non-SARS-CoV-2 causes of acute dyspnea are non-specific, are also not immediately resulted, and are of limited value during the initial hospital presentation.The role of imaging during the SARS-CoV-2 outbreak is still being established. A study of patients diagnosed with COVID-19 in Wuhan, China, demonstrated a progression of disease by CT imaging from early subclinical/asymptomatic patients with unilateral and multifocal ground-glass opacities to patients with less than one week of symptoms showing bilateral disease and transition to consolidation and interstitial changes.7POCUS holds some distinct advantages over other imaging modalities especially in times of disaster or pandemic. The characteristic ultrasonographic findings of interstitial pneumonia near the pleura are accessible, rapidly attained and reliable markers of pathology. Lung ultrasound has been shown to be more sensitive than CXR for pneumonia and pulmonary edema.While the majority of patients infected with SARS-CoV-2 will experience only mild illness, a subset will progress to multifocal pneumonia, acute respiratory distress syndrome, and cardiomyopathy15The above case highlights the utility of a multiorgan approach in the evaluation of the acutely dyspneic patient during the SARS-CoV-2 pandemic. Along with lung ultrasound findings that have been described in China and Italy, we believe that the evaluation of the heart and IVC are easily obtained and extremely useful for two important reasons. First, this approach allows to rapidly determine other common causes of dyspnea in the undifferentiated patient. Second, with a more protocolized pathway on early presentation, we hope to reduce the reliance on other imaging modalities (chest radiographs and CT) in a time when infection control is imperative. In our experience, a multi-organ ultrasound first approach for all severely dyspneic patients is an ideal approach during the global SARS-CoV-2 pandemic and especially as healthcare resources become increasingly strained."} +{"text": "The COVID-19 pandemic remains an evolving disease posing a challenge of incomplete understanding escalated by random atypical clinical presentations. Numerous challenges still exist with accessibility and availability of standard COVID-19 viral testing using real-time Polymerase Chain Reaction (RT-PCR), in low- and middle-income countries, especially in several hospital settings. The clinical information of three select patients at a major health facility in Southwestern Nigeria with unusual COVID-19 clinical presentation and clinical management dilemma related to challenges with COVID-19 viral laboratory testing, were retrospectively reviewed. The medical history in all three cases closely mimicked that of other medical conditions because of assumptions created by red herrings like an acute exacerbation of an underlying non-communicable disease (diaphragmatic eventration) in case 1, re-activation of a previously treated lung condition (tuberculosis) in case 2 and a sequalae of a previously diagnosed but poorly-managed chronic non-communicable disease (decompensated hypertensive heart disease). Also, viral testing was challenging in all cases due to reasons ranging from late turn-around time to inconsistent results. However, thoracic imaging was employed in all cases to heighten suspicion of COVID-19 infection, resolve management dilemma and limit intra-hospital spread. Thoracic imaging can play a major role within hospital settings in low-and middle-income countries in resolving diagnostic challenges of atypical COVID-19 clinical presentations, raising suspicion for early institution of intra-hospital disease containment measures, limiting exposure among hospital staff and guiding clinical case management of COVID-19; especially where challenges with confirmatory viral testing remain persistent. Equalountries ,6. WhileWidely considered vital to accurate diagnosis of this disease that has a considerable number of random atypical clinical presentations, has been viral laboratory testing (VLT) employing SARS-CoV-2 real-time Polymerase Chain Reaction (RT-PCR) testing of nasal and throat swabs. Several challenges still exist in the way of deploying RT-PCR on a large scale at many LMICs, for general public infection prevention and control (IPC) . Many COThe clinical information of three unique cases managed at a major health facility in Southwestern Nigeria, University College Hospital, Ibadan, Nigeria; was retrospectively reviewed. The peculiar scenario used to select the cases reviewed included atypical pattern of clinical presentation of COVID-19 and the presence of management dilemma related to challenges of obtaining confirmatory real-time Polymerase Chain Reaction (RT-PCR) COVID-19 test.Specifically, in each of the three selected case scenarios, the review focused on the atypical features of their medical history and clinical examination, presence and nature of any underlying medical condition, findings on diagnostic investigations especially serial chest X-rays, chest computed tomographic scan and naso- and oropharyngeal swab real-time Polymerase Chain Reaction (RT-PCR) COVID-19 test results; and identification of any management dilemma and rationale behind clinical decision making to resolve the situation.The COVID-19 viral real-time Polymerase Chain Reaction (RT-PCR) testing challenges were evaluated considering the transmission dynamics and overall national response in the country at the time of each patient\u00b4s presentation to the hospital. Lengthy result turn-around time associated with low laboratory capacity was peculiar in the period when there were a few clusters of cases in the country in early April and mid-May 2020 when cases 1 and 2 presented. Case 3 was managed in early July 2020 at the community transmission phase of the infection in the country. At this stage, laboratory testing capacity had improved but intermittent shortage of test kits was still prevalent in many parts of the country.Patients and descriptions: the patients were all males, aged 45 to 80 years. A case-by-case review of the three scenarios is detailed below.Scenario 1: a 67 year old man, a known hypertensive and newly diagnosed diabetic inpatient, developed an intermittent left chest pain, 3 days after surgery for a locally-advanced pelvic tumour which was performed in the Trendelenburg\u00b4s position to improve intraoperative access. Pre-operatively, he had a background history of an asymptomatic left diaphragmatic eventration discovered incidentally during a routine health screening conducted 20 years previously. He had no fever, frequent sneezing, cough, abdominal pain or swelling but developed a progressive shortness of breath with poor oxygen saturation (ranging from 90-93% in room air) over the next three days after surgery. At the time, he was on routine chemoprophylaxis for venous thromboembolism. He arrived for the surgical operation from one of the COVID-19 endemic states in the country at the time, but reported no contact with any active COVID-19 case and so with the disease not yet at the community transmission stage during that period, there was no reasonable suspicion of COVID-19 infection. As well, there were only a few clusters of cases of the disease existing in the country at this time mostly related to external arrivals from western countries but his most recent foreign travel was over a year earlier.The major remarkable finding on clinical examination was tachypnoea (respiratory rate of 28/minute) with a marked reduction in breath sounds over most of the middle and lower areas of the left hemithorax with background audible bowel sounds. Initial laboratory panels revealed normal complete blood count, elevated D-dimers of 24mcg/ml and mild elevation in serum creatinine of 1.8mg/dl . Other serum electrolytes were within normal limits. Serial chest radiographs done over three days consistently revealed a thinned out and markedly elevated left hemidiaphragm (diaphragmatic eventration) with mass effect of the sub-phrenic abdominal contents causing ipsilateral left lung collapse and contralateral tracheo-mediastinal shift (tension viscero-thorax). In comparison to the pre-operative chest radiograph, the degree of eventration appeared to have increased as well as the pressure effect. The working diagnosis was acute exacerbation of a previously asymptomatic left diaphragmatic eventration complicated by tension viscero-thorax while pulmonary thrombo-embolism was a differential diagnosis. He was nursed head-up with supplemental oxygen support. He also had institution of full anticoagulation with enoxaparin at 1mg/kg/day dosing. However, the left chest pain progressed from an intermittent nature to a more persistent and intolerable form accompanied by deterioration in his clinical parameters {oxygen saturation dropped below 90% with persistent tachycardia (pulse rate >110/minute), tachypnoea respiratory rate >30/minute and low-grade fever (up to 38\u00b0C)}. Repeat laboratory panels revealed white cell count of 14,800 cells/\u03bcl with relative lymphopenia and elevated C-reactive protein of 105.7 mg/L. At that point, strong consideration was given to the possibility of bowel strangulation underneath the eventrated hemidiaphragm with need for expeditious surgical management. A chest Computed Tomographic (CT) scan was performed on the s2) of 1. He also had a high-grade fever (peak temperatures of 39.8\u00b0C) despite ongoing broad-spectrum systemic antibiotic, corticosteroid therapy and maintenance of therapeutic dose of enoxaparin. Post-operative chest radiograph in the Intensive Care Unit (ICU) but he maintained poor oxygen saturation (88-93%) despite a high fraction of inspired oxygen , poor room air oxygen saturation of 90%, tachycardia (pulse rate of 100/minute) and systemic hypertension (blood pressure of 165/96mmHg). All initial laboratory blood panels were within normal limits except for borderline elevation in serum creatinine of 1.6mg/ml and low estimated glomerular filtration rate of 45.5ml/min/1.73m2 indicating low renal reserve.The chest radiograph done on admission revealed dextrocardia with features of multiple consolidations in both lung fields demonstrating peripheral disposition. There was no evidence of pleural or pericardial effusion . A 12-leth day of admission (12th day from the onset of illness) which revealed diffuse ill-defined ground glass densities in both lungs with multiple peripherally-distributed non-enhancing peri-bronchovascular consolidations especially in the lower lobes. There was bilateral pleural thickening with mild cardiomegaly (CTR=54%), rightward cardiac apex, and bovine branching pattern of a rightward aortic arch consistent with dextrocardia. The liver was located on the left and the spleen on the right, in keeping with a situs inversus scan on the 5inversus . These iScenario 3: a 45 year old gentleman had reported to our hospital with progressive exercise intolerance and shortness of breath of 2 weeks duration. There was an intermittent cough, productive of mucoid sputum, but he had no fever or sore throat. He also had occasional palpitations, orthopnoea and mild but progressive bilateral leg swellings. He was diagnosed with hypertensive heart disease three years previously but was poorly-compliant with prescribed medications. He presented when community transmission of COVID-19 was present in the state where the hospital is located but had reported no contact with any confirmed or suspected case. The remarkable findings on clinical examination include mild bilateral ankle oedema, tachypnoea , room air oxygen saturation of 89-92% with activity-related deterioration, tachycardia of 110-118/minute pulse rate with a regular rhythm, bilateral basal lung crepitations and tender, mild hepatomegaly with no demonstrable ascites.His initial laboratory panels revealed elevated white cell count of 13,400 cells/\u03bcl with relative lymphopenia of 9% differential count . Serum D-dimer was elevated at 10mcg/ml as well as C-reactive protein (CRP) of 74mg/L . Twelve-lead electrocardiogram revealed left ventricular hypertrophy and left axis deviation with sinus tachycardia. The 2-dimensional trans-thoracic echocardiography revealed concentric left ventricular hypertrophy with borderline left ventricular ejection fraction (EF) of 55% and grade I diastolic dysfunction. The TAPSE was 1.8cm.nd day of admission done on the 2dmission , which rThe patient also made a full recovery after 12 days in the infectious disease isolation facility. Except for a close caregiver who also tested positive but remained asymptomatic while in isolation, no hospital staff among the primary contacts of the patient was reported to have tested positive to COVID-19.The global profile of the COVID-19 viral infection has demonstrated a progressive change in the epicenter from China at the onset, to western Europe at the initial peak and later to North-America (United States of America) before the recent surges recorded in Latin America . Currently, there is a growing anxiety about a second wave of the global pandemic suggesting the presence of a rapidly changing disease dynamics. Therefore, there is heavy reliance on new insights gained from patients and meticulous scientific researches that are underway in different countries of the world at this time. Indeed, with the World Health Organization (WHO), frequently providing a global direction and data-driven guideline for disease surveillance, transmission control and case management; it has become imperative that developing countries grappling with the socio-economic and clinical sequalae of the pandemic begin to provide evidence for local adaptation of global protocols to meet peculiar demands of their environments at this time .From available literature, the typical and common pattern of clinical presentation of COVID-19 infection is fairly well documented and includes low grade fever, productive cough, loss of taste and smell, fatigue and shortness of breath . Other lIn many countries including LMICs, COVID-19 viral laboratory testing (VLT) of throat and nasal swabs remains the most utilized platform for disease detection or confirmation -18. DespThoracic imaging in form of plain chest radiography/ X-ray and chest computed tomographic scanning (CT) appears to have proven diagnostic and screening relevance in COVID-19 pneumonia among patients requiring hospitalization or hospital-based care ,24. ThouEven in developing and LMICs, computed tomography scanners are becoming commonplace especially in large cities and urban areas ,28, but COVID-19 infection occurring in individuals with underlying or pre-existing medical conditions may become difficult to diagnose if it presents unusually with similar and overlapping clinical features to those conditions. This diagnostic challenge can be further aggravated in the presence of a problematic COVID-19 viral laboratory testing system. Thoracic imaging using chest CT scan is highly sensitive for screening patients with unclear clinical diagnosis either in the early or late stage of COVID-19 infection while chest X-ray is particularly useful during the late phase. The crucial role of this imaging modalities in COVID-19 screening becomes more apparent when real-time RT-PCR testing for COVID-19 is a challenge as can be found in many hospital settings of most low- and middle-income countries (LMICs).COVID-19 remains a disease in evolution with more information coming through on daily basis to explain the disease epidemiology, pattern of presentation, case management and to guide public health control;Atypical presentations of COVID-19 are not uncommon;These atypical COVID-19 clinical presentations appear to be more common and follows a more severe course among patients with certain pre-existing medical conditions.Atypical presentations of COVID-19 are not uncommon but may present a huge diagnostic challenge or difficulty with containment of intra-hospital disease transmission particularly where viral real-time PCR (RT-PCR) testing capabilities are difficult or limited. This is particularly important in resource-challenged hospital settings in low- and middle-income countries;The use of thoracic imaging especially chest computed tomographic scan in early evaluation of suspected COVID-19 cases, potentially has far-reaching clinical and public health benefits within a hospital setting, where and when possible and should be given strong considerations in situations where viral testing for COVID-19 is problematic and clinical presentation is atypical; regardless of the severity of the disease;Chest X-ray may not show classic radiological features of COVID-19 at the early stage of the disease. Therefore, the use of serial chest radiograph is advised in low-and middle-income countries where RT-PCR test kits or computed tomography (CT) are not readily available, bearing in mind the increasing diagnostic yield of chest X-ray as the disease progresses towards the late stage (averagely about day 8 - 12 from onset of symptoms)."} +{"text": "Treponema pallidum particle agglutination assay. A test for human immunodeficiency virus was positive and his CD4+ count (248 cells/mL) was below the reference range . The patient was administered intravenous penicillin G for 21 days as well as highly active antiretroviral therapy. The serum VDRL test result fell in response to treatment and a VDRL test of his cerebrospinal fluid revealed negative results. The patient was discharged 21 days after admission with residual right hemiparesis and diplopia. A 26-year-old man presented with acute-onset right hemiparesis, diplopia on horizontal gaze, and fever. Brain magnetic resonance imaging (MRI) with high-resolution vessel wall imaging (HR-VWI) showed left hemipons infarction and concentric parietal thickening of the basilar artery, consistent with vasculitis and 2. C-Neurosyphilis can occur at any stage of the disease and may be associated with occlusive large vessel infarcts"} +{"text": "Lesbian, gay, and bisexual (LGB) Veterans report stress and mental health conditions that may increase risk for neurocognitive changes like dementia. Subjective cognitive decline (SCD) can be an early indicator of neurocognitive change \u2013 yet no known studies have examined SCD in LGB Veterans. Cross-sectional data from the Vietnam Era Health Retrospective Observational Study (VE-HEROeS) were examined for 260 LGB and 17,796 heterosexual Veterans. VE-HEROeS is the latest probability-based survey of Vietnam Era Veterans (1961\u20131975) as older adults (2016-2017). SCD was assessed using two subscales of the Functional Assessment of Cancer Therapy-Cognitive Instrument Version-3 (FACT-Cog). Good reliability was observed in this sample: Cronbach\u2019s alpha =.94 for the 7-item Perceived Cognitive Abilities subscale and .88 for the 4-item Comments from Others. Analyses were weighted to account for the complex survey design. LGB Veterans were slightly younger than heterosexual Veterans ; were more likely to be female ; and had fewer people living in the household . LGB Veterans were also more likely than heterosexual Veterans to report feeling depressed most or all of the time over the past 30 days on a single 5-point Likert-scale. SCD indicators did not vary by Veteran sexual orientation and were elevated compared to published studies in healthy adult samples. More work is needed to examine neurocognitive risk factors in aging LGB Veterans."} +{"text": "Living arrangements are critical for intra-family exchanges such as physical, financial, and emotional supports influencing older adults\u2019 health and well-being. Existing research is largely based on short-term observations of living arrangements. This study aims to explore longer term dynamic patterns of intergenerational living arrangements among older Americans and their sociodemographic and health determinants. Data came from the 1998-2016 Health and Retirement Study. Sequence analysis was employed to identify long-term patterns of intergenerational living arrangements for 3,025 individuals who were age of 51-64 at the baseline (ages of 69-82 at the last wave), have at least one child, and were observed 10 consecutive times . Living arrangements were categorized into co-residence, proximate residence , and nursing home. Multinomial logistic regressions were used to evaluate the associations of individual characteristics with the different living arrangements sequences. Four patterns of eighteen-year living arrangement trajectories were identified: Transition to proximate residence (17%), stable in distant residence (24%), stable in proximate residence (38%), and stable in co-residence (22%). Younger age and working (vs. retired) status were associated with stable coresidence rather than proximate or distant residence. Respondents who retired during the study period were more likely to move close to their children. Contrary to expectations, changes in self-rated health and functional status had no significant effect in long-term living arrangement sequence patterns. These findings suggest that intergenerational living arrangements among older Americans tend to be stable and not to be significantly affected by their caregiving needs."} +{"text": "Dear Editor,Anaplastic large cell lymphoma (ALCL) is the third most common peripheral T cell lymphoma and is dWe present an unusual case of a 38-year-old female patient with challenging diagnostic workup of an ALK-positive ALCL due to the variable histology and clinical course of this lymphoma. The patient initially complained of lower back pain and fever. FDG-positron emission tomography and computerized tomography (PET-CT) of the thorax and abdomen revealed multiple bone lesions Fig. . The patSince the discovery of ALCL by Stein et al. due to tThis case shows the difficulties in diagnosing ALK-positive ALCL due to the variable clinical course including bone infiltration. A major challenge is a histological diagnosis since anaplastic large cell lymphoma may present with heterogeneous morphology, expansion of inflammatory cells, and few CD30-positive cells, especially if limited biopsy material is warranted, contributing to delayed diagnosis. In patients with bone lesions and unspecific histological result, ALCL should be considered with high priority in differential diagnosis."} +{"text": "Background: The Preferences for Everyday Living Inventory (PELI) was developed to assess the psychosocial preferences of older adults receiving home care (PELI-HC) and then revised for nursing home residents (PELI-NH). While the PELI-HC has been tested to identify patterns in preference ratings by race, the PELI-NH has not. We sought to explore whether the PELI-NH tool captures differences in preference ratings of African-American and White NH residents. Methods: Preference assessment interviews were conducted with NH residents (n = 317). Analysis via a Mann-Whitney U test, results show that 46 of 72 (63.88%) a preference importance items were not statistically different between African-American and White NH residents. Additionally, African-Americans reported greater importance than White older adult NH residents in 26 of 72 (36%) preference importance items. Conclusion/Implications: It appears that the PELI-NH can test group differences in preference importance among African-American and White NH residents; implications for practice will be discussed. Part of a symposium sponsored by the Research in Quality of Care Interest Group."} +{"text": "There have been significant advances in the management of acute ischemic stroke (AIS), autoimmune encephalitis, and anoxic brain injury in recent years. This Research Topic, Multimodality Monitoring and Evaluation of Neuro-Function in Modern Neurological Intensive Care Unit (NICU), presents eight original research articles and two mini reviews to highlight the applicability of novel multimodality monitoring and clinical evaluation in the management and prognostication of severe neurological disorders.Wang et al. investigated the predictive value of 40-Hz SSR in patients with large hemispheric infarction. Bilateral abnormal 40-Hz SSRs were found to have a high specificity and positive predictive value for 30-day mortality and 90-day poor prognosis.Non-invasive electroencephalography (EEG) can capture sensory cortical neurons' entrainment to rhythmic sound stimuli known as the auditory steady-state response. The 40-Hz steady-state response (SSR) reflects early sensory processing and has the potential to differentiate disease severity. Liu et al. used continuous EEG and CBF velocity monitoring to investigate neurovascular coupling in patients with stroke from large vessel occlusion (LVO). A phase-amplitude cross-frequency coupling (CFC) algorithm was applied to assess how CBF velocities interact with the EEG amplitude. The degree of hemispherical asymmetry of CFC was found to correlate with the degree of arterial stenosis.Neurovascular coupling is a dynamic physiological process that adjusts cerebral blood flow (CBF) to match neuronal activity needs. Huang et al. investigated the correlation between hyperchloremia and outcome in patients with severe stroke. Out of 405 study patients, 35 (8.6%) and 69 (17.0%) were found to have hyperchloremia at NICU admission and within 72 h, respectively. New-onset hyperchloremia and every 5 mmol/L increment in Cl\u2212 were associated with increased 30-day mortality and poor 6-month outcome. However, hyperchloremia was not an independent predictor of poor outcome in multivariate models.Taken together, EEG has great potential for evaluating LVO and outcomes from large hemispheric infarction. In contrast, hyperchloremia may be iatrogenic from the use of hypertonic saline in the NICU and is not an independent predictor of poor outcome.Vitt et al. provided an excellent overview of stroke pathophysiology and current BP management. Ideal BP target after recanalization therapy depends on the degree of reperfusion and extent of infarction. Following complete recanalization, lower BP target is reasonable to prevent reperfusion injury. However, randomized clinical trials are warranted to define optimal BP goals during and after recanalization therapy.Extreme blood pressure (BP) and hemodynamic instability in stroke patients are associated with worse outcome. Melinosky et al. analyzed beat-to-beat variation of electrocardiogram (ECG) and photoplethysmogram (PPG) as well as waveform features during the first 15\u201360 min to identify physiologic parameters associated with future ND. Among 191 patients, 33 (17%) developed ND. Both ECG and PPG analyses during the first 15 min predicted ND better than did clinical characteristics. Predictive probability for ND by a PPG analysis at 15 min (p = 0.03) was independently associated with inpatient mortality. Early vital sign variation appears to be a promising biomarker of outcome prognostication in TBI.In patients with traumatic brain injury (TBI), one of the major goals is to identify and prevent secondary neurological decline (ND). Nguyen et al. provided an excellent review of targeted temperature management (TTM) and multimodality monitoring in modern NICU. TTM is neuroprotective for patients with anoxic brain injury. Current guidelines recommend the use of TTM for comatose survivors after out-of-hospital cardiac arrest from a shockable rhythm. Neurointensivists are central in the patient evaluation, management, and prognostication. Established prognostic tools include clinical exam, somatosensory evoked potential (SSEP), EEG, and MRI. Currently, functional MRI and invasive monitoring are not validated in prognostication, and further studies on biomarkers of poor outcomes are warranted.2) measured by near-infrared spectroscopy (NIRS) can be used to monitor brain oxygenation and acute brain injury (ABI) in extracorporeal membrane oxygenation (ECMO). Khan et al. evaluated the association between rScO2 and ABI in ECMO patients. Among 18 study patients, 11 (61%) experienced rScO2 desaturations and 6 (33%) exhibited ABI. All ABI patients experienced rScO2 desaturation as compared with 42% patients without ABI (p = 0.04). The presence and burden of cerebral desaturations noted on NIRS cerebral oximetry are associated with secondary ABI in ECMO patients. Monitoring of rScO2 may be applicable in ECMO and TBI patients.Regional cerebral oxygen saturation and transient evoked otoacoustic emissions (TEOAEs) were measured in cardiac arrest patients and 10 patients with myocardial infarction as controls. Compared with controls, cardiac arrest patients had significantly less preserved DPOAE . TEOAEs were not statistically different between the two groups. Despite convenience, otoacoustic emissions were unreliable prognostic markers in cardiac arrest survivors.Yuan F et al. reported a retrospective study of 94 patients with SE from autoimmune encephalitis. There were 23.4% SRSE and 76.6% non-SRSE. Cortical or hippocampal abnormality on neuroimaging and Encephalitis-Non-convulsive Status Epilepticus-Diazepam Resistance-Image Abnormalities-Tracheal Intubation (END-IT) score were found to be independent predictors of progression to SRSE. Recurrent clinical or EEG seizures, tracheal intubation, and emergency resuscitation predict poor functional outcome.Status epilepticus (SE) is the most serious complication of acute encephalitis. Early progression to super-refractory SE (SRSE) is associated with poor outcome. Jiang et al. reported the use of quantitative EEG (qEEG) to predict the outcome of anti-N-methyl d-aspartate receptor (anti-NMDAR) encephalitis. Twenty-six patients were divided into critically ill (n = 14) and non-critically ill (n = 12) group on the basis of ICU admission. All patients underwent 2-h 10-channel qEEG recordings at the acute stage. No difference in qEEG parameters was observed between the two groups. A logistic regression analysis revealed that a narrower parietal amplitude-integrated EEG bandwidth was associated with favorable long-term outcomes .These studies suggest that neuroimaging and qEEG may be used together to predict outcome of acute encephalitis.In summary, multimodality monitoring has been rigorously investigated in patients with TBI and subarachnoid hemorrhage in the last two decades. Although invasive multimodality monitoring may provide evidence of pathophysiological changes in a local area near the implanted probe, it is associated with risk of periprocedural complication and low sensitivity for the detection of changes in other brain regions. The articles in this Research Topic collection have presented new insight on non-invasive multimodality monitoring and vital sign variability analysis in prognostication of patients with large hemispheric infarction, acute encephalitis, and acute brain injury. The collection has also included judicious appraisal of targeted temperature management after cardiac arrest and blood pressure goals after endovascular thrombectomy. Currently, it remains challenging to predict secondary brain injury and outcome. This Research Topic article collection will stimulate future research on the development of integrated and reliable non-invasive monitoring and clinical evaluation tools in modern NICU.LL and WY contributed to the drafting of this Editorial for the Research Topic that they edited. WY made critical revision and finalized the editorial.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Genetic heterogeneity of tumor is closely related to its clonal evolution, phenotypic diversity and treatment resistance, and such heterogeneity has only been characterized at single-cell sub-chromosomal scale in liver cancer. Here we reconstructed the single-variant resolution clonal evolution in human liver cancer based on single-cell mutational profiles. The results indicated that key genetic events occurred early during tumorigenesis, and an early metastasis followed by independent evolution was observed in primary liver tumor and intrahepatic metastatic portal vein tumor thrombus. By parallel single-cell RNA-Seq, the transcriptomic phenotype of HCC was found to be related with genetic heterogeneity. For the first time we reconstructed the single-cell and single-variant clonal evolution in human liver cancer, and dissection of both genetic and phenotypic heterogeneity will facilitate better understanding of their relationship. The genetic heterogeneity in hepatocellular carcinoma (HCC) has been extensively studied by bulk or multi-region sequencing , 2, and Great inter-tumor genetic heterogeneity of HCC was revealed by pseudo-bulk whole exome sequencing (WES), with different somatic mutations and mutational signatures observed among patients database. The synonymous mutations were further filtered. This table is related to Fig S2.Additional file 4: Table S2. Mutation sites and amplification primers for single-cell target sequencing. This table shows the full list of target sites and PCR primers used in single-cell target amplification for HCC1, HCC2, HCC9 and HCC8. The primer sequences include the adaptor sequences that can be used for downstream library preparation with illumina Nextera XT Index Kit and multi-plexed sequencing."} +{"text": "Mycobacterium tuberculosis complex (MTBC) comprise seven phylogenetic lineages originally associated with their geographical distribution. Here, we report the genomes of three drug-resistant clinical isolates of the Latin American-Mediterranean (LAM) family collected in Kazakhstan. We utilised whole-genome sequencing to study the distribution and drug resistance of these isolates. Phylogenetic analysis grouped the genomes described in this study with the sequences from Russia, Uzbekistan, and Kazakhstan belonging to the LAM family. One isolate has acquired extensive drug resistance to seven antituberculosis drugs. Our results suggest at least two multi-drug resistant (MDR)/extensively drug-resistant (XDR)-associated genotypes of the LAM family circulate in Kazakhstan.The human-adapted strains of the Mycobacterium tuberculosis is a human pathogen with diverging lineages initially associated with a specific geographic region.M. tuberculosis complex (MTBC) are distinguished as ancient and modern. The ancestral lineages include lineage 1 (Indo-Oceanic), lineage 5 (West Africa 1), lineage 6 (West Africa 2), while recently discovered lineage 7 (Ethiopia) appears to be intermediate between the ancient and modern ones.,M. tuberculosis observed in Kazakhstan after the Beijing family.6110 into the plcA gene.M. tuberculosis Beijing genotype.,M. tuberculosis isolates from 12 provinces of Kazakhstan (51/470 = 10.85%).,6110 insertions.Kazakhstan is among the 30 countries with the highest burden of multidrug-resistant tuberculosis in the world.M. tuberculosis isolates collected in Nur-Sultan city, Kazakhstan. Epidemiology of M. tuberculosis including lineage 4 is routinely studied by the analysis of single nucleotide polymorphisms (SNP), RD loci, IS6110-restriction fragment length polymorphisms (RFLP), spoligotyping, and/or mycobacterial interspersed repetitive units (MIRU)-typing.in silico analysis of the epidemiological characteristics of the local LAM isolates.Thus, we provide the whole-genome sequencing data of three LAM isolates from a collection of drug-resistant M. tuberculosis strains was isolated in Nur-Sultan, Kazakhstan, from sputum of patients with clinically suspected tuberculosis. The drug susceptibility was tested using a Bactec MGIT 960 culture system according to the manufacturer\u2019s protocol. DNA was extracted using the cetyltrimethylammonium (CTAB) procedure.fbpC codon 103 (Rv0129c) was carried out using the CFX96 Touch System . Three LAM isolates were SNP-confirmed for sequencing .A collection of 28 drug-resistant de novo assembly with SPAdes v.3.14.1.,,Isolates no. 3538 and 4142 were sequenced using a MiSeq platform and the other LAM isolate no. 4330 using an Ion Torrent platform (Thermo). For the MiSeq sequencing, libraries with an average fragment size of 600 bp were prepared using a Nextera DNA Flex Library Prep kit (Illumina) according to the manufacturer\u2019s instructions. A barcoded library for the isolate no. 4330 was prepared using an Ion Xpress Plus fragment library kit and an Ion Xpress barcode adapters 1-16 kit (Thermo). The median library size of 480 bp for the adapter-ligated 400-base-read library was size-selected with E-Gel SizeSelect II Agarose Gel . The sequencing was conducted on the Ion Torrent PGM sequencing platform using a Hi-Q sequencing kit (Thermo) and a 318 Chip (Thermo) as described previouslyin silico spoligotyping was performed by SpoTyping 2.1 and the assignment of regions of deletion was accomplished by TB-Profiler.,6110 insertions, and spoligoprofiles with a set of primers by Kamerbeek, J et al.An Supplementary data (Table)]. The filtered sequence reads were mapped using the BWA-MEM program with M. tuberculosis H37Rv (NC_000962.3) reference genome sequence.,Mycobacterium canettii as an out-group. The phylogenetic tree was visualised with FigTree software v.1.4.4.An SNP matrix was produced by comparing SNPs found between the studied genomes, and sequences of 81 MTBC isolates . This data set included fifty published genomic sequences representing phylogeny of M. tuberculosis lineage 4 according to Coll et al.Finally, we conducted a maximum-likelihood phylogenetic analysis. A phylogenetic tree was constructed based on overall SNPs extracted from 84 MTBC genomic DNA sequences including WGS data from this study [in silico spoligotyping, assignment of RD loci as well as IS6110 insertions. The obtained genomes have provided new data on the genetic variations occurring in the drug-resistant LAM family isolates circulating in Central Asia. We found two MDR/XDR-associated genotypes of the LAM family circulating in Kazakhstan (SIT42 and SIT42/LAM-RUS). We are deeply concerned with the acquired extensive and multi-drug resistance in the local LAM family isolates. Further expansion of these drug-resistant clones represents a threat to regional TB control and the effectiveness of standardised treatment strategy. One of the limitations of the current research was the collection of genomic sequences that is not comprehensive to confirm the origin and migration pathways of the studied LAM isolates. A further comparison of the obtained WGS data with the other circulating LAM sublineage 4.3.3 isolates is needed to reveal the genetic differences responsible for the pathogenicity and transmission success of the LAM isolates.Contribution of the present data when comparing to earlier studies is WGS-based genotypic prediction of drug-resistance combined with epidemiological genotyping that covered Accession numbers - This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. JABACH000000000, JABACG000000000, and JABACF000000000. The raw Whole Genome Shotgun data was submitted to the NCBI SRA. SRA accession numbers are listed in"} +{"text": "This was a cross-sectional study describing HIV testing uptake and ART initiation for pregnant women and HIV-exposed infants after one-off clinical mentorship training in 2013 for nurses in 56 peripheral health-facilities, Zimbabwe. Between 2014-2018, 92% of 106411 pregnant women were HIV tested and 98% of HIV-positive women initiated antiretroviral therapy (ART). There were 15846 HIV-exposed infants, of whom 96% had dried blood spots collected for virologic diagnosis and 51% of those diagnosed HIV-positive initiated ART. In conclusion, this one-off clinical mentorship training in 2013 was associated with consistently high HIV testing and ART initiation in pregnant women and their children. Despite good global progress in the prevention of mother-to-child transmission of HIV (PMTCT), implementation is still inadequate with an estimated 180,000 new HIV infections in children and just 52% of HIV-infected children accessing antiretroviral therapy (ART) in 2017 . We wereThis was a cross-sectional study using routinely collected secondary aggregate data. The clinical mentorship training for nurses included five-days of classroom training by clinicians and nurses, seven-days when the nurse was attached to a clinician involved in ART care and four-months of supervision from a clinical mentor and multidisciplinary team observing nurse\u00b4s practices in HIV and ART management and care . EGPAF oFrom 2014-2018, there were 106411 pregnant women enrolled in antenatal care, 97829 (92%) were HIV tested, 6097 (6%) were HIV-positive and 6004 (98%) were started on ART. Annual HIV testing uptake ranged from 91%-93%. ART initiation in those diagnosed HIV-positive ranged from 97%-99%. Characteristics associated with HIV testing uptake and ART initiation are shown in Following the clinical mentorship training in 2013, annual HIV testing uptake in pregnant women was consistently high >90% and ART initiation in HIV-positive women was also consistently high >95%. These findings align with national reports, and compThis may be due to our use of aggregate rather than individual cascade data, possible data documentation errors or a true reflection of MTCT in rural Zimbabwe. A recent review in Ethiopia showed that while the pooled MTCT prevalence was 10%, this ranged from 5-15% in different parts of the country . Study sAfter one-off clinical mentorship training for nurses on PMTCT in 56 health-facilities in Zimbabwe, there was consistent high uptake of HIV testing and ART initiation in pregnant women and collection of DBS in HIV-exposed children. However, initiation of ART in children was sub-optimal. With changing PMTCT practices in Zimbabwe and a move from paper-based to electronic data-capture systems further clinical mentorship training for nurses should be considered.Clinical mentorship program involving a change from doctor-led to nurse-led task shifting is feasible and results in improvement in HIV testing uptake and ART initiation for both pregnant mothers and their HIV exposed babies;Nurse led-ART has been shown to improve both HIV testing uptake and ART initiation of pregnant women and their HIV positive babies.A one-off clinical mentorship programme has the potential to maintain consistently high annual HIV testing (at > 90%) and ART initiation in HIV positive pregnant mothers (at >95%) even three to four years post mentorship;Both accessibility to health facilities and dose-responses to DBS uptake and ART initiation were observed as urban facilities and facilities with at least one trained nurses showed a higher performance of DBS uptake and ART initiation."} +{"text": "Neurosarcoidosis (NS) is a mimicker of many infectious, neoplastic, and inflammatory diseases. It most commonly involves the cranial nerves followed by meninges, ventricles, hypothalamic-pituitary axis, spinal cord, and brainstem/cerebellum. While NS myelopathy has been increasingly recognized, pathophysiological/prognostic and management principles in NS-mediated cauda equina (CE) and conus medullaris (CM) syndromes, which constitute a small and rare minority of this subset, remain elusive. We present the case of a 49 -year-old Hispanic man who developed a peripheral facial palsy and primary hypogonadism within a span of 12 months and eventually got diagnosed with NS after he presented with CE syndrome. We also performed an extensive literature review, with a discussion on the underlying pathophysiology and current management recommendations for NS-mediated CE/CM syndrome. CE/CM syndromes in a middle-aged man should prompt the consideration of NS as a possible differential diagnosis. While steroid responsive, the majority of NS-CE/CM patients are left with residual neurodeficits with quick relapses when steroids are tapered, making the case for early institution of immunosuppressive therapies. Sarcoidosis is an autoimmune multi-organ inflammatory disorder histologically characterized by diffuse infiltration of non-caseating granulomas, with an estimated incidence of 7.6-8.4/100, 000 2010-2013) in the United States > II [21%] > V [12%] > VIII [11%]), headache in 32%, sensory symptoms in 29%, and motor weakness in 19% [A diagnosis of NS is typically established via a neural/non-neural biopsy demonstrating the pathologic hallmark of non-caseating epithelioid granulomas in the absence of an infection , inflammation (inflammatory bowel disease), malignancy (lymphoma), and foreign body/elements (silica) . ConsensLiterature reviewMost patients with systemic sarcoidosis do not require therapy . HoweverInvolvement of the spinal cord in NS is rare. The current body of evidence on the management and prognosis of patients with NS-CE/CM syndrome is based on short case series and suggests that while the disease is steroid responsive, the vast majority of these patients will be left with residual neurological deficits with quick relapses when steroids are tapered. Prospective studies evaluating the role of IS at initial presentation of spinal cord disease in patients with NS are urgently required to minimize the morbidity caused by this disorder."} +{"text": "Although cardiac involvement is an important prognostic factor in patients with sarcoidosis, cardiac sarcoidosis (CS) is often difficult to diagnose. Cardiac magnetic resonance (CMR) imaging with late gadolinium enhancement (LGE) is considered to be useful in identifying CS early.We investigated LGE characteristics in patients with CS.The study included 17 patients who were diagnosed with CS by Japanese Ministry of Health and Welfare criteria and underwent CMR. Among the 17, 15 had LGE and were evaluated retrospectively. We obtained LGE images using an inversion recovery segmented gradient-echo sequence 10 minutes after we administered gadolinium-DTPA (0.15 mmol/Kg or 20 mL). We analyzed patterns (patchy or band-like appearance) and locations of LGE in LV using a 17-segment model. We also assessed the extent of LGE in each segment of LV . We evaluated relationships between LGE characteristics and LV function using cine MR images.We observed band-like LGE with distinct margin in 14 patients and patchy LGE in one. The band-like pattern correlated well with pathological findings in biopsy-proven CS. Transmural LGE (T-LGE) was observed in 7 patients. All patients with T-LGE also had subepicardial lesion. In the patients without T-LGE, LGE was most common in the subepicardial layer (74% of enhanced segments) and most frequently observed in the basal septal wall, especially on the RV side. The number of LGE segments of the patients with T-LGE was significantly larger than that of patients without T-LGE . The ejection fraction of the LV (LVEF) of the patients with T-LGE was significantly lower than that of patients without T-LGE , and the end-diastolic volume of the LV of the patients with T-LGE was significantly larger than that of patients without T-LGE .Characteristic LGE pattern and location allow accurate diagnosis of CS. CMR with LGE is useful for diagnosing CS and predicting LV function."} +{"text": "Each PED area was divided into peak and slope regions. RPE70 area ratios were compared with the maximum PED height, PED area, PED volume, and slope area ratio (area of slope region/area of whole PED). RPE-melanin OCT images were consistent with near-infrared autofluorescence images. The RPE70 area ratio in the slope region was significantly negatively correlated with the slope area ratio. Development of active RPE lesions in the slope region was correlated with the PED configuration. Multi-contrast OCT is useful for objective evaluation of changes in the RPE in patients with age-related macular degeneration.The purpose of this study was to quantitatively evaluate retinal pigment epithelium (RPE) changes in serous pigment epithelial detachment (PED) among patients with age-related macular degeneration by means of prototype multi-contrast optical coherence tomography (OCT), which is capable of simultaneous collection of OCT angiography, polarization-sensitive OCT, and standard OCT images. We evaluated 26 eyes of 21 patients with serous PED. RPE-melanin OCT images were calculated from the multi-contrast OCT dataset and compared with near-infrared autofluorescence images. An active RPE lesion was defined as an area of thickened RPE-melanin (\u2265\u200970\u00a0\u03bcm; RPE Alterations of the retinal pigment epithelium (RPE) are an important sign of AMD4. Pigment epithelial detachment (PED) is a common finding in patients with AMD5. In eyes with a PED, especially those with a drusenoid PED, RPE cells show various responses, including sloughing, shedding, hypertrophy, and intraretinal migration9. These RPE changes are presumed to be important indicators of RPE function7. Therefore, clinical evaluation of RPE changes in PED is crucial for the clinical management of AMD.Age-related macular degeneration (AMD) is a leading cause of vision loss in elderly adults12. AF signals in short-wavelength AF imaging are presumed to originate from lipofuscin or melanolipofuscin13, while AF signals in near-infrared AF imaging are presumed to originate from melanin or melanolipofuscin16. Simultaneous hyper-AF lesions in both SW-AF and NIR-AF are presumed to arise from an increased concentration of melanolipofuscin in RPE cells12, as well as RPE dysmorphia (greater cell height) and intraretinal RPE migration8. Although clinical AF imaging is widely used to evaluate RPE changes, the absence of topographic information remains an important limitation of AF imaging.Clinical autofluorescence (AF) imaging is widely used to evaluate RPE changes in AMD17. Some intraretinal hyperreflective foci in standard OCT images have been attributed to intraretinal RPE migration18, which might be the origin of hyper-AF lesions8. If RPE cells are lost because of RPE migration, one would expect hypo-AF in the RPE layer18. One class of thickened RPE-Bruch\u2019s membrane band in standard OCT might represent RPE dysmorphia and stacked RPE cells19. Standard OCT can provide important information concerning RPE changes; however, the evaluation of RPE cells using standard OCT is limited by the lack of specific contrast to RPE cells, which impedes direct comparisons with AF images.Intensity-based optical coherence tomography is another essential clinical tool for evaluation of RPE changes21. Multiple scattered lights from melanin in the RPE induce depolarization or scrambled polarization22. Comprehensive evaluation of RPE changes in AMD can be performed using a combination of polarization-sensitive OCT and AF imaging24. However, the evaluation of RPE changes by polarization-sensitive OCT has some limitations, including a lack of discriminability between melanin in the RPE (RPE-melanin) and melanin in the choroid. In projection images captured by polarization-sensitive OCT, RPE changes are obscured by depolarization involving choroidal melanin25. To overcome this limitation, we developed an automatic highlighting algorithm for RPE-melanin using multi-contrast OCT (MC-OCT)26, which enables simultaneous collection of OCT angiography, polarization-sensitive OCT, and standard OCT images29. From the MC-OCT dataset, we derived RPE\u2013melanin-specific contrast OCT (RPE-melanin OCT) images, which we used to evaluate RPE changes26. In our previous studies of patients with AMD26 and patients with Vogt\u2013Koyanagi\u2013Harada disease25, we confirmed similarities between NIR-AF images and RPE-melanin OCT projection images. Thus, the combination of RPE-melanin OCT and AF imaging might be useful for evaluation of RPE changes in PED. In this study, we evaluated RPE changes in serous PEDs by means of AF and MC-OCT imaging. We also analyzed the relationships of RPE changes with PED parameters.Polarization-sensitive OCT is a functional extension of OCT technology that permits advanced tissue differentiation in retinal disease30 data from a single measurement. Standard OCT B-scan images showed a thickened RPE band and intraretinal hyper-reflective foci in hyper NIR-AF lesions on each A-line in the three-dimensional dataset. The resulting chorioretinal melanin thickness map represents the overall thickness of melanin in the choroid and RPE. DOPU B-scan images in polarization-sensitive OCT clearly showed melanin accumulation in the RPE band, as well as intraretinal melanin migration based on the concept of feature engineering by the presence or absence of blood flows26. Melanin in both the RPE and choroid showed low DOPU due to depolarization. However, the OCT angiography signal in the RPE cells was low because vascularization was absent, whereas the choroid showed a high OCT angiography signal because of its dense vasculature. The presence of high FRPE is presumed to indicate the presence of RPE-melanin. The RPE-melanin B-scan images were used to determine the distribution of FRPE in the B-scan images, which enabled evaluation of the depth-resolved distribution of RPE-melanin. RPE-melanin thickness maps were created by counting the number of pixels with high FRPE (\u2265\u20090.15) on each A-line in the volume dataset. RPE-melanin thickness maps clearly showed the en face distributions of these melanin changes. Greyscale RPE-melanin thickness maps were similar to both NIR-AF and SW-AF images in all patients were distributed in both the peak and slope regions in 19 eyes revealed that the RPE70 areas in both whole PED and the slope region showed significant positive correlations with PED volume were calculated. First, simple linear regression analysis was performed between RPE70 area ratios and morphometric PED parameters in both the whole PED and the slope region ; the RPE70 area was significantly greater in the slope region than in the peak region. This frequent occurrence of RPE changes in the slope region was also reported in drusenoid PEDs6, despite a possibly larger contribution of hypoxia with the presence of drusenoid material. The development of RPE activation in the slope region suggests the presence of induction factors other than hypoxia. One possible explanation involves size: there was a close relationship between the RPE70 area and the PED area, according to simple linear regression analysis in MC-OCT imaging was used to calculate the area of RPE melanin defects, in accordance with the method used in our previous studies26. With this threshold, the RPE-melanin line at the normal RPE band occasionally became unclear . Among them, three patients were treated for hypertension, one patient was treated for diabetes, and one patient was treated for both hypertension and diabetes. To exclude the influence of these systemic diseases, eyes with retinal diseases other than AMD were excluded. Patients were considered to have \u201cserous PED\u201d when they exhibited serous PED without retinal hemorrhage, hard exudates, or choroidal neovascularization. OCT angiography images obtained from commercial OCT and MC-OCT were used to exclude eyes with choroidal neovascularization. To avoid the possible influence of treatments for AMD, eyes with prior intravitreal injection or laser treatment were excluded. Eyes with severe cataract or other eye diseases that could significantly compromise the image quality were also excluded from this study.http://www.umin.ac.jp/ctr/index-j.htm). Written informed consent was obtained from each participant before any study procedures or examinations were performed.This prospective, observational, cross-sectional study followed the tenets of the Declaration of Helsinki, and Institutional Review Board approval was obtained from the Tokyo Medical University Institutional Review Board (IB-1615 and T2019-0072). The study was registered in a public database was defined as the peak region, while the outer residual area of the PED was defined as the slope region was computed using an attenuation coefficient43, the DOPU, and the blood flow signal in OCT angiography, as follows26:b is the binarized OCT angiography signal. This index was computed to selectively represent RPE-melanin by the absence of blood flow in the RPE. The RPE-melanin B-scan images were computed as the distribution of FRPE in the B-scan images; this enabled evaluation of the depth-resolved distribution of RPE-melanin. RPE-melanin thickness maps were created by counting the number of pixels with high FRPE (\u2265\u20090.15) on each A-line in the volume dataset. The area of thickened RPE-melanin (RPE70:\u2009\u2265\u200970\u00a0\u03bcm) was calculated from RPE-melanin thickness maps using image-processing software (FIJI)41 and SW-AF images were obtained using an HRA2 , and were saved in eight-bit greyscale images. For comparison of AF images and MC-OCT images, retinal vascular architecture was manually aligned across images using image processing software . A retina specialist (T.I.) subjectively evaluated the distribution of hyper-AF lesions.Supplementary Information."} +{"text": "Pseudomonas aeruginosa and Staphylococcus aureus . The 30-day case-fatality of VAP was 46% (78/171). In multivariable analysis, septic shock at VAP onset and acute respiratory distress syndrome at VAP onset were associated with fatality. In conclusion, VAP is frequent in critically ill COVID-19 patients. The related high fatality is likely the sum of the unfavorable prognostic impacts of the underlying viral and the superimposed bacterial diseases.The primary objective of this multicenter, observational, retrospective study was to assess the incidence rate of ventilator-associated pneumonia (VAP) in coronavirus disease 2019 (COVID-19) patients in intensive care units (ICU). The secondary objective was to assess predictors of 30-day case-fatality of VAP. From 15 February to 15 May 2020, 586 COVID-19 patients were admitted to the participating ICU. Of them, 171 developed VAP (29%) and were included in the study. The incidence rate of VAP was of 18 events per 1000 ventilator days . Deep respiratory cultures were available and positive in 77/171 patients (45%). The most frequent organisms were Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Most clinically detectable infections are mild to moderate, but cases of severe pneumonia requiring intensive care unit (ICU) admission may be observed ,4.The clinical presentation of COVID-19 pneumonia includes fever, leukocytosis, severe hypoxemia, bilateral infiltrates, and multisystemic inflammatory syndrome with possible multiorgan failure (MODS-CoV-2) ,6. Some The primary objective of this observational, multicenter study was to assess the incidence rate of VAP in COVID-19 patients. The secondary objective was to assess predictors of 30-day case-fatality of VAP in COVID-19 patients.The present multicenter, observational, retrospective study was conducted in 11 intensive care units (ICU) across 9 centers in Italy , and specific informed consent was waived due to the retrospective nature of the study. The other participating centers followed the local ethical requirements.The diagnosis of COVID-19 was made in presence of at least one positive real-time polymerase chain reaction (RT-PCR) test for SARS-CoV-2 on respiratory specimen/s . VAP was defined as new or changing chest X-ray infiltrate/s occurring more than 48 h after initiation of invasive mechanical ventilation, plus both of the following: (i) new onset of fever (body temperature \u2265 38 \u00b0C)/hypothermia (body temperature \u2264 35 \u00b0C) and/or leukocytosis /leukopenia / > 15% immature neutrophils; (ii) new onset of suctioned respiratory secretions and/or need for acute ventilator support system changes to enhance oxygenation /mL) rather than qualitative information from positive BALF cultures, as well as quantitative data from endotracheal aspirate cultures . We acknowledge this was an arbitrary decision in order to identify what we thought was the best subgroup for a more plausible estimation of etiological diagnosis considering the limited available data collected during routine practice in the first months of the COVID-19 pandemic. In this regard, the lack of many microbiological data certainly remains a major limitation of the present study, since all of this lacking microbiological information could have been exploited either for a more precise selection of the subgroup of patients with microbiological diagnosis of VAP or for exploring the possible prognostic effects of different CFU/mL counts. Third, in line with the used VAP definition , and besVAP may be frequent in critically ill COVID-19 patients, but its clinical diagnosis remains difficult. The high 30-day case fatality of VAP we observed likely represents the sum of the prognostic effects of the underlying viral and the superimposed bacterial diseases. Further investigation is needed to precisely characterize the relative contribution of these effects and further improve our therapeutic approach to both COVID-19 and superimposed VAP."} +{"text": "N-(2-hydroxypropyl)methacrylamide] in an in vivo animal solid tumor model. We used radiolabeled biodegradable hydroxyapatite NPs as a model nanoparticle core within this study and we anchored the polymers to the NPs core by hydroxybisphosphonate end groups. The general suitability of polymers for coating of NPs intended for solid tumor accumulation is that poly(2-ethyl-2-oxazoline) and poly(ethylene oxide) gave comparably similar very good results, while poly[N-(2-hydroxypropyl)methacrylamide] was significantly worse. We did not observe a strong effect of molecular weight of the coating polymers on tumor and organ accumulation, blood circulation time, biodistribution and biodegradation of the NPs.Nanoparticles (NPs) represent an emerging platform for diagnosis and treatment of various diseases such as cancer, where they can take advantage of enhanced permeability and retention (EPR) effect for solid tumor accumulation. To improve their colloidal stability, prolong their blood circulation time and avoid premature entrapment into reticuloendothelial system, coating with hydrophilic biocompatible polymers is often essential. Most studies, however, employ just one type of coating polymer. The main purpose of this study is to head-to-head compare biological behavior of three leading polymers commonly used as \u201cstealth\u201d coating materials for biocompatibilization of NPs poly(ethylene oxide), poly(2-ethyl-2-oxazoline) and poly[ HoweverHydrophilic poly(2-oxazoline)s such as poly(2-ethyl-2-oxazoline) are modeN-(2-hydroxypropyl)methacrylamide] is, except for biocompatibilization of nanoparticles, often used for the construction of water-soluble drug delivery systems -based and poly(2-ethyl-2-oxazoline)-based doxorubicin delivery systems in in vivo animal tumor models [99mTc-hydroxyethylidene diphosphonate (99mTc-HEDP) [N-(2-hydroxypropyl)methacrylamide] with weight-average molecular weights (wM) typically used for coating NPs were selected. The polymer-coated radiolabeled NPs were compared in an in vivo animal solid tumor model. To the best of our knowledge, no such study was published in literature in an in vivo animal solid tumor model. This study therefore offers general comparison of in vivo biological applicability of the three most often used biocompatible polymers for coating of inorganic core-based nanoparticles for diagnostics, therapy and theranostics of various diseases such as cancer demonstrating it on in vivo animal model.Majority of studies however employ just one type of coating polymer while head-to-head comparison of different biocompatible polymers is largely missing for most biomedical applications related to various diseases. Recently, we published a comparison of antitumor efficacy of poly (wM 5 kDa - PHPMA5000). For the coating to the polymer solution (0.2 g in 4.4 mL of water) was added 0.07 g of the HAP NPs powder, the mixture was sonicated for 5 min and stirred under ambient conditions for 24 h. Coated NPs were purified by centrifugation and characterized with dynamic light scattering (DLS) and thermogravimetric analysis (TGA) .The HAP NPs were synthesized and coated as reported previously . Briefly99mTc-HEDP (~100 \u00b5L corresponding to 100\u2013150 MBq) as described previously (PHPMA) displayed slightly higher retention in lungs and almost no uptake in the tumor, probably due to too fast uptake into reticuloendothelial system given by worse protection of the HAP NPs core by PHPMA compared to the other polymers involved not giving the system enough blood circulation time to allow solid tumor accumulation. These results show similar high quality of polymer coating protecting the HAP nanoparticles from unwanted interactions in bloodstream and suitable in vivo stability of the nanoparticles on the nanoparticles. As all polymers possess the same HAP-anchoring terminal hydroxybisphosphonate moiety, the differences among the PHMPA-coated HAP NPs and the POX- and PEG-coated NPs is purely given by the nature of the coating polymer. We did not show the accelerated blood clearance (ABC) phenomenon for the PEG-coated HAP NPs sometimes observed for the PEG-based systems, probably because the mice were not pre-exposed to PEG-based system.Ex vivo biodistribution studies in healthy animals showed that n et al. and Khmen et al. . In cont99mTc-HEDP labeled HAP NPs tested 99mTc-PEG5000-HAP revealed the most favorable tumor-blood ratio (6.14 for 24 h p.i.) and 99mTc-PHPMA5000-HAP (0.99 for 24 h p.i.) the most unfavorable. Tumor-muscle ratios were in the range of 2.52 \u2013 6.91 for all PEG and POX coated HAP NPs at 24 h post injection. 99mTc-PHPMA5000-HAP showed again the lowest tumor-muscle ratio (1.01 for 24 h p.i.) from tested NPs. Based on these findings 99mTc-HEDP labeled PEG and POX HAP NPs were used for SPECT/CT imaging of tumor-bearing mice and PHPMA coated HAP NPs were excluded from further experiments.We have also not observed significant dependence of the biological behavior on the molecular weight of the polymer used for coating, so most plausibly event he lower molecular weight polymer is able to provide sufficiently dense coating to prevent unwanted interactions with the biological environment. Among the 99mTc-HEDP labeled HAP NPs coated with PEG or POX revealed pharmacokinetic properties as expected from ex vivo biodistribution studies: high activity uptake was observed in liver and spleen during all imaging time points and certain activity was present in heart and urinary bladder or human colorectal carcinoma (HCT116) was performed. Although, ex vivo biodistribution studies in HT-29 xenografted mice displayed clear uptake of 99mTc-PEG5000-HAP in the tumor and highest tumor-blood ratio among studied HAP NPs, we were not able to image either HT-29 or HCT116 tumor in mice with 99mTc-PEG5000-HAP using small animal SPECT/CT imaging system in any of studied time points after injection. The same results were obtained also for other PEG and POX coated HAP NPs.SPECT/CT scans performed with healthy mice injected with 99mTc labeled HAP NPs under study was not successful to visualize tumors, we started to reflect on the use of positron emitters for the radiolabeling of HAP NPs for positron emission tomography (PET) imaging. The main advantage of PET over SPECT is its spatial resolution, the ability of absolute quantification and higher sensitivity coated HAP NPs displayed significantly lower uptake in tumor tissue. Unfortunately, SPECT imaging was not successful in visualizing the tumor. We did not observe strong effect of molecular weight of the coating polymers on tumor and organ accumulation, blood circulation time, biodistribution and biodegradation of HAP NPs under the study.We have shown that HAP NPs coated with different polymers of varying molecular weights can be radiolabeled with"} +{"text": "F12 gene in a patient with angioedema induced by angiotensin-converting enzyme inhibitors. The reference described by Bork et al. as a new causal gene (Bork et al., PLG for variants in eight unrelated index patients from Germany with HAE-nC1-INH with unknown genetic causes (Dewald, Another recent WES study in families with HAE-nC1-INH with unknown genetic causes identified the plasminogen gene ( Dewald, . They alThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Introduction: Students in the Frontiers in Human Aging course at UCLA participate in service-learning (SL) with older adults. In 2020, completion of SL coincided with the outbreak of the novel coronavirus disease (COVID-19) pandemic. We evaluated the impact of SL on student attitudes on aging and community service in the context of the pandemic. Methods: Students were assigned to senior residential and daycare programs for 18-20 hours of SL. A retrospective pretest-posttest survey asked about attitudes and interests before and after SL and how the COVID-19 pandemic affected these perceptions; 73 (of 103) students responded. Mean differences before and after SL were tested and differences were assessed within groups reporting COVID-19 effects. Results: SL improved students\u2019 attitudes and ability to engage with older adults, knowledge about aging concepts, interest in future work with older adults, attitudes on community service, social well-being and feelings of usefulness (p<0.001). There was no significant change in overall anxiety about aging (p=0.1), however, students showed increased anxiety about losing independence and finances when older (p<0.05). At least 50% of students reported that the COVID-19 pandemic increased their awareness of needs of older adults (81.9%) and decreased connection to their peers (50.7%); the impact of SL remained unchanged by these effects. Conclusion: Despite the overall benefits of SL, increased anxiety about aspects of aging suggests the need to address these concerns. While the COVID-19 pandemic did not seem to affect the impact of SL, this event did seem to influence perceptions about aging and social integration."} +{"text": "This study assessed the anterior chamber depth (ACD) and iridocorneal angle using a portable smart eye camera (SEC) compared to the conventional slit-lamp microscope and anterior-segment optical coherence tomography (AS-OCT). This retrospective case-control study included 170 eyes from 85 Japanese patients. The correlation between the ACD evaluations conducted with the SEC and conventional slit-lamp was high (r = 0.814). The correlation between the Van-Herick Plus grade obtained using two devices was also high (r = 0.919). A high kappa value was observed for the Van-Herick Plus grading (Kappa = 0.757). A moderate correlation was observed between the ACD measured using AS-OCT and the slit-lamp image acquired with the conventional slit-lamp microscope and SEC (r = 0.609 and 0.641). A strong correlation was observed between the trabecular-iris angle (TIA) measured using AS-OCT and Van-Herick Plus grade obtained with the conventional slit-lamp microscope and SEC (r = 0.702 and 0.764). Strong correlations of ACD evaluation and high kappa value of the Van-Herick Plus grading indicated the adequate subjective assessment function of the SEC. Moderate correlations between the ACD objective measurement and evaluation and strong correlation between the TIA and Van-Herick Plus grade suggested the good objective assessment function of the SEC. The SEC demonstrated adequate performance for ACD evaluation and angle estimation. The slit-lamp microscope is the most commonly used diagnostic instrument in daily ophthalmological practice . One of The retrospective study adhered to the tenets of the Declaration of Helsinki. The clinical trial was registered with the University Hospital Medical Information Network Center (UMIN-CTR: UMIN000040321). The study protocols were approved by the institutional ethics review board (IRB) of Keio University School of Medicine, Tokyo, Japan (IRB No. 20200021). Written informed consent was obtained from all patients via an agreement document.A fellow (T.K.) and resident (R.S.) reviewed the database of the Department of Ophthalmology, Keio University School of Medicine, to screen for eligible patients.A fellow or resident recorded the eye images by SEC for the prediagnosis and an attending physician used the conventional slit-lamp microscope for confirming the diagnosis. The inclusion criteria were as follows: (1) Japanese men and women (above 20 years of age), (2) patients who underwent slit-lamp examination with both conventional slit-lamp microscopy and SEC, and (3) patients who underwent AS-OCT examinations on the same visiting date. The exclusion criteria were as follows: (1) pseudophakic eyes, (2) aphakic eyes, and (3) eyes with mydriasis because it could possibly alter the spherical curve of the lens. Sample size calculation yielded a required sample size of 146 eyes . Therefore, we enrolled 170 eyes from 85 Japanese patients between August and September 2020. A fellow (T.K.) and resident (R.S.) extracted all the data from the electronic medical records . The extracted data were randomized by a random digit panel to avoid any bias and classified into the following datasets: (I) slit-lamp photographs obtained using the conventional slit-lamp microscope, (II) slit-lamp videos obtained using the SEC, and (III) the objective anterior chamber value in the form of AS-OCT findings (ACD and TIA). An attending physician (S.S.) subjectively evaluated all the (I) slit-lamp images and (II) SEC videos after data curation in a masked manner to avoid bias and determined whether the depth of the anterior chamber was deep or shallow subjectively. Next, the physician evaluated the Van-Herick Plus grade by focusing on the inferior corneal angle. To facilitate performance of the two devices, the correlation analysis and reproducibility calculation were performed between the conventional slit-lamp microscope and the SEC (the depth of the anterior chamber and Van-Herick Plus grading). Moreover, to confirm similar performance between the two devices, the correlation analysis was performed between (III) the objective anterior chamber value from AS-OCT (ACD or TIA) and either subjective depth of the anterior chamber or Van-Herick Plus grading.Several conventional slit-lamp microscopes were used for anterior chamber image acquisition: the SL130 , 700GL , and SL-D301 . These slit-lamp microscopes are non-portable and are normally used in the conventional examination room . Each anCorneal/AS-OCT was performed using the CASIA2 Advance system . All participants were examined by several certified optometrists until at least two sets of images of sufficient quality were recorded. All the OCT scans were centered on the pupil and acquired along the vertical axis , using the CASIA system\u2019s standard anterior-segment scan protocol . The ACDAll data were analyzed using SPSS . The sample size calculation was performed based on the previous data [This study enrolled 170 eyes from 85 Japanese patients (45 men and 40 women). The participant\u2019s mean age was 44.393 \u00b1 19.798 years (range: 20\u201396 years). The size of a single ocular photograph acquired with the conventional slit-lamp and evaluated by the ophthalmologist was 696.364 \u00b1 103.571 kilobyte. The length of the video recorded by the SEC was 10.940 \u00b1 2.464 s . The ACDA total of 148 eyes were included in the correlation analysis. The correlation coefficient between the ACD measured with the conventional slit-lamp and SEC was high in the right, left, and both eyes , which addresses the problem of whether a disease is a public health problem , primary"} +{"text": "We describe a case of an acute myocardial infarction with an atypical electrocardiogram showing a de Winter T-wave pattern suggesting the 100% proximal left anterior descending artery occlusion seen on emergent cardiac catheterization.Timely recognition of acute myocardial ischemia is paramount for emergency providers. As highlighted in this case, It is important to be mindful of atypical electrocardiogram findings, such as de Winter T-waves, which suggest acute myocardial ischemia. A 56-year old male with a history of hypertension presented to the emergency department with one hour of crushing chest pain radiating to the left arm and neck. The symptoms began following exertion, but failed to alleviate with rest. Initial electrocardiogram (ECG) demonstrated hyperacute T-waves with associated ST-segment depression in the precordial leads, consistent with a de Winter T-wave patternEmergent cardiac catheterization was performed and revealed a 100% occlusion of the proximal left anterior descending artery . After sDe Winter T-waves are characteristic prominent, symmetric precordial T-waves with associated upsloping ST-segment depression at the J-point.3Diagnosis of AMI can be challenging. Emergency physicians are well trained to recognize the pattern of contiguous ST-segment elevations with reciprocal depressions that define traditional criteria for an ST-elevated myocardial infarction (STEMI)What do we already know about this clinical entity?De Winter T-waves are hyperacute precordial T-waves with associated upsloping ST-segment depressions that indicate acute anterior myocardial infarction (MI).What is the major impact of the image(s)?The electrocardiogram (ECG) demonstrates the de Winter T-wave pattern that emergency physicians must recognize as a ST-segment elevated MI equivalent.How might this improve emergency medicine practice?Recognition of atypical ECG patterns consistent with acute MI can facilitate prompt coronary intervention and salvage at-risk myocardium."} +{"text": "Targeted therapy of solid tumors represents a great challenge because of heterogeneity of tumor-associated antigen expression. To overcome this obstacle we propose a dual targeting therapy based on protein preparations capable of recognizing different of tumor-associated antigens on a tumor cell producing a directed cytotoxic effect. The dual specific therapy of breast carcinoma-bearing mice using the designed preparations eliminates both the primary tumor and distant metastases. The mono-targeting therapy aimed at single tumor-associated antigen did not suppress metastases at all. The proposed approach can serve as a potential therapeutic strategy that surpasses mono-specific targeting strategies in the anti-cancer efficacy.Pseudomonas aeruginosa exotoxin A and ribonuclease Barnase from Bacillus amyloliquefaciens. The delivery of toxins to cancer cells was carried out by targeting designed ankyrin repeat proteins (DARPins). We have shown that both target agents efficiently accumulate in the tumor. Simultaneous treatment of breast carcinoma-bearing mice with anti-EpCAM fusion toxin based on LoPE and HER2-specific liposomes loaded with Barnase leads to concurrent elimination of primary tumor and metastases. Monotherapy with anti-HER2- or anti-EpCAM-toxins did not produce a comparable effect on metastases. The proposed approach can be considered as a promising strategy for significant improvement of cancer therapy.We report here a combined anti-cancer therapy directed toward HER2 and EpCAM, common tumor-associated antigens of breast cancer cells. The combined therapeutic effect is achieved owing to two highly toxic proteins\u2014a low immunogenic variant of Cancer is a second leading cause of death globally and one of the biggest challenges facing biomedical scientists. Despite the considerable progress made in targeted cancer treatment, the heterogeneity of solid tumor greatly limits precision oncology therapy. Dual targeting strategies applying targeting moieties recognized different receptors in tumor population can be a solution of this problem.Tumor targeting with naked antibodies and antibody-drug conjugates has become an established strategy for cancer-related therapy in clinics, particularly if conventional therapies have failed ,2. HowevPreviously designed ankyrin repeat proteins (DARPins), a novel class of non-IgG scaffolds based on naturally occurring ankyrin repeats have beeThe transmembrane protein HER2 is one of the most well-studied tumor markers; its overexpression represents a hallmark of many types of tumors associated with an increased risk of metastasis and resistance to chemotherapy . The epiBacillus amyloliquefaciens /Vcontrol, where V is the tumor volume at a selected time point. Twelve days after the inoculation, when tumor volumes reached ~100 mm2/str).In vivo bioluminescence imaging was performed on IVIS Spectrum CT system . The BT-474/NanoLuc bearing mouse was placed in an anesthesia chamber and isoflurane inhalation was performed using the RAS-4 Rodent Anesthesia System . Furimazine was administered i.p. at a dose of 7 \u03bcg per animal, the mouse was then moved to the IVIS Spectrum CT imaging chamber, and data acquisition started one minute after the introduction of the substrate. All bioluminescence data were normalized to the acquisition conditions and are displayed in radiance (photons/s/cmThe data (MTT-test and tumor volume measurements) were statistically processed using one-way analysis of variance (ANOVA). The present study provides evidence that dual targeting therapy of solid tumors with protein-based toxic preparations recognizing different tumor-associated antigens is effective not only in eliminating the growth of primary tumor, but also in preventing the development of distant metastases. The proposed approach can be considered as a potential strategy with the efficacy significantly exceeding that of the mono-specific targeting therapy."} +{"text": "The pathophysiology of chronic obstructive pulmonary disease (COPD) relies on airway remodelling and inflammation. Alterations of mucociliary clearance are a major hallmark of COPD caused by structural and functional cilia abnormalities. Using transcriptomic databases of whole lung tissues and isolated small airway epithelial cells (SAEC), we comparatively analysed cilia-associated and ciliopathy-associated gene signatures from a set of 495 genes in 7 datasets including 538 non-COPD and 508 COPD patients. This bio-informatics approach unveils yet undescribed cilia and ciliopathy genes associated with COPD including NEK6 and PROM2 that may contribute to the pathology, and suggests a COPD endotype exhibiting ciliopathy features (CiliOPD). Cilia dysfunction is a hallmark of chronic obstructive inflammatory lung diseases . AlteratCellular processes related to cilia dysfunction such as autophagy may reprhttps://www.uniprot.org; date of retrieval July 27th 2020): (i) cilia-associated genes: \u201ccilia AND reviewed:yes AND organism:\"Homo sapiens (Human) [9606]\"\u201d yielded 447 entries; (ii) ciliopathy-associated genes: \u201cciliopathy AND reviewed:yes AND organism:\"Homo sapiens (Human) [9606]\"\u201d yielded 171 entries. Both lists of genes were compared and completed with the lists of cilia-associated genes and ciliopathy-associated genes described in the data from the 100,000 Genomes Project, CentrosomeDB, CilDB, SysCilia, and CiliaCarta.Human cilia-associated genes (n\u2009=\u2009447) and ciliopathy-associated genes n\u2009=\u2009189) were extracted from the reviewed (Swiss-Prot) records were ext, and thehttp://www.ncbi.nlm.nih.gov/geo; accession numbers: GSE47460, GSE57148, GSE76925, GSE103174, GSE11784, GSE37147, GSE56341). The expression of the genes of interest (human cilia-associated genes and ciliopathy-associated genes) was analysed depending on COPD status and expressed as fold-change compared to non-COPD. Associations with clinical/functional characteristics were searched. Analyses were performed separately in the lung compartment and in small airway epithelial cells (SAEC) .Previously published datasets of gene expression of whole lung tissue samples and small airways bronchoscopic samples obtained from non-COPD and COPD patients, that were available online, were collected .GSE plots contain all the genes of the genesets for each dataset. The y-axis is the log10 ratio obtained by dividing the mean of each gene\u2019s value in lung tissues or SAEC of non-COPD patients by its value in COPD patients. The Venn Diagram were designed with a tool from VIB/UGent correction was applied.A total of 7 public datasets of transcriptomic analysis of either whole-lung tissues (238 non-COPD and 391 COPD patients) or SAEC (300 non-COPD and 117 COPD patients) were analysed to identify an alteration of cilia- and ciliopathy-associated genes expression in COPD patients when compared with non-COPD patients and in all 3 SAEC databases , both being upregulated in COPD. Using single cell sequencing analysis, we confirmed that all commonly dysregulated genes (14 in lung datasets and 10 in SAEC datasets) were mainly expressed by multiciliated cells (motile cilia) and non-differentiated epithelial cells (primary cilia) and quiescence (ciliogenesis). Although experimental validation of the gene candidates that we identified will be needed, our results suggest alteration of cilia-related cellular and tissular processes that might have a role in COPD pathophysiology.Ciliopathies refer to genetic disorders that are caused by the abnormal formation or function of cilia. Since cilia and cilia-associated genetic signature are abnormal in COPD patients, COPD could be included in the spectrum of ciliopathies and ciliopathy-associated COPD (CiliOPD) may be considered as a COPD endotype.Additional file 1. Additional figures and tables."} +{"text": "Bacillus anthracis. Resilience to oxidative stress is essential for the manifestation of B. anthracis pathogenicity. Here, we announce transcriptome data sets detailing global gene expression in B. anthracis wild-type and htrA-disrupted strains following H2O2-induced oxidative stress.The high-temperature requirement chaperone/protease (HtrA) is involved in the stress response of the anthrax-causing pathogen Bacillus anthracis. Resilience to oxidative stress is essential for the manifestation of B. anthracis pathogenicity. Here, we announce transcriptome data sets detailing global gene expression in B. anthracis wild-type and htrA-disrupted strains following H2O2-induced oxidative stress.The high-temperature requirement chaperone/protease (HtrA) is involved in the stress response of the anthrax-causing pathogen Bacillus anthracis is the etiological cause of anthrax. The lethality of B. anthracis is attributed to its exotoxins and its optimal adaptation to tolerate stress constraints encountered in the course of infection and an htrA-disrupted strain, in biological triplicate or duplicate cultures . Total RNA was extracted using the RNeasy kit (Qiagen), and residual DNA was digested using RNase-free DNase (Qiagen). RNA-seq was performed in-house . Libraries were generated using the TruSeq RNA library prep kit version 2 (Illumina), assessed for correct sizing using a high-sensitivity Bioanalyzer DNA chip (Agilent), quantified by quantitative PCR (qPCR), and normalized to 2\u2009nM. Pooling and clustering of libraries were performed using the Illumina cBot system; 35-bp single-end sequencing was performed on the Illumina Genome Analyzer IIx system with TruSeq sequencing-by-synthesis (SBS) kit version 2 reagents. FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control of the data. Reads were mapped to the B. anthracis Ames Ancestor reference genome (GenBank accession number NC_007530) using Novoalign, version 3.02.07. The HTSeq software induced upon treatment in both strains (792 genes), (ii) repressed in both strains (868 genes), (iii) uniquely upregulated in the WT strain (271 genes), (iv) uniquely downregulated in the WT strain (221), (v) uniquely upregulated in the mutant (330 genes), and (vi) uniquely downregulated in the mutant (648 genes). Further inspection of these classes of genes will enable a better understanding of the response of B. anthracis to oxidative stress in general and the regulatory role of the protein HtrA in particular. Furthermore, this database may facilitate identification of proteins for the future development of countermeasures against B. anthracis.The analysis revealed the following categories of HThe transcriptomic data have been deposited in the NCBI database, and their SRA and GEO accession numbers are provided in"} +{"text": "Scientific Reportshttps://doi.org/10.1038/s41598-020-66406-x, published online 15 June 2020Correction to: In this Article, the legend of Figure\u00a02 is incorrect:sdY by real-time qPCR. Number of sdY copies detected within the linear dynamic range (LDR) of the real-time qPCR assay in phenotypic males and phenotypic females , and outside of the LDR in phenotypic females .indicates a phenotypic female with no sdY copies detected. (a) data for all 176 Tasmanian Atlantic salmon used in this study; (b) magnified view of individuals with low numbers of target copies.\u201d\u201cQuantification of Should read:sdY by real-time qPCR. Number of sdY copies detected within the linear dynamic range (LDR) of the real-time qPCR assay in phenotypic males and phenotypic females , and outside of the LDR in phenotypic females .indicates a phenotypic female with no sdY copies detected. (a) data for all 176 Tasmanian Atlantic salmon used in this study; (b) magnified view of individuals with low numbers of target copies.\u201d\u201cQuantification of"} +{"text": "Experiments with a prototypical implementation on top of the Storm model checker show encouraging results for both model types and indicate a substantial improved performance over existing multi-objective long-run MDP model checking based on linear programming.This paper presents an efficient procedure for multi-objective model checking of long-run average reward (aka: mean pay-off) and total reward objectives as well as their combination. We consider this for Markov automata, a compositional model that captures both traditional Markov decision processes (MDPs) as well as a continuous-time variant thereof. The crux of our procedure is a generalization of Forejt"} +{"text": "A 60-year-old female with diabetes presented to the department of internal medicine with a 1-month history of headache. The patient had an Eastern Cooperative Oncology Group performance score of 1. Moderate tenderness was observed by soft palpation of the skull. Laboratory investigations revealed an elevated level of alkaline phosphatase (604 U/L) which was far above normal range (100-350 U/L). The serum level of hemoglobin, creatinine and calcium were within normal range. Plain radiography and computed tomography (CT) showed many punched-out osteolytic lesions in the skull . CranialPunched-out lesions are osteolytic lesions without sclerotic rim on X-ray examination which are considered as hallmarks of multiple myeloma. Punched-out lesions are created by the absence of reactive bone formation as a consequence of tumor factors that combine to activate osteoclasts and inhibit osteoblasts . TherefoCholangiocarcinoma is a heterogeneous group of tumor derived from bile ducts cells, and represents the second most frequent malignant liver cancer. Incidence is globally increasing with a rate of 2.1/100,000 person-years in Western countries. Patients with cholangiocarcinoma are known to commonly present locally advanced diseases ."} +{"text": "Kr). Inadvertent blockade of this channel by drug-like molecules represents a key challenge in pharmaceutical R&D due to frequent overlap between the structure-activity relationships of hERG and many primary targets. Building on our previous work, together with recent cryo-EM structures of hERG, we set about to better understand the energetic and structural basis of promiscuous blocker-hERG binding in the context of Biodynamics theory. We propose a two-step blocker binding process consisting of:The initial capture step: diffusion of a single fully solvated blocker copy into a large cavity lined by the intra-cellular cyclic nucleotide binding homology domain (CNBHD). Occupation of this cavity is a necessary but insufficient condition for ion current disruption.Kr disruption step: translocation of the captured blocker along the channel axis, such that:The head group, consisting of a quasi-rod-shaped moiety, projects into the open pore, accompanied by partial de-solvation of the binding interface.One tail moiety packs along a kink between the S6 helix and proximal C-linker helix adjacent to the intra-cellular entrance of the pore, likewise accompanied by mutual de-solvation of the binding interface .closed channel become trapped upon closing, as do blockers terminating prior to this region.Blockers containing a highly planar moiety that projects into a putative constriction zone within the A single captured blocker copy may conceivably associate and dissociate to/from the pore many times before exiting the CNBHD cavity.The IThe human ether-a-go-go-related voltage-gated cardiac ion channel (commonly known as hERG) conducts the rapid outward repolarizing potassium current in cardiomyocytes (Iin vivo-relevant strategy factoring in:Benefit/risk.undiseased human ventricular cardiomyocyte).The predicted arrhythmogenic fractional hERG occupancy simulations of the Alteration of the safety threshold due to underlying disease.Risk of exposure escalation toward the predicted arrhythmic limit due to patient-to-patient pharmacokinetic (PK) variability, drug-drug interactions, overdose, and use for off-label indications in which the hERG safety parameters may differ from their on-label counterparts.Lastly, we highlight possible flaws in the current hERG safety index (SI), and propose an alternate Kr) of the human ether-a-go-go gene product K+ channel (hERG) on slowinoff speeding due to decreased blocker re-solvation cost during dissociation via the deletion of (or decreased polarity of) a polar BC, BP, or BY blocker group .kon due to reduced pKa of a basic group within the BP moiety.Slowed kSignificant increase in the percent inhibition of a given blocker analog, resulting from:on speeding due to decreased blocker de-solvation cost incurred during association via the deletion of (or decreased polarity of) a polar BC, BP, or BY blocker group .koff slowing due to increased blocker and/or hERG re-solvation cost during dissociation via the addition of (or decreased polarity of) a non-polar blocker group .kon speeding due to increased pKa of a basic group (or addition thereof) within the BP moiety.kSignificant on due to the loss of H-bonds of polar group solvation transferred to bulk solvent. We note that key local solvation effects may be masked in global changes in scalar logP and solubility. Non-trappable blocker-induced expulsion of this solvation is expected to slow koff, minimally to the rate of channel closing (below which channel closing becomes rate-determining). koff slowing in the case of shorter BP groups falling short of the Y site depends on the expulsion of H-bond depleted solvation from the C region .We inferred certain structure-kinetics relationships from the structure-activity relationships of two proprietary in-house datasets based on the aforementioned principles. A large activity cliff in dataset 1 is attributable to the increased de-solvation cost of the pyridazyl versus pyridyl moieties predicted to bind in site C and the The concept of blocker trappability was proposed by Starmer et al. and StorTrappable and non-trappable blockers occupy a common region of P in the open state of the channel (referenced to the parent propafenone moiety of the series).The shape and volume of P differs between the open and closed channel states, which is necessarily localized to the region occupied by the terminal para moiety of the piperidine/piperazine ring of the substituted propafenone analogs (denoted as PT).PT is partially constricted in the closed state of the channel. Trappable blockers are sterically compatible with this putative constriction zone, whereas non-trappables are not (resulting in expulsion of the latter during channel closing).It then follows that:Occupation by a planar moiety (e.g. phenyl group).Alignment of the planar moiety with the pore axis, as determined by the geometric relationship between the planar moiety and the moiety to which it is bonded .In summary, blocker binding is driven largely by:Concurrent steric shape complementarity to the C (L- or Y-shaped blocker moieties), P (quasi-linear blocker moieties), and Y regions of the channel.blocker de-solvation costs during translocation from the outer vestibule into the C, P, and Y regions of the channel.Principally, channel re-solvation costs at the Y and C sites incurred during blocker dissociation from P.Principally, Electrostatic interactions with basic blockers that are capable of projecting their charged group along the longitudinal axis of P Figs , right.intra-cellular free Cmax, whereas non-trappable blocker occupancy builds and decays within the ventricular hERG population during each cycle total(cell)\u2212[blocker]bound(cell) into bound(cell) information:However, it is apparent that the TFPCTTICmax) . Substit\u03b32 to \u03b31 is necessarily less than 1 because [blocker]total(cell) in free(cell):However, the ratio of total(cell) = 5 [blocker]free(cell):For example, at a [blocker]max (= TTICmax), which serves to buffer exposure and occupancy escalation between the TFPCmax and arrhythmic FPCmax stemming from DDI, overdose, and other factors. A wide safety margin of this nature is arguably justified given the life and death implications of drug-induced TdP (exacerbated in the presence of pre-existing cardiac impairment), although possibly tempered by questionable assumptions in the Redfern SI derivation.Viewed in this light, the Redfern SI equates to approximately zero safe hERG occupancy at the TFPCmax (which correlates with the TFPCmax) and hERG safety margin necessarily translate to a maximum FICmax far below our predicted arrhythmic FICmax (AFICmax) in the undiseased heart. The hERG IC50/30 criterion derived by Redfern et al. free(t) is the time-dependent free intra-cellular blocker concentration, Poand Pi are the open and inactive state probabilities, \u03b2 is the channel opening rate constant, and \u03bc is the channel inactivation rate constant [blocker]free is overestimated by on is less than the channel opening rate, and [blocker]free is below the saturating level. Trappable blocker occupancy is described by off \u2265 koff floor . The in vivo-relevant percent inhibition for both trappable and non-trappable blockers is ideally measured via manual patch clamp experiments performed at the physiological gating frequency. Given the fast rate of channel opening (the peak amplitude is reached in a few ms), the kon requirement for high percent inhibition among non-trappable blockers is necessarily fast [in static channels via a radio-ligand displacement approach [on and koff were deconvoluted by the authors from the measured kobs = kon [blocker]free + koff and the IC50).Blocker occupancy is channel state- and time-dependent, and therefore out of the scope of constant . Non-traily fast . Zu et aapproach . Using cStatus quo hERG mitigation and preclinical safety assessment is typically guided by high throughput in vitro IC50 data and animal PK data. hERG mitigation depends on guidance from accurate data capable of unambiguously resolving the true SAR [in vitro experimental methods (50 > the detectability limit) among clinical drug candidates. However, total hERG mitigation, combined with optimal primary target potency and other requirements, is rarely achieved in practice, relegating high uncertainty to both terms of the Redfern IC50/exposure ratio. Uncertainty on top of uncertainty is especially problematic for safety assessment of clinical candidates in advance of in vivo cardiotoxicity evaluation.true SAR , which i methods (noting max in humans is putatively overestimated by the in vitro IC50-based Redfern SI in patients with uncompromised cardiac function (a key assumption in our simulations). Uncertainty in the hERG safety of late stage lead compounds exhibiting residual activity is often further complicated by the lack of confirmed quantitative hERG data . Instead, we propose the following guidelines:As addressed above, pro-arrhythmic risk at exposures \u2265 the TFPCmax via kinetically tuned drug-target binding, defined as the optimization of kon to the rate of binding site buildup .percent inhibition, rather than IC50 data . Sufficient accuracy is needed to confirm critical SAR and inform safety assessment. Data accuracy can be gauged via the following criteria:orthogonal assays (e.g. patch clamp and radio-ligand binding).Similarity in observed trends between replicate runs in each assay.Convergence of Self-consistency of hERG SAR .Basing SAR and safety assessment on on , while maintaining on-target activity, etc.Increasing the de-solvation cost of ton and minimize undesirable collateral lysosomal trapping and membrane partitioning effects manifesting as high volume of distribution (Vss).Attenuating the pKa of basic group(s) in BP (when unavoidably present) in order to slow kmax .Maximally decreasing percent hERG inhibition at the projected TFPCmax and hERG IC50 (noting that in vitro potency may be overestimated for non-trappable blockers). Our simulated general dose-response relationship for trappable and non-trappable blockers as a function of kon and koff (for non-trappables) and IC50 (for trappables) is shown in Assessing pro-arrhythmicity based on \u0394(exposure) between the projected TFPCin vitro hERG IC50 data to humans, although the normal inward-outward ion current balance is certainly disrupted by MICE .Attenuating blockade of other cardiac channels (when present), noting that hERG blockade in the absence of multiple ion channel effects (MICE) is pro-arrhythmic, as is blockade of other single cardiac ion channels. The emphasis by other workers on MICE may reflChloroquine and its hydroxy derivative are currently of interest as potential SARS-CoV-2 anti-viral therapies Fig 19)Fig 19). 50s for chloroquine and HCQ are 2.5 \u03bcM [50 of HCQ is consistent with the expected greater incremental de-solvation cost of the hydroxyl group, which is predicted by our model to reside on BP. Neglecting the additive effects of azithromycin or other drug combinations, the maximum safe TFPCmax for chloroquine and HCQ under the Redfern SI equates to 83 and 187 nM (i.e. 2.5E-6/30 and 5.6E-6/30 \u03bcM), respectively. The mean total plasma concentration of orally administered HCQ in one COVID-19 study is 0.46 \u03bcg/ml [at therapeutic COVID-19 dosing levels is essential for accurate hERG safety assessment. The high Vss of HCQ and its metabolites [1/2 of 40\u201350 days), raising the possibility of multi-dose accumulation. The estimated TFPCmax of HCQ adjusted for an ~50% plasma protein bound fraction [max in humans . Chloroquine and HCQ lack definitive preclinical hERG safety margins vis-\u00e0-vis the Redfern criterion, which is exacerbated by putative hERG trappability and low plasma protein binding . Both d46 \u03bcg/ml , equatin46 \u03bcg/ml ), which abolites results fraction is ~700 l uptake ). HCQ hal uptake and autotransient excursions in exposure \u2265 the arrhythmic threshold . The high potential for cardiovascular impairment in COVID-19 patients may result in a downward shift of our predicted arrhythmic hERG occupancy level (which was predicted from simulations of the undiseased human ventricular cardiomyocyte).That arrhythmia can result from even 50 = 219 \u03bcM [+ loading [Co-administration with other pro-arrhythmic drugs, including azithromycin (hERG IC= 219 \u03bcM ), may lo= 219 \u03bcM have bee loading ).1/2.That HCQ metabolites likewise block hERG and exhibit long tThe high potential for impaired clearance due to renal compromise in COVID-19 patients.The potential for DDIs in COVID-19 patients undergoing multi-drug therapies.50, equating to ~67% inhibition (well above our predicted arrhythmic level).That intravenous HCQ administration results in up to 19-fold higher blood levels in the C-linker and pore cavities. This hypothesis is consistent with our previous ligand-based analysis of hERG blocker chemical space (based on the Redfern dataset [We used non-equilibrium structure-free energy (Biodynamics) principles, combined with a three-dimensional ligand-based alignment of a set of trappable and non-trappable hERG blockers and published cryo-EM structures of hERG and Nav1.4 ,31, to u dataset and inte dataset .hERG safety assessment and mitigation are necessarily weighted toward the prevention of false negatives over false positives (erring on the side of caution), which is entirely justified given the acute, life-threatening implications of TdP, combined with:Uncertainty in the true cause-effect relationship between measured hERG inhibition and arrhythmic risk.in vivo ECG and PK data needed to establish a human-relevant safety margin. Critical unknown parameters during this stage include:max in humans.The predicted TFPCmax at the TFPCmax in humans, noting that percent hERG inhibition cannot be assessed from IC50s in the absence of TFICmax information. Furthermore, TFICmax may be influenced by potentially unquantifiable lysosomal trapping, membrane binding, primary target binding, and off-target binding.The predicted TFIC50 and percent inhibition data, noting that such data is typically measured using less accurate high throughput techniques and efficacious therapeutic target binding criteria is extremely challenging, time-consuming, and failure prone. The question is whether absolute hERG safety at all possible exposures, and across all indications and patient populations is an acceptable tradeoff against slowed progress and failure among hERG-afflicted R&D programs addressing unmet medical needs .Simultaneous satisfaction of the highly stringent Redfern criterion . We define the human-relevant SI in terms of the \u0394(exposure) between the true TFICmax and the arrhythmic exposure, which may be significantly less in the presence of cardiac dysfunction. The actual safety margin depends on the maximum \u0394(exposure) due to PK variability, DDIs, overdose, or dose escalation , and dissociation is driven largely by mutual blocker and binding site re-solvation costs . We further propose a drain-plug-like canonical binding mode, in which blockers straddle the pore and C-linker cavities , projec"} +{"text": "Mass isotopolome analysis for mode of action identification (MIAMI) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopomer distribution-based (MID) similarity network and incorporates the data into metabolic reference networks. By identifying MID variations of all labeled compounds between different conditions, targets of metabolic changes can be detected.We implemented the data processing in C++17 with Qt5 back-end using MetaboliteDetector and NTFD libraries. The data visualization is implemented as web application. Executable binaries and visualization are freely available for Linux operating systems, the source code is licensed under General Public License version 3. Additionally, all date can be exported in various formats.We implemented the data analysis back-end in C++17 using MetaboliteDetector and NTFD libraries for GCMS data processing. The front-end is implemented in Qt5 and data visualization in JavaScript using D3.js library (Bridging the gap between non-targeted and targeted data processing of stable-isotope labeled MS data is essential for the interpretation of metabolic changes in biological processes. With MIAMI, we combine targeted and non-targeted approaches to generate metabolic networks and propose potential metabolic targets based on MID variability. We extended MID similarity-based network visualization with reference pathways. This enables the inclusion of non-targeted detected metabolites into a known biological context. MIAMI also provides a highly customizable and dynamic network visualization to aid data interpretation. The extensive export options enable further data processing with other data processing software.Financial Support: none declared.Conflict of Interest: none declared."} +{"text": "Treatment with tenofovir disoproxil at 245 mg/day was therefore initiated. HBV DNA levels decreased progressively and reached undetectable levels within 1 year. At the time of this report, he is on ibrutinib and tenofovir treatment with HBsAg (+), anti-HBc IgG (+), anti-HBs (-), HBeAg (+), and negative HBV DNA. The course of the disease is summarized in Immunosuppression in patients with hepatitis B virus (HBV) infection may result in viral reactivation. This risk is higher in patients with present than past HBV infection (hepatitis B surface antigen (HBsAg)-positive vs. HBsAg-negative, anti-HBc positive) and in patients with hematological malignancies and related treatments ,2. IbrutIbrutinib has B-cell signaling inhibitory activity that might be more potent than anti-CD20 monoclonal antibodies. HBVr in the case of chronic HBV carrier state or past HBV infection could be a potential complication of treatment with this agent . In our"} +{"text": "This symposium takes an interdisciplinary perspective in order to address psychological and behavioral benefits of various arts-based programs for older adults including persons living with dementia. Presenters in this symposium specialize in diverse disciplines including psychology, social work, cognitive neuroscience, education, and sociology. Using novel approaches and various research methods, the presenters will speak to the specific outcomes of arts-based interventions. The positive outcomes include: 1) improved cognitive health rediscovered identities among cognitively normal older adults; and 2) better communication and reduced agitation for persons with dementia. The first two presentations concern cognitively intact participants. Brown will present a mixed-methods study that examined cognitive benefits and differential experiences of 11 older adults who participated in a 12-week, arts-based intervention. Chow will identify the themes in the \u2018Tree of Life\u2019 drawings of 144 Hong Kong Chinese older adults, who re-authored their sense of self transcending life challenges. Next, Mohan will discuss results from an analysis of communication exchanges among 6 older participants in a 6-week, creative group storytelling program (TimeSlips) offered in a memory care community. Halpin-Healy will explain the research-based practices used in museum programming (Arts & Minds) for persons with dementia and their care partners. She will summarize the assessments of the programs that have served approximately 500 participants over a decade. As a discussant, Kim will summarize common threads that lead to effective arts-based interventions for older adults regardless of their cognitive status. She will also highlight implications regarding the benefits of arts-based interventions in late life development."} +{"text": "Communication is fundamental for daily care activities in nursing homes (NHs). Second-by-second behavioral coding of video observations is an ideal approach to examine the interactive nature of communication but requires a reliable coding scheme. Recent studies have adapted the Peron-Centered Behavioral Inventory (PCBI) and Task-Centered Behavioral Inventory (TCBI) to analyze caregiver communication during mealtime interactions, but their use for coding general daily caregiving activities has not been widely evaluated. This pilot study adapted the PCBI and TCBI of video observations and determined their inter-rater reliability for measuring caregiver verbal communication with persons with dementia (PwD). We analyzed videos from a randomized controlled trial of an intervention to improve caregiver communication in NHs. We selected one 1-minute segment from 12 videos that included interactions of caregiver-resident dyads. One research assistant transcribed caregivers\u2019 verbal communication and segmented the communication into utterances. Two other research assistants independently coded each utterance using the adapted PCBI and TCBI. The coding scheme was expanded by modifying the existing operational definitions, adding three new codes, and developing a coding decision guide. Residents were Caucasian (100%), mean age 86 years with dementia and resistive behaviors. The adapted PCBI and TCBI had an inter-rater reliability of Kappa=0.656 (p<.001) across the 12 videos. Overall, our adapted PCBI and TCBI showed substantial inter-rater reliability. The results support the use of our adapted PCBI and TCBI to distinguish between person-centered and task-centered communication in video observations, which, in turn, allows for sequential analysis to examine the impact of caregiver communication on PwD."} +{"text": "Significance: Label-free quantitative phase imaging is a promising technique for the automatic detection of abnormal red blood cells (RBCs) in real time. Although deep-learning techniques can accurately detect abnormal RBCs from quantitative phase images efficiently, their applications in diagnostic testing are limited by the lack of transparency. More interpretable results such as morphological and biochemical characteristics of individual RBCs are highly desirable.Aim: An end-to-end deep-learning model was developed to efficiently discriminate thalassemic RBCs (tRBCs) from healthy RBCs (hRBCs) in quantitative phase images and segment RBCs for single-cell characterization.Approach: Two-dimensional quantitative phase images of hRBCs and tRBCs were acquired using digital holographic microscopy. A mask region-based convolutional neural network (Mask R-CNN) model was trained to discriminate tRBCs and segment individual RBCs. Characterization of tRBCs was achieved utilizing SHapley Additive exPlanation analysis and canonical correlation analysis on automatically segmented RBC phase images.Results: The implemented model achieved 97.8% accuracy in detecting tRBCs. Phase-shift statistics showed the highest influence on the correct classification of tRBCs. Associations between the phase-shift features and three-dimensional morphological features were revealed.Conclusions: The implemented Mask R-CNN model accurately identified tRBCs and segmented RBCs to provide single-RBC characterization, which has the potential to aid clinical decision-making. Thalassemia is an inherited anemia that has a high prevalence (3.6%)2We acquired 2-D quantitative phase images of RBCs using off-axis DHM. Details of the optical setup are described in Ref.\u00a0This study was approved by the Institutional Review Board of National Taiwan University Hospital, and an informed consent was obtained from each subject. We imaged 210 hRBCs from 11 healthy subjects and 475 tRBCs from 29 adult thalassemia-minor patients. About 10 interference images were acquired from each RBC to expand the dataset. In total, 2001 hRBCs and 4268 tRBCs interference images were collected. Phase images were retrieved from the interference images by bandpass filtering in the spatial frequency domain and inverse Fourier transform without zero-padding,\u2013Since the number of tRBC images was about two times more than that of hRBC images, we adopted data augmentation by random rotation, to enlarge the hRBC dataset to balance data for XGBoost classifier training and Mask R-CNN model building. Furthermore, the operation of random rotation increased the variation in datasets, to prevent overfitting during Mask R-CNN model training.33.1The Mask R-CNN model was developed using the Deep-Learning-Framework Keras (v2.3.1) and TensorFlow (v1.12.0) as the backend, and accelerated using NVIDIA CUDA (v10.0) and cuDNN (v7.5). The architecture of the Mask R-CNN model, shown in We partitioned the augmented dataset described in Sec.\u00a03.2,To benchmark the performance of the proposed Mask R-CNN model in distinguishing tRBCs from hRBCs, we built an optimal classifier with features extracted from manually segmented RBC quantitative phase images. 3.3Exemplary results of segmenting RBCs with the Mask R-CNN model are illustrated in 4\u2013To unveil the underlying characteristics of RBCs that enable the accurate classification of tRBCs and to demonstrate an advantage of Mask R-CNN\u2019s in performing instance segmentation, we took the segmentation results of the Mask R-CNN model to train a second XGBoost classifier for discriminating tRBCs from hRBCs. Then, we performed the SHAP analysis to evaluate the relative impact of each feature on the XGBoost classifier.5Results shown in 5.1CCA is a statistical method for exploring correlations between two sets of variables acquired on the same experimental units.The top four 2-D QPI features identified by the SHAP analysis Sec.\u00a0 includedSince the canonical correlation is calculated between a pair of canonical variates that are linear combinations of the original variables, it is desirable to analyze associations between the canonical variates and the original variables. We followed the method described by Arifler5.2The canonical correlations (6We successfully applied Mask R-CNN to build a classification model to accurately (\u2013,To realize high-throughput screening of RBCs for clinical applications, both the hardware and the software reported in this paper need to be improved. First, the QPI instrument can be integrated with microfluidic devices to automate the dilution and pumping of blood samples for optimal acquisition speed with sufficient image quality.In conclusion, we demonstrated simultaneously the automatic delineation of RBC phase images for single-cell analysis and highly accurate detection of tRBCs using Mask R-CNN. The developed Mask R-CNN model efficiently processed massive amounts of QPI data and greatly simplified the process of developing an automatic method for detecting RBC-related abnormalities from the QPI data. Moreover, the instance segmentation capability of the Mask R-CNN model was very useful for single-cell characterization, and combined with a classifier and the SHAP analysis, provided invaluable insights into the relationship between RBC QPI features and diseases. To help interpret the QPI features, CCA was performed to elucidate associations between the statistics of the phase shift and the more intuitive RBC 3-D morphology. We believe that Mask R-CNN has the potential to improve the efficiency of hematological examinations and achieve single-RBC characterization to aid clinical decision-making."} +{"text": "To evaluate the development and implementation of clinical practice guidelines for the management of depression globally.We conducted a systematic review of existing guidelines for the management of depression in adults with major depressive or bipolar disorder. For each identified guideline, we assessed compliance with measures of guideline development quality and implementation . We compared guidelines from low- and middle-income countries with those from high-income countries.We identified 82 national and 13 international clinical practice guidelines from 83 countries in 27 languages. Guideline development processes and funding sources were explicitly specified in a smaller proportion of guidelines from low- and middle-income countries relative to high-income countries . Fewer guidelines from low- and middle-income countries, relative to high-income countries , were authored by a multidisciplinary development group. A systematic review of comparative effectiveness was conducted in 31%\u00a0(9/29) of low- and middle-income country guidelines versus 71%\u00a0(41/58) of high-income country guidelines. Only 10%\u00a0(3/29) of low- and middle-income country and 19%\u00a0(11/58) of high-income country guidelines described plans to assess quality indicators or recommendation adherence.Globally, guideline implementation is inadequately planned, reported and measured. Narrowing disparities in the development and implementation of guidelines in low- and middle-income countries is a priority. Future guidelines should present strategies to implement recommendations and measure feasibility, cost\u2013effectiveness and impact on health outcomes. We searched titles and abstracts using medical search heading terms and keywords. Text keywords used include, for example: bipolar disorder, depressive disorder, mood disorders, depressi*, practice guidelines, evidence-based medicine, guideline*, AND . The full search records and details of the grey literature and manual searches are available in the data repository.International statistical classification of diseases and related health problems, 10th edition (ICD-10) and the Diagnostic and statistical manual of mental disorders . We excluded guidelines published exclusively for the treatment of depressive symptoms in the absence of major depressive or bipolar disorder; developed for use in local regions, hospitals, states or provinces; developed before 1994 ; or with inaccessible full-texts (we approached authors for access to full-text publications of relevant guidelines). Guidelines with original and updated recommendations were considered duplicates (the most recent update was reviewed). Additional selection and data extraction processes are available in the data repository.We included national and international guidelines for the management of depression in adults (aged approximately 18\u201370 years) with major depressive or bipolar disorder defined by standardized diagnostic criteria. Diagnostic criteria included the We evaluated the quality of the guideline development process by assessing compliance to the Institute of Medicine\u2019s eight standards for clinical practice guidelines: (i)\u00a0transparency in guideline development processes and funding; (ii)\u00a0disclosure, management and divestment of conflicts of interest; (iii)\u00a0multidisciplinary and balanced composition of development group; (iv)\u00a0recommendations based on a systematic review; (v)\u00a0rating of evidence quality and strength of recommendation grading; (vi)\u00a0articulation of recommendations; (vii)\u00a0external review process; and (viii)\u00a0schedule for guideline update.,We adopted measures from the GuideLine Implementability Appraisal and other published criteria to evaluate how amenable each guideline was to implementation.The data extraction form is available in the data repository.\u2013\u2013We compared outcome measures between guidelines from high-, upper-middle- and low- or lower-middle-income countries, as classified by the World Bank for the fiscal year of the publication date.We evaluated to what extent differences in access to quality health care predict disparities in the quality of guideline development processes observed across income classifications. The median Healthcare Access and Quality index was computed for each income classification group using the most recently published index estimates.We compared outcomes between income classifications usingglm for logistic regressions. We computed incident rate ratios (IRRs) using msm::deltamethod and robust (White\u2013Huber) standard errors (SE) using sandwich::vcovHC to evaluate the association between Healthcare Access and Quality index and guideline development quality. We present numbers and percentages of total number of guidelines across or within income groups, as relevant. We conducted statistical analyses using R software version 3.4.4 , with \u03b1\u2009=\u20090.05.http://www.who.int/bulletin/volumes/98/10/20-251405). http://www.who.int/bulletin/volumes/98/10/20-251405) illustrates all countries with at least one depression guideline; the countries are grouped by income classification. There were 82 national guidelines\u2013Our database searches yielded 9833 records. After screening the titles and abstracts of non-duplicate records, we reviewed the full texts of 312 records for eligibility . A total\u2013\u2013,,Of the 13 international guidelines, five were from countries in the same income group.Fifty-two guidelines were specifically developed for major depressive disorder and 33 for bipolar disorder. One guideline was developed for the treatment of mood disorders, four for psychiatric disorders, one for psychiatric and neurological disorders, one for medical and psychiatric disorders, and three for depression in special populations . Guidelines most often targeted psychiatrists and primary care providers . Only 19 (20%) and 13 (14%) of guidelines targeted policy-makers and payers , respectively .The majority of guidelines recommended the use of the two-item Patient Health QuestionnaireRecommendations for the primary prevention of depression were included in 16 guidelines (17%), most of which were developed in high-income (10 guidelines) or upper-middle-income countries (four guidelines). These guidelines described risk factors, strategies for reducing risk and methods for early detection. Few guidelines evaluated the literature on the effectiveness of different interventions for primary prevention or cited limitations of current evidence.,,,,,,,,,,,,,,,,,,Fifteen guidelines (16%) provided decision support or recommendations for assessing work ability, sick leave or return to work; all were published by high-income or upper-middle-income countries . Eleven The quality of the guideline development processes varied across country income classifications. The median number of standards met was five (interquartile range: 3\u20137) for high-income country guidelines, two (interquartile range: 1\u20134) for upper-middle-income country guidelines and one (interquartile range: 0\u20131.5) for low- or lower-middle-income country guidelines. The World Health Organization (WHO) guidelines, developed specifically for low- and lower-middle-income countries,Sixty-eight guidelines (72%) provided specific, unambiguous and actionable recommendations, representing 44 of 58 (76%), 13 of 22 (59%) and three of seven (43%) of guidelines from high-, upper-middle- and low- or lower-middle-income countries, respectively .The guideline development processes and funding sources were explicitly specified in 51 guidelines (54%), only two of which originated in low- or lower-middle-income countries. Potential conflicts of interest were openly declared and managed in a higher proportion of guidelines from high-income versus upper-middle-income and low- or lower-middle-income countries .Only 25 guidelines (26%) were developed by a multidisciplinary group comprising subject experts, clinicians and patients or patient advocates. Development groups often lacked patient or patient advocacy representation. None of the low- or lower-middle-income country guidelines had a multidisciplinary development group.A systematic review of comparative effectiveness of interventions being recommended had been carried out by 57 guidelines (60%), all of which were developed by international authorship groups or in high- or upper-middle-income countries. Some guidelines from low- or middle-income countries were based on recommendations of other published international guidelines. Only 10 guidelines (11%), all from high- and upper-middle-income countries, had conducted a systematic review of cost\u2013effectiveness of a particular intervention or set of recommendations. Forty guidelines (42%) included with their recommendations ratings of evidence, harms, benefits, and confidence level. More guidelines from high-income countries met the Institute of Medicine\u2019s standard for strength of recommendation grading. Thirty-five guidelines (37%) had been externally reviewed ; none of these guidelines originated in low- or lower-middle-income countries.,,Thirty-eight guidelines (40%) stated plans to renew or update their recommendations, excluding three guidelines that were withdrawn past the scheduled updating date.2\u03c7\u2009=\u2009156.2, degrees of freedom\u2009=\u200972; P\u2009<\u20090.001; The median Healthcare Access and Quality index was significantly greater among guidelines from high-income countries relative to those from upper-middle-countries and low- or lower-middle-income countries and 79 (83%) guidelines, respectively. The authors of 75 guidelines (79%) met criteria for credibility with the intended audience . Most ofTarget users or patient representatives evaluated enablers and barriers to the implementation of 24 guidelines (25%); 11 guidelines involved both target users and patient representatives, 11 guidelines involved target users without patient representatives and two guidelines involved only patient representatives in the evaluation of enablers and barriers. None of the guidelines from low- or lower-middle-income countries evaluated enablers and barriers to implementation.Twenty-one guidelines (22%) evaluated patient preferences by conducting literature reviews of patient preferences or by including patient representatives in the guideline development group, as external reviewers or as members of focus groups. None of the low- or lower-middle-income country guidelines evaluated patient preferences.Twenty-four guidelines (25%) ordered their recommendations by ease of use . For management of mild depression, these guidelines recommended low-intensity psychosocial and psychological interventions before pharmacological interventions or high-intensity psychological interventions . Whether a guideline had ordered recommendations by ease of use varied across income classifications.,,,,,,,,,Eighteen guidelines (19%), mostly from high-income countries (15 guidelines), evaluated the resource implications of implementing guideline recommendations. Five guidelines described personnel, infrastructure and training requirements for each recommendation in detail.The number of guidelines that considered legal or ethical issues did not vary across income classifications. Twenty-five guidelines (26%) discussed various legal aspects of patient care, such as involuntary treatment of psychiatric patients, certification requirements for professionals providing psychotherapy, availability of antidepressants across national regulatory agencies, national work or disability legislations and statutory patient rights. Twenty-one guidelines (22%) discussed ethical considerations relevant to care provision, such as risks versus benefits of taking medications while pregnant or breastfeeding and obtaining informed patient consent before initiating electroconvulsive therapy or off-label drug usage.Thirty-nine guidelines (41%) discussed social aspects affecting patient care or illness presentation, such as race or ethnicity, and advised clinicians to consider patient factors, such as social support availability, interpersonal relationship quality, workplace or other factors influencing recovery, childhood trauma and developmental disabilities. Other guidelines, for example, emphasized the importance of adapting guidelines to local contexts and training end-users to be culturally sensitive. Some guidelines commented on the lack of availability of personnel with sufficient training in some areas of the country and the implications of this for clinical care. More guidelines from high-income countries were informed by social considerations when compared to upper-middle-income and low- or lower-middle-income (none) countries.Thirty-three guidelines (35%), mostly from high-income countries (25 guidelines), operationalized monitoring or auditing criteria for assessing the implementation of guidelines. These guidelines suggested quality indicators or measures of guideline concordance, such as the proportion of patients prescribed lithium or a selective serotonin reuptake inhibitor for at least four weeks.Fifteen guidelines (16%), none of which were from low- or lower-middle income countries, described plans for assessing implementation of guidelines or adherence to guideline recommendations . HoweverGuidelines described, for example, available health administrative data sets or national electronic medical records that could be used to assess measures of guideline implementation and quality indicators. The Swedish National Quality Register for Bipolar Disorder included longitudinal data from 244 active health-care providers and approximately 30% of patients with bipolar disorder in Sweden.Sixty-five guidelines (68%) provided tools for guideline application, such as a quick reference summary. More high-income country (47/58) and international (6/8) guidelines provided implementation tools. Twenty-four guidelines (25%) described plans for disseminating guidelines, 29 of which originated in high-income countries.\u2013,We found that many low- and lower-middle-income countries, especially in Africa, lacked published clinical practice guidelines for the management of depression. However, international guidelines exist that cover or specifically target these countries.While the overarching aim of guidelines is to improve health outcomes and cost\u2013effectiveness, it remains unclear to what extent guidelines for the management of depression are being implemented and improving health outcomes, particularly in low- and lower-middle-income countries.,,,,\u2013\u2013The disparities in availability, development processes and quality of guidelines underscore an unmet need for decision support in low- and middle-income countries.,,Low- and middle-income countries are differentially affected by multimorbidity, which drastically reduces life expectancy and increases personal, social and economic burden.Most guidelines for the management of depression provided tools for the application of guideline recommendations, such as a summary document or a quick-reference guide. However, less than one fifth of the guidelines we identified provided materials for patients; fewer targeted policy-makers or payers. Guideline implementation requires diversity in the engagement of target audiences and stakeholders, as well as realistic and relevant implementation plans.,,,,Guideline development groups should include experts in experimental, observational and contextual evidence and knowledge users (such as clinicians and patient advocates).\u2013Guidelines endeavour to comprehensively review and corroborate knowledge of intervention efficacy, effectiveness, safety and tolerability. Guidelines must also be informed by an evaluation of the determinants, processes and outcomes of implementing evidence-based recommendations.The main aim of our initiative was not to synthesize a consensual set of implementation measures across low- and middle-income countries. However, lessons learnt from implementation science across other noncommunicable diseases could be a starting point for determining policy and implementation principles for depression management. For example, internet access may be needed to facilitate guideline dissemination, especially in low- and middle-income countries. The integration of technology may also facilitate chronic disease management. The guiding principles include prioritizing the involvement of stakeholder and end-user input in any policy around implementation, identification of those people most at risk, and appraisal of local health-care resources.The paucity of depression guidelines from low-income countries may reflect limitations in our search strategy . We were more likely to identify guidelines available online than in print only. To mitigate this possibility, we contacted members of the Global Alliance for Chronic Diseases and members of national psychiatric or other medical associations across geographical and linguistic world regions. Database searches may miss guidelines published as government reports or in formats other than peer-reviewed journal articles or meeting abstracts. To improve the likelihood of detecting such guidelines, we manually searched the websites of multiple national and international medical associations and ministries of health and included experts from 27 countries across all continents in our collaboration. Thus, the possible selection bias in our search is unlikely to confound our findings of differences in guideline quality and development across economic strata. Our large number of evaluators may have resulted in differences in data extraction. However, we completed blinded evaluations in duplicate using structured evaluation forms; a third reviewer independently evaluated all forms. In addition, guidelines were evaluated by two or three reviewers who had not been involved in their development.The focus of our analysis on guidelines may inadequately capture separate implementation studies of guidelines. Future research should primarily evaluate implementation studies of guidelines. We limited our inclusion criteria to national and international guidelines, which may not capture more regional or local differences in guideline development or implementation. Our comparison of guidelines by country-level income classification and Healthcare Access and Quality index did not consider differences in the availability and accessibility of health care within individual countries. Much of the available research informing guideline recommendations has been conducted in high-income countries, with an over-representation of Caucasian groups, often overestimating patient access to expensive medications and specialized care. In conclusion, the implementation of guidelines for the management of depression is inadequately planned, reported and measured. As a result, it remains unknown to what extent guidelines are acceptable to patients and other target users; are feasible and cost\u2013effective; and improve health outcomes. Narrowing the disparities in the development and implementation of guidelines, particularly in low- and middle-income countries, is a priority. Refinement of decision support processes in depression is a critical first step towards the aim of reducing morbidity, especially in low- and middle-income countries. Future guidelines should present strategies to implement recommendations and measure feasibility, cost\u2013effectiveness and impact on health outcomes, co-designed by stakeholders and experts with practical knowledge from low- and middle-income countries."} +{"text": "This diagnostic study describes an online tool created with actual severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus copy number data to help policy makers understand how pooled testing compares with single-sample testing in different populations. This study follows the 2015 Standards for Reporting of Diagnostic Accuracy to count SARS-CoV-2 copy numbers in patient samples and create quantitative curves for 3 US Food and Drug Administration Emergency Use Authorized SARS-CoV-2 reverse transcriptase\u2013PCR qualitative tests. We used these curves to convert positive nasopharyngeal PCR cycle threshold (Ct) values to droplet digital PCR\u2013harmonized VCNs for these tests. We created an online tool that allows users to define the sample size, pool size, positivity rate, and test characteristics and to compare pooled testing with single-sample testing using actual VCN data . The tool uses VCNs from preprocedural screening samples and outpatient diagnostic samples to simulate asymptomatic and symptomatic SARS-CoV-2\u2013positive patients. The tool generates random virtual pools with positive samples pulled from VCN data mirroring the expected positivity rate and calculates pool VCNs with the expected dilution. The tool uses VCNs and user-defined test characteristics to predict which positive pools and samples are detected or missed, the sensitivity of pooled and single sample testing, and the number of tests performed. Additional details are shown in the eAppendix in the We used this tool to compare pooled testing with single-sample testing via a common reverse transcriptase\u2013PCR assay , with a 95% limit of detection of 100 VCNs/mL and an absolute limit of detection of 2 VCNs/mL, for detection of asymptomatic and symptomatic SARS-CoV-2\u2013positive patients at various positivity rates. A screenshot of the COVID19 Pool Tool user interface is shown in eFigure 1 in the Calculation of VCNs from Ct values was performed using Excel software version 2016 (Microsoft). Figures were created in Prism software version 6.0c (GraphPad) and Excel. Data analysis was performed in August 2020 using data collected from March to July 2020.10 RNA copies/mL) and 2910 outpatient diagnostic sample VCNs used to simulate asymptomatic and symptomatic SARS-CoV-2\u2013positive patients in the tool. Pooled testing can extend SARS-CoV-2 test supplies and increase the number of patients tested and cases detected, making it useful for population screening and resource-constrained settings. The complicated workflow, lower sensitivity for low-VCN patients, and need to repeat tests for positive pools are drawbacks. Sequential 2-stage pooling could reduce the burden of retesting from positive large pools . The lack of clinical data for laboratory samples is a potential limitation of this study. This tool offers policy makers an easy to use tool to inform regional and national decision-making about the pros and cons of pooled testing."} +{"text": "Systemic homeostasis is maintained by the robust bidirectional regulation of the neuroendocrine-immune network by the active involvement of neural, endocrine and immune mediators. Throughout female reproductive life, gonadal hormones undergo cyclic variations and mediate concomitant modulations of the neuroendocrine-immune network. Dysregulation of the neuroendocrine-immune network occurs during aging as a cumulative effect of declining neural, endocrine and immune functions and loss of compensatory mechanisms including antioxidant enzymes, growth factors and co-factors. This leads to disruption of homeostasis and sets the stage for the development of female-specific age-associated diseases such as autoimmunity, osteoporosis, cardiovascular diseases and hormone-dependent cancers. Ovarian hormones especially estrogen, play a key role in the maintenance of health and homeostasis by modulating the nervous, endocrine and immune functions and thereby altering neuroendocrine-immune homeostasis. Immunologically estrogen's role in the modulation of Th1/Th2 immune functions and contributing to pro-inflammatory conditions and autoimmunity has been widely studied. Centrally, hypothalamic and pituitary hormones influence gonadal hormone secretion in murine models during onset of estrous cycles and are implicated in reproductive aging-associated acyclicity. Loss of estrogen affects neuronal plasticity and the ensuing decline in cognitive functions during reproductive aging in females implicates estrogen in the incidence and progression of neurodegenerative diseases. Peripherally, sympathetic noradrenergic (NA) innervations of lymphoid organs and the presence of both adrenergic (AR) and estrogen receptors (ER) on lymphocytes poise estrogen as a potent neuroimmunomodulator during health and disease. Cyclic variations in estrogen levels throughout reproductive life, perimenopausal surge in estrogen levels followed by its precipitous decline, concomitant with decline in central hypothalamic catecholaminergic activity, peripheral sympathetic NA innervation and associated immunosuppression present an interesting study to explore female-specific age-associated diseases in a new light. This reciprocal communication among the homeostatic systems is essential for the maintenance of health, and any dysregulation in the communication leads to susceptibility and development of disease Aging is marked by decline in homeostatic maintenance in the neuroendocrine-immune network. Several studies have reported that age-associated dysregulation in the cross-talk between the neuroendocrine and immune system contributes to the development of diseases, in both rodents and humans 2.+) neurons by a reduction in the ability of estrogen to induce neurochemical changes associated with pre-ovulatory surge in GnRH and LH + neurons in the hypothalamus through decline in hypothalamic stimulatory molecules such as glutamate, NE, vasoactive intestinal peptide (VIP) and increase in inhibitory signals such as gamma-amino butyric acid (GABA) and opioids In females, reproductive aging is one of the first hallmarks of age-associated decline in the neuroendocrine-immune network. The depletion of ovarian follicles, hypothalamic deficits and the ensuing decline in the hypothalamo-pituitary-gonadal (HPG) axis and its mediators involving neurotransmitters, neuropeptides, releasing hormones [gonadotropin releasing hormone (GnRH) and luteinizing hormone (LH)] and target organs (ovaries) lead the transition into menopause 3.In women, regular menstrual cycles in the young give way to irregular cycles by middle-age, leading to perimenopausal estrogen surge, onset of menopause leading to the final menstrual period. Rhythmic cyclicity of ovarian hormones including estrogen are implicated in the alteration of cell-mediated immune responses in follicular and luteal phases of the menstrual cycle. Cell-mediated immune functions including mitogen-induced proliferation and cytokine production were significantly enhanced during follicular phase of the menstrual cycle in young women compared to the luteal phase 4.The presence of sympathetic NA nerve fibres in synaptic association with immune organs, and the expression of adrenergic and steroid hormone receptors on immune cells renders immune cells susceptible to the immunomodulatory effects of both neurotransmitters and steroid hormones alike. Of interest here is the interesting crosstalk between NE signals released from the sympathetic fibres and circulating estrogen, both of which have shown contradictory effects on immune cells.\u22123 M, 10\u22126 M and 10\u22129 M) while \u03b12-AR agonist clonidine (10\u22126 M and 10\u22129 M) inhibited splenocyte proliferation, phosphorylated-extracellular signal regulated kinase (p-ERK) and phosphorylated-cAMP response element binding protein (p-CREB) expression \u22126 M and 10\u22129 M) significantly decreased splenocyte proliferation and interleukin-6 (IL-6) expression in splenic lymphocytes \u22129 M 17 \u03b2-estradiol reverses phenylephrine-mediated decline in IFN-\u03b3 expression, clonidine-mediated decline in proliferation, p-ERK and p-CREB expression and terbutaline-mediated decline in proliferation and IL-6 expression The expression of adrenergic receptor (AR) subtypes including \u03b11-, \u03b12-, \u03b21-, \u03b22-adrenoceptors have been characterised in several immune cell subsets including splenic lymphocytes (T cells and B cells) and natural killer (NK) cells 5.+ T cells while ER\u03b2 predominantly expressed on B cells, playing a role in maturation and differentiation of thymic T cells and B lymphopoiesis in the bone marrow + T cells in normal rodents and experimental autoimmune disease model of myasthenia gravis Intracellular (genomic and non-genomic) effects of estrogen are mediated by specific intracellular and membrane receptors namely ER\u03b1 and ER\u03b2. ER\u03b1 is predominantly expressed on CD4in vitro study conducted in our laboratory, estrogen [10\u22126 M] treatment of splenic lymphocytes reversed immunosuppression mediated by adrenergic agonists and enhanced cell-mediated immune functions Crosstalk between estrogen and adrenergic signalling has also been implicated in the expression of proinflammatory cytokines by peritoneal macrophages Centrally, the effects of estrogen are transduced through the activation of ERK and CREB in the hypothalamus and hippocampus, activation of Akt signalling pathways in the striatum or mediating anti-inflammatory effects through inhibition of NF-\u03baB 6.+) nerve fibers in the medial prefrontal cortex of old rats + fiber density and TH activity in the hippocampus and frontal cortex have been implicated in memory and cognitive functions The role of 17 \u03b2-estradiol in neuroprotection in young and old females has been widely explored in a number of studies. We have shown that estrogen exerts a dual role by mediating neuroprotective effects in specific brain areas while causing sympathetic denervation in the periphery esp. lymphoid organs 7.\u221212 M, 10\u221210 M and 10\u22128 M) plays a potent antioxidant function in splenic lymphocytes by increasing the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) in vitroAging takes a toll on cellular processes through increased allostatic load of reactive oxygen species and decline in antioxidant machinery leading to impaired functions and cellular distress. Peroxides and superoxide anions can bind to cell membrane lipids through malondialdehyde adducts leading to impaired structural integrity that eventually compromise functional integrity of the cell 8.The brain is a glucose-intensive organ and hence places a huge physiological demand for energy currency on the systemic metabolic process +/K+/ATPase pump that is energy intensive and is crucial for the maintenance of ionic gradients, resting potentials and triggering action potentials that is also regulated by catecholamines mainly NE and serotonin (5-HT) +/K+/ATPase activity in the frontal cortex and hypothalamus conferring neuroprotection against amyloid-\u03b2-induced oxidative stress and suppressing lipid peroxidation Another target of estrogen is the Na9.The diverse effects of estrogen on the neuroendocrine network and the dependence of the female physiology on the robustness of estrogen-associated regulatory functions during reproductive life and aging places women at risk of developing autoimmune diseases, heart diseases, osteoporosis, neurodegenerative diseases, and breast cancer. While loss of neuroendocrine-immune homeostasis shares a cause-effect relationship with impaired hormone secretion, immunosenescence, peripheral denervation and central neurodegeneration, decline in neurotransmitters etc, the cumulative effects set the stage for age-associated disease pathology . Age-ass"} +{"text": "Viral emergence is an unpredictable but obvious event, particularly in the era of climate change and globalization. Efficient management of viral outbreaks depends on pre-existing knowledge and alertness. The potential hotspots of viral emergence often remain neglected and the information related to them is insufficient, particularly for emerging viruses. Viral replication and transmission rely upon usurping the host metabolic machineries. So altered host metabolic pathways can be exploited for containment of these viruses. Metabolomics provides the insight for tracing out such checkpoints. Consequently introspection of metabolic alteration at virus-host interface has evolved as prime area in current virology research. Chromatographic separation followed by mass spectrometry has been used as the predominant analytical platform in bulk of the analyses followed by nuclear magnetic resonance (NMR) and fluorescence based techniques. Although valuable information regarding viral replication and modulation of host metabolic pathways have been extracted but ambiguity often superseded the real events due to population effect over the infected cells. Exploration of cellular heterogeneity and differentiation of infected cells from the nearby healthy ones has become essential. Single cell metabolomics (SCM) emerges as necessity to explore such minute details. Mass spectrometry imaging (MSI) coupled with several soft ionization techniques such as electrospray ionization (ESI), laser ablation electrospray ionization (LAESI), matrix assisted laser desorption/ionization (MALDI), matrix-free laser desorption ionization (LDI) have evolved as the best suited platforms for SCM analyses. The potential of SCM has already been exploited to resolve several biological conundrums. Thus SCM is knocking at the door of virus-host interface. The enormous genetic diversity of existing viruses and unpredictability of viral behavior complemented by inadequacy of knowledge about global virome database always poses potential threats over the entire living world to acquire infection from any emerging or re-emerging viruses. Rapid climate change, increased traveling in the era of globalization and frequent mingling of sylvatic and urban lifecycle have also potentiated the viruses for genetic undulation, emergence and re-emergence to become pandemic at occasions . Keen in\u201cOmics\u201d technologies pertain to the entire sets of molecules expressed at cellular or tissue level, or within an organism under specific set of condition. However cellular heterogeneity in multicellular organisms is often masked in pooled analyses. There the importance of single cell omics can be apprehended because it holds the potential to identify several targets expressed within a single individual cell or a cell population of interest individually at a specified time, or analyze handful of parameters in the same cells over time . The enoMetabolites are smaller molecules, usually of lesser than 1.5 kD in size reflecting various cellular pathways which include sugar, lipids, glycolytic products , phosphate compounds , xenobiotics etc., but generally excludes nucleic acids, minerals, and salts , b. TheyResearch related to virus host interaction and information regarding susceptibility, virulence, mechanisms of gene regulation and metabolic pathway modulation under variable environmental factors such as temperature, humidity, light color, intensity and also radiation etc. are mostly lacking that may be useful to combat the incidences of outbreaks from novel viral emergence. Although metabolomics has found its value in virology research but mostly in population study whereas SCM intervention is almost yet to be started to introspect virus-host interaction and is reached upto the level of cell lines only, may be due to the hardship of SCM in terms of single cell isolation and handling, structural diversity and rapid metabolite turnover, lack of amplification opportunity, sensitivity and repeatability of the analytical platforms etc. . HoweverThe most common hurdle in SCM analyses is the isolation of single target cell followed by its careful handling and delivery to the downstream analytical platforms because it is directly reflected over the precision of SCM data. Limiting dilutions, manual cell-picking by micromanipulator and laser micro dissection are the common manual methods having relatively low throughput yet applied for single cell analyses where as fluorescence-based cell sorting, high-density microarrays and microfluidics are the most popular automatic high throughput single-cell isolation techniques employed for SCM . High coFluorescence-activated cell sorting isolates the target cells specifically labeled with antibody coupled with a fluorescent tags. This technique prefers the samples that are naturally suspended in liquid media, such as blood, bone marrow cells, semen, ovum, secretions, yeast, protoplast, bacteria, and viruses . Time-laImmune-magnetic separation using antibody-coated magnetic beads or attached with other ligands for capturing the target cells is also an important single cell isolation method. Dynabeads or MACS (Dynabeads Magnetic Separation Technology) employs such isolation principle .Aptamer-based cell isolation relies upon the precise binding of aptamers to its target using structural conformation and ease the isolation of single cells . FluoresSingle-cell printing technique like \u201cBlock-Cell-Printing\u201d is another example of high throughput single cell isolation technique yet to find ample application .Microfluidics or Lab-on-a-Chip devices provide excellent opportunity for simultaneous isolation of target single cells along with its handling and manipulation followed by SCM suitable platforms with high end automation . SeveralDirect sampling through nano-electrospray ionization tips followed by mass spectrometric analyses method is gaining popularity in recent times due to its minimum sample requirement and processing along with high throughput data generation. Pipette tip column electrospray ionization (PTC-ESI) or ballpoint electrospray ionization (BP-ESI) followed by simultaneous mass spectrometry or live single-cell video-mass spectrometry are the SCM platforms where the technique has been used .The precision and coverage of SCM analysis depends upon the \u201cresolution\u201d and \u201csensitivity\u201d of the analytical platform. Although theoretically SCM analyze the entire set of cellular metabolites but more often it is restricted to qualitative or quantitative analysis of a cluster of metabolites under certain condition. \u201cTargeted\u201d for acquiring information regarding specific metabolite(s) or \u201cuntargeted\u201d SCM approach for obtaining the maximum coverage can be chosen according to the requirement and selection of the analytical platform should be done accordingly. Mass Spectrometry Imaging (MSI)-based methods are arguably the most sensitive and thus preferred SCM platform. However, the compromised reliability, restricted quantitation option, and poor resolution for structural characterization are the certain limitations need to be taken care of. Other SCM platforms include but not limited to separation-based methods like capillary electrophoresis (CE), liquid chromatography (LC), or gas chromatography (GC) combined with MS or fluorescent tagging approach which are mostly used for \u201ctargeted SCM\u201d due to the sensitivity issue ; Table 2Xenopus laevis to depict more than 80 metabolites (Capillary electrophoresis coupled with electrospray ionization and mass spectrometry (CE-\u03bcESI-MS) has been employed to analyze single 8-cell embryo of abolites . Similarifornica . CE-ESI-nM range . High-Re(\u223c11 nm) . TargeteTorenia hybrida petal cell based analysis has yielded 5 anthocyanins from 2-4picolitervolume of individual tal cell . Gas chrironment . Thus chironment . Ultra-hironment . Gut metironment . AlthougExtreme sensitivity, vast coverage and the opportunity of label-free analysis has rendered MSI as one of the most preferred method of SCM analysis, particularly for untargeted approach. Improvement in resolution is going on in terms of reducing the laser spot area by lowering the diameter of optical fiber along with providing multiplexing option by integration of multiple mass analyzers. Matrix-Assisted Laser Desorption Ionization (MALDI)-MSI and Electrospray Ionization (ESI)-MSI are the two conventional platforms applied for SCM analyses .Closterium acerosum (in situ hybridization (FISH) microscopy combined with high-resolution atmospheric pressure-MALDI-MSI of Bathymodiolus puteoserpensis epithelial cells has also been used to understand host-microbe symbiosis . Fluoresymbiosis . Lipidomsquitoes . Thus thPelargonium zonale leaf cell has depicted over16 metabolites from 1to 5pL of sample is another important soft ionization technique where the analytes after ionization, evaluated by MS to facilitate metabolite characterization. ESI-MS is equipped with simultaneous detection at both positive and negative ion mode yielding enormous sensitivity. Live nano-ESI-LTQ-MS analyses of f sample . Probe Eepa cell . ESI-Q-Tepa cell .Allium cepa and Narcissus pseudonarcissus bulb epidermis and single eggs from Lytechinus pictus has been evaluated through LAESI to detect 35 prominent metabolites including anthocyanidins, flavonoids, and their glucosides depicting its potential in SCM analysis (Laser ablation electrospray ionization (LAESI) employs mid-infrared (mid-IR) laser to generate gas phase metabolites. Large plant cells or cluster of animal cells are preferred subjects for this platform but high sensitivity, little chemical background and a direct sample delivery to MS platform has made it a desired choice for SCM analysis. Metabolites from single cells or cluster of analysis . LAESI-Manalysis . LAESI canalysis .Live Single-Cell Video-Mass Spectrometry using micro sampling method by video microscopy and micromanipulator guided gold-coated glass capillary nano-ESI tip along with Nano-ESI-Q-TOF platform has demonstrated good potential for SCM analysis .in vivo metabolism has been followed by using NMR (CIVM-NMR) coupled with high-resolution-magic angle spinning to elucidate branched-chain amino acid metabolism in human chronic lymphoid leukemia cells detection has been employed for detection of chiral amino acids and neurotransmitters from mouse brain and neuron cells . CapillaChlamydia trahomatis and Neisseria gonorrheoae along with associated extra-cellular metabolite changes (Surface Enhanced Raman Scattering (SERS) employs laser in the visible, near-infrared, or near-ultraviolet range for label free detection of the metabolites within the cells . SERS ha changes . Raman s changes . Recentl changes .Secondary Ion Mass Spectrometry Imaging with spatial resolution capacity at the range of 50\u2013100 nm is a potential future tool for SCM as well as sub-cellular metabolite analyses . The matin vitro antiviral activity against SARS-CoV-2 infection and warrants rapid further in vivo introspection to combat current COVID-19 pandemic. This is also an example of drug repurposing relying upon the virus-exploited common pathways. Because in earlier research, ivermectin has depicted efficacy against multiple RNA viruses such as DENV 1-4, West Nile Virus, influenza virus, Venezuelan equine encephalitis virus (VEEV) and human immunodeficiency virus-1 (HIV-1) by destabilizing the importin (IMP) \u03b1/\u03b21 heterodimer and blocking IMP \u03b1/\u03b21-mediated nuclear import of viral proteins viruses, Ebola and Marburg filoviruses, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome coronavirus (MERS CoV) are the emerging viruses as evidenced in recent times . Severalproteins .Metabolite profiling can also provide an idea about the disease severity and predictive outcome of the viral infection. Serum metabolite analyses of H7N9 infected subjects have revealed that increase in palmitic acid, erucic acid, and phytal level is related to virus-induced repression of fatty acid metabolism and negatively correlated with the disease outcome .Aedes albopictus mosquito which serves as the vector of ZIKV infection. Glucose influx has been increased through glycolysis in both the cases, however, it is mainly diverted toward tricarboxylic acid (TCA) cycle and amino acid synthesis in human cells whereas glucose contribution to TCA cycle gets reduced to augment the intermediates of pentose phosphate pathway in mosquito cells. Further, ZIKV infection depletes ATP level in HFF-1 cells leading to elevated AMPK phosphorylation and increased caspase-mediated cell death whereas neither such increase in AMP/ATP and ADP/ATP ratios as well as AMPK phosphorylation nor decreased cell viability has been evidenced in infected C6/36 mosquito cells. Such difference in cell viability may be contributed by both altered pentose phosphate pathway and AMPK activation induced metabolic reprogramming of human foreskin fibroblast cells (HFF-1) shapes differently from C6/36 cells of tivation . So metaConsiderable numbers of researches have followed such path providing metabolomic insight at virus-host interface. Chromatography (LC/GC) coupled with tandem mass spectrometry (MS/MS) is the most common method employed for metabolomics introspection followed by NMR, FTIR and fluorescence based methods . Most ofHowever, the inherent challenges of SCM techniques require to be surmounted with diligence and passion for proper utilization of the potential of single-cell analyses. The difficulty in single cell isolation along with rapid turnover, transport and degradation of the cellular metabolites are the key challenges of SCM analyses. Rapid metabolite turnover can produce random noise which may create analytical error and difficulty in differentiating infected cells from the healthy one. Thus normalization of such random error must be performed during the experimental set-up for SCM data acquisition to differentiate the deterministic effects from the stochastic one. Similar type of random fluorescence noise normalization has been performed by Rapid development in single cell isolation and handling methods, persistent improvement in sensitivity and resolution of the analytical platforms along with growing database and data interpretation programs are smoothening the hurdles of SCM to introduce it at the virus-host interface as early as possible. The SCM derived precise information regarding the altered metabolism of infected cell over the healthy cells may assist to investigate the virulence, survival, and progression of diseases. The exploration of cellular heterogeneity can illuminate the aspects which remain concealed in population study. Thus SCM holds the promise as a key tool of future to introspect virus-host interaction and assist in efficient management of emerging viral disease.MP and MG conceptualized the manuscript. RK and SK wrote the manuscript. MP critically analyzed and improved the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Nine cases exhibited primary and eight cases secondary AI resistance. Both ORR and CBR were higher in patients with secondary AI resistance . The median TTF was 6.2 months in the entire AI-resistant group (n = 17) and was longer in the secondary resistance subgroup than in the primary resistance subgroup . High-dose TOR appears to be most effective for postmenopausal breast cancer cases with secondary resistance to AIs, cases without prior AI treatment, and cases without liver metastasis. The detailed mechanisms of AI resistance and the clinical features of responsive cases need to be further clarified to identify the best candidates for HD-TOR.There are currently no established second- and later-line therapies for postmenopausal women with hormone receptor-positive advanced or metastatic breast cancer. We examined the efficacy of high-dose toremifene (HD-TOR) for this patient group and whether aromatase inhibitor (AI) resistance influences HD-TOR treatment outcome. This retrospective analysis investigated the outcomes of 19 women with postmenopausal hormone-sensitive recurrent or metastatic breast cancer who received HD-TOR, defined as 120\u2009mg daily from 2012 to 2016. The median follow-up duration was 9.67 months. The overall response rate (ORR) and clinical benefit rate (CBR) were compared between various clinical subgroups, including patients exhibiting primary or secondary AI resistance as defined by the timing of recurrence or progression. Time to treatment failure (TTF) was estimated by the Kaplan\u2013Meier method and compared between subgroups by the log-rank test. The overall ORR was 21.1%, and the CBR was 31.6%. CBR was significantly higher for patients without liver metastasis (50% vs. 0%, Aromatase inhibitors (AIs) have long been the primary first-line endocrine treatment for postmenopausal women with hormone receptor-positive metastatic or locally advanced breast cancer , 2. ReceHigh-dose toremifene therapy (HD-TOR) has attracted attention as an effective and relatively low-cost endocrine therapy for metastatic breast cancer. Toremifene is a selective estrogen receptor modulator (SERM) used alone as an adjuvant endocrine therapy to treat hormone receptor-positive breast cancer in Japan. The standard dose is 40\u2009mg/day orally, and a higher dose is used to treat metastatic breast cancer that is unresponsive to other endocrine therapies. Although the precise mechanism underlying the anticancer efficacy of HD-TOR in cases with prior endocrine therapy failure is not yet clear, a recent report suggested the dose-dependent inhibition of the MAPK/ERK signaling pathway in addition to hormone receptor blockade . SeveralOne aim of the present study is to examine the effectiveness of HD-TOR against postmenopausal hormone-sensitive progressive or recurrent breast cancer. In addition, we examined whether AI resistance influences HD-TOR efficacy because AIs are still the most frequently used first-line treatments.A retrospective analysis was conducted to investigate the outcomes of women with postmenopausal hormone-sensitive recurrent or metastatic breast cancer who received HD-TOR (120\u2009mg/day). We reviewed age, hormone receptor, and human epidermal growth factor receptor 2 (HER2) expression status at the latest biopsy, site(s) of metastasis at the beginning of HD-TOR therapy, therapies used before HD-TOR, and the antitumor effects of HD-TOR. The antitumor effects were judged on the basis of RECIST 1.1. The overall response rate (ORR) and clinical benefit rate (CBR) were calculated and compared between clinical subgroups defined by HER2 status, history of endocrine therapy, metastatic organ, presence of AI resistance, and type of AI resistance (primary or secondary) by Fisher's exact test.We classified AI resistance as primary or secondary on the basis of the following definitions. Primary resistance was defined as recurrence within 2 years after the start of adjuvant endocrine therapy with AIs or progression within 6 months from the start of AI therapy for metastatic breast cancer. Secondary resistance was defined as recurrence later than 2 years after the start of adjuvant endocrine therapy with AIs until 12 months from the end of AI adjuvant endocrine therapy or progression later than 6 months after the start of AI therapy for metastatic breast cancer [6]. TimIn all, 21 consecutive patients (19 women and 2 men) received HD-TOR for hormone-sensitive recurrent or metastatic breast cancer at our institution from September 2012 to August 2016 . The medp = 0.035; CBR: 100% vs. 24%, p = 0.088). The CBR was also significantly higher in the subgroup of patients without liver metastasis . The ORR and CBR tended to be higher in patients who had developed secondary resistance to AIs .The ORR was 21.1%, and the CBR was 31.6% . The ORRp = 0.159).The 17 cases with AI resistance consisted of nine cases with primary and eight cases with secondary resistance. The primary resistance subgroup had a higher frequency of previous chemotherapy and a lower frequency of lung metastasis than the secondary resistance subgroup . There were no significant differences in the other factors between the primary and secondary AI resistance subgroups . Figurede novo) or secondary (acquired) on the basis of the timing of recurrence or progression .\u201316.12\u201316This study has several limitations. First, the study population was too small to evaluate HD-TOR efficacy between the known risk factor subgroups. The small study population also precluded detailed side effect evaluation. In addition, side effect comparisons were limited by the retrospective study design. However, we found no obvious side effects even after an extensive review of the medical records.High-dose toremifene appears to be effective for advanced breast cancer with secondary resistance to AIs but is not effective in advanced cases with liver metastasis. Further studies are warranted to identify additional factors predictive of HD-TOR efficacy for advanced breast cancer."} +{"text": "Signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) are often limited in first-pass myocardial perfusion images due to the demands for ultra-fast image acquisition and the use of parallel imaging techniques. Spatial or temporal low pass filtering can enhance SNR but may blur boundaries and generate artifacts. The Karhunen-Loeve Transform (KLT) filter takes advantage of temporal correlation to remove random noise without compromising either spatial or temporal resolution, thereby enhancing SNR in dynamic images , 2, but The purpose of this study is to demonstrate that the combination of non-rigid registration and KLT filtering significantly improves CNR between normal and abnormally perfused myocardium without introducing blurring or other image artifacts.nornal - Sabnormal)/\u03c3n, where Snornal, Sabnormal are the mean signal intensities of normal and abnormal myocardium and \u03c3n is the standard deviation of the noise from a region outside the body. Identical ROI's were drawn on filtered (registration + KLT) and unfiltered images for evaluation of CNR improvement. In order to assess blurring or other artifacts induced by filtering, KLT filtered images both with and without prior non-rigid registration were evaluated by two experienced observers. Artifact level relative to the unfiltered image series was scored as: (1) none, (2) mild, (3) moderate and (4) severe.Ten consecutive first-pass perfusion datasets interpreted positive for ischemia or infarction were processed and analyzed retrospectively. All images were acquired using GRE-EPI with TSENSE acceleration rate 2 on a 1.5 T MR system . For each subject, all slices showing clinically interpreted perfusion defect were included in the analysis. Non-rigid body registration was firsThe overall SNR of perfusion images increased with filtering. Figure The combination of non-rigid registration and KLT filtering was shown to increase the SNR of GRE-EPI perfusion images, with a direct increase of CNR between normal and abnormal regions. Subjective evaluation of image artifacts revealed no significant blurring or other artifacts caused by filtering, provided non-rigid registration was performed first."} +{"text": "The aim of our study is to explore the relationship of rabbit anti-thymocyte globulin (R-ATG) on development of post-transplant lymphoproliferative disease (PTLD) and its aggressive forms (monomorphic PTLD and Hodgkin lymphoma) in renal transplant recipients.All patients diagnosed with PTLD post-renal transplant in the United States\u2019 Organ Procurement and Transplantation Network from 2003 till 2013 and followed up till 2017 were retrospectively reviewed. Multi-variable logistic regression analysis assessed association of R-ATG to development of PTLD and its aggressive form.p\u2009=\u2009.02) and is associated with higher risk of development of aggressive PTLD .Risk of developing PTLD post renal transplant is 1.35%. In comparison to interleukin-2 blocker induction therapy, R-ATG is associated with increased risk of development of PTLD . Careful monitoring for development of PTLD in renal transplant recipients receiving R-ATG induction therapy is advised. Post-transplant lymphoproliferative disease (PTLD) is one of the most common cancers occurring after solid organ transplantation, accounting for almost 20% of all cancers ,2. It isvia disrupting cancer immune-surveillance and immunological control of oncogenic viruses [The initial treatment of PTLD is the reduction or withdrawal of immunosuppression which may lead to resolution of early lesions . Other t viruses ,22. HoweThe study was exempt from ethical approval by Liverpool university. All renal transplant patients registered in organ procurement and transplantation network (OPTN) from January 2003 until January 2013, received R-ATG or interleukin-2 receptor antagonist induction therapies and discharged on calcineurin inhibitors maintenance therapy were retrospectively reviewed. Patients were followed up till June 2017. Exclusion criteria were patients who had transplants other than the kidneys, multiple organ transplant, previous renal transplant, patients who received treatment for post-operative acute rejection episodes, patients who received monoclonal antibody alemtuzumab (Campath) or any type of ATG for treatment of acute rejection till the end of follow-up period. Muromonab-CD3 antibody (OKT3) and high doses of R-ATG induction therapies have been commonly used in the USA in 1980s and early 1990s. However, afterwards, OKT3 has been commercially unavailable and lower doses of R-ATG has been widely used . By 2003Collected data included recipient and donor age, sex, ethnicity, donor type (living/non living), extended criteria donors, type of induction therapy, maintenance immunosuppression medications at time of discharge, type of PTLD, panel reactive antibody (PRA) titer, cold ischemia time, HLA mismatches, EBV status, CMV, HBV, HCV and HIV status for the transplant recipient. Types of PTLD were defined according to the 2008 WHO classification [p value less than .05 was a cutoff point for poor fit model. Patients with missing data about induction therapy were excluded while performing multi-variable logistic regression analysis. R-ATG was compared to IL2-RA induction therapy in the logistic regression models.STATA package-15 was used for the analysis. The starfiles used from OPTN database were kidpan, immunosuppression_discharge, immunosuppression_follow and kidney_malig_followup_data. Duplicates from each file were removed separately and then the files were merged into one file using 1:m merge command. Continuous variables were reported as means and standard deviation while categorical variables were reported as percentages or frequencies. To prove association, multi-variable logistic regression analysis was used to assess the impact of R-ATG induction therapy on the development of PTLD and aggressive PTLD (monomorphic PTLD and Hodgkin lymphoma) in the presence of other cohort characteristics that are well-known to affect development of PTLD. Performance and calibration of the model were assessed using AUC analysis and Pearson goodness-of-fit tests. After deduplicating selected files from OPTN database and removing patients who lack data about transplant date, 82838 patients were found to have renal transplantation since January 2000 till June 2017. Out of these patients, 1119 developed PTLD (1.35%). Types of PTLD are shown in p\u2009=\u2009.026). Area under the curve for this model equals 0.59. There is no evidence for poor fit in this model (p\u2009=\u20091).After applying inclusion and exclusion criteria to the merged files, sample size of the study was equal to 14,988 patients (8360 patients received R-ATG induction therapy and 6628 patients received IL2-RA induction therapy). Multi-variable logistic regression analysis assessing the impact of R-ATG induction therapy on development of PTLD is shown in p\u2009=\u2009.048). Area under the curve for this model equals 0.63. There is no evidence for poor fit in this model (p\u2009=\u20091).Multi-variable logistic regression analysis assessing the impact of R-ATG induction therapy on development of aggressive PTLD (monomorphic PTLD and Hodgkin lymphoma) is shown in et\u00a0al., showed that equine anti-thymocytic globulin (E-ATG) increased the risk of PTLD, while R-ATG did not [This retrospective study utilized the OPTN database and demonstrated that R-ATG induction therapy was associated significantly with increased risk of PTLD and a higher risk of developing the aggressive forms of PTLD. Our study analyzed a large cohort of PTLD-affected renal transplant recipients with 10-years recruitment period (2003-2013) allowing us to produce strong results. Similarly, previous studies utilized OPTN database to study the effect of immunosuppression (IS) on incidence of PTLD. Although concurring with our results, no study focused on subgroup analysis of different types of PTLD and its association with R-ATG use . Also, w did not . This is did not . Althoug did not . Concurr did not . Intereset\u00a0al., found that polyclonal induction is not associated with a statistically significant higher risk of PTLD [et\u00a0al., conducted a retrospective review on all PTLD patients after kidney transplant documented in the Australia & New Zealand Dialysis and Transplant Registry from 1970 to March 2003 [et\u00a0al., used the UNOS registry to find the incidence & risk factors of early onset (within two years from date of transplant) & late onset PTLD (two or more years post-transplant) among kidney transplant recipients from 1999-2007 [On the other hand, several other studies failed to show a link between ATG and PTLD. Cherikh of PTLD . However of PTLD . Moving rch 2003 . They forch 2003 . Quinlan999-2007 . These avia disrupting cancer immunosurveillance and immunological control of oncogenic viruses and this concludes plausibility [We used R-ATG at time of induction to ensure that it was administered at a specific time point before development of PTLD and its aggressive form (monomorphic PTLD and Hodgkin lymphoma). Furthermore, we excluded all patients that received treatment of post-operative acute rejection episodes or received Campath or any type of ATG for treatment of acute rejections during follow-up. This allowed us to exclude effect of treatment for acute rejection episodes as a confounding factor on our results. R-ATG can increase the risk of PTLD sibility ,22.Our study is unique in several ways. We analyzed the association of R-ATG to different subtypes of PTLD and included a very large cohort of PTLD affected renal transplant recipients abstracted from the OPTN data. In addition, our long recruitment period of 10-years further enhanced our results. The present results are important in improving our understanding of immunosuppressive therapies and PTLD.Limitations of using registry data include missing data and presence of non-measured confounders. Since monomorphic lymphoma is an aggressive disease mostly with poor outcome , we beliWe conclude that R-ATG induction is associated with a higher risk of PTLD and its aggressive form (monomorphic PTLD and Hodgkin lymphoma). Careful monitoring for development of PTLD in renal transplant recipients receiving R-ATG induction therapy is advised."} +{"text": "Adoptive cell transfer (ACT) has long been at the forefront of the battle with cancer that began last century with the therapeutic application of tumor-infiltrating lymphocytes (TILs) against melanoma. The development of novel ACT approaches led researchers and clinicians to highly efficient technologies based on genetically engineered T lymphocytes, with chimeric antigen receptor (CAR)-T cells as the most prominent example. CARs consist of an extracellular domain that represents the single-chain variable fragment (scFv) of a monoclonal antibody (mAb) responsible for target recognition and the intracellular domain, which was built from up to several signaling motifs that mediated T cell activation. The number of potential targets amenable for CAR-T cell therapy is expanding rapidly, which means that the tremendous success of this approach in oncology could be further translated to treating other diseases. In this review, we outlined modern trends and recent developments in CAR-T cell therapy from an unusual point of view by focusing on diseases beyond cancer, such as autoimmune disorders and viral infections, including SARS-CoV-2. Adoptive cell transfer (ACT) has a rich history in the development of cancer treatments. Last century, an immune therapy approach against melanoma was developed based on enhancement of tumor-infiltrating lymphocytes (TILs). Nowadays, the development of ACTs led researchers and clinicians to technologies based on genetically engineered T lymphocytes . One of CARs are synthetic constructs that consist of extracellular domains for target cell recognition represented by a single-chain variable fragment (scFv) from a monoclonal antibody (mAb). The intracellular part includes up to several signaling motifs capable of T cell activation . One of The number of available targets for CAR-T cell therapy is expanding rapidly . Major sPathogenesis of many autoimmune diseases (AIDs) has still not been determined precisely, but there is no doubt that T cell tolerance failure plays a central role in this process . The mecThe chimeric autoantibody receptor (CAAR), also known as the B cell antibody-targeting receptor (BAR), represents a variation of modified CAR. Unlike the scFv domain, CAAR functions as a target for autoreactive B cells and defines the selective cytotoxicity of CAAR-T cells only against immune cells that carry receptors to specific autoantigen without inducing immunosuppression ,7. Such Another interesting concept for the restoration of immune tolerance implies \u201cswitching\u201d T cell phenotype from cytotoxic to regulatory, since Tregs are usually suppressed in AIDs. CAR-Tregs represent CAR-T cells converted to Tregs by transduction of FOXP3 , which is a member of the FOX protein family that controls pathways responsible for the development and function of regulatory T cells . CAR-TreThese approaches were tested in a number of preclinical studies, e.g., Ellebrecht et al. tried to use CAAR-T cells to treat AIDs in case of pemphigus vulgaris (PV), an autoimmune disease that causes painful blistering on the skin and mucous membranes . PV is aA similar concept was proposed by Parvathaneni et al. for the treatment of Hemophilia A (HA) . RecombiMany studies related to CAR-T therapy against AIDs are focused on Type 1 diabetes (T1D), a T cell-mediated autoimmune disease in which both CD4+ and CD8+ T cells are involved in the destruction of insulin-producing islet \u03b2 cells. Fishman et al. proposed the design of a peptide/\u03b22m/CD3-\u03b6 receptor that targets CD8+ T cell clones carrying TCRs specific to the peptide of interest, e.g., fragments of insulin-B chain InsB15\u201323, or islet-specific glucose-6-phosphatase catalytic subunit-related protein IGRP206\u2013214 . They reThe abovementioned concept was also examined as a potential treatment for multiple sclerosis (MS) since one of the central roles in its pathogenesis is autoreactive T cells recognizing myelin epitopes. Fransson et al. designed CAR-Tregs to target myelin oligodendrocyte glycoprotein (MOG) in which the role of the CAR-\u03b1MOG receptor was to bring Tregs in close proximity with MOG+ oligodendrocytes to prevent immune attacks against them . CAR-TreCAR-Tregs were also reported to be effective for the treatment of ulcerative colitis associated with overexpression of carcinoembryonic antigen (CEA), a well-known tumor marker of colon inflammation . Blat etImportantly, three ongoing clinical trials are focused on the application of CAR-T cell therapy against autoimmune diseases by depleting the whole B cell population instead of the point autoreactive clone elimination. NCT04146051 evaluates autologous Descartes-08 CAR-T cells that target B cell maturation antigens (BCMA) for the treatment of generalized myasthenia gravis, which is a chronic, autoimmune, and neuromuscular condition that causes muscle weakness in different parts of the body. NCT03030976 is based on classical anti-CD19 CAR-Ts to deplete B cells in CD19+ systemic lupus erythematosus (SLE), in which the immune system attacks its own tissues, causing widespread inflammation and tissue damage in the affected organs. Another clinical study (NCT03605238) used tandem anti-CD19 and anti-CD20 CAR-Ts to treat neuromyelitis optica spectrum disorder (NMOSD), which is a chronic disorder of the brain and spinal cord dominated by inflammation of the optic nerve (optic neuritis) and inflammation of the spinal cord (myelitis). In addition, the NCT04561557 study is based on anti-BCMA CAR-T cells for elimination of plasma cells in patients with AQP4-IgG-seropositive NMOSD who suffer recurrent attacks from conventional treatments.Allergic diseases (ADs) and asthma are characterized by the domination of the Th2 immune response, which can be modulated by Tregs . IgE proThe main event in the initiation of allergic reactions is the binding of IgE to its respective IgE receptor Fc\u03b5RI, which are expressed on mast cells, eosinophils, and basophils that cause degranulation and release of inflammatory mediators resulting in type I hypersensitivity reactions and allergic symptoms . Ward etPathogenesis of allergic asthma is associated with a low number of Tregs and reduced immunosuppressive activity, as well as excessive Th2 cell-dominated responses to allergens leading to airway inflammation, hyper-reactivity, and reversible obstruction . SkuljecThe main function of CD8+ T cells is their ability to eliminate foreign cells and agents, making them attractive CAR-Ts for treating infectious diseases . PatientChronic hepatitis C virus (HCV) infection is a medical indication for liver transplantation for end-stage chronically infected patients who are nonresponsive to current therapies. For many HCV cases, there remains a high risk of post-treatment reinfection, which implies a need for the development of alternative therapeutic approaches. Sautto et al. developed CAR-T cells that recognize HCV E2 glycoprotein (HCV/E2), a major target of the host immune response and one of the most variable viral proteins exposed on the surface of infected cells . These aInfection by human cytomegalovirus (HCMV) and its reactivation is a major cause of mortality after hematopoietic stem cell and solid organ transplantation. Proff et al. attempted to redirect T cells to HCMV-glycoprotein B (gB); however, despite the activation, anti-gB CAR-T cells were not able to lyse infected cells in vitro . Anti-gBThe Influenza A virus, which gave rise to swine flu and avian flu, was studied by Talbot et al. as a potential therapeutic application for CAR-T cells . In thisHuman immunodeficiency virus type 1 (HIV-1) replication can be successfully suppressed via combination antiretroviral therapy (cART); however, complete elimination of the latent reservoir of infected cells still remains a major problem. CD8+ T cellular cytotoxic activity against HIV-1 infected cells plays a critical role in managing HIV-1 infection; therefore, attempts to apply CAR-Ts for HIV-1 treatment provide a promising new therapeutic avenue that catches up with its use in oncology ,25.The main target for anti-HIV-1 CAR-T therapy is considered to be the gp120 region of the HIV Envelope (Env) glycoprotein expressed on the surface of HIV infected cells . Deeks eSince the early trials began, the structure and function of clinically tested CARs have vastly improved. Sahu et al. developed a second generation CD4+ CAR-Ts that, in vitro, eliminated not only infected and HIV-producing cells but the entire latent cell population . LeibmanDespite the overall limited in vivo efficacy, the interest towards the application of anti-HIV CAR-T has significantly intensified over the past few years due to the outstanding success of CAR-T therapy in cancer treatment. Anti-HIV CARs based on a single-chain fragment of the human anti-gp120 mAb were used by Masiero et al., who designed and tested such constructs in vitro and achieved promising results . An inteSeveral research groups attempted to combine CD4-based and BNAbs-based CARs into one construct to allow dual specificity and produce highly potent anti-HIV CAR-T cells. Liu et al. reported bispecific CD4+ CAR-Ts consisting of human CD4 (binds native Env on virions) attached to an scFv of the human anti-gp120 mAb . This apCurrently, two Phase I clinical trials are recruiting to evaluate the safety and efficacy of CAR-T cell therapy for HIV treatment. The NCT03240328 trial enrolls HIV patients whose plasma HIV has been successfully suppressed after cART and is expected to enhance the reconstitution of HIV-specific immune function to assist the eradication of HIV reservoirs. The NCT03980691 trial evaluates the combined effect of chidamide with CAR-T or TCR-T cell therapy on HIV-1 latent reservoirs. The NCT04648046 trial that will evaluate the efficacy of bispecific anti-gp120 CAR-T cells has not yet started.The approach of using CAR-transduced immune cells against virus infected cells has recently attracted the attention of the scientific community for the treatment of COVID-19, a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A promising therapeutic approach is based on natural killer (NK) cells, which are effector lymphocytes of the innate immunity with the main function to destroy tumor and virally infected cells. NK cells function through either direct recognition of viral proteins or inhibitory NK receptor signaling in the case of downregulated MHC class I on the infected cell surface .Ma et al. tried to develop CAR-NK cells to target the SARS-CoV-2 spike protein with the CR3022 scFv domain, which is a strong neutralizing antibody for SARS-CoV-1 and SARS-CoV-2 . They foCurrently, there is only one clinical trial (NCT04324996) evaluating bispecific NKG2D-ACE2 CAR-NK cells as a promising COVID-19 therapy. NKG2D is the universal activating receptor of NK cells that recognize the infected cells, while ACE2 is the receptor that binds the SARS-CoV-2 spike protein .In addition to the expanding scope of clinical applications, lessons learned from CAR-T therapy helped us tackle the complications in other diseases. An interesting example is the cytokine release syndrome (CRS) caused by hypersecretion of proinflammatory cytokines by CAR-T cells activated in response to tumor recognition . CRS is Fibrosis is a pathological process associated with the hyperactivation and expansion of fibroblasts, as well as the deposition of extracellular matrix components. Many pathological stimuli can lead to cardiac fibrosis and the progression of heart failure. Currently, there is still no available targeted therapy to treat cardiac fibrosis. Aghajanian et al. assessed the potency of CAR-T cells that target activated heart fibroblasts through the recognition of fibroblast activation protein (FAP) in mice with induced hypertensive cardiac injury and fibrosis ,39. TheyThe ever-growing progress in our understanding of various pathologies and their fundamental molecular mechanisms pushes the application boundaries of cellular immunotherapy far beyond oncology. A plethora of molecules confirmed as therapeutic targets for a wide range of diseases renders immune cell therapy as an attractive and highly promising treatment option . The rapThe application of CAR-T cell technology is eagerly awaited in numerous fields, e.g., for the treatment of viral infections in patients with primary immune deficiency (PID) . CurrentIn addition, investigation of CAR-T cell action in immune dysfunction caused by autoimmune diseases or HIV can help understand mechanisms of tumor immune evasion. For example, exploring migration of CAR-T cells into the tumor stroma and the lymph node HIV sanctuaries will generate mutually complementary new knowledge about the molecular mechanisms involved in both pathogenic conditions .Despite a large number of common issues associated with CAR-T cell therapy that still remain largely unresolved , the overall great promise of this approach is supported by encouraging clinical results and solid technological basis . The ong"} +{"text": "EML4-ALK fusions are targetable oncogenic drivers in a subset of advanced non-small cell lung cancer (NSCLC) patients that can benefit from selected ALK inhibitors. Precise detection of ALK fusions may yield critical information for selection of appropriate therapy and hence improve patient survival. Analysis of circulating tumor DNA (ctDNA) in liquid biopsies using next generation sequencing (NGS) prior to or during treatment hold great promise for disease monitoring and treatment guidance of various cancers including NSCLC. Herein, we report a case of a 21-year-old advanced lung adenocarcinoma patient with a low abundance (0.03%) of EML4-ALK rearrangement identified in plasma ctDNA upon progression on two lines of chemotherapy that demonstrated long-term complete response to alectinib (>13 months) including metastatic brain tumors. Patient's clinical and pathologic characteristics, computerized tomography (CT) scans and brain magnetic resonance imaging (MRI) were reviewed retrospectively. Taken together, our report not only reinforces the translational utility of NGS-based genomic sequencing of liquid biopsy in guiding clinical practice, but also highlights the superior efficacy of alectinib than chemotherapy in ALK+ NSCLC with brain metastases, albeit at a low variant allele abundance. ALK rearrangements have been recognized as central oncogenic drivers for many solid malignancies. EML4-ALK fusions occur in ~2\u20137% of advanced non-small cell lung cancer (NSCLC) patients, and are more frequently detected in lung adenocarcinoma as well as in never- or light- smokers or young adults in liquid biopsies using next generation sequencing (NGS) provide a non-invasive approach to tumor molecular profiling and is increasingly utilized to screen presence of disease, guide therapy selection, and evaluate treatment response (EML4-ALK fusion in plasma ctDNA.Aberrant g adults . Despiteresponse . However2) and cisplatin (75 mg/m2) and achieved a partial response (PR) according to the RECIST guideline version 1.1(2). The patient demonstrated a progression-free survival (PFS) of about 20 months in total during the course of first-line chemotherapy until the disease progressed with the occurrence of bone metastases in October 2017, although the primary lung lesion remained stable and carboplatin (6 mg/ml/min). In January 2018, the patient was switched to single-agent pemetrexed due to severe allergic reactions to carboplatin. The primary lung tumor demonstrated durable complete response to second-line chemotherapy (EML4-ALK fusion variant (E6:A20) was detected at a low allele frequency (AF) of 0.03% in plasma ctDNA using the same targeted NGS panel in March 2019 upon the diagnosis of multiple brain metastases by brain magnetic resonance imaging ablation for the primary lung lesion in October 2017, followed by two cycles of second-line pemetrexed was reported to be lower than that for mutations or indels , and difbenefits , 11, a tnt NSCLC \u201314. TogeALK-rearranged NSCLC, the disease inevitably relapses in the clinic mainly owing to acquired therapy resistance mediated by multiple mechanisms. A number of ALK inhibitors including brigatinib . In brief, genomic DNA were extracted from cervical lymph node biopsy specimen using the DNeasy Blood & Tissue kit (Qiagen) according to the manufacturer's protocols. Cell-free (cfDNA) from pericardial effusion or plasma samples was extracted using the QIAamp Circulating Nucleic Acid kit (Qiagen). Approximately 200 ng of cfDNA was used for subsequent library preparation using the KAPA Hyper Prep kit (KAPA Biosystems) according to manufacturer's suggestions for different sample types. Sequencing library preparation, targeted gene enrichment, and sequencing data processing were carried out following the methods as previously described .EML4-ALK fusion demonstrated a durable complete response to alectinib.An advanced lung adenocarcinoma patient with a low abundance of Analysis of plasma ctDNA changes using NGS-based liquid biopsy assays holds great promise for tracing disease progression or recurrence and guiding treatment decision-making.The datasets generated for this study are available on request to the corresponding author.The studies involving human participants were reviewed and approved by the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China. The patients/participants provided their written informed consent to participate in this study. Written informed consent was obtained from the patient for publication of this case report and any accompanying images.YZhu and RJ conducted data curation and project management. YS, LZ, QO, and XW reviewed and analyzed data. YZha designed the concept and methodology and supervised the entire study. QO, MY, and YZha wrote the manuscript and all authors read and approved the final manuscript. All authors contributed to the article and approved the submitted version.YS and LZ are the employees of Nanjing Geneseeq Technology Inc., China. QO, MY, and XW are the employees of Geneseeq Technology Inc., Canada. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Halomonas titanicae strain TAT1, isolated from production water of the Romashkinskoe oilfield (Russia) is presented. The genome is annotated for elucidation of the metabolic pathways involved in hydrocarbon degradation and nitrate reduction in petroleum-contaminated hypersaline environments.The draft genome sequence of a moderately halophilic bacterium, Halomonas titanicae strain TAT1, isolated from production water of the Romashkinskoe oilfield (Russia) is presented. The genome is annotated for elucidation of the metabolic pathways involved in hydrocarbon degradation and nitrate reduction in petroleum-contaminated hypersaline environments.The draft genome sequence of a moderately halophilic bacterium, Halomonas titanicae strain TAT1 (VKM B-3500D) was isolated from highly mineralized production water of the Romashkinskoe oilfield (Russia) , and low-quality reads were trimmed using Trimmomatic v. 0.36 , and cells were harvested after 7\u2009days of cultivation. DNA was purified from the cell biomass using the cetyltrimethylammonium bromide (CTAB) method under accession number SRR11977805. The genomic version described in this paper is version JABWTB010000000.This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the BioProject accession number"} +{"text": "Recombinant human granulocyte-macrophage colony stimulating factor (hGM-CSF) is a glycoprotein and hematopoietic growth factors that regulates the proliferation of myeloid precursor cells and activates mature granulocytes and macrophages. In a previous study, we reported that hGM-CSF could be produced in transgenic rice cell suspension culture, termed rhGM-CSF. In the present study, we examined the repeated dose toxicity of rhGM-CSF in SD rats. The repeated dose toxicity study was performed at each dose of 50 and 200 \u00b5g/kg subcutaneous administration of rhGM-CSF everyday for 28-days period. The results did not show any changes in food and water intake. There were also no significant changes in both body and organ weights between the control and the tested groups. The hematological and blood biochemical parameters were statistically not different in all groups. These results suggest that rhGM-CSF may show no repeated dose toxicity in SD rats under the conditions."} +{"text": "Following entry into host cells, the KSHV genome undergoes circularization and chromatinization into an extrachromosomal episome ultimately leading to the establishment of latency. The KSHV episome is organized into distinct chromatin domains marked by variations in repressive or activating epigenetic modifications, including DNA methylation, histone methylation, and histone acetylation. Thus, the development of KSHV latency is believed to be governed by epigenetic regulation. In the past decade, interrogation of the KSHV epitome by genome-wide approaches has revealed a complex epigenetic mark landscape across KSHV genome and has uncovered the important regulatory roles of epigenetic modifications in governing the development of KSHV latency. Here, we highlight many of the findings regarding the role of DNA methylation, histone modification, post-translational modification (PTM) of chromatin remodeling proteins, the contribution of long non-coding RNAs (lncRNAs) in regulating KSHV latency development, and the role of higher-order episomal chromatin architecture in the maintenance of latency and the latent-to-lytic switch.Kaposi\u2019s sarcoma-associated herpesvirus (KSHV) is an oncogenic Accurate epigenetic status is essential for normal development and maintenance of tissue-specific gene expression in mammals, and disruption of epigenetic regulation can cause aberrant gene expression and diseases, such as cancer. Different from genetic variation, epigenetics is a reversible mechanism that modifies the genome, and thus, repair of epigenetic lesions has been envisioned to be more feasible than correction of DNA mutations. Epigenetic therapies are therefore emerging as an active area of preclinical and clinical cancer research.There are three primary interconnected epigenetic mechanisms , includi(i)de novo methylation. 5-mC within CpG islands in mammalian promoter regions is associated with transcription repression and aberrant DNA methylation is a common lesion related to carcinogenesis (Methylation of the 5th carbon on cytosine (5-mC) was the first identified, and one of the most well-studied epigenetic marks related to cancer . DNA metogenesis . Cytosinogenesis . 5-hmC sogenesis .(ii)acetylating the \u03b5-amino group of lysine (Lys) using histone acetyltransferases (HATs), acetylation neutralizes the net positive charge on histones, leading to the unfolding of chromatin and exposure of negatively charged DNA to DNA-binding proteins, and consequently activation of gene transcription residues are known to be methylated. Arg can be mono- or di-methylated, with the latter in a symmetrical or asymmetrical manner, by protein arginine methyltransferases (PRMTs) (Histone (PRMTs) . Lys has (PRMTs) . In rece (PRMTs) . Histone(iii)Non-coding RNAs (ncRNAs) are RNA transcripts that do not encode proteins. Based on the length, ncRNAs are divided into two classes, (i) small ncRNAs (sncRNAs), with transcripts shorter than 200 nucleotides (nts), and (ii) long ncRNAs (lncRNAs), with transcripts longer than 200 nts that are devoid of protein-coding potential , though (iv)Architectural/spatial epigenetics considers the three-dimensional (3D) structure of a genome and its impact on gene expression and other nuclear activities. How the 3D organization of a genome operates with the addition of dynamics across time and its relationship to nuclear processes including transcription, DNA replication, and chromosome segregation are included in this class of mechanisms .\u03b3-herpesvirus Kaposi\u2019s sarcoma-associated herpesvirus is one of the seven recognized human oncogenic viruses and has been linked to Kaposi\u2019s sarcoma (KS) (The human oma (KS) , primaryoma (KS) , and an oma (KS) . KSHV isoma (KS) . After ede novo infection (de novo infection. This notion was supported by a report from DNA methylation on CpG islands is associated with gene silencing. It has been shown that the DNA methyltransferase inhibitor 5-Azacytidine (5-AzaC) is a stimulator of KSHV lytic reactivation , suggestnfection . They shnfection , indicatIt is important to note that both de novo infection. Initially with the help of K-Rta, KSHV genomes rapidly acquired the active histone marks H3K4me3 and H3K27-ac. This was followed by (1st to 3rd dpi) sequential deposition of repressive histone marks H3K27me3 by PRC2 and H2AK119-Ub by Polycomb repressive complex 1 (PRC1). It is believed that binding of CBX in PRC1 to H3K27me3 deposited by PRC2 helps recruit PRC1 to the KSHV genome and RING1B in PRC1 ubiquitinated H2A at K119 modification, were initially identified as reversible protein modifications that regulate signal transduction. Among the PTMs, accumulating evidence suggests that the SUMO system plays an important role in regulating chromatin organization and transcription . In addiAs SUMO modifications regulate chromatin organization, we showed that SUMOylation of the chromatin binding protein Kr\u00fcppel-associated box domain-associated protein-1 (KAP-1) is essential for its association with the KSHV genome and for maintaining viral latency. Phosphorylation of KAP-1 by KSHV vPK (ORF36) counteracts KAP-1 SUMOylation-dependent binding and thereby facilitates viral reactivation . BindingIn 2015, the genome-wide landscape of SUMO paralog modifications on the KSHV genome was revealed using ChIP-seq assays. The results showed similar SUMO-1 and SUMO-2/3 binding patterns on KSHV latent viral genomes and detailed a significant increase of SUMO-2/3 deposition upon reactivation . MechaniGene expression profiling of the KSHV life cycle using real-time PCR, oligonucleotide arrays, and Northern blotting has dete5 copies per cell assay, Interaction of PAN RNA with additional viral factors has also been examined. Through direct interaction with LANA, PAN RNA dissociates LANA from the KSHV genome and disrupts viral latency . Using aThe development of high-resolution chromosome conformation capture (3C)-based methodologies has estade novo infection. Although de novo infection, detailed mechanisms of the initial high-order structuring and nuclear residences of KSHV episomes are unknown.The looping/conformation model described above has only been studied in the context of latently infected cells and, as such, attempts to explain the maintenance of latency and the latent-to-lytic switch. However, it is currently not known how initial episomal chromatin conformations are established following de novo infection, the KSHV IE protein K-Rta may help viral episomes acquire active histone marks (Genome-wide analysis of KSHV episomes have revealed distinct temporal and spatial chromatin modification patterns on the viral genome. In summary, following ne marks and cellne marks . The binne marks and hSETne marks onto thene marks . Howeverne marks , 2017, rne marks . As the ne marks and at tne marks suggestiThe compartmentalization of the epigenetic marks on the KSHV genome might be beneficial for transcription regulation of viral gene expression during its distinct life cycle. The well-organized DNA methylation and different histone modification patterns on the KSHV genome reflects the precise recruitment of cellular chromatin modifying complexes employed by the virus. KSHV latency is essential for persistent infection as well as the development of KSHV-associated malignancies. In recent years, more and more epigenetic modifications and the corresponding modifying enzymes have been identified. Drugs targeting epigenetic modification enzymes have now evolved into a potential viable strategy for controlling persistent viral infections . Thus, eMC wrote and edited the manuscript. W-SY helped writing the manuscript. C-HK constructed the figures. P-CC worked on the constructs and the manuscript writing. WY contributed to the final revision with modification of manuscript and The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Despite several proposed mechanisms for the pathophysiology of cardiorenal syndrome (CRS), the exact mechanism remains unclear. Nitrosative stress has been argued as a key mechanism recently. Nebivolol is a beta-blocker with nitric oxide (NO)-releasing effect. In the present study, NO-mediated effects of two different treatment regimes of nebivolol in CRS were studied. Rats were divided into: sham-operated (sham-control), myocardial infarction (MI)-induced, (MI-control) early nebivolol-treated (MI-neb1) and late nebivolol-treated (M\u0131-neb2) groups. The effects of nebivolol were assessed both in the early and late period of MI by histologic, hemodynamic and biologic studies.Developed MI model was in line with the heart failure with preserved ejection fraction. Focal and total tubular damage findings were observed in MI-control group both in early and late period of MI. In parallel, subclinical functional damage was transformed into chronic renal dysfunction in this group. Increased inducible nitric oxide synthase (iNOS) and endothelial NOS (eNOS) together with decreased neuronal NOS (nNOS) levels were in parallel with the increased inflammation and nitrosative stress biomarkers. Nebivolol effectively prevented both subclinical and clinical nephropathy. There was no statistical difference between the nebivolol treatment regimes.The beneficial effects of nebivolol were closely related to the reduction of nitrosative damages as well as hemodynamic alterations. The NO-mediated effects were: prevention of nitrosative damage by decreasing iNOS, preservation of nNOS in order to maintain glomerular filtration rate (GFR), and restoration of eNOS in the late period of MI. On contrary to our previous work, early nebivolol administration had a similar effect with delayed administration of nebivolol on CRS. It is known that heart and kidney diseases affect each other through different mechanisms. Although complex interplay between the heart and kidneys is known from the beginning of the nineteenth century , this wa2) and other highly oxidizing reactive oxygen species (ROS) and sympathetic system activation . Althouges (ROS) . The rolNebivolol is a beta-blocker agent. Although NO-mediated effects of nebivolol have been demonstrated in different cardiovascular pathologies, these effects on renal dysfunction are unknown. In this study, we aimed to evaluate the NO-mediated effects of two different treatment strategies of nebivolol in the development and progression of CRS. Animals and dose selectionSprague-Dawley rats were divided into 4 groups of 18 each: Sham operated control (sham-control); MI induced control (MI-control); MI induced and immediate intravenous load followed by oral nebivolol-treated group (MI-neb1) and MI induced and oral nebivolol-treated group (MI-neb2)Nebivolol dose was selected as the minimum beta-blocker dose (characterized by the absence of significant effect on blood pressure and heart rate) in a preliminary dose-response study ) in which, the hemodynamic effects were compared to metoprolol, a \u03b21-selective adreno-receptor antagonist . AccordiAll experimental procedures were performed in accordance with the Guide for the Care and the Use of Laboratory Animals published by the US National Institutes of Health. The local animal ethic committee approval was obtained for all experimental procedure. Induction of myocardial infarctionMI was induced by the ligation of the left anterior descending coronary artery as described previously . The shaLeft ventricular function and hemodynamic parametersLeft ventricular (LV) function was evaluated by echocardiography in lightly anesthetized animals as described previously . Two-dimHemodynamic measurements were performed according to our previous study . LV systBiochemical assessments\u00b0C until analysis. Kidneys were snap-frozen in liquid nitrogen and stored at -70 \u00b0C for subsequent biochemical assays. The biochemical parameters were assayed in freshly prepared homogenates.Animals were anesthetized, abdomen was opened and blood samples were collected from the inferior vena cava, and the kidneys were dissected out, cleaned off the extraneous tissue and weighed. Blood samples were centrifuged and kept at -20 Kidney functions As a representation of renal function, serum creatinine (Cr) and blood urea nitrogen (BUN) levels were measured by a standard technique using an Olympus AU 2700 Analyzer . Plasma was analyzed for C-reactive protein (CRP) in order to assess the systemic inflammation using an automated analyzer .Tissue total antioxidant capacity, total oxidant status and oxidative stress index 2O2 equivalent/milligram protein for TOC.Tissue total antioxidant capacity (TAC) and total oxidant capacity (TOC) were measured spectrophotometrically using commercially available kits according to manufacturer\u2019s instruction . The results were expressed as nanomole Trolox equivalent/mg protein for tissue for TAC and nanomole H2O2 equivalent/milligram protein)/ (The percent ratio of TOC level to TAC level was accepted as the oxidative stress index (OSI) and calculated according to the following formula: (nanomole Hprotein) .Malondialdehyde (MDA), and glutathione (GSH) levels as oxidative damage biomarker and superoxide dismutase (SOD) level as antioxidant defense system biomarker were measured using commercially available kits according to manufacturer\u2019s instruction. Tissue NO, ONO2- and cyclic guanylate cyclase levels NO was measured in the tissue supernatants as nitrite/nitrate (NOx) concentration by spectrophotometry .2- or NO/ cyclic guanylate cyclase (cGMP) pathway, ONO2- and cGMP levels were measured by using enzyme-linked immunoassay (ELISA) . Tissue protein levels were determined using the method proposed by Folin-Lowry and masson-trichrome (MS). The tissues were investigated under a light microscope (Olympus BH-2). Severity of heart damage was examined as the early coagulative necrosis parameters and late signs of MI . et al. and glomerular (widening of the Bowman space) alterations. Severity of renal damage was scored with grading system of 0 to 3, developed by Chatterjee et al. on a bliImmunohistochemistry\u00b0C according to the manufacturer instructions. Sections were examined under light microscope and labeling intensity was graded using a semi-quantitative scale of 1+ (weak), 2+ (moderate) or 3+ (strong) labeling on a blinded basis.The immunohistochemical studies were performed according to the developed technique as described previously (6). Samples were incubated using endothelial nitric oxide synthase (eNOS) Ab-1 (dilution 1:200) and inducible NOS (iNOS) Ab-1 (dilution 1:200) antibodies (Abcam UK) for 2 hr at room temperature and neuronal NOS (nNOS) (dilution1: 100) (Abcam UK) for overnight at 4 Statistical analysispost-hoc Bonferroni test and P<0.05 was considered statistically significant.Statistical analysis was performed with SPSS 24.0 software program . All variables were expressed as mean\u00b1standard deviation. Echocardiographic, hemodynamic and biochemical measurements were analyzed by ANOVA and P>0.05). A total of 54 animals were included in the study. MI was confirmed by the increase in troponin T levels. However, troponin T levels were insignificant between groups . This trend continued for 28 days and functional abnormalities (characterized by decreased EF and CO) were significant in MI-control group as early as 2 day of MI ( 28 days . Compare 28 days . Hemodynamic parameters P>0.05) (Hemodynamic parameters are shown in P>0.05) . Biochemical assessmentsP=0.001, for all comparisons) . In this group, plasma CRP levels were also significantly higher than sham-control animals (arisons) . P<0.003). Although the OSI of MI-neb2 was lower than of MI-neb1, this decrease was not reached the statistically significant level (P>0.05) .P<0.05 for all comparisons). This trend continued throughout the study period. Nebivolol treatment prevented the decrease in SOD and GSH and increase in MDA levels . There was no statistically significant difference between MI-neb groups (P>0.05) th day of MI) . However, this difference reached the statistically significant level at the late period of MI (28 y of MI) Histologic assessmentsThe light microscopic images of sham-control rats showed normal myocardium, which demonstrated the normal orderly arrangement of myocytes and scant interstitial fibrosis. MI-control group was characterized by coagulative necrosis followed by typical inflammatory response and repair.\u00a0The changes of coagulative necrosis become evident early after MI (2 day of MI). Wavy cardiac muscle cells represented the coagulative necrotic cells and the presence of neutrophils represented that the inflammation could be recognized on HE-stained slices of MI-control rats. Collagen accumulation was also observed in MS-stained sections too Histopathological evaluation revealed that the renal tissues of the sham-control group had normal structure with no pathological changes. In the MI-control group, focal tubular damage characterized by focal brush border loss, tubular cell swelling, nuclear condensation and loss was prominent in the early period of MI (2 day of MI). Extensive tubular damage characterized by flattening in epithelial cells, and total brush border loss in proximal tubules was recognized in the late period of MI (28 day of MI) in this group. Compared to MI-control, regeneration signs were observed in nebivolol-treated groups. These changes were more prominent in MI-neb2 group. Especially at the late period of MI (28 day of MI), renal tissues of MI-neb2 animals were almost same as sham-control rats .nd day of MI). However, at the late period of MI (28th day of MI), iNOS-labeling intensities were weaker than sham-control (labeling intensity 1+ for both MI-neb groups) in these groups. Immunolabeling intensities of all groups are given in Cytoplasmic-membranous eNOS immunoreactivity both in juxtamedullary region and brush borders of proximal tubules was observed. Moderate eNOS staining was observed in sham-control group throughout the study (labeling intensity 2+ for both periods of MI) . Althougnd and 28th day of MI respectively). In nebivolol-treated groups, nNOS immunolabeling intensities were same as sham-control for both periods of MI (Cytoplasmic and partly nuclear nNOS immunolabeling in juxtamedullary region was observed. Strong nNOS immunoreactivity was observed in sham-control through the study (labeling intensity 3+ for both periods of MI). nNOS immunoreactivity was decreased early after MI in MI-control group. This decrease was continued throughout the study (labeling intensities were +2 and 1+ for the 2ds of MI .MI-caused heart failure with preserved ejection fraction (HFpEF)Bidirectional communication between the heart and kidney is well known. Under normal circumstances, this communication coordinates the modulation of the cardiac output, vascular tone and volume status and excretion of metabolic waste products . Disruptet al. . As discussed earlier, in order to increase the GFR, afferent vasodilation together with efferent vasoconstriction occurs as a compensatory mechanism in response to venous congestion. According to recent study on a rat spontaneous hypertension model, this compensatory mechanism is regulated by nNOS, and while SOD activates the effect of nNOS on afferent arterioles, O2\u2212 inhibits the regulatory effect of nNOS on the afferent arterioles and that these simultaneously produced radicals caused the formation of ONO2\u2212 by competing with SOD in the cytosol. In the same study, researchers also showed that ROS and RNS overproduction caused further mitochondrial damage by further disrupting cellular ATP production and emphasized the basic mechanism of tubular damage as a mitochondrial-induced cytopathic hypoxia , which adjusts absorption of salt and water in proximal tubules in proportion to changes in GFR . Unlike gulation . Brush bgulation . In the gulation , 49. MorThe beneficial effects of nebivolol were closely related to the reduction of nitrosative damages as well as hemodynamic alterationsA number of drugs, such as RAAS antagonists, vasodilators, vasopressin, adenosine antagonists, inotropes, nesiritide (recombinant form of B-type natriuretic) and diuretics have been studied in the treatment of CRS. Some of the studies in which heterogeneous results were obtained reported positive results on heart failure; however, a stable improvement in the prognosis of nephropathy could not be provided. The main target in these studies was usually hemodynamic parameters and neurohumoral activation. In addition to preclinical observations, clinical trials with diuretics and vasodilators have failed to record improvements in the nephropathy parallel to the improvement of hemodynamic parameters. Furthermore, the tendency of nephropathy to worsen with intensive diuretics and RAAS antagonist treatments indicates the necessity of different mechanisms in treatment. Strategies to reduce inflammation and oxidative stress are limited. To the best of our knowledge, this is the first study investigating the NO-mediated effects of nebivolol on both Type I and Type II CRS in a rat model of MI. According to our results, significant improvements were achieved in hemodynamic parameters with nebivolol. In the nebivolol groups, EF significantly improved compared to the MI-control. However, the improvement in LVEDP provided by nebivolol was much more pronounced. Despite the effective reduction in LVEDP with nebivolol in both periods of MI, the mean values \u200b\u200bwere still significantly higher compared to the sham-control group. Thus, a partial improvement with nebivolol may be mentioned, especially in diastolic functions. On the other hand, the effect of nebivolol on oxidative stress parameters was stable and evident. Nebivolol effectively prevented both subclinical and clinical nephropathy developed after MI. Contrary to significantly elevated Cr levels in MI-control group in the late period of MI (1.4 milligram/deciliter), unchanged Cr levels in nebivolol-treated groups in both periods of MI (0.9 milligram/deciliter) support this result. It should also be emphasized that the nebivolol dose used in this study was the minimum beta-blocker dose . The NO-mediated effects of nebivolol based on its source can be summarized as1. Prevention of oxidative/nitrosative damage by decreasing iNOS activity2\u2212, and ONO2\u2212 regulate water reabsorption in tubules on LV dysfunction in a rat MI model in our previous studies prevention of oxidative/nitrosative damage by decreasing iNOS activity; 2) preservation of nNOS activity in order to maintain GFR; 3) restoration of eNOS activity in the late period of MI."} +{"text": "A cluster of patients of novel coronavirus pneumonia (NCP) have been identified in Wuhan in December 2019 and soon this virus spread at a tremendous rate which swept through the whole China and more than 93 countries and regions around the world ) and the area under ROC curve was 0.962 (data unpublished). Our retrospective analysis of cases in Jiangsu Province proved a good consistency between early screening of SpOion Fig. .Fig. 1EaSince there have been no effective antiviral treatments for COVID-19 , 8, the Clinical experts-guided hierarchical management strategy(1) For patients with ARDS or pulmonary extensive effusion in CT scan, high-flow nasal cannula oxygen therapy (HFNC) or non-invasive mechanical ventilation (NIV) was used to maintain positive end expiratory pressure (PEEP) to prevent alveolar collapse even if some of these patients did not have refractory hypoxemia. 2) Restrictive fluid resuscitation under the premise of adequate tissue perfusion is performed to relieve pulmonary edema. (3) Although previous study proved prone position\u2019s benefit in moderate-to-severe ARDS patients with invasive mechanical ventilation (IMV) , we atte RestrictRational allocation of materials and human resourcesAt the outset of epidemic situation, a clinical experts-guided, multidisciplinary, province-wide hierarchical management group was established to provide medical guidance for all NCP patients . The memHealth authorities attached great importance to epidemic and deployed disease prevention and control measures effectively , 15. AllSince the outbreak of COVID-19, Jiangsu takes effective measures to curb the spread of the virus and gives normative treatments for infected patients, which shows significant disease control and treatment effects. From our experience, early screening of critically ill patients and critical care-guided early intervention are prominent in reducing NCP patients\u2019 mortality. At this critical moment in the global outbreak of NCP, we hope our valid management and treatment bundles can help us achieve the victory in the battle against COVID-19."} +{"text": "Robo2 regulates synaptic oxytocin content by affecting actin dynamics. Published 10, June 2019In the published article, Figure 6F inadvertently presented the wrong confocal Z-stack image of Tg and Tg(UAS:mCherry-Utrophin-CH) expression in the neurohypophysis of 5-dpf transgenic larvae. The corrected Figure 6 is now shown. No further changes were made to the text and figure legend. Please note that this correction does not affect the results and conclusions of the original paper.The corrected Figure 6 is shown here:The originally published Figure 6 is also shown for reference:The article has been corrected accordingly."} +{"text": "Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events associated with AML relapse in primary cells from 41 AML patients at time of diagnosis. Patients were defined as relapse-free if they had not relapsed within a five-year clinical follow-up after AML diagnosis. Relapse was associated with increased expression of RNA processing proteins and decreased expression of V-ATPase proteins. We also observed an increase in phosphorylation events catalyzed by cyclin-dependent kinases (CDKs) and casein kinase 2 (CSK2). The biological relevance of the proteome findings was supported by cell proliferation assays using inhibitors of V-ATPase (bafilomycin), CSK2 (CX-4945), CDK4/6 (abemaciclib) and CDK2/7/9 (SNS-032). While bafilomycin preferentially inhibited the cells from relapse patients, the kinase inhibitors were less efficient in these cells. This suggests that therapy against the upregulated kinases could also target the factors inducing their upregulation rather than their activity. This study, therefore, presents markers that could help predict AML relapse and direct therapeutic strategies. Acute myeloid leukemia (AML) is an aggressive and heterogeneous malignancy, the two main subsets being acute promyelocytic leukemia (APL) and the heterogenous group non-APL AML ,2. The ACEBPA, FLT3, NPM1 and TP53) are implemented in the routine prognostic evaluation and risk adapted treatment of AML patients procedures . B. Bg at 4 Image J . StatistThis study describes the proteomics profiles of patient-derived AML cells collected at the first time of diagnosis that differ between patients that are long-term relapse free survivors and patients that relapse. The relapse-associated group displayed decreased expression of V-ATPases and the increased activity of CDKs and CSK2. Furthermore, our results suggest a subset of transcriptional and metabolic regulators that could be considered as predictors of prognosis and therapeutic targets in AML."} +{"text": "Correction to: Arch Public Health (2020) 78: 3https://doi.org/10.1186/s13690-019-0385-6In the original publication of this article , the autFig. 1 Rescaling severity distributions that include asymptomatic cases to obtain symptomatic severity distributions. Example derived using GBD 2016 global health state prevalence estimates for cocaine dependenceFig. 2 Potential variation in disability weight for the 20 leading non-communicable diseases of YLD in the European region, 2017. YLD denotes Years Lost to Disability; 20 leading causes based on ranking of YLD rate for the European region; Non-communicable diseases only; Causes ordered ascendingly according to the number of YLDThe publisher apologizes to the readers and authors for the inconvenience."} +{"text": "The global burden of coronavirus disease 2019 (COVID-19) to public health and global economy has stressed the need for rapid and simple diagnostic methods. From this perspective, plasmonic-based biosensing can manage the threat of infectious diseases by providing timely virus monitoring. In recent years, many plasmonics\u2019 platforms have embraced the challenge of offering on-site strategies to complement traditional diagnostic methods relying on the polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). This review compiled recent progress on the development of novel plasmonic sensing schemes for the effective control of virus-related diseases. A special focus was set on the utilization of plasmonic nanostructures in combination with other detection formats involving colorimetric, fluorescence, luminescence, or Raman scattering enhancement. The quantification of different viruses with particular attention to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reviewed from the perspective of the biomarker and the biological receptor immobilized on the sensor chip. Technological limitations including selectivity, stability, and monitoring in biological matrices were also reviewed for different plasmonic-sensing approaches. Viral infections can be transmitted among human populations in a short period of time via droplets, aerosols, contact with abiotic surfaces, and even fecal matter ,2,3. TheTraditionally, viral diagnosis has relied upon culture-based methods and serological tests that detect either direct (intact viruses or their components: proteins or nucleic acids) or indirect virus infectious diseases .More recently, the advances of molecular techniques in viral diagnosis have permitted that nucleic acid-based amplification methods such as the polymerase chain reaction (PCR) and the reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) have consolidated as the gold standard methods for the routine diagnosis of a wide range of viruses (human immunodeficiency virus (HIV), hepatitis B and C viruses, and cytomegalovirus (CMV)) ,11,12,13Consequently, the requirement for fast and cost-effective viral diagnostic methods has led to putting the focus on the development of real-time biosensing platforms. Among the variety of biosensor technologies that have arisen in the last decades for virus detection, plasmonic applications have gained significant attention, owing to their versatility, label-free monitoring, and low time of response ,10,14. TOn the other hand, the chemical activation of the surface plays a major role for improving the sensing efficiency of single virus particles ,21. The Thus, nanoplasmonic biosensors provide a promising approach to attain ultra-low detection limits of viral particles, antigens, or nucleic acids from clinical specimens . The vast majority of virus sensing plasmonic applications are based on the well-known operation principles of surface plasmon resonance (SPR) biosensors. Nonetheless, the success in achieving optimal biosensing performance requires the design of novel biosensing strategies capable of maintaining the specificity and sensitivity of measurements while preserving the biocompatibility of the immobilized biological receptor.Therefore, the aim of this review was to present recent advances in plasmonic biosensing schemes for the detection of virus on the basis of signal enhancement. This review specially focused on the utilization of sensing surfaces comprising nanomaterials-based approaches. Current progress in the development of plasmonic-based applications involving the combination with colorimetric, electrochemical, fluorescence, or fiber-optic detection principles is also discussed.The fundamental principles of plasmonic biosensors rely on the propagation of surface plasmons along the interface of a thin, metal layer and a dielectric (aqueous medium). A detailed description of the optical working principles was comprehensively reviewed in previous works and it is beyond the scope of this review ,23,24. IThis special characteristic allows enhancing the spatial resolution of LSPR configurations by designing the geometry and composition of metallic nanostructures, laying the basis for colorimetric plasmonic biosensing ,28. The Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section.Nanomaterials provide the signal amplification of plasmonic biosensing due to their interesting optical, magnetic, and electrical properties. The biocompatibility and easy chemical activation are also significant advantages. Likewise, the large surface area-to-volume ratio provides a higher loading of biological receptors ,34,35,36Plasmonic nanomaterials can be classified regarding their chemical composition in organic and inorganic materials. Among the latter ones, noble-metal nanoparticles have been extensively applied to plasmonic biosensing due to the strong absorption of light resulting from the oscillation of the free electrons. The size and shape of nanoparticles along with the interparticle distance determine the amplitude of oscillation and the position of the SPR band . Likewis\u22121 [LSPR sensing is the most common sensing scheme that exploits noble-metal nanoparticles in analytical applications. LPSR biosensors employing gold nanoparticles (AuNPs) have been successfully applied to clinical diagnostics, environmental monitoring, and food safety . Particu\u22121 . First, Another LSPR platform takes advantage of a hollow Au spike-like nanoparticle (hAuSN) to detect avian influenza virus (AIV H5N1) using a multi-functional DNA three-way unction (3WJ) . This me\u22121, which is within the clinical levels observed in the first days of dengue infection. Despite the proposed method making use of spiked, whole blood samples instead of patient samples, the blood-plasma separation-integrated strategy represents a great advance toward the development of lab-on-chip devices and point-of-care virus diagnostics.The LSPR effect of silver nanostructures has also been reported to detect dengue NS1 antigen using an immunoassay format . The crePseudomonas aeruginosa and adenovirus [A singular LSPR immunosensor approach compares the capability of antibody-functionalized gold, silver, and copper nanoparticles for the detection of respiratory syncytial virus (RSV) in the presence of enovirus . The cha\u22121 levels.Plasmonic nanoparticles have also been exploited by SERS biosensors. The sensing scheme of SERS benefits from the enhancement of Raman scattering by providing the modulation of surface plasmon polaritons at a greater distance from the metallic nanoparticle surface, thereby offering higher sensitivity than that of SPR and LSPR. Lebedev et al. reported a SERS platform applied to the detection of viral DNA using nanoclusters (NC) of gold nanoparticles . SERS ex\u22121 with a limit of detection of 0.05 pg mL\u22121 . The applicability of the proposed method for clinical analysis was evaluated by testing HBsAg in spiked, real serum samples from nine patients showing recovery values between 96 and 104%.Another virus SERS-based strategy has been proven to detect hepatitis B surface antigen HBsAg . The bioHeavy metal quantum dots are semiconductor nanomaterials that have gained prominence in recent years for multiplex detection due to their broad adsorption and narrow emission band. The possibility of tuning the emission spectra over a wide range of wavelengths and the resistivity to external physico-chemical conditions are also significant advantages . Among t\u22121) and human serum (0.4 pg mL\u22121) (\u22121. The same quenching effect was observed when using CdSeTeS QDs/AuNPs\u2019 nanocomposites for detecting norovirus-like particles (NoV-LPs) [\u221214 to 10\u22129 g mL\u22121 range, showing a limit of detection of 12.1 \u00d7 10\u221215 g mL\u22121. The selectivity for the detection of the target NoV-LPs was evaluated with influenza virus A (H3N2) and Zika viruses, demonstrating the nanobiosensor specificity . The effNoV-LPs) . As the cificity .\u22121, depending on the composition of the nanohybrids: Alloyed AuAgNP-Qdot646-MB (molecular beacon) (1.7 copies mL\u22121) > CS Au/AgNP-Qdot646-MB (LOD = 2.4 copies mL\u22121) > AuNP-Qdot646-MB (LOD = 2.9 copies mL\u22121) > AgNP-Qdot646-MB (LOD = 7.6 copies mL\u22121) . The worCarbon nanomaterials are graphite structures that can adopt different dimensions ranging from cylindrical nanotubes to plane nanosheets. Graphene-based nanostructures provide numerous benefits for plasmonic applications due to their physicochemical properties including a high surface and biocompatible area that facilitate surface functionalization ,61.Several SPR graphene-based applications have been developed by Mahdi\u2019s group for the quantification of dengue virus at picomolar levels. A composite of reduced graphene oxide and polyamidoamine (PAMAM) dendrimers is described for the detection of the E-proteins of the serotype 2 of dengue virus (DENV 2). The detection format consisted of an immunoassay in which monoclonal antibodies were immobilized on self-assembled, dithiobis (succinimidyl undecanoate) amine-activated layers . The cha\u22121. Likewise, the same sensing scheme involving binary nanoparticle-graphene structures, although with the combined effect of gold and magnetic nanoparticles, was presented to detect norovirus-like particles [\u22121.Other plasmonic immunosensing approaches have exploited the potential of binary nanoparticle-graphene hybrid structures for the detection of virus in biological samples. For example, a magnetofluorometric platform made use of the combined effect of SERS and fluorescence of quantum dots to assist nanoparticle-decorated carbon graphenes in monitoring the presence of hemagglutinin (HA) protein in the surface of H1N1 influenza virus . The immarticles . In thisFinally, another composite consisting of gold nanorods and graphene oxide and gold nanorods (GO-GNRs) was applied to the determination of hepatitis B surface antigen using surface-enhanced Raman spectroscopy (SERS) as described above .The fabrication of plasmonic structures also relies on lithographic approaches, which enable the design of ordered arrays of metallic nanoapertures, such as nanoholes, nanoantennas, nanoslits, or nanodisks. The interaction of light with periodic arrays of nanoholes exhibits extraordinary optical transmission (EOT) effects, thus enhancing the transmission efficiency of light at certain wavelengths. These spectral features have facilitated the development of optical arrangements that support high bulk sensitivities and permit their integration into microfluidic systems and their application for the detection of single molecules ,63,64,65\u22121 levels, which significantly improved the recommended immunoassay-best test for the Ebola virus antigen detection.For instance, Zang et al. presented an interesting approach for single-molecule detection of Ebola virus antigens. The biosensor consisted of a 3D plasmonic nanoantenna array, which used a sandwich-immunoassay format with fluorescent intensity enhancement Figure . The nanAnother plasmonic nanohole-based assay was developed for capturing single dengue virus-like particles . The dimSimilarly, another study measured the adsorption of a small virus particle of 25 nm (PhiX174) using double nanohole apertures in a gold film by the extraordinary acoustic Raman (EAR) method . As withSPR and LSPR biosensors that integrate optical fibers for coupling optical excitation of surface plasmons offer an interesting alternative to classical prism-based configurations. The possibility of driving the propagation of the electromagnetic field radiation through a fiber-optic system permits the improvement of the wavelength modulation and the development of compact structures. Many optical fiber SPR/LSPR platforms have provided miniaturized sensing approaches for the determination of clinical biomarkers . Most re4 to 108 EID 50/0.1 mL (EID: embryo-infectious dose), showing a detection limit of 5.14 \u00d7 105 EID 50/0.1 mL.In particular, a fiber-optic SPR system has been described for the analysis of avian influenza virus subtype H6 . To optiThe combination of the optical properties of gold nanostructures-LSPR surfaces with the achievement of total internal reflection via optical fiber configurations can provide signal enhancement and better spatial sensitivities. The integration of nanorod-modified surfaces into a fiber-optic LSPR platform have permitted the development of an immunosensor for the determination of a nonclinical application in plant viruses: Cymbidium mosaic virus (CymMV) and Odontoglossum ringspotvirus (ORSV) . The limFinally, the coating of an excessively tilted fiber grating surface (Ex-TFG) with gold nanospheres has permitted the development of an immunosensor for detecting Newcastle disease virus (NDV) . The modThe utilization of colorimetric assays is becoming more important in clinical diagnosis for detection of either organic or inorganic molecules . The fabrication of plasmonic colorimetric nanosensors relies mainly on noble metal nanoparticles due to their high LSPR extinction coefficients in the visible range ,30. MostA plasmonic colorimetric sensor based on the aggregation of colloidal nanoparticles was described for the detection of influenza virus . The app\u22121 while H5N1 virus antigen was detected at 1 pg mL\u22121 levels using a sandwich-immunoassay format. The improvement in sensitivity in comparison with other methods was attributed to the high index faceted on the tips of the gold nanobipyramids with regard to gold nanorods.Another plasmonic colorimetric application for influenza virus detection (lineage H5N1) employed gold nanobipyramids (Au NBPs) as noble metal nanostructures . This ap2O2). A limit of detection of 10 pg mL\u22121 was obtained in buffer solution while the determination of HEV in real samples collected from fecal matter of HEV-infected monkey was in good correlation with RT-qPCR conventional methods .Similarly, a plasmonic platform consisting of silver deposition on antibody-conjugated gold nanoparticles was applied for monitoring hepatitis E virus (HEV) . A nanozFinally, a colorimetric assay approach based on the LSPR changes of silver nanoparticles induced by the hybridization chain reaction of the microRNA biomarker (miR-29a-3p) was described to detect H1N1 influenza A virus at picomolar levels . The hybThe effect of collective oscillations of free electrons on the surface of metal nanostructures displayed in LSPR sensing can enhance the optical signal of a luminophore near noble metal nanoparticles ,73. Plas3O4 yolk/Au shell (M@Au) was reported for the detection of a mouse sarcoma virus oncogene [3O4 nanoparticles and the stability and low toxicity of graphite quantum dots to detect nucleic acids in the 1-fM\u22121-nM range as clinical nanosensors. For example, an ECL assay based on magnetic-plasmonic Feoncogene . The stunM range . The eff2 nanosheets to enhance the ECL signal of sulfur-doped boron nitrogen QDs (S-BN QDs) [2 nanosheets and S-BN QDs reduced the energy transfer while strengthening the surface plasma-coupling effect. Specifically, the assay was applied to the detection of hepatitis C virus (HCV) gene. The so-called hybridization chain reaction was used as an isothermal enzyme-free DNA amplification method to quantify DNA HCV with a limit of detection (LOD) of 0.17 pmol L\u22121.Another plasmon-based ECL strategy utilizes the strong surface plasmon-coupling nonmetallic MoS-BN QDs) . The appThe SARS-CoV-2 is an enveloped, nonsegmented \u03b2-coronavirus that causes a new, severe, acute respiratory syndrome and coronavirus disease COVID-19) [9 1,3,7575,78. SiNevertheless, the search for rapid and reliable point-of-care devices has triggered the development of plasmonic methods based on the latest technological advancements. For example, a novel approach combines the plasmonic photothermal (PPT) effect and LSPR sensing to detect DNA-selected sequences via hybridization to DNA receptors immobilized on two-dimensional gold nanoislands (AuNIs) . This du\u22121 of RNA with SARS-CoV-2 viral load. The main advantage of the proposed method was the possibility of being applied to target other regions of the viral genomic material, such as S-gene (surface glycoprotein), E-gene (envelope protein), and M-gene (membrane glycoprotein) without using sophisticated instrumental techniques.Another innovative approach for COVID-19 diagnosis comprised the development of a colorimetric assay based on gold nanoparticles (AuNPs) functionalized with thiol-modified antisense oligonucleotides (ASOs) specific for N-gene (nucleocapsid phosphoprotein) of SARS-CoV-2 . The bioThe uncertain proportions of pandemic outbreaks have triggered the need for reliable and cost-effective protocols easily adaptable to the changing virulence of virus strains. In recent years, plasmonic biosensors are being increasingly applied for clinical diagnosis of viral and other infectious diseases. Typical plasmonic biosensing strategies rely on the versatility of SPR and LSPR as label-free detection systems capable of monitoring binding interactions in a short period of time. Nevertheless, the incorporation of technological advancements has precipitated the development of nanomaterial-based applications for improving the sensitivity and specificity of classical configurations. The unique optical properties of plasmonic nanostructures has been exploited in combination with SERS colorimetric, fluorescence, or luminescence enhancement for viral diagnosis. Likewise, the development of plasmonic virus-sensing approaches has also benefitted from the variety of virus biomarkers. Thus, a high number of virus plasmonic biosensors have prompted the advance of novel functionalization strategies to achieve the effective coverage of the biological receptor while ensuring the affinity and specificity towards the target viral nucleic acids, proteins, or whole virus.Despite this substantial progress, current plasmonic applications have not yet outpaced conventional laboratory-based sequencing and immunoanalytical techniques. The improvement of sensing schemes has led to the attainment of ultrasensitive, robust, and reproducible analytical performances. However, the automation and integration of microfluidics as well as the prevention of nonspecific proteins\u2019 adhesion in complex media still remains a challenge in many cases. On the one hand, the fabrication of automatable point-of-care devices is strongly dependent on both the design of reliable microfluidics and the integration of advanced software in miniaturized platforms. In this sense, the utilization of novel flexible materials via nanopatterning lithographic approaches may facilitate the incorporation of microchannels that enable the delivery of microvolume samples without requiring additional equipment. Secondly, plasmonic virus detection from clinical specimens is still limited due to the lack of universal methods that prevent the interference of biomolecules present in undiluted body fluids. From this perspective, the design of effective antifouling coatings, which take into account either the composition of the media or the biological receptor\u2019s characteristics, will contribute to fill the gap between traditional analytical methods and plasmonics\u2019 applications. By addressing these challenges, the huge potential for single virus detection along with the effectiveness and simplicity of current plasmonic configurations will impact on the routine surveillance of virus in clinical settings during this decade."} +{"text": "We present an improved stochastic finite-fault method controlled by the fault rupture process (NNSIM) which can make the simulated strong ground motion at a broad frequency band similar to real ground motion of the Ms 7.0 Lushan earthquake by introducing the fault physical rupture process into the stochastic finite-fault method. Two obvious improvements are obtained: 1) the non-uniform time window functions produce various shape of the simulated time series instead of one single spindle shape; 2) the non-uniform stress drops and the non-uniform time window functions improve obviously simulated pseudo-spectral acceleration (PSA), especially, the low-frequency part.\u2022We present an improved stochastic finite-fault method controlled by the fault rupture process (NNSIM) which can make the simulated strong ground motion at a broad frequency band similar to real ground motion by introducing the fault physical rupture process into the stochastic finite-fault method. Its validity was tested by the comparisons with records of Lushan earthquake.\u2022The non-uniform time window functions produce various shape of the simulated time series instead of one single spindle shape.\u2022The non-uniform stress drops and the non-uniform time window functions improve obviously simulated pseudo-spectral acceleration (PSA), especially, the low-frequency part. Specification Table1)Time window functionsStochastic finite-fault methods are effective ground-motion time-series simulation methods. The rupture process of a large fault has a non-uniform slip, a non-uniform stress drop, a non-uniform rupture velocity, and a non-uniform source time function at different points in the fault. Its implement in the stochastic finite-fault method makes the simulated strong ground motion hold the specific physical meaning and reproduce the real ground motion. Thus the new method of non-uniform stochastic finite-fault method (abbreviated as NNSIM) causes two main modifications: 1) Replace the predetermined time function with different source time functions for each subfault to improve low-frequency results including the envelopes of accelerations and velocities. 2) Replace the uniform stress drop with a distribution of non-uniform stress drops to reduce the dependence of simulated results on a single stress drop. In order to simulate the ground motion some key parameters need to be obtained as follows:1)Stress drop/ Stress parameterFor one actual earthquake, the fault rupture process including low-frequency slip rate time function, seismic moment on the finite fault model can be inversed based on seismic records. The slip rate time functions with different time history shapes are normalized, then used as the time window functions substituting the Saragoni-Hart function for simulating the ground motion. The normalized slip rate time functions containing the low frequency characters of the source such as multiple rupture peaks make the shape of the simulated time series more similar to real ground motion.Stress drop/ Stress parameter d motion . Based od motion . SubstitBesides the above two main source parameters, the non-uniform slip rate time functions also provide various rupture delays and different seismic moment release in the finite fault. The various rupture delays reflect the change of the rupture velocities. The rupture delay can be obtained by the first-arrival picking technique. After the determination of all the source parameters, the ground motion can be calculated following the steps of the pre-existing stochastic finite-fault method .On April 20, 2013, an Ms 7.0 earthquake struck Lushan County in China at 8:02 am Beijing time. We obtain source parameters, including non-uniform stress drop distribution, non-uniform slip rate time function, non-uniform rupture velocity and non-uniform seismic moment, based on Zhang et al.\u2019s inversion results using teleseismic data. Combining these source parameters with stochastic finite-fault methods, we simulate the ground motions of the Ms 7.0 Lushan Earthquake, which are compared with observed records and results simulated by stochastic finite-fault methods (Version of EXSIM12). The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."} +{"text": "In a recent editorial by Gattinoni et al. [The clinical presentation of coronavirus 2 (SARS-CoV-2) ranges from asymptomatic to severe respiratory failure, and correspondingly requirement for respiratory support ranging from varying levels of supplementary Oi et al. , it is pWe propose that the direct effects on pulmonary tissue by SARS-CoV-2 in COVID-19 pneumonia in ARDS COVID-19 patients resembles neonatal respiratory distress syndrome (NRDS), caused by surfactant deficiency.SARS-CoV-2 enters and replicates in the alveolar type II cells impacting the production and turnover of pulmonary surfactants. This results in alveolar collapse and inflammation leading to increased capillary permeability, edema, and microvascular thrombosis; where the associated ARDS clinical picture closely resembles NRDS. Of importance, as ARDS progresses, vascular permeability increases and surfactant deactivates making the lung increasingly unstable . These pTreatment of NRDS with rescue surfactant and continuous positive airway pressure (CPAP), when compared to mechanical ventilation, results in reduced development of pulmonary fibrosis; a complication also reported in intubated COVID-19 patients. Antenatal corticosteroid treatment may also accelerate fetal lung maturation in the risk of preterm birth. A multicentre trial evaluates whether surfactant plus budesonide improves survival in NRDS . In COVIWe suggest assessment of surfactant levels should be added to the evaluation of COVID-19 patients. A point-of-care test for fast measuring surfactant at birth in premature babies has been developed . This me"} +{"text": "The folding of certain proteins into perfectly defined 3D conformations via multi-orthogonal interactions is critical to their function. Concerning synthetic polymers chains, the \u201cfolding\u201d of individual polymer chains at high dilution via intra-chain interactions leads to so-called single-chain nanoparticles (SCNPs). This review article describes the advances carried out in recent years in the folding of single polymer chains into discrete SCNPs via multi-orthogonal interactions using different reactive chemical species where intra-chain bonding only occurs between groups of the same species. First, we summarize results from computer simulations of multi-orthogonally folded SCNPs. Next, we comprehensively review multi-orthogonally folded SCNPs synthesized via either non-covalent bonds or covalent interactions. Finally, we conclude by summarizing recent research about multi-orthogonally folded SCNPs prepared through both reversible (dynamic) and permanent bonds. The compaction process of a biological linear polypeptide chain to its functional, native conformation is called protein folding . The folConcerning synthetic polymers chains, the \u201cfolding\u201d of individual polymer chains at high dilution via intra-chain interactions leads to so-called single-chain nanoparticles (SCNPs) ,17,18,19R \u2248 N1/3 is found where R is the protein size and N is the number of residues in the polypeptide chain . Th. Th75]. A dual photoreactive precursor polymer entailing equal number of antracene and styrylpyrene units was synthesized by Barner-Kowollik and colleagues . This poDimers of SCNPs of high purity were isolated by sorting via exclusive self-assembly (ESA) by Chen and coworkers 77]. Fi. Fi77]. b-poly(vinylpyridine) (PI-b-P4VP) diblock copolymer was selected containing two different cross-linkable blocks for sequential cross-linking. In the first step, the PI block was modified with 2-mercaptoethylamine hydrochloride to introduce an electrostatic interaction along the chain. The intramolecular cross-linking was performed with 1,6-hexanediisothiocyanate. In the second step, the P4VP block was reacted with iodoethane to introduce an electrostatic interaction along the P4VP chain. Afterward, the intramolecular cross-linking was performed with 1,5-diiodopentane. A dimer of SCNPs was thus achieved whose two domains were different in composition: the PI domain containing residual amine and cyanate groups, and the P4VP domain containing residual pyridine and quaternized groups by Yang and coworkers through electrostatically-mediated intramolecular cross-linking of diblock copolymers . The synd groups .Attempts to produce highly compact SCNPs folded via two orthogonal procedures were recently carried out by Temel and coworkers . A firstSimilar to the case of multi-folded SCNPs via non-covalent bonds, attempts to produce more compact SCNPs through the involvement of multiple covalent bonds are expected to grow in next years. One significant advantage of the use of covalent bonds is that robust SCNPs for a variety of applications are obtained . HoweverMulti-folded SCNPs via covalent and non-covalent interactions offer the advantage of being partially dynamic and responsive due to the presence of non-covalent bonds but retaining most of the stability imparted by the covalent interactions.co-cyclooctadiene) copolymer synthesized via ring-opening metathesis polymerization (ROMP) was used as SCNP precursor polymer. In a first step, the anhydride handles of the copolymer were decorated with an aniline tetramer (AT) that induced folding via supramolecular interactions between the AT pendant groups. The remaining anhydride groups were cross-linked with p-aminoaniline as external linker providing the second folding step. The last folding step was carried out in the presence of a dithiol linker via thiol-ene click chemistry involving the cyclooctadiene repeat units of the copolymer. Overall, the hydrodynamic volume of the SCNP was 70% smaller than that of the original coil.Berda and coworkers pioneered the use of multiple sequential orthogonal intra-chain covalent and non-covalent interactions for the controlled folding of a novel electroactive polyolefin . A poly(\u03b2-ketoester units were synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization. The experimental results obtained from SEC measurements techniques for the computational design of SCNPs, i.e., (i) generating data of a given property at a moderate computational cost through the simulation in a reduced space of chemical sequences, (ii) using this information to train the ML model, and (iii) predicting and optimizing the property out of the space generated in step (i). Recent work has applied this strategy, which should be transferrable to SCNPs, to target specific molecular conformations of heteropolymer models using the size distribution of a small number of simulated sequences . As afor"} +{"text": "Backgrounds Frailty is a common geriatric condition leading to poor surgical outcomes. Having a valid frailty measure has the potential to improve surgical care quality. Objectives To test the ability of the Reported Edmonton Frailty Scale-Thai version (REFS-Thai) in predicting hospital outcomes compared with the American Society of Anesthesiologists physical status classification (ASA) and the Elixhauser Comorbidity Measure (EMC) in older Thai orthopedic patients. Methods A prospective study was conducted on hospitalized older adults scheduled for elective orthopedic surgery. Multiple Firth logistic regression modeled the effect of frailty on postoperative complications, postoperative delirium (POD), and discharge disposition, while the length of stay (LOS) was examined by Poisson regression. The area under the receiver operating characteristic curve (AUC) and mean squared errors (MSE) were used to compare the predictive ability of the instruments. Results Two hundred participants with mean age of 72 (range 60-94 years) were mostly female, 23% were frail. Adjusting for other variables, frailty was significantly associated with postoperative complications , POD , and prolonged LOS . The REFS-Thai alone shows good performance in predicting postoperative complications and POD . The combination of REFS-Thai with ASA and EMC demonstrates an improved predictability. Conclusion The REFS-Thai was useful in predicting adverse outcomes in surgical orthopaedic older adults. Integrating the REFS-Thai for preoperative assessment may be useful for enhancing care quality."} +{"text": "Tourette syndrome (TS) and persistent motor/vocal tic disorders are neurodevelopmental conditions characterised by the chronic presence of motor and/or vocal tics. Patients with TS often present with co-morbid disorders, especially attention-deficit and hyperactivity disorder (which tends to improve after childhood), and obsessive-compulsive disorder (which can persist in adulthood). We set out to explore pharmacotherapy for tics in adult patients with TS and persistent motor/vocal tic disorders, as well as its relationship with the presence of co-morbid conditions.n\u2009=\u2009187), persistent motor tic disorder (n\u2009=\u20093) and persistent vocal tic disorder (n\u2009=\u20092) attending a specialist clinic in the UK.We retrospectively reviewed the clinical characteristics and pharmacotherapy of 192 adult patients with TS (n\u2009=\u200965) and alpha-2-agonists (n\u2009=\u200950) were the most commonly prescribed pharmacotherapy for tic management. A sub-group analysis revealed that co-morbid obsessive-compulsive disorder and sub-threshold obsessive-compulsive behaviours were significantly more common in patients treated with anti-dopaminergic medications than patients taking alpha-2-agonists .Anti-dopaminergic medications (The use of pharmacotherapy options for tic management observed at a specialist clinic for adults with TS reflects guideline recommendations. We found that the presence of co-morbid obsessive-compulsive disorder/behaviours correlates with the choice of anti-dopaminergic medications over alpha-2-agonists, in line with available evidence on the efficacy of anti-dopaminergic medications for the treatment of specific tic\u2013related behavioural symptoms. Tourette syndrome (TS) is a neurodevelopmental disorder characterised by the presence of both motor and vocal tics with a chronic course . IndividThe recently published American Academy of Neurology guidelines on the assessment and treatment of tics in patients with TS and other chronic tic disorders recommend the use of alpha-2-agonists and anti-dopaminergic medications as pharmacotherapy of choice for the treatment of tics [We recruited 192 consecutive patients attending the specialist Tourette Syndrome Clinic, Department of Neuropsychiatry, National Centre for Mental Health, Birmingham, UK. All patients fulfilled current diagnostic criteria for TS or other chronic tic disorders. Patients under 16\u00a0years of age, with limited understanding of English and with severe autism spectrum disorder/learning disability were excluded from the study.Each patient underwent a comprehensive clinical assessment using the National Hospital Interview Schedule (NHIS) for TS . The NHIAll statistical analyses were conducted using parametric testing on continuous variables that were normally distributed and non-parametric testing on continuous variables that were not normally distributed. The chi-square test was used for non-continuous variables.Out of the 192 adult patients in our clinical sample, 187 had a diagnosis of TS, 3 persistent motor tic disorder and 2 persistent vocal tic disorder. The demographic and clinical characteristics of the sample are shown in Table n\u2009=\u200965) and alpha-2-agonists (n\u2009=\u200950) were the most commonly prescribed pharmacological classes. All patients taking alpha-2 agonists were prescribed clonidine, the most commonly used tic-suppressing medication.About two thirds of the patients (66.7%) were on some form of pharmacotherapy for their tics Table . Anti-don\u2009=\u200955) with those of patients taking alpha-2-agonists only (n\u2009=\u200940). The only significant difference between the two sub-groups was identified when analysing the presence of co-morbidities: patients with OCD were more likely to be taking anti-dopaminergic medications than alpha-2-agonists . The same difference was observed with sub-threshold obsessive-compulsive behaviours .A sub-group analysis compared the clinical characteristics of patients taking anti-dopaminergic medications only (The use of pharmacotherapy for tic management observed in a large and representative clinical sample of adult patients with TS and other chronic tic disorders reflects current guideline recommendations . The DCIWe found that the presence of co-morbid OCD/obsessive-compulsive behaviours correlates with the choice of anti-dopaminergic medications over alpha-2-agonists, in line with available evidence on the efficacy of anti-dopaminergic medications for the treatment of specific tic\u2013related behavioural symptoms. In a recent study on adults with TS, aripiprazole significantly improved OCD and showed a trend toward improvement of other behavioural co-morbidities . In the The main limitations of the present study include its retrospective approach and referral bias, as participants were recruited from a tertiary referral centre and may therefore not be representative of the wider community. Future research is needed to fully understand how the phenotypic heterogeneity of patients with TS and other chronic tic disorders affects pharmacotherapy across the lifespan."} +{"text": "Hospitalization processes related to patient mobility and food-intake significantly affect outcomes of older adults. Nurses are the front-line personnel responsible for promoting performance of these functioning-preserving processes. The degree to which nursing skill-mix is related to their performance is unclear. We investigated the association between staffing and hospitalization processes in a cohort of 836 older adults aged 70+ admitted to internal units for non-disabling conditions. Mobility and food-intake were assessed within 2 days of admission using validated questionnaires. Nurse-patient ratios and nursing skill-mix were assessed using administrative and payroll/roster data. Decision-trees were developed for mobility and food-intake applying classification and regression tree analysis. The mobility decision-tree identified four characteristics that subdivided the patients into eight segments (nodes) . The food-intake decision-tree identified five characteristics that subdivided the patients into ten nodes. Percent of advanced practice nurses and the percent of nurse aids classified low functioning patients: higher percent of advanced practice nurses (>30% vs. \u226430%) was associated with higher probability of walking in corridors (20.7%) versus inside the room (4.3%), and higher percent of nurse aids (>23% vs. \u226423%) was associated with higher probability of eating more than half of the served meals (83.9%) versus others (66.3%). This study shows that staffing levels are associated with better performance of functioning-preserving processes. Future studies should investigate staffing interventions improving functioning-preserving processes."} +{"text": "This short review addresses the evidence behind dispatcher-assisted CPR (DA-CPR) and whether it contributes to overall survival of out-of-hospital cardiac arrest (OHCA). Six papers directly addressed the review question and were selected for appraisal, including one systematic review. The outcomes of these studies demonstrate variable results from the implementation of DA-CPR strategies. While DA-CPR has some utility as a substitute for spontaneously delivered bystander CPR, available evidence suggests there is scope to improve. Further work should focus on the identification and adoption of more effective protocols. In [adult patients suffering out-of-hospital cardiac arrest (OHCA)] does [emergency medical services dispatcher-assisted CPR (DA-CPR)] improve [clinical outcomes]?A 65-year-old man is found by passers-by on a riverside path. He is unresponsive and not breathing. The bystanders contact emergency medical dispatch for assistance but do not attempt CPR. The patient has persistent asystole and no return of spontaneous circulation, and is declared dead. Would emergency medical DA-CPR have increased the odds of a favourable outcome?((basic life support) OR (cardiopulmonary resuscitation) OR CPR OR ) AND (coaching OR dispatcher) AND OR (depth) OR (rate) OR (compression*) OR (ventilation*) OR (Return of Spontaneous Circulation) OR (ROSC) OR (Length of Stay) OR OR OR (recovery)).Limits: January 2008\u2013November 2018.Studies examining the administration and/or quality of DA-CPR in relation to clinical outcomes in adults were included. Non-English papers, conference abstracts, letters, case reports or studies conducted exclusively in paediatric populations or simulated scenarios were excluded.Out of 189 results, 75 potentially relevant titles were identified, of which seven papers met the inclusion criteria and were selected for appraisal . This inSearch results are presented in The use of national registries facilitated collection of large amounts of data in all five primary research studies included. However, studies were conducted in a range of international systems where differences in dispatch and emergency medical services (EMS) response protocols may limit external validity. Only one prospective study was identified.Six out of seven identified studies suggest that DA-CPR may modestly improve the odds of both survival to discharge and favourable neurological outcome from OHCA. Three studies independently report that DA-CPR was inferior to spontaneously delivered bystander CPR. Explanations for the latter may include the presence of trained responders, more rapid initiation of chest compressions and higher quality chest compressions. A single study attempted to assess DA-CPR administration at the time of EMS arrival, and found chest compressions to be of poor quality.Future work should focus on the comparative effectiveness of DA-CPR protocols in terms of quality of CPR delivery, and effect on clinical outcomes. This may allow for the identification and more widespread adoption of effective protocols or highlight the need for further development in this area. As spontaneously delivered CPR seems superior to DA-CPR, provision of the latter should not be seen as a substitute for widespread public training initiatives.Current DA-CPR strategies modestly improve the odds of favourable outcome from OHCA. However, DA-CPR may be inferior to spontaneously delivered bystander CPR. Based on current evidence, opportunities for public training should be maximised and supported by evidence-based DA-CPR protocols.None declared.None."} +{"text": "This review focuses on in vivo detection and monitoring of various regulatory immune cell types administered for allograft tolerance induction in both pre-clinical animal models and early human clinical trials. We discuss the current status of various non-invasive methods for tracking regulatory cell products in the context of organ transplantation and implications for enhanced understanding of the therapeutic potential of cell-based therapy in the broad context of control of immune-mediated inflammatory disorders.Application of cell-based immunotherapy in organ transplantation to minimize the burden of immunosuppressive medication and promote allograft tolerance has expanded significantly over the past decade. Adoptively transferred regulatory immune cells prolong allograft survival and transplant tolerance in pre-clinical models. Many cell products are currently under investigation in early phase human clinical trials designed to assess feasibility and safety. Despite rapid advances in manufacturing practices, defining the appropriate protocol that will optimize Non-invasive, accurate, and durable techniques to monitor exogenous cell products after infusion in both pre-clinical and clinical human studies are critical in addressing 1) variability in clinical outcomes, 2) potential cell toxicity and adverse side effects of infusion, 3) anatomic localization and 4) duration and magnitude of desired tolerogenic activity and polyclonally expanded Tregs (pTreg), regulatory macrophages (Mreg), regulatory dendritic cells (DCreg), and mesenchymal stromal cells (MSCs). Findings from the recent ONE Study, the largest multi-center consortium to date assessing adoptive cell therapy in kidney transplant patients, have confirmed the safety of infusing various regulatory immune cells, paving the way for further development . The maiin vivo cell monitoring using whole-body imaging with novel reporter systems, initially developed for cancer immunotherapy, are increasingly being incorporated into both pre-clinical and clinical transplant studies. This review will discuss current techniques used to track and monitor the major regulatory immune cells under clinical investigation for tolerance induction . In addition to these thymic Tregs (tTregs), na\u00efve Foxp3-CD4+ T cells can differentiate in the periphery to become Foxp3+ cells, that are known as induced Tregs (iTregs) or peripheral Tregs. Distinctions between tTregs and iTregs have been reviewed recently dye or on Treg generated from green fluorescent protein (GFP) transgenic donors to study tissue homing and survival of these cells after intravenous administration -mismatched vascularized composite allotransplant rat recipients and visually tracked using bioluminescence imaging (BLI) longitudinally. In contrast to the limited detection of labeled Tregs in cross-sectional samples of earlier studies, real-time in vivo imaging allowed Cheng et. al to identify migratory patterns of infused Tregs first to draining LNs and then to grafted tissue over a prolonged period of 42 weeks (ex vivo-expanded Tregs with technetium-99m pertechnetate (99mTcO4-) was performed both directly and indirectly via retroviral transduction with a construct expressing the hNIS glycoprotein ion channel gene -labeling and subsequent flow cytometric analysis of the labeled cells in peripheral blood, mesenteric and inguinal LNs, and spleen at various timepoints post-infusion (Tregs have been well-characterized in nonhuman primates (NHP) , 33\u201335.Tinfusion , 21. Phainfusion , 23. Theex vivo-expanded autologous Tregs support their efficacy in prolonging allograft survival and function. In addition, multiple Treg infusions in NHP pretreated with anti-thymocyte globulin (ATG) and post-operative rapamycin prolonged renal allograft survival modified Tregs as a more potent and targeted cellular method of tolerance induction after transplantation. Investigators have demonstrated that adoptive transfer of genetically engineered donor HLA-specific CAR Tregs successfully prevents the rejection of transplanted allogeneic cells and graft tissue in humanized mouse models , 38, 39.AR Tregs or mAb-dTregs analysis to measure deuterium enrichment in circulating Tregs. Infused Tregs peaked within 7 days of infusion and were detected by deuterium signals at 30 days. Deuterium-labeled cells fell to the limit of detection within 3 months of infusion (111Indium tropolonate (111In) . Serial (111In) . This prThe myeloid cell lineage includes multiple regulatory immune cell subsets under active investigation to induce and maintain transplant tolerance in solid organ transplantation, including DCregs, Mregs, and myeloid-derived suppressor cells (MDSCs) -dependent manner , 44 howescanning .-CD63+HLA-DR+ phenotype and IL-10 production, have been demonstrated to suppress T cell proliferation in vitro cells cells . Thus, t111In prior to infusion allowing for in vivo Mreg tracking in real-time using SPECT-CT scanning. Scintigrams reconstructed from SPECT imaging demonstrated initial trapping of labeled Mregs in the pulmonary vasculature, but after 2.5 h re-distributed to the peripheral blood, liver, and spleen. 24 h after infusion, Mregs were no longer detectable in the lungs or peripheral blood and were seen to accumulate in lymphoid and non-lymphoid organs grants R01 AI118777, U01 AI 136779, and U19 AI131453 to AT, and by an NIH institutional research training fellowship to LT (T32 AI074490). Additionally, the University of Pittsburgh holds a Physician-Scientist Institutional Award from the Burroughs Wellcome Fund, which supports LMT.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Besides the cross-coupling, we also examined the competitive pathways of \u03b2-hydrogen elimination to give the corresponding alkene byproduct. The DFT study on the reaction pathways explains the cross-coupling selectivity over the elimination in terms of FeI/FeII/FeIII mechanism which involves the generation of alkyl radical intermediates and their propagation in a chain reaction manner. The present study gives insight into the detailed molecular mechanic of the cross-coupling reaction and revises the FeII/FeII mechanisms previously proposed by us and others.To explore plausible reaction pathways of the cross-coupling reaction between a haloalkane and an aryl metal reagent catalyzed by an iron\u2013phosphine complex, we examine the reaction of FeBrPh(SciOPP) Transition-metal-catalyzed cross-coupling reaction is one of the most versatile synthetic tools for constructing carbon frameworks of various functional molecules, e.g., pharmaceuticals, agrochemicals, and organic electronic materials. Iron catalysts have emerged as a sustainable alternative for conventional palladium and nickel catalysts and have attracted significant attention due to their practical merits of cost-effectiveness, low toxicity, and the abundance on the earth ,2,3,4. DMore specifically, iron catalysts have proven useful for cross-coupling reactions of non-activated haloalkanes, a synthetically valuable yet challenging substrate, which is prone to undergo \u03b2-hydrogen elimination in the conventional palladium-catalyzed cross-couplings to form undesired alkene byproducts ,21,22,23IIX2(SciOPP), FeIIXAr(SciOPP), FeIIAr2(SciOPP), where X = halide and Ar = Ph or Mes which is formed from iron(II)-precatalyst and they proposed a low-coordinate iron(I)-phosphine species is involved in the cross-coupling reactions . T. TI/FeIInclusion . DespiteIIBrPh(SciOPP) complex reacts with a haloalkane to give the corresponding cross-coupling product selectively, but the detailed mechanism has remained unclear )Br(SciOPP)) was also predicted correctly [IIBrPh(SciOPP) complex. Hence, the B3LYP-method reliably predicts the spin state of the current system and is used in this study. Further, we have also checked the effect of long-range-corrected (LC) exchange functional on barrier height [The spin-state energies of iron complexes computed by a DFT method depend on the choice of the exchange-correlation functional ,51. Variin state ,34. Addiorrectly . Furtherorrectly gave conr height using CAIIBrPh(SciOPP) and bromocycloheptane by using DFT methods and identified iron species of different oxidation states involved in a catalytic cycle of the iron-bisphosphine-catalyzed haloalkane couplings. The reaction mechanism follows the FeI/FeII/FeIII pathway, where iron(I) activates the C\u2013Br bond of the haloalkane substrate, another molecule of FeIIBrPh(SciOPP) traps the generated alkyl radical species to form iron(III) species leading to the formation of the cross-coupling product and iron(I) species. The iron(I) species then again react with haloalkane generating alkyl radical and the reaction propagates through a radical chain mechanism. The current mechanism mirrors our previous mechanistic study on a chiral bisphosphine-catalyzed enantioselective cross-coupling despite the change of bisphosphine ligand from BenzP* to SciOPP.We have studied the mechanism of the reaction between FeII/FeII and FeII/FeIII pathways proposed previously. Furthermore, we have found that an alkyl radical prefers to coordinate to the FeIIBrPh(SciOPP) species, instead of the \u03b2-hydrogen-atom abstraction ending with the alkene byproduct. The generated FeIIIBrPh(SciOPP) species favors reductive elimination to give the corresponding coupling product over the alkene byproduct. These results deepen our understanding of the iron-SciOPP catalysis and provide insights into the probable root for the side product formations. Further understanding of the mechanism of alkene formation with FeIIPh2(SciOPP) catalyst will help design better catalysts and synthetic methodology. The theoretical and experimental research in this line is now actively pursued in our laboratory and will be reported in due course.The reaction of haloalkane with iron(II) species and the reaction of the alkyl radical with iron(III) species have a higher energy barrier than those of Iron(I) species and iron(II) species, respectively. The obtained energetics exclude the possibility of Fe"} +{"text": "Participant outcomes to be measured include: Quality of Recovery (QoR-15); Oral Morphine Equivalent Daily Dose (OMEDD) at 24-h post-operatively; time to first opioid (TTFO) dose; post-operative nausea and vomiting (PONV); Post Anesthetic Care Unit length of stay (PACU-LOS); and hospital length of stay (LOS). The findings may challenge the essentiality of opioids in the peri-operative period, which in turn would influence the future intra-operative management of surgical patients. Ultimately, a reduction in anesthesia-associated opioid use will support a more general decline in opioid use.The administration of opioids is a central element in contemporary anesthetic techniques in Australia; however, opioids have a range of side effects. As an alternative, opioid-free anesthesia (OFA) is an emerging mode of anesthesia intended to avoid these side effects. This study is the first to publish the use of OFA in Australia and is conducted in a regional Queensland Health Service. The design will utilize a randomized clinical trial (RCT) to investigate the impact of OFA for patients having an elective laparoscopic cholecystectomy ( Historical records indicate that humans have used opioids for at least 8000 thousand years as a mood enhancer, analgesic and hypnotic agent . EvidencTraditionally in Australia, peri-operative analgesia has been provided by opioid analgesics, and current anesthetic practice is heavily dependent on opioid use during and after anesthesia for post-operative pain relief. However as White indicateA non-opioid analgesic multimodal approach (opioid-free anesthesia (OFA)) is aimed at optimizing adjunctive options intra-operatively, utilizing anesthetic techniques targeting different neuroanatomical circuits and multiple neurophysiological mechanisms ,11. The Contemporaneous anesthetic practice calls for patient-centered approaches to assessing the recovery of patients after surgery. OFA has been shown to be an effective anesthetic technique for patients undergoing laparoscopic cholecystectomy and, in The research has been approved by the Royal Brisbane and Women\u2019s Hospital Human Research Ethics Committee (HREC/2020/QRBW/62398), Queensland, Australia, and is registered with the Australian New Zealand Clinical Trials Registry (ANZCTR), trial number ACTRN12620000714987.This is an investigator-initiated, single site, prospective, randomized, parallel group, single-blind study, with concealed allocation of participants scheduled for elective laparoscopic tubal ligation or cholecystectomy surgery, randomized on a 1:1 basis to receive either a standard or opioid-free anesthesia protocol. The aim of this study is to compare clinical outcomes for participant\u2019s receiving opioid-free anesthetic (OFA) with those receiving standard opioid-containing anesthesia.The primary objective is to compare the quality of recovery from general anesthesia and surgery using the quality of recovery 15 item scale (QoR-15) . The QoR\u25cbRespiratory depression;\u25cbNausea and vomiting;\u25cbDelirium/hallucinations;\u25cbPruritus;\u25cbParticipant pain scores;\u25cbFunctional activity scores;\u25cbSedation level;\u25cbLocal anesthetic toxicity.Post-operative complications of medication administration including:\u25cbTime post-operatively to first analgesia;\u25cbType of analgesia;\u25cbOral Morphine Equivalent Daily Dose (OMEDD).The use of analgesia:Time until post-operative mobilization.Length-of-stay in PACU.Hospital length-of-stay.Peri-operative adverse events.The secondary objectives and endpoints include comparing:All patients presenting for an elective cholecystectomy or tubal ligation (with or without oophorectomy) will be identified by the research team as per n = 20 OFA cholecystectomy and n = 20 OFA tubal ligation participants) and 40 in the non-OFA group .Current literature reports that mean change QoR-15 scores (difference between baseline and Day 1 post-operative) is approximately 22 with a standard deviation of four . A diffeEligible participants will be randomly selected to receive OFA surgery or non-OFA surgery on a 1:1 basis. Treatment allocations will be randomized into blocks of six and stratified by type of surgery . Following consent, participants will be allocated a study participation identification number (ID). An envelope with corresponding ID will be opened by the anesthetist just prior to surgery. This envelope will contain the random allocation of OFA or standard treatment and the respective treatment protocol for the allocation.Allocation to standard or OFA protocol will be completed prior to surgery as designated by the chief investigator. The participant and the outcome assessors (recovery and ward nurses) will be blinded to the allocation group. The chief investigator will not conduct any outcome assessments. The allocation/randomization arms will be as follows:Group A: Investigational treatment\u2014opioid-free anesthesiaGroup B: Standard treatment\u2014non-opioid-free anesthesiaInduction and maintenance anesthesia will be given according to The recovery room staff will be blinded to the participant\u2019s anesthetic grouping. The intraoperative anesthetic charts (AARK) records will be printed without \u201canesthetic medications/agents administered intraoperatively\u201d. The recovery nurses will receive the AARK print out with all other data, including procedure details, intraoperative monitoring and anesthetic notes. The recovery nurse will receive the Identification, Situation and Status, Background, Assessment and Actions, Recommendations and Responsibilities (ISBAR) handover from the anesthetic doctor/nurse. The recovery room staff will use the standard Post-anesthetic Pain Management Protocol for all QoR-15 questionnaire (baseline and 24-h post-operatively).Preoperative anesthetic clinic assessment form.AARK.Post-anesthetic care unit (PACU) documents.National In-patient Medication Charts (NIMC).Queensland Hospital Admitted Patient Data Collection.Intravenous Patient Controlled Analgesia Order\u2014Adult.Analgesia monitoring forms, intravenous, PCA, epidural and regional analgesia.Queensland Adult Deterioration Detection System (Q-ADDS).Clinical notes.Data will be collected and transcribed onto an electronic data collection sheet using Google Docs. A cloud-stored electronic database within Google Docs has been purpose built for this research by a research team member. Access is via two-factor authentication and password security. This methodology has been risk assessed by the Queensland Health Cyber Security team as meeting the needs for the storage of sensitive data.Outcomes are measured at baseline, then at the induction of anesthesia and at Day 1 post-operatively. The post-operative assessment will be conducted on the ward or by phone . The primary outcome is the 15-item quality of recovery (QoR-15) score . Each quAll participants randomized will be included in the analyses on an intention-to-treat basis. Ten percent of data collected and entered will be independently verified. If more than 0.5% disagreement between data collected/data entry exists, then a further 10% of data will be checked. This process will continue until no disagreement is found by the independent verifier.Data distribution will be assessed. Descriptive statistics, including frequencies and percentages for categorical data, and means, standard deviations or medians, and ranges for continuous data, will be assessed to ensure randomization has succeeded, and to describe differences between groups.\u00ae version 20.0 (IBM\u00ae SPSS\u00ae Statistics 20) for Windows will be used for all analyses. All analyses will be reported at the 0.05 statistical significance level, unless Bonferroni corrected levels are appropriate.Mean and total QoR-15 scores will be calculated per participant at baseline and on Day 1. QoR-15 change scores will be calculated to determine the difference between Day 1 and baseline scores for each participant. The effect of OFA versus non-OFA on recovery (QoR-15 score) will be evaluated using a mixed model with random effects to estimate the effect of OFA on QoR-15 scores, accounting for baseline QoR-15 scores type of surgery and 24-h peri-operative opioid use. If there are no statistically significant random effects in the mixed-method model (tested using likelihood ratio test), univariate and multivariate linear regression models using the QoR-15 change score will be used for group comparisons and to estimate factors associated with outcomes. Interaction effects will be investigated and eliminated where possible through data transformation and the inclusion of interaction terms in the models. Stata 14 and SPSSThe intent of this research is to consider the hypothesis that opioids are an essential component in the suite of anesthetic medications. In Western contemporary health care practices, the use of opioids during anesthetic is evidenced-based, or is it? The Australian and New Zealand College of Anesthetists is cognizant of the rising prescription and risk of opioids. Their position statement around tThe evidence provided by this research will contribute to the growing body of knowledge around the efficacy of newer opioid-free anesthetic techniques."} +{"text": "Existing data from several reports on the association between lipid profile and ovarian tumour (OT) suggests divergent conclusions. Our aim was to examine whether circulating lipid profile: total cholesterol (TC), triglyceride (TG), high-density lipoprotein (HDL) and low-density lipoprotein (LDL) differed between cases and non-cases of OT.I2 statistics, the effect of individual studies on the overall effect size was tested using sensitivity analysis and funnel plot was used to evaluate publication bias.Electronic repositories; PUBMED, EMBASE and Cochrane library were explored through December 2019 to retrieve published articles for inclusion in the meta-analysis after quality assessment. Heterogeneity was assessed using I2 statistics ranged between 97 and 99%. Mean circulating TC and HDL were significantly lower among OT cases compared to non-OT cases.Twelve studies, involving 1767 OT cases and 229,167 non-cases of OT were included in this meta-analysis and Decreased TC and HDL profiles were observed among subjects with OT in this collection of reports. The implications of TC and HDL in tumour manifestations and growth need to be validated in a large multi-ethnic longitudinal cohort adjusting for relevant confounders. Ovarian cancer is the most deadly gynaecological malignancy among women, comprising diverse groups of neoplasm . It accoSeveral studies have reported the relationship between lipid profiles; total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL) and low-density lipoprotein cholesterol (LDL) and ovarian tumour (OT) with different conclusions. For example, Camuzcuoglu et al. and BukhDrawing vivid inferences from prior population-based studies on lipid profile and OT risk appears difficult because of disparities in participants\u2019 selections, study designs, etc. In addition, scientific evidence on this subject is of great significance to clarify whether alterations in circulating lipid profiles are sufficient to promote OT risk or these alterations are only a reflection of previously compromised health status.To this effect, a comprehensive analysis, comprising previous studies across diverse population would be necessary. Therefore, this study investigated the true difference in circulating lipid profiles among subjects with and without OT using a meta-analytical approach.https://www.crd.york.ac.uk/PROSPERO/display_record.php?ID=CRD42018099728) and conducted using the MOOSE guidelines of serum lipid profile were extracted independently by two reviewers and differences in data extractions were resolved in recourse to a third reviewer. To ensure uniformity of estimates, mean values of TC were transformed to (mg/ into SD .I2 test statistics. A random-effects model was used to obtain mean estimates under considerable heterogeneity (i.e I2-test >\u200950% or P\u2009<\u20090.05), but a fixed-effect model was applied to obtain mean estimates when I2-test <\u200950% or P\u2009>\u20090.05. The random effect model postulates mean estimates of lipid profile(s) differed across studies, but follow a distribution and pooled mean is estimated as the average mean difference with an assumption that differences in mean estimates are symmetrically distributed. However, the fixed effect estimates assumed that observed differences are primarily an after-effect of chance [Heterogeneity of pooled effect estimate and the magnitude of variation across studies was assessed using f chance , 15.P\u2009<\u20090.05 was considered statistically significant. Sensitivity analysis of pooled mean estimates was assessed using a leave-one-out method and publication bias was assessed using a funnel plot.Statistical analysis was conducted using Review Manager 5.3 and two-tailed Of the 1619 records obtained from the primary literature search, 377 duplicates and 1079 records were excluded after examining titles and abstracts. Also, 151 records were excluded after full-text evaluation and 12 studies comprisimg/dL, P\u2009=\u20090.04 was significantly lower among OT cases compared to non-OT subjects among OT subjects with malignant and/or advanced tumours. TC and LDL profiles were insignificantly different, but HDL profile was significantly lower between OT and non-OT subjects in studies with low risk of bias.Stratifying our meta-analysis by age Table\u00a0, TG profFifty percent of studies included in the meta-analysis suggested a low risk of bias Table S. The biaThere was no significant evidence of publication bias from the funnel plots Figure S in the mOverall pooled mean estimates differed insignificantly upon the exclusion of a single study at a time Table S, but fewTo the best of our knowledge, this is the first meta-analytical study reporting true mean differences of circulating lipids and OT risk. Total cholesterol and HDL profiles were significantly lower among OT subjects, but TG and LDL profiles were insignificant in OT risk. We opined that these results highlight the significance of lipids in OT outcomes. The quality of reports included in our meta-analysis may largely influence these associations, but the findings of the stratified analysis represent a significant strength and modest evidence for significant alterations of lipid profile in OT risk is likely.Whether altered lipid profiles are a causal or consequential factor of OT risk is debatable. However, our findings aligned with the plausibility of the latter. Circulating lipid profiles are largely subject to alterations in the occurrence of tumour events . CholestHDL and LDL are prominent cholesterol-transporting agents vital in evaluating lipid profile in cancer signalling , 30. In In addition, there is evidence of a modest inverse association between TC or HDL and breast cancer risk . The antAlso, LDL differed insignificantly between OT and non-OT subjects in this current meta-analysis. This finding has been well reported in studies , 45 fromOur study has both strengths and limitations. Our report is the first meta-analysis highlighting the significance of lipid profile and risk of ovarian neoplasm. The higher statistical power arising from a large number of participants in our report potentially offer credibility to our findings. In addition, our funnel plots could not rule out the potential for publication bias in this meta-analysis. However, most studies included in our meta-analysis were cross-sectional (owing to limited cohort reports) and limited studies age-matched cases with controls in the eligible studies. The number of studies on this subject is comparatively rare, making the clarification of our findings quite challenging. Our findings must be interpreted with caution given a temporal sequence of causal association cannot be inferred and perhaps prone to reverse causality. In spite of the biological plausibility of the association between lipid profile and OT risk, there are many confounders involved in OT carcinogenesis. Overweight/obesity and its associated co-morbidities significantly promote OT risk among women . SimilarOur meta-analysis presents evidence of a modest significant association between circulating HDL and risk of OT. It is vital to elucidate the implications of HDL in tumour manifestations and growth. There is a need to validate these findings using large multi-ethnic longitudinal cohorts effectively adjusting for age, menopausal status, preclinical prejudice and other key confounding factors.Additional file 1. Supplementary Table S1: Critical assessment of included studies using the Newcastle-Ottawa Scale (NOS). Supplementary Figure S1: Funnel plot of lipid profile; total cholesterol (A), triglyceride (B), HDL (c) and LDL (D) between cases and non-cases of ovarian tumours; summarizing the publication bias in the meta-analysis. Supplementary Figure S2: Graphical illustration of the results of the critical assessment of studies; Is the Case Definition Adequate? (S1), representativeness of the Cases (S2), selection of Controls (S3), definition of Controls (S4), comparability of cases and controls on the basis of the design or analysis (C1), ascertainment of exposure (E1), same method of ascertainment of exposure for cases and controls (E2), overall risk of bias of all studies included. Supplementary Table S2: Sensitivity Analysis (using one study leave out method) of pooled mean differences of Lipid profiles between cases and non-cases of ovarian tumour.Additional file 2. A Meta-analysis Of Observational Studies in Epidemiology (MOOSE) Checklist."} +{"text": "Uterine cancer is the sixth most common malignancy in women worldwide, with the majority of cases originating from the endometrium . The proAs with other types of endometrial cancer, the mainstay of treatment in women with G3 endometrioid adenocarcinoma is surgery including total hysterectomy, bilateral salpingo-oophorectomy, and staging. The optimal adjuvant treatment remains less defined, and National Comprehensive Cancer Network (NCCN) Guidelines offer several options for each stage . Women wTargeted therapy remains an area of exploration for development of new agents such as antibody-drug conjugates (ADCs), targeted monoclonal antibodies linked to a cytotoxic agent. Sacituzumab govitecan, an ADC that is comprised of a humanized anti-trophoblast cell surface antigen (Trop-2) antibody, conjugated with the active metabolite of irinotecan (SN-38) through the cleavable CL2A linker, has shown promising results against epithelial cancers overexpressing Trop-2 in Phase II trials -9. Trop-et al. recently investigated Trop-2 expression in 143 patients with G3 endometrioid endometrial adenocarcinomas and studied the cytotoxic effects of sacituzumab govitecan against these tumors in the preclinical setting [in vitro model, the authors demonstrate both antibody-dependent cellular toxicity as well as cytotoxic effects of sacituzumab govitecan in tumors expressing Trop-2. The same toxic effects were not seen in Trop-2 negative cell lines. The authors also noted a bystander effect, which is a unique characteristic of ADCs with cleavable linkers that provides an opportunity for destruction of not only the antigen-positive target cells but also the surrounding antigen-negative cells. This is especially beneficial in tumors that demonstrate high heterogeneity in the expression of target antigens such as uterine cancer. In the xenograft model, intravenous administration of sacituzumab govitecan twice weekly for a total of six injections resulted in a significant tumor growth inhibition.Perrone setting . ModeratThese promising preclinical results strongly suggest that sacituzumab govitecan may represent a novel, potentially effective treatment option for poorly differentiated endometrial cancer patients with recurrent/metastatic disease resistant to standard treatment modalities. The results of the first clinical trial of trop-2 targeted therapy in uterine cancer (NCT04251416) are eagerly awaited and will shed more light into this topic."} +{"text": "Ting Wang et al. describe a defective variant of hepatitis B virus (HBV) with a very high replication capacity comprising a large deletion in the preS1 domain of the open reading frame encoding the three HBV surface proteins [In this issue of Virus Genes, The variant showed the typical mutations A181T and N236T in the reverse transcriptase domain of the viral polymerase protein leading to adefovir resistance after previously failed lamivudine therapy. The first lamivudine-selected mutation (A181T) happens to generate the stop mutation W172* in the overlapping S domain of the HBs proteins causing carboxyterminal truncation and intracellular retention of all three HBs proteins. While this is an additional stop mutation in the S domain (C69*) that prevented the formation and release of enveloped HBV particles encoded by the variant, HBV DNA and HBsAg of the variant could nevertheless be detected in the patient serum. This indicated that the patient\u2019s hepatocytes replicating the variant via circular covalently closed (ccc) HBV DNA contained HBV genes encoding functional HBs proteins as well, most likely as linear-integrated HBV DNA fragments. Transcomplementation with functional HBs genes of defective ccc DNA has recently been shown in CHB patients by Peiffer et al. [Surprisingly, the variant described in with theBoth effects are probably linked together. The preS1 sequence aa 42-110) deleted in the variant of 2-110 del. After nAt the first glance, the variant may appear irrelevant because it cannot generate infectious HBV progeny. However, the large amounts of partially double-stranded HBV DNA accumulating in the nucleus in absence of functional HBs proteins are subject to potentially detrimental cellular DNA repair processes including integration of HBV DNA fragments. Thus, mutated HBs proteins may directly contribute to pathogenesis of HBV-related diseases like hepatocellular carcinoma (HCC) via the effect of intranuclear accumulation of HBV DNA. In fact, HBV variants with altered HBs structure including preS deletions have increasingly been identified in patients with active HBV disease including HCC . Besidest, have been linked to the development of hepatocellular carcinoma (HCC) [t [Already decades ago, secretion-defective HBs mutants, e.g., a truncated form of the middle HBs protein MHBsma (HCC) . Accumulma (HCC) . However(HCC) [t or of WT(HCC) [t . The pre(HCC) [t . Althoug(HCC) [t did not (HCC) [t , 11 have(HCC) [t .Seemingly contrary to the published association of preS2 with HCC , 11, a hThe fact that the highly replicating HBV variant of ref was foun"} +{"text": "Limited empirical evidence suggests that caregiver burden is greater for informal care partners (family and friends) in assisted living (AL) compared with other long-term care settings, particularly within context of end of life. Using qualitative data from a larger 5-year, 7-site study of end-of-life care in AL funded by the National Institute on Aging (R01AG047408), we investigate informal care partners\u2019 involvement in end-of-life care and identify challenges related to informal caregiving that might contribute to care burden. Grounded theory analysis of ethnographic data and in-depth interviews (average interview length = 97 minutes) with 59 racially and ethnically diverse informal care partners (mean age = 60) shows that informal care partner involvement in end-of-life care varies across participants and over time and is shaped by multiple intersecting social and structural determinants. At individual levels, these include many personal, situational, and relational factors. Personal factors include but are not limited to care partners\u2019 own physical and mental health and material resources . Situational and relational factors include care partners\u2019 awareness (or lack thereof) of residents\u2019 impending death and the quality of the caregiving relationship. AL and wider community-level factors include understaffing, staff turnover, inadequate hospice support, and lack of access to these services. We find that informal care partners navigate these caregiving challenges through a basic social process we conceptualize as \u201cnegotiating risks.\u201d Strategies for easing caregiver burden and improving informal care partner and resident quality of life at end of life are implicated."} +{"text": "More supportive social relationships are protective of cognitive decline in older adulthood. Although supportive social relationships are hypothesized to promote cognitive reserve , it is unknown whether CR mediates associations between social support and risk of developing mild cognitive impairment or dementia (MCI/dementia). Data from 815 women (aged 73-87 years) participating in the Women\u2019s Health Initiative Memory Study-MRI cohort (WHIMS-MRI) and Women\u2019s Health Initiative Study of Cognitive Aging (WHISCA) were analyzed to examine whether domain-specific estimates of CR mediate associations between social support and incident MCI/dementia risk. Women completed the Medical Outcomes Study Social Support Scale (MOS-SS) in 2004-2005, a structural MRI (sMRI) of the brain in 2005-06, and annual extensive neuropsychological examinations till 2018. CR (6-months after completing the MOS-SS) was estimated across different domains as the residual variance after regressing out effects of sMRI variables, sociodemographic factors, and measurement error. Structural equation models were constructed to examine whether CR mediate associations between social support and MCI/dementia risk while adjusting for covariates. Higher social support was associated with lower MCI/dementia risk , higher language reserve and verbal memory reserve . Language and verbal memory reserve each significantly explained approximately 14% of the protective effect of social support. Findings illustrate the heterogeneous effect of social support on CR, highlighting the importance of language and verbal memory reserve as mediators of the association between social support and MCI/dementia risk."} +{"text": "Cell Discovery (2021) 7:8Correction to: 10.1038/s41421-020-00238-x Published online 02 February 20211, the description of data source and reference for the identification of epithelial cell lineages of pigs were missing and should be added in Materials and methods section as follows.In the original publication of this articleLineage identification of cells in Pig2.The expression matrix of the endometrial epithelium, including the pregnant glandular epithelium (GSM2946041-44), the pregnant luminal epithelium (GSM2946045-48), the control glandular epithelium (GSM2946030-33), and the control luminal epithelium (GSM2946034-37), was downloaded from GSE1095392 should be cited in the main text as shown below.The newly added reference45 to predict the ligand\u2013receptor interactions between pregnant womb epithelium 2 and PostL-EPIs or PostL-TEs during the elongation stages\u201d.\u201cTo investigate potential roles of the endometrial epithelium may play in pig embryo elongation, we used CellPhoneDBIn addition, in the last Venn diagram of Fig."} +{"text": "Over seven million U.S. adults are estimated to have undiagnosed diabetes and are at heightened risk of diabetes complications and poorer long-term glycemic control. Key to addressing undiagnosed diabetes is identifying how persons encounter diabetes testing in everyday life and the contextual factors that lead to consulting a health care provider. As part of the NIA-funded Subjective Experience of Diabetes Study we examined the pathways through which community-living African-American and non-Hispanic White older adults with type 2 diabetes (T2D) (N=75) received their T2D diagnosis. Systematic, thematic analyses using ATLAS.ti reveals three primary routes to diabetes diagnosis: diagnosis through continuity of primary care, diagnosis through happenstance testing, and diagnosis following the exacerbation of symptoms. While diagnosis as part of routine care was the least reported (N=13), participants\u2019 accounts suggest diagnosis in primary care validates the patient-provider relationship and provides an occasion to calmly establish a treatment plan. More frequently, however, diagnosis occurs through fortuitous encounters with glucose tests, e.g., through work or community research projects (N=15) or after symptoms become alarming and disrupt daily life (N=47). Participants\u2019 experiences in these latter two categories reveal the critical role of insurance and social prompts in the decision to consult a clinical provider regarding symptoms. At the same time, the abundance of over-the-counter therapies treating conditions commonly found early in the emergence of diabetes can delay clinical follow up. These findings highlight the importance of social prompts and community-based testing in the fight to reduce undiagnosed diabetes."} +{"text": "To the Editor: In their recent article, Nakaminami et al. describe a case of human infection caused by Panton-Valentine leucocidin (PVL)\u2013positive livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (MRSA CC398) in Japan , lincosamides (clindamycin), macrolides (clarithromycin), and tetracyclines (tetracycline). We therefore suspect that the isolate belongs to the human variant of MRSA CC398.In recent years, Denmark has witnessed increased importation of PVL-positive MRSA CC398 from mainland Asia because of international travel, in 1 case leading to a large hospital outbreak among mothers and infants in a maternity ward ("} +{"text": "Gametophytic mutants share very small proportion of the total mutants generated by any mutagenic approach; even rarer are the fertilization-defective gametophytic mutants. They require an efficient and targeted strategy instead of \u2018brute force\u2019 screening approach. The classical gametophyte mutant screening method, mainly based on the segregation distortion, can distinguish gametophytic mutants from the others. However, the mutants pooled after the screening constitute both fertilization-defective and developmental-defective gametophytic mutants. Until recently, there has not been any straightforward way to screen the former from the latter. Additionally, most of the mutations affecting both gametes are lost during the screening process. The novel gametophyte screening approach tends to circumvent those shortcomings. This review discusses on the classical approach of gametophytic mutant screening and focuses on the novel approach on distinguishing fertilization-/developmental-defective gametophytic mutants . It offers an empirical basis of screening such mutants by taking in the consideration of earlier studies on fertilization failure, initiation of seed coat formation, and fertilization recovery system in plants. Arabidopsis suggest that a distinct group of genes (known as imprinted genes) is essential for the successful seed development. Their active allele is restricted either to the maternal or to the paternal line. Moreover, their expression is mostly limited to the endosperm after fertilization in few T-DNA insertional mutants. Such segregation pattern was later termed as \u2018segregation distortion\u2019 and has since been regularly used to screen the gametophytic mutants ratio. Additional reciprocal crosses of the mutants with their wild-type (WT) counterparts separates the female gametophyte (FG)-specific, male gametophyte (MG)-specific, and zygotic mutants from each other burst and successful double fertilization at the FG can be affected by MG mutation thereby bringing a significant variation in the seed-set pattern . Numerouduo1, duo2 (duo3 (drop1drop2 (gcs1/hap2 (gcs1/hap2) PT in the beginning -attracts additional PT to salvage the failed fertilization (hap2-1/+ pollens), only half of the ovules receiving second PTs may get fertilized and develop into seeds thereby bringing the seed-set rate up to 75% (50% of the ovules fertilized with first PT + 25% of them fertilized with second PT) may not necessarily receive the second PT before they (the ovules) degenerate. This is why the seed-set rate in a fully penetrant fertilization defective hemizygous MG-mutants ranges between 60 and 75% (When the mutation causes defects in sperm cell (SC) development or function, the self-pollinated hemizygous mutants show a significant drop in seed sets. Few mutants are known to affect SC development, which include o1, duo2 , duo3 . Additiocond PT) in hap2- and 75% .It should be noted that any potential mutant with no defect in SC but defective in PT burst may also show ~75% seed-set. The rapid expulsion right after PT burst is appar). In such cases, any observed seed-set rate in the self-pollinated hemizygous mutants would be insufficient to determine the gametophytic mutants conclusively.Studies show that gametophytic mutations are rare and comprise mere 1\u20139% of the total mutant pool . AdditioClassical screening method greatly depends on the selection marker segregation and close linkage of the marker to the mutated gene in the chromosome. Chromosomal rearrangements (and insertions elsewhere in the genome) leading to the development of positive selection marker progenies without mutation in the gene in question is a possible unwanted consequence of the method . Screenigcs1/+ mutants, as explained in Since pollen tube content (PTC) release in the ovule triggers seed coat formation and the successful fertilization allows its continued and complete formation , the fer1) Carrying out self-cross and check the seed-set pattern in the mutants and 2) using the siliques of the mutants for vanillin staining 3 days after pollination and check the proportion of fully stained, partially stained, and unstained ovules. The fertilization defective mutants will show no unstained ovules while the developmental-defective mutants will show no partially stained ovules. Additional crosses (other than the self-cross) shown in gcs1/+ (\u2642) in Expected maximum seed-set rates and proportions of vanillin staining within a silique of either developmental- or fertilization-defective MG and/or FG-mutants are shown in gcs1/+ (\u2642) would show 37.5% seed-set. The vanillin staining would show the ratio of 3:5:0 , with ~37.5 and ~62.5% seeds/ovules showing full and partial staining, respectively (A fertilization-defective FG mutant will show ~50% seed-set upon self-cross (or crossing with WT (\u2642)). The vanillin staining will exhibit the ratio of 1:1:0 for the ovules in each silique. Additionally, its cross with ectively . Hence, ectively . The ~37A fertilization-defective MG mutant, on the other hand, will show ~75% seed-set upon self-cross or crossing with WT (\u2640). Subsequent vanillin staining would show the ratio of 3:1:0 for the ovules in each silique (It should be noted that the seed-set rates and vanillin staining proportions shown in Vanillin staining combined with the consideration of the fertilization recovery system offers a strong clue for screening gametophytic mutants (except for the fertilization-defective MG-mutants vs zygotic mutants) in a single generation. When selection marker segregation analysis is added , this screening approach can effectively separate any of the zygotic and fertilization-/developmental-defective MG/FG mutants. Moreover, starting the screening process (after mutagenesis) from vanillin-staining of the self-crossed mutant siliques provides a rough clue on the mutant type and allows a researcher to prepare a gametophytic mutant enriched pool for their targeted gametophytic studies.PA prepared the data figures and wrote the manuscript. XL carried out the vanillin staining experiments, and RK checked and confirmed the data and manuscript.This work was supported by start-up funds from the School of Life Sciences, Fujian Agriculture and Forestry University (Grant #: 114-712018008 to RK) and the FAFU-UCR Joint Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University. This work was also supported by Chinese NSFC fund (Grant #: 31970809). This work was also supported by the Precursory Research for Embryonic Science and Technology .The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Electrospinning is one of the most widely used techniques for the fabrication of nano/microparticles and nano/microfibers, induced by a high voltage applied to the drug-loaded solution. The modification of environmental conditions, solution properties or operation parameters results in different fiber properties, thus enabling the fine-tuning of functionality-related characteristics of the final product. The latter includes the alteration of the rate and extent of the solubility of drugs, hence the rapid or prolonged onset of absorption.This Special Issue serves to highlight and capture the contemporary progress of electrospinning techniques, with particular attention to their further pharmaceutical application as conventional and novel drug delivery systems or for tissue regeneration purposes. It comprises a series of 12 research articles and one review, illustrating the versatile researches and teams from 13 different countries, making profound contributions to the field.Palo et al. investigated a combined technique for the fabrication of bi-layered carriers from a blend of polyvinyl alcohol (PVA) and sodium alginate (SA). The bi-layered carriers were prepared by solvent casting in combination with two surface modification approaches, electrospinning or three-dimensional (3D) printing. An initial inkjet printing trial for the incorporation of bioactive substances for drug delivery purposes was performed. The solvent cast (SC) film served as a robust base layer. The bi-layered carriers with electrospun nanofibers (NFs) as the surface layer showed improved physical durability and decreased adhesiveness compared to the SC film and bi-layered carriers with a patterned three-dimensional (3D) printed layer. The bi-layered carriers presented favorable properties for dermal use with minimal tissue damage. In addition, electrospun NFs on SC films (bi-layered SC/NF carrier) provided the best physical structure for cell adhesion, and proliferation as the highest cell viability was measured compared to the SC film and the carrier with a patterned 3D printed layer (bi-layered SC/3D carrier) .Cherwin et al. developed a novel oxygen therapeutic made from a pectin-based hydrogel microcapsule carrier mimicking red blood cells. The study focused on three main criteria for developing the oxygen therapeutic to mimic red blood cells: Size (5\u201310 \u03bcm), morphology (biconcave shape), and functionality ). The hydrogel carriers were generated via the electrospraying of the pectin-based solution into an oligochitosan crosslinking solution using an electrospinning setup. The pectin-based solution was investigated first to develop the simplest possible formulation for electrospray. The production process of the hydrogel microcapsules was also optimized. The microcapsule with the desired morphology and size was successfully prepared under the optimized condition. The encapsulation of Hb into the microcapsule did not adversely affect the microcapsule preparation process, and the encapsulation efficiency remained high (99.99%). The produced hydrogel microcapsule system offers a promising alternative for creating a novel oxygen therapeutic .Staphylococcus aureus and Escherichia coli. Consequently, PCL-GEL/CLV nanofiber mats can be potential candidates for antibiotic-free wound healing applications [Unalan et al. prepared antibacterial poly(\u03b5-caprolactone) (PCL)-gelatin (GEL) electrospun nanofiber mats containing clove essential oil (CLV) using glacial acetic acid (GAA) solvent. The addition of CLV increased the fiber diameter from 241 \u00b1 96 nm to 305 \u00b1 82 nm. Along with the increase of the CLV content of nanofibers, the wettability of PCL-GEL nanofiber mats was also increased. Fourier-transform infrared spectroscopy (FTIR) analysis confirmed the presence of CLV, and the actual content of CLV was determined by gas chromatography\u2013mass spectrometry (GC-MS). It was confirmed that the CLV-loaded PCL-GEL nanofiber mats did not have cytotoxic effects on normal human dermal fibroblast (NHDF) cells, while the fibers exhibited antibacterial activity against Viet Nguyen et al. developed novel amphiphilic electrospun nanofibers (NFs) loaded with haemanthamine (HAE), phosphatidylcholine (PC), and polyvinylpyrrolidone (PVP), intended for a stabilizing platform of self-assembled liposomes of the active agent. The NFs were fabricated with a solvent-based electrospinning method. The HAE-loaded fibers showed a nanoscale size ranging from 197 nm to 534 nm. The liposomes with a diameter between 63 nm and 401 nm were spontaneously formed as the NFs were exposed to water. HAE dispersed inside liposomes showed a tri-modal dissolution behavior. Amphiphilic NFs loaded with HAE are an alternative approach for the formulation of a liposomal drug delivery system and stabilization of the liposomes of the chemically instable and poorly water-soluble alkaloid [v/v) and formic acid solution (90% v/v) . The fiber diameter and morphology of the nanofibrous DDSs were modulated by varying ultrasonic parameters in the USES process . The authors found that the USES technology produced nanofibers with a higher fiber diameter (402 \u00b1 127 nm) than TES (77 \u00b1 21 nm). An increase in burst count in USES increased the fiber diameter (555 \u00b1 265 nm) and the variation in fiber size. The slight-to-moderate changes in a solid state were detected in comparison to the nanofibers generated by TES and USES. In conclusion, USES provides a promising alternative for aqueous-based fabrication of nanofibrous DDSs for various pharmaceutical and biomedical applications [Hakkarainen et al. investigated nozzleless ultrasound-enhanced electrospinning (USES) as a means to generate nanofibrous drug delivery systems (DDSs) for pharmaceutical and biomedical applications. Traditional electrospinning (TES) equipped with a conventional spinneret was used as a reference method. High-molecular polyethylene oxide (PEO) and chitosan were used as carrier polymers and theophylline anhydrate as a water-soluble model drug. The nanofibers were electrospun with the diluted mixture (7:3) of aqueous acetic acid -loaded polymeric nanofibers in situ and determined the solid-state of the drug during dissolution. Hydroxypropyl methylcellulose (HPMC) and polydextrose (PD) were used as carrier polymers for electrospinning (ES). The initial-stage dissolution of the nanofibers was monitored in situ with three-dimensional white light microscopic interferometry (SWLI) and high-resolution optical microscopy. They confirmed that PRX recrystallizes in a microcrystalline form immediately after wetting of nanofibers, which could lead to enhanced dissolution of the drug. Initiation of crystal formation was detected by SWLI, indicating that PRX was partially released from the nanofibers, and the solid-state form of PRX changed from amorphous to crystalline. The amount, shape, and size of the PRX crystals depended on the carrier polymer used in the nanofibers and the pH of the dissolution media. The PRX-loaded nanofibers exhibited a quasi-dynamic dissolution via recrystallization. SWLI enabled a rapid, non-contacting, and non-destructive method for in situ monitoring of the early-stage dissolution of nanofibers and regional mapping of crystalline changes during wetting .Preem et al. tested and compared different drug release model systems for electrospun chloramphenicol (CAM)-loaded nanofiber (polycaprolactone (PCL)) and microfiber (PCL in combination with polyethylene oxide) mats with different drug release profiles. The CAM release and its antibacterial effects in disc diffusion assay were assessed by bacterial bioreporters. The release into buffer solution showed larger differences in the drug release rate between differently designed mats compared to the hydrogel release tests. The UV imaging method provided an insight into the interactions with an agarose hydrogel mimicking wound tissue, thus providing information about early drug release from the mat. Bacterial bioreporters showed clear correlations between the drug release into gel and antibacterial activity of the electrospun CAM-loaded mats .Lactobacillus and one of Lactococcus were characterized. The electrospinning of polymer solutions containing ~10 log colony forming units (CFU)/mL of lactic acid bacteria enabled the successful incorporation of all bacterial species tested, from the smallest to the largest , into poly(ethylene oxide) nanofibers with an average diameter of ~100 nm. All of these lactobacilli were viable after incorporation into nanofibers, with 0 to 3 log CFU/mg loss in viability, depending on the species. Viability correlated with the hydrophobicity and extreme length of lactic acid bacteria, whereas a horizontal or vertical electrospinning set-up did not have any role. Therefore, electrospinning represents a promising method for the incorporation of lactic acid bacteria into solid delivery systems, while drying the bacterial dispersion at the same time [Zupan\u010di\u010d et al. investigated the effect of electrospinning on the viability of bacteria incorporated into nanofibers. The morphology, zeta potential, hydrophobicity, average cell mass, and growth characteristics of nine different species of w/w triethanolamine, 15% w/w PVPK90) were found to be suitable for obtaining orally dissolving webs of fast dissolution and potential oral absorption [Sipos et al. formulated aceclofenac-loaded poly(vinyl-pyrrolidone)-based nanofibers by electrospinning to obtain drug-loaded orally disintegrating webs to enhance the solubility and dissolution rate of the poorly soluble anti-inflammatory active that belongs to the Biopharmaceutical Classification System (BCS) Class-II. Triethanolamine-containing ternary composite of aceclofenac-poly(vinylpyrrolidone) nanofibers was formulated to exert the synergistic effect on the drug-dissolution improvement. The nanofibrous formulations had diameters in the range of a few hundred nanometers. FT-IR spectra and DSC thermograms indicated the amorphization of aceclofenac, which resulted in a rapid release of the active substance. The characteristics of the selected ternary fiber composition . The presence of crystalline mannitol and the low water content enabled appropriate grinding of the fibrous sample without secondary drying. The ground powder was mixed with commonly used tabletting excipients and was successfully directly compressed. \u03b2-galactosidase remained stable in the course of the whole processing and after one year of storage at room temperature in the tablets. The results demonstrate that high-speed electrospinning is a viable alternative to traditional biopharmaceutical drying methods, especially for heat-sensitive molecules, and further processing of electrospun fibers to tablets can be successfully achieved [Vass et al. developed a processable, electrospun formulation of a model biopharmaceutical drug, \u03b2-galactosidase. They demonstrated that higher production rates of drug-loaded fibers could be achieved by using high-speed electrospinning compared to traditional electrospinning techniques. An aqueous solution of 7.6 achieved .d,l-lactide-co-glycolide) (PLGA)/gelatin polymer solutions for the simultaneous release of recombinant human epidermal growth factor (rhEGF) and gentamicin sulfate at the wound site to hasten the process of diabetic wound healing and inactivation of bacterial growth. The bacterial inhibition percentage and detailed in vivo biocompatibility for wound healing efficiency was performed on diabetic C57BL6 mice with dorsal wounds. The scaffolds exhibited excellent wound healing and continuous proliferation of cells for 12 days, thus providing a promising means for the rapid healing of diabetic wounds and ulcers [Dwivedi et al. designed a nanocomposite carrier using Poly(d ulcers .co-polycaprolactone (PLA-PCL) electrospun nanofibers; quantification and in vitro drug release profiles in static and dynamic conditions were investigated. The kinetics of the GS release from nanofibers was studied using mathematical models. A preliminary microbiological test was carried out towards Staphylococcus aureus and Escherichia coli bacteria. The prolonged effect of the antibiotic at the site of action can reduce administration frequency and improve patient compliance [Pisani et al. studied electrospun nanofibers as antibiotic release devices for preventing bacteria biofilm formation after surgical operation. In their work gentamicin sulfate (GS) was loaded into polylactide-mpliance . Pant et al. summarized that electrospinning has emerged as a potential technique for producing nanofibers. The use of electrospun nanofibers in drug delivery has increased rapidly over recent years due to their valuable properties, which include a large surface area, high porosity, small pore size, superior mechanical properties, and ease of surface modification. A drug-loaded nanofiber membrane can be prepared via electrospinning using a model drug and polymer solution; however, the release of the drug from the nanofiber membrane in a safe and controlled way is challenging as a result of the initial burst release. Employing a core-sheath design provides a promising solution for controlling the initial burst release. This paper summarizes the physical phenomena, the effects of various parameters in coaxial electrospinning, and the usefulness of core-sheath nanofibers in drug delivery. It also highlights the future challenges involved in utilizing core-sheath nanofibers for drug delivery applications . All the articles presented in this Special Issue represent a small fraction of the great research interest in the field of nanofibrous system applications as drug delivery bases or for tissue engineering purposes. Their diverse and tunable features enable a wide variety of use, which opens a new dimension in the case of their feasible scaling-up."} +{"text": "Hepatitis C virus (HCV) and hepatitis B virus (HBV) co-infection can be encountered in either virus endemic countries. Co-infection can also be found in populations at risk of parenteral transmission. Previous studies demonstrated a high risk of liver disease progression in patients with HCV/HBV co-infection; thus, they should be treated aggressively. Previous evidence recommended therapy combining peginterferon (pegIFN) alfa and ribavirin for co-infected patients with positive HCV RNA. Recent trials further advise using direct-acting antivirals (DAAs) for the clearance of HCV in the co-infected patients. Reactivation of HBV has been observed in patients post-intervention, with higher risks and earlier onset in those having had HCV cured by DAA- versus pegIFN-based therapy. The mechanism of HBV reactivation is an interesting but unsolved puzzle. Our recent study revealed that in vitro HBV replication was suppressed by HCV co-infection; HBV suppression was attenuated when interferon signaling was blocked. In vivo, the HBV viremia, initially suppressed by the presence of HCV super-infection, rebounded following HCV clearance by DAA treatment and was accompanied by a reduced hepatic interferon response. In summary, major achievements in the treatment of HCV/HBV co-infection have been accomplished over the past 20 years. Future clinical trials should address measures to reduce or prevent HBV reactivation post HCV cure. In hepatitis B virus (HBV) or hepatitis C virus (HCV) endemic countries, patients are exposed to the risk of being co-infected with both viruses ,2,3. ParPrevious clinical trials suggested that peginterferon (pegIFN) alfa plus ribavirin (RBV) was effective for clearing HCV in patients with HBV/HCV co-infection ,12,13,14Patients may experience HBV reactivation after the cure of their HCV by pegIFN- or DAA-based therapy, the risk of HBV reactivation being higher and onset being earlier in the latter, as warned by the US FDA years ago . Our triUntil now, the mechanism of this HBV reactivation, post-HCV cure, remained an interesting mystery. Our recent study provided evidence that HBV suppression was attenuated when IFN signaling was blocked in vitro . ClinicaManagement of HBV activity, including the prevention of HBV reactivation post HCV cure, is a clinical issue that needs to be dealt with in further clinical trials. The lack of supportive evidence is reflected by the differences among the recommendations by the EASL (European Association for the Study of the Liver), AASLD (American Association for the Study of Liver Diseases) or APASL (Asian Pacific Association for the Study of the Liver) community regarding the prevention of HBV reactivation in co-infected patients ,19,20.This article will review recent updates about the clinical outcomes and treatment of patients with hepatitis C and B co-infection, with emphasis on the risks and mechanisms of HBV reactivation.The adverse effect of HCV/HBV co-infection has been demonstrated previously by a long-term community-based study in Taiwan showing the combined effect of HCV/HBV co-infection on the cumulative incidence of HCC . Our recThe fibrosis 4 parameters (FIB-4) index has been investigated widely for the assessment of the liver fibrosis stage and the clinical outcomes in patients with chronic hepatitis C . To examOvert HBV infection (indicated by positive serum HBsAg) adversely affects the clinical outcomes of chronic HCV infection . Occult In short, recent studies have reached a consensus that overt, but not occult, HBV co-infection may accelerate the progression of HCV-related liver diseases. FIB-4 index can help to predict adverse clinical outcomes in CHC patients receiving DAA.Our previous data confirmed the efficacy of pegIFN plus RBV in the treatment of co-infected patients with active hepatitis C ,25,26,27For patients with HCV/HBV co-infection, we hope treatment can decrease the risk of HCC development and liver-related mortality in the long term. In Taiwan, we analyzed nationwide databases and conducted a case-control study. We found that the treatment of co-infected patients using pegIFN plus RBV indeed reduced risk of HCC development and liver-related mortality .With the arrival of the DAA regimen, which has proven to be a simple, time-saving, highly tolerated and effective treatment option for HCV , two queTo answer these questions, we conducted a multi-center study in Taiwan using sofosbuvir/ledipasvir to treat HCV/HBV co-infected patients . OverallUnlike the HCV treatment response, the outcomes of co-existing HBV infection were still unclear. One study followed the serial HBsAg and HBV DNA levels in 79 HCV/HBV co-infected patients receiving DAAs (13 receiving anti-HBV nucleos(t)ide analogue [NUC] therapy simultaneously) . The autp = 0.03). Cirrhosis risk was numerically higher among HBV/HCV co-infected patients than among HCV mono-infected patients, but became lower among those who attained SVR .A recent study reported on whether the clearance of HCV by DAA could improve the clinical outcomes of co-infected patients . For perHBV activity may reactivate during anti-HCV therapy in co-infected patients . Our prin = 779) was similar between those treated with IFN-based therapy and DAAs . Interestingly, HBV reactivation was noted to occur much earlier in those treated with DAAs in comparison to those receiving IFN-based therapies. The risk of hepatitis due to HBV reactivation was also higher in those receiving DAA versus IFN-based therapy (12.2% vs. 0%).After the introduction of DAA for the treatment of chronic hepatitis C, there is an increased awareness of HBV reactivation in CHC patients co-infected with HBV treated with DAAs. An earlier systematic review and meta-analysis compared the rate of HBV reactivation in CHC patients co-infected with HBV treated with IFN-based therapy, versus those with DAAs . OverallTo clarify the chronological profile and risk of HBV reactivation during and after the DAA treatment, we followed the HBV virological parameters prospectively for 108 weeks following the end of treatment . We foun10 IU/mL) ranging from 25% to 87.5% (mean: 41.1%) in HBsAg-positive patients treated by DAAs and HBV/HCV co-infection (n = 78) were both enrolled. The authors found that compared with HCV mono-infection, the HBV/HCV co-infection group showed significantly lower HCV neutralizing antibody responses and a decreased frequency of circulating Th1-like Tfh cells. The clinical implications of these immunologic interactions between the two viruses await further study.A recent study has investigated the impact of co-existing HBV on circulating T follicular helper cell (Tfh) distribution and the HCV neutralizing antibody response . PatientTo further explore the molecular mechanisms behind this viral interaction and resultant HBV reactivation, our recent in vitro and in vivo investigations were conducted with major inputs from virologists . In co-iAnother study investigated potential mechanism of HBV reactivation after HCV elimination by DAA treatment in HCV/HBV co-infected patients . Murai eIn short, recent studies have provided evidence regarding the in vivo and in vitro interactions between HCV and HBV. These interactions partly explained why HBV reactivates after the clearance of HCV. However, more studies are needed to fully clarify this issue.EASL guidelines suggest AASLD practice guidance has diffRecent APASL guidelines suggest that for these co-infected patients, careful attention should be paid to HBV reactivation for 24 weeks post-treatment .All guidelines agree that the status of HBV infection should be monitored closely if IFN-free regimens are adopted, since HCV DAA is anticipated to have no direct or immunomodulatory effect on the replication of HBV. Anti-HBV therapy should be timely implemented if clinically indicated .Despite being suggested by EASL guidelines, whether prophylactic NUC would be beneficial in comparison to the therapeutic strategy for HBV reactivation remains unclear. We therefore conducted a prospective multicenter trial in Taiwan investigating the effect of prophylactic NUC on the prevention of HBV reactivation after the start of DAA for CHC [NCT04405011]. The data will be available soon and will further the understanding and management of HCV/HBV co-infection.HCV/HBV co-infection is commonly encountered in endemic areas and among individuals at risk of parenterally transmissible infections. How the two viruses interact with each other in the liver is partly understood. In addition to academic interest, these data will help develop more effective antiviral therapy and efficient strategies to prevent HBV reactivation post HCV cure by DAA.For HCV/HBV co-infected patients, the same genotype-dependent treatment recommendations for single chronic hepatitis C can be applied. The value of DAA-based therapy in co-infected patients has been demonstrated in a recent clinical trial and prolonged follow-up . The lon"} +{"text": "The transformation in cells at genetic levels stimulatesthe proliferation of cancer. The current review highlights the role of miRNA in management of cancer by altering processes of body at cellular levels. A deep research on the literature available till date for miRNA in cancer was conducted using various medical sites like PubMed, MEDLINE from internet and data was collected. The articles were majorly preferred in English language. The development of normal cells into cancerous cells is a multivalent procedure highlighting numerous responsible factors. During the progression of cancer, the role of oncogene and tumor suppressor genes outshines at different levels of tumorogenesis. Metastasis poses highest threat in cancer progression and fabricates obstacles to clinicians and researchers in preventing formation of tumor on secondary sites. The mesenchymal-epithelial transition (MET) and epithelial mesenchymal transition (EMT) induce dissemination and ultimately progression of cancer. A comprehensive knowledge of the altered genes and the mechanism by which they induce formation of tumor is essential as they contribute in proliferating cancer at various stages, aggravating clinical symptoms. Hence miRNAs can be efficiently employed as an emerging treatment therapy for cancer. Cancer in itself is a very broad term and condition. It can be described as a disease in which the cellular modifications in the body lead to uncontrolled abnormal growth and proliferation of the cells that accumulate and protrude towards tumor formation. There is not always rapid cell growth but cell growth may be suppressed in certain scenarios as well. The tumor growth cancers can be detected much easily when compared to malignant like blood caners which are hard to diagnose. In a study in USA in 2014, it has been estimated that over 480,000 people die with cancer each year. It is still one of the most debilitating disease worldwide and therapy advances in management of cure of cancer are much needed.C. elegans, and were later established for their presence in human and other eukaryotes . It has also been assumed that the human genome comprises of nearly 1-5% of miRNAs which evidently regulates about 30% of genes that code for specific proteins . Various studies established the significant functioning of miRNA in regulating genetic expression of metabolic and cellular origin pathways . de Croce\u2019s team was the first to state the part of miRNA in proliferating cancer and identified genes that suppress tumor in chronic stage of B-cell lymphocytic leukemia. In latter cases, miR-16-1 and miR-15a, two major miRNAs downregulated . Further studies conducted stated that they not only suppressed the growth of tumor but also promoted apoptosis via manipulation of Bcl-2 and anti-apoptotic proteins, hence increasing expression of non dividing malignant B cells . The miRNA manifestation is highly regulated by transcription factors. Hence, miRNA illustrationscould bealtered by modifying the factors responsible for transcriptionsuch as p53 and c-Myc. In malignant cases c-Myc is elevated and guides cell proliferation by stimulating transcription . Alterations in genes with simultaneous modification in phenotype of the individual are linked with metastasis of cancer cells . The non-coding miniature endogenous RNAs also called micro RNAs (miRNAs) regulates a wide array of metabolic processes that are indulged in induction of carcinogenesis. MiRNAs were primarily revealed in Biogenesis of miRNA MicroRNAs (miRNAs) comprise of a long 20\u201322 nucleotide chain of non-translating RNAs. About 1\u20135% of miRNA genome undergoes transcription on interaction with enzyme RNA-polymeraseII . Biogenesis is a long procedure and occurs at nucleus and cytoplasmic compartments. The transcribed genes initiate capped 5\u2019 end and polyadenylated 3\u2019 end generating the first primary transcript namely pri- miRNA. Its a large stem-loop like formation and fabricates the formation of single stranded 5\u2019 and 3\u2019 RNA that projects theformation of functional miRNA . Pri-miRNA further branches to precursor miRNA (Pre-miRNA) via nuclear RNAse III or Drosha comprising complex microprocessors along with DGCR8. The pre-miRNA formed migrates to cytoplasm via GTP complex Exportin-5 and Ran from nucleus . The latter on reaction with dicer associated TRBP or TAR RNA-binding protein and enzyme RNase III generate long double stranded ~22 nucleotide miRNA . An enzyme named helicase unzips the doublyentangled miRNA and develops two single strands, one of which engages itself in formation of RNA induced silencing complex (RISC) comprising of Argonaute-2 (AGO2) protein degrading other. Upon binding to 3\u2019UTR\u2019s, the miRNA induced silencing complex (miRISC) suppresses translation causing degradation of mRNA targets . Single miRNA directs numerous pathwaysand have a tendency to extinguish multiple transcripts. Disturbed transcription regulation may synthesize and express abnormal and diversified proteins. Hence, miRNA\u2019sare recognized as important determinants of cell fate in response to cellular expression during cancer progression.Involvement of miRNAs in cancer Various studies conducted in previous decade clearly explained miRNA and its part in regulating malignancies in humans. Abnormal miRNAs manifestations cause gene dysfunction and are responsible for pathological conditions of various diseases. They have ability to regulate the genetic expression via repression of pre-transcription or directing deletion and destruction of target gene by messenger RNA (mRNA) . Some studies identified miRNAs as a standardized element in transcriptional regulation of metastasis , arresting cell cycle and inducing apoptosis . In this article we will emphasize thecontribution of miRNA in modulating and abolishing proliferation of cancer and cell survival. Restraint of miRNA in Transcriptional controlRegulating transcription is an essential factor for cell survival. Convoluted interactions between the controls of transcription and post-transcription proteins regulate gene expression leading to manifestation ofgenes explicit to cell-type patterns ascertained by the stages of development and differentiation of etiological conditions. Biological system directly or indirectly has connected signaling pathways. Theoncogenic and tumor suppressive transcription factors become dysfunctional, resulting in cell transformation due tochanges in transcriptional factors, for example,P-TEFb can be stimulated by c-Mycwhich activates the enzyme RNA polymerase II and maintains transcription . c-Mycis a factor oftranscription thatrepresses and activatestarget genes. A tumor gene suppressor called phosphatase and tensin homology (PTEN) is activated by c-Myc on transcriptionwhich further dephosphorylates PI3K and its products named phosphatidylinositol 3,4,5-triphosphate (PIP3) by inhibiting PI3 kinase mediated growth signals. Failure of expression of PTEN inhibits AKT activation further prohibitingpromotion of proliferation of cells and apoptosis . Inhibition of miRlet-7 increases proliferation of cells , whereasmanifestation of mature miRlet-7 arrests the cell cycle . Interestingly another miRNA named miR-145is capable to arrest development of tumor cells by aiming c-Myc, mucin-1 and other related genes . Contrivedthe miR-143 functioning whilst interacting with native miR-145inhibits the major signaling molecules like p68/p72/\u03b2-catenin (Wnt), ERK5/c-Myc, hence preventing the development of intestinal tumor . Therefore, impaired expression of miRNAs could be involved in alteration of transcription factors that may support or cease the cancer development and progression.miRNA in cell cycle Appropriate regulation of cell cycle assures genetic adherence while mitotic division. Inaccurate cell cycle and disturbed genetic profiles may protrude incomplete replication and arrest cell cycle thereby causing cell apoptosis. The cell cycle is directed by two main molecular mechanisms: a cascade of protein phosphorylation polished by cyclin dependent kinase (CDK) and cyclin complex besides restriction points such as G1/S/G2/, metaphase . The principal hallmark of proliferation and progression of cancer are the mutations in genes due to dysregulated gene expressions andirregular cell cycle. Oncogenic miRNAs wreck CDK inhibitors and assist the succession of entry of cell cycle and suppress transcription of the retinoblastoma family .A miR-137 self-manifestation is repressed by hypermethylation and is associated with the expression of CDK6 in oral carcinogenesis cases . The miR-449a/breinforces negative feedback on signaling of Rb/E2F, and stimulate transcription of miR-499a/b by E2F, declining the levels of CDK6 and Cdc25A implied in regulation of cell cycle. A huge emphasis is given on miR-126 as it is beautifully of brews signaling of PI3K via IRS-1 VEGF . In hypoxic conditions, miR-210 interacts with hypoxia-inducible factor 1-alpha or HIF-1a. HIF-1a mediated cell-cycle arrest antagonizes transcriptional activity of c-Myc transcriptional preventing signaling of canonical Wnt, thereby reducing malignancy .miRNA in EMT/MET The fundamentalcharacter of MET and EMT in invading cancer has recently been investigated. Through various studies it has been found that modification in individuality of cells upon transformationmanifest cancer. Epithelium, a cellular phenotype, acts as a surface barrier and cells possessing invasive and migratory properties are referred as mesenchyme. The incidence of transition of epithelial mesenchymal cells is popular and cells tend to gain migratory properties by exploiting the process besides change in itsadhesive property. Impressive rearrangement of the cytoskeleton of actin besides the simultaneous formation of prominence memberis must for invading proliferation. The cells divide themselves from region of primary tumor and spread around the associated tissues.The cancerous cells through extracellular matrix pursue a chemo alluring pathway as they lose cell to cell contact thereby remodeling adhesion sites of cell-matrix. EMTexhibitsa remarkable attribute in proliferation of cancer and its invasion. Regulating genes by EMTcan prove to be amazing therapeutic targets for management of cancer. Various stages of metastasis express the processes commonly undergone by EMT . On the other hand, MET is reciprocal of EMT and is fundamental for cellular proliferation. The cells of cancer invade through EMT processes and relapse to epithelial state by MET to proliferate to secondary surrounding sites, hence act smartly . The markers of EMT are highlighted by failure of adhering cells, repressingexpression of E-cadherin, an associated marker for acquisition of mesenchyma like N-cadherin, Vimentin, and Fibronectin, and elevated motility of cells . Numerous miRNAs are stated for their indulgence in single or multistep event of metastasis since the past decade. Some of the miRNAsare linked with the EMT like family of miR-205 and mir-200,therefore targeting genes namely SIP1 and ZEB1. The ZEB1,also called deltaEF1 and SIP1 also called ZEB2 are suppressors of E-cadherin . Suppressing miRNAs issufficient to execute thefamily of miR-200 expressionandavoid EMT induced by TGF-beta . Many miRNAs acting as inhibitors and inducers of EMT in management of cancer have also been documented, for example, miR-21 , miR-7 , miR-10b, miR-125b , miR-155 , miR-9 , miR-497 , and miR-5003-3p. The examples of miRNA linked with MET include miR-34a, miR-34b and miR-34c .Apoptosis regulated miRNA p53 gene which lacks cell line of murine myeloid leukaemia. Apoptosis can be classified under two categories: \u201cintrinsic\u201d and \u201cextrinsic\u201d . The former path requires Cytochrome Cfor recruiting procaspase-9 complex. The pathway for apoptosis is moderately influenced by bcl family members linked to mitochondrial membrane . The Bcl-2-antagonist/killer namely Bak and Bax are involved in retotion to the apoptotic impetus . The extrinsic pathway sparks on activation of receptors of dependence and death. The ligands for receptors of dependence and death bind to their relative membrane receptors, likeFas ligand (FasL), tumor necrosis factor (TNF-\u03b1), TNF-like weak inducer of apoptosis (TWEAK) and TNF-related inducing ligand (TRAIL) . Death receptor ligands stimulate the death inducing signaling complex (DISC), that further activates CASP8 and regulate its function . The dependence receptor family consist, netrin 1 (NTN1), unc-5netrin receptor A (UNC5A) and the neurotrophin receptor tyrosin kinase 3 (NTRK3). DNA damage induced disturbance or alteration in signaling pathways seize the cycle of cell growth, modifying phenomenon of apoptosis. Apoptosis or commonly called programmed cell death is widely studied and targeted phenomenon in cancer research. Itirreversibly kills the damaged cells and exhibits beneficial effects in organism. The apoptotic events occur through equilibrium between the pro- and anti-apoptotic family of proteins . Apoptosis is induced by changes in physiological or pathological conditions in body or in response tocertain stimuli. The enzyme p53 exhibits a significantrole in apoptosis induced death of cells which wasoriginallystatedin year 1991 by M. Oren with the help of Bcl2. The miR-145 via dependent TP53 manner has been identified in establishing death induced pro-apoptotic effect. miR-145 on stimulation activate TP53 level and increase their levels which inversely proliferate the tumor grades in cancer of breasts . Restoring miR-133a expression suppresses tumorigenicity in bone cell sarcoma via cell apoptosis . Augmented concentrations of miR-210 in hypoxic conditions induce existence of cells .Various reports have suggested participation of miRNA in functioning and apoptosis of cell. Thorough studies showhigh manifestations of miR-221 and miR-222 which tends to regulate extrinsic pathways via TRAIL induced apoptosis of cell . The miR-K10 is an onco-miR and encourages tumor cell existence by down- regulating TNF-like weak apoptosis inducing (TWEAK) receptors . Similarly, decreased concentrations of miR-15 and miR-16 assisst Bcl2 expression in the Chronic lymphocytic leukemia (CLL) and activate apoptotic pathway signaling and can be strategizedas an approach for treatment of tumors due to over expression of miRNA in therapeutics To fabrictate therapeutic strategies, a thorough knowledge ofvarious mechanisms like transcription regulation, epigenetic or chromosomal changes and miRNAs mediated defects in cancer progression is must. Since past decademiRNAs have been in limelight and attention for their targettingto develop new treatment approaches. The miRNA are fundamentally active in major cellular functions like proliferation, differentiation, growth and metabolism.The miRNAs are also engaged in cancer biology and asa regulatory genetic element. Studies done till date pose miRNA to exhibit mainpart in proliferating tumor malignancy by acting as oncogenes modulator or tumor suppressor element. Different miRNA express and flourish development of individual diseases on alterations. Fate of the disease and functioning of genes is regulatedby overexpression or down expression of miRNA in varied medical complications . However, restoring their function can reduce or even abolish tumor growth .PDCD4, PTEN, and Akt/Rb signaling (SPRY1) . Therefore, miRNA mediated anti-cancer therapy can be usedalone or combined with conventional medicines. miR-100 possesses chemo-resistance properties incancerous cells of lungs . Hindering epigenetics of miR-199b-5p increases the sensitivity to drug in ovarian cancer resistant to chemotherapy . miR-21 was established as an onco-miRdisplaying high levelsin cancer, comprising target genes in association like miRNA expression and prompt functioning of genes that have ability to suppress tumor .Researchers are intended to design adjuvant molecular approach along with chemotherapy to control oncogenic In conclusion, alterations in genetic makeup of a human promote cancer cell growth. The carcinoma progression is a multistep process;therefore a deep knowledge the mechanisms at molecular and microenvironmental level that trigger growth of tumorare highly essential.Molecular investigations of cancer cells atvaried levels of cancer progression display the diversity in genes that suppress tumor and other oncogenes correlated with the clinical pugnacity of cancer and its proliferation. A decade of research and pieces of evidence suggest the emergence of micro RNA. Through extensive studies, the precisepathway and functions of the miRNA has been established. Differentially dysregulated miRNA leads to cancer progression and severity. Involvement of miRNA and their expression in cancer related pathwaysmust be understood. However, the role of miRNA role has been defined in regulation of cancer and its related pathways towards malignancy and metastasis of the tumor. The current article explainsmiRNA and itsfunction ina variety of biological events like transcription, metastasis, cycle of cell growth, cancer progression and apoptosis. The emerging scenario suggests that miRNA also have propulsive indication in cell differentiation and act as a critical element in determining fate of cell and fundamental oncogenesis. Therefore, targeting the oncogenic miRNA or revitalization of mi-RNA induced tumor suppression could be a novel concept in advanced therapy. To develop miRNA inhibitors and restoring levels of miRNA, we must determine the principal miRNA that possesses clinical importance at different stages in various cancers."} +{"text": "Throughout May 2020, I conducted a quantitative literature review of the Web of Science database, with search terms including \u201cpsychological anxiety,\u201d \u201cemotional distress,\u201d \u201csocial isolation stress,\u201d and \u201cmental health disorders.\u201d As I focused on research published exclusively this year, only 104 various types of articles met the eligibility criteria. By removing those whose results were inconclusive, unconfirmed by replication, or too general, and because of space constraints, I selected 49, mainly empirical, sources. The inspected collected findings prove that the COVID-19 pandemic has resulted in greater degrees of psychological distress in the affected populations. The COVID-19 outbreak may generate emotional distress and anxiety, aggravating preexisting mental health disorders and shaping stress-related disturbances for affected people. Individuals having severe mental illness tend to be hurt emotionally by social problems heightening their vulnerability. Both COVID-19 infected patients and the general affected population may develop severe depressive symptoms. Significant degrees of fear may heighten the damage generated by such a highly infectious disease. The volume of recovered patients may diminish COVID-19-related apprehension and panic. Future research should investigate whether COVID-19-related reduced care provision and prolonged self-isolation and quarantine will have long-term impact on mental and psychological health.This review enhances the existing literature on the emotional and mental health of COVID-19 patients and affected persons who have spent prolonged time intervals in self-isolation or quarantine. My article cumulates previous research findings on adverse physical COVID-19 causes severe psychological anxiety and social isolation stress . As a reEmotions of anxiety around COVID-19 are associated with limited health resources to keep the pandemic under control, social self-isolation, and the prevalent unpredictability with regard to the length of the crisis . AdjustiThe COVID-19 pandemic has resulted in greater degrees of psychological distress in the affected populations, generating symptoms of anxiety and depression, and instability in immune function . ClinicaThe practice of physical/social distancing associated with COVID-19 leads to alterations in behavioral patterns and discontinuances of routine functioning with possible long-term effects for mental health and psychological well-being . The emoand psychological consequences developed from the COVID-19 pandemic. The prolonged COVID-19-related restrictions on social interactions have detrimental consequences on the mental health of affected individuals , particuAs The public health effects of restricting close human links during the COVID-19 pandemic may comprise severe mental health issues . PhysicaSignificant research has considered lately how affected persons are experiencing a deterioration in physical and psychological health throughout the COVID-19 crisis. My article extends previous work by focusing on how such individuals are exposed to temporally undetermined stress that may increase anxiety and depression. The conclusions drawn from the above analyses are that COVID-19-related behavioral and emotional reactions consolidate detrimental consequences of psychological stress as a result of lengthy negative events. As limitations in the current review, by focusing only on articles published in journals indexed in the Web of Science database, I inevitably disregarded other valuable sources. Future research should investigate whether COVID-19-related reduced care provision and prolonged self-isolation and quarantine will have a long-term impact on mental and psychological health.The author confirms being the sole contributor of this work and has approved it for publication.The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Complex phenotypes captured on histological slides represent the biological processes at play in individual cancers, but the link to underlying molecular classification has not been clarified or systematised. In colorectal cancer (CRC), histological grading is a poor predictor of disease progression, and consensus molecular subtypes (CMSs) cannot be distinguished without gene expression profiling. We hypothesise that image analysis is a cost-effective tool to associate complex features of tissue organisation with molecular and outcome data and to resolve unclassifiable or heterogeneous cases. In this study, we present an image-based approach to predict CRC CMS from standard H&E sections using deep learning.Training and evaluation of a neural network were performed using a total of n=1206 tissue sections with comprehensive multi-omic data from three independent datasets , n=430 patients). Ground truth CMS calls were ascertained by matching random forest and single sample predictions from CMS classifier.Image-based CMS (imCMS) accurately classified slides in unseen datasets from TCGA =0.84) and rectal cancer biopsies . imCMS spatially resolved intratumoural heterogeneity and provided secondary calls correlating with bioinformatic prediction from molecular data. imCMS classified samples previously unclassifiable by RNA expression profiling, reproduced the expected correlations with genomic and epigenetic alterations and showed similar prognostic associations as transcriptomic CMS.This study shows that a prediction of RNA expression classifiers can be made from H&E images, opening the door to simple, cheap and reliable biological stratification within routine workflows. Previous research has shown that there are four distinct colorectal cancer subtypes defined by common patterns of gene expression.Clinicians hope that these consensus molecular subtypes (CMSs) of colorectal cancer could support patient stratification for precision therapy.Currently, colorectal cancer subtype is established through RNA analysis, which is not widely used due to high costs and the need for specialist knowledge to interpret the data.Computational models can predict transcriptional subtypes of colorectal cancer from standard histology sections.Image-based CMS (imCMS) makes sequencing information interpretable through association of tile level predictions with morphology, molecular features and outcome data.imCMS classifies samples previously unclassifiable by RNA expression profiling, gives a novel insight into tumour heterogeneity and shows similar prognostic associations as transcriptomic CMS.imCMS classifies endoscopic biopsies and resection specimens of colorectal cancer laying the methodological basis for patient stratification in diverse clinical settings.A prediction of RNA expression classifiers can be made from H&E images, opening the door to simple, cheap and reliable biological stratification within routine workflows and existing retrospective cohorts.Colorectal cancer (CRC) is a disease with heterogeneous molecular subtypes, variable clinical course and prognosis.et alThe application of traditional image analysis to histopathology facilitates the quantitative assessment of tissue architecture, cell distribution and cellular morphology by light microscopy to generate feature libraries of unprecedented resolution and detail.In CRC, it is well known that tumour morphology, growth pattern and architecture hold important clues to differentiating biological subtypes with clinical impact.Ongoing research is investigating associations between clinical interventions and CMS subgrouping, and so this classification has the potential to guide treatment allocation in future clinical practice.The study design, cohorts and aims are outlined in 10.1136/gutjnl-2019-319866.supp1Supplementary dataGut in 2018.https://gut.bmj.com/content/67/1/179%23DC1. Draft papers developed by each working group were evaluated by a 20-strong patient panel. A final list of RGs and research recommendations (RR) was endorsed by all participants. Key RGs were identified in the pathological assessment of CRC (RG7). The working group highlighted the importance of integrating genomics, big data science and digital pathology methods to improve the morpho-molecular taxonomy and biological stratification of CRC . The present study aims to address these recommendations through the development of multiparameter algorithms for analysis of routine H&E slides in the pathology laboratory. Results from this study were communicated to the patient community through Bowel Cancer UK.This project is tackling research gaps (RGs) identified by authors of this study in the Bowel Cancer UK \u2018Critical research gaps and recommendations to inform research prioritisation for more effective prevention and improved outcomes in colorectal cancer\u2019 research project, published in The aim of this study was to develop an image analysis framework to associate features of tissue organisation on standard histology slides with molecular classification and outcome data in patients with CRC. Training and test cohorts were selected to represent relevant clinical scenarios in the management of patients with CRC including postoperative resection specimens (FOCUS and TCGA) and endoscopic biopsy material (GRAMPIAN). A total of 1540 slides from three independent datasets were utilised in this study including 666 slides of resection specimens from 362 patients in the FOCUS cohort, 468 slides of resection specimens from 463 patients in the TCGA cohort and 406 slides from preoperative biopsies of 223 patients in the GRAMPIAN cohort . Tumour 10.1136/gutjnl-2019-319866.supp12Supplementary dataThe imCMS classifier was trained against CMS calls on the transcriptionally classified samples of the FOCUS cohort and tested on the TCGA and GRAMPIAN cohorts . With th10.1136/gutjnl-2019-319866.supp2Supplementary dataWe systematically compared the performance of the imCMS classifier across all three cohorts. For benchmarking against molecular data, all unclassified samples were excluded from the test set. Classification performance was compared using image tiles derived at (a) 3\u00d7 and (b) 12\u00d7 magnification to determine the effect of detail levels. In the FOCUS training cohort, a robust imCMS classification performance of 0.88 AUC was reached . imCMS c10.1136/gutjnl-2019-319866.supp13Supplementary data10.1136/gutjnl-2019-319866.supp14Supplementary dataCRC resection specimens and biopsies (GRAMPIAN) were used for algorithm training and testing. Samples from these cohorts have been prepared in separate institutions using different protocols and exhibit the expected range of morphological differences due to discrete preprocessing and preparation steps. The combination of these three specific cohorts captures sample variability as commonly encountered in pathology practice and provides an excellent opportunity to evaluate the generalisability of imCMS. Domain adversarial learning, a machine learning method that promotes the emergence of features that are discriminative for imCMS classification and indiscriminate of preanalytical variation between resection specimens,; we furt10.1136/gutjnl-2019-319866.supp15Supplementary data10.1136/gutjnl-2019-319866.supp16Supplementary data10.1136/gutjnl-2019-319866.supp17Supplementary data10.1136/gutjnl-2019-319866.supp18Supplementary data10.1136/gutjnl-2019-319866.supp3Supplementary data10.1136/gutjnl-2019-319866.supp19Supplementary data10.1136/gutjnl-2019-319866.supp4Supplementary data10.1136/gutjnl-2019-319866.supp20Supplementary dataTo understand which specific morphological patterns associate with imCMS, we extracted and visually reviewed tiles with the highest prediction confidence for each imCMS subtype. The large-scale histology patterns corresponded well with the biological characteristics of the CMS1 and CMS4 classes as predicted from the molecular assay10.1136/gutjnl-2019-319866.supp5Supplementary dataFailure of the transcriptional CMS classification might represent a transition phenotype, intratumoural heterogeneity or might represent technical failure to classify.10.1136/gutjnl-2019-319866.supp6Supplementary data10.1136/gutjnl-2019-319866.supp21Supplementary dataCRC tumours exhibit intratumoural variability in transcriptional features leading to a bias in transcriptional CMS calls introduced by the regions sampled for molecular analysis.10.1136/gutjnl-2019-319866.supp7Supplementary data10.1136/gutjnl-2019-319866.supp8Supplementary data10.1136/gutjnl-2019-319866.supp10Supplementary data10.1136/gutjnl-2019-319866.supp11Supplementary dataWe performed univariate Cox proportional hazard analysis to assess the prognostic associations of the imCMS classification compared with its molecular counterpart. The trend of patient survival outcomes stratified by imCMS was largely in agreement with those of the transcriptional classification and imCM10.1136/gutjnl-2019-319866.supp22Supplementary data10.1136/gutjnl-2019-319866.supp9Supplementary dataH&E slides are generated as part of the standard work-up of any CRC treated by surgical resection. In the assessment of this histologic material, pathologists are presently limited to a strictly defined set of morphologic and anatomic criteria.We trained and tested the imCMS approach towards consensus molecular subtyping of CRC on three independent and well-characterised patient cohorts with availability of digital slides and transcriptional information from the MRC CRUK S:CORT consortium and TCGA. We specifically focused on relevant clinical scenarios in the management of patients with CRC and investigated the imCMS classification of both preoperative biopsies and resection specimens. Our analysis demonstrates the feasibility of imCMS classification of both primary colon and rectal resection specimens in the FOCUS and TCGA cohorts. imCMS calls closely matched transcriptional classification for survival stratification, underlining the potential of imCMS to aid pathologists in the identification of aggressive disease for intensified follow-up and chemotherapy trials.Small biopsy fragments have previously proven difficult to analyse using genomic technologies due to the limited amount of tissue available and pathologist assessment is usually restricted to the diagnosis of cancer, a select panel of immunohistochemical studies and a limited assessment of additional prognostic features.The robustness of image analysis algorithms is a well-recognised problem in the setting of limited training sets and poorly annotated reference data. We addressed the problem of sample diversity by training the imCMS classifier on histological samples sourced from multiple institutions (n=59) participating in the FOCUS trial. We also included endoscopic biopsies and surgical resections as two diverse examples of CRC tissue specimens with different preprocessing procedures. Biopsy tissue undergoes relevant compression stress during capture by endoscopic forceps leading to architectural distortion and variable alteration of cellular morphology. We show that imCMS classification is relatively stable across these settings. Domain adversarial training was used to further minimise learning features that are attributed to a specific cohort.Transcriptomic CMS was released as the most robust molecular classification in CRC and the basis for clinical stratification and targeted intervention.Tumour heterogeneity introduces important challenges in designing optimal treatment strategies for patients with cancer.Prospective validation of imCMS in independent studies will be critical to clinical translation. A first application will be its use as a tool to call CMS in large clinical trial cohorts in whom funding for gene expression profiling is not available. This will build the evidence base to show whether or not imCMS can be used as a predictive biomarker for treatment response or patient enrichment for certain research studies. We hypothesise that the general principle can be applied not only to other cancer types but also to other diseases. It will therefore lay the foundation of a more systematic integration of image-based morphological analysis and molecular stratification."} +{"text": "From both weldments, cylindrical tensile specimens of cross-weld configuration were machined. The room-temperature tensile tests were performed for the individual welds\u2019 PWHT states in both hydrogen-free and electrolytically hydrogen-charged conditions. The results indicated higher hydrogen embrittlement susceptibility for the renormalized-and-tempered weldments, compared to the conventionally tempered ones. The obtained findings were correlated with performed microstructural and fractographic observations.In the present work, the effects of electrolytic hydrogen charging of T92 steel weldments on their room-temperature tensile properties were investigated. Two circumferential weldments between the T92 grade tubes were produced by gas tungsten arc welding using the matching Thermanit MTS 616 filler material. The produced weldments were individually subjected to considerably differing post-welding heat treatment (PWHT) procedures. The first-produced weldment was conventionally tempered (i.e., short-term annealed below the Ac The 9 wt.% Cr creep strength enhanced ferritic (CSEF) steels represent advanced structural materials for application in high-efficiency power engineering. However, for constructing complex power generation equipment, fusion welding technologies are needed for joining individual functional parts. In accordance with the numerous research studies and ex-service experience, e.g., ,4,5, it 2-based Laves phase within the failure location [Depending on several factors including the welding metallurgy-related material properties and outer loading and/or environmental conditions, the fusion weldments can be susceptible to some of several typical failures . The \u201cTylocation ,18. The location showed tlocation ,21. Thislocation . The meclocation .23C6 carbides and MX carbo-nitrides. The direct consequence of performing the subcritical PWHT procedure is related to the decrease of unallowably high hardness in FZ/CG-HAZ and improvement of the overall weld fracture resistance [In common industrial practice, the weldments of CSEF steels are necessarily subjected to conventional PWHT, i.e., the subcritical tempering below the steel Ac1 critical transformation temperature. The main aim of such PWHT is to relieve residual stresses and thermally stabilize the weld microstructure with secondary phase precipitates, typically the Msistance ,24. Howesistance that thesistance ,26 suggeOur previous investigations ,28 were Our present study represents a continuous research work to our aforementioned former studies. It deals with investigation of the effects of initial PWHT conditions and subsequent electrochemical hydrogenation on the resulting room-temperature tensile properties and fracture behavior of T92/T92 welded joints. Mutual correlations between varying microstructural characteristics induced by different initial PWHT regimes and resulting mechanical properties of the weldments in either hydrogen-free or hydrogen-charged conditions are discussed.Four segments of industrially normalized and tempered T92 tubes were circumferentially welded in the company SES a.s. Tlma\u010de, Slovakia. The welded joints were produced by gas tungsten arc welding (GTAW) technique using T92-based filler metal Thermanit MTS 616 to prepare two equivalent T92/T92 weldments. The T92/T92 welds geometry was the same as also used in our previous study about long-term ageing effects on room-temperature tensile behavior of quenched and tempered T92/TP316H dissimilar weldments [The chemical compositions in The two prepared weldments were individually subjected to mutually differing post-welding heat treatment (PWHT) procedures. 1 temperature of T92 steel) for 60 min and then slowly cooled within the tempering furnace (see the PWHT-1 in 3 temperature of T92 steel) for 20 min and subsequently cooled on still air, followed by its conventional subcritical tempering at a crosshead speed of 0.05 mm/min. Three tensile test specimens per each state were investigated. The hydrogen-charged samples were tested immediately after the electrolytic hydrogen charging. The evaluation of c-w tensile properties involved the calculation of their average values and corresponding standard deviations. Local mechanical properties of studied weldments were characterized by means of hardness measurements which were performed using a Vickers 432 SVD hardness tester on plain surfaces of longitudinal sections of fractured tensile specimens. This procedure was also helpful for indication of local strain hardening effects within the studied weldments during the tensile tests. The referential, i.e., un-deformed samples corresponding to both initial PWHT states were also tested for hardness. All the hardness measurements were performed at 98 N loading for 10 s per measurement.3COOH, 20 mL HCl, 3 g picric acid, and 144 mL CH3OH) using the light optical microscope OLYMPUS GX71 and the scanning electron microscope (SEM) JEOL JSM-7000F . Fractographic analyses were carried out using the SEM Tescan Vega-3 LMU .Microstructural analyses of the studied weldments were performed on the conventionally prepared metallographic samples carbides and intragranular MX carbo-nitrides [2 Laves phase is not to be expected in the currently studied material states (PWHT-1 and PWHT-2) due to insufficient time for its creation related to slow diffusion kinetics of the tungsten and molybdenum atoms in the ferrite solid solution. This assumption has already been evidenced in our several former studies [The phase composition of normalized and tempered martensitic steels of T/P92 grade is generally known and consists of ferritic matrix and strengthening precipitates of intergranular Mnitrides ,39,40,41 studies ,28,29 ab1-Ac3 range). Accordingly, the IC-HAZ is formed of fine-grained microstructure consisting of over-tempered martensite and newly formed martensite created on cooling from fine-grained non-saturated austenite. The FG-HAZ microstructure is formed in the region of BM heated up during the welding to peak temperatures just above Ac3 up to about 1100 \u00b0C. After subsequent cooling, the resulting FG-HAZ consists of newly formed martensite created from fine-grained non-saturated austenite and coarsened precipitates of original undissolved carbides. As shown in By comparison of individual microstructures in The effects of initial PWHT conditions in combination with subsequent electrolytic hydrogenation of the studied T92/T92 weldments on their room-temperature tensile properties are shown in RA0 and xRA are the values of reduction of area at fracture of two considered material states, and the subscripts \u201c0\u201d and \u201cx\u201d refer to the states selected as initial and final, respectively [RA values SC-HAZ in the location of tensile test fracture. Thus, the originally softer areas within the T92/T92 weldment in the PWHT-1 material state represent the locations of the localization of the highest plastic deformation during tensile testing. f, as it follows:A0 and fA are the values of original cross-sectional area and final cross-sectional area at the point of fracture of the tensile test specimen. The calculated \u03b5f values indicating the level of accumulated plastic deformation at the location of final fracture are shown in The necking-related hardness peaks at fracture locations are the result of strain hardening due to the localization of plastic deformation after reaching plastic instability during tensile testing. This can be supported by the fact that the more ductile samples after the PWHT-1 induced by plastic instability at local microstructural heterogeneities , namely the HAZ microstructural gradient and WM microstructural heterogeneity in the PWHT-1 and PWHT-2 material states, respectively. For the sake of completeness, it should be noted that for the weldments in PWHT-1 material state, the increased strain hardening effects were observed not only at the final fracture locations but also at the locations of the concurrent necking areas a. The reThe detailed discussion on mutual correlation between the fractographic and microstructural characteristics of studied T92/T92 weldments will be provided within the following section.As already discussed, and shown in On the other hand, the observation of rather brittle failures c,d withiThe fracture paths in As already shown in previous section, the hardness profile of undeformed c-w sample of T92/T92 weldment after the PWHT-2 showed sThe observed microstructural variations of studied weldments induced by different initial PWHT conditions had crucial effects on their resulting tensile deformation and fracture behavior in both the hydrogen-free and hydrogen-charged conditions. The weldments after the tempering PWHT-1 exhibited a typical HAZ microstructural gradient consisting of the CG-HAZ, FG-HAZ, IC-HAZ, and SC-HAZ, whereas the weldments after the renormalizing-and-tempering PWHT-2 showed quite homogenized microstructure of former HAZ. In addition, the regions of WM and former CG-HAZ showed certain microstructural refinement compared to the rest of the BM.The effects of both the PWHT conditions applied and electrolytic hydrogenation on the resulting strength properties, i.e., the YS and UTS values of studied weldments, were rather insignificant. A small increase of the measured strength properties has been observed after the renormalizing-and-tempering PWHT-2 compared to the tempering PWHT-1, which was reasonably attributed to the overall suppression of the former HAZ microstructural gradient with its soft microstructural sub-regions as indicated by c-w hardness measurements. As expected, some small hydrogen-induced hardening effects were observed for the weldments in both the PWHT-1 and PWHT-2 states.The used renormalizing-and-tempering PWHT-2 of studied weldment resulted in a significant decrease of its plastic properties, i.e., the EL and RA values, compared to those of the weldment after the conventional tempering PWHT-1. Thus, the use of renormalizing-and-tempering PWHT-2 was found to be quite inappropriate for improving the microstructure and mechanical properties of the investigated T92/T92 weldments. The application of electrolytic hydrogenation of the studied weldments in their both PWHT conditions led to additional detrimental effects of their plastic properties. Although the results indicated recognizably higher hydrogen embrittlement susceptibility for the renormalized-and-tempered weldments compared to the conventionally tempered ones, it can be concluded that all studied weldments show sufficient resistance against hydrogen embrittlement in conditions of the present investigation.In present study the T92/T92 weldments in two different initial PWHT states were investigated in terms of the electrolytic hydrogenation effect on their room-temperature tensile properties and fracture behavior. Here are the main conclusions:"} +{"text": "Increasing evidence has demonstrated that circular RNA (circRNA) exerts important function in the pathogenesis of some diseases. While, the contributions of circRNAs to aseptic loosening after total hip arthroplasty (THA) remain largely unknown. Our research is to explore the differentially expressed circRNAs (DEcircRNAs) and elucidate complex regulated mechanism of circRNAs in aseptic loosening. The DEcircRNAs were identified by RNA sequencing (RNA-seq) analysis. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was adopted to corroborate these DEcircRNAs. The potential function of circRNAs in aseptic loosening tissue was identified by competing endogenous RNA (ceRNA) analysis. Enrichment analysis was performed for target mRNAs and host genes of the DEcircRNAs by Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). 257 DEcircRNAs were obtained from RNA-seq results. Following the RT-qPCR corroboration, 6 circRNAs were selected for further analysis. By circRNA-miRNA and miRNA-mRNA prediction, 6 circRNAs, 138 miRNAs and 1667 mRNAs were identified. Then, circRNA-miRNA-mRNA network was established. The result of GO and KEGG enrichment analysis suggested that the circRNAs were related with some biological functions and pathways of aseptic loosening. A novel pathogenesis and treatment strategy about aseptic loosening after THA was revealed from our study of circRNA-miRNA-mRNA network. Total hip arthroplasty (THA) is one kind of successful treatment for the management of pain and function 7 There is growing evidence that circRNAs have multiple biological functions, including microRNA sponges, regulating target gene transcription, and forming RNA-protein complexes Circular RNA (circRNA) is a special type of endogenous noncoding RNA and formed by intron or exon circularization The underlying mechanism of circRNAs in aseptic loosening after THA was investigated in our reseach. First, the RNA-seq analysis of circRNAs was used to detect the differentially expressed circRNAs (DEcircRNAs) profiles in aseptic loosening and non-aseptic loosening synovial tissue of the hip joint. Then, the DEcircRNAs were corroborated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). We predicted their target miRNAs and target mRNAs, then constructed a circRNA-miRNA-mRNA network to reveal whether DEcircRNAs acting as ceRNAs in aseptic loosening. We conducted Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the downstream mRNAs and host genes of the DEcircRNAs to reveal the possible pathogenesis of aseptic loosening. Therefore, our finding might further elucidate the complex RNA regulatory mechanism by constructing ceRNA network and provide a novel perspective for the pathogenesis and latent diagnosis of aseptic loosening.The experimental specimens were obtained from the hip joint synovial tissues of patients, who received revision operations for aseptic loosening after THA. The hip joint synovial tissues from patients with femoral neck fracture during their primary THA were acting as control specimens. 6 aseptic loosening tissues and 6 non-aseptic loosening tissues were obtained between January 2018 and November 2019 from the First Affiliated Hospital of China Medical University. 3 pairs of specimens were selected for RNA-seq, and the 6 paired specimens were used to identify the accuracy of the RNA-seq results by RT-qPCR. All specimens were quick-freezing and preserved at - 80 \u00b0C before use. Our study meet the specification of the Declaration of Helsinki, and approved by the Research Ethics Committee of the First Affiliated Hospital of China Medical University.Total RNA from specimens for RNA sequencing was isolated by a TRIzol\u2122 reagent as per the manufacturer's instructions. NanoDrop ND-1000 was used for determinating the RNA quality and quantity. Denaturing agarose gel electrophoresis was used for testing the RNA integrity and gDNA contamination. The remnant RNA was preserved at - 80 \u00b0C for later use.Approximately 1-2 \u03bcg total RNA from each specimens was used for library construction. Extracted mRNA was enriched with NEB Next\u00ae Poly (A) mRNA Magnetic Isolation Module (New England Biolabs). KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used for the library construction. RNA-seq libraries were subjected to quality control analysis by Agilent 2100 Bioanalyzer. Libraries were quantified by qRT-PCR. Samples were sequenced using Illumina X-ten/NovaSeq. The RNA-seq data were deposited in GEO (Accession code: GSE149315).Illumina X-ten/NovaSeq produced raw sequencing data in FASTQ format. The raw sequencing data were submitted to sequencing quality control by FastQC to assess whether to be used for subsequent data analysis. The trimmed data generated by the pre-processing and filtering steps were mapped to the reference genome. First, StringTie software was used to compare the results to the known transcriptome and calculate the transcriptional abundance. Then, Ballgown was used for quantification of gene expression levels, as well as analysis of intergroup differential expression of genes. The differentially expressed genes were screened with a width of the difference \u22651.5 times, a P-value \u2264 0.05 and an internal FPKM (Fragments Per Kilobaseof gene/transcript model per Million mapped fragments) mean value \u22650.5. Backsplice junction reads count of circRNA was quantified by STAR software through mapping to the reference genome, and its backsplice junction reads detection and reads count statistics were done by the CIRCexplorer2 software. EdgeR package was used for determining the significantly DEcircRNAs with the filter criteria of P-values <0.05 and |log2FC| \u2265 0.585.-\u0394CT method. GAPDH was used as internal control. Primer 5.0 software was used for the design of primer sequences in our study. Paired T-test was adopted for analysis of significance between experimental and control group by SPSS 22.0. And P-value < 0.01 indicates a statistical significance.We selected six aseptic loosening synovial tissues, matched with 6 control samples. Total RNA from specimens was isolated by a TRIzol\u2122 reagent following the manufacturer`s instruction. To quantify the amount of each circRNA, cDNA was synthesized by reverse transcription using SuperScript\u2122 III Reverse Transcriptase (Invitrogen) on Gene Amp PCR System 9700 (Applied Biosystems) from 1 \u03bcg of total RNA. Subsequently, ViiA 7 Real-time PCR System (Applied Biosystems) was used for qRT-PCR by 2X PCR master mix (Arraystar) following the manufacturer`s instruction. The relative expression of each circRNA was determined by 2http://www.targetscan.org/vert_72/) http://www.microrna.org/microrna/) https://cytoscape.org/index.html) CeRNA hypothesis that the circRNA shared the same miRNA with mRNA was acted as the theoretical basis for network construction. MREs were the miRNA binding sites which were foundation of ceRNA hypothesis, and crosstalk of RNA transcripts can be caused by competing for common miRNAs with same MREs. Home-made miRNA target prediction software based on TargetScan (http://david.abcc.ncifcrf.gov/) Database for Annotation, Visualization and Integrated Discovery (DAVID) included in circBase; (2) |log2FC| >2; 3) p-value <0.05; (4) exonic-related circRNAs; and (5) CPM value was not zero. RT-qPCR was performed in 6 pairs aseptic loosening and non- aseptic loosening tissues to validate the expression of the 10 DEcircRNAs. Nine of ten selected DEcircRNAs were the same change tendency though the data from RNA-seq and RT-qPCR. Among them, 1 upregulated circRNA (hsa_circ_0007482) and 5 downregulated circRNAs were statistically significant and these 6 circRNAs were candidates for further study were enrichment in cGMP-PKG signaling pathway, and the target mRNAs of downregulated circRNAs were enrichment in chemokine signaling pathway and Toll-like receptor signaling pathway. According to current study, activation of cGMP-PKG pathway could promote rat osteoblast differentiation and maturation In general, 171 circRNAs were upregulated and 86 circRNAs were downregulated in aseptic loosening synovial tissues compared to non-aseptic loosening synovial tissues. GO and KEGG analysis of the DEcircRNAs host genes shows that PI3K-Akt signaling pathway, Rap1 signaling pathway, and autophagy are the most common terms. CeRNA network was constructed based on the 6 validated DEcircRNAs. Enrichment analysis of the target genes of these 6 validated DEcircRNAs shows that the target genes mainly took part in the Toll-like receptor signaling pathway and chemokine signaling pathway. The signaling pathways mentioned above are closely related to osteolysis. Therefore, the ceRNA network may reveal novel mechanisms for aseptic loosening, and circRNAs may serve as candidates in aseptic loosening. The functions of DEcircRNAs from our RNA-seq data warrant further investigations."} +{"text": "Epidemiological and genomic analyses uncover viral mutational dynamics and transmission bottleneck size during the early COVID-19 pandemic in Austria. et al. examined the fine-scale dynamics of viral spread within and from Austria in the spring of 2020. Epidemiologically defined phylogenetic clusters and viral mutational profiles provided evidence of the ongoing fixation of two viral alleles within transmission chains and enabled estimation of the SARS-CoV-2 bottleneck size. This study provides an epidemiologically contextualized, high-resolution picture of SARS-CoV-2 mutational dynamics in an early international transmission hub.Austria was an early hotspot of SARS-CoV-2 transmission due to winter tourism. By integrating viral genomic and phylogenetic analyses with time-resolved contact tracing data, Popa 3 SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2 and to gain fundamental insights into mutational dynamics and transmission properties.Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first wave of infections in Austria, a country that played a major role in initial virus transmissions in Europe. Capitalizing on Austria\u2019s well-developed epidemiological surveillance system, we identified major SARS-CoV-2 clusters during the first wave of infections and performed deep whole-genome sequencing of more than 500 virus samples. Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020. Moreover, we exploited epidemiologically well-defined clusters to quantify SARS-CoV-2 mutational dynamics, including the observation of low-frequency mutations that progressed to fixation within the infection chain. Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 10 The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has already infected more than 20 million people in 188 countries, causing 737,285 deaths globally as of 11 August 2020 and extraordinary disruptions to daily life and national economies . The selOf the 572 samples, 427 passed our sequencing quality controls , and after the removal of cell culture samples, 420 samples were considered for low-frequency analysis. Of the 420 samples, 345 corresponded to unique SARS-CoV-2 cases and were further integrated in our phylogenetic analyses, as they corresponded to unique patient identifiers with complete sample annotation at the time of the analysis (fig. S1E). For these 345 samples, we assembled SARS-CoV-2 genome sequences, constructed phylogenies, and identified low-frequency mutations based on high-quality sequencing results with >5 million reads per sample and >80% of mapped viral reads .To obtain robust quantifications of minor variants in all 420 samples, we validated our sample processing workflow and pipeline with additional experimental controls including synthetic SARS-CoV-2 genome titrations, technical replicates for sample preparation and sequencing runs, and dilution experiments (data file S1). Matched controls were highly consistent with each other, indicative of excellent assay performance and a highly reproducible analysis pipeline . For an alternative allele frequency of 0.01, we obtained an average accuracy of 90.92% (ranging from 68 to 97%). In addition, the shared percentage of detected variants between control pairs ranged from 50 to 90.97% for a cutoff of 0.02 of the allele frequencies. The high specificity of detection even at low frequencies, as well as the large overlap of detected variants, supported the choice of a 0.02 frequency cutoff for calling high-confidence variants (data file S1).To investigate the link between local outbreaks in Austria and the global pandemic, we performed phylogenetic analysis of 345 SARS-CoV-2 genomes from Austrian cases and 7666 global genomes from the GISAID database (data file S2). Similar mutation profiles, together with information of geographical proximity of the samples and time of infection, are strong indicators of possible transmission links. Therefore, groups of virus sequences were annotated as phylogenetic clusters when they all shared a homogeneous mutation pattern and originated from the same geographical location and time period. Among the distinct phylogenetic clusters identified, six could be linked to specific geographic locations of the probable region of infection . Three oIndependently, contact tracing surveillance assigns SARS-CoV-2 cases to epidemiological clusters based on the identification of transmission lines. In Austria, an extensive centralized tracing program was implemented during the COVID-19 outbreak. This program facilitated grouping of positive cases with a common exposure history and a comparable time frame of infection into epidemiological clusters. Integration of the phylogenetic analysis of Austrian SARS-CoV-2 sequences with epidemiological data resulted in strong overlap of these two lines of evidence, with 199 of the 345 sequences (65%) assigned to epidemiological clusters (data file S3). All sequenced samples from epidemiological cluster A mapped to the relatively homogeneous phylogenetic cluster Vienna-1 with an Our largest phylogenetic cluster, Tyrol-1 (fig. S3B), contained samples originating mainly from Austria\u2019s Tyrol region (73 of 90 samples) and overlapped with epidemiological cluster S . This phylogenetic cluster included resident and travel-associated cases to the ski resort Ischgl or the related valley Paznaun . AlthougTo reveal possible transmission lines specifically between European countries in February and March 2020, we performed phylogenetic analysis using all 7731 European high-quality SARS-CoV-2 sequences sampled before 31 March that were available in the GISAID database (data file S2). Using this approach, we identified several samples matching the Tyrol-1 cluster mutation profile from a local outbreak in the region Hauts-de-France in the last week of February , for exaOur results integrating epidemiological and sequencing data emphasize that phylogenetic analyses of SARS-CoV-2 sequences empower robust tracing from interindividual to local and international spreading events (nsp6), open reading frame 3a (ORF3a), and ORF8 and the pool of low-frequency variants of each one of our samples. More than half of the fixed mutations in the Austrian SARS-CoV-2 genomes were nonsynonymous , most frand ORF8 . An analand ORF8 .We assessed the pool of variants for both low-frequency and fixed mutations and obseOn the basis of our phylogenetic analysis, we identified a subcluster inside the phylogenetic Tyrol-1 cluster that was defined by a fixed nonsynonymous G > U mutation at position 15,380 . This muThrough several telephone interviews, we followed up with the members of both families to reconstruct the timeline of the infection events (data file S4). Both grandparents of family 1 were exposed to infected case CeMM1056 during a recreational indoor event on 28 February and subsequently tested positive for SARS-CoV-2 , and 5A.The emergence and potential fixation of mutations in the viral populations within a patient depend on interhost bottlenecks and intrahost evolutionary dynamics . In particular, we computed bottleneck size using the beta-binomial method . To analyze intrahost viral dynamics, we focused on variants observed in at least two samples from the same patient. This approach resulted in a pool of high-confidence mutations (>0.02) with high coverage across same-patient samples (fig. S5A). Same-patient samples shared more variants than unrelated sample pairs (fig. S5B). In addition, variants shared between samples from the same patient were unlikely to be found in unrelated samples (fig. S5C).P = 0.075) , whereas cases CeMM0108, CeMM0172, CeMM0251, CeMM0269, CeMM0299, and CeMM0221 exhibited higher variability, including the fixation and loss of individual mutations (= 0.075) .3. Our estimated bottlenecks are based on a substantial number of defined infector-infectee pairs and in agreement with recent studies implying larger bottleneck sizes for SARS-CoV-2 compared with estimates for the influenza A virus was processed for genome consensus sequence reconstruction and variant calling as approved by the ethics committee of the Medical University of Vienna. Additional analyses on subsets of samples consisted of the profiling of the mutational patterns across the genome and bottleneck size estimates based on transmission pairs. Data presented in this study are based on epidemiological and contact tracing data from the Austrian Department of Infection Epidemiology & Surveillance at the Austrian Agency for Health and Food Safety (AGES).Patient samples were obtained from the Medical Universities of Vienna Institute of Virology, Medical University of Innsbruck Institute of Virology, Medical University of Innsbruck Department of Internal Medicine II, Central Institute for Medical-Chemical Laboratory Diagnostics Innsbruck, Klinikum Wels-Grieskirchen, and AGES. Samples were obtained from suspected or confirmed SARS-CoV-2 cases or contact persons of these. Sample types included oropharyngeal swabs, nasopharyngeal swabs, tracheal secretion, bronchial secretion, serum, plasma, and cell culture supernatants. RNA was extracted using the following commercially available kits by adhering to the manufacturers\u2019 instructions: MagMax (Thermo Fisher Scientific), EasyMag (bioM\u00e9rieux), AltoStar Purification Kit 1.5 (Altona Diagnostics), MagNA Pure LC 2.0 (Roche), MagNA Pure Compact (Roche), and QIAsymphony (Qiagen). Viral RNA was reverse transcribed with Superscript IV Reverse Transcriptase (Thermo Fisher Scientific). The resulting complementary DNA was used to amplify viral sequences with modified primer pools from the Artic Network initiative (Amplicons were cleaned up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio. Amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies), and the size distribution was assessed using the 2100 Bioanalyzer system (Agilent). Amplicon concentrations were normalized, and sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer\u2019s instructions. Library concentrations again were quantified with the Qubit Fluorometric Quantitation system (Life Technologies), and the size distribution was assessed using the 2100 Bioanalyzer system (Agilent). For sequencing, samples were pooled into equimolar amounts. Amplicon libraries were sequenced on the NovaSeq 6000 platform (Illumina) using S Prime (SP) flowcell with a read length of 2 \u00d7 250 base pairs in paired-end mode.http://jgi.doe.gov/data-and-tools/bbtools). Overlapping read sequences within a pair were corrected for using BBMERGE function from BBTools. Read pairs were mapped on the combined Hg38 and SARS-CoV-2 genome using the BWA-MEM software package with a minimal seed length of 17 (v0.7.17) (https://github.com/lh3/seqtk). For calling low-frequency variants, the viral read alignment file was realigned using the Viterbi method provided by LoFreq (v2.1.2) using FastQC (v.0.11.8) (The investigation of transmission chains (contact tracing) was conducted by the Department of Infection Epidemiology & Surveillance at the AGES. Epidemiological clusters were defined as accumulations of cases within a certain time period in a defined region and with common source of exposure. The required information for cluster annotation and resolution in chains of transmission was collected during the official case contact tracing by the public health authorities, resulting in identification of the most likely source cases and successive cases of the index cases. Contact tracing was performed according to technical guidance relating to this measure produced by the European Centre for Disease Prevention and Control (ECDC) and the 345 sequences obtained in this publication. GISAID sequences were filtered for entries from human hosts with complete sampling dates. Metadata information for patient age and sex was excluded from the analysis. Multiple sequence alignments were performed using mafft ; clusters of Austrian strains were identified on the basis of shared mutation profiles and patient location from epidemiological data.Phylogenetic analysis was conducted using the Augur package (version 7.0.2) . Nineteen of 31 cases had only two samples per patient. For each of the 31 cases, we only considered variants with an alternative frequency greater than 0.02 and that were shared across at least two of the intrapatient samples. We retrieved the depth of coverage of the selected variants for each sample for each patient. To compare how many variants were shared intrapatient as opposed to unrelated samples, we first identified potentially unrelated cases by eliminating all samples from the same patient, as well as all the samples in the transmission chains in For shared mutations with defined infector-to-infectee transmission, we determined those mutations present in both samples and calculated their absolute difference in frequency. Similarly, we performed the same computations between time consecutive pairs for serially sampled patients. If multiple samples were obtained on the same day, the sample with the lowest Ct value was considered. Note that the time-consecutive pairs had a differing number of days between samples. To these genetic distances obtained from the shared variants, we added the sum of the frequencies of the variants detected in only one of the pairs of shared samples; that is, we calculated the l1-norm of the variant frequencies. Statistical difference between the genetic distances from transmission pairs versus consecutive pairs from serially sampled patients was determined by a Wilcoxon (one-sided) rank sum test.R2 was reported. For mutational patterns analyses, a statistical test was devised to compare the deviation of the observed number of mutations from the expected distribution as detailed in Materials and Methods. The frequency of mutations in overlapping windows across the genome was statistically assessed with a log-likelihood test. For bottleneck size computations, a maximum likelihood approach was applied. The comparison of genetic diversity between groups was performed with a standard Wilcoxon test. Significance was inferred for P values \u22640.05.Control samples were compared with a linear regression method, and the corresponding"} +{"text": "Listeria monocytogenes sequence type 1247 strain (VLTRLM2013) that was isolated from a vacuum-packaged sliced salted salmon product of an Estonian fish-processing company that was obtained from an Estonian retail outlet in 2013.We sequenced the genome of a multicountry outbreak-related Listeria monocytogenes sequence type 1247 strain (VLTRLM2013) that was isolated from a vacuum-packaged sliced salted salmon product of an Estonian fish-processing company that was obtained from an Estonian retail outlet in 2013.We sequenced the genome of a multicountry outbreak-related Listeria monocytogenes than any other RTE food category in Estonia (Ready-to-eat (RTE) fish products from retail outlets have higher prevalence and counts of Estonia . RTE fis Estonia . An anal Estonia .L. monocytogenes strain VLTRLM2013 was isolated in accordance with Estonian Centre for Standardisation standard EVS-EN ISO 11290-1:2000/A1:2004 v4.11 (The reported P) v4.11 with defJABGCT000000000. The version described in this paper is the first version, JABGCT010000000. The raw sequencing reads have been deposited in the SRA under the accession no. SRR11789329.This whole-genome shotgun project has been deposited in GenBank under the accession no."} +{"text": "To provide an overview of randomized controlled trials (RCTs) in primary total hip arthroplasty summarizing the available high-quality evidence.Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA), we searched the Cochrane Central Register of Controlled Trials , Ovid MEDLINE, and Embase. We excluded nonrandomized trials, trials on neck of femur fractures or revision surgery, systematic reviews, and meta-analyses. Trials that met our inclusion criteria were assessed using a binary outcome measure of whether they reported statistically significant findings. These were then classified according to the intervention groups .Three hundred twelve RCTs met the inclusion criteria and were included. The total number of patients in those 312 RCTs was 34,020. Sixty-one RCTs (19.5%) reported significant differences between the intervention and the control groups. The trials were grouped into surgical approach 72, fixation 7, cement 16, femoral stem 46, head sizes 5, cup design 18, polyethylene 25, bearing surfaces 30, metal-on-metal 30, resurfacing 20, navigation 15, robotics 3, surgical technique 12, and closure/drains/postoperative care 13 RCTs.The evidence reviewed indicates that for the vast majority of patients, a standard conventional total hip arthroplasty with a surgical approach familiar to the surgeon using standard well-established components and highly cross-linked polyethylene leads to satisfactory clinical outcomes. This evidence also offers arthroplasty surgeons the flexibility to use the standard and cost-effective techniques and achieve comparable outcomes. However, significant advances have been achieved in metallurgy and manufacturing processes, particularly with the highly cross-linked polyethylene (PE) ensuring excellent long-term outcomes of THA.3 Nonetheless, debate continues over the optimal surgical approach, implant fixation, head sizes, or bearing surfaces. National joint registry data play an important role in monitoring implants, measuring performance and survivorship nationwide such as the Scandinavian registries and the United Kingdom national joint registry, which also collects patient-reported outcome measures' data.4 However, in clinical research, high-quality randomized controlled trials (RCTs) provide strong evidence for the efficacy of healthcare interventions and inform evidence-based medicine.6 In particular, RCTs with results demonstrating clinically or statistically significant differences between two interventions indicate a positive effect of one intervention over another.8 A large number of RCTs have been conducted in THA over the years with only few reporting significant findings reflecting the lack of marginal effects of evaluated surgical interventions.9Total hip arthroplasty (THA) is one of the most successful and cost-effective interventions in orthopaedic surgery.In this systematic review of the literature, we therefore aim to evaluate published RCTs in primary THAs summarizing the available high-quality evidence.10 we carried out the electronic searches in January 2018 and updated searches in January 2020. We searched the Cochrane Central Register of Controlled Trials , Ovid MEDLINE (1946-20 January 2020), and Embase (1980-20 January 2020). We limited our searches to the English language literature. In MEDLINE, we combined the subject-specific search strategy with the sensitivity maximizing version of the Cochrane Highly Sensitive Search Strategy for identifying randomized trials.11 The following search strategy was used .Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA),We examined the titles and abstracts of articles identified in the search as potentially relevant trials. We obtained the full texts of trials that fulfilled our inclusion criteria and those that were unclear from perusal of the abstracts. We excluded nonrandomized trials, trials on neck of femur fractures/revision surgery, systematic reviews, and meta-analyses. Trials that met our inclusion criteria were assessed by two authors (H.E.M. and S.R.P.) using a binary outcome measure of whether they reported statistically significant findings. These were then classified according to the intervention groups in a narrative review summarizing the evidence. The results were expressed descriptively in numbers and percentages. SPSS 16.0 software (SPSS) was used for descriptive statistical analysis.The electronic searches produced 5141 records, and additional 6 records were identified from reference lists of some included studies. After removing duplicates and screening abstracts, 952 studies were assessed for eligibility, and 312 RCTs met the inclusion criteria and were included at a 28-month follow-up and reported better outcomes and less dislocations with trans-osseous repair compared with gluteus medius/short rotators tendon-to-tendon repair. Finally, Kruse et al16 compared radiographic outcomes of posterior and lateral approaches in 80 patients and reported that the femoral offset and abductor moment arm were significantly increased when using posterior compared with lateral approach.Seventy-two RCTs with 6728 patients evaluated different surgical approaches or related aspects with only five RCTs (6.9%) reporting significant differences between the intervention groups . The cementless tapered stem had an extremely good survival rate of 99%. Radiographs showed evidence of mild stress-shielding around 95% of the cemented stems and 88% of the cementless stems; stress-shielding of grade 3 or greater was seen around the remaining 12% of the cementless stems. The remaining six RCTs reported no significant differences between cemented and cementless THA although their follow-up was only up to 5 years.Seven RCTs compared cemented and cementless THA of different brands with a total of 1271 patients. Only one trial, Corten et al,19 evaluated a modified cementing technique to reduce the intramedullary pressure in 120 patients and measured the embolic events using continuous perioperative transesophageal echocardiography reporting significant embolic events with conventional cementing techniques although no patient developed frank fat embolism syndrome. Visser et al20 compared three types of cement restrictors in 93 patients measuring their postoperative radiographs efficiently and reported significant failures with the Biosem restrictor (SEM). Degradable cement restrictors were reported to have significantly worse outcomes in three RCTs. Freund et al21 reported more failures with a resorbable restrictor with a longer cement plug although no difference was observed in stem loosening at a 2-year follow-up. Schauss et al22 also reported a shorter cement plug with nondegradable plugs in 130 patients compared with degradable restrictors. Finally, Wembridge et al23 compared PE with biodegradable cement restrictors in 32 patients and reported worse migration and longer cement plug with the biodegradable restrictors.Sixteen RCTs with a total of 979 patients evaluated cement comparing different viscosities or different types of cement restrictors with five RCTs 31.3%) reporting significant findings , three RCTs comparing fluoride-containing acrylic cement with conventional cement, Palacos, or Palacos G cement. Additional six RCTs made the following comparisons between different types of cement with no significant differences reported; low/medium Simplex P cement versus high-viscosity Simplex AF cement (Stryker-Howmedica), Cemex Rx versus Palaces R cement , Palamed G (Biomet Merck) versus Palacos R cement , SmartSet HV (DePuy CMW) versus Palacos R cement (Schering Plough), Palacos R (Schering Plough) versus Palacos R + G (Schering-Plough), and Palacos versus Palamed cement (Biomet Merck).The remaining 11 RCTs reported no significant differences, including one RCT comparing 24 reported a significantly lower rate of cement mantle deficiencies when using stem centralizer in 60 patients (P < 0.001). In their trial of 39 patients at a 2-year follow-up, Tanzer et al25 assessed femoral bone remodeling using dual-energy radiograph absorptiometry after a titanium proximally porous-coated femoral implant with or without hydroxyapatite (HA)-tricalcium phosphate coating. The HA-tricalcium phosphate-coated stems had significantly less femoral bone loss. Luites et al26 compared 22 titanium and 20 HA-coated ProxiLock stems at a 2-year follow-up and reported significantly higher early failures with the ProxiLock stems requiring revision surgery.Forty-six RCTs with 5242 patients evaluated aspects specifically related to femoral stems. Only three RCTs reported significant differences. Berger et alThe remaining 43 trials reported no significant differences . These i27 reported significant findings. They compared the dislocation rate between 28 and 36 mm metal heads on highly cross-linked polyethylene (HXLPE) at a 1-year follow-up in 533 patients with primary THA: 4.4% (12/275) versus 0.8% (2/258) (P = 0.024). The remaining four RCTs reported no significant differences including 28 versus 32 mm ceramic-on-ceramic (CoC) THA; 32 versus 36 mm ceramic-on-PE THA, 28 versus 36 mm metal-on-cross-linked PE, and small head 28 mm metal-on-metal versus metal-on-PE.Five RCTs compared different head sizes in 889 patients. Only one large multicentre RCT, Howie et al,28 evaluated the use of all-PE cemented cups (407 THA) with or without integrated cement spacers attached at the back of the cup to ensure a uniform cement mantle. They reported a significantly higher rate of failure with integrated spacers compared with no spacers at a 6.5-year follow-up. Stilling et al29 compared titanium uncemented cups with first-generation HA-coated cups at a 15-year follow-up with a significantly higher revision rate for HA-coated cups.Eighteen RCTs with 1778 patients evaluated aspects of acetabular component designs with two RCTs reported significant findings (11.2%). Faris et alThe remaining 16 RCTs were a heterogeneous group that made the following comparisons with no significant differences between the interventions in either clinical or radiographic outcomes, including solid versus cluster hole cups; scientific versus Omnifit cups; tantalum versus titanium cups; porous tantalum monoblock cup versus porous-coated titanium monoblock cup; trabecular metal cups versus titanium fiber-mesh cups; porous titanium versus conventional titanium cups; solid-backed versus cluster-hole cups all without screws; HA-coated versus porous-coated cups; cementless cup with or without screws; uncemented 61% high porosity versus 45% low porosity cups; BICON-PLUS versus BICON-PLUS NT cup; finger-packing versus cement pressurization cemented cups; cemented Charnley versus uncemented Duraloc 1200 cups; cemented PE versus uncemented porous-coated cups; cemented cups versus porous-coated cups, and all-poly press-fit RM cup with or without screw fixation.30\u201332 Similarly, HXLPE consistently shown to have significantly better wear characteristics across different trials up to a 12-year follow-up3334353637383940 versus Durasul-poly liner with no significant differences (Twenty-five RCTs with 2216 patients compared different types of PE particularly the effect of cross-linking on wear rates with a long-term follow-up (multiple publications). Ten RCTs , reported a less wear rate with metal-on-cross-linked polyethylene compared with metal-on-UHMWPE.Thirty RCTs with 5425 patients compared different bearing surfaces in THA with only four RCTs (13.3%) reporting significant findings THA with other bearing surfaces in 2912 patients. This was a unique group of trials where nearly all RCTs that looked at metal ions in their reported outcomes found statistically significant higher levels of ions with MoM but similar clinical outcomes and patient-reported outcome measures. Trials that did not report on metal ion levels (10 RCTs) found no significant differences in their reported outcomes comparing MoM with other bearings .47 compared Articular Surface Replacement (ASR) hip resurfacing prosthesis with THA at a 2-year follow-up in 38 patients and found higher consistently higher metal ions levels with ASR (P \u2264 0.001). The remaining 19 trials reported no statistically significant differences although the majority were short-term follow-ups (2 to 5 years). These included 15 RCTs comparing outcomes of hip resurfacing versus THA; two RCTs compared hip resurfacing with MoM THA; one RCT compared cemented versus cementless femoral stem; and one RCT compared posterior versus anterolateral approach in hip resurfacing (Twenty RCTs looked at hip resurfacing in 1762 patients. Only one RCT (5%) reported statistically significant differences. Penny et alurfacing .Navigation was evaluated in 15 RCTs with a total of 1158 patients. Three RCTs (20%) reported significant differences with improved cup positioning Table . The rem48 randomized 154 patients to conventional or robotic-assisted THA and compared 2-year outcomes using Harris, Merle d'Aubign\u00e9, and the Mayo scores with no significant differences reported. However, the duration of robotic procedures was longer with 18% of attempted robotic implantations converted to manual implantations as a result of system failure. Dislocation was more frequent with robotics 11/61 versus 3/80 (P < 0.001) as well as revision surgery 8/61 (P < 0.001). Lim et al49 evaluated the effects of robotic milling versus manual rasping on the accuracy of short femoral stem positioning and on the clinical outcomes in 54 patients at a 2-year follow-up and reported no significant differences. Finally, Bargar et al50 reported a mean 14-year follow-up outcomes of 67 patients from 2 U.S. Food and Drug Administration trials who underwent conventional versus active robotic system THA. No statistically significant difference was observed in probability of a revision for wear or loosening. The robotic group had statistically significant higher Health Status Questionnaire pain and Harris pain scores but lower Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores.Furthermore, three RCTs evaluated the use of robotics in THA in 275 patients. In their early robotic RCT, in 2003, Honl et al51 high-efficiency particulate air to reduce colony-forming units within 5 cm of the surgical wound,52 better acetabular component positioning measured on postoperative CT scan with the use of patient-specific instrumentations,53 the use of transverse acetabular ligament for cup anteversion and inclination,54 and the use of digital inclinometer-assisted cup insertion technique55 reported significant findings in favor of using a measuring device to minimize leg length discrepancy,55 Table .The remaining seven RCTs reported no significant differences and made the following comparisons: sequential versus simultaneous bilateral THA; removal versus retention of subchondral bone plate for cemented cups in two trials; cup insertion with or without inclinometer; the use of abductor shuck versus trans-osseous pins versus patella electrocardiogram leads to measure intraoperative leg length; plasma-rich platelets versus no plasma-rich platelet in bilateral THA; and autologous impaction bone grafting versus traditional technique in cementless THA .56 compared staples versus absorbable subcuticular suture for skin closure at a 3-month follow-up in 165 patients. They reported no infections in sutures group versus 2 superficial infections (2.4%) in the staples group. A statistically significant difference was observed in favor of the suture group for time to dry surgical incisions , hospital stay , and cost saving $82.2 per case. Although shorter surgical time to use staples , no difference was observed in patients' satisfaction. However, two additional RCTs made similar comparisons and reported no significant difference between staples and sutures (There were 13 RCTs in this group with 2287 patients included. Only one RCT (7.7%) reported significant findings. Rui et al sutures .Four RCTs evaluated the use of surgical drain postoperatively comparing it to no drain and reported no significant differences in their measured outcomes. Different postoperative care instructions were also evaluated in six RCTs with no significant differences including weight-bearing status after cementless THA (unrestricted versus protected) across four RCTs and hip precautions after the posterolateral approach in two RCTs .In this study, we provide a comprehensive overview of 312 RCTs in primary THA. The total number of patients included in those RCTs was 34,020. The most important finding is that only 19.5% of trials reported significant differences between the intervention and the control groups for the outcome measures used by those trials.Different surgical approaches were evaluated in 72 trials, the largest subgroup of trials, with \u223c93% reporting no significant differences in their reported outcomes. This evidence supports surgeons' preference based on their familiarity with a particular approach that allows adequate exposure to perform THA safely acknowledging that each surgical approach has its own pros and cons. The majority of modern THA cementless acetabular components are hemispheric press-fit with improved modular liner congruity and fixation. Furthermore, the use of HXLPE liners seems to have substantially reduced wear rate and osteolysis. This was a consistent finding in a large number of RCTs included. Fixation of THA and stem designs, once fiercely debated topics, are covered by a variety of RCTs with no clear advantage of the comparators. Forty-six RCTs evaluated various designs of femoral stems, both cemented and cementless, with similar clinical outcomes reported at short to medium term. Here lies one of the limitations of RCT evidence where long-term survivorship data, most pertinent to stem survivorship, are lacking.57 Clinical outcomes of hip resurfacing were evaluated in 20 trials in comparison with THA, and functional outcomes were similar at short- to medium-term follow-ups. Trials of navigation techniques show no difference in clinical outcomes although some reported significant differences in radiological outcomes, particularly cup positioning, and a long-term follow-up is needed to see whether this leads to improved clinical outcomes. Finally, skin closure techniques, use of drains, and postoperative weight-bearing status or hip precautions were evaluated in a small number of trials with no significant differences.In total, 60 RCTs compared different bearing surfaces including metal-on-metal bearings that have consistently shown raised levels of metal ions and the familiar mode of failure of this particular bearing. The evidence reviewed equally supports the use of metal-on-PE, CoC, and ceramic-on-PE bearings; the latter is further supported by emerging long-term survivorship and registry data.58 Long-term observational studies and data registries, despite their inherent limitations, prove more practical in evaluating long-term outcomes of THA such as survivorship and reoperations and provide a pragmatic overview of clinical practice.59\u201361 In its 16th annual report, the UK's national joint registry has collated data for over 1 million primary THA with up to a 15-year follow-up. Ceramic-on-polyethylene bearings performing particularly well and the overall revision rates after primary THA have reduced over the last 10 years after the peak of metal-on-metal bearings.57 Similar trends have been reported in other national registries and long-term follow-up studies3; the RCTs included in this study support those findings.Evidence derived from RCTs is based on highly selective populations in a tightly controlled settings and deemed to have the highest reliability. However, most RCTs are short or medium term as obtaining a long-term follow-up is complicated by cost, co-intervention, loss to follow up, and postrandomization variables.62 The majority of trials included in this study used PROMs as a primary or secondary measure. A number of studies have demonstrated a ceiling effect of those PROMS where a considerable proportion of patients score the best/maximum or worst/minimum score, making the measure unable to discriminate between subjects at either extreme of the scale.64 However, more recent registry-based observational studies have demonstrated that population-wide data do not exhibit a ceiling or floor effect of these PROMs.65 Others have found only weak-to-moderate correlation between PROMs and patient satisfaction.66 The International Society of Arthroplasty Registries PROMs working group acknowledges the variation in the specific PROMs used and does not make specific recommendations about which PROMs to use in arthroplasty registries.67 PROMs are used in many registries to support quality assurance and provide information on value-based care. However, in the context of RCTs, they may not detect the marginal effects of the evaluated interventions.Patient-reported outcome measures (PROMs) play an important role in evaluating interventions in terms of outcomes that matter to patients and widely used in clinical research.68 The prospective registration of trials and public access to study data via results databases had been introduced to minimize the impact reporting bias.69 The true scale of this bias in the clinical literature is unclear. However, \u223c80% of published RCTs in THA reported no significant differences \u201cnegative trials,\u201d which may indicate that there is no tendency to overestimate the efficacy and underestimate the risks of the interventions evaluated in those trials.This is the first study to undertake a comprehensive overview of RCTs in THA. We do, however, acknowledge limitations to its findings. We did not calculate the treatment effect of individual trials with significant statistical findings and whether this correlated with clinically measurable effects. Furthermore, the quality of reporting trials was not addressed as this aspect falls outside the scope of this study. However, reporting bias or publication bias in clinical research is a known phenomenon where data from trials with negative findings are not publicized, and so they remain inaccessible.To conclude, THA is a successful and durable operation that has helped millions of patients worldwide. The early failures encountered in the 1970 to 1980s had been largely addressed in the 1990s and the early 2000s with improved metallurgy and manufacturing processes. The RCT evidence presented indicates that for the vast majority of patients, a standard conventional THA with a surgical approach familiar to the surgeon using standard well-established components and highly cross-linked polyethylene leads to satisfactory clinical outcomes. This evidence also offers arthroplasty surgeons the flexibility to use the standard and cost-effective techniques and achieve comparable outcomes. Future trials should also focus on preoperative interventions to improve clinical outcomes, an area that is currently lacking in THA trials."} +{"text": "Innate immune surveillance of cancer involves multiple types of immune cells including the innate lymphoid cells (ILCs). Natural killer (NK) cells are considered the most active ILC subset for tumor elimination because of their ability to target infected and malignant cells without prior sensitization. NK cells are equipped with an array of activating and inhibitory receptors (IRs); hence NK cell activity is controlled by balanced signals between the activating and IRs.\u00a0Multiple myeloma (MM) is a hematological malignancy that is known for its altered immune landscape. Despite improvements in therapeutic options for MM, this disease remains incurable. An emerging trend to improve clinical outcomes in MM involves harnessing the inherent ability of NK cells to kill malignant cells by recruiting NK cells and enhancing their cytotoxicity toward the malignant MM cells. Following the clinical success of blocking T cell IRs in multiple cancers, targeting NK cell IRs is drawing increasing attention. Relevant NK cell IRs that are attractive candidates for checkpoint blockades include KIRs, NKG2A, LAG-3, TIGIT, PD-1, and TIM-3 receptors. Investigating these NK cell IRs as pathogenic agents and therapeutic targets could lead to promising applications in MM therapy. This review describes the critical role of enhancing NK cell activity in MM and discusses the potential of blocking NK cell IRs as a future MM therapy. Multiple myeloma (MM) is characterized by the accumulation of malignant plasma cells (PCs), resulting in increased monoclonal protein in the blood and urine . MM reprIn recent years, there have been several notable therapeutic advancements for MM. Hematopoietic stem cell transplantation (HSCT) , proteasNatural killer (NK) cells are an intriguing immune cell type in MM given the recent development of monoclonal antibodies (mAbs), elotuzumab (anti-SLAMF7), and daratumumab (anti-CD38) that enhance NK cell-mediated tumour cell toxicity by activating the antibody dependent cellular cytotoxicity (ADCC) mechanism \u201315. AlthGiven the success of blocking T cell IRs in multiple cancer types, blocking the IRs on NK cells offers another possibility to enhance anti-myeloma cell immunity. This review discusses NK cell IRs Figure 1NK cells are a cytotoxic subset of innate lymphoid cells (ILCs). They are the first responders against malignant and infected cells and are functionally classified by their innate capacity to eliminate cells without prior sensitization or recognition of presented antigens , 17. NK +veCD3\u2212ve and classified into two major populations\u2014CD56dim and CD56bright. The CD56dim cells are considered the cytotoxic population and express more immunoglobulin-like receptors to detect stressed cells and induce cell death. CD56bright cells are known as the pro-inflammatory cytokine releasers and specialize in promoting other components of the immune system through IFN-\u03b3 and TNF-\u03b1 production and cytokine production that are important for both innate and adaptive immune responses in early stage patients, but not the immature subset, forecasts good outcomes that is important for ADCC against mAb-coated cancer cells patients, supporting the notion that CAR-NK cells could be a safe alternative to CAR-T cells in hematological malignancies . The firin-vitro and in-vivo studies have shown that the combination of elutuzumab and lenalidomide enhanced anti-proliferative effects more than any single agent and was associated with increase NK cell activation as demonstrated by the stimulation of activating cytokine production and induction of MM cell death in in vitro co-culture assays. Interestingly, in in-vivo established MM xenografts, although NK cells recruitment to tumor sites was not associated with lenalidomide, this recruitment could be enhanced by the addition of elotuzumab, likely through an ADCC-mediated mechanism (in-vitro study on BM mononuclear cells from MM patients have been shown that combination of daratumumab-IPH2102 anti-killer cell immunoglobulin-like receptors (anti-KIR) with lenalidomide have improved the NK cell ADCC activity and myeloma cell lysis , T-cell immunoglobulin and mucin-domain containing-3 (TIM-3), T-cell Ig and ITIM domain (TIGIT), V-domain Ig-containing suppressor of T cell activation (VISTA), programmed death-1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA4) and lymphocytic-activation gene 3 (LAG-3) Figure 1KIRs are a group of inhibitory and activating type I transmembrane glycoproteins expressed on most NK cells and some T-cell subsets showed a surprising decrease in NK cell activity and KIR2D expression that is NKG2A is an inhibitory receptor that belongs to the C-type lectins. It is a type II membrane receptor that forms a heterodimer with CD94 patients showed that monalizumab restored their cytotoxicity , CEACAM-1 (carcinoembryonic antigen cell adhesion molecule 1), PtdSer (phosphatidylserine), and galectin-9 showed a manageable safety profile and positive clinical response. Functional studies assessing how anti-TIGIT mAbs affect NK cells activity through cytokine production and NK cell degranulation in preclinical and clinical MM models may lead to an improved understanding of how to utilize NK cells in MM therapy.PD-1 is a surface receptor initially marked for its inhibitory function in T lymphocytes but is expressed on both T and NK cells recruiting patients to explore the safety and efficacy of BCMA-PD1-CAR-T cells in RRMM. BCMA-PD-1-CAR-T cell therapy works by administering T cells modified to target BCMA and secrete a PD-1Fc fusion protein capable of blocking the PD-L1/PD-1 inhibitory axis.Given that low numbers of anti-MM T cells are a commonality amongst relapsed patients while NK cell-mediated MM cytotoxicity can be enhanced by anti-PD-1 therapy , the potLAG-3 is a transmembrane protein expressed on activated T cells, NK cells, B cells, and dendritic cells . Another phase I clinical trial of anti-KIR in combination with lenalidomide demonstrated positive objective responses in a subset of patients (NCT01217203). Although some of the phase II trials did not report significant patient responses, we argue that a lack of understanding regarding the expression of KIRs limits our ability to predict positive responses in clinical trials.In this review, we have highlighted the preclinical evidence that IRs on the NK cell such as KIRs, NKG2A, TIGIT, TIM-3, PD-1, and LAG-3 may impact MM biology and response to treatments. KIRs remain the most promising target. Not only were anti-KIR antibodies shown to be well tolerated, but they were also shown to enhance NK cell function , 134. Asvia the TCR using restricted receptors produced by gene rearrangement followed by a second activating, costimulatory signal. NK cells, on the other hand, are equipped with a repertoire of receptors to initiate activating signals that lead to NK cell-mediated cytotoxic cell lysis and cytokine production . Similarly, IR-targeted therapy not only has implications for the intrinsic cytotoxic capabilities of NK cells, but can also be used within an ADCC and CAR-NK cell context. Considering the unique characteristic of the NK cells, which mediating ADCC, combining mAb against specific antigens expressed on myeloma cells with mAb targeting specific NK IRs according to their functional level and their cognate ligands on myeloma cells could enhance the NK cells killing. The combination of PD-1 blockade with mAbs daratumumab or elotuzumab are intriguing possibilities currently under investigation . SimilarTo conclude, we can say that there is a body of knowledge supporting the role of NK cells, IRs and cancer progression, although the evidence characterizing NK cells and their subpopulations in myeloma patients or the myeloma-NK cell interaction is still lacking. Therefore, we envision some key steps and factors to be considered in order to build on the foundation of myeloma-NK cell biology:Profile NK cell receptors and subpopulations, NK cell activity and abundance, and NK cell function in myeloma.Profile the expression of NK cell receptor cognate ligands in myeloma.The immunosuppressive nature of myeloma poses a general challenge to immunotherapies in myeloma including those involving NK cells, and understanding and overcoming this challenge is critical to success.Investigate the mechanisms that control specific ligands on the surface of myeloma.Study ligand expression at the transcriptional and protein levels.Evaluate the role of chemokines and soluble factors released in the microenvironment and if they positively or negatively mediate NK receptors and/or their ligands.Explore the integration of NK cell-based therapies with traditional myeloma therapies pre-clinically to optimize clinical trial design.Pursue the promise of CAR-NK cells in clinical trials.In vitro and in vivo models should be used to study:-Myeloma\u2013NK cell interaction-Impact of NK cell receptor targeting on the effectiveness of mAb therapy for myeloma-Personalizing approaches to NK cell-based therapies using knowledge of NK cell function and myeloma-NK cell ligand expression heterogeneity.-Approaches to building CAR-NK cells as myeloma therapeutics Mobilizing NKs in MM is particularly attractive due to their natural capacity to distinguish damaged cells from healthy cells, allowing them to specifically eliminate only the damaged cells. Utilizing NK-based immunotherapy in MM remains an interesting and understudied area of research. This review highlights the important role that NK IRs may play in MM. With more research, we propose the development of a patient-specific strategy that incorporates precise IR blocking that can be adjusted according to patient-specific responses and changes due to different treatments regiments. This will involve more investigation into NK cell characteristics, their related ligands and NK cells subpopulations in MM patients as well as the MM microenvironment throughout disease stages. With this understanding comes the potential for novel IR-blockade immunotherapies regimen that could improve disease control and thus increase survival outcomes.All authors contributed to the article and approved the submitted version. HA and TR conceptualized and designed the manuscript. JW and HA designed and created the figures and generated the clinical trial table. SG critically edited the manuscript.This work is supported by a grant from The Canadian Institutes of Health Research (CIHR)-The New Brunswick Health Research Foundation (NBHRF) iCT SPOR grant SMC-151513, Canadian Cancer Society (CCS) 706194 and The Terry Fox Research Institute (TFRI) 1067.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Although intraocular lens (IOL) dislocations have been reported after uneventful cataract surgeries, no sequential changes have ever been demonstrated. Our case showed the sequential changes to IOL dislocation caused by vigorous ocular massage.A 42-year-old man complained of blurred vision in the left eye 8 years after uneventful phacoemulsification. The IOL was still well-centered, but curvilinear tears of the anterior and posterior capsule along the optic border of IOL and vitreous herniation were noted. In the following month, the IOL subluxated inferiorly. A careful history taking revealed a recent habit of vigorous ocular massage. The subluxation was stable for 2 years after avoiding ocular massage, but dislocation into vitreous occurred after taking a spring water bath (spa) bath with massage.IOL dislocation.Pars plana vitrectomy to remove the dislocated IOL and implantation of a 3-piece IOL into sulcus were performed.The IOL was well-centered. The visual acuity returned to 20/20.Ocular massage might cause tear of the intact fibrotic capsule and dislocation of IOL. The capsule along the border of the optics might be a weak point against ocular massage. To our knowledge, only 5 cases of rubbing-related IOL dislocation have been reported (3 in-the-bag IOL dislocations and 2 anterior chamber IOL posterior dislocations).45645 Our report is the first to demonstrate the sequential progression to IOL dislocation. Written informed consent for the publication of this case and any additional related information was taken from the patient involved in the study.Intraocular lens (IOL) dislocation is a rare late complication of cataract surgery. The cumulative risk of late posterior chamber IOL dislocation is between 0.1% and 1.7%.2A 42-year-old high myopic professor visited our clinic with the chief complaint of blurred vision in his left eye for a long time. He had undergone cataract extraction and IOL implantation in his right eye at another hospital before. Best corrected visual acuity (BCVA) was 20/20 in the right eye (OD) and 20/200 in the left eye (OS). Biomicroscopic examination showed pseudophakia (OD) and anterior cortical opacity and nuclear sclerosis (OS). The patient then underwent uneventful phacoemulsification in his left eye with a smooth round continuous curvilinear capsulorrhexis (CCC), intact posterior capsule and in-the-bag IOL implantation . The post-operative corrected visual acuity was 20/20. The condition was quite well until 8 years later when he came back with the complaint of mild blurred vision in his left eye. He denied any ocular trauma or any dangerous sports. The corrected visual acuity was still 20/20 in his left eye. Biomicroscopic examination revealed some feathery whitih material behind the pupil but in front of the IOL Fig. A. After 3 The posterior capsule rupture occurred and progressed during the habit of ocular massage and came to a halt after stopping the ocular massage. Therefore, we believe that ocular massage was the culprit of the out-of-the-bag IOL dislocation.Our patient had no risk factors for out-of-the-bag dislocation as reported. In 2004, Gross et al reported another in-the-bag IOL dislocation from eye rubbing in a 75-year-old female, which was managed by IOL removal in exchange for anterior chamber IOL. In 2005, Poh et al reported a 61-year-old Chinese man with bilateral anterior chamber IOL posterior dislocation into the vitreous cavity after uncontrolled eye rubbing, which was treated by IOL removal via pars plana vitrectomy. In 2007, G\u00fcrl\u00fc et al reported another anterior chamber IOL posterior dislocation after habitual eye rubbing in a 77-year-old woman. In 2016, Bassily et al reported a 36-year-old woman with atopic eczema suffered from bilateral posterior capsule rupture and IOL dislocation after excessive eye rubbing, which were managed by replacing the dislocated IOL with an iris-claw IOL. In contrast, our patient suffered from posterior capsule rupture and subsequent out-of-the-bag dislocation during the habit of vigorous ocular massage, and received removal of the dislocated IOL and sulcus IOL implantation.Literature review revealed 5 cases of IOL subluxation or dislocation associated with eye rubbing. In 2001, Yamazaki et al reported the first IOL in-the-bag subluxation into the anterior chamber in a 66-year-old Japanese with atopic dermatitis after forceful eye rubbing, which was treated by IOL removal and contact lens wear. However, our case beautifully demonstrated that the original posterior capsule tear was along the optic border rather than from the sharp edge of the haptic. Hence, the posterior square edge of optic prevents the formation of posterior capsular opacity, but the square edge might cut the posterior capsule when a forceful pressure is applied on the anterior optic of IOL. The curvilinear tear along the optic border did not only appear on the posterior capsule but also on anterior capsule outside the original CCC. The edge of the optic and a rebound force form the vitreous together might lead to the curvilinear tear of the fibrotic anterior capsule.Bassily et al suggested that the mechanism of the posterior capsule tear could have been focal digital pressure on the eye that displaced the IOL vertically, causing the sharp edge of the haptic to rupture the posterior capsule.Although IOL subluxation or dislocation could be managed with surgical intervention, the best strategy is prevention from happening or progression. We recognized the curvilinear capsule tear when the IOL was still in its original position but failed to prevent its further progression to IOL dislocation in our patient because of the initial lack of thorough history taking. Therefore, both early recognition and a careful history taking of the lifestyle are mandatory.Our report demonstrated progressive sequential changes to IOL dislocation caused by ocular massage. The initial tears were along the optic border of IOL. Patients should be advised to avoid vigorous ocular massage or excessive eye rubbing, even long after the operation.Conceptualization: Yuan-Chieh Lee.Data curation: Wei-Shan Tsai, Yuan-Chieh Lee.Formal analysis: Yuan-Chieh Lee.Supervision: Yuan-Chieh Lee.Validation: Yuan-Chieh Lee.Writing \u2013 original draft: Wei-Shan Tsai.Writing \u2013 review and editing: Yuan-Chieh Lee."} +{"text": "This article mainly describes the preclinical research of RosA on inflammatory diseases and depicts a small amount of clinical research data. The purpose of this review is to discuss the anti-inflammatory effects of RosA in inflammatory diseases and its underlying mechanism.Inflammatory diseases are caused by abnormal immune responses and are characterized by an imbalance of inflammatory mediators and cells. In recent years, the anti-inflammatory activity of natural products has attracted wide attention. Rosmarinic acid (RosA) is a water-soluble phenolic compound that is an ester of caffeic acid and 3, 4-dihydroxyphenyl lactic acid. It is discovered in many plants, like those of the Boraginaceae and Lamiaceae families. RosA has a wide range of pharmacological effects, including anti-oxidative, anti-apoptotic, anti-tumorigenic, and anti-inflammatory effects. The anti-inflammatory effects of RosA have been revealed through Inflammation is an integral part of innate immunity. It includes the body\u2019s removal of harmful signals and the initiation of protective responses and tissue healing processes . The infThe pattern-recognition receptors (PRRs) on immune cells sense \u201cdanger\u201d from protein-associated molecular patterns (PAMPs) linked to a pathogen or from danger-associated molecular patterns (DAMPs) triggered by a large number of endogenous stress signals from the host . The intin vitro and in vivo studies have reported the anti-inflammatory effects of RosA in inflammatory diseases. This review systematically describes the therapeutic potential of RosA for inflammatory diseases and discusses its possible mechanisms.Rosmarinic acid RosA, Figure 1Arthritis is an inflammatory disease that involves damage to one or more joints. It has more than one hundred types, the most common of which are osteoarthritis and rheumatoid arthritis . OsteoarOA is a multifactorial disease described primarily as the destruction of articular cartilage . Collage+CD25+ activated T cell apoptosis in 57.1% of RA patients in a dose-dependent manner, and RosA showed stronger apoptotic activity against the CD4+CD45RO+ effector T cell subset than the CD4+CD45RA+ naive T cell subset. In addition, RosA inhibited MMP destruction, reduced Bcl-2 expression, and induced Cyt c release from mitochondria to the cytoplasm. These results supported the view that RosA induced the apoptosis of activated T cells from RA patients through the mitochondrial pathway. Another experiment found that RosA can improve arthritis symptoms in the mouse model of collagen-induced arthritis (CIA) . RosA cois (CIA) .Inflammatory bowel disease (IBD) is a chronic recurrent intestinal inflammation that includes Crohn\u2019s disease (CD) and ulcerative colitis (UC). IBD is thought to be caused by an abnormal and sustained immune response to microorganisms in the intestine caused by the genetic susceptibility of the individual . UC is aStudies have found that RosA can improve dextran sulfate sodium (DSS)-induced colitis . In thisSome researchers have modified RosA to reduce its hydrophilicity, effectively inhibiting hypoxia-inducible factor-prolyl hydroxylase-2 (HPH) and causing the activation of hypoxia-inducible factor (HIF)-1 to exert anti-TNBS-induced colitis effects in rats .Atopic dermatitis (AD), also known as atopic eczema, is a chronic recurrent inflammatory skin disease . The cli+ T cells, which chiefly secrete the Th2 cytokines IL-4, IL-5, and IL-13. However, in the chronic phase, Th1 cells secrete interferon-\u03b3 (IFN-\u03b3) . Some re (IFN-\u03b3) . The aut studies . This efAsthma is a common chronic airway disease described as a complicated interaction between airway obstruction, bronchial hyperresponsiveness (BHR), and airway inflammation . Lots ofRosA has been found to inhibit ovalbumin (Ova)-stimulated airway inflammation in a mouse model of asthma . The mitOcimum gratissimum (Og) and RosA in a mouse respiratory allergy model caused by Blomia tropicalis (Bt) mite mite . This exBt) mite . It was Allergic rhinitis (AR) is a symptomatic nose inflammation caused by immunoglobulin E (IgE)-mediated endocardial inflammation . AR is oRosA improved inflammation in the OVA-induced AR animal model . AdminisPerilla frutescens extract led to a marked augment in responder rates for itchy nose, watery eyes, itchy eyes, and total symptoms. RosA could effectively treat mild SAR at least in part by inhibiting the infiltration of polymorphonuclear leukocytes (PMNLs) into the nostrils.Some researchers have studied whether oral RosA is effective in patients with SAR through clinical trials, and animal experiments have estimated the anti-inflammatory mechanism of RosA in the ear edema model . In clinPeriodontal disease (PD) is thought to be a multifactorial disease caused by pathogenic infections, promoted by inflammation, and immune responses to bacteria, and altered by different environmental and genetic factors . The comAn article has reported the effects of the topical anti-inflammatory drugs ebselen and RosA on plaque-induced gingivitis progression in a rhesus monkey model . NonparaPrunella vulgaris L. (PVE) and its composition RosA on oxidative damage and inflammation in human gingival fibroblasts induced by LPS is an inflammatory disease described as acute inflammation and necrosis of the pancreatic parenchyma . AP is cvia suppressing the activation of NF-\u03baB.RosA may have a protective effect on sodium taurocholate (NaTC)-induced AD . The patMastitis is a breast inflammation which is usually caused by a bacterial infection and is able to influence any mammal that is lactating . Human evia RosA. Therefore, RosA can attenuate LPS-induced mastitis through suppressing the TLR4/MyD88/NF-\u03baB signaling pathway.Recently, an article reported the anti-inflammatory effect of RosA on LPS-induced mouse mastitis . This exIn addition, studies have found that RosA has been reported in Japanese encephalitis and neuritis. RosA reduced the mortality of murine infected with Japanese encephalitis virus (JEV). The viral load and pro-inflammatory cytokine levels of JEV-infected animals receiving RosA were significantly reduced 8 to 9 days after infection compared to the levels of untreated infected mice . RosA grIn addition to its therapeutic effects in inflammatory diseases, RosA also exerts an anti-inflammatory effect on other diseases. The anti-inflammatory effects of RosA on different disease models are presented in Inflammation is an acute reaction to infection and tissue lesion to prevent damage to the body . ExcessiAll the authors have written, reviewed the manuscript and agreed the ultimate version.This work was supported by Liaoning provincial department of education project (LZ2019013) and Special Program of Talents Development for Excellent Youth Scholars in Tianjin (TJTZJH-QNBJRC-2-7).SS is employed by Tianjin Institute of Pharmaceutical Research New Drug Evaluation Co Ltd.The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Transcatheter pulmonary valve implantation (TPVI) is now an established alternative to surgery in patients with congenital heart disease and dysfunctional right ventricular outflow tract (RVOT) conduit. However, there is recognition of a higher incidence of infective endocarditis in the patients after TPVI. Transthoracic and transesophageal echocardiography is limited in the evaluation of prosthetic pulmonary valve endocarditis secondary to a metallic artifact and degenerative calcified conduit. Additionally, the anterior position of RVOT also limits evaluation by echocardiography. Conventional single-energy CTA can also be sub-optimal in evaluating prosthetic pulmonary valve stent frame due to streak artifacts from the metallic cage\u00a0and poor contrast to noise ratio if higher kV is used for single-energy CTA to avoid metallic artifacts. Dual-energy CTA can overcome these limitations using reconstructed virtual monoenergetic and iodine-only images for metal artifact reduction and improve intra-stent luminal visualization. Reconstructed iodine perfusion maps may also help\u00a0differentiate vegetation from a thrombus. In this case report, we discuss the diagnostic utility of dual-energy cardiac CT in the evaluation of endocarditis after TPVI and discuss the imaging protocol. Transcatheter pulmonary valve implantation (TPVI) is an established alternative to surgery for patients with dysfunctional (stenotic/regurgitant) right ventricular outflow tract (RVOT) conduit . HoweverThe use of dual-energy CTA is steadily increasing in the field of cardiovascular applications like coronary plaque evaluation and myocardial perfusion. These have been made possible due to significant improvement in temporal resolution and superior spectral separation using tin filter at high kVp image -5.Despite these advantages, the role of DECT in the evaluation of endocarditis after TPVI has not been studied earlier. Using case examples, we discuss our initial experience in the challenging clinical situation of suspected endocarditis after TPVI.Case 1Staphylococcus aureus (MSSA). TTE was suboptimal presented with fever three years later. Blood culture was positive for methicillin-sensitive DECT (DLP 201.6 mGycm) showed circumferential hypodensity in the stent frame Figure , 2B. QuaThe patient underwent surgical replacement with a homograft. Histopathology of explanted conduit Figure confirmeCase 2A 16-year-old female with TPVI for congenital stenosis presented with a fever a month later and positive blood culture for gram-positive cocci. Transthoracic echocardiogram was non-diagnostic. DECT was ordered to evaluate the stent frame integrity and to rule out any pseudoaneurysm. DECT (DLP 156.2 mGycm) with blended single-energy images showed metallic artifacts obscuring the lumen Figure A, B. ReNo other complications like infective pseudoaneurysm or dehiscence were seen. She was managed conservatively using IV antibiotics and was discharged in a stable condition after two weeks. The patient was clinically afebrile and asymptomatic at a three-month\u00a0follow-up evaluation.Cardiac DECT TechniqueThe cases were performed on a dual-source CT scanner with a tube voltage of 90 and 150 kVp and automated tube current modulation (Caredose 4D). ECG-gating with dose modulation was performed. Scan range extended from the level of carina to the diaphragm.Injection TechniqueA biventricular or triphasic injection protocol was employed for the simultaneous evaluation of aorta and pulmonary artery. In this technique,\u00a0the half dose of total contrast volume (Iohexol 350 mgI/ml) was followed by the remaining contrast volume mixed with saline (50:50)\u00a0and saline chase flush. This method is commonly used in patients where the evaluation of both right- and left-sided cardiac chambers is required. The scan was triggered using bolus tracking (descending aorta at 100 HU), providing adequate opacification of cardiac chambers and RVOT conduit.Image ReconstructionPost-processing was performed on Siemens Syngovia software. The CT images were reconstructed over 10 phases per cardiac cycle for dynamic valve and functional analysis. Six data sets were reconstructed: single-energy data set at 90 kVp Figure and 150 Virtual Monoenergetic ImagesVirtual monoenergetic (VM) images were reconstructed, ranging from 40 to 190 keV. High keV data were useful for evaluating the structural integrity of the stent frame, while low keV (40-70) images improved RVOT contrast enhancement Figure 6].\u00a0Vir.\u00a0Vir6].\u00a0Virtual Non-Contrast ImagesVirtual non-contrast images are reconstructed by subtraction of the iodine from contrast-enhanced images; hence providing an artificially created non-contrast images. These images are useful for examining prosthetic material and post-surgical changes. This prevented performing an unenhanced CT, thus reducing radiation exposure .Iodine ImagesIodine-only images involve accentuation of the iodine attenuation by post-processing. Iodine-only images improved visualization of the intrastent lumen by avoiding metallic artifacts Figure and enabIodine uptake is useful to differentiate vegetation from a thrombus (Case 1) and is not affected by window-level Figure .TPVI is FDA approved since 2010) for patients with dysfunctional RVOT conduit . The ann for patiF-18 FDG PET-CT or white cell-labeled SPECT-CT are commonly used to evaluate for the source of infection when other modalities, including echocardiogram/computed tomography, fail to localize the site of endocarditis. PET-CT is more sensitive but has low specificity, whereas SPECT-CT has high specificity in endocarditis evaluation [The choice of test depends upon the goal of the study and the clinical status of the patient. A transthoracic echocardiogram is the initial test of choice for the management and monitoring of these patients. It provides a quick, bed-side assessment of cardiac function in unstable patients. However, both transthoracic and transesophageal echocardiograms are frequently limited in the evaluation of endocarditis affecting intracardiac devices or prosthetic valves . Cardiacaluation . CTA shoaluation .Conventional single energy CT in patients with metallic prosthetic valve evaluation is usually limited due to streak artifacts. Dual-energy CT angiography (DE-CTA) can overcome these limitations and has distinct, complementary advantages like virtual monoenergetic images, metal artifact reduction, and iodine quantification, which allows for better visualization and appropriate disease characterization in such patients. CT is fast, non-invasive, and is also excellent in detecting paravalvular complications of prosthetic valve endocarditis. The radiation dose with single-energy and dual-energy cardiac CT is comparable , 16. TheUnlike single-energy CTA, DECT may help differentiate thrombus from infective vegetation based on the presence or absence of iodine uptake. We found iodine uptake in the filling defect in Case 1 (1.2 mgI/ml), and it was confirmed as infected vegetation on histopathology. Prior studies have proposed that iodine uptake at a concentration above 0.5 mgI/ml suggests true enhancement . CurrentEndocarditis after TPVI is a high-risk situation requiring early diagnosis and treatment. Echocardiography is frequently suboptimal in these patients due to the metallic valve frame. Conventional single-energy CT in these patients is also poor due to streak artifacts from the metallic valve cage. Cardiac DECT enables reconstructions like virtual monoenergetic and iodine-only images that overcome the limitations of single-energy CTA. Quantitative iodine uptake is also possible with DECT, which allows differentiation of a bland thrombus versus infective vegetation improving the specificity of the diagnosis. The use of DECT for assessment of endocarditis after TPVI is a new and novel use of CT and should be validated in future studies."} +{"text": "Correction to: J Eat Disordhttps://doi.org/10.1186/s40337-019-0249-zIn the publication of this article , there iThe last sentence of the results paragraph in the abstract reads as follows: \u201cWhile measures of WE related more to weight gain and general ED Psychopathology, indices including lowest weight were stronger predictors of changes in slimness ideal and inappropriate compensatory behaviors.\u201d Instead of WE (weight elevation), however, the abbreviation should say WS (weight suppression). This has now been included in this correction article."} +{"text": "Small molecule inhibitors and peptide inhibitors are identified for therapeutic intervention of JNK signaling pathway. SP-600125, an anthrapyrazole small molecule inhibitor for JNK with high potency and selectivity has been widely used for dissecting JNK signaling pathway. CC-401 is the first JNK inhibitor that went into clinical trial for inflammation and leukemia. Inhibitor for mixed lineage kinase (MLK), CEP-1347 also negatively regulates JNK signaling, and tried for potential use in Parkinson\u2019s disease. Cell-permeable peptide inhibitor D-JNKI-1 is being developed for the treatment of hearing loss. The current status of these JNK inhibitors and safety issue is discussed in the minireview.Targeting protein kinases has been active area in drug discovery. The c-Jun N-terminal kinases (JNKs) have also been target for development of novel therapy in various diseases, since the roles of JNK signaling in pathological conditions were revealed in studies using"} +{"text": "Escherichia coli (ESBLEC) were isolated from healthy Thoroughbred racehorse feces samples in Japan. Some ESBL genes were predicted to be located on the conjugative plasmid. PCR-based replicon typing (PBRT) is a useful method to monitor and detect the association of replicons with specific plasmid-borne resistant genes. This study aimed to evaluate the plasmid replicon associated with ESBLEC isolated from healthy Thoroughbred racehorses at Japan Racing Association Training Centers in Japan. A total of 24 ESBLECs isolated from 23 (10.8%) individual Thoroughbred racehorse feces samples were used in this study. ESBL gene transfer was performed using a conjugation assay. Then, replicon types of ESBLEC isolates and their transconjugants were determined using PBRT. Pulsed-field gel electrophoresis (PFGE) was performed to look at the clonality of the ESBLECs isolates. ESBLECs were detected from 10.8% of healthy Thoroughbred racehorses. The blaCTX-M-2 was identified as the dominant type of ESBL gene, followed by blaCTX-M-1 and blaTEM-116. In this study, only the blaCTX-M-2 and the IncI1 plasmid were transferred to transconjugants. The PFGE results showed that ESBL genes were distributed in diversity of ESBLECs. This finding suggested that the IncI1 plasmid was associated with the dissemination of blaCTX-M-2 in Thoroughbred racehorses in Japan.In our previous study, extended spectrum \u03b2-lactamase (ESBL)-producing The emergence of resistance to third-generation cephalosporin, mediated mainly by extended spectrum \u03b2-lactamase (ESBL), has become a major health problem . CTX-M iEscherichia coli (ESBLEC) have received special attention in the area of equine medicine ), polypeptide (colistin [CL]), quinolone and folate antagonist-sulfonamide (trimethoprim- sulfamethoxazole [STX]), by determining the minimum inhibitory concentration (MIC) of these antibiotics based on recommendations from the Clinical Laboratory Standard Institute guidelines . In the -, Nar) of E. coli DH5\u03b1 was used as the recipient strain, while all the ESBLECs sensitive to NA served as donors. Conjugation experiments were performed based on our previous study [The transfer of ESBL genes was studied using a conjugation assay for all ESBLEC isolates. A plasmid free and nalidixid acid-resistant (Fus study . All traThe replicon types of ESBL-producing bacteria (donor) and their transconjugants were determined using a previous report . BrieflyPulsed-field gel electrophoresis (PFGE) was carried out as described previously . DNA fra"} +{"text": "Alzheimer\u2019s disease (AD) is a devastating disorder primarily affecting older adults and is the most common neurodegenerative disease in the US. More than one in three AD patients experience AD-associated urinary dysfunction (ADUD), which directly contributes to their institutionalization. While ADUD has been clinically regarded as a result of poor cognitive control over urinary function, the physiology underlying loss of urinary control remains unknown. We hypothesize that beta-amyloidosis in the CNS results in pathologic changes in urinary structure and function. Male and female Tg-APP/PS1DE9 mice were used before plaque deposition (4-6 months) and after plaque accumulation (8-10 months) and compared to their WT littermates. Pressure-flow cystometry was conducted under urethane anesthesia to assess urinary performance at the level of the autonomic nervous system in the absence of cortical control. Pharmacomyography was performed on bladder strips to determine tissue-level changes in the absence of CNS input. In Tg-APP/PS1DE9 mice, plaque accumulation resulted in diminished volume sensitivity and decreased voiding efficiency. Pharmacologic studies showed aberrant drug responses, altered cholinergic signaling, and decreased resilience of tissue longevity after plaque accumulation. Based on our findings, we conclude that the AD-related pathology of A\u03b2 accumulation results in a distinct urinary phenotype in our model, analogous to the ADUD observed in AD patients. Establishing and expanding models of ADUD to other mouse models of AD-associated pathology may improve the efficacy of treating ADUD and increase quality of life for patients and their caregivers."} +{"text": "Background: Patients with different molecular subtypes of breast cancers have different recurrence risks and prognoses. Clinical support and evidence to guide management are absent for patients with breast cancer coexisting with HER-2 amplification and EGFR mutations.Case presentation: We report a case of breast cancer coexisting with HER-2 amplification and EGFR exon 19 deletion (E19 del). The patient presented with solitary pulmonary nodule and enlargement of hilar and mediastinal lymph nodes 2 years after radical mastectomy. Biopsy of the subcarinal lymph node showed suspected adenocarcinoma. The specimen was too small for further immunohistochemistry, but an EGFR E19 del was discovered. Due to the primary diagnosis of EGFR-mutant lung adenocarcinoma, EGFR-TKI gefitinib was administered and resulted in 1 year of stable disease until the patient developed progression in the right pulmonary nodule with new metastatic cervical lymph nodes. According to histopathological findings of re-biopsy of the pulmonary nodule and left cervical and subcarinal lymph nodes, the patient was diagnosed with breast cancer with lung metastasis and multiple lymph node metastases. The patient received multiple anti-HER-2-targeted therapies and survived for more than 36 months after lung metastasis.Conclusions: This case suggested that breast cancer coexisting with HER-2 amplification and EGFR E19 del may be driven by both HER-2 and EGFR signaling pathways, and patients can benefit from EGFR-TKI and anti-HER-2 therapy. Breast cancer, as the most common cancer in females, is reported to have had about 252,710 new cases in the United States during 2017, accounting for 30% of all new cancer diagnoses in women . PatientHigh heterogeneity is a hallmark of breast cancer. Patients with breast cancers with different molecular subtypes have different recurrence risk and survival prognosis. About 20\u201325% of breast cancer patients have HER-2 protein overexpression or gene amplification, which is considered an effective predictor for anti-HER-2 therapy . ReportsTo our knowledge, this may be the first case report to discuss the efficacy of EGFR-TKIs as first-line therapy for HER-2-positive advanced breast cancer with EGFR co-mutation. Therefore, we summarized the diagnosis and treatment of this patient and discussed the experience and lessons learned from it.in situ hybridization (FISH) for HER-2 amplification. The patient had early stage disease and underwent 8 cycles of adjuvant chemotherapy (CE \u00d74 \u2192 T\u00d74) without trastuzumab followed by tamoxifen.A 50-year-old female patient was clinically diagnosed with left breast cancer and received a radical mastectomy in February 2014. Pathological findings supported invasive ductal carcinoma with immunohistochemistry (IHC) for ER 80%+, PR 70%+, Ki-67 20%+, and fluorescence Follow-up chest computed tomography (CT) in November 2016 showed a nodule in the upper lobe of the right lung. The patient complained of chest pain but denied fever, cough, hemoptysis, and weight loss. She had no family history of cancer. She had menarche at 13 and was not currently in menopause. Further positron emission tomography CT (PET-CT) showed a lobulated nodule with diameter 0.8 \u00d70.9 cm in the upper lobe of the right lung with intense fluorodeoxyglucose (FDG) uptake (SUVmax = 8.32) . The enlBased on the pathological and molecular results and CT findings, a primary lung adenocarcinoma was suspected. Since radical surgery was not available, the patient started receiving EGFR-TKI gefitinib (250 mg once daily) and stopped taking tamoxifen since November 2016. Follow-up chest CT indicated stable disease until November 2017, when the patient presented left neck swelling at physical examination.Further PET-CT in November 2017 revealed more intense FDG uptake in the right lung nodule and hilar and subcarinal lymph nodes . EnlargeAccording to pathological findings, primary lung adenocarcinoma was excluded. The patient had breast cancer with lung metastasis and multiple lymph node metastases. She received 6 cycles of combination treatment with trastuzumab, vinorelbine, and capecitabine from December 2017. Repeated PET-CT in May 2018 indicated that all metastatic lesions significantly shrank . ThereafIn this case report, a patient had HER-2-amplified and ER-expressing breast cancer. The patient received a radical mastectomy, postoperative adjuvant chemotherapy, and endocrine therapy without anti-HER-2-targeted therapy. Metachronous thoracic metastases occurred 33 months after mastectomy, with a solitary nodule in the right upper lobe and right hilar and subcarinal metastatic lymph nodes. The primary diagnosis of EGFR-mutant lung adenocarcinoma was made based on the insufficient immunohistochemistry and atypical CT appearance of lung metastasis. The first-line administration of EGFR-TKI gefitinib unexpectedly resulted in 1 year of stable disease. The patient benefited from both EGFR-TKI and anti-HER-2 therapy and survived more than 3 years after lung metastasis.Currently, subtype classification based on molecular biomarkers is recommended to guide breast cancer treatment. In addition, multigene panel testing is deemed a useful supplement for deciding on postoperative adjuvant therapy for patients with early breast cancer . Differein vitro . One year later, new metastases in the left cervical lymph nodes were found and biopsied for histopathological diagnosis. HE staining, IHC and FISH (HER-2 amplification) suggested metastatic cervical lymph nodes derived from breast cancer. A second CT-guided biopsy of the nodule in the upper lobe of the right lung was performed. Irregular adenoid and cord-like cancer cells were found in the biopsy tissue of the nodule in the upper lobe of the right lung with IHC results of positive expression for ER (80%), PR (20%), HER-2 (2\u20133+), Ki-67 (10%), and Gata-3, but negative expression for TTF-1, Napsin A, and P40. This result helped to confirm the diagnosis of lung metastasis of breast cancer after EGFR-TKI therapy failure in November 2017. Limited results from pathologic diagnosis and atypical imaging of lung metastasis led to the misdiagnosis. Pathology is considered an indispensable diagnostic tool for differential diagnosis. Histopathological and immunohistochemical analyses and genetic testing of biopsy tissues are crucial for accurate diagnoses, especially when patients have atypical metastatic tumor imaging.This case suggested that breast cancer coexisting with HER-2 amplification and EGFR E19 del may be driven by both signaling pathways and patients can benefit from EGFR-TKIs and anti-HER-2 therapy. Early identification and accurate diagnosis are not only fundamental principles of cancer therapy but also crucial for determining therapeutic schemes and prognostic survival.Written informed consent was obtained from the patient for publication of this case report and accompanying images. This report adhered to the tenets of the Declaration of Helsinki and was reviewed and approved by our center's ethics committee .WJ was mainly responsible for the article writing. C-BH was the corresponding author. WJ and J-TM were responsible for patients' clinical data and analysis.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "As we illustrate through a variety of examples, this method identifies those binding sites that are sensitive to the cellular context or post-translational modifications, and may serve as regulatory points of cellular pathways.Interactions between disordered proteins involve a wide range of changes in the structure and dynamics of the partners involved. These changes can be classified in terms of binding modes, which include disorder-to-order (DO) transitions, when proteins fold upon binding, as well as disorder-to-disorder (DD) transitions, when the conformational heterogeneity is maintained in the bound states. Furthermore, systematic studies of these interactions are revealing that proteins may exhibit different binding modes with different partners. Proteins that exhibit this context-dependent binding can be referred to as fuzzy proteins. Here we investigate amino acid code for fuzzy binding in terms of the entropy of the probability distribution of transitions towards decreasing order. We implement these entropy calculations into the FuzPred ( Great advances have been made in the last several decades in deciphering how the behavior of proteins is encoded in their amino acid sequences. A variety of sequence-based prediction methods have been developed to estimate a wide range of properties of proteins, including secondary structure propensity, native state structures, preference for being disordered and tendency to aggregate. Much less is known, however, about the rules that regulate the conformational changes of proteins upon binding. In particular, many proteins change their binding modes upon interacting with different partners, or as a consequence of post-translational modifications or changes in the cellular milieu. Here we address the problem of how amino acid sequences can encode different binding modes depending on their binding partners, and describe the FuzPred method of predicting context-dependent binding modes. With the advent of fast sequencing methods there has been an explosion in the number of proteins of known amino acid sequence. As the number of proteins whose sequences have been determined currently vastly exceeds that of proteins with known structures, especially in functional forms, one can exploit this asymmetry of information to develop sequence-based predictors of protein conformational behaviour. Great advances have been made in this area, with several methods introduced in the last two decades \u20134.Another major recent advance in molecular biology has been the discovery of disordered proteins, which do not fold into well-defined three-dimensional structures but remain conformationally heterogeneous in their native states , 6. ThisIn addition, certain proteins have evolved the ability to adopt different binding modes depending on their binding partners, which has been termed context-dependent binding . DisordeHow can different binding modes be encoded in the same sequence? While a repertoire of methods for predicting the degree of disorder in the monomeric state of proteins are available , 8, we hIn this work, we considered three types of binding modes for interactions of disordered regions . Disordehttp://protdyn-database.org) is the number of binding regions with a binding mode pDO(R). To define nR[pDO(Ri)] we have binned pDO(R) into 0.1 intervals.Here we address how the predicted binding mode of a given residue lues Eqs and 3 chAi, we compute the Shannon entropy (f[pDO(R)] is the frequency of a given binding mode with a given pDO(R) (pDO(R).Using the frequencies of all the possible binding modes of a given residue entropy SAi=\u2212\u2211f. As. AspDO apDO and pDD values further support changes in binding modes conveys unfolded protein response signals via oligomerization, which activates both its kinase and RNase domains . Ire1 trrylation . The preng modes .The nonsense-mediated decay factor regulator of nonsense transcripts 2 (UPF2) binds its partner regulator of nonsense transcripts 1 (UPF1) in a bi-partite manner. The linker (1130-1166-residue), which connects the structured binding elements however, remains disordered in the bound state , yet conng modes . This fing modes .pDD and pDD values; whereas the y axis defines the number of binding modes, or fuzziness indicate a large variability of binding modes. Indeed, this segment is also engaged in interactions with the high mobility group box 1 (HMGB1) protein , representing the whole spectrum of binding modes (pDO(Ri)}N distribution informs on the number and preference of binding modes.Using running windows from 5 to 9 residues provide 35 ng modes . The modpDO(Ri)}N distribution was calculated for each residue using frequencies of pDO(Ri) values. Thus, the pDO(Ai) characterizes interactions of a residue. Low pDO(Ai) and pDO(Ri) distribution. Using more bins (> 10) would require defining more binding sites, including longer interfaces. This is, however, not typical for disordered proteins [The Shannon entropy associated with the {proteins , 51 and We also eliminated potential artefacts owing the reduced number of hypothetical binding sites at the N- and C-terminal regions as compared to the middle of the sequence . We did Receiver operating characteristic (ROC) curves were computed using the R program. The true positive rate (TPR) was calculated as a function of the false positive rate using the experimentally observed disorder-to-order, disorder-to-disorder and context-dependent regions. The area-under-the-curve (AUC) was determined by the R program. Only disordered residues were included in the distinct binding mode classes.S1 Text(DOCX)Click here for additional data file.S2 Text(DOCX)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S1 Fig(DOCX)Click here for additional data file.S2 Fig(DOCX)Click here for additional data file.S3 Fig(DOCX)Click here for additional data file."} +{"text": "This study examined the association between leadership styles and resident quality and financial performance in under-resourced nursing homes. Survey data from 391 Directors of Nursing were merged with secondary data from LTCFocus, Area Health Resource File, Medicare Cost Reports, and Nursing Home Compare. Two multivariate regressions were used to model the relationship between leadership styles and the dependent variables: nursing home star ratings (1-5) and operating margin. The independent variables were composite scores for leadership styles, while control variables included organizational and county-level factors. Results show that compared to autocratic leadership, the consultative autocrat was associated with lower quality (p < 0.05), while the consensus manager (delegates authority to the group) was associated with lower profit margin (p < 0.05). Under-resourced facilities need to recognize trade-offs of different decision making styles for performance."} +{"text": "Fusarium equiseti, was sequenced. The circular molecule is 53,411\u2009bp long with a GC content of 32.81%. It contains 22 protein-coding genes, 4 ribosomal RNA (rRNA), and 24 transfer RNA (tRNA) genes. Phylogenetic reconstructions confirmed that it has the closest relationship with Fusarium equiseti. The mitogenome analysis of Fusarium equiseti provides a molecular basis for further studies on molecular systematics and evolutionary dynamics.The complete mitochondrial genome of plant pathogenic fungus, Fusarium cause diseases in many crops and wild plants. The isolate of Fusarium equiseti is a strongly virulent strain, which can cause leaves wilting. We sequenced the complete mitogenome of the Fusarium equiseti strain 2018BL08 (GenBank accession number MN199625) isolated from Nelumbo nucifera in Guangchang City of Jiangxi Province and the specimens were stored at the Plant Pathology Lab in Jiangxi Agricultural University. DNA isolation using an improved extraction method was used to identify any potential genes in the uncoding regions. The mitochondrial genes were annotated using homology alignments and de novo prediction. Transfer RNA (tRNA) genes and ribosome RNA (rRNA) genes were predicted by tRNAscan-SE , and 24 transfer RNA (tRNA) genes. The tRNA genes contain codons for all 20 standard amino acids. Most amino acids are represented by only one tRNA gene, however, two trnL (trnL-UAA and trnL-UAG), two trnG (trnG-ACC and trnG-UCC), two trnR (trnR-ACG and trnR-UCU), and two trnS (trnS-GCU and trnS-UGA) genes are found in this mitochondrial genome.Fusarium. Maximum likelihood (ML) were used to construct the phylogenetic trees with all protein-coding genes and rRNA by PhyML v3.0 (http://www.atgc-montpellier.fr/phyml/) , Fusarium gerlachii (KM486533), and Fusarium culmorum (KP827647) are determined as sisters of Fusarium equiseti with strong support. High bootstrap and posterior probability values show that presented relations are stable. The mitochondrial genome of Fusarium equiseti will contribute to the understanding of phylogeny.As shown in"} +{"text": "Introduction: Recent proposed major construction projects in New York City\u2019s Chinatown often last multiple years. Little is known about the health impact of construction on vulnerable populations such as older adults. In Chinatown, approximately 20% of residents are older adults, live below the poverty level (34%), have a disability (47%), and nearly half report limited English proficiency. Objectives: We are conducting a mixed methods study to describe possible health and psychosocial outcomes of construction on older adults in Chinatown. Methods: We used a community-engaged modified Delphi process to identify priority areas related to construction and older adults which included: 1) a scoping review of the health impact of long-term construction; 2) key informant interviews of academic experts; and 3) convened community stakeholder leaders to review key focus areas and evidence-informed, culturally-relevant mitigation strategies. Five priority topics were identified: 1) Construction site emissions; 2) Noise; 3) Outdoor nocturnal lighting; 4) Neighborhood changes; and 5) Relocation. Results: Long-term construction contributes to adverse effects of air pollution, noise, and changes in the environment, with exposure to particulate matter and unwanted noise associated with higher morbidity and mortality. Unsafe sidewalk due to construction increase the risk of falling, the leading cause of death among NYC seniors. Construction-related stressors may isolate older adults from vital services and social networks. Conclusion: Long-term construction poses serious health implications for older adults. Stakeholders should adopt a community-engaged approach and identify meaningful community priorities to inform practical solutions to mitigate the impact of construction on vulnerable Chinatown older adults."} +{"text": "Metabolism can directly drive or indirectly enable an aberrant chromatin state of cancer cells. The physiological and molecular principles of the metabolic link to epigenetics provide a basis for pharmacological modulation with the anti-diabetic biguanide metformin. Here, we briefly review how metabolite-derived chromatin modifications and the metabolo-epigenetic machinery itself are both amenable to modification by metformin in a local and a systemic manner. First, we consider the capacity of metformin to target global metabolic pathways or specific metabolic enzymes producing chromatin-modifying metabolites. Second, we examine its ability to directly or indirectly fine-tune the activation status of chromatin-modifying enzymes. Third, we envision how the interaction between metformin, diet and gut microbiota might systemically regulate the metabolic inputs to chromatin. Experimental and clinical validation of metformin\u2019s capacity to change the functional outcomes of the metabolo-epigenetic link could offer a proof-of-concept to therapeutically test the metabolic adjustability of the epigenomic landscape of cancer. Global changes in the topology of the epigenetic landscape are a hallmark of cancer \u20133. MetabMore than 60 years after its introduction as a first-line therapy for managing type 2 diabetes, the biguanide metformin is emerging as an archetypal drug capable of targeting most of the epigenetic traits of cancer \u201316 and \u03b2-hydroxyglutarate for histone deacetylases (HDACs), acetyl-CoA for histone acetyltransferases (HATs), \u03b1-ketoglutarate/succinate for histone/DNA demethylases (HDMs), and s-adenosyl-methionine/homocysteine (SAM/SAH) for DNA/histone methyltransferases (DNMTs/HMTs), among others inhibition and its inhibitory action on the mitochondrial electron transport chain (ETC), and can be attributed both to its AMP-activated protein kinase (AMPK)-dependent and -independent actions. There are numerous examples that illustrate the ability of metformin to alter the pools of metabolic intermediates acting as activity modulators of a variety of epigenome-modifying enzymes, including nicotinamide adenine dinucleotide , to decre (SAHH) . The tare (SAHH) , 29\u201331. Beyond promoting fluctuations in the abundance of metabolites that can positively or negatively influence the activities of certain chromatin-modifying enzymes, metformin can modulate the levels of specific epigenetic modifications by indirectly or directly targeting the activation status of core epigenetic enzymes Figure 2via the multifunctional kinase effects of AMPK (O-linked \u03b2-N-acetylglucosamine (O-GlcNAc) transferase to inhibit histone O-GlcNAcylation. There are already some encouraging examples of how metformin-induced AMPK activation regulates the activity of DNA methyltransferases/demethylases and histone-modifying enzymes to translate the metformin-driven transient decrease in cellular energy status into epigenetically-regulated transcriptional events. At the level of DNA methylation, metformin can protect the AMPK-mediated phosphorylation of the TET2 demethylating enzyme, which increases TET2 stability and 5-hydroxymethylcytosine (5 hmC) levels, thus impeding the ability of certain metabolic environments to aberrantly reprogram the epigenome, thereby maintaining genomic stability to repress ribosomal RNA (rRNA) transcription and cell proliferation . MoreoveDH ratio , 39, 40.low NAD+ . Althouglow NAD+ , 43, thelow NAD+ and KDM6low NAD+ at milliEnvironmental factors including diet and microbiota can regulate HMTs and HATs by modulating the intracellular pools of their substrates SAM and acetyl-CoA, respectively. Dietary methionine and other nutrients feeding into one-carbon and methionine metabolism can modulate the levels of SAM and SAH to reprogram the landscape of DNA and histone methylation , 45\u201347. The bidirectional interaction between diet and gut microbiota can drive microbiota metabolomes to alter systemic metabolic physiology and influence epigenetic programs \u201362 Fig\u201366. LessC. elegans and by an unrestricted research grant from the Fundaci\u00f3 Oncolliga Girona . EC is a recipient of a research contract \u201cMiguel Servet\u201d (CP20/00003) from the Instituto de Salud Carlos III, Spanish Ministry of Science and Innovation (Spain).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "The red-eared slider (RES) ranavirus (RESRV) was isolated from a free-ranging RES turtle that died with evidence of respiratory disease. The RESRV genome sequence was determined, and phylogenetic analysis revealed that it is a common midwife toad virus (CMTV) strain. This study is the first report of CMTV in RES. The red-eared slider (RES) ranavirus (RESRV) was isolated from a free-ranging RES turtle that died with evidence of respiratory disease. The RESRV genome sequence was determined, and phylogenetic analysis revealed that it is a common midwife toad virus (CMTV) strain. This study is the first report of CMTV in RES. Trachemys scripta elegans) are semiaquatic turtles with a native range extending from the southeastern United States to northern Mexico. They are listed as an invasive alien species (IAS) by the European Union legislation (Terrapene carolina heart (TH-1) cells (CCLV-RIE 1131), as previously described .Viral DNA served as the template for constructing a DNA library using a TruSeq Dual Index high-throughput (HT) DNA PCR-free library preparation kit (Illumina), followed by sequencing on an Illumina MiSeq sequencer using a v3 chemistry 600-cycle kit. rameters . BLASTN http://iqtree.cibiv.univie.ac.at) with default parameters and 1,000 bootstrap replicates. The resulting ML tree supported the Polish RESRV as a strain of CMTV (The genome of the red-eared slider ranavirus (RESRV) was annotated using the Genome Annotation Transfer Utility with default parameters, and the CMTV strain PEV was used as the reference genome. Additional putative open reading frames (ORFs) were identified using GeneMarkS, and gene functions were predicted based on BLASTP searches against the NCBI GenBank nonredundant protein sequence database. A total of 101 putative ORFs were predicted in RESRV, compared to strains of CMTV predicted to encode between 98 and 112 ORFs \u201312. An a\u2013 of CMTV .Ranavirus (family Iridoviridae) are globally emerging viruses that have been reported in wild and captive populations of ectothermic vertebrates databases under accession no."} +{"text": "Haemophilus influenzae type b conjugate (DTaP-HepB-IPV/Hib) vaccine, measles, mumps, and rubella (MMR) vaccine, and pneumococcal conjugate 7-valent (PCV7) or 13-valent (PCV13) vaccines. Of this, 16% (n = 8) of the studies reported significantly more adverse events following immunization (AEFI) while in 10% (n = 5) significantly fewer adverse events were found in the co-administration groups. Statistically significant differences between co-administration and separate administration were found for 16 adverse events, for 11 different vaccine co-administrations. In general, studies briefly described safety and one-third of studies lacked any statistical assessment of AEFI. Overall, the evidence on the safety of vaccine co-administrations compared to separate vaccine administrations is inconclusive and there is a paucity of large post-licensure studies addressing this issue.The growing number of available vaccines that can be potentially co-administered makes the assessment of the safety of vaccine co-administration increasingly relevant but complex. We aimed to synthesize the available scientific evidence on the safety of vaccine co-administrations in children by performing a systematic literature review of studies assessing the safety of vaccine co-administrations in children between 1999 and 2019, in line with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Fifty studies compared co-administered vaccines versus the same vaccines administered separately. The most frequently studied vaccines included quadrivalent meningococcal conjugate (MenACWY) vaccine, diphtheria and tetanus toxoids and acellular pertussis (DTaP) or tetanus toxoid, reduced diphtheria toxoid and acellular pertussis (Tdap) vaccines, diphtheria and tetanus toxoids and acellular pertussis adsorbed, hepatitis B, inactivated poliovirus and With new vaccines becoming available and added to pediatric immunization schedules, these schedules become increasingly crowded ,2. SinceImmunization schedules are typically designed based on evidence of efficacy and safety from clinical trials. However, both the number and types of vaccines co-administered in routine immunization practices, as well as the vaccinated populations, may differ from the ones investigated in pre-licensure trials. In addition, the small sample size of clinical trials, the many possibilities of vaccine co-administrations, and the low incidence of adverse events following immunization (AEFI) make it challenging to find and interpret evidence on the safety of vaccine co-administrations compared to separate administrations. Both healthcare providers and parents require more information about vaccine co-administrations . TherefoPopulation: Infant OR child OR adolescent OR newborn OR minors OR teenager;Intervention: Vaccination OR vaccines OR immunization OR immunization schedule OR immunization OR immunization, secondary/trends OR mass vaccination/trends OR vaccines/administration & dosage OR vaccines/pharmacology; andOutcome: ((Safety drug-related side effects OR adverse reactions OR adverse effects OR vaccination/adverse effects OR vaccines/complications OR vaccines/adverse effects) OR safety OR tolerability) AND (co-administration OR co-administered OR concomitant administration OR simultaneous administration).We performed a systematic literature review of studies assessing the safety of vaccine co-administrations in children in line with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Our search strategy aimed to retrieve studies in the pediatric population, who received more than one vaccine at the same time for which adverse outcomes were reported. We searched Pubmed (including Medline), Embase, and the Cochrane library for articles in English, published between 1999 and 2019 to cover vaccines and co-administrations relevant to actual immunization practices, combining the following keywords:This translated in the following search string for Pubmed: \u201c(Infant OR child OR adolescent OR newborn OR minors [MeSH terms]) AND AND ((safety drug-related side effects OR adverse reactions OR adverse effects OR vaccination/adverse effects OR vaccines/complications OR vaccines/adverse effects [MeSH terms]) OR safety) AND (co-administration OR co-administered OR concomitant administration OR simultaneous administration)\u201d. The most recent search was performed on 28 January 2019. We screened the included articles\u2019 reference lists for additional articles. Full text articles were obtained through the University of Basel\u2019s library and references were managed using Zotero .Articles were eligible when study participants were under 18 years of age or the study population included both under and over 18 year olds, co-administration of at least two vaccines was indicated in the title and/or abstract, and safety data were reported. After removing duplicates, the following data was collected from the included articles by three independent reviewers (J.B. (Jorgen Bauwens), L.-H.S., A.R.). Study population: Minimum and maximum age of children included, sample size, selected inclusion and exclusion criteria applied . Intervention: Vaccines co-administered and comparator vaccines. Outcome: All AEFIs observed, reported differences in AEFI between co-administration and comparator groups . Study characteristics: Study design, countries, statistics reported to assess differences in AEFI, potential sources of bias. Coding, completeness, and consistency of variables in the data extraction forms were checked among the reviewers and data were compiled in a structured database.The safety assessment was limited to studies comparing co-administered vaccines with the same vaccines administered separately. Studies where the comparator group did not receive exactly the same vaccines separately as the vaccines co-administered were excluded. For studies comparing co-administration with separate administration of the same vaccines, the collected data was analyzed to obtain the following summary measures: Vaccines investigated in co-administration versus separate administration of the same vaccines and their frequencies of occurrence among the included studies; frequencies of study designs used to assess co-administration versus separate administration; minimum, maximum, and mean sample sizes of the included studies by study design; minimum and maximum ages of children in the included studies; number of studies per country; number of studies with statistically more or statistically fewer AEFI between both groups, number of studies with more or fewer AEFI between both groups without statistical assessment provided; AEFI that were reported statistically significantly more or less between both study groups; use of statistical measures in the included studies; occurrence of potential sources of bias including health status of the study population, exclusion of children with known previous reaction or allergies to vaccines or vaccine components; and method for reporting and collecting AEFIs. Analyses were performed in R .From 391 retrieved articles, 185 studies reported safety data for co-administration of at least two vaccines in children. Of these, 50 studies (27%) compared co-administration with separate administration of the same vaccines and were included in our analysis. Other studies meeting the initial inclusion criteria, but not allowing a direct comparison between co-administration and separate administration, compared co-administered vaccines versus only a part of the same vaccines administered separately , versus the same antigens but combined in one vaccine , versus other vaccines , or looked at co-administered vaccines without comparison . The most frequently investigated co-administered vaccines included MenACWY vaccine , DTaP or Tdap vaccines , DTaP-HepB-IPV/Hib vaccine , MMR vaccine , and PCV7 or PCV13 vaccines . SupplemThe median sample size of the 50 studies comparing co-administration with separate administration of the same vaccines was 726 (interquartile range (IQR) 328-1199). Forty-five (90%) of these studies were randomized clinical trials with a sample size between 64 and 2648 children. One case-control study included 590 children. One prospective observational study had a study size of 530 children and one retrospective observational study included 36,844 children. One study used surveillance data covering 128,197 vaccinations and one study used case reports from 883 children. Only healthy children were enrolled in 37 (74%) studies and 20 studies (40%) excluded children with known allergies or hypersensitivity to vaccines or vaccine components. In 37 (74%) studies, the safety data relied on parental self-reporting of AEFI.Thirteen (26%) studies comparing co-administered vaccines with the same vaccines administered separately found statistically significant safety differences. Of these, eight studies 16%) reported significantly more and five studies 10%) reported significantly fewer AEFI in the respective co-administration groups. Of the eight studies identifying significantly more AEFI, two found significant increases in pyrexia: One when co-administering PCV13 + IIV3 and one when co-administering DTaP-HepB-IPV/Hib + PCV7 compared to separate administration of these vaccines ,10. One % reporte% reporteOf the five studies identifying significantly fewer AEFI, one study reported significantly less diarrhea and pyrexia following co-administration of DTaP-IPV + RV5 . One stuThirty-three (66%) of studies comparing co-administered vaccines versus the same vaccines administered separately reported safety differences without providing a statistical assessment: In 29 (58%) of these studies increased AEFI were found in the co-administration groups and in 17 (34%) of these studies decreased AEFI were found in the co-administration groups.Risk of AEFI and differences between groups were statistically evaluated and reported in studies comparing co-administration with separate administration of the same vaccines by assessing confidence intervals (48%), p-values (28%), risk differences (10%), relative risks (4%), Fisher test (2%), adjusted relative risk (aRR) (2%), IR (1%), or odds ratios (2%). Seventeen (34%) studies reported no statistical assessment. Of those, two studies (4%) listed observed AEFI without reporting absolute numbers or percentages.The evidence about the safety of co-administered vaccines compared to separately administered vaccines is mainly based on clinical trials that were primarily designed to evaluate efficacy rather than safety differences. The safety of co-administering vaccines was assessed in 185 studies over the last 20 years. Of these, only 50 directly compared the safety of co-administration with separate administration of the same vaccines. Most occurred in Europe and the USA, reflecting the regions where the most clinical trials take place and wherFor the majority of co-administered vaccines, only one study directly assessing the safety of vaccine co-administration versus separate administration was available. Co-administrations of MenACWY + Tdap ,12,13,23We only found statistically significant differences between co-administration and separate administration for some AEFI, and for a limited number of vaccine co-administrations. Furthermore, multiple studies on the same co-administered vaccines did not confirm each other\u2019s findings, as indicated in For the co-administered vaccines where only one study could be retrieved, almost three times more cases of injection site tenderness and almost four times more headaches were reported following co-administration of Td + MMR + HepB , more thSome studies found fewer AEFI after co-administration compared to separate administration: Half the cases of diarrhea and half the cases of pyrexia following co-administration of DTaP-IPV + RV5 , less inDespite the few studies on the same co-administered vaccines, it is remarkable that none of the reported increased adverse events following co-administration were contradicted by another study that would report a significant decrease following the same co-administration, and vice versa. In general, the studies indicate differences in less severe AEFI. Therefore, these insights might not influence immunization practices that much but can be meaningful to correctly inform patients and parents.The lack of repeated studies for the majority of vaccine co-administrations and the absence of confirmatory findings of significant results indicate a scarcity of strong evidence about the safety of co-administration versus separate administration. This lack of evidence can be partly explained by the inability to demonstrate statistically significant safety differences. Two-thirds of studies reported differences in safety between vaccine co-administration and separate administration but these were not significant or a statistical assessment was missing. Typically, safety was briefly described and one-third of studies lacked any statistical assessment of AEFI. Most of the studies were randomized clinical trials (RCTs) mainly designed to demonstrate efficacy, with sample sizes that were too small for assessing particularly rare and very rare adverse events with sufficient statistical power . This maOur findings indicate that dedicated studies on vaccine co-administration with a larger sample size are required to obtain statistical evidence on a potential increase or decrease of adverse events following co-administration. Particularly for co-administered vaccines for which an increased or decreased risk compared to separate administration was observed, confirmatory studies specifically designed to assess the safety of co-administration would be useful. Such studies should aim at assessing AEFIs with sufficient statistical power and would benefit from standardized data collection of AEFIs and established methodologies for the assessment of adverse events following vaccine co-administration compared to separate administration.Evidence about no increased risk of adverse events when co-administering vaccines compared to separate vaccine administration is indispensable to improve immunization rates. Opposition to vaccination and under-vaccination are crucial threats to herd immunity , which c"} +{"text": "Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant\u2019s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis. RNA-triggered gene silencing is a highly conserved mechanism in eukaryotes. The key feature of RNA silencing is the production of 21\u201325 nucleotides (nt) long small RNAs (sRNAs) downregutrans-acting siRNAs (ta-siRNAs), involved in endogenous gene regulation. Resistance against DNA viruses and regulation of transposons/or repetitive elements are conferred by 24-nt siRNAs produced by DCL3, whereas DCL2 produces 22-nt siRNAs and coordinates with DCL4 in conferring antiviral response. DCL1 is involved in the production of endogenous sRNAs, called miRNA duplex, in the nucleus . AGO 2/3/7 interact with vsiRNAs, miRNAs, and most importantly tasiRNAs and are involved in plant defense and morphogenesis. AGO 4/6/8/9 proteins bind to 24-nt siRNAs and other endogenous siRNAs and recruit DNA methyltransferase DRM2 to effect RNA-dependent DNA methylation (RdDM) (The trigger for RNA silencing is either double stranded RNA (dsRNA) or hairpin RNA (hpRNA) or fold-back structures formed by ssRNAs derived from the pathogens. These RNA structures are recognized by the plant host-derived ribonucleases, Dicer-like (DCL) enzymes, which cleave the dsRNA into siRNA duplexes . The Ara nucleus . The resn (RdDM) . The RISn (RdDM) and in tRDR1 and RDR6 contribute to the accumulation of vsiRNAs in the infected cells , jasmonic acid (JA), ethylene, and nitric oxide, suggestive of its role in systemic acquired resistance (RDR1 expression in tobacco resulted in systemic spread of potato virus X (PVX) , whereas vsiRNAs associated with RDR6 were mapped to the 3\u2032-ends in rdr1 mutant plants and appears to be RDR6-dependent also play major roles by producing secondary siRNAs . The RDRed cells ; RDR2 antructure ; RDR6 prate RNAs . RDR1 hasistance . Downreg X (PVX) . RDR1 faependent . The rolependent . Thus, p\u2217) via precursor miRNA (pre-miRNA) intermediate. The mature miRNA duplex is exported from nucleus to cytoplasm via HASTY-1 (HST-1) by the activity of plant RNA polymerase II. The coordinated activity of plant-derived enzymes such as DCL1, DAWDLE, HYPONASTIC LEAVES-1 (HYL1), SERRATE (SE) processes pri-miRNA into mature miRNA duplex (miRNA:miRNA (HST-1) . Either equences . Thus, mIt is increasingly evident that sRNAs, comprising mainly of siRNAs and miRNAs, at the virus\u2013plant interface are the major determinants of an outcome of disease reaction Figure . AdditioArabidopsis thaliana infected with tobacco mosaic virus\u2013Cg (TMV-Cg) divulged multiple host genes as potential targets for the vsiRNAs. However, TMV-Cg-derived siRNA-mediated cleavage sites were detected only for two target genes, namely, cleavage and polyadenylation specificity factor (CPSF30), and a protein similar to translocon-associated protein alpha using RLM-RACE involved in chlorophyll biosynthesis resulting in yellow symptoms. Corroboratively, expression of RNA silencing constructs targeting Y sat RNA also caused yellowing symptoms. Moreover, incorporation of RNA silencing gene constructs with the chll sequence of Arabidopsis and tomato manifested typical yellow mosaic symptoms in an otherwise non-responsive host. Thus, this study demonstrated the role of sub-viral agent and associated vsiRNAs in inducing characteristic symptoms in the natural host model. It was known that yellow mosaic symptom appears when CMV-Y sat infects ral host . Furthercumented . CMV-2b-rocesses .N. benthamiana model. Among the differentially expressed genes, 11 (nine of them were chloroplastic genes) were found to be involved in inducing chlorosis. Also, the eukaryotic translation initiation factor 4A (NbeIf4A) was downregulated resulting in leaf twisting and stunting symptoms associated in RSV infection. Interestingly, vsiRNA-4A derived from RSV showed sequence complementarity with NbeIf4A mRNA, and artificial miRNA expression of these vsiRNAs demonstrated silencing of NbeIf4A gene in susceptible tomato cultivars. However, this sequence complementarity is lacking in the resistant plants due to the 14 nt deletion in the host genome. The viral siRNAs derived from the IR have the ability to silence the SILNR1 in susceptible cultivars actuating the stunting and curling leaf traits. Further, SILNR1 overexpressing lines showed reduced accumulation of TYLCV suggestive of the negative crosstalk between the vsiRNAs and the lncRNAs , causing characteristic symptoms and suppressing the host defense network infecting N. benthamiana neither elicit the host DCL induction nor the RDR6 activity to mount antiviral defense; however, PLPV vsiRNAs, representing the entire genome of the virus, are abundant in the non-symptomatic plants. Despite the abundance of vsiRNAs, accumulation of the host mRNAs is not affected. Infection caused alterations in host miRNA concentrations; nonetheless, it is not correlated with any phenotypic abnormalities. Hence, it is pertinent to investigate other host factors that remain uncharacterized yet but could be associated with viral pathogenesis and symptom appearance to nucleotide binding site\u2013leucine-rich repeats (NBS-LRR) involved in host defense pathways has the ability to overcome the vsiRNA-mediated targeting of NBS-LRR class R-genes. The wide range of host mRNA targets indicate that vsiRNAs are not mere pathogenicity factors but also are the determinants of the outcome of host\u2013virus interaction (Laodelphax striatellus) were investigated to gain insights about the regulatory roles of vsiRNAs in different hosts. Among the downregulated genes of RSV-infected rice, 70% of the genes had potential vsiRNA target sites, and these genes were found to be enriched in carbohydrate binding and kinase activity. Similarly, 47.5% of downregulated genes in RSV-infected plant hoppers were potential targets for vsiRNAs and were involved in activities such as cuticle formation, peptidase, and oxido-reductase. vsiRNA profiles of the same virus instigate different molecular responses depending on the host system reflecting diverse biological requirements -derived siRNAs from infected tomato identified that 2,450 unique vsiRNAs have potential to interact with tomato transcriptome. It is noteworthy that tomato cultivars exhibited differential molecular response to the TSWV-derived vsiRNAs that potentially targeted the host mRNAs. Tomato cultivar (Red Defender) containing the virus resistance-conferring loci involved in callose deposition in pollen mother cell walls and during pathogen infection from the virulence modulating genomic region of PSTVd specifically targets multiple callose synthase genes of the host involved in host defense process were identified. Transient expression of all the three vd-siRNAs using a VIGS model based on osa-MIR528 backbone mimicked viroid infection phenotypes (Understanding the interaction between enotypes .MYB TF caused enhanced (>threefold) CLCuD viral DNA accumulation (vsiRNAs from the antisense strand of sugarcane mosaic virus (SCMV) exhibited multiple target sites in the maize transcriptome compared to the siRNAs from the sense strand denoting the strand-specific role of vsiRNAs in host gene regulatory pathways. Furthermore, a broad range of host transcriptome targets involving various pathways such as gene regulation, energy metabolism, cellular defense, and plant signaling underlines the predominance of vsiRNAs in enhancing the virulence of pathogen . Cotton mulation . Though mulation . Thus, tN. benthamiana plants co-infected with a polerovirus, brassica yellows virus (BrYV), and an umbravirus, pea enation mosaic virus 2 (PEMV 2), showed differences in their target pathways enhancing the synergistic infection and virulence and SCMV in maize revealed possible roles of vsiRNAs in synergistic infection . In SCMVirulence . Similarirulence . Chineseirulence . It estairulence .HDA6) led to the postulate that favorable transcriptional changes are induced in the viroid infected cells so as to recognize the pathogenic RNA as an RNA pol II template so that viroid replication is enhanced (Viroid genomic RNAs are lncRNAs that subenhanced . Infectienhanced . Additiopulus L. . Computapulus L. . Five ges (PARE) . These gFRL3 mRNA by PARE sequencing and RLM-RACE techniques. Thus, it provided the direct evidence for the role of a vd-siRNA in modulating the expression of host-mRNA wherein, vd-siRNA not only downregulated FRL3 mRNA but also induced early flowering in tomato was shown to enter plant nuclei and viral genome-derived miRNA (hcrsv-miR-H1-5p) was identified to be involved in the regulation of viral replication play main role in growth and development of organisms. Animal-infecting DNA viruses encode miRNAs that modulate the expression of host genes and to regulate self gene expression . miRNAs V genome . TuMV-desic acid . Similarlication . In anotredicted .Computational analysis of SCSMV also revealed the hairpin-RNA structured miRNA precursor in its genome. The predicted miRNA precursor, pre-miR-16, was present in the 3\u2032UTR region of the viral genome and its expression was demonstrated. Furthermore, the reduced chlorophyll and carotenoids content in SCSMV-infected leaves was co-related with the virus-derived miRNA-mediated silencing of plastidial isoprenoid biosynthesis pathway . RecentlThese studies thus unravel hitherto an unknown mode of counter-defense strategy employed by the plant-infecting viruses. Plant virus-derived miRNAs is a rarity when compared to miRNAs of animal viruses . VirusesGeminiviridae) infecting Cassava and Jatropha revealed nine pre-miRNAs from the genomes of African cassava mosaic virus (ACMV) and five pre-miRNAs from East African cassava mosaic virus- Uganda (EACMV-UG). In addition, DNA A-derived ORFs AC1, AC2, AC4, and IR regions of the begomoviruses exhibited miRNA-coding potential. Viral -derived miRNAs were also validated through stem-loop RT-PCR are considered to be of recent origin and exhibit wide nucleotide sequence diversity across the virus species. VSRs interfere in all the crucial steps of RNA silencing right from the recognition of viral RNA , dsRNA d genomes . Thus, Vin vivo conditions is the prevalence of VSRs. Many VSRs possess sRNA sequestration capability so that it bind siRNA duplexes or miRNA:miRNA\u2217 thereby limiting the active pool of siRNAs in effecting trans-silencing of host transcripts efficiently affects host miRNA and siRNA pathways. Correspondingly, sub-cellular localization of a 126-kDa replicase protein of severe and mild isolates of pepper mild mottle virus (PMMoV) has been attributed with differential symptoms expression in N. benthamiana. Although, the authors reasoned that interaction of 126 kDa protein with unknown host factors for differences in the intensity of symptoms, differential impact of the proteins on the PMMoV-derived siRNAs cannot be ruled out. Moreover, suppressors enhance the virulence of viral pathogens by aiding in the accumulation of viral nucleic acids. Nonetheless, as already stated, viral genomic RNA titers do not always correlate with the symptom severity even in the presence of a strong or a weak suppressor protein in the susceptible cultivar whereas manifestation of resistance trait of a tomato cultivar is due to the deletion of vsiRNA target site in SILNR1 thereby affecting the callose deposition in pollen mother cells disrupting not only the reproductive pathways of hosts but also augmenting the entry point of secondary pathogens -derived sRNAs selectively target immunity-conferring genes of hosts, Arabidopsis and tomato technique revealed that long dsRNAs are precursors of vsiRNAs . MoreoveFeatures like 5\u2032terminus nucleotide of siRNA also play important role in the efficacy of RNA silencing activity of vsiRNA. AGO 1 preferentially incorporates siRNAs with nucleotide \u201cU\u201d at 5\u2032 terminus. Furthermore, recruitment of vsiRNAs onto AGO and RISC lacking proper \u2018slicer\u2019 activity also diminishes the cleavage potential of the sRNAs. Above all, the degree of vsiRNA activity against the host transcripts is also influenced by its relative abundance . DiffereEnormous quantum of data is being generated concerning the nature of vsiRNAs and vd-siRNAs encompassing wide variety of plant and pathogen species. It is also possible for vsiRNAs to act on host chromosome in TGS manner involving RNA directed DNA methylation. However, little research evidences are available to prove this probability, even though sequence-specific epigenetic modification of viral genomic regions mediated by siRNAs is common . DevelopFunctional miRNAs derived from viral genomes are generally identified in DNA viruses not in RSVR, SY, PG, SC, SW, and HRP performed the data mining and drafted the various sections of the manuscript. All the authors have read and approved the final version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Primary central nervous system lymphomas (PCNSLs) are extranodal variant forms of non-Hodgkin lymphoma arising within the brain parenchyma, leptomeninges, or spinal cord. PCNSL can present with varied neurological symptoms and imaging findings, making diagnosis without biopsy difficult. PCNSLs are highly aggressive, causing rapid deterioration, but are responsive to chemotherapy and radiotherapy making early diagnosis important.Crossed cerebellar diaschisis (CCD) is mostly seen with cerebral cortex vascular insults and is rarely reported with thalamic lesions and even rarer with thalamic lymphoma. However, CCD has also been described in other brain tumors (including primary glioma), chronic subdural hematoma, congenital insults, intracranial infections, and various dementia subtypes.We present a rare case of thalamic lymphoma evaluated with positron emission tomography/computed tomography that showed hypermetabolism of thalamus and associated hypometabolism in ipsilateral cerebral cortex and contralateral cerebellum representing CCD. Primary central nervous system lymphoma (PCNSL) is a rare neoplasm, accounting for 0.5 to 2% of all primary brain tumors and 1 to 3% of all non-Hodgkin lymphoma, with approximately 95% of PCNSLs being diffuse large B cell lymphomas (DLBCLs). PCNSL is a \u201cwhole-brain disease\u201d from a pathological point of view, with involvement of the brain, eye, leptomeninges, and rarely spinal cord with subacute presentation in form of typical symptoms as cognitive decline or personality changes without evidence of systemic involvement.The PCNSL is a vasocentric neoplasm with an infiltrative tumor extending beyond the primary lesion, with multifocality in more than 50% cases. Focal neurological deficits with involvement of the parenchyma or leptomeninges needing rapid imaging are seen in approximately 70% of the patients.A 65-year-old male presented with a history of lethargy, memory loss, and hemiparesis of right lower limb. Gadolinium-enhanced T1-weighted magnetic resonance axial and cori67 stain (D) and absent expression of CD3 (C) and CD10. The phenotype in combination with morphology was supportive of a diagnosis of DLBCL type of PCNSL.Biopsy showed diffuse proliferation of medium-to-large lymphoid cells (18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) and fused18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) axial axial andC a) axial andC s) axial andC a18F-FDG-PET has an important role in PCNSL staging at diagnosis or in the follow-up, as it can diagnose systemic disease with higher sensitivity than conventional imaging.The PCNSLs are commonly seen with a median age of 60 year in immune-competent patients and at a younger age in immune-compromised patients.CCD is defined as decreased neuronal activity by focal structural lesions or disturbance remotely from the structures likely due to interruption of afferent and efferent pathways. CCD is a well-recognized phenomenon after cerebral infarction and reported contralateral to the focal supratentorial lesion likely due to disruption of the cortico-ponto-cerebellar tract.Vascular insult of the subcortical structures is rarely reported cause of CCD, as basal ganglia or thalamus is not usually connected to the cortico-ponto-cerebellar tract and the remote effect is usually not observed. Deep-seated thalamic infarcts have been reported to cause CCD due to their direct effect on cerebellar efferent pathways or indirect effect from the affected cerebral cortex.Basal ganglia hematoma has been seen to cause CCD directly due to interruption of inhibitory GABAergic axons to globus pallidus and to thalamus through cerebellar efferent pathways resulting in reduced regional cerebral blood flow in cerebellumSimilar mass effect resulting in CCD has also been described in other brain tumors (including primary glioma), chronic subdural hematoma, congenital insults, intracranial infections, and various dementia subtypes.This case is a rare demonstration of PCNS thalamic lymphoma with ipsilateral cerebral hypoperfusion and contralateral CCD likely due to the compression effect of posterior limb of internal capsule and interruption of cortico-ponto-cerebellar tract.18F-FDG PET plays an important role in diagnosis of patients who cannot undergo brain biopsy due to surgical risks, older age, or comorbidities, with PET/magnetic resonance imaging having good accuracy for the assessment of inoperable PCNSL.The"} +{"text": "Cardiac rehabilitation (CR) is an evidence-based intervention that improves event-free survival in patients with cardiac conditions, yet <27% of all eligible patients use CR in the United States. CR is traditionally delivered in clinic-based settings where implementation barriers abound. Innovative nontraditional program designs and strategies are needed to support widespread CR uptake.This study aimed to demonstrate how user-centered design (UCD) and implementation science (IS) principles and methods can be integrated into the early-stage development of nontraditional CR interventions.As part of a NewYork-Presbyterian Hospital (NYPH) quality improvement initiative (March 2020-February 2022), we combined UCD and IS principles and methods to design a novel home- and clinic-based telehealth-enhanced hybrid CR (THCR) program. We co-designed this program with multilevel stakeholders using an iterative 3-step UCD process to identify user and contextual barriers and facilitators to CR uptake , design an intervention prototype that targets contextual and user factors and emulates the evidence-based practice (through design workshops and journey mapping [step 2]), and review and refine the prototype . The UCD process was informed by the Theoretical Domains Framework and Consolidated Framework for Implementation Research.At step 1, we conducted semistructured interviews with 9 provider- and system-level stakeholders at 3 geographically diverse academic medical centers, which revealed behavioral and contextual barriers to uptake; hybrid delivery was a key facilitator. Step 2 involved conducting 20 design workshops and 3 journey-mapping sessions with multidisciplinary NYPH stakeholders where we identified key design elements , yielding an initial THCR prototype that leveraged NYPH\u2019s telehealth infrastructure. At step 3, we conducted usability testing with 2 CR clinicians administering home-based sessions to 3 CR patients , which revealed usability themes and design solutions to be included in the final THCR prototype.Combining UCD and IS methods while engaging multidisciplinary stakeholders in an iterative process yielded a theory-informed THCR program targeting user and contextual barriers to real-world CR implementation. We provide a detailed summary of the process and guidance for incorporating UCD and IS principles and methods into the early-stage development of a nontraditional CR intervention. The feasibility, acceptability, appropriateness, and usability of the final THCR prototype is being evaluated in an ongoing study. Emotion was a key behavioral barrier for clinic-based CR.For clinic-based CR, key contextual barriers , available resources , and compatibility . Key behavioral barriers to home-based CR related to knowledge , beliefs about capabilities , beliefs about consequences , and decision-making .For home-based CR, key contextual barriers to implementation included external policies , leveraging existing CR workflow or electronic health record (EHR) and telemedicine infrastructure and initiatives , and intervention adaptability .Two key clinician stakeholders agreed to complete a series of in-depth interviews to enable us to understand the local context of CR and telehealth at Columbia University Irving Medical Center or NYPH. The barriers and facilitators to clinic- and home-based CR from step 1 were confirmed, with hybrid CR emerging as the ideal model to implement at NYPH . When asked about telehealth and documenting remote visits, both stakeholders mentioned that all video visits and data collection happen in the Epic cloud-based EHR and that the staff are familiar with technology, but learning to adopt a new system may be challenging . Contextual inquiry also revealed that the primary CR patient population in the Washington Heights neighborhood of New York City consists of predominantly Hispanic Spanish-speaking patients with varying levels of socioeconomic status and digital health literacy.Informed by our design concept, 20 design intervention prototype workshops or meetings were conducted to design an initial nontraditional CR prototype that addressed the contextual (informed by the CFIR) and behavioral (informed by the TDF) determinants of CR implementation that emerged in step 1, as well as offered the same core components of traditional CR. Of these 20 sessions, 2 (10%) focused solely on nontraditional CR programming , 7 (35%) focused solely on telehealth , 6 (30%) focused on both nontraditional CR programming and telehealth, and 5 (25%) focused on eliciting feedback from additional stakeholders . A total of 7 follow-up email threads among design team members and additional stakeholders were used to facilitate prototype design between the workshops or meetings.The co-design process revealed that the initial nontraditional CR prototype should include the following key design elements: (1) combination of home- and clinic-based CR sessions , (2) fewer total number of CR sessions , (3) reduction in total duration of direct clinician supervision or monitoring , (4) real-time remote patient monitoring (RPM) of resting and exercise vital signs , (5) comparable home- and clinic-based exercise dose , (6) alignment with existing clinical workflow and telehealth infrastructure , and (7) provision of training for clinicians and patients. Table S3 in Throughout the design process, details of the initial prototype design evolved based on stakeholder feedback, NYPH infrastructure, and ability of the proposed design elements to address user and contextual determinants; for instance, the commencing version of the initial prototype leveraged Epic Systems\u2019 MyChart Video Visits, which aligned with existing clinical workflow and infrastructure but required patients to (1) have their own electronic device, (2) have access to Wi-Fi, and (3) independently log in to their Epic portal. Specifically, MyChart Video Visits did not support interoperability between commercial patient monitoring devices and the EHR, hindering the ability to provide real-time RPM during home-based sessions. Accordingly, we leveraged the expertise from our digital health team members and decided to partner with NYPH\u2019s investment in Philips Healthcare\u2019s RPM platform, which included (1) freely available RPM devices that wirelessly transmit BP and HR data to a web-based tracking database during CR sessions or exercise, (2) real-time integration of HR and BP data into the EHR (eCC interfaces with Epic), and (3) telemonitoring-enabled CR support via 2-way video calls. Moreover, to address key determinants highlighted by stakeholders in step 1 , this platform was chosen to ensure that patients had access to reimbursable resources (vs out-of-pocket expenses) that support both cellular and Wi-Fi connectivity (vs requiring Wi-Fi access or a cellular data plan).Ultimately, this process yielded an initial THCR prototype to offer 24 CR sessions, each lasting 60 minutes , over 12 weeks. The prototype combined home-based CR with NYPH\u2019s existing clinic-based CR , EHR , and telemonitoring infrastructure. Home-based exercise equipment included a stationary cycle-ergometer for aerobic exercise and ankle and wrist weights for strength training. Education and counseling about exercise, nutrition, psychosocial support, and risk factor management aligned with NYPH\u2019s existing clinic-based CR programming, which included one-on-one counseling with CR clinicians during sessions and self-administered educational videos between sessions. The home-based CR protocol and telehealth monitoring platform from this initial prototype were user tested in step 3.We conducted 8 usability sessions (multiple sessions per patient) to simultaneously troubleshoot the patient and clinician experiences when using the eCC platform, RPM devices, and home-based exercise equipment, as well as patient-clinician communication during the sessions. As the end users engaged in >1 session throughout the program , multiple usability sessions were conducted per patient . At least 1 clinician participated in each usability testing session. All sessions were conducted in English and aligned with real-world clinical workflow . The NYPH design team completed intermittent design team workshops (n=24) and journey mapping sessions (n=3) to refine elements of the protocol and create a final prototype.codes) for different prototype intervention components and technology disruptions (Wi-Fi/\u200bBluetooth connectivity), whereas themes for exercise were related to comfort with ability to perform or use exercise modality or equipment (capability/comfort and safety) and flexibility with exercise experience (adaptations/flexibility). CR clinician\u2013level themes for the eCC platform were ease of using the telehealth platform to remotely monitor patients (visibility and navigation), technology disruptions (Wi-Fi/\u200bBluetooth connectivity), and confidence in using the telehealth platform to safely monitor patients (confidence in technology and safety concerns). Each of these themes aligned with key usability constructs and principles identify user and contextual factors of CR implementation; (2) engage key stakeholders within a health care system to co-design a prototype that targets relevant implementation determinants while retaining core components of the evidence-based practice; and (3) address real-world usability concerns based on clinician and patient experiences. The CFIR and TDF helped to focus the identification of contextual- (outer setting and inner setting) and user-level (motivation and capability) implementation determinants, respectively, for general clinic- and home-based CR (step 1). Design team workshops and journey mapping enhanced our ability to design the initial prototype (step 2) and refine the nontraditional CR model based on usability themes that emerged from each patient- and clinician-facing experience during usability testing (step 3). Collectively, this iterative multilevel stakeholder\u2013focused process yielded a theory-informed 12-week THCR program prototype. The final program prototype has been implemented at NYPH, where we are examining the program\u2019s potential to optimize end-user experiences and implementation potential in a real-world hospital setting serving racially, ethnically, and socioeconomically diverse populations.This is the first study to apply 2 complementary IS frameworks to examine stakeholder perspectives on behavioral and contextual determinants of both home- and clinic-based CR implementation, an essential first step to help inform the iterative co-design process. Although ample pre\u2013COVID-19 pandemic research exists on clinic-based CR determinants , our theEngaging multilevel stakeholders in the design process ensured that the final prototype embodied design elements responsive to patient-, provider-, and system-level perspectives and experiences; for instance, the reimbursement of home-based CR has been documented as a persistent structural barrier in the literature and was nontraditional CR model. Although scientific calls have been made to use novel approaches to address the research-practice gap in CR [A unique contribution of this study is the combination of theory-informed IS frameworks and usability testing methods to examine patient- and clinician-level experiences with an innovative ap in CR , and comap in CR ,26, few ap in CR performeap in CR engaged ap in CR . Two othap in CR or self-ap in CR . Althougap in CR because By contrast, Funahashi et al applied This study has several strengths. First, this study expands the literature on the use of theory-informed implementation frameworks to characterize multilevel determinants of CR implementation to inform intervention development. Moreover, we provide an applied example of using the CFIR and TDF as complements to each other in the context of CR. The use of these frameworks provides a foundation to develop future multilevel implementation strategies. Second, this is among the first studies to combine both UCD and IS methods at the early stages of nontraditional CR development . Third aAdditional research is needed to understand the optimal design by which a nontraditional CR model can improve multilevel CR implementation, patient and provider experiences, and clinical outcomes in racial and ethnic and socioeconomically diverse settings, with the goal to mitigate inequities that exist in access to CR. Accordingly, future research should consider equity recommendations at the early stages of intervention development, as well as consider costs to implement and sustain the program in real-world settings . MoreoveThis paper provides an applied example for integrating UCD and IS principles into the early-stage development of a THCR model while aligning with the behavioral and contextual factors of a real-world clinical setting. We found that IS frameworks can help to identify user and contextual factors of CR implementation; design team workshops and journey mapping can engage key stakeholders within a health care system to co-design a prototype that targets relevant implementation determinants while retaining core components of the evidence-based practice; and patient- and clinician-level usability testing can unveil real-world usability concerns to be addressed when refining the prototype. This process may serve as a useful model for future CR clinics that aim to design and implement a nontraditional CR program for their specific organizational or health care infrastructure and patient population."} +{"text": "VHL) tumor suppressor gene activates hypoxia inducible factor (HIF) and vascular endothelial growth factor (VEGF) pathways. The first-line TKIs that predominantly target VEGF receptor (VEGFR) and platelet-derived growth factor receptor (PDGFR) have been clinically used since late 2000s, and the second-line TKIs such as cabozantinib, which targets more receptor tyrosine kinases including MET and TAM kinases as well as VEGFR, have been further applied to the treatment of advanced RCC since early 2010s in which the first-line TKIs are ineffective. The mTOR (mechanistic target of rapamycin) protein kinase pathway is also a crucial axis involved in the pathogenesis of RCC including both ccRCC and non-ccRCC, the latter mainly consists of papillary and chromophobe types of RCC, and mTOR inhibitors everolimus and temsirolimus are applied to the treatment of non-ccRCC [Renal cell carcinoma (RCC) is a major adult kidney cancer, which is often incidentally discovered as an asymptomatic disease on imaging in the developed countries . RCC hason-ccRCC . While tin vivo tumor formation of sunitinib-resistant RCC cells in mice, suggesting the TKI-facilitating effects of DPP4i in RCC pathophysiology.While several molecular mechanisms underlying TKI resistance have been characterized, the oncogenic roles of proinflammatory cytokines interleukin-6 (IL6) and IL8 are of particular interest as prognostic factors, particularly in ccRCC . The sec"} +{"text": "Histone deacetylase (HDAC) inhibitors have enormous therapeutic potential as effective epigenetic regulators, and now with the focus on the selective HDAC6 inhibitor in ongoing clinical trials, more advantages over other non-selective pan-HDAC inhibitors are foreseeable. As it is of paramount importance to understand the complex regulatory web of mutual interactions involving epigenetic machinery and non-coding genome in regulating gene expression, herein, we investigated the intriguing interactions between HDAC6-induced lncRNA (LINC00152) and its possible sponge miRNA (hsa-miR-499a-5p) in multiple myeloma.The online version contains supplementary material available at 10.1186/s12920-023-01724-3. The intriguing interactions between the non-coding genome and the epigenetic machinery that regulate gene expression have preoccupied researchers over the past decades. Certainly, the question of how organisms/cells have adapted to these multiple regulatory mechanisms continues to resurface. Despite the fact that the functional existence of microRNAs relies exclusively on miRNA-mRNA interactions, another obvious concern is why the crosstalk of lncRNAs and microRNAs is so pivotal and what is the rationale behind the involvement of epigenetic enzymes in this complexity. With recent advances, it is undeniable that a deregulated noncoding genome poses a critical factor in diseases , particuSince it is of utmost importance to understand the complex regulatory web of these mutual interactions, Wu and colleagues presented some interesting results on this concept using glioblastoma model . The autUndeniably, HDAC6 as a selective inhibitor has more advantages over other non-selective pan-HDAC inhibitors . While tBelow is the link to the electronic supplementary material.Supplementary Material 1Supplementary Material 2Supplementary Material 3"} +{"text": "Figure 12 as published.In the published article, there was an error in the legend for . The corrected legend appears below.\u201cColocalization of MBP-EP-CBS cargos and pGFP-CaM during comparison of the internalization of the five MBP-EP-CBS cargos at two concentrations. Simultaneous internalization of the five 550-labeled MBP-EP-CBS cargos with equimolar pGFPCaM at complex concentrations of (A) 1000 nM or (B) 200 nM. Equimolar adaptor/cargo complexes were internalized in growth media containing NucBlue and imaged with the complex present between 40\u201360 min.\u201dThe authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated."} +{"text": "Machine learning (ML) approaches are a promising venue for identifying vocal markers of neuropsychiatric disorders, such as schizophrenia. While recent studies have shown that voice-based ML models can reliably predict diagnosis and clinical symptoms of schizophrenia, it is unclear to what extent such ML markers generalize to new speech samples collected using a different task or in a different language: the assessment of generalization performance is however crucial for testing their clinical applicability.In this research, we systematically assessed the generalizability of ML models across contexts and languages relying on a large cross-linguistic dataset of audio recordings of patients with schizophrenia and controls.We trained ML models of vocal markers of schizophrenia on a large cross-linguistic dataset of audio recordings of 231 patients with schizophrenia and 238 matched controls . We developed a rigorous pipeline to minimize overfitting, including cross-validated training set and Mixture of Experts (MoE) models. We tested the generalizability of the ML models on: (i) different participants, speaking the same language (hold-out test set); (ii) different participants, speaking a different language. Finally, we compared the predictive performance of: (i) models trained on a single language (ii) MoE models, i.e., ensemble of models (experts) trained on a single language whose predictions are combined using a weighted sum (iii) multi-language models trained on multiple languages .Model performance was comparable to state-of-the art findings (F1: 70%-80%) when trained and tested on participants speaking the same language (out-of-sample performance). Crucially, however, the ML models did not generalize well - showing a substantial decrease of performance (close to chance) - when trained in a language and tested on new languages . MoE and multi-language models showed a better increase of performance (F1: 55%-60%), but still far from those requested for achieving clinical applicability.Our results show that the cross-linguistic generalizability of ML models of vocal markers of schizophrenia is very limited. This is an issue if our first goal is to translate these vocal markers into effective clinical applications. We argue that more emphasis needs to be placed on collecting large open datasets to test the generalizability of voice-based ML models, for example, across different speech tasks or across the heterogeneous clinical profiles that characterize schizophrenia spectrum disorder.None Declared"} +{"text": "Correction : Orphanet Journal of Rare Diseases (2023) 18:177 10.1186/s13023-023-02780-9Following publication of the original article [1], we have been notified that the sentence on equal contribution of the first authors was missed. It should be as follows:Ali Zare Dehanavi and Maryam Bemanalizadeh have contributed equally to this work."} +{"text": "This study analyzed KISS1 and its receptor KISSR for peptide sharing with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It was found that SARS-CoV-2 shares numerous minimal immune pentapeptide determinants with KISSR only. The peptide sharing has a high immunologic potential since almost all the common peptides are present in 101 SARS-CoV-2-derived immunoreactive epitopes. Data are in favor of configuring molecular mimicry as an epigenetic factor that can alter KISSR thus causing the hypogonadotropic hypogonadism syndrome with which altered KISSR associates. The human kisspeptin protein (here referred to as KISS1) and the human kisspeptin receptor protein (here referred to as KISSR) form the hypothalamic system that regulates the gonadotropic axis at puberty and in adulthood.Recently, clinical reportsBased on these observations, the present study posed a question: could SARS-CoV-2 infection/vaccination play a causal role via molecular mimicry and cross-reactivity in the diseases canonically ascribed to potential genetic variants of KISS1 and KISSR?www.uniprot.org/www.iedb.org/)Consequently, molecular mimicry analyses were performed as follows. The amino acid (aa) sequences of KISS1 and KISSR were retrieved fromThe results of the molecular mimicry analyses are reported inThen, the peptide commonality between SARS-CoV-2 and KISSR finds a logical scientific explanation in the close phenetic relationship between viruses and the origin of the eukaryotic cell. In fact, according to the endosymbiotic theory,A second noteworthy point of the present study is the high immunological potential of peptide sharing. Indeed, exploration of IEDB revealed that all shared pentapeptides but one recur in 101 experimentally validated immunoreactive SARS-CoV-2-derived epitopes . That iStarting from 2000,In essence, this study scientifically explains the clinical reports"} +{"text": "Nature Nanotechnology (2023)10.1038/s41565-023-01446-82 can memorize the reconfigurable photoresponse weight and perform the calculation using the electricity generates in situ. Furthermore, scaling the neuromorphic hardware to larger dimensions is conceptually feasible due to the simple device structure and provides various training possibilities for neuromorphic vision applications. Further work on ionic-optical-electronic coupled device can be applied in other semiconducting materials to develop neuromorphic photonic chips.The real-time image processing proliferation places specific information computing and energy conservation demands on sensor-rich platforms. Fabrication of reconfigurable image sensors allowing for in-sensory computing usually requires a sophisticated architecture of multiple layers integration. A team of researchers from the State Key Laboratory of Infrared Physics at Shanghai Institute of Technical Physics, Chinese Academy of Sciences in China and from Department of Electrical and Systems Engineering at University of Pennsylvania in United States, has found a very promising approach that integrating sensing, memory, and computing within a simple two-terminal metal/semiconductor/metal architecture. Such neuromorphic photovoltaic detectors driven by S vacancy migration in 2D MoS"} +{"text": "This study aimed to decrease unnecessary long-term antimicrobial use in primary care by identifying and highlighting patients with long-term or repeated exposure to antibiotics to GP teams for review. The broad spectrum antimicrobial co-amoxiclav was targeted following data showing rising DDD per prescription in our Health Board.Community antibiotic prescribing from the national Prescribing Information System (PIS) was searched for NHS Lothian (126 GP practices) using DDD to identify patients. Long courses of co-amoxiclav were defined as \u226563 DDD. Ninety-eight patients were identified with high antimicrobial usage and a data collection form was sent to the Primary Care Pharmacy teams to voluntarily collate data for each patient.Clostridioides difficile. Forty-one patients had multiple courses of co-amoxiclav and 39 patients were prescribed co-amoxiclav as prophylaxis; of these 59% were for urinary tract infection (UTI). Thirty-four of 94 patients (36%) had been on prophylaxis for over 5 years with 9 patients on co-amoxiclav for over 20 years. Of note in 39 of 94 patients no microbiology samples were available and where samples were available (n=55), narrower spectrum options were available in 38 patients (69%) and 17 patients (31%) had samples showing resistance to co-amoxiclav. Following this intervention to highlight use, the number of patients on long-term courses or prophylaxis with co-amoxiclav reduced by 70% in the following year.The data collection form had a 97% response rate. Of the 94 patients with full data 62 (66%) patients had co-amoxiclav initiated due to secondary care specialist advice and 26 (28%) had been initiated by primary care. Forty-four patients (47%) were aged 65 or over, putting them at high risk of Patients on long-term antibiotics are priorities for antimicrobial stewardship interventions. This work demonstrated that ongoing appropriateness and efficacy of long-term antibiotic courses were not routinely reviewed. Using pharmacy data proved an effective method to highlight patients and ultimately reduce patient antibiotic exposure. UTI prophylaxis was the majority patient group in this study and interventions to review and decrease long-term UTI prophylaxis in our Board using this method are underway."} +{"text": "Streptococcus (GAS) is a leading human pathogen for which there is no licensed vaccine. Infections are most common in young children and the elderly suggesting immunity accumulates with exposure until immune senescence in older age. Though protection has been postulated to be strain type specific, based on the M-protein (emm-type), the antigenic basis of population-level immunity remains poorly understood. Naturally acquired GAS antibody responses were investigated using intravenous immunoglobulin (IVIG), which contains pooled immunoglobulins from thousands of healthy human donors, as a surrogate for population immunity. Functional opsonophagocytic killing assays were conducted with GAS strains (n = 6) representing the three major emm-pattern types . While IVIG induced opsonophagocytic killing of all GAS strains tested, specificity assays showed the profile of protective antibodies differed considerably between emm-types. Antibodies targeting the M-protein were a major component of the functional IVIG antibody response for emm12 and emm53 strains but not for emm75 strains. The striking differences in the contribution of M-protein specific antibodies to killing suggest naturally acquired immunity differs between strains from the major emm-patterns. This challenges the dogma that M-protein is the primary protective antigen across all GAS straintypes.Group A Streptococcus (GAS) is a globally important pathogen. With the surge of invasive GAS infections that have occurred in multiple countries, contemporaneous with the relaxation of COVID-19 pandemic restrictions, there is increased interest in the mechanisms underpinning GAS immunity. We utilized intravenous immunoglobulin (IVIG), pooled immunoglobulins from thousands of healthy donors, as a surrogate for population-level immunity to GAS, and explored the contribution of strain-specific (M-type specific) antibodies to GAS immunity using functional killing assays. This revealed striking differences between major strain types as to the contribution of strain specific antibodies to killing. For GAS strains belonging to the E pattern group, M-type specific antibodies do not mediate killing and immunity, which contrasts with strains belonging to pattern A\u2013C and D groups. This challenges the historical dogma, originally proposed by Rebecca Lancefield in the 1950\u20131960s, that the M-protein is the major protective antigen across all GAS strain types.Group A Streptococcus pyogenes (group A Streptococcus [GAS]) is associated with a significant global burden of disease, across a diverse spectrum of clinical syndromes ranging from pharyngitis and impetigo to severe invasive infections and serious post-infectious sequelae such as acute rheumatic fever . Functional, emm-type-specific antibodies (where function is defined as the induction of phagocytosis) have been detected in humans decades after infection of the protein is the basis of strain typing and included two clinical isolates for each (Table S1). The presence of emm-type-specific antibodies in IVIG was confirmed using ELISA to 50-mer peptides derived from the HVR as well as the matched full-length recombinant M-proteins following published protocols (To explore the contribution of (OPKAs) (Supplem (OPKAs) . IVIG isimmunity . The preimmunity . We inverotocols ; Fig. S2rotocols . Complete (100%) inhibition of killing was achieved for emm12 and emm53 when rabbit sera were pre-adsorbed with homologous M-protein and very little or no inhibition was observed with heterologous M-protein pre-absorption and emm53 (79.5%) when IVIG was pre-adsorbed with homologous M-proteins, and little or no inhibition was observed with heterologous M-protein pre-adsorption and showed markedly reduced binding of matched anti-M-protein sera to emm75 compared with emm12 and emm53 (emm75 strains in contrast to strains from the other major emm-pattern types examined (A\u2013C and D). The antigenic basis of emm75 killing remains to be determined, but the recently developed emm75 human challenge model provides a novel means for further investigation (The absence of functional, strains , 11. Flond emm53 . This sutigation .emm75 E pattern strains in this study challenges the dogma that M-protein is the major protective antigen across all GAS strain types. This study was limited by the number of strains investigated. The findings may not be reflective of all pattern E strains, but the findings nevertheless suggest that naturally acquired, protective antibodies found in IVIG target alternative antigens on some GAS strains. This does not preclude the possibility that future vaccines, based on either type-specific or conserved vaccine antigens, will be broadly protective across the spectrum of GAS strains. There are likely to be significant differences between infection- and vaccine-acquired immunity, as has been shown for other vaccine preventable diseases, including S. pneumoniae(The lack of M-protein mediated killing of the neumoniae. Overall"} +{"text": "Heterologous priming with the inactivated SARS-CoV-2 vaccine (CoronaVac) and boosting with mRNA-based COVID-19 vaccine (Moderna or Pfizer) is currently recommended in Indonesia. The reactogenicity data of these heterologous vaccine regimens are not entirely available, particularly in young adults. The present study, therefore, aimed to evaluate the solicited local and systemic reactions in the first seven days post-vaccination either with Moderna or Pfizer vaccine among previous recipients of two doses of CoronaVac.An electronic-based cross-sectional study was conducted among medical students at the Pelita Harapan University, Banten, Indonesia, who received mRNA-based COVID-19 vaccine following two doses of CoronaVac. Samples were collected using a cluster sampling technique. Comparison between groups was performed by Fisher\u2019s exact test.A total of 72 participants, 23 (32%) of which received the Moderna vaccine and 49 (68%) received the Pfizer vaccine, were included in this study. The median age of participants was 21 (IQR 19-22) years old. The most common local and systemic events for mRNA-based COVID-19 vaccines were injection site pain, fever, headache, fatigue, myalgia, and arthralgia. Solicited local and systemic reactions were reported more frequently in Moderna recipients than Pfizer recipients. Most local and systemic reactions were graded as mild to moderate and did not lead to hospitalization.The reactogenicity of the heterologous prime-boost with CoronaVac and mRNA-based COVID-19 vaccine booster among young adults is reassuring, and no unexpected concerns were identified. In Indonesia, the inactivated SARS-CoV-2 vaccine was [P1]the first vaccine made available and has been widely administered since January 2021. Although the immunogenicity of two doses of CoronaVac vaccine has been shown by a previous study . However, the increased reactogenicity was [P2]frequently reported in heterologous vaccine regimens and was more common in younger age groups .[P3] Continued monitoring of reactogenicity after heterologous booster administration in young participants may provide valuable information for the health care practitioner and the public about expected local and systemic reactions following the current available heterologous vaccine regimens.The heterologous COVID-19 vaccine booster has been implemented for the general population in Indonesia since January 2022 to overcome the potential of waning immunity. Heterologous booster with mRNA-based COVID-19 vaccine (Moderna and Pfizer) has been recommended for fully vaccinated individuals with CoronaVac due to its capacity to elicit a robust humoral and cellular immune response and provide immunity against SARS-CoV-2 variants . Written informed consent was obtained from all participants prior to data collection. A total of 72 participants who received two doses of the inactivated COVID-19 vaccine (CoronaVac) were included in this study. Approximately after 6 months, all the fully vaccinated participants received the third dose of the COVID-19 vaccine either with Moderna (mRNA-1273) or Pfizer (BNT162b2).Safety assessment included monitoring the solicited local and systemic adverse reactions reported by the participants within seven days following the third vaccination. Baseline data on demographics and safety assessment were collected by electronic questionnaire. Perceived severity was evaluated using a modified 4-point Food and Drug Administration Toxicity Grading Scale.[P5] The severity of the adverse reactions was classified into four categories [P6].The median age of participants was 21 years , and 71% of which were females. The majority of participants had no underlying diseases . Of the 72 study participants, 23 (32%) individuals previously vaccinated with the CoronaVac series received heterologous regimens with Moderna, whereas 49 (68%) fully vaccinated individuals acquired Pfizer booster. Detailed characteristic of participants is provided in Panel A shows the percentage of Moderna (n = 23) and Pfizer (n = 49) booster recipients that reported any solicited local and systemic reactions in the first seven days after vaccination. Panel B shows the percentage of participants with local adverse reactions , and panel C shows the percentage of participants with systemic adverse reactions after booster vaccination. Local and systemic adverse reactions were graded into four categories . Comparison between groups is performed by Fisher\u2019s exact test.Figure 1B). As shown in Figure 1C, a higher percentage of systemic adverse reactions were reported from Moderna recipients than from Pfizer recipients. Further analysis revealed there was a statistically significant association between solicited adverse reactions with vaccine type (p<0.05). Most of the systemic reactions were mild to moderate and did not lead to hospitalization.The most common local adverse reaction was pain at the injection site by 17 (74%) of 23 for Moderna and 24 (49%) of 49 for Pfizer. Tenderness at the injection site was also frequently reported in 15 (65%) of 23 Moderna recipients and 25 (51%) of 49 Pfizer recipients. Most local reactions were graded as mild or moderate. A small number of participants had severe local reactions and its more commonly found in participants who received the Moderna vaccine . The higher reactogenicity was found in Moderna booster recipients than in those who received the Pfizer vaccine. The findings of this study are in line with the findings reported in the COV-BOOST study, in which greater reactogenicity was identified in Moderna booster recipients than in Pfizer recipients .In the current study, heterologous vaccine regimens with CoronaVac and mRNA-based COVID-19 vaccine were found to be well-tolerated among young individuals (19 to 22 years of age). There were no participants who reported grade 4 local and systemic reactions that required hospitalization or medical attention. The most frequently reported solicited local and systemic reactions in the first seven days after mRNA-based COVID-19 vaccination was pain at the injection site, fever, fatigue, headache, myalgia, and arthralgia. This result was generally consistent with previous studies of mRNA-based COVID-19 vaccine safety (Polack Although the local and systemic reactions of the COVID-19 vaccine were common among the young age group, our study showed that the administration of mRNA-based COVID-19 vaccine in young adults vaccinated with CoronaVac was well-tolerated. Identifying expected local and systemic reactions after mRNA-based COVID-19 vaccination was important to alleviate the participants\u2019 anxiety regarding the vaccination experience and increase the acceptance of the current heterologous COVID-19 vaccine regimens.The authors have declared that no competing interest exists.COVID-19:Coronavirus Disease 2019.,mRNA:Messenger RNA.,SARS-CoV-2:Severe Acute Respiratory Syndrome Coronavirus 2."} +{"text": "Heart transplant recipients undergo extensive invasive and non-invasive postoperative screening to exclude complications, such as allograft rejection and vasculopathy. Cardiac magnetic resonance imaging is a non-invasive, non-irradiating, diagnostic tool for monitoring graft health and identifying possible tissue rejection or myocardial fibrosis. We describe the case of a 29-year-old female heart transplant recipient admitted to our care center with a worsening clinical condition. The patient underwent clinical evaluation, blood tests, including troponin I and N-terminal pro brain type natriuretic peptide, transthoracic echocardiography, invasive coronary angiography, and cardiovascular magnetic resonance imaging. Cardiovascular magnetic resonance imaging showed widespread sub-epicardial hyperintensity of the myocardial segments along the course of the coronary arteries. T2 mapping sequences showed an elevated value and the myocardial native T1 values and extracellular volume percentage were significantly increased. Late gadolinium enhancement demonstrated a diffuse sub-epicardial hypersignal along the lateral, free, and left ventricular walls. All the sequences evidenced widespread hyper-enhancement of epicardial fat along the course of the thickened main coronary artery walls. One month later, the recipient underwent re-transplantation due to progressive worsening of the clinical condition and refractoriness to intravenous medication. The anatomopathological findings of the explanted heart provided impressive visualization of structural and histopathological changes. These results could guide the tailoring of preventive therapeutic strategies and non-invasive monitoring of cardiac grafts. Cardiac transplantation remains the most effective treatment for end-stage heart failure with excellent short- and long-term survival rates . CardiacA 29-year-old female heart transplant recipient presented to our care center with a generalized poor health condition. The patient was affected by congenitally corrected transposition of the great arteries with a subpulmonary interventricular defect and right ventricular hypoplasia. In 1998 at the age of twelve the patient underwent Glenn atrial switch procedure. In September 2015, heart transplantation was performed for severe heart failure refractory to therapy and episodes of paroxysmal supraventricular tachycardia that required frequent hospitalization. Due to residual claudication caused by severely impaired lower limb muscles, the patient was unable to undergo a stress test during periodical follow-up or during hospitalization. Upon admission to our care center, the patient appeared pale and complained of dizziness and fatigue. The patient's blood pressure was 123/70\u2005mmHg with a heart rate of 105\u2005beats/min. The 12-lead electrocardiogram (ECG) showed sinus tachycardia, first degree atrioventricular block, right bundle branch block, and diffuse non-specific abnormalities of ventricular repolarization. Transthoracic echocardiography revealed a slightly reduced left ventricular ejection fraction (46%). Laboratory findings showed a normal cardiac troponin I level (5.4\u2005pg/ml) and an elevated terminal pro brain type natriuretic peptide level (353\u2005pg/ml). Invasive coronary angiography showed severe stenosis at the distal portion of the circumflex coronary artery and diffuse sclerosis of the left anterior descending coronary artery. Intravascular ultrasonography showed a Stanford scale IV score . ConsequCMR imaging-based myocardial tissue characterization with T1 and T2 mapping has emerged as a non-invasive and highly sensitive method of detecting cardiac allograft rejection, with numerous studies demonstrating good correlation between CMR-based mapping and histopathology-determined rejection . CMR imaTo our knowledge, this is the first report on the CMRI findings in allograft failure and its relation to histopathological specimens. This concept could raise the possibility of tailoring preventative therapies."} +{"text": "Supported by spatially resolved tissue analysis of established glycolytic biomarkers, this study provides the rationale for multicenter trials of tumor metabolic imaging as an auxiliary tool to support PCa treatment decision-making.While radical prostatectomy remains the mainstay of prostate cancer (PCa) treatment, 20 to 40% of patients develop postsurgical biochemical recurrence (BCR). A particularly challenging clinical cohort includes patients with intermediate-risk disease whose risk stratification would benefit from advanced approaches that complement standard-of-care diagnostic tools. Here, we show that imaging tumor lactate using hyperpolarized BCR pretabolism \u20137. Whiletergrade and intrtergrade tumor di13C-MRI prior to RP (Top). Preoperatively, all patients had intermediate risk of BCR development according to the European Association of Urology and D\u2019Amico risk groups (Top). The same was true for the matched secondary cohort of 14 PCa patients who were followed up for a minimum of 6 y after RP with a total of 41 tumor cores sampled for the spatial metabolomics analysis (Bottom). Two patients in each cohort developed BCR at 16 and 22 mo (HP-13C-MRI cohort), as well as 11 and 18 mo after surgery, respectively. In both cohorts, one BCR-positive patient had pT3a disease, and both BCR-positive patients had positive surgical margins; importantly, these two adverse histopathological characteristics were also noted in some BCR-negative patients ratio , an enzy4) ratio , an inde4) ratio and tisslabeling . Importalabeling .13C-MRI) novel clinical metabolic imaging tools in intermediate-risk PCa patients to identify men harboring metabolically active lesions at increased risk of surgical failure. In addition to reporting imaging findings, we attempted to mechanistically explain our observations through spatially resolved tissue analysis of established glycolytic biomarkers, corroborated by the direct epithelial lactate readout using spatial metabolomics. Future work will involve multi-institutional validation of our preliminary findings in larger cohorts to prospectively determine the clinical impact of metabolic imaging on PCa care.This prospective study suggests the feasibility of using both invasive (DESI-MSI) and noninvasive and involved presurgical HP-13C-MRI acquisition, biological analysis of surgical samples, and postsurgical follow-up reported in this study. The DESI-MSI analysis was conducted under an Institutional Review Board-approved prospective national study , which involved prospective collection of fresh frozen radical prostatectomy samples from patients who provided written informed consent for their subsequent retrieval and analysis under the study protocol. Detailed imaging and tissue analysis protocols for the HP-13C-MRI cohort are provided in the original cohort description Click here for additional data file."} +{"text": "Escherichia coli. We utilized experimental evolution in E. coli to test the effect of the evolution of phage T7 resistance on populations resistant to excess iron (III) and populations without excess iron resistance. Phage resistance evolved rapidly in both groups. Dual-resistant (iron (III)/phage) populations were compared to their controls (excess iron (III)-resistant, phage-resistant, no resistance to either) for their performance against each stressor, excess iron (III) and phage; and correlated resistances to excess iron (II), gallium (III), silver (I) and conventional antibiotics. Excess iron (III)/phage-resistant populations demonstrated superior 24 h growth compared to all other populations when exposed to increasing concentrations of iron , gallium (III), ampicillin, and tetracycline. No differences in 24 h growth were shown between excess iron (III)/phage-resistant and excess iron (III)-resistant populations in chloramphenicol, sulfonamide, and silver (I). The genomic analysis identified selective sweeps in the iron (III) resistant , phage-resistant and iron (III)/phage resistant populations . E. coli selected for resistance to both excess iron (III) and T7 phage showed some evidence of a synergistic effect on various components of fitness. Dual selection resulted in correlated resistances to ionic metals {iron (II), gallium (III), and silver (I)} and several conventional antibiotics. There is a likelihood that this sort of combination antimicrobial treatment may result in bacterial variants with multiple resistances.The prevalence of multidrug-resistant bacteria and their increased pathogenicity has led to a growing interest in metallic antimicrobial materials and bacteriophages as potential alternatives to conventional antibiotics. This study examines how resistance to excess iron (III) influences the evolution of bacteriophage resistance in the bacterium E. coli could rapidly evolve resistance to gallium (III) nitrate and iron (II) sulfate, which subsequently demonstrated correlated resistance to conventional antibiotics . RN. RNwaaC ner core 49]. An. AnwaaC ic drugs . Other mE. coli rpoS subunit of RNA polymerase was also detected in the phage-resistant population family of ATPases [ClpX is required for adaptation to and extended viability in the stationary phase, as well as growth in SDS [clpX may be common in adaptation to minimal medium is that these mutations were routinely observed in the Lenski LTEE . In addpulation . UxaB is sources .lapC, formerly yejM , is a major variant also found in phage-resistant populations. It encodes an essential inner membrane protein implicated in lipopolysaccharide (LPS) homeostasis. A lapC allele (lapC1163) has been reported to increase outer membrane permeability. Mutations in phage-resistant and iron (III)/phage-resistant populations majorly target the LPS, essential to Escherichia T7 phage infection. Pgi expression has been reported to be induced by oxidative stress as a pgi deletion mutant is hypersensitive to oxidative stress induced by paraquat [E. coli K-12 [yjbEFGH operon produces extracellular polysaccharide [YjbH may be a lipoprotein and/or an outer membrane porin, and the expression has been reported to be higher in rpoS mutants, which was detected in all samples of phage-selected populations both as selective sweep and major variant [rcsA is a positive DNA-binding transcriptional regulator that belongs to the LuxR/UhpA family of transcriptional regulators. Its detection in the phage-resistant population might be responsible for some of the success of this population in antibiotics. Members show moderately increased resistance to kanamycin and 2-fold increased \u03b2-lactam resistance via increased ampC expression [A mutation in paraquat . Pgi beloli K-12 . The yjbccharide ,56. YjbH variant . A rcsA pression .E. coli K-12 MG1655 can rapidly evolve in succession resistance to excess iron (III) followed by that to bacteriophage. In addition, this selection regime subsequently enhanced the resistance of the bacteria to conventional antibiotics and metallic antimicrobial materials. These previous substantiated studies in this bacterium show the pleiotropic impacts of genomic variants associated with excess iron resistance. We did not, however, show the repetition of specific mutations in the ompC gene encoding an outer membrane protein C. Thus, this experiment showed no evidence of dramatic fitness epistasis or a possible tradeoff between excess iron (III) and T7 phage resistance. Furthermore, as the selection in this design was sequential, we do not know whether trade-offs between excess iron (III) and phage T7 might not evolve in a simultaneous selection design. In summary, more studies are needed to determine if a combination therapy of metal and phage will be effective in preventing the evolution of resistance.These studies have shown that"} +{"text": "Tumor-associated carbonic anhydrases IX (CAIX) and XII (CAXII) have long been in the spotlight as potential new targets for anti-cancer therapy. Recently, CAIX/CAXII specific inhibitor SLC-0111 has passed clinical phase I study and showed differential response among patients with colorectal cancer (CRC). CRC can be classified into four different consensus molecular subgroups (CMS) showing unique expression patterns and molecular traits. We questioned whether there is a CMS-related CAIX/CAXII expression pattern in CRC predicting response. As such, we analyzed transcriptomic data of tumor samples for CA9/CA12 expression using Cancertool. Protein expression pattern was examined in preclinical models comprising cell lines, spheroids and xenograft tumors representing the CMS groups. Impact of CAIX/CAXII knockdown and SLC-0111 treatment was investigated in 2D and 3D cell culture. The transcriptomic data revealed a characteristic CMS-related CA9/CA12 expression pattern with pronounced co-expression of both CAs as a typical feature of CMS3 tumors. Protein expression in spheroid- and xenograft tumor tissue clearly differed, ranging from close to none (CMS1) to strong CAIX/CAXII co-expression in CMS3 models . Accordingly, response to SLC-0111 analyzed in the spheroid model ranged from no (CMS1) to clear (CMS3), with moderate in CMS2 and mixed in CMS4. Furthermore, SLC-0111 positively affected impact of single and combined chemotherapeutic treatment of CMS3 spheroids. In addition, combined CAIX/CAXII knockdown and more effective treatment with SLC-0111 reduced clonogenic survival of CMS3 modelling single cells. In conclusion, the preclinical data support the clinical approach of targeted CAIX/CAXII inhibition by showing linkage of expression with response and suggest that patients with CMS3-classified tumors would most benefit from such treatment. The mean values and the SD of all measured IC50 values were then calculated for each spheroid model. For the co-treatment trials, IC50 values in both the control and the inhibitor group were calculated via equation: [inhibitor] vs. normalized response - variable slope. The IC50 values of both groups (Gaussian distribution assumed) were then compared using a Welch test or an unpaired t-test, depending if the variances were significantly different or not. Additionally, the relative viability of the spheroids in the control and inhibitor groups were compared at two different chemotherapeutic concentrations. The concentration was chosen closest to the peak plasma concentration of the respective agent in vivo and the second concentration was chosen at 10% of the first concentration . The relative spheroid viability was compared using a Welch test or an unpaired t-test, as described above. For the combination treatment, the control groups and their respective inhibitor groups were compared to each other using traditional one-way ANOVA .Statistical analysis was carried out using GraphPad Prism 8. The used This section is not mandatory but can be added to the manuscript if the discussion is unusually long or complex."} +{"text": "We present the case of a 75-year-old female in which a pulmonary tumor embolism was detected incidentally on a prostate-specific membrane antigen positron emission tomography-computed tomography restaging scan. This occurred on the background of renal cell carcinoma in remission with pazopanib systemic therapy and a right nephrectomy 4 years prior. An avidity to prostate-specific membrane antigen in the superior lingula of the left upper lobe of the lung coupled with contrast-enhanced computed tomography findings found the lesion to be a tumor thrombus. This case serves to highlight the effectiveness of incorporating contrast-enhanced computed tomography with prostate-specific membrane antigen positron emission tomography and to consider the rare diagnosis of a pulmonary tumor embolism. The development of novel second-generation radiotracers targeting prostate-specific membrane antigens (PSMA) has led to increased diagnostic and staging capacity in both prostatic and non-prostatic cancers. An emerging gold standard is 2-(3-{1-carboxy-5-[(6-18F-fluoro-pyridine -3-carbonyl)-amino]-pentyl}-ureido)-pentanedioic acid (18F-DCFPyL), and when used in combination with positron emission tomography-computed tomography (PET/CT) hybrid imaging, it bestows the clinician tremendous diagnostic ability A 75-year-old female presented with recent onset dyspnea and left-sided chest pain. Her history included a right nephrectomy for clear renal cell carcinoma which had renal vein involvement (pT3N0) 4 years earlier. Previous staging imaging had demonstrated thoracic mediastinal nodal metastases and she was subsequently treated with pazopanib systemic therapy (tyrosine kinase inhibitor). She had a complete radiological response based on serial contrast-enhanced CT and 18F-DCFPyL PET imaging and the patient had then been off treatment given remission. Given her new onset of symptoms, restaging combined hybrid contrast-enhanced CT and 18F-DCFPyL PSMA PET was performed. Hybrid imaging demonstrated focal abnormal PSMA tracer expression in the superior lingula segment of the left upper lobe of the lung. This was confirmed on high-resolution fused PET/CT images to be within an eccentric filling defect in the lingula segmental pulmonary artery . Given tRenal cell carcinoma (RCC) is the most common cancer of the kidney and accounts for roughly 2% of global cancer diagnoses Prostate-specific membrane antigen is a transmembrane glycoprotein that is classically overexpressed in cancerous prostate cells In this case report, the patient displayed pulmonary PSMA-avidity on PET/CT. Naturally, with PSMA-avidity at the lungs on staging PET/CT, one may be inclined to presume pulmonary metastases, especially if nodular in appearance and numerous. However, given the exhaustive list of pathology that expresses PSMA, this presumption cannot be made necessarily. Inflammatory and infectious lung conditions can display PSMA-avidity and thereby mimic potential pulmonary metastases . Autopsy studies revealed its presence in 3%-26% among patients with solid tumors RCC is a malignancy associated with tumor thrombus formation where 4-10% of patients possess a degree of tumor extension into the renal vein or inferior vena cava [9]Two other case reports were found describing PTE secondary to RCC. Manley et\u00a0al. To our knowledge, this is the first case report of a PTE secondary to RCC detected by PSMA-PET/CT. It underscores the importance of high-quality novel PSMA radiotracers and the clinical utility of CECT in hybrid imaging for detecting incidental findings. But most importantly, it alerts even the most senior clinicians to judiciously assess CECT and consider the possibility of PTEs in the context of pulmonary PSMA-avidity for RCC patients, especially if they are dyspneic.The development of novel PSMA-targeting agents in PET/CT has empowered imaging specialists and oncologists with profound diagnostic capability, but in doing so, it opens the doors to a multitude of previously unconsidered diagnoses. As demonstrated in this case, the finding of PSMA-avidity in the lungs is not limited to only parenchymal metastases. It highlights that if there is pulmonary PSMA-avidity on PET, especially in a patient with known RCC and dyspnea, it should prompt the clinician to evaluate the CECT to assess for nonmetastatic findings, including but not limited to PTE.Written, informed consent was obtained from the patient under the knowledge that their case would be described in this publication."} +{"text": "Correction: Antimicrobial Resistance & Infection Control (2022) 11:152 10.1186/s13756-022-01165-0Following publication of the original article, the ESCMID Study Group for Nosocomial Infections (ESGNI) was mistakenly added as a separate author, whereas all authors were acting on behalf of the study group. The author list has been updated in this correction article and the original article has been"} +{"text": "The curative potential of allogeneic hematopoietic stem cell transplant for hematologic malignancies and nonmalignant conditions was first explored during the 1950s . In contThe review conducted from the American University of Beirut Medical Center examined innovative strategies for preventing and managing relapse following allo-HCT in patients with ALL. The group showed that the use of maintenance tyrosine kinase inhibitors (TKIs) after allo-HCT in patients with Philadelphia chromosome (Ph+) ALL in first complete remission (CR1) prolongs survival and reduces the risk of relapse, as recommended by the consensus statement from the European Society for Blood and Marrow Transplantation (EBMT). While donor lymphocyte infusion (DLI) has a limited remission rate of no more than 15% in patients with B-cell ALL (B-ALL), prophylactic or pre-emptive DLI may play a role in preventing leukemia relapse, involving multiple escalated doses guided by the occurrence of GVHD. Although CAR-T therapy for B-ALL achieves an early CR rate of nearly 70-80%, more than half of the patients progress within 1 year. Novel sequencing of CAR-T and allo-HCT to reduce relapse rates are being explored. In this regard, a large CIBMTR analysis showed that consolidation allo-HCT after CAR-T results in significant reduction in leukemia relapse with a trend towards better leukemia-free survival (LFS) in 62 patients with R/R B-ALL . In a stA systematic review and meta-analysis demonstrated the efficacy and safety of vedolizumab, a monoclonal antibody that impedes the interaction between \u03b14\u03b27 integrins on T-lymphocytes and MAdCAM1 on gut endothelial cells, for the treatment and prevention of gastrointestinal acute GVHD (GI-aGVHD). The study found that patients receiving vedolizumab for treatment exhibited a higher response rate and lower incidence of adverse events during the early stages of GI-aGVHD.Besides preemptive and maintenance treatment following allo-HCT, optimizing donor selection in a risk-adapted manner can also mitigate the relapse risk. Two large CIBMTR analyses demonstrated a noteworthy decrease in relapse rates among adult patients with B-ALL and AML who underwent allo-HCT with younger matched unrelated donors (MUD), as opposed to older matched sibling donors , 10. TheThis Research Topic offers a valuable forum for advancing novel approaches and mechanisms to address relapse following allo-HCT.YS and LH: study concept, design, and drafted the manuscript. MBA provided expert input. All authors contributed to the article and approved the submitted version."} +{"text": "Panels A and B, asterisks). Computed tomography angiography revealed a localized cross-sectional luminal narrowing in the abdominal aorta (Panel C and arrow in Panel D), compared to the lumen of the more proximal descending aorta (Panel C and arrowhead in Panel E). A bypass graft to the iliac artery and numerous collateral arteries were also visualized. Although his symptoms were improved after the placement of transanal ileus tube, he died of sepsis due to gastrointestinal and urinary tract infection on Day 20 after admission. Autopsy revealed the severe narrowing of the abdominal aortic lumen at the level of superior mesenteric artery (SMA) (Panel F). Histological examination demonstrated marked fibrous thickening of the aortic intima resulting in the abdominal aortic stenosis and occlusion of SMA . The cross-sectional area luminal narrowing of the most stenotic abdominal aorta was calculated as 94.8% (Panel H). Middle aortic syndrome (MAS) is a rare vascular disease characterized by the hypoplasia or coarctation of distal descending thoracic aorta and/or abdominal aorta. Although typical symptoms of MAS include severe hypertension, headache associated with high blood pressure, bilateral lower-limb claudication, and renal failure, megacolon as a main symptom of MAS is extremely rare. Clinicians should recognize MAS as a possible cause of megacolon.A 72-year-old man, who had a history of treatment-resistant hypertension due to aortic stenosis and underwent subclavian-iliac bypass surgery 20 years before, visited the emergency department due to abdominal pain and distention. Abdominal X-ray and sagittal computed tomography showed prominent dilatation of the ascending colon (Panels A and B): (Panel A) Abdominal X-ray and (Panel B) computed tomography showing megacolon. (Panels C\u2013E) Computed tomography angiography showing a localized luminal narrowing in the abdominal aorta. (Panels F\u2013H) (Panel F) Macroscopic and (Panels G and H) microscopic images showing a severe stenosis in the abdominal aorta and a total occlusion of the superior mesenteric artery.X-ray, computed tomography, and pathology in a case of middle aortic syndrome presenting with megacolon. ("} +{"text": "Febrile neutropenia (FN) is associated with a high risk for infections in patients receiving chemotherapy. Mortality estimates in pediatric patients with FN range from 0.4-3%. Extended infusion (EI) of beta-lactam antibiotics leads to improved pharmacodynamic parameters and is associated with enhanced antimicrobial activity. A recent study demonstrated significantly better overall treatment response in adult patients with documented infections and high-risk FN who received EI vs. standard infusion (SI) piperacillin-tazobactam. There are currently no studies evaluating clinical outcomes of EI beta-lactam use in pediatric patients with FN.This study was a single-center retrospective cohort study with a time frame between September 2016-September 2022. The primary objective was to assess the time to fever resolution in patients with FN who received EI vs. SI of beta-lactam antibiotics. Secondary objectives included the difference in 30-day mortality and hospital length of stay (LOS) between the EI and SI groups. This study included patients admitted to pediatric hematology, oncology, or BMT services at Michigan Medicine who were (1) diagnosed with FN during hospital admission or admitted for FN following chemotherapy and (2) treated with EI or SI cefepime, piperacillin-tazobactam, or meropenem for at least 48 hours.A total of 87 patients were included in the study analysis (40 in the EI group and 47 in the SI group). Baseline characteristics were similar between the groups. There was no significant difference in the time to fever resolution for the cohort . There were numeric non-significant differences favoring EI for 30-day mortality , and avoiding need to escalate antibiotic therapy due to treatment failure .The small sample size limited the ability to detect differences in time to fever resolution between EI and SI beta-lactams. Although not statistically significant, secondary endpoints showed numerically lower mortality and lower rates of therapy escalation in the EI group.Madeleine King, PharmD, BCOP, Elsevier, Inc: Board Member"} +{"text": "Affective episodes often emerge in adolescence and young adulthood. Identification of factors subjectively associated with their onset may improve aetiological models and targeted intervention.To examine precipitating conditions of (hypo-)manic and depressive episodes in adolescents and young adults from the general population.A random sample of 14-21 year-olds was drawn from the population registry of Dresden, Germany, and N=1180 were assessed in 2015/2016 (response rate: 21.7%). Lifetime depressive and (hypo-)manic symptoms as well as full-threshold depressive and (hypo-)manic episodes (DSM-5) were identified using standardized interview. Participants reporting depressive or (hypo-)manic symptoms were asked whether and which events or conditions they associate with episode onset. Besides responses on a list providing potential triggering conditions a free answer was possible. Qualitative content analysis preceded quantitative logistic regression analyses (significance level p<.05). Considered categories were: negative life events , events requiring adaptation, positive life events, internal factors, and other factors.and at least one reported precipitating condition, multiple regression models including all condition categories showed that in particular internal factors, interpersonal problems and other factors were associated with the occurrence of a full-threshold depressive episode (n=199) and positive life events as well as internal factors were associated with the occurrence of a full-threshold (hypo-)manic episode (n=21).The vast majority of participants reporting depressive (n=682) respectively (hypo-)manic (n=200) symptoms also reported a precipitating condition . There was no significant association between any triggering condition and the occurrence of a full-threshold depressive (n=206) or (hypo-)manic (n=25) episode. However, the number of reported categories of precipitating conditions was associated with full-threshold depressive and (hypo-)manic episodes. Among those with depressive or (hypo-)manic symptoms Adolescents and young adults from the general population usually associate the onset of phases with affective symptoms with precipitating conditions but these do not necessarily signal the emergence of a diagnostically relevant episode. Nevertheless, a greater number of and the presence of particular precipitating conditions may indicate the emergence of full-blown depressive or (hypo-)manic episodes. Thus, asking for subjective triggers appears relevant and may guide early identification and intervention.None Declared"} +{"text": "Scientific Data 10.1038/s41597-023-02040-2, published online 20 March 2023Correction to: In this article funding from preproposal phase of the Einstein Center Climate Change and Climate Change Center Berlin Brandenburg for Nikola Milojevic-Dupont was omitted. Also, funding from CircEUlar project of the European Union\u2019s Horizon Europe research and innovation program under grant agreement 101056810 for Florian Nachtigall was omitted. The original article has been corrected."} +{"text": "Cardiac surgery-associated acute kidney injury (CSA-AKI) is frequent. While two network meta-analyses assessed the impact of pharmacological interventions to prevent CSA-AKI, none focused on non-pharmacological interventions. We aim to assess the effectiveness of non-pharmacological interventions to reduce the incidence of CSA-AKI.We searched PubMed, Embase, Central and clinical trial registries from January 1, 2004 (first consensus definition of AKI) to July 1, 2023. Additionally, we conducted manual screening of abstracts of major anesthesia and intensive care conferences over the last 5 years and reference lists of relevant studies. We selected all randomized controlled trials (RCTs) assessing a non-pharmacological intervention to reduce the incidence of CSA-AKI, without language restriction. We excluded RCTs of heart transplantation or involving a pediatric population. The primary outcome variable was CSA-AKI. Two reviewers independently identified trials, extracted data and assessed risk of bias. Random-effects meta-analyses were conducted to calculate risk ratios (RRs) with 95% confidence intervals (CIs). We used the Grading of Recommendations Assessment, Development, and Evaluation to assess the quality of evidence.I2\u2009=\u20090%; Phet\u2009=\u20090.44) and remote ischemic preconditioning . Pulsatile flow during cardiopulmonary bypass was associated with a significant reduction in CSA-AKI incidence but with very low quality of evidence . We found high quality of evidence for lack of effect of restrictive transfusion strategy and tight glycemic control .We included 86 trials evaluating 10 non-pharmacological interventions to reduce the incidence of CSA-AKI. No intervention had high-quality evidence to reduce CSA-AKI. Two interventions were associated with a significant reduction in CSA-AKI incidence, with moderate quality of evidence: goal-directed perfusion (RR, 0.55 [95% CI 0.40\u20130.76], Two non-pharmacological interventions are likely to reduce CSA-AKI incidence, with moderate quality of evidence: goal-directed perfusion and remote ischemic preconditioning.The online version contains supplementary material available at 10.1186/s13054-023-04640-1. The development of acute kidney injury (AKI) after cardiac surgery, known as cardiac surgery-associated acute kidney injury (CSA-AKI), is frequent. The incidence is estimated at 20\u201340% of patients undergoing cardiac surgery, with renal replacement therapy (RRT) required in 1.6\u20135.8% of cases . The occMany mechanisms are involved in the development of CSA-AKI. Cardiac surgery is frequently associated with low systemic output secondary to cardiopulmonary bypass (CPB) , 10 leadMany pharmacological and non-pharmacological interventions have been tested to reducing the incidence of CSA-AKI. However, randomized controlled trials (RCTs) have presented discordant results . SeveralIn this systematic review and meta-analysis, we assessed the effectiveness of non-pharmacological interventions to reduce the incidence of CSA-AKI.This article follows the PRISMA statement . The proWe included only RCTs. There was no restriction on publication status or language, but we selected trials published after 2004, the year of publication of the RIFLE criteria for AKI ). Most trials included patients with an on-pump procedure (n\u2009=\u200974 [86%]) , some concerns for 13 (15%) and low for 47 (55%) had a definition of AKI using a consensus classification: AKIN (n\u2009=\u200923 [27%]), KDIGO (n\u2009=\u200917 [20%]) or RIFLE (n\u2009=\u20096 [7%]). Among trials using consensus classification of AKI, only 25 (54%) were based on both creatinine and urine output assessment. Severity of AKI was reported in 28 (61%) trials including 7842 patients. Among them, 2283 (29%) developed AKI: 64% of patients (n\u2009=\u20091467) had mild AKI (stage 1 or Risk), 23% (n\u2009=\u2009520) had moderate AKI (stage 2 or injury) and 13% (n\u2009=\u2009293) had severe AKI (stage 3 or failure). The other definitions of AKI included elevated creatinine level (n\u2009=\u200925 [29%]) or the use of RRT (n\u2009=\u20093 [4%]). Twelve trials (14%) did not state how CSA-AKI was defined patients developed CSA-AKI. Half of the trials , RIPc and pulsatile flow during CPB Fig.\u00a0.Fig. 2FoWe included 2 trials (601 patients), both at low risk of bias. The definition of AKI was KDIGO for one trial and AKIN for the other. In both trials, the GDP strategy was to maintain oxygen delivery (DO2) above a minimal target (280 or 300 mL/min/m2) during CPB.I2\u2009=\u20090%; Phet\u2009=\u20090.44) . Heterogeneity was low , 6 (19%) high risk of bias and 5 (16%) some concerns. The definition of AKI was a consensus classification in 24 trials (77%) .RIPc was evaluated in 31 RCTs (7738 patients). Most trials were at low risk of bias , with slight heterogeneity for only one trial; 6 trials used elevated creatinine level; and 3 did not report the definition of AKI. Pulsatile flow during CPB was associated with a significant reduction in incidence of CSA-AKI , with heterogeneity and 1.51 (0.16\u201314.27), respectively. However, the interaction test was not statistically significant as in the subgroup analyses by risk of bias and definition of CSA-AKI . were included, most at some concerns regarding risk of bias. AKI was defined with the AKIN classification in 5 trials and RIFLE in 1 trial. MECC was not associated with a significant reduction in CSA-AKI incidence as compared with standard CPB , with low heterogeneity . Three trials were at low risk of bias and 2 high risk of bias. The definition used for AKI was AKIN, KDIGO or RIFLE for 4 trials. A restrictive transfusion strategy was not associated with a significant reduction in CSA-AKI incidence as compared with a liberal transfusion strategy , and no heterogeneity was detected . Five trials were at low risk of bias. Only one trial used a consensus definition of AKI. Tight glycemic control was not associated with a significant reduction in CSA-AKI incidence as compared with standard glycemic control , with slight heterogeneity , as was MECC . No other intervention was associated with a reduction in stroke incidence , with moderate heterogeneity exhibited high quality of evidence for the lack of benefit on reducing the incidence of CSA-AKI had high quality of evidence for a lack of effect on reducing CSA-AKI incidence. Although we restricted our search to recent trials, the definition of CSA-AKI was heterogeneous across trials with nearly half of the trials using a non-consensus definition of AKI, despite a trend to increased use of a consensus definition of AKI over the years.This is the first meta-analysis synthesizing all non-pharmacological interventions during the peri-operative period to reduce the risk of CSA-AKI. Our search strategy was extensive, without language restriction, thus limiting the risk of missing important trials, with a robust and standardized methodology based on the Cochrane Handbook including the GRADE approach for evaluating the certainty of evidence. The protocol was prospectively registered in PROSPERO. Our meta-analysis brings new insights into the prevention of CSA-AKI, with important implications for clinical practice and future research. We provide a comprehensive summary of non-pharmacological interventions for prevention of CSA-AKI including an evaluation of their level of evidence. While recent meta-analyses focused on specific interventions such as RIPc, pulsatile flow during CPB or GDP, no previous meta-analysis has concentrated on CSA-AKI prevention for the following interventions: red blood cell transfusion strategies, tight glycemic control, minimally invasive extracorporeal circulation, epidural analgesia, KDIGO care, targeting high-arterial pressure or hyperoxia during CPB.In our meta-analysis, GDP was significantly associated with reduced incidence of CSA-AKI. GDP is a recent intervention , derivedRIPc was the most evaluated intervention in our meta-analysis, with more than 30 trials, and was associated with decreased incidence in CSA-AKI. RIPc is a simple, non-invasive and inexpensive strategy. During the last 2 decades, several trials and meta-analyses assessing RIPc in cardiac surgery were published, with discordant results. In 2015, 2 large multicenter RCTs with no benefit in reducing CSA-AKI incidence and with high quality of evidence. However, many trials of cardiac surgery did not consider CSA-AKI among outcomes even though it is one of the most frequent complications after cardiac surgery. Also, when trials did consider the CSA-AKI outcome, the definition of AKI was heterogeneous across trials despite the development and validation of consensus definitions.Additional file 1:\u00a0eTable 1. Changes between the protocol and the article in the Outcome and the Data Analysis. Supplemental eMaterial 1. Search algorithm in PubMed. eTable2. Detailed characteristics of each included trial by intervention. eTable3. Characteristics of chronic kidney disease population for each intervention. eFigure 1. Risk of bias of randomized controlled trials assessing a non-pharmacological intervention to prevent cardiac surgery associated - acute kidney injury. eFigure 2a. Definition of cardiac surgery associated acute kidney injury in all included RCTs according to each intervention. eFigure 2b. Acute kidney injury definition according to the year of publication of the trials. eFigure 3. Meta-analysis of the effect of goal directed perfusion (GDP) on cardiac surgery associated acute kidney injury. eFigure 4. Subgroup analysis of the effect of Remote ischemic preconditioning (RIPc) on cardiac surgery associated acute kidney injury according the Risk of bias. eFigure 5. Subgroup analysis of the effect of Remote ischemic preconditioning (RIPc) on cardiac surgery associated acute kidney injury according the definition of acute kidney injury (AKI). eFigure 6. Subgroup analysis of the effect of Remote ischemic preconditioning (RIPc) on cardiac surgery associated acute kidney injury according the type of surgery. eFigure 7. Funnel plot for random effects meta-analysis of cardiac surgery associated acute kidney injury outcomes in trials of Remote ischemic preconditioning. eFigure 8. Meta-analysis of the effect of pulsatile flow on cardiac surgery associated acute kidney injury. eFigure 9. Subgroup analysis of the effect of pulsatile flow on cardiac surgery associated acute kidney injury according the modality of pulsatility. eFigure 10. Subgroup analysis of the effect of pulsatile flow on cardiac surgery associated acute kidney injury according the definition of acute kidney injury (AKI). eFigure 11. Subgroup analysis of the effect of pulsatile flow on cardiac surgery associated acute kidney injury according the risk of bias. eFigure 12. Funnel plot for random effects meta-analysis of CSA-AKI outcomes in RCTs of Pulsatile flow during CPB. eFigure 13. Meta-analysis of the effect of Minimally invasive extracorporeal circulation (MECC) on cardiac surgery associated acute kidney injury. eFigure 14. Subgroup analysis of the effect of Minimally invasive extracorporeal circulation (MECC) on cardiac surgery associated acute kidney injury according the risk of bias. eFigure 15. Subgroup analysis of the effect of Minimally invasive extracorporeal circulation (MECC) on cardiac surgery associated acute kidney injury according the definition of acute kidney injury (AKI). eFigure 16. Subgroup analysis of the effect of Minimally invasive extracorporeal circulation (MECC) on cardiac surgery associated acute kidney injury according the type of surgery. eFigure 17. Funnel plot for random effects meta-analysis of cardiac surgery associated acute kidney injury outcomes in trials of Minimally invasive extracorporeal circulation (MECC). eFigure 18. Meta-analysis of the effect of restrictive transfusion strategy on cardiac surgery associated acute kidney injury. eFigure 19. Subgroup analysis of the effect of restrictive transfusion strategy on cardiac surgery associated acute kidney injury according the risk of bias. eFigure 20. Subgroup analysis of the effect of restrictive transfusion strategy on cardiac surgery associated acute kidney injury according the definition of acute kidney injury (AKI). eFigure 21. Meta-analysis of the effect of tight glycemic (BG) control on cardiac surgery associated acute kidney injury. eFigure 22. Subgroup analysis of the effect of tight glycemic (BG) control on cardiac surgery associated acute kidney injury according the risk of bias. eFigure 23. Subgroup analysis of the effect of tight glycemic (BG) control on cardiac surgery associated acute kidney injury according the definition of acute kidney injury (AKI). eFigure 24. Funnel plot of tight glycemic control on cardiac surgery associated acute kidney injury. eFigure 25. Meta-analysis of the effect of Epidural analgesia on cardiac surgery associated acute kidney injury. eFigure 26. Subgroup analysis of the effect of Epidural analgesia on cardiac surgery associated acute kidney injury according the risk of bias. eFigure 27. Subgroup analysis of the effect of Epidural analgesia on cardiac surgery associated acute kidney injury according the definition of acute kidney injury (AKI). eFigure 28. Meta-analysis of the effect of KDIGO bundle of care on cardiac surgery associated acute kidney injury. eFigure 29. Subgroup analysis of the effect of KDIGO care on cardiac surgery associated acute kidney injury according the risk of bias. eFigure 30. Meta-analysis of the effect of high-target arterial pressure (MAP) target on cardiac surgery associated acute kidney injury. eFigure 31. Subgroup analysis of the effect of high-target arterial pressure (MAP) target on cardiac surgery associated acute kidney injury according the definition of acute kidney injury (AKI). eFigure 32. Meta-analysis of the effect of hyperoxia on cardiac surgery associated acute kidney injury. eFigure 33. Subgroup analysis of the effect of hyperoxia on cardiac surgery associated acute kidney injury according the risk of bias. eFigure 34. Forest plot of non-pharmacological interventions for efficacy in reducing risk of mortality. Interventions were tested with standard medical care as control. eFigure 35. Forest plot of non-pharmacological interventions for efficacy in reducing risk of RRT. Interventions were tested with standard medical care as control. eFigure 36. Forest plot of non-pharmacological interventions for efficacy in reducing lenght of hospital stay. Interventions were tested with standard medical care as control. eFigure 37. Forest plot of non-pharmacological interventions for efficacy in reducing length of Intensive care unit stay. Interventions were tested with standard medical care as control. eFigure 38. Forest plot of non-pharmacological interventions for efficacy in reducing risk of post-operative stroke. Interventions were tested with standard medical care as control. eFigure 39. Forest plot of non-pharmacological interventions for efficacy in reducing risk of post-operative myocardial infarction. Interventions were tested with standard medical care as control. eFigure 40. Forest plot of non-pharmacological interventions for efficacy in reducing risk of post-operative atrial fibrillation. Interventions were tested with standard medical care as control. eTable 4. Summary of quality of evidence for the effect of each intervention on CSA-AKI according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE)."} +{"text": "Understanding how a virus interacts with cellular targets in an animal model provides critical information in developing therapeutic targets and vaccines for humans. The Syrian hamster model of SARS-CoV-2 infection, the causative agent of COVID-19, is one of the most widely used animal models for this disease. While extensive work on vaccine and therapeutic interventions have been performed in this animal model, the initial viral targets and spread throughout the respiratory tract has been poorly documented. We sought to evaluate the viral spread by microscopic examination of tissues as early as 6 hours post intranasal inoculation through the development of lung lesions at 3 days post inoculation.Coronavirus Infectious Disease 2019 (COVID-19) initiated a global pandemic that thus far has resulted in the death of over 6.5 million people internationally. Understanding the viral tropism during the initial, subclinical phase of infection is critical to develop targeted vaccines and therapeutics. With the continued emergence of variants of concern, particularly those that appear to have a tropism for the upper respiratory tract, understanding the complete pathogenesis is critical to develop more effective interventions. Thus far, the Syrian hamster has served as the most consistent small animal model of SARS-CoV-2 infection for mild to moderate respiratory disease. Herein, we utilize histopathology and immunohistochemistry to characterize the peracute phase of disease initiating at 6-h-post-inoculation in the intranasal inoculation route Syrian hamster model. Inflammation and viral replication initiates in the respiratory epithelium of nasal turbinates as early as 12-h-post-inoculation and moves caudally through the nasal cavity by 36-h-post inoculation. Lower respiratory involvement can be detected as early as 12-h-post inoculation in the intranasal inoculated hamster model. These data highlight the importance of rostral nasal cavity sampling at early timepoints for detection of SARS-CoV-2 in the Syrian hamster model. A severe, contagious, pneumonic disease emerged from Wuhan, China on 19 December 2019. A novel betacoronavirus, SARS-CoV-2, was rapidly recognized as the source of respiratory disease . A humanNonhuman primate models of SARS-CoV-2 infection initiated in the rhesus macaque evaluating two timepoints by necropsy: three- and 21-days post inoculation . This waA well-studied and widely utilized model of respiratory disease in SARS-CoV-2 infection is the Syrian hamster. The Syrian hamster ACE2 receptor naturally supports SARS-CoV-2 interaction and facilitates viral cellular entry . To datead libitum. All infectious work with SARS-CoV-2 was performed in the high biocontainment laboratory of the Integrated Research Facility at the Rocky Mountain Laboratories (RML), Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) in accordance with standard operating procedures approved by the Institutional Biosafety Committee (IBC). Samples were inactivated prior to removal from biocontainment according to validated procedures approved by the IBC [Animals were housed and cared for in accordance with standard operating procedures approved by Rocky Mountain Laboratories Institutional Biosafety Committee, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health. All animal work was approved by the Institutional Animal Care and use Committee and performed in strict accordance with the recommendations described in the guide for the care and use of laboratory animals of the National Institutes of Health, the Office of Animal Welfare, the United States Department of Agriculture in an association for assessment and accreditation of laboratory animal care-accredited facility. Animals were group housed in HEPA-filtered cage systems enriched with nesting material. Commercial food and water were available the IBC .SARS-CoV-2 isolate nCoV-WA1-2020 (MN985325.1) (Vero passage 3) was obtained through CDC and propagated once in Vero E6 cells in DMEM supplemented with 2% fetal bovine serum , 1 mM L-glutamine , 50 U/mL penicillin and 50 \u03bcg/mL streptomycin (Gibco) (virus isolation medium) as previously described . The virMesocricetus auratus) 8-weeks-of-age were utilized in the study. Thirty hamsters were inoculated with 103 TCID50 WA1 isolate of SARS-CoV-2. Six hamsters, evenly distributed between male and female, were euthanized at each of the predetermined times: 6-, 12-, 36-, 48- and 72-h post inoculation (HPI). In addition, 3 hamsters were mock-inoculated with MEM and 6 hamsters were inoculated with 103 TCID50 of gamma irradiated, WA1 SARS-CoV-2. Three gamma-irradiated and three DMEM inoculated hamsters were euthanized at 6 HPI and the remaining 3 gamma-irradiated virus inoculated hamsters were euthanized at 12 HPI. A total inoculum volume of 20 \u00b5L divided equally between each naris was utilized for all inoculations. Hamsters were evaluated daily for signs of clinical disease. Euthanasia was performed by bilateral thoracotomy and exsanguination under deep anesthesia. At the time of euthanasia, a mid-sagittal section of the skull, oral section of trachea and all lung lobes were harvested for histopathologic evaluation. A subsection of nasal turbinates, trachea and caudal lung lobes were collected for molecular evaluation.Thirty-nine Syrian golden hamsters . Embedded tissues were sectioned at 5 \u00b5m and dried overnight at 42 \u00b0C prior to staining. Anti-SARS-CoV-2 N-protein immunoreactivity was detected using U864YFA140-4/CB2093 NP-1 at a 1:1000 dilution. The secondary antibody is the Vector Laboratories ImPress VR anti-rabbit IgG polymer (cat# MP-6401). The tissues were then processed for immunohistochemistry using the Discovery Ultra automated processor with a ChromoMap DAB kit . Histopathology slide readouts and immunohistochemical analysis were performed blindly by a board certified veterinary anatomic pathologist. Representative images of each timepoint were captured.qPCR was performed on RNA extracted from swabs collected immediately prior to euthanasia using QiaAmp Viral RNA mini kit according to the manufacturer\u2019s instructions. Tissues (30 mg or less) were homogenized in RLT buffer and RNA was extracted using the RNeasy kit according to the manufacturer protocol. Viral RNA was detected with a one-step real-time RT-PCR assay using primers and probes generated to amplify the E gene and with custom primers designed against the SARS-CoV-2 E protein as previously described ,17.Clinical signs of disease were not observed during the course of the study. No grossly observable lesions were observed in either the upper or lower respiratory tract at 6-HPI in experimentally inoculated hamsters, gamma-irradiated virus inoculated and mock inoculated negative control hamsters. Early evidence of broncho-interstitial pneumonia was grossly observed as early as 12-HPI and were characterized by well-demarcated, variably sized, red foci disseminated throughout the cranial portions of both left and right lung lobes in experimentally inoculated hamsters. Grossly observable pulmonary changes persisted through 72-HPI.3 SARS-CoV-2 WA-1 isolate inoculated hamsters. Low numbers of neutrophils infiltrated the lamina propria-submucosa and rarely extended into the overlying mucosa of evaluated hamsters at 36-HPI. Rhinitis was characterized by moderate numbers of neutrophils and lymphocytes infiltrating and expanding the lamina-propria-submucosa and occasionally extending through the mucosa and into the lumen a. OlfactMild to severe histopathologic lesions were observed throughout the nasal turbinates in both ciliated respiratory epithelium a and olfModerate to severe histopathologic lesions were observed throughout the nasal turbinated at 72-h-post inoculation, both in ciliated and olfactory epithelium a,b. HistAt the time of euthanasia, whole blood, nasal swabs, oral swabs, nasal turbinates, rostral trachea, and lungs were collected for molecular analysis. To elucidate the viral load associated with replicating virus, PCR for subgenomic E protein was performed . A very In this study, we sought to define the natural history of the peracute infection of SARS-CoV-2 in the Syrian hamster model using a clinically derived, human isolate (WA-1). In contrast to human infections, clinical signs of respiratory disease were not observed in any hamster at the timepoints evaluated in this model. In this intranasal inoculation model, we show through immunohistochemistry, infection initiates in the upper respiratory tract within respiratory epithelium, not olfactory epithelium. Previous work with the same viral stock in similarly sourced Syrian hamsters within the same facility showed viral antigen in the olfactory epithelium at 24 HPI following intranasal inoculation . In thisInterestingly, conducting airway and lower respiratory tract infection can be observed within conducting airways as early as 12 HPI. This may be an artifact of the model, as the virus is diluted in 20 \u00b5L of media and slowly deposited into each naris under general anesthesia, which may overwhelm the conducting airways of the upper respiratory tract and allow some movement into the lower respiratory tree. However, the lack of viral detection by PCR in the lower respiratory tree at 6 HPI with limited detection in the upper respiratory tree at this time suggests that the viral spread is not due to the route of inoculation. This hypothesis is supported by the presence of viral RNA in the oral swabs of WA-1 inoculated but not media inoculated or irradiated virus inoculated hamsters suggesting robust, early viral replication and secretion in fluids that drain toward to oropharynx as early as 6 HPI.Importantly, rodents have defined gross and microanatomic differences in the upper respiratory tract relative to humans. Rodents have a small vestibule, branched and scrolling ethmoturbinates, transverse lamina with an olfactory recess and lack of nasopharyngeal tonsillar tissue relative to humans and nonhuman primates . RodentsImportantly, this work shows evaluation of respiratory epithelium in the rostral nasal passage rather than the olfactory epithelium in the caudal nasal passage is critical to detect peracute viral replication. The microanatomic difference, with less surface area occupied by respiratory epithelium in the hamster relative to humans, may explain why early viral shedding is not detected rapidly or at a high copy number with exterior nasal swabs in the hamster model. Interestingly, respiratory epithelial inflammation is relatively mild and transient compared to olfactory epithelial inflammation in the hamster model. True denudation of respiratory epithelium was never observed in this peracute study through 72 HPI while olfactory epithelial sloughing and full epithelial erosion was consistently observed at later time points. This intense inflammatory response was accompanied with abundant immunoreactivity for SARS-CoV-2 within olfactory epithelial cells. Interestingly, respiratory epithelium was capable of regeneration and viral clearance while abundant virus remained detectable within the olfactory epithelium.In infectious disease research, immunohistochemistry is best suited for qualitative imaging analysis to accompany molecular assays as a quantitative analytic tool. In natural history studies, immunohistochemical analysis coupled with histopathologic evaluation is of particular importance as it provides insight into early cell targets and pathways of systemic spread. In the case of SARS-CoV-2 in the intranasally inoculated Syrian hamster model, immunohistochemistry highlights the rapid spread of viral antigen from the respiratory epithelium of the upper respiratory tree, the site of inoculation, to the conducting airways in the lower respiratory tree. Additionally, immunohistochemical evaluation highlights the delayed viral tropism for the abundant olfactory epithelium. This information provides key insight into critical early microanatomic sites of peracute infection, guiding decisions on microanatomic regions that need to be analyzed for evaluation of early phase interventional therapies. Importantly, this work supports the combined use of molecular assays, histologic imaging and immunohistochemical analysis on sampled tissue sets.Taken together, molecular analysis and immunohistochemical analysis support early viral replication in the respiratory epithelium of the Syrian hamster with limited, virus associated, tissue damage in the infected microanatomic regions. Additionally, immunohistochemistry aids molecular analysis in identifying varying viral tropism during the progression of upper respiratory tract infection associated with SARS-CoV-2 infection."} +{"text": "Cucumis melo L.) is one of the important horticultural crops of the Cucurbitaceae family. Global production of melon fruits was approximately 27 million tons, with the United States production yielding 616,050 tons , produced through the methylerythritol phosphate pathway (MEP) in the chloroplast and converted to geranyl pyrophosphate (GPP\u2014C10) by plastidial GPP synthase. Monoterpene synthases (MTPS) synthesize monoterpenes from GPP. The large family of terpene synthases has been divided into eight clades (TPS-a to TPS-h) and are ten-carbon aromatic compounds. The protective role of terpenoids in foods has been suggested because of the broad antimicrobial activity of terpenoids, which led to the application of terpenoid-containing essential oils for food preservatives. Monoterpenes are formed from the CMentha spicata) L-limonene synthase (GenBank accession No. L13459) as a query sequence. The genome annotation of each hit was inspected and corrected using RNA-seq data, resulting MTPS1-MTPS9, which are clustered on chromosome 11 is highly expressed during fruit development of Western shipper (F39) and Tuscan (da Vinci) varieties\u00a0 were excluded from the alignment. Arrowhead indicates cleavage site for transit peptide for MsLS. The red box indicates a conserved catalytic motif (DDxxD)."} +{"text": "BMC Genomic Data (2023) 24:1310.1186/s12863-023-01111-yFollowing publication of the original article [1], it was reported that the article entitled \u201cProcessing genome-wide association studies within a repository of heterogeneous genomic datasets\u201d was published in the regular issue of this journal instead of in the supplement issue.The details of the supplement in which this article ought to have been published are given below:About this supplementhttps://bmcgenomdata.biomedcentral.com/articles/supplements/volume-24-supplement-1.This article has been published as part of BMC Genomic Data Volume 24 Supplement 1, 2023: Selected articles on Conceptual Modeling for Life Sciences (CMLS 2021 workshop and ER 2021 conference): genomic data. The full contents of the supplement are available online at The publisher apologizes for any inconvenience caused."} +{"text": "Suicidal thinking is relevant in patients with First Episode Psychosis (FEP). However, longitudinal studies specifically examining treatment response for suicidal ideation in FEP are still relatively scarce, especially with long-term design and in real-world clinical settings.The aims of this research were (A) to longitudinally assess suicidal thoughts in people with FEP along a 2-year follow-up period and (B) to overtime investigate any significant association of suicidal ideation levels with the specific treatment components of an \u2018Early Intervention in Psychosis\u2019 (EIP) protocol along the 2 years of follow-up.At entry, 232 FEP participants (aged 12\u201335 years) completed the Brief Psychiatric Rating Scale (BPRS), including a \u2018Suicidality\u2019 item subscore. Multiple linear regression analysis was then performed.Across the follow-up, FEP subjects showed a relevant decrease in suicidal thinking levels overtime. This was specifically predicted by the total number of individual psychotherapy sessions offered within the 2-year EIP protocol and antidepressant dose (at least as regards the first year of our intervention).Image:Suicidal ideation is clinically relevant in FEP but seems to improve overtime together with the provision of specific, patient-tailored and integrated EIP treatments, especially individual psychotherapy.None Declared"} +{"text": "Postpartum depression (PPD) affects about 1 in 8 women in the months after delivery . In thisWe used 2 publicly accessible LLMs, GPT-4 (using ChatGPT) and LaMDTwo board-certified physicians (author JL is board certified in pediatrics and pediatric gastroenterology and author FC is board certified in pediatrics) compared the LLM responses and Google Search results to the ACOG FAQ responses and rated the quality of responses using a GRADE -informed scale . We calc\u03c722=12.2; P=.002; Z=2.143; adjusted P=.048) and Google Search . There was no difference in the quality of responses between Bard and Google Search .ChatGPT differed in the quality of responses against others and nonhomoscedastic for each category .Raters showed perfect agreement for ChatGPT and near-perfect agreement for Bard and Google Search . Data were not normally distributed (This study expands an earlier investigation on chatbot advice for PPD , showingOverall, LLMs showed promise in terms of providing clinically accurate or better-quality responses than Google Search results. This finding is consistent with the prior investigation on the appropriateness of LLM-based medical advice . Our fin"} +{"text": "Panels A and B).A 62-year-old man was scheduled for left-sided permanent pacemaker implantation for post-operative complete heart block. A peripheral venogram showed patency of the axillary and proximal subclavian veins. After access was obtained, the micropuncture wire did not follow the typical course expected of a left brachiocephalic vein. A venogram was therefore performed through a 5 Fr short sheath\u2014this revealed a U-shaped course with eventual drainage into the superior vena cava (These represent a dilated left superior intercostal vein that drains into the accessory hemiazygous vein, followed by the azygous vein and finally the superior vena cava. The prominence of this vessel can occur with congenital or acquired obstruction of the proximal veins. In this case, a dialysis catheter-associated thrombus likely caused acute left brachiocephalic vein occlusion and consequent increase in collateral flow.Pursuing left-sided device implantation was not deemed feasible, given the long and meandering venous course visualized. Hence, a dual-chamber pacemaker was implanted on the right side instead. The invasive electrophysiologist should be aware of these uncommon but impressive venous anomalies in the planning and execution of cardiac device implantations.https://www.escardio.org/Education/E-Learning/Clinical-cases/Electrophysiology.The full-length version of this report can be viewed at:"} +{"text": "Scientific Reports 10.1038/s41598-023-44046-1, published online 11 October 2023Correction to: The Acknowledgements section in the original version of this Article was incomplete,\u201cThe research was funded by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) through \u2018Harnessing Opportunities for Productivity Enhancement (HOPE II) for Sorghum and Millets in sub-Saharan Africa\u2019 project (OPP1198373), funded by the Bill & Melinda Gates Foundation (BMGF).\u201dnow reads:\u201cThe research was funded by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) through \u2018Harnessing Opportunities for Productivity Enhancement (HOPE II) for Sorghum and Millets in sub-Saharan Africa and CIMMYT through the Accelerated Varietal Improvement and Seed delivery of legumes and cereals in Africa (AVISA) (grant number OPP1198373), funded by the Bill & Melinda Gates Foundation (BMGF).\u201dThe original Article has been corrected."} +{"text": "External ventricular drain (EVD)-related ventriculitis is a serious complication associated with poor patient outcomes. We aim to: (1) characterize patient-level factors and outcomes of individuals with EVD-related ventriculitis and (2) identify differences by type of infection and indication of EVD-placement.This study is a single center, case series of adults hospitalized with a diagnosis of EVD-related ventriculitis between January 2018 to February 2023. EVD-related ventriculitis was defined as having a positive cerebrospinal fluid culture from an EVD consistent with CDC/NHSN criteria for ventriculitis. Several covariates were extracted from patient charts to characterize patient outcomes. Further stratification by type of infection (gram-positive versus gram-negative ventriculitis) and indication (traumatic versus non-traumatic EVD placement) were performed to identify any differences in characteristics between the two groups.Twenty-two patients were identified in the study. The majority of patients were infected with gram-positive bacteria (54.5%) rather than gram-negative bacteria (41%) with 1 case of fungus. The most common indication for EVD placement was trauma (59%) and most were placed at bedside (91%) rather than an operating room (9%). The mean length of stay (LOS) was 42.14 days. (Table 1)There was a statistically significant difference in the CSF to serum glucose ratio between gram-negative and gram-positive infections with gram negative ventriculitis having a lower ratio compared to patients with gram positive ventriculitis . However, LOS, interval from catheterization to infection, and other CSF parameters were similar between the two groups as well as those whose EVDs were placed in the setting of traumatic vs non-traumatic settings. (Table 2 and 3)Characteristics stratified by trauma vs non-trauma patientsPatients with EVD-related ventriculitis had double the LOS compared to neurosurgical patients without EVD-related ventriculitis reported in the literature. Patients with gram-negative ventriculitis had a lower CSF to serum glucose ratio than those with gram-positive ventriculitis. Otherwise, patient characteristics and outcomes were similar when stratified by type of infection and indication.All Authors: No reported disclosures"} +{"text": "Editorial on the Research TopicInsights in neuropathic pain: 2022Neuropathic pain refers to a type of chronic that arises from damage or dysfunction in the sensory nervous system . It affeVelzen et al. highlights the challenges associated with neuropathic pain, including its prevalence among a large and diverse population of patients, as well as the instability of efficacy due to unacceptable side effects and variations in disease characteristics and patient severity antibody-associated ON (AQP4-ON), myelin oligodendrocyte glycoprotein (MOG) antibody-associated ON (MOG-ON), and idiopathic demyelinating optic neuritis (IDON) (The research conducted by s (IDON) . MagnetiWeeks et al. investigated the mechanism of HIV-associated distal neuropathic pain (DNP) by examining the functional connectivity alterations in the salience network (SN) and default mode network (DMN) using functional neuroimaging: resting state functional magnetic resonance imaging (rs-fMRI) (The study by rs-fMRI) . Their rYamamoto et al.'s research article evaluated the lipidomic analysis of fatty acids (FAs) metabolites changes over time following peripheral nerve injury (PNI) . Their rGandhi et al.'s study offered a novel perspective on neuronal function in diabetic peripheral neuropathy (DPN) . Using p"} +{"text": "Alzheimer\u2019s disease (AD) was described over a century ago as a disease of dementia with the presence of amyloid and tau pathologies , but theThough aducanumab was the first AAA approved in June 2021), controversy ensued rapidly thereafter owing to questionable efficacy and Biogen\u2019s ASO strategy for tauopathy [https://www.biospace.com/article/biogen-successfully-targets-tau-in-phase-ib-study-for-alzheimer-s/] have shown sustained protein knockdown in cerebrospinal fluid (CSF) in the ranges of 60\u201390%, respectively.Other targets and strategies are also beginning to bear fruit. Alnylam\u2019s antisense oligonucleotide (ASO) strategy for APP [Triggering receptor expressed on myeloid cells 2 (TREM2) is beingThese talking points were drafted as an intended service to the private patients of the author, and no endorsement(s) by the author\u2019s employer(s) is/are implied. The views represented here are entirely the personal views of the author."} +{"text": "Diarrhea is a common complication of hematopoietic stem cell transplantation (HSCT) and associated with substantial morbidity, but the etiology is often not identified. The objectives of this study were to evaluate 1) whether the introduce of FilmArray GI panel would increase diagnostic yield, 2) the degree to which pre-transplantation colonization predicts post-transplantation infection.From November 2019 and February 2021, a total of 158 patients undergoing HSCT were prospectively included in the study . Stool specimens were obtained from all HSCT recipients prior to conditioning therapy, on 28 \u00b1 7 days after transplantation and at any new episode of diarrhea. All stool samples were tested by FilmArray GI panel, and other clinical microbiological assays were also performed as requested by the treating physician.Flowchart of patients\u2019 recruitment. A total of 158 patients were recruited from 175 patients undergoing HSCT during the study period. Eighty-four of the 158 patients underwent diarrhea episodes after transplantation, while the other 74 patients did not.C. difficile , EPEC , and norovirus . The incidence of infectious diarrhea is significantly higher in colonized patients than that in non-colonized patients (p < 0.001) . Pre-transplantation colonization of norovirus was at the highest risk of developing post-transplantation diarrhea .Eighty-four (53.16%) of the 158 patients developed diarrhea after transplantation. The primary cause of post-transplantation diarrhea was infection , followed by medication and graft-versus-host disease . Ninety-five (60.13%) of 158 patients were colonized with at least one gastrointestinal pathogen before conditioning therapy, and the most common colonized pathogens detected were Etiologies of diarrhea after transplantation. (A) Etiologies of diarrhea in 84 patients who underwent diarrhea episodes after transplantation; (B) Etiologies of diarrhea that combined all factors, including infection, GVHD and medication; (C) The incidence of diarrhea and infectious diarrhea in colonized and non-colonized patients.Pathogens detected by FilmArray GI panel in pre- and post- transplantation stool samples. The number of patients who had a clinical relevant post-transplantation diarrheal infection due to pre-transplantation colonization is shown for each pathogen (red part in bar plot).Impact of different underlying diseases on pathogen colonization and subsequent development of infectious diarrhea due to the colonized pathogens. (A) The number and proportions of patients with different underlying diseases who were colonized with gastrointestinal pathogens pre-transplantation. (B) The number and proportions of patients in the colonized group who developed infectious diarrhea due to their colonized pathogens. HM: Hematological malignancies; PI: Primary immunodeficiency; AA: Aplastic anemia; IMD: Inherited metabolic disorders.FilmArray GI panel can increase the detection rate of diarrheal pathogens in pediatric HSCT patients, and further studies assessing its clinical impact and cost-effectiveness are needed.All Authors: No reported disclosures"} +{"text": "The risk of intussusception related to percutaneous endoscopic gastrostomy with jejunal extension (PEG-J) in patients with severe motor and intellectual disabilities (SMID) remains unknown. In a cross-sectional study, a review of 26 patients with SMID who underwent PEG-J was performed. During the follow-up period, 6 of 26 (23%) patients developed intussusception. The median period from PEG-J to the onset of intussusception was 364 days. No significant difference was observed in the Cobb angle between the intussusception and nonintussusception groups; however, body mass index at the time of PEG-J was significantly lower in the intussusception group. Intussusception related to PEG-J occurs relatively frequently in patients, and it is possibly attributable to factors such as deformity caused by undernutrition and weight loss. If enteral nutrition via PEG-J has been established, earlier enterostomy can be recommended because of the high risk of intussusception in patients with SMID. Percutaneous endoscopic gastrostomy with jejunal extension (PEG-J) is an alternative technique for patients with severe motor and intellectual disabilities (SMID). The incidence of intussusception in children with SMID is unknown.About one-fifth of patients with SMID developed intussusception. Long-term PEG-J insertion is not recommended in patients with SMID because of increased risk of intussusception development by PEG-J.Pediatric patients with severe motor and intellectual disabilities (SMID) occasionally experience oral feeding difficulties. Thus, feeding methods such as tube feeding and percutaneous endoscopic gastrostomy (PEG) are chosen. As patients grow, various factors such as repeated aspiration because of gastroesophageal reflux disease (GERD), decreased gastric motility, and intestinal obstruction caused by scoliosis may lead to difficulties with tube and PEG feeding 2. PEG wiP < 0.05. Institutional review board approved was obtained (2020-1242).In a cross-sectional study, the outcomes of 26 patients who underwent PEG-J following unsuccessful gastric feeding at Osaka Women\u2019s and Children\u2019s Hospital between April 2012 and March 2019 were retrospectively reviewed. All patients fulfilled the criteria of classes 1\u20134 of Ohshima\u2019s classification (P = 0.004). In Kaplan\u2013Meier survival analysis, almost half of the patients developed intussusception approximately 1500 days after PEG-J (Fig. Patient characteristics are listed in Table Tube feeding or gastrostomy is commonly used if oral intake is insufficient or impossible for patients with SMID . HoweverPhysicians should consider the possibility of intussusception if patients undergoing PEG-J feeding exhibit unexplained vital changes. Additionally, low body weight and low BMI may predispose patients to intussusception, and enterostomy should be introduced as necessary."} +{"text": "The dC5 could be effectively removed from the ZN pores by either high-temperature calcination or UV irradiation in air at room temperature but not by the piranha solution treatment. Ultrathin ZN-laminated membranes (ZNLMs) were fabricated by sandwiching a UV-activated multilayered ZN film between two recast Nafion\u00ae layers (ZNLM-Nafion) and by filtration coating from a suspension of thermally activated ZNs on a nonionic porous PVDF (ZNLM-PVDF). The ZNLMs on both supports demonstrated the ability of highly proton-selective ion conduction with low resistances in aqueous electrolyte solutions. The ZNLM-PVDF with PVDF binder was structurally stable, and it achieved a comparably low ASR but much higher proton selectivity compared with a Nafion membrane of same overall thickness. However, detachment between the ZNLM and Nafion layers occurred when the ZNLM-Nafion operated in aqueous electrolyte solutions. Results of this study show the potential for developing ZNLMs as efficient proton-conducting membranes without using expensive ionic polymer matrices. However, the development of polymer-supported ZNLMs is hindered by the current inefficiency in preparing well-dispersed suspensions of open-pore ZNs. Future development of efficient methods for synthesizing open-pore ZNs in dispersed states is key to realizing high-performance ZNLMs on polymers.Single crystalline ZSM-5 ZNs with thicknesses around 6 nm were obtained by secondary growth of silicalite nanoparticles using diquaternary bis-1,5(tripropyl ammonium) pentamethylene diiodide (dC This liquid phase activation process provided well-dispersed open-pore ZN suspensions. The preactivated ZN suspension was used for coating binder-free ZNLMs on porous polybenzimidazole supports by vacuum filtration. The binder-free ZNLM had minimized n-butane and i-butane. However, the binder-free multilayered ZNLM is likely to lack structural stability in liquid phase, especially in electrolyte solutions where the layered ZNs could disintegrate and redisperse upon surface solvation or ionization.To avoid the solid-state irreversible aggregation, Zhang et al. activate2) during pervaporation desalination of brines with total dissolved salts of ~22 wt.%. The efficient ion rejection was achieved because the nanometer-scale n-/i-butane because its In a previous work, we synthesized aluminum-containing MFI ZNLM on porous polyvinylidene fluoride (PVDF) support using a minimal amount of PVDF as binder to prevent the multilayered ZNs from dissociation in concentrated slat solutions (Br2) (C22-6-6Br2) SDA in air to activate multilayered ZNs under dry conditions \u2212H+) b.2SO4 and acidic vanadyl ion solution for over two weeks. The SEM images of ZNLM-PVDF showed no visible changes in the surface morphology and multilayered structure films for highly selectivity proton conductions in aqueous electrolyte solution with low resistances. The ZSM-5 ZN-laminated membrane (ZNLM), formed on the nonionic macropore PVDF substrates using the same PVDF as a binder, was able to achieve a comparably low ASR but much higher proton selectivity compared with the Nafion membrane of similar thickness. This indicates the potential for development of ZNLMs as efficient proton-conducting membranes without using expensive ionic polymer matrices. However, the development of such new ZN-laminated membranes on ubiquitous polymer is limited by the inefficiency in preparing well-dispersed suspensions of open-pore ZNs, which are necessary for coating membranes on polymer supports. Our current research efforts are focused on developing methodologies for synthesizing dispersible open-pore ZNs and investigating the ZNLM performance as an ion separator for aqueous flow batteries."} +{"text": "Postoperative colorectal anastomotic strictures are not uncommon and often require endoscopic or surgical interventionA 59-year-old man underwent anterior resection and loop colostomy for sigmoid colon diverticulitis with perforation. A follow-up colonoscopy within 3 months revealed the formation of circular scars and stricturing at the anastomotic site . The stInstead of endoscopic balloon dilation, we employed an innovative technique calledsnare-tipped endoscopic radical incision and cutting (STERIC) to address the postoperativeanastomotic stricture. We used the tip of the snare ,sticking out by 2 mm in length, to perform the radical incision and cutting. The snare tip wasplaced at the edge of the stricture ring at the 6-o\u02bcclock position and then used to make acircumferential incision with the assistance of the electrosurgical unit inEndocut Q mode , employing a step-by-step excision along thearc of the lumen . FollowSnare-tipped endoscopic radical incision and cutting (STERIC) is performed for a postoperative colorectal anastomotic stricture.Video 1The patient subsequently underwent loop transverse colostomy closure, with no signs of restenosis during follow-up.Endoscopy_UCTN_Code_TTT_1AQ_2AF"} +{"text": "The association between insight, stigma and self-concept has been considered as a potential predictor of poor clinical outcomes and global functioning in psychosis. In patients with delusional disorder (DD), the effects of stigma and self-stigma have been poorly explored.Our main goal was to systematically review studies addressing stigma and self-stigma in DD to assess whether these phenomena have an impact on clinical symptoms.A systematic review was conducted through PubMed and Google Scholar databases from inception to 2022 (PRISMA guidelines). Search terms: (Stigma OR self-stigma) AND . Studies were considered eligible if they included patients with DD.A total of 875 records were retrieved, from which 18 were included.Stigma: (1) Stigma is associated with poor quality of life, poor adherence to medications and acceptation of diagnosis. (2) Support at workplaces would improve stigma and discrimination in DD. (3) Poor interpersonal competence may increase stigma experience in DD.Self-stigma: (1) Women show higher level of self-stigma than men. (2) Higher rates of psychiatric hospitalizations and higher severity of symptoms associated with greater degree of self-stigma. (3) Suicidal ideation was associated with negative self-schema but not self-stigma, particularly in patients with persecutory delusions. (4) Self-stigmatization negatively associated with quality of life. (5) Depressive symptoms associated with higher levels of self-stigma. (6) Promotion interventions should address self-stigma content.Further longitudinal studies are needed to test the influence of stigma and self-stigma on adherence to follow-up and specific interventions to improve them.None Declared"} +{"text": "We report a rare case of central retinal artery occlusion (CRAO) with triple cilioretinal artery sparing in a 76-year-old male with hypertension who presented with sudden diminution of vision in the left eye (OS) for one day. Optical coherence tomography angiography (OCTA) demonstrated the presence of three cilioretinal arteries and the absence of flow signals in the rest of the macula. Primary ophthalmic treatment was instituted immediately in the form of ocular massage, and acetazolamide 500 mg per oral (PO) stat was given. Systemic investigations revealed a significant blockage in coronary circulation on coronary angiography and an atheromatous plaque at the origin of the left internal carotid artery with 50% stenosis on digital subtraction angiography. Systemic anticoagulants and lipid-lowering agents (statins) were initiated by the cardiologist. Percutaneous transluminal coronary angioplasty was subsequently performed.At the eight-week follow-up visit, best-corrected visual acuity had improved to 2/60 OS. Fundus examination of the OS revealed optic disc pallor with normal retinal background. Spectral-domain optical coherence tomography showed diffuse retinal thinning except in the area supplied by the three patent cilioretinal arteries. En face OCTA OS showed restoration of retinal flow signal in the macula.Non-invasive imaging (OCTA) is critical in establishing early diagnosis and initiating prompt treatment in this ocular emergency with underlying potentially life-threatening systemic associations. Central retinal artery occlusion (CRAO) is caused by obstruction of the central retinal artery, most commonly due to emboli originating from atheromatous plaques in the cardiac valves and carotid arteries, resulting in retinal ischemia . The comHerein, we report a unique case of CRAO with sparing of three cilioretinal arteries, possibly the first of its kind.A 76-year-old male with a history of hypertension (controlled on anti-hypertensive medication) presented with painless, sudden diminution of vision in the left eye (OS) for one day.\u00a0The best-corrected visual acuity (BCVA) was 6/9 in the right eye (OD) and counting fingers close to face (CFCF) in the OS. A relative afferent pupillary defect in the OS was noted. Intraocular pressure was normal in both eyes (OU) . Anterior segment examination was unremarkable OU. Fundus examination OD was normal. OS showed a normal-appearing optic disc with a cup-to-disc ratio of 0.3:1, arteriolar narrowing with segmental blood flow (box-carring), and diffuse background pallor with a small area of normal-appearing retina temporal to the optic disc, corresponding to patent cilioretinal arteries Figures , 1B. SpeA clinical diagnosis of CRAO with triple cilioretinal artery-sparing OS was made. Primary treatment was immediately instituted in the form of ocular massage, and acetazolamide 500 mg per oral (PO) stat was given. Systemic investigations revealed mildly deranged glycated hemoglobin (HbA1c) at 6.7% with a deranged lipid profile and renal function test (serum creatinine = 1.4 mg/dL). The patient was referred to the cardiology and neurology specialists to rule out systemic co-morbidities and any potential sources of thrombi or emboli. He underwent coronary angiography, which revealed significant (>70%) blockage in the left proximal ramus intermedius artery Figure . DigitalThe vision had improved to 2/60 OS after eight weeks.\u00a0Fundus examination of the OS revealed optic disc pallor with arteriolar attenuation with a normal retinal background Figures , 2B. SD-At the latest follow-up visit at six months, the patient maintained status quo OU. Anti-hypertensive drugs, statins, and systemic anticoagulants continued to be administered under the supervision of the cardiologist.CRAO is not only an ophthalmic emergency but also a medical emergency due to its potentially life-threatening systemic associations such as carotid artery disease and coronary artery disease . The incCilioretinal arteries are defined as retinal artery branches, not continuous with the central retinal artery . They maMacular supply is defined as the cilioretinal artery reaching a circle centered on the fovea with a radius of fovea-to-optic disc rim distance minus one-disc diameter . MacularTo the best of our knowledge, ours is the first case report of CRAO with triple cilioretinal artery sparing. Invasive and relatively time-consuming investigations such as fluorescein angiography were not performed at presentation due to the emergent nature of the clinical presentation and the presence of potential unknown systemic risk factors such as nephropathy. OCTA provided a crucial advantage in this emergency owing to its fast acquisition time and non-invasive nature. Prompt systemic evaluation led to the timely diagnosis and treatment of the underlying ominous coronary and carotid artery disease."} +{"text": "The Third Report of the Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults, Adult Treatment Panel III (ATP III) encouraged reduced low-density lipoprotein (LDL) cholesterol levels for a greater number of patients and reemphasized the benefits of high-density lipoprotein (HDL) cholesterol. The purpose of this study was to compare 2 regimens achieving simultaneous LDL and HDL goals.A decision-analytic model compared the cost-effectiveness of simvastatin and lovastatin/extended-release niacin. The perspective of the analysis was that of a health system. Product labeling was used to determine changes in cholesterol concentrations and frequencies of clinically important adverse events. The Third National Health and Nutrition Examination Survey (NHANES III) adult data were used for baseline cholesterol levels. Each product was titrated to achieve LDL and HDL goals unless an adverse effect occurred. Direct medical costs were determined for each treatment to determine cost-effectiveness.For both the 130 mg/dL and 100 mg/dL LDL goal analyses (and HDL e40 mg/dL), lovastatin/extended-release niacin had higher success rates and lower estimated direct-medical costs than simvastatin. Simvastatin had the highest success rate in achieving LDL level less than160 mg/dL and HDL e40 mg/dL; however, its estimated direct-medical cost was approximately twice that of lovastatin/extended-release niacin ($665 versus $333).For the LDL goals less than130 mg/dL and less than100 mg/dL (and HDL e40mg/dL) required of the majority of U.S. residents, lovastatin/extended-release niacin was both more successful and less costly than simvastatin."} +{"text": "Correction: BMC Genomics 23, 357 (2022)https://doi.org/10.1186/s12864-022-08551-3Analysis of conserved structural domains and conserved motifs of thePeDoGs section.Following publication of the original article , a typesThe paragraph currently reads:DoGDoGDoGDoGTo study the structural domains of the The paragraph should read:DoG\u00a0family of moso bamboo, the GFF annotation file of the whole genome of moso bamboo was used to extract the structural information of the moso bamboo DoG family genes. The structural domains of the moso bamboo DoG family were analyzed by NCBI Conserved Domain (https://www.ncbi.nlm.nih.gov/cdd/), and the gene structures and protein structural domains were mapped by TBtools software. The conserved motifs of the DoG family of Moso bamboo were predicted by using the online amino acid conserved motif analysis software MEME (http://meme-suite.org/tools/meme) with the following parameter settings: the motif discovery mode was classical with a predicted number of motifs of 5, and each motif occurred 0 or 1 times.To study the structural domains of the The original article has been"} +{"text": "Information on craniosynostosis and non-craniosynostosis-related admissions, cumulative length of hospital stay (cLoS), intensive care unit, and emergency department\u2013related admissions were extracted from the hospitalization dataset and linked to other data sources. These associations were examined using negative binomial regression presented as annual percent change and associations of hospitalizations by age groups, demographic, and perinatal factors were expressed as incidence rate ratio (IRR). We found an increasing trend in incident hospitalizations but a marginal decline in cLoS for craniosynostosis over the observed study period. Perinatal conditions, feeding difficulties, nervous system anomalies, respiratory, and other infections contributed to majority of infant non-CS-related admissions.Respiratory infections accounted for about twice the number of admissions for individuals with CS (IRRs 1.94\u20132.34) across all observed age groups. Higher incidence of non-CS hospitalizations was observed among females, with associated anomalies, to families with highest socioeconomic disadvantage and living in remote areas of the state.Understanding hospital service use among children with a diagnosis of craniosynostosis (CS) is important to improve services and outcomes. This study aimed to describe population-level trends, patterns, and factors influencing hospitalizations for craniosynostosis in Western Australia. Data on live births (1990\u20132010; \u00a0 Conclusion: Marginal reduction in the cLoS for CS-related admissions observed over the 21-year period are potentially indicative of improved peri-operative care. However, higher incidence of respiratory infection-related admissions for syndromic synostosis is concerning and requires investigation.The online version contains supplementary material available at 10.1007/s00431-023-04922-4. Children born with craniosynostosis (CS) often require early neurosurgical intervention, ideally between 4 and 13\u00a0months of age, with syndromic cases undergoing additional timed craniofacial corrections from childhood into early adulthood . HoweverA previous Australian-based population-based study reported a stable trend in hospitalization rates and a marginal decrease in the average length of stay for people with craniosynostosis using the total population separation data from the publicly available Australia-wide National Hospital Morbidity Database . HoweverGiven the knowledge gaps in the literature regarding the hospital service use for craniosynostosis, it is important to build comprehensive evidence to inform research, clinical and surgical practice, and planning and improve patient care. Hence, this study investigated trends, age-specific patterns, and factors influencing hospital admissions for people with craniosynostosis utilizing the Western Australian linked population data.This retrospective cohort study utilized record-linked deidentified data from four data collections made available by the Western Australian Data Linkage System (WADLS). As a result of this linkage, each individual record is provided with a common unique identification number (linkage key) which was used to link the four data collections to facilitate the analysis.Cases of craniosynostosis were principally identified from Western Australian Register of Developmental Anomalies (WARDA), with additional cases identified from the Hospital Morbidity Data Collection (HMDC). WARDA is a statutory population-based statewide register of congenital anomalies that identifies eligible cases using multiple sources of ascertainment. It includes structural and functional anomalies diagnosed in stillbirths and livebirths to six years of age . Midwiven\u2009=\u2009554,624). Among them, all infants born with craniosynostosis were largely identified from WARDA using the BPA-ICD9 codes with diagnostic descriptions for craniosynostosis (75600), Crouzon syndrome (75601), Apert syndrome (75550), Pfeiffer syndrome (75601), Carpenter syndrome (75984), Saethre-Chotzen syndrome (75550), Muenke syndrome (75600), and Baller-Gerold syndrome (75600)]. Some additional cases not identified in WARDA from 1998 onwards were extracted from the separation data of HMDC, provided the individual separation data had both a principal diagnostic code and procedure codes directly corresponding to craniosynostosis diagnostic codes used included Q75.0 (Craniosynostosis), Q75.01 , Q75.02 , Q75.03 (metopic synostosis), Q75.04 (multiple suture synostosis), Q75.09 (unclassified synostosis), and Q75.1 . The Australian Classification of Health Interventions (ACHI) procedure codes for identifying craniosynostosis included 40115\u201300, 40118\u201300 [other procedure for craniosynostosis], and 45785\u201303 [total cranial vault reconstruction]. Considering the International Classification of Diseases-9th revision system-clinical modification (ICD-9-CM) codes do not specifically identify craniosynostosis, case identification from HMDC was restricted to births following the introduction of the ICD-10-AM system in 1998.Our overall study population comprised all infants born in WA between 1990 and 2010 non-syndromic (isolated single/multiple suture synostosis); (ii) syndromic synostosis .The comparison cohort included all live-born individuals over the same period but not diagnosed with craniosynostosis. The comparison cohort was extracted from the MNS.th revision system-clinical modification (ICD-9-CM) codes and procedure codes to the Australian Classification of Health Interventions (ACHI) to allow comparisons across the study period.The primary outcome of this study was the number of incident hospitalizations per total person-years. Individual person time under observation was obtained by subtracting either the final date of follow-up or date of death, whichever occurred earlier, from the date of birth. The value was then summed among the study population to ascertain the total person-years. Hospitalizations in our study were defined as craniosynostosis or non-craniosynostosis-related admissions that included both surgical and non-surgical admissions. All principal diagnoses codes were mapped to the International Classification of Diseases-9Craniosynostosis-related admissions (CS-related) considered for this study included surgical and non-surgical admissions that were identified using principal diagnostic codes for craniosynostosis or where relevant principal and additional procedure codes, indicating craniosynostosis repair regardless of principal diagnosis code (Supplementary Table All admissions not categorized as craniosynostosis-related were broadly considered as non-craniosynostosis (non-CS) related. We specifically considered admissions for ocular, auricular, dental, respiratory infections, other respiratory conditions, and sleep-related disorders reasons separately as these admissions are common or previously reported among children with craniosynostosis . FurtherSecondary outcomes for this study were as follows:Length of stay: calculated as the time between admission and discharge. The length of hospital stay was considered as 0.5\u00a0days when the admission and discharge occurred on the same day to reflect some period of hospitalization . We repoFrequency of intensive care unit (ICU) admissions: data were extracted from the HMDC and additionally included individual length of stay in intensive care.Frequency of emergency department (ED) admissions: this information was collected from the HMDC.As was done previously , 16, infDescriptive statistics were used to summarize the frequency of admitted individuals (craniosynostosis and non-craniosynostosis-related), intensive care admissions, and emergency admissions. Linear trends in hospitalizations adjusted for age at separation, sex, Indigenous status, remoteness, and socioeconomic disadvantage were estimated using negative binomial regression, and annual percent change (APC) was reported. The APC was calculated by exponentiating the coefficient of the year of birth and then subtracting 1 .Furthermore, we conducted the analysis by type of craniosynostosis (non-syndromic and syndromic) for four age groups. As was done previously , the fouA similar modeling approach was used to determine the association between each relevant explanatory variable and hospitalizations and IRRs with 95% CIs were reported. All analyses were carried out using Stata 16.0 .As done in our previous work involving missing data, a complete case analysis was also used in this study , Western Australian Aboriginal Health Ethics Committee (HREC#2015/613) and The University of Western Australia (RA/4/20/5843).As presented in Table The median cumulative length of stay (cLoS) was lowest for those with non-syndromic coronal synostosis and highest for those with Apert syndrome. Furthermore, about three-fifths of the admitted individuals with CS had an emergency admission, and more than two-fifths required intensive care ], more pronounced for syndromic CS, than those born without this condition ] prominently for non-syndromic CS but not for non-craniosynostosis-related admissions. Individuals with craniosynostosis spent three and a half times more total days in hospital for any cause [IRR 3.56 higher than for males Supplementary file2 (DOCX 23 KB)Supplementary file3 (DOCX 46 KB)Supplementary file4 (DOCX 18 KB)Supplementary file5 (DOCX 17 KB)Supplementary file6 (DOCX 21 KB)Supplementary file7 (DOCX 21 KB)Below is the link to the electronic supplementary material."} +{"text": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants are expected to be resistant to Bebtelovimab (BEB) monoclonal antibody (MAb) and the real-world experience regarding its effectiveness is scarce. This retrospective cohort study reports a data analysis in Banner Healthcare System (a large not-for-profit organization) between 4/5/2022 and 8/1/2022 and included 19,778 Coronavirus disease-19 (COVID-19) positive (by PCR or direct antigen testing) patients who were selected from Cerner-Electronic Health Record after the exclusions criteria were met. The study index date for cohort was determined as the date of BEB MAb administration or the date of the first positive COVID-19 testing. The cohort consist of COVID-19 infected patients who received BEB MAb compared to propensity score (PS) matched control . The primary composite outcome was the incidence of 30-day all-cause hospitalization and/or mortality. All statistical analyses were conducted on the paired (matched) dataset. For the primary composite outcome, the event counts and percentages were reported. Ninety-five percent Clopper-Pearson confidence intervals for percentages were computed. The study cohorts were 1:1 propensity matched without replacement across 26 covariates using an optimal matching algorithm that minimizes the sum of absolute pairwise distance across the matched sample after fitting and using logistic regression as the distance function. The pairs were matched exactly on patient vaccination status, BMI group, age group and diabetes status. Compared to the PS matched control group , BEB MAb use did not significantly reduce the incidence of the primary outcome (p = 0.67). In the subgroup analysis, we observed similar no-difference trends regarding the primary outcomes for the propensity rematched BEB MAb treated and untreated groups, stratified by patient vaccination status, age (<65 years or \u226565), and immunocompromised status . The number needed to treat (1/0.026\u20130.022) with BEB MAb was 250 to avoid one hospitalization and/or death over 30 days. The BEB MAb use lacked efficacy in patients with SARS-CoV-2 Omicron subvariants in the Banner Healthcare System in the Southwestern United States. Coronavirus disease 2019 (COVID19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents with a spectrum of infection severity, ranging from asymptomatic to severe/critical . The indSARS-CoV-2 continues to evolve into new variants of concern (VOC) characterized by mainly spike receptor binding domain mutations, which are the target of authorized neutralizing monoclonal antibodies (MAb) to reduce hospitalization and death . The spiIn our system, the Banner Healthcare System, a multidisciplinary team reviews patients\u2019 eligibility for antiviral therapy (remdesivir and nirmatrelvir-ritonavir as the first line agents) and an alternative MAb treatment, guided by the FDA EUA. BEB is indicated for high-risk patients at risk for severe disease and/or death who are unable to receive remdesivir 3-days IV treatment due to logistic challenges or have contraindications for the use of nirmaltrevir/ritonavir due to severe drug-drug interactions. The high-risk patients with underlying medical conditions are defined by the Center for Disease Control and Prevention (CDC), such as age>50 years old, obesity infection, chronic lung/ kidney/ liver diseases, etc. . BEB washttps://covid.cdc.gov/covid-data-tracker/#variant-proportions) and CoVariants database (https://covariants.org/per-country?region=United+States) to decide on prevalent Omicron subvariants in the areas of U.S. where Banner Healthcare System operates during the study period, not based on the viral genotype sampling from the study cohort.In this study, we assessed the composite outcome in high-risk patients in the outpatient setting, who received BEB MAb compared to the propensity score (PS) matched untreated control group for COVID-19 in the Banner Healthcare System (a large not-for-profit organization) in the Southwestern United States, during a period (4/5/2022-8/1/2022) dominated by SARS-CoV-2 Omicron BA.2, BA.2.12.1, and BA.5 subvariants . We primThis study was approved by the Institutional Review Board of the University of Arizona with a waiver of patient consent given the retrospective nature of the study. The study adhered to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement See .This observational retrospective cohort study of positive COVID-19 patients was conducted between April 5, 2022, and August 1, 2022. Patients\u2019 follow-up date was censored on August 31, 2022. All data pertaining to BEB MAb treated patients and untreated patients were captured from electronic health records (Cerner EHR) in the Banner Health Care System, which houses thirty hospitals and several clinics across the Southwestern United States, mainly in Arizona. A multidisciplinary team formed under the Banner Health Care System Monoclonal Antibody Treatment program reviews patients\u2019 eligibility for antiviral therapy (remdesivir and nirmatrelvir-ritonavir as the first line agents) and an alternative MAb treatment, guided by the FDA EUA. The alternative BEB MAb therapy (175 mg administered as a single intravenous injection over 30 seconds) is indicated for mild-to-moderate SARS-CoV-2 infection (within 7 days of symptom onset) in adults who are at high-risk for progression to severe disease and in children older than 12 years-old and weighing 40 kg or above.During the study period, 19,778 COVID-19 positive (by PCR or direct antigen testing) patients were retrieved from Cerner-EHR after exclusions were met and wereThe primary composite outcome was the incidence of all-cause hospitalization and/or mortality and the within 30-days of the index date among the post-propensity matched cohort.Propensity score methods are commonly used in non-randomized observational data analysis to balance covariate differences between treatment groups and reduce bias in estimating treatment effects (pseudo-randomization) . The goaThe cohorts in this study were 1:1 propensity matched without replacement across 26 covariates using an optimal matching algorithm (a logistic regression model) that minimizes the sum of absolute pairwise distance across the matched sample. Optimal matching is a generalized linear model with a logit link function to calculate propensity scores. MatchIt package from the statistical computing software R was used for optimal pair matching . This alAll statistical analyses were conducted on the paired (matched) dataset. For each outcome, event count, percentage with the event and ninety-five percent Clopper-Pearson confidence intervals have been reported. These confidence intervals for percentages were computed using the R package Exactci. Exact McNemar\u2019s test was used to compare the proportions in the paired dataset and the 95% confidence intervals for proportions were calculated. P-values <0.05 was considered statistically significant . AdditioAdditional analyses were conducted on subgroups under the propensity matched cohorts to assess the differences on BEB MAb effectiveness on these subgroups. For this purpose, the post-match BEB treated and untreated cohorts were combined and then stratified by vaccination status (fully vaccinated and not fully vaccinated), age groups (age <65 and age \u226565), and immunocompromised status . The same algorithm and model that were used for the initial propensity matching were employed to rematch based on subgroups and the incidence of the composite outcome was reported alongside the percent difference in between the treated and untreated cohorts and its significance level . FinallyData on missing vaccination status of patients was labeled as unknown and was included in the initial propensity matching .In the subgroup analysis, we observed similar no-difference trends regarding the primary composite outcomes for the propensity rematched BEB MAb treated and untreated groups, stratified by patient vaccination status, age (<65 years or \u226565), and immunocompromised status , see In this retrospective propensity matched analysis, the incidence of the primary composite outcome was low (2.2%-2.6%) and treatment with the BEB MAb lacked efficacy against SARS-CoV-2 Omicron during an era dominated by BA.2, BA.2.12.1, and BA.5 subvariants to reduce the all-cause hospitalization and mortality over 30 days in Banner Health Care System in the Southwestern United States. Moreover, in the subgroup analysis for the primary composite outcome stratified by patient vaccination status, age category, and immunocompromised status between the PS matched groups, BEB MAb use failed to show significant efficacy. The hazards for the composite outcome were lower in the BEB MAb group but not statistically significant. However, fully vaccinated status continued to be protective while age >65 and immunosuppressed status increased the hazards for primary outcome two to four folds, respectively. Similar finding from epidemiological study showing possible protective immunity from previous infections and vaccinations, and that older age can result in worse outcomes during the Omicron wave . Such fiThe only published (non-peer-reviewed data) on the efficacy of BEB MAb comes from the Phase II Blaze 4 clinical trial during the period of alpha and delta waves, which showed that the incidence of the primary outcome in the BEB MAb arm compared with the control arm was similar, around 3% . While iOn November 10, 2022, the NIH COVID-19 Treatment Guidelines Panel reportedHuman genetic predisposition can explain why some individuals are severely affected upon infection by SARV-CoV-2 resulting in severe inflammatory lung injury \u201330. The Observational data analysis in the post-propensity matched cohort cannot be used to prove causality nor propensity score methods can eliminate unmeasured confounding as randomize controlled trials do. Quality of propensity score adjustment depends on propensity model, selection of variables, and sample size. If the propensity model is appropriately constructed and sample size large enough, propensity score methods can approximate treatment effects accurately. By using optimal matching algorithm, a large sample size. very small SMDs (<0.1) across 26 covariates, we feel confident that our results reflect a reasonable approximation of BEB treatment effect.rd or 4th booster); 5) lack of specific SARS-Cov-2 Omicron subvariant genotype sampling; 6) not capturing patients may have received Ritonavir-boosted nirmatrelvir (Paxlovid) and other approved therapies by healthcare providers outside our healthcare system.Large observational studies are necessary to show the efficacy assessment of MAbs in the setting of continuously mutating SARS-Cov-2 when conducting conventional randomized controlled clinical trials may not be practical. However, our study has several limitations: 1) retrospective study design not allowing to rule residual confounding; 2) lack of symptom severity assessment among patients (possibility of more symptomatic patients on the BEB MAb group vs. asymptomatic patients on the control arm); 3) not measuring the impact of immunity through prior COVID-19 infection(s); 4) not knowing patients\u2019 vaccination booster status in the Southwestern United States. Under the light of the current study findings and an expectation of the majority of Omicron subvariants becoming resistant, the continuing use of BEB MAb may no longer be justified. Continuing real-world research from other large healthcare organizations in the different regions of the United States would be needed to assess generalizability.S1 File(PDF)Click here for additional data file."} +{"text": "Staphylococcus aureus (MRSA) and methicillin-susceptible SA (MSSA) infections are a public health threat; MSSA is a growing problem requiring targeted attention. Socioeconomically disadvantaged patients face disparate outcomes. We analyzed SA infection trends in NYC.Methicillin-resistant Hospitalization data for NYC residents were obtained from the NY SPARCS database for 2009-19. Trends in hospitalization rate by resistance (MSSA vs MRSA), clinical syndrome (bacteremia (BAC), pneumonia (PNA), all other infections (OTH)) and setting (community-associated (CA) vs healthcare-associated (HA)) were assessed with Poisson regression. Associations between baseline variables and death were assessed with multivariable logistic regression. CA SA cases were defined as those: 1) with no prior hospitalization in the past year; 2) with a SA diagnosis present on admission; 3) not admitted for complications from a surgery; 4) with no comorbid chronic conditions.The overall rate of hospitalization with SA infection declined by 7.8% from 2009 to 2019. The hospitalization rate for all MSSA infections increased significantly (F1). The rate of MRSA PNA increased significantly but MRSA BAC and OTH MRSA hospitalizations significantly declined (F1). CA cases declined as a proportion of all SA hospitalizations, from 18.4% in 2009 to 12.4% in 2019 (F2).Age, living in a high-poverty area (HPA), and Medicaid or Medicare insurance were significantly associated with higher odds of in-hospital death for CA cases. Non-Hispanic Black and Hispanic Black patients had lower odds of death for HA but not CA cases; the effect of living in a HPA appeared to attenuate the association between race/ethnicity and death. A logistic regression model with demographic predictors was discriminative in predicting in-hospital death for CA cases (area under the curve: 0.87).Crude Hospitalization RatesCrude Hospitalization Rates by Pathogen and Clinical Syndrome Total counts of hospitalizations by resistance and setting While hospitalization with SA is declining overall, the relative burden of MSSA has increased compared to MRSA. Further studies and interventions are needed to understand this and baseline risk factors for SA mortality in vulnerable populations.Mandatory disclaimer for publications using NYS Department of Health data and/or produced under auspices of NYC Department of Health and Mental HygeineAll Authors: No reported disclosures"} +{"text": "Healthcare-associated infections (HAI) constitute a significant burden to patient outcomes and healthcare costs. Ventilator-associated pneumonia (VAP) carries a high mortality and represents one of the costliest HAI. There is uncertainty if treating this subgroup of patients in For-Profit (FP) hospitals portents better outcomes than Nonprofit (NP) hospitals.A retrospective cohort of patients admitted from January 2016 through December 2020 was extracted from the National Inpatient Sample database. We compared two cohorts of patients with a primary diagnosis of VAP: patients admitted to FP hospitals and patients admitted to NP hospitals. The primary end-point was all-cause inpatient mortality. A multivariate logistic regression analysis was conducted. The secondary end-points included: comparing the requirement of vasopressor use and Acute Kidney Injury (AKI) requiring hemodialysis (HD); describing associated comorbidities; and comparing if there was a difference in length of stay (LoS) and hospital cost between the 2 groups. In order to compare LoS and hospital cost, a multivariate linear regression was conducted.A total of 6 155 hospitalizations under the primary diagnosis of VAP were included. No statistically significant difference in mortality was noted , but age and Charlson Comorbidity Index(CCI) were modest predictors of mortality for both groups (FP vs. NP). There was no statistically significant difference in mean LoS between these two groups . CCI and admission to large-size hospitals were predictors of LoS for both groups. Admission to for-profit hospitals predicted higher hospitalization costs (p = 0.020). Furthermore, admission to medium-size hospitals, large-size hospitals, and urban hospitals were also predictors of higher hospital cost (p < 0.05). No statistically significant difference was found in vasopressor use and AKI requiring HD among both groups (FP vs. NP) (p < 0.05).Admission to For-Profit hospitals did not portend better outcomes compared to Nonprofit hospitals. Conversely, admission to For-Profit hospitals predicted higher total hospital costs.All Authors: No reported disclosures"} +{"text": "MicroRNAs (miRNAs) are RNA molecules consisting of approximately 21 nt and are known for their roles in target transcript cleavage or translational regulation . PrimaryThe regulatory roles of miRNA have been widely discussed. For example, plant miRNAs act as regulators of plant\u2013environment interactions . ArsenicArabidopsis thaliana) , arsenic [As(III)] treatment, or LS + As(III) treatment, miPEP408-35aa inhibited seedling growth. To further confirm the negative role of miR408 in seedling growth under these stresses, Arabidopsis lines overexpressing miR408 or carrying knocked out miR408 were generated. The overexpression of miR408 inhibited seedling growth while knockout of miR408 promoted tolerance to these stresses. In addition to the stress tolerance phenotypes, the authors also measured cellular sulfate and GSH levels. Overexpression of miPEP408 promoted the cellular level of sulfate but reduced the cellular level of GSH. Since sulfate is the oxidized form of sulfur, the promoted sulfate level reflects repressed sulfur reduction, an important step for GSH biosynthesis . Whereasynthesis .Plantacyanin (ARPN) and Laccase-3 (LAC3) transcripts (Glutathione S-Transferase TAU 25 (GSTU25) as an additional target of miR408. By analyzing the 5\u2032 RNA Ligase Rapid Amplification of cDNA Ends (RLM-RACE) products, the authors showed miR408 mediates the cleavage of GSTU25 transcripts. The application of miPEP408-35aa also downregulated the expression of GSTU25. Overexpression of miR408 downregulated the expression levels of sulfur reduction pathway genes including Adenosine 5\u2032-Phosphosulfate Sulfurylases (ATPS) and Adenosine 5\u2032-Phosphosulfate Reductase (APR) in Arabidopsis. The effects of miR408 on gene expression are consistent with the miR408-mediated promotion of cellular sulfate level and the repression of cellular GSH level. Moreover, when miR408 was overexpressed, the reduced cellular GSH level was in line with the increased sensitivity to LS, As(III), and LS + As(III) stresses.Previously, miR408 was reported to mediate the cleavage of nscripts . In thisTriticum aestivum), soybean (Glycine max), rice (Oryza sativa), barley (Hordeum vulgare), and maize (Zea mays) . The negea mays) ."} +{"text": "Comparative studies of immune-active hot and immune-deserted cold tumors are critical for identifying therapeutic targets and strategies to improve immunotherapy outcomes in cancer patients. Tumors with high tumor-infiltrating lymphocytes (TILs) are likely to respond to immunotherapy. We used the human breast cancer RNA-seq data from the cancer genome atlas (TCGA) and classified them into hot and cold tumors based on their lymphocyte infiltration scores. We compared the immune profiles of hot and cold tumors, their corresponding normal tissue adjacent to the tumor (NAT), and normal breast tissues from healthy individuals from the Genotype-Tissue Expression (GTEx) database. Cold tumors showed a significantly lower effector T cells, lower levels of antigen presentation, higher pro-tumorigenic M2 macrophages, and higher expression of extracellular matrix (ECM) stiffness-associated genes. Hot/cold dichotomy was further tested using TIL maps and H&E whole-slide pathology images from the cancer imaging archive (TCIA). Analysis of both datasets revealed that infiltrating ductal carcinoma and estrogen receptor ER-positive tumors were significantly associated with cold features. However, only TIL map analysis indicated lobular carcinomas as cold tumors and triple-negative breast cancers (TNBC) as hot tumors. Thus, RNA-seq data may be clinically relevant to tumor immune signatures when the results are supported by pathological evidence. Th. Th32]. age in R .p value was less than 0.05 and the log2 fold change was greater than 2. Genes with a log2 fold change of less than 2 yet with a significant p value were considered minimally differentially expressed. The overlapping upregulated and downregulated genes from the comparisons between cold tumors and either hot tumors or GTEx samples were checked for their correlation with the lymphocyte score using the Pearson product-moment correlation ) (https://david.ncifcrf.gov/ (accessed on 24 May 2023)) was used to identify transcription factors. T effector, T exhausted, and T cell functionality genes were manually curated based on the T cell literature [To identify significantly enriched processes and pathways, we did an enrichment analysis on immune-related pathways from KEGG and GO terms using the Bioconductor packages Pathview and Gage in R ,72. For y 2023)) . DAVID (terature ,74.RNA-seq-based assignment of breast tumor types to either hot or cold category was further tested against tumor-infiltrating lymphocyte maps from TCGA and H&E whole-slide pathology images under TCIA . The datp values were calculated by comparing the distribution of samples in the hot and cold groups for each category to the distribution of remaining samples in these two groups (p value of 0.05 was used to determine statistical significance.To investigate whether certain clinical characteristics would associate with the immunological coldness or hotness of breast tumors, we conducted Fisher\u2019s exact tests in R. The o groups . A cutofSurvival curves were estimated using the Kaplan\u2013Meier method and the statistical comparison was done using the log-rank test. The log-rank test is used to test the null hypothesis of no difference in survival between two or more independent groups.In summary, this study analyzes the immune microenvironment in hot and cold breast tumors, their adjacent normal tissues, and normal healthy breast tissues based on TCGA RNA-seq and GTEx data. The hot/cold assignment of breast tumors was verified using pathology image-derived TIL maps. We demonstrated that infiltrating ductal carcinoma and estrogen receptor ER-positive tumors were significantly associated with cold phenotypes. However, RNA-seq results should be interpreted with caution and accompanied with pathological evidence for meaningful clinical decision-making.We provided evidence for high levels of pro-tumorigenic M2 macrophages in cold tumors and showed that T cell suppression is the main immune evasion mechanism in hot breast tumors. We hypothesize that elevated levels of M2 macrophages and ECM rigidity may restrict lymphocyte infiltration into the cold tumor core. Our findings also indicate M2 macrophages are a promising immunotherapeutic target in human breast cancer."} +{"text": "Sulfur homeostasis is of vital importance for plant health and human nutrition. Sulfur nutrition strongly impacts plant resilience and nutritional quality traits in agricultural crop production. Recent discoveries provide dynamic perspectives on biological processes and mechanistic models delineating biochemical diversity and genetic regulation of plant sulfur metabolism. Invited reviews and articles in this Special Issue highlight current knowledge and ongoing research in sulfur biology.In the sulfur cycle in nature, plants are producers of the essential amino acids cysteine (Cys) and methionine (Met), both of which are incorporated into storage proteins serving as a dietary source consumed by animals (2\u2013) and O-acetylserine (OAS), the substrates for Cys biosynthesis, modulate formation of the Cys synthase complex and sulfate assimilation complex which optimizes plant growth lyase (OAS-TL) highlights the importance of the proposed sulfur-sensing function of the Cys synthase complex in As tolerance , cadmium (Cd), lead (Pb), and mercury (Hg), are significant threats to global food security, deteriorating plant performance and human health. Plants exposed to these toxic metals and metalloids detoxify them through conjugation, sequestration, and avoidance mechanisms . In this2\u2013 in plant Cd responses. As the product of sulfate assimilation and Cys catabolism, the potential signaling function of this highly reactive small molecule draws increasing attention. The prevalence of its biological impact may well be explained by translational and post-translational regulations associated with protein persulfidation ..2\u2013 from Sulfur-containing cofactors play pivotal roles in metabolism . They arCys desulfurase is the enzyme which is central to the extraction of sulfur from Cys, facilitating subsequent sulfur transfer or \u2018sulfur trafficking\u2019 in the Fe\u2013S cluster and Moco biogenesis pathways. 2\u2013 released after disassembly of Fe\u2013S clusters could rely on Cys biosynthesis locally in this organelle.Fe\u2013S cluster formation in mitochondria parallels its essentiality in chloroplasts. OAS is arguably the compound gaining traction over the past few decades in this research area. While it serves as a substrate for Cys biosynthesis, it is also recognized categorically as a signaling molecule triggering dissociation of the Cys synthase complex . OAS accS-methyl-Met cycle as a possible strategy to improve seed quality. They further mention the OAS cluster gene regulations in developing seeds of pea and wheat grains hexamers and O-acetylserine(thiol)lyase (OAS-TL) dimers form this multienzyme complex. SAT/SERAT hexamers within the Cys synthase complex (blue) are free from feedback inhibition by Cys and remain active to synthesize OAS from Ser. OAS-TL dimers within the Cys synthase complex are catalytically inactive (gray). Free OAS-TL dimers (green) catalyze synthesis of Cys from OAS and S2\u2013. Under sulfur-deficient conditions (\u2013Sulfur), S2\u2013 gradually becomes unavailable and OAS accumulates in the cell. OAS promotes dissociation of the Cys synthase complex. SAT/SERAT hexamers dissociated from the complex are inactive (gray) because they are sensitive to feedback inhibition by Cys. Illustration modified based on work by Under sulfur-replete conditions (+Sulfur), S42\u2013 and synthesize Cys, GSH, and sulfur-containing specialized metabolites. These metabolites contribute to maintaining the redox status and stress mitigation. The seed storage protein composition will become sulfur rich. Under sulfur-deficient conditions (right), plants activate SO42\u2013 uptake and promote sulfur recycling. Sulfur-rich seed storage proteins will become less abundant and replaced by sulfur-poor storage proteins. The OAS cluster genes are co-regulated and play important roles in these processes.Boxes highlight responses to changes in sulfur conditions: under sulfur-replete conditions (left), plants accumulate SO"} +{"text": "International Journal for Equity in Health (2022) 21(Suppl 3):16710.1186/s12939-022-01767-5After publication of this article , the autThe statement in the Funding information section was incorrectly given as \u2018The WHO surveillance database and dashboards are funded by WHO funds, including publication charges\u2019 and should have read \u2018The WHO surveillance database and dashboards are funded by the WHO. Funding for the journal special issue has been provided by Global Affairs Canada (GAC).\u2018The author name Henry Laurenson-Schafer was incorrectly written as Henry Laurenson-Schaefer.The original article has been"} +{"text": "Objectives: To evaluate the total and outpatient economic burden of aspergillosis, and to describe the outpatient antifungal treatment of aspergillosis within a large, commercially-insured population in the United States.Methods: Adults with at least one medical claim with an aspergillosis diagnosis between 07/01/04-03/01/11 were identified from the MarketScan Research Databases. Patients had \u22656 months of pre-index and \u22651 month of post-index continuous health plan and pharmacy benefit enrollment and no pre-index diagnosis of aspergillosis. Aspergillosis cases were propensity score-matched to a sample of controls without aspergillosis. Outpatient antifungal therapy and total and outpatient healthcare resource utilization were evaluated in the post-index period. General linear models were used to estimate costs, which were adjusted by the length of follow-up. Incremental costs were calculated between cohorts and a bootstrap procedure was used to produce corresponding variation and 95% confidence interval estimates.Results: Aspergillosis cases were matched to 5,499 controls . Two-thirds of the aspergillosis cases had no outpatient prescription for an antifungal within 30 days of index; for those with outpatient antifungal therapy, voriconazole was the most commonly prescribed agent (60.9%). Average adjusted total and outpatient expenditures were greater for aspergillosis patients during follow-up than those of the matched controls .Conclusions: The economic burden of aspergillosis is substantial. Patients with aspergillosis utilize significantly more healthcare resources and thus incur greater healthcare costs than do similar patients without aspergillosis."} +{"text": "The new coronavirus had a huge impact on individuals from a social, economical and psychological point of view. In march 2020 The World Health Organization declared the coronavirus diseases 2019 (COVID-19) a pandemic and highlighted its psychoemotional implications.The aim of this study was to investigate the psychological distress during the COVID-19 pandemic in patients with cutaneous manifestations and SARS-CoV-2 infection.Data was collected from one first-line infectious diseases hospital from northeastern Romania. All patients with cutaneous manifestations and SARS-CoV-2 infection who accepted to answer the quality of life questionnaire (QLQ) were included in the study. The descriptive data analysis was conducted with the SPSS.A total of 191 patients with cutaneous manifestations and COVID-19 completed a questionnaire concerning their psychological distress and financial burden during the pandemic. Patients with chronic dermatological diseases (psoriasis) \u2013 31% reported the highest level of psychological distress and financial burden compared to patients with acute cutaneous manifestations . Furthermore, this patients showed generalized anxiety disorder, depressive symptoms, post-traumatic stress disorder (PTSD), sleep disturbances and they attributed their individual psychological distress to the COVID-19 pandemic. This patients received psychological/psychotherapeutic treatment due to the COVID-19 crisis, during hospitalization and after discharge.During the pandemic, patients with dermatological diseases needs not only medical support but also psychological and psychosocial support. This study results emphasize the importance of monitoring the psychological impact of the COVID-19 pandemic on patients with cutaneous manifestations.None Declared"} +{"text": "Antimicrobial stewardship (AS) is critical to effectively treat infections and combat antibiotic resistance. Our Healthcare-Associated Infections/Antimicrobial Resistance (HAI/AR) program used state-level data to set public health priorities for AS across diverse acute care (ACH) and critical access (CAH) hospital settings.Infographic describing antimicrobial stewardship goals and priority actions for Colorado hospitalsHospitals reported antibiotic use (AU) data and implementation of priority core elements of AS to the National Healthcare Safety Network (NHSN). The Colorado Department of Public Health and Environment (CDPHE) accessed the data according to a data use agreement with NHSN. We used these data and antibiotic resistance surveillance data to inform state public health goals for AS.Staphylococcus aureus (MRSA) by 5% in five years by encouraging facilities to evaluate their empiric anti-MRSA ABS and provide PAF. Goal Three is to increase NHSN AU/AR reporting to 100%/75% of ACH and 75%/50% of CAH with support through virtual AU/AR office hours and financial grants. Finally, we identified an increase in carbapenemases as an urgent threat and will encourage facilities to review use of broad-spectrum ABS and provide PAF, while monitoring rates of carbapenemases. These initiatives will be promoted through AS collaborations and feedback reports, with progress monitored through the AU Targeted Assessment for Stewardship reports.AU data were available for 47/53 ACH (88%) and 18/31 (58%) CAH. Three antibiotics (ABS) of highest use were ceftriaxone , vancomycin (14%), and piperacillin-tazobactam (10%). Data from the NHSN Patient Safety Survey indicated prospective audit and feedback (PAF) occurred in 79% of ACH and 47% of CAH. Monitoring discharge duration of therapy was reported in 27% of ACH and 37% of CAH. We developed three goals: Goal One is to decrease broad-spectrum ABS used for community-acquired infections (BSCA) by 5% in five years by encouraging hospitals to achieve 75% adherence to facility-specific treatment guidelines by 2025. Goal Two is to reduce the use of ABS active against methicillin-resistant These novel state-wide AS initiatives are tailored by local data and best practices to support a common vision for action for hospital AS providers.All Authors: No reported disclosures"} +{"text": "The new coronavirus disease (COVID-19) has important physical and mental health implications at short and long term. Some inflammatory parameters are implicated in the maintenance of psychiatric symptoms, especially those of anxiety and depression. Additionally, growing literature attributes a role to interoception in several mental health conditions.We investigated the involvement of the interoception in COVID-19 survivors and its possible associations with psychopathological and inflammatory variables.Our study included 57 people surviving COVID-19 at one month follow-up after recovery. Individual interoceptive accuracy (IA) measure was obtained through heart-beat perception task. A measure of accuracy in external time perception (TA) was also obtained asking people to mentally produce a duration of 10s. Each participant completed State-Trait Anxiety Inventory - STAI-Y; Zung Self-Rating Depression Scale - ZSDS; Beck Depression Inventory - BDI-II; Impact of Events Scale - IES-R and Multidimensional Assessment of Interoceptive Awareness - MAIA. Peripheral inflammation markers were obtained in a subsample of 40 people by a blood sampling conducted at the time of admission and discharge from hospital. Correlation, regression and GLM analyses were performed with SPSS. Mediation analysis were performed with Hayes\u2019 Process tool.TA is not associated with IA, symptomatological measures and bodily awareness. Trusting is the only aspect of body awareness associated with IA (p=.021). Noticing (p=.010), Not-distracting (p=.009), Not-worrying (p=.012) and Trusting (p=.001) predict anxiety psychopathology. Poor IA predict anxiety symptomatology (p=.004) and part of this effect is mediated by Trusting [Fig.1]. In the end, platelets count at the time of hospitalization negatively correlates with anxiety symptoms (p=.003).Image:COVID-19 hospitalization could be considered a psychophysical traumatic experience which involved mental and physical health and the connection and integration between them. It\u2019s necessary to deepen the different facets of body awareness and IA in post-covid stages and to study how interoceptive dimensions change over time. Further research is needed to investigate the specific role of platelets in prominent anxiety psychopathology detected in COVID-19 survivors, wondering about their possible involvement in the dysfunctional interoception process too.None Declared"} +{"text": "The American Society of Heating, Refrigeration, and Air-Conditioning Engineers (ASHRAE) recommends that hospital operating rooms (OR) are controlled for temperature and humidity with established ranges but does allow for exceedances for surgeons and surgical procedures. There is currently no clear consensus or established thresholds for out-of-range temperature and humidity ranges in relation to risk for surgical site infections (SSI). A study was performed at Memorial Sloan Kettering Cancer Center (MSKCC) to further examine if temperature and humidity deviations pose a patient safety risk.p < 0.05.The study included 5600 surgical procedures that were performed at MSKCC between September 2021 and January 2022 where temperature and humidity logs were available. Procedures were broken into groups based on in- (n=4419) and out-of-range (n=1187) temperatures and in- (n=5225) and out-of-range (n=381) humidity. SSIs following the procedure were identified using targeted positive microbiology cultures and within NHSN surveillance periods. Chi-square and Fisher\u2019s exact statistical tests were used to determine if there was a significant difference between groups where Breakdown of eligible procedures and follow upTable represents the total number of eligible procedures with environmental parameters and SSI follow up period.p=0.15). There was a significantly higher SSI rate observed for out-of-range temperatures (p=0.04) more specifically low out- of-range temperatures (p=0.02). A sub-analysis was performed for low temperatures based on procedures by duration. Significance of the finding was lost when surgery duration was 4 hours or greater.There was no significant impact on SSI for out-of-range humidity (If there was a true correlation between SSI and low ambient temperature, we would have expected to see a strengthening of SSI risk with longer procedures. This study suggests that temperature and humidity deviations out of the recommended guidelines in the operating room do not pose additional risks for surgical site infections and limited exceedances can be permitted without risking patient safety.All Authors: No reported disclosures"} +{"text": "Patients with chemo-refractory metastatic colorectal cancer (mCRC) have poor prognoses. The application of programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) inhibitors encouragingly improved the survival of mCRC patients with microsatellite instability-high (MSI-H)/mismatch repair-deficient (dMMR). Unfortunately, it was ineffective for mCRC with microsatellite-stable (MSS)/proficient mismatch repair (pMMR), which accounted for 95% of mCRC. Radiotherapy can promote local control by directly killing tumor cells and inducing positive immune activities, which might help synergistically with immunotherapy. We present the report of an advanced MSS/pMMR mCRC patient who had progressive disease (PD) after first-line chemotherapy, palliative surgery and second-line chemotherapy combined with targeted therapy. Then the patient received the therapy of PD-1 inhibitor combined with radiotherapy and granulocyte-macrophage colony-stimulating factor (GM-CSF). According to Response Evaluation Criteria in Solid Tumors version 1.1 (RECIST1.1), the patient showed a complete response (CR) after triple-combined therapy with progression-free survival (PFS) for more than 2 years so far. The patient had no other significant adverse reactions except for fatigue (Grade 1). The triple-combination therapy provided a promising strategy for metastatic chemo-refractory MSS/pMMR mCRC patients. By 2021, colorectal cancer (CRC) was the third most common cause of cancer mortality worldwide. Meanwhile, metastasis was found at the first diagnosis in 20% of CRC patients , 4. The We present the report of a refractory mCRC patient with MSS/pMMR who received PD-1 inhibitor combined with Radiotherapy and GM-CSF. The patient demonstrated a sustained tumor response and prolonged progression-free survival (PFS) for over 2 years so far.A patient in his mid 40s was diagnosed with ascending colon adenocarcinoma through colonoscopy biopsy and pathological examination on 21 January 2020. Further Positron Emission Tomography/Computed Tomography (PET/CT) imaging showed metastasis of retroperitoneal and celiac lymph nodes in February 2020. All of the primary lesion and the part of the mesenteric lymph nodes were resected. The mesenteric and retroperitoneal lymph nodes were not resected. Then the patient received six cycles of chemotherapy of capecitabine plus irinotecan (mXELIRI) combined with Bevacizumab from March to July 2020. CT scan observed new lymph node metastases at mesenteric and retroperitoneal in August 2020, which indicated progressive disease (PD). It suggested the patient was insensitive to chemotherapy combined with vascular-targeted Therapy. In addition, neutropenia and gastrointestinal reaction (Grade 2) were observed during chemotherapy.http://www.chictr.org.cn/index.aspx). We defined the triple-combined therapy of PD-1 inhibitor combined with Radiotherapy and GM-CSF as PRaG therapy. The patient underwent three cycles of PRaG therapy in August 2020 and September 2020. In the PRaG cycle, radiotherapy was delivered for lymph node metastases, followed by subcutaneous injection of GM-CSF and intravenous injection of toripalimab . PRaG regimen was repeated every three weeks inhibitor combined with Radiotherapy and GM-CSF (Recombinant Human Interleukin-2(I) for Injection) in patients with advanced metastatic solid tumors on 10 August 2020 was delivered for celiac metastatic lymph node and retroperitoneal metastatic lymph node. Considering the tolerance dose constraints of normal tissues, the radiation dose was reduced to 5Gy/d (d1-3) for celiac lymph node in the third cycle.After the PRaG therapy, the CT scan showed that lymph node metastases in retroperitoneal and celiac almost disappeared compared with before Figure\u00a02Backline treatment of MSS mCRC is a hard nut to crack. Regorafenib or trifluridine and tipiracil (TAS-102) were recommended, but the survival benefit was still limited. A phase II trial of TAS-102 combined with nivolumab showed no tumor response in MSS/pMMR mCRC . The mPFin-situ vaccines that can promote tumor cells to release tumor-associated antigens (TAAs) and induce immunogenic cell death (ICD) . The PEMth (ICD) . The samth (ICD) .GM-CSF is a cytokine used to promote the growth of leukopenia or neutropenia and is widely used to promote the production of granulocytes or APCs. Preclinical studies supported that GM-CSF combined with immune checkpoint inhibitors (ICI) can improve the activity of innate immune cells, and indirectly recruit T cells by promoting the antigen cross-presentation , 17. IpiThe doses and frequency of radiation have not been standardized when radiotherapy is combined with PD-1/PD-L1 inhibitors. Preclinical studies have shown that hypo-fractionated radiotherapy (5Gy \u00d7 3f) boosted more proliferation and activation of antigen-presenting cells compared with conventionally fractionated radiotherapy (2Gy \u00d7 5f) . The conConsidering the heterogeneity of the tumor, irradiation of a single site may not induce sufficient exposure to TAAs. Chang et\u00a0al. suggested multisite radiotherapy of metastases to enhance the synergistic effect . HoweverAfter three irradiation cycles achieved an excellent local control effect with a significant decrease in the irradiated lymph node metastases. At the same time, the regression of the nonirradiated lesion was also observed. Regression of the nonirradiated tumor was called the abscopal effect, which was not frequently in patients with radiotherapy alone , 29. HowThe MSS mCRC patient achieved terrific results through PRaG triple-combination therapy with well-tolerated. The efficacy and safety of PRaG therapy for MSS mCRC patients need to be confirmed in future prospective studies.The original contributions presented in the study are included in the article/The studies involving human participants were reviewed and approved by the Ethics Committee of the Second Affiliated Hospital of Soochow University. The patients/participants provided their written informed consent to participate in this study. Written informed consent was obtained from the individual(s) for the publication of any potentially identifiable images or data included in this article.JY composed the manuscript as the first authorship. LZ designed and conducted the study as corresponding authors. PX and YK helped with data collection and interpretation. MX collected and sorted out part of the image data. All authors read and approved the final manuscript."} +{"text": "BMC Public Health (2023) 23:104210.1186/s12889-023-15960-wIn the original publication of this article the corresponding authorship of Zahid Ahmad Butt was not indicated. The original publication has been updated to amend this."} +{"text": "Dear Editor,With interest we read the article by Sobreira et al. about the thromboembolic complications of COVID-19 vaccines.Coagulopathy is a common feature of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its incidence increases in severe cases.The mechanisms of thrombotic events are multifactorial and platelets play a major role in this phenomenon. Beyond hemostasis and thrombosis, platelets are also capable of sensing and responding to invading pathogen and immune signals.Both positive and negative effects depend on the interaction between viral proteins and host cell receptors. Interactions can occur directly via various immune receptors in platelets or indirectly through plasma proteins. Platelets also express angiotensin-converting enzyme 2 (ACE2) which serves as the primary receptor for SARS-CoV-2 and facilitates virus entry into host cells.COVID-19 thrombotic complications may be the result of direct or indirect impacts of viral infection. SARS-CoV-2 can directly activate ACE2 and potentiates platelet activation. Moreover, the SARS-CoV-2 spike protein enhances the potential of thrombosis and recombinant human ACE-2 protein can suppress virus-induced platelet activation. The virus can also directly induce platelet releasing coagulation factors and inflammatory cytokines and increases formation of leukocyte-platelet aggregates.Platelets may also be activated indirectly, through sensing of an inflammatory microenvironment and subsequent dysfunction of vascular endothelium, which are induced by viral infection. The inflammatory milieu may cause uncontrolled platelet activation which consecutively may lead to pathophysiological effector activities. Moreover, immune complex containing viral particles may impact on the platelet hyperactivity in COVID19 patients.Altogether, platelets may be affected by SARS-CoV-2. Therefore, understanding of the underlying mechanisms can be beneficial in promoting assessment and treatment of COVID-19 patients. Dear Editor,We would like to thank you for the important points on the topic of our article about thromboembolic complications of COVID-19 vaccines, which are quite relevant and help update knowledge on the issue.The interactions described in relation to the pathophysiological role of platelets in activating the alleged potential thrombotic trigger are initiated by vaccine-induced thrombocytopenia, as occurs with thrombotic predisposition accompanying infection caused by COVID19.Much remains to be discovered about the pathophysiology of COVID-19 infection, particularly the potential predisposition to thrombotic events. Thank you for sharing this data about complex platelet mechanisms and interactions that enhances the content of our article and helps us to understand and clarify the best assessment and treatment of COVID-19 patients.Covid-19 vaccines and thromboembolic complications"} +{"text": "The effects of preeclampsia superimposed on chronic hypertension (CHTN-PE) on the structure and function of the human brain are mostly unknown. The purpose of this study was to examine altered gray matter volume (GMV) and its correlation with cognitive function in pregnant healthy women, healthy non-pregnant individuals, and CHTN-PE patients.Twenty-five CHTN-PE patients, thirty-five pregnant healthy controls (PHC) and thirty-five non-pregnant healthy controls (NPHC) were included in this study and underwent cognitive assessment testing. A voxel-based morphometry (VBM) approach was applied to investigate variations in brain GMV among the three groups. Pearson\u2019s correlations between mean GMV and the Stroop color-word test (SCWT) scores were calculated.Compared with the NPHC group, the PHC and CHTN-PE groups showed significantly decreased GMV in a cluster of the right middle temporal gyrus (MTG), and the GMV decrease was more significant in the CHTN-PE group. There were significant differences in the Montreal Cognitive Assessment (MoCA) and Stroop word scores among the three groups. Notably, the mean GMV values in the right MTG cluster were not only significantly negatively correlated with Stroop word and Stroop color scores but also significantly distinguished CHTN-PE patients from the NPHC and PHC groups in receiver operating characteristic curve analysis.Pregnancy may cause a decrease in local GMV in the right MTG, and the GMV decrease is more significant in CHTN-PE patients. The right MTG affects multiple cognitive functions, and combined with the SCWT scores, it may explain the decline in speech motor function and cognitive flexibility in CHTN-PE patients. Hypertensive disorder of pregnancy (HDP), including preeclampsia/eclampsia, gestational hypertension, chronic hypertension, and preeclampsia/eclampsia superimposed on chronic hypertension, continues to be among the major causes of maternal and fetal morbidity and mortality around the world . HDP affThe effects of pregnancy on the structure and function of the human brain are poorly understood. The voxel-based morphometry (VBM) method was utilized in the current investigation, which can fairly and comprehensively evaluate the anatomical differences in gray matter (GM) throughout the entire brain . VBM is With the increase in sex hormones during pregnancy, women often show cognitive and subjective emotional changes, as well as a slight decline in cognitive function . StudiesThe objectives of this study were, first, to discuss the characteristics of decreased GMV in pregnant healthy women and CHTN-PE patients and, second, to summarize the characterization of GMV reductions associated with cognitive dysfunction.This prospective and cross-sectional study was approved by Jinan Maternity and Child Care Hospital\u2019s institutional review board. Twenty-five CHTN-PE patients (age 32.24 \u00b1 5.00 years), thirty-five non-pregnant healthy controls (NPHC) (age 32.29 \u00b1 4.99 years) and thirty-five pregnant healthy controls (PHC) (age 30.34 \u00b1 5.73 years) from July 2020 to April 2021 were enrolled in this cross-sectional study. All participants were clear about the detailed experimental procedures and signed informed consent forms. CHTN-PE patients were recruited from the obstetric ward and had to be clinically stable to complete the MRI examination. No subjects were diagnosed with eclampsia, either before or after participating in the study. All pregnant participants had blood pressure (BP) measured, blood and urine sampling, and MRI examinations within 12 h after study enrollment. BP was measured in the right arm after subjects had been supine for 15 min. Routine blood and urinary tests were performed in all pregnant participants. The CHTN-PE patients included in this study did not demonstrate hypertension crisis after the evaluation of clinicians and could be examined by MRI. MRI examinations and cognitive assessments for all pregnant women were completed after admission, before delivery, and under clinically stable conditions.The inclusion and exclusion criteria are shown in All participants underwent detailed neurological examinations by professional neurologists. The Beijing version of the Montreal Cognitive Assessment (MoCA) was used to evaluate cognitive functions , which i\u00b0; and isotropic voxel size: 1 mm3]. Furthermore, T2-weighted (T2W) turbo spin echo, T2W fluid-attenuated inversion recovery (FLAIR) and diffusion-weighted images (DWI) were obtained and used to identify brain abnormalities. The average scanning time of each sequence is about 5 min, and the total imaging time did not exceed 20 min.Magnetic resonance imaging scanning was performed on a 1.5-T MR scanner using a 16-channel head coil for signal reception. A three-dimensional (3D) T1-weighted (T1W) high-resolution sequence with the following parameters was used to generate the structural images [repetition time (TR): 25 ms; echo time (TE): 6.1 ms; inversion time (TI): 900 ms; flip angle: 301 toolbox after data acquisition based ont-test was applied to assess differences in gestational weeks between the NPHC and PHC groups, and one-way analysis of variance (ANOVA) and least significant difference (LSD) post-hoc tests were used to examine differences in other demographic and clinical parameters among the three groups using the Statistical Package for the Social Sciences . The SPM8 toolbox was used to perform one-way analysis of covariance (ANCOVA) with age and total intracranial volume (TIV) as covariates to compare GMV differences among the three groups, and the family-wise error (FWE) correction based on Random Field Theory (RFT) method was applied to control multiple comparisons curve analysis using MedCalc Statistical Software.en index , 2018. Tpost-hoc tests, and a two-sample t-test was performed to assess differences in gestational week. The mean MoCA and Stroop word scores were significantly different among the three groups. The CHTN-PE group had lower MoCA scores and higher Stroop word scores than the NPHC and PHC groups, and the PHC group had lower MoCA scores and higher Stroop word scores than the NPHC group. No significant differences were found in age, gestational week, Stroop color and Stroop color-word scores among the three groups. No abnormality was found in routine magnetic resonance imaging in three groups . The mean GMV values within the right MTG cluster were extracted, and follow-up LSD post-hoc tests revealed that the CHTN-PE group had significantly lower GMV than the NPHC and PHC groups and that the PHC group had lower GMV than the NPHC group in the right MTG cluster . There were no significant correlations between the GMV and Stroop color-word scores in all subjects for all subjects. Correlation analysis revealed a significant positive correlation between the mean GMV of the right MTG and MoCA while suppressing interference from a task that was more automated (reading words) . In fact2) in CHTN-PE patients has not been evaluated. CBF and CMRO2 can be obtained by adding multi-delay arterial spin labeled images of Jinan Maternity and Child Care Hospital (20190618). The patients/participants provided their written informed consent to participate in this study.CS wrote the main manuscript text. CS and HW performed the statistical analysis. JH, TC, YG, and YW prepared the clinical data and imaging data. LY and LG revised the main manuscript text. All authors reviewed the manuscript."} +{"text": "Macroautophagy , a highly programmed process maintains cellular homeostasis by degrading over-copious or damaged organelles, large macromolecular aggregates, and invading pathogens via the lysosomal system. Autophagy is generally activated by a variety of extracellular or intracellular stresses, such as oxygen- or energy-deprivation, drugs, infections, etc. In addition to non-selective bulk degradation of cytosolic contents, autophagy selectively recycles specific organelles including mitochondria (mitophagy), endoplasmic reticulum (ER) (ER-phagy), lysosomes (lysosomophagy) and intracellular lipid droplets (lipophagy) . AutophaAlim Al-Bari et al. describe the mechanistic intricacies of selective autophagy and its impact on liver physiology and pathology and suggest modulation of selective autophagy as key to therapeutic interventions against several hepatic diseases.In a detailed review presented here, Qi et al. report how curcumol, an active constituent of the Rhizoma Curcumae roots control AFLD development by targeting hepatocyte senescence. They found that curcumol suppresses lipid accumulation in an ethanol liquid diet-induced liver injury mouse model and in ethanol-treated LO2, human fetal hepatocyte cell line via inhibition of hepatocyte senescence. Mechanistically, the senescence-related suppressive activity of curcumol in AFLD is associated with inhibition of cytoplasmic chromatin fragments (CCF) formation and subsequent inactivation of the cyclic GMP\u2013AMP synthase (cGAS) stimulator of interferon gene (STING) signaling pathway, resulting in a significant reduction in senescence-associated secretory phenotype (SASP) in hepatocytes. The authors concluded anti-AFLD activity of curcumol might be attributed to its blocking of LC3B-lamin B1 interaction for inhibition of CCF formation and subsequent inactivation of the CCF-cGAS-STING signaling pathway, and curcumol is proposed as a therapeutic molecule for hepatocyte senescence.In the first research article; Yan et al. report that cajaninstilbene acid (CSA), a natural stilbene compound derived from the leaves of pigeon pea [Cajanus cajan (L.) Millsp.] commonly used in traditional medicine alleviates AILI pathology in a mouse model. Since the emergence of the COVID-19 pandemic, it is common clinical practice to advise patients to take APAP to relieve headache and fever (In developed countries acetaminophen (APAP or paracetamol)-induced liver injury (AILI) is the predominant cause of acute liver failure . In theind fever . Althougnd fever .Li et al. investigates this cross-talk and describe a beneficial effect of the FDA-approved anti-T2DM drug empagliflozin in ameliorating hepatic steatosis. Empagliflozin is a sodium-glucose co-transporter-1/2 (SGLT1 and 2) inhibitor and synthetic analog of the natural flavonoid phlorizin, isolated from apple trees , rose hips (Rosa canina L.), strawberry fruits (Fragaria x ananassa Duch.), or pear tree (Pyrus communis L.) and reduces triglyceride content and lipid accumulation in the hepatocyte steatosis model via activation of autophagy through the AMPK-Ten-Eleven Translocation-2 (TET2) signaling pathway. Interestingly, previous study in a rat model of T2DM, empagliflozin was shown to prevent hepatic steatosis, via proposed mechanisms involving activation of SIRT1 and AMPK pathways (MAFLD is the fatty-liver pathology associated with metabolic disorders like obesity and T2DM. The manuscript by unis L.) . In the pathways . In addipathways . Based oAlim Al-Bari et al. on this Research Topic summarizes the mechanistic details of selective autophagy in the context of liver and its impact on abnormal liver function in patients including that of COVID-19. In addition, this review proposes the pharmacological targeting of autophagy as a viable strategy against liver pathologies, which is supported by the findings of the three research articles in the Research Topic. While modulation of autophagy seems to be a sought-after strategy for treating several diseases, focus on selective autophagy pathways and development of specific inhibitors for the same will be the way forward. We hope the research articles and the comprehensive review on this Research Topic presented here generate more interest in research aimed at understanding molecular mechanisms of autophagy-related liver pathologies, finally providing reasonable clinical treatment options.In conclusion, the review article by"} +{"text": "Dear Editor,The global prevalence of chronic lung diseases is increasing, with a significant number of people affected by chronic obstructive lung disease (COPD), asthma and interstitial lung diseases.\u00ae , which employs the multi-breath helium dilution method for measuring static lung volume, with the MiniBox. All subjects provided written informed consent according to a protocol approved by the Institutional Review Board of National Hospital Organization Osaka Toneyama Medical Center, Osaka, Japan (TNH-R-2020048). The study included 60 participants categorised into three groups: 12 healthy volunteers, 24 patients with restrictive lung disease and 24 patients with obstructive lung disease. The baseline clinical characteristics of the participants is shown in An alternative tool is the MiniBox\u2122 , which is a table-top plethysmography system that offers a reliable means of measuring spirometry, flow-volume loop, static lung volume and diffusion capacity. It is cost-effective, space-efficient and simple to operate, making it suitable for primary care sites.MB), expiratory reserve volume (ERVMB) and inspiratory reserve volume (IRVMB) measured using the MiniBox were not significantly different from the values obtained on the Chestac-8900 (MB) and forced expiratory volume in the first second (FEV1MB) measured using the MiniBox did not differ significantly from the values obtained using the Chestac-8900 (MB), functional residual capacity (FRCMB) and residual volume (RVMB) measured using the MiniBox were significantly greater than the values measured by the Chestac-8900 (CT) was similar to the TLC measured by the Chestac-8900 (TLCChestac). The mean discrepancy was \u20130.397 L (95% LoA \u20132.077 to 1.284) (MB) was significantly greater than TLCCT (MB and TLCChestac was negatively correlated with the ratio of FEV1 to FVC (FEV1/FVC) and positively correlated with the percentage of emphysematous lesions on CT (low-attenuation areas [LAA%]) derived from morphometric analysis . In contan TLCCT . The meaanalysis . This suMB) using spirometry data and flow-interruption transients through a machine learning algorithm.MB showed good correlation with TLC measured using both helium dilution (TLCChestac) and chest CT scan (TLCCT). However, TLCMB consistently yielded higher values than TLCChestac or TLCCT, particularly in patients with obstructive lung disease. For the MiniBox, the predictive equation for static lung volume was generated from data based on the original set of individuals, whose static lung volumes (measured using plethysmography) served as the reference.The MiniBox is a compact device with a flow-interruption feature used for measuring lung volumes. It calculates total lung capacity (TLCCO) and diffusion capacity of the lungs for carbon monoxide (DLCO) , carbon monoxide transfer coefficient (Ke (DLCO) . However devices . The MinCurrently, whole-body plethysmography is the gold standard for measuring lung volumes, but each method has limitations.15Click here for additional data file."} +{"text": "Here, we investigated if divergent sites in the CR and IRD are involved in the interaction between these two begomoviruses. ToSRV clones were constructed containing the same nucleotides as ToRMV in the CR (ToSRV-A(ToR:CR)), IRD (ToSRV-A(ToR:IRD)) and in both regions (ToSRV-A(ToR:CR+IRD)). When plants were co-inoculated with ToRMV and ToSRV-A(ToR:IRD), the infectivity and accumulation of ToSRV were negatively affected. In mixed inoculation of ToRMV with ToSRV-A(ToR:CR), high infectivity of both viruses and high DNA accumulation of ToSRV-A(ToR:CR) were observed. A decrease in viral accumulation was observed in plants inoculated with ToSRV-A(ToR:CR+IRD). These results indicate that differences in the CR, but not the IRD, are responsible for the negative interference of ToRMV on ToSRV.Mixed infection between two or more begomoviruses is commonly found in tomato fields and can affect disease outcomes by increasing symptom severity and viral accumulation compared with single infection. Viruses that affect tomato include tomato severe rugose virus (ToSRV) and tomato rugose mosaic virus (ToRMV). Previous work showed that in mixed infection, ToRMV negatively affects the infectivity and accumulation of ToSRV. ToSRV and ToRMV share a high degree of sequence identity, including Begomovirus (family Geminiviridae) comprises plant viruses with a genome consisting of one (monopartite) or two (bipartite) single-stranded circular DNA molecules encapsidated separately by a single structural protein in twinned icosahedral particles and ToSREscherichia coli by electroporation, and three clones of each genomic component were sent for commercial sequencing by primer walking . Sequences were assembled using DNA Baser v. 3.5 and organized to begin at the nicking site in the invariant nonanucleotide at the origin of replication (5\u2032-TAATATT//AC-3\u2032). Pairwise sequence comparisons of DNA-A and DNA-B, CRs and ORFs between ToRMV and ToSRV were performed using Sequence Demarcation Tool (SDT) v.1.2 to a total of 144 ToSRV isolates from different hosts to see how common the observed variations in the CR and IRD are among isolates of the virus. Analyzing the IRD nucleotide sequence, we found that only five of these isolates contained a single variable nucleotide and that only two out of these five isolates lack cytosine as the first base of the fifth Rep codon (like ToSRV-[BR:PG1:Pep:03] does) . For the(ToR:IRD) that could be related to the virus-specific recognition of the iterons, an in silico prediction was performed using the AlphaFold2 program. As mutations in the CR would not affect the structure of any virus-encoded protein, ToSRV(ToR:CR) and ToSRV(ToR:CR+IRD) were not considered in the modeling. All models generated by the program had high confidence metrics ((ToR:IRD). The TM-score value for ToSRV(ToR:IRD) in relation to wt ToSRV was 0.96. To investigate possible conformational differences in the structure of the Rep protein of ToRMV, ToSRV wt and ToSRV metrics . The sim(ToR:IRD) clone was evaluated with single changes: ToSRV(Pro>Thr) and ToSRV(Lys>Arg). ToSRV(Pro>Thr) had a TM-score of 0.62, 0.94 and 0.98 in relation to ToRMV, wt ToSRV and ToSRV(ToR:IRD), respectively. ToSRV(Lys>Arg) yielded TM-scores of 0.62, 0.97 and 0.97 in relation to ToRMV, wt ToSRV and ToSRV(ToR:IRD), respectively.The ToSRVBegomovirus) in the same plant are very common in nature was obtained from pepper rather than tomato. The differences observed in the CR sequence of ToSRV-[BR:PG1:Pep:03] may be the result of viral adaptation to a new host, and this adaptation may have incurred a fitness cost. Although ToSRV naturally infects tomato and pepper, infection in tomato is much more prevalent in the field. New studies comparing ToSRV isolates from various hosts may provide additional insights into viral evolution in terms of adaptation to new hosts and potential fitness effects."} +{"text": "Greenness exposure has been associated with many health benefits, by providing opportunities for physical activity. Longitudinal studies are lacking, and most studies overlook the varying effects of different greenness types on physical activity (PA) and sedentary behavior (SB). We investigated 9-year associations of greenness characterized by overall greenness, vegetation type, and mix, with PA and SB using data from the ORISCAV-LUX study and the MET\u2019HOOD project.The PA and SB outcomes were measured using the International Physical Activity Questionnaire (IPAQ) short form. PA is expressed as MET-minutes/week and log-transformed, and SB is expressed as sitting time in minutes/day. The exposure variables were Tree Cover Density (TCD), Soil-adjusted Vegetation Index (SAVI), and Green Land Use Mix (GLUM). The study population consisted of 628 adults, who completed the questionnaires between January 2007-2009 and January 2016-July 2017. Missing data were imputed. Greenness exposure was collected within 800-meter street network buffers based on participants\u2019 exact residential address. Associations between TCD, SAVI and GLUM and PA and SB were estimated using a Random Effects Within-Between (REWB) model. Interaction by gender and SES were explored. Sensitivity analyses were performed on smaller (500 meter buffer) and larger definitions of the residential neighborhood.We found evidence of between-individual associations of GLUM and PA , and within-individual associations of TCD with PA (in 800 meter buffers). There was no evidence for associations between greenness exposure and SB. Sensitivity analysis using varying buffer sizes showed similar associations.Our study found evidence of associations of GLUM and TCD with PA, and no associations between greenness exposure and SB. Promoting different types of greenness may result in different PA levels and behaviors. Replication studies are needed to inform urban planning interventions.This study is funded by the EU Horizon2020 Program under\u00a0grant agreement number 956780 (SURREAL). The\u00a0ORISCAV-LUX study is funded by the Luxembourg Ministry of Health and Ministry of Higher Education and Research. The MET'HOOD project is funded by the Luxembourg National Research Fund as part of the CORE 2020 programme (C20/BM/14787166)."} +{"text": "Our clinical research unveiled chronic heart failure with preserved ejection fraction (HFpEF) as a long-term sequel in survivors of severe pediatric burn injury due to a yet unknown molecular pathomechanism. Applying a standardized rat model, we systematically determined the pathophysiological impact of burn injury on long-term cardiac performance to uncover systemic and molecular pathomechanisms that may cause post-burn HFpEF development.Male adolescent SD-rats were subjected to a 60 % total body surface area (TBSA) full-thickness burn- or sham-trauma and subsequently characterized after burn-injury by serial transthoracic echocardiography, bulk myocardial next-generation sequencing and proteomics as well as RT-PCR, immuno-blotting (IB), histology and plasma proteomics for cardiac performance and molecular alterations, respectively, at 3, 7, 30 and 90days.In comparison to the sham-group (SG), animals from the burn-group (BG) recapitulated typical post-burn clinical traits, such as significant loss in body weight or skeletal muscle wasting in accord with elevated molecular atrophy markers. We show post-burn cardiac muscle wasting and persistent markers of cardiac dysfunction in accord with significant histological cardiomyocyte hypotrophy and significantly diminished left ventricular (LV) global longitudinal strain and isovolumic relaxation time in BGs, while LV-EF remained unchanged. Weighted gene network correlation analysis from bulk myocardial NGS and clinical traits related activation of immunological and pro-fibrotic pathways in post-burn injury hearts to cardiac dysfunction in BGs. Subsequent RT-PCR and histology confirmed significant myocardial accumulation of cardio-depressive damage associated molecular patterns and infiltration by granulocytes and monocytes as well as significant LV fibrosis. Serial plasma proteomic analysis indicated elevated plasma levels of S100A8 and A9 and other heart failure markers that mirrored similar changes in human post-burn plasma samples.Here we report the development of HFpEF as a novel systemic consequence of severe burn injury in a rodent model, which warrants further mechanistic and translational studies. Cardiac inflammation and fibrosis are known to negatively impact cardiac performance and may be mechanistic key findings that will guide further therapeutic studies and subsequent validation of post-burn heart failure biomarkersThis model is part of a translational and interdisciplinary experimental and clinical effort to inform pathophysiology and mechanistics of long-term heart failure in burn patients. Echocardiographic data and parameters from this model are currently being used to evaluate adult survivors of severe burn injury for signs of HFpEF."} +{"text": "The incidence of incisional self-harm of the upper limbs is increasing, and recurrence rates are high. It is not known whether different wound treatment strategies (dressings only vs. surgery) or the operative setting (main theatre vs. non-main theatre) affect wound or mental health-related outcomes.Four electronic databases were searched from inception to 14/09/2021 for studies which describe the management of incisional self-harm wounds of the upper limb(s) in adults and children. Dual-author screening and data extraction were conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.In total, 19 studies (1477 patients) were included. Overall, the evidence was limited by a paucity of comparative data on wound management strategy and setting, and poor-quality outcome reporting. Only four studies clearly identified the operative setting for definitive wound management . Few studies inconsistently reported surgical outcomes (n=9) or mental health outcomes (n=4), hindering evidence synthesis.Further investigation is needed to determine the most cost-effective management strategies and settings for these injuries. The recently drafted National Institute for Health and Care Excellence (NICE) guidelines for self-harm (NG10148) emphasise the importance of a psychosocial assessment after every episode of self-harm at the earliest opportunity Decision-making for operative vs. best non-operative care should be discussed with patients on an individual basis.The primary aim of this review is to compare the management of incisional self-harm wounds of the upper limb , with respect to surgical and mental health outcomes. Our secondary aims include comprehensively describing the epidemiology of incisional self-harm injuries of the upper limb, regarding patient and injury characteristics, psychological and surgical management approaches, and their outcomes.This systematic review adheres to a prespecified protocol and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 checklist.Appendix; Table S1). Studies returned by database searches were compiled and de-duplicated using Covidence\u00a9 software. Two reviewers (AL and AS) independently screened articles against prespecified inclusion and exclusion criteria in two stages . Discrepancies between reviewers were resolved through discussion; a third author (JNR) was consulted if consensus was not reached.The inclusion and exclusion criteria are shown in Two reviewers (AL and AS) independently extracted data using a piloted data extraction form developed for the purpose of the review. This included study details , participant demographics , injury characteristics and management approach . Information was extracted per injured structure and in commonly encountered groups of structures, i.e. radial triad and ulnar triad . Upper limb structures were also classified into superficial, middle and deep anatomical layers, as previously described.Extracted outcomes were mental health related and surgical/functional. Mental health outcomes included further attempted self-harm (any), further suicide attempt and further episode(s) of incisional self-harm. Post-operative outcomes included clinically diagnosed wound infection, any re-operation related to the original injury (including re-repair and tenolysis) and adherence to surgical follow-up. Functional outcomes included any patient-reported outcome measure for the upper limb and any measure of tendon, intrinsic muscle or motor/sensory nerve function.The following were summarised narratively: study details; patient and injury characteristics; management approach (operative vs. non-operative) and setting of operative wound management. Suitability for meta-analysis of surgical and mental health outcomes was determined by author consensus based on the clinical and statistical heterogeneity of the included studies. Quantitative synthesis was not appropriate; hence, narrative synthesis was undertaken following the synthesis without meta-analysis (SwiM) guidance.The National Institutes of Health Quality Assessment Tool was used to assess the risk of bias for Observational Cohort and Cross-Sectional Studies.Database searches returned 932 non-duplicate citations, of which 19 were included in the review .Figure 1Table S1. Most (n=17) were retrospective cohort studies and two were prospective cohort studies. There were no randomised-controlled trials or comparative cohort studies. Eleven studies only included patients with self-inflicted injuries; six also included accidental or non-self-inflicted wounds. Most studies (n=17) aimed to describe the characteristics and/or surgical outcomes of upper limb incisional self-harm injuries. One study specified factors relating to post-closure wound infection as the primary outcome.,A list of included studies is provided in Table S2).The overall risk of bias for the included studies was fair , poor and good were male, and the mean age ranged from 16 to 57 years. Some studies specified their population, for example, self-inflicted stab wounds,Table S3).Where specified, 356 (82%) patients had unilateral self-inflicted upper limb injuries and 78 (18%) had bilateral injuries. Where injury characteristics were described in detail, 381 (36%) were superficial with no structural injury. A total of 894 structures were injured, or 0.84 structures per patient . One study reported wound infection in 2/3 self-inflicted wounds closed in the emergency department.Seven studies described psychiatric management. Those that did offered same-day psychosocial assessment to 296 (76%) patients and follow-up to 102 (26%) patients. Four studies reported mental health outcomes within the study period. One study reported further attempted or completed suicide , and three studies reported further instances of self-harm . One study described \u2018several\u2019 repeated incisional self-harm episodes but did not quantify this further.Our key finding is that there is a paucity of comparative data for different management approaches for incisional self-harm injuries of the upper limb and underreporting of mental health assessment and outcomes.We were unable to compare theatre and non-theatre settings for wound management (our primary outcome) because most studies did not describe the operative setting. However, a notable proportion of the injury patterns described in the included studies would not necessarily need formal surgical exploration and repair . If these patterns are generalisable, then non-operative or non-theatre management might be appropriate in some circumstances. This is an area that may merit further investigation. It is unclear whether wound management approach or setting affects functional outcomes, recurrent self-harm risk or other mental health outcomes. Inconsistent surgical, functional and mental health outcome reporting hindered evidence synthesis and could be standardised. This may be partly facilitated by a core outcome set for flexor tendon injuries (currently in development),The proportion of patients offered psychosocial assessment during admission and follow-up was short of NICE standards and was likely overestimated given that two-thirds of included studies did not describe psychiatric management. Few studies reported rates of further attempted or completed suicide and recurrent self-harm within the study period. Where reported, events were rare. However, the reported figures may be underestimates due to underreporting, given repetition rates of up to 50% in the non-surgical literature,Patients with incisional self-harm injuries have the highest recurrence rates,The near-equal gender distribution in this study may be explained by men being more likely to use sharp objects in non-fatal suicide attempts,The strengths of this review include the comprehensive search of four electronic databases and dual-author screening and data extraction, according to PRISMA methodology.Incisional self-harm of the upper limb is prevalent in both genders with high rates of psychiatric comorbidity. There is a paucity of comparative data on different treatment approaches (operative vs. non-operative) and settings for wound management (theatre vs. non-theatre), and the effect (if any) on wound-related outcomes, mental health-related outcomes and health economic outcomes; this warrants further investigation. Few studies reported surgical, and particularly mental health, outcomes, with inconsistent outcome measures, hindering evidence synthesis. High-quality comparative studies with standardised outcome reporting are warranted. All healthcare professionals have a responsibility to ensure an appropriate psychosocial assessment is performed prior to discharge.National Institute for Health Research (NIHR) Doctoral Research Fellowship (NIHR300684) for this research project. Jeremy N. Rodrigues is funded by an NIHR postdoctoral fellowship (PDF-2017-10-075). This document presents independent research funded by the NIHR. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.Conrad J. Harrison is funded by a Not required.None declared."} +{"text": "Correction to: Clinical Rheumatology (2022) 42:75-8210.1007/s10067-022-06375-w\u201cMusculoskeletal ultrasound (MSUS) can detect inflammation within the synovium the joint, and quantification of active synovitis through Power Doppler (PDUS) in RA patients has been well established. PDUS has been utilized to predict RA therapeutic response, RA flares, and clinical remission; and may be more sensitive than clinical examination in detecting active joint inflammation. In the current work, we evaluated an association of PDUS synovitis signal with HDL function and structure in patients with RA treated in two independent clinical therapeutic trials.\u201dThe final paragraph of the Introduction section as shown below should have been removed in the original published version of the above article.The original article has been corrected."} +{"text": "Clinical trials have demonstrated that levofloxacin prophylaxis during periods of neutropenia in hematopoietic stem cell transplantation (HSCT) reduces the frequency of bacteremia in adults and febrile episodes in children. Therefore, levofloxacin prophylaxis may also have a role in reducing empiric intravenous antibiotic (EIA) use.This retrospective review assessed the impact of levofloxacin prophylaxis for patients < 18 years undergoing HSCT at a Canadian children\u2019s hospital. The primary outcome was antibiotic days of therapy (DOT) during the pre-engraftment period comparing the pre-levofloxacin era to the levofloxacin era . Patients were excluded if they were receiving EIA at the time of transplant, received chimeric antigen receptor T-cell therapy, or if levofloxacin use was discordant with their era. Secondary outcomes included the number of positive blood cultures and clinical deterioration episodes .Fifty-four of 152 patients (36.5%) and 55 of 147 patients (37.4%) were included in the pre-levofloxacin and levofloxacin eras respectively. The most common reasons for exclusion were EIA use at the time of transplant and levofloxacin use discordant with the patient's era . Baseline characteristics were not significantly different between groups (Table 1). Mean DOT/pre-engraftment days (%) were significantly lower in the levofloxacin era for piperacillin-tazobactam and amikacin , while there was no significant difference for meropenem, vancomycin, or all other antibiotics combined. There was also no significant difference in the number of positive blood cultures or clinical deterioration episodes .Levofloxacin prophylaxis in children undergoing HSCT reduced percent pre-engraftment days on piperacillin-tazobactam and amikacin, with no significant impact on the number of positive blood cultures or clinical deterioration episodes. Therefore, levofloxacin prophylaxis may facilitate antimicrobial stewardship activities through reduced use of certain broad-spectrum antibiotics.Kathryn E. Timberlake, PharmD, Avir Pharma: Advisor/Consultant"} +{"text": "This article refers to data derived from a research article entitled \u201cPrediction of narrow HT-SMA thermal hysteresis behaviour using explainable machine learning\u201d The datasets are provided as supplementary files and the second dataset is also visualised as an intuitive marginal effects plot. We believe that these data will find applications in advancing experimental and theoretical HT-SMA research. Specifications Table1\u2022The main dataset is valuable because it consolidates significant prior published data on narrow HT-SMA thermal hysteresis behaviour;\u2022The second dataset is valuable because it improves the generalized understanding of the influence of the Ti-, Ni-, Pd-, Pt-, V-, Hf-, Zr-, Cu-, and Co- contents have on the narrow HT-SMA thermal hysteresis behaviour\u2022Some materials used in the development of Ti-Ni-based HT-SMAs are rare-precious metals that are scarce and prohibitively expensive, researchers working on HT-SMA development can significantly benefit from the availability of these consolidated and simulated datasets.\u2022As demonstrated in the original paper , these s\u2022Finally, these datasets are part of a case study curated to demonstrate the benefits of interpreting ML-predicted outcomes in the advanced materials and engineering field.The value of the data is summarised below:2The work grows from a need to develop prediction models that are not only accurate but explainable from a practical metallurgical persuasion. The objective of the work was to produce results and outcomes that communicate usable knowledge to the advanced materials and metallurgical community. The data reported in this article are intended for practitioners \u2013 those researchers busy planning, conducting, or interpreting their own experimental or computational work. The consolidated main dataset will find applications in advancing experimental and theoretical HT-SMA developments while the simulated dataset will summarise our findings 3The data presented in this article are divided into two components. That is, (i) the main dataset which consolidates significant prior published data on narrow HT-SMA thermal hysteresis behaviour of novel Ti-Ni-based HT-SMAs, (ii) an auxiliary dataset simulated based on the related research article findings ,3, and a4The main dataset is constructed from HT-SMA thermal hysteresis behaviour observations reported in experimental peer-reviewed research reports. It also builds upon data published by Yamabe-Mitarai , Frenzel(a) An ML-based XG-Boost model was developed using the Scikit-Learn and XGBoost libraries in the Python environment.(b) The model inputs data collected from experimental reports in the public domain to predict the narrow hysteresis behaviour (< 60 \u00b0C) in novel Ti-Ni HT-SMAs. The data is structured as a dataframe herein each row defines an alloy's multicomponent elemental composition as taught in our previous work .ous work .(c) The ML model development and implementation involves the prediction of the narrow hysteresis behaviour in novel Ti-Ni HT-SMA. The model follows a conventional ML-supervised regression where the accuracy of the model is assessed by comparing the ML predictions against true (previously known) values. SeeFig.\u00a02.(d) The ALE post-hoc analysis technique was implemented in the Python environment using the PyALE package to analyze the marginal effects of each element's composition on the narrow hysteresis behaviour. The implementation of the ALE method produces a dataset showing how see how the ML prediction (y-axis) changes as a function of the predictor features (x-axis) i.e., Ti-, Ni-, Pd-, Pt-, V-, Hf-, Zr-, Cu-, and Co- amounts in the alloy. seeFig.\u00a01.(e) The dataset has nine sets of simulated samples. More specifically, the y-axis is the predicated expected change in ML predicted \u0394T value that affects the predictions of the model while holding the values of all the other compositions constant.The reported auxiliary data are simulated, and not necessarily secondary data; the data were acquired following machine learning and post-hoc ALE computations using the above-described hardware and software.Lastly, ALE plots see were genThe research work did not involve human or animal subjects or the collection of data from social media or similar platforms. The use of artificial intelligence (AI) tools reported in this article, and the original study, is responsible and in line with the highest ethical standards including Australia's AI Ethics Principles . None ofR. Machaka (RM): Conceptualization (lead), Funding acquisition (lead), Data curation (supporting), Methodology (lead), Hardware & computations (lead), Visualisation (lead), Writing \u2013 original draft (lead), Writing \u2013 review & editing . P.M. Radingoana (PMR): Data collection (lead), Methodology (supporting), formal analysis , Writing \u2013 review & editing ."} +{"text": "To evaluate variation in the prescription of guideline-recommended medications across Medicare Advantage (MA) plans and to determine whether such variation is associated with increased mortality.Observational study of 111,667 patients aged 65 years or older receiving care in 203 MA plans. We linked data from the Medicare Health Outcomes (HOS) Survey cohort 9 (April 2006\u2013May 2008) with the Medicare Part D prescription benefit files to examine variation in treatment across MA plans and its association with differences in observed (O)/expected (E) mortality ratio for 5 high-volume chronic conditions: diabetes, coronary artery disease (CAD), congestive heart failure (CHF), chronic obstructive pulmonary disease (COPD)/asthma, and depression.Analysis of variance confirmed that the 203 MA plans differed significantly in their use of guideline-recommended treatment (P\u22640.02). Those MA plans with higher use of angiotensin-converting enzyme inhibitors/angiotensin II receptor blockers and beta-blockers in patients with CHF were significantly associated with lower O/E mortality ratios. Those MA plans with higher use of multiple guideline-recommended medications were significantly associated with lower O/E mortality ratios in CHF and diabetes . There were no significant associations between the variation in performance indicators and mortality ratios in patients with CAD and COPD/asthma. Those MA plans with higher use of antidepressant medications had significantly higher O/E mortality ratios .There was wide variation across MA plans in the prescription of guideline-recommended medications that had a measurable relationship to the mortality of elderly patients with CHF and diabetes. These findings can serve to both motivate and target quality improvement programs."} +{"text": "The left atrium had a mobile intracavitary mass with dynamic mitral valve stenosis. The mass was mildly heterogeneous and predominantly hyperintense on T2 short-inversion-time inversion-recovery and T1-weighted images.A 71-year-old woman with a history of endometrial cancer was referred for CMR imaging for precise assessment of left ventricular (LV) function after the surgical removal and pharmacological treatment of the tumour. The patient was asymptomatic. The CMR protocol included cines, T1 mapping, T2 mapping, first-pass perfusion, late gadolinium enhancement, and 4D flow imaging. The LV was normal in size . A diastolic LV vortex is formed in the low-pressure areas near the basal mitral annular area inside the LV. This doughnut-like vortex preserves the kinetic energy of blood flow during early and late filling (Video S2). A lack of it would plausibly mean further loss of diastolic function and cardiac efficiency. The absence of LV diastolic vortex formation has been linked with aging and other cardiovascular diseases. The patient had successful surgical removal and confirmed histological diagnosis of myxoma .On 4D flow two-dimensional vector visualization, during early and late filling, the blood flow accelerates through the anterior leaflet of the mitral valve. There was evidence of E/A flow reversal and absence of diastolic vortex formation (This case highlights the importance of not only multi-parametric tissue characterization by CMR to facilitate the diagnosis of myxoma but also the use of emerging 4D flow CMR visualization and quantification tools to allow enhanced assessment of transvalvular flow and associated flow-related patterns. However, more work must be done to develop our comprehensive understanding of how vortex formation is dependent on LV geometry, pressure gradients, and mitral annulus.ytad298_Supplementary_DataClick here for additional data file."} +{"text": "Vascular endothelial growth factor (VEGF) is linked with Non-small cell lung carcinoma (NSCLC). Therefore it is of interest to document data on the molecular dockinganalysis of VEGF with compounds from tomato for consideration drug discovery. Data shows that compounds Kaempferol-3-O, Quercetin, Naringenin & Rutin show optimalbinding. Lung cancer is a serious threat to human health. This condition has been the world's most dangerous malignancy . Every yThe X-ray crystal structure of VEGF (PDB code: 1FLT) was downloaded from the Brookhaven Protein Data Bank (www.rcsb.org/pdb).10 compounds (Table 1 - see PDF) known from the tomato plant were collected from the literature. The structures of these compounds were dowmloaded from the PubChemCompound Database in the Spatial Data File (SDF) format and translated to the PDB file format by using Online Smile Translator. Energy minimization of ligands wascompleted using Open Babel software with a steepest 139 descent using uniform force fields and then translated to PDBQT format.AutoDock (V. 4.0) could be used in the PyRx GUI to validate the binding capability of the selected ligands to the selected target .The griIn order to recognize the interaction of the selected compounds with the active VEGF site, the compounds have been submitted to molecular docking simulation studiesperformed using the PyRx docking method using the Autodock VINA program. The molecular docking of bioactive compound at the VEGF binding site was carried out on the basisof the reported VEGF (PDB code: 1FLT) and complex structures, and the highest suitable binding modes of the best compounds were shown in Figure 1(see PDF). The bindingenergy and H-bond information have been shown in Table 2(see PDF), where the created docked complexes have been examined on the basis of binding affinity values and bonding interaction patterns . Compounds have strong hydrogen bonding interactions through amino acid residues GLN-22,THR-31, LEU-32, GLN-37, CYS-57, GLY-59, ASN-100 and CYS-102. By using pymol, the docking results were then compared to see the interaction produced the best bindingenergy, out of 10 dockings performed. Many of the compounds showed very strong interactions with the VEGF receptor. We sorted the four compounds on the basis of thebinding energy. The strongest docking interaction between VEGF and four compounds was shown in Figure 1(see PDF), with binding energy ranging from-7.2 to 5.9 kcal /mol.Analysis of the docking results showed that selected compounds interact with VEGF protein via H bond interactions. These compounds showed the strong interaction withactive site residues. The presence of the H-bond interactions enabled the complex to attain the specified configuration of the complex structure. The selected fourcompounds showed very close interactions with the VEGF receptor . As per Data shows that compounds Kaempferol-3-O, Quercetin, Naringenin & Rutin show optimal binding with VEGF."} +{"text": "Characterization of coronavirus disease 2019 (COVID-19) vaccine breakthrough infections are limited. This study aims to characterize breakthrough infection hospitalized in a tertiary hospital in the Philippines and identify risk factors associated with severe and critical outcomes.A retrospective cohort study was done on 133 vaccinated adult individuals with COVID-19 breakthrough infection hospitalized in a tertiary hospital since the start of the vaccination roll out in the Philippines. Demographic, clinical and vaccination profile were obtained and statistically correlated with outcome of severe and critical COVID-19 illness.Work Flow DiagramWork Flow Diagram of Determining COVID-19 Breakthrough InfectionsA total of 133 patients were reviewed: the mean age was 53 years. The mean time to SARS CoV2 detection from full dose vaccination is 107 days. Most of the patients have hypertension (n=76), diabetes mellitus (n=49) and chronic kidney disease (n=30). Majority have moderate severity (n=56). Age of more than 65 , presence of acute coronary syndrome , active cancer , and diabetes mellitus , symptomatology of cough , shortness of breath , and fatigue and a high baseline sensitivity C-reactive protein were associated with increased risk of developing severe and critical COVID-19 breakthrough infection. On the other hand, receipt of Pfizer as primary series vaccination and a high baseline PaO2/FiO2 ratio were associated with decreased risk of developing severe and critical illness.Demographic and Clinical Profile of patients with COVID-19 Breakthrough Infections hospitalized in Philippine General HospitalDemographic and Clinical Profile of patients with COVID-19 Breakthrough Infections hospitalized in Philippine General HospitalDemographic and Clinical Profile (Continuous Variables) of patients with COVID-19 Breakthrough Infections hospitalized in Philippine General HospitalDemographic and Clinical Profile (Continuous Variables) of patients with COVID-19 Breakthrough Infections hospitalized in Philippine General HospitalLaboratory Profile (Cycle Threshold) of COVID-19 Breakthrough Infection Hospitalized in Philippine General HospitalLaboratory Profile (Cycle Threshold) of COVID-19 Breakthrough Infection Hospitalized in Philippine General HospitalMajority of the COVID-19 breakthrough infections have moderate disease. Age more than 65 years old, presence of co-morbidities such as acute coronary syndrome, active cancer and diabetes mellitus, symptoms of cough, shortness of breath and fatigue on initial presentation and high baseline high sensitivity CRP were associated with increase chance of developing severe and critical COVID-19 among breakthrough patients, while a primary series vaccination with Pfizer and a high baseline PaO2/FiO2 ratio were associated with decreased risk.Association of Demographic and Clinical Profile and Laboratory Profile of COVID-19 Breakthrough Infection in developing Severe and Critical COVID-19Association of Demographic and Clinical Profile and Laboratory Profile of COVID-19 Breakthrough Infection in developing Severe and Critical COVID-19All Authors: No reported disclosures"} +{"text": "Scientific Data 10.1038/s41597-023-02124-z, published online 17 April 2023Correction to: In this article the affiliation details for Rui Zhang were incorrectly given as Xiamen University but should have been BGI-Qingdao; the affiliation details for Weidong Li were incorrectly given as BGI-Qingdao but should have been Xiamen University; and the affiliation details for Haipeng Liu were incorrectly given as BGI-Qingdao but should have been Xiamen University. The original article has been corrected."} +{"text": "Walking balance is central to independent mobility, and falls due to loss of balance are a leading cause of death for people 65 years of age and older. Bipedal gait is typically unstable, but healthy humans use corrective torques to counteract perturbations and stabilize gait. Exoskeleton assistance could benefit people with neuromuscular deficits by providing stabilizing torques at lower-limb joints to replace lost muscle strength and sensorimotor control. However, it is unclear how applied exoskeleton torques translate to changes in walking kinematics. This study used musculoskeletal simulation to investigate how exoskeleton torques applied to the ankle and subtalar joints alter center of mass kinematics during walking. We first created muscle-driven walking simulations using OpenSim Moco by tracking experimental kinematics and ground reaction forces recorded from five healthy adults. We then used forward integration to simulate the effect of exoskeleton torques applied to the ankle and subtalar joints while keeping muscle excitations fixed based on our previous tracking simulation results. Exoskeleton torque lasted for 15% of the gait cycle and was applied between foot-flat and toe-off during the stance phase, and changes in center of mass kinematics were recorded when the torque application ended. We found that changes in center of mass kinematics were dependent on both the type and timing of exoskeleton torques. Plantarflexion torques produced upward and backward changes in velocity of the center of mass in mid-stance and upward and smaller forward velocity changes near toe-off. Eversion and inversion torques primarily produced lateral and medial changes in velocity in mid-stance, respectively. Intrinsic muscle properties reduced kinematic changes from exoskeleton torques. Our results provide mappings between ankle plantarflexion and inversion-eversion torques and changes in center of mass kinematics which can inform designers building exoskeletons aimed at stabilizing balance during walking. Our simulations and software are freely available and allow researchers to explore the effects of applied torques on balance and gait. Walking balance is central to independent mobility, and falls due to loss of balance are a leading cause of death for people 65 years of age and older. Wearable robotic devices, or exoskeletons, could help people with reduced muscle strength and motor control avoid falls by providing stabilizing torques at lower-limb joints. However, it is currently unclear how exoskeleton torques change walking motions. In this study, we used computer simulation to investigate how exoskeleton torques applied to the ankle change the motion of the body\u2019s center of mass. We first created realistic simulations of walking using a biomechanically accurate model. We then simulated the effect of exoskeleton torques applied to the model that plantarflexed , inverted, or everted the ankle. We found that plantarflexion torques moved the center of mass backwards or forwards, depending on when the torque was applied during the walking cycle. Plantarflexion torques also moved the center of mass upwards. Eversion and inversion torques produced left-right motions of the center of mass. Finally, we found that the force-generating properties of muscles in our model reduced the center of mass changes from exoskeleton torques. Our results can help exoskeleton designers create devices that stabilize walking balance. Walking balance is central to human health and mobility. Balance ability is especially critical to older adults who face significant health problems and injuries when mobility is impaired . In partExoskeleton devices may help prevent undesired center of mass motions by providing the corrective torques that individuals with muscle weakness or sensorimotor impairments are unable to produce. Ankle exoskeletons could also be used to replicate the effect of ankle plantarflexor muscles on changes in medio-lateral ground reaction forces during stance . FurtherPrevious studies have used simulation to study walking balance using a variety of approaches , 24\u201338. The goal of this study was to understand the effect of ankle plantarflexion and inversion-eversion exoskeleton torques on center of mass kinematics and center of pressure positions during unperturbed walking. To this end, we first created realistic muscle-driven simulations of walking using optimal control that track experimental gait data. We then modeled exoskeleton devices using massless actuators that applied plantarflexion and inversion-eversion torques to the ankle and subtalar joints and used forward integration to simulate their effect on walking kinematics. We analyzed these simulations to achieve two goals. First, we sought to determine how changes in center of mass kinematics and center of pressure positions differed based on different exoskeleton devices and different timings of exoskeleton torque during the gait cycle. Second, we sought to determine how intrinsic muscle properties alter center of mass and center of pressure changes induced by exoskeleton torques.We utilized a two-step approach to simulate the effect of ankle plantarflexion and inversion-eversion exoskeleton torques during walking . We firs-1 to create our tracking simulations.We used a previously-collected dataset from 5 healthy individuals walking on a treadmill . SubjectWe used a generic musculoskeletal model with 31 degrees-of-freedom and 80 lower-extremity muscles and a torque-actuated upper-extremity developed for gait simulation . The mod-1 kg-1), bending (1.5 Nm rad-1 kg-1), and rotation (0.5 Nm rad-1 kg-1) coordinates based on experimental measurements of bending moments applied to the lumbar joint [-1 based on experimental ankle impedance measurements [-1 [-1 coefficient were also applied to the lumbar, subtalar, and metatarsophalangeal joints, since the lumbar joint was not muscle-actuated and the subtalar and metatarsophalangeal joints did not track any experimental data . For the remaining joints in the model, we applied passive rotational exponential spring and linear damping forces to represent ligament forces [Passive force elements were included in our model to represent contributions from ligaments and soft tissue structures. Torsional spring forces were added to the lumbar extension and controls (muscle and torque excitations) were constrained to be periodic across the gait cycle. This also avoided unconstrained state variables from taking on large values at the beginning of the trajectory. We prevented the arms from intersecting with the torso and the feet from intersecting with each other by imposing a minimum distance between pairs of the respective bodies via path constraints added to the problem. Finally, the average walking speed over the gait cycle was constrained to match the experimental walking speed.The tracking problems were solved with CasADi . We used-1 because it was both large enough to produce an effect on center of mass motion and small enough to be used for closed-loop control of balance in real devices without destabilizing the user. In addition, we found that torque magnitudes of 0.2 Nm kg-1 or greater often produced kinematics which led to joints hitting the range of motion limits in the model. The exoskeleton device torques had peak times between 20% and 60% of the gait cycle at 5% intervals which occurred between the average times of foot-flat and toe-off of the five subjects. Each simulation began at the onset of exoskeleton torque, and the model initial state was set using the state from the normal walking simulation. The effect of each exoskeleton device was evaluated using forward simulation performed with a 4th-order Runge-Kutta-Merson time-stepping integrator (integrator accuracy: 1e-6) [We simulated five different exoskeleton devices that applied one or two torques to the ankle and/or subtalar joints. The first device applied a plantarflexion torque to the ankle joint, where equal and opposite body torques were applied to the tibia and the talus. Two exoskeleton devices applied torque in eversion and inversion to the subtalar joint, where equal and opposite body torques were applied to the talus and calcaneus. The last two exoskeleton devices applied torque to the ankle and subtalar joints simultaneously . Each exoskeleton device was modeled using massless torque actuators with a a rise time equal to 10% of the gait cycle and a fall time equal to 5% of the gait cycle based on a common four parameter control design used in previous exoskeleton experimental studies . We chosy: 1e-6) . The forIn each exoskeleton simulation, the contributions from muscles were applied to the model using two different approaches that addressed both goals of our study. In the first approach, we applied the muscle excitations from the tracking simulation to the original model with muscle actuators included . In this approach, muscle forces could change based on muscle intrinsic properties as the applied exoskeleton torque produced changes in kinematics. In the second approach, we first computed the moments generated by the muscles in the normal walking simulations. We then replaced the muscles in the model with torque actuators that applied the muscle-generated moments . In this approach, the joint torques applied to the model could not change in response to the exoskeleton devices. The differences between the muscle-driven simulations and the torque-driven simulations reveal the influence of the intrinsic muscle properties.hCOM, 1.03 \u00b1 0.02 m) and accelerations were normalized by gravitational acceleration (g). Center of mass velocities were normalized by the term We computed changes in center of mass kinematics and right foot center of pressure positions to assess the effect of each exoskeleton device in the forward simulations. Changes in center of mass acceleration and in center of pressure were computed at the time of peak exoskeleton torque , since these quantities were most related to force-level information . We comp\u03b1 = 0.05 [We performed two sets of statistical tests to address the goals of our study. The first set of tests compared the effects of the exoskeleton devices on changes in center of mass kinematics and center of pressure positions relative to the normal walking simulations. For these tests, we employed a linear mixed model with 25 observations for each test (5 subjects and 5 exoskeleton devices). Individual tests were performed for each time point in the gait cycle, model actuator type (muscle-driven or torque-driven), and direction of center of mass or center of pressure change . The second set of tests evaluated if the changes in center of mass kinematics and center of pressure positions from the torque-driven simulations were significantly different from the changes produced from the muscle-driven simulations. We again employed a linear mixed model with 50 observations for each test . Individual tests were performed for each time point in the gait cycle and direction of center of mass or center of pressure change. For each linear mixed model, we performed analysis of variance (ANOVA) tests and Tukey post-hoc pairwise tests with a significance level of \u03b1 = 0.05 . The sta\u03b1 = 0.05 \u201367.Plantarflexion, eversion, and inversion torques produced changes in fore-aft and medio-lateral center of mass velocity in the muscle-driven simulations compared to the normal walking condition and toe-off (63.6 \u00b1 1.4% of the gait cycle) from the tracking simulations matched well to those reported by Perry and Burnfield (2010) . The tim-1, which is 6% of the 1.25 m s-1 walking speed used in our simulations. Vlutters et al. (2016) found larger velocity changes after applying force perturbations to the pelvis [This study provides relationships between ankle and subtalar exoskeleton torques and three-dimensional changes in center of mass velocity during the stance phase of walking. We found that plantarflexion torque had a stronger effect on center of mass velocity during mid-stance compared to toe-off. In addition, plantarflexion torque reduced the forward velocity of the center of mass during mid-stance and increased forward velocity at push-off. Eversion and inversion torques primarily affected the medio-lateral velocity of the center of mass. The medio-lateral effects from subtalar torques were stronger than those from ankle plantarflexion torques, while plantarflexion torque had a stronger effect on vertical velocity compared to the subtalar torques. Plantarflexion plus eversion and plantarflexion plus inversion torques combined the kinematic changes we observed from individual exoskeleton torques. The maximum change in the magnitude of center of mass velocity we observed in the muscle-driven simulation was 0.072 m se pelvis .During mid-stance, changes in the right foot center of pressure positions were generally in the opposite direction of the changes in center of mass kinematics. Inversion-eversion exoskeleton torques produced the largest medio-lateral changes in center of pressure which led to the medio-lateral changes in center of mass kinematics. Similarly, plantarflexion exoskeleton torque produced larger forward changes in center of pressure compared to inversion-eversion torques. Center of pressure changes were reduced as fewer contact spheres were in contact with the ground during the late mid-stance and push-off phases. The largest forward change in center of mass velocity occurred at the end of push-off when the center of pressure could no longer shift forward and produce a backwards change in center of mass velocity. In addition, ankle plantarflexion velocity peaked near toe-off and provide quantitative comparisons specific to ankle devices that exoskeleton designers may find useful. For example, we found that including muscle properties could reduce the change in center of mass velocity by nearly a factor of two after applying ankle plantarflexion torque. Therefore, exoskeletons aimed at inducing kinematic changes may need torques larger than estimations from torque-driven simulations because muscles will produce forces that tend to reduce the effects of exoskeleton torques.Some limitations of our simulation approach should be considered when interpreting our results. First, we only simulated the effect of exoskeleton torques when applied during normal walking at a single speed. Therefore, it is unclear whether the relationships we observed between exoskeleton torque and center of mass state would apply to walking conditions that differ from typical gait or are much faster or slower than the walking speed we simulated. Second, since muscle activations were unchanged by the applied exoskeleton torques, we only simulated center of mass and center of pressure changes over a short time window (15% of the gait cycle or 165 ms on average). This time window was chosen to be a compromise between previously reported delays in muscle activity response after perturbation (100\u2013150 ms) and torqFuture studies could build upon our simulations to improve predictions of the effect of exoskeletons on walking kinematics. Models of human motor control should be incorporated in simulations to elucidate how both reflexes and voluntary neural commands drive human kinematic responses to exoskeleton torques. Simulations that train neural control models using approaches based on single-shooting , 73 or rWe chose to simulate healthy, unperturbed walking in this study since no comprehensive mapping between ankle exoskeleton torque and center of mass motion existed for any type of gait prior to this study. Future studies focusing on participants with neuromuscular deficits and other conditions that lead to minimal gait deviations from normal walking may still benefit directly from our results, and studies focusing on larger gait deviations can use these results to generate hypotheses for new assistance strategies to aid balance. Additionally, this study can be a useful reference for future work studying how to optimally assist perturbed walking, which can encompass a wide variety of motions that stem from normal walking. Finally, future studies can leverage our simulation framework to study optimal balance assistance strategies targeted at gait pathologies or perturbed walking.Exoskeleton designers may use the results from this study as a guide for developing devices to control the center of mass during walking. We recommend applying plantarflexion exoskeleton torque during mid-stance to control the center of mass velocity primarily in the fore-aft direction. While we only simulated plantarflexion torque which decreased fore-aft velocity, dorsiflexion torque (or a reduction in an applied plantarflexion torque) could be used to produce the opposite velocity change at a specific time in the gait cycle . While previous work from simple biped models has suggested that plantarflexion torque has a strong effect on medio-lateral kinematics , our reshttps://simtk.org/projects/balance-exo-sim) and software to build upon our work.We used musculoskeletal simulation to evaluate the effect of ankle plantarflexion and inversion-eversion exoskeleton torques on walking kinematics. This work clarifies how exoskeleton torques applied to the ankle and subtalar joints can alter center of mass kinematics and center of pressure positions during walking. Our results showed that the exoskeleton torques we applied produced clear trends in center of mass kinematics. In addition, when we removed muscles from the exoskeleton simulations, the changes in center of mass kinematics increased, highlighting how muscle properties influence the dynamics of human-device interactions. Designers can use these results as a guide for building exoskeletons aimed at improving gait stability. We invite researchers to use our freely available simulation results (S1 Appendix(PDF)Click here for additional data file.S1 Fig-2.The change in center of mass acceleration, calculated at exoskeleton torque peak time, projected onto the transverse plane. The arrows represent acceleration changes normalized by gravitational acceleration and averaged across subjects. Columns represent acceleration changes for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). Thick arrows with filled heads represent changes using the muscle-driven model; thin arrows with open heads represent results using the torque-driven model. Each column includes acceleration changes at different exoskeleton timings, ranging from 20% (bottom) to 60% (top) of the gait cycle. The horizontal arrow directions are medio-lateral changes in acceleration, and the vertical arrow directions are fore-aft changes in acceleration. The horizontal axes provide scales for medio-lateral acceleration changes, and the fore-aft changes represented by each arrow are scaled to match the horizontal axis. The maximum transverse acceleration change observed across both muscle-driven and torque-driven conditions was 0.55 m s(TIF)Click here for additional data file.S2 Fig-2.The change in center of mass acceleration, calculated at exoskeleton torque peak time, projected onto the sagittal plane. The arrows represent acceleration changes normalized by gravitational acceleration and averaged across subjects. Rows represent acceleration changes for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). Thick arrows with filled heads represent changes using the muscle-driven model; thin arrows with open heads represent results using the torque-driven model. Each row includes acceleration changes at different exoskeleton timings, ranging from 20% (left) to 60% (right) of the gait cycle. The horizontal arrow directions are fore-aft changes in acceleration, and the vertical arrow directions are vertical changes in acceleration. The vertical axes provide scales for vertical acceleration changes, and the fore-aft changes represented by each arrow are scaled to match the vertical axis. The maximum sagittal acceleration change observed across both muscle-driven and torque-driven conditions was 0.93 m s(TIF)Click here for additional data file.S3 FigThe change in center of mass position, calculated at exoskeleton torque end time, projected onto the transverse plane. The arrows represent position changes normalized by center of mass height and averaged across subjects. Columns represent position changes for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). Thick arrows with filled heads represent changes using the muscle-driven model; thin arrows with open heads represent results using the torque-driven model. Each column includes position changes at different exoskeleton timings, ranging from 25% (bottom) to 65% (top) of the gait cycle. The horizontal arrow directions are medio-lateral changes in position, and the vertical arrow directions are fore-aft changes in position. The horizontal axes provide scales for medio-lateral position changes, and the vertical changes represented by each arrow are scaled to match the horizontal axes. The maximum transverse position change observed across both muscle-driven and torque-driven conditions was 0.002 m.(TIF)Click here for additional data file.S4 FigThe change in center of mass position, calculated at exoskeleton torque end time, projected onto the sagittal plane. The arrows represent position changes normalized by center of mass height and averaged across subjects. Rows represent position changes for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). Thick arrows with filled heads represent changes using the muscle-driven model; thin arrows with open heads represent results using the torque-driven model. Each row includes position changes at different exoskeleton timings, ranging from 25% (left) to 65% (right) of the gait cycle. The horizontal arrow directions are fore-aft changes in position, and the vertical arrow directions are vertical changes in position. The vertical axes provide scales for vertical position changes, and the fore-aft changes represented by each arrow are scaled to match the vertical axis. The maximum sagittal position change observed across both muscle-driven and torque-driven conditions was 0.004 m.(TIF)Click here for additional data file.S5 Fig-2.The change in center of mass acceleration, calculated at exoskeleton torque peak time, for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). The bars represent acceleration changes normalized by gravitational acceleration and averaged across subjects; error bars represent standard deviations across subjects. The left column represents changes using the muscle-driven models, and the right column represents changes using the torque-driven models. Asterisks above bars represent statistically significant changes relative to normal walking condition; diamonds above bars in the right column represent changes from torque-driven simulations that were statistically different from changes from muscle-driven simulations. The maximum acceleration change observed across both muscle-driven and torque-driven conditions was 0.93 m s(TIF)Click here for additional data file.S6 Fig-1.The change in center of mass velocity, calculated at exoskeleton torque end time, for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). Velocity changes are normalized to the dimensionless Froude number. The bars represent normalized velocity changes averaged across subjects; error bars represent standard deviations across subjects. The left column represents changes using the muscle-driven models, and the right column represents changes using the torque-driven models. Asterisks above bars represent statistically significant changes relative to normal walking condition; diamonds above bars in the right column represent changes from torque-driven simulations that were statistically different from changes from muscle-driven simulations. The maximum velocity change observed across both muscle-driven and torque-driven conditions was 0.072 m s(TIF)Click here for additional data file.S7 FigThe change in center of mass position, calculated at exoskeleton torque end time, for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). The bars represent position changes averaged across subjects; error bars represent standard deviations across subjects. The left column represents changes using the muscle-driven models, and the right column represents changes using the torque-driven models. Asterisks above bars represent statistically significant changes relative to normal walking condition; diamonds above bars in the right column represent changes from torque-driven simulations that were statistically different from changes from muscle-driven simulations. The maximum position change observed across both muscle-driven and torque-driven conditions was 0.004 m.(TIF)Click here for additional data file.S8 FigThe change in right foot center of pressure position, calculated at the exoskeleton torque peak time, for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). The bars represent position changes averaged across subjects; error bars represent standard deviations across subjects. The left column represents changes using the muscle-driven models, and the right column represents changes using the torque-driven models. Asterisks above bars represent statistically significant changes relative to normal walking condition. No significant differences in center of pressure changes between torque-driven and muscle-driven simulations were detected. The maximum center of pressure position change observed across both muscle-driven and torque-driven conditions was 0.024 m.(TIF)Click here for additional data file.S9 FigJoint angles computed from experimental data using inverse kinematics (black) compared to joint angles from the tracking simulations (blue). Solid lines represent averages across subjects, and shaded bands represent standard deviations across subjects. The subtalar and metatarsophalangeal (mtp) joints did not track any reference experimental data.(TIF)Click here for additional data file.S10 FigExperimental ground reaction forces (black) compared to model-generated ground reaction forces from the tracking simulations (blue). Solid lines represent averages across subjects, and shaded bands represent standard deviations across subjects.(TIF)Click here for additional data file.S11 FigExperimental electromyography recordings compared to muscle activations from the tracking simulations (blue). To account for electromechanical delays, a 40 ms delay was applied to the experimental EMG recordings. Solid lines represent averages across subjects, and shaded bands represent standard deviations across subjects.(TIF)Click here for additional data file.S12 FigAverage positive and average negative plantarflexion exoskeleton powers for the following exoskeleton torque conditions: plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue). Power is averaged over the full simulation time range when exoskeleton torque was applied. Exoskeleton timings are denoted by the time of peak exoskeleton torque. For the plantarflexion plus eversion and plantarflexion plus inversion exoskeletons, only the power produced by the plantarflexion torque component is shown. Each bar represents the average positive (top) or average negative (bottom) power normalized by body mass and averaged across subjects; error bars represent standard deviations across subjects. The left column represents changes using the muscle-driven models, and the right column represents changes using the torque-driven models. Torques during push-off (60% of the gait cycle) produced the largest average positive powers, which corresponded with the largest forward center of mass velocity changes we observed. Early mid-stance torques (20% of the gait cycle) produced the largest average negative powers. Backward changes in center of mass velocity were observed throughout mid-stance, but large average negative powers did not persist beyond early mid-stance.(TIF)Click here for additional data file.S13 FigThe change in fore-aft center of mass velocity, calculated at exoskeleton torque end time, for the plantarflexion exoskeleton torque condition. The x-axis represents the fore-aft center of mass position relative to the fore-aft center of pressure position, normalized by center of mass height and calculated at exoskeleton torque onset time. The filled circles represent mean values across subjects; error bars represent standard deviations across subjects. The left column represents changes using the muscle-driven models, and the right column represents changes using the torque-driven models. From left to right, the circles represent measurements from 25% to 65% of the gait cycle, corresponding to the nine exoskeleton timings we simulated. As the center of mass passed in front of the center of pressure , the velocity changes remained negative (backward) until the latest exoskeleton timings. This suggests that changes in fore-aft center of mass velocities were not strongly related to the position of the center of mass relative to the center of pressure.(TIF)Click here for additional data file.S14 FigThe changes in the 2-norm of the 3-dimensional center of mass position, velocity, and acceleration for the ankle plantarflexion exoskeleton torque condition versus exoskeleton peak torque. The kinematic changes were computed relative to the exoskeleton torque profile as described in (TIF)Click here for additional data file.S15 Fig2 s-1.The change in whole-body angular momentum (WBAM), calculated at exoskeleton torque end time, for each exoskeleton torque condition: eversion (light orange), plantarflexion plus eversion (dark orange), plantarflexion (black), plantarflexion plus inversion (dark blue), and inversion (light blue). WBAM was normalized by mass, center of mass height, and g*hCOM , 77. The(TIF)Click here for additional data file."} +{"text": "Background: Despite guidelines recommending shorter durations of therapy and empiric coverage of Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus (MRSA) only for patients with certain risk factors, optimizing therapy for community-acquired pneumonia (CAP) remains a challenge for antimicrobial stewardship (AMS) teams. We investigated the impact of a multimodal AMS initiative on the rate of guideline-discordant empiric antibiotic selection and total duration of therapy for CAP. Methods: A quality improvement initiative was implemented at 9 community hospitals in 2022 to optimize CAP therapy. Education was provided to pharmacists and providers. Alerts were implemented within the electronic medical record to prompt the AMS team to review fluoroquinolones, antipseudomonal \u03b2-lactams, and anti-MRSA agents ordered for CAP. Clinical pharmacists reviewed antibiotic orders for CAP at hospital discharge and encouraged providers to prescribe a total antibiotic duration of 5\u20137 days. For the preintervention period (July\u2013 September 2021) and the postintervention period (July to September 2022), a random sample of 320 patients with an antibiotic order for CAP were evaluated retrospectively via chart review. Patients treated for an indication other than CAP were excluded. The primary outcome was the proportion of patients with a total duration of therapy >7 days. Secondary outcomes included average duration of therapy, rate of guideline-discordant empiric therapy, and type of guideline discordance. Results: In total, 317 patients were included. The proportion of patients with a total duration of therapy >7 days decreased from 29% to 14% (P < .01). Average duration of therapy and guideline-discordant empiric therapy also decreased significantly (Table 1). Conclusions: This multifaceted AMS initiative was associated with decreased guideline-discordant empiric therapy and decreased total duration of therapy for CAP.Disclosures: None"} +{"text": "Alcohol Use Disorders (AUDs) are highly prevalent psychiatric disorders with often a poor treatment outcome in terms of high dropout rates and relapses. A vulnerability to disinhibition or a lack of self-regulation/low Effortful Control (EC) seems to be a core risk factor associated with both the initiation and continuation of AUDs. EC is the regulative dimension of temperament that involves attentional control, inhibitory control and activation control, and reflects self-regulation abilities that develop later in life parallel with the maturation of the prefrontal cortex.In this study we want to investigate whether EC, operationalised in terms of self-report and in terms of behavioral measures, can predict relapse. When a low EC indeed turns out to be a significant contributor to relapse, treatment interventions aiming at strengthening EC could result in better treatment outcomes and less relapse in AUD patients.The sample consisted of 75 adult patients with AUD admitted at a specialized, inpatient treatment unit for addiction. To assess the regulative temperament dimension, we used the Effortful Control Scale (ECS) from the Adult Temperament Questionnaire Short-Form), a self-report questionnaire as well as five behavioral/neuropsychological tasks using the Cambridge Neuropsychological Test Automated Battery: Cambridge Gambling Task (CGT), Stop-Signal Task (SST), Intra-Extradimensional Set Shift (IED), Spatial Working Memory (SWM) and Spatial Span (SSP).We performed binary logistic regression analyses with EC/CANTAB measures as predictors and relapse/no relapse (during treatment and after 3 months follow up) as dependent variable. According to these analyses, the self-report measure of EC nor the behavioral tasks CGT, SST, SWM and SSP (CANTAB) were able to significantly predict relapse neither during treatment nor after 3 months follow-up. Only the IED (outcome measure stages completed) was significant in predicting relapse (p<0.05) during follow-up.In our study we investigated whether self-regulation as measured by self-report questionnaires and behavioral tasks could predict relapse during treatment and after 3 months follow-up in a sample of inpatients with AUD. In contrast to some findings in literature, in our sample most of the used measures were not able to predict relapse. One hypothesis for these findings is that our sample of inpatients at a specialized addiction treatment unit is too homogeneous, all presenting lower levels of self-regulation. Future research should thus focus on larger samples and less homogeneous population. Only the IEC (outcome measure stages completed) was able to predict relapse during follow-up.None Declared"} +{"text": "Brain-derived neurotrophic factor (BDNF) has been associated with both emotionally unstable personality disorder (EUPD) and suicidal behavior. No study has yet investigated BDNF-associated epigenetic alterations in severely impaired EUPD and suicidal patients.The main goal of the present study was to investigate whether epigenetic dysregulation in BDNF, CRP, IL-1, IL-2 and IL-6 were associated with EUPD and severity of suicidal behavior.The discovery cohort consisted of 97 women with emotionally unstable personality disorder (EUPD) with at least two serious suicide attempts (SA) and 32 healthy women. The genome-wide methylation pattern was measured by the Illumina EPIC BeadChip and analyzed by robust linear regression models to investigate mean BDNF methylation levels in a targeted analysis conditioned upon severity of suicide attempt. The validation cohort consisted of 60 female suicide attempters, stratified into low- (n=45)and high-risk groups (n=15) based on degree of intent-to-die and lethality of suicide attempt method, and occurrence of death-by-suicide at follow-up.Mean BDNF methylation levels exhibited hypermethylation in relation to EUPD. Similarly, this locus was confirmed as hypermethylated in an independent cohort of women with severe suicidal behavior (p=0.0469). Results were independent of age and BMI.This study elicits emerging evidence of epigenetic dysregulation of BDNF in relation to phenotypes known to increase risk of suicide . Further studies investigating epigenetic and genetic effects of BDNF on severe suicidal behavior and EUPD are needed to elucidate the role of epigenetic regulatory mechanisms and neurotrophic factors in relation to suicide risk.None Declared"} +{"text": "Community-acquired pneumonia (CAP) is a common infectious disease state that provides multiple opportunities for antimicrobial stewardship interventions to optimize therapy management.This retrospective cohort study evaluated the impact of a service-level scorecard with prescribing feedback on the rate of guideline concordant therapy and order set utilization in non-immunocompromised, adult patients with CAP and admitted to internal medicine and family medicine services. Scorecards were shared with teams as part of a larger antimicrobial stewardship \u201cbundle\u201d that included order set and guideline development, and clinician education. The primary outcome was the proportion of guideline concordant therapy defined as meeting three of our four scorecard domains: appropriate duration of therapy, appropriate empiric therapy, and inpatient IV to PO transition. Secondary outcomes included individual scorecard components of appropriate treatment duration, empiric therapy, inpatient IV to PO transition, and order set utilization.239 patients were included consisting of 182 in the pre-dissemination of scorecard group (December 2022 \u2013 February 2023) and 57 in the post-dissemination group (March 2023). Median age in both groups were 68-69 years with 49% males in the pre-dissemination group and 63% males in the post-dissemination group. The majority of patients were treated under the internal medicine service (Table 1). Proportion of guideline concordant therapy in the pre-dissemination group was 9% (n=16) and 25% (n=14) in the post-dissemination group (p=.007). Appropriate empiric therapy was utilized in 77% (n=140) patients in the pre-dissemination group and in 95% (n=54) in the post-dissemination group (p=.003) (Table 2).Service-level scorecard distribution increased the rate of guideline concordant therapy amongst internal medicine and family medicine services and provided insight into creative solutions to optimize future disease state-based antimicrobial stewardship interventions.All Authors: No reported disclosures"} +{"text": "Scientific Reports 10.1038/s41598-022-22055-w, published online 17 November 2022Correction to: The Acknowledgments section in the original version of this Article was incomplete.\u201cThe US authors gratefully acknowledge support from a DOE Basic Energy Sciences Grant DE-FG02-99ER14982 for the experimental setups and measurements, the Physics Frontier Center grant PHY1734006 for the correlative ARPES measurements, and STROBE STC Grant . We thank Dr. Michael Gerrity for his laser expertise and aid and Yingchao Zhang for his thoughtful insights.\u201dThe original Article has been corrected."} +{"text": "Surgical face masks were originally developed to contain and filter droplets containing microorganisms expelled from the mouth and nasopharynx of healthcare workers during surgery, thereby providing protection for the patient. However, there are several ways in which surgical face masks could potentially contribute to contamination of the surgical wound, e.g. by incorrect wear or by leaking air from the side of the mask due to poor string tension. To determine whether disposable surgical face masks worn by the surgical team during clean surgery prevent postoperative surgical wound infection. We searched The Cochrane Wounds Group Specialised Register (searched 14 September 2011); The Cochrane Central Register of Controlled Trials (CENTRAL) ; Ovid MEDLINE (2008 to August Week 5 2011); Ovid MEDLINE ; Ovid EMBASE (2008 to 2011 Week 35); and EBSCO CINAHL (2008 to 9 September 2011). Randomized controlled trials (RCTs) and quasi-randomized controlled trials comparing the use of disposable surgical masks with the use of no mask. Two review authors extracted data independently. Three trials were included, involving a total of 2113 participants. There was no statistically significant difference in infection rates between the masked and unmasked group in any of the trials. From the limited results it is unclear whether the wearing of surgical face masks by members of the surgical team has any impact on surgical wound infection rates for patients undergoing clean surgery. This is the abstract of a Cochrane review published in the Cochrane database of systematic reviews (CDSR) 2012, issue 1, art. No.: CD002929. DOI: 10.1002/14651858.CD002929 (http://onlinelibrary.wiley.com/doi/10.1002/14651858.CD002929/abstract). For full citation and authors\u2019 details see The full text is freely available from:http://www.cochranejournalclub.com/masks-for-preventing-wound-infection-in-surgery/pdf/CD002929.pdf"} +{"text": "The availability of high-fidelity animal models for oncology research has grown enormously in recent years, enabling preclinical studies relevant to prevention, diagnosis, and treatment of cancer to be undertaken. This has led to increased opportunities to conduct co-clinical trials, which are studies on patients that are carried out parallel to or sequentially with animal models of cancer that mirror the biology of the patients\u2019 tumors. Patient-derived xenografts (PDX) and genetically engineered mouse models (GEMM) are considered to be the models that best represent human disease and have high translational value. Notably, one element of co-clinical trials that still needs significant optimization is quantitative imaging. The National Cancer Institute has organized a Co-Clinical Imaging Resource Program (CIRP) network to establish best practices for co-clinical imaging and to optimize translational quantitative imaging methodologies. This overview describes the ten co-clinical trials of investigators from eleven institutions who are currently supported by the CIRP initiative and are members of the Animal Models and Co-clinical Trials (AMCT) Working Group. Each team describes their corresponding clinical trial, type of cancer targeted, rationale for choice of animal models, therapy, and imaging modalities. The strengths and weaknesses of the co-clinical trial design and the challenges encountered are considered. The rich research resources generated by the members of the AMCT Working Group will benefit the broad research community and improve the quality and translational impact of imaging in co-clinical trials. The Co-clinical Imaging Research Resource Program (CIRP) of the National Cancer Institute (NCI) focuses on the optimization and dissemination of quantitative imaging methods and protocols employing genetically engineered mouse models (GEMM) and patient-derived xenografts (PDX) to improve co-clinical precision medicine research . The CIR13C MRI.The members of the AMCT WG possess a wealth of experience in applying a multitude of imaging technologies to diverse animal models treated using a variety of therapies. Cancers targeted include triple-negative breast cancer, estrogen receptor-positive breast cancer, small cell neuroendocrine prostate cancer, osteosarcomas, high-risk localized soft tissue sarcoma of the extremity, colorectal cancer, pancreatic ductal adenocarcinoma, and non-small cell lung cancer and myelofibrosis. Murine hosts of PDX include SCID/beige, athymic nude, and NOD scid gamma (NSG) immunocompromised mice, and immunocompetent Balb/c, C57BL/6J and 129/SvJae mice are used for GEMM and murine tumors. Sites of tumors targeted for therapy and imaging include the orthotopic mammary fat pad, bone and muscle, and metastatic sites of the bone and liver. The biological fidelity of models has been confirmed by characteristics such as histologic appearance, genomics, transcriptomics, proteomics, metabolomics, and clinical progression . Treatments utilized in the co-clinical trials range from standard chemo- and immuno-therapies , targeted therapies (anti-EGFR antibody panitumumab), hormonal therapy, surgery, and radiotherapy, to a novel CD47 monoclonal antibody, glutaminase inhibition, the JAK2 inhibitor ruxolitinib, a vitamin D receptor ligand, the CDK4/6 inhibitor abemaciclib, and an inhibitor of CXCL1/2. Endpoints selected for the co-clinical trial include tumor growth inhibition, local recurrence-free survival, metastasis-free survival, and disease-free survival. Imaging technologies include ultrasound, micro-computed tomography (CT), positron emission tomography (PET), magnetic resonance imaging (MRI), and hyperpolarized An overview of the co-clinical studies in the CIRP network is provided in The co-clinical study at UCSF focuses on small cell neuroendocrine prostate cancer (SCNC), a lethal variant of metastatic castration-resistant prostate cancer (mCRPC) that is becoming increasingly prevalent in the era of treatment with second-generation androgen signaling inhibitors (ASI) . While lClinicalTrials.gov ID: NCT04346225) aims to assess the response of SCNC to standard-of-care carboplatin chemotherapy using hyperpolarized (HP) [1-13C]pyruvate MRI. Patients who have mCRPC and prior progression on ASI undergo standard-of-care cross-sectional imaging of the abdomen/pelvis using either CT or MRI to guide the selection of a target lesion. Following baseline HP 13C MRI, patients undergo paired CT image-guided percutaneous core needle biopsies of metastases within 14 days to confirm the presence of SCNC and are given carboplatin. Consistent with standard clinical practice, the patients undergo re-staging with cross-sectional imaging of the abdomen/pelvis every 8 weeks thereafter to determine tumor response (defined as >30% reduction in longest diameter of target lesion). Patients undergo follow-up HP 13C MRI after 1 cycle of treatment (carboplatin area under the curve (AUC) 5 through intravenous (IV) line every 3 weeks) to investigate the reduction in the HP 13C MRI metric as an early marker of response to chemotherapy. The multiparametric (mp) 1H MRI/dynamic HP 13C MRI protocol used includes T1- and T2-weighted anatomic, diffusion weighted, and dynamic contrast-enhanced (DCE) imaging and 2D dynamic HP [1-13C]pyruvate MRI for both clinical and preclinical protocols.The corresponding clinical study at UCSF EPI acquisition used clinically and comparing it with standard 2D Dynamic HP 13C chemical shift imaging to evaluate the impact of motion/respiration in test\u2013retest studies.The preclinical trial provides several advantages compared to the clinical study, including a vehicle-treated control, the standardization of the initial volume of tumors, and the ability to image mice more frequently than patients to quantitatively measure tumor response over time. Importantly, the study permits the reverse engineering of clinical acquisition and processing protocols for the development and optimization of associated preclinical protocols. The SCNC PDX have a more homogeneous phenotype compared to the mixed adenocarcinoma/SCNC and/or other variants often observed in mCRPC patients, which may be advantageous for preclinical studies but is not completely representative of the clinical presentation. The implantation of PDX cells into the bone or liver does not capture the metastatic process but does enable more clinically relevant studies on the treatment of SCNC than models involving the implantation of non-human cells or immortalized cell lines at sites that have significantly different microenvironments, such as the murine flank. Organ-specific prostate cancer responses have been observed in both clinical and preclinical studies ,10,11,12ClinicalTrials.gov ID: NCT03092323) investigating whether the addition of neoadjuvant and adjuvant pembrolizumab, a monoclonal antibody targeting programmed cell death protein-1 (PD-1), to preoperative radiotherapy (RT) and surgical resection improves disease-free survival compared to neoadjuvant RT (50 Gy in 25 fractions) and surgery for patients with high-risk soft tissue sarcoma of the extremity (undifferentiated pleomorphic sarcoma [UPS] or dedifferentiated/pleomorphic liposarcoma [LPS]) ) . ClinicaTP53 observed in human UPS and dedifferentiated/pleomorphic LPS [Trp53, followed by injection of 3-methylcholanthrene (MCA) into the gastrocnemius muscle (p53/MCA model). Tumors developed in the hind limb 7\u201312 weeks after induction. Primary p53/MCA sarcomas resemble human UPS in both histologic appearance and gene expression profile [To mimic gradual sarcoma development under immune surveillance and the frequent development of lung metastases in sarcoma patients, the preclinical arm of the co-clinical trial utilized a carcinogen-induced GEMM of sarcoma that devphic LPS , primary profile . Without3: isotype control antibody (ISO), anti-PD-1 antibody, ISO + 20 Gy (ISO + RT), and anti-PD-1 + 20 Gy (anti-PD-1 + RT). Anti-PD-1 or the isotype control antibody (200 \u03bcg) was administered by intraperitoneal injection on Day 0 (pre-amputation), Day 7 (day of amputation), and Day 14 (post-amputation). Sarcomas were treated with sham RT or 20 Gy (single fraction) on Day 0. Due to rapid p53/MCA tumor growth, the fractionated 5-week RT regimen and the every 3-week dosing of 200 mg pembrolizumab utilized in the clinical trial was not feasible. Primary sarcomas were imaged using micro-MRI, and respiratory-gated micro-CT was used to detect lung metastases with high spatial resolution [Sarcoma-bearing mice were randomized into four treatment groups when tumors reached 75\u2013125 mmsolution . Comparesolution . Mice trFor patients enrolled in the clinical trial SU2C-SARC032, pre-treatment tumor samples are undergoing both whole exome sequencing and RNA sequencing. The surgical resection specimen obtained after neoadjuvant radiation (with or without neoadjuvant anti-PD-1 therapy) is also undergoing RNA sequencing. While some patients have developed new metastases after undergoing sequencing, these results remain blinded. For the murine co-clinical trial, a subset of sarcoma samples obtained from hind limb amputation after neoadjuvant radiation with or without neoadjuvant anti-PD-1 therapy underwent whole exome sequencing. The mice received one additional dose of anti-PD-1 antibody or isotype control after amputation. Tumor samples were taken from mice who developed local recurrences after amputation of the tumor-bearing hind limb, and the recurrent tumor also underwent whole exome sequencing. These mice did not develop new metastases after genetic sequencing.KRAS colorectal cancer (CRC) patients.The co-clinical study at MDACC utilizes PET imaging and radiotracers of glutamine metabolism to assess the response of individualized cancer therapeutics for wild-type (WT) KRAS gene, indicating that the remaining 50% of CRC patients might respond to anti-epidermal growth factor receptor (EGFR)-targeted therapy [KRAS tumors with or without BRAF mutations, which are usually mutually exclusive with KRAS mutations, represent 5\u201315% of advanced CRC [Approximately 50% of CRC are known to have a mutated therapy ,20. Howenced CRC and do nnced CRC ,23. To o18F-fluorodeoxyglucose (FDG) PET preclinically [The mitogen-activated protein kinase (MAPK) pathway, one of the most frequently deregulated signaling cascades in CRC, follows the ligand-mediated activation of EGFR and requires glutamine; furthermore, glutamine can induce MAPK-mediated proliferation in an EGFR-independent manner ,25. Indeinically and clininically ,28.11C-Glutamine and (S)-4-(3-18F-Fluoropropyl)-L-glutamic acid (18F-FSPG) in WT KRAS CRC. In collaboration with the Vanderbilt University Medical Center, we are conducting a Phase II clinical trial combining an anti-EGFR antibody, panitumumab, with a glutaminase (GLS1) inhibitor, CB-839 . Patients participating in this trial receive glutaminase inhibitor CB-839 orally twice a day and immunohistochemistry (IHC) data. In the second study, a Phase I clinical trial, baseline glutamine PET imaging with 11C-Glutamine and 18F-FSPG is evaluated in patients with metastatic WT KRAS CRC undergoing treatment with EGFR-targeted antibody therapy . The goal is to identify a predictive imaging biomarker of response which would guide therapy selection for patients.Currently, we are conducting two clinical trials using PET imaging with 3), at which point mice will be sacrificed. The preclinical PET/CT scans with 18F-4-fluoro-glutamine and 18F-FSPG are conducted pre- and 1-week post-treatment. We are also using RNA-seq data from these PDX to develop imaging-derived gene signatures associated with treatment response. These gene signatures could provide rationale and guidance for the appropriate treatment selection with combined blockade of EGFR and glutamine metabolism.The preclinical trial uses avatar PDX athymic nude mouse models . Gene seThe overall goal of the project at Stanford University is to optimize and validate preclinical and clinical quantitative imaging techniques for in vivo quantification of tumor associated macrophages (TAM) in osteosarcomas. This goal will be accomplished by optimizing and validating preclinical quantitative imaging methods for TAM imaging, implementing the optimized methods in a co-clinical trial, and populating a web-accessible research resource.TM) [While the outcome of patients with localized bone sarcomas has significantly improved over the last two decades, the overall survival of patients with metastatic disease continues to be less than 30% ,35,36,37TM) ,47,48,49TM) ,51. The The Stanford co-clinical trial design is outlined in Animals undergo MRI scans before and after treatment as well as before and after undergoing intravenous infusion of ferumoxytol or Mega Pro iron oxide nanoparticles. Doses of CD47 mAb and iron oxide nanoparticle are adjusted according to the weight of the mouse or patient ,51. Ferup = 0.03). In addition, the tumor DT2 * enhancement positively correlated with the quantity of CD80 and inducible nitric oxide synthase (iNOS)-positive TAM on the histology and the tumor size on post-treatment scans. Reproducibility studies are ongoing to determine variables that might affect our quantitative measures. Preliminary results demonstrated less than 10% inter- and intra-individual variations in quantitative MRI measures of TAM. Important variables that affected quantitative T2 * mapping results included magnetic field strength, tumor type, tumor size, and nanoparticle type, as well as pulse sequence parameters and the approach for image analysis. Statistical analyses of these variables are ongoing.Results have shown stronger hypointense (dark) nanoparticle enhancement of intratibial osteosarcomas after treatment with CD47 mAb compared with IgG1 control antibody. The DT2 * enhancement, quantified as the difference between pre- and post-contrast T2 *-values, was significantly higher in CD47 mAb-treated tumors compared to IgG1-treated tumors , as expected based on results from our preclinical studies. While the accrual of patients is ongoing, the imaging findings will be correlated with the degree of tumor necrosis after tumor resection.Next, the team developed a web-based server application with detailed records of both individual images and experimental data relevant to our project, which includes a web-based 3D/4D image viewer to easily and quickly view and evaluate images. The application uses a data-driven, bottom-up approach to record each piece of data and its relationship to specific experiments, studies, and projects. The original unstructured data collected from various imaging modalities and related animal preparation experiments are annotated and stored in a structured hierarchical database. Data can be managed, accessed, and shared through either private or public web clients for better data security and accessibility. The application also includes a robust image viewer and modular processing tools for various computationally intensive and artificial intelligence (AI) applications. A centralized distributed data storage is used for accessibility, scalability, security, and performance. The application provides easy access to send images to a publicly accessible image repository portal. Using this web portal, data sharing can be performed easily, provided the receiver has authorized login credentials for the application. Users can choose to send their private images to this image gallery for public viewing. Images in the public portal can be searched for using search parameters, such as user info and date of acquisition, and by selected keywords. Data sharing is fully controlled and protected by credentials accessible only to authorized users. An integrated image viewer can be used to visualize one or more selected images. The viewer features an easily navigable set of standard medical image viewing tools, such as annotation and segmentation tools. The viewer is capable of loading and overlaying multiple images in both 3D and 4D image formats, making it easy to view and compare multiple related images simultaneously.This quantitative imaging (QI) tool for TAM imaging is readily clinically translatable and will provide important quantitative information about tumor response to cancer immunotherapy, which will inform personalized treatment protocols. Therefore, this new QI tool test will have significant impact on clinical outcomes and enable broad applications beyond the team\u2019s immediate research focus.ClinicalTrials.gov ID: NCT03519308) , employs a GEMM in the preclinical arm, and enrolls resectable PDA patients in the clinical trial (3519308) . The denPatients with resectable PDA are randomized into one of two arms: chemoimmunotherapy , or chemoimmunotherapy plus vitamin D receptor ligand, Paricalcitol. After two cycles of treatments, patients undergo surgical resection of PDA and tumor specimens are examined by IHC. DW-MRI and DCE-MRI are performed at baseline and after one cycle of treatment.G12D:Trp53R172H:Pdx1-Cre), referred to as KPC, and resemble key features of human PDA including a dense stroma [3 confirmed by MRI were enrolled in the treatment study. In GEMM, the initiation and progression of PDA are driven by pancreatic epithelial-specific mutations of the KRAS oncogene and the TP53 tumor-suppressor gene and Day 7 followed by scheduled drug treatments, and finally, T2W and DW-MRI are applied on Day 14 followed by euthanasia and the harvesting of tumor tissues for IHC and for single cell RNA-seq.KPC mice are randomized and enrolled in one of four groups: (1) control ; (2) chemotherapy only; (3) chemotherapy + Calcipotriol (a synthetic vitamin D for mice); (4) chemotherapy + Calcipotriol + PD-L1 mAb, where chemotherapy is a combination of three agents (gemcitabine/cisplatin/nab-paclitaxel administered at dose of 266/8/4 mg/kg), PD-L1 antibody (200 \u00b5g/mouse), and Calcipotriol (60 \u00b5g/kg). Treatment and MRI study last for 2 weeks for the preclinical trial arm. Chemotherapeutic drugs are administered on Day 0 and Day 7; calcipotriol on Monday to Friday skipping Saturday and Sunday; and PD-L1 mAb twice a week. Ttrans, Ve, and T1 relaxation time of the tumor are obtained for the co-clinical trial. We developed motion-resistant radial k-space sampling acquisition and image reconstruction protocols [trans maps are shown in Quantitative imaging biomarkers (QIB) including tumor size, apparent diffusion coefficient (ADC), Krotocols ,56. Furtrotocols ; a deep-Strengths of the co-clinical trial design include: (1) the neoadjuvant setting of the clinical trial allows for mechanistic insights of the treatment by detailed IHC analyses; (2) GEMM captures the stromal and other key features of human PDA; (3) there are closely matched clinical and preclinical trial designs in treatment and endpoints, while animal studies include more groups to dissect the effect of chemo, immune and stromal treatment; and (4) the co-clinical trial allows for the assessment of fibrosis and tumor immune microenvironment in both human subjects and in KPC mice. Weaknesses include the fact that resectable PDA accounts for only 20% of all PDA, and subtyping a biopsied tumor is required before enrollment, limiting the sample size of the clinical trial and impacting the statistical power.The University of Michigan co-clinical study centers on myelofibrosis (MF), a chronic, ultimately fatal hematologic cancer that arises either as a primary malignancy or secondary to other rare myeloproliferative neoplasms (MPNs), polycythemia vera (PV), or essential thrombocythemia (ET). Major driver mutations causing MPNs constitutively activate JAK2 kinase signaling in hematopoietic stem and progenitor cells (HSCs). Patients with primary or secondary MF commonly develop debilitating systemic inflammatory symptoms, progressive fibrosis of bone marrow and other organs, and clonal proliferation of HSCs in organs outside of bone marrow. These hallmark phenotypes distinguish MF from other MPNs. Treatment options for MF remain very limited. The U.S. Food and Drug Administration (FDA) has approved only three drugs for MF, which alleviate symptoms in ~50% of patients but do not eliminate malignant HSCs or reverse major organ pathologies. Most of these patients discontinue treatment within three years because of side effects or drug resistance.Biopsy remains the current standard for analyzing bone marrow in patients. This technique has notable limitations, including sampling only a very small amount of bone marrow from one site (iliac crest) in a disease known to exhibit marked heterogeneity within bone marrow. In patients with advanced MF, biopsy may yield no diagnostic information, inflicting the pain of the procedure on a patient without any benefit. Imaging in clinical trials for MF has been restricted to quantifying changes in spleen volume, with a 35% reduction after six months of treatment being the standard for FDA approval of a therapy. Imaging has not been part of clinical management of patients with MF. The objective of this research is to develop quantitative imaging methods which can be validated for use in analyzing bone marrow pathology in MF, the major site of disease, in mouse models and human participants undergoing therapy. If the establishment of validated quantitative imaging biomarkers is successful, we anticipate the establishment of a new paradigm for staging MF patients and monitoring the response to therapy. Employing quantitative MRI methods for the detection of stabilization or reversion of bone marrow toward a healthy state would provide a new and important approach for clinical patient management.ClinicalTrials.gov ID: NCT01973881) is currently open and enrolling participants with MF who are beginning treatment with a new drug. Patients typically undergo DNA sequencing for somatic mutations associated with myelofibrosis. There is no repeat sequencing after therapy. Studies to date have focused on patients beginning treatment with the JAK2 inhibitor ruxolitinib dosed according to the clinical judgement of the oncologist. MR imaging studies are conducted within one month of therapy initiation and follow-up scans are acquired after 1, 3, and 6 months of treatment. If a participant remains on the same therapy, they may opt to have additional imaging studies at 12 and 24 months of treatment. For all imaging studies, measurement of spleen volume is accomplished by anatomic imaging and bone marrow is monitored using the following MRI parameters in the lumbar spine, pelvis, and proximal femurs: (1) ADC for changes in cellularity; (2) magnetization transfer ratio (MTR) for extracellular macromolecules such as reticulin and collagen fibrosis; and (3) proton density fat fraction (PDFF) for amounts of fat and water (cells) content in the bone marrow. MTR images are only acquired in the pelvis because of imaging time and energy (radiofrequency deposition) constraints. MRI parameters are quantified to determine site-specific anatomic changes over the course of therapy. In addition, imaging data are also evaluated for correlation with multiple clinical metrics, including complete blood counts, biopsy, clinical symptom score according to the Dynamic International Prognostic Scoring System (DIPSS), and somatic mutations identified by targeted genomic sequencing. These data will enable the determination of the extent of response to therapy that quantitative bone marrow MRI metrics detect and the evaluation of discordance between effects of therapy on spleen volume versus bone marrow changes.The clinical study at the University of Michigan (Mouse models of MF consist of a bone marrow transplantation model to establish MF in immunocompetent mice . In thisWashington University (WU) School of Medicine in St. Louis has two projects focused on predicting response to therapy in breast cancer (BCa) under the umbrella of the Washington University Co-Clinical Imaging Research Resource (WU-C2IR2). The first project focused on predicting response to carboplatin/docetaxel therapy in triple-negative breast cancer (TNBC), while the new project is focused on predicting response to endocrine therapy (ET) in advanced estrogen receptor-positive (ER+) BCa. The resource generates PDX matched to the patient\u2019s tumor subtype and PDX generated from patient-specific tumor biopsies/engraftments. The use of PDX enables bi-directional translation as a test-bed for both imaging and therapeutic strategies, mindful of the limitations of PDX as summarized previously . QI algoClinicalTrials.gov ID: NCT02124902). In clinical studies, docetaxel was administered intravenously at a dose of 75 mg/m2 over 60 min on Day 1 of each 21-day cycle. Carboplatin AUC 6 was administered intravenously over 30 min on Day 1 of each 21-day cycle immediately following docetaxel infusion. A total of six cycles were given. In preclinical studies, PDX were treated with combined docetaxel (20 mg/kg) and carboplatin (50 mg/kg) weekly for six weeks, during which period the tumor growth profile was monitored. A multi-parametric PET/MR imaging protocol including FDG-PET, T1w\u2013T2w, DWI- and DCE-MRI was implemented in the clinical setting to predict response to therapy. Subjects were imaged at baseline (B) and again at the conclusion of the first cycle of NAC, and before starting the second cycle (1-weighted and T2-weighted MR imaging [TNBC is a highly heterogeneous and aggressive tumor characterized by poor outcome and higher relapse rates compared to other subtypes of BCa. Pathologic complete response (pCR) is often used as an important endpoint in the treatment of TNBC following neoadjuvant chemotherapy (NAC) as it is often associated with favorable long-term outcome. Therefore, it is critical to identify patients who will respond to NAC, and thus avoid the use of ineffective treatments in nonresponding patients with an opportunity to devise adaptive treatment strategies. Patients with newly diagnosed clinical stage II or III BCa with complete surgical excision of the cancer after NAC were recruited to the now completed clinical trial -PET and 18F-fluorofuranylnorprogesterone (FFNP)-PET QI strategies to assess the heterogeneity of hormone receptor status as predictors of response to ET in a panel of subtype-matched PDX to assess and compare the efficacy of FES-PET- and FFNP-PET-optimized QI metrics to predict response to therapy, and to correlate with mutation status and gene signatures of ER and PgR response to therapy. The co-clinical trial will interface with a recently funded phase II multicenter translational BCa research consortium (TBCRC) trial sponsored by the breast cancer research foundation (BCRF) to assess the accuracy of FFNP-PET in predicting response to abemaciclib, a CDK4/6i, plus ET in patients with ER+/HER2- metastatic BCa . ET reduatic BCa A. Patienatic BCa B. Biopsihttps://c2ir2.wustl.edu (accessed on 20 January 2023).Overall, these projects aim to have high, far-reaching impact on the implementation of co-clinical imaging strategies in identifying, stratifying, and predicting response to therapy in TNBC and ER+/HER2 \u2212 BCa, integrating QI with genoproteomic discovery. In addition, high-value, multi-scale analytic data will be generated to interrogate and characterize tumor heterogeneity. All publications, data, and protocols are available through the WU-C2IR2 Resource website at https://miraccl.research.bcm.edu/miraccl), a web-based resource to store, manage, analyze, and display comparative imaging and omics analyses in co-clinical trials. MIRACCL integrates three existing web platforms: (1) the BCM PDX Portal , (2) ePad [The collaborative team at Baylor College of Medicine (BCM)/UT Austin/Stanford University is building MIRACCL ePad , and (3)(2) ePad . The ultscidLystbg-J) mice [3). Once tumors are visible and/or palpable, caliper measurements are used to determine the size (LxW2/2).TNBC PDX models are chos-J) mice . On aver3, the animals are randomized (n = 3) onto one-week or four-week treatment arms and pre-treatment MRI is performed appears to reduce these artifacts. Additionally, this location makes identification of an arterial input function for quantitative MRI difficult, yielding data that can only be analyzed with a semi-quantitative metric or by a reference region method .fl/fl/Lkb1fl/fl (PL) mouse model of lung squamous cell carcinoma will be utilized as adenocarcinomas and squamous cell carcinomas together account for >90% of all NSCLC.The University of Washington and Fred Hutchinson Cancer Center are collaborating on a co-clinical study of immune checkpoint inhibitor (ICI) therapies in non-small cell lung cancer (NSCLC). This project uses a GEMM of lung adenocarcinoma to develop, test, and implement ICI therapies of this deadly disease. The Houghton lab has developed a novel mouse model of lung cancer suitable for the study of immunotherapies by exposing LSL-Kras mutant mice to cigarette smoke (KSM) . Tumors The scheme of the co-clinical trial is illustrated in The number of different types of animal models and their relative value for translation research in oncology have grown enormously in recent years ,79. UsinThe co-clinical quantitative imaging projects of the AMCT WG of the CIRP network aim to incorporate many of these recommendations. Notable strengths among the various projects include high fidelity between tumors targeted in the clinical trial and PDX or GEMM in the co-clinical study, attempts to use human-equivalent doses of therapeutic drugs, the orthotopic location of tumors or tumors grown at cancer type-specific sites of metastases, immunocompetent hosts for murine models, and gender-appropriate murine hosts. Preclinical studies offer certain advantages compared to clinical trials, including the ability to add additional control arms, standardization of tumor volume at initiation of therapy, and more frequent imaging. Some projects take advantage of the opportunity to reverse engineer clinical acquisition and processing protocols for the optimization of associated preclinical protocols, or to optimize imaging methods preclinically for translation to human studies. The co-clinical trials aim to employ therapeutic outcomes similar to those in the clinical studies, such as tumor regression or recurrence-, disease-, and metastasis-free survival. Quantitative imaging biomarkers are sought to predict response, provide early evidence of treatment efficacy, or monitor response and/or recurrence. Several projects focus on imaging the tumor microenvironment to monitor the response of TAMs to immunotherapy or to evaluate changes in microvascular perfusion and fibrosis in response to a stromal-targeted therapy. Most projects include correlative biological studies to validate the imaging findings.Common drawbacks among the projects include difficulty in capturing cancer heterogeneity with the small number of animal subjects in preclinical studies, the more rapid growth rate of tumors in mice compared to humans, the age of mice versus humans, and the absence of an immune microenvironment in PDX propagated in immunocompromised mice. Depending on the location of the tumors, respiratory motion impacts imaging. Means to overcome this problem include faster acquisition of images and respiratory gating.Together with the Imaging Acquisition and Data Process (IADP) and Informatics and Outreach (IMOR) WGs, the activities of the AMCT WG contribute to the mission of the NCI CIRP to advance the practice of precision medicine by establishing consensus-based best practices for co-clinical imaging and developing optimized state-of-the-art translational quantitative imaging methodologies to enable disease detection, risk stratification, and assessment/prediction of response to therapy. The web-based resources generated by each project, including methods, protocols, software, and imaging data, will advance the efforts of the cancer research community to develop clinically translatable imaging biomarkers.This article is meant to serve as a resource or handbook to investigators interested in designing co-clinical trials involving quantitative imaging. The intent is to highlight the ongoing activities of the nine teams that are part of the CIRP network and provide examples that might serve as templates for other co-clinical studies. Each section describes the associated clinical trial, the experimental approach, the rationale for the animal models selected, the imaging platforms, and pros and cons of the various elements of the co-clinical trial of each team. Work is in progress and findings will be the subject of future publications."} +{"text": "Correction to:Crit Care 27, 274 (2023). https://doi.org/10.1186/s13054-023-04561-zFollowing publication of the original article , the autThe Results section currently reads:ResultsA total of severe RCTs involving 1689 patients were included in this study.The Results section should read:ResultsA total of seven RCTs involving 1689 patients were included in this study.The Results section has been updated in this correction and the original article has been"} +{"text": "Retraction Note: BMC Infectious Diseases (2020) 20:94910.1186/s12879-020-05630-2The Editor has retracted this article because the authors have been unable to provide documents confirming that ethics approval was obtained for the study. None of the authors have responded to correspondence from the Editor about this retraction."} +{"text": "The financial sustainability of regional burn centers is essential to the health of the populations they serve, and to the broader development of burn prevention and care innovations. Additionally, per capita out-of-pocket personal health expenditures (OOP) have risen steadily over the last decade. Lower pre-injury income has been shown to predict poorer post-injury quality of life and higher risk of financial toxicity. Given these multi-level dynamics, we aimed to characterize the changing payor landscape and OOP from 2010-2020 at an American Burn Association-verified center to delineate the financial implications of these changes on the health system and per-patient financial liability.We merged burn registry and financial data from 2010 to 2020. Financial variables included payor status, pay-to-charge ratio , financial liability (remainder of charges after insurance reimbursement), and patient payment (dollars). Analyses of trend were performed using Pearson\u2019s chi-squared analysis for counts and ANOVA for means.The percentage of self-pay patients decreased from 2010 to 2020 from over 13% to under 4% of the total number of patients annually (p< 0.001), corresponding with an increase in the percentage of Medicaid patients from 30% to over 40% of the total number of patients annually (p< 0.001). This change became significantly more pronounced in 2014. Notably, most major provisions of the Affordable Care Act were phased in by January 2014, including state-level Medicaid eligibility expansion. Medicaid consistently displayed a lower pay-to-charge ratio (30-40%) than both commercial insurance (~70%) and Medicare (50-80%) across the decade (p< 0.001). Total financial liability increased across the decade for commercial insurance (p< 0.001), Medicaid (p=0.013), and Medicare (p=0.015). From a patient perspective, the average payment burden did not change significantly across the decade despite rising healthcare costs. The average per-patient owed amount ranged from $0-$1000 for self-pay, $150-$200 for Medicare patients, and $500-$600 for patients with commercial insurance.Burn centers must remain financially sustainable to continue serving their communities. The shifting landscape of healthcare with a population increasingly reliant on Medicaid impacts a hospital\u2019s financial sustainability. This change demonstrates that minor differences in OOP for the average patient may have large implications for hospital systems given the low pay-to-charge ratio of Medicaid.This work highlights the changing payor landscape and the impact it may have on burn center financial sustainability and risk of patient financial toxicity, particularly among already vulnerable Medicaid recipients."} +{"text": "Infection control practices are imperative to mitigate COVID-19 transmission, and adherence likely depends on accurate understanding of their effectiveness along with the risks associated with COVID-19 infection. This is particularly important in people living with HIV (PLWH) as they may be at increased risk for severe disease and worse outcomes. There is limited understanding of the knowledge, attitudes, and practices (KAP) regarding COVID-19 risks and infection control measures among PLWH in sub-Saharan Africa.A questionnaire with Likert scale responses for COVID-19 knowledge/attitudes and binary responses for practices was administered beginning Mar 2022 to participants enrolled in the African Cohort Study (AFRICOS), a prospective cohort of adults and adolescents living with or at risk for HIV in Kenya, Nigeria, Tanzania, and Uganda. Multivariable logistic regression with generalized estimating equations was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for associations between demographics and COVID-19 knowledge/attitudes with self-reported facemask use and social distancing in the preceding month.As of 1 Dec 2022, 962 PLWH enrolled in AFRICOS had COVID-19 KAP data. Facemask use was reported by 784 participants (81.5%) and social distancing by 600 (62.4%). Compared to participants in Uganda, participants in Kenya or Tanzania had lower odds of facemask use and social distancing (Table 1). Participants with lower self-assessed general health status and who were less concerned about the spread of COVID-19 had lower odds of facemask use or social distancing. Participants who more highly agreed that facemasks reduce the risk of COVID-19 had higher odds of facemask use. Compared to 176 participants not living with HIV, PLWH had higher odds of facemask use and social distancing.These results provide important insight into COVID-19 KAP among PLWH in sub-Saharan Africa and suggest potential population and messaging targets to enhance future COVID-19 infection control efforts.The views expressed are those of the author(s) and do not reflect the official policy of the Department of the Army, Department of Defense, or U.S. Government. The investigators adhered to policies for protection of human subjects prescribed in AR 70\u201325.All Authors: No reported disclosures"} +{"text": "The substitution of generic treatment alternatives for brand-name drugs is a strategy that can help lower Medicare beneficiary out-of-pocket costs. Beginning in 2011, Medicare beneficiaries reaching the coverage gap received a 50% discount on the full drug cost of brand-name medications and a 7% discount on generic medications filled during the gap. This discount will increase until 2020, when beneficiaries will be responsible for 25% of total drug costs during the coverage gap.To examine the cost variability of brand and generic drugs within 4 therapeutic classes before and during the coverage gap for each 2011 California stand-alone prescription drug plan (PDP) and prospective coverage gap costs in 2020 to determine the effects on beneficiary out-of-pocket drug costs.Equivalent doses of brand and generic drugs in the following 4 pharmacological classes were examined: angiotensin II receptor blockers (ARBs), bisphosphonates, HMG-CoA reductase inhibitors (statins), and proton pump inhibitors (PPIs). The full drug cost and patient copay/coinsurance amounts during initial coverage and the coverage gap of each drug was recorded based on information retrieved from the Medicare website. These drug cost data were recorded for 28 California PDPs.The highest cost difference between a brand medication and a Centers for Medicare Medicaid Services (CMS)-suggested generic treatment alternative varied between $110.53 and $195.49 at full cost and between $51.37 and $82.35 in the coverage gap. The lowest cost difference varied between $38.45 and $76.93 at full cost and between -$4.11 and $18.52 during the gap.Medicare beneficiaries can realize significant out-of-pocket cost savings for their drugs by taking CMS-suggested generic treatment alternatives. However, due to larger discounts on brand medications made available through recent changes reducing the coverage gap, the potential dollar savings by taking suggested generic treatment alternatives during the gap is less compelling and will decrease as subsidies increase."} +{"text": "Skilled nursing facilities (SNFs) have significant opportunity to improve antibiotic use and reduce multidrug-resistant organism transmission. In the summer of 2022, the Southeast Pennsylvania Long-Term Care Resiliency, Infrastructure Supports, and Empowerment (LTC-RISE) team and the Philadelphia Department of Public Health (PDPH) distributed a survey to all Philadelphia SNFs to understand strengths and opportunities for improvement of antibiotic stewardship programs (ASPs).A REDCap survey was distributed via phone or video call to 47 SNFs addressing all elements in the CDC's Checklist for Core Elements of Antibiotic Stewardship in Nursing Homes. SNFs self-reported survey responses. Survey results were used to provide individualized feedback highlighting SNF performance against peers, and to implement broad-based interventions to strengthen ASPs.Thirty-eight SNFs (81%) responded to the survey. All 7 ASP core elements were reported present by 55% of respondents. Only one SNF did not have any core elements present. The elements most commonly reported present and absent were tracking measures of antibiotic use (97%), and monitoring outcomes of antibiotic use (79%), respectively. The ASP lead(s) most commonly identified was the Infection Preventionist (66%), Director/Assistant Director of Nursing (55%), or Medical Director (37%). Infection-specific interventions and resident educational materials were provided in only 42% and 34% of SNFs, respectively. Customized ASP reports were sent to all participating SNFs, with feedback obtained at 3 months after distribution. Survey results were used to create an educational webinar and UTI-focused resource package.A majority of Philadelphia SNFs reported having ASPs with all CDC core elements in place, and almost all facilities tracked at least one measure of antibiotic use. Opportunities for improvement included tracking outcomes of antibiotic use, providing infection-specific interventions, and providing educational materials to residents. Insights provided from the survey helped to guide individualized and broad-based ASP interventions across facilities.All Authors: No reported disclosures"} +{"text": "We report the electroencephalography (EEG) showing an intermittent generalized polyspike pattern in EEG due to an aseptic meningoencephalitis in a 71-year-old soporous patient. Initially, she presented with word-finding disturbances and later with generalized tonic\u2013clonic seizures. The cerebrospinal fluid (CSF) showed pleocytosis of 99 leukocytes/\u03bcL (primarily neutrophils) and an increased protein level of 1240 mg/L (CSF/serum glucose ratio and lactate unremarkable). Pathogens and autoimmune antibodies in CSF were not found. Brain imaging was unremarkable. After antibiotic, antiviral and anticonvulsive therapy, the pattern in the EEG was no longer detectable. The patient was discharged to go home due to absence of any residues."} +{"text": "Prevention of unplanned pregnancies through modern contraceptives among HIV-positive women is one of the essential strategies for reducing mother-to-child transmission of HIV. Family planning and HIV services integration is a national strategy designed to scale-up modern contraceptives among HIV-positive women. This study aims to evaluate the success of a service integration strategy by comparing the prevalence of modern contraceptive use among HIV-positive women receiving ART within integrated services and those not on integrated services (HIV-negative women and HIV-positive women unaware of their status).We used data from the Tanzania HIV impact survey (THIS) of 2016/17. THIS provided HIV counselling and testing with a return of results in over 30,000 adults over 15\u00a0years of age. Women tested positive self reported their enrollment into ARV with further confirmation through laboratory analysis for any detectible ARV in their blood. All non-pregnant women reported their contraceptive use. Univariate and multivariate logistic regression was used to assess the effect of accessing integrated services controlling for potential confounders.p-value\u2009=\u20090.0014). The most common contraceptive methods in HIV-positive women were injectables (32%) and male condoms (31%), while in HIV-negative women, injectables (39%) and implants were the most preferred methods. Among HIV-positive women, enrolment into integrated services (currently on ART) demonstrated an increase in the odds of modern contraceptives by 85% .A total of 14,986 women were included in the analysis; HIV-positive women were 1,066 and HIV-negative women were 13,830. Modern contraceptive use prevalence was 35% among HIV-positive women and 30% among HIV-negative women. Among HIV-positive women, those enrolled in integrated services (ART) had a higher prevalence of modern contraceptive (40%) compared to HIV-positive women unaware of their status (27%, This study found relatively low modern contraceptive use among HIV-positive women in the general population despite the existance of service integration program and guidelines to guide its implementation.Our study therefore calls for the evaluation on the implementation of the integration programme to identify factors that constrain or facilitate programme effectiveness. Women and their reproductive actions are essential for the success of HIV prevention and control programs. Over half of 38 million people infected with HIV/AIDS globally are women . Women oNational governments and international organizations endorsed integrating family planning and HIV services as a strategy to reduce unintended pregnancies and MTCT of HIV . Quasi- Tanzania endorsed the strategy and is implementing family planning and HIV services integration at all facility levels. During routine HIV care and PMTCT visits, all women of reproductive age should be assessed for pregnancy status and family planning needs, to facilitate FP counseling and provision of contraceptives or referrals.Over 90% of HIV-positive women access ART through HIV treatment and PMTCT clinics . HIV-posUsing data from a large household-based HIV impact survey in Tanzania, we tested this hypothesis by comparing modern contraceptive use among women on ART (integrated services) with HIV-positive women not on treatment and HIV-negative women. This assessment will provide information on the performance of the service integration strategy in Tanzania and the need for its evaluation. While few facility-based surveys have examined the prevalence of modern contraceptives among HIV-positive women, to our knowledge, there is no national survey analysis on this subject in Tanzania.The United Republic of Tanzania comprises Tanzania mainland and Zanzibar Islands. The total population in 2022 was estimated at 59.8 million, where 69% of the people live in rural areas . The aveTanzania is among the countries with the highest levels of HIV and unmet need for modern contraception in sub-Saharan Africa. Current modern contraceptive prevalence among married women stands at 31% . Nearly This study utilized data from the Tanzania HIV impact survey (THIS) 2016/2017. THIS is a nationally representative household-based cross-sectional survey covering Tanzania's Mainland and Zanzibar Islands . THIS waTHIS employed a two-stage stratified cluster sampling design, with the first stage involving sampling enumeration areas (EA) and the second stage sampling households. Sampling was stratified by residency and 31 geographical regions. The sampling frame for THIS survey was the 2012 Tanzania population and housing census survey. Sampling weights were generated and were used to account for survey design, selection probabilities and non-responses in statistical analysis.https://phia.icap.columbia.edu/.THIS used adult, adolescent, and household questionnaires to collect social, demographic and household information. Our analysis focuses on data collected from household and adult questionnaires from households with women of reproductive age. The household questionnaire collected various members' data, including basic social and demographic information. The adult questionnaire was completed for one household member to capture, among others, sexual activity, pregnancy, and childbearing information and service utilization data, including family planning, ANC, and self-reported HIV status. Non-pregnant women responded to the contraceptive access and use modules. Data is achieved by the Population-Based HIV Impact Assessment (PHIA) project. We accessed the data from the project\u2019s portal at Modern contraceptive use among women of reproductive age is the primary outcome of this analysis. Non-pregnant women were asked whether \u201cyou or your partner are currently doing something or using any method to delay or avoid getting pregnant\u201d. Those who responded yes were further asked to report their contraceptive method. Contraceptive methods were divided into modern methods , traditional methods and non-use.This study's primary predictor of modern contraceptives is the enrollment into integrated family planning and HIV service. HIV treatment guidelines require healthcare providers to offer family planning services when providing HIV treatment. Therefore, in this study, enrollment in HIV treatment is the primary predictor variable of interest. Enrolment in ART treatment was identified by asking HIV-positive respondents whether they were on ART treatment. Blood samples of all HIV-positive women were further screened for detectable levels of ARVs to confirm self-reported responses. The final service integration variable is binary indicators 1 if the respondent has detectable ARVs and 0 otherwise. Confounding predictor variables of interest were identified and grouped into social-demographic, reproductive, and HIV-related characteristics. Social-demographic variables collected by THIS include age, marital status, education level, place of residency , wealth quintiles, and occupation status, among many others. Reproductive characteristics included the number of pregnancies, children, births, and sexual partners. HIV-related characteristics included awareness of HIV status (partners status and self-status), duration of ARV treatment and suppression.p-value less than 0.05. The data were analyzed using STATA version 15.We used descriptive statistics to show the distribution of respondents' social-demographic, reproductive and HIV-related characteristics. Modern contraceptive prevalence was calculated by dividing the number of non-pregnant women who reported using any modern contraceptive (numerator) and the total number of non-pregnant women (denominator). The Pearson chi-square test was used to assess the differences in modern contraceptive use between the study groups. The univariate logistic regression model was used to assess the strength of the association between modern contraceptive use and one potential predictor at a time. We re-assessed the strength of association using a multivariate logistic regression model, which simultaneously accounts for multiple predictors in a single model. In multivariate analysis, we only included predictors with a p-value equal or less than 0.25 in univariate analysis. Sampling weight was applied to descriptive and regression analyses to account for survey design, selection probabilities and response rates. Odds ratios with 95% confidence intervals were computed to assess the strength of associations. Statistical significance was considered at a The final analysis includes 14,896 women; 1066 were HIV-positive, and 13,830 were HIV-negative. Among those diagnosed with HIV, 61% self-reported being aware of their HIV status. After combining self-report and ART detection in blood, 65% of HIV-positive women were estimated to be aware of their HIV status. Over 90% of women diagnosed with HIV are on ART. Viral suppression had been attained in most women on HIV treatment (79%) compared to those not on HIV treatment (20%).Age distribution substantially differed among HIV-positive and negative women. Over 50% of HIV-positive women were older adults (35\u201349), while the majority of HIV-negative women (44%) were youth 15\u201324). Other characteristics differentiating the two groups were attainment of secondary education and above (HIV-positive\u2009=\u200913% vs HIV negative\u2009=\u200926%), living in urban areas (HIV-positive\u2009=\u200950% vs HIV-negative\u2009=\u200939%), and divorced/widow/separated marriage status (HIV-positive\u2009=\u200935% vs HIV-negative\u2009=\u200912%). Table 5\u201324. OthThere was a slight difference in the proportion of women who were sexually active in the past 12\u00a0months (HIV-positive\u2009=\u200977% vs HIV-negative\u2009=\u200984%). Multiple sexual partnerships in the past 12\u00a0months were more prevalent among HIV-positive (16%) than HIV-negative (9%). On the other hand, more HIV-positive women (34%) frequently reported condom use during non-marital sexual intercourse than HIV-negative women (26%). Pregnancies are fewer among HIV-positive (7%) than HIV-negative (12%) at the time of the survey. Birth histories in the past five years indicate fewer HIV-positive women (8%) gave birth to more than two children than HIV-negative women (14%). Table p-value\u2009=\u20090.004). In women diagnosed with HIV, the contraceptive prevalence was higher among women who were aware of their HIV status (41%) compared to those who were not aware of their HIV status (27%) . Furthermore, in HIV-positive women, contraceptive prevalence was higher in those enrolled on integrated services (on ART) (40%) than those not on ART (28%) . Women with viral suppression had higher contraceptive prevalence than those with unsuppressed viral loads. Contraceptive prevalence appears comparable by ART duration and HIV-negative women (39%). Implants were more common among HIV-negative (30%) than HIV-positive (23%). HIV-positive women reported the highest male condom use 31%) relative to HIV-negative women (12%). Both groups have similarities in using IUDs, pills, and sterilization. Both groups mostly preferred short-acting contraceptives, 69% (237) and 61% (2288), by HIV-positive and HIV-negative women, respectively , women who knew their HIV-positive status had higher odds of modern contraceptives than HIV negtive women or HIV positive not knowing their status (Table In HIV-positive women (Model 2), enrolment into integrated services (currently on ART) demonstrated an increase in the odds of modern contraceptives by 85% . Model 2 was adjusted for six variables, of which statistical significance were observed for age, formal education, number of sexual partners and number of pregnancies. HIV-positive women with only one sexual partner had 79% higher odds of modern contraceptive use compared to those with multiple partners . Additionally, those with more than three pregnancies had 6 times higher contraceptive use than those with fewer pregnancies ; being aged 35\u00a0years and above, ; and having primary education, had significantly higher odds of modern contraceptive use is associated with increased modern contraceptive use among HIV positive women. Contraceptive prevalence by HIV status shows that approximately one-third of HIV-positive women (35%) used modern contraceptives. The prevalence was higher among those on integrated services (ART) (40%) compared to those not on ART or unaware of their status (27%) and HIV-negative women (30%).This indicates a 13% higher contraceptive prevalence among HIV-positive women on integrated services compared to those not on ART and unaware of their HIV status, and a 10% higher prevalence than HIV-negative women. This increase may be attributed to the integration of family planning and HIV services and or reduced desire for more children following HIV diagnosis , 22. PriIn our multivariate analysis that combined HIV-positive and negative women (Model 1), HIV-positive status awareness increased the odds of modern contraceptives by 33%. In HIV-positive women (Model 2), being on integrated service increased the odds of modern contraceptives by 85%. These findings are consistent with the results reported among HIV-positive women in Malawi . The incThis study presents a precise and reliable situation of modern contraceptive use among HIV-positive women and in the general population in Tanzania. Our findings are comparable with studies from sub-Saharan African countries where low modern contraceptive prevalence was observed. These studies are from Kenya (32%) , NortherOne facility-based study in Kilimanjaro, Tanzania, reported a modern contraceptive prevalence of 54% among HIV-positive women attending HIV care and treatment clinics (CTCs) . The higThe differences in the distribution of preferred contraceptive methods may be associated with many factors, such as contraceptive availability, individual preferences, and perceived risks by providers and users. Concerning perceived risks, the National Guideline on Family Planning in Tanzania cautions providers when prescribing oral contraceptives and implants due to reported reduced contraceptive efficacy among HIV-positive women treated with some ARV . High-riContraceptive choice limitations in the family planning guidelines for HIV-positive may have contributed to high injectables and male condom use. Injectables and male condoms were the most common methods of contraceptives among HIV-positive women. The order of preference is consistent with a similar study from Malawi, where injectables (20%) and male condoms (13%) were the most popular methods of contraception among HIV-positive women . A compaThe family planning and fertility modules of THIS 2016/17 survey collected data on a few variables, thus missing potential variables such as family planning knowledge, fertility intentions, male involvement, uptake of family planning counselling, and the sources of family planning information. The missing variables could have provided additional and valuable information for assessing the determinants of modern contraceptives among HIV-positive women. Morever, majority of HIV positive women (94%) were on ART, hence we can not make a definitive conclusion on weather being on ART was the only factor responsible for the observed difference in contraceptive use between women on ART and those not on ART.Despite the availability of the national guidelines for integrating family planning and HIV services, our study found lower modern contraceptive use among HIV-positive women in Tanzania than anticipated following integration. This suggests a gap in program effectiveness. As previously described, family planning is a cost-effective intervention for reducing unintended pregnancies and MTCT of HIV. These findings provide insight into why unintended pregnancies and MTCT of HIV persist in Tanzania. Therefore, we recommend a thorough evaluation of the family planning and HIV services integration program to identify factors that hinder or enhance its effectiveness in Tanzania."} +{"text": "New advances in bedside assessment and monitoring of acute respiratory failure patients.\u201d This editorial will highlight their major strengths and messages.Four manuscripts were selected in the Research Topic titled \u201cTang et al. evaluated the outcomes of early using of Central Venous Pressure (CVP) in ARDS patients at ICU admission. They used retrospective info from the medical Information Mart for Intensive Care IV (MIMIC-IV) database. Their primary outcome was the 28-day mortality cut off . Modern ICUs use invasive and non-invasive cardiac output measurements and the dynamic parameters of fluid responsiveness, such as stroke volume (SV), stroke volume variation (SVV), and pulse pressure variation (PPV), following the concept of functional hemodynamic monitoring to give fluids (p < 0.001). Multivariate logistic regression confirms this trend , while the incidence of Acute Kidney Injury (AKI) was comparable between the two groups. Among the study limitations the patients in the CVP group showed lower severity of illness scores and fewer comorbidities, suggesting less impairment of overall function. The authors concluded that the association found does not necessarily imply causation and further prospective studies will be required to confirm whether CVP use is useful in ARDS patients.In the first manuscript, e fluids , 2. In pe fluids \u20135. ThereGirard et al. measured the regional pleural strain related to invasive mechanical ventilation using ultrasound elastography. This is order to non-invasively evaluate the Ventilator Induced Lung Injury (VILI) and to measure if the US elastography would correlate with varying tidal volumes . Pleural and diaphragmatic measurements are valuable tools used to indirectly check the lung parenchyma for consolidations and strength during mechanical ventilation and weaning off it in predicting the development of respiratory failure (RF) in patients with Community-acquired-pneumonia (CAP) and its feasibility and benefit in emergency department (ED) . In partnography , 10. TheErlebach et al.). The V-VA ECMO provides both respiratory and hemodynamic support potentially representing a therapeutic option for patients with ARDS who develop secondary severe hemodynamic impairment. In this retrospective study among three ECMO centers, the authors aimed to describe the short and long-term outcomes of ARDS patients receiving V-V ECMO plus V-VA ECMO. The femoral-site for venous drainage and the jugular-site for venous return was the most frequent configuration of V-V ECMO. The femoral and subclavian artery cannulation was used in V-VA ECMO upgrade. The V-VA and V-V ECMO were successfully weaned in 47 (64%) and 40 (55%) patients. Thirty-five (48%) V-VA ECMO patients died during their ICU stay. An overall 2 year-mortality of 58% (39/67) was observed. In the final multivariable model, SOFA score >14 and lactate level were significantly associated with 60-day ICU-mortality. The favorable ICU survival rate of 52% is remarkable, underling the message that in highly specialized centers, the upgrade of V-V ECMO patients suffering from ARDS to V-VA ECMO should not be rendered as futile per se.Finally, the last study describes an upgrade of the V-V-system using an additional arterial return cannula (termed V-VA ECMO) to retain sufficient organ perfusion (GA wrote the manuscript. PP and LV conceived the content, gave important intellectual contributions to the manuscript, and revised the draft critically. All authors contributed to manuscript revision, read, and approved the submitted version."} +{"text": "Retraction Note: BMC Cancer (2020) 21:210.1186/s12885-020-07670-yThe Editors have retracted this article due to the authors\u2019 inability to provide documentation of approval from the ethics committee. The authors have not responded to correspondence from the publishers about this retraction."} +{"text": "Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses. miRNAs regulate plant immunity through repression of mRNAs encoding nucleotide binding-leucine-rich repeat intracellular receptors (NLRs), often triggering production of siRNAs that reinforce repression and direct silencing of additional NLRs. Plants use cell surface and intracellular receptors to detect potential pathogens. Activation of membrane-anchored pattern recognition receptors (PRRs) is typically associated with perception of pathogen-associated molecular patterns (PAMPs) and elicits pattern-triggered immunity (PTI). Intracellular nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLRs) detect pathogen-derived effectors, thereby activating effector-triggered immunity (ETI). Pathogen effectors act intracellularly to manipulate host processes and facilitate pathogen spread. The immune response triggered by the activation of NLRs, known as ETI, is fast and robust, and is often accompanied by activation of localized programmed cell death known as the hypersensitive response (HR) (Shao etResistance (R) genes that mediate gene-for-gene resistance to pathogens carrying cognate effectors, in this case known as avirulence factors or a protein that mimics its target protein (decoy model), or through direct modification by the effector of a decoy domain integrated within the NLR protein . Activat2+ fluxes to drive intracellular signaling cascades (+ into nicotinamide (Nam) -tailed and m7G-capped primary miRNA transcripts (pri-miRNAs) containing a hairpin-like structure family . miRNAs tructure . Pri-miRtructure . Subsequtructure , in a process assisted by the proteins suppressor of gene silencing 3 (SGS3) and silencing defective 5 (SDE5) (asiRNAs) . ProductasiRNAs) does so in Arabidopsis (cis and trans modes); (iv) the trigger miRNA levels are modulated during pathogen\u2013host interactions to allow for an increase in NLR expression; and (v) this modulation influences the outcome of the host\u2013pathogen interaction. In the following, we expand on each of these important points, and discuss the use of the small RNA\u2013NLR repression network to modulate pathogen detection and the plant responses through changes in NLR levels.The first reports of NLR regulation via miRNAs used 5\u02b9-RNA ligase-mediated (RLM)-RACE to demonstrate that miR482 guides cleavage of NLR-encoding transcripts in bidopsis ; (iii) pNLR genes and the total number of genes in a plant genome and secondary NLR targets (trans silencing) were found and secondary (trans) NLR target genes (Brassica napus phasiRNA (phasiR130-4) whose production is triggered by the miR1885\u2013BraTIR1 mRNA interaction, mediates trans silencing of BraCP24 mRNA, at least when the two are transiently co-expressed in Nicotiana benthamiana leaves mRNA . A modified version of the 5\u02b9RLM-RACE technology in which the ligated products are subjected to high-throughput sequencing. This approach is useful to detect cleavage of RNA targets in a transcriptome-wide manner.miRNA (or phasiRNA) reporter activity. Analysis of the expression of a modified version of a reporter gene (e.g. GFP or GUS) that harbors the miRNA target site of interest and thus is under miRNA-mediated regulation. When using this methodology, it is important to analyze in parallel a modified version of this construct carrying mutations that prevent miRNA (or phasiRNA) pairing without altering the protein sequence, as a control (non-regulated version of the reporter). This technique allows detection of both mRNA cleavage and translational inhibition, the latter not detected by techniques such as 5\u02b9RLM-RACE or PARE.Box 2.Reducing miRNA levels. Target Mimics (MIMs), Short Tandem Target Mimics (STTMs), and Central mismatches Molecular Sponges (cmSPs) technologies constitute the toolkit used in plant research to reduce mature miRNA levels. These three techniques make use of a non-coding RNA that harbors 1\u201315 non-cleavable altered miRNA target sites (mismatches or bulges) promoting miRNA knockdown, through a process known as target-directed miRNA degradation (TDMD). The main differences between the three methodologies are the sequence/structure of the non-coding RNA, the mismatch region, and the number of miRNA target sites per molecule of RNA decoy.Increasing miRNA levels. Overexpression (e.g. 35S promoter) of the genomic sequence of the miRNA precursor (pri-miRNA) or use of artificial miRNAs (amiRNAs) in which the precursor of a known miRNA (e.g. miR319) is modified to harbor and render the mature sequence of the miRNA of interest.The mode of action of small RNAs is governed by its AGO partner . ClearlyMovement of siRNAs affects silencing effectiveness and has broad implications for plant development and immunity , activated upon perception of PAMPs such as bacterial flagellin, are canonical elements of PTI . HoweverPruitt RDR6 and AGO1 mRNA levels have been shown to rapidly decrease in Arabidopsis leaves and seedlings upon flg22 treatment or fungal PAMPs (Arabidopsis) (ng genes . In thisP. syringae DC3000 hrcC mutant (which fails to introduce effectors into the host cell and therefore does not induce ETI) in Arabidopsis. The authors proposed that increases in the dosage of so many TIR genes could lead to an increased production of small molecules with defense signaling activities even in the absence of effector detection, assuming a certain degree of NLR misfiring, thus activating downstream TIR signaling pathways to a level sufficient to reinforce PTI responses without triggering cell death prior to infection with either P. syringae or B. cinerea, although this decrease is only statistically significant if pathogen infection follows ISR activation (i.e. treatment with B. cereus followed by P. syringae or B. cinerea infection) (Both miR472 and miR825-5p have been linked to the activation of the induced systemic response (ISR) in Arabidopsis Are phasiNLR more prone to operate through translational repression or by cleaving the target mRNA? (ii) Can phasiNLRs move in a non-cell-autonomous manner reaching miRNA-free tissues as has been reported for other siRNAs? And if so, is this a relevant aspect on immune regulation? Moreover, there are additional open questions on the field that are relevant for understanding how this mechanism of regulation operates. A deeper search into sRNA libraries in selected species via the CRISPR /Cas (CRISPR-associated protein) technology would provide valuable information.MIR loci and mature miRNA levels is clear; however, the signaling elements involved are still unknown. Additionally, mature miRNA levels have been shown to drop as soon as 30 min after PAMP treatment (IPS1 during phosphate starvation (TAS5 in tomato (Another aspect important for understanding the relevance of this type of regulation in plant defenses that has not been investigated at the molecular level is how NLR-targeting miRNAs and phasiNLRs respond to PRR-mediated pathogen perception. The link between PAMP perception and decreases in transcription of the Solanaceae-specific 22 nt miR6019 triggers the production of phasiNLR from the target NLR N gene conferring resistance against TMV in Nicotiana tabacum (N mRNAs and increased N-mediated resistance against TMV in tobacco plants, a mechanism that may be conserved in other Solanaceace species (Much have been discovered about the role of 22 nt miRNA and phasiNLR regulation in plant immunity in the last decade. This, in conjunction with the developments in the last few years in defense signaling, make this a hot and exciting topic with a great potential to be unlocked in generating new strategies for crop protection, in which much is yet to be learnt."} +{"text": "Our single-molecule real-time sequencing-based methylome analysis revealed multiple AamA-mediated DNA methylation sites and proposed a potent census target motif (TTTRAATTYAAA). Loss of Dam led to modulation of genome-wide gene expression, and several Dam-target sites including the promoter region of the trmD operon were identified through our methylome and transcriptome analyses. AamA methylation also appeared to control the expression of many genes linked to membrane functions , replication (dnaA) and protein synthesis (trmD operon) in the strain ATCC 17978. Interestingly, cellular resistance against several antibiotics and ethidium bromide through functions of efflux pumps diminished in the absence of the aamA gene, and the complementation of aamA gene restored the wild-type phenotypes. Other tested phenotypic traits such as outer-membrane vesicle production, biofilm formation and virulence were also affected in the aamA mutant. Collectively, our data indicated that epigenetic regulation through AamA-mediated DNA methylation of novel target sites mostly in the regulatory regions could contribute significantly to changes in multiple phenotypic traits in A. baumannii ATCC 17978.Individual deletions of three genes encoding orphan DNA methyltransferases resulted in the occurrence of growth defect only in the Transcriptomic data have been deposited in the NCBI database under Gene Expression Omnibus (GEO) accession GSE195621. Methylome data have been deposited in the NCBI database under Sequence Read Archive (SRA) accession SRR25365149 (Lab-WT) and SRR25365148 database at the time of writing this article, their genome-wide methylome analysis and AamA-recognition sites have been poorly explored. Our data revealed putative novel census AamA target motifs, which are densely positioned in 12 regions in the genome of A. baumannii strain ATCC 17978. Further methylome analyses and studies of AamA-controlled genes remain warranted because the size and structure of AamA proteins differ even among A. baumannii strains, and bacterial methylation patterns are known to vary under different conditions. Nevertheless, this study establishes a foundation for understanding the impact of AamA-mediated epigenetic control on the survival and virulence of A. baumannii.Although the emergence of multidrug pathogenic Escherichia coli, encoded by the dam gene produces N-6-methyladenine (6mA), the most prevalent DNA modification in prokaryotes pyridinium dibromide; Molecular Probes, Eugene, OR, USA and Life Technologies, Carlsbad, CA, USA). The lipophilic dye FM4-64, which intercalates into the outer membrane, is commonly used to stain and observe membranes of bacteria / [h\u00d7100]) in LB (5\u2009ml), but no significant growth defects were observed in other dcm mutants (\u2206aamA/pRK415::aamA) and the vector controls , the growth retardation of the aamA mutant remained the same under all test conditions except for the R2A (2\u2009x) broth media, and the aamA complemented strain failed to restore the growth rate . Failure of our complementation assay and the absence of any growth defect in aamA mutant under certain conditions suggested that fine-tuning the expression of the aamA gene and AamA is necessary for the epigenetic control of target sites in the genome of A. baumannii. Scanning electron microscopic (SEM) image analyses showed no significant differences in the sizes of WT and the aamA mutant mid-exponentially grown in LB , but large holes were often detected on the surfaces of both the aamA mutant and the aamA complemented strains suggesting possible destruction of membrane structure (aamA mutant and the complemented strains under the R2A (2\u2009x) broth condition, indicating strong linkage AamA protein abundance and surface structure of A. baumannii cells. Although the underlying molecular mechanisms of AamA-controlled membrane maintenance remain elusive, Aam protein deficiency suggested novel insights into cell surface modification . Loss of mutants 47\u201349]..aamA, dcwth rate and S2. tructure . Interesfication .aamA mutant strains were more abundant than methylated adenine residues , our study focused on the 6mA-type of adenine methylation, because growth defect was only observed in the aamA mutant and 6mA was prevalent in all bacterial methylome analysis rnpA geneaamA mutant strains were sequenced under the same conditions used for methylome analysis to understand AamA-mediated changes in genome-wide gene expression patterns , metabolic processes , and antioxidant activity , and the upregulated genes were mainly involved in other metabolic processes (lolAB) and porin protein-folding (bamAD) pathways might affect the membrane stability and rigidity of AamA-mediated methylation (trmD operon (rpsP-rimM-trmD-rplS) having motif IV in the promoter region mirrors that in E. coli, and its expression was down-regulated (0.30\u20130.75-fold) in aamA mutant, partly supporting the defective growth phenotype in aamA mutant due to the linkage between this trmD operon and the 16S rRNA processing for translation and the rbtA-like gene , which are predicted to encode membrane proteins, were upregulated in the aamA mutant, although it is not clear how such modifications are linked to changes in gene expression (Transcriptomes of both WT and the nd pcaF) . Interesnslation 62, 63]aamA mutapression .aam mutant, and the aamA complementation strains in the aamA complementation strain compared to WT to have the same levels of aamA expression in both WT and aamA complementation strains were upregulated (1.5\u20132.4-fold) when the aamA gene was deleted. Although the aamA gene was successfully complemented, and its gene expression levels were restored in the aamA complementation strain, the expression levels of the three target genes tested did not reach those observed in WT, which is consistent with growth test results obtained with the same strains (mltA gene (1.6-fold), otsAB operon (0.4\u20130.8-fold) and trmD operon (0.2\u20130.6-fold) in aamA mutant were successfully recovered to the levels observed in WT were not recovered in aamA complemented strain, because AamA-mediated on/off switch for gene expression might be attributed to the competitive target site binding of DNA-binding proteins (transcription factors [TFs] and nucleoid-associated proteins [NAPs]) at methylated or unmethylated sites rather than directly regulated genes ) codons, and the deletion of the trmD gene results in increased antibiotic susceptibility (e.g. KAN) due to defects in membrane lipoprotein and efflux pumps biosynthesis . In. IntrmD oniae) . Loss of. coli . Interesynthesis . ConsistClick here for additional data file.Click here for additional data file."} +{"text": "Background: With new variants challenging the effectiveness of preventive measures, we are beginning to recognize the reality that COVID-19 will continue to pose an endemic threat. The manifestations of COVID-19 in lung transplant recipients during index admission are poorly understood with very few cases reported in recent lung transplant recipients. Optimal management of immunosuppression and antiviral therapy in recent transplant recipients is challenging. Methods: We performed a retrospective analysis identifying lung transplant recipients at our institution who contracted COVID-19 in the immediate postoperative period (within index admission). In addition, we performed a systematic review from January 2020 to August 2023 identifying all publications on the PUBMED database regarding COVID-19 infection in lung transplant recipients during index admission. Results: We report four cases of COVID-19 pneumonia in lung transplant recipients in the immediate postoperative period and we describe the clinical course, treatment options, and immunosuppression changes to manage this unique clinical problem. All patients made a full recovery and were eventually discharged home. Within our review of the literature, the most prevalent presenting symptoms were cough, dyspnea, and fatigue. Six (75%) patients decreased or held their antimetabolite. The two most common treatments were monoclonal antibodies (38%) and remdesivir (63%). Conclusion: Although previous literature demonstrates that COVID-19 can be deadly in recent lung transplant recipients, rapid treatment with anti-viral therapy/immunotherapy, deescalating immunosuppression, and treatment of respiratory decompensation with Decadron was effective in our patients. COVID-19 caused by the novel SARS-CoV-2 virus has a wide clinical spectrum, ranging from asymptomatic infection and mild upper respiratory tract illness to acute respiratory distress syndrome and multisystem organ dysfunction. Lung transplant recipients are at increased risk for infection and progression to fulminant disease given their frequent comorbidities and high levels of immunosuppression. The immediate postoperative period is of particular concern due to targeted T-cell induction immunotherapy. Initial reports of COVID-19 in patients with a remote history of lung transplantation show very poor outcomes . DespiteWe performed a retrospective analysis of all adult patients undergoing primary lung transplantation with immediate postoperative COVID-19 infection at our institution from January 2020 to August 2023. Patients who underwent concomitant cardiac procedure, solid organ transplantation, or lung retransplantation were excluded from this study. Immediate postoperative COVID-19 infection was defined as having a positive test during index admission.A systematic review was performed using PubMed database from January 2020 to August 2023. This systematic review followed guidelines established by the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA). The search was restricted to publications in English. The following search terms were applied: ((lung transplantation) AND (COVID-19)), ((lung transplantation) and (coronavirus)), ((lung transplantation) and (SARS-CoV-2)). In addition, references from original papers were manually searched for relevant citations. We only included papers that contained patients with COVID-19 infection during their index admission in the postoperative setting. Publications regarding preoperative COVID-19 infection and postoperative outside of index admission were excluded from the analysis. A PRISMA flow diagram is included in 2 support method. All studies were available for synthesis and variables of interest that were not reported, were marked as \u201cNR\u201d for the respective study. A meta-analysis could not be performed due to the heterogeneity of literature collected and the limited quantity of literature in this area. The protocol for this systematic review was not registered.Primary outcomes were mortality and changes in immunosuppression. The data collected also included the number of patients included, average age, patient(s) sex, transplant indication, time to diagnosis, comorbidities, presenting symptoms, COVID-19 diagnostic methods, imaging modality, imaging findings, hospital length of stay, antibiotic/antiretroviral treatment, and OA pre-planned risk of bias was not assessed within this systematic review due to the lack of high-quality evidence investigating immediate postoperative COVID-19 infection in lung transplant recipients. The systematic review consists of case reports and case series studies that contain inherent biases and the lack of a control group.Four patients tested positive for COVID-19 within their index hospitalization after primary lung transplantation. Three tested positive in early 2021 and one in early 2022. All four were transplanted for restrictive lung disease. The average LAS was 40 and the average age was 62 years. Three were diagnosed by routine nasal swab prior to discharge to acute rehab with no other symptoms, while one was tested for new mild shortness of breath and cough. Computed tomography (CT) in two patients showed multi-lobar opacities concerning for multi-lobar pneumonia. Two patients showed classical ground glass opacities on imaging . Case 1 A total of 40 records were identified and eligible for full-text review. After reviewing for eligibility, we found two case series and four case reports of patients with COVID-19 infection in the immediate post-operative period (within index admission) after lung transplantation, totaling 18 patients ,3,4,5,6.Of lung transplantation patients with immediate post-operative COVID-19 and available data, the mean age at the time of COVID-19 diagnosis was 59 years (range: 37\u201371 years) and 50% were male. Reasons for transplantation in the cohort with immediate post-operative COVID-19 were as follows: idiopathic pulmonary fibrosis (50%), hypersensitivity pneumonitis (33%), and cystic fibrosis (17%). The mean interval between the date of transplant and the date of COVID-19 diagnosis was 12 days (range: 1\u201322 days). All patients were under immunosuppressive therapy for rejection prophylaxis at time of COVID-19 diagnosis.The most prevalent presenting symptoms were as follows: dyspnea (80%), cough (60%), and fatigue (60%). GI symptoms were less common at 20%. All patients had RT-PCR tests run on samples collected via nasopharyngeal swab with fewer having additional samples collected via oropharyngeal swab (33%), saliva (17%), and bronchioalveolar lavage (17%) . All patients diagnosed in the immediate postoperative period tested positive via RT-PCR. The majority of patients underwent CT scans (88%) and to a lesser degree chest X-ray (25%). The most common findings on radiographical imaging were ground glass opacities (75%) and consolidation (38%). Chest X-ray was clear in one (13%) patient.The management of COVID-19 infections in lung transplantation recipients is summarized in The mean hospital length of stay for patients with available data was 52 days (range: 14\u2013122 days). Of the eight cases of COVID-19 infection in the immediate post-operative period after lung transplantation, three (37.5%) succumbed to infection.Here, we report four cases of lung transplant recipients diagnosed with COVID-19 during their initial hospitalization an average of 26 days post-transplant, despite both donor and recipient testing negative at time of the initial operation. The initial diagnosis of COVID-19 in recent lung transplant recipients is challenging. Classical signs and symptoms may be masked due to the recency of the transplant operation, initiation of new medications, primary graft dysfunction, or other infectious etiologies. Three of the four patients displayed no symptoms at the time of diagnosis and the remaining patient reported mild shortness of breath and worsening cough. No patients developed objective fever over the course of the acute infection. However, in the reported literature, fever is not a common presentation in lung transplant recipients who contract COVID-19 ,4,5. DesWithout consensus guidelines to define treatment algorithms in this cohort, treatment decisions were made by a multidisciplinary COVID team, in conjunction with transplant surgery. Treatment strategies with antiviral and neutralizing antibody modalities continue to rapidly evolve with no clear gold-standard treatment. Two of our patients received Bamlanivimab as neutralizing antibody monotherapy, while the other two patients received a 5-day course of Remdesivir. This was in accordance with the literature review demonstrating that monoclonal antibody and Remdesivir were the two most common treatments. Patient treatment selection depends upon the COVID-19 disease severity and Remdesivir is indicated in patients with severe disease while Bamlanivimab is recommended for patients with mild to moderate disease severity at risk of progression . Both BaBalancing immunosuppression against the risk of infection is a challenging clinical problem under normal circumstances. Infection with SARS-CoV-2 complicates the matter further. In the transplant literature, pausing antimetabolite therapy, but continuing calcineurin inhibitors is a common management strategy ,2,4,5,12In the current review of eight lung transplant recipients with COVID-19 infection in the immediate postoperative period, the mortality rate was 37.5%, which is disparate from our case series where all four patients survived to discharge. The mortality results of our literature review are in general agreement with the current COVID-19 literature as this viral infection has been found to be associated with increased risk of both postoperative complications and 30-day mortality in patients who contract the COVID-19 virus in an immediate postoperative setting ,17,18. DAll four of our patients were stable for discharge despite continuing to test positive for COVID-19. Moderately or severely immunocompromised individuals may produce replication-competent virus beyond 20 days ,5. It isThere are several limitations associated with our case series and literature review findings. First, due to the rarity of the current topic, the outcomes reported in the current study are based on a small group of patients and may lack power. Due to the small sample size, the effects of variations in lung transplant practices as well as treatment strategies across centers can confound the results. Lastly, because of the short follow-up associated with the studies included, we can only report on immediate results and cannot offer any insight into important clinical questions such as the long-term effects of the COVID-19 virus on graft survival in lung transplant recipients. Despite these limitations, we include the most comprehensive group of lung transplant recipients who have contracted the COVID-19 virus during their index admission to date. To increase statistical power and identify risk factors associated with poor outcomes, a large multicenter investigation into the impact of COVID-19 on lung transplant recipients in the immediate postoperative period is warranted. In addition, investigating the long-term overall survival, graft survival, and pulmonary function in lung transplant recipients who acquire COVID-19 during the index hospital admission will inform post-discharge care and follow-up visit intervals.Recommendations for the treatment of COVID-19 in lung transplant patients defer to those for the general population where treatment is based on disease severity. Here, we describe four cases of COVID-19 immediately after lung transplantation. Although COVID-19 pneumonia can be deadly in this unique cohort, rapid treatment with anti-viral therapy/immunotherapy, deescalating immunosuppression, and treatment of respiratory decompensation with Decadron was effective in our patients. Despite reduction in immunosuppression, no patient developed episodes of acute rejection."} +{"text": "Body dysmorphic disorder (BDD) is defined in DSM5 as a preoccupation with one or more perceived defects or flaws in physical appearance causing significant distress or impairment in social and occupational functioning. Despite many studies on mental health disorders related to BDD, the diagnosis is still frequently overlooked.Previous studies have examined the general personality characteristics of BDD. The objective of this study is to find out how socially aversive personality traits are related.Total of 86 mentally and physically healthy adults participated. BDD was assessed by BDDE-SR, and aversive personality was assessed by Short Dark Triad , Assessment of Sadistic Personality (ASP), and paranoid (PAR), borderline (BOR), and antisocial (ANT) features of the clinical subscales of Personality Assessment Inventory(PAI). Correlations between the reported scores were investigated using Pearson\u2019s and regression was performed on relevant scales.Thirty seven males and 49 females (mean age 23.8 years) showed no statistically significant difference in total BDDE-SR was reported based on sex(p=0.18) or BMI. BDDE-SR, SD3 and ASP were not statistically correlated, but all of the subscales of PAR, BOR and ANT were associated with BDDE-SR. Regression results demonstrated in Table 1 show that BOR-I and PAR-R predict BDDE-SR. Correlation of BOR-I and PAR-R with BDDE-SR factors was shown in Table 2.This study shows that BDD symptoms are associated with borderline-identity problems and paranoia-resentment and suggests that we should consider the diagnosis of BDD for individuals with high BOR and PAR scores.None Declared"} +{"text": "Personalized treatment of metastatic non-squamous non-small cell lung cancer (NSCLC) requires detailed molecular characterization of the tumour including detection of predictive driver mutations and programmed death ligand 1 (PD-L1) expression. Complete detection is influenced by the amount of tumour cells sampled as well as their quality. Different sampling techniques may be necessary to provide sufficient tumour material for comprehensive molecular characterization. Missing the detection of targetable molecular genetic aberrations would have a serious impact on the quality of life and prognosis of a patient. This case report highlights the importance of biopsy technique in a patient with NSCLC. Several procedures\u2014pleural puncture, transthoracic lung biopsy and endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA)\u2014could not provide sufficient tumour material for precise tumour characterization. Only the addition of EBUS-guided transbronchial lymph node cryobiopsy (EBUS-TBLNC) enabled complete immunohistochemical and genetic tumour characterization, demonstrating PD-L1 expression in 100% of the tumour cells in the absence of actionable genetic alterations. Based on these results, immunotherapy was initiated. Mutational analysis and programmed death ligand 1 (PD-L1) expression are required for personalized treatment of metastatic non-small cell lung cancer (NSCLC). The detection of a targetable driver mutation has prognostic and predictive relevance, giving the patient the opportunity to receive highly effective first line targeted treatment with a kinase inhibitor ,3. The bTissue sampling is affected by size and/or localization of tumour lesions, which may result in insufficient biopsy samples, both in terms of quantity and quality. In cases of mediastinal or hilar lymph node involvement, cytological specimens obtained by EBUS-TBNA can often confirm malignancy , but cytEndobronchial and transbronchial cryobiopsy can yield large tissue samples allowing exact tumour characterization and may be superior to other biopsy techniques . EBUS-TBWe describe the case of a patient in whom several attempts of characterization of a lung tumour by different sampling techniques were unsuccessful due to low cellularity of the samples. Only EBUS-TBLNC yielded sufficient tumour material for detailed immunohistochemical and molecular tumour characterization and allowed to determine the optimal systemic therapy for this patient\u2019s non-squamous NSCLC.In an 83-year-old male former smoker (30 pack-years) with multiple comorbidities but with a good performance status (ECOG 1), the work-up of a symptomatic left pleural effusion led to the detection of a lung lesion in the left lower lobe accompanied by lymphangiosis, as well as discrete hilar and mediastinal lymphadenopathy. Drainage of the pleural effusion revealed single cells of a thyroid transcription factor 1 (TTF-1)-positive pulmonary adenocarcinoma. Further molecular analysis was not possible due to the scarcity of tumour cells in the cyto spin. For further classification of the non-squamous NSCLC, cytological material was obtained by EBUS-EBNA from mediastinal lymph nodes (LN) in position 4L, the best accessible site according to the staging CT A. DespitTherefore, we suggested tissue sampling with the aim of extracting solid tissue from the mediastinal LN by EBUS-TBNLC. The patient was informed about potential side effects and the limited experience with this technique. He agreed to undergo the procedure.Under EBUS guidance, tunnelling through the bronchial wall in the direction towards LN 4L was made using a monopolar electric needle knife A. A 1.1 Extensive infiltrates of TTF1 positive adenocarcinoma cells were seen C. MolecuBased on these findings and the positive risk-benefit ratio, first-line PD-1-directed therapy was initiated with Pembrolizumab as monotherapy ,16,17. UWe present a case in which, after several unsuccessful sampling attempts for NSCLC characterization, EBUS-TBLNC succeeded in adequate tumour sampling for molecular characterization, thereby allowing personalized treatment of the patient. EBUS-TBNLC may contribute to optimized molecular workup of NSCLC in the future, thereby providing important information for patient treatment."} +{"text": "Single-cell RNA sequencing (scRNA-seq) has revolutionized the transcriptomics field by advancing analyses from tissue-level to cell-level resolution. Despite the great advances in the development of computational methods for various steps of scRNA-seq analyses, one major bottleneck of the existing technologies remains in identifying the molecular relationship between disease phenotype and cell subpopulations, where \u201cdisease phenotype\u201d refers to the clinical characteristics of each patient sample, and subpopulation refer to groups of single cells, which often do not correspond to clusters identified by standard single-cell clustering analysis. Here, we present PACSI, a method aimed at distinguishing cell subpopulations associated with disease phenotypes at the single-cell level.PACSI takes advantage of the topological properties of biological networks to introduce a proximity-based measure that quantifies the correlation between each cell and the disease phenotype of interest. Applied to simulated data and four case studies, PACSI accurately identified cells associated with disease phenotypes such as diagnosis, prognosis, and response to immunotherapy. In addition, we demonstrated that PACSI can also be applied to spatial transcriptomics data and successfully label spots that are associated with poor survival of breast carcinoma.PACSI is an efficient method to identify cell subpopulations associated with disease phenotypes. Our research shows that it has a broad range of applications in revealing mechanistic and clinical insights of diseases.The online version contains supplementary material available at 10.1186/s12915-023-01658-3. Single-cell RNA sequencing (scRNA-seq) is revolutionizing whole-transcriptomic studies from the tissue resolution to the cell resolution . DespiteThere are multiple statistical methods that have been developed to explore single-cell data. Seurat utilizes unsupervised clustering to identify cell types and then associate cell types with disease phenotypes . HoweverTo address these challenges, Scissor was purposed to dissect phenotype-specific cell subsets from heterogeneous single-cell data . The keyTherefore, we have developed PACSI (Phenotype-Associated Cell Subpopulation Identification), a novel network-based method to identify cell subpopulations associated with disease phenotypes of interest. PACSI takes a single-cell transcriptome dataset, a bulk gene expression matrix, phenotype labels and protein-protein interaction (PPI) networks as inputs. PACSI consists of three steps: (1) cell/sample signatures in the form of gene sets are constructed using the highly expressed genes of a cell/sample relative to the others in the single-cell or bulk gene expression matrix; (2) network-based proximity is calculated to define similarity between cells and the disease phenotype of interest; (3) the significance of the proximity-based similarity between a cell and the phenotype of interest is assessed by randomly assigning genes in the cell signature. We tested PACSI on multiple datasets of various disease phenotypes to ascertain the broad utilities of PACSI. Our studies suggest that PACSI allows scientists to generate more biological insights into the underlying mechanisms of complex diseases, which can promote the development of precision medicine.To develop a general-purpose algorithm that is suitable for many disease phenotypes, we integrated single-cell expression matrices, bulk gene expression data, bulk sample phenotype labels, and PPI networks to identify cells related to disease phenotypes Fig. A. The fiTo evaluate the performance of PACSI in a controlled context, we implemented splatter to generHead and neck squamous cell carcinoma (HNSC) are the most common malignant tumors that arise in the head and neck . The ideCDH3 . In TCGA-HNSC, there are in total of 522 tumors, 44 normal samples, and 2 metastatic samples. After removing two metastatic samples, the remaining 566 samples were used as the input of PACSI.The TCGA-HNSC bulk data and phenotype information were downloaded using the GDCRNATools R package . Read coThe independent HNSC dataset (accession numbers: GSE143083) was downloaded from the GEO database , 72. The2-transformed.The single-cell dataset of 1534 cells from six triple-negative breast cancer tumors was downloaded from the GEO (accession number: GSE118389) , 73. TheThe breast carcinoma bulk fragments per kilobase of transcript per million fragments mapped (FPKM) gene expression data and survival information were downloaded from UCSC Xena . When maThe three external bulk BRCA microarray expression data were downloaded from the GEO \u201376 with The scRNA-seq data of 7186 cells from 31 melanoma tumors was downloaded from GEO (GSE115978) , 81. In Twenty-three melanoma patients with known clinical response information were collected from the GEO (accession number: GSE78220) , 82. ThiThe independent dataset was downloaded from the GEO (accession number: GSE91061) , 84. TheThe single-cell expression data was obtained from the GEO (accession number: GSE157344) , 85. In The COVID-19 bulk gene expression matrix was downloaded from GEO (accession number: GSE196822) , 87. We 2-transformed.The independent dataset was downloaded from the GEO (accession number: GSE206263) , 89 to thttps://www.10xgenomics.com/resources/datasets). Read counts per gene were first converted into transcripts per million (TPM) quantification using the IOBR package. Then, the main preprocessing analysis was performed using the Seurat package. The dataset was normalized by variance stabilizing transformation using the SCTransform function. Spot clusters were generated through dimensionality reduction and clustering.The spatial transcriptomic dataset of breast carcinoma was retrieved from the 10x website downloaded from the Molecular Signatures Database (MSigDB) are used to perform gene set enrichment analyses (GSEA) using the clusterProfiler package [P values for multiple hypothesis testing. Reactome pathway enrichment analyses are performed using the hypergeometric test as implemented in ReactomePA [The differentially expressed genes are computed using the Wilcoxon rank-sum test as applied in the FindMarkers function in Seurat . DEGs ar package . The cluactomePA .2 fold-change > 2 and FDR < 0.01). And then, the ssGSEA method implemented in GSVA [To demonstrate the characteristic of cells identified by PACSI, we compare PACSI-derived signature scores between groups of samples with distinct phenotypes in the independent dataset. We define the genes significantly upregulated in PACSI-identified cells relative to other cells as PACSI-derived gene signatures . The Wilcoxon rank-sum test is used to identify DEGs. For Hallmark pathway enrichment analysis, le tests . If the Additional file 1:\u00a0Supplementary Fig 1. A, The UMAP visualization of simulated single-cell data. B, The distribution of PACSI-identified cells by cell clusters. C, The PR curves of three methods on the simulated dataset. Supplementary Fig 2. Violin plots show the expression level of the CDH3 gene in PACSI-identified cells (n = 46) and all the other cells (n = 4198). Supplementary Fig 3. The expression of vital genes in the melanoma single-cell data. Supplementary Fig 4. Differential gene expression analysis. The x-axis shows the difference in the percentage of cells expressing the gene between PACSI-identified cells associated with COVID-19 and the others, the y-axis represents the log2 fold-change. Supplementary Fig 5. The top five Reactome enrichment of genes that were expressed higher in the PACSI-identified spots, ordered by -log10(FDR). Supplementary Fig 6. The ROC curves of PACSI on simulated data with and without dropout. Supplementary Fig 7. Box plots of HNSC case (A), BRCA case (B), melanoma case (C) and COVID-19 case (D) show the P values between PACSI-identified cells and the disease phenotype of interest or control phenotype. Supplementary Table 1. The run time and memory requirements of PACSI on real cases. Supplementary Table 2. The run time and memory requirements of PACSI for different numbers of cells.Additional file 2. Table with differential expression genes in PACSI-identified cells associated with HNSC versus all other cells. Table with Hallmark pathways enrichment of differential expression genes between PACSI-identified cells associated with HNSC versus all other cells. Table with full list of genes in HNSC signature. Table with the specificity scores of regulons in PACSI-identified cells associated with HNSC.Additional file 3. Table with differential expression genes in PACSI-identified cells associated with poor survival versus all other cells. Table with the Reactome pathways enrichment of upregulated genes in PACSI-identified cells associated with poor survival. Table with full list of genes in prognostic signature. Table with the specificity scores of regulons in PACSI-identified cells associated with poor survival.Additional file 4. Table with differential expression genes in PACSI-identified cells associated with good immunotherapy response versus all other cells. Table with Hallmark pathways enrichment of differential expression genes between PACSI-identified cells associated with good immunotherapy response versus all other cells. Table with full list of genes in PACSI-derived signature associated with good immunotherapy response. Table with the specificity scores of regulons in PACSI-identified cells associated with good immunotherapy response.Additional file 5. Table with differential expression genes in PACSI-identified cells associated with COVID-19 versus all other cells. Table with the Reactome pathways enrichment of upregulated genes in PACSI-identified cells associated with COVID-19. Table with full list of genes in COVID-19 signature. Table with the specificity scores of regulons in PACSI-identified cells associated with COVID-19.Additional file 6. Table with differential expression genes in PACSI-identified spots associated with poor survival versus all other spots. Table with the Reactome pathways enrichment of upregulated genes in PACSI-identified spots associated with poor survival. Table with full list of the upregulated genes in PACSI-identified spots associated with poor survival versus all other spots."} +{"text": "Accurate clinical differentiation of deep partial-thickness (DPT) and full-thickness (FT) wounds is essential in justifying appropriate treatments for heterogeneous burns. Only recently has non-invasive burn depth imaging been ground-truthed with tissue punch biopsies; an endeavor that will no doubt improve AI imaging algorithms in the near future. Prior literature supports unique apoptotic and necrotic properties of DPT and FT wounds, suggesting a use for not only standard stains (H&E), but apoptotic marker staining in assisting clinical diagnosis of burn depth, progression and/or conversion.The aim of this study was to evaluate the presence of apoptotic cells in DPT and FT samples previously diagnosed by a burn biopsy algorithm (BBA-V2) for burn depth and severity by expert review of H&E-stained slides. Eight paired biopsies were collected from DPT and FT wounds in four patients within 72 hours of thermal injury and were immunofluorescently labeled for apoptosis markers by detection of deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) and cleaved caspase-3 (CC-3) staining. Fluorescence intensity in dermal appendages within images was used to quantify signal at 40x magnification for CC-3. % positive TUNEL cells were graded by an investigator blinded to the burn severity. A higher grade indicated higher % positivity. TUNEL grading was evaluated by Chi square test. CC-3 intensity was evaluated by Student\u2019s t-test.Across all four patients, FT burns had higher levels of CC-3 in dermal appendages compared to DPT burns . Within each patient, all FT biopsy sites had significantly higher levels of CC-3 versus DPT biopsy sites (p< 0.05)(Table). DPT burns had a greater proportion of patients with increasing grades of TUNEL positive cells .CC-3 and TUNEL levels within dermal appendages align with burn depth classification by H&E staining, wherein appendages graded as necrotic had higher levels of CC-3 and lower levels of TUNEL. Therefore, CC-3 and TUNEL are potential secondary histological markers for burn depth. Further analysis of isolated, individual dermal appendages is underway to identify what additional information this secondary marker may add to the diagnosis of burn depth.For the first time there is access to a large tissue repository of biopsies from burn wounds. Although staining from these samples has been used to build diagnosis algorithms with success, much more can be learned from the cellular pathophysiology when secondary analyses are performed. These assays may help us understand the processes of burn conversion."} +{"text": "The through-the scope (TTS) helix tack-and-suture device is a newer endoscopic suturing device used for closure of large defects after endoscopic resectionA 74-year-old man with a benign duodenal peptic stricture presented for removal of a previously placed fully covered lumen-apposing metal stent that had been fixated using the TTS tack and suture device in stent-mucosa-mucosa-stent fashion. An upper endoscopy was performed and showed the previously placed stent in the first portion of the duodenum with four helical tacks and suture in place. The suture was cut using endoscopic scissors followed by tack removal using a TTS rotatable endoclip and a rotatable rat tooth forceps . The stVideo\u20061\u2002Approaches to helical tack removal in a patient who underwent stent fixation with the X-tack device.The TTS tack-and-suture device was initially designed as a mucosal-based tissue closure device but more recently has been used for endoscopic device fixationEndoscopy_UCTN_Code_TTT_1AR_2AG"} +{"text": "Immune checkpoint inhibitors (ICIs) are frequently used as treatment for many malignancies. Immune-related adverse events (irAEs) due to use of ICIs are common. Thyroid involvement is the most common endocrine irAE. Here, we present an unusual case of Graves' disease potentially cured due to destructive thyroiditis caused by inflammation due to ICIs. Thyroid irAEs are more common with programmed cell death protein-1 (PD-1) inhibitor or programmed cell death-ligand 1 (PD-L1) inhibitors than cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) inhibitors. Baseline and serial monitoring of thyroid function tests is recommended. Immune checkpoint inhibitors (ICIs) are commonly used for treatment of many cancers . The thyA 66-year-old man with metastatic lung cancer was referred to the endocrine clinic for suppressed thyroid-stimulating hormone (TSH) of <0.01\u2005uIU/mL. He was first found to have low TSH about 3 years earlier. At that time, investigations showed suppressed TSH (0.02\u2005uIU/mL), positive thyroid peroxidase (TPO) antibodies, heterogeneous thyroid with no nodules on sonogram and normal 24-hour uptake (12%) on radioactive scan without hot or cold nodules. Antithyroid drugs (ATD) were not prescribed as he was asymptomatic. The patient was subsequently diagnosed with metastatic poorly differentiated squamous cell carcinoma of lung and received chemotherapy with carboplatin and paclitaxel for 4 months. Because of inadequate response, he was switched to the immune checkpoint inhibitor (ICI) pembrolizumab (a programmed cell death protein-1 [PD-1] inhibitor). Pembrolizumab was stopped after 8 cycles due to immune-mediated hepatitis that was treated with prednisone and mycophenolate mofetil. He was not re-challenged with pembrolizumab again. Thyroid function tests prior to starting pembrolizumab were consistent with primary hyperthyroidism (TSH < 0.004\u2005uIU/mL). He was also started on the beta blocker Atenolol by the oncology team for hypertension and low TSH. During initial evaluation in the endocrinology clinic (after the fourth cycle of pembrolizumab), he was diagnosed with autoimmune thyroid disease, likely Graves' disease based on suppressed TSH for the past 3 years, positive TPO antibodies, and family history of Graves' disease in his mother. Thyroid-stimulating immunoglobulin (TSI) came back positive at 1.84 confirming the suspicion of Graves' disease. Atenolol was continued and thyroid function tests were followed closely. TSH was found be significantly elevated prior to the seventh cycle of pembrolizumab . At thatSince starting levothyroxine, the dose has been adjusted a few times and patient is doing well. His thyroid antibodies/TSI are now negative at 0.10 . TSH receptor antibody and thyroid peroxidase antibodies are also negative. Serial thyroid function tests and dates of starting ICI and levothyroxine are detailed in Immune checkpoint inhibitors (ICIs) have changed the paradigm of cancer therapy . Since tICI therapy is associated with immune-related adverse events (irAEs) with frequent involvement of the endocrine system . Among tIn summary, serial monitoring of thyroid tests and close surveillance is important to distinguish autoimmune thyroid disease induced by ICI therapy and Graves' disease. Baseline thyroid tests are recommended prior to initiation of ICI therapy . ICI-indThis is a unique case of a patient with Graves' disease who went into a prolonged remission or potentially cured because of immune-related adverse events from use of immune checkpoint inhibitor therapy.Immune checkpoint inhibitor (ICI) therapy is commonly and frequently used in many malignanciesEndocrine immune-related adverse events (irAEs) are common and the thyroid is the most common organ involvedBaseline and serial monitoring of thyroid function tests is very important"} +{"text": "Electronic nicotine delivery systems (ENDS) or electronic cigarettes (e-cigarettes) have propylene glycol (PG) and vegetable glycerin (VG) as humectants, flavoring chemicals, and nicotine. Nicotine naturally occurs in two isomers R- and S-nicotine, with both tobacco-derived nicotine (TDN) composed of S-nicotine and synthetic nicotine (TFN) composed of a racemic mixture of R- and S-nicotine. Currently there is limited knowledge of the potential differences in the toxicity of TFN vs TDN. We hypothesized that exposure of TFN salts to C57BL/6J mice will result in a differential response in inflammation and lung protease and antiprotease imbalance compared to TDN salts exposed mice. We studied the toxicological impact of these isomers by exposing mice to air, PG/VG, PG/VG with TFN salts, or PG/VG with TDN salts by nose-only exposure and measured the cytokine levels in BALF and lung homogenate along with MMP protein abundance in the lungs of exposed mice. Exposure to the humectants, PG/VG, used in e-cigarettes alone was able to increase cytokine levels- IL-6, KC, and MCP-1 in BALF and KC levels in lung homogenate. Further, it showed differential responses on exposure to PG/VG with TDN salts and PG/VG with TFN salts since PG/VG with TDN salts did not alter the cytokine levels in lung homogenate while PG/VG with TFN salts resulted in an increase in KC levels. PG/VG with TDN salts increased the levels of MMP9 protein abundance in female exposed mice, while PG/VG with TFN salts did not alter MMP9 levels in female mice. The metabolism of nicotine or the clearance of cotinine from TFN may differ from the metabolism of nicotine or the clearance of cotinine from TDN. Thus exposure of humectants alone to induce an inflammatory response while PG/VG with TFN salts and PG/VG with TDN salts may differentially alter inflammatory responses and lung proteases in acute exposures. These data suggest the harmful effects of synthetic/natural nicotine and PG/VG and potential toxicological risk for users."} +{"text": "Correction to: Annals of Hematology10.1007/s00277-023-05196-4, the authors have learned that the National Comprehensive Cancer Network (NCCN) requires some editorial changes relating to how their guidelines are referenced within the paper.Following the online publication of this paperThe original article has been corrected."} +{"text": "There are serious adverse effects on the physical and mental wellbeing of patients with alcohol use disorders.It is important to screen and provide brief intervention for these group of patients during their inpatient admission.Prompt identification and treatment of patients with alcohol use disorders are contingent on the attitudes of healthcare workers towards them.Non-psychiatric doctors and nurses might respond inadequately due to negative attitudes and beliefs.We examined the attitudes of non-psychiatric workers in the medical and surgical wards.The Alcohol & Alcohol-Problems Perceptions Questionnaire (AAPPQ) was administered to 128 doctors and 785 nurses from the medical and surgical disciplines in a tertiary hospital.75.5% of doctors and 51.9% of nurses endorsed the domain of role legitimacy in the AAPPQ.However both groups reported low-levels of role-adequacy (combined: 41.2%), role-support (combined: 36.9%), motivation (combined: 36.5%), task-specific self-esteem (combined: 25.1) and work satisfaction (combined: 20.5%) in the AAPPQ.While non-psychiatric healthcare workers acknowledged the importance to initiating intervention for patients with alcohol-use disorder in daily work, there were low levels of therapeutic commitments towards patients with problematic alcohol-use.It is vital to introduce in-house programmes to educate, empower and emphasise the importance of therapeutic contact with patients for alcohol intervention.None Declared"} +{"text": "Sap et al. review the role of the ubiquitin-proteasome system (UPS) in Huntington\u2019s disease, suggesting that defects in Huntingtin (HTT)-UPS targeting might be alleviated through understanding differential ubiquitination of \u201cnormal\u201d versus polyQ-expanded mutant HTT. Zhu et al. review small ubiquitin-like modifiers (SUMO) signalling in cancer stem cells. Small molecules that alter flux through SUMOylation cascades and influence cancer cell metastatic properties point towards potential therapeutic targets. These reviews point to the need for specific inhibitors of ubiquitinating and deubiquitinating enzymes (DUBs) as well as new protein-targeting chimeras (PROTACs) to direct the degradation of misregulated or pathogenic proteins.This collection of reviews highlights the central role that ubiquitin, and ubiquitin-like proteins, play in biology and how hypothesis driven use of new and existing biochemical tools continues to expand our understanding of cellular physiology. We begin with two reviews that focus on proteostasis in specific disease states. Kennedy et al. discuss recent developments in fragment-based drug discovery for the Ubiquitin system in their mini-review. Typically, covalent fragments target the catalytic cysteines of Ubiquitin E2 conjugating enzymes (E2s), cysteine dependent E3 ubiquitin ligases (cys-E3s) and DUBs. Kennedy and colleagues suggest that fragments which target non-cysteine nucleophiles may be the basis for the next-generation of tool compounds.There is a considerable gap between clinically useful drugs and tool-compounds for the ubiquitin system. Remarkable progress has been made in both areas. De Cesare provides a timely personal perspective on dissecting the Ubiquitin system with matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). She and others have put this technique to use in identifying DUBs and E2s with non-lysine activity (in vitro experiments are likely to reveal more surprising substrates. We anticipate that new biochemical tools will be required to validate these observations in vivo.activity . Key queKelsall provides an in-depth review of ubiquitination beyond lysine. Transfer of ubiquitin to serine, threonine, and non-proteinaceous substrates has re-entered the spotlight in recent years. Bacterial effector proteins in the SidE family bypass the ubiquitination cascade completely to link ubiquitin to serine via a phosphoribosyl linkage (in vitro (in vitro (Continuing this theme, linkage . In euka linkage . A caveain vitro . The prein vitro . Given tin vitro . Ubiquit"} +{"text": "While E (HER-2) . TNBC tr (HER-2) . Althoug (HER-2) . Natural (HER-2) . The preWei et al. studied the effect of Cordycepin (an active phyto-constituent present in Cordyceps mushroom) on metastasis modulation in mouse TNBC model. The study highlighted that Cordycepin inhibits cellular growth and decreases migration and invasion potential in TNBC cells (BT549 and 4T1 cells) at micromolar concentrations. Mechanistically the study showed that Cordycepin treatment of TNBC cells reversed the expression profile of epithelial to mesenchymal transition markers E-cadherin (increased) and N-cadherin (decreased) in concentration dependent manner. Further, the study showed that Cordycepin treatment reduces the expression of EMT-related transcription factors in TNBC cells significantly compared to non-treated cells. Furthermore, the authors utilize the 4T1 mouse allogenic tumor model to study the metastasis inhibition potential of Cordycepin in vivo. The immune system plays an important role in cancer metastasis and thus selection of the animal experimental model with the intact immune system provides decent translational pre-clinical data on the anti-metastatic potential of Cordycepin. Overall, the study highlights Cordycepin as a natural lead compound managing metastasis and invasion in mouse TNBC model.In the present research article Wang et al. studied the effect of Ailanthone on bone metastasis in TNBC and attempted to search for the underlying mechanism(s). Interaction between breast cancer cells (by secreting osteolytic factors) and bone microenvironment is largely involved in breast cancer metastasis. Interestingly, the study focused on the effect of Ailanthone on osteoclast differentiation which was induced by TNBC cells mediated cytokine secretion. The study reported that Ailanthone treatment can potentially inhibit osteoclasts production by inhibiting the osteolytic factors secretion in RANKL-dependent manner, thereby inhibiting the downstream molecular signaling pathways involved in TNBC cell metastasis. Overall, these findings reveal a natural compound mediated novel therapeutic strategy for managing breast cancer metastases.In the next research article Zhou et al. studied the effect of Polyphyllin III or dioscin (Paris polyphylla rhizome saponin) in vitro TNBC model. The study also explored the underlying anticancer mechanism(s) of this natural compound. Polyphyllin III has the potential to induce ferroptosis in TNBC cells at micromolar concentration. Studies were performed using the transmission electron microscopy-based morphological assessment of the mitochondrial membrane/cristae density ratio in TNBC cells. Further examination of hallmarks of ferroptosis, including accumulation of cellular lipid reactive oxygen species and decrease in GSH levels in Polyphyllin III, treated TNBC cells, substantiates these findings. The study proposed that increasing the expression of Acyl-CoA synthetase, a long chain family member 4 (ACSL4), by Polyphyllin III treatment might be a possible ferroptosis inducing mechanism in TNBC cells. In an important observation, the study pointed out that KLF4-mediated overexpression of xCT in TNBC cells acts as a protective response during ferroptosis in TNBC cells in response to therapeutic drugs and may result in enhancing drug resistance. The study proposed that this protective response could be diminished by using xCT inhibitors combined with Polyphyllin III to counter balance the protective response in TNBC cells during ferroptosis. The study also showed that the combination treatment significantly increased Polyphyllin III treatment susceptibility in TNBC cells.In the following article, Zhang et al. studied the effect of Ursolic acid, a naturally occurring triterpenoid acid, in in vitro and in vivo TNBC models. The author strikingly utilized a combination of computer-based and pre-clinical experiments to decipher the anti-TNBC effect of Ursolic acid and its underlying mechanism(s). The compound has the potential to reverse the drug-resistance in cancer cells. The study further proved that Ursolic acid can significantly inhibit the proliferation of TNBC cells. The compound selectively kills TNBC cells, compared to normal cells. Furthermore, Ursolic acid has the potential to arrest the cells in the G2/M phase, reduce migration/invasion (by decreasing MMP2 and MMP9 levels), and induces apoptosis . Pharmacology-based network analysis identified the enrichment of PLK1 and CCNB 1 in the p53 signaling pathway in TNBC cells. Treatment of TNBC-xenograft mice with Ursolic acid resulted in a protective effect and reduced tumor growth through the PLK1-CCNB1-p53 axis.The last research article by In this Research Topic, some natural compounds are highlighted with the mechanisms of action, demonstrating their effectiveness against triple-negative breast cancer. Future research focusing on more detailed studies can open new horizons in breast cancer prevention and/or treatment, which could enhance the overall survival and quality-of-life of breast cancer patients."} +{"text": "Nutraceuticals are products based on the nutrient content of foods derived from dietary or medicinal plants . BecauseLuo et al. used a middle cerebral artery occlusion rat model and comparative transcriptomics to determine the molecular targets and mechanisms underlying the beneficial effects of laminarin in ischemic stroke . Their results demonstrated the involvement of laminarin targets in blood circulation, oxygen supply, and anti-inflammatory responses in the normal brain. More importantly, laminarin treatment attenuated the brain damage and neuro-deficits caused by an ischemic stroke. Using bioinformatics analysis, they found that the beneficial effects of laminarin occur through the regulation of blood vessel development and brain cell death, suggesting that laminarin could be a novel nutraceutical for treating ischemic stroke.Vaughan-Shaw et al. performed a feasibility study to evaluate whether high-dose cholecalciferol (vitamin D3) had a beneficial effect on the survival of patients with CRC . We recruited 122 colorectal cancer (CRC) patients, 41 of whom were administered high-dose vitamin D3 daily. Serum 25-hydroxyvitamin (25OHD) levels were measured using liquid chromatography-tandem mass spectrometry and compared with untreated CRC controls. They found that high-dose vitamin D supplementation was associated with higher perioperative 25OHD levels, lower rates of vitamin D insufficiency, and reduced early postoperative C-reactive protein levels. These findings suggested that vitamin D has beneficial effects on CRC survival outcomes.Temraz et al. investigated the prognostic value of vitamin C in patients with mCRC, recruiting adults with metastatic CRC (mCRC) (n = 46) and cancer-free controls (n = 45) . They found no significant difference in vitamin C intake between the two groups; however, patients have lower plasma vitamin C levels than healthy controls.Another prospective cohort study conducted by Sannappa Gowda et al. used an in vivo mouse mammary carcinoma model and an in vitro human breast cancer cell line model to study the hepatoprotective role of quercetin in breast cancer via the vitamin D receptor (VDR) . Their results showed that quercetin treatment significantly decreased tumor volume, tumor angiogenesis, hepatic inflammation, and fibrosis. Furthermore, the results of the docking analysis confirmed the VDR-quercetin interaction, suggesting the involvement of VDR in anti-breast cancer activity.In conclusion, this issue suggests using nutraceuticals such as vitamin D3 and laminarin to treat cancers and neurodegenerative diseases. Several studies have delineated the molecular mechanisms underlying the beneficial effects of these nutraceuticals. However, further preclinical studies are required to confirm these findings before the clinical use of these nutraceuticals.The author confirms being the sole contributor of this work and has approved it for publication."} +{"text": "Correction: Pilot Feasibility Stud 8, 92 (2022)https://doi.org/10.1186/s40814-022-01054-8Following publication of the original article , an erroThe sentence currently reads:We designed an outline of the web-based self-learning program, which included six modules for acquiring knowledge and skills related to local healthcare planning based on adult learning theory [31], a review of the relevant Japanese literature [14],The sentence should read:We designed an outline of the web-based self-learning program, which included six modules for acquiring knowledge and skills related to local healthcare planning based on adult learning theory [31], a review of the relevant Japanese literature [13],The original article has been"} +{"text": "Studies have acknowledged the prevalence of amputation in patients with electrical burns; however, the exact probability of amputation as a result of electrical injuries and the effect of amputation on the long-term health remain unclear. The purpose of this study was to analyze electrical burn survivors with amputation using a large multi-center database and assess their corresponding long-term physical and mental health, compared with a non-electrical burn population with amputation.Retrospective reviews of burn patients from 1993 to 2021 were performed using the Burn Model System National Database, that yielded 408 patients with electrical etiology and 6341 with non-electrical etiology. The variables for analysis included the Veterans RAND 12-Item Health Survey and the Patient-Reported Outcomes Measurement Information System 29, collected at discharge, six months, 12 months, 24 months, and five years post-burn.Electrical burn patients showed a higher amputation rate (30.3%) than non-electrical burn patients (6.6%) (p < 0.0001). Electrical burn patients with amputation showed significantly lower physical component scores (PCS=34.1) and physical function scores (PFS=37.1) at discharge than electrical burn patients without amputation (p < 0.05). No significant differences were found in mental component scores, anxiety, depression, sleep, or fatigue between patients regardless of burn type or amputation. Electrical burn patients experienced similar post-injury trends compared with non-electrical burn patients. Non-electrical burn survivors with amputation had the worst outcomes of all patient groups. The Hispanic population comprised the largest percentage of the electrical burn group (80%).This study shows that patients with amputation need extra attention to their physical impairment at discharge. Early rehabilitation in electrical burn patients with amputation should be emphasized. Non-electrical burn survivors with amputation need the most support from both physical and psychological perspectives. This study like many others supports that regardless of burn etiology, all burn survivors require psychological support at discharge. The study also accentuates the need for better electrical injury prevention and rehabilitation program for those who speak Spanish.More intensive and comprehensive interventions for electrical burn survivors with amputation in the earlier stages of rehabilitation can help ensure better long-term physical, psychological, and social outcomes. In contrast, rehabilitation plans for patients with non-electrical burns with amputation should concentrate more on the long-term management for up to a minimum of two years post injury, as these patients face significantly longer and severe difficulties than electrical burns patients with and without amputation."} +{"text": "Correction: Insights into Imaging 14, 176 (2023)https://doi.org/10.1186/s13244-023-01512-8Figure 1 of the originally published article [\"Poster used as part of the SOLACE project to promote women's participation in lung cancer screening.The SOLACE project is co-funded under the EU4Health Programme 2021\u20132027 under grant agreement no. 101101187. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or HaDEA. Neither the European Union nor the granting authority can be held responsible for them.\""} +{"text": "In the Post Antibiotic era with the ongoing Silent pandemic of AMR, early detection of the resistant gene exhibited by the offending pathogen causing the ailment is of paramount importance. Early diagnosis and formulating the choice of antibiotics in treatment of Multi drug and Pan drug resistant bacteria helps in reducing the hospital stay and the overall outcome of the patients.Carbapenems serve as the first line drugs for the treatment of drug resistant Gram-negative bacilli (GNB) infections.However, carbapenem resistance (CR) among GNB is quite common in India.CR can be due to carbapenemase production.The most common carbapenemases areblaKPC, blaNDM, blaVIM, blaIMP-1, and blaOXA-4.The present study aims to find the prevalence of Carbapenem resistance thereby aiding in initiating the empirical therapy. By studying the resistance patterns we would be able to know whether the isolate expresses single carbapenemase or multiple carbapenemases which has direct influence in the choice of antimicrobials and patient outcomes.Enterobacteriales, Pseudomonas aeruginosa, Acinetobater baumanii and Stenotrophomonas maltophilia isolated during the period of Jan2022- April 2023 (15 months) were included in the study. Carbapenem resistance was confirmed by Vitek 2 automated AST system.These isolates were further subjected to X-pert Carba -R Real Time Multiplex PCR Assay to detect the type of carbapenamses expressedA total of One hundred and seventy seven clinical isolates which were Carbapenem non-susceptible NDM,bla fourteen isolates(20%) produced OXA-4bla.One isolate produced blaIMP-1.Twenty four isolates produced both NDMbla and OXA-4.blaOut of one hundred and seventy seven clinical isolates, one hundred and eight isolates did not produce carbapenemases by X-pert Carba -R Real Time Multiplex PCR Assay. A total of sixty nine isolates(38%) were positve for carbapenemases. Among the sixty nine isolates, thirty isolates(43%) produced In Madras Medical Mission , New Delhi Metallo-Betalactamase -1 is the most common carbapenemase produced by the clinical isolates from Cardio-Vascular patients.Second most common carbapenemase is OXA-48.All Authors: No reported disclosures"} +{"text": "Helicobacter Pylori (BOSTON-HP) study included 1002 patients with confirmed Helicobacter pylori (HP) via gastric histopathology from 2016-2022 to evaluate the effects of a Multidisciplinary Division Wide Program. Our previous data showed that demographic factors, such as race/ethnicity and preferred language, are associated with treatment, test-of-cure, and eradication outcomes. We hypothesize that given an unlikely even geographic distribution of demographic factors, HP outcomes may cluster geographically.The BIDMC Optimization & Standardization for Treatment Outcomes in New England for The BOSTON-HP cohort patient addresses were transformed to georeferenced coordinates which were mapped using QGIS (3.30 's-Hertogenbosch) onto OpenStreetMap. We calculated the maximum Euclidean distance matrix to assign heatmap weights for each outcome, and calculated global spatial autocorrelation to evaluate the extent of spatial clustering.Eight hundred and sixty-eight patients (86.6%) received treatment with confirmed eradication in 416 (47.9%) of them. A statistically significant positive spatial autocorrelation of clusters was observed for the likelihood of treatment. Layering transportation and healthcare units revealed key clustering patterns . Clusters in the vicinity of Longwood Medical Area (LMA), and South Cove Medical Center (SCMC) were more likely to receive treatment, while those in the Brighton collegiate area (BCA) and along the Red Line Axis in Roxbury-Dorchester (RLRD) were less likely to receive treatment. Test-of-cure and eradication success were not statistically significant for clustering , respectively.A moderate and significant spatial correlation existed between the likelihood of HP treatment and the geographic location of the patient\u2019s residence. Identification of groups for targeted quality improvement interventions (RLRD) and models of success within the system (SCMC) can help improve treatment outcomes and reduce geographic disparities.Javier Villafuerte-G\u00e1lvez, MD, Milky Way Biosciences: Partial Research Support."} +{"text": "In addition to this, the butyrylation reaction (butyrate (Bu) esterification\u2014short-chain fatty acid) using native or oxidized starch was analyzed under reactive extrusion (REx) conditions with and without the addition of a green food-grade organocatalyst (l(+)-tartaric acid) with the purpose of developing potentially health-promoting spaghetti-type pasta systems in terms of increasing its resistant starch (RS) values. These would be due to obtaining organocatalytic butyrylated starch or not, or the manufacture of a doubly modified starch or not. To this end, six pasta systems were developed and characterized by solid-state 13C cross-polarization magic angle spinning nuclear magnetic resonance (CP MAS NMR) spectroscopy, degree of substitution (DS), attenuated total reflectance Fourier transform infrared (ATR/FTIR) spectroscopy, X-ray diffraction (XRD), thermogravimetric analysis (TGA), pancreatic digestion, free Bu content analysis and in vitro starch digestibility. The results obtained here suggest that starch oxidation hydrolytically degrades starch chains, making them more susceptible to enzymatic degradation by \u03b1-amylase. However, the oxidized starch-based pasta systems, once esterified by Bu mainly on the amylose molecules (doubly modified pasta systems) increased their RS values, and this was more pronounced with the addition of the organocatalyst . Interestingly, despite the checked chemical changes that took place on the molecular structure of starch upon butyrylation or oxidation reactions in corn starch-based spaghetti-type pasta systems, and their incidence on starch digestibility, the orthorhombic crystalline structure (A-type starch) of starch remained unchanged.Extruded spaghetti-type pasta systems were obtained separately either from native or oxidized starch prepared Spaghetti-type pasta (noodle) is a widely consumed food in the world, which is manufactured industrially by extrusion from wheat semolina (starchy food ingredient containing gluten)/water mixtures . HoweverZea mays) starch was selected as gluten-free feedstock .A Bruker AV WB 400 spectrometer (HCl = volume (mL) of HCl needed for sample titration). The percent esterified Bu (butyryl group\u2014%Bu) was determined as follows .,49.\u03b8 = 1.7829 \u00c5) . The effsystems) . These rsystems) . Thus, to et al. for low-= 5.73%) . Therefoc values . In cont = 1.34) . It coula system .vs. NSt pasta system). Hence, the addition of the used organocatalyst (TAc) could preferentially establish H-bonding interactions with the amylose molecules before giving rise to the organocatalytic butyrylation reaction, thus increasing thermal stability in the NSt + Bu + TAc pasta system compared to the NSt + Bu pasta system. This is in accordance with the discussion previously made from the correlative analysis between the DS values and the XRD patterns for referred pasta systems. Nonetheless, the butyrylation reaction in the absence of the organocatalyst showed an opposite trend for the OSt-based pasta system (NSt + Bu pasta system) compared to its analogous control pasta system (OSt pasta system). This was even more marked after adding the organocatalyst (OSt + Bu + TAc pasta system vs. OSt pasta system). In this context, a negative relationship between thermal stability and DS values was in general viewed for the pasta systems analyzed. A similar trend was informed by Li et al. [The TGA curves evidenced the following increasing order of thermal stability for the spaghetti-type pasta systems: NSt < OSt + Bu + TAc < NSt + Bu < OSt + Bu \u2248 NSt + Bu + TAc < OSt . Starch i et al. for butyi et al. . It can p \u2265 0.05) were found in the free Bu content values upon pancreatic digestion of the butyrylated starch-based pasta systems (vs. OSt + Bu + TAc pasta system). Therefore, adding the organocatalyst had a positive effect on promoting the butyrylation reaction for the OSt-based pasta system, but not for the NSt-based pasta system.No markedly significant changes (systems) . This fisystems) . In partsystems) . This disystems) . With reWith regard to RS content, the OSt pasta system had lower RS content values compared to the NSt pasta system . This faTaking into consideration the classification given by Go\u00f1i et al. , the potRegarding the variations in the RDS and SDS content values for the pasta systems studied here, a clear trend was not observed for these digestibility parameters, as to establish an adequate explanation for this. This is probably related to the poor understanding of the relationship between short-range ordered structures and starch digestibility.l(+)-tartaric acid\u2014TAc). This was evidenced by solid-state 13C CP MAS NMR spectroscopy, (2) 13C NMR spectra elucidated that unesterified Bu and organocatalyst unavoidably persisted embedded in the REx-processed pasta systems, thereby limiting the proper determination of DS values. Notwithstanding, the estimated quantification of DS values obtained by titration, in general, agrees well with all the findings found in this research and (3) the orthorhombic crystalline structure (A-type starch) in corn starch-based spaghetti-type pasta systems remained unchanged regardless of the butyrylation or oxidation reaction under the conditions studied.The following points can be established as general conclusions from this research work: (1) all the butyrate (Bu)-containing corn starch-based spaghetti-type pasta systems were butyrylated, both in the absence and in the presence of the organocatalyst used (The butyrylation reaction apparently occurred on the amorphous regions of the starch (amylose), regardless of the starch used: native or oxidized starch, thus resulting in more crystalline pasta systems, in which their thermal resistance was reduced, due to the breaking of the starch\u2013starch H-bonding interactions provoked by the esterification reaction of hydrophobic Bu groups on the starch structure.The oxidation reaction led to the production of more amorphous and thermal degradation-resistant spaghetti-type pasta systems compared to native starch (NSt)-based pasta systems. Regardless, the enzymatic resistance by \u03b1-amylase was lower in the oxidized starch (OSt)-based pasta system compared to the NSt-based pasta system, thus reducing RS values. Noteworthily, DS values by butyrylation were inferior in the OSt-based pasta system compared to the NSt-based pasta system in the absence of the organocatalyst. This suggests that the sites with the potential to be esterified (available -OH groups on the starch structure) were previously occupied (oxidized) by carbonyl (C=O) and carboxyl (O\u2212C=O) groups.via wet chemistry followed by organocatalytic butyrylation) and reduction of the free butyrate content values. Therefore, potentially health-promoting spaghetti-type pastas were prepared from organocatalytically doubly modified (oxidized-butyrylated) starch. Nevertheless, an opposite trend was observed once the organocatalyst was added to the NSt-based pasta systems. These findings suggest that organocatalyst\u2013amylose hydrogen bonding interactions could limit the butyrylation reaction.The addition of the organocatalyst (TAc) had a positive result on the increase of the DS values by butyrylation in the OSt-based pasta system, which caused increases in RS values in this pasta system made from doubly modified (oxidized-butyrylated) starch (starch oxidation From the analysis of the results obtained, and based on the three main objectives previously established in the introduction, the following three specific conclusions of this work emerge:"} +{"text": "Mental health problems are common in children and young people (CYP) in England, yet evidence suggests high levels of unmet need in this group. Understanding of the determinants of mental health-related service contact is needed to identify gaps in service provision and areas for targeted intervention to improve access.To determine the relationship between CYP characteristics and mental health-related support and service contact in England.A secondary analysis of the 2017 NHS Digital Mental Health of Children and Young People (MHCYP-2017) cross-sectional survey dataset was performed. MHCYP-2017 was a national survey investigating the mental health of CYP using a stratified multistage random probability sampling approach, providing the official national statistics for England. Multi-informant data were collected through a combination of questionnaires and interviews. Expert clinical rating took place to formally identify the presence of mental disorders, according to established diagnostic criteria. This secondary analysis describes mental health-related support and service contact amongst 6681 participants aged 5-16 recruited to the MHCYP-2017 study. A range of socio-demographic and clinical characteristics were analysed as explanatory variables and their relationships with different types of support/service contact were examined through multivariable multinomial logistic regression. Analyses were stratified by age group: 5-10- and 11-16-year-olds.Overall, around 25% of parents reported CYP mental health-related contact with one or more types of support/service in the past 12 months due to concerns regarding CYP \u201cemotions, behaviour, concentration or difficulties in getting along with people\u201d. Age stratified multivariable analyses revealed several statistically significant associations between participant socio-demographic/clinical characteristics and mental health-related support and service contact, independent of CYP mental health status and parental perception of difficulties. These associations were not necessarily consistent across mental health support categories, suggesting that several of the measured characteristics have differential relationships with different types of support and service contact. Whilst there were some differences between the 5-10 and 11-16 age groups, similar associations were seen for many of the explanatory variables. Socioeconomically disadvantaged and black and minority ethnic CYP were less likely to have had professional contact for mental health problems.There may be higher levels of unmet need in socioeconomically disadvantaged and black and minority ethnic CYP, warranting further investigation and efforts to address inequalities. Further longitudinal studies are needed to elucidate causal associations and mechanisms underlying these observations.None Declared"} +{"text": "Staphylococcus aureus (MRSA) bloodstream infection (BSI). Limited data and few recommendations exist regarding combination treatment for MRSA BSI outside of prosthetic valve endocarditis (PVE). The alternative treatment option of combining daptomycin with ceftaroline for its synergistic mechanism possibly through \u03b2-lactam-induced reduction in cell wall cross-linking has been pursued. This regimen is less feasible for home administration and more information on when to de-escalate to monotherapy after blood culture clearance is needed. This study evaluated clinical outcomes for patients with MRSA BSI who received combination therapy with daptomycin and ceftaroline.IDSA MRSA Treatment Guidelines recommend vancomycin or daptomycin as first-line therapy for methicillin-resistant This was a single-center, retrospective study evaluating hospitalized patients mostly with persistent MRSA BSI from 1/2019 to 7/2022 who received a combination of daptomycin and ceftaroline. Patients with a diagnosis of pneumonia, PVE or polymicrobial bacteremia were excluded. The primary endpoint assessed in-hospital mortality for patients on combination therapy. Secondary endpoints included readmission within 90 days, reoccurrence of bacteremia within 30 days, length of stay and adverse drug reactions during treatment.Of 73 patients screened, 14 patients were included with the primary reason for exclusion being diagnosis of PVE. Notably, half of the patients had a history of IVDU, with the majority of patients (71%) being started on initial therapy with vancomycin. Blood culture clearance occurred within 3 days of starting the combination for 11 of 14 patients. Only 4/14 patients received combination therapy for > 14 days, in which one patient died on a total duration of 26 days.This study demonstrated a variable duration of combination therapy for MRSA BSI in low-risk patients. The in-hospital mortality rate observed was low. All had microbiological cure. However, further exploration is needed to determine the optimal time for de-escalation after blood culture clearance. Future studies could contribute to creating stewardship efforts to de-escalate patients for MRSA BSI.All Authors: No reported disclosures"} +{"text": "Escherichia coli induce specific stress responses through the activation of specialized transcription factors. Each transcription factor and downstream regulon (e.g. SoxR) are linked to a unique stress (e.g. superoxide stress). Cells starved of phosphate induce several specific stress regulons during the transition to stationary phase when the growth rate is steadily declining. Whereas the regulatory cascades leading to the expression of specific stress regulons are well known in rapidly growing cells stressed by toxic products, they are poorly understood in cells starved of phosphate. The intent of this review is to both describe the unique mechanisms of activation of specialized transcription factors and discuss signalling cascades leading to the induction of specific stress regulons in phosphate-starved cells. Finally, I discuss unique defence mechanisms that could be induced in cells starved of ammonium and glucose.Toxic agents added into the medium of rapidly growing In nature, environmental conditions can change frequently as a result of fluctuations in growth parameters \u2212 e.g. carbon source , phosphaChanges in environmental conditions can directly (e.g. addition of toxic products) and indi70 holoenzyme to promoters of genes required for stress survival. Each transcription factor and downstream regulon are specific to a unique type of stress cluster in SoxR . TherefopoxB in a strictly RpoS-dependent manner cluster, thereby entering into a new redox cycle [\u2022+ develops to miscoding lesion (8-oxoGua) and noncoding lesion \u2212 fragmentation of guanine into FapyGua blocks DNA replication [The hydroxyl radical readily abstracts one electron (hydrogen atom) from proteins and nucleic acids (HO\u2022 + RCH \u2192 HOolecules . The priH + G\u2022+) . ActivatH + G\u2022+) of one e SoxRox) Fig. 2)\u2022\u2022H + RC\u2022ox cycle . If not lication .E. coli evolved two complementary envelope stress responses, CpxR and RpoE, whose aim is primarily to prevent the integration of misfolded proteins into inner and outer membranes [embranes . The Cpxembranes .Pi) induces primarily genes required for the elimination of abnormal proteins in the periplasm. CpxRPi can also repress the transcription of genes implicated in ETC biogenesis, namely nuo and cyo encoding NADH:quinone reductase I and cytochrome-quinol oxidase bo3, respectively [nuo and cyo by CpxR decreases the excretion of protons (from a maximum of 8 H+/2 e- with the Nuo-Q-Cyo combination down to 2 H+/2 e- with the Ndh-Q-Cyd combination), which decreases the internal pH (pHi). The repression of nuo and cyo can explain that induction of the CpxR envelope stress response by the antibiotic gentamicin decreases the pHi [In growing cells, the CpxA/CpxR two-component system (TCS) is activated under environmental conditions that damage envelope proteins . ATP-depectively . The comectively . ETCs ar the pHi . Globall the pHi . Inducti the pHi .In Pi-starved cells, induction of the CpxR regulon is independent of the CpxA kinase activity but is dependent upon PhoB activity . There iCarbon source responsive), which somehow senses the accumulation of PYR and responds with induction of the ackA-pta operon [During rapid growth on glucose, PYR and AcCoA flux is mainly directed towards the fermentative phosphate acetyltransferase-acetate kinase (Pta-AckA) pathway, so-called overflow metabolism, rather than toward the aerobic TCA-ETC pathway . Pta cona operon Fig. 1)Carbon soPi) [AcP transiently accumulated in cells grown in rich medium supplemented with glucose can therefore phosphorylate CpxR (CpxRPi) . The samPi) . The PtaPi) .phosphate specific transporter PstSCAB (PST) activate the PhoR/PhoB TCS [ackA-pta operon and the production of AcP at three different levels . RpoE (\u03c3E) activity depends on its release from the anti-sigma factor RseA. The protease DegS, activated by the presence of abnormal proteins in the periplasm, degrades RseA, which frees RpoE. The RpoE regulon encodes proteins ensuring the integrity of the outer membrane through the synthesis of lipopolysaccharide and proteolysis of misfolded outer-membrane porins [rpoH, which encodes the heat-shock protein regulator RpoH (\u03c332). Heat-shock proteins include ATP-dependent molecular chaperones and proteases (e.g. the ClpXP degradation complex and Lon) that refold and eventually degrade proteins damaged by high temperature, extreme pH and oxidative stress [In growing cells, the RpoE envelope stress response is primarily induced by high temperature . The Rpoe porins . Moreovee stress .E holoenzyme is independent of RseA and PhoB [Carbon storage regulation) system. High levels of ppGpp increase the RNAP\u03c370-dependent transcription of csrB and csrC; the CsrB and CsrC small RNAs bind to and inactivate the activity of CrsA, which inhibits the translation of the rpoE mRNA [E holoenzyme [csrB and csrC genes [Pi and ppGpp might be required to increase RpoE levels and RNAP\u03c3E activity independently of RseA activity in Pi-starved cells and later on of the PoxB pathway (when cells enter into stationary phase). Each pathway contributes equally to Ace final concentration in the presence of excess glucose [phoBR mutants \u2212 as suggested by inhibition of the CpxR activity \u2212 induction of poxB by the RNAP\u03c3S holoenzyme could occur prematurely as a result of a rapid drop in growth rate and entry into stationary phase. PoxB-dependent production of Ace could induce the BarA/UvrY TCS, which might account for induction of the RpoE regulon in phoBR mutants starved of Pi [ytfK should play a minor role. Loss of YtfK-dependent activation of SpoT could be compensated by activation of RelA (and SpoT) in response to a rapid drop in growth rate [How is the RpoE regulon induced in glucose . If Pta ed of Pi . If highwth rate .lexA, recA, dinB, polB and umuDC) results from the (auto)cleavage of the LexA repressor when free LexA molecules interact with short RecA-ATP filaments built on ssDNA organized by the ssDNA-binding protein (SSB) [In rapidly growing cells, the LexA response is induced when DNA bulky lesions \u2212 produced for instance by the antibiotic mitomycin C \u2212 stall the replicative DNA polymerase Pol III. Reinitiating replication beyond lesions generates single-stranded DNA (ssDNA) gaps . Inductiin (SSB) . The Lexin (SSB) . Gap filin (SSB) .The LexA regulon can be induced when cells approach the stationary phase in the absence of added genotoxic products in the medium. This occurs when cells are grown in rich LB medium \u2212 pH sharply increases at the approach of the stationary phase as a result of amino-acid degradation \u2212 and when cells are starved of Pi but not when they are starved of ammonium or glucose . ContrarTherefore, the LexA regulon can be markedly induced in Pi-starved cells in the absence of the ssDNA signalling system through an increase in the pHi, which decreases the binding affinity of LexA to LexA box . In cont-) and protons (H+) inside the cell [+/H+ ion balance.Ace excreted into the medium decreases the pH of the medium during prolonged incubation of Pi-starved cells. At moderate acidic pH, acetic acid present in the medium diffuses across the membrane and dissociates into acetate (AcOthe cell . However+:H+ symport), is the most abundant intracellular cation. Potassium helps to control key physiological parameters such as osmotic pressure, ionic strength and pHi. When the concentration of potassium falls into the micromolar range in the medium, activation of the KdpD/KdpE TCS induces the kdpFABC operon, which encodes the Kdp high-affinity ATP-dependent K+ pump. Upon osmotic upshift, potassium uptake through the Trk and Kdp systems increases dramatically, which triggers the extrusion of protons and a transient alkalinization of the cytoplasm [Potassium, which is normally transported by the Trk system could account for the non-canonical induction of the LexA regulon in Pi-starved cells . The components of the PTSNtr system are mainly in dephosphorylated form in cells incubated in a minimal medium containing excess ammonium [x interacts with and favours the active phosphorylated forms of both PhoRPi and KdpDPi [Activation of the and KdpE , and for complex Fig. 1)kdp operoammonium . In dephd KdpDPi .+ ions specifically bind to and increase the activity of NADH:quinone reductase I (Nuo) [+ excretion by ETC [kdp operon, K+ accumulation and stimulation of Nuo activity could account for alkalinization of the cytoplasm in Pi-starved cells (K I (Nuo) , which cn by ETC . Therefoed cells .70 to promoters of osmo-regulated genes and eventually with \u03c3S [70 to promoters that bind SoxRox and CpxRPi, and to promoters made accessible following the release of the LexA repressor from LexA box , NadB could be a primary source of ROS in Pi-starved cells [2\u2022-) [2O2) and prevent the formation of toxic hydroxyl radicals (HO\u2022) [Flavoenzymes adventitiously produce ROS in Pi-starved cells. However, redirection of PYR metabolism from the PDH-TCA-ETC aerobic pathway towards the PDH-Pta-AckA fermentative pathway decreases the production of ROS by Sdh and Ndh in TCA and ETC, respectively. Because of activation of the NADed cells Fig. 2)+ biosyntls [2\u2022-) . The perls (HO\u2022) . TherefodinB encoding the Pol IV TLS DNA polymerase could play a key role. DinB helps to skip single-strand nicks generated through hydroxyl radical-mediated oxidative degradation of 2-deoxyribose moiety [In the LexA regulon, e moiety . In the e moiety . Finallye moiety .70 holoenzyme to promoters of a limited number of genes. In sharp contrast, the RpoS-dependent general stress response dramatically remodels the transcriptome, which allows non-growing cells to fight against many stresses [katE, sodC, gor, dps, dinB, poxB and pdhR. However, the switch from RpoD (\u03c370)- to RpoS (\u03c3S)-dependent transcription might be a risky investment. Exit from the stationary phase upon dilution into a rich medium requires a lag period to change metabolic pathways from a survival (RpoS-dependent) to a growth (RpoD-dependent) regimen [Why did such mechanisms evolve since the RpoS response can efficiently protect Pi-starved cells against multiple stresses including oxidative stress? SoxR-, OxyR-, LexA- and CpxR-specific stress responses are induced through the activation of specialized transcription factors that recruit the vegetative RNAP\u03c3stresses . At firs regimen . In a po regimen .70 to RNAP\u03c3S notably during incubation at low temperature [70 (RpoD) to \u03c3S (RpoS) (70-dependent expression of the LexA regulon in Pi-starved cells.The H-NS protein can delay the switch from RNAP\u03c3perature . High leperature could acperature . High leS (RpoS) , and lowS (RpoS) , both coE. coli should adapt to frequent and rapid environmental changes in Pi concentrations, the so-called \u2018feast and famine cycle\u2019 [Taken together, these data support the idea that specific stress regulons could protect Pi-starved cells against oxidative stress before the RpoS switch. Specific stress regulons can protect notably DNA and proteins essential for metabolism and envelope structure. Such a protection might be critical whether Pi-starved find a new source of Pi and start growing rapidly. In other words, specific stress regulons can afford a transient protection against oxidative stress whether e cycle\u2019 , which oe cycle\u2019 .E. coli evolved unique regulatory processes leading to induction of specific stress regulons before oxidative damage totally compromise protein synthesis [x and PhoRPi, thereby allowing a co-ordinated induction are poorly expressed with the remarkable exception of the Ntr system, which is mainly phosphorylated in ammonium-starved cells [enolpyruvate phosphotransferase system (PTSGlc) for the common phosphoryl donor, phosphoenolpyruvate (PEP) (Pi increases the activity of both Trk (K+:H+ symport) and CvrA (K+ efflux) [+ accumulation) and indirectly (competition for PEP) account for the strong induction of the SoxRS regulon and the weak induction of the CpxR, RpoE and LexA regulons in ammonium-starved cells.The source of ROS is probably the same in ammonium- and Pi-starved cells because ammonium-starved cells also continue to consume glucose, but at a rate twice lower than in Pi-starved cells . A simpled cells , competete (PEP) . Slow tr efflux) rather tGlc system triggers the accumulation of cyclic AMP (cAMP). Binding of cAMP to the cAMP-receptor protein (CRP) induces genes that help to scavenge and metabolize glucose through PTSGlc (pts), PDH (aceEF-lpd) and TCA (acnB and sdh) [poxB \u2212 rather than sodA and zwf as in Pi-starved cells \u2212 whereas PdhR without ligand inhibits the synthesis of PDH [ahpCF katE) or weakly affected (katG katE dps) under glucose-starvation conditions. However, the viability of oxyR single mutants and oxyR rpoS double mutants decreases markedly at the entry into stationary phase, which suggests that induction of gene(s) of the OxyR regulon could help glucose-starved cells to resist to low levels of ROS during the transition to stationary phase [When cells begin the transition to stationary phase because of a decrease in glucose levels in the medium, the PTSand sdh) . Metaboland sdh) before mand sdh) . The burand sdh) . Cra wits of PDH . Switchis of PDH . The hypry phase .Ferric uptake regulator) controls the transcription of ryhB [Glucose-starved cells accumulate high levels of the sRNA RyhB, whereas RyhB is not detected in Pi-starved cells (Julia Bos and PLM unpublished results). The repressor Fur .The activity of iron transporters requires a PMF and ATP . However3+) complexes [sufA-E operon is negatively controlled by Fur and positively controlled by OxyR [sufA-E operon, which could help to synthesize FeS proteins required to mitigate oxidative stress.RyhB helps maintain the viability of iron-starved cells both by stimulating the synthesis of enterobactin that scavenges iron, and by inhibiting the synthesis of most Fe-proteins but a few \u2018essential\u2019 FeS proteins \u2212 e.g. ribonucleotide reductase that permits dNTP synthesis . The synomplexes . Suf canomplexes . A role by OxyR . It is tl-methionine (SAM), and arginine to putrescine, thereby producing spermidine [Pi-starved cells degrade both threonine to S-adenosyl-ermidine . Spermidermidine . Oxidatiermidine . It is termidine could beIn sharp contrast, glucose-starved cells degrade threonine but not arginine (PLM unpublished results), which could improve SAM rather than spermidine synthesis. Glucose-starved do not accumulate TBARS . If glucConsidering the accumulation of SAM and activation of the Suf system, it is tempting to speculate that the synthesis of SAM-dependent iron-sulphur enzymes could play a key role in the viability of glucose-starved cells. Radical SAM methyltransferases such as RlmN and MiaB methylate tRNAs, which enhances translational fidelity and thus prevents the synthesis of abnormal proteins . It has An increase in translational fidelity could therefore prevent the synthesis of misfolded proteins sensitive to oxidative damage. The pre-emptive role of radical SAM methyltransferases could be critical if glucose-starved cells would contain low ATP levels, which could prevent the activity of ClpP and Lon ATP-dependent proteases that normally degrade misfolded proteins .E. coli can be starved of Pi in the small intestine [E. coli evolve different strategies to survive during the transition from the exponential growth phase to the stationary phase. Pi- and ammonium-starved cells, which can metabolize high levels of glucose, should fight against high levels of ROS. Pi-starved cells, which produce the unmodified form of PtsN, use several stress regulons in addition to SoxRS and OxyR oxidative stress regulons to mitigate oxidative damage. Ammonium-starved cells, which produce the phosphorylated form of PtsN, rely primarily on the SoxRS-Rsx system to mitigate oxidative damage. Glucose-starved cells could use a new strategy based primarily on the production of SAM/FeS methyltransferases that could help to prevent the synthesis of abnormal proteins prone to oxidation.In nature, ntestine and, folntestine . E. co"} +{"text": "Background: Western State Hospital (WSH) is an 800-bed, state-owned psychiatric hospital in Washington State which services individuals in 20 counties. WSH provides services and inpatient treatment to patients referred via behavioral health providers and/or the civil court system. Because many patients are admitted with serious, long-term illness, WSH also provides primary care and addresses infectious syndromes encountered in admitted patients. In January 2016, WSH officially began their antimicrobial stewardship program (ASP). In 2017 WSH joined the UW Center for Stewardship in Medicine (UW-CSiM) to grow and optimize their ASP. Methods: The lead pharmacist at WSH participated in weekly hour-long education and tele-mentoring sessions through the UW-CSiM program. Educational materials were adapted from UW-CSiM didactics and delivered to providers during regular meetings and grand rounds. Daily pharmacist led prospective audit with feedback was conducted. Antibiotic use data were collected and measured by days of therapy (DOT) per 1000-patient days from pharmacy dispensing records from 2015 to 2022. Results: From 1/1/15 to 12/31/22, there was a consistent trend of decreasing antibiotic consumption annually. In particular, antibiotic use decreased by over 65% ranging from 35-43 DOT per 1000 patient-days in 2015 to 9-11 DOT per 1000 patient-days in 2022 . This translates to approximately 1000 antibiotic days of therapy in 2015 and 200 days of antibiotic therapy in 2022. As of 2022, the two most common antibiotics used were cephalexin and sulfamethoxazole/trimethoprim Conclusion: Although treating infections is not a principal focus of a psychiatric hospital, patients receiving care in inpatient psychiatric facilities do experience common infections and receive antibiotics during their stay. At WSH, initiation of an antimicrobial stewardship program was associated with sustained decrease in total antibiotic DOT over 7 years. These data highlight the impact of tele-education and tele-mentoring in infectious diseases and antimicrobial stewardship as a path to build a successful antimicrobial stewardship even without formal infectious diseases training. Our single center experience at a large psychiatric hospital demonstrates the use of antimicrobials in these facilities and the opportunity for a large impact of an antimicrobial stewardship program in inpatient psychiatric facilities.Disclosures: None."} +{"text": "Correction to: Behav Res10.3758/s13428-022-01843-2mean RTs across conditions. This mistake can actually serve as an instructive reminder, because whether standardization is performed on raw data (LISAS) versus on averaged data (BIS) affects the suitability of the combined measure to control for speed\u2013accuracy trade-offs as demonstrated in the paper.A subtle but crucial mistake was introduced in Eq. 2 during copy-editing: LISAS is calculated using the standard deviation of RTs across trials and conditions ("} +{"text": "Antibiotic misuse can lead to poor patient outcomes, including ineffective treatment of infections, increased adverse effects, and development of antibiotic resistance. Implementing an antimicrobial stewardship program (ASP) is a vital strategy to improve and measure the appropriate use of antibiotics. This study aimed to assess the impact of pediatric ASP implementation on the reduction of restricted antibiotic usage and the improvement of patient outcomes.A single-center retrospective-prospective study was conducted at a children\u2019s hospital and included patients admitted to general pediatric or pediatric intensive care units receiving one or more restricted antibiotics. Prior-authorization of these restricted antibiotics was implemented as the ASP strategy. A three-month pre- and post-implementation chart review was completed. The primary outcome was optimizing restricted antibiotic usage. Secondary outcomes included provider compliance, antibiotic days of therapy (DOT), hospital length of stay (LOS), and readmissions within 30 days.Table 1Restricted antibiotics50 patients were included in the study. Restricted antibiotic orders for 18 out of 24 patients in the post-implementation group (75%) were compliant with obtaining pre-approval. Vancomycin, cefepime, and metronidazole were the most common agents ordered. The most common indications were skin and soft tissue infections, musculoskeletal infections, and preemptive sepsis coverage. Patients receiving restricted antibiotics decreased by two (-7.7%) while total restricted antibiotic orders increased by five (16.7%) following ASP implementation. Mean antibiotic DOT increased by 2.02 days (42.7%) and mean hospital LOS increased by 1.8 days (31.0%) in the post-implementation group. There was no difference in 30-day readmissions.Figure 1Restricted antibiotics ordered post-implementation of a pediatric antimicrobial stewardship program.Figure 2Use of restricted antibiotics pre- and post-implementation of a pediatric antimicrobial stewardship programThe results of this study not only aided in establishing baseline data but also provided a starting point for future efforts concerning the appropriate use of restricted antibiotics. While the findings were inconsistent with those of other institutions, incomplete program compliance and patient complexity in the post-implementation group likely contributed to the increase in DOT and hospital LOS. A longer study duration is needed to assess the true impact of this program.All Authors: No reported disclosures"} +{"text": "Enterobacteriaceae (CRE) colonization is an important risk factor for CRE infection. Most of Infection prevention control (IC) strategies to reduce CRE colonization were recommended to implement in a private room setting. Data on effectiveness of IC program in general medicine wards is limited.Carbapenem-resistant During February-October 2021, a cluster-randomized controlled trial was conducted among high risk for CRE-adult patients at six general medical wards, Siriraj Hospital. Six wards were randomized to receive either the standard IC care (sIC) or the enhanced CRE prevention program (eIC) plus sIC. The active CRE surveillance of stool or rectal swab specimen was performed in both groups within the first 72 hours of enrollment and then every 7 days. The eIC included a monthly healthcare education and feedback session, a real-time alert of CRE-acquisition from the active surveillance, and the CRE contact precaution visual reminder. The sIC included the cohorting and contact precaution of a CRE-acquisitioned patient, and a real-time alert of CRE-acquisition from the clinical specimen.p=0.059). The incidence rate of CRE-acquisition was significantly lower in the intervention group . The median [range] of CRE-acquisition free time were comparable. K. pneumoniae was the most common CRE pathogen isolated from the surveillance and clinical specimens. No difference in all-cause mortality and length of stay between the two groups was observed.There were 174 patients (with 1684 patient-days) in the intervention group and 189 patients (with 1517 patient-days) in the control group. Baseline characteristics were comparable between two groups. The cumulative incidence of CRE-acquisition was slightly lower in the intervention group (36.8% (64/174) vs. 46.6% (88/189);The incidence of CRE acquisition at our institute was remarkably high. The eIC could reduce the incidence of CRE-acquisition and lengthen the CRE-acquisition free time. Future study should be done to explore the benefit on morbidity and mortality outcomes.All Authors: No reported disclosures"} +{"text": "Pilot-ignited direct-injected NG (PIDING)combustion uses a small pilot injection of diesel to ignite a late-cycle maindirect injection of NG, resulting in significant reduction of unburnedCH4 emissions relative to port-injected NG. Previous works haveidentified NG premixing as a critical parameter establishing indicatedefficiency and emissions performance. To this end, a recent experimentalinvestigation using a metal engine identified six general regimes of PIDING heatrelease and emissions behavior arising from variation of NG stratificationthrough control of relative injection timing (RIT) of the NG with respect to thepilot diesel. The objective of the current work is to provide comprehensivedescription of in-cylinder fuel mixing of direct injected gaseous fuel and itsimpacts on combustion and pollutant formation processes for stratified PIDINGcombustion. In-cylinder imaging of OH*-chemiluminescence (OH*-CL) and PM(700\u2009nm), and measurement of local concentration of fuel is considered for 11different 4 emissionspreviously observed for stratified-premixed PIDING combustion in previous investigations are due to: (i) very rapid reaction zone growth(Gaseous fuels for heavy-duty internal combustion engines provide inherentadvantages for reducing CO Typically, the main PIDING combustion process is non-premixed,which allows for higher compression ratios, providing high efficiency and very lowuHC emissions at the cost of increased PM and NOX emissions relative tohighly premixed (i.e. port-injected) NG systems.11Because the main constituent of NG, CH The fraction of fuel converted in the partially-premixed fraction,In PIDING combustion, a portion of the NG also reacts in a rapid partially-premixedmode in parallel to establishment of a quasi-steady jet flame. and McTaggart-Cowan et al.15) and (ii) stratified-premixedPIDING modes where one or more NG injections are performed during the compressionstroke to generate highly premixed conditions . For both these approaches, late-cycle where X or CH4emissions, however with advancing X and CH4 increased significantly. The decreased PM emissions were attributed to the increased NG premixing timeprior to NG ignition resulting in less NG with an equivalence ratio, 15 The major drawbacks of theSPC mode were indicated to be increased cycle-to-cycle variability and demonstratedincreased efficiency with decreased PM and CO relative to non-premixed PIDINGcombustion and acceptable CCV (COV of indicated mean effective pressure limited toless than 2%). Based on numerical simulation, the authors describe the Relative to port-injected NG operation, a 75% reduction in the emissions ofCH4 was achieved. However, CH4 emissions rapidly increasedfor 17 Emissions of NOX were also observed to besignificantly higher for X, inagreement with earlier experimental investigations.16Stratified-premixed PIDING combustion was investigated by advancing 19 Increased efficiency and areduction of PM and CO were reported for these strategies, although limiting uHCemissions was a challenge. These investigations indicated that the increasedturbulent mixing rates produced by the late NG injection supported higher flamepropagation speeds and reduced CH4 emissions from slow flame extinction, which has also been noted for DISI combustion.2022Splitting the main NG injection into early- and late-cycle injections has also beenconsidered as a strategy to control NG stratification.1215 and/or the time delay betweenNG injection and the start of partially-premixed NG combustion, 24 In-cylinder OH*-chemiluminescence (OH*-CL) imaging of PIDINGcombustion with \u22126 ms A subsequent non-optical measurement campaign defined Investigations of stratified-PIDING combustion have used where These previously introduced metrics to characterize the NG premixing are graphicallysummarized in 25). However, the majority ofpublished investigations are limited to subsets of the full spectrum of NG premixingthat is possible with PIDING fuel systems, where The identified regimes of PIDING combustion motivate and guide the currentwork and are summarized below.All investigations of stratified PIDING combustion have noted transitions in thecharacteristic behavior of PIDING combustion for different degrees of NG premixing(e.g. transition of PM sensitivity to A constant engine speed (1000\u2009RPM) was considered, so the range ofTo classify regimes of PIDING combustion, AHRR and emissions behavior wasanalyzed for \u221226.5\u2009ms 26 Combustion regimes were considered to be domains of11 SPC,131527 and port-injected dual-fuel combustion strategies, respectively. Of particular interest is thestratified-premixed (late-cycle) regime or outside thepiston bowl (early-cycle), which significantly influenced injection controlstrategy, combustion behavior, and emissions as noted in otherinvestigations.Two early-cycle PIDING regimes were distinguished by For late-cycle operating conditions more fundamentalinvestigations of single pilot-NG jet pairs in rapid compression/expansionmachines (RCEMs).34 These investigations have been valuable forcharacterizing the structure of typical non-premixed PIDING combustion, howeveronly a subset of these investigations address PIDING combustion withThe above description of the spectrum of stratified PIDING combustion connectsinvestigations of different stratified PIDING combustion strategies into asingle generalized framework. To develop and refine this framework into a usefulconceptual tool for PIDING, complementary measurements investigating thestratification and structure of NG mixing and combustion processes are needed.To address this gap, investigators have performed in-cylinder imaging of PIDINGcombustion processes following one of two general approaches: (i)optically-accessible engines fitted with production multi-jet PIDINGinjectors,34 Inparticular, quenching of the pilot reactants by the cold NG jet has shown toincrease variability in the ignition phasing and location of both fuels, whichimpacts NG premixing and main combustion behavior, as has been noted in opticalengine experiments.31 Crucially, these fundamental studies only considerunbounded NG jets, and do not provide insight to the effects of NG jetimpingement on combustion chamber surfaces (i.e. the piston bowl).Study of single pilot-NG jet pairs in RCEMs has demonstrated that This resulted in increased NG premixing and more rapid heat release.In-cylinder OH*-CL imaging for a slightly wider range of which corroborates numerical modeling results.Decreasing 24 Finally, comparison of in-cylinder NG stratificationand reaction zone structures to combustion and emissions performance isneeded.RCEM and optically-accessible engine measurements of stratified PIDING combustionto date have provided significant insight to the role of pilot-NG interactionsand the effects of increased NG premixing on PIDING combustion behavior.However, the range of NG premixing conditions investigated is narrowly focusedon the transition between the minimally-premixed and variable premixed fractionregimes. Additional consideration of the role of combustion chamber geometry isneeded as this is a critical parameter for stratified PIDINGcombustion.The objectives of this work are to: (i) support and refine the previouslyidentified regimes of PIDING combustion and associated critical injectionphasings and (ii) describe the in-cylinder mixing processes of direct injectedgaseous fuel and its impacts on combustion and in-cylinder pollutant formationprocesses. These objectives are addressed by applying in-cylinder imaging andlocal fuel concentration measurements to stratified PIDING combustion conditionsranging from homogeneously-premixed to nominally non-premixed in anoptically-accessible engine.The optical research engine facility, measurement diagnostics, and selectedstratified PIDING combustion conditions are described first. Discussion ofresults is divided into 3 parts addressing adjacent domains of the spectrum ofstratified PIDING combustion: (i) Minimally-premixed and variable premixedfraction regimes, (ii) Variable premixed fraction and stratified-premixed(late-cycle) regimes, and (iii) Early-cycle regimes. Last, a summary of theimportant in-cylinder processes is presented for all combustion regimes. Details of the optical engine configuration are presented in The experimental facility used in this investigation is based on a 2.0\u2009L,single-cylinder, optically-accessible Ricardo Proteus engine, the specifications ofwhich are given in These observations have been made for non-premixed PIDING combustion, and itshould be noted they may not apply to the wide range of stratified PIDING conditionsconsidered in the current work.The research engine facility is fitted with a first generation Westport Fuel Systems(WFS) High-Pressure Direct-Injection (HPDI) injector and commercial WFS dome-loadedself-relieving regulator (DLSR). A custom programmable engine control unit (ECU) andHPDI injector with independently actuated concentric needles allows arbitraryrelative injection timing of the diesel and NG injections. The injector is mountedvertically and concentric to the piston bowl with 9 equally-spaced NG orifices and 9pilot diesel orifices midway between each NG orifice see . Diesel A Bowditch piston with a flat-bottomed, cylindrical piston bowl housing a quartzwindow offset from the cylinder axis by 4\u2009mm provides a 78\u2009mm diameter opticalaccess to the combustion chamber see . This piTwo imaging systems were used to simultaneously record: (i) OH*-CL at 310\u2009nm and(ii) emission from PM at 700\u2009nm. The imaging systems were synchronized to oneanother with a constant framerate of 15,000\u2009Hz and focused to the horizontal midplane of the combustion chamber atTDC. All imaging is line-of-sight and although it is not possible to infervariations along the optical path, they provide qualitative indication of theposition and intensity of reaction zones and soot clouds. Specifications of theimaging system hardware is provided in The presence of PM has also been shown to significantly attenuate OH*-CL,which must be considered when analyzing OH*-CL for non-premixed combustion systems. Further detail on the analysis of OH*-CL images is provided in OH*-CL measurements are used to analyze ignition, main combustion reaction zonestructure and growth rates. The 700\u2009nm images are used as an indicator of PM,with broadband incandescence from PM being the dominant emitter at 700\u2009nm.Due to the wide range of combustion conditions imaged the exposures were adjusted for eachoperating condition in order to maximize the dynamic range used on each camerasensor without incurring sensor saturation was used to measure the local CH3 measurement volumeprotruding from the cylinder head. Light introduced to the measurement volume isreflected by a mirrored surface, transmitted back to a second fiber optic cableand 3.4\u2009The ICOS measures absorption of light sent via fiber optic cable from aquartz-tungsten-halogen lamp to a 20\u2009mmIn the current work, the relative magnitude of Where Analysis of the phasing of CH4 consumption to allow the window tocool. Images were recorded on the alve see , the intIn this work, characterization of the NG mixture development and the resultingfeatures of the combustion structure(s) are investigated to refine descriptions ofthe regimes of PIDING combustion previously proposed based on emissions and AHRRanalysis. Local relative fuel-air ratio, Minimally-premixed \u2192 variable-premixedVariable-premixed \u2192 stratified-premixed (late-cycle)Stratified-premixed (early-cycle) \u2192 RIT-insensitive premixedTo describe the spectrum of premixed PIDING combustion regimes, a summary ofThe NG mixture stratification is a key parameter influencing ignition, maincombustion, and emissions behavior for all regimes of PIDING combustion.Following direct injection of the NG, complex fluid mixing processes will causethe fuel-air mixture to develop from a highly stratified state (i.e. pure fuelin the core of the NG jet) toward a fully-developed homogeneous state. Thetransient fuel-air mixture states are a function of the NG premixing time,In For all non-fired operating conditions shown in For all conditions with late-cycle injections and PM (700\u2009nm) imaging is compared for In ,NG see . The rel For the stratified-premixed conditions, the peak PM signal is alsolocalized in the 9 pilot ignition regions, indicating the pilot ignition processis more significant for PM production than the premixed NG combustion processfor these operating conditions. For the initial peak in the For all conditions shown in there is a single peak in the In The single-cycle images presented in However, for With early-cycle The development of For 4 emissions measuredusing the thermodynamic engine tooutside the piston bowl (early-cycle). Across this transition, the max(AHRR) and To support in-cylinder imaging, local measurement of relative molar fuelconcentration was performed for reacting and non-reacting engine operation tocharacterize gaseous fuel mixing evolution. The objectives of this investigationwere to: (i) support and refine the previously identified regimes of PIDINGcombustion and critical injection phasings and (ii) describe the in-cylinder mixingprocess of direct injected gaseous fuel and its impacts on combustion andin-cylinder pollutant formation processes. Detailed descriptions of the in-cylinderprocesses of each regime are given in In-cylinder imaging of OH*-CL (310\u2009nm) and PM (700\u2009nm) was performed for 11 PIDINGoperating conditions, representing 5 regimes of stratified PIDING combustionpreviously identified based on AHRR and emissions behavior.The in-cylinder imaging and relative fuel concentration measurements provided animproved understanding all PIDING combustion regimes and critical injection phasingsPIDING combustion regimes (SPC and 17 elsewhere) is likely due to very rapid reactionzone growth rates (4emissions; this is a recommended area of focus for future investigation.Early-cycle PIDING combustion: For homogeneously-premixed PIDINGcombustion, flame propagation speeds decrease from approximately 15 to10\u2009m/s as This investigation has validated the previously identified regimes of PIDINGcombustion and has augmented them with description of the in-cylinder NG mixturedevelopment and its impacts on combustion and pollutant formation processes. Furtherinvestigation of NG mixing, pilot-NG interactions, and the implementation ofnumerical modeling of stratified-premixed PIDING combustion is needed to furthersupport and extend the conclusions presented in the current work. These results,combined with recommended future areas of research offer significant opportunity fordeveloping higher-efficiency gaseous fuel direct-injection combustion strategieswith low pollutant emissions."} +{"text": "Background: Until recently, the lack of clinical outcomes information for rheumatoid arthritis (RA) in administrative claims databases limited their use in comparative effectiveness research. A validated claims-based algorithm has been developed to estimate the effectiveness of biologics for RA, allowing for estimation of cost and effectiveness in the same database.Objectives: To implement a validated claims-based effectiveness algorithm in a US managed care claims database to compute the 1-year biologic cost per effectively treated patient among first-line biologics approved for moderate-to-severe RA .Methods: This retrospective cohort study used administrative claims data for individuals in the HealthCore Integrated Research Database (HIRDSM). The first claim for a first-line biologic between July 1, 2009, and January 31, 2013, after 6 months of continuous enrollment, was defined as the index event and date. Patients were aged 18-63 years on the index date and had at least one claim for RA in the 6-month pre- index period. Biologic costs included plan and patient paid amounts on claims for the biologic drug and administration. The algorithm defined effectiveness during the 12-month post-index period as achieving all six of the following: high adherence (medication possession ratio \u226580% or infusions consistent with the product label); no increase in biologic dose or decrease in dosing interval; no new biologic; no new nonbiologic disease-modifying antirheumatic drug; no new or increased oral glucocorticoid use; and \u22641 glucocorticoid injection. Cost per effectively treated patient was calculated as the total biologic cost (drug and administration) divided by the number of patients categorized by the algorithm as effectively treated.Results: The cohort comprised 4844 patients . Average first-year biologic cost ranged from $14 795 (golimumab) to $19 520 (abatacept). Average first-year biologic cost per effectively treated patient was significantly lower for etanercept ($50 217) than for golimumab adalimumab , abatacept , certolizumab pegol , and infliximab .Conclusions: In this application of a validated claims-based algorithm to a large managed care population, etanercept had the lowest 1-year biologic cost per effectively treated patient among first-line biologics."} +{"text": "Design and Identification of seed regions for Golden Gate assembly and Expression of synthetic sRNAs in Bacteria. The SEEDling tool predicts optimal sRNA seed regions in combination with user-defined sRNA scaffolds for efficient regulation of specified mRNA targets. Results are passed on to the G-GArden tool, which assists with primer design for high-fidelity Golden Gate assembly of the desired synthetic sRNA constructs.Synthetic small RNAs (sRNAs) are gaining increasing attention in the field of synthetic biology and bioengineering for efficient post-transcriptional regulation of gene expression. However, the optimal design of synthetic sRNAs is challenging because alterations may impair functions or off-target effects can arise. Here, we introduce DIGGER-Bac, a toolbox for In bacteria, small RNAs (sRNAs) are versatile regulators that can be exploited for modulation of gene expression at the post-transcriptional level. Hence, sRNAs have gained attention as regulatory tools in bacteria using synthetic biology approaches . A typicIn recent years, type IIS restriction enzyme-based cloning, Golden Gate cloning, became popular because type IIS enzymes recognize specific sequences but cut in a directed and defined distance outside the motif, allowing scar-free assembly. Using Golden Gate assembly, several DNA parts can be combined in a one-pot, single-step reaction with high precision . The metEscherichia coli (Design and Identification of seed regions for Golden Gate cloning and Expression of synthetic sRNAs in Bacteria) toolbox supports the process of seed region/scaffold identification (SEEDling) and guides the primer design for high-fidelity Golden Gate cloning (G-GArden) (We have recently established an easy-to-use plasmid toolset for efficient Golden Gate-based generation of synthetic sRNA TUs in hia coli . The pla-GArden) .SEEDling predicts the best possible synthetic sRNA sequence for the target(s) of choice. The lowest sRNA\u2013mRNA hybridization energy does not necessarily provide the best function; therefore, SEEDling integrates hybridization energy, off-target activity, and sRNA structure to predict the optimal synthetic sRNA. In order to do so it requires the following user inputs: (i) an annotated target genbank file (single gene to whole genome), (ii) the reference genome of the used model organism, and (iii) a config file . Based osaved_data file that is constantly expanded by the user (e.g. by feeding in SEEDling results and acceptor plasmids). Within the GUI, four DNA parts are typically selected for construction of an sRNA TU: (i) a Golden Gate-compatible cloning plasmid, (ii) a promoter, (iii) a seed sequence, and (iv) a scaffold sequence (primer3 tool (https://github.com/primer3-org) may be applied for primer design (https://ggtools.neb.com/getset/run.cgi) for optimization of overhangs (.txt), (ii) files for ordering of oligodeoxynucleotides (.txt and .csv), (iii) and genbank files of the final constructs for documentation purposes (.gb). Exemplary saved_data and output files can be found in The G-GArden tool is a stand-alone application for primer design in Golden Gate-based cloning strategies. It is implemented as a graphical user interface (GUI) that is launched by an executable file on both Linux and Windows operating systems. G-GArden is written in python and bundled separately for both operating systems using PyInstaller so it can be executed without time-consuming installation of interpreters or modules. To take advantage of the DIGGER-Bac toolbox results from SEEDling are preferably used as input . G-GArdesequence . By seler design . By defaverhangs , 2018b. The Design-Build-Test-Learn cycle is at the heart of synthetic biology approaches. The DIGGER-Bac toolbox offers user-friendly solutions for the Design-Build phase of synthetic sRNA-related projects. While existing tools compute complementary RNA sequences (i.e. seed regions) for target regulation and search for potential off-target effects , SEEDlinFinally, G-Garden assists with primer design for cloning, which\u2014together with our recently published plasmid tool set \u2014speeds ubtad285_Supplementary_DataClick here for additional data file."} +{"text": "Objectives: Over the past 2 years, many infection prevention and control (IPC) resources have been diverted to manage the COVID-19 pandemic. Its impact on the incidence of antimicrobial-resistant organisms has not been adequately studied. We investigated the impact of the pandemic on the incidence of carbapenem-resistant Enterobacterales (CRE) in Singapore. Methods: We extracted data on unique CRE isolates and patient days for 6 public hospitals in Singapore from the carbapenemase-producing Enterobacteriaceae (CaPES) study group database, and we calculated the monthly incidence of CRE . Interrupted time-series (ITS) analysis was conducted with the pre\u2013COVID-19 period defined as before February 2020, and the COVID-19 period defined as after February 2020. Statistical analyses were performed using Stata version 15 software. Results: From January 2017 to March 2021, 6,770 CRE isolates and 9,126,704 patient days were documented. The trend in CRE monthly incidence increased significantly during the pre\u2013COVID-19 period but decreased during the COVID-19 period without stepwise change in the incidence . The trend in monthly incidence rate of CRE clinical cultures increased significantly during the pre\u2013COVID-19 period and decreased significantly during COVID-19 period with no stepwise change in the incidence . The trend in monthly incidence rate of CRE surveillance cultures decreased during the pre\u2013COVID-19 period and the COVID-19 period without stepwise change in the incidence . Conclusions: The rate of CRE in clinical cultures decreased during COVID-19 but not the rate in surveillance cultures. Further studies are warranted to study the impact of COVID-19 on CREs.(DUPLICATE DELETED)"} +{"text": "Staphylococcus aureus. Given its virulence, patients may experience serious complications that can be difficult to diagnose at the time of the infection leading to increased morbidity and mortality. The objective of this study is to evaluate the incidence of hospital-acquired Staphylococcus aureus bacteremia (HA-SAB) and its risk factors associated with mortality among hospitalized patients in Universiti Malaya Medical Centre (UMMC), a tertiary teaching hospital in MalaysiaHospital acquired bacteremia is predominantly caused by This is a retrospective analysis of patients with HA-SAB admitted to UMMC over three time periods (P) in relation to the COVID-19 pandemic; P1 beginning of the pandemic (July 2020-May 2021), P2 during the peak of pandemic (June 2021-June 2022) and P3 recovery phase (July 2022-March 2023). We included patients \u226518 years old who fulfilled the criteria for HA-SAB. HA-SAB was defined as the first positive blood culture performed \u226548 hours after admission in patients with no evidence of infection at the time of admission. HA-SAB rates per 100 days admission and its risk factors associated with mortality were analyzed.A total of 287 cases of HA-SAB were identified and the overall mortality rate was 31%. The HA-SAB rate increased by 42% from 0.19 (P1) to 0.33 (P2) per 100 admission days and decreased to 0.15 per 100 admission days (P3). On multivariate analysis, risk factors associated with mortality among patients with HA-SAB were older age , use of arterial lines and secondary bloodstream infection (BSI) .The COVID-19 pandemic was associated with substantial increase in HA-SAB rate. This was likely due to changes in infection control measures in general and line care prevention bundle specifically to cope with the pandemic such as extended use of personal protective equipment (PPE), and non-adherence to the 5-moments of hand hygiene especially changing gloves between patients. Older age, use of arterial lines and secondary BSI were significantly associated with mortality among patients with HA-SAB.All Authors: No reported disclosures"} +{"text": "Patients receiving B-cell-depleting therapies (BCDT) are at an increased risk for severe COVID-19. Passive antibody therapy (PAT), including COVID-19 convalescent plasma (CCP) and monoclonal antibodies (MAB), is hypothesized to be an effective treatment in this population. However, real-world data on their effectiveness is limited.We conducted a retrospective chart review of patients who contracted COVID-19 within a year from their last BCDT treatment and later received PAT (Table 1). Response to treatment was assessed by 90-day COVID-related mortality and all-cause morbidity, defined through number of hospitalizations .Sixty-five patients met initial criteria. Five were excluded from analysis due to non-COVID related death within 90 days from COVID diagnosis. Cause of death was established in the chart and confirmed by review of two investigators.From 60 included patients, the majority were Caucasians (97%), females (57%), and vaccinated (67%) (Table 2). Most patients received rituximab (53%) for treatment of a hematological malignancy (37%) or multiple sclerosis (37%) . Overall morbidity and mortality were low. All hospitalized and deceased patients were elderly Caucasian males receiving rituximab for underlying hematological malignancy. All deceased patients received inpatient treatment, 2 with CCP and one with MAB .Demographics, vaccination status and number of comorbidities excluding the condition which is the indication for B-cell depleting therapy.COVID-19 patients undergoing BCDT and treated with PAT had low morbidity and mortality in our study, suggesting a possible benefit of PAT in this patient population. All deaths occurred in patients hospitalized at the time of treatment with PAT, implying advanced COVID-19 infection and highlighting the importance of early PAT administration. All deceased patients and 2/3 hospitalized patients were receiving rituximab, suggesting that rituximab may be a risk factor for severe COVID . All deceased and hospitalized patients had an underlying hematological malignancy, suggesting that the presence of hematologic malignancy may impact the outcome of COVID-19. In our study, elderly Caucasian males with multiple medical comorbidities and underlying hematological malignancy treated with BCDT, particularly rituximab, may have an increased risk for severe COVID-19. Early PAT administration may improve outcomes in this group of patients, and they should be prioritized for treatment when access to PAT is limited.All deaths were among patients being treated with rituximab for hematological malignancy.All Authors: No reported disclosures"} +{"text": "This Research Topic includes 10 articles related to applications of nuclear medicine techniques in different fields of medicine.18F]FDG) is the most common radiopharmaceutical used for positron emission tomography (PET) and it allows to evaluate the glucose metabolism for oncological and non-oncological indications.Fluorine-18 fluorodeoxyglucose . A total of 162 NSCLC patients from two centers were included. A model combining visual assessment of lymph node status and tumor maximal standardized uptake values (SUVmax) was selected. The authors demonstrated that primary tumor SUVmax improves lymph node status prediction and could allow a better selection of NSCLC patients who are candidates for minimally invasive approaches .18F]FDG, other PET radiopharmaceuticals evaluating different metabolic pathways can be used for oncological indications as radiolabelled choline which is useful to assess the cell membrane turnover.Beyond [Ghidaglia et al. assessed the influence of key histological characteristics on [18F]FDG PET and [18F]fluorocholine PET positivity in 62 patients with hepatocellular carcinoma (HCC). The authors clearly demonstrated that, among different key histological characteristics, [18F]FDG PET and [18F]fluorocholine PET positivity appear driven by both the grade and microvascular invasion components in HCC .The study of 18F]fluorocholine PET/computed tomography (PET/CT) but for a non-oncological indication. Imperiale et al. investigated the value of presurgical [18F]fluorocholine PET/CT in detecting additional hyperfunctioning parathyroids despite a positive [99mTc]Tc-sestamibi parathyroid scintigraphy in 64 patients with primary hyperparathyroidism (pHPT). [18F]fluorocholine PET/CT resulted more accurate and useful than [99mTc]Tc-sestamibi scintigraphy in pHPT patients with positive scintigraphic results. Positive parathyroid scintigraphy could be not satisfactory before neck surgery particularly in patients with multiglandular disease. Based on these findings, [18F]fluorocholine PET/CT outperforms [99mTc]Tc-sestamibi scintigraphy in detecting hyperfunctioning parathyroid glands and its role in the diagnostic algorithm of pHPT patients should be highlighted.Another article included in this collection was focused on [18F]FDG PET/CT in bacteremia or bloodstream infections. [18F]FDG PET/CT should be considered in suspected complex bloodstream infections, in patients at high risk of metastatic spread, and in bloodstream infection in patients hospitalized in intensive care units. As a matter of fact, in these patients [18F]FDG PET/CT has an impact on the management, treatment strategy, and outcome, mainly by directing the diagnostic process ameliorating the detection of infectious foci or by modifying treatment regimens, resulting in reduced relapse and mortality rates. Interestingly, a negative [18F]FDG PET/CT has a positive prognostic value and may obviate the need for further workup in patients with bloodstream infections (Hess).Another example of non-oncological application of PET imaging is reported by a review article included in this collection which summarizes the potential role and recommendations of Ga-EDTA) PET and evaluating its performance in healthy mice and murine models of renal dysfunction. Dynamic [68Ga]Ga-EDTA PET provided a reliable and precise means of evaluating renal function in two murine models of renal injury, supporting the possible clinical application of this imaging technique in the near future .In a preclinical study included in this collection Beyond PET, nuclear medicine imaging includes also planar scintigraphy and single-photon emission computed tomography (SPECT) techniques which can be used in oncological and non-oncological fields.Boccalini et al. investigated the effects of manual and semi-automatic methods for assessing semi-quantitative indices in myocardial innervation imaging using iodine-123 metaiodobenzylguanidine ([123I]MIBG) scintigraphy in 35 patients with idiopathic Parkinson's disease. The semi-automatic method evaluated by the authors improved the agreement among raters in classifying scintigraphic images as normal or abnormal. These findings have important implications for semi-quantitative assessment of [123I]MIBG scintigraphy in clinical routine.The study of Nuclear medicine does not include only imaging techniques but also therapeutic applications.Trautwein et al. analyzed prognostic risk factors in 62 patients with NETs treated with PRRT. The authors found that PET-based molecular tumor volume at somatostatin receptor PET and chromogranin A in combination were significant prognostic factors for long-term overall survival. Furthermore, an interim somatostatin receptor PET/CT after two cycles of PRRT had the potential in identifying non-responders who may benefit from a change in therapy at an early stage .Peptide receptor radionuclide therapy (PRRT) is an effective and well-tolerated treatment option for patients with NETs that prolongs progression-free survival. In their retrospective study In conclusion, the articles included in this Research Topic clearly highlight the bright future of nuclear medicine and radiopharmaceutical sciences.GT drafted the manuscript and revised the final version. The author contributed to the article and approved the submitted version."} +{"text": "Abutilon fruticosum in order to detect antibiotic resistance genes (ARGs) along with their antibiotic resistance mechanisms and to detect potential risk of these ARGs to human health upon transfer to clinical isolates. The study emphasized the potential risk to human health of such human pathogenic or commensal bacteria, being transferred via food chain or horizontally transferred to human clinical isolates. The top highly abundant rhizospheric soil non-redundant ARGs that are prevalent in bacterial human pathogens or colonizers included mtrA, soxR, vanRO, golS, rbpA, kdpE, rpoB2, arr-1, efrA and ileS genes. Human pathogenic/colonizer bacteria existing in this soil rhizosphere included members of genera Mycobacterium, Vibrio, Klebsiella, Stenotrophomonas, Pseudomonas, Nocardia, Salmonella, Escherichia, Citrobacter, Serratia, Shigella, Cronobacter and Bifidobacterium. These bacteria belong to phyla Actinobacteria and Proteobacteria. The most highly abundant resistance mechanisms included antibiotic efflux pump, antibiotic target alteration, antibiotic target protection and antibiotic inactivation. antimicrobial resistance (AMR) families of the resistance mechanism of antibiotic efflux pump included resistance-nodulation-cell division (RND) antibiotic efflux pump , major facilitator superfamily (MFS) antibiotic efflux pump (for soxR gene), the two-component regulatory kdpDE system (for kdpE gene) and ATP-binding cassette (ABC) antibiotic efflux pump (for efrA gene). AMR families of the resistance mechanism of antibiotic target alteration included glycopeptide resistance gene cluster (for vanRO gene), rifamycin-resistant beta-subunit of RNA polymerase (for rpoB2 gene) and antibiotic-resistant isoleucyl-tRNA synthetase (for ileS gene). AMR families of the resistance mechanism of antibiotic target protection included bacterial RNA polymerase-binding protein (for RbpA gene), while those of the resistance mechanism of antibiotic inactivation included rifampin ADP-ribosyltransferase (for arr-1 gene). Better agricultural and food transport practices are required especially for edible plant parts or those used in folkloric medicine.A metagenomic whole genome shotgun sequencing approach was used for rhizospheric soil micribiome of the wild plant The online version contains supplementary material available at 10.1186/s13568-023-01597-w. A. fruticosum to human gut was exploredRisk of transfer of rhizosphere resistome of The most common resistance mechanism in this resistome is antibiotic efflux pumpRhizobiome is a source of new antibiotics with feasible therapeutic interventionsThe online version contains supplementary material available at 10.1186/s13568-023-01597-w. Abutilon fruticosum is a perennial medicinal plant species of family Malvaceae that is native to northern America, Africa and southwestern and western Asia including Saudi Arabia is an approach to detect accurate signature of soil microbiome down to the strain level existing in rhizospheric microbiomes, especially those of native or wild plant species to pathogenic bacteria in human gut.The present study aimed to detect resistome signature of soil-dwelling rhizospheric bacteria of the wild plant species Abutilon fruticosum plants growing naturally in the North Western region of Mecca district, Saudi Arabia were shipped to Novogene Co. (Singapore) for whole metagenome shotgun sequencing. Based on the quality control criterion, reads with low quality bases of\u2009\u2265\u200940\u00a0bp and with N nucleotides of\u2009>\u200910\u00a0bp were removed. Then, library preparation was done and clean data were sequenced on Illumina HiSeq 2500 platform as described (812 gene queries) or from re-assembled less abundant reads of all samples (NOVO_MIX) (1025 gene queries) was used to detect unique ORFs referring to the antibiotic resistance genes (ARGs) in rhizosphere (R) and bulk (S) soil microbiomes of mtrA, soxR and vanRO genes, while the least are arr-1, ileS and iri genes. List of ARGs in rhizospheric soil of Abutilon fruticosum that are prevalent in human bacterial pathogens/colonizers along with their phyla is shown in Additional file Abutilon fruticosum and bulk (S) soil microbiomes of A. fruticosum are shown in Additional file Mycobacterium (255), Pseudomonas (117) and Nocardia (81). The results for the 13 selected genera indicate higher abundance and relative abundance of ARG queries in rhizosphere soil of A. fruticosum compared with those of bulk soil , Pseudomonas (17378), Nocardia (3607) and Bifidobacterium (3452) with\u2009>\u200915 non-redundant queries were detected , major facilitator superfamily (MFS) antibiotic efflux pump (for soxR gene), the two-component regulatory kdpDE system (for kdpE gene) and ATP-binding cassette (ABC) antibiotic efflux pump (for efrA gene). AMR families of the resistance mechanism of antibiotic target alteration include glycopeptide resistance gene cluster (for vanRO gene), rifamycin-resistant beta-subunit of RNA polymerase (for rpoB2 gene) and antibiotic-resistant isoleucyl-tRNA synthetase (for ileS gene). AMR families of the resistance mechanism of antibiotic target protection include bacterial RNA polymerase-binding protein (for RbpA gene), while those of the resistance mechanism of antibiotic inactivation include rifampin ADP-ribosyltransferase (for arr-1 gene) families along with resistance mechanisms of the 10 selected ARGs are shown in Additional file Abutilon fruticosum are shown in Additional file mtrA (3452), soxR (498), vanRO (461), RbpA (286) and rpoB2 (266) and bulk (S) soil microbiomes of , soxR 49, vanRO and Proteobacteria (genus Vibrio), while soxR gene belongs to members of phylum Proteobacteria , golS gene belongs of members of phylum Proteobacteria , kdpE gene belongs to members of phyla Actinobacteria (genus Mycobacterium) and Proteobacteria , and efrA gene belongs to members of phylum Proteobacteria (genera Cronobacter and Klebsiella) gene that is highly abundant in rhizospheric microbiome of A. fruticosum -like sensor family is made of membrane and membrane-associated proteins that transports drugs extracellularly. In the ABC system, ATPases hydrolyze ATP to release energy required for the translocation (efflux) of substrates or drugs across membranes , rifamycin-resistant beta-subunit of RNA polymerase (for rpoB2 gene) and antibiotic-resistant isoleucyl-tRNA synthetase (for ileS gene) that kill bacteria by inhibiting synthesis of cell wall and VanRO is the response regulator (RR). The vanHOX gene cluster exists head-to-head to the vanSO/vanRO gene cluster. The VanSO/VanRO cluster promotes biosynthesis of the VanHOX cluster in two steps, where VanS senses the accumulation of substrates in order to inhibit glycosyltransferase activity, then VanR is activated by ATP-dependent phosphorylation. VanR, then, initiates expression of the vanHOX gene cluster, where vanH gene encodes a dehydrogenase enzyme that participates in the biosynthesis of new peptidoglycan precursors, while vanX gene encodes an enzyme that removes the normal D-Ala-D-Ala-ending precursors, and vanO gene encodes a ligase to synthesize a new altered D-Ala-D-Lac substrate of penicillin binding protein (PBP) with low binding affinity of vancomycin \u03b2 subunit and share 88.8% identity. RpoB-encoded protein is rifampin sensitive, whereas RpoB2-encoded protein contains amino acid substitutions at the rifampin-binding site that enable bacteria to resist this antibiotic of Bifidobacteria, it confers resistance against the narrow-spectrum antibiotic mupirocin that is firstly discovered in Pseudomonas fluorescens via food chain to pathogens or human clinical isolated in gut. These commensal bacteria can also be converted to opportunistic pathogens when they incorporate abundant ARGs in their cells. Risk to human health can be larger if these ARGs are prevalent in human pathogens (or opportunistic pathogens) that already exist in rhizosphere soil microbiome of A. fruticosum. These types of bacteria can be a direct threat to human health without the need to be horizontally transferred to genetically-related or -unrelated bacteria.Based on the results of the present study, there are two types of bacteria that exist in the rhizospheric soil of A. fruticosum to the environment and possible threat to human health. Attention should also be given to rhizobiome signature of different wild plant species that can help isolate new antibiotics with feasible therapeutic interventions.In conclusion, the present study provides insights into the signature and possible horizontal transfer and/or dissemination of rhizospheric resistome determinants of the wild plant Additional file 1.Table S1. Alignment results of non-redundant gene queries generated from rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. NOVO_MIX refers to reassembled low-copy ORF that is usually found in \u2265 2 of the six microbiome samples, while that preceded by S or R refers to a unique ORF.Additional file 2.Table S2. Annotation results of non-redundant queries of antibiotic resistance genes (ARG) generated from rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. NOVO_MIX refers to reassembled low-copy ORF that is usually found in \u2265 2 of the six samples, while that preceded by S or R refers to a unique ORF.Additional file 3.Table S3. Number and description of non-redundant queries of antibiotic resistance genes (ARG) generated from rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. NOVO_MIX refers to reassembled low-copy ORF that is usually found in \u2265 2 of the six samples, while that preceded by S or R refers to a unique ORF. ARGs with query no. of \u2264 15 (in red) were not analyzed further.Additional file 4.Table S4. Pathogens or bacterial colonizers harboring antibiotic resistance genes (ARGs) that are prevalent in human. The data were generated using the resistance gene identifier (RGI) that is a tool for putative AMR gene detection from submitted sequence annotation data in the comprehensive antibiotic resistance database (CARD). Species in red refers to a microbe acting as a biocontrol agent and later was placed into the low risk group 1 from the German Federal Institute for Occupational Safety and Health, TRBA 466 \u201cClassification of prokaryotes (bacteria and archaea) into risk groups\u201d) as cited by Nelkner et al. with query number of \u2265 16 harbored by known human microbial pathogens/colonizers that were detected in soil microbiomes of Abutilon fruticosum. N/A refers to ARGs that are not prevalent in known human bacterial pathogens/colonizers. These ARGs were not analyzed further as the risk of their direct transfer to human bacterial pathogens/colonizers is low. Species in blue are not in the list of human pathogens/colonizers, while that in red refers to a microbe acting as a biocontrol agent as described of the different antimicrobial resistance mechanisms (AMR) at the phylum level of soil microbiomes of Abutilon fruticosum. Rows in red refer to less abundant mechanisms that were not analyzed further.Additional file 7.Table S7. Abundance of non-redundant gene queries at bacterial genus/species level of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum.Additional file 8.Table S8. Abundance of Mycobacterium genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold rows refer to bacterial pathogens/colonizers whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 9.Table S9. Abundance of Vibrio genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold row refers to a bacterial pathogen/colonizer whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 10.Table S10. Abundance of Klebsiella genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold row refers to a bacterial pathogen/colonizer whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 11.Table S11. Abundance of Stenotrophomonas genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold row refers to a bacterial pathogen/colonizer whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 12.Table S12. Abundance of Pseudomonas genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold rows refer to bacterial pathogens/colonizers whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 13.Table S13. Abundance of Nocardia genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold rows refer to bacterial pathogens/colonizers whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 14.Table S14. Abundance of Salmonella genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold row refers to a bacterial pathogen/colonizer whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 15.Table S15. Abundance of Escherichia genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold rows refer to bacterial pathogens/colonizers whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 16.Table S16. Abundance of Citrobacter genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold rows refer to bacterial pathogens/colonizers whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 17.Table S17. Abundance of Serratia genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold row refers to a bacterial pathogen/colonizer whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 18.Table S18. Abundance of Shigella genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold rows refer to bacterial pathogens/colonizers whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 19.Table S19. Abundance of Cronobacter genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold row refers to a bacterial pathogen/colonizer whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 20.Table S20. Abundance of Bifidobacterium genus/species in terms of non-redundant gene queries of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. Bold row refers to a bacterial pathogen/colonizer whose ARGs are prevalent in human. The total list of human bacterial pathogens/colonizers is shown in Table S4.Additional file 21.Table S21. Number of non-redundant gene queries of bacterial genera with species existing in the list of bacterial human pathogens/colonizers shown in Table S4 in rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum.Additional file 22.Table S22. Information retrieved from CARD site (https://card.mcmaster.ca/ontology/) for the top highly abundant ARGs (> 15 gene queries) in samples of rhizosphere and bulk soil microbiomes of Abutilon fruticosum.Additional file 23.Table S23. Number of the most abundant non-redundant antibiotic resistance gene queries (ARGs) of rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. These ARGs are prevalent in bacterial human pathogens or colonizers.Additional file 24.Table S24. Highly abundant non-redundant antibiotic resistance gene queries (ARGs) in rhizosphere (R) and bulk (S) soil microbiomes of Abutilon fruticosum. These ARGs are prevalent in bacterial human pathogens or colonizers."} +{"text": "Nuclear chromosome compaction is non-random and dynamic. The spatial distance among genomic elements instantly modulates transcription. Visualization of the genome organization in the cell nucleus is essential to understand nuclear function. In addition to cell type-dependent organization, high-resolution 3D imaging shows heterogeneous compaction of chromatin organization among the same cell type. Questions remain to be answered if these structural variations were the snapshots of dynamic organization at different time points and if they are functionally different. Live-cell imaging has provided unique insights into dynamic genome organization at short (milliseconds) and long (hours) time scales. The recent development of CRISPR-based imaging opened windows for studying dynamic chromatin organization in single cells in real time. Here we highlight these CRISPR-based imaging techniques and discuss their advances and challenges as a powerful live-cell imaging method that poses high potential to generate paradigm-shifting discoveries and reveal functional implications of dynamic chromatin organization. Traditional methods used to study chromatin organization have been largely \u201csnapshot\u201d-based, while these methods have advanced our knowledge of genome architecture, our understanding of dynamics and heterogeneity across a cell population is still in its infancy. Elucidating the temporal genome organization is key for understanding genome function. Direct visualization of chromatin dynamics endogenously in living cells is essential to advance our understanding of chromatin movement, structure, and function.Genetic information coded by DNA is highly regulated to express cell type-specific genes. To achieve this regulation, DNA dynamically associates with proteins forming a complex known as chromatin. Chromatin is hierarchically folded to maintain homeostasis and allow rapid response to stimuli . To fullin-situ hybridization (FISH) and chron (FISH) enabled n (FISH) , visualin (FISH) , and, mon (FISH) ]. Despitn (FISH) and chann (FISH) . Data din (FISH) , reflectin vivo. Deactivating the CRISPR-associated (Cas) proteins converts a CRISPR system from a genome editing tool to an imaging tool. In the type-II CRISPR/Cas9 system from Streptococcus pyogenes, the two substitution mutations, D10A and H840A, deactivated Cas9 to the nuclease-dead Cas9 (dCas9) which binds to DNA but does not generate double strand breaks (DSBs) (trans-activating crRNA (tracrRNA), Cas protein, and protospacer adjacent motifs (PAMs). While the crRNA guides the Cas protein to the target by base pairing, the tracrRNA serves as the glue that holds crRNA, and Cas together. Genetic fusion of the crRNA and tracrRNA creates single guide RNAs (sgRNAs); this is a common strategy to simplify the CRISPR systems as one of the most influential breakthroughs and powerful techniques for precise genome editing of the 21st century . Beyond s (DSBs) . This sy systems . The PAMChen et al., 2013) (Streptococcus pyogenes (Sp), Neisseria meningitidis (Nm), and Streptococcus thermophilus (St1) CRISPR-dCas systems for a three-color imaging system , or SpdCas9 with Staphylococcus aureus (Sa) dCas9 for a two-color system . More recently, Sun and colleagues demonstrated that cellular DNA and mRNA can be visualized simultaneously in single cells by combining fluorescent CRISPR-dCas9 and CRISPR-dCas13 systems (The first CRISPR imaging used a GFP fused dCas9 (dCas9-GFP) to label specific genomic loci as a monochromatic system . CRISPR- systems . Using CCASFISH, the earliest application of CRISPR in a FISH setting, has allowed FISH experiments to be conducted without global denaturation of chromatin by high temperature as in conventional FISH experiments . SimilarThe breakthrough of CRISPRainbow is the color expansion (up to seven colors simultaneously using one CRISPR-dCas system) . CRISPRaSignal amplification of CRISPR-based imaging techniques has allowed scientists to track low- or non-repetitive genomic regions with fewer sgRNAs ; this improves the labeling efficiency and expands the applications of the technology. A common strategy to improve the fluorescence signal is to use an array of tandem repeats of fluorophores. Imaging low- and non-repetitive genomic loci was reported by inserting tandem \u00d714 MS2 stem loops at the 3\u2032 end of the sgRNA . HoweverInstead of tagging sgRNAs with fluorescent protein fused RNA coat proteins , fluorogenic sgRNAs can be made by directly tagging small commercial dyes to the 5\u2019 end of the sgRNA, such as Alexa488-sgRNA . These sC. elegans.The dCas9-SunTag system has been used to visualize genomic loci with 21 or 15 copies of repeats [, For infCRISPR-Casilio amplifies the fluorescence signal of sgRNAs by fusing unique repeats of Pumilio/FBF (PUF)-binding sites (PBS) to 3\u2032 end of the sgRNA (sgRNA-\u00d720 PBSc) . PumilioMUC4 locus (Combining molecular beacons (MBs) as a fluorescence resonance energy transfer (FRET) pair with the CRISPR-dCas9 system have allowed visualization of non-repetitive DNA sequences in living cells. CRISPR/dual-FRET MB used two distinct molecular beacons as a FRET donor and acceptor pair to minimize the noise background of non-specific interacting events in cells since the FRET signals will only be detected when the FRET pairs are in proximity and released from their quenchers. As few as three sgRNAs is sufficient to clearly visualize the non-repetitive C4 locus .in vitro applications, it only needs two CRISPR-Cas complexes to detect one specific non-repetitive sequence. The future development of CasPLA for live-cell imaging will be a great advance of this field.Precisely detecting single-nucleotide variations (SNVs) helps to understand aging-related diseases. Zhang and colleagues designed CRISPR/Cas9-mediated proximity ligation assay (CasPLA), allowing SNVs to be visualized in single cells . CasPLA spdCas9 targeting have been bioinformatically predicted in human cells (ZNF358 (TPM (transcription per million) = 37.2) treated with DRB, but not on the silenced gene locus CYP4F12 (TPM = 0). In mouse embryonic cells (mESC), Gu and colleagues observed increased mobility on the loci with transcription activation using CARGO (chimeric array of gRNA oligonucleotides). Of note, increased genomic locus and chromatin domain dynamics were also observed by single-nucleosome tracking in HeLa cells and by insertion of LacO as the labeling site in fibroblasts , telomeres have been successfully visualized in human osteosarcoma cells (U2OS), human retinal pigment epithelium (RPE), HeLa, HEK293T, plant, mouse epiblast-like (mEpiLCs), and mouse embryonic stem (mESCs) cells by CRISPR-imaging techniques . Howeveran cells . The coman cells . Interesan cells . Similarroblasts . UltimatWang and colleagues tracked chromosomal translocations using LiveFISH . The twoChromosomal compaction can be quantitatively described by the compaction exponent, the scaling exponent of a power-law relation between genomic distance and spatial distance . This meLive-cell imaging of two or more specific genomic loci simultaneously labeled on a single chromosome was used to quantitatively study dynamic chromatin domains and folding . The spaWe have discussed different CRISPR-based imaging techniques that have been improved significantly in brightness and ease of use in the past few years. However, difficulties remain for labs to adopt these techniques. Here we summarize limitations and disadvantages of CRISPR-based imaging techniques that could be further improved in the future: 1) a sgRNA can have different labeling efficiency in different cell types. Optimizations are necessary for each research project. 2) Lentiviral transduction is often used for generating stable cell lines with consistent locus signals. However, lentiviral transduction is more labor-intense, compared to transfection, and the efficiency depends on quality of the viral particles. 3) CRISPR-based imaging techniques have not yet been made for high-throughput applications. 4) High sensitivity of the microscope system is required to detect weak fluorescence signals at low noise background for imaging low- and non-repetitive sequences. Further improvements in CRISPR-dCas delivery, sgRNA design, fluorophore size, and microscopy will expand the applications and facilitate the adoption of these techniques. Nevertheless, CRISPR-based imaging techniques are not replaceable by other imaging techniques. Studying spatio-temporal dynamics of genome organization non-invasively under physiological conditions and endogenous sequences in single chromosomes in single cells cannot be achieved by approaches using fixed cells or whole genome labeling methods."} +{"text": "Background:Epilepsy is a common chronic brain disorder globally affecting people of all ages, with the majority living in developing countries. The introduction of epilepsy self-management approaches to help people with epilepsy is urgently needed to influence epilepsy-related outcomes. This 2-site randomised controlled trial building on promising preliminary data is intended to explore this further.Methods:A total of 188 adult people with epilepsy (PWE) attending the neurology clinics at Mulago and Mbarara hospitals and consent to participate in the study. They will be randomised into intervention versus enhanced treatment control (eTAU) study groups. The intervention group will receive 12-week \u201cintensive\u201d educational sessions and a 12-week remotely accessed telephone follow-up stage. The controls will continue in their usual care supplemented by written materials on epilepsy in their preferred language and tailored to the reading level of most patients at the clinic. SMART-U consists of 2 main components: a 12-week \u201cintensive\u201d group format stage and a 12-week remotely accessed telephone follow-up stage. SMART-U will be assessed for acceptability, fidelity, and efficacy compared to eTAU. The primary study outcome is the mean change in cumulative past 24-week seizure frequency (24 weeks prior to the study baseline compared to the 24-week follow-up). Seizure frequency will be via self-report with corroboration by family/support system informants whenever possible. Participants will self-report their seizure frequency (numeric count) that they experienced between baseline and 13 weeks and again between 13 and 24 weeks and the mean change from baseline to 24 weeks in QOL.Discussion:The curriculum-guided Self-Management intervention for Reducing The epilepsy burden among Ugandans (SMART-U) program is anticipated to reduce the epilepsy burdenseizure frequency and improve other health outcomes, including depression, functional status and health resource use.Trial Registration Number (TRN): NCT06139198Date of registration: 14thNovember 2023"} +{"text": "Bipolar disorder (BD) is higher in developing countries. Childhood trauma exposure is a common environmental risk factor in Colombia and might be associated with a more severe course of bipolar disorder in Low-Middle Income-Countries. We carried out the first case-control study (114 BD patients and 191 controls) in Colombia using a structural clinical interview and the Childhood Trauma Questionnaire-Short Form (CTQ-SF) to describe the prevalence and association between trauma exposure during childhood with a severe course of illness in a sample of BD patients.to describe the prevalence and association between trauma exposure during childhood with a severe course of illness in a sample of BD patients.A case-control study (114 controls versus 191 controls) that assessed outpatients between 18 and 65 years old, at a teaching hospital in Barranquilla, Colombia was carried-out. All participants were assessed with the SCID-5-CV, the Young Mania Rating Scale (YMRS), and the Bipolar Depression Rating Scale (BDRS). Additionally, exposure to childhood trauma was assessed using The Childhood Trauma Questionnaire-Short Form (CTQ-SF). The CTQ-SF is a brevity 28-item Likert-type, with a five-factor structure: emotional abuse EA, physical abuse PA, sexual abuse SA, physical neglect PN, and emotional neglect EN, self-administered instrument in order to assess multiple types of trauma during childhood.We generate an outcome variable named severe bipolar disorder defined by course severe of bipolar disorder as the presence of any clinical indicator of severity, previously delimited by the research team . Also, we carried out bivariate and regression analyses with each clinical indicator of severity as an outcome.Cases included 61.4% BD type I and 38.6% BD type II. The median age was 31.5 years for BD patients and 31 years old for healthy controls. A higher prevalence of childhood trauma was evidenced in cases compared to controls.Multivariate logistic regression model in severe bipolar disorderThis is the first association study between childhood trauma exposure as a higher risk for a severe course of illness in BD patients in Colombian. Our findings highlight the importance of screening and evaluating childhood trauma exposure during the course of BD patients.None Declared"} +{"text": "Posttraumatic stress disorder is characterized by deficits in cognitive flexibility related to dysfunction of the medial prefrontal cortex (mPFC). Exposure therapy can effectively reverse these deficits. Fear extinction in rodents bears similarity to exposure therapy. Extinction reverses chronic stress\u2013induced deficits in cognitive flexibility on the attentional set-shifting test (AST), an mPFC-mediated process. This therapeutic effect requires activity of pyramidal neurons and brain derived neurotrophic factor (BDNF) signaling in infralimbic cortex (IL). However, the circuit mechanisms governing BDNF-mediated plasticity initiated by extinction in IL are unknown. The ventral hippocampus (vHipp) plays a role in regulating IL activity during extinction, and plasticity in vHipp is necessary for extinction memory consolidation. Therefore, we investigated the role of vHipp input to IL in the effects of extinction in reversing stress-induced cognitive deficits.vHipp input to IL was silenced using a Gi-Designer Receptors Exclusively Activated by Designer Drugs (DREADD) via local infusion of clozapine-N-oxide (CNO) into IL before extinction. A day later, rats were tested on AST. In a separate experiment, we tested whether vHipp input to the IL induces BDNF signaling to exert therapeutic effects. We activated the vHipp using a Gq-DREADD, and injected an anti-BDNF neutralizing antibody into IL. Rats were tested on the AST 24 hours later.Silencing the vHipp input to IL prevented the beneficial effects of extinction in reversing stress-induced cognitive deficits. Activating vHipp input to IL in the absence of extinction was sufficient to reverse stress-induced deficits in set-shifting. The beneficial effects were blocked by local infusion of a neutralizing anti-BDNF antibody into IL.vHipp-driven BDNF signaling in IL is critical for extinction to counteract the deleterious cognitive effects of chronic stress. In this work, we report the importance of ventral hippocampal input to the infralimbic cortex for the therapeutic-like effects of fear extinction learning in stressed rats. We demonstrate that BDNF plays a pivotal role in inducing plasticity via the ventral hippocampal-IL circuit in stressed animals. Such findings elucidate a potential therapeutic target for the treatment of posttraumatic stress disorder.Posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) are debilitating illnesses that affect millions every year. Such disorders are characterized by behavioral disruptions associated with dysfunction of the medial prefrontal cortex (mPFC), such as maladaptive coping and cognitive deficits . CognitiAvailable pharmacological treatments for PTSD and MDD are ineffective for a large portion of patients and often fail to address cognitive symptoms . BehavioFear extinction in rodents engages circuits similar to those activated by exposure therapy . Fear exde novo protein synthesis in the IL is necessary for the effects of extinction to reverse stress-induced deficits in set shifting during extinction attenuates the effects of extinction in reversing stress-induced deficits on set-shifting performance and active coping . Furthershifting . TogetheWe recently demonstrated the necessity of brain derived neurotrophic factor (BDNF) signaling in the IL for the therapeutic effects of extinction on set shifting in stressed animals . BDNF plSpecifically, it is unknown if extinction-induced BDNF signaling in the IL is dependent on afferent input from another region, such as the ventral hippocampus (vHipp). Activity-dependent release of BDNF in hippocampal-prefrontal circuits regulate fear extinction learning and behavioral perseverance . vHipp nA total of 109 male and female rats were housed on a 12-hour light/dark cycle. After 1-week acclimation, rats were single housed. Experiments took place during the lights-on portion of the cycle. All procedures followed National Institutes of Health guidelines and were approved by the UTHSA Institutional Animal Care and Use Committee. Group sizes were determined by power analysis using estimates of effect size from previous data. Males and females were included in all groups. As per National Institutes of Health mandate, after the primary analyses, secondary analyses were conducted separately after disaggregating by sex, and results were shown separately for males and females. These experiments, however, were not explicitly powered to study sex differences.Two days before beginning chronic unpredictable stress (CUS), rats were habituated to 2 contexts in sound-attenuating chambers for 15 minutes each, as previously described . ContextRats received fear conditioning or tone control treatment in Context A. Fear conditioning consisted of 4 pairings of a tone coterminus with a footshock , with an inter-trial interval of 120 seconds. Freezing during each tone was quantified using FreezeView . Tone control rats did not receive footshocks during tone exposures.All rats received fear extinction in Context B, consisting of 16 tone trials with no shock, with average inter-trial interval of 120 seconds.CUS was conducted as previously described . In maleThe AST was used to measure cognitive flexibility on the extradimensional set-shifting task as previously described . Rats weHabituation day: Rats were trained to dig in pots filled with sawdust to retrieve a food reward, one-half of a Honey Nut Cheerio .Training day: Rats were trained to locate the reward in 1 of 2 pots by discriminating cues in 2 stimulus dimensions: the odor applied to the rim of the pot or the texture of the digging medium that filled the pot.Treatment day: Rats received bilateral microinjections and extinction or tone control treatment.Testing day: Rats were tested on a series of discrimination stages in which a criterion of 6 correct consecutive trials were required to proceed to the next stage of either AAV5-CaMKIIa-hM4D(Gi)-mCherry or the control AAV5-CaMKIIa-EGFP (Addgene) at a rate of 0.1 \u03bcL/min into the ventral hippocampus of either control AAV5-CaMKIIa-EGFP or the excitatory DREADD, AAV5-CaMKIIa-hM3D(Gq)-mCherry into the ventral hippocampus as above. Subsequently, rats were implanted with microinjection guide cannulae targeting vHipp terminals in the IL, as above. Rats recovered for 7 days after surgery, then underwent CUS. On the third day after CUS (1 day before testing), rats received bilateral microinjections of CNO into the IL in lieu of extinction and subsequently received bilateral microinjections of either sheep control IgG or sheep anti-BDNF . This dose of anti-BDNF previously was shown to block BDNF signaling . The injIn previous experiments, we observed phosphorylation of TrkB 30 minutes after extinction . Therefot test, t16\u2009=\u20092.140, P\u2009=\u2009.0328; To assess whether inhibiting ventral hippocampal terminals during extinction affects the phosphorylation of the receptor TrkB at the Y515 residue, 9 males (4\u20135 per group) and 10 female rats (4\u20136 per group) were used in 2 groups: (1) a control group with the control EGFP construct injected in the vHipp (Ext-EGFP); and (2) a group injected with the Gi DREADD in vHipp (Ext-Gi). Inhibiting ventral hippocampal input to the infralimbic cortex during extinction significantly attenuated the induction of phosphorylated TrkB in the IL . ANOVA was used to compare performance on the ED set-shifting test between groups. In the primary analysis, ANOVA revealed a significant group effect . Inhibiting vHipp terminals in nonstressed animals at the time of extinction had no behavioral effect on the AST tested 24 hours later . Consistent with our previous work, extinction reversed stress-induced deficits in set shifting . Silencing vHipp terminals in the IL at the time of extinction blocked the effects of extinction on set shifting after CUS . Thus, chemogenetically inhibiting vHipp terminals in the IL during extinction blocked the therapeutic effects of extinction in stressed animals. Analyzed separately after disaggregating by sex, males also showed a significant group effect , and extinction reversed the effects of stress . Inhibiting vHipp terminals in the IL during extinction blocked the effects of extinction, although the effect was marginally significant due to reduced power after disaggregation . Similarly, females showed a significant group effect , which was reversed by extinction, although this effect was again marginally significant due to reduced power after disaggregation . Inhibiting vHipp terminals in the IL blocked the therapeutic effects of extinction .To test if inhibiting ventral hippocampal terminals in the IL prevented the effects of extinction in reversing stress-induced deficits in set shifting, 25 males (3\u20138 per group) and 23 females (3\u20136 per group) were used in 5 groups. The groups were defined by virus injection, stress condition, and extinction treatment: (1) control group with EGFP injected in the vHipp (no stress/extinction/EGFP); (2) control group with Gi DREADD in the vHipp (no stress/extinction/Gi); (3) stress group, with CUS + tone control and EGFP in the vHipp (CUS/tones/EGFP); (4) stress plus extinction group, with CUS + extinction and EGFP in the vHipp (CUS/extinction/EGFP); and (5) a group to test the necessity of vHipp terminal activity in IL during extinction after stress (CUS/extinction/Gi). Microinjections were administered 24 hours before testing, immediately before extinction. Within-session freezing during extinction did not differ between fear-conditioned groups . Pairwise comparisons using the Holm Sidak test showed a significant stress effect . Chemogenetic activation of vHipp terminals in the IL reversed the effects of stress . Infusion of anti-BDNF antibody into the IL prevented the beneficial effects of activating vHipp terminals . Stress induced a set-shifting deficit , which was nonsignificantly reversed by Gq activation . Likewise in females, set-shifting performance significantly differed between groups . In females, stress induced a deficit on set-shifting performance , which was also nonsignificantly reversed by Gq activation.We next investigated whether (1) chemogenetically activating vHipp input to the IL is sufficient to reverse stress-induced deficits in set shifting, and (2) if these effects are dependent on BDNF signaling in the IL. To address these questions, 19 males (3\u20136 per group) and 23 females (3\u20138 per group) were used in 5 groups. The groups were defined by virus injections in the vHipp, IgG injection in the IL, and CUS: (1) no stress with EGFP in vHipp and control sheep IgG in IL (no stress/EGFP/IgG); (2) no stress with EGFP in vHipp and anti-BDNF in IL (no stress/EGFP/anti-BDNF); (3) CUS with EGFP in the vHipp and control sheep IgG; (4) CUS with Gq in the vHipp and sheep IgG injected in IL, to test the sufficiency of activating vHipp terminals to reverse stress-induced set shifting deficits (CUS/Gq/IgG); and (5) a group to test the necessity of BDNF signaling in the IL for the effects of activating vHipp terminals (CUS/Gq/anti-BDNF). ANOVA revealed a significant effect of group on performance in the ED task (FThese results demonstrate the necessity of glutamatergic vHipp input to the IL for extinction to reverse stress-induced deficits in set-shifting performance, consistent with literature highlighting the importance of plasticity in these regions for successful extinction memory recall . AlthougWe have shown that extinction induces phosphorylation of the BDNF receptor TrkB in the IL . In the Chemogenetically activating vHipp terminals in the IL in lieu of extinction treatment was sufficient to reverse stress-induced impairments in set-shifting performance tested 24 hours later. This observation aligns with studies showing the antidepressant-like effects of activating the vHipp-mPFC pathway and withOur work highlights the crucial role of activity in the vHipp-IL pathway during extinction that is necessary to counteract the detrimental effects of stress. Extinction learning is a complex process involving distinct brain regions working in concert . Regions"} +{"text": "Lung transplant (LT) recipients with high risk cytomegalovirus (CMV) mismatched donors have been found to have worse early and late outcomes. In our institution, high risk CMV mismatch patients are managed in a protocolized manner consisting of proactive utilization of antiviral agents and immune augmentation with CMV immune globulin.We reviewed our institutional LT database. The study group consistent of all patients who underwent single or bilateral lung transplant between January 2012 to December 2016 (n=319). The CMV serostatus of both recipients and donors was reviewed and patients were classified into two groups: High risk CMV mismatch (R-/D+): n=82 (25.7%) and non-high risk CMV mismatch (n=237). We compared patient demographics, co-morbidities, pre and port-transplant variables among the two groups. Three-year survival was analyzed as the primary outcome variable. With three-year survival as the dependent variable, we analyzed the association of CMV status with survival using multivariate logistic regression analysis.There was no difference in the baseline and post-transplant characteristics of LT recipients with and without CMV mismatch donors. Overall one-year and three-year survival was 89.96% and 72.7% respectively. Recipients transplanted with CMV mismatch status and managed with a proactive CMV prophylaxis protocol experienced similar one one-year and three-year survival as the non-CMV mismatch recipients.After adjustment for demographics, comorbidities and post-transplant course, CMV mismatch was not associated with three-year survival. Post-LT development of AKI the only independent variable to be independently associated with three-year survival . Kaplan Meier analysis showed very similar survival curves for recipients with and without CMV mismatched donors.Use of a proactive multimodality CMV prophylactic regimen consistent of antiviral agents and immune augmentation with CMV immune globulin may improve outcomes among high risk CMV mismatch LT recipients.All Authors: No reported disclosures"} +{"text": "Volatile organic compounds (VOCs) produced by human cells reflect metabolic and pathophysiological processes which can be detected with the use of electronic nose (eNose) technology. Analysis of exhaled breath may potentially play an important role in diagnosing COVID-19 and stratification of patients based on pulmonary function or chest CT.Breath profiles of COVID-19 patients were collected with an eNose device (SpiroNose) 3 months after discharge from the Leiden University Medical Centre and matched with breath profiles from healthy individuals for analysis. Principal component analysis was performed with leave-one-out cross validation and visualised with receiver operating characteristics. COVID-19 patients were stratified in subgroups with a normal pulmonary diffusion capacity versus patients with an impaired pulmonary diffusion capacity (DLCOc\u2009<\u200980% of predicted) and in subgroups with a normal chest CT versus patients with COVID-19 related chest CT abnormalities.The breath profiles of 135 COVID-19 patients were analysed and matched with 174 healthy controls. The SpiroNose differentiated between COVID-19 after hospitalization and healthy controls with an AUC of 0.893 . There was no difference in VOCs patterns in subgroups of COVID-19 patients based on diffusion capacity or chest CT.COVID-19 patients have a breath profile distinguishable from healthy individuals shortly after hospitalization which can be detected using eNose technology. This may suggest ongoing inflammation or a common repair mechanism. The eNose could not differentiate between subgroups of COVID-19 patients based on pulmonary diffusion capacity or chest CT. The outbreak of the COVID-19 pandemic resulted in more than 620\u00a0million confirmed cases globally and at least 6.5\u00a0million deaths . HistopaAnalysis of volatile organic compounds (VOCs) in exhaled breath with the use of electronic nose technology (eNose) is a relatively new and emerging diagnostic tool that already demonstrated its capability to diagnose patients with interstitial lung disease and sarcoidosis , 6. VOCsWe aimed to evaluate whether VOCs in exhaled breath detected with eNose technology can differentiate between previously hospitalized COVID-19 patients and healthy individuals, and discriminate subgroups with impaired lung diffusion capacity or patients with COVID-19-related CT abnormalities.In this single-centre cross-section study, adult survivors of COVID-19 discharged from the Leiden University Medical Centre (LUMC) between March 2020 and April 2021 were invited for follow-up 3 months after discharge. Patients aged 18 years and older were eligible for inclusion after laboratory-confirmed diagnosis of SARS-CoV-2. Patients were excluded upon decline of informed consent, refusal of follow-up, a history of lung disease or inability to perform breath analysis. The study was approved by the local ethics committee for COVID-19 related research (protocolnumber 2020-059). Demographics and clinical characteristics were obtained from electronic medical records. Healthy controls were volunteers without a history of pulmonary diseases who gave informed consent for collection of their breath profile.Breath profiles were collected in real-time with the SpiroNose , a technically and clinically validated cloud-connected device that integrates spirometry and eNose technology . The SpiPulmonary function tests were conducted together with the collection of breath profiles by clinical technicians at the department of pulmonary function. Forced vital capacity (FVC), forced expiratory volume in one second (FEV1) and diffusion capacity of the lungs for carbon monoxide adjusted for hemoglobin (DLCOc) were measured according local standard protocol. Impairment of lung diffusion capacity was defined as a DLCOc of <\u200980% of predicted. Radiological evaluation was performed with non-enhanced CT of the chest. Chest CT was defined as abnormal in patients with presence of at least one of the following COVID-19 related findings: parenchymal consolidation, ground-glass opacities (GGO), reticulation, bronchiectasis and curvilinear bands. COVID-19 patients were stratified in subgroups with a normal pulmonary diffusion capacity versus patients with an impaired pulmonary diffusion capacity and in subgroups with a normal chest CT versus patients with COVID-19 related chest CT abnormalities.Prior to analysis, sensor data was processed as described by the Vries . This meBreath profiles of COVID-19 patients were randomly matched with a computer algorithm for age, sex and BMI with breath profiles of healthy individuals for comparison. Between-group comparisons were analysed with Mann-Whitney U tests. Retained principal components were used as feature of linear discriminant analysis. Generated models were validated with leave-one-out cross validation and outcomes were visualized with confusion matrices and receiver operating characteristics (ROC) . Area unIn total, 167 patients with PCR-confirmed COVID-19 diagnosis were discharged from the LUMC between March 2020 and April 2021 of whom 35 (19%) patients were excluded. 22 (13%) patients had a history of lung disease and 10 (6%) patients were unable to perform breath analysis mostly due to difficulty with following PFT instructions. The remaining 135 (81%) patients were included in this analysis and their breath profiles were matched with breath profiles of 174 healthy controls.Baseline characteristics of COVID-19 patients and healthy controls are shown in Table\u00a0All patients and healthy individuals were included in this analysis. The first three principle components (PCs) were retained and represented 75% of the variance. Comparison of PCs between groups resulted in p-values ranging from <\u20090.001\u20130.013 had impairment of lung diffusion.The first three PCs were retained and represented 73.3% of the variance. Comparison of PCs between groups resulted in p-values ranging from 0.129 to 0.227. Breath profiles of COVID-19 patients with impaired diffusion and patients with normal diffusion were similar with an AUC of 0.544 patients had an abnormal CT. The first three PCs were retained and represented 73% of the variance. Comparison of PCs between groups resulted in p-values ranging from 0.796 to 0.880. Breath profiles of COVID-19 patients with abnormal CT and patients with normal CT were similar with an AUC of 0.585 tests. Detection of SARS-CoV-2 in samples of exhaled breath is a relatively fast and cost-effective technique like eNose technology. However, the diagnostic performance of eNose devices appears to be superior with a sensitivity ranging from 81 to 100% compared to detection rates of 11\u201370% in studies with PCR tests of aerosolized SARS-CoV-2 \u201315. The In addition to the diagnostic performance of eNose technology in the acute phase of infection, a few studies also demonstrated that COVID-19 patients with chronic complaints had a distinguishable pattern of VOCs, indicating that eNose could potentially improve follow-up assessments of COVID-19 . Our stuVOCs with the potential of being a biomarker of COVID-19 infection are yet unknown. The different cell types that play dominant roles in COVID-19 infection, like inflammatory neutrophils and monocyte-derived macrophages in the lung promote proinflammatory cytokines and chemokines with a principal role in the early cytokine storm could explain a production of different VOCs . In lateAlthough cytokines and chemokines associated with COVID-19 infection are known, it is difficult to detect them with GC-MS since their small size. Therefore, our data cannot be one-on-one correlated with prior data on cytokine and chemokine levels, but the VOCs in exhaled breath could be produced by these cells as resumed in the review article by Schulte-Schrepping J et al . For exaA strength of this study was the selection and pulmonary evaluation of all discharged COVID-19 patients regardless of complaints or symptoms. Unfortunately, the SpiroNose is unable to present which groups of VOCs act as a specific biomarker for COVID-19. This hampers generalizability between different brands of eNose devices. This study was limited by the relatively small number of patients and uneven distribution of patients in subgroups which made it impractical to divide cohorts in a preferred training and validation set. Another limitation is the absence of patients with other lung diseases as reference group. Further studies are warranted to validate eNose technology in post-COVID-19 patients and to evaluate if these breath profiles are different compared to other lung diseases.In conclusion, eNose technology is able to distinguish between breath profiles of previously hospitalized COVID-19 patients and heathy controls. These patterns may suggest ongoing inflammation or remodelling mechanisms at play 3 months after COVID-19. Within the COVID-19 group, there were no differences in breath profiles based on lung diffusion capacity or abnormalities on chest CT."} +{"text": "Accurate insights into CSS prognostic determinants for NMIBC necessitate large cohorts within multicenter studies. Presently, comprehensive real-world data concerning survival outcomes and prognostic factors in NMIBC are deficient. We aimed to evaluate real-world CSS in NMIBC and to develop a prognostic nomogram based on identified risk factors.5The majority of prognostic models and nomograms for non-muscle-invasive bladder cancer (NMIBC) classify individuals based on their risk of recurrence and progression.5Our population-based analysis using the Surveillance, Epidemiology, and End Results database encompassed 98,238 patients with NMIBC\u00a0who underwent transurethral resection of bladder tumor (TURBT) between 2004 and 2015. Our findings reveal significant disparities in cancer-specific mortality (CSM) across different NMIBC stages. Notably, T1HG and carcinoma in situ (CIS) were associated with the highest CSM rates within the observed follow-up of 124\u00a0months [interquartile range (IQR) 81\u2013157], reaching 19.52% and 15.56%, respectively. The study also highlighted the relatively high risk of CSM for rarely diagnosed T1LG and TaHG tumors; the risk being approximately 10%. Our nomogram underlines the crucial relevance of T stage, grade and age in CSM prediction. Sociodemographic factors also influence the CSM, which underscores the disparity in oncological care and should alarm the healthcare providers and policymakers. Estimation of\u00a0long-term CSM based on identified risk factors might help in patient counseling and aid clinical decision making regarding treatment intensification in ones and de-intensification in others.4 Potentially synergistic adjuvant regimens after TURBT, accompanied by vigilant cystoscopic monitoring, might offer more effective bladder-sparing approaches, minimizing the need for radical cystectomy. The forthcoming outcomes from ongoing trials involving combinations of Bacillus Calmette\u2013Gu\u00e9rin (BCG) vaccine and promising immunotherapies have the potential to reshape the current therapeutic landscape for high- and very high-risk NMIBC subgroups, thereby amplifying the significance of robust risk stratification strategies.4The anticipation of CSS, representing the paramount ultimate endpoint within oncological investigations, holds profound significance within the context of NMIBC. Future research endeavors pertaining to the prediction of progression-free and cancer-specific survival in NMIBC should be directed towards identifying strategies for precisely categorizing the subset of patients with the highest risk, necessitating intensified therapeutic interventions and meticulous surveillance. The development and implementation of innovative therapeutic paradigms remains an unmet need, particularly for individuals with high- and very high-risk NMIBC."} +{"text": "Comorbidity with Obsessive Compulsive Disorder (OCD) in patients with bipolar disorder (BD) affects from 10 to 20% of the clinical samples considered. The pharmacological treatment of these patients emphasizes the clinical issue of the use of serotonergic anti-obsessive agents, which may increase the risk of manic/mixed episodes or may accelerate a rapid cycle course. In some cases, the addition of a second stabilizer drug results in improvement in both mood disorder and comorbid obsessive psychopathology. Although off-label, the use of II generation long-acting injectable antipsychotics (LAI-2) in type I BD is widespread in clinical practice but data regarding their efficacy in improving obsessive symptoms of the eventual comorbid disorder are still lacking.The aim of this open-label naturalistic study was to evaluate the efficacy and safety of adjunctive treatment with LAI-2 monthly paliperidone palmitate (PP1M-LAI) and monthly aripiprazole (ARI-LAI) in 24 bipolar type I BD patients with OCD comorbidity, in a real-world clinical setting of 3 outpatient services located in the 3 macro-areas of Northern, Central and Southern Italy.Twenty-four patients diagnosed with type I BD and comorbid OCD were recruited and observed over a 24-week period after the add-on of PP1M-LAI or ARI-LAI to stabilizing therapy. Psychopathology assessment was performed by means of Yale-Brown Obsessive Compulsive Scale (YBOCS), Hamilton Depression Rating Scale (HDRS), Brief Psychiatric Rating Scale (BPRS), Young Mania Rating Scale (YMRS), Hamilton Anxiety Rating Scale (HARS). The mean PP1M-LAI dosage was 117.8 mg/month while that of ARI-LAI was 400 mg/month.At the end of the observation period, all patients who completed the study demonstrated a consisten reduction in obsessive symptoms while maintaining effective mood stability in the absence of signs of hypomanic/manic change . The relatively small number of patients recruited did not allow to detect significant differences in the performance of PP1M and ARI-LAI. Overall tolerability was good for both treatments, in line with the tolerability profiles of each drug.While considering the limitations of the relatively small sample and the open-label design, the results of this study indicate that the two LAI-2, PP1M and ARI-LA,I can be considered an effective and well-tolerated treatment in type I BD patients with OCD comorbidity, confirming efficacy in mood stabilization and reducing obsessive symptoms. Further studies on larger samples will be needed to confirm these preliminary findings and to detect any performance difference between the two antipsychotics.None Declared"} +{"text": "Paediatric heart transplant patients are disproportionately affected by Epstein-Barr virus (EBV)-related post-transplant lymphoproliferative disease (PTLD) compared with other childhood solid organ recipients. The drivers for this disparity remain poorly understood. A potential risk factor within this cohort is the routine surgical removal of the thymus\u2014a gland critical for the normal development of T-lymphocyte-mediated antiviral immunity\u2014in early life, which does not occur in other solid organ transplant recipients. Our study aims to describe the key immunological differences associated with early thymectomy, its impact on the temporal immune response to EBV infection and subsequent risk of PTLD.Prospective and sequential immune monitoring will be performed for 34 heart transplant recipients and 6 renal transplant patients (aged 0\u201318 years), stratified into early (<1\u2009year), late (>1\u2009year) and non-thymectomy groups. Peripheral blood samples and clinical data will be taken before transplant and at 3, 6, 12 and 24 months post-transplant. Single cell analysis of circulating immune cells and enumeration of EBV-specific T-lymphocytes will be performed using high-dimensional spectral flow cytometry with peptide-Major Histocompatibilty Complex (pMHC) I/II tetramer assay, respectively. The functional status of EBV-specific T-lymphocytes, along with EBV antibodies and viral load will be monitored at each of the predefined study time points.Ethical approval for this study has been obtained from the North of Scotland Research Ethics Committee. The results will be disseminated through publications in peer-reviewed journals, presentations at scientific conferences and patient-centred forums, including social media.ISRCTN10096625. This is the first prospective study to monitor the temporal immune response to Epstein-Barr virus (EBV) infection within a group of patients known to be at a high risk of developing post-transplant lymphoproliferative disease.The integration of data from clinical parameters, in-depth immunophenotyping and EBV-specific T-lymphocyte functional assay permits robust analysis of potential predictive immune biomarkers.The multicentre study design optimises recruitment of participants.The primary study limitation is the low incidence of paediatric heart transplantation, which may affect the rate of study recruitment.Post-transplant lymphoproliferative disease (PTLD) is the most common childhood cancer in paediatric recipients of a solid organ transplant. This heterogeneous group of life-threatening lymphoid malignancies is typically driven by Epstein-Barr virus (EBV) infection.1 3PTLD has one of the worst clinical outcomes among childhood lymphomas. The estimated 2-year event-free survival (EFS) is 70% compared with 94% in sporadic cases within the general paediatric population.9The pathogenesis of PTLD is complex and multifactorial. It involves the interplay between EBV-driven lymphoproliferation, iatrogenic immunosuppression and the suspected functional exhaustion of T-lymphocytes due to graft-initiated chronic antigen stimulation.10In paediatric heart transplant patients, cardiac surgery via median sternotomy in early childhood often requires routine thymectomy in order to access the heart and great vessels. Our earlier study retrospectively examined risk factors for PTLD in the largest UK cohort of paediatric orthotopic heart transplant patients to date.12 13During the first year of life, the thymus plays a crucial role in the development of cell-mediated immunity, providing a microenvironment for precursor T-lymphocytes to proliferate and differentiate into mature (na\u00efve) T-lymphocytes.This study aims to investigate the development of EBV-specific immune responses following childhood heart transplant. Specifically, it aims to identify the impact of early thymectomy\u2014compounded by iatrogenic immunosuppression\u2014on EBV immunology and the risk of PTLD.We hypothesise that a combination of early thymectomy and lifelong immunosuppression therapy establishes a tolerogenic immune profile consisting of dysregulated, exhausted and senescent immune cell subsets, poorly able to control EBV infection. This dysfunctional immune microenvironment permits the uncontrolled proliferation of EBV-infected B-lymphocytes and the subsequent development of PTLD.The Immunology of THymectomy And Childhood CArdiac transplant (ITHACA) study is a prospective nationwide cohort study recruiting children (0\u201318 years) from the two UK centres currently commissioned to provide paediatric heart transplant services: The Freeman Hospital, Newcastle upon Tyne and Great Ormond Street Hospital for Children, London. The study cohort will consist of 34 prospective heart transplant recipients and a non-thymectomy age-matched control group made up of 6 renal transplant recipients. All patients meeting the study\u2019s eligibility criteria will be identified and recruited through their local transplant teams at the time of listing for cardiac or renal transplantation. The study opened to patient recruitment in March 2022 and is expected to recruit until June 2024.Aged 0\u201318 years.Actively listed on the National Health Service Blood and Transplant (NHSBT) waiting list for a primary organ transplant or awaiting transplant with a living related donor kidney or recently transplanted with pretransplant blood samples available.Written informed consent.Has a pre-existing diagnosis of an inherited or acquired immunodeficiency.Has an underlying thymic disorder.Has previously received a bone marrow or organ transplant.Has had a previous cancer diagnosis.Withheld consent.Weight under 2.5 kg.Informed consent will be obtained from the parent/carer of the eligible child or from the patient themselves if over the age of 16 years. Assent may be given by children<16 years of age who wish to do so.A deferred consent approach will be employed for potential study participants who attend a research site\u2019s transplant service for transplantation in a critical/life-threatening clinical situation. This will involve the collection of baseline study samples from potential participants at the point of presurgical workup without written informed consent being received. Discussion about the study, the giving of participant information sheet (PIS) and receiving of written informed consent/assent will be offered at a more appropriate time before further follow-up blood tests are taken. Such cases will require that the clinical team considers obtaining informed consent prior to transplant to be inappropriate. This will be documented in the patient\u2019s clinical notes. Study samples collected under such circumstances will be processed for storage but not analysed until written informed consent is obtained. Any patient who has study samples collected by deferred consent but subsequently declines enrolment in the study will have their samples destroyed in a timely manner according to local laboratory standard operating procedures. Additional consent will be sought to store specimens for future ethically approved research.Children will undergo blood sampling for study-specific investigations during routine clinical visits prior to transplant and at 3, 6, 12 and 24 months post-transplant . No addi10.1136/bmjopen-2023-079582.supp1Supplementary dataStudy investigations will consist of:Immunophenotyping of circulating immune cell subsets.EBV serology.EBV-specific T-lymphocyte quantification.EBV-specific T-lymphocyte functional analysis.Circulating immune cell populations will be analysed in Newcastle University laboratories. Mononuclear cells (MNCs) will be isolated and cryopreserved from blood samples taken at each study time point. In addition, biobanked MNC samples from age-matched healthy children will be included for analysis as non-thymectomy, non-transplant controls. Circulating immune cell subsets will be identified within samples using high-dimensional spectral flow cytometry (Aurora system (Cytek)). The 5-laser Aurora spectral cytometer enables an in-depth analysis of up to 40 cell surface markers at a time.Major innate/adaptive cell lineages.Main T-lymphocyte subsets as well as putative T-helper subsets.Recent thymic activity.Cellular exhaustion and senescence.Key innate/adaptive cells involved in immune response to EBV infection.Two full spectrum flow panels have been validated for this purpose. A 24-colour panel has been designed to probe the wider circulating immune landscape of the study cohort . This isRoutine blood samples for evaluation of EBV serology will be tested centrally in the Newcastle upon Tyne NHS Hospitals Foundation Trust (NUTH) virology laboratories. EBV and CMV viral load will be measured from whole blood using PCR assays. Serum and/or plasma will be tested for antibody response to key EBV proteins including IgM/IgG for viral capsid antigen and IgG for EBV Nuclear Antigen 1. The results for viral load assay will be reported as total titres while antibody testing will be reported as a binary detected/not detected based on NUTH laboratories reference cut-off values.An optimised panel of Human Leucocyte Antigen (HLA)-restricted peptide-Major Histocompatibility Complex (pMHC) I/II tetramers will be used to evaluate EBV-specific CD8 and CD4 T-lymphocyte immunity at the time points outlined in To assess the functional capacity of EBV-specific T-lymphocytes in an HLA-unbiased manner, effector cytokine production of interferon gamma will be determined by ELISpot following stimulation with pools of overlapping peptides (JPT PepMix) representing the full sequences of a panel of EBV latent and lytic cycle proteins.20 21Study data will be collated and managed using Research Electronic Data Capture (REDCap) electronic case report forms.23Primary outcomes measures:Proportions of circulating innate and adaptive immune cell subsets before and at 3, 6, 12 and 24 months post-transplant.Frequency of detectable EBV-specific T-lymphocyte immunity.Functional capacity of EBV-specific T-lymphocytes.Secondary outcome measures:Incidence of EBV infection.Time from transplantation to EBV viraemia.Time from EBV viraemia to seroconversion.As the study objectives are largely descriptive, no sample size calculation is necessary. Instead, we selected our sample size such that the study is feasible and large enough to conduct comprehensive analyses. Therefore, our sample size is based on a national average of 30 childhood cardiac transplants per year,https://www.omiq.ai/). Automated clustering and dimensionality reduction will be used to identify immune cell populations by FlowSOM and Uniform Manifold Approximation and Projection, respectively. These techniques overcome the practical challenges associated with manual gating and user bias when analysing datasets from large flow panels.Data from spectral flow cytometry will be analysed using the OMIQ platform . Continuous variables will be assessed by Pearson correlation using the single linkage method to group patients by expression values, and non-continuous variables by non-parametric Spearman correlation, as appropriate. Viral loads will be serially quantified at each study time point to correlate changes in immune responses with the volume of circulating virus-infected cells. Tetrameric frequencies for population groups will be compared using Mann-Whitney U test and between time points for paired patient sample using Wilcoxon signed-rank test.The Young Person\u2019s Advisory Group North England (YPAGne) was involved in the development of the study design, patient facing documents and the informed consent process. Ongoing consultation with YPAGne will continue to influence participant recruitment, outcome measure priorities and the acceptability of study methods.The ITHACA study has both research governance and ethical approvals and is adopted onto the National Institute for Health Research Clinical Research Network portfolio. Study organisation and sponsorship will be provided by The Newcastle upon Tyne Hospitals NHS Foundation Trust including coverage of insurance and NHS indemnity.No significant risks are anticipated for enrolled participants. Study samples will be taken at the same time as routine transplant investigations during clinic visits, thereby avoiding any additional discomfort or hospital attendance. The estimated volume of study-related blood samples required at each assessment time point is based on guidance from the WHO for trial-related blood volumes in children.Study findings will be disseminated widely through publications in high impact peer-reviewed journals, national and international conferences, and stakeholder events. We will engage YPAGne to identify patient-centred forums to facilitate discussion of study progress and any relevant findings with the general public. Published data will be made available via a public data repository, with a digital object identifier included in any published manuscript to aid discovery and outline access conditions. Potentially identifiable data, including patient sex, date of birth and date of transplant, will not be shared. Any unpublished data will only be shared with other parties where a data access agreement has been negotiated by Newcastle University Legal Services team on behalf of the study\u2019s chief investigator."} +{"text": "Antimicrobial stewardship (AS) programs aim to slow the growing threat of antimicrobial resistance. The majority of antibiotic prescribing occurs in outpatient settings. This study examines the effect of an AS intervention bundle on the proportion of inappropriate antibiotic prescriptions given to adult patients with bronchitis in outpatient settings of a large healthcare system.The Institutional Review Board approved this retrospective study of antibiotic prescription rates for adults (\u226518 years old) diagnosed with bronchitis (identified using ICD-10 codes J20.9 or J20.8) during 2020 and 2021 in outpatient settings. An AS intervention bundle involving training and auditing of physicians\u2019 antibiotic prescribing habits was enacted in January of 2021. A total of 8,176 encounters were reviewed for appropriateness of antibiotic prescriptions. Instances where no antibiotics were prescribed or antibiotics were prescribed for a comorbid condition were considered appropriate. Percentages of inappropriate antibiotic prescribing pre- and post-intervention were then compared via Chi-square analysis using SAS Enterprise Guide version 7.15 software.The proportion of inappropriate antibiotic prescribing for bronchitis decreased significantly from 44.9% pre-intervention to 32.5% post-intervention (p< 0.0001). Comparison of inappropriate prescribing rates by month showed significant decreases between the pre- and post-intervention periods in March , October , and November .AS activities can decrease inappropriate antibiotic prescribing for bronchitis in outpatient settings. Further analyses on site-specific, seasonal and demographic differences on the effect of our AS intervention bundle may further enlighten on how programs can decrease unnecessary antibiotic use for respiratory tract infections.All Authors: No reported disclosures"} +{"text": "An 84-year-old man presented to the emergency department with sudden, left lower quadrant cramping pain. Because critical hypotension was noted, point-of-care ultrasonography (POCUS) was performed immediately. The study revealed a pulsatile flow extravasating from the left common iliac artery into the left psoas muscle with hypoechoic para-aortic fluid collection.Common iliac artery rupture is rare and has nonspecific clinical presentations. A quick disposition can be made with a combination of clinical manifestations and POCUS results. An 84-year-old man with a history of hypertension and peripheral arterial occlusive disease presented to the emergency department (ED) with sudden onset of left lower quadrant (LLQ) cramping abdominal pain. The patient was in stable condition with blood pressure 129/61 millimeters of mercury (mm Hg), heart rate 78 beats per minute, and 99% oxygen saturation on room air without respiratory distress on arrival to the ED. Physical examination disclosed mild tenderness over LLQ of abdomen. There was a sudden drop in blood pressure to 66/41 mm Hg with altered consciousness with a Glasgow Coma Score of three , while waiting for lab results.Point-of-care ultrasound (POCUS) over the LLQ of the abdomen showed a left common iliac artery with a demarcated arterial mural defect . PulsatiCommon iliac artery rupture is rare and often results from iliac artery aneurysms, dissection, connective tissue disorders , atherosclerosis, or even iatrogenesis.4What do we already know about this clinical entity?Common iliac artery rupture is a rare but serious condition often associated with aneurysms, dissection, or connective tissue disorders.What is the major impact of the image(s)?The images obtained through point-of-care ultrasonography (POCUS) help in timely diagnosis and guide emergent percutaneous angioplasty, potentially preventing fatal outcomes.How might this improve emergency medicine practice?Increased awareness of this condition and liberal use of POCUS can lead to quicker diagnosis and prompt intervention, improving patient outcomes in cases of common iliac artery rupture.Video 1Point-of-care ultrasound over the left lower quadrant of the abdomen showed a left common iliac artery with demarcated arterial mural defect.Video 2Point-of-care ultrasound in transverse view over left lower quadrant of abdomen demonstrating a pulsatile extravasating flow from the left common iliac artery with hypoechoic para-arterial fluid collection."} +{"text": "Plant biology research has currently entered the post-genomics era with the advances in genomic technologies. The unprecedented development of genomics and application in crops is driving a new \u201cgreen revolution\u201d in agriculture. With the high-quality genomes of many important crops , numerous genes controlling the agronomically important traits have been identified and the underlying mechanisms have been revealed.Modern plant genomics can boost research progress in several aspects: (1) omics data provide a comprehensive exploration of a given gene family in a genome-wide, sometimes genus-wide manner; (2) high-quality genomes and large-scale sequencing data allow the identification of single nucleotide polymorphism (SNP) and structural variations, facilitating quantitative trait loci (QTL) or genome-wide association (GWAS) studies to rapidly identify genetic loci for agronomic traits; (3) combining with other omics, such as metabolomics, quantitative proteomics, epigenomics and epitranscriptomics, multi-omic approaches can gain new insights into a biological question even without an available reference genome.Triticum aestivum L.), rice (Oryza sativa L.), maize (Zea mays L.), soybean (Glycine max L.), cotton (Gossypium hirsutum L.), rapeseed (Brassica napus L.), tea plant (Camellia sinensis (L.) O. Kuntze), flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) and many others. These studies fall into four themes of plant genetics and genomics: (1) Genome-wide characterization of gene families in plants; (2) Functional studies of genes regulating various traits in plants; (3) Dissecting important agronomic traits through population genetics; (4) Multi-omic analysis facilitates plant functional genomic and genetic improvement studies. This Editorial paper aims to showcase the Topic and discuss the related perspectives.In this context, the present Topic \u201cPlant Functional Genomics and Crop Genetic Improvement\u201d provides a forum for researchers to communicate their latest findings related to plant functional genomics and the corresponding applications in crop genetic improvement. We collaborate with several related journals, including Agronomy, Crops, International Journal of Molecular Sciences, Life and Plants, to cover such a broad-range theme. This Topic has collected a set of 51 papers (three reviews and 48 research articles) with a relatively low acceptance rate (~25%), covering several species including wheat (SHMT), 227 genes of basic leucine zipper (bZIP) and 10 genes of catalases (CATs) were identified in wheat, and the members with potentially regulating plant growth and the responses to various abiotic stresses were explored in several studies varieties with contrasting resistance to the pseudo-rust revealed the regulatory networks responsive to the pseudo-rust, highlighting that oxidation-reduction process, flavonoid biosynthesis and ABA signaling genes may be associated with the response to pseudo-rust infection [Panax ginseng) cultivars suggested that 22 candidate genes involved in ginsenoside Rb1 biosynthesis [Vicia sativa L.) seeds [Gossypium stocksii (purple fiber) and Gossypium arboreum (white fiber) revealed that the key PA biosynthetic genes are responsible for fiber coloration in G. stocksii, which improved our understanding in the molecular mechanisms of cotton fiber coloration [Calotropis gigantea and zoysiagrass (Zoysia japonica), respectively, also helped to obtain insights into the molecular responses to Cd stress and rust resistance, respectively [Comparative transcriptome analysis of two pueraria [nfection . The traynthesis . By comb.) seeds , Li et aloration . Two comectively ,44.Verticillium dahliae stress, providing several candidate genes for further improving Verticillium wilt resistance of cotton [In addition to transcriptomic analysis, multi-omic approaches combining multiple omic datasets are more powerful in gaining insights from a system biology point of view. The integrative omic analysis of mRNA and miRNA expression in cotton revealed some key genes/modules involved in the response to f cotton .Camellia sinensis cv. Zikui) by metabolomics and transcriptomics. Three anthocyanins, petunidin 3-O-glucoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside, were the major anthocyanins in the leaves of Zikui. CsMYB90 was identified as an important regulator controlling the synthesis of the three anthocyanins [Cai et al. revealed the mechanism of anthocyanin biosynthesis in the purple-leaf tea cultivar Zikui and their promoters in hexaploid triticale using cas9-targeted nanopore sequencing (nCATS) technology, disclosing the potential of the nCATS approach for sequencing target genes in large genome size plants [Besides the omics and sequencing tools, other molecular techniques showcase their promising use. Kirov et al. sequenced the full-length glutenin genes The genome-wide analysis may be enhanced by comparative analysis in multiple evolutionarily related species to take advantage of the evolution, family expansion/contraction, and expression conservation and divergence between species; (2) Omics data facilitate the narrow down of genetic loci and the underlying candidate genes, thus improving the efficiency of QTL mapping and GWAS studies; (3) Multi-omic analysis could rapidly gain novel insights into a particular biological process, especially in less-studied species. in turn, the identified key candidate genes or regulatory relationships may be functionally characterized in model plants . Utilizing the research trends will certainly strengthen the quality of plant functional genomic studies or genetic improvements. Moreover, application of the cutting edge technologies will further push forward crop functional genomics."} +{"text": "To profile immunological changes in healthy and acute myeloid leukemic (AML) patients\u2019 ex vivo cell cultures, we correlated the cell biological data with the profiles of cell culture supernatant-derived VOCs. DC/DCleu from leukemic or healthy whole blood (WB) were generated without (Control) or with immunomodulatory Kit M (Granulocyte macrophage-colony-stimulating-factor (GM-CSF) + prostaglandin E1 (PGE1)) in dendritic cell cultures (DC culture). Kit-pretreated/not pretreated WB was used to stimulate T cell-enriched immunoreactive cells in mixed lymphocyte cultures (MLC culture). Leukemia-specific adaptive and innate immune cells were detected with a degranulation assay (Deg) and an intracellular cytokine assay (InCyt). Anti-leukemic cytotoxicity was explored with a cytotoxicity fluorolysis assay (CTX). VOCs collected from serum or DC- and MLC culture supernatants (with vs. without Kit M pretreatment and before vs. after culture) were measured using eNose. Compared to the Control (without treatment), Kit M-pretreated leukemic and healthy WB gave rise to higher frequencies of mature (leukemia-derived) DC subtypes of activated and (memory) T cells after MLC. Moreover, antigen (leukemia)-specific cells of several lines (innate and adaptive immunity cells) were induced, giving rise to blast-lysing cells. The eNose could significantly distinguish between healthy and leukemic patients\u2019 serum, DC and MLC culture supernatant-derived volatile phases and could significantly separate several supernatant -derived VOCs within subgroups . Interestingly, the eNose could indicate a Kit M- and culture-associated effect. The eNose may be a prospective option for the deduction of a VOC-based profiling strategy using serum or cell culture supernatants and could be a useful diagnostic tool to recognize or qualify AML disease.Volatile organic compounds (VOCs) reflect the metabolism in healthy and pathological conditions, and can be collected easily in a noninvasive manner. They are directly measured using electronical nose (eNose), and may qualify as a systemic tool to monitor biomarkers related to disease. Myeloid leukemic blasts can be transformed into leukemia-derived dendritic cells (DC AML is a clonal stem cell disorder of the hematopoiesis, which comes with uncontrolled proliferation of myeloid progenitor cells (blasts) . Cytocheleu, leukemia-derived DC; without induction of blast proliferation) from AML patients\u2019 WB in the presence of different combinations of response modifiers (Kits) . Its 32 sensors have a variation of coefficient of 2\u201310%. The addition of all 32 signals and the determination of the precision of the total signal finally resulted in a mean coefficient of variation of 4.64%. Digitally sensed VOCs using an electronic nose have the potential to become a rapid, immediate, and non-invasive diagnostic tool. With the advent of inexpensive, environmentally friendly, and biocompatible sensor systems, health monitoring using VOCs may transform laborious or invasive procedures that currently can only be used in facilities specialized for this purpose into a technology that can be used anywhere and anytime by individuals.An electronic nose such as the one used here utilizes a standardized approach. An important requirement is that its sensors work correctly, and the 32 sensors of the eNose indicate correct reference ranges. Moreover, sensors must be trained with a training set before the start of measurements and must be regularly calibrated. In contrast to other methods, such as ion mobility spectrometry or mass spectrometry, identification of the individual component in a mixture is usually not possible here or is only possible under very restricted conditions . Consequmat secrete different exosomes compared to immature DCs . Exosomes from mature DCs (compared to immature DCs) can be enriched with MHC class II, B7.2, and ICAM-1, and depleted in MFG-E8 [Analyses of different cellular/humoral, soluble factors ,22,23,24n MFG-E8 .p = \u22120.0158) (A culture effect could be detected by the eNose in leukemic MLC culture supernatant-derived VOCs. VOCs collected before culture were significantly different compared to after culture (leukemic MLC: \u0394\u22120.0158) . These VWith respect to culture effects, we found significant differences in the VOC profiles of healthy DC culture supernatants (independent of the addition of Kit M), whereas the culture effects of AML samples in the same settings were not different. These findings might be explained by the different compositions of DC culture supernatants in healthy vs. AML DC culture supernatants; healthy samples contain higher frequencies of \u2018healthy cells\u2019, and AML samples contain high frequencies of blasts. After culture, different releases of VOCs in the different settings might explain the good differentiation of healthy DC supernatant VOCs, but not AML DC culture supernatant VOCs.With respect to Kit M-mediated effects, we found significant differences in the VOC profiles of healthy DC culture supernatants when comparing Kit M-pretreated vs. non-pretreated samples, whereas the culture effects of AML samples in the same settings were not different. These findings might be explained by different DC compositions in healthy vs. AML DC culture supernatants; healthy samples yield higher frequencies of mature monocyte-derived DCs, and AML samples yield (in addition) leukemia-derived DCs and blasts, which may proliferate/differentiate and produce leukemia-associated VOCs.Moreover, AML patients\u2019 DC supernatants might contain traces of drug (derivates) after chemotherapy and antibiotic/antimycotic therapy, which could be responsible for alternated VOC profiles compared to healthy DC culture supernatant-derived VOCs.With respect to culture effects, we found no significant differences in the VOC profiles of healthy MLC supernatants (independent of Kit M addition), whereas the culture effects of AML samples in the same settings were significantly different. These findings might be explained by different MLC-related supernatants in healthy vs. AML MLC supernatants .With respect to Kit M-mediated effects, we did not find significant differences in the VOC profiles of healthy MLC supernatants when comparing Kit M-pretreated vs. non-pretreated samples, whereas the culture effects of AML samples in the same settings were significantly different. These findings might be explained by the different compositions of immune cells in AML vs. healthy cells; the activation of leukemia-specific immune reactive cells in AML cases might yield significantly different VOCs under the influence of Kit M vs. Control.We could deduce the following culture and Kit M-related effects detectable by VOC profiles in healthy and AML cultures:This means that culture alone gives rise to other changes in healthy and AML VOC profiles; the presence of Kit M changes the setting and produces different results in AML and healthy VOC samples. We have shown that the role and metabolic influences of drugs of different cellular compositions with respect to qualitative/quantitative differences in VOC release profiles are complex, although our chosen technology yielded differences in different settings. Other strategies or more standardized settings might contribute to more refined VOC-based monitoring strategies in the future. According to our results, eNose analyses might then yield a prospective option for deriving a VOC-based disease profiling strategy using serum or cell culture supernatants from patients with leukemia. Due to rapid sample collection and analysis, the present study shows good reproducibility of data. It could therefore be recommended to include VOC analyses as an additional component to monitor the course of disease, and potentially to guide therapy-related decisions."} +{"text": "Development of resistance to androgen deprivation therapy (ADT) is a major obstacle for the management of advanced prostate cancer. Therapies with androgen receptor (AR) antagonists and androgen withdrawal initially regress tumors but development of compensatory mechanisms including AR bypass signaling leads to re-growth of tumors. MicroRNAs (miRNAs) are small regulatory RNAs that are involved in maintenance of cell homeostasis but are often altered in tumor cells.In this study, we determined the association of genome wide miRNA expression (1113 unique miRNAs) with development of resistance to ADT. We used androgen sensitive prostate cancer cells that progressed to ADT and AR antagonist Casodex (CDX) resistance upon androgen withdrawal and treatment with CDX. Validation of expression of a subset of 100 miRNAs led to identification of 43 miRNAs that are significantly altered during progression of cells to treatment resistance. We also show a correlation of altered expression of 10 proteins targeted by some of these miRNAs in these cells.We conclude that dynamic alterations in miRNA expression occur early on during androgen deprivation therapy, and androgen receptor blockade. The cumulative effect of these altered miRNA expression profiles is the temporal modulation of multiple signaling pathways promoting survival and acquisition of resistance. These early events are driving the transition to castration resistance and cannot be studied in already developed CRPC cell lines or tissues. Furthermore our results can be used a prognostic marker of cancers with a potential to be resistant to ADT. Prostate cancer is the most commonly diagnosed cancer and a leading cause of cancer related death in men in developed countries. Because androgen is required for normal growth and functioning of the prostate gland and also for development of cancer androgen deprivation therapy (ADT) has become the mainstay for advanced prostate cancer . AlthougDevelopment of resistance to ADT, which includes reduction in androgen synthesis and direct antagonism of the androgen receptors (AR), can occur as a result of high expression and activation of AR . Activathttp://www.mirbase.org Nov 2011). Genes encoding miRNAs are located in the intergenic regions or within the protein-coding genes either alone or in clusters [The role of small noncoding microRNAs (miRNAs) in regulation of gene expression, which is mediated by inhibition of translation or degradation of target mRNAs is an established phenomenon . MiRNAs clusters . There iclusters ,17. The clusters . Becauseclusters . BecauseA number of studies indicated aberrant expression of miRNAs in CRPC compared to AD prostate cancer cells ,21. SeveWe used genome-wide miRNA array (1113 unique primers) profiling approach to identify specific miRNAs that are involved in development of resistance to Casodex (CDX). A clonal subline of LNCaP cells LNCaP-104S (-104S) and its androgen-independent derivative LNCaP-104R1 (-104R1) were used for monitoring differential expression of miRNAs upon treatment with CDX. LNCaP-104S cells are CDX-sensitive, whereas LNCaP-104R1 cells are not despite expressing AR at a basal level higher than LNCaP-104S cells . LNCaP-12 transformed expression data values of four treatment conditions compared to -104S untreated cells showed two distinct clusters of up and down regulated miRNAs, which includes 307 down regulated and 197 up regulated miRNAs for different time periods. Two sample Welch t-test with a 2 transformed FC in expression of 100 miRNAs showed three distinct clusters displaying common expression changes in 2 time points of two eatment conditions. Two clusters contained miRNAs with increased expression and one cluster containing down regulated miRNAs and down-regulated miRNAs (miR-15b-3p and miR-18b). Although we noted differential expression of miRNAs between CS-FBS and CDX treated LNCaP cells we selected only miRNAs that showed either up regulation or down regulation in all treated samples for analysis of their putative targets. Despite similar expression profile of specific miRNAs in CS-FBS and CDX treated samples, some the targets such as DOK4 and VEGF showed differential expression in CSFBS and CDX treated cells. Presumably, this could be the effect of regulation of multiple targets by a given miRNA, which may indirectly affect the net expression of DOK4 and VEGF.Over expression of miR-146a was noted in all treated cells contrary to the study showing loss of expression of miR-146a in CRPC . IncreasThe EGFR signaling pathway could be activated also in the early stages of androgen blockade and CDX treatment. The evidence of EGFR pathway activation in the treated -104S cells is from our results showing an increased expression of EGFR, down regulation of miR-7 and up-regulation miR-222, which are the miRNA regulators of EGFR. Decreased expression of p27Kip1 and Cbl, as two other targets of the up-regulated miR-222, further aid activation of EGFR signaling. C-Cbl, an E3 ubiquitin ligase, inactivates ligand-bound EGFR through EGFR-Cbl complex formation leading to its degradation . C-Cbl aActivation of PI3K/AKT signaling axis also could be predicted in treated -104S cells, as a result of down regulation of miR-7, which inhibits tumor growth and metastasis through inhibition of PI3K/AKT pathways ,140. DowOther than modulation of specific signaling axis, altered expression of miRNA clusters is also evident in our study. Members of the miR-17-92 and its paralogous miR-106a-363 clusters, miR-17, miR-18a, miR-18b, miR-20a and miR-106a showed ~9-10-fold down regulation upon CDX treatment and androgen blockade. In support of our observation, loss of expression of miR-17 , miR-18aAdditional miRNAs such as miR-518b, miR-205 and miR-596 showed\u2009>\u200910-fold loss of expression upon CDX treatment or androgen withdrawal. In support of our observation, loss of expression and tumor suppressor functions of mir-518b and miR-596 has been documented in other cancers . MiR-124Functional contribution of some of the identified microRNAs in development of CRPC has been previously reported. Over expression of miR-222/221 in AI LAPC4 cells was shown to promote androgen independent cell growth, which was abrogated upon expression of anti-miR-222/221 inhibitors . Down reAnalysis of the altered cellular processes during progression towards CDX resistance and androgen independence showed a decreased percentage of miRNAs involved in cancer but an increased percentage in reproductive system, endocrine system, hepatic system and metabolic diseases. It can be speculated that up regulated oncomirs at earlier stages aid in transformation of cells through suppression of tumor suppressors. Whereas, at later stages accumulation of abnormal cellular events triggers expression of additional sets of miRNA, which inhibit key regulatory proteins involved in metabolic process, hormone response and other cellular events. Our qRT-PCR FC data indicate differential expression of miRNAs between 1wk and 3wks treatment, which would have been undetected had the profiling been done only in CDX sensitive/AD and \u2013resistant/AI cells. In silico analysis identified a number of targets that are potentially regulated by one or more altered miRNAs. This includes, two mitosis regulatory proteins CCNJ and CHAMP1 (ZNF828) ,121, twoIn summary, our results and in silico network analysis suggest that inhibition of expression of TP53, BRCA, Toll like receptors, IRAK1, STAT1, CHUK and FADD by the up regulated miRNAs, and increased synthesis of EGFR, NFkB1/RelA, E2F family members, BCL2L2, ZBTB7A, EGO2 (EIF2C2) and ZEB2 as the targets of down regulated miRNAs are part of the events that support growth and survival of AI LNCaP cells. During treatment with AR antagonist in androgen-deprived condition, additional inhibition of expression of DDX20, URF1, IRF5 and CDKN3 as the targets of the up regulated miRNAs and increased expression of PRDM1, DOK4, TNFSF9 and NOTCH2 as a result of down regulated miRNAs may provide additional protection against CDX induced cell death. In-depth studies are needed to accurately determine the activation and inactivation of specific signaling pathways during development of insensitivities of prostate cancer cells to AR antagonistic drugs.The overall evaluation of the changes in expression profiles of miRNAs during transition of CDX sensitive and AD cells to the CDX resistant and AI ones demonstrates that not any one or two miRNAs are responsible for development of drug-resistant prostate cancer. Instead, a complex network of activation and inactivation of specific signaling pathways aided by degradation or accumulation of the target mRNAs as a result of differential expression of a significant number of miRNAs plays the pivotal role. Also, there are transient changes in the expression of miRNAs as well as their target proteins during transition of cells towards ADT resistance, which may provide growth and survival advantage to a subset of cancer cells; and these changes in miRNA/mRNA signature may be missed in already developed castration resistant prostate cancer. This study provides a predictive tool for monitoring the susceptibility of development of anti-androgen therapy resistant prostate cancer.The androgen responsive LNCaP-104S and androgen independent LNCaP-104R1 cells were generous gifts from Dr. Shutsung Liao, University of Chicago. These LNCaP sublines were isolated and characterized as previously described . LNCaP-1Total RNA was extracted from untreated and treated cells using the Cell-to-Cts kit (System Biosciences) according to the manufacturer\u2019s instructions. Total RNA was converted to cDNA utilizing the QuantiMir RT Kit (System Biosciences) according to the manufacturer\u2019s instructions. Briefly, small RNAs were first tagged with polyA-tails; oligo-dT primers were annealed next, and converted to cDNA by reverse transcription.Expression of mature miRNAs in untreated and treated LNCaP cells was determined by quantitative real-time PCR (qRT-PCR) using the miRNome microRNA Profiling Kit (System Biosciences) and cDNAs according to the manufacturer\u2019s instruction. The kit provides specific primers for 1,113 mature miRNAs and 3 internal control snRNAs. MiRNA IDs listed in the text are based on Sanger miRBase identifiers. Primers were designed to maintain uniform amplification efficiencies. qRT-PCR was conducted using the Applied Biosystems 7900HT thermal cycler and data analyzed using and SDS2.3 software. DNA concentrations were reported through SYBR Green fluorescence and normalized to that of the passive reference dye, ROX.Ct values generated by the SDS2.3 software were normalized according to the average Ct values of the three internal controls provided with the miRNome Profiler kit using qbasePLUS software (Biogazelle). In order to ensure the integrity of the \u2206Ct values, we utilized the Genorm software (Biogazelle) to identify 7 additional miRNAs displaying stable expressions between samples. The Ct values of all miRNAs were then normalized to these 10 controls. The relative expression values were then generated using qbasePLUS software and used in additional analysis . Hierarchical clustering of the miRNAs was based on the average linkage of the Pearson\u2019s correlation values. The relative expression values were Log2 transformed and used for evaluation of differences among groups of treated and untreated cells by performing a Welch t-test using MultExperiment Viewer (MEV) software. Results of the t-test were displayed in Volcano plots using -log10 P values of the log2 transformed values. The K-median clustering of the normalized values were performed using MEV software.Clustering was performed using loghttp://bioinfogp.cnb.csic.es/tools/venny/index.html). The miRNA-protein network generated by the core analysis was overlayed with different cancer types and members of the network that displayed alterations in those cancers were identified using the Interactive Pathway Analysis (IPA) software (Ingenuity Systems). All connections made in the networks are based on previously published results.Next, identification of target mRNAs, creation of miRNA-protein networks, and identification of altered cellular processes were conducted using the IPA software (Ingenuity Systems). The \u2206\u2206Ct values were used for a core analysis by selecting all tissue and cell types and using a stringent filter and generating direct relationships only. From the core analysis, mRNA targets were identified for each sample and these mRNAs were used to generate the Venn diagrams using online tool , PSA , Cbl (C-15) , TRAF6 , p27Kip1 (C-19) , IRAK1 (F-4) , ZFAND1 (A-14) (Santa Cruz Biotechnology), FGD4 , ABHD3 , DOK4 (C-16) (Santa Cruz Biotechnology), EGFR (1005) (Santa Cruz Biotechnology), VEGFA (A-20) (Santa Cruz Biotechnology), \u03b1-tubulin , GAPDH . Total extracts (30\u201350\u00a0\u03bcg) were directly mixed with Lammeli sample buffer and separated on SDS-PAGE. Immunoblotting was performed using appropriate primary and horseradish peroxidase conjugated respective secondary antibodies. Positive signals were detected using a chemiluminiscence ECL kit .ADT: Androgen deprivation therapy; AR: Androgen receptor; MiRNA: MIcroRNA; AD: androgen dependent; AI: Androgen independent; CRPC: castration resistant prostate cancer; AS: Androgen sensitive; -104S: LNCaP-104S cells; -104R1: LNCaP-104R1 cells; CDX: Casodex; CDXR: Casodex resistant; V plot: Volcano plot; CSFBS: Charcoal stripped FBS; FC: Fold change; PSA: Prostate specific antigen.The author(s) declare that they have no competing interests.RO performed cell treatments, profiling and all validation experiments including western blots. He also did the hierarchical clustering and in silico analysis of the targets. He participated in manuscript writing. CN analyzed data using IPA software and performed cell treatment related experiments. RL analyzed data including data normalization, z score calculation and Venn diagrams. RC conceived the idea, wrote the manuscript and performed data analysis. All authors read and approved the final manuscript.Light micrograph images of LNCaP cells before and during treatment with CS-FBS and CDX.Click here for fileListing normalized and log-transformed values of the miRNA expression.Click here for fileHierarchical clustering of the data from genome wide miRNA profiling.Click here for fileListing the p-values, expression patterns and IDs of significant miRNAs identified in t-tests (supple Figure\u00a0Click here for fileVolcano plots of the two samples t-tests of the normalized values of untreated and treated LNCaP cells.Click here for fileListing the log-transformed fold change values of the up regulated and down regulated miRNAs identified in miRNA profiling.Click here for fileListing miRNAs in specific clusters identified in K-median cluster analysis.Click here for fileListing the p-values, expression profile and IDs of significant miRNAs from the list of validated miRNAs identified in two samples t-tests.Click here for fileListing the log-transformed values of the fold change in expression of the validated miRNAs.Click here for fileListing the up and down regulated subset of the validated miRNAs in specific clusters identified in K-median cluster analysis.Click here for fileAnalysis of association of deregulated miRNAs with canonical pathways and cellular processes.Click here for fileSupplemental methods and figure legends.Click here for file"} +{"text": "Delayed neutrophil apoptosis is often detected in inflammatory pathologies, including sepsis . CD24 isStaphylococcus aureus or heat-killed Escherichia coli and CD24 expression assessed by flow cytometry. Neutrophils were cross-linked with anti-human CD24 and assessed for apoptosis after 24 hours of culture. In some experiments, neutrophils were preincubated with caspase inhibitor (z-VAD-fmk) before crosslinking.Blood samples were either collected from healthy donors or from sepsis patients at the onset of sepsis and the two following days and surface CD24 expression on neutrophils was analyzed by flow cytometry. Peripheral blood neutrophils were purified from sepsis patients and healthy individuals by positive selection. Whole blood or neutrophils were challenged with lipopoplysaccharide (LPS), TNF, granulocyte-macrophage colony-stimulating factor (GM-CSF), heat-killed Ex vivo death responses after CD24 ligation in neutrophils from sepsis patients are currently under study.Surface expression of CD24 assessed by flow cytometry was significantly altered in neutrophils from sepsis patients compared with healthy controls. Activation of neutrophils with LPS or heat-killed bacteria in whole blood triggers a strong upregulation of CD24 at surface level despite no enhanced expression being observed when the activation was carried out in purified neutrophils. In contrast, TNF and GM-CSG upregulated CD24 in whole blood and in purified neutrophils. CD24 cross-ligation induces caspase-independent apoptosis in human neutrophils. This is the first report studying the role of CD24 in sepsis patients, linking homeostasis and apoptosis."} +{"text": "Purpose. To present a series of retinal disease cases that were imaged by spectral domain optical coherence tomography (SD-OCT) in order to illustrate the potential and limitations of this new imaging modality. Methods. The series comprised four selected cases (one case each) of age-related macular degeneration (ARMD), diabetic retinopathy (DR), central retinal artery occlusion (CRAO), and branch retinal vein occlusion (BRVO). Patients were imaged using the Heidelberg Spectralis in SD-OCT mode. Patients also underwent digital fundus photography and clinical assessment. Results. SD-OCT imaging of a case of age-related macular degeneration revealed a subfoveal choroidal neovascular membrane with detachment of the retinal pigment epithelium (RPE) and neurosensory retina. Using SD-OCT, the cases of DR and BRVO both exhibited macular edema with cystoid spaces visible in the outer retina. Conclusions. The ability of SD-OCT to clearly and objectively elucidate subtle morphological changes within the retinal layers provides information that can be used to formulate diagnoses with greater confidence. Over the past decade, the development of high-speed, wide-bandwidth tuneable light sources in conjunction with high-speed photodetectors has resulted in major gains in the horizontal and depth resolution of optical coherence tomography (OCT) based instrumentation, thereby dramatically improving visualization capabilities during retinal and optic nerve examination , 2. As aThe principle of OCT is based on interferometry , 4. In a\u03bcm, thereby permitting the acquisition of high-resolution, histological detail of the retina captured from the living human eye over a wide field of view. The much improved scan speed of SD-OCT also permits 3D scanning, with minimal impact of eye movements. The SD-OCT scans can also be referenced to simultaneously acquired 2D en-face images, thereby ensuring the accurate spatial location of each OCT A-scan within the 3D image. An example of SD-OCT imaging of a healthy retina is shown in SD-OCT has dramatically improved image resolution. Using SD-OCT, broadband interference is measured with spectrally distinct detectors using Fourier analysis , thereby avoiding path length adjustment of the reference arm. The avoidance of depth scanning results in dramatic gains in imaging speed and improved signal-to-noise ratio , with anIn this study, we report on the clinical application of SD-OCT using a series of case reports of patients with clinically defined common and/or classic eye diseases in order to highlight some of the potential, the limitations, and the clinical utility of this technology.\u03bcm). Patients also underwent pupil dilation, digital fundus photography, and clinical assessment. Digital fundus photography was undertaken using a Canon digital fundus camera with a resolution of 12.8 mega pixels. Clinical assessment comprised visual acuity, stereo fundus biomicroscopy, and binocular indirect ophthalmoscopy, as appropriate.Patients were imaged using the Heidelberg Spectralis HRA + OCT in SD-OCT mode, using a scan field of 30 degrees horizontally and 15 degrees vertically and 19 to 25 OCT horizontal sections can be used in any one of six imaging modes, that is, SD-OCT, fluorescein angiography, indocyanine green angiography, autofluorescence, and red-free and infrared imaging. This paper details use of the instrument in SD-OCT mode only. The Heidelberg Spectralis utilizes a broadband light source centered at 870\u2009nm to simultaneously measure multiple wavelengths, a prerequisite of SD-OCT imaging (Heidelberg Retina Angiograph 2 Operating Instructions). Simultaneous confocal scanning laser ophthalmoscopy is used to generate high-resolution images of the retinal surface, thereby providing precise location information of each A-scan within a cross-sectional SD-OCT image. SD-OCT scanning generates 40,000 A-scans/second with an axial resolution of 3.5\u2009microns/pixel digital and a transverse resolution of 14 microns [This series comprised four selected cases (one case each) of age-related macular degeneration (ARMD), diabetic retinopathy (DR), central retinal artery occlusion (CRAO), and branch retinal vein occlusion (BRVO). A 81-year-old female patient had a 20-year history of hypertension and a one-year history of type 2 diabetes. At first presentation, her best corrected visual acuity (VA) in the right (OD) and left (OS) eyes was 20/50 and 20/70, respectively. Intraocular pressures (IOPs) were 18\u2009mmHg OD and 20\u2009mmHg OS. Retinal examination revealed a large choroidal neovascular membrane (CNVM) and a probable serous pigment epithelium detachment (PED) OD and soft macular drusen OS (not shown). A 51-year-old male patient presented with a 15 year history of type 2 diabetes, having taken oral medications for the first 11 years and having used insulin for the past 4 years. Past ocular history included laser photocoagulation in both eyes. At the initial visit, the best corrected visual acuity was 20/30 (OD) and 20/70 (OS) with IOPs of 20 mmHg OD and OS. A 69-year-old male patient had a medical history of stroke and type 2 diabetes for fifteen years. He presented in the clinic with sudden and absolute vision loss OD. Visual acuity was Counting Fingers at 0.3\u2009meters OD and 20/40 OS. A 78-year-old male patient had a 10 year history of hypertension. His past ocular history included cataract surgery to both eyes. The patient complained of blurry vision OS for the past 4 months. At the initial visit, the visual acuity was Counting Fingers at 0.07 meters OD and 20/200 OS with an intraocular pressure of 24 mmHg and 18 mmHg. SD-OCT imaging technology was used to acquire images of patients with various retinal diseases in order to evaluate the clinical utility, potential, and limitations of the technique. Both SD-OCT and conventional clinical techniques showed choroidal neovascular membrane and pigment epithelial detachment (case of ARMD); neovascularisation at the disc and elsewhere, fibrosis, epiretinal membrane, and laser scars (case of DR); retinal edema and haemorrhages (case of BRVO). In some circumstances, SD-OCT provided visualization of morphological changes associated with retinal diseases that were either not immediately visible or not at all visible, using conventional clinical techniques. For example, SD-OCT revealed neurosensory retinal detachment and Bruch's/retinal pigment epithelium wrinkling (case of ARMD); cystoid spaces localised in the outer retina (case of DR); thickening and increased reflectance of inner retina (case of CRAO); localisation of depth of macular edema and of haemorrhages (case of BRVO). Thus, SD-OCT revealed structural retinal changes that are not visible by 2-dimensional limited fundus photography. Conversely, the presence of colour information within the digital fundus photography images may be advantageous, while SD-OCT uses a narrow spectrum of wavelengths and therefore has limited colour information. For example, in the case of the CRAO, conventional digital fundus photography showed the presence of infarction more prominently than the cSLO and SD-OCT imaging.Previous studies have shown that SD-OCT reveals retinal pathology that was not visible using TD-OCT, such as intra-retinal cysts and subretinal fluid . SD-OCT The ability of SD-OCT to clearly and objectively elucidate subtle morphological changes within the retinal layers provides information that could potentially be useful in the treatment of retinal diseases. This feature provides SD-OCT with a clear superiority over other clinical techniques that do not possess the same resolution. First, high-resolution cross-sectional images allow better visualization of the vitreoretinal interface, the vitreous, retinal structures, and the choroid. Furthermore, 3D images depict volumetric topographic retinal morphology that can be registered relative to images acquired at a different time point and, therefore, change in retinal morphology can be calculated. Second, while taking a follow-up image of a particular patient, the software is capable of automatically and accurately registering images so that the identical retinal area is used to calculate change. This added functionality eliminates the possibility of human error and makes it easier to analyze the data with greater validity. However, automated segmentation of the internal limiting membrane and Bruch's membrane sometimes requires manual adjustment prior to analysis in patients with retinal diseases.\u03bcm, it was hard to discern the underlying pathology and choroid.Nevertheless, SD-OCT has its limitations. This paper clearly demonstrates that hyperreflective lesions such as exudates and haemorrhages, as well as major retinal vessels, resulted in shadowing of the underlying retinal structures, and thereby details of the underlying morphology are lost. In the case exhibiting choroidal neovascular membrane , and diabetic retinopathy/macular edema where the retinal thickness was over 400\u2009 SD-OCT imaging technology offers a previously unattainable resolution of retinal morphology. The ability of SD-OCT to clearly and objectively elucidate subtle morphological changes within the retinal layers provides information that can be used to potentially formulate diagnoses earlier and with greater confidence. The current generation of SD-OCT instruments will not replace clinical retinal evaluation but do offer further information that can be valuable from a clinical perspective.This study illustrates the potential and limitations of SD-OCT imaging technology. It demonstrated the ability of SD-OCT to clearly and objectively elucidate subtle morphological changes within the retinal layers that are not visible using conventional clinical techniques. Such information may be useful for the earlier diagnosis and treatment of retinal diseases."} +{"text": "Eucalyptus species, including interspecific hybrids, has been extended from the traditional interest of pulp and paper production to the emergent areas of bio-fuels and bio-materials. New genomic resources and high throughput technologies have provided the Eucalyptus research international community with the opportunities to identify genomic regions of interest in order to comprehensively dissect, catalogue and characterize genes involved in the determination of wood formation and quality. Similar strategies can be now applied to identify key regulator genes and better understand the cellular mechanisms by which they modulate the complex molecular events occurring in xylogenesis.The economic importance of some wqGeneglob project (2006-2010) produced and used a set of genomic tools which, associated with Next Generation Sequencing (NGS) technologies, allowed us to expand the knowledge of the Eucalyptus genome by focusing on regions potentially involved in the determination of wood properties, namely pulp yield and lignin content. We first start to characterize two E. grandis BAC libraries [http://www.jgi.doe.gov/sequencing/why/99176.html], and two E. globulus BAC libraries made available by RAIZ [http://www.raiz-iifp.pt/]. We than used 3D-pools of BAC libraries and BAC macroarrays to characterize genomic environment of several lignin and lignin-regulator genes both in E. grandis and E. globulus. The shotgun sequencing of selected BAC clones containing those genes generated a high amount of sequencing data that made it possible to map the E. globulus BAC sequenced clones against the E. grandis genome (8X coverage). These comparative analyses showed extended microlinearity between both genomes, at least in the studied regions. Additionally, we have sequenced and annotated the chloroplast genome of E. grandis (GeneBank Accession NC_014570) [The t 2006-200 producet 2006-200 produceE. globulus transcriptome dynamics has also been included and structured in the wqGeneglob project, aiming at the identification of genomic hotspots of transcription activity. Various E. globulus xylogenesis \u201cmodels\u201d have been considered comprising several paired, contrasting wood forming tissues (provided by RAIZ): i) xylem samples collected along the year (season variation); ii) juvenile and adult individuals of a single genotype; iii) contrasting genotypes for pulp yield. Samples from these tissues were used for transcriptome sequencing using IlluminaHi-Seq technology (mRNA-SEQ). The same E. globulus genotype used for both E. globulus BAC libraries (a parent tree used in controlled crosses by RAIZ) has been re-sequenced (pair-end 100bp), and provided the first draft of an E. globulus genome. This resequencing data was mapped against the E. grandis Brasuz S1 reference genome. Transcriptomic data were also blatted against the gene models annotated in E. grandis genome, to evaluate in silico the expression of each gene.A global approach to unravel microEGo project (2010-2012) started the identification and characterization of Eucalyptus globulus microRNAs and their target genes, involved in the regulation of wood formation. The E. globulus season variation xylogenesis \u201cmodel\u201d was used considered for this project as well as an E. globulus reaction wood \u201cmodel\u201d. The latter comprises reaction wood tissues (tension / opposite wood) formed in bent trees at different kinetic times of gravitropic stimulation and control wood (non-bent trees). Small RNA libraries have been generated from those tissues and sequenced using IlluminaHi-Seq technology . The sequencing data from both microEGo and wqGeneglob projects together with a genome wide bioinformatics analysis of E. grandis reference genome and E. globulus genome are being used for identification of miRNA gene and putative their putative target-genes.More recently, the Eucalyptus community, providing insights into the nature of the molecular machinery involved in wood formation and most importantly in the identification of key players determining the variability of wood characteristics and its end-uses.These projects will hopefully constitute an important piece in the assemblage of whole new categories of knowledge and genomic resources for the"} +{"text": "Current MRI methods for radiofrequency ablation (RFA) visualization have problems in accurately delineating the extent of lesions at an early phase. The aim of this study is to evaluate a non-gadolinium enhanced (NGE) multi-contrast inversion recovery steady state free precession (IR-SSFP) imaging method to visua15 lesions were created in the endocardium of 13 pigs using approved animal protocols. NGE IR-SSFP and T2-w black-blood (double IR-FSE) images were acquired in <60min after ablation. Then, Gd-DTPA was injected and LGE images were acquired repeatedly over one hour. Gross pathology was used as the reference for lesion size measurements. Two regions were measured in this reference: the pale \"inner\" lesion core and the \"outer\" lesion border including the dark rim on pathology (see Results).All DIR-FSE images showed large hyper-intense regions in and around the lesion likely due to edema, making, the lesion borders hard to distinguish Fig . The lesThe lesion sizes measured in LGE images were always larger than those in IR-SSFP images. While the lesion sizes in IR-SSFP images were better correlated with the size of the inner lesion core on gross pathology Fig , the lesIR-SSFP images without Gd enhancement demonstrated good contrast between the ablation lesions and normal myocardium. The lesion size from IR-SSFP images also correlated well with lesion size in gross pathology. Among the imaging methods used in this study, IR-SSFP provided the most reliable and consistent data for RFA lesion characterization.We gratefully acknowledge support from GE Healthcare, the Ontario Research Fund, and Canadian Institutes of Health Research."} +{"text": "Our objective was to evaluate the association between the use of sedative and analgesic agents during paediatric intensive care unit (PICU) treatment and long-term neuropsychological outcome in children who survived meningococcal septic shock (MSS).This study is part of a medical and psychological follow-up study of all consecutive MSS survivors requiring PICU treatment between 1988 and 2001 at the Erasmus MC - Sophia Children's Hospital, a tertiary-care university hospital. This follow-up study revealed that MSS survivors showed long-term (at least 4 years after PICU admission) impairments on several domains of neuropsychological functioning. Severity of illness was no significant predictor of adverse neuropsychological outcome. The use of sedatives and analgesics was retrospectively evaluated.n = 40), median age 25 months at time of PICU admission). In 45 patients (58%) one or more analgesic and/or sedative drugs were administered during PICU admission. Benzodiazepines were the most commonly used drugs , followed by opioids . In total 15 different kinds of analgesic or sedative drugs were given. There was a statistically significant correlation between the use of opioids (both as continuous (cumulative dose) and dichotomous variable) and adverse outcome on multiple domains of neuropsychological functioning , verbal IQ , verbal reasoning , social comprehension , visual-motor integration ). After univariate analysis, correcting for socioeconomic status, age at follow-up and severity of illness, these correlations remained significant.The study population consisted of 77 patients (52% male (The use of opioids during PICU admission was significantly associated with long-term adverse neuropsychological outcome in MSS survivors."} +{"text": "Approaches to simplify and streamline the construction of full-length infectious cDNA clones (FL-cDNAs) are needed. Among desirable improvements are the ability to use total nucleic acids (TNA) extracts from infected hosts for the direct one-step amplification of large FL-cDNAs, the possibility to inoculate plants with uncloned FL-cDNAs and the simplified cloning of these large molecules.Apple chlorotic leaf spot trichovirus (ACLSV) approaches allowing the rapid generation from TNA extracts of FL-cDNAs under the control of the T7 promoter and the successful inoculation of plants using in vitro transcripts obtained from these uncloned amplification products have been developed. We also show that the yeast homologous recombination system permits efficient cloning of FL-cDNAs and the simultaneous one-step tailoring of a ternary Yeast-Escherichia coli-Agrobacterium tumefaciens shuttle vector allowing efficient inoculation of both herbaceous and woody host plants by agroinfiltration.Using the 7.55 kb genome of The fast and efficient strategies described here should have broad applications, in particular for the study of \"difficult\" plant viruses, such as those infecting woody hosts, and potentially for other, non plant-infecting viral agents. Over the past 25 years, our ability to discover and characterize viral agents has steadily improved, leading to a constant flow of discovery of novel plant viruses as testified by the literature and by the constant increase in the number of viral species described in successive reports of the International Committee for the Taxonomy of Viruses . The devin vitro or in vivo . Following incubation overnight at 28\u00b0C under agitation, bacteria were collected by centrifugation at 6000 g for 15 min at room temperature, re-suspended in infiltration medium and the bacterial suspension adjusted to an optical density of 0.6 at 600 nm. The suspension was then incubated for 3 h at room temperature before being infiltrated in the intercellular spaces of young C. quinoa or N. occidentalis leaves, using a syringe directly placed on the lower leaf surface. Alternatively, young GF305 peach seedlings were inoculated by injections of the Agrobacterium cells suspension in their stems using a syringe and a small gauge needle. Following their inoculation, plants were monitored weekly for symptoms appearance and ACLSV infection was confirmed as described above.For agroinfiltration of plants, Apple chlorotic leaf spot virus; ApLV: Apricot latent virus; CLBV: Citrus leaf blotch virus; DAS-ELISA: double-antibody sandwich enzyme-linked immunosorbent assay; DEPC: diethylpyrocarbonate; dsRNA: double stranded RNA; FL-cDNA: full-length infectious cDNA clone; LB: T-DNA left border; LD-PCR: long distance PCR; MES: 2N-morpholino-ethane sulfonic acid; NGS: next generation sequencing; NosT: Nopaline synthase gene terminator; RB: T-DNA right border; SD: minimal synthetic defined base; TNA: total nucleic acids; YAC: yeast artificial chromosome70SP: duplicated CaMV 35S promoter; ACLSV: The authors declare that they have no competing interests.All authors contributed to the results presented. FY, AM, PG and TC contributed to and edited the manuscript. All authors read and approved the final manuscript."} +{"text": "Aedes aegypti mosquitoes are the main vectors of dengue viruses to humans. Understanding their biology and interactions with the pathogen are prerequisites for development of dengue transmission control strategies. Mosquito salivary glands are organs involved directly in pathogen transmission to vertebrate hosts. Information on the spatial distribution of gene expression in these organs is expected to assist in the development of novel disease control strategies, including those that entail the release of transgenic mosquitoes with impaired vector competence.in situ patterns of 30 transcripts expressed in the salivary glands of adult Ae. aegypti females. Distinct spatial accumulation patterns were identified. The products of twelve genes are localized exclusively in the proximal-lateral lobes. Among these, three accumulate preferentially in the most anterior portion of the proximal-lateral lobe. This pattern revealed a salivary gland cell type previously undescribed in Ae. aegypti, which was validated by transmission electron microscopy. Five distinct gene products accumulate in the distal-lateral lobes and another five localize in the medial lobe. Seven transcripts are found in the distal-lateral and medial lobes. The transcriptional product of one gene accumulates in proximal- and distal-lateral lobes. Seven genes analyzed by quantitative PCR are expressed constitutively. The most abundant salivary gland transcripts are those localized within the proximal-lateral lobes, while previous work has shown that the distal-lateral lobes are the most active in protein synthesis. This incongruity suggests a role for translational regulation in mosquito saliva production.We report here the hybridization Ae. aegypti salivary glands has been shown to reduce prevalence and mean intensities of viral infection. We anticipate greater efficiency of viral suppression if effector genes are expressed in all lobes of the salivary glands. Based on our data, a minimum of two promoters is necessary to drive the expression of one or more anti-dengue genes in all cells of the female salivary glands.Transgenic mosquitoes with reduced vector competence have been proposed as tools for the control of dengue virus transmission. Expression of anti-dengue effector molecules in the distal-lateral lobes of Aedes aegypti [[http://exon.niaid.nih.gov/transcriptome.html].Mosquito salivary glands have been studied extensively for their roles in blood feeding and pathogen transmission to vertebrate hosts. A number of morphological -6 and biaegypti [-15, httpAe. aegypti have a distinctive tri-lobed structure consisting of a single medial and two lateral lobes. Each lobe comprises a secretory epithelium surrounding a salivary duct into which saliva is released.The salivary glands of adult mosquitoes are sexually dimorphic and it is clear that their structural and functional differences enable females to engage successfully in hematophagy ,17. The The complex mosquito saliva is produced by secretory cells of the proximal and distal regions of the lateral lobes and the distal region of the medial lobe. The secretory products collect in extracellular secretory cavities that are connected by openings to the salivary duct. The mosquito salivary glands produce and secrete molecules with diverse enzymatic, anti-hemostatic and anti-inflammatory activities, which help in the acquisition of blood meals from vertebrate hosts, as well as for the digestion of sugar and nectar meals ,18. Addiin situ patterns of 30 genes expressed in the salivary glands of adult Ae. aegypti females, the identification of a new cell type located in the proximal portion of the lateral lobes, and discuss the application of such knowledge for enhancing efforts to interfere with dengue virus transmission.Despite the extensive knowledge acquired thus far about mosquito saliva components and their functions, little is known about the spatial-specificity of expression of the corresponding genes in the salivary glands. Here we report the hybridization Ae. aegypti (L.) was used for all gene amplification and hybridization in situ experiments and the PPCampos strain was used in the transmission electron microscopy experiments. Standard rearing procedures were used [The Liverpool strain of ere used . Briefly2O and treated for 30 min at 37\u00b0C with RQ1 DNAse .Salivary glands were dissected from adult females in phosphate-buffered saline (PBS), frozen in Trizol reagent and stored at -80\u00b0C prior to RNA extraction. Total RNA was extracted, dissolved in RNAse-free Hhttp://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi to amplify products of a minimum of 500 nucleotides whenever possible. Sequences of all oligonucleotide primers are listed in Additional file \u00ae4-TOPO\u00ae cloning vector (Invitrogen) and sequenced to confirm their identity. Digoxygenin (DIG)-labeled antisense RNA probes for salivary gland gene products were synthesized in vitro using T3 or T7 RNA polymerases .The One-step RT-PCR kit was used for cDNA amplification reactions. Primer pairs were designed using the Primer3 Plus primer design software Salivary glands were dissected in PBS from adult female mosquitoes 4 days post emergence. Tissues were fixed with 4% formaldehyde in PBS immediately after dissection. Post-fixation treatment, hybridization and signal detection were conducted as described previously , with th\u00ae JEM-1011 electron microscope .Salivary glands of 3-5 day old female mosquitoes were dissected and fixed for 2 hours in 2.5% glutaraldehyde in 0.1 M cacodylate buffer, pH 7.2. Samples were post-fixed in 1% osmium tetroxide in 0.8% potassium ferricyanide and 0.1 M cacodylate buffer, pH 7.2, dehydrated in a series of acetone (30 to 100%) and embedded in EPON-812 resin . Thin sections (60-70 nm) were stained with uranyl acetate and lead citrate, and were examined in a Jeol\u00ae JEM-1011 electron microscope.Alternatively, salivary glands were fixed in glutaraldehyde as described above, rinsed in PBS, dehydrated in graded ethanol (30 to 100%) and immersed for 48 hours in 2.0% phosphotungstic acid (PTA) in absolute ethanol. Glands were washed subsequently in ethanol (2X for 10 min), ethanol and acetone (1:1) for 10 min and absolute acetone (2X for 10 min). After dehydration the material was embedded in EPON-812 resin (Electron Microscopy Sciences), and thin sections (60-70 nm) were examined in a JeolrpL32). Quantitative PCR was performed with an iQ5 real-time PCR detection system (BioRad) with iQ-SyberGreen Super Mix (BioRad). The relative 2-\u0394\u0394Ct method [P value of \u22640.05 was considered to be significant.Salivary glands were dissected from adult female mosquitoes at various time points: 1 day and 4 days post emergence (PE), and 6 h, 24 h, and 48 h post blood feeding. Mosquitoes were blood-fed on anesthetized mice for 30 min, 4-5 days PE. Three biological replicates, each consisting of salivary glands from 20 mosquitoes, were collected for each time point. cDNA was synthesized from DNAse-treated total RNA from pooled samples of 20 salivary gland pairs using SuperScript III (Invitrogen) and oligo dT. All primers were designed to flank the start of the 3'-end untranslated region to increase target specificity. Oligonucleotide primers were designed to amplify a 97 nucleotide fragment of AAEL003396, a constitutively-expressed reference gene encoding the 60 S ribosomal protein L32 ; a lysozyme (AAEL009670); amylase 1 (AAEL006719); a salivary chymotrypsin-like gene (AAEL015294); two putative vacuolar-type H+-ATPase subunits (AAEL009808 and AAEL007777); three genes with unknown functions ; carbonic anhydrase (AAEL010893); gambicin (AAEL004522); and a putative serine protease (AAEL005596). The last three genes belong to a sub-class of the proximal-lateral lobe group that is transcribed within the anterior-most portion of the proximal-lateral lobes ; putative 30 kDa allergen-like proteins, 30K a (AAEL010228) and aegyptin (AAEL010235), which also has been designated 30K b [Culex quinquefasciatus. The mRNAs of these genes accumulate only in the cells of the distal-lateral lobes, except for the transcripts of aegyptin, which also accumulate in the intermediate region and distal tip of the proximal-lateral lobes ; a gene encoding a predicted protein with angiopoietin-like features (AAEL000726); a putative C-type lectin (AAEL000533) and two genes with unknown functions (AAEL008310 and AAEL009852) Figure .serpin (AAEL003182), salivary apyrase (AAEL006347), D7L1 (AAEL006417), D7L2 (AAEL006424), a salivary purine nucleosidase (AAEL006485) and two genes with unknown functions (AAEL083050 and AAEL003601) Figure . The las) Figure .The spatial patterns of transcript accumulation determined in this study support previously-described, functionally-distinct regions of the mosquito salivary glands ,3,10,16.Transmission electron microscopy of PTA-stained sections showed two distinguishable cell types in the proximal regions of the lateral lobes Figure . The celThe distal regions of the lateral and medial lobes display an overall architecture consistent with previous morphological descriptions of the organ, with cells surrounding secretory cavities containing uniform and electron-dense secretory material Figure and 6F. rpL32 was used to determine relative fold changes in transcript accumulation for genes of four spatial groups of salivary gland-expressed genes. Genes selected for analysis include two expressed in proximal-lateral lobes, a lysozyme gene (AAEL009670) and a gene encoding a putative 18.5 kDa secreted protein (AAEL007986); one gene from the distal-lateral group, antigen-5 member (AAEL000793); two from the medial group, a gene encoding an angiopoietin-like protein (AAEL000726) and sialokinin (AAEL000229); and two genes from the distal lateral and medial group, D7L2 (AAEL006424) and salivary apyrase (AAEL006347). All genes except for salivary apyrase were expressed at levels greater than rpL32 and for the majority of genes analyzed, fold-changes in gene expression did not vary significantly over the experimental time course. However, the two medial group genes, angiopoietin-like and sialokinin, did show significantly (p \u2264 0.05) lower accumulation levels following blood feeding based on ANOVA analysis and Dunnett's test with pair-wise comparisons using 1 dPE as the calibrator , distal-lateral (five genes), medial (five genes), distal-lateral/medial (seven genes), all lateral (one gene), and one subclass of the proximal-lateral group in which gene products accumulate in the anterior-most portion of the proximal-lateral lobe (three genes). This diversity of spatially-restricted expression patterns reveals a more elaborate picture of salivary gland-specific gene regulation and an alternative to the view of a simplified tri-regional compartmentalization of the salivary gland [Transcript localization patterns within chniques -30. Herery gland . Moreovein situ analyses to be expressed in the proximal-lateral lobes of Ae. aegypti salivary glands, such as 1,4-alpha-glucosidase and amylase 1, are related to the digestion of the sugar meal [in situ results presented herein.Constituents of female mosquito saliva have various functions related to their secretion during sugar- or blood-feeding, and from previous observations it has been postulated that these salivary constituents are compartmentalized in their expression to particular lobes of the salivary glands. Genes shown previously by both enzymatic and hybridization gar meal ,28,32,33Ae. aegypti salivary glands [Ae. aegypti [Aedes albopictus, a near relative of Ae. aegypti, also expresses a salivary lysozyme [in situ and real-time RT-PCR. We propose based on amino acid similarity and tissue localization that these genes are orthologous and correspond to the activity detected by Rossignol and Lueders [Lysozyme is another abundantly-expressed gene product in the proximal regions of the lateral lobes that was identified previously by biochemical analysis of female y glands . It was aegypti . Aedes alysozyme . This co Lueders .gambicin, carbonic anhydrase and a putative serine protease accumulate in a novel functional region within the anterior-most portion of the proximal-lateral lobes. Transmission electron microscopy shows that this region contains a cell type that is distinct morphologically from cells in other regions of the salivary gland. Previous work also describes two well-defined cellular types in the most proximal portion of the salivary glands of Anopheles darlingi [gambicin, an anti-microbial gene product involved in mosquito innate immune response, supports the hypothesis that this region of the glands may produce other salivary components that prevent microbial infection during sugar-feeding.Three transcripts, encoding darlingi . These falpha-glucosidase, amylase 1, lysozyme, and gambicin support the conclusion that genes expressed in the proximal-lateral lobes correspond to sugar-feeding and nectar-related digestive and bacteriocidal functions. However, serine protease-like gene products (AAEL015294 and AAEL005596) containing secretory signal peptides also are expressed in the proximal-lateral lobes. While the majority of protein ingested by female mosquitoes is obtained during blood-feeding it is possible that gene products are needed to metabolize low abundance proteins ingested during sugar feeding. Alternatively, these and other products in the proximal-lateral lobes could be involved in blood feeding, for example enzymes could interact with vertebrate host hemostatic factors. The leech Haementeria ghilianii produces a proteolytic enzyme, Hementin, in its salivary glands, which has an anticoagulant activity [The localization patterns described for activity . The mecin situ confirms the role of the distal-lateral and medial lobes in the expression of genes involved with blood-feeding. Genes such as salivary apyrase (AAEL006347), salivary purine nucleosidase (AAEL006485), serpin (AAEL003182), an antigen-5 family member (AAEL000793), aegyptin (AAEL010235), 30-kDa allergen (AAEL0010228), and the D7 family genes all have been shown previously to be major components of hematophagous mosquito saliva and play roles in suppressing human host wound responses, preventing hemostasis and causing host hypersensitivity responses [in situ patterns for three members of the D7 gene family show that the mRNA of one short isoform D7s2 (AAEL006423) is localized only in the distal-lateral lobes, while transcripts of two long isoforms, D7L1 (AAEL006417) and D7L2 (AAEL006424), accumulate in distal-lateral and medial lobes. The D7 gene family encodes proteins that bind biogenic amines including histamine, serotonin and norepinephrine and thereby inhibit vasoconstriction and platelet aggregation, while promoting blood-feeding [In contrast to the proximal regions, the distal regions of the lateral and medial lobes have been shown previously to produce salivary products such as platelet aggregation inhibitors, anticoagulants and vasodilatory agents involved in hematophagy ,30,37,38esponses ,35,37-421 AAEL0067 and D7Langiopoietin-like (AAEL000726), restricted spatially to only the medial lobe, have described functional domains. Sialokinin is a potent vasodilatory tachykinin that has been shown to help maintain blood flow during hematophagy and increase the likelihood of venipuncture during host probing by enlarging target venules and arterioles [angiopoietin-like gene product investigated here was identified through proteomics approaches and is one of a family of angiopoietin-like variants that are involved in immunity-related responses [sialokinin and the angiopoietin-like medial-lobe gene products were decreased following a blood meal. The reasons for this observation are as of yet unknown.Two of five genes, sialokinin (AAEL000229) and terioles ,43,44. Tesponses ,45. Whilin situ analyses showed that transcripts of two different V-ATPase subunits (AAEL007777 and AAEL009808) accumulate in the proximal-lateral lobes, not in the intermediate regions. The presence in the proximal-lateral lobe of these molecules, which serve a basic tissue function for solute transport, support the hypothesis that the proximal regions of the lateral lobes are most similar to the tubular salivary glands of non-hematophagous mosquitoes [The intermediate regions of the lateral lobes are not thought to be associated with saliva production ,3. The msquitoes ,47. Moresquitoes .Ae. aegypti salivary glands [35S -methionine labeling showed that the distal regions of the lateral lobes followed by the medial lobe were the most translationally active, while the proximal regions of the lateral lobe were much less active [Another surprising finding from our studies is that transcripts identified previously as the most abundant in y glands are locas active . The difAe. aegypti broadens its range across the Mexico-US border [Dengue is the most prevalent mosquito-borne viral disease of humans worldwide, with 3 billion people at risk of infection and ~50 million annual cases of dengue fever . ChanginS border ,55. ConvS border . These sS border .Anti-pathogen effector genes that block or kill viral pathogens, and promoters that target effector gene expression to key tissues where the virus and mosquito host interact are essential components of population replacement strategies to control dengue transmission. Dengue viral invasion of mosquito host tissues is ubiquitous, however important tissue barriers relevant for mosquito infection and subsequent transmission include the midgut and the salivary glands . Express30K b promoter, was limited spatially to only the distal lateral lobes. Since dengue viruses infect and replicate in all lobes of the salivary gland [Ae. aegypti females will enhance efforts to interfere with dengue virus transmission within the mosquito vector.Recent work showed that salivary gland promoter-directed expression of an anti-dengue siRNA effector molecule also results in reduced virus prevalence and mean intensities of infection in transgenic mosquitoes . Howeverry gland , it is pAe. aegypti mosquitoes. We postulate that effector molecule expression in all lobes of the salivary glands can be achieved best with the use of two promoters, one each from the proximal-lateral and distal-lateral/medial groups. A combination of promoters, from the medial group and the all-lateral group also can be used. Quantitative RT-PCR results indicate that a promoter from each of these groups should permit constitutive expression of effector molecules, before and after a blood meal. However, it is worth mentioning the moderate decrease in transcript abundance following a blood meal observed for two genes in the medial group.Our findings have implications to the design of multiple and/or combinatorial promoter-effector molecule constructs that would target dengue virus throughout the entire salivary gland of Global transcriptome analyses of mosquito salivary gland responses to blood-feeding have been performed ,62 and cAe. aegypti mosquitoes. Quantitative RT-PCR analysis indicates that seven selected genes are expressed constitutively and that salivary gland gene expression is not modulated significantly by blood-feeding except for genes in the medial group, which were observed to be down-regulated. Additionally, a morphologically-distinct cell type was identified in the anterior-most region of the proximal lateral lobe. Our findings emphasize the importance of investigating further the complex transcriptional and potentially translational regulation of gene expression in the salivary glands of mosquitoes. Genetically-modified mosquitoes expressing anti-dengue effector molecules exclusively in the distal lateral lobes resulted in decreased virus prevalence and mean intensities of infection. Dengue virus transmission potential of those transgenic mosquitoes was reduced strongly. Here we propose the use of at least two promoters to drive expression of anti-dengue molecules within the entire salivary gland to more efficiently reduce, or block disease transmission.The work described here identifies five distinct groups of transcript localization patterns in the salivary glands of Authors declare that they have no competing interests.in situ probes, performed hybridization in situ experiments, conducted quantitative real time RT-PCR experiments and analyses, participated in the design and coordination of the study and drafted the manuscript. UN-U and AM performed RT-PCR amplifications and cloning, prepared hybridization in situ probes and performed hybridization in situ experiments. BAMG carried out the transmission electron microscopy experiments. JC dissected salivary glands. PFPP interpreted transmission electron microscopy images and helped to draft the manuscript. WA and AAJ read and helped to draft the manuscript. OM conceived of the study, participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.JJ prepared hybridization Oligonucleotide primers for in situ probes and oligonucleotide primers for quantitative real-time RT-PCR.Click here for file"} +{"text": "Cardiac involvement of patients with systemic lupus erythematosus (SLE) is one of the main complications contributing to morbidity and mortality, however a significant portion of patients presents with subclinical disease. Non-invasive contrast-enhanced cardiovascular magnetic resonance (CMR) imaging is a well-established diagnostic tool to identify myocardial tissue alterations and morphological and functional changes. In this study, we aimed to assess cardiac abnormalities in SLE patients using LGE-CMR and, furthermore, the relation of serological inflammatory biomarkers to the cardiac LGE-CMR findings.We studied 27 SLE patients and 30 healthy age-matched volunteers who served as a control group . Cine MRI with 32 channel image acquisition and vector-ECG gated short axis, two and four chamber cine slices with parallel image acquisition covering the entire left ventricle (LV) were acquired using a regular SSFP sequence on a 1.5T Whole Body MRI scanner . LGE-CMR was performed and analyzed by two blinded experienced observers. Analysis of the presence and distribution of LGE forms was compared to serum levels of anti-ds DNA, C- reactive protein as markers of disease activity and inflammation. Groups were compared using the Student's t-test or the Mann-Whitney test and Fisher's exact test. P-values \u2264 0.05 were considered statistically significant.Nineteen SLE patients (70%) showed LV myocardial LGE (14 patients with infarct-atypical pattern, 2 patients with infarct-typical and 3 patients with mixed pattern, (Figure Presence of myocardial LGE in SLE patients is a common finding and may be associated with a chronic and exacerbated inflammatory process. Taking into consideration the significant cardiovascular morbidity and mortality in SLE patients, and the difficulty in the early detection of cardiac manifestations, CMR could serve as a non-invasive diagnostic tool to assess cardiac SLE involvement and to aid in the cardiovascular risk stratification of these patients.none"} +{"text": "The novelty of this work is the construction of such artificial architectures with a non-conducting building block. Furthermore a detailed study of the size influence of silica nanoparticles is performed with regard to formation and electrochemical behavior of these systems.For bioanalytical systems sensitivity and biomolecule activity are critical issues. The immobilization of proteins into multilayer systems by the layer-by-layer deposition has become one of the favorite methods with this respect. Moreover, the combination of nanoparticles with biomolecules on electrodes is a matter of particular interest since several examples with high activities and direct electron transfer have been found. Our study describes the investigation on silica nanoparticles and the redox protein cytochrome c (cyt c) immobilized by the use of modified silica nanoparticles (SiNPs) to act as an artificial matrix. The layer-by-layer deposition technique has been used for the formation of silica particles/cytochrome c multilayer assemblies on electrodes. The silica particles are characterized by dynamic light scattering (DLS), Fourier transformed infrared spectroscopy (FT-IR), Zeta-potential and transmission electron microscopy (TEM). The modified particles have been studied with respect to act as an artificial network for cytochrome c and to allow efficient interprotein electron transfer reactions. We demonstrate that it is possible to form electro-active assemblies with these non-conducting particles. The electrochemical response is increasing linearly with the number of layers deposited, reaching a cyt c surface concentration of about 80 pmol/cm2 with a 5 layer architecture. The interprotein electron transfer through the layer system and the influence of particle size are discussed.We report on interprotein electron transfer (IET) reaction cascades of cytochrome c multilayer assemblies by using carboxy-modified silica nanoparticles. Thus it can be shown that functional, artificial systems can be build up following natural examples of protein arrangements. The absence of any conductive properties in the second building block clearly demonstrates that mechanisms for electron transfer through such protein multilayer assemblies is based on interprotein electron exchange, rather than on wiring of the protein to the electrode.This study demonstrates the ability to construct fully electro-active cyt The construction strategy of this multilayer system provides a new controllable route to immobilize proteins in multiple layers featuring direct electrochemistry without mediating shuttle molecules and controlling the electro-active amount by the number of deposition steps. Raising the number of layers a continuous increase of the voltammetric cyt c signal has been achieved with this system and can be used for the detection of superoxide radicals with enhanced sensitivity from QCM frequency shift [\u0394f (Hz)] of fixed films by using the Sauerbrey equation [\u0394m = 1.03 \u0394f. According to this a layer mass increase can be estimated. Since measurements have been performed in solution, these values are estimated due to unknown amount of bound water.A Q-Sense-D E4 piezoelectric instrument was used for the quarz crystal microbalance measurements. A clean gold covered quarz sensor chip was incubated in ethanol solution containing 5 mM MUA/MU (1:3) for 24 h, then rinsed with water and mounted into the QCM flow system. The solutions containing SiNPs and cyt equation . Taking equation , this eqAll electrochemical measurements were carried out in a 1 mL cell using an Ag/AgCl/1 M KCl reference and Pt-wire counter electrode. The working electrodes were modified gold wires (diameter 0.5 mm) obtained from Goodfellow which are modified according to the procedures described above. Cyclic voltammetric experiments were carried out with CH Instruments CHI 660D device . Scan rates were varied between 0.01 and 50 V/s, but a scan rate of 100 mV/s was normally used. The potential range has been chosen between -0.3 and +0.3 V vs. Ag/AgCl. Data analysis has been performed using CHI 660D software.APTES: (4-aminopropyl triethoxy silane); CV: (cyclic voltammetry); ccyt : (cytochrome c); effectiveD: (effective diffusion coefficient); DET: (direct electron transfer); DLS: (dynamic light scattering); DNA: (desoxyribonucleic acid); FT-IR: (Fourier transformed infrared spectroscopy); IET: (interprotein electron transfer); ex: k(self-exchange rate constant); KPP: (potassium phosphate buffer); MU: (mercaptoundecanol); s: k(dissociation constant); MUA: (mercaptoundecanoic acid); PASA: (polyaniline sulfonic acid); pH: (potentia hydrogenii); PI: (polydispersity index); QCM: ; SAM: (self-assembling monolayer); SiNPs: (silica nanoparticles); TEM: (transmission electron microscopy); TEOS: (tetraethyl orthosilicate).The authors declare that they have no competing interests.SCF carried out all the experiments and prepared the manuscript. FL supervised the design of the study and the drafting of the manuscript. All authors read and approved the final manuscript."} +{"text": "Many viruses target cytoplasmic polyA binding protein (PABPC) to effect widespread inhibition of host gene expression, a process termed viral host-shutoff (vhs). During lytic replication of Epstein Barr Virus (EBV) we observed that PABPC was efficiently translocated from the cytoplasm to the nucleus. Translocated PABPC was diffusely distributed but was excluded from viral replication compartments. Vhs during EBV infection is regulated by the viral alkaline nuclease, BGLF5. Transfection of BGLF5 alone into BGLF5-KO cells or uninfected 293 cells promoted translocation of PAPBC that was distributed in clumps in the nucleus. ZEBRA, a viral bZIP protein, performs essential functions in the lytic program of EBV, including activation or repression of downstream viral genes. ZEBRA is also an essential replication protein that binds to viral oriLyt and interacts with other viral replication proteins. We report that ZEBRA also functions as a regulator of vhs. ZEBRA translocated PABPC to the nucleus, controlled the intranuclear distribution of PABPC, and caused global shutoff of host gene expression. Transfection of ZEBRA alone into 293 cells caused nuclear translocation of PABPC in the majority of cells in which ZEBRA was expressed. Co-transfection of ZEBRA with BGLF5 into BGLF5-KO cells or uninfected 293 cells rescued the diffuse intranuclear pattern of PABPC seen during lytic replication. ZEBRA mutants defective for DNA-binding were capable of regulating the intranuclear distribution of PABPC, and caused PABPC to co-localize with ZEBRA. One ZEBRA mutant, Z(S186E), was deficient in translocation yet was capable of altering the intranuclear distribution of PABPC. Therefore ZEBRA-mediated nuclear translocation of PABPC and regulation of intranuclear PABPC distribution are distinct events. Using a click chemistry-based assay for new protein synthesis, we show that ZEBRA and BGLF5 each function as viral host shutoff factors. Viruses promote a widespread reduction of host cell gene expression to reduce competition for cellular resources, to decrease expression of cellular factors that elicit an immune response to viral infection, and to facilitate the establishment of viral latency. This process, termed viral host shutoff (vhs), is mediated by modulation of transcription, mRNA splicing, nuclear export of mRNA, mRNA decay, translation, and proteolysis vhs protein, an endonuclease with sequence homology to the FEN-1 family of nucleases, which rapidly degrades mRNAs vhsAmong herpesviruses, the alphaherpesvirus herpes simplex virus type 1 (HSV-1), and the gammaherpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV), murine gammaherpesvirus 68 (MHV68), and Epstein-Barr virus (EBV), all induce vhs characterized by accelerated global host mRNA decay during the lytic phases of replication. Betaherpesviruses, like human cytomegalovirus (HCMV), in contrast, do not shut-off host macromolecular synthesis ShutOff and eXonuclease), a viral alkaline nuclease (AN) encoded by ORF37, a gene that is conserved among all herpesvirus family members During lytic infection by KSHV, vhs and translocation of PABPC is mediated by SOX -tails and by sequestering hyperadenylated mRNAs in the nucleus, intranuclear PABPC precludes translation of cellular mRNAs After SOX was shown to be the primary inducer of vhs by KSHV, the AN homologs in EBV (BGLF5) and MHV68 (muSOX) were also found to induce host shutoff and to translocate PABPC from the nucleus to the cytoplasm when transiently transfected into cells lacking virus In this study, we examined in detail the nuclear translocation of PABPC during the early stages of lytic EBV infection. We report that in addition to BGLF5, the major lytic cycle regulatory protein, ZEBRA, controls the intracellular localization of PABPC and regulates host shutoff during lytic infection. ZEBRA is a member of the bZIP family of transcription factors, and is expressed from the BZLF1 gene as an early lytic protein. As an essential transcription factor and replication protein, ZEBRA binds DNA at specific sequences termed ZEBRA response elements (ZRE), and activates or represses downstream lytic viral genes. In cells lacking the EBV genome, the combination of BGLF5 and ZEBRA were sufficient to re-locate PABPC in the nucleus in a pattern seen during lytic infection. ZEBRA and BGLF5 each individually elicited a distinct nuclear distribution pattern of PABPC; ZEBRA co-localized with intranuclear PABPC, whereas BGLF5 did not. While both ZEBRA and BGLF5 were capable of promoting PABPC accumulation in the nucleus, ZEBRA was dominant in influencing a diffuse intranuclear distribution of PABPC. We also show that both BGLF5 and ZEBRA function as regulators of host shutoff. Each protein caused a global inhibition of endogenous host protein synthesis.In preliminary experiments, the localization of PABPC was examined in HH514-16, a cell line derived from Burkitt lymphoma, untreated or treated with sodium butyrate to induce the EBV lytic cycle . In untrThe lytic cycle of EBV progresses through distinct temporal stages: the early stage is defined by expression of viral \u201cearly genes\u201d many of which encode proteins required for DNA replication; early gene expression is followed by the onset of viral DNA replication in which viral DNA is synthesized in subnuclear globular domains called replication compartments; viral DNA replication permits entry into the late stage of lytic infection in which viral \u201clate genes\u201d are expressed and virions are produced. Lytically induced cells were co-stained with antibodies to PABPC and to EA-D (early antigen-diffuse), a viral gene product whose intranuclear distribution differs during the early and late phases of the EBV life cycle. EA-D is diffusely present throughout the nucleus during early phases of the life cycle and concentrates in replication compartments during and after DNA replication. Three hundred-forty-four cells expressing EA-D, chosen at random, were scored for the localization of EA-D and PAPBC . PABPC wWe asked whether BGLF5, the EBV homologue of KSHV SOX and MHV68 muSOX, functions similarly to translocate PABPC to the nucleus These results suggested that an EBV lytic cycle product other than BGLF5 regulates the intranuclear distribution of translocated PABPC characteristic of the lytic cycle. To test this hypothesis, BGLF5-KO cells were co-transfected with BGLF5 and with ZEBRA to induce the lytic cycle and thereby provide additional lytic cycle proteins . Under tUsing 293 cells lacking EBV, we studied whether BGLF5 or ZEBRA could mediate nuclear translocation of PABPC in the absence of all other viral products. In 293 cells, PABPC remained exclusively cytoplasmic after transfection of an empty vector . TransfeTransfection of BGLF5 expression vectors promoted nuclear translocation of PABPC in all 293 cells that expressed BGLF5 protein . The cluTo investigate the specificity of ZEBRA's effect on the localization of PABPC, we tested the ability of Rta, another EBV early viral transcription factor that localizes exclusively to the nucleus, to regulate the distribution of translocated PABPC Several aspects of the translocation of PABPC in 293 cells transfected with ZEBRA and BGLF5, individually or in combination, were quantitated . First, A FLAG-tagged version of PABPC aberrantly mis-localizes to the nucleus of uninfected 293 cells and distributes unevenly in clumps and aggregates . When FLDuring the EBV lytic phase, diffusely distributed intranuclear PABPC was often concentrated at the nuclear periphery; some subnuclear regions were spared of PABPC iv, vii The distributions of ZEBRA, BGLF5, and translocated PABPC with respect to nucleoli seen during lytic induction are the same in cells lacking EBV. In 293 cells co-transfected with ZEBRA and BGLF5 and co-stained for ZEBRA and nucleolin, ZEBRA was distributed diffusely and exhibited its characteristic propensity to spare nucleoli . Cells cPABPC was excluded from certain nuclear subregions present during lytic infection of EBV. These subregions were enriched in BGLF5 and nucleolin and contained viral replication compartments , indicatIn 2089 cells that were lytically induced by transfection of ZEBRA or co-trDuring EBV lytic infection, SC35 co-localized with BGLF5 in punctate foci i-iii anEBV BMLF1 exports viral mRNAs from the nucleus to the cytoplasm To investigate mechanisms by which activities of ZEBRA regulate translocation and intranuclear distribution of PABPC, we used three point mutants of ZEBRA, Z(N182K), Z(S186A), and Z(S186E), each defective for transcriptional activation of downstream lytic viral genes To assess the ability of the ZEBRA mutants to distribute PABPC re-localized within the nucleus, each was co-transfected with FLAG-BGLF5. Z(S186A) and Z(S186E) distribute evenly and diffusely in the nucleus similarly to WT ZEBRA; Z(N182K) is diffusely yet unevenly distributed. Some clumping of the Z(N182K) mutant was seen [24], and [iv-vi] depict the same field of view. Arrows in panels denote cells undergoing viral lytic induction.(TIF)Click here for additional data file.Figure S2Levels of PABPC during induction of the lytic phase, and during expression of ZEBRA and BGLF5. (A) BZKO cells were transfected with vector (pHD1013) or pCMV-gZ expressing wild type ZEBRA. Cell extracts were prepared 48 h after transfection. Immunoblots were probed with antibodies to ZEBRA, PABPC and tubulin. (B) 293 cells were transfected with vector, ZEBRA or FLAG-BGLF5. Cell extracts were prepared 43 h after transfection. Immunoblots were probed with antibodies to FLAG, PABPC and \u03b2-actin.(TIF)Click here for additional data file.Figure S3Rta does not redistribute intranuclear PABPC. 293 cells were transfected with Rta and FLAG-BGLF5. Cells were fixed and stained with antibodies specific for PABPC and Rta, and fluorescent secondary antibodies. Reference bar in each panel equals 10 \u03bcM in length.(TIF)Click here for additional data file.Figure S4ZEBRA but not c-Jun relocalizes FLAG-PABPC. 293 cells were co-transfected with: (A) FLAG-PABPC, (B) ZEBRA and FLAG-PABPC, (C) c-Jun and FLAG-PABPC. Cells were fixed and stained with antibodies specific for ZEBRA, FLAG, and c-Jun, and fluorophore-conjugated secondary antibodies. Each of the following sets of panels depicts the same field of view: [i-iii], [iv-vi], [vii-ix], [x-xii], [xiii-xv], [xvi-xviii]. Reference bar in each panel equals 10 \u03bcM in length.(TIF)Click here for additional data file.Figure S5The DNA-binding deficient aggresome-inducing mutant of ZEBRA, Z(R183E), relocalizes PABPC. 293 cells were (A) transfected with Z(R183E) or (B) co-transfected with Z(R183E) and FLAG-BGLF5. Cells were fixed and stained with antibodies specific for ZEBRA and PABPC, and fluorophore-conjugated secondary antibodies. Each of the following sets of panels depicts the same field of view: [i-iii], [iv-vi], [vii-ix]. Reference bar in each panel equals 10 \u03bcM in length.(TIF)Click here for additional data file.Figure S6BGLF5 and ZEBRA inhibit endogenous nascent protein synthesis on a global scale; point mutations in the basic region impair ZEBRA's host shutoff activity. 293 cells were transfected with pHD1013, or vectors expressing BGLF5, ZEBRA, Z(N182K), or Z(S186E). Cells were incubated in methionine-free, cysteine-free media containing HPG, then fixed. Using click-chemistry based reagents, incorporated HPG was covalently bound to Alexa Fluor 555. Cells were stained with antibodies specific for ZEBRA and lamin B, and fluorophore-conjugated secondary antibodies. (A) Each of the following sets of panels depicts the same field of view: [i-iv], [v-viii], [ix-xii], [xiii-xvi], [xvii-xx], [xxi-xxiv]. Blue arrows denote cells expressing transfected protein. In panels [xiii-xvi], purple arrows denote cells expressing relatively high levels of ZEBRA, yellow arrows denote cells expressing relatively low levels of ZEBRA. Reference bar in each panel equals 10 \u03bcM in length.(TIF)Click here for additional data file."} +{"text": "Several studies of critically ill patients have suggested an association of the D/D genotype of the insertion/deletion (I/D) angiotensin-converting enzyme (ACE) polymorphism with poor outcome probably by enhancing the inflammatory response and leading to a procoagulant state. Our aim was to evaluate the effect of both the ACE I/D polymorphism and its gene product, on the clinical outcome of critically ill septic patients.The study cohort included 186 consecutive Caucasian patients with sepsis, severe sepsis or septic shock. Epidemiological, clinical data and co-morbidities along with severity scores were recorded. Measurements of serum ACE activity and genotyping for ACE I/D polymorphism were carried out in all patients. The primary outcomes were the 28-day and 90-day mortalities; secondary outcomes included the number of days without renal or cardiovascular failure, and ventilation-free days over the 28-day period following the study enrollment. One hundred and eighty healthy blood donors were genotyped and used as controls.P = 0.45). ACE I/D polymorphism and circulating ACE levels were not associated with mortality (P > 0.05) or with secondary outcomes including ventilation-free days and days without cardiovascular or renal failure among septic critically ill patients (P > 0.05). See Figure The genotype distribution in the patients' group was comparable with that observed in controls (Neither the ACE I/D polymorphism nor the serum ACE levels seem to be significant prognostic factors of the outcome of sepsis in critically ill patients."} +{"text": "Magnetic Resonance Imaging (MRI) has emerged as a promising noninvasive imaging modality for the serial assessment of vessel wall thickness in the carotid artery as an early marker of atherosclerosis. For clinical application of this technique, Scan-Rescan reproducibility is paramount. Currently, a multicontrast protocol, including a combination of MR-weightings is used as reference standard for quantitative and morphologic measurements.To investigate Scan-Rescan reproducibility for each of the commonly used weightings analyzed separately. To investigate which of the MR-weightings approximates best the combined multicontrast protocol (reference standard).2). Scan-Rescan analysis was performed in the third slice of the imaging stack, representing a slice in the common carotid artery. An example is provided in Figure 2) and lumen area (mm2) were assessed by one blinded observer for the different contrast weightings and compared with the rescan acquisition. Furthermore, vessel wall- and lumen areas from the different contrast weightings were compared with the reference standard.5 healthy volunteers underwent repeated MRI examinations of the left carotid artery with five contrast-weighted scans to image lumen and vessel wall Table . The scaReproducibility of the repeated assessment was high for all MR-weightings, for both lumen area and vessel wall areas. Table . The BlaT1-TFE showed highest correlation for lumen (r=0.97) and vessel wall area (r=0.90) assessment when compared with the reference standard.This pilot Scan-Rescan study showed best reproducibility of lumen and vessel wall area assessment for the T1-TFE and T2-TSE weightings. T1-TFE showed highest correlation to the reference standard."} +{"text": "Retrieval of myocardial biopsies under X-ray guidance in patients with unclear myocardial dysfunction or acute myocarditis is a difficult and potentially hazardous procedure since soft tissues only offer low X-ray contrast during the procedure and extraction of biopsies could cause myocardial rupture and concomitant haemopericardium. In contrast, cardiac magnetic resonance imaging provides excellent soft-tissue and anatomic information, especially for inflamed and fibrotic areas. MR-guided myocardial biopsies would therefore be attractive but could not be performed until now due to incompatible bioptome catheters leading to substantial image artifacts and significant device heating.Evaluation a novel MR-compatible bioptome in in-vitro experiments to assess potential artifacts, safety aspects and performance of MR-guided navigation under real-time imaging in a cylindrical 1.5T system.The bioptome was evaluated in a series of in-vitro experiments in an 1.5T MRI system (Philips Achieva). The specific device design (non-disclosure) avoided inducible currents and subsequent heating. The bioptome was introduced and navigated inside a) plastinated cow and swine hearts and b) a plastic heart model. The first model forms a true anatomic environment containing all relevant morphological structures (figure The metal tip of the bioptome produced an artifact that allowed constant and precise ex-vivo tip localization. The artifact size was approximately 3.3x3 cm (figure With the novel MR compatible bioptome, the superior CMR soft tissue visualization can be made available for MR-guided myocardial biopsies overcoming the limited soft tissue contrast on X-ray images. Clinically, this could significantly reduce the high amount of necessary specimen to overcome the sample error under X-ray and secondly improve the specificity and reliability of cardiac biopsies. Thirdly, MR-guided biopsies would minimize X-ray dose for the patient and especially the interventionalist.None."} +{"text": "Panax notoginseng, was widely used for the treatment of cardio- and cerebro-vascular diseases in China. This study develops a simple and global quality evaluation method for the quality control of XST.Xuesaitong (XST) injection, consisting of total saponins from n).High performance liquid chromatography-ultraviolet detection (HPLC-UV) was used to identify and quantify the chromatographic fingerprints of the XST injection. Characteristic common peaks were identified using HPLC with photo diode array detection/electrospray ionization tandem mass spectrometry (HPLC-PDA/ESI-MSRepresentative fingerprints from ten batches of samples showed 27 'common saponins' all of which were identified and quantified using ten reference saponins.P. notoginseng products such as the XST injection.Chemical fingerprinting and quantitative analysis identified most of the common saponins for the quality control of Panax notoginseng (Sanqi), was widely used for the treatment of cardiovascular and cerebrovascular diseases in China. As total saponins (including ginsenosides and notoginsenosides) in the XST injection are its active ingredients, quality control of total saponins in the XST injection is critical for its safety, efficacy and stability. Single or simultaneous determination of main components of the total saponin extracts from P. notoginseng using high performance liquid chromatography-ultraviolet detection (HPLC-UV) , (B) [Journal of Pharmaceutical and Biomedical Analysis 48 (2008) 1361-1367], (C) [Journal of Pharmaceutical and Biomedical Analysis 38 (2005) 45-51], (D) [Journal of Chromatography A 1011 (2003) 77-87], (E) , and (F) Click here for fileThe method validation for simultaneous determination of the twenty-seven saponins in XST injection. The quantitative and semi-quantitative methods were validated and the semi-quantitative principle were discussed in detail.Click here for filePrecisions and repeatability. The results of precision and repeatability for simultaneous determination of the twenty-seven saponinsClick here for fileRecovery. The results of recovery for simultaneous determination of the twenty-seven saponinsClick here for filePlots of slopes of calibration curves vs molecular weights (MW) with different chromatography columns. (A) Ultimate\u2122 XB-C18 , (B) Zorbax Eclipse SB-C18 and (C) Zorbax Eclipse SB-C18 Click here for fileRegression equation using different columns. Columns: Zorbax Eclipse SB-C18 and Zorbax Eclipse SB-C18 Click here for file"} +{"text": "Cavernous hemangiomas are the most frequent neoplasms of the liver and in routine clinical practice they often need to be differentiated from malignant tumors and other benign focal lesions. The purpose of this study is to evaluate whether diagnostic accuracy of magnetic resonance imaging (MRI) of hepatic hemangiomas, showing atypical pattern on US, improves with the use of Gd-BOPTA in comparison with contrast-enhanced multi-phase computed tomography (CT).178 consecutive patients with ambiguous hepatic masses showing atypical hyperechoic pattern on grey-scale US, underwent unenhanced and contrast-enhanced multi-phase multi-detector CT and MR (1.5T) with the use of liver-specific contrast medium gadobenate dimeglumine (Gd-BOPTA). After intravenous contrast administration arterial (HAP), venous-portal (PVP), equilibrium phases (EP) both in CT and MR and additionally hepatobiliary phase (HBP) in MR were obtained. 398 lesions have been detected including 99 hemangiomas and 299 other lesions.In non-enhanced MDCT examination detection of hemangiomas was characterized by sensitivity of 76%, specificity of 90%, PPV of 71%, NPV of 92% and accuracy of 86%.Non-enhanced MR examination showed sensitivity of 98%, specificity of 99%, PPV of 99%, NPV of 99% and accuracy of 99%.After intravenous administration of contrast medium in MR the mentioned above parameters did not increase significantly.Gd-BOPTA-enhanced MR in comparison with unenhanced MRI does not improve diagnostic accuracy in discriminating hemangiomas that show non-specific appearance in ultrasound examination. Unenhanced MR as a method of choice should directly follow US in course of diagnostic algorithm in differentiation of hemangiomas from other liver tumors. Cavernous hemangiomas are the most frequent benign neoplasms of the liver, found in autopsy examinations within 0.4% to 20% of population ,2. Such Great technological development concerning both multi-detector computer tomography and hepatocyte-specific contrast agents in magnetic resonance imaging (MRI) has been observed in recent years.Computed tomography is a well established procedure of imaging of hepatic hemangiomas. Most hemangiomas show typical enhancement pattern: nodular or globular peripheral enhancement in arterial phase with a progressive fill-in in portal venous and equilibrium phases.In particular cases the use of magnetic resonance imaging leads to specification of diagnosis based on US and CT findings.Many studies have been dedicated to differential diagnosis of hemangiomas from malignant tumors -8. PreviThe purpose of this study is to evaluate whether assessment by means of MRI of hepatic hemangiomas, showing atypical appearance on gray-scale US, improves with the use of Gd-BOBTA in comparison with contrast-enhanced multiphase CT.178 consecutive patients with non-specific hepatic foci observed in US were included in this prospective study and spiral CT and MR examinations were performed in those patients within the period not exceeding 3 weeks.Inclusion criteria were as follows: presence of focal liver lesion that in grey-scale US did not present typical features of a simple cyst (anechoic focus with posterior acoustic enhancement) or a typical hemangioma in axial and coronal plane with and without contrast enhancement in equilibrium and hepatobiliary phase, T2-weighted Express sequence in axial plane, T2-weighted FSE in coronal plane, performed also with fat saturation and T1-weighted out of phase sequence without and after contrast administration in hepatic arterial dominant phase (HAP), portal venous dominant phase (PVP), equilibrium phase (EP) and hepatobiliary phase (HBP). Slice thickness was 5mm, intersection gap - 0.5, matrix 256 \u00d7 256. Dynamic MRI was obtained immediately after a bolus injection of Gd-BOPTA (dosage of 0.1 mmol per kilogram of body weight), followed by saline solution flush of 25mL through a 20G venous catheter positioned in the antecubital vein. Similarly to the multiphase CT study HAP, PVP, and EP were performed after respectively 25, 60 and 180sec. HBP was acquired 60min after contrast agent administration. The phase-encoding direction was anterior-posterior for all sequences. All images were acquired during breath-hold.Multi-phase multi-detector (6 and 32-row) CT examination of the liver has been conducted first unenhanced, then after application of a contrast agent in HAP, PVP and EP. 100ml of iodinated contrast agent at a rate of 4mL/sec through an 20G venous catheter positioned in an antecubital vein using a power injector was administrated. The CT section thickness was 2.5mm, images interval - 2.5mm and pitch - 1.0.Spiral CT and MRI were then interpreted by three independent radiologists with at least 10-years and 5-years (AS) experience in abdominal imaging, who had no previous knowledge of patients' medical history. The interval between CT and MR examinations was from 3 to 5 weeks. Final assessment was based on the observers' consensus in case of disagreement.Radiological parameters assessed in CT and MR analysis were: size of detectable lesions, their density, signal intensity and type of enhancement.Signal intensity of each lesion in relation to adjacent liver parenchyma in T2-weighted TSE images was assessed. A 4-point scale has been used: 1-hypointense, 2-isointense, 3-hyperintense and 4-bright lesion consisted only of liver hemangiomas, the second group (nonHH group) included focal liver lesions other than hemangiomas.All lesions were also classified as small or large according to their medians by the study coordinator (ES).P values less than 0.05 were considered as statistical significant.The interobserver agreement was measured with Cohen's kappa coefficient. Statistical analysis of size of detectable lesions, their density, signal intensity and type of enhancement of hemangiomas and other lesions in unenhanced, gadolinium-enhanced MR and CT studies has been performed with Statistica 8 software and McNemar's test with Bonferroni correction for multiply comparison. The research was approved by Independent Bioethic Committee for Scientific Research of Medical University of Gdansk (NKEBN/649/2001-2002). All patients gave their written consent to participate.The study has been partially financed from the research grant ST-82 given by authorities of the Medical University of Gdansk to MS.178 patients were qualified for the study, amongst this group 161 underwent further analysis .In case of 17 patients we failed to establish the final diagnosis - 2 of the patients passed away, 15 did not show for the follow-up.High interobserver agreement confirmed the methodology as reliable and reproducible.In 100 patients the final diagnosis was based upon histopathological examination results (66 cases by the means of surgery and 34 cases with biopsy) which disclosed: 41 cases of HCC, 21 FNHs, 28 cases of liver metastases, 4 cavernous hemangiomas, 4 solitary adenomas and 2 cases of peripheral cholangiocarcinoma.In the remaining 61 patients, the final diagnosis was based upon the clinical and diagnostic imaging follow-up. In this group we observed: 30 hepatic hemangiomas (confirmed in contrast-enhanced US examination and follow-up MR examination), 18 FNHs (confirmed in Gd-EOB-DTPA-enhanced MR), 13 cases of liver metastases (treated with chemotherapy and confirmed in follow-up CT examinations) and 2 inflammatory lesions (follow-up CT examinations showed no lesions).The HH group consisted of 99 liver hemangiomas, recognized in 34 patients. 21 patients with HH had isolated liver lesions and multifocal HHs were recognized in 13 people.The nonHH group included 127 patients with 299 focal liver lesions other than hemangioma: 144 metastases, 100 cases of hepatocellular carcinoma, 4 adenomas, 44 FNHs and 7 other lesions.The diameter of foci ranged from 6mm to 125mm (median 21mm). According to the mean foci diameter, all lesions were divided into two groups: small lesions (<2cm) - 199 foci and large lesions (\u22652cm) - 199 foci. In the HH-group, 40 foci of cavernous hemangiomas were large lesions and the rest of 59 tumors were small lesions.Small hemangiomas more frequently (30/59) showed homogenous enhancement pattern in all three phases, while large hemangiomas (25/40) presented nodular or globular peripheral enhancement pattern in HAP and progressive fill-in in PVP and EP in dynamic MR study table . The typGd-BOPTA - enhanced MR and multi-phase spiral CT evaluation of hepatic hemangiomas was based upon typical enhancement pattern in three phases table :- homogenous in HAP and PVP or EP figure ,- nodular peripheral or globular in HAP with progressive fill-in enhancement in PVP and EP figure .In the hepatobiliary phase of MR examination all hemangiomas showed a lower signal in comparison to the adjacent liver tissue figure . 233 nonSpiral CT correctly characterized 75 hemangiomas.Signal intensity observed in moderately and heavily T2-weighted images in hemangiomas and other liver lesions is presented in table In unenhanced MR false-negative diagnosis was obtained in one case of hemangioma and one false-positive diagnosis of hemangioma was noted in case of cystic metastasis from ovarian carcinoma.Gd-BOPTA-enhanced MR study allowed to correctly diagnose cystic metastasis from ovarian carcinoma and therefore revealed 98 hemangiomas. Still one hemangioma was unrecognized figure .p < 0.0001 for both modalities), also in case of small and large lesions assessed separately (p = 0.0055 for unenhanced MR and p = 0.0009 for Gd-BOPTA-enhanced MR).Unenhanced MR and Gd-BOPTA-enhanced MR show higher diagnostic accuracy in differentiation of hemangiomas than CT and high signal intensity in T2-weighted images -14.In dynamic examination the enhancement pattern of hemangiomas does not differ in neither CT nor MR study.Distinction between metastases and cavernous hemangiomas on the basis of different patterns of enhancement is well described, but to our knowledge, only few reports focus on the type of enhancement, diagnosed with hepatocyte-specific contrast-enhanced MRI .In presented study the assessment of focal lesions in MR was performed with the use of moderately and heavily T2-weighted sequences and dynamic examination after Gd-BOPTA administration.Ultrasound was the initial examination qualifying patients into this study as it allowed to distinguish a group of patients with ambiguous focal liver lesions, some of suspected malignant nature.Patients presenting lesions of typical ultrasound appearance of hemangiomas and simple cysts were excluded from further studies as such lesions may be successfully monitored in grey-scale ultrasound examinations.To assess foci in moderately T2-weighted images qualitative criteria proposed by Fenlon were used . In modeA high diagnostic efficacy of marked hyperintensity in moderately and heavily T2-weighted images as a feature allowing to diagnose hepatic hemangiomas was proven with indexes of diagnostic efficacy reaching 99% table .Similar observation was made by Ito et al. , who gaiFenlon et al. compared qualitative and quantitative analysis of hepatic tumors using heavily T2-weighted SE technique and they noted that quantitative method with measurement of T2-relaxation times allowed significantly better differentiation between benign and malignant neoplasms with accuracy about 100% than that of the subjective visual assessment of focal liver lesions .In our series a false-negative diagnosis concerned one case of hemangioma with areas of fibrosis and hyalinization, which mimicked a solid part of malignant necrotic neoplasm. One false-positive diagnosis of hemangioma was reported in case of cystic metastasis from ovarian cancer. We did not observe characteristic strong hyperintensity typical for hemangiomas in other cases of malignant tumors especially in necrotic or hypervascular metastases as noted in literature ,28.The next radiological feature that allows recognition of HH is the type of enhancement observed in successive phases of dynamic CT or MR examination after extracellular iodine or gadolinium based contrast medium administration. Ros et al. distingu- early homogenous enhancement seen in foci of less than 1.5 cm in diameter,- nodular peripheral enhancement in HAP with a progressive centripetal fill-in pattern, to homogenous enhancement in the late phase (foci from 1.5 to 5cm in diameter),- nodular peripheral enhancement in HAP with a hypointense center of the lesion in the late phase (foci larger than 5 cm in diameter).Essentially in our study two types of enhancement patterns in HAP were stated: nodular peripheral and homogenous table . At the In hemangiomas greater than 2cm in diameter a nodular peripheral enhancement pattern in HAP with progressive slow centripetal fill-in during next phases has been observed. This type of enhancement has been described as specific for hemangiomas since 1986 -37.The value of PPV and accuracy and sensitivity in differentiation of hemangiomas from other focal liver lesions based of enhancement pattern presented in multi-phase sCT study are 0.71, 0.86 and 0.76 and noticeably lower than all indexes of diagnostic efficacy obtained by using unenhanced-MRI (PPV-0.99). In the group of lesions smaller than 2cm, sensitivity of diagnostic methods based on contrast CT enhancement pattern is even lower, at the range of 0.66.Presented study in accordance to the other authors ,38 showsIn this study all hemangiomas presented weaker enhancement in hepatobiliary phase in comparison to the adjacent liver parenchyma, similarly to metastases and the majority of HCCs. This results from the characteristic of applied hepatocyte-specific contrast media - Gd-BOPTA. Gadobenate dimeglumine (Gd-BOPTA) is a gadolinium-based paramagnetic contrast with a vascular-interstitial distribution during first few minutes. The majority of this contrast agent is excreted by the kidneys in the urine, however, about 4% of the injected dose is taken up by the hepatocytes and eliminated via anionic transporter across the sinusoidal membrane into the bile .Due to contrast agent presence within hepatic cells, it is possible to observe the enhancement of the liver parenchyma that persists for 1-3 hours after its administration and this period is called hepatobiliary phase.A tumor that does not contain functioning hepatocytes in which hepatobiliary metabolism is active, is not able to uptake Gd-BOPTA.Hemangiomas consist of multiple vascular channels limited by single layer of endothelial cells within a thin fibrous stroma and the enhancement in hepatobiliary phase is not observed, what makes hemangiomas impossible to differentiate from other hepatocyte-devoided liver tumors ,40,41.Main restrictions of this study are a small number of cases of hemangiomas confirmed in histological examination, lack of quantitative analysis of focal liver lesions signal intensity as described by other authors and no iOur results indicate that qualitative analysis of signal intensity of hepatic lesions in moderately and heavily T2-weighted images is the most sensitive method of differentiation between liver hemangiomas of non-specific appearance in ultrasound from malignant tumors. Assessment of the enhancement pattern provides information about vascularity of the lesion although the type of enhancement pattern itself is not as important in characterization of hemangiomas as the intensity of the lesion in T2-weighted images.Application of contrast-enhanced MR, especially with administration of liver-specific contrast agents in diagnosing liver hemangiomas is not advisable as it leads to elongation of examination time and unnecessary exposure to potential side effects of intravenous contrast agents.Gd-BOPTA-enhanced MR in comparison with unenhanced MRI does not improve diagnostic accuracy in discriminating hemangiomas that show non-specific appearance in ultrasound examination. Unenhanced MR as a method of choice should directly follow ultrasound examination in course of diagnostic algorithm in differentiation of hemangiomas from other liver tumors.CT: computer tomography; EP: equilibrium phase; FNH: focal nodular hyperplasia; FSE: fast spin echo; HAP: hepatic arterial dominant phase; HBP: hepatobiliary phase; HH: hepatic hemangioma; MDCT: multidetector computer tomography; MR: magnetic resonance; MRI: magnetic resonance imaging; nonHH: other lesion than hemangioma; NPV: negative predictive value; PPV: positive predictive value; PVP: portal venous dominant phase; ROI: region of interest; sCT: spiral computed tomography; SE: spin echo; TE: echo time; TR: repetition time; US: ultrasound.The authors declare that they have no competing interests.ES has had substantial contribution to study design, data collection and interpretation, statistic analysis and manuscript preparation. TN has contributed to statistic analysis and manuscript preparation. EIS has contributed to data collection and interpretation, as well as manuscript preparation. JW and ADJ has contributed to study design and manuscript preparation. AS has contributed to data collection and interpretation. KM has contributed to manuscript preparation. MS has contributed to study design and has coordinated research team. All authors have read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-230X/11/43/prepub"} +{"text": "Epitopes displayed by MHC-I come from the multistep degradation of proteins by intracellular peptidases such as proteasome and aminopeptidases or cathepsins in the exogenous pathway. We hypothesize that due to structural homologies HIV protease inhibitors (PIs) used in antiretroviral therapies may affect activities of cellular peptidases involved in epitope processing and may affect epitope presentation to immune cells.Using a fluorogenic assay the effect of 5 HIV-1 PIs on proteasome, aminopeptidase and cathepsin activities was tested in PBMCs from at least 6 healthy donors. Using PBMC cytosol as a source of peptidases and HPLC and mass spectrometry to define and quantify the degradation products, the effect of HIV PIs on HIV peptide processing kinetics and HIV epitope half-life was assessed. Finally we assessed the impact of PIs on the endogenous processing and presentation of epitopes by infected cells to CD8 T cells using a fluorescence-based cytotoxicity assay.HIV PIs variably altered proteasome, post-proteasomal aminopeptidases and cathepsin activities. Depending on the PI, some activities were inhibited , enhanced , and others not changed. These PI-induced changes in protease activities modified HIV peptide processing patterns and HIV epitope intracellular half-life prior to MHC-I loading. Depending on the PI and the epitope the half-life was increased 1.5 fold (p<0.01) or decreased 1.3 fold (p<0.05). Furthermore HIV PI altered the presentation of HIV epitopes and recognition by epitope-specific CD8 T cells.These findings suggest that in HIV-infected patients an antiretroviral therapy including PIs might -by altering host proteases function- modify the pattern of epitope presentation, leading to the elicitation of additional CTL responses against HIV and potentially against other pathogens co-infecting HIV+ persons.This project was supported by NIH-NIAID grant R01-A1084106."} +{"text": "The separation and purification of peptides and proteins using chromatography can make up more than half the amount of the total purification costs of a biotechnological process . The devTo explore the power of computer science in supporting experimentally based process development, we applied a combined force field approach with subsequent Density Functional Theory (DFT) calculations. As a first step, we examined the adsorption of the amino acids glycine (gly), l-alanine and l-lysine (lys) on MFI-type zeolite (MFI). Experimental data from adsorption isotherms and Isothermal Titration Calorimetry (ITC) have proved the adsorption to be strongly pH-dependent. Therefore, we applied the amino acids in their protonated and neutral state in order to simulate low and medium pH values in our computational study. A T33 cluster containing all potential binding regions was used as a model of MFI.3 code (Accelrys Inc.) using the generalized-gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the double numerical plus polarization (DNP) basis set.Initial geometries for DFT calculations were prepared with force field methods in order to speed up the search in conformational space. Low energy adsorption sites were determined using Adsorption Locator and Forcite modules of Materials Studio 6.0 (Accelrys Inc.). Subsequently, the structures were optimized with DMollow_pH >> low_pH ~ lysmedium_pH)) >> medium_pH. Furthermore, calculated adsorption energy ratios between protonated amino acids agree very well with the enthalpy ratios derived from low pH ITC experiments: , , . Additionally, the adsorption mechanisms of neutral and protonated amino acids were found to be qualitatively different. Neutral amino acids bind via neutral amino group and proton transfer to the active site in zeolite, whereas protonated amino acids bind via carboxyl group.Calculated energies strongly mirror the adsorption affinities derived from experimental adsorption isotherms: (lysThese results illustrate that a judiciously designed combination of atomistic modeling methods can be used as a reliable first step in the design of cost-efficient industrial processes."} +{"text": "This study has shown that in patients with suspected and confirmed CAD, estimates of MBF by perfusion-CMR are significantly higher in diastole than systole during maximal hyperemic stress.Differences in myocardial blood flow (MBF) between systole and diastole have been reported in healthy volunteers but the impact of cardiac phase on detecting coronary artery disease (CAD) is unknown . This stFollowing invasive coronary angiography, 40 patients underwent stress perfusion-CMR (1.5T Philips) acquired at mid-systole and end-diastole simultaneously [Twenty-one patients (53%) had CAD. A typical example of a patient with ischemia is shown in Figure Estimates of stress MBF and MPR by perfusion-CMR in this study were greater in diastole than systole in normal and CAD patients. Although the diagnostic accuracy of both phases was similar, the MPR cut-off values were different. These observations are particularly important in the emerging field of 3D perfusion-CMR where the acquisition phase may be specifically chosen. Different estimates of MBF and different MPR cut-off values between phases mean a universal standard needs to be agreed for 3D acquisitions.S.P is funded by a British Heart Foundation fellowship (FS/10/62/28409).S.P and J.P.G received an unrestricted educational research grant from Philips Healthcare."} +{"text": "Drosophila melanogaster, high-resolution recombination maps show an excess of DSBs within annotated transcripts relative to intergenic sequences. The impact of active transcription on recombination landscapes, however, remains unexplored in a multicellular organism. We then investigated the transcription profile during early meiosis in D. melanogaster females to obtain a glimpse at the relevant transcriptional dynamics during DSB formation, and test the specific hypothesis that DSBs preferentially target transcriptionally active genomic regions.Evidence in yeast indicates that gene expression is correlated with recombination activity and double-strand break (DSB) formation in some hotspots. Studies of nucleosome occupancy in yeast and mice also suggest that open chromatin influences the formation of DSBs. In Our study of transcript profiles of early- and late-meiosis using mRNA-seq revealed, 1) significant differences in gene expression, 2) new genes and exons, 3) parent-of-origin effects on transcription in early-meiosis stages, and 4) a nonrandom genomic distribution of transcribed genes. Importantly, genomic regions that are more actively transcribed during early meiosis show higher rates of recombination, and we ruled out DSB preference for genic regions that are not transcribed.D. melanogaster genome. We propose that a model where variation in gene expression plays a role altering the recombination landscape across the genome could provide a molecular, heritable and plastic mechanism to observed patterns of recombination variation, from the high level of intra-specific variation to the known influence of environmental factors and stress conditions.Our results provide evidence in a multicellular organism that transcription during the initial phases of meiosis increases the likelihood of DSB and give insight into the molecular determinants of recombination rate variation across the AA performed the experiments and data collection. Correspondence and requests for materials should be addressed to JC (josep-comeron@uiowa.edu). Both authors read and approved the final manuscript.Table S2: Top Enriched GO Terms among genes with parent-of origin effects with maternal-like transcript levels.Top Enriched GO Terms among genes with parent-of origin effects with maternal-like transcript levels for Early- and Late-Ovarian samples. Click here for fileFPKM distribution density across genes. Blue region: Early-ovarian transcriptome; Orange region: Late-ovarian transcriptome.Click here for fileVolcano plot of genes by significance and fold change.Click here for file2 fold difference histogram following normalization.Early vs Late LogClick here for fileP-value distribution following normalization and testing with CuffDiff v2.0.2 before correcting for multiple tests. This histogram displays the approximate expected distribution of significance following proper normalization\u2014harboring signals of true positives enriched at the low-end, while enrichment in the highest bin is due to genes with low read counts.Click here for file"} +{"text": "HTLV-1 is classified in seven subtypes (a-g) most of them restricted to specific regions (b-e), while the Cosmopolitan subtype (a) is worldwide distributed. Cosmopolitan subtype has experimented a degree of molecular diversity giving rise to five subgroups: Transcontinental (A), Japanese (B), West African (C), North African (D) and Black Peruvian (E).to confirm the classification of four HTLV-1 highly divergent strains as a new subgroup within the Cosmopolitan subtype.http://www.R-project.org).LTR sequences from 65 HTLV-1 positive Buenos Aires residents were retrospectively studied. Phylogeny of LTR region was studied by three different methods . A similitude index (SI) was estimated as the mean number of nucleotide substitutions from each subgroup (intra-subgroup) or between sequences from a given subgroup against all from other subgroups (inter-subgroup) previously described as divergent, branching off all known subgroups . The similitude analysis showed a SI intra-subgroup similar to those obtained for A-D subgroups and a SI inter-subgroup similar to subgroups A and D. Following nomenclature, it was named subgroup F.This study confirms the existence of a highly divergent monophyletic clade within the Cosmopolitan subtype composed of sequences from Peruvian and Brazilian individuals and suggest that more studies should be performed in this South-American area where the last subgroups (E and F) has been detected."} +{"text": "Mucuna pruriens (mucuna) seeds contain 3-6% L-DOPA, and have been used in traditional Ayurvedic medicine to treat diseases resembling Parkinson\u2019s disease (PD). Pilot studies in PD show that mucuna seed powder has similar effects to conventional levodopa/carbidopa medication. Formulations of mucuna seed are readily available through the internet, and are used by some PD patients as an alternative to conventional levadopa/carbidopa medication. The purpose of this study was to examine the L-DOPA content of a range of popular mucuna products in order to assess the veracity of label claims.Six different brands of mucuna product were ordered through the internet. Certificates of analysis were obtained where possible. A standard amount of each product was extracted using methanol: formic acid for analysis using reversed-phase high performance liquid chromatography (HPLC) with ultraviolet and fluorescence detection. L-DOPA content was calculated using a standard curve prepared using L-DOPA (Sigma-Aldrich) as reference.The claimed L-DOPA content ranged from 25 to 250mg per dose for the six products. HPLC analysis revealed that only two of the products had L-DOPA values close to the value claimed. The remaining products contained considerably less L-DOPA , <10% in two cases, than implied on the label. Certificates of analysis suggested that not all manufacturers routinely measure L-DOPA content of their mucuna product.Four of six products examined showed a large discrepancy between label claim and L-DOPA content, independently measured by HPLC. This finding warrants further investigation as these deficiencies could impact both patients, and the outcome of clinical studies using these products."} +{"text": "Significantly, the role of sRNAs in the stress response remains poorly understood at the genome-scale level. It was previously shown that toxic-metabolite stress is one of the most comprehensive and encompassing stress responses in the cell, engaging both the general stress response as well as specialized metabolic programs.Small non-coding RNAs (sRNA) are emerging as major components of the cell\u2019s regulatory network, several possessing their own regulons. A few sRNAs have been reported as being involved in general or toxic-metabolite stress, mostly in GramC. acetobutylicum in response to the native but toxic metabolites, butanol and butyrate. 7.5% of the RNA-seq reads mapped to genome outside annotated ORFs, thus demonstrating the richness and importance of the small RNome. We used comparative expression analysis of 113 sRNAs we had previously computationally predicted, and of annotated mRNAs to set metrics for reliably identifying sRNAs from RNA-seq data, thus discovering 46 additional sRNAs. Under metabolite stress, these 159 sRNAs displayed distinct expression patterns, a select number of which was verified by Northern analysis. We identified stress-related expression of sRNAs affecting transcriptional and translational (tmRNA & SRP-RNA) processes, and 65 likely targets of the RNA chaperone Hfq.Using RNA deep sequencing (RNA-seq) we examined the sRNome of Clostridium organisms, whether related to normophysiology, pathogenesis or biotechnological applications.Our results support an important role for sRNAs for understanding the complexity of the regulatory network that underlies the stress response in The prehybridization and hybridization of the membrane with labeled oligo probes was carried using the ULTRAhyb hybridization solution (Ambion) at 42\u00b0C.Northern analysis of select sRNAs was performed as described previously using single stranded oligo DNA probes . The proB. subtilis promoter consensus sequences [Lactococcus promoters, we used the promoter HMM model from the PPP tool [http://www.softberry.com). Secondary structures of sRNAs were predicted using Vienna RNAfold [Promoter prediction in the upstream region of the sRNAs were carried out using PSSMs of equences . For thePPP tool . Rho indPPP tool , Erpin [PPP tool and Find RNAfold ,93.The sRNA nomenclature for the newly identified sRNAs was done in the same manner as described previously .+ reductase; AhrC/ArgR: Arginine repressor; Hfq: Host factor-I protein from Q8 bacteriophage; TFBS: Transcriptional factor binding site; SRP: Signal recognition particle; tmRNA: Transfer and messenger RNA; SAM: S-adenosyl methionine; adhe: Alcohol/aldehyde dehydrogenase 1; ctf: Co-enzyme A transferase; adc: Acetoacetate decarboxylase; SmpB: Small protein B; EF-Tu/Tuf: Elongation factor Tu; rpsA: Ribosomal protein A.SIPHT: sRNA identification protocol using high-throughput technologies; ABE: Acetone-bytanol-ethanol; Q-RT-PCR: Quantitative reverse transcriptase polymerase chain reaction; IOR: Interoperonic region; IGR: Intergenic region; ORF: Open reading frame; UTR: Untranslated region; PSSM: Position specific scoring matrix; HMM: Hidden Markov model; FNR: Ferredoxin-NADPThe authors declare that they have no competing interests.KPV and SWJ carried out the fermentations and RNA isolations. KPV carried out Northern analysis and drafted the manuscript. SGK constructed the libraries for RNA-seq. KPM processed the data and built the web browser. KPV and KPM analysed the data. KPV and MTR carried out the identification of new sRNAs and other computational analyses. BCM and ETP helped with data analysis and interpretation, and participated in the manuscript preparation. ETP conceived the study, participated in its design and coordination. All authors read and approved the final manuscript.Detailing the information on the sequenced libraries and the list of newly identified 46 sRNAs.Click here for fileC. acetobutylicum. Pair-wise and point by point by comparison of each stress level to the no stress control using DEseq at a p-value\u2009\u2264\u20090.05. Table S2: Probes sequences used for Northern analysis.Differential expression of annotated mRNAs of Click here for fileC. acetobutylicum hfq with the Hfq from E. coli (3GIB_B), reveals conservation in the secondary structure on the Hfq monomeric unit. (A) The \u03b1-\u03b21-5 structural unit can be found to be conserved. (B) The corresponding conservation in the protein sequence is displayed below.CBLAST of the Click here for fileContaining the Hfq binding model.Click here for fileHierarchical clustering of the 65 sRNAs belonging to the Hfq constellation (see text for details).Click here for filesolB to the sol (adhE1-ctfA-ctfB) operon.Putative antisense binding of Click here for fileHierarchical clustering of 159 sRNAs under both butanol and butyric acid stress.Click here for file"} +{"text": "We have demonstrated that cardiac magnetic resonance (CMR) myocardial feature tracking (FT) and natural radial strain correlate and correspond to inotropic stimulation. CMR-FT has the potential for quantitative wall motion assessment at rest and during dobutamine stress magnetic resonance (DSMR) imaging.CMR-FT is a recently introduced technique for tissue voxel motion tracking on standard steady-state free precession (SSFP) images to derive radial myocardial mechanics. CMR-FT has the potential to facilitate DSMR analysis however has not yet been compared to external reference standards (with stress) such as SSFP derived natural radial strain.10 healthy subjects were studied at 1.5 Tesla. LV short-axis radial strain ErrSAX was derived from SSFP cine images using dedicated CMR-FT software at rest and during dobutamine stress (10 and 20 \u03bcg * kg-1* min-1). Natural radial strain values were calculated in identical segments as analysed for ErrSAX using commercially available software . 95% confidence intervals (CI) of the difference and p-values were calculated to compare the 2 techniques.In all volunteers strain parameters could be derived from the SSFP images at rest and stress. ErrSAX values showed significantly increased contraction with DSMR . Natural radial strain values increased with dobutamine .There was reasonable agreement between mean ErrSAX and natural radial strain at rest and with dobutamine stress figure as deterCMR-FT correlates with natural radial strain derived from SSFP cine imaging. Both measures correspond to inotropic stimulation. CMR-FT holds promise of easy and fast quantification of wall mechanics and strain.AS receives grant support from the British Heart Foundation (BHF) (RE/08/003 and FS/10/029/28253) and the Biomedical Research Centre (BRC-CTF 196). SK receives grant support from the American College of Cardiology Foundation, the Edna Ittner Pediatric Foundation, and the Children\u2019s Hospital and Medical Center Foundation."} +{"text": "Of those 33 neurons, 15 (45%) began to discharge before hand-target contact, while the remaining neurons were tonically active after contact. Thirty-percent (n\u200a=\u200a15/48) of studied neurons responded to both passive somatosensory stimulation and to the motor task. A consistent percentage of task-related neurons in SII/pIC was selectively activated during finger exploration (FE) and precision grasping (PG) execution, suggesting they play a pivotal role in control skilled finger movements. Furthermore, hand-manipulation-related neurons also responded when visual feedback was absent in the dark. Altogether, our results suggest that somato-motor neurons in SII/pIC likely contribute to haptic processing from the initial to the final phase of grasping and object manipulation. Such motor-related activity could also provide the somato-motor binding principle enabling the translation of diachronic somatosensory inputs into a coherent image of the explored object.The posterior inner perisylvian region including the secondary somatosensory cortex (area SII) and the adjacent region of posterior insular cortex (pIC) has been implicated in haptic processing by integrating somato-motor information during hand-manipulation, both in humans and in non-human primates. However, motor-related properties during hand-manipulation are still largely unknown. To investigate a motor-related activity in the hand region of SII/pIC, two macaque monkeys were trained to perform a hand-manipulation task, requiring 3 different grip types both in light and in dark conditions. Our results showed that 70% ( Whenever retrieving a key or lipstick from the bottom of a purse, we usually identify the searched object by hand-finger exploration in the absence of vision In both humans and non-human primates, the secondary somatosensory cortex (area SII) and the adjacent posterior insular cortex (pIC) is believed to play a pivotal role in high-level haptic perception In non-human primates, area SII and adjacent pIC show multiple digits and hand representations In order to answer these questions we investigated hand-manipulation-related neurons in SII/pIC in monkeys trained to perform a hand-manipulation motor task, using three different grip types and precision grasping (PG) execution. Furthermore, a subset number of hand-manipulation-related neurons increased their discharge in the dark. The temporal profile of task-related responses enabled us to segregate three possible components of haptic processing in SII/pIC, namely: 1) Prediction of the hand-finger movement; 2) Hand-object contact detection; 3) Hand-finger exploration. Such somato-motor haptic processing could also provide the somato-motor binding principle enabling the translation of diachronic somatosensory inputs into a coherent image of the explored object.Macaca mulatta) were used in this study. We recorded from both hemispheres in one monkey and from the left hemisphere in another monkey . All experimental protocols were approved by the Ethical Committee for Animal Research of the University of Parma and by the Superior Institute for Health . The authorization for conducting our experiments was delivered by the Animal Health and Veterinary Medication Division of the Department of Public Veterinary Health, Nutrition and Food Safety of the Italian Ministry of Health . The monkeys were housed and handled in strict accordance with the recommendations of the Weatherall Report about good animal practice. For example, the monkeys were fed a variety of vegetables, fruits, and grains everyday. Supplementary pellets were also provided for maintaining their nutritional health. Their health condition was carefully checked by experimenters everyday. The monkeys were kept in individual primate cages in an air-conditioned room where was maintained a consistent temperature at approximately 25\u201326 degrees Celsius. Our routine laboratory procedures also included an environmental enrichment program where monkeys had access to toys, mirrors and swings. They also had visual, auditory and olfactory contact with other animals and, they could touch/groom each other. Any possible pain associated with surgeries was pharmacologically ameliorated. The well-being and health conditions of the monkeys were constantly monitored by the institutional veterinary doctor of the University of Parma.Two male macaque monkeys were implanted over both hemispheres based on stereotaxic coordinates of the cortical regions to be recorded . The surIn the case of MK2, the targeted area was identified on MRI images prior to the experiment. The first surgery was performed to enable head fixation under the above-described anesthesia. A \u201cK-letter\u201d shaped stainless steel head post was implanted on the occipital skull to allow attachment of a head-fixation bar on the primate chair. Following training, a cylindrical-recording chamber was implanted under above-described anesthesia.The center of the chamber and angle in stereotaxic coordinates were as follows: in MK1 over both hemispheres and in MK2 over the right hemisphere . The position of all chambers allowed recording from the rostral to the middle part of the upper bank of the lateral sulcus, including the hand regions of SII/pIC see .Single-unit recording was performed extracellularly using varnish-insulated tungsten microelectrodes advanced perpendicularly into the cortex through the dura matter. In the MK1, the terminal of hydraulic microdrive manipulator was attached to a stereotaxic arm and fixed to the monkey\u2019s head fixation apparatus on the monkey\u2019s chair. In the MK2, the microelectrode was mounted on an electrode-driving terminal fixed onto the recording chamber. Neuronal activity was amplified and monitored on an oscilloscope. Single neuron action potentials were isolated on-line with a dual voltage-time window discriminator to test properties of single neurons. Raw analog signal, isolated action potentials and the digital events related to the behavioral paradigm, were acquired and stored on-line by means of CED1401 mk-II and Spike2 software . A waveform of single spike was further extracted and sorted off-line using the same software.After recording chamber implantation, physiological boundaries of hand regions in area SII/pIC were identified on the basis of stereotaxic coordinates and previously described neuronal properties [17]\u2013. Moreover, the temporal pattern of discharge was similar for the three tested grips but its firing rate being higher during the execution of PG and SG than during the FE execution . p<.001], but neither epochs showed any significant difference between each other . Moreover, this neuron did not show any grip-selectivity . p<.00001]; it was broadly tuned by grasp execution . Also p<.0001]. In contrast to neuron of p<.0001, following Bonferroni correction, for each p<.001].p<.0001] and between Grip and Epoch . p<.01), POS-type neurons showed significantly stronger activity in \u2018post-contact epoch\u2019 (p<.01) and MID-type neurons did not showed any significant difference between the two epochs. Moreover, just MID-type neurons did not show any significant interaction with types.To clarify both grip-selectivity and temporal profile discharge of these types of neurons, a 2\u00d73\u00d73 repeated measure ANOVA with Epoch , Grip and Type as factors was applied. The analysis did not show any significant main effect but it showed significant interactions both between Epoch and Type but not for Epoch (p\u200a=\u200a0.06). Furthermore, it also showed a significant interaction between factors . Activity of Best-grip population was significantly stronger in post-contact epoch than in pre-contact one (p<.0001), while Second best- and Worst-grip populations did not show any significant difference between epochs. Furthermore, the pre-contact epoch activity of both Best- and Second best-grip populations was significantly stronger than that of the Worst-grip population . In the post-contact epoch, Best-grip population showed significantly stronger activity than both Second best- and Worst-grip population .Since population analysis showed significant main effect for grips , we furtp\u200a=\u200a.017). This neuron showed tactile RF on the contralateral palm. During the execution of the motor task, it was maximally activated during post-contact epoch and it showed significantly stronger responses during FE than during PG execution (p<.0001). This response likely reflected somatosensory stimulation evoked when the fingers but not the thumb touched the palm, a hand configuration typically occurring during FE and SG execution.p<.0001).\u03c72\u200a=\u200a17.4, df\u200a=\u200a4, p<.01). Furthermore, a residuals analysis showed that the statistically largest proportion was represented by FE in the Best-grip , by PG (n\u200a=\u200a6) in the Second best-grip category , and by SG (n\u200a=\u200a6) in the Worst-grip category .To clarify differences between the two populations in the hand-manipulation-related activity, first we investigated the composition of Best-, Second best- or Worst-grip in SS population by submitting these neurons to the same analysis described above. Five out of 15 SS-related neurons were excluded from further analysis because they did not show any significant main effect for the Grip factor. p<.001] and Epoch . It also showed a significant interaction between factors . Activity of three populations was stronger in the post-contact epoch than in the pre-contact one (p<.0001). Importantly, in contrast to hand-manipulation-related neurons (see p<.001).rons see , SS-relan\u200a=\u200a33) and SS-related neurons . For all 48 neurons we added up the activity both in pre- and post-contact epochs and then calculated the mean values of net normalized activity for each grip . We next evaluated their correlation coefficient (p<. 01). Although pairs among PRE, MID and SOM type neurons or pair between SOM and POS ones did not show any significant correlations with others , POS type neurons showed significantly negative correlations with PRE and MID type neurons .Since population analysis demonstrated an evident difference both in grip-selectivity and discharge temporal profile between grip-selective hand-manipulation-related neurons and grip-selective SS-related neurons , we furtfficient . Correlan\u200a=\u200a33) were tested while monkeys performed PG and/or FE in the Dark condition.In order to investigate the effect of visual feedback, most of the hand-manipulation-related neurons and Epoch was applied. In 16 neurons tested during PG execution in both Light and Dark conditions, 8 neurons (50%) showed statistically stronger response in the dark, 3 neurons (19%) showed the opposite effect, and 5 neurons (31%) did not show any significant difference between the two conditions. On the other hand, in the 20 neurons tested during FE execution in both conditions, 6 neurons (30%) showed statistically stronger response in the dark than in the light, 6 neurons (30%) showed the opposite effect, and 8 neurons (40%) did not show any significant difference between the two conditions.p<.0001], Epoch and also interaction between factors . Baseline activity was not significantly different between Light and Dark conditions. However, while activity in the pre-contact epoch did not show any significant difference with its baseline in Light condition, that activity in the Dark condition was significantly stronger than during baseline . Furthermore, activity in post-contact epoch in the Dark condition showed the best response among task-related epochs (for each comparison p<.01). p<.001], Epoch and interaction between factors . As the previous example, although activity in baseline was not significantly different between conditions, the neuron showed significantly stronger responses in the dark than in the light during both pre- and post-contact epochs .To examine how much hand-manipulation-related neurons in SII/pIC hand region do show somato-motor context-dependent activity, we analyzed 16 neurons in two different conditions: a) FE grip with a target (FEt), and b) the same grip performed without a target (FEwt). Monkey performed both conditions in the dark . The resp<.005], Epoch and also interaction between factors . Importantly, the pre-contact epoch activity was not statistically different between FEt and FEwt (p<.0001), while activity in post-contact epoch was significantly stronger in FEt than in FEwt condition (p<.0001). This result may suggest that the additive discharge after contact in FEt condition could be partly due to an object-displacement effect.Converging findings from non-human primates and humans brain studies suggested that secondary somatosensory cortex (SII) and the adjacent posterior insular cortex (pIC) could play a pivotal role in somato-motor haptic processing. Although hodological studies in macaque monkey brain revealed that hand regions within SII/pIC have reciprocal connections with the parieto-premotor grasping-related areas, such as ventral premotor area F5 and anterior intraparietal area AIP, the physiological somato-motor properties of SII/pIC during hand-manipulation are still largely unknown.n\u200a=\u200a33/48) of task related recorded neurons were only activated during monkeys\u2019 active hand-manipulation. Of those 33 neurons, 15 (45%) became active before hand-target contact, while the remaining neurons were mostly activated after contact. (2) Thirty-percent (n\u200a=\u200a15/48) of studied neurons responded to both passive somatosensory stimulation and motor task execution. (3) A consistent percentage of all tested neurons was selectively active during finger exploration (FE) and precision grasping (PG) execution. (4) A subset of hand-manipulation-related neurons increased their discharge when visual feedback was absent. (5) Correlation analysis revealed that all tested neurons in this region could be involved in haptic processing during object grasping and hand-manipulation.The original aim of this study was to determine whether neurons in SII/pIC hand regions show hand-manipulation-related properties. We formally tested a total of 48 single units from SII/pIC in two macaque monkeys. The main results of our study can be summarized as follows. (1) Focusing on motor responses, 70% as showing the effect of active touch during task execution. On the basis of this interpretation, the significant activity enhancement in the FEt task (FEt>FEwt) likely reflects the presence of the target and the following target displacement movements Both PRE and MID type consisted of neurons discharging prior to the hand-target contact. In particular, as epitomized by the neuron shown in The small number of SS-related neurons was due to our strict criterion to select neurons to be recorded. In fact, since the present study focused on purely motor responses of SII/pIC neurons, we only recorded neurons if we observed stronger responses during active hand-manipulation than during passive somatosensory stimulations. Additionally, we did not test neurons by means of the motor task if they showed strong baseline activity during the set period. In contrast to our study, Gardner and co-workers demonstrated grasping-related activity of somatosensory neurons in SI and posterior parietal cortex, recording neurons with high baseline activity even before motor execution. In our study the baseline activity of SS-related neurons was as low as that of hand-manipulation-related ones .Both hand-manipulation-related and SS-related neurons showed grip-selectivity and 7. OOn the other hand, activity of SS-related neurons may correlate with duration of hand-manipulation time B and S2Naturally, exploring an object in the dark without any visual feedback is much harder than in the light. Our behavioral analysis showed that the hand-manipulation execution time in the Dark was longer than in the Light condition . MoreoveIt is well known that reward system including SII and insular cortices is activated by eating and food anticipation The present findings suggest that both hand-manipulation-related and SS-related neuronal populations likely contribute to haptics processing from the initial to the final phase of grasping and object manipulation .As mentioned above, hodological studies show strong reciprocal connections between ventral premotor cortex (PMv) and the hand region of SII/pIC. Given this evidence, we posit that the activity of both PRE and MID type neurons might likely reflect efference copy or corollary discharge of selected motor commands from PMv. When a movement is made, an efference copy of the motor command is used to make a prediction of the sensory consequences of the movement. This sensory prediction can then be compared with the actual sensory feedback or kinesthesia during movement used to optimize motor control.We also posit that post-contact dominant activity of both SS- and POS-type neurons might likely be involved in hand-object contact detection and hand-finger exploration after the contact respectively. Hand-object contact signals the end of the reaching movement. It provides an important tactile cue for the timing of the hand-object interaction sequence Unlike SI and superior parietal cortex (areas 2 and 5), the SII/pIC region shows dense reciprocal connections with the ventrolateral prefrontal cortex. In particular, both the intermediate area 12r Figure S1Functional mapping of somato-motor properties in SII/pIC. Unfolded view of the lateral sulcus of both right and left hemispheres of MK1 (Left). Example of one coronal section (AP 9) showing the position of anatomical markers to build the unfolded map (Right). The 2D reconstruction of the upper bank of the lateral sulcus (UBLs) and of the posterior insula was aligned along its fundus, indicated by a straight dashed line . The continuous lines mark the lips of the upper (R1), the starting point of the circular region (R2), and the wall of the middle insular region (R4). Arrows mark the most anterior tip of the intraparietal (IPs) and central sulcus (Cs). Each color dot indicates the entrance point of the electrode. Green dot: Mouth; blue dot: face; red dot: hand/fingers; yellow-green dot: arm; black dot: lower body part; cyan dot: hemi-body; pink dot: whole body somatosensory representation. Red dot within black circle indicates the recording site of hand-manipulation-related neurons. Calibration bar: 10 mm.(TIF)Click here for additional data file.Figure S2Kinematic analyses in Light and Dark conditions. (A) Maximal finger aperture (cm) during the execution of three different grips both in the Light and Dark conditions. (B) Reaching and pre-shaping time (msec) for three grips both in the Light and Dark conditions. (C) Hand-manipulation execution time (msec) for three grips both in Light and Dark conditions. (D) Bringing to the mouth execution time (msec) for three grips both in Light and Dark conditions. For each parameter, error bars indicate \u00b1 SEM (standard error of the mean), *p<.001.(TIF)Click here for additional data file.Figure S3Kinematics analyses in FE advance task. (A) Maximal finger aperture (cm) during the execution of FEt and FEwt. (B) Reaching and pre-shaping time (msec) of FEt and FEwt. (C) Hand-manipulation execution time (msec) of FEt and FEwt. For each parameter, error bars indicate \u00b1 SEM (standard error of the mean), *p<.001.(TIF)Click here for additional data file.Text S1Text of supporting informaiton for (DOC)Click here for additional data file.Text S2Text of supporting information for (DOC)Click here for additional data file.Text S3Text of supporting information for (DOC)Click here for additional data file."} +{"text": "The country of Georgia has a high prevalence of tuberculosis (TB) and hepatitis C virus (HCV) infection. To determine whether HCV co-infection increases the risk of incident drug-induced hepatitis among patients on first-line anti-TB drug therapy.Prospective cohort study; HCV serology was obtained on all study subjects at the time of TB diagnosis; hepatic enzyme tests were obtained at baseline and monthly during treatment. Among 326 study patients with culture-confirmed TB, 68 (21%) were HCV co-infected, 14 (4.3%) had chronic hepatitis B virus (HBV) infection (hepatitis B virus surface antigen positive [HBsAg+]), and 6 (1.8%) were HIV co-infected. Overall, 19% of TB patients developed mild to moderate incident hepatotoxicity. In multi-variable analysis, HCV co-infection was found to be an independent risk factor for incident anti-TB drug-induced hepatotoxicity. Survival analysis showed that HCV co-infected patients developed hepatitis more quickly compared to HCV seronegative patients with TB.A high prevalence of HCV co-infection was found among patients with TB in Georgia. Drug-induced hepatotoxicity was significantly associated with HCV co-infection but severe drug-induced hepatotoxicity (WHO grade III or IV) was rare. The World Health Organization (WHO) estimates there were 8.6 million new cases of tuberculosis (TB) globally in 2012 and 1.3 million deaths due to TB. In 2012Hepatitis C virus (HCV) has also emerged as an important global public health problem. WHO estimates that 3% of the world\u2019s population is infected with HCV and that more than 170 million chronic carriers are at risk of developing liver cirrhosis and/or liver cancer . A high Globally, the prevalence of HCV infection among patients with TB has not been extensively investigated, and very limited data on rates of HCV co-infection among patients with TB exists. In Georgia, a previous study reported a high prevalence (22%) of HCV infection among patients with TB; in that study HCV co-infection was independently associated with previous incarceration, tattoo, and previous sexually transmitted infections .Hepatotoxicity is the major adverse effect of three of the first-line anti-TB agents: isoniazid (INH), rifampin (RIF), and pyrazinamide (PZA). Underlying liver disease may increase the risk of developing drug-induced hepatotoxicity and there is concern that HCV and/or HIV co-infection may increase the risk of anti-TB drug-induced hepatotoxicity. There rThe Institutional Review Board (IRB) at Emory University and at the National Center for Tuberculosis and Lung Diseases (NCTBLD) reviewed and approved the study. >18 years of age) with pulmonary TB who had received <2 weeks of WHO-recommended directly observed short course (DOTS) therapy. Treatment included an intensive phase of four drugs for two months, followed by a continuation phase of RIF and INH for four months activity during first-line anti-tuberculosis therapy does not appear to be warranted based on data from our study."} +{"text": "B cell depletion therapy is effective in the treatment of various autoimmune diseases. However, this therapy is shown to be associated with increased risk of adverse effects such as opportunistic infections. Therefore, in this study, we developed and analyzed the selective depletion therapy of pathogenic B cells using peptide tetramers in collagen-induced arthritis model.Since the antigenic targets of pathogenic antibodies are identified in collagen-induced arthritis (CIA) model, we developed toxin-conjugated peptide tetramers, which contained pathogenic epitope of mouse type II Collagen (CII). The male DBA/1J mice were immunized with bovine CII and injected with toxin-conjugated peptide tetramers on day 10 and day 20 after CIIimmunization.We analyzed the effect of toxin-conjugated peptide tetramers on the production of autoantibodies and clinical course of arthritis.P < 0.05) in the tetramer-treated group than in the control group. The mean serum antibody levels for CII did not differ significantly, but there were significant differences in the anti-peptide antibodies over time.The incidence of arthritis was significantly lower (Peptide tetramer is effective in the selective depletion of antigen-specific B cells and decreased the incidence of arthritis in CIA model. Therefore, depletion of antigen-specific B cells using this strategy might be a new therapeutic intervention of autoimmune diseases."} +{"text": "This observational pilot project was performed as background to eventually create a rapid, automated and accurate assessment of RV systolic function in variable clinical subgroups. We propose new parameters that characterize the global systolic function of the right ventricle with a simple linear measurement.The tricuspid annular plane systolic excursion (TAPSE), which has been used for over a quarter century as a quick estimate of RV systolic function, was revisited using CMR. It shows good correlation with invasive hemodynamics. MRI is the current gold standard to assess the volumes and anatomy of the heart and we can measure TAPSE more precisely with cardiac MRI to accurately detect any current problems TAPSE measurements may suffer from.We studied 61 patients with adequate, high quality, clinical CMR scans using a conventional 1.5T GE scanner were studied. In addition to simulating the echo-TAPSE parameter, additional semi-automated CMR parameters were obtained from manually identified phasic anatomic landmarks that honored the trajectory of the tricuspid annulus (TA) and right ventricle apex (RVA):1. TAPSE -Distance traveled by the TA along the direction of the fixed line joining the TA and RVA at end-diastole (simulates echo measure).2. \u0394 TA-RVA - Difference between lengths of line segments joining the (RVA) and TA at end-diastole and end-systole (recognizes cardiac translation).3. TA Excursion (TAE) - Euclidean distance traveled by the TA from end-diastole to end-systole (measures just the TA motion).The correlation of these parameters with conventional RVEF was obtained using linear regression analysis, and a p-value less than 0.05 was considered significant.In general, there is a weak correlation between TAPSE and RVEF and a moderate correlation using the newer parameters of \u0394 TA-RVA and TAE. In clinically relevant subgroups such as RV pressure overload (RVPO) and RV volume overload (RVVO), there are statistically significant differences between the traditional and conventional parameters , but this correlation can be significantly improved using the rapid, semi-automated \u0394 TA-RVA or TAE method. Very importantly, the choice of parameter has diametrically opposed influences on RVVO and RVPO sub-groups . These findings suggest variable alteration of longitudinal RV myocardial contraction and warrants further investigation.A portion of Dr. Sorrell's support for this project was provided by the Allan C. Hudson and Helen Lovaas Endowed Chair of Cardiac Imaging."} +{"text": "Clinicians have long appreciated the distinct phenotype of systemic juvenile idiopathic arthritis (SJIA) compared to polyarticular juvenile idiopathic arthritis (POLY). We hypothesized that gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with each disease would reveal distinct biological pathways when analyzed for significant associations with elevations in two markers of JIA activity, erythrocyte sedimentation rate (ESR) and number of affected joints .t-test analyses were performed to identify transcripts significantly associated with clinical parameters (ESR and JC) in SJIA or POLY samples. These transcripts were used to find related biological pathways.PBMC RNA from SJIA and POLY patients was profiled by kinetic PCR to analyze expression of 181 genes, selected for relevance to immune response pathways. Pearson correlation and Student's t-test analyses, we found 91 ESR-related and 92 JC-related genes in SJIA. For POLY, 20 ESR-related and 0 JC-related genes were found. Using Ingenuity Systems Pathways Analysis, we identified SJIA ESR-related and JC-related pathways. The two sets of pathways are strongly correlated. In contrast, there is a weaker correlation between SJIA and POLY ESR-related pathways. Notably, distinct biological processes were found to correlate with JC in samples from the earlier systemic plus arthritic phase (SAF) of SJIA compared to samples from the later arthritis-predominant phase (AF). Within the SJIA SAF group, IL-10 expression was related to JC, whereas lack of IL-4 appeared to characterize the chronic arthritis (AF) subgroup.Combining Pearson and The strong correlation between pathways implicated in elevations of both ESR and JC in SJIA argues that the systemic and arthritic components of the disease are related mechanistically. Inflammatory pathways in SJIA are distinct from those in POLY course JIA, consistent with differences in clinically appreciated target organs. The limited number of ESR-related SJIA genes that also are associated with elevations of ESR in POLY implies that the SJIA associations are specific for SJIA, at least to some degree. The distinct pathways associated with arthritis in early and late SJIA raise the possibility that different immunobiology underlies arthritis over the course of SJIA. Systemic juvenile idiopathic arthritis (SJIA) is currently classified as a subtype of juvenile idiopathic arthritis , and is There are also unique immunophenotypic features in SJIA compared to other JIA subtypes, such as the lack of human leukocyte antigen (HLA) class II allele association, low or absent autoantibodies , a tendDespite our knowledge of some important immunological characteristics of active SJIA, the pathogenesis of SJIA remains unknown. One of the unanswered questions is whether independent biological processes underlie the systemic symptoms and the arthritis. Evidence from clinical studies shows that earlier in the disease, IL-1 inhibitors are efficacious, especially against systemic symptoms, but at a later stage, where arthritis may predominate, patients may develop resistance to these therapies -20. ThesTranscriptional profiling of peripheral blood cells has been a useful approach for identifying biological pathways involved in SJIA and other complex diseases, such as polyarticular JIA (POLY), rheumatoid arthritis (RA), systemic lupus erythematosus and Kawasaki disease -24. PrevWe hypothesized that distinct gene expression patterns may be associated with individual clinical parameters used as measures of the systemic inflammation and the arthritis. We analyzed expression in peripheral blood mononuclear cells (PBMC) of a panel of inflammation-associated genes to determine patterns associated with elevations in two markers of disease activity in JIA, erythrocyte sedimentation rate (ESR) and number of active joints . ESR is a marker of inflammation that is elevated in association with systemic as well as organ-specific inflammation, including arthritis . Active We asked if common or unique expression profiles are associated with ESR and JC in SJIA. In order to assess the specificity of our results for SJIA, we also asked whether the expression of the panel of tested genes differed in SJIA patients compared to patients with polyarticular course JIA (POLY), which is characterized by chronic polyarthritis. We then analyzed if JC associated genes differ during the early and late phase of SJIA. Based on the gene expression patterns, we identified candidate biological pathways associated with the systemic and arthritis components of SJIA.The study was approved by the Stanford University Administrative Panel on Human Subjects in Medical Research (protocol ID 13932). Informed consent was obtained from patients or parents or guardians before blood sample collection. Venous blood samples from all subjects were treated anonymously throughout the analysis. All JIA patients were followed at the Pediatric Rheumatology Clinic at Lucile Packard Children's Hospital. SJIA and POLY patients met amended ILAR criteria for diagnosis ,31,32 with sodium citrate . Peripheral blood mononuclear cells (PBMCs) were isolated within three hours of collection by centrifugation of CPT tubes, per the manufacturer's instructions.Purified PBMCs were lysed in RLT reagent and lysate was stored at -80\u00b0C until RNA extraction. RNA was isolated using the RNeasy mini kit (Qiagen), per the manufacturer's instructions with an additional on-column DNase I (Qiagen) treatment for 40 minutes. The RNA concentration was measured by the Ribogreen assay or by absorbance at 260 nm. The purity of RNA was assessed by the ratio of the absorbance readings at 260 and 280 nm. The integrity of the RNA samples was also checked by either agarose gel electrophoresis or with the Agilent 2100 Bioanalyzer .http://www.pantherdb.org/) to categorize their biological functions. This analysis showed that the largest functional category is inflammatory chemokine and cytokine signaling pathways (14.6% of the genes), followed by interleukin signaling pathways (10.8%), apoptosis signaling pathways (9.9%) and toll receptor signaling pathways (6.2%). A full list of categories covered is shown on Additional file In a pilot study, paired flare/remission PBMC samples from 14 SJIA patients were processed for RNA as described and analThe kinetic RT-PCR assay was performed as described . Brieflyt-test, as explained in the Results section.Genes significantly associated with SJIA and POLY were determined using Pearson's correlation and Student's http://www.ingenuity.com). The significance of either ESR or JC related pathways was analyzed using sparse linear discriminant analysis method, as previously described . Given the immunosuppressive effect of IL-10, association of this gene with arthritis in SJIA may represent an attempt by the immune system to reduce inflammation. The level of IL-10 may be inadequate to deal with the inflammatory challenge, as the frequency of a promoter allele associated with low IL-10 expression is increased in SJIA patients [In the systemic plus arthritic stage of SJIA, we found that expression of IL-10 in PBMC was positively associated with arthritis. In d others ,29 obserpatients ,70. We fpatients .A striking finding of this study is that deficiency in IL-4-related pathways correlates with JC in the arthritic phase of SJIA. IL-4 has been implicated in protection against arthritis. Polymorphism in the IL4R\u03b1 gene that confers reduced responsiveness to IL-4 is associated with worse outcome in RA . Low levIL-4 inhibits expression of pro-inflammatory cytokines, such as IL-1\u03b2, TNF\u03b1 ,79 and Iet al. 2009 showed that RF+ and RF- patients can share a similar gene signature [We found no gene association or correlation linked with POLY joint count, and a limited number of somewhat different genes were associated with elevated ESR in POLY-JIA subjects. Our gene panel was largely derived from a SJIA-based microarray study and, as such, it has a significant bias towards SJIA-related genes. Further, the systemic nature of SJIA predicts more changes in peripheral blood than for POLY, where pathology is more localized. Our POLY cohort was itself heterogeneous, including RF+ and RF- patients, which were analyzed as one group. Most gene expression studies have analyzed RF- patients only ,84,85; signature .It will be of interest to determine the cell type within PBMC that is responsible for particular transcripts. Based on correlated expression patterns with more lineage specific genes, it is most likely that IL-4 transcripts derive from CD4 T cells; the IL-4 message expression is correlated with expression of CD40LG and IL2RG (not shown). In contrast, the IL-10 expression correlates with expression of IL-1, IL-1-related genes and IL-6 (not shown), suggesting IL-10 transcripts are expressed in monocytes. Further studies are also needed to determine the specificity of the SJIA gene signature in relation to other acute inflammatory diseases, such as bacterial and viral infections and other rheumatologic pediatric diseases . NonetheThis study demonstrates that analysis of individual clinical parameters in a complex disease like SJIA may reveal unique and informative molecular associations. In addition to elucidating disease immunopathology, this approach may help identify therapeutic targets and strategies tailored to the different phases of SJIA.AF: arthritis-predominant phase; AOSD: Adult Onset Still Disease; BAFF: B cell activating factor; CPT: cell preparation tubes; CRP: C-reactive protein; EEF1A1: eukaryotic translation elongation factor 1 alpha1; ESR: erythrocyte sedimentation rate; F: SJIA flare; FDR: false discovery rate; GEO: Gene Expression Omnibus; GC: glucocorticoid; GCR: glucocorticoid receptor; IL: interleukin; JC: joint count; LPS: lipopolysaccharide; MAS: macrophage activation syndrome; PANTHER: Protein ANalysis THrough Evolutionary Relationships) Classification System; PBMC: peripheral blood mononuclear cells; PCR: polymerase chain reaction; PKR: protein kinase receptor; PLT: platelets; POLY: polyarticular juvenile idiopathic arthritis; PPP1CC: protein phosphatase 1, catalytic subunit, gamma isoform; Q, SJIA quiescence; qPCR: quantitative PCR; RA: rheumatoid arthritis; RF: rheumatoid factor; RPL12: ribosomal protein L12; RPL41: ribosomal protein L41; SAF: systemic plus arthritic phase; SAM: Significance Analysis of Microarrays; SJIA: systemic onset juvenile idiopathic arthritis; WBC: white blood count.The authors declare that they have no competing interests.XBL performed the statistical analysis and wrote the paper. CM performed statistical analysis, interpreted the data and wrote the paper. HCA, S-YPC and ABB designed and performed the kinetic PCR. QW and EC performed statistical analysis. YS and CD processed patients' samples, prepared RNA, performed and analyzed the microarrays. K-HP, RL, C-JL and SHP performed microarray and initial data analysis. TL and CS provided patients' samples and clinical information. SNC helped design the study and the initial strategy for data analysis. EM contributed to study design, interpreted data and wrote the manuscript. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1741-7015/10/125/prepubSupplementary Figure 1. Unsupervised hierarchical clustering analysis of a subset of differentially expressed genes from SJIA flare and quiescence samples studied by microarray. Paired samples from 14 subjects at flare (red) and quiescence (green) were studied. Independent samples from the same individual are indicated by *. Each column represents a separate sample; each row represents a separate gene.Click here for fileSupplementary Table 1. The 181 immune-related genes analyzed in this study.Click here for fileSupplementary Table 2. Annotation of the 181 analyzed genes into different functional categories using PANTHER software.Click here for fileSupplementary Table 3. SJIA ESR, SJIA JC and POLY ESR related gene lists.Click here for fileSupplementary Figure 2. The fold changes in expression of the genes that differ between groups and between quartiles of ESR or JC. (A) The probability density of fold changes with the selected ESR-related genes between F1 + Q and F2 of SJIA; (B) The probability density of fold changes with the selected ESR-related genes between quartiles (the first quartile to the third quartile) of SJIA; (C) The probability density of fold changes with the selected JC-related genes between Q and F of SJIA; (D) The probability density of fold changes with the selected JC- related genes between quartiles (the first quartile to the third quartile) of SJIA; (E) The probability density of fold changes with the selected ESR-related genes between F2 and F1 + Q of POLY; (F) The probability density of fold changes with the selected ESR-related genes between quartiles (the first quartile to the third quartile) of POLY.Click here for file"} +{"text": "PLEC) cause two distinct autosomal recessive subtypes of epidermolysis bullosa: EB simplex (EBS) with muscular dystrophy (EBS-MD), and EBS with pyloric atresia (EBS-PA). Previous studies have demonstrated that loss of full-length plectin with residual expression of the rodless isoform leads to EBS-MD, whereas complete loss or marked attenuation of expression of full-length and rodless plectin underlies the more severe EBS-PA phenotype. However, muscular dystrophy has never been identified in EBS-PA, not even in the severe form of the disease. Here, we report the first case of EBS associated with both pyloric atresia and muscular dystrophy. Both of the premature termination codon-causing mutations of the proband are located within exon 32, the last exon of PLEC. Immunofluorescence and immunoblot analysis of skin samples and cultured fibroblasts from the proband revealed truncated plectin protein expression in low amounts. This study demonstrates that plectin deficiency can indeed lead to both muscular dystrophy and pyloric atresia in an individual EBS patient. \u00a9 2010 Wiley-Liss, Inc.Plectin is a cytoskeletal linker protein which has a long central rod and N- and C-terminal globular domains. Mutations in the gene encoding plectin ( Plectin is a 500-kDa protein of the plakin family, which interlinks different element of the cytoskeleton . PlectinPLEC (MIM# 601282), have been known to be causal for two subtypes of autosomal recessive EBS (EBS with muscular dystrophy (EBS-MD) and EBS with pyloric atresia (EBS-PA)) and for one subtype of autosomal dominant EBS (EBS-Ogna) (Epidermolysis bullosa (EB) comprises a group of heterogeneous congenital disorders characterized by dermal- epidermal junction separation. EB is subdivided into the three major groups of EB simplex (EBS), junctional EB and dystrophic EB, and the one minor group of Kindler syndrome, based on the level of blister formation . So far,BS-Ogna) .PLEC in EBS-MD patients . The pro exon 31 .PLEC mutations, the pathomechanisms distinguishing two subtypes were unclear. Recently, our group and others demonstrated that EBS-MD patients typically express a rodless plectin isoform, although the full-length plectin is absent of 4, dehydrated, and embedded in Epon 812. The samples were sectioned at 1 um thickness for light microscopy and thin-sectioned for electron microscopy (70 nm thick). The thin sections were stained with uranyl acetate and lead citrate, and examined by transmission electron microscopy.Skin biopsy samples were fixed in 2% glutaraldehyde solution, post-fixed in 1% OsOPLEC exons and intron-exon borders, followed by direct automated sequencing using an ABI PRISM 3100 genetic analyzer . The oligonucleotide primers and PCR conditions used in this study were derived from a previous report was isolated from peripheral blood leukocytes of the proband and her parents. The mutation detection was performed after polymerase chain reaction (PCR) amplification of all s report . The gDNhttp://www.hgvs.org/mutnomen) according to the reference sequence NM_000445.3, with +1 as the A of the ATG initiation codon.The mutation nomenclature follows the journal's guidelines and six non-chromosome 8 markers . All microsatellite markers were amplified with fluorescently labeled oligonucleotides and used under conditions recommended by the manufacturer. Electrophoretic analysis was performed on an ABI Prism 310 Genetic Analyzer with Performance Optimized Polymer 4 (POP4) using GeneScan software (Applied Biosystems). The allele sizes were analyzed using Genotyper software (Applied Biosystems).Genotype analysis of this family to establish the Immunofluorescence analysis was performed using skin specimens from the proband as previously described . Briefly+CIV22 against type IV collagen ; and S1 193 and mAb HDD20 against BP230 and type XVII collagen, respectively. mAbs PN643, HD1-121 and PC815 were generously donated by Prof. K. Owaribe of Nagoya University, and antibody S1 193 by Prof. J. R. Stanley of the University of Pennsylvania. C20, a goat polyclonal antibody against the C-terminus of plectin, was purchased from Santa Cruz. Anti-beta-actin mAb was used to confirm equal protein loading.The following antibodies against basement membrane zone (BMZ) components were used: monoclonal antibody (mAb) PN643 against the N-terminal actin-binding domain of plectin; mAb HD1-121 against the rod domain of plectin; C20 and mAb PC-815 against the C-terminal globular domain of plectin ; mAbs GoCell culture and immunoblot analysis was performed as previously described . CultureSemi-quantitative reverse transcription PCR (RT-PCR) analysis was performed as previously described . Total RThe medical ethics committee of Hokkaido University Graduate School of Medicine approved all of the described studies. The study was conducted according to The Declaration of Helsinki Principles. Participants gave their written informed consent.The proband was a first child of non-consanguineous Japanese parents. There was no family history of bullous diseases. He was born by cesarean section after a 39-week gestation because of non-reassuring fetal status. Clinically the proband showed extensive blistering and aplasia cutis on the extremities . RoutineElectron microscopy of the skin samples from the proband showed that the skin separation localized to the base of the basal keratinocytes . HemidesPLEC mutational analysis demonstrated that the proband was compound heterozygous for maternal c.10984C>T (p.Glu3662X) and de novo c.11453_11462del in exon 32, the last exon of PLEC . To check plectin expression patterns in the skin specimens from the proband, we used four antibodies: PN643 , HD1-121 (rod domain), PC815 and C20 . Normal Immunoblot analysis of lysates from normal human cultured fibroblasts revealed that two closely spaced bands, corresponding to two forms of plectin (500kDa full-length and 390kDa rodless), reacted with PN643 and C20 antibodies recognizing the N- and C-termini of plectin , as prevUsing RT-PCR, the presence of mRNA that encodes full-length or rodless plectin was demonstrated in the normal human control as well as in the proband's cultured fibroblasts , 6. JudgThis is the first report of EB complicated with both MD and PA. Skin detachment within basal keratinocytes was demonstrated by electron microscopy, which indicated the simplex subtype of EB. The proband's skin sample and cultured fibroblasts showed reduced and truncated plectin expression .PLEC. Nonsense-mediated mRNA decay (NMD) is a quality-control mechanism that selectively degrades mRNAs with PTCs (Both of the premature termination codon (PTC)-causing mutations detected in our case are within exon 32, the last exon of ith PTCs . When thith PTCs . Reducedth plectin repeat and is predicted to cause a frameshift followed by a premature termination codon. The age of onset for MD in the patient with c.13458_13473dup was 4 years (th and 6th plectin repeat (One reported EBS-MD case was homozygous for a PTC-causing mutation (c.13458_13473dup) in exon 32 . c. 1345 4 years ; in our n repeat . Therefon repeat .PLEC mutations (PTC-causing mutations or in-frame insertions/deletions) influences the timing of MD onset the integrity of basement membrane and hemidesmosomes, and 2) the control of the normal process of fibrosis in the course of wound healing . The seqIt had been predicted that some cases of EBS-PA would develop MD, although no such case had been reported in the literature . One posIn summary, this study clearly shows that plectin mutations lead to both MD and PA phenotypes in an individual EBS patient."} +{"text": "Conceptually, this strategy seeks to increase efficacy and minimize toxicity through the appropriate selection of patients for either therapy escalation or de-escalation . Preliminary evidence with tailoring both chemotherapy and radiotherapy (omission or inclusion) is varied; however, numerous clinical trials seeking to validate this approach are ongoing. This paper summarizes the available evidence and active protocols involving PET response-adapted therapy for adult (early and advanced stages) Hodgkin's lymphoma.Risk-adaptive therapy for Hodgkin's lymphoma focuses on treatment modifications based on assessment of response. [ Treatment of Hodgkin's lymphoma (HL) with modern combination chemotherapy and radiation therapy has increased long-term survival to greater than >75% . In the In an effort to tailor treatment towards both favorable and unfavorable-risk patients, response-adaptive therapy involves modifications based upon response assessment. The prognostic value of PET, both during and after completion of treatment, has been demonstrated . As a reStudies in high-grade non-Hodgkin's lymphoma, with the inclusion of a few HL patients, first demonstrated a strong predictive value of PET scan performed after 1-2 cycles of chemotherapy \u201310. In aP < .01). PET-2 response was the strongest predictor of PFS on multivariate analysis, and PET was proved superior to conventional computer tomography (CT) imaging . This trial also tests randomizations for PET-2 negative patients receiving BEACOPPesc chemotherapy and PET-2 positive patients .PET response is strongly prognostic for treatment outcome in HL. As a result, interest has developed in tailoring treatment based upon PET assessment. While this approach has the potential to identify appropriate patients for either intensifying or deintensifying therapy, the mechanisms to do so remain largely undefined. Treatment de-escalation strategies carry a risk of negatively impacting the overall highly favorable outcomes in this disease. Likewise, there is no consensus regarding the appropriate treatment of PET-avid disease (interim or after completion of therapy), in which these patients may require intensive therapy. An active interest in PET response-based treatment strategies is demonstrated through widespread incorporation into Hodgkin's lymphoma protocols, but the variety of strategies being employed reflect a relative lack of experience with this approach. The results of these upcoming studies will hopefully answer the combined questions of whether and how treatment can be safely modified based on PET response."} +{"text": "Although intra-amniotic(IA) infection is present in both preterm labor and intact membranes(PTL) and preterm premature rupture of membranes(preterm-PROM), it is more common in preterm-PROM than in PTL. Microorganisms and their products in the amniotic-cavity can elicit an inflammatory-response in fetus as well as in amniotic-cavity in the progression of acute histologic chorioamnionitis(acute-HCA). A fundamental question is whether a fetal and an IA inflammatory-response is more severe in preterm-PROM than in PTL, in the same-context of acute-HCA with or without fetal-involvement. The purpose of current-study was to answer this-question.Study population consisted of 213 singleton preterm-gestations(<34 weeks) delivered within 4 days of amniocentesis due to PTL(120 cases) or preterm-PROM(93 cases). The intensity of fetal and IA inflammatory-responses was compared between PTL and preterm-PROM, according to placental inflammatory conditions:1)placenta without inflammatory-lesion;2)acute-HCA without funisitis;3)acute-HCA with funisitis. IA inflammatory response was assessed by amniotic-fluid(AF) matrix metalloproteinase-8(MMP-8), and fetal inflammatory response(FIR) by umbilical-cord plasma(UCP) C-reactive protein(CRP) at birth.p<.01 for each);2) there were no significant differences in the intensity of fetal and IA inflammatory-responses and the rate of cervical dilatation\u22653 cm or 4 cm between patients with PTL and those with preterm-PROM in the context of both placenta without inflammatory-lesion and acute-HCA without funisitis(p>.05 for each);3) however, acute-HCA with funisitis was associated with a significantly higher median AF MMP-8 and UCP CRP concentration and higher rate of cervical dilatation\u22653 cm or 4 cm in PTL than in preterm-PROM, despite less common IA infection in PTL than in preterm-PROM.1) Patients with preterm-PROM had higher rates of IA infection, acute-HCA, and acute-HCA with funisitis than those with PTL did(A fetal and an IA inflammatory-response is more severe in PTL than in preterm-PROM in the context of funisitis, despite less common IA infection. This unexpected observation may indicate the fundamental difference in the pathogenesis between PTL and preterm-PROM. Microbial invasion of amniotic cavity (MIAC) can be present in both patients with preterm labor and intact membranes (PTL) and those with preterm premature rupture of membranes (preterm-PROM) Study population consisted of 213 singleton-gestations who delivered preterm-neonates at the Seoul National University Hospital between January 1993 and December 2007 and who met the following criteria: (1) gestational age (GA) at delivery <34 weeks; (2) preterm births due to PTL (120 cases) or preterm-PROM (93 cases); (3) available results of placental histopathologic examination after delivery; (4) delivery within 4 days of amniocentesis. This criterion of amniocentesis-to-delivery interval was used to preserve a meaningful temporal relationship between the results of amniotic fluid (AF) studies, and the results of placental pathology and umbilical cord plasma C-reactive protein (CRP) concentrations obtained at birth. The intensity of fetal and IA inflammatory response was compared between patients with PTL and those with preterm-PROM according to the following placental inflammatory conditions: 1) placenta without inflammatory lesion (n\u200a=\u200a71); 2) acute-HCA but without funisitis (n\u200a=\u200a61); and 3) acute-HCA with funisitis (n\u200a=\u200a81). At our institution, we routinely recommended and performed trans-abdominal amniocentesis, umbilical cord blood collection at birth, and placental histo-pathologic examination in all patients admitted with the diagnosis of PTL or preterm-PROM after written informed consent was obtained. Trans-abdominal amniocentesis was performed to evaluate either the microbiologic or inflammatory status of the amniotic cavity and/or the fetal lung maturity. The Institutional Review Board of Seoul National University Hospital approved the collection and use of these samples and information for research purposes. The Seoul National University has a Federal Wide Assurance with the Office for Human Research Protections (OHRP) of the Department of Health and Human Services of the United States. Many of patients in this study were included in our previous studies.The demographic and clinical characteristics of the mothers and their neonates were examined through a review of the medical records. We investigated maternal age, parity, GA at amniocentesis, GA at delivery, birth weight, 1 min and 5 min Apgar score as demographic and clinical characteristics.3), maternal tachycardia (>100 beats/min), and fetal tachycardia (>160 beats/min).Clinical chorioamnionitis was diagnosed when maternal temperature was elevated to 37.8\u00b0C and \u22652 of the following criteria were present: uterine tenderness, malodorous vaginal discharge, maternal leukocytosis for the evaluation of MIAC according to methods previously described AF was cultured for aerobic and anaerobic bacteria and for genital mycoplasmas concentration at birth. Umbilical cord plasma CRP concentrations were measured with a commercially available enzyme-linked immunosorbent assay . The sensitivity of the test was 0.02 ng/mL. Both intra- and inter-assay coefficients of variation were <10%. Details about this assay and its performance have been previously described Mann-Whitney U test was used for comparison of continuous variables. Comparisons of proportions were performed with the Fisher\u2019s exact test. Statistical significance was defined as a p<0.05.p>0.05 for each) (see p<0.01 for each) (see p<0.01 for each) (see There were no significant differences in parity (\u22651), maternal age, clinical chorioamnionitis, birth weight, GA at amniocentesis, 1 min Apgar score (<7) and 5 min Apgar score (<7) between patients with PTL and those with preterm-PROM (ach) see . Howeverach) see .p>0.05 for each) (see There were no significant differences in parity (\u22651), maternal age, clinical chorioamnionitis and GA at amniocentesis between patients with PTL and those with preterm-PROM, in the context of each placental inflammatory condition (ach) see . Howeverach) see . Table 3There were no significant differences in a median AF MMP-8 concentration and umbilical cord plasma CRP concentration at birth between patients with PTL and those with preterm-PROM, in the context of both placenta without inflammatory lesion see and acutThe principal findings of this study are as following. Firstly, patients with preterm-PROM had higher rates of IA infection, acute-HCA, and acute-HCA with funisitis than those with PTL did. Secondly, there were no significant differences in the fetal and IA inflammatory responses and the cervical dilatation between patients with PTL and those with preterm-PROM in the context of both placenta without inflammatory-lesion and acute-HCA but without funisitis. Thirdly, acute-HCA with funisitis was associated with a significantly higher fetal and IA inflammatory response and increase in cervical dilatation in PTL than in preterm-PROM, despite less common IA infection in PTL than in preterm-PROM.Our previous studies reported that a fetal inflammatory response was stronger in patients with MIAC than in those without MIAC among cases with both preterm-PROM and IAI Major strengths of this study are: (1) its large cohort (n\u200a=\u200a213) of consecutive singleton preterm gestations (<34 weeks) due to PTL or preterm-PROM; (2) it included several markers of infection and an inflammatory response, including AF culture, AF MMP-8 concentration, umbilical cord plasma CRP concentration at birth and acute-HCA with or without funisitis, and therefore, this study analyzed the inflammatory responses in the relevant potential compartments among study groups; and (3) it compared a fetal and an IA inflammatory response between PTL and preterm-PROM, in the same context of various aspects as followings: (1) delivery within 4 days of amniocentesis; (2) the extent of placental inflammatory conditions ; (3) others: maternal age, parity (\u22651) and GA at amniocentesis. Therefore, patients with PTL and those with preterm-PROM can be comparable groups for analyzing a fetal and an IA inflammatory response by virtue of obstetric management. The potential weaknesses of the study are: (1) it did not analyze neonatal morbidity according to PTL or preterm-PROM, in the context of each placental inflammatory condition, due to the following reasons: the relatively small sample size for the evaluation of neonatal morbidity and extending beyond the scope of this study; and (2) it did not perform the broad range PCR or more sophisticated techniques of microbial identification in addition to culture technique. Culture is fairly insensitive and mistakes in organism identification are not uncommon. Therefore, the results on the differences in microorganisms between PTL and preterm-PROM in current study are thought to be extremely preliminary.Our data demonstrated the novel finding that PTL was associated with greater fetal and.IA inflammatory responses than preterm-PROM, in the context of acute-HCA with fetal involvement, despite less common IA infection in PTL than in preterm-PROM. This finding has clinical and patho-physiologic implications in that the differences in the intensity of a fetal and an IA inflammatory response between PTL and preterm-PROM may suggest the fundamental difference in the pathogenesis between the two conditions, although the exact mechanisms responsible for this unexpected clinical observation should be investigated.The differentiation between PTL and preterm-PROM should be made in the research about the patho-physiology of preterm births as well as in the management of patients at risk for preterm births. Moreover, it should be determined whether the mere PTL itself may increase a more IA inflammatory response than preterm-PROM, or whether much higher intensity of AF MMP-8 concentration may act preferentially on the production of prostaglandin for PTL, rather than on the degradation of extracellular matrix in the chorio-amniotic membranes for preterm-PROM. However, it is difficult to perform these studies in human population, and therefore, in vitro or animal experiments regarding above unexplained issues may be required."} +{"text": "Contrast-enhanced mammography is a relatively novel technique. We describe a single-centre experience with use of the technique to facilitate the detection and characterisation of lesions in the breast by triangulation of contrast-enhanced mammography, biopsy/gross pathological specimen and MR findings.Retrospective review of the pathological and imaging findings of consecutive patients undergoing contrast mammography was performed. Sixty-four contrast mammograms were performed on 61 patients over a 15-month period. Technique involves a dual energy acquisition of CC and MLO views following the administration of contrast medium, then digital subtraction (GE Senographe DS).At contrast-enhanced digital mammography, enhancement was observed in 37 of 43 patients with biopsy-proved cancers. Of the six patients with a cancer diagnosis but no enhancement, three were post neoadjuvant treatment. Three patients without a tissue diagnosis of malignancy demonstrated mammographic enhancement. Fourteen patients also underwent gadolinium-enhanced breast MR. Nine out of 10 patients with MR enhancement also demonstrated enhancement on contrast mammogram. One patient with no MRI enhancement had enhancement on contrast mammography. Morphology generally correlated with the pathologic diagnosis.The results of this study demonstrate the utility of contrast-enhanced mammography in the identification, evaluation and follow-up of breast lesions. It offers similar enhancement characteristics to MRI and represents a feasible alternative in centres without onsite MRI."} +{"text": "The identities of toxic aggregate species in Huntington\u2019s disease (HD) pathogenesis remain unclear. While polyQ-expanded mutant huntingtin (Htt) is known to accumulate in compact inclusion bodies inside neurons, this is widely thought to be a protective coping response that sequesters misfolded conformations or aggregated states of the mutated protein.in vitro [To define the spatial distributions of fluorescently-labeled Htt-exon1 species in the cell model PC12m , we employed highly sensitive single-molecule-based and stimulated emission depletion (STED) super-resolution fluorescence imaging modalities. In addition to inclusion bodies and the diffuse pool of monomers and oligomers, fibrillar aggregates ~100 nm in diameter and up to ~1-2 \u00b5m in length were observed for pathogenic polyQ tracts (expression experiments with 46 and 97 repeats) after targeted photo-bleaching of the inclusion bodies [Definition of the diverse Htt structures in cells will provide an avenue to link the impact of pharmacological agents to aggregate populations and morphologies. The latest observations w.r.t. co-localization of Htt with various quality control proteins such as the chaperone Hsp70 will be presented."} +{"text": "Structures of HIV-1 reverse transcriptase (RT) have been reported in several forms, but only one contains an RNA/DNA hybrid, the conformation of which has been controversial. We have been successful in obtaining three structures of HIV-1 RT complexed with a non-nucleoside RT inhibitor (NNRTI) and an RNA/DNA hybrid [Although the single-subunit RT of Moloney murine leukemia virus (Mo-MLV) has been extensively characterized biochemically, structural information is lacking that describes the substrate binding mechanism for this RT species. We also present data on the first crystal structure of a complex between an RNA/DNA hybrid and the 72 kDa single-subunit RT from the related xenotropic murine leukemia virus-related virus (XMRV) ["} +{"text": "Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs, which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. The functional role of many of the members of this class has been an enigma, except a few of them like Malat and HOTAIR. Little is known regarding the regulatory interactions between noncoding RNA classes. Recent reports have suggested that lncRNAs could potentially interact with other classes of non-coding RNAs including microRNAs (miRNAs) and modulate their regulatory role through interactions. We hypothesized that lncRNAs could participate as a layer of regulatory interactions with miRNAs. The availability of genome-scale datasets for Argonaute targets across human transcriptome has prompted us to reconstruct a genome-scale network of interactions between miRNAs and lncRNAs.We used well characterized experimental Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) datasets and the recent genome-wide annotations for lncRNAs in public domain to construct a comprehensive transcriptome-wide map of miRNA regulatory elements. Comparative analysis revealed that in addition to targeting protein-coding transcripts, miRNAs could also potentially target lncRNAs, thus participating in a novel layer of regulatory interactions between noncoding RNA classes. Furthermore, we have modeled one example of miRNA-lncRNA interaction using a zebrafish model. We have also found that the miRNA regulatory elements have a positional preference, clustering towards the mid regions and 3\u2032 ends of the long noncoding transcripts. We also further reconstruct a genome-wide map of miRNA interactions with lncRNAs as well as messenger RNAs.This analysis suggests widespread regulatory interactions between noncoding RNAs classes and suggests a novel functional role for lncRNAs. We also present the first transcriptome scale study on miRNA-lncRNA interactions and the first report of a genome-scale reconstruction of a noncoding RNA regulatory interactome involving lncRNAs. Recent advances in sequencing technologies have enabled genome-scale mapping of transcriptional potential feasible at single-nucleotide resolutions The ncRNA class now encompasses a wide diversity of subclasses organized based on their size, structure, function and conservation. MicroRNAs (miRNAs) have been one of the recently discovered and well characterized classes of ncRNAs and are small regulatory RNA molecules processed from larger precursors through a highly coordinated pathway Though much of the focus in ncRNA research is directed towards understanding the regulation of protein-coding genes mediated by them, it has been suggested previously that ncRNAs could form a well-orchestrated regulatory interaction network 7sl lncRNA with miR-125b in a zebrafish model, thus adding confidence to our hypothesis. Furthermore, we have also integrated miRNA-target information to suggest a network of interactions between lncRNAs, miRNAs and protein-coding transcripts. To our knowledge this is one of the first transcriptome scale study on miRNA-lncRNA interactions and the first report of a genome-scale reconstruction of a noncoding RNA regulatory interactome involving lncRNAs.We employed datasets in public domain for lncRNA annotations recently made available from the ENCODE project along with genome-wide cross-linking with immunoprecipitation (CLIP-Seq) datasets for four Ago proteins The PAR-CLIP reads for HEK293 cells were downloaded from the NCBI Short Read Archive , which amounted to a total of 19,301,715 CLIP-seq reads for Ago 1-4. The reads were further mapped to hg19 version of the human genome using a quality-aware reference mapping algorithm: Mapping and Assembly with qualities (MAQ). Mapping was performed with stringent criteria and allowed no mismatches. The Agos significantly overlap in their biological function. Ago1 has been shown to be involved in RNA-mediated post-transcriptional gene silencing, Ago2 shows slicer activity, Ago3 and Ago4 are required for RNA-mediated gene silencing (RNAi). Since there have been no significant differences reported between the mappings of reads for each of the Ago datasets, and since biologically their functions overlap, we merged the datasets as previously used for the analysis Ago proteins are a component of the RNA induced silencing complex and are intricate components modulating the function of the complex. CLIP-seq allows one to identify the miRNA recognition elements in the transcriptome. To understand the biological interactions between miRNAs and their cognate target transcripts, it is imperative to identify the miRNAs corresponding to each of the miRNA recognition elements. We used miRanda 7sl lncRNA , which had 91.64% similarity with human 7sl lncRNA. The miRanda software identified potential binding sites of miR-125a, miR-125b, miR-125c, miR-17a*, miR-20a*, miR-210*, miR-2187, miR-29a, miR-29b and miR-457a in the predicted zebrafish l lncRNA . MiR-1257sl lncRNA in developing zebrafish embryos, we investigated the expression of the predicted zebrafish 7sl lncRNA during zebrafish embryonic development using reverse transcriptase PCR technique. The predicted zebrafish 7sl lncRNA was expressed in 24 and 48 hpf (hour post fertilization) zebrafish embryos (data not shown). The interaction of miR-125b and 7sl lncRNA was investigated by ectopic overexpression of miR-125b mimic in zebrafish embryos 7sl lncRNA was assayed in miR-125b injected embryos using quantitative real-time PCR. MiR-125b injected embryos displayed reduction in expression of the predicted 7sl lncRNA by approximately 1.72 fold (0.42\u00b10.26 SD) compared to non-injected embryos (NIC) (7sl lncRNA were not significantly affected in case of control injected miRNA (7sl lncRNA in zebrafish embryos.Prior to examining the interaction of miR-125b with the predicted os (NIC) . Howevered miRNA . In summAnalysis of the positional preference of miRNA regulatory elements in lncRNAs revealed a positional preference of the Ago binding sites in mid regions and at the 3` ends of the lncRNAs . Such prThe present analysis suggests lncRNAs also harbor potential miRNA regulatory elements and could participate in the miRNA regulatory network. We reconstituted a comprehensive genome-wide network of RNA mediated interactions putting together the interactions from genome-wide analyses and validated miRNA-mRNA interactions. The network brings to light hitherto unknown complexity of RNA regulatory interactions and how lncRNAs could play regulatory roles in the miRNA mediated interactions with mRNAs . The recZebrafish experiments were performed in strict accordance with the recommendations and guidelines laid down by the CSIR-Institute of Genomics and Integrative Biology, India. The protocol was approved by the Institutional Animal Ethics Committee (IAEC) of the CSIR Institute of Genomics and Integrative Biology, India . All necessary efforts were made to minimize animal suffering.Zebrafish used in this study were housed at the CSIR-Institute of Genomics and Integrative Biology following standard husbandry practices We used transcriptome wide interaction data for miRNA-Ago available from PAR-CLIP studies http://www.gencodegenes.org/) The manually annotated lncRNAs from GENCODE version 9 sequences were downloaded from lncRNAdb database MiRNA injections were performed following a published protocols The injected and non-injected control embryos were observed and imaged in white light with an upright Zeiss Axioscope 40 microscope using 2.5X magnification and 0.075 numerical aperture. Images were processed with Zeiss AxioVision 4.6 and Adobe Photoshop CS software. Identical modifications and adjustment were applied to all the images in the same experiment.7sl lncRNA was p1942F (5\u2032-GTAATCCAAGCTACTGGGAGGC-3\u2032) and p1943R (5\u2032-AGGCGCGATCCCACTACTGATC-3\u2032). The fold change were calculated by \u0394\u0394CT method 5\u2032-ACTAAAATTGGAACGATACAGAGA-3\u2032) and U6R (5\u2032-AAAGATGGAACGCTTCACG-3\u2032).RNA derived from miRNA injected and control embryos were obtained using Qiagen miRNeasy Mini Kit (cat no. 217004) according to manufacturer described protocol. One microgram of RNA was reverse transcribed into cDNA using Superscript II , and diluted by 1\u22365 for RT-PCR assay. The assay was performed using Sybr Green mix . The oligonucleotide primers used for RT-PCR assay of predicted zebrafish The present analysis illustrates the potential integration of genome-wide experimental datasets to provide insights into novel biological regulatory interactions in the cell. Interactions for miRNAs with lncRNAs have been suggested to play an important role in modulating regulation mediated through miRNAs. This analysis also provides a genome-scale report and reconstruction of miRNA interaction with mRNAs as well as lncRNAs. We also show how such a network approach could potentially suggest the lncRNAs for functional validation. In addition we have also experimentally validated a miRNA-lncRNA interaction using a zebrafish model, which suggest that miRNA-lncRNA interaction networks are biologically active . We haveThe study is not without caveats. The first being limitation in the diversity of CLIP-seq datasets available in public domain. The datasets used in the analysis are limited to HEK293 cells. The second major caveat is that majority of miRNA recognition elements could not be tracked back to their cognate miRNAs. With the advent of faster and cheaper sequencing technologies Figure S1Schematic of the proposed hypothesis.(TIF)Click here for additional data file.Figure S2List of all transcripts with the Ago binding sites.(DOC)Click here for additional data file.Figure S3Distribution of Ago binding sites across the length of lncRNAs divided in bins of 10 percent. A) The panel shows the number of Ago sites in each bin. B) The panel shows the individual Ago binding sites in lncRNAs transcripts.(TIF)Click here for additional data file."} +{"text": "A 53-year-old man with a diagnosis of gastric non-Hodgkin lymphoma (NHL) underwent PET/CT scans both prior to starting chemotherapy and immediately following completion of chemotherapy to evaluate the response to therapy. Pre-therapy PET/CT images showed intense FDG uptake in the antral region of the stomach. Biodistribution of FDG was otherwise unremarkable. The patient was started on metformin in the middle of his therapy period to provide glycemic control. Post-therapy PET/CT study performed after 6 courses of chemotherapy showed complete resolution of the disease with no evidence of residual FDG uptake. However, intense and diffuse FDG accumulation is observed in the bowel, which was interpreted as physiological and most probably due to metformin administration. It should be borne in mind that there are a number of physiological variants of FDG biodistribution seen on PET/CT imaging. Recognizing physiologic bowel activity is crucial for the accuracy of PET image interpretation. Conflict of interest:None declared. F-18 fluorodeoxyglucose (FDG) positron emission tomography (PET) imaging is a commonly used method for diagnosis or staging of malignancy as well as for evaluating treatment response. FDG competes with glucose for hexokinase phosphorylation to FDG-6- phosphate and FDG-6-phosphate becomes trapped in tissue in proportion to the rate of glycolysis or glucose utilization of that tissue . In thisA 53-year-old man with a diagnosis of gastric non- Hodgkin lymphoma (NHL) underwent PET/CT scans both prior to starting chemotherapy and immediately following completion of chemotherapy to evaluate response to therapy. Pre-therapy PET/CT images showed intense FDG uptake in the antral region of the stomach. Biodistribution of FDG was otherwise unremarkable. The patient was started on metformin in the middle of his therapy period to provide glycemic control. Post-therapy PET/CT study performed after 6 courses of chemotherapyAfter a ten-hour fasting (serum glucose level 66 mg/dL), the patient underwent PET/CT imaging from the skull base to mid thigh at 1 hour post injection of 16,6 mCi (614 MBq) FDG using a dedicated full-ring LSO based PET scanner integrated with a 6-slice CT. No intravenous contrast was given for CT portion of the study. However, a 50 mL of iodinated contrast diluted into 1500 ml water was orally administered starting from the midnight, to make the bowel visible on CT scans. The pre-therapy PET/CT images confirmed gastric involvement of the disease with no other pathological FDG accumulation throughout the body including the bowel. On the post-therapy PET/CT images (Dimethylbiguanide metformin or \"metformin\", a biguanide molecule with a half-life of 6 h, is an orally administered drug that lowers the blood glucose concentration and improves the insulin sensitivity in type 2 diabetes. It is the first-line drug of choice for the treatment of type 2 diabetes. It acts by increasing glucose uptake, oxidation and glycogenesis by muscle, increasing glucose metabolism to lactate by the intestine, reducing hepatic gluconeogenesis and possibly a reducing rate of intestinal glucose absorption . An inte"} +{"text": "Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified.To investigate the relationship between proliferation and immune gene signatures, we analyzed an integrated dataset of 1,954 clinically annotated breast tumor expression profiles randomized into training and test sets to allow two-way discovery and validation of gene-survival associations. Hierarchical clustering revealed a large cluster of distant metastasis-free survival-associated genes with known immunological functions that further partitioned into three distinct immune metagenes likely reflecting B cells and/or plasma cells; T cells and natural killer cells; and monocytes and/or dendritic cells. A proliferation metagene allowed stratification of cases into proliferation tertiles. The prognostic strength of these metagenes was largely restricted to tumors within the highest proliferation tertile, though intrinsic subtype-specific differences were observed in the intermediate and low proliferation tertiles. In highly proliferative tumors, high tertile immune metagene expression equated with markedly reduced risk of metastasis whereas tumors with low tertile expression of any one of the three immune metagenes were associated with poor outcome despite higher expression of the other two metagenes.These findings suggest that a productive interplay among multiple immune cell types at the tumor site promotes long-term anti-metastatic immunity in a proliferation-dependent manner. The emergence of a subset of effective immune responders among highly proliferative tumors has novel prognostic ramifications. Expression profiling studies in human tumors have enabled new insights into the genes and pathways that contribute to tumorigenesis and spurred the development of gene expression signatures prognostic of patient outcomes. Genes comprising prognostic signatures often provide clues to the pathobiological mechanisms that drive cancer progression. With the aim of discovering genes with statistical associations with breast cancer recurrence, we and others have identified a number of genes with roles in cellular proliferation -6, incluIn recent years, we and others have observed that elevated expression levels of many genes involved in immune response pathways are associated with reduced risk of breast cancer recurrence -19. ThesIn this report, we investigate the biological origins of coordinately expressed genes in breast cancer that exhibit statistical associations with patient distant metastasis-free survival (DMFS). We identify gene clusters indicative of tumor-immune cell interactions that organize into three distinct immunity-related gene signatures, or metagenes, and shed light on their prognostic implications for tumors of differing proliferative capacity with an emphasis on highly proliferative breast cancers and the most aggressive intrinsic molecular subtypes in particular.To characterize prognostic gene modules, we created a multi-study microarray database of 2,116 breast tumor expression profiles of which 1,954 were annotated with corresponding clinicopathological data including DMFS -adjusted; Additional file Further inspection of the cluster architecture revealed a large reproducible cluster of genes associated with immune cell functions that exhibited negligible correlation with the proliferation cluster Figure . Gene onWe hypothesized that the immune gene subclusters likely reflect the relative abundance of tumor-infiltrating immune cells. We employed several strategies to investigate this hypothesis. First, we investigated the expression patterns of the immune cluster genes in the microarray dataset of Abbas and colleagues, comprising a comprehensive collection of human leukocyte gene expression profiles . StrikinNext, we examined the immune gene subclusters for gene-level enrichment of GO terms . Numeroun = 35) at another institution , with breast tumor samples assigned to the closest subtype centroid based on Euclidean distance.Intrinsic breast cancer subtypes were assigned to samples using the Single Sample Predictor (SSP) algorithm described by Hu et al. and util [et al. . Affymett et al. and the t et al. . BrieflyP-value for survival difference > 0.99, and < 10% standardized difference for each of the listed variables.The 1,954 survival-annotated cases were dichotomized into training and testing sets comprising 977 cases each. Cases were iteratively randomized to two groups with monitoring of intergroup survival rates (log-rank test) and standardized differences for the P-values less than 0.01 and FDR-adjusted q-values less than 0.10 [Associations between gene expression and patient survival (DMFS) were assessed by Cox proportional hazards regression (likelihood ratio test) using the R survival package or by thhan 0.10 were ide2 expression data were mean centered (on genes only), and genes and tumors were hierarchically clustered by average linkage using uncentered Pearson correlation as the distance metric. Clustered data were visualized by TreeView using default color saturation settings.Supervised hierarchical clustering and heatmap visualization of breast tumor and leukocyte gene expression profiles were conducted using Eisen's Cluster (v2.11) and TreeView (v1.60) software ,91. BrieSelection and construction of the immune metagenes was carried out essentially as previously described ,28. BrieIGKC, IGLL5 and IGHA1 (the B/P metagene) and LCK, CD3E and CD27 (the T/NK metagene). Four housekeeping genes were included for normalization. Normalized expression ratios were generated by dividing the background-subtracted expression values by the geometric mean of the housekeeping genes. Lastly, the expression ratios were averaged to generate metagene values, and these values were correlated to total leukocyte abundance by Pearson correlation.Thirty FFPE tissue blocks from surgically resected primary ER+ breast tumors were selected from a biobank of primary breast tumors representing recurrent cases and controls maintained at Aarhus University Hospital, Denmark (SJHD and TLL) . The bloThe DAVID Bioinformatics Resource ,95 versiL, I, H: low, intermediate, or high proliferation tertile; T/NK: T cell/natural killer cell.B/P: B cell/plasma cell; CL: Claudin-Low; DAVID: database for annotation, visualization and integrated discovery; DMFS: distant metastasis-free survival; ER: estrogen receptor; FDR: false discovery rate; FFPE: formalin-fixed paraffin-embedded; GO: Gene Ontology; H&E: hematoxylin and eosin; HER2-E: and human epidermal growth factor receptor 2-enriched; HLA: human leukocyte antigen; LN: lymph node; LumA: luminal A; LumB: luminal B; M/D: monocyte/dendritic cell; MHC: major histocompatibility; PThe authors declare that they have no competing interests.SN and LDM conceived of the project and analytical strategy. MAB and LDM qualified and curated the breast cancer microarray datasets. MAB processed the microarray data and assigned cases to breast cancer subtypes. JWC contributed to data curation, quality control and subset analysis. JB and CS contributed microarray and clinical data, and contributed to manuscript development. TLL, SJHD and MCW provided paraffin blocks and pathological guidance, and contributed to methods development. SN, JR, PD, JPV and LDM vetted content and wrote the manuscript. All authors read and approved the final manuscript.Table S1 - Data table of patient populations comprising the breast cancer microarray database. Reference data for each breast cancer population is provided.Click here for fileSpreadsheet S1 - Distant metastasis-free survival-associated genes selected from patient groups 977A and 977B. Selected probe sets and their corresponding Cox regression coefficient, hazard ratio, confidence interval and FDR q-value are shown for 977A (1st tab) and 977B (2nd tab).Click here for fileFigure S1 - Hierarchical clustering of distant metastasis-free survival-associated genes in group 977B. The heatmap (far left) shows the hierarchical clustering of the 3,304 genes (probe sets) associated with distant metastasis-free survival. A zoomed in view of the proliferation and immune gene clusters are shown with gene dendrograms (right). Clustered genes having average correlations of approximately 0.6 are indicated by colored branches. Heatmap coloring: mean gene expression is colored black, red indicates above-mean expression, green denotes below-mean expression and the degree of color saturation reflects the magnitude of expression relative to the mean.Click here for fileFigure S2 - The proliferation metagene score is highly correlated with tumor cell proliferation rate. Two hundred and thirty-two primary breast tumors from the Uppsala population [(A) proliferation metagene and mitotic index and (B) Ki-67 staining. The metagene is depicted in (C), and tumor samples are ordered from left to right in ascending order, according to the proliferation metagene score (average log intensity of the proliferation genes). The Pearson product-moment correlation coefficient (r) and P-value are shown .pulation were annClick here for fileTable S2 - Ontology analysis and gene components of the immune gene cluster. Table A: Gene Ontology analysis of 161 gene probe sets comprising the large immune gene cluster demarcated in Figure Click here for fileSpreadsheet S2 - Table of Affymetrix probe sets and corresponding genes that comprise the proliferation and immune metagenes.Click here for fileFigure S3 - Concordance among gene clusters derived from patient groups 977A and 977B. (A) Expression patterns of probes comprising the proliferation (P) and immune clusters (IC) were compared between 977A and 977B. All selected probes (n = 210) and tumors were hierarchically clustered, then the tumors were partitioned (in cluster order) by patient group. Genes comprising the proliferation and immune clusters are distinguished by color according to the key shown. (B) Proliferation and immune cluster metagene values , derived from 977A and 977B, were compared to one another by Pearson correlation. Pearson coefficients (r) are represented by heatmap and described by the color key. r values corresponding to the cognate clusters are shown in white font. Biological titles equated with the immune clusters elsewhere in the manuscript are shown for continuity.Click here for fileFigure S4 - Breast cancer immune and proliferation gene clusters differentiate specific leukocyte cell types. This figure is derived from Figure Click here for fileFigure S5 - Magnitude of immune metagene expression correlates with abundance of immune cell infiltrate. Histological characterization of immune cell abundance was previously conducted for 35 tumors from Guy's Hospital, London [(A) Distributions of mean-centered metagene values (977A) are shown as box and whisker plots for each measure of immune cell abundance . Shaded rectangles define the interquartile ranges. The midline of each rectangle marks the median value. T-bars extending from the interquartile range mark the 5th and 95th percentiles, and outliers are indicated by open circles. P-values for differential distributions were generated by Kruskal-Wallis one-way analysis of variance by ranks (Sigma Plot 11.0). (B-D) Genes representative of the T/NK and B/P metagenes were prospectively analyzed for expression in a panel of 28 ER+ breast tumors using the Panomics QuantiGene Plex 2.0 assay system . H&E-stained, FFPE breast tumor samples exhibiting (B) high or (C) low levels of infiltrating immune cells are shown. Red arrows indicate small, darkly staining nuclei of leukocytes; blue arrows mark tumor cell nuclei. (D) Distributions of mean-centered metagene values are shown as a function of immune cell abundance . Box and whisker plot parameters and statistical method are the same as for (A)., London , for whi, London . (A) DisClick here for fileFigure S6 - The immune metagenes are prognostic of outcome in the aggressive intrinsic subtypes. (A) Intrinsic subtype distributions are shown relative to the proliferation metagene, whereby tumors are ranked by the proliferation metagene from left to right in ascending order. (B) The percentage of each tumor subtype comprising the three proliferation tertiles is shown. (C) Kaplan-Meier plots show the PH HER2-enriched (left), luminal B (middle) and Basal-like (right) populations stratified by the B/P metagene.Click here for fileTable S3 - Metagene value thresholds defined by tertile cut-points in the training set and subsequently applied to the test set.Click here for file"} +{"text": "Anopheles gambiae, has uncovered an array of components and mechanisms involved in defence against pathogen infections. Two of these immune factors are LRIM1 and APL1C, which are leucine-rich repeat (LRR) containing proteins that activate complement-like defence responses against malaria parasites. In addition to their LRR domains, these leucine-rich repeat immune (LRIM) proteins share several structural features including signal peptides, patterns of cysteine residues, and coiled-coil domains.The discovery and characterisation of factors governing innate immune responses in insects has driven the elucidation of many immune system components in mammals and other organisms. Focusing on the immune system responses of the malaria mosquito, LRIM1 and APL1C revealed putatively novel innate immune factors and furthered the understanding of their likely molecular functions. Genomic scans using the shared features of LRIM1 and APL1C identified more than 20 LRIM-like genes exhibiting all or most of their sequence features in each of three disease-vector mosquitoes with sequenced genomes: An. gambiae, Aedes aegypti, and Culex quinquefasciatus. Comparative sequence analyses revealed that this family of mosquito LRIM-like genes is characterised by a variable number of 6 to 14 LRRs of different lengths. The \"Long\" LRIM subfamily, with 10 or more LRRs, and the \"Short\" LRIMs, with 6 or 7 LRRs, also share the signal peptide, cysteine residue patterning, and coiled-coil sequence features of LRIM1 and APL1C. The \"TM\" LRIMs have a predicted C-terminal transmembrane region, and the \"Coil-less\" LRIMs exhibit the characteristic LRIM sequence signatures but lack the C-terminal coiled-coil domains.The identification and characterisation of genes related to The evolutionary plasticity of the LRIM LRR domains may provide templates for diverse recognition properties, while their coiled-coil domains could be involved in the formation of LRIM protein complexes or mediate interactions with other immune proteins. The conserved LRIM cysteine residue patterns are likely to be important for structural fold stability and the formation of protein complexes. These sequence-structure-function relations of mosquito LRIMs will serve to guide the experimental elucidation of their molecular roles in mosquito immunity. Disease-vector mosquitoes transmit some of the most devastating diseases of humankind including malaria, dengue, and filariasis. The ability of different mosquito species to transmit these and other pathogens varies greatly and much of this variation in vectorial capacity can be attributed to the success or failure of the mosquito immune system to recognise and eliminate the pathogen. The availability of complete mosquito genome sequences has facilitated both large-scale and targeted experiments, which together with hypotheses generated from extensive comparative genomic analyses have driven dramatic advances in the understanding of vector biology. These studies have revealed key components and underlying mechanisms that constitute the dynamically evolving repertoire of the mosquito's systemic and local epithelial immunity .An. gambiae have linked three major antiparasitic factors together in a complement-like pathway that mediates parasite killing xC). This distinctive terminal LRR pattern is also observed among the Short and Coil-less LRIMs.The Short LRIMs and the majority of Coil-less LRIMs contain 6 or 7 recognisable LRRs while the LRR domains of the Long, TM, and remaining 3 Coil-less LRIMs are made up of 10 to 14 repeats and the third 'L' of its 11-residue LRR consensus is almost always replaced by a less bulky alanine (A) residue. The mosquito LRIM-like genes are thus characterised by a variable number of 6 to 14 recognisable LRRs of different lengths, with a subset of LRIMs that exhibit an unusually short LRR of only 19 amino acids.Examining the lengths of the LRIM LRRs revealed the exceptionally short LRR-g Figure . The majg Figure . Althougg Figure . The LRRAgLRIM1 and AgAPL1C highlights several well-conserved patterns of cysteine residues is incomplete in AaLRIM2 and missing from the frameshift-disrupted AgAPL1A. This frameshift is present in the sequenced An. gambiae PEST genome assembly but may not occur in other populations where anti-parasitic effects of AgAPL1A have been observed [The comparison of protein sequences most closely related to s Figure . The leaobserved . The douobserved . A doublobserved . This moAgLRIM1 and AgAPL1C. Examining the behaviour of AgLRIM1 and AgAPL1C using specific antibodies under non-reducing conditions revealed major protein bands of a high molecular weight complex that resolved into expected monomer sizes under reducing conditions [An. gambiae shows specificity in regulating resistance to P. falciparum [As well as forming the N-and C-terminal LRR caps, the patterns of cysteine residues may also be important in stabilising LRIM-LRIM interactions as in the case of nditions . Thus, tnditions . The MD-nditions . At leaslciparum . Thus, cThe LRIM1 and APL1/LRIM2 proteins all exhibit a double coiled-coil C-terminal domain Figure , while tAn. gambiae LRIM1 and APL1C are ~55 kD and ~80 kD, respectively, the disulphide-bridged complex migrated at ~260 kD suggesting the presence of a functional multimer in the hemolymph [While the predicted monomer sizes of emolymph . HoweverAn. gambiae LRIM1/APL1C complex, some R-proteins require the formation of homo-or heteromeric complexes to achieve effective activation. LRRs of the related nucleotide-binding leucine-rich repeat (NLR) proteins are believed to sense Pathogen Associated Molecular Patterns (PAMPs) such as flagellin, initiating amino-terminal domain recruitment of downstream effectors such as pro-caspases to trigger immune responses [Drosophila immunity, the Toll LRRs similarly perform a recognition function but rather than directly sensing PAMPs, the receptor is activated by the cytokine, Spaetzle. The remarkable potential of LRR domains for diverse recognition properties is exploited in the jawless vertebrates, lamprey and hagfish, where LRRs have been shown to form the basis of their adaptive immune system [AgLRIM1 and AgAPL1C in An. gambiae hemolymph.The identification and feature characterisation of the family of mosquito LRIM-like genes revealed several putatively important sequence-structure-function relations. Notably, their variable LRRs suggest a stable arc or horseshoe-like fold with potential for surface structural plasticity that could facilitate multiple interactions. Interaction properties of LRRs are extremely diverse, exemplified by plant R-proteins that may sense parasites by binding to avirulence proteins or to host proteins that have been perturbed by the presence of parasite effectors . As in tesponses . TLR ectesponses . In Drose system . Combinae system . Interese system , as do AMany thousands of LRR-containing proteins have been found in a wide range of organisms from viruses to eukaryotes where the repeat structures appear to provide versatile recognition and/or interaction functionality often in combination with a variety of other functional, often signalling, domains . Some ofAgLRIM1 with AgAPL1C. Under this model, the Coil-less LRIMs may act as promiscuous family members that are less restricted in their choice of interaction partner. The LRIM coiled-coil domains may also facilitate important interactions with other components of the mosquito complement-like system. The An. gambiae LRIM1/APL1C complex interacts with the processed form of TEP1 and promotes its localisation to parasite surfaces [While the LRRs are likely to be responsible for pathogen sensing, the LRIM coiled-coil domains may be important for driving additional interactions. The oligomerisation properties of coiled-coils mean that they can serve as protein-protein interaction domains, as in the case of the SNARE proteins where a four-helix bundle brings three proteins together to facilitate the processes of membrane fusion . Interacsurfaces ,3. Such The known characteristics of the LRR domains of R-genes, NLRs, TLRs, and VLRs, together with functional data from mosquitoes and the interaction properties of coiled-coil domains support the role of LRIM proteins as putative recognition receptors of the mosquito innate immune system. This family of LRIM-like genes appears to be unique and expanded in mosquitoes with more than 20 members in each species but no clearly related genes in other insects. Nevertheless, both LRR and coiled-coil domains are tolerant of high levels of sequence variation that may obscure ancestral relations to genes in other organisms. The 6 to 14 variable-length LRRs that characterise the LRIM proteins may facilitate multiple interactions, which in turn may be augmented by the formation of LRIM protein complexes mediated by coiled-coils and stabilised by disulphide bridges. The appreciation of these relations between key protein sequence and structural features and their likely molecular functions will drive experimental elucidation of their roles in the biology of the mosquito complement-like system and innate immunity.An. gambiae LRIM1 and APL1C gene products both have signal peptide sequences followed by a stretch of LRRs. The C-terminal sequences of both these genes exhibit characteristic 7-residue repeats that define the primary structure of coiled-coil domains. A distinctive cysteine-rich pattern can be identified in the hinge region between the LRR and the coiled-coils. These characteristic shared features served as the basis for comparative genomic searches to identify putative LRIM-like genes. Official predicted protein sets for An. gambiae, Ae. aegypti, Cx. quinquefasciatus and the fruitfly, Drosophila melanogaster, were scanned for the distinctive cysteine-rich pattern of the hinge region using Perl regular expressions. Hits that also exhibited LRR and coiled-coil domains were then used as seeds for searches of the genomes of the three mosquito species, as well as D. melanogaster, Apis mellifera (honey bee), and Pediculus humanus (body louse). Homology-based gene predictions were then performed for each region using multiple approaches with sequence profiles or individual protein sequences. These predictions were manually examined with available supporting data (e.g. expressed sequence tags) to confirm LRIM-like gene models.LRIM-like genes in each of the three mosquito species were examined using the VectorBase [A. mellifera, Bombyx mori (silk moth), D. melanogaster, and Tribolium castaneum (flour beetle). The VectorBase expression data BioMart facility (database release 1.1.2) was employed to identify An. gambiae LRIMs that exhibited transcriptional responses to malaria parasite infections or blood feeding.The architectures of the identified LRIM-like genes were analysed using InterProScan , REP 4040, PCOILctorBase genome bAgAPL1C PANGGL repeat region: gcggatccaccATGTGCTGGTTACACGCCGTATC and ACCTATATGGGTTGGAGTTC. Products were analysed on a 2% agarose gel.Genomic DNA was prepared from single male mosquitoes from three laboratory strains; G3, L3-5 and Yaounde. Mosquitoes were placed in a tube containing 100 \u03bcL of a 50% w/v suspension of Chelex 100 beads (Sigma) in water. Mosquitoes and beads were homogenised using a disposable pestle and samples were incubated at 100\u00b0C for 10 minutes. Homogenates were spun at 20,000 xg for 1 minute. 1 \u03bcL of an 800 unit/mL stock of Proteinase K (Sigma) was added to 10 \u03bcL of the cleared supernatant and the samples were incubated at 37\u00b0C for 30 minutes, and then at 100\u00b0C for 5 minutes. 10 uL PCR reactions were run using 0.5 \u03bcL of the genomic DNA, GoTaq master mix (Promega) and the following primers flanking the Anopheles-Plasmodium-responsive leucine-rich repeat protein; BRACA: breast cancer susceptibility protein; cDNA: complementary deoxyribonucleic acid; GNEF: guanine nucleotide exchange factor; LRIM: leucine-rich repeat immune protein; LRL: leucine-rich leader; LRR: leucine-rich repeat; MD: myeloid differentiation protein; NBD: nucleotide-binding domain; NLR: nucleotide-binding leucine-rich repeat protein; PAMP: pathogen associated molecular pattern; SNARE: soluble N-ethylmaleimide-sensitive factor attachment protein receptor; TE: transposable element; TEP: thioester-containing protein; TIR: toll-interleukin receptor; TLR: toll-like receptor; TM: transmembrane; VLR: variable lymphocyte receptor.APL: The authors declare that they have no competing interests.RMW conceived and designed the study, carried out the computational comparative genomic analyses, and wrote the manuscript. MP performed the PANGGL repeat polymorphism experiments, participated in the design of the study and helped to write the manuscript. GKC coordinated the study, participated in the design, and helped to write the manuscript. All authors read and approved the final manuscript.LRIM gene features and expression dataSupplementary tables of . A table listing the sequence features of each of the identified LRIM genes in the mosquitoes Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus, and a table listing Anopheles gambiae LRIM genes with experimental evidence of transcriptional responses to malaria parasite infections or blood feeding.Click here for file"} +{"text": "N-acetyl-p-aminophenol reduces the paracellular transport activities of itself and co-administered substances. The aim of this study was to find out how APAP reduces the bioavailability of small molecules which pass paracellularly, and which tight junction proteins are involved in the regulation of paracellular transport using a Caco-2 barrier model.Drugs and diet interact with each other in mutually influencing their bioavailability. In our previous work we have shown that in vitro model is widely used by the pharmaceutical industry to predict the absorption of orally administered drugs. To construct a Caco-2 barrier model, the Caco-2 cell line, a continuous line of heterogeneous human epithelial colorectal adenocarcinoma cells, was seeded onto inserts for 21 days. After differentiation, the cells were treated topically with 10 mM APAP for 24 h. The cell transepithelial electrical resistance (TER) and capacitance (Ccl) were determined by two different impedance-measuring systems. The membrane permeability was tested by differently sized molecules: Lucifer Yellow (520 Da), 3\u20135 kDa and 40 kDa Fluorescein thiocarbamoyl (FITC)-dextran. The tight junction proteins were investigated using Western blot analysis and immunofluorescence staining.The Caco-2 i.e. membrane integrity, which correlated significantly with the decrease of permeability of the small molecules Lucifer Yellow (ca. 520 Da) and FITC-dextran (3\u20135 kDa) but not of large molecules (40 kDa FITC-dextran). The tight junction protein ZO-1 and its tyrosine phosphorylation were up-regulated after 24 h treatment with APAP.APAP increased the TER value, Tight junction proteins play an important role in maintaining the intestinal barrier function. We assume that APAP affects the paracellular transport pathway through disassembly of the tight junction. We suppose that APAP leads to remodelling of the tight junction protein ZO-1 through changes in the level of protein expression and in tyrosine phosphorylation. APAP may reduce the bioavailability of co-administered substances through remodelling the tight junction by regulating ZO-1 and its tyrosine phosphorylation. As a result, the paracellular transport activity for small molecules is decreased as is net intestinal absorption."} +{"text": "People with type 2 diabetes (T2D) struggle with their chronic disease, and few reach recommended targets for self-care activities and clinical risk factors. We explored the experience of using adjunctive naturopathic care (ANC) in people with T2D to better understand the role ANC may play in facilitating health behavior change and improving self-care.A phenomenologic qualitative study was embedded within a one-year prospective observational trial of ANC for people with inadequately controlled T2D. Focus groups and key informant interviews were audio-recorded, transcribed, coded, and analyzed using an inductive content analysis approach. We explored rationale, process, and outcomes from receiving ANC.Twenty-two of the 40 trial participants were interviewed. Participants differed non-participants only in their lower rating of satisfaction with ANC (p=0.03). The majority (64%) perceived limitations in usual care, which influenced their participation in the trial. The most striking characteristics of the experience of receiving ANC were the: (1) collaborative communication style, (2) holistic perspective, and (3) pragmatic approach to addressing behavioral change. Many participants reported feeling increased hope knowing they had new options and tools to take control of their health. Participants reported improved self-care behaviors, specifically, engaging in health promoting activities , improved self-efficacy, and better understanding the impact of psychosocial factors on their self-care. These findings were corroborated with statistically significant improvements in measures of mood and behavioral change in the parent study. A minority of participants expressed uncertainty about value of dietary supplements given the out-of-pocket costs.A variety of important benefits were reported by persons with inadequately controlled T2D who tried ANC. These findings are noteworthy because the trial participants had no previous knowledge of or experience with naturopathic care."} +{"text": "M. tuberculosis are urgently required as adducts in the present treatment regimen. Using THP-1 cells we have analyzed and compared the global protein expression profile of broth-cultured and intraphagosomally grown drug resistant and sensitive M.tuberculosis clinical isolates.Tuberculosis (TB) is the most threatening infectious disease globally. Although progress has been made to reduce global incidence of TB, emergence of multidrug resistant (MDR) TB threatens to undermine these advances. To combat the disease, novel intervention strategies effective against drug resistant and sensitive subpopulations of On comparing the two dimensional (2-DE) gels, many proteins were found to be upregulated/expressed during intracellular state which were identified by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). Four proteins were present in both intracellular MDR and sensitive isolates and three of these belonged to intermediary metabolism and respiration category. Two proteins of intracellular MDR isolate and two (glucose-6-phosphate isomerase and ATP synthase epsilon chain) of intracellular sensitive isolate belonged to intermediary metabolism and respiration category. One protein of intracellular MDR and three of sensitive isolate belonged to virulence, detoxification and adaptation category. ESAT-6 of intracellular MDR belonged to cell wall and cell processes category. Two proteins (Antigen 85-C and Antigen 85-A) of intracellular sensitive isolate were involved in lipid metabolism while probable peptidyl-prolyl cis-trans isomerase A was involved in information pathways. Four of intracellular MDR and two proteins (Rv2896c and Rv2558c) of sensitive isolate were hypothetical proteins which were functionally characterized using bioinformatic tools. Bioinformatic findings revealed that the proteins encoded by Rv0036, Rv2032c, Rv0635, Rv1827 and Rv2896c genes are involved in cellular metabolism and help in intracellular survival.M. tuberculosis during intraphagosomal growth showed that majority of commonly upregulated/expressed proteins belonged to the cellular metabolism and respiration category. Inhibitors of the metabolic enzymes/intermediate can therefore serve as suitable drug targets against drug-resistant and sensitive subpopulations of M. tuberculosis.Mass spectrometry and bioinformatic analysis of both MDR and sensitive isolates of Mycobacterium tuberculosis, one of the most successful human pathogens. Inappropriate treatment regimens and patient poor-compliance have led to the appearance of drug resistant TB. Multi Drug Resistant TB (MDR-TB) is caused by bacteria that are resistant to the most effective anti-TB drugs (Isoniazid and Rifampicin) with or without resistance to other drugs. 50% of MDR-TB cases in world are estimated in India and China .Method of Shevchenko et al. was follDigested samples were desalted and concentrated on C-18 ZipTips using the manufacturer's protocol. ZipTips were eluted on MTP 384 target plate with 2 \u03bcl of a-cyano-4-hydroxycinnamicacid (HCCA) saturated solution dissolved in 50% ACN and 0.2% TFA. Mass spectra of digested proteins were acquired using Autoflex II TOF/TOF 50 in positive reflectron mode, in the detection range of 500-3000 m/z. External calibration to a spectrum, acquired for a mixture of peptides with masses ranging from 1046 to 2465 Da, was done prior to acquisition. The proteolytic masses obtained were then processed through Flex Analysis v.2.4 programme for peak detection of proteins. Peak detection in MALDI spectra and submission of peak lists to the Peptide mass fingerprint (PMF) Mascot server were done using the Mascot Wizard program . Peptide mass tolerance was set to 50 ppm with carbamidomethyl-cystein set as fixed modification, oxidation of methionine as variable modification and 1 missed cleavage site was allowed.http://genolist.pasteur.fr/TubercuList/ hosted by Pasteur Institute, Paris for whole annotated genome of H37Rv.Computational analysis of the differentially expressed hypothetical proteins was carried out using softwares and web-servers like BLASTp, MotifScan and Conserved Domain Database (CDD). Protein sequences of all hypothetical proteins were retrieved from Tuberculist server http://blast.ncbi.nlm.nih. Protein sequence of hypothetical proteins was retrieved from Tuberculist server http://genolist.pasteur.fr/TubercuList. Top five BLAST hits were selected for annotating the function. BLAST runs were performed at NCBI server using the default threshold E-value of 10 and inclusion of threshold value of 0.005.The prediction of probable function of hypothetical proteins was done using BLASTp search performeThe motif search was done using HAMAP profiles and PROSITE patterns motif databases .http://www.ncbi.nlm.nih.gov/cdd.The Conserved Domain Database (CDD) of NCBI which is a database of multiple sequence alignment was usedThe authors declare that they have no competing interests.NS carried out the experiments, participated in the data analysis and drafted the manuscript. PS helped in mass spectrometric experiments and MK in bioinformatic analysis. BJ helped in carrying out cell line experiments and critical review of the manuscript. DB conceived and designed the study, interpreted the experiment data and drafted the manuscript. All authors read and approved the final manuscript."} +{"text": "Spleen Tyrosine Kinase (SYK) is a key activator of signaling pathways downstream of multiple surface receptors implicated in asthma. SYK function has been extensively studied in Last cells downstream of the high-affinity IgE receptor (Fc\u03b5R1). Most studies evaluating SYK function in preclinical models have relied on poorly selective compounds, anti-sense oligonucleotides, or SYK knockout mice. Here we describe the characterization of SYK mechanism in multiple in vivo model settings.The effect of SYK inhibitor MRK-A on allergic airway responses was evaluated in IgE-mediated tracheal extravasation in rat, Brown Norway Ova rat models of allergic inflammation and the sheep inhaled ascaris allergen challenge model.MRK-A dose-dependently blocked IgE-mediated tracheal extravasation in rat. In a Brown Norway rat ovalbumin-sensitized airway challenge model oral dosing of MRK-A led to a dose-dependent inhibition of airway inflammation. Intravenous dosing of MRK-A was able to significantly inhibit both early and late allergen- induced changes in airway resistance in an ascaris-sensitive sheep allergen challenge model as well as airway hyper responsiveness.Here we demonstrated that SYK mechanism plays a significant role in several in vivo allergen challenge models. This ranges from simple PK/PD mast cells driven models such as the IgE-mediated tracheal extravasation to the more complex and clinically relevant sheep inhaled allergen challenge model."} +{"text": "Increased concentrations of free-circulating plasma DNA (cpDNA) are observed in patients with invasive cancer, including lung cancer. Whether cpDNA levels are elevated in subjects with high-grade pre-invasive lesions of lung squamous cell carcinoma (SqCC) and whether its detection may be of value for identifying subjects at the highest risk of developing lung SqCC is currently unknown. The present study assessed cpDNA levels in subjects with high- and low-grade pre-invasive squamous endobronchial lesions relative to patients with clinically overt lung SqCC and healthy controls using real-time quantitative PCR methodology. The median cpDNA levels of the patients with invasive lung SqCC (n=16) were significantly higher compared with those of the healthy controls , whereas the cpDNA levels in the subjects with pre-invasive lesions (n=20) did not differ from those of the controls (P=0.29). The cpDNA levels in subjects with high-grade pre-invasive lesions were highly similar to those diagnosed with low-grade pre-invasive lesions (P=0.85). Our data suggest that cpDNA levels are not increased during the pre-invasive stages of lung squamous carcinogenesis. Early lung cancer detection is an important approach for reducing disease mortality rates. Low-dose spiral computed tomography (CT) scanning has demonstrated effectiveness in detecting early-stage peripheral lung cancers \u20133. HowevAnalysis of free-circulating plasma DNA (cpDNA) levels is a non-invasive method that has shown the potential to detect patients with lung cancer \u201315. SignPeripheral blood was collected with informed consent from i) subjects with pre-invasive squamous endo-bronchial lesions; ii) patients diagnosed with invasive lung SqCC (stage I\u2013IV); and iii) cancer-free, healthy individuals. Characteristics of the study population are shown in Peripheral blood was processed within 1 h of collection. The plasma component was carefully separated by centrifuging twice at 3,000 rpm for 10 min at room temperature. The plasma specimens were stored in 1-ml aliquots at \u221280\u00b0C until use. DNA isolation was performed essentially as described previously . BrieflycpDNA levels were determined in quadruplicate by means of quantitative real-time PCR amplification of the human Fra-1 gene on the ABI/Prism 7300 Real-Time PCR system and further quantified using a standard calibrator curve of human placental DNA . HPV16-sin situ (CIS) were categorized into high-grade pre-invasive disease (HGD). Statistical analyses were performed using the SPSS Statistics v17.0 software package . Differences in the frequencies of patient characteristics between groups were examined using Fisher\u2019s exact and Mann-Whitney U tests. Median plasma DNA levels between groups were compared using non-parametrical Kruskal-Wallis testing.cpDNA quantification assays were performed in a blinded fashion, and afterwards the results were correlated with disease category. For analysis, the pre-invasive lesions graded as hyperplasia, squamous metaplasia, mild dysplasia and moderate dysplasia were categorized into low-grade pre-invasive disease (LGD), and severe dysplasia and carcinoma A total of 52 plasma samples were used for comparison of cpDNA levels from i) 20 subjects with AFB-visualized preinvasive endobronchial lesions ; ii) 16 patients with clinically overt, invasive SqCC ; and iii) 16 cancer-free, healthy individuals (controls). The patients with clinically overt lung cancers demonstrated significantly higher levels of cpDNA as compared with the controls P<0.01; . By contThe results of our study suggest that cpDNA levels are not increased during the pre-invasive stages of lung squamous carcinogenesis. Although cpDNA levels were significantly higher in clinically overt lung cancer, consistent with previous data \u201315, noneet al cancerous lesions that well complement previous results from studies, mainly including the adenocarcinoma histotype ,22. A liIn conclusion, although the median cpDNA levels of patients with invasive lung SqCC were significantly higher as compared with those of healthy controls, no elevated levels of cpDNA were observed in subjects with either LGD or HGD. cpDNA quantification does not appear to be a prognostic marker in potentially malignant conditions and is unlikely to be of value as an alternative or addition to the diagnostic algorithm of AFB for identifying patients at highest risk of developing lung cancer. Our study highlights the need to continue research efforts aiming to identify biomarkers that can be appplied to non- or less invasively collected biomaterial for the early prediction of invasive cancer in the respiratory airways to improve screening and/or diagnostic algorithms."} +{"text": "MEN-I is a rare genetic disorder classically characterized by a predisposition to tumors of the parathyroid glands, anterior pituitary gland, and pancreatic islet cells. We present a case of MEN-I syndrome diagnosed using predominantly nuclear medicine imaging followed by radionuclide therapy, thus emphasizing the role of nuclear imaging in diagnosing and treating MEN-I. Multiple Endocrine Neoplasia-I (MEN-I) is an autosomal dominant disease with a broad spectrum of clinical manifestations , 2. ParaThere is a very few case reports of the development of pancreatic neuroendocrine tumors (PNETs) in patients diagnosed with MEN-I syndrome related tumors. A carcinoid tumor in this case was located in the head of the pancreas, along with macroadenoma of the pituitary gland. This is the first paper to report the occurrence of PNETs in the association of a pituitary adenoma diagnosed by PET and treated with radionuclide targeting somatostatin receptors.71-year-old normotensive female, non diabetic presented with abdominal pain and increasing jaundice. Patient was admitted for evaluation and management. Endoscopic ultrasound revealed a periampullary mass measuring 5 x 5 cm in close proximity to the distal common bile duct (CBD). Fine needle aspiration cytology demonstrated metastatic deposits of a round cell tumor, morphologically resembling a neuroendocrine carcinoma. Magnetic Resonance Cholangiopancreatography performed for assessment of loco-regional disease revealed a lobulated mass lesion (2.7 x 2.3 cm) in the head and uncinate process of the pancreas .As a palliative procedure, papillotomy was done and stent was introduced into the CBD during Endoscopic Retrograde Cholangiopancreatography. Hemogram, liver and kidney function returned to normal levels within a week after the procedure.68Ga-DOTANOC PET-CT study for staging and identification of distant metastases. There was evidence of somatostatin receptor expression on the tumor located in head of pancreas. Surprisingly, other intracranial lesion with intense radiotracer uptake was noted corresponding to enlarged pituitary gland with 177Lu-DOTATATE and co-administered with the reno-protective amino acid mixture containing 25 g of Arginine and 25 g of Lysine. Post therapy whole body planar scans revealed intense uptake of radiotracer in head of pancreas and pituitary (177Lu-DOTATATE reduced serum Chromogranin A by 23%. The patient has been scheduled for next therapy 6 weeks later.The patient atient was thereafter referred to the Nuclear Medicine Department for ry gland . Serum Try gland . Serum Pid gland . Biochemituitary . Single Neuroendocrine tumors (NETs) constitute a heterogeneous group of neoplasms with common characteristics and biological features. NETs were previously referred as APUDomas, by Pearse in 1968 when he described peptide secreting endocrine cells that share an ability to take up the precursors of biologically active amines, to produce active amine through subsequent intracellular decarboxylation, hence APUD (amine precursor uptake and decarboxylation) . Though MEN-I or Multiple Endocrine Neoplasia \u2013 Type 1, also called Wermer Syndrome, is a familial multiglandular endocrine tumor syndrome which can be variable in its presentation. The epidemiology of MEN-1 demonstrates a prevalence of 2-10 per 100,000 . It is 9Pituitary tumors occur in approximately 40% of patients with MEN-I. These occur more commonly in women than men, and they are often more aggressive macro adenomas as compared to sporadic pituitary tumors. The most common type of pituitary adenoma in MEN-I is a prolactinoma . But nonPancreatic neuroendocrine tumors occur in the majority of patients with MEN-I . Nonsecr99mTc-sestamibi, 111In-penterotide, 18-fluorodeoxyglucose (18F-FDG) and 131I-meta-iodobenzylguanidine (131I-MIBG). Each of these tracers has advantages and disadvantages. 99mTc-sestamibi, for example, concentrates on cells with high mitochondrial content and is very useful in detecting parathyroid adenomas; it has a sensitivity of approximately 90%. 111In-penterotide is extremely beneficial in detecting NET because it acts on somatostatin receptors, making it highly tumor-specific. In contrast, FDG accumulates in any region with increased glucose metabolism, such as areas of inflammation, therefore making it less tumor-specific are present in several organ systems and have an important function in the regulation of both endocrine and exocrine secretion. SSRs are expressed in the majority of tumors of neuroendocrine origin. So far five SSRs subtypes have been identified and cloned. Several somatostatin analogs have been successfully radiolabeled for diagnostic and therapeutic use. The relative usefulness of these radiolabeld somatostatin analogs is a function of their sensitivities and specificities of receptor binding and the characteristics of the associated radioisotope .68Ga-labeled peptides show a rapid renal clearance and rapidly accumulate in the tumors (80% within 30 minutes). Concentration in tissues without expression of SSRs is low, providing higher contrast imaging. The activity administered in adults is 100-150 MBq and imaging is acquired 60 to 90 minutes after injection. 68Ga-DOTANOC that we have used being a PET tracer is an excellent tracer for neuroendocrine tumor imaging, and provides a high target-to-nontarget ratio that allows for the detection of very small lesions (Positron emission tomography (PET) for imaging somatostatin receptor positive tumors is desirable because of its improved spatial resolution. lesions .111In-DTPA0] octreotide in patients with metastatized NET are encouraging, although partial remissions (PRs) were exceptional. This is not surprising because 111In-coupled peptides are not ideal for peptide receptor radionuclide radiotherapy (PRRT) because of the small particle range and, therefore, short tissue penetration of the Auger electrons in a 71-year-old female.68Ga-DOTANOC scan is particularly helpful for identifying pituitary and pancreatic lesions in MEN-I. Uptake of 177Lu-DOTATATE on post therapy scan and decrease in serum chromogranin A after single administration indicate an alternative non-surgical option for treatment of patients with MEN-I.Nuclear medicine diagnostic imaging namely"} +{"text": "Fasting is a recognized trigger of headache in susceptible individuals. Leptin is a peptide hormone encoded by the mouse obese gene (ob) and is mTo study the effect of acute administration of leptin on activity in the trigeminocervical complex (TCC) in response to middle meningeal artery (MMA) stimulation.Adult male Sprague-Dawley rats were anesthetized with pentobarbitone (60 mgkg-1) and cannulated for measurement of blood pressure and intravenous administration of supplementary anesthesia with propofol (15-20 mgkg-1hr-1). The parietal bone was removed over the MMA for electrical stimulation of the dura mater and electrophysiological recording of second order neurons in the TCC using a tungsten electrode. Rats received either rat recombinant leptin in a dosage of 1 mgkg-1 (i.v.) dissolved in sterile water, or sterile water alone as the control group. The effects of leptin on TCC activity in response to MMA stimulation were recorded.Leptin significantly reduced cell firing in response to trigeminovascular activation within the TCC (p < 0.05). This effect reached a maximum inhibition of nearly 12% at 45 minutes post-infusion of leptin. Infusion of sterile water alone had no significant effect on MMA stimulation-evoked firing.The data show leptin treatment inhibits stimulus-evoked trigeminal activity, which might explain, in part, why fasting, a condition characterized by low levels of circulating leptin, may have a role in headache. Exploring the interaction between feeding physiology and trigeminovascular nociceptive mechanisms may contribute to our understanding of this very common trigger."} +{"text": "Reduced expression in immortalized cells (REIC)/Dickkopf (Dkk)-3 is a tumor suppressor and therapeutic gene and has been studied with respect to the application of cancer gene therapy. Our previous studies demonstrated that the intratumoral injection of an adenovirus vector carrying the human REIC/Dkk-3 gene (Ad-REIC) suppresses tumor growth in mouse models of prostate, breast and testicular cancer and malignant mesothelioma. The mechanisms underlying these antitumor therapeutic effects have only been clarified recently. It has been demonstrated that Ad-REIC treatment inhibits cancer progression via the upregulation of systemic anticancer immunity. Under experimental conditions, autologous cancer vaccination via cancer-specific apoptosis and anticancer immune activation is a possible therapeutic mechanism. The robust anticancer effects observed in previous preclinical studies support the clinical utility of Ad-REIC. At present, a phase I\u2013IIa study of Ad-REIC gene therapy in prostate cancer patients is ongoing. The current study reviews the observations of previous fundamental studies and summarizes the anticancer mechanisms of intratumoral Ad-REIC treatment in terms of cancer vaccination. A number of therapeutic cancer vaccines have been previously developed and evaluated in phase II/III clinical trials \u20133. The sA good strategy to address these issues is to kill the cancer cells at the tumor site via the direct injection of anticancer agents. In this way, the various TAAs released from the dead cancer cells are exposed to the individual immune system. The released TAAs are taken up by antigen-presenting cells (APC) and activated APCs upregulate the anticancer immune response by presenting the TAAs to immune effector cells ,2. This Gene therapy has been utilized in a number of previous clinical trials of human cancer and exhibits an innovative and attractive therapeutic potential. Adenovirus-mediated gene delivery continues to be the preferred treatment for cancer as the vectors indicate the high transduction efficacy of the therapeutic gene and the safety of the procedure when used for direct local injection \u20137. A numin vitro and in vivo using several mouse tumor models. Under these experimental conditions, autologous cancer vaccination via cancer-specific apoptosis and anticancer immune upregulation is a potential therapeutic mechanism. We herein review the previously reported observations of fundamental studies and summarize the anticancer mechanisms of intratumoral Ad-REIC treatment in terms of cancer vaccination.The reduced expression in immortalized cells (REIC) gene is identical to Dickkopf (DKK)-3 and REIC/Dkk-3 expression is significantly downregulated in a broad range of human cancer cells \u201317. In oThe REIC gene was originally identified at Okayama University and reported in 2000 as a genThe REIC/Dkk-3 gene is located on human chromosome 11p15.1 and contains 9 exons spanning >50 kbp . The REIPreviously, the physiological functions of the REIC/Dkk-3 protein have been intensively investigated using knockout or overexpression of intracellular proteins. Previous studies have demonstrated that Dkk-3 modulates fibroblast growth factor and activin/nodal signaling to regulate the mesoderm induction of Xenopus. This suggests that physiological Dkk-3 is required for transforming growth factor \u03b2 (TGF-\u03b2) signaling during early Xenopus development . PreviouThese results indicate that intracellular REIC/Dkk-3 protein plays a pivotal role in biology, involved in cell differentiation and proliferation and the development of specific organs via the regulation of the Wnt and TGF-\u03b2 signaling pathways. Notably, REIC/Dkk-3 protein acts as an inhibitor or inducer of the Wnt and TGF-\u03b2 signaling pathways based on the cellular conditions of various tissues and organisms, from amphioxus to vertebrates . The bin+ monocytes were incubated with recombinant proteins at a concentration of 10 \u03bcg/ml. Recombinant REIC/Dkk-3 protein was found to induce monocyte differentiation to a DC phenotype. The morphological features of the REIC/Dkk-3-induced cell phenotype and its expression pattern of dendritic markers on the cell surface are similar to those of interleukin (IL)-4- and granulocyte macrophage-colony stimulating factor (GM-CSF)-induced DCs. Consistent with these observations, unpublished data indicates that recombinant REIC/Dkk-3 protein intraperitoneally administered in mice significantly upregulate the ratio of circulating DCs on flow cytometry. Recombinant REIC/Dkk-3 protein also possesses a cytokine-like function in the activation of STAT1 and STAT3 during dendritic phenotype differentiation in vitro. In terms of the expression of CD1a and CD14 surface markers, the REIC/Dkk-3-induced dendritic phenotype and IL-4- and GM-CSF-induced DCs are distinctly different. It is likely that these cells are categorized into DC subgroups. In addition, the direct cytotoxic effects of exogenous REIC/Dkk-3 protein were examined in several cancer cell lines. Even at a concentration of 20 \u03bcg/ml, no significant cytotoxic effects were associated with REIC/Dkk-3 protein treatment . The CAGin vitro ,18\u201320. Bin vitro ,18,20. Tin vitro \u201317,22, tThe molecular mechanisms underlying the apoptosis induced by Ad-REIC have been previously investigated and the pathway is shown in Previously, differences in ER stress signaling following Ad-REIC treatment have also been studied in cancer and normal cells ,19,21,40in vivo, mouse tumor models of several cancer types were established by transplanting the cancer cell line and treating the tumor-bearing mice with Ad-REIC . The aim of this clinical study is to verify the safety, efficacy and anticancer immunological effects of Ad-REIC-based gene therapy in prostate cancer patients. In particular, evidence of the concept of autologous cancer vaccination via Ad-REIC is being tested in clinical trials to clinically develop the agent for large-scale application. The safety and efficacy of Ad-REIC-mediated gene therapy have been verified in patients and the initial impression of the clinical trial has been good. We hypothesize that Ad-REIC-based medicine is likely to provide anticancer immunological effects via the application of autologous cancer vaccination, which is likely to become a promising therapeutic option for treating a wide range of human malignancies as a cancer vaccine."} +{"text": "After systemic administration, both compounds were cleared rapidly from the bloodstream but maintained plasma levels well above the active concentrations required in vitro for inhibition of Sp TF activity and cell proliferation. Consistently, MTM-SDK and MTM-SK inhibited transcription of Sp-regulated genes in prostate tumor xenografts and exhibited potent antitumor activity in subcutaneous and metastatic tumor xenograft models with no or minimal toxicity. Taken together, these data indicate that MTM-SDK and MTM-SK possess significantly improved pharmacological and toxicological properties compared to MTM-A and represent promising drugs for treatment of advanced prostate cancer.Deregulated activity of transcription factors (TFs) of the Sp/KLF family, like Sp1, Sp3 and Sp4, and consequent over-expression of Sp-regulated genes occur frequently in human cancers. This provides the rationale for development of inhibitors of Sp TFs as cancer therapeutics. Mithramycin A (MTM-A) is a natural polyketide that binds GC-rich DNA sequences, inhibits activity of Sp TFs and exhibits potent antitumor activity in experimental systems. However, clinical use of MTM-A is limited by the severe toxicity of the compound. Here, we studied two MTM-A analogues, which had been generated by genetically engineering of the MTM-A biosynthetic pathway, and evaluated their activity in human prostate cancer in cell cultures and mouse models. The compounds, named MTM-SDK and MTM-SK, were highly effective Tumor initiation and progression are mediated by multiple signaling pathways and the therapeutic benefits achievable by targeting individual pathways may be limited Streptomyces species Mithramycin A (MTM-A) is a natural polycyclic aromatic polyketide produced by various In this study, we evaluated the activity of the MTM-A analogues MTM-SDK and MTM-SK in experimental models of human prostate cancer. Prostate cancer is the most common cancer and the second leading cause of cancer death in men in western countries Human prostate cancer PC3, DU145, 22Rv1 and LNCaP cells were maintained in RPMI 1640 GAPDH and B2M were used as internal controls. Expression data were expressed as a percentage of control gene expression as described Total RNA from cultured cells and tumor tissues was isolated and reverse transcribed as described Cells were collected, cross-linked with formaldehyde and processed following a modified EZ-ChIP kit protocol (Upstate Biotechnology) as described Cell viability was determined using the MTT colorimetric assay as described ad libitum and their general health status was monitored daily. All protocols involving laboratory animals were conducted in conformity with the institutional guidelines and in compliance with national and international laws and policies. Experimental procedures and study protocols have been reviewed and approved by the Swiss Cantonal Veterinary Authority . To establish subcutaneous tumor xenografts, PC3 cells (2\u00d7106 cells) were inoculated in the flank of mice. For the metastatic xenograft model, PC3 cells (0.6\u00d7106) were injected twice into the tail vein with a 24-h interval between injections.Athymic male nude mice were purchased from the Harlan Laboratories. Mice were maintained under pathogen-free conditions with food and water provided Healthy CD-1 mice provided by the University of Oviedo Animal Facility were treated with single or repeated IV injections of MTM-SK, MTM-SDK and MTM-A. Each group consisted of 4 mice. For repeated doses, drugs were administered by IV injections every two or three days for a total of 10 injections. Body weight, deaths, changes in behaviour, motility, eating and drinking habits, and any other sign of local or systemic toxicity were recorded daily.Healthy CD-1 mice were injected IV with MTM-SK (18 mg/Kg) and MTM-SDK (2 mg/Kg). Blood was collected at five time-points between 5 and 120 min. At each time point 3 mice per group were analyzed. Plasma samples were diluted with 4 volumes of acetonitrile, vortexed and centrifuged to eliminate any insoluble precipitate. The supernatant was then used to measure MTM-SDK and MTM-SK by LC-MS. Plasma levels were assessed after intraperitoneal (IP) and IV injection of MTM-SK (18 mg/Kg) also by HPLC-UV.To evaluate the effects on transcription in tumor tissues, mice bearing subcutaneous tumours were treated with MTM-SDK (1.2 mg/kg) and MTM-SK (8 mg/kg) or saline solution by IV injection. Animals were sacrificed after 1, 3 and 7 days from the injection. Tumors were immediately collected and snap frozen for RNA isolation. qRT-PCR was performed as described above. At each time point 4 mice were analyzed in each experimental group and qRT-PCR performed in triplicate for each sample.Mice bearing subcutaneous tumors were treated with compounds or vehicle. Each experimental group consisted of 10 mice. Drugs were prepared in sterile saline solution and given by IP injections every 3 days. Control mice received IP injection of sterile saline solution. Tumor size was measured with a caliper twice a week. Data represent average \u00b1 SD of 10 mice per group.n\u200a=\u200a3 per group) were sacrificed after 1 and 2 weeks from the injection to confirm implantation and growth of metastatic cells. Control and drug treated mice (n\u200a=\u200a3 per group) were then sacrificed after 1 and 2 weeks from the beginning of the treatment. Lung tissues were collected for qPCR analysis and histological examination after H&E staining. Lung metastases were quantified using a previously described qPCR based method To evaluate the compounds ability to block metastatic tumor growth, mice received tail vein injections of tumor cells to establish lung metastasis. Then mice were treated with MTM-SDK (1.2 mg/kg), MTM-SK (8 mg/kg) or sterile saline given by IP injections every 3 days starting two weeks after the tail vein injection of tumor cells. Two groups of untreated mice and androgen-independent (AI) prostate tumors. LNCaP cells are androgen receptor (AR) positive and depend on AR signaling. 22Rv1 are AR positive but AI. PC3 and DU145 are AR negative and AI. Growth of all the cell lines tested, independent of their AR state, was strongly inhibited by both compounds, with MTM-SDK being more effective than MTM-SK . The IC5Systemic toxicity is a major limitation to the clinical use of MTM-A. Therefore, we assessed the doses at which MTM-SDK and MTM-SK could be safely administered to mice upon both acute and chronic administration. The maximum tolerated doses (MTD) of MTM-SDK and MTM-SK after a single IV injection were 4 mg/kg and 32 mg/kg, respectively . The MTDin vitro for cell growth inhibition and suppression of Sp1 dependent transcription. Next, we compared pharmacokinetics of MTM-SK following single IV and IP injections. Beside the initial peak seen with the IV injection, the kinetics following IV and IP administration were quite similar, reaching comparable drug levels in the plasma within 15\u201330 min and maintaining similar levels over the 2-h period of the analysis , MTM-SK (8 mg/kg) or saline solution. Tumors were excised at 1, 3 and 7 days after the injection and RNA levels of selected Sp regulated genes were measured by qRT-PCR. Expression of at 24 h . HoweverThe anti-tumor activity of MTM-SDK and MTM-SK was examined using subcutaneous tumor xenografts of PC3 prostate cancer cells. PC3 cells are AI, highly tumorigenic and metastatic. Thus, these cells represent a good model of advanced castration-resistant prostate cancer. Mice bearing PC3 tumor xenografts received MTM-SDK and MTM-SK every 3 days by IP injections. The IP administration was chosen as it is commonly used for prolonged treatments with anticancer compounds. Furthermore, IV and IP injections were nearly equivalent in terms of plasma levels and pharmacokinetics. Doses and schedule of administration were also based on the pharmacodynamic and MTD data described above. The treatment was terminated when mice in control groups had to be sacrificed due to excessive tumor burden. Drug-treated mice were followed for another week after the end of the treatment. Treatment with MTM-SDK and MTM-SK reduced tumor growth . The difWe were interested in determining whether treatment with the MTM-A analogues was also effective in a metastatic model of prostate cancer. To this end, we used an experimental lung metastasis model to study the effects of the treatment on disseminated human cancer cells in immunodeficient mice. PC3 cells were injected in the tail vein of mice and the growth of lung metastasis was monitored by qPCR over a 4-week period in vivo pharmacological and toxicological profiles. Genetic manipulation of the MTM-A biosynthetic pathway to generate new compounds with an array of structural modifications may provide the means to produce analogues more active and more suitable for clinical use than MTM-A Sp family transcription factors control many cellular processes essential for development of human tumors In this study, we investigated the pharmacological activity of MTM-SDK and MTM-SK in prostate cancer cell lines and prostate tumor xenografts. The two compounds were effective inhibitors of the transcription of Sp1-regulated genes both in vitro and in vivo. Toxicity studies revealed that MTM-SDK and MTM-SK were well tolerated upon systemic administration in mice. The MTDs for single injections of MTM-SDK and MTM-SK were, respectively, 4- and 32- fold higher than that of MTM-A. Repeated treatment with both compounds using two different schedules of administration was also well tolerated. Using doses and schedules of treatment that could be safely administered , both compounds exhibited potent antitumor activity in subcutaneous prostate tumor xenografts. Even at the lowest dose tested, treatment with MTM-SDK and MTM-SK significantly reduced tumor growth. Prolonged treatment was well tolerated also in tumor bearing mice with minimal reduction of body weight. Only at the highest dose of MTM-SDK there were signs of toxicity in few animals at the end of the treatment. MTM-SDK and MTM-SK were also very active in a metastatic prostate cancer xenograft model. Although lung is not a primary site for prostate cancer, this experimental model approximates the clinical situation of advanced disease with multiple metastatic foci growing at ectopic sites. Advanced prostate cancer is difficult to treat and the finding that the MTM analogues arrested the expansion of metastatic foci in the lung could be clinically relevant. The metastatic cascade comprises several steps. This experimental model requires cancer cells to survive in the bloodstream, extravasate, form micro-metastasis and then expand into clinically evident macro-metastasis. In our experiments treatment was initiated at the stage when multiple micro-metastatic foci were present in the lung of control animals in vitro studies We assessed pharmacokinetics and pharmacodynamics properties of the MTM-A analogues to guide the choice of dose and schedule of administration for the antitumor activity assays. We found that MTM-SK and MTM-SDK were cleared rapidly from the bloodstream after IV administration according to a typical exponential decay. The pharmacodynamic data suggest a rapid uptake in cells and tissues that would compensate for the short half-life in the bloodstream as indicated also by previous The activity of MTM-SDK and MTM-SK demonstrated here in prostate cancer cell lines and prostate tumor xenografts is highly encouraging. Along with previous data in other tumor types, these results indicate that these MTM-A analogues could be good candidates for treatment of cancers in which Sp TFs play an important role in driving the disease. Recent studies also have expanded the potential of Sp TF targeting compounds like MTM-A as cancer therapeutics. MTM-A was shown to have synergistic activity in combination with other anticancer drugs in various experimental models of human cancers Methods S1Bioinformatics analysis of Sp transcription factors in prostate cancer.(DOC)Click here for additional data file.Figure S1Gene set enrichment analysis of Sp target genes in prostate cancer.(PDF)Click here for additional data file.Figure S2Cell viability following 24-h incubation with MTM-SK and MTM-SDK.(PDF)Click here for additional data file.Figure S3Pharmacokinetics profile of MTM-SK following intravenous (IV) and intraperitoneal (IP) injection in mice.(PDF)Click here for additional data file.Table S1Genes with experimental evidence of control by Sp transcription factors and implication in prostate cancer development according to analysis of recent literature.(PDF)Click here for additional data file.Table S2Microarrays data sets downloaded from GEO.(PDF)Click here for additional data file.Table S3PCR primer sets and sequences.(PDF)Click here for additional data file."} +{"text": "Natriuretic peptides increase in heart failure. C-type natriuretic peptide (CNP) generates cyclic 3\u2019,5\u2019 guanosine monophosphate (cGMP) by activating the NPR-B receptor in cardiomyocytes. There are studies showing CNP-induced negative inotropic and positive lusitropic responses in normal hearts, but less is known about the effects of CNP in failing hearts.2+ removal from cytosol and thus less Ca2+ available for the myofilaments during contraction. Cyclic GMP levels, contraction and relaxation, Ca2+ transients, troponin I (TnI) and phospholamban (PLB) phosphorylation were measured in left ventricular muscle strips or cardiomyocytes from Wistar rats with heart failure 6 weeks after myocardial infarction. CNP increased cGMP levels and evoked negative inotropic and positive lusitropic responses concentration-dependently. TnI and PLB phosphorylation also increased in the presence of CNP. The functional responses to CNP were reduced in the presence of a PKG-blocker/cGMP-analogue (Rp-8-Br-Pet-cGMPs), demonstrating activation of the PKG pathway. In the presence of CNP, Ca2+ transient amplitude and Ca2+ extrusion rate were increased. CNP elicited both negative inotropic and positive lusitropic responses in the presence of the L-type Ca2+ channel activator BAY K 8644, whereas in the presence of full activation of the cAMP system by isoproterenol these responses were not seen. This indicates that the downstream targets causing functional responses to CNP were already activated in the presence of isoproterenol. All these results could be explained by an increased SERCA activity and a reduced myofibrillar sensitivity to Ca2+ in the presence of CNP, due to increased phosphorylation of PLB and TnI, respectively. An obligatory role of SERCA activation was revealed in a mouse model with cardiomyocyte-specific excision of the SR Ca2+-ATPase gene (SERCA-KO). The functional responses to CNP were abolished in 8-week SERCA-KO mice compared to 4-week SERCA-KO mice still possessing some SERCA activity.We investigated the functional effects of CNP in heart failure and suggested that increased activation of SERCA is the main mechanism of CNP-induced negative inotropic and positive lusitropic responses. Increased SERCA activity could cause a faster CaThe functional responses to CNP are mediated through the PKG pathway. Activation of SERCA thus seems to be the major and indispensable mechanism of CNP-induced functional responses in failing hearts."} +{"text": "Atrial fibrillation (AF) is the most common cardiac arrhythmia affecting more than 5 million people in North America and Europe. Radio-frequency ablation (RFA) is effective in symptomatic, drug refractory AF. Reported success rates of the procedure vary significantly with AF recurrences ranging from 25-40%. The transmural extent of left atrial (LA) wall injury is difficult to assess with conventional electro-physiological (EP) measurements. Late gadolinium enhancement (LGE) and double inversion recovery T2-weighted TSE (DIR-T2w-TSE) and HASTE have been proposed to evaluate acute LA wall injury. In this study, we examine the evolution of acute (< 30 hours after RFA) atrial lesions in LGE and DIR-T2w-TSE MRI with time after the procedure. The main goals of this project are to study changes in acute lesion appearance with time after RF ablation and to determine the time interval after ablation when MRI achieves the best visibility of acute LA lesions.LB) and between LA lesion and normal myocardium (CNRLM) were evaluated for these patients using immediately and next day post-ablation DIR-T2w-TSE and LGE images. Signal intensity for LA lesion/blood/normal myocardium was measured in LA posterior wall/LA cavity/LV wall, correspondingly. Standard deviation of noise was assumed to be equal to standard deviation of blood signal in the LA cavity.From January 2010 to September 2011, 224 AF patients who underwent pulmonary vein isolation and debulking of the septal and posterior walls under EAM guidance were imaged on a 3 Tesla MR scanner . Typical time interval between the conclusion of the ablation procedure and patient in the scanner was less than an hour. MRI studies were performed to rule out procedure complications and assess the extent of injury to LA wall. The study protocol included DIR-T2w-TSE, contrast enhanced MR angiography , and 3D LGE scans. Ten patients underwent an additional MRI study on the next day after ablation (22.0\u00b12.6 hours) to follow-up on significant enhancement of the anterior wall of the esophagus in vicinity of LA wall, detected by immediately post-ablation LGE-MRI. Contrast-to-noise ratio (CNR) between LA lesion and blood (CNRQuantitative analysis Table and visuThe presented results indicate a fast physiological response of LA wall to injury. Edema is noticeably reduced 24 hours after RF ablation. Kinetics of contrast agent in injured regions changes considerably during the first 24 hours after RF ablation. Our results demonstrate that MRI study should be performed as soon as possible after conclusion of the RFA procedure to achieve high contrast between ablated LA wall and the other tissues.Ben B. and Iris M. Margolis Foundation."} +{"text": "Cell type and TF specific interactions between Transcription Factors (TFs) and cofactors are essential for transcriptional regulation through recruitment of general transcription machinery to gene promoter regions and their identification heavily reliant on protein interaction assays.in vivo through enrichments of non target cofactor binding site motifs within ChIP-seq peaks. We observe enrichments in both known and novel cofactor motifs.Using TF targeted chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) data from Encyclopedia of DNA Elements (ENCODE), we report cell type and TF specific TF-cofactor interactions captured Given the regulatory implications which TF and cofactor interactions have on a cell's phenotype, their identification is necessary but challenging. Here we present the findings to our analyses surrounding the investigation of TF-cofactor interactions encoded within TF ChIP-seq peaks. Novel cofactor binding site enrichments observed provides valuable insight into TF and cell type specific interactions driving TF interactions. Transcription Factors (TFs) are protein complexes responsible for the recruitment of basic transcription machinery to DNA . At the Distinct transcriptional programs made of interacting networks of TFs each regulating a subset of genes work cooperatively to generate the diversity of cells seen in multicellular organisms.Mapping of TF interactions within such net- works are important for understanding of their control over gene expression and higher order functions such as cell fate determination . AlthougCell type agnostic interactions do exist between TFs and are TF specific where master regulator TFs like the Signal Transducer and Activator of Transcription (STAT) bind with its cofactors to activate transcription of gene targets regardless of cell types ,5.in vivo conditions [While existing methods of discovering TF-cofactor interactions require protein interaction assays, such as protein complex immunoprecipitation, or two hybrid screens which are low throughput, costly and non-indicative of nditions -10.Specificity of TFs to their cognate binding sites have been well studied and with ChIP-sequencing (ChIP-seq) for chromatin immunoprecipitation (ChIP) coupled to ultra-high throughput massively parallel sequencing . During Sequenced regions include those bound by cofactors is largely due to the fixation step during ChIP where fixation not only occurs between the antibody targeted TFs and bound region but similarly with cofactors in a TFBS-TF-Cofactor-TFBS manner . As a rein vivo for transcription factor binding sites (TFBS) can be achieved and their co-occurrences used as a proxy for their interactions. While analysis of TF ChIP-seq peaks data is much more scalable for investigating far larger libraries of TFs.Thus, identification and scanning of bound genomic regions by the ChIP targeted TFs and cofactors in silico alternatives to analysing Cell type and TF specific TF-cofactor interactions from TFBS motif enrichments within ChIP-seq peaks. For cell type specific enrichments, we screened peaks for enrichments in non-canonical motifs, motifs with no known associations with the immuno-targeted TFs, across mutliple cell types (> 10). Whereas for TF specific enrichments >20% again in non-canonical motifs in > 3 cell types targeting the same TF.Given the existence of cell type and TF specific TF-cofactor interactions as well as the challenges in conventional methods of TF-cofactor discovery, we set out to explore In our study we used human ChIP-seq data from The Encyclopedia of DNA Elements (ENCODE) Project . In the In contrast to previous reports of cofactor sig-natures within TF ChIP-seq peak data for our For this study, we aim to identify TF-cofactor interaction networks through careful screening and analysis of transcription cofactor motifs captured by TF ChIP-seq as well as uncover nuances in their interaction specificities relating to cell types, and individual TFs.Cell type as well as TF specificity upon applying criteria specific filters.In the following, we begin with an overview of analyses conducted on the ChIP-seq dataset as well as report significant co-occurring TFBS motifs belonging to both validated and predicted cofactors. Of these, some exhibit Using ENCODE's recent release, a total of 425 ChIP-seq experiments studying 122 TFs in 95 different cell cultures were considered initially for this study totaling 1,702,787 unique ChIP-seq peaks.We removed experiments investigating basic transcription machinery Polymerase I, II and III and non-canonical TF CTCF. Peaks belonging to high occupancy regions, that is being ubiquitous across ChIP-seq experiments regardless of conditions were also not considered. Finally, TFs investigated in only a single cell type as well as those without matched DNA binding site motifs were also removed. Also excluded from analysis were peaks showing extensive overlaps with peaks of other TF ChIP-seq experiments targeting different TFs . Accumulation of functionally unrelated DNA binding factors in regions known as 'High-Occupancy Target' (HOT) regions have been documented . NucleatThe resulting dataset containing 1,022,885 peaks from 81 unique ChIP-seq experiments across 46 unique cell cultures of various tissue types was chosen. 28 unique TFs remained after curation with a total of 56 mapped canonical TFBS motif position weight matrix (PWMs).Finally, we looked for cell type specific as well as TF specific co-occurrences and identified a total of 134 such motifs Tables . ExamplePeaks were later classified based on presence of canonical TFBS motifs belonging to the ChIP targeted TF and a total of 75,955 non-canonical motifs were identified. Co-occurring motifs identified within peaks present and absent for the targeted TF's canonical motifs are thus classified as proximal and distal Figure .p-values < 0.05. Potentially novel as well as known TF-cofactor pairs have been identified and selected examples will be discussed in the following. For the complete list of co-occurring motifs identified please refer to the supplementary tables provided motif abundance; the enrichment of the co-occurring motif in the ChIP-seq peaks, 2) motif ubiquity; the presence of the co-occurring motif across peaks from different TF ChIP-seq experiments and the (3) uniqueness or dis-similarity the targeted TF's canonical motif(s) using similarity scores with motif ab motif ubThe most striking cell type specific enrichment observed belonged to the motif of Hepatocyte nuclear Factor 4 alpha (HNF4\u03b1) . The motHNF4\u03b1 belongs to the superfamily of nuclear receptors known to be expressed endogenously in adult liver cell lines. Functionally, HNF4\u03b1 is a ligand-dependent transcription factor which is a master regulator for liver-specific gene expression and forms homodimers as well as heterodimers with other TFs via its AF-2 transactivation domain .Co-occurring with HNF4\u03b1 motifs are the canonical motifs of 11 cofactor TFs both proximally and distally located peaks.More cell type specific co-occuring TF motifs can be found in Additional file As in the earlier section, we selected co-occurring motifs fulfilling the specific criteria of motif enrichment (>20%) across > 3 cell types targeting the same TF.108 TF specific motifs were identified with the majority (~ 83%) proximal to target TFBS motifs. Of these are experimentally verified co-factors of the target TFs as well as those whose identity as a co-factor has not been experimentally verified .Upon applying the screening process, five TFBS motifs where found to be enriched proximally with canonical TFBS motifs of the Signal Transducer and Activator of Transcription Three STAT3) (Jaspar motif ID: MA0144.1) regardless of cell type but not so in experiments targeting other TFs (Jaspar motif ID: MA0099.2) and its subunits c-Fos and c-Jun (Jaspar motif ID:MA0099.1 and Uniprobe motif ID: UP00103 secondary). Associations between STAT3 and AP-1 complexes are well characterised and their binding site motifs known to co-occur proximally together ,25. In a in vivo -29.AP-1 and STAT3 are known to be responsible for regulating the expression of genes mediating tissue repair and regeneration ubiquitously across cell types. The co-occurrences in the two's TFBS motifs in a cell type independent manner therefore is not surprising.p-value: 1.15405e-15) [Of the remaining two motifs, one is a Saccharomyces cerevisiae homologue of the AP-1 sub-unit c-Jun, GCN4 (Jaspar motif ID: MA0303.1) which binds to the AP-1 specific sequences (405e-15) . The oth405e-15) -34.Saccharomyces cerevisiae homologues HAP3, HAP4 and HAP5 in proximal peaks of ChIP-seq experiments targeting SP1 across cell types In a separate example of a TF specific co-occurrence of TFBS motifs, we observed the enrichment of 'CCAAT' family of TFs namely NFY, and the The positive identification of AP-1 and its subunits' motifs in ChIP-seq peaks studying to STAT3 but not in peaks studying SP1 and vis versa acts simultaneously as a positive internal control as well as a negative internal control for this study.TF specific motif co-occurrences identified in our analysis which have not been experimentally validated to our knowledge previously as a cofactors belong to EBF1 (Jaspar motif ID: MA0154.1). The co-occurrence was observed in the proximal peaks of ChIP-seq targeting NF\u03baB (Jaspar motif ID: MA0105.1) and the enrichment is fairly uniform across lymphocytes, embryonic stem cells, hepatocytes and human leukemia cells as shown in Figure EBF1 has been found to be important in the regulation of genes responsible for the normal progression of B cell development. Similarly, NF\u03baB too has been shown to be essential for proper B cell development ,40. HencThe motif of Plagl1 (Uniprobe motif ID: UP00088) was found enriched within peaks from ChIP-seq experiments targeting c-Myc across cervix adenocarcinoma cells (HeLa), human leukemia cells (K562), hepatocytes (HepG2), human breast adenocarcinoma cells (Mcf-7), lymophocytes (GM12878) and promyelocytic cells (NB4).Plagl1 and c-Myc are known regulators of the cell cycle and Plagl1 have been associated with inducing cell cycle arrest and apoptosis while c-Our analyses have uncovered enrichments of known and novel TF cofactors combinations occurring in cell-type and TF specific manner worth investigating. Through the examples discussed we've shown the retrieval of 3 verified cofactors including HNF4A in hepatocytes, STAT3 and AP-1, and NFY-A and SP1 as well as novel co-occurrences such as EBF1 and NFKB suggesting the possibility of the two being cofactors.Thus, it is apparent following critical examination of enrichments in non-canonical TFBS motifs in ChIP-seq data that cofactor motifs signatures are indeed detectable and retrievable through rigorous screening as described in our study.In conclusion, we have shown through careful examination of motif enrichment in ChIP-seq data that not only are global cofactors of TFs be identified but also criteria specific binding partners. This could potentially be used for quick identification of potential cofactors of newly characterised TFs not only in humans but also other model organisms.Such analyses as described in our study will prove be invaluable as more TFs are interrogated using ChIP-seq as the cost of next generation sequencing continues to become more affordable.To identify potential cofactor TFBS motifs from ChIP-seq data, we began with the collection of TF ChIP-seq experimental data as well as a representative list of known TFBS motifs. Next, we applied a series of procedures to process and screen for significant motifs exhibiting any of the two qualities: Cell type and TF specificity.In our analysis, we used TF ChIP-seq experimental data retrieved from the Integrated Transcription Factor Track in the Data Coordination Center of the ENCODE project ,46. The BSgenome.Hsapiens.UCSC.hg19 package in R [All 1,702,787 peaks were mapped to their appropriate DNA sequences belonging to the latest human genome assembly (GRCh37/hg19) ,46 usingage in R .Identification of co-occurring TFBS motifs using motif finding algorithms requires consensus Position Weight Matrices (PWMs) which summarise DNA profiles of DNA sites bound by the DNA binding domain (DBDs) of a TF. We retrieved curated PWMs from two leading open-access TFBS motif databases: JASPAR CORE 2009 and UniPROBE Mouse ,49. EntrA curated list of Tar-get TF canonical TFBS PWM(s) was retrieved from Ensembl .nature of the targeted TF, the number of experiments targeting the same TF, peak density of genomic regions and associated peaks, and the availability of target TF TFBS motif PWM(s).We begin by examining data from each ChIP-seq experiment based on the following: the Thereafter, we searched for proximally and dis-tally located co-occurring motifs by scanning for motifs in peaks positive for the target TFBS motif and peaks negative for the target TFBS motif. Motifs identified in the former represent motifs found in close proximity with the target TFBS while the motifs identified in the later represent motifs located distally from the target TFBS.Cell type and TF specificity.Finally, we determined significant and non-ubiquitous co-occurrences and screened them for: non-canonical TF such as CTCF were also removed.For meaningful analysis of TF-cofactor interactions, ChIP-seq experiments targeting general transcription machinery such as Polymerase II, III and the TATA-binding protein (TBP) were not considered for analysis. Similarly, the Justifications for considering CTCF as a non-canonical TF Initially considered as a canonical TF, CCCTC-binding Factor (CTCF) shows similar genomic distributions with TFs such as STAT1 and NRSF . However'Orphan' ChIP-seq experiments without 'sister' experiments investigating the same TF but in different cell types were not selected for further analysis as we were unable to ascertain occurrence specificity of the co-occurring motifs.HOT and COLD regions Individual peaks from each ChIP-seq experiment were curated based on the TF occupancy of the regions they are found in. Regions observing significant overlaps in peaks from multiple TFs (ChIP-seq experiments), henceforth referred to as High-Occupancy-Target (HOT) regions, are known to se-quester DNA binding factors but yet not much is known about their formation. As we were unable to determine if the motifs in the DNA sequences co-immunoprecipitated were truly bound by a cofactor or simply by another factors in the larger protein aggregates we chose not to include the peaks coming from these HOT regions into our analysis.The arbitrary cutoff set to delimit such HOT regions requires the overlapping of peaks from more than 50% of all ChIP-seq experiments investigated. Peaks found in these HOT regions will be henceforth referred to as \"HOT peaks\" and the rest as \"COLD peaks\" for nomenclatural reasons. Availability of Target TF TFBS motif PWM(s) Experiments targeting TFs without any matched TFBS motif PWM(s) from the curated list of TF PWMs retrieved from Ensembl earlier were removed from analysis.TFs which were matched to multiple canonical motifs were also observed due to multiple DBDs or have DBDs with alternative conformational states.As shown in Figure Enrichment of TFBS motifs excluding that of the target TF's in positive peaks were considered to be proximal co-occurrences where the both target TF motif and enriched motif share the same ChIP-seq peak. Motifs enriched in peaks negative for the target TF's motif(s) were grouped as distally co-occurring. See Figure Abundance scores for each of the identified co-occurring motifs were assigned based on the motif's presence across the ChIP-seq peaks investigated regardless of its enrichment within each peak.non-specific motifs were discarded from further analysis as we proceeded to screen for various criteria specific co-occurrences of TFBS motifs in the second part of our analyse.Some motifs were observed to co-occur in ChIP-seq peaks both abundantly within a ChIP-seq experiment as well as ubiquitously across ChIP-seq experiments regardless of the cell type or the targeted TF. Such This was achieved using two arbitrary thresholds, such that the selected motifs would not be co-occurring abundantly within an experiment (95th percentile) as well as be not too ubiquitous across ChIP-seq experiments . The second threshold was chosen based upon the relative abundance of co-occurring motifs across experiments after applying the first threshold.Cell type specific Motifs must co-occur in ChIP-seq peaks of experiments investigating the same cell type but across TFs (>3) and enriched with abundances above 15%. Motifs must co-occur in at least ten individual ChIP-seq experiments investigating the same cell type but different TF.TF specific Motifs must co-occur with the same tar-get TF motif in at least three or more 'sister' experiments investigating other cell types. The motif must also have enrichment abundances above 20% in all experiments.p-value representing the probability of a true match. A corresponding q-value is generated using a bootstrap method to determine the mini-mal false discovery rate at which the p-value will be deemed significant [To scan for the relative occurrence of TFBS motif PWMs within ChIP-seq peaks, we used the TFBS motif identification software, FIMO, for Find Individual Motif Occurrences. FIMO is found as a part of the MEME suite of motif analysis algorithms and requires PWM(s) of the queried TFBS motif for scanning and identifying TFBS motifs in the sequences provided. When comparing two motifs, FIMO assigns a log-likelihood ratio score to each sequence position matched and the scores are converted into a nificant .p-value describing the significance of the match against the rest of the motifs in the database. [The varying degrees of similarity between motifs found in the compiled list of motifs were determined using the motif similarity comparison software, TOMTOM. TOMTOM creates ungapped alignments between queried motifs against a database of PWMs and determines a atabase. . For thip-values scores less than 0.05, when compared with the target TF's motif(s) were considered to be false positives.Motifs with The authors declare that they have no competing interests.Experimental design by CX and PL and data analysis by GCL with assistance from CX. Manuscript written by GCL with input from CX and PL. All authors read and approved the final manuscript.Proximal co-occurring motifs. List of co-occurring motifs identified in proximity (in the same ChIP-seq peak) with a target TF canonical motif with accompanying parameters. (.csv)Click here for fileDistal co-occurring motifs. List of co-occurring motifs identified distally (in different ChIP-seq peak) with a target TF canonical motif with accompanying parameters. (.csv)Click here for fileCell type specific motifs. List of cell type specific co-occurring motifs. (.csv)Click here for fileTF specific motifs. List of TF specific co-occurring motifs. (.csv)Click here for file"} +{"text": "Animals co-evolve with their gut microbiota; the latter can perform complex metabolic reactions that cannot be done independently by the host. Although the importance of gut microbiota has been well demonstrated, there is a paucity of research regarding its role in foliage-foraging mammals with a specialized digestive system.Petaurista alborufus lena). Phylogenetic compositions of the cecal microbiota derived from 3 flying squirrels were dominated by Firmicutes. Based on end-sequences of fosmid clones from 1 flying squirrel, we inferred that microbial metabolism greatly contributed to intestinal functions, including degradation of carbohydrates, metabolism of proteins, and synthesis of vitamins. Moreover, 33 polysaccharide-degrading enzymes and 2 large genomic fragments containing a series of carbohydrate-associated genes were identified.In this study, a 16S rRNA gene survey and metagenomic sequencing were used to characterize genetic diversity and functional capability of cecal microbiota of the folivorous flying squirrel (Cecal microbiota of the leaf-eating flying squirrel have great metabolic potential for converting diverse plant materials into absorbable nutrients. The present study should serve as the basis for future investigations, using metagenomic approaches to elucidate the intricate mechanisms and interactions between host and gut microbiota of the flying squirrel digestive system, as well as other mammals with similar adaptations. Although ancestors of mammals are believed to have been small carnivores, primarily feeding on invertebrates or other vertebrates, dietaryPetaurista), which are adapted to a leaf-eating niche in forest trees in the montane areas of Taiwan, primarily consists of leaf parts of diverse tree species; fosmid end-sequence [JS583577-JS587049]; and fosmid insert sequence [JQ335997-JQ335998].CAZy: Carbohydrate-Active enZYmes; CBM: Carbohydrate-binding modules; CE: Carbohydrate esterase; COG: Clusters of Orthologous Groups of proteins; GH: Glycoside hydrolase; GI: Gastrointestinal; KEGG: Kyoto Encyclopedia of Genes and Genomes; MG-RAST: Meta Genome Rapid Annotation using Subsystem Technology; NCBI-nr: Non-redundant protein database of National Center for Biotechnology Information; ORF: Open reading frame; OTU: Operational Taxonomic Unit; PCoA: Principal coordinates analysis; Pfam: Database of protein families.The authors declare that they have no competing interests.HP Lu, CH Hsieh and HT Yu conceived the study design; HP Lu and HT Yu collected the samples; HP Lu, SW Huang, and M Wu did the molecular experiments and sequencing; YB Wang, CY Lin and M Wu carried out the bioinformatics analyses; and HP Lu and HT Yu wrote the first draft. All authors contributed to data interpretation and preparation of the final manuscript. All authors read and approved the final manuscript.Rarefaction curves of observed species (a) and Chao1 diversity (b).Click here for filePrincipal Coordinates Analysis (PCoA) based on the UniFrac metric comparing the phylogenetic composition of various gut microbiota. FS1 and FS2 represent cecal microbiota of 2 flying squirrels; M1, M2, and M3 represent cecal microbiota of 3 mice[f 3 mice; C8, C64f 3 mice.Click here for fileFunctional categories of the cecal microbiota of the flying squirrel, according to the COG database.Click here for fileFunctional categories of the cecal microbiota of the flying squirrel, according to the KEGG database.Click here for filePutative functions and taxonomic assignments of predicted ORFs of 2 fosmid inserts: Scaffold_56 (GenBank: JQ335997) and Scaffold_90 (GenBank: JQ335998).Click here for file"} +{"text": "Live Attenuated SIV confers potent protection against wild-type SIV challenge. However the mechanism of protection is poorly understood and does not appear to correlate with adaptive immune responses. We have constructed a novel conditionally live SIVmac239 variant that replicates exclusively when doxycycline(dox) is administered ,2. This Mauritian cynomolgus macaques were vaccinated with SIV-rtTA and subsequently challenged with the heterologous wild-type virus SIVsmE660. Indian rhesus macaques were vaccinated with SIV-rtTA and subsequently challenged with wild-type SIVmac239.In naive cynomolgus macaques, SIVsmE660 establishes high peak and steady-state viraemia. After 20 weeks vaccination with SIV-rtTA in the presence of dox, 6/6 animals were protected against SIVsmE660. By contrast only 1/6 animals were protected after 3 weeks vaccination in the presence of dox. The role of persisting vaccine virus replication was investigated by vaccinating for 3 weeks with SIV-rtTA in the presence of dox, removing doxfor 17 weeks and subsequent challenging with SIVsmE660. In this group, 3/6 vaccinates were protected against detectable infection with SIVsmE660 in the periphery. These data demonstrate that live attenuated SIV can protect against a vigorously replicating, heterologous challenge virus (SIVsmE660) and that a longer duration of vaccination is beneficial, even when the vaccine-virus is apparently 'switched-off'.Vaccination of rhesus macaques with the same SIV-rtTA vaccine for 6 months in the presence of dox protected only 2/8 vaccinates against homologous challenge with wild-type SIVmac239. Remarkably, both protected animals demonstrated more persistent viral load kinetics upon vaccination, which confirms that prolonged replication of the vaccine virus improves protection. Sequence recovery of SIV-rtTA indicated an absence of mutations in the rtTA gene that would impact on doxycycline dependency. The presence of only minimal changes elsewhere indicated that SIV-rtTA was genetically stable in vivo. Since the genetics and antigenic relatedness of vaccine and challenge virus does not appear to predict the outcome of these vaccine studies, the kinetics and relative persistence of vaccine virus replication and the role of innate anti-retroviral responses are being evaluated."} +{"text": "P. falciparum genome has become available in 2002, reverse vaccinology represents a new opportunity to identify novel malaria vaccine candidate antigens. Screening of predicted P. falciparum open reading frames for proteins that could elicit parasite-inhibitory antibodies has led to the identification of the Cysteine-Rich Protective Antigen (CyRPA) as promising blood-stage candidate protein for inclusion in a malaria subunit vaccine.The development of an effective malaria vaccine is recognized as one of the most promising approaches that would provide a cost-effective intervention for addition to the currently available malaria control measures. Since the fully annotated in vivo growth inhibition was assessed by passive immunisation experiments in P. falciparum infected NOD-scid nullIL2R\u03b3 mice engrafted with human erythrocytes [On the basis of available genome-wide transcriptomic and proteomic information generated since 2002, we have selected uncharacterized ORFs for evaluation of their potential as vaccine candidate antigens. To generate tools for the characterization of candidate antigens, we have developed a cell-based approach for monoclonal antibody production: (I) generation of stably transfected mammalian cells, expressing high levels of target antigen on their surface in a native conformation; (II) immunisation of mice with transfected cells; (III) hybridoma cell generation by screening with the transfectants . Stage-sin vitro and in vivo. Thus, CyRPA represents a promising malaria blood-stage vaccine candidate antigen. It fulfills three key criteria applied to select asexual blood-stage antigens as vaccine candidates: (I) the protein is conserved; (II) Abs against the antigen inhibit parasite growth in vitro and (III) are protective in animal models. We expect that characterization of further parasite proteins with this strategy will identify additional vaccine candidate antigens from the extracellular stages of P. falciparum. This will extend the panel of vaccine antigens for incorporation into an effective multivalent, multi-stage malaria subunit vaccine.Our data on localization, stage-specific expression pattern, and functional assays suggest a role of CyRPA in erythrocyte invasion by the merozoite. Importantly, CyRPA elicits Abs that inhibit merozoite invasion"} +{"text": "A 60-year-old male with a long-lasting history of palpitations was referred to our hospital for further evaluation. His family history was negative for sudden cardiac death at a young age. Transthoracic echocardiography and exercise treadmill test ruled out structural heart disease. Baseline ECG showed sinus rhythm and frequent premature ventricular contractions (PVCs) displaying rS pattern in leads V1 through V3, late transition zone in lead V4 and inferior axis. QTc interval (Bazzet's formula) was normal. Ambulatory ECG monitoring showed frequent monomorphic PVCs and bigeminy without episodes of ventricular tachycardia. After obtaining an informed consent, an electrophysiological study was carried out. A detailed activation mapping of the PVCs at the right ventricular outflow tract (RVOT) was performed with a 4-mm tip deflectable catheter using a 3-dimentional electroanatomical mapping system . The earliest activation site of the PVCs was identified at the anterior aspect of the RVOT free wall. Pace-mapping at this location demonstrated \"perfect match\" (12 of 12 leads) with the morphology of the PVCs. Shortly after the delivery of the radiofrequency (RF) energy, an episode of non-sustained monomorphic VT and an episode of sustained polymorphic VT (>30s) necessitating cessation of the ablation and external defibrillation were developed . Both epThe large majority of idiopathic RVOT tachycardias are due to cyclic AMP-mediated triggered activity . ApplicaRVOT PVCs and/or tachycardia in subjects without structural heart disease are generally considered benign ,6. Howev"} +{"text": "The application of advanced 3T MRI imaging techniques to study recovery after subarachnoid hemorrhage (SAH) is complicated by the presence of image artifacts produced by implanted aneurysm clips. To characterize the effect of these artifacts on image quality, we sought to: 1) quantify extent of image artifact in SAH patients with implanted aneurysm clips across a range of MR sequences typically used in studies of volumetry, blood oxygen level dependent signal change (BOLD-fMRI), and diffusion-weighted imaging (DW-MRI) and 2) to explore the ability to reconstruct white matter pathways in these patients.T1- and T2-weighted structural, BOLD-fMRI, and DW-MRI scans were acquired at 3T in two patients with titanium alloy clips in ACOM and left ACA respectively. Intensity-based planimetric contouring was performed on aligned image volumes to define each artifact. Artifact volumes were quantified by artifact/clip length and artifact/brain volume ratios and analyzed by two-way (scan-by-rater) ANOVAs. Tractography pathways were reconstructed from DW-MRI at varying distances from the artifacts using deterministic methods.Artifact volume varied by MR sequence for length (p = 0.007) and volume (p < 0.001) ratios: it was smallest for structural images, larger for DW-MRI acquisitions, and largest on fMRI images. Inter-rater reliability was high , and reconstruction of white matter connectivity characteristics increased with distance from the artifact border. In both patients, reconstructed white matter pathways of the uncinate fasciculus and inferior fronto-occipital fasciculus were clearly visible within 2 mm of the artifact border.Advanced 3T MR can successfully image brain tissue around implanted titanium aneurysm clips at different spatial ranges depending on sequence type. White matter pathways near clip artifacts can be reconstructed and visualized. These findings provide a reference for designing functional and structural neuroimaging studies of recovery in aSAH patients after clip placement. Recent advances in aneurysmal subarachnoid hemorrhage (aSAH) management have led to consistent improvement in survival, with case fatality rates decreasing 0.9% every year without a rebound increase in the proportion of survivors with severe disabilities . Most pu3) structural MRI volumes to measure cortical thickness and gray/white matter density using voxel based morphometric techniques [The acquisition of advanced neuroimaging sequences and application of recently developed analysis techniques promises to shed more light on the relationship between brain changes following aSAH and specific cognitive deficits. Such techniques include 1) high spatial resolution hichniques to measuchniques ,11 and tchniques , and 3) chniques -16. A rechniques -20. Howechniques ), vasospchniques -24.in vivo at high field (> 1.5 tesla) in aSAH patients, although basic characteristics of artifacts have been reported for imaging obtained with clips in phantoms at 1.5 tesla and higher [Treatment of many aSAH patients involves the surgical placement of non-ferromagnetic intracranial aneurysm clips ,26. Thesd higher ,34,45,46in vivo with patients who have a history of SAH, and that artifact size is quantified across a range of acquisitions using parameters that are typically found in advanced research MRI studies of cognitive function. The major motivation to characterizing the MR artifact in vivo rather than in phantoms is that the results can be interpreted from a clinically-relevant perspective in order to give neurosurgeons, neuroradiologists and researchers alike an idea of how much signal loss varies across these acquisitions before they embark on large-sample imaging studies of neurocognitive recovery after SAH. A description of artifact characteristics obtained in vivo across a range of advanced image acquisition sequences is necessary in order to understand the extent of signal integrity around the aneurysm clip. Only after the boundary of signal loss around the clip is quantified can the signal changes arising from damage due to the hemorrhage, normal signal change from healthy brain tissue, and connectional neuroanatomy near implanted clips, like that made possible by DW-MRI tractography, be adequately summarized.Given previous studies of MRI artifacts from aneurysm clip implants in humans conducted at low field strength and studies at both low and high field strengths conducted with phantoms, we expected at the outset of this study to find that artifact size depends on the type of pulse sequence. The novelty of our study is that it is conducted at 3T in vivo data is available from aSAH patients to guide clinicians and researchers in estimating the extent of aneurysm clip artifact in images reconstructed from advanced high-field (> 1.5 tesla) MR sequences. In this paper, we test the null hypothesis that the resulting artifact from implanted titanium alloy clips is spatially similar across high-resolution T1- and T2-weighted structural, T2* echo-planar BOLD-fMRI, and DW-MRI images when clinical characteristics related to the extent of aSAH and clip characteristics are similar. We also explore the ability to reconstruct temporal and frontal lobe white matter fiber pathways reconstructed using deterministic tractography methods from the DW-MRI acquisitions, and quantify pathway density at different distances from the artifact border.Image artifact due to the presence of titanium alloy aneurysm clips is generally acknowledged to be minimal. Yet no in-vivo clip orientation, and dimensions . The two patients were similar in terms of the degree and distribution of SAH, its intraparenchymal component, the degree and severity of vasospasm , the sur2), (4) a set of functional images obtained with a gradient-recalled echo-planar imaging (EPI) sequence sensitive to the blood-oxygen level dependent (BOLD) signal . These particular sequence parameters were selected for use here because they are commonly applied in structural and functional studies of cognition in both healthy controls [The following brain scans were obtained using a 3T Philips Intera scanner : (1) T2-weighted turbo-spin echo 3D volume acquisition , (2) high-resolution 3D T1-weighted magnetization-prepared rapid acquisition turbo field echo sequence , (3) a set of diffusion-weighted image volumes (32-directions high angular resolution) using the gradient overplus option with one B0 (non-diffusion weighted) image volume acquired before the acquisition of one repetition of the diffusion-weighted scans . In the first ANVOA, the dependent variable was the artifact length/clip length ratio, and the two fixed factors were rater (2-levels: rater 1 & 2) and scan sequence . In the second ANOVA, the dependent variable was the artifact volume/brain volume ratio, and the two fixed factors were rater (2-levels: rater 1 & 2) and scan sequence . These ANOVAs had 3 and 15 numerator and denominator degrees of freedom, allowing for To quantify how the number of white matter tractography pathways varied as a function of distance from the artifact, diffusion tractography pathways were computed from the set of aligned diffusion-weighted images according to previously described methods ,55. ThenThe means and standard deviations of the two raters' measurements of each patient's artifact are listed by imaging sequence in Table For both patients, the artifact appeared smallest on T2-weighted structural volume and the largest on the EPI functional image . = 8.51, p = 0.007), and the ANOVA of artifact volume/brain volume ratio = 22.25, p < 0.001) supporting the hypothesis the artifact size varies among the different MR acquisition sequences. Further evidence was found by computing post-hoc tests for significant (p < 0.05) differences among the means (Bonferroni corrected for multiple comparisons). These showed differences between the structural (T1 and T2) and EPI sequences for the artifact length/clip length ratios, and between the structural (T1 and T2) and EPI and DW sequences for the artifact volume/brain volume ratios. Differences between the EPI and DW artifact volume/brain volume ratios trended toward but failed to reach significance (p = 0.11).Significant main effects of scan type were found by the ANOVA of artifact length/clip length ratio . There were no significant main effects of rater found in either the ANOVA of artifact length/clip length ratio or the ANOVA of artifact volume/brain volume ratio, showing that estimates of artifact size were consistent and did not differ systematically by individual rater.Inter-rater reliability for all measurements was very high demonstrating objective differentiation between raters of the artifact size as a function of MR sequence. In general, inter-rater variability in estimation of artifact length was low and artifact volume was relatively high , computed from a group of similar aged controls published recently [Computed whole-brain volumes were 229,705 and 242,419 mmrecently . To helpThe ability to reconstruct nearby white matter fiber pathways as a function of distance from the artifact border was examined in both patients. The artifact mask delineated on the diffusion-weighted sequence was expanded by 3D morphological dilation incrementally in 2 mm steps analyses and between-group (SAH vs. matched control) can be conducted in future larger-sample studies. For functional imaging, there is a necessary tradeoff between high spatial and temporal resolution when acquiring fMRI-BOLD sequences. In our echo-planar fMRI sequence, we used a 2 second repetition time, meaning that hemodynamic activity throughout 34 slices representing the entire volume of the brain is captured every two seconds. This acquisition speed is common for task-evoked and rest state designs. Fast fMRI acquisitions require larger voxel sizes of ~ 3 mm in order to image most of the brain. Advances in head coil design, including the number of channels to record the signal, will in the future allow acquisition of higher spatial resolution scans in a shorter time, but the spatial-temporal tradeoff will remain.Artifact size in the fMRI-BOLD sequence acquired here is also significantly magnified by a susceptibility artifact at the base of the brain, near where many aneurysm clips are likely to be placed. This well-known dropout of signal due to a large static magnetic field inhomogeneity that occurs near air/brain interfaces is also present in echo-planar acquisitions in healthy controls. The interaction between clip location and signal dropout due to the brain tissue/air cavity susceptibility complicated delineation of the clip artifact because both artifacts appeared as low intensity regions and overlapped to some extent. However, the tissue-air artifact extends outside the border of the brain, so by constraining our artifact delineation to within-brain borders as defined by the high-resolution anatomical images we were able to minimize this error to some extent.Outside the boundary of our artifact masks, imaging signal integrity recovers quickly. This was demonstrated by reconstructing diffusion tensor tractography fiber pathways as the artifact mask volumes were parametrically dilated in three dimensions. As we used standard diffusion tensor imaging methods here with relatively few gradient orientations, future investigations should evaluate the feasibility of collecting higher direction diffusion-weighted sequences in order to more accurately reconstruct white matter pathways in SAH patients using methods like Q-ball and diffIn summary, we show that artifact due to the presence of titanium clips differs across a range of advanced high-field (3 tesla) MR imaging sequences in aneurysmal subarachnoid hemorrhage patients. This artifact is easily quantifiable and 3D volumes of confidence can be produced outside of which the MR signal for measuring structure, function, and diffusion-weighted connectivity information may be obtained. We also show that DW-MRI tractography can reveal white matter pathways in close proximity to the artifact borders. These results have important methodological implications for studying brain changes with advanced neuroimaging tools in patients who recover from subarachnoid hemorrhage after neurosurgical treatment.This project was supported by the Brain Aneurysm Foundation and the Vivian L. Smith Foundation for Neurological Research. Partial funding for the purchase of the Philips 3T scanner used to collect the imaging data was provided by NIH S10 RR19186. No funding was provided by manufacturers of clips studied.3T: three tesla; AFNI: Analysis of Functional Neuroimages; ANOVA: analysis of variance; ACA: anterior cerebral artery; ACOM: anterior communicating artery; aSAH: aneurysmal subarachnoid hemorrhage; BOLD: blood oxygen level dependent; DTI: diffusion tensor imaging; DW-MRI: diffusion-weighted magnetic resonance imaging; EPI: echo-planar imaging; ETL: echo train length; FA: flip angle; fMRI: functional magnetic resonance imaging; FOV: field of view; GOS: Glasgow Outcome Scale; mRS: modified Rankin Scale; MRI: magnetic resonance imaging; TE: echo time; TR: repetition timeThe authors declare that they have no competing interests.FK, FR, and TME collected the MRI data. DK did the surgeries and referred patients for research. FK and TME analyzed the data. SS helped interpret the imaging data. FK and TME wrote the paper. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2342/11/19/prepub"} +{"text": "Although transthoracic echocardiography (TTE) is the initial and best validated modality for the assessment of aortic valve stenosis severity, both cardiovascular magnetic resonance (CMR) and transesophageal echocardiography (TEE) provide valuable complimentary information, particularly when patients are being assessed for Transcatheter Aortic Valve Implantation (TAVI). It is increasingly recognised that aortic valve area normalised to body surface area may better represent the severity of aortic stenosis than estimates derived from measurements of peak flow velocity as these can be load-dependent. In addition, Doppler-derived measurements may be limited by errors arising from misalignment of Doppler jet and poor windows. This study sought to determine the agreement and variability between CMR-, TEE- and TTE-derived measures of aortic stenosis severity.One hundred and twenty three patients assessed by CMR and TTE prior to TAVI were studied. Aortic-valve stenosis severity was assessed by TTE with traditional Doppler measurements and computed using the continuity equation. By CMR, the severity of aortic stenosis was assessed using a contiguous stack of steady-state free precession (SSFP)-based, small field of view, short axis cines and quantified by planimetry of aortic valve area (AVA) at peak-systole . TEE, performed just prior to TAVI insertion, was also used to measure AVA by planimetry. Agreement and variability between each imaging modality were assessed by Bland-Altman analysis.2; -0.47 cm2 to 0.58 cm2, (Bias (SD of Bias); 95% Limits of agreement)). CMR- and TEE-based planimetry also showed close agreement with no clinically significant bias (0.096 (0.33) cm2; -0.54 cm2 to 0.73 cm2).Of one hundred and twenty three patients assessed by CMR and TTE prior to TAVI, 55 also underwent TEE. Close agreement and almost negligible bias was observed between CMR- -derived planimetry of AVA and TTE-continuity-equation-derived AVA (0.06 (0.27) cmPlanimetry of aortic valve area in patients with severe aortic stenosis by CMR shows close agreement and negligible bias when compared with continuity equation-derived AVA measures by transthoracic echocardiography. Furthermore, CMR and transesophageal echocardiography-derived AVA by planimetry also show close agreement. AV planimetry is important in the assessment of aortic stenosis severity in TAVI patients undergoing CMR.This project was supported by the NIHR Cardiovascular Biomedical Research Unit of Royal Brompton and Harefield NHS Foundation Trust, the British Heart Foundation, and CORDA. Dr. Jabbour was supported by a Postdoctoral Research Fellowship from the National Health and Medical Research Council of Australia, a Vincent Fairfax Family Foundation Research Fellowship from the Royal Australasian College of Physicians, the St. Vincent\u2019s Clinic Foundation, and the Victor Chang Cardiac Research Institute."} +{"text": "Endocrine therapy is an effective treatment of estrogen receptor-positive (ER+) breast tumors, significantly reducing mortality. However, approximately 30% of patients receiving adjuvant endocrine therapy will experience recurrence within a 15-year period. The mechanisms of endocrine resistance are poorly understood. Understanding the underlying genetic diversity of breast cancers responding differently to endocrine therapy is important for the development of more optimal and individualized treatments strategies.In the current study, a panel of isogenic MCF-7-derived human breast cancer cell lines -3 that aA small panel of somatic point mutations potentially associated with acquired endocrine resistance were identified. Future experimental validation will reveal which of the detected mutations that are causatively involved in resistance to endocrine therapy."} +{"text": "Vascular screening including the coronary, carotid, renal arteries and aorta using non-contrast MRA in 300 asymptomatic subjects detected atherosclerosis lesions including the coronary artery in 5% of participants.Atherosclerosis is a systemic disease affecting arteries in a whole body and a major cause of death in the world. There are few data, however, on the extent of the diseases associated with atherosclerosis in asymptomatic subjects.Objective of this study was to identify the prevalence of cardiovascular diseases in asymptomatic subjects using non-contrast MRA.We performed vascular screening including the coronary, carotid, renal arteries and aorta using MRA and biochemistry tests in asymptomatic subjects from October 2008 to July 2011. Imaging of carotid arteries was performed by time of flight methods. Imaging of coronary arteries was performed by corrected respiratory-triggered and cardiac-triggered steady-state-free-precision (SSFP) sequence with fat suppression and T2 preparation. The data of the magnetic resonance coronary angiography (MRCA) was transferred to the workstation with image reconstruction software . Imaging of renal arteries was performed by steady-state-free-precision (SSFP) sequence with time-SLIP pulse. The diseases of the aorta were detected by sagittal images of the coronary artery and coronal images of the renal artery by which the whole aorta from the ascending aorta to common iliac arteries was covered.There were 186 males and 114 females with a mean age of 59\u00b110 and 64\u00b19, respectively. Six subjects (2%) had coronary diseases, six (2%) had carotid artery diseases , two (0.7%) had renal artery disease, two had aortic disease (thoracic aortic aneurysm), and two had peripheral artery (common ileac artery) aneurysms. Two had atherosclerotic diseases in 2 lesions simultaneously. Thoracic aortic aneurysm was detected by sagittal images of MRCA, and common iliac artery aneurysm by coronal images of the renal artery.Asymptomatic atherosclerosis lesions including the coronary artery were detected by non-contrast MRA in 5% of participants. Non-contrast MRA is a useful and non-invasive technique without radiation exposure for vascular screening.None."} +{"text": "The Mortality in Emergency Department Sepsis (MEDS) score has been gradually accepted as a reliable tool for bedside risk prediction of sepsis patients in the emergency department. Despite its clinical usefulness, the MEDS score did not take advantage of the prognostic information of biomarkers.We compared the clinical utility of MEDS score with and without CRP or PCT among participants in a prospective cohort of patients. All adult patients fulfilling the criteria for SIRS with a presumed infectious etiology were eligible for inclusion. Serum PCT and CRP were evaluated at admission. Initial severity was assessed with the MEDS score. Each patient was followed for at least 30 days for the 30-day survival. We built three extended models, including MEDS plus natural log PCT model (MEDS-LnPCT), MEDS plus natural log CRP model (MEDS-LnCRP), and MEDS plus natural log PCT and natural log CRP model (MEDS-LnPCT & LnCRP) for comparison. The values of CRP and PCT were transformed to natural log scale to normalize the distributions. We assessed whether adding CRP, PCT or both biomarkers to the MEDS model significantly reclassified patients into more appropriate risk categories. The reclassification was then evaluated by comparison of the observed incidence of events in the cells of the reclassification table with the predicted probability from the original MEDS model.P = 0.047). MEDS-CRP and MEDS-CRP & PCT models improved model fit but did not improve calibration . All three models did not improve model discrimination as measured by c-statistics.The 63 patients who died (10.6%) had significantly increased levels of PCT and CRP. Adjusting for MEDS predictors, either high levels of CRP or PCT was independently associated with 30-day mortality. We fitted PCT-incorporated (MEDS-PCT), CRP-incorporated (MEDS-CRP), and PCT & CRP incorporated (MEDS-PCT & CRP) models for comparison. The MEDS-PCT model was the favored model as it improved model fit and calibration as measured by the Net Reclassification Improvement (NRI) score (14.1%, Adding PCT levels to the MEDS score reclassified patients into groups that better predict actual 30-day mortality. Inclusion of CRP or both biomarkers offers limited additional predictive value. Further validation studies are needed to corroborate these findings."} +{"text": "Immunotherapy represents a novel treatment approach for cancer; however, a longer maturation time and the lack of immunological markers are major obstacles in the development and characterization of immunological therapies. This study aims to identify gene expression profile on CD8+ T cells between the responder (completely regressed tumors) and non-responder (progressively growing tumors) groups of mice helpful in predicting the outcome of immunotherapy treatment. Using a preclinical mouse model for prostate cancer, subcutaneous tumors were established and the mice were treated with Ad-PSA+PSCA bivalent vaccine. Splenic CD8+ T cells purified from the responder and non-responder groups of mice were subjected to Affymetrix microarray to obtain gene expression profile. Pooling the data sets from two independent experiments revealed an up-regulation of 85 genes and down-regulation of 1768 gene in CD8+ T cells from the non-responder mice. Gene network analysis showed a coordinated expression of genes implicated in cell-mediated immune response, cell-to-cell signaling and interaction, and immune cell trafficking. The mRNA expression levels for the selected transcripts were verified using semi-quantitative RT-PCR method suggesting a panel of genes specific to CD8+ T cells differentially expressed between the responder and non-responder mice. Further studies are warranted to determine the potential of these identified genes as immunological biomarker to predict immunotherapy response."} +{"text": "The prognostic importance of the ischaemic and scar burden, and their impact on coronary heart disease (CHD) patient management is well established from single photon emission computed tomography (SPECT) studies. Recently, cardiac magnetic resonance (CMR) has been shown to have superior sensitivity for the detection of CHD compared with SPECT . HoweverFrom the prospective CE-MARC study, all patients who had significant coronary artery stenosis (\u226570% of a first order coronary artery or \u226550% of the left main artery) on quantitative invasive coronary angiography and ischaemia on both CMR and SPECT were selected. The summed stress score (SSS), the summed rest score (SRS) as well as the summed difference score (SDS) were assessed based on a 5-point scoring scale for perfusion defects and/or late gadolinium enhancement (LGE) using a 16-segment model; comparisons were made between the two modalities. Bland-Altman limits of agreement (BA) were calculated.One-hundred-and six of the 752 CE-MARC patients fulfilled the inclusion criteria for this analysis. The median SSS was similar between CMR and SPECT and the difference in cardiac coverage for perfusion assessment. Further studies will have to show the impact of these findings on patient outcome.The CE-MARC study was funded by a British Heart Foundation Programme Grant (RG/05/004). S.P is funded by British Heart Foundation fellowship (FS/10/62/28409)."} +{"text": "Ketamine hydrochloride is a noncompetitive antagonist of the NMDA receptors and produces a dissociative state described as a 'functional and neuro-physiological dissociation between the neocortical and limbic systems' ,2.We describe long-term use of ketamine in the pediatric intensive care unit (PICU) inducing pyramidal liberation in a septic shock patient.A 15-month-old boy with congenital cardiopathy and developmental delay without previous chronic encephalopathy history. He was admitted with septic shock and during the PICU stay received association of multiple analgesic-sedative agents and high doses of ketamine intravenous infusion . The patient presented after 10 days of PICU stay symptoms associated with pyramidal liberation: deep hyperreflexia with sinreflexia, Babinski sign on both sides, opisthotonus, trismus. The clinical signs were not associated with new metabolic or structural intracranial lesion. The patient was discharged from hospital after 36 days receiving pericyazine that was interrupted 1 week after hospital discharge.The ketamine side effects after short-term use include ,2: hyper"} +{"text": "The concept of bioprospecting for bioactive peptides from keratin-containing materials such as wool, hair, skin and feathers presents an exciting opportunity for discovery of novel functional food ingredients and nutraceuticals, while value-adding to cheap and plentiful natural sources. The published literature reports multiple examples of proline-rich peptides with productive bio-activity in models of human disease including tumour formation, hypertension control and Alzheimer\u2019s disease. Bioactive peptides have been identified from food and other protein sources however the bioactivity of keratin-related proteins and peptides is largely unknown. Considering the high representation of proline-rich peptides among proven bioactive peptides, the proline-rich character of keratinous proteins supports current research. A selection of mammalian and avian (chicken feather) keratinous materials were subjected to enzymatic hydrolysis using established processing methods. A bio-assay of determining inhibition of early stage amyloid aggregation involved using a model fibril-forming protein \u2013 reduced and carboxymethylated bovine K-casein (RCMk-CN) and quantitation of fibril development with the amyloid-specific fluorophore, Thioflavin T (ThT). The assay was fully validated for analytical repeatability and used together with appropriate positive controls. Peptide library products derived from chicken feather (n=9), sheep wool (n=9) and bovine epidermis (n=9) were screened in the fibril inhibition assay based on K-casein. 3 of 27 products exhibited interesting levels of bio-activity with regard to fibril inhibition. HPLC profiles provide an indication of the complexity of the assemblage of peptides in the three active products. We conclude the bioprospecting research using keratinous materials shows promise for discovery of useful bioactive peptides. Proline-rich peptides are an important ingredient of a balanced human diet. The modern Western diet is often lacking in these peptides. While dairy products are a major traditional source of these peptides, other low-cost potential sources for dietary supplementation are desirable.The concept of \u201cbioprospecting\u201d for bioactive peptides from keratin-containing materials such as wool, hair, skin and feathers presents an exciting opportunity for discovery and value-addition. The published literature (scientific and patent) reports multiple examples of proline-rich peptides with protective bioactivity in models of human disease, including tumor formation, hypertension control and Alzheimer\u2019s disease. Bioactive peptides have been identified from food and other protein sources. However, the bioactivity of keratin-related proteins and peptides is largely unknown.Considering the high representation of proline-rich peptides among proven bioactive peptides , the proA selection of mammalian and avian (chicken feather) keratinous materials were subjected to enzymatic hydrolysis using established processing methods for library production.A bioassay for determining inhibition of early-stage amyloid aggregation involved using a model fibril-forming protein and quantification of fibril development with the amyloid-specific fluorophore, Thioflavin T ThT, see . Progresn=9), sheep wool (n=9) and bovine epidermis (n=9) were screened in the fibril inhibition assay based on kappa-casein. Twenty-seven products were identified; three exhibited sufficient bioactivity to warrant enrichment and identification of active peptides within this sample set [Peptide library products derived from chicken feather (mple set .Results from the primary screening of keratinous peptide libraries in assays related to hypertension, including ACE inhibition and angiotensin II receptor inhibition, also indicate promising bioactivity. As fibril inhibition requires stoichiometric interaction between peptide and kappa-CN, the bioactivity is likely to be associated with most abundant peptides.High-performance liquid chromatography was used to provide an indication of the complexity of the assemblage of peptides in the three active products .Keratinous containing substances such as feather, wool and skin, often discarded after animal slaughter, can now be considered as important future neutraceuticals.Furthermore, the model systems currently used allow characterization of the molecular properties of fibril-inhibiting peptides and will allow us to elucidate the mechanism and molecular properties of the keratinous peptides responsible for fibril inhibition. Bioprospecting research using keratinous materials facilitates the discovery of useful bioactives in research and product development."} +{"text": "Rho family GTPases are critical regulators of many important cellular processes and the dysregulation of their activities is implicated in a variety of human diseases including oncogenesis and propagation of malignancy. The traditional methods, such as \u201cpull-down\u201d or two-hybrid procedures, are poorly suited to dynamically evaluate the activity of Rho GTPases, especially in living mammalian cells. To provide a novel alternative approach to analyzing Rho GTPase-associated signaling pathways in vivo, we developed a series of bioluminescent biosensors based on the genetically engineered firefly luciferase. These split-luciferase-based biosensors enable non-invasive visualization and quantification of the activity of Rho GTPases in living subjects. The strategy is to reasonably split the gene of firefly luciferase protein into two inactive fragments and then respectively fuse the two fragments to Rho GTPase and the GTPase-binding domain (GBD) of the specific effector. Upon Rho GTPase interacting with the binding domain in a GTP-dependent manner, these two luciferase fragments are brought into close proximity, leading to luciferase reconstitution and photon production in the presence of the substrate. Using these bimolecular luminescence complementation (BiLC) biosensors, we successfully visualized and quantified the activities of the three best characterized Rho GTPases by measuring the luminescence in living cells. We also experimentally investigated the sensitivity of these Rho GTPase biosensors to upstream regulatory proteins and extracellular ligands without lysing cells and doing labor-intensive works. By virtue of the unique functional characteristics of bioluminescence imaging, the BiLC-based biosensors provide an enormous potential for in vivo imaging of Rho GTPase signaling pathways and high-throughput screening of therapeutic drugs targeted to Rho GTPases and (or) upstream molecules in the near future. Rho GTPases constitute a large subfamily of the Ras superfamily and include several isofonns of CDC42, Rac and Rho. They function as intracellular molecular switches, cycling between a GDP-bond state (inactive) and a GTP-bound state (active). Rho GTPase signaling pathways regulate various cell biological processes Molecular imaging, especially optical imaging, provides a new platform for noninvasive visualization of biological processes at molecular level in the whole organism. This technique bridges the gap between the identification of biomarkers and their clinical applications. Fluorescence marking techniques and fluorescence resonance energy transfer (FRET) analysis are being widely used in characterizing the spatiotemporal dynamics of Rho GTPases in living cells Accumulating evidence indicates that Rho GTPases are involved in the formation and progression of tumors in vivo Bioluminescence imaging, which harnesses the light-emitting reactions of enzymes such as luciferase by oxygenating a substrate molecule, is a sensitive imaging modality that enables in vivo analysis of cellular and molecular events. It offers important opportunities for investigating a vide variety of disease in intact animal models and systems All experimental procedures with animals used in this study had been given prior approval by the Experimental Animal Manage Committee of Sichuan University under Contract 2011-0138472. Animal handling and all procedures on animals were carried out strictly according to the guidelines of the Animal Care and Use committee of Sichuan University and the Animal Ethics Committee Guidelines of the Animal Facility of the West China Hospital. The nude mice were maintained under specific pathogen free (SPF) conditions. Mice were gas anesthetized with isofluorane using the XGI-8 Gas Anesthesia Unit during all injection and imaging procedures.Restriction and modification enzymes and DNA ligase were purchased from Fermentas . TransStart FastPfu DNA polymerase was obtained from TransGen Biotech . The plasmids pGL3-Basic and pRL-tk purchased from Promega were used as templates for the amplification of the luciferase fragments. All BiLC-based biosensors were constructed in a pcDNA3.1 (+) vector backbone (Invitrogen). Site-directed mutagenesis was performed using the QuickChange\u2122 site-directed mutagenesis kit . Plasmid extraction kits and DNA gel extraction kits were purchased from Qiagen . Lipofectamine 2000 transfection reagent was obtained from Invitrogen . Bradykinin acetate salt (BK), insulin and lysophosphatidic acid (LPA) were purchased from Sigma-Aldrich . D-Luciferin potassium was from Xenogen . Coelenterazine was purchased from Regis .2S)2\u223c4 or (G4S)1\u223c2(F37A), Cfluc398-CDC42(G12V), Cfluc398-CDC42(T17N), Cfluc398-CDC42(WT), Cfluc398-RacI(F37A), Cfluc398-RacI(G12V), Cfluc398-RacI(T17N), Cfluc398-RacI(WT), Cfluc398-RhoA(F39A), Cfluc398-RhoA(G14V), Cfluc398-RhoA(T19N), Cfluc398-RhoA(WT), Nfluc416-WASP, Nfluc416-PAK and Nfluc416-PKN are KC736072-KC736086.The renilla luciferase (RL) plasmid, which was cotransfected to normalize transfection efficiency, is pRL-tk . The N and C portions of the firefly luciferase (FL) gene for each split point were amplified by PCR from pGL3-Basic . The coding sequences of the Rho GTPases and their related proteins were amplified from the corresponding plasmid vectors kindly provided by Y. Zheng . All the CDC42 biosensors were constructed by first generating the vectors pcDNA3.1-Nfluc and pcDNA3.1- Cfluc, following by insertion of PCR-amplified coding sequences of the interacting proteins (CDC42 and WASP GBD (AA 220\u2013288)) in frame and with a short flexible linker . All these cells were cultured in Dulbecco modified Eagle medium supplemented with 10% fetal bovine serum (Gibco). Cell cultures were maintained in a 37\u00b0C incubator with 5% CO2/sr) was measured by the charge-coupled device (CCD) camera of IVIS spectrum using the following parameters: 1-min exposure; emission filter, 600 nm; f-stop, 1; binning, 8; field of view, 15 cm. Renilla luciferase (RL) activity was measured by adding coelenterazine with the CCD camera . The measure of RL activity was preferential in order to avoid mutual interference, because RL emission signal intensity is almost negligible at 600 nm. Data for each well are expressed in the relative luminescence ratio, which is calculated as the ratio of the luminescent intensity of firefly luciferase (FL) at 600 nm to that of renilla luciferase (RL) at 500 nm (FL/RL). For the analysis of GEF and GAP activities in 96-well plates, 100 ng/well of expression vectors encoding these regulatory proteins or, as a control, the corresponding empty expression vector (pCMV-HA) were cotransfected with renilla luciferase vector and the biosensor pairs (Nfluc416-WASP/Cfluc398-CDC42(WT), Nfluc416-PAK/Cfluc398-RacI(WT) or Nfluc416-PKN/Cfluc398-RhoA(WT)). For the respond analysis of extracellular factors, NIH3T3 cells were plated on white, clear-bottom 96-well plates and transfected with 50 ng of the biosensor pairs (Nfluc416-WASP/Cfluc398-CDC42(WT), Nfluc416-PAK/Cfluc398-RacI(WT) or Nfluc416-PKN/Cfluc398-RhoA(WT)) per well. The cells were serum-starved (growth in serum-free DMEM medium for 6 h) and then detected the luminescence intensity. When the luminescence intensity became steady, we stimulated the cells with insulin (2 mg/ml), lysophosphatidic acid (LPA) (40 ng/ml) or bradykinin (100 ng/ml), which are the known activator of Rac1, RhoA and Cdc42, respectively Transfections were performed in 80% confluent 24-h-old cultures of HEK 293 or NIH 3T3 cells, which were plated on white, clear-bottom 96-well plates . For transfection, 50 ng/well of biosensors (a pair of plasmid vectors) as indicated were transfected using Lipofectamine 2000 reagent according to the manufacturer's instructions. The renilla luciferase plasmid was cotransfected to normalize transfection efficiency. The cells were assayed after 24-h incubation at 37\u00b0C at 5% CO2. To image in living cells, after administration of D-luciferin , luminescent signal intensity . One part of the whole-cell lysates was directly subjected to SDS-PAGE and probed with a 1\u22361000 dilution of goat anti-luciferase polyclonal antibody to confirm the expression of the biosensors. The primary antibody was detected with a 1\u22362000 dilution of HRP-conjugated donkey anti-goat IgG . Blots were developed using enhanced chemiluminescence (ECL) reagent (Amersham BioSciences). The proteins in the remaining lysates were coimmunoprecipitated with mouse anti-myc antibody . The immune complexes were captured using protein G-coupled magnetic beads (Millipore) and then fractionated by SDS-PAGE. Nfluc-effectors and Cfluc-Rho GTPases were detected with anti-myc and anti-luciferase polyclonal antibody, respectively.HEK 293 cells were plated on 100-mm culture dishes, grown to 80% confluence and then transfected with 2 ug of BiLC biosensors. After incubation for 24 h, the cells were harvested in cell lysis buffer of implantation were confirmed by luminescent intensity of RL activity in vitro, making sure the relative consistency among different groups. After a residence time of 24 hours, D-luciferin was injected intraperitoneally at 150 mg/kg BW. The mice were imaged using IVIS spectrum .All the mice used were 6-week-old. 293 cells plated in 100-mm dishes were transiently cotransfected with pRL-tk vector and BiLC biosensors as indicated and implanted subcutaneously 24 h later. The cell numbers 2\u223c4 or (G4S)1\u223c212 of CDC42 and Rac1 or Gly14 of RhoA was replaced with Val to inactivate the GTPase activity, resulting in constitutively activated forms (dominant positive mutants). In T17N or T19N mutants, Thr17 of CDC42 and Rac1 or Thr19 of RhoA was replaced with Asn. These mutations are known to reduce the affinity of G proteins for guanine nucleotides and downregulate Rho GTPase activity (dominant negative mutants) 37 or Phe39 in the effector domain of Rac and Cdc42 or RhoA, which is essential for the binding to the specific effector (effector-loop mutants) The split luciferase fragment-assisted complementation technique is thought to have the most sensitive and highest dynamic range due to the enzymatic amplification of signals and the optimized bio-compatible substrate (high cell permeability and high quantum yield) among all the protein-protein interaction (PPI) detection methods To demonstrate the feasibility of BiLC-based biosensors for imaging Rho GTPase signaling pathways, a pair of known interacting proteins (CDC42 and the GBD (AA 220\u2013288) of its effector WASP) was selected beforehand to put this strategy into practice, attempting to explore and construct the optimal configuration. The three dimensional structure (PDB ID: 1EJ5) of WASP GBD bound to Cdc42 indicates that if the amino terminal fragment of firefly luciferase (FN) was fused upstream of WASP-GBD and the carboxyl terminal fragment (FC) was added downstream of CDC42, the two luciferase fragments could be sufficiently brought together by the interaction of CDC42 and WASP and then yield significant complemented luciferase enzyme signal. We speculated that this configuration (Nfluc-WASP/CDC42-Cfluc) may be a good domain arrangement. As with other protein complementation assay methods, one of the key prerequisites for the split luciferase complementation strategy is an appropriate dissection site . Hence, to search for the configuration most suitable for the Rho GTPase biosensors, we constructed biosensors with all possible configurations based on the preferred dissection site (Nfluc416/Cfluc398) of the interacting proteins (such as CDC42 and WASP) need to be fused to which luciferase fragments (FN or FC) fluc398) . All theTo demonstrate the universality of BiLC strategy in visualizing Rho GTPases pathways, we further used this optimal configuration (Nfluc416-effector/Cfluc398-RhoGTPase) to construct Rac1 biosensor (Nfluc416-PAK/Cfluc398-Rac1 and mutants thereof) and RhoA biosensor (Nfluc416-PKN/Cfluc398-RhoA and mutants thereof). Therefor, we obtained a Rho GTPase biosensor system which can image the three best characterized Rho GTPases . All these sensors were studied in 293 cells by transient cotransfection under appropriate conditions. Firefly luciferase activities were imaged using the CCD camera of IVIS spectrum, and the pseudo-color images representing light intensities were generated by the Living Image\u00ae 4.2 software program . As is shown in Unlike FRET, photon is produced by luciferase oxygenating the substrate in BiLC. Because no excitation is used, there is no autofluorescent background, no bleaching of the donor fluorophores and no co-excitation of the acceptor fluorophores by the energy used to excite the donor But just as a coin has two sides, BiLC probes usually require several minutes to respond to the stimulus, and an even longer time to return to the baseline level. In contrast, FRET provide a high temporal resolution for Rho GTPase activity in live cells on the order of single secondsIn the BiLC sensor, the fragment of luciferase is fused to the Rho GTPase. This can affect the interaction of GTPase with downstream effectors and upstream regulatory proteins (such as GEFs and GAPs). By trial and error, we obtained the optimal configuration (Nfluc416-GBD/Cfluc398-WASP) and successfully apply this configuration to develop a system which can image the three best characterized mammalian Rho GTPases. The restoration of luciferase activity and the coimmunoprecipitation see have demIn the aforementioned studies, we only used different mutants to manipulate the activity states of Rho GTPases and demonstrated the restoration of luciferase enzyme activity in a GTP-dependent manner. This doesn't necessarily justify the Cfluc-RhoGTPase fusion proteins can correctly interact with upstream regulatory proteins. To test the rigorous validity of our BiLC-based biosensors, we further tested the responses of these biosensors to upstream regulatory proteins (GEFs and GAPs) and extracellular ligands in living cells. Because BiLC strategy is generally performed as plasmid-based transfections, it works well in conjunction with other target genes requiring transfection, such as plasmid encoding regulatory proteins of GTPases. Thus, in this section, we experimentally tested the responses of this biosensor system to GEFs and GAPs, to justify its sensitivity to the upstream signal transduction. The catalytic domains of six well-known GEFs and five GAPs were used as the representatives. Through these molecules, we can objectively test the sensitivity of this system to monitor GEF-catalyzed nucleotide exchange and GAP-stimulated GTP hydrolysis in living cells. Data are expressed as a ratio of experimental to control values, in order to facilitate comparison between activities from different regulator molecules. 2/sr. First, we proved that without stimulation, there was no obvious increase of luciferase activity restoration after luminescences became steady, and this steady signal began to gradually decrease after about 20\u223c30 min (data not shown). However, when we administrated the stimulators, the feature of response is completely different. As is shown in To further validate whether the system is sensitive to the upstream signals, we tested its responses to the stimulations of extracellular ligands. In this experiment, we use insulin, lysophosphatidic acid and bradykinin as the extracellular stimulators, which are the known activator of RacI, RhoA and CDC42, respectively The experiments above completely demonstrated that the BiLC biosensor systems can correctly response to the upstream signaling, and the sensitivity is very high. Thus, we can easily reveal or quantify the signal change in the Rho GTPase pathways, by estimating the changes of luminescent intensity, without lysing cells and doing labor-intensive works inherent to \u2018pull-down\u2019. Although this system can't entirely displace the function of the tradition method, it saves a great deal of time and effort as a screening method. And unlike the bimolecular fluorescence complementation (BiFC) biosensors, BiLC biosensors do not assemble irreversibly In this study, a new type of biosensor system for Rho GTPases based on bimolecular luminescence complementation has been established by optimizing the split site and the configuration. These genetically encoded biosensors are induced by Rho GTPase activation in a GTP-dependent manner. It's robustness has been demonstrated through visualizing the three best characterized Rho GTPases in living cell and in vivo. It has also been proved that this system is sensitive to the upstream regulatory proteins (GEFs and GAPs) and the extracellular ligands. As a novel alternative method to investigate Rho GTPase-associated signaling pathways, it takes a lot less effort than traditional ways, such as \u201cpull-down\u201d or two-hybrid analysis. And, more importantly, due to its high sensitivity and no autofluorescent background, it can be directly applied to living mammalian cells and in vivo. These merits make it as a good supplement to traditional technologies and fluorescent imaging. Application of these BiLC-based biosensors or combination with other methods will facilitate our research works: for example, exploring how Rho GTPase signaling pathways operate in living cells and deciphering the complex function of Rho GTPase signal transduction in living animal (such as in tumor model). Meanwhile, by virtue of the properties and advantages of bioluminescence imaging, this system makes it possible to carry out high-throughput screening assay for identifying therapeutic agents targeted to Rho GTPase pathways. We also hope that the BiLC biosensors generated here may provide principles and basic methods for proper application of BiLC strategy to shed light on other small G proteins."} +{"text": "These cancers have a poor prognosis, are highly metastatic and often resistant to current therapeutic approaches. Viscum album L. (mistletoe) is one of the most widely used complementary cancer therapies in Germany but little is known about its actual effects on paediatric solid cancers. Approved Viscum album L. extracts (VAE) basically contain water soluble compounds of the plant . However, mistletoe also contains triterpene acids (mainly oleanolic- and betulinic acid) that are water-insoluble. The anti-tumorigenic properties of these solubilized triterpene acids are the subject of ongoing research. The aim of this study is to determine the effects of different VAE containing either lectins (viscum), triterpene acids (TT) or a combination thereof (viscum TT) on solid tumor models In vivo efficacy was determined in the spontaneous NXS2 metastases model.Ewing\u00b4s-, osteo- and rhabdomyosarcoma as well as neuroblastoma cell lines were treated with the above-mentioned different VAE. The cytotoxicity and the induction of apoptosis were determined using mitochondrial membrane potential measurements (JC-1) and Annexin/PI assays. The mechanism of apoptosis was further analyzed by Western blot analysis and caspase inhibitors. in vivo will be presented at the meeting.First experiments have shown diverse but effective levels of sensitivity for triterpene acid containing mistletoe extracts among the tested tumor cell lines. The JC-1 assays revealed a mitochondria-dependent apoptosis induction. Results on the efficacy of treatment with VAE in neuroblastoma in vivo, supporting the effectiveness of these extracts as adjuvant tumor therapy. Furthermore, the results revealed cell-line-specific differences of the apoptosis rate induced by VAE.We could demonstrate that Viscum album L. extracts inhibit cell proliferation in different paediatric solid cancers cell lines and in a neuroblastoma model"} +{"text": "The term polyp refers to any overgrowth of tissue from the surface of mucous membranes. Intestinal polyps grow out of the lining of the small and large bowels. The polyps that arise as a result of proliferative dysplasia are termed as adenomatous polyps or adenomas. They are true neoplastic lesions and are precursors of carcinoma. The hamartomatous polyps are formed as a result of abnormal mucosal maturation. They are non-neoplastic and do not have malignant potential. There are several hereditary diseases that produce large numbers of intestinal polyps. These disorders include: familial adenomatous polyposis of the colon (MIM 175100), familial adenomatous polyposis type 2(MIM 608456), Lynch's syndrome (MIM 120435), Peutz-Jeghers syndrome (MIM 175200), Juvenile polyposis syndrome (MIM 174900) PTEN Hamartoma Tumor Syndrome (PHTS) PHTS Includes: Bannayan-Riley-Ruvalcaba Syndrome (MIM 153480), Cowden Syndrome (MIM 153480), PTEN-Related Proteus Syndrome, Proteus-Like Syndrome. Here we present spectrum of mutation detected in over six hundred Polish families with intestinal polyposis. The studies have encompassed over 30 families with Juvenile polyposis syndrome and PHTS, over 40 families with Peutz-Jeghers syndrome and almost 600 families with familial adenomatous polyposis of the colon. The study was in part financed by the Ministry of Education and Science, Poland, grant number N402 481537, N401 331936."} +{"text": "The cause of multiple sclerosis (MS), its driving pathogenesis at the earliest stages, and what factors allow the first clinical attack to manifest remain unknown. Some imaging studies suggest gray rather than white matter may be involved early, and some postulate this may be predictive of developing MS. Other imaging studies are in conflict. To determine if there was objective molecular evidence of gray matter involvement in early MS we used high-resolution mass spectrometry to identify proteins in the cerebrospinal fluid (CSF) of first-attack MS patients (two independent groups) compared to established relapsing remitting (RR) MS and controls. We found that the CSF proteins in first-attack patients were differentially enriched for gray matter components . Myelin components did not distinguish these groups. The results support that gray matter dysfunction is involved early in MS, and also may be integral for the initial clinical presentation. The cause of Multiple Sclerosis (MS) The most common MS clinical subtype is relapsing remitting MS (RR-MS), characterized by discrete attacks resulting in neurologic deficits. This is how 85% of MS patients present, with the first attack considered a clinically isolated syndrome (CIS) Some imaging studies suggest gray rather than white matter changes occur early, and predict the development of MS but other imaging studies are in conflict Cerebrospinal fluid (CSF) is an important body fluid to examine in MS because recent evidence suggests cell processing within the central nervous system (CNS) is a crucial component to the damage process. Meningeal and subarachnoid inflammation have been associated with cortical lesion development in very early MS patients MS, italicized this to distinguish it from the disease multiple sclerosis which is abbreviated as MS non-italicized) based proteomics offers an effective tool to evaluate CSF proteins. Using advanced proteomic techniques, we have previously examined CSF collected from healthy controls CFS) and neurologic post treatment Lyme disease syndrome (nPTLS) Mass spectrometry . We compared the results to CSF analysis from our published pooled healthy normals and pooled other neurologic diseases (ONDs) . We identified 2,820 proteins in MS CSF and determine whether the CSF proteins could distinguish between groups, we performed direct LC- mass spectrometry analysis of all the individually immunodepleted samples of the three groups included in this study, and quantified peptide and protein abundances employing the accurate mass and time (AMT) tag label-free quantification approach. The term , , We then selected the CNS-specific proteins detected in CSF which showed significant quantitative differences in the first-attack CIS MS group compared to established RR-MS and controls and direct LC-MS analyses CFS from nPTLS, as well as from healthy control CSF Our application of immunoaffinity depletion and the AMT tag strategy combining both offline 2D-LC-Although the use of our mass spectrometry based proteomics method was for research purposes, they may have added value to current magnetic resonance imaging (MRI) because conventional MRI generally does not detect gray matter lesions. That requires non conventional advanced imaging technologies In conclusion, although this is an early investigation, it has raised intriguing findings which suggest that the CIS/true first-attack presentation of MS may not be random. The data also indicate that the CSF proteome of these patients is distinguishable from established RR-MS, particularly by gray matter components , and that gray matter rather than myelin is more proximally involved in the initiation of MS.Approval for the conduct of this study was obtained from the Institutional Review Board of New Jersey Medical School, the Institutional Review Board of Pacific Northwest National Laboratory, the Human Ethics Committee at the Faculty of Medicine of Uppsala University, and the Human Investigation Review Board of the University of Szeged (in agreement with the Declaration of Helsinki). Written consent was obtained from subjects.MS/MS and direct LC-MS analyses were employed to provide both broad proteome coverage and reliable protein identification and quantitation. The offline 2D-LC-MS/MS analysis, where immunoaffinity-depleted CSF samples were fractionated into 30 fractions and each fraction was analyzed by highly sensitive LC-MS/MS on high-resolution Orbitrap Velos mass spectrometer, offers the broadest CSF proteome coverage. However, the use of immunoaffinity depletion and offline fractionation (30 fractions in this study) requires a large amount of starting material; hence it is best suited for deep profiling of the pooled MS sample for qualitative comparisons with the deep proteomes that were previously established for two ONDs and healthy controls. The direct LC- mass spectrometry analysis of individual CSF samples for label-free quantitation provides both high throughput measurements and good quantitation of relative protein abundance, and therefore uniquely suited for analysis of the entire set of individual CSF sample in the CIS, RR and control groups. Therefore, combining both the offline 2D-LC-MS/MS and direct LC- mass spectrometry analyses maximized the findings possible from size-limited CSF sample sets, contributing to truly comprehensive characterization of the CSF proteome in MS.Proteomics analysis of CSF samples faces two major analytical challenges: extremely high dynamic range in protein concentration and low overall protein concentration . To maximize the findings possible from size-limited CSF sample sets, immunoaffinity depletion and the AMT tag strategy that combines both offline 2D-LC-We collected CSF from three subject groups with IRB approvals. Group 1 involved 9 first-attack CIS patients who eventually met the criteria for MS We analyzed a separate group of 10 patients with CIS- first-attack MS. Because of limited volume, it did not have the advantage of the current methods of immunoaffinity depletion of abundant proteins (which can mask less abundant proteins) and high fractionation of the sample. Nevertheless, this independent group permitted us to evaluation whether the gray matter proteins described in the Results in the immunoaffinity-depleted patients was also found in this group.3.All CSF samples were immediately processed and frozen at \u221280\u00b0C. RBC counts were less than 10 per mm4HCO3 . The volume of the samples was then adjusted using 50 mM NH4HCO3 to ensure that all samples had the same volume for in-solution digestion.All CSF samples in the primary groups had the 14 most abundant proteins removed employing immunodepletion as previously described Both the flow-through (lower abundance proteins) and bound fractions from the group pooled CSF samples were collected and processed identically by high-resolution two-dimensional liquid chromatography coupled to high performance tandem mass spectrometry (2D-LC-MS/MS) analysis. These analyses produced the in-depth characterization of the CSF proteome, and the combined results of abundant protein and less abundant protein fractions were used in the creation of an AMT tag database 4HCO3. Following dilution, 1 mM CaCl2 from Sigma was added. Sequencing grade modified trypsin from Promega was then added in a 1\u223650 trypsin-to-protein ration. The samples were incubated for 3 hour at 37\u00b0C. Following trypsin digestion and SPE clean-up utilizing C-18 SPE cartridges from Supelco samples were concentrated in a Speed-Vac and the final peptide concentration was determined. Lastly all tryptic digests were snap frozen in liquid nitrogen and stored at \u221280\u00b0C until further processing and analysis.Proteins isolated from CSF were digested with trypsin and processed as previously described MS CSF samples were fractionated by High pH reversed phase (HPRP) LC as previously described MS/MS analysis. HPRP fractions of the IgY14 bound fraction samples were analyzed on an LTQ linear ion trap, and HPRP fractions of the IgY14 flow-through fraction samples were analyzed on an LTQ-Orbitrap Velos (ThermoFisher) instrument, operated in data-dependent mode and same LC conditions as previously described 6) were collected from 400\u20132000 m/z at a resolution of 30,000 while data dependent ion trap CID MS/MS spectra were acquired for the ten most abundant ions. A dynamic exclusion time of 180 sec was used to discriminate against previously analyzed ions.A total of 300 \u03bcg of tryptic peptides from both the IgY14 bound and flow-through fractions from the pooled 6) while MS/MS spectra were acquired for the six most abundant ions .Label-free quantification of proteins in individual CSF samples was performed as previously described MSn and analyzed with the SEQUEST algorithm searching the MS/MS data against the human IPI database (Version 3.40). Precursor mass tolerance of 3 daltons and 1 dalton for MS/MS ion masses without an enzyme defined, as well as static carboxyamidomethylation of cysteine and dynamic oxidation of methionine were used for the database search. The LTQ-Orbitrap Velos MS/MS data were first processed by in-house software DeconMSn The LTQ raw data from the pooled samples was extracted using Extract_MS/MS peptide identifications obtained from the 2D-LC-MS/MS analyses of all pooled CSF samples were included in an AMT tag database with their theoretical mass and normalized elution time recorded. LC- mass spectrometry datasets were then analyzed by in-house software VIPER The AMT tag strategy MS/MS or direct LC- mass spectrometry analysis were further processed by ProteinProphet software The resulting lists of peptides from 2D-LC-Data normalization and quantification of the changes in protein abundance between the normal CIS-MS and RR-MS CSF samples were performed and visualized using in-house software DAnTE www.ingenuity.com Accessed 2013), as we have done before Pathway Analysis of the data was performed with Ingenuity Pathways Analysis .(PDF)Click here for additional data file.Table S2Proteins with significant difference in abundance by ANOVA .(PDF)Click here for additional data file."} +{"text": "Gastrulation is a key transition in embryogenesis; it requires self-organized cellular coordination, which has to be both robust to allow efficient development and plastic to provide adaptability. Despite the conservation of gastrulation as a key event in Metazoan embryogenesis, the morphogenetic mechanisms of self-organization are poorly understood.Caenorhabditis elegans gastrulation that reveals mechanisms of self-organization. Cells that internalize during gastrulation show apical contractile flows, which are correlated with centripetal extensions from surrounding cells. These extensions converge to seal over the internalizing cells in the form of rosettes. This process represents a distinct mode of monolayer remodeling, with gradual extrusion of the internalizing cells and simultaneous tissue closure without an actin purse-string. We further report that this self-organizing module can adapt to severe topological alterations, providing evidence of scalability and plasticity of actomyosin-based patterning. Finally, we show that globally, the surface cell layer undergoes coplanar division to thin out and spread over the internalizing mass, which resembles epiboly.We report a modular structure of cell internalization in C. elegans gastrulation can be unified with the general notions of monolayer remodeling and with distinct cellular mechanisms of actomyosin-based morphogenesis.The combination of coplanar division-based spreading and recurrent local modules for piecemeal internalization constitutes a system-level solution of gradual volume rearrangement under spatial constraint. Our results suggest that the mode of During gastrulation, an embryo is dramatically restructured by cell and tissue movements to positDrosophila, Xenopus, zebrafish, and mouse. In this process,, cells at the epithelial margin form dynamic lamellipodial and filopodial protrusions, and assemble a supracellular actomyosin cable that draws the hole closed, in a similar way to a purse-string.Contractile actomyosin networks are probably the best-studied common molecular assemblies driving morphogenesis . A promiBoth oscillatory contractility and purse-string closures in their canonical form invoke mechanical coherence of individual dynamic components to result in supracellular force-generating systems ,7. InterCaenorhabditis elegans, gastrulation begins at the 26-cell stage, when the 2 endodermal cells Ea and Ep internalize on the ventral side of the embryo to form the gut primordium . Shapes were measured from two-dimensional (2D) confocal images . (B) Ea/Ep are arc-shaped during internalization. Ventral (blue), sagittal (green)m and transverse (yellow) views of the Ea/Ep apical surfaces generated by projecting three-dimensional (3D) volume data in the respective direction. (C) Flows of contractile foci on Ea shortly after cell birth and during internalization. Superimposition of five consecutive frames from cortical projection stills recorded at 2-second intervals. Streams of non-muscle myosin (NMY)-2 foci are highlighted by arrowheads. (D) Kymographs of contractile flows on Ea starting at time points corresponding to (A), and generated along a line similar to the white dashed line in Figure (E) Transient covering of cells by lateral extensions. (Top) Cortical views of ABplapp. Dashed lines outline the extensions of surrounding cells, and progression of covering and resurfacing is shown in the bottom right frame. (Bottom) Quantification of the degree of covering over time . (F) Apical dynamics of Partitioning defective (PAR)-6 Repolarization of Ea/Ep during internalization. (Left) Side view of Ea with average projection of 2 focal planes at 1 um apart in the middle of the embryo. (Right) Quantification of PAR-2::GFP along the perimeter of Ea (inside the white dashed lines) in counterclockwise direction from the gray arrow to the black arrow.Click here for fileCovering depended on surrounding cells. Irradiation of(A) P3 or (B) other neighboring AB cells prevented Ea/Ep internalization. (Top panels) Time-lapse microscopy with three-dimensional (3D) projection still images. Lightning marks the irradiated cells. Mesoderm is outlined with dashed lines, non-internalized endoderm is marked with a white circle, and arrow points to the center of the rosette. (Bottom panels) Schematic illustration depicting the embryo in the same orientation as above, and highlighting the irradiated cell.Click here for fileCellular dynamics during rosette formation and its developmental plasticity. (A) Cortex rupture and bleb formation in Ea/Ep. (Top) Side view of two-dimensional (2D) confocal slices. White arrows point to breakpoints in the cortex, while the red arrow marks a reemerging NMY-2 focus at the tip of the bleb. (Bottom left) Schematic representation of blebbing events in a representative embryo. Blebs are indicated by arrows, and the dashed white line indicates the initial position of Ea/Ep apices. (Bottom right) Size distribution of blebs shown on the left. (B) Effect of non-muscle myosin (NMY)-2 RNA interference (RNAi) on blebbing and internalization dynamics. (Top) Cortical views overlaying cellular membranes (gray) with color-coded NMY-2 intensities. (Right) Covering kinetics and number of blebs in wild-type and nmy-2 RNAi-treated embryos. (C) Cells in rosettes divided along the long axis. (First panel) three-dimensional (3D)projection image shows polarization of cells in rosettes. (Second panel) Quantification of long and short axis of cells from 3D still images . (Third panel) Cell polarization during rosette formation. (Fourth panel) Division orientation in the same embryos as in third panel (double arrows) (n = 5). (D) Cellular topology during endoderm internalization in three different nematodes. Color code for tissues is indicated on the bottom left, and direction of covering with black arrows.Click here for file"} +{"text": "MTHFR) gene, in particular the C677T polymorphism were recently associated to steatosis and fibrosis. We analyzed the frequency of MTHFR gene in a cross-sectional study of patients affected by Chronic Hepatitis C (CHC) from Northeast of Brazil.Hyperhomocysteinemia due to Methylenetetrahydrofolate Reductase levels were determined by chemiluminescence method. All patients were negative for markers of Wilson's disease, hemochromatosis and autoimmune diseases and have current and past daily alcohol intake less than 100 g/week.One hundred seven-four untreated patients with CHC were genotyped for the C677T MTHFR genotypes TT was 9.8% versus 4.4% genotype 1 (p = 0.01). Nevertheless, association was found between the MTHFR genotype TT \u00d7 CT/CC polymorphism and the degree of steatosis and fibrosis in both hepatitis C genotype (p < 0.05). A significant difference was found on plasma Hcy levels in patients with steatosis regardless of HCV genotype (p = 0.03).Among subjects infected with CHC genotype non-1 the frequency of MTHFR C677T polymorphism was more common in CHC genotype non-1 infected patient regardless of histopathological classification and genotype TT+CT frequencies were significant in the presence of fibrosis grade 1+2 and of steatosis in CHC infected patients from the northeast of Brazil regardless of HCV genotype. The genetic susceptibility of MTHFR C677T polymorphism should be confirmed in a large population.Our results indicate that plasma Hcy levels is highly prevalent in subjects with chronic hepatits C with steatosis regardless of HCV genotype and vitamin deficiency. The presence of genotype TT of Homocysteine (Hcy) belongs to a group of molecules known as cellular thiols. It is considered a \"bad thiol\" because its association with a variety of health conditions including cardiovascular disease, end-stagMTHFR gene like C677T result in amino acids substitutions that lead to a decreased enzyme activity : fasting insulin (U/mL) fasting glucose (mmol/L)/22.5) ) (p = 0.001) and of steatosis (No Steatosis [n = 70] versus Steatosis [n = 104]) (p = 0.04) regardless of HCV genotype in the multi regression analysis. It should be understood because the high plasma levels of Hcy have been reported to negatively influence normal cell function in many different tissues, such as vascular endothelium and smooth muscle cells and the liver. These effects, in turn, may explain the association of hyperhomocysteinaemia with vascular disease [Other important finding of our study was the higher Hcy level in patients with steatosis, although the lerosis) -36 and mlerosis) .MTHFR enzyme has fundamental importance in plasmatic Hcy regulation [Hcy is a toxic non-protein sulfur containing amino acids in humans. It is formed exclusively upon demethylation of the essential amino acid- methionine. The Hcy metabolism occurs through the junction of the remethylation and transsulfuration pathways. These pathways are strongly influenced by enzymes polymorphisms. gulation ,39.in vitro to increase the expression of monocyte chemoattractant protein 1 (MCP-1) which may enhance intravascular monocyte recruitment and lead to accelerated lesion formation [Hcy decreases the expression of a wide range of antioxidant enzymes -42 and iormation .There is evidence that Hcy induced endoplasmic reticulum (ER) stress causes dysregulation of the endogenous sterol response pathway, thereby leading to increased hepatic biosynthesis and uptake of cholesterol and triglycerides without impairing the hepatic export of lipids . SimilarWe also observed lower concentrations of serum total cholesterol in CHC patients genotype non-1. Similar results have been described by Corey at al., who demonstrated that serum lipids play a role in hepatitis C virion circulation and hepatocyte entry. In a cohort of 179 patients with CHC this author showed that patients with HCV had lower concentrations of total cholesterol than in the control group. These data support the hypothesis that the lipo-viral particles use the LDL-C receptors of hepatocytes as points of entry of the virus. Once inside into hepatocyte, the replication dependents of the lipid environment of the host -47.MTHFR C677T polymorphism was more common in CHC genotype non-1 infected patient regardless of histopathological classification and genotype TT+CT frequencies were significant in the presence of fibrosis grade 1+2 and of steatosis in CHC infected patients from the northeast of Brazil. The genetic susceptibility of MTHFR C677T polymorphism should be confirmed in a large population.In summary, our study had important implications. According to our data, Hcy levels were highly prevalent in subjects with chronic hepatits C with steatosis regardless of HCV genotype and vitamin deficiency. The presence of genotype TT of MTHFR C677T polymorphism frequencies were significant in the presence of fibrosis and of steatosis in CHC infected patients from the northeast of Brazil regardless of homocysteine levels and HCV genotype.The ALT: alanine aminotransferase; AP: alkaline phosphatase; AST: aspartate aminotransferase; BMI: body mass index; CHC: Chronic Hepatitis C; ER: endoplasmic reticulum; GGT: gamma-glutamyl transferase; HCC: hepatocellular carcinoma; HCV: human hepatitis C virus; HCY: homocysteine; HDL: high-density lipoprotein; HOMA-IR: homeostasis model assessment-insulin resistance; LDL: low-density lipoprotein; MCP-1: monocyte chemoattractant protein 1; MTHFR: methylenetetrahydrofolate reductase; NAFLD: nonalcoholic fatty liver disease; NO: nitric oxide; PCR-RFLD: polymerase chain reaction restriction fragment length polymorphism; ROS: reactive oxygen species; 5,10-mTHFR: 5,10: metilenetetraidrofolate; 5-mTHFR: 5-metiltetraidrofolate; Tg: triglyceride.The authors declare that they have no competing interests.ERFS- participated in the all steps of study, including design of the study, performed the statistical analysis and wrote the manuscript.CPMSO- critical revision of the manuscript for important intellectual content.MTCM-carried out the molecular genetic studies, participated in the sequence alignment and drafted the manuscript.FSS- acquisition of data; analysis and interpretation of data.LMMBP- conceived of the study, and participated in its design and coordination and helped to draft the manuscript.FJC-study supervisionAll authors read and approved the final manuscript."} +{"text": "In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia. The tenth InCoB , an official conference of the Asia-Pacific Bioinformatics Network (APBioNet) , was helBMC Bioinformatics or BMC Genomics (BMC track) and Immunome Research (IR) [We offered authors three tracks to submit manuscripts for potential publication in the supplement issues of rch (IR) . Of 110 rch (IR) which coThe 25 articles selected for this issue represent a cross-section of scientific and technological innovations accelerating bioinformatics in the areas of databases, software tools, RNomics, next-generation sequencing, sequence analysis, evolution, proteome analysis and disease informatics. The remaining 24 accepted BMC articles are published as a BMC Bioinformatics supplement .Papers presenting a wide variety of databases and software tools were accepted -12. PartFour papers make use of next-generation sequencing (NGS) -16 to adAcacia mangium small RNAs in secondary xylem samples of varying lignin content. The obtained small RNA profiles, which include 82 novel miRNAs may open venues to silence monolignol biosynthesis-associated genes without compromising the fitness of the tree.Fast-growing trees from plantations are used in pulp and fiber production. Lignin, an essential component of the tree structure, is undesired in this process. Ong and Wickneswari applied ab initio various short linear motifs that are specific for certain exosome-enriched RNAs.Secretory proteins are important players in host-pathogen interactions. Existing prediction tools do not support the identification of secretory protein candidates from NGS data, thus hampering the identification of non-classical secreted protein candidates. Garg and Ranganathan developeE. coli than common enzymes [et al. [C. elegans. The results indicate a duplication age-dependent relationship of alternative splicing and an evolutionary constraint among duplicates. Alternative splicing was more frequently observed among ancient than recent duplicates.The growing number of complete genome drafts and protein sequence data allows to re-visit questions on the origin of vertebrate promoters, evolutionary conservation of enzymes, as well as the generation of functional diversity through gene duplication and alternative splicing. Profiling of ascidian promoters revealed a primordial vertebrate promoter type that appears to be partially methylated with a high but limited extent of CpG scores and G+C content . Phyloge enzymes . Chen et [et al. analysedThe increasing scale and speed of whole-genome sequencing requires faster and high-accuracy genome mapping methods. A new method that utilizes perfect Hamming Code with a hash table significantly reduces the number of hash keys required for searching genome positions . The UniM. tuberculosis H37Rv bacterial two-hybrid (B2H) data seemed to contain numerous false positives and false negatives, while the H37Rv STRING predicted PPIs included many none-direct interactions. Yet, stringently predicted H37Rv STRING PPI data appeared to be suitable as a reference for analysing functional associations rather than physical interactions. To understand the behaviour of proteins in PPI networks, PPIs are often correlated with gene expression parameters. The correlation of high-confidence human PPIs derived from the HitPredict database with gene expression stability improved the classification of transient obligatory hubs and revealed functionally distinct, previously unknown type of hubs [Knowledge of protein-protein interaction (PPI) data quality and their limitations is critical for interpreting results and essential for using them as a reference set. Zhou and Wong found th of hubs .et al. [All protein domains common to mouse-infecting viruses and mice were analyzed and published as MusVirus database and tool . Biochemet al. implemenBeta-D-mannosidase mutations cause lysosomal storage disease. A comparative structural bioinformatics analysis of inherited mutations in \u03b2-D-mannosidase across multiple species revealed a geno-phenotpye correlation . The ideet al. [et al [Papers on the discovery and analysis of biomarkers and disease gene candidates focussed on copy number variations (CNVs) , cut-ciret al. examined. [et al developeet al. [Lack of clinically applied biomarkers for the early diagnosis and aggressiveness of lung adenocarcinoma inspired the development ECD to select features in paired gene expression samples, and to identify genes that are essential for reprogramming lung tissue cells . Compareet al. proposedth InCoB in Bangkok or at the 2nd ISCB-Asia conference.In recent years numerous Asian bioscience conferences have added bioinformatics sessions to their program. Yet, higher-profile annual conferences dedicated to bioinformatics remained largely in North America and Europe. The high number of manuscript and poster submissions to InCoB/ISCB-Asia 2011 suggests that the joint conference model ISCB-Asia may indeed invigorate regional bioinformatics-themed meetings in Asia, which are necessary to advance bioinformatics research, particularly in South and Southeast Asia. The strengthening of these regional conferences should lead to a gradual and healthy consolidation of smaller meetings that will benefit participants. Towards this end, we expect to see you again at the 11The authors declare that they have no competing interests.CS and SR (Program Committee Co-chairs) wrote the introduction and managed the review and editorial processes. CS, SR, JK , BR, TWT and SN (Conference Chair) jointly contributed to the scientific program development and its implementation. TWT supported the post-acceptance manuscript processing.List of Program Committee Members and Additional Reviewers in Alphabetical OrderClick here for fileA. Submission and Acceptance Statistics by Regions and Countries B. Acceptance Rate for Submissions to BMC trackClick here for file"} +{"text": "Although myocardial fibrosis identified by late gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) may predict adverse outcomes among patients with hypertrophic cardiomyopathy (HCM), its precise role in risk stratification for sudden cardiac death (SCD) remains unresolved. Previous studies have relied on broad surrogate composite endpoints and were underpowered to assess SCD risk or to adjust for confounding variables. To address this, we studied the prognostic significance of LGE in a large HCM cohort with long-term follow-up.Consecutive patients with HCM underwent LGE-CMR and were prospectively followed for a median of 3.5 years. This amounted to a total of 2852 patient-years of follow-up. The primary endpoint was SCD or aborted SCD. The principal secondary endpoint was a composite of cardiovascular mortality and aborted SCD. LGE imaging was performed in two orthogonal phase-encoding directions ~10 min after 0.1 mmol/kg gadolinium using an inversion recovery-prepared gradient echo sequence. The amount was quantified using the full-width at half-maximum method.Patients with LGE had more significant left ventricular hypertrophy and lower left ventricular ejection fraction (LV-EF) than those without LGE Table . The medNeither the presence nor the amount of LGE independently predicted SCD risk after adjusting for confounders. In contrast, LV-EF was the best independent predictor of SCD and cardiovascular mortality, and should therefore be considered as part of the routine risk stratification of patients with HCM.This work is supported by the NIHR Cardiovascular Biomedical Research Unit at the Royal Brompton and Harefield NHS Foundation Trust, and Imperial College. Dr Ismail is supported by the British Heart Foundation."} +{"text": "The aim was to determine whether aggregated MAVS protein is present in blood cells from SLE patients.Patients with systemic lupus erythematosus (SLE) often have evidence of excessive type I interferon production, with increased interferon levels and activation of interferon-inducible genes (interferon signature). The mitochondrial adaptor protein MAVS is a key intermediary in the RIG-I pathway, where viral RNA triggers a conformational change in RIG-I, leading to MAVS activation and activation of IKK and TBK1, with subsequent interferon production driven by IRF-3 and NF\u03baB activation and translocation. A recent report using Peripheral blood mononuclear cells (PBMC) were isolated from 17 patients fulfilling ACR criteria for SLE, and from nine controls. Thirty million PBMC were lysed and pellets loaded onto semi-denaturing detergent vertical 1.5% agarose gels. After electrophoresis, the proteins were transferred to Immobilon membranes for immunoblotting with anti-MAVS antibody or anti-\u03b2-actin.Six of 17 SLE patients showed clear MAVS aggregation, with essentially all of their MAVS protein in a high-molecular-weight form. None of nine controls had abnormal MAVS. Three of the four SLE patients had nephritis and the fourth had lung involvement. SLEDAI scores of MAVS-aggregate positive SLE patients did not differ from patients with normal molecular weight MAVS. Patient 4 (P-4) shows the aggregated MAVS phenotype in the western blot (Figure This is the first report of aggregated MAVS in human cells. The relationship of this abnormality to disease needs further investigation, but suggests the possibility that prolonged and increased IFN-I production could result from MAVS aggregation, with the formation of poorly degradable prion-like protein that could signal IFN-I production for prolonged periods."} +{"text": "Dear Editor,I read with interest the article by Yilmaz et al. regarding the value of aspartate aminotransferases (AST)-to-platelet ratio index (APRI score) for the noninvasive assessment of liver fibrosis in chronic hepatitis, which was published in Hepatitis Monthly . The autRegarding hepatitis B virus (HBV) infection, a recently published study from China showed t"} +{"text": "Up to 50% of oral squamous cell carcinomas (OSCCs) recur following surgical resections with conventional \u201chistologically-negative\u201d margins. Three members of the SIBLING family of proteins: dentin sialophophoprotein (DSPP); bone sialoprotein (BSP); and osteopontin OPN are upregulated in OSCCs. In this study, we aimed to correlate the expression of DSPP, OPN and BSP as well as three SIBLING-partners, matrix metalloproteinase-2 (MMP-2), matrix metalloproteinase-3 (MMP-3), and matrix metalloproteinase-9 (MMP-9), at histologically-negative margins of OSCCs with tumor recurrence. Immunohistochemical analyses of the SIBLINGs and MMP expressions at histologically-negative margins of OSCC was carried out in a retrospective study of 20 patients, and the results correlated with tumor recurrence. Each protein was dichotomized as \u201cpresent\u201d (\u226510% staining) or \u201cabsent\u201d (< 10% staining). The Sensitivity, Specificity, Positive Predictive Value(PV+) and Negative Predictive Value (PV\u2212) for recurrence was calculated for each protein, along with their overall diagnostic accuracy, calculated as: (number of true positives + number of true negatives)/ number of patients. OSCC recurred in 9 of 20 patients (45%), a ratio not significantly different from the estimated population recurrence rate of 50% (p = 0.664). Among the SIBLINGs, DSPP and OPN showed the greatest Accuracy with DSPP being more Sensitive (89%) and OPN more Specific (64%). MMP-9 showed the greatest overall Accuracy (80%), slightly less Sensitivity (67%) and more Specificity (100%), than either DSPP or OPN. MMP-9 showed a superior positive PV than either DSPP or OPN. The negative PVs of OPN and MMP-9 were almost identical, and inferior to DSPP. We conclude that DSPP, OPN, or MMP-9 expressions at histologically-negative surgical margins predict OSCC recurrence with MMP-9 being the preferred predictor. These proteins may identify patients who could benefit from more extensive resection, or from adjunct treatments such as radiotherapy. Most mortality in oral squamous cell carcinoma (OSCC) patients is due to local recurrent disease and regional spread following surgical treatment failure at the primary site -5. In trHowever, up to 50% of OSCCs recur following surgical intervention even with \u201cadequate tumor-free\u201d margins, usually within 2 years of initial surgical intervention , 5. ThisDentin sialophosphoprotein (DSPP), bone sialoprotein (BSP), and osteopontin (OPN) are three members of the Small Integrin-Binding LIgand N-linked Glycoprotein (SIBLING) family of proteins reportedThree members of the SIBLING gene family also have been determined to specifically bind and activate three different matrix metalloproteinases (MMPs): BSP with MMP-2; OPN with MMP-3; and DMP-1 with MMP-9 . The binIn the present retrospective study, we investigate the expression, at histologically-negative resection margins of primary OSCCs, all of the three oral cancer-associated SIBLINGs as well as three MMPs and correlate expression with the clinical outcome parameters, recurrence and survival.I) shown in Figures +) from histologically negative and DSPP/MMP-9 negative (-) portions of the margins. This demarcation also provided an in-section negative control.A total of 200 histologically negative surgical mucosal margin sections (average of 10 sections per case), obtained at several consecutive levels, from the 20 cases of OSCCs were each subjected to immunohistochemistry analysis for the expressions of each of the SIBLINGs , and MMPs . As shown in Table Of the 20 cases in the present study, 9 (45%) had clinical documentation of recurrence of OSCC. This rate does not differ significantly from the estimated population recurrence rate of 50% (p = 0.664). Time between initial surgical resection of primary tumor and initial recurrence ranged from 6-17 months with an average RFT (ARFT) of 10.5 months Table with DSPp-values: DSPP=0.040; OPN=0.050; MMP-9<0.001).Based on the Fisher's Exact and Fisher-Freeman-Halton tests Table , tumor sFollowing Fisher's Exact and Fisher-Freeman-Halton test analyses, no patient characteristics or clinical variables were found to be significantly associated with OPN or DSPP status (data not shown). On the other hand, tumor size and node metastasis were significantly associated with MMP-9 expression at negative margins ], both MMP-9 and LVI were negatively associated with recurrence-free survival after adjusting for the other factor and tumor size (T) were also independently predictive when included with MMP-9 in multivariate analyses, their predictive association was not as strong as that of MMP-9. When one considers sensitivity, specificity, and predictive value, dichotomized MMP-9 had the greatest overall accuracy, comparable sensitivity, and greater specificity than the SIBLINGs or the other MMPs when predicting recurrence. MMP-9 was superior in terms of positive predictive value (PV+) and comparable in terms of negative predictive value (PV-). As shown in Table To the best of our knowledge, this is the first study investigating the potential significance of the expression of the oral cancer-associated SIBLINGs with their cognate MMPs at histologically-negative surgical resection margins of primary OSCC. Our results indicate that the expression of MMP-9 at histologically-negative surgical resection margins is the preferred predictor of recurrence of OSCC, although it was always co-expressed with DSPP and/or OPN.The prevailing management philosophy that advocates complete surgical excision with \u201cadequate\u201d tumor-free margins for primary solid tumors such as OSCCs presumes the homogeneity and rectilinear progression of such tumors at the advancing edge . The empThe complexity in understanding the biology of tumor recurrence at histologically negative resection margins of primary OSCCs is further compounded by the concept of \u201cfield cancerization\u201d well documented in human OSCCs ,24. FielAlthough recent studies have reported molecular signatures at conventional histologically negative surgical resection margins predictive of the recurrence of OSCC at primary sites, their utility is hampered by their limited practical clinical applications. For example, elf4E and p53 expression at surgical resection margins of primary OSCCs have been suggested as being of predictive value for recurrence at histologically negative resection margins , 8. In tThe studies reported by Nathan et al. analyzedOur current results cast DSPP, OPN, and MMP-9 expression at histologically negative resection margins as potential predictors of recurrence at primary OSCC resection sites, suggesting that true tumor-free margins consistent with RFS may be redefined as histologically-negative-DSPP-OPN-MMP-9-negative resection margins. Multicenter prospective cohort designs are however required to further assess the utility and clinical applicability of the expressions of DSPP, OPN and MMP-9, singly or in combination with DSPP in the overall estimation of tumor-free resection margins consistent with RFS in the surgical management of primary OSCC. Such prospective studies will compare long-term recurrence status of patients with histologically-negative (H-N) surgical resection margins with that of histologically-negative-and DSPP-OPN-MMP-9 negative margins of primary OSCC.A retrospective study was carried out on archived paraffin surgical resection specimens obtained from patients who underwent surgical resection of their primary OSCC with a curative intent. Only resections with histologically-negative margins were selected for this study. The cases are from patients seen and treated in the Department of Otolaryngology/Head and Neck Surgery at the Georgia Health Sciences University (GHSU) between January 2004 and December 2007. Only cases with adequate follow-up records of at least 4 years were selected for this study. Prior to commencement of study, the required Institutional Review Board (IRB) approval was obtained.Twenty consecutive cases meeting the inclusion criteria were selected using the archived, initial diagnostic hematoxylin and eosin (H&E) sections. These were reviewed independently by two board-certified Oral and Maxillofacial Pathologists in order to verify the original diagnosis. All the paraffin blocks relating to each case were retrieved and matched with corresponding H&E stained sections. Five micron sections of the histologically negative resection margins were made for immunohistochemistry and analyses for the expression of BSP, DSPP, OPN, MMP-2, MMP-3, and MMP-9 following the steps schematically illustrated in Figures Antibodies for the SIBLINGs and MMPs used were produced in the laboratory of one of the authors (LWF) and have been previously published , 15, 16.Immunostaining was carried out to localize the SIBLINGs and MMPs on sections using the Zymed ST5050 automated system as previously described , 15, 16.Immunoreactivity to each SIBLING and MMP was scored semiquantitatively by two independent pathologists who were blinded to the clinicopathological details of all cases until after the completion of the scoring. A co-investigator (PW) not involved with the immunohistochemistry scoring retained the clinical data . For statistical analysis, each scoring set for SIBLING and MMP was dichotomized as \u201cpresent\u201d \u226510%) or \u201cabsent\u201d (<10%). The Sensitivity, Specificity, Positive Predictive Value (PV+) and Negative Predictive Value (PV-) for recurrence of OSCC were calculated for each dichotomized SIBLING and MMP. The overall diagnostic accuracy for each SIBLING and MMP was calculated as (number of true positives + number of true negatives) / number of patients. The exact binomial test with mid-p correction was used to determine any significant difference between OSCC recurrence rate observed on the present sample and the estimated population recurrence rate of 50%. Fisher's exact test (two categories) and the Fisher-Freeman-Halton test (more than two categories) were used to examine the associations between clinical variables (summarized in Table 0% or \u201cab"} +{"text": "The purpose of this study was to evaluate feasibility and obtain preliminary efficacy estimates comparing craniosacral therapy (CST) with an attention-control condition for the adjunctive treatment of migraine.Individuals with moderate to severe migraine were recruited from specialty clinics, family practices, and the university community. After confirmatory clinical evaluation and an 8-week run-in phase, those meeting study criteria were randomized to 8 weekly CST or low-strength static magnet therapy (LSSM) treatments. Study participants were followed for 4 weeks after the conclusion of therapy. Primary outcome measures included headache frequency and headache-specific quality of life (HIT-6). Secondary headache-specific measures include headache-related disability (MIDAS), headache intensity, and abortive medication use.At baseline, participants reported a mean 14 headache days per month and severe headache-related quality-of-life impact and disability. Compliance with study procedures was excellent, with 60 of 69 randomized individuals completing 8 weeks of therapy. Individuals in both treatment groups appeared to benefit from the therapy. A significant difference, favoring CST, was noted by treatment group in mean headache hours per day 30 days post treatment . HIT-6 scores decreased significantly in both groups, but without a between-group difference at the last treatment visit. MIDAS scores improved in the CST, but not the LSSM group at 4 weeks post treatment. Headache intensity was reduced more in the CST compared with the LSSM group, but the difference was not statistically significant. Abortive medication use decreased substantially in both groups during treatment.Our results show that conducting a randomized clinical trial of CST for migraine using a standardized protocol is feasible and that adjunctive CST may reduce headaches in those with severe migraine. Protocol modifications may enhance future investigations of CST for migraine."} +{"text": "Survivin is a component of the chromosomal passenger complex (CPC) that is essential for accurate chromosome segregation. Interfering with the function of Survivin in mitosis leads to chromosome segregation errors and defective cytokinesis. Survivin contains a Baculovirus IAP Repeat (BIR) and therefore was originally classified as inhibitor of apopotosis protein (IAP), yet its role in apoptosis after cellular stress remains largely unknown. We demonstrate here, that Survivin predominantly suppresses anoikis, a form of programmed cell death induced by loss of cellular adhesion to extracellular matrix. Interestingly, cells ectopically overexpressing EGFP-Survivin showed after loss of cell-matrix-interaction a decreased expression of I\u03baB-\u03b1. Subsequent subcellular protein fractionation and immunoprecipitation experiments revealed that XIAP interacts with detergent-soluble Survivin which is known to cooperatively activate NF-\u03baB signaling. Examination of the expression levels of detergent soluble Survivin in colorectal cancer cell lines and in colorectal cancerous tissues revealed that detergent soluble cytoplasmic Survivin levels correlated inversely with anoikis susceptibility in colorectal cancer. Therefore, the detergent soluble cytoplasmic Survivin might be a promising predictive biomarker for lymph node and distant metastases of colorectal cancer. We conclude that an anti-apoptotic function of detergent-soluble Survivin in interphase cells experiencing anoikis is mediated at least via XIAP/I\u03baB-\u03b1/NF-\u03baB signaling. During cancer development, metastatic cells detach from neighboring tumor cells, acquire cell motility, invade and enter the lymph system or blood circulation, survive and form metastatic lesions. These steps involve many genes and pathways, and yet these biological processes are poorly understood despite many scientific approaches Xenopus laevis and S. pombeSurvivin is a member of the chromosomal passenger protein complex (CPC) that is a key regulator of mitosis. Survivin and other CPC components, Aurora-B, inner centromere protein (INCENP), and Borealin (Dasra B) are essential for the CPC functions including kinetochore attachment error corrections and completion of cytokinesis Survivin is periodically expressed during the cell cycle peaking in mitosis In our study we show for the first time that detergent-soluble Survivin suppresses anoikis in anchorage-dependent cells, a form of programmed cell death induced by loss of adhesion from the surrounding extracellular matrix. Subcellular fractionation experiments provided evidence that detergent soluble Survivin of the cytosol was responsible for suppressing anoikis. The mechanism of anoikis suppression involves activation of XIAP/I\u03baB-\u03b1/NF-\u03baB signaling and inactivation of c-Jun. A further important finding of this study is that detergent-soluble Survivin is correlated to the invasive phenotype of colorectal cancer cells. Therefore, detergent-soluble Survivin might be of clinical value since it likely predicts lymph node and distant metastases in colorectal cancer patients.In initial studies we sought to analyze the impact of Survivin overexpression in p53-deficient Chinese hamster embryonic diploid fibroblasts (CHE cells) and isogenic CHE cells harboring wild type p53. For monitoring transfection we used an enhanced green fluorescence protein-tagged Survivin (EGFP-Survivin). Yet, the ectopic overexpression of EGFP-Survivin had no effect on apoptosis in CHE-p53+/+ cells treated with DNA damaging ionizing radiation (IR) and UV-C when compared to CHE-p53+/+-EGFP cells as measuin vivo physiological conditions of disseminating tumor cells such as anchorage-independent situation and nutrient starvation.So far transfection of pEGFP-Survivin does not inhibit radiation\u2013induced apoptosis in CHE-cells, irrespective of p53 status and expression levels of Survivin but on the other hand only CHE-p53\u2212/\u2212 cells overexpressing EGFP-Survivin caused metastatic disease in mice. We therefore hypothesized that overexpression of Survivin might increase the survival of CHE-p53\u2212/\u2212 -EGFP-Survivin cells under stress conditions which likely more resembles the i.v. injection of tumor cells in mice we revealed that the number of surviving CHE-p53\u2212/\u2212 cells in the lung was significantly increased when compared to the number of surviving control cells expressing EGFP . The quantitative data demonstrated the effective suppression of suspension culture-induced anoikis in EGFP-Survivin-expressing cells when compared to control cells expressing EGFP . We then focused on the second mitochondria-derived activator of caspase/direct inhibitor of apoptosis-binding protein with low pI (Smac/DIABLO) which has been demonstrated to bind to Survivin Smac/DIABLO). Another IAP family member, the X-linked inhibitor of apoptosis protein (XIAP) has been reported to form heterodimers with Survivin XIAP, I\u03baB-\u03b1, and NF-\u03baB). Concomitantly, augmentation of phosphorylation of pro-apoptotic transcription factor, c-Jun, was suppressed by overexpression of EGFP-Survivin in detached culture condition , and c-Jun). These data suggest that overexpression of EGFP-Survivin decreases the I\u03baB-\u03b1 level in detached cells and subsequently lead to the activation NF-\u03baB and on the same time to a suppression of c-Jun-mediated transcription. However, we could not found a contribution of focal adhesion kinase (FAK) to anoikis suppression in this cell system although FAK auto-phosphorylation site at Y397 has been reported to be important for anti-apoptotic activity of FAK We next asked which signaling pathways could be involved in the anoikis-suppression in EGFP-Survivin-expressing CHE-p53\u2212/\u2212 cells. Survivin has been described to inhibit pro-apoptotic Bcl-2-associated X protein (BAX)-induced apoptosis IB: anti-XIAP). Yet, the majority of EGFP-Survivin was found in the detergent-insoluble pellet fraction containing chromatin but was also found to a lesser extend in the detergent-soluble nuclear and cytosolic fractions (IB: anti-Survivin and IB: anti-EGFP). Thus, an interaction of XIAP and Survivin obviously was restricted to the detergent soluble fraction of the cytosol. Indeed we found a stable protein-protein interaction between XIAP and Survivin by applying immunoprecipitation experiments using the detergent-soluble cytoplasmic fraction of CHE-p53\u2212/\u2212 cells with ectopic expression of EGFP-Survivin . Among the colorectal cancer cell lines, Survivin was found in the detergent-soluble fractions although the expression levels varied considerably . SubsequWhich biological behaviors in colorectal cancer are related to detergent-soluble cytoplasmic Survivin is important for its diagnostic or therapeutic availabilities. In our previous immunohistochemical analyses of colorectal cancer tissues, the absence of nuclear Survivin and the existence of cytoplasmic Survivin have found to be significant predictors of mortality in colorectal cancer patients C. elegansXenopus laevisD. melanogasterNowadays, it is unanimously accepted that Survivin is an essential component of the CPC regulating chromomal segregation and cytokinesis In cultured cell systems, an increased apoptotic susceptibility, which appeared spontaneously or by apoptotic agents, is conferred by loss-of-function or knock-down of Survivin. Survivin knock-out in a T-cell lineage induced p53-dependent phenotypes, resulting in thymocyte developmental defect When exposed to the DNA damaging agent etoposide, Survivin knocked-out DT40 cells showed normal sensitivity to this agent In line with previous reports, we show here that Survivin regulates caspase-3 activity. It has been reported that Survivin inhibits caspase-3 activation in physiological situations during apoptosis, but this effect is likely not due to the direct inhibition of caspase-3 The detergent-soluble cytoplasmic Survivin was important to induce anoikis suppression in our experimental system. There is a proposal that Survivin releases from mitochondria in response to cell stresses, resulting in Survivin/XIAP heterodimer formation under the regulation by phosphorylation of Survivin at serine 20 The regional lymph node metastasis as well as the distant metastasis are well recognized in colorectal cancer staging and are known to be a common determinant of long-term outcome in the cancer patients. The metastasis-related factors, genes, or proteins, which have the prognostic significance and clinical impact in patients with colorectal cancer, still need identifying. The information promises to advance the understanding, treatment, and prevention of colorectal cancer. The detergent-soluble cytoplasmic Survivin is a candidate such a factor from our analysis. Anoikis resistance is a key for cancer cell survival not only in the primary tumor microenvironment but also for invaded and extravasated cancer cells . Our datin vitro cell transformation assay p53 were used as CHE-p53+/+ cells, and clone A1/p60/clone #3 with a modal chromosome number of 23 containing one t marker chromosome having mutated p53 at codon 245 (GGC/AGC) in both alleles were used as CHE-p53\u2212/\u2212 cells. CHE-p53\u2212/\u2212 cells are non-metastatic when injected subcutaneously or intravenously into nude mice, but become metastatic by introducing certain metastasis-relating genes 2 at 37\u00b0C.CHE cells were isolated from Chinese hamster whole embryos during Whole cell lysates were prepared by lysed with Laemmli SDS-PAGE sample buffer. Nuclear and cytoplasmic extracts from cultured cells or human tissues were prepared using a Nuclear Extraction Kit (Active Motif), according to the manufacturer's instructions. The pellet was used as the detergent-insoluble fraction after solubilization by Laemmli SDS-PAGE sample buffer. This fraction contains detergent-insoluble cytoplasmic and nuclear fractions. SDS-PAGE and immunoblotting were performed according to the procedures described previously The activated caspase-3-specific bands were quantitatively measured by a fluorescence imaging system using immnoblots developed by ECF Western Blotting Reagent Pack . The protein levels of activated caspase-3 were calculated by the following formula: (estimated activated caspase-3 level)\u200a=\u200a(immunofluorescence intensity of activated caspase-3-specific band)/(immunofluorescence intensity of \u03b1-tubulin-specific band on the same blot).Cells were transfected with pEGFP or pEGFP-Survivin (pEGFP with the full-length mouse Survivin cDNA) by using Lipofectamine 2000 (Life Technologies). The transfected cells were exposed to serum-starvation at 24 h after transfection. For anoikis induction, transfected cells were suspended in serum-free medium . ApoptosDNA fragmentation analysis was performed as described Transfected cells were fixed with 4% formaldehyde-containing Formaldehyde Neutral Buffer Solution (Nakarai Tesque). The fixed cells were then stained with 200 U/ml rhodamine phalloidin (Molecular Probes) plus 0.1 \u00b5g/ml 4\u2032,6-Diamidino-2-phenylindole (DAPI), mounted onto an anti-fade fluorescent mounting medium (DakoCytomation), and observed under a FV1000D laser scanning microscope (Olympus).The detergent-soluble cytoplasmic fraction was used for Immunoprecipitation analysis. The cleaned extract was incubated with affinity-purified Rabbit anti-XIAP polyclonal antibody coupled to protein A Dynabeads (Life Technologies). The beads were washed and were processed for immunoblot analysis with monoclonal anti-GFP antibody. Immunoprecipitation of GFP-Survivin was carried out under the same conditions using anti-XIAP antibody.5 PKH26-labeled cells. After 24 h, the mice were sacrificed to measure fluorescence intensity of PKH26 extracted from the lungs. The retention of injected cells in the lung was determined by calculating the percentage of the injected fluorescence intensity that was found in the lung extract immediately after injection.The retention of tumor cells in the lung was measured as previously described This study was carried out in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocol was approved by the Committee on the Ethics of Animal Experiments of the Prefectural University of Hiroshima (Permit Number: H21-002 and H24-017). All surgery was performed under sodium pentobarbital anesthesia, and all efforts were made to minimize suffering.Cancerous tissues and their surrounding normal tissues were obtained from 40 colorectal cancer patients. The samples were initially obtained from surgical resection, endoscopic resection, or biopsy between 2000 and 2004 at Tsuchiya General Hospital in Hiroshima.The fresh cancerous and normal tissues were lysed and the detergent-soluble cytoplasmic fraction, the detergent-soluble nuclear fraction, and the detergent-insoluble (cytoplasmic- and nuclear-mixed) fraction were generated by subcellular fractionation . SurviviThe detergent-soluble cytoplasmic pool of Survivin was quantitated by immunoblot experiments using three different anti-Survivin antibodies . The Survivin bands in the detergent-soluble cytoplasmic fraction for each antibody were measured by a fluorescence imaging system as described above. The protein levels of Survivin were calculated by the following formula: (estimated detergent-soluble cytoplasmic Survivin level)\u200a=\u200a(immunofluorescence intensity of Survivin-specific band)/(immunofluorescence intensity of \u03b1-tubulin-specific band on the same blot). Three different Survivin antibodies were used for three different blots, and the average level was calculated. Positivity for the detergent-soluble cytoplasmic pool of Survivin was graded according to the protein level of the detergent-soluble cytoplasmic Survivin of colorectal cancer HCT116 cells, as follows: +++ (>60% of HCT116 level); ++ (20\u201360% of HCT116 level); + (>1% and <20% of HCT116 level); or \u2212 (<1% of HCT116 level). The cases showing +++, ++, and + were classified as tumor without the detergent-soluble cytoplasmic Survivin, and the cases showing - were as tumor with the detergent-soluble cytoplasmic Survivin.This study was reviewed and permitted by both the Tsuchiya General Hospital Human Research Ethics Committee and the Prefectural University of Hiroshima Human Research Ethics Committee. The study protocol followed the ethical guidelines of Tsuchiya General Hospital and Prefectural University of Hiroshima. The individual in this manuscript has given written informed consent (as outlined in the PLoS consent form) to publish these case details.Figure S1Outline of the experimental procedure.(TIF)Click here for additional data file.Figure S2Schematic illustration of the experimental procedure for detection of Survivin fractionated into the detergent-soluble cytoplasmic fraction in human tissue.(TIF)Click here for additional data file.Table S1a.Tumorigenicity and spontaneous metastatic potential of stable transfectants expressing EGFP and EGFP-Survivin after subcutaneous injection into nude mice(PDF)Click here for additional data file."} +{"text": "Cicer arietinum L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea.Chickpea (EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity (<1E-06) in the NCBI non-redundant (nr) database. Gene ontology functional classification terms (BLASTX results and GO term), were retrieved for 2006 (92.0%) sequences, and 656 sequences were further annotated with 812 Enzyme Commission (EC) codes and were mapped to 108 different KEGG pathways. In addition, expression status of 830 unigenes in response to terminal drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay.Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated) associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea. Cicer arietinum L.), the fourth most important grain-legume crop, is grown in more than 45 countries, mostly in arid and semiarid zones. Approximately 90% of the crop is grown under rainfed conditions, wherein yield is significantly affected by abiotic stresses such as drought, heat, and cold dCTP and used as probes. The nylon membrane were prehybridized with formamide hybridization buffer for 42\u00b0C for 6 h, the denatured probe was added, and hybridized for 24 h. Washed membranes were exposed to X-ray film and developed after 7 days of incubation at -80\u00b0C. The image of the developed film was acquired by SYNGENE-G-Box gel documentation and analysis system and signal intensity of each spot was calculated by the Gene tool software. Transcript levels for each unigenes were calculated as the average intensity from triplicate experiments. The intensity of each spot was normalized with respect to the intensity of actin gene. Change in level of expression was expressed as the expression ratio of normalized signal intensities of respective unigenes in control versus treatments. On the basis of macroarray results, genes exhibiting significant induction were validated by Northern blotting.Equal amounts of purified PCR amplified products (100 ng) was spotted onto nylon membranes , using the dot-blot apparatus in 96 formats. Each blot was prepared in duplicate. PCR-amplified products of actin cDNA from WW and WS plants was separated by electrophoresis on a 1.2% FA agarose gel and transferred to an Immobilon\u2122-Ny+ membrane following the method of Sambrook et al. . PCR-ampTm > 55-65\u00b0C, primer length 18-30 nucleotides, and an expected amplicon size of 80-200 bp . The unigene (UG) set developed in this study is henceforth referred to as UG-TDS . CAP3 assembly analysis of our datasets with all chickpea EST sequences deposited in NCBI dbESTs identified 1576 unigenes as singlets and are new entries to the chickpea database.A total 5494 high-quality sequences (average length 505 bp) were generated after removing short and low-quality sequences. A total of 3062 unigenes (638 contigs and 2424 singletons) were derived from cluster assembly and sequence alignment; each contig had 2-113 ESTs with an average length of the 527 bp. The majority of contigs (84.9%) contained 5 or fewer ESTs, whereas only 2.97% contigs were made from 20 or more ESTs . There were 592 unigenes specific to forward-subtracted libraries and 876 unigenes to reverse-subtracted libraries. Although 125 assemblies contained ESTs from both forward and reverse libraries, this indicates very low level of redundancy between both libraries , followed by Glycine max (72.0%), Phaseolus (53.7%), Lotus (53.4%), Populus (43.6%), Arabidopsis (29.4%), and Oryza sativa (28.5%) ESTs than those of other species such as soybean and Medicago . The low nucleotide similarity observed between chickpea and other plant species does not necessarily represent phylogenetic relationships, but could depend on the coverage of EST sequences. A significant percentage of unigenes (14.6-47.5%) showing weak or no similarity for Medicago, Glycine, Lotus, and Phaseolus, indicating a considerable divergence in chickpea gene content within other leguminous species.BLASTN analysis of UG-TDS revealed significant identity with aseolus 5.7%, Lotutic tree . As expeGlycine max and Medicago truncatula ; only 6% (132 unigenes) matched with Cicer arietinum, indicating the novelty of the chickpea unigenes dataset. Among nonlegume species, majority of matches were with proteins of Vitis vinifera , Ricinus communis and Populus trichocarpa . The availability of the whole genome and predicted proteins of these species and limited sequence information of legumes in the database may have led to the highest homology of chickpea sequences with these nonlegume genomes database with E value <1E-06. A majority of top matches were from proteins of legume species, with maximum hits from Of the 1808 annotated sequences, 656 were annotated with 812 Enzyme Commission (EC) codes and mapped to 108 different KEGG pathways. Of the 108 pathways contained within the metabolism category (metabolic pathways), 46 were represented by 43.44% of the 656 unigenes. KEGG metabolic pathways well represented by unigenes were biosynthesis of plant hormones (44 enzymes), biosynthesis of phenylpropanoids (29 enzymes) and terpenoids and steroids (24 enzymes), biosynthesis of alkaloids derived from histidine and purine (25 enzymes) and from the shikimate pathway (24 enzymes), starch and sucrose metabolism (24 enzymes), and arginine and proline metabolism (10 enzymes). Several hormone pathways, such as of abscisic acid, ethylene, salicylic acid, and jasmonic acid, are involved in one or more environmental stresses, including drought stress and other abiotic stresses processes -42. A reIdentification of overrepresented and underrepresented GO terms from a given list of genes from different libraries may help elucidate the functional relevance of these genes under drought stress. GO enrichment analysis found that 60 GO terms were differentially represented between AB1-1 and AB2-1 Figure : 50 wereGO enrichment analysis was also performed between ESTs derived from the parental genotype library and RILs library to determine differential responses between parents and RILs. Compared with parental genotype libraries, 13 GO terms were significantly overrepresented in RILs bulk libraries and pyrroline-5-carboxylate synthetase (P5CS) were upregulated under drought stress Figure . The conr stress . Differer stress , Arabidobidopsis , and ricbidopsis . Unigenebidopsis .HVA1 in wheat and rice increases drought tolerance were found highly up regulated in drought stress , 5 unigenes encoding tonoplast intrinsic protein 2 unigenes encoding NOD26-like intrinsic protein (UG-TDS HO066903 and HO062732). The maximum numbers of the unigenes encoding aquaporin were found in root libraries and downregulation of one of the member (HO062890) under drought stress was conformed in northern blot analysis down-regulated gene. High level of BR is accompanied by a very low level of RAV1 transcripts and vice versa and also these genes shown to be involved in drought response in several other plants ,72. Upre stimuli ,74 indic stimuli .Cluster III contained unigenes that were upregulated in ICC 1882 but not ICC 4958. One upregulated unigene encoded fructose-bisphosphate aldolase (HO063129), whose downregulation could inhibit gluconeogenesis for conserving energy in drought-stressed plants (41).To validate the results of dot blot analysis, 10 differentially expressed unigenes were analyzed by qPCR. Real-time PCR confirmed the differential expression of these genes under terminal drought stress conditions Figure . The genWe report the sequencing, assembly, and annotation of 5494 high-quality drought-responsive EST sequences from chickpea. This dataset was generated from SSH libraries constructed using drought-tolerant and -susceptible chickpea genotypes and bulks of their progenies exhibiting HRB and LRB phenotypes. SSH libraries allowed cloning genes that are specifically up- and downregulated from the roots and shoots of chickpea in response to terminal drought. Moreover, we identified more than 1500 novel unigenes in chickpea that are associated with terminal drought stress. Besides several transcripts coding for known stress-related proteins, several novel genes with unknown functions that may have a potential role in drought tolerance in chickpea were also identified. This study also provides a comparative overview of genotype-specific expression patterns of more than 830 unigenes in root tissues of chickpea in response to drought. The up- and downregulation of some unigenes was confirmed by real-time qPCR. The EST dataset and the information about transcription of several genes can be useful for the research community and help identify potential candidate genes for drought tolerance in chickpea. Our study can also serve as an important resource for developing functional markers, full-length gene isolation, TILLING, drought-responsive promoter isolation, and in drought functional genomic studies involving overexpression, e-QTL, and manipulation of drought tolerance in chickpea.RS, RV, PKJ, SMK and AAD planned the experiments. VV, AAD and VK were involved in setting up drought experiments and isolation of RNA. AAD, VK were involved in cloning and sequencing of cDNA SSH libraries, dot blot, northern blot and real time PCR experiments. AAD, NLR and RV were involved in bioinformatics analysis. AAD, RS and RV analyzed the experiments. AAD and RS prepared the manuscript. All authors read and approved the final manuscript.Summary of earlier work done towards identifying ESTs associated with drought stress in chickpea.Click here for filePrimer sequences for qPCR analysis. All primer sequences used for qPCR analysis in the manuscript are listed.Click here for fileDaily NTR ratio of each well watered (WW) and water stressed (WS) ICC 4958, ICC 1882 and RILs. (A) Change in NTR ratio of well watered (WW) and water stressed (WS) ICC 4958 and ICC 1882 plants. (B) Change in NTR ratio of high root biomass and low root biomass RILs along with parental lines under water stressed (WS) condition.Click here for fileGraphical representation of Chickpea unigene assembly UG-TDS. (a) Distribution of chickpea EST members in contigs after the assembly process. (b) Distribution of contigs according to the EST numbers. Each contig categories represents number of ESTs per contig. Green bars indicate the EST size and the blue bars indicate number of contigs belonging to respective EST size categories.Click here for fileUG-TDS BLASTN analysis results. Table showing BLASTN analysis results of UG-TDS dataset with EST datasets of EST datasets of Mt (Medicago Truncatula), Gm (Glycine max), Pv (Phaseolus vulgaris), Lj (Lotus japonicus), Pa , Os (Oryza Sativa) and At with corresponding details of GB ID numbers, descriptions and E-value.Click here for fileBLASTX similarity search of the UG-TDS against the NCBI non-redundant protein database. (A) Distribution of top matches against the NCBI taxonomic domains. (B) Distribution of e-value scores.Click here for fileFunctional annotation of UG-TDS results. Table showing functional categorization results of UG-TDS dataset using Blast2go tool. Table represent corresponding details of sequence description of BLASTX hit, E-values, Gene Ontology terms and Enzyme Commission entries.Click here for fileKEGG pathway for Biosynthesis of plant hormones: 78 differentially expressed unigenes under drought stress were identified as a candidates involves in different plant hormones such as Jasmonic acid, ethylene and salicylic acid and gibberellin.Click here for fileGO enrichment analysis using GOSSIP module of BLAST2GO program. Table S1: Results of GO enrichment analysis done using transcripts generated from AB1-1 library as test set and AB2-1 as reference set with the FDR filter value 0.05. The 60 GO terms were differentially represented in these two libraries. Out of then 50 were over represented and 10 were under represented. Table S2: Results of GO enrichment analysis done using transcripts generated from bulks of RILs as test set and SSH unigenes from individual parental libraries as reference set with the FDR filter value 0.05. The 13 GO terms were over represented in libraries from bulk of RILs. Table S3: Results of GO enrichment analysis done using transcripts generated from up regulated libraries (AS1-1 and AR1-1) as test set and unigenes from down regulatory libraries (AS2-1 and AR2-1) as reference set with the FDR filter value 0.05. The 10 Go terms were overrepresented in up regulated libraries and three GO terms were under represented.Click here for fileDifferential Gene Ontology terms between parental line (ICC 4958 & ICC 1882) and bulks of RILs under drought stress. GO enrichment analysis between ESTs generated from parental line (From AS and AR libraries) and ESTs form bulks of RILs using Fisher's exact test with a false discovery rate (FDR) cutoff of p \u2264 0.05. The numbers of transcripts associated with a specific GO term are represented as percentage of functionally annotated EST in their respective librariesClick here for fileGenotype specific response of chickpea unigenes in response to terminal drought stress. Expression profiling of differentially expressed ESTs generated by SSH libraries were analysed in drought stressed ICC 4958 and ICC 1882 using dot-blot expression analysis. Differential responses of unigenes are represented in normalised signal intensities values. Standard deviations are calculated from three different experiments. Signal intensity of Actin (GenBank: EU529707) used for normalisation of the signals between the blots and NPTII was used for signal background correction. Unigenes are listed according to their annotation generated in present work.Click here for file"} +{"text": "In the current study, we compare the different preparation methods for the generation of HPV pseudovirions for their ability to efficiently infect cells. We also compare the antigen-specific CD8+ T cell immune responses generated by different DNA delivery methods and several commonly used forms of vaccination with that of HPV pseudovirions.Human papillomavirus (HPV) pseudovirions have recently been shown to deliver DNA efficiently We found that the preparation method of pseudovirions is important for the efficient delivery of encapsidated DNA. We have shown that vaccination with DNA encoding model antigen ovalbumin (OVA) delivered by HPV-16 pseudovirions was capable of generating therapeutic antitumor effects against OVA-expressing tumor. In addition, vaccination with DNA encoding OVA delivered by HPV-16 pseudovirions generated the highest number of OVA-specific CD8+ T cells in mice in our system compared to DNA delivered by other delivery methods. We also found that vaccination with OVA DNA delivered by HPV-16 pseudovirions generated the highest number of OVA-specific CD8+ T cells in mice compared to other forms of antigen-specific vaccines. Furthermore, HPV-16 pseudovirions were capable of carrying DNA vaccine encoding clinically relevant antigen, telomerase reverse transcriptase, to generate antigen-specific CD8+ T cell immune responses.Our data suggest that DNA vaccines delivered by HPV-16 pseudovirions may be advantageous compared to other delivery methods and other forms of antigen-specific vaccines for application to antigen-specific immunotherapy. Therefore, an optimized and efficient delivery system that improves the transfection efficiency of DNA vaccines into cells in vivo may significantly improve the antigen-specific immunity generated by DNA vaccination for the control of virus-associated infections and/or tumors.DNA vaccination has emerged as a promising way to generate antigen-specific T cell immunity due to its safety, stability, and capacity for repeated administration. However, naked DNA vaccines suffer from limited vaccine potency due to poor transfection efficiency in vivo /6.The OVA-expressing B16/OVA murine tumor model has been described previously . 5-8 weet test. A p value < 0.05 was considered significant.Data expressed as means \u00b1 standard deviations (SD) are representative of at least two different experiments. Comparisons between individual data points were made by 2-tailed Student's (BMDCs): Bone marrow-derived dendritic cells; (HPV): Human papillomavirus; (OVA): Ovalbumin; (psV): pseudovirions; (VLPs): virus-like particles.The authors declare that they have no competing interests.SP was involved in the design of the study and acquired and analyzed the data. SHC analyzed and interpreted the data. BM and TCW analyzed and interpreted the data and drafted the manuscript. CFH and TCW conceived and designed the study as well as provided general supervision of the research group. All authors gave final approval of the manuscript."} +{"text": "The soluble CD14 subtype (sCD14-ST: renamed presepsin), which is approximately 13 kDa, has been identified as a protein whose levels increase specifically in the blood of sepsis patients. In this study, we evaluated the clinical performance of a point-of-care assay for measurement of presepsin in admitted sepsis patients.We obtained 43 cases with blood culture test-positive from patients admitted to our hospital and compared presepsin levels with procalcitonin (PCT), CRP and white blood cell count.P < 0.05). Presepsin levels reflected the blood culture test and sepsis severity more than other biomarkers.Positive ratios of presepsin levels of patients with Gram-negative bacterial infection, Gram-positive bacterial infection and fungal infection were higher than those of PCT. When 43 cases were divided into four groups , presepsin levels were only significantly different between sepsis/infection group and severe sepsis group (This assay has sufficient clinical performance in patients admitted to the hospital in addition to the emergency room and ICU."} +{"text": "Objective: To determine site specific carotid intima-media thickness: common\u2013carotid artery and carotid bifurcation in hypercholesterolemia patients as a marker for atherosclerosis.Methods: Fifty patients with hypercholesterolemia and twenty controls were selected after getting informed consent regarding the investigation of carotid- intima media thickness by B-mode ultrasound. All the patients of hypercholesterolemia with LDL-C > 160mg/dL had family history of coronary artery diseases. This procedure was carried out in the Radiology Department of Dr. Ziauddin Hospitals. Measurement of carotid -intima media thickness, B-mode ultrasonography of common carotid artery, carotid bifurcation and internal carotid artery (left and right carotid arteries) was performed with Toshiba (M# SSA-580A/E2) ultrasound scanner with linear probe. The posterior or far wall of the carotid artery is, the distance between the leading edge first bright line (lumen -intima interface) and the leading edge of the second bright line (media-adventitia interface) of far wall was recorded as intima -media thickness. The average mean of six segments of intima-media thickness was taken as mean CIMT of right and left common carotid, bifurcation and internal carotid arteries.Results: Maximal CIMT was significantly increased at sites common carotid, carotid bifurcation and internal carotid arteries in fifty patients with hypercholesterolemia as compared to controls. At carotid bifurcation mean of maximal CIMT was (0.9+ 0.3mm). Range of maximum CIMT in hypercholesterolemia patients was (0.8- 3.3mm) and in controls (0.4- 0.8 mm). The thickness was more frequently increased at site of bifurcation.Conclusions: Carotid intima- media thickness in hypercholesterolemia patients was increased and carotid bifurcation was site that has shown greater increase in intima-media thickness and plaques in these patients predict high risk for atherosclerosis. Risk factors contribute to atherosclerosis through gradual arterial changes that may produce ischemia by either progressive luminal narrowing or more commonly, by sudden plaque rupture or intimal erosions with formation of an in situ occlusive thrombus.13 The use of mean maximum CIMT rather than mean common CIMT as the primary outcome measure in Randomized Control Trials designed to evaluate the efficacy of pharmacological and non- pharmacological interventions in carotid artery atherosclerosis.4A widely accepted, convenient marker of atherosclerosis is carotid artery intima-media thickness (IMT).5 Carotid intima-media thickness has been measured to determine risk of atherosclerosis.6-12 Studies have shown that increased carotid intima-media thickness is high risk for cardiovascular diseases.13-15 B-mode ultrasound imaging (Carotid Doppler) can visualize noninvasively the superficial arteries in every stage of arthrosclerosis. As observed by de Groot et al an average healthy person will have IMT of 0.78mm at 76 years of age while FH patient has this CIMT at 40 years of age.15 CIMT assessment used in randomized control trials to determine effects of therapy.16 CIMT can be used as a surrogate end point for intervention trials.Atherosclerotic changes can be measured by carotid intima-media thickness by B-mode ultrasound is surrogate end point in cardiovascular outcomes in clinical trials.The aim of this study was to determine carotid intima- media thickness at different sites, common carotid artery and carotid bifurcation in hypercholesterolemia patients as marker for atherosclerosis.Fifty cases with hyperlipidemia were from National Institute of Cardiovascular Diseases and Dr.\u00a0Ziauddin Hospitals and twenty controls were selected after getting informed consent regarding the investigation of carotid- intima media thickness by B-mode ultrasound. Age range of cases and controls was 22 to 60 years. All the patients of hyperlipidemia with LDL-C >160mg/dL (lipid profile done after 12 hours fasting) had family history of coronary artery diseases. This study was approved by Ethical Committee of Ziauddin University.Sites for measurement of Carotid Intima- Media Thickness: This procedure was carried out in the Radiology Department of Dr. Ziauddin Hospitals. Measurement of carotid -intima media thickness, B-mode ultrasonography of common carotid artery, carotid bifurcation and internal carotid artery (left and right carotid arteries) was performed with Toshiba (M# SSA-580A/E2) ultrasound scanner with linear probe. The posterior or far wall of the carotid artery is, the distance between the leading edge first bright line (lumen-intima interface) and the leading edge of the second bright line (media-adventitia interface) of far wall was recorded as intima -media thickness.17 Frozen images of these segments were of carotid intima- media thickness mean and maximum values were calculated by the computer.The average mean of six segments of intima-media thickness was taken as mean CIMT. Wall thickness was defined as the distance from the leading edge of lumen-intima thickness interface of the far wall of leading edge of media-adventitia interface of far wall.Assessment of CIMT at multiple sites determines frequent plaque thickening that are common in carotid bifurcation in patients with high levels of total cholesterol and LDL-Cholesterol. Statistical analysis: Comparison was done with mean and maximum of CIMT of hypercholesterolemia patients and controls. For carotid intima- media thickness the mean and maximum values were calculate by applying student\u2019s t-test for right and left mean IMT of common carotid, bifurcation and internal carotid arteries. Using student\u2019s t-test for comparison of quantitative data (CIMT thickness) compared between hypercholesterolemia patients and controls (controls .Images of the segments of carotid intima-media thickness of common carotid, carotid bifurcation and internal carotid arteries were taken by B- mode. Mean of maximum values were calculated by the computer. Assessment of CIMT at multiple sites determines frequent plaque thickening that are common in carotid bifurcation and internal carotid artery in patients with risk of cardiovascular diseases. It is a reproducible study assessment was done by two observers. Plaque seen mostly at bifurcation were reveled in eleven cases with familial hypercholesterolemia.Maximal CIMT was significantly increased in subjects with hypercholesterolemia as given in The present study shows increased Carotid intima-media thickness in patients with FH and most of these patients have shown to have developed early coronary and cerebrovascular diseases. 18 values from the near wall are less reliable. It is possible to visualize plaques in the artery with ultrasound technique. Plaque is a focal structure encroaching into the arterial lumen.CIMT should be measured preferably on the far wall19 Bifurcation was found to have the highest correlation with CIMT. If a single ultrasound is to be used, bifurcation should be the preferred site.20In clinic an CIMT >0.9 mm or presence of plaque may support a more intensive risk factor and intervention at individual level.This study shows an increase in mean carotid intima-media thickness more in area of bifurcation. Also calcified plaques were seen in patients with very high LDL-cholesterol levels .21, shows that CIMT should be measured preferably on the far wall. Carotid intima-media thickness values from the near wall are less reliable. It is possible to visualize plaques in the artery with ultrasound technique. Plaque is a focal structure encroaching into the arterial lumen of at least 0.5 mm or 50% of the surrounding CIMT. Several studies have shown a significant relationship between CIMT and cardiovascular risk. Also the number of cardiovascular risk factors correlation with CIMT. Cardiovascular diseases risks slow down as CIMT progression is reduced. This is most clearly shown when cholesterol and LDL-cholesterol levels are lowered. Increased CIMT and plaque predicts risk of stroke and acute myocardial infarction.22In this study the CIMT was measured on the far wall. Study by Agewall et alIn these patients having high LDL-C and increased carotid intima media thickness more significant at carotid bifurcation predicts an increased risk of early atherosclerosis.Increased carotid intima- media thickness in hypercholesterolemia. Carotid bifurcation has shown greater increase in intima-media thickness and plaques. Carotid- intima media thickness at bifurcation is most important site for measurement of IMT for determination of early atherosclerosis."} +{"text": "Cardiovascular magnetic resonance myocardial feature tracking (CMR-FT) is a promising novel method for quantification of myocardial wall mechanics from standard steady-state free precession (SSFP) images. We sought to determine whether magnetic field strength affects the intra-observer reproducibility of CMR-FT strain analysis.We studied 2 groups, each consisting of 10 healthy subjects, at 1.5 or 3 Tesla. Analysis was performed at baseline and after 4 weeks using dedicated CMR-FT prototype software to analyse standard SSFP cine images. Right ventricular (RV) and left ventricular (LV) longitudinal strain (EllRV and EllLV) and LV long-axis radial strain (ErrLAX) were derived from the 4-chamber cine, and LV short-axis circumferential and radial strains from the short-axis orientation. Strain parameters were assessed together with LV ejection fraction (EF) and volumes. Intra-observer reproducibility was determined by comparison of the first and the second analysis in both groups.In all volunteers resting strain parameters were successfully derived from the SSFP images. There was no difference in strain parameters, volumes and EF between field strengths (p>0.05). In general EccSAX was the most reproducible strain parameter as determined by the coefficient of variation (CV) at 1.5 Tesla and 3 Tesla . The least reproducible parameter was EllRV .CMR-FT results are similar with reasonable intra-observer reproducibility in different groups of volunteers at 1.5 and 3 Tesla. CMR-FT is a promising novel technique and our data indicate that results might be transferable between field strengths. However there is a considerable amount of segmental variability indicating that further refinements are needed before CMR-FT can be fully established in clinical routine for quantitative assessment of wall mechanics and strain.AS receives grant support from the British Heart Foundation (BHF) (RE/08/003 and FS/10/029/28253) and the Biomedical Research Centre (BRC-CTF 196). SK receives grant support from the American College of Cardiology Foundation, the Edna Ittner Pediatric Foundation, and the Children's Hospital and Medical Center Foundation. EN receives grant support from BHF (RE/08/003), the Wellcome Trust and Engineering and Physical Sciences Research Council and the National Institute for Health Research (NIHR) via the comprehensive BRC award to Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London."} +{"text": "The NO/cGMP signal transduction is involved in the regulation of a variety of physiological processes e.g. smooth muscle relaxation, inhibition of platelet aggregation and synaptic plasticity. Nitric oxide (NO) is produced by NO synthases and acts mainly on NO-sensitive guanylyl cyclase (NO-GC), the most important NO receptor. NO stimulation of NO-GC leads to production of the second messenger cGMP which exerts its effects via cGMP-dependent kinases, channels or phosphodiesterases.Recently, we have generated mice lacking NO-GC (GCKO). We showed that lack of NO-GC resulted in arterial hypertension concomitant with a totally abolished NO responsiveness of vascular and gastrointestinal smooth muscle.Global deletion of a protein in mice does not allow identification of the cell/tissue type responsible for a certain phenotype. We therefore generated a mouse line in which NO-GC was specifically deleted in smooth muscle cells (SM-GCKO). These mice should provide more detailed information on the role of NO and cGMP with regards to smooth muscle relaxation.Here we examined the role of NO/cGMP signaling with regards to the smooth muscle relaxation of corpus cavernosum. NO failed to relax corpus cavernosum from GCKO in organ bath experiments: neither exogenously produced NO by NO donors nor endogenous NO release from neurons induced by electrical field stimulation led to relaxation. Similar results were observed in the corpus cavernosum of SM-GCKO mice. To our surprise, both KO models were fertile and produce offspring.Our data show that deletion of NO-GC globally or exclusively in smooth muscle abolishes corpus cavernosum relaxation, but nevertheless, does not impair fertility."} +{"text": "Purpose. To report an association between reticular pseudodrusen, located above the retinal pigment epithelium (RPE), and Early Onset Drusen (EOD) as described using Spectral-Domain Optical Coherence Tomography (SD-OCT). Methods. Eight patients (16 eyes) with EOD were examined. EOD were classified into three entities called Large Colloid Drusen (LCD), Malattia Leventinese (ML), and Cuticular Drusen (CD). Best-corrected visual acuity, fundus examination, color fundus photographs, fundus autofluorescence (FAF), fluorescein angiography (FA), indocyanine green angiography (ICGA), and SD-OCT were performed in all study patients. Results. Four patients had LCD, 2 had ML, and 2 had CD. Reticular pseudodrusen were observed with SD-OCT in all study patients; all these patients had hyperreflective lesions above and below the RPE. Conclusion. Early Onset Drusen appear to be associated with reticular pseudodrusen. SD-OCT is helpful in distinguishing the location of the deposits that are above and below the RPE in EOD. Further studies are needed to understand the role of reticular pseudodrusen in the pathophysiology of EOD. These l Patients with Early Onset Drusen underwent a comprehensive ophthalmologic examination which included best-corrected visual acuity (BCVA), fundus examination, color fundus photographs, multicolor images, fundus autofluorescence (FAF), fluorescein angiography (FA), indocyanine green angiography (ICGA), and Spectral-Domain Optical Coherence Tomography (SD-OCT). Informed consent was obtained as required by the French bioethical legislation (CE_20130319_11_BWF), in agreement with the Declaration of Helsinki for research involving human subjects. The diagnosis of the specific EOD entity was based on fundus biomicroscopy, angiography, and OCT features . In MalaA total of 8 patients presenting with EOD were included in this study . All theSD-OCT of the 4 LCD patients showed 2 kinds of deposits at different locations from the RPE: (i) convex colloid drusen with variable reflectivity classically described in LCD were observed between the RPE and Bruch's membrane similar to soft drusen Figures , and ii; the locPatients with ML also showed 2 distinct kinds of deposits on SD-OCT. The first kind was large and round colloid-like drusen corresponding to focal or diffuse deposition of hyperreflective material between the RPE and Bruch's membrane within the posterior pole. These deposits were associated with a focal dome-shaped or diffuse RPE elevation above Bruch's membrane. The second kind of deposit was a hyperreflective lesion located above the RPE Figures and 8.In Cuticular Drusen (CD), SD-OCT again showed 2 different kinds of deposits: confluent small \u201cdome-shaped\u201d RPE elevations and \u201csawtooth\u201d RPE elevations . In the The diagnosis of Early Onset Drusen (EOD) is classically based on fundus examination and angiographic features. Recently, SD-OCT has been used to detect the different EOD entities and to define drusen as deposits observed under the RPE \u20136. Our sReticular pseudodrusen in AMD have been described by Querques et al. using SD-OCT as hyperreflective material located not below but above the RPE . In 2007 In conclusion, soft drusen and reticular pseudodrusen seem to be frequently associated in EOD. SD-OCT is helpful in distinguishing the location of the deposits above and below the RPE in EOD. Soft drusen are located below the RPE layers while reticular pseudodrusen are located above the RPE. These two distinct lesions frequently occur simultaneously in young patients affected by hereditary drusen. A new clinical classification of Early Onset Drusen should include the presence of reticular pseudodrusen. Further studies are needed to understand their role in the physiopathology of EOD."} +{"text": "Methanohalophilus mahii is the type species of the genusMethanohalophilus, which currently comprises three distinct species with validly published names.Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism.The type strain SLPT was isolated from hypersaline sediments collected from the southern arm of Great SaltLake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bpgenome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteriaand Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahiiwith other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species. T (= DSM 5219T = ATCC 35705T) is the type strain of the moderately halophilic methanogen Methanohalophilus mahii hydrogenases (ech) for the uptake of H2 were not detected in the annotated genome sequence, thus confirming the strict methylotrophy of this species. For the activation of acetate for methanogenesis Methanosarcina species use either acetate kinase (ack) and phosphotransacetylase (pta) or an ADP-forming acetyl-coenzyme A synthetase (acdAB). However, none of these genes were identified in the Mhp. mahii genome.Genes encoding enzymes for the utilization of alternative substrates for methanogenesis, like formate dehydrogenase and F420 (F420H2) are probably oxidized by the membrane-bound Ech hydrogenase and the cytoplasmic Frh F420-hydrogenase, respectively. The produced H2 is in turn oxidized by a membrane-bound methanophenazine-reducing hydrogenase (Vht/Vho). Finally, the reduced methanophenazine (MPH2) is used by the membrane-bound heterodisulfide reductase HdrED for reduction of CoM-S-S-CoB and concomitant proton translocation across the membrane that is subsequently combined with 2-hydroxyphenazine or its precursor. In Msc. mazei the synthesis of all-E geranylfarnesyl diphosphate is catalyzed by an prenyl diphosphate synthase encoded by the gene MM_0789 whereas a homologous enzyme producing the C-20 geranylgeranyl diphosphate is probably encoded by MM_1767 .Supplementary Table 2. Classification and general features of Evidence codes: TAS: Traceable Author Statement ; NAS: Non-traceable Author Statement . These evidence codes are from the Gene Ontology project [74].Methanomicrobia\u201d was created to replace the class Methanococci, whose definition seems to be in conflict with current analyses of complete genome data.\u2217 In version 4.0 of the BMSB Taxonomic Outline [18] the class \u201cClick here for additional data file."} +{"text": "The last author wishes to add the following to the Funding Statement concerning their funding sources: \"Gunter Schuman is also part-funded by the European Union-funded FP6 Integrated Project IMAGEN (LSHM-CT- 2007-037286), the FP7 projects ADAMS (Genomic variations underlying common neuropsychiatric diseases and disease related cognitive traits in different human populations) (242257) and the Innovative Medicine Initiative Project EU-AIMS (115300-2), as well as the Medical Research Council Programme Grant \"Developmental pathways into adolescent substance abuse\" (93558) and the Swedish Research Council (FORMAS).\""} +{"text": "Enterobacteriaceae bacterium strain FGI 57 was isolated from a fungus garden of the leaf-cutter ant Atta colombica. Analysis of its single 4.76-Mbp chromosome will shed light on community dynamics and plant biomass degradation in ant fungus gardens.The Enterobacteriaceae bacterium strain FGI 57 was isolated in 2009 from a fungus garden of the leaf-cutter ant Atta colombica on Pipeline Road in Panama. Leaf-cutter ants are dominant herbivores in the Neotropics that derive nutrition from plant biomass by culturing specialized fungus gardens on foliar material Joint Genome Institute (JGI) using a combination of Illumina pipeline -based comparison . Phylogenetic analysis of the 16S rRNA genes using FastTree (Enterobacteriaceae. The availability of the complete genome of this bacterium will facilitate future investigations of the symbiotic microbial community residing in leaf-cutter ant fungus gardens.The complete genome of the pipeline . A totalmparison of its 1FastTree failed tEnterobacteriaceae bacterium strain FGI 57 has been deposited at DDBJ/EMBL/GenBank under the accession number CP003938.The complete genome sequence of"} +{"text": "Botulinum toxin A (BTX-A) has been approved for treatment of movement disorders and migraine. The widely assumed peripheral mechanism of action has been questioned by recent studies which demonstrated an axonal transport in the facial nerve and within central nerves. Findings in our laboratory suggested a central antinociceptive activity following axonal transport in the sciatic nerve.To characterize the axonal transport of BTX-A, the toxin's enzymatic activity in the CNS was assessed using immunofluorescent detection of its cleaved substrate synaptosomal-associated protein 25 (SNAP-25) following injections into the rat whisker pad and hind-paw, intramuscular injection into the gastrocnemius and intraneural injections into the sciatic nerve. Intraneural and intraganglionic colchicine was employed to block axonal transport. To investigate the significance of axonal transport for antinociceptive activity of BTX-A, we assessed the effect of peripheral and intraganglionic injections of low dose BTX-A in orofacial formalin-induced pain in rats.Following whisker pad BTX-A injection, cleaved SNAP-25 was observed in the dorsal horn of the medulla. Cleaved SNAP-25 following subcutaneous, intramuscular and intraneural toxin injection in rat hind limbs was observed in corresponding segments of ipsilateral dorsal and ventral horn. Central SNAP-25 cleavage following BTX-A injection into the sciatic nerve was prevented by colchicine. In the ventral horn, BTX-A protease was localized within cholinergic neurons. Facial and intraganglionic injections of BTX-A prevented orofacial pain dependent on axonal transport in the trigeminal sensory nerve.Our results suggest that the axonal transport of BTX-A in different sensory and motor nerves commonly occurs after peripheral administration. Axonal transport in sensory neurons followed by central enzymatic activity is involved in botulinum toxin's antinociceptive effects. The possible functional role of axonal transport in motor neurons remains to be examined."} +{"text": "The 15th International Conference on Human Retrovirology: HTLV and Related Retroviruses was organized in Belgium in the cities of Leuven and Gembloux from June 5 to June 8, 2011. The main topics of the meeting were human T-lymphotropic virus (HTLV), Xenotropic murine leukemia virus-related virus (XMRV) and endogenous retroviruses. The following abstracts were presented."} +{"text": "However, delivery systems able to differentially target both subsets in vivo are still missing as well as demonstration for efficient immuno-modulation. The present work aims at providing evidences for the selective delivery of a siRNA-containing lipid formulation to the Ly-6Chigh monocyte population and at evaluating the therapeutic potential of targeting this subset as well as their human counterpart for immuno-intervention in a prototype IMID like rheumatoid arthritis (RA). The pre-B-cell colony enhancing factor (PBEF/visfatin/Nampt) is an essential enzyme in the NAD biosynthetic pathway that exerts a key role in the persistence of inflammation through the induction of the expression of the TNF-\u03b1 and IL-6 pro-inflammatory cytokines and is highly expressed in patients with a variety of IMID. Mice with collagen-induced arthritis (CIA) display Ly-6Chigh monocytosis in the circulation that infiltrate into the inflamed joints. The systemic delivery of siRNAs formulated with the cationic liposome DMAPAP provides specific and functional down-regulation of PBEF within inflammatory monocytes. Moreover, decreased production of the PBEF-induced pro-inflammatory cytokines TNF-\u03b1 and IL-6 was evidenced in both mouse and human inflammatory monocytes. PBEF gene silencing within Ly-6Chigh monocytes resulted in reduced disease severity in mice with CIA, associated with an overall systemic immuno-modulation of the effector T cell balance. These results identify PBEF as a critical target to modulate autoimmune responses and inflammation in arthritis and provide novel evidence that silencing of a master gene within inflammatory monocytes is a promising strategy for future therapeutic intervention in the context of IMID.Inflammatory mouse Ly6C"} +{"text": "Abuse of anabolic steroids to induce skeletal muscle hypertrophy is widespread amongst recreational bodybuilders, however, the cardiac effects of such drugs have not been systematically documented. The ability of cardiovascular magnetic resonance (CMR) to image the myocardium in any plane and achieve full myocardial coverage renders it the gold standard for assessing LV volumes and mass.We sought to investigate the cardiac effects of anabolic steroid use with CMR hypothesising that significant hypertrophy and distinct LV remodelling would be seen in steroid users relative to non-users.A total of 23 recreational bodybuilders were studied - 15 anabolic steroid users and 8 non-users. CMR was undertaken on a 1.5T Avanto using breath-hold steady-state free precession cine sequences. Three long-axis images were obtained followed by sequential short axis cines from the AV-groove to the apex. Late gadolinium enhancement (LGE) imaging was performed ~10 min after intravenous Gadovist 0.1 mmol/kg . Indexed LV and RV ventricular volumes, ejection fraction and indexed LV mass were determined using a semi-automated threshold-based algorithm after manual tracing of epicardial and endocardial borders . LV remodelling index was calculated as the ratio of LV-mass to LV end-diastolic volume (LV-EDV).None of the subjects exhibited any late gadolinium enhancement. Mean indexed LV and RV volumes and EF were comparable for the two groups Table . HoweverAnabolic steroid use amongst bodybuilders can induce significant left ventricular hypertrophy. The pattern and severity of remodelling can mimic hypertrophic cardiomyopathy. The use of such drugs should be considered in the differential diagnosis of significant otherwise unexplained left ventricular hypertrophy, particularly in the athletic cohort.This work is supported by the NIHR Cardiovascular Biomedical Research Unit at the Royal Brompton and Harefield NHS Foundation Trust, and Imperial College. Dr Ismail is supported by the British Heart Foundation."} +{"text": "The presence of ischemia-induced microvascular obstruction (MVO) despite successful coronary revascularization, has been associated with poor functional recovery and adverse left ventricular remodeling after acute myocardial infarction (AMI). Additionally, the extent of the infarct gray zone is a strong independent predictor of post-AMI mortality. However, the evolution of gray zone after AMI has not been investigated and its relationship with MVO in terms of risk stratification is unknown.To characterize the evolution of gray zone and determine its correlation with the presence of MVO during infarct healing in patients treated with primary percutaneous coronary intervention (PCI).Patients were enrolled post-PCI and underwent MRI examination on a 1.5T scanner (GE Signa Excite) at day 2, week 4 and month 6 following AMI. Cardiac function was evaluated using a steady-state-free-precession (SSFP) sequence in cine mode. A T1-weighted IR-GRE sequence was used for delayed-hyperenhancement (DHE) of infarcted myocardium. Infarct core (IC) and gray zone (GZ) volumes were quantified using the full-width-half-maximum technique as previously described; both quantities were expressed as a percentage of myocardial volume. MVO\u2019s were manually traced and included in the infarct core calculation.r = 100*GZ/(GZ+IC) increased in the MVO group at month 6 while it remained stable in the non-MVO group; (d) EF was reduced in the MVO group compared to the non-MVO at all time points (p<0.05). The percent change in GZr (\u0394GZr) at week 4 and month 6, relative to day 2 is shown in Figure Ten patients who completed MRI exams at all three time points were included in the study . Figure The increase in infarct gray zone or arrhythmogenic substrate may be one of the possible mechanisms responsible for adverse remodeling and poor clinical prognosis in patients with MVO. Monitoring the early evolution of gray zone in the high-risk patients could also potentially help identify the optimal timing and candidates for placement of implantable cardioverter-defibrillator."} +{"text": "Our laboratory is blending new RNA chemistries, largely directed at the ribose 2'-hydroxyl group, with quantitative interpretation to create new kinds of chemical microscopes for accurate RNA structure analysis. This seminar will focus on two examples from retroviral biology. All retroviral RNAs contain a packaging element that directs the genome into nascent virus particles through a mechanism that has been unclear. Using SHAPE, we probed the structure of murine leukemia virus RNA inside virus particles and identified the binding site for the nucleocapsid domain of Gag. The RNA structural context is critical: High-affinity binding requires two specific UCUG-UR-UCUG motifs flanked by base-paired elements. Mutation of four guanosine residues in these two motifs - only 4 nucleotides per genomic RNA - reduced packaging to non-specific levels. These motifs only form in genomic RNA dimers; thus analysis of authentic full-length RNA was critical. This work illustrates how local context and RNA structure can create information-rich recognition signals from simple single-stranded sequence elements. In the second example, we discovered strong correlations between shRNA-mediated inhibition of HIV-1 replication in a cell-based assay and both the energetic cost of breaking secondary structures and the overall annealing energy between guide strand and folded target RNA. These correlations were only apparent when the energetic cost of disrupting pre-existing structure in the HIV-1 RNA was calculated using a secondary structure model derived from SHAPE probing information. We verified these correlations by design and evaluation of additional shRNAs and could achieve consistent inhibition of HIV-1 production by 90%. This approach emphasizes the profound, but ultimately predictable, role of RNA structure in tuning RNAi function and is likely to prove broadly useful in understanding large-scale biological recognition involving RNA."} +{"text": "Pogostemon cablin possesses two morphologically and ontogenetically different types of glandular trichomes, one type of bristle hair on the surfaces of leaves and stems and one type of internal gland inside the leaves and stems. The internal gland originates from elementary meristem and is associated with the biosynthesis of oils present inside the leaves and stems. However, there is little information on mechanism for the oil biosynthesis and secretion inside the leaves and stems. In this study, we identified three kinds of glandular trichome types and two kinds of internal gland in the Pogostemon cablin. The oil secretions from internal glands of stems and leaves contained lipids, flavones and terpenes. Our results indicated that endoplasmic reticulum and plastids and vacuoles are likely involved in the biosynthesis of oils in the internal glands and the synthesized oils are transported from endoplasmic reticulum to the cell wall via connecting endoplasmic reticulum membranes to the plasma membrane. And the comparative analysis of the development, distribution, histochemistry and ultrastructures of the internal and external glands in Pogostemon cablin leads us to propose that the internal gland may be a novel secretory structure which is different from external glands. The Lamiaceae comprise many commercially important species because of their high content of essential oils, which are widely used in pharmaceutical preparations, perfumery and cosmetics. The development and histochemistry of glandular trichomes occurring in plants of the Lamiaceae was well documented Most published studies on the Lamiaceae had concentrated on the ultrastructure of peltate trichomes or capitate trichomes in relation to the secretory process Pogostemon cablin is one of the tropical, aromatic crops in Lamiaceae, and cultivated mainly in Southeast Asia, India and Brazil. Previous studies on Pogostemon cablin have shown that there are external or internal glands in leaves and stems Pogostemon cablin deserves to be studied for elucidate the relationship between the external and internal glands.Pogostemon cablin showed numerous glandular trichomes and bristle hairs and peltate trichome (type II) and one was long-stalked capitate trichome (type III) in Pogostemon cablin. Internal glands were found in the palisade tissue of leaves (type IV) and in ttype IV) . Every etype IV) . Varioustype IV) indicatetype IV) . The heaInternal glands in leaves with a length of 40 \u00b5m (\u00b19) distributed among palisade cells , arrow. 4 for unsaturated lipids distributed among cortex cells of stems . The int4 , leaves and stems at various developmental stages were fixed in glutaraldehyde . Sectional material was washed in the phosphate buffer (pH 7.3). Dehydration was done in an acetone dilution series . After critical drying with Leica EM CPD300 automated critical point dryer, the samples were mounted on double-sided carbon tape on stubs. They were then plasma coated with 10 nm gold and viewed with a Hitachi S-3400N scanning electron microscope. For cryo-SEM, samples were fixed in liquid nitrogen, sublimated and gold-coated in Quorum PP2000T Cryo-SEM system. For transmission electron microscopy, samples were fixed in glutaraldehyde , post-fixed in osmium tetroxide , dehydrated in an acetone dilution series and infiltrated with Eponate 12 resin. Sections for transmission electron microscopy were cut to a thickness of 70 nm with diamond knives and a Leica EM UC6 ultramicrotome. The sections were stained with either 1% (w/v) aqueous uranyl acetate and 1% (w/v) lead citrate. Specimens were viewed with a JEM-1230 transmission electron microscope.The development and histochemistry of external trichomes and internal glands were studied with light microscopy. Sections for light microscopy were cut to a thickness of 0.5 to 1 \u00b5m with glass knives and stained with toluidine blue. The main classes of metabolites in secreted material of glandular trichomes were observed in fresh and fixed hand-sections, using following different histochemical tests. Neutral red and Sudan black B were used to localize total lipids, osmium tetroxide for unsaturated lipids, Naturstoffreagent A for detection of flavonoids (under UV 365 emission LP 397), periodic acid-Schiff (PAS) reagent for polysaccharides, Sudan III for lipids, NADI reagent for terpenes, ruthenium red for pectins. The observations were made under an Olympus microscope.Figure S1Morphology and distribution of glandular trichomes on the surface of Pogostemon cablin. (A\u2013F) (SEM): Adaxial surface (A) and abaxial surface (B) view with peltate glandular trichomes and short-stalked capitate glandular trichomes in secretory phase. (C) The surface view of stems showing long-stalked capitate trichomes (arrows). (D) Long-stalked capitate trichomes (arrows) among glandular trichomes and non-glandular trichomes on the leaf veins. (E) Distribution of glandular trichomes on stem apex of Pogostemon cablin. (F) Higher magnification of (E) showing fully developmental peltate glandular trichomes and short-stalked capitate glandular trichomes and the tuberculate epidermal cells depicted by arrows.(TIF)Click here for additional data file.Figure S2SEM micrographs showing the morphology and the secretion of three glandular trichome types in Pogostemon cablin. (A\u2013C) The secretion of short-stalked capitate glandular trichomes: (A) Pre-secretory stage with the secretory centre (arrow); (B) beginning of the secretory release (arrow); (C) the secretory droplets are getting bigger and the number increase to two (arrows). (D\u2013F) The secretion of long-stalked capitate glandular trichomes: (D) beginning of the secretory release and the oil droplet is small (arrow); (E) the oil droplet is getting bigger (arrow); (F) the small oil droplet (arrow) outside the apical cell. (G\u2013I) The secretion of peltate glandular trichomes: (G) Pre-secretory stage without thickened cuticle; (H) secretory stage with protruding cuticle; (I) the collapse of the sub-cuticular space after secretion.(TIF)Click here for additional data file.Figure S3Semithin sections of three glandular trichome types in different developmental phases showing the process of development. (A\u2013E) The development of short-stalked capitate glandular trichomes: (A) protruding epidermal cell with an asymmetrical cytoplasmic distribution containing vacuolate basal portions and cytoplasmically dense apical portions; (B) two-celled stage with one cytoplasmically dense apical cell and one vacuolate cell; (C) three-celled stage with one big cytoplasmically dense apical cell; (D) four-celled stage with two cytoplasmically dense apical cells without cuticle; (E) mature short-stalked capitate glandular trichomes with one sub-cuticular space containing essential oil (arrow). (F\u2013J) The developmental process of long-stalked capitate glandular trichomes: (F) protruding epidermal cell with a vacuolate basal region and an apical region containing the nucleus; (G) glandular trichome initial after periclinal cell divisions with a vacuolate basal cell and a apical cell containing the nucleus in the apical region; (H) three-celled stage showing a vacuolate basal cell,a vacuolate stalk cell, and an apical region containing the nucleus; (I) glandular trichomes in pre-secretory stage with a cytoplasmically dense apical cell, a narrow stalk cell and an elongated stalk cell; (J) mature long-stalked glandular trichomes with one sub-cuticular space containing essential oil (arrow). (K\u2013O) The developmental process of peltate glandular trichomes: (K) protruding epidermal cell with a vacuolate basal region and an apical region containing the nucleus; (L) two-celled stage with one cytoplasmically dense apical cell and one vacuolate basal cell; (M) three-celled stage with one cytoplasmically dense apical cell containing two nucleus, one narrow stalk cell and one vacuolate basal cell; (N) mature peltate glandular trichomes with one sub-cuticular space (arrow); (O) post-secretory glandular trichomes with the collapse of the sub-cuticular space.(TIF)Click here for additional data file.Figure S4Bright field and fluorescence micrographs of three glandular trichome types showing histochemical characterization of secretory products. (A\u2013H) Histochemistry of the short-stalked capitate glandular trichomes: (A) Ruthenium Red test showing the apical cells stained red; (B) gold-yellow secondary fluorescence observed with Neutral Red under UV light; (C) positive staining reaction with Sudan III in the apical cells and weak reaction in the stalk cell; (D) the apical cells stained blue with Sudan Black B and the stalk cell stained black; (E) OsO4 test showing the apical cells and the droplet (arrow) stained black; (F) NADI staining for terpenes is positive in the apical cells; (G) the apical cells react positively with Naturstoffreagent A; (H) PAS test for polysaccharides in apical cells. (I\u2013O) Histochemistry of the long-stalked capitate glandular trichomes: (I) ruthenium Red test showing the apical cells stained red; (J) yellow staining of secretion in sub-cuticular space with Neutral red; (K) secretory material stained with Sudan III; (L) positive staining reaction with Sudan Black B; (M) black staining of secretion with OsO4, secretory process is visible; (N) secretory material reacts positively for terpenes with NADI; (O) mature trichome reacts positively in PAS test for polysaccharides in the head cell and stalk cell. (P\u2013T) Histochemistry of the peltate glandular trichomes: (P) gold-yellow secondary fluorescence observed with Neutral Red under UV light; (Q) secretory material in the sub-cuticular space positive stained with Sudan III; (R) staining for total lipids with Sudan Black B; (S) positive staining reaction with OsO4 in the head cells and weak reaction in the narrow stalk cell; (T) NADI staining for terpenes is positive in the sub-cuticular space.(TIF)Click here for additional data file.Figure S5EM micrographs showing the cuticle of mature external and internal glands in Pogostemon cablin. (A) A random fibrillar network (arrow) on the reticulate cuticle of short-stalked capitate glandular trichomes is evident; (B) the thin cuticle of long-stalked capitate glandular trichomes; (C) TEM and (D) SEM micrographs showing the gaps (arrow) between the spherical accumulations of cutin at the apex of peltate glandular trichomes; (E) the cuticle of internal glands in leaves with high electron density; (F) the cuticle of internal glands in stems.(TIF)Click here for additional data file."} +{"text": "Cancer metastasis is the most common cause of death in cancer patients. Although surgical resection remains the only potentially curative treatment for lung cancer, lung cancer patients after curative surgery still have high risk of cancer recurrence. If we can perform any prophylactic strategy during the perioperative period for cancer recurrence, surgical outcome for lung cancer could be improved significantly.Atrial natriuretic peptide (ANP) has been used clinically for the treatment with heart failure in Japan, and exhibits a wide range of biological activities including beneficial effects on cardiovascular system through binding the guanylate cyclase-A (GC-A) receptor. We previously reported that ANP administration during the perioperative period had a prophylactic effect on postoperative cardiopulmonary complications in lung cancer patients. We performed the follow-up survey in these patients, and found that the incidence of cancer recurrence after curative surgery for lung cancer was significantly lower in the ANP-treated patients compared to the control patients . The objective of the present study was to investigate the mechanism of ANP in the prevention of cancer metastasis.We used B16 mice melanoma cell line, which don't have the GC-A receptor, in the experimental hematogenous metastasis model in mice. ANP infusion was started one day before the injection of B16 cells. This dose does not change blood pressure and heart rate in mice.5 cells) were intravenously injected into C57/B6 mice, 100-150 of visible lung macrometastasis occurred in two weeks. In this hematogenous metastasis model, administration of ANP notably inhibited metastasis in the lung compared to the control mice . Furthermore, lung metastasis significantly increased in the vascular endothelial cell specific GC-A knock-out mice, and decreased in the vascular endothelial cell specific GC-A overexpression mice compared to the wild-type mice. These studies indicate that ANP/GC-A signaling in the vascular endothelial cells plays crucial roles in the inhibition of cancer metastasis.When B16/F10 cells (5 x 10We found that ANP inhibits cancer metastasis through GC-A receptor in the vascular endothelial cells. Our data provide novel insights into the prophylactic therapy for various kinds of cancer metastasis."} +{"text": "A 49 year-old-man presented to the emergency room with sudden onset palpitation of four hourduration. He also complained of retrosternal chest discomfort and giddiness. There was nohistory of palpitations in the past. Twelve lead ECG showed r"} +{"text": "Amyloid-beta related angiitis (ABRA) of the central nervous system (CNS) is a rare disorder with overlapping features of primary angiitis of the CNS and cerebral amyloid angiopathy. We evaluated a 74-year-old man with intermittent left sided weakness and MRI findings of leptomeningeal enhancement, vasogenic edema, and subcortical white matter disease proven to have ABRA. We discuss clinicopathological features and review the topic of ABRA. A 74-year-old man with a past medical history of chronic lymphocytic leukemia (CLL) stage 0 (not receiving treatment), renal cell carcinoma , hypertension, and hyperlipidemia awoke one morning with numbness of the thumb and first two fingers of the left hand \u201cmarching\u201d up to the left arm over the course of few seconds. This was immediately followed by drooling from the left corner of his mouth. The entire episode lasted <15\u2009s and was followed by complete resolution. The following day, he had an episode of slurred speech and left facial weakness, which prompted evaluation at a local hospital where his symptoms again completely resolved. He was admitted for further investigation. Contrast-enhanced brain MRI showed leptomeningeal enhancement and increased signal intensity on T2 fluid attenuated inversion recovery (FLAIR) sequences on the right temporal lobe, as well as moderate subcortical and periventricular T2 signal abnormalities suggestive of white matter disease , 6. Pati(CAA-RI) , 6. BothThe pathophysiology of ABRA is not fully understood. Whether amyloid-beta deposits initiate a vasculitic response or rather angiopathic-mediated inflammation leads to beta-amyloid deposition remains debatable. One theory suggests an immunologic response toward amyloid-beta, resulting in leptomeningeal and parenchymal inflammation with increased amyloid-beta deposition and clearance of amyloid-beta in the parenchyma . DecreasAmyloid-beta related angiitis usually presents in the seventh decade of life (mean age of 67\u2009years) \u2013 without gender predilection . The maiAn abnormal ESR has been reported in 12\u201338% of patients with ABRA . CSF floThe most common neuroimaging findings of ABRA are gadolinium-enhancing leptomeninges . Other fTreatment of ABRA and CAA-RI include corticosteroids and immunosuppression, primarily with cyclophosphamide , 2, 5, 6Amyloid-beta related angiitis and CAA-RI are unusual neuropathological diagnoses. Mental status or cognitive changes, gadolinium-enhancing meninges, and elevated CSF protein content are frequent findings. In contrast to PACNS, patients with ABRA have better response to immunosuppressive therapy. Differentiating prognostic and management features between ABRA and CAA-RI require further refinement.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Staphylococcus aureus (MRSA) is an important nosocomial and community-associated pathogen. Recently, livestock-associated MRSA (LA-MRSA) has emerged and disseminated in Europe and North America and now constitutes a considerable zoonotic burden in humans with risk factors of pig exposure, whereas the extent of the livestock reservoir is relatively unknown on other continents.Methicillin-resistant lukF-lukS genes encoding Panton-Valentine leukocidin, and were resistant to multiple non-\u03b2-lactam antimicrobials. However, unlike other Asian LA-MRSA-ST9 variants, they were spa type t337 and harbored a different staphylococcal cassette chromosome mec IX.From March through April 2011, MRSA was identified in pigs from 3 out of 30 production holdings in Chang Mai Province, Thailand. Representative isolates were subjected to molecular characterization and antimicrobial susceptibility testing; all isolates had genotypic and phenotypic characteristics of LA-MRSA previously characterized in the region: they belonged to ST9, lacked the A novel MRSA-ST9 lineage has been established in the pig population of Thailand, which differs substantially from LA-MRSA lineages found in other areas of the continent. The emergence of novel LA-MRSA lineages in the animal agriculture setting is worrisome and poses a serious threat to global public health. Staphylococcus aureus (MRSA) in livestock, particularly pigs, and in humans with contact to livestock provided the first evidence of the existence of a true livestock-associated MRSA (LA-MRSA) reservoir throughout Europe Recent reports of methicillin-resistant mec elements encoding \u03b2-lactam resistance; they exhibit co-resistance to many non-\u03b2-lactam antimicrobials including those commonly used in animal production.LA-MRSA isolates have unique characteristics that distinguish them from community- and healthcare-associated MRSA isolates showed that closely related sequence types (STs) within clonal complex (CC)398 predominate in Europe and North America, whereas the vast majority of LA-MRSA isolates from Asia belongs to CC9 (ST9 and single-locus variants thereof).There is still a comparative lack of information on the emergence of LA-MRSA and its burden on human disease in South-East Asia. The purpose of this study was to investigate whether pigs constitute an MRSA reservoir in Thailand. We present evidence that a novel MRSA-ST9 lineage has been established in the pig population of Thailand, which differs substantially from LA-MRSA lineages found in other areas of the continent.mecA, using PCR assays and primers that have been described elsewhere From March through April 2011, nasal swabs were taken from 4 pigs from each of 20 small-scale and 10 large-scale confined production holdings located in Chiang Mai Province . The dif(spa) typing was performed using the Ridom Staph Type standard protocol (http://www.ridom.com) and the Ridom SpaServer (http://spa.ridom.de/index.shtml), and MLST types were determined as described previously http://www.mlst.net). The eBURST algorithm was used to assign individual STs to specific CCs (http://www.mlst.net). Presence of lukF-PV and lukS-PV genes (encoding PVL) was investigated by a PCR assay that has been reported elsewhere mec (SCCmec) was performed using a PCR-based multiplex assay described by Kondo et al. A single MRSA colony from each positive holding was selected for further analysis. Staphylococcal protein A The antimicrobial susceptibility profiles were determined by the agar dilution method using Neo-Sensitabs , in accordance with the Clinical Laboratory Standards Institute guidelines spa type t337 and carried SCCmec IX. In comparison, none of the 10 large-scale confined production holdings were positive for MRSA (lukF-lukS genes encoding PVL.Three (15%) of 20 small-scale confined production holdings were positive for MRSA ; analysifor MRSA . The t33This study provides the first evidence of a porcine reservoir of MRSA-ST9-IX in Thailand. However, the extent and diversity of the MRSA reservoir in animals remains speculative because of the limited sample size and analysis of only a single colony per holding. It should be noted that the 3 positive holdings were located in the village of Tamao , which sspa type t337) in Thailand is not known. The distribution of spa types associated with LA-MRSA-ST9 shows rather distinct geographic patterns with t899 and t4358 being the most common spa types in pigs from China and Malaysia, respectively mec V predominates among LA-MRSA-ST9 from other Asian countries The origin of LA-MRSA-ST9-IX (mec IX has only been described in a single MRSA-ST398 isolate (spa type t034) recovered from a Thai participant at the 19th International Pig Veterinary Conference in Denmark mec IX is geographically restricted. Notably, the 18-kb J1 region of the large SCCmec IX contains a cadDX operon, a copB gene, and two arsenate resistance operons, arsRBC and arsDARBCTo date, SCCS. aureus (MSSA) lineages with spa types t034 (CC398), t1333 (CC30), and t337 (CC9) are predominant in the pig population spa type t337 through local acquisition of SCCmec IX. If this is the case, other MSSA CC9 (and CC30) populations circulating in the animal agriculture setting around the world may also have the propensity to acquire SCCmec, thereby expanding the porcine MRSA reservoir.Methicillin-susceptible mec IX in LA-MRSA CC9 and CC398 from Thailand suggests that SCCmec transfer can occur between these lineages, although the direction of transfer remains unclear. However, it is also possible that other MRSA types or methicillin-resistant coagulase-negative staphylococci are the source of SCCmec IX in S. aureus CC9 and CC398. Additional studies investigating the role and direction of horizontal transfer in the evolution of S. aureus CC9 and CC398 are currently under way.The presence of SCCThe carriage rate among humans with contact to pigs was not investigated in this study. Nevertheless, zoonotic transmission of LA-MRSA-ST9 from pigs to humans with contact to pigs has been previously reported in China and Malaysia spa type t899) and MRSA-ST834 have been isolated from sporadic cases of infection in China and Cambodia, respectively mec IV; it exhibits high rates of resistance to rifampin (90%) and trimethoprim-sulfamethoxazole (90%), whereas rates of resistance to gentamicin (15%), chloramphenicol (3%), and ciprofloxacin (20%) are low S. aureus CC398 Cases of MRSA-CC9 carriage and infections in human populations have not been reported in Thailand, unlike in other countries of the region where MRSA-ST9 (In conclusion, our findings demonstrate that MRSA is present in the Thai pig population. However, the extent of the porcine MRSA reservoir and its implications for MRSA carriage and disease in humans in Thailand and other Asian countries has still to be determined."} +{"text": "Tcl1-Deficient ES Cells\" In the Results section, the subheading \"Generation of -deficient ES cells\" is incorrect. The corrected subheading is \"Generation of"} +{"text": "The assessment of global left-ventricular (LV) parameters from a stack of multiple slices is usually performed in short-axis orientation, whereas transversal orientation is commonly preferred for the assessment of right-ventricular (RV) parameters. Other choices carry the risk of inaccuracies due to hindered delineation of valvular planes. The purpose of our study was to reconstruct 3D cine data sets in short-axis orientation from transversal image data and vice versa, and to assess the accuracy of global LV and RV parameters derived from these reconstructed data sets as compared to that from data sets with targeted acquisition in both orientations.In 10 patients with congenital heart disease , multi-slice cine data sets encompassing both ventricles were acquired in both short-axis and transversal orientation . LV and RV end-diastolic volumes (EDV), end-systolic volumes (ESV), and ejection fraction (EF) were derived from the acquired data sets. Using a custom-built CMR analysis program (CAIPI), transversal data sets were reconstructed from images acquired in short-axis orientation, and short-axis data sets were reconstructed from images acquired in transversal orientation. The same biventricular parameters were then derived from the reconstructed data sets using a semi-automatic contour detection tool from CAIPI.On the acquired data sets, mean differences between ventricular parameters as assessed from short-axis and transversal orientation ranged from 0.4+/-10.4% (RV EF) to 12.3+/-9.7% (RV ESV). Bland-Altman comparison showed better agreement between LV parameters derived from reconstructed short-axis and acquired short-axis data sets than between acquired transversal and acquired short-axis data sets. In concordance, there was higher agreement between RV parameters derived from reconstructed transversal and acquired transversal data sets than between acquired short-axis and transversal data sets.The use of reconstructed 3D cine data sets allows for using optimal analysis planes for both ventricles with high diagnostic accuracy and without the need for time-consuming acquisition of two separate cine data sets.DFG, BMBF."} +{"text": "In temperate zones, the seasonal cycling of perennials comprises two main steps: a growing period when environmental conditions are favourable and a non-growing period in winter. Winter dormancy consists of two phases: endodormancy and ecodormancy . The forThe objective of this study was to characterize the transcriptome of endo- and eco-dormant sessile oaks (a major broadleaf species in Europe) by RNA-seq and to identify differentially expressed genes between these two dormancy stages. Four cDNA libraries were generated using total RNA extracted from apical buds harvested during endo- or ecodormancy of two contrasted populations. Transcriptome characterization was performed on a Roche 454 FLX platform. Digital expression analysis leads us to identify a set of 48 genes differentially regulated between these two developmental phases (there was no differences between populations). Their function was identified by sequence homology and this result contributes to the characterization of the molecular network underlying vegetative bud dormancy, an important life history traits of these long lived organisms.Quertus petreae (Matt) Lieb.) were collected in 2006 on two populations from Northern France: Longchamp (LC) and Saint Jean (SJ). These populations are contrasted for their bud burst date (early vs. late flushing). We obtained 560 and 468 seedlings for the SJ and the LC populations, respectively. A forcing test experiment was performed in a greenhouse from July 30th 2007 to February 25th 2008 located at the INRA forestry research station (southwestern France). For each population, approximately 25 seedlings were selected each week. Ten apical buds from 10 seedlings were used for RNA extraction. The 15 remaining seedlings were transferred in a greenhouse with the following parameters: a 16-hours photoperiod and a day/night temperature of 25/18 \u00b0C. For each batch of seedlings, bud burst date was evaluated three times a week allowing us to determine the number of days necessary to induce bud burst. We, thus, identified periods corresponding to eco- and endodormancy.Acorns of sessile oak (r statistics [TM reverse transcription system (Promega) according to the manufacturer\u2019s instructions. Q-PCR reaction and quantification were performed on a Chromo4 Multicolor Real-Time PCR Detection System (Bio-Rad)Total RNA from apical buds harvested on September 17th, 24th and October 1st for endo-dormancy as well as on January 14th, 28th and February 11th for eco-dormancy were extracted independently, and mixed equimolarly to obtain a composite cDNA library for each population and developmental stage. The libraries were sequenced on a Roche 454 FLX to produce 495,915 reads in total. After cleaning and removal of duplicated reads, reads were mapped onto oak unigenes [atistics and R BioWe identified 48 common contigs that showed differential expression by three bioinformatic programs and selected 13 genes for Q-PCR analysis with the main goal to validate the result obtained in silico. One gene (heat shock protein) showed multi-banding pattern and discarded from the analysis. Among the 12 remaining genes, only one gene (cold shock protein) showed contradictory expression pattern between in silico and Q-PCR analysis. The high success rate of Q-PCR analysis (11/13 = 84.6 %) indicates that the verified genes are likely to represent endo- and ecodormancy stages. Two genes (Globulin and XET) were confirmed as up-regulated in endodormancy, while nine genes were found to be up-regulated in ecodormancy .Analysis in terms of GO showed genes responsible to abiotic and endogenous stimulus as well as stress related were enriched in the set of 48 genes. Similar trend was observed in expression analysis for raspberry bud dormancy, where high percentage of stress-response/defense/detoxification-related genes were identified . Althoug"} +{"text": "Human immunodeficiency virus (HIV)- infected patients are at risk of acquiring viral hepatitis, due to common routes of transmission. As the introduction of highly active antiretroviral therapy (HAART) reduced the frequency of opportunistic infections and improved survival, viral hepatitis emerged as an important cause of morbidity and mortality in HIV-infected cases. Occult hepatitis B virus (HBV) infection is characterized by presence of HBV infection without detectable hepatitis B surface antigen (HBsAg). There are conflicting reports on the impact of occult HBV infection on the natural history of HIV disease. In this review, we described the findings of studies on HIV and hepatitis B co-infection with focus on the prevalence of occult HBV infection. The results of this review demonstrated the importance of prevention, diagnosis and treatment of occult HBV infection in HIV-positive patients. Hepatitis B virus (HBV) infection is a serious global health problem, with two billion people infected worldwide and 360 million suffering from chronic HBV infection . HBV infHIV- infected patients are at risk of acquiring parenterally- or sexually-transmitted viruses including HBV. Approximately 20% of HIV-positive patients who acquire acute HBV infection develop chronic HBV infection compared to only 5% of HIV-negative persons . ChronicThe prevalence of OBI in HIV-positive patients varies considerably from 0% to 89.5% in different geographical regions 18]19][[19][18][[[19][18]Thirty-five million people have HIV infection worldwide, and approximately 20% of them had chronic hepatitis C (HCV) infection . HCV infHepatic abnormalities are common in HIV-infected subjects. Due to shared routes of transmission, chronic HBV and HCV infections frequently complicate HIV disease. To date, there are controversial evidences regarding the influence of HBV infection on HIV disease progression. While some early studies suggested that HBV-related liver disease may be less severe among HIV-infected patients, recent studies indicate an increased risk of liver-related morbidity and mortality among HIV-HBV co-infected patients. Current evidences demonstrated that OBI is relatively frequent in HIV-infected individuals. These data emphasize the importance of prevention, diagnosis and treatment of OBI in HIV-positive cases and all HIV-infected patients should be screened for evidence of resolved or active HBV infection. HCV infection is also common in HIV-infected individuals with parenteral exposure such as IDUs and recipients of blood products. Although the majority of HCV-HIV co-infected cases are asymptomatic, HCV infection may lead to the development of hepatic fibrosis, cirrhosis and hepatocellular carcinoma. There are conflicting reports on the impact of HCV infection on the natural history of HIV disease. With the advent of HAART, there has been a significant decrease in opportunistic infections so HCV has emerged as an important cause of morbidity and mortality in HIV-infected patients. Taken together, these data provide evidences of the increasing importance of HCV among HIV-infected subjects. There is limited information on the clinical impact and management of HIV-infected patients with OBI. Further studies to provide sufficient data for management of the clinical consequences of these patients are suggested."} +{"text": "Soy-derived isoflavones potentially protect against obesity and depression. In five different studies we examined the influence of soy-containing diets or equol injections on depression, serotonin levels, body weight gain (BW) and white adipose tissue (WAT) deposition in female Long-Evans rats at various stages of life .In general, animals fed a soy-rich diet (Phyto-600) and/or administered equol (@ 5 mg/kg/day) displayed significant decreases in BW and WAT compared to a low-soy diet. When equol was injected alone (5 mg/kg/day), experiments 1, 4, and 5 demonstrated that body weight was significantly decreased. Equol has body weight control effects in females that are dependent on ovarian status and/or age of diet initiation. Experiments 1-4 all displayed no significant differences in depressive-related behavior as measured by the Prosolt forced swim test (PFST) when soy-rich (Phyto-600) or low-soy diets (Phyto-low) or equol treatments (5 mg/kg/day) were tested in female rats at various ages or hormonal status. Results of all the experiments are not presented here due to space limitations, but data from experiment 5 are presented. From conception female rats were exposed to either: a) a soy-rich (Phyto-600) or b) low-soy diet (Phyto-low). After 290 days all rats experienced NOF. At 330 days-old the animals were examined in the Porsolt forced swim test (PFST). One month later a second PFST was performed [after Phyto-low fed animals were injected with equol (5 mg/kg/day) for one week prior to the second PFST]. At the first PFST, serotonin and mobility levels were significantly decreased in the Phyto-low fed animals compared to animals that consumed the Phyto-600 diet. After equol injections at the second PFST, mobility and serotonin levels significantly increased in aged NOF rats fed the Phyto-low diet .Consumption of dietary isoflavones or equol exposure in rats has body weight controlling effects and equol specifically may have antidepressant potential dependent upon diet initiation and/or dosage of treatments. The current study demonstrates that equol is able to decrease body weight, abdominal WAT, and depressive-related behavior. While other factors and mechanisms may play a role, in part, the present results provide a greater understanding of how isoflavonoid molecules modulate the brain's influence on behavior. Following the 2002 Women's Health Initiative (WHI), concerns about hormone replacement therapy (HRT) amplified interest in alternative therapies for the treatment of menopausal symptoms -3. PolypIsoflavones, such as daidzein and genistein, are selective estrogen receptor modulators (SERM) or biochemical compounds that are able to agonize or antagonize estrogen receptors (ER) . DaidzeiMenopausal symptoms such as hot flashes, insomnia, depression, and weight gain are associated with the loss of ovarian steroid production and availability ,12-14. HIn a series of reports we demonstrated that soy-derived isoflavones can significantly decreased body weight, adipose tissue deposition, skin tail temperature and produce anxiolytic effects -20. NotaThus, this stimulated us to examine whether isoflavones (particularly equol) may be used as both an antidepressant and an anti-obesity treatment in intact female rats and two animal models of menopause .In five different experiments we examined the influence of soy-containing diets and equol administered via subcutaneous (s.c.) injections on depressive-like behaviors, serum serotonin levels, weight gain (BW) and white adipose tissue (WAT) deposition in female Long-Evans rats at various stages of postnatal life.All animals had free access to food (diet treatment) and tap water. Only the animals in Experiment 3 were not bred at our facilities. [The Experiment 3 rats were purchased ovariectomized (at approximately 45-50 days-old) from Charles River Laboratories (CRL) and following surgery/recovery the animals were shipped to our facilities.] All other male and female rats purchased from the supplier were allowed time to adapt to their new surroundings and diet treatments before being bred in our animal facilities at approximately 90 days old for each experiment (outlined below). Mating was performed by a protocol previous reported by our laboratory . In brieFrom conception the female rats were exposed to either a soy-rich (Phyto-600) diet that contained 600 ppm of isoflavones or a low-soy (Phyto-low) diet that contained approximately 10 ppm of isoflavones , . Each diet protocol is outlined below by experiment number and descriptor. Furthermore, the diet formulations (ingredient list) have been published previously -19. NotaIn general, before running the last Porsolt Forced Swim Tests rats received subcutaneous (s.c.) injections (@ nape of the neck) of either dimethyl sulfoxide @ 100% that served as controls or 5.0 mg/kg body weight of equol in DMSO. Daily injection volume was 0.1 cc (see specific experiment number below for injection schedule). While the length of time injected differed between experiments the equol concentration remained at 5 mg/kg in each experiment. [Notably: in other experiments an equol dose of 2.5 mg/kg yielded similar results].Animals in Experiment 4 were ovariectomized in our laboratory between 96-100 days of age. Animals were anesthetized with a combination of at 0.05 cc per 100 grams body weight. Body temperature was maintained with a warm water blanket. Both ovaries were surgically removed (with the assistance and supervision of our university veterinarian), the incision was closed with sterile surgical staples and animals were given acetaminophen [20 ml of pediatric elixir (32 mg/ml) per 500 ml tap water] in their drinking water for approximately 4-5 days post-surgery during recovery.We utilized the Porsolt forced swim test (PFST) that has become a standard antidepressant test in pharmaceutical laboratories worldwide and in academic laboratories for investigating the neurobiology of depression and of antidepressant agent action ,22. It t\u00ae computer software .Each rat was placed in a plastic cylindrical container containing water at a depth of 35.6 cm for 8 minutes. Rats were unable to touch the bottom of the container with their tails . The behBody weight (in grams) was recorded at different intervals for each experiment (see below). At the end of each experiment, trunk blood was collected, serum prepared and then stored at -20\u00b0C until assayed for serotonin or isoflavone concentrations. WAT was dissected from just below the diaphragm to the base of the pelvic cavity and recorded in grams.Serum serotonin levels were quantified using ELISA kits (Cat# IB89527-121610) purchased from Immuno Biological Laboratories . Serum was analyzed for all of the experiments except experiment 3.Serum was analyzed via gas chromatography/mass spectrometry (GC/MS) and the circulating isoflavones: genistein, daidzein, and equol concentrations were determined (ng/ml) using internal control standards, as previously reported in other studies by our laboratory ,19.All methods associated with animal use/surgery were approved by the Institutional Animal Care and Use Committee at Brigham Young University.This experiment examined the influence of diet on body weight, WAT, serotonin levels, isoflavone levels, and behavior as measured in the PFST. From conception to young adulthood, 23 female rats representing 6 litters were fed the Phyto-low diet. At age 120 days animals were run on the Porsolt forced swim test (PFST) to obtain baseline levels for depressive-like behaviors in Phyto-low fed female rats. Following this PFST, 12 animals were switched to a Phyto-600 diet while 11 animals remained on the original Phyto-low diet. The animals remained on these diet treatments (Phyto-600 or Phyto-low) until the end of this experiment. When animals were age 155 days they were run a second time on the PFST and behavioral parameters were recorded. From age 194 to 200 days, the Phyto-low fed animals received 5 mg/kg (body weight) injections of equol while the Phyto-600 animals received vehicle-DMSO injections. At age 200 days the animals were run on a third PFST and behavioral parameters were recorded. The dietary and treatment injections continued until the animals were sacrificed at age 210 days when body and WAT weights were recorded and blood was collected for serotonin and isoflavone quantification or a soy-rich (Phyto-600) diet from conception to adulthood (145 days-old) in intact rats for the study parameters. Animals were fed either the Phyto-low or the Phyto-600 diet. Animals were weighed three times a week. When the rats were 115 days-old the rats were run on the first PFST. After 3 weeks the Phyto-low fed animals were injected for 4 days (136 to 142 days-old) prior to second PFST with 5 mg/kg of equol while the Phyto-600 fed animals received vehicle-DMSO injections. At 142 days-old the animals were run on a second PFST. These injections continued until the animals were sacrificed at 145 days-old when body and WAT weights were recorded and trunk blood was collected for quantification of serotonin and isoflavones concentrations diet from approximately 50-55 days of age until 80-85 days of age in twenty-two ovariectomized rats purchased from Charles River Laboratories. The animals were weighed daily during this experiment. At approximately age 85 days eleven animals were changed to a soy-rich (Phyto-600) diet while the other eleven animals remained on the original soy-low or Phyto-low diet for approximately two weeks. When the animals were approximately age 100 days they were tested in the PFST. The animals were then sacrificed and body and WAT weights were recorded and blood collected for subsequent analysis of isoflavone concentrations or a soy-rich (Phyto-600) diet from conception to adulthood (222 days-old) on the study parameters. Animals were initially intact rats and later ovariectomized (in our laboratory) as young adults. The females were fed either the Phyto-low (n = 8 from 4 litters) or Phyto-600 (n = 8 from 3 litters) diet. Animals were weighed three times a week. Animals were ovariectomized at approximately age 100 days. At age 150 days animals were run on the PFST and behavioral parameters were recorded. The animals continued on their respective diet treatments until age 200 days when they were run on a second PFST. However, four days prior to this second PFST (from age 197 to age 200 days) the Phyto-low fed animals received s.c. injections of 5 mg/kg of equol and the Phyto-600 fed animals were administered vehicle-DMSO injections. After the second PFST animals continued to received daily s.c. injections by dietary treatments until being run on a third PFST age 220 days. The injections by dietary treatments continued until animals were sacrificed at age 222 days when the study parameters were collected (body/WAT weights) and quantified (serum serotonin and isoflavone levels) or a soy-rich diet from conception to mid-age on the study parameters in intact rats (representing at least 2 to 3 litters by dietary treatment) that experienced natural ovarian failure (NOF). Intact, Long-Evans female rats were exposed to a Phyto-low diet or a Phyto-600 lifelong from conception to mid-age (> 300 days-old). The animals were weighed at selected time intervals in this experiment. At approximately 300 days-old all animals (regardless of diet treatment) experienced NOF as detected by vaginal histological/microscopic examination of the epithelial cells over a 10-day interval (from 295 to 305 days-old). Twenty-seven days later approximately one half of the animals in each treatment group had blood collected via tail vein for baseline serotonin and isoflavone levels. At 330 days-old the animals (by dietary treatment group) were run on the first PFST. Twenty-four days later (@ approximately 353 days-old) the Phyto-low fed animals received daily s.c. injections of equol (@ 5 mg/kg) while the Phyto-600 fed animals received vehicle-DMSO injections for 7 consecutive days. Two hours after the last injection on the seventh day the animals were again run for a second time on the PFST (by diet and injection treatments). Injections continued until animals were sacrificed at 365 days-old; body and WAT weights were recorded and trunk blood was collected for quantification of serotonin and isoflavones concentrations and significance are shown in Table In general, the animals fed the Phyto-600 diet displayed lower body weight gain. However, statistically significant differences were only seen following the diet change in experiment 1 and following ovariectomy in experiment 4.In experiment 1: Phyto-low diet exposure from conception to 120 days post-birth with diet change of one-half of the animals to a Phyto-600 diet until 210 days of age.The Phyto-600 animals displayed significantly decreased weight gain following the change to the Phyto-600 diet Figure . Within In experiment 4: Phyto-low or Phyto-600 diet exposure from conception to approximately 100 day old when all animals were ovariectomized. Then the animals remained on their respective diet treatments (Phyto-low or Phyto-600) until 222 days of age.The Phyto-600 females had significantly lower body weights following ovariectomy and in experiment 3 had lower average body weights than the Phyto-low fed animals but these differences were not significant. The animals in experiment 2 were culled to remove any outliers prior to treatment and had the shortest treatment periods (see methods). We believe that had treatment continued the Phyto-600 animals would have displayed significantly lower body weights due to the observed change in slopes of the body weights.In experiment 3 Phyto-600 WAT was significantly lower (p < 0.001); however when normalized to body weight (WAT/BW) this was not significant (p < 0.086). Equol injections in the Phyto-low animals decreased body weight as shown in Figure Experiments 1-4 demonstrated no significant differences between treatment groups for any behavioral study parameters in any of the PFSTs performed in these experiments . Serum equol levels of the equol-injected Phyto-low animals were less than half the levels of the intestinally produced equol in the Phyto-600 fed animals Table . In expeThere were no significant differences in serum serotonin values between treatment groups for experiments 1-4 . These values were obtained at the end of each experiment; prior serotonin values were not determined .Animal body weight measurements were only recorded at specific points during this experiment and these points and respective ages are marked in Figure In the first PFST, time immobile Figure , swimminAll isoflavone values are shown in Table The Phyto-low fed animals displayed lower serum serotonin values prior to the first PFST vs. Phyto-600 values Figure . HoweverIn general, this study demonstrates that either dietary isoflavone exposure or equol alone effectively decreased body weight and WAT deposition in females regardless of ovarian status, which is similar to that reported previously -20,24. OThis study also demonstrated that equol decreases depressive-related behavior in NOF females. Prior to equol injections in experiment 5, the Phyto-low animals demonstrated greater immobility and lower serotonin levels. These differences were reversed following equol injection as time immobile significantly decreased and serum serotonin levels significantly increased in the Phyto-low animals. This study is the first to test and report equol's potential effectiveness as an antidepressant using the PFST. The testing of other isoflavones such as quercitin or resveratrol in the PFST, while few in number, demonstrate that isoflavones have potential as antidepressant treatments ,37.Equol's antidepressant potential demonstrated in the PFST, may be attributed to equol's estrogenic actions in the brain. ER\u03b2 is found in four brain regions associated with behavioral and mood disorders, the frontal cortex, amygdala, hippocampus, and the hypothalamic region -41. FollRemarkably, equol could potentially affect the concentration of serotonin. For example, Dewar et al., reported that equol was an effective inhibitor of rat liver monoamine oxidase . Since mIt is noteworthy that ER\u03b2-deficient mice express increased anxiety while adHowever, the use of animals with varying ovarian status demonstrated that equol appears to have a defined range of effectiveness. For instance, ovarian status plays a role in equol treatment effectiveness. Equol is ineffective at decreasing depressive-related behavior in intact females or females ovariectomized shortly after puberty. Experiments 1-4 all displayed no significant differences in depressive-related behavior as measured by the PFST. Only experiment 5 showed any significant differences. Conversely, from this study it appears that equol has potential as an anti-obesity treatment regardless of ovarian status; however, as an antidepressant it appears to be effective only following NOF.Menopause/ovarian failure is a normal part of the aging process . DepressThe current study demonstrates that equol and/or isoflavonoids can decrease body weight, abdominal WAT, and depressive-related behavior dependent on age at initiation of diet and changes in ovarian status. However, equol's effectiveness as an antidepressant may be dependent upon the changes/timing of ovarian status with aging. This study demonstrated that equol's beneficial effects are most clearly seen in female rats that have undergone NOF. Further studies determining equol's exact mechanisms of action and potential as an antidepressant are required.The authors declare that they have no competing interests.CB- participated in the experiment design, performed the experiments, analyzed the data and authored the text, etc; KMF- participated in the experiment design, performed the experiments, analyzed the data; KDRS- performed the isoflavone blood analysis; TDL- performed the experiments and data analysis of the Porsolt results; EDL- participated in the experimental design, performed the experiments, data analysis, authoring of the text, etc. All authors read and approved the final manuscript."} +{"text": "The left ventricular (LV) lead in cardiac resynchronization therapy (CRT) can be placed on any non-septal LV wall, most commonly the lateral wall. Presence of myocardial scar adversely affects CRT outcome, particularly if it involves the LV pacing site. It is increasingly important to identify and localize myocardial scar in CRT candidates, the majority of whom have left bundle branch block (LBBB). We aimed to describe the diagnostic performance of electrocardiographic (ECG) criteria based on the Selvester QRS score in localizing myocardial scar into 5 LV wall segments and in detecting non-septal scar in patients with LBBB using Cardiac Magnetic Resonance as the gold standard.In 39 cardiomyopathy patients with strictly defined LBBB , late gadolinium enhancement cardiac magnetic resonance images (CMR-LGE) and 12-lead ECGs were analyzed for scar presence in 5 LV wall segments. Using stepwise regression analysis, multiple subsets of the Selvester QRS score ECG criteria were identified for each of the 5 individual segments and for the 4 non-septal segments together. The diagnostic performance of each of these subsets is displayed in the graph below. The one subset for each location that had the highest combination of sensitivity plus specificity was selected.The best identified subset of Selvester QRS score criteria for screening of non-septal scar had 75% (95% CI: 51-90%) sensitivity, 95% (78-99%) specificity, 92% (67-99%) positive predictive value and 84% (65-94%) negative predictive value. For each individual wall segment, 40-60% sensitivities and 77-100% specificities were found.The 12-lead ECG can convey information about scar presence and location in patients with cardiomyopathy and LBBB. ECG screening criteria for scar in potential CRT LV pacing sites were identified. Further exploration is required to determine the clinical utility of the 12-lead ECG in combination with other imaging modalities to screen for scar in potential LV pacing sites in CRT candidates.The study was supported by the National Heart, Lung, and Blood Institute, National Institutes of Health , the DW Reynolds Foundation and the FDA Critical Path Initiative."} +{"text": "Although some neurophysiological studies have showed cortical excitability changes during different phases of the migraine cycle, the pathophysiological mechanisms underlying attacks recurrence remain unknown. Here we evaluated the response of the migraine motor-cortex to brief trains of 5-Hz repetitive transcranial magnetic stimulation (rTMS) in order to study, indirectly, presynaptic mechanisms of glutamatergic neurotransmission across the different phases of the migraine cycle.40 migraine with aura (MwA) and 40 migraine without aura (MwoA) patients underwent suprathreshold (130% of the resting motor threshold) brief trains of 5-Hz-rTMS to the motor-cortex, recording Motor Evoked Potentials (MEPs) at each train stimulus. Patients were studied whatever the phase of the migraine cycle: interictal (n=51), preictal (n=9), ictal (n=10) or postictal (n=10).As we previously showed , in the Our results support the hypothesis that in migraine a transient increase in intracortical glutamatergic activity could trigger the migraine attack. Inhibitory homeostatic mechanisms of glutamate release could be involved in the resolution of the migraine attack and in preventing further attacks."} +{"text": "To evaluate the profile of genetic markers, childhood abuse and personality in eating disorders (EDs) and compare this to the profiles found in their healthy sisters. Gene environment interactions (G*E) were also assessed for sexual abuse and various candidate genes.Participants were 147 discordant sister pairs for EDs. The semi-structured EATATE interview [designed to assess ED symptomatology and obsessive-compulsive personality traits (OCPD)], the Temperament and Character Inventory (TCI-R) and the Oxford Risk Factor Interview (ORFI) were used. DNA was also collected and three candidate genes were genotyped.p<.01).Compared to the sisters, the ED group revealed more significant associations between different personality measures and the candidate genes 5-HTTLPR and 5-HT2A (p<.05). Sexual abuse also occurred more commonly in the ED group compared to the sisters. The only personality traits associated with sexual abuse were adulthood OCPD traits (p <.05). Finally, for the G*E interaction effects, even though no significant results were obtained for either of the 3 candidate genes, the likelihood of an ED increased by roughly 4.5 times for those patients with the presence of the LS-5-HTTLPR genotype and sexual abuse.ED patients presented with significantly more adulthood OCPD traits, higher levels of harm-avoidance and lower levels of self-directedness and cooperativeness than their healthy sisters (Our findings indicate that EDs are complex genetic disorders of multi-factorial aetiology, where liability may result from the accumulation of psychosocial risk factors that trigger the illness in genetically vulnerable individuals.Understanding and Treating Eating Pathology stream of the 2013 ANZAED Conference.This abstract was presented in the"} +{"text": "Oncorhynchus mykiss) to investigate the influence of genotype and developmental stage on genetic responses (i.e. dominant vs. recessive) and specific physiological pathways.Release of domesticated strains of fish into nature may pose a threat to wild populations with respect to their evolved genetic structure and fitness. Understanding alterations that have occurred in both physiology and genetics as a consequence of domestication can assist in evaluating the risks posed by introgression of domesticated genomes into wild genetic backgrounds, however the molecular causes of these consequences are currently poorly defined. The present study has examined levels of mRNA in fast-growing pure domesticated (D), slow-growing age-matched pure wild (Wa), slow-growing size-matched pure wild (Ws), and first generation hybrid cross (W/D) rainbow trout (Highly significant differences in mRNA levels were found between domesticated and wild-type rainbow trout genotypes (321 mRNAs), with many mRNAs in the wild-domesticated hybrid progeny showing intermediate levels. Differences were also found between age-matched and size-matched wild-type trout groups (64 mRNAs), with unique mRNA differences for each of the wild-type groups when compared to domesticated trout , illustrating an influence of fish developmental stage affecting findings when used as comparator groups to other genotypes. Analysis of differentially expressed mRNAs (found for both wild-type trout to domesticated comparisons) among the genotypes indicates that 34.8% are regulated consistent with an additive genetic model, whereas 39.1% and 26.1% show a recessive or dominant mode of regulation, respectively. These molecular data are largely consistent with phenotypic data assessed in domesticated and wild trout strains.The present molecular data are concordant with domestication having clearly altered rainbow trout genomes and consequent phenotype from that of native wild populations. Although mainly additive responses were noted in hybrid progeny, the prevalence of dominant and non-additive responses reveals that introgression of domesticated and wild genotypes alters the type of genetic control of mRNA levels from that of wild-type, which may lead to disruption of gene regulation systems important for developing phenotypes for optimal fitness in nature. A clear influence of both fish age and size on mRNA levels was also noted in this study, which highlights the importance of examining multiple control samples to provide a comprehensive understanding of changes observed between strains possessing differences in growth rate. Domestication is a natural process that occurs in organisms subjected to rearing in animal husbandry, horticulture and aquaculture, adapting them to artificial environmental conditions which differ from those their progenitor wild strains evolved within. Domestication is often coupled with selective breeding to further accentuate desired phenotypic traits such as enhanced growth rate -3. Salmosp with GEO platform accession number [GSE45151].The data set supporting the results of this article is available in Gene Expression Omnibus (GEO) repository [GEO; The authors declare that they have no competing interest.SLW wrote the manuscript and performed all bioinformatics and statistical analysis. DS produced the British Columbia family crosses and conducted all microarray hybridizations. RHD, RGD and SLW were involved in the design of the study and data interpretation. All authors read and commented on the manuscript.Significant mRNA entity list (including replicate mRNAs) of domesticated relative to age-matched wild-type rainbow trout .Click here for fileSignificant mRNA entity list (including replicate mRNAs) of domesticated relative to size-matched wild-type rainbow trout .Click here for fileSignificant mRNA entity list (including replicate mRNAs) of wild-domesticated relative to domesticated rainbow trout .Click here for fileSignificant mRNA entity list (including replicate mRNAs) of wild-domesticated relative to age-matched wild-type rainbow trout .Click here for fileSignificant mRNA entity list (including replicate mRNAs) of wild-domesticated relative to size-matched wild-type rainbow trout .Click here for fileSignificant mRNA entity list (including replicate mRNAs) of age-matched wild relative to size-matched wild-type rainbow trout .Click here for fileP \u2264 0.01 with fold change of \u2265 2. Bar chart shows the amount of up-regulated and down-regulated mRNAs found in each group pairing of fast-growing domesticated (D), slow-growing age-matched wild (Wa), slow-growing size-matched wild (Ws), and first generation hybrid cross (W/D) rainbow trout.Significant differences found in mRNA levels between group pairings as determine by ANOVA Click here for filePhysiological pathways found significant in pairings of domesticated (D) and wild-domesticated (W/D) relative to either age- (Wa) or size-matched (Ws) trout populations. S2a.) the physiological pathways up- or down-regulated, unique to D relative to Wa (blue) or Ws (red). S2b.) the physiological pathways up- or down-regulated in W/D relative to Wa (blue), Ws (red) and D (grey) populations.Click here for file"} +{"text": "Motivation: Experimental spatial proteomics, i.e. the high-throughput assignment of proteins to sub-cellular compartments based on quantitative proteomics data, promises to shed new light on many biological processes given adequate computational tools.Results: Here we present pRoloc, a complete infrastructure to support and guide the sound analysis of quantitative mass-spectrometry-based spatial proteomics data. It provides functionality for unsupervised and supervised machine learning for data exploration and protein classification and novelty detection to identify new putative sub-cellular clusters. The software builds upon existing infrastructure for data management and data processing.Availability:pRoloc is implemented in the R language and available under an open-source license from the Bioconductor project (http://www.bioconductor.org/). A vignette with a complete tutorial describing data import/export and analysis is included in the package. Test data is available in the companion package pRolocdata.Contact:lg390@cam.ac.uk The software includes state-of-the-art statistical machine-learning algorithms and bundles them in a consistent framework, accommodating any experimental designs and quantitation strategies.Knowledge of the spatial distribution of proteins is of critical importance to elucidate their role and refine our understanding of cellular processes. Mis-localization of proteins have been associated with cellular dysfunction and disease states clustering, (ii) novelty detection and (iii) classification are proposed along with visualization functionalities. package for dataThe unsupervised machine-learning techniques are used, among other aims, as exploration and quality control tools. Several critical factors such as feature-level quantitation values, the extent of missing values and organelle markers can be overlaid on the data clusters as effective data exploration and quality control.pRoloc provides the implementation for the phenoDisco novelty detection algorithm , can be used for the classification using the SVM algorithm (with a Gaussian kernel). The algorithms parameters are first optimized and then subsequently applied in the actual classification. Finally, the plot2D function is used to generate an annotated scatter plot along the two first principal components (library(pRoloc)library(pRolocdata)data(dunkley2006)res <- phenoDisco(dunkley2006)p <- svmOptimisationres <- svmClassificationplot2DA typical pipeline is summarized below using data from mponents .libraryR and Bioconductor ; BBSRC Tools and Resources Development Fund (Award BB/K00137X/1); Prospectom project .Conflict of Interest: none declared."} +{"text": "Understanding where mutant CFTR is localised in airway epithelia is essential in guiding the best therapeutic approach to correct the dysfunction of the CFTR protein. The widely held paradigm is that CF patients harbouring the commonest mutation, CFTR-delF508, trap CFTR within the endoplasmic reticulum and target it for degradation. However there are conflicting reports concerning expression and localisation of CFTR-delF508 in lung tissue. To attempt to resolve this fundamental issue we developed a novel approach to measure CFTR-delF508 in the lower airways of patients who have undergone lung transplantation for advanced CF. By sampling CF and non-CF epithelium simultaneously from the same individual, confounding factors of different airway microenvironments which may have influenced previous observations can be overcome.Epithelia sampled by bronchial brushing above (CF) and below (non-CF) the bronchial anastomosis were stained for CFTR and the localisation and level of expression assessed (n\u200a=\u200a12).There was no significant difference in the proportion of tall columnar cells showing CFTR immunostaining as a discrete band at the apical membrane in cells harbouring the CFTR-delF508 mutation compared to non-CF cells . However, the amount of CFTR expressed at the apical surface was reduced by \u223c50% in CF cells compared to non-CF cells .Our novel observation challenges the prevailing paradigm that CFTR is essentially absent from the apical membrane of respiratory cells harbouring the CFTR-delF508 mutation. Moreover, it raises the possibility that the new generation of CFTR potentiators may offer a realistic therapeutic option for CF patients. Cystic Fibrosis (CF) is the most common autosomal recessive disease in Caucasians and the most common heritable cause of death during teenage and young adulthood in-vivo. However, the sensitivity of CFTR to its microenvironment and the difficulties in accurately localising it has led to conflicting reports and suggestions that localisation might differ between tissues The mislocalisation of CFTR has been observed in epithelial tissues from the lung To investigate CFTR localisation in the lower airway, we developed a novel approach of sampling the lower respiratory tract epithelia in CF patients who have undergone lung transplantation. This approach allows both non-CF cells and cells carrying the CFTR-delF508 mutation to be obtained from the same airway microenvironment simultaneously. This approach overcomes many of the significant limitations of previous studies, and may provide a possible testing ground for novel therapies.The Newcastle and North Tyneside Local Regional Ethics Committee approved the study (REC reference no 2001/179), and written informed consent was obtained from each subject.Bronchial brushings were obtained using a protected specimen single-sheathed nylon cytology brush from at least 2 cm above the airway anastomosis in the left main bronchus and at least 2 cm below the airway anastomosis in the segmental bronchus of the left lower lobe. Brushings were obtained from twelve (8F\u22364M) lung transplant recipients between 79 and 357 days post bilateral lung transplantation for advanced CF lung disease. Standard immnuosuppression protocol after transplantation comprises a calcineurin inhibitor (ciclosporin/tacrolimus), a cell cycle inhibitor (azathioprine/mycophenolate mofetil) and oral corticosteroids (maintenance dose 0.1 mg/kg). All subjects showed no evidence of infection or acute or chronic rejection (grade A2 or above (ISHLT classification) and were bronchiolitis obliterans syndrome stage 0 (FEV1 >90% of baseline)).xl Genetic Analyser and data analysed using Genemapper v3.7 (Applied Biosystems).See Cells isolated by bronchial brushing were smeared onto microscope slides and fixed with 4% paraformaldehyde. Cells were incubated with either MATG1061 (RD-Biotech), 570 (raised against amino acids 731\u2013742 in the R-domain) or 596 (raised against amino acids 1204\u20131211 in nucleotide binding domain 2) (both Cystic Fibrosis Foundation) anti-CFTR monoclonal antibodies and anti-Interferon regulatory factor-1 (IRF-1 - Santa Cruz) or anti-\u03b2-tubulin polyclonal antibodies (Sigma). Antigen-antibody complexes were detected using appropriate flourochrome-linked secondary antibodies with DAPI as a nuclear counterstain. Laser settings for each patient were optimised using the non-CF cells and the same settings used to compare CFTR expression in the CFTR-delF508 cells. Images acquired using a Leica TCS-SP-2UV laser scanning confocal microscope. Isotype matched immunoglobulins were employed as negative controls.The percentage of tall columnar epithelial (TCE) cells expressing CFTR as a distinct apical band was examined in multiple randomly selected fields and compared above and below the airway anastomosis from each individual. Patients with <100 cells were excluded. Results were validated by counts from two blinded individuals. Total and average pixel intensity of CFTR staining was quantified using Photoshop CS3 (Adobe) in multiple randomly selected fields and compared above and below the airway anastomosis from each individual. At least 20 cells/sample were assessed. The difference between groups was assessed by a one way ANOVA using SPSS 14.0. Differences with a p-value of <0.05 were considered statistically significant.Normal control tissue was obtained from unused donor lungs. Lung samples were fixed in 10% formalin, embedded, sectioned and stained with antibodies against E-cadherin (BD Bioscience) and CFTR (RD-Biotech). Antibodies were detected using appropriate flourochrome-linked secondary antibodies with DAPI as a nuclear counterstain. Areas of intact epithelium were identified and images acquired using a LSM 510 laser scanning confocal microscope. Isotype matched immunoglobulins were employed as negative controls.To investigate CFTR expression in both non-CF and CF cells from the lower airway in the same individual, epithelia were sampled by bronchial brushing from above (CFTR-delF508 mutation) and below (non-CF) the airway anastomosis joining the native bronchus and the transplanted lung . Cells fnd mutations on CFTR localisation/expression levels. Furthermore, due to the limited number of CF patients who undergo transplantation it would be extremely difficult to generate sufficient data sets to achieve significance using any individual second mutation.To quantify the number of non-CF and CF TCE cells expressing CFTR at the apical pole we collected data from at least 100 cells/sample, and the number of CFTR positive cells was quantified by two blinded observers. An example of a typical image is shown in Consequently we analysed the results from CFTR-delF508 homozygous patients alone. Again, there was no significant difference in the percentage of TCE cells expressing apical CFTR above and below the airway anastomosis . These rTo confirm the results above with the MATG1061 antibody we proceeded to compare the number of non-CF and CF TCE cells expressing CFTR at the apical pole with 2 further well characterised per se, but the mutation does markedly reduce the quantity of protein localised to the membrane.The finding that CFTR was detected in the same proportion of non-CF and CF lower airway cells was unexpected since impaired trafficking of CFTR-delF508 is thought to be the hallmark of CF in airway epithelial cells via the endoplasmic reticulum-associated degradation pathway (ERAD) in vitro studies in cells expressing exogenous mutant CFTR as well as CFTR localisation studies in both fixed excised lung tissue and cultured nasal epithelium in vivo in CF patients, and uncertainty exists as to the relation of CFTR expression in the upper and lower airway. We therefore developed a novel approach which overcomes these problems to assess CFTR localisation in lower airway epithelial cells from patients who have undergone lung transplantation for advanced CF.The rationale for developing gene therapy and small molecule drug corrector approaches to treat CF lung disease is the reported absence of CFTR from the apical membrane of airway epithelium in the commonest mutation, CFTR-delF508. This is believed to occur due to inefficient biosynthetic maturation of the mutant protein and its rapid degradation Cells brushed from above the bronchial anastomosis in CFTR-delF508 homozygous individuals were confirmed to be 100% CFTR-delF508 homozygous and those from below were confirmed non-CF. We found no significant difference in the percentage of TCE cells expressing apical CFTR when sampled from below (non-CF) and above (CFTR-delF508) the airway anastomosis. However, apical CFTR staining showed a significant reduction in both average and total pixel intensity in CFTR-delF508 affected cells compared to non-CF cells. This suggests that, when TCE cells are isolated from the same airway microenvironment, an equal proportion of CFTR-delF508 and non-CF cells express CFTR at the apical membrane. In contrast to some previous reports, the quantity of CFTR expressed at the apical membrane of TCE cells was the only distinguishing feature in the lower airway.et al also found indistinguishable levels of CFTR expression in pseudostratified columnar epithelium covering nasal polyps, and in submucosal glands of nasal polyps et al found no evidence of CFTR protein expression in the bronchial surface epithelium, apart from localised expression in a small number of flask-like cells et al found no evidence of expression of CFTR-delF508 CFTR in TCE cells of human bronchial cryosections obtained from homozygous individuals despite detecting CFTR expression in the same cells from non-CF tissue There have been conflicting reports regarding CFTR expression in excised native airway tissues. Using the same antibody as in the present study, frozen sections of excised nasal polyps were shown to express CFTR predominantly in the apical membrane and sub-membranous compartment of ciliated epithelial cells. This pattern of expression was also seen in CFTR-delF508 homozygous tissues, but with additional accumulation along the basolateral and mitochondrial membranes et al. found CFTR to be localised mainly in the apical region of ciliated and non-ciliated TCE cells et al. confirmed these findings using a panel of 7 anti-CFTR antibodies and a range of processing and fixation techniques et al found a distinct peri-nuclear staining in TCE cells obtained by nasal brushing from CFTR-delF508 homozygous individuals, and similar proportional expression of apical CFTR from CF/non-CF individuals et al. using the same antibody and fixation technique Studies utilising detached airway epithelial cells, in particular nasal epithelial cells, have generally demonstrated identifiable differences in CFTR expression between CFTR-delF508 homozygous and non-CF individuals. Penque A possible alternative explanation for our findings is that the particular microenvironment in the transplanted lung may correct the CFTR-delF508 trafficking defect. Pharmacological therapy is common in the lung transplant recipient, particularly the use of various immunosuppressants, and this may affect CFTR maturation and trafficking. Ciclosporin has been demonstrated to correct processing mutations of other ATP-binding cassette proteins, particularly P-glycoprotein, but failed to demonstrate any such effect in cell lines expressing CFTR-delF508 Our novel observation challenges the prevailing paradigm that CFTR is essentially absent from the apical membrane of respiratory cells in CF patients harbouring the CFTR-delF508 mutation. Instead these data suggest that CFTR is widely expressed at the apical membrane in epithelial cells from the lower airway but at a significantly reduced level compared to non-CF cells. This raises the exciting possibility that the new generation of drugs which potentiate mutant CFTR activity Figure S1Comparison of CFTR localisation using 3 different CFTR antibodies. Bronchial brushings of non-CF and CF cells were stained for CFTR ) - FITC/Green) and IRF-1 (TRITC/Red) with a nuclear counter stain (DAPI/Blue). CFTR is localised predominantly to the apical membrane of tall columnar epithelial cells in both non-CF and CF cells for all 3 antibodies tested. Images acquired on a Leica confocal microscope (\u00d720 magnification).(TIF)Click here for additional data file.Supporting Information S1Supplementary Material and Methods.(DOCX)Click here for additional data file."} +{"text": "Feline immunodeficiency virus (FIV) is a widespread pathogen of the domestic cat and an important animal model for human immunodeficiency virus (HIV) research. In contrast to HIV, only limited information is available on the transcriptional host cell response to FIV infections. This study aims to identify FIV-induced gene expression changes in feline T-cells during the early phase of the infection. Illumina RNA-sequencing (RNA-seq) was used identify differentially expressed genes (DEGs) at 24\u00a0h after FIV infection.After removal of low-quality reads, the remaining sequencing data were mapped against the cat genome and the numbers of mapping reads were counted for each gene. Regulated genes were identified through the comparison of FIV and mock-infected data sets. After statistical analysis and the removal of genes with insufficient coverage, we detected a total of 69 significantly DEGs (44 up- and 25 down-regulated genes) upon FIV infection. The results obtained by RNA-seq were validated by reverse transcription qPCR analysis for 10 genes.Out of the most distinct DEGs identified in this study, several genes are already known to interact with HIV in humans, indicating comparable effects of both viruses on the host cell gene expression and furthermore, highlighting the importance of FIV as a model system for HIV. In addition, a set of new genes not previously linked to virus infections could be identified. The provided list of virus-induced genes may represent useful information for future studies focusing on the molecular mechanisms of virus-host interactions in FIV pathogenesis. However, HIV encodes four additional accessory genes not present in FIV: vpr, vpu, tat and nef. In contrast, the orf-A gene can be found uniquely in FIV. Despite these differences on the genome level, FIV induced pathogeneses display striking similarities to human AIDS under accession number E-MTAB-2083.Cellular RNA was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research) including an on-column DNase I digestion for the removal of gDNA. RNA quality control was performed by capillary electrophoretic separation of the samples on the Agilent 2100 Bioanalyzer and subsequent estimation of RNA integrity numbers. 1\u00a0\u03bcg of total RNA were used as the starting material for the preparation of cDNA libraries utilizing the TruSeq RNA Sample Prep Kit v2 following the recommended protocol. Sequencing was performed on a Genome Analyzer IIx instrument (Illumina) with reagents taken from the TruSeq SR Cluster Kit v5 and TruSeq SBS Kit v5 (Illumina). The lengths of the generated sequencing reads were 37\u00a0bp. The raw sequencing data are available in the ArrayExpress database [ftp://ftp.ensembl.org/pub/release-72/genbank/felis_catus/] and the FIV Petaluma genome (Genbank: M25381) using the QSeq v5 analysis software implementing the default options for Illumina short reads (matching of a minimum of 20 bases and at least 80% of bases within each read). The numbers of raw reads mapping to annotated genes on the genome reference were counted and fold changes were calculated by comparing the mean values of four FIV infected samples to four control samples. P-values (Student\u2019s t-test) were calculated in QSeq v5 and adjusted according to the Benjamini-Hochberg method under accession number E-MTAB-2083.The RNA-sequencing reads reported in this paper have been deposited in the ArrayExpress database [DEGs: Differentially expressed genes; FIV: Feline immunodeficiency virus; HIV: Human immunodeficiency virus; hpi: Hours post infection; IFN: Interferon; MOI: Multiplicity of infection; qPCR: Quantitative PCR; RNA-seq: RNA-sequencing; RPKM: Reads per kilobase per million mapped reads; RT-qPCR: Reverse transcription quantitative PCR.The authors declare that they have no competing interests.RE and DK conceived and designed the experiments. RE performed the experiments, analyzed the data and wrote the manuscript. All authors edited and approved the final manuscript.2) represent the mean values of four replicate samples. P-values were adjusted according to the Benjamini-Hochberg method.List of differentially expressed genes in FIV infected T-cells at 24 hpi as detected by RNA-seq analysis. Fold changes refer to mock-infected cells. Read counts (logClick here for filePrimers used for quantitative PCR.Click here for file"} +{"text": "Conclusion: IDLVs provide an attractive platform for the tolerogenic expression of intracellular or secreted proteins in the liver with a substantially reduced risk of insertional mutagenesis. Lentiviral vectors are attractive tools for liver-directed gene therapy because of their capacity for stable gene expression and the lack of preexisting immunity in most human subjects. However, the use of integrating vectors may raise some concerns about the potential risk of insertional mutagenesis. Here we investigated liver gene transfer by integrase-defective lentiviral vectors (IDLVs) containing an inactivating mutation in the integrase (D64V). Hepatocyte-targeted expression using IDLVs resulted in the sustained and robust induction of immune tolerance to both intracellular and secreted proteins, despite the reduced transgene expression levels in comparison with their integrase-competent vector counterparts. IDLV-mediated and hepatocyte-targeted coagulation factor IX (FIX) expression prevented the induction of neutralizing antibodies to FIX even after antigen rechallenge in hemophilia B mice and accounted for relatively prolonged therapeutic FIX expression levels. Upon the delivery of intracellular model antigens, hepatocyte-targeted IDLVs induced transgene-specific regulatory T cells that contributed to the observed immune tolerance. Deep sequencing of IDLV-transduced livers showed only rare genomic integrations that had no preference for gene coding regions and occurred mostly by a mechanism inconsistent with residual integrase activity. Liver-directed gene therapy has the potential to treat metabolic diseases and plasma protein deficiencies, including hemophilia.8In previous studies, we showed that immune tolerance induction with LVs is dependent on stringent targeting of transgene expression to hepatocytes, which can be achieved by a combination of transcriptional and posttranscriptional microRNA-based regulation.8Although these studies have demonstrated the feasibility of gene replacement therapy and immune tolerance induction with LVs, concerns remain about the potential long-term adverse effects of vector integration due to insertional mutagenesis. Although advanced LV design potentially reduces this risk,2- to 103-fold) without compromising other steps in the transduction pathway and was thus adopted for this study.Integrase-defective lentiviral vectors (IDLVs) are typically generated by the packaging of the vector with catalytically inactive human immunodeficiency virus (HIV) integrase.Plasmids pCCLsin.cPPT.ET. cFIX.142T, pCCLsin.cPPT.PGK.OVA, and pCC Lsin.cPPT.ET.OVA.142T were constructed with standard cloning techniques. Details are available upon request.Green fluorescent protein (GFP)\u2013expressing integrase-competent lentiviral vectors (ICLVs) and IDLVs were administered to 7-week-old female BALB/c mice by tail vein injection. Six-week-old female and male C57BL/6 FIX-knockout mice were injected intravenously on 2 consecutive days with a total p24 dose of 260 \u03bcg (2 \u00d7 500 \u03bcL) in FIX-expressing ICLVs or IDLVs supplemented with 40 mg/mL polybrene. For 70% partial hepatectomy, mice were anesthetized with isoflurane. Liver sections were snap-frozen for genomic DNA extraction . FIX activity in citrated plasma was quantified according to the manufacturer's instructions with normal dog plasma as a reference (detection limit > 0.1%). All animal experiments were approved by the Animal Ethics Committee of the University of Leuven or the San Raffaele Institutional Animal Care and Use Committee (321).To analyze ICLV and IDLV integration, we used standard and nonrestrictive, 5\u2032-long terminal repeat (5\u2032-LTR)\u2013mediated and 3\u2032-LTR\u2013mediated linear amplification\u2013mediated polymerase chain reaction (LAM-PCR) as previously described.22Further details can be found in the Supporting Information.in vitro. To drive transgene expression, we used a hepatocyte-specific chimeric promoter (designated as ET).ad hoc quantitative polymerase chain reaction (PCR) that selectively amplified the reverse-transcribed vector genome and discriminated it from plasmid DNA, which was carried over from the transfection used to produce the vectors (Supporting Information + cells and the mean fluorescent intensity (MFI) of GFP were lower in IDLV-transduced cells versus ICLV-transduced cells , and this indicated less efficient expression from the former vector. Analysis of the same cultures 2 weeks after transduction showed a nearly complete loss of vector genomes and GFP+ cells in the IDLV-transduced cells, as expected for an episomal form.We generated GFP-expressing LVs with either integrase-defective (IDLV) or integrase-competent (ICLV) packaging constructs and compared their transduction efficiency and transgene expression levels in human cell lines and primary hepatocytes We then tested the same vectors on human primary hepatocytes, which do not proliferate in culture, and showed that IDLVs attained similar levels of transduced vector genomes vector copy number (VCN) 1 week after transduction but expressed GFP at substantially lower levels in comparison with matched doses of ICLVs n = 2; . Overallin vivo, we injected increasing doses of GFP-expressing IDLVs (ET.GFP.142T) intravenously into adult mice and measured GFP expression in hepatocytes and vector DNA contents in the liver 5 weeks post-injection of GFP-expressing IDLVs and ICLVs (ET.GFP.142T) intravenously to adult mice (n = 20 for IDLV mice and n = 4 for ICLV mice in three independent experiments) and measured GFP expression and vector DNA contents in the liver at different times post-injection (+ hepatocytes and the vector content progressively decreased with increasingly longer times post-injection for the IDLV-treated groups.To ascertain that IDLVs could be used to transduce hepatocytes njection . A vectonjection . One weede novo induction of hepatocyte proliferation (data not shown). In the recovering mice, FIX levels remained comparable to those measured before hepatectomy in the ICLV-treated group of IDLV- or ICLV-expressing canine FIX complementary DNA (ET.FIX.142T) to adult hemophilia B mice . We then applied nonrestrictive and standard, 5\u2032- and 3\u2032-LTR\u2013mediated LAM-PCR strategiesBecause the D64V mutation reduces LV integration by 2 to 3 log see also ,13 low-lP < 10\u22129) with an almost 100-fold lower frequency of retrieval nuclear B2 repeat sequences that are scattered throughout the mouse genome increased in the liver after treatment with both IDLV types 3 weeks after vector administration; however, the ratio of Tregs to CD8+ effector cells was much higher in the mice treated with miR-142-regulated vector than in control vector treated mice and secondary challenges (intramuscular plasmid). In addition, residual levels of vector genomes and GFP expression were still detectable in the livers of mice previously treated with IDLV.142T after rechallenge were, therefore, first transduced with hepatocyte-targeted ICLVs (ET.GFP.142T) to obtain robust GFP expression in hepatocytes. A pool of splenocytes and liver lymphocytes derived from naive, control IDLV-treated or IDLV.142T-treated animals was transferred 1 month later. Although comparable amounts of GFP-expressing hepatocytes were detected in the mice reconstituted with naive cells or cells derived from tolerant (IDLV.142T-treated) mice, a complete clearance of GFP+ hepatocytes was observed in recipient mice reconstituted with cells derived from control, unregulated IDLV-treated mice, and this was accompanied by a loss of vector DNA. These results indicate that only those cells derived from control mice exhibited the full effector potential upon adoptive transfer, whereas the effector cells derived from tolerized mice (IDLV.142T-treated) were kept in check by the induced regulatory compartment. Taken together, these data indicate that GFP-specific immunological tolerance was established.To further confirm that IDLV.142T is able to direct the immune system toward the induction of immune tolerance to transgene antigens, we reconstituted immune-deficient recipients through the adoptive transfer of immune cells derived from either immunized (IDLV-treated) or tolerized (IDLV.142T-treated) mice . Rag2\u2212/\u2212To assess whether immune tolerance could be induced by IDLVs toward a therapeutically relevant secreted antigen, we evaluated the anti-FIX immune response in hemophilic mice treated with FIX-encoding IDLV.142T. Activated partial thromboplastin time (aPTT)\u2013based Bethesda assays showed no anti-FIX inhibitory activity . Importa+FOXP3\u2212 T cells into FOXP3+ Tregs was evaluated. To this end, we adoptively transferred naive CD4+ T cells obtained from double-transgenic mice for an OVA-specific T cell receptor and a GFP reporter knock-in downstream of the Foxp3 promoter. OTII CD4+ FOXP3-GFP Ly5.2 T cells were isolated, FACS-sorted to deplete FOXP3+ cells, and adoptively transferred into naive Ly5.1 recipient mice before the injection of OVA-encoding IDLVs or IDLV.142T and model antigens (GFP and OVA), by IDLVs can result in a state of transgene-specific immunological tolerance due to a strong contraction of the transgene-specific effector compartment and the induction of the transgene-specific regulatory compartment.IDLVs are emerging as an attractive platform for transgene expression for several purposes.The declining transgene expression of IDLVs in proliferating cells has been mostly ascribed to the progressive loss of episomal DNA from the cell nucleus during mitosis versus the stably integrated provirus of ICLVs. Here, we have reliably quantified the contents of reverse-transcribed vector genomes and the transgene expression level in transduced dividing or quiescent cells, and we have shown that the expression efficiency per genome copy is significantly lower for IDLVs versus ICLVs in hepatocytes. This may be due to diffusion of the episomes to nuclear areas that are not involved in active transcription, inefficient chromatin deposition, or enrichment with histone modifications typical of transcriptionally silenced chromatin.in vivo expression is mostly mediated by the episomal forms.We have shown that IDLV background integration occurs by mechanisms incompatible with residual activity of the mutant integrase because they often present deletions in the LTR ends and lack the typical flanking genomic repeats at the insertion site. These events may be mediated by nonhomologous end joining of linear episomes to sites of chromosomal breakage.The significantly lower expression of IDLVs versus ICLVs represents a limiting factor for their application to stable therapeutic gene replacement in the liver, at least in the current design. However, IDLVs may be considered whenever reversible gene transfer is preferable , especially if the clinical setting imposes high safety bars in the face of existing treatment options or the biological effects of gene-based delivery are difficult to predict or may entail substantial toxicity. Here we demonstrate the therapeutic potential of inducing a prolonged window of FIX expression in the plasma of hemophilic mice. Apparently, FIX expression was more prolonged than GFP expression after hepatic transduction with IDLVs. This possibly reflects the higher vector doses and/or differences in the detection limits of the assays used to quantify the expression of the respective transgene products. IDLVs may also be used for hepatic expression of therapeutic proteins, such as interferon (IFN) and other cytokines, in chronic viral hepatitis or hepatic tumors; gene-based delivery may provide therapeutic concentrations of the factor at the disease site with limited systemic exposure and only for a defined window of time.27in vivo induction of antigen-specific Tregs by microRNA-regulated IDLVs may well represent their most attractive feature to date, and it provides an intriguing contrast to the immunogenic nature of unregulated IDLV delivery, which is currently being explored for the design of improved virus-based vaccines.Hepatic gene transfer has been associated with the induction of immunological tolerance to the transgene product with several vector platforms.A broad application of hepatocyte-targeted expression by ICLVs for immune modulation is currently limited by the concerns associated with integration in the target cell genome. IDLVs are advantageous for this purpose and could be exploited in inverse vaccination strategies to tolerize individuals to protein replacement or gene therapies and prevent the development of autoimmune disease in at-risk individuals."} +{"text": "Caenorhabditis elegans (C. elegans) is comprised of 302 sensory, motor and inter-neurons. Near-complete connectivity data for the gap junctions and chemical synapses connecting these neurons (its connectome) have been resolved [+ action potentials in C. elegans neurons [The neuronal network of the nematode resolved . In addicomputationally relating the sensory input with the resultant dynamical behavior of the inter- and motor-neurons. Figure Our study combines the known connectome data with a p"} +{"text": "Chlamydia trachomatis is a major cause of sexually transmitted disease in humans. Previous studies in both humans and animal models of chlamydial genital tract infection have suggested that the hormonal status of the genital tract epithelium at the time of exposure can influence the outcome of the chlamydial infection. We performed a whole genome transcriptional profiling study of C. trachomatis infection in ECC-1 cells under progesterone or estradiol treatment.omcB, trpB, cydA, cydB, pyk and yggV), which suggest a stress response similar to that reported previously in other models of chlamydial persistence. We also observed morphological changes consistent with a persistence response. By comparison, progesterone supplementation resulted in a general up-regulation of an energy utilising response.Both hormone treatments caused a significant shift in the sub-set of genes expressed . Overall, estradiol treatment resulted in the down-regulation of 151 genes, including those associated with lipid and nucleotide metabolism. Of particular interest was the up-regulation in estradiol-supplemented cultures of six genes (Our data shows for the first time, that the treatment of chlamydial host cells with key reproductive hormones such as progesterone and estradiol, results in significantly altered chlamydial gene expression profiles. It is likely that these chlamydial expression patterns are survival responses, evolved by the pathogen to enable it to overcome the host's innate immune response. The induction of chlamydial persistence is probably a key component of this survival response. Chlamydia trachomatis is an obligate intracellular bacterial pathogen that infects the genital and ocular mucosa of humans causing sexually transmitted disease and trachoma respectively. In 2010 the World Health Organization reported 140 million cases of C. trachomatis infections occurred worldwide , UDP-N-acetylmuramoylalanine-D-glutamate ligase, putative (murC/ddlA) [9.31 fold], V-type ATPase, subunit D, putative (atpD) [10.23 fold], arginine transport system substrate-binding protein (artJ) [10.96 fold], and putative glycerol-3-phosphate acyltransferase (plsX) [16.53 fold]. In addition, the five genes that showed the largest down-regulation of mRNA expression profile include cell division protein FtsI (pbp3) [35.54 fold], nucleoside-triphosphatase (yggV) [31.84 fold], ribonucleoside-diphosphate reductase alpha chain (nrdA) [30.06 fold], GTP-dependent nucleic acid-binding protein (ychF) [21.29 fold], and succinate dehydrogenase iron-sulfur subunit (sdhB) [18.82 fold].In the estradiol-exposed cultures, 151 genes were down-regulated more than 2-fold, while 63 genes were up-regulated more than 2-fold during the same period. Of these 213 altered genes, more than 52% were hypothetical proteins, with no known homologues outside the chlamydiae. Even though nearly 30% of the chlamydial genome is composed of hypothetical genes, the fact that 52% of these genes altered their expression by more than 2-fold in response to estradiol exposure suggests that many of the key changes are uniquely associated with http://www.genome.jp/kegg/pathway.html, using the known or predicted chlamydial pathway information, some clustering of transcriptional responses was evident . Estradiol also resulted in a marked down-regulation of the genes involved in chlamydial nucleotide (purine and pyrimidine) metabolism . In addition, we also observed a more minor down-regulation in cofactor and vitamin metabolism pathways .When the up- and down-regulated genes were input into the KEGG Pathway database nt Table . EstradiTaken together, this overall down-regulation of key pathways is suggestive of a persistence phenotype. The normal chlamydial developmental cycle can be altered under stressful conditions, leading to the formation of aberrant bodies (ABs) which are inhibited in their differentiation back to infectious EBs . MoleculomcB and trpB genes are currently the most reliable general markers of chlamydial persistence , the putative glycerol-3-phosphate acyltransferase (plsX) [16.17 fold], glucose inhibited division protein (lplA_2) [11.9 fold], NADH-quinone reductase complex (nqr2) [10.95 fold] and polynucleotide adenylyltransferase (pcnB_1) [10.75 fold]. In addition to these 85 genes, 135 chlamydial genes were observed to have a reduced gene expression profile in response to the presence of progesterone. The five top down regulated genes include exoribonuclease II (vacB) [67.96 fold], isopentenylpyrophosphate transferase (miaA) [33.91 fold], cysteinyl-tRNA synthetase (cysS) [33.64 fold], thioredoxin reductase (trxB) [33.44fold], and ribonucleotide-diphosphate reductase subunit alpha (nrdA) [29.25 fold]. 103 genes had unknown annotated functions .Overall, 85 chlamydial genes were observed to have two-fold or greater up-regulated gene expression levels in the presence of progesterone. The five top genes that were observed with this mRNA expression profile encode for proton or sodium-glutamate symport protein H and free-radicals. The association with the top five down-regulated genes appears to align with control at the transcriptional/translational level. For example, the gene encoding miaA and cysS have associated functions with translation, through transfer RNA molecules. nrdA plays an important role in nucleotide regeneration and our observation that expression of this gene was down 29-fold, suggests that one mechanism being employed by C. trachomatis is to reduce cellular multiplication.The progesterone-mediated response mounted by stradiol , and aftet al., manuscript submitted) we have analysed the host cell response to these hormones and have found a cascade of changes. It is likely therefore that the chlamydial transcriptome changes are in response to these host cell changes. It is known that hormones have a major effect on host cell innate immune pathways. For example, the expression of antimicrobial peptides such as human defensin 5 suggesting that the chlamydial changes may be in response to the altered host cell environment. In the present study we analysed the effects of either progesterone or estradiol separately. In reality, both hormones are continually present, but their levels fluctuate during the various stages of the estrous cycle. This hormonal cycling may have the effect of causing the chlamydiae to alternate between cycles of productive growth and cycles of persistence or dormancy. Given the 28 day duration of the human female menstrual cycle and the 2-3 day growth cycle of C. trachomatis, such cycling is a real possibility and may be of survival benefit to the chlamydiae.While these chlamydial transcriptome changes might be a direct result of the effect of the hormones on the chlamydiae it is likely that the major effects are indirect, via the host cells. As an intracellular pathogen, most of the chlamydial response to the hormones is most likely an indirect response to changes in the host cells. In a parallel study (Wan 5 (HD-5 ), lactof 5 C. trachomatis gene expression and (b) the type of inclusions that develop. In our experiments, evidence of long-term persistent chlamydial infections was observed. Collectively our data suggest that hormonal supplementation; estradiol in particular, may directly or indirectly play an important role in the development of chlamydial persistence. The data may help to explain why infections are more common in the estrogen-dominant phase of the menstrual cycle and suggest that estradiol favours the development of persistent infections that may allow Chlamydia to; (a) resist common antibiotic therapy and (b) survive the innate immune response to infection, thereby facilitating repeated reactivation of infection that drives damaging immunopathology.This is the first study to demonstrate transcriptional analysis of The authors declare that they have no competing interests.AA carried out the molecular genetic and microarray studies, participated in the microarray analysis and drafted the manuscript. CW designed microarray chip and participated in the microarray analysis. KB conceived the study and revised the manuscript critically for important intellectual content. JL participated in the cell culture and provided the initial samples. IS revised the manuscript critically for important intellectual content. PT participated in the design of the study, project coordination and helped to draft the manuscript. All authors read and approved the final manuscript."} +{"text": "Spina bifida aperta (SBA) is associated with shunt-dependent hydrocephalus and with meningomyelocele (MMC). Fetal endoscopic closure of the MMC may reduce shunt-dependency, but the benefit upon motor function in individual patients is still unclear. An increase in differentiated muscle ultrasound density (dMUD) provides an objective parameter for the extent of muscle damage caudal to the MMC. In this perspective, we aimed to compare dMUD and neurological function between SBA children treated by fetal endoscopic closure (fSBA) and by neonatal closure (nSBA) of the MMC.We included 12 [age- and (level of) MMC-] matched pairs of fSBA and nSBA children . All 12 fSBA patients were delivered by caesarean section, all 12 nSBA patients by vaginal delivery. To compensate for the effect by delivery mode, we also compared separate (age- and MMC-) matched pairs of nSBA children born by caesarean section and by vaginal delivery . Neurological parameters consisted of dMUD ; motor- and sensory function and shunt-dependent hydrocephalus and Chiari-II (C-II) malformation. fSBA and nSBA patients were treated at Bonn and Groningen/Cologne, respectively.dMUD was significantly lower in fSBA than nSBA . Assessment of motor and sensory function indicated a lower segmental spinal function in fSBA than nSBA . Shunt-dependent hydrocephalus appeared less frequent in fSBA than in nSBA , whereas the incidence of C-II malformation did not significantly differ between fSBA and nSBA . Comparing the neurological parameters between nSBA-SC and nSBA-VD revealed no significant differences.Assessment of dMUD and neurological function in fSBA and nSBA children indicates a moderately improved neuromuscular outcome in fSBA. It remains to be established by long-term functional and cognitive outcome parameters to determine whether the suggested neurological benefit is maintained and outweighs the risks of iatrogenic complications by the fetal endoscopic surgery."} +{"text": "The hierarchical growth of straight ZnO nanorods on the core-shell NWs eventually reduced the defect (green) emission and enhanced the near band edge (ultraviolet) emission of the ZnO.Silicon/zinc oxide (Si/ZnO) core-shell nanowires (NWs) were prepared on a p-type Si(111) substrate using a two-step growth process. First, indium seed-coated Si NWs (In/Si NWs) were synthesized using a plasma-assisted hot-wire chemical vapor deposition technique. This was then followed by the growth of a ZnO nanostructure shell layer using a vapor transport and condensation method. By varying the ZnO growth time from 0.5 to 2 h, different morphologies of ZnO nanostructures, such as ZnO nanoparticles, ZnO shell layer, and ZnO nanorods were grown on the In/Si NWs. The In seeds were believed to act as centers to attract the ZnO molecule vapors, further inducing the lateral growth of ZnO nanorods from the Si/ZnO core-shell NWs via a vapor-liquid-solid mechanism. The ZnO nanorods had a tendency to grow in the direction of [0001] as indicated by X-ray diffraction and high resolution transmission electron microscopy analyses. We showed that the Si/ZnO core-shell NWs exhibit a broad visible emission ranging from 400 to 750 nm due to the combination of emissions from oxygen vacancies in ZnO and In The Si/ZnO core-shell NWs revealed a broad range of PL at spectral range of 400 to 750 nm due to the combined emission of nanocrystallite Si, oxygen deficiency in InThe authors declare that they have no competing interests.SK carried out the experimental parts on the sample preparation and characterization and drafted the manuscript. CF and SA participated in the statistical analysis and revised the manuscript. All authors read and approved the final manuscript.a) FESEM image and (b) TEM micrograph of the newly grown ZnO NRs. (c) High magnification TEM micrographs of In seed-capped ZnO NRs. Figure S2. HRTEM micrograph of the amorphous In2O3 and ZnO interface enlarged from a TEM micrograph of an In seed-capped ZnO NR. The TEM micrograph of the In seed-capped ZnO NR is inserted in the figure.Initial growth stage of ZnO NRs on In/Si NWs. (Click here for file"} +{"text": "The organization of eukaryotic DNA into chromatin has a strong influence on the accessibility and regulation of genetic information. The locations and occupancies of a principle component of chromatin, nucleosomes, are typically assayed through use of enzymatic digestion with micrococcal nuclease (MNase). MNase is an endo-exo nuclease that preferentially digests naked DNA and the DNA in linkers between nucleosomes, thus enriching for nucleosome-associated DNA. To determine nucleosome organization genome-wide, DNA remaining from MNase digestion is sequenced using high-throughput sequencing technologies (MNase-seq). Unfortunately, the results of MNase-seq can vary dramatically due to technical differences and this confounds comparisons between MNase-seq experiments, such as examining condition-dependent chromatin organizations.In this study we use MNase digestion simulations to demonstrate how MNase-seq signals can vary for different nucleosome configuration when experiments are performed with different extents of MNase digestion. Signal variation in these simulations reveals an important DNA sampling bias that results from a neighborhood effect of MNase digestion techniques. The presence of this neighborhood effect ultimately confounds comparisons between different MNase-seq experiments. To address this issue we present a standardized chromatin preparation which controls for technical variance between MNase-based chromatin preparations and enables the collection of similarly sampled (matched) chromatin populations. Standardized preparation of chromatin includes a normalization step for DNA input into MNase digestions and close matching of the extent of digestion between each chromatin preparation using gel densitometry analysis. The protocol also includes directions for successful pairing with multiplex sequencing reactions.S. cerevisiae. Results from our matched preparation consistently produced MNase-seq datasets that were more closely correlated than other unstandardized approaches. Additionally, we validated the ability of our approach at enabling accurate downstream comparisons of chromatin structures, by comparing the specificity of detecting Tup1-dependent chromatin remodeling events in comparisons between matched and un-matched wild-type and tup1\u0394 MNase-seq datasets. Our matched MNase-seq datasets demonstrated a significant reduction in non-specific differences between experiments and were able to maximize the detection of biologically-relevant (Tup1-dependent) changes in chromatin structure.We validated our method by comparing the experiment-to-experiment variation between biological replicates of chromatin preparations from DNA-histone interactions are the first order of chromatin structure, and both the strength and locations of these interactions have significant influence on the accessibility and regulation of genetic information ,2. DNA-hSaccharomyces cerevisiae (baker\u2019s yeast) model was the first organism to have its chromatin mapped using MNase-seq, and it remains the most extensively studied model with dozens of MNase-seq datasets available today.Technical approaches to the measurement of chromatin structure generally consist of two phases: collection of DNA associated with a particular type of chromatin and characterization of the isolated nucleic acid pool . CollectS. cerevisiae by Weiner et al. and Xi et al. has demonstrated the presence of easily digested nucleosomes and/or other protein complexes present in the chromatin pool of under-digested nuclease preparations that were absent in preparations using greater digestion levels, \u0394h4-2[LEU2+]/pUK499) were prepared using our standardized protocol (matched digestions) including cross-linking and complete digestion of chromatin samples. Cells were fixed during log phase and asynchronized growth in rich media with galactose as the carbon source (YPG). All other MNase-seq datasets were downloaded from SRA and processed identically [Saccharomyces cerevisiae Genome Database using the Bowtie alignment algorithm allowing only unique matches with up to 2 mismatches. [tup1\u0394 datasets were calculated at 100-bp resolution in Microsoft ExcelTM.Biological replicates for Strain #1 and linker (15\u2009bp) DNAs sized according to the average sizes of a ng et al.. Additioerevisiae,32. Simuerevisiae. MNase cFollowing randomized cut distributions (i.e. simulated digestion), potential mono-nucleosomal DNA fragments (sized 115\u2009<\u2009bp >195) were then size-selected from the remaining fragment sizes in the entire chromatin template population and aligned to the template sequence for signal tabulation. This assumes that the entire length of each fragments was sequenced, the functional equivalent to a paired-end run, and bypasses the need for sequence tag extension which would introduce additional and unnecessary assumptions into our simulations. The count of aligned mono-nucleosome fragments was standardized between simulations to control for differences in fragment numbers between experiments and long linker sizes were defined as exceeding this range and extending to include sizes ~1.5X the size of an average nucleosome template (21\u2009<\u2009bp\u2009>\u2009221). The averaged MNase protection profiles in Figure\u2009Nucleosome configurations in Figure\u2009ng et al.. ReferenHanlon et al.[2 ratio) profiles were generated by ChIPOTle's sliding window approach [tup1\u0394 chromatin. The statistical significance of these values was tested by comparing the distribution of Tup1-binding values for dissimilar windows against the binding values for 10,000 random regions of chromatin, using a one-tailed heteroscedastic t-test.Tup1 binding data overlapping dissimilar chromatin regions was taken from ChIP-chip experiments by on et al.. Continuapproach . Averageapproach . Only reNone declared.JMR performed the experiments and analyses. JEB created the MNase digestion simulator used in the analysis. JMR and MJB designed the study and wrote the manuscript. All authors read and approved the final manuscript.Supplementary Protocol. Matched Micrococcal Nuclease Digestions.Click here for fileSupplemental Figure 1. Unmatched preparations show poor consistency in identifying changes in MNase protection signals. Supplemental Figure 2. Matched MNase digests identify biologically relevant differences in chromatin structure. Supplemental Figure 3. Comparison between wild-type and tup1? MNase-seq experiments at a single region of Tup1-dependent chromatin. Supplemental Figure 4. The ability of matched MNase digests to specifically detect biologically-relevant differences in chromatin structure is NOT dependent on dissimilarity cutoff values used in analysis. Supplemental Figure 5. MNase cut probability function for nucleosomal DNA templates. Supplemental Table 1: MNase-seq datasets used in this study.Click here for fileSupplemental Methods: Standardized MNase-seq Analysis.Click here for file"} +{"text": "Streptococcus pneumoniae but the mechanisms underlying this relationship are unclear. The objective of this study is to describe a comprehensive picture of the cellular interaction between the adhering bacteria and host cells in the presence or absence of a viral co-infection.Viral upper respiratory tract infections are associated with increased colonization by S. pneumoniae strain TIGR4 (serotype 4) in the presence of either mock- or viral-infected cells was analyzed by pneumococcal microarray. Significantly regulated genes were identified by both significance analysis of microarray (SAM) and a\u2009\u2265\u20092-fold change ratio cut-off. The adherence of S. pneumoniae to human pharyngeal cells was significantly augmented in the presence of RSV or HPIV3 infection. Global gene expression profiling of the host cells during infection with RSV or HPIV3 revealed increased transcription of carcinoembryonic antigen-related cell adhesion molecules (CEACAM1), CD47, fibronectin, interferon-stimulated genes and many other host cell adhesion molecules. Pneumococci increased transcription of several genes involved in adhesive functions , choline uptake and incorporation (lic operon), as well as transport and binding.Gene expression profiles of Detroit-562 pharyngeal cells, which were either mock-infected or infected with human respiratory syncytial virus (RSV) or human parainfluenza virus 3 (HPIV3), were analyzed using human microarrays. Transcription response of We have identified a core transcriptome that represents the basic machinery required for adherence of pneumococci to D562 cells infected or not infected with a virus. These bacterial genes and cell adhesion molecules can potentially be used to control pneumococcal adherence occurring secondary to a viral infection. Viruses play a pivotal role in modulating host cells, consequently mediating bacterial superinfection -8. Howevin vitro adhesion assays. This suggests separate or additional mechanisms of action that are independent of immune mechanisms. Studies of polymicrobial interactions have revealed that cellular receptors such as CD14, CD15, CD18, carcinoembryonic antigen-related cell adhesion molecule (CEACAM), macrophage receptor (MARCO), platelet-activating factor (PAFR), fibronectin (FN) and fimbriae-associated receptors are likely to be involved in increased bacterial adherence after viral infection and we have confirmed this observation with regard to HPIV3. CEACAM1 binds meningococcal and gonococcal opacity-associated (Opa) proteins and mediates internalization of the bacteria into several cell types in vitro. It alsoningitis .glnQ was highly up-regulated in TIGR4 in contact with virus-infected cells. The symmetry of these observations suggests that virus-induced up-regulation of fibronectin type III induced a reciprocal response in S. pneumoniae in the form of up-regulation of a ligand to match the newly up-regulated host receptor. This is a specific hypothesis worth pursuing in future functional experiments.Interestingly, the gene encoding a fibronectin type III domain-containing protein was up-regulated by the host in response to both viruses (significantly in RSV and moderately in HPIV3). In our pneumococcal gene expression studies, a fibronectin-binding gene, E. coli[Other genes that were significantly up-regulated in our study include several interferon-stimulated genes (ISGs) and the urokinase plasminogen activator (PLAU), which mediates a response to the inflammation induced by the virus. Induction of ISGs and NOD-like receptor family Table\u00a0 in our sE. coli. Up-reguS. pneumoniae to the host cells by a factor of 1.3-2.0; (c) infection with both RSV and HPIV3 enhanced the transcription of host cell adhesion molecules that facilitate or mediate bacterial adhesion in general; and (d) there is a core transcriptome (at least in the TIGR4 strain) that represents the basic machinery required for adherence of pneumococci to D562 cells regardless of whether the cell is infected with a virus or not. Further elucidation of these mechanisms is most likely to be obtained by specific inhibition of the expression of the host cell receptors or by bacterial gene knockout experiments.In summary, we have shown that: (a) D562 cells were permissive to RSV and HPIV3; (b) these viruses augmented the adherence of CEACAM: Carcinoembryonic antigen-related cell adhesion molecule; CPE: Cytopathic effect; D562 cells: Detroit 562 cells; FN: Fibronectin; HCL: Hierarchical clustering; HPIV3: Human parainfluenza virus 3; ISGs: Interferon-stimulated genes; MARCO: Macrophage receptor; NA: Neuraminidase; PAFR: Platelet-activating factor; RSV: Respiratory syncytial virus; SAM: Significance analysis of microarrays.JAGS reports receiving a grant from GlaxoSmithKline Biologicals for a study entitled: \u2018A phase IV multi-site observational epidemiology study to assess potential risk for adverse events following immunization that may be associated with misuse of a two-dose vial of 10-valent Pneumococcal Conjugate Vaccine (Synflorix) in Kenya\u2019.SZKM carried out the adherence assays and pneumococcal microarray experiments, analyzed the data and drafted the manuscript. TCTP participated in the design and performance of viral adherence assays. NK performed the human microarray experiments and qRT-PCR experiments. SRS participated in the design and performance of bacterial adherence assays and RNA extractions and drafting of the manuscript. JCDH participated in the design and analysis of all experiments involving molecular work in this manuscript. NI participated in the pneumococcal microarray experiments. VGH performed qRT-PCR experiments. DRR participated in the bioinformatics analysis of microarray work. DDE, GMC, JS participated in the design of the study. JAGS and HT conceived the study, participated in the study design and development, analysis and drafting of the manuscript. All authors read and approved this manuscript.Table S1. is a table listing the primers used for qRT-PCR analysis of human genes. Table S2. is a table listing the primers used for qRT-PCR analysis of pneumococcal genes. Table S3. is a table listing genes commonly significantly regulated by TIGR4 in contact with either viral- or mock-infected human pharyngeal cells. Figure S1. is a figure depicting the correlation of the log2 ratios of TIGR4 adherent to mock-infected cells and to HIPV3-infected cells. Figure S2. is a figure showing graphs of qRT-PCR validation of human and pneumococcal microarray results.Click here for file"} +{"text": "The development of novel techniques and systems to study human infectious diseases in both an in vitro and in vivo settings is always in high demand. Ideally, small animal models are the most efficient method of studying human afflictions. This is especially evident in the study of the human retroviruses, HIV-1 and HTLV-1, in that current simian animal models, though robust, are often expensive and difficult to maintain. Recently significant advances have been made to use human stem cells in immunocomprimised animals and follow the course of infection. HTLV-1-infected humanized non-obese diabetic severe combined immunodeficiency (HU-NOD/SCID) mice have been shown by inoculation of NOD/SCID mice with CD34(+) hematopoietic progenitor and stem cells (CD34(+) HP/HSCs) infected ex vivo with HTLV-1 ["} +{"text": "Axonal branching is a key principle for the establishment of neuronal circuitry that allows an individual neuron to innervate several target areas thus providing a physical framework for parallel processing of information. Our previous search for molecular determinants of axonal branching unravelled a cGMP signalling pathway in embryonic dorsal root ganglion (DRG) neurons composed of the ligand C-type natriuretic peptide (CNP), the receptor guanylyl cyclase B , and the cGMP-dependent protein kinase I\u03b1 (cGKI\u03b1) that is essential for the bifurcation of sensory axons at the dorsal root entry zone of the spinal cord. Absence of any of these components causes a complete loss of bifurcation where sensory axons only turn in either a rostral or a caudal direction Figure . ConsequTo examine whether the cGMP signalling system that underlies axon bifurcation in DRG neurons may also extend to other neuronal subpopulations we generated a GC-B-lacZ reporter mouse line for a detailed analysis of the GC-B expression pattern during embryonic development. A strong expression of GC-B that correlated with the localization of cGKI\u03b1 was detected in neurons of all cranial sensory ganglia (CSG) at early embryonic stages when their central afferents enter the brainstem. Furthermore, a complimentary distribution of the ligand CNP at the entry zones of these axons in the hindbrain was observed.To analyze the impact of GC-B-mediated cGMP signalling on axonal branching of CSG neurons we applied a genetic strategy for sparse labelling of GC-B-expressing neurons. For this purpose we generated a mouse mutant (GC-B-CreERT2) encoding a tamoxifen-inducible variant of Cre recombinase under control of the GC-B promoter that in combination with a conditional alkaline phosphatase reporter (Z/AP) enables the visualization of individual neurons within the genetically defined subset of GC-B-expressing cells. Comparing the branching patterns of GC-B heterozygous mice which resemble the wild-type phenotype with those of homozygous GC-B-deficient animals we found that in the absence of GC-B the bifurcation of axons of CSG neurons upon entering the hindbrain is impaired and only an ascending or a descending arm is formed Figure .Our data demonstrate that neurons of CSG - similar to DRG neurons - use GC-B-mediated cGMP signalling to trigger axonal bifurcation."} +{"text": "Catheter ablation is a first-line treatment for many cardiac arrhythmias and is generally performed under X-ray fluoroscopy guidance. However, current techniques for ablating complex arrhythmias such as atrial fibrillation and ventricular tachycardia are associated with sub-optimal success rates and prolonged radiation exposure. Pre-procedure 3-D magnetic resonance imaging (MRI) has improved understanding of the anatomic basis of complex arrhythmias and is being used for planning and guidance of ablation procedures. A particular strength of MRI compared to other imaging modalities is the ability to visualize ablation lesions. Post-procedure MRI is now being applied to assess ablation lesion location and permanence with the goal of identifying factors leading to procedure success and failure. In the future, intra-procedure real-time MRI, together with the ability to image complex 3-D arrhythmogenic anatomy and target additional ablation to regions of incomplete lesion formation, may allow for more successful treatment of even complex arrhythmias without exposure to ionizing radiation. Development of clinical grade MRI-compatible electrophysiology devices is required to transition intra-procedure MRI from preclinical studies to more routine use in patients. Radiofrequency (RF) catheter ablation has advanced over the last 25 years from an experimental procedure to the first-line treatment for a number of cardiac arrhythmias including atrioventricular re-entrant tachycardia, accessory pathway-associated tachycardias, and typical atrial flutter.3The clinical indications for anatomy-based catheter ablation have since expanded to more complex arrhythmias such as atrial fibrillation and scar-based ventricular tachycardia.Modern imaging techniques such as magnetic resonance imaging (MRI), intracardiac ultrasound, and X-ray computed tomography (CT) are increasingly used to approach the shortcomings of current mapping and ablation systems. Cardiac MRI (CMR) is a particularly flexible imaging modality that offers excellent soft tissue contrast, well characterized gadolinium enhancement techniques for myocardial scar visualization, 3-D imaging of complex cardiovascular anatomy, real-time 2-D imaging along arbitrary imaging planes, and the ability to quantify cardiac motion and blood-flow. This article will review the application of CMR to current clinical procedures and on-going advances toward full CMR guidance of electrophysiology procedures.MRI has been used most extensively to assist planning and guidance of atrial fibrillation (AF) ablation procedures. AF is the most common clinically relevant arrhythmia affecting 0.4% of the general population.8In an effort to improve procedural success and reduce complications, 3-D MRI angiography (MRA) has been used to assist planning of AF ablation. Kato and colleagues used MRA to study left atrial anatomy in normal subjects and patients with paroxysmal atrial fibrillation and found that 38% of people had pulmonary vein anatomic variants.CMR also has the potential to guide the treatment of scar-based monomorphic ventricular tachycardia (MVT), a potentially lethal arrhythmia that is difficult to treat medically or with current ablation techniques. Ventricular tachycardia that results in uniform repetitive electrical activation of the heart arises from anatomically fixed arrhythmia substrate that can be targeted for ablation. Myocardial scarring due to infarction, cardiomyopathy, sarcoidosis, arrhythmogenic right ventricular dysplasia, or cardiac surgery is a common cause of MVT.ex-vivo delayed enhancement MRI (DEMRI) to assess the relationship of MVT electrical propagation to scar morphology. Detailed scar imaging revealed numerous previously unseen features including 3-D tracts of viable myocardium within scar and scar within viable myocardium that visually correlated with the MVT isthmus identified by electrical activation mapping. Ciaccio et al. complemented these findings by computationally predicting suitable locations for MVT ablation with the use of high-resolution DECMR scar imaging.The use of CMR for assisting MVT ablation is still in the investigational stages but shows promise. Delayed enhancement CMR (DECMR) has been used extensively to characterize regions of scar in ischemic and non-ischemic cardiomyopathy . A numbeThe detailed anatomic information available from CMR is now being used as a road map for guiding placement of ablation lesions.32These sub-optimal results call attention to limitations of this current state-of-the-art in 3-D image-guided cardiac ablation. First, pre-acquired road map images may not correspond to the anatomy during the procedure. Changes in cardiac chamber size associated with variations in heart rate, rhythm, and volume status are not accounted for by pre-acquired imaging and could lead to catheter position registration errors.36Intracardiac echocardiography (ICE) addresses some of these shortcomings and is increasingly used in clinical practice.There are a number of reasons why intra-procedure CMR is an attractive option for guiding future electrophysiology procedures. First, CMR offers a number of ablation lesion imaging techniques. In addition, the ability to obtain images in arbitrary orientations opens the potential for high-quality visualization of catheters, anatomy, and electrode tissue contact. Further, the position errors introduced by registering catheter position to pre-acquired 3-D images can be largely avoided because both real-time CMR images and 3-D CMR images are acquired in the same co-ordinate system and 3-D images can be reacquired during the procedure if needed.Over the last 15 years the basic techniques to enable fully MR-guided electrophysiology (EP) procedures have been developed. Lardo and colleagues introduced the potential of CMR for guiding EP procedures in 2000.Subsequent work in our lab has demonstrated the ability to use real-time CMR to perform basic diagnostic EP studies.Other techniques relevant to EP procedures have also been performed using real-time CMR guidance. Trans-septal catheterization is required for left atrial catheter ablation. While generally safe, the procedure can be difficult in the setting of distorted atrial anatomy and carries the risk of serious complications such as aortic puncture. The ability of real-time CMR to guide trans-septal punctures under direct visualization of the needle, atria, fossa ovalis, and surrounding vasculature has been nicely demonstrated.42Recent advances promise to take MR-guided EP from these initial feasibility studies to safe, efficient practice. These advances include 1) intra-procedure ablation lesion monitoring techniques, 2) faster 2-D and 3-D imaging, 3) improved device visualization, 4) intuitive 3-D anatomy and intracardiac electrogram visualization, and 5) MRI-safe device construction techniques.Perhaps the most significant advantage of CMR-guided ablation therapy is the potential to visualize ablation lesions with high spatial and temporal resolution. The typical end-point of current ablation procedures is absence of electrical conduction across the ablated region and/or an in-ability to reinduce the clinical arrhythmia with cardiac pacing and medications. However, propagation of electrical signals through the heart is affected by a number of factors including the tissue temperature change induced by ablation.A 500 kHz radiofrequency (RF) current is the most commonly used ablation source used for electrophysiology procedures. Cryothermy, ultrasound, laser, and microwave ablation are also being investigated. Ablation lesions can be visualized because CMR is able to detect specific changes in proton precession and relaxation properties resulting from heating and heat-induced biophysical changes in cardiac tissue including interstitial edema, hyperemia, protein conformational changes, cellular shrinkage, and tissue coagulation.T1-weighted non-contrast-enhanced MR imaging of RF ablation lesions has also been investigated.46Gadolinium delayed enhancement CMR (DECMR) can provide better visualization of RF ablation lesions compared with non-contrast imaging techniques . The timOther methods for monitoring ablation lesion formation during RF energy application are also being investigated. Proton resonance shift thermography is an MRI technique that takes advantage of the decrease in the proton resonance frequency with increasing temperature.56While most cardiac ablation lesion MRI studies have been performed in roughly 10 mm thick ventricle, imaging the less than 3 mm thick human atria is of particular clinical interest given the difficulty of achieving long-term pulmonary vein isolation following atrial fibrillation ablation. Peters et al. demonstrated 3-D DECMR of left atrial ablation lesions 10 to 15 minutes after contrast injection using image-based respiratory gating.2. The target temporal resolution is 7 frames per second (fps), the usual X-ray fluoroscopy frame rate for clinical EP procedures.While cardiac gating can be used to generate MR images with excellent spatial resolution by splitting data collection over multiple heart-beats, real-time CMR requires a more deliberate trade-off between temporal and spatial resolution. To visualize catheters adequately, MRI-guided EP procedures require an in-plane spatial resolution of around 2 mmSince the initial 1 fps imaging used to guide the first MR-guided EP procedure61While the current imaging rates are adequate for a single 2-D image plane, ideal visualization of the device, target anatomy, and surrounding reference anatomy may require multiple 2-D image planes or even 3-D imaging. Other techniques that can improve imaging speed while balancing imaging quality include non-Cartesian k-space sampling, temporal data sharing between images, and adjusting the trade-off between temporal and spatial resolution.65While fluoroscopy provides projection images where the entire catheter body and tip are easily visualized, 2-D MR images typically depict a slice through the body that is around 5\u201310 mm thick. Curved devices such as catheters may pass in and out of the MR imaging plane leading to mis-interpretation of the device tip position. We have noted in preclinical studies that poor delineation of the tip position can result in tissue contact trauma, such as local hemorrhage. In addition, for electrophysiology ablation procedures the device tip contains the energy source. Misestimating the tip/tissue contact region can lead to inaccurate placement of ablation lesions.During our feasibility studies, tip location has mostly been performed using interactive real-time sequences with a user interface that permits adjustment of the scan plan during image acquisition. Part of the catheter is first identified on some imaging plane, and the plane is manually adjusted until the tip is located. For vascular procedures where the device is constrained to a co-planar segment of blood-vessel, manual plane manipulation is acceptable since only minor image plane translations are needed to visualize the device tip and relevant anatomy. For navigation in cardiac chambers where the device tip location is less constrained, the frequent need for manual plane manipulation necessitates a skilled operator for image plane manipulation and can distract from efficient procedure work flow.x, y, and z directions to identify the 3-D position of small receiver coils located in a catheter tip.One approach to this problem is to automatically direct imaging to the device location using position sensors located in the catheter. Fifteen years ago Dumolin et al. described using 1-D projection MR imaging along the An alternative technique for device visualization uses non-slice-selective imaging to produce an effect similar to projection X-ray fluoroscopy.Another factor that affects device navigation in the MRI environment is the physical constraint of performing procedures near and within the narrow MRI bore. The availability of shorter, wider-bore, high-field MRI scanners is making this less of an issue. Remote catheter steering is also gaining interest in the EP field to facilitate point-by-point electrical mapping of the cardiac chambers and assist stable device placement during ablation.83The ability to generate real-time images with arbitrary orientations in addition to anatomically detailed 3-D images with flexible tissue contrast makes CMR well suited for navigating complex arrhythmia anatomy and delineating complex ablation patterns. This flexibility also introduces the potential for disorientation and information overload. Appropriate displays and user-interfaces tailored to the work flow of an EP procedure are needed to manage this flexibility. Because thin-slice real-time imaging can intersect anatomy in unfamiliar ways, 3-D visualizations that plot real-time images oriented relative to reference images can be helpful . A basicThe most important consideration for any new diagnostic or therapeutic approach is safety. While a number of studies have been performed to determine the safety of conventional MRI with regard to electromagnetic energy exposure and tissue heating,91An additional safety concern particular to CMR-guided cardiovascular procedures is the significant heating that can result from RF transmission-induced current in extended metallic objects such as guide-wires, wired electrodes, and metal-braided catheters.Transitioning proof of concept studies to clinical electrophysiology procedures requires collaboration between academic centers, imaging and device companies, and regulatory agencies. The first CMR-guided electrophysiology procedure in a patient was performed using custom catheters made to clinical specifications by a clinical catheter manufacturer.in-vitro and animal MR imaging, and experience is growing for safe cardiac MRI scanning in patients with selected devices under controlled scanning conditions.The compatibility of MRI with implanted devices such as pace-makers and implantable cardiac defibrillators (ICDs) is also an important consideration in performing interventional MRI studies in the electrophysiology patient population. Particular concerns include static magnetic field-induced movement of the device and scanning-induced programming changes, device inhibition, activation of tachyarrhythmia therapies, and lead currents leading to heating or cardiac stimulation.Increasing knowledge of the anatomic basis for cardiac arrhythmias has extended the role of catheter ablation to curing even complex rhythms such as atrial fibrillation and scar-based ventricular tachycardia. CMR has demonstrated a number of uses for procedural planning, particularly for treatment of atrial fibrillation. The use of DEMRI for planning VT ablation procedures also shows promise. Real-time CMR combined with intra-procedural lesion imaging could allow physicians to accurately guide devices and establish completeness of ablation lines without concern for radiation exposure. This could significantly improve the way current ablation procedures are performed and open the way to ablative cure of arrhythmias such as permanent atrial fibrillation that currently respond poorly to minimally invasive approaches.7"} +{"text": "Many studies have examined MRSA control measures, but few have been planned prospective single intervention studies in the endemic setting. We asked whether active surveillance & contact precautions (CP) reduced MRSA transmission. We collected & analysed data to avoid confounding (of MRSA acquisition with length of stay) & serial dependence due to colonisation pressure (CoPr) in accordance with ORION guidelines.This was an interrupted time series in a tertiary ICU. Standard precautions only were used for control patients regardless of MRSA status. In the intervention period, rapid PCR was used to detect MRSA colonised patients, who were then cared for in CP. We used a generalised estimating equation (GEE) with each patient-day being the unit of interest. The predictor variables were both time-dependent & time-invariant covariates & intra-individual risk correlation was adjusted for using the GEE framework.The primary outcome measure was the effect of the intervention on MRSA acquisition, adjusting for CoPr & individual & ward covariates. The relative risk of MRSA acquisition was 0.40 (95%CI 0.24-0.65). Secondary measures include the effect of colonised patients in the ward & the phase-colonised patient interaction, with a reduced risk from colonised patients in the intervention phase to 0.41 (95% CI 0.14-1.18) compared with the control phase.We demonstrated a clinically significant effect of isolation on MRSA transmission. Our planned single intervention study is unique because of near-complete observations due to short intervals between swabs & full documentation of CoPr & time varying risk factors.None declared."} +{"text": "Aging of the male reproductive system leads to changes in endocrine signalling and is frequently associated with the emergence of bothersome conditions owing to prostate hyperplasia and bladder dysfunctions. Recent findings suggest that urogenital organs are promising targets for therapeutic interventions with inhibitors of the cGMP-degrading phosphodiesterase 5 (PDE5) . HoweverWestern blot analyses aimed to characterize the levels of PDE5, soluble (sGC) and particulate guanylyl cyclases, endothelial nitric oxide synthase (eNOS) and cGMP-dependent protein kinase I (cGKI) in membrane and cytosolic protein fractions. Data revealed a strikingly low abundance of all these proteins in prostate. In contrast, the bladder was distinguished by exceptionally high levels of PDE5, cGKI and eNOS, each resembling those in lung tissue. The epididymis was characterized by a predominance of particulate (in particular GC-B) versus soluble (sGC) guanylyl cyclases and lowest PDE5 tissue concentrations.As evidenced also by membrane guanylyl cyclase assays, ageing did not affect the three cGMP-generating enzymes in all organs. However, and supported by PDE activity studies, we recognized a pronounced age-related decrease (by nearly 50%) of PDE5 in bladder. Membrane-associated (but not cytosolic) cGKI concentrations were markedly reduced in the aged epididymis. On the other hand, prostatic cGKI increased with ageing. Androgen withdrawal during temporary Leydig cell elimination induced a massive (>12-fold) upregulation of cGKI in prostate but not other androgen-dependent organs. Castration elicited an equally organ-selective upregulation of cGKI in prostate. Neither EDS treatment nor castration evoked increases in other kinases examined. Testosterone supplementation reduced the increased cGKI levels in prostates of castrated rats in a dose-dependent manner.The findings may have significance for ageing-associated pathologies in the male lower urinary tract and identify cGKI as an androgen-sensitive signalling protein in prostate."} +{"text": "Distal myopathy with rimmed vacuoles/hereditary inclusion body myopathy is clinically characterized by the early involvement of distal leg muscles. The striking pathological features of the myopathy are muscle fibers with rimmed vacuoles. To date, the role of aquaporin-4 water channel in distal myopathy with rimmed vacuoles/hereditary inclusion body myopathy has not been studied.Here, we studied the expression of aquaporin-4 in muscle fibers of a patient with distal myopathy with rimmed vacuoles/hereditary inclusion body myopathy. Immunohistochemical and immunofluorescence analyses showed that sarcolemmal aquaporin-4 immunoreactivity was reduced in many muscle fibers of the patient. However, the intensity of aquaporin-4 staining was markedly increased at rimmed vacuoles or its surrounding areas and in some muscle fibers. The fast-twitch type 2 fibers were predominantly involved with the strong aquaporin-4-positive rimmed vacuoles and TAR-DNA-binding protein-43 aggregations. Rimmed vacuoles with strong aquaporin-4 expression seen in the distal myopathy with rimmed vacuoles/hereditary inclusion body myopathy patient were not found in control muscles without evidence of neuromuscular disorders and the other disease-controls.Aquaporin-4 might be crucial in determining the survival or degeneration of fast-twitch type 2 fibers in distal myopathy with rimmed vacuoles/hereditary inclusion body myopathy. N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) gene, which encodes a bifunctional enzyme catalyzing the 2 exclusive rate-limiting reactions of sialic acid synthesis in the cytosol[Autosomal recessive distal myopathy with rimmed vacuoles (DMRV)/hereditary inclusion body myopathy (hIBM) is clinically characterized by preferential involvement of the distal leg muscles in the very early stage, and later of most proximal muscles. One of the striking pathological features of this myopathy is muscle fibers with rimmed vacuoles (RVs),2. DMRV/ cytosol,4. HowevGNE mutation. Furthermore, we investigated accumulation of TAR-DNA-binding protein-43 (TDP-43), a pathological hallmark of vacuolar myopathies[Aquaporin-4 (AQP4) is the main water channel of the neuromuscular system. In the skeletal muscle, AQP4 is predominantly localized to the sarcolemma of fast-twitch type 2 fibers-7. AQP4 opathies,12, in tGNE revealed a homozygous 1714 G>C mutation.A 20-year-old man was admitted to our hospital with gait disturbance. He had no family history of neuromuscular disorders. He first noticed leg dragging at the age of 14. Neurological examination showed marked weakness and atrophy in the distal leg muscles and moderate atrophy in the proximal leg muscles. Cranial muscles were not involved and sensory examination was unremarkable. No deformity of the spine and feet was noted. Serum creatine kinase level was 599 IU/L with no other routine biochemical abnormalities including renal, liver, and thyroid functions and a battery of immunological markers were all negative. Electromyography showed myogenic changes with some neurogenic changes in all muscles tested. Nerve conduction studies were unremarkable. Muscle magnetic resonance imaging studies showed atrophies and degenerations in the muscles of both anterior and posterior compartments of the legs fibers in serial sections FigureA-3C. DoSubsequently, we performed a disease-control study of muscle AQP4/dystrophin expression. RVs with intensive AQP4 expression and sarcoplasmic AQP4 aggregates frequently seen in the DMRV/hIBM patient were not found in a female carrier of Duchenne muscular dystrophy (DMD) or in an ALS patient (FigureTo the best of our knowledge, this is the first report on AQP4 expression in the skeletal muscle of a DMRV/hIBM patient. We showed that sarcolemmal AQP4 immunoreactivity was reduced in many muscle fibers of the DMRV/hIBM patient, a female carrier of DMD, and an ALS patient. It is interesting to note that AQP4 staining was markedly increased in the areas of the RVs and in some muscle fibers in DMRV/hIBM. The most striking findings were that the fast-twitch type 2 fibers were predominantly involved with the strong AQP4-positive RVs and TDP-43 aggregations in DMRV/hIBM.GNE mutations[GNE knockout mouse are preferentially involved[GNE-mutated DMRV/hIBM. Further studies are needed to clarify the genotype/phenotype correlations in DMRV/hIBM patients.Our DMRV/hIBM case showed unusual involvement of the quadriceps muscles. In general, even at the advanced stage of DMRV/hIBM, quadriceps muscles are relatively spared. However, an earlier study has described a DMRV/hIBM patient with weakness of quadriceps. Intriguutations. On the involved. It remaOur results about downregulation of AQP4 are consistent with the results reported in other studies-10. We sIn conclusion, we found that many muscle fibers of a patient with DMRV/hIBM showed a reduction of sarcolemmal AQP4 immunoreactivity, while fast-twitch type 2 fibers were predominantly involved with strong AQP4-positive RVs and TDP-43 aggregation. Although the functional role of AQP4 in skeletal muscle is not well understood, AQP4 might be crucial in determining the survival or degeneration of fast-twitch type 2 fibers in DMRV/hIBM.Written informed consent was obtained from the patient for publication of this Case report and any accompanying images.The authors declare that they have no competing interests.AH conceived the study and drafted the manuscript. In addition, he reviewed medical report of the patients and analyzed the neuropathological findings. KS and ST contributed to the analysis of muscle pathology. TY and YU are senior authors and oversaw all aspects of the paper, including a careful review of the final product. KS performed routine muscle histochemistry, immunohistochemistry, and immunofluorescence of the patients. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2377/12/22/prepubMethod of immunohistochemical and immunofluorescence study.Click here for file"} +{"text": "Relationship with age and comparison of phase-contrast-CMR and Doppler-echocardiography derived left ventricular diastolic function parameters in asymptomatic individuals with preserved ejection fraction.Recent studies suggest the ability of phase-contrast cardiovascular magnetic resonance (PC-CMR) to provide velocity and flow-related left ventricular diastolic function parameters in good agreement with Doppler echocardiography (DE). Furthermore, DE diastolic parameters are known to change with aging. The aim of the present study is to assess whether the age-related variations of diastolic parameters are comparable when assessed by DE and PC-CMR.We studied 80 asymptomatic volunteers who underwent DE and PC-CMR exams on the same day. Transmitral EDE and ADE and lateral mitral annulus E\u2019DE peak velocities were assessed by DE.For PC-CMR analysis, a custom software was used for semi-automated segmentation of mitral annulus velocities and transmitral flow throughout the cardiac cycle and for automated extraction of diastolic parameters from velocity and flow rate curves. Flow rate curves provided: 1) early diastolic peak filling rate and peak atrial filling rate , 2) peak filling rate to filling volume ratio , and 3) deceleration time (DTMR), while maximal velocity curves provided the early to late peak velocities ratio EMR/AMR. Myocardial velocity curves provided peak early diastolic E\u2019MR myocardial longitudinal velocity.Table Our automated method provided PC-CMR diastolic parameters which were strongly related to age. These age-related variations of diastolic parameters appear to be comparable when assessed by DE or PC-CMR with a slight superiority of the PC-CMR flow-related parameters. These findings suggest the usefulness of PC-CMR diastolic data when analyzed automatically as an additional CMR tool for the evaluation of left ventricular function.Nothing to disclose."} +{"text": "Autopsy data has demonstrated that the abdominal aorta offers a valuable early window for the study of atherosclerosis. Current MRI strategies often suffer from long scan times or require slice gaps. We sought to implement a small field-of-view approach (zoom imaging) , to allow complete coverage of the thoracic and abdominal aorta. To improve blood signal nulling before and after contrast administration for identical imaging parameters, we combined zoom imaging with a quadruple inversion recovery (QIR) pre-pulse .To demonstrate the feasibility of the novel zoom QIR technique for plaque imaging in the abdominal aorta.b) for T1 values up to 2000ms. The effective TR was set to equal the RR-interval for heart-rates between 30 and 120bpm at 5bpm intervals. For each heart-rate, the optimal TI1 and TI2 values were calculated by minimizing the integral of Mzb between 200 and 1400ms.The QIR pre-pulse consists of a double inversion recovery (DIR) pre-pulse and a time delay (TI1) followed by a second DIR pre-pulse and a second time delay (TI2). Simulations in MATLAB were performed to study the steady-state longitudinal magnetization of blood sequence Five selected slices were then imaged with the DIR pre-pulse replaced by the QIR pre-pulse with imaging parameters maintained Approximately 10-15 minutes after the injection of a double dose of Gadovist, the zoom 2D DIR-TSE and QIR-TSE sequences were repeated in the same five slices.Zoom imaging allowed a reduced field-of-view without wrap-around artifact and the QIR pre-pulse achieved blood signal nulling before and after contrast administration using identical imaging parameters in all volunteers (an example is shown in figure The QIR pre-pulse has successfully been combined with ECG gating and zoom imaging. Preliminary data has shown that direct comparison of pre and post contrast imaging of abdominal aortic plaques is feasible."} +{"text": "Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed.The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought. Crop productivity is significantly impacted by abiotic constraints, especially water availability . Given tSorghum bicolor L. Moench) is an excellent model for the study of plant response to abiotic stress, particularly drought stress. With the exception of millet, sorghum is the cereal best adapted to water-limited environments and ranks amongst the most drought tolerant of all crops grown in the U.S. ; ; Ortholose. a; ; Ortholoa[b[c[d[eClick here for filecis-element enrichment in 1000 bp upstream of the transcriptional start site for sorghum genes with unknown function conserved in function and expression across speciesp-Values for . \u2020B (CGT); D (AGT); H (ACT); K (GT); M (AC); N (ACGT); R (AG); S (CG); V (ACG); W (AT); Y (CT)Click here for filecis-element enrichment in 1000 bp upstream of the transcriptional start site for rice, maize, and Arabidopsis genes with unknown function conserved in function and expression to sorghump-Values for . \u2020B (CGT); D (AGT); H (ACT); K (GT); M (AC); N (ACGT); R (AG); S (CG); V (ACG); W (AT); Y (CT)Click here for fileNumber of genes within read count binsClick here for file"} +{"text": "To evaluate the ability of velocity encoded magnetic resonance imaging (VENC-MRI) to identify the presence of a restrictive filling pattern in patients with reduced systolic left ventricular (LV) function.A restrictive filling pattern is an independent prognostic marker for an increased mortality in patients with reduced systolic LV function. The diagnosis is currently established by characterization of transmitral and pulmonary-venous flow using Doppler-echocardiography. VENC-MRI enables robust quantification of transmitral as well as pulmonary-venous flow.The study included 41 patients with reduced systolic LV function (ejection fraction 29\u00b112 %). All patients underwent VENC-MRI and Doppler-echocardiography to assess the transmitral and pulmonary-venous flow characteristics. Figure There was a very good correlation between VENC-MRI and Doppler-echocardiography for the E/A ratio . The correlation was moderate between both methods for the S/D ratio . VENC-MRI identified 10 (24 %) and Doppler-echocardiography 7 (17 %) patients with restrictive filling pattern. The agreement between both methods was moderate (kappa= 0.49). Left atrial volumes were larger in patients with restrictive filling pattern than in patients without restrictive filling pattern . Higher NT-proBNP levels were found in patients with restrictive filling pattern compared to patients without restrictive filling pattern . VO2max was lower in patients with restrictive filling pattern compared to patients without restrictive filling pattern VENC-MRI has the ability to identify the presence of a restrictive filling pattern and may be a useful tool for the evaluation of patients with reduced systolic LV function."} +{"text": "Populus tremula) and birch (Betula pubescens) are the fast-growing trees successfully used for the aim of plantation forestry. These species have the great potential in Russia to meeting the need for paper, timber and other wood-based products. However, enhanced growth rate, decreased lignin content and herbicide resistance are the required properties of new trees for plantation forestry. Breeding of forest trees is a slow process due to the long generation intervals typical of most forest trees and because many traits can only be properly assessed at rotation age. Genetic modification is an alternative method that can be used for new trees creation.Aspen(Agrobacterium tumefaciens strain CBE21. pBI-4CL plasmid contains the expression cassette harboring inverted fragments of 4-coumarat-CoA-ligase gene (GeneBank AY043494). pBI-Xeg vector was constructed using cDNA of xyloglucanase gene cloned from Penicillium canescens. pGS and pBIBar vectors contains pine glutamine synthetase gene (GS) and phosphinothricin acetyltransferase gene (bar). For transcription control of expression 35S promoter used in all cassettes harboring the gene of interest.Genetic transformation experiments were carried out using vectors pBI-4CL, pBI-Xeg, pGS and pBIBar and supervirulent in vitro aspen plants (Populus tremula) and leaves from in vitro birch plants (Betula pubescens) cultivating on WPM medium were used as an explants for Agrobacterium-mediated transformation [Internodes from ormation ,2. TransTo detect DNA fragments from binary vectors transformants were analysed by PCR. Expression of recombinant genes was detected by RT-PCR. Lignin content determination performed by using the Klason method.Agrobacterium-mediated transformation experiments with pGS vector 56 and 27 transgenic lines of birch and aspen have been produced respectively. Presence of recombinant glutamine synthetase GS gene confirmed by PCR in 52 birch and 23 aspen lines. GS gene expression at the RNA level demonstrated RT-PCR analysis (Figure As a result of two s Figure .Most of GS lines have resistance to subletal dose of phosphinotricin as well as in the in vitro and greenhouse conditions. Comparative biometric analysis of GS plants in a greenhouse makes it possible to select 7 and 3 superior lines of birch and aspen respectively. Growth rate enhancement of selected lines was 20-25 %.Genetic transformation of aspen plants for 4-coumarat-CoA-ligase gene down-regulation and xyloglucanase overexpression has been performed using pBI-4CL and pBI-Xeg binary vectors respectively. 11 transgenic lines with inverted fragments of 4CL gene and 15 lines harboring Xeg1 gene have been produced. DNA fragments of 4CL RNAi-construct were detected in all lines. 14 out of 15 transformants produced with pBI-Xeg vector harboring Xeg1 gene. Chemical analysis of stem wood of 4CL lines demonstrated decreased lignin content Table .bar gene coding resistance against herbicide phosphinotricin were also created. Transformation experiments were carried out using vector pBIBar. 19 aspen and 9 birch lines were selected as a result of transformation. Presence of bar gene was confirmed in all lines. Herbicide resistance was observed at 16 and 7 lines of aspen and birch respectively. Lines tested in a greenhouse demonstrated normal phenotype without somaclonal variations and may be recommended for the field trials.Aspen and birch transgenic plants with To combine several new properties in one plant the co-transformation method was developed. This method allows transferring recombinant DNA fragments from three T-DNAs of two plasmids independently . Efficie"} +{"text": "A funding organization and grant were incorrectly omitted from the Funding Statement. The following sentence should be included in the Funding Statement: We thank the EC for co-funds, NanoReg (FP7-310584)."} +{"text": "Membrane fusion is the central molecular event during the entry of enveloped viruses into cells. The critical agents of this process are viral surface proteins, primed to facilitate cell bilayer fusion. The important role of Dendritic-cell-specific ICAM3-grabbing non-integrin (DC-SIGN) in Dengue virus transmission makes it an attractive target to interfere with Dengue virus Propagation. Receptor mediated endocytosis allows the entry of virions due to the presence of endosomal membranes and low pH-induced fusion of the virus. DC-SIGN is the best characterized molecule among the candidate protein receptors and is able to mediate infection with the four serotypes of dengue virus (DENV). Unrestrained pair wise docking was used for the interaction of dengue envelope protein with DC-SIGN and monoclonal antibody 2G12. Pre-processed the PDB coordinates of dengue envelope glycoprotein and other candidate proteins were prepared and energy minimized through AMBER99 force field distributed in MOE software. Protein-protein interaction server, ZDOCK was used to find molecular interaction among the candidate proteins. Based on these interactions it was found that antibody successfully blocks the glycosylation site ASN 67 and other conserved residues present at DC-SIGN-Den-E complex interface. In order to know for certain, the exact location of the antibody in the envelope protein, co-crystallize of the envelope protein with these compounds is needed so that their exact docking locations can be identified with respect to our results. DENV belongs to flavivirus genus of the Flaviviridae family, including numerous other important human pathogens such as tick-borne encephalitis (TBE), yellow fever (YF), West Nile (WN) and Japanese encephalitis (JE) viruses Developing world is victim of largest vector-borne viral disease burden caused by the four serotypes of dengue virus (DENV) Lipid bilayer envelops the virus particles which are enclosed within an icosahedral scaffold of envelope glycoprotein E Three distinct domains constitute its structure . DI contReported DENV receptors include heat shock protein 70 (Hsp 70) and Hsp90 DC-SIGN is the best characterized molecule among the candidate protein receptors and is able to mediate infection with the four serotypes of DENV. DENV replication occurs in the skin followed by intradermal injection of DENV-2 in mice through an infected mosquito bite The CRD recognizes fucose and high-mannose N-glycans containing blood group antigens The identification of this and other receptors can open a way to the development of specific, receptor-based prophylaxis and therapy as well as, potentially, the early genetic identification of individuals at increased risk of developing dengue fever or, more importantly, dengue hemorrhagic fever or dengue shock syndrome. This study focus on identifying conserved residue (may or may not be epitopes) of Dengue virus serotypes 1\u20134 that interact with DC-SIGN receptors and designing peptide and ligand based inhibiters against those interfacing residues to block dengue and DC interaction.http://www.uniprot.org/help/uniprotkb). All images were resized and developed by Adobe Photoshop CS3.ClustalW based on progressive alignment methods available in MEGA 5 http://www.imtech.res.in/raghava/bcepred/index.html).The ABCpred server based on partial recurrent neural network with a single hidden layer was used to predict B cell epitopes High resolution X-Ray 3D crystal structure of dengue virus serotype 2 (pdb code: 1OK8), DC-SIGN CRD (pdb code: 1SL4) and Antibody 2G12 (pdb code: 3OAU) were retrieved form pdb database. We employed ProQ We used unrestrained pairwise rigid body docking for dc-CRD-DEN-E and 2G12-envelope protein of dengue virus. Pre-processed the PDB coordinates of dengue envelope glycoprotein (PDB ID: 1OK8); DC-SIGN CRD domain (PDB ID: 1SL4) and Antibody 2G12 (PDB ID: 3OAU) were used prior than docking procedure for energy minimization through AMBER99 force field distributed in MOE 2011.10 software with 0.05 gradient on default parameters.Protein-protein docking software, ZDOCK An important role is played by B-cell epitope in synthetic vaccine design and also in humoral response. Sequence-based methods are limited to the prediction of continuous epitopes. The majority of the sequence-based methods assume that epitopes have to be accessible for antibody binding and, hence, are based on using epitope properties related to surface exposure. The epitopes predicted by ABCpred database in dengue virus envelope protein are listed in Using multiple physiochemical parameters and different analysis software, Epitopes at 65\u201383 and 57\u201374 amino acids are consider good for Dengue E protein. Physiochemical properties of B cell epitope including turns, exposed surface, polarity, accessibility, flexibility, and hydrophilicity are shown in supplementary data models having no intersection in domain II of dengue E protein were omitted; (ii) only those shared models were included where the binding region is explained with experimental data The ZDOCK ranking of all the optimal models along with buried surface interaction area are shown in supplementary data in Dengue virus transmission makes it an attractive target to interfere with Dengue virus Propagation.Detailed interaction of DC-SIGN has been investigated here with Dengue virus envelope glycoprotein. Envelope residues at the interface of DC-SIGN-Den-E complex are conserved in all four serotypes of dengue virus and are found in conserved continuous predicted B cell epitopes. Based on these interactions it was found that antibody in this study successfully blocks the glycosylation site ASN 67 and other conserved residues present at DC-SIGN-Den-E complex interface. In order to know for certain, the exact location of the antibody in the envelope protein, co-crystallization of the envelope protein with these compounds is needed so that their exact docking locations can be identified with respect to our results.File S1Includes Figures S1 and S2.(DOCX)Click here for additional data file.File S2Includes Tables S1 and S2.(DOCX)Click here for additional data file."} +{"text": "A 22-year-old male presented with recurrent upper gastrointestinal bleeding along with pain in the abdomen. An upper gastrointestinal endoscopy revealed Menetrier's disease affecting the body of the stomach, which was confirmed histopathologically . There w"} +{"text": "To investigate possible mechanism(s) of the extract\u2019s hypotensive effects, the contractile or relaxant responses to EKE in the absence or presence of reference drugs were evaluated in Wistar rat isolated aortic rings precontracted with methoxamine hydrochloride .The purpose of this study was to examine the Acute intravenous administration of EKE elicited hypotensive responses in anaesthetised animals, while sub-chronic treatment with the extract averted the development of high blood pressure in weanling DSS rats. Isometric recordings of methoxamine hydrochloride (ME) pre-contracted, isolated, endothelium-intact and -denuded aortic rings revealed concentration-dependent relaxation responses to EKE (1\u2013160 mg/ml). The potency was significantly less in the endothelium-denuded rings. Inhibitors of endothelium-derived relaxing factor (EDRF), L-NAME, methylene blue and indomethacin significantly reduced EKE-evoked vasorelaxations in endothelium-intact aortic rings.These results indicate that the vasorelaxant effect of EKE was in part mediated via EDRF-dependent or -independent pathways. These observations suggest that the hypotensive effect of EKE was in part mediated via modulation of total peripheral resistance of the vascular smooth muscles. Ekebergia capensis Sparrm (Meliaceae), a fairly large tree and widespread in southern Africa, plays an important role in various communities.E capensis extracts are used for heartburn, coughs and respiratory complaints, and decoctions made from the wood of the plant are used by the Zulus in KwaZulu-Natal as oxytocic agents.4The World Health Organisation and many developing countries have significant interest in complimentary health systems, perhaps due to the integral part played by ethnomedicinal plants in folkloric healthcare.E capensis extracts in folk medicine and the availability of a reasonable number of scientific observations on its medicinal properties, we could not find any report on its effects on the cardiovascular system. Ekebergia senegalenensis A Juss which belongs to the Meliaceae family has, however, been reported to contain bioactive chemical compounds such as glycosides, polyphenols, tannins, triterpenes and saponins.E capensis leaf extract on the blood pressure of rats, based on the knowledge that Ekebergia spp extracts contain glycosides, and the fact that cardiac glycosides used therapeutically to increase cardiac contractility are of plant origin.6In spite of the widespread use of E capensis leaf extract on blood pressure of normotensive Wistar and weanling genetically hypertensive Dahl salt-sensitive (DSS) rats, which develop hypertension as they age. Since we needed more information about the mechanism(s) of action of the extract, we also evaluated the in vitro cardiovascular effects of E capensis leaf extract (EKE) on rat isolated atrial muscle strips, and its vasorelaxant effects on isolated thoracic aortic rings and portal veins of normotensive Wistar rats. We envisaged that establishment of the mechanism(s) of its cardiovascular effects would provide scientific evidence for the development of a cheap and accessible source of novel drugs for the treatment of cardiovascular disorders in impoverished, developing populations.The main aim of this study was therefore to assess the effects of G-nitro-L-arginine-methyl-ester (L-NAME), methylene blue, atropine sulphate (ATR), glibenclamide, (\u00b1)-propranolol hydrochloride, (-)-noradrenaline hydrochloride (NA), prazosin, reserpine and nifedipine . All chemicals were of the analytical grade and supplied by Merck Chemicals, South Africa.The reference drugs used in the present study were: methoxamine hydrochloride (ME), acetylcholine chloride (ACh), indomethacin, NIndomethacin and glibenclamide were separately dissolved in 0.5% sodium bicarbonate (1 ml) and dimethyl sulphoxide , respectively, and deionised water (19 ml) before use. All other drug solutions, including Kreb-Henseleit solution (KHS) were freshly prepared in deionised water daily at the beginning of our experiments.Ekebergia capensis Sparrm (Meliaceae), identified by Prof H Baijnath, former chief taxonomist/curator of the Department of Botany, University of KwaZulu-Natal were collected on the Westville Campus of the University between January and June 2005. A voucher specimen of the plant has been deposited in the Botany Department Herbarium.Leaves of ad libitum. Ethical clearance was obtained for this study from the University Ethics Committee.Normotensive male Wistar (250\u2013300 g) and weanling Dahl salt-sensitive rats (100\u2013150 g) bred and housed at the Biomedical Research Unit, University of KwaZulu-Natal were used in this study. The rats were maintained on a 12-h light/12-h dark regime, and given both food and water E capensis leaf extracts (1 kg) were prepared as previously described by Musabayane et al.Ethanolic in vivo in the Wistar and DSS rats, respectively. The effect of EKE on myocardial contractile performance was evaluated on rat isolated atrial muscle strips, whereas the vasodilatory effects were determined on isolated thoracic aortic rings and portal veins of the Wistar rats. Arterial blood pressure and heart rate were measured in anaesthetised Wistar and conscious DSS rats as previously described by Musabayane et al.7The acute and chronic effects of EKE on the mean arterial blood pressure (MAP) and heart rate were examined Acute effects of EKE: Wistar rats anaesthetised by intraperitoneal injection of inactin were placed on a thermally controlled heating table (37 \u00b1 1\u00b0C). After tracheotomy, a catheter was inserted into the jugular vein for intravenous infusion of 0.077 M NaCl at 9 ml/h . An additional heparinised catheter was also inserted into the left carotid artery for blood pressure and heart rate measurement at 30-min intervals via a pressure transducer compatible with PowerLab System ML410/W .Following a 3-h equilibration period, measurements were recorded over the 4-h post-equilibration period of the 1-h control, 1 h 30-min treatment and 1 h 30-min recovery periods. In those animals in which the effects of the extract were studied, EKE was added to the infusate at 360 \u03bcg/h for 1.5 h (treatment period), resulting in a total dose of 18 mg/kg (for a 300-g rat), before the animals were returned to infusate alone for the last 1.5 h (recovery period). Depth of anaesthesia was monitored throughout the experiments and additional intravenous bolus doses of inactin (0.05 g/kg body weight) were administered when necessary.Chronic effects of EKE: Mean arterial blood pressure (MAP) and systolic and diastolic pressures were measured every third consecutive day for seven weeks at 09:00, in separate groups of untreated control and EKE-treated (120 mg/kg po) DSS rats (n = 8 per group). Control rats were similarly treated with deionised water (3 ml/kg). The cardiovascular effects of EKE were measured by the tail-cuff method with computerised blood pressure monitoring . The method was standardised and used routinely in our laboratory as described previously.Inotropic and chronotropic effects of EKE: The effects of EKE on myocardial contractile performance were evaluated on rat isolated atrial muscle strips of Wistar rats as previously described.7To evaluate the effects of EKE on the myocardial contractile force (inotropic), electrically driven left atria were impaled on thin platinum wire electrodes and stimulated (5\u201310 mV) with square wave pulses of 5-ms duration at a frequency of 3 Hz, via an SRI stimulator . To examine the extract\u2019s effect on atrial pacemaker activity (chronotropic), isolated spontaneously beating right atria of rats were set up under the same experimental conditions. Two isolated electrically driven left atrial muscle strips and two isolated spontaneously beating right atrial muscle preparations were set up each time to allow for changes in the atrial muscle sensitivity.n = 8 preparations for each concentration).Concentration\u2013response curves to EKE (1\u201340 mg/ml) and/or reference agonist drugs were obtained. Control atrial muscle strips were treated with volumes of deionised water equivalent to the volumes of bath-applied EKE solution (0.1\u20130.6 ml). The electrically provoked and spontaneous contractions of the atrial muscles, as well as the EKE- and reference agonist drug-induced responses of the muscle preparations were recorded isometrically by means of Ugo Basile force\u2013displacement transducers and pen-writing Gemini recorders (model 7070). The effects of EKE and reference drugs were expressed as percentages of the baseline values . Satisfactory removal of the functional endothelium was checked by at least 10% and 70% relaxation, respectively, to 10-6 M ACh.G-nitro-L-arginine methyl ester, L-NAME (100 \u03bcM), nitric oxide synthase inhibitor, methylene blue (10 \u03bcM), guanylate cyclase inhibitor, and indomethacin (10 \u03bcM), a nonselective cyclooxygenase inhibitor].After a sustained, stable, tonic contraction was obtained with ME, concentration-response curves for EKE (1\u2013160 mg/ml) and/or the reference agonist drugs were obtained. The involvement of endothelium-derived relaxing factor in EKE-induced relaxation was examined in intact aortic rings pre-treated with appropriate antagonists [N+ (20 mM) and high K+ concentrations (80 mM), respectively, in the presence glibenclamide, as previously described.To assess the role of potassium or calcium in the vasorelaxant effect of the extract, concentration\u2013response curves of EKE were constructed in endothelium-intact aortic rings precontracted with low Ktrations 0 mM, resIsolated portal veins: The Wistar rats were sacrificed and the isolated portal vein preparations were prepared as previously reported,7 and graded concentrations of EKE were added to the bath fluid. To investigate whether the effects of EKE were mediated through modulation of alpha-1 adrenergic receptors or voltage-operated calcium channels, some of the portal vein preparations were pre-treated with either an alpha-1 adrenergic receptor blocker, prazosin (1 \u03bcM), or an L-type voltage-operated calcium channel blocker, nifedipine (1 \u03bcM), five minutes before re-establishing the cumulative concentration\u2013response curves to EKE.n = 8 preparations for each concentration).Control venous muscle strips were treated with deionised water equivalent to the volumes of bath-applied EKE solution. Two isolated venous tissue preparations (one control and the other EKE- or reference drug-treated test) were set up in order to make allowance for changes in the venous tissue sensitivity. The plant extract and/or reference drug-induced responses of the muscle preparations, recorded by means of Gemini recorders, were calculated as percentage of the baseline values . Statistical comparison of the differences between treated means (EKE and reference drugs) and control means was performed with GraphPad InStat Software , using one-way analysis of variance , followed by Tukey-Kramer multiple comparison tests. A value of Acute intravenous infusion of EKE (360 \u03bcg/h) in the normotensive Wistar rats induced a transient fall in MAP within 30 min without a significant effect on the heart rate Isolated atrial muscles: Sequential administrations to the bath fluid of low to high concentrations of EKE (2.5\u201340 mg/ml) produced significant (p < 0.05), concentration-dependent, positive inotropic and positive chronotropic effects of EKE on isolated electrically driven left and spontaneously beating right atrial muscles taken from the normotensive rats, respectively p < 0.05) partial abolition of the positive inotropic and chronotropic effects of EKE Isolated aortic rings: Exogenous additions of graded concentrations of EKE (1\u2013160 mg/ml) to aortic ring strips pre-contracted with ME, an alpha-1 adrenergic receptor agonist, evoked concentration-dependent relaxation responses of the muscle strips + did not modify the vasorelaxant effect of EKE To evaluate the role of potassium channels in the vasorelaxant effects of EKE, studies were conducted on endothelium-intact aortic rings pre-contracted with low K+ concentrations (20 mM). EKE induced significant and concentration-dependent vasorelaxations in these aortic rings. Pretreatment with glibenclamide before inducing contraction with low K+ concentrations (80 mM). The vasorelaxant effects of graded EKE concentrations were not statistically different in these aortic rings precontracted with low or high K+ concentrations + have been used to study compounds with Ca2+ entry-blocking properties.To evaluate the role of calcium channels in the vasorelaxant effects of EKE, experiments were conducted in endotheliumintact aortic rings pre-contracted with high Ktrations 0 mM. TheIsolated portal veins: EKE concentration-dependently increased the amplitude of spontaneous contractions of the rat portal vein preparations isolated from the normotensive rats p < 0.05) reduced the stimulant, contractile effect induced by the high concentration of EKE (40 mg/ml) E capensis leaf extract possesses hypotensive properties, since acute and sub-chronic administrations of the extract reduced blood pressure in normotensive Wistar and hypertensive DSS rats, respectively. The DSS rat, which progressively develops hypertension with age, is a genetic rat model of salt-sensitivity hypertension,in vivo reduction in blood pressure by the extract occurred without significant alterations in heart rate, possibly suggesting that the in vitro cardiovascular effects of EKE significantly contributed to its hypotensive effects. This speculation is corroborated by the fact that the vasorelaxant effects of EKE were demonstrated in isolated vascular smooth muscles The findings of this study indicate that The results obtained in this study also suggest that the EKE-evoked vasorelaxations in aortic ring preparations were mediated through both EDRF-dependent and -independent mechanisms. Indeed, graded concentrations of the extract elicited dose-dependent vasorelaxations in endothelium-intact and -denuded aortic ring preparations, although the EKE vasodilatory effect was less in the latter protocol. Furthermore, the vasorelaxations produced by EKE in endothelium-intact aortic rings were pharmacologically modulated by L-NAME, a non-selective nitric oxide synthase inhibitor,2+-activated (Kca) channels directlyEndothelial NO synthesis is regulated by a variety of stimuli that trigger release of multiple vasoactive substances, including nitric oxide synthase (NOS).+ concentrations (20 mM), we speculate that this effect was mediated via endothelium-derived hyperpolarising factor (EDHF), which opens K+ voltage-sensitive channels.+ depolarises smooth muscle cells to facilitate Ca2+ influx, and subsequent vasoconstriction.+ concentrations (< 30 mM) are usually mediated via the opening of KCa-activated channels.2+ voltage-sensitive channels participate in the process of excitation\u2013contraction coupling25Removal of the functional aortic endothelium did not completely abolish EKE-evoked vasorelaxations, suggesting the involvement of endothelium-independent relaxing factor. Since EKE concentration dependently evoked vasorelaxations in the endothelium-intact aortic rings pre-contracted with low Ktrations mM, we strations mM, we s+ concentration (80 mM), suggesting the participation of calcium channels in the vasorelaxant effects of the extract. The contractile responses induced by high K+ concentrations (80 mM) in K+-depolarised muscles are due to the influx of extracellular Ca2+ through L-type voltage-sensitive channels (VOCs).2+ entry into cells. The vasorelaxant action induced by EKE in K+-contracted rings therefore appears to be mediated via inhibition of Ca2+ entry, leading to decreased intracellular calcium concentrations. The fact that EKE relaxed pre-contracted endothelium-intact thoracic aortic rings via both endothelium-dependent and -independent mechanisms suggests that the hypotensive action of the extract was elicited, in part at least, by reducing the total peripheral vascular resistance through dilatation of the blood vessels.EKE produced concentration-dependent vasorelaxation in the endothelium-intact aortic rings pre-contracted with a high K2+ channels, since nifedipine, a Ca2+ channel antagonist,1-adrenergic system, since the vasorelaxant effects of EKE were not altered by pre-treatment of the venous muscle preparations with prazosin, an \u03b11-adrenergic receptor antagonist.1-adrenergic receptor activation.27The present results suggest that the vasorelaxant effects of EKE in the portal vein preparations were in part mediated via L-type voltage-dependent CaAlthough the chemical constituents of EKE were not evaluated in this study, compounds reported to be present in the extract include saponins,33E capensis in the management of hypertension and other cardiovascular disorders. The findings may be helpful in the development of an antihypertensive agent from E capensis leaves.This study has provided the mechanistic basis for the use of"} +{"text": "Digital breast tomosynthesis (DBT) increases the sensitivity and specificity of detecting invasive breast carcinoma. Integration into screening raises questions. Should we perform two-view full-field digital mammography (FFDM) and two-view DBT or two-view FFDM and single-view DBT at every screening? DBT is shown to offer greatest benefit in the assessment of a soft tissue lesion. We routinely use two-view DBT in combination mode for all patients recalled from screening for a soft tissue abnormality. The aim of our study is to assess the need for two-view DBT in the detection of breast cancer.We retrospectively queried our histopathology database for all screen-detected invasive cancers between 2011 and 2012. The study sample was 254 cases. Comparisons were made between the visibility of the cancer on MLO/CC DBT and histological type/grade, molecular profile and breast density (BIRADS).The mean age was 59 years. In total, 4/254 cancers were visible on one-view DBT (1.6%). (Two seen on MLO DBT [spiculated masses] and two seen only on the CC view [distortions]). A total of 11/254 had greater visibility on one view in comparison with the other view on DBT (4.3%). Two of 254 cases were occult on FFDM and DBT. Recall was for clinical symptoms, both lobular invasive carcinoma (0.79%). There was no relationship between histological type, grade or molecular characteristics and the visibility on one-view versus two-view DBT.A total 98.4% of cancers were seen on two-view FFDM and MLO-DBT. Integration of MLO-DBT into breast cancer screening with two-view FFDM is a consideration."} +{"text": "Natural rubber latex allergy (NRL-A) is an international problem of public health. About 50-60% of NRL-A patients may present adverse reactions after ingestion cross-reacting vegetable foods. This condition is called \"Latex-fruit Syndrome\" and is matter of research. The aim of our study is distinguishing between clinical/subclinical latex-fruit syndrome and cross-sensitization to latex and food/pollens allergens on the basis of latex recombinant allergens. We studied 19 patients with food hypersensitivity and serological evidences of NRL sensitization. They underwent an accurate allergological evaluation . The patients were divided in two groups: group 1) 9 patients allergic to fruits/vegetables and/or pollens, with serological, but not clinical NRL-A; group 2) 10 patients with clinical and serological latex and fruits/vegetables allergy. The same number of patients was positive to pollens in each group. All group 1 patients presented negative provocation challenges and a monosensitization to Hev b8 (and other recombinant profilins), probably linked to a cross-sensitization to pollens and foods. These data suggest that profilin sensitization determines false positivity from NRL-A diagnostic test. Consequently the observed in vitro reactivity to NRL is not clinically relevant in patients with adverse food reactions and it does not determine always a latex-fruit syndrome. Instead, in group 2 we observed positive NRL provocation challenges and sensitization to rHev b 8 , but also to other recombinant latex allergens . These patients probably presented a latex-fruit syndrome.We supposed that the available panel of recombinant latex allergens could be effective to demonstrate a significant difference between latex-fruit syndrome and cross-sensitization to latex and food/pollens allergens. So further investigations are needed with a larger group of patients."} +{"text": "A high rate of response to treatment with epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) has been observed in certain patients with mutations in exons 18 to 21 of the tyrosine kinase domain of EGFR. Some cases of high-grade neuroendocrine carcinoma of the lung harboring mutations have been sporadically reported.We describe the case of a 78-year-old woman with large-cell neuroendocrine carcinoma of the lung, with mutation in exon 21 L858R and co-expression of adenocarcinoma markers.A mass (3.0 cm in diameter) was identified in the inferior lobe of the left lung, accompanied by metastases into ipsilateral mediastinal lymph nodes and elevations of serum pro-gastrin-releasing peptide and carcinoembryonic antigen. Initial transbronchial brushing cytology suggested high-grade neuroendocrine carcinoma favoring small-cell carcinoma in poorly smeared and degenerated preparations, and revealed exon 21 L858R mutation. Re-enlargement of the cancer and bone metastases was observed after chemotherapy, and further testing suggested large-cell neuroendocrine carcinoma with immunoreactivity to markers of primary lung adenocarcinoma and L858R mutation. High-grade neuroendocrine carcinoma with mutations in the tyrosine kinase domain of EGFR may be associated with adenocarcinoma, as reviewed from the literature and may also apply to our case.EGFR-TKI could provide better quality of life and survival in patients with advanced or relapsed high-grade neuroendocrine carcinoma with EGFR gene mutations. Further studies in this respect are warranted. Clinical trials have revealed significant variability in response to EGFR-TKIs, and patient characteristics such as sex, dominantly female, East Asian ethnicity, non-smoking history, and adenocarcinoma (ADC) histology have been associated with an increased likelihood of EGFR-TKI effectiveness [The entry of tyrosine kinase inhibitors (TKIs) gefitinib harboring EGFR gene mutation and apparently responding to EGFR-TKI have sporadically appeared since 2005 -27. The 2) for three months, at the end of which the size of the tumor decreased by one half. Lumbago developed after six months, and metastases to the left iliac bone and the femur were detected by MRI. Focal radiotherapy (39Gy/13Fr) was carried out. The primary lesion had doubled again during the following four months with enlargement of mediastinal lymph nodes. Histopathologic and cytologic follow up examinations were carried out: Papanicolaou smears revealed cells larger than those at previous examinations, and numerous scattered sheet-like arrangements. The cells had fine granular nuclear chromatin and prominent large nucleoli of a high nuclear/cytoplasm ratio and relatively rich cytoplasm was positive with past histories of pulmonary tuberculosis and uterine leiomyoma had been under medical treatment for chronic heart failure with atrial fibrillation, unstable angina, eosinophilic myocarditis, bronchial asthma, hyperuricemia, hyperlipidemia, and hypothyroidism. At a follow-up examination one and half year earlier, chest computed tomography showed a mass (1.5 cm in diameter) in the inferior lobe of the left lung. It had doubled in size within the following four months, and positron emission tomography (PET) and magnetic resonance imaging (MRI) revealed metastases to ipsilateral mediastinal lymph nodes. Serum tumor markers were as follows: pro-gastrin-releasing peptide 105 pg/ml (standard range 0 \u2013 80), carcinoembryonic antigen (CEA) 21.8 ng/ml (0 \u2013 5.2), and cytokeratin 19 fragment 3.0 ng/ml (0 \u2013 2). Transbronchial brushing and needle aspiration against the tumor demonstrated small cells with a high nuclear/cytoplasm ratio and fine granular nuclear chromatin scattered around a large cell cluster in poorly smeared Papanicolaou stains, suggesting high-grade neuroendocrine carcinoma favoring small-cell carcinoma along with anti-EGFR exon 21 L858R mutation antibody [An additional therapeutic choice for high-grade neuroendocrine carcinoma showing poor prognosis is expected, and EGFR-TKI that is now available commercially should naturally be considered even for this carcinoma, much more than for one with adenocarcinomatous characteristics. Presently there is no regimen of chemotherapy for high-grade neuroendocrine carcinoma harboring EGFR gene mutation. Nonetheless, the detection of this disease needs to be attempted through further study. The prerequisite to administering EGFR-TKI for NSCLC is the presence of EGFR gene mutation, as opposed to resistance mutation such as that of exon 20 T790M, exon 19 D761Y, and exon 21T854A ,31,32. Tantibody ,34. AntiThe fact that patients with lung cancer have as many therapeutic choices as possible is gratifying. High-grade neuroendocrine carcinoma generally shows more aggressiveness and rapid relapse than NSCLC. Interestingly, our case suggests the presence of high-grade neuroendocrine carcinoma harboring EGFR gene mutation: EGFR-TKI may provide better quality of life and survival in patients with advanced or relapsed high-grade neuroendocrine carcinoma, particularly that with EGFR gene mutation. EGFR gene mutation-specific immunostaining is potentially effective and should be utilized for easy detection and further study of this rare disease.Written informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.The authors have no grant for this research and no competing interest to declare.All authors read and approved the final manuscript."} +{"text": "MicroRNA (miRNA) and endogenous small interfering RNA (endo-siRNA) are two essential classes of small noncoding RNAs (sncRNAs) in eukaryotes. The class of miRNA is diverse and there exist noncanonical miRNAs that bypass the canonical miRNA biogenesis pathway. In order to identify noncanonical miRNAs and endo-siRNAs responding to virus infection and study their potential function, we sequenced small-RNA species from cells lytically infected with murine gammaherpesvirus 68 (MHV68). In addition to three novel canonical miRNAs in mouse, two antisense miRNAs in virus and 25 novel noncanonical miRNAs, including miRNAs derived from transfer RNAs, small nucleolar RNAs and introns, in the host were identified. These noncanonical miRNAs exhibited features distinct from that of canonical miRNAs in lengths of hairpins, base pairings and first nucleotide preference. Many of the novel miRNAs are conserved in mammals. Besides several known murine endo-siRNAs detected by the sequencing profiling, a novel locus in the mouse genome was identified to produce endo-siRNAs. This novel endo-siRNA locus is comprised of two tandem inverted B4 short interspersed nuclear elements (SINEs). Unexpectedly, the SINE-derived endo-siRNAs were found in a variety of sequencing data and virus-infected cells. Moreover, a murine miRNA was up-regulated more than 35 fold in infected than in mock-treated cells. The putative targets of the viral and the up-regulated murine miRNAs were potentially involved in processes of gene transcription and protein phosphorylation, and localized to membranes, suggesting their potential role in manipulating the host basal immune system during lytic infection. Our results extended the number of noncanonical miRNAs in mammals and shed new light on their potential functions of lytic infection of MHV68. MicroRNAs (miRNAs) are \u223c22-nt small noncoding RNAs (sncRNAs) that are encoded in virus, plants and animals miRNA biogenesis is complex; a collection of diverse miRNAs can be generated through noncanonical pathways that bypass Drosha/Dgcr8 processing. One example is the class of miRtrons Another type of noncanonical miRNAs originates from small nucleolar RNAs (snoRNAs) through their internal hairpin-shaped folding structures Over 200 viral miRNAs have been reported for a variety of DNA viruses, predominately in the Herpesviridae family. These include 25 miRNAs in human Epstein-Barr virus (EBV) and 12 in Kaposi's sarcoma herpesvirus (KSHV) In contrast to miRNAs, endo-siRNAs are derived from long dsRNAs in the form of annealed natural antisense transcripts (NATs) or long hairpin RNAs (hp-RNAs). Processing of long dsRNAs is directly performed by Dicer along dsRNAs to consecutively produce multiple siRNAs. Diverse sources for dsRNA formation have been identified in animals and plants; for review, see ref In this study, we prepared and sequenced small-RNA libraries of cells lytically infected with MHV68 and of mock-treated cells, and searched for canonical and noncanonical miRNAs as well as endo-siRNAs in the MHV68 and mouse genomes. A total of 30 novel miRNAs were identified, which include two antisense miRNAs (miRNAs on the antisense strands of known miRNAs) in the MHV68 genome, and 3 canonical miRNAs and 25 noncanonical miRNAs derived from tRNAs, snoRNAs and introns of the mouse genome. The hairpin structures of virus pre-miRNAs and that of snoRNA- and shRNA-derived pre-miRNAs in mouse were observed to lack loop-distal regions and to be shorter than canonical miRNA hairpins. Atypical base pairings outside the seed regions and a predominant preference of Adenosine as the first nucleotides were observed for noncanonical miRNAs. Furthermore, we also identified a novel endo-siRNA-generating locus in a B4 SINE-inverted repeat region of the mouse genome. Moreover, a set of endo-siRNAs was found in a collection of our data from MHV68-infected cells and previously published sequencing data. Besides the expression of all known and novel miRNAs in the virus, a noncanonical miRNA in mouse was significantly up-regulated in infected cells than in mock-treated cells. The viral and highly up-related miRNAs were predicted to have a large number of target genes, many of which were involved in processes of gene transcription and protein phosphorylation and localized to cell membranes, suggesting their potential role in manipulating the host basal immune system during lytic infection.Three MHV68-infected and two mock-treated small-RNA libraries were prepared from NIH 3T12 cells. The five small-RNA libraries were sequenced separately using Illumina Genome Analyzer II. Both the biological triplet of infected samples and the biological duplicate of mock samples were of a high fidelity and the deep sequencing experiments were highly reproducible; the Pearson's correlation coefficients of a pair of biological duplicates range from 0.8939 to 0.9849. The deep-sequencing profiling experiments resulted in a total of more than 74 million raw sequence reads and 28,268,434 qualified sequence reads, among which 274,266 mapped to the MHV68 genome and 21,364,827 aligned to the mouse reference genome and cDNAs perfectly with no mismatches. Of the reads mapped to MHV68, 241,683 came from the known MHV68 pre-miRNA sequences; of the reads mapped to the host genome, 19,701,917 were from the known murine pre-miRNA sequences. In total, the currently annotated MHV68 and host miRNAs produced 92% of the total mappable reads present in 3T12 cells and S2. We performed a comprehensive search of new miRNA genes in the virus and mouse genomes see based onA total of 30 novel miRNAs were identified in the virus and host genomes, including two virus miRNAs and 28 murine miRNAs . The newPreviously, we used part of the sequencing data that is presented here to identify five novel miRNAs in the MHV68 genome Both miR-M1-8-AS and miR-M1-10-AS were distinct from their sense counterparts with regard to precursor and mature miRNA sequences. Nevertheless, the sense and antisense miRNA precursors also shared high sequence similarities . Both mimiRNA sequence variances, known as miRNA isoforms or isomiRs, have been observed in previous studies We identified 3 novel canonical miRNAs in the mouse genome . DespiteSnora7a and yielded 1,159 sequencing reads from the 10- to 13-nt within the miRNA/miRNA* duplex, whereas the seed region is nearly perfectly paired . Such atWe next examined small RNA reads that aligned to the tRNAs in the mouse genome. The well-conserved murine miRNA, miR-1983, derived from murine tRNA-IIeTA The authenticity of this tRNA SerAGA-derived miRNA candidate as a genuine noncanonical miRNA is supported by several observations. First, the tRNA sequence with a 15-nt 3\u2032 extension was predicted to yield an alternative miRNA-like hairpin structure , right iA total of 15 candidate new miRtrons, including three typical miRtrons and twelve tailed ones, were identified in the mouse genome ; File S1Plod3, has homogeneous 5\u2032 clustered reads starting with dinucleotide GU and the most abundant 3\u2032 clustered reads ending with dinucleotide AG, which are characteristic of intron splice sites where two tandem B4 SINEs are arranged in a convergent fashion . FoldingBesides the newly identified endo-siRNA from B4 SINEs, three previously annotated endo-siRNAs from B1 SINEs in mouse were detected in our virus-infected small-RNA libraries . RelativMus Musculus (mouse) or Rattus norvegicus (rat). In addition, six out of nine snoRNA-derived, the tRNA-derived, and four out of 22 canonical miRNAs, as well as six out of 15 miRtrons were found conserved beyond Rat and further down to Monodelphis domestica (opossum), exemplified by the well-conserved sno-miR-#1 and sno-miR-#9. As for the endo-siRNAs, the three B1 SINE-derived siRNAs appeared only in mouse, while the newly identified B4 SINE-derived siRNA was conserved in rat We studied the conservation of the novel miRNAs and endo-siRNAs via a comparative genomics analysis across seven species in mammals. As listed in d in rat . This miMaking use of all the noncanonical miRNAs we identified and detected, we were able to study their sequence and structural features. Indeed, they have several characteristics, making them distinct from the canonical miRNAs.i.e., the miRNA duplexes were still located at the hairpin ends, different from the canonical miRNA hairpins with loop-distal regions.We observed that all the noncanonical miRNA hairpins were missing 5\u2032 and 3\u2032 arm loop-distal regions, marked as I and V regions of a canonical miRNA hairpin (the foldback structure before Drosha and Dgcr8 processing) in Noncanonical miRNAs have atypical base pairings that appear more frequently in the central regions from 9- to 14-nt or near both ends within miRNA duplexes . The mosA large portion of noncanonical miRNAs have Adenine or Cytosine as the first nucleotides, exemplified by the MHV68 miRNAs with \u223c90% of the total reads starting with A or C in the host genome exhibited more than 35-fold up-regulation in lytically infected cells in reference to mock-treated cells with the percentage of false positive (pfp) less than 0.001 see .Expressed viral miRNAs have the potential to target transcripts in the virus and/or the host to exert their functions. To appreciate their potential regulatory roles, we searched for putative targets of virus miRNAs and isomiRs see . This reFurthermore, the significance of the differential expression of mouse miRNA, miR-142-3p, suggests involvement in gene regulation during lytic infection of MHV68; thus its targets are of primary interest for further investigation. A total of 240 mRNA genes in the mouse genome were predicted to be putative targets of miR-142-3p . On the The large number of putative targets made it possible to further analyze which cellular and signaling pathways may be potentially regulated by the viral and viral-responsive miRNAs. We thus examined Gene Ontology (GO) terms enriched in the putative target genes identified. Among many biological processes revealed by the GO analysis were transcription and protein amino acid phosphorylation . These bPhenotypic differences between Dicer-null and Drosha-null mutants have been observed in recent studies, which implied a potential role for noncanonical miRNAs and endo-siRNAs We identified two novel miRNAs that reside antisense to two known miRNAs in MHV68. Antisense miRNAs have been previously reported in human, Drosophila, KSHV and herpes simplex virus type1 (HSV-1) We observed a substantial amount of sequence variations of virus miRNAs and recognized that one third of virus miRNAs had 5\u2032 heterogeneous isoforms or isomiRs. Some of the isomiRs had comparable abundances as the major miRNAs. This is crucial because 5\u2032 heterogeneity could shift miRNA seed regions and thus alter their downstream target binding. The large amount of miRNA isoforms that we observed may due to the different cells and conditions used in our and previous experiments. The annotation of some of the MHV68 miRNAs in miRBase was based on sequencing data of MHV68-infected murine NIH3T3 and S11 cells It is surprising that the mouse genome encodes so many noncanonical miRNAs in loci of a variety of small noncoding RNAs (sncRNA), including snoRNAs and tRNAs, through alternative RNA folding of cognate transcripts. The flexibility of producing miRNAs from such sncRNAs implies the potential of cognate sncRNA transcripts to derive alternative regulatory functions. Indeed, a murine ACA45-derived miRNA has been recently shown to share seed region similarities with canonical miRNAs, which implied a regulatory role of gene regulation Besides those pre-miRNAs piggybacking on other annotated sncRNA transcripts, intergenic shRNAs originated from unannotated transcripts provided more examples that pre-miRNAs are broadly encoded in mammalian genomes. We also observed that individual members of single shRNA family tend to follow the same biogenesis pathway. For example, the members of miR-344 family were all produced from shRNAs .Distinct from canonical miRNAs, most noncanonical miRNAs shared some common features of their hairpin structures, lengths, base pairings and first nucleotide preferences. All the noncanonical miRNA hairpins that we analyzed were observed to lack distal-loop regions, thus, having an average length of 64.5-nt. Such a structural property is in agreement with the observation that noncanonical miRNA hairpins are similar to pre-miRNAs.Typical miRtrons and tRNA-derived miRNAs tend to have longer hairpin structures, which can give rise to two adjacent miRNA species. One example, miRtron miR-3102 precursor, is 104-nt long and can generate two distinct miRNA/miRNA* duplexes, namely outer and inner miRNAs (close to the loop end) More unpaired bases appeared in snoRNA-derived miRNAs and miRtrons than well-conserved canonical miRNAs. Nonetheless, instead of being inside seed regions, the extra unpaired bases occurred more often at the first nucleotides, in the central regions and near the 3\u2032 ends of miRNAs . Such paConstructed at a particular time during MHV68 lytic infection, the five small-RNA libraries that we analyzed in the current study may be too small to draw a concrete conclusion on the functions of noncanonical miRNAs. Despite this limitation, the data and results, particularly those on the targets of viral miRNAs and the differentially expressed murine miRNA, offered a glimpse into the possible functional roles they may play. As listed in We identified one locus comprising two tandem B4 SINEs to yield a long hairpin and further to give rise to endo-siRNAs. These endo-siRNAs were enzymatically Dgcr8-independent but Dicer-dependent, as expected for endo-siRNAs. Previous studies also revealed a number of examples of endo-siRNAs derived from either B1 SINEs or long terminal retrotransposons (LTRs) in mouse stem cells or oocytes endo-siRNAs were presumed to be largely absent from mammalian cells, a notion bolstered by the assumption that long double stranded RNAs (dsRNAs), a rich source for siRNA generation, would trigger an interferon (IFN) response endo-siRNAs have been reported to originate from other diverse sources including cis-NATs, trans-NATs and Piwi-associating loci previously Identification of noncanonical miRNAs and endo-siRNAs can be difficult due to the plausible presence of heterogeneous small RNAs originating from the same genomic loci, as shown by the snoRNA- and tRNA-derived miRNAs as well as SINE-derived siRNAs. Additionally, atypical folding of corresponding transcripts complicated the discovery procedure. To increase the sensitivity of the procedure, we proposed an integrative computational method by considering multiple features of these small RNAs. The examination of the enzymatic dependency of both individual sequence reads and clustered aligned reads helped differentiate small RNAs derived from different origins. Furthermore, the presence of sequence reads characteristic of Dicer cleavage provided additional information for accurate identification. Such characteristics included the length distribution, 5\u2032 or 3\u2032 end homogeneity, characteristic 5\u2032 or 3\u2032 end of clustered reads that we explored in our study.Total RNA from mock- and MHV68-infected NIH 3T12 cells were prepared as previously described http://www.mirbase.org/ftp.shtml), murine snoRNA and repeats regions .Individual deep sequencing libraries were each processed separately as follows. Reads containing no sequencing adaptor sequence, reads having a substring of adapter strictly shorter than 6-nt, or reads whose trimmed sequences were shorter than 17-nt were removed from further analysis. Adaptor-trimmed reads were mapped to the MHV68 The qualified reads were mapped to the known miRNA loci by Bowtie Candidate miRNAs were prioritized based on (1) occurrence of sequencing reads on the stem of a predicted hairpin structure with minimum folding energy less than -18 kcal/mol To identify miRtrons, a 160-nt intronic sequence adjacent to exon/intron boundary was extracted for each intron in the mouse genome . The same procedure for finding miRNAs as described above was then applied to identify miRtrons. In addition, the presence of sequencing reads starting or ending at intron splice sites was examined as a signal of miRtrons. The suboptimal secondary structures within an folding energy difference of 5 kcal/mol predicted by RNAsubopt The EINVERTED program To identify authentic endo-siRNAs derived from long dsRNAs, we calculated the length distribution of reads uniquely mapped to each candidate and required that more than 60% of the mappable reads must be 21- to 23-nt long, as typically expected for siRNAs Mus musculus (mouse), Rattus norvegicus (rat), Homo sapiens (human), Pongo pygmaeus abelii (Orangutan), Canis lupus familiaris (dog), Equus caballus (horse), Monodelphis domestica (opossum), and Gallus gallus (chicken) \u2013 for each novel sncRNA. Next, based on the multiple alignments of the eight species, we calculated the number of insertions, deletions and mismatches when each non-murine sequence was compared to the murine sncRNA . The hairpin sequences of novel and newly annotated noncanonical miRNAs, provided in sample be the number of qualified reads that aligned to the mouse genome (mm9 build) in each sample, C the average of all Nsample, and Msample the number of qualified reads in each sample aligned to each sncRNA. Thus, the normalized number of reads for each sncRNA in a given sample is (Msample*C)/(Nsample). Fold changes were calculated from the average normalized read counts in each category (MHV68-infected or mock-treated). We identified differentially expressed genes using Rank Product (RP) implemented in R We collected the newly identified sncRNAs and the known murine miRNAs (miRBase version 17) for differential expression analysis. Reads aligned perfectly to the set of sncRNAs with 3-nt extension on either end, in order to include their possible isoforms, were considered in the analysis. Reads mapped to multiple genomic loci were attributed to all derivative small RNAs. Read counts in each sample were normalized to adjust for variation in total read count between samples. Let Ni.e., virus miRNAs and differentially expressed host miRNAs, to find their putative targets. We set a minimum length cutoff greater than 160-nt and no mismatches in miRNA seed regions to predict targets.Sequences for MHV68 ORFs were downloaded from NCBI website (NC_001826.2). Sequences for host murine 3\u2032 UTRs were fetched from the Refseq table in UCSC genome browser (mm9 build). The two sets of sequences were then combined as a whole for target prediction. We applied miRanda p-value, before and after multiple-test corrections, based on a modified Fisher's exact test.The GO term analysis was performed using the online tool DAVID All small-RNA deep-sequencing data have been deposited into NCBI/GEO databases, and the accession number is GSE36639.Figure S1Flowchart describing the major steps for novel miRNAs identification.(PDF)Click here for additional data file.Figure S2Normalized reads in wide-type, Dicer- and Dgcr8-knockout mice (GSE12521). (A) snoRNA-derived miRNA candidate #3. (B) snoRNA-derived miRNA candidate #9. (C) tRNA-derived miRNA discussed in the main text. (D) endo-siRNA derived from inverted B4 SINEs.(PDF)Click here for additional data file.Figure S3Sequence reads aligned to sno-miR-#3. Reads corresponding to snoRNA fragments (in blue) appeared in both Dgcr8- and Dicer-knockout mice, while representative miRNA reads were found in Dgcr8- but not in Dicer-knockout mice.(PDF)Click here for additional data file.Figure S4Examples of known and novel snoRNA-derived miRNAs bearing atypical folding structures. (A) Folding structure of snoRNA HBI-100 carrying an annotated miRNA,mmu-miR-1843 with 4.5 unpaired bases in the central bulge, indicated inside the red ellipsis. (B) Folding structure of SNORA1 carrying novel sno-miR-#9 with 5 unpaired bases in the central bulges.(PDF)Click here for additional data file.Figure S5A murine miRNA derived from tRNA-SerAGA. (A) Alignment of reads representing the tRNA fragments and miRNA sequences. The tRNA is annotated in blue with the putative Pol III transcription terminal signal (in orange). Untemplated reads derived from tRNA CCA addition end with blue characters, while miRNA reads are annotated in red. The arrows indicate the RNase P (left) and RNase Z (right) processing. (B) The tRNA folding structure (left) and the alternative miRNA hairpin structure (right) with the miRNA annotated in red, with folding energy being presented below each structure. (C) Multiple sequences alignments of tRNA-SerAGA sequence among eight mammalian species with the miRNA indicated in the red rectangle.(PDF)Click here for additional data file.Figure S6Sequence reads mapped to the (A) mmu-miR-702 and (B) mmu-miR-5132 hairpins. Sequence in blue represents intron region, while in yellow represents flanking exon regions. Reads comprising GU or AG dinucleotide, which is characteristic of intron splice sites, were marked in red.(PDF)Click here for additional data file.Figure S7Six of 17 previously annotated cis-NATs in the previous study appeared in the current MHV68-infected data. All of the loci are based on UCSC mouse reference genome (version mm8). Mapping of reads and numbers of reads (log2 based) in current data set (GSE36639) and in oocyte (GSM261957) are shown in the top two tracks. RefSeq and Ensembl Gene annotations, repeat elements and conservation scores are shown (see USCS genome browser for details of track information).(PDF)Click here for additional data file.Figure S8The relationship between the copy number and the percentage of all genomic-aligned reads included.(PDF)Click here for additional data file.File S1Read alignments for 49 novel miRNAs in and The first column on the left indicates the number of reads in the sequencing data; the second column indicates the length of the read; the third column indicates how many loci in the MHV68 or mouse genome (version mm9) the read can be mapped to.(TXT)Click here for additional data file.File S2Read alignments for the novel and previously annotated murine endo-siRNA in current sequencing data. The genome information was based on UCSC mouse genome annotation (mm9 build).(TXT)Click here for additional data file.File S3Multi-species alignments of sncRNAs among seven species. The number of insertion (ins), deletion (del) and mismatches (mis) compared to mouse sncRNAs are listed. The multi-species include mouse (mm9), rat (rn4), human (hg18), orangutan (ponAbe2), dog (canFam2), horse (equCab1) and opossum (monDom4). Small RNAs from the sequencing data of human psoriatic skin (GSE31037) were aligned to human homologous sequences.(TXT)Click here for additional data file.Table S1Reads mapped to the known miRNAs (miRbase version17).(XLSX)Click here for additional data file.Table S2Abundance of MHV68 miRNA, miRNA* and their isoforms. The sequences underlined indicate the most abundant read. The annotated miRNA sequences (miRbase version 17) were indicated in column miRbase. Five miRNAs showing 5\u2032 isoforms are marked in yellow.(XLSX)Click here for additional data file.Table S3Twenty-eight novel miRNAs in the mouse genome represented by normalized reads from wide-type (wt), Dicer- (dicer) and Dgcr8-knockout (dgcr8) mice .(XLSX)Click here for additional data file.Table S4Newly annotated and previously described noncanonical miRNAs. The column of # Reads represents the number of reads in the current sequencing data for each mature miRNA sequence. Normalized reads from wide-type (wt), Dicer- (dicer) and Dgcr8-knockout (dgcr8) mice (XLSX)Click here for additional data file.Table S5A set of miRNA candidates identified in the mouse genome (build mm9). The columns of # reads represent the number of reads in all samples perfectly mapping to mature miRNA and hairpin sequences, respectively. The column of location indicates the names of host genes overlapping with miRNAs.(XLSX)Click here for additional data file.Table S6Conservation of noncanonical miRNAs and endo-siRNAs that were analyzed.(XLSX)Click here for additional data file.Table S7MHV68 open reading frames targeted by MHV68 virus miRNAs. The number at the end of the miRNA name represents the digital counts of the miRNA and indicates the corresponding isoform. Annotation of MHV68 open reading frame can be downloaded from NCBI with accession number NC_001826.2.(XLSX)Click here for additional data file.Table S8List of genes in mouse genome targeted by MHV68 virus miRNAs.(XLSX)Click here for additional data file.Table S9List of genes in mouse genome targeted by the differentially expressed murine miRNA (miR-142-3p).(XLSX)Click here for additional data file.Table S10Representative Gene Ontology functions of predicted genes targeted by virus and differentially expressed miRNAs.(XLSX)Click here for additional data file."} +{"text": "Fc-mediated inhibitory activity of neutralizing antibodies has been shown to participate in HIV protection . In addition, a non-neutralizing antibody F240 was found to partially protect macaques from SHIV vaginal transmission . However, mechanisms involved in this protection need further investigations. In this study, two non-neutralizing antibodies have been selected on the basis of their Fc-mediated inhibitory functions in vitro for further analysis of their protective role on vaginal challenge in non-human primate (NHP).We have assessed and scored various in vitro HIV-inhibitory activities of non-neutralizing antibodies: Fc-mediated inhibition of macrophages through phagocytosis of immunecomplexes, ADCC in primary infected CD4+ T lymphocytes by autologous NK cells, capture of native primary virus particles. Efficacy of two anti-PID antibodies with high in vitro functional scores has been tested in NHP. The combination of two antibodies formulated in 1.6% HEC gel has been topically applied in the vagina of macaques (n=6), 1 hour before vaginal challenge with high dose (10 AID50) of SHIVSF162P3.Infection was followed by assessing viral load in the plasma.Although unable to block virus entry at mucosal site as all treated animals became persistently infected, the antibody treated macaques have significant decrease of plasma viral load .Decrease in viral load following antibody treatment strongly suggests that non-neutralizing inhibitory antibodies could interfere with early viral replication and dissemination through Fc-mediated inhibitory functions. Additional studies will be required to optimize this inhibition, and combined strategies should be developed to assess the potential synergy between neutralizing and non-neutralizing inhibitory antibodies."} +{"text": "Because of the frequent interchange of patients between acute hospitals and rehabilitation hospitals, infections caused by multidrug-resistant bacteria will continue to emerge. There are limited data concerning the epidemiology of nosocomial infection among patients admitted for rehabilitation in non acute hospitals after stabilization of an acute surgical or neurological event. Recognition of such threats has prompted new interest in the prevention and control of infections associated with those health-care facilities.To evaluate the impact of an intervention on rates of methicillin-resistant Staphylococcus aureus (MRSA) colonization or infection in a geriatric-rehabilitation hospital.Quasi-experimental analysis before/after.A 160 bed geriatric-rehabilitation hospital in Guadarrama (Madrid), Spain.All patients admitted to the hospital during two periods: 2003-2004 and 2010.A multimodal intervention consisting on active surveillance for MRSA in all patients admitted and a comprehensive hand hygiene promotion programme is studied.The preintervention rate of MRSA colonization or infection was 1.02 cases per 1,000 patient-days . The rate decreased significantly to 0.21 cases per 1,000 patient-days after the intervention.None declared."} +{"text": "The recent identification of another modified form of cytosine, 5-hydroxymethylcytosine (5-hmC), in both stem cells and post-mitotic neurons, raises new questions as to the role of this base in mediating epigenetic effects. Genomic studies of these marks using model systems are limited, particularly with array-based tools, because the standard method of detecting DNA methylation cannot distinguish between 5-mC and 5-hmC and most methods have been developed to only survey the human genome.Methylation on the fifth position of cytosine . Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressor genes finds 76 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Similarly, adapting the assay to detect 5-hmC finds highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus >> mouse). Annotation of 5-hmC with respect to gene structure reveals a significant prevalence in the 3'UTR and an association with chromatin-related ontological terms, suggesting an epigenetic feedback loop mechanism for 5-hmC.We show that non-human data generated using the optimization of a widely used human DNA methylation array, designed only to detect 5-mC and 5-hmC, greatly improving the utility of mammalian model systems to study the role of epigenetics in human health, disease, and evolution.Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both DNA methylation and histone modifications are essential epigenetic components in the establishment of the transcriptional state of eukaryotic genes throughout the genome. The best understood of these epigenetic modifications is DNA methylation, which occurs primarily at cytosines located 5' to guanosine in the CpG dinucleotide of differentiated eukaryotic nuclei . This mo5-hmC), in both stem cells and post-mitotic neurons, raises new questions as to the role of this base in mediating epigenetic effects. 5-hmC is mediated by members of the ten-eleven translocation (TET) family of proteins, which each contain a C-terminal oxidase domain. Recently, a highly efficient and selective chemical approach to label and capture 5-hmC revealed the first distribution map of 5-hmC in a mammalian brain genome (mouse) and showed that 5-hmC is enriched in the gene bodies of active or highly transcribed genes , where \u03b2 ranges from 0 (unmethylated) to 1 (methylated). For human samples, quality control of data resulted in removal of samples with aberrantly low signal intensity (mean\u2009<\u20092000) or with fewer than 99% of CpG loci detected, where a given locus was deemed not detected if the detection P-value was >\u20090.01 . For rhesus, chimp and mouse samples, the data for only the \u2018competent\u2019 probe-set (ref. section \u2018Assay optimization\u2019) for each species was taken. Furthermore, any probes having more than 20% of samples with detected P-values\u2009>\u20090.01 were discarded from the analysis. Assay controls were inspected to remove samples with poor bisulfite conversion, staining, extension (single nucleotide extension assay), hybridization, or specificity. Outliers identified by hierarchical clustering and/or dissimilarity matrices were removed. Additionally, one control DNA replicate was run on each BeadChip to assess overall assay reproducibility. Methylation profiles of the control DNA correlated well, with an average Pearson correlation coefficient (R) of 0.990 between human replicates.To analyze DNA methylation differences associated with cancer, we fit a separate regression for each CpG site. Although samples were randomly distributed across BeadChips and experiments with respect to disease, BeadChip was also included as a random effect covariate in all analyses to account for potential batch effects. The package \u201cnlme\u201d in R (Cran) was used for the mixed effect model. Fixed effects included intensity in the model. To correct for multiple hypothesis testing, we applied a Benjamini-Hochberg False Discovery Rate (FDR) correction using the R function \u201cp.adjust,\u201d but to avoid false positives due to the small sample size, we used conservative Bonferroni adjustment for our ultimate determination of significance.All permutation analyses were conducted in R using the same linear model as the actual analysis, where BeadChip was treated as a mixed-effects covariate, but in each permutation the tissue type of the sample was randomly reassigned. In total, 100 permutations were conducted. Permutation P-values for each CpG locus were calculated by assessing the number of times each locus was more significantly associated with fetal tissue in the 100 permuted data sets than the actual.5-hmC were assessed using both Fisher\u2019s exact test and permutation analysis, which corresponded well (data not shown). Permutation P-values were determined as described previously [5-hmC loci on a chromosome to the proportions obtained using the permuted loci (termed \u201cpermuted proportions\u201d). To correct for multiple hypotheses (i.e. 24 chromosomes and both over and underrepresentation) the actual proportion of each chromosome was compared to the permuted proportions of any chromosome for each permutation. Thus the permutation P-value is the number of times a permuted proportion is more significant than the actual proportion, divided by the number of permutations .Loci were mapped to chromosome location using the Illumina annotation files for the HumanMethylation450 panel based on the NCBI Human Genome (build 37). Over- and underrepresentation of CpG loci with\u2009>\u200920% median eviously , by compWe have submitted the data generated from the monkey, chimp, human and mouse samples for this study to the Gene Expression Omnibus (GEO), which can be found under the Gene Series: GSE49177.The authors declare that they have no competing interests.PC conceived of the study, analyzed the data and wrote the manuscript. LAP performed experiments and wrote the manuscript. ATJW and AH performed the validation experiments. RMB developed the software to display the validation data. PHR, MAG, and TGG selected and acquired samples. STW provided critical conceptual advice and the arrays, and helped write the manuscript. RSA conceived of the study, analyzed the data and wrote the manuscript. All authors read and approved the final manuscript.Optimized probe sets for each species. The list of Illumina probe identification names that were used for each non-human species. Header indicates the species and whether these probes were identified as exact matches or mismatches (see Methods).Click here for fileArray-based assay probe distribution and validation. A) The density (y-axis) of genes and the number of probes for each gene are shown for human (blue), rhesus (orange), and mouse (black) genomes. B) Permutation analysis of placenta-associated differential methylation. Scatter plot of permuted (100 permutations) placental-associated P-values (x-axis) compared to asymptotic P-values (y-axis) calculated using the linear model (Pearson R\u2009=\u20090.9852). C-M) Independent assay validates the accuracy of the array for 5-mC (rhesus) and 5-hmC (human and rhesus) C-G) Bar charts showing the side-by-side comparison of the methylation levels (y-axis) of CpG loci near genes (denoted above each chart) in different monkey tissues that were determined by either sodium bisulfite treatment, cloning, and sequencing (white bars) or the HumanMethylation450 BeadChips (black bars). H-M) Circle plots showing the 5-mC and 5-hmC status of individual CpG loci in human (H-K) and monkey (L-M) genes (denoted above each plot) from brain tissue. Each circle represents the methylation status of an independent clone . The numbers along the left of each panel indicates the percent methylation that was determined using either the HumanMethylation450 BeadChips (Array) or the independent assay . The numbers along the left indicates the nucleotide number from the transcription start site of each gene, as referenced from UCSC build 37/hg19. Each row of the panels indicates a different clone.Click here for fileDifferentially methylated loci identified between rhesus placental and fetal tissue using genes previously investigated by Chui et al. [. Header descriptions include: the Illumina assay probe identification (cgid); the Bonferroni corrected P-value (bonferroni); the false discovery rate (fdr); uncorrected P-value (none); permutation P-value ; the genome build that the probe was designed on (Genome_Build); the human chromosome that the probe is located on (CHR); the genomic coordinates on the human chromosome (MAPINFO); the gene name as annotated by the University of California Santa Cruz genome browser (UCSC_RefGene_Name); the UCSC accession number for the gene (UCSC_RefGene_Accesssion); the location of the locus in relation to the UCSC gene structure (UCSC_RefGene_Group); and the location of the locus in relation to a UCSC annotated CpG island .et al. . Header Click here for fileGenome-wide differentially methylated loci identified between rhesus placental and fetal tissue. Header descriptions include: the Illumina assay probe identification (cgid); the Bonferroni corrected P-value (bonferroni); the false discovery rate (fdr); uncorrected P-value ; the genome build that the probe was designed on (Genome_Build); the human chromosome that the probe is located on (CHR); the genomic coordinates on the human chromosome (MAPINFO); the gene name as annotated by the University of California Santa Cruz genome browser (UCSC_RefGene_Name); the UCSC accession number for the gene (UCSC_RefGene_Accesssion); the location of the locus in relation to the UCSC gene structure (UCSC_RefGene_Group); and the location of the locus in relation to a UCSC annotated CpG island .Click here for fileOutput results from gene ontology and KEGG analysis. This table has five pages that can be accessed using the labeled tabs at the bottom. The first two tabs are gene ontology or KEGG analysis using the 6,102 loci identified with the genome-wide regression analysis. The header descriptions include: the gene ontology or KEGG identification number (GOBPID or KEGGID); the P-value associated with finding this term ; the Odds ratio for the term (OddsRatio); the expected number of genes to be associated with the term (ExpCount); the actual number of the differentially methylated genes that are associated with the term (Count); the total number of genes on the assay associated with the term (Size); and the term name (Term). The other three pages of this file are the output results from a gene ontology analysis using the X-linked CpG loci with\u2009>\u200940% 5-hmC in primates and 5hmc_Chr_X_Rhesus_GeneOntology_; tab 4 (monkey)) or\u2009>\u200920% in mice . Header descriptions are the same as above for tab 1.Click here for fileDifferentially methylated loci identified between rhesus placental and fetal tissue using genes annotated to oncogenes and tumor suppressor genes. Header descriptions include: the Illumina assay probe identification (cgid); the Bonferroni corrected P-value (bonferroni); the false discovery rate (fdr); uncorrected P-value ; the genome build that the probe was designed on (Genome_Build); the human chromosome that the probe is located on (CHR); the genomic coordinates on the human chromosome (MAPINFO); the gene name as annotated by the University of California Santa Cruz genome browser (UCSC_RefGene_Name); the UCSC accession number for the gene (UCSC_RefGene_Accesssion); the location of the locus in relation to the UCSC gene structure (UCSC_RefGene_Group); and the location of the locus in relation to a UCSC annotated CpG island .Click here for fileMammalian DNA methylation levels detected on the human array are highly correlated. Scatter plots of human (A), chimpanzee (B), rhesus (C), and mouse (D) methylation data (5-mC) generated from biological replicates run on the HumanMethylation450 BeadChips are shown for mismatch species-competent probes ; 360,491 (B); 154,030 (C), or 9,734 (D)). The diagonal red line indicates the regression line and the x and y-axes indicate the methylation level for each individual. The correlation level (R2) is denoted above each plot.Click here for file5-hmC distinguishes species and is highly reproducible among mammals. Unsupervised hierarchical cluster analyses of 5-mC (A) and 5-hmC (B) probe data common to all species that was generated from brain tissue of human (E06 samples), monkey (r# samples), and mouse individuals are shown. The length of the branches using the scale shown indicates relatedness. Scatter plots of rhesus (C) and mouse (D) brain methylation data (5-hmC) generated from biological replicates run on the HumanMethylation450 BeadChips are shown to have a mean R2\u2009>\u20090.92. Data for each probe is represented as a blue dot. For all scatter plots, the diagonal red line indicates the regression line and the x and y-axes indicate the methylation level for each replicate.Click here for fileGene structure specific probe distribution among species. The density (y-axis) of probes at each annotated gene structure (x-axis) using the human (blue), rhesus (orange), and mouse (black) optimization of the array.Click here for fileThe distribution of DNA methylation with respect to CpG islands. The density (y-axis) of probes at each methylation level in monkey (A-E) and mouse (F-J) brain samples that were either interrogated for total methylation (5mc\u2009+\u20095hmc (black line)) or 5-hmC levels (5hmc (blue line)). Profiles shown are delineated for the island, the island shores (N_shore (5\u2019 end) and S_shore (3\u2019 end)) or the island shelves , monkey , and mouse . The last three tabs are the results from our chromosomal analysis on human , monkey , and mouse . All of the pages in this file have the following header descriptions: a genomic description of the locus location (Region (tabs 1-3); Chromsome (tabs 4-6)); whether the data is filter for probes\u2009>\u200920% or\u2009>\u200940% 5-hmC (Cutoff); the total number of probes in the dataset (NumProbes_Dataset); the number of probes after the filter has been applied (NumProbes_Cutoff); the number of probes in the genomic description of interest (NumProbes_Region or NumProbes_Chr); the number of probes that meet the genomic description and the filter criteria (NumCommonProbes); the Fisher\u2019s exact test P-value ; the odd ratio for the result (OddsRatio); and the permuted P-value . The tabs showing the chromosomal analysis also have a column that shows the variance that the data has for each chromosome (Variance). See text for definitions of the regions.Click here for fileThe distribution of DNA methylation with respect to gene structures. The density (y-axis) of probes at each methylation level in monkey (A-F) and mouse (G-L) brain samples that were either interrogated for total methylation (5mc\u2009+\u20095hmc (black line)) or 5-hmC levels (5hmc (blue line)). Profiles shown are delineated relative to a gene, including the distance to the gene transcription start site and TSS200), 5\u2019UTR, 1st exon, body, and 3\u2019UTR. The number of probes is indicated for each island and gene category.Click here for fileThe range of 5-hmC levels on each chromosome. The distribution of 5-hmC in monkey and mouse brain tissues is shown using box and whisker plots depicting the 5-hmC level (y-axis) of probes by chromosome (x-axis).Click here for file"} +{"text": "Recent our microRNA (miRNA) expression signature revealed that expression of microRNA-218 (miR-218) was reduced in cancer tissues, suggesting a candidate of tumor suppressor in head and neck squamous cell carcinoma (HNSCC). The aim of this study was to investigate the functional significance of miR-218 and its mediated moleculer pathways in HNSCC. Restoration of miR-218 in cancer cells led to significant inhibition of cell migration and invasion activities in HNSCC cell lines (FaDu and SAS). Genome-wide gene expression analysis of miR-218 transfectants and in silico database analysis showed that focal adhesion pathway was a promising candidate of miR-218 target pathways. The laminins are an important and biologically active part of the basal lamina, the function of that are various such as influencing cell differentiation, migration and adhesion as well as proliferation and cell survival. Interestingly, all components of laminin-332 are listed on the candidate genes in focal adhesion pathway. Furthermore, we focused on LAMB3 which has a miR-218 target site and gene expression studies and luciferase reporter assays showed that LAMB3 was directly regulated by miR-218. Silencing study of LAMB3 demonstrated significant inhibition of cell migration and invasion. In clinical specimens with HNSCC, the expression levels of laminin-332 were significantly upregulated in cancer tissues compared to adjacent non-cancerous tissues. Our analysis data showed that tumor suppressive miR-218 contributes to cancer cell migration and invasion through regulating focal adhesion pathway, especially laminin-332. Tumor suppressive miRNA-mediated novel cancer pathways provide new insights into the potential mechanisms of HNSCC oncogenesis. Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and approximately 650,000 new cases occur and 350,000 patients dying from HNSCC annually . DespiteThe discovery of non-coding RNA in human genome is a topic in post genome sequencing era . The recA growing body of evidence indicated that miRNAs also contributed to the initiation and development of various types of cancers , 6. ManyWe previously identified tumor suppressive miRNAs based on miRNA expression signatures of various types of cancer, such as hypopharyngeal, maxillary sinus, esophageal, and lung SCCs, and renal cell carcinoma and bladder cancer -13. We hmicroRNA-218 (miR-218) was significantly reduced in cancer tissues and TargetScan release 6.2 [http://www.targetscan.org/] were used to identify predicted target genes and their miRNA binding site seed regions. Sequences of the predicted mature miRNAs were confirmed using miRBase release 18.0 [http://microrna.sanger.ac.uk/].A genome-wide screen was performed to identify gene targets for Written consent for tissue donation for research purposes was obtained from each patient before tissue collection. The protocol was approved by the Institutional Review Board of Chiba University. Thirty-five pairs of primary tumor tissues and corresponding normal epithelial tissues were obtained from patients with HNSCC in Chiba University Hospital from 2007 to 2012. The normal tissue was confirmed to be free of cancer cells by pathologic examination. The specimens were immersed in RNAlater and stored at \u221220\u00b0C until RNA was extracted. The patients were classified according to 2002 Union for International Cancer Control TNM staging criteria before treatment.http://rsbweb.nih.gov/ij/index.html).Cells were harvested and lysed 48 h after transfection. Each cell lysate (50 \u03bcg of protein) was separated using Mini-PROTEAN TGX gels and transferred to PVDF membranes. Immunoblotting was performed with polynoclonal LAMA3 antibody , polyclonal LAMB3 antibody and monoclonal LAMC2 antibody . GAPDH antibody was used as an internal control. The membrane was washed and incubated with anti-rabbit IgG, HRP linked antibody or anti- mouse IgG, HRP linked antibody . Complexes were visualized with an Immun-Star\u2122 WesternC Chemiluminescence Kit (Bio-Rad), and the expression levels of these proteins were evaluated by ImageJ software Partial sequences of the LAMB3 3' untranslated region that contains miR-218 target sitewere inserted between the XhoI and PmeI restriction sites in the 3'UTR of the hRluc gene in the psiCHECK-2 vector . FaDu and SAS were then transfected with five ng vector, 10 nM mature miRNA molecules, Pre-miRNA miR-218 (Applied Biosystems), and one \u03bcL Lipofectamine 2000 (Invitrogen) in 100 \u03bcL Opti-MEM. Firefly and Renilla luciferase activities in cell lysates were determined using a dual-luciferase assay system . Normalized data were calculated as the quotient of Renilla/firefly luciferase activities.The relationships between two groups and the numerical values obtained by qRT-PCR were analyzed using the Mann-Whitney U test or the paired t-test. The relationship among more than three variables and numerical values was analyzed using the Bonferroni adjusted Mann-Whitney U test. All analyses were performed using Expert StatView ."} +{"text": "Small studies with composite endpoints show that midwall fibrosis, identified by late gadolinium enhancement cardiovascular magnetic resonance (LGE-CMR), predicts short term adverse prognosis in dilated cardiomyopathy (DCM). We hypothesized that midwall fibrosis is an independent predictor of mortality over a long follow-up period.Consecutive patients with DCM referred for CMR between 2002-2008 were prospectively enrolled. The diagnosis of DCM was made using clinical, CMR and coronary angiographic findings. Patients with ischemic heart disease, primary valvar disease and infiltrative CM were excluded. LGE-CMR at 1.5T was performed in 2 phase-encoding directions. The presence of midwall LGE was determined by a specialist blinded to all outcome data. The primary endpoint was all-cause mortality. The secondary endpoint was a composite of cardiovascular (CV) mortality or cardiac transplantation.Two hundred and thirty patients were followed up for a median duration of 44 months. Midwall fibrosis was identified in 87 (38%) patients. No patient was lost to follow-up. There were 33 deaths and 7 patients underwent cardiac transplantation. Kaplan-Meier analysis demonstrated a significant association between the presence of midwall fibrosis and both the primary (p=0.02, Fig.Midwall fibrosis is a significant independent predictor of both all-cause mortality and CV mortality/transplantation in DCM. Detection of midwall fibrosis by LGE-CMR represents an important and novel marker for the risk stratification of DCM patients.This work was supported by the NIHR Cardiovascular Biomedical Research Unit at the Royal Brompton and Harefield NHS Foundation Trust and Imperial College London. Dr Ankur Gulati receives salary support from CORDA."} +{"text": "Translational Stroke Research gives readers a timely update on the emerging roles of glutamate receptor-independent ion channels and transporters in ischemic brain injury. This issue has collected contributions from the leading research laboratories with expertise on the most important ion transport targets. For example, Khanna et al. [N-methyl-d-aspartate-independent ion transporters and channels that mediate apoptotic volume decrease or cytotoxic cell swelling [This special featured issue of a et al. provide swelling . Norenbeswelling report n+ channels [+ channel Hv1 in microglial activation [+/H+ exchangers and alkaline pHi in perinatal brain injury. Pignataro et al. discuss a strategy of targeting increased Ca2+ efflux mediated by Na+/Ca2+ exchanger in stroke intervention [The second half of the issue include comprehensive discussions of voltage-gated Kchannels and the channels , 6 in istivation , followitivation present rvention . Chen etrvention .In summary, these timely papers illustrate exciting new findings in the area of glutamate receptor-independent mechanisms of ischemic ionic injury in the nervous system, and reveal the critical role of dysregulated ion transport, mediated by diverse ion transport proteins, in the neurogliovascular unit. These reports show that ischemia-induced ion channel/transporter dysfunction affects multiple critical cell processes, including cell volume regulation , intraceTranslational Stroke Research.Perhaps nowhere closer is the reality of clinical translation of basic findings more apparent than in the story of the SUR1-regulated TRPM4 ion channel, and its role in the pathogenesis of cerebral edema and hemorrhagic transformation following ischemic stroke . Glibenclamide, an FDA-approved drug commonly used in patients with type 2 diabetes, inhibits SUR1-TRPM4, and several robust preclinical studies have demonstrated the efficacy of glibenclamide in reducing edema and hemorrhagic conversion in rodent models of ischemic stroke. This has in turn prompted the study of the potential protective effects of glibenclamide in humans in an ongoing prospective phase II clinical trial, and preliminary data from this effort suggests glibenclamide also significantly reduces ischemic cerebral edema and hemorrhagic conversion . Many ot"} +{"text": "Baseline characteristics of women suffering from ST-elevation myocardial infarction (STEMI) diverge compared to men. Therefore the presence and extent of microvascular obstruction (MO), which has been shown to be a prognostic marker for adverse clinical outcome after STEMI, might differ between genders. Up to date gender differences of MO after STEMI have not been evaluated.STEMI patients reperfused by primary angioplasty (n=423) within 12 hours after symptom onset underwent contrast-enhanced-MRI at a median of 3 days after the index event. MO was measured 15 minutes after gadolinium injection with late enhancement sequences and evaluated qualitatively and quantitatively (as percentage of left ventricular mass [%LV]).A total of 105 women and 318 men were analysed . In comparison to men, women were significantly older , displayed longer symptom-onset-to-reperfusion times , a higher prevalence of diabetes mellitus and arterial hypertension . Complete epicardial reperfusion defined as post-PCI TIMI-flow III did not differ significantly between genders.The prevalence and extent of MO, infarct size and left ventricular ejection fraction were similar in women and men .Despite longer ischemic time and a more disadvantageous cardiovascular risk profile in women the prevalence and extent of MO do not differ between genders."} +{"text": "In contrast to adults with coronary artery disease (CAD), the use of CMR adenosine stress perfusion in pediatrics and in adults with congenital heart disease (CHD) is not well established. The medical literature reveals an absence of experience evaluating the effects of CMR adenosine stress perfusion on clinical decision making and outcomes in these populations.Evaluate whether CMR adenosine stress perfusion in pediatrics and adults with CHD affects clinical decision making and outcomes.Consecutive patients, who completed CMR adenosine stress perfusion and were < 21yo or > 21yo with CHD, were enrolled. SSFP cine and delayed enhancement CMR (DE-CMR) were performed in a standard manner. Adenosine stress perfusion was performed with administration of adenosine (140 ug/kg/min) for 2-4 minutes and gadolinium (0.1 mmol/kg) using a standard adult protocol. Perfusion defects matching infarct size on DE-CMR and defects corresponding to DE-CMR at the right ventricular insertion site or post-surgical changes were considered negative for ischemia.51 studies were performed in 46 patients . Diagnoses and symptoms are listed in Tables A negative finding on CMR adenosine stress perfusion often results in no further testing, indicating confidence in the result. A positive result can lead to further work-up and positively affect patient outcomes.Institutional."} +{"text": "A good correlation has been found between the extent of late gadolinium enhancement (LGE) and clinical outcome in patients who have undergone radiofrequency (RF) ablation for atrial fibrillation (AF). However, there can be strong residual blood signal in the traditional inversion-recovery (IR) sequence, which hampers scar visualization and causes poor repeatability of scar size measurements. The dual-IR sequence has previously been shown to improve blood suppression in LGE images of ventricular scar. We aimed to assess whether the superior blood suppression in the dual-IR pre-pulse improved the inter-observer variability of left atrial scar measurements compared with the IR sequence.The dual-IR pre-pulse consists of two non-selective inversion pre-pulses separated by two time delays TI1 and TI2. The TI1 and TI2 delays were optimized to achieve signal suppression in the T1-range 250-1400ms. Whereas the IR sequence can only null one T1 species , the dual-IR pre-pulse simultaneously suppresses both the blood and normal myocardium whilst maintaining high signal in the scar.11 patients underwent MR imaging using a 1.5T MR scanner approximately 3 months after RF ablation for AF. Dual-IR imaging was performed at 20 minutes and compared to standard IR imaging at 25 minutes after 0.2 mmol/kg of Magnevist was administered. For each 3D image set, two blinded, independent, experienced readers used ITK-SNAP software to manually segment areas of LGE around the left atrial wall.Dual-IR images achieved superior blood suppression at an earlier time point compared with IR images Figure . There wThe dual-IR technique improves blood signal suppression and definition of the edges and boundaries of LGE areas. This leads to improved inter-observer variability in scar size quantification. As imaging can be performed earlier, it also has the potential to reduce the overall scan time.This work was funded by the British Heart Foundation award RE/08/003. The authors also acknowledge financial support from the Department of Health via the National Institute for Health Research (NIHR) comprehensive Biomedical Research Centre award to Guy's & St Thomas' NHS Foundation Trust in partnership with King's College London and King's College Hospital NHS Foundation Trust and the Centre of Excellence in Medical Engineering funded by the Wellcome Trust and EPSRC under grant number WT 088641/Z/09/Z."} +{"text": "Background and Purpose. Cerebral white matter hyperintensities (WMHs) are regarded as typical MRI expressions of small-vessel disease (SVD) and are common in hypertensive patients. Hypertension induces pathologic changes in macrocirculation and in microcirculation. Changes in microcirculation may lead to SVD of brain and consequently to hypertensive end-organ damage. This damage is regarded the result of interactions between the macrovascular and microvascular levels. We sought to investigate the association of cerebral WMHs with ultrasonographic parameters of cerebral macrocirculation evaluated by carotid duplex ultrasound (CDU) and transcranial doppler (TCD). Subjects and Methods. The study was prospective, cross-sectional and consecutive and included hypertensive patients with brain MRI with WMHs. Patients underwent CDU and TCD. The clinical variables recorded were demographic characteristics and vascular risk factors . Excluded from the study were patients with history of clinical stroke (including lacunar stroke and hemorrhagic) or transient ischemic attack (either hemispheric or ocular), hemodynamically significant (>50%) extra- or intracranial stenosis, potential sources of cardioembolism, and absent transtemporal windows. WMHs were quantified with the use of a semiquantitative visual rating method. Ultrasound parameters investigated were (1) common carotid artery (CCA) diameter and intima-media thickness, (2) blood flow velocity in the CCA and internal carotid artery (ICA), and (3) blood flow velocity and pulsatility index of middle cerebral artery (MCA). Results. A total of 52 patients fulfilled the study inclusion criteria . The only two ultrasound parameters that were independently associated with WMH score in multivariate linear regression models adjusting for demographic characteristics and vascular risk factors were increased mean common carotid artery (CCA) diameter and increased middle cerebral artery pulsatility index . Among all ultrasound parameters the highest AUC (areas under the receiver operating characteristic curve) were documented for MCA-PI and mean CCA diameter . Conclusions. Our study showed that in hypertensive individuals with brain SVD the extent of structural changes in cerebral microcirculation as reflected by WMHs burden is associated with the following ultrasound parameters of cerebral macrocirculation: CCA diameter and MCA-PI. There is accruing data indicating that white matter hyperintensities (WMHs), the most common imaging biomarker of small-vessel disease (SVD), are longitudinally associated with increased risk of cognitive decline and gait disturbance . Older aHigh-resolution B-mode ultrasonography can non-invasively and reliably detect the hypertension-induced structural changes in extracranial macrocirculation that affect common carotid artery intima-media thickness (CCA-IMT), common carotid artery (CCA) diameter, and presence of carotid artery plaques , 5. TranLimited studies have assessed the relation between WMHs on brain MRI and ultrasound assessments of structural macrocirculation-vessel changes with partly conflicting findings \u201310. ThesThe study was prospective, cross-sectional and consecutive and included all hypertensive patients who have had a brain MRI with white matter disease (white matter changes on MRI in concordance with SVD), referred to the cerebrovascular ultrasound laboratory of our department for assessment of extracranial and intracranial arteries between the years 2006 and 2007.We excluded patients with: (1) history of clinical stroke (including lacunar stroke and hemorrhagic) or transient ischemic attack either hemispheric or ocular, (2) a >50% stenotic disease of extracranial carotid and/or absence of flow or reversed flow of vertebral arteries on ultrasonography, (3) inadequate temporal windows on TCD permitting acquisition of flow velocities or an asymmetrical middle cerebral artery (MCA) blood flow velocities and/or focal >50% stenosis, (4) cardiogenic sources of emboli, and (5) WMH of non-atherosclerotic etiology.Clinical variables were recorded on all individuals including demographic characteristics and vascular risk factors as previously described , 12. Brain MRI was performed in all patients using axial T1-weighted, T2-weighted, fluid-attenuated inversion recovery (FLAIR), and proton-density-weighted scans on 1.0-Tesla MRI scanner in the axial and sagittal planes with the slice thickness of 5\u2009mm. We used the previously validated method by Leys et al. to quantify the extent of WMH . This meTwo experienced in neurosonology investigators , 14 perfThe degree of stenosis was calculated according to the Consensus Criteria of Society of Radiologists in Ultrasound as previThe CCA-IMT was assessed as previously described . The CCAProximal anterior circulation intracranial arteries were evaluated using a single-channel, 2\u2009MHz TCD . An insonation depth of 50\u201360\u2009mm and 60\u201365\u2009mm was used for the identification of proximal (M1) middle cerebral artery (MCA) and for measurement of flow velocity (FV) and pulsatility index (PI) and termr). The null hypothesis was tested at a level of P < 0.05. Univariate and multivariate linear regression models were used to evaluate which ultrasound parameters were independently associated with WMH score (entered as a linear variable in the models) after adjusting for clinical confounders. All factors that contributed to the outcome in the initial univariate analyses at P < 0.1 were included in the multivariate linear regression model as candidate variables and then removed by backward stepwise selection procedure. In the final multivariate analyses, statistical significance was achieved if P < 0.05. To confirm the robustness of multivariate models, we repeated all multivariate analyses using a forward procedure. For the evaluation of the predictive value of ultrasound parameters to identify patients with high burden of WMH score, the area under the receiver operating characteristic (ROC) curve (AUC) was calculated and corresponding 95%\u2009CI was computed. Accuracy parameters including sensitivity, specificity, positive predictive value, negative predictive value and overall accuracy were also calculated. Multivariate logistic regression models were used to identify independent associations between ultrasound parameters and high WMH score burden (entered as a binary variable in the models). Statistical analyses were performed using the SPSS Version 19, Chicago, IL, USA.Continuous variables with normal and skewed distribution are presented as mean (SD) or as median (interquartile range (IQR)). Correlation calculations between ultrasound parameters and WMH score were performed by Spearman's correlation coefficient (P = 0.003). Of the 158 patients considered, 52 met the inclusion criteria . Demograr = 0.501\u20130.508, P < 0.001 for all three correlations). The former association still retained its statistical significance (P < 0.001) even after adjustment for gender.WMH score ranged from 10 to 41, with a mean score of 22.1 \u00b1 9.1 . The correlation of ultrasound parameters with WMH is shown in r = 0.228, P = 0.104) and CCA-MFV was documented. ICA-EDV and ICA-MFV were negatively correlated to WMH score . A positive correlation of WMH score with of MCA-PI was observed, but not with of MCA-MFV . No association of CCA-IMT mean (P < 0.001), MCA-PI , and extracranial ICA MFV . Finally, in the multivariate linear regression models (adjusting for demographic characteristics and vascular risk factors), only two ultrasound parameter were independently associated with WMH score: increased mean CCA diameter and increased MCA-PI .In the initial univariate linear regression analysis, the following three ultrasound parameters were associated with WMH score in descending order: mean CCA diameter had higher CCA-Dmean (P = 0.001) and MCA-PI (P = 0.003) when compared to the low WMH score groups. Conversely, CCA-PSV (P = 0.024), ICA-EDV (P = 0.009) and ICA-MFV (P = 0.005) were lower in the high WMH score group.The median value of WMH score (20 points) was selected as the cut-off point to subdivide patients into two groups with high (>20 points) and low (\u226420 points) WMH score. No significant differences in any of the patients' baseline characteristics were found between the two groups of patients (data not shown). Patients with high WMH score (P < 0.001) and CCA-Dmean . Clinically important cut-off points for all these parameter s were also determined by the ROC curve analysis , the area under ROC curve (AUC) was computed . The higanalysis . The corP < 0.001). Similarly high MCA-PI values (\u22651.063) yielded an odds ratio of WMH score >20 points of 6.90 .In multivariate logistic regression analysis, after adjustment for demographic characteristics including gender and vascular risk factors, CCA-Dmean and MCA-PI remained the significant independent predictors for high WMH-score; high CCA-Dmean values (\u22650.666\u2009cm) yielded an odds ratio of WMH score >20 points of 15.94 and the We observed that increased CCA diameter was linearly associated with greater WMH score on brain MRI. To the best of our knowledge, there is no prior study evaluating the relationship of white-matter lesions as well as symptomatic or clinically silent brain infarctions with CCA diameter. The available literature focuses on CCA remodeling and indicates that thickening of the arterial wall due to hypertension may be accommodated by outward remodeling of the vessel, thereby preserving the luminal area . InteresWe also recorded an independent association between increased MCA-PI and more extensive WMHs on brain MRI. This observation is in line with a previous North-American study that assessed MRI manifestations of small-vessel disease with TCD indices and also found that MCA-PI positively correlated to MRI scores for hemispheric small-vessel disease . HoweverPrevious reports have yielded conflicting results regarding the potential association between CCA-IMT and WMHs on brain MRI. A French and a JaOur study has limitations including the cross-sectional design that does not allow us to ascertain any causal relationship between ultrasound parameters and the extent of WMH burden. Furthermore the presence and extent of microbleeds on brain MRI, which have also been established as an imaging biomarker of small-vessel disease , were noIn conclusion, our pilot study points to an independent association of higher MCA-PI and larger mean CCA diameter with more extensive WMH burden on brain MRI in hypertensive, asymptomatic patients. Further observational studies are needed to verify this potentially intriguing association in a longitudinal fashion and to investigate whether these ultrasound parameters may constitute imaging biomarkers that could predict extensive small-vessel disease in cerebral circulation leading to cognitive impairment and gait disturbance."} +{"text": "Pathogenesis of aortic valve calcificationis a multifunctional processassociated with various risk factors, while heart valve replacement is the only established treatment.Unfortunately, the real mechanism of the valve calcification remains still unknown. Herewith, we investigate the changes in molecular levelof aortic valve tissues in order to characterize the mineral deposits and understand the mechanism of aortic valve mineralization and stenosis.30 aortic valves samples of patients (65-80 years), who underwent surgical aortic valve replacement due to aortic valve stenosis. A Nicolet 6700 thermoscientific spectrometer was used to record the infrared (FT-IR) spectra. The aortic valve surfaces were studied with Scanning Electron Microscopy (SEM-EDX), without any coating of the samples.4 and amorphous hydroxyapatite, depending on the chemical factors of the cells\u2019 microenvironment. In the case of SEM showed that the cross-link bonds of collagen are the targetingsites where the minerals start the deposition.The infrared spectra showed intensity changes and shifts of characteristic bands concerning the peroxidation of lipids suggesting inflammation character of stenosis. The proteins and collagen changed their \u03b1-helix to random one.The mineral deposits were consistent of calcium phosphates, CaHPO10(PO4)6(OH)2), Ca2HPO4 and calcium phosphate of phospholipoprotein fragments. SEM-EDX data show substitution of calcium cations from magnesium cations leading to amorphous hydroxyapatites. This finding suggested that magnesium supplements could prevent the re-calcification of the implants.The characteristic FT-IR absorption bands of calcified stenotic aortic valves showed hyperoxidation of membranes (a pro-inflammation stage), while the mineral deposits were consistent of low crystallinity biological HA (Ca"} +{"text": "We generated a mouse model (MIP-Luc-VU-NOD) that enables non-invasive bioluminescence imaging (BLI) of beta cell loss during the progression of autoimmune diabetes and determined the relationship between BLI and disease progression. MIP-Luc-VU-NOD mice displayed insulitis and a decline in bioluminescence with age which correlated with beta cell mass, plasma insulin, and pancreatic insulin content. Bioluminescence declined gradually in female MIP-Luc-VU-NOD mice, reaching less than 50% of the initial BLI at 10 weeks of age, whereas hyperglycemia did not ensue until mice were at least 16 weeks old. Mice that did not become diabetic maintained insulin secretion and had less of a decline in bioluminescence than mice that became diabetic. Bioluminescence measurements predicted a decline in beta cell mass prior to the onset of hyperglycemia and tracked beta cell loss. This model should be useful for investigating the fundamental processes underlying autoimmune diabetes and developing new therapies targeting beta cell protection and regeneration. Type 1 diabetes (T1D) results from the autoimmune destruction of the insulin-producing pancreatic beta cell. The nonobese diabetic (NOD) mouse, the predominant pre-clinical model of type 1 diabetes, is characterized by immune cell infiltration of the pancreatic islet, known as insulitis, followed by beta cell destruction and the development of diabetes A major challenge in the study of T1D in both humans and the NOD mouse is the heterogeneity of disease. The degree of beta cell destruction prior to the onset of hyperglycemia varies among individuals with T1D A second challenge in the study of T1D is the inability to measure \u03b2 cell mass non-invasively and repeatedly in the same mouse or human Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. Animal protocols were approved by the Institutional Animal Care and Use Committee at Vanderbilt University Medical Center .Animal studies were performed according to guidelines in the http://www.cidr.jhmi.edu/mouse/mmset/html. Using speed congenics, integration of the NOD background was achieved in nine backcrosses and confirmed from chromatogram data using GeneMapper 3.5 software . The MIP-Luc-VU-NOD line is being deposited in The Jackson Laboratory Induced Mutant Resource Repository and can be found by searching the JAX Mice database (http://jaxmice.jax.org/query).Male MIP-Luc-VU mice Bioluminescence imaging (BLI) was performed using an IVIS 200 CCD camera as previously described Dissected mouse pancreata were fixed using methods previously described To determine beta cell mass in the pancreas of MIP-Luc-VU-NOD mice, pancreatic sections spaced by 250 \u00b5m from three different levels of the pancreatic tissue block were immunolabeled for insulin, as described above. Following overnight incubation with insulin primary antibody, slides were incubated for 2 hours in 1\u2236200 HRP-conjugated donkey anti-guinea pig antibody. DAB substrate was applied for 1 minute, washed with distilled water, and counterstained for eosin. Pancreatic beta cell area measurements were performed using a ScanScopeCS brightfield slide scanner and ImageScope software . ImageScope software was used to calculate the insulin- and eosin-positive areas of each cross-section, and the pancreatic beta cell area was defined as (insulin area)/(insulin area plus eosin area). The beta cell mass was then determined by multiplying the relative beta cell area by the total pancreatic weight.Insulitis was determined from H&E stained pancreatic sections Blood glucose measurements were obtained using tail vein blood measured with an Accu-chek glucose meter . Hyperglycemia was defined as blood glucose above 200 mg/dl. For glucose tolerance testing, baseline blood glucose was measured after a six hour fast and then mice were challenged with an I.P. injection of 2 g/kg of glucose followed by blood glucose measurement at 15, 30, 60, 90, and 120 minute increments. For insulin secretion, mice were challenged with an I.P. injection of 2 g/kg glucose/arginine after a six hour fast. Retro-orbital eye bleeds were performed prior to injection and at 15 minutes after injection. Samples were centrifuged at 4\u00b0C for 15 minutes and clear supernatants were collected for insulin measurement by radioimmunoassay Pancreata were excised and cleaned of connective tissue, blotted dry, and weighed. Tissue was homogenized in acid alcohol (1 ml 12 M HCL/110 mL 95% ethanol) and incubated for 48 h at 4\u00b0C under mild agitation, as described Data are expressed as means \u00b1 standard error of the mean (SEM). An unpaired, two-tailed t test was used to compare experimental results between two groups. For experiments with more than two groups, ANOVA was used with post-hoc Tukey\u2019s honest significance test or test for linear trend, as indicated . For predictive modeling, a binary logistic regression analysis was performed using SPSS software .MIP-Luc-VU-NOD mice developed the insulitis characteristic of the NOD mouse model. For example, an islet from a representative 22 week-old female MIP-Luc-VU-NOD mouse displayed lymphocyte infiltration of the islet by both H&E staining and immuRepeated bioluminescence imaging of female MIP-Luc-VU-NOD revealed a decline in bioluminescence intensity as mice aged. Weekly BLI, initiated when mice were between five and seven weeks old, was maximum in the first, second, or third week of measurement and then declined in every MIP-Luc-VU-NOD mouse imaged . In contIn order to determine whether bioluminescence correlates with measures of beta cell mass, BLI, serum insulin measurements, blood glucose, morphometric measurement of insulin immunostaining, and pancreatic insulin content measurements were performed at serial time points in female MIP-Luc-VU-NOD mice. Mice were randomly selected for these assays from a cohort of 20 mice. Normalized bioluminescence intensity decreased with increasing mouse age . Serum iSince the NOD mouse model displays heterogeneity in the occurrence, severity, and age of onset of diabetes, four female MIP-Luc-VU-NOD mice were followed with biweekly BLI and glucose tolerance testing at 15, 17, 19, and 21 weeks of age. Glucose tolerance testing (GTT) revealed variability in the progression toward diabetes in these mice . BLI likBlood glucose measurements of female MIP-Luc-VU-NOD mice that became diabetic were initially normoglycemic despite a gradual decline in bioluminescence over the period of several weeks prior to the onset of hyperglycemia . This isMale MIP-Luc-VU-NOD that became diabetic also demonstrated a decline in bioluminescence intensity prior to the onset of hyperglycemia . The onsA binary logistic regression analysis was conducted to predict the incidence of diabetes in female MIP-Luc-VU-NOD mice using bioluminescence intensity as a predictor. Bioluminescence intensity at three weeks prior to the onset of diabetes was a reliable predictor for distinguishing mice that became diabetic from mice that did not become diabetic. The odds ratio of developing diabetes was small given the limited sample size, but significant (p\u200a=\u200a0.024).A predictive binary logistic model based upon the bioluminescence value at three weeks prior to diabetes incidence was constructed using the following equation:We report the development of a new mouse model in which autoimmune diabetes can be non-invasively predicted by bioluminescence imaging (BLI). Building upon our previous experience using bioluminescence imaging to measure beta cell mass Longitudinal studies of bioluminescence intensity and blood glucose in the same MIP-Luc-VU-NOD mice reveal that bioluminescence decreases weeks before the onset of hyperglycemia. Indeed, at the onset of hyperglycemia the bioluminescence intensity has decreased by an average of 90%. A drastic reduction in beta cell mass prior to the onset of hyperglycemia has previously been noted in other rodent models The decline in bioluminescence in MIP-Luc-VU-NOD mice correlates with morphometric measurements of beta cell mass, plasma insulin, and pancreatic insulin content. A caveat of bioluminescence imaging is that the spatial resolution is incapable of resolving individual islets; instead the BLI signal reflects the sum of all beta cell bioluminescence. Bioluminescence measurements of this new model reflect beta cell mass during the progression of the NOD diabetic phenotype. This contrasts with a previous report using an inducible activator of luciferase to monitor the NOD mouse, which found that the decline in bioluminescence outstripped the decline in beta cell mass In the sample of mice imaged, the incidence of spontaneous diabetes in female MIP-Luc-VU-NOD agrees with the 60% to 80% incidence reported for female mice while the incidence in male mice was higher than the figure of 20% to 30% reported for males in the small sample examined The monitoring of type 1 diabetes developed in the MIP-Luc-VU-NOD model should allow for studies that increase our understanding of the NOD model as well as testing new interventions and monitoring disease. The combination of bioluminescence measurements of beta cell mass with longitudinal monitoring of insulitis Figure S1MIP-Luc-VU-NOD mice display increasing insulitis with age. A) H&E stain shows lymphocyte infiltration of the pancreatic islet. B) Immunofluorescence staining for insulin (green) and the CD45R/B220 pan B lymphocyte marker (red) reveal lymphocyte infiltration and beta cell loss in MIP-Luc-VU-NOD islets. C) Insulitis scoring from H&E sections of MIP-Luc-VU-NOD mice at 8, 12, and 22 weeks of age displays increased islet infiltration with mouse age . Sections from 3 mice at each age were scored for insulitis. D) Representative islet of each score outlined with a blue dashed line.(TIF)Click here for additional data file.Figure S2Immunocytochemistry for insulin (green) and luciferase (red) shows staining of beta cells for luciferase.(TIF)Click here for additional data file.Figure S3Heterogeneity of diabetes incidence in female MIP-Luc-VU-NOD mice is reflected by glucose tolerance testing. Glucose tolerance tests was performed on four female MIP-Luc-VU-NOD mice at A) 15, B) 17, C) 19, and D) 21 weeks of age. Note that mouse #1 died prior to week 21.(TIF)Click here for additional data file.Figure S4Female MIP-Luc-VU-NOD mice that did not become hyperglycemic by 32 weeks of age were followed with weekly bioluminescence and blood glucose measurements. A) Bioluminescence intensity declined but then stabilized at approximately 40% of the maximum BLI. Blood glucose measurements remained normal. B) Glucose and arginine-stimulated insulin secretion revealed the maintenance of insulin secretion in these animals.(TIF)Click here for additional data file."} +{"text": "Clinical data from the HVTN-080 study demonstrated that intramuscular electroporation (EP) delivery of PENNVAX\u00ae-B DNA vaccine and the plasmid adjuvant IL-12 generated strong antigen specific cellular immune responses in humans with nearly 90% response rate. We have now developed minimally invasive EP delivery technologies (MID-EP) to target dermal tissue and demonstrate their ability to generate strong antibody (Ab) responses in animal models with DNA antigens \u2013 including small pox, influenza, dengue \u2013 and have shown protection from viremia and lethality following challenge.We demonstrate MID-EP delivery of consensus HIV gp140 antigens and show the generation of cross-clade neutralizing responses in guinea pigs and rabbits. These EP enhanced humoral responses were significantly broader and higher than naked DNA delivery alone or with a protein antigen. We demonstrated NAb titers against a broad panel of 15 Tier-1 HIV viruses from Clades A-D in the range of 20 -200 measured in the Tzm-Bl neutralization assay. The magnitude but not the breadth of the responses was boosted to 20-1000 range using a MID-EP DNA prime-protein boost regimen.We further developed a surface EP device (SEP) for the simultaneous, but spatially segregated, delivery of multi-component HIV vaccines. The SEP device operates under substantially lower voltage parameters than conventional EP devices resulting in significant improvements in tolerability. The separation of multi-component HIV vaccines avoids potential issues with plasmid interference at the transcriptional or translational levels. SEP produces Ab responses comparable to the penetrating DNAEP devices.Our results suggest that MID/SEP electroporation devices offer safe, tolerable and potent methods to administer HIV DNA vaccinations in a prophylactic clinical setting. Combined with the design of novel HIV consensus based Env antigens these DNA-EP combination vaccines are suitable for further HIV vaccine product development."} +{"text": "Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Evidence also suggests that many pre-mRNAs undergo unproductive alternative splicing resulting in incorporation of in-frame premature termination codons (PTCs). The destinies and potential functions of the PTC-harboring mRNAs remain poorly understood. Unproductive alternative splicing in circadian clock genes presents a special case study because the daily oscillations of protein expression levels require rapid and steep adjustments in mRNA levels.Arabidopsis thaliana circadian clock-associated genes are alternatively spliced. Results were confirmed using reverse transcription polymerase chain reaction (RT-PCR), quantitative RT-PCR (qRT-PCR), and/or Sanger sequencing. Intron retention events were frequently observed in mRNAs of the CCA1/LHY-like subfamily of MYB transcription factors. In contrast, the REVEILLE2 (RVE2) transcript was alternatively spliced via inclusion of a \"poison cassette exon\" (PCE). The PCE type events introducing in-frame PTCs are conserved in some mammalian and plant serine/arginine-rich splicing factors. For some circadian genes such as CCA1 the ratio of the productive isoform to its PTC counterpart shifted sharply under specific environmental stress conditions.We conducted a systematic survey of alternative splicing of plant circadian clock genes using RNA-seq and found that many CCA1 across phyla [2] indicates a potential role of nonsense transcripts in regulation of circadian rhythms. Most of the alternatively spliced isoforms harbor in-frame PTCs that arise from full or partial intron retention events. However, a PTC in the RVE2 transcript is introduced through a PCE event. The conservation of AS events and modulation of the relative abundance of nonsense isoforms by environmental and diurnal conditions suggests possible regulatory roles for these alternatively spliced transcripts in circadian clock function. The temperature-dependent expression of the PTC transcripts among members of CCA1/LHY subfamily indicates that alternative splicing may be involved in regulation of the clock temperature compensation mechanism.Our results demonstrate that unproductive alternative splicing is a widespread phenomenon among plant circadian clock genes that frequently generates mRNA isoforms harboring in-frame PTCs. Because LHY and CCA1 are core components of the plant central circadian oscillator, the conservation of alternatively spliced variants between CCA1 and LHY and for This article was reviewed by Dr. Eugene Koonin, Dr. Chungoo Park (nominated by Dr. Kateryna Makova), and Dr. Marcelo Yanovsky . Arabidopsis thalianaPopulus (poplar), Brachypodium, and Oryza (rice). Furthermore, the core circadian clock genes of Oryza subspecies japonica and indica displayed nearly indistinguishable oscillation profiles and phase calls .Click here for fileOligonucleotide primer sequences and PCR conditions.Click here for file"} +{"text": "Xenopus embryos.Dynamics of polyadenylation vs. deadenylation determine the fate of several developmentally regulated genes. Decay of a subset of maternal mRNAs and new transcription define the maternal-to-zygotic transition, but the full complement of polyadenylated and deadenylated coding and non-coding transcripts has not yet been assessed in To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts and putative long non-coding RNAs (lncRNA). These lncRNA transcripts were stringently selected as spliced transcripts generated from independent promoters, with limited coding potential and a codon bias characteristic of noncoding sequences. Many lncRNAs are conserved and expressed in a developmental stage-specific fashion.These data reveal dynamics of transcriptome polyadenylation and abundance and provides a high-confidence catalogue of novel and long non-coding RNAs. Innovations in sequencing technology have allowed deep sequencing of complementary DNA (cDNA), known as ribonucleic acid sequencing (RNA-seq), enabling transcriptome assembly and identification of coding and non-coding transcripts across many cell types -4.+) selected messenger RNA (mRNA). These studies have reported identification of thousands of maternal genes and identified the earliest set of embryonic transcripts. They also identified a large number of novel transcribed regions in annotated and unannotated regions of the zebrafish genome , and indeed, their PA/RZ ratios faithfully reflect their fertilization-induced deadenylated state . We validated the adenylation states of transcripts using RT-qPCR in combination with oligo(dT)20 primers and random hexamers , polyA+ ribonucleic acid sequencing (RNA-seq) data and RT-qPCR with oligo(dT)20 primers correlated very well. To analyze the deadenylated transcripts more systematically, we filtered the log ratio of two measures (PA/RZ) to be less than or equal to -0.5 for oocyte, stage 6 and stage 9 respectively. This filtering gave us sets of genes that are highly enriched in RZ data compared to the polyA+ data , known to mediate sequence-specific mRNA deadenylation region; Xtev: Xenopus tropicalis experimentally validated; lncRNAs: Long non-coding RNAs; ORF: Open reading frame; PA: PolyA+; RiboZero, RZ: Ribosomal RNA depleted total-RNA; RPKM, see Materials and methods: Reads per kilobase of exon model per million mapped reads; GO: Gene ontology; BP: Biological processes; EST: Expressed sequence tags; GM: Gene models; NGM: New gene models; NGM-vv: New gene models with validation support; NGM-vvo: Manually curated new gene models with ORF less than 100 amino acids; LLR: Log likelihood ratio; JGI: Joint Genome Institute; rRNA: Ribosomal RNA; BWA: Burrows-Wheeler Aligner; PCR: Polymerase chain reaction; H3K4me3: Histone H3 lysine 4 tri-methylation; RZ: Ribosomal RNA depleted total RNA; RNAPII: RNA polymerase II; ChIP-seq: Chromatin immuno-precipitation sequencing; TSS: Transcription start-site.The authors declare that they have no competing interests.Xenopus tropicalis experimentally validated (Xtev) pipeline and performed the conservation analysis. GJCV performed ORF length and codon bias analysis. SSP and GJCV wrote the manuscript. All authors read and approved the final manuscript.SSP, UGJ and GJCV conceived and designed the study, UGJ performed the RNA-seq experiments, SSP did the analysis and performed the validation experiments. SJvH performed transcriptome assembly, designed and assembled the Supplementary tables (S1 and S2) and figures (S1-S9).Click here for fileMulti-page list of genes expressed inXenopus tropicalis.Click here for fileMulti-page Xtev annotation pipeline gene list with genomic co-ordinates.Click here for fileSingle-page list of codon usage frequencies used for calculating codon bias score.Click here for fileSingle-page list of primers used for real-time qPCR validation of highly conserved lncRNAs from the NGM subset.Click here for file"} +{"text": "Here, we use transgenic mice expressing Lifeact-EGFP to visualize F-actin in ECs. We show that in the retina, Lifeact-EGFP expression is largely restricted to ECs allowing detailed visualization of F-actin in ECs in situ. Lifeact-EGFP labels actin associated with cell-cell junctions, apical and basal membranes and highlights actin-based structures such as filopodia and stress fiber-like cytoplasmic bundles. We also show that in the skin and the skeletal muscle, Lifeact-EGFP is highly expressed in vascular mural cells (vMCs), enabling vMC imaging. In summary, our results indicate that the Lifeact-EGFP transgenic mouse in combination with the postnatal retinal angiogenic model constitutes an excellent system for vascular cell biology research. Our approach is ideally suited to address structural and mechanistic details of angiogenic processes, such as endothelial tip cell migration and fusion, EC polarization or lumen formation.Angiogenesis requires coordinated changes in cell shape of endothelial cells (ECs), orchestrated by the actin cytoskeleton. The mechanisms that regulate this rearrangement Our knowledge on the organization and regulation of the endothelial actin cytoskeleton is mainly based on in vitro studies, which are missing essential physiological features, such as composition of the ECM, blood flow and mechanical input from the tissue Sprouting angiogenesis, the formation of new blood vessels from pre-existing ones, is required for organogenesis and contributes to the progression of many diseases including cancer in vitro and in vivoLifeact is a 17-amino-acid-long actin-binding peptide derived from yeast that specifically labels F-actin without affecting actin organization. It has been extensively used to visualize F-actin and to study actin dynamics Lifeact-EGFP transgenic mice have been previously described Embryos were dissected in PBS at embryonic day (E) 10.5 and fixed overnight in fixation buffer . Embryos were stained as whole mounts as previously described Eyes were collected between postnatal (P) day 5 and P10 and fixed in 4% paraformaldehyde (PFA) for 2 hours at room temperature. Retinas were dissected and stained as whole mounts as previously described Samples were collected, fixed and stained as previously described in vivo microscopy was performed as described previously in vivo microscopy, the muscle was superfused with warm buffered saline. After in vivo microscopy, the tissue was fixed in 2% paraformaldehyde and immunostained as whole mount.Microsurgical preparation of the cremaster muscle and in vivo microscopy was centered on an AxioTech-Vario 100 Microscope (Zeiss), equipped with LED excitation light (Zeiss) for fluorescence epi-illumination. Microscopic images were obtained with a water dipping objective and acquired with an AxioCam Hsm camera and Axiovision 4.6 software.The setup for in vivo models extensively used to study the mechanisms that regulate EC behaviour during angiogenesis The expression level and cellular expression pattern of Lifeact-EGFP in the vascular system of the Lifeact-EGFP mice is not known. Mouse embryos and early postnatal mouse retinas are in vivo model to study dynamic morphogenetic microvascular events such as leukocyte-EC interactions and leukocyte extravasation in vivo visualization of rolling and adherent leukocytes at the vessel walls of postcapillary venules staining of whole-mounted E10.5 transgenic Lifeact-EGFP embryos. Lifeact-EGFP: green. (A) 3-dimensional reconstruction images. (B) Confocal sections. Arrows point to intersomitic vessels and arrowheads indicate epithelial actin-rich apical site. Scale bars: 50 \u00b5m. Ep: Epithelial cell; Me: Mesenchymal cell; NT: Neural tube.(TIF)Click here for additional data file.Figure S2Lifeact-EGFP expression is practically absent in retinal astrocytes. GFAP (in red) and VECad (blue) double labelling of retinas. Lifeact-EGFP: green. Arrowheads indicate short actin filament protrusions in ECs. Scale bars: 20 \u00b5m.(TIF)Click here for additional data file.Figure S3Confocal images of endothelial actin cytoskeleton in retinal vasculature.(A and B) Visualization of endothelial actin cytoskeleton (Lifeact-EGFP: white) during anastomosing of tip cells. Arrowheads point to short actin filament protrusions during the tip cell fusion process. (C) 3-dimensional reconstruction of an EC sprout. Lifeact-EGFP: white. Arrow points to an actin filament protrusion. Scale bars: 20 \u00b5m.(TIF)Click here for additional data file.Table S1Antibodies and reagents used for staining.(DOCX)Click here for additional data file.Video S1Postcapillary venules in the cremaster muscle from Lifeact-EGFP mouse.(AVI)Click here for additional data file."} +{"text": "The discovery of copy number variations (CNV) in the human genome opened new perspectives in the study of the genetic causes of inherited disorders and the etiology of common diseases. Differently patterned instances of somatic mosaicism in CNV regions have been shown to be present in monozygotic twins and throughout different tissues within an individual. A single-cell-level investigation of CNV in different human cell types led us to uncover mitotically derived genomic mosaicism, which is stable in different cell types of one individual. A unique study of immortalized B-lymphoblastoid cell lines obtained with 20 year interval from the same two subjects shows that mitotic changes in CNV regions may happen early during embryonic development and seem to occur only once, as levels of mosaicism remained stable. This finding has the potential to change our concept of dynamic human genome variation. We propose that further genomic studies should focus on the single-cell level, to understand better the etiology and physiology of aging and diseases mediated by somatic variations. Many forms of human genome variations are known and described including single-nucleotide polymorphisms, small insertion-deletion polymorphisms, variable numbers of repetitive sequences and genomic structural alterations. Recent developments in the genome-wide targeted technologies used to analyze structural variations have led to the identification of thousands of heritable copy number variations (CNV) occurring in both phenotypically normal and affected subjects . These aCCL3L1 copy number was a major determinant for enhanced HIV susceptibility /45,X[48], pod-FISH assessed the parental origin of the normal and derivative chromosomes 7 with two BACs (RP11-533E18 and RP11-45N9) of the 15 BACs tested . UnipareAML1\u2013ETO-positive acute myeloid leukemia (AML). After bone-marrow (BM) transplantation from a female donor, the cellular chimerism in BM was determined in 60% donor vs 40% recipient cells using a centromeric probe for the X chromosome. Surprisingly, no signal intensity variation for RP11-367L15 was found in 55% of the donor cells. The remaining 45% of donor cells showed the identical pod-FISH signal pattern as those of the recipient cells .pod-FISH and PDP-P > 0.05). The results of this study suggest that somatic variation of CNV regions occurs in early embryogenesis [2). Statistical analysis was performed using t-test . As in previous studies also here we found two cell types with different signal intensity of the same BAC ranging from 0% to 100%. Interestingly, the variation ratio of BACs remained equal in LCL from different time points within a subject and varied between the two individuals studied [Intraindividual differences detectable by pod-FISH turn out to be a common observation rather than an exception. To test whether different cell types have specific CNV patterns when studied at the single-cell level, we used chromosome-specific pod-FISH on metaphase spreads from 10 healthy individuals . Three cogenesis . To inveogenesis . The ageogenesis , 27. Theogenesis ; the app studied . The mechanisms underlying the establishment of CNV mosaicism and their transmission through \u2018mitosis remain unclear. Single-cell-CNV-focused approaches might only uncover a tip of the iceberg in the recently reported background of extensive chromosomal instability in human cleavage-stage embryos . Severalin vitro-fertilized embryos [Overall, the presence of somatic CNV mosaicism in different individuals has been confirmed by several studies: Here we approach the problem of CNV mosaicism in different cell types and tissues of the same organism in different cell types and tissues of the same organism at differentially stages. The stable variation ratios of CNV detectable by pod-FISH have been shown to differ between individuals but not within healthy individuals. We suggest that the somatic recombination of polymorphic regions might occur at least at a relatively early time point in embryogenesis because all the well-differentiated cells studied have similar CNV mosaic patterns . This hy embryos . InteresUnderstanding these phenomena in more and finer details should open new perspectives in developmental physiology and in personalized medicine. The intraindividual specific mosaicism ratio at a certain disease susceptibility gene might have a higher impact than previously expected, especially for so-called \u2018multi-factorial diseases\u2019, and might also explain clinical genetic phenomena like diminished penetrance in autosomal dominant diseases or clinical signs without apparent mutations when only a single tissue is screened."} +{"text": "The enteric nervous system contains excitatory and inhibitory neurons which control contraction and relaxation of smooth muscle cells and gastrointestinal (GI) motor activity. Nitric oxide (NO) plays an important role as a non-adrenergic non-cholinergic inhibitory neurotransmitter in the enteric nervous system, which activates the NO-GC/cGMP/PKG signalling pathway and thus relaxation of the smooth musclulature in the GI tract. Interstitial cells of Cajal (ICC) act as pacemaker cells in the GI tract by generating slow waves of depolarisation to induce rhythmic smooth muscle contractions. In addition, our previous work established a surprising role of ICCs in excitatory and inhibitory nitrergic neurotransmission. The aim of the present study was to investigate molecular and cellular mechanisms, which mediate regeneration of intestinal slow-waves and inhibitory nitrergic neurotransmission upon acute damage of the ICC network.CreERT2c-Kit knock-in allele at the endogenous c-Kit locus. This tamoxifen inducible mouse model enables genetic manipulation and depletion of ICC as well as regeneration studies at defined time points during development and in adults in vivo. To investigate the role of ICC in transducing the nitrergic inhibitory signal, we deleted cGMP-dependent protein kinase I (Prkg1), the central mediator of the non-adrenergic, non-cholinergic neurotransmission in ICC using floxed Prkg1 animals. Furthermore we crossed CreERT2/c-Kit+ mice with conditional DTA/LSL-R26+ animals, which carry a latent diphtheria toxin A (DTA) expression cassette to deplete the ICC network. Using these models, we subsequently investigated molecular and cellular mechanisms which mediate regeneration of slow-waves and GI motility over time.To evaluate the role of ICC in excitatory and NO-dependent inhibitory neurotransmission after acute damage, we generated a Prkg1 in ~40% of all ICC abolished specifically the NO-dependent component of the inhibitory junction potential in colonic circular smooth muscle cells. This resulted in a significantly disturbed GI motility with a profound increase in total GI transit time, as seen in animals with a disruption of the ICC network due to expression of DTA. Interestingly, GI motility, slow-wave activity and enteric neurotransmission recovered completely within 5 weeks. However, we found no overt recovery of ICC cell number, reexpression of Prkg1 or proliferation of precursor cells.Deletion of in vivo genetic evidence for a surprising plasticity of ICC which restores normal gut function after damage of the ICC network.Our results suggest that adaptive mechanisms of the remaining ICC restore pacemaker activity and enteric neurotransmission. Therefore, we provide first"} +{"text": "Here, we study the significance of PI in GI pathophysiology using the zebrafish mutant hi559cdipt, which lacks PI synthesis, and unravel a crucial role of PI in intestinal mucosal integrity and inflammation. The hi559cdipt mutants exhibit abnormal villous architecture and disorganized proliferation of intestinal epithelial cells (IECs), with pathologies reminiscent of inflammatory bowel disease (IBD), including apoptosis of goblet cells, abnormal mucosecretion, bacterial overgrowth and leukocyte infiltration. The mutant IECs exhibit vacuolation, microvillus atrophy and impaired proliferation. The hi559cdipt gene expression profile shows enrichment of acute phase response signaling, and the endoplasmic reticulum (ER) stress factors hspa5 and xbp1 are robustly activated in the mutant GI tissue. Temporal electron micrographic analyses reveal that PI-deficient IECs undergo sequential ER-Golgi disruption, mitochondrial depletion, macroautophagy and cell death, consistent with chronic ER-stress-mediated cytopathology. Furthermore, pharmacological induction of ER stress by inhibiting protein glycosylation or PI synthase inhibition in leukocyte-specific reporter lines replicates the hi559cdipt inflammatory phenotype, suggesting a fundamental role of PI metabolism and ER stress in mucosal inflammation. Antibiotics and anti-inflammatory drugs resolved the inflammation, but not the autophagic necroapoptosis of IECs, suggesting that bacterial overgrowth can exacerbate ER stress pathology, whereas persistent ER stress is sufficient to trigger inflammation. Interestingly, the intestinal phenotype was partially alleviated by chemical chaperones, suggesting their therapeutic potential. Using zebrafish genetic and pharmacological models, this study demonstrates a newly identified link between intracellular PI signaling and ER-stress-mediated mucosal inflammation. The zebrafish cdipt mutants provide a powerful tool for dissecting the fundamental mechanisms of ER-stress-mediated human GI diseases and a platform to develop molecularly targeted therapies.Dysregulated phosphatidylinositol (PI) signaling has been implicated in human gastrointestinal (GI) malignancies and inflammatory states, underlining the need to study pathophysiological roles of PI in an Intestinal epithelial cells (IECs) play a major role in mucosal homeostasis, barrier function and immunity in addition to their digestive functions. Physiological stress to the IECs affects intestinal mucosal integrity, making the host susceptible to various gastrointestinal (GI) diseases. Epithelial disruption is a hallmark pathological feature of GI inflammatory disorders, particularly inflammatory bowel diseases (IBD) and necrotizing enterocolitis (NEC) .XBP1 locus confer an increased risk for both Crohn\u2019s disease (CD) and ulcerative colitis (UC) (HSPA5 is reported in human IBD tissues (Endoplasmic reticulum (ER) stress leading to epithelial dysfunction is believed to contribute to GI inflammation . ER stretis (UC) . In muritis (UC) . Differe tissues , and ER tissues . However tissues , indicatDanio rerio, has been an effective tool in deciphering mechanisms of human GI diseases, due to the similarity in basic GI tissue structure, function and gene expression profiles and cancers of the gastrointestinal tract. IBD is a debilitating chronic disorder, with a peak incidence in early adult life, that often requires lifetime prescriptions of drugs that cause significant side effects. Although IBD is believed to result from an inappropriate inflammatory response to commensal microbes in a genetically susceptible host, we only have limited insights into its pathogenesis, underlining the importance of finding novel genes and pathways that might contribute to the inflammatory process. Notably, genes that affect the cellular stress response pathway have recently been implicated in IBD pathogenesis. Zebrafish provide an attractive tool for unraveling the underlying mechanisms in gastrointestinal disease, given the similarity with the mammalian system in terms of the basic architecture of the digestive system, cell types and function. The model also allows Resultshi559cdipt zebrafish, which are deficient in de novo PI synthesis, to elucidate the importance of PI signaling in gastrointestinal physiology. Mutant zebrafish demonstrated persistent ER stress and disrupted intestinal architecture, epithelial restitution and homeostasis. The unresolved ER stress sequentially leads to reduced mucosecretion, goblet cell apoptosis, autophagy, bacterial overgrowth and myeloid inflammation in the mucosa, resembling IBD pathologies. The authors show that pharmacological induction of ER stress is sufficient to elicit similar inflammatory phenotypes. Interestingly, suppression of inflammation by anti-inflammatory drugs failed to resolve the ER stress pathologies, whereas ER stress alleviation by chemical chaperones resolved the mutant phenotype.To explore the underlying mechanisms driving cellular stress and inflammation, the authors used a zebrafish genetic model linking phosphatidylinositol (PI) signaling to these processes, as PI signaling is known to be associated with a number of gastrointestinal diseases and malignancies. The authors used Implications and future directionsin vivo approach, this study unravels novel mechanistic insights into the pathophysiology of gastrointestinal diseases. The data described provide the first evidence to link a deficiency in PI synthesis with ER-stress-mediated intestinal mucosal injury and inflammation. The ER homeostasis and inflammatory pathways appear to be conserved between zebrafish and humans, suggesting that modulation of PI signaling and ER stress components might alleviate gastrointestinal inflammation. This work thereby provides new avenues for therapeutic strategies to treat IBD and associated diseases. The zebrafish genetic and pharmacological model presented here is amenable to treatment with commonly tested anti-inflammatory drugs and chemical chaperones, indicating that it can be used as a preclinical platform to develop molecularly targeted therapies for gut-related inflammatory diseases and cancer.Using a whole organism hi559cdipt (hi559), which is defective in PI synthesis. Cdipt (CDP-diacylglycerol\u2013inositol 3-phosphatidyltransferase) is a highly conserved enzyme with its active site on the cytoplasmic face of the ER and is responsible for synthesis of intracellular PI from myo-inositol and CDP-diacylglycerol. PI synthesis has been suggested to occur in a dynamic domain of the ER positioned at the leading edge of the ER tubules P] and phosphatidylinositol -bisphosphate [PIP2] to exert their secretory functions.Phosphatidylinositol (PI) signaling has been linked to a variety of human diseases and cancer. PI is a crucial phospholipid synthesized in the ER and in highly dynamic ER-derived compartments. PI is rapidly metabolized and its levels are tightly controlled in the cell to exert its spatiotemporal intracellular signaling functions . Phospho tubules . Our earteatosis . Despitecdipt mutant zebrafish develop consistent GI defects during late larval stages after tissue differentiation, exhibiting a complex pathology in the intestine: abnormal IEC proliferation and apoptosis, villous atrophy, GC depletion, bacterial overgrowth and inflammation, all of which are hallmarks of human IBD. The hi559 IECs show disruption of ER architecture followed by mitochondrial defects and increased autophagy and cell death, consistent with ER-stress-induced cytopathology. Pharmacological induction of ER stress in wild-type larvae results in similar inflammatory pathologies, suggesting a contributory role of aberrant PI synthesis in ER-stress-mediated GI inflammation. In addition, akin to IBD treatment strategies, the mutant phenotype is partially ameliorated by antibiotic and anti-inflammatory drugs. This highlights the utility of this system as a tool for studying the pathogenesis of ER stress and mucosal inflammation. These studies facilitate novel insights into the mechanistic relationships between intracellular PI signaling, ER stress and GI pathophysiology in a whole-organism in vivo setting.The hi559 homozygous mutant lacks Cdipt expression due to a retroviral insertion within the cdipt gene. Larvae develop normally until 5 dpf, when they begin to exhibit hepatic defects, including hepatomegaly and steatosis (hi559 larvae expressing green fluorescent protein (GFP) in the gut [hi559Tg(gut:gfp)] confirmed that the hi559 mutation is fully penetrant, consistently presenting with a significantly smaller intestine at 5 dpf (lopcdipt (lop) , but exhibited a milder, delayed phenotype. They developed normally until 7 dpf, subsequently exhibiting similar gross and histological intestinal abnormalities as seen in hi559 larvae and dying at about 10 dpf. Both hi559 and lop failed to rescue each other in a complementation assay , supporting the conclusion that lop is a hypomorphic allele of hi559. In homozygous hi559 and lop mutants, Cdipt function is eliminated, resulting in abrogation of de novo PI synthesis . In addiop (lop) , which cynthesis . The simhi559 intestine is evident from whole-mount staining and histology . Incorporation of Nile Red was diminished in the mutants, indicating decreased luminal volume . The intestinal epithelial structure was reduced in size, as demonstrated by Cy3-streptavadin (Cy3-SA) immunostaining (hi559 larvae by whole-mount in situ hybridization (ISH) using RNA probes against the intestine-specific markers fabp2, vil1 and anxa2b . The observed decrease in marker gene expression suggests loss of structural and functional components of the hi559 intestine by 5 dpf. There was no difference in expression of intestinal markers or Nile Red staining until 4 dpf in hi559 compared with wild type (data not shown), suggesting no gross physical defects during early intestinal development. Intestinal expression of cdipt in wild-type larvae implicate an important role of PIS in intestinal integrity and function.The hypomorphic nature of staining , suggeste larvae and the hi559 intestine . TEM analysis of the 5.5-dpf intestinal mucosa demonstrated that the wild-type IECs exhibit a highly elaborate apical brush border with microvilli projecting into the lumen, whereas the hi559 IECs had enlarged cytoplasmic vesicles, abnormal brush border, reduced terminal web and microvillus atrophy . Interestingly, there was no difference in numbers of GCs at 5 dpf (P=0.667), supporting normal IEC differentiation. However, the population of esophageal GCs declined by 6 dpf . Concomitant with GC depletion, nearly all hi559 larvae (>90%) showed histological features of bacterial overgrowth in the intestine by 6 dpf . These vacuoles did not show PAS or Oil-Red-O staining, suggesting that they were neither mucinous nor steatotic (data not shown). Taking the results together, we conclude that PI deficiency impedes proliferation and induces apoptosis of IECs, causing villous atrophy and intestinal hypoplasia.We studied the fate of the IECs by analyzing their cell-cycle status by BrdU incorporation and TUNEL assays. In the wild-type intestine, BrdU-positive cells occur frequently, typically at the base of the epithelial villi; TUNEL-positive cells are rare . AlthougP=0.006; and the epletion . In the hi559 intestine exhibited increasing bacterial overgrowth coinciding with depletion of the GCs . To quantify leukocyte infiltration, we utilized the leukocyte-specific reporter line Tg(lyzc:egfp). Analysis of hi559 Tg(lyzc:egfp) mutant larvae revealed significantly higher leukocyte aggregation in the 6-dpf intestine compared with wild-type Tg(lyzc:egfp) , further substantiating the hypothesis that deficient PI synthesis leads to mucosal inflammation.During larval development, the the GCs . Becauserophages . Necro-iP=0.008; . Intereshi559 gene expression identified acute phase response (APR) signaling as the most significantly upregulated canonical pathway, suggesting activated transcription of pro-inflammatory factors .Pathway analysis of P=0.002; . In addihi559 larvae . The elevation of both unspliced and spliced transcripts of xbp1 indicated that there was ongoing ER stress in the hi559 GI tissues. To further clarify the ER stress within tissues, we performed immunohistochemistry to detect active Hspa5 protein. Robust enrichment of Hspa5 protein was seen within hi559 GI tissues, specifically in the mucin secreting GCs and subsequently in the IECs of the intestinal mucosa . In addil mucosa .hi559 GI tissues to dissect the sequence of ER-stress-mediated pathology at cellular level. We performed extensive TEM analysis of the intestinal mucosa at different stages of the phenotype . Disrupted ER architecture, grossly expanded ER lumens and vacuolization, consequent mitochondrial damage, and autophagy are consistent with ER-stress-induced cytopathology. These results demonstrate that unresolved ER stress in the highly secretory GI cells is the major etiology of the hi559 phenotype, implying that the lack of de novo PI impedes secretory function, leading to pathological ER-stress-induced GI defects in cdipt mutants.Because these ER stress UPR factors are associated with molecular pathogenesis of IBD , we wanthenotype . At 5 dpmponents . Large dmponents . At 6 dpmponents . The lumP\u22640.003; . ER-streP\u22640.003; . ER expahi559 mutants has not yet addressed the sequence of events leading to the overt phenotype: is the ER stress a direct consequence of functional loss of Cdipt, or induced by another unrecognized process such as inflammation? To help distinguish between these possibilities, we tested whether tunicamycin, a compound known to induce ER stress by inhibition of N-glycosylation, can cause GI inflammation. Chronic treatment of wild-type zebrafish with 1 \u03bcM tunicamycin from 3.5 dpf through to 6 dpf resulted in a smaller intestine (P=0.002) and defects in intestinal architecture . Interestingly, tunicamycin-treated larvae exhibited increased bacterial growth (P=0.0006), GC depletion (P\u22640.02), and increased intestinal macrophage and neutrophil infiltration . Necro-inflammatory lesions containing large numbers of vacuolated or autophagic IECs in tunicamycin-treated Tg(lc3-gfp) larval intestines were clearly evident . These results clearly suggest that chronic ER stress is sufficient to trigger necro-inflammatory injuries in the zebrafish intestine, leading to hi559-like GI pathology.Our analysis of cdipt mutants to human inflammatory states and as an in vivo system in which to assay potential suppressors of the inflammatory pathology, we assessed the response of hi559 mutants to antibiotics and anti-inflammatory drugs.Recruited macrophages and neutrophils are potent sources of cytokines and tissue destructive enzymes, contributing to necro-inflammatory injury by loss of IEC integrity. Anti-inflammatory agents, such as 5-aminosalicylic acid (5-ASA) and prednisolone, are thus widely used therapies for alleviating human inflammatory disorders, and remain an important option for treating patients presenting with moderate to severe IBD. In recent years, co-administration of antibiotics or probiotics with anti-inflammatory drugs is also being prescribed as an effective regimen for IBD treatment . To illuhi559 intestinal phenotype and did not increase gut size , although leukocyte infiltration was effectively reduced . Co-administration of anti-inflammatory drugs 5-ASA and prednisolone together with antibiotics from 3.5 to 6 dpf resulted in marginal alleviation of hi559 intestinal size, as seen by ISH with fabp2, showing a minor increase in gut size compared with the mutant is a small chemical chaperone and a well-established drug proven to reduce ER stress in both in vivo and in vitro studies larvae showed reduction of IEC autophagosomes , which probably contributes to inflammation and other disparate diseases (including cancer) that have been linked with chronic inflammation. Phospholipids are believed to have potential anti-inflammatory roles and can suppress activation of pro-inflammatory cells tivation , and admtivation . Interestivation . Recentltivation . The \u03bc-otivation . We hypocdipt mutants could provide an excellent platform for preclinical in vivo whole-organism studies evaluating the therapeutic potential of such compounds in ameliorating epithelial injury and inflammation.This study provides the first evidence linking PI synthase to ER-stress-mediated GI pathologies, including bacterial overgrowth, mucosal apoptosis and inflammation, that are reminiscent of human IBD. In addition to genes regulating the immune system, mutations in genes affecting epithelial ER stress and function have been associated with IBD risk factors . Becausehi559cdipt was isolated from a large-scale insertional mutagenesis screen to generate a transgenic zebrafish line. A 1.2-kb upstream fragment of the fabp2 promoter was cloned into the plasmid vector pEGFP. The plasmids pEGFP-fabp2 and pTOL2 (pT2KxIG in) were double-digested with BamHI and XhoI. The linearized ~3.5-kb fragment from pEGFP-fabp2 and the 6.8-kb fragment from pTOL2 were ligated using the T4 DNA ligase. The linearized construct pTOL2-EGFP-fabp2 was micro-injected into single-cell zebrafish embryos to obtain a germ-line transgene integration of fabp2-TOL2-EGFP. The founder fish were screened for the stable integration of the transgene, and subsequent transgenic fish generations were maintained.We used the regulatory region of the zebrafish hi559 heterozygotes with Tg(gut:gfp) and Tg(lyzc:egfp) lines. The Tg(gut:gfp) transgenic zebrafish line expresses GFP throughout the digestive system and is used as a tool to analyze development of the GI tract and digestive organs (Tg(lyzc:egfp) transgenic line expresses enhanced green fluorescent protein (EGFP) under the regulatory regions of the zebrafish lysozyme-C (lyzc) gene, and is used to study infiltration of myeloid-derived inflammatory cells, representing a subset of macrophages and granulocytes (Tg(mpx:gfp) transgenic line expresses GFP under the neutrophil-specific myeloperoxidase promoter and is used effectively to analyze intravital inflammatory response in vivo in zebrafish larvae (Tg(lc3:gfp) transgenic line expresses GFP-fused Lc3 (GFP-Lc3), which can be visualized in vivo to monitor autophagy as Lc3 specifically labels the growing phagophores and completed autophagosomes (Double transgenic fish used in this study were generated by crossing e organs . The Tg(ulocytes . The Tg(h larvae . The Tg(agosomes .n\u226512).Live imaging of zebrafish larvae was done by brightfield or fluorescent microscopy (Leica or Zeiss Axiovert). Confocal imaging was performed using a laser scanning confocal microscope (Leica or Zeiss), and the acquired images were analyzed using ImageJ . The GFP intensity and puncta were quantified to assess leukocytes and autophagosomes in the GI tract of the respective transgenic larvae (in situ hybridization were performed as described previously (Tg(gut:gfp) or Tg(fabp2-egfp) transgenic fish.For Nile Red staining, larvae were treated with 10 ng/ml Nile Red in E3 medium, starting at 3 dpf. The size and morphology of the gut lumen was assessed at different stages by observing Nile Red incorporation using fluorescent microscopy (Leica). Cy3-SA labeling and whole-mount eviously . Quantitn\u226515) and larvae from DMSO control and drug treatment groups (n\u22657). This allowed us to cover the analyses of histological features of the entire GI tract. For GC enumeration, PAS- and H&E-stained sections prepared at various time points during larval growth were imaged, and the total numbers of IECs and PAS-positive cells were determined for at least 12 alternate sections (4 \u03bcM) representing at least eight different larvae each from wild-type, mutant, DMSO and drug treatment groups. Phenotypically mature GCs were assessed according to the intensity of staining, the size of the apical region, the location in the intestinal epithelium and morphological appearance.Histological sectioning and hematoxylin and eosin (H&E) staining were performed as described previously . The IECTo assess the differential expression of Hspa5, sagittal cryosections (8 \u03bcM) through the entire GI tract of wild-type and mutant larvae were used for fluorescent immunohistochemistry using anti-HSPA5 primary antibody (Sigma) and FITC-conjugated anti-rabbit IgG secondary antibody (Sigma) and counterstained with DAPI (Sigma) for nuclear staining. Fluorescent image acquisition was performed using a confocal microscope (Zeiss) followed by analyses using ImageJ.TEM was performed in the EM facility at the Center for Biological Imaging, University of Pittsburgh. For semithin sections, the epoxy resin-embedded larvae were transverse sectioned (350 nm) and stained with toluidine blue. At least ten ultrathin sections (70 nm) were collected, corresponding to the esophageal and intestinal region, for TEM staining and analyses. Sectioning depth from the beginning of the tissue as reference point and visualization of toluidine blue stained sections at regular intervals allowed us to select TEM sections from the same area of the tissue for wild type and mutants. The number of mitochondria, autophagosomes and lysosomes were counted from a set field of specific magnifications facilitating observation of GI cells and represented as numbers per field of observation. GI cells containing double or multi-membrane autophagosomes were considered positive and counted manually. Data were presented as percentage of IECs with autophagy in each field of observation. Mitochondrial counts were presented as total number of mitochondria per IEC.n=5) was isolated using RNA purification kit (Stratagene). cDNA was prepared by reverse transcription using Superscript II (Invitrogen). RT-PCR to detect xbp1 splicing was performed as described previously and the isolated gut tissues were washed three times with sterile PBS followed by homogenization with 500 \u03bcl PBS in sterile microfuge tubes with disposable microfuge pestles. Serial log10 dilutions of the homogenates were plated on LB agar plates and incubated overnight at 28.5\u00b0C. Intestinal bacterial density was enumerated based on total colony forming units (cfu) per individual gut.Quantification of intestinal bacterial density was adapted from previously described methods with applicable modifications . Zebrafiin vivo labeling with 5-bromo-2 -deoxy-uridine and apoptosis was quantified by TUNEL assay on histological sections using the ApopTag peroxidase kit (Chemicon). Larvae were incubated in E3 with 10 mM BrdU for 6 h at 28.5\u00b0C and fixed in 4% PFA overnight. Incorporated BrdU was detected with an anti-BrdU antibody (Amersham) and visualized with peroxidase substrate kit (Vector). Quantification of proliferating and apoptotic cells was represented in percentages of relative proportion of BrdU-positive and TUNEL-positive IECs to the total number of IECs in at least ten alternate sagittal sections (5 \u03bcm) representing the entire GI tract of at least eight different larvae.Cell proliferation was estimated by Tunicamycin is known to prevent N-linked glycosylation of proteins, affecting their proper folding and accumulation in the ER, thus inducing ER stress in eukaryotic cells . The tunTg(gut:gfp), Tg(lyzc:egfp) or Tg(lc3:gfp) larvae were treated with 5 \u03bcM \u03b4-HCH (Sigma) from 3.5 to 6 dpf and analyzed at 6 dpf.\u03b4-Hexachlorocyclohexane (\u03b4-HCH), a compound with similar configuration to myo-inositol, inhibits PI synthesis by affecting the incorporation of myo-inositol into PI . Wild-tyFor antibiotic treatment, zebrafish larvae were exposed to a cocktail of antibiotics from 3.5 to 6 dpf. Antibiotics consisted of ampicillin , kanamycin , and penicillin-streptomycin pre-mix in E3 media. Anti-inflammatory drugs consisted of 5-aminosalysilic acid and 6-\u03b1-methylprednisolone dissolved in 0.05% DMSO v/v in E3 media.For chemical chaperone treatment, sodium 4-PBA (Sigma) was dissolved in E3 water and the fish exposed to various dosages of 4-PBA to optimize a nontoxic dosage that did not cause any developmental defects. A final concentration of 50 \u03bcM 4-PBA (from 3.5 dpf until 9 dpf) was used for the rescue experiments in this study. For control groups, larvae were treated with equivalent concentration of DMSO alone. The drug treatments were performed in 12-well plates containing 15 larvae each from three different biological clutches.t-test; P values of less than 0.05 were considered significant. The results are expressed as means, and standard deviations are indicted by error bars in the figures.Data are representative of larvae from at least three different biological clutches. Statistical significance was calculated using a two-tailed Student\u2019s http://www.ingenuity.com) and the Gene Set Enrichment Analysis tool after adjusting for false discovery rate was considered significant.Gene expression and pathway analyses were performed as described previously using our microarray data deposited with GEO (GSE17711) . We usedu/gsea/) to decip"} +{"text": "To conduct a systematic review and meta-analysis to evaluate the efficacy of peer-led interventions in reducing unprotected anal intercourse (UAI) among men who have sex with men (MSM).Randomized clinical trials (RCTs), quasi-experimental studies, pre- and post-intervention studies without control groups, and serial cross-sectional assessments involving peers delivering interventions among MSM and published as of February 2012 were identified by systematically searching 13 electronic databases and cross-referencing. Effect sizes (ES) were calculated as the changes of standardized mean difference (SMD) in UAI between groups or pre-post intervention.P<0.01). Subgroup analyses demonstrated a statistically significant reduction on UAI in quasi-experimental studies and serial cross-sectional intervention studies , but non-significant reduction in RCTs or pre- and post-intervention studies . Heterogeneity was large across these 15 studies , largely due to pre-and-post intervention studies and serial cross-sectional intervention studies.A total of 22 studies met the eligibility criteria, including five RCTs, six quasi-experimental studies, six pre-and-post intervention studies, and five serial cross-sectional intervention studies. We used 15 individual studies including 17 interventions for overall ES calculation; peer-led interventions reduced UAI with any sexual partners in meta-analysis (mean ES: -0.27; 95% confidence interval [CI]: \u22120.41, \u22120.13; Peer-led HIV prevention interventions reduced the overall UAI among MSM, but the efficacy varied by study design. More RCTs are needed to evaluate the effect of peer-led interventions while minimizing potential bias. Men who have sex with men (MSM) continue to represent the largest number of new HIV infections in North America and other parts of the world Peer-led HIV intervention typically involves members of a specific at-risk group to influence and support members of the same group to maintain healthy sexual behaviors, change risky sexual behaviors, and modify norms In 1991, a peer-led intervention study among MSM was reported to successfully increase condom use and reduce the number of sexual partners A systematic literature search was performed to identify randomized clinical trials (RCTs), quasi-experimental studies, pre- and post-intervention studies without control groups, and serial cross-sectional intervention studies involving peers delivering interventions among MSM published as of February 29, 2012. The search was conducted in 13 electronic databases: AMED , BIOSIS Previews , British Nursing Index , EMBASE , EconLit , ERIC , Ovid Medline , PsycINFO , Scopus , Web of Science , CNKI , CQVIP , and Wanfang Data . Keywords used in the database search included: [(men who have sex with men) OR (MSM) OR OR (gay men) OR OR (transgender women) OR (money boy)] AND [(HIV) OR (AIDS) OR OR ] AND [(peer) OR (opinion leader)]. All publications were exported to an Endnote file , and the duplicates were deleted.Studies were selected if they met the following inclusion criteria: original RCTs, quasi-experimental intervention studies, pre- and post-intervention studies without control groups, or serial cross-sectional intervention studies of interventions among cohorts of MSM ; utilized MSM peers as intervention deliverers; reported UAI or condom use during anal sex before and after intervention between arms , or only in intervention arm .All abstracts were independently reviewed by two authors (SY and LY), and full texts were reviewed for determining eligibility if abstracts were incomplete. Manuscripts that met inclusion criteria were retained for full analysis. Any disagreements were resolved by further discussion involving an additional author (HZQ).For all eligible studies, two authors extracted the following information independently, using common abstraction forms: authors, publication year, study country, study design, description of interventions in study arms, training of peers, theoretical basis of intervention, sample sizes and retention rates in study arms, durations of follow-up, type and HIV status of sex partners, position of anal sexual intercourse , and proportions and mean frequencies of UAI. Disagreements were discussed until a consensus was reached.We assessed the rigor of the study design of each included study using an 8-point scale We used UAI as the outcome variable in this meta-analysis as this was the most common and HIV-relevant outcomes included in other studies. UAI was measured as continuous or categorical variable in the included studies. We adopted a conservative approach for calculating the proportion of UAI where the denominator was the number of total sample instead of the number of participants who reported UAI, as the latter may potentially overestimate the proportion of UAI. We calculated standard mean difference (SMD) in each study arm as a fraction of dividing the difference of two means at follow-up and baseline (or post- versus pre-intervention) by the pooled standard deviation (SD) of these two means. When studies reported dichotomous outcomes, odds ratios were transformed into SMD using Cox transformation We calculated the effect size (ES) of individual intervention as the difference of SMDs between study arms in RCTs and quasi-experimental studies, as well as in pre- and post-intervention studies and serial cross-sectional studies where we assumed a value of zero for SMD in the comparison arm Several planned subgroup analyses of studies were performed to examine effect sizes of any sexual partners, which were conducted by study design ; characteristics of risk assessment ; intervention characteristic , as well as by other study characteristics including study country (US and Canada or China), number of study cities (one or multiple), venue of recruiting participants (establishment-based or other venues), sample size at baseline (\u2264300 or >300), publication year (prior to year 2000 or year 2000 or later), duration of follow-up , retention rate at the last follow-up (<80% or \u226580%), and rigor score (<6 or \u22656). We evaluated overall effect size based on 15 papers (17 interventions) as they reported UAI with any sexual partners; we included other 7 papers in subgroup analyses as they provided additional information such as UAI with regular or casual or with HIV negative or/and unknown status sexual partners I2 statistic Heterogeneity in overall efficacy and within specific subgroups was assessed by the Sensitivity analyses were conducted to determine the stability of intervention efficacy by evaluating whether the overall effect size was sensitive to inclusion of any given individual study. Studies excluded in iterative sensitivity analyses included those producing outliers identified by standardized deleted residuals analyses, involving two active intervention arms contrasted to the same control arm in the same study, involving only HIV-infected MSM participants, studies with low rigor score, or those with poor data reporting. All meta-analyses were performed in the R/S plus Software version 2.15.1.The initial search of 13 individual electronic databases yielded 1,320 entries meeting our predefined inclusion criteria; 775 duplicates were identified and removed . Of the Among the 22 studies included, 5 were RCTs As indicated in Nine studies developed the intervention based on Kelly's diffusion of innovation theory Nine studies did not provide information on selection and training of peer educators The change in UAI by study arm, type of sexual partner, and position of anal sex (insertive or receptive) were described in P<0.01), with significant heterogeneity across studies . While quasi-experimental studies and serial cross-sectional intervention studies showed statistically significant reduction in UAI, RCTs and pre- and post-intervention studies did not. No publication bias was detected based on the funnel plot .nel plot as well Subgroup analyses and sensitive analyses showed peer-led interventions reduced UAI with casual sexual partners but not with regular sexual partners or with HIV negative or unknown status sexual partners . StudiesIn standardized deleted residual analysis, two individual studies were identified as outliers Our systematic review of 22 studies and our meta-analysis of 17 interventions from 15 studies with qualifying UAI outcomes of peer-led interventions targeting MSM showed an overall beneficial effect on reducing UAI. Sensitivity analyses also showed reduction of UAI in all four types of study design, but the subtotal efficacy from RCTs (average SMD\u200a=\u200a-0.15) is not statistically significant and is smaller than those from other three study designs: serial cross-sectional intervention studies (SMD\u200a=\u200a\u22120.33), quasi-experimental studies (SMD\u200a=\u200a\u22120.30) and pre- and post-intervention studies (SMD\u200a=\u200a\u22120.29). High heterogeneity observed in these 15 included studies; and those employing serial cross-sectional or quasi-experimental design appeared to contribute significantly to the overall positive effect. Future studies should use more rigorous study design RCT to reduce potential bias. In this meta-analytic review, we did not assess the impact of pee-led interventions on disease rates such as HIV incidence Our meta-analysis found that follow-up assessments within 12 months showed a statistically significant relationship with reduction of UAI among MSM, whereas the few that examined longer-term intervention effects did not have a significant average effect. Whether this reflects true dissipation of intervention effects or another factor is unknown. Given the scarcity of data for long-term outcomes, high quality peer-delivered intervention research that characterizes risk behavior beyond 12 months is needed.UAI with casual sexual partners is known as a high risk factor for HIV acquisition. Recent research has indicated that higher levels of UAI may be associated with one's level of perceived familiarity with casual sexual partners Our stratified analysis by the format of delivering intervention found a 32% reduction of UAI for group-based interventions, but only a 4% (non-significant) increase for individual-based interventions. A previous meta-analysis found that individual-based interventions were more effective than group-based interventions to reduce UAI (51% vs. 34%), but it only included the studies published between 1988 and 2004 and focusing on HIV-infected persons The diffusion of innovation model served as the theoretical basis for many peer interventions Our study is the first meta-analysis of the efficacy of peer-led interventions on UAI among MSM. Our analyses adjusted baseline data between study arms and combined continuous and categorical outcomes of UAI as reported in original studies. Therefore, our study has an advantage over previous reviews that failed to correct varying denominators In summary, our meta-analysis suggests that peer-led HIV prevention interventions have an overall impact on reducing UAI among MSM, but the efficacy varied by study design. Future peer-led intervention studies targeting MSM population should use RCT design for controlling the baseline difference between intervention and comparison arms, have a long follow-up period for assessing long-term effects of interventions, and use biological outcomes such as HIV seroconversion to reduce information bias.Table S1Efficacy of 22 peer-led interventions on unprotected anal intercourse (UAI) among men who have sex with men.(DOCX)Click here for additional data file.Table S2List of relevant studies excluded from this meta-analysis by category of reasons.(DOCX)Click here for additional data file.Checklist S1CONSORT checklist.(DOC)Click here for additional data file."} +{"text": "The basal-like subtype of human breast cancers has no clinically defined marker profile. Recent studies have shown that Met as well as certain Src family kinases are over-expressed in basal-like breast cancers and correlate with disease progression and poor prognosis. Our group has also demonstrated a potential regulatory role of Stat3 on Met activation or turnover, adding to the previously identified roles of Stat3.We have elected to test the efficacy of inhibitors of Met (PF-02341066), Src family kinases (Dasatinib), and Stat3 (CPA7) in blocking the invasive potential of breast cancer cells, using the human basal-like breast cancer cell line MDA-MB-231 transfected with a constitutively active Src mutant (MDA-Src cells). The efficacy of inhibitors in disrupting the invasive capacity of cells was assessed using transwell invasion assays and colony growth in a 3D Matrigel culture model mimicking basement membrane matrices.Treatment of MDA-Src cells with Stat3 or Src inhibitors markedly reduced branching extensions, and induced growth arrest and cell death of colonies in a dose-dependent manner. Interestingly, treatment with the Met inhibitor also decreased branching extensions but failed to inhibit cell colony forming ability or proliferation. Furthermore, we have found that induction of morphological responses in 3-D culture occurs at ~15-fold lower concentration of the inhibitors than is necessary to observe decreased expression of drug targets in 2D culture. Transwell assays also showed a decrease in invasion of CPA7 and Dasatinib treated cells. Interestingly, PF2341066 treatment of cells did not affect transwell invasive potential, suggesting that other effectors than Met may be involved.Our findings further implicate a rate-limiting role of Src, Stat3 and Met in the process of invasion in human basal-like cells, and may lead to improved predictive biomarkers for targeting of aggressive breast cancer subtypes which exploit this pathway.Terry Fox Transdisciplinary Studentship in Partnership with CIHR (EC), Ontario Graduate Studentship (EC), Canadian Breast Cancer Foundation (LR), and Canadian Institutes of Health Research (BEE)."} +{"text": "In this technical report, we present an approach for defining a subset of interest in a mixed cell population by flow cytometric detection of intracellular antigens. We have developed a fully validated protocol that enables the co-detection of cluster of differentiation (CD) surface antigens on fixed, permeabilized neural cell populations defined by intracellular staining. Determining the degree of co-expression of surface marker candidates with intracellular target population markers on neuroblastoma cell lines -M17) yielded a combinatorial CD49f-/CD200high surface marker panel. Its application in fluorescence-activated cell sorting (FACS) generated enriched neuronal cultures from differentiated cell suspensions derived from human induced pluripotent stem cells. Our data underlines the feasibility of using the described co-labeling protocol and co-expression analysis for quantitative assays in mammalian neurobiology and for screening approaches to identify much needed surface markers in stem cell biology.Surface molecule profiles undergo dynamic changes in physiology and pathology, serve as markers of cellular state and phenotype and can be exploited for cell selection strategies and diagnostics. The isolation of well-defined cell subsets is needed for A percentage value of 0.1% was assigned where no cells were present in a quadrant . Surface antigens co-stained with DCX were quantified on SH-SY5Y cells. Surface antigens co-stained with TUJ1 were quantified on SH-SY5Y cells and neuronally differentiating cultures derived from human iPS cells, and surface antigens co-stained with GFAP were quantified on SNB-19 cells. (B) Using the conditional formatting function in Microsoft Excel, a dark to light-green color scale was applied to each one of the intracellular co-stained data sets to generate co-expression heatmap (see (tmap see 6D. Note(TIF)Click here for additional data file."} +{"text": "Pseudomonas aeruginosa PAO1 follows the Wzy-dependent pathway, beginning with translocation of undecaprenyl pyrophosphate-linked anionic O-Ag subunits (O units) from the inner to the outer leaflets of the inner membrane (IM). This translocation is mediated by the integral IM flippase Wzx. Through experimentally based and unbiased topological mapping, our group previously observed that Wzx possesses many charged and aromatic amino acid residues within its 12 transmembrane segments (TMS). Herein, site-directed mutagenesis targeting 102 residues was carried out on the TMS and loops of Wzx, followed by assessment of each construct's ability to restore B-band O-Ag production, identifying eight residues important for flippase function. The importance of various charged and aromatic residues was highlighted, predominantly within the TMS of the protein, revealing functional \u2018hotspots\u2019 within the flippase, particularly within TMS2 and TMS8. Construction of a tertiary structure homology model for Wzx indicated that TMS2 and TMS8 line a central cationic lumen. This is the first report to describe a charged flippase lumen for mediating anionic O-unit translocation across the hydrophobic IM.Heteropolymeric B-band O-antigen (O-Ag) biosynthesis in Pseudomonas aeruginosa is an opportunistic Gram-negative bacterial pathogen that often infects individuals with compromised defences resulting from such conditions as AIDS, cancer, severe burn wounds or cystic fibrosis (P. aeruginosa PAO1 synthesizes both a homopolymeric common polysaccharide antigen (A band) and a heteropolymeric O-specific (B band) O-Ag glycoform, with the latter composed of repeating trisaccharide O units each containing a proximal d-fucosamine sugar followed by two dideoxy-mannuronic acid derivatives capping motif. 1, or 40\u201350 units regulated by Wzz2 proteins believed to form a complex . Followi by Wzz2 , producipolysaccharide transporter (PST) protein family, which in turn is one of four members of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily (Wzx flippases belong to the prokaryotic erfamily . Inter-fP. aeruginosa PAO1 (WzxPa) was the presence of numerous charged and aromatic amino acids in these domains compared with models based on topology prediction algorithms was observed compared with the native construct in the complementation assay (multidrug and toxin extrusion (MATE) family of proteins, which pumps out drugs and other toxic compounds from the cytoplasm aligns well with the second half of the protein (residues 207\u2013411) in the HHpred fold-recognition search . NorM isytoplasm . WzxPa dhomology and hydrhomology to NorMV207\u2013411) , a consiof WzxPa .Pa structural model was assessed using genetic, biochemical and bioinformatic approaches, beginning with the sequence comparison of homologues. Residue pairs in homologous proteins that are distantly separated in primary structure but in direct contact via tertiary structure have a high propensity to maintain amino acids at these positions that have similar physicochemical and steric properties to match polarities or conserve molecular volume , while tPa model .Pa structure was determined through filling of the internal void space with dummy atoms using HOLLOW were found to be in direct contact with the lumen, whereas others were partially buried within the tertiary structure in the current conformation of the flippase family family , which hnd WzxPa , it was in LacY .Pa function . HoweverxEc) half of the protein, even though many mutants were made that map to the distal (periplasmic) half . DespitePantoea stewartii (Stewart's wilt disease) and Erwinia amylovora (fire blight disease) was successfully co-crystallized with NorMVc, leading He et al. to propose a mechanism for NorMVc function -linked GlcNAc residue via simple diffusion previously shown to not impede protein function with linear regression and local background subtraction. The ratio of the density of the B-band O-Ag banding to that of the outer core oligosaccharide was compared between cells of P. aeruginosa PAO1 \u0394wzx complemented with the native 8wzx-gfp-his construct versus the various mutant constructs. Initial screens were performed using three independent singly-analysed samples, with statistical significance calculated in comparison with the native construct using the Student's t-test. Mutant constructs displaying densitometric complementation differences compared with the native construct but with non-statistically significant initial t-test results (due to high variability in the density ratio comparisons) were further examined through the use of cultures from three independently isolated clones (n = 3), each analysed in triplicate and averaged, before comparison with the native construct via the Student's t-test (The band LPS . LPS samband LPS respectis t-test . Membrans t-test was carrpsi-blast profile generated using the non-redundant protein database from NCBI. TMhit (http://bio-cluster.iis.sinica.edu.tw/TMhit/) using both the higher-threshold L/5 and lower-threshold L/2 settings. Model restraints for each program were introduced based on established Wzx core TMS boundaries was used to identify 31 prokaryotic Wzx homologues with minimal alignment gaps possessing 22\u201335% sequence identity (43\u201360% similarity). MUSCLE was used to generate a multiple sequence alignment (MSA) (Vc (GenBank Locus: AE003852) to identify 43 NorM homologues possessing 53\u201368% sequence identity (72\u201385% similarity). MSAs of WzxPa and NorMVc, respectively, with other homologues were aligned via MUSCLE to verify the alignment of stringent positions between the two sets of proteins and then compared using AlignMe (Vc structure using iMembrane (Vc (i.e. those in the same plane as the membrane lipid acyl chains). The TMS core regions of WzxPa and its 31 homologues were analysed with MEMSAT3 to ident AlignMe . Results MEMSAT3 , yielding HOLLOW with the"} +{"text": "Because it is known that nef by RT-PCR. The amplified products were cloned into a plasmid and subsequently sequenced. A representative nef clone was selected for each patient and cloned into an NL43 proviral plasmid backbone. Infectious recombinant viruses were prepared by transfecting 293T cells with these resultant proviral clones and tested for their viral replication capacity in PBMCs obtained from multiple healthy donors. Viral replication was monitored by measuring the concentration of p24 Gag in the culture supernatant by p24 ELISA every 3 days. The same virus stocks were further tested for their infectivity using TZM-bl cells.Viral RNAs were extracted from plasma samples of 45 ECs and 48 chronic progressors (CP) and used for amplification of nef alleles isolated from EC and CP had intact ORFs. Phylogenetic analysis revealed no specific lineage or clustering, suggesting the absence of common genetic defects in EC-derived nef alleles. All viruses expressing patient-derived nef showed a wide range of viral replication in PBMC, confirming the importance of nef alleles in the enhancement of viral replication capacity. The viruses harboring EC-derived nef replicated and peaked on Day 12 after infection or even later; whereas the viruses harboring CP-derived nef peaked on Day 9. Also, the peak level of p24 values was significantly lower in the EC-nef viruses than in the CP-nef viruses. Because Nef activity is highly dependent on PBMC donors, we tested 4 different donors' PBMC and compared the initial burst of their viral replication at Day 9. In all donors'PBMC, viruses carrying EC-nef displayed lower p24 values than those carrying CP-nef, suggesting that the viral replication capacity was much impaired by nef alleles in EC. Corroboratively, in viral infectivity assay in TZM-bl cells, the EC-nef viruses showed significantly lower infectivity than the CP-nef viruses.All nef alleles present in circulating plasma viruses in EC are much impaired in boosting viral replication, suggesting that such phenotypic alterations in Nef function play a role, at least partly, in the sustained maintenance of low viral load in vivo.Taken together, our data indicate that"} +{"text": "Arsenic is a well-known human carcinogen, which potentially affects ~160 million people worldwide via exposure to unsafe levels in drinking water. Lungs are one of the main target organs for arsenic-related carcinogenesis. These tumors exhibit particular features, such as squamous cell-type specificity and high incidence among never smokers. Arsenic-induced malignant transformation is mainly related to the biotransformation process intended for the metabolic clearing of the carcinogen, which results in specific genetic and epigenetic alterations that ultimately affect key pathways in lung carcinogenesis. Based on this, lung tumors induced by arsenic exposure could be considered an additional subtype of lung cancer, especially in the case of never-smokers, where arsenic is a known etiological agent. In this article, we review the current knowledge on the various mechanisms of arsenic carcinogenicity and the specific roles of this metalloid in signaling pathways leading to lung cancer. In. In17]. uaporins ,20. Insisynthase . As a panjugates . Mono- aepletion -25. IncrInorganic arsenic does not interact directly with DNA and is not considered to be mutagenic at non-toxic doses . HoweverIII and AsV[III)-mediated inhibition of mitochondrial complexes II and IV [-), hydrogen peroxide (H2O2), and hydroxyl radicals (OH\u2022) [Arsenic-induced ROS may be generated by either cycling of AsI and AsV or throuI and AsV ,38. Arseeroxide HO2, and hls (OH\u2022) -41.Arsenic can also induce generation of reactive nitrogen species (RNS). The mechanisms involved are not completely understood; however, they are thought to occur in a tissue-specific manner . The incIII species generated by the biotransformation process impair the expression and activity of human PARP1, a promoter of NER that acts in response to DNA damage [Arsenic can affect cellular DNA repair capacity, by altering both nucleotide- (NER) and base-excision repair (BER) mechanisms Figure\u2009. ArsenicA damage . ArsenicA damage . In arseA damage .Arsenic-treated cells demonstrate significantly increased micronuclei formation as well as chromosomal aneuploidy, likely by an effect on sulfhydryl groups of tubulin and microtubule-associated proteins and consequential cell spindle assembly disruption -57. AddiArsenic detoxification requires the use of S-Adenosyl methionine (SAM) as a methyl donor Figure\u2009; consequInterestingly, individuals chronically exposed to high yet non-lethal levels of arsenic exhibit a significantly higher degree of DNA methylation in promoter regions of P53 and CDKN2A compared to non-exposed controls . Lung caArsenic-mediated reduction of global levels of H4K16 acetylation, a mark of gene activation, has been demonstrated in cell models . FurtherA study using human bronchial epithelial cells (HBEC) demonstrated that chronic arsenic exposure of P53-knock down cells induced malignant transformation accompanied by epithelial-to-mesenchymal transition (EMT) . A reducArsenic exposure can alter miRNA expression levels in vitro and in vivo in other cell types and tissues. For example, in a study using chick embryos, arsenic decreaseD expression of miR-9, -181b, -124, and -125b. Decrease of miR-9 and miR-181b resulted in expression of their common target Nrp1, leading to cell migration, tube formation and angiogenesis . ArsenitAlteration in the EGFR pathway can result from mutation and/or amplification events at the epidermal growth factor receptor (EGFR) locus. The consequence of either genetic event is a structural alteration that destabilizes the auto-inhibitory loop of EGFR, forcing the receptor into a constitutive and ligand-independent active state .III activates STAT3 through c-Jun NH2 kinase (JNK), contributing to Akt activation [III is capable of activating Rac1 GTPases resulting in downstream engagement of the JNK pathway and increased cell survival and proliferation [Similar states of EGFR constitutive activation can be induced by even moderate levels of arsenic, similar to those registered in contaminated U.S. drinking water, affecting the lungs and other target organs of arsenic carcinogenesis ,95 Figu. Arsenictivation . Arsenicferation ,104. Thiferation .Signaling through the PI3K/AKT pathway starts with the activation of receptor tyrosine kinases (RTK\u2019s) through binding to an extracellular growth factor. Binding of the extracellular ligand to its receptor leads to the dimerization and activation of the RTK . The conIII can induce phosphorylation of EZH2 at serine 21 in human bronchial epithelial cells and such phosphorylation of EZH2 requires AsIII-activated signalling through JNK and STAT3 leading to phosphorylation of AKT [III-induced AKT activation [III can stimulate AKT and the consequent release of vascular endothelial growth factor (VEGF), inducing cell migration through different mechanisms [Acute exposure to arsenite can stimulate the PI3K/AKT phosphorylation cascade, leading to cellular transformation characterized by increased proliferation and anchorage-independent growth -109 Fig. AsIII cn of AKT . Arsenicn of AKT . Additiotivation . In HBECchanisms ,112,113.chanisms .Although acute activation of this pathway is thought to be mediated by arsenic-induced ROS, the specific role of arsenic on PI3K/AKT signalling during chronic exposure remains to be clearly demonstrated .The transcription factor nuclear factor erythroid-derived factor 2\u2013related factor 2 (NRF2) plays a key role in the activation of oxidative stress response. NRF2 contains a leucine-zipper DNA binding domain capable of binding to both antioxidant response elements (ARE\u2019s) and electrophile response elements (ERE\u2019s). Under normal conditions, NRF2 is actively sequestered by KEAP1 and targeted for proteolytic degradation ; howeverIII and MMAIII[It has been proposed that activation of the NRF2 pathway confers protection against toxic effects induced by both Asnd MMAIII. Patholond MMAIII. Arsenitnd MMAIII. It is pnd MMAIII. This apnd MMAIII.Lung cancer is the leading cause of cancer-related deaths in North America, affecting over 200,000 men and women each year . ArsenicV into AsIII and its methylated conjugates plays a crucial role in arsenic carcinogenicity at both genetic and epigenetic levels. Genetic changes are acquired mainly through the induction of ROS during the biotransformation process, while the competition for methyl groups between AsV detoxification enzymes and DMT\u2019s contribute to epigenetic abnormalities.Undoubtedly, the biotransformation of AsArsenic species directly modulate several oncogenic pathways\u2009-\u2009most notably the EGFR, PI3K/AKT and the NRF2/KEAP1 pathways\u2009-\u2009and these specific pathways possess actionable targets for therapy in lung cancer. A greater understanding of the molecular mechanisms governing arsenic-related lung tumorigenesis may therefore yield promising translatable findings. Deep characterization of arsenic-related tumors and/or cell models at both the genetic and epigenetic levels, and the comparison of arsenic-related and unrelated SqCC tumors may provide such insights. On the other hand, mechanisms associated with anti-tumoral effects of As2O3 in the treatment of APL (not discussed in this review) should also be considered in order to increase the understanding of the molecular effects of arsenic in the human body.In conclusion, arsenic can induce specific alterations affecting pathways that drive malignant transformation in lung cells. Current evidence suggests that arsenic-induced lung tumors represent a unique class of lung cancer, based on histology and underlying molecular characteristics. Further characterization of the mechanisms by which arsenic affects its targets will certainly give support to preventing and/or reducing the effects of arsenic toxicity, especially among those populations chronically exposed to arsenic.AsIII: Arsenite; AsV: Arsenate; EGFR: Epidermal Growth Factor; HBEC: Human Bronchial Epithelial Cells; MMAIII: Monomethylarsonous Acid; NRF2: NFE2-Related Factor 2; PIK3: Phosphatidylinositol 3-kinase; ROS: Reactive Oxygen Species; RTK: Receptor Tyrosine Kinase; SAM: S-Adenosyl Methionine; SCC: Small Cell Carcinomas; SqCC: Squamous Cell Carcinomas.All authors declare no conflict of interest on the topics covered by this review.RH and DBS contributed to manuscript conception and writing. KE and DR contributed to literature search and manuscript writing. SL and WLL contributed to manuscript writing and critically revised the paper. All authors read and approved the final manuscript. VM contributed to study conception, manuscript writing and critically revised the paper."} +{"text": "O-methyl-substituted derivative of the clinically used MOP analgesic oxymorphone, namely 14-O-methyloxymorphone, and its 5-methyl-substituted analogue, 14-methoxymetopon. The focus of the present work is on structure-activity relationship (SAR) studies and in vitro and in vivo pharmacological investigations on a series of opioid ligands differently substituted in positions 5 and 14 of the morphinan skeleton.Opioid analgesics are the cornerstone drugs for the treatment of moderate-to-severe pain. Morphine and other analgesics like fentanyl, oxycodone and oxymorphone activate the \u00b5 opioid (MOP) receptor, the main type targeted for pharmacotherapy of pain. These drugs share the same pharmacological profiles including severe adverse effects such as respiratory depression, constipation, tolerance and physical dependence. Chemical approaches towards the identification of novel MOP analgesics with reduced side effects include structural modifications of morphinan-6-ones in key positions that are important for binding, selectivity, potency and efficacy at opioid receptors. A representative example is the development of the 14-35S]GTP\u03b3S functional assays with Chinese hamster ovary (CHO) cells expressing human opioid receptors were used to assess opioid agonism. Antinociceptive properties were established using hot-plate and writhing tests in mice after subcutaneous (s.c.) administration.Radioligand binding assays were performed using rodent brain membranes. Mouse vas deferens (MVD) and guinea-pig ileum (GPI) bioassays, and [N-methylmorphinan-6-ones produced marked antinociceptive effects in mice when given s.c., being several-fold more potent than morphine. On the basis of the SAR that has emerged, certain modifications in the substitution pattern, e.g. introduction of an alkyl or arylalkyl group in position 14 and/or in position 5, result in interesting alterations in opioid activity by influencing the pharmacological properties of ligands interacting with opioid receptors. Analysis of the in vitro and in vivo opioid profile for this series of 14-alkoxymorphinans leads to an improved understanding of the relationship between affinity and/or selectivity for opioid receptors, agonist activity, antinociceptive potency and the nature of substituents in morphinans.Binding studies showed that all derivatives display affinities in the subnanomolar range at the MOP receptor and were MOP receptor-selective. In smooth muscle preparations and CHO cells transfected with MOP receptors they behaved as potent agonists. The differently substituted These results represent a useful and valuable outcome for the design and optimization of existing structural templates increasing the chance of identifying clinically useful analgesics for superior management of pain."} +{"text": "Individuals with acquired immunodeficiency are at heightened risk for multiple subtypes of cancer. Among sarcomas, increased risk in both adults and children has been identified only for Kaposi\u2019s sarcoma (KS), and in HIV-infected children for leiomyosarcoma. In contrast, broader diversity in subtypes of lymphomas and carcinomas has been reported. Sarcomas constitute <1% of all incident cancers in the general population. Modest increases in risk of rare sarcoma categories in the immunocompromised may thus be difficult to capture. We therefore reviewed published data from case reports/series to describe sarcoma subtypes in HIV-infected individuals and solid organ transplant recipients.Literature review of sarcoma case reports in people with HIV and recipients of organ transplants were conducted using PubMed and citation searches. Surveillance Epidemiology and End Results (SEER) data (1974-2008) were queried to obtain counts of each type of sarcoma, and the age distribution of leiomyosarcomas.3. All 14 cases of transplant-related angiosaromas were in renal transplants. Ninety three percent (13) occurred in males. Half of transplant-related angiosarcomas occurred at the site of an arteriovenous fistula.A total of 152 cases of sarcomas (other than KS) were identified in people with HIV/AIDS (n=62) and in recipients of solid organ transplants (n=90). Leiomyosarcomas represented the bulk of all sarcomas (98/152), followed by angiosarcoma (16/152) and fibrohistiocytic tumors (15/152). Compared to the distribution of sarcomas in SEER, leiomyosarcoma was overrepresented by 4-fold . Ages of HIV-related leiomyosarcoma cases suggested a bimodal distribution with an early peak among 0-9 year olds (36%) and later among 30-39 year olds (34%). More than 80% of immunodeficiency-related leiomyosarcomas were Epstein-Barr virus (EBV)-positive. Most HIV-related leiomyosarcomas (>93%) were in people with AIDS diagnoses and the majority of transplant-related leiomyosarcomas (>62%) were reported in renal transplant recipients. Leiomyomas were also reported in people with immunodeficiency (n=37), and >65% of leiomyomas and leiomyosarcomas reported in people with HIV infection occurred with CD4 counts of <50 cells/mmEBV-positive smooth muscle tumors are frequently reported in people with immunosupression. Both children and adults are at risk for leiomyosarcomas. Leiomyomas and leiomyosarcomas occurred with the same propensity in people with CD4 counts below 50. Angiosarcomas occurred specifically in males in renal transplant recipients and may be related to an arteriovenous fistula."} +{"text": "Immune evasion by suppression of host immunity is one of the major mechanisms that tumors use to promote its own survival. We have reported an abundance of immunosuppressive monocytes (CD14+HLA-DRlow/neg) in lymphoma (LYM), multiple myeloma (MM), glioblastoma multiforme (GBM), prostate cancer and renal cell carcinoma (RCC). The number of these cells increases with more aggressive disease and is associated with decreased survival. In this study, we examine the RNA expression profile of monocytes from cancer patients compared to healthy donors (CNTRL) to identify differentially affected functional pathways.Monocytes were isolated from peripheral blood using anti-CD14 immunomagnetic beads. RNA was extracted from the monocytes and analyzed via whole genome expression array (Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays). The number and frequency of the HLA-DRlow/neg phenotypes were quantified, but the population was not purified. Data was analyzed using packages assembled from R and Bioconductor. Probe-level data from the GeneChips was background-corrected, normalized and summarized into a set of expression measures via the Robust Multi-array Average with GC-content background (GCRMA) method. Several search strategies were employed to find interesting gene expression differences: (1) Directed searches for specific genes, (2) Hypergeometric testing for Gene Set Enrichment Analysis and (3) Gene Set Enrichment Analysis using liner models. A variety of gene set was employed: (A) Gene Sets derived from the Gene Ontology (GO) database, (B) Gene Sets derived from the Kyoto Encyclopedia of Genes and Genomics (KEGG) database and (C) Gene Sets curated by the Broad Institute.Monocytes RNA expression profiles were obtained from 5 CNTRL, 5 LYM, 6 MM, 4 GBM, 5 RCC, 1 ovarian cancer. Comparison of the differences in monocyte RNA expression in cancer patients to normal controls found statistically highly significant under-expression of immune function genes such as those in the TLR and TNFaR superfamily and overexpression of genes regulating cell metabolism. These genes lie at the intersection of several oncogenic and immunogenic gene sets and their roles in immunosuppressive monocytes are under active investigation. Gene Set Enrichment analysis of gene expression profiles is a promising exploratory avenue towards identifying novel immuno-regulatory pathways of CD14+HLA-DRneg/low monocytes."} +{"text": "Arabidopsis genome through complicated interaction pathways, and have been found to be significantly disrupted by biotic and abiotic stress treatments, complicating treatment-response gene discovery methods due to clock pattern mismatches in the fold change-based statistics. The PRIISM algorithm outlined in this paper is designed to separate pattern changes induced by different forces, including treatment-response pathways and circadian clock rhythm disruptions.Circadian rhythm pathways influence the expression patterns of as much as 31% of the Using the Fourier transform, high-resolution time-series microarray data is projected to the frequency domain. By identifying the clock frequency range from the core circadian clock genes, we separate the frequency spectrum to different sections containing treatment-frequency (representing up- or down-regulation by an adaptive treatment response), clock-frequency (representing the circadian clock-disruption response) and noise-frequency components. Then, we project the components\u2019 spectra back to the expression domain to reconstruct isolated, independent gene expression patterns representing the effects of the different influences.Arabidopsis microarray dataset under a cold treatment, we systematically evaluated our method using maximum fold change and principal component analyses. The results of this study showed that the ranked treatment-frequency fold change results produce fewer false positives than the original methodology, and the 26-hour timepoint in our dataset was the best statistic for distinguishing the most known cold-response genes. In addition, six novel cold-response genes were discovered. PRIISM also provides gene expression data which represents only circadian clock influences, and may be useful for circadian clock studies.By applying PRIISM on a high-resolution time-series PRIISM is a novel approach for overcoming the problem of circadian disruptions from stress treatments on plants. PRIISM can be integrated with any existing analysis approach on gene expression data to separate circadian-influenced changes in gene expression, and it can be extended to apply to any organism with regular oscillations in gene expression patterns across a large portion of the genome. Differential gene expression studies typically use the fold change statistic (the ratio of mRNA quantities between two samples) as input, and have been used to discover genes involved in adaptive stress responses which have not been previously characterized . SpecifiIn this paper, we present the PRIISM algorithm to perform novel stress-response gene discovery analyses which correct for differential gene expression patterns induced by the circadian clock. As described previously , althougBiological approaches such as the use of constant light and clock component genetic knockout mutants are applied in order to attempt to remove the influences of the circadian clock on target gene expression. However, constant light is an unnatural condition which reduces the applicability of the results, because natural biotic and abiotic genetic stress-response patterns depend on the time-of-day (the point in the light/dark cycle) at which the treatment is applied ,18,19. LMost existing computational approaches for studying differential gene expression in microarray datasets involve clustering algorithms designed to group genes with similar expression profiles, with the goal of identifying potential annotations for unknown genes -17. HoweArabidopsis genome is influenced by circadian clock genetic components . Similarly, we compute where Note that because the entire warm and cold gene expression datasets are mean-shifted based on their relative amplitudes in each component, the reconstructed time-zero fold change values may not necessarily be equal to zero Figure.Arabidopsis Affymetrix ATH1 microarray dataset generated by Espinoza et al. (2010), which consists of 16 timepoints collected over the course of 58 hours in both warm (20\u2009\u00b0C) and cold (4\u2009\u00b0C) conditions under a 16-hour light/8-hour dark cycle starting at ZT14 (14 hours after dawn) [Arabidopsis[This study analyzes an er dawn) . This daabidopsis,20,50,51Bioconductor software package and annotated using annotation data available from TAIR . The gene expression data were interpolated to every 2 hours using B-spline regression, and were segmented into four overlapping gene expression time frames (from both the warm and cold treatments), which were combined using a weighted average were geel et al by distiel et al . This diPrincipal component analysis (PCA) is a linear component composition method that has been applied to summarize different gene expression influences under different conditions, and consequently has been used for differential gene expression studies in microarray datasets . PCA wasThese results showed that, in both maximum fold change and PCA analyses, the ranked treatment-frequency fold change analyses produce fewer false positives than the original methodology by distinguishing more COS-upregulated genes Table.In the previous section, it was shown that gene discovery in the treatment-frequency data produced by PRIISM constantly outperforms the same analyses on the original data. Although these approaches are useful for poorly studied treatment responses, a knowledge-based approach may be used to identify more treatment-response genes with a lower false positive rate.C-repeat/DRE Binding Factor genes CBF1, CBF2 and CBF3[, which are induced in parallel with the cold transcription factors RAV1 and ZAT12[CBF transcription factors include Cold-Responsive (COR) genes COR15A, COR15BCOR47, and COR78[Cold treatments have been shown to induce the expression of the transcription factors and CBF3, which aand ZAT12. Some ofand COR78,50,58,59and COR78,20,23.In the treatment-frequency data, a peak in the fold change patterns can be observed in the well-studied cold response transcription factors and cold regulated (COR) response genes at the start of the first night (at approximately 26 hours) Figure, 5D. TheThis data shows that the fold change value at 26 hours in the treatment-frequency data is the best predictor of whether a gene is involved in adaptive cold response. The top 25 ranked genes based on fold changes at 26 hours in the treatment-frequency dataset are shown in TableATGolS3 (AT1G09350), the gene with the largest fold change in the treatment-frequency data at 26 hours are shown in FigureThe results of a case study on To test the statistical significance of PRIISM\u2019s ability to discover treatment-response genes, P-values were calculated using a Z-test for both the maximum fold change from the original dataset and the fold change values at 26 hours in the treatment-frequency dataset. FigureThe clock vectors calculated by Equation\u20093 under both warm and cold conditions for each of the time frames are shown in FigureT-test P-values indicating the probability that an input pattern matches a gene expression model, and provides several types of cyclic clock pattern models to use for comparison [To study whether the clock-frequency data produced by PRIISM successfully isolated cyclic clock influences from treatment-response influences, the clock-frequency gene expression patterns of eight well-studied cold response genes were matched with standard clock patterns according to the pattern-matching algorithm HAYSTACK . This almparison . This anmparison . The resArabidopsis genome through complicated interaction pathways, and have been found to be significantly disrupted by biotic and abiotic stress treatments, complicating treatment-response gene discovery methods due to clock pattern mismatches in the fold change statistic. The PRIISM algorithm outlined in this paper is designed to separate pattern changes induced by different forces, including treatment pathways and circadian clock rhythm disruptions. By applying PRIISM on a cold-response dataset, we systematically evaluated our method using maximum fold change and PCA analyses. The results of this study showed that the ranked treatment-frequency fold change analyses produce fewer false positives than the original methodology, and the 26 hour timepoint in the PRIISM produced dataset was the best statistic for distinguishing the most known cold-response genes. In addition, PRIISM also provides gene expression data which represent only circadian clock influences, and may be useful for circadian clock studies. In fact, any existing analysis approach on gene expression data can utilize PRIISM to separate circadian-influenced changes in gene expression. In conclusion, PRIISM is a novel approach for overcoming the problem of circadian disruptions from stress treatments on plants. PRIISM can be integrated with any existing analysis approach on gene expression data to separate circadian-influenced changes in gene expression, and it can be extended to apply to any organism with regular oscillations in gene expression patterns across a large portion of the genome. In future work, we will apply the discrete wavelet transforms (DWT) on higher resolution datasets in order to further enhance the ability of PRIISM to distinguish circadian clock disruption influences from treatment-response pathway influences.Circadian rhythm pathways influence the expression patterns of as much as 31% of the The authors declare that they have no competing interest.JC, YJ, BR conceived and designed the algorithm. YJ designed MATLAB code for algorithm. BR performed pre-processing and post-processing of data. BR and YJ wrote the manuscript, which was edited by JC, BM, SO and WQ. BM and SO also provided biological knowledge and research of circadian and cold response genes. All authors read and approved the final manuscript.Figure S1: Time frames used to generate FFT results. Frame sizes and positions are shown in (A) and the contribution of each frame to the weighted average at each timepoint is shown in (B). Figure S2: Principal Component Analysis (PCA) Plots. Principal component analysis (PCA) plots for the original data (A) and the first components of the clock-frequency and treatment-frequency data (B) are shown. COS-upregulated genes are shown in black circles, COS-downregulated genes are shown in white diamonds and all other genes are shown as grey dots. Figure S3: The original, mean-shifted, PRIISM-reconstructed and Butterworth-filter reconstructed gene expression patterns ofAtGolS3. (A) The original (black) and mean-shifted (grey) expression values of AtGolS3. (B) Comparison between the treatment-frequency-reconstructed gene expression patterns for AtGolS3 using PRIISM (Black line) and using a fifth-order Butterworth low-pass filter (grey line). Figure S4: The frequency spectra of the original, the PRIISM-reconstructed and the Butterworth-filter reconstructed gene expression patterns ofAtGolS3. (A) The Frequency Spectrum of the original gene expression pattern of AtGolS3. (B) Comparison of the frequency spectra of AtGolS3 after processing using PRIISM (white circles) and the fifth-order Butterworth low-pass filter (grey diamonds). The original treatment-frequency spectrum of AtGolS3 is also shown (red bars). Figure S5: The Bode plot of a fifth-order Butterworth low-pass filter forAtGolS3.Click here for file"} +{"text": "We assessed the prognostic importance of right ventricular (RV) involvement in patients with acute inferior myocardial infarction (MI).RV infarction contributes markedly to hemodynamic instability, atrioventricular conduction block and in-hospital mortality in patients with inferior MI. Cardiac magnetic resonance imaging (MRI) is the superior imaging technique for assessing RV involvement because of its high spatial resolution.th, 75th percentiles) of 6 months. We assessed the association of RV function with length of cardiac care unit (CCU) treatment as an index of short-term prognosis by using multiple regression analysis, and used Kaplan-Meier analysis to demonstrate the association of RV dysfunction with occurrence of heart failure (HF) after discharge as an index of long-term prognosis.We analyzed 20 consecutive patients with first acute inferior MI due to proximal right coronary lesion. All patients were assessed with cardiac MRI after primary percutaneous coronary intervention and followed up for a median (25RV involvement was diagnosed with delayed enhancement MRI in 11 patients (55%). Patients with RV involvement had lower RV ejection fraction (EF) and longer duration of CCU treatment than those without RV involvement, although there were no significant differences regarding clinical, angiographic and the other MRI characteristics such as left ventricular parameters. By multiple regression analysis, RVEF was an independent predictor of length of CCU treatment . Kaplan-Meier analysis demonstrated that RVEF <30% was associated with increased occurrence of HF in chronic phase (p = 0.003).RVEF in patients with acute reperfused inferior MI is an important predictor of short-term prognosis and patients with lower RVEF had more occurrence of HF at long-term follow-up than those without lower RVEF. Evaluation of RV with cardiac MRI can improve risk stratification and patient management after acute inferior MI."} +{"text": "To compare parenting stress between mothers of children with spina bifida and mothers of able-bodied controls, and to explore factors other than the disease that moderate stress.81 mothers of children with spina bifida and 69 mothers of children with acute, non-disabling illnesses aged 1-18 years completed the Parenting Stress Index Short Form (PSI/SF) and General Health Questionnaire-12 (GHQ). Each child\u2019s adaptive skills was assessed using the Vineland Adaptive Behaviour Scales (VABS). Medical and sociodemographic data were collected from a combination of case notes\u2019 reviews and direct interviews. Multiple regression analysis was used to determine factors related to Parental Distress (PD), Parent-Child Dysfunctional Interaction (P-CDI) and Difficult Child (DC) sub domains of the PSI.Compared to controls, mothers of children with spina bifida had lower educational levels and were more likely to be the main caregiver and not working. They also had significantly higher mean scores for the GHQ, Total PSI/SF and the PD (Parent Domain), DC (Difficult Child) and P-CDI sub scales. Children with spina bifida had lower VABS scores, indicating poorer adaptive skills, than controls. Single parent status, having a child with spina bifida and higher Life Stress scores were associated with higher PD scores. Single parent status, higher Life stress and GHQ scores were associated with higher DC scores. The only factor associated with higher P-CDI scores was lower VABS scores.Factors such as life stress events, single parent status, maternal mental health status and the child\u2019s adaptive skills appear to moderate the impact of spina bifida on various aspects of parenting stress."} +{"text": "HIV-infected patients demonstrate premature and more severe vascular disease relative to controls. Therefore, development of a reproducible non-invasive vascular imaging biomarker in this population is important. The purpose of this study was to assess coronary artery wall thickness in young HIV-infected patients who acquired HIV in early life compared to healthy controls using a novel black-blood coronary vessel wall MR imaging technique.We prospectively studied 20 young HIV-infected adults and 12 HIV-uninfected control subjects. Participants were free of known active cardiovascular disease or symptoms at the time of the scan. MR imaging of the proximal right coronary artery (RCA) vessel wall was performed using phase-sensitive dual inversion-recovery (PS-DIR) black-blood vessel wall imaging. Group comparisons were performed to evaluate differences in proximal RCA wall thickness and potential associations between clinical variables and wall thickness were evaluated using linear regression analyses.HIV-infected subjects ranged in age from 15-29 years, with an average age of 21.1 years . HIV-uninfected subjects ranged in age from 23 to 47 years, with an average age of 29.3 years . The average RCA wall was significantly thicker in HIV-infected patients compared to controls , despite the fact that controls were significantly older (p=0.0001). In HIV-infected subjects, linear regression analysis did not show significant correlation between the RCA wall thickness and duration of disease, current or nadir CD4 counts, levels of total cholesterol, LDL cholesterol or triglycerides.We have demonstrated statistically significant increased proximal RCA wall thickness as a likely surrogate marker of generalized vascular disease in a group of young patients who acquired HIV in early life compared to HIV-uninfected subjects. Although we did not find a significant correlation between the vessel wall thickness and markers of infection such as CD4 counts, we believe studying a larger sample size is warranted to determine more definitively if such a correlation exist.This work has been funded by the National Institutes of Health"} +{"text": "Training in screening brief intervention, and referral to treatment (SBIRT) for substance abuse is being widely disseminated and implemented in a variety of health-care settings. Use of motivational interviewing (MI) techniques is thought to enhance BI effectiveness. The science of BI-MI training has not yet established optimal training doses for interventionist trainees to reach beginning competence. This study evaluated two training packages for teaching BI-MI, an eight-week comprehensive and a four-week accelerated training in primary care medical settings. Interventionist trainees were medical social workers (n = 22) in primary care clinics serving safety-net patients with drug abuse. Trained coders evaluated post-training BI and MI performance during standardized patient role-play interviews using a checklist of BI clinical tasks and the Motivational Interviewing Treatment Integrity (MITI) 3.0 coding system. Both training models yielded similar end-point MI skill levels. The proportion of learners who reached beginning proficiency on MI skills by the end of training was comparable to that reported in similar MI training studies (between 25% and 65%). Results suggest that some practitioners working in busy medical settings can learn BI and reach beginning proficiency in MI in as little as one month. Adherence to BI content and MITI outcomes with patients in primary care settings will also be presented."} +{"text": "Neuroimaging community usually employs spatial smoothing to denoise magnetic resonance imaging (MRI) data, e.g., Gaussian smoothing kernels. Such an isotropic diffusion (ISD) based smoothing is widely adopted for denoising purpose due to its easy implementation and efficient computation. Beyond these advantages, Gaussian smoothing kernels tend to blur the edges, curvature and texture of images. Researchers have proposed anisotropic diffusion (ASD) and non-local diffusion (NLD) kernels. We recently demonstrated the effect of these new filtering paradigms on preprocessing real degraded MRI images from three individual subjects. Here, to further systematically investigate the effects at a group level, we collected both structural and functional MRI data from 23 participants. We first evaluated the three smoothing strategies' impact on brain extraction, segmentation and registration. Finally, we investigated how they affect subsequent mapping of default network based on resting-state functional MRI (R-fMRI) data. Our findings suggest that NLD-based spatial smoothing maybe more effective and reliable at improving the quality of both MRI data preprocessing and default network mapping. We thus recommend NLD may become a promising method of smoothing structural MRI images of R-fMRI pipeline. Partial Differential Equation (PDE), a well-established mathematical theory, has given its advances on denoising images in terms of the strong theoretical framework with simple and efficient numerical strategies Currently, the ISD is the most popular method used to reduce noise in structural and functional images of both 3D brain volume Here, we collected MRI data from 23 normal healthy controls and performed such comparisons by using volume-based brain image analysis . Specifically, we first applied ISD, ASD and NLD to smooth individual T1 brain images to statistically evaluate their abilities to remove image noise and subsequent effects of structural brain processing. Three common steps of processing structural MRI data were chosen to demonstrate smoothing effects: brain extraction Twenty-three participants were scanned on a Phillips Achieva 1.5 Tesla scanner. For each participant, a high-resolution T1 anatomical image was obtained and 240 EPI R-fMRI images were collected. Among these subjects, nine subjects were scanned twice separated by one year, i.e., a one-year test-retest design. Of note, to keep the scanner's settings as consistent as possible between the test/retest scans, no any updates of hardware/software occurred to the scanner during the one-year duration. All participants are college students from Henan University of Traditional Chinese Medicine and had no history of psychiatric or neurological illness, as confirmed by clinical assessments. All subjects gave written, informed consent to participate in the study, which was approved by the Neuroimaging Acupuncture Research Center of Henan University of Traditional Chinese Medicine.The intensity of an MRI image can be defined in a bounded domain The ISD of image A gaussian smoothing is optimal for harmonic functions. However, it performs poorly on edges or texture where its Laplacian is large. To avoid this drawback , ASD smoothes the image http://www.fmrib.ox.ac.uk/fsl, version 4.1) consisting of various comprehensive tools for brain imaging data, 2) Analysis of Functional NeuroImaging mainly designed for fMRI analysis and 3) Voxel-based morphometry (VBM) extent of Statistical Parametric Mapping . Another reason of using FSL and AFNI is that they both are the packages employed in the R-fMRI pipeline of our interest Both ISD and ASD are local neighborhood filters, which mean they average the intensity of voxels within a small spatial neighborhood. With such a strategy, it is difficult to maintain image texture \u2013 not a local feature of images. NLD addresses this problem by generalizing the diffusion domain to whole image domain To evaluate the effect of three spatial smoothing approaches, we chose the three most frequently used preprocessing steps in both anatomical and functional MRI applications and quantify their performance on the denoised data: 1) brain extraction (BET) is widely employed as a preprocessing step in both computational anatomy and functional MRI analyses The brain extraction was done by using a command bet in FMRIB Software Library (FSL) To check the effects of these denoising methods on spatial normalization, for each smoothing approach, a fully automated robust and accurate tool for linear registration between individual T1 brains and the standard MNI152 brain was first computed in FMRIB's Linear Image Registration Tool (FLIRT). Based on this affine transformation, FMRIB's Non-linear Image Registration Tool (FNIRT) spatially normalized the T1 brain to match the standard brain by using a local spline basis deformation model FMRIB's Automated Segmentation Tool (FAST) was used to segment the T1 image into three tissues For each of the three structural processing , paired t-tests were performed to show if there is any statistical difference in above measures between each pair of smoothing approaches.http://www.nitrc.org/projects/fcon_1000 was selected as our R-fMRI pipeline of mapping resting state functional networks The 1000 Functional Connectomes Project scripts Functional preprocessing includes: 1) discarding the first 5 EPI volumes from each scan to allow for signal equilibration, 2) slice timing correction, 3) 3D motion correction, 4) co-registration between individual functional and anatomical brain images using a 6-degrees-of-freedom linear affine transformation, 5) spatial smoothing (6 mm FWHM Gaussian kernel), 6) 4D mean-based intensity normalization, 7) band-pass temporal filtering (0.01\u20130.1 Hz), 8) removal of linear and quadratic trends, 9) removal of nine nuisance covariates . The resultant 4D residual time series was used for subsequent mapping of participant-level default network. The final maps of individual default network were spatially normalized to the 3 mm MNI152 standard space.For each smoothing method, we first employed it to denoise all individual T1 images. The denoised T1 images were then fed into the R-fMRI pipeline of producing individual default network maps. The core seed of default network was adopted from Using one-year test-retest R-fMRI datasets from the 9 subjects, we assess if any of the three spatial smoothing methods can improve the test-retest reliability of default network mapping As we demonstrated in our previous work To demonstrate the impact of different smoothing methods on brain extraction of T1 images, we extracted the brain masks from each smoothed T1 image and calculated overlap ratios Brain registration via FNIRT resulted in different matching quality when the various methods of spatial smoothing were applied to denoise T1 brain data . ASD demAs indicated by the grey matter probability map in Consistent with many previous R-fMRI studies see . Figure Using ReML-based ICC, the test-retest reliability maps of default network connectivity maps generated by the R-fMRI pipeline with the three spatial smoothing were calculated. We statistically compared the differences in performance of three PDE-based spatial smoothing for MRI image processing and demonstrated the feasibility of the non-local mean diffusion technique in denoising T1 images and in improving accuracy and test-retest reliability of MRI image processing. The NLD approach tends to not only increase robustness of structural MRI processing but improve the quality and reliability of mapping default network. It is particularly valuable to adopt NLD in fMRI studies because these studies often use T1 data polluted by unknown scanning noise from a low-strength magnetic field . Indeed, as we present in our previous study Although NLD has been extensively studied in several 2D image processing fields, only a few recent studies have demonstrated the utility of NLD for effectively denoising MRI datasets. In A limitation of the current study is that we did not compare the performance of PDE-based filters by directly applying them to R-fMRI data. To our best knowledge, there is no study to examine the impacts of directly applying NLD to fMRI images. In contrast, there was a study employing ASD for detection of fMRI activation In summary, our study confirmed the utility of non-local diffusion equations in denoising degraded T1 MRI images. This approach demonstrates a promising potential to improve various fundamental MRI analytic processes including brain extraction, tissue segmentation, registration and subsequent functional MRI analyses. NLD method could serve as an initial preprocessing step in future MRI studies.Figure S1One-year Test-Retest Reliability Maps for Default Network Mapping with Raw Structural Smoothing. This figure depicts the voxel-wise one-year test-retest reliability of PCC-derived resting-state functional connectivity or default network. The axial views of the reliability maps are displayed in radiological convention. The ICC map is thresholded at ICC(TIF)Click here for additional data file.Figure S2One-year Test-Retest Reliability Maps for Default Network Mapping with ISD Structural Smoothing. This figure depicts the voxel-wise one-year test-retest reliability of PCC-derived resting-state functional connectivity or default network. The axial views of the reliability maps are displayed in radiological convention. The ICC map is thresholded at ICC(TIF)Click here for additional data file.Figure S3One-year Test-Retest Reliability Maps for Default Network Mapping with ASD Structural Smoothing. This figure depicts the voxel-wise one-year test-retest reliability of PCC-derived resting-state functional connectivity or default network. The axial views of the reliability maps are displayed in radiological convention. The ICC map is thresholded at ICC(TIF)Click here for additional data file.Figure S4One-year Test-Retest Reliability Maps for Default Network Mapping with NLD Structural Smoothing. This figure depicts the voxel-wise one-year test-retest reliability of PCC-derived resting-state functional connectivity or default network. The axial views of the reliability maps are displayed in radiological convention. The ICC map is thresholded at ICC(TIF)Click here for additional data file."} +{"text": "The present special issue was aimed at elucidating the role and the effects of glucagon-like peptide-1 (GLP-1) in type 2 diabetes. GLP-1 is a gastrointestinal hormone, mainly secreted after meals, capable of increasing glucose-stimulated insulin release and inhibits food intake. The physiological activity of this hormone has been demonstrated to be impaired in obese subjects and in patients with type 2 diabetes in comparison with healthy subjects.Available data suggest that GLP-1 plays a relevant role in the regulation of postprandial glucose metabolism in physiologic conditions. Several new drugs act through the GLP-1 signaling system to stimulate insulin release and regulate blood glucose levels in patients with diabetes. Therefore, a special issue exploring the physiological properties of GLP-1 and the possible applications in several clinical settings is particularly warranted. This special issue is composed of 5 articles: two mechanistic studies and three systematic reviews and meta-analyses, exploring GLP-1-induced signaling mechanisms and molecular identification and cloning of the GLP-1 receptor. The reviews and meta-analyses are focused on the promising beneficial extraglycaemic effects of the incretin-based therapy, including those on lipid profile and cardiovascular risk.Matteo MonamiMatteo MonamiGiovanni Di PasqualeGiovanni Di PasqualeAnna RowzeeAnna RowzeeCarlo Maria Rotella Carlo Maria Rotella Edoardo Mannucci Edoardo Mannucci"} +{"text": "We hypothesized that quantitative PET parameters may have predictive value beyond that of traditional clinical factors such as the International Prognostic Score (IPS) among Hodgkin's disease (HD) patients.Thirty HD patients treated at presentation or relapse had staging and interim-treatment PET-CT scans. The majority of patients (53%) had stage III-IV disease and 67% had IPS \u2265 2. Interim-treatment scans were performed at a median of 55 days from the staging PET-CT. Chemotherapy regimens used: Stanford V (67%), ABVD (17%), VAMP (10%), or BEACOPP (7%). Hypermetabolic tumor regions were segmented semiautomatically and the metabolic tumor volume (MTV), mean standardized uptake value (SUVmean), maximum SUV (SUVmax) and integrated SUV (iSUV) were recorded. We analyzed whether IPS, absolute value PET parameters or the calculated ratio of interim- to pre-treatment PET parameters were associated with progression free survival (PFS) or overall survival (OS).int/pre (p < 0.01), SUVmeanint/pre (p < 0.05), SUVmaxint/pre (p = 0.01), and iSUVint/pre (p < 0.01). Absolute value SUVmax from interim-treatment scans was associated with PFS (p = 0.01). Three calculated PET parameters were associated with PFS: MTVint/pre (p = 0.01), SUVmaxint/pre (p = 0.02) and iSUVint/pre (p = 0.01). IPS was associated with PFS (p < 0.05) and OS (p < 0.01).Median follow-up of the study group was 50 months. Six of the 30 patients progressed clinically. Absolute value PET parameters from pre-treatment scans were not significant. Absolute value SUVmax from interim-treatment scans was associated with OS as determined by univariate analysis (p < 0.01). All four calculated PET parameters were associated with OS: MTVCalculated PET metrics may provide predictive information beyond that of traditional clinical factors and may identify patients at high risk of treatment failure early for treatment intensification. The alymphoma or magnelymphoma -8. The h studies -12. Fuse studies .18F]FDG-PET in predicting clinical outcome for patients with Hodgkin's disease. Advani et al showed that a positive [18F]FDG-PET scan following completion of Stanford V chemotherapy was predictive of freedom from progression, even after controlling for bulky disease and International Prognostic Score (IPS) greater than 2 [18F]FDG-PET scan may be extended even further. Although the optimal timing for evaluating early response to treatment is yet to be defined, a recent joint Italian-Danish study has prospectively shown that [18F]FDG-PET scan following two cycles of AVBD chemotherapy is superior than IPS in predicting progression-free survival in patients with Hodgkin's disease FDG-PET scans were qualitative in these studies. Variability in interpretation of PET-CT scans, particularly in cases with faint residual uptake or \"intermediate-positive\" scans, limits the broad clinical utility of this tool. Whether quantitative PET parameters is a predictive factor for disease progression in Hodgkin's disease is not well established. Metabolic tumor volume (MTV) has been described in a previous study incorporating patients with Hodgkin's disease and non-Hodgkin's lymphoma to be an independent prognostic factor, but this study had a short follow-up period of 12.7 months and it did not examine the prognostic value of interim-treatment PET parameters [Evaluation criteria of [rameters . We hypo18F]FDG-PET scanning at Stanford Hospital and Clinics between January 2003 and June 2005 in order to maximize the length of clinical follow-up. During this study period, 3, 548 [18F]FDG-PET scans were performed. Of the patients scanned, we identified 57 adult and pediatric patients who were evaluated for Hodgkin's disease at presentation or relapse and had interim-treatment PET-CT scans as previously described . In briemean), maximum SUV (SUVmax) and integrated SUV (iSUV), defined as a product of MTV and SUVmean FDG-PET scan following two cycles of AVBD chemotherapy predicts progression-free survival in Hodgkin's disease patients. The interpretation of the PET-CT scans differs in our study in that we employ quantitative analysis rather than qualitative assessment. The establishment of quantitative methods of assessing PET-CT scans may aid in the interpretation of scans with minimal residual uptake or with \"intermediate-positive\" disease. It also has the potential for standardizing the interpretation of scans to reduce the variability in technique among clinical trials and across different institutions. Since a PET-CT is generally performed to assess the extent of disease before and during treatment for patients with Hodgkin's disease, quantitative analysis would be a practical and cost-effective strategy for incorporating these data into clinical practice.Our results although preliminary, are consistent with the joint Italian-Danish study showing that [The limitations of our study are the relatively small number of patients, relatively small number of clinical events (progression and/or death), and retrospective method. Due to the small number of patients, we were not able to select a more homogenous population of patients receiving identical chemotherapy regimen, e.g. our stage I-II patients. Due to the low numbers of events we were also unable to perform a multivariate analysis to exclude the influence of other clinical and treatment related prognostic factors as compared to our quantitative PET metrics. In spite of these limitations, we present statistically significant data correlating quantitative interim-treatment PET metrics with clinical progression.In conclusion, quantitative assessment of FDG-PET status after chemotherapy will likely be helpful for identifying patients at high risk of treatment failure at an early time point when treatment intensification could be considered. The preliminary findings of our study supports the quantitative interpretation of FDG-PET images as possibly an important tool guiding the design of prospective clinical trials of functional imaging for Hodgkin's disease.The authors declare that they have no competing interests.DT and LPR carried out the clinical review required in the study, analyzed the data and drafted the manuscript. ZS preformed the statistical analysis. RA, SH, RTH and AQ participated in the treatment of the patients included in the study. RA, RTH, AQ and EEG participated in the review of the drafted manuscript. BWL and PTT conceived of the study, participated in its design, performed the analysis and coordinated and helped to draft the manuscript. All authors read and approved the final manuscript."} +{"text": "A 56-year-old man presented with hypothermia and hypotension after being found by emergency medical services (EMS) on his basement floor. A 12-lead electrocardiogram (ECG) revealed normal sinus rhythm with a rate of 62 bpm, right bundle branch block, prolonged QT interval (QTc of 564 ms), wide QRS (110 ms), and a prominent J wave in the precordial leads . After tAmerican Journal of Physiology on experimental hypothermia (The J wave is also known as an Osborn wave, camel-hump sign, late delta wave, hathook junction, and hypothermic wave . The proothermia .An Osborn wave is characterized as an extra deflection of the terminal junction of the QRS complex and the start of the ST segment . Typical"} +{"text": "Brachypodium distachyon, Oryza sativa ssp. japonica, Sorghum bicolor, Zea mays) and four dicots reveals the structural organization of the core promoter in relation to the TATA-box as well as with respect to other CPEs. The distribution of known CPE motifs with respect to transcription start site (TSS) exhibited positional conservation within monocots and dicots with slight differences across all eight genomes. Further, a more refined subset of annotated genes based on orthologs of the model monocot (O. sativa ssp. japonica) and dicot genomes supported the positional distribution of these thirteen known CPEs. DNA free energy profiles provided evidence that the structural properties of promoter regions are distinctly different from that of the non-regulatory genome sequence. It also showed that monocot core promoters have lower DNA free energy than dicot core promoters. The comparison of monocot and dicot promoter sequences highlights both the similarities and differences in the core promoter architecture irrespective of the species-specific nucleotide bias. This study will be useful for future work related to genome annotation projects and can inspire research efforts aimed to better understand regulatory mechanisms of transcription.Transcription initiation, essential to gene expression regulation, involves recruitment of basal transcription factors to the core promoter elements (CPEs). The distribution of currently known CPEs across plant genomes is largely unknown. This is the first large scale genome-wide report on the computational prediction of CPEs across eight plant genomes to help better understand the transcription initiation complex assembly. The distribution of thirteen known CPEs across four monocots ( Despite numerous technological advances in biological and computational sciences in the post- genome era, our basic understanding of gene regulatory mechanisms remains primitive. Currently, the fundamental need to understand RNA polymerase II (polII) mediated transcription initiation is well recognized for developing system level understanding of the condition-specific gene regulatory networks (GRNs). It is now well known that the TATA-box motif, once thought to be necessary for formation of polII pre-initiation complex (PIC) assembly, only accounts for a small fraction of the expressed genome Saccharomyces cerevisiae, Drosophila melanogaster, and mammals, several other CPEs have been identified in TATA and TATA-less promoters that include the initiator (Inr) element located at or surrounding the TSS which is recognized by TAF1 and TAF2 subunits of the TFIID complex Promoter regions can be categorized into two classes: core and extended . The core promoter is the primary docking site of polII PIC and directs basal transcription D. melanogasterCaenorhabditis elegansRattus norvegicusMus musculusHomo sapiensVery little is known about the cis-regulatory elements of transcription control in plants. In the past decade, considerable work has focused on model animal species like in silico prediction is still in its early stage. Though the number of computational motif discovery methods has significantly increased in last two decades Due to the complexity, diversity and inherent degenerate nature of regulatory motifs within promoters, the prediction of cis-regulatory elements is quite challenging and We performed a genome-wide prediction of known CPEs in eight plant species spanning both monocots and dicots, by developing a systematic and unbiased high-throughput methodology using PWMs, DNA free energy profiles, and homology to significantly reduce the false positive rate of motif discovery. The CPE profiles were compared to see the similarities and differences in promoter sequence architecture within and across monocots and dicots.Core promoter regions are generally reported within a tight window of TSS\u00b150bases www.gramene.org]. These eight plant genomes included four monocots (Brachypodium distachyon (Bdi), Oryza sativa ssp. japonica (Osa), Sorghum bicolor (Sbi), Zea mays (Zma)) and four dicots , Populus trichocarpa (Ptr), Vitis vinifera (Vvi), Glycine max (Gma)). For each genome, only the transcripts annotated with a 5\u2032 untranslated region (5\u2032UTR) and high quality filtered gene-set (after discarding transposable elements) were used for CPEs predictions for four monocots and four dicots . To see cross-species conservation of CPEs based on orthologs, A.thaliana and O.sativa ssp japonica orthologous protein coding genes with sequence identity \u226550% with their respective dicots and monocots were selected for orthologous conservation study. 9225 and 7958 orthologous protein coding genes for Ath and Osa were selected for this study. The ortholog dataset was retrieved from Gramene biomart The core promoter sequences [TSS\u00b1500] of protein coding genes with known 5\u2032UTR information were extracted from the Gramene core databases (version 34b) [Drosophila melanogaster were extracted from Eukaryotic promoter database [http://epd.vital-it.ch/] The promoter sequences for DNA free energy profiles of the promoter regions and randomly generated background sequences as negative control related to eight plant genomes were constructed using PromPredict \u2013 an algorithm based on GC content of the genome as well as difference in the GC content of the promoter region and the genomic sequence flanking the promoter region Arabidopsis thaliana as a dicot model and Oryza sativa ssp. japonica as a monocot model were selected as mentioned before. It provided an additional approach to increase the confidence in putative CPEs predictions made based on the positional conservation.For positional conservation, we analyzed the promoters for which 5\u2032UTR information was available for all eight genomes. For orthologous conservation, Search Tool for Occurrences of Regulatory Motifs (STORM) was used to identify motifs based on predefined PWMs in silico according to the real nucleotide composition of the genomes in our data set. It established motif's positional signal detection base-line threshold. The range in which foreground CPE abundance was at least 1.5 standard deviations higher than the background CPE abundance was considered as a candidate binding site region. Further, overlaying of individual species frequency distribution profiles within monocots and dicots provided positional conservation of the binding site region across species. Overlaying of frequency distribution profiles based on A. thaliana orthologous gene promoters among dicots and O. sativa japonica orthologous gene promoters among monocots provided further confidence in cross species conservation of CPEs. Based on these approaches, the consensus range for each CPE was determined independently in the monocots and dicots.We generated and tested several background models specifically derived from corresponding real genomic sequences from non-regulatory regions as well as a pseudo random background model designed from a large set of sequences that had been generated artificially For each genome, a list of each core promoter element's putative distribution range was determined based on the qualitative and quantitative measures as mentioned earlier. Custom perl scripts were used to determine the specific core element present in each promoter sequence of the genome. The set of core elements found to be present in a particular promoter sequence defined that promoter's combinatorial module. Though, with this approach one combinatorial module per promoter was obtained, however often a combinatorial module was found to be present in more than one promoter. Therefore, only the set of unique combinatorial modules was analyzed. To further determine prevalent CPEs contributing to the majority of the combinatorial modules, this dataset was partitioned with respect to the presence and absence of the TATA-box.A. thaliana protein coding genes in TATA, TATA-less, and CPE-less categories were analyzed for gene ontology functional enrichment by using BiNGO Figure S1The distribution of the number of transcripts with respect to 5\u2032UTR length across dicots and monocots. The panel A shows the distribution of 5\u2032 UTR length in four dicots: Arabidopsis thaliana (Ath - solid navy blue), Glycine max (Gma-solid dark blue), Populus trichocarpa (Ptr \u2013solid blue sapphire), and Vitis vinifera (Vvi -solid blue green). The panel B shows the distribution of 5\u2032UTR length in four monocots: Brachypodium distachyon (Bdi-solid bronze yellow), Oryza sativa ssp. japonica (Osa-solid red), Sorghum bicolor (Sbi-solid bronze), and Zea mays (Zma -solid purple). X-axis shows bins of 5\u2032 UTR length, where each bin is 10 base-pair long. Y-axis shows the number of transcripts.(TIF)Click here for additional data file.Figure S2The GC content distribution across dicots and monocots. X-axis shows the percentage GC across eight genomes whereas Y \u2013axis shows the number of transcripts. GC percentage in monocots and dicots showed the demarcation of GC content distribution between dicots and monocots.(TIF)Click here for additional data file.Figure S3Arabidopsis thaliana).The distribution of all known core promoter elements in dicot model , Inr (dark-grey), GC-box (black), CCAAT-box (purple), DPE (dark-green), BREu (brown), BREd (sky-blue), DCE-S1 (yellowish-green), XCPE1 (blue), TATA-box (red), MED-1 (light-grey), and Y-patch (green).(TIF)Click here for additional data file.Figure S4Oryza sativa ssp. japonica).The distribution of all known core promoter elements in monocot model , Inr (dark-grey), GC-box (black), CCAAT-box (purple), DPE (dark-green), BREu (brown), BREd (sky-blue), DCE-S1 (yellowish-green), XCPE1 (blue), TATA-Box (red), MED-1 (light-grey), and Y-patch (green).(TIF)Click here for additional data file.Figure S5Drosophila melanogaster.The distribution of selected known core promoter elements in Genome-wide motif distribution profiles of core elements \u2013 TATA-box (solid red), Inr (solid blue), MTE (solid black), and DPE (solid green) in D. melanogaster genome showing positional conservation of these CPEs with respect to TSS. X-axis shows promoter region that is binned into 20 base-pair bins, where each bin is represented by the bin-center. Y-axis shows the frequency distribution of the elements along the promoter with respect to TSS.(TIF)Click here for additional data file.Table S1Genomic information of the eight plant species from Gramene.(XLSX)Click here for additional data file.Table S2Brief information on core promoter elements with sequence logo of the respective position weight matrix.(XLSX)Click here for additional data file.Table S3Position weight matrix specific score threshold cut off for each core promoter element for eight plant species.(XLSX)Click here for additional data file.Table S4Putative binding site distribution of the core promoter elements relative to transcription start sites based on positional and orthologous gene conservation across species.(XLSX)Click here for additional data file.Table S5Percentage distribution of the core promoter elements in eight plant genomes.(XLSX)Click here for additional data file.Table S6CPE combinatorial modules selected based on the positional distribution range across dicots.(XLSX)Click here for additional data file.Table S7CPE combinatorial modules selected based on the positional distribution range across monocots.(XLSX)Click here for additional data file.Table S8Prevalence of core promoter elements in combinatorial CPE modules in TATA(+) and TATA(\u2212) promoter genes.(XLSX)Click here for additional data file.Table S9Functional annotation based on gene ontology molecular function enrichment of TATA, TATAless and Coreless genes.(XLSX)Click here for additional data file.Table S10Functional annotation based on gene ontology biological process enrichment of TATA, TATAless and Coreless genes.(XLSX)Click here for additional data file."} +{"text": "An increasing body of behavioral and physiological evidence shows that cortical activity operates optimally within a limited range of dopamine (DA) transmission within a broader inverted-U shaped relationship . HoweverIn the current study, we incorporated DA's modulation of NMDA conductance at a network level and analyzed whether DA's modulation of NMDA currents could lead to an inverted-U shaped relationship with cortical activity. With this motivation, we simulated a neural network with 200 excitatory and 40 inhibitory quadratic integrate-and-fire neurons coupled with biologically realistic probabilities. In the simulated network, the effects of DA were implemented through varying the NMDA conductances in various combinations of synaptic types including excitatory-excitatory and excitatory-inhibitory. The network synchronization was analyzed through examining gamma band power in the local field potential. Parametrically varying the NMDA conductance revealed an inverted-U shaped relationship, with lower gamma band power at both low and high conductance levels and optimal synchronization occurring at intermediate conductance levels. Our findings reveal that DA's modulation of NMDA currents at the single cell level gives rise to a non-monotonic relationship between cortical gamma band synchrony and DA levels. These results together with those of ["} +{"text": "The t chromosomal translocation activates aberrant expression of the AML1-ETO (AE) fusion protein and is commonly associated with core binding factor acute myeloid leukaemia (CBF AML). Combining a conditional mouse model that closely resembles the slow evolution and the mosaic AE expression pattern of human t CBF AML with global transcriptome sequencing, we find that disease progression was characterized by two principal pathogenic mechanisms. Initially, AE expression modified the lineage potential of haematopoietic stem cells (HSCs), resulting in the selective expansion of the myeloid compartment at the expense of normal erythro- and lymphopoiesis. This lineage skewing was followed by a second substantial rewiring of transcriptional networks occurring in the trajectory to manifest leukaemia. We also find that both HSC and lineage-restricted granulocyte macrophage progenitors (GMPs) acquired leukaemic stem cell (LSC) potential being capable of initiating and maintaining the disease. Finally, our data demonstrate that long-term expression of AE induces an indolent myeloproliferative disease (MPD)-like myeloid leukaemia phenotype with complete penetrance and that acute inactivation of AE function is a potential novel therapeutic option. Acute myeloid leukaemia (AML) is a heterogeneous group of severe haematological diseases characterized by a block in myeloid differentiation and the unrestrained proliferation of immature myeloid cells and the ETO gene (RUNX1T1 or MTG8) generates the 752 amino acid long chimeric AML1-ETO (AE) protein translocation, a fusion between the DNA-binding In recent years leukaemic stem cells (LSCs) have attracted major attention as critical therapeutic targets as these cells have been proposed to drive leukaemia initiation, progression and maintenance , as illustrated by targeted therapeutics like Imatinib population of committed myeloid cells. Finally, we demonstrate that long-term expression of AE consistently induces a phenotype of indolent myeloproliferative disease (MDP)-like myeloid leukaemia with complete penetrance and report that inactivation of AE function is a potential novel therapeutic option.Using a novel experimental mouse model that recapitulates the slow disease evolution and mosaic expression of AE found in human AML, we report the first We initiated this study with the aim to analyse global signalling pathways and cellular mechanisms that operate during the progressive disease evolution downstream of the t translocation. In the past several mouse models for t-associated leukaemia have been developed [reviewed in haematopoietic progenitor cells and to different adult blood lineages , short-term repopulating haematopoietic stem cells , common myeloid progenitors , granulocyte macrophage progenitors , megakaryocyte erythrocyte progenitors and common lymphoid progenitors of R26/AE reconstituted recipients from compound ROSA26-iM2-tetO-GFP/TgPtet-AML1-ETO (R26/AE) mice into lethally irradiated recipients .A growing body of evidence suggests that the t translocation is only leukaemia-initiating but not sufficient for the induction of AML T lymphoid cells colony formation . Conversely, although control and GFP\u2212 CMP, GMP, MEP and GFP+ CMP were not significantly different, GFP+ GMP were augmented and GFP+ MEP decreased . These findings highlighted differences between GFP\u2212 and GFP+ GMP and MEP populations and thus support the interpretation that transgene activation promoted the expansion of GMP and reduced MEP in a cell-autonomous fashion. Importantly, the finding that LT- and ST-HSC as well as CLP and CMP did not significantly differ between controls, GFP\u2212 and GFP+ populations provides direct in vivo evidence that conditional transgene induction did not expand the number of HSC, CLP or CMP pools in our mice. To reveal potential differences in cells with activated transgene expression, we separately analysed GFPin vivo evidence that persistent AE expression promoted an invasive MPD-like myeloid leukaemia phenotype in mice translocation can persist for years before any signs of AML become apparent translocation suggests a direct role of AE for the pathogenesis of this disease. However, it is not known if continued AE expression is essential for maintaining leukaemia. We therefore asked what would be the consequence of an acute ablation of AE function during overt disease. To this end long-term induced leukaemic BM cells together with supportive BM were injected into lethally irradiated recipients that were continued on DOX. Of note, by choosing a fairly advanced AE induction time, we sought to mimic a progressed disease stage that might have a high probability to be refractory to therapy. Three month after transplantation all mice showed abnormal peripheral blood parameters and had circulating blasts. At this point, seven out of ten animals were switched to a DOX-free diet A. Four mes +DOX, B and a nes +DOX, C. Moreoves +DOX, D and we es +DOX, E. Direct\u2212K+S+CD150+ containing both malignant and normal HSC) and leukaemic GMP to propagate the disease. Following a previously established protocol . Also in line with the different composition of immature und more mature myeloblasts seen in the BM sections of low granulocytes in both L-HSC- and L-GMP-reconstituted mice and a significant drop of Gr1high mature granulocytes in L-HSC animals . Because in mice adoptively transferred GMP can produce myeloid progeny for only a limited period of about four weeks from non-AE-expressing controls (Ctrl-GMP), from mice that had been short-term DOX-induced during 10 days (ST-GMP) and from overtly leukaemic animals (L-GMP) were sorted and subjected to whole transcriptome sequencing (RNA-Seq). After alignment to the mouse reference genome and normalization, we identified a total number of 18097, 18435 and 15181 transcripts in Ctrl-, ST- and L-GMP . This information was used to evaluate differences between each GMP pool. As seen in R2\u2009=\u20090.1602) between Ctrl- and L-GMP, whereas Ctrl- and ST-GMP transcriptomes had a smaller correlation-based distance (R2\u2009=\u20090.3623) and ST- and L-GMP were most similar (R2\u2009=\u20090.8328). These results document an incremental transcriptional shift between Ctrl-, ST- and L-GMP and demonstrate that global transcriptome changes immediately following conditional AE expression were stronger than those occurring during the transition from ST- to L-GMP. To further define molecular differences in gene expression, we compared common and differentially expressed mRNAs. Comparison between Ctrl-, ST- and L-GMP mRNA pools documented that the majority of gene coding transcripts were commonly expressed in all three groups (13915) and identified 691 uniquely expressed transcripts for Ctrl-, 974 for ST- and 254 for L-GMP translocation can persist in a non-leukaemic mode for years before the transcriptional rewiring required for leukaemic transformation has occurred and malignant disease progression can start off.The above determination of global transcriptome changes provides the interesting opportunity to identify specific pathways that are needed for leukaemic transformation and disease progression. To gain more insight into these programs, transcripts only deregulated, extinguished or newly activated in L-GMP were subjected to Ingenuity Pathway Analysis (IPA). Validation of these gene sets unveiled striking changes in cancer-related networks. As shown in Tablep\u2009=\u20090.0215) in t AML patients CBF AML patients and healthy controls CBF AML. Analysis of this model revealed several key cellular and molecular mechanisms operating immediately downstream of AE and during leukaemic progression. In addition, we applied next generation sequencing to unveil the dynamics of global transcriptome changes occurring during the trajectory to overt disease. Our findings provide direct evidence that the succession of events that take place downstream of the t chromosomal translocation is essentially characterized by two basic mechanisms: lineage instruction of HSC followed by the substantial fine adjustment of transcriptional programs needed for the progression to leukaemia.in vivo evidence \u2013 both during pre-leukaemia and manifest disease \u2013 that aberrant AE activation specifically expanded the GMP population but that despite an activated DOX-switch in LT- and ST-HSC the pool of HSC did not increase. By gating on the GFP+ and GFP\u2212 cells, our results further suggest that the expansion of GMP and the reduction of other progenitor populations are substantially sustained by the transgene expressing population. Our results thus lead to the concept that the main function of aberrant AE expression is to modify the lineage potential of HSC resulting in the selective expansion of the myeloid compartment.Our experiments demonstrate that expression of AE changes the developmental output of HSC by promoting the selective expansion of myeloid cells at the expense of normal erythroid and lymphoid lineage maturation. These results further extend previous reports about AE-specific lineage skewing AML patients and healthy individuals. Examining sets of genes that were highly upregulated in murine cells, we found that many orthologous human genes were also significantly upregulated in t AML patients. These findings indicate that not only the phenotypic manifestation of the disease but also major alterations in gene expression were similar between human patients and our model. Using transcripts selectively upregulated in murine L-GMP, we identified 17 orthologous human genes that were predominantly expressed in t AML patients, poorly transcribed in healthy donors and absent from or only marginally transcribed in normal haematopoietic cells. The identification of candidates fulfilling these criteria suggests that at least some of these genes might represent future therapeutic targets and that interfering with their function should not produce unwanted haematotoxic effects.In summary, using a model that recapitulates the slow disease evolution and mosaic expression of AE in t CBF AML, we report several molecular and cellular principles governing the dynamic disease progression downstream of the initial activation of AE. The exhaustive analysis presented here thus represents a good starting point for developing and testing novel therapeutic strategies needed for a better and more effective treatment of t-associated leukaemia.2O or 600\u2009mg DOX/kg as food pellets. All experiments were approved by the Ethical Committee of the Landesuntersuchungsamt Rheinland-Pfalz under the reference number 23 177-07/G 09-1-047.ROSA26-iM2-GFP (R26) and the TgPtet-AML1-ETO (AE) mouse lines were on a C57BL/6 background and have been previously described and analysed with the FlowJo software (TreeStar). Cell sorting was performed on a FACSAria I cell sorter (BD). A detailed description of all flow cytometric materials and methods can be found online in the Supporting Information section.http://www.ebi.ac.uk/arrayexpress) under E-MTAB-1820 and under the ENA Accession Number ERP003759. A detailed description of the RNA-Seq materials and methods can be found online in the Supporting Information section.RNA-Seq data are available in the ArrayExpress database .For calculating A description of Materials and Methods for quantitative real-time PCR, BM transplantation, isolation and functional characterization of LSC, acute ablation of AE expression in leukaemic mice, colony-forming unit assay, routine haematologic assays and histopathology and the conversion and comparison of murine ST AE- and leukaemia-associated transcripts with human t CBF AML and non-leukaemic profiles is available in the online the supplemental material section.PROBLEM:Determinants governing initiation, progression and establishment of t-associated leukaemia have not been studied in a mouse model that recapitulates the slow disease evolution and mosaic AE expression found in patients. Moreover, the dynamics of progressive transcriptome alterations and the nature of LSC are unknown. Finally, proof-of-principle experiments testing the therapeutic benefit of AE inactivation are missing.RESULTS:Using a mouse model that closely recapitulates the slow pathogenesis of human CBF AML we report the evolution of transcriptome-wide alterations following AE activation. AE expression initially promoted the specific expansion of myeloid cells followed by secondary transcriptional changes associated with the upregulation of leukaemia-promoting and anti-apoptotic programs. We also find that both HSC- and GMP-like cells act as LSC. Finally, we demonstrate that long-term expression of AE induced leukaemia and that inactivation of AE function is a potential novel therapeutic option.IMPACT:Our results reveal several novel mechanisms operating downstream of the initial AE activation and proof that both cells with HSC and GMP markers can initiate and maintain leukaemia in mice. The finding that inactivation of AE function is a potential therapeutic option will warrant the future development of AE-specific therapeutic strategies.EB, LE, TK, CM, BK, JCC, AT and US conceived the idea; EB, AH, NC-W and JC wrote the paper; NC-W performed most of the experiments of the paper; NC-W, VE, LE, YA, RH and SO performed mouse experiments; RS, SW and D-EZ contributed genetically modified mice, JdG and NC-W performed the NGS experiments; ML, AH, AKD and JCC performed the bioinformatics analysis; AL, AK and JL performed the pathology; NC-W and SS performed the flow cytometric analysis."} +{"text": "In this commentary we discuss how an optimized functional imaging protocol could assist new clinical trials using fetal cell transplantation in Parkinson's disease.Clinical trials aiming to assess the safety and efficacy of fetal cell transplantation in Parkinson's disease rely on the hypothesis that the grafted tissue will survive and grow, restore striatal dopaminergic neurotransmission, improve the connectivity between striatum, thalamus and cortex and, thereby, produce long-lasting clinical improvement while avoiding the development of adverse effects. Although transplantation of human fetal ventral mesencephalic tissue has been reported as one of the most effective reparative therapies in Parkinson's disease patients to date, different studies have shown inconsistent results causing a paucity of new trials over the last decade. However, during this period, functional imaging alongside other scientific developments from clinical observations and animal work has significantly aided in understanding the mechanisms responsible for the success or failure of grafting human fetal tissue. Recent advances in functional imaging including both positron emission tomography and functional magnetic resonance imaging could be proven useful This notion could explain the differences in the outcomes between open-label trials reporting an average of 50 to 85% increase in 18F-DOPA uptake associated with good clinical improvement of PD motor symptoms and reductions in medication requirements [18F-DOPA uptake associated with poor clinical outcomes during the first periods post-transplantation [There are now up to 16 years of post-transplantation M tissue ,13-15. Airements -8, and tantation ,10.18F-DOPA PET can also help facilitate patient selection and screening as patients with baseline reductions in 18F-DOPA uptake extending to the ventral part of the striatum and patients with reductions in 18F-DOPA uptake consistent with atypical or secondary Parkinsonism should be excluded from these trials [post-hoc analysis, raises the possibility of a time window for optimal transplantation outcomes as preoperative preservation of DA innervation in ventral striatal areas seems to be predictive of a better outcome.e trials ,17. This18F-DOPA PET. However, in line with the inconsistent results observed in post-mortem studies with regard to DAT expression in the grafted neurons [76Br-FE-CBT PET failed to visualize DAT in grafted striata enhancing 18F-DOPA [123I-IPT [123I-FP-CIT [18F-DOPA.During past years, a small number of studies have been undertaken in order to demonstrate imaging of DA transporters (DAT) in the grafted striatum. Imaging of DAT with PET or single photon emission computed tomography (SPECT) could be used as an alternative technique to neurons , 76Br-FE18F-DOPA , whereas123I-IPT and 123II-FP-CIT SPECT sh11C-raclopride PET have shown several cases where graft-derived DA cells were able to restore the release of endogenous DA in the striatum of PD patients [215O we learned that despite an early stabilization of DA reinnervation in the striatum, graft function and integration continue and symptomatic relief may also require the functional reafferentation of striato-thalamo-cortical circuitries in the host brain [Up to 10 years post-transplantation follow-up data using patients ,17. The st brain .11C-PK11195 PET or any of the other recently developed translocator protein (TSPO) PET ligands.Immunosuppression could be another factor related to the outcomes of clinical trials, although the role of neuroinflammation in influencing the outcome of transplantation procedures in PD is not known. There is evidence showing that long-term immunosuppresion can be withdrawn without interfering with graft survival or the motor recovery induced by transplantation . Additio11C-DASB PET and a clinical trial with an agent dampening transmitter release from 5-HT neurons was used to show a causal relationship between mishandling of DA release from the graft-derived 5-HT hyperinnervation in the striatum of PD patients and the occurrence of GIDs [GIDs are a severe adverse effect of fetal cell transplantation in PD hindering the further development of cell transplantation trials ,15,22-25 of GIDs ,15. Furt of GIDs ,15,25. TRecent advances in MRI techniques allow us to examine the brain in a way that was not previously possible. The examination of functional connectivity between brain regions is now possible using resting-state functional MRI (fMRI). These resting state networks (RSNs) are believed to reflect functional communication between brain regions and could be very informative in providing insights of large-scale neuronal communication during restorative therapies such as fetal cell transplantation in PD -29. FMRIhttp://www.transeuro.org.uk. Functional imaging protocols for this or any other future trials employing fetal or stem cells will undoubtedly benefit from the lessons learned from over two decades of research.A new European Commission-funded multicenter trial under the name Transeuro was recently launched for a new round of fetal cell transplantation trials in vivo imaging results with PET and SPECT have been inconsistent. 11C-dihydrotetrabenazine (DTBZ) PET measuring the density of the vesicular monoamine transporter (VMAT2) could serve as an alternative, but to date there are no 11C-DTBZ PET data on the expression and survival of VMAT2 in VM tissue grafts and VMAT2 is also present in other monoaminergic systems. Therefore, 18F-DOPA PET remains today the standard for monitoring survival and growth of grafted DA cells. According to data from open-label and double blind trials it appears that a short-term increase in 18F-DOPA uptake of more than 50% from baseline is necessary to achieve clinically valuable antiparkinsonian effects. Measures of 18F-DOPA uptake at baseline can also provide valuable information to assist in the selection of patients for trials of cell-based DA therapies in PD by excluding those showing reduced uptake in the ventral striatum. 11C-raclopride PET together with a competitive displacement challenge could be used to visualize a graft's ability to release DA. 11C-DASB PET together with 18F-DOPA PET and markers of DAT availability can be used to calculate binding ratios reflecting proportions of 5-HT to DA neurons and SERT to DAT binding sites and, therefore, assist in the preparation of grafts during preoperational screening and, hence, prevent and monitor the development of GIDs postoperational. Inflammatory and immune responses around the graft alongside the effect of immunosuppressive therapy on transplantation outcomes could be assessed with 11C-PK11195 or one of the other recently developed TSPO PET ligands. Moreover, the new MRI techniques such as RSNs fMRI and DTI could assist in the assessment of functional and WM structural connectivity between the graft and the host brain while ME tasks could be employed replacing previous paradigms with H215O PET.An optimized functional imaging protocol Table using PEin vivo tool alongside clinical observations. It is worth noting, however, that previous knowledge has shown that in order to efficiently monitor cell replacement therapies in PD with functional imaging, long period follow-up assessments are needed and conclusions cannot be ultimately achieved with short follow-up periods.Although functional imaging cannot currently be used as a primary endpoint in clinical transplantation trials, if used appropriately, it can provide researchers with an additional valuable 11C-DTBZ: 11C-dihydrotetrabenazine; DA: dopamine; DAT: dopamine transporter; DTI: Diffusion Tensor Imaging; fMRI: functional magnetic resonance imaging; GIDs: graft-induced dyskinesias; ME: motor execution; PD: Parkinson's disease; PET: positron emission tomography; RSNs: resting state networks; SERT: serotonin transporter; SPECT: single photon emission computed tomography; TSPO: translocator protein; VM: ventral mesencephalic; VMAT2: vesicular monoamine transporter 2; WM: white matter.5-HT: serotonin; The author declares that they have no competing interests.MP is entirely responsible for the content of this article.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1741-7015/9/50/prepub"} +{"text": "The \u03b22-adrenergic receptor agonist, albuterol, has been reported beneficial in treating several forms of congenital myasthenia. Here, for the first time, we examined the potential benefit of albuterol in a mouse model of anti-Muscle Specific Kinase (MuSK) myasthenia gravis. Mice received 15 daily injections of IgG from anti-MuSK positive patients, which resulted in whole-body weakness. At neuromuscular junctions in the tibialis anterior and diaphragm muscles the autoantibodies caused loss of postsynaptic acetylcholine receptors, and reduced the amplitudes of the endplate potential and spontaneous miniature endplate potential in the diaphragm muscle. Treatment with albuterol (8 mg/kg/day) during the two-week anti-MuSK injection series reduced the degree of weakness and weight loss, compared to vehicle-treated mice. However, the compound muscle action potential recorded from the gastrocnemius muscle displayed a decremental response in anti-MuSK-injected mice whether treated with albuterol or vehicle. Ongoing albuterol treatment did not increase endplate potential amplitudes compared to vehicle-treated mice nor did it prevent the loss of acetylcholine receptors from motor endplates. On the other hand, albuterol treatment significantly reduced the degree of fragmentation of endplate acetylcholine receptor clusters and increased the extent to which the remaining receptor clusters were covered by synaptophysin-stained nerve terminals. The results provide the first evidence that short-term albuterol treatment can ameliorate weakness in a robust mouse model of anti-MuSK myasthenia gravis. The results also demonstrate that it is possible for albuterol treatment to reduce whole-body weakness without necessarily reversing myasthenic impairment to the structure and function of the neuromuscular junction. Most cases of autoimmune myasthenia gravis (MG) are caused by autoantibodies against the nicotinic acetylcholine receptor (AChR). Anti-AChR IgG reduces the efficacy of synaptic transmission at the neuromuscular junction (NMJ) by blocking AChR channels, accelerating AChR degradation and activating complement Drugs that activate the \u03b2-adrenoceptor offer therapeutic benefit in certain forms of congenital myasthenia syndrome that share some features with anti-MuSK MG. Ephedrine has been in clinical use for myasthenic disorders at least since the 1930 s Current treatment options for the anti-MuSK form of MG have significant drawbacks. Clinical series of anti-MuSK MG patients have confirmed the utility of antibody based therapies (plasmapheresis being more effective than IVIG) and immunosuppression with corticosteroids, antiproliferative agents and rituximab. However these treatments are associated with significant risks and many are expensive Autoantibodies specific for MuSK seem to cause MG by disrupting MuSK-dependent maintenance of the NMJ. Active immunization of animals with MuSK, or passive transfer of IgG from anti-MuSK-positive MG patients resulted in whole-body weakness that was associated with impaired neuromuscular transmission In common with the Dok-7 congenital myasthenia, anti-MuSK MG is thought to interfere with MuSK signaling in the postsynaptic membrane. Ephedrine is a restricted drug, being a precursor of amphetamine while albuterol, a selective \u03b22 adrenergic agonist, is widely used as a bronchodilator All mouse experiments described in this paper were conducted at the University of Sydney with the approval of The University of Sydney Animal Ethics Committee in accordance with the New South Wales Government Animal Research Act 1985, associated regulations (2005) and the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes, 7th edition . In relation to the collection of plasma, informed, written consent was obtained from patients in accordance with the Declaration of Helsinki . The project was approved by the Human Research Ethics Committee of the Sydney South West Area Health Service.Female C57BL/6J mice received 15 daily intraperitoneal (I.P.) injections of anti-MuSK-positive patient IgG (25 mg filter-sterilized in PBS) as previously described Mice were treated with albuterol infused steadily for 2-weeks via an Alzet minipump that was implanted beneath the skin of the mid back on day 0 of the IgG injections. Albuterol sulfate (Sigma) was dissolved in sterile water (vehicle). To implant the pump, mice were anaesthetized with 1\u20133% isoflurane/oxygen. Mice received buprenorphine for analgesia at the completion of surgery and 24 h later, as previously described Mice were inspected daily for general health and fatigue and were weighed and graded for muscle weakness before and after an exercise regime that involved the mouse walking backwards 12 times over a wire cage grid Repetitive stimulation of the sciatic nerve and compound muscle action potential (CMAP) recordings were performed on mice anaesthetized with isoflurane/oxygen as previously described 2, 2 mM CaCl2) as previously described Spontaneous miniature endplate potential (mEPP) and evoked endplate potential (EPP) recordings were made from phrenic nerve-hemidiaphragm preparations at physiological calcium levels (1 mM MgClhttp:rsb.info.nih.gov/ij) was used to measure the fluorescence intensities.To compare AChR staining intensities, transverse sections (12 \u00b5m) of the tibialis anterior and diaphragm muscles were fixed for 15 min in 2% paraformaldehyde/phosphate buffered saline (PBS) at room temperature. Sections were blocked for 1 h in 2% bovine serum albumin (BSA)/PBS and then incubated with Alexa488-\u03b1-bungarotoxin for 1 h at room temperature. Slides were washed three times with PBS between every step. For comparisons of staining intensities, all slides were stained in the same batch, and confocal optical sections of endplates were collected in the same imaging session using fixed gain and black level settings . ImageJ 1.31 v software . Sections were fixed as described above and nerve terminals were labeled using a cocktail of rabbit anti-neurofilament antibody and rabbit anti-synaptophysin antibody overnight at 4\u00b0C. After washing three times with PBS, sections were incubated with fluoresceine isothiocyanate (FITC)-conjugated donkey anti-rabbit IgG and Alexa555-\u03b1-bungarotoxin for 1 h at room temperature. Image stacks (for maximum-intensity Z-projection images) were collected enface to the endplate in the same imaging session. Metamorph software was used to measure the area and intensity of the postsynaptic AChR cluster and presynaptic nerve terminal staining. The co-localization plug-in of the Metamorph program was used to determine the area of overlap (pixel by pixel) Photomicrographs of endplates from anti-MuSK-injected mice often revealed dim staining. To improve visibility the brightness was increased in the final figures. Changes in brightness were applied in equal proportion to the control and experimental panels of the figure in question.The cross-sectional areas of muscle fibers were measured from transverse sections (12 \u00b5m) of the tibialis anterior and diaphragm muscles. Sections were fixed for 15 min in 4% paraformaldehyde/PBS and pre-incubated for 1 h in 10% BSA/PBS. Rabbit anti-laminin antibody followed by FITC-conjugated donkey anti-rabbit IgG were used to label the basement membrane. The laminin-stained basement membrane was used to frame the cross-sectional area of each muscle fiber, which was then measured using ImageJ software.Graphpad Prism was used for statistics. Comparison of two groups was by unpaired, two-tailed Student\u2019s t-test where n was the number of mice in the treatment group. The cross-sectional area of fibers in the tibialis anterior muscle did not follow a normal distribution. Therefore one-tailed Mann-Whitney tests (n\u200a=\u200anumber of mice per group) were used to test the hypotheses: 1/that anti-MuSK IgG injections would reduce fiber cross-sectional area, and 2/that albuterol treatment would increase cross-sectional area compared to vehicle treatment. One-way ANOVA with Bonferroni\u2019s multiple comparison post-test was used for comparison of multiple treatment groups. P<0.05 was considered statistically significant.Mice received daily injections of anti-MuSK-positive patient IgG (25 mg/day I.P.). This led to weight loss and the onset of whole-body weakness between days 12 and 15 of the injection series, consistent with previous findings To assess the degree of AChR loss from motor endplates we compared the intensity of endplate AChR staining in mice that received injections of anti-MuSK IgG, with and without albuterol treatment. In transverse sections of healthy naive mice, endplates appeared as intensely fluorescent crescents of AChR staining . After 1Enface images of the motor endplates from healthy diaphragm muscles typically reveal pretzel-shaped AChR plaques, each covered by a branched nerve terminal . Key chaIn healthy muscles of anaesthetized mice repetitive stimulation of the nerve produces compound muscle action potentials (CMAPs) of consistently high amplitude. After 15 daily injections of anti-MuSK IgG, CMAP recordings from the gastrocnemius muscle revealed a decrementing response during repetitive stimulation of the sciatic nerve (3 stimuli per sec), suggesting impaired neuromuscular transmission .The phrenic nerve-hemidiaphragm muscle preparation from the same mice was then used to record endplate potentials. As expected, the amplitudes of nerve-evoked EPPs and spontaneous mEPPs were rather low in anti-MuSK injected mice (\u223c0.3 mV), compared to values previously recorded in healthy mice \u223c0.6 mV; . For mic2 . Injection of anti-MuSK IgG significantly reduced the mean cross-sectional area of diaphragm muscle fibers to 620\u00b143 \u00b5m2 (n\u200a=\u200a4 mice) when compared with healthy naive mice was not significantly different to naive mice . In the tibialis anterior muscle of albuterol-treated mice an increase in median fiber cross sectional area (1859 \u00b5m2) compared to vehicle treated-mice did not reach significance throughout the two-week anti-MuSK IgG injection series showed areas and intensities of endplate AChR staining as well as EPP amplitudes that were similar to vehicle-treated myasthenic mice. The primary pathogenic mechanism of anti-MuSK IgG in rodent models seems to be a decline in endplate AChR density/number Long-term treatment with albuterol has been successful in improving strength for patients with forms of congenital myasthenia that have common features with anti-MuSK MG. These include patients with mutations in the ColQ and Dok-7 genes ex vivo EPP recordings from the diaphragm revealed no functional improvement in those anti-MuSK-injected mice that were treated with albuterol. In the diaphragm muscle of mice that became weak after injections of anti-MuSK IgG there were reductions in the number of endplates per photomicrograph, suggesting the complete loss of many NMJs Loss of postsynaptic AChR appears to be a primary cause of synaptic failure in animal models of anti-MuSK MG Several caveats need to be considered in assessing the results. Our passive IgG transfer protocol involved injecting mice with large amounts of patient IgG (25 mg/day for 15 days). This model yields a robust and reproducible onset of synaptic failure and myasthenic weakness within two weeks By what other mechanism/s might albuterol have reduced weakness in our anti-MuSK injected mice? Firstly, it remains possible that albuterol positively influenced aspects of synaptic function other than those that we have measured. It is also conceivable that albuterol might enhance neural drive to myasthenic muscles. However, in healthy rodents albuterol was found to reduce spontanous locomotor activity, rather than increasing mobility While albuterol did not improve the function of the NMJs in our recordings, it did produce significant improvements to two out of eight measures of NMJ integrity in anti-MuSK-injected mice. Anti-MuSK injections cause the break-up of the large postsynaptic AChR plaque into multiple small (fragmented) AChR clusters. Albuterol reduced the extent of AChR cluster fragmentation. Secondly, in albuterol-treated mice a higher proportion of the surviving endplate AChRs retained coverage by nerve terminal staining, suggesting more-complete innervation. These two positive effects of albuterol lay the groundwork for further studies in other animal models of myasthenias where the onslaught might be more gradual and the subtle beneficial effects of albuterol may improve the function of the myasthenic NMJ."} +{"text": "B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt's lymphoma (BLUI) is a recently added entity to the World Health Organization (WHO) classification to address a grey zone between large B-cell lymphoma (DLBCL) and Burkitt's lymphoma (BL). These are rare aggressive lymphomas, which were previously also known as Burkitt's-like lymphoma (BLL). BL and BLUI/BLL of the colon mostly involve the ileocecal region. In the rectum, BL and BLUI/BLL almost always affect patients with the acquired immune deficiency syndrome (AIDS). We report the first case of rectal BLUI/BLL in an immunocompetent patient who is also negative for MYC abnormalities and the EBV early RNA (EBER) in situ hybridization. The border between classical Burkitt's lymphoma (BL) and classical diffuse large B-cell lymphoma (DLBCL) has been a field of diagnostic uncertainty . The upd\u2009mm in greatest dimension was noted in the distal rectum about 2\u2009cm from the anal verge. Histopathological examination revealed a monomorphic mucosal lymphoid proliferation with numerous mitotic figures , primary gastric lymphomas are most common, whereas large intestinal lymphomas are rare . With reBL is a rare aggressive form of NHL composed of monomorphic medium-sized B cells with basophilic cytoplasm and numerous mitotic figures. It is also characterized by c-MYC translocation and CD10+/bcl-2\u2013/bcl-6+ with a very high Ki-67 proliferation index [Morphology, immunophenotypic features, and gene expression studies suggest that BL and DLBCL are extreme ends of a spectrum of diseases , 8. A grWe present a case of MYC negative rectal BLUI/BLL in an immunocompetent patient. A literature search through PubMed did not reveal any case of rectal BLUI/BLL in an immunocompetent patient. However, it revealed one case of rectal BL in an immunocompetent patient that was positive for EBER in situ hybridization (unlike the present case) . Adult MClinicians and pathologists must be aware of this rare aggressive entity while dealing with B-cell lymphomas of the rectum in immunocompetent patients."} +{"text": "Cardiac magnetic resonance (CMR) imaging enables characterization of myocardial scar and the \u2018grey zone', an admixture of scar and healthy myocardium, which is an independent predictor of ventricular arrhythmia. We explored the relationship between the grey zone and ventricular tachycardia circuits (VT) in ischaemic cardiomyopathy.Two patients with previous myocardial infarct underwent high-resolution late gadolinium enhanced CMR scar imaging (1.2x1.2x2.6mm) and a VT-stimulation study. The LV scar core was segmented using full-width-half-maximum method; and the grey zone was segmented with a cut-off signal intensity below that of the scar core and above 2 standard-deviation of the remote healthy myocardium. A multi-electrode array (MEA) was positioned in the LV cavity for simultaneous electroanatomical mapping during the study. The MEA shell was registered with the CMR-derived LV shell using anatomical landmark registration Figure for compSustained monomorphic VT (SMVT) was induced in both patients. Scar core and grey zone regions correlated well with the low voltage area (\u2264 30% maximum voltage) seen on the MEA Figure . The exiWe have demonstrated that the critical substrate of re-entrant SMVT lies within the grey zone in the two ischemic cardiomyopathy study cases. CMR characterization of scar heterogeneity may provide useful information predicting the location of the critical substrate in re-entrant VT observed in patients with a previous history of myocardial infarction.N/A"} +{"text": "The history of specific therapy for hereditary tumors dates back to mid 1980s and involves a number of reports demonstrating regression of familial colon polyps upon administration of sulindac. Virtually no clinical studies on other hereditary cancer types were available until the year 2009, when Byrski et al. presented the data on unprecedented sensitivity of BRCA1-associated breast malignancies to cisplatin. This breakthrough has revived interest to the treatment of cancer in germ-line mutation carriers. Recent trials and clinical observations have confirmed the efficacy of platinating agents and PARP inhibitors in BRCA1/2-driven breast, ovarian and pancreatic carcinomas. Pegylated liposomal doxorubicin may be considered as a promising treatment option for BRCA1/2-related ovarian cancer after the failure of platinum-containing therapy. Several novel drugs have been recently introduced in the management of rare familial tumor syndromes. Vandetanib, a low-molecular weight RET kinase inhibitor, demonstrated substantial efficacy in the treatment of hereditary and sporadic medullary thyroid cancer. Vismodegib, an inhibitor of SMO oncoprotein, caused regression of basal-cell carcinomas in patients with Gorlin syndrome. Down-regulation of mTOR kinase by everolimus has been successfully used for the therapy of subependymal giant-cell astrocytomas in patients with tuberous sclerosis. The achievements in the prevention, diagnostics and treatment of hereditary cancers may serve as an excellent example of triumph of translational medicine. Virtually all major hereditary tumor types differ from their sporadic counterparts with respect to the underlying biological mechanisms, and thus may be considered as a somewhat distinct disease entity. First reports on specific therapy of familial tumors date back to mid 1980s . Here weThere are over 10 genes causing hereditary forms of breast cancer (BC), however only BRCA1- and BRCA2-related disease has been studied with sufficient level of comprehension. It is commonly stated that BRCA-driven malignancies are triggered by somatic inactivation of the remaining (wild-type) BRCA allele, thus providing an unique opportunity for a tumor-specific therapy. Indeed, while normal tissues of BRCA mutation carriers retain a non-altered copy of the gene, the transformed cells are characterized by complete loss of BRCA function. Absence of the BRCA1 or BRCA2 compromises DNA repair and increases sensitivity of the cell to particular DNA damaging agents .Clinical studies on breast cancer demonstrated an unique sensitivity of BRCA1-accociated tumors to cisplatin . The avaTaxanes exert antitumor action via BRCA1-mediated apoptosis, therefore BRCA1-deficiency may mediate resistance to docetaxel or paclitaxel. Two systematic studies on BC provided strong support to this hypothesis. Kriege et al. investigA number of issues may be considered while designing the BC studies for the near future. The list of known BC genes is rapidly expanding, with the CHEK2 being apparently the most frequent cause of hereditary BC after BRCA1 and BRCA2. Drug response of CHEK2-related BCs has not been evaluated yet, neither in laboratory experiments nor in the patients -16. It iApproximately 15% of ovarian cancers (OCs) arise due to inherited BRCA1 or BRCA2 mutation. In addition, a significant portion of serous OCs demonstrate somatic inactivation of BRCA1/2 genes and therefore have similar biological properties . BRCA dend- and 3rd-line PLD in proven BRCA1/2-carriers versus presumably non-hereditary OC patients; the objective response rates were 68% versus 49%, and the median time to treatment failure was 15.8\u00a0months versus 8.1\u00a0months. Adams et al. , while the Food and Drug Administration states in the drug label that there is no evidence of a relationship between RET mutations and efficacy of this compound [http://www.accessdata.fda.gov/drugsatfda_docs/label/2011/022405s001lbl.pdf].Hereditary forms of medullary thyroid cancer (MTC) develop due to inherited mutation in the RET oncogene and demonstrate pronounced sensitivity to the RET tyrosine kinase inhibitor, vandetanib . VandetaBasal-cell nevus (Gorlin) syndrome is a rare hereditary disorder which is caused by mutation in the PTCH1 gene. PTCH1 inactivation abolishes its negative regulation of the SMO oncogene and thus initiates the growth of multiple basal-cell carcinomas. Clinical administration of a specific SMO inhibitor, vismodegib, prevented the appearance of new malignancies and resulted in the regression of existing neoplasms. None of the lesions progressed during the treatment, however the systemic tumor disease quickly relapsed after discontinuation of the therapy .Tuberous sclerosis is caused by germ-line mutations in TSC1 or TSC2 suppressor genes. Disruption of TSC1 or TSC2 leads to uncontrolled activation of mTOR kinase, and, consequently, to neoplastic growth. Tumors arising in patients with tuberous sclerosis are usually benign, however some of the neoplasms, especially if located in the brain, may cause severe disability and death. Recent development of specific mTOR inhibitors provided novel opportunities for the management of tuberous sclerosis. In particular, promising results have been achieved with everolimus: administration of this drug to the patients with serial subependymal giant-cell astrocytomas led to the marked tumor reduction in 21 (75%) of 28 enrolled patients .Recent studies have convincingly demonstrated that hereditary and sporadic tumors may indeed require distinct treatment approaches. Ongoing revolution in technologies of DNA analysis, particularly the invention of next-generation sequencing, allows to expect that dozens of new familial cancer genes will be identified in the near future. Furthermore, dramatic increase of velocity and cost-efficiency of germ-line mutation testing provides the hope that virtually every cancer patient will soon be undergoing genetic examination right at the time of tumor diagnosis . AdvanceAT: Anthracycline-taxane combinations; BC: Breast cancer; CRC: Colorectal cancer; OC: Ovarian cancer; pCR: Pathological complete response; MMR: DNA mismatch repair; MSI: Microsatellite instability; MTC: Medullary thyroid cancer; PC: Pancreatic cancer; PLD: Pegylated liposomal doxorubicinThe authors declare that they have no competing interests.ENI and TB, drafted the manuscript. Both authors read and approved the final manuscript."} +{"text": "Accumulating data indicate that inappropriate activation of type I interferon (IFN) plays a key role in the pathogenesis of systemic lupus erythematosus (SLE). Given that IFN can influence B-cell lymphopoiesis in murine bone marrow (BM), we explored the hypothesis that IFN activation in SLE BM has direct effects on B-cell development. Additionally, the impact of B cells on pDC production of IFN was examined.Peripheral blood mononuclear cells (PBMC) and bone marrow mononuclear cells (BMMC) were isolated from 28 patients fulfilling ACR criteria for SLE and from 20 healthy controls. RNA isolates were analyzed for the expression of three to five IFN-regulated genes by quantitative PCR and IFN-regulated chemokines CXCL10 (IP-10), CCL2 (MCP-1), and CCL19 (MIP-3\u03b2) defined in serum and BM supernatant. B-cell subsets were delineated in single-cell suspensions of PBMC and BMMC by multi-parameter flow cytometry. BM and PB pDCs were stimulated with TLR9 (CpG ODN 2006 or 2216) or TLR7 (R848) agonists and intracellular IFN and TNF measured by flow cytometry.+, IgD- switch memory B cells. SLE patients with a BM IFN signature were enriched for a high number of autoantibody specificities (P = 0.003 compared with IFN low), and the degree of IFN activation in the BM correlated with peripheral lymphopenia (P = 0.019) and disease activity (P = 0.05). In order to understand the etiology of IFN activation in SLE BM, we examined the production of IFN by pDCs. CpG induced IFN production in pDCs in a dose-dependent fashion. Notably, a higher proportion of BM pDCs produced IFN compared with paired PB. Moreover, pDCs produced 59% more IFN in the presence of B cells.The majority of SLE patients had an IFN signature in the BM (57%), which was even more pronounced than the paired PB. Notably, the early B-cell compartment in SLE BM with an IFN signature was associated with a reduction in the fraction of pro/pre B cells, suggesting an inhibition in early B-cell development. However, at the transitional B-cell stage this inhibition was reversed with enhanced selection of B cells into the transitional compartment. The composition of the mature B-cell compartment in IFN-activated SLE BM was notable for an expansion of CD27This is the first demonstration of an IFN signature in SLE BM. These results suggest that the BM is an important but previously unrecognized target organ in SLE with critical implications for B-cell ontogeny and selection. We postulate that in the setting of IFN activation the stringency of negative selection of autoreactive B cells in the BM may be reduced. Circulating immune complexes and apoptotic fragments in SLE BM may serve as ligands for Toll-like receptors on pDCs contributing to aberrant IFN production and, in turn, B cells may be critical regulators of pDC function."} +{"text": "A recent large-scale clinical trial has indicated that an initial invasive strategy does not improve cardiac outcomes beyond optimized medical therapy in patients with stable coronary artery disease (CAD). Therefore, novel methods to stratify at-risk patients may refine therapeutic decisions and improve outcomes. We sought to test the hypothesis that stress cardiac magnetic resonance (CMR) imaging effectively prognosticates and reclassifies patient risk in a consecutive clinical cohort of patients with known or suspected CAD across a spectrum of guideline-determined risk categories.In a prospective observational study of 815 consecutive patients clinically referred for stress CMR between 2001-2011, we studied the association of inducible ischemia on a composite of cardiac mortality and acute non-fatal myocardial infarction (MACE). We constructed Cox regression models to measure the independent and incremental association of inducible ischemia with our composite outcome beyond traditional markers of risk (including prior CAD). In addition, we quantified net reclassification improvement across guideline-based 3-year risk categories of MACE: low (<3%), moderate (3-9%), and high (>9%) by inducible ischemia by CMR, incremental to clinical risk models.Inducible ischemia was the strongest predictor of MACE in the overall cohort and in patients with prior CAD . Absence of inducible ischemia was associated with low annual rates of MACE and cardiac death . Addition of inducible ischemia to the best clinical risk model (age and prior CAD adjusted) improved discrimination of MACE . Inducible ischemia reclassified 91.5% of patients at moderate pre-test risk , with corresponding changes in annual event rates . Categorical net reclassification index was 0.229 (95% 0.063-0.391). For patients with prior CAD, inducible ischemia reclassified 44% of patients at moderate pre-test risk and 37% at high pre-test risk to lower post-test risk, with a low annual rate of MACE (1.2%/year in both groups).The presence and extent of inducible ischemia by stress CMR effectively reclassifies patient risk beyond standard clinical risk factors, specifically in patients at moderate-to-high pre-test risk and in patients with prior CAD.Dr. Shah is supported by an American Heart Association Post-Doctoral Fellowship Award (11POST000002) and a training grant from the Heart Failure National Institutes of Health Clinical Research Network (U01-HL084877). Dr. Heydari is supported by a Clinical Fellowship Award from the Alberta Heritage Foundation for Medical Research. Dr. Murthy is supported by National Institutes of Health training grant T32-HL094301. Dr. Kwong is supported by a National Institutes of Health grant R01-HL091157 and a research grant from Astellas Pharmaceuticals."} +{"text": "Smed-APC-1(RNAi) or Smed-ptc(RNAi) lose anterior fate but form previously described ectopic anterior brain structures. Later these animals form peri-pharyngeal brain structures, which in Smed-ptc(RNAi) grow out of the body establishing a new A/P axis. Combining double amputation and hydroxyurea treatment with RNAi experiments indicates that early ectopic brain structures are formed by uncommitted stem cells that have progressed through S-phase of the cell cycle at the time of amputation. Our results elaborate on the current simplistic model of both AP axis and brain regeneration. We find evidence of a gradient of hedgehog signalling that promotes posterior fate and temporarily inhibits anterior regeneration. Our data supports a model for anterior brain regeneration with distinct early and later phases of regeneration. Together these insights start to delineate the interplay between discrete existing, new, and then later homeostatic signals in AP axis regeneration.The current model of planarian anterior regeneration evokes the establishment of low levels of Wnt signalling at anterior wounds, promoting anterior polarity and subsequent elaboration of anterior fate through the action of the TALE class homeodomain PREP. The classical observation that decapitations positioned anteriorly will regenerate heads more rapidly than posteriorly positioned decapitations was among the first to lead to the proposal of gradients along an anteroposterior (AP) axis in a developmental context. An explicit understanding of this phenomenon is not included in the current model of anterior regeneration. This raises the question what the underlying molecular and cellular basis of this temporal gradient is, whether it can be explained by current models and whether understanding the gradient will shed light on regenerative events. Differences in anterior regeneration rate are established very early after amputation and this gradient is dependent on the activity of Hedgehog (Hh) signalling. Animals induced to produce two tails by either The process of regeneration is widely observed across metazoan phyla; with most clades having members that possess some ability to replace lost or damaged tissues as adults. In recent years the study of regenerative mechanisms has become increasingly tractable in a number of experimental systems that all hold promise for informing how we might one day regenerate lost or damaged human tissues S. mediterranea, loss of Wnt activity leads to ectopic regeneration of anterior structures at all wounds and a gradual homeostatic anteriorisation of the whole axis if animals are left unwounded We now know that correct A/P axis specification is dependent on correct Wnt and Hedgehog (Hh) signalling to establish regenerative polarity Many planarian species can regenerate a head from a decapitation made anywhere along the A/P axis, however the rate of regeneration decreases more posteriorly S. mediterranea has a clear gradient of anterior regenerative rate along the A/P axis Here, we show that the widely used laboratory model planarian S. mediterranea. We created eight positionally matched transverse sections staining at the two mitotic maxima med-GluR , n\u200a=\u200a18 and Smed-\u03b2catenin-1(RNAi) (see Smed-\u03b2catenin-1(RNAi) animals regenerated posterior facing heads Smed-hedgehog(RNAi) phenotype in pre- and post-pharyngeal fragments Smed-hedgehog in more anterior fragments .We performed both Smed-\u03b2catenin-1(RNAi) had no effect on the anterior regeneration gradient (Smed-hedgehog(RNAi) completely eliminated any difference between more anterior and more posterior cut sites. Post-pharyngeal anterior regeneration rates increased to match those of pre-pharyngeal pieces animals maintained a temporal difference in the extent of Smed-sFRP-1 expression, with pre-pharyngeal fragments showing more extensive Smed-sFRP-1 staining around the anterior blastema than post-pharyngeal fragments at 24 hR (To test this further we used the ragments . We interagments as repreragments . Smed-\u03b2cSmed-hedgehog(RNAi) resulted in loss of the difference in Smed-sFRP-1 expression, with equivalent early expression observed between pre- and post-pharyngeal fragments (Smed-hedgehog(RNAi) animals regenerate their photoreceptors at the same rate.Smed-ptc(RNAi) and Smed-APC-1(RNAi) as controls as knockdown of these genes leads to ectopic Wnt and Hh signalling, ectopic posterior fate and loss of Smed-sFRP-1 expression also results in a higher incidence of the tailless phenotype in more anterior fragments also supports the existence of lower pre-existing levels of hedgehog signalling in anterior regions. Alternatively it remains possible that Smed-hedgehog(RNAi) may have pleiotropic functions effecting early Smed-sFRP-1 expression and the later formation of photoreceptors and neither effect is reflective of anterior regeneration events in between.Taken together these data suggest that the anterior regenerative rate is controlled by a pre-existing hedgehog signalling gradient. This difference is not due to differences in stem cell proliferation . While pSmed-GluR and Smed-GpasSmed-GluR or Smed-Gpas at 48 and 72 hours of regeneration in both Smed-hedgehog(RNAi) and Smed-\u03b2catenin-1(RNAi) compared to control animals (Smed-hedgehog(RNAi) and Smed-\u03b2catenin-1(RNAi) at 48 hours and Smed-ptc(RNAi) animals always regenerated Smed-GluR and Smed-Gpas positive early brains at anterior wounds and Smed-ptc(RNAi) animals still regenerate early brains at anterior wounds. An array of phenotypes for Smed-APC-1(RNAi), ranging from hypermorphic cyclopic animals, reminiscent of weaker classes of Smed-prep(RNAi) phenotypes to animals with two tails, has previously been reported. We found that injection doses of 1 \u00b5g/\u00b5l of Smed-APC-1 dsRNA led to the formation of animals with two tails, ectopic posterior structures (Smed-sFRP-1 expression at anterior blastemas (Smed-fz-4 (Smed-GluR and Smed-Gpas positive brain structures in the post-blastema (dsRed(RNAi) animals which also leads to the formation of two tails, ectopic posterior structures animals, early brains appeared to be clearly positioned in the anterior blastema whereas in Smed-APC-1(RNAi) animals brain structures differentiated in the post-blastema (Smed-ptc(RNAi) animals have significantly more anteriorly positioned brain structures than Smed-APC-1(RNAi) animals, in a similar average position to controls. Performing double Smed-APC-1(RNAi);Smed-ptc(RNAi) phenocopied the Smed-APC-1(RNAi) phenotype by limiting ectopic brain structures to the post-blastema (see In tema see .Smed-prep(RNAi) phenotype. Previous work has shown that correct anterior and brain regeneration requires Smed-Prep activity in regions of low Wnt activity Smed-prep might be required for early polarity independent brain formation. While Smed-prep(RNAi), as previously described, led to the complete loss or severe reduction of brain structures at 12 days of regeneration (dR), early brain structures were detected at 72hR (Smed-ptc(RNAi) animals. Later, by 120hR, these early brain structures either disappeared (Smed-prep(RNAi) phenotype later in regeneration. This suggests that early polarity independent brain regeneration is not a peculiarity caused by ectopic high levels Wnt or Hh signalling, but also occurs in the absence of the instructive Smed-prep signal. We also note that early Smed-prep(RNAi) brain structures were always smaller than those observed in either Smed-ptc(RNAi) or Smed-APC-1(RNAi) worms.Our data are in agreement with a previous study that also observed polarity independent brain regeneration and reveal that brains form independently of regenerative polarity and ultimate regenerative fate Smed-prep activity. Instead, we find that that early brain regeneration occurs at anterior facing wounds that will ultimately have posterior fate. This early ectopic brain regeneration also displays differential rates along the A/P axis.Together our data show that while Hh signalling does affect differences in the rate of anterior regeneration along the A/P axis an early phase of brain regeneration proceeds regardless of ultimate regenerative polarity controlled by Wnt and Hh or elaboration permitted by dsRed(RNAi) animals regenerated normally with anterior bilobed cephalic ganglia together with two photoreceptors and a central pharynx (Smed-APC-1(RNAi) trunk regenerates (Smed-APC-1(RNAi) animals we observed the regeneration of a second pharynx in opposite orientation to the original pharynx with paired brain structures around this new pharynx. We found that 76% of these animals displayed peri-pharyngeal brain structures around both the new and the old pharynx (Smed-APC(RNAi) and Smed-axins(RNAi)We wished to observe what happened to early ectopic brain structures later during regeneration in animals that regenerated two tails. Control pharynx . However pharynx . These fSmed-ptc(RNAi) animals regenerated trunk and tail pieces with centrally positioned outgrowths containing well developed brain structures and eventually photoreceptors (Smed-ptc(RNAi) phenotype was dose dependent with increased concentrations of dsRNA injection leading to an increased frequency of new A/P axis formation (eceptors and invoormation . It is pSmed-APC-1(RNAi);Smed-ptc(RNAi) phenotype, the later phenotype of these animals phenocopy Smed-APC-1(RNAi) animals (Smed-ptc or Smed-hedgehog have homeostatic phenotypes (i.e. generated without amputation) we suggest that the effect of Hedgehog signalling may be specific to regeneration and act through modulation of a Wnt signalling gradient Like the early animals , suggestptc(RNAi). In addition our data provide evidence that ventral nerve cord (VNC) regions around the pharynges may have the most anterior positional identity in animals with two tails induced by ectopic Wnt signalling as pASCs differentiate into brain tissue in these regions.Together these data suggest that planarians are able to homeostatically regulate A/P axis identity as long as Wnt signalling components are left intact, as is the case for animals that have two tails due to We next wished to know the source of the cells forming early brain structures. Our data thus far implicate a Wnt and Hh independent mechanism in existing tissue in directing the differentiation of pASCs to form early brain structures at the anterior wound site, although the ultimate position of these structures is Wnt activity dependent .Smed-GluR or Smed-Gpas expression, in both Smed-APC-1(RNAi) and Smed-ptc(RNAi) animals (Smed-APC-1(RNAi) and Smed-ptc(RNAi), 7/7 for controls). Thus, at this time the double cut anterior blastema has the properties of a posterior blastema, with respect to early brain regeneration. This suggests the signals in existing tissue directing early brain regeneration may have been reprogrammed by 16hR. Control, dsRed(RNAi) animals form normal brains after double cuts, showing this is not an effect of the procedure and Smed-ptc(RNAi) double cut animals and found that they developed later peri-pharyngeal brain structures and full anterior outgrowths with brains respectively, whilst control dsRed(RNAi) animals regenerated as normal (We continued to observe Smed-APC-1(RNAi) and Smed-ptc(RNAi) backgrounds prompted us to consider the cellular source of early brain structures. As early ectopic brain structures form all along the A/P axis we hypothesised that brain structures were likely to be formed from uncommitted pASCs or progeny in response to decapitation. These cells would be capable of reading their position as being at the most anterior point in remaining tissue and be initially non-responsive to ectopic Wnt and Hh signals with respect to differentiation decisions (but not migration to he blastema in the case of Smed-APC(RNAi) animals). Given that 16 hours is after the first proliferative peak and this peak consists of many cells in S-phase, G2 and M at the time of wounding (The observation that double cuts stop the formation of early brains in wounding we hypotSmed-APC-1(RNAi) and Smed-ptc(RNAi) HU treated animals were all still able to regenerate brain structures (To investigate this hypothesis further we used hydroxyurea (HU) to block the transition of pASCs through the cell cycle at S-phase. We confirmed the efficacy of this treatment by monitoring mitotic activity and analructures , althougSmed-\u03b2catenin-1(RNAi) animals that form anterior structures at all amputation sites. We reasoned that if signals instructing early brain structures are specifically directed at anterior stem cells progressed through S-phase, then ectopic anterior structures caused by Smed-\u03b2catenin-1(RNAi) would not have a contribution from this cell population at posterior wounds present at the time of amputation. This predicts that Smed-\u03b2catenin-1(RNAi) HU treated animals will form early anterior brain structures but no brain structures in the posterior. We observed that while Smed-\u03b2catenin-1(RNAi) animals produced brains in both blastemas, HU treated Smed-\u03b2catenin-1(RNAi) animals only produced brains in anterior blastemas results in no difference in anterior regenerative rates or Smed-sFRP-1 expression between anteriorly and posteriorly positioned amputations. However, abrogation of Smed-hedgehog(RNAi) signalling removes differences in regenerative rates and early differences in Smed-sFRP-1 expression. Together our data suggest that differences in anterior regeneration rate are established very early after amputation and are dependent on a gradient of hedgehog signalling. The finding that we also observe a difference in the Smed-hedgehog(RNAi) \u201ctailless\u201d phenotype between anterior and posterior pieces also supports the existence of a pre-existing gradient. AP axis . We obseSmed-APC-1(RNAi) and Smed-ptc(RNAi) animals. Although, we note that Yawaza et al Dj-ndk expression in the early anterior blastemas of Dj-ptc(RNAi) worms and do suggest that Dj-ptc(RNAi) and ectopic Hh signalling leads to a transition from anterior to posterior fate.Our observation that early brain structures regenerate at all anterior amputations, including those that will regenerate to form tail structures, reveals an early phase of brain regeneration that is Wnt and Hh independent. This has also been recently described by a study investigating the role of Smed-Axin molecules Smed-APC-1(RNAi);Smed-ptc(RNAi) with and without HU treatment we show that ectopic brain ganglia and anterior fate at posterior blastemas do not involve this early phase of regeneration. These data also suggest that the early phase of brain regeneration we have uncovered maybe be redundant for the ultimate restoration of anterior structures, and that low Wnt signalling activity alone is sufficient to instruct correct anterior regeneration, agreeing with the proposal that anterior fate may be the default state of blastemas. Redundancy of regenerative mechanisms in planarians has not been described by direct experimental means before. One intriguing possibility is that the early brain regeneration phase uncovered here may represent part of the mechanism for beginning the regeneration of anterior structures during post-pharyngeal fission. Before the fission process this would be a region of relatively high Wnt signal and thus refractory to the de novo regeneration of anterior structures. This remains to be tested by looking at early brain regeneration during the process of fission with molecular markers in asexual animals.By combining HU treatment with Smed-APC-1(RNAi) and Smed-ptc(RNAi) indicates a difference in the timing of fate specification in the blastema (Smed-APC-1(RNAi) animals brain structures are limited to the post blastema (Smed-ptc(RNAi) animals (Smed-hh(RNAi) or Smed-ptc(RNAi) without inducing regeneration by amputation and two previous studies did not report homeostatic effects on the A/P axis The observations that early brain structures differentiate in different relative positions in blastema A\u2013D. In blastema , while t animals . This suSmed-APC-1(RNAi) and Smed-ptc(RNAi) animals homeostatically regenerate brain tissue around new pharynges (Smed-ptc(RNAi) animals anterior regeneration takes place without further wounding from central body regions and the new pharynx re-orientates animals. The implications of these observations are twofold. Firstly, it suggests that in the absence of anterior fate the new and old pharynx represent the most anterior tissues and may instruct pASC to brain neuron differentiation. Evidence in support of this possibility includes the observation that Smed-prep, required for anterior regeneration, and Smed-sFRP-1 a marker of anterior fate, without as yet an ascribed function, are also expressed around and in the pharyngeal region Smed-APC-1(RNAi) (Smed-ptc(RNAi) animals a gradient of Wnt activity appears to be restored (Smed-APC-1(RNAi);Smed-ptc(RNAi) animals phenocopy Smed-APC-1(RNAi) animals and form ectopic peri-pharyngeal brain structures but not anterior outgrowths and a new A/P axis (Smed-ptc(RNAi) and Smed-APC-1(RNAi) animals is mediated at the level of Smed-prep activity in the region around the pharynx, but this remains to be formally tested (Both two tailed harynges E-J. In ates see . Interes-1(RNAi) prevent -1(RNAi) . Howeverrestored , with hirestored . In agreA/P axis . We wouly tested J\u2013L.ndk leads to expansion of brain tissues without affecting other A/P fates ndk is somehow responsible and has led to the Brain Activator hypothesis of brain regeneration ndk or FGF-receptors in early brain regeneration directly. However, we do observe that in Smed-prep(RNAi) animals early brain structures are smaller than in Smed-ptc(RNAi), Smed-APC-1(RNAi) or HU treated animals. Given that one role of Smed-Prep is to allow pASC progeny to form brain tissue in the suppressive presence of ndk Smed-prep(RNAi) animals as indirect evidence that ndk is active at this early stage of brain structure differentiation, and is suppressing brain fates. However, whether ndk and FGF signalling will also be implicated in controlling anterior regeneration rates remains to be tested. Another possible clue as to the Wnt independent mechanisms controlling anterior regenerative rate and early brain regeneration comes from work on gap junction function et al, demonstrated that either intact VNC connections to the brain or active gap junction signalling are required to limit anterior regeneration to the anterior rather than all amputation sites. In this scenario it is tempting to speculate that the requirement for intact VNC to brain connections or functioning gap junctions reflects the need for an active form of the mechanism mediated by ndk to inhibit anterior fates. These ideas await direct testing with combinatorial RNAi and gap junction blockers Future work will be focused on identifying the molecular components that control the early Wnt/Hh independent gradient of anterior regeneration rates and early phase of brain regeneration we describe here. Clues to what these might be exist in the data presented here and in the findings of previous studies. It has been previously shown that loss of In summary we reveal an early phase of brain regeneration that relies on stem cells through S-phase and suggests for the first time that pASCs may respond to regenerative signals differentially according to their position in the cell cycle. This early phase may be functionally redundant with respect to regenerative outcomes as it is not required for posterior brain structures induced by abrogation of Wnt signalling. We show that the roles of Hh and Wnt signalling are not equivalent during regeneration or homeostasis of posterior fates and that planarians can remodel their A/P axis to produce anterior tissues from central body regions given an intact Wnt signalling gradient. Overall we have revealed previously unappreciated but important layers of complexity in the A/P and brain regeneration processes.Schmidtea mediterranea were fed organic veal liver and starved for at least one week prior to experiments or amputation. The animals were not fed for the duration of the experiments.Asexual All animals used in experiments to investigate the anterior regeneration rate were 1.5 cm in length . AnimalsFor RNAi experiments all animals were 1.3 cm (to the nearest 500 \u00b5m) in length to control for the any effect of size on overall regeneration rates. In these experiments pre- and post-pharyngeal fragments were kept within the same size limits (\u223c1.4 mm) as experiments investigating anterior regeneration rate in wild type animals.Smed-APC-1, Smed-ptc, Smed-\u03b2catenin-1 and Smed-prep sequences have previously been submitted to GenBank with accession numbers EU130785, GQ337475, EU082826 and GU290186 respectively. Double stranded RNA (dsRNA) was produced as previously described for Smed-APC-1, Smed-ptc, Smed-\u03b2catenin-1, Smed-prep and a control fragment of dsRed, which has no homology to the planarian genome dsRed(RNAi) controls over the course of up to several weeks. Animals were observed and bright field images were taken on a Zeiss Discovery V8 from Carl Zeiss using Axio Cam MRC from Carl Zeiss. All scoring of photoreceptor regeneration rates was performed blind and bright field images taken to allow later independent blind scoring by a second individual. No differences in scoring for individual images were detected.The in situ hybridisation was carried out on regenerating pieces and were fixed and stained using methods previously described Smed-sFRPSmed-GluR, Smed-GpasDugesia japonica, which specifically labels the brain lateral branches and the pharyngeal cuff H.10.2fSmed-porcupine1Whole mount For immune-staining animals were killed, fixed and processed as previously described 2 was determined using Adobe Photoshop CS4. The average number of proliferative cells per mm2 was calculated from pooled samples at each regeneration and homeostasis time point.To assess proliferation, animals were stained with anti-phospho-Serine10 histone H3 as described above. For each regenerating piece or homeostatic worm the number of mitotic cells and the area in mmHydroxyurea (Sigma) was used as previously described Planarian cell dissociation was performed following a protocol based on that previously used Figure S1Schematic of RNAi experiments. For all experiments animals were injected on each of three consecutive days, followed by a 4 days break, and then three further days of injection. On each day 3 injections of 32 nl were applied. Animals were amputated as described in the text 10 days after initial injection and observed(PDF)Click here for additional data file.Figure S2Controls for Smed-sFRP-1 expression. Control experiments showing that (A) Smed-APC-1(RNAi) and (B) Smed-ptc(RNAi) animals maintain Smed-sFRP-1 expression in the anterior of head fragments even though expression is absent from anterior amputation sites (on sites .(PDF)Click here for additional data file.Figure S3Proliferation in regenerating pre- and post- pharyngeal fragments. In order to test if differences in the timing of anterior regeneration along the A/P axis were due to proliferation we counted mitotic cells in these fragments in control (dsRed injected) and experimental animals. Only Smed-ptc(RNAi) animals showed significant effects (previously reported in (PDF)Click here for additional data file.Figure S4Ultimate Regeneration of two tails in Smed-APC-1(RNAi) and Smed-ptc(RNAi) animals. In situ analysis with Smed-porcupine-1 in (A) control and experimental animals to show that both (B) Smed-APC-1(RNAi) and (C) Smed-ptc(RNAi) animals regenerate two tails with two characteristic major posterior branches as previously reported (PDF)Click here for additional data file.Figure S5Expression of the posterior marker Smed-Fz-4 in Smed-APC-1(RNAi) and (B) Smed-ptc(RNAi) animals. The expression of the posterior marker Smed-Fz-4 is localized to the posterior of control injected animals. Expression in Smed-APC-1(RNAi) and Smed-ptc(RNAi) animals is expanded as posterior fate expands in these animals. Scale bar represent 250 \u00b5m.(PDF)Click here for additional data file.Figure S6Formation of peri-pharyngeal brain structure in Smed-APC-1(RNAi) animals. (A) All regenerating truck fragments form Smed-GluR (shown) or Smed-Gpas positive peri-pharyngeal brain structures (see ures see . (B) In (PDF)Click here for additional data file.Figure S7Formation of a new anterior and A/P axis in Smed-ptc(RNAi) worms. (A\u2013D) All dsRed(RNAi) control worms and Smed-ptc(RNAi) head fragments regenerate normally while Smed-ptc(RNAi) trunk and tail fragments initially regenerate tails. By 14dR Smed-ptc(RNAi) animals begun to develop distinct centrally positioned outgrowths, These outgrowths progress and eventually form a new head with photoreceptors and a brain ( a brain .(PDF)Click here for additional data file.Figure S8Schematic explaining double cut experiments. Trunk pieces were amputated as depicted and both early blastemas re-amputated after regeneration had been allowed to proceed for a set time. These animals were then stained with Smed-Gpas, and Smed-GluR to assay early brain formation events.(PDF)Click here for additional data file.Figure S9Hydroxyurea treatment leads to depletion of cycling cells in G2 and M phase. (A\u2013K) Control animals maintain cells in G2 and M phase and pASCs continue to cycle over the first 72hR. (L\u2013V) Treatment with HU before amputation leads to a significant depletion of cells progressing through S-phase (blue box in plot M) and results in eventual depletion of G2 and M cells, as these compartments fail to be renewed.(PDF)Click here for additional data file.Figure S10Control in situ hybridization for HU treated Smed-APC-1(RNAi) and Smed-ptc(RNAi) worms. Control in situ hybridization images of Smed-GluR expression in head fragments of e(A) Smed-APC-1(RNAi) and (B) Smed-ptc(RNAi) worms.(PDF)Click here for additional data file.Figure S11Effect of colchicine treatment on brain regeneration. Colchicine blocks cells transiting M phase and also blocks early brain regeneration (B) that proceeds normally in control worms (A). We cannot rule out that the effect of colchicine on brain regeneration is through blocking the differentiation of post-mitotic pASC progeny. Scale bars 100 \u00b5m.(PDF)Click here for additional data file."} +{"text": "Eczema is a chronic relapsing atopic dermatitis (AD) associated with pruritus, sleep disturbance and poor quality of life of the patient. Treatment of eczema includes use of emollient, topical and systemic antimicrobial agents, corticosteroid or immunomodulating agents. Many patients also seek alternative treatments such as dietary avoidance, supplementation or both. This article reviews the basic pathophysiology of eczema and clinical trials involving Chinese medicine in the treatment of eczema. Research reports on Chinese herbal medicine for eczema were retrieved from PubMed and the Cochrane Database for Systematic Reviews for this review. Only a few RCTs demonstrated the efficacy (or lack of efficacy) of Chinese medicinal herbs in treating atopic eczema. Further larger scale trials are warranted. Aboutvailable . As thervailable . Howevervailable . A limitvailable -14.Pathogenesis of AD involves complex interactions between susceptible genes (filaggrin genes), immunological factors , skin barrier defects, infections, neuroendocrine factors (brain derived neurotrophic factor) and environmental factors ,2,15,16.Changes in the epidermis are attributed to the xerotic skin in AD patient. Essential fatty acids (EFAs) are important components of the epidermis. Loss of EFAs results in increased transepidermal water loss and subsequent xerosis (dryness). Defects in the epidermal barrier also lead to increased susceptibility to allergens such as house dust mites, grass or pollen. When such allergens are in contact with susceptible skin, they stimulate Th2 lymphocytes to produce cytokines such as IL-4, IL-5 and IL-13 which in turn promote an increase in IgE synthesis ,18. AD pStaphylococcus aureus colonization, stress, anxiety, systemic illness and xerosis, exacerbate or trigger AD [AD patients also often have defective cell-mediated immunity, which is attributed to increased susceptibility to many bacterial, viral and fungal infections of the skin . Certainigger AD .Cortex Moutan Radix (Danpi), Radix Paeoniae Alba (Bai Shao), Potentilla Chinensis Ser (Weilingcai) and Radix Glycyrrhizae (Gan Cao) are common treatments for allergy [Flos Lonicerae (Jingyinhua) and Herba Menthae (Bohe) clear 'damp-heat' from the exterior, Cortex Moutan (Danpi) clears 'heat' from blood while Rhizoma Atractylodis (Cangzhu) and Cortex Phellodendri (Huangbai) clear the 'damp-heat' from the interior. Pharmacological studies indicate that these herbs have anti-allergic, anti-inflammatory and sedative action for itchiness [According to Chinese medicine theory , Qi can allergy . Flos Lotchiness ,23,24.This article aims to review randomized trials, case series and bench studies in Chinese medicine for eczema.For this review, as of December 2010, we retrieved 47 articles from PubMed using the keywords \"'Chinese herbal medicine' and ('atopic dermatitis' or 'eczema')\". We also searched the Cochrane Database for Systematic Reviews. Using PubMed Clinical Queries, we retrieved 9, 2 and 9 references under Clinical Study Categories, Systematic Reviews and Medical Genetics respectively. All RCTs and relevant case series and bench studies were included. Review articles that did not provide any information on eczema and Chinese medicine were excluded.There have been only a few randomized trials in this region on Chinese medicine treatment for AD Table . Cochranet al. carried out a randomized placebo-controlled double-blind trial of a specific prescription formulated for widespread non-exudative atopic eczema [In the early 1990s, a decoction was efficacious for the treatment of AD in both children ,26 and ac eczema . Forty-sThe opportunity to continue treatment was offered to the parents of 37 children who had completed a double-blind placebo-controlled trial of the same formulation of Chinese medicinal herbs for atopic eczema . The parP = 0.005 and P = 0.002 for erythema and surface damage respectively). At the end of the 12-month period, no patient in group 1 discontinued treatment although eight patients were on an alternate-day regimen by six months and remained on this regimen until the end of the 12-month period, and seven were able to control their eczema with treatment throughout the period. The remaining two patients continued on daily treatments. Toxicology screening revealed no abnormalities in either blood counts or biochemical parameters in all patients under continued treatment. Improvement in disease was not associated with any significant change in the levels of serum IgE or peripheral blood lymphocyte subsets.The adult patients with severe atopic eczema who had completed a similar double-blind placebo-controlled crossover trial were offered continued treatment for one year . Out of Despite the efficacy reported in the UK trials, a subsequent randomized placebo-controlled, cross-over trial (RCT) of the same decoction in Hong Kong failed to demonstrate beneficial effects on Chinese patients with recalcitrant AD in Hong Kong . Forty ret al. evaluated the clinical and biochemical effects of a Chinese medicine capsule (PentaHerbs capsule) in children with AD [P = 0.069). No clinical or biochemical evidence of any adverse drug reaction was found during the study period. The PentaHerbs capsules were well tolerated by the children and apparent (reduction of disease severity) were noted clinically. The authors concluded that a larger, randomized placebo-controlled study is required to confirm the efficacy of this formulation for AD.In a pilot study, Hon with AD . After aFlos lonicerae (Jinyinhua), 1 gram of Herba menthae (Bohe), 2 grams of Cortex moutan (Danpi), 2 grams of Rhizoma atractylodis (Cangzhu) and 2 grams of Cortex phellodendri (Huangbai). The dosage calculation was based on the standard Chinese medicine prescription for children [The PentaHerbs capsules were manufactured, packaged and labeled by the Chinese Medicine Industry Development Centre, the Hong Kong Institute of Vocation Education . The composition of each herb in the formulation was standardized. The formula comprised 2 grams of bal tea) and is ebal tea) under thbal tea) .n = 42; P = 0.003) and from 56.9 to 46.9 in the placebo group . However, there was no significant difference in the scores at the corresponding time points between the two groups. The CDLQI of PentaHerbs-treated group was more significantly improved than that of the placebo group at the end of the 3-month treatment and 4 weeks after stopping therapy (P = 0.008 and 0.059 respectively). The total amount of topical corticosteroid used was also significantly reduced by one-third in the PentaHerbs group (P = 0.024). The formulation was palatable and well tolerated. No serious adverse effects were observed between the groups. The investigators concluded that the PentaHerbs formulation is efficacious in improving quality of life and reducing topical corticosteroid use in children with moderate-to-severe AD.In a subsequent double-blinded randomized placebo-controlled trial, the researchers assessed the efficacy and tolerability of the decoction in children with AD . Followiet al. evaluated the effects and safety of Shuangfujin (SFJ) on acute eczema [Bai e eczema . One hunHochu-ekki-to, a Kampo formula , is effective for patients with Kikyo constitution. Previous case reports suggested that this herbal drug was effective for a subgroup of AD patients. Kobayashi et al. evaluated the efficacy and safety of Hochu-ekki-to in the long-term management of Kikyo patients with AD [Kikyo patients with AD were enrolled. Kikyo condition was evaluated by a questionnaire scoring system. All patients continued their ordinary treatments before and after their protocol entry. Hochu-ekki-to or placebo was orally administered twice daily for 24 weeks. The skin severity scores, total equivalent amount (TEA) of topical agents used for AD treatment, prominent efficacy (cases with skin severity score = 0 at the end of the study) rate and aggravated rate were monitored and evaluated. Seventy-seven out of 91 enrolled patients completed the 24-week treatment course . The TEA of topical agents in the Hochu-ekki-to group and 5% (2 of 40) in the placebo group (P = 0.06). The aggravated rate was significantly lower in the Hochu-ekki-to group than in the placebo group . Only mild adverse events such as nausea and diarrhea were noted in both groups without statistical difference. This placebo-controlled study demonstrated that Hochu-ekki-to was a useful adjunct to conventional treatments for AD patients with Kikyo constitution. Use of Hochu-ekki-to significantly reduced the dose of topical steroids and/or tacrolimus used for AD treatment without aggravating AD. with AD . In a muet al. reported that fifty-six cases of 'stubborn' eczema treated by oral administration and topical application of herbal medicine; [In the last decades, a number of case series reported the efficacy of herbal medicine on childhood AD. Luo edicine; .et al. assessed the effectiveness of the combination of Chinese herbal medicine and acupuncture for the treatment of atopic dermatitis [Salameh rmatitis . Twenty rmatitis mild-to-et al. performed a single-center open label trial to assess the efficacy and tolerability of a Chinese medicine syrup in younger children with AD [Hon with AD . Childre with AD were rec with AD and all with AD . At base with AD ,30. Enro with AD -39 at ev with AD formed tP < 0.001) whereas the placebo extract had no significant effect on CD23 expression. This inhibition was dose-dependent, and PentaHerbs was effective at a concentration of 250 \u03bcg/ml (P = 0.001). If PentaHerbs or placebo was added after IL-4, the action of PentaHerbs was still observed at 12 hours. This inhibition was not due to cell death, as peripheral blood mononuclear cells (PBMCs) cultured with PentaHerbs or placebo at a concentration used in these experiments had a similar viability to control cultures. Down-regulation of the low affinity receptors for IgE on antigen-presenting cells in patients with eczema may contribute to the benefit observed following treatment with PentaHerbs [To delineate the actions of PentaHerbs on AD, the authors analyzed the effects of an extract of these herbs on interleukin 4 (IL-4)-induced CD23 expression on peripheral blood monocytes collected from non-atopic subjects. They found that PentaHerbs inhibited CD23 expression up to 60% upon study completion. The invetsigators concluded that PentaHerbs possessed in vitro and in vivo immunomodulation that might mediate the clinical efficacy observed in AD treatment with PentaHerbs [Laboratory studies also demonstrated favorable immunomodulatory effects ,42. Leunreatment on cytotntaHerbs .Cortex Moutan and Herba Menthae significantly attenuated histamine release and prostaglandin D(2) synthesis from RPMC activated by anti-IgE and compound 48/80. While Flos Lonicerae and Rhizoma Atractylodis suppressed only mediator release from compound 48/80 activated RPMC, Cortex Phellodendri potentiated only anti-IgE induced mediator release. However, with the exception of Cortex Moutan, PentaHerbs and the other four component herbs failed to affect cytokine production in Human Mast Cell HMC-1. The investigators concluded that individual herbs of PentaHerbs modulated mast cells and inhibited the inflammatory mediators from mast cells thereby achieving the therapeutic efficacy of PentaHerbs.The actions of PentaHerbs on mast cell activation was also investigated . Effectset al. received reports of 11 cases of liver damage following the use of Chinese herbal medicine for skin conditions [et al. reported that a patient with eczema developed a severe cardiomyopathy after a 2-week course of Chinese herbal medicine [Adverse effects of some Chinese herbal medicine have been reported ,43-49. Pnditions . There wmedicine . The conOnly a few RCTs demonstrated the efficacy (or lack of efficacy) of Chinese medicinal herbs in treating AD. Further larger scale trials and laboratory studies are warranted.hytohemagglutinin; RCT: Randomised controlled trial; SCORAD: SCORing Atopic Dermatitis; SD: Standard deviation; SEB: Staphylococcal enterotoxin B; SFJ: Shuangfujin; TARC: Thymus and activation-regulated chemokine; TEA: Total equivalent amount; Th1: T Helper 1; Th2: T Helper 2; TNF: Tumour necrosis factor; UK: United Kingdom; VAS: Visual analogue scale.AD: Atopic dermatitis; AST: Aspartate aminotransferase; BDNF: Brain derived neutrotrophic factor; CD: Cluster designation; CDLQI: Children Dermatology Life Quality Index; CS: Corticosteroid; CTACK: Cutaneous T cell-attracting chemokine; DLQI: Dermatology Life Quality Index; EASI: Eczema Area and Severity Index; ECP: Eosinophil cationic protein; EFA: Essential fatty acid; HMC Human mast cell; IFN: Interferon; IL: Interleukin; IgE: Immunoglobulin E; MDC: Macrophage-derived chemokine; PBMCs: Peripheral blood mononuclear cells; PHA: PThe authors were involved in the design and trials of the PentaHerbs formulation.KLH drafted the manuscript. BCLC and PCL revised this manuscript. All authors read and approved the final version of the manuscript."} +{"text": "Our understanding of genomic regulation was revolutionized by the discovery that the genome is pervasively transcribed, giving rise to thousands of mostly uncharacterized non-coding ribonucleic acids (ncRNAs). Long, ncRNAs (lncRNAs) have thus emerged as a novel class of functional RNAs that impinge on gene regulation by a broad spectrum of mechanisms such as the recruitment of epigenetic modifier proteins, control of mRNA decay and DNA sequestration of transcription factors. We review those lncRNAs that are implicated in differentiation and homeostasis of metabolic tissues and present novel concepts on how lncRNAs might act on energy and glucose homeostasis. Finally, the control of circadian rhythm by lncRNAs is an emerging principles of lncRNA-mediated gene regulation. This paradigm was fundamentally called into question by results obtained from whole-transcriptome sequencing efforts over thnsortium . Althougnsortium , recent nsortium . One lognsortium , to Drososophila , plants osophila and humaosophila . Given tosophila . It was osophila and goesXIST . Interestingly, lncRNAs on one hand exhibit many similarities with protein-coding transcripts: As true for mRNAs, lncRNAs are transcribed by RNA-polymerase (Pol) II II , spliced(Pol) II , are par(Pol) II and even(Pol) II . Further(Pol) II . It is n(Pol) II . On the (Pol) II . Further(Pol) II .Currently, intensive research efforts are underway to better understand the molecular basis of gene regulation by lncRNAs. To date, four major paradigms have emerged on how lncRNA impinge on gene regulation:cis- or trans. Indeed, early insights into lncRNA-based gene regulation have revealed the recruitment of the inhibitory polycomb repressive complex (PRC) 2 and the activating Trithrorax/MLL chromatin modifiers to specific genomic loci by the lncRNAs HOTAIR , which control the expression of neighboring protein-coding genes. Elegant follow-up studies using chromosome conformation capture (3C) technology revealed that the co-activator complex Mediator is involved in tethering eRNAs to their gene targets. Hence, lncRNAs regulate the three-dimensional (3D) structure of chromosomes via Mediator-dependent chromosome looping that acts as BACE1 ceRNA and concomitantly increases Bace1 mRNA stability and leads to augmented deposition of A\u03b2-plaques in Alzheimer\u2019s disease and are required for AR-dependent gene transcription. In androgen-refractory prostate cancer, PRNBR1 and PCGEM1 are robustly expressed and are implicated in the ligand-independent activation of AR signaling into changes in gene expression. NFkB activation induces the transcription of a specific subset of lncRNAs, apart from the induction of classical inflammatory protein-coding genes. Among this subset of TNF-regulated lncRNAs, a lncRNA termed Lethe is recruited to the NFkB effector subunit RelA in an inducible fashion and inhibits RelA from DNA-binding and target gene activation 1alpha transcription factors. This HIF1a-linc-p21 circuit controls the hypoxia-evoked increases of the glycolytic \u201cWarburg effect\u201d in tumor cells . Key to the understanding of whole-body metabolism are the pleiotropic effects of the anabolic master regulator insulin which simultaneously controls peripheral as well as central-nervous system-related aspects of metabolism . ResistaCRNDE ] points H19 is involved in the intergenerational transmission of diabetes mellitus [gestational diabetes mellitus (GDM)] and the GDM-associated impairments of islet infrastructure and function . Concomitantly, RNAi-mediated SRA loss-of-function interfered with in vitro differentiation of 3T3-L1 preadipocytes serves as storage organ for excess nutrients, brown adipose tissue (BAT) dissipates the proton gradient across mitochondrial membranes to generate heat via the BAT-intrinsic uncoupling protein 1 UCP1; . The accipocytes . In a seipocytes of whichAlu elements located within the 3\u2032UTR of an SMD target and an Alu site localized within a class of lncRNAs called 1/2sbsRNAs (1/2-STAU1-binding site RNAs) triggered SMD , a condition of reduced terminal differentiation of myoblasts. Reinstating DMD-associated downregulation of linc-MD1 expression via lentiviral delivery led to improved maturation of DMD myoblasts. In a study published by Braveheart (Bvht) was demonstrated to be required for differentiation of mesodermal progenitors toward mature cardiomyocytes via interaction with PRC2 epigenetic modifiers. This report for the first time implicated a tissue-specific lncRNA in maintaining cell fate during mammalian organogenesis.The differentiation of skeletal muscle cells (myogenesis) is regulated by a complex, yet well understood, evolutionarily conserved circuitry of protein-coding genes which control the timely growth, morphogenesis, and terminal maturation of muscle progenitors , a CNS-controlled genetic disorder circadian rhythm with an associated dysregulation of metabolism and the development of obesity, was shown to be influenced by a PWS-associated lncRNA called 116G. After splicing, a lncRNA consisting of the remnants of 116G (termed 116HG) bound to the transcriptional activator RBBP5 and ensures a physiological circadian rhythm in the brain. Mice deficient for 116HG exhibit metabolic disorders due to the dysregulation of diurnally expressed circadian genes like Clock, Cry1, and Per2 in the CNS such as miRNAs can be packaged into exosomes and released after binding to recipient cells, thus constituting a novel and intriguing way for ncRNAs to regulate systemic aspects of metabolism . Similarin vivo -mediated inhibition of disease-associated lncRNAs effectively improves degenerative diseases like myotonic dystrophy type 1 (DM1) in mice efficiently silence the expression of ncRNAs such as miRNAs and are generally well tolerated in vivo . These ain vivo and adopin vivo with unpc health . In conte models ] showcas in mice .The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Intrinsic plasticity (IP) is a ubiquitous activity-dependent process regulating neuronal excitability and a cellular correlate of behavioral learning and neuronal homeostasis. Because IP is induced rapidly and maintained long-term, it likely represents a major determinant of adaptive collective neuronal dynamics. However, assessing the exact impact of IP has remained elusive. Indeed, it is extremely difficult disentangling the complex non-linear interaction between IP effects, by which conductance changes alter neuronal activity, and IP rules, whereby activity modifies conductance via signaling pathways. Moreover, the two major IP effects on firing rate, threshold and gain modulation, remain unknown in their very mechanisms. Here, using extensive simulations and sensitivity analysis of Hodgkin-Huxley models, we show that threshold and gain modulation are accounted for by maximal conductance plasticity of conductance that situate in two separate domains of the parameter space corresponding to sub- and supra-threshold conductance . Analyzing equivalent integrate-and-fire models, we provide formal expressions of sensitivities relating to conductance parameters, unraveling unprecedented mechanisms governing IP effects. Our results generalize to the IP of other conductance parameters and allow strong inference for calcium-gated conductance, yielding a general picture that accounts for a large repertoire of experimental observations. The expressions we provide can be combined with IP rules in rate or spiking models, offering a general framework to systematically assess the computational consequences of IP of pharmacologically identified conductance with both fine grain description and mathematical tractability. We provide an example of such IP loop model addressing the important issue of the homeostatic regulation of spontaneous discharge. Because we do not formulate any assumptions on modification rules, the present theory is also relevant to other neural processes involving excitability changes, such as neuromodulation, development, aging and neural disorders. Over the past decades, experimental and theoretical studies of the cellular basis of learning and memory have mainly focused on synaptic plasticity, the experience-dependent modification of synapses. However, behavioral learning has also been correlated with experience-dependent changes of non-synaptic voltage-dependent ion channels. This intrinsic plasticity changes the neuron's propensity to fire action potentials in response to synaptic inputs. Thus a fundamental problem is to relate changes of the neuron input-output function with voltage-gated conductance modifications. Using a sensitivity analysis in biophysically realistic models, we depict a generic dichotomy between two classes of voltage-dependent ion channels. These two classes modify the threshold and the slope of the neuron input-output relation, allowing neurons to regulate the range of inputs they respond to and the gain of that response, respectively. We further provide analytical descriptions that enlighten the dynamical mechanisms underlying these effects and propose a concise and realistic framework for assessing the computational impact of intrinsic plasticity in neuron network models. Our results account for a large repertoire of empirical observations and may enlighten functional changes that characterize development, aging and several neural diseases, which also involve changes in voltage-dependent ion channels. Ion channels of neuron membranes undergo long-term experience-dependent modifications of their biochemical and biophysical state induced by on-going neuronal activity, a process called intrinsic plasticity IP; . RegulatIP involves a causal loop between electrical activity and the channels' state. Indeed, activity-induced signaling pathways modify the channels' state, a process commonly termed IP rules Actually, getting a global picture of the possible computational role of IP loops remains problematic for two reasons. First, IP loops are diverse. IP involves virtually all known ion channel types and many different signaling pathways Although the ubiquitous scheme has emerged that electrical activity implicates calcium signaling and kinase/phosphatase pathways to regulate channels' state To avoid such specificities, we propose an alternative modeling strategy devised to provide the generic framework required for a global picture of the IP loop and its functional role. Ideally, this framework should describe IP effects and IP rules with the highest possible generic character. Here, we develop an extensive analysis of generic IP effects on firing rate. This theory is to be combined with generic descriptions of IP rules to enlighten IP loop interactions. In particular, we view the present study as a complement to the aKP model In the following, we perform a sensitivity analysis to systematically quantify how changes in the maximal conductance of a generic voltage-gated conductance affects the threshold and gain of the We address the issue of how the firing frequency of a neuron, In this context, the effect of IP on firing rate is captured by the frequency sensitivity, On the one hand, On the other hand, This initial analysis thus suggests that IP effects arise from two mechanisms underlain by conductance with distinct biophysical properties, according to whether they activate independent of, or correlative to spiking. Moreover, it suggests that such conductance should respectively exhibit strong threshold versus inverse gain sensitivities. In the following, we examine the biophysical plausibility of these suggestions by exploring the parameter space of the X conductance using extensive numerical simulations of HH neuron models see to 1) unWe ran extensive simulations of a single-compartment HH neuron model endowed with the X conductance submitted to a constant input current, rent see . We comped and . As a ge large threshold sensitivity is characteristic of conductance with large activation at We then examined the inverse gain sensitivity, tivities . In this of the ; arrow. f the , the persistent (INaP) and slowly-inactivating (INaS) sodium, the low-threshold calcium (ICaT), or the muscarinic (IM) and slowly-inactivating (IKs) potassium conductance display biophysical parameters typically situated in the domain of high threshold sensitivity. Consistently, empirical studies indicate that modifications of the persistent sodium Together, these results provide a unifying framework to account for and interpret IP experiments. Indeed, we have determined that voltage-gated conductance with large threshold versus large inverse gain sensitivities can be discriminated on the basis of a simple and generic criterion, i.e. an activation of CaL, ICaR), calcium-activated (IAHP) or fast-potassium potassium (IA) conductance that are directly or indirectly activated by APs should essentially affect the In contrast, modifications of pharmacologically identified conductance types such as the high-threshold calcium conductance , whereas several IP studies show that IH exclusively increases the The dichotomy we have unraveled and which appears to beneficiate from experimental support appeals several remarks. First, our results indicate that mixed modifications of the In addition to interpreting existing results, the present theoretical framework represents a valuable tool for experimentalists to target putative conductance involved in IP, based on the observation of hreshold or the Ihreshold , S9, S10We have ascertained that the present results are robust. Indeed, shifting half-activation potentials of AP sodium and potassium currents by a few mV shifts sensitivity maps by the same amount along the Besides, the dichotomy we have unraveled appears to extend to the general case of voltage-dependent activation time constants, commonly encountered in real conductance. Hence, sensitivity maps obtained with voltage\u2013dependence activation time constants were consistent with our previous understanding of sensitivities' dependence on time constants. Indeed, we found (not shown) that 1) threshold sensitivity is globally unaffected by the voltage-dependence of the activation; 2) large time constants at ISI potentials (below voltage AP threshold) increase the impact of the post-spike relaxation and delay the build-up effect, thus augmenting the post-spike mechanism and diminishing the pre-spike mechanism; 3) large time constants at spike potentials (above AP voltage threshold) diminish the activation increase during the spike, reducing the post-spike effect, but have no impact on the pre-spike mechanism.Finally, an important question is whether the IP effects we unravel are robust in the general case where several voltage-gated conductance are present, even though exploring this issue in depth is largely out of the present scope. Actually, we have achieved a preliminary exploration suggesting that threshold and inverse gain modifications behave as the linear sum of individual conductance effects. If confirmed, this result would be noteworthy, given the degree of non-linearity commonly encountered in neurons at the level of the membrane potential or gating variables. Moreover, such linearity would open the possibility to capture complex interactions between conductance in a simple way in terms of frequency coding in neuron and neural network models.Although robust, our results should be extended with respect to several dimensions, including 1) IP effects on spike-timing properties , in particular by also considering type II excitability neuron models, 2) multi-compartmental neuron models to address IP effects on dendritic integration This analysis complements recent analyses of parameter robustness of excitability in Hodgkin-Huxley (HH) models, using sensitivity analysis or stochastic search methods Here, we have focused on IP effects to escape the entanglement of IP effects and IP rules in empirical and theoretical studies and provide a manageable framework for the comprehensive study of IP loops. Hence, our goal is attainable by coupling the present IP effect equations with IP rules equations describing the causal mechanisms relating on-going spiking activity to conductance changes. In our mind, realistic signaling pathways models are desirable as they share the same - molecular - level of description. IP processes display gradation Introducing these coupled equations in neural networks offers the possibility to assess the impact of IP on dynamical and computational network properties. The present results allow studying IP of real conductance with known biophysical parameters in firing rate neural networks with explicit threshold and/or gain, and spiking neural networks embedded with conductance parameters, using event-based schemes As a concluding remark, the present results are independent of the regulatory processes modifying conductance parameters and thus relevant to a larger class of processes than IP, possibly including neural development The present study is aimed at providing a description of the effects of conductance parameter modification on neuronal excitability. Characterizing neuronal excitability requires criteria to evaluate activity in response to stimulatory inputs. Here, we do not study possible changes in dynamical regimes of firing that can result from IP regulation Spiking rate and spike timing represent two complementary dimensions by which information can be carried by neurons in a regular spiking mode and that can be analyzed to this end 7 conditions: we computed >10 maps (see Parametric exploration), each map incorporated >103 points at which sensitivities were computed from \u223c30 simulated Reaching present conclusions required evaluating the response of the standard model in >10Here, we study a single-compartment neuron model endowed with leak, AP currents and a generic voltage-dependent X current to assess the effect of its plasticity on firing rate of the model neuron. The membrane potential (V) evolves according toThe kinetics formalism we employ offers two decisive advantages to reach the present goal of unraveling the effect of IP on firing rate. First, this formalism is simple enough to derive tractable analytic expressions of Assessing the effect of plastic conductance modifications on firing rate requires in principle the exploration of a 9-dimensional space with the present formalism, the X conductance being described by the parameter vector To estimate the threshold models, the objective was to reach analytical expressions of the threshold Theoretical threshold sensitivity map derived from the threshold IAF theory computed from equation (1.3). (B) Threshold sensitivity map of the standard HH model with(TIF)Click here for additional data file.Figure S2Threshold sensitivity and reversal potential. (A) Threshold sensitivity map of the standard HH model with potassium currents ((TIF)Click here for additional data file.Figure S3Threshold sensitivity and inactivation. (A) Threshold sensitivity map of the standard HH model in the presence of inactivation ((TIF)Click here for additional data file.Figure S4Inverse gain sensitivity and activation power. (A) Inverse efficacy sensitivity map of the standard HH model, (TIF)Click here for additional data file.Figure S5Inverse gain sensitivity in the pre- and post-spike IAF theories. (A) Theoretical inverse gain sensitivity map derived from the post-spike IAF theory with sodium conductance. (B) Theoretical inverse gain sensitivity map derived from the pre-spike IAF theory with sodium conductance.(TIF)Click here for additional data file.Figure S6ISI dynamics for a sodium X conductance in the domain of large inverse gain sensitivities. (A) Mean membrane potential dynamics of the standard HH model for increasing (TIF)Click here for additional data file.Figure S7ISI dynamics for a sodium X conductance in the large domain of moderate inverse gain sensitivities. (A) Mean membrane potential dynamics of the standard HH model for increasing (TIF)Click here for additional data file.Figure S8ISI dynamics for a sodium X conductance in the pre/post-spike theory. (A) Theoretical membrane potential dynamics in the pre/post-spike IAF theory, with parameters similar to those used in (TIF)Click here for additional data file.Figure S9ISI dynamics for a potassium X conductance in the pre/post-spike theory. (A) Mean membrane potential dynamics of the standard HH model with potassium conductance, for increasing (TIF)Click here for additional data file.Figure S10Inverse gain sensitivity and reversal potential. (A) Inverse gain sensitivity map of the standard HH model with calcium conductance. (B) Theoretical inverse gain sensitivity map derived from the pre/post-spike IAF theory with calcium conductance. (C) Inverse gain sensitivity map of the HH model, with potassium conductance. Colorbar as in (D). (D) Theoretical inverse gain sensitivity map derived from the pre/post-spike IAF theory with potassium conductance. (TIF)Click here for additional data file.Figure S11Inverse gain sensitivity and activation time constant. (A) Inverse gain sensitivity map of the standard HH model with instantaneous activation. Colorbar as in (B). (B) Inverse gain sensitivity map of the standard HH model with sodium conductance with activation time constant (TIF)Click here for additional data file.Figure S12Inverse gain sensitivities and inactivation. (A) Inverse gain sensitivity map of the standard HH model in the presence of inactivation ((TIF)Click here for additional data file.Figure S13Net frequency effects arising from threshold and inverse gain modulation. (A) Map of the common logarithm of maximal conductance limit for sodium conductance. Colorbar as in (B). (B) Map of the common logarithm of maximal conductance limit for potassium conductance. (C) Net frequency effects from threshold modulation for sodium conductance. Colorbar as in (D). (D) Net frequency effects from inverse gain modulation for sodium conductance. (E) Net frequency effects from threshold modulation for potassium conductance. Colorbar as in (F). (F) Net frequency effects from inverse gain modulation for potassium conductance.(TIF)Click here for additional data file.Text S1The threshold IAF theory(DOC)Click here for additional data file.Text S2Threshold sensitivity and activation kinetics(DOC)Click here for additional data file.Text S3Threshold sensitivity and reversal potential(DOC)Click here for additional data file.Text S4Threshold sensitivity and inactivation(DOC)Click here for additional data file.Text S5Inverse gain sensitivity and activation power(DOC)Click here for additional data file.Text S6The pre-spike IAF theory(DOC)Click here for additional data file.Text S7Comparison of dynamics in the standard HH and pre-spike IAF theory(DOC)Click here for additional data file.Text S8The post-spike IAF theory(DOC)Click here for additional data file.Text S9Activation dynamics during the spike(DOC)Click here for additional data file.Text S10Comparison of dynamics in the standard HH and post-spike IAF theory(DOC)Click here for additional data file.Text S11The pre/post-spike IAF theory(DOC)Click here for additional data file.Text S12Comparison of dynamics in the standard HH and pre/post-spike IAF theory(DOC)Click here for additional data file.Text S13Inverse gain sensitivity and reversal potential(DOC)Click here for additional data file.Text S14Inverse gain sensitivity and activation time-constant(DOC)Click here for additional data file.Text S15Inverse gain sensitivity and inactivation(DOC)Click here for additional data file.Text S16Maximal net modifications on the threshold, the inverse gain and firing frequency(DOC)Click here for additional data file.Text S17Action potential and leak conductance efficacies and modifications(DOC)Click here for additional data file."} +{"text": "A multiple-test strategy in often needed in the evaluation of patients (pts) with suspected coronary artery disease (CAD). Cardiac magnetic resonance (CMR) has potential advantages in this context allowing simultaneous evaluation of ventricular function, myocardial perfusion and scar detection with high spatial resolution and no ionizing radiation exposure. We aimed to compare the diagnostic accuracy of adenosine stress CMR myocardial perfusion imaging (CMR-MPI) with exercise treadmill test (ETT) for detection of CAD using invasive fractional flow reserve (FFR) as the reference standard, and to assess the best performing diagnostic algorithm using these tests in patients with suspected CAD.Prospective single-center study with enrollment of symptomatic pts referred to cardiology to suspected CAD assessment. All pts underwent a sequential protocol including: ETT, CMR-MPI and X-ray coronary angiography (XA). The ETT was dichotomously classified and deemed suggestive of CAD if reproduction of clinical symptoms during effort or additional ST-segment depression \u22651 mm. CMR-MPI exams were evaluated by two independent cardiologists blinded to the results of ETT. Functionally significant CAD was defined by the presence of occlusive/sub-occlusive stenosis or FFR measurements <0.8 in vessels >2 mm. Multiples protocols integrating ETT and CMR-MPI were tested using ROC curves.80 pts were recruited, 68% male and with mean age of 61 \u00b1 8 years. All pts were symptomatic and had at least one cardiovascular risk factor. CAD was detected in 37 pts (47%). CMR-MPI and ETT showed similar sensitivity for CAD detection (81 vs. 80%), but with higher specificity for CMR-MPI (93 vs. 56%), translating into a greater diagnostic accuracy of CMR-MPI . In the best performing protocol (AUC = 0.83), pts with both clinical and electrically positive ETT would be directly referred to XA while all the remaining pts would be managed according to CMR-MPI results. The other protocols, including referral to CMR-MPI only the pts with borderline positive or inconclusive ETT or with negative or inconclusive ETT had worst performances .CMR-MPI has high sensitivity and specificity for detection of obstructive CAD. In our pts with high probability of CAD, the inclusion of CMR-MPI in an integrated protocol for the detection of CAD improved the overall diagnostic accuracy, particularly in those pts with negative, borderline positive or inconclusive ETT.No conflict of interests/financial disclosures."} +{"text": "Although the advent of ultra-deep sequencing technology allows for the analysis of heretofore-undetectable minor viral mutants, a limited amount of information is currently available regarding the clinical implications of hepatitis B virus (HBV) genomic heterogeneity.To characterize the HBV genetic heterogeneity in association with anti-viral therapy, we performed ultra-deep sequencing of full-genome HBV in the liver and serum of 19 patients with chronic viral infection, including 14 therapy-na\u00efve and 5 nucleos(t)ide analogue(NA)-treated cases.Most genomic changes observed in viral variants were single base substitutions and were widely distributed throughout the HBV genome. Four of eight (50%) chronic therapy-na\u00efve HBeAg-negative patients showed a relatively low prevalence of the G1896A pre-core (pre-C) mutant in the liver tissues, suggesting that other mutations were involved in their HBeAg seroconversion. Interestingly, liver tissues in 4 of 5 (80%) of the chronic NA-treated anti-HBe-positive cases had extremely low levels of the G1896A pre-C mutant , suggesting the high sensitivity of the G1896A pre-C mutant to NA. Moreover, various abundances of clones resistant to NA were common in both the liver and serum of treatment-na\u00efve patients, and the proportion of M204VI mutants resistant to lamivudine and entecavir expanded in response to entecavir treatment in the serum of 35.7% (5/14) of patients, suggesting the putative risk of developing drug resistance to NA.Our findings illustrate the strong advantage of deep sequencing on viral genome as a tool for dissecting the pathophysiology of HBV infection. Hepatitis B virus (HBV) is a non-cytopathic DNA virus that infects approximately 350 million people worldwide and is a main cause of liver-related morbidity and mortality The major goals of antiviral therapy in patients with HBV infection are to prevent the progression of liver disease and inhibit the development of hepatocellular carcinoma in vivo dynamics of HBV drug resistant variants in response to anti-viral treatment remains to be clarified. Moreover, intrahepatic viral heterogeneity in patients that achieved the clearance of circulating HBV is largely unknown.There has been a recent advance in DNA sequencing technology By taking the advantage of an abundance of genetic information obtained by utilizing the Illumina Genome Analyzer II as a platform of ultra-deep sequencing, we determined the whole HBV sequence in the liver and serum of patients with chronic HBV infection to evaluate viral quasispecies characteristics. Moreover, we investigated the prevalence of rare drug-resistant HBV variants as well as detailed dynamic changes in the viral genetic heterogeneity in association with NA administration. Based on the abundant genetic information obtained by ultra-deep sequencing, we clarified the precise prevalence of HBV clones with G1896A pre-C mutations in association with HBe serostatus in chronically infected patients with or without NA treatment. We also detected a variety of minor drug-resistant clones in treatment-na\u00efve patients and their dynamic changes in response to entecavir administration, demonstrating the potential clinical significance of naturally-occurring drug-resistant mutations.The Kyoto University ethics committee approved the study, and written informed consent for participation in this study was obtained from all patients. The study was conducted in accordance with the principles of the Declaration of Helsinki.The liver tissues of 19 Japanese patients that underwent living-donor liver transplantation at Kyoto University due to HBV-related liver disease were available for viral genome analyses. These individuals included 13 men and 6 women, aged 41 to 69 years and all but one were infected with genotype C viruses. Participants comprised 19 patients with liver cirrhosis caused by chronic HBV infection, including 14 antiviral therapy-na\u00efve cases (chronic-na\u00efve cases) and 5 cases receiving NA treatment, with either lamivudine or entecavir (chronic-NA cases) . Serum HDNA was extracted from the liver tissue and serum using a DNeasy Blood & Tissue Kit . To define the consensus reference sequences of HBV in each clinical specimen, all samples were first subjected to direct population Sanger sequencing using the Applied Biosystems 3500 Genetic Analyzer . Oligonucleotide primers for the HBV genome were designed to specifically amplify whole viral sequences as two overlapping fragments using the sense primer 169_F and antisense primer 2847_R to yield a 2679-bp amplicon (amplicon 1), and the sense primer 685_F and antisense primer 443_R to yield a 2974-bp amplicon , the 64 base-pair reads obtained from the Genome Analyzer II were aligned with the reference sequences of 3215 bp that were determined by direct population Sanger sequencing of each clinical specimen. Reads with 90% or more bases matching a particular position of the reference sequences were aligned. Furthermore, two quality filters were used for sequencing reads: the reads with a median quality score of more than 30 and no more than 3 uncalled nucleotides were allowed anywhere in the 64 bases. Only sequences that passed the quality filters, rather than raw sequences, were analyzed and each position of the viral genome was assigned a coverage depth, representing the number of times the nucleotide position was sequenced.To determine the relative proportion of the G1896A pre-C mutant, allele-specific quantitative real-time PCR was performed based on the previously described method P values less than 0.05 were considered statistically significant.Results are expressed as mean or median, and range. Pretreatment values were compared using the Mann-Whitney U-test or the Kruskal Wallis H-test. n is the number of different species identified, fi is the observed frequency of a particular variant in the quasispecies, and N is the total number of clones analyzed The viral quasispecies characteristics were evaluated by analyzing the genetic complexity based on the number of different sequences present in the population. Genetic complexity for each site was determined by calculating the Shannon entropy using the following formula:http://www.ddbj.nig.ac.jp/index-e.html) under accession number DRA000435.All sequence reads have been deposit in DNA Data Bank of Japan Sequence Read Archive irrespective of their HBeAg serostatus, while the G1896A pre-C mutant were detectable in substantial proportion before treatment in all cases chronic-na\u00efve cases possessed the M204VI mutants in their liver tissues and the proportion of mutant clones among the totally infected viruses ranged from 0.3% to 1.1% among the M204VI mutant-positive patients. In chronic-NA cases, 4 of 5 (80.0%) liver tissues harbored the M204VI mutants with the proportion among the totally infected viruses ranging from 0.4% to 18.7% , while tTo clarify the risk of latent expansion of drug-resistant mutations due to NA treatment, we next examined the early dynamic changes of the prevalence of M204VI mutants in the serum of treatment-na\u00efve patients in response to entecavir treatment. Ultra-deep sequencing provided a mean 40,791- and 38,823-fold coverage of readings, which were mapped to the M204VI nucleotide position at the YMDD sites of each reference sequence in patients before and after entecavir treatment.Five of 14 (35.7%) patients harbored the M204VI mutations prior to entecavir treatment. Although the serum HBV DNA levels were significantly reduced in response to entecavir in all cases, the M204VI mutant clones were detected in 9 cases (64.3%) after entecavir administration . NotablyDirect population sequencing is the most common method for detecting viral mutations Because of its ability to handle abundant viral genome information, ultra-deep sequencing allowed us to evaluate low-abundant virus variants of patients with chronic HBV infection in detail. It is widely accepted that HBe seroconversion is highly associated with the emergence of G1896A pre-C and/or A1762T and G1764A core promoter mutant clones One thing to be noted is that the majority of the chronic-NA cases had extremely low levels of the G1896A pre-C mutant in their liver tissues, even though those cases were serologically positive for anti-HBe and negative for HBeAg. Moreover, entecavir administration significantly reduced the proportion of the G1896A pre-C mutant in the serum of the majority of patients irrespective of their HBeAg serostatus, while the G1896A pre-C mutant clones were detectable in a substantial proportion before treatment in all cases. These findings suggest that the G1896A pre-C mutant have higher sensitivity to NA than the wild-type viruses. Consistent with this hypothesis, several previous studies reported that NA is effective against acute or fulminant hepatitis caused by possible infection with the G1896A pre-C mutant Ultra-deep sequencing has a relatively higher sensitivity than conventional direct population sequencing and is thus useful for detecting drug-resistant mutations not detected by standard sequencing The current ultra-deep parallel sequencing technology has limitations in the analyses of viral quasispecies. First, because the massively-parallel ultra-deep sequencing platform is based on a multitude of short reads, it is difficult to evaluate the association between nucleotide sites mapped to different genome regions in a single viral clone. Indeed, potential mutational linkages between the pre-C and reverse transcriptase regions were difficult to elucidate due to the short read length of the shotgun sequencing approach. Second, accurate analysis of highly polymorphic viral clones by ultra-deep sequencing is also difficult because the identification of mutations depends strongly on the mapping to the reference genome sequences.In conclusion, we demonstrated that the majority of patients positive for anti-HBe and negative for HBeAg lacked the predominant infection of the G1896A pre-C mutant in the presence of NA treatment, suggesting that the G1896A pre-C mutant have increased sensitivity to NA therapy compared with wild-type HBV. We also revealed that drug-resistant mutants are widely present, even in the liver of treatment-na\u00efve HBV-infected patients, suggesting that the preexisting low-abundant mutant clones might provide the opportunity to develop drug resistance against NA through the selection of dominant mutations. Further analyses utilizing both novel and conventional sequencing technologies are necessary to understand the significance and clinical relevance of the viral mutations in the pathophysiology of various clinical settings in association with HBV infection.Figure S1Comparison of the viral complexity between the liver and serum of the same individual. Shannon entropy values throughout the whole viral genome of the liver and serum of the representative two cases are shown. . preC-C: pre-core\u223ccore, preS: pre-surface, P: polymerase.(TIF)Click here for additional data file.Table S1The oligonucleotide primers for amplifying HBV sequences in each clinical specimen.(DOCX)Click here for additional data file.Table S2Error frequency of Ultra-deep sequencing for the expression plasmid encoding wild-type genotype C HBV genome sequences by the three control experiments.(DOCX)Click here for additional data file.Table S3The sensitivity and accuracy of detecting the low abundant minor clones in association with the different coverage numbers.(DOCX)Click here for additional data file."} +{"text": "On delayed-enhancement (DE-CMR), both fat and infarcted myocardium appear bright making them difficult to differentiate. Standard chemical shift fat-suppression (FatSatCS) consists of a fat-frequency selective saturation followed by readout. This approach is suboptimal in clinical DE-CMR sequences which typically have long readout times (100-200ms) and as a result, fat magnetization has significantly recovered when the center of k-space is acquired for linear reordering. Centric reordering can overcome this limitation, but at the cost of blurring artifacts.The phase sensitive inversion recovery (PSIR) variant of DE-CMR avoids the need to precisely set inversion time through the acquisition of a reference data set interleaved between image acquisitions. We hypothesized that modifying the reference acquisition via a Dixon-type approach could provide PSIR images that simultaneously show dark fat without added acquisition time. The result is a virtual chemically selective inversion (FatSatVCSI), without increased SAR and at no cost to signal-to-noise from pulse imperfections.DE-CMR images in phantoms and patients (n=7) were acquired at 3T (Siemens) with a segmented gradient-echo readout. In phantoms, we studied the relationship of readout duration (by varying the number of lines per segment) to fat signal. FatSatCS efficacy was studied for both centric and linear reordering. In patients, three sequential PSIR images were acquired: no fat suppression, FatSatCS and the FatSatVCI with the same parameters including inversion time. Regions of interest (ROIs) were drawn in pericardial and subcutaneous fat and left ventricular blood pool. The performance of each technique was evaluated by comparing the fat-to-blood signal ratios.Phantom results demonstrate that increasing readout time reduces the efficacy FatSatCS with linear reordering, but not for centric figure . With ceBy modifying the reference acquisition of a PSIR scan, we provide PSIR images with and without fat suppression in a single acquisition. No additional data acquisition, RF pulses, or increased scan time is required.NIH grant 5R01HL064726-07."} +{"text": "Interstitial myocardial fibrosis is a histological hallmark of non-ischemic dilated cardiomyopathy (DCM), and may play an important role in adverse remodelling and progressive systolic dysfunction. T1-mapping enables non-invasive assessment of diffuse fibrosis by quantification of myocardial extracellular volume fraction (ECV). We hypothesized that CMR would identify a raised ECV in DCM which would correlate with the degree of systolic dysfunction.Consecutive DCM patients referred for CMR and age/sex-matched healthy controls were prospectively enrolled. Exclusion criteria included a history of recent myocarditis, ischemic heart disease, diabetes, severe hypertension and primary valvular disease. All subjects underwent CMR according to a standardized protocol which included T1-mapping and late gadolinium enhancement (LGE) imaging. Mid-ventricular short-axis T1-maps were acquired using a Modified Look-Locker Inversion recovery sequence prior to contrast and 20 minutes after gadolinium administration (Gadovist 0.1mmol/kg). The pre- and post-contrast T1-maps were co-registered and used with the patient's hematocrit to generate an ECV map.In total, 85 patients and 35 controls were studied. Baseline clinical and CMR characteristics for the cohort are summarized in Table ECV is expanded in DCM in proportion to the degree of LV systolic dysfunction. An increased ECV in sections of the heart without clinically obvious LGE suggests the presence of low level myocardial fibrosis or possibly myocardial edema. This technique offers potential for the evaluation of interstitial fibrosis in DCM, although important challenges include the substantial overlap of ECV values between patients and normals. Further work should aim to corroborate these findings with histological validation.This project was supported by the NIHR Cardiovascular Biomedical Research Unit of Royal Brompton and Harefield NHS Foundation Trust, the British Heart Foundation, and CORDA (research charity).Dr Peter Kellman and Dr Andrew Arai are funded by the National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA."} +{"text": "More and more evidence has showed that wild-type Htt plays important roles in maintaining normal functions of neuronal system. The clearance of mutant Htt has been studied extensively; however, little is known about the mechanisms regulating accumulation and turnover of endogenous wild-type Htt. Puromycin-sensitive aminopeptidase (PSA) was recently identified as a major peptidase digesting TAU protein and protecting against TAU-induced neurodegeneration. PSA was also found as the peptidase responsible for digesting polyglutamine sequences released by proteasomes and removal of neurotoxic polyglutamine-expanded Htt exon-1, ataxin-3, mutant synuclein and superoxide dismutase 1 via autophagy system. These results suggest that PSA might represent a novel degradation mechanism targeting aggregate-prone neurotoxic protein substrates, including mutated Htt. However, the effects of PSA on endogenous wild-type Htt abundance remain unclear. Here, we investigated the effects of PSA on endogenous wild-type Htt clearance in vivo using a human PSA (hPSA) transgenic mouse model, which was generated using bacterial artificial chromosome (BAC) mediated technology. For measuring the Htt expression in hPSA transgenic mice and control mice, the brain tissues were dissected and separated, and then were homogenized by sonication followed with centrifugation at 100,000 g at 4oC. Htt in supernatants were analyzed by Western blot using anti-Htt antibodies. Immunohistochemistry was also performed using perfused brains from both hPSA and control mice according to standard protocols. And we tested whether PSA overexpression is able to reduce the abundance of endogenous Htt in human neuroblastoma cells SH-SY5Y in vitro. SH-SY5Y cells were transfected with hPSA overexpression vectors pCMV6-XL-hPSA or blank vectors and then the endogenous Htt was analyzed with Western blot and immunocytochemistry. We also investigated the effect of inhibition of PSA expression using RNA interference on endogenous Htt levels in SH-SY5Y cells. Cells were transfected with siRNA oligonucleotides specific for hPSA. Efficient hPSA silencing was confirmed with both real-time RT-PCR and Western blot analysis.We first determined whether PSA regulates Htt abundance In vivo studies, Western blot analysis showed that Htt is significantly decreased in human PSA transgenic mice. Immunohistochemical experiment also showed Htt expression is decreased in all the transgenic brain regions tested. In vitro studies, Western blot analysis demonstrated decrease of endogenous Htt in response to PSA overexpression and accumulation of Htt in response to PSA slicing with Stealth-RNAi in human neuroblastoma cell line SH-SY5Y. And immunocytochemistry demonstrated notable decrease and rapid accumulation of Htt in response to PSA overexpression and PSA slicing respectively in SH-SY5Y cells.in vivo and in vitro data implicate that PSA may be a key physiological regulator of clearance and turnover of wild-type Htt in neuronal system, and may play important roles in pathogenesis of HD through regulating clearance of wild-type or and mutated Htt as well.These combined"} +{"text": "Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this \u2018siRNA omics\u2019 approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense.Virus-infected plants accumulate abundant, 21\u201324 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Furthermore, we show that bioinformatics analysis of viral siRNA population allows for the identification of the master genome and its microvariants in viral quasispecies. We also used this technology to reconstruct a newly emerged single-stranded DNA virus and two viroids associated with the red blotch disease of grapevines in the United States. Thus, deep siRNA sequencing can be used for identification and reconstruction of the consensus master genome of any plant virus or viroid, and for studying virus diversity and evolution. Moreover, our analysis of siRNAs derived from DNA viruses and viroids contributes to further understanding the mechanisms of siRNA biogenesis and RNAi-based antiviral defense and raises new questions for future research.Owing to error-prone replication, viruses accumulate microvariants which deviate from a consensus master genome by one or more SNPs (single-nucleotide polymorphisms) and/or indels (insertions/deletions) and comprise a viral quasispecies that can rapidly evolve in changing environment Arabidopsis plants infected with Cauliflower mosaic virus (CaMV) Cabbage leaf curl virus (CaLCuV) Caulimoviridae and the Geminiviridae families, respectively. Bioinformatic analysis of the redundant sRNA reads revealed that the hotspots of viral siRNA production cover only portions of the viral genome in both cases. The non-redundant reads, however, cover the entire circular genomes of CaMV and CaLCuV in the sense and antisense orientations without gaps RNA precursors covering the entire viral genome sequences out gaps , albeit out gaps . This sude novo assemble viral siRNAs, we tested different algorithms using Velvet followed by Oases or Metavelvet for assembling redundant or non-redundant reads and Seqman for merging the resulting contigs. In some cases, we also used mapping to the plant genome as a filtering step before Seqman to separate the viral siRNA contigs from the plant sRNA contigs , the RNA virus for which an available cDNA clone was not infectious de novo as a single contig from two independent sRNA libraries (To determine if such \u2018siRNA omics\u2019 (siRomics) approach is applicable for identification of a master genome in viral \u2018quasispecies cloud\u2019, we sequenced sRNAs from ibraries . This reibraries . SNP calibraries A. We coibraries . Thus, aArabidopsis thaliana. Note, that for identification of the SNPs listed in rdr1/2/6 triple mutant plants with diminished RDR activities Interestingly, SNP calling revealed that ORMV, CaMV and CaLCuV do not differ drastically in the frequency of SNPs or the average degree of deviation (in %) from the master genome nucleotides A-D. ThiVitis vinifera cv. Pinot noir) grown at vineyards in Oregon, some of which exhibited severe leaf red blotch disease symptoms of unknown etiology, and from control plants with green, healthy-looking leaves. De novo reconstruction revealed that both infected and healthy-looking vines harbored Grapevine yellow speckle viroid 1 (GYSVd-1) and Hop stunt viroid (HSVd), whose small circular RNA genomes were assembled as single terminally-redundant contigs and verified by redundant sRNA coverage and confirmed its presence in DNA samples from 12 of 16 symptomatic vines from the same vineyard, but not from any of 18 symptomless vines. Intriguingly, the most recent reports describe Grapevine red blotch-associated virus (GRBaV) and Grapevine red leaf-associated virus (GRLaV) that severely affect vineyards in States of California To evaluate the potential of siRomics for diagnostics of an unknown disease, we deep sequenced sRNAs from grapevines (coverage . Previoucoverage . In addicoverage . Phylogecoverage E. Notabcoverage B. We deC), DNA viruses that are transcribed in the nucleus spawn 21-, 22- and 24-nt siRNAs and Cabbage leaf curl virus or by mechanical inoculation with sap from Oilseed rape mosaic virus (ORMV)-infected Nicotiana benthamiana. A previously constructed plasmid containing ORMV cDNA downstream of the T7 promoter (kindly provided by Dr. Fernando Ponz) was modified using synthetic DNA fragments and suitable restriction sites to correct the cloning errors and obtain the reconstructed wild type ORMV genome clone (deposited to the Genbank as KF137561). The resulting and the original clones were linearized downstream of the ORMV sequence and used as templates for in vitro transcription reactions to produce a capped viral genomic RNA. The reaction mixtures were used for mechanical inoculation. Symptom development at day 10 post-inoculation is shown in Growth conditions and virus infections of Samples of the red leaves displaying leafroll-like disease symptoms (named \u2018red blotch\u2019 disease) and healthy-looking green leaves of grapevine cv. Pinot noir plants were collected in a privately owned vineyard near Newberg, Oregon, USA in summer, 2011. The samples were scion clone 777 grafted onto rootstock 44\u201353 and collected with permission of the owner.et al. de novo reconstruction of the viral genomes using the algorithms summarized in www.ebi.ac.uk/~zerbino/velvet) www.ebi.ac.uk/~zerbino/oases) k-mer values (13 through 23). 100% coverage of a virus genome could be achieved either with single k-mers or certain combinations thereof, as exemplified for CaMV, CaLCuV and ORMV in www.broadinstitute.org/igv) k-mer values or their selected combinations were merged using the Seqman module of Lasergene DNASTAR 8.1.2 Core Suite . If required, the filtering step before Seqman (or Velvet) was done by mapping contigs (or sRNA sets) to the Arabidopsis thaliana genome (TAIR9) or Vitis vinifera genome (PRJNA33471) using Burrows-Wheeler Aligner (BWA) 0.5.9 de novo reconstructed viral genomes were scanned for SNPs and indels using IGV with redundant reads. Finally, single-base resolution maps of viral sRNAs on the virus genomes were created using BWA and a sRNA map tool MISIS at several positions. These apparent sequencing errors were confirmed by re-sequencing of the three clones. The original ORMV clone (confirmed by re-sequencing) differs at the three positions , which we reconstructed from each of the two green and three red leaf samples of grapevine cv. Pinot noir (Grapevine yellow speckle viroid 1 (GYSVd-1) reconstructed from the two green leaf samples is most closely related to the GYSVd-1 isolate from Germany , while GYSVd-1 reconstructed from the three red leaf samples to the GYSVd-1 isolate from Japan . The genome sequence of grapevine geminivirus (GVGV) reconstructed from the red leaves was deposited to the Genbank as KF137562.The analysis of siRNAs and complete genome contigs revealed that the infectious DNA-B clone of CaLCuV differs from its reference sequence U65530.2 by a single nucleotide deletion at the last position of the reference (making the genome 1 nt shorter), the infectious clone of CaMV differs from its reference sequence V00140 by two substitutions (C6175A and T6281C), while the original non-infectious ORMV clone differs from its reference sequence , CaLCuV-infected Arabidopsis (Table S1B), ORMV-infected Arabidopsis (Table S1C), and healthy-looking green and red blotch disease-infected leaves of grapevine cv. Pinot noir plants (Table S1D).Counts of viral and endogenous sRNAs in the sRNA deep-sequencing libraries from mock-inoculated and CaMV-infected (XLSX)Click here for additional data file.Dataset S2Arabidopsis plants and of 20\u201325 nt viral (GVGV) and viroid siRNAs from red blotch disease-infected red leaves (BPO-105) and healthy-looking green leaves (BPO-104) of grapevine cv. Pinot noir plants. The numbering of nucleotide positions are according to the NCBI Genbank reverence sequences of CaMV , CaLCV DNA-A (U65529.2), CaLCuV DNA-B , ORMV (KF137561), GVGV (KF137562), HSVd (KF137565), GYSVd1_green (KF137564) and GYSVd1_red (KF137563). Note that the positions of 5\u2032-terminal nucleotide of sense sRNAs and 3\u2032-terminal nucleotide of antisense sRNAs along the reference sequence are given, and the read counts are given for each sRNA of 20-, 21-, 22-, 23-, 24- and 25-nt classes mapped to the forward strand and the reverse strand with zero mismatches, along with the total counts of 20\u201325 nt sRNAs mapped on the forward and reverse strands and on both strands . The last column contains the total number of 20\u201325 nt sRNA mapped to the reference sequence with up to two mismatches.MISIS-generated, single-base resolution maps of 20\u201325 nt viral siRNAs from CaMV -, CaLCuV (BPO-57)- and ORMV - infected (XLSX)Click here for additional data file.Dataset S3Table S3A: SNPs at positions of the mismatches between the reconstructed wild-type ORMV genome and the original ORMV genome clone as well as SNPs in the wild type ORMV viral quasispecies; Table S3B: SNPs in CaMV; Table S3C: SNPs in CaLCuV DNA-A; Table S3D: SNPs in CaLCuV DNA-B; Table S3E: SNPs at the positions of the mismatches between the GVGV-Oregon and the GVGV-New York genomes as well as other SNPs in the GVGV-Oregon quasispecies; Table S3F: SNPs in the GYSVd-1 (red) and green) quasispecies; Table S3G: SNPs in the GYSVd-1 (green) quasispecies; Table S3H: SNPs in the HSVd quasispecies.SNPs in viral and viroid quasispecies. (XLSX)Click here for additional data file.Dataset S4Arabidopsis. Coverage (in %) of the viral genome sequences with the siRNA contigs is calculated for single k-mer values and combination thereof.Analysis of the contigs generated by Velvet and Oases using non-redundant 20\u201325 nt sRNA libraries from CaMV (BPO-20 and BPO-21)-, CaLCuV (BPO-57)- and ORMV (BPO38 and BPO44)-infected (XLSX)Click here for additional data file."} +{"text": "Research on tumor-induced lymphangiogenesis has predominantly focused on alterations and abnormal growth of peritumoral and intratumoral lymphatic vessels. However, recent evidence indicates that lymphangiogenesis of sentinel lymph nodes might also contribute to cancer progression. In clinical oncology, the sentinel lymph nodes play an important role in diagnosis, staging and management of disease. The prognostic value that may be placed in the analysis of various parameters in tumor-free lymph nodes is still under debate. We, therefore, chose to investigate genetically fluorescent MDA-MB-435/green fluorescent protein human cancer cells transfected to overexpress VEGF-C in a nude mouse model and investigated metastasis, lymph node lymphangiogenesis, lymph node angiogenesis and size of sentinel lymph nodes. The nature of MDA-MB-435, identified as a breast cancer cell line for several decades, has recently been reidentified as being from melanoma origin. Vascular endothelial growth factor-C overexpression induced early metastasis and significantly increased the lymphatic vessel area in sentinel lymph nodes even before the tumor metastasis. At early time-points, expansion of the lymphatic network was observed even though no difference of blood vessel area and lymph node size was detected. These results suggest that primary tumors -via secretion of VEGF-C- can induce hyperplasia of the sentinel lymph node lymphatic vessel network and thereby promote their further spread. In cases of tumor-free lymph nodes the increased lymphatic network of sentinel lymph nodes is a very early premetastatic sign and may provide a new prognostic indicator and target for aggressive diseases. Tumor-induced lymphangiogenesis has primarily been investigated concentrating on peritumoral and intratumoral lymphatic vessels at primary sites. Studies in animal tumor models have shown that lymphatic vessels promote the metastatic spread of tumors \u20133, and tPreviously, were able to show that lymphangiogenesis of sentinel lymph nodes might also play a role in cancer progression. VEGF-A and VEGF-C expressing skin tumors maintained their lymphangiogenic activity after metastasizing to the sentinel lymph node and even induced sentinel lymph node (LN) lymphangiogenesis before the tumor has metastasized ,11. LN-lIn clinical oncology, the sentinel lymph nodes play an important role in diagnosis, staging and management of disease. Especially in breast cancer and melanoma the involvement of regional lymph nodes is an excellent prognostic indicator. But about two thirds of the invasive cancers have no regional lymph node involvement and of those another third will recur ,14. StudLymph nodes constitute a critical crossroad between drained proteins, antigen-presenting cells, lymphocytes and even tumor cells. Also in the absence of tumor metastasis draining lymph nodes can undergo hyperplasia in number and size , becauseTo investigate the earliest changes of the sentinel lymph nodes we injected genetically modified fluorescent MDA-MB-435/green fluorescent protein human melanoma cancer cells transfected to overexpress VEGF-C or control vector in nude mice. The MDA-MB-435 cell line, which has been reclassified from breast to melanoma, has been derived from the M14 melanoma cell line ,22. In t\u03bcg/ml zeocin and 400 \u03bcg/ml geneticin. All animal studies were approved by the Massachusetts General Hospital Subcommittee on Research Animal Care.As tumor cells we used a previously published cell line . The MDA6 cells/100 \u03bcl serum-free culture medium). Two mice of each group (VEGF-C transfected MDA-MB-435 and control vector transfected MDA-MB-435) were sacrificed every two weeks until week ten. The two sentinel lymph nodes and the superficial inguinal lymph nodes were removed from each mouse and paraffin embedded , CD31 , Prox-1 , F4/80 and corresponding secondary antibodies labeled with Alexa Fluor 488 or 594 . Cell nuclei were counterstained with Hoechst-bisbenzimide (Sigma-Aldrich). Specimens were examined by using a Nikon E-600 microscope and images captured with a SPOT digital camera . At autopsy, all axillary and inguinal lymph nodes were examined for the presence of metastases. In addition, we determined the presence of metastases by fluorescence microscopic analysis and H&E staining for each lymph node.Representative H&E stained slides of the inguinal and axillary lymph nodes, obtained from the two groups (n=10 for each group) and 4 controls, were analyzed for the highest diameter, sections were examined by a Nikon E-600 microscope (Nikon) and images captured with a SPOT digital camera (Diagnostic Instruments). Further sections were stained with lymphatic and blood vessel markers (LYVE-1/CD31) to examine the lymphatic and blood vessel network. Images were captured with a Spot digital camera (Diagnostic Instruments). Computer-assisted morphometric analyses of the lymph node size, lymphatic network (lymphatic plus medullary sinuses) and blood vessel area were performed using the IP-LAB software . Statistical analyses were performed using the two-sided, unpaired Student\u2019s t-test.For distinguishing lymphatic endothelium from blood vessel endothelium in lymph nodes for computer-assisted evaluation we identified the lymphatic endothelial cell expression profile. We investigated the expression of known lymphatic markers, using antibodies against Lyve-1, Prox-1 and PECAM-1 reviewe. The lymLymphatic sinuses of the cortical and paracortical zone are indicated by the asterisk . Interesin vivo did not lose their GFP vector every section was in addition evaluated by an H&E stain (To investigate the effect of VEGF-C on tumor growth and sentinel lymph node size we used the previously published human cell line MDA-MB-435 transfected with human VEGF-C . We exam&E stain . Metasta*p<0.05). We further observed no evidence of an increased blood vessel area in percent of the lymph node in mice carrying VEGF-C overexpressing tumors versus control tumors .To investigate the effect of VEGF-C on the draining sentinel lymph node we determined differences of the lymphatic vessel area between the VEGF-C transfected and the control cell line. We evaluated the effect only on lymph nodes without presence of metastatic cells until week 4, an observation point with no visible and statistical difference in general tumor and lympl tumors . Double-l tumors . In lympl tumors . These cl tumors drained l tumors . The numl tumors . VEGFR-3Lymph nodes are the primary site of immune response and are a critical crossroad, since tumor cells, inflammatory and stroma cells could migrate towards and into them. Although morphological changes of lymph nodes involved and uninvolved in metastasis have been studied in various types of cancers, the prognostic significance of immune response and lymph node size of tumor-free sentinel lymph nodes of breast carcinoma patients is unclear \u201317,31\u201337et al recently observed this in VEGF-C overexpressing skin tumors (et al(Based on this observation it could be hypothesized that LN-lymphangiogenesis facilitates tumor cell metastasis, an early event of distant organ metastasis. Hirakawa n tumors , but thers (et al. It has rs (et al. The finrs (et al. Althougrs (et al. Especiars (et al\u201345. In ors (et al. We deters (et al,46. We fImportantly, our study reveals that the lymphatic network of sentinel lymph nodes should be specifically evaluated by using specific lymphatic endothelial markers. In agreement with the previously published finding by Hattori , we recoOur findings provide additional data to the previously proposed \u2018seed and soil hypothesis\u2019 , inasmucEarly changes of the lymphatic sinuses and lymphangiogenesis might predict an unfavorable outcome of an individual carcinoma patient. The lymphatic sinus network of sentinel lymph nodes could even be an important target for future therapies."} +{"text": "A direct pharmacological stimulation of soluble guanylate cyclase (sGC) is an emerging therapeutic approach to the management of various cardiopulmonary disorders associated with endothelial dysfunction. Novel sGC stimulators, including riociguat (BAY 63-2521), have a dual mode of action: they sensitize sGC to endogenously produced nitric oxide (NO) and also directly stimulate sGC independently of NO. Little is known about their effects on tissue remodelling and degeneration and survival in experimental malignant hypertension.Mortality, hemodynamics and biomarkers of tissue remodelling and degeneration were assessed in Dahl salt-sensitive rats maintained on a high salt diet and treated with riociguat (3 or 10 mg/kg daily) for 14 weeks. Riociguat markedly attenuated systemic hypertension, improved systolic heart function and increased survival . Histological examination of the heart and kidneys revealed that riociguat significantly ameliorated fibrotic tissue remodelling and degeneration. Correspondingly, mRNA expression of the pro-fibrotic biomarkers osteopontin (OPN), tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) and plasminogen activator inhibitor-1 (PAI-1) in the myocardium and the renal cortex was attenuated by riociguat. In addition, riociguat reduced plasma and urinary levels of OPN, TIMP-1, and PAI-1.Stimulation of sGC by riociguat markedly improves survival and attenuates systemic hypertension and systolic dysfunction, as well as fibrotic tissue remodelling in the myocardium and the renal cortex in a rodent model of pressure and volume overload. These findings suggest a therapeutic potential of sGC stimulators in providing organ protection in diseases associated with impaired cardiovascular and renal functions."} +{"text": "To investigate the association between oral health literacy (OHL) and oral health-related quality of life (OHRQoL) and explore the racial differences therein among a low-income community-based group of female WIC participants.rho and zero-inflated negative binomial modeling.Participants enrolled in the Carolina Oral Health Literacy (COHL) study completed the short form of the Oral Health Impact Profile Index and REALD-30 (a word recognition literacy test). Socio-demographic and self-reported dental attendance data were collected via structured interviews. Severity (cumulative OHIP-14 score) and extent of impact (number of items reported fairly/very often) scores were calculated as measures of OHRQoL. OHL was assessed by the cumulative REALD-30 score. The association of OHL with OHRQoL was examined using descriptive and visual methods, and was quantified using Spearman's rho = -0.14 ; extent rho = -0.14 ; severity rho = -0.10 . \"Low\" OHL (defined as < 13 REALD-30 score) was associated with worse OHRQoL, with increases in the prevalence of OHIP-14 impacts ranging from 11% for severity to 34% for extent. The inverse association of OHL with OHIP-14 impacts persisted in multivariate analysis: Problem Rate Ratio (PRR) = 0.91 for one SD change in OHL. Stratification by race revealed effect-measure modification: Whites--PRR = 1.01 ; AA--PRR = 0.86 .The study group included a substantial number of African Americans (AA = 41%) and American Indians (AI = 20%). The sample majority had a high school education or less and a mean age of 26.6 years. One-third of the participants reported at least one oral health impact. The OHIP-14 mean severity and extent scores were 10.6 and 1.35 , respectively. OHL scores were distributed normally with mean REALD-30 of 15.8 (5.3). OHL was weakly associated with OHRQoL: prevalence Although the inverse association between OHL and OHRQoL across the entire sample was weak, subjects in the \"low\" OHL group reported significantly more OHRQoL impacts versus those with higher literacy. Our findings indicate that the association between OHL and OHRQoL may be modified by race. Oral Health in America underscores and emphasizes the importance of OHRQoL, and its improvement on a population-level is defined as a goal , whereas (using race-specific estimates from Table Considering the high versus those with higher literacy. Within the limitations of our study among low-income female caregivers, our findings indicate that the association between OHL and OHRQoL appears to be modified by race.We found a high prevalence of perceived oral health impacts in this sample of low-income female WIC participants. Although the inverse association between OHL and OHRQoL across the entire sample was weak, subjects in the \"low\" OHL group reported significantly more OHRQoL impacts The authors declare that they have no competing interests.KD conducted the data analysis and prepared the first draft of the manuscript. JL conceived the study, overviewed the data analysis, contributed to the interpretation of results and assisted in preparation of the first draft of the manuscript. ADB participated in data collection, and critically revised the manuscript. WFV contributed to the interpretation of results and critically revised the manuscript. All authors read and approved the final manuscript."} +{"text": "FIGLA gene and its regulation during early embryogenesis. Bovine FIGLA mRNA expression is restricted to gonads and is detected in fetal ovaries harvested as early as 90 days of gestation. FIGLA mRNA and protein are abundant in germinal vesicle and metaphase II stage oocytes, as well as in embryos from pronuclear to eight-cell stage but barely detectable at morula and blastocyst stages, suggesting that FIGLA might be a maternal effect gene. Recent studies in zebrafish and mice have highlighted the importance of non-coding small RNAs (microRNAs) as key regulatory molecules targeting maternal mRNAs for degradation during embryonic development. We hypothesized that FIGLA, as a maternal transcript, is regulated by microRNAs during early embryogenesis. Computational predictions identified a potential microRNA recognition element (MRE) for miR-212 in the 3\u2019 UTR of the bovine FIGLA mRNA. Bovine miR-212 is expressed in oocytes and tends to increase in four-cell and eight-cell stage embryos followed by a decline at morula and blastocyst stages. Transient transfection and reporter assays revealed that miR-212 represses the expression of FIGLA in a MRE dependent manner. In addition, ectopic expression of miR-212 mimic in bovine early embryos dramatically reduced the expression of FIGLA protein. Collectively, our results demonstrate that FIGLA is temporally regulated during bovine early embryogenesis and miR-212 is an important negative regulator of FIGLA during the maternal to zygotic transition in bovine embryos.Factor in the germline alpha (FIGLA) is an oocyte-specific basic helix-loop-helix transcription factor essential for primordial follicle formation and expression of many genes required for folliculogenesis, fertilization and early embryonic survival. Here we report the characterization of bovine During oocyte growth and follicular development, oocytes accumulate maternal effect factors necessary for oocyte maturation, fertilization and early embryogenesis . IdentifZp1, Zp2 and Zp3) that form the extracellular matrix that surrounds growing oocytes, ovulated eggs and pre-implantation embryos . Si. SiXenop targets \u201349. As s targets . StudiesmiR-212 and miR-132 are evolutionary conserved tandem miRNAs, well known for their essential role in the development, maturation and function of neurons . DeregulCollectively, our results provide novel information regarding the temporal expression of FIGLA during bovine oocyte maturation and early embryonic development. We also provide several lines of evidence to support a new role for miR-212 as a bona fide negative regulator of FIGLA during early embryogenesis. First, the expression of miR-212 is inversely correlated to the expression of FIGLA during bovine early embryonic development. Second, miR-212 represses the expression of bovine FIGLA protein in HeLa cells. Third, miR-212 suppresses the activity of a luciferase reporter fused with the 3`UTR of FIGLA in a MRE dependent manner, and finally, ectopic expression of miR-212 mimic in bovine early embryos significantly represses FIGLA protein expression. Our report is the first to identify a miRNA that directly regulates FIGLA and display a novel potential role for miR-212 during early embryogenesis.Figure S1Cloning of bovine FLGLA cDNA.(A) Schematic illustration of two isoforms of bovine FIGLA mRNA. Isoform 2 results from alternative splicing of exon 4. (B) Confirmation of two isoforms by RT-PCR analysis. PCR was performed using primers flanking exon 4 and PCR products were separated by 3% agarose gel electrophoresis.(DOC)Click here for additional data file.Figure S2Multiple alignment of deduced amino acid sequences of bovine (bFIGLA-1 and bFILGA-2), human (hFIGLA) and mouse (mFIGLA) FIGLA proteins by ClustalW analysis.The conserved helix-loop helix domain is boxed.(DOCX)Click here for additional data file.Table S1List of primers used in the study.(XLSX)Click here for additional data file.Table S2FIGLA gene.Genomic organization of bovine (XLSX)Click here for additional data file."} +{"text": "T-tube placement following bile duct exploration remains commonplace.Iohexol contrast media is injected with pressure through the cutaneous opening of the T-tube sinus tract. Post-contrast imaging helps to identify the location of T-tube tract . Using xThe technique of drainage tube reinsertion using x-ray fluoroscopy is a safe and effective method for restoring the patency of a T-tube sinus tract and may avoid reoperation or ERCP."} +{"text": "Prophylactic vaccine strategies against HIV-1 must effectively prevent virus transmission, infection and cell-to-cell spread during the earliest stages of acute infection. Since the genital mucosa is the primary site of entry, mucosal defense is critical for early control of infection. Recent identification of transmitted/founder (T/F) HIV-1 genomes has demonstrated a consistent genetic bottleneck during mucosal transmission and suggests that T/F viruses may exhibit distinct phenotypes. HIV-1 Env gp41-specific responses are among the first to be generated in natural HIV infection.Previously, we developed chimeric virus-like particle (VLP) immunogens that elicit potent systemic and mucosal antibodies against two highly conserved regions of gp41, by employing an optimized immunization strategy. The ELDKWA and QARVLAVERY epitopes are found with the membrane proximal external region (MPER) and the coiled coil region of gp41, respectively. Importantly, the epitope-specific IgG and IgA fractions derived from immunized mice were shown to be effective in neutralizing and preventing transcytosis of HIV in vitro. In particular, the QARVLAVERY epitope is remarkably conserved and induced unusually high and early levels of anti-QARV IgA, making it an attractive candidate for generation of broadly reactive mucosal antibodies.In this study, we assessed the effectiveness of mucosal and systemic mouse antibodies elicited against these gp41 epitopes to inhibit T/F Env function. For this, we employed recombinant infectious molecular clones (Env-IMC) of HIV-1 that encode mucosally transmitted/founder env genes. Our results show that the gp41-specific IgG and IgA fractions effectively prevented the infection of TZM-bl cells and inhibited HIV transcytosis in an assay measuring the passage of infectious virus across an epithelial monolayer. Interestingly, the T/F Env-IMC tested were more sensitive to the antibodies than the R5 lab-adapted strains included as controls.These results highlight the potential of gp41-based immunogens to impart effective mucosal protection in the earliest stages of HIV transmission and infection."} +{"text": "Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species. Recent advances in high-throughput sequencing (HTS) technologies have allowed research groups to produce unprecedented amounts of genomics data that have been of great use in exploring the genetic variability among and within any kind of species and in determining the genetic causes of phenotypic variation. These technologies have been successfully applied to make significant discoveries in highly dissimilar research fields such as human genetics , cancer Supplementary Figure S1). Several algorithms and software tools have been recently developed to resolve the different steps of this pipeline ; the Agentschap voor Innovatie door Wetenschap en Technologie (IWT) Flanders ; the European Commission (EC) 7th Framework program (NEMO project) (to J.M.T.); the Katholieke Universiteit Leuven (KU Leuven) Industrieel Onderzoeksfonds (IOF) Knowledge platform IKP/10/002 [ZKC1836 to J.M.T.], Bijzonder Onderzoeksfonds (BOF) Program financing (project NATAR) (to J.M.T.); the European Research Council (ERC) [Young Investigator grant 241426 to K.J.V.]; the Vlaams Instituut voor Biotechnologie (VIB); the Fonds Wetenschappelijk Onderzoek (FWO) Vlaanderen (to K.J.V.); the Odysseus program (to K.J.V.); and the European Molecular Biology Organization (EMBO) International Youth Initiative Program (YIP) (to K.J.V.). Funding for open access charge: International Center for Tropical Agriculture (CIAT) Core Funding.Conflict of interest statement. None declared."} +{"text": "Several evidences have suggested the potential therapeutic value of cannabinoids (CBs) in the treatment of MS and their experimental models. However, the effects of endocannabinoids on VCAM-1 regulation are poorly understood. In the present study we investigated the effects of anandamide (AEA) in the regulation of VCAM-1 expression induced by Theiler's virus (TMEV) infection of brain endothelial cells using in vitro: VCAM-1 was measured by ELISA in supernatants of brain endothelial cells infected with TMEV and subjected to AEA and/or cannabinoid receptors antagonist treatment. To evaluate the functional effect of VCAM-1 modulation we developed a blood brain barrier model based on a system of astrocytes and brain endothelial cells co-culture. ii) in vivo: CB1 receptor deficient mice (Cnr1-/-) infected with TMEV were treated with the AEA uptake inhibitor UCM-707 for three days. VCAM-1 expression and microglial reactivity were evaluated by immunohistochemistry.i) 1 receptors. The study of leukocyte transmigration confirmed the functional relevance of VCAM-1 inhibition by AEA. In vivo approaches also showed that the inhibition of AEA uptake reduced the expression of brain VCAM-1 in response to TMEV infection. Although a decreased expression of VCAM-1 by UCM-707 was observed in both, wild type and CB1 receptor deficient mice (Cnr1-/-), the magnitude of VCAM-1 inhibition was significantly higher in the wild type mice. Interestingly, Cnr1-/- mice showed enhanced microglial reactivity and VCAM-1 expression following TMEV infection, indicating that the lack of CB1 receptor exacerbated neuroinflammation.Anandamide-induced inhibition of VCAM-1 expression in brain endothelial cell cultures was mediated by activation of CB1 receptor dependent VCAM-1 inhibition is a novel mechanism for AEA-reduced leukocyte transmigration and contribute to a better understanding of the mechanisms underlying the beneficial role of endocannabinoid system in the Theiler's virus model of MS.Our results suggest that CB Vascular cell adhesion molecule-1 (VCAM-1), an endothelial receptor belonging to the immunoglobulin superfamily is a key player in leukocyte extravasation in multiple sclerosis (MS) . High lThe endocannabinoid system (ECS), consists of endogenous ligands (AEA and 2-AG) and congeners, target receptors, synthesis , and degradation enzymes and proteins involved in their transport, and intracellular trafficking . Increas1 receptor (Cnr1) gene, susceptible to TMEV-IDD development, gently gifted by Dr. Baker (University College London). Mice were maintained on food and water ad libitum in a 12 hours dark-light cycle. Four-to six week-old mice were inoculated intracerebrally in the right cerebral hemisphere with 106 plaque forming units (PFU) of Daniel's (DA) TMEV strain, in 30 \u03bcl of Dulbecco's modified Eagle's medium supplemented with 10% of fetal calf serum (FCS) as previously described . Activa pathway and in aeceptors .1 receptor leads to an exacerbation of microglial response to TMEV infection in the ipsilateral hemisphere. Thus, microglial activation was observed from prefrontal cortex to hippocampal levels instead of maintaining it exclusively in the area close to the injection site. Currently, we unknown the meaning of the extensive microglial activation in Cnr1-/- mice, but it is likely to be associated with the facilitation of spreading viral antigens as microglia/macrophages are an important virus reservoir [1 receptors previous studies have reported that CB1-knockout mice develop more severe CREAE [Cnr1 gene could represent a genetic risk factor for both the primary progressive [An important finding of the present study is that the lack of CBeservoir . In linere CREAE ,62. Moregressive and relagressive .1 receptors. More relevant is that the inhibitor of anandamide uptake, UCM-707 reduced VCAM expression in TMEV infected mice with the participation of CB1 receptors. Available data from MS patients subjected to success natalizumab therapy showed downregulation of sVCAM-1 which is considered a good biomarker of endothelial activity [In summary, mechanisms underlying the decreased cellular infiltration on the CNS by CBs in animal models of MS are not yet clear but the present study showed that anandamide was effective in reducing endothelial VCAM-1 expression and BBB permeability via CB2-AG: 2-Arachidonoylglycerol; AEA: N-arachidonoylethanolamine or anandamide; BBB: blood brain barrier; CBs: cannabinoids; CNS: central nervous system; CREAE: chronic experimental autoimmune encephalomyelitis; DAG lipase: Diacylglycerol lipase; EAE: experimental autoimmune encephalomyelitis; ECS: endocannabinoid system; FAAH: Fatty acid amide hydrolase; FBS: Fetal bovine serum; FCS: Fetal calf serum; MAGL: monoacylglycerol lipase: MS: multiple sclerosis; NAPE-PLD: N-acyl phosphatidylethanolamine phospholipase D; NGS: normal goat serum; PFU: plaque forming units; PPARs: peroxisome proliferator-activating receptors; RT: room temperature; SR1: SR141716A; TMEV: Theiler's murine encephalomyelitis virus; TMEV-IDD: TMEV-induced demyelinating disease; TRPV1: transient receptor potential cation channel: subfamily V: member 1; VCAM-1: vascular cell adhesion molecule-1; VLA-4: very late antigen-4.The authors declare that they have no competing interests.in vitro experiments. JB participated in the design of the study, in the statistical analysis and revising manuscript draft. CG conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.LM performed the majority of all experiments, participated in the design of the study, participated in the statistical analysis and drafted the manuscript. PMI participated in the adhesion experiments and revising manuscript draft. MM helped to immunohistochemistry studies and participated in the interpretation of data and revising manuscript draft. FC, FL and FD participated in the design of the study, interpretation of data and revision of manuscript draft. MH helped to performed in vitro BBB model performance and experimental designSchematic drawing of the . Schematic drawing of the BBB model, experimental design and confirmation of BBB characteristic by Evan's blue permeability assay and Zonula occludens 1 immunocytochemistry.Click here for filein vitro BBB model performance and experimental designSchematic drawing of the . Schematic drawing of the BBB model, experimental design and confirmation of BBB characteristic by Evan's blue permeability assay and Zonula occludens 1 immunocytochemistry.Click here for file"} +{"text": "MSH1 (MutS 1 homolog), lending itself to detailed study of de novo mitochondrial genome activity. In the present study, we investigated the underlying basis for unusual plant features as they contribute to rapid mitochondrial genome evolution.The mitochondrial genome of higher plants is unusually dynamic, with recombination and nonhomologous end-joining (NHEJ) activities producing variability in size and organization. Plant mitochondrial DNA also generally displays much lower nucleotide substitution rates than mammalian or yeast systems. Arabidopsis displays these features and expedites characterization of the mitochondrial recombination surveillance gene msh1 mutants on the basis of data generated by Illumina deep sequencing and confirmed by DNA gel blot analysis. On a larger scale, with mitochondrial comparisons across 72 Arabidopsis ecotypes, similar evidence of DSB repair activity differentiated ecotypes. Forty-seven repeat pairs were active in DNA exchange in the msh1 mutant. Recombination sites showed asymmetrical DNA exchange within lengths of 50- to 556-bp sharing sequence identity as low as 85%. De novo asymmetrical recombination involved heteroduplex formation, gene conversion and mismatch repair activities. Substoichiometric shifting by asymmetrical exchange created the appearance of rapid sequence gain and loss in association with particular repeat classes.We obtained evidence of double-strand break (DSB) repair, including NHEJ, sequence deletions and mitochondrial asymmetric recombination activity in Arabidopsis wild-type and Extensive mitochondrial genomic variation within a single plant species derives largely from DSB activity and its repair. Observed gene conversion and mismatch repair activity contribute to the low nucleotide substitution rates seen in these genomes. On a phenotypic level, these patterns of rearrangement likely contribute to the reproductive versatility of higher plants. While producing a circular genetic map, plant mitochondrial chromosomes comprise a heterogeneous population of highly branched, circularly permuted linear molecules ,2. In plde novo events. Mitochondrial DNA replication in plants is not well-detailed, but both rolling circle and recombination-mediated replication have been suggested , and intermediate repeats are annotated. Generated raw sequence data are available from the sequence read archive [GenBank:SRA039856].Illumina Solexa Sequencing Technology paired-end reads of Col-0 were assembled using the comparative assembler AMOScmp version 2.08 software program (with default parameters) with theameters) and SHORameters) to obtaiameters) . The annmsh1 was about 600\u00d7{and for advanced-generation msh1 it was about 200\u00d7. Reads of the Illumina Solexa Sequencing Technology paired-end sequencing for first- and advanced-generation msh1 (Col-0) mutants were mapped to the mitochondrial genome of Col-0 using Velvet software [msh1 lines were selected, and putative repeats were identified by BLAST analysis [msh1 lines and DNA gel blot data, we determined the putative direction of strand invasion around the repeats. For nucleotide sequence analysis of the intermediate repeats in the msh1 mutants, we used a custom-made script to derive the consensus sequence.The Illumina Genome Analyzer was used with paired-end reads of 36 bp, a mean library length of 220 and a standard deviation of about 20. This length spanned approximately half of the repeats in the mitochondrial genome. Coverage for first-generation software and SHORsoftware , and recanalysis of the shttp://www.1001genomes.org/). Aligned sequence data against the C24 mitochondrial genome with SHOREmap version 0.5 software [http://code.google.com/apis/maps/documentation/staticmaps/). Deletions were identified by analyzing the coverage data, and recombination polymorphisms were identified by grouping paired-end reads whose ends map to regions separated by more than 1,000 bp with a custom-made script. Data for the 80 ecotypes are available at \"1001 Genomes: A Catalog of Arabidopsis thaliana Genetic Variation: MPICao2010: 80 Arabidopsis thaliana accessions\" (http://www.1001genomes.org/projects/MPICao2010/index.html) [Illumina Solexa Sequencing Technology paired-end sequence data for 80 ecotypes was produced by the Weigel laboratory at the Max Planck Institute for Developmental Biology .bp: base pair; kb: kilobase; Mbp: megabase pair; PCR: polymerase chain reaction; SNP: single-nucleotide polymorphism.The authors declare that they have no competing interests.msh1, Col-0, Ler, and C24. JC, JH and DW generated total genomic sequence from 72 Arabidopsis ecotypes. SAM designed and coordinated the study, participated in data analysis and prepared the manuscript. All authors read and approved the final manuscript.JID participated in computational analysis, genome assembly, literature screening and manuscript preparation. MAM carried out PCR and gel blot hybridization analyses and genome mapping. YW, VS and YZX participated in mitochondrial genome sequencing experiments in msh1 first- and advanced-generation mutants reveal recombination differencesFigure S1. Clusters of recombinant paired ends in wild-type and . x- and y- axes represent the coordinates of the first part and second part, respectively, of the paired-end read. The radius of the circle represents the number of reads that cluster around such coordinates. The graphs correspond to wild-type (a), msh1 first-generation (b) and msh1 advanced-generation lines (c). Small-radius circles in the wild-type lines were taken as background and subtracted from the graphs of the mutants. Increased levels of recombination are observed across generations of the mutant. The red circle represents a structural feature present in wild types and mutants at the same level used as controls.Click here for filemsh1 mutants across generationsFigure S2. Fate of genomic environments around repeats in . y-axis represents the percentage changes in coverage across each copy of the repeat with respect to wild type. The pink and red squares represent the recombinant forms gained in msh1 first- and advanced-generation lines. The turquoise and blue triangles represent the parental forms lost in msh1 first and advanced generations. These were calculated as the difference in coverage of right versus left flanking regions of each repeat relative to wild type. A gradient, as well as a correspondence, between gain of recombinant and loss of parental forms is observed across generations.Click here for filemsh1 mutantTable S1. Changes in coverage and putative strand invasion polarity for intermediate repeats in the . Coverage data are shown for first- and advanced-generation mutants. The data show changes in coverage with respect to Col-0 for regions flanking each repeat, along with deduced order of strand invasion (strand polarity). Confirmation by gel blot analysis is indicated for several sites.Click here for fileFigure S3. Potential outcomes of double-strand break repair during break-induced replication. With the occurrence of a double-strand break (DSB) during replication, 5' to 3' strand recession occurs, followed by strand invasion to a homologous duplex for reestablishment of the replication fork. (1) Occurrences of the DSBs at a unique region. (2) When the DSB occurs at a repeated region, two outcomes are possible: (a) strand invasion at homologous repeats or (b) strand invasion across different copies of the repeat to produce a new genomic environment as the recombinant MSH1 prevents DNA exchange beyond the region of sequence homology within the repeated sequence.Click here for fileTable S2. Primers used in the study.Click here for file"} +{"text": "Rosiglitazone is a thiazolidinedione derivative oral hypoglycemic agent active in both diabetic animal models and type 2 diabetic patients. Rosiglitazone is a high affinity ligand for the peroxisome proliferator-activated receptor gamma, which is responsible for the insulin-sensitizing action of the compound. Recent large clinical trials found an association between the antidiabetic drug rosiglitazone therapy and increased risk of cardiovascular adverse events.The aim of this report is to elucidate the cardiac electrophysiological properties of rosiglitazone on control and diabetic murine ventricular papillary muscles using conventional microelectrode technique.90) and increased the AP amplitude (APA) in a concentration-dependent manner. Moreover, rosiglitazone reduced the maximum velocity of depolarization (Vmax). In diabetic animals we detected very similar effects.In control histidine-decarboxylase knock-out mice (HDC-KO) as well as in their wild-types (WT) rosiglitazone (1\u201330 \u03bcM) shortened AP duration at the 90% level of repolarization (APDThe action potential changes caused by rosiglitazone probably can be explained by ion channel effects. The observed alterations may carry a serious proarrhythmic risk in case of overdose intoxication with rosiglitazone, especially in patients having multiple cardiovascular risk factors, like elderly diabetic patients."} +{"text": "Assessment of regional and global left ventricular (LV) function and strain are important in the setting of prior myocardial infarction (MI). Feature tracking (FT-MRI) is a novel cardiac MRI method for assessment of myocardial strain, similar to speckle tracking in 2-D echocardiography, which provides multi-planar strain data without the need for tagged images.The goal of our study was to characterize LV global and regional strains in patients with prior MI using FT-MRI and determine the relationship of strains to infarct size, location and LV ejection fraction (EF).Eighty patients with history of past MI were grouped by MI coronary territory {left anterior descending (LAD), left circumflex (LCX), right coronary (RCA)}. Scar quantification was done by computer-assisted planimetry (Medis Qmass v7.2) of gadolinium enhanced delayed images and MI percentage was determined. Global and regional circumferential subendocardial (Ecc Endo) and subepicardial (Ecc Epi) and longitudinal (Ell) strains were derived from three long axis and three short axis steady state free procession cine planes. Semi-automated tracing of endocardial and epicardial borders using FT-MRI was performed and strains were mapped to a 17 segment AHA model. Repeated measures ANOVA was used to compare normal strain values from 60 healthy subjects to MI patients controlling for scar percentage.The mean age was 64.412) years and mean EF was 42.1%(11). Peak global Ecc Epi and Ecc Endo were decreased in all MI patients, except in Ecc endo LCx infarcts, compared to normals (Table 2 years aFT-MRI permits detailed assessment of global and regional strains in patients with MI. Global Ecc was decreased in all MI patients, while Ell was preserved in the majority on infarcts except LAD infarcts. The best predictor of reduced LV EF was reduced global Ecc Endo strain, which was superior to infarct size."} +{"text": "Recruiting patients to palliative care randomised controlled trials (RCTs) is particularly challenging. This paper describes and analyses the differing recruitment trajectories for patients with advanced malignant and non-malignant disease to a palliative care RCT, outlining activities undertaken to achieve targets. It will outline the lessons learned in order to inform design and conduct of future studies.Analysis of descriptive recruitment statistics to a Phase II pilot pragmatic single-blind fast track RCT, and subsequent Phase III RCT, of a breathlessness intervention service for advanced disease. Phase II piloted with chronic obstructive pulmonary disease (COPD) patients only, whereas the Phase III RCT incorporated two sub-protocols: one for patients with malignant and one for non-malignant disease. Documentary analysis of: recruitment activity log, Trial Management and Advisory Group minutes and field notes.Recruitment targets for patients with non-malignant disease were achieved. The pathway to recruitment was through referral to the service therefore referral rates impacted on recruitment alongside response rates. Recruitment of cancer patients was considerably slower despite concerted efforts to increase referrals by raising the service profile. Referrals only improved for the latter when a researcher attended clinics, supporting clinical staff in patient identification: recruitment tripled from 0.8 to 2.4 patients per month. Three possible reasons for the effectiveness of this are (1) dedicated time, (2) reciprocity & (3) established relationships. Predictably, response rates remained lower for patients with malignant disease than for those with non-malignant disease.Recruitment was partly referral-driven, therefore gate-keeping did not explain the differences. Clinical inter-professional relationships consolidated in Phases 0-II drove early referrals of non-malignant disease patients. Local palliative care services were available for patients with cancer. Consideration of the natural history and context of a service is therefore important when predicting recruitment. Pilot trials are informative, but should include qualitative elements and all disease groups. Placing researchers in relevant clinical settings is helpful."} +{"text": "HBsAg-positive DLBCL patients treated with RCHOP had a significantly higher OS rate (79.6%) compared with the 41 CHOP-treated patients . HBsAg-positive DLBCL patients with an earlier median onset age and elevated HBV-DNA during chemotherapy had poorer prognoses. HBsAg and HBV-DNA during chemotherapy may be used as prognostic indicators for patients with DLBCL. Rituximab improves the outcome of HBsAg-positive DLBCL patients when administered in combination with anti-viral lamivudine.The aim of this study was to analyze the clinical features of hepatitis B surface antigen (HBsAg)-positive and negative diffuse large B-cell lymphomas (DLBCLs) and to compare the outcomes and serum hepatitis B virus (HBV)-DNA loads of patients treated with cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP) regimens with rituximab (RCHOP) or without. A total of 451 DLBCL patients, of which 90 were HBsAg-positive and 361 were HBsAg-negative, were retrospectively reviewed. We compared onset age, gender, Ann Arbor stage, international prognostic index (IPI), lactate dehydrogenase (LDH) and \u03b22-microglobulin (\u03b22-M) levels, as well as overall survival (OS) rates and HBV-DNA loads under CHOP or RCHOP regimens. The OS rate of the HBsAg-positive DLBCL patients was significantly lower than that of HBsAg-negative DLBCL patients and the HBsAg-positive DLBCL patients had an earlier median onset age. HBsAg-positive DLBCL patients had poorer OS rates compared with HBsAg-negative patients . HBsAg-positive DLBCL patients with HBV-DNA loads >10 Diffuse large B-cell lymphoma (DLBCL) is defined by the World Health Organization (WHO) classification as a heterogeneous entity, encompassing morphologic and genetic variants with variable clinical presentations and outcomes, while constituting the most common type of non-Hodgkin\u2019s lymphoma (NHL) in adults. More than one-third of the world\u2019s population has been infected with the hepatitis B virus (HBV), with the vast majority living in developing regions \u20133. ChinaHBV-carrying DLBCL patients are at a higher risk of reactivating hepatitis B with reactivation rates of 20\u201350% and rela+, which is an antigen expressed in the majority of B lymphocytes, including malignant lymphomatous B cells and normal B lymphocytes. The incorporation of rituximab into standard chemotherapies has been shown to improve the clinical outcomes of CD20+ DLBCL regimen was once the classical frontline treatment for DLBCL; however, the development of monoclonal antibodies has led to further improvement of DLBCL treatment outcomes. Currently, patients with DLBCL are medicated with an additional immunochemotherapy, usually the rituximab plus CHOP (RCHOP) regimen. Rituximab is a chimeric mouse human monoclonal antibody against CD200+ DLBCL ,17. Howe0+ DLBCL ,19. LamiIn this retrospective study, we compared the clinical features of DLBCL patients with or without HBV infections and evaluated the potential prognostic factors in HBsAg-positive DLBCL patients. We also compared the treatment outcomes and HBV reactivation rates of patients who received CHOP or RCHOP regimens.We reviewed 536 consecutive newly diagnosed patients with DLBCL who were hospitalized in the First and Second Affiliated Hospitals of the Medical School of Zhejiang University between January 2006 and April 2011. All diagnoses were confirmed by histopathological staining with hematoxylin and eosin (H&E), as well as determination of the immunophenotypes according to the WHO classification. Complete clinical profiles were obtained from 451 patients who received chemotherapy and completed the follow-up. Clinical staging and diagnostic methods included clinical history and physical examinations, chest, abdominal and pelvic computed tomography (CT) scans, digital full-body color Doppler ultrasound diagnosis, marrow aspirate and biopsy, as well as serum lactate dehydrogenase (LDH) and serum \u03b22-microglobulin (\u03b22-M) level measurements . Enzyme-Routine liver function tests included determinations of alanine aminotransferase (ALT), aspartate aminotransferase (AST), galactosylhydroxylysyl glucosyltransferase (GGT) and bilirubin (direct and indirect forms) levels. These assays were first performed within one week prior to the start of each chemotherapy cycle.3 cps/ml, which is the upper normal limit in the First Affiliated Hospital of Medical School of Zhejiang University, was regarded as an elevated value. The research was approved by the ethics committee of The First Affiliated Hospital of the Medical School of Zhejiang University and informed consent was obtained from all participants.The HBV-DNA loads of all 96 HBsAg-positive patients were determined and an HBV-DNA load >10Of the 451 patients, for economical reasons, 156 patients were treated only with a CHOP regimen and 295 cases were treated with an RCHOP regimen . Lamivudine prophylaxis was prescribed for all HBsAg-positive patients prior to chemotherapy. Once patients presented an abnormal liver function, they were treated with hepatinica and all chemotherapies were restarted only in cases where the liver function had recovered.Following treatment, routine clinical follow-up was conducted every 3 months for the first 2 years and then every 6 months for the additional 3 years. Ultrasound or CT scans were performed every six months during the first two years and then afterwards annually during the follow-up period. The median follow-up time was 27 months .Significant differences in the baseline clinical parameters and treatment characteristics between the HBsAg-positive patients and HBsAg-negative patients were evaluated by either Chi-square test or Fisher\u2019s exact test for categorical parameters. Overall survival (OS) rates and survival curves were calculated by the Kaplan-Meier method. The OS rate calculation was performed from the date of diagnosis to the date of mortality or the last follow-up. The multivariate analysis of outcome in terms of OS was performed by Cox regression, which included the variables that were significant in a univariate analysis. Two-tailed P-values <0.05 were considered to indicate a statistically significant difference. All statistical analyses were performed with the SPSS software for Windows v.19.0 .Of the 451 patients, 90 were HBsAg-positive and 361 were HBsAg-negative. The clinical characteristics of these two groups are summarized in At a median follow-up time of 27 months, we compared the OS rates between HBsAg-positive and HBsAg-negative patients with Kaplan-Meier analyses. HBsAg-negative patients demonstrated a higher OS rate was significantly higher compared with that in the second subgroup , Ann Arbor stages III/IV (P=0.002) and elevated LDH levels (P=0.001) were poor prognostic factors for HBsAg-positive DLBCL patients. A multivariate analysis revealed that positive B symptoms [hazard ratio (HR), 14.434; 95% confidence interval (CI), 3.063\u201368.013; P<0.001), elevated LDH levels and male gender were poor prognostic factors for OS rates .In the 90 HBsAg-positive patients, 41 patients were treated with CHOP and 49 patients with RCHOP . We compared the therapeutic efficacies and the reactivation rates of HBV between the DLBCL patients were treated with CHOP and those who were treated with RCHOP.For a prognosis evaluation, we used the Kaplan-Meier method to compare the OS rates between the CHOP and RCHOP groups and identified that the OS rate of the RCHOP group (79.6%) was higher compared with that of the CHOP group and 31 RCHOP (63.3%) patients, without statistical difference between the two groups in the RCHOP group. Due to the anti-viral efficacy of lamivudine, the percentages of patients with HBV-DNA levels >103 cps/ml declined in the two groups when compared with their status before chemotherapy; however, there was no significant difference between the two groups whose HBV-DNA level was >10P=0.403; . Therefo3 cps/ml during chemotherapy had poorer prognoses compared with patients with HBV-DNA loads <103 cps/ml , Ann Arbor stages III/IV (P=0.002) and elevated LDH levels (P=0.001) were poor prognostic factors for HBsAg-positive DLBCL patients and a multivariate analysis revealed that positive B symptoms (P<0.001), elevated LDH levels (P=0.003) and male gender (P=0.028) were poor prognostic factors for the OS rates in HBsAg-positive DLBCL patients.We compared therapeutic efficacies and HBV reactivation rates between CHOP and RCHOP treatments in the present study. Regarding HBV-reactivation, we did not identify any patient whose HBsAg status changed from negative to positive following chemotherapy. We also compared the CHOP and RCHOP groups\u2019 serum HBV-DNA values of HBsAg-positive DLBCL patients before and during chemotherapy and identified that there was no significant difference between the two groups , indicatSince RCHOP has an advantage over CHOP on the OS rate and since the management of lamivudine with the RCHOP regime did not increase the risk of HBV reactivation, our study demonstrated that a RCHOP treatment was appropriate for HBsAg-positive patients and resulted in a better prognosis."} +{"text": "Success of most periodontal treatment modalities as demonstrated by clinical parameters is well-established. These measurements, however, do not capture the full impact of treatment on the oral health status and health-related quality of life (QoL) of the patients. This study aims to assess the effectiveness of periodontal treatment provided at selected government specialist dental clinics using patient-reported outcomes.This prospective study involved patients who visited five randomly selected government periodontics clinics in Malaysia for treatment of periodontitis. Following ethics approval, all patients meeting the selection criteria were recruited over a period of eight months and comprehensive periodontal treatment ensued for a period of twelve months. Diagnosis of periodontitis was based on presence of periodontal pockets at least 4mm deep. At the end of the study period periodontal treatment outcomes were assessed using two patient-centred outcome measures: Oral Health Impact Profile (OHIP-14S) and Euroqol EQ-5D-3L index.A total of 145 patients started periodontal treatment but only 139 (95.8%) completed the 12-month study period. At post-treatment, patients had significantly improved oral health-related QoL (P<0.001) Wilcoxon Signed Rank Test; median OHIP-14S score of 7.0 at post-treatment vs 22.0 at baseline). Further, Cohen\u2019s effect size was calculated to be 1.1, suggesting practical significance. Improvement in general health status was indicated by gain in EQ5D-utility and Visual Analogue scores at post-treatment . Improvements in clinical parameters also reflected positive outcomes consistent with that of patient-reported outcomes.Periodontal treatment provided at the selected government periodontics clinics in Malaysia is effective in improving oral health status and health-related quality of life of the patients. Employing patient reported outcome measures in assessing effectiveness of dental health services will be an added value in providing high quality patient-centred healthcare."} +{"text": "High-resolution ocular coherence computed tomography enables unprecedented visualization of the retinal microarchitecture. To the best of our knowledge, this is the first report of high-resolution ocular coherence tomography findings in the healed form of photic post-cataract retinopathy.A 76-year-old Caucasian man complained of paracentral scotoma, persisting for six weeks after cataract surgery.Ocular coherence tomography demonstrated a localized juxta-foveal area of retinal atrophy involving the photoreceptor layer, and the retinal pigment epithelium layer. Operating microscope light-induced foveal damage is a well recognized occurrence following ocular surgery including complicated or lengthy cataract extraction and complex anterior segment procedures -5. WhileA healthy 76-year-old Caucasian man underwent phacoemulsification under retrobulbar anesthesia in his right eye with torn posterior capsule at the completion of cortex aspiration. Anterior vitrectomy was performed and a 5 \u00d7 6 mm intra-ocular lens was implanted in the sulcus. A coaxial illuminated microscope was used for surgery that lasted 45 minutes. At six weeks postoperatively, his best corrected visual acuity was 0.5. His main complaint was a paracentral scotoma confirmed by perimetry Figure . FundoscMost mild phototoxic retinal injuries probably remain undiagnosed in routine postoperative examination -5. Retinet al. [Acute histological changes in photic injuries have included localized necrosis of the retinal pigment epithelium, extensive disruption of the outer lamellae of the photoreceptors, and edema of the inner segments . Rodriguet al. presenteWe present, to the best of our knowledge, the first report of high-definition OCT findings in the healing stage (six weeks and nine months after surgery) of photic post-cataract retinopathy, showing atrophy of the photoreceptor and retinal pigment epithelium layers.Written informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.The authors declare that they have no competing interests.AM analyzed and interpreted our patient's fluorescein angiography and OCT data. MY performed the surgery and eye examinations of our patient. WM was a major contributor in writing the manuscript. All authors read and approved the final manuscript."} +{"text": "Increasing evidence indicated astroglia-derived neurotrophic factors generation might hold a promising therapy for Parkinson's disease (PD). Resveratrol, naturally present in red wine and grapes with potential benefit for health, is well known to possess a number of pharmacological activities. Besides the antineuroinflammatory properties, we hypothesized the neuroprotective potency of resveratrol is partially due to its additional neurotrophic effects. Here, primary rat midbrain neuron-glia cultures were applied to investigate the neurotrophic effects mediated by resveratrol on dopamine (DA) neurons and further explore the role of neurotrophic factors in its actions. Results showed resveratrol produced neurotrophic effects on cultured DA neurons. Additionally, astroglia-derived neurotrophic factors release was responsible for resveratrol-mediated neurotrophic properties as evidenced by the following observations: (1) resveratrol failed to exert neurotrophic effects on DA neurons in the cultures without astroglia; (2) the astroglia-conditioned medium prepared from astroglia-enriched cultures treated with resveratrol produced neurotrophic effects in neuron-enriched cultures; (3) resveratrol increased neurotrophic factors release in the concentration- and time-dependent manners; (4) resveratrol-mediated neurotrophic effects were suppressed by blocking the action of the neurotrophic factors. Together, resveratrol could produce neurotrophic effects on DA neurons through prompting neurotrophic factors release, and these effects might open new alternative avenues for neurotrophic factor-based therapy targeting PD. Parkinson's disease (PD) is one of the most common neurodegenerative diseases characterized by a selective dopamine (DA) neuronal loss in the substantia nigra (SN) of the ventral midbrain. Although current treatments are mainly used for symptomatic controls, their long-term application is associated with complications and could not halt the neurodegeneration . A growiResveratrol , a natural nonflavonoid polyphenol, is naturally present in red wine and grapes with a widely potential benefit for health . It was Our previous studies indicated that resveratrol produced neuroprotection against lipopolysaccharide- (LPS-) induced DA neurodegeneration through its anti-inflammatory activities and increased neurotrophic factors release in primary astroglia cultures , 15. BesFemale Wistar rats (200\u2013300\u2009g) were purchased from the Experimental Animal Centre of the Third Military Medical University . Housing and breeding of the animals were performed in strict accordance with Animal Care and Use Guidelines in China. Resveratrol and the polyclonal antityrosine hydroxylase (TH) antibody (1\u2009:\u20091000) were bought from Sigma Chemical Co. . The polyclonal anti-BDNF (1\u2009:\u20091000) and anti-GDNF (1\u2009:\u20091000) antibodies were obtained from Abcam . The Vectastain avidin-biotin complex (ABC) kit was purchased from Vector Laboratories . Enzyme-linked immunosorbent assay (ELISA) kits were obtained from Promega . All the cell culture materials were purchased from Invitrogen . 6/mL in poly-D-lysine-coated 24-well plate. Seven-day-old cell cultures were performed for drug treatments. At the time of treatment, cultures were composed of 10% microglia, 50% astrocytes, 40% neurons, and 1% TH-immunopositive neurons DA in Krebs-Ringer buffer for 20\u2009min. Liquid scintillation counting was performed to detect the radioactivity. Mazindol was used to block the nonspecific uptake for DA uptake. After the cultures were washed for three times with ice-cold Krebs\u2013Ringer buffer and lysed with NaOH, the lysate was mixed with scintillation fluid, and radioactivity was measured through the liquid scintillation counter. The specific [3H] DA uptake was calculated by subtracting the radioactivity amount obtained in the presence of mazindol from that obtained in the absence of mazindol DA uptake assay and immunocytochemical staining. The [3H] DA uptake assay indicated that resveratrol treatment increased the capacity of dopaminergic neurons to take up DA by approximately 160% compared with the control cultures (Rat primary midbrain neuron-glia cultures were treated with resveratrol (25\u2013100\u2009cultures . To invecultures . From thcultures . \u03bcM) on the first day. Seven days later, as shown in To investigate which cell type participated in resveratrol-mediated neurotrophic effects, three types of cultures including neuron-enriched, neuron-astroglia, and neuron-microglia reconstituted cultures were prepared and treated with resveratrol (100\u2009\u03bcM) and incubated for 48\u2009h. The conditioned medium in the absence (ACM) or presence of resveratrol (ACM-resveratrol) were collected and dialyzed and then added to the neuron-enriched cultures. Seven days later, the [3H] DA uptake assay indicated that ACM and ACM-resveratrol increased DA uptake capacity compared with the control group in the neuron-enriched cultures. Additionally, compared with ACM-treated cultures, a significant increase in DA uptake capacity was discerned in ACM-resveratrol-treated cultures was prepared from primary astroglia-enriched cultures. Primary astroglia were treated with resveratrol (100\u2009cultures .\u03bcM) for 48\u2009h. The BDNF and GDNF production in the culture medium was detected by ELISA. As shown in Rat primary neuron-glia cultures were treated with resveratrol resveratrol failed to exert neurotrophic effects on DA neurons in primary cultures without the presence of astroglia; (2) the astroglia-conditioned medium prepared from primary astroglia-enriched cultures treated with resveratrol produced neurotrophic effects in primary neuron-enriched cultures; (3) resveratrol increased neurotrophic factors release in the concentration- and time-dependent manners; (4) resveratrol-mediated neurotrophic effects were suppressed by the inhibition of neurotrophic factors production. These findings suggest that resveratrol could produce neurotrophic effects on cultured DA neurons through prompting astroglial BDNF and GDNF release.Astroglia, the most abundant cell type in the higher mammalian nervous system, were present in all regions of the brain and appeared to be organized in the strategic positions closely associated with the neuronal structures . A wealtFurther studies indicated that the increased neurotrophic factors such as BDNF and GDNF production participated in resveratrol-mediated astroglial neurotrophic effects. It has been demonstrated that the neurotrophic factors are responsible for the development, maintenance, and survival of neurons, microglia, astroglia, and oligodendrocytes . A largeSeveral clinical trials aimed at reviving DA neurons through direct infusion of GDNF to PD patient brains were conducted in the past few years. However, few of these clinical trials succeeded due to the occurrence of severe sided effects \u201336. In c"} +{"text": "Previous therapy with anthracyclines (ANT) and conditioning regimen followed by hematopoietic stem cell transplantation (HSCT) represents a high risk for development of cardiotoxicity. The aim of this study was to assess subclinical myocardial damage after HSCT using echocardiography and cardiac biomarkers - high sensitive cardiac troponin T (hs-cTnT) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) and to identify patients at risk of developing clinical cardiotoxicity.Thirty-seven patients who were treated with allogeneic HSCT for hematologic diseases at median age of 28 years at time of HSCT were studied. Conditioning regimen included either chemotherapy without total body irradiation (TBI) or combination of chemotherapy with TBI. Twenty-nine patients were pretreated with ANT therapy. Cardiac biomarkers were serially measured before conditioning regimen and at days 1, 14 and 30 after HSCT. Cardiac systolic and diastolic functions were assessed before conditioning regimen and 1 month after HSCT by echocardiography.P < 0,01 v.s. P < 0,01). Persistent elevations of NT-proBNP and hs-cTnT simultaneously for a period exceeding 14 days after HSCT were found in 29,7% patients. Serum concentrations of cardiomarkers were significantly elevated in ANT group compared to non-ANT group. These observations were underscored by the echocardiographic studies which did reveal significant changes in systolic and diastolic parameters. Five of 37 patients developed clinical manifestation of cardiotoxicity.The changes in plasma NT-proBNP and hs-cTnT levels during the 30 days following the HSCT were statistically significant (Elevations in both cardiac biomarkers were found before clinical signs of cardiotoxicity developed. Persistent elevations in NT-pro-BNP and hs-cTnT concentrations simultaneously for a period exceeding 14 days might be used for identification of patients at risk of developing cardiotoxicity and requiring further cardiological follow up. Stem cells are widely used in the treatment of malignant and nonmalignant diseases . AdvanceHowever, HSCT survivors are at risk of developing long-term complications. A fifth of HSCT survivors develop severe or life-threatening conditions . CardiacCardiac biomarkers are routinely evaluated only in patients before HSCT with increased cardiac risk ,7. FuturThis prospective study involved 37 consecutive patients with a median age of 28 years (range: 19-58 years) who underwent an allogeneic hematopoietic stem cell transplantation (HSCT) from June 2009 to February 2011 at the Transplantation Centre of Hematology Department at University Hospital Bratislava. There were 24 males and 13 females. Their diagnosis included acute myeloid leukemia (AML) in 13 patients, acute lymphoblastic leukemia (ALL) in 14 patients, chronic myeloid leukemia (CML) in 2 patients, Hodgkin's lymhoma in one patient, myelodysplastic syndrome (MDS) in 3 patients, osteomyelofibrosis in one patient and severe aplastic anemia in 3 patients.Twenty-seven patients were conditioned with myeloablative regimens including cyclophosphamide (CY) 60 mg/kg body weight intravenously on 2 consecutive days in combination with fractionated total body irradiation (TBI) 12 Gy in six fractions of 2 Gy over 3 days in 12 patiens or in combination with peroral busulphan 4 mg/kg body weight daily for 4 days in 15 patients. The remaining 10 patients were conditioned with nonmyeloablative regimens . Fifteen patients received hematopoietic stem cells from an HLA-matched related donor and 22 patients from an HLA-matched unrelated donor.2, range: 100-470). Characteristics of patients are summarized in Table Cyclosporine A and short-term methotrexate were administered for the prophylaxis of graft-versus-host disease (GVHD). Two patients had arterial hypertension, 2 patients had diabetes mellitus and 14 patients had dyslipidemia before transplantation. One patient had a prior history of a cardiac disease because of leukemic infiltration of the heart (at the time of diagnosis of acute leukemia). The cumulative dose of anthracyclines (ANT) was calculated as the equivalent dose of doxorubicin. Twenty-nine patients were previously treated with ANT , the day after HSCT (D + 1), 14 days after HSCT (D + 14) and 30 days after HSCT (D + 30) in all patients. Venous blood samples were obtained from an indwelling catheter in the morning and serum concentrations of biomarkers were measured immediately by electrochemiluminescence immunoassay on Elecsys 2010 analyzer (Roche Diagnostics). The upper reference limit (99th percentil) for hs-cTnT was 0.014 \u03bcg/L and cut-off values for NT-proBNP excluding acute heart failure were 450 and 900 pg/mL for ages < 50 and 50-75 years [Echocardiography was performed before the conditioning regimen and 1 month after HSCT. Parameters of systolic and diastolic left ventricular (LV) function were evaluated. Systolic LV dysfunction was defined as ejection fraction (EF) less than or equal to 50%. To evaluate LV diastolic function, the following parameters were recorded: peak flow velocity of early filling (E), peak flow velocity of late filling (A), ratio of peak early to peak late flow velocities (E/A), E-wave deceleration time (DT) and isovolumetric relaxation time (IVRT). Diastolic LV dysfunction was defined as E/A inversion and DT above 220 ms on the transmitral Doppler curve (impaired relaxation).P-value less than 0,05 was considered statistically significant.Continuous variables (echocardiographic parameters) are presented as mean \u00b1 SD (standard deviation) and cardiac biomarkers as median and interquartile range. Comparisons between continuous or categorical variables were performed using the Student's t-test, Mann-Whitney and Wilcoxon test. Friedman test was used to test the difference between variables. Correlations were evaluated with Spearman correlation coefficient. A P < 0,01). The highest values were detected on day 1 after HSCT in 26 patients with a gradual decline, but without normalization to baseline . There were no differences between patients with or without TBI as a part of conditioning regimen . Levels of NT-proBNP showed no correlation with fever in the last week , with plasma creatinine level and arterial hypertension .The changes in plasma NT-proBNP level during the 30 days following the HSCT were statistically significant P < 0,0. The higP < 0,01). We found persistent elevations in hs-cTnT levels 1 day, 14 days and also 30 days after HSCT . The concentrations of hs-cTnT in all measurements were significantly higher in patients previously treated with ANT , but not in patients receiving TBI as a part of the conditioning regimen . Levels of hs-cTnT showed no correlation with fever in the last week , with plasma creatinine level and arterial hypertension . Levels of NT-proBNP showed positive correlation with hs-cTnT .The differences in plasma hs-cTnT level during the 30 days following HSCT were also statistically significant . The mean E/A ratio decreased significantly over time, whereas DT and IVRT remained unchanged . Levels of NT-proBNP showed negative correlation with LV EF .In the early period after HSCT, we found a statistically significant decrease in systolic LV function developed a cardiac event. All of these patients exhibited elevated plasma NT-proBNP and hs-cTnT levels prior to clinical signs occuring and these elevations persisted at least 30 days after HSCT. Characteristics of patients are described in Table The results of this prospective and single-center study revealed, that persistently elevated cardiac biomarkers have important implications for identifying high-risk patients, particularly if levels of cardiac troponins and natriuretic peptides are simultaneously elevated for a period exceeding 14 days. We found that NT-proBNP and hs-cTnT might be a useful diagnostic tool for early detection of cardiotoxicity before its clinical manifestation. All patients with clinical cardiotoxicity had contemporary elevations in both cardiac biomarkers before clinical signs developed.Natriuretic peptides elevations have been shown to reflect wall stress, and thus provide functional information. Although the usefulness of NT-proBNP is well known in detection of chemotherapy-induced cardiotoxicity, only a few reports have assessed the detection of cardiotoxicity using BNP/NT-proBNP after allogeneic HSCT -13 or afCardiac troponins have been defined as the biomarkers potentially useful for assessing minimal myocyte damage or loss of cell membrane integrity, and thus give structural information. The recently introduced highly sensitive troponin tests will expand the diagnostic potential to the detection of minor injuries of the heart and also higher cTnT levels, below the detection range of currently available assays may be considered as a marker of \"end organ\" cardiovascular damage ,18. For Persistent elevations in cardiac biomarkers may reflect the presence of an underlying reduced functional myocardial reserve or reduced cardiac tolerance to cardiac stressors. Serial measurements of plasma NT-proBNP and hs-cTnT concentrations might be a useful tool for identification of patients at risk of developing cardiotoxicity after allogeneic HSCT and requiring cardiological follow up. Further studies are needed to clarify whether combination of both biomarkers improve detection of cardiotoxicity. Continued follow up is required to bring more insight into the predictive value of these biomarkers.A: Peak flow velocity of late filling; ALL: Acute lymphoblastic leukemia; AML: Acute myeloid leukemia; ANT: Anthracyclines; CY: Cyclophosphamide; DT: E-wave deceleration time; E: Peak flow velocity of early filling; EF: Ejection fraction; GVHD: Graft-versus-host disease; HSCT: Hematopoietic stem cell transplantation; hs-cTnT: High sensitive cardiac troponin T; IVRT: Isovolumetric relaxation time; LV: Left ventricular; MDS: Myelodysplastic syndrome; NT-proBNP: N-terminal pro-B-type natriuretic peptide; TBI: Total body irradiation.The authors declare that they have no competing interests.LR designed the study, collected informations about patients, performed statistical analysis and drafted the manuscript, EB performed daily clinical evaluation of patients, revised the manuscript, MM revised the manuscript, JD performed echocardiography study and helped to revise the article, JG carried out biochemical studies and helped to revise the article, NL carried out biochemical studies, BM conceived the idea, revised the manuscript and supervised the study. All authors read and approved the final manuscript."} +{"text": "The treatment of patients suffering from the neuroischemic diabetic foot syndrome (DFS) comprises arterial revascularization (e.g. below-knee bypass surgery), minor amputations, debridements, as well as long-term specialized wound care. Following premature discharge to the homecare sector, the quality of postoperative care is often inadequate. Many patients are readmitted. We studied the influence of a trans-sectoral case management (CM), ensuring outpatient care according to our clinical standards, on the readmission rate, length of hospital stay (LOS) and the hospital's costs/benefit situation.DFS patients after implementation of the CM (Case Management Group (CMG); n = 202; 2007-2008) were compared with a historic control group . All patients had high maintenance foot wounds as well as healing incisional wounds following bypass surgery. Both groups were matched for the principal diagnosis, a patients clinical complexity level (PCCL) of 4, and G-DRG-related flat rate. From the 202 CMG patients evaluated, 54 received long-term trans-sectoral care by the CM.The rehospitalization rate in the CMG was significantly reduced versus the HCG . The reduction of the revolving door effect in the CMG significantly improved the costs/revenue situation for the hospital. The LOS was unchanged.The implementation of a hospital-based trans-sectoral CM significantly reduces the rehospitalization rate in patients with neuroischemic DFS requiring bypass surgery. Hospital economics are improved.None declared."} +{"text": "In order to analyze when multi-infection first occurs during a lentivirus infection and how the distribution of multi-infection evolves during the disease course, we now determined the SIV copy numbers from splenocytes of 11 SIVmac251-infected rhesus macaques cross-sectionally covering the time span of primary infection throughout to end-stage immunodeficiency.Recombination is an important mechanism in the generation of genetic diversity of the human (HIV) and simian (SIV) immunodeficiency viruses. It requires the co-packaging of divergent RNA genomes into the same retroviral capsid and subsequent template switching during the reverse transcription reaction. By HIV-specific fluorescence SIV multi-infection of single splenocytes was readily detected in all monkeys and all stages of the infection. Single-infected cells were more frequent than double- or triple- infected cells. There was no strong trend linking the copy number distribution to plasma viral load, disease stage, or CD4 cell counts.in vivo throughout the disease course.SIV multi-infection of single cells is already established during the primary infection phase thus enabling recombination to affect viral evolution The human (HIV) and simian (SIV) immunodeficiency viruses exhibit phenomenal genetic diversity. This diversity is generated by 3 different mechanisms, (i) error-prone replication by the reverse transcriptase that occurs without proofreading , (ii) hyDue to the structure of the retrovirus particle and the low processivity of the reverse transcriptase, recombination is extraordinary frequent in HIV and SIV . In factin situ hybridization (FISH) on splenocytes of infected patients [To have an impact on virus evolution, recombination needs to proceed between non-identical RNA strands. The requirements and biological steps for the generation of such virus particles with non-identical genomes have been described. First, multi-infection of single cells occurs via direct and via cell-mediated entry pathways . Second,patients . Third, patients . Howeverpatients -23.in vivo during a lentivirus infection and how the distribution of multi-infection evolves during the disease course. To answer these questions, we determined the SIV copy number in splenocytes from SIVmac251-infected rhesus macaques (Macaca mulatta) by specific fluorescence in situ hybridization.While features of the basic steps in the generation of HIV/SIV recombinants have been described in various experimental conditions, it is still unknown when multi-infected single cells first appear In vitro SIVmac239-infected CEMx174 cells served as positive control to test the sensitivity of the biotin-labelled SIV DNA-probe while un-infected CEMx174 cells as well as spleen cells from an un-infected rhesus macaque were used as negative controls. Only after detecting bright signals in the interphase nuclei of the infected CEMx174 cells with no nonspecific background in the negative samples, the splenocytes of the infected animals were analyzed under the same conditions.To determine the SIV copy number of splenocytes from SIVmac251-infected animals by FISH, DNA from SIVmac239 was used as a probe. This was possible due to the high sequence homology between SIVmac239 and SIVmac251 . In vitrMulti-SIV-infected cells were observed for all animals and throughout the entire observation period from primary infection (2 weeks post infection) to the AIDS state . Approximately 10% of U1 cells showed only one copy. Thus it would appear that we underestimated the real values by ~10%. Within the same experiments, we very rarely detected 3 proviruses (< 0.5% of cells). Likewise, using either HIV DNA or SIV DNA as probes, non-infected monkey splenocytes rarely gave a positive signal (< 0.5%) suggesting that the number of false positive events is very small. Extrapolating these findings to the SIV FISH experiments with splenocytes from infected monkeys, the real SIV proviral copy number may be around 10% higher than indicated.4-fold in plasma virus titres but showed a similar provirus distribution in their splenocytes of a SIVmac251-derived virus stock prepared in rhesus monkey peripheral blood mononuclear cells [Splenocytes were analyzed from 11 SIVmac251-infected monkeys that had been used in previously published infection studies . Animalsar cells . They weThe authors declare that they have no competing interests.RS and AS performed the work. SS and US performed animal studies and collected the samples. RS and AM designed the study and wrote the paper. All authors read and approved the final manuscript.Detailed protocol for the preparation of cells for fluorescence in situ hybridization.Click here for fileDetailed protocol for the SIV-specific fluorescence in situ hybridization.Click here for file"} +{"text": "The rising prevalence of allergic disease in the last decades is unexplained. However, it has been postulated that the widespread introduction of genetically modified (GM) foods since 1996 may play a role in this evolving allergic disease epidemic. Currently, the most common GM plant is the genetically engineered Bacillus thuringiensis (Bt)-corn. This transgene confers resistance against corn borers leading to an enormous economic benefit. Corn products are found in a diverse variety of foodstuffs. Our hypothesis is that Bt-corn consumption influences allergic disease. We sought to determine whether feeding Bt-corn to mice would influence allergen-induced disease to a non-crossreactive allergen. To examine the influence of GM corn feeding on, the initiation and exacerbation of ovalbumin (OVA)-induced allergic asthma, we injected female BALB/c mice on days 0 and 21 with OVA intraperitoneally and nebulized them with OVA on days 28 and 29 to initiate disease and then allowed mice to recover until they were re-exposed to OVA for the induction of a disease exacerbation. We fed mice pellets containing 33% Bt (MON810)- or isogenic-corn vs. normal mouse food containing no corn for 4 weeks prior to inducing disease or inducing disease exacerbation. To evaluate the effects of the Bt-corn on OVA-induced disease, we measured lung and airway inflammation, mucus hypersecretion and OVA-specific antibodies. We observed that Bt-corn feeding had no effect on OVA-induced allergic disease or exacerbations indicating that Bt-corn using this protocol has no effect on the propensity for another allergen to initiate allergic disease or induce disease exacerbations in mice."} +{"text": "NMD is often triggered by alternative splicing (AS) modifications introducing such codons. NMD plays an important regulatory role in brain neurons, but the Here, we report exon arrays analysis of leukocyte mRNA AS events prior to and following Deep Brain Stimulation (DBS) neurosurgery, which efficiently improves the motor symptoms of Parkinson\u2019s disease (PD), the leading movement disorder, and is increasingly applied to treat other diseases. We also analyzed publicly available exon array dataset of whole blood cells from mixed early and advanced PD patients. Our in-house exon array dataset of leukocyte transcripts was derived from advanced PD patients\u2019 pre- and post-DBS stimulation and matched healthy control volunteers. The mixed cohort exhibited 146 AS changes in 136 transcripts compared to controls, including 9 NMD protein-level assessed events. In comparison, PD patients from our advanced cohort differed from healthy controls by 319 AS events in 280 transcripts, assessed as inducing 27 protein-level NMD events. DBS stimulation induced 254 AS events in 229 genes as compared to the pre-DBS state including 44 NMD inductions. A short, one hour electrical stimulus cessation caused 234 AS changes in 125 genes compared to ON-stimulus state, 22 of these were assessed for NMD. Functional analysis highlighted disease-induced DNA damage and inflammatory control and its reversal under ON and OFF stimulus as well as alternative splicing in all the tested states.The study findings indicate a potential role for NMD both in PD and following electrical brain stimulation. Furthermore, our current observations entail future implications for developing therapies for PD, and for interfering with the impaired molecular mechanisms that underlie PD and other neurodegenerative and neurological disorders, as well as DBS-treatable conditions in general. NMD is an eukaryotic mRNA surveillance process that detects, and selectively degrades, mRNA transcripts which harbour premature termination codons , increaThe pre-mRNA splicing machinery recognizes a termination codon as premature when it is located more than about 50 nucleotides upstream of the final intron position. Therefore, NMD can result from somatic DNA rearrangements, the presence of upstream open reading frames, the use of alternative open reading frames or the presence of UGA codons -7. More That NMD functions as a quality control mechanism tentatively suggested involvement of this particular RNA surveillance process in both the initiation and progression of neurodegenerative diseases and in treatment-induced modifications of disease symptoms. Specifically, we considered the rapid changes occurring following Deep Brain Stimulation (DBS) treatment, a functional stereotactic neurosurgery that is most commonly applied to ameliorate Parkinson\u2019s disease (PD) motor symptoms through targeting of the Sub-Thalamic Nucleus (STN) brain region . FollowiAlthough PD is a central nervous system disease, the current estimation is that it initiates up to decades prior to the appearance of the motor symptoms , includiIn our current study, we zoomed in to profile NMD events in leukocyte transcripts from PD patients before and after DBS neurosurgery and under disconnected electrical current, aiming to challenge the hypothesis that NMD may be actively involved in the impaired brain-to-body signalling processes that accompany PD and in the correction of such impairments under DBS which mitigates PD symptoms. We predicted NMD profile changes in PD leukocytes compared to healthy volunteers and in post-DBS compared to pre-DBS preparations, and surmised that disconnecting the electrical stimulus would again alter the NMD profile. To challenge these predictions, we integrated a web-available exon array data set of human PD blood samples with ourTo characterize alternative splicing changes in exon array datasets from PD patients, we first studied our in-house exon array leukocyte dataset by measuring the exon level splicing index and assessing functional protein-level implications of these measures in our data-set, as well as in an additional independent exon array dataset of whole mRNA extracted from blood samples of mixed early and advanced PD patients and healthy control volunteers . Exon leOur dataset differed from the published one in two principal points: both the clinical characteristics of recruited patients (advanced stage as compared to mixed composition) and the population of blood cells from which RNA was extracted . Overall, 319 AS events were detected in the advanced patients compared to control volunteers Figure\u00a0Bi. TheseFunctional analysis of the PD AS-modified transcripts using EASE identifiWe have further challenged these observations using the robust FIRMA analysis approach . While iAlthough there was no overlap between the specific genes identified by the SI and the FIRMA analysis methods, we noted that there was an overlap in terms of gene families between the two lists. For example, the solute carrier (SLC) as well as zinc finger and WD repeat domain-containing genes were detected as significantly changed by both methods. Notably, there was also an overlap between the functional enriched terms of the SI and FIRMA detected genes, for example \u2013 alternative splicing, with the SwissProt keyword phosphoprotein as the top detected functional enriched term in both lists, found in 69 of the SI, and 70 of the FIRMA detected genes. The biological process protein transport also appeared as significantly enriched in both lists.Next, we addressed the question of whether the observed splicing changes are correlated with treatment efficacy. We have conduced exon-level SI analysis of blood leukocyte transcripts from PD patients post-DBS, upon symptoms stabilization, and under electrical stimulation (PD-Stim-ON) as compared with one day prior to DBS neurosurgery . While Of the DBS-modifiable AS transcripts, 23 were also detected in the PD patients pre-DBS and 2 of those showed DBS-inducible NMD change: the TATA Box gene TAF1D (with inclusion of exon E9-7) and VDAC3, where inclusion of exon E5-1 was predicted to affect functional NMD decay. Four of the DBS-induced AS genes also showed expression change in the same patients: the tumorigenic protein TPRG1, the keratin KRT7, the vesicular trafficking protein EXOC7 and the NMD factor UPF3A, which also changed in patients compared with controls. The treatment-induced AS genes also included interleukin (IL) 19, suggesting immune and NMD relevance to the DBS-induced improvement of motor functions. Although inducing less exon level AS changes as compared with PD, DBS increased the diversity of the detected events to 631 functional predictions . FIRMA analysis of the post-DBS ON- stimulus state as compared with the pre-DBS state detected 110 AS events in 106 transcripts . We noted 133 AS changes within only one hour following disconnection of the stimulus Figure\u00a0E, reinfoTo further challenge the power of the observed differences, we performed hierarchical classification analysis on all of those AS regions that were implicated to cause NMD in the mixed patients\u2019 cohort, and found correct classification of all samples except for 2 misclassifications Figure\u00a0A. In comPost-hoc functional enrichment analysis of the AS genes detected in the mixed published PD cohort revealed enrichment in nucleotide-binding, metal-binding, Natural killer cell mediated cytotoxicity, ATP-binding, transition metal ion binding, ATP binding, gene silencing and positive regulation of immune response , the Swissprot database term alternative splicing , acute inflammatory response and mitochondrion and cause truncation in accordance with the Declaration of Helsinki principles. Following oral agreement, all participants signed informed consent prior to inclusion. The decisions regarding the DBS treatment were taken solely by physicians at the Hadassah Ein Kerem Hospital and the PD patient volunteers were only subsequently recruited for the study.28 exon array raw CEL files of whole blood mRNA from 17 mixed early and late PD patients (time from diagnosis: 2\u201323\u00a0years) and 11 healthy control volunteers (HC) were obtSeven PD male patients nominated for bilateral DBS neurosurgery were recruited to the study and six healthy age-matched male controls (HC). Subjects were assessed for their clinical background and state and fulfilled detailed medical history questionnaires. Patients with other medical conditions were excluded, including depression and past and current DSM Axis I and II psychological disorders (SM), chronic inflammatory diseases, coagulation irregularities, previous malignancies or cardiac events, or any other surgical procedure up to 1\u00a0year pre-DBS. Exceptions were hyperlipidemia (present in two patients and three control volunteers), hypertension and diabetes (two patients each). All patients went through bilateral STN-DBS electrode implantation and were under dopamine replacement therapy (DRT) both pre- and post- DBS, with a significantly reduced dosage post-DBS (t-test p\u2009<\u20090.01). The last medication was administrated at least 5\u00a0hours pre-sampling. The patients and healthy volunteers also exhibited similar total white and red blood cell counts. Further clinical details are given under the supporting information of . Blood sMicroarray probe-set summation of the input CEL files was conducted using Affymetrix Power Tools (APT) through AltAnalyze.http://www.ensembl.org). Briefly, AS targeted analysis was conducted using both Splicing-Index (SI) [Splicing targeted analysis of both sets of exon array data was conducted using the software AltAnalyze using the Ensembl human database (#37) (dex (SI) ,79 and Fdex (SI) . Prior thttp://www.biocarta.com/).Pathway post-hoc analysis on the detected AS transcripts was conducted through the DAVID ,81 EASE http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23676 and http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18838.The data-sets supporting the results of this article are available in the GEO repository, AS: Alternative plicing; BP: Biological process; DBS: Deep brain stimulation; GO: Gene Ontology; GEO: Gene Expression Omnibus; MF: Molecular Function; NMD: Nonsense-Mediated decay; FIRMA: Finding Isoforms using Robust Multichip Analysis; PD: Parkinson\u2019s disease; PTC: Pre-termination codon; SI: Splicing Index; UTR: Un-Translated Region.The authors declare that they have no competing interests.LS, HB, ZI and HS designed the study, HB, ZI and LS submitted for Helsinki ethics committee approval and recruited patients and healthy control volunteers to the study, LS signed the participants of agreement forms, produced the blood leukocyte samples and RNA and conducted the bioinformatic data analyses. LS drafted the manuscript with the help of HS and all the co-authors approved the final manuscript. All authors read and approved the final manuscript.Alternatively spliced genes detected by splicing-index exon level analysis of the independent mixed early-late PD patients and healthy control volunteers (HC) cohort.Click here for fileFunctional terms, functions and processes found as enriched in the detected external cohort alternatively spliced genes.Click here for fileAlternatively spliced genes detected by splicing-index exon level analysis of the in-house advanced PD patients and HC cohort.Click here for fileFunctional terms, functions and processes found as enriched in the in-house PD cohort alternatively spliced genes detected upon comparison to HC.Click here for fileAlternatively spliced genes detected by robust isoform finding analysis (FIRMA) of the exon microarray data of the in-house advanced PD patients and HC.Click here for fileAlternatively spliced genes detected by splicing-index (SI) exon level analysis of the in-house advanced PD patients cohort post-DBS as compared with pre-DBS (pre-treatment) state.Click here for fileFunctional terms, functions and processes found as enriched in the in-house PD cohort alternatively spliced genes detected upon comparison of pre- to post-DBS (treatment) states.Click here for fileAlternatively spliced genes detected by FIRMA analysis of the exon microarray data of the in-house advanced PD patients cohort post-DBS as compared with pre-DBS (pre-treatment) state.Click here for fileAlternatively spliced genes detected by splicing-index exon level analysis of the in-house advanced PD patients cohort post-DBS ON-Stim as compared to one hour off stimulation state .Click here for fileFunctional terms, functions and processes found as enriched in the in-house PD cohort alternatively spliced genes detected upon splicing-index analysis of the two tested post-DBS states .Click here for fileAlternatively spliced genes detected by robust isoform finding analysis (FIRMA) of the exon microarray data of the in-house advanced PD patients in the two post-DBS states .Click here for file"} +{"text": "Data are scarce on long-term effects of Bentall procedure on left ventricular systolic function and functional status. Aim was to assess long-term effects of Bentall procedure on left ventricular (LV) systolic function and functional status.Study group consisted of 90 consecutive patients who were operated using elective Bentall procedure for the aneurysm of the ascending aorta and aortic valve disease from 1997 to 2003 in a single tertiary care center. Patients were followed for eight years for mortality, LV ejection fraction and volume indices, as well as functional capacity as assessed by NYHA class. Echocardiographic measurements were made according to the recommendations given by the American Society of Echocardiography.Study group consisted of 71 male and 19 female patients, mean age 54+/-10 years. There were no operative deaths. Survival rate was 73.3% during eight-year follow-up (11 cardiac and 13 non-cardiac deaths). Echocardiography was performed before index procedure and after 96+/-9 months. Statistically significant improvement in the LV ejection fraction was noted at follow-up examinations as compared to preoperative values . Similarly, statistically significant reduction in the LV end-systolic and end-diastolic volumes were observed. NYHA class improved from baseline during the follow-up . Univariate analysis identified ejection fraction on admission and the presence of postoperative complications as predictors of long-term LV ejection fraction.Bentall procedure significantly improves long-term LV systolic function and functional status."} +{"text": "We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations.Next-generation sequencing (NGS) studies in cancer are limited by the amount, quality and purity of tissue samples. In this situation, primary xenografts have proven useful preclinical models. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC), a malignancy often diagnosed from small biopsy or needle aspirate samples. Using an Although the application of NGS technology to cancer research has led to dramatic advances in the understanding of the genomic basis of these diseases, the depth and complexity of sequencing data is negatively correlated to the amount and quality of tumour specimen used for analysis One approach to overcome this problem is the use of primary xenograft models, in which small tissue samples can be directly engrafted, expanded and passaged in immunodeficient mice without exposure to conventional tissue culture conditions et al.Based on these data, primary xenografts could represent a useful platform for NGS analysis when cancer tissue is limiting. Ding post-hoc during bioinformatic analyses, which unequivocally identify species-of-origin reads. This issue has been previously discussed for ultra high-throughput cDNA sequencing (RNA-Seq) by Conway et al.et al.in silico workflow designed to definitively assign species-of-origin to NGS reads in several previously characterized primary and cell line-derived xenograft models of SCLC, and compared these results with published datasets.In our view, the presence of contaminating mouse DNA and RNA affects the sensitivity and specificity of NGS analysis in these tumour models which should not be based on cellularity estimates, but should be accurately and systematically addressed. Additionally, since most current NGS techniques use shotgun-sequencing methodology, resolution of any potential artifact could be performed All experiments involving animals were approved in advance by an Animal Ethics Committee at Monash University and were carried out in accordance with \u201cAustralian Code of Practice for the Care and Use of Animals for Scientific Purposes.\u201din vivo as described above and cells were injected into the flanks of athymic nude mice in Matrigel. Passaged and snap frozen tumours samples were routinely characterised for histopathologic and immunohistochemical features of the parent tumour The SCLC primary xenograft lines LX22, LX33 and LX36 were passaged as previously described in vitro and in vivo as described in Watkins et al.Authenticated NCI-H209 cell line was purchased from ATCC, re-derived from a single cell clone using the single cell cloning by serial dilution and then cultured Exome and low-coverage whole-genome DNA re-sequencing: Target DNA (3ug) was firstly sheared using a focal acoustic device . DNA fragment libraries for exome re-sequencing and low-coverage whole-genome sequencing were constructed from sheared DNA by sequential steps of end-repair, A-tailing and ligation of indexed lllumina compatible adapter sequences . For exome re-sequencing, PCR amplified fragment libraries were enriched for exonic DNA by long oligonucleotide hybridisation capture according to the manufacturer\u2019s protocol . For low-coverage whole-genome, PCR-amplified libraries were size selected to capture DNA of 500\u2013700nt length, using an automated electrophoresis platform . All sequencing libraries were quantified using real-time PCR against a library of known concentration and then processed for cluster generation and sequencing according to standard protocols .total RNA was checked for quality and yield by automated microfluidic electrophoresis and spectrophotometer . Non-directional RNA-Seq libraries were created according to the manufacturers protocol . Briefly this method involved sequential steps of mRNA enrichment from 3ug total RNA, RNA fragmentation by heating in the presence of divalent cations, a randomly primed reverse transcription and second-strand cDNA synthesis followed by preparation of DNA fragment libraries using Illumina compatible adapters and PCR amplification as previously described for DNA libraries.http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and low quality reads were filtered and were hard trimmed using Trimmomatic .et al.via collecting and comparing the read ids of the host/graft alignments, producing reads in FASTQ format. As a result, identified graft-specific reads were re-aligned to the graft genome.The proposed strategy resembles that described by Conway i. e., reads that could only be mapped to the human genome, reads that were exclusively mapped to the mouse genome and reads that mapped to both genomes. In addition to analysing RNA-Seq read sets, we further verify this strategy for low-coverage whole-genome and exome-capture sequencing experiments. A complete overview describing all the steps included in the proposed strategy is shown in http://seqanswers.com/forums/showpost.php?p=25302&postcount=3] and the cmpfastq_pe software, that compared raw pair-end fastq files and reported common and unique reads (http://compbio.brc.iop.kcl.ac.uk/software/cmpfastq_pe.php).Subsequent alignments produced three separate aligned datasets, Mapping scores were used to assess the mapping quality of the processed samples and to further discard multiple-hit reads. As a general rule, it was assumed that a higher mapping quality means a more \u201cunique\u201d aligned read and for most of the samples, a high percentage of the read-pairs had a mapping quality above 20 ., San Diego, CA, USA). The experiment was paired-end with 100nt read length (300nt average insert size). The targeted minimum number of reads per sample was 40 million reads and host (mouse) reads, processed sample reads were sequentially aligned to both graft [complete hg19 human genome ] and host [complete mm9 mouse genome ] genomes using Bowtie-TopHat and host [complete mm9 mouse genome ] genomes using the Burrows-Wheeler Alignment tool and host [complete mm9 mouse genome ] genomes using the Burrows-Wheeler Alignment tool [(BWA), bwa aln algorithm used, seed length of 22nt; maximum edit distance in the seed of 0 Intra- and inter-chromosomal rearrangements discovery of the identified human specific reads was performed using FusionMap [span and split read count threshold of 3 and split minimum anchor of 4 reads Copy number variations (CNV) and allelic content in genomic regions were detected using Control-Freec i.e., those reads that aligned to both the human and the mouse genome, was found to be similar for all methods, ranging from 4% (RNA-Seq) to 1.5% (Exome-capture). A complete summary of the alignments performed is described in As shown in As expected, the sequence depth of coverage of the samples subjected to low-coverage whole-genome sequencing was above 3 times for all analysed samples A. Howevbeta allele frequency profiles for both sample types family. A complete list of the intra- and inter-chromosomal rearrangements common to both cell line and the xenograft samples can be found in Comparable results could be observed for intra- and inter-chromosomal rearrangements A, wherein vivo model.The data presented above supports our hypothesis that a thorough CNV and structural variant analysis can be performed when both the cell line and xenograft samples were used. We found that when correctly accounting for mouse-specific contamination, the results obtained using uncontaminated cell lines can be accurately reproduced using xenograft samples, with the additional benefits of the usage of an i. e., peripheral blood, cell line and xenograft) detected a total of 53,186 SNPs. Those variants that were found in the peripheral blood were considered of germline origin, and were no further processed for tertiary analysis.A mean sequence depth of coverage in the targeted captured regions in all samples of over 100 times was achieved, with more than 80% of the bases covered at least 30 times B. In thet alA total of 946 somatic variants, 351 of these novel, were common to both the cell line and xenograft samples A. Of thFor the 946 variants common to both cell line and xenograft, the SnpEff effect predictor reported a total of 1806 A & B. FESPN, KAZN, APEH, MUC20, MUC17, AQP7, ZNF808 and LUZP4. In order to identify the cause of these discrepancies between the variants detected in the cell line and the xenograft samples, the genomic regions surrounding the variants detected were examined. In order to exclude the possibility that these variants arose from contaminating mouse sequence, we performed the following analysis. First, we isolated the sequencing reads adjacent to the region of interest within a range of 1,000bp resulted in non-synonymous coding region changes with a predicted moderate impact on protein function showed a strong correlation with a previously published gene-expression array data set in the same tumor models using human-specific cDNA probesets BGN, COL1A1, COL1A2, COL5A1, FN1, NID2, COL10A, COL11A1, COL3A1, MMP2, POSTN, SPARC, DST and THBS2, produced high number of RPKM and positively correlated with the gene expression array data cell line and a xenograft tumour derived from it (B).(PDF)Click here for additional data file.Figure S2Analysis of xenograft-specific variants. Local pairwise alignment of the human (hg19) and mouse (mm9) genomes compared against the sequencing read alignments of genomic regions surrounding the variants detected. Representative detected variants are shown for AQP7 (A), APEH (B), MUC17 (C) and MUC20 (D) genes. Genomic locations for the variants shown are described in supplementary Table 4 A. In the local pairwise alignments, vertical lines, and the number above them, represent sequence gaps and its length respectively; dots represent conserved human-mouse sequences. Variant position is highlighted by black parallel bars. Nucleotide residues are shown in red (thymine), blue (cytosine), green (adenine) and yellow (guanine). Heterozygous variants are indicated in the depth of coverage track and show both reference and alternative alleles. Forward and reverse sequencing reads are shown in pink and blue respectively. Sequence base mismatches are highlighted with its corresponding nucleotide colour.(PDF)Click here for additional data file.Figure S3Analysis of xenograft-specific variants. Sequence depth of coverage and allele frequency comparisons between the xenograft and cell line samples. Both samples were aligned to the human reference genome hg19. Representative detected variants are shown for AQP7 (A), APEH (B), MUC17 (C) and MUC20 (D) genes. Genomic locations for the variants shown are described in supplementary Table 4 A. Variants position is highlighted by black parallel bars. Nucleotide residues are shown in red (thymine), blue (cytosine), green (adenine) and yellow (guanine). Heterozygous variants are indicated in the depth of coverage track and show both reference and alternative alleles. Forward and reverse sequencing reads are shown in pink and blue respectively. Sequence base mismatches are highlighted with its corresponding nucleotide colour.(PDF)Click here for additional data file.Figure S4Analysis of cell line-specific variants. Sequence depth of coverage and allele frequency comparisons between the cell line and xenograft samples. Both samples were aligned to the human reference genome hg19. Representative detected variants are shown for HIF1A (A), TRIM22 (B), GPR64 (C) and MAML2 (D) genes. Genomic locations for the variants shown are described in supplementary Table 4 A. Variants position is highlighted by black parallel bars. Nucleotide residues are shown in red (thymine), blue (cytosine), green (adenine) and yellow (guanine). Heterozygous variants are indicated in the depth of coverage track and show both reference and alternative alleles. Forward and reverse sequencing reads are shown in pink and blue respectively. Sequence base mismatches are highlighted with its corresponding nucleotide color.(PDF)Click here for additional data file.Table S1Summary of the total and post QA/QC number of sequenced reads from each NGS experiment performed. Control: peripheral blood BL209, Cell line: NCI-H209; Xenograft: xenograft sample derived from the NCI-H209 cell line. LX22, LX33 and LX33: SCLC primary xenograft lines LX22, LX33 and LX36. The number of mapped reads for the xenograft samples are human-specific only. PE: pair-ends.(PDF)Click here for additional data file.Table S2Summary of the alignments statistics of each NGS experiment performed. LX22, LX33 and LX33: SCLC primary xenograft lines LX22, LX33 and LX36.Control: peripheral blood BL209, Cell line: NCI-H209; Xenograft: xenograft sample derived from the NCI-H209 cell line. The number of mapped reads for the xenograft samples are human-specific only. For the exome capture and low-coverage whole genome analyses of the xenograft sample concordantly paired reads were analyzed.(PDF)Click here for additional data file.Table S3Summary of the depth of coverage obtained for the exome capture (A) and low pass whole genome (B) experiments. Control: peripheral blood BL209, Cell line: NCI-H209; Xenograft: xenograft sample derived from the NCI-H209 cell line. The results of the xenograft sample only represent those reads that were human specific. Depth of coverage was estimated on whole reads.(PDF)Click here for additional data file.Table S4Table describing sample-specific single nucleotide variants. (A) Xenograft-specific non-synonymous coding variants. (B) Cell line specific non-synonymous coding variants. For sample-specific variants, approximate read depth is shown (reads with MQ\u200a=\u200a255 or with bad mates were filtered). Read and allelic depth of the sample were the variant was not identified were calculated on de-duplicated reads. NSC: non-synonymous coding variant.(PDF)Click here for additional data file.Dataset S1Detected copy number variations in the NCI-H209 cell line sample.(PDF)Click here for additional data file.Dataset S2Detected copy number variations in the xenograft sample derived from the NCI-H209 cell line.(PDF)Click here for additional data file.Dataset S3nter- and intrachromosomal rearrangements common to both the NCI-H209 cell line and its derived xenograft sample.I(PDF)Click here for additional data file.Dataset S4Somatic variants detected in both the cell line and xenograft samples.(PDF)Click here for additional data file.Dataset S5SNPs effects common to both the cell line and xenograft samples (only one transcript of the moderate and high impact effects are reported.(PDF)Click here for additional data file."} +{"text": "Sensitive antibody-based tumor targeting has the potential not only to image metastatic and micrometastatic disease, but also to be the basis of targeted therapy. The vast majority of pancreas cancers express carcinoembryonic antigen (CEA). Thus, we sought to evaluate the potential of CEA as a pancreatic cancer target utilizing a rapidly clearing engineered anti-CEA scFv-Fc antibody fragment with a mutation in the Fc region [anti-CEA scFv-Fc H310A].In vivo tumor targeting was evaluated by tail vein injection of I124-labeled anti-CEA scFv-Fc(H310A) into mice harboring CEA-positive and -negative xenografts. MicroPET/CT imaging was performed at successive time intervals. Radioactivity in blood and tumor was measured after the last time point. Additionally, unlabeled anti-CEA scFv-Fc(H310A) was injected into CEA-positive tumor bearing mice and ex vivo IHC was performed to identify the presence of the antibody to define the microscopic intratumoral pattern of targeting.Immunohistochemistry (IHC) with the antibody fragment was used to confirm expression of CEA on human pancreas cancer specimens. Moderate to strong staining by IHC was noted on 84% of our human pancreatic cancer specimens and was comparable to staining of our xenografts. Pancreas xenograft imaging with the radiolabeled anti-CEA scFv-Fc(H310A) antibody demonstrated average tumor/blood ratios of 4.0. Immunolocalization demonstrated peripheral antibody fragment penetration of one to five cell diameters (0.75 to 1.5 \u03bcm).We characterized a preclinical xenograft model with respect to CEA expression that was comparable to human cases. We demonstrated that the anti-CEA scFv-Fc(H310A) antibody exhibited antigen-specific tumor targeting and shows promise as an imaging and potentially therapeutic agent. Pancreatic cancer is one of the most lethal cancers as incidence approximates mortality . Signs aOne such strategy to improve our ability to detect cancer is by using labeled antibodies targeting cancer-specific antigens. Antibodies offer high specificity for tumor antigens on the cell surface and thus can be used for positron emission tomography (PET) imaging once radiolabeled with a positron-emitting radionuclide (immunoPET). This offers great potential to achieve specific molecular imaging of cancer. Although very stable and specific, intact monoclonal antibodies are limited for imaging purposes by their extended serum half-life causing a high background signal. To circumvent this issue, recombinant, domain-deleted, antibodies with varying size and half-life can be engineered . These rin vivo antigen-specific tumor targeting of our xenograft models with microPET imaging. Lastly, we investigated the microscopic pattern of tumor targeting of the intravenously injected antibody fragment with ex vivo immunolocalization studies to detect the exact location of the fragment within the tumor, which may have important ramifications for development of antibody-based therapeutics.CEA is a 180-kDa GPI-linked glycoprotein expressed on the cell surface of the normal adult colon at very low levels. However, during carcinogenesis, this oncofetal protein becomes much more highly expressed on the cell surface. Additionally, this protein can be shed into the circulation and measured as a serum tumor marker, reflective of the burden of disease . High le7 NS0 murine myeloma cells were transfected by electroporation with 40 \u03bcg of the pEE12 vector containing the anti-CEA scFv-Fc(H310A) construct and selected in glutamine-deficient DMEM/high modified media as previously described . Als. Als5]. CEA expression was determined for four different pancreatic cell lines using flow cytometry Figure . MiaPacaExpression of CEA on human pancreas cancer specimens was evaluated by performing IHC utilizing the anti-CEA scFv-Fc H310A) antibody fragment upon a tissue microarray containing 107 1-mm-tissue cores of pancreatic adenocarcinomas. Of the 107 cancer specimens, 90 demonstrated moderate to strong staining for CEA expression antibody fragment. Nude mice with a CEA-positive tumor and CEA-negative tumor (MiaPaca-2) were injected via the tail vein with approximately 50 \u03bcg of radiolabeled antibody fragment (120 \u03bcCi of radioactivity). Three mice per positive cell line were used for imaging purposes. Average tumor weight for all positive tumors was approximately 220 mg . Whole body microPET scans were obtained at 4 and 20 h post-injection. MicroCT was obtained at 20 h only. Figure Radioiodination with in vivo incubation period. Sections were examined for the presence of the human Fc portion of the anti-CEA fragment. Intratumoral staining was largely localized to tumor cells at the periphery of the microtumor nodules surrounded by stroma and vessels antibody fragment and a 20-h Targeting cancer with antibodies is a rapidly expanding field seeking to provide new technology for diagnosis and therapy. Considering molecular imaging applications such as immunoPET, intact antibodies are limited due to their extended serum persistence resulting in a high background signal. However, the growing knowledge of antibody interactions with FcRN receptors resulting in prolonged serum persistence have allowed for development of engineered antibody fragments possessing shorter half-lives while providing the same specific binding to their antigen. In such a way, these engineered antibodies can overcome the limitations of intact antibodies. Indeed, many recent studies have demonstrated that smaller size antibody fragments as well as decreased serum persistence are better imaging agents owing to their improved tumor penetration and rapid blood clearance ,13-15. PCEA serum levels have been used clinically for many years to diagnose, stage, and follow patients with colorectal cancer. Although CEA serum levels are not widely elevated in pancreatic cancer, this antigen is expressed on the cell surface of the vast majority of pancreatic cancers. Many reports of CEA on pancreas cancer specimens describe expression ranging from 70% to 98% . In addi124I-labeled anti-CEA scFv-Fc (H310A) antibody and imaged at 4 and 20 h after injection with microPET/CT. Our microPET images at 4 h demonstrate quick targeting of the antibody fragment to all CEA-positive pancreatic tumors (data not shown). Moreover, microPET images at 20 h show persistence of signal at the site of the tumor with low blood background signal. Accordingly, biodistribution data at 20 h after injection provides objective confirmation of the microPET images. We were able to achieve positive tumor to negative tumor ratios greater than 17 demonstrating antigen-specific tumor targeting of the anti-CEA scFv-Fc (H310A) antibody fragment. Furthermore, a tumor to blood ratio of 4.0 at 20 h is evidence of the imaging benefit afforded by the decreased serum half-life of the fragment. Overall, these data are very supportive regarding the immunoPET imaging potential of the anti-CEA scFv-Fc (H310A) antibody fragment in pancreas cancer.Using our pancreatic cancer mouse xenograft model, we injected mice with To assess the potential ability of converting an antibody-based imaging agent into a tumor-targeting therapeutic, we additionally wanted to define the microscopic pattern of tumor targeting of the anti-CEA scFv-Fc (H310A) antibody fragment in mice xenografts by performing \"immunolocalization\" studies. These studies provided confirmatory evidence of the microPET images demonstrating the physical presence of the anti-CEA scFv-Fc (H310A) antibody protein in the tumor sections. Furthermore, the intratumoral staining pattern demonstrated localization of antibody to the periphery of microscopic tumor nodules comprising the macroscopic tumor xenograft with antibody penetration approximately one- to five-cell-layers deep from the intervening stroma and vessels. Additionally, antibody tumor penetration models describe a number of factors including antigen density, antibody binding affinity, and antibody metabolism along with physical properties of the cancer tissue (e.g. tumor vascularity) as impacting antibody localization -21. Depein vivo imaging potential and targeting capability of this antibody fragment in pancreatic cancer xenografts. Although CEA expression appears to be similar between our xenografts and the majority of human pancreas cancer specimens, data from xenograft models are limited secondary to lack of a competent immune system. Historically, the majority of murine monoclonal antibodies have failed to be translated to the clinical setting because of the human anti-mouse antibody (HAMA) response. This resulted in the advent of chimeric antibodies with murine variable regions (VL and Vh) and human constant domains (CH2 and CH3) as well as humanized and fully human antibodies. Of note, the anti-CEA scFv-Fc (H310A) antibody fragment is a chimeric protein, which should decrease the incidence of the HAMA response, although it may still occur with repeated administration of the protein [This work demonstrates the utility of the anti-CEA scFv-Fc (H310A) antibody fragment for imaging pancreas cancer with possible applications for therapy. We show the protein .in vivo antigen-specific molecular imaging. Furthermore, we define the microscopic pattern of tumor targeting which may have implications regarding radioimmunotherapy. The versatility of this antibody construct, based on the presence or absence of an Fc domain mutation, provides for improved pharmacokinetics in both imaging and therapy making it a very attractive fragment for continued study and development.In summary, antigen-specific molecular imaging has the potential to provide a more accurate assessment of the tumor burden for pancreatic cancer patients. CEA is strongly expressed in the majority of pancreas cancers and thus is a potential target for antibody-based molecular imaging and therapy. Using the novel mutated anti-CEA scFv-Fc (H310A) antibody fragment with a reduced serum half-life, we demonstrated The authors declare that they have no competing interests.MG carried out immunoassays, biochemical characterization, functional characterization and drafted the manuscript. TO participated in animal studies and manuscript preparation. VK participated in design of the study and animal studies. KM participated in animals studies and biochemical characterization. AM participated in design of the study and manuscript preparation. JT performed animal studies, carried out immunoassays, conceived the study and helped prepare the manuscript. All authors read and approved the final manuscript."} +{"text": "A good correlation has been found between the extent of late gadolinium enhancement (LGE) and clinical outcome in patients who have undergone radiofrequency (RF) ablation for atrial fibrillation (AF). Residual blood signal with the traditional inversion-recovery (IR) sequence often hampers scar visualization in these patients and causes poor repeatability of scar size measurements. The dual-IR sequence has previously been shown to improve blood suppression in LGE images of myocardial infarction. We sought to assess whether the superior blood suppression with the dual-IR sequence would improve atrial scar definition in a swine model of chronic atrial radiofrequency ablation scar.A 30 kg female G\u00f6ttingen minipig pig underwent linear RF ablation from the SVC to the IVC under general anesthesia. MR imaging was performed two months later using a 1.5T MR scanner . After administering 0.2 ml/kg of Gadovist , dual-IR imaging (imaging every heartbeat) was performed at 10 and 15 minutes and compared with standard IR imaging (imaging every 2 heartbeats) at 35 minutes.The dual-IR pre-pulse consists of two non-selective inversion pre-pulses separated by two time delays (TI1 and TI2). The TI1 and TI2 delays were optimized to achieve signal suppression in the T1-range of 250-1400 ms. Whereas the IR sequence can only null one T1 species , the dual-IR pre-pulse simultaneously suppresses both the blood and normal myocardium whilst maintaining high signal in the scar.Dual-IR images achieved superior blood suppression at an earlier time point compared with IR images Figure . The enhThe dual-IR technique improves blood signal suppression and definition of the edges and boundaries of LGE areas. As dual-IR images were performed every heartbeat and taken earlier after contrast administration, it also has the potential to reduce the overall scan time.This work was funded by the British Heart Foundation award RE/08/003 and EU COST Action: TD1007. The authors also acknowledge financial support from the Department of Health via the National Institute for Health Research (NIHR) comprehensive Biomedical Research Centre award to Guy's & St Thomas' NHS Foundation Trust in partnership with King's College London and King's College Hospital NHS Foundation Trust and the Centre of Excellence in Medical Engineering funded by the Wellcome Trust and EPSRC under grant number WT 088641/Z/09/Z."} +{"text": "The discovery of novel anti-viral restriction factors illuminates unknown aspects of innate sensing and immunity. We identified RNA-associated Early-stage Anti-viral Factor (REAF) using a whole genome siRNA screen for restriction factors to Human Immunodeficiency Virus (HIV) that act in the early phase of viral replication.We observed more than 50 fold rescue of HIV-1 infection, using a focus forming unit (FFU) assay, following knockdown of REAF by specific siRNA. Quantitative PCR was used to measure the effect of REAF knockdown on two steps in the replication cycle - production of reverse transcripts and integration of viral cDNA. Both steps were strongly enhanced. Conversely, when REAF is over expressed in target cells fewer reverse transcripts are produced. Human REAF can also inhibit HIV-2 and simian immunodeficiency virus (SIV) infection. REAF associates with viral nucleic acid and may act to prevent reverse transcription.This report firmly places REAF alongside APOBECs and the recently described SAMHD1 as a potent inhibitor of HIV replication acting early in the replication cycle, just after cell entry. We propose that REAF is part of an anti-viral surveillance system destroying incoming retroviruses. This novel mechanism could apply to invasion of cells by any intracellular pathogen."} +{"text": "The Aromascan A32S conducting polymer electronic nose was evaluated for the capability of detecting the presence of off-flavor malodorous compounds in catfish meat fillets to assess meat quality for potential merchantability. Sensor array outputs indicated that the aroma profiles of good-flavor (on-flavor) and off-flavor fillets were strongly different as confirmed by a Principal Component Analysis (PCA) and a Quality Factor value (QF > 7.9) indicating a significant difference at (P < 0.05). The A32S e-nose effectively discriminated between good-flavor and off-flavor catfish at high levels of accuracy (>90%) and with relatively low rates (\u22645%) of unknown or indecisive determinations in three trials. This A32S e-nose instrument also was capable of detecting the incidence of mild off-flavor in fillets at levels lower than the threshold of human olfactory detection. Potential applications of e-nose technologies for pre- and post-harvest management of production and meat-quality downgrade problems associated with catfish off-flavor are discussed. Most prannually . The incannually .The current method for detecting off-flavor in catfish meat usually involves quality control evaluations by expensive human inspectors (assessors). The training of assessors for sensory evaluation is necessary for almost all sensory methods used to grade meat quality . The degMallotus villosus (capelin) [Merluccius hubbsi (Argentinean hake) [Thunnus albacares (yellowfin tuna) [Salmo salar [Gadus morhua (Atlantic cod) [Sardina pilchardus (Moroccan sardines) [Sparus aurata (sea bream) [Trichiurus lepturus (hairtail or cutlassfish) [Hypophthalmichthys molitrix (silver carp) [Oreochromis niloticus (tilapia) [Ctenopharyngodon idellus (grass carp) [Most previous studies involving the e-nose evaluation of meat quality have been concerned with the detection of microbial and chemical contamination (particularly the presence of human pathogens and toxins in meat), meat age (freshness), spoilage, and authenticity of meat types to avoid fraud and adulterations with cheaper meats ,10\u201319. Ecapelin) , Merluccan hake) , Thunnusin tuna) , Salmo s salmon) ,24, Gadutic cod) , Sardinaardines) \u201329, Spara bream) , and Triassfish) . Meat quassfish) and octoassfish) . Previouer carp) , Oreochrtilapia) , and Ctess carp) .We evaluated the efficacy of utilizing a conducting polymer (CP) electronic-nose (e-nose) device for the detection of off-flavor in catfish as a quality control for grading meat. The objectives of this study were to determine the capabilities of the Aromascan A32S e-nose: (1) to detect the presence of off-flavor compounds in catfish meat; (2) to discriminate between good-flavor (on-flavor) and off-flavor meat samples; and (3) to assess the potential feasibility of using this or similar e-nose instruments for managing pre-harvest off-flavor problems in catfish ponds and for post-harvest assessments of catfish meat quality and merchantability based on the presence of off-flavor compounds in harvested fish.2.Ictalurus punctatus Rafinesque (channel catfish), the most numerous and abundant catfish species marketed in the southern United States.The catfish meat samples, utilized for testing the efficacy of the Aromascan A32S e-nose for the detection of off-flavor in this study, were obtained from fresh catfish, randomly collected from several 0.04 ha experimental catfish ponds of the Thad Cochran National Warmwater Aquaculture Center in the Mississippi Delta region located near Stoneville, Mississippi. The fish samples used in this study were all of one species, 2.1.base). The sorption of headspace volatiles, composed of specific VOC mixtures, to the conducting polymer sensor surfaces induce a change in the electrical resistance to current flow which is detected by a transducer to produce the output from the sensor array. Sensor responses varied with the type of plastic polymer used in the sensor matrix coating, produced by electropolymerization of either polypyrrole, polyanaline or polythiophene derivatives, which have been modified with ring-substitutions of different functional groups and with the addition of different types of metal ions to the polymer matrix in order to improve and modulate sensor response. All measurements were statistically compared using normalized sensor outputs from the sensor array. The conducting polymer analysis (CPA) methods used with this instrument employ application-specific reference libraries for aroma pattern-recognition and neural-net training algorithms.The AromaScan 32S is a conducting polymer (CP) electronic nose that contains an organic matrix-coated polymer-type 32-sensor array, designed for general use applications with 15 v across sensor paths. The sensor-array response of the A32S e-nose to VOCs from different chemical classes was tested and reported previously . Sensors2.2.3 uncapped glass vial inserted into a 500 mL Pyrex glass sampling bottle no. 1395 fitted with reference air, sampling, and exhaust ports on a polypropylene bottle cap. Reference air entered the sampling bottle through a 3 mm-diameter polypropylene tube extending to just above the bottom of the sampling bottle. The sampling bottle was held in the sampling chamber within the instrument at a constant air temperature of 25 \u00b0C and purged with moisture-conditioned reference air for 2 min prior to building headspace. The sampling bottle was sealed and volatiles from each meat analyte were allowed to build headspace and equilibrate for 30 min prior to each run. Prerun tests were performed as needed to determine sample air relative humidity compared with that of reference air. Reference air was set at 4% relative humidity at 25 \u00b0C. The sampling bottle cap and exhaust port were opened between runs to purge the previous sample with conditioned reference air. A reference library (recognition file) for off-flavor vs. good flavor meat types was constructed using neural net training by defining aroma classes using reference databases of known sample types. This recognition file then was used to identify unknown samples.Fresh catfish (approximately 18 months old and 570\u2013900 g), were randomly sampled by netting from local research ponds after being stunned by a custom built, 40-volt electric pulse shocker . The heads were removed mechanically using a Baader Model 166 Heading Machine , eviscerated manually, filleted and skinned by a Baader Model 184 fillet machine (Baader), and trimmed manually. The fish were immediately frozen at \u221220 \u00b0C for long-term storage prior to e-nose analysis of individual samples. Immediately prior to CPA tests, individual fish were removed from the freezer and thawed to room temperature on clean tissue paper to air dry. Small meat core samples were taken from individual fresh catfish using a sharp stainless steel coring tool, pressed into the side flesh of each fish fillet at the thickest point, and the meat core was removed from the corer using a clean glass rod. Each meat core was blotted on tissue paper to remove free moisture and analyzed separately by placing individual meat cores into a 14.8 cm2.3.3/min using a ADM 3000 flow meter . The instrument was interfaced with a personal computer via an RS232 cable controlled with Aromascan Version 3.51 software. The instrument plumbing (reference airflow route through the instrument) was altered from conventional architecture and configured for static sampling of the headspace by allowing air flow, maintained at 605 cm3/min flow rate, to be released out of the external vent port of the instrument during analytical runs, and closing the exhaust port on the sampling bottle so that headspace volatiles were taken by suction from a homogeneous static air mass within the sampling bottle.Electronic-nose analyses of catfish off-flavor compounds in meat were conducted with an Aromascan A32S intrinsically conducting polymer (ICP) e-nose. Eight sensors, that did not respond or contribute to the discrimination of catfish volatiles, were turned off. The block temperature was maintained at a constant 30 \u00b0C. Reference air was preconditioned by passing room air sequentially through a carbon filter, silica gel beads, inline filter, and Hepa filter to remove organic compounds, moisture, particulates, and microbes, respectively, prior to humidity control and introduction into the sampling bottle. The flow rate of sampled air at the sampling port was maintained at 702 cm2.4.Data from the sensor array were collected at 1 s intervals using a 0.2 detection threshold (y-units), a 15\u201320 y-max graph scale, and with a pattern average of five data samples taken per run during data acquisition. A uniform run schedule was used consisting of reference air 20 s, sampling time 90 s, and wash 20 s, followed by 90 s of reference air for a total run time of 220 s. A 2 min reference air purge was completed between runs after each sample was removed from the sampling bottle. Sensors were rinsed between runs with a 2% isopropanol solution to remove any residual analyte compounds that had adsorbed to the surface of individual sensors from the previous analysis.2.5.et al. [A catfish-specific aroma signature reference library was constructed from ten separate meat samples from separate catfish. All database files were linked to specific (designated) aroma classes defining each sample type or category. All databases were constructed from sensor-array output data collected during a 20 s interval, 85\u2013105 s into the run cycle, immediately prior to the closing of the reference air valve to the sensor array. The following recognition network options were used for each training session: training threshold = 0.60, recognition threshold = 0.60, number of elements allowed in error = 5, learning rate = 0.10, momentum = 0.60, error goal = 0.010 (P = 0.01), hidden nodes = 5, maximum iterations (epochs) = 10,000, using normalized input data, not actual intensity data. Some parameters were modified for improvement of recognition accuracy. A typical training required 2\u201335 min, depending on the size of the database applied, using an IBM-compatible personal computer with a minimum of 64 Mb of RAM and 350 MHz run speed. Artificial neural net (ANN) trainings were validated by examining training results that compare individual database files for compatibility or by similarity matches to each specific odor classes by test-assigned odor class distributions among related odor classes included in each library. The specific detailed analytical methods used for identification of unknowns, data processing, and statistical determinations followed the procedures and specifications indicated by Wilson et al. .2.6.Individual sensor output values from the sensor array were normalized using bell-shaped curve statistical analysis algorithms within the data-processing module of the Aromascan Version 3.51 software. Sensor output values from different samples and replications of each sample type (aroma class) were used to determine mean percentage change in electrical resistance values \u00b1 one standard deviation (SD) for each sensor within the aroma signature pattern (aroma profile) of each aroma class.2.7.vs. off-flavor catfish meat samples. The mapping parameters for three-dimensional PCA were: iterations = 30, units in Eigen values (%), and use of normalized input data. The degree of relatedness between meat aroma types was determined using three-dimensional PCA of headspace volatiles with each axis of the aroma map representing a separate principal component of headspace volatiles within sample-analyte mixtures.Detailed comparisons of relatedness of odor classes (meat types) were determined using principal component analysis (PCA) algorithms provided by the Aromascan 3.51 software. Three-dimensional PCA was used to distinguish between headspace volatiles of good-flavor 3.The utilization of filleted meat core samples from fresh pond-raised catfish provided sufficiently strong sensor-responses from the A32S e-nose sensor array for effective detections of off-flavor compounds in the meat to assess meat quality. The building of sample headspace volatiles from meat samples for 30 min prior to analysis resulted in data outputs that allowed effective discriminations of samples types based on the presence or absence of off-flavor compounds in individual fish samples.3.1.The typical graphics outputs from the Aromascan A32S e-nose sensor array, derived from analyses of catfish headspace volatiles, were strong with well-separated intensity readings from individual sensors . All senSensor responses to headspace volatiles from catfish meat samples were quite diffuse, but showed relatively low to moderate intensities. Instrument operation was significantly affected by sample air relative humidity (RH). Sensors were overloaded by excess moisture in the sample. This problem was controlled by maintaining a relatively dry reference air stream (\u22644% RH) with minimal impact on sensor sensitivity. Maintaining a low reference air RH assured positive sensor responses in most cases because any additional moisture added to the analyzed headspace was derived from the sample. Effective control of reference air RH by the instrument humidity control device required that sample hydration was properly maintained to avoid free moisture. Standardizing sample preparation and equilibration methods controlled the sample size releasing volatiles and headspace accumulation. Reference air prefilters provided assurances of air quality introduced into the sampling chamber. Instrument precision was very high when these controls were strictly maintained.3.2.vs. off-flavor aroma classes varied widely within the 2 to 8 sensor-intensity range with very good precision as indicated by low standard deviations (SD) of mean values. Among both sample types, the lowest sensor intensities were recorded for sensors 4\u20136 and the highest intensities occurred for sensors 27\u201329. Sensors 30 had no response to headspace volatiles of meats from either aroma class. Sensor 20 could only detect headspace volatiles from off-flavor meat samples. Thus, twenty sensors provided response outputs for both aroma classes.Two distinct aroma classes, good-flavor and off-flavor, were identified from catfish meat samples based on electronic aroma signature patterns (aroma profiles) derived from the A32S e-nose sensor array. Significant differences in sensor-response intensities were found between good-flavor and off-flavor meat samples types (aroma classes) for most sensors used in the analyses . Individvs. off-flavor sample types, identified as separate aroma classes of the differences recorded between good-flavor and off-flavor sensor outputs in \u201cdifference mode\u201d were positive for 18 out of 20 sensors producing an output, including sensors 1\u20139, 13\u201319, 28, and 29. The percentage difference in sensor intensities for all positive outputs in \u201cdifference mode\u201d were less than 0.5%, indicating relatively low variations among individual sensors, although cumulative differences between all twenty sensors provided a high level of overall difference in the aroma signature patterns (profiles) of good-flavor Three separate trials (batches) of catfish meat samples were run to test the efficacy of aroma class discrimination between the good-flavor and off-flavor meat sample types. The Aromascan A32S electronic nose provided consistent correct identifications for the majority of the samples tested in three trials based on differences in sensor-array responses to headspace volatiles . The insA large proportion (91.4%) of all catfish fillet unknowns from three trials was correctly identified to the proper aroma class. The lowest level (90.7%) of correct identifications that occurred with off-flavor meat samples were above the statistical level required for a confident determination. All other trial tests for both good-flavor and off-flavor meat types were well above the statistical level necessary for confident determinations. These levels of discriminations were achieved with a sampling rate of ten to twenty replications per unknown meat type in each trial.3.3.vs. off-flavor catfish samples using 3-dimensional PCA indicated significant differences between these two sample groups based on sensor-response patterns (aroma profiles). The differences between the aroma profiles of off-flavor vs. good flavor catfish (aroma classes) based on PCA, was graphed in the form of an aroma map , were as follows: PC 1 = 89.9%; PC 2 = 8.8%; and PC 3 < 0.5%, representing the x-, y-, and z-axis of the aroma map, respectively. Thus, a high proportion (98.7%) of the variation was explained by the first two principal components (PC 1 and PC 2). Almost all of the data points for individual samples of each aroma class (good-flavor and off-flavor) were closely clustered for most sample replicates on the aroma map.vs. off-flavor aroma classes were determined using a statistical algorithm called Quality Factor (QF) analysis that determines statistical distances between aroma profiles of aroma classes, measured using Euclidean distance units. The greater the QF value determined from headspace volatiles, the greater the difference (or distance) between the aroma signature profiles of the two aromas being compared. A QF value of 2.0 is roughly equivalent to a statistical difference at P = 0.10 level of significance. The QF value determined between the headspace volatiles of the off-flavor vs. the good flavor aroma class was 7.92, indicating good discrimination between the two classes at a statistical difference of P < 0.05 level of significance. This QF value indicates that these two aroma classes were distinguished with a high level of confidence and that some of the chemical components of the headspace mixtures of these two aroma classes are not chemically related. Even though cluster groups B (off-flavor) and cluster group C (good-flavor) are in close proximity, there is still sufficient differences among some of the compounds present in the headspace of the off-flavor aroma class that are not present in the good-flavor aroma class.The statistical level of difference between sensor array output pattern of headspace volatiles from good-flavor 4.The Aromascan A32S e-nose provided strong sensor responses to headspace volatiles from fresh catfish meat samples. These results suggest that the time allowed for building headspace volatiles prior to analytical runs might be significantly reduced from 30 min without an appreciable loss of signal strength. Individual sensor outputs derived from CP-analysis of headspace volatiles from catfish core samples were diffuse and well separated, similar to those produced from analyses of headspace volatile metabolites from bacteria, but at lower relative intensities . This ditrans-dimethyl-trans-(9)-decanol) and 2-methylisoborneol (MIB) [The most likely chemical compounds responsible for differences in aroma profiles between good-flavor and off-flavor catfish aroma classes have been identified previously. The two chemical compounds most frequently associated with off-flavor in catfish meat are geosmin ,40. Geosol (MIB) . These col (MIB) ,43. The ol (MIB) . This huet al. [et al. [Previous studies utilizing electronic-nose devices in catfish meat analyses have been very limited. Korel et al. tested tet al. ,44. Totaet al. . Pacquit [et al. develope [et al. . Trimeth [et al. . The enz [et al. \u201349. The [et al. ,51.vs. off-flavor aroma classes revealed three separate data clusters based on differences in aroma profiles with most of the variation represented by only two principal components represented by the x- and y-axes. The occurrence of the strongly off-flavor data cluster A at significant Euclidean distances from the strongly good-flavor data cluster B showed well separation of samples types at the extremes of aroma class sample types. However, the occurrence of data cluster B was interpreted as indications of catfish fillets that contained mostly good flavored aroma elements, but were contaminated by low-levels of off-flavor compounds that rendered the e-nose determination of off-flavor due to sufficient differences generated by the apparent detection of these abnormal malodorous compounds at low concentrations in the meat. Low-level detections of off-flavor compounds in some fillets are viewed as equivalent to incipient detections when off-flavor compounds are just beginning to accumulate in the meat tissue. These data provide evidence that the e-nose has the capability of detecting off-flavor in catfish meat at early stages of contamination. Such samples found in cluster B data were not the same as in-determinant samples because the e-nose clearly distinguished these samples as off-flavored at good levels of statistical confidence.The use of PCA to generate an aroma map of good-flavor There are at least two major potential applications of e-nose instruments to help manage and mitigate off-odor and off-flavor meat problems associated with commercial catfish production. First, portable e-nose instruments could be useful to detect and manage the preharvest occurrences of off-flavor in live fish within catfish ponds. The e-nose monitoring of off-flavor incidence in catfish by the periodic random sampling of catfish in individual ponds could be used for the early detection of off-flavor before it builds up to unmanageable levels. Early detection of off-flavor in catfish ponds allows the application of water-management methods to control the build-up of aquatic microbes causing off-flavor before off-flavor compounds began to accumulate within the meat of preharvest catfish. Once the treatment of pond water resources are maintained at sufficient levels of quality, the fish could then be continuously monitored over to time to determine when all traces of off-flavor have disappeared from the fish population in each pond prior to harvest. This process could minimize economic losses to the fish producer by reducing the incidence of catfish off-flavor in the final harvest. Secondly, e-nose devices could be used in the post-harvest meat-production and processing steps for quality control to effectively screen individual fresh catfish fillets for the presence of off-flavor compounds that essentially render affected fish fillets unmerchantable. This screening protocol could facilitate the culling of unsalable meats to assure that only the highest quality product is sold to fish suppliers in commercial meat markets. The use of effective quality assurance and quality control (QA-QC) procedures using e-nose devices could help maintain a producer's high-quality product and associated buyer's brand recognition.The current study has provided evidence to demonstrate that the CP Aromascan A32S e-nose has the capability to effectively discriminate between good-flavor and off-flavor in catfish fillets. However, the application of similar e-nose instruments to commercial production of catfish fillets would require the use of portable devices with much shorter analysis and recovery times in order to screen fillets with sufficient speed for rapid modern meat-production lines when fish are not prescreened in cultivation ponds prior to harvest. This could be achieved with the use of MOS sensors that not only provide faster recovery times, but also have much longer sensor lives than CP e-nose devices . Once ad"} +{"text": "Catheter-based transmyocardial injection offers a minimally invasive method to deliver therapeutics to the heart. It is typically performed under X-ray fluoroscopic guidance, which suffers from poor demarcation of myocardial boundaries and an inability to assess myocardial viability. MRI-guided intramyocardial delivery of therapeutics at 3T offers the potential for more precise targeting of these therapies with superior tissue contrast. Our group has been actively involved with microencapsulated stem cell therapy to improve cell retention and prevent stem cell rejection. However, conventional microencapsulated stem cell products are too large to be administered transmyocardially. We demonstrate here intramyocardial injection of a prototype single stem cell therapeutic into the myocardium of a normal swine using real-time MR guidance and a custom active injection catheter.ex vivo pig heart, and an in vivo swine study at 3T (Siemens TimTrio). For the in vivo study, a breath-hold, multi-slice cine TrueFISP short-axis stack was obtained, which was segmented and converted to a 3D model impregnated with iron oxide (MyeOne) were produced using a custom microfluidic device. A custom MR- trackable, steerable intramyocardial injection catheter with four built-in tracking coils Figure was visul Figure for an ol Figure . The catl Figure . After el Figure . Deliverl Figure . RelevanLeft ventricular catheterization and guidance to four target sites in the myocardium was achieved. Confirmation of microbead delivery on FLASH images was possible but difficult due to the small volume and low iron concentration delivered. Follow-up imaging at one week post-delivery was unable to visualize the iron oxide-labeled therapeutic. No adverse events from transmyocardial delivery were observed.in vivo heart.A real-time interface with active catheter tip tracking enabled successful 3T MRI-guided transmyocardial delivery of a prototype therapeutic to the MD Stem Cell Research Foundation (2011-MSCRFII-0043) and Siemens Corporation"} +{"text": "Factors affecting host immunity are important variables during cancer growth. The immunosuppressive tumor microenvironment perturbs numerous immune regulatory networks and usurps host antitumor immune responses. We discovered that tumor interferes with host hematopoietic Notch system. Tumor-induced decrease in Notch signaling in host immune cells could be a major causative link in the inadequate induction of anti-tumor immunity. Interestingly, we found that tumor-induced decrease in immune Notch could be restored therapeutically by the following two agents. Administration of a novel Delta-like ligand 1 (DLL1) multivalent cluster, and FDA-approved proteasome inhibitor drug bortezomib - which also sensitizes tumors to death signals - could activate Notch 1 signaling in lymphoid cells of tumor-bearing mice without increasing tumor cell proliferation or clonogenicity. Systemic activation of DLL1-Notch signaling could attenuate tumor vascularization as well as increase T cell infiltration in tumor, decrease proportion of regulatory T cells and enhance antitumor T cell function and memory in multiple mouse tumor models. This resulted in significant suppression of tumor growth in wild type mice as well as provided therapeutic benefit following an adoptive T cell transfer into tumor-bearing SCID-NOD mice. New data also show that bortezomib affects the expression of notch receptors and ligands differentially in lymphocytes and in a wide range of solid tumor cells: 4T1, PyMT, MDA-MB-231, C26, LLC, D459, and Renca-HA. Moreover, bortezomib administration increased the expression of Notch target Hes1 in thymus, lymph node and spleen of tumor-bearing mice, suggesting a potential synergistic action of bortezomib and DLL1 activation of Notch signaling. This new role of Notch in the development of effective antitumor immunity and the potential of its modulation by a novel prototypic agent DLL1 in combination with bortezomib present exciting opportunities to uncover multi-pronged immune stimulatory regimens. Reagents based on the multivalent forms of Notch ligands thus need to be explored for the therapeutic modulation of Notch signaling. Therapeutic restoration of immune Notch signaling could provide effective treatment and recurrence-free survival in cancer patients by breaking tumor resistance and induction of robust antitumor immunity."} +{"text": "According to the 2004 WHO Annual Report, abdominal sepsis (AS) is one of the most dangerous diseases of the 21st century. But the issue of its treatment including immunotherapy is very far from being completely solved. Our aim was the demonstration of specific immunotherapy efficacy in AS.We investigated activity of immunogenesis (production of specific antibodies) in AS in 50 patients under impact of hyperimmune plasma infusion obtained from the donors who recently endured acute inflammatory abdominal diseases. The control group was made up of 10 healthy people.Escherichia coli, anti-Pseudomonas aeruginosa, anti-Staphylococcus aureus, anti-bacteroids, anti-peptococci immunity. Introducing hyperimmune plasma obtained from such donors evidently increases specific antibody titer in AS patients increases titer of specific antibodies, and increased concentration of specific antibodies improves forecast of survival in AS."} +{"text": "This study aimed at evaluating the early effects of successful elective percutaneous coronary intervention (PCI) on systolic and diastolic function.We consecutively studied the systolic and diastolic function in 21 patients with stable coronary artery disease (CAD) and left ventricular ejection fraction (LVEF) > 40% before and 48 hours after successful elective PCI.p-value = 0.008) following PCI. Diastolic velocities, E/A ratio, deceleration time (DT), early and late diastolic velocities of mitral annulus in TDI, pulmonary vein systolic (PVs) and diastolic flow velocity (PVd) did not show significant improvement.Tei index and systolic indices did not change significantly. Among the diastolic indices, only velocity propagation (Vp) improved significantly (from 42.9 \u00b1 10.8 to 51.8 \u00b1 10.7, Propagation velocity of mitral inflow was the earliest index to recover following successful PCI in patients with stable CAD. Percutaneous coronary intervention (PCI) is a very common revascularisation procedure performed in patients with stable coronary artery disease (CAD).Echocardiography provides a feasible and non-invasive technique for assessment of global and regional myocardial function.The present study was designed to evaluate the early effects of successful elective PCI on systolic and diastolic function globally and regionally through thorough echocardiographic examinations, including two-dimensional (2-D), M-mode, colour Doppler and TDI.Our study participants were recruited from 31 consecutive patients with stable CAD who were scheduled for elective PCI in Rajaie Heart Centre. Patients were considered for inclusion if they had angiographically documented coronary artery stenosis > 70% in diameter in the culprit lesion by visual assessment, and documented ischaemia. Ischaemia was documented using stress testing in patients with typical stable angina, according to the Canadian Cardiovascular Society (class I or II).Exclusion criteria were bundle branch block, pacemaker implantation, left ventricular ejection fraction (LVEF) < 40%, valvular heart disease, cardiomyopathy, history of coronary artery bypass grafting (CABG), refractory angina or acute myocardial infarction (MI) requiring emergency revascularisation, and left main stem disease.All patients were evaluated by an experienced echocardiologist, using conventional and tissue Doppler echocardiography examinations one day before and 48 hours after successful PCI, in order to assess cardiac systolic and diastolic function. Successful revascularisation was defined as a residual stenosis of < 30% in luminal diameter with TIMI flow grade 3. Patients with unsuccessful PCI (10 people) were excluded.All patients were on an optimal medical regimen consisting of nitrates, aspirin, \u03b2-blockers, angiotensin converting enzyme inhibitors and lipid-lowering agents (statins) along with a low-fat diet on an individual basis.The institutional review board of the hospital approved the study protocol. All participants gave written informed consent. This investigation was in accordance with the Declaration of Helsinki.Direct stenting or stenting after successful angioplasty was performed in all the participants according to published guidelines.Echocardiographic data were obtained using a commercially available ultrasound system Vivid-3 (GE) equipped with a 3-MHz transducer. Measurements were obtained by averaging values recorded in three consecutive cycles, according to the current American Society of Echocardiography guidelines.14For two-dimensional and M-mode echocardiography, 2-D images were obtained in standard parasternal and apical views. All patients were examined at rest in the left lateral decubitus position.The LV end-diastolic and end-systolic dimensions (LVEDD and LVESD) were measured at the level of the mitral leaflet tips from the parasternal long-axis with two-dimensional targeted M-mode echocardiography. LVEF was calculated from the apical two- and four-chamber views using the modified Simpson\u2019s rule.The regional wall motion abnormality (RWMA) score of the LV was assessed for each LV segment individually, and the wall motion abnormality score index (WMSI) was obtained using the 16-segment model, according to the American Society of Echocardiography recommendations.For RV systolic functional assessment, the tricuspid annular plane systolic excursion (TAPSE) was measured using two-dimensionally guided M-mode imaging from the apical four-chamber view.Mitral inflow velocities were measured with pulsed-wave colour Doppler echocardiography, with the sample volume positioned between the tips of the mitral leaflets in the apical four-chamber view. Peak early diastolic velocity (E), peak late diastolic velocity (A), E/A ratio and deceleration time (DT) were obtained.Mitral inflow propagation velocity (Vp) was measured as the maximum slope of the first aliasing velocity during early filling from the mitral valve plane to 4 cm distal to the LV cavity in the apical four-chamber view using colour M-mode Doppler.Pulmonary vein systolic flow velocity (PVs) and diastolic flow velocity (PVd) were measured from the apical four-chamber by placing a sample volume in the right upper pulmonary vein with Doppler echocardiography. Isovolumetric contraction time (IVCT), isovolumetric relaxation time (IVRT) and ejection time (ET) were assessed by simultaneously measuring the flow into the LV outflow tract and the mitral inflow, using Doppler echocardiography. The index of myocardial performance (IMP or Tei index) was calculated by dividing the sum of IVRT and IVCT by ET.Pulsed-wave TDI was performed by activating the tissue Doppler function in the same echocardiographic machine. Mitral annulus velocities were measured using the pulsed-wave TDI technique, by placing a 1\u20132-mm sample volume at the levels of septal, lateral, inferior, anterior and posterior annulus.Peak systolic velocity of the mitral annulus (Sa), and early (Ea) and late diastolic (Aa) velocities of the mitral annulus were determined from septal, lateral, inferior, anterior and posterior aspects. Peak systolic velocity of the tricuspid annulus (TA-Sa) was also derived from pulsed Doppler tissue imaging of the lateral tricuspid annulus.t-test. The Wilcoxon signed rank test was used to test for the difference between the mean RWMA scores before and after PCI. The statistical software SPSS-13 for Windows was used for all analyses; p-values < 0.05 were considered statistically significant.Continuous variables are presented as means \u00b1 standard deviations (SD) and categorical data are expressed as frequencies and percentages. Comparisons of continuous variables pre and post PCI were carried out using the paired-samples p = 0.008). Other diastolic indices did not show improvement A total of 21 patients who had had successful PCI were considered for the study analysis. Baseline characteristics of participants are summarised in This study presents a comprehensive echocardiographic assessment of regional and global myocardial function, both systolic and diastolic, following blood flow restoration with PCI electively performed in patients with stable CAD. Our findings indicate that the propagation velocity of early flow into the LV cavity (Vp), measured by colour M-mode Doppler, was the most sensitive index to recover after successful PCI.LV ejection fraction calculated by the biplanar Simpson\u2019s method, along with other parameters of myocardial systolic function including the regional wall motion index evaluated by 2-D and TDI-derived systolic myocardial velocities at the mitral (Sa) and tricuspid annulus (TA-Sa), did not change significantly early after PCI. Previous studies have shown different results regarding systolic functional improvement following PCI. In a study performed in 41 patients with stable CAD, successful elective PCI did not improve ejection fraction at the one-day and six-month follow up.5However, in another study, peak systolic velocities of three annular sites, but not the ejection fraction, showed substantial improvement.It is postulated that patients with severely depressed ventricular dysfunction (LVEF < 40%) benefit most from revascularisation.et al.16Among various echo-technique parameters assessing diastolic function, only colour M-mode Vp was found to have improved significantly 48 hours after PCI. There have been various reports on improvements observed in diastolic parameters following PCI. Diller A study performed on 31 patients with chronic CAD showed that most echocardiographic diastolic indices, including IVRT, EDT, E/A ratio, IVCT and diastolic indices of both the mitral and tricuspid annulus sites on TDI improved significantly 24 hours following elective PCI.9There is evidence that abnormalities in diastolic function may precede systolic dysfunction during myocardial ischaemia.et al.21Vp, which was initially proposed by Brun The reason for persistence of abnormal indices of LV performance (other than Vp) may be the duration of disease before PCI.A limitation to the current study could have been the relatively small number of patients evaluated. Moreover, since functional improvement following PCI may increase over time,Unlike studies that showed an improvement in TDI parameters of systolic and diastolic function in patients with stable CAD after successful PCI, in our population only the colour M-mode Doppler parameter improved 48 hours after successful elective PCI in patients with stable CAD. More studies should be done to corroborate the results presented here."} +{"text": "An elevated level of EMMPRIN in cancer tissues have been correlated with tumor invasion in numerous cancers including oral cavity and larynx. Although EMMPRIN's effect has been generally attributed to its MMP inducing activity, we have previously demonstrated in breast cancer model that EMMPRIN can also enhance invasion by upregulating uPA. In this study, the role of EMMPRIN in regulating uPA and invasion was investigated in oral squamous cell carcinoma (OSCC) progression.Precancerous and invasive oral tumoral tissues were used as well as the corresponding cell lines, DOK and SCC-9 respectively. The paracrine regulation of uPA by EMMPRIN was investigated by treating culture cells with EMMPRIN-enriched membrane vesicles. UPA expression was analyzed by qPCR and immunostaining and the consequence on the invasion capacity was studied using modified Boyden chamber assay, in the presence or absence of EMMPRIN blocking antibody, the uPA inhibitor amiloride or the MMP inhibitor marimastat.OSCC tumors were shown to express more EMMPRIN and uPA compared to dysplastic lesions. The corresponding cell models, SCC-9 and DOK cells, displayed similar expression pattern. In both cell types EMMPRIN upregulated the expression of uPA as well as that of MMP-2 and MMP-9. EMMPRIN treatment led to a significant increase in cell invasion both in the invasive SCC-9 and in the less invasive dysplastic DOK cells, in an MMP and uPA dependent manner.Our results suggest that the upregulation of uPA contributes to EMMPRIN's effect in promoting oral tumor invasion. Oral squamous cancer cell carcinoma (OSCC) ranks among the top ten most frequently cancers, and 500 000 people per year are world widely diagnosed . OSCC isIn addition to increasing invasion through proteinase induction, EMMPRIN induces several other malignant properties associated with cancer. These include, amongst others, the stimulation of cell survival signaling, including Akt, Erk and FAK, through the increased production of the pericellular polysaccharide hyaluronan . Also, EThe role of EMMPRIN in tumor growth and invasion was illustrated by the accelerated growth and increased invasiveness of EMMPRIN-overexpressing human breast cancer cells ,19. The Microarray analyses of primary oral tumors have identified uPA and its receptor (uPAR) as key genes associated with human OSCC progression ,20,21. HIncreased expression of EMMPRIN in oral squamous cell carcinoma has been shown to correlate with lymphatic metastasis and tumor progression . EMMPRINfetal bovine serum (FBS) and 2mML-glutamine. Chinese Hamster Ovary (CHO) cells were cultured in DMEM/F12 (Invitrogen) supplemented with 10% FBS and 2mML-glutamine.Two cell lines representing two stages of oral tumour progression were used: DOK, a precancerous dysplastic cell line and SCC-CHO cells were stably transfected with a plasmid containing full-lengh EMMPRIN cDNA (CHO-Emp cells) or empty vector (CHO-Mock cells) . CHO-EmpEMMPRIN small interfering RNA(siRNA) oligos (Ambion/Applied Biosystems) or scrambled siRNA oligos (25 nmol/L) were transfected into DOK and SCC-9 cells using the BLOCK-iT transfection kit and Lipofectamine-2000 (Invitrogen), according to the manufacturer's protocol. Cells were then incubated for 24 hours prior to the measurements of uPA mRNA by qRT-PCR and invasion assays.Western blot was preformed as previously described . MembranGelatin or casein-plasminogen zymography was performed as described previously . Serum-f9 molecules/\u03bcl. The copy number of unknown samples was calculated by setting their PCR cycle number to the standard curve. Data were normalized to the TBP (TATA-box binding protein) housekeeping gene transcripts. Primers and probes are available under request. All experiments were performed in duplicate.Transcript quantification for EMMPRIN, uPA, MMP-2 and MMP-9 was conducted using TaqMan technology and standard curve quantification method. Quantitative PCR were performed using Perfect Master Mix-Probe on LightCycler system2.0 according to the manufacturer's techniques. Briefly, cDNAs for EMMPRIN, uPA, MMP-2 and MMP-9 were prepared from total RNA, amplified by RT-PCR, and cloned using TOPO II TA cloning kit (Invitrogen). A standard curve for each transcript was generated using serial dilutions of cloned products ranging from 1 to 104 cells/insert for 24-well plate) were plated onto Matrigel-coated cell culture inserts together with either anti-EMMPRIN antibody (20 \u03bcg/mL), non-immune IgG, uPA inhibitor amiloride or the MMP inhibitor marimastat . Three hours later CHO-Emp mb or CHO mb were added (20 \u03bcg/ml). After 48 hours of incubation, cells on the underside of insert filters were fixed, stained with Diff Quik (Dade Behring) and counted under a bright-field microscope. Migration assay was performed as above, omitting matrigel coating.In vitro invasion was assessed using a modified Boyden chamber assay. SCC-9 and DOK cells (2 \u00d7 10DOK and SCC-9 cells were grown in microscope slide chambers to 50-60% confluence. CHO-Emp mb or CHO mb were then added (20 \u03bcg/ml) and 24 hours later, cells were washed in PBS and fixed in 4% paraformaldehyde for immunofluorescence detection of EMMPRIN or uPA. Slides were probed with mouse anti-human EMMPRIN antibody (HIM6 BD Pharmingen) or with goat anti human uPA antibody (American diagnostica). After incubation with the corresponding secondary antibody (Alexa 488 and 594) the slides were examined with a laser-scanning confocal microscope . Cells were counterstained with DAPI (Sigma).Tissues of normal oral mucosa were collected from healthy donors attending for tooth extraction. All patients gave their informed consent. Protocols were approved by our institution research ethics committee. Total Formalin-fixed paraffin-embedded (FFPE) tissue sections of 6 normal oral mucosa, 4 intra epithelial neoplasia, 8 micro-invasive OSCC and 8 invasive OSCC, were analysed for EMMPRIN and uPA expression using qRT-PCR and immunohistochemistry assays. For immunohistochemistry, FFPE sections were stained with a mouse anti-human EMMPRIN antibody (BD-Pharmingen) and a goat anti human uPA antibody (American diagnostica). Staining was visualized using the streptavidin-biotin-HRP detection method, followed by counterstaining with Mayer's hematoxylin. Three-amino-9-ethyl-carbazole was used as the chromogen. For transcript quantification levels, RNA was extracted using TRIzol reagent (Invitrogen). First-strand cDNA was synthesized using the High-Capacity cDNA Archive Kit (Applied-Biosystems). Transcript levels were measured in each tissue by qPCR using Perfect Master Mix-Probe on LightCycler 2.0 System (Roche). The expression levels of interesting transcripts were normalized to the housekeeping TATA-box binding protein (TBP) gene transcripts. All experiments were performed in duplicates and Spearman's rank correlation was used to evaluate the association between mRNA levels in oral dysplastic, micro-invasive and invasive tumor tissues.Tumor samples were collected from 20 patients with oral squamous carcinoma or dysplastic tissues. Data are expressed as mean F SD. Mann-Whitney and Student's t tests were used to compare differences between groups in various experiments.and compared with to their expression in normal oral mucosa (6). QRT-PCR analysis has shown that both EMMPRIN and uPA transcripts were proportionally increased with the invasive stage of the tumors micro-invasive (8) or invasive lesions (8) s Figure . An averEMMPRIN and uPA expression was also evaluated by immunohistochemical analysis of tumors obtained from OSCC patients. Figure The association of both EMMPRIN and uPA transcript with oral tumor progression and their colocalization within tumor tissues prompted us to look for a regulation of uPA by EMMPRIN. For that, two cell lines, DOK and SCC-9, representing the dysplastic and the invasive stages respectively were studied. These two cell models present a differential expression of EMMPRIN Figure , with SCThe role of EMMPRIN in the regulation of uPA production in these two cell lines was investigated by treating the cells with exogenously added EMMPRIN. EMMPRIN contained within membrane vesicles was obtained from CHO cells previously transfected with EMMPRIN full length cDNA. The incubation of DOK and SCC-9 cells with 20 \u03bcg/ml of EMMPRIN-containing membranes (designated CHO-Emp) increased uPA protease activity (by 40% for DOK and 26% for SCC-9) and RNA levels (5 fold for DOK and SCC- 9) when measured by casein-plasminogen zymography and qRT-PCR respectively, whereas those prepared from mock-transfected CHO cells (CHO) had no effect Figure . This waTo evaluate the specificity of EMMPRIN's effects, blocking anti-EMMPRIN antibody was added with the EMMPRIN containing membranes and the effect on uPA production was examined by zymography. As shown in Figure The regulation of uPA by EMMPRIN was also investigated by inhibiting endogenous EMMPRIN expression using RNA interference strategy. EMMPRIN siRNA transfection of DOK and SCC-9 cells showed a significant reduction in the transcript level of uPA Figure .Hence, EMMPRIN regulated uPA in both the dysplastic and the invasive tumor cell lines, suggesting a regulatory mechanism involved even at the early tumorogenesis stagesEMMPRIN has already been implicated in tumor cell invasion ,29. ThisEMMPRIN also had a more significant effect on the Invasion Indices of SCC-9 compared to DOK. This emphasizes the protease inducing function of EMMPRIN in the invasion process Figure .Since EMMPRIN is mostly known to upregulate MMPs, we investigated the relative contribution of the uPA and MMP systems to the invasion capacity of both cell lines. For that, we used 20 nmol/L amiloride (for uPA inhibition) and 10 \u03bcmol/L marimastat which were added alone or in combination. As expected, an inhibition of invasion was observed in both cell lines in the presence of either amiloride or marimastat, the inhibition was greater when the inhibitors were used in combination. However, EMMPRIN treatment did not restore invasion in any of these conditions Figure . These rEMMPRIN is widely distributed in many human and mammalian cells, with notably high expression in some of solids cancers including oral squamous cell carcinoma. It's over-expression is associated with malignancy and \u2044 or poor prognosis in many tumor types, and several studies suggest that EMMPRIN is an important factor which contributes to oral squamous cell carcinoma growth, invasion, and metastasis . EMMPRINThe functional importance of EMMPRIN during tumor progression has been related mainly to its ability to promote tumor cell invasion by stimulating MMP and VEGF cytokine production expression . We haveThe MAP kinase P38 was implicated in the regulation of uPA, certain MMPs and EMMPRIN itself and may represent a common mechanism for their regulation . As EMMPuPA gene has already been reported in oral tumors and cultured OSCC cells and tumors with high levels of both uPA and uPAR were shown to be more invasive [Silencing EMMPRIN in head and neck squamous carcinoma (HNSCC) cells was shown to result in significant suppression of tumor growth . Furtherinvasive ,33,34. CAlthough the role of EMMPRIN in tumor growth and metastasis has been studied in detail, the mechanisms by which it exerts its effects in OSCC tumorogenesis are not completely understood. Our results showing the induction of the uPA system provide important insights into the mechanism by which EMMPRIN contributes to oral tumor cell invasion and progression.The authors declare that they have no competing interests.GL: carried out in vitro experiments; SM (S Menashi): participated in the design of the study, data analyses and writing of the manuscript; BCB: coordinated tissue specimens study and analyzed Immunohistochemistry data; FK: carried out experiments; CQ: carried out experiments; MPP: carried out qPCR analyses; BN: developed analytical tools; FC: participated in the design of the study and research discussions; CL: participated in the design of the study and data analyses; SM (S Mourah): participated in the design of the study, statistical and data analysis and writing of the manuscript. All authors read and approved the finalmanuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2407/12/115/prepub"} +{"text": "Recent studies have shown that basic leucine zipper factor (HBZ) gene was transcribed in all adult HTLV-1 infected individuals examined, including ATL and HAM/TSP patients, whereas tax mRNA was only transcribed in a half of these groups. The amount of HBZ mRNA expression per provirus was higher than tax mRNA expression in HAM/TSP and adult asymptomatic carriers. Nevertheless, there are no data on HBZ and tax mRNA expression in child and adolescent carriers. The aim of this study was to quantify the HBZ and tax mRNA expression levels in infective dermatitis associated with HTLV-1 (IDH).RNA was extracted from PBMC of 31 patients with IDH and 8 adolescent asymptomatic carriers. The mRNA expression levels were quantified by real-time quantitative PCR. For HBZ gene, spliced (HBZ-SI) and non-spliced (HBZ) transcripts were analyzed.The HBZ mRNA expression levels were higher than the tax mRNA expression levels in patients with IDH and in the asymptomatic carriers, for both HBZ-SI and HBZ (p=0.0019 and p=0.005) transcripts. The HBZ-SI mRNA load was greater than the expression of the HBZ transcript (p=0.0005) only in IDH patients. HBZ-SI and HBZ mRNA load positively correlated with tax mRNA load in IDH patients but not in asymptomatic carriers. There was no correlation between the expression of these genes and proviral load in the two groups evaluated.These findings suggest that expression of HBZ gene plays a role in early stages of HTLV-1 infection."} +{"text": "The crystal structures of human placental aromatase in complex with the substrate androstenedione and exemestane have revealed an androgen-specific active site and the structural basis for higher order organization. However, X-ray structures do not provide accounts of movements due to short-range fluctuations, ligand binding and protein-protein association. In this work, we conduct normal mode analysis (NMA) revealing the intrinsic fluctuations of aromatase, deduce the internal modes in membrane-free and membrane-integrated monomers as well as the intermolecular modes in oligomers, and propose a quaternary organization for the endoplasmic reticulum (ER) membrane integration. Dynamics of the crystallographic oligomers from NMA is found to be in agreement with the isotropic thermal factors from the X-ray analysis. Calculations of the root mean square fluctuations of the C-alpha atoms from their equilibrium positions confirm that the rigid-core structure of aromatase is intrinsic regardless of the changes in steroid binding interactions, and that aromatase self-association does not deteriorate the rigidity of the catalytic cleft. Furthermore, NMA on membrane-integrated aromatase shows that the internal modes in all likelihood contribute to breathing of the active site access channel. The collective intermolecular hinge bending and twisting modes provide the flexibility in the quaternary association necessary for membrane integration of the aromatase oligomers. Taken together, fluctuations of the active site, the access channel, and the heme-proximal cavity, and a dynamic quaternary organization could all be essential components of the functional aromatase in its role as an ER membrane-embedded steroidogenic enzyme. Cytochrome P450 aromatase catalyzes the biosynthesis of estrogens from their androgenic precursors by converting the partially unsaturated A-ring to an aromatic A-ring. Structure-function relationships of aromatase have been studied for more than thirty years, but many issues remain unresolved. The recent crystal structure of human placental aromatase showing a compact active site cleft \u03b1) at much less computational costs However, the dynamical properties of aromatase that may play critical functional roles, such as membrane integration and active site access channel opening, have not yet been addressed. Availability of the crystal structure of aromatase has opened the door for investigating the dynamics by high resolution atomic/coarse-grained simulated models, such as molecular dynamics (MD) simulations and normal mode analysis (NMA). NMA proves to be a very powerful tool to gain insights into the protein dynamics at a reasonable resolution membrane integration. The two major intramolecular normal modes in the monomer are likely to be responsible for the active site access channel \u201cbreathing\u201d. The root mean square fluctuation (RMSF) from EN-NMA provides a measure for the intrinsic molecular flexibility and the analysis elucidates the rigid core structure of aromatase, regardless of its self-association and membrane integration.A tetramer is built using the crystallographic symmetry and then\u03b1) are computed from the mean square fluctuation (MSF), for the green monomer and compared with the X-ray B-factors has reduced amplitudes for the membrane integrating regions is calculated and visualized in a rendered ribbon diagram where red represents the lowest RMSF (at the heme group), and blue the highest RMSF (at the H-I loop) . The H-IAlthough the substrate is in direct contact with the catalytic cleft residues The C\u03b1-RMSFs calculated for a membrane-integrated aromatase monomer , a channel of dynamically disordered solvent and detergent, thereby providing some rationale as to why the N terminus is disordered.The calculations were repeated for the crystallographic tetramer with the N-terminal helices were scaled to the experimental B factor data. Prior to scaling, the calculated MSF of each node was reasonably up shifted away from the origin to account for the translational and rotational rigid body motions in the lattice cell.Root mean square fluctuation (RMSF) was used to characterize protein flexibility. The mean square fluctuation (MSF) of the kT/e to 7kT/e.The software Adaptive Poisson-Boltzmann Solver (APBS) The atomic model of aromatase with the N-terminal helix was used to build by collapsing a linear chain of two units of crystallographically related trimers into a cFigure S1The slowest normal mode of crystallographic tetramer of aromatase and the residue fluctuations against crystal contact interactions.(TIF)Click here for additional data file.Figure S2Ribbon diagrams showing the structure of a crystallographic tetramer.(TIF)Click here for additional data file.Figure S3Intermolecular motions of aromatase dimers from normal mode analysis.(TIF)Click here for additional data file.Figure S4Monomer-to-monomer docking computation.(TIF)Click here for additional data file.Figure S5The flexibility of a membrane-free aromatase monomer.(TIF)Click here for additional data file.Figure S6Membrane integration of aromatase and flexibility.(TIF)Click here for additional data file.Figure S7The flexibility of aromatase upon oligomerization.(TIF)Click here for additional data file.Figure S8Model for the N-terminal helix.(TIF)Click here for additional data file.Text S1Probing of other possible oligomeric structures by protein-protein docking computation.(DOCX)Click here for additional data file.Text S2Fluctuations in an oligomeric aromatase.(DOCX)Click here for additional data file.Movie S1Mode 12 of a crystallographic tetramer shows the motions of the N-terminal helices.(MOV)Click here for additional data file.Movie S2Two modes of intramolecular motion of a membrane-free aromatase monomer deduced from normal mode analysis: (A) hinge-bending mode and (B) twisting mode.(MOV)Click here for additional data file.Movie S3Two modes of intramolecular motion of a membrane-embedded aromatase monomer deduced from normal mode analysis: (A) hinge-bending mode and (B) twisting mode.(MOV)Click here for additional data file.Movie S4Three slowest modes of a membrane-embedded aromatase monomer: (A) and (B) bending and (C) twisting modes.(MOV)Click here for additional data file.Movie S5Two modes of intermolecular motion of the green-gold dimer deduced from normal mode analysis: (A) hinge-bending mode and (B) twisting mode.(MOV)Click here for additional data file.Movie S6Two modes of intermolecular motion of the blue-green-gold trimer deduced from normal mode analysis: (A) hinge-bending mode and (B) twisting mode.(MOV)Click here for additional data file.Movie S7Two modes of intermolecular motion deduced from normal mode analysis of the blue-green-gold trimer in the presence of the fourth gray monomer, simulating crystal packing conditions: (A) hinge-bending mode and (B) twisting mode.(MOV)Click here for additional data file."} +{"text": "The LDE225 and nilotinib combination more effectively inhibited tumor growth in mice compared to either vehicle- or nilotinib- or LDE225-treated mice. Histopathologic analysis of tumor tissue from LDE225 plus nilotinib-treated mice demonstrated an increased number of apoptotic cells detected by TUNEL staining. To investigate combined effects of LDE225 and nilotinib on primary Ph-positive acute lymphocytic leukemia (ALL) cells, NOD/SCID mice were injected i.v. with bone marrow mononuclear cells from a Ph positive ALL patient. Treatment with LDE225 and nilotinib demonstrated a marked segregation of apoptotic cells in both the central bone-marrow cavity and the endosteal surface. These results suggest that the combination with a Smo inhibitor and ABL TKIs may help to eliminate the Ph positive ALL cells. Taken together, the present study shows that the combination of LDE225 and nilotinib exhibits a desirable therapeutic index that can reduce the in vivo growth of mutant forms of BCR-ABL-expressing cells.Recent studies have demonstrated that hedgehog pathway is activated in chronic myeloid leukemia (CML) stem cells via up-regulation of Smoothened (Smo), a seven transmembrane domain receptor protein. LDE225 is a small molecule Smo antagonist which has entered Phase I clinical evaluation in patients with solid tumors. We performed a comprehensive drug combination experiment using a broader range of concentrations for LDE225 and nilotinib. Compared with single agents, the combination of LDE225 and nilotinib was more effective at reducing the outgrowth of resistant cell clones. No outgrowth was observed in the presence of 2 \u03bcM nilotinib plus 20 \u03bcM LDE225. Also co-treatment with LDE225 and nilotinib resulted in significantly more inhibition of growth than treatment with either agent alone in BaF3 cells expressing wt-BCR-ABL and BCR-ABL mutants . The observed data from the isobologram indicated the synergistic effect of simultaneous exposure to LDE225 and nilotinib even in BaF3 cells expressing T315I. To assess the in vivo efficacy of LDE225 and nilotinib, athymic nude mice were injected s.c. with BaF3 cells expressing random mutagenesis for BCR-ABL mutation. 7 days after injection (average tumor volume, 100 mm"} +{"text": "Cardiac motion self-gating is a technique where MRI signal is used to derive motion triggers instead of ECG, which might be problematic in high B0 field or cases where ECG is not accessible . However, the performance of existing cardiac self-gating approaches have not yet enabled clinical utility. We propose and evaluate here a novel cardiac self-gating strategy that potentially improves the trigger detection accuracy and reliability.Conventional cardiac self-gating uses the k-space center from a radial acquisition to represent the cardiac motion and derive triggers. However, this strategy suffers from signal drifting and distortion shown in Fig.Fig.Fig.Our data demonstrates that the proposed cardiac self-gating method can significantly reduce the drift and distortion of the self-gating signal and therefore improve cardiac trigger detection accuracy and reliability. Future work will be focused on implementing the technique in an imaging sequence as Fig.The authors acknowledge research-funding support from AHA (10SDG4200076), NIH (1R21HL113427)."} +{"text": "Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown.de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning.To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians.Transcriptome sequencing of short reads allowed for the simultaneous The limited regenerative capabilities of humans call for therapies that can replace or heal wounded tissues. The treatment of neurodegenerative diseases has been a major focus of regenerative medicine, as these diseases can cause irreversible damage to the central nervous system (CNS). It is crucial, therefore, to understand the molecular mechanisms of regeneration and the intrinsic and extrinsic signals that induce and promote this process.Planarian flatworms are one of the few animals that can regenerate their CNS. Planarians are free-living Platyhelminthes with a relatively simple CNS consisting of a bilaterally symmetrical brain made from two cephalic ganglia, and two longitudinal ventral nerve cords, which extend along the body axis and send out axonal projections into nearly any micrometer of the body (reviewed in ). DespitPlanarians are characterized by their large pool of pluripotent adult stem cells that facilitate the regeneration of whole animals from only small pieces of their body (reviewed in ). Strikiin vivo have made planarians an attractive model organism for investigating the molecular processes that underlie regeneration and stem cell biology iewed in ,11). Oneomosomes .S. mediterranea genome sequencing project ). To test where in the animal smed-egr-like1 was expressed, we performed whole mount in situ hybridization of intact and regenerating animals. We did not detect smed-egr-like1 mRNA in either intact animals or in animals after 6 or 24 h of regeneration , as we found at least one more putative Runx transcription factor (Gene_20170), which mapped to genomic contigs v31.007764 and v31.028733 but did not seem differentially expressed at the time points tested after 6 h, and maintained a high expression level during the first 48 h of regeneration, before slowly returning to near basal levels after 1 week Figure . Sequencsmed-runt-like1-positive cells could no longer be detected in posterior-facing blastemas. Instead, smed-runt-like1 was expressed in a subset of cells along the regenerating brain into the gut of planarians. mRNA levels of smed-runt-like1 were strongly reduced, but not completely eliminated after RNAi, possibly due to very rapid kinetics of its induction after decapitation , its high repetitiveness, and the redundant representation of genomic locations on multiple supercontigs. The assembly of short reads into longer transcripts simplifies the alignment and offers novel opportunities to improve the genomic assembly by identifying supercontig-spanning genes and [GenBank:JF914965], respectively.All next generation sequencing data are available through the ArrayExpress repository at the European Bioinformatics Institute (accession number [E-MTAB-607]). The GenBank accession numbers for dj: Dugesia japonica; dsRNA: double-stranded RNA; EGR: early growth response gene family; EST: expressed sequence tag; GO: gene ontology; nr: non-redundant; PBST: phosphate-buffered saline with Tween 20; PCR: polymerase chain reaction; qRT-PCR: quantitative reverse transcriptase PCR; RNAi: RNA interference; TNFR: tumor necrosis factor receptor; TRAF: tumor necrosis factor receptor associated protein.bp: base pair; CNS: central nervous system; KB designed the study and wrote the manuscript. MB designed the study. TS designed the study, performed SOLiD sequencing and analyzed the next generation sequencing data and wrote the manuscript. MCV performed the experiments and wrote the manuscript. SO performed the experiments and wrote the manuscript. All authors have read and approved the manuscript for publication.Transcriptome assembly from public 454 data. (a-c) Schematic overview of 454 transcriptome assembly approaches. Publicly available 454 reads were assembled either separately or as a combined dataset (c) using the Newbler 2.5 assembler. Colors indicate the three different assemblies: yellow, Abril et al. [et al. [(d) Kernel densities of the length distributions for the assembled sequences. For multi-isoform loci, only the longest isoform was considered. Colors as in (a-c). (e) Kernel densities of ortholog hit ratios obtained by comparing sequences from the different assemblies or computational prediction to the Schistosoma mansoni proteome using blastx. For multi-isoform loci, only the longest isoform was considered. Colors as in (a-c).l et al. (a); ora [et al. (b); redClick here for fileGenomic supercontigs. This histogram shows the sequence length distribution of all genomic S. mediterranea supercontigs (version 3.1 [sion 3.1 ). The reClick here for fileIdentification of supercontig-spanning transcripts. Illustration of 413 high-confidence supercontig-joining transcripts identified, with a description of the procedure.Click here for fileExperimental validation of the continuity of genomic supercontigs v31.005068 and v31.000152. (a) Agarose gel electrophoresis showing the PCR amplicon produced with forward and reverse primers annealing to supercontigs v31.005068 and v31.000152, respectively. (b) The amplicon sequence was verified by Sanger sequencing. (c) Blastn results showing the 5' end of the sequence aligning to supercontig v31.000152 and the 3' end matching supercontig v31.005068.Click here for fileExperimental validation of detected transcripts by RT-PCR. (a) Agarose gel electrophoresis of amplicons amplified using primers designed against 14 different sequences from the Illumina+ assembly and two control sequences. (b) Primer sequences used in the PCRs.Click here for filede novo transcriptome sequences with the NCBI non-redundant protein databaseBlastx comparison of . (a) Distribution of similarity detected in the best blastx hit for each transcript . (b) Distribution of blastx e-values for the best blastx hit for each transcript. For multi-isoform loci, only the longest isoform was used as a blastx query.Click here for fileIllumina+ assembly annotations and expression data. A spreadsheet containing the length, annotation and differential gene expression data for all sequences of the Illumina+ assembly.Click here for fileMapping statistics of Illumina and SOLiD raw reads. Statistics of mapping raw Illumina and SOLiD reads onto the Illumina+ assembly.Click here for fileMA plots illustrating differential gene expression from both Illumina and SOLiD data. For the longest isoform of each locus from the Illumina+ assembly, the expression fold change relative to the control (0 h) is plotted against its log average abundance (MA plot). Statistically significant up- or down-regulation ) is indicated in yellow and blue, respectively. Genes chosen for qRT-PCR validation MA plots show a comparison of Illumina transcriptome sequencing (RNAseq) data from 0.5 to 1 h samples (a), 2 to 3 h samples (b), 4 to 8 h samples (c), 10 to 18 h samples (d) and 24 to 72 h (e) relative to controls. SOLiD reads from control or regeneration samples were aligned to the genomic supercontigs with Bioscope. MA plots show a comparison of SOLiD RNAseq data from 1 h sample (f) and 6 h sample (g) relative to controls.n Figure are labeClick here for fileGene ontology enrichment analysis for each temporal expression class. Gene ontology term enrichment and depletion of each cluster compared to the full set of annotated sequences using GOSeq.Click here for filesmed-runt-like1Conservation, knockdown efficiency, and RNAi phenotype of . (a) Alignment of Runt domains of proteins from vertebrate and invertebrate species: Danio rerio ; Homo sapiens ; Hydra magnipapillata ; Drosophila melanogaster ; Schmidtea mediterranea . The planarian Runt domain shares at least 45% sequence identity with Runt domains from other organisms. (b) qRT-PCR analysis of smed-runt-like1 expression levels in intact and regenerating planarians 6 h after head and tail dissection. Prior to dissection, animals had been injected with three pulses of 32.2 nl of a 1.5 \u03bcg/\u03bcl dsRNA solution containing either dsRNAs against smed-runt-like1 or a control gene (gfp), for three days in a row for two consecutive weeks . Expression levels were normalized against those of a housekeeping gene (AY068123). Error bars represent standard deviations of the mean of three independent biological replicates of five worms each. Note that the smed-runt-like1 mRNA levels are reduced but not completely abolished upon RNAi in regenerating animals. (c) Immunofluorescence analysis (anti-Arrestin) of photoreceptor neurons in regenerating control and smed-runt-like1 RNAi animals at day 14 after decapitation. Note that smed-runt-like1 RNAi animals have severe eye patterning defects. Animals were treated as described in the Materials and methods section of the main text.Click here for fileExpression data mapped onto computational gene predictions. Differential gene expression data for all gene models predicted by MAKER.Click here for fileCustom perl script used for quality filtering of Illumina reads. Custom perl script used for quality filtering of Illumina reads.Click here for fileIllumina+ assembly sequences in fasta format. Compressed .fasta file containing all Illumina+ assembly sequences.Click here for filePrimers used for experimental validation of expression profiles by qRT-PCR. Primer sequences used for qRT-PCR analysis.Click here for file"} +{"text": "Detection of chromosomal aberrations from a single cell by array comparative genomic hybridization (single-cell array CGH), instead of from a population of cells, is an emerging technique. However, such detection is challenging because of the genome artifacts and the DNA amplification process inherent to the single cell approach. Current normalization algorithms result in inaccurate aberration detection for single-cell data. We propose a normalization method based on channel, genome composition and recurrent genome artifact corrections. We demonstrate that the proposed channel clone normalization significantly improves the copy number variation detection in both simulated and real single-cell array CGH data. Array analysis of single-cell copy number variations (CNVs) is a recently developed experimental technique for the detection of chromosomal rearrangements in single cells -4. Two-cAmong existing array CGH normalization methods, global loess normalization is commonly used . Global In this paper, we present a new normalization approach based on channel and clone-specific artifact corrections, named channel clone normalization, to remove the amplification bias caused by the different natures of test and reference samples. Moreover, this approach removes genome artifacts that obscure the detection of real aberrations. The explorations of the amplification bias and genome artifacts are shown in the Results section. Furthermore, we compare our newly developed method to several existing normalization methods as well as to the methods combining normalization and segmentation , and circular binary segmentation (CBS) combined normalization) ,15,16. TTo quantify the effect of the channel clone normalization, we simulated 15 samples including 23 artificial aberrations based on 7 real Epstein-Barr virus (EBV)-transformed samples as described in the Application section. The simulation details are presented in the Materials and methods section. This simulation data set is comparable to real genome profile features of the single-cell array CGH data with known artificial aberrations. The overall performance of all normalization methods on the simulation data set is demonstrated in Figure An example shown in Figure We analyzed seven single EBV-transformed lymphoblastoid cells amplified according to the previously described protocol . Each ofOur normalization approach mainly consists of three steps: channel standardization, genome composition artifacts correction and recurrent genome artifacts correction. All of these three steps are necessary to improve single-cell CNV detection. The investigation of the single-cell amplification bias is covered in the 'Exploration of the amplification bias' section and the exploration of genome artifacts is covered in the 'Detection of copy number variation' section.y-axis and x-axis of a MA plot represent the log2 ratios and average log2 intensities between two hybridized samples, respectively. The points of a MA plot should be randomly located around zero in the y-axis if no large aberrations or artifacts exist in the data. The density plot and QQ plot are graphical techniques to show the similarity between intensity distributions from test and reference samples. If the test sample intensities are distributed similarly to reference intensities, the density plot of two hybridized samples should overlap and the QQ plot should be located along the 45-degree line.We first explored the amplification bias caused by the different natures of the test and reference samples with the help of graphical plots. MA, density, and quantile-quantile (QQ) plots are used to check for potential artifacts before and after normalization. The An obvious intensity-dependent pattern is observed in the MA plot of all single-cell array CGH experiments Figure . The patAfter the data are normalized by the channel standardization step, the pattern between averaged intensity and log2 ratio disappears and the lowess curve fitted to the data is close to horizontal Figure . The intAfter the exploration of the amplification bias, we checked the impact of genome composition artifacts and recurrent genome artifacts on the performance of single-cell CNV detection using the CBS algorithm . Genome We therefore use a genome composition correction step to correct the artifacts caused by GC content and a recurrent artifact correction step to correct unknown recurrent artifacts. For the genome composition correction step, we considered two possible methods: correction based on the GC content of (1) the probe sequence itself or (2) an enlarged window around the probe. Similarly, for the recurrent genome artifact correction we also considered two methods: (1) CBS segmented residuals followed by the recurrent genome artifact correction and (2) an artifact correction without the CBS segmentation in advance. The details of the channel clone normalization are introduced in the Materials and methods section. We compare our channel clone approach with four sub-methods to show that the combination of channel standardization, genome composition artifact correction and recurrent genome artifact correction together give the best single-cell CNV detection performance: CG (channel plus genome composition correction using enlarged window GC contents); CA (channel plus recurrent genome artifact correction without CBS segmentation); CGprobeA (channel plus genome composition correction using probe GC contents plus recurrent genome artifact correction without CBS segmentation); CGACBS ; channel clone (channel plus genome composition correction using enlarged window GC contents plus recurrent genome artifact correction without CBS segmentation).The genome profiles before and after genome composition correction are shown in Additional file et al. . GSE31219 contains single EBV-transformed lymphoblastoid cell array and human blastomere array data. The previously published human blastomere data are accessible through Gene Expression Omnibus series accession number [GSE11663].The parameters of the CBS algorithm were optimized to detect validated known CNVs of EBV-transformed single cells. The CGHcall program was used to call the CNVs in single cells. It fits each CBS segment to a mixture model with four states and calls each segment as a duplication, deletion, amplification or normal state . We calcCBS: circular binary segmentation; CGH: comparative genomic hybridization; CNV: copy number variation; EBV: Epstein-Barr virus; FPR: false positive rate; GADA: genome alteration detection analysis; QQ: quantile-quantile; SD: standard deviation; SNP: single nucleotide polymorphism; TPR: true positive rate.JRV designed the novel single-cell experiment and critically reviewed the manuscript. EV and TV designed the novel single-cell experiment, carried out the single-cell experiments and generated the array data and critically reviewed the manuscript. PK was involved in the statistical discussion and critically reviewed the manuscript. YM conceived of the study, guided JC to develop the algorithm and critically reviewed the manuscript. JC performed the analysis and wrote the manuscript. All authors have read and approved the final manuscript.Figure S1 - MA plot of single-cell array CGH. MA plot of EBV-transformed cell 1160. The spots in the plot are the clones excluding internal control and incomplete physical annotated clones. The red spots represent clones with intensities more than five-fold lower than the median background intensity.Click here for fileFigure S2 - genome profile of single-cell array CGH before and after genome composition correction. Genome plots of EBV-transformed cell 1168. Genome plots of chromosomes 1 and 10 before genome composition correction. Genome plots of chromosomes 1 and 10 after genome composition correction. The red line represents a lowess curve fitted to the data.Click here for fileFigure S3 - genome profile of single-cell array CGH before and after recurrent genome artifacts correction. (a) Genome plot of chromosome 3 from EBV-transformed cell 1168 before recurrent genome artifact correction. The red line represents the CBS segmentation. (b) Estimated common profile trend of chromosome 3 across all the EBV-transformed cells. The red line represents a lowess curve. (c) Genome plot of chromosome 3 from EBV-transformed cell 1168 after recurrent genome artifact correction. The red line represents the CBS segmentation.Click here for fileFigure S4 - genome-wide copy number variation detection of single EBV-transformed cell 1168 using existing normalization methods. (a-d) Single-cell CNV detection of EBV-transformed cell 1168 after global loess (a), CGHnormaliter (b), poplowess (c) and Haarseg normalization (d). The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigure S5 - genome-wide copy number variation detection of single EBV-transformed cell 1151 using existing normalization methods. (a-d) Single-cell CNV detection of EBV-transformed cell 1151 after global loess (a), CGHnormaliter (b), poplowess (c) and Haarseg normalization (d). The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigure S6 - genome-wide copy number variation detection of single EBV-transformed cell 1160 using existing normalization methods. (a-d) Single-cell CNV detection of EBV-transformed cell 1160 after global loess (a), CGHnormaliter (b), poplowess (c) and Haarseg normalization (d). The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigure S7 - genome-wide copy number variation detection of single EBV-transformed cell 1162 using existing normalization methods. (a-d) Single-cell CNV detection of EBV-transformed cell 1162 after global loess (a), CGHnormaliter (b), poplowess (c) and Haarseg normalization (d). The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigure S8 - genome-wide copy number variation detection of single EBV-transformed cell 614 using existing normalization methods. (a-d) Single-cell CNV detection of EBV-transformed cell 614 after global loess (a), CGHnormaliter (b), poplowess (c) and Haarseg normalization (d). The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigure S9 - genome-wide copy number variation detection of single EBV-transformed cell 617 using existing normalization methods. (a-d) Single-cell CNV detection of EBV-transformed cell 617 after global loess (a), CGHnormaliter (b), poplowess (c) and Haarseg normalization (d). The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigure S10 - genome-wide copy number variation detection of single EBV-transformed cell 1013 using existing normalization methods. (a-d) Single-cell CNV detection of EBV-transformed cell 1013 after global loess (a), CGHnormaliter (b), poplowess (c) and Haarseg normalization (d). The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigures S11 - genome-wide copy number variation detection of single EBV-transformed cell 1168 using the channel clone normalization method. Single-cell CNV detection of EBV-transformed cell 1168 after channel clone normalization. The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigures S12 - genome-wide copy number variation detection of single EBV-transformed cell 1151 using the channel clone normalization method. Single-cell CNV detection of EBV-transformed cell 1151 after channel clone normalization. The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigures S13 - genome-wide copy number variation detection of single EBV-transformed cell 1160 using the channel clone normalization method. Single-cell CNV detection of EBV-transformed cell 1160 after channel clone normalization. The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigures S14 - genome-wide copy number variation detection of single EBV-transformed cell 1162 using the channel clone normalization method. Single-cell CNV detection of EBV-transformed cell 1162 after channel clone normalization. The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigures S15 - genome-wide copy number variation detection of single EBV-transformed cell 614 using the channel clone normalization method. Single-cell CNV detection of EBV-transformed cell 614 after channel clone normalization. The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigures S16 - genome-wide copy number variation detection of single EBV-transformed cell 617 using the channel clone normalization method. Single-cell CNV detection of EBV-transformed cell 617 after channel clone normalization. The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigures S17 - genome-wide copy number variation detection of single EBV-transformed cell 1013 using the channel clone normalization method. Single-cell CNV detection of EBV-transformed cell 1013 after channel clone normalization. The y-axis represents the log2 ratios and the x-axis the probe position along the chromosome. The blue line represents the CBS segmentation line. The red region represents the deletion and the green region represents the duplication called by CGHcall.Click here for fileFigure S18 - genome-wide copy number variation detection of single EBV-transformed cells using the GADA algorithm. Single-cell CNV detection of all seven EBV-transformed cells. Each row represents the profile of one EBV-transformed cell and each column represents one probe across all the EBV-transformed samples. Different colors in the profile represent the breakpoints of single-cell CNVs detected by GADA.Click here for fileR code to implement channel clone normalization approach.Click here for file"} +{"text": "Most studies on the dynamics of recurrent cortical networks are either based on purely random wiring or neighborhood couplings -3. NeuroWe ask to what extent such geometric traits influence the 'idle' dynamics of cortical network models. Assuming an enlarged spatial scale we consider distinct network architectures, ranging from purely random or purely locally coupled neurons to distance dependent connectivities that also include patchy projections. Approximately 50000 neurons are spatially embedded in a 2D sheet of cortex with a side length of five millimeters in order to account for remotely established synapses. Neurons are implemented as conductance based integrate-and-fire neurons with distance-dependent synaptic delays. Network dynamics are simulated with NEST/PyNN .Analyzing the characteristic measures describing spiking neuronal networks (e.g. the correlation coefficient or the coefficient of variation), we explore and compare the phase spaces and activity patterns of our simulation results. As expected from random networks, different dynamical states (e.g. synchronous regular 'SR' or asynchronous irregular 'AI' firing) occur in dependence of the input rate and the relation between exc. and inh. synaptic strengths -3. Non-rWe conclude that (the amount of) local distance-dependent connections is an important structural feature of cortical networks since it induces rather complex activity patterns compared to random connectivities. However, we found no clear differences in the dynamics of networks with randomly distributed compared to spatially clustered long-range projections. Further analysis is needed to explore the functional aspects of patchy projection patterns."} +{"text": "To investigate the phenotypic relationships between aortic stiffness and left ventricular (LV) stroke volume (SV) and modes of deformation at rest and stress, with preserved and compromised contractile capacity.Increased aortic stiffness, measured by pulse wave velocity (PWV), is linked to a range of cardiovascular (CV) risk factors and acts as predictor of CV events, independently of age-related increase in pulse pressure. As an integrated marker of the pulsatile component of LV afterload, PWV has been linked to prognostically adverse cardiac phenotypes, including LV systolic dysfunction and post-infarct remodelling. Evidence suggests that longitudinal mode of deformation is particularly important to overcome the superimposed afterload. Thus, reduced LD due to myocardial ischaemia or scar may influence the capacity to offset the LV afterload in patients with increased aortic stiffness.At total of 124 cardiac patients underwent a high-dose dobutamine-stress/perfusion magnetic resonance (DS(P)MR) protocol with simultaneous late gadolinium enhancement (LGE) imaging and aortic pulse wave velocity (PWV) measurements MR/LGE outcome as negative (n=68) or positive for ischaemia (n=25), or post-infarct LV remodelling with scarring (n=31). All three groups showed a significant within-subject increase in HR and cardiac output with similar HR*BP products (p>0.05) in all 4 stages of the protocol Figure . SV incrOur findings reveal that modes of deformation to increased aortic stiffness differ at rest and dobutamine-stress and with compromised LV contractility: intact myocardium relies on longitudinal function to displace volume and offset the afterload, whereas with LV dysfunction, increased LV wall stress reveals a role for radial component."} +{"text": "Hippo pathway controls the organ size by modulating cell proliferation and apoptosis. However, the upstream regulation of hippo signaling by actin cytoskeleton is not clear. To elucidate the role of actin as an upstream regulator of Hippo signaling, the levels of F (filamentous)-actin in cells were elevated using jasplakinolide, an actin-stabilizing drug. Induction of F-actin formation in HeLa cells resulted in decreased phosphorylation of YAP, a key effector molecule for Hippo signaling. The activated YAP is localized to the cell nucleus and YAP increase was associated with increased expression of downstream CCN growth factors CCN1/CYR61 and CCN2/CTGF. The effect of the actin-stabilizing drug was blocked when YAP levels were suppressed in YAP \u201cknock-down\u201d cells. In summary, using an actin-stabilizing drug we show that actin cytoskeleton is one of the upstream regulators of Hippo signaling capable of activating YAP and increasing its downstream CCN growth factors. Drosophila using genetic screening Drosophila and vertebrates Tissue growth and organ size are regulated by cell proliferation and cell death controlled by several developmental pathways Drosophila have shown the regulation of Hippo signaling by the actin cytoskeleton. Deletion of actin binding capping proteins or overexpressing constitutively active version of actin nucleation factor Diaphanous Recent studies in In the present study, we extended earlier studies by directly measuring G-actin and F-actin ratios following treatment of HeLa cells with an actin-stabilizing drug. We further analyzed the role of YAP in the induction of downstream CCN growth factors CTGF and CYR61.Jaspis johnstoni, is a potent inducer of actin polymerization Jasplakinolide (Jasp), a naturally occurring cyclic peptide extracted from the marine sponge, YAP is a potent oncogene and one of the main effectors of the Hippo signaling pathway; YAP is activated in different human cancers The phosphorylation of YAP at Ser127 retains YAP in the cytoplasm The CCN family of secreted proteins consists of six members designated as CCN1 to CCN6. CCN family of secreted proteins are involved in various biological functions including cell proliferation, migration, survival, differentiation, and angiogenesis To further determine if increases of CCN family growth factors after Jasp treatment is mediated through YAP, the levels of YAP were suppressed using siRNA . The supDrosophila cells demonstrated the important role of actin polymerization in Hippo signaling disruption Although genome-wide screening studies in Drosophila studies, the effect of F-actin on Yorkie/Yki was shown to be mediated through Wts/LATS but not hpo/MST Under high cell density culture conditions, the levels of F-actin in the cells are low and the Hippo signaling pathway is active. In the current study using actin stabilizing drug jasplakinolide, the monomeric G-actins in the cell were converted to F-actin . The bunJasplakinolide treatment rapidly converted the monomeric G-actin to F-actin; the levels of F-actin were maintained for long period of time . For celAntibodies to pYAP (Ser127) (#4911), YAP (#4912) and GAPDH (#2118) were obtained from Cell Signaling Technology . Jasplakinolide, CYR61 (SC-13100) and CTGF (SC-14939) were from Santa Cruz Biotechnology . G-actin/F-actin in vivo assay kit was from Cytoskeleton Inc. . YAP siRNA was from Qiagen .HeLa cells were cultured in Dulbecc\u00f3s Modified Eagle Medium supplemented with 10% fetal bovine serum, penicillin and streptomycin. The cells were serum starved overnight and treated with jasplakinolide for 10 min. After treatment the cells were washed with medium twice and further cultured for different time periods, except for 5 and 10 min. time point during which the treatment was continuous. siRNA was transfected to cells using HiPerFect transfection reagent (Qiagen). The cells were transfected with siRNA in the complete medium and cultured for 48 h.HeLa cells were cultured to confluency and were serum-starved overnight before treatment with jasplakinolide. The cells were treated with jasplakinolide for 10 min. and washed twice with serum-free medium before further culture. Before immunoblotting, cells were lysed in M-PER lysis buffer supplemented with protease inhibitors. The cell lysates were run on SDS-PAGE and transferred to PVDF membranes. To measure secreted proteins in the medium, culture media from the wells were collected and concentrated using centrifugal filter units (Millipore). The reducing sample buffer was added to the final concentrated media and run on SDS-PAGE. Densitometry analysis was done using ImageJ .AGCCTCGCATCCTATACAACC and TTCTTTCACAAGGCGGCACTC, hCTGF: GCGTGTGCACCGCCAAAGAT and CAGGGCTGGGCAGACGAACG, hYAP: TCAGACAACAACATGGCAGGA and TTCATGGCTGAAGCCGAGTT, hGAPDH: GGTGAAGGTCGGAGTCAAC and CCATGGGTGGAATCATATTG.Total RNA was extracted from cells using RNeasy kit (Qiagen). The first strand synthesis was done using Sensiscript RT kit (Qiagen) and quantitative PCR was performed in triplicates using iTaq SYBR Green Supermix kit (Bio-Rad). Transcript levels were normalized based on GAPDH levels. The primers used are: hCYR61: Cells were grown on cover slips. After jasplakinolide treatment the cells were fixed in 4% paraformaldehyde and permeabilized with 0.1% Triton x-100. The primary and secondary antibodies were diluted in the blocking buffer (1% BSA/PBS). Cells showing nuclear YAP staining was quantified by counting the cells from five different fields. The mean of each treatment group from two independent experiments were plotted. Hoechst 33342 (Invitrogen) was used for staining the nucleus and the coverslips were mounted on microscope slides using Vectashield mounting medium (Vector shield).The amount of G-actin and F-actin in HeLa cells was quantified using G-actin/F-actin in vivo assay kit according to the manufacturer instructions. Briefly, the cells were lysed in pre-warmed lysis/F-actin stabilizing buffer supplemented with protease inhibitor and ATP. The cell lysate was centrifuged for 5 min. at 350\u00d7g to remove the cell debris. Cell lysate (100 ul) was ultracentrifuged at 100,000\u00d7g for 1 h at 37\u00b0C to pellet the F-actin with G-actin remaining in the supernatant. F-actin in the pellet was resuspended in 100 ul of F-actin destabilizing buffer on ice for 1 h with frequent pipetting. Equal volumes of G-actin and F-actin fractions were mixed with 5\u00d7 SDS sample buffer and run on SDS-PAGE. Western blot was done using anti-actin antibody provided in the kit. Densitometry analysis was done using ImageJ.P<0.05.All experiments were repeated at least three times. For comparisons the differences between groups were calculated with Student\u2019s t-test, and a difference was considered significant if"} +{"text": "The functional impairment caused by peripheral arterial disease (PAD) is difficult to evaluate objectively and quantitatively. Current methods used to assess the efficacy of therapeutic interventions in patients with PAD are limited by variability and changes representing the placebo effect. Recently, Gadolinium-enhanced first-pass (FP) MRI has emerged as a new method to assess perfusion in peripheral muscles at peak exercise.We seek to demonstrate that calf muscle perfusion index measured with FP MRI at peak exercise correlates with treadmill exercise measures of ischemia in patients with PAD.82 patients with PAD were included in the study. Patients exercised until fatigue inside the 1.5T MR scan using an MR-compatible plantar-flexion ergometer. Images were acquired at peak exercise using a dynamic, first-pass, dual-contrast sequence. The dual contrast sequence acquires two interleaved slices; an inversion-prepared slice in the calf muscle, and a saturation-prepared slice in the popliteal artery (8 cm superior). Time-intensity curves (TIC) were acquired from the dynamic images by placing ROI's in the popliteal artery on the saturation-prepared slices in the brightest calf muscle group on the inversion-prepared slice . The PI was not correlated with resting ABI.MR-based calf muscle PI correlates significantly with treadmill exercise parameters. MRI PI could be a valuable tool to objectively and quantitatively assess improvement in exercise perfusion in response to therapeutic intervention in patients with PAD.Funding was provided by a grant from the National Institutes of Health ."} +{"text": "The selective pressure of antiretroviral therapy invariably results in the emergence of drug-resistant HIV variants that acquire mutations which can compromise the replication capacity of the virus. Recently, we showed that impaired replication of ritonavir-resistant HIV can be rescued by cellular activation. Ritonavir-resistance mutations in HIV protease prevent complete proteolysis of the Gag polypeptide, and the accumulation of uncleaved capsid-spacer peptide1 (CA-SP1) in maturing virus particles decreases the ability of HIV to replicate in human thymocytes and nonactivated cell lines. We confirmed that ritonavir-resistant HIV replication was arrested after virus entry but before complete proviral DNA synthesis. Using a functional genetic screen, we identified the abundant cellular chaperone Hsp90 as a host factor that can rescue the impaired replication of ritonavir-resistant HIV. We confirmed that Hsp90 expression increases in response to cellular activation and that pharmacologic inhibition of Hsp90 blocks HIV replication. Previous work has shown that altering key residues in structural domains of the HIV core prevents uncoating of the CA lattice in an infected cell. The CA mutations render the core either unstable or too stable, in each case resulting in abortive HIV replication at the uncoating stage of the virus life cycle. The nature of our genetic screen was based on the ability of a host factor to rescue a replication-impaired HIV isolate with a defective CA morphology. To verify Hsp90 as a potential host factor in HIV uncoating, we tested its ability to rescue the impaired replication of HIV with different destabilizing CA mutations.Titrated virus stocks with mutations in different structural domains of HIV CA were generated. Jurkat T cells were transduced with WT and mutant Hsp90-expressing retrovirus and subsequently inoculated with the different CA mutants. Productive virus replication was monitored over 8 days.Although the CA mutants replicated poorly in normal Jurkat T cells (0\u201327% relative to infectivity of WT HIV), they displayed varying degrees of impairment (32\u201375% relative to WT HIV) in PHA-activated human peripheral blood mononuclear cells and activated Jurkat T cells. Further, productive replication of several CA mutants were observed in Jurkat T cells transduced with WT Hsp90.The ability of CA-mutant HIV to replicate in Hsp90-transduced Jurkat T cells suggests a potential role for Hsp90 as an uncoating factor in postentry HIV replication. The increased expression of Hsp90 in activated T cells may override the destabilizing effects of CA mutations that arise in response to immune surveillance or drug therapy.This project has been funded in part with Federal funds from NIAID, NIH, under Contract No. HHSN26620070002C/N01-AI-70002 and the California HIV/AIDS Research Program (CHRP) Grant No. ID09-SF-051 to C.A.S."} +{"text": "To determine the reproducibility of axial versus short axis methods for measurement of right ventricular volumes and ejection fraction (RVEF) in adults after Mustard palliation for complete transposition of the great arteries (TGA).The most common cause of a systemic right ventricle is atrial redirection surgery (Mustard repair) in the setting of complete TGA. Decreased RVEF is common and is a predictor of morbidity and mortality. Cardiac magnetic resonance (CMR) cine imaging is the reference standard for assessment of right heart size and function. However, the optimal method of RV planimetry using CMR in patients with Mustard palliation for complete TGA remains unclear.Consecutive adult patients with atrial redirection surgery (Mustard procedure) for complete TGA were identified from an existing database and steady state free-precession cine images acquired on 1.5 T commercially available scanners were reviewed. To obtain RVEF, both end-diastolic volumes (EDV) and end-systolic volumes (ESV) were measured in two orientations, axial and short axis, by two experienced, independent readers who were blinded to other results. One reader reanalyzed the RV volumes and function \u2265 14 days after the first set of measurements. Intra- and inter-observer variabilities were determined using Bland-Altman analysis.A total of 25 patients were identified between 2008 and 2010. All images had sufficient quality for analysis. From the axial stack, the medians (interquartile ranges) were RVEDV 243cc (198-297), RVESV 142cc (101-174) and RVEF 44% (38-50). From the short axis stack, medians (interquartile ranges) were RVEDV 236cc (181-281), RVESV 127cc (90-157) and RVEF 44% (41-50). Volumes derived from short axis and axial stacks were significantly different (p=0.001 for RVEDV and p<0.001 for RVESV) but there was no statistical difference in RVEF between the methods (p=0.38). Bland Altman analysis for evaluation of intra and inter-observer variabilities are summarized in table Following Mustard palliation for complete TGA, RVEF measurements derived from axial and short axis stacks are similar, although both RVEDV and RVESV values are significantly higher based on the axial acquisition. Intra-observer measurements appear to be more reliable using the axial as compared with the short axis method."} +{"text": "The T box riboswitch controls bacterial transcription by structurally responding to tRNA aminoacylation charging ratios. Knowledge of the thermodynamic stability difference between two competing structural elements within the riboswitch, the terminator and the antiterminator, is critical for effective T box-targeted drug discovery.Terminator - \u0394GAntiterminator) values were compared.The \u0394G of aminoacyl tRNA synthetase (aaRS) T box riboswitch terminators and antiterminators was predicted using DINAMelt and the resulting \u0394\u0394G (\u0394GAverage \u0394\u0394G values did not differ significantly between the bacterial species analyzed, but there were significant differences based on the type of aaRS.The data indicate that, of the bacteria studied, there is little potential for drug targeting based on overall bacteria-specific thermodynamic differences of the T box antiterminator vs. terminator stability, but that aaRS-specific thermodynamic differences could possibly be exploited for designing drug specificity. The T box riboswitch is an important regulatory mechanism found in Gram-positive bacteria including many pathogens -3. The r2+ binds via a diffuse, outer-sphere interaction [We have been investigating the structure-function relationship of the T box antiterminator element and the key recognition features necessary for ligands to specifically bind the antiterminator and disrupt its function. There are few detailed medicinal chemistry studies of ligands targeting RNA and thiseraction . In vitreraction and tRNAeraction indicateAminoglycosides bind AM1A in a structure-specific manner, most likely via electrostatics ,14. In cB. subtilis tyrS T box [From a drug discovery perspective, a key factor to determine is the range of ligand-induced stabilization that can be accommodated without overly stabilizing the antiterminator element and precluding terminator formation. The goal of our T box drug discovery project is to determine the key ligand features that lead to specific antiterminator binding, but that do not result in excessive stabilization of the antiterminator secondary structure. These ligands could then potentially compete with tRNA for binding to the antiterminator, but still allow terminator formation such that transcription of a T box gene critical for bacterial survival would be terminated Figure . The prerS T box . HoweverBacillus cereus (BC), Bacillus subtilis (BS), Clostridium botulinum (CB), Clostridium difficile (CDF), Clostridium perfringens (CPE), Staphylococcus aureus Mu50 (SA), Streptococcus agalactiae (SAG), and, Streptococcus pyogenes (SPY) [Terminator - \u0394GAntiterminator. The % suboptimal setting was adjusted as necessary to obtain the lowest free energy antiterminator fold that had the consensus secondary structure of the core seven-nucleotide bulge containing the 5' -UGGN-3' nucleotides that are complementary to the tRNA acceptor end nucleotides [The thermodynamic stability of T box antiterminator and terminator structural elements was calculated using the DINAMelt server . The DINes (SPY) . The \u0394G leotides .The free energy values for the antiterminator and terminator structural elements of the T box genes analyzed were calculated using the DINAMelt webserver . The preThe free energy of T box riboswitch antiterminator and terminator elements was predicted and compared for a series of aaRS T box genes. The observed aaRS-specific stability differences between these key riboswitch structural elements could potentially be targeted to effect ligand-specificity in future drug discovery efforts.Bacillus cereus; (BS): Bacillus subtilis; (CB): Clostridium botulinum; (CDF): Clostridium difficile; (CPE): Clostridium perfringens; Mu50 (SA): Staphylococcus aureus; (SAG): Streptococcus agalactiae and, Streptococcus pyogenes (SPY).(aaRS): Aminoacyl tRNA synthetase; (BC): JH is a co-inventor on U.S. Patent number 7,005,441 for T box binding assays and ligands.FJ carried out the sequence folding and free energy predictions. JH conceived of the study, designed and coordinated the study and prepared the manuscript.Predicted \u0394G values for aaRS T box terminators and antiterminators.Click here for file"} +{"text": "HTLV-1 is associated with the development of HAM/TSP and overactive bladder (OB). A higher prevalence of helminthic coinfection has been observed among those infected with HTLV-1. Because helminthic infection may modify the immune response and influence clinical outcomes in HTLV-1 infection, we investigated the development of HAM/TSP and OB in HTLV-1 positive individuals with and without helminthic coinfection.HTLV-1 patients enrolled in a cohort study between 2004-2010 were classified as coinfected and non-coinfected based on stool samples. All patients were followed at least two years from initial evaluation, with yearly clinical assessments. Disease-free survival for OB was estimated using the Kaplan-Meier method, and the relationship between helminthic infection and development of OB was assessed by Cox proportional hazard modeling.Seventy-four coinfected and 79 non-coinfected patients were followed. A total of 92 helminthic infections were observed in the coinfected group. One patient from each group developed HAM/TSP during followup. Fourteen and 17 patients developed OB from the coinfected and non-coinfected groups, respectively. There was no association between helminthic infection and risk of OB .We found no difference in the risk of development of OB in HTLV-1 and helminthic coinfected and non-coinfected patients. The incidence of HAM/TSP was low in each group. These data indicate that general helminthic infection does not modify development of HAM/TSP or OB. Future studies should address the potential association between specific helminthic infections and risk of neurologic disease in HTLV-1 infection."} +{"text": "Deregulation of long non-coding RNAs (lncRNAs) expression has been proven to be involved in the development and progression of cancer. However, expression pattern and prognostic value of lncRNAs in breast cancer recurrence remain unclear. Here, we analyzed lncRNA expression profiles of breast cancer patients who did or did not develop recurrence by repurposing existing microarray datasets from the Gene Expression Omnibus database, and identified 12 differentially expressed lncRNAs that were closely associated with tumor recurrence of breast cancer patients. We constructed a lncRNA-focus molecular signature by the risk scoring method based on the expression levels of 12 relapse-related lncRNAs from the discovery cohort, which classified patients into high-risk and low-risk groups with significantly different recurrence-free survival . The 12-lncRNA signature also represented similar prognostic value in two out of three independent validation cohorts. Furthermore, the prognostic power of the 12-lncRNA signature was independent of known clinical prognostic factors in at least two cohorts. Functional analysis suggested that the predicted relapse-related lncRNAs may be involved in known breast cancer-related biological processes and pathways. Our results highlighted the potential of lncRNAs as novel candidate biomarkers to identify breast cancer patients at high risk of tumor recurrence. MALAT1 function as an oncogene whose high expression was associated with high metastatic potential and poor patient prognosis of lung cancerMEG3 expression in many primary human tumors and tumor cell lines, providing substantial evidence that supported lncRNA MEG3 as a tumor suppressor14151617181920212223The increasing attention to various types of non-coding RNAs (ncRNAs) has highlighted their well-adapted and specialized biological roles during past years14Breast cancer is a frequent malignant gynecologic cancer accounting for 29% of all newly diagnosed cancers among women in 2014, and is one of the major causes of cancer death among women3435In this work, we performed a comprehensive analysis of lncRNA expression profiles across 473 breast cancer patients who did or did not develop recurrence by repurposing the publicly available microarray expression profiles from the Gene Expression Omnibus (GEO) database. A comparison between the groups of patients who did and did not develop recurrence identified a set of 12 lncRNAs overexpressed or downregulated in relapsed patients. Finally, we defined a 12-lncRNA signature by risk scoring method that is highly predictive of tumor recurrence and recurrence-free survival of breast cancer patients.In this study, we included four breast cancer patient cohorts with recurrence information for biomarker discovery and validation see . The patTo identify potential lncRNA biomarkers associated with tumor recurrence of breast cancer patients, the patients from discovery cohort were classified into two groups according to recurrence status. We first compared the lncRNA expression profiles of breast cancer patients who did and did not develop recurrence, and identified 12 differentially expressed lncRNAs between the two patient groups see . Among tRP1-34M23.5)\u2009+\u2009\u2009+\u2009\u2009+\u2009\u2009+\u2009\u2009+\u2009\u2009+\u2009\u2009+\u2009\u2009+\u2009\u2009+\u2009\u2009+\u2009\u2009+\u2009. We calculated a BCSigLnc-12 risk score for each patient in the discovery cohort and ranked them according to increased risk score. To obtain the best cutoff value of the risk score, the various cutoff values were evaluated using time-dependent ROC curveSince these 12 differentially expressed lncRNAs exhibited distinct expression patterns in patients who did and did not develop recurrence, these 12 lncRNAs were integrated into a predictive signature by risk scoring method to predict the risk of tumor recurrence of breast cancer patients (hereafter inferred as BCSigLnc-12) (see Methods), as follows: BCSigLnc-12 risk score\u2009=\u2009 whose high expression was associated with good recurrence-free survival, while high expression of the remaining six was associated with poor recurrence-free survival.Distribution of BCSigLnc-12 risk scores, the relapse status and expression pattern of 12 lncRNA biomarkers of 104 breast patients in the discovery cohort was shown in To evaluate the robustness of BCSigLnc-12 in predicting the risk of tumor recurrence of breast cancer patients, the BCSigLnc-12 was then tested for its predictive power in the test cohort-1 of 204 patients. With the same model and cutoff point as those derived from the discovery cohort, 204 patients of the test cohort-1 were classified into the high-risk group (n\u2009=\u2009113) and low-risk group (n\u2009=\u200991). As in the discovery cohort, Kaplan-Meier recurrence-free survival curves based on BCSigLnc-12 prediction were significantly different. Patients in the high-risk group had significantly shorter recurrence-free survival than those in the low-risk group . The fivAnother validation of the predictive power of BCSigLnc-12 was conducted using independent test cohort from Loi\u2019s study (termed test cohort-2). Similar to the findings from the discovery cohort and test cohort-1, the BCSigLnc-12 was again shown capable of predicting the risk of tumor recurrence in the test cohort-2. Using the risk score formula, the BCSigLnc-12 was able to stratify 77 patients of the test cohort-2 into the high-risk group (n\u2009=\u200939) and low-risk group (n\u2009=\u200938) with significantly different recurrence-free survival (log-rank p\u2009=\u20090.042) and relapse status using the same cutoff as in the discovery cohort. The recurrence-free survival was significantly worse in the high-risk group compared with the low-risk group . At fiveFurther validation of the BCSigLnc-12 in the test cohort-3 from Dedeurwaerder\u2019s study showed that recurrence-free survival was different between the high-risk and low-risk groups and the proportions of recurrence-free survival in the high-risk and low-risk groups were 59.9% and 65% after five years. However, the p-value of the log-rank test is 0.289 indicating that the BCSigLnc-12 is not significantly associated with recurrence-free survival in the test cohort-3 .The distribution of BCSigLnc-12 risk scores, relapse status and expression pattern of lncRNA biomarkers from breast cancer patients in the test cohort-1,test cohort-2 and test cohort-3 have been shown in We used multivariate Cox regression analysis to determine whether predictive capacity of BCSigLnc-12 was independent of other clinicopathological factors of breast cancer patients in the discovery cohort, test cohort-2 and test cohort-3 , such as age, tumor size, tumor grade, estrogen receptor (ER) status and lymph node status. The results from the discovery cohort showed that the BCSigLnc-12 , ER status and lymph node status were independent prognostic factors for patients with breast cancer . In the We further performed data stratification analysis for breast cancer patients according to ER status and lymph node status. Patients with ER status information in four patient cohorts were first stratified into either the ER-positive group or the ER-negative group. Log-rank test of ER-positive patients showed that the BCSigLnc-12 could further classify ER-positive patients into the high-risk group (n\u2009=\u200993) and low-risk group (n\u2009=\u200993) with significantly different recurrence-free survival . For ER-We performed functional enrichment analysis for GO terms and KEGG pathways to predict potential biological processes and pathways involved in relapsed-related lncRNA biomarkers. For this purpose, we first measured the co-expressed relationships between 12 relapse-related lncRNA biomarkers and protein-coding genes (PCGs) by calculating the Pearson correlation coefficient of paired lncRNA and PCG expression profiles, and identified highly positively or negatively correlated PCGs (ranked top 1%) with at least one of 12 relapse-related lncRNAs. The functional enrichment analysis of GO and KEGG pathway revealed that PCGs positively correlated with lncRNAs were involved in RNA metabolic process and spliceosome pathway, while PCGs negatively correlated with lncRNAs were enriched in five GO function clusters and six pathways . The BCSigLnc-12 associated biological processes and pathways can be found as Although great efforts have been made to improve clinical management of breast cancer leading to a reduction in mortality rate, a substantial number of patients still faced the risk of tumor recurrence span 20 years38404141In this study, we analyzed and mined lncRNA expression profiles of breast cancer patients with recurrence information by repurposing the publicly available microarray expression profiles from GEO database to determine whether there are significantly different lncRNA expression patterns in breast patients with and without tumor recurrence. By first separating breast cancer patients into two groups according to relapse status, we identified 12 lncRNAs whose expression levels were significantly different between the two patient groups with and without recurrence. Hierarchical clustering and Cox regression analysis revealed that 12 differentially expressed lncRNAs were significantly correlated with tumor recurrence and recurrence-free survival of breast cancer patients. By focusing on these differentially expressed lncRNAs, we constructed a lncRNA expression-based molecular signature, termed BCSigLnc-12, which was able to accurately predict recurrence-free survival in breast cancer patient. Patients with high-risk signature scores have a 2.7-fold hazard ratio for recurrence compared to those with low-risk signature scores. The predictive value and robustness of the BCSigLnc-12 were successfully validated in two out of three additional independent breast cancer patient cohorts. Notably, the BCSigLnc-12 clearly distinguished breast cancer patients with good recurrence-free survival for those with poor recurrence-free survival. Furthermore, when tested together with other clinical factors in multivariate Cox regression analysis, a certain degree of independence of predictive capacity of BCSigLnc-12 from clinicopathological factors was found, including age, tumor size, tumor grade, ER status and lymph node status. These results suggested that the BCSigLnc-12 may be candidate biomarkers for recurrence-free survival prediction in breast cancer.SNHG7, one of 12 relapse-related lncRNAs, is a known lincRNA belonging to endogenous retrovirus families and may play a role in trophoblasts syncytialization47More than ten thousand lncRNAs have been discovered in human during the past years. In contrast, the number of well-studied lncRNAs appears to be quite rare. LncRNA However, some limitations should be aware in our study. First, only a fraction of lncRNAs was analyzed in our study because of limited available lncRNAs expression profiles. Second, only three of four independent cohorts confirmed the predictive value of this lncRNAs signature. Therefore, larger cohorts are needed to validate this signature. Finally, the biological implication of the BCSigLnc-12 was predicted using the bioinformatics analysis in our study and experimental studies need to be carried out to investigate the functional roles of the BCSigLnc-12 in breast cancer recurrence in the further work.In conclusion, we have shown distinct expression patterns of lncRNAs in breast patients with relapse compared with those with relapse-free, and identified 12 differentially expressed lncRNAs that were closely associated with tumor recurrence of breast cancer patients. We therefore constructed a lncRNA-based molecular signature using the expression levels of these 12 relapsed-related lncRNAs that predicts the risk of tumor recurrence of breast cancer independently of clinicopathological factors, and validated it in two out of three independent breast cancer cohorts derived from different studies. Our study not only indicated the potential of lncRNAs as novel candidate biomarkers to provide additional recurrence risk stratification for breast cancer patients beyond the known clinical prognostic factors, but also improved our understanding of the molecular mechanism underlying breast cancer recurrence with further prospective validation.GSE42568) (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568)GSE12276) (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12276)GSE9195) (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9195)GSE20711) (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20711)The gene expression profiles data generated by Affymetrix HG-U133 Plus 2.0 platform from four independent cohorts of breast cancer patients with relapse information were obtained from the publicly available GEO database. After removal of the patients without recurrence status, a total of 473 breast cancer patients were analyzed in this study see , includihttp://www.affymetrix.com) and re-mapped to the human genome (GRCh38) using SeqMap tool1617The raw microarray data (.CEL files) of breast cancer patients in three cohorts were downloaded from the GEO database, and were background corrected, log2-transformed and normalized using the Robust Multichip Average (RMA) algorithmThe expression profiles of three cohorts were standardized by the Z-score transformation to avoid systematic error across different experimentsThe Cox regression analysis was used to evaluate the association between expression levels of differentially expressed lncRNAs and patients\u2019 recurrence-free survival. The selected differentially expressed lncRNAs were fitted in a multivariate Cox regression analysis in the discovery dataset. Then the lncRNA-focused molecular signature, termed BCSigLnc-12, was built using the linear combination of expression levels of prognostic lncRNAs with the estimated regression coefficients derived from the above multivariate Cox regression analysis as the weight to calculate the recurrence risk score for each patient as previously described60https://david.ncifcrf.gov/, version 6.7)We calculated the Pearson correlation coefficients between lncRNAs and protein-coding genes, and identified protein-coding genes positively or negatively correlated with prognostic lncRNAs. Functional enrichment analysis for these protein-coding genes was performed using DAVID Bioinformatics Tool ."} +{"text": "Dear Editor,Therapy-related myeloid neoplasms (t-MNs) are a unique clinical entity occurring as late complication of chemotherapy and radiotherapy administered for a primary disease . AccordiTP53 gene which is frequently mutated in t-AMLs exhibiting a potentially important role in leukemogenesis [In this study, we selected patients with therapy-related AML (t-AML) following cytotoxic treatment of malignant lymphomas as bone marrow (BM) biopsies are routinely performed during their initial staging procedures. We focused on the ogenesis . We idenogenesis . HoweverTP53 mutation in the patient\u2019s BM obtained at the time of the lymphoma staging which showed that the relative proportion of mutated cells increased substantially in the t-AML specimen Below is the link to the electronic supplementary material."} +{"text": "AbstractGryllotalpidae, and the NHM collection holds plaster casts of the burrows of two species. These recordings and burrows have until now not been made available through the NHM's collection database, making it hard for researchers to make use of these resources.The Natural History Museum (NHM) sound archive contains recordings of Gryllotalpagryllotalpa and Gryllotalpavineae Bennet-Clark, 1970 have been made available via the NHM Data Portal.Eighteen recordings of mole crickets (three identified species) held by the NHM have been made available under open licenses via BioAcoustica. 3D scans of the burrows of Orthoptera: Gryllotalpidae) are subterranean insects, rarely seen above ground apart from adults flying during breeding season. The Natural History Museum has a collection of sound recordings and burrow casts of the genus GryllotalpaG.vineae:Gryllotalpamajor in the United States are based on its song.Mole Crickets . They are presented now for the following reasons; (1) they are the only representatives of the super-family Gryllotalpoidea, and future planned publications on the Orthoptera sound collection are being written at super-family level; (2) the only burrow casts held by the NHM are of Gryllotalpa, and (3) the importance of Gryllotalpagryllotalpa for both conservation (in the UK) and as an invasive pest (in the USA) makes publication timely.The collection of Orthoptera have been digitised and made available on the BioAcoustica platform (http://bio.acousti.ca/taxonomy/term/178).Online libraries of recorded wildife sound are useful in taxonomic studies award SDF 14011.Gryllotalpagryllotalpa, Gryllotalpavineae), Africa and Asia . Locations are summarised in Fig. Recordings are held from Europe Licence. 3D models are made available under the Creative Commons Attribution Non-Commercial (CC BY-NC) licence following standard NHM policy. Other resources on BioAcoustica may use different licenses.Burrow cast and sound data for NHM Gryllotalpidaehttp://dx.doi.org/10.5519/00021201NHM Specimens relating to sound recordings of GryllotalpidaeCSV6http://data.nhm.ac.uk/dataset/burrow-casts-of-the-mole-cricket-genus-gryllotalpa-latreille-1802/resource/e0e36679-9a6b-4da4-8b82-eabaa6f7f147NHMUK-BMNH(E)-010210942: recording) which B. C. Townsend considered (via a specimen label) has male genitalia conspecific with G.africana Palisot de Beauvois, 1805, but which has a unique song may indicate the presence of cryptic species within the genus.The existence of a specimen . Recently the museum has moved away from the classic BMNH coden to NHMUK, while entomology specimens have been given unique identifiers of the form BMNH(E). This results in the rather long DarwinCore identifiers NHMUK-BMNH(E)-########. These specimens are currently being enterred into the Museum's collection managaement system.For specimens where we have recordings that can be georefrenced and dated, but there is known to be no corresponding specimen in the NHM collection, the identifiers of the observation are given the format BioAcoustica-Collector-#."} +{"text": "Juvenile Justice-Translating Research Interventions for Adolescents in the Legal System seeks to reduce unmet substance use disorder (SUD) needs by assisting JJ agencies in their efforts to implement best practices and improve SUD service utilization along a behavioral health cascade . Such efforts require systems-level change; thus, the JJ-TRIALS study targets JJ agencies and the behavioral health partners to which juveniles are referred .Aaron\u2019s implementation science framework providesUsing a clustered randomized design, JJ-TRIALS will compare two implementation interventions: a Core Intervention, involving DDDM strategies to promote change across the EPIS phases, versus an Enhanced Intervention, providing support for DDDM through facilitation and inter-agency change teams. A total of 36 sites representing 7 states and the District of Columbia will be randomized to Core (n = 18) or Enhanced (n = 18) and to one of three start times. Primary research questions address whether DDDM strategies and facilitation of DDDM tools/implementation teams improve: a) the provision and quality of services along a behavioral health cascade ; and b) attitudes toward/use of best practices among staff working with justice-involved youth. Exploratory research questions focus on aspects of the implementation process, inter-organizational collaboration, costs associated with each study arm, and youth outcomes."} +{"text": "Bronchoalveolar lavage (BAL) has a stable place in the diagnostics of various forms of the diffuse parenchymal lung disease. The analysis of cellular components of the bronchoalveolar lavage fluid (BALF) informs us about inflammatory and immune processes in the alveolar space. This can be very helpful in the diagnostics of many interstitial lung diseases (ILDs), but also in the diagnostics of pulmonary haemorrhage and bronchoalveolar carcinoma or lymphomas. The aim of study is to present our experience in cellular analysis of BALF.Lymphocyte subsets were determined by flow cytometry. We utilized monoclonal antibodies directed against the CD3, CD4, CD8 (T-lymphocytes), CD19 (B-lymphocytes), CD16 (NK cells), and HLA-DR antigen to determine the degree of lymphocyte activation.Over the past 10 years (2003\u20132013) we have analysed 4540 BALFs. We evaluated total cell count, immunocompetent cells profile and phenotype of lymphocytes.An increased percentage of lymphocytes (above 15%) were found in 1680 BALFs (37%). The phenotypes of these cases of lymphocytic alveolitis were determined via monoclonal antibodies as mentioned above. CD3+T-lymphocytic alveolitis was established in 1677 BALFs (99.8%). This represents an overwhelming majority of BALFs with elevated lymphocyte count in patients with interstitial lung diseases. CD19+B-lymphocytic alveolitis was found in 2 BALFs only. These interesting accidental findings resulted in the establishment of B-lymphocyte hematopoietic infiltrative neoplasm in patients suspected of interstitial lung diseases. CD16+NK cells alveolitis was found in 1 BALF only of a patient with histologically confirmed pulmonary fibrosis type of UIP.We concluded that lymphocytic alveolitis is a nonspecific pathological finding to be followed by detailed lymphocyte phenotype analysis. Owing to the fact that the phenotypes of an overwhelming majority of the cases of lymphocytic alveolitis in our group (99.8%) were CD3+, we conluded that T-lymphocytes almost exclusively persist within the alveolar structures and play an important role in the pathogenesis of many interstitial lung diseases. Consequently, monoclonal antibodies directed against the CD3 antigen (T-lymphocytes), against the CD4 and CD8 antigens (T-lymphocytes subsets), perhaps even the antibody against the HLA-DR molecule (the T-lymphocyte activation marker) are sufficient for routine BALF lymphocyte phenotype analysis."} +{"text": "The feature of distinct transcriptomes between ECRSwNP and non-ECRSwNP suggests the necessity to develop specific biomarkers and personalized therapeutic strategies. Our findings lay a solid foundation for subsequent functional studies of mRNAs and lncRNAs as diagnostic and therapeutic targets in CRSwNP by providing a candidate reservoir.Chronic rhinosinusitis with nasal polyps (CRSwNP), one of the most prevalent chronic diseases, is characterized by persistent inflammation of sinonasal mucosa. However, the pathogenesis of CRSwNP remains unclear. Here, we performed next-generation RNA sequencing and a comprehensive bioinformatics analyses to characterize the transcriptome profiles, including mRNAs and long noncoding RNAs (lncRNAs), in patients with eosinophilic and noneosinophilic CRSwNP. A total of 1917 novel lncRNAs and 280 known lncRNAs were identified. We showed eosinophilic CRSwNP (ECRSwNP) and noneosinophilic CRSwNP (non-ECRSwNP) display distinct transcriptome profiles. We identified crucial pathways, including inflammatory, immune response and extracellular microenvironment, connected to the pathogenetic mechanism of CRSwNP. We also discovered key lncRNAs differentially expressed, including lncRNA XLOC_010280, which regulates CCL18 and eosinophilic inflammation. The qRT-PCR and Chronic rhinosinusitis (CRS) is one of the most prevalent chronic diseases with a heavy socioeconomic burden12122561012Global gene expression has been studied using complementary DNA microarray techniques in CRS populations, primarily CRSwNP14151617212324Our aim in this study was to delineate a more complete transcriptome picture and identify key pathways that are dysregulated in eosinophilic and noneosinophilic CRSwNP. Therefore, we analyzed the profiles of gene expression in nasal polyps from ECRSwNP (n\u2009=\u20093), non-ECRSwNP (n\u2009=\u20093), and normal nasal mucosa from control subjects . We used next-generation high-throughput RNA sequencing (RNA-Seq), an unbiased technology that depicts the whole set of transcriptional deviations in a disease, including novel transcripts not annotated in the database or measured by conventional assaysTo comprehensively identify lncRNAs and mRNAs related to CRSwNP, we applied whole transcriptome strand specific RNA-Seq on rRNA-depleted RNAs from 3 ECRSwNP, 3 non-ECRSwNP and 3 CTRL sample tissues. We obtained a total of 1.017\u2009billion raw reads, from which 969\u2009million clean reads were isolated . More thThen, we developed a CRSwNP transcripts computational identification pipeline. For mRNAs, we chose RefSeq database (Build 37.3) as the annotation reference. For lncRNAs, we chose GENCODE v19 database as the annotation reference. Through the transcripts identification pipeline , we obtaTo examine chromatin features of lncRNA loci, we analyzed the publically available epigenetic modification information across nine ENCODE cell lines27We characterized the basic features of the lncRNAs and compared them with protein-coding genes where appropriate. Our data show that average lncRNA expression was lower than protein-coding gene expression . LncRNAsIn the ECRSwNP group, 151 lncRNA transcripts (26 up-regulated and 125 down-regulated) and 1921 mRNA transcripts (1058 up-regulated and 863 down-regulated) were differentially expressed compared to the control group . In non-To confirm the reliability of our RNA-Seq data, we randomly selected five lncRNAs transcripts from all dysregulated lncRNAs and analyzed expression levels by qRT-PCR in another independent cohort of 32 ECRSwNP subjects, 28 non-ECRSwNP subjects and 31 control subjects. The qRT-PCR fold change values for each lncRNA were calculated and compared with data obtained from RNA-Seq. The qRT-PCR results were consistent with the RNA-Seq data with the same trends (up- or down-regulated) for each lncRNA , confirmTo ascertain the functions of the differentially expressed mRNAs and connections among them, we performed GO term and KEGG pathway enrichment analyses. We drew directed acyclic graphs (DAGs) for the significantly over-represented GO terms to clarify the relationship , in whicThe KEGG pathway analyses mapped the dysregulated protein-coding genes to KEGG reference pathways to infer systemic biological behaviors. The KEGG pathway analysis of the differentially expressed mRNAs between ECRSwNP and control group revealed that phagosome, TNF signaling pathway, staphylococcus aureus infection, and asthma are significantly over-represented ; compariAlthough the same over-represented terms appeared in multiple comparison groups, the genes enriched in the terms were distinct among different comparison groups. For example, cytokine activity and chemokine activity were over-represented in all three comparison groups, but IL-13 and CCL26 were specifically highly expressed in ECRSwNP patients, while CXCL1 and CXCL5 were specifically highly expressed in non-ECRSwNP patients . TherefoTo gain insights into the common pathophysiological mechanism of ECRSwNP and non-ECRSwNP, we analyzed the 623 common dysregulated mRNAs of the 1cis and regulate the expression of nearby protein-coding genes22trans and regulate the expression of remote genes29cis regulatory function of lncRNAs, we calculated the Pearson correlation coefficient (PCC) between the expression levels of lncRNAs and neighboring protein-coding genes (lncRNA:cis-mRNA pairs) and compared with those of mRNA:cis-mRNA pairs and random protein-coding gene pairs (cis-mRNA pairs (mean PCC\u2009=\u20090.107) and mRNA:cis-mRNA pairs (mean PCC\u2009=\u20090.127) had a significantly positive correlation . However, we did not observe a stronger correlation of lncRNA:cis-mRNA pairs compared with mRNA:cis-mRNA pairs . Taken together, these results suggest that lncRNAs perform a cis regulatory role on neighboring protein-coding genes, but not stronger than that of mRNAs. We performed the GO enrichment analysis of cis-mRNAs to predict the function of dysregulated lncRNAs, but no significant enrichment was found since the number of cis-mRNAs was relatively small.Most of the known lncRNAs are not functionally annotated in current databases. Previous studies demonstrated that lncRNAs act in ne pairs . There wtrans. The function of differentially expressed lncRNAs can be predicted by their closely correlated trans-regulated target protein-coding genestrans-regulated potential target protein-coding genes. To clarify the functional categories with which the differentially expressed lncRNAs were associated, we performed GO enrichment analysis on their trans-regulated target mRNAs and metallopeptidase activity. In the common differentially expressed mRNAs analysis, ECRSwNP and non-ECRSwNP share many common dysregulated genes in inflammatory and immune response and extracellular matrix microenvironment, including staphylococcus aureus infection, HIF-1 signaling pathway, and cell adhesion molecules, but they also have their own distinctive characteristics. For instance, on the cytokine and chemokine side, we found IL-13 and eotaxins highly expressed in ECRSwNP, while IFN-\u03b3 and IL-8 highly expressed in non-ECRSwNP . This su1We compared the most differentially expressed mRNAs between ECRSwNP and non-ECRSwNP in our study with pre404140414045381cis or in transcis- and trans- regulated target protein-coding genes. The neighbor gene correlation suggests that lncRNAs perform a cis regulatory role on neighboring protein-coding genes, but not stronger than that of mRNAs. The enrichment of cis-regulated target protein-coding genes was not significant because of limited number of target genes. The trans-regulated target protein-coding genes of the three comparison group commonly enriched in terms about cellular process regulation, cell communication and signal transduction, cell movement and migration, and cytokine activity. The identified enriched function categories of dysregulated lncRNAs are closely related to those of the dysregulated protein-coding genes, suggesting that lncRNAs play an important part in regulating the expression of protein-coding genes in CRSwNP.Among the numerous uncharacterized transcripts identified by our study, we obtained 1917 novel and 280 known GENCODE v19 lncRNAs transcripts through our pipeline. The high ratio of novel to known lncRNAs may have resulted from the high tissue specificity of lncRNA20cis-regulated target CCL18 were highly correlated. CCL18 plays a vital role in Th2 inflammation and is mainly produced by M2 macrophage in nasal polyps in Caucasian CRSwNP patients1P value\u2009<\u20090.0017) (cis-regulated target CCL18 (PCC\u2009=\u20090.89). The results of qRT-PCR and in situ hybridization showed that XLOC_010280 was also highly expressed in ECRSwNP. Both XLOC_010280 and CCL18 are located in chromosome 17q11.2-q12 CC chemokine gene cluster . Further cluster . This geThere are several advantages of using RNA-Seq over microarrays: 1) the ability to identify novel transcripts, not confined to annotated transcripts in databases; (2) sensitive detection and reliable quantification of coding and noncoding transcripts, which is particularly important because of the low expression level of lncRNAs. However, our study has several limitations. First, the sample size was relatively small and the gender of the RNA-Seq subjects was heterogeneous. Nevertheless, the consistency between our results and the previous research the abil12141635363738394546In conclusion, the dysfunction of inflammatory and immune response and extracellular microenvironment are the key pathogenic mechanisms of CRSwNP. Differences in the pathophysiology of two subtypes of CRSwNP demonstrate the significance and necessity of developing specific biomarkers and personalized therapeutic strategies. The high consistency between predicted functions of dysregulated lncRNAs and functions of dysregulated mRNAs indicates lncRNAs play a critical role in regulating the expression of protein-coding genes in CRSwNP. This study lays a solid foundation for subsequent functional studies of mRNAs and lncRNAs as diagnostic and therapeutic targets in CRSwNP by providing a candidate reservoir.An expanded Method section is available in the The study was approved by the Ethics Committee of Peking Union Medical College Hospital. All study participants provided written informed consent and were recruited at Peking Union Medical College Hospital. All experiments were performed in accordance with approved guidelines. A total of 35 patients with ECRSwNP, 31 patients with non-ECRSwNP and 34 control subjects were recruited for the study. The diagnosis of CRSwNP was based on standard criteria issued in the European Position Paper on Rhinosinusitis and Nasal Polyps 2012 guidelinesThe CRSwNP patients were classified based on the tissue eosinophil number, counted in the lamina propria of the polyps in five random microscopic high power fields . We defined ECRSwNP as subjects whose tissue eosinophil number per HPF was more than twentyTotal RNAs from 3 ECRSwNP, 3 non-ECRSwNP and 3 control subjects were isolated and quality controlled. The preparation of whole transcriptome libraries and deep sequencing were performed by Novogene Bioinformatics Technology Cooperation . Ribosomal RNA (rRNA) was removed and strand-specific sequencing libraries were generated following manufacture\u2019s recommendations. RNA-Seq was performed on an Illumina Hiseq 2000 platform and 100\u2009bp paired-end reads were generated according to Illumina\u2019s protocol. Detailed procedures are in the P value\u2009<\u20090.05 adjustment) was used as the cut-off for significantly differentially expressed genes. Differentially expressed genes were analyzed by enrichment analyses to detect over-represented functional terms present in the genomic background. See the The adapter sequences were removed from the raw sequencing data and the individual libraries were converted to the FASTQ format. Sequence reads were aligned to the human genome (hg19) with TopHat2 and the resulting alignment files were reconstructed with Cufflinkscis and trans target mRNAs. We defined potentially cis-regulated target genes as protein-coding genes within 100kb in genomic distance from the lncRNA, and potentially trans-regulated target genes as protein-coding genes coexpressed with the lncRNA with Pearson correlation coefficient (PCC) >0.95 or <\u22120.95 and beyond 100\u2009kb in genomic distance from the lncRNA or in different chromosomes. We analyzed the expression correlation of lncRNA:cis-mRNA pairs and lncRNA:trans-mRNA pairs by calculating PCC.Most of the lncRNAs in current databases have not yet been functionally annotated. Thus, the prediction of their functions is based on the functional annotations of their related All primers qRT-PCR for qRT-PCR experiments are listed in In situ hybridization analyses for lncRNA XLOC_010280 were performed on paraffin-embedded sections by using digoxigenin (DIG)-labeled XLOC_010280 antisense probe or sense control probe. More information is provided in the Method section in Accession codes: Data for the RNA-Seq experiments are deposited in the NCBI Gene Expression Omnibus as GSE72713.How to cite this article: Wang, W. et al. Transcriptome Analysis Reveals Distinct Gene Expression Profiles in Eosinophilic and Noneosinophilic Chronic Rhinosinusitis with Nasal Polyps. Sci. Rep. 6, 26604; doi: 10.1038/srep26604 (2016)."} +{"text": "Pseudomonas putida CBF10-2 is a microorganism isolated from farmland soil in Fairchild, TX, found to degrade high-impact xenobiotics, including organophosphate insecticides, petroleum hydrocarbons, and both monocyclic and polycyclic aromatics. The versatility of CBF10-2 makes it useful for multipurpose bioremediation of contaminated sites in agricultural and industrial environments. Pseudomonas putida is a Gram-negative gammaproteobacterium ubiquitous to contaminated soil environments and is well known for its tolerance and degradation capacity for organic solvents . The metabolic pathways of aromatic and heterocyclic compounds were examined using the KEGG databases . The clo glucose . While a glucose and filt glucose , with a glucose Web resoatabases . This drPseudomonas putida CBF10-2 whole-genome shotgun (WGS) project has the project accession no. LUCV00000000. This version of the project (01) has the accession number LUCV01000000 and consists of sequences LUCV01000001 to LUCV0100073.The"} +{"text": "Lymantria dispar) biopesticide Virin-ENSh. The genome sequence is 161,712\u00a0bp, and its structure and sequence similarity indicate that the virus used in Virin-ENSh is a strain of the species Lymantria dispar multiple nucleopolyhedrovirus.We report the genome sequence of an alphabaculovirus from the gypsy moth ( Lymantria dispar (Lepidoptera: Noctuidae), is a worldwide pest of trees and forests , designated the species Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) . The com(LdMNPV) . Partial(LdMNPV) . However(LdMNPV) , and res(LdMNPV) .hrs) and baculovirus repeated ORFs (bros). The two LdMNPV genomes contain 12 (LdMNPV-3029) or 13 (LdMNPV 5-6) hrs and 16 bros found in 8 clusters distributed throughout the genome sequences. Large indels occurring in these locations provide a likely explanation for the appearance of significantly different restriction endonuclease fragment patterns reported for these two strains of LdMNPV. We conclude that the virus used in the Virin-ENSh biopesticide is a strain of the previously defined baculovirus species Lymantria dispar multiple nucleopolyhedrovirus.To resolve issues surrounding the identity of the virus found in Virin-ENSh, occlusion bodies of a sample of Virin-ENSh isolate 3029 of a USDA insect virus collection maintained in Beltsville, Maryland, USA, were grown in New Jersey Standard Strain gypsy moth larvae. Viral DNA was isolated from the occlusion bodies and subjected to 454 sequencing as previously described . AssemblKM386655.The genome sequence was deposited in GenBank under the accession number"} +{"text": "The aim was to compare the accuracy of standard supplementary views and GE digital breast tomosynthesis (DBT) for assessment of soft tissue mammographic abnormalities.Women recalled for further assessment of soft tissue abnormalities were recruited and received standard supplementary views and two-view GE DBT. The added value of DBT in the assessment process was determined by analysing data collected prospectively by unblinded radiologists working up the cases.Following anonymisation of cases, there was also a retrospective multireader review. The readers first read bilateral standard two-view digital mammography (DM) together with the supplementary mammographic views and gave a combined score for suspicion of malignancy on a five-point scale. The same readers then read bilateral standard two-view DM together with two-view DBT. Pathology data were obtained. Differences were assessed using ROC analysis.The study population was 342 lesions in 322 patients. Final diagnosis was malignant in 113 cases (33%) and benign/normal in 229 cases (67%). In the prospective analysis, the performance of two-view DM plus DBT was at least equivalent to the performance of two-view DM and standard mammographic supplementary views--area under the curve (AUC) was 0.946 and 0.922 respectively, which did not reach statistical significance. Similar results were obtained for the retrospective review--AUC was 0.900 (DBT) and 0.873 (supplementary views), which did not reach statistical significance.The accuracy of GE DBT in the assessment of screen-detected soft tissue abnormalities is equivalent to the use of standard supplementary mammographic views."} +{"text": "To assess the combined antitumor effect of STAT3-blocking/TLR9-triggering in immunocompetent host, we used syngeneic Cbfb/MYH11 AML. The i.v. administration of CpG-STAT3dODN over two weeks resulted in long-term survival of the majority of mice. These potent antitumor effects resulted from the increased immunogenicity of leukemic cells rather than host antigen-presenting cells as suggested by the comparable extent of tumor regression in wild-type and TLR9-deficient mice. These finding support further development of CpG-STAT3dODN strategy for treatment of AML and potentially B cell lymphoma.STAT3 transcription factor is persistently activated in cancer cells and in diverse tumor-associated immune cells being an important oncogene and an essential immune checkpoint regulator. It is a highly desirable but challenging therapeutic target for pharmacological intervention. We previously demonstrated that ligand for the intracellular receptor TLR9 (CpG ODN) allows for the uptake and cytoplasmic delivery of siRNA into specific target cells-3. Now, This project described was supported by the National Cancer Institute of the National Institutes of Health under award number R01CA155367 to M.K."} +{"text": "Diabetes mellitus (DM) is a chronic disease with an ever-increasing incidence in world and has become the object of scientific research into the search for novel therapeutic alternatives. Bauhinia forficata Link, known locally as cow foot, has been traditionally used as tea in folk medicine of Brazil for treatment of DM.The purpose of this study is to explore the possible homology between the AA sequences of ribulose 1,5-biphosphate carboxylase large subunit, partial (chloroplast) [Bauhinia forficata subsp. pruinosa] and pancreatic beta-cell specific transcriptional activator [Homo sapiens], using databanks of proteins of National Center for Biotechnology Information (NCBI).Were performed the comparison between the AA sequence of the GenBank: CAA94019.1-ribulose 1,5-biphosphate carboxylase large subunit, partial (chloroplast) [Bauhinia forficata subsp. pruinosa] and GenBank: BAC20389.1-pancreatic beta-cell specific transcriptional activator [Homo sapiens], available in the database of NCBI with the Basic Local Alignment Search Tool (BLASTp) software.The homology between the ribulose 1,5-biphosphate carboxylase large subunit, partial (chloroplast) [Bauhinia forficata subsp. pruinosa] and the pancreatic beta-cell specific transcriptional activator [Homo sapiens] ranged from 48.0% to 63.0% [Bauhinia forficata subsp. pruinosa] and pancreatic beta-cell specific transcriptional activator [Homo sapiens], and studies on this plant are important to the safe, effective development of pharmaceutical products for the treatment of diabetes."} +{"text": "This effect was clear during the first 40 days of treatment and was lost during the last stages of treatment. Administration of RFX+SFZ to chronically SIVsab\u2013infected PTMs had no discernible effect on infection. Our data thus indicate that early RFX+SFZ administration transiently improves the natural history of acute and postacute SIV infection, but has no effect during chronic infection.Increased chronic immune activation and inflammation are hallmarks of HIV/SIV infection and are highly correlated with progression to AIDS and development of non-AIDS comorbidities, such as hypercoagulability and cardiovascular disease. Intestinal dysfunction resulting in microbial translocation has been proposed as a lead cause of systemic immune activation and hypercoagulability in HIV/SIV infection. Our goal was to assess the biological and clinical impact of a therapeutic strategy designed to reduce microbial translocation through reduction of the microbial content of the intestine (Rifaximin-RFX) and of gut inflammation . RFX is an intraluminal antibiotic that was successfully used in patients with hepatic encephalopathy. SFZ is an antiinflammatory drug successfully used in patients with mild to moderate inflammatory bowel disease. Both these clinical conditions are associated with increased microbial translocation, similar to HIV-infected patients. Treatment was administered for 90 days to five acutely SIV-infected pigtailed macaques (PTMs) starting at the time of infection; seven untreated SIVsab-infected PTMs were used as controls. RFX+SFZ were also administered for 90 days to three chronically SIVsab-infected PTMs. RFX+SFZ administration during acute SIVsab infection of PTMs resulted in: significantly lower microbial translocation, lower systemic immune activation, lower viral replication, better preservation of mucosal CD4 + T cells and lower levels of hypercoagulation biomarkers throughout acute SIV infection. Our results thus support the use of therapeutic approaches to reduce microbial translocation, improve the clinical outcome of HIV-infected patients receiving antiretroviral therapy and prevent non-AIDS comorbidities. Our results also reinforce the importance of early therapeutic management of HIV infection.We report that administration of the intraluminal antibiotic Rifaximin and the gut-focused anti-inflammatory drug Sulfasalazine to acutely SIV-infected pigtailed macaques is associated with a transient disruption of the vicious circle of inflammation-microbial translocation-immune activation which is pathognomonic to pathogenic HIV/SIV infection and drives HIV disease progression and non-AIDS comorbidities in HIV-infected patients. This therapeutic approach resulted in transient lower microbial translocation, lower systemic immune activation, lower viral replication, better preservation of mucosal CD4 Differences in microbiome composition between infant subsets were quantified by the Bray-Curtis beta-diversity index using the adonis function of the vegan R package, which performs a non-parametric multivariate analysis of variance [The Explicit sequence analysis software package (v.2.7) and R-stmplings) . IndividApproximately 25 mg aliquots of stool were weighed, and then DNA purified using the UltraClean Fecal DNA kit . 16S rRNA gene copy numbers were measured in duplicate for each sample using a panbacterial quantitative PCR TaqMan assay . 16S copWe compared microbial translocation, cytokine and other immune parameters between RFX+SFZ-treated and control animals at two time periods separately: acute phase and post-acute phase. To improve the power of these analyses, we used linear mixed-effects models . In thisDuring the acute phase the behavior of the different parameters assayed over time is variable, so to allow for a general pattern of dependency of the variable on time, we considered the number of days since infection as a categorical factor . For thihttp://cran.r-project.org/).Assumptions on the distribution of residuals and appropriateness of the fitted values were checked by visual inspection of residual and fitted plots. The best model for the data (with or without the interaction term) was chosen comparing the log likelihood. For these analyses we used the lme function of the nlme package of R , precluding the use of mixed-effects models, we used a Mann-Whitney test.Finally, to compare the percentage of CD4+ T-cells, we analyzed fold-changes from baseline for all variables studied. P-values<0.05 were considered to be significant.With the exception of viral loads and peripheral CD4S1 Fig(PDF)Click here for additional data file.S2 Fig(a) Comparison between plasma LPS levels in SIVsab-infected PTMs receiving RFX+SFZ (red) and untreated controls (black). (b) Comparison between plasma sCD14 levels in SIVsab-infected PTMs receiving RFX+SFZ (red) and untreated controls (black).(PDF)Click here for additional data file.S3 Fig+ T cells (a) and CD8+ T cells (b). Conversely, Ki-67 expression by CD4+ T cells (c) and CD8+ T cells (d) was not statistically different between the two groups.Significant differences were observed between SIVsab-infected PTMs receiving RFX+SFZ (red) and untreated controls (black) with regard to CD38 and HLA-DR expression by CD4(PDF)Click here for additional data file.S4 FigLevels of proinflammatory cytokines were consistently lower in SIVsab-infected PTMs receiving RFX+SFZ (red) compared to untreated controls (black): TNF-\u03b1 (a); I-TAC (b); and C-reactive protein (CRP) (c).(PDF)Click here for additional data file.S5 Fig+ T cells (b), a less prominent depletion of mucosal CD4+ T cells could be observed in treated PTMs (c).Levels of viral replication were significantly lower in SIVsab-infected PTMs receiving RFX+SFZ (red) compared to untreated controls (black) (a). While no significant impact of RFX+SFZ treatment could be observed in circulating CD4(PDF)Click here for additional data file.S6 FigLevels of d-dimer (a) and tissue factor (b) were significantly lower in SIVsab-infected PTMs receiving RFX+SFZ (red) compared to untreated controls (black). Shown are the average values for each group and standard error of means.(PDF)Click here for additional data file."} +{"text": "Stem Cell Research and Therapy by Wagh and colleagues reports a novel regulatory role for miR-363 in cardiomyocyte specification. By employing microRNA expression profiling and functional knockdown studies on human embryonic stem cell-derived cardiomyocytes, the authors identified miR-363 as an upstream negative regulator of left ventricular specification transcription factor HAND1.MicroRNAs regulate target gene expression post-transcriptionally in a myriad of cell types and play critical roles in diverse physiological and pathological processes, including cardiomyocyte development, differentiation, and regeneration. The recent publication in The efficient derivation of specialized and functional cardiomyocytes (CMs) from pluripotent stem cells is a primary goal for stem cell-based cardiac regenerative therapies. Such a prospect is currently hampered, however, in part by an incompletely defined complex of molecular regulators of cardiac cell development and differentiation.Stem Cell Research and Therapy demonstrating a critical role for miR-363 in post-transcriptional regulation of CM differentiation via the hand and neural crest derivative expressed HAND1 transcription factor [This commentary discusses the findings from Wagh and colleagues published in this issue of n factor . There iin vivo CM proliferation in rat and mouse models [MicroRNAs (miRNAs) are small noncoding RNAs (~22 nucleotides in length) that regulate gene expression post-transcriptionally by imperfect binding to the 3\u2032 untranslated region of target mRNAs in a wide variety of cell types. Given the notion that a single miRNA may have multiple cellular targets and given the existence of vast numbers of miRNAs , we can expect to witness the discovery of novel miRNA-dependent regulation in the modulation of versatile biological functions . Recentle models , 7. miRNin vitro[in silico analysis) of the CM subtype specification transcription factors , and found that a subset of miRNAs was expressed at a higher level in hESC-derived non-CMs compared with CMs. These novel findings were confirmed by real-time polymerase chain reaction analysis: higher expression of HAND genes correlated with lower expression of miR-363, miR-367, miR-181a and miR-181c. Using an elegant dual-reporter assay, the authors further showed that miR-363 specifically inhibits HAND1 gene expression through 3\u2032 untranslated region binding. Perhaps more heartening, overexpression of antisense oligonucleotide directed against miR-363 (anti-miR-363) during hESC differentiation promoted more HAND1-expressing CMs, confirming the role of miR-363 in dorso-ventral patterning and interventricular septum formation in the embryonic heart [hESCs are a unique source for deriving cardiac cells in a specialized manner and also offer a unique opportunity to study the mechanisms and derivation of different cardiac cell types in vitro, 9. The in vitro. To thisic heart , 11 (FigHAND1 transcription factor and extends the role of miRNAs in cardiac cell biology (Figure\u00a0In summary, Wagh and colleagues demonstrated for the first time that miR-363 acts as an upstream negative regulator of in vivo? To what extent does this regulation affect the cardiac cell specification during development? Is it safe to use anti-miR-363 for cardiac regenerative therapies? What are the additional miRNA networks that cooperate with miR-363 to form a high-order regulatory complex in determining cardiac cell specification? Most importantly, how can we derive the desired functional cardiac subtype without any genetic manipulation? These are just a few of the myriad questions that are emerging from this exciting study. Answering these questions may identify more druggable targets and might help push cardiac research much closer to human cardiac regenerative therapy.Nevertheless, Wagh and colleagues\u2019 study opens new areas of research and presents several unanswered questions for future investigations. The current study is impressive, but does the miR-363-mediated repression of HAND1 occur"} +{"text": "There are limited prospective, prognostic data for cardiovascular magnetic resonance (CMR) in the same patients with suspected coronary heart disease (CHD). CE-MARC established the diagnostic performance of CMR (and SPECT), with a predefined objective to determine both modalities' ability to predict major adverse cardiovascular events (MACE).All CE-MARC patients underwent annual follow-up for 3 years to assess the occurrence of MACE . Time to MACE was assessed by univariate (log-rank test) and multivariate analysis after adjustment for major cardiovascular risk factors. Net reclassification improvement (NRI) and discrimination (IDI) of the risk of MACE with CMR, incremental to standard clinical risk factors was calculated.747(99.3%) of 752 patients recruited had complete follow-up. Of 633 who underwent both CMR and SPECT, 41(6.5%) had at least 1 MACE event. Abnormal CMR findings were strong and independent predictors of MACE ."} +{"text": "Compressed sensing (CS) is an efficient tool that accelerates the data acquisition in MRI through the significant reduction of required measurements for image reconstruction. In recent years, there have been significant interests in the use of Compressed Sensing (CS) in Dynamic applications . Since CIn this study we obtain Temporal Estimation (TE) from Temporal Information (TI) using forward-backward motion estimation (F-B ME) to highly accelerate dynamic MRI acquisition.We implement CS on TE in the first step and then use these reconstructed frames with under-sampling K-space data in aModified CS (MCS) scheme. Figure The results of the proposed algorithm were compared to those of conventional CS, CS -TI and origWe proposed a new method to highly accelerate Cine cardiac images using spatial and temporal sparsity based on CS theory. The proposed method high efficiency under-sampling rate and fidelity in CS theory. The results show the efficiency and accuracy of the proposed methods compared to other conventional CS methods. Concluding that proposed method outperforms other methods in both SNR and SSIM with 10% and 8%, respectively."} +{"text": "Cardiac MR (CMR) has emerged as the gold standard for the evaluation of biventricular systolic function. Semi-automated algorithms for investigating left ventricular systolic function exist, but application to the right ventricle (RV) is challenging. Recently, feature tracking has been developed to semi-automatically track the tricuspid annulus on 4-chamber cine imaging. The purpose of this feasibility study is to determine the ability of semi-automated quantification of the CMR tricuspid annular plane systolic excursion (CMR-TAPSE) to predict normal RV systolic function, comparing to echocardiography determined TAPSE (echo-TAPSE) and quantitative assessment of RV systolic function at CMR.Retrospective analysis of 15 patients referred for cardiac MR and transthoracic echocardiography with suspected infiltrative heart disease. MR images were acquired at 1.5T . A high temporal resolution 4-chamber segmented cine bSSFP acquisition was acquired . Standard temporal resolution bSSFP cine short axis images were acquired for quantitative evaluation of RV systolic function . 4-chamber HR bSSFP cine images were analyzed using prototype software evaluating deformation fields to semi-automatically identify and track the tricuspid base plane at the lateral tricuspid insertion determining CMR-TAPSE. The CMR RV ejection fraction (RVEF) was determined on a dedicated workstation by two reviewers. A single reviewer calculated echo-TAPSE on a dedicated PACS workstation . CMR-TAPSE and Echo-TAPSE were correlated with the CMR RVEF using Pearson's correlation. ROC analysis was performed using a TAPSE threshold of 15 mm and defining normal RV systolic function as a RVEF\u226540%.There was a significant correlation between CMR-TAPSE and CMR RVEF Figure . CorrelaCMR-TAPSE shows promise for efficient prediction of normal RV systolic function with similar performance to Echo-TAPSE and good correlation with CMR derived RVEF. Work is ongoing to validate our results in a larger cohort.None."} +{"text": "A challenge for drug of abuse testing is presented by \u2018designer drugs\u2019, compounds typically discovered by modifications of existing clinical drug classes such as amphetamines and cannabinoids. Drug of abuse screening immunoassays directed at amphetamine or methamphetamine only detect a small subset of designer amphetamine-like drugs, and those immunoassays designed for tetrahydrocannabinol metabolites generally do not cross-react with synthetic cannabinoids lacking the classic cannabinoid chemical backbone. This suggests complexity in understanding how to detect and identify whether a patient has taken a molecule of one class or another, impacting clinical care.Cross-reactivity data from immunoassays specifically targeting designer amphetamine-like and synthetic cannabinoid drugs was collected from multiple published sources, and virtual chemical libraries for molecular similarity analysis were built. The virtual library for synthetic cannabinoid analysis contained a total of 169 structures, while the virtual library for amphetamine-type stimulants contained 288 compounds. Two-dimensional (2D) similarity for each test compound was compared to the target molecule of the immunoassay undergoing analysis.2D similarity differentiated between cross-reactive and non-cross-reactive compounds for immunoassays targeting mephedrone/methcathinone, 3,4-methylenedioxypyrovalerone, benzylpiperazine, mephentermine, and synthetic cannabinoids.In this study, we applied 2D molecular similarity analysis to the designer amphetamine-type stimulants and synthetic cannabinoids. Similarity calculations can be used to more efficiently decide which drugs and metabolites should be tested in cross-reactivity studies, as well as to design experiments and potentially predict antigens that would lead to immunoassays with cross reactivity for a broader array of designer drugs. Immunoassays (antibody-based assays) are widely employed for drug of abuse/toxicology screening on urine or other bodily fluids. Immunoassays may utilize polyclonal or monoclonal antibodies, with a trend towards monoclonal antibody-based designs ,2. Many A challenge for drug of abuse testing is presented by what are widely termed \u2018designer drugs\u2019, a heterogeneous group of psychoactive compounds typically discovered by modifications of existing clinical drug classes such as amphetamines -10. Two N-methylamphetamine . Immunalysis, Inc. markets two assays for synthetic cannabinoids . Neogen Corporation markets ELISAs for synthetic cannabinoids [Synthetic Cannabinoids (SPICE) ELISA kit], benzylpiperazine (Benzylpiperazine Forensic ELISA), and mephentermine (Mephentermine Forensic ELISA). Two publications report extensive cross-reactivity testing of immunoassays targeted at synthetic cannabinoids and amphFor the Neogen Synthetic Cannabinoids ELISA, Randox Synthetic Cannabinoids ELISA, the Immunalysis synthetic cannabinoids assays, and two synthetic cannabinoids assays reported in the literature by Arntson et al. , there iThe virtual chemical libraries curve analysis were carried out in EP Evaluator release 9 . Sensitivity was defined as: (number of true positives)/. Specificity was defined as: (number of true negatives)/. Efficiency was defined as: (number of true positives\u2009+\u2009number of true negatives)/. ROC curve analysis plots the true positive rate (sensitivity) on the y-axis versus the false positive rate (1-specificity). EP Evaluator calculates the true and false positive rate at a range of thresholds for the 2D similarity in discriminating experimental determined assay cross-reactivity (positive) compared to lack of cross-reactivity (negative). ROC curve analysis was only performed if there were five or more cross-reactive compounds for a given assay. EP Evaluator does not allow for ROC curve analysis if less than five datapoints are available in either the positive or negative groups. This is to avoid erroneous conclusions based on ROC curve analysis of samples with small study size .The authors declare that they have no competing interests.MDK and SE conceived and designed the experiments and analyzed the data. MDK wrote the initial manuscript. Both authors read and approved the final manuscript.Cross-Reactivity and Similarity Data for Amphetamine-like Compounds: Contains common and scientific names and SMILES identifiers for compounds, along with cross-reactivity data of immunoassays and 2D similarity measures for the amphetamine-like compounds analyzed in this study.Click here for fileCross-Reactivity and Similarity Data for Cannabinoids: Contains common and scientific names and SMILES identifiers for compounds, along with cross-reactivity data of immunoassays and 2D similarity measures for the cannabinoid compounds analyzed in this study.Click here for file"} +{"text": "Polybrominated diphenyl ethers (PBDEs) are widely used as flame-retardant additives in consumer and household products and can escape into the environment over time. PBDEs have become a global environmental organic pollutant due to the properties of persistence, toxicity, and bioaccumulation. The well-studied toxic effects of PBDEs mainly include thyroid hormone disruption and neurotoxicity. There is no consistent conclusions on the carcinogenic potential of PBDEs to date. Here, we explored the toxic effects of BDE-209 on human embryonic kidney cells (HEK293T). The comparison of the gene expression profiles of HEK293T cells with BDE-209 treatment and the negative control found that BDE-209 exposure may alter nucleosome organization through significantly changing the expression of histone gene clusters. The remodeled chromatin structure could further disturb systemic lupus erythematosus as one of the toxic effects of BDE-209. Additionally, gene sets of different cancer modules are positively correlated with BDE-209 exposure. This suggests that BDE-209 has carcinogenic potential for a variety of tumors. Collectively, BDE-209 has a broader toxicity not limited to disruption of thyroid hormone-related biological processes. Notably, the toxic effects of BDE-209 dissolved in dimethyl sulfoxide (DMSO) is not the simply additive effects of BDE-209 and DMSO alone. Polybrominated diphenyl ethers (PBDEs) are a major type of brominated flame retardants. PBDEs have been widely used in a variety of consumer and household products to delay the ignition of materials , 3,3\u2032,5-triiodothyronine (T3) and 3,3\u2032,5,5\u2032-tetraiodothyronine (T4). The metabolites of PBDEs compete with thyroid hormones to bind to thyroid hormone receptors (TR) cultured in the normal medium, and the medium added with DMSO (the solvent) and with BDE-209 dissolved in DMSO. Pairwise comparisons identified significantly expressed genes between each two samples. The functional analysis of these genes found that BDE-209 exposure may alter nucleosome arrangement through changing the expression of histone gene clusters. In addition to this, BDE-209 exposure could increase the risk for tumorigenesis of a number of tumors. Our results also found that the total toxic effects of BDE-209 dissolved in DMSO led to a more complex toxic effects than the additive effects of BDE-209 and DMSO alone.2 as adherent monolayer in Dulbecco modified Eagle medium (DMEM) (Hyclone) that was supplemented with L-glutamine and 10% fetal bovine serum (FBS) (Hyclone). BDE-209 was dissolved in the dimethyl sulfoxide (DMSO) and added to the culture medium. The final concentration of BDE-209 and DMSO is 10\u22126 and 10\u22123 M, respectively. The negative control is the HEK293T cells cultured in the normal medium. The DMSO treatment sample is the HEK293T cells cultured in the medium added with DMSO. The BDE-209 treatment sample is the HEK293T cells cultured in the medium added with BDE-209 dissolved in DMSO. All samples were cultured for 48 h.We cultured human embryonic kidney 293 cells (HEK293T) at 37\u00b0C in 5% COWe extracted the total RNA w from each sample using Trizol reagent (Invitrogen) according to the manufacturer's instructions. Then, BGI-Shenzhen (the sequencing service provider) enriched the mRNA by polyA tail, prepared the library, and did the sequencing using Illumina HiSeq2000. Sequencing method was 49 bp single-end reads. RNA-seq data can be accessed through GEO database under accession number GSE56361.q-value \u2265 0.6 were defined as the differentially expressed (DE) genes. Gene ontology (GO) and pathway analysis for DE genes were performed using the tool DAVID . We also generated transcriptomic profiles of HEK293T cell treated with the solvent DMSO (10\u22123 M) and normal medium as negative control, respectively. Pairwise comparison of the gene expression profiles of the three samples will allow us not only to analyze the impacts of BDE-209 and DMSO alone on gene expression but also the additive effects of two organic chemicals. More than 86% of reads were mapped to the reference genome . The KEGG pathway annotation shows that nucleosome and histone gene clusters are the upstream factors in the pathway systemic lupus erythematosus. Therefore, the perturbation of BDE-209 to systemic lupus erythematosus is likely attributed to the differentially expressed gene clusters encoding histones in the BDE-209 treatment samples identified 117 significantly differentially expressed genes (defined gene Set I hereinafter), 72 up-regulated genes and 45 down-regulated genes. Similarly, we obtained 96 significantly differentially expressed genes (defined gene Set II hereinafter) between BDE-209 dissolved in DMSO and the negative control samples, 54 up-regulated genes and 42 down-regulated genes. We defined the above identified 94 significantly differentially expressed genes between BDE-209 dissolved in DMSO and DMSO samples as gene Set III. There are only about 20 common genes (~25%) shared by each two of the gene sets, respectively Figure . Gene SeThe standard 2-year rodent bioassays found dose-related increase in liver and thyroid tumors in both rats and mice with deca-BDE treatment NTP, . HoweverPBDEs consist of more than 200 possible congeners. The commercial use of PBDEs as flame-retardant additives is actual in a mixture of congeners that are slowly released over time. PBDEs with different levels of bromination possess distinct properties. The fully brominated deca-BDE congeners are likely one of the least bioactive PBDEs because they are relatively poorly absorbed, rapidly removed, and not bioaccumulative (Hooper and McDonald, As noted earlier, many bioassays on the toxic effects of PBDEs mainly focused on disruption of TH homeostasis and TH-induced biological processes. In this study, we used a not TH-related human cell HEK239T to investigate the toxic effects of PBDEs, and discovered that PBDE exposure could affect nucleosome organization. Additionally, BDE-209 has carcinogenic potential effects in HEK293T cells. Interestingly, a previous study showed that BDE-209 exposure can cause mouse sperm DNA damage in a dose dependent manner (Wang et al., The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Multiple studies have documented the presence of systemic osteopenia in AIS. Osteopenia was associated with severe curves and was reported to be one of the significant prognostic factors for curve progression in AIS. This study aimed to evaluate bone quality and bone strength parameters including rod-plate configuration and finite element analysis (FEA) with in vivo High-Resolution Peripheral Quantitative Computed Tomography (HR-pQCT) and to investigate their relationship with osteopenia in AIS Vs normal controls.101AIS and 105 controls between 11-14 years old were recruited. Areal bone mineral density (aBMD) of bilateral femoral necks was measured with Dual Energy X-ray Absorptiometry (DXA). Subjects were classified into the osteopenic (Z-score-1) group. Bone Morphometry, volumetric bone mineral density (vBMD) and Trabecular Bone Mcro-architecture were measured using HR-pQCT Structural Model Index (SMI) quantifying the trabecular rod/plate configuration (a higher index indicating more rod-like configuration) and FEA in terms of Stiffness, Failure Load and Apparent Modulus were calculated with a standard algorithm.In the AIS group, osteopenic subjects showed higher SMI, lower Stiffness, lower Failure Load and lower Apparent Modulus when compared with non-osteopenic subjects . Similar differences in FEA profiles were noted between osteopenic and non-osteopenic subjects in the control group. In contrast, no significant difference in SMI was found between osteopenic and non-osteopenic controls. When all osteopenic subjects were considered, osteopenic AIS subjects had higher SMI when compared with osteopenic controls .This study showed that osteopenia was associated with lower bone strength and a specific pattern of SMI indicating preponderance of rod-like configuration in AIS subjects. Notably the association of higher SMI with osteopenia was seen in AIS but not in normal controls, thus providing strong evidences that osteopenia in AIS was different from osteopenia in non-AIS controls. Further investigations exploring the underlying biochemical and biomechanical mechanisms that bring about these specific endophenotypes are warranted for gaining further understanding of the etiopathogenesis of AIS.This study was supported by Research Grants Council of the Hong Kong S.A.R., China (Project no: 468809 and 468411)"} +{"text": "In vivo fluorescence microscopy and electron cryo-tomography have revealed that chemoreceptors self-assemble into extended honeycomb lattices of chemoreceptor trimers with a well-defined relative orientation of trimers. The signaling response of the observed chemoreceptor lattices is remarkable for its extreme sensitivity, which relies crucially on cooperative interactions among chemoreceptor trimers. In common with other membrane proteins, chemoreceptor trimers are expected to deform the surrounding lipid bilayer, inducing membrane-mediated anisotropic interactions between neighboring trimers. Here we introduce a biophysical model of bilayer-chemoreceptor interactions, which allows us to quantify the role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. We find that, even in the absence of direct protein-protein interactions, membrane-mediated interactions can yield assembly of chemoreceptor lattices at very dilute trimer concentrations. The model correctly predicts the observed honeycomb architecture of chemoreceptor lattices as well as the observed relative orientation of chemoreceptor trimers, suggests a series of \u201cgateway\u201d states for chemoreceptor lattice assembly, and provides a simple mechanism for the localization of large chemoreceptor lattices to the cell poles. Our model of bilayer-chemoreceptor interactions also helps to explain the observed dependence of chemotactic signaling on lipid bilayer properties. Finally, we consider the possibility that membrane-mediated interactions might contribute to cooperativity among neighboring chemoreceptor trimers. The chemotaxis system allows bacteria to respond to minute changes in chemical concentration, and serves as a paradigm for biological signal processing and the self-assembly of large protein lattices in living cells. The sensitivity of the chemotaxis system relies crucially on cooperative interactions among chemoreceptor trimers, which are organized into intricate honeycomb lattices. Chemoreceptors are membrane proteins and, hence, are expected to deform the surrounding lipid bilayer, leading to membrane-mediated interactions between chemoreceptor trimers. Using a biophysical model of bilayer-chemoreceptor interactions we show that the membrane-mediated interactions induced by chemoreceptor trimers provide a mechanism for the observed self-assembly of chemoreceptor lattices. We find that the directionality of membrane-mediated interactions between trimers complements protein-protein interactions in the stabilization of the observed honeycomb architecture of chemoreceptor lattices. Our results suggest that the symmetry of membrane protein complexes such as chemoreceptor trimers is reflected in the anisotropy of membrane-mediated interactions, yielding a general mechanism for the self-assembly of ordered protein lattices in cell membranes. The chemotaxis signal transduction pathway in vivo electron cryo-tomography have revealed From a structural perspective, chemoreceptors are homodimers, which interact strongly to form trimers-of-dimers What are the molecular mechanisms yielding attraction between chemoreceptor trimers and, hence, self-assembly of chemoreceptor lattices? Chemoreceptors are transmembrane proteins localized in the cytoplasmic membrane of bacteria. In general, membrane proteins deform the surrounding lipid bilayer In our analysis of membrane-mediated interactions between chemoreceptor trimers we follow the standard membrane-mechanical framework In general, neighboring membrane proteins are expected to induce overlapping deformation fields of the bilayer membrane, yielding gies see .Our biophysical model of membrane-mediated interactions between chemoreceptor trimers is based on the standard framework of membrane mechanics E. coli cytoplasmic membrane is Results section). For a given value of The thickness deformation energy in Eq. (2) scales approximately with the square In the absence of detailed structural information on the transmembrane region of chemoreceptor trimers, we adopt a highly simplified model designed to capture two key features of chemoreceptor trimers: (1) As described above, we assume that chemoreceptors have a hydrophobic mismatch with the lipid bilayer, which induces membrane-mediated interactions between neighboring chemoreceptor trimers . (2) In Our simple model for the shape of chemoreceptor trimers is consiin vivo signaling response of chemoreceptors implies Multiple lines of evidence E. coli, we find three regimes of membrane-mediated interactions between chemoreceptor trimers (We followed the approach developed in Refs. trimers : (1) ForE. coli cytoplasmic membrane Click here for additional data file.S2 FigureThickness deformation fields of chemoreceptor trimers. Thickness deformations (TIF)Click here for additional data file.S3 FigureThickness deformation profile around a cylindrical membrane inclusion. The thickness deformation field (TIF)Click here for additional data file.S4 FigureSchematic of chemoreceptor lattice symmetries. (A) Hexagonal lattice. (B) Face-on honeycomb lattice. (C) Tip-on honeycomb lattice.(TIF)Click here for additional data file.S5 FigureMembrane-mediated interactions in chemoreceptor lattices. Calculated elastic interaction energy per trimer, E. coli cytoplasmic membrane ). For the main panels in (B\u2013D) we set (TIF)Click here for additional data file.S6 FigureEffect of higher-order interactions on lattice energies. Lattice energies for face-on honeycomb, tip-on honeycomb, and hexagonal lattices of chemoreceptor trimers allowing for up to nearest-neighbor Click here for additional data file.S7 FigureMembrane contribution to the transition energy of a single chemoreceptor trimer. For the main panel we set E. coli cytoplasmic membrane.(TIF)Click here for additional data file.S1 VideoVideo of gateway to assembly of face-on trimer configuration. Gateway states in (AVI)Click here for additional data file.S1 TextSI sections 1\u20133.(PDF)Click here for additional data file."} +{"text": "Molecular epidemiological surveys of CA-MRSA revealed a wide diversity of genetic backgrounds with only sporadic identification of USA300 isolates during the period 1994-2012.We conducted a comparative genomics approach to trace origin, spreading and diversity of CA-MRSA USA300 clones accounting for 50% of CA-MRSA isolates identified in 2013.mec structure, and mobile elements were documented and enriched with patient information. Published genomes of USA300 were used for comparison purposes and for investigating the relationship between isolates.Solexa-Illumina was used for whole genome sequencing (WGS) of all USA300 isolated in 2013. Comparative genomics identified genomic alterations in this \u201cclonal\u201d population. All features including single-nucleotide polymorphisms (SNPs), ACME gene cluster, SCC mec IVc element.From 1994 to 2005, only 4 USA300 strains were identified in our institution. In 2013, among the 46 cases of CA-MRSA, USA300 were found in 22 patients . WGS allowed identifying two groups: (i) ACME positive (n=12) and (ii) ACME negative (n=10). In contrast to ACME-neg, the ACME-pos strains were resistant to ciprofloxacin and erythromycin. Comparison with a reference genome revealed that the ACME-pos group was more homogeneous that ACME-neg showing reduced genome plasticity. Two clusters of 2 strains were identified describing familial transmission events. The vast majority of ACME neg strains were isolated from patients traveling to South America in the 12 last months. SNP position allowed tracing the geographical origin of strains and to observe that ACME-neg group is composed by strains harboring a SCC In 2013, we observe a sudden and worrisome increase in CA-MRSA USA300 isolates in Geneva. WGS showed that acquisition of mobile elements and smaller genomic alterations are signatures of strain origin, probably related to antibiotic utilization. Our epidemiology is rapidly changing. Considering that most of USA300 result from importation events, its emergence coincides probably with loss of fitness of ancient clones.None declared."} +{"text": "Border-ownership selectivity (BOS) codes for the direction of a foreground object relative to the background . Attenti"} +{"text": "April 20th-22nd 2016. The Partners Meeting entitledThe \"Umbrella Consortium for Assessment Network (UCAN)\" is celebrating its tenth anniversary onCompetence. Cooperation. Communications.10 Years in Medical Assessment Networksas well as an anniversary celebration will be held at the Schlosshotel Molkenkur, and a pre-conference is scheduled in the Medical Clinic Heidelberg. 30th November 2015:We are looking forward to your contribution and invite you to submit your abstracts on the following topics until Competence-based assessmentQuality assurance of medical examsThe implementation of the NKLM in assessment networksInnovative assessment formatsProgrammatic Assessment (Gesamtpr\u00fcfungsprogramm)Competence-based Progress TestReview of foreign professional qualificationsTechnical trends in assessment, implementation and evaluationAssessing communicative, professional and inter-professional competenciesDiscipline-specific cooperations in the field of assessmentwww.ucan-assess.org/cms/de/p10.For more information please see our conference website The author declares that she has no competing interests."} +{"text": "Tyrosine kinase inhibitors (TKIs) have improved overall survival of patients with chronic myeloid leukemia (CML). Moreover, it has been reported that some of the patients achieve treatment-free remission (TFR) after cessation of TKIs, even though leukemic stem cells (LSC) of CML are considered to be resistant to TKIs. Therefore, these findings suggest that remaining LSCs could be eradicated by immune system after withdrawal of TKIs. In order to clarify the role of anti-LSC immunity in achieving TFR, we tried to detect cytotoxic T cells against one of the LSC antigens, KU-MEL9 in CML patients.in vitro, then stained with anti-KU-MEL9-specific dextramer and analyzed by flow cytometry. Immunophenotype of lymphocytes was also determined by flow cytometry.Fresh blood samples were obtained from 16 CML patients who stopped imatinib after maintained complete molecular response (CMR) for more than two years at 0,3, and 6 months after cessation of imatinib. Mononuclear cells were stimulated with LSC antigen, KU-MEL9-derived nanomer peptide twice + CD25+ cells was higher in patients who experienced loss of CMR.We detected KU-MEL9-specific CTLs in 3 of 16 patients (Table We found LSC antigen-specific T cells only in patients who achieved TFR. Although the patient size is small, these data suggest that anti-LSC CTLs may play a role in eradicating remaining LSCs after imatinib treatment and LSC antigen-specific immunotherapy could be useful to increase TFR rate.Written informed consent was obtained from the patients for publication of this abstract and any accompanying images. A copy of the written consent is available for review by the Editor of this journal."} +{"text": "Cytotoxic mechanisms are involved in most forms of drug-induced skin diseases, but till now only a small number of studies has been addressed the question whether in vitro detection of cytotoxic drug-specific response could be helpful in drug hypersensitivity diagnosis. The aim of this study was to assess and compare different cytotoxic tests as an alternative nonradioactive approach which may be more appropriate for routine testing and may provide in addition more information about the pathophysiology of the reaction than proliferation-based assays, like the lymphocyte transformation test (LTT).Number of granzyme B secreting cells by ELISpot (GrB-ELISpot), perforin concentrations in the supernatants (Per-ELISA) and intracellular expression of granulysin in NKp46+ cells by means of flow cytometry (Grl-NK) were evaluated in drug-stimulated cultures of peripheral blood mononuclear cells from 34 patients in remission state, suspected of antiepileptic drug-induced maculopapular exanthema and 24 drug-exposed healthy controls. Lymphocyte transformation tests with corresponding drugs were performed in all investigated individuals.In 18/36 patients tested drugs elicited granzyme B release in ELISpot. Staining for granulysin was positive in 15/36 patients, whereas increased secretion of perforin was detected in 3/36 patients. 11/36 patients showed positive proliferative response to the drug, measured in lymphocyte transformation test. None of the 24 drug-exposed healthy donors reacted to the tested drugs in perforin assay and LTT, however one reacted in GrB-ELISpot and another one in granulysin assay. Obtained data correspond to the following sensitivities and specificities, respectively: GrB-ELISpot: 53% and 96%; Grl-NK: 44% and 96%; Per-ELISA: 9% and 100%; LTT: 32% and 100%.In vitro cytotoxic assays of drug-specific GrB-ELISpot and granulysin production in NK cells, but not Per-ELISA offer potential for use as effective diagnostic tests and advantages over the LTT, including a shorter assay time and a greater sensitivity. As a significant percentage of included patients suspected of drug-induced skin reaction did not show any positive response in any test, we can assume that causal relationship between drug exposure and common exanthemas is often overestimated."} +{"text": "We aim to establish a non-invasive, clinically translatable imaging approach for in vivo monitoring of adoptively transferred T cells engineered with selected TCRs. We have previously isolated several TCRs specifically recognising peptides derived from diverse tumor associated antigens and selected one TCR recognising lymphoma cells with defined HLA-DR restriction.Transfer of T lymphocytes genetically modified with T-cell receptors (TCR) specific for tumour-associated antigens is a novel therapeutic approach for diverse malignant diseases. However, efficacy as well as safety of this therapy still needs to be improved. In order to understand T cell trafficking and functionality in vivo, the development of non-invasive and sensitive cell-tracking technologies would be of high value. Moreover, clinical translation of such technologies would further provide possibilities to improve this therapeutic approach in humans124I-TCRmu or 89Zr-TCRmu. Specific in vivo binding was evaluated by co-injection of an excess of unlabelled antibody or isotype control antibody. In vivo uptake was confirmed by autoradiography and immunostaining for human CD3 on tumour frozen sections.Peripheral blood mononuclear cells from healthy donors were retrovirally transduced with the selected TCR. To track transduced T cells, we used an anti-murine TCR\u03b2 monoclonal antibody (TCRmu), which binds to the murinzed region of the introduced TCR. This antibody was either radioiodinated with Iodine-124 or conjugated with a bifunctional chelator and labelled with Zirconium-89. Labelled antibodies were tested for stability and specific binding in vitro. A xenogenic mouse model was established using Nod/SCID mice injected intraperitoneally with lymphoma cells. After tumour inoculation, we transferred TCR-transduced human T cells and PET imaging was performed at different time points post injection of 89Zr-anti-TCRmu. These results correspond to autoradiographic signals and detection of human T cells on the tumour border. Injection of an excess of unlabelled TCRmu showed depletion of human T cells in vivo, enabling a possible approach to control potentially autoreactive T cells in vivo.We established labelling of TCR transduced T cells using a specific antibody (TCRmu) marked with Iodine-124 or Zirconium-89. After the radio-labelling, affinity and specificity of the antibody was maintained while viability and functionality of T-cells remained unaffected. In vivo imaging of TCR-transduced T cells in the xenograft tumor model revealed strong uptake on the tumour area. Improved signal detection and reduced background was observed using In summary, we developed a non-invasive imaging model for tracking specifically human TCR-engineered lymphocytes in vivo. This model will be useful to monitor adoptive transfer of TCR transgenic T cells in vivo and therefore giving important information for further optimisations regarding efficacy and safety of immunotherapeutic approaches."} +{"text": "In the Preventive Angioplasty in Myocardial Infarction trial , immediate multivessel PCI (MV-PCI) of non-IRA (infarct related artery) lesions in patients with acute ST elevation myocardial infarction (STEMI) and multivessel coronary disease (MVD) improved long term prognosis. We assessed infarct distribution and size in a pre-specified cardiac magnetic resonance (CMR) sub-study.2) using a signal intensity threshold of >5SDs above a remote region, and expressed as a % of total LV mass. The incidence of new LGE in non-infarct related artery territories at baseline and 1 year were assessed. Data were analysed by an independent statistician.In this single centre prospective sub-study, PRAMI participants were invited to undergo 1.5 Tesla CMR 1 week and 1 year after primary PCI. The CMR scans were analysed using semi-automated software by a clinician blinded to treatment group assignment and clinical outcomes. The presence and extent of infarction were assessed quantitatively with late gadolinium enhancement (LGE) imaging . The infarct was delineated as an area of myocardial enhancement were enrolled in Glasgow. Of these 80 patients underwent CMR 1 week post primary PCI of whom 41 (51%) were in the multi-vessel PCI group and 39 (49%) were in the IRA-only group. At 1 year, 69 (86%) patients had a follow up CMR scan. Infarct size and distribution are described in Table Infarct size and distribution were similar in patients treated by MV-PCI or IRA-only PCI. MV-PCI is not associated with additional MI acutely which supports the safety of this procedure in line with the benefits observed with preventive PCI in PRAMI.Golden Jubilee National Hospital; PRAMI was funded by Barts and the London Charity."} +{"text": "Accurate measurement of maximal aortic root dimensions is important for informed decision making on the timing/nature of aortic valve replacement surgeries in pediatric patients. Currently, the observer manually measures the following metrics to quantify maximum aortic root dimensions: 1) Cusp to Commisure (Cu-Co), and 2) Cusp to Cusp (Cu-Cu) lengths. This introduces significant inter-observer variability (IOV), especially if a followup study is performed in a different institution than the previous study. Hypothesis: A simple post-processing tool that allows the observer to perform semi-automated measurements using reproducible landmarks will enable accurate quantification of maximal aortic root dimensions as well as decrease IOV, thereby leading to reproducibility of measurements.An image analysis tool was developed using MatlabTM that can automatically measure the Cu-Cu and Cu-Co lengths from easily reproducible landmarks traced by an observer namely: 1) location of the commissures, and 2) the external margin of the sinuses and aortic circumference (Figure The manual measurements under-estimated aortic root dimensions Figure . The r vManual measurements under-estimate aortic root dimensions and present a statistically significant higher IOV when compared to semi-automated measurements. Using an automated tool will reduce the visual subjectivity induced by different observers. We demonstrate that a simple semi-automated tool consistently captures the maximum dimension of the aortic root when compared to the conventional method, and significantly improves IOV. While its benefit might not be substantial in a single center studies, this will be useful in detecting subtle interval change on serial studies conducted at varying imaging centers.None."} +{"text": "Buprenorphine (Subutex) and buprenorphine/naloxone (Suboxone) received Food and Drug Administration approval in 2002 for the treatment of opioid dependence. Introduction of these drugs expanded the availability of opioid-dependence treatment options to reduce the morbidity and mortality associated with opioid abuse, and buprenorphine has become an increasingly prescribed component of office-based treatment. However, unsupervised ingestion of buprenorphine-containing products by children is a growing concern .During 2010\u20132011, the National Electronic Injury Surveillance System \u2014 Cooperative Adverse Drug Event Surveillance project of ED visits and 59.5% (CI = 38.9%\u201380.2%) of emergent hospitalizations for opioid product ingestions.Ingestions of buprenorphine-containing products by children are serious and have increased rapidly nationally. Fatalities have been reported in children after unsupervised ingestions of single doses . Innovat"} +{"text": "Sjogrens syndrome (SS) is a chronic autoimmune disorder, characterised by lymphocytic infiltration resulting in exocrine gland destruction and other extra-glandular manifestations . CurrentA microRNA screen had been conducted in peripheral blood mononuclear cells (PBMCs) from healthy controls and SS patients. From this screen a set of microRNAs were analysed by bioinformatics using online platforms including miRWalk, MiRDB and miRanda Tools. Primers were designed and optimised by PCR for the miRs and their predicted gene targets. As part of ongoing work in the lab PBMCs were isolated and transfected with a sequence that mimics miR-155 (a pro-inflammatory miR). The effect miR-155 on target genes was analysed qPCR.Bio-informatic studies identified several novel miRs whose expression is altered in SS patients compared to healthy controls. Two miRs that were focused on were down-regulated in the patient sample and are hsa-miR-132-3p and hsa-miR-4535 and their target genes are ESRRG (Estrogen related receptor gamma) and ATRN (Attractin) respectively; and one up-regulated miR which is Hsa-miR-185-3p and its target gene is IRF5 (Interferon regulatory factor 5). Primers for these novel miRs and gene targets were optimised.Since these specific miRs have altered expression in SS patients, and have a direct effect on inflammatory genes, this indicates that these miRs may have biomarker potential and further study of these miRs might increase our understanding of the underlying pathology of Sjogrens syndrome and other autoimmune diseases."} +{"text": "Preterm delivery is a leading cause of perinatal morbidity. Reasons are diverse, but immunologic fetal rejection has repeatedly been postulated to be involved. Myeloid derived suppressor cells (MDSC) are myeloid progenitor cells, characterized by their T cell suppressive capacity. They have predominantly been described under pathological conditions like cancer or infectious diseases, yet their role for materno-fetal tolerance remains elusive. We aimed to quantify and characterize MDSC in cord blood (CB) and in pregnancy.+/CD33+/CD14-/HLA-DR+ cells) and monocytic MDSC were quantified, expression of enzymes arginase I (ArgI) and inducible NO-Synthetase (iNOS) was analysed by flow cytometry and production of reactive oxygen species (ROS) tested. Suppressive capacity of GR-MDSC on T cells was analysed in CFSE proliferation assay.Cord blood mononuclear cells (CBMC) and peripheral blood mononuclear cells (PBMC) were prepared from CB of healthy newborns and blood of healthy pregnant women. Proportions of granulocytic MDSC (GR-MDSC, CD66bPercentages of GR-MDSC were up to tenfold higher in CBMC and in PBMC from pregnant women in all three trimesters compared to non-pregnant controls, whereas proportions of MO-MDSC did not change. GR-MDSC from CB and pregnant women expressed the enzymes ArgI and iNOS and produced high amounts of ROS. Addition of CB-GR-MDSC or GR-MDSC from pregnant individuals to PBMC from non-pregnant controls reduced the CD4 and CD8 T cell proliferation rate significantly compared to T cell proliferation alone.We describe for the first time an expansion of GR-MDSC in CB and during normal human pregnancy. Increased MDSC activity could play a role for induction and maintenance of materno-fetal immune tolerance and serve as a target for the therapy of immunologic pregnancy complications thereby preventing premature delivery."} +{"text": "Routine blood volume quantification is generally performed by using two-dimensional velocity-encoded phase-contrast magnetic resonance imaging (PC-MRI). Due to their long acquisition times averaging of flow information occur leading to underestimation of peak velocities and preventing the examination of respiration-related stroke volume (SV) variations.Non-electrocardiographic triggered real-time PC-MRI using EPI combined with half-Fourier technique was applied to study respiration-driven SV fluctuations in the ascending aorta (AAo) and both caval veins under natural and forced breathing in 34 healthy children and 10 pediatric Fontan patients. Data were collected during a 12-14 s time interval. The subject's physiological data (ECG & respiration) were recorded simultaneously for matching with flow data. Virtual stroke volumes were generated dividing the respiration curve in four segments: expiration, breathing in, inspiration and breathing out. Spirometric measurements were performed to validate respiratory volumes. Statistical differences were analyzed by using ANOVA, paired Student t-test and Bland-Altman statistics.Stroke volume variability in healthy subjects was around 6% for AAo and >15% for SVC and IVC while breathing naturally. Under forced breathing variability increased to 9% and >34%, respectively. In Fontan patients a two to three-fold augmentation was observed in both respiratory maneuvers. Whereas in volunteers aortic SV was elevated during expiration (6%) and decreased during inspiration (-6%) in relation to mean respiratory SV, highest blood flow was detected during breathing in SVC (10%) and IVC (20%) and lowest blood flow during breathing out . Differences were increased under forced breathing. All differences were statistically significant. Regarding patients SV variability was drastically increased and had to be related to the patient's individual quality of Fontan circulation. Intraobserver and interobserver varability of the four separated respiration-dependent SV was below 5%.Due to its non-averaging character real-time PC-MRI allows a physiological assessment of respiratory-related SV fluctuations in healthy subjects as well as in Fontan patients and demonstrates its capability for detection of short-term effects in clinical routine work. It can be expected that real-time PC-MRI has the potential to classify the quality of Fontan hemodynamics.None."} +{"text": "Pre-surgical planning for Fontan procedures involves time-consuming patient-specific vascular segmentation and non-intuitive virtual surgical modeling which has encumbered utility in the clinic by surgeons. We present an interactive platform to design virtual surgical options and visualize pericardial enlargement strategy for Fontan connections, starting with patient-specific vascular templates.We demonstrate the utility of our novel virtual surgical construction tool in a patient-specific case of retrospectively identifying an optimal extra-cardiac (EC) Fontan connection strategy starting with post-operative cine cardiac MRI scans of a pediatric patient with a Lateral Tunnel (LT) Fontan connection. First, a 3D vascular model of the LT Fontan , left & right pulmonary arteries ) was segmented at end-diastole (in ITK-SNAP). A virtual pre-Fontan Glenn vascular model was derived from this LT model by virtually clipping the LT connection away using Paraview (Kitware Inc.) and fitting a smooth surface to the remaining geometry using a Poisson Surface Reconstruction (PSR) algorithm. A series of experimental EC Fontan options were interactively prepared by employing PSR to stitch together the pre-operative Glenn model with an EC conduit template in a range of feasible positions (see Figure The ideal tested EC connection anastomosis was offset toward the RPA (see Figure We demonstrate the feasibility of a novel virtual surgery tool to retrospectively create and hemodynamically evaluate a range of feasible patient-specific EC Fontan connections starting with a virtual Glenn anatomosis model. This presented methodology may be applied to prospective surgical planning starting with pre-Fontan CMR imaging of the Glenn anatomosis.N/A."} +{"text": "MEN syndrome is one of the most important familial causes of neuroendocrine tumours. Radiological screening and follow-up for syndrome-related tumours play an important role in the life-long surveillance. Liver metastases (LM) from neuroendocrine tumours are common (75%) and significantly reduce the prognosis. Characterisation of liver lesions in these patients is a challenge for radiologists as LM are difficult to differentiate from benign liver lesions such as of haemangioma. In this study we aimed to give an overview of the radiological presentation of LM in MEN patients by different imaging modalities.We retrospectively evaluated 30 genetically-proven cases of MEN syndrome (type 1+ 2), who had a hepatic lesion. The findings of contrast-enhanced computer tomography (CE-CT) as well as ultrasound (US) were considered for the main diagnosis. The findings of other imaging techniques such as contrast-enhanced ultrasound (CEUS), magnetic resonance imaging (MRI) as well as PET-CT were evaluated and compared individually.The most common liver lesions were haemangioma (40%) followed by LM (30%). The radiological findings in LM varied from hypodense lesions with low marginal contrast-enhancement to disseminated calcified lesions. The most common CT finding in early stage LM was hyperarterialised lesion with marginal contrast-enhancement in the portal venous phase as well as hyperechogenic appearance in US which mainly mimic the classic haemangioma.Better understanding of the radiological appearance of LM in patients with MEN syndrome will help in early tumour-detection and adjusted treatment. For this purpose multimodal imaging, primarily CE-CT in addition to CEUS or CE-MRI are essential for screening as well as follow-up controls."} +{"text": "Veno-arterial extracorporeal membrane oxygenation (VA ECMO) has been introduced in the management of critical conditions caused by severe cardiac failure. However, literary evidence for the use of VA ECMO in non-surgical patients remains insufficient.To analyze a group of non-surgical patients with cardiogenic shock and refractory cardiac arrest treated with VA ECMO in cardiovascular center.Between January 2006 and March 2015 one hundred and thirty-eight patients were treated in our institution with mini-invasive active circulatory support or VA ECMO for circulatory failure. We analyzed data from a subgroup of 87 primarily non-surgical patients (mean age 61 (31-84) years, 80% were males), treated by VA ECMO.The major indication for circulatory support therapy was cardiogenic shock, followed by refractory cardiac arrest, arrhythmic storm, and support of high-risk interventions. Median duration of circulatory support was 3 days, maximum 62 days. The all-cause 30-day mortality in our group was 34.5%; in the subgroup of patients with severe refractory cardiogenic shock the 30-day mortality was 49.4%. In patients with refractory cardiac arrest, where ECMO was introduced during continuous chest compressions, 4 individuals from 18 treated survived with good neurological outcome. We found significant survival differences between subgroup with urgent circulatory support introduction and patients with semi-urgent support . We observed significantly higher lactate levels prior to ECMO insertion in survivors in comparison with non-survivors (P < 0.05); other baseline characteristics including age or left-ventricle ejection fraction were comparable. We evaluated also the role of cerebral/peripheral near-infrared spectroscopy (NIRS) oximetry in the non-invasive monitoring of global circulatory status in patients with mini-invasive circulatory support.VA ECMO is a promising tool in the management of severely compromised patients with rapidly progressing cardiogenic shock or refractory cardiac arrest. Frequently the circulatory support therapy in these high-risk patients represents the last chance to survive.This study was supported by the grant from the Czech Ministry of Health, Nr. 12153 and by the Institutional grant MH CZ - DRO"} +{"text": "Platinum compounds are the mainstay of chemotherapy for lung cancer. Unfortunately treatment failure remains a critical issue since about 60\u00a0% of all non-small cell lung cancer (NSCLC) patients display intrinsic platinum resistance.in silico by Ingenuity Pathway Analysis (IPA). Further validation was done using siRNA.We analyzed global gene expression profiles of NSCLC clones surviving a pulse treatment with cisplatin and mapped deregulated signaling networks DKK1), DNA repair machinery (XRCC2) and cell-cell/cell-matrix interaction were among the top deregulated genes by microarray in these replicates and were validated by q-RT-PCR. We focused on DKK1 which previously was reported to be overexpressed in NSCLC patients. IPA network analysis revealed coordinate up-regulation of several DKK1 transcriptional regulators in cisplatin-surviving clones from that biological replicate. Knockdown of DKK1 by siRNA sensitized for cisplatin in two different NSCLC cell lines and in ovarian A2780 cells, but not in the A2780 cis subline made resistant to cisplatin by chronic exposure, suggesting a role of DKK1 in intrinsic but not acquired platinum refractoriness.The pooled cisplatin-surviving NSCLC clones from each of the biological replicates demonstrated heterogeneous gene expression patterns both in terms of the number and the identity of the altered genes. Genes involved in Wnt signaling pathway contains supplementary material, which is available to authorized users. Lung cancer (LC) is the tumor type with the highest number of cancer-associated deaths worldwide . LC is hCisplatin resistance is still a major obstacle for the clinical management of NSCLC. At the molecular level, a cisplatin-refractory phenotype can be a result of: (I) failure to reach the DNA (pre-target resistance), (II) impeded induction of DNA lesions (on-target resistance), (III) malfunctioning of cell death pathways (post-target resistance), and (IV) activation of pro-survival signaling pathways that are not directly influenced by cisplatin, but abolish its death-inducing capacity (off-target resistance), reviewed in .ERCC1) and ribonucleotide reductase M1 (RRM1), respectively. NSCLC cases whose specimen lacked ERCC1 expression had a more prominent response to adjuvant cisplatin treatment and hence ERCC1 expression holds promise as a predictive biomarker. .The data set supporting the results of this article is available in NCBI's Gene Expression Omnibus reposito"} +{"text": "Gastrointestinal (GI) motility originates from the complex coordination of smooth muscle contraction and relaxation. GI diseases affecting motility are often associated with impaired nitrergic signaling. In the enteric nervous systems, NO is released from nitrergic neurons as a major inhibitory neurotransmitter. NO acts via NO-sensitive guanylyl cyclase (NO-GC) in different GI cell types such as smooth muscle cells (SMC) and interstitial cells of Cajal (ICC). The precise mechanism of nitrergic signaling through these two cell types to regulate colonic spontaneous contractions is not fully understood yet.Longitudinal smooth muscle of the proximal colon from WT mice exhibits spontaneous contractile activity in vitro. Colon from global and ICC-specific GCKO animals also exhibited spontaneous rhythmic contractions. Yet, in both genotypes, duration and amplitude of the rhythmic contractions were increased compared to WT. In line with that, colon from WT revealed an arrhythmic contractile pattern which was transformed into a uniform motor pattern after addition of L-NAME or ODQ. Electrical field stimulation induced off-contractions in WT and high amplitude on-contractions in global GCKO colon.Our results prove that basal NO release participates in the regulation of spontaneous contractions in the murine proximal colon. NO-GC activity in ICC converts the contraction pattern from periodic into irregular. Thus, NO-GC in ICC is the major effector for NO in the proximal colon."} +{"text": "To understand the role of FDG PET/CT imaging in the multimodality investigation of gynecological and genitourinary cancers.2. To describe the mechanism of action and technical pitfalls of FDG-PET/CT.3. To highlight key imaging features of physiological and non-physiological FDG uptake and show how this is essential for interpretation of gynecological and genitourinary FDG-PET/CT studies.4. to review the pathophysiological mechanisms leading to potentially false-positive and false-negative assessments.Introduction of FDG-PET/CT\u2218 Mechanism of action\u2218 Role in gynecological and genitourinary oncological imaging\u2218 FDG-PET/CT imaging protocolsFalse positives in gynecological and genitourinary oncological imaging:\u2218 Physiological FDG-PET uptake \u2013 pictorial examples of uptake in endometrium and ovaries\u2218 Non-physiological FDG-PET uptake \u2013 pictorial examples of pelvic inflammatory disease, fibroids, endometriosisFalse negatives in gynecological and genitourinary oncological imaging:\u2218 Physiological FDG-PET uptake \u2013 pictorial examples of urinary excretion masking malignant lesions\u2218 No/low FDG uptake \u2013 pictorial examples of necrotic lymphadenopathy and low grade tumours\u2218 ArtefactsPearls explaining how to minimise false interpretationFDG-PET/CT has a useful role in gynecological and genitourinary oncological imaging. However, understanding of physiological and non-physiological FDG- PET uptake is vital to understand potential false positive and false negatives in interpretation.FDG PET/CT should be used as one part of the multimodality investigation of gynecological and genitourinary cancers."} +{"text": "Linaclotide binding to the extracellular receptor domain of GC-C activates the intracellular catalytic domain of GC-C, resulting in the generation of cyclic GMP (cGMP). cGMP, via a pathway leading to activation of the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel, stimulates Cl- and HCO3-secretion and concomitant inhibition of Na+ absorption by sodium/hydrogen exchanger 3 (NHE3), driving the efflux of water into the lumen and accelerating bowel transit. However, the effect of linaclotide on electrolyte transport in the lower gastrointestinal tract has not yet been characterized. This study specifically examined the effect of linaclotide on electrolyte transport in the colon. We used an Colonic mucosa was isolated using either sharp (human) or blunt (rat) dissection and ion transport was monitored by measuring short-circuit current (Isc).Stimulation with linaclotide elicited a concentration-dependent short-circuit current across rat colonic epithelium. The Isc response reached its maximum at 100 nM of linaclotide with an EC50 of 9.8 nM in rat colonic mucosa. Linaclotide at concentrations of 30 nM and 1000 nM added to human colonic mucosa also induced a trans-epithelial current. As the CFTR ion channel and Na-K-Cl co-transporter NKCC1 are well-characterized transporters regulating the flux of Cl-anions across the intestinal epithelium, we further studied the effects of NKCC1 and CFTR antagonists on GC-C\u2013mediated short-circuit current. Addition of NKCC1 inhibitor bumetanide (100 \u03bcM) to the basolateral bath significantly inhibited linaclotide-induced transepithelial current in human colonic mucosa. In contrast, bumetanide had no effect on linaclotide-induced transepithelial current in rat colonic mucosa, suggesting that in the rat proximal colon, flux of Cl-anions is mediated by alternate transporters. Preincubation of rat colonic mucosa with the CFTR antagonist GlyH-101 attenuated the sustained increase in Isc observed in response to treatment with 100 nM linaclotide. The effect of GlyH-101 on Isc inhibition was more profound after the colonic epithelium was stimulated with a sub-EC50 (6 nM) concentration of linaclotide.We have demonstrated that linaclotide treatment induces a transepithelial ion current in the human ascending colon and rat proximal colon. This ion current is in part driven by Cl-anion secretion into the intestinal lumen."} +{"text": "Atg7) in dopamine receptor D2 (DRD2) neurons were used to test our hypothesis using a mouse model with striatal FC infusion. The result showed that the levels of autophagic cell death and injury severity were higher in male than in female mice. Pre-treatment of FC-infused females with rapamycin increased the FC-induced behavioral deficit and DRD2 neuron death. However, DRD2 neuron-specific knockout of Atg7 decreased FC-induced injury severity and the number of TUNEL(+) DRD2 neurons in males. These results suggest that autophagy in FC-infusion males is overactive with maladaptive consequences and inhibition of autophagy decreases the severity of FC-induced striatal injury in males. These findings present prospects for male-specific therapeutic strategy that targets autophagy in patients suffering from iron overload.Men exhibit a worse survival rate than premenopausal women after intracerebral hemorrhage (ICH), however, no sex-specific management has been concerned. In a rat model involving infusion of ferrous citrate (FC) that simulates iron accumulation after hemorrhage, a higher degree of autophagy associated with higher injury severity was observed in striatum of males than in females. Since the imbalance between the levels of autophagy and energy demand may lead to cell death, we proposed that FC-induced autophagy is detrimental in a male specific manner and autophagy modulation affects injury severity in a sex-dependent manner. Rapamycin, an autophagy inducer, and conditional knockout gene of autophagy-related protein 7 ( Primary intracerebral hemorrhage (ICH) results in the highest mortality of all stroke subtypes and less than 40% of ICH survivors regain their independence . The incAtg7 to address the issue whether autophagy inhibition is beneficial for patients suffering from neurodegeneration caused by iron overload in a male-specific manner.Following ICH, accumulation of ferrous iron causes oxidative damage and contributes to the long-term neurological deficits , 11 and 2) after castration were used to study the contribution of E2 to the sex difference in FC-induced autophagy and injury in striatum. For the female mice, ovariectomy involved a small incision in both flanks after which the ovaries were removed. In the male mice, the skin and body wall caudal to the penis were incised with a scissor, and the testicles were retracted through the incision. The exposed testicular artery and vein were double-ligated and cut., RO, RO27], PI3K/Akt , rapamycAtg7 in DRD2 neurons decreased the percentage of TUNEL(+) DRD2 neurons and diminished FC-induced injury severity in males, while slightly increased the FC-induced injury severity in females. These results strongly suggested that, in males, the inhibition of FC-induced autophagy could switch a maladaptive or harmful autophagy to a response in favor of neuroprotection. Whereas, in females, the moderate level of FC-induced autophagy might be sufficient for supplying energy demand, thus inhibition of autophagy deprived the protective machinery under oxidative stress. Accordingly, male-specific inhibition of autophagy might be a useful therapeutic strategy for patients with iron overload.On the other hand, conditional knockout of In conclusion, over-activation of the autophagic machinery plays a maladaptive and harmful role in FC-induced striatal injury in males but not in females. Inhibition of autophagy could represent a useful therapeutic target for iron-induced brain injury in men or postmenopausal women who have lost the limitation of autophagy by estrogen. Therefore, this study presents new paths for exploring sex-specific therapeutic strategies that address the maladaptive over-activation of autophagy, such as gene therapy targeting autophagy-related genes.S1 FigTwo days after FC infusion, the brain tissue containing striatum was sectioned and stained by working solution which is a mixture of equal parts of hydrochloric acid and potassium ferrocyanide prepared immediately before use. Arrows in the lower left panel indicate dark blue deposits that confirmed the iron overload after FC infusion.(TIF)Click here for additional data file.S2 Fig(A) Striatum without FC infusion; (B) Lesion site; (C) Around lesion site. Bal/c mice were stereotaxically infused with 3 \u03bcL FC into the right striatum. Two days after FC infusion, the brain tissue containing striatum was sectioned and stained by LC3 antibody for LC3-II aggregation (green dots) as an autophagic marker; NeuN for neuron marker; and DAPI for nuclei. Bright green spots (arrow) showed in the lower raw of right panel indicate LC3 aggregation, which are exhibited in both neuron and non-neuronal cells.(TIF)Click here for additional data file.S3 FigBal/c mice were stereotaxically infused with 3 \u03bcL FC into the right striatum. Two days after FC infusion, the brain tissue containing striatum was sectioned and stained by LC3 Ab (Green), in the left panel; TUNEL (Green) and GFAP Ab (Red) in the left panel; and TUNEL (Green) and NeuN Ab (Red) in the right panel. DAPI (Blue) was used to identify nucleus simultaneously. Bright green spots showed in the left panel indicate LC3 aggregation, which is a detection marker of autophagy. Arrow showed in the lower raw of right panel indicates the TUNEL positive astrocyte; arrowhead showed in the lower raw of right panel indicates the TUNEL positive neuron.(TIF)Click here for additional data file.S4 FigThe paraffin-embedded tissues were serially sectioned into 10-\u03bcm thick slices. After hematoxylin and eosin (HE) staining, the extents of the histological lesions were analyzed using Image-proPlus according to the staining intensity in the enclosed area. The ratio of ipsilateral hemispheric volume of the striatum to the contralateral hemispheric volume served as an index of histological lesion. The images at the upper panel indicate the higher magnifications the histological injury is more obvious. The scale bars represent the different magnifications under microscope.(TIF)Click here for additional data file.S5 FigThe paraffin-embedded tissues were serially sectioned into 10-\u03bcm thick slices. After hematoxylin and eosin (HE) staining, the extents of the histological lesions in every fifteenth section of the striatum were analyzed using Image-proPlus software, according to the staining intensity in striatum. The ratio of ipsilateral hemispheric volume of the striatum to the contralateral hemispheric volume served as an index of histological lesion.(TIF)Click here for additional data file."} +{"text": "Introduction. Autoimmune encephalitis (AE) is a clinically challenging diagnosis with nonspecific neurological symptoms. Prompt diagnosis is important and often relies on neuroimaging. We present a case series of AE highlighting the importance of an early [18F]-fluoro-deoxy-glucose positron emission tomography (FDG-PET) scan. Methods. Retrospective review of seven consecutive cases of autoimmune encephalitis. Results. All patients had both magnetic resonance imaging (MRI) and FDG-PET scans. Initial clinical presentations included altered mental status and/or new onset seizures. Six cases had serum voltage-gated potassium channel (VGKC) antibody and one had serum N-methyl-D-aspartate (NMDA) antibody. MRI of brain showed mesial temporal lobe hyperintensity in five cases of VGKC. The other two patients with VGKC or NMDA AE had restiform body hyperintensity on MRI brain or a normal MRI, respectively. Mesial temporal lobe hypermetabolism was noted in three cases on FDG-PET, despite initial unremarkable MRI. Malignancy workup was negative in all patients. Conclusion. A high index of suspicion for AE should be maintained in patients presenting with cognitive symptoms, seizures, and limbic changes on neuroimaging. In cases with normal initial brain MRI, FDG-PET can be positive. Additionally, extralimbic hyperintensity on MRI may also be observed. Autoimmune encephalitis (AE) is a clinically challenging diagnosis usually suspected in cases of altered mental status or seizures after excluding other more common diagnoses. Anderson 2008) Common presenting signs are nonspecific-memory impairment, hallucinations, anxiety, irritability, depression, seizures, or sleep alterations , 2. Thes008 Commo18F]-fluoro-deoxy-glucose positron emission tomography (FDG-PET).Voltage-gated potassium channel (VGKC) and N-methyl-D-aspartate (NMDA) antibodies are increasingly being recognized as associations of AE due to easy availability of serological testing. Since the presenting symptoms are nonspecific, establishing neuroimaging correlates to guide diagnostic workup may allow for timely therapeutic interventions. We present seven patients (six positive for VGKC and one positive for NMDA antibodies) with AE highlighting the importance of early neuroimaging with brain magnetic resonance imaging (MRI) and [We screened medical records of patients evaluated at a tertiary academic medical center between 2004 and 2010 billed under ICD-9 codes 276.1 and 323.9. A retrospective review of 848 case records with clinical diagnosis of AE and/or limbic encephalitis upon presentation was done. Of these, 102 patients had paraneoplastic panel results available with 7 being positive (6 positive for VGK and 1 positive for NMDA antibodies). All panels were processed by Mayo Medical Laboratories . The cases were further reviewed for historical information, diagnostic workup, medications administered, and neuroimaging findings. The Institutional Review Board approved the study protocol.\u03bcU/mL) and free T4 (1.4\u2009\u03bcU/mL) in addition to VGKC antibody. None of the patients had diabetes. Computed tomography (CT) of chest, abdomen, and pelvis was negative in all patients. CSF was significant in three patients with elevation of white cell count in two patients and mild elevation of protein in a third patient.Patient characteristics are described in The mean time of symptom onset to positive antibody serology was 102.1 days . MRI of the brain was the first modality in four cases . CT of hFDG-PET scans were available in six of the patients. All six patients had hypermetabolism of mesial temporal structures . In threThis case series of VGKC and NMDA autoimmune encephalitis illustrates the importance of neuroimaging with emphasis of early FDG-PET particularly in cases of initial nondiagnostic MRIs. It also demonstrates the extralimbic nature that may occur with VGKC antibody positive AE.It is accepted that paraneoplastic and nonparaneoplastic antibodies can present at distant sites from the limbic system, but they usually do so in addition to limbic involvement . The impWhy VGKC antibodies caused mostly limbic hyperintensity on MRI and the NMDA antibodies did not is not entirely known. It has been suggested that the restricted diffusion seen on the diffusion weighted images (DWI) is due to the presence of abundant number of inflammatory cells along with increased amounts of interstitial water which accounts for the relative normal apparent diffusion coefficient (ADC) images . The hypAnother important finding in this case series is the lag time in developing noticeable changes on MRI. Two cases showed mesial temporal lobe hypermetabolism on FDG-PET prior to changes on brain MRI. Additionally, the patient with NMDA AE showed mesial temporal lobe hypermetabolism without MRI findings. The utility of FDG-PET in the diagnosis and monitoring of autoimmune encephalitis has been shown to be significant \u201317. FDG-In conclusion, FDG-PET is a useful tool in the diagnostic workup of autoimmune encephalitis, such as in patients with VGKC or NMDA receptor antibodies. FDG-PET can be positive despite an unremarkable brain MRI. Additionally, maintaining awareness of extralimbic hyperintensity on MRI is also recommended."} +{"text": "Cluster headache (CH) is a painful and debilitating disorder for which non-invasive vagus nerve stimulation (nVNS) may be a treatment option.Compare the efficacy of gammaCore\u00ae, a handheld nVNS device, with the standard of care (SoC) in chronic CH subjects in the randomized phase of the Prevention and Acute (PREVA) Treatment of Chronic Cluster Headache study.PREVA was a multicenter study comprised of 3 phases: 2-week run-in, 4-week randomized , and 4-week extension. Subjects randomized to nVNS delivered stimulations prophylactically twice daily (mandatory) and optionally for the rescue treatment of CH attack. The primary efficacy end point was the reduction in number of CH attacks/week during the last 2 weeks of the randomized phase versus the run-in phase. Additional end points included the proportion of subjects with >50% reduction in CH attacks/week (response rate) and rescue medication use; safety was assessed by monitoring the frequency of adverse events.Ninety-seven subjects were randomized; data from 93 subjects were included in the intention-to-treat population. Number of CH attacks/week was significantly reduced in subjects treated with nVNS compared with patients treated with SoC only . Further, significantly more nVNS- than SoC-treated subjects were considered treatment responders . nVNS was associated with less use of rescue medications and demonstrated a favorable safety/tolerability profile.Prophylactic treatment of chronic CH with nVNS is safe and, compared with SoC, reduces frequency of CH attacks/week. Sham-controlled studies are warranted and underway to confirm these data.Abstract submitted on behalf of the PREVA Study Investigators."} +{"text": "Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10\u201315 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse Allele mining is an efficient strategy to unlock a wealth of largely untapped natural and functional allelic variation/diversity existing within wild and cultivated genetic resources for crop genetic enhancement, thereby improving the productivity and sustainability of global agriculture. The vast available germplasm (core and mini-core) repositories and different recently developed high-throughput array-based next-generation sequencing (NGS) and sequence-based marker genotyping strategies are found expedient in large-scale mining and genotyping of genome/gene-based SNP (single nucleotide polymorphism) alleles among these germplasm accessions for driving genomics-assisted crop improvement through genetic and association mapping. The allele mining strategies commonly adopted in laboratories equipped with advanced infrastructural facilities , require prior information of SNP alleles (nature/types and flanking sequences) for their discovery, validation and genotyping in the targeted gene/genomic regions of multiple crop accessions. Conversely, EcoTILLING , a rapid, inexpensive and well-established allele mining approach is found much proficient in large-scale mining and high-throughput genotyping of novel natural and functional allelic variants of known and candidate genes related to useful agronomic traits in diverse crop germplasm accessions polymorphism. Most of the EcoTILLING studies utilize the advanced genotyping platforms for efficient resolution of fluorescent dye (IRDye 700/800 and SYBR green)-labeled CEL-I cleaved heteroduplex PCR amplified fragments. Consequently, these efforts led to the discovery and genotyping of novel potential alleles specifically derived from the trait-associated known and candidate genes in natural population of diverse crop plants with a wealth of trait diversity and wild chickpea accessions for identifying novel functional/natural allelic variants in the candidate and known genes associated with multiple traits of agricultural importance in chickpea.Chickpea, a member of genus desi, kabuli and wild accessions that are adapted to diverse agro-climatic conditions for genomics-assisted crop improvement of chickpea.The agarose gel-based EcoTILLING strategy mostly utilizes pooling of genomic DNA isolated from two diverse accessions rather than multiple accessions for robust mining and genotyping of alleles in the view of anticipating more allelic variations between distant accessions of crop plants , which were specifically selected from the previous studies of Jhanwar et al. (desi chickpea accession (ICC 4958) as per the detail PCR protocol described by Jhanwar et al. in a diploid crop species like chickpea with narrow genetic base and low intra-/inter-specific genetic polymorphism. Henceforth, this agarose-based detection assay has potential utility not only for the analysis of EcoTILLING using the pools of natural germplasm accessions but also for TILLING involving the pools of available EMS (ethyl methanesulfonate)-induced mutant lines of desi accession of chickpea. At the most, we could expect clustering of 192 accessions into two distinct population groups at K = 2, in accordance with our preliminary genetic distance-based phylogenetic tree analysis. Using population genetic structure, the average likelihood value [Ln P(D)] against each K across 20 independent replications was estimated and plotted. The optimal value of K was determined following ad hoc and delta K procedures of Pritchard et al. among accessions was performed using GAPIT -values and adjusted P-value threshold of significance were performed in accordance with Kujur et al. . The TF gene-derived SNP loci exhibiting significant association with SW trait at lowest FDR adjusted P-values (threshold P < 10\u22124) and highest R2 were identified in chickpea.To perform candidate gene-based association analysis, the genotyping information of 1133 TF gene-derived SNP alleles mined by EcoTILLING was integrated with multi-location replicated SW field phenotyping (100 seed weight: 6\u201363 g), principal component analysis (P), population genetic structure (Q), and kinship (K) matrix of 192 d et al. and Evand et al. , respectr et al. . The degP \u2264 10\u22124 , whereas one SNP mapped on the unanchored scaffold of desi genome (Table bZIP (Basic-leucine zipper), SBP (Squamosa promoter binding protein) protein, Zinc finger-domain containing protein, NAC , bHLH (Basic helix-loop-helix) protein, AP2-EREBP (APETALA-2/ethylene response element binding protein), ARF (auxin response factor), and mTERF ] among 192 desi and kabuli accessions belonging to an association panel varied from R2: 10 to 15% (Table bZIP TF gene (R2: 15% with P: 1.3 \u00d7 10\u22125) with SW was observed in desi and kabuli chickpea -derived SNPs mapped on chromosomes 1 and 2, has been ascertained by recent studies in chickpea through identification of similar gene models-containing TFs, integrating seed weight trait-specific association analysis with QTL mapping, differential expression profiling and LD (linkage disequilibrium)-based marker haplotyping (Kujur et al., The CMLM and P3D/EMMAX-based association analysis at a FDR cut-off \u2264 0.05 detected eight TF gene-derived SNPs exhibiting significant association with 100-seed weight at a \u22124 Table . Seven ame Table . The pro5% Table . All sigea Table . The SW-ea Table . EspeciaCollectively, the present study demonstrated the efficacy of an optimized pool-based agarose gel-EcoTILLING strategy Figure for highDB, RS, and MN conducted experiments and drafted the manuscript. ST, CB, and HU helped in constitution of association panel and performed phenotyping. SP and AT conceived and designed the study, guided data analysis and interpretation, participated in drafting and correcting the manuscript critically and gave the final approval of the version to be published. All authors have read and approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Alzheimer Disease (AD) is characterized by progressive cognitive decline and dementia. Earlier diagnosis and classification of different stages of the disease are currently the main challenges and can be assessed by neuroimaging. With this work we aim to evaluate the quality of brain regions and neuroimaging metrics as biomarkers of AD. Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox functionalities were used to study AD by T1weighted, Diffusion Tensor Imaging and 18FAV45 PET, with data obtained from the AD Neuroimaging Initiative database, specifically 12healthy controls (CTRL) and 33 patients with early mild cognitive impairment (EMCI), late MCI (LMCI) and AD (11 patients/group). The metrics evaluated were gray-matter volume (GMV), cortical thickness (CThk), mean diffusivity (MD), fractional anisotropy (FA), fiber count (FiberConn), node degree (Deg), cluster coefficient (ClusC) and relative standard-uptake-values (rSUV). Receiver Operating Characteristic (ROC) curves were used to evaluate and compare the diagnostic accuracy of the most significant metrics and brain regions and expressed as area under the curve (AUC). Comparisons were performed between groups. The RH-Accumbens/Deg demonstrated the highest AUC when differentiating between CTRLEMCI (82%), whether rSUV presented it in several brain regions when distinguishing CTRL-LMCI (99%). Regarding CTRL-AD, highest AUC were found with LH-STG/FiberConn and RH-FP/FiberConn (~100%). A larger number of neuroimaging metrics related with cortical atrophy with AUC>70% was found in CTRL-AD in both hemispheres, while in earlier stages, cortical metrics showed in more confined areas of the temporal region and mainly in LH, indicating an increasing of the spread of cortical atrophy that is characteristic of disease progression. In CTRL-EMCI several brain regions and neuroimaging metrics presented AUC>70% with a worst result in later stages suggesting these indicators as biomarkers for an earlier stage of MCI, although further research is necessary."} +{"text": "The aim of current work was to automatically derive a body-lung-air three-valued material map from MRI images for pre-clinical PET attenuation correction. Our goal was also to measure the effect of attenuation on corresponding pre-clinical PET images.12 mouse and 9 rat PET/MRI images were acquired by nanoScan PET/MRI (Mediso). Each MRI image was filtered with edge-preserving Non-Local Means filter.Two segmentation stages were determined: the first stage separated the body and the air. The gravitational center of each disjunctive region determined by histogram-derived value ranges of the body and the air were inputs of two independent fuzzy-based affinity map generation steps. The fuzzy maps were merged with simple maximum into an initial binary body-air material map. In the second stage the gravitational center of disjunctive air regions laid inside the body mask were the seed points of the third fuzzy affinity map generation. Three fuzzy maps were merged with maximum operation into a three-valued mask.The three-valued material map was given as input for the Tera-Tomo 3D PET reconstruction engine to serve as the base for attenuation correction.Mouse and rat material map segmentation result were validated by two experienced pre-clinical researchers who manually drawn the ideal mask boundaries. The ratio of voxel misclassification was measured as 2.23% (mouse) and 1.87% (rat). Quantitative ROI measurements shown 1.3 - 2.7% AC and NAC PET differences.An automated and robust segmentation method was designed to provide a material map for pre-clinical PET attenuation correction. Although current work operated with PET/MRI images, the same method can be applied for nanoScan SPECT/MRI acquisitions. Results show that on the level of real quantitative measurements, attenuation correction of PET makes sense. As the next step of our future work we will investigate the effects of AC on pre-clinical nanoScan SPECT/MRI images."} +{"text": "The trait-related hypoconnectivity of DMN-salience network and hyperconnectivity of DMN-executive control network across the menstrual cycle featured a dynamic transition from affective processing of pain salience to cognitive modulation. The altered DMN-sensorimotor network may be an ongoing representation of cumulative menstrual pain. The findings indicate that women with long-term PDM may develop adaptive neuroplasticity and functional reorganization with a network shift from affective processing of salience to the cognitive modulation of pain.Primary dysmenorrhea (PDM) is the most prevalent gynecological problem. Many key brain systems are engaged in pain processing. In light of dynamic communication within and between systems (or networks) in shaping pain experience and behavior, the intra-regional functional connectivity (FC) in the hub regions of the systems may be altered and the functional interactions in terms of inter-regional FCs among the networks may be reorganized to cope with the repeated stress of menstrual pain in PDM. Forty-six otherwise healthy PDM subjects and 49 age-matched, healthy female control subjects were enrolled. Intra- and inter-regional FC were assessed using regional homogeneity (ReHo) and ReHo-seeded FC analyses, respectively. PDM women exhibited a Between 40 to 90% of female adolescents have experienced PDM and 10\u201320% describe their suffering as so severe and distressing that it requires absence from school or workstate- and trait-related structures456State-related changes are menstrual pain-primed, whereas trait-related changes exist even without symptoms. Notably, pain-related regions, such as the medial prefrontal cortex (mPFC), posterior cingulate cortex and insula, exhibit abnormal functional and structural changes in otherwise healthy women with PDM461113We have previously reported that long-term PDM is associated with alterations in brain metabolism and functional connectivity (FC) in pain modulatory systems, as well as in trait-related changes in response to different affective states. Furthermore, PDM may feature functional interactions between large-scale brain networks.Many key brain systems are engaged for menstrual pain processing; many key regions of these systems are also neural substrates of pain matrix that participate substantially in central processing of pain. Recent studies have demonstrated that the FC of large-scale brain systems/networks may be dynamically altered in patients with PDM and other chronic pain disorders and that these alterations can be either adaptive or maladaptive71515181521In this study, we implemented a hierarchical approach to study the FC constructs of PDM. We reasoned that FC changes could be manifested as intra-regional and inter-regional (long- distance) FC changes. To study the neuroplasticity of intra-regional FC, we used regional homogeneity (ReHo) analyses to estimate the local synchronization of resting brain activity within a segregated brain regionp\u2009=\u20090.351), age at menarche , years of menstruating , or average duration of one menstrual cycle . For the menstrual pain experience, PDM subjects had in average 9.22\u2009\u00b1\u20092.85 years of pain history; 65.2% of them had absenteeism from school or works and 41.3% of them had taken analgesics occasionally. The PDM group had been experiencing moderate cyclic menstrual pain .In brief, 46 PDMs and 49 controls (CON) were enrolled in the current neuroimaging study. There were no significant between-group differences regarding age and helplessness scores of the Pain Catastrophizing Scale (PCS), Beck Anxiety Inventory , the state anxiety of Spielberger State-Trait Anxiety Inventory (STAI), and Beck Depression Inventory . No significant group-phase interactions were found in the rumination and magnification scores of the PCS, and trait anxiety of STAI . Significant main effects of group were found in the total , rumination , helplessness and magnification scores of the PCS, BAI , the state anxiety and trait anxiety of STAI, and BDI . Significant main effects of phase were found in the BAI , state anxiety of STAI and BDI . No main effects of phase were found in the total , rumination , helplessness and magnification scores of the PCS, and the trait anxiety of STAI -phase (menstruation [MENS] vs. periovulatory [POV]) interactions were found in the total and left superior parietal lobe (SPL) of DAN network during the MENS phase vs. the POV phase , and lesser ReHo alterations in the left aIPS/SPL in the PDM group ; Fig. 1AOV phase and S1. For the interaction effect, the PDM group as compared to the CON group exhibited greater left vmPFC -For the interaction effect, no group-phase interaction was found when the left aIPS/SPL was seeded. For the main effects, please refer to the In the PDM group, the FC of the left vmPFC-bilateral posterior-mid insula (DMN-pain matrix connectivity) and -dACC (DMN-pain matrix connectivity) were more correlated with BAI during the POV phase when compared to the MENS phase ; Table 4state- and trait-related intra- and inter-regional FC alterations that collectively may result in subclinical central modulations of pain in otherwise healthy women with PDM. In our study, we observed a decreased ReHo, or a reduced local synchrony, in the vmPFC, which indicates increased intra-regional functional segregations in reaction to long-term menstrual pain. We also measured changes of inter-regional FC (both intrinsic and extrinsic network connectivity) in the PDM group, which may represent network reorganization in the context of strengthened DMN-ECN FC and attenuated DMN-SN FC when compared to the CON group. In addition, functional interaction between aIPS/SPL and pain-related regions (DAN-pain matrix connectivity) might be associated with a top-down regulation of pain transmission. Finally, we observed an inverse correlation between the vmPFC-posterior/mid insula FC (DMN-pain matrix connectivity) and anxiety scores across different phases. This suggests an adaptive neuroplasticity that is related to pain-primed mental state changes.Using ReHo and ReHo-seeded FC analyses, the current study demonstrated The vmPFC of PDM group manifested a relative lack of resilience across t10143637The functional expression and engagement of DAN throughout the menstrual cycle differed between PDM and CON groups, as reflected by the interaction effect of group and phase. The aIPS/SPL services attention shifting and saliently driven sensory discrimination and is a cardinal substrate of the DAN that participates in the top-down attention to painGreater ReHo (MENS vs. POV) of the declive and the orbitofrontal cortex (OFC) in the PDM as compared to the CON group could be17et al.22The functional interplay between the three core networks might reorganize after stress eventstrait-related decrease of FC with right vmPFC 20\u201330-year-old Taiwanese (Asian) females; 2) a regular menstrual cycle of approximately 27\u201332 days; 3) a history of menstrual pain longer than 6 months; 4) averaged menstrual pain under regular treatment with a rating at least higher than 4 on a verbal numerical scale in the last 6 months; and 5) right-handedness, as confirmed by the Edinburgh Handedness Inventory. All subjects in the PDM group underwent pelvic ultrasonography to exclude secondary dysmenorrhea that was caused by organic pelvic diseases, such as endometriosis or adenomyosis. All participants were clinically examined and diagnosed in the gynecology clinic by the same gynecologist. The inclusion criteria for the healthy female control subjects were similar to those for the PDM group, with the exception that the members of the control group must have no pain during menses (VNS\u2009=\u20090). The exclusion criteria for all the participants were: 1) using oral contraceptives, hormonal supplements, Chinese herbal medicine, or any central-acting medication within 6 months prior to the study; 2) pathological pituitary gland disease; 3) organic pelvic disease; 4) any psychiatric or neurological disorders; 5) brain trauma or brain surgery; 6) immediate plans for pregnancy or a positive pregnancy test; 7) a history of childbirth; and 8) having a metal/pacemaker implant, claustrophobia, or any contraindications to magnetic resonance imaging (MRI). No analgesics were used within 24\u2009hours of the scans. The study was conducted in accordance with the Declaration of Helsinki and was approved by the Institutional Review Board of Taipei Veterans General Hospital. Written informed consents were obtained from all participants.MRI scanning was individually scheduled according to the commencement day of menstruation for each subject. Psychological assessments, blood samples for gonadal hormone assays and MRI images (T1 and resting-state fMRI images) were obtained at two time points during the menstrual cycle: the MENS phase and the POV phase . Ovulation was confirmed using a urinary luteinizing hormone test (Han Chiun Proper LH Rapid Test).The patients in the PDM group completed the PCS and recounted their overall menstrual pain by using the McGill Pain Questionnaire during the inception interview. Then, during the MENS phase, subjects were assessed for their present experience of menstrual pain using the McGill Pain Questionnaire. All participants completed the BDI, BAI and STAI during the MENS and POV phases to assess their psychological status.The serum that was extracted during both phases was stored for batch analysis using commercialized assays . The total serum concentrations were assayed using a chemiluminescence immunoassay technique for estradiol and progesterone and a radioimmunoassay technique for the testosterone. As gonadal hormones may affect resting-state FC3, in-plane matrix size\u2009=\u2009224\u2009\u00d7\u2009256\u2009\u00d7\u2009192, in-plane resolution\u2009=\u20091\u2009mm) and T2*-weighted gradient echo sequence were conducted to obtain high-resolution anatomical T1 images and functional MRI images. The first four functional scans of each resting-state functional MRI series were discarded for signal saturation and magnetic field stabilization. Participants remained awake during the scan and were instructed to maintain open eyes and relaxed, still heads without thinking about any topic in particular. Head cushions and earplugs were applied to reduce head motion and noise.Resting-state functional MRI images were acquired using a 3.0 Tesla MRI scanner with a 12-channel head coil. High-resolution T1-weighted 3-dimensional structural images using a magnetization-prepared rapid-acquired gradient echo sequence to extract the low-frequency oscillations. The following nuisance variables were regressed out: 1) the six head movement parameters computed based on rigid body translation and rotation during the realignment in SPM8; 2) the mean signal within the lateral ventricles for cerebral spinal fluid; and 3) the mean signal within a deep white matter region . Brain activity was activated in clusters, or contiguous voxels, rather than in a few voxels. ReHo maps were generated by calculating the Kendall\u2019s coefficient of concordance (KCC) of the time series between a given voxel with its nearest neighbors (26 voxels) in a voxel-wise manner. The ReHo maps were spatially smoothed using a 3D Gaussian kernel of 6\u2009mm full-width at half-maximum (FWHM). For standardization purposes, each individual subject\u2019s ReHo map was divided by its own global mean. The peaks of significant clusters were then selected as the ReHobased seeds.Preprocessing was performed by using the Data Processing Assistant for Resting-State fMRI (DPARSF) V2.3 Advanced Edition The preprocessing of the functional connectivity analysis protocol was as same as in the ReHo analysis, except that the images were 1) coregistered to individuals\u2019 anatomical image and then normalized to the standard T1 MNI template; 2) spatially smoothed using a 3D Gaussian kernel of 8\u2009mm FWHM; and 3) treated with the global mean signal for additional nuisance variables. We performed global signal regression because it has been shown to maximize the specificity of positive resting-state correlations when using real and simulated data717For the network assignments for the significantly altered ReHo and FC regions, we conducted the inverse validation by means of FC analyses, using peaks of significant clusters as the seeds. The FC was considered significant if family-wise error level was p\u2009<\u20090.05 at voxel level. The FC map of each seed was visually compared with the FC map of the key brain systems as published previouslyet al.SPSS Statistics 20.0 was used for all analyses. Two-sample t-tests were conducted for the between-group (PDM vs. CON) differences in demographic characteristics and Edinburgh Handedness Inventory scores. To test the group-phase interactions, we used mixed design two-way ANOVA. The significance was thresholded at p\u2009=\u20090.05. For more comprehensive statistical analyses and results, please refer to our previous paper by Lee trait- and state-related neuroplasticity, we focused on the planned contrasts of between-group differences of respective phase and between-phase differences of respective group rather than the main effects for ReHo values and ReHo-seeded FCs5t test, respectively. Main effects analyses were also conducted for reference only. Three gonadal hormone levels were treated as non-interest covariates. Significance was thresholded at the uncorrected voxel level p\u2009=\u20090.005 followed by the FWE-corrected cluster level p\u2009=\u20090.05.For the interaction effects of group and phase, we compared the phase difference (MENS phase vs. POV phase) of mean ReHo values and ReHo-seeded FCs between the PDM and CON groups by the factorial design module of SPM8. To elucidate the respective Since studies have reported that state anxiety correlate with mPFC-insula FCHow to cite this article: Wu, T.-H. et al. Dynamic Changes of Functional Pain Connectome in Women with Primary Dysmenorrhea. Sci. Rep.6, 24543; doi: 10.1038/srep24543 (2016)."} +{"text": "PERIANTHIA (PAN) regulates the formation of the floral organ primordia as revealed by the pan mutant forming an abnormal pentamerous arrangement of the outer three floral whorls. The Arabidopsis TGA bZIP TF family comprises 10 members, of which PAN and TGA9/10 control flower developmental processes and TGA1/2/5/6 participate in stress-responses. For the TGA1 protein it was shown that several cysteines can be redox-dependently modified. TGA proteins interact in the nucleus with land plant-specific glutaredoxins, which may alter their activities posttranslationally. Here, we investigated the DNA-binding of PAN to the AAGAAT motif under different redox-conditions. The AAGAAT motif is localized in the second intron of the floral homeotic regulator AGAMOUS (AG), which controls stamen and carpel development as well as floral determinacy. Whereas PAN protein binds to this regulatory cis-element under reducing conditions, the interaction is strongly reduced under oxidizing conditions in EMSA studies. The redox-sensitive DNA-binding is mediated via a special PAN N-terminus, which is not present in other Arabidopsis TGA TFs and comprises five cysteines. Two N-terminal PAN cysteines, Cys68 and Cys87, were shown to form a disulfide bridge and Cys340, localized in a C-terminal putative transactivation domain, can be S-glutathionylated. Comparative land plant analyses revealed that the AAGAAT motif exists in asterid and rosid plant species. TGA TFs with N-terminal extensions of variable length were identified in all analyzed seed plants. However, a PAN-like N-terminus exists only in the rosids and exclusively Brassicaceae homologs comprise four to five of the PAN N-terminal cysteines. Redox-dependent modifications of TGA cysteines are known to regulate the activity of stress-related TGA TFs. Here, we show that the N-terminal PAN cysteines participate in a redox-dependent control of the PAN interaction with a highly conserved regulatory AG cis-element, emphasizing the importance of redox-modifications in the regulation of flower developmental processes.The Arabidopsis TGA transcription factor (TF) PERIANTHIA (PAN) regulates the initiation of floral organ primordia in the outer three floral whorls and belongs to the TGACG (TGA) motif-binding family. Loss-of-function pan plants form pentamerous flowers with five sepals, five petals and five stamens, compared to the development of four sepals, four petals and six stamens in wild-type flowers (cis-regulatory elements comprising the name-giving TGACG core recognition sequence. A well-characterized TGA TF binding element is the activation sequence-1 (as-1) motif, first described in bacterial and viral promoters . The. ThePERIromoters . VariatiSE (GST) \u20138. UsingOUS (AG) , 10. Thesequence Fig 1B)PERIANTHIsequence and has sequence . The imp element . In Arabth whorl . Additiogulation , 14. Thegulation , 11.as-1-like element . TheAAGAAT motif from the floral TF AG, prompted us to analyze the evolutionary relationships between the N-terminus and the AAGAAT motif. Earlier studies on conserved elements in the AG intronic regions identified AAGAAT motifs in diverse angiosperm species [Picea abies and the bryophyte Physcomitrella patens. AAGAAT motif is indicated for the investigated species and sequence alignments are shown in AAGAAT motif comprising the AAGAAT sequence but lacking the core TGA TF binding site already exists in the basal-most analyzed land plant, the bryophyte Physcomitrella patens. Such partial AAGAAT motifs were also identified in representatives of basal angiosperms (Amborella trichopoda), gymnosperms (Picea abies) and monocots . In asterids, partial motifs exist in the Phrymaceae and Lentibulariaceae and complete AAGAAT motifs, where an AAGAAT sequence precedes the TGA binding site, were identified in the Solanaceae. All analyzed rosids comprise a complete AAGAAT motif.The observation that the PAN N-terminus mediates a redox-dependent interaction with the species , 12. HerTarenaya hassleriana from the Cleomaceae family, sister to the Brassicaceae, two TGA TFs with high similarity to PAN were identified. One homolog comprises two and the other homolog three N-terminal cysteines Click here for additional data file.S2 FigAAGAAT motif from the second Arabidopsis AG intron is indicated in bold. The blue box marks the characteristic AAGAAT sequence and the orange box the core TGA TF binding site. The first position of the AAGAAT motif is variable [Aethionema arabicum motif originated from a BLAST result, indicated by a star symbol. The Oryza sativa AAGAAT motif (circle) was obtained from [Arabidopsis thaliana; Al Arabidopsis lyrata; Cr Capsella rubella; Ag Arabis gunnisoniana; Br Brassica rapa; Bo Brassica oleracea; Aa Aethionema arabicum; Th Tarenaya hasseleriana; Tc Theobroma cacao; Gr Gossypium raimondii; Pt Populus trichocarpa; Gm Glycine max; Md Malus domestica; Fv Fragaria vesca; Pp Prunus persica; Eg Eucalyptus grandis; St Solanum tuberosum; Mg Mimulus guttatus; Ug Utricularia gibba; Ma Musa acuminata; Os Oryza sativa; Atr Amborella trichopoda; Pa Picea abies; Ppa Physcomitrella patens.Comparison of sequences from plant species listed in variable . The Aetned from . At Arab(TIF)Click here for additional data file.S3 FigArabidopsis thaliana PAN sequence is indicated in bold. Cysteines at positions equivalent to the PAN cysteines are highlighted in red. At Arabidopsis thaliana; Al Arabidopsis lyrata; Cr Capsella rubella; Aal Arabis alpina; Br Brassica rapa; Bo Brassica oleracea; Aa Aethionema arabicum; Th Tarenaya hasseleriana; Tc Theobroma cacao; Gr Gossypium raimondii; Pt Populus trichocarpa; Gm Glycine max; Md Malus domestica; Fv Fragaria vesca; Pp Prunus persica; Eg Eucalyptus grandis; St Solanum tuberosum; Mg Mimulus guttatus; Ug Utricularia gibba; Ma Musa acuminata; Os Oryza sativa; Atr Amborella trichopoda; Pa Picea abies; Ppa Physcomitrella patens.Amino acid sequences from the plant species listed in the (TIF)Click here for additional data file.S1 Table(PDF)Click here for additional data file."} +{"text": "Diabetic retinopathy (DR) is a neovascular, inflammatory and neurodegenerative disease. The neovascular component is treatable but no therapeutic agents are available for the other two components. Early changes in the diabetic retina include neuronal death of amacrine and retinal ganglion cells (RGC), and elevated levels of inflammatory mediators . Nerve Growth factor (NGF) receptors, namely TrkA and p75NTR, are expressed in RGC. The TrkA receptor activates prosurvival, while p75NTR activates inflammatory and apoptotic pathways . Dehydroepiandrosterone (DHEA) binds to both receptors, mimicking NGF. It affords anti-apoptotic, neuroprotective and anti-inflammatory effects in the retina . The therapeutic use of DHEA is restricted due to its metabolic products. The main objective of this study was to investigate and compare the neuroprotective and anti-inflammatory effects of DHEA and its spiro-epoxy derivatives BNN27 and BNN20 (not metabolized to estrogens and androgens), in the rat streptozotocin model of DR. BNN27, via TrkA activation, protected in a dose-dependent manner bNOS (brain nitric oxide synthetase) and TH (tyrosine hydroxylase) expressing amacrine cells and ganglion axons (NFL immunoreactivity) similar to DHEA\u2019s actions, while BNN20 was less effective. BNN27 activated the TrkA prosurvival signaling pathway ERK1/2 kinase. It reduced the activation of SAPK/JNK kinase and the expression of p75NTR. BNN27 also increased the expression of anti-inflammatory cytokines (IL10). These results suggest that NGF TrkA receptor is involved in the neuroprotective and anti-inflammatory effects of BNN27 and is a valuable target via which BNN27 could afford efficacious therapeutics for the treatment of DR."} +{"text": "These observations have thus challenged the classical picture of specific protein-DNA binding and strongly suggest the existence of additional recognition mechanisms that affect protein-DNA binding preferences. We have previously demonstrated that repetitive DNA sequence elements characterized by certain symmetries statistically affect protein-DNA binding preferences. We call this binding mechanism nonconsensus protein-DNA binding in order to emphasize the point that specific consensus TFBSs do not contribute to this effect. In this paper, using the simple statistical mechanics model developed previously, we calculate the nonconsensus protein-DNA binding free energy for the entire C. elegans and D. melanogaster genomes. Using the available chromatin immunoprecipitation followed by sequencing (ChIP-seq) results on TF-DNA binding preferences for ~100 TFs, we show that DNA sequences characterized by low predicted free energy of nonconsensus binding have statistically higher experimental TF occupancy and lower nucleosome occupancy than sequences characterized by high free energy of nonconsensus binding. This is in agreement with our previous analysis performed for the yeast genome. We suggest therefore that nonconsensus protein-DNA binding assists the formation of nucleosome-free regions, as TFs outcompete nucleosomes at genomic locations with enhanced nonconsensus binding. In addition, here we perform a new, large-scale analysis using in vitro TF-DNA preferences obtained from the universal protein binding microarrays (PBM) for ~90 eukaryotic TFs belonging to 22 different DNA-binding domain types. As a result of this new analysis, we conclude that nonconsensus protein-DNA binding is a widespread phenomenon that significantly affects protein-DNA binding preferences and need not require the presence of consensus (specific) TFBSs in order to achieve genome-wide TF-DNA binding specificity.Recent genome-wide experiments in different eukaryotic genomes provide an unprecedented view of transcription factor (TF) binding locations and of nucleosome occupancy. These experiments revealed that a large fraction of TF binding events occur in regions where only a small number of specific TF binding sites (TFBSs) have been detected. Furthermore, nonconsensus protein-DNA binding in order to describe protein-DNA interactions that occur in the absence of specific protein-DNA binding motifs. Here we demonstrate that the identified nonconsensus effect is highly significant for a variety of organismal genomes and it affects protein-DNA binding preferences and nucleosome occupancy at the genome-wide level.Interactions between proteins and DNA trigger many important biological processes. Therefore, to fully understand how the information encoded on the DNA transcribes into RNA, which in turn translates into proteins in the cell, we need to unravel the molecular design principles of protein-DNA interactions. It is known that many interactions occur when a protein is attracted to a specific short segment on the DNA called a specific protein-DNA binding motif. Strikingly, recent experiments revealed that many regulatory proteins reproducibly bind to different regions on the DNA lacking such specific motifs. This suggests that fundamental molecular mechanisms responsible for protein-DNA recognition specificity are not fully understood. Here, using high-throughput protein-DNA binding data obtained by two entirely different methods for ~100 TFs in each case, we show that DNA regions possessing certain repetitive sequence elements exert the statistical attractive potential on DNA-binding proteins, and as a result, such DNA regions are enriched in bound proteins. This is in agreement with our previous analysis performed for the yeast genome. We use the term It has been known for a long time, since the seminal studies of Iyer and Struhl , [aXa], [aXXa], and [aXXXa], where a represents each amino acid type and X represents an arbitrary amino acid , [Arg-Arg] , and [Leu-X-Leu] (pks \u2243 0.01) into two groups. The first group contained 41 TFs with the strongest negative correlation between the free energy and the measured TF occupancy. The second group contained the remaining 41 TFs. We have analyzed the amino acid correlation properties in these two groups of TFs. Our working hypothesis here is that enhanced amino acid sequence correlations in TF sequences are responsible for enhanced nonconsensus TF-DNA binding. We use the term \u201csequence correlations\u201d in order to describe repetitive sequence patterns. We have previously used a similar analysis in order to investigate protein sequence features responsible for enhanced level of protein structural disorder and protein-protein interaction promiscuity . In partino acid . For exa \u2243 0.05) . In addi \u2243 0.01) . The facTwo conclusions can be drawn from our results. First, that the intrinsic propensity for nonconsensus protein-DNA binding is imprinted both into the DNA and the protein. Since our simple nonconsensus binding model treats proteins as random binders, it captures general trends in the binding profiles of most, but not all, TFs. Second, nonconsensus and specific (consensus) protein-DNA binding mechanisms are tightly interlinked, and both of these mechanisms cooperate in determining the overall protein-DNA binding preferences in eukaryotic genomes. The fact that our simple random-binder model (without any fitting parameters and without any protein-DNA binding specificity built in) provides such a good statistical description of the measured DNA binding strength for the majority of TFs strongly suggests that the nonconsensus mechanism is quite general and it represents the statistical law rather than the exception. However, more accurate, atomistic models describing nonconsensus protein-DNA binding interactions are necessary in order to improve the accuracy of our predictions for different proteins.C. elegans and 30 TFs in D. melanogaster are significantly, negatively correlated with the predicted nonconsensus free energy landscape experiments showed an ccupancy . The latccupancy . In partis group . The latstatistically similar way by entirely different DNA sequences containing similar repetitive patterns constitutes the key difference between the nonconsensus and specific protein-DNA recognition modes.Importantly, in this study, our random-binder statistical mechanics model for protein-DNA interactions does not use any experimentally pre-determined information on either low-affinity or high-affinity TF-DNA binding sites. The genomic DNA sequence constitutes the only experimental parameter of the model. In addition, our model does not have any fitting parameters. Contrary to the case of specific protein-DNA binding that requires the presence of a 6 to 20-bp long specific DNA motif , the nonconsensus protein-DNA binding effect stems from multiple nonspecific interactions between the TF and a relatively long (few tens of bp) DNA fragments enriched with repetitive sequence patterns. The fact that different TFs are affected in a What exactly is the interplay between nonconsensus DNA repetitive sequence elements and consensus (specific) sequences and how their combination influences the overall binding of proteins to the DNA and the expression levels of genes are important questions yet to be explored. We suggest that repetitive nonconsensus sequence elements might have similar influence on TF-DNA binding and on gene expression as repeats of consensus (specific) DNA sequence elements (i.e. homotypic clusters) . HoweverC. elegans Hlh-1 protein as an example demonstrating that nonconsensus DNA sequence elements might stabilize the binding to specific consensus elements in vivo (C. elegans) demonstrates that only 5% of the total number of Hlh-1 specific motifs in the genome is bound by Hlh-1 sequence elements embedded in different nonconsensus DNA backgrounds, should shed more light on this hypothesis.Repetitive sequence elements located near the consensus (specific) motif, could increase the TF association rate, by inducing the one-dimension \u201csliding\u201d of the TF, and improving its search for the specific binding site , 58. The in vivo . The anaby Hlh-1 . We sortnificant . This exin vitro measurements of binding preferences for additional TFs , [aXa], [aXXa], and [aXXXa], where a represents each amino acid type and X represents an arbitrary amino acid. The second table contains the average amino acid content in each group of TFs. The presented p-values represent the Kolmogorov-Smirnov p-values.The first group (1st average) contained 41 TFs with the strongest negative correlation between the free energy and the measured TF occupancy. The second group (2nd average) contained the remaining 41 TFs. We have analyzed the frequency of occurrence of the following repetitive amino acid sequence patterns in each TF group: [(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file."} +{"text": "Securing the airway by endotracheal intubation (ETI) is a key issue in civilian and military pre-hospital critical care. Night vision goggles (NVG) are used by personnel operating in low-light tactical environments. We examined the feasibility of an anaesthesiologist performed ETI using binocular NVG in a helicopter setting.Twelve anaesthesiologists performed ETI on a manikin in an emergency room (ER) setting and two helicopter-settings, with randomization to either rotary wing daylight (RW-D) or rotary wing in total darkness using binocular NVG (RW-NVG). Primary endpoint was intubation time. Secondary endpoints included success rate, Cormack-Lehane (CL) score and subjective difficulty according to the Visual Analogue Scale (VAS).The median intubation time was shorter for the RW-D compared to the RW-NVG setting . We found no difference in median intubation time for the ER and RW-D settings . For all scenarios success rate was 100%. CL and VAS varied between the ER setting , RW-D setting and RW-NVG setting .This study suggests that anaesthesiologists successfully and quickly can perform ETI in a helicopter setting both in daylight and in darkness using binocular NVG, but with shorter intubation times in daylight.The authors have no conflicts of interests"} +{"text": "TNF-\u03b1 inhibitors plus MTX appear to have benefit in the longer-term reduction of RA. Boolean long-term remission under drug-free conditions is rare. The therapeutic mechanism and the factor of predicting response have not been clarified yet.A 24-year-old female rheumatoid arthritis (RA) patient, who once attained complete remission (CR) with the combination therapy with tumor necrosis factor alpha inhibitor adalimumab (ADA) and methotrexate (MTX), showed the occurrence of Epstain- Barr virus (EBV)-associated lymphoproliferative disorder (LPD). Pulse treatment with methylprednisolone after the termination of anti TNF-\u03b1 therapy resulted in the remission of EBV-associated LPD. The administration of prednisolone (PSL) was tapered off after the improvement of clinical symptoms and laboratory data. The patients achieved drug-free 12 months after urgent hospitalization and delivered healthy baby 2 years after hospital discharge. She has been complete drug-free Boolean remission for 5 years.The purpose of this brief case is report that we experienced the remission of LPD after CR with combined therapy with ADA and MTX. We believe this case report will be one of the paths for unveiling the pathogenesis and improving the treatment for RA.We believe this case report will be one of the paths for unveiling the pathogenesis and improving the treatment for RA. Tumor necrosis factor-alpha (TNF-\u03b1) inhibitors have revolutionized the management of RA and other chronic inflammatory diseases. TNF-\u03b1 inhibitors plus MTX appears to have benefit in the longer-term reduction of RA signs/symptoms in MTX-resistant patients, with no unexpected safety concerns. Nonetheless, Boolean defined disease remission occurred in 5.0-10.1% of RA, and long-term remission under drug-free conditions is rare . Flow-cytometric analysis of infiltrating lymphocytes in lymph node showed an abundant population of CD38 positive B cell. In addition to routine blood test and urine cultures, the histories of infection were collected . The examinations for all these infections agents were negative except for high titers of anti-EBV antigen IgG (Table\u00a0A 24-year-old Japanese woman with one year history of active rheumatoid arthritis (RA) who complained in March 2007 with pain and swelling of bilateral wrists, elevation of the inflammatory markers such as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and matrix metalloproteinase-3 (MMP3). The blood examination showed anti-agalactosyl IgG antibody CARF positive, which is known as the early diagnosis marker for RA (Wong et al. In this case, we experienced the remission of LPD after CR with combined therapy with ADA and MTX. RA is a polygenetic disease, it makes difficult to unveil the pathogenesis of RA and treatment. More evidence and further investigations are required for elucidating the mechanism of complete remission and establishing optimal treatment strategies."} +{"text": "T cells have proven to be effective for the treatment of leukaemias in form of donor lymphocyte infusions (DLI). However, those DLI are of unknown specificity and often associated with graft versus host disease. New effector tools in form of T cell receptor (TCR)-transgenic T cells with specificity for leukaemia-derived human leukocyte antigen (HLA) ligands are highly promising tools for the treatment of life-threatening, therapy refractory leukaemias.in vitro and in vivo leukaemia reactivity as well as their in vitro on- and off-target reactivity.In order to identify leukaemia-derived HLA ligands, we performed the immunopeptidomic approach on seven samples from patients with myeloproliferative neoplasias (MPN). HLA ligands derived from genes with expression restricted to the hematopoeitc system were identified by database searches and literature research and validated by quantitative PCR (qPCR) and immunohistochemistry (IHC). For isolation of peptide-specific TCR, naive T cells of healthy blood donors were primed with single HLA-mismatched dendritic cells, pulsed with synthetic counterparts of selected HLA ligands. Peptide specific T cells were isolated using HLA multimers and cloned by limiting dilution. TCR were isolated out of peptide-specific T cell clones and characterised for their B*07:02 restricted ligand MPO5 could be isolated. TCR2.5D6-transgenic T cells show in vitro leukaemia reactivity including colony forming leukaemic progenitor cells. Strikingly, anti-leukaemic reactivity could be observed in a murine model of human acute myeloid leukaemia with HLA-B*07:02-transgenic NB4 cells, resulting in significantly prolonged survival and reduced bone marrow infiltration by leukaemic cells. However, strong immune pressure led to the development of tumours that lost transgene expression in the TCR treated group. Extensive experiments regarding safety of the TCR2.5D6 revealed lack of reactivity against MPO- cells including healthy hematopoietic stem cells. Experiments with alanine variants of the MPO5-peptide resulted in a recognition pattern that is unique for the MPO-specific peptide.Using the immunopeptidomic approach on seven MPN samples, we were able to identify 4386 unique HLA ligands. Nineteen of those ligands are derived from seven genes with restricted expression to the hematopoietic system and are presented on six different HLA molecules. We exemplarily selected the antigen myeloperoxidase (MPO) (five identified ligands) and confirmed restricted expression to myeloid cells. A TCR (named TCR2.5D6) with high specificity for the HLA-In conclusion, as shown for the MPO-specific TCR, combination of the immunopeptidomic identification of leukaemia-derived HLA ligands with the isolation of TCR in the single HLA-mismatched setting is suitable to generate highly specific, leukaemia-reactive TCR-transgenic T cells. Further TCR are isolated and characterized at the moment to allow therapeutic application for a broad patient population."} +{"text": "In patients with hemodynamically significant atrioventricular (AV) blocks of unknown etiology, cardiac MRI (CMR) with tissue characterization can provide incremental diagnostic information. Correlation of initial CMR findings with future events recorded by permanent pacemakers (PPM) can characterize the natural history of these serious and potentially life-threatening cardiac conditions.We studied a total of 78 patients with complete heart block, high-grade second degree heart block and symptomatic bundle branch blocks. In all patients, initial cardiac work-up was non-revealing for potential etiology, and CMR with late gadolinium enhancement (LGE) was performed. Following CMR, most of these patients underwent clinically indicated PPM placement. The interrogated PPM events were followed up for 1-4 years to monitor significant arrhythmias or long-term pacemaker dependence.In patients with heart block, CMR identified a myocardial infiltrative process in 44%. In patients with symptomatic LBBB or RBBB, CMR identified a plausible etiology in approximately 25%. Presence of myocardial LGE by CMR had 90% sensitivity and 80% negative predictive value for long-term pacemaker dependence in patients with complete or high-grade AV blocks.In addition to the indications attributed in the current diagnostic algorithm, CMR can identify potential cause of hemodynamically significant AV-blocks in over 40% of the patients. Presence of LGE or other major diagnostic findings on CMR can uniquely identify patients with long-term pacemaker dependence.N/A."} +{"text": "Accurate quantification of the ischemic myocardium at risk (MaR) in patients with ST- elevation myocardial infarction (STEMI) is paramount in studies of therapies seeking to reduce infarct size expressed as percent of MaR. Cardiac magnetic resonance (CMR) is an important clinical research tool for determination of MaR and infarct size in the same examination within one week after STEMI. Recent data suggest that cardioprotective interventions such as ischemic postconditioning or remote conditioning reduce infarct size, but may also reduce the extent and severity of edema detected with T2-weighted imaging. Such an effect might limit the value of determining MaR using T2-weighted sequences. Contrast enhanced steady-state free precession (CE-SSFP) imaging for quantifying MaR in STEMI has previously been validated compared to single photon emission computed tomography following radiotracer injection prior to reperfusion. The aim of the current study was to compare extent and severity of signal intensity changes in MaR determined from CE-SSFP in patients with STEMI randomized to postconditioning or standard percutaneous coronary intervention (PCI).Patients eligible for primary PCI due to STEMI were randomized to standard PCI or postconditioning (n=38) consisting of four cycles of 60 sec reperfusion and 60 sec of re-occlusion before permanent reperfusion. CMR was performed 7.8\u00b11.2 days after myocardial infarction using a protocol in which the contrast agent was administered before acquisition of short-axis CE-SSFP images. MaR was determined by manual delineation, in end-diastole and end-systole, as the contrast-enhanced myocardial volume in relation to left ventricular mass (Figure Postconditioning affects neither the extent nor severity of signal intensity changes in MaR quantified by CE-SSFP performed one week after STEMI. This indicates that CE-SSFP is an accurate and appropriate imaging method to quantify MaR in patients with STEMI, even in the setting of treatment with postconditioning.Swedish Heart and Lung Foundation."} +{"text": "Drosophila melanogaster males, the expression of X-linked genes is regulated by mechanisms that operate on a chromosomal scale. One such mechanism, male-specific lethal complex-dependent X-linked dosage compensation, is thought to broadly enhance the expression of male X-linked genes through two-fold transcriptional upregulation. The evolutionary consequences of this form of dosage compensation are not well understood, particularly with regard to genes more highly expressed in males. It has been observed the X chromosome arrangement of these male-biased genes is non-random, consistent with what one might expect if there is a selective advantage for male-biased genes to avoid dosage compensation. Separately, it has been noted that the male-specific lethal complex and its dosage compensation mechanism appear absent in some male tissues, thus providing a control for the selection hypothesis. Here we utilized publicly available datasets to reassess the arrangement of X-linked male-biased expressed genes after accounting for expression in tissues not dosage compensated by the male-specific lethal complex. Our results do not corroborate previous observations supporting organismal-wide detrimental effects by dosage compensation on X-linked male-biased expressed genes. We instead find no evidence that dosage compensation has played a role in the arrangement of dosage compensated male-biased genes on the X chromosome.In Drosophila melanogaster males and females have revealed a vast number of traits to be sexually dimorphic. Technological advances have enabled similar contrasts of molecular endophenotypes, and again sexual dimorphism has been shown to be widespread, especially within the transcriptome Drosophila sex-biased expressed genes, with an emphasis on X-linked male-biased expressed genes (MBGs) X-linked gene expression.Phenotypic contrasts between Drosophila, two primary mechanisms are thought to broadly modulate X-linked gene expression in males: meiotic sex chromosome inactivation (MSCI) X chromosome is rendered inactive in meiotic tissue; in DC, transcriptional activity on the male X chromosome is generally upregulated in somatic tissues in order to compensate for male X monosomy. The extent to which these operate remains a subject of debate X-linked MBGs; likewise, many meiotically expressed X-linked MBGs are thought to be negatively impacted by MCSI. Evidence supporting these hypotheses is indirect. First, throughout the Drosophila genus, there appears to be a deficit of both meiotically and mitotically expressed MBGs on the X chromosome XMale-specific Lethal) complex, whose role in dosage compensation is discussed below In Drosophila dosage compensation , MSL-2 , MSL-3 , MOF and MLE ) as well as two redundant yet unique non-coding RNAs (roX1 and roX2). The histone modification associated with dosage compensation, H4K16Ac Drosophila and its putative impact on the organization of the X chromosome. The prevailing argument for how DC has influenced the X hypothesizes selection against MBGs that are both dosage compensated and further upregulated by non-DC mechanisms X chromosomes carry a signature conistent with such migrations; however, other inconsistencies persist. There remains debate as to whether the X chromosome is truly depauperate for MBGs, with some suggesting the observation is confounded by the absence of DC in the testis X chromsome, there remains debate as to why. The arguments in the literature have been fueled by analyses utilizing increasingly rich datasets that have yielded seemingly contradictory results X chromosome, explicitly controlling for the absence of any MSL complex-like dosage compensation in meiotic tissues This manuscript focuses on DC in X-linked MBGs near CESs and found the degree of male bias to be greater for MBGs more distant from their nearest CES roX1 mutant . Concerned that the increased distance of non-dosage compensated testis-biased MBGs from their nearest CES , we filtered these genes from our analysis and in doing so abolished any relationship among MBGs between CES proximity and either transcript abundance or degree of male bias. Thus, it is possible that this spatial bias was the driver behind previous observations. It is also noteworthy that Bachtrog and colleagues X-linked MBGs to be significantly further from their nearest chromatin entry site than either X-linked FBGs and UBGs. They moreover found the degree of male bias to increase with distance from the nearest chromatin entry site. On the surface, these observations would seem to contradict our attribution of whole-body signal to germline tissue; however, we suggest an explanation that rectifies our conclusions with those of Bachtrog et al Our study is meant to complement previous work in which Bachtrog and colleagues X-linked MBGs. For example, differential MSL-complex binding patterns were shown to exist among various relevant classes of X-linked genes . Genes were partitioned into testis-biased expressed and somatically expressed using tissue-specific expression data from FlyAtlas X-linked or autosomal based on the FB2013_04 Release gene map table from FlyBase Data were collected from their respective latest public release. Specifically, probe-set-based expression measurements from third instar larval males in both the las see 0.9. SexX-linked genes, 348 of which were male biased.Custom Perl scripts were created (available upon request) to merge all of the collected data into a single table. Specifically, all genes, regardless of the identification system they were made available in, were converted to FBgn IDs using the FB2013_02 Release FBgn annotation file form Flybase Custom R scripts (available upon request) using standard R functionality were created for statistical analysis. All Figure S1Distances of X-linked testis-biased and non-testis-biased male-biased expressed genes from their nearest chromatin entry site.X-linked MBGs were classified as testis-biased or non-testis-biased base on tissue specificity calculated using tissue-specific data from FlyAtlas. Testis-biased X-linked MBGs tend to be significantly further from their nearest CES (mean distance: 72909 bp) than non-testis-biased X-linked MBGs (mean distance: 34980 bp)((EPS)Click here for additional data file.Figure S2Relationship between transcript abundnace and dosage compensation for X-linked FBGs and UBGs. A combined set of X-linked FBGs and UBGs do not show any compatibility between transcript abundance and probability of dosage compensation. Interestingly there is instead a positive correlation suggesting that more highly transcribed genes show a stronger signature of dosage compensation ((EPS)Click here for additional data file.Figure S3Relationship between sex-bias magnitudes and distance from nearest CES using whole fly expression data from Innocenti and Morrow, 2010. Using whole body expression from Innocenti and Morrow, 2010 we found a significant positive correlation between sex-bias magnitude and distance from the nearest CES including all X-linked MBGs Click here for additional data file.Figure S4Relationship between sex-bias magnitudes and distance from nearest CES using whole fly expression data from Wyman et al., 2010. Using whole body expression from Wyman et al., 2010 we found a significant positive correlation between sex-bias magnitude and distance from the nearest CES when considering all X-linked MBGs Click here for additional data file.Figure S5Relationship between sex-bias magnitudes and distance from nearest CES using whole fly expression data from Ayroles et al., 2009. Using whole body expression from Ayroles et al., 2009 we found a significant positive correlation between sex-bias magnitude and distance from the nearest CES when considering all X-linked MBGs Click here for additional data file.Figure S6Relationship between sex-bias magnitudes and distance from nearest CES using head-specific expression data from Goldman et al., 2007. Using head-specific expression from Goldman et al., 2007 we could not find a significant positive correlation between sex-bias magnitude and distance from the nearest CES when considering all X-linked MBGs Click here for additional data file.Figure S7Relationship between sex-bias magnitudes and distance from nearest CES using whole fly expression data from Stolc et al., 2004. Using whole body expression from Stolc et al., 2004 we found a significant positive correlation between sex-bias magnitude and distance from the nearest CES when considering all X-linked MBGs Click here for additional data file.Figure S8Relationship between sex-bias magnitudes and distance from nearest CES using gonadectomized carcass expression data from Parisi et al., 2004 Using gonadectomized carcass expression from Parisi et al., 2004 we found a significant positive correlation between sex-bias magnitude and distance from the nearest CES when considering all X-linked MBGs Click here for additional data file."} +{"text": "Right ventricular (RV) function holds important prognostic value in both right- and left-sided acquired and congenital heart diseases. However, assessment of RV function remains challenging due to its complex chamber geometry and physiology. 4D flow CMR permits assessment of multidimensional intraventricular flow. We hypothesized that 4D flow specific markers of RV function can detect subtle impairment of RV function in primary left ventricular (LV) disease.Eighteen patients with mild ischemic heart disease and eleven healthy controls were enrolled. 4D flow CMR and standard morphological images were acquired on a 3T-scanner (Philips Ingenia). The patients were stratified into two groups (n=9 each) based on LV end-diastolic volume index (EDVI) from CMR: lower LVEDVI and higher LVEDVI, respectively. The RV volume was segmented from morphological images at end-diastole (ED) and end-systole (ES) and matched to the velocity data. Pathlines were emitted from the ED volume and traced forwards and backwards in time, to the time of ES, encompassing the cardiac cycle. The blood volume was separated into functional flow components Figure . The DirResults are displayed in Table These findings suggest that in primary LV disease, mild impairment of RV function can be detected by 4D flow CMR, but not by the majority of conventional CMR and echocardiographic indices. These flow-specific alterations propose novel pathophysiological aspects of interventricular function that could add to the assessment of integrated cardiac function in the context of medical, pacing and surgical strategies.The Swedish Heart-Lung Foundation."} +{"text": "Listeria and Yersinia gain initial entry by binding to host target cells and stimulating their internalization. Bacterial uptake entails successive, increasingly strong associations between receptors on the surface of bacteria and hosts. Even with genetically identical cells grown in the same environment, there are vast differences in the number of bacteria entering any given cell. To gain insight into this variability, we examined uptake dynamics of Escherichia coli engineered to express the invasin surface receptor from Yersinia, which enables uptake via mammalian host \u03b21-integrins. Surprisingly, we found that the uptake probability of a single bacterium follows a simple power-law dependence on the concentration of integrins. Furthermore, the value of a power-law parameter depends on the particular host-bacterium pair but not on bacterial concentration. This power-law captures the complex, variable processes underlying bacterial invasion while also enabling differentiation of cell lines.Pathogenic bacteria such as Uptake of bacteria by mammalian cells is highly variable within a population of host cells and between host cell types. A detailed but unwieldy mechanistic model describing individual host-pathogen receptor binding events is captured by a simple power-law dependence on the concentration of the host receptors. The power-law parameters capture characteristics of the host-bacterium pair interaction and can differentiate host cell lines. This study has important implications for understanding the accuracy and precision of therapeutics employing receptor-mediated transport of materials to mammalian hosts. Yersinia pseudotuberculosis and Listeria monocytogenes exploit a latent phagocytic activity in gut epithelia to pass into deeper tissues that are optimal for survival and proliferation /GFPo). (E) Simulations. Cell receptors are pre-incubated with 0.15 \u03bcg/mL of antibody for 60 minutes of simulation time followed by 90 minutes with the indicated MOI of bacteria. (Left) Relationship between bacterial uptake and A-R. (Right) Relationship between probability (uptake/MOI) and A-R calculated from simulated data. These results show that the dependence of bacterial uptake on the concentration of antibody-bound receptors is qualitatively the same as the dependence on total receptor Flow cytometry demonstrating that qualitative relationship between uptake and host receptors is recapitulated with a different bacterial strain. Experiments were performed as described in 1-integrin antibody and the indicated MOI of GFP-expressing E. coli also expressing INV from the plasmid pSCT7Inv. EM algorithm was used to assign cells to the GFP+ subpopulation (colored). (G) Fractional uptake. For each MOI sample in (F), data points in GFP+ mode within 2.5 standard deviations of the mean Alexa647 signal were extracted, placed into 15 contiguous bins, and the fraction of GFP+ cells were plotted. (H) Uptake and probability. Shown for each MOI sample in (F) are the (left) major axes and mean or (right) GFP values scaled by bacterial MOI.Click here for additional data file.S6 FigHeLa cells (A) were co-cultured with bacteria harboring pTetGFP alone (B), pTetGFP and pBACr-AraInv without arabinose induction (C), or with induction at the indicated concentrations of arabinose (D-G). The blue line denotes auto-fluorescent GFP signal from HeLa cells, and is overlaid for comparison with GFP signals in other conditions (shown in red). (TIF)Click here for additional data file.S7 Figinvasin expression induced by arabinose. Top10F\u2019 cells containing pBACr-AraINV and pTetGFP were either uninduced or induced with 0.1% arabinose and harvested after 5 hours. qPCR was conducted with primers targeting invasin and FFH was used as a reference gene for normalization. The fold change in the average expression level of invasin was then calculated using the standard curve method for relative quantification. The average expression level of invasin in the induced sample was 25 times greater than that in the uninduced sample. The average level of invasin expression is calculated from either 3 or 4 replicates.Quantification of (TIF)Click here for additional data file.S8 FigA) Flow cytometry. Mammalian cells were labeled with \u03b21-integrin antibody for 60 minutes, washed, then co-incubated with GFP-expressing E. coli also expressing Invasin from pBAC-AraInv (cultured in 0.1% arabinose) at the indicated MOI along with fluorescent-conjugated secondary antibody (Alexa647) for 90 minutes prior to washing. Scatter plots show the relationship between uptake (Log GFP) and \u03b21-integrins (Log Alexa647) in individual cells. (B) Statistical summary of data in (A). Shown are the major axes and mean of GFP+ subpopulations from (A). (C) Power-law parameters for calculated from samples presented in (A) and data in (B). (D) Flow cytometry. Indicated mammalian cells were co-cultured with the indicated GFP-expressing strain of E. coli as described in (A). Shown on right are the major axes of GFP+ subpopulations scaled by their respective MOI.((TIF)Click here for additional data file.S9 FigA) For each parameter, the zipper model simulates several perturbations over two orders of magnitude. This results in quasi-parallel lines consistent with the emergence of the power-law, analogous to that of B) Apparent linear correlation between fitted power-law parameters is defined by the quasi-constant locus , which determines the slope and intercept for the lines of best fit. Every point will fall along the same trajectory, as described by equation ((TIF)Click here for additional data file.S1 Text(DOCX)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file."} +{"text": "CI = 0.24\u20130.79) for the main outcome \u201caccuracy of naming\u201d in language assessment. No heterogeneity was observed (I2 = 0%). More multicenter RCTs with larger populations and homogenous intervention protocols are required to confirm these and the longer-term effects.Chronic communication impairment is common after stroke, and conventional speech and language therapy (SLT) strategies have limited effectiveness in post-stroke aphasia. Neurorehabilitation with non-invasive brain stimulation techniques (NIBS)\u2014particularly repetitive transcranial magnetic stimulation (rTMS) or transcranial direct current stimulation (tDCS)\u2014may enhance the effects of SLT in selected patients. Applying inhibitory NIBS to specific homologous language regions may induce neural reorganization and reduce interhemispheric competition. This mini review highlights randomized controlled trials (RCTs) and randomized cross-over trials using low-frequency rTMS or cathodal tDCS over the non-lesioned non-language dominant hemisphere and performs an exploratory meta-analysis of those trials considered combinable. Using a random-effects model, a meta-analysis of nine eligible trials involving 215 participants showed a significant mean effect size of 0.51 (95% Post-stroke aphasia accounts for around 85% of all cases of aphasia, is present in 21\u201338% of post-stroke patients and transcranial direct current stimulation (tDCS) may be viable approaches to augment the clinical efficacy of conventional SLT strategies. Two separate meta-analyses of published randomized controlled trials (RCTs) in post-stroke aphasia rehabilitation have recently evaluated the clinical efficacy of tDCS over the unaffected non-language dominant hemisphere as an adjunct to SLT for post-stroke aphasia rehabilitation, and where outcome measures are considered comparable, to combine these in an exploratory meta-analysis. This study allows us to specifically examine the neuroplastic process underlying aphasia recovery in adults considering the concept of reducing interhemispheric competition.The language network includes (i) Broca's and Wernicke's areas in the left hemisphere (dominant hemisphere); (ii) homologous areas in the right side of the brain (non-dominant hemisphere); (iii) the prefrontal and premotor areas in the frontal regions; and, (iv) the lower part of the parietal region increases cortical excitability and cathodal (c-tDCS) decreases cortical excitability .Intervention: inhibitory NIBS technique over the unaffected non-language dominant hemisphere as an adjunct to SLT.Control group: sham NIBS with SLT.Outcome measures were reported with continuous scales that evaluated the accuracy of naming (as degree of language impairment) immediately after treatment.One review author (BO) read the titles and abstracts of the records identified from the electronic searches and eliminated obviously irrelevant studies. Two independent authors (MO and BO) examined whether the potentially relevant publications fitted our inclusion criteria and assessed them for methodological quality and risk of bias using the 11 item PEDroI2 statistic, and this review considered 25% low, 50% moderate, and 75% high We identified 67 unique records from the database searches see . After fWe included six RCTs involving 183 participants investigating the effect of low-frequency rTMS over the non-lesioned hemisphere vs. sham rTMS (control group) in combination with SLT. Three of the included studies were conducted with German-speakers and used the Aachen Aphasia Test (AAT) as an outcome measure vs. sham tDCS (control group) in combination with SLT. Two of these three studies were randomized cross-over trials . Between study heterogeneity was negligible (I2 = 0%).Figure Our work complements recent systematic reviews of rTMS targeting the right IFG (mainly PTr). There is some indication that an inhibitory NIBS effect might be more relevant on the right homologs of Broca's area, right PTr but not POp we did not include any unpublished or non-English language studies; (2) too few inhibitory NIBS trials were included to generalize the results; (3) publication and selection bias might have affected our results.Our results indicate low levels of heterogeneity between studies in the meta-analysis with low This exploratory meta-analysis suggests potential benefits of low-frequency rTMS and c-tDCS over right hemispheric homologous language regions in post-stroke aphasia, though the effects of c-tDCS still need to be confirmed in RCTs with larger cohorts of patients and more homogenous protocols. Further RCTs of c-tDCS modulating the right Broca's homolog in the subacute phase may be relevant to allow more realistic comparisons vs. low-frequency rTMS. Additionally, RCTs directly comparing low-frequency rTMS vs. c-tDCS may provide insight in assessing which inhibitory technique is most clinically effective and best tolerated. More well-designed longitudinal studies and standardized region location methods are necessary to determine the effect duration and long-term impact in language recovery of both techniques.There is a lack of information comparing the clinical efficacy of trials of rTMS and tDCS as an adjunct to conventional SLT utilizing combinable protocols and outcome measures in post-stroke aphasia. By using stringent inclusion criteria, this exploratory meta-analysis combines existing randomized trials of these two inhibitory NIBS techniques in combination with SLT. Our results reflect that low-frequency rTMS and c-tDCS over the unaffected non-language dominant hemisphere may be a promising approach compatible with the concept of interhemispheric inhibition. Further multicenter RCTs with larger populations and homogenous intervention protocols are required to confirm these and the longer-term effects.AF was the principle investigator on one of the trials reviewed. During the time of the trial, AF was supported by German Science Foundation (Fl-379-4/2 379-8/1) and the Federal Ministry for Education and Science (FKZ 0315673A). The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Rapid drug desensitization (RDD) is widely used to re-introduce medications that have caused an IgE-mediated hypersensitivity in allergic patients. However, RDD protocols are largely based on empiric experience and few in vitro models have explored the rationale guiding the rate at which the dose should be increased, what the starting dose should be and how the time elapsed between doses affect the effectiveness of desensitization. This study addresses these issues in a new humanized in vitro model of rapid desensitization.Bone marrow-derived mast cells (BMMCs) from transgenic Balb/c mice expressing the human high affinity IgE receptor alpha chain (hFcRI) were sensitized with human serum containing IgE against dust mites. Sensitized BMMCs were challenged with Dermatophagoides pteronyssinus administered at once (activation) or through a step-wise progressive increase in concentration (desensitization). The influence of the concentration fold-increase per step, of the starting concentration and of the time elapsed between steps on the inhibition of mediator release (-hexosaminidase) induced by desensitization was assessed.Inhibition of -hexosaminidase release correlated with the fold-increase per step, the starting concentration and the time elapsed between steps. A two-fold increase per step protocol induced 81% inhibition compared to 51% (p=0.001) and 19% (p=0.003) for four-fold and ten-fold increase per step protocols. Maximal inhibition was reached with a starting concentration below the activation threshold (80%) and a progressive reduction in inhibition was observed with starting concentrations above that threshold. One-minute intervals between steps induced a small degree of inhibition (15%) that was maximal with 10-minute intervals (81%) (p<0.001).in vitro humanized mast cell/IgE-mediated desensitization model will allow evaluation of drug hypersensitivity patients and provide the basis for adjusting the fold-increase per step, the starting concentration and the time between steps necessary for safe rapid drug desensitization. These three factors independently influence the inhibition of mediators release and should be taken into account in all RDD protocols.This"} +{"text": "Alcohol consumption causes nicotinic acid deficiency. The present study was undertaken to determine whether dietary nicotinic acid supplementation provides beneficial effects on alcohol-induced endotoxin signaling and the possible mechanisms at the gut-liver axis. Male Sprague-Dawley rats were pair-fed the Lieber-DeCarli liquid diets containing ethanol or isocaloric maltose dextrin for eight weeks, with or without dietary supplementation with 750 mg/liter nicotinic acid. Chronic alcohol feeding elevated the plasma endotoxin level and activated hepatic endotoxin signaling cascade, which were attenuated by nicotinic acid supplementation. Alcohol consumption remarkably decreased the mRNA levels of claudin-1, claudin-5, and ZO-1 in the distal intestine, whereas nicotinic acid significantly up-regulated these genes. The concentrations of endotoxin, ethanol, and acetaldehyde in the intestinal contents were increased by alcohol exposure, and niacin supplementation reduced the intestinal endotoxin and acetaldehyde levels. Nicotinic acid supplementation upregulated the intestinal genes involved in aldehyde detoxification via transcriptional regulation. These results demonstrate that modulation of the intestinal barrier function and bacterial endotoxin production accounts for the inhibitory effects of nicotinic acid on alcohol-induced endotoxemia and hepatic inflammation. Alcohol abuse causes alcoholic liver disease (ALD), but the mechanisms of disease pathogenesis have not been well defined. Alcohol is metabolized mainly in the liver and the process of alcohol metabolism generates acetaldehyde and reactive oxygen species, which are critical mediators in the pathogenesis of ALD ,2,3,4. AEndotoxin is derived from the cell wall of Gram-negative bacteria that inhabit in the lumen of the distal intestine. Only trace amounts of endotoxin can penetrate through the intestinal barrier into the circulation system at physiological conditions . However+ [+, nicotinic acid deficiency may worsen alcohol-induced redox imbalance. Indeed, our previous report showed that nicotinic acid supplementation attenuated alcoholic steatosis through increasing cellular NAD+ level [Alcohol consumption is frequently associated with malnutrition, and the deficiencies of water-soluble vitamins and minerals are among the major changes detected in patients with ALD . Nicotin+ . Since VD+ level . The obj+ and CD163+ macrophages in the liver of the AF rats, which was alleviated by dietary nicotinic acid supplementation and qualitative (dysbiosis) changes of the GI microbiome have long been associated with liver diseases including ALD . DisturbBacteroidetes and higher ones of Proteobacteria in the colon as compared to alcoholic patients without liver disease [Bacteroidetes and Firmicutes phyla, with a proportional increase in the Gram-negative Proteobacteria and Gram-positive Actinobacteria phyla in mice feces [Proteobacteria phylum includes Gram-negative bacteria, most of which are regarded as pathogenic species. Therefore, alcohol exposure-induced Proteobacteria expansion in the intestine strongly indicates a link between alcohol-induced alterations of gut microbiota and the elevated plasma endotoxin level and hepatic inflammation. Indeed, dietary supplementation with probiotics corrected alcohol-induced perturbation of the intestinal microbiota in association with reduced plasma endotoxin level [Alcohol consumption not only results in quantitative changes of the intestinal microbiota, but also leads to an imbalance in the intestinal bacteria composition, namely enteric dysbiosis. Clinical studies have shown that patients with alcoholic cirrhosis had a lower proportion of disease . An animce feces . The Proin level . These oIn vitro studies have shown that acetaldehyde disassembles the distribution of tight junction proteins including occludin and ZO-1 and dissociates these proteins from the actin cytoskeleton in Caco-2 cell monolayers [ex vivo [Alcohol consumption increases the level of acetaldehyde in the intestinal lumen. Increasing evidence suggest that acetaldehyde may play a crucial role in mediating alcohol-induced disruption of the intestinal barrier . In vitrnolayers ,43. The [ex vivo . The pre[ex vivo ,46. Metr[ex vivo . On the [ex vivo . However[ex vivo ,50. AlthMale Sprague-Dawley rats were obtained from Charles River and treated according to the experimental procedures approved by the Institutional Animal Care and Use Committee of the institution. Three-month-old rats were pair-fed with the liquid control diet , alcohol diet or alcohol diet with nicotinic acid supplementation at 750 mg/L (AF/NA group), as described previously .The endotoxin levels in the plasma and intestinal contents were assessed by a chromogenic kinetic limulus ameobocyte lysate (LAL) assay kit following the manufacture\u2019s instruction. The concentration of endotoxin was expressed in endotoxin units (EU) per milliliter for plasma samples and EU per milligram weight of the intestinal contents for intestinal luminal samples.Total RNA was isolated from liver or ileum mucosa, and reverse transcribed with TaqMan Reverse Transcription Reagents . The gene expression of related mRNA was measured in triplicate by the comparative cycle threshold method using the 7500 real-time PCR system (Applied Biosystems). The primers sequences are shown in For detection of macrophages in the liver, cryostat sections of liver were incubated with anti-CD68 or anti-CD163 antibody overnight at 4 \u00b0C, respectively, followed by incubation with Alexa Fluor 594-conjugated donkey anti-mouse IgG for 30 min at room temperature. The nuclei were counterstained by 4',6-diamidino-2-phenylindole .The concentrations of ethanol and acetaldehyde in the intestinal luminal contents were measured by headspace gas chromatography-mass spectrometry as described previously.post hoc test. Differences between groups were considered significant at p < 0.05.All data are expressed as mean \u00b1 standard deviation (SD). The data were analyzed by analysis of variance (ANOVA) followed by Newman-Keuls\u2019 In summary, the present study demonstrates that dietary nicotinic acid supplementation ameliorates alcoholic endotoxemia and hepatic inflammation, which provides novel experimental evidence that nicotinic acid possesses therapeutic potential in treating ALD. The protection of nicotinic acid against ALD is at least partially achieved through modulation of the intestinal barrier function and the intestinal bacteria."} +{"text": "Tobacco mosaic virus (TMV) using dominant negative inhibition of myosin activity. We found that interference with the functions of three class VIII myosins and two class XI myosins significantly reduced the local and long-distance transport of the virus. We further determined that the inactivation of myosins XI-2 and XI-K affected the structure and dynamic behavior of the ER leading to aggregation of the viral movement protein (MP) and to a delay in the MP accumulation in plasmodesmata (PD). The inactivation of myosin XI-2 but not of myosin XI-K affected the localization pattern of the 126k replicase subunit and the level of TMV accumulation. The inhibition of myosins VIII-1, VIII-2 and VIII-B abolished MP localization to PD and caused its retention at the plasma membrane. These results suggest that class XI myosins contribute to the viral propagation and intracellular trafficking, whereas myosins VIII are specifically required for the MP targeting to and virus movement through the PD. Thus, TMV appears to recruit distinct myosins for different steps in the cell-to-cell spread of the infection.Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles in the specific infection steps have not been addressed. Here we investigated the replication, cell-to-cell and systemic spread of N. benthamiana myosins during the infection by Tobacco mosaic virus (TMV). Our results show that class XI myosins play specific roles in the reproduction and intracellular movement of TMV in association with the dynamic endoplasmic reticulum network, whereas class VIII myosins support the specific targeting of the viral movement protein to plasmodesmata and thus the cell-to-cell movement of the virus. Together these results indicate that TMV interacts with distinct myosins during specific infection steps.Viruses are parasites that require the host cell machinery for their propagation within and between cells. Myosins are molecular motors involved in the trafficking of cargos along actin filaments. Plant viruses have evolved to borrow this transport mechanism to aid their infection and spread within the plant. However, little is known about which of the many plant myosins are essential and at which specific steps they act to support virus infection. Here we investigated the role of different Tobacco mosaic virus (TMV) exemplifies a widespread mechanism in which the MP acts as a chaperone for the viral RNA and increases the SEL of PD. Another important mechanism involves reorganization of the PD structure and is exemplified by Grapevine fanleaf virus (GFLV). The MP of this virus assembles into tubules within the PD cavity and thus forms a dedicated transport structure for the passage of assembled virions Viruses are obligate intracellular parasites that depend on host cell functions for replication and movement. Upon infection of a plant cell, viruses replicate and spread to the adjacent cells (cell-to-cell movement) to reach the phloem and infect distal parts of the plant (systemic movement). Cell-to-cell movement occurs through specialized channels in the cell wall called plasmodesmata (PD). PD provide symplastic continuity of the cytoplasm, endoplasmic reticulum (ER) and the plasma membrane (PM) between cells and regulate the intercellular transport of macromolecules by dilation or closure, i.e. through modification of their size exclusion limit (SEL) Phylogenetic analysis revealed that all plants encode two distantly related classes of unconventional myosins, VIII and XI, with reference plant Arabidopsis possessing four myosins VIII and 13 myosins XI In contrast, functions of the myosins XI are relatively well investigated using dominant negative inhibition and gene knockout approaches. It was found that several of these myosins provide overlapping contributions to both the polar and diffuse cell growth, as well as to plant growth and development Beet yellows closterovirus, a virion component required for the viral cell-to-cell movement. Subsequent studies showed that other diverse viruses also require either class VIII or class XI myosins for their movement Several studies indicated that myosins exert important functions in the PD targeting of viruses. First experimental support came from Avisar et al. To gain deeper mechanistic insight into the contributions of myosin motors to TMV infection, we investigated the roles of class VIII and XI myosins using dominant negative inhibition, which is achieved by overexpression of the myosin tails encompassing dimerization and cargo-binding domains. Although the mechanistic details of dominant-negative inhibition are not entirely understood, the inhibitory effect is likely caused by the retention of the cargo-binding activity and lack of the head domain possessing the motor and actin-binding activities. Thus, in binding cargo but not actin the expressed myosin tails sequester the cargo without contributing to its transport. In addition, by forming dimers with endogenous myosins without contributing a motor domain, the expressed tails may dominantly block the processivity of the associated myosin and, thus, cargo transport along the actin filaments. Dominant negative inhibition generally results in stronger functional effects than inactivation of individual myosins N. benthamiana plants were inoculated with TMV-GFP, an engineered TMV variant expressing GFP in place of the CP N. benthamiana myosin tail in one half of the leaf blade and for expression of free RFP as control in the other half . As expected, no effect on the subcellular distribution of MP:GFP was observed upon co-expression with either RFP or with the myosin XI-F tails . AlthougN. benthamiana plants expressing an ER marker (GFP:HDEL) revealed that the MP aggregates are associated with ER and therefore are likely ER-derived assays. Upon bleaching the MP:GFP fluorescence at PD, the rate of the MP:GFP fluorescence recovery over time reflects the efficiency with which MP:GFP is delivered to PD. Using the approach outline above, we also studied the role of class VIII myosins in the PD localization of MP. Strikingly, expression of the myosin VIII-1, VIII-2 or VIII-B tails drastically reduced the localization of MP at PD and caused redistribution of the MP along the cell wall , MP:RFP To further investigate the TMV MP redistribution upon co-expression with myosin VIII-B tails, we in addition co-expressed remorin:GFP, which is targeted to PD and to plasma membrane (PM) lipid rafts independently of myosins XI and VIII Interestingly, myosin VIII tails were previously reported to localize to specific regions at the PM TMV encodes two replicase subunits, the 183 kDa (183k) and the 126 kDa (126k) proteins. The larger subunit is produced by read-through of an amber stop codon that terminates the translation of the shorter protein and harbors the RNA-dependent RNA polymerase (RdRp) domain required for replication. Although the 183k subunit is sufficient for TMV replication, the 126k subunit increases the replication rate Many plant and animal viruses depend on cytoskeletal elements for the entry, replication and movement within and between the cells Tobacco rattle virus. This work implied a significant role of myosin XI-2 in TMV cell-to-cell movement, whereas reduced levels of the myosins XI-F, VIII-1, or VIII-2 had no apparent effect on this process. It should be noted, however, that research into myosin functions is significantly impeded by functional redundancy of these molecular motors such that even complete elimination of the individual myosins XI in corresponding gene knockouts results in little or no phenotypic effect Recently, Harries et al. modus operandi of the dominant negative inhibition is not entirely understood. However, we show here that the expression of myosin tails does not interfere with the accumulation of corresponding endogenous myosins and used for agroinfiltration with agrobacteria grown to a final optical density (OD 600 nm) of 0.2 for expression of MP:GFP, MP:RFP and remorin:GFP and of 0.4 for expression of myosin tails The binary vectors designed to express HA-epitope-tagged N. benthamiana leaf disks in Laemmli buffer, separated by 12.5% SDS-PAGE and blotted onto polyvinylidene difluoride membrane (Millipore). Immunoblot labeling was performed with anti-HA-peroxidase antibodies (Sigma-Aldrich) or with anti-GFP antibody (Invitrogen) and peroxidase-labeled secondary antibodies (Invitrogen) for luminescence detection (Roche).Total protein extracts were obtained by grinding N. benthamiana leaves transiently expressing RFP in one half leaf and myosin tails in the other half were taken under UV light at 4 dpi, and the level of fluorescence as well as the areas of fluorescent infection sites in each half leaf were measured using ImageJ (1.47s) software. All imaging was conducted under identical illumination and exposure conditions to allow comparisons. Mean values of areas of at least 23 infection sites per treatment and representing three independent experiments were calculated. The mean values of infection site areas in half leaves expressing myosin tails were compared to mean values of infection site areas in half leaves expressing free RFP. The same infection site areas were used to measure and compare the GFP fluorescence intensity between half leaves expressing myosin tails and free RFP. To compare virus replication, the fluorescence intensity of the infection sites in leaf areas expressing myosin tails was normalized to the fluorescence intensity of the infection sites in leaf areas expressing free RFP. Statistical analyses were performed with R software. In addition, statistical ANOVA or Student's t-tests where applied where appropriate.Photographs of TMV-GFP fluorescent infection sites in t-test.Virus quantification was carried out according to Niehl et al. To visualize PD-located callose, leaf disks were vacuum infiltrated with aniline blue solution (0.1% aniline blue in 67 mM phosphate buffer pH 8). Leaf disks were incubated in the dark at room temperature for 15 minutes before imaging using a Zeiss LSM780 laser scanning confocal microscope.Excised leaf disks were mounted on a microscope slide and vacuum infiltrated with water and epidermal cells imaged using a Zeiss LSM780 laser scanning confocal microscope under multitrack mode. Excitation/emission wavelengths were 488 nm/505 to 545 nm for GFP and 543 nm/585 to 615 nm for RFP. Confocal images were processed using ImageJ (1.47s) software.FRAP was performed with a Zeiss LSM780 laser scanning confocal microscope. PD labeled with MP:GFP in leaves expressing myosin tails or RFP as control were imaged with a 488 nm laser at 20% intensity before bleaching. Selected PD were then bleached using the 488 nm laser at 100% intensity. Subsequently, the fluorescence of the photobleached PD was recorded each minute during 50 min at 20% 488 nm laser intensity. Images were analyzed with ImageJ (1.47) software. To obtain recovery profiles corrected for potential X, Y and Z-axis drift during the acquisition time, serial Z sections over a typical distance of 6 \u00b5m were acquired at each time point. Maximum intensity projections were prepared for every time point across the time series. The projected images were then further registered with the StackReg ImageJ plugin http://biotools.umassmed.edu/bioapps/primer3_www.cgi) and specific for the myosin motor region, which is not present in the expressed myosin tails. . Aliquots of reverse transcription products from myosin XI-2 or VIII-B tails- or their RFP control-treated samples were used to amplify the corresponding endogenous myosins and GAPDH as housekeeping gene. Aliquots taken after 30 and 40 PCR cycles were loaded in a 2% agarose gel and stained with ethidium bromide.Leaf disks of agroinfiltrated leaf areas expressing myosin XI-2 or VIII-2 tails at 2 dpa were used to extract total RNA with TR-Reagent (SIGMA) according to the manufacturer's instructions. Leaf disks of agroinfiltrated leaf areas expressing RFP were used as control. After DNase treatment, the total RNA was used for reverse transcription using random hexamer primers. The subsequent PCR reactions were carried out with specific primers that were designed by Primer3 software , myosin VIII-2 tails (B), or VIII-B tails (C) at 2 dpa. Scale bars, 20 \u00b5m.(TIF)Click here for additional data file.Figure S2Expression of myosin XI-F, VIII-1, VIII-2 or VIII-B tails does not disrupt the normal subcellular localization of 126k:GFP. A-D, Localization pattern of 126k:GFP in N. benthamiana epidermal cells in the presence of myosin XI-F tails (A), myosin VIII-1 tails (B), myosin VIII-2 tails (C), or myosin VIII-B tails (D). Proteins were expressed by co-agroinfiltration and observed at 2 dpa. Scale bars, 20 \u00b5m.(TIF)Click here for additional data file.Figure S3The 126k:GFP and the MP:RFP colocalize near the nucleus upon expression of myosins XI-2 and XI-K tails. A-C, 126k:GFP (A) and MP:RFP (B) colocalize in the vicinity of the nucleus upon expression of myosin XI-2 tails (C). D-F, 126k:GFP (D) colocalizes with the MP:RFP (E) in some aggregates . Proteins were expressed by co-agroinfiltration and observed at 1 dpa. Scale bar: 10 \u00b5m.(TIF)Click here for additional data file.Figure S4Time-lapse video frames showing expression of the 126k:GFP and the actin marker ABD:RFP in the absence (A-D) and presence of myosin XI-2 tails (E-H). In the absence of myosin XI-2 tails the 126k:GFP-containing aggregates move along actin . Expression of myosin XI-2 tails impaired the movement of the 126k:GFP-containing aggregates along actin . Proteins were expressed by co-agroinfiltration and observed at 2 dpa. Scale bar, 10 \u00b5m.(TIF)Click here for additional data file.Figure S5Expression of myosin tails does not trigger silencing of the corresponding endogenous myosins. A, immunoblot analysis of leaf sections using HA- antibodies revealed the expression of the HA-tagged myosin tails at 2 dpa. Immunostained bands corresponding to class XI (\u2248100 kDa) and class VIII (\u224840 kDa) myosin tails are marked by asterisks. Coomassie blue staining (bottom panel) is shown as loading control. B, semiquantitative RT-PCR analysis of endogenous myosin mRNA. Expression of myosin XI-2 and VIII-2 tails, which are representatives of their corresponding myosin class, did not trigger silencing of the endogenous corresponding myosins in the same leaf areas also used for immunoblot analysis (A). The expression of endogenous myosins remains similar as in the control, RFP-expressing tissue.(TIF)Click here for additional data file.Video S1Live video microscopy of reduced ER dynamics upon transient expression of myosin XI-2 tails.(AVI)Click here for additional data file.Video S2Live video microscopy showing drastic reduction in ER dynamics upon transient expression of myosin XI-K tails.(AVI)Click here for additional data file.Video S3Live video microscopy showing the absence of changes in ER dynamics upon transient expression of RFP.(AVI)Click here for additional data file.Video S4Representative live video microscopy showing the absence of changes in ER dynamics upon transient expression of myosin XI-F tails. A similar absence of effects on the structure and dynamic behavior of the ER was observed upon transient expression of myosins VIII-1, VIII-2 or VIII-B tails.(AVI)Click here for additional data file."} +{"text": "Larimichthys crocea) genome were identified using restriction-site associated DNA sequencing (RAD-seq). Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04%) of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs) evenly distributed across the large yellow croaker ( Larimichthys crocea ) is a temperate-water migratory fish that is mainly distributed in the coastal areas of East China and Southeast China . We . We 9]. A high-density genetic linkage map of 5451.3 cM was constructed. Immunity-related genes (1274) and hypoxia-related genes (195) were mapped to the 24 pseudo-chromosomes of large yellow croaker. These results provide a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits such as disease- and hypoxia-resistances."} +{"text": "In the setting of acute myocardial infarction (AMI), therapeutic and spontaneous reperfusion of ischemic myocardium can lead to interstitial intramyocardial hemorrhage (IMH) which is associated with microvascular obstruction (MVO) and subsequent adverse clinical outcomes. Imaging without contrast agents (native imaging) can be used in AMI patients for additional myocardial tissue characterization. Native T1 and T2 weighted imaging and quantitative measurements have been reported to detect myocardial edema and depict the myocardial area at risk. IMH affects T1, T2 and T2* relaxation as well as susceptibility and the feasibility of several MR image contrasts has been demonstrated for the depiction of IMH. Susceptibility weighted imaging (SWI) uses a type of image contrast different from traditional spin density, T1 or T2 weighted MR imaging.In the present work, we report our experience with myocardial SWI imaging (combined gradient-echo magnitude and phase imaging) for the detection of IMH. We propose TE image averaging and gray-scale inversion as a means of providing a single image with good image SNR and excellent contrast for the detection of IMH.Eleven AMI subjects were studied at 1.5T before contrast agent administration with a dark blood double inversion recovery multiple spoiled gradient-echo sequence and conventional CINE and late gadolinium-enhanced (LGE) imaging. Magnitude, susceptibility weighted and TE-averaged images were reconstructed from raw data k-space data. Contrast and signal-difference-to-noise were measured and compared between SWI methods for IMH detection. Volumes of LGE, IMH and MVO were measured and reported as a percentage of LV myocardial volume.There were six patients with microvascular obstruction (MVO) and four patients with IMH detected by TE-averaged SWI imaging. TE-averaged SWI images from a representative AMI subject with IMH are given in Figure TE-averaged SWI imaging is a promising method for myocardial tissue characterization in the setting of AMI for the detection of IMH. Along with gray-scale colormap inversion, it combines not only magnitude and phase information, but also images across TEs to provide a single image sensitive to IMH with characteristics similar to LGE imaging.American Heart Association scientist development grant (0635029N)."} +{"text": "Temporal lobe epilepsy represents a high proportion of whole epilepsy patients. Medial temporal lobe epilepsy (MTLE) is generated from internal structures like hippocampus, and patients with MTLE are poorly controlled by antiepileptic drugs . RecentlIn this paper, we propose a hippocampal network model which portrays seizure-like events (SLEs) recorded in in-vitro experiments. The model is composed of excitatory and inhibitory neurons interconnected following the well-known synaptic pathway to form a small world network . Each neThe effectiveness of the model is confirmed by comparing the simulation results with experimental data which were recorded in rat hippocampal slice in 4-AP bath application using micro-electrode array (MEA). Below Figure"} +{"text": "Active soluble Fas ligand (sFasL) accumulates in lung fluid of patients with acute respiratory distress syndrome (ARDS), and causes apoptosis and inflammation in lung epithelial cells . AlveolaDetermine whether sFasL increases protein permeability of the alveolar epithelium by mechanisms involving disruption of the tight junction proteins in ARDS.lpr (Fas deficient) mice were treated with an intratracheal dose of rh-sFasL (25 ng/g b.w.) or PBS, and the lungs were studied 16 h later. We performed immunofluorescence double staining for the detection of tight junction proteins (ZO-1 and Occludin) and apoptosis .Primary human pulmonary alveolar epithelial cells were cultured in permeable transwell chambers. After reaching maximal confluency, the cells were incubated for 0.5, 1, 2 or 4 h with medium with or without human recombinant sFasL (rh-sFasL). Protein permeability of the cell monolayer was measured by using fluorescein-labeled albumin (FITC-Albumin). C56BL/6 wild-type mice and lpr mice, altered the distribution of ZO-1 and Occludin, and induced apoptosis in cells of the alveolar walls only in wild-type but not in lpr mice.In vitro, human sFasL increased protein permeability of the alveolar epithelial cell monolayer , altered the distribution of the tight junction proteins ZO-1 and Occludin, and induced apoptosis. In vivo, intratracheal instillation of rh-sFasL, which increases pulmonary protein permeability in wild-type but not in in vitro and in vivo. This increased permeability was associated with disruption of tight junctions and apoptosis. These results provide a mechanism that could be targeted for the prevention of lung edema in ARDS.Activation of the Fas/FasL system increased protein permeability of the pulmonary alveolar epithelium"} +{"text": "The delivery of systemically administered drugs and genes to the CNS is hindered by both the blood-brain barrier (BBB), which limits transport from the bloodstream to the brain to only a few privileged molecules, and the nanoporous electrostatically charged tissue space, denoted here as the \u201cbrain tissue barrier\u201d (BTB). Our group engineers targeted drug and gene delivery approaches, capable of overcoming both of these physical barriers, for the treatment of brain tumors and neurodegenerative diseases. We focus on nanoparticle (NP) delivery systems, as they offer the potential for enhanced transfection efficiencies and controlled-drug release.To deliver drug- and gene-bearing NPs across the BBB, we use focused ultrasound (FUS) and contrast agent microbubbles (MBs). FUS may be applied using either MR-guidance or with a simple table-top system. We and others have shown that activating MBs with FUS yields safe and transient BBB opening in the FUS focal zone. Technologies for overcoming the BTB center on coating the drug and gene bearing NPs with an extremely dense brush layer of polyethylene glycol (PEG). NPs are injected at the time of BBB opening to permit their delivery to the CNS.Drug Bearing NP Delivery \u2013 PEG-coated polystyrene (PS) tracer NPs (60 nm diameter) and biodegradable polylactide-co-glycolide (PLGA) NPs (75 nm) were engineered to penetrate brain tissue and then delivered across the BBB in rats using 1 MHz FUS. NPs were delivered to endothelium and as \u201cclouds\u201d to brain tissue. PS-NP delivery through the brain continued over 24 hours, yielding enhancements of cloud size and intensity Figure . FUS at Gene Bearing NP Delivery \u2014 We used a blend of non-PEGylated and highly PEGylated polymers at an optimized ratio to engineer brain-penetrating DNA NPs with a polyethylenemine (PEI) core polymer. We delivered PEI-NPs (~50 nm in diameter) carrying either luciferase or mCherry plasmid DNA (driven by the unmethylated CpG-free \u03b2-actin promoter) across the BBB in rats using MR-guided FUS and MBs. Robust luciferase transgene expression, corresponding to a single focal site of FUS exposure, was visible (Figure e Figure , and thee Figure . After de Figure . mCherrye Figure , demonst"} +{"text": "Venoarterial (VA) ECMO is used for mechanical support in patients with cardiogenic shock (CS) unresponsive to medical therapy. Long-term survival and quality of life after hospital discharge have not yet been well analyzed.We performed a retrospective observational study of patients admitted to the ICU for refractory CS from January 2010 to November 2014. Patients with postcardiotomy and/or post-transplant CS were excluded. Demographic, clinical and biochemical variables were collected. Continuous variables are presented as mean (standard deviation) and categorical variables as percentage. Long-term outcome and quality of life were assessed during scheduled follow-up evaluations or telephonic interviews.We analyzed 23 consecutive patients undergoing VA ECMO for refractory CS. Etiologies of cardiac collapse were: 11 acute myocarditis, five acute myocardial infarctions and seven acute decompensation of chronic cardiomyopathies (CCM). Thirteen patients died during the hospital stay and 10 survived. The main cause of ICU death was progressive multiple organ dysfunction (12/13). Baseline variables are presented in Table VA-ECMO is an effective treatment tool for refractory CS in patients with acute life-threatening heart failure. Patients affected by acute decompensation of CCM had poorer outcomes characterized by multiple organ dysfunction, as already known in the literature."} +{"text": "Core biopsies of the prostate and both seminal vesicles revealed diffuse involvement by small cell carcinoma. Therapy could not be instituted due to a rapid deterioration in the patient\u2019s clinical condition.Extrapulmonary primary small cell carcinomas arising from the urogenital tract is infrequent. It can rarely arise from the prostate and even more rarely from the seminal vesicles. We present a 79-year-old male who was admitted due to acute renal failure with a history of radical radiotherapy for prostate adenocarcinoma 13 years ago. The prostate specific antigen level was not elevated. An abdominopelvic computed tomography (CT) scan showed markedly enlarged seminal vesicles causing bilateral ureteral obstruction and a mildly enlarged prostate. Further evaluation with fluorine-18-fluorodeoxyglucose ( Nevertheless, the primary site can rarely be outside the lungs and pleural spaces, which are referred to as extrapulmonary small-cell carcinoma (EPSCC) . Herein,18F-FDG PET/CT demonstrated intense 18F-FDG uptake (SUVmax: 7.2) throughout the bilateral markedly enlarged seminal vesicles with diffuse involvement of the prostate (18F-FDG PET/CT. Percutaneous core biopsies of the prostate and both seminal vesicles revealed diffuse small cell carcinoma (A 79 year-old male was admitted with acute renal failure with a history of radical radiotherapy for prostate adenocarcinoma 13 years ago. The prostate specific antigen level was not elevated. The abdominopelvic CT scan showed markedly enlarged seminal vesicles occupying most of the pelvic cavity causing bilateral ureteral obstruction, and loss of fat plane between seminal vesicles and a mildly enlarged prostate gland indicating local invasion of the tumor. prostate . There warcinoma . The pat18F-FDG uptake in primary small cell carcinoma of urogenital origin indicates that there may be a role for 18F-FDG PET/CT scan in the staging and probable response assessment of EPSCC.Small-cell carcinoma usually originates from the lung and accounts for 18% of lung cancers, but very rarely the primary site is detected outside the lungs and pleural spaces, which is called EPSCC . Seminal"} +{"text": "Systems neuroscience has identified a set of canonical large-scale networks in humans. These have predominantly been characterized by resting-state analyses of the task-unconstrained, mind-wandering brain. Their explicit relationship to defined task performance is largely unknown and remains challenging. The present work contributes a multivariate statistical learning approach that can extract the major brain networks and quantify their configuration during various psychological tasks. The method is validated in two extensive datasets (n = 500 and n = 81) by model-based generation of synthetic activity maps from recombination of shared network topographies. To study a use case, we formally revisited the poorly understood difference between neural activity underlying idling versus goal-directed behavior. We demonstrate that task-specific neural activity patterns can be explained by plausible combinations of resting-state networks. The possibility of decomposing a mental task into the relative contributions of major brain networks, the \"network co-occurrence architecture\" of a given task, opens an alternative access to the neural substrates of human cognition. Assuming the central importance of canonical brain networks for realizing human cognitive processes, the present work demonstrates the quantifiability of relative neural networks involvements during psychological tasks. This is achieved by a machine-learning approach that combines exploratory network discovery and inferential task prediction. We show that activity levels of network sets can be automatically derived from task batteries of two large reference datasets. The evidence supports the often-held suspicion that task-specific neural activity might be due in large part to distinct recombinations of the same underlying brain network units. The results further discourage the frequently embraced dichotomy between exteroceptive task-associated versus interoceptive task-unspecific brain systems. Standard fMRI brain scans can thus be used to reconstruct and quantitatively compare the entire set of major network engagements to test targeted hypotheses. In the future, such network co-occurrence signatures could perhaps be useful as biomarkers in psychiatric and neurological research. There is uncertainty about pertinent concepts of functional brain architecture. Systems neuroscience has established the existence of a set of fluctuating yet robust brain networks in humans , 2. It hdescriptive statistical analyses used by many previous neuroimaging studies are extended in the present work by introducing an inferential statistical approach for the network involvement during task and at rest. On the other hand, the proposed approach combines deriving and predicting mutually overlapping network patterns , whereas existing neuroimaging methods frequently focus on non-overlapping voxel and region patterns.The central hypothesis of the present work is that network patterns can effectively describe fMRI data in both a resting mind-wandering and goal-directed task context. We introduce a methodological approach that enables formal assessment of this task-rest correspondance. On the one hand, the mostly constellation of relative network involvements as an under-appreciated unit of functional brain organization.Identical neural networks have repeatedly been observed across cognitive domains using diverging neuroscientific methods. These observations prompted widely-adopted notions, including for instance the \u201cdefault-mode network\u201d , \u201csalienIn line with this contention, the onset of a given cognitive task might induce characteristic changes in functional coupling of large-scale networks. For instance, the salience network and dorsal attention network tend to display blood-oxygen-level-dependent (BOLD) signal increases due to experimental stimulation, while the default-mode network often decreases across a wide range of tasks . WhetherThe neuroarchitectural difference underlying the task behaviors and the idling brain has been investigated by what one can summarize as \u201cdichotomy\u201d and \u201cmanifold\u201d hypotheses. The dichotomic view advocates functional antagonism between so-called \u201ctask-positive\u201d and \u201ctask-negative\u201d neural networks . Task-pIn contrast, the \u201cmanifold\u201d view advocates a fluctuating equilibrium of functionally distinct large-scale networks that is perturbed at task onset . This ffunctional integration account of human brain organization, it will also be explicitly contrasted with the functional segregation account more frequently embraced by previous fMRI studies. Functional integration emphasizes brain function as an emergent property of complex connections between distinct brain regions based on the vectorized SVM weights of all 18 classes. This parsimony-based metric of model \"effectiveness\" ranged between 8.55 and 13.19 for ICA and sparse PCA (a lower number indicates a sparser weights of the SVM model), whereas it ranged between 13.33 and 14.51 for PCA and factor analysis. We thus found that activity maps can be described more correctly (according to model performance metrics) and more effectively (according to a model sparsity metric) by the learned network sets based on ICA and sparse PCA compared to components obtained from PCA and factor analysis. More generally, the observation of many zeros among the averaged model weights suggests that the \u201ctrue\u201d decomposition of task activity maps is a linear combination of few network components. Indeed, 18 diverse cognitive tasks could be very well distinguished solely based on 40 loadings of large-scale networks. The approach has been validated using four different decomposition methods in both HCP [We first assessed the predictive accuracy of network co-occurrence models across methodological choices and datasets Figs \u20135. Withoboth HCP and ARCHAfter validating the proportional implication of large-scale networks as a salient property of task activity, we aimed at the interpretability of the network co-occurrence models from task maps (without any recourse to rest maps). The 18-task classification problem was solved by l2-penalized SVM of the selected k most important network loadings for each task . As an efit for purpose [network- and region-based reconstruction performances were compared to fitting the same l1-penalized support vector machine models on all 61,472 gray-matter voxels without the initial feature-learning step, that is, without recourse to global spatiotemporal components or local voxel clusters. Neurobiologically uninformed support vector machines applied to the raw voxel features (89% out-of-sample performance for HCP and 93% for ARCHI), otherwise identical to above classifier training by multi-class, one-versus-rest, and leave-one-participant-out design, achieved correlations between z-scored class average maps and z-scored model weights of r = 0.24 (across-task SD = 0.04) for HCP and r = 0.11 (across-task SD = 0.05) for ARCHI. Consequently, cluster-based and voxel-based multivariate predictive models were less successful in capturing the original task activity patterns than network co-occurrence models.We then inspected the learned classification models based on task-derived network dictionaries as to whether they were purpose . The fitAfter evaluating network co-occurrence models, they were put into practice by testing explicit hypotheses about the difference between functional brain architecture of the human brain during tasks and at rest. In contrast to the above results, these experiments also performed regions/network discovery step and region/network-based task classification step based on non-identical data: HCP task maps, ARCHI task maps, and rest maps Figs \u20138.We formally tested whether given task activity patterns can be accounted for by network sets obtained from a diverging task battery and from the task-free resting brain Figs and S12.between canonical brain networks is more context-sensitive than functional coupling within a same network [We confirm the central hypothesis that fMRI brain activity can be formally assessed in sets of macroscopical network units in a goal-direct task and an idlying rest mindset. The proposed statistical approach effectively exploits the recently increasing neurobiological evidence that functional coupling network \u201317.Two large datasets allowed for direct comparison of 36 diverse experimental tasks. A large proportion of activity patterns evoked by experimental tasks is shown to reflect combinations of stereotypical network patterns. Despite their diverging statistical assumptions , all used decomposition methods allowed for generative network models that can express neural activity maps as combinations of spatiotemporal activity components. We thus computed neurobiologically interpretable stratifications of large-scale network recruitment specific to cognitive tasks without relying on assumptions from cognitive theory cf. . We valiThe novelty of the present approach consists in direct modeling of task activity by combinations of canonical brain networks and formal inference on changed neural activity of distinct networks. The involvement of major brain network ensembles in a given psychological task can be explicitly quantified at once and used for model-based prediction in independent or future neuroimaging studies. The term \"network co-occurrence\" thus refers to the signature of network involvements specific to a given psychological task.Functional coupling between brain regions and coupling changes between task and rest has been investigated in several previous studies e.g., , 56, 57), 5756, 5unconstrained mind-wandering by imposing this behavior on the participants as the task to follow while lying in a brain imaging scanner cf. [exploratory, hypothesis-free fashion [inference on the implication of the ensuing network maps during psychological experiments [network notions have so far hardly been formally tested for generalization to the population-level.Up to now, the relationship between brain activity during task and rest has predominantly been addressed by three neuroscientific tools : i) targnner cf. , 59, 60.nner cf. . Seed conner cf. , 108. Mo fashion . There ieriments , 47. Alteriments \u2013100, conIt is an important limitation of the presented statistical framework that it ignores local within-network processes. The over-simplified quantification of brain activity at the network-level cannot account for relevant brain signal differences in circumscribed brain regions. Network co-occurrence modeling is hence insensitive to activity variance due to less distributed subnetwork effects underlying psychological tasks , 107. Firest network dictionaries have been shown to reflect sufficiently rich directions of variation to encode and reconstruct whole-brain task images with minimal information loss. It follows that a single major brain network may not be task-specific but the entire activity pattern of the various brain networks may be a distinctive correlate underlying each cognitive process. Indeed, an interplay of limited entities generates an infinity of different observations in numerous natural systems [In the present study, the reconfiguration of large-scale networks was identified as a characteristic property of fMRI activity during experimental tasks. Multivariate decomposition of neural activity into 40 major networks allowed distinguishing 18 typical tasks in up to 90% (HCP dataset) and 93% (ARCHI dataset) of unseen activity maps. Selecting only the loading of the single most distinctive of 40 total networks for each task, classification still scored at up to 83% (HCP dataset) and 72% (ARCHI dataset). In particular, ICA and sparse PCA appeared most successful in searching the space of plausible network co-occurrence architectures. Neurobiological pertinence was suggested by overall best task classification scores, highest parsimony in model parameters, and model-derived recovery of most realistic task activity maps. This suggests that the underlying statistical assumptions of these models reverse-engineer critical properties of brain network constellation. In this way, present results would favor large-scale patterns to parsimoniously distribute in space (reflected by sparse PCA models) and vary independently (reflected by ICA models), whereas orthogonality (reflected by PCA) and different variances seem less important. Notably, attempting the reconstruction of statistically coherent source signals operates with a network definition that is not strictly neurobiological in nature . Neverth systems , formali systems . This coFinally, we have demonstrated the usefulness of constructing and comparing network co-occurrence models to test specific hypotheses about network architecture in fMRI data. We tested between what one can summarize as \u201cdichotomy\u201d and \u201cmanifold\u201d hypotheses on the neuroarchitectural difference between task behaviors and the idling brain . While tOnly recently, systems neuroscience has transitioned the interpretational focus from regional segregation to network integration , 37, 72.www.humanconnectomeproject.org). HCP is an international long-term project dedicated to network exploration [The first of two task batteries was drawn from the Human Connectome Project . Each of the task and rest maps was hence represented by 61,472 voxels with z-values in gray matter.unsupervised discovery of latent structure by matrix decomposition and clustering methods. The components of variation identified in the data allowed for feature engineering from biological structures. In the second step, we applied supervised classification algorithms to the other half of the activity maps to predict cognitive tasks. The winning models for classifying 18 cognitive tasks were compared by cross-validation. This inferential statistical framework is the gold standard to obtain an unbiased estimate of how well a trained classifier generalizes beyond the data samples at hand [leave-one-participant-out cross-validation scheme ensured model fitting of task effects, rather than interindividual differences. In the third and last step, the averaged winning models were back-projected into realistic task activity maps as face validity for the reduced representation of task activity patterns.Data folding and model selection were performed in the following fashion. In the first step, one half of the task datasets and the entire rest dataset were used for at hand , 81. TheThe first step uncovered hidden structure in large quantities of neural activity maps. To this end, each dataset was used to capture the main directions of variation in the activity maps [sparse PCA was used to separate the activity maps into network components with few regions [factor analysis (FA) generalizes (probabilistic) PCA by a heteroscedastic noise model [ormation . This itormation . Second,ity maps . This noity maps . An implity maps performe regions , which s regions . Fourth,se model . Similarall the original voxel signals.Note that all four decomposition methods implicitly assume large variance to be indicative of impor- tant structure. They reflect different ways to model sets of partially-overlapping major brain networks without access to any task information. All decompositions are soft in that each voxel with its BOLD signals can be part of the support in more than one network component. For most but not all (sparse PCA) decompositions, the ensuing components are linear combinations of Clustering into brain regions. The decompositions into spatially overlapping network components were evaluated against clustering of the same data into non-overlapping regional components. That is, the similarity between voxels in neural activity changes across maps was indicative of coherent regional compartments, rather than distributed spatiotemporal networks. On the one hand, Ward clustering is a bottom-up hierarchical clustering approach [approach . A spatiapproach . On the approach . It diviapproach .Note that the clustering methods thus yielded a regional scaffold of functional brain architecture with emphasis on functional specialization by segregation into disjoint region units. Yet, the decomposition methods yielded a spatially distributed scaffold with emphasis on functional integration by separation into overlapping network units. Please note however that clustering methods impose stricter constraints on the estimation of relevant structure, including the flat partition of the voxel space and the compulsory assignment of each voxel to one cluster , 88, 91.The extracted hidden components were subsequently used to reduce each task activity map to a much smaller number of component loadings. 61,472 voxels from gray-matter voxels of each map were thus condensed into 40 component loadings that quantify task-related network co-occurrence or region co-occurrence involvements. For network co-occurrence models, the presence of large-scale networks in every task map was determined by ridge regression based on a component design matrix . 40 component loadings were thus computed by projection of each task map onto the 40 network components. Note that the proposed approach is thus related to dual regression analysis . For regIn particular, linear-SVM classification was performed with regularization by l1- and l2-penalty terms. Both shrinkage methods were used to search for parsimonious, more interpretable models . First, In one subanalysis, ANOVA was used for explicit univariate component selection of the k most important component loadings for each given task comparing to other tasks. That is, fitting the multivariate classifier was preceded by a univariate feature-selection procedure on the training data in each cross-validation fold. In particular, the feature space was reduced to the k component loadings most relevant for each task. As we had already selected variables in this feature space, it was fed to l2-penalized, rather than l1-penalized, SVM to delineate their task-specific contribution. From a neurobiological perspective, this approach acknowledged the assumption that the balanced contribution of few large-scale networks should be sufficient to disentangle cognitive tasks. Note that all other reported results were based on the full set of 40 network or region loadings without ANOVA-based subselection.We finally evaluated whether the obtained explicit models capture genuine properties of fMRI task activity. Complementing sparsity and predictive performance, this provides a face-validity criterion to disambiguate whether task-immanent aspects of neural activity or arbitrary discriminative aspects explain the models\u2019 success. To this end, artificial maps were generated from the explicit network co-occurrence or region co-occurrence models of each task. The 40 features describing large-scale network or region implications in a given task were transformed back into the original gray-matter voxel space with 61,472 voxels. In network decomposition, the product was computed between the SVM weights and the support of each component. In region clustering, the mean activity of each region was projected into each voxel of that region. Importantly, back-projection from an abstract, highly reduced space to the original task activity space should succeed as a function of the construct validity of each model. For each of 18 tasks, Pearson\u2019s correlation between the model-derived activity map and the mean across first-level activity maps quantified the recovery performance. Consequently, the recovery performance indexed the neurobiological validity of quantitative network co-occurrence and region co-occurrence models.http://nipy.org/). Scikit-learn [http://scikit-learn.org). This general-purpose machine-learning library [http://github.com/nilearn/nilearn). 3D visualization of brain maps was performed using PySurfer (http://pysurfer.github.io/). All analysis scripts of the present study are readily accessible to the reader online (http://github.com/banilo/taskrest2016).Python was selected as scientific computing engine. Capitalizing on its open-source ecosystem helps enhance replicability, reusability, and provenance tracking. Nipy performeit-learn provided library was inteS1 Fig40 network components underlying 18 HCP tasks (left) have been discovered by sparse PCA (Comp1-40). The ensuing network loadings from the second half of the HCP task data were submitted to classification of the psychological tasks based on the implication of brain networks . l2-contrained support vector machines were employed to choose the most discriminatory network variables by a classical univariate test in a discrete fashion rather than by soft variable selection based on l1 penalization (cf. methods section). This diagnostic analysis (right) revealed the most distinctive k = 1, 5, 10, and 20 network features (red cubes) for each experimental condition of the task battery cf. . The thu(PNG)Click here for additional data file.S2 Fig40 network components underlying 18 HCP tasks (left) have been discovered by ICA (Comp1-40). The ensuing network loadings from the second half of the HCP task data were submitted to classification of the psychological tasks based on the implication of brain networks . l2-contrained support vector machines were employed to choose the most discriminatory network variables by a classical univariate test in a discrete fashion rather than by soft variable selection based on l1 penalization (cf. methods section). This diagnostic analysis (right) revealed the most distinctive k = 1, 5, 10, and 20 network features (red cubes) for each experimental condition of the task battery cf. . The thu(PNG)Click here for additional data file.S3 Fig40 network components underlying 18 ARCHI tasks (left) have been discovered by ICA (Comp1-40). The ensuing network loadings from the second half of the ARCHI task data were submitted to classification of the psychological tasks based on the implication of brain networks . l2-contrained support vector machines were employed to choose the most discriminatory network variables by a classical univariate test in a discrete fashion rather than by soft variable selection based on l1 penalization (cf. methods section). This diagnostic analysis (right) revealed the most distinctive k = 1, 5, 10, and 20 network features (red cubes) for each experimental condition of the task battery cf. . The thu(PNG)Click here for additional data file.S4 FigSparse PCA decomposition was used to derive the 40 most important modes of variation (Comp1-40) in the rest data (cf. methods section). These parsimonious spatial patterns are depicted in coronal, sagittal, and axial slices rendered on the Colin MNI template. Combinations of this dictionary of overlapping major brain networks were used to explain task-evoked neural activity patterns.(PNG)Click here for additional data file.S5 FigICA decomposition was used to derive the 40 most important modes of variation (Comp1-40) in the rest data (cf. methods section). These independent spatial patterns are depicted in coronal, sagittal, and axial slices rendered on the Colin MNI template. Combinations of this dictionary of overlapping major brain networks were used to explain task-evoked neural activity patterns.(PNG)Click here for additional data file.S6 FigLeftmost column: Average whole-brain activity from 18 experimental tasks of the HCP dataset. The voxel-wise mean was computed across the first-level contrast activity maps from 498 participants. Right columns: Four different network models were derived from the task activity during the 18 HCP tasks. First, four different network decompositions were applied to the first half of the HCP task data. Second, the ensuing sets of 40 brain networks served as a basis for feature engineering to automatically learn distinguishing the 18 tasks in the second data half based on network loadings alone. Third, the quantitative models of task-specific network loadings allowed generating a synthetic whole-brain activity map for each experimental task. The correlation values r quantify the voxel-wise similarity between the reconstructed activity map and the average activity map for each task and network decomposition method. This measure of recovery performance indicates the information loss incurred when first expressing activity maps as 40 network loading values and then translating these values back into whole-brain space. The similarity between real HCP task maps (leftmost column) and synthetic model-derived task maps (right columns) indicates that 40 network loadings can well describe task-evoked neural activity patterns in the HCP task battery.(JPG)Click here for additional data file.S7 FigLeftmost column: Average whole-brain activity from 18 experimental tasks of the ARCHI dataset. The voxel-wise mean was computed across the first-level contrast activity maps from 78 participants. Right columns: Four different network models were derived from the task activity during the 18 ARCHI tasks. First, four different network decompositions were applied to the first half of the HCP task data. Second, the ensuing sets of 40 brain networks served as a basis for feature engineering to automatically learn distinguishing the 18 tasks in the second data half based on network loadings alone. Third, the quantitative models of task-specific network loadings allowed generating a synthetic whole-brain activity map for each experimental task. The correlation values r quantify the voxel-wise similarity between the reconstructed activity map and the average activity map for each task and network decomposition method. This measure of recovery performance indicates the information loss incurred when first expressing activity maps as 40 network loading values and then translating these values back into whole-brain space. The similarity between real HCP task maps (leftmost column) and synthetic model-derived task maps (right columns) indicates that 40 network loadings can well describe task-evoked neural activity patterns in the ARCHI battery.(JPG)Click here for additional data file.S8 Fig40 clusters of homogeneous neural activity patterns across tasks and across participants. Spatially constrained ward and spatially unconstrained k-means clustering were applied to the first half of the task maps from the HCP and ARCHI dataset. Each cluster is depicted in a unique, arbitrary color. This grey-matter atlas of non-overlapping brain regions was used to explain task-evoked neural activity patterns.(PNG)Click here for additional data file.S9 FigLeftmost column: Average whole-brain activity from 18 experimental tasks of the HCP dataset. The voxel-wise mean was computed across the first-level contrast activity maps from 498 participants. Right columns: Two different region models were derived to explain the task activity during the 18 HCP tasks. First, two different clustering algorithms were applied to the entirety of the HCP task data. Second, the ensuing sets of 40 coherent activation clusters served as a basis for feature engineering to automatically learn to distinguish the 18 tasks based on cluster loadings alone. Third, the quantitative models of task-specific cluster loadings allowed generating a synthetic whole-brain activity map for each experimental task. The correlation values r quantify the voxel-wise similarity between the reconstructed activity map and the average activity map for each task and region clustering method. This measure of recovery performance indicates the information loss incurred when first expressing activity maps as 40 region summary values and then translating these values back into whole-brain space. The frequently low similarity between real HCP task maps (leftmost column) and synthetic model-derived task maps (right columns) indicates that 40 cluster loadings might not well describe task-evoked neural activity patterns in the HCP battery.(JPG)Click here for additional data file.S10 FigLeftmost column: Average whole-brain activity from 18 experimental tasks of the ARCHI dataset. The voxel-wise mean was computed across the first-level contrast activity maps from 78 participants. Right columns: Two different region models were derived to explain the task activity during the 18 ARCHI tasks. First, two different clustering algorithms were applied to the entirety of the ARCHI task data. Second, the ensuing sets of 40 coherent activation clusters served as a basis for feature engineering to automatically learn distinguishing the 18 tasks based on cluster loadings alone. Third, the quantitative models of task-specific cluster loadings allowed generating a synthetic whole-brain activity map for each experimental task. The correlation values r quantify the voxel-wise similarity between the reconstructed activity map and the average activity map for each task and region clustering method. This measure of recovery performance indicates the information loss incurred when first expressing activity maps as 40 region summary values and then translating these values back into whole-brain space. The frequently low similarity between real ARCHI task maps (leftmost column) and synthetic model-derived task maps (right columns) indicates that 40 cluster loadings might not well describe task-evoked neural activity patterns in the ARCHI battery.(JPG)Click here for additional data file.S11 FigFour different network co-occurrence models (upper and middle row) were computed based on decomposition based on sparse PCA, ICA, PCA, and factor analysis (FA). They capture functional brain architecture with emphasis on functional integration as opposed to regional specialization. Two different region co-occurrence models (lower row) were computed based on ward clustering and k-means clustering . They capture functional brain architecture with emphasis on regional specialization. The recovery performance of all 18 tasks is measured by the Pearson correlation r between the model-derived task activity maps and the average first-level task map. As a first conclusion, modeling task-specific neural activity appears to be more successful based on functional network units than on functional region units. Additionally, network and region dictionaries were derived from i) identical task-data as positive test (dark blue), ii) non-identical task-data (medium blue), iii) resting-state data (light blue), and iv) Gaussian noise as negative test (red). As a second conclusion, network dictionaries derived from non-identical task maps and rest maps are similarly successful in recovering whole-brain activity during divering experimental tasks. This was confirmed by univariate t-tests between the task-wise correlation values r (cf. results section).(PNG)Click here for additional data file.S12 FigParallel coordinate plots that depict the recovery performance by one line for each of the 18 tasks in both datasets. The network dictionaries were derived from i) identical task-data , ii) non-identical task-data (medium blue), iii) resting-state data , and iv) Gaussian noise , analogous to (PNG)Click here for additional data file."} +{"text": "While blood flow in the majority of arteries peaks in systole, the rhythmic squeezing of the coronary arteries and microcirculation as the heart beats results in left anterior descending artery (LAD) flow being diastolic-predominant while for the right coronary artery (RCA), there is approximately equal flow in systole and diastole. These temporal flow patterns can provide important information on disease state. The aim of this study is to assess the inter-breath hold reproducibility of parameters of coronary haemodynamics using a high temporal resolution spiral phase velocity mapping technique and to compare automatic and manual analyses.Two breath-hold coronary velocity maps were acquired in the proximal arteries of 10 LAD and 5 RCA : pixel size 1.4 x 1.4 x 8mm, true temporal resolution 19 ms, 1-1 water excitation (WE), 17 cardiac cycle breath-hold, retrospective ECG gating (reconstructed 50 phases). Extraction of coronary flow velocity-time curves was performed using a custom MATLAB program by two independent observers. Following Hough transformation, a circular coronary region of interest (ROI) was automatically defined on a through-plane segmented gradient echo scout image. This was copied to the spiral velocity maps and automatically shifted from frame to frame to track motion of the coronary through the cardiac cycle. For the LAD, a tracked arc-shaped ROI in nearby myocardium was used to correct for the through-plane motion of the vessel itself. For the RCA, the adjacent myocardium was too thin and a tracked ROI in the epicardial fat surrounding the vessel in a 1-1 fat-excitation (FE) breath-hold was used instead. Temporal flow profiles were extracted for each breath-hold acquisition and mean velocity (MV), peak systolic and diastolic velocities (PSV and PDV) and times to peak velocities (TPSV and TPDV) were determined. Bland Altman analysis and intraclass correlation coefficients (ICCs) were used to determine the inter breath-hold reproducibility of each parameter for each observer, and also to compare manual and automatic analyses. Results are quoted as mean +/- SD of signed differences between paired values.Example data are shown in Figure The automatic analysis technique reliably generates through-plane corrected temporal flow profiles with minimal user interaction and results agree well with those from manual analyses. Inter breath-hold reproducibility of MV, PSV, PDV, TPSV and TPDV (both observers) is excellent. Temporal patterns of coronary blood flow can be automatically assessed with high temporal resolution spiral phase velocity mapping.N/A."} +{"text": "The pathogenesis of idiopathic normal pressure hydrocephalus (iNPH) may take place in structures close to the cerebral ventricular system. Suprachiasmatic nucleus (SCN), situated close to the third ventricle, is involved in circadian rhythm and is therefore of interest to study. One of the main symptoms of iNPH is cognitive impairment. Diurnal disturbances are a well-known phenomenon of patients with dementia. Diurnal rhythm has never been studied in iNPH. The aim was to study any changes of the diurnal rhythm and diurnal activity amplitude, before and after shunt operation in iNPH-patients.Twenty consecutive iNPH patients fulfilling the criteria of American iNPH guidelines from 2005, 9 males and 11 females, mean age 73 (49-81) years were included. The patients underwent a pre-operative clinical work-up including 10 meters walk time (w10mt) steps (w10ms), TUG-time (TUGt) and steps (TUGs) and for cognitive function an MMSE score was measured. In order to receive circadian rhythm data actigraphic recordings were performed using the SenseWear 2 actigraph. Cosinor analyses of accelerometry data were performed in \u201cR\u201d using non-linear regression with Levenburg-Marquardt estimation. Pre- and post-operative data regarding mesor, amplitude and circadian period were compared using Wilcoxon-Mann-Whitney test for paired data.Twenty patients were evaluated before and three month post-operatively. Motor function was significantly improved while MMSE was not significantly changed . Actigraphic measurements showed no significant changes after the shunt operation.This is the first systematic study of circadian rhythm in iNPH-patients. There were no significant changes in circadian rhythm after shunt surgery. This is in line with the results from our previous actigraphic study showing that the patients did not improve their ambulatory activity in spite of improved motor function. Cognition measured with MMSE remained unchanged. These findings underscore the need of more active post-operative rehabilitation."} +{"text": "Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV-27) was isolated from dead larvae of a Western Siberian (WS) population of gypsy moths (Lymantria dispar L.). We report the complete genome sequence of this strain, comprising 164,108\u00a0bp and double-stranded circular DNA encoding 162 predicted open reading frames.A novel strain of Alphabaculovirus, are pathogenic for invertebrates, particularly insects of the order Lepidoptera. Lymantria dispar multiple NPV is the lethal viral infection of gypsy moths that causes epizootics in wild host populations. The gypsy moth (Lymantria dispar L.) is a widespread forest defoliator species inhabiting Europe, Asia, North America, and the northern part of Africa. There is no strong food specialization for the gypsy moth, so this herbivore species is one of the most important forest pests in the world.The nuclear polyhedrosis viruses (NPV), which belong to the genus Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV-27), isolated from dead larvae of a Western Siberian (WS) population of gypsy moths. The LdMNPV-27 natural isolate was passed through the larvae of a wild WS population of gypsy moths under laboratory conditions in 2006. Virus DNA was phenol-chloroform extracted from purified viral polyhedral inclusion bodies (de novo with CLC GW version 7.0 software (CLC Bio).Here, we present a complete genome for a novel strain of n bodies . The virThe LdMNPV-27 strain has a double-stranded circular 164,108-bp DNA genome with an average 57.4% GC content. Potential open reading frames (ORFs) were identified by using the GeneMarkHMM and subsAt least 162 ORFs of the total 174 predicted for the virus genome seem to be functional based on a genome comparative analysis with other known NPV genomes. The closest relative is LdMNPV strain 3029 (KM386655) (KP027546.The genome sequence of LdMNPV-27 has been deposited in GenBank under the accession number"} +{"text": "It is known that postnatal functional maturation of the small intestine is facilitated by microbial colonization of the gut. Preterm infants exhibit defects in gut maturation, weak innate immunity against intestinal infection and increased susceptibility to inflammatory disorders, all of which may be related to the inappropriate microbial colonization of their immature intestines. The earliest microbes to colonize the preterm infant gut encounter a na\u00efve, immature intestine. Thus this earliest microbiota potentially has the greatest opportunity to fundamentally influence intestinal development and immune function. The aim of this study was to characterize the effect of early microbial colonization on global gene expression in the distal small intestine during postnatal gut development.Gnotobiotic mouse models with experimental colonization by early (prior to two weeks of life) intestinal microbiota from preterm human infants were utilized. Microarray analysis was used to assess global gene expression in the intestinal epithelium.Multiple intestinal genes involved in metabolism, cell cycle regulation, cell-cell or cell-extracellular matrix communication, and immune function are developmental- and intestinal microbiota- regulated. Using a humanized gnotobiotic mouse model, we demonstrate that certain early preterm infant microbiota from prior to 2 weeks of life specifically induce increased NF-\u03baB activation and a phenotype of increased inflammation whereas other preterm microbiota specifically induce decreased NF-\u03baB activation. These fundamental differences correlate with altered clinical outcomes and suggest the existence of optimal early microbial communities to improve health outcomes. In hubacteria . Early abacteria ,12. Thisbacteria ,14.Studies on fecal samples collected from term and preterm infants suggest that early gut colonization influences infant health and disease, and that microbial interventions may affect disease risk both early and late in life ,16. StudMany disorders of preterm newborns are inflammatory in nature including chronic lung disease and neonPI . This experimental design revealed both age-dependent and microbial colonization induced changes in small intestine gene expression. Differences in influence of certain microbial communities on intestinal inflammatory and immune pathways suggest existence of optimal communities to modulate the exaggerated inflammatory response of the immature gut. Our studies present a powerful model for dissecting the function of the microbiota and microbiota/host relationships in ways that would not be possible in human infants. Furthermore, our studies suggest that early colonization patterns in certain preterm infants lead to an exaggerated inflammatory state that may affect growth and susceptibility to the multiple morbidities of inflammatory origin seen in preterm infants.GeneChip profiling of transcripts in ileal mucosal RNAs was used to assess the effects of microbiota on gene expression in the murine intestine during postnatal development. Three classes of mice of the same C57B6 genetic background but with distinct intestinal microbial phenotypes were used: GF mice ; SPF mice or GF-MPI-H) and low growth (MPI-L) were collected for further analysis and transfaunation studies. At the time the samples were obtained, both were receiving total parenteral nutrition (TPN) intravenously, as well as their own mother\u2019s non-fortified breast milk from frozen stores via nasogastric tube.This study was designed to investigate the influence of early microbiota on the developing gut using gnotobiotic mice transplanted with early microbiota from preterm infants. Subjects were recruited from the neonatal intensive care unit (NICU) at The Comer Children\u2019s Hospital of the University of Chicago. As growth can be used as a marker of health in infants, we arbitrarily selected two preterm human infants with normal >10gm/k/day weight gain or decreased <10gm/kg/day weight gain as the donors for microbiota transplantation. The two preterm infants were comparable in gestational age (27-week GA), mode of delivery (cesarean section), feeding pattern (breast fed) and exposure to antibiotics (48 hour administration of ampicillin and gentamicin immediately after birth). Based on our previously published work demonstrating a temporal progression of preterm infant microbiota with distinct clustering at <2 weeks of life, the earSpecimen collection procedures involved minimal physical risk to subjects. The procedures were approved by the Institutional Review Board (IRB), approval 14991B, and written consent was obtained from patient parents.All procedures were carried out in accordance with Institute guidelines at the University of Chicago. Germ free (GF) C57BL/6J mice were maintained in the gnotobiotic facility of the Digestive Disease Research Core Center (DDRCC) at the University of Chicago. GF colonies are routinely tested for microbes and parasites by the facility\u2019s staff to ensure germ-free conditions. Conventional C57BL6J mice (From the Jackson Laboratory) were bred and housed in the animal care facilities of the University of Chicago under specific pathogen free environment (SPF) conditions. All groups of mice were allowed ad-libitum access to Harlan Teklad 7012 (SPF) or its autoclaved equivalent NIH 31 (GF) chow. All animal studies were approved by the Institutional Animal Care and Use Committee of the University of Chicago (permit number 71703).PI-L, MPI-H). Pups delivered spontaneously and naturally acquired the microbiota of interest. Litters remained with the mother to allow natural passage of intestinal microbes. These pups were studied in parallel with age-matched SPF and GF controls.To initiate microbial colonization, pregnant GF female 8- to 9-week-old mice (estimated between E15-17) were gavaged with 0.25 ml of freshly prepared fecal homogenate from frozen fecal samples of the preterm human infant donors (M5\u2019-GTGCCAGCMGCCGCGGTAA-3\u2019 and 806R: 5\u2019- GGACTACHVGGGTWTCTAAT-3\u2019) and contained Illumina 3' adapter sequences as well as a 12 bp barcode [http://mg-rast.mcs.anl.gov/linkin.cgi?metagenome .DNA was extracted from stool samples using the QIAamp Stool DNA kit (Qiagen) according to manufacturer\u2019s instruction. PCR primers used were specific for the 533\u2013786 base pair (bp) region of the 16S rRNA encoding gene .Total RNA from small intestinal mucosal scrapings was extracted from pre and postweaned GF and SPF using the RNeasy kit and RNase-free DNase I (QIAGEN) digestion based on the manufacturer's protocol. RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies). Microarray was done by Onearray . Six micrograms of total RNA was reverse transcribed to cDNA by Ambion Amplification then transcribed into biotin-labeled cRNA with the One-Cycle Target Labeling Kit ). Hybridization was done in triplicate to the Mouse Array (mouse v2), and chips were scanned with a Molecular Devices GenePix Scanner and Image quality analysis performed with Rosetta Resolver. The database has been submitted to the GEO repository . For in-depth functional analysis of the microarray data, all differentially expressed genes (p<0.05) were imported into MetaCore analytical software (GeneGo) to generate gene enrichment reports based on http://pga.mgh.harvard.edu/primerbank) [RNAs were isolated from ileal tissues as described above. qRT-PCR was performed using mouse-specific primers with SYBR-Green PCR master mix (Applied Biosystems). For all the genes tested, the primer sets were selected and obtained from the Harvard primer Bank (merbank) . cDNA saPI, SPF and GF mice was collected and inflammatory cytokines were measured by BioPlex assay (BioRad) according to manufacturer's instructions.Sera from 3 wk old M2O2 (3% in methanol). Antigen retrieval was performed by microwave in a citrate buffer and endogenous avidin-biotin blocked . Primary antibodies or isotype control were added to the sections, followed by biotinylated secondary antibody and ABC detection kit (Vector Laboratories). Sections were counterstained with hematoxylin and examined on a BioRad Axiophot fluorescence photomicroscope.Distal ileum segments were fixed in formalin and paraffin embedded for sectioning and histological examination. For immunohistochemistry, 5-\u03bcm paraffin sections were dehydrated and endogenous peroxidase was quenched with HPI-L and MPI-H. Differences were considered significant when p<0.05. ANOVA analysis and a post-hoc Tukey honest significance (HSD) test were used to compare differences among groups. Findings are presented as the mean \u00b1 standard error and a p<0.05 was considered statistically significant.The \u0394\u0394\u2019 (CTs) were used to calculate the expression levels of amplified genes and were normalized to expression levels of GAPDH. The nonparametric Kruskal-Wallis test was used for comparing \u0394\u0394\u2019 (CTs) between MWe hypothesized that temporal development and bacterial colonization affect small intestinal gene regulation in early life. First, a genome-wide expression analysis was used to examine the patterns of gene expression profiles and to identify functional networks corresponding to temporal development (preweaned vs. postweaned). To separate developmental changes from alterations due to microbial colonization, postweaned vs preweaned was examined in both GF and SPF mice. Out of a total 14626 genes, 4228 genes in GF and 2782 genes in SPF mice were differentially expressed with at least two-fold change between pre and postweaned (2 weeks vs 4 weeks) ileum, (p<0.05). We have termed the difference between pre and post weaned the developmental difference.p values. The top scored Gene ontology (GO) processes overrepresented by differentially expressed gene sets are shown in The age-dependent differentially expressed genes (preweaned vs postweaned) were subjected to integrated pathway enrichment analysis using MetaCore knowledge-based annotation to extract functional gene expression patterns in GF or SPF ileum. Ranking of relevant integrated pathways was based on hypergeometric Next, to examine the role of gut microbiota on gene expression pattern separate from developmental changes, we compared the pre or postweaned ileal mRNA expression profiles of SPF to that of GF mice. Gut microbiota colonization had a greater effect in preweaned ileum (preweaned SPF vs. preweaned GF) than in postweaned ileum (postweaned SPF vs. postweaned GF) with 4516 vs 2825 genes affected respectively. Our data indicate that gut microbiota induce large effects on metabolic processes, phosphorylation, organ (heart) development and apoptosis in preweaned SPF vs preweaned GF ileum, whereas the microbiota invoke a strong effect on immune system process, response to stress, positive regulation of biological process and immune response in postweaned SPF vs postweaned GF ileum .A large number of differentially expressed genes were shared between GF- and SPF-dev (preweaned vs. postweaned) suggesting that these genes were development-associated and not influenced by microbiota colonization. Similarly, we identified 1206 microbiota-associated differentially expressed genes (\u2265\u00b1 2) shared by preweaned and postweaned SPF vs GF, suggesting that these were mainly influenced by microbiota irrespective of developmental stage. We further analyzed these flagged genes in GO biological processes networks. Using GOMiner software in combination with Venn Master,33, we iPI-L and the sample from the infant with normal growth is indicated as MPI-H. The composition of the microbial community in the fecal samples obtained from these preterm infants was analyzed and the frequencies of sequences from each subject were grouped according to public database NCBI and RDP-II. Growth of the preterm infant is a surrogate for health . To inveProteobacteria and Firmicutes with a small portion of Bacteroidetes and Actinobacteria.Consistent with what has been shown in other analysis of preterm infant fecal microbiota , these tPI) to facilitate colonization from birth of the resulting pups with the microbiota of interest. Fecal samples from MPI and SPF pups were sequenced and grouped according to their taxonomic group (Firmicutes (59.9% relative abundance) and Bacteroidetes (39.6%), MPI-colonized mouse pups exhibited a very different composition reflecting the input human preterm infant microbiota dominated by Proteobacteria and Firmicutes in both MPI-L and-H colonized mice. There is a greater contribution of Bacteroidetes (8.30 vs. 3.42) and Actinobacteria (8.53 vs. 0.57) in MPI-H-colonized mice compared to MPI-L mice. Principal Coordinates Analysis based on Bray Curtis Dissimilarities revealed clear separation of MPI-L (red) from MPI-H (blue) by grouping into one side of the PCA plot in MPI-H mouse pups. The differentially expressed genes in MPI-L and MPI-H were further analyzed using GeneGo MetaCore Gene Enrichment analysis. The top scored GO processes and networks overrepresented by differentially expressed genes are presented in PI with GF mouse ileum, MPI-L affected primarily innate immune/inflammatory responses with many genes involved in leukocyte adhesion, migration and chemotaxis. In contrast, MPI-H had little or no effect on these processes.To gain insights into effects of preterm infant microbiota, we collected ileal RNA from preweaned mouse pups transfaunated with preterm infant microbiota for a genome-wide analysis of gene expression profiles. Results were compared to expression data from preweaned GF mouse pups. This comparison yielded a total of 461 differentially expressed genes in which transcript levels had at least twofold change (452 up and 9 down) in MPI-L and 154 genes in MPI-H overlapped with the microbiota-associated genes identified in the SPF vs GF analysis. These genes were further analyzed using Ingenuity Pathway Analysis (IPA) which confirmed the findings that MPI-L-upregulated genes in inflammatory response networks in general and leukocyte adhesion, migration and chemotaxis in particular is shown in PI-L compared to that in MPI-H mouse ileum tissues.We next selected inflammation-associated genes that were differentially expressed by gene expression array analysis in MPI-L for furtPIs and SPF mice by immunohistochemistry staining. VCAM-1 and MCP-1 are two NF-\u03baB target-genes whose expression levels were upregulated in MPI-L based on gene expression array and qPCR. Moreover, they are important molecules implicated in many inflammatory states [PI-L ileum compared to GF and SPF ileum tissues, while MPI-H ileum showed a qualitative decrease in the levels of VCAM-1 and MCP-1 expression compared to MPI-L and SPF at weaning. As shown in PI-L compared to MPI-H mice. These data suggest an elevated basal systemic inflammatory response in MPI-L mice.Using a multiplex immunoassay we next examined immune and inflammatory cytokine expressions in blood sera collected from GF, Min vivo evidence of persistent activation of NF-\u03baB in the ileum of MPI-L, -H mice, immunohistochemistry analysis was performed to examine baseline nuclear localization of phosphorylated p65 as an indicator of NF-\u03baB activation. The number of phosphorylated p65 positive nuclei in the tissue was quantified using the ImmunoRatio tool from Image J software. As shown in Fig PI-L mouse ileum displayed an increased level of phospho-p65 indicating increased NF-\u03baB activation as compared to GF and SPF mice, while MPI-H showed decreased NF-\u03baB activation as compared SPF mice by ImmunoRatio counting. Tukey\u2019s HSD test indicated a significant increase of NF-\u03baB nuclear translocation in MPI-L compared to GF, SPF and MPI-H mouse ileum induced a significant upregulation of genes and pathways associated with innate immune/inflammatory responses, particularly in chemotaxis, chemokine/ cytokine signaling, chemokine receptor expression and phagocyte-, monocyte-, and leukocyte-rolling and adhesion in the transfaunated pups. Many of these genes are targets (either direct or indirect) of the NF-\u03baB complex and the changes in their expression levels were associated with increased NF-\u03baB activation . However, the growth phenotype we observed in human infants was transferred to GF mouse pups via our fecal transfer model. Furthermore, the transfaunated mice reproduced their original hosts\u2019 growth patterns throughout the study. Thus, our data suggest a potential link between improved growth present in MPI-L mice. Importantly these results suggest that certain microbial communities may decrease inflammation and thus protect infants from inflammatory based morbidity of prematurity.Importantly these differences in inflammation phenotype, including elevation of systemic inflammatory cytokines, occurred under basal conditions without any secondary inflammatory stimulus. We thus speculate that the different initial microbiota may influence initial inflammatory basal states that could influence susceptibility to inflammatory morbidities of prematurity. The mechanisms by which the microbiota alter the inflammatory phenotype as well as the factors that influence microbiota characteristics in different patients are important next steps for future investigation. The gene enrichment analysis in In this study, growth was used as a marker of overall well-being or health. The two patients selected for this study were not intended to link a specific microbial community with a specific clinical outcome. Rather these studies support our main conclusions: 1. Microbiota from a human preterm infant can be transfaunated to a germ free mouse and transfer a phenotype representative of that infant and thus represents a powerful model for studying microbiota function. 2. Early microbiota influence inflammatory potential of the intestinal epithelium. As inflammation is the root of much of the morbidity of prematurity, these studies demonstrate the potential for optimal initial colonization to influence fundamental processes to improve multiple health outcomes. Future investigation will focus on understanding the mechanisms by which early microbiota influence the priming of immune and inflammatory responses of the developing preterm gut. Our goal is to define the causal association between early microbiota and health outcomes of preterm infants. Defining this optimal colonization may enable interventions to influence this earliest microbial colonization to down-regulate inflammatory responses and minimize morbidities of prematurity.S1 FigS1A: Area-proportional Euler diagram of development-associated-genes generated from differentially expressed genes in post vs preweaned GF and SPF ileum is shown. A total of 10 ontology categories were significantly enriched among the changed genes. The analysis revealed that those categories strongly overlap with metabolic process-related categories. S1B: Area-proportional Euler diagram of microbial-colonization-associated-genes generated from differentially expressed genes in SPF vs GF ileum. A total of 8 ontology categories were significantly enriched. The analysis revealed that the categories strongly overlap into 2 major categories: cytokine biosynthesis and innate immune response-NF-\u03baB signaling.(TIF)Click here for additional data file.S2 FigPIL_GF (145 genes) vs MPI-H_GF (154 genes) by Ingenuity Pathway Analysis (IPA). Orange line: activation; Blue line: inhibition; Grey: not present.Overrepresentation of inflammatory response-related networks in common differentially expressed microbial-associated-genes in M(TIF)Click here for additional data file.S3 FigPI-L (n = 20), MPI-H (n = 15), GF (n = 9) and SPF (n = 9) from birth to weaning. The daily weights are presented as mean (g) \u00b1 SEM. One-way ANOVA with post-hoc Tukey\u2019s HSD test was used to compare the groups.Growth curve of M(TIF)Click here for additional data file."} +{"text": "Transthyretin (TTR) Val30Met-associated familial amyloid polyneuropathy is the most common form of FAP and has become prevalent in areas other than conventional endemic foci. The clinicopathological features of FAP ATTR Val30Met are known to vary between endemic foci and non-endemic areas in Japan. Characteristic features of early-onset cases from Japanese endemic foci include the presence of sensory dissociation and marked autonomic dysfunction associated with a predominant loss of small-diameter myelinated and unmyelinated nerve fibers. These characteristics are uncommon in late-onset cases from non-endemic areas.We examined sural nerve biopsy specimens from 42 patients with FAP ATTR Val30Met using electron microscopy, particularly focusing on the morphology of nerve microvascular endothelial cells. This study included 5 early-onset cases from endemic foci (3 men and 2 women) and 37 late-onset cases from non-endemic areas (33 men and 4 women).Greater amyloid deposition was observed in early-onset cases than in late-onset cases, whereas reduced nerve fiber density was more conspicuous in late-onset cases than in early-onset cases. Retraction of the processes of Schwann cells associated with amyloid fibrils was observed, particularly in early-onset cases. In addition, basement and cytoplasmic membranes of Schwann cells associated with amyloid fibrils were indistinct, indicating that direct invasion of amyloid to Schwann cells had resulted in predominantly small-fiber axonal loss characteristic of early-onset cases. In late-onset cases, nerve microvascular endothelial cell morphology was frequently found to be abnormal with loss of tight junctions and fenestrations.These findings suggest that, in addition to direct invasion of amyloid to Schwann cells, the disruption of the blood\u2013nerve barriers contributes to the pathogenesis of neuropathy in FAP."} +{"text": "Total Anomalous Pulmonary Venous Connection (TAPVC) is a rare form of congenital heart disease (CHD) in which all pulmonary veins connect to the systemic veins, right atrium or the coronary sinus. Echocardiography is a good screening modality in picking up majority of these cases. Cross sectional imaging is often utilized to establish the anatomy and confirm the diagnoses. In this study we looked at the prevalence and pattern of TAPVC and Partial Anomalous Pulmonary Venous Connection (PAPVC) in Indian patients with CHD.Retrospective analysis of all Multi Detector Computed Tomography (MDCT) and Cardiac Magnetic Resonance (CMR) examinations performed in our center over 8-year period (2006-2013). Patients with Anomalous Pulmonary Venous Connection (APVC) were classified into TAPVC and PAPVC. Patients with TAPVC were sub-classified into supra-cardiac, cardiac, infra-cardiac and mixed type based on the site of drainage.A total of 3983 patients with CHD had cross sectional imaging during this period. Of these, 411 (10.3%) patients had APVC, 232 (6%) had TAPVC and 172 (4.3%) had PAPVC. The most common type of TAPVC was supra-cardiac in 106 (46%), followed by cardiac in 55 (24%) and mixed type of TAPVC in 51 (22%) patients. Infra-cardiac TAPVC was present in 20 (8%) cases. Cross sectional imaging was able to recognise all pulmonary veins accurately in these patients. It was also particularly useful in picking up cases with obstruction that required urgent surgical management.Anomalous pulmonary venous connection is a common form of CHD in Indian patients. Cross sectional imaging plays an important role in diagnosis and establishing the anatomy in these patients."} +{"text": "Among human T-lymphotropic virus type 1 (HTLV-1)-infected individuals, the lifetime risk of developing HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) differs between ethnic groups, also, there is an association between HTLV-1 tax gene subgroups and the risk of HAM/TSP. In an attempt to understand the molecular mechanism responsible for this association, we studied the full-length proviral genome sequences of various HTLV-1-infected cell lines and patient samples, the functional difference in the viral transcriptional regulator Tax and HBZ between each subgroup, and the relationship between tax subgroups and the clinical and laboratory characteristics of HAM/TSP patients. The results indicated that (1) the distinct nucleotide substitutions corresponding to each tax subgroup are also associated with the nucleotide substitutions of viral structural, regulatory, and accessory genes; (2) mRNA expression of HBZ in HTLV-1-infected cells was significantly higher in HAM/TSP patients with tax-B than those with tax-A; (3) there was a positive correlation between HBZ and the expression of its target FoxP3 in HAM/TSP patients with tax-B but not in patients with tax-A; (4) transcriptional changes in inducible cells that express each subgroup of Tax or HBZ protein under the control of an inducible promoter showed different target gene profiles; however, (5) there were no clear differences in clinical and laboratory characteristics between HAM/TSP patients with tax-A and tax-B; and (6) there were no functional differences in Tax and HBZ between each subgroup evaluated by reporter gene assays. Our results indicate that although different HTLV-1 tax subgroups cause different patterns of viral and host gene expression in HAM/TSP patients via independent mechanisms of direct transcriptional regulation, these differences do not significantly affect the clinical and laboratory characteristics of HAM/TSP patients. Further studies on other viral genes, as well as clinical samples of asymptomatic carriers and adult T-cell leukemia (ATL) patients, are in progress to clarify the role of HTLV-1 tax subgroups."} +{"text": "Adverse cardiac remodeling is a key component of the failing heart. Increased diastolic wall stress plays a pivotal role in the development and progression of adverse cardiac remodeling. The forces generated by the left ventricular (LV) myocardium initiate blood flow, while the moving blood itself also exerts a force on the ventricular wall and heart valves. Abnormal hemodynamic forces may contribute to increased diastolic wall stress. We calculated LV hemodynamic forces from the moving blood, and hypothesized that these forces are mostly directed along the \"mitral valve (MV) to apex axis\" in the healthy LV, while the distribution is altered in myopathic LVs.3. The LV was segmented from the morphological images using Segment (http://www.segment.heiberg.se). The LV pressure gradients were computed from the 4D flow data using the Navier-Stokes equations. By integrating the pressure gradients over the LV volume at every time frame, the LV hemodynamic force was calculated . The ratio between the LV hemodynamic forces acting in the LV SAx and LAx directions was used to calculate the \"SAx-max/LAx-max force-ratio\" for the early (E-wave) and the late (A-wave) diastolic filling (figure Ten dilated cardiomyopathy (DCM) patients with mild to moderate ventricular dysfunction and ten healthy subjects underwent a cardiac CMR examination at 1.5T (Philips Achieva), where morphological short- (SAx) and long-axis (LAx) images and 4D flow data was acquired. 4D flow MRI was acquired with retrospective cardiac gating; acquired temporal resolution 50.4ms and spatial resolution 3x3x3mmThere was no significant difference in age or heart rate between the groups, while LV ejection fraction , LV end-diastolic volume and LV sphericity index was significantly different. The \"SAx-max/LAx-max\"ratio (figure 4D flow CMR data allow quantification of hemodynamic forces acting on the LV myocardium. The present data show that the distribution of hemodynamic forces is altered in LVs of DCM patients compared to LVs of healthy subjects.This study was funded by the Swedish Heart-Lung foundation, the Swedish Research Council and the European Research Council."} +{"text": "Our results demonstrate that PHx of a chronically inflamed liver directed tumor development to a discrete pathway characterized by amplification of specific chromosomal regions and expression of specific tumor-promoting genes. Crem is a new candidate HCC oncogene frequently amplified in this model and frequently over-expressed in human HCC.Resection of hepatocellular carcinoma (HCC) tumors by partial hepatectomy (PHx) is associated with promoting hepatocarcinogenesis. We have previously reported that PHx promotes hepatocarcinogenesis in the Mdr2-knockout (Mdr2-KO) mouse, a model for inflammation-mediated HCC. Now, to explore the molecular mechanisms underlying the tumor-promoting effect of PHx, we compared genomic and transcriptomic profiles of HCC tumors developing in the Mdr2-KO mice either spontaneously or following PHx. PHx accelerated HCC development in these mice by four months. PHx-induced tumors had major chromosomal aberrations: all were amplifications affecting multiple chromosomes. Most of these amplifications were located near the acrocentric centromeres of murine chromosomes. Four different chromosomal regions were amplified each in at least three tumors. The human orthologs of these common amplified regions are known to be amplified in HCC. All tumors of untreated mice had chromosomal aberrations, including both deletions and amplifications. Amplifications in spontaneous tumors affected fewer chromosomes and were not located preferentially at the chromosomal edges. Comparison of gene expression profiles revealed a significantly enriched expression of oncogenes, chromosomal instability markers and E2F1 targets in the post-PHx compared to spontaneous tumors. Both tumor groups shared the same frequent amplification at chromosome 18. Here, we revealed that one of the regulatory genes encoded by this amplified region, Crem, was over-expressed in the nuclei of murine and human HCC cells Tumor resection and ablation are currently the main treatment options for an early-stage hepatocellular carcinoma (HCC), while tumor recurrence is the main complication following these treatments . ChronicIn order to delineate the roles of gender and time of PHx in the development of HCC in the chronically inflamed liver, we performed 70% PHx in male and female Mdr2-KO/FVB mice at either three or six months of age; sham operations served as controls . PHx sigTo determine the effect of genetic background on the development of HCC in the chronically inflamed liver following PHx, we performed 70% PHx in male Mdr2-KO/B6 mice at six months of age and sacrificed these animals for tumor score at 14 months of age. Surprisingly, there was no significant difference in liver tumor development between the PHx-treated and control groups . Both PHTo explore the mechanisms of the accelerated HCC development by PHx, we compared liver tumors and their matched non-tumor liver tissues between 9-month-old hepatectomized and 13-14-month-old untreated Mdr2-KO mice. From each experimental group, we selected six well differentiated HCC tumors similar in size range and morphology between groups. All tumors were well protruding from the liver and contained at least 90% of tumor cells on histological sections. We compared cell proliferation and DNA damage markers in tumors and their adjacent non-tumor (surrounding) as well as distant non-tumor (non-tumor) liver tissues between both experimental groups. BrdU inclusion in hepatocytes for all three tissue types was significantly higher in the post-PHx compared to the untreated (spontaneous) group Figure . However2= 0.8527; Figure To understand the molecular mechanisms of the accelerated tumor development in post-PHx mice, we compared, using aCGH, genomic aberrations in six tumors from each of the experimental groups described above . Most amGenome-scale gene expression analysis of the PHx-induced tumors and their distant non-tumor liver tissues using PCA and hierComparison of the genome-scale gene expression profiles of these six post-PHx tumors with those of spontaneous tumors of the 16-month-old Mdr2-KO mice which were analyzed previously revealedversus non-tumor liver: in females, it was similar in the post-PHx tumors, while it significantly decreased in spontaneous tumors to the process of HCC development/recurrence in patients, we analyzed the significance of the known appropriate gene expression signatures in the tumor and non-tumor samples of the post-PHx Mdr2-KO/FVB mice. Recently, it was shown that in tumors removed by curative surgery, up-regulation of the Racgap1 together with several other genes of its interactome is associated with the early HCC recurrence . Here weThe most common amplified region among both post-PHx and spontaneous tumors was the one on chromosome 18, containing 22 unique genes: it was amplified in 4/6 post PHx tumors and in 3/6 spontaneous tumors Figure . We focuCrem has multiple splicing isoforms . Using iin vitro.Several Crem isoforms were detected by immunoblotting in five out of nine tested human and mouse HCC cell lines Figure . Human lWe have revealed strain-specificity of the effect of PHx on tumor acceleration in Mdr2-KO males operated at the age of six months: in the FVB/N strain, the tumor-promoting effect of PHx could be already detected at the age of nine months, whereas in the B6 strain, no effect of PHx on HCC development could be observed even at the age of 14 months. This result correlates with our previous findings of a reduced inflammation at the early age and retarded tumor development at the adult age in the Mdr2-KO/B6 compared to the Mdr2-KO/FVB strain . ImportaRecently, it was demonstrated that HCCs from Mdr2-KO/FVB mice are similar to pediatric HCCs of similar etiology in terms of low frequency of point mutations and high frequency of gene amplifications . In contDetermination of causative cancer genes in chromosomal aberrations is complicated by the known examples of cooperation between both co-amplified oncogenes and co-dPrediction of tumor recurrence which jeopardizes survival of about 70% of HCC patients within 5 years following tumor resection or ablation is of high clinical importance . SeveralValidation of H19 expression on an expanded set of liver samples by qRT-PCR revealed different expression patterns between PHx-induced and spontaneous tumors for Mdr2-KO/FVB females, but not for males Figure . The H19in vitro revealed its pro-proliferation role in two human HCC cell lines, thus demonstrating that CREM is a new candidate HCC oncogene.In our search for candidate cancer-causing genes in frequently amplified regions, we focused on the gene Crem because it was amplified in 4/6 post PHx tumors and in 3/6 spontaneous tumors, and also due to its involvement in cancer , 13, incIn summary, we demonstrated that PHx of the chronically inflamed murine liver accelerated HCC development by a specific pathway characterized by amplification of chromosomal regions located near the acrocentric centromeres of murine chromosomes and by expression of specific tumor-promoting genes, including those of the \u201cpoor prognosis\u201d HCC signatures. We also identified Crem as a new candidate HCC oncogene frequently amplified and up-regulated in this murine HCC model and frequently over-expressed in human HCC.Full details are available in the Supplemental Materialtm1Bor (Mdr2-KO/FVB) and the C57Bl/6 Mdr2-KO (Mdr2-KO/B6) mice were described previously [All animals received human care. All animal experiments were performed according to national regulations and guidelines of the Institutional Animal Welfare Committee . The FVB.129P2-Abcb4eviously . The 70%TM cDNA Synthesis Kit (#95047) and Perfecta Sybr Green Fast Mix ROX (#95073) . The quantitative PCR assay was performed on an AB 7900 HT fast real-time PCR system or CFX384TM Real-Time System with C1000 Touch Thermal Cycle . The semi-quantitative RT-PCR and the primers used for RT-PCR are described in the Total RNA was isolated from frozen liver tissues and subjected to gene expression profiling using GeneChip Mouse Gene 1.0 ST Array as described . Data weTotal DNA was isolated from frozen tumors and their matched non-tumor liver tissues as described and subjProtein detection by immunoblotting and immunohistochemial staining was performed as described in the in vitro experiments were performed in triplicates, excluding the cell proliferation rate assay using a xCELLigence system, which was performed in duplicates; in the in vivo experiments, at least 3 mice per group were used. All parameters were evaluated with the two-tailed t-test. Statistical evaluation of differential expression between the experimental groups was performed using the ANOVA test. A p-value of 0.05 or less was considered significant. t-test, correlation test, and f-test were performed using the GraphPad Prism version 6.04 for Windows . Stained hepatocytes IHC sections were counted by the NIS-Elements Microscope Imaging Software . The results of protein immunoblotting and semi-quantitative RT-PCR were calculated using ImageJ . To evaluate the effect of PHx on tumor incidence, the Fisher exact test was calculated online (http://www.quantpsy.org/fisher/fisher.htm). The Pearson's correlation coefficient (All the fficient was calc"} +{"text": "Cabbage leaf curl virus interacts with all three NIKs from Arabidopsis to suppress their kinase activity [Tomato golden mosaic virus), TCrLYV (Tomato crinkle leaf yellows virus) and ToYSV (Tomato yellow spot virus) [in vitro and in vivo, and interacts with the ribosomal proteins L10 (rpL10) and L18 (rpL18) [The NSP-interacting kinase (NIK) receptor-mediated antiviral signaling has been identified as a virulence target of the begomovirus nuclear shuttle protein (NSP) ,2. NSP sactivity . The NSPt virus) ,2. Severt virus) . Second,t virus) ,3. In adt virus) . NIK exh (rpL18) . NIK-med (rpL18) . The con (rpL18) ,7. Our dTo identify novel regulators of NIK-mediated defense response, we screened a two-hybrid library for partners of rpL10. We discovered a novel transcriptional factor, which interacts with rpL10 in the nucleus of plant cells to down-regulate the expression of ribosomal genes. These data are consistent with the observation that constitutive activation of the NIK receptor by replacing Thr-474 with aspartate impairs global translation in Arabidopsis and tomato transgenic lines and confers broad-spectrum tolerance to begomovirus infection. Our data also indicate that the NIK immune receptor-mediated antiviral signaling operates through a bipartite module. One defense signal-transducing branch is mediated by the regulated nucleocytoplasmic transport of ribosomal protein to impair translation and the second branch of the antiviral signaling transduces a typical defense signal through induction of the plant immune system. We will discuss novel insights into the regulation of the NIK-mediated antiviral signaling and an efficient-acquired defense against begomovirus by modulating the activity of the immune defense receptor NIK in tomato plants."} +{"text": "A 77 year old male with history of renal lithiasis leading to right nefrectomy and end stage renal disease (ESRD) secondary to possible vascular nephropathy and focal segmental glomerulosclerosis diagnosed in 2009, started ambulatory peritoneal dialysis (APD) due to clinical decline. Insufficient drainage of the peritoneal dialysis solution with progressive bilateral testicular edema (more severe in right side) was observed from the first APD session. As a consequence, the patient needed temporarily hemodialysis. In order to diagnose a patent peritoneal-vaginal duct, a dynamic 99mTc-Phytate scintigraphy was performed after introduction of peritoneal dialysis solution labelled with 74 MBq of 99mTc-Phytate in the abdominal cavity. A total of 60 images (30 seconds per image) were acquired and a hypogastric uptake of radiotracer was observed and 3 weThe peritoneal-scrotal dialysate leakage is the major non-infectious catheter-related complication in patients receiving APD, caused by increased intraperitoneal pressure and the loss of integrity of the peritoneal membrane, although the most common cause is fluid extra-vasation from an indirect hernial sac or patent peritoneal-vaginal duct . PleuralSeveral diagnostic methods including intraperitoneal infusion of contrast, abdominal x-ray, computed tomography or peritoneal scintigraphy are employed when the leak diagnosis is uncertain. The peritoneal scintigraphy has proven to be a useful tool for the diagnosis of the peritoneal leakage ,3, being"} +{"text": "Systemic onset Juvenile Idiopathic Artritis (sJIA), also known as Still's disease, is characterized by arthritis with symptoms of systemic inflammation such as spiking fever, rash and serositis. It is considered an autoinflammatory disease with a major role for the innate immune system, reflected by extremely high serum levels of S100 proteins and interleukin (IL)-18. How the number of monocytes and neutrophils relate to the increased levels of S100-proteins and IL-18 and to sJIA disease progression is still unknown.To study the role of monocytes and neutrophils in the inflammatory cascade of sJIA.ex vivo cell frequencies and cell surface activation markers of sJIA patients at disease onset, in remission and healthy controls by flow cytometric analysis. For the in vitro assessment of neutrophils, we stimulated whole lysed blood or isolated neutrophils with S100-proteins, IL-18, platelet-activating factor (PAF) with or without Formyl-Methionyl-Leucyl-Phenylalanine (fMLP) or phorbol 12-myristate 13-acetate (PMA) and determined intracellular ROS production, degranulation and apoptosis. To investigate the role of monocytes, we stimulated peripheral blood mononuclear cells (PBMCs) from sJIA patients and healthy controls with S100-proteins (+/- ATP) or other TLR-ligands and determined the concentration of cytokines in the supernatant by multiplex immunoassays.We determined ex vivo expression of Fc-gamma receptors (CD32 and CD64), markers of secretory vesicles (CD35) and specific granules (CD66b) compared to healthy controls. Neutrophils from new onset sJIA showed enhanced ROS production and degranulation and appeared to be more resistant to apoptosis. In contrast to the hyperactivated status of neutrophils in active sJIA,, PBMCs from these patients produced less IL-18 upon S100 stimulation compared to PBMCs from the same patient in remission or healthy controls. The same trend was observed when PBMCs from sJIA patients were stimulated with LPS, TLR2- or TLR7/8 ligands, suggesting cross-tolerance in these patient cells.Patients with new onset sJIA had significantly elevated neutrophil counts compared to healthy controls and sJIA patients with clinically inactive disease, while the amount of monocytes was not significantly different between the groups. Neutrophils from new onset sJIA patients showed an activated phenotype, reflected by higher Although monocytes from sJIA patients with active disease are less responsive towards stimulation, neutrophil counts, ROS production and degranulation are clearly elevated. The exact role of each cell type and activity and their interaction in sJIA pathology is currently under investigation."} +{"text": "The targeted integration of transgenes into a pre-characterized genomic locus enables predictable protein expression to occur, which reduces the need for the screening of transfected clones. We previously developed an accumulative site-specific gene integration system (AGIS), which enabled the repeated integration of multiple transgenes into a pre-determined locus of the cell genome ,2. We acWe constructed a donor plasmid encoding a DsRed gene upstream of a scFv-Fc expression unit flanked by a wild-type loxP and a mutated loxP (P2R-scFvFc). An insulator element derived from the CHO cell genome was located either side of the scFv-Fc expression cassette. Recombinant CHO cells (CHO/P1G) containing EGFP flanked by compatible target sites were used as founder cells . CHO/P1GFollowing transfection of the donor plasmid with a Cre expression vector (5 ng) into founder cells, we screened recombinant cells exhibiting a fluorescent color shift from green to red via the Cre/loxP reaction Figure . A totalTransgenes were integrated into a predetermined chromosomal locus of CHO cells using AGIS. The rapid screening of recombinant cells using a FACS device was based on a shift in fluorescence. RMCE-completed clones exhibited similar levels of scFv-Fc productivity and fluorescent protein expression. Moreover, higher and more stable scFv-Fc production was achieved using the insulator insertion.This work was partially funded by a project to build infrastructure for creating next-generation drugs for personalized medicine from the Ministry of Economy, Trade and Industry (METI), Japan; and the Kato Memorial Bioscience Foundation. The insulator element derived from the CHO cell genome was provided by Toyobo ."} +{"text": "Single bolus quantitative myocardial perfusion is sensitive to systematic errors due to the non-linear relationship between contrast agent concentration and MR signal. These errors can be minimised by using a low dose contrast bolus or by altering the imaging sequence parameters. However, these approaches substantially reduce the contrast to noise ratio of the images increasing the noise in the myocardial blood flow (MBF) values. This study compared two techniques proposed to address these issues; the dual-bolus technique and dual-sequence imaging.Seven patients undergoing outpatient investigation for suspected coronary artery disease underwent rest and adenosine induced stress dynamic contrast enhanced myocardial perfusion CMR. A pre-bolus of 0.005mmol/kg of Gadovist\u00ae was used followed by a main bolus of 0.05mmol/kg. Injection volumes and rates were matched. Imaging was performed using a saturation-recovery prepared turbo gradient echo (SR-TGE) sequence to acquire three slices through the heart with a pre-pulse delay (PPD) of 95.9ms. The Philips instantaneous scan-switching/interleaving capability was used to acquire an additional low resolution (64x64 acquisition matrix) image directly after the first-slice saturation pulse with a PPD of 24.3ms. Pre-contrast proton density weighted (PDW) images were acquired using the same pulse sequence with the saturation pulse turned off. Enhancement curves were converted to concentrations using the pulse sequence equation and parameters in addition to the pre-contrast signal and PDW values. Curves were selected for the two analyses as shown in the figure and the area under the curve (AUC) of each AIF was calculated. MBF values were generated using Fermi-constrained deconvolution.The quantitative perfusion results are summarised in the table. Dual-bolus MBF values were significantly smaller than dual-sequence values (p<0.05) and gave a greater MPR (borderline significance p=0.06). The AUC of the dose corrected pre-bolus was significantly greater than that for the bolus (p<0.05).Both methods generated MBF estimates that are within literature ranges. However, the values between the two methods differed significantly. The AUC of the main bolus was lower than that of the dose corrected pre-bolus. This would be consistent with a reduced dose ratio, perhaps due to dilution of the main bolus in the line, or inaccuracies in the concentration conversion procedure, due to the limitations of the imaging sequence (e.g. an imperfect saturation and/or readout pulses). These results call into question the accuracy of these techniques and highlight the need for future studies to isolate the causes of these discrepancies.During this work S Plein was funded by a British Heart Foundation fellowship (FS/10/62/28409). S Plein received an educational research grant from Philips Healthcare. David Broadbent was funded by an NIHR fellowship NIHR-DRF-2012-005-155."} +{"text": "MR dual bolus (DB) perfusion imaging has been effectively shown to eliminate signal saturation of the arterial input function (AIF) and allow more reliable quantification of myocardial (Myo) blood flow (MBF). Single bolus (SB) protocols are prone to AIF signal saturation but have been widely used in clinical studies. The Fermi model has been well established for MBF quantification. The distributed parameter (DP) model has been implemented in a recent study to measure additional physiological parameters (PP) such as intravascular (vb) and extravascular-extracellular space (ve) of the coronary arteries (CAs). Our study aims to a) validate absolute values, correlations and differences between SB versus DB estimates and b) assess which model more reliably fits SB data.After informed consent, 8 healthy volunteers underwent adenosine stress-rest MR myocardial perfusion imaging . A dilute (0.006 mmol/kg) Gd-based contrast agent was injected to allow extraction of the AIF for the DB analysis followed by a standard (0.03 mmol/kg) Gd dose for the extraction of Myo signal intensity curves . Images were acquired in mid-diastole. SB AIF data were generated by extracting the AIF from the standard Gd dose component of the DB data. Signal intensity AIF and Myo curves were converted to Gd concentration curves . The Fermi model was used to quantify MBF as a reference standard against DP-MBF . DP and Fermi values were examined both in SB and DB data. Bland Altman plots and paired t-test were used for data analysis.The most significant difference between SB and DB parameter estimates was observed in the Fermi model during stress Table p < 0.01DP-MBF and PP values were not significantly affected when SB AIF was used which suggests that DP model might more reliably model SB data than Fermi. This should be further investigated in larger populations. PS was low compared to previous mid-systole analysis, suggesting that DP may show potential in detecting decreased permeability of the CAs in mid-diastole.This work was made possible through funding and continued support from the British Heart Foundation."} +{"text": "Levels of myostatin expression and physical activity have both been associated with transcriptome dysregulation and skeletal muscle hypertrophy. The transcriptome of triceps brachii muscles from male C57/BL6 mice corresponding to two genotypes (wild-type and myostatin-reduced) under two conditions was characterized using RNA-Seq. Synergistic and antagonistic interaction and ortholog modes of action of myostatin genotype and activity level on genes and gene pathways in this skeletal muscle were uncovered; 1,836, 238, and 399 genes exhibited significant activity-by-genotype interaction, genotype and activity effects, respectively. The most common differentially expressed profiles were (i) inactive myostatin-reduced relative to active and inactive wild-type, (ii) inactive myostatin-reduced and active wild-type, and (iii) inactive myostatin-reduced and inactive wild-type. Several remarkable genes and gene pathways were identified. The expression profile of nascent polypeptide-associated complex alpha subunit (Naca) supports a synergistic interaction between activity level and myostatin genotype, while Gremlin 2 (Grem2) displayed an antagonistic interaction. Comparison between activity levels revealed expression changes in genes encoding for structural proteins important for muscle function and for fatty acid metabolism . Conversely, comparison between genotype groups revealed changes in genes associated with G1-to-S-phase transition of the cell cycle of myoblasts and the expression of Grem2 proteins that modulate the cleavage of the myostatin propeptide. A number of myostatin-feedback regulated gene products that are primarily regulatory were uncovered, including microRNA impacting central functions and Piezo proteins that make cationic current-controlling mechanosensitive ion channels. These important findings extend hypotheses of myostatin and physical activity master regulation of genes and gene pathways, impacting medical practices and therapies associated with muscle atrophy in humans and companion animal species and genome-enabled selection practices applied to food-production animal species. Genetic and non-genetic conditions impact the molecular pathways and physiology of the skeletal muscle. The myostatin (Mstn) gene encodes a growth and differentiating factor and hormonal protein responsible for inhibition of muscle growth and proliferation in vertebrates. Myostatin negatively regulates muscle fiber number during skeletal muscle development \u20132 and inPhysical activity influences muscle fiber in manners akin to the effect of myostatin deficiency . ContracWhile targeted genetic and non-genetic studies have associated skeletal muscle hypertrophy to dysregulation of the IGF1-Akt-mTOR and myostatin-Smad2/3 signaling pathways, muscle atrophy has been associated to dysregulation of the autophagic-lysosomal and proteasomal pathways . StudiesFew studies have evaluated the simultaneous effects of physical activity and myostatin genotype on the transcripts in the skeletal muscle of mice , 15. ResThis study characterizes the complete transcriptome of triceps brachii muscles from C57/BL6 mice representing one of two genotype transcript levels and one of two physical activity levels (high and low) using massive parallel next-generation RNA sequencing. Synergistic, antagonistic and ortholog modes of action of the factors myostatin genotype and activity on genes and gene pathway profiles were investigated. This study is supported by: (a) mapping RNA sequencing reads to the mouse genome, identification of differentially expressed genes, and testing for differential expression among activity-genotype combination groups; (b) identification and interpretation of gene profiles revealing significant interaction between genotype and activity; (c) identification and interpretation of gene profiles revealing significant genotype (or activity) effect irrespective of activity (or genotype); and (d) functional analysis in support of the identification and interpretation of biological processes and pathways associated with genotype and activity levels. Our findings provide a basis to understand multifactorial gene regulation and dysregulation in triceps brachii and other skeletal muscles of mice.ad libitum access to food and water and kept in a 12-hour dark cycle. Myostatin-reduced mice were developed from C57/BL6 mice with floxed myostatin that was activated using Cre recombinase. At 4 months of age, all mice were fed chow with 0.025% tamoxifen content for 6 weeks to activate the Cre Recombinase enzyme and deplete myostatin only in mice with floxed myostatin genes. Myostatin was under-expressed (approximately 85%) in the myostatin-reduced mice. One week after the end of the tamoxifen feeding (approximately 6 months of age), mice in the active group were moved to be housed individually and given free access to running wheels during the last 12 weeks of the study. Physical activity was monitored and the sum over 1-hour periods was recorded. At the end of the wheel-running period, all mice were euthanized and samples taken from their triceps brachii muscles were frozen in melting isopentane and stored at \u221270\u00b0C. Muscles were sampled from myostatin-reduced and control mice that were matched for running behavior; this was done to ensure that the amount of physical activity performed was not a contributor to differences in gene expression between control and myostatin-reduced mice. Polyadenylated RNA was extracted as directed by Invitrogen using a Trizol reagent, converted to cDNA, and amplified with an Illumina TruSeq RNA library preparation kit following manufacturer instructions.Profiling information stems from an experiment comparing the transcriptome of a skeletal muscles, triceps brachii muscle of adult (6 months of age) male C57/BL6 mice. Difference in gene expression associated with two factors were studied. The factor termed genotype encompasses two levels: wild-type mice exhibiting baseline expression of the myostatin gene and myostatin-reduced mice exhibiting lower expression of the myostatin gene. The factor termed activity encompasses two levels: inactive and active. Four physical activity-by-genotype combination groups of mice were compared (n = 3/group): (1) active and myostatin-reduced, (2) inactive and wild-type (control genotype); (3) inactive and myostatin-reduced; and (4) active and wild-type. Prior to the trial, mice were housed in standard cages in groups of 2 or 3, given http://www.ncbi.nlm.nih.gov/refseq/) of transcripts were counted. Exon-level data was consolidated to gene-level read counts and summarized. Data normalization was performed so trimmed column means (excluding the highest and lowest 5th percentiles) were equal for all samples. In total, 13 protein-coding mtDNA transcripts were mapped to NC_005089.1, counted separately, and normalized to the trimmed mean of the non-mitochondrial transcripts. The transcriptome data, additional experimental details and preliminary analysis are available in the National Center for Biotechnology Information, Gene Expression Omnibus database, accession number GSE31839 [Triceps brachii muscle transcriptome was studied using Illumina Genome Analyzer IIx producing 65-base long single-end reads. Data processing was performed using CASAVA software. The 65-base sequence reads were mapped to the mouse genome (mm9) using default settings and reads mapping to exons in the Refseq database (GSE31839 . Resultshttp://genome.ucsc.edu). Prior to mapping, FastqGroomer was used to convert file format to FastqSanger [Mus musculus mitochondrion, complete genome), counted separately, and normalized to the trimmed mean of non-mitochondrial transcript counts. Sequence reads were mapped using Tophat (v1.4.0), transcript isoforms were identified, quantified in number of fragments per kilobase of exon per million mapped reads (FPKM) [The 65-base, single-end sequence reads from FastQ files were mapped to the mouse mm10 genome assembly accessed from the UCSC Genome Browser database (tqSanger and FasttqSanger . Using Fs (FPKM) , and difs (FPKM) . Differes (FPKM) \u201321. Falss (FPKM) \u201324. The s (FPKM) \u201327. Comps (FPKM) .http://david.abcc.ncifcrf.gov). The Gene Ontology (GO) functional categories investigated included biological process (BP) and molecular function (MF), the biological objective to which the gene or its product contributes or the biochemical activity of a gene product, respectively [Enrichment of functional categories and pathways among the differentially expressed genes was explored using the web service Database for Analysis, Validation, and Integrated Discovery activity-by-genotype interaction, alternative profiles of over- and under-expression or non-significant differential expression in each of the six contrasts between pairs of activity-genotype combinations were identified. The concept of synergism and antagonism has been used previously in studies on expression and regulation . While pPresentation of findings. Findings are presented and discussed in a sequence starting with genes exhibiting significant activity-by-genotype interaction, followed by genes exhibiting significant main effects of activity or genotype. Genes corresponding to transcripts exhibiting significant > |1.3|) differential expression are identified in the Results section and their profiles are discussed in the Discussion sections. Broader lists of genes reaching a lower significance threshold are presented in the supplementary materials . Of these, 5,013,631 (28.7%) had multiple alignments .Overall, 1,836 genes exhibited significant activity-by-genotype interaction. Patterns of differential gene expression across activity-genotype contrasts. The number of differentially expressed genes for AW-IM, AM-AW, AM-IM, IW-AW, IW-AM, and IW-IM was 1,051, 86, 711, 119, 238 and 390, respectively. Several interpretations can be made from the progression of number of differentially expressed genes starting with the highest number in AM-IM followed by AM-IM, followed by IW-IM followed by AM-AW. Firstly, activity level was associated with more differentially expressed genes in myostatin-reduced mice than in the wild-type mice. Also, genotype was associated with more differentially expressed genes in active relative to inactive mice. Among all activity-genotype combination groups, inactive myostatin-reduced mice exhibited the most number of differentially expressed genes relative to other activity-genotype combinations, including the highest number of over-expressed genes at FDR-adjusted P-value < 0.01. On the other hand, active wild-type mice exhibited the fewest number of differentially expressed genes relative to all other activity-genotype combinations, and these genes were overexpressed at FDR-adjusted P-value < 0.01.Among active mice, the genotype difference was associated with the fewest number of differentially expressed genes among all pairwise contrasts. Likewise, among wild-type mice, activity level was associated with the second lowest number of differentially expressed genes among all pairwise contrasts. In contrast, changes in activity level elicited more differentially expressed genes in myostatin-reduced mice than in wild-type mice.Functional enrichment analysis of activity-genotype contrasts. Functional enrichment analysis was performed on genes exhibiting differential expression between pairs of activity-genotype combination groups for each of the six contrasts individually. Clusters of categories exhibiting enrichment scores > 3.0 were considered for discussion. These functional enrichment results can be found in Tables B to F in Notably, some functional categories enriched among the genes differentially expressed in the IW-IM contrast The genes exhibiting the most significant interaction effect including the log2 fold change between pairs of activity-by-genotype groups and the overall FDR-adjusted P-value are presented in Other genes that exhibited a significant interaction did not reach high significance in particular contrasts; however, the integration of consistent borderline significant contrasts resulted in a significant overall interaction effect . ExampleThe interaction pattern of cysteine and glycine-rich protein 3 (CSRP3) and Myozenin 2 (Myoz2) were characterized by highest expression in inactive myostatin-reduced mice relative to all other activity level-genotype groups. The consistent interaction patterns of Myosin, light polypeptide 2 (Myl2) and myosin, light polypeptide 3 (Myl3) can be summarized by over-expression in inactive myostatin-reduced mice relative to all other activity level-genotype groups. The pathways of these Myosin genes could result in this consistent profile. Myosin light chains (Myls) modulate muscle contraction and may be involved in myogenesis or muscle regeneration \u201337.Clusters of expression profiles among genes exhibiting significant activity-by-genotype interaction. Within the genes that exhibit significant interaction, various profiles of over- and under-expression were identified. However, the joint functional analysis of these groups may hinder or bias the discovery of enriched categories. Thus, discretizing the pairwise contrasts into over-, under- and non-differentially expressed identified clusters of genes exhibiting common expression profiles across the six contrasts. Profiles including more than 100 genes were subjected to functional enrichment analysis in DAVID. Tables Gene under-expression in active wild-type and active myostatin-reduced relative to inactive myostatin-reduced is a clear example of activity-by-genotype interaction because the combination of inactivity and myostatin-reduced genotypes was associated with higher gene expression than activity (regardless of genotype). Among genes sharing the first profile (under-expression in active wild-type and active myostatin-reduced relative to inactive myostatin-reduced) one highly enriched functional cluster (enrichment score = 16.28) was identified . This clAmong the profile cluster characterized by genes under- or over-expressed in the AW-IM contrast and not differentially expressed in all other contrasts , five fuAmong the profile characterized by genes under- or over-expressed in the AM-IM contrast and not differentially expressed in all other contrasts , the funClusters of functional categories enriched (enrichment score > 3.0) among the genes differentially expressed between genotypes are listed in Clusters of functional categories enriched (enrichment score > 3.0) among the genes differentially expressed between activity levels are listed in Both genotype and activity level were associated with significant changes in gene expression, irrespective of the remainder factor indicating main effects. The more extreme fold change estimates observed in the genotype relative to the activity contrasts indicate that the genotypes considered in this study have a higher impact on gene expression than the physical activity levels evaluated Tables and 9.Common expression profiles. The patterns of differential gene expression across activity-genotype contrasts provided insight into activity-by-genotype interaction effect on gene expression in triceps brachii muscles. The identification of 33 genes shared between one set of the three orthogonal contrast groups including the baseline group set, inactive wild-type mice suggests a specific role of these genes in inactive wild-type mice that are sensitive to changes in the activity-genotype condition were associated with the fewest number of differentially expressed genes (86 genes), suggesting that activity may be picking up and modulating or compensating some expression regulated by myostatin. The second lowest number of differentially expressed genes (119 genes) was related to differences in activity level within wild-type mice (contrast IW-AW), indicating that activity alone was associated with more limited changes in gene expression than those observed in the combination of activity and myostatin reduction. Finally, considering the fact that activity level elicited more differentially expressed genes in myostatin-reduced than in wild-type mice along with the finding that the greatest number of differentially expressed genes is in the AW-IM contrast confirms the hypothesized synergistic impact of physical activity and the silencing of myostatin on gene expression.Functional enrichment within profiles. Functional enrichment analysis of the activity-genotype contrasts offered insights into the impact of the activity-genotype combinations on GO MF and BP categories and KEGG pathways. Differentially expressed genes in the AM-IM and the IW-AW contrasts exhibited enrichment of the tricarboxylic acid cycle TCA cycle (mmu00020) KEGG pathway and a number of GO MF terms linked to metabolism of cofactors and vitamins that are also linked to these metabolic pathways. These enriched categories are consistent with the higher metabolism of active muscles; elevated amino acid and energy metabolism are seen in muscles of physically active mice, and presumably this elevated amino acid metabolism maintains the TCA cycle intermediates needed for fatty acid metabolism [tabolism .Muscle cell differentiation (GO:0042692) and muscle organ development (GO:0007517) were two BP terms enriched among the genes differentially expressed in the IW-IM and AM-AW contrasts. These categories are consistent with the known role of myostatin on cell differentiation and proliferation in triceps. Multiple studies have confirmed the direct impact of myostatin on these muscles. Specifically, myostatin-deficient mice have significantly larger tricep muscles than wild-type mice \u201341. MyosEnrichment of hypertrophic and dilated cardiomyopathy KEGG pathways was observed among genes differentially expressed in the IW-IM and AM-AW contrasts. Although hypertrophic cardiomyopathy is characterized by an hypertrophied heart muscle while tricep samples were used in this study, our results suggest that the expression of genes in similar biological processes are altered by myostatin genotype regardless of activity level. Our result is consistent with a previous report that a hypertrophic cardiomyopathy mutation is expressed in the messenger RNA of skeletal as well as cardiac muscle .Finally, enrichment of the vasculature development BP (GO:0001944) among the genes differentially expressed in the AM-IM and IW-IM contrasts suggests that activity level within myostatin-reduced mice and myostatin genotype within inactive mice have comparable impact on the expression of genes in the vascular development pathway. While inactivity may have counteracted the effect of myostatin reduction in the former contrast, myostatin reduction may have counteracted the effect of inactivity in the latter contrast. Our results offer support at the gene expression level to claims that the processes that regulate blood vessel development can also enable the adult to adapt to changes in tissues that can be elicited by activity or pathologies .Notable genes. Consideration of individual genes exhibiting significant activity-by-genotype interaction further augmented the understanding of the interplay between activity and myostatin genotype on the triceps brachii muscle transcriptome in C57/BL6 mice. PAK1 displayed consistent borderline significant differential expression across multiple contrasts, resulting in a significant overall interaction effect. A study of target genes of myostatin loss-of-function in muscles of bovine fetuses identified PAK1 [ied PAK1 . The comied PAK1 may leadied PAK1 . This fuied PAK1 . The expied PAK1 and thisCSRP3 and Myoz2 shared the same interaction pattern of highest expression in inactive myostatin-reduced relative to all other activity level genotype groups. The parallel expression profiles of these two genes detected in the present study is in agreement with previous reports. The expression of CSRP3 and Myoz2 is high in skeletal muscles \u201350, posiClusters of expression profiles among genes exhibiting significant activity-by-genotype interaction were identified as well. Among genes sharing the first profile , KEGG pathways for several inflammation-associated neurodegenerative conditions including Parkinson\u2019s disease, Alzheimer\u2019s disease, and Huntington\u2019s disease were enriched. Our results are in agreement with reports that myostatin causes sporadic inclusion body myositis (sIBM), a muscle-wasting disease that has pathogenesis similar to that of Alzheimer\u2019s and Parkinson\u2019s diseases . Also, aAdditionally, oxidative phosphorylation, electron transport chain, energy generation, and mitochondrial ATP synthesis GO terms were enriched among the profile characterized by genes under- or over-expressed in the AW-IM contrast and not differentially expressed in all other contrasts. These findings are consistent with the electron transport chain, or the flow of electrons resulting from NADH and FADH2 oxidation, that establishes an electrochemical gradient vital in powering ATP synthesis in oxidative phosphorylation, the final stage of aerobic cell respiration. Myostatin reduction, although not affecting phosphorylated compound concentrations and intracellular pH at rest, causes up to a 206% increase in ATP cost of contraction as well as limiting the shift toward oxidative metabolism during muscle activity . Muscle Antagonistic and synergistic expression patterns. Finally, using genes exhibiting significant genotype-by-activity interaction effects, antagonistic and synergistic expression patterns were identified. Synergistic effects occur when the expression of a gene under a combination of genotype and activity levels is more extreme than the average expression under each level separately. Antagonistic effects occur when the expression of a gene under a combination of genotype and activity levels is less extreme than the average expression under each level separately. An example of synergistic pattern would be when a gene that has high over-expression (e.g. 4 fold) in myostatin inactive relative to the average of all other groups meanwhile the expression in myostatin relative to wild type and the expression in inactive relative to active are less or non-significant (e.g. less than 2 fold). An example of antagonistic pattern would be a gene that is not or less differentially expressed (e.g. 1 fold) in myostatin inactive mice relative to the average of all other groups meanwhile the expression in myostatin relative to wild type and the expression in inactive relative to active are more significant or extreme (e.g. more than 3 fold).Examples of synergistic or antagonistic mode of action of genotype and activity factors on gene expression are listed in The identification of significant interactions enabled the detection of synergistic effects between genotype and activity. For genes Naca, Dusp23, and Dhcr24, the difference in expression between myostatin genotype groups was more extreme than between activity groups > |1.3|) between myostatin-reduced and wild-type mice , the fun) of differentially expressed genes between myostatin-reduced and wild-type mice in triceps brachii muscles can be found in Table G in Among the rest of the genes differentially expressed between genotype groups, four provided remarkable insight into myostatin\u2019s effects on the gene networks of muscle development. The protein coded by the Piezo-type mechanosensitive ion channel component 1 (Piezo1) allows cells to react to physical stimuli. Mechanosensitive ion channels play a key role in the physiology of smooth muscle ,76\u201377. CMany of the differentially expressed genes between active and inactive mice, unsurprisingly, are associated with the biological processes of contractile response of muscles to activity. A notable finding is that Ercc2 was differentially expressed between genotype groups and between activity groups as well, yet this gene did not exhibit a significant activity-by-genotype interaction effect. A similar molecular mechanism is speculated for both comparisons. Among other genes differentially expressed between activity groups, Tnnt1 plays anNovel associations between differentially expressed genes and activity level were also identified in this study. Many of these genes have indirect links to muscle function and activity, but the actual mechanism uncovered is unique and unexpected. The differentially expressed gene 3-hydroxybutyrate dehydrogenase (Bdh1) encodes an enzyme involved in the interconversion of acetoacetate and (R)-3-hydroxybutyrate, essential for fatty acid catabolism. Also, Bdh1 mRNA is found in all forms of muscle . The rolThe enrichment of GO biological process terms related to vasculature development among the genes differentially expressed in the AM-IM and IW-IM contrasts suggests that the combination of activity and myostatin-reduced genotype has comparable impact to the combination of inactivity and wild-type typical myostatin genotype on the expression of genes in the vascular development pathway. A link between vascular development and muscle development is expected based on the logical physiological association of the two organ systems. Vasculature is modified in order to meet the metabolic requirements of tissue cells in response to changes in metabolic rate; oxygen is a major control element of this adaptation, as hypoxia initiates various signals which in turn lead to an increase in vessel growth . Given tThe study of the impact of physical activity and myostatin level on gene expression in the triceps brachii muscles of C57/BL6 mice uncovered novel and confirmed known associations at the gene and gene network levels. Novel and significant interaction effects were observed for some genes including synergistic effects and antagonistic effects . Functional analysis of genes presenting significant interaction effects uncovered novel (e.g. angiogenesis) and expected enriched pathways and biological processes.Among the genes exhibiting significant main genotype effect, known and novel associations were detected. Functional analysis of genes presenting significant genotype effect uncovered novel (e.g. dilated and hypertrophic cardiomyopathy) and expected enriched pathways and biological processes. Likewise, among the genes exhibiting significant main activity effect, known associations were detected. Functional analysis of genes presenting significant activity effect uncovered novel and expected enriched pathways and biological processes. While several genes and functional categories enriched among the differentially expressed genes uncovered in this study were consistent with previous reports, the identity and profile of the genes exhibiting the most extreme interaction and main genotype and activity effects opened new avenues of inquiry on the role of specific genes in skeletal muscle development and the effects of myostatin and physical activity on muscle function. The present study centered on the comparison of four genotype-activity groups based on transcriptome information from a specific skeletal muscle type, mouse strain, gender, and age. Consideration of additional muscle types, genotypes, activities, ages, and genders would help identify additional synergistic and antagonistic relationships between these factors.The findings from the present study could have medical implications on preventive practices and therapies associated with muscle atrophy in humans and companion animal species and genome-enabled selection practices applied to food-production animal species. The study of changes in gene expression in response to myostatin gene expression level in skeletal muscle tissue involved genes that code for a number of proteins that are feedback regulated by the myostatin molecule. The functions of the genes exhibiting differential expression between genotype groups are primarily regulatory. This functional category includes microRNA and Piezo proteins that make the list of the top 10 differentially expressed genes, side-by-side with Grem2 proteins that modulate the metalloprotein BMP-mediated cleavage of the myostatin propeptide. The role of genes regulated by microRNAs was unanticipated, especially because these genes seem to impact central functions such as the G1 to S phase transition of the cell cycle of myoblasts. The role of genes coding for Piezo proteins that make mechanosensitive ion channels, which in turn regulate cationic currents in the cells, was also remarkable and unanticipated, especially because of the consistent profile of the genes in this family. The study of changes in gene expression patterns in response to activity level revealed enrichment of genes that code structural proteins important for muscle function, including troponin, tropomyosin and myoglobin proteins. Activity was also associated with differential expression of genes important for fatty acid metabolism, some linked to type II diabetes and obesity and others to DNA-repair capacity, stem cell renewal, and various forms of cancer.Our results provide evidence supporting the role of myostatin as a master regulator and the hypothesis that physical activity affect the expression of genes associated with homeostatic balance between storage of fat and muscle growth. Down-regulation of myostatin expression enables muscle growth at full expense of storage of fat, a condition that is hardwired at the regulatory level . During activity, the changes in gene expression associated with balance between storage of fat and growth appears more instantaneous and subtle. This balance involves the regulation of metabolic pathways of fatty acid synthesis and does not impinge on oxidative phosphorylation pathways. The master regulatory functions of myostatin identified in this study should now be explored at the biochemical level to identify details of the regulatory networks, especially because of their potential to assist in the development of muscular disorders.S1 FileTable A: Differentially expressed genes across activity-genotype contrasts.Table B: Enriched (enrichment score > 3) clusters of Gene Ontology (GO) biological process (BP), molecular function (MF) Functional Annotation Tool (FAT) categories, and KEGG pathways among differentially expressed genes in the active myostatin-reduced vs jnactive myostatin-reduced contrast group.Table C: Enriched (enrichment score > 2.0) clusters of Gene Ontology (GO) biological process (BP), molecular function (MF) Functional Annotation Tool (FAT) categories, and KEGG pathways among differentially expressed genes in the inactive wild-type vs active wild-type contrast group.Table D: Enriched (enrichment score > 3) clusters of Gene Ontology (GO) biological process (BP), molecular function (MF) Functional Annotation Tool (FAT) categories, and KEGG pathways among differentially expressed genes in the inactive wild-type vs inactive myostatin-reduced contrast group.Table E: Enriched (enrichment score > 3) clusters of Gene Ontology (GO) biological process (BP), molecular function (MF) Functional Annotation Tool (FAT) categories, and KEGG pathways among the genes differentially expressed between active and inactive mice clusters of Gene Ontology (GO) biological process (BP), molecular function (MF) Functional Annotation Tool (FAT) categories, and KEGG pathways among differentially expressed genes in the active wild-type vs inactive myostatin-reduced contrast group.Table G: Genes differentially expressed between myostatin-reduced and wild-type mice in triceps brachii muscle.Table H: Enriched (enrichment score > 3) clusters of Gene Ontology (GO) biological process (BP), molecular function (MF) Functional Annotation Tool (FAT) categories, and KEGG pathways among differentially expressed genes between triceps brachii muscle of myostatin-reduced and wild-type mice.Table I: Genes differentially expressed between active and sedentary mice in triceps brachii muscle.Table J: Enriched (enrichment score > 2) clusters of Gene Ontology (GO) biological process (BP), molecular function (MF) Functional Annotation Tool (FAT) categories, and KEGG pathways among differentially expressed genes between triceps brachii muscle of active and sedentary mice.(DOCX)Click here for additional data file."} +{"text": "Knee joint distraction (KJD) is a novel, but poorly understood, treatment for osteoarthritis (OA) associated with remarkable \u2018spontaneous\u2019 cartilage repair in which resident synovial fluid (SF) multipotential mesenchymal stromal cells (MSCs) may play a role. We hypothesised that SF hyaluronic acid (HA) inhibited the initial interaction between MSCs and cartilage, a key first step to integration, and postulate that KJD environment favoured MSC/cartilage interactions.Attachment of dual-labelled SF-MSCs were assessed in a novel in vitro human cartilage model using OA and rheumatoid arthritic (RA) SF. SF was digested with hyaluronidase (hyase) and its effect on adhesion was observed using confocal microscopy. MRI and microscopy were used to image autologous dual-labelled MSCs in an in vivo canine model of KJD. SF-HA was investigated using gel electrophoresis and densitometry.Osteoarthritic-synovial fluid (OA-SF) and purified high molecular weight (MW) HA inhibited SF-MSC adhesion to plastic, while hyase treatment of OA-SF but not RA-SF significantly increased MSC adhesion to cartilage These differences were linked to the SF mediated HA-coat which was larger in OA-SF than in RA-SF. OA-SF contained >9\u2005MDa HA and this correlated with increases in adhesion (r=0.880). In the canine KJD model, MSC adhesion to cartilage was evident and also dependent on HA MW.These findings highlight an unappreciated role of SF-HA on MSC interactions and provide proof of concept that endogenous SF-MSCs are capable of adhering to cartilage in a favourable biochemical and biomechanical environment in OA distracted joints, offering novel one-stage strategies towards joint repair. End stage osteoarthritis (OA) is inevitably associated with severe articular cartilage loss and joint failure.10There is an emerging interest in the use of multipotential mesenchymal stromal cells, also termed mesenchymal stem cells (MSCs) and/or scaffolds for joint repair.We and others previously described a synovial fluid (SF) resident MSC population in OA, rheumatoid arthritic (RA) and non-arthritic joints, where elevated numbers were seen in early and advanced OA14Key endogenous factors leading to intrinsic cartilage repair are likely associated with SF-MSCs, joint biomechanics and SF homeostasis including growth factors and hyaluronic acid (HA) composition. Given that SF-MSCs highly express CD44,All samples were collected following written informed consent with relevant ethical approval. Cartilage samples were obtained during total knee replacement surgery. OA-SF and RA-SF was collected from patients undergoing joint replacement or aspirated during routine clinics. For SF samples, cells were pelleted at 16\u2005000\u2005rcf for 5\u2005min and SF frozen at \u221280\u00b0C. SF-MSCs were derived and expanded as previously described.164 per OC plug) were resuspended in either a culture medium, OA-SF or RA-SF with or without addition of hyaluronidase before being added to the OC plug and incubating overnight at 37\u00b0C. Thereafter, the cartilage surface was gently washed and adherent SF-MSCs were fixed in 3.7% formalin. Confocal microscopy was used to image attached cells.SF-MSCs were dual-labelled with fluorescent micro-sized particles of iron oxide . Macroscopically normal osteochondral (OC) plugs (8\u2005mm diameter) were placed into a preformed 8\u2005mm diameter well of sterile 2% agarose. FMPIO-SF-MSCs .6 autologous cells injected into the synovial cavity in 1\u2005mL saline supplemented with 5% canine serum 72 h after placement of the external fixation frames. Each animal was allowed to continue normal daily activities before euthanising 48 h after MSC injection, whereby the joints were dissected and fixed in formalin.Canine Groove model of OA was bilaterally induced in the right and left stifle joints in three dogs.Statistics were performed using SPSS Statistics V.21 . Unless otherwise stated, all data were treated as non-parametric. Where applicable, paired analysis was done using the Wilcoxon Signed Ranks and non-paired using the Mann-Whitney U test. Correlations were calculated using the Spearman's rank correlation coefficient for non-parametric data. For further details please see online supplementary information.Recovery and expansion of SF-MSCs directly from SF was poor; however, by replacing SF with culture medium, cells readily adhered and proliferated on tissue culture plastic A. To invHA is known to mediate cell adhesion;To further clarify the role of HA and to specifically exclude another unanticipated effect of hyase, we used purified, commercially obtained preparations of high and low MW HA to supplement culture medium. We observed that, only HMWHA inhibited SF-MSC adhesion from three different donors E.We used FMPIO labelled-MSCs in a novel in vitro adhesion model with OA derived cartilage, SF and SF-MSCs. Labelled SF-MSCs (see online supplementary figure S1) were added to the joint-facing surface of OC plugs in RA-SF or OA-SF with or without prior digestion of SF with hyase A. So as Each in vitro adhesion assay included a positive control whereby SF-MSCs were resuspended and added to OC plugs in culture medium used to normalise adhesion seen in SF and SF+hyase experiments (culture medium samples representing 100% adhesion). Representative confocal images from one adhesion assay using OA-SF are shown in The HA-coat is an important mediator in the initial stages of cell adhesion.Having identified a clear difference between OA-SF and RA-SF on the adhesion and induction of HA-coat formation with SF-MSCs, we further analysed the HA component of SFs. Agarose gel electrophoresis and densitometry were used to investigate the HA content of OA-SF and RA-SF F, G, comWe next sought to determine if this difference in VHMWHA correlated with the difference seen between changes in MSC adhesion to cartilage upon hyase digestion. A direct correlation between the proportion of VHMWHA in native SF and the fold change in adhesion after digestion of SF with hyase was seen against the hyperintense contrast (light areas) of the thin cartilage layer F in fourGel electrophoresis and densitometry were used to determine the HA content of SF from control and distracted joints J. SF-HA Remarkable yet poorly understood repair following KJD has been reported.We evaluated SF-HA and MSC adhesion in distracted and non-distracted OA canine joints. Using autologous labelled MSCs, adhesion to cartilage defects in these joints was observed. KJD was accompanied by a decrease in SF-HA in each animal when compared with the control, non-distracted joints, suggesting that increasing the joint space is accompanied by plasma effusion and equilibration of joint pressure, effectively diluting SF-HA. Joint effusion is also seen accompanying KJD in humans throughout the distracted period . Consistent with our in vitro data, the abundance of HMWHA species had a negative impact on cell adhesion within these defects. Thus confirming that in vivo HA also influences MSC/cartilage interactions. Finally, in long-term follow-up experiments (without addition of MSCs), KJD showed improved structural outcomes and reduced synovial inflammation indicating restoration of joint function (see online supplementary figure S4),HA is a major SF constituent, the concentration and MW of which determines SF viscosity. It is known to be reduced in RA and other inflammatory conditions.16The biology of HA has been investigated over several decades with a large body of knowledge having accrued in several fields but its role in MSC adhesion has been neglected. HA interacts with a variety of cell types via CD44 which is highly expressed on SF-MSCs.19Inflammation and tissue injury is associated with HA breakdownTo conclude, this work opens up novel possibilities for use of both minimally manipulated endogenous as well as culture expanded allogeneic MSCs, allowing their use in more favourable environments encouraging MSC/cartilage interactions. The recognition that joint resident MSCs may be capable of adhering to cartilage in a HA-dependent manner when placed in the correct mechanical environment also provides a potentially novel explanation for the success of KJD in human OA and encourages the development of cost-effective, one-stage joint saving therapies."} +{"text": "Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the protein-coding genes for CALD1, FTX, and HNRNPH1. In conclusion, a number of differentially expressed lncRNAs have been identified with relation to cancer-related protein-coding genes. We applied a custom expression microarray interrogating previously identified lncRNAs regulated in tumor-relevant pathways A custom expression microarray (GEO accession number GPL13648) was used to analyze the expression patterns of protein-coding and non-coding transcripts in total RNA from 26 well characterized breast tumor samples bona fide non-coding (subsequently referred as non-coding), if they did not exhibit any evidence for encoding functional open reading frames, as predicted by RNAcode significantly differentially expressed (DE) between normal and tumor samples DE-probes that mapped to 8282 unique genomic loci in intergenic or intronic space were non-coding, i.e. without any bioinformatic evidence for functional open reading frames or sequence similarity to known proteins. Non-coding DE-probes located antisense to exons of known protein-coding genes mapped to 1365 unique genomic loci.cis lncRNA expression changes. Correlation analysis of the 26 tumor samples utilizing data from 109k Illumina SNP array did not detect any in-cis correlation between copy number and lncRNA expression . FollowiTo investigate the biological variation of lncRNAs within tumor samples independent of known mRNA subtypes, we applied unsupervised hierarchical clustering. Uncertainty of derived clusters was assessed by random sampling with replacement . Hierarchical clustering based on probes mapping to protein-coding exons largely reproduced the known mRNA subtypes and reflected TP53 status, while hierarchical clustering based on non-coding probes revealed a different pattern . HoweverAn F-test was employed to assess, if the mean expression of a probe is equal for all five mRNA-based subtypes in our sample set. We identified 3175 probes that were significantly differentially expressed between any subtype odds ratios for DE-probes upregulated (downregulated) in tumor samples and transcriptionally active sites (H3K36 trimethylated) - as opposed to DE-probes downregulated (upregulated) in tumor samples and transcriptionally inactive sites (H3K27 trimethylated) - might be a consequence of the unequal composition of ENCODE ChIP-Seq data, which is mainly derived from normal cell lines .A less pronounced, but significant, enrichment was observed for transcription factor binding sites Within tumor samples, non-coding DE-probes, which were upregulated in Basal-like tumors compared to Luminal A and B tumor samples, were significantly enriched in promoters (H3K4 monomethylation), enhancers (H3K27 acetylation), and in regions known to be actively transcribed together with reports of previous studies about frequent We detected 416 protein-coding genes in nearest genomic proximity of 782 intergenic non-coding DE-probes, where both displayed significant differential expression variation between normal and breast tumor tissue and in introns of protein-coding genes (5088), further in antisense or bidirectional genomic location relative to protein-coding genes (1365). Several of the detected differentially expressed lncRNAs were well described members of cancer-related pathways, including tumor suppressors and oncogenes oncogenes in a direct or indirect way, and thus contribute to tumorigenesis. Overall, we found a significantly smaller distance of differentially expressed non-coding regions to the proximal protein coding gene than expected by randomly drawing from the transcripts represented on the custom array. We detected a massive deregulation of non-coding transcription from regulatory DNA sites upstream of protein coding sequences. These may partly correspond to short RNAs (50bp to 200 bp length) that are transcribed upstream of coding genes, which are known to be a target of polycomb proteins and can induce repression of coding genes in cisSeveral lncRNAs have been found to regulate gene expression in Further, we identified 311 protein-coding genes with proximal long non-coding RNAs in intergenic space and non-synonymous expression changes, suggesting that these lncRNAs may interfere with mRNA expression. Synonymous pairs were only assessed for RNAs on opposite strands to avoid counting of unknown mRNA exons and these synonymous pairs were significantly fewer than non-synonymous pairs. For the majority of non-synonymous pairs the protein-coding gene was found down- and the intergenic lncRNA was identified being upregulated in tumors samples. We noticed an enrichment of tumor suppressor protein-coding genes for mRNAs downregulated in tumor. Together with the fact that the majority of mRNAs were down- and the majority of non-coding transcripts were upregulated in tumors one may speculate whether the upregulation of lncRNAs contributes to the downregulation of tumor suppressor genes and thus to the progress of cancer.Cabili et al. 2011 found that the expression patterns of lincRNAs and their nearest protein-coding neighbour are not more correlated than pairs of two neighbouring protein-coding genes \u00d8rom et al. 2010 report intergenic non-coding RNAs acting as enhancers for their nearest protein-coding gene, which results in synonymous expression changes between non-coding RNAs and mRNAs In few cases, non-synonymous expression in opposite reading direction, exhibiting overexpression of breast cancer-associated mRNAs along with an antisense lncRNA downregulated in tumor samples, was detected. An example for a strongly anticorrelated, non-synonymous pair with a tumor-downregulated mRNA is HDAC3 and its antisense lncRNA transcript. We found HDAC3 expression in normal samples and strongly downregulated but detectable in tumor tissue samples. Class I histone deacetylases, like HDAC3, are repressing the transcription machinery for various genes in cancer cis by mediating chromatin modifications in close genomic proximity. We identified downregulated CARs in vicinity or overlapping the oncogenes IGF1R, MYLK trans through establishing repressive chromatin marks at distant sites cis or trans.In the breast cancer samples used for our investigations, we observed a massive downregulation of lncRNAs previously described to be a component of chromatin In summary, the observed massive deregulation of lncRNAs may be an important characteristic of breast cancer development and progression. The frequently observed anticorrelation between lncRNAs and adjacent breast cancer relevant onco- and tumor suppressor genes may give rise to novel drug targets at the non-coding RNA level. Finally, the perturbation of chromatin-associated lncRNAs encourages for a more detailed investigation of the role of lncRNAs in epigenetic reprogramming in breast cancer etiopathology.All studies are approved by the Norwegian Regional Committee (REC) for Medical and Health Research Ethics . All patients are informed and have declared written informed consent that their samples are used for research.Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study - Oslo I from various hospitals between 1995 and 1998 We used the nONCOchip, a custom-designed Agilent microarray containing 203,527 probes covering protein-coding and non-coding genomic loci (GEO accession number GPL13648). The nONCOchip interrogates probes for lncRNAs regulated by three tumor-relevant pathways , known lncRNAs, as well as mRNAs https://earray.chem.agilent.com/earray/). eArray design was performed according to the base composition methodology where probes are equally distributed across the target sequence, and uniqueness of probes have been checked against all known RefSeq (m)RNAs. Target sequences were grouped into three length categories defining the required number of probes. Target sequences of length In detail, probes of 60bp length have been designed following Agilent's standard design protocol for expression exon microarrays as available from eArray . In addition, a probe must exhibit a nonspecific change of expression of at least IQR Differentially expressed probes were identified by using R For quality control of the expression data, we investigated whether the subtype classification obtained in previous studies for the same set of tumor samples was reproducible using the nONCOchip. Gene expression of PAM50 genes was compared to previous profiling of the same samples using Agilent's Whole Human Genome Oligo 44k Microarrays The genotypes aCGH dataset has been published previously bona fide set of non-coding probes in intergenic and intronic regions was constructed from the significantly differentially expressed probes as follows: (1) All probes overlapping with at least one nucleotide with protein-coding exons (independent of reading strand) as annotated in Gencode release v12 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/ and split into shorter alignments of at most 400bp length to enable parallel processing. Each multiple alignment was assessed by RNAcode in all six possible reading frames, and the longest segment in the reference sequence of maximal score reported. All segments with an RNAcode bona fide non-coding probes in intergenic regions and 71,228 in introns of protein-coding genes. For simplicity, we termed probes passing these three filters as non-coding probes.A Probes antisense to a protein-coding exon, but not containing a significant RNAcode hit was used to check for unspecific primer matches.For quantitative real time PCR 250 ng of total RNA was reverse transcribed using random primers and the High-Capacity cDNA Reverse Transcription Kit following the manufacturer's recommendations . Transcript expression analysis was performed using Fast SYBR Green Master Mix according to the manufacturer's instructions . 5Figure S1Expression changes recovered mRNA based subtype classification, and were independent of copy number changes. (A.) Heatmap of Pearson's correlation coefficients of expression levels of the protein-coding genes that define the five known mRNA subclasses of breast cancer on the custom microrarray compared to expression levels of these genes in the same set of tissue samples on Agilent 4\u00d744k arrays B.) Smoothed scatterplot of expression changes and copy number variations for non-coding DE-probes regulated between normal and tumor samples ((PDF)Click here for additional data file.Figure S2Differential expression of non-coding probes in breast tumor. Heatmap of non-coding probes with significant expression variation between molecular tumor subtypes ; histological grade 1, 2 or 3 (Grade); TP53 mutational status Click here for additional data file.Figure S3Unsupervised clustering of tumor samples. Hierarchical clustering of probes passing unspecific filtering, i.e. A.) Hierarchical cluster tree of probes located in exons of protein-coding genes (B.) of non-coding probes ((PDF)Click here for additional data file.Figure S4Differential expression of lncRNAs. Heatmap of lncRNA (Gencode v12) expression changes between normal and tumor tissue. For each lncRNA and patient sample, the median expression of all significantly differentially expressed probes ; histological grade 1, 2 or 3 (Grade); TP53 mutational status Click here for additional data file.Figure S5RT-qPCR validation of differentially expressed chromatin-associated lncRNAs. Subsequent analysis of three chromatin-associated lncRNAs Click here for additional data file.Figure S6Sequence conservation and hybridisation intensities. Empirical cumulative distributions (ECDF) of average PhastCons scores of DE-probes or to array probes located in genomic loci with conserved secondary structures \u2013 RNAz B.). (C.) ECDF of maximal microarray hybridisation intensities of probes located in loci with conserved secondary structure motifs compared to all remaining probes on the custom microarray.(PDF)Click here for additional data file.Figure S7Genomic distance of intergenic non-coding DE-probes to protein-coding genes. Empirical cumulative distribution function (ECDF) of genomic distances of intergenic non-coding probes either significantly differentially expressed between tumor and normal samples (A.) or between Basal-like and Luminal tumors (B.) to their nearest protein-coding gene (Gencode v12), not taking the reading direction into account.(PDF)Click here for additional data file.Table S1Clinical, pathological, and immunohistochemical data of presented breast tumor samples. Column headings indicate sample identifier (Sample ID); Age at onset ; tumor cell content in percentage ; status of breast tumor ; status of estrogene receptor Click here for additional data file.Table S2KEGG pathway enrichment analysis for protein-coding genes significantly differentially expressed . Most enriched KEGG pathways (ID), significance of enrichment , odds ratios (Odds ratio), expected number of genes associated with tested pathway (Exp. count), number of significantly differentially expressed genes associated with this pathway (Count), number of genes from the gene universe that are annotated in that pathway (Size), name of the pathway (Pathway Name), and a list of genes which are regulated in that pathway and were significantly differentially expressed. Analysis was done by using the Bioconductor GOstats package. Mapping of genes to Entrez IDs is based on the NCBI gene information table . Significance of enrichment was assessed by a one-sided hypergeometric test where the universe contains all genes of the custom microarray which passed unspecific filtering .(PDF)Click here for additional data file.Table S3Known non-coding RNAs differentially expressed between normal versus tumor samples. Summary of known non-coding RNAs (Gencode v12) significantly differentially expressed between normal and tumor patient samples (Gene name), Gencode identifier (Gene ID), if ncRNA transcript is bona fide non-coding , position of transcript in human genome version hg19 (Position of transcript), position of probe in human genome version hg19 (Position of probe), custom array probe ID (Probe ID), and fold change in log2 scale (logFC). A fold change of (XLSX)Click here for additional data file.Table S4DE-Probes overlap with genomic annotation. Number of DE-Probes significantly differentially expressed between normal and tumor samples and the data Click here for additional data file.Table S5Chromatin-associated lncRNAs differentially expressed between normal versus tumor. Summary of chromatin-associated lncRNAs bona fide non-coding , genes the CAR overlaps with , position of probe in human genome version hg19 which overlap CAR in either reading direction (Probe - Genomic locus), custom array probe ID (Probe - ID), fold change in log2 scale (Probe - logFC), and genes the custom array probes overlap with (Probe - overlaps gene). A fold change of AS (antisense), NC , NMD (nonsense mediated decay), PC (protein coding), PG (pseudogene), PT (processed transcript), RI (retained intron), SI (sense intronic), and SO (sense overlapping).(XLSX)Click here for additional data file.Table S6KEGG pathway enrichment analysis for mRNAs with intergenic, intronic, or antisense non-coding DE-probes. Most enriched KEGG pathways (ID), significance of enrichment , odds ratios (Odds ratio), expected number of genes associated with tested pathway (Exp. count), number of significantly differentially expressed genes associated with this pathway (Count), number of genes from the gene universe that are annotated in that pathway (Size), name of the pathway (Pathway Name), and a list of genes which are regulated in that pathway and significantly differentially expressed. Analysis was done by using the Bioconductor GOstats package. Mapping of genes to Entrez IDs is based on the NCBI gene information table . Significance of enrichment was assessed by a one-sided hypergeometric test where the universe contains all genes of the custom microarray which passed unspecific filtering .(PDF)Click here for additional data file.Table S7Detailed documentation of used annotation categories. Column headings Annotation, Abbreviation, Source/URL, Assembly, Citation, and Comment indicate the according genomic feature, the abbreviation used in figures and tables throughout the paper, the online source of the annotation data set, the human genome assembly for which annotation was available, references, and comments about preprocessing of the annotation data, respectively.(PDF)Click here for additional data file.Table S8RT-qPCR primers. LncRNA expression was validated by RT-qPCR with primers designed using Primer3 (v0.4.0) with default parameters.(PDF)Click here for additional data file.Methods S1Description of genomic annotation categories. Detailed description of all genomic annotation categories used to investigate the genomic location of DE-probes.(PDF)Click here for additional data file."} +{"text": "Individuals with alpha-1 antitrypsin (AAT) deficiency (AATD) are predisposed to early-onset emphysema and neutrophils are the primary effector cells responsible for the pathological manifestations of AATD lung disease. As AAT interacts directly with the circulating neutrophil membrane [Circulating neutrophils were purified from blood of patients with AATD and from healthy control individuals (n=7). Membranes and cytosols were isolated from neutrophils by sucrose-gradient ultracentrifugation. Cholesterol and calcium levels were fluorometric quantified and calpain levels measured using a calpain activity assay. Caveolin-1 expression was examined by Western blot analysis. Statistical comparisons were performed by Student's t-test.Neutrophil cytosols of AATD individuals had increased calcium concentrations and activation of the calcium dependent protease calpain . Furthermore, levels of the cholesterol trafficking protein caveolin-1 were significantly lower in AATD neutrophil cytosols leading to significantly decreased membrane cholesterol content when compared to healthy control cells .In summary, our findings have demonstrated for the first time increased calcium, increased calpain activity causing proteolytic cleavage of caveolin-1, and decreased membrane cholesterol content of AATD neutrophils. This novel data may in part explain the dysregulated activity of this innate immune cell in AATD."} +{"text": "Tuberculosis (TB), the disease caused by Mycobacterium tuberculosis (Mtb) remains a global health concern. The evolution of various multi-drug resistant strains through genetic mutations or drug tolerant strains through bacterial persistence renders existing antibiotics ineffective. Hence there is need for the development of either new antibiotics or rationalizing approved drugs that can be utilized in combination with existing antibiotics as a therapeutic strategy. A comprehensive systems level mapping of metabolic complexity in Mtb revels a putative role of NDH-I in the formation of bacterial persistence under the influence of front-line antibiotics. Possibilities of targeting bacterial NDH-I with existing FDA approved drug for type-II diabetes, Metformin, along with existing front-line antibiotics is discussed and proposed as a potential combination therapy for TB. Mycobacterium tuberculosis (Mtb), the main etiological agent of human tuberculosis. The problem of antibiotic resistance therefore renders current therapeutic interventions for the treatment of TB ineffective and hence urges the discovery or development of new and alternate strategies to counter its impact. Bacteria can develop antibiotic resistance either through genetic mutations [Mtb are well established and understood, the aspect of bacterial persistence, which may result into drug tolerant phenotypes of Mtb is seldom addressed.Tuberculosis (TB) remains a leading global health concern with 5.4 million new cases reported in 2013 by WHO. Globally, 5% of TB cases are estimated to have Multi-Drug resistance TB (MDR-TB). The current anti-TB therapy constitutes a combination of 4 different antibiotics, which is extremely lengthy (6\u20139 months) and non compliance has resulted into the evolution of various MDR and extensively drug resistant strains of in silico systems approach, we probed the metabolism in Mtb to identify various metabolic mechanisms that may potentiate the formation of persister phenotype in Mtb when challenged with current front-line antibiotics of TB therapy and respiratory chain complex \u2013 I in Mtb as a possible alternate mechanism of ATP generation that may facilitate the formation of a persister phenotype and hence demonstrate antibiotic tolerance translocating subunit, H+ - NADH-Q oxidoreductase (designated as NDH-I); b) sodium (Na+) translocating subunit, Na+ - NADH-Q oxidoreductase (designated as Na+ - NADH) and c) NADH-Q oxidoreductase that lacks energy coupling site and designated as NDH-II [The bacterial respiratory chain complex NADH-Q oxidoreductase is classified into three main subunits a) proton an attractive combination target along with targets of existing front-line antibiotics for TB therapy. Designing new ligands or re-purposing the existing compounds that can inhibit nadA\u2009~\u2009E operon in Mtb in combination with front-line anti-TB antibiotics therefore might result into novel therapeutic interventions that can substantially aid in the ongoing efforts of TB translation research.Furthermore, our previous systems level analysis also suggest a possible role of gure\u00a0Mtb mediated"} +{"text": "Stevens-Johnson syndrome (SJS) and drug-induced hypersensitivity syndrome are life-threatening drug hypersensitivity reactions. Previous studies on genetic predictors for SJS and HSS were focused on immune-related genes and on known, frequent polymorphisms in the genome. For the anticonvulsant carbamazepine (CBZ), genetic markers for CBZ-induced SJS and HSS have been identified in the HLA region . However, many patients carriyng HLA-B*15:02 or HLA-A*31:01 tolerate CBZ, resulting in a low positive predictive value of a predictive test based on these genetic markers alone. In this pilot study, we aimed to identify rare genetic variants potentially associated with CBZ-induced SJS and HSS using whole exome sequencing in seven children with CBZ-induced SJS and five children with CBZ-induced HSS. Whole exome sequencing was performed using Illumina TruSeq exome capture and sequencing technology. Paired-end sequence reads were aligned and variants within 150 bp of the 64 Mb target region were identified using Bowtie, BWA and GATK. DNA samples from 95 CBZ-tolerant Canadian children were pooled and sequenced to a median depth of 300-fold to estimate frequencies of sequence variants identified in the hypersensitivity cases. All study participants were recruited through the Canadian Pharmacogenomics Network for Drug Safety. Children with CBZ-induced SJS or HSS were of European, Asian and First Nations ancestry with three SJS cases of Asian origin carrying HLA-B*15:02 and two HSS patients of European and First Nations origin carrying HLA-A*31:01. No individual rare single nucleotide variant (SNV) was strongly overrepresented in the SJS or HSS cases either in combined or in hypersensitivity reaction-specific analyses. Gene-based analyses revealed several candidate genes with rare nonsynonymous SNVs observed in a majority of SJS or HSS cases, respectively, which require follow-up in additional patients. With a hypothesis-free, comprehensive genetic screening approach, we identified new candidate genes and variants potentially involved in the development of CBZ-induced SJS or HSS for further investigation. The identified genes and pathways may lead to novel hypotheses for the pathomechanisms of these serious dermatologic reactions, potentially opening up new possibilities for prevention and treatment strategies."} +{"text": "Eating disorders (EDs) are serious mental disorders which have significant physical and psychological impacts. The aim of this study is to determine whether ED prevention programs are effective across the age spectrum.Electronic databases were searched for published randomised controlled trials (RCTs) designed for preventing ED. Included trials were classified as both broader prevention strategies and more specific prevention program ). Quantitative meta-analyses were conducted.A total of 3790 titles were retrieved via the initial search strategy. Ninety-eight RCTs were included in the meta-analysis. Most of studies used self-report measurements of ED risk factors, and did not report final outcomes of cases of ED prevented. For universal prevention, media literacy (ML) interventions demonstrated a significant reduction in ED risk factors (e.g. weight and shape concern) at up to 30 months after interventions for both male and female adolescents. For selective prevention CBT (delivered by class or online) and ML interventions have significantly reduced bulimic symptoms at 3- to 8- month follow up , and thin-ideal internalisation at 3-month follow up , respectively. CBT and cognitive dissonance (CD) interventions for indicated prevention showed strong evidence and substantial effect in reducing both ED risk factor and ED symptoms. A healthy weight program which was designed to prevent both ED and obesity as an indicated prevention intervention was found to significantly reduce ED risk factors and body mass.The study supported the conclusions that indicated prevention interventions using CBT and CD approaches are effective for ED prevention while universal and selective prevention using media literacy and selective prevention using CBT are promising. Combined ED and obesity prevention interventions require further research."} +{"text": "Strongyloides antibody . He received two doses of ivermectin 2 weeks apart.A 57-year-old Samoan man with large B-cell gastric lymphoma presented with fatigue, anemia, and melena. A positron emission tomography (PET) with 18-fluoro-2-deoxyglucose (FDG) showed no gastric activity but marked hypermetabolic activity in the cecum and ascending colon (S. sterocoralis nematodes typically inhabit the small bowel; therefore, involvement of the cecum and ascending colon in this patient suggests a hyperinfection syndrome. Diagnosis of Strongyloides may be established by detection of larvae in stool or a biopsy or by serology. PET and CT are not typically used for diagnosis. However, this case shows Strongyloides hyperinfection syndrome by PET as an incidental finding and reinforces the need to maintain a high index of suspicion for this infection in immigrants from endemic regions."} +{"text": "Breast metastasis from lung cancer has been reported, but not from SCLC that is transformed from lung adenocarcinoma during maintenance treatment with epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI). Transformation to small cell lung cancer(SCLC), although uncommonly seen, has been associated with resistance to EGFR-TKI therapy in lung adenocarcinomas.We describe a case of a 49-year-old man with lung adenocarcinoma harboring L858R point mutation at the exon 21 of the epidermal growth factor receptor (EGFR). During the maintenance treatment with EGFR-TKI, the patient presented with a right breast mass, which was accompanied by elevated serum neuron specific enolase (NSE) level. The histological examination of biopsies from the breast mass and enlarging lung mass revealed SCLC that was less sensitive to standard SCLC treatment. The breast tumor was positive for thyroid transcription factor-1 (TTF-1), consistent with a lung primary cancer.This is the first case report of small cell transformation and metastatic to the breast in a patient with lung adenocarcinoma following EGFR-TKI treatment. Repeat biopsy is important for evaluation of evolving genetic and histologic changes and selection of appropriate treatment. and serum NSE measurement may be useful for detection of small cell transformation in cases with resistance to EGFR-TKI therapy. Activating mutations in the epidermal growth factor receptor (EGFR) gene have been shown to be associated with a dramatic clinical response to EGFR tyrosine kinase inhibitors (EGFR-TKIs) in patients with lung adenocarcinomas , 2. The A 49-year-old man with 20 years\u2019 history of smoking presented with cough and shortness of breath in September 2012. Chest computed tomography (CT) scan revealed a mass in the lingular segment of the left lung with mediastinal lymphadenopathy and moderate left pleural effusion Fig. . Serum tThe incidence of metastatic lung cancer to the breast is very low . MirrielTransformation to SCLC following EGFR-TKI treatment is uncommon. To date, there are only a few case reports or small series. Zakowski et al first described a case of a 45-year-old female non-smoker with lung adenocarcinoma that was transformed to SCLC after acquired resistance to EGFR TKI therapy . The patWe here reported a rare case of the patient who had small cell transformation and breast metastasis following EGFR-TKI treatment. Immunophenotypic analysis including TTF-1 is crucial to establish the diagnosis of breast metastasis from primary lung cancer. Measurement of serum NSE level may be helpful for suggesting small cell transformation. Repeat biopsy is important to enable histological and molecular analysis and guide appropriate treatment.EGFR-TKI, Epidermal growth factor receptor tyrosine kinase inhibitor; ER, Estrogen receptor; HGF, Hepatocyte growth factor; NSCLC, Non-small cell lung cancer; NSE, Neuronspecific enolase; ProGRP, Pro-Gastrin-releasing peptide; SCLC Small cell lung cancer"} +{"text": "Intravascular large B-cell lymphoma (IVLBCL) is a rare and aggressive subtype of systemic extranodal non-Hodgkin diffuse large B-cell lymphoma (DLBCL). We report a rare case of IVLBCL who showed diffuse 18F-fluorodeoxyglucose (FDG) uptake in the lung in FDG-positron emission tomography/computed tomography (PET/CT) without respiratory symptoms or chest CT abnormalities. Serum biochemical studies showed a raised level of lactate dehydrogenase (LDH) and serum soluble interleukin-2 receptor (sIL-2R), which suggested the presence of malignant lymphoma strongly. A non-contrast CT showed no abnormalities in the lung fields, no lymphadenopathy was found. FDG-PET/CT revealed diffuse FDG uptake in the both lungs and in spleen as well as multiple hot spots in the liver. Under the suspicion of IVLBCL especially by the diffuse FDG uptake in the lung, a random skin biopsy was performed from three regions, the left forearm, right abdomen and left thigh in which there had been no evidence of FDG uptake. The definite diagnosis of IVLBCL was made based on the pathological analysis of the specimen from the left thigh. She achieved complete remission (CR) after combined chemoimmunotherapy. FDG-PET/CT was useful for the early detection of IVLBCL even without respiratory symptoms or any abnormal findings by chest CT. Intravascular large B-cell lymphoma (IVLBCL) is a rare subtype of systemic extranodal non-Hodgkin diffuse large B-cell lymphoma (DLBCL), occurring less than 1% of all lymphomas has emerged as a powerful functional imaging tool in the assessment of non-Hodgkin lymphoma (lymphoma . HoweverWe present here a case of IVLBCL who had no respiratory symptoms which could occur in the near future nor chest computed tomography (CT) abnormalities. Diffuse FDG uptake in the lung on FDG-PET/CT was helpful in the early diagnosis of IVLBCL.A 53-year-old woman was suspected a hematologic disease in a medical checking. She presented with nocturnal sweating 1 week before consulting. Her past and family history was unremarkable. Clinical examination was also unremarkable, lymphadenopathy was absent. Her hematological profile was as follows: hemoglobin: 10.4 g/dl, hematocrit: 30.9%, white blood cell count: 3.0 \u00d7 10A non-contrast enhanced CT of chest, abdomen and pelvis was performed, some low density areas in the liver and splenomegaly were detected and no lymphadenopathy was found. No abnormalities were detected in the lung fields, although high-resolution CT was not applied. FDG-PET/CT was undertaken within two weeks after CT, revealed diffuse FDG uptake in the both lungs and in spleen as well as multiple hot spots in the liver . She hadAn R-CHOP chemotherapy regimen was started immediately. She received two courses of high dose-methotrexate (HD-HTX) and Rituximab as prophylaxis for central nervous system relapse after total of six cycles of R-CHOP. FDG-PET/CT after these therapies demonstrated complete disappearance of all abnormal uptakes including the diffuse uptake in the lungs. She achieved complete remission (CR) .We reported a case of IVLBCL in whom abnormal FDG uptake was shown in the lung, spleen and liver. The diffuse lung uptake of FDG was especially suggestive of ILVBCL and she could be sent to random skin biopsy for definite diagnosis and prompt immunochemotherapy before emerging of respiratory or systemic symptoms.To the extent of our search 15 case reports have been reported to date -18. MiurIn this case report no abnormal FDG uptake was detected in the cutaneous lesions, but it is reasonable to apply a random skin biopsy for the definite diagnosis of IVLBCL suggested by FDG-PET. The usefulness of random skin biopsy from unaffected skin for the definite diagnosis of IVLBCL has been proposed . FurtherIn conclusion we reported a case of IVLBCL with diffuse FDG uptake in the lung without respiratory symptoms or chest CT abnormalities, which could be diagnosed early by a random skin biopsy and achieved CR with combined chemoimmunotherapy. FDG-PET provided an important information for recalling IVLBCL and could indicate random skin biopsy which could diagnose early, and lead to prompt chemotherapy, contributing to CR and long-term survival."} +{"text": "Myocardial infarction (MI) leads to heart failure in a substantial number of patients. Investigation of perfusion in the infarct-adjacent segments can offer better insights into left ventricular remodeling. It is the aim of this study to compare myocardial blood flow (MBF) with cardiac magnetic resonance (CMR) in the infarct borderzones (BZ) and the remote myocardium (RM) in a large patient population in the acute phase of MI.In this substudy of the NOMI-trial using the placebo arm, 68 patients underwent CMR with restperfusion within 48 to 72 hours of acutely revascularized ST-elevation MI in a 1.5 tesla MR scanner . TIMI 2-3 flow was achieved in all patients after PCI. MBF was quantified using Fermi deconvolution with a dual bolus analysis technique ) in basal and midventricular short axis perfusion slices. A segmental model was applied on corresponding images of perfusion, late gadolinium enhancement (LGE) and T2-weighted images (T2W). The MBF of the infarct zone (IZ) was calculated as the mean perfusion of segments with LGE. The adjacent 30 degree segments were defined as BZ, and were also classified in BZ-inAAR and BZ-outAAR, depending on their location in- or outside the area at risk, respectively, as determined by T2W imaging. The MBF of the RM was calculated as the mean perfusion of the remaining segments. Apical slices seldomly included more than one myocardial zone and were excluded from analysis.One hundred thirty six slices were analyzed. Restperfusion was not significantly different in BZ and RM . BZ-inAAR restperfusion however, was significantly lower than BZ-outAAR and RM perfusion in the acute phase of MI. (cf. Table)Myocardial restperfusion in infarct-adjacent segments is lower in- than outside the area at risk in acute MI. This regional myocardial perfusion inhomogeneity may impact subsequent LV remodeling, thereby offering new opportunities for targeted interventions.No disclosures."} +{"text": "In line with the Kidney Disease: Improving Global Outcomes (KDIGO) clinical practice guideline on the management of chronic kidney disease-mineral and bone disorder (CKD-MBD) , recent"} +{"text": "A 10-year-old boy presented with torticollis and neck pain for 2 months without fever. His physical examination showed torticollis and limitation of flexion/extension and cervical rotation without neurological deficit. Family and past histories were unremarkable. Cervical spine radiographs showed a cervical scoliosis with loss of the normal cervical lordosis and partial collapse of C3 vertebral body (A and B). Cervical computed tomography-scan and magnetic resonance imaging demonstrated a destruction of C3 vertebral corpus (vertebra plana) without discitis or spinal cord compression (C and D). A malignant bony tumor was suspected. Routine blood tests showed a mildly elevated erythrocyte sedimentation rate. Other skeletal X-rays revealed a well-defined solitary metaphyseal lytic lesion in the medial femoral condyle (E). An anterior cervical corporectomy was performed and the spine was stabilised with a tricortical iliac crest graft with plate/screws fixation (F). Histological features were consistent with eosinophilic granuloma. The patient was discharged home pain free with a good outcome. Eosinophilic granuloma (EG) is a benign and solitary bony lesion of unknown etiology. EG, Letterer-Siwe, and Hand-Schuller-Christian disease represent a spectrum of the same disease entity now known as Langerhans cell granulomatosis or histiocytosis X. EG predominantly affects the skull, the ribs, the pelvis, the mandible, and the metaphyses of other long bones. Although rare, EG should always be included in the differential diagnosis for osteolytic lesions of the spine in children."} +{"text": "Hepatocellular carcinoma (HCC) is an aggressive liver tumor that occurs with chronic liver disease. Surgical resection is the mainstay of therapy for localized disease whereas therapeutic options for advanced disease are limited. The innovative blockade of immune checkpoints with targeted immunotherapies, such as monoclonal antibodies against programmed death receptor 1 (PD-1), have shown promise in the treatment of solid malignancies. The PD-1 inhibiting antibodies, nivolumab and pembrolizumab prolonged overall survival in randomized trials in metastatic melanoma and advanced non-small cell lung cancer. This is a report of a 75-year-old male patient with metastatic HCC who was initially treated with the standard of therapy sorafenib. After failure of sorafenib therapy, pembrolizumab was started. There was a dramatic response to pembrolizumab with decrease in tumor size and drop in alfa fetoprotein. To the best of our knowledge, this is the first case report of metastatic HCC responsive to pembrolizumab after failure of sorafenib. Hepatocellular carcinoma (HCC) is an aggressive tumor of the liver that usually occurs with chronic liver disease. HCC is frequently diagnosed late in its course with a median survival following diagnosis of approximately 6\u201320 months -2. ExtraSubstantial progress has been made in the development of immunotherapy for the treatment of a variety of solid malignancies. The immune checkpoint proteins, programmed death receptor 1 (PD-1) and programmed death receptor ligand (PD-L1), play a major role in the immune resistance of tumor cells . PD-1 isA 75-year-old male patient presented with abdominal pain and with a past medical history significant for hypertension, gastroesophageal reflux disease, and anemia. An abdominal exam was positive for right upper quadrant tenderness. Laboratory findings revealed normal complete blood count, normal renal panel, but mildly elevated liver enzymes (aspartate aminotransferase (AST) = 66, alanine aminotransferase (ALT) = 38). A computerized tomography (CT) scan of the abdomen and pelvis showed a hyper-vascular mass in the left lobe of the liver. CT-guided biopsy of the mass showed HCC. The patient underwent exploratory laparotomy, total left hepatic lobectomy, and cholecystectomy. Active post-surgical surveillance with alpha fetoprotein (AFP) and CT scan of the abdomen was done for three years with no evidence of disease recurrence. Three years after initial presentation, the patient noticed a mass below the xiphoid process. AFP was elevated at 2751 mcg/L . A CT scan of the abdomen showed a large anterior subxiphoid abdominal wall soft tissue mass measuring 8 x 6 cm with multiple small satellite lesions consistent with metastatic disease was initiated. After six cycles of therapy, a CT scan of the abdomen showed a major decrease in subxiphoid mass size from 8 x 6 cm to 4 x 1.6 cm score of zero.Our case revealed the potential efficacy of an anti-PD-1 antibody for treatment of metastatic HCC. An open-label, single-institution, non-randomized, single-arm study titled \"Phase II study of Pembrolizumab (Keytruda) in Advanced Hepatocellular Carcinoma (HCC)\" is currently evaluating the efficacy of pembrolizumab therapy in patients with advanced HCC. Results from this trial will contribute to determination of the benefit of PD-1 blockade in HCC.A promising avenue of clinical research in HCC is the use of immune checkpoint inhibitors. As far as we know, this is the first case report of advanced HCC responsive to pembrolizumab after failure of sorafenib therapy. Pembrolizumab and other immune checkpoint inhibitors could be a new developing therapy for patients with advanced HCC resistant to sorafenib."} +{"text": "Smed-boule, a member of the DAZ family of germline RNA-binding proteins, revealed that egg capsule (or capsule) production and deposition occurs independently of the presence of gametes in the planarian flatworm Schmidtea mediterranea. Reduction of Smed-boule expression by RNA-interference (RNAi) causes ablation of spermatogonial stem cells and the inability of ovarian germline stem cells to undergo oogenesis. Although animals subjected to Smed-boule RNAi lose their gametes and become sterile, they continue to lay egg capsules. Production of sterile capsules is even observed in virgin Smed-boule(RNAi) and control planarians maintained in complete isolation, demonstrating that egg production in S. mediterranea occurs independently of ovulation, fertilization, or mating. Evidence suggests that this is a conserved feature amongst Platyhelminthes, and therefore relevant to the pathology and dissemination of parasitic flatworms. These findings demonstrate that Smed-boule functions at different stages during male and female germline stem cell development, and also demonstrate that egg capsule production by planarian flatworms occurs independently of signals produced by mating or ova.Few animals are known to lay eggs in the absence of ovulation or copulation, as it is presumably energetically wasteful and subjected to negative selection. Characterization of Schmidtea mediterranea, a hermaphroditic species of flatworm that develops germ cells post-embryonically. These findings surfaced from the characterization of Smed-boule, a member of the Deleted in AZoospermia gene family of RNA-binding proteins required for germline development in a broad range of animals. These findings lead to a better appreciation of the evolutionary diversity in approaches to oviparity. Additionally, discovering that egg capsule production occurs independently of germline or mating activities may carry a potential applied aspect with regards to regulating the dissemination and pathology of parasitic flatworms (such as blood flukes and tapeworms), if conserved in these organisms.Our work shows that production and deposition of egg capsules by planarian flatworms does not require fertilization, mating, ovulation, or even the existence of gametes. We also uncovered evidence for the existence of gender-specific germline stem cells in The characterization of developmental processes involved in sexual reproduction has important implications towards reproductive medicine, stockbreeding, farming, and for controlling the dissemination of infectious disease. Evolutionarily conserved molecular processes involved in metazoan germline development have been identified through decades of research using model organisms. For example, post-transcriptional regulation of gene expression by conserved germline-specific RNA-binding proteins is one of the conserved molecular processes that ensure development of gametes \u20133. On thPlanarian flatworms belong to the phylum Platyhelminthes, and are well known for their extraordinary regenerative abilities, which are founded in the availability of a pluripotent stem cell population throughout their life \u20139. The eSchmidtea mediterranea, germline stem cells are first detected as dorsolateral clusters in the area where testes develop [Dugesia ryukyuensis, germline stem cells are first detected in the area of the ovaries [Planarian flatworms have become useful models for the study of metazoan germline development ,15. In g develop . In othe ovaries ,20. Upon ovaries ,19. Germ ovaries ,15. Even ovaries ,22.Deleted in AZoospermia (DAZ) gene family, which is required for germ cell development in species ranging from sea anemone to humans [DAZ family homologs contribute to germline development in planarians remains unknown. In this study, we characterize a Boule homolog in the planarian Schmidtea mediterranea and demonstrate that it functions at different stages during male and female germline development. Functional analyses by RNA-interference (RNAi) revealed that Smed-boule is required for development and maintenance of spermatogonial stem cells, but disposable for the existence of their oogonial counterparts, uncovering the presence of sex-specific germline stem cells in planarian hermaphrodites. Long-term analysis of Smed-boule knockdowns revealed that egg capsule deposition in planarians is not triggered by gametogenesis, ovulation, oocyte activation, fertilization, or mating. These results demonstrate that egg capsule formation occurs regardless of signals from sexual activity or germ cell activity in S. mediterranea. These findings also provide a unique opportunity to identify internal mechanisms that influence capsule production in Platyhelminthes, which is central in the dissemination and pathology of parasitic members of this phylum.The development of planarian germline stem cells depends on conserved post-transcriptional regulators such as Nanos and Bic-C ,18. Boulo humans ,24. How boule homolog in the planarian flatworm S. mediterranea with a region of amino acid sequence 55% identical with that of the RNA recognition motif of human BOLL was detected by whole-mount in situ hybridization (ISH) in testes and ovaries of sexually mature planarians that are actively laying egg capsules with the germline stem cell marker Smed-nanos [Smed-boule mRNA overlapped with that of Smed-nanos in testes ..boule hon testes and partn testes . The pree testes . DetectiSmed-boule in planarian germline development and sexual reproduction we subjected planarians to three months of RNAi. Planarians continuously turn over all cells in their body from a continuous population of pluripotent stem cells, which allowed us to assess whether Smed-boule is required for normal germline development in sexually mature adults using germ cell markers (Smed-boule knockdowns (Smed-boule(RNAi)) were compared to control(RNAi) planarians. DsRNA corresponding to a planarian Cytoplasmic Polyadenylation Element Binding Protein 1 homolog (CPEB1), which is required for yolk gland development and egg capsule production (below), was administered to an additional group (CPEB1(RNAi)) as readout of RNAi effectiveness overtime. At the end of three months of RNAi, we observed that both oocytes (Smed-boule(RNAi). No defects in oocyte or sperm development were observed in control(RNAi) planarians (CPEB1(RNAi) samples were fully developed and Smed-boule(RNAi) animals (CPEB1(RNAi) animals was severely reduced (Smed-boule(RNAi) (CPEB1(RNAi) planarians, which were on average 30.8% larger than control animals maintained under the same conditions was further supported by quantitative analyses of egg capsule production (below).Neoophoran flatworms rely on a particular approach to oviparity in which nutrients for the developing embryo (yolk) are not accumulated in the developing ova. Instead, nutritional support is contributed by yolk cells (vitellocytes), which are transferred from yolk glands to the planarian uterus and encapsulated with embryos during egg capsule deposition. We checked for the presence of yolk glands using the yolk cell marker actant b , which p animals . However reduced . We lookle(RNAi) , which ile(RNAi) . There wCPEB1(RNAi) ceased laying eggs within a month of RNAi (Smed-boule(RNAi) was unaffected during the three months of RNAi treatment (control(RNAi) and Smed-boule(RNAi) groups continuously laid eggs for the entirety of the experiment (Smed-boule(RNAi) when compared to control(RNAi) planarians during the second and third months of RNAi treatment, respectively groups hatched 22% to 48% of the time planarians planarians were capable of producing sterile egg capsules in the absence of germ cells (and therefore fertilization events), we hypothesized that control animals would also produce sterile egg capsules in the absence of fertilization events. To test this hypothesis, we obtained \u2264 1 week-old hatchlings and maintained them in isolation for four months under continuous RNAi regimens. Planarians were maintained in isolation throughout the experiment, which allowed us to test whether egg capsule production is independent of signals produced during mating or the presence of potential mates altogether. Since planarians in this experiment were subjected to Smed-boule RNAi within a week of being born, which is a point when no sperm has developed, this approach also allowed us to verify that lingering sperm in adult knockdowns used in the previous experiment was not contributing to egg capsule production. Two categories of isolated virgins were maintained on either liver containing Smed-boule dsRNA or control dsRNA and were fed twice per week. These animals were expected to grow and eventually reach sexual maturity under these husbandry conditions. The production of egg capsules would only occur if independent from stimuli produced during mating, fertilization, embryonic development and, in the case of Smed-boule(RNAi), the absence of gametes.Given the fact that Smed-boule(RNAi) isolated animals produced egg capsules during the third and fourth months of the experiment (Smed-boule(RNAi) (Smed-boule(RNAi) individuals were fertile (n = 0/28 capsules). Capsules produced by control RNAi animals were also completely sterile (n = 0/43 capsules), suggesting that the production of egg capsules in these animals were not due to self-fertilization or parthenogenesis. We verified that normal gamete development was present in control animals at the end of the isolation experiment (Smed-boule(RNAi) flatworms (Smed-boule(RNAi) planarians raised in isolation planarians suggests that this trigger is detached from signals originating from sperm and oocyte development or ovulation.Indeed, both control and periment . The numperiment . The ave = 0.25) . As expe = 0.25) , none ofperiment and abselatworms , which wlatworms . We alsosolation . CollectSmed-boule RNAi. The most severe phenotype would be the loss of germline stem cells, which are specified and maintained post-embryonically through neoblast differentiation [germinal histone H4 and nanos [control(RNAi) and Smed-boule(RNAi) by nanos ISH after 3\u20134 months of RNAi animals planarians and Smed-boule(RNAi) planarians were readily detectable were also lost after Smed-boule RNAi (Smed-boule(RNAi) are due to the absence of male germline stem cells, whereas defects in oogenesis occur further downstream in the differentiation pathway.We decided to evaluate the severity of germline development defects caused by ntiation . Germlinnd nanos ,20,25,26als Figs and 8A. ans Figs and 8B. ble Figs . Identicsolation . Furtherule RNAi . From thSmed-boule(RNAi) ovaries, we analyzed control and Smed-boule knockdowns stained with DAPI by confocal microscopy (Smed-boule(RNAi) flatworms reveal that these are two fundamentally distinct germline stem cell populations that require Smed-boule function at different developmental stages. Smed-boule function is necessary for neoblast differentiation into male germline stem cells and/or maintenance of male germline stem cells, whereas ovarian germline stem cells only require Smed-boule for progression through early stages of oogenesis . Studies in S. polychroa have shown that siblings emerging from a single egg result from different fertilization events, which is possible because sperm from one or more partners can be stored for at least a month after insemination [Smed-boule(RNAi) planarians when compared to control planarians (which contained both oocytes and precursors). Nevertheless, current and previous observations do support a model by which a sustainable approach to oviparity could rely on a trigger for capsule formation that is independent of mating, fertilization, or ovulation.How can triggering egg production independently of fertilization be an efficient approach to survival of planarian populations? First, we must consider that in terms of sexual reproduction, nd Brown who obsemination . The abiS. mediterranea) are evolutionarily distant from members of parasitic groups . However, the non-causative relationship between ovulation/fertilization and capsule production appears to be conserved in some cestodes and trematodes, whose dissemination and pathology depend on the continuous production of egg capsules. Parasitic flatworms of the genus Schistosoma have been reported to produce egg capsules from females after single-sex infections of mammalian hosts [in vitro [Inside the phylum Platyhelminthes, free-living species . A PCR product corresponding to Smed-boule ORF sequence was amplified from oligo(dT)-primed total RNA cDNA using 5\u2019-GTTGTTTCAACGGTTCTACTGGCATC -3\u2019 and 5\u2019- GATTATTCCGGACAAAGCTGGACAAG -3\u2019 forward and reverse primers (respectively) and ligated to pJC53.2 [g reads , Smed-nanos, were also synthesized from a pJC53.2-based construct [Smed-synaptotagmin XV, Smed-granulin (grn), Smed-surfactant b, germinal histone H4, and a tuba/oviduct marker were synthesized from pBluescript-based clones uEscherichia coli ccdB sequence, which does not affect planarian development or behavior was used for unaffected control groups. For isolated RNAi samples, each planarian was fed individually and in isolation. For other experiments, planarians were maintained in groups of seven animals.Double-stranded RNAi feedings were performed twice every seven days and the protocol was followed as previously described . DsRNA cSmed-boule dsRNA twice per week, at which point any capsules present were collected and isolated. DsRNA corresponding to E. coli ccdB sequence was used for control samples. Egg capsules were monitored for hatchling events weekly for a period of three months after deposition.Groups of seven sexual planarians of 0.5 to 0.7 cm size and with a visible gonopore were maintained in glass Petri dishes and subjected to dsRNA feedings as described above. For isolated experiments, single \u2264 1 week-old hatchlings were maintained in isolation in glass Petri dishes throughout the experiment, under the husbandry conditions described above. Isolated planarians were fed liver containing control or S1 Fig(A) Double-fluorescence in situ hybridization (ISH) and confocal microscopy detection of synaptotagmin XV(A\u2019) and Smed-CPEB1(A\u201d) mRNAs in oocytes of S. mediterranea. Oocytes are distinguished by DAPI staining (A) as large cells with condensed chromosomes in the ovary. (A\u201d\u2019) Merged image. (B) Whole-mount ISH on sexual strain specimens of S. mediterranea reveals timing and distribution of Smed-surfactant b expression resembling that of yolk glands in the largest animal. Scale bars = 25 \u03bcm in (A) and 1 mm in (B).(TIF)Click here for additional data file.S2 FigCPEB1 whole-mount in situ hybridization (ISH) in sexual planarians subjected control RNAi reveals the presence of oocytes (A), which are absent in Smed-boule RNAi planarians (B). Images of DAPI staining in these individuals show the ventral side of control (A\u2019) and Smed-boule(RNAi) animals (B\u2019), and the presence of testes in the dorsal side of control animals (A\u201d), but not in Smed-boule(RNAi)(B\u201d). The fraction of animals displaying the phenotype represented by the image is shown at the bottom-left corner of each frame. Scale bars = 1 mm.(TIF)Click here for additional data file.S3 Figt-test (p < 0.05) in CPEB1(RNAi) animals compared to the size of control or Smed-boule(RNAi).Average size (cm) of sexually mature sized planarians after three months of RNAi treatment reveal a significant enlargement (*) using unpaired two-tailed (TIF)Click here for additional data file.S4 Fig(A-D) Whole-mount in situ hybridization analysis of germline stem cell (GSC) distribution visualizing nanos expression in the testes (A-B) and ovary (C-D) regions of planarian hatchlings raised in isolation and subjected to continuous control or Smed-boule RNAi. GSCs were specifically absent in the testes region of Smed-boule knockdowns (B), but present in the ovary region of both control (C) and Smed-boule(D) knockdowns. The fraction of animals displaying the phenotype represented by the image is shown at the bottom-left corner of each frame. Scale bars = 1 mm.(TIF)Click here for additional data file.S5 FigSmed-boule (right). Magnified views show detection of GSC clusters in control samples, but not in Smed-boule(RNAi). The fraction of animals displaying the phenotype represented by the image is shown at the bottom-left corner of each frame. Scale bars = 1 mm.Detection of germline stem cell (GSC) clusters (white arrows) in presumptive testes primordia of asexual planarians subjected to three weeks of control RNAi (left) or (TIF)Click here for additional data file.S6 Fig(A), or on separate and independent pathways (B), for initiating ovulation/fertilization and capsule deposition.Models of planarian oviparity that could rely on a shared upstream trigger (TIF)Click here for additional data file.S1 MovieProgression through 3.3 \u03bcm confocal sections revealing normal oocyte development in control ovaries stained with DAPI.(MOV)Click here for additional data file.S2 MovieSmed-boule(RNAi) ovaries stained with DAPI.Progression through 3.3 \u03bcm confocal sections revealing the absence of oogenesis in (MOV)Click here for additional data file."} +{"text": "Mycobacterium tuberculosis which presented as multidrug resistant in New Zealand, and describe a number of single-nucleotide polymorphisms in genes relating to drug resistance.Multidrug resistance constitutes a threat worldwide to the management of tuberculosis (TB). We report the draft whole-genome sequence of a lineage 3 (East-African Indian) isolate of Mycobacterium tuberculosis complex (MTBC) isolates, through improvements in diagnostic technologies, would facilitate early optimal selection of anti-TB drugs in MDR cases.Tuberculosis (TB) is a leading cause of infectious mortality worldwide, killing in the region of 1.3 million people each year (M.\u00a0tuberculosis strain H37Rv reference genome (accession no. AL123456.3) by Burrows-Wheeler alignment for whole-genome analysis of drug-resistance mutations in a New Zealand clinical isolate of MDR-TB from 2011 which belongs to lineage 3 (East-African Indian) (rpoB) which has previously been shown to have high specificity for rifampin phenotypic resistance (katG), and , the former having high specificity for isoniazid phenotypic resistance (A non-synonymous mutation was identified in the gene Rv0667 (embC) and Rv3795 (embB) although their specificities with respect to ethambutol resistance remain to be established. Nonsynonymous mutations were not detected in genes associated with pyrazinamide resistance, i.e., Rv2043c (pncA), Rv1630 (rpsA), and Rv3601c (panD) . The S95T mutation has been demonstrated to have low specificity with respect to fluoroquinolone resistance (rrs) of NZ3MDR1.Regarding second-line drug resistance, SNPs were identified in Rv0006 (To our knowledge, this is the first published genome sequence of a lineage 3 MTBC isolate from New Zealand. The drug-resistance gene SNP data generated correlate with earlier phenotypic DST data but were obtained within a considerably shorter turn-around-time. In addition, deletions were detected in known MTBC virulence and immune modulatory genes in NZ3MDR1, the significance of which will be investigated further. This underlines the value that NGS could offer clinical diagnostics in the routine characterization of TB isolates.CCSJ00000000.This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no."} +{"text": "The E3 ubiquitin ligase cbl-b has been identified as a key intracellular checkpoint limiting T and NK cell activation. Concordantly, blockade of cbl-b function by genetic deletion strongly enhances anti-tumor immune responses, thereby validating cbl-b as target for immunotherapy. We have recently shown in the B16-OVA model that transfer of transiently cbl-b silenced murine T cells together with DC vaccination could suppress tumor growth. This provides a rationale to combine administration of cbl-b silenced PBMCs with an established DC vaccination protocol. We present here a case study for the treatment of a patient suffering from lung metastases originating from pancreatic cancer.PBMCs were isolated ex vivo from the cancer patient and transfected with cbl-b siRNA by electroporation. DCs were pulsed with lysates of pancreatic tumor cell lines serving as antigen source and co-administrated with the PBMCs intranodally to the cancer patient. The composition and phenotype of the immune compartment of the patient was regularly monitored at each treatment by flow cytometry. The phenotype and activation of DCs and cbl-b silenced PBMCs was assessed by flow cytometry and ELISA. Tumor progression was monitored by determination of CA19-9 blood levels and computer tomography.Ex vivo Transfection of cancer patient PBMCs with cbl-b si RNA resulted in strong suppression of cbl-b expression and enhanced T cell activation. No adverse events were observed when cbl-b silenced PBMCs (up to 1.5*10^8) were administrated to the patient. When cbl-b silenced PBMCs were co-administrated with activated DCs, no worsening of DC-associated slight fever and local DTH reactions was observed. Overall, 2 vaccination cycles (each 10 single treatments with DCs and cbl-b silenced PBMCs) were administrated. During the treatment, massive fluctuations in the PBMC immune compartments were observed, indicating the impact on the patient`s immune system. Tumor progression was slowed during the treatment periods, resulting in disease control over a period of more than 30 months.The adoptive cell therapy protocol combining DC vaccination and ex vivo cbl-b silencing was shown to be feasible and well tolerated. Moreover, immunologic effects and slowed tumor growth suggest beneficial effects of the treatment. Based on these results, a Phase I trial for adoptive cell therapy with larger numbers of cbl-b silenced PBMCs was started at Wake Forest University."} +{"text": "The lengths of the sarcomeric thin filaments vary in a skeletal muscle-specific manner and help specify the physiological properties of skeletal muscle. Since the extent of overlap between the thin and thick filaments determines the amount of contractile force that a sarcomere can actively produce, thin filament lengths are accurate predictors of muscle-specific sarcomere length-tension relationships and sarcomere operating length ranges. However, the striking uniformity of thin filament lengths within sarcomeres, specified during myofibril assembly, has led to the widely held assumption that thin filament lengths remain constant throughout an organism's lifespan. Here, we rigorously tested this assumption by using computational super-resolution image analysis of confocal fluorescence images to explore the effects of postnatal development and aging on thin filament length in mice. We found that thin filaments shorten in postnatal tibialis anterior (TA) and gastrocnemius muscles between postnatal days 7 and 21, consistent with the developmental program of myosin heavy chain (MHC) gene expression in this interval. By contrast, thin filament lengths in TA and extensor digitorum longus (EDL) muscles remained constant between 2 mo and 2 yr of age, while thin filament lengths in soleus muscle became shorter, suggestive of a slow-muscle-specific mechanism of thin filament destabilization associated with aging. Collectively, these data are the first to show that thin filament lengths change as part of normal skeletal muscle development and aging, motivating future investigations into the cellular and molecular mechanisms underlying thin filament adaptation across the lifespan. In skeletal muscle fibers, contractile force is generated via crossbridge interactions between the myosin (thick) filaments and actin (thin) filaments in the sarcomeres arranged in series along contractile myofibrils. The capacity for a sarcomere to generate force is best described by the sliding filament theory of muscle contraction, which states that the extent of overlap between the thick and thin filaments determines the number of crossbridge interactions and, hence, the extent of active force production. The sliding filament theory can be quantified by the sarcomere length-tension relationship, which depicts a sarcomere's force output as a function of sarcomere length, and whose shape can be accurately modeled from thick and thin filament lengths were sacrificed at P7, P14, P21, 2 months after birth, or 2 years after birth. Mice sacrificed at P7, P14, and P21 were C57Bl/6J mice, while mice sacrificed at 2 months or 2 years after birth were BALB/cBy mice. Two different mouse strains were used to test whether thin filament lengths in adult skeletal muscle vary with mouse strain . Mice were sacrificed by isoflurane inhalation followed by cervical dislocation, in accordance with ethics guidelines set forth by the Institutional Animal Care and Use Committee at The Scripps Research Institute.Mice signal across the Z-lines of adjacent half-sarcomeres (I-Z-I arrays), as previously described . In the TA and EDL, no statistically significant differences in thin filament lengths were observed between 2-mo-old vs. 2-yr-old muscles (~1.11 \u03bcm in both muscles at both time points) Figure .in vivo (Ochala et al., in vitro (Broschat et al., This study provides the first evidence that skeletal muscle thin filaments undergo adaptive remodeling to alter their lengths during the mouse lifespan, implying age-dependent alterations in sarcomere length-tension relationships and optimum sarcomere length ranges. What molecular mechanisms might drive these changes in thin filament lengths? When examining neonatal muscles, we observed thin filament shortening between P7 and P21 in both the TA and GAS Figure . The preWhen comparing 2-mo-old and 2-yr-old muscles, we observed no statistically significant changes in thin filament length in the TA or EDL, but a marked decrease in thin filament length was observed in the 2-yr-old soleus Figure . The facAn alternative mechanism for slow-muscle-specific thin filament shortening in aging involves preferential induction of proteolytic pathways in slow-twitch muscles (Sultan et al., The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "The input of the above mentioned nutritional data in a computer supported, individual rotation diet plan (FOOD ALLERGY CONTROL\u00ae) ensures a gradual improvement of the symptoms and stabilization of the clinical course during and after therapy.Our experience in the treatment of over 20,000 atopic eczema, urticaria and psoriasis patients shows that besides allergic reactions to foods an increasing number of pseudoallergic reactions caused by toxic-irritative pollutants are responsible for the inflammatory process behind the complex symptoms. Intrauterine and postnatal environmental influences were also reported. The routine analysis of specific IgE- and IgG4-factors in our atopic patients by means of ELISA-assays after challenge meals (CM) showed an increased frequency of specific IgE- and IgG4-antibodies after repeated CM. In 60% of the patients, we simultaneously found raised concentrations of the IgE- and IgG-CIC (p< 0.005) responsible for the delayed allergic reactions in the same group. Further inflammation markers like acute phase proteins showed a surprisingly rapid increase after CM (p< 0.01) in the atopic group; by contrast the control samples remained in the normal range. Serum histamine levels (RIA-Test) also showed a significant increase 1/2 hour after CM and after individual oral provocation with lactose, sucrose, tyramine, serotonine or phenylethylamine, respectively. The carbohydrate intolerance reactions (H2-test) were in good correlation to the significantly lowered disaccharidase activites in the gut of atopic eczema patients (p< 0.001). This was closely related to chronic intestinal dysbiosis with toxic microbial breakdown products leading to an increased intestinal permeability, histamine release and impairment of liver detox functions. On the other side, we found both in atopic eczema and in psoriasis patients pseudoallergic reactions against biogenic amines and constantly raised serum histamine levels , suggesting an inhibition of catabolic enzymes . Previously published results from our laboratory showed significantly reduced DAO (p< 0.001) and Type B MAO- (p< 0.05) activities in thrombocyte-rich plasma of atopic eczema and psoriasis patients explaining their intolerance reactions to histamine, tyramine and octopamine rich foods. Last, but not least, the chronic increased levels of free radicals in whole blood and plasma of all patient groups showed significant changes after oral intake of different food homogenates/ juices dependent on their ROS-blocking or ROS-increasing effects (enhanced chemoluminescence test). Our current research shows that appropriate combinations of hypoallergenic protein hydrolysates with particular sugar alcohols and omega-3 fatty acids (EQUIDERM PLUS\u00ae) are dramatically enhancing the anti-inflammatory and free radical quenching properties of the mixture, demonstrating an excellent compliance and therapy efficiency in atopic, psoriasis and geriatric patients. With the emergence of affordable microarray gene expression profiling methods, the opportunity arises to"} +{"text": "The hybrid positron emission tomography/computed tomography (PET/CT) or positron emission tomography/magnetic resonance imaging (PET/MRI) has become routine practice in clinics. The applications of multi-modality imaging can also benefit research advances. Consequently, dedicated small-imaging system like dual-head small-animal PET (DHAPET) that possesses the advantages of high detection sensitivity and high resolution can exploit the structural information from CT or MRI. It should be noted that the special detector arrangement in DHAPET leads to severe data truncation, thereby degrading the image quality. We proposed to take advantage of anatomical priors and total variation (TV) minimization methods to reconstruct PET activity distribution form incomplete measurement data. The objective is to solve the penalized least-squares function consisted of data fidelity term, TV norm and medium root priors. In this work, we employed the splitting-based fast iterative shrinkage/thresholding algorithm to split smooth and non-smooth functions in the convex optimization problems. Our simulations studies validated that the images reconstructed by use of the proposed method can outperform those obtained by use of conventional expectation maximization algorithms or that without considering the anatomical prior information. Additionally, the convergence rate is also accelerated."} +{"text": "Profiling technologies allow the simultaneous measurement and comparison of thousands of cell components without prior knowledge of their identity. In the present study, we used two-dimensional gel electrophoresis combined with mass spectrometry to evaluate protein expression of Brazilian genetically modified maize hybrid grown under different agroecosystems conditions. To this effect, leaf samples were subjected to comparative analysis using the near-isogenic non-GM hybrid as the comparator.In the first stage of the analysis, the main sources of variation in the dataset were identified by using Principal Components Analysis which correlated most of the variation to the different agroecosystems conditions. Comparative analysis within each field revealed a total of thirty two differentially expressed proteins between GM and non-GM samples that were identified and their molecular functions were mainly assigned to carbohydrate and energy metabolism, genetic information processing and stress response.To the best of our knowledge this study represents the first evidence of protein identities with differentially expressed isoforms in Brazilian MON810 genetic background hybrid grown under field conditions. As global databases on outputs from \u201comics\u201d analysis become available, these could provide a highly desirable benchmark for safety assessments. Genetically modified organisms (GMO) are widely grown and consumed in a number of countries. According to the industry agency, The International Service for the Acquisition of Agri-biotech Applications, biotech crops reached 170 million hectares planted with transgenic soybeans, maize and cotton in 2012 -1-propanesulfonate; DTT: Dithiothreitol; GAPDH: Glyceraldehyde-3-phosphate dehydrogenase; GMO: Genetically modified organisms; GM: Genetically modified; IEF: Isoelectric focusing; IPG: Immobilized pH gradient; MS/MS: Tandem mass spectrometry; MW: Molecular weight; pI: Isoelectric point; PCA: Principal component analysis; PCR: Polimerase chain reaction; PMF: Peptide mass fingerprinting; Q-TOF: Quadrupole time-of-flight; SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis.The authors declare that they have no competing interests.SZA and RON designed the study. SZA, MPG, OW and RON were responsible for data analysis and interpretation and drafted the manuscript; SZA carried out the 2D gel analysis and excised the protein spots; MPG and OW were responsible for mass spectrometry analysis and manuscript editing. All authors read and approved the final manuscript."} +{"text": "The complete genome sequence of an isolate of tomato mottle mosaic virus (ToMMV) infecting tomatoes in New York was obtained using small RNA (sRNA) deep sequencing. ToMMV_NY-13 shared 99% sequence identity with isolates from Mexico and Florida. Broader distribution of this emerging virus is a cause for concern to the tomato industry. Tobamovirus in the family Virgaviridae and tomato mosaic virus (ToMV) have been two of the most common recognizable tobamoviruses infecting tomatoes. These seed-borne and mechanically transmitted viruses are managed through the breeding of tobamovirus-resistant tomato cultivars and in the use of certified, virus-tested seed lots. However, a novel tobamovirus, tomato mottle mosaic virus (ToMMV), was first identified in tomatoes in Mexico in 2013 . Based oaviridae , 6. Totaaviridae and sequaviridae . A contiKT810183.The complete genome sequence of ToMMV_NY-13 has been deposited in GenBank under the accession number"} +{"text": "This work focuses on the study of simultaneous dynamic MR-PET acquisition in brain tumour patients. MR-based perfusion-weighted imaging (PWI) and PET [18F]-FET are dynamic methods, which allow to evaluate tumour metabolism in a quantitative way. In both methods, arterial input function (AIF) is necessary for quantification. However, the AIF estimation is a challenging task. In this work, we explore the possibilities to combine dynamic MR and PET AIF.Data of 11 brain tumour patients was acquired in a hybrid 3TMR-BrainPET (Siemens). The PET acquisition took one hour while several MRI sequences were simultaneously acquired, including DSC-MRI (Dynamic Susceptibility Contrast MRI) and MPRAGE. Two DSC-MRI sequences for PWI were investigated: 1) echo planar imaging (EPI) and 2) EPI Keyhole (EPIK). For three patients venous blood samples were available at later times. For DSC-MRI AIF estimation an automatic in-house algorithm was used and for PET AIF estimation an automatic segmentation of the carotid arteries in MPRAGE images was used. Furthermore, several anatomical-based partial volume correction (PVC) methods were applied to images using the carotid artery segmentation.The gamma fitting is useful in MR studies where the first pass of the bolus is used for quantification and can also aid the estimation of the peak of the PET AIF due to the similar peak shape. For the later PET frames, a three exponential model provided a good fitting. The iterative Yang PVC provided results closer to the venous blood samples than the other PVC methods.PET quantification can be improved by using MR data for: automatic carotid segmentation, partial volume correction and estimation of AIF using dynamic MRI. Furthermore, the estimation of MR AIF using EPIK instead of EPI was more robust and consequently PET AIF."} +{"text": "There is a need for assessment of adverse event (AEs) after hospital discharge in RCTs in surgery. Currently, measures to assess patient-reported AEs are limited. The EORTC quality of life questionnaires (QLQ) cover AEs and functions.This research aimed to assess if AEs covered in EORTC QLQ upper gastrointestinal (GI) modules could be used to assess AEs post-discharge after surgery.Questionnaire items and scales in the EORTC QLQ-C30 and the five validated upper GI modules were analysed. Items not relevant to surgical AEs were excluded. Items and scales with overlapping content were scrutinised. Published validation papers were reviewed for associations between module and core questionnaire scales and items. Semi-structured interviews were then conducted with patients to ensure the questionnaire covered relevant AEs.There were 134 items identified from the C30 and five modules. Methods initially excluded 17 items/scales relevant only to chemoradiation treatment or psycho-social issues. There were 13 overlapping scales/items in the five modules, so one scale/item was selected. The disease-specific pain and fatigue scales were moderately correlated with scales in the C30, so only the C30 scales were retained. The shorter physical functioning scale in the EORTC QLQ-C15-PAL was used. The final questionnaire comprised of 34 items. Interviews with 18 patients showed sufficient coverage except for wound-related problems.Existing validated disease-specific EORTC modules can be utilised to form an upper GI questionnaire to measure AEs in surgical patients in RCTs. Further work is under way to identify clinically important thresholds.\u201cThis abstract presents independent research funded by the National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Reference Number RP-PG-0611-20008). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. We also acknowledge support from the MRC ConDuCT-II Hub.\u201d"} +{"text": "Background: Liver transplantation (LT) is the standard treatment of end-stage liver diseases (ESLD). Invasive fungal infection is one of the important causes of morbidity and mortality after transplantation.Objective: To determine the incidence of late-onset (after 6 months of LT) Candida infection in recipients. Methods: A retrospective study was conducted to evaluate 50 pediatric patients after LT for 8 years at the LT Unit of Nemazee Hospital affiliated to Shiraz University of Medical Sciences, Shiraz, Iran. We followed the patients until 6 months post-LT for episodes of Candida infection proven by culture. Results: One recipient (2%) developed late-onset esophageal candidiasis with improvement after intravenous amphotricin therapy but finally expired with a diagnosis of post-transplant lymphoproliferative disorder (PTLD).Conclusions: The incidence of late-onset Candida infection is not significant in pediatric liver recipient, but it still remains a significant problem. Control of Candida colonization would reduce the risk of invasive fungal infections and possibly more fatal complications. Several types of chronic liver diseases in the pediatric population need liver transplantation (LT)\u2014the standard and life-saving treatment in this age group , 2. Due Although life-saving, LT is not curative\u2014to get rid of a fatal disease, the recipient needs life-long consumption of immunosuppressive medications . But, coAlthough multiple centers investigate early-onset Candia infection (during the first six months of transplantation), few studies have examined the late-onset (six months after LT) infection.The objective of this study was to evaluate the incidence of late-onset Candida infection in pediatric liver recipients. A cross-sectional study was conducted in 50 pediatric LT patients in the LT center of Nemazee Hospital, Shiraz University of Medical Sciences (SUMS), Shiraz, Iran. All the studied children aged between 1 and 18 years and were followed in LT clinic, Nemazee Hospital, by LT surgeons and pediatric hepatologists for 6 to 96 months. If the patients had any signs or symptoms of gastrointestinal candidiasis including dysphagea, odynophagea, prolonged diarrhea without improvement, they were evaluated for Candida infections. oC. After 48\u201372 hours, if the result was positive, the colony was re-cultured for purity onto potato dextrose agar and incubated at 35 oC for an additional 48 hours. Specimens were collected and cultured on Sabouraud dextrose agar supplemented with chloramphenicol (50 mg/L) and incubated at 35 Species identification of the isolates were performed by standard methods and by the API 20 C system for sugar assimilation. The studied patients included 32 (64%) boys and 18 (36%) girls with mean\u00b1SD age of 10.6\u00b14.6 (range: 1\u201318) years. The most common causes of LT were extra-hepatic biliary atresia (EHBA) . Other causes of LT in our patients are presented in One patient (2%) developed fever and dysphagea. She was five years old. The LT was done eight months prior to admission. She had been receiving tacrolimus for immunosuppression (with monitoring of blood level). The patient had also been receiving prednisolone that was tapered and finally discontinued. Due to fever and dysphagea, she was admitted to Pediatric Hepatology ward; upper endoscopy (esophago-gastro-duodenoscopy) showed multiple whitish patchy lesions suggestive of esophageal candidiasis.Stain of esophageal brushing was showed hyphae. The specimen was also cultured (as described above), the results of which were in favor of candidiasis. Intravenous amphotricin (1 mg/kg/day for three weeks) was started for her; fever and dysphagea subsided and the patient discharged with no problem. The patient had a past history of acute rejection of liver; she had been admitted and responded well to pulse of methyl-prednisolone. The patient had regular follow-up visits (with monitoring of tacrolimus blood level). Finally, after about two months she again developed fever and anorexia. After admission, in physical examination, she had submandibular lymphadenopathy (LAP). Biopsy revealed post-transplantation lymphoproliferative disorder (PTLD). Unfortunately, the patient did not response to treatment and expired.Multiple studies showed that infection is one of the most important causes of morbidity and mortality after pediatric LT . Based oInfection in the early post-transplant period (<1 month) is most commonly bacterial, although the risk of fungal infection is also high , 9. ThisSeveral studies revealed that infectious complications become relatively uncommon after six months of LT (if the recipient is on a stable immunosuppressant therapy) and that these types of infections are primarily associated with chronic rejection, re-transplantation, or large doses of immunosuppressive therapy [5].Risk factors for Candida infection after LT include complicated transplantation, repeated surgery, prolonged broad spectrum antimicrobials consumption, critically ill , and CMV disease. These risk factors show that Candida infection usually occurs during early months after LT. Several studies showed that fungal infections commonly occur during the first six months of LT.One study revealedOur study showed that one child (2%) developed late-onset Candida infection\u2014after six months of transplantation. The incidence is somewhat higher than other studies reported. This finding may indicate that late-onset Candida infection may be an alarming sign for evaluation of more invasive complications (including PTLD). Therefore, particular attention should be paid to make the diagnosis and institute an appropriate treatment for late-onset Candida infection in pediatric patients after LT."} +{"text": "Direct hemoperfusion with polymyxin-B has been reported to improve hemodynamics in postsurgical patients. In 2012, the Japanese Guidelines for the Management of Sepsis were published and mention the efficacy of polymyxin-B direct hemoperfusion. But how to use and the target patients are varied by facilities. We investigated the effective use of polymyxin-B direct hemoperfusion in nonsurgical patients.We analyzed retrospectively all septic shock patients who were treated with polymyxin-B hemoperfusion between January 2008 and December 2012.We checked their mean arterial pressure (MAP), and vasopressor requirement every 30 minutes until stopping treatment.There were 32 patients under treatment and 11 patients did not need surgical treatment. Even in the nonsurgical group, hemodynamic states and vasopressor requirement was improved after polymyxin-B hemoperfusion started. And the effects were continued over 120 minutes. A second plolymyxin-B hemoperfusion treatment underwent in nine patients. In second treatment, MAP increased in the nonsurgical group greater than in the postsurgical group.Polymyxyn-B direct hemoperfusion improves hemodynamic status even in nonsurgical patients. A second polymyxin-B direct hemoperfusion is effective especially in nonsurgical septic shock patients. And if its hemodynamic effect was significantly, long-time treatment should be considered."} +{"text": "Patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD) may need ventilatory support (VS) due to respiratory failure. Risk stratification on admission could identify patients at higher risk of deterioration. Cardiac biomarkers are associated with outcome in AECOPD but were not studied as predictors for VS.The aim of this study was to evaluate association between admission NT-proBNP and ventilatory support (VS) in the patients with AECOPD.The prospective observational study included 139 patients with a clinical diagnosis of AECOPD and Global Initiative for Chronic Obstructive Lung Disease (GOLD) stages III-IV. NT-proBNP was determined from venous blood samples on patient admissions to the hospital with the use of a quantitative electrochemiluminescence assay on an Elecsys 2010 analyzer (Roche Diagnostics) according to established methods. The VS was defined as any form of invasive or noninvasive VS applied during index hospital stay.Patients who did not require (no.:108) vs. those who required VS (no.:31) and patients with invasive (no.:15) vs. those with noninvasive VS (no.:16) were of similar age, gender and GOLD stage . NT-proBNP was higher in patients who required VS then in those without VS . Patients with noninvasive VS had higher NT-proBNP then those without VS . The difference between patients treated with noninvasive vs. invasive VS was not significant . Patients receiving invasive VS had similar admission NT-proBNP as those without VS .Admission NT-proBNP may predict need for noninvasive VS in patients with AECOPD."} +{"text": "Osteoma is a benign bone-forming tumor that usually arises in the craniofacial bones and rarely in the long bones. Clavicular involvement is extremely rare. We report a 51-year-old woman with osteoma of the left clavicle. Radiograph of the left shoulder showed a well-defined lobulated blastic mass in the proximal and mid-portion of the left clavicle. Bone scintigraphy was performed 4 hours after an intravenous injection of Tc-99m hydroxymethylene diphosphonate (HMDP). Whole-body image showed a focus of intensely increased uptake in the clavicle. Single photon emission computed tomography / computed tomography (SPECT/CT) images were also acquired and clearly showed intense uptake at the tumor site. Integrated SPECT/CT imaging supplies both functional and anatomic information about bone the SPECT imaging improves sensitivity compared with planar imaging, the CT imaging provides precise localization of the abnormal uptake, and information on the shape and structure of the abnormalities improves the specificity of the diagnosis. Osteoma is a benign bone-forming tumor and clavicular involvement is extremely rare. We report a case of clavicular osteoma undergoing bone scintigraphy who demonstrated intense uptake in the clavicle, for which further single photon emission computed tomography / computed tomography (SPECT/CT) imaging was performed to characterize and localize the lesion.The present case was a 51-year-old woman who presented with a left clavicular mass. The tumor had grown very slowly since the age of 21 years when the lesion was detected incidentally on plain chest X-ray. Radiograph of the left shoulder showed a 70\u00d735 mm, well-defined lobulated blastic mass in the proximal and mid-portion of the left clavicle. Bone scintigraphy was performed 4 hours after an intravenous injection of Tc-99m hydroxymethylene diphosphonate (HMDP). Whole-body image showed a focus of intensely increased uptake in the clavicle . SPECT/COsteoma is a benign ostogenic tumor that usually arises in the craniofacial bones and rarely in the long bones , 2. Clav"} +{"text": "Multi-disciplinary team (MDT)-working is recognized as a key modality for providing cancer services in the province of Quebec (Canada) and elsewhere . EvidencData were collected in 2010-11 in 15% of Quebec\u2019s oncology outpatient clinics. Sites (n=9) were purposely selected on the basis of the intensity level of MDT (higher or lower). The sample included 1379 adult cancer patients (response rate 80%). Perceived experience of care was documented by means of a self-administered questionnaire divided into six validated sub-scales: timeliness of services (TIM), communication (COM), patient-centered care (PCC), quality of physical environment (QPE), continuity (CONT) and results of care (RES). Multiple logistic regression models were used to estimate the extent to which patients\u2019 ratings of their care experience differed between levels of MDT-working.Patients who were treated in clinics where the MDT-working level is high were 3.99 times (95% CI: 1.89-8.41) more likely to rate positively TIM and also more likely to have a positive opinion of COM , of PCC and of CONT . Patients\u2019 perception of QPE and RES were not related to the level of MDT-working. Various patients\u2019 characteristics and organizational attributes were associated with patients\u2019 ratings of their care experience.This study suggests that MDT-working can improve various aspects of perceived patients\u2019 care experience. Significant challenges remain in order to draw clear conclusions about the key elements of MDT-working and its benefits and they will be discussed."} +{"text": "To analyze the distribution of Middle East respiratory syndrome coronavirus (MERS-CoV)\u2013seropositive dromedary camels in eastern Africa, we tested 189 archived serum samples accumulated during the past 30 years. We identified MERS-CoV neutralizing antibodies in 81.0% of samples from the main camel-exporting countries, Sudan and Somalia, suggesting long-term virus circulation in these animals. Betacoronavirus genus lineage C and causes severe respiratory disease in humans has caused an ongoing epidemic on the Arabian Peninsula. The designated Middle East respiratory syndrome (MERS)-CoV belongs to the A serum sample from each of 189 dromedary camels was collected by trained personnel as previously described as previously described Figure 1A total of 159 of 189 dromedary camels were positive for MERS-CoV antibodies in the rELISA , Table 1MERS-CoV antibody\u2013carrying dromedaries were present in all 3 countries in 1983, 1984, and 1997 , 2. The Our study complements and supports the latest findings on long-term and widespread circulation of MERS-CoV or MERS-like CoV in dromedaries in Africa recombinant ELISA (rELISA) cutoff and correlation of the MERS-CoV rELISA and the virus neutralization test."} +{"text": "Diabetic retinopathy (DR) is the most serious ocular complication of type 1 diabetes (T1D) and leading cause of acquired blindness in working aged adults. Although various interventions have been trialled to prevent the development or progression of DR, the evidence to support many of these remains unclear. We systematically reviewed the evidence for primary and secondary interventions, to guide the management of DR in people with T1D.Systematic searches were performed using MEDLINE, EMBASE and CENTRAL databases (from January 1990 to June 2014) to identify randomised controlled trials and controlled cohort studies reporting the incidence or progression of DR following administration of systemic interventions. English-language studies with a minimum follow-up of one year were eligible. Meta-analyses of extracted data were performed to determine pooled relative risk (RR) reduction.Twenty-three studies met the inclusion criteria. Intensive insulin therapy significantly reduced the risk of both incident DR and progression of DR compared with conventional therapy. Continuous subcutaneous insulin infusion (CSII) pumps provided significantly greater protection than multiple daily injection therapy . Angiotensin-converting enzyme inhibition had no impact on DR incidence but reduced progression . Conversely, angiotensin receptor blockade was effective in decreasing DR incidence but had non-significant effect on progression. Both pancreas-alone and combined pancreas-kidney transplantation retarded progression of DR . Islet cell transplantation provided no benefit compared with either intensive or conventional insulin therapy.In people with T1D, there is strong evidence supporting intensive insulin therapy for prevention of DR. Anti-hypertensives also provide protection against DR in normotensive, normoalbuminuric adults but their effectiveness in other populations is yet to be investigated. In patients with T1D of longer duration, pancreas transplantation slows progression of DR. There is insufficient evidence to recommend the use of anti-lipid therapy or other medical interventions."} +{"text": "Diffusion tensor imaging (DTI) has been shown to be exb = 770 smm-2 (+b0) with 1 mm isotropic resolution.3D DTI of a whole human heart was performed on a 3T Siemens Skyra using a monopolar spin echo sequence with 30 diffusion directions at ky-kz plane of the 3D Cartesian acquisition was applied retrospectively to the fully-sampled DTI dataset with sampling ratios 50, 33, 25, and 20% .Efficient variable-density under-sampling of the Diffusion tensor data was reconstructed and the left-ventricular wall was analyzed. Maps of fractional anisotropy (FA), mean diffusivity (MD), and helix angles (HA) were computed for the fully-sampled and reconstructed under-sampled datasets. To evaluate the accuracy of FCSA CS, root mean square errors (RMSEs) of FA, MD, and HA were estimated between the full-sampled and the accelerated data-sets. All computations were performed using custom-made software in Matlab.Figure We have demonstrated that CS using FCSA has potential to shorten acquisition times of cardiac DTI without compromising accuracy. These results can be used to minimize patient discomfort and mitigate growing healthcare costs through increasing contemporary scanner throughput.This work was supported by the National Institute of Health Research Cardiovascular Biomedical Research Unit at the Royal Brompton Hospital and Imperial College, London."} +{"text": "Clinical transcranial MR-guided focused ultrasound (TcMRgFUS) brain treatment systems compensate for skull-induced beam aberrations by adjusting the phase and amplitude of individual ultrasound transducer elements. These corrections are currently calculated based on a pre-acquired CT scan of the patient\u2019s head. The purpose of the work presented here is to demonstrate the feasibility of using ultrashort echo-time (UTE) MRI instead of CT to calculate and apply aberration corrections on a clinical TcMRgFUS system.ex vivo human skulls filled with tissue mimicking hydrogel. Each skull phantom was imaged with both CT and UTE MRI. The MR images were then segmented into \u201cskull\u201d and \u201cnot-skull\u201d pixels using a computationally efficient, threshold-based algorithm, and the resulting three-dimensional binary skull map was converted into a series of two-dimensional virtual CT images. Each skull was mounted in the head transducer of a clinical TcMRgFUS system , and transcranial sonications were performed using a power setting of approximately 750 Acoustic Watts at several different target locations within the electronic steering range of the transducer. Each target location was sonicated three times: once using aberration corrections calculated from the actual CT scan, once using corrections calculated from the MRI-derived virtual CT scan, and once without applying any aberration correction. MR thermometry was performed in conjunction with each 10-second sonication, and the highest single-pixel temperature rise and surrounding-pixel mean were recorded for each sonication.Phantom experiments were performed in three Fig."} +{"text": "Resistance against diseases affects profitability of rainbow trout. Limited information is available about functions and mechanisms of teleost immune pathways. Immunogenomics provides powerful tools to determine disease resistance genes/gene pathways and develop genetic markers for genomic selection. RNA-Seq sequencing of the rainbow trout spleen yielded 93,532,200 reads (100 bp). High quality reads were assembled into 43,047 contigs. 26,333 (61.17%) of the contigs had hits to the NR protein database and 7024 (16.32%) had hits to the KEGG database. Gene ontology showed significant percentages of transcripts assigned to binding (51%), signaling (7%), response to stimuli (9%) and receptor activity (4%) suggesting existence of many immune-related genes. KEGG annotation revealed 2825 sequences belonging to \u201corganismal systems\u201d with the highest number of sequences, 842 (29.81%), assigned to immune system. A number of sequences were identified for the first time in rainbow trout belonging to Toll-like receptor signaling (35), B cell receptor signaling pathway (44), T cell receptor signaling pathway (56), chemokine signaling pathway (73), Fc gamma R-mediated phagocytosis (52), leukocyte transendothelial migration (60) and NK cell mediated cytotoxicity (42). In addition, 51 transcripts were identified as spleen-specific genes. The list includes 277 full-length cDNAs. The presence of a large number of immune-related genes and pathways similar to other vertebrates suggests that innate and adaptive immunity in fish are conserved. This study provides deep-sequence data of rainbow trout spleen transcriptome and identifies many new immune-related genes and full-length cDNAs. This data will help identify allelic variations suitable for genomic selection and genetic manipulation in aquaculture. Teleost fish are the first class of vertebrates that have the elements of both innate and adaptive immune responses Whyte, . Innate The ability of fish to combat viral, bacterial or parasitic pathogen is affected by genetic factors. Thus, genetic selection can improve disease resistance and provide prolonged protection against pathogens are widely distributed and cultured aquaculture species used as a food and sport fish characterize the transcriptome of rainbow trout spleen and (2) identify spleen-specific and immune-relevant genes (including full-length cDNAs) that could be used to develop genetic markers for disease resistance. Identifying the networks associated with such genes will be helpful in generating new technologies to improve aquaculture high quality reads were obtained and assembled into 43,047 contigs with an average contig length of 1154 nt and N50 equal to 1306 nt.The spleen transcriptome was sequenced from an apparently healthy single homozygous doubled-haploid fish from the Swanson clonal line, the same line used for BAC library construction contigs with hits to the NR database (Table Contigs were searched against the NCBI's non-redundant protein (NR) database using the BLASTX program with se Table . The conse Table , limitedse Table . FurtherE-value distribution of the top hits to the NR database showed that 28% of the assembled contigs showed significant homology to previously deposited sequences (less than 1.0E-50), and 72% ranged from 1.0E-50 to 0. The assembled contigs have been submitted to the NAGRP Aquaculture Genome Projects .Data statistics of the sequencing, assembly and annotations are presented in Table Gene ontology (GO) categorizes gene products and standardizes their representation across species annotated sequences with the highest number of sequences assigned to immune system followed by endocrine system , nervous system , digestive system and development . Assignments of the organismal systems to the last four categories support the previously reported relationships between function of the spleen and other systems of the body. For example, a subset of genes with functions relevant to neurodevelopment was identified in the spleen transcriptome of the house finch , followed by Oreochromis niloticus (16.64%), Maylandia zebra (16.47%) and Danio rerio (16.12%) and Oryzias latipes (5.17%). Rainbow trout itself fell in the seventh position of the top-hit species distribution. This may be explained by identification of a large number of new genes in this study and/or and existence of a limited number of rainbow trout proteins (6965 proteins) that currently available at NCBI database. The model fish species in the list, D. rerio, T. rubripes and O. latipes, have large number of proteins available in the NCBI database. All first nine species were fish, starting with S. salar from the family Salmonidae to which rainbow trout belongs. Therefore, these results support the high quality and high level of phylogenetic conservation of the assembled spleen transcriptome. Other species with known genome sequences appearing in the BLASTX top-hit species distribution were mammals including Homo sapiens, Mus musculus, and Rattus norvegicus, Gallus (chicken) and the amphibian Xenopus laevis.A BLASTX top-hit species distribution of gene annotations showed highest homology to Our transcriptome analysis identified 842 immune-related transcripts in 15 KEGG immune pathways, Table . Many ofToll-like receptors (TLRs) activate the innate immune response through recognition of pathogen associated molecular patterns (PAMPs) including lipopolysaccharides or peptidoglycan in bacterial cell wall, \u03b2-1,3-glucan on fungal cell wall and dsRNA from viruses and costimulatory molecules such as CD28 are required for T cell activation. The cytotoxicity of Cytotoxic T lymphocytes in fish is obscure due to lack of suitable experimental systems even though few studies have depicted the lysis of virus-infected cells by NK-like cells in rainbow trout . The coordinate IDs of the spleen-specific transcripts were determined using BLASTN against our spleen transcriptome . The assembled contigs were submitted to the NAGRP Aquaculture Genome Projects (me Table . As showH. mexicanus) spleen transcriptome in neurodevelopment through a subset of genes has been already reported Immune proteins include 5 transcripts such as Fc receptor-like protein 3-like, thrombopoietin receptor precursor, P-selectin precursor, nuclear factor, interleukin 3 regulated (NFIL3), and lectin precursor. (2) Respiratory gas transport proteins include 4 most highly expressed transcripts assigned to hemoglobin and one transcript assigned to carbonic anhydrase II. A large representation of iron-binding proteins was reported in spleen of virus infected Turbot . These data indicate that many of the spleen-specific genes may have immune functions. Further research is still needed to test if the other spleen-specific gene functions are related to immunity.Full-length cDNAs are a crucial tool for many genetic and genomic studies including alternative splicing and characterization of gene duplications or pseudogenes by androgenesis , 901 West Illinois street Urbana, IL 61801 USA. A RiboMinusTM Eukaryote Kit V2 was used to deplete rRNA from the total RNA. cDNA libraries were constructed using ~1 \u03bcg of rRNA depleted RNA following the protocol of the Illumina TruSeq RNA sample preparation Kit (Illumina). The resulting double-stranded manufactured cDNA was used in the preparation of the Illumina library. The standard end-repair step was carried out first, followed by the standard ligation reaction where the end-repaired DNA along with a single A base overhang were ligated to the adaptors using T4-DNA Ligase . The products of the ligation reaction were purified and exposed to size selection of the target length (400\u2013450 bp) from the gel for carrying out the ligation-mediated PCR. Cluster generation and sequencing were carried out following the cluster generation and sequencing manual from Illumina . All sequenced raw data were first exported in FASTQ format and are currently being uploaded to the NCBI short read archive (SRA).http://www.clcbio.com/products/clc-genomics-workbench/). The raw data were filtered by removing short, duplicated and low quality reads. CLC was run using the default settings for all parameters including a minimum contig length of 500 bp.De novo assembly of the expressed short reads was carried out by CLC Genomics Workbench was used for the functional annotation and analysis of the assembled contigs according to molecular function, biological process and cellular component ontologies. BLASTX search for sequence homology was carried out against NCBI's non-redundant protein database (NR). GO terms related to the established hits were extracted and modulated. The functional annotations were analyzed and statistical analysis of GO distributions was performed.Blast2Go version 2.6.5 (http://www.genome.jp/tools/kaas/). The functional annotation of genes was carried out by searching local BLAST against KEGG database.Assembled consensus sequences were uploaded to the KEGG Automatic Annotation Server (KAAS) against the genome protein dataset method was used to analyze and identify the immune molecules that were present and absent in the seven immune pathways containing the highest number of transcripts that showed high similarity to different members of each pathway. Transcripts were mapped to a newly assembled genome reference. The coordinate genome reference IDs of the immune-related transcripts were determined using BLASTX . For distinction of tissue-specific genes, FDR value was set as 5% and fold change was at least 20 fold higher in spleen relative to the other 12 tissues. The spleen-specific genes were mapped to the newly assembled genome reference completely sequenced or not.All contigs annotated in the interesting KEGG immune pathways, including Toll-like receptor signaling pathway, T-cell receptor signaling pathway, B-cell receptor signaling pathway, chemokine signaling pathway, Fc gamma R-mediated phagocytosis, Leukocyte transendothelial migration and NK cell mediated cytotoxicity, in addition to spleen-specific genes were analyzed using the online TargetIdentifier server (Min et al., The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Myasthenia gravis (MG) is often categorized into thymoma-associated MG, early-onset MG with onset age <50 years, and late-onset MG with onset age \u226550 years. However, the boundary age of 50 years old between early- and late-onset MG remains controversial, and each category contains further subtypes. We attempted to classify MG from a statistical perspective.We analyzed 640 consecutive MG patients using two-step cluster analysis with clinical variables and discrimination analysis, using onset age as a variable.Two-step cluster analyses categorized MG patients into the following five subtypes: ocular MG; MG with thymic hyperplasia (THMG); generalized anti-acetylcholine receptor antibody (AChR-Ab)-negative MG; thymoma-associated MG; and generalized AChR-Ab-positive (SP) MG without thymic abnormalities. Among these 5 subtypes, THMG showed a distribution of onset age skewed toward a younger age (p<0.01), whereas ocular MG and SPMG without thymic abnormalities showed onset age skewed toward an older age . The other 2 subtypes showed normal distributions. THMG appeared as the main component of early-onset MG, and ocular MG and SPMG without thymic abnormalities as the main components of late-onset MG. Discrimination analyses between THMG and ocular MG and/or SPMG without thymic abnormalities demonstrated a boundary age of 45 years old.From a statistical perspective, the boundary age between early- and late-onset MG is about 45 years old. Myasthenia gravis (MG) is an autoimmune disease mediated by autoantibodies against molecules in the neuromuscular junction (NMJ), such as anti-acetylcholine receptor antibody (AChR-Ab) or anti-muscle-specific receptor tyrosine kinase antibody (MuSK-Ab) Among 676 consecutive MG patients surveyed in the Japan MG registry study of 2012 The following clinical factors were used as variables: sex; age at onset; disease duration; presence of thymoma; presence of thymic hyperplasia; positivity for AChR-Ab or MuSK-Ab; positivities for other concurrent autoantibodies (see below); MG Foundation of America (MGFA) clinical classification All study protocols were approved by the ethics committee of Tohoku University School of Medicine, the ethics committee of Sendai Medical Center, the ethics committee of Hanamaki General Hospital, the ethics committee of Keio University School of Medicine, the ethics committee of Kyushu University School of Medicine, the ethics committee of Sapporo Medical University, the ethics committee of Nagasaki Institute of Applied Science, the ethics committee of Saitama Medical Center, the ethics committee of Toho University Medical Center Oh-hashi Hospital, the ethics committee of Tokyo Medical University or the ethics committee of Nagasaki Kawatana Medical Center. These clinical investigations have been conducted according to the principles expressed in the Declaration of Helsinki. Written informed consent was obtained from all patients prior to participation in the study.The regular cluster analysis divides subjects into classes simply according to distances (e.g. Euclidean distances) among variables, which may not be fitted for analysis simultaneously of both categorical and continuous variables with various levels of measurement and scale. On the other hand, two-step cluster analysis estimates log-likelihood and measures probability distribution of each variable, which is more suitable for the present clinical analysis.Therefore, to classify the patients, we conducted two-step cluster analysis using SPSS Statistics Base 22 software , which can extract clusters with high accuracy 2 test for categorical variables. Values of p<0.05 were considered statistically significant.Correlations between clinical factors were evaluated using the Spearman rank correlation. The boundary age between early- and late-onset MG was determined by discrimination analysis. Differences between groups were evaluated using the Mann-Whitney U test for continuous variables and the \u03c7First, two-step cluster analysis for the whole dataset and onset age until a specific age. Such changes in correlations are shown regarding ocular MG/(ocular MG + THMG) -A, SPMG Second, we performed discrimination analysis with onset age as a variable to further establish the boundary age between early- and late-onset MG. The boundary age for discriminating THMG and SPMG without thymic abnormalities was calculated as 44.9 years old, and predictive values of the analysis were about 74%; these values were not particularly high, but were at the significant level for setting the boundary. In the same way, the boundary ages between THMG and ocular MG and between THMG and SPMG without thymic abnormalities + ocular MG were 44.8 and 47.5 years old .According to the findings from the two models, the boundary age between early- and late-onset MG was around 45 years old.The present cluster analyses, without using early- and late-onset MG as variables, extracted THMG, ocular MG, and SPMG without thymic abnormalities as subtypes of MG. Distributions of onset age for THMG or ocular MG and SPMG without thymic abnormalities skewed toward younger or older ages. Given that ages at onset of the other two subtypes showed normal distributions and that TAMG is widely accepted as an independent unique subtype As clustering analyses are basically tools of exploratory data analysis for extracting data analogies, the present results need to be validated from the viewpoint of clinical utility and rationality. The separation of ocular MG with the strongest significance seems plausible, because patient backgrounds, clinical symptoms, and therapeutic responsiveness of ocular MG were totally different from those of other MG subtypes The boundary onset age between early- and late-onset MG was calculated to be around 45 years old by analyses between THMG and ocular MG and/or SPMG without thymic abnormalities, somewhat younger than but still relatively close to the often-used cut-off at 50 years old In conclusion, MG was classified into ocular MG, THMG, generalized AChR-Ab-negative MG, thymoma-associated MG, and generalized SPMG without thymic abnormalities by two-step cluster analyses. THMG appeared to represent a component of early-onset MG, and ocular MG and SPMG without thymic abnormalities appear to represent components of late-onset MG. The boundary age between early- and late-onset MG was suggested as 45 years old. These results await external cross-validation with a different large-sized dataset in the future.Figure S1Frequency histograms for onset age in generalized AChR-Ab-negative MG.(PDF)Click here for additional data file.Figure S2Frequency histograms for onset age in TAMG.(PDF)Click here for additional data file.Figure S3Frequency histograms for onset age in THMG.(PDF)Click here for additional data file.Figure S4Frequency histograms for onset age in ocular MG.(PDF)Click here for additional data file.Figure S5Frequency histograms for onset age in SPMG without thymic abnormalities.(PDF)Click here for additional data file.Table S1The whole dataset (n\u200a=\u200a640) subjected to the present analysis.(PDF)Click here for additional data file."} +{"text": "Mycobacterium tuberculosis (MTB). INH-resistant MTB clinical isolates are frequently mutated in the katG gene and the inhA promoter region, but 10 to 37% of INH-resistant clinical isolates have no detectable alterations in currently known gene targets associated with INH-resistance. We aimed to identify novel genes associated with INH-resistance in these latter isolates.Isoniazid (INH) is a highly effective antibiotic central for the treatment of katG, inhA, kasA and ndh genes and the regulatory regions of inhA and ahpC. Twelve INH-resistant isolates with no mutations, and 17 INH-susceptible MTB isolates were subjected to whole genome sequencing. Phylogenetically related variants and synonymous mutations were excluded and further analysis revealed mutations in 60 genes and 4 intergenic regions associated with INH-resistance. Sanger sequencing verification of 45 genes confirmed that mutations in 40 genes were observed only in INH-resistant isolates and not in INH-susceptible isolates. The ratios of non-synonymous to synonymous mutations (dN/dS ratio) for the INH-resistance associated mutations identified in this study were 1.234 for INH-resistant and 0.654 for INH-susceptible isolates, strongly suggesting that these mutations are indeed associated with INH-resistance.INH-resistant clinical isolates of MTB were pre-screened for mutations in the The discovery of novel targets associated with INH-resistance described in this study may potentially be important for the development of improved molecular detection strategies. Mycobacterium tuberculosis (MTB) is a leading cause of mortality globally, with about 8.7 million new cases of tuberculosis and 1.4 million deaths reported in 2011 INH is a highly effective anti-tuberculosis drug, central for the treatment of MTB. The mode of action of INH is to inhibit mycolic acid synthesis katG gene, with mutations resulting in diminished activation of INH inhA, ahpC, kasA and ndhkatG mutations INH is a prodrug activated by the catalase-peroxidase enzyme, KatG Between 10 to 37% of INH-resistant clinical isolates have no detectable alterations in any of the currently known gene targets Clinical isolates of MTB were from the Central Tuberculosis Laboratory, Department of Pathology, Singapore General Hospital. Phenotypic drug susceptibility testing was done with the BACTEC 460 system , as previously described katG, inhA, kasA, ndh genes, and the regulatory regions of inhA and ahpC, and had no detectable mutations st Base Pte Ltd, Singapore.All INH-resistant isolates had previously been screened for known mutations found in Mycobacterium tuberculosis H37Rv (GenBank accession no. AL123456.2) using BWA 0.5.9, which takes into account read quality during alignment, resulting in low quality reads not being aligned SOLiD 3 single-end reads and Illumina paired-end reads were aligned against Mycobacterium canetti as an outlier Phylogenetically related mutations could affect the accuracy in selecting the INH resistance associated genes and intergenic regions. Phylogenetic analysis of 29 isolates that were whole genome sequenced was carried out using TreeBeST, which uses a maximum likelihood approach for phylogenetic tree construction. Filtering of phylogenetically related mutations was performed in the following way, as has been described previously in mutations that were present only within one single clade of the tree were remmutations that were present in two or more subclades and in wp<0.05) was used to identify mutations in coding and intergenic regions, not occurring by chance. The Normal distribution (p<0.05) was used to select mutations that were present in a higher proportion in INH-resistant isolates than in INH-susceptible isolates of the INH-resistance associated genes as well as whole genome sequences of both INH-resistance and INH-susceptible isolates was determined Taq polymerase and the PCR products were purified with FastAP and Exonuclease I enzyme (Fermentas), according to the manufacturer's instructions. Sanger sequencing was performed using the standard dye terminator chemistry , and analysed on a 3130xl Genetic Analyser (Applied Biosystems). Sequencing results were aligned to the MTB H37Rv sequence (GenBank accession no. AL123456) using SeqMan Pro Lasergene 8 software .Specific primers were designed to amplify regions of \u223c300 to 600 base pairs flanking mutations detected from whole-genome sequencing . Polymerhttp://www.ebi.ac.uk/ena/) under accession number ERP001993.Raw sequence data has been submitted to the European Nucleotide Archive with no detectable mutations in the utations .The average depth of coverage for the twelve INH-resistant MTB isolates was 33-fold (19- to 41-fold), with an average of 86% of bases with at least 8-fold coverage. For the 17 INH-susceptible MTB isolates, the average depth of coverage was 534-fold, and an average of 94% bases had at least 8-fold coverage. As whole-genome sequencing had been performed using two sequencing platforms, the 11 INH-susceptible isolates sequenced in the second stage had higher read coverage, as the more advanced Illumina HiSeq2000 Sequencing System was utilized. The overall higher coverage for INH-susceptible MTB isolates resulted in a higher specificity in detecting INH-resistant specific mutations.In total, we detected 8087 mutations of which 1054 were found only in INH-resistant strains . Of thesA total of 2,365 non-synonymous and 144 intergenic variants were identified in INH-resistant and INH-susceptible strains, after excluding phylogenetically related and synonymous mutations . We furtgpsA, gnd1, atsB, Rv1069c and Rv2869c) had mutations in INH-susceptible isolates regions of The ratio of non-synonymous mutations to synonymous mutations (dN/dS) suggests the rate of evolution of genes and such rates play a major role in identifying potential drug targets One limitation of this study is that the small number of isolates that were whole-genome sequenced (12 INH-resistant and 17 INH-susceptible isolates) may have led to the identification of only some INH-resistant mutations, which occur in very low frequencies. It is anticipated that whole genome sequencing of more MTB isolates could potentially reveal additional novel mutations associated with INH-resistance. In addition, due to the limited number of clinical isolates in this study, statistical confirmation that the INH-resistance associated mutations are indeed linked to the INH-resistant phenotype, has not been shown.Another limitation of this study is that cloning of each mutant allele and determination of their functional effect in INH resistance has not been performed. Functional analysis will be required to conclusively show that each of these mutations is associated with INH resistance. Allelic exchange has also been proposed as an approach for validating the effect of mutations associated with antibiotic resistance In conclusion, the search for identification of the additional genes associated with INH-resistance as described in this current study, will be important for the development of comprehensive molecular detection strategies, more efficient than current susceptibility testing methods based on culture. Such molecular screening methods could aid in more appropriate treatment given earlier to patients and have the potential to decrease transmission of the resistant strains. In addition, the discovery of the new loci reported here may reveal novel targets suitable for the development of alternative therapeutic options.Table S1List of primers used for PCR amplification and Sanger sequencing.(XLSX)Click here for additional data file.Table S2List of nonsynonymous and nonsense mutations, insertions and deletions identified by whole genome sequencing in INH-resistant isolates.(XLSX)Click here for additional data file.Table S3List of nonsynonymous, stoploss and stopgain mutations with Poisson distribution p-value<0.05.(XLSX)Click here for additional data file.Table S4List of nonsynonymous, stoploss and stopgain mutations with Normal distribution p-value<0.05.(XLSX)Click here for additional data file.Table S5List of intergenic mutations with Poisson distribution p-value<0.05.(XLSX)Click here for additional data file.Table S6List of intergenic mutations with Normal distribution p-value<0.05.(XLSX)Click here for additional data file.Table S7List of mutations verified using Sanger sequencing.(XLSX)Click here for additional data file.Table S8Drug susceptibility of 101 INH-resistant isolates & 99 INH-susceptible isolates tested.(XLSX)Click here for additional data file."} +{"text": "Prognosis following MI has been shown to be strongly associated with small changes in left ventricular remodeling. Omega-3 fatty acid (PUFAs) supplementation may have a number of beneficial pleiotropic effects, including enhancement of myocardial relaxationThe OMEGA-REMODEL study was a randomized, double-blinded, placebo controlled trial of PUFA supplementation post acute MI. A total of 358 patients were randomized to study therapy with PUFAs (n=180) or matching placebo (n=178) and underwent baseline assessment by CMR 4-28 days following MI, with follow-up after 6 months of randomized therapy. The primary endpoint was changes in left ventricular end-systolic volume indexed to body surface area (LVESVI). Secondary outcomes included a) change in total infarct size, b) expansion of MECVF within noninfarcted myocardium, and c) changes in systemic biomarkers.Baseline demographics for the entire cohort and both treatment arms are shown in Table 1. CMR characteristics, PUFAs levels, and biomarkers for baseline and 6-month post-treatment values of each treatment arm are shown in Table 2 and Figure The results of this study demonstrated a significant reduction in LVESVI and MECVF for patients treated with high-dose PUFAs as compared to placebo. Further assessment of systemic biomarkers demonstrated a substantial reduction in biomarkers of inflammation, and fibrosis for the PUFAs treated arm. These findings represent the first description of the effect of PUFAs on myocardial tissue phenotypes during the convalescent phase post MI and may suggest potentially important pathophysiological pathways for their pleiotropic effects.National Institutes of Health Heart, Lung and Blood Institute (NHLBI)."} +{"text": "LMNA-related Congenital Muscular Dystrophy (L-CMD) is a rare genetic disorder characterized by the onset of selective axial weakness and wasting in the first year of life with limited motor achievements, associated with multiple severe contractures and frequent respiratory failure requiring early ventilatory support. We identified heterozygous de novo mutations in LMNA, encoding lamins A/C, as responsible for this sub-group of CMD in which no therapeutic treatment is available[delK32Lmna) reproducing a LMNA mutation identified in L-CMD patients. Homozygous mice die within the first 3 weeks of life from striated muscles maturation delay and severe metabolic defects[in vitro in C2C12 cells and in vivo using Adeno-Associated Virus (AAV) transduction in tibialis anterior of WT mice. We will now determine the ability of the best PTM to restore normal muscular phenotype, in vitro in KI myoblasts/myotubes and in vivo after injection of AAV-PTM vectors in new born homozygous and adult heterozygous mice. Histological and metabolic parameters will be monitored to evaluate the degree of phenotype rescue.available. Lamins"} +{"text": "We hypothesized that intraluminal signal intensity (SI) of coronary total occlusion (CTO) lesions at coronary MR angiography (CMRA) may reflect the degree of the softness of the lesion with or without the presence of microvessels. The purposes of our study were to report the CMRA findings of CTO lesions and to compare success rates of percutaneous coronary intervention (PCI) for CTO lesions according to different SI patterns at CMRA.Ninety-one consecutive CTO patients who underwent steady-state free precession CMRA (free-breathing whole-heart and breath-hold volume-targeted) and late gadolinium enhancement imaging using a 1.5-T scanner before PCI were included. We analyzed the images of CMRA and PCI results of the patients. Ninety-three CTO lesions were analyzed for this study. Lesions were graded according to CMRA findings of CTO segment: (Gr. 1) tubular appearance with homogeneously high SI (HSI), (Gr. 2) continuous HSI areas with moderate irregularity in contour, (Gr. 3) heterogeneous SI lesion with interrupted HSI areas, (Gr. 4) intermediate or low SI lesion. Lesions were classified into two groups with regard to the presence of the continuity of HSI areas. Angiographic findings including lesion length, collateral grades, and thrombolysis in myocardial infarction (TIMI) grades were recorded at invasive coronary angiography. Multivariable statistical test was performed to identify variables associated with successful PCI.Seventy-three lesions (78%) of 93 CTO lesions were successfully treated with PCI. On CMRA images, the presence of continuity of HSI areas was found in 60 lesions (64.5%) including lesions of Gr. 2 (n = 13). Fifty-four lesions (90%) of the 60 lesions were successfully treated with PCI. The others (Gr. 3 or 4) were 33 lesions . Nineteen lesions (58%) of the 33 lesions were successfully treated with PCI. At multivariable analysis, the presence of continuity of HSI areas in CTO segments proved to be the only independent predictor of PCI success , while angiographic findings did not significantly correlate with PCI outcomes.The CMRA findings showing continuity of HSI areas in CTO segments predict better success rates of PCI.No."} +{"text": "In primary care settings difficult-to-treat asthma may be interpreted as severe asthma. Little is known about diagnostic outcomes in children referred to secondary paediatric referral centres with an established primary care doctor's diagnosis of difficult-to-treat bronchial asthma. The objective of the present study was to assess diagnostic outcome in school age children referred to a secondary paediatric referral centre with an established primary care doctor's diagnosis of difficult-to-treat bronchial asthma.482 consecutively referred children aged 5-14 (mean 7.9) years, 99 girls (21%) and 383 boys (79%) with a primary care doctor's referral diagnosis of difficult-to-treat asthma were included from the prospective Asthma in a Secondary Pediatric Referral Centre Study (ASP 2002) in the present survey. At referral and during a 6 months evaluation period patient characteristics, history, symptoms, signs and results of type 1 allergy tests, spirometry, post bronchial beta-2 agonist dilation tests, 4-weeks daily measurement of peak flow rates, corticosteroid reversibility trials and exercise challenge tests were entered into a pre-defined electronic form. The secondary referral centre (SRC) diagnosis of asthma was based on these data.A diagnosis of asthma was confirmed in 200 (41%), whereas it could not be confirmed in 282 (59%) of the children. Allergic rhinoconjunctivitis was diagnosed in 96 (48%) in the confirmed group, in 87 (31%) in the not confirmed group. A variety of differential diagnoses was made in the children in whom asthma was not confirmed.In more than half of school age children with a primary care doctor's diagnosis of difficult-to-treat asthma referred to a secondary paediatric referral centre the diagnosis may not be confirmed. Sensitivity and specificity of the diagnosis of asthma in schoolchildren made in primary care settings need further improvement."} +{"text": "However, TEE requires esophageal intubation and cannot fully assess the complex 3D pattern of flow in the LA. In addition, a systematic analysis of the impact of beat-to-beat variations on LA flow characteristics and thus thromboembolic risk is lacking, particularly in the presence of arrhythmia. To better elucidate the role of beat-to-beat flow variations in different AF phenotypes (arrhythmia vs. sinus) we utilize a recently introduced real-time 2D flow imaging method which has shown promising results3. The goal of this feasibility study was to investigate different measures of LA flow to better understand the impact of different AF phenotypes on LA hemodynamics.Atrial fibrillation (AF) is a common cardiac arrhythmia, affecting 33.5 million patients worldwide. The most serious complication is stroke, which is generally attributed to embolism of thrombus from the left atrium (LA). Studies utilizing transesophageal echocardiography (TEE) have shown that decreased blood flow velocities in the LA are risk factors for stroke in AF3. Data analysis included the calculation of LA flow-time and mean velocities-time curves in a region of interests delineating the LA boundary (see figure).In 7 AF patients , highly accelerated real-time 2D flow imaging with through plane velocity encoding (venc=80-150cm/s) was performed. Images were acquired during breath-holding in 2D planes along the LA short axis to investigate the impact of irregular heart rate in AF on LA flow and velocities . To achieve sufficiently high frame rates needed for real-time flow acquisitions (45-50ms), the 2D flow imaging pulse sequence combines an echo planar imaging (EPI) readout module and with parallel acceleration in the temporal direction (T-PAT) and a novel reconstruction algorithm, shared velocity encodingAs shown in the figure, real-time flow imaging could reliably assess LA flow variations over multiple heart beats for both sinus-rhythm and arrhythmia. Quantification of average and beat-to-beat variability of mean LA flow, peak mean LA velocities, and maximum LA through plane velocities Fig clearly The findings of this study demonstrate the feasibility of real-time flow imaging to measure beat-to-beat flow variation in AF patients with arrhythmia and compared to sinus rhythm. Noticeably, there was high inter-individual variability in peak LA velocities and their beat-to-beat variability indicating the potential of real-time flow MRI to identify individual patients with altered AF induced flow characteristics.AHA (12GRNT12080032) and NIH-NHLBI (1R21HL113895)."} +{"text": "Sarcoidosis is a multisystem disorder with cardiac involvement in 25% of cases . Diagnos30 patients meeting Japanese Ministry of Health & Welfare guidelines for clinFDG-PET and CMRI were positive in 10 patients; FDG-PET +ve and CMRI -ve in 3; FDG-PET -ve and CMRI +ve in 4; both -ve in 13. Distributions of FDG and LGE throughout the myocardium are summarized in Figure Previous single modality studies have suggested sensitivity and specificity for FDG-PET of 89% and 78% and CMRI of 75% and 77% respectively. In our study, 43% showed no cardiac sarcoidosis by either modality and half of these had minimal or no FDG-PET evidence of active sarcoidosis elsewhere. Are these false -ve FDG-PET/CMRI studies or are the clinical criteria too sensitive? Our findings suggest FDG-PET and CMRI-LGE show different degrees of cardiac sarcoid involvement: FDG-PET indicating active inflammatory disease, LGE showing severe edema and scar. Those patients with LGE and no myocardial FDG uptake appear to have 'burnt-out' disease.None."} +{"text": "One in a thousand pregnancies will be complicated by serious maternal morbidity warranting intensive care unit (ICU) admission before, during or after delivery. Between 2007 and 2009 maternal mortality in France was one in ten thousand, about half of them are considered preventable.In order to assess and improve avoidable severe maternal morbidity (SMM), whether lethal or not, a prospective analysis was undertaken in a tertiary care obstetric ICU (TCO-ICU) over a six year period.Between January 2007 and December 2012 data were collected on all obstetric and post-partum admissions in the Strasbourg (France) TCO-ICU.Among the 305 TCO-ICU admissions, 2 patients presented with avoidable (iatrogenic) non-lethal morbidity and 8 patients died, all of them from non-avoidable causes. No deaths occurred in the 2 main groups, hypertensive disorders of pregnancy and major obstetric hemorrhage.Optimal cooperation between our tertiary facilities and non-teaching hospitals and clinics as well as the prehospital transport systems allows significant limitations in avoidable obstetric maternal morbidity and mortality. Cerebral hemorrhage and amniotic fluid embolism carry the heaviest toll in non-avoidable deaths."} +{"text": "A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity , and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database , which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between In recent years, a significant progress has been made concerning the development of numerous genomic and transcript-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers at a genome-wide scale and their deployment in multi-dimensional genomics-assisted breeding applications in chickpea . This suLength polymorphism of SSR markers in the coding sequence (CDS) and non-CDS components of genes are known to affect transcription and translation, and may have significant consequences on gene function . The expindica and japonica rice following the criteria (at least six repeats of di-nucleotides and five repeats of tri- to hexa-nucleotides) as described earlier present in the coding and non-CDS components of genes, and intergenic regions were amplified via PCR using genomic DNA of 31 desi and 15 kabuli chickpea genotypes to evaluate their amplification and polymorphic potential. These desi and kabuli genotypes with diverse useful yield contributing and stress tolerance traits, have been primarily utilized as contrasting parents in various cross-breeding varietal improvement programs for developing improved cultivars of chickpea in India. The touchdown thermal cycling profiling and standard constituents used for PCR amplification were as described previously and degree of admixture within and between population groups at optimal K (population number) value was determined.A total of 160 informative SSR markers were used for determining functional molecular diversity and establishing phylogenetic relationships among chickpea genotypes based on Nei\u2019s genetic distance by neighWe developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB), to provide browsable access to the SSR data. The web pages of CMsDB have been written using Perl-CGI on the Apache Tomcat (version 5.5.29) Web server application. The information regarding SSRs, their flanking sequences and primer details are cataloged in the MySql server (version 5.0.77). The database is currently hosted on Sun Workstation running CentOs (version 5.4) Linux operating system with two Intel Xeon quad core processors and 12 GB of random access memory. The database is compatible with various browsers like Internet Explorer, Mozilla Firefox, and Google Chrome.desi and kabuli chickpea genomes, respectively, were utilized for mining and characterization of SSR motifs. Based on these analyses, 74941 and 81845 perfect SSRs (excluding mono-nucleotides) were identified in desi and kabuli chickpea with an average density of 0.144 SSR/kb and 0.157 SSR/kb, respectively (Table 1). The overall frequency of compound SSRs identified in desi and kabuli chickpea was almost comparable with each other. In both the genomes, di-nucleotide repeat-motifs were most prevalent followed by tri- and tetra-nucleotides (Table 1). In terms of proportion of total number of SSRs identified, the long hyper-variable class I repeats varied from 49.8% (40789) in kabuli to 50.3% (37737) in desi chickpea. The class I and class II di-nucleotide repeat-motifs were present in maximum fraction varying from 49.1 (18537) to 62.3% (25568) in desi and kabuli chickpea . Next, the tri-nucleotide SSR repeat-motifs were most abundant (varied from 34.2 to 38.4%) in both class I and class II SSRs, while tetra-, penta-, and hexa-nucleotide motifs were completely absent in case of class II SSRs. The frequency of AT-rich di-nucleotide repeat-motifs was maximum in both desi and kabuli chickpea followed by AAT/ATT-rich tri-nucleotide SSRs and AAAT/ATTT-rich tetra-nucleotide SSRs . The structural annotation of identified SSRs in desi genome revealed their highest frequency in intergenic regions (64961 SSRs) followed by introns (6762), exons (3218), CDS (1816), and upstream regions (3289) . All five different classes of SSR repeat-motifs (di- to hexa-nucleotides) were predominant particularly in the intergenic regions as compared to various coding and non-CDS components of genes. However, within genes, the frequency of di- (4191), tetra- (462), and penta-nucleotide (84) SSR repeat-motifs were maximum in the intronic and upstream sequences, whereas tri- (2100) and hexa-nucleotide (76) motifs were abundant in the exons . Maximum number of tri-nucleotide SSR repeat-motifs was found in the CDS (1673 SSRs), whereas upstream regions (3029), and 5\u2019- (703) and 3\u2019-UTRs (168) were rich in di-nucleotide repeat-motifs.A total of 519.8 and 522.3 Mb sequences of desi and kabuli chickpea based on their expansion/contraction of SSR repeat-length . Among the polymorphic SSRs obtained, the di-nucleotide repeat-motifs were most abundant followed by tri-nucleotide motifs . With the increase of SSR repeat-length variation, the number of SSRs showing polymorphism decreased, which indicates inverse correlation between fragment length polymorphism and frequency of polymorphic SSRs identified in desi and kabuli chickpea . Maximum number of polymorphic SSRs showed \u22652-bp repeat-unit variation and 287 SSRs with >20-bp variation between desi and kabuli chickpea were identified. The AT/TA di-nucleotide repeats were maximum followed by TTA/TAA , AAT/ATT , and TAT/ATA . All the identified 1835 polymorphic SSRs were structurally annotated in intergenic regions, and coding and non-CDS components of genes. Maximum number of polymorphic SSR repeats were identified in the intergenic regions , . The polymorphic SSRs identified within genes included highest number in the upstream sequences followed by introns , exons and minimum in 3\u2032-UTRs of genes. All classes of polymorphic SSR repeats including di- to hexa-nucleotide motifs were maximum in the intergenic sequences . The di-nucleotide followed by tri-nucleotide SSR repeats were abundant in the upstream regions (139 di- and 49 tri-nucleotide) and intronic (126 di- and 15 tri-nucleotide) sequences of genes, whereas tri-nucleotide repeats were maximum in the coding regions. About 85% of the polymorphic SSRs were present on the eight chickpea chromosomes, whereas other 15% were located on the scaffolds of kabuli chickpea genome polymorphic SSRs, which included 1151 (78.3%) in the intergenic regions, 150 (10.2%) in the upstream regulatory sequences, 125 (8.5%) in the introns, 31 (2.1%) in the exons, 17 (1.2%) in the 5\u2032-UTRs, 11 (0.75%) in the CDS, and 3 (0.20%) in the 3\u2032-UTRs in total located in different components of genes and intergenic regions to evaluate their amplification efficiency as well as potential for detecting polymorphism among 31 desi and 15 kabuli chickpea genotypes . It included 130 of 176 class I and 30 of 76 class II SSR markers. The remaining 92 (36.5%) markers exhibited monomorphic amplification among chickpea genotypes used. A total number of 764 alleles were amplified by 160 polymorphic SSR markers with a mean allele number of 4.8. The number of alleles amplified per locus varied from 2 to 12. The PIC ranged from 0.23 to 0.86 with an average of 0.75, while gene diversity varied from 0.25 to 0.89 with a mean of 0.77 of 164 markers derived from intergenic regions also showed polymorphism between the two chickpea types . Remarkably, 120 and 107 markers revealed polymorphism within desi and kabuli chickpea genotypes too, respectively. Overall, eight different representative allele types were detected based on fragment length polymorphism patterns of all the 160 SSR markers in 46 desi and kabuli genotypes .We utilized 341 SSR markers to 0.94 with an average of 0.68. Maximum average genetic distance was observed particularly among the accessions belonging to desi chickpea (0.65) in contrast to that detected within kabuli (0.57). The phylogenetic relationship among 31 desi and 15 kabuli chickpea genotypes has been depicted in an unrooted dendrogram . This set of informative genome-wide physically mapped SSR markers (160) clearly discriminated all 46 genotypes from each other and resulted in definite desi and kabuli cultivar-specific groupings. Most of the desi and kabuli genotypes were grouped in separate clusters (I and II), which further corresponded well with their known pedigree relationships and parentage with slight deviations. However, desi genotypes included under cluster I were further grouped into four different sub-clusters , while kabuli genotypes belonging to cluster II classified into two different sub-clusters .The pair-wise distance matrix among 46 desi and 15 kabuli chickpea genotypes was determined using 160 validated polymorphic SSR markers with varying levels of population numbers (K = 2\u201310) with 20 replications. The optimization of K inferred that at K = 5, the average estimate of Ln P(D) across 20 independent replications plateaus and also best replicate giving maximum log likelihood values with sharp peak was obtained. All 46 chickpea genotypes were majorly classified into two distinct high resolution population groups . The population groups, I (31 desi and one kabuli chickpea) and II (14 kabuli chickpea) contained the genotypes mostly from desi and kabuli chickpea, respectively. The desi population group (I) was further classified into four sub-population groups; Ia (10 desi and one kabuli chickpea genotypes), Ib (10 desi), Ic (8 desi), and Id (3 desi) . The cultivar-specific classification and geographical origin of 46 chickpea genotypes belonging to all the five individual population groups are provided in the Supplementary Table FST varied from 0.16\u20130.91 with an average of 0.64) among five population groups. The genetic variation among the five population groups (mean FST: 0.62) was higher than that estimated within populations (0.53). Higher molecular diversity of population group I (mean FST: 0.86) as compared to group II (0.69) was evident. Within population groups I and II, maximum divergence was observed in population groups Ib (mean FST: 0.83) and IIb (0.65), respectively. All the 46 chickpea genotypes clearly belonged to a structured population of five distinct groups in which about 74.2% of inferred ancestry of each group was derived from one of the model-based population and remaining \u223c25.8% contained admixed ancestry. Maximum admixtures (20.3%) of the three desi population groups with kabuli population (II) were observed.The population genetic structure among 31 http://www.nipgr.res.in/CMsDB.html. The database provides browsable access to all the SSRs identified in desi and kabuli chickpea types, and polymorphic SSRs between them. CMsDB can be used to retrieve SSRs in desi and kabuli genomes using various simple [genomic location (chromosome number and position) and genomic feature (genic and/or inter-genic)] and advanced search parameters. Multiple parameters can be combined also to search for a specific set of SSRs as per user requirement. The output lists all the SSRs meeting the user-selected parameters(s) in tabulated format along with various information, including SSR identifier, chromosome number, motif type and length, genomic location (start and end position in bp) and location in the genomic features . An option for downloading the flanking sequences (50\u2013250 bp) of individual/multiple SSRs has also been provided. Polymorphic SSRs between desi/kabuli can also be searched/retrieved using similar parameters. Further, CMsDB provides information on the primers designed for the polymorphic SSRs. In addition to download the flanking sequences (50\u2013250 bp), an option for viewing/downloading the designed primers for individual/multiple polymorphic SSRs has also been provided. Whole datasets have also been made available for download for high-throughput genotyping applications. We aim to update the database as the new versions of desi and kabuli reference genome sequence data set(s) will become available for chickpea. Figure 8 provides snapshots of various features and utilities of the CMsDB.We developed a public data resource, CMsDB, to provide a searchable interface to the SSR data reported in this study. CMsDB is publicly available at desi and kabuli genotypes is required for marker-assisted genetic improvement of chickpea. In this context, we discovered 74941 and 81845 SSRs from the desi and kabuli chickpea genomes, respectively, and inferred their frequency and genomic distribution in the intergenic regions and within protein-coding genes. Subsequently, 1835 polymorphic (based on SSR repeat-length variation) SSRs between desi and kabuli genomes from different coding and non-CDS components were identified and characterized. CMsDB provides an integrated web interface to search, browse and filter the SSRs in desi and kabuli chickpea genomes and polymorphic SSRs between them. Recently, the CicArMiSatDB comprising SSR markers identified from coding and non-coding regions of kabuli genome between them, Thus, CMsDB will assist molecular breeders in rapid selection of gene-based polymorphic SSR markers for use in large-scale genotyping applications of chickpea.The development and large-scale validation of informative genome-wide SSR markers showing high intra-specific polymorphic potential among i genome has beeni genome . CMsDB ddesi and kabuli chickpea developed in our study will serve as an immediate resource for mapping whole genome and targeted mapping of trait-specific genes/QTLs for marker-assisted genetic improvement in chickpea. These polymorphic SSR markers being derived from different coding and non-CDS components that regulate cellular and biological functions have significance in developing functional genetic markers for rapidly establishing marker-trait linkages and identification of genes/QTLs associated with important agronomic traits. The association of gene-based SSR markers based on their expansion/contraction of repeats with many traits of agricultural importance including seed weight in chickpea have been well studied showing polymorphism between studied , 2014.desi and kabuli chickpea. This may also result from frequent association of transposable elements with the intronic and intergenic SSRs as previously documented in rice than that within desi or kabuli genotypes. Henceforth, the developed genome-wide SSR markers being more informative than SSR markers identified till now would be of immediate use in efficient large-scale genotyping applications in chickpea. Considering requirement of functional SSR markers showing high intra-specific polymorphism among desi and kabuli genotypes for chickpea marker-assisted genetic enhancement, the large-scale experimentally validated polymorphic SSR markers developed by us will be highly relevant.Higher (\u223c74%) amplification success rate of polymorphic SSR markers in chickpea genotypes suggested their immense use in various genotyping applications in chickpea. The remaining \u223c26% of SSR markers derived mostly from the introns and intergenic regions of genes showed null amplification in chickpea genotypes. It could be due to insertion\u2013deletions in the primer-binding sites of corresponding genomic sequences of in rice . The ext in rice and poly in rice . The max in rice , 2010. IFST varied from 0.16 to 0.94 with a mean of 0.68) obtained among 46 chickpea genotypes belonging to five population groups was comparable/higher than the previously detected level (0.03\u20130.82) with the genomic and genic SSR markers and kabuli (15) population groups had distinct agro-morphological features that are commonly observed in desi and kabuli (white flower and large seed size with beige colored seed coat) chickpea, respectively. The grouping of one kabuli chickpea genotype ICC 8261 (originated from Turkey) with the desi genotypes (originated from India) of population group Ia reflected more influence of its geographical origin rather than cultivar-specific classification. However, complex breeding history involving introgression, cross-breeding efforts and sequential evolutionary bottlenecks among desi genotypes possibly led to their clustering in four population sub-groups. The informative genome-wide SSR markers developed by us are significant in establishing distinctness and evolutionary relationships as well as assaying broader molecular diversity among desi and kabuli chickpea genotypes and therefore, will be useful for many applications in chickpea genetics, genomics and breeding.The distinctness and phylogenetic relationships established by informative genome-wide SSR markers in desi and kabuli chickpea from different coding and non-CDS components of genes and intergenic regions. These genome-wide physically mapped markers with relatively high experimental validation success rate and intra-/inter-specific polymorphic potential have immense utility in large-scale genotyping applications in chickpea. A wider molecular diversity including parentage- and cultivar-specific phylogenetic relationships assayed by these informative SSR markers in a structured desi and kabuli population suggested their significance in chickpea structural, functional and comparative genomics, and breeding. We anticipate that web resource CMsDB will be very useful to scientists/breeders to search, browse and query SSRs in chickpea to facilitate molecular breeding strategies in chickpea.We developed a large set of polymorphic SSR markers between The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "To develop and evaluate a fast and accurate Monte Carlo simulation (MCS) based scatter correction for PET/MR imaging, based on Geant4 using graphical processing units (GPUs).The GPU implementation by Bert et al. includinFor Compton scatter correction the reconstructed emission image, the patient MR-derived attenuation map and a CT-derived attenuation template of the MR coils are used as input for the simulation. The resulting simulated projection data are scaled to the normalized measured projection data. Thus, the often unstable fit to the distribution tails, necessary for single scatter simulation (SSS), is circPhantom results suggest an improved contrast with our new MC-based scatter correction, especially for measurements including the MR coils, where the contrast recovery was improved by 10-14%. First patient images also show improved grey/white matter contrast.The new GPU-accelerated MCS allows for fast and accurate estimation of scattered coincidences in PET studies using the Siemens MR-BrainPET with a major speed-up compared to standard MCS and superior image quality compared with the standard correction based on SSS."} +{"text": "Neurohormonal pathways are of critical importance in the pathogenesis and progression of heart failure. Current heart failure therapies mainly focus on blocking the detrimental effects of long-term neurohormonal activation and largely ignore the physiological compensatory effect of the natriuretic peptide system and other endogenous vasodilator systems. Natriuretic peptides exert their effects by activating membrane-bound guanylyl cyclase-coupled receptors (NPR-A and -B), resulting in increased concentrations of the second messenger cyclic guanosine monophosphate (cGMP) .LCZ696 exhibits the novel mechanism of action of an angiotensin receptor neprilysin inhibitor (ARNI) by simultaneously inhibiting neprilysin via LBQ657, the active metabolite of the prodrug sacubitril (AHU377), and blocking the angiotensin II type-1 receptor via valsartan . The carIn the PARADIGM-HF study of 8442 patients with heart failure and reduced ejection fraction (HFrEF), LCZ696 reduced the primary endpoint of cardiovascular death or heart failure hospitalization by 20% and reduced death due to any cause by 16% (both p<0.001) compared with the ACE-inhibitor enalapril. Symptoms and physical functioning, as assessed by the Kansas City Cardiomyopathy Questionnaire (patient assessment) and NYHA classification (physician assessment), were also favourably impacted by LCZ696 vs. enalapril. LCZ696 increased levels of cGMP and BNP while decreasing NT-proBNP and troponin levels ,4.LCZ696 is currently under investigation in patients with heart failure with preserved ejection fraction (HFpEF). Of note, hypertrophy signalling, diastolic relaxation and stiffness, and vasorelaxation are favourably modified by cGMP-dependent protein kinase phosphorylation, suggesting that agents that raise cGMP levels may have a role in the treatment of HFpEF . In the"} +{"text": "The results of this study suggest that the transfer of placental C19MC miRNAs into maternal pNK cells occurs during pregnancy. The present study provides new insight into maternal NK cell functions.Although recent studies have demonstrated that microRNAs (miRNAs or miRs) regulate fundamental natural killer (NK) cellular processes, including cytotoxicity and cytokine production, little is known about the miRNA-gene regulatory relationships in maternal peripheral blood NK (pNK) cells during pregnancy. In the present study, to determine the roles of miRNAs within gene regulatory networks of maternal pNK cells, we performed comprehensive miRNA and gene expression profiling of maternal pNK cells using a combination of reverse transcription quantitative PCR (RT-qPCR)-based miRNA array and DNA microarray analyses and analyzed the differential expression levels between first- and third-trimester pNK cells. Furthermore, we constructed regulatory networks for miRNA-mediated gene expression in pNK cells during pregnancy by Ingenuity Pathway Analysis (IPA). PCR-based array analysis revealed that the placenta-derived miRNAs [chromosome 19 miRNA cluster (C19MC) miRNAs] were detected in pNK cells during pregnancy. Twenty-five miRNAs, including six C19MC miRNAs, were significantly upregulated in the third- compared to first-trimester pNK cells. The rapid clearance of C19MC miRNAs also occurred in the pNK cells following delivery. Nine miRNAs, including eight C19MC miRNAs, were significantly downregulated in the post-delivery pNK cells compared to those of the third-trimester. DNA microarray analysis identified 69 NK cell function-related genes that were differentially expressed between the first- and third-trimester pNK cells. On pathway and network analysis, the observed gene expression changes of pNK cells likely contribute to the increase in the cytotoxicity, as well as the cell cycle progression of third- compared to first-trimester pNK cells. Thirteen of the 69 NK cell function-related genes were significantly down-regulated between the first- and third-trimester pNK cells. Nine of the 13 downregulated NK-function-associated genes were NK cein vitro . The synMicroRNAs (miRNAs or miRs) are small non-coding RNAs that play a pivotal role in post-transcriptional gene regulation by targeting the 3\u2032-untranslated region (3\u2032-UTR) of specific target mRNAs for endonucleolytic cleavage or translational repression . With reIn the present study, to determine the roles of miRNAs within gene regulatory networks of maternal pNK cells during pregnancy, we performed comprehensive miRNA and gene expression profiling of NK cells isolated from the peripheral blood of healthy pregnant females and analyzed these differential expression levels between first- and third-trimester pNK cells. We explored NK cell function-associated genes that were negatively correlated with miRNA expression levels and computationally predicted to be miRNA targets. Finally, we constructed a regulatory network for miRNA-mediated gene expression in pNK cells during pregnancy using miRNA and gene expression profiles.Samples of peripheral blood were obtained from pregnant females after obtaining informed consent. For the comprehensive analysis of mRNA and gene expression profiles in pNK cells, samples were obtained from the same healthy pregnant females during the first , second (19\u201323 weeks) and third (36\u201338 weeks) trimesters of gestation (n=5 each), and from other females who had a normal pregnancy 4 days following delivery (n=5). For the validation of miRNA expression levels by reverse transcription quantitative PCR in pNK cells, a different set of experiments with other healthy pregnant females was performed; samples were obtained from the same females in the first, second and third trimesters of gestation (n=5 each), and from other females who had a normal pregnancy 4 days following delivery (n=5). The study protocols were approved by the Ethics Committees of Jichi Medical University and Nippon Medical School . Peripheral blood mononuclear cells were isolated from heparinized venous blood using Lymphoprep as previously described . NK cellTotal RNA within the cells was extracted using RNAiso reagent according to the manufacturer\u2019s instructions. The integrity of the RNA was determined using an Agilent 2100 Bioanalyzer ; samples with an RNA integrity number >7 were used.RNU6-2.We performed real-time PCR-based array analysis to quantitatively and comprehensively examine the expression levels of 756 miRNAs in the pNK cells obtained from pregnant females. Total RNA from each specimen (each 30 ng) was reverse transcribed using Megaplex RT Primers . The cDNA was then pre-amplified using Megaplex PreAmp Primers (Applied Biosystems). The pre-amplified products were subjected to real-time PCR using TaqMan Array Human MicroRNA Cards on a 7900HT Fast Real-Time PCR System (Applied Biosystems) according to the manufacturer\u2019s instructions. The miRNA sequences were annotated using the Sanger database (miRBase), release 14. Data obtained with this assay were analyzed using RQ Manager 1.2 (Applied Biosystems). The relative Ct method (\u0394\u0394Ct method) was applied for the quantification of each miRNA expression level, as previously described and miR-518b (assay ID 001156) were from Applied Biosystems.Real-time PCR for miRNA expression was carried out using TaqMan MicroRNA Assays on a 7300 Real-Time PCR System (both from Applied Biosystems). Briefly, total RNA (each 10 ng) was reverse transcribed with a High Capacity cDNA Reverse Transcription kit (Applied Biosystems). The RT products were subsequently subjected to real-time PCR using TaqMan 2X Universal PCR Master Mix (Applied Biosystems). To normalize the expression levels of the miRNAs, http://www.ncbi.nlm.nih.gov/geo/).We performed microarray analysis of the gene expression levels in the first- and third-trimester pNK cells. Of the total RNA obtained, 20 ng was used in a labeling reaction with a Low-Input Quick Amp Labeling kit, one-color (Agilent Technologies), and the quality and yield of the labeled cRNA were evaluated on an Agilent 2100 Bioanalyzer. Gene expression profiling was conducted using an Agilent Microarray . The resulting signals were normalized relative to the 75th percentile signal intensity and spots with low reproducibility were omitted (coefficient of variation <50%). The processed data were filtered for P<0.05 (paired t-test) using the GeneSpring GX software . The mRNA array data are publicly available . A total of 715 NK cell function-related genes have been previously reported (http://www.microrna.org/microrna/getMirnaForm.do) was also used to predict the targets of miRNAs.Molecular networks of the selected molecules and specific pathways were analyzed by the Core Analysis of fold change for the third- vs. first-trimester pNK cell group in Ingenuity Pathway Analysis . The significance of between-group differences was assessed using ANOVA followed by Tukey\u2019s test, or the Kruskal-Wallis test, and a value of P<0.05 was considered to indicate a statistically significant difference.We performed real-time PCR-based array analysis of the expression levels of 756 miRNAs in pNK cells at different time points of pregnancy . Among the 756 miRNAs examined, 293, 293, 294 and 325 miRNAs were detected in the pNK cells obtained from females in the first, second and third trimester of gestation, and post-delivery, respectively. Of the 47 mature chromosome 19 miRNA cluster (C19MC) miRNAs, which are expressed exclusively in the placenta \u201318, probmiR-7-2# [currently defined as miR-7-2-3p in miRBase release 21 (http://www.mirbase.org/)], was significantly downregulated in the third-trimester pNK cells compared to those in the first trimester. Subsequently, a comparison of the miRNA expression profiles between the third-trimester and post-delivery pNK cells identified nine miRNAs, including eight C19MC miRNAs (89% of the downregulated miRNAs), which were significantly downregulated in the post-delivery pNK cells compared to the third-trimester pNK cells . Among the 1,173 genes, 264 genes were significantly downregulated in the third- compared to the first-trimester cells. On the other hand, the expression of 909 genes was found to be significantly increased in the third- compared to the first-trimester cells.KIR2DL4) showed significantly a decreased expression in the third- compared to the first-trimester cells. By contrast, the expression levels of leukocyte Ig-like receptor (LILR) genes in the third-trimester cells were significantly higher than those in the first-trimester cells. With regard to cell cycle and proliferation, the third-trimester pNK cells showed a high-level expression of a group of genes involved in regulating cell cycle transitions . Thirteed CCNA1) .\u22127), as well as cell cycle regulation pathways . The NK cell signaling pathway contained downregulated KIR genes .We then used the IPA tool to search for molecular pathways associated with pNK cells during pregnancy. A data set of 69 NK cell function-associated genes mentioned above was included in the IPA Core Analysis that allowed us to interpret the data set in the context of biological processes, pathways and gene networks. The top canonical pathways and gene networks that were most significantly affected in the pNK cells during pregnancy are shown in \u221210), the quantity of cells , the activation of leukocytes and cytotoxicity . Downstream Effects Analysis (as defined in IPA) for visualization of the biological trends in this study revealed that the proliferation of immune cells and quantity of cells were predicted to decrease in the third- compared to the first-trimester pNK cells (1L1R1 and CEACAM1) and that KIR genes were downregulated (We found that 136 gene-related functions with a minimum of ten genes per category in the IPA defined Diseases and Bio Functions category (an IPA data set of the 136 functions is available upon request). Moreover, we filtered the 136 functions by NK cell context with a minimum of ten genes per category. The filtering found 16 functions for NK cells; 54 genes were selected among the 69 NK cell function-associated genes . Among tNK cells . By contNK cells . The comegulated .http://www.microrna.org/microrna/getMirnaForm.do) to search for over-represented miRNA seed sequences. We identified 27 seeds originating from the 12 miRNAs that were significantly upregulated in the third- compared to the first-trimester pNK cells . Althougt, PRKG1 . We hypomiR-517a-3p and miR-518b differed significantly before and after delivery , while CD56bright CD16neg NK cells primarily produce cytokines. The pNK cells are mainly CD56dim CD16pos ((KIR2DS4) and activating receptor NKG2-D type II integral membrane protein gene (KLRK1) showed a significantly decreased expression during pregnancy, and inhibitory KIR genes simultaneously showed a decreased expression (LILRA2) and inhibitory LILR genes (LILRB2 and LILRB3) in the third-trimester pNK cells were significantly higher than those in the first-trimester cells (in vivo (NK cells consist of two distinct subsets based on the levels of expression of the low-affinity Fc \u03b3 receptor IIIA (CD16) and neural cell adhesion molecule (CD56) receptors. CD56 CD16pos ,31. The pression . By conter cells . These d, were significantly upregulated in the third- compared to the first-trimester pNK cells. pNK cells incorporated C19MC miRNAs, and these interactions were possibly mediated via exosomes. The rapid clearance of C19MC miRNAs also occurred in the NK cells following delivery. DNA microarray analysis revealed that 69 NK cell function-related genes were differentially expressed between the first- and third-trimester pNK cells. Pathway and network analysis suggested that these gene expression changes of pNK cells contribute to the increase in the cytotoxicity, as well as the cell cycle progression of third-trimester pNK cells. Thirteen of the 69 NK cell function-related genes were significantly downregulated between the first- and third-trimester pNK cells. Nine of the 13 downregulated NK function-associated genes were feration ,35, the"} +{"text": "Virus-induced gene silencing (VIGS) is an effective tool for gene function analysis in plants. Over the last decade, VIGS has been successfully used as both a forward and reverse genetics technique for gene function analysis in various model plants, as well as crop plants. With the increased identification of differentially expressed genes under various abiotic stresses through high-throughput transcript profiling, the application of VIGS is expected to be important in the future for functional characterization of a large number of genes. In the recent past, VIGS was proven to be an elegant tool for functional characterization of genes associated with abiotic stress responses. In this review, we provide an overview of how VIGS is used in different crop species to characterize genes associated with drought-, salt-, oxidative- and nutrient-deficiency-stresses. We describe the examples from studies where abiotic stress related genes are characterized using VIGS. In addition, we describe the major advantages of VIGS over other currently available functional genomics tools. We also summarize the recent improvements, limitations and future prospects of using VIGS as a tool for studying plant responses to abiotic stresses. This gene was identified from a subtracted cDNA library for drought-stress-responsive genes in chili pepper resulted in increased susceptibility of silenced plants to mannitol-induced osmotic stress. Leaf disks from CaPO2-silenced leaves showed severe bleaching and higher chlorophyll loss than vector control plants alone or together with OXIDOREDUCTASE (CaOXR1), using the TRV-VIGS vector, conferred reduced tolerance to mannitol-induced osmotic stress compared to vector control plants and OSMOTIN (CaOSM1) in drought tolerance in chili pepper. Silencing of CaMLO2 using the TRV-VIGS vector in chili pepper plants showed lower levels of transpirational water loss and lipid peroxidation in dehydrated leaves compared to wild-type plants. This study showed that CaMLO2 acts as a negative regulator under drought stress conditions.VIGS is a valuable tool for functional validation of drought-responsive genes identified from transcript profiling of plants exposed to drought stress. TRV-VIGS-mediated silencing of NAC TRANSCRIPTION FACTOR 2 (RhNAC2) and A-TYPE EXPANSIN 4 (RhEXPA4) in rose petals and petal disks reduced the recovery of petals and petal disks during rehydration in rose petals has resulted in a decrease in cell expansion of the petals during rehydration along with concomitant down-regulation of several stress- and cell-expansion-related genes in the silenced petals compared to the vector control and ACC SYNTHASE 2 (RhACS2) genes individually or co-silencing of both genes suppressed dehydration- and rehydration-induced ethylene in the sepals and gynoecia. Reduced ethylene production resulted in improved petal cell expansion during dehydration. On the contrary, silencing of an ethylene receptor, RhETR3, enhanced the inhibitory effect of dehydration on petal cell expansion and INOSITOL POLYPHOSPHATE 1-PHOSPHATASE , were individually silenced in wheat using the BSMV-VIGS vector. Era1 gene encodes the \u03b2-subunit of farnesyltransferase involved in ABA mediated stomatal closure by activating the guard cell S-type anion-channels and increasing the cytosolic Ca2+ concentration. The loss-of-function of Era1 has been shown to enhance ABA sensitivity and hence reduced stomatal conductance and water loss and better vigor compared to vector-inoculated plants. This suggests that down-regulation of Era1 and Sal1 genes enhances drought tolerance in wheat by decreasing sensitivity to ABA. In another study, H. VULGARIS ABUNDANT PROTEIN (HvHVA1) and DEHYDRIN 6 (HvDhn6), genes encoding the LEA class of proteins, were individually silenced in wheat using the BSMV-based VIGS vector gene in wheat resulted in a decreased plant survival rate, less free proline content, less RWC and increased membrane leakage compared to vector control plants under drought stress from Triticum dicoccoides (wild emmer wheat) resulted in reduced chlorophyll content and an increase in malondialdehyde (MDA) content in silenced plants under drought stress gene in wheat to test its involvement in tolerance to photo-inhibition under high light treatment. High light inhibited the net photosynthesis and affected the maximal quantum yield of Photosystem II (Fv/Fm) in the silenced plants. Also, silenced plants showed increased membrane damage, anthocyanin accumulation and higher MDA, suggesting the role of TaPGR5 in oxidative stress tolerance. In pea, PEBV-VIGS-mediated co-silencing of thioredoxin genes, TRX-F/TRX-M, resulted in a significant reduction in Mg-chelatase activity and 5-aminolevulinic acid synthesizing capacity. This was associated with reduced chlorophyll and carotenoid pigment contents, lowered photosynthetic capacity and reduced expression of tetrapyrrole biosynthesis pathway genes, leading to the accumulation of ROS iron-inefficient line, Isoclark, a Bean pod mottle virus (BPMV)-based VIGS vector was used to silence a REPLICATION PROTEIN A (GmRPA3) gene. GmRPA3-silenced plants had smaller leaves, decreased internode length and higher chlorophyll content, and failed to respond to increased iron nutrition, suggesting a role of the GmRPA3 gene in iron acquisition was studied in tomato roots , a Pea early browning virus (PEBV)-based vector was used to study arbuscular-mycorrhizal-fungi (AMF)-associated phosphate acquisition. Silencing of a symbiotic gene, PsSym19, reduced the development of both arbuscules and vesicles at the root cortex. Similarly, silencing of a putative Pi transporter gene, PsPT4, using the PEBV-vector, reduced the phosphate uptake , Cucumber mosaic virus (CMV), Tobacco mosaic virus (TMV) and TRV delayed the appearance of drought symptoms in various plant species The virus vector may accumulate to high levels in the silenced plant if the silenced target gene is involved in the immunity of plants against the virus and such plants can become highly susceptible to subsequent abiotic stress. This will adversely influence studying the specific effect of gene silencing on abiotic stress tolerance. Quantification of viral load (Senthil-Kumar and Mysore, VIGS, as both a forward and reverse genetics tool, offers opportunities for rapid functional analysis of abiotic-stress-related genes in both dicotyledonous and monocotyledonous crop species. Utilization of VIGS for understanding the mechanisms of abiotic stress tolerance and crop improvement is depicted in Figure Venkategowda Ramegowda and Muthappa Senthil-Kumar wrote the manuscript, and Kirankumar S. Mysore edited the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Piwi-interacting piRNAs are a major and essential class of small RNAs in the animal germ cells with a prominent role in transposon control. Efficient piRNA biogenesis and function require a cohort of proteins conserved throughout the animal kingdom. Here we studied Maelstrom (MAEL), which is essential for piRNA biogenesis and germ cell differentiation in flies and mice. MAEL contains a high mobility group (HMG)-box domain and a Maelstrom-specific domain with a presumptive RNase H-fold. We employed a combination of sequence analyses, structural and biochemical approaches to evaluate and compare nucleic acid binding of mouse MAEL HMG-box to that of canonical HMG-box domain proteins (SRY and HMGB1a). MAEL HMG-box failed to bind double-stranded (ds)DNA but bound to structured RNA. We also identified important roles of a novel cluster of arginine residues in MAEL HMG-box in these interactions. Cumulatively, our results suggest that the MAEL HMG-box domain may contribute to MAEL function in selective processing of retrotransposon RNA into piRNAs. In this regard, a cellular role of MAEL HMG-box domain is reminiscent of that of HMGB1 as a sentinel of immunogenic nucleic acids in the innate immune response. Integrity of the germ cell genome is central to sexual reproduction. Gamete development presents an ideal environment for the selfish propagation of transposable elements (TEs) such as LINE-1 (L1) . In mammDrosophila and mice ; sequence-specific HMG proteins ; non-sequence-specific HMG proteins . Codon alignment was performed using the ClustalW algorithm built-in MEGA6 package, without changing pre-set parameters. The aligned nucleotides were translated to protein using standard genetic code and the alignment of protein repeated using built in ClustalW algorithm. No changes to codon alignment occurred. This alignment was manually refined using experimentally determined structural information to account for the secondary characteristics such as helices and loops. Following PDB structures were used: SRY\u20141j46 . Li. Li39]. Drosophila Mael HMG-box domains . When appropriate, we utilized competition assays, where the protein concentration was kept constant along with the concentration of the hot substrate, and instead the unlabeled (cold) substrate was titrated in. This allowed us to estimate the competitor dissociation constant (KC) that is directly related to the dissociation constant obtained from the binding assay. Considered together these two constants provide an estimate of the observed binding kinetics obtained by gel shifts.To evaluate the biochemical activity and validate our previous analysis of MAEL HMG-box domain, we expressed HMG-box domains of SRY (SS), HMGB1a (NSS) and murine, and bacteria . The recbacteria . To evalD = \u223c12 nM) and specifically forming a single complex , or dsDNA methylated at CpGs -mouse, d at CpGs \u2014mouse. Wnditions . Likely nditions . Even thnd dsDNA . The pre present . We haveA common observed characteristic of the HMG-box domains is the ability to bind to DNA four-way junctions (4WJ) in their open conformation , 63, 64.D = \u223c14 nM, Taken together, the above experiments show that MAEL HMG-box domain does not bind to dsDNA, however it is able to form a single strong and specific complex with DNA 4WJ along the helix-1 and the arginine (R8) in N-terminus of the helix-1 to see whether polar residues within these regions are also important for binding . MutatioThe overall mutational analysis of the MAEL HMG-box domain has revealed that arginines in the \"hook\" and \"propeller\" regions are essential for binding, supporting our sequence and structure analyses and the interpretation of previous binding experiments. Taken together, our results point towards structured RNA as the preferred substrate for the MAEL HMG-box domain.The apparent preference of MAEL HMG-box domain for structured RNA is in agreement with the results of our analysis of MAEL immunoprecipitates (IP). MAEL protein complexes immunoprecipitated from the adult mouse testis lysate are specifically enriched for the fragments of piRNA precursor RNAs and retrotransposon mRNAs . TherefoThese observations suggested that the removed stem somehow contributes to binding. Perhaps the double-stranded region constrains the ends of the RNA molecule allowing for unambiguous formation of the dual hairpin regions in the center. In this way, the ensemble of structures would be smaller with greater proportion of the preferred substrate. This would also explain the presence of the weak complexes and the lack of complete binding seen with shorter RNAs. Presence of additional RNA in reactions with the RNA 4WJ has led to full formation of large complexes, most likely also affecting the ensemble of structures . ImportaThe aim of the study is to shed light onto the biochemical function of MAEL, a protein indispensable for the function of the piRNA pathway , 30, 85.in vitro despite the presence of the consensus HMG-box binding sites in the tested substrates. Of the DNA substrates, MAEL HMG-box domain only binds DNA 4WJs, where it likely interacts with the structured center like many other HMG-box domains [A plethora of non-sequence specific RNA binding domains have been described , but ver domains , 64. On domains , 88. Furin vitro preference of MAEL HMG-box domain for structured nucleic acids, including RNA hairpins, four way junctions, and large structured RNAs are all in agreement with this hypothesis. We believe that the combination of new in vitro with inTS-CLIP, ) in the in vitro is reminiscent of that of HMGB1a in terms of structure-directed binding. Interestingly, in addition to their prominent structural role in the nucleus, HMGB proteins have been shown to function as sentinels of immunogenic nucleic acids in innate cellular response [Lastly, a biochemical activity of the MAEL HMG-box domain response , 43. A presponse .S1 FigAn amino acid multiple sequence alignment of candidate HMG-box domains. The candidates were selected based on their substrate specificity (sequence vs. non-sequence specific) with at least four candidates per group, and with preferences for well-described and mouse HMG-box domains. Aligned codons were translated to protein sequences (MEGA6), and then the alignment was adjusted to account for the secondary structural characteristics found in solved structures within each group . The residues were pseudo-colored according to Taylor color scheme to provide contrast to groups of residues. Conserved secondary structure characteristics and residues are shown below the alignment.(TIF)Click here for additional data file.S2 FigDrosophila MAEL HMG-box, D) SRY HMG-box, and E) HMGB1a domains.(A) Purification scheme employed for all recombinant HMG-box domain proteins. Shown are example gels demonstrating purity of acquired proteins. (B) Circular dichroism (CD) measurements of recombinant wild-type and point-mutant mouse MAEL HMG box domain proteins. All proteins are folded and helical. Only mutant R8A shows change in ellipticity (arrow) indicating that this mutation somehow affects folding of the protein. CD traces of C) (TIF)Click here for additional data file.S3 FigSRY). Top gel shows the titration series for SRY HMG-box domain protein. The bottom gel shows cold competition with unlabeled dsDNA demonstrating strength and specificity of binding. The average KD \u223c12 nM is close to previously reported values. (B-C) The mouse MAEL HMG-box does not bind to 25-nt ssDNA or dsDNA modified with symmetrical cytosine methylation. (D) Predicted (Robetta) tertiary structure of Drosophila melanogaster (Dm) Mael HMG-box domain. Based on the predicted structure, this domain closely resembles canonical HMG-box domains without any apparent novel regions. Despite the homology and contrary to previous observations dsDNA [D \u223c14 nM.(A) Binding of SRY HMG-box domain to dsDNA with its consensus recognition sequence Click here for additional data file.S4 FigD = 0.638 \u03bcM). (B) Cold competition of MAEL HMG-box domain with RNA 4WJ leads to increased formation of the large complex instead of competition. Presence of more RNA likely influences structural ensemble, making the formation of large complex more favorable. (C) Model summarizing structural transition of RNA 4WJ tested here based on previous analysis [(A) Strength of MAEL HMG-box domain interaction with RNA 4WJ is moderate Click here for additional data file.S5 Fig(A) Multiple sequence alignment of regions identified through analysis of MAEL RIP-Seq datasets. Sequences correspond to L1_Md_F2 retrotransposon, are located on different chromosomes, and are highly conserved. Colored by percent identity . (B) Traces for individual regions after manual refinement of the alignment showing genomic locations and corresponding read coverage in each examined dataset. (C) Single, thermodynamically stable secondary structures generated in Mfold provided with covariance information for each identified genomic region. Shown are dG values of each structure as calculated by Mfold.(TIF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.S6 Table(XLSX)Click here for additional data file."} +{"text": "Serum specimens were also collected and serological test were performed. Results from the first swab sample were inconclusive while the second swab was strongly positive for MERS-CoV RNA by rRT-PCR and confirmed positive by RT-PCR and partial gene sequencing. Positive serologic test results further confirmed MERS-CoV infection. Full-length nucleocapsid and spike gene coding sequences were later obtained from the positive swab sample. Phylogenetic analysis revealed that the virus was closely related to recent human-derived MERS-CoV strains obtained in Jeddah and Makkah, Saudi Arabia, in April 2014 and dromedary camels in Saudi Arabia and Qatar. These findings were consistent with the patient\u2019s history. We also identified a unique amino acid substitution in the spike receptor binding domain that may have implications for receptor binding efficiency. Our initial inconclusive rRT-PCR results highlight the importance of collecting multiple specimens from suspect MERS-CoV cases and particularly specimens from the lower respiratory tract.Rapid and reliable laboratory diagnosis of persons suspected of Middle East respiratory syndrome coronavirus (MERS-CoV) infection is important for timely implementation of infection control practices and disease management. In addition, monitoring molecular changes in the virus can help elucidate chains of transmission and identify mutations that might influence virus transmission efficiency. This was illustrated by a recent laboratory investigation we conducted on an imported MERS-CoV case in Greece. Two oropharyngeal swab specimens were collected on the 1 Since its discovery in Saudi Arabia in 2012, the Middle East respiratory syndrome coronavirus (MERSCoV) has been implicated in 1042 laboratory confirmed cases of human infection, including 419 deaths. Among these cases, 14 were reported by European countries, including 8 imported cases and 3 local person-to-person transmissions and negative, respectively, and the specimen was determined to be inconclusive for MERS-CoV RNA detection. In contrast, specimen B was found to be positive by both UpE and ORF-1a assays with Ct values 30.2 and 32.5, respectively. The presence of MERS-CoV RNA was also confirmed on specimen B by RT-PCR and partial sequencing of the RdRp and N genes.Greece-Saudi Arabia_2014 S differed by 0.1\u20130.9% nucleotides (nt) and 0.1\u20131.3% amino acids (aa) from 68 other published human and camel derived MERS-CoV sequences. One unique nt change present as a mixed base at position 1533 (G>C) of the S ORF confers a predicted aa change of arginine (R) with proline (P) at position 511 (R511P). The Greece-Saudi Arabia_2014 N differed by 0.1\u20130.9% nt and 0\u20130.8% aa from 69 other published MERS-CoV sequences. No unique nt changes were identified.Full genome sequencing was not possible due to the limited available sample volume. However, sequences of the S and N protein coding regions were successfully obtained. The Greece-Saudi Arabia_2014 sequences clustered most closely with human derived MERS-CoV strains obtained in Jeddah and Makkah, Saudi Arabia, in April 2014. MERS-CoV sequences recently obtained from dromedary camels in Saudi Arabia and Qatar also clustered with the Greece-Saudi Arabia_2014 sequences.Phylogenetic analyses of the MERS-CoV S and N ORFs are shown in Serology identified specific anti-MER-CoV IgM (titer 1/100) and IgG (titer 1/320) antibodies in the patient\u2019s serum sample.6 copies/mL of MERS-CoV RNA were present in lower respiratory tract specimens, whereas only small amounts of viral RNAs could be detected in upper respiratory tract specimens [The present study describes the laboratory investigation of an imported MERS-CoV case in Greece. Discrepancy of the rRT-PCR results between specimens A and B may be due to different sampling techniques, although detection attributable to increasing viral load with infection progression cannot be ruled out for specimen B. Collection of additional specimens, particularly from the lower respiratory tract and at different time points over the disease course is highly recommended when there is strong clinical and epidemiological suspicion of MERS-CoV infection and initial results from upper respiratory tract specimens are negative or inconclusive. Drosten et al. pointed out that up to 10pecimens .According to World Health Organization recommendations, partial sequencing of the RdRp and N genes is an acceptable alternative for confirmation of MERS-CoV infection . AlthougDetection of MERS-CoV-specific antibodies in the patient\u2019s serum was consistent with recent MERS-CoV infection. Ideally, however, for serological confirmation of acute MERS-CoV infection, a second serum specimen taken two weeks or more after onset of illness should also be tested.Our findings revealed a genomic subpopulation in the swab sample that possessed a unique amino acid substitution in S protein receptor-binding domain (RBD) as compared with other published human and camel sequences. The above substitution was confirmed independently by two separate CDC laboratories, ruling out the possibility of its introduction during the RT-PCR. The R511P substitution is located within a region (residues 484 to 567) of the MERS-CoV RBD that directly interacts with the dipeptidyl peptidase4 (DPP4) receptor on the host cell surface for viral attachment \u201312. RecePhylogenetic analysis revealed that the Greek strain was most closely related to Jeddah and Makkah strains circulating during the recent burst of MERS-CoV activity in the Arabian Peninsula . This waThe ongoing outbreak of MERS-CoV suggests that the risk of importation of the virus in countries is expected to continue, although the number of incident cases has been steadily declining . In that"} +{"text": "Recent guidelines have advocated for step-wise treatment of increasing invasiveness in the management of ischaemic priapism though with low-level evidences. In the past, proximal shunts were favoured as first-line treatment. We present an African man who had proximal shunt three decades ago for ischaemic priapism and subsequently had long-term morbidity over the three decades with adverse effect on his quality of life. Recent guidelines appear to be sound despite their limitations and more invasive cavernoso-spongiosal shunts may be associated with significant long-term morbidities and poor quality of life. It is only in the last decade or two that evidences and guidelines have advocated for a step-wise pattern of increasing invasiveness in the surgical treatment of acute episodes of ischaemic priapism . This isA 30-year-old African man with sickle cell trait (AS) developed ischaemic priapism in 1981. He had cavernoso-spongiosal shunt with complete detumescence. However, he developed urethro-cutaneous fistula in the early post-operative period which was repaired after six months with Devine-Horton urethroplasty technique. He was subsequently lost to follow-up. Thirty-one years later, he was referred back to the same hospital where he previously had his shunt created by his family physician. The referral followed the finding of a bladder stone in a Pelvic X-ray done when he complained of recurrent pelvic and perineal pains. On further evaluation, he described three decades-long history of bothersome lower urinary tract symptoms (LUTS) and he also had erectile dysfunction(ED) often improvising with digital support for successful vaginal penetration. This resulted in a recurrent acrimonious relationship with his spouse due to unsatisfying sexual intercourse. He was however able to father eight children during this period despite the ED. His International prostate symptom score (IPSS) was 18 and International index of erectile function-5 (IIEF-5) score was 12. Physical examination revealed meatal stenosis, a 5cm ventral midline distal penile scar of prior penile surgery and distal penile urethral induration.Prostate examination revealed no enlargement. A diagnosis of Postpriapism erectile dysfunction and shunt-related urethral stricture was made. He had abdominopelvic ultrasound done which showed no upper urinary tract abnormality, prostate volume of 30 mLs and a 3.5cm echogenic oval structure in the bladder casting an acoustic shadow. Retrograde urethrogram revealed irregularity and some narrowing in the distal-penile urethra . His ProIschaemic priapism is an emergency urologic condition and presents as persistent painful penile erection that continues hours beyond or is unrelated to sexual stimulation . IschemiIn earlier times, proximal shunts were created as first-line treatment often with dismissal of the usefulness of less invasive measures as providing only temporary relief . At the Guidelines advocating step-wise treatment of increasing invasiveness for ischaemic priapism appear to be sound despite low-level evidence. The more invasive cavernoso-spongiosal shunts may be associated with morbidities not only in the immediate post operative period but also long-term."} +{"text": "Deep venous thrombosis is a common vascular problem with long-term complications including post-thrombotic syndrome. Post-thrombotic syndrome consists of leg pain, swelling and ulceration that is related to incomplete or maladaptive resolution of the venous thrombus as well as loss of compliance of the vein wall. We examine the role of metalloproteinase-9 (MMP-9), a gene important in extracellular remodeling in other vascular diseases, in mediating thrombus resolution and biomechanical changes of the vein wall.in vivo murine model of thrombus resolution using the FVB strain of mice. MMP-9 expression and activity significantly increased on day 3 after DVT. The lack of MMP-9 impaired thrombus resolution by 27% and this phenotype was rescued by the transplantation of wildtype bone marrow cells. Using novel biomechanical techniques, we demonstrated that the lack of MMP-9 significantly decreased thrombus-induced loss of vein wall compliance. Biomechanical analysis of the contribution of individual structural components showed that MMP-9 affected the elasticity of the extracellular matrix and collagen-elastin fibers. Biochemical and histological analyses correlated with these biomechanical effects as thrombi of mice lacking MMP-9 had significantly fewer macrophages and collagen as compared to those of wildtype mice.The effects of targeted deletion of MMP-9 were studied in an MMP-9 mediates thrombus-induced loss of vein wall compliance by increasing stiffness of the extracellular matrix and collagen-elastin fibers during thrombus resolution. MMP-9 also mediates macrophage and collagen content of the resolving thrombus and bone-marrow derived MMP-9 plays a role in resolution of thrombus mass. These disparate effects of MMP-9 on various aspects of thrombus illustrate the complexity of individual protease function on biomechanical and morphometric aspects of thrombus resolution. The biology of venous thrombus resolution plays a central role in a number of significant cardiovascular diseases. Deep venous thrombosis (DVT) is an exceedingly common and serious problem with between 350,000 to 600,000 cases annually in the U.S. and 200,000 deaths from pulmonary embolism (PE) . The acuThere is no specific therapy to prevent or treat post-thrombotic syndrome. Defining the cellular and molecular mechanisms of venous thrombus resolution is critical to developing such therapy to potentially restore vein wall structure and function after thrombosis. Experimental thrombus resolution is defined as decreasing thrombus mass but therin-vivo [14 [1413] 16] [17 [1716] [in-vivo [13]. MMin-vivo and macrin-vivo . One priin-vivo . We recein-vivo . The bioin-vivo , which c-/- mice , in in vivo. Specifically we note a 27% increase in thrombus size in mice lacking MMP-9, which is comparable in magnitude to changes noted during thrombus resolution in mice lacking TLR-9 (20% increase) . Th. Thin vi-/- animals is consistent with the key role of MMP-9 in macrophage migration in vivo in models of peritonitis, spinal cord injury and aortic aneurysms [18 [18-/- aneurysms [18] [39ammation [18] [39ammation and ischammation . It is aammation 19]..-/- animSeveral specific factors and mediators contribute to the detrimental biomechanical changes (e.g. stiffening) of the vein wall induced by thrombus resolution. Inhibition of plasmin, a known proteolytic activator of pro-MMP-9, results in decreased vein wall stiffness and decreased MMP-9 activity . In the -/- mice correlated with decreased amounts of collagen noted by immunohistochemical staining. However the magnitude of biomechanical changes exceeds the immunohistochemical differences in collagen content. This suggests that MMP-9 plays a greater role in remodeling of extracellular matrix and collagen fibers to induce vein wall stiffness than can be discerned by immunohistochemical analysis, and demonstrates that direct biomechanical analysis of mouse vein wall detects more subtle changes than immunochemistry. Standard quantitative techniques such as immunohistochemistry Click here for additional data file.S1 Data(XLSX)Click here for additional data file."} +{"text": "We previously reported the secretion of C-type natriuretic peptide (CNP) from vascular endothelial cells and proposed the existence of vascular natriuretic peptide system composed of endothelial CNP and vascular smooth muscle guanylyl cyclase-B (GC-B), the selective receptor for CNP, and implicated in the regulation of vascular tone, remodeling and regeneration -5. HowevIn the present study, we have assessed the functional significance of this system in the regulation of blood pressure in vivo using vascular endothelial cell-specific CNP knockout (CNP ecKO) and vascular smooth muscle cell-specific GC-B knockout (GC-B smcKO) mice generated using the Cre/loxP system. These mice showed neither the skeletal abnormality nor the early mortality observed in systemic CNP or GC-B knockout mice . CNP ecKThese results demonstrate that endothelium-derived CNP contributes to the chronic regulation of vascular tone and systemic blood pressure by maintaining endothelial function independently of vascular smooth muscle GC-B and indicate the implication of the vascular natriuretic peptide system in blood pressure control."} +{"text": "Malaria is a major cause of death and has been one of the strongest selective forces on the human genome selecting variants that influence pathogenesis, host response and may protect against disease severity . Previous studies suggest the association between malaria and red blood cell (RBC) glucose-6-phosphate dehydrogenase (G6PD) and pyruvate kinase (PK) deficiencies in humans . This stP. falciparum 3D7 was maintained in continuous synchronous cultures. Invasion ratios and maturation ratios were determined. Samples were prepared for proteomic analysis by FASP and GelC-MS. LC-MS and CID-MS/MS of peptides were carried out by nano-RP-LC-MS/MS. Data were analyzed for identification of peptides and quantification through comparison of normalized peak area/intensity of each identified peptide.Only results from parasite proteome are available so far. There was an over-expression of defensive molecules against oxidative stress (heat shock proteins and chaperones) in parasites growing in G6PD-deficient RBC, and an under-expression of global proteins (mostly proteins involved in haemoglobin catabolism and trafficking/RBC remodelling) in parasites growing in PK-deficient RBC. The study will still look into infected RBC proteome and assess the influence of these alterations in the putative protective effect against malaria."} +{"text": "Hypothesis: HCC detectability is independent of whether the study is performed as part of a larger one-stop-shop CMR or as a traditional focused MRI. Objective: We evaluated the 'detectability' of HCC using cardiac MRI for pre-operative evaluation of OLT candidates in a CMR suite performing assessment of cardiac structure, function and viability, along with simultaneous evaluation of thoracoabdominal vasculature and liver anatomy and compared with histopathology in explanted livers.Precise diagnosis and staging of hepatocellular carcinoma (HCC) is crucial in the selection and timing of orthotopic liver transplantation (OLT) patients, especially cirrhotics. The preoperative workup of OLT patients is logistically cumbersome and expensive given the need for separate cardiac, vascular, and abdominal imaging. We have recently demonstrated the value of a 'one-stop-shop' approach combining the attributes of a nuclear stress, echocardiogram and abdominal MRI into one single pre-op CMR evaluation. However, this approach requires further validation as accurate detection of HCC is critically important. In this pilot study, patients (n = 51) underwent a standard cardiac exam, stress CMR, and abdominal MRI on a dedicated CMR scanner during a single imaging session. Abdominal MRA along with liver parenchymal imaging was obtained via a Liver Acquisition with Volume Acquisition (LAVA) technique. Another representative cohort (n = 26) underwent standard abdominal MRI in a Radiology Suite. Pathological results at explanations were compared to interpretation of the CMR/MRI exams.Over 3 years, 51/77 OLT candidates underwent MRI in a dedicated CMR suit as a part of an integrated pre-operative evaluation of liver and heart. The remaining 26 pts underwent traditional pre-op evaluation of liver while cardiac stress testing was performed elsewhere via nuclear/echo. All referred pts completed standard dynamic CMR, 98% completed stress CMR, 94% completed liver MRI and 45 pts (88%) completing entire CMR exam. Nine pts (20%) in the combined CMR group and 12 (46%) in the traditional group proceeded to OLT. Of these, 2/9 pts in the CMR group and 2/12 pts in the traditional group were found to have lesions suggestive of HCC. These findings were all confirmed at explant surgical pathology with 100% detection/exclusion for HCC (100% NPV/PPV).In this Proof-of-Concept study, it appears feasible to perform a comprehensive pre-operative liver transplant evaluation in a CMR suite for the detection of HCC lesions. Our study confirmed that MRI evaluation of the liver along with cardiac preoperative evaluation is equivalent to traditional testing for the detection of HCC lesions, which was confirmed with 100% histopathological concordance. This is an important next step towards validation of the CMR One-Stop-Shop concept for pre-op evaluation for potential OLT recipients. The final step is a cost-effective analysis.Internal."} +{"text": "Over the last decades ICU survival is increasing. As a consequence, post ICU sequelae with (persistent) functional dependency in long-stay ICU patients become a topic of interest. However data on specific fields of physical performance and the potential influence of rehabilitation programmes remain scarce .To establish the course of functional dependency and specific fields of physical performance in patients with and without a (non ICU-specific) rehabilitation programme in long-stay ICU patients.We performed a single centre prospective observational study in mixed ICU patients with a length of stay ICU > 48 hours. Patients were evaluated at ICU discharge and re-evaluated after a 3-months period in a specific post-ICU outpatient clinic. At both time points a Barthel score (BS) and grip strength (GS) were recorded. Additionally the 6 minutes walking test (6MWT), the Berg balance scale (BBS) and characteristics of individual rehabilitation programmes were assessed in the outpatient setting. Non-parametric tests for comparison between dependent and independent datasets were used. A Bonferroni correction was used for multiple comparison.In a 1-year period during 2014 80 patients were included. Baseline characteristics are provided in Table In long-stay ICU patients overall physical performance considerably improved in 3 months from ICU discharge. However, there are large differences in the recovery of specific fields of physical performance, irrespective of participation in non ICU-specific rehabilitation programmes. Further research to unravel the specific rehabilitation needs of long-stay ICU patients is needed."} +{"text": "Mohammadali F, Pourfathollah AA. Changes in frequency of HBV, HCV, HIV and syphilis infections among blood donors in Tehran province 2005 - 2011. Arch Iran Med 2014; 17(9)613-620The routine screening of blood donors for potentially transmissible infections has reduced transfusion-associated infection whilst providing an insight into disease prevalence. This retrospective cross-sectional study evaluates the prevalence of hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency (HIV) and syphilis infection in 2,026,628 potential blood donors screened at Tehran Blood Transfusion Centre from 2005 to 2011. One or more transmissible infections were identified in 0.52% of donors with greater prevalence in first time donors. The average prevalence rate of HBV, HCV, syphilis and HIV was 388, 112, 10.5 and 5.4 per 100,000 respectively. A decreasing prevalence rate of HBV was identified from 2005 to 2011 and of HCV from 2007 to 2011. This may have resulted from increased vaccination, screening and health education. Although an interesting insight into disease prevalence in the donor population, caution should be exercised in extrapolating these results to the wider population in view of sampling bias.De BK et al. Pentoxifylline plus prednisolone versus pentoxifylline only for severe alcoholic hepatitis: a randomised controlled clinical trial. Ann Med Health Sci Res 2014;4(5):810-816Pentoxifylline and prednisolone are individually useful in the management of severe acute alcoholic hepatitis (Maddrey discriminant function (MDF) \u226532) but their combined efficacy is unclear. This single-centre randomised controlled trial investigated the short and medium term outcomes of treatment with pentoxifylline and prednisolone compared to pentoxifylline alone in 60 patients with severe alcoholic hepatitis from 2010 to 2012. During the 12 month follow up period 33% and 20% of patients died in the dual therapy and monotherapy groups respectively. Overall there was no significant difference in mortality and morbidity between the treatment groups. The study could have been enhanced by including a third prednisolone monotherapy group for comparison.Iwaisako K et al. Origin of myofibroblasts in the fibrotic liver in mice. Proc Natl Acad Sci USA 2014;111(32):E3297-3305.4) administration and common bile duct ligation (BDL) respectively. Myofibroblast activation and the degree of hepatic fibrosis was similar in both types of liver injury. In CCL4- or alcohol-induced fibrosis, activated hepatic stellate cells (aHSCs) comprised >92% of myofibroblasts whereas in BDL-induced liver injury myofibroblasts originated from activated portal fibroblasts (aPFs) and aHSCs in similar proportions. Of note, the genotype of BDL-aHSCs was more similar to aPFs than CCL4-aHSCs suggesting that following cholestatic liver injury aHSCs may mimic aPFs. In BDL-induced liver injury PF activation may lead to cytokine production causing subsequent HSC activation. The observation that mesothelin expression is unregulated in aPFs following BDL injury may offer a novel target for future anti-fibrotic therapy. Hepatotoxic and cholestatic liver injuries activate distinct subsets of fibrogenic myofibroblasts, preferentially aHSCs and aPFs respectively. Activated hepatic myofibroblasts are responsible for fibrous scar formation in chronic liver disease although their origin is unclear. Using transgenic reporter mice this study investigates the origin of myofibroblasts and quantifies their number in hepatocellular and cholestatic-type chronic liver disease induced by carbon tetrachloride :e107466Hepatorenal syndrome (HRS) is a severe, progressive renal failure associated with end-stage liver disease which may require splanchnic vasoconstrictor therapy whilst liver transplantation is awaited. In some countries the cost and poor availability of terlipressin has prompted search for an alternative splanchnic vasoconstrictor with similar efficacy. This systematic review and meta-analysis of four studies comprising 154 adult patients compared the efficacy and safety of norepinephrine with terlipressin in the management of HRS. Both HRS type 1 and 2 was analysed and all patients received intravenous albumin and central venous pressure monitoring. There was no difference in the reversal of HRS , mortality at 30 days and recurrence of HRS between the norepinephrine and terlipressin treatment groups. Adverse events were less common with norepinephrine although all were of minor importance. Although norepinephrine appears an attractive alternative to terlipressin with favourable cost and availability in some countries, the authors highlight significant bias. A large randomised controlled trial is needed to further evaluate splanchnic vasoconstrictor therapy in HRS. Johal AS, et al. Endoscopic ultrasound-guided liver biopsy in pediatric patients. Endosc Ultrasound 2014:3(3)191-194Endoscopic ultrasound-guided liver biopsy (EUS-LB) requires further evaluation in the pediatric population. This case series reports EUS-LB using a 19-gauge aspiration needle in three pediatric patients aged 9, 14 and 17 years for the evaluation of deranged liver enzymes. All patients were sedated with propofol. Colour doppler imaging determined a safe needle path prior to puncture. In all cases EUS-LB yielded sufficient tissue to make an accurate histopathologic diagnosis . No immediate or delayed complications were reported. The authors conclude that EUS-LB is a safe, diagnostically useful technique in the pediatric population. This should be confirmed in further studies with larger patient cohorts. Celikbilek M et al. Circulating microRNAs in patient with non-alcoholic fatty liver disease. World J Hepatol 2014;6(8):613-620There is a need for accurate minimally invasive tests to inform the diagnosis of non-alcoholic fatty liver disease (NAFLD) and reduce reliance on liver biopsy. The serological measurement of microRNAs (miRNA) is attractive but further work is needed to characterise those miRNA specific for NAFLD and whether levels correlate with disease severity. This cross-sectional study investigates the expression of several miRNAs sampled serologically in 20 adult patients with histologically proven NAFLD and 20 healthy age-matched controls between 2010 and 2012. The expression of miR-181d, miR-99a, miR-197 and miR-146b was significantly lower in patients with NAFLD compared to controls (p<0.05). Levels of miR-197 and miR-10b inversely correlated with the degree of inflammation (p<0.05) and miR-181d and miR-99a inversely correlated with serum gamma glutamyl transferase levels in NAFLD (p<0.05). The expression of miR-10b, miR-122, miR-34a and miR-29a did not differ between NAFLD and control groups. Overall this study identifies an altered serum miRNA expression pattern associated with NAFLD. By further characterising NAFLD-associated miRNAs future work should aim to develop a serological diagnostic test for NAFLD.Shi M, et al. Statin use and risk of liver cancer: an update meta-analysis. BMJ open 2014;4:e005399In addition to their principle cholestrol-lowering action statins may offer anti-cancer benefits. This meta-analysis of 12 studies investigated the effect of statins in 35,756 patients with liver cancer from 2005 to 2013. Statin use was associated with a reduced risk of liver cancer only when data from observational studies was sub-analysed . There was a trend towards a greater liver cancer protective effect with statin use in patients at high risk of liver cancer . Overall the observed risk reduction in liver cancer cannot be clearly attributed to a direct statin-mediated effect due to several confounding factors including inter-study variability in statin indications and contraindications and other confounding lifestyle changes which may accompany statin use. The effect of statins in patients at high risk for liver cancer requires further evaluation before statins can be considered an adjuvant treatment for liver cancer.Dr Ishaq Ahmad and Luke Materacki, Alexandra Hospital, UKOther contributors to this page are"} +{"text": "Increasing numbers of patients with immunodeficiencies, malignant diseases, advanced surgeries and prolonged stays in intensive care units are at risk for developing infections by enteric bacteria, which often are systemic (sepsis) and caused by multidrug resistance isolates. Intestinal bacteria provide also a constant antigenic stimulation for the synthesis of natural anti-carbohydrate antibodies such as those targeting blood group-associated antigens or galactose \u03b11,3 galactose . Enteric bacteria that cause sepsis are more likely to bind anti-Gal antibodies than those isolated from stools, which appears related to the higher resistance to serum killing evidenced by the former microorganisms.Investigate the impact of removing anti-Gal antibodies in the sepsis after cecal ligation and puncture (CLP) in \u03b11,3 galactosyltransferase knockout mice. These mice produce from four months of age natural anti-Gal antibodies as humans without the need of any additional Gal antigen exposure.in vivo using a soluble Gal trisaccharide-polylysine conjugate (GAS914) and determined by ELISA. Binding of serum antibodies to Escherichia Coli isolated from Gal-KO mice blood was performed by FACS and serum bactericidal activity was determined by a complement-mediated assay. The pattern of 40 cytokines and antibodies against 577 carbohydrate and bacterial antigens before and after GAS914 was evaluated by two different arrays.Anti-Gal antibodies were removed Escherichia Coli in 83% of mice carrying anti-Gal antibodies and 87.5% of the animals lacking them. Pulse field electrophoresis did not show differences between E. Coli blood isolates from GAS914-treated and untreated mice. Removal of anti-Gal antibodies was associated with a significant increase in serum IgG binding and bactericidal activity to E. Coli. GAS914 administration was associated in the glycan array with the removal of anti-Gal antibodies and the significant augment of binding to several bacterial antigens. Finally, GAS914 also significantly reduced the level of several proinflammatory and anti-inflammatory cytokines prior to CLP in Gal-KO mice.GAS914 at 10 mg/kg subcutaneously every other day for two weeks led to the removal of anti-Gal antibodies in Gal-KO mice from day one. Removal of anti-Gal antibodies with GAS914 significantly improved survival in Gal-KO mice subsequently subjected to CLP on day 3 . On day one after CLP there was a reduction of 50% in the level of anti-Gal antibodies in untreated Gal-KO mice. Blood cultures obtained 24 h after CLP were positive for Removal of natural anti-Gal antibodies with GAS914 enhances humoral immunity against enteric bacteria expressing Gal-antigen isolated from the blood preventing sepsis mortality after CLP in mice. Depletion of existing antibodies may be a new approach to boost immunity and prevent or treat infection diseases and other disorders."} +{"text": "Evaluation of lymphomatous bone marrow infiltration on 18F-FDG PET can usually distinguish between normal regenerating marrow following chemotherapy by a characteristic pattern of uptake.The use of 18F-FDG PET scan revealed apparent progression of marrow disease. Subsequent investigations were performed including bone marrow biopsies, repeat 18F-FDG PET scanning and a white cell scan. These revealed the interim 18F-FDG PET scan appearance was due to a highly unusual pattern of scattered islands of regenerating normal marrow, rather than progressive lymphoma.Here we report the case of a 51-year-old Caucasian woman with mixed low- and high-grade lymphoma with biopsy confirmed marrow infiltration. An interim post-three cycle chemotherapy 18F-FDG PET scans in lymphoma patients treated with chemotherapy are not always due to disease. Clinicians should retain a high index of suspicion for benign causes when 18F-FDG PET scan results appear incongruent with clinical response.Our case report highlights that apparent severe bone marrow abnormalities on As a emission -8.18F-FDG not being specific to lymphoma or malignancy, a false positive finding on interim PET scanning is generally low and in equivocal cases can often be resolved with tissue sampling and histological correlation.Although spurious results can occur due to cellular uptake of 18F-FDG PET scanning is quite sensitive for detecting bone marrow involvement in higher grade lymphomas and is typically associated with a heterogeneous pattern of increased marrow activity within the skeleton [skeleton ,10. In cskeleton .In February 2013, a 51-year-old Caucasian woman presented with a several month history of back pain, hot flushes, sweats and weight loss. A subsequent CT scan demonstrated multiple enlarged cervical nodes, as well as confluent paravertebral soft tissue masses in the region of the thoracic spine and anterior to L5 to the presacral region. A CT-guided core biopsy of the presacral mass was performed and histology confirmed low grade B-cell non-Hodgkin lymphoma based on immunostaining results.18F-FDG PET scan which demonstrated moderate to markedly FDG-avid right upper and bilateral lower thoracic para-spinal, lower lumbar para-spinal and presacral soft tissue masses with extension into several right lower lumbar and sacral neural foramen. Heterogeneous increased FDG uptake was also seen in a right external iliac node and throughout the skeleton, most marked and intense in the trochanteric region of the right femur and right ilium, consistent with marrow infiltration chemotherapy with pegfilgrastim support every three weeks. This was followed by two cycles of high-dose methotrexate due to the perceived higher risk for central nervous system disease from direct neural foramen invasion.Despite the presacral mass core biopsy demonstrating low grade B-cell small lymphocytic lymphoma, clinical symptoms, bone marrow biopsy and 18F-FDG PET scan to assess treatment response was performed at this point which demonstrated resolution of FDG-avid right upper and bilateral lower thoracic para-spinal, lower lumbar para-spinal and pre-sacral soft tissue masses and right external iliac node . The range of This case highlights assessment of treatment response in bone marrow on PET scanning can be confounded in cases where the lymphoma has caused significant disruption to normal marrow architecture, resulting in islands of normal residual rapidly regenerating marrow giving a \u2018pathological\u2019 appearance. In this circumstance a further bone marrow scan, in this case a white cell scan, is useful in discriminating between bone marrow regeneration and progressive disease by the degree of its congruence with the FDG PET study.Our case is unusual as the focal increased marrow and bony FDG uptake in the trochanteric region of the right femur and right ilium was consistent with disease involvement on the baseline pretreatment PET scan. FDG uptake in the remainder of the skeleton appeared relatively normal despite mixed lytic and sclerotic lesions scattered throughout the skeleton on CT. The lack of FDG-avidity at these sites suggested an underlying lower grade lymphoma, with the more FDG-avid sites representing sites of transformed higher grade disease. The interim post-three cycle chemotherapy PET scan was most concerning for a mixed response to therapy, with the new highly heterogeneous appearance in the marrow being suspicious for disease progression despite metabolic resolution of the femoral and ilial bone lesions and sites of nodal disease.The typical normal reactive marrow appearance seen following chemotherapy is that of diffusely increased relatively uniform FDG uptake throughout the marrow . In patiAs our patient likely has mixed low- and high-grade lymphoma, the interim and post-therapy PET/CT scan appearances possibly represent a partial flip-flop variant, with photopenic sites representing either sites of successfully treated disease or non FDG-avid less chemotherapy responsive lower grade lymphoma.A further likely contributing factor in this case is the timing of PET scanning post-pegfilgrastim administration. The post-three cycle interim PET scan was performed four days following pegfilgrastim administration. At this time point, pegfilgrastim was likely having its maximal stimulatory effect on granulopoiesis, resulting in any residual islands of normal bone marrow appearing particularly FDG-avid, further mimicking disease progression in the marrow ,16. In cApparent new focal bone marrow abnormalities on PET scans in lymphoma patients treated with chemotherapy and pegfilgrastim are not always due to progressive disease. Clinicians should retain a high index of suspicion for benign causes, particularly if PET results show metabolic remission of soft tissue and/or nodal disease. In such cases, an additional bone marrow scan, such as a white cell scan or a Tc-99m sulphur colloid scan , may be Written informed consent was obtained from the patient for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.18F-FDG PET: 18F-fluorodeoxyglucose positron emission tomography; CT: Computed Tomography; Tc-99m WCC: Technetium-99m labelled white cell scan.The authors declare that they have no competing interests.MC was involved in the analysis and interpretation of medical imaging and drafting the manuscript. SP was involved in treating the patient and revising the manuscript. PB and VK were involved in performing, analysis and interpretation of medical imaging and revising the manuscript. All authors read and approved the final manuscript."} +{"text": "Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950\u2009m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling. The contribution of marine archaea to the ocean's carbon cycle is unclear. Here, Li et al. analyse the genomes and transcriptomes from five deep-sea archaeal groups to reveal their metabolic characteristics, suggesting a crucial role in modulating the carbon cycle in deep oceans. Archaea are ubiquitous members of marine microbial communities122446Out of the four major groups of planktonic archaea, only representatives of MG-I have been cultured, which led to the discovery that they oxidize ammonia9111210141514In this study, we reconstructed 59 partial to near-completed genomes and transcriptomes of several ubiquitous uncultured archaea groups from deep-sea hydrothermal plumes and surrounding background seawater at three distinct locations. Hydrothermal vent plumes are hotspots of biogeochemical activity in the deep oceans2122De novo assembly of metagenomic reads , comprising 70.5%, 72% and 52% of total extracellular peptidase genes in deep-sea MG-I, -II and -III, respectively . TranscrIn contrast to MG-I, -II and -III, the genomic bins of Parvarchaeota and DHVEG-6 contained only one gene related to the S01C family (DegP peptidase) and two genes affiliated with M48B family (HtpX peptidase), and no transcripts of these genes were detected . These rAlthough many of the peptidases identified here are divergent from experimentally studied proteins, family-level classifications offer clues to their broad functions. S08A peptidases, one of the largest groups of serine endopeptidases37The archaeal genomes also contained diverse and transcriptionally active carbohydrate-active enzymes . In MG-I40Archaeal genes involved in beta-oxidation of fatty acids were present and abundantly expressed in deep-sea MG-II and -III, suggesting that straight chain lipids may also be organic substrates for these groups . A recenGenes involved in cell mobility were identified in deep-sea MG-I, \u2013II and \u2013III genomes . ParticuFinally, genes related to central carbon metabolism were also identified in these genomes and transcriptomes, including the tricarboxylic acid cycle and glycolysis/gluconeogenesis pathway in MG-II and MG-III, and the modified 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle in deep-sea MG-I . These rOverall, the genomic and transcriptomic results presented here indicate that widespread deep-sea archaea utilize diverse proteins, carbohydrates and straight chain lipids as substrates for heterotrophic growth . Althoug2125292 and lipids. Because archaea are ubiquitous across varying geochemical regimes and depths of the world's deep oceans30Microbial degradation of organic matter in the pelagic ocean-water column strongly influences the export of carbon from the surface oceans, and converts labile carbon into refractory organic matter that can be preserved in deep-sea sediments or as dissolved organic carbon (DOC)48495051R/V Atlantis in January 2010. Samples at different depths of the rising plumes from Von Damm and Beebe hydrothermal vent fields as well as their background were collected using a Suspended Particle Rosette Samples (SUPR) mounted on remotely operated vehicle ROV Jason II, which can be used for sampling rising plumes55in situ (in situ filtration with the SUPR sampler (Lau)255657Samples from Mid-Cayman Rise in the Caribbean Sea were collected on the cruises abroad 5in situ . Samplesg, clear supernatant was transferred to a Montage PCR purification filter unit and centrifuged at 1,000\u2009g until all of the liquid passed through (\u223c15\u2009min). The flow-through was discarded, and 400\u2009ml of TE buffer was added to the filter unit and it was centrifuged for 15\u2009min at 1,000\u2009g. The DNA was then eluted in 100\u2009ml of TE and quantified using RiboGreen (Invitrogen). RNA was extracted using the mirVana mRNA Isolation kit (Ambion), treated with DNase I to remove DNA and concentrated and repurified using the RNeasy MinElute Kit (Qiagen). Total RNA was quantified using RiboGreen (Invitrogen). RNA amplification by random priming and complementary DNA synthesis was performed using the MessageAmp II-Bacteria Kit (Ambion). Shotgun sequencing of DNA and complementary DNA were performed with Illumina HiSeq2000 at the University of Michigan DNA Sequencing Core, and results are shown in DNA and RNA were extracted from \u00bc filters following procedures21https://github.com/najoshi/sickle). Samples from the eight vent sites , Beebe (Cayman Deep), Kilo Moana, Abe, Mariner, Tahi Moana, Tui Malila) were each assembled de novo to obtain eight separate assemblies (de novo assemblies were performed using IDBA-UDhttp://img.jgi.doe.gov/cgi-bin/w/main.cgi).The raw shotgun sequencing metagenomic reads were deprelicated (100% identity over 100% lengths) and trimmed using Sickle Parvarchaea acidiphilium ARMAN-4 (PRJNA38567)Comparative genomics of the deep-sea archaea identified in this study was performed against the representative archaeal genomes within each group . GenomicE-value <10\u221210 by BLASTP. All hits were compared against the non-redundant NCBI protein database. Only those that had top hits to peptidases and carbohydrate active enzymes were considered. The extracellular peptidases were further confirmed based on the identification of extracellular transport signals using SignaIP17For genes encoding peptidases and carbohydrate-active enzymes, all annotated genes in deep-sea archaea genomic bins were searched against public databases of peptidases (MEROPS)Alignment of amino acid sequences for extracellular peptidase of S08A, M28 and M14A families was performed by MUSCLE using default parameters followed by manual refinementAccession codes: The nucleotide sequences have been deposited in the DOE JGI-IMG/MER database under the following Taxon Object IDs: 3300001680 (Kilo Moana), 3300001681 (Abe), 3300001678 (Mariner), 3300001679 (Tahi Moana), 3300001676 , 3300001683 (Guaymas), 3300001781 (Cayman Deep) and 3300001835 .How to cite this article: Li, M. et al. Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea. Nat. Commun. 6:8933 doi: 10.1038/ncomms9933 (2015).Supplementary Figures 1-13 and Supplementary Tables 1-12"} +{"text": "Introduction: Amyloid A (AA) amyloidosis is a systemic form of amyloidosis secondary to chronic infections and inflammatory disorders. An acute-phase protein produced by the liver, serum amyloid A (SAA) is the precursor of AA amyloid fibrils. AA amyloid deposition occurs predominantly in the kidneys, spleen, adrenal glands, liver and gastrointestinal tract. The manifestations of AA amyloidosis involving the kidneys include proteinuria, tubular dysfunction and progressive loss of renal function.Case: We report a 47-year-old drug addict who developed AA amyloidosis as a result of recurrent suppurative skin infections secondary to subcutaneous drug injection. Elevated C-reactive protein concentrations attested to the presence of a chronic systemic inflammatory state. He suffered from the nephrotic syndrome and insidious loss of renal function. Isosthenuria and glycosuria were indicative of renal tubular dysfunction. Renal biopsy demonstrated AA amyloidosis involving the glomeruli, tubular basement membranes and blood vessel walls.Conclusion: Superimposed acute tubular necrosis due to concomitant endocarditis and cocaine use accelerated his renal disease. Case presentation is followed by a brief discussion of clinical features, natural history and outcome of AA amyloidosis with a particular emphasis on AA amyloidosis as a complication of subcutaneous drug abuse. Amyloid A (AA) amyloidosis is a systemic form of amyloidosis secondary to chronic infections and inflammatory disorders. An acute-phase protein produced by the liver, serum amyloid A (SAA) is the precursor of AA amyloid fibrils. We report a 47-year-old drug addict who developed AA amyloidosis as a result of recurrent suppurative skin infections secondary to subcutaneous drug injection. Renal biopsy demonstrated AA amyloidosis involving the glomeruli, tubular basement membranes and blood vessel walls. Superimposed acute tubular necrosis due to concomitant endocarditis and cocaine use accelerated his renal disease. Case presentation is followed by a brief discussion of clinical features, natural history and outcome of AA amyloidosis with a particular emphasis on AA amyloidosis as a complication of subcutaneous drug abuse.A 47-year-old Caucasian man presented with a right arm abscess as a consequence of subcutaneous injection of narcotics. He was found to have proteinuria and renal insufficiency. The past medical history was notable for subcutaneous injection of heroin and cocaine complicated by skin abscesses in the upper and lower extremities over the past five years. In addition, he had hepatitis C infection diagnosed in 1998 and psoriasis. He never received treatment for hepatitis C. Review of systems was negative for fevers, chills, chest pain, shortness of breath, hematuria, dysuria, headaches, or blurry vision. He was homeless and snorted cocaine for 25 years.2. Examination of upper and lower extremities demonstrated multiple needle marks, several localized cutaneous scars, and hyperkeratotic plaques on the elbows , tubular basement membranes (black arrow) and blood vessel walls (arrowhead) (A). Accumulation of amorphous material in the tubular basement membranes (white arrows) (B). Polarizing microscopy of a Congo red-stained tissue section revealed apple-green birefringence of deposits in the glomerular mesangial areas (white arrows) and tubular basement membranes (black arrows) . Immunohistochemistry using antisera specific for serum amyloid A demonstrating strong staining of deposits in glomeruli (E). Ultrastructural examination revealing fine non-branching fibrillary material in the expanded glomerular basement membrane (GBM) (F). Tissue sections stained with Masson\u2019s trichrome (A), periodic acid-Schiff (B), Congo red (C) and anti-sera against serum amyloid A (E) were examined with a light microscope , an immunofluorescence microscope (D) and an electron microscope (F).Renal AA amyloidosis was believed to be secondary to chronic suppurative skin infections complicating subcutaneous drug injection. Acute tubular necrosis was probably secondary to infections and cocaine use. The patient received supportive care for renal disease and did not require renal replacement therapy. He received counseling for drug addiction and is currently awaiting aortic valve replacement.We present a middle-aged man with a 5-year history of intravenous and subcutaneous drug use resulting in recurrent skin abscesses. He developed isosthenuria, proteinuria, and progressive renal insufficiency. Renal biopsy demonstrated AA amyloidosis.Amyloidoses are a heterogeneous group of disorders characterized by the extracellular deposition of insoluble abnormal proteins in a \u03b2-pleated sheet configuration with distinctive tinctorial properties . AA amylet al, the average duration of intravenous and subcutaneous drug abuse was 16 and 3 years, respectively . As stated above, CRP concentrations usually parallel those of SAA.The natural history and outcome of AA amyloidosis was evaluated in a study involving 374 patients followed for a median of 86 months have been completely observed by the author.This work received no funding from public, commercial or not-for-profit organizations."} +{"text": "Transit-Time Flow Measurement (TTFM) is a valid method of intraoperative graft verification. TTFM shows a low diagnostic accuracy due to high number of false positive.High-Resolution Epicardial Ultrasonography (HR-ECUS) is a well-recognized procedure for coronary anastomosis and stenosis evaluation with high sensitivity and specificity.The aim of the study is to verify if the combined use of TTFM and HR-ECUS in intraoperative graft verification process can increase the diagnostic accuracy of procedure itself.From November 2009 to December 2014, 741 patients underwent isolated CABG. A total number of 1733 grafts were performed; all the grafts were intraoperatively verified by means of both TTFM and HR-ECUS.Among all grafts considered functioning at TTFM, 7 (0.4%) were failing at HR-ECUS and promptly redone. These were confirmed as true positive at graft revision due to technical error. HR-ECUS confirmed the good functioning of the remaining grafts already demonstrated by TTFM; among them, 8 showed high troponin I release , whereas the remaining had no high TnI release . In 2 of 39 grafts malfunctioning at TTFM, HR-ECUS confirmed the graft failure. Finally, in 35 cases, HR-ECUS did not confirm TTFM diagnosis demonstrating a full patency of the anastomosis; these grafts had an uneventful clinical course (true negative). The main result of this study is the increase of PPV from 10% with TTFM to almost 100% of TTFM + HR-ECUS, avoiding many unnecessary graft revisions.In intraoperative graft verification procedure the combined use of TTFM and HR-ECUS increase diagnostic accuracy of the verification process close to 100%. Both methods should be used intraoperatively in order to achieve the best outcome for the patient."} +{"text": "Reduced white matter (WM) integrity is a fundamental aspect of pediatric multiple sclerosis (MS), though relations to resting-state functional MRI (fMRI) connectivity remain unknown. The objective of this study was to relate diffusion-tensor imaging (DTI) measures of WM microstructural integrity to resting-state network (RSN) functional connectivity in pediatric-onset MS to test the hypothesis that abnormalities in RSN reflects changes in structural integrity.This study enrolled 19 patients with pediatric-onset MS and 16 age- and sex-matched healthy controls (HC). All subjects underwent 3.0T anatomical and functional MRI which included DTI and resting-state acquisitions. DTI processing was performed using Tract-Based Spatial Statistics (TBSS). RSNs were identified using Independent Components Analysis, and a dual regression technique was used to detect between-group differences in the functional connectivity of RSNs. Correlations were investigated between DTI measures and RSN connectivity.Lower fractional anisotropy (FA) was observed in the pediatric-onset MS group compared to HC group within the entire WM skeleton, and particularly the corpus callosum, posterior thalamic radiation, corona radiata and sagittal stratum . Relative to HCs, MS patients showed higher functional connectivity involving the anterior cingulate cortex and right precuneus of the default-mode network, as well as involving the anterior cingulate cortex and left middle frontal gyrus of the frontoparietal network . Higher functional connectivity of the right precuneus within the default-mode network was associated with lower FA of the entire WM skeleton , genu of the corpus callosum , and left and right sagittal stratum.Loss of WM microstructural integrity is associated with increased resting-state functional connectivity in pediatric MS, which may reflect a diffuse and potentially compensatory activation early in MS. Multiple sclerosis (MS) is an inflammatory demyelinating and neurodegenerative disease of the central nervous system associated with diffuse damage to white matter (WM) tracts. Approximately 5% of all MS patients experience pediatric-onset MS \u20133. PediaDiffusion tensor imaging (DTI) is a technique that characterizes microstructural tissue integrity based on properties of diffusion, and this information is represented mathematically in a diffusion ellipsoid , 5. The 2-hyperintense lesions, but also in normal-appearing, non-lesional WM on a voxel-wise level. Tract-Based Spatial Statistics (TBSS) analysis [3 standard space (FMRIB58_FA), followed by creation of a mean FA image which was further refined to create a mean FA WM skeleton thresholded at a FA value of 0.2. As all subject\u2019s FA images were in a standard space, the WM skeleton was applied yielding FA skeletonized images for each subject. The same WM skeleton was applied to the AD and RD images. For voxelwise analyses of DTI measures , differences between groups were tested in a general linear model (GLM) framework with unpaired t-tests using nonparametric permutation testing (number of permutations = 5000), FSL\u2019s randomise [DTI processing was conducted using FMRIB Software Library (FSL) software library tools (uk/fsl/) . First, uk/fsl/) and enteanalysis created andomise and contandomise . The gen3 voxels. The transformation was done using a combination of 12-parameter affine transformation and nonlinear registration tools and incorporating the T1-weighted image; (f) regression of the functional data against six motion parameter timeseries as well as four WM and four cerebrospinal fluid voxel timeseries in order to remove non-neural contributions to the BOLD signal; and (g) temporal filtering in order to retain frequencies between the range of 0.01 to 0.1 Hz.Functional MRI data preprocessing was conducted using a mixture of Analysis of Functional NeuroImages (AFNI) and FSL randomise [The functional connectivity analysis utilized an ICA-based approach in combination with a dual regression technique . The preandomise nonparamandomise . ClusterDemographic, disease-related, and structural MRI data are reported in 2- lesion volume as well as with thalamic volumes .Within the MS group, none of the DTI metrics showed a significant association with age, sex, age of disease onset, disease duration, or EDSS. All FA, AD, and RD measures correlated significantly with TPediatric-onset MS patients demonstrated lower WM FA compared to healthy controls of the entire WM skeleton . We also show that reduced WM microstructural integrity is associated with higher functional connectivity of the precuneus suggesting particular disruption of the default mode network with WM damage.2-lesion volume suggesting Wallerian degeneration as a possible substrate for reduced white matter tract integrity.The reduced WM FA seen in our cohort is congruent with other reports in pediatric MS \u201315, 18. Higher levels of resting state functional connectivity has similarly been observed in cognitively intact adults with early relapsing-remitting MS \u201347. Our Within our pediatric MS cohort, higher default mode network functional connectivity was associated with reduced FA and higher RD of WM. Similar findings of reduced tissue integrity being associated with heightened connectivity of the default mode network during resting state has also been reported in studies of adult MS , 49, sugIn summary, we show both anatomical DTI and functional resting-state fMRI abnormalities in pediatric MS. More extensive loss of WM integrity was associated with increased default mode network connectivity at the level of the precuneus which could be interpreted to represent a compensatory response in a cohort of MS patients studied both at a younger age and at an early stage of their disease. DTI and functional connectivity analysis in a larger sample of pediatric-onset MS patients with longer disease duration and more variable cognitive impairment will provide further insight into the relationship between functional network characteristics, structural damage, and cognitive performance.S1 FigWM skeleton (green) depicting areas in which the pediatric-onset MS group demonstrated higher (blue) AD and RD compared to the healthy control group (p < .01 corrected). MNI152 template slice coordinates are also reported.(TIF)Click here for additional data file."} +{"text": "T) (amplitude of lung deformation) and Inspiratory Flow (V') (rate of lung deformation) augments incidence of Ventilator-Induced Lung Injury (VILI) [Increasing both Tidal Volume (Vy (VILI) .T augments incidence of VILI.To clarify whether increasing V' at constant VT and one of two groups of V'. Lower and higher V' were obtained by setting inspiratory-to-expiratory time ratio as high as 1:2 or as low as 1:9. Respiratory rate was always 15 breaths per minute. Interplay between VT and V' was assessed at the beginning of the study as airway pressure-volume loop area (or dynamic respiratory system hysteresis). VILI was defined as pulmonary oedema (lung weight gain \u226510% across the study period).Twenty-eight healthy piglets were mechanically ventilated for up to 54 hours. Each animal was assigned to one of three groups of VMain findings are reported in Table rate of lung deformation) while maintaining VT (amplitude of lung deformation) constant augments incidence of VILI. Further studies are needed to clarify whether dynamic respiratory system hysteresis is an independent predictor of VILI.Increasing V' ("} +{"text": "The risk factors for post-operative intra-abdominal abscess (IAA) formation after laparoscopic appendectomy (LA) remain debatable. Some advocate that a perforated appendicitis or Diabetes Mellitus may increase the incidence of post-operative IAA; however, the existing evidence is insufficient.This study aimed to identify risk factors and non-risk factors for IAA formation in patients receiving LA.From January 2010 to December 2013, all patients who underwent three-port LA and who were histologically diagnosed with appendicitis were included. We classified these patients into two groups according to their development of post-operative IAA and then analyzed the differences between the groups.Overall, 1790 patients showed no post-operative complications and were assigned to the non-complication group, whereas 27 patients suffered from IAA postoperatively and were assigned to the IAA group. The incidence of IAA after LA was 1.4% and the only identified risk factor for IAA was dirty fluid collection in the peritoneal cavity observed during the operation. (P < 0.001) On logistic regression analysis of those patients who demonstrated dirty fluid collection, the non-placement of a peritoneal drain had statistical significance for the development of IAA. (P < 0.001)In the present study, the presence of dirty fluid collection in the peritoneal cavity rather than the type of appendicitis was demonstrated as a risk factor for the development of post-operative IAA after LA. When such fluid collection is observed, surgeons should consider deploying peritoneal drainage and post-operative antibiotics treatment including anti-anaerobic treatment."} +{"text": "Purpose. To describe the first reported case of West African crystalline maculopathy (WACM) from a member of the Benin tribe and explore the association with sickle cell retinopathy. Methods. Full ophthalmic examination and high-resolution ocular coherence tomographic imaging. Patients. 61-year-old patient from an academic retina practice. Results. The patient demonstrated bilateral yellow-green birefringent crystals localized to the inner retina on optical coherence tomography, as well as sickle cell-related neovascularization in the right eye. She reported no consumption of kola nuts. Conclusions. Associated retinal vascular disease may be important in the pathogenesis of crystalline maculopathy. A 61-year-old female with hypertension, diabetes mellitus type II, and sickle cell presented with visual acuity of 20/50 (right eye) and 20/40 (left eye). Dilated fundus examination revealed bilateral foveal refractile yellow-green crystals that were more abundant in the right eye Figures and regrWest African crystalline maculopathy was originally described in 2003 by Sarraf et al. in six patients from the Igbo tribe of Southeast Nigeria . Since tMany theories have been raised regarding the origin of these crystals. A genetic component has been entertained, as this condition is exclusive to West Africans. However, a limited number of eye exams in family members have all been negative. The seminal study implicated West African foods , but fur"} +{"text": "Solanum melongena L.) and turkey berry (S. torvum Sw.), a wild ally of eggplant with promising multi-disease resistance traits, are of great economic, medicinal and genetic importance, but genomic resources for these species are lacking. In the present study, we sequenced the transcriptomes of eggplant and turkey berry to accelerate research on these two non-model species.Eggplant contains supplementary material, which is available to authorized users. Solanum melongena L.) is the third most agriculturally important crop from the genus Solanum after potato (S. tuberosum) (eggplant) and [SRA: SRR1104128] (turkey berry). Transcripts are available through the NCBI TSA under accession number GBEF00000000 (eggplant) and GBEG00000000 (turkey berry).Figure S2: Distributions of depth of reads and densities of genes on tomato genome. Figure S3: Distributions of depth of reads and densities of genes on potato genome. Figure S4: Maximum likelihood trees based on 276 single-copy genes. Figure S5: Estimation of divergence time using the first and second codon positions. (DOCX 2 MB)Additional file 1: Figure S1: Distributions of genomic elements of potato eggplant and turkey berry on potato genome."} +{"text": "To conduct an RCT of 3 school-based programs to evaluate if one or more could reduce both eating disorder and obesity risk factors. Method: N = 1,316 Grade 7 and 8 girls and boys (M age = 13.21 years) from three Australian states were randomly allocated to: Media Smart; Life Smart; Helping, Encouraging, Listening and Protecting Peers Initiative (HELPP) or control . Risk factors were measured at baseline, post-program (5-weeks later), 6-month follow-up, and 12-month follow-up.Media Smart girls had half the rate of onset of clinically significant concerns about shape and weight as control girls at 12-month follow-up. Media Smart and HELPP girls reported significantly lower weight concern and shape concern than Life Smart but not control girls at 12-month follow-up. Media Smart girls experienced additional benefits on eating concerns and perceived pressure to be thin compared to HELPP girls and also on levels of physical activity compared to control girls. Media Smart and HELPP boys experienced significant benefit on media internalization compared to control boys while Media Smart boys reported additional benefits including significantly lower screen time at 12-month follow-up compared to the other interventions.Media Smart was the only program to show benefit on both disordered eating and obesity risk factors.Prevention & Public Health stream of the 2014 ANZAED Conference.This abstract was presented in the"} +{"text": "DNA methylation is an important epigenetic mechanism in several human diseases, most notably cancer. The quantitative analysis of DNA methylation patterns has the potential to serve as diagnostic and prognostic biomarkers, however, there is currently a lack of consensus regarding the optimal methodologies to quantify methylation status. To address this issue we compared five analytical methods: (i) MethyLight qPCR, (ii) MethyLight digital PCR (dPCR), methylation-sensitive and -dependent restriction enzyme (MSRE/MDRE) digestion followed by (iii) qPCR or (iv) dPCR, and (v) bisulfite amplicon next generation sequencing (NGS). The techniques were evaluated for linearity, accuracy and precision.MethyLight qPCR displayed the best linearity across the range of tested samples. Observed methylation measured by MethyLight- and MSRE/MDRE-qPCR and -dPCR were not significantly different to expected values whilst bisulfite amplicon NGS analysis over-estimated methylation content. Bisulfite amplicon NGS showed good precision, whilst the lower precision of qPCR and dPCR analysis precluded discrimination of differences of < 25% in methylation status. A novel dPCR MethyLight assay is also described as a potential method for absolute quantification that simultaneously measures both sense and antisense DNA strands following bisulfite treatment.Our findings comprise a comprehensive benchmark for the quantitative accuracy of key methods for methylation analysis and demonstrate their applicability to the quantification of circulating tumour DNA biomarkers by using sample concentrations that are representative of typical clinical isolates.The online version of this article (doi:10.1186/1471-2164-15-1174) contains supplementary material, which is available to authorized users. The methylation of CpG dinucleotides is a common epigenetic mechanism in eukaryotes that plays an essential role in the regulation of gene activity. Defects in methylation have been described in several human diseases, most notably cancer (reviewed in ). Alteraet al. ,,Shows t .(DOCXShows a summary of primers and probes.(DOCX 19 KB)Additional file 6:Shows the assay performance for qPCR in accordance with the MIQE guidelines.(PPTX 2 MB)Additional file 7:Shows the Digital MIQE checklist for authors, reviewers and editors .Additional file 9:"} +{"text": "SUNY Upstate Medical University entered a contract with Health Research, Inc. and the New York State Department of Health to implement an intervention using academic detailing and practice facilitation to increase colorectal cancer screening rates within primary care practices, and to assess the outcomes and barriers to intervention success. The project was conducted within a large multi-organizational framework, led by the Studying-Acting-Learning-Teaching Network in partnership with the Upstate New York Network and the Greater Rochester PBRN , under the auspices of the Upstate New York Translational Research Network (UNYTE).Nine primary care practices enrolled in the project. Practices received a 1-hour academic detailing session on colorectal cancer screening guidelines, and two months of practice facilitation services to implement evidence based strategies to increase patient screening, with a particular focus on initiating and/or streamlining the use of electronic health record (EHR)-based patient screening registries. The impact of project participation on colorectal cancer screening as assessed through pre-and post-intervention screening rates.Primary intervention activities completed by participating practices included efforts to address the data recording issues within practice EHR systems, provider feedback and assessment activities, streamlining of provider reminder systems, and patient education and outreach interventions. The difference between mean pre-and post-intervention screening rates was statistically significant (mean pre-rate 24.7% (SD 20.6%) vs. mean post-rate 26.4% (SD 20.5%), p = 0.028). A preliminary assessment indicates a mean relative increase of 30% between the pre-and post-screening rates.This project evaluates the efficacy of a targeted intervention to implement evidence-based practices in a primary care setting to increase colorectal cancer screening rates, and provides tangible information on facilitators and barriers to implementing these practices in safety net clinics."} +{"text": "Osteoarthritis (OA) is considered the most prevalent form of arthritis. The aim of this study was to verify potential protein OA biomarkers by applying Selected Reaction Monitoring (SRM) assays to protein extracts obtained from Bone Marrow-Mesenchymal Stem Cells (BM-MSCs) isolated from OA patients.BM aspirates were obtained from the femoral channel of OA patients at the time of surgery and from the femoral channel of hip fracture subjects without OA during hip joint replacement surgery for the treatment of subcapital fracture.SRM results verified the differential expression of several protein biomarkers in BM-MSCs from OA patients. Proteomic approaches have proposed numerous protein factors potentially involved in pathological processes including osteoarthritis (OA) , the mos6 confluent cells at the third passage were obtained. Then the cells were lysed, protein concentration was measured as previously described [BM aspirates were obtained from two OA patients (age: 52 and 89\u00a0years) and three hip fracture subjects without OA during hip joint replacement surgery. Hip fracture subjects without OA had a densitometric T-score\u2009>\u20092.5 SD (Hologic QDR-4500C) performed after surgery. All samples were obtained after patients gave their informed consent, and this study was approved by the local institutional ethics committee. After culturing the cell-containing fraction of BM aspirates as previously described , five peparametric Student\u2019s t test and/or non-parametric Mann\u2013Whitney U test. Values with p\u2009<\u20090.05 were considered significant.Since peptide precursor and fragment data from our previous, DIGE-based experiments were genSRM results enabled the verification of a five-protein set for which significant differences were measured between patients and controls Table\u00a0. The ratBased on SRM we have verified the differential expression of potential protein biomarkers in BM-MSCs from OA patients. Results reinforce the hypothesized preactivation of these cells by signaling events produced by the subchondral bone and corroborate the feasibility of using SRM for the quantitation of biomarker sets in clinically relevant samples.BM: Bone marrow; DIGE: Differential in-gel electrophoresis; ESI: Electrospray ionization; MALDI: Matrix-assisted laser desorption/ionization; MSC: Mesenchymal stem cell; MS/MS: Tandem mass spectrometry; OA: Osteoarthritis; SDS-PAGE: Sodium dodecylsulfate polyacrylamide gel electrophoresis; SRM: Selected reaction monitoring; XIC: Extracted ion chromatogram.The authors have no conflicts of interest to declare.CNIC is supported by the Ministerio de Econom\u00eda y Competitividad and the Fundaci\u00f3n Pro CNIC. Support was also provided by FIS PI10/00178 and RETICS Program, RD08/0075 (RIER) from Instituto de Salud Carlos III (ISCIII). JRL is a recipient of Miguel Servet Program from Instituto de Salud Carlos III (ISCIII).EmC: SRM performing, writing of the manuscript and discussion of results. JRL: obtaining of mesenchymal stem cells and discussion of results. EC: SRM performing and discussion of results. PTE: obtaining of mesenchymal stem cells and discussion of results. JAL: SRM performing and discussion of results. BFG: selection of patients, writing of the manuscript and discussion of results. All authors read and approved the final manuscript."} +{"text": "Pyrenophora graminea (Pg), is a worldwide crop disease that results in significant loss of barley yield. The purpose of the present work was to use transcriptomic profiling to highlight barley genes and metabolic pathways affected or altered in response to Pg infection and consequently elucidate their involvement and contribution in resistance to leaf stripe.Barley leaf stripe disease, caused by the fungus Pg suggested the involvement of 15 upregulated genes during the immunity response. By using network-based analyses, we could establish a significant correlation between genes expressed in response to Pg invasion. Microscopic analysis and quantitative PCR (qPCR) profiling of callose synthase and cellulose synthases revealed a direct involvement of cell wall reinforcement and callose deposition in the Pg-resistant phenotype.Our study examined and compared the transcriptomes of two barley genotypes using an established differential display reverse-transcription polymerase chain reaction (DDRT-PCR) strategy at 14 and 20\u00a0days post-inoculation (dpi). A total of 54 significantly modulated expressed sequence tags (ESTs) were identified. The analysis of gene expression changes during the course of infection with Pg fungus, 15 of which are specifically expressed in Pg-resistant plants. Collectively, our results suggest that the resistance to leaf stripe in barley proceeds through callose deposition and different oxidation processes.We have identified a number of candidate genes possibly involved in the host-pathogen interactions between barley and The online version of this article (doi:10.1186/s12864-016-2573-x) contains supplementary material, which is available to authorized users. Hordeum vulgare) ranks among the most important cereals cultivated by humans in diverse environmental conditions worldwide [Pyrenophora graminea Ito & Kuribayashi [anamorph Drechslera graminea (Rabeneh. Ex. Schlech. Shoem)] (Pg) the leaf stripe disease agent is a seed-borne pathogen that systemically spreads in infected barley plants . All the supporting data of selected DEGS are included as additional files in Additional file"} +{"text": "Bordetella bronchiseptica KU1201 identified 6,358 protein-coding sequences. This will give us an insight into the catabolic variability of this strain for aromatic compounds, along with the roles of arylmalonate decarboxylases in nature.The analysis of the 6.8-Mbp draft genome sequence of the phenylmalonate-assimilating bacterium Bordetella bronchiseptica KU1201 was isolated from soil sample through enrichment culture on phenylmalonate as a sole carbon source , followed by further purification by phenol:chloroform:isoamyl alcohol extraction. Shearing and library preparation were done in accordance with Illumina\u2019s TruSeq DNA PCR-Free Sample Preparation Guide .This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession numbers"} +{"text": "By randomly allocating goodprognosis patients between mini-IVF with singleET and conventional IVF with double ET, the authors found lower cumulative C-LBRs (6 months)with the mini-IVF protocol , albeit no incidence of ovarian hyperstimulation syndrome. The proposed strategies,therefore, need further evaluation through RCTs,by directly comparison of its LBRs per single ET(fresh or frozen), as well as C-LBRs with those ofconventional IVF.The publication by Zhang et al. was not The bulk of evidence of better LBRs and superior perinatal outcomes in frozen ET are largely derived from studies with conventional IVF . Acompr"} +{"text": "The national sentinel surveillance (NSS) system in Vietnam captures only cases presenting to sentinel sites, limiting our understanding of burden of disease in the communityTo identify self-reported cases of influenza-like illness (ILI) and severe acute respiratory infection (SARI) in the community and describe healthcare utilization to better estimate the burden of influenza-associated illnessA cross-sectional survey was conducted in Thai Binh Province. A two-stage cluster sample was used to select households. Standardized questionnaires were used to screen households for episodes of self-reported ILI in the previous month and SARI in the previous 12 months and health seeking behavior for each episodeWe surveyed 2,100 households and 6,760 residents in May 2013, including 1,470 households and 4,666 residents in rural Kien Xuong District and 630 urban households and 2,094 residents in Thai Binh City. Overall, we identified 582 episodes of self-reported ILI and 121 episodes of self-reported SARI cases. The proportions of both self-reported ILI and SARI were significantly (p< 0.05) lower in Thai Binh City than in Kien Xuong. The proportion of cases of seeking healthcare outside the home for an ILI episode within the last month was 89% (95% CI: 84-94). Only 18% (95% CI: 10-27) of household members with a self-reported ILI episode sought healthcare at the ILI NSS site. The estimated proportion of SARI cases that sought healthcare within the last year at a SARI burden study site was 25%.In Thai Binh Province the majority of cases with self-reported ILI sought healthcare outside the home. However, less than 1/5 of self-reported ILI cases came to a national ILI NSS site. Similarly, only 1/4 of SARI cases treated at a SARI burden study site. The studies depend on healthcare seeking behavior of the populations that will underestimate burden of influenza-associated disease in Vietnam. Adjustment for healthcare utilization practices will accurately estimate the incidence of influenza in the communityNone declared."} +{"text": "Anti-vascular endothelial growth factor (anti-VEGF) therapy used as adjunctive to glaucoma filtration surgery may help filtering bleb survival because vascular endothelial growth factor has an important role in the angiogenesis of new vessels and in the fibrogenesis, which lead to scar formation and bleb failure. Bevacizumab is a non-selective monoclonal antibody against all isoforms of VEGF-A.We present the case of an inflammatory glaucoma of a 67-year-old female, with uncontrolled intraocular pressure on maximal tolerable medical treatment, who underwent trabeculectomy and received 1.25 mg/0.05 ml of bevacizumab (Avastin) subconjunctivally at the end of the surgery and an additional injection one month later. Right eye intraocular pressure (IOP) was 26 mm Hg at preoperative visit and after surgery, it decreased and remained normal at each postoperative examination with no additional IOP-lowering medication. A localized avascular bleb with moderate elevation was observed six months postoperatively.Abbreviations: VEGF = vascular endothelial growth factor, IOP = intraocular pressure, 5-FU = 5-Fluorouracil, MMC = Mitomycin-C Because of the wound healing process, the success rate of filtering surgery is limited in time [2-4].Surgical intervention in glaucoma is often done after topical treatment and laser surgery have failed to control pressure or in case of poor compliance. Trabeculectomy, the gold standard in glaucoma filtering surgery, has undergone modifications and refinements over time, with a view to improve the patient outcomes and visual recovery [5-7].In order to reduce scar formation, antimetabolites are frequently used (5-Fluorouracil and Mitomycin-C) nowadays. The introduction of antimetabolites (5-FU and MMC) has improved the success rate and has lowered IOP compared to trabeculectomy without such agents, but the frequency of postoperative complications such as hypotony or bleb-related infections have raised .With the aim of reducing these complications, new compounds are being investigated. Anti-vascular endothelial growth factor (anti-VEGF) therapy used as adjunctive to trabeculectomy may help filtering bleb survival because vascular endothelial growth factor has an important role in the angiogenesis of new vessels and in the fibrogenesis, which lead to scar formation and bleb failure. Bevacizumab is a non-selective monoclonal antibody against all isoforms of VEGF-A and is currently being used off-label to treat various ocular pathology, including refractory glaucoma [A 67-year-old woman with a history of inflammatory glaucoma presented to our department for trabeculectomy surgery without phacoemulsification due to uncontrolled IOP. This patient was under maximum tolerated medical therapy (Cosopt and Travatan). The preoperatory ophthalmologic examination included: best corrected visual acuity (BCVA) in the right eye (RE) was 20/ 60 and in the left eye (LE) was 60/ 60, intraocular pressure (IOP) using Goldmann applanation tonometry was 26 mm Hg (RE) and 19 mm Hg (LE), computerized visual field revealed superior Bjerrum scotoma in the RE, fundus examination revealed increased cup-to-disc (C/ D) ratio of 0.7 with inferior neuroretinal rim thinning and Optical Coherence Tomography found decreased RNFL in the inferior quadrant.Fig. 1). The bleb conjunctiva appeared more avascular than preoperatively, with a moderate elevation and also seemed less hyperemic than the surrounding non-operated conjunctiva.A signed informed consent was obtained and trabeculectomy was performed after the administration of the peribulbar anaesthesia with lidocaine. At the end of the surgery, 1.25mg/ 0.05 ml subconjunctival bevacizumab (Avastin) was injected adjacent to the bleb by using a single-use 30-gauge needle and a tuberculin syringe. One month after the glaucoma surgery, the administration of bevacizumab injection was repeated in the temporal region of the bleb. The postoperative regimen included Netildex, Indocollyre and Tropicamida three times per day for 1 month. One day post-injection, the IOP on the RE was 15 mm Hg and at each follow-up visit did not increase more than 17 mm Hg. The final BCVA was 40/ 60. At each visit, bleb photographs were taken to evaluate the filtering bleb morphology by using the Indiana Bleb Appearance Grading Scale [Additional follow-up and further studies on multiple patients are mandatory to evaluate the long-term efficiency of this multiple administration of bevacizumab.In this case of refractory glaucoma, bevacizumab was an useful agent for the improvement success and for the limitation of scar tissue formation after trabeculectomy.Subconjunctival injections of bevacizumab seem to improve the function of the filtering bleb in inflammatory glaucoma because they control the bleb vascularization by blocking the angiogenesis and fibroblast modulation.No additional anti-glaucoma therapy was needed after surgery. No injection-related complications or drug related side effects were observed.AcknowledgementsThis study was supported by the Sectoral Operational Programme Human Resources Development (SOPHRD), financed from the European Social Found and by the Romanian Government under the contract number POSDRU/159/1.5/S/137390 (author #1)."} +{"text": "Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Since patients with high-risk RMS have limited treatment options and a poor prognosis, and late complications including growth disturbance and secondary cancer induced by chemotherapy or radiation therapy are essential problems, novel therapies are urgently needed. C-type natriuretic peptide (CNP) has physiological activity mainly for mesenchymal cells to inhibit cell proliferation. We hypothesized that CNP attenuates proliferation of human RMS, a malignant mesenchymal tumor and provide rationale for using CNP to treat RMS.Gene expression of guanylyl cyclase B (GC-B), receptor of the CNP in rhabdomyosarcoma clinical samples and cell lines was assessed by using quantitative polymerase chain reaction. To ascertain biological activity of CNP in RMS cells, cyclic guanosine monophosphate (cGMP), the second messenger molecule which is produced by the activation of GC-B and serves as the major signaling molecule was measured following addition of CNP. However, cGMP is quickly degraded by phosphodiesterases and thereby biological activity becomes deactivated. Therefore, sildenafil, a selective inhibitor of phosphodiesterase 5 (PDE5) was added to CNP to prolong or enhance the effects of physiological processes mediated by cGMP by inhibiting its degradation. The in vitro and in vivo efficacy of CNP and sildenafil was evaluated alone and in combination.GC-B expression was seen in all alveolar and embryonal clinical samples which had higher GC-B expression than RMS cell lines. Since RD and RMS-YM cell lines had considerably lower GC-B expression than the clinical samples and KYM-1 and RH30 had no detectable expression, GC-B stable expression cell lines, RD-GC-B was established to mimic the clinical samples. CNP increased the rate of cGMP accumulation in RMS cells depending on concentration of this peptide. Combinations of CNP and sildenafil synergistically inhibited cell growth of RD-GC-B cells by inhibiting extracellular-signal-regulated kinase (Erk), the major signal for cell proliferation in RMS. The synergistic effect on growth and reduction of phosphorylated Erk as tumor pharmacodynamic biomarker were also confirmed in a mouse xenograft model.These results suggest that CNP in combination with sildenafil may have clinical efficacy for treating RMS patients."} +{"text": "Enterobacteriaceae are on the increase worldwide and their spread has become a global challenge. Escalating the challenge is the possibility that many of these are Carbapenemase-producing Enterobacteriaceae (CPE). This further complicates patient management. The magnitude of MDR-CPE in many developed settings has been reported, however, there is paucity of data from resource limited settings.Multi-drug resistant (MDR) We evaluated the epidemiology of MDR-CPE of clinical origin in South Western Uganda.Enterobacteriaceae isolated from diverse specimens obtained from patients attending Mbarara Regional Referral Hospital, South-western Uganda, were screened for MDR in a laboratory-based cross sectional study. Isolates found to be MDR were screened for carbapenem susceptibility/resistance phenotypically by Kirby Bauer disc diffusion method following EUCAST guidelines and genetically using the multiplex real-time Polymerase Chain Reaction (RT-PCR).From September 2013 to June 2014, all blaVIM and blaOXA-48 genes were detected among the genetically resistant isolates.Of the 658 strains isolated, 183 (27.8%) were MDR and 68 (37.15%) of those MDR exhibited at least one form of carbapenem resistance with 23 (12.57%) and 56 (30.60%) isolates expressing phenotypic and genetic resistance, respectively. Eleven MDR-CPE (6.01%) isolates exhibited both phenotypic and genotypic resistance to carbapenems. Only The high prevalence of MDR-CPE calls for aggressive infection control and prevention strategies, including reinforcement of hand hygiene, using contact precautions and early detection of CPE through use of targeted surveillance and molecular techniques in resource limited settings.None declared."} +{"text": "We report a case of widespread unilateral drusen in a healthy 31 year old Caucasian woman using multi-modal imaging including ultra-high resolution optical coherence tomography (UHR-OCT). Dilated fundus exam showed multiple drusen-like lesions in the posterior pole without heme or fluid. Fundus auto fluorescence demonstrated hyperautofluorescent at the deposits. Fluorescein angiography revealed mild hyperfluorescence and staining of the lesions. Spectral-domain optical coherence tomography (SD-OCT) OS showed accumulations in the temporal macula at Bruch\u2019s membrane. UHR-OCT provided improved axial resolution compared to the standard 5 \u03bcm on the commercial SD-OCT and confirmed the presence of deposits in Bruch\u2019s membrane, consistent with drusen. The retinal layers were draped over the excrescences but did not show any disruption. Drusen was first described by Dr. Franciscus Donders in 1855 via histopathological observations as round accumulations under the retinal pigment epithelium (RPE) in Bruch\u2019s membrane . In the We report a case of widespread unilateral drusen in a healthy 31 year old Caucasian woman.A 31 year old Caucasian woman with a history of prematurity was referred to New England Eye Center for drusen-like deposits in the left eye (OS). She denied smoking, renal disease, or a family history of retinal disorders.The patient\u2019s uncorrected visual acuity was 20/20 in the right eye (OD) and 20/20-1 OS. Dilated fundus exam showed a normal fundus OD and multiple drusen-like lesions in the posterior pole without heme or fluid OS. Fundus Autofluorescence (FAF) OS demonstrated hyperautofluorescence at the deposits. Fluoresce in Angiography (FA) OS revealed mild hyperfluorescence and staining of the lesions . SpectraA prototype ultra-high resolution SD-OCT (UHR-OCT) system was employed to provide improved axial resolution of 2\u20133 \u03bcm compared to the standard 5 \u03bcm on the commercial SD-OCT . The higThis report describes a case of unilateral drusen in a healthy 31 year old non-smoking Caucasian woman with no family history of retinal pathology. It is unusual to have extensive macular and extra macular unilateral drusen in young patients. To our knowledge this is the only reported case of widespread unilateral drusen in a patient in her 30s.The patient had no family history of retinal diseases to suggest an inherited disorder, and lacked the characteristic radial pattern of malattia leventinese . Althoug"} +{"text": "Sarcoidosis is systemic granulomatous disease of unknown etiology. Most patients present with pulmonary involvement, but association of cardiac sarcoidosis (CS) is critical factor determining prognosis. Recently, cardiac magnetic resonance imaging (CMR) and 18F-fluoro-2-deoxyglucose positron emission tomography (18F-FDG PET) can detect cardiac lesions in asymptomatic sarcoidosis patients. On the other hand, Conduction abnormalities and ventricular tachycardia are the most common arrhythmias with CS. With the experience of CS pointed out accidentally in PET medical examination at earlier stage got us to recognize the usefulness of CMR, we conducted a study to figure out real-world prevalence of CS in advanced atrioventricular block (AVB) cases and to assess the usability of \"aggressive\" diagnosis of CS by cardiac MRI.Between June 2009 and May 2013, one thousand four hundred eighty-seven patients underwent CMR. We underwent CMR to advanced AVB cases that have been the adaptation of pacemaker implantation of five years if at all possible. CMR was performed by using 1.5-T magnet MR systems with 5-element cardiac coils. In cases with temporary pacing, CMR scan were performed just behind extraction temporary pacing lead with confirmation of spontaneous beat, which followed by pacemaker implantation. We excluded cases over 85 years old or in severe circulatory failure with AVB.Sixty-six AVB cases of all fourteen hundred eighty-seven CMR cases underwent CMR for five years. On the other hand, in one hundred fifty-four cases, a pacemaker was newly implanted for AVB and one hundred twenty-five were under 85 years old. Among these cases, CMR scan were performed in fifty (40% of one hundred fifty-five) cases. Thirteen cases (20% of sixty-six) indicate the pattern of CS with late Gd enhancement (LGE). Nine of thirteen cases were diagnosed as CS with criteria and FDG-PET scan. Five cases received steroid therapy and three cases showed improvement of AVB. Especially, pacemaker implantation was able to avoid in one case. Unfortunately one case did not receive steroid therapy at early phase and developed congestive heart failure. In addition, FDG-PET is more useful than Ga scintigram for assessment activity of CS.CMR in advanced AVB has been accompanied with difficulty because of the bradycardia. Even if only few cases were found as CS in all cases newly pacemaker implanted, its impact on the therapeutic strategy is enormous. In diagnosis of CS, sign of positive LGE and positive PET have important implications. CMR is useful as screening tool for CS and should be performed as far as possible in advanced AVB cases.N/A."} +{"text": "Background: Cryopreservation of ovarian tissues and pre-antral follicles is a promising prospect for preservation of women fertility.Objective: The aim of this study was to evaluate the in vitro developmental competence of mouse vitrified pre-antral follicles in comparison to isolated pre-antral follicles derived from vitrified ovaries in the presence of alpha lipoic acid (ALA).Materials and Methods: Pre-antral follicles derived from fresh, vitrified-warmed ovarian tissues and vitrified\u2013warmed pre-antral follicles were cultured individually with or without ALA, followed by adding hCG to induce ovulation. The follicle growth, oocyte maturation, and embryo development were assessed.Results: The diameter and development of follicles, oocyte maturation and embryo development rates were significantly higher in ALA supplemented groups compared to the respective ALA-free conditions groups. Aforementioned parameters were significantly higher in vitrified-warmed follicles in comparison to follicles derived from vitrified-warmed ovaries.Conclusion: These findings support a superior performance of pre-antral follicles when vitrified rather than when isolated from vitrified ovaries with regard to increasing the rates of developmental parameters. Moreover, ALA improves the in vitro maturation of pre-antral follicles in vitrified and non-vitrified samples.This article extracted from M.Sc. thesis. (Sahar Hatami) In recent years, preservation of female fertility in cancer patients who are facing chemotherapy or radiotherapy has been done in several ways such as cryopreservation of ovarian tissue, oocytes and embryos. Cryopreservation of ovarian tissue rather than cryopreservation of oocytes and embryos has many advantages . It willThis method is also appropriate for pre-pubertal girls and patients with premature ovarian failure , 4. In rThis procedure not only increases cooling rate through reducing sample size, but also reduces the risk of transmission of cancer cells from vitrified ovarian tissue back into recipients and also provides the assessment of follicles quality during culture period after warming . Nowadayin vivo condition, generation of ROS is equilibrated by enzymatic and no enzymatic antioxidant defense systems of cells level of follicles throughout culture period , glutathione peroxidase 4 (GPx4) and superoxide dismutase (SOD) . To dateReagentsAll reagents were purchased from Sigma-Aldrich, UK unless otherwise stated and all media were made with Mili-Q water.AnimalsoC) and they provided with food and water ad libitum. In this experimental animal study, female National Medical Research Institute (NMRI) mice were purchased from Pasteur Institute, Iran. Animals were cared for and used according to the Animal Ethics Committee. The mice were housed and bred in the Animal House of Damghan University under light and temperature controlled conditions supplemented with 10% fetal bovine serum , 2.2 g/l sodium bicarbonate, 25 mM HEPES, 100 IU/ml penicillin and 75 \u00b5g/ml streptomycin. The ovaries were randomly divided into 3 groups: 1) those that not vitrified (control), 2) those that vitrified and 3) those which their follicles were isolated and then vitrified. Isolated pre-antral follicles of each group were cultured in the presence or absence of 100 \u00b5M of ALA. Pre-antral follicles isolationoC.The preantral follicles of fresh and vitrified-warmed ovaries were isolated mechanically by using a 29 gauge needle under a stereomicroscope at 10X magnification. Isolated follicles were selected according to the following criteria: rounded follicular structure with 140-150 \u00b5m diameters, containing visible centrally located healthy oocyte surrounded with intact several layers of granulosa cells, an intact basement membrane, at least one layer of theca cells and no antral cavity. During the operating procedures the culture medium was always kept at 37Vitrification and warming of ovarian tissue and pre-antral folliclesThe vitrification procedure was based on a method described previously with some modifications. Exposure time to the equilibrium solution (ES) and vitrification solution (VS) for ovarian tissue and pre-antral follicles were also based on the methods described previously , 24.In brief, ovarian tissues and isolated pre-antral follicles were initially incubated for 10 and 5 minutes respectively in ES containing 7.5% (v/v) ethylene glycol (EG) and 7.5% (v/v) dimethylsulfoxide (DMSO) in Dulbecco phosphate-buffered saline medium with 20% fetal bovine serum (FBS), then incubated in vs. for another 2 min and 30 sec for ovarian tissue and isolated pre-antral follicles, respectively. After dehydration, the ovarian tissues and pre-antral follicles were immediately drawn into a Pasteur pipette with minimum volume of VS (<0.1\u00b5l) and were individually placed on top of a polypropylene strip of cryotop carrier and immediately immersed into LN2. oC for another 10 min before placing in culture medium.The thin strip of cryotop was covered with cap and stored in LN2 tank for at least 1 week. All equilibration and vitrification steps were carried out at room temperature. For warming, the cryotop cap was removed while it was still immersed in LN2, then the strip directly submerged in DPBS medium containing 1M sucrose. The pre-antral follicles and ovarian tissue were left in the warming solution (1M sucrose in DPBS) for 30 sec and 5 min respectively and transferred into droplets of DPBS medium containing 0.5 and 0.25M sucrose at an interval of 5 min and 3 min respectively at room temperature. After this, ovarian tissue and pre-antral follicles were pipetted into fresh \u03b1-MEM medium supplemented with 10% FBS at 37In vitro culture of isolated pre-antral folliclesIn vitro culture of the isolated fresh and vitrified/warmed pre-antral follicles was performed according to our previous methodology for up to 12 days. At 48h intervals, 10 \u00b5l of culture medium from each drop was replenished by fresh medium.hodology . BrieflyEvaluation of morphological and developmental parameters of cultured pre-antral folliclesThe survival rate of the pre-antral follicles was assessed microscopically based on the morphology of the pre-antral follicle every other day under inverted microscope during culturing period and they were compared at the end of the study as described previously . BrieflyAntral-like cavity formation was considered as visible lucent area in the granulosa cell mass around the oocyte. Follicles diameter was measured only in healthy follicles on day 2 and 4 of culturing period, mean follicle diameter was assessed by measuring and averaging two perpendicular cross sectional diameters of each follicle with pre-calibrated ocular micrometer under inverted microscope . In vitro ovulation inductionIn the twelfth day of culture, ovulation and final oocyte maturation were induced by substitution of culture media with fresh maturation medium supplemented with 1.5 IU/ml human chronic gonadotropin . 24 h after hCG addition in all groups, released oocytes were classified as germinal vesicle (GV), germinal vesicle breakdown (GVBD) when the GV was absent, and metaphase II oocytes (MII) when the first polar body was extruded. In vitro fertilizationoC in 5% CO2 to allow the spermatozoa to swim out and capacitate. Capacitated sperm suspension was added to MII oocyte to give the final motile sperm concentration of 1-2\u00d7106 /ml. The fertile NMRI male mice were sacrificed by cervical dislocation and their caudae epididymides dissected and placed into a 500-\u00b5l drop of modified Tyrods medium (mT6) supplemented with 5% bovine serum albumin (BSA) under mineral oil. The caudae epididymides were ripped with the aid of 28 gauge needle and the spermatozoa squeezed out gently by using forceps and incubated for 90 min at 37oC under 5% CO2 for 6h. Oocytes presenting two pronuclei (2PN) were considered normally fertilized. Fertilized oocytes were washed and gently pipetted to remove spermatozoa and attached cumulus cells. Zygotes were then transferred to drops of fresh KSOM-AA medium supplemented and cultured at 37oC under 5% CO2 with maximum humidity until day 5. Day of insemination was considered as day 0. MII oocytes and spermatozoa were co-incubated in modified KSOM-AA medium at 37oC) of an inverted microscope . The numbers of zygotes that reached to two cells, morula and blastocytes were counted.Embryos were observed on the heated stage . All proportional data were analyzed after arcsine of sqtr transformation. Differences in groups were evaluated by one-way analysis of variance (ANOVA) and Tukey's HSD was used as The morphological and maturational parameters of the cultured vitrified and non-vitrified isolated pre-antral follicles with or without ALA are summarized in As show in The survival (94.3%) and antrum formation (92.3%) rates were significantly higher in fresh pre-antral follicles supplemented with ALA than the other groups . The ratNevertheless, the differences were all significant compared to that of pre-antral follicles which were cultured in the presence of ALA (53.9%). Fertilization and embryo developmental rates of MII oocytes derived from cultured isolated follicles in non-vitrified and vitrified groups in the presence of ALA are shown in Significant higher rates of fertilization and blastocyte were observed in vitrified-warmed pre-antral follicles group in comparison with vitrified-warmed ovaries groups; however both were statistically lower than control group. There were no significant differences in the rates of fertilization and blastocyst formation between vitrified-warmed pre-antral follicles samples and pre-antral follicles derived from vitrified-warmed ovaries which were cultured in the presence of ALA. Also, these situations were observed between cultured vitrified-warmed pre-antral follicles samples in the presence of ALA and ALA-free fresh pre-antral follicles samples.In the present study, vitrification of isolated mouse pre-antral follicle was more effective in comparison with vitrification of whole ovarian tissue due to improving follicular survival, antrum formation and oocyte maturation rates. This difference in the cryobiological features of vitrified-warmed pre-antral follicles and pre-antral follicles derived from vitrified-warmed ovarian tissue may be attributed to their morphological differences. In this regard, it seems that vitrification of ovarian tissue compared to vitrification of pre-antral follicles is facing to some obstacles such as the high volume ratio to low surface area of a whole ovary, which will slow down the cooling and warming rates . This feature of ovarian tissue causes temperature transition from the central region of the ovary to be slowly driven, which in turn will lead to increased possibility of ice crystal formation thus be at a greater risk of severe damage , 26. FurThus, it appears that differences between maturational competence of vitrified-warmed pre-antral follicles and pre-antral follicles obtained from vitrified-warmed ovarian tissue are due to the small size of the pre-antral follicles and increased surface to volume ratio, which in turn will overcome obstacles mentioned above. Effect of cryopreservation on ultra-structural properties of vitrified ovaries has been investigated previously -29. In tOur explanation for different developmental competence among vitrified groups and fresh samples is that, mitochondrial disorders that are occurred throughout cryopreservation could increase ROS generation in vitrified samples and it seems that these disorders were minor in vitrified-warmed pre-antral follicles than pre-antral follicles derived from vitrified-warmed ovary, because development rate was higher in vitrified-warmed pre-antral follicles than those of pre-antral follicles dived from vitrified-warmed ovaries. Several defense mechanisms against ROS are present including non-enzymatic antioxidants and enzymatic defense mechanisms within cells . in vitro maturation of vitrified-warmed pre-antral follicles and pre-antral follicles derived from vitrified-warmed ovaries. The present study showed that ALA could improve the rates of survival, antrum formation and MII oocytes of vitrified-warmed and fresh pre-antral follicles after long-term in vitro culture. We reported useful impact of ALA as a potent antioxidant on the developmental competence of isolated pre-antral follicles in fresh samples . HoweverSeveral hypotheses can be considered for the role of ALA on improving the development of vitrified-warmed and fresh pre-antral follicles. Some investigators attributed the efficiency of ALA to unique antioxidant properties of lipoate/ dihydrolipoate system, i.e. ROS scavenging ability , 22, 31.+, and coenzyme A. In this sense, sodium pyruvate routinely is a constant component of culture media like KSOM-AA medium . ALA may be involved in improving development of cultured pre-antral follicles via metal chelation, antioxidant recycling, and gene expression (To test this hypothesis, further studies must be designed to determine monergic coenzymatic role or possible synergic coenzymatic roles of ALA combined with the rest of coenzymes of pyruvate dehydrogenase complex like thiamine pyrophosphate, FAD, NADpression . The othpression . Also, ipression . CAT and GPx are two fundamental enzymes can be used as a biomarker of oxidative stress . Also itFuture mechanistic studies on the identification of metabolic role of ALA involved in follicular maturation beside its antioxidative activity in assisted reproduction techniques should therefore be conducted."} +{"text": "Juvenile idiopathic arthritis (JIA) is the most common disease associated with uveitis of childhood. The pathogenesis of JIA-associated uveitis (JIAU) is undefined, although there is evidence for a B-cell-mediated autoimmune process with a probably pathogenetic role for autoantibodies.This study intended to analyze the antiocular autoantibodies in serum and their correlation with disease course.Serum samples from children with JIAU (n = 47), JIA without uveitis (n = 67), idiopathic anterior uveitis and healthy controls (n = 52) were collected. The binding patterns of serum antibodies to ocular cryosections from swine eyes were analyzed by indirect immunohistochemistry, and were correlated to epidemiological, clinical and laboratory test results.The patient groups differed with respect to their presence of antibody-binding to the sections: JIAU (94%), JIA (75%), IAU (75%), and healthy controls (29%) to uveal and/or retinal structures. Serum antibodies of JIAU patients predominantly bound at iris (74%) and ciliary body . Iris/cb positive staining correlated with the presence of uveitis complications (p < 0.005) in JIAU patients, but not with positivity for serum anti-nuclear antibodies (ANA), rheumatoid factor (RF) or HLA-B27, and was independent from uveitis activity or type of anti-inflammatory treatment.In JIAU patients, anti-ocular serum antibodies can be detected more frequently than in control groups. Binding patterns to ocular tissue correlate with complicated uveitis course but not with uveitis activity and anti-inflammatory treatment. Antibody-binding is not specific for this uveitis entity, and does not correlate with ANA-positivity.None declared."} +{"text": "Familial Mediterranean fever (FMF) and cryopyrin-associated periodic syndrome (CAPS) are rare inherited autoinflammatory diseases (AID). Chronic inflammation may result in severe organ damage. Beyond the physical burden of the disease, its impact on psychosocial well-being affects all areas of life. Patients may encounter rejection resulting in isolation and the risk of psychological disorders. While the positive effects of IL-1 inhibition on the physical aspects of AID are well documented little is known about the psychosocial condition of these patients. Therefore, the aim of the study was to evaluate HRQL in patients with FMF and CAPS.A single centre study of consecutive patients diagnosed with autoinflammatory diseases age \u2265 4 years was performed. Semi-structured interviews focussing on domains of burden of disease, activities of daily life, family, school and job, participation in social life and self-management were conducted. In addition, patients completed validated HRQL questionnaires including KINDL-R (children) and SF-36 (adults). Questionnaires were analyzed using descriptive statistics. Results were correlated with patient-related variables.Interviews were conducted with 55 patients, 24 males and 31 females. Age distribution: 10 children age 4-7 years, 30 adolescents age 8-18 years and 15 adults. Diagnoses: FMF in 21, CAPS in 30 and unclassified AID in four. A total of 80 questionnaires were completed by affected children , adolescents , and adults in addition to 28 unaffected parents (35%).Overall, the patients' social well-being was impaired. The experience of not being believed was rated worst by almost all patients. Lack of understanding by doctors on their odyssey to diagnosis was experienced by 70%. Challenges in school and job were: above average times of absence (67%), impaired ability to concentrate (80%) and limited productivity (65%). The discrepancy between self-perception (feeling ill very often) and perception of others (not noticing the patients' disease) causes self-doubt (30%).Children and adults with autoinflammatory diseases report significantly impaired HRQL. Patients identified challenges in school and job as the key concern. Targeted interventions like school visits by trained social workers may address this area of need."} +{"text": "These data are in concordant with the clinical data showing that the differential expression profiles of miRNA in tumour tissues and blood associate strongly with drug response and overall survival. Furthermore, another line of studies indicate that the chemopreventive effects of a variety of natural compounds may involve miRNAs. The present review aims to discuss the therapeutic capacity of miRNAs in relation to recent discoveries on EGFR-TKI resistance, including chronic drug exposure and mutations.Non-small cell lung cancer (NSCLC) represents about 85% of the reported cases of lung cancer. Acquired resistance to targeted therapy with epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib, is not uncommon. It is thus vital to explore novel strategies to restore sensitivity to gefitinib. Provided that microRNAs (miRNAs) negatively regulate their gene targets at the transcriptional level, it is speculated that miRNA mimetics may reduce the expression, activity and signal transduction of EGFR so that sensitization of tumour sites to gefitinib-induced cytotoxicity can be achieved. Indeed, a growing body of evidence has shown that the manipulation of endogenous levels of miRNA not only attenuates the EGFR/PI3K/Akt phosphorylation cascade, but also restores apoptotic cell death in Non-small cell lung cancer (NSCLC) makes up about 85% of the reported cases of lung cancer. Approximately 10% of NSCLC patients manifest mutations of epidermal growth factor receptor (EGFR), resulting in hyperactivation of downstream oncogenic pathways related to cell proliferation and survival . CurrentMature microRNAs (miRNAs) are single-stranded, non-coding RNAs composed of 19\u201322 nucleotides which have tremendous impact on the transcriptome. Activation of miRNA involves the \u201ctrimming\u201d of a primary transcript consisting of hundreds of nucleotides through the action of Drosha, which is a RNA-specific endonuclease, to premature pre-miRNA that is approximately 80 nucleotides in length. Furthermore, pre-miRNA is subject to modification by Dicer protein in the cytoplasm as double-stranded miRNA, but only one of the strands would eventually incorporate with the RNA-induced silencing complex (RISC). Provided that miRNAs induce transcriptional repression through complementary pairing of the 3\u2032-untranslated region (UTR) with the transcripts of interest, it is plausible to postulate that the introduction of miRNA mimetics may reduce the expression, activity and signal transduction of EGFR such that the cytotoxicity of gefitinib can be restored in tumours exhibiting impaired drug response [Thr1068, AktSer473 and MAPKThr202 and augmented apoptotic cell death measured as Bim and cleaved PARP in BID007 cells harbouring the A763_Y764insFQEA variant of exon 20 [Reversible EGFR-TKIs, such as gefitinib and erlotinib, are considered the frontline treatment for advanced NSCLC patients harbouring EGFR mutations. Unfortunately, the therapeutic efficacies of EGFR-TKIs are known to be impeded by mutations of EGFRs. Activating mutations, such as deletions in exon 19 and amino acid substitutions in exon 21 including the well-documented L858R point mutation, elevate the intrinsic tyrosine kinase activity of EGFRs, an effect which establishes the rationale of treatment with EGFR-TKI to reduce competitive binding of adenosine triphosphate (ATP) . Notablyvs. erlotinib: rash: 28% vs. 13%; diarrhoea: 22% vs. 5%) [in vitro (H157 > H460 > A549), thereby suggesting that up-regulation of VEGF may represent a pathogenic mechanism that contributes to the resistance to EGFR-TKIs [in vitro model of gefitinib resistance harbouring both L858R and T790M mutations, researching VEGF effectors may have important translational implications in clinical oncology.The phenomenon of EGFR-TKI resistance has called for intense efforts in search of novel, alternative therapeutic opportunities. The fact that T790M mutation increases recruitment and binding of ATP but not EGFR-TKIs and is found in 68% of NSCLC patients with defective responses to EGFR-TKIs [ vs. 5%) . A recen vs. 5%) . These r vs. 5%) . These dGFR-TKIs . PhosphaIt has also been proposed recently that disruptions of mitochondrial function by oxidative stress may modulate gefitinib resistance. Chronic exposure to gefitinib reduced mitochondrial number and respiration and up-regulated remarkably vimentin, a marker indicative of drug resistance in H1650 cells whereas these alterations were reversed by mTempo, which is a free radical scavenger . Under ain vitro model of head and neck tumour, uncovered that apoptotic activation and repression of phosphorylated EGFR/Akt/MAPK were more pronounced in the cetuximab plus gefitinib group compared with the gefitinib-treated group [Thr1135 in H1650 was not paralleled by elevated cleavages of caspase 3 and PARP in response to gefitinib treatment [Emerging evidence suggests that the anti-tumour activity of EGFR-TKIs in resistant NSCLC cell lines can be enhanced by combined therapy with other regimens. Early efforts have shown that cetuximab, which is an EGFR-targeting monoclonal antibody, produced synergistic anti-proliferative effects in various tumour cell lines including H226 when used in combination with gefitinib or erlotinib . Furthered group . These ded group . CompareAnother conflicting line of evidence suggests that dual treatment may not necessarily followed by synergistic therapeutic effects. While substantial growth delay and down-regulation of proliferating cell nuclear antigen (PCNA) in H226 tumours were more evident in athymic mice subject to combined therapy with cetuximab and gefitinib/erlotinib relative to their counterparts receiving single treatment with either of the drugs studied , these retc.) were due to direct degradation of the target of study or secondary to the repression of other regulatory molecules, inactivation of EGFR/MET appears to be a common mechanism of various miRNAs (MicroRNAs (miRNAs) have gained increasingly attentions from researchers worldwide due to its known transcriptional silencing effects by which may modulate multiple signalling cascades. While the centre of attention of the current work is to review miRNA regulation in gefitinib-resistant NSCLC, further readings are recommended for readers interested in the implications of miRNAs in other cancer types and reces miRNAs .in vivo revealed that miR-34a induced regression of gefitinib-resistant tumours in conjunction with gefitinib intervention, an effect that could be ascribed to reduced expression of MET and phospho-EGFRTyr1068 [50 of gefitinib [i.e., a 14-fold reduction) among other miRNA members studied, transfection with miR-7 abolished the elevation of EGFR and restored drug sensitivity in A549 cells exposed to long-term escalating doses of gefitinib [Restoration of gefitinib sensitivity has been observed in different NSCLC cell lines with chronic gefitinib exposure in response to miRNA stimulation. It has been reported recently that miR-34a reversed gefitinib resistance in HCC827 cells induced by concomitant incubation with hepatocyte growth factor (HGF) and gefitinib . This coRTyr1068 . Althougefitinib . In lineefitinib .Tyr1173 and AktSer473 in H1975 cells, despite the fact that these effects were less pronounced relative to those induced by EGFR-targeting small-interfering RNA (siRNA) [The pro-apoptotic capacity of miRNAs has also been supported by data obtained from experimental models of acquired gefitinib resistance. Transfection with miR-138-5p mimics induced a dramatic sensitizing response to gefitinib in H1975 cells, which is in line with the observation that 6-month gefitinib exposure reduced miR-138-5p expression by 10 folds . Incubat (siRNA) . It is n (siRNA) . Further (siRNA) . Recent (siRNA) . Taken i (siRNA) . These rThe functional role of miRNAs in gefitinib resistance has also been characterized by epigenetic approaches. Experiments involving methylation-specific PCR analyses have demonstrated that the promoter of miR-9-3 was hypermethylated in H1975 cells . Demethyin vitro: transfection with miR-150 potentiated while forced expression of SRCIN1 alleviated cell migration [in vitro enhanced phosphorylation of AktSer473 and cell viability [in vitro. A representative example of the claim would be that further stimulation with miR-101 in H157, a NSCLC cell line in which the expression of miR-101 is remarkably high, was not accompanied by reductions in surviving fraction and protein content of ATM (a target of miR-101 known to be involved in DNA repair) in response to ionizing radiation [in vivo: miR-101 blunted the growth of A549 and H1975 xenografts whereas the size of H157 tumours did not differ significantly with ectopic expression of miR-101 [A growing body of opposing data suggests that not every miRNA would induce sensitizing drug response. Over-expression of miR-210 attenuated the expression of genes related to oxidative phosphorylation and induced enlargement of the mitochondria; these observations were coincident with the stabilization of hypoxia-inducing factor 1 alpha (HIF-1\u03b1) in A549 cells . Furtherigration . In accoiability . The notiability . Experimiability . In addiadiation . Similar miR-101 . Intrigu miR-101 . Subsequ miR-101 .in vitro [A growing body of evidence has proposed the use of miRNAs as markers of diagnosis and prognosis. In NSCLC patients, the expression of miR-21 in the serum was elevated and more importantly, patients with higher circulating levels of miR-21 had shorter survival time compared with those with lower levels . This obin vitro , the expin vitro . It is win vitro , thus imEmerging evidence also suggests that miRNAs may mediate the chemopreventive effects of natural, dietary compounds and thusSer473, JAK1/2Tyr1002/Tyr1007 and STAT3Tyr705 and stimulated apoptosis indicated by increased expression of pro-apoptotic Bax and cleavage of caspase 3 and down-regulation of anti-apoptotic Bcl2 in H441 cells [Ser473 [Antrocin is one of the most abundant small molecules of medicinal mushroom believed to confer preventive effects against the development of cancer. Recent attempts have demonstrated that antrocin mitigated phosphorylations of various survival-related kinases including Akt41 cells . What is41 cells . This po41 cells . Compell [Ser473 . Recent [Ser473 . Extrapo [Ser473 .etc.) [in vitro models of pancreatic cancer [Previous efforts have also shown that resveratrol, which is a natural antioxidant in grapes and red wine, modulated an array of miRNAs in A549 cells. In particular, the expression of various miRNA members changed abruptly with resveratrol stimulation . Using betc.) . MicroRNetc.) . In concetc.) . It is aetc.) . Given tc cancer whereas c cancer , it is tc cancer . All theCurcumin, a bioactive ingredient in curry, has been demonstrated to elevate significantly the contents of miR-192-5p and miR-215 concomitantly with pro-apoptotic p53 and cell-arresting p21 in H460 cells . ExperimNevertheless, it remains largely unknown whether the therapeutic values of these natural compounds would be augmented by simultaneous treatment with their putative miRNA mimetics. An encouraging study has shown that combined injection of resveratrol and miR-200c prolonged the survival of H460-bearing mice more remarkably than either treatment alone; by which this effect could be in part ascribed to the increases in caspase 3, caspase 9 and CHOP . Taken tin vitro and in vivo, meaning these effects can be attributed largely to the manipulation of EGFR/MET pathway and apoptotic cell death (Whilst overcoming the mutations causing gefitinib resistance in NSCLC patients are apparently infeasible at the present moment, researching molecules associated with proliferation, survival and cell death offers an alternate approach for biomarker discovery and the development of novel therapeutic regimens. A growing body of data points out that various miRNAs impede the growth of gefitinib-resistant tumours both ll death . Recent"} +{"text": "Phleum pratense p 5, Merck/ALK-Abell\u00f3).Seasonal allergic rhinitis/rhinoconjunctivitis symptoms are dependent on pollen exposure and may impact the observed treatment effect of drugs used to treat seasonal allergic rhinitis. We conducted a post-hoc analysis to investigate the impact of pollen exposure on the overall magnitude of the recorded immunotherapy treatment effect across multiple seasons and trials of Timothy grass sublingual immunotherapy tablet MK-7243 . We assessed the correlation of between-treatment difference in total combined score per trial or trial year to the first-20-days-of-GPS cumulative grass pollen count and entire-GPS average pollen count.Data from seven North American and European randomized placebo-controlled trials of MK-7243 were included in the analysis . Boundaries of three consecutive days with a pollen count \u226510 grains/m2=0.803). A correlation was also seen between TCS and average pollen count over the entire GPS (R2=0.464).Data from 1798 subjects on MK-7243 and 1765 subjects on placebo were included in the analysis. TCS for both groups increased with grass pollen counts. The treatment effect in TCS in each trial was correlated to the cumulative grass pollen count during the first 20 days of GPS (RPost-hoc analysis of seven MK-7243 trials demonstrates that the magnitude of the treatment effect observed in the trials was highly correlated to the early-season grass pollen exposure observed in each trial. Therefore, differences in pollen exposure levels should be considered when comparing results among pollen immunotherapy trials and may contribute to observed differences in magnitude of efficacy between trials using the same immunotherapy formulation.ClinicalTrials.gov Identifiers: NCT00227279; NCT00408616; NCT00562159; NCT00550550; NCT01385371, 2 trials not registered"} +{"text": "In the last decade, various kinds of clinical trials of hematopoietic stem cell transplantation (HSCT) have been performed for ATL patients, and showed therapeutic effects with long-term remission in a part of recipients. Our previous finding of activation of CD8+ Tax-specific cytotoxic T-lymphocytes (CTL) in post-HSCT ATL patients indicated the presence of Tax expression in vivo and potential contributions of CTL to GVL effects. These findings let us attempt developing an anti-ATL therapeutic vaccine consisting of autologous dendritic cells (DC) pulsed with Tax peptides corresponding to the major epitopes of Tax-specific CTL previously identified from HLA-A2, A24 or A11-possessing post-HSCT ATL patients. In preliminary experiments, the DC induced with a conventional method showed matured phenotype and produced IL-12 in 2 of 3 ATL patients tested. Under the official approval by the institutional ethical committees, we conducted the phase-I clinical study of anti-ATL immunotherapy for ATL patients at stable conditions after other therapy. The peptide-pulsed DC was subcutaneously injected for three times with 2 weeks intervals. The first patient showed a significant reduction in the proviral loads in 1 week after administration of DC, which gradually increase during the treatment, then decreased again at 8 weeks after the initiation of the therapy. Reduction in the size of surface lymph nodes by CT confirmed the therapeutic effects. So far two patients completed the course of the study without severe side effects except for fever and skin rash, and their clinical outcomes were partial remission and stable disease respectively."} +{"text": "The 131 RD centers of expertise (CE) initiated then various IT projects to register electronically their RD patients. The CEMARA project [The proposed national architecture incorporates a national minimum data set for all rare diseases (F-MDS-RD) into hospital information care systems to enable electronic patient files re-use for epidemiological studies or research . To ensuThe minimum data set for rare diseases is now being implemented in several local systems, and connectors are being rolled out with several database suppliers. Data re-entry is nowadays a major concern for clinicians. Enabling data re-use is not only an interoperability problem; data must be structured, qualified, standardized and suit"} +{"text": "Molecular nuclear imaging agents enable the comprehensive characterization of therapeutic intervention and can be used in patient selection, pharmacokinetic, dosage-finding, and proof-of-concept studies. The effort in image-guided cell therapy and theranostic approaches in parallel with instrumentation development would be more comprehensive in the outcome assessment of patient response to treatment. To extend the threshold of being able to provide personalized therapy for patients, the integration of imaging findings to genomic and proteomic systems profiling is essential to validate targeted pathways.18F- and 68Ga-radiopharmaceuticals. The Pharmaceutical Inspection Convention and Pharmaceutical Inspection Cooperation Scheme (jointly referred to as PIC/S) are two international instruments between countries and pharmaceutical inspection authorities, which provide together an active and constructive cooperation in the field of Good Manufacturing Practice (GMP). PIC/S' mission is to lead the international development, implementation, and maintenance of harmonized CGMP standards and quality systems of inspectorates in the field of medicinal products. They reviewed FDA and PIC/S guidelines for the synthesis of radiopharmaceuticals. Two examples, 68Gallium--D-Phe1,Tyr3-octreotate (68Ga-DOTATATE) and 18F-fluorodeoxyglucose (18F-FDG), were manufactured under CGMP process. They have reviewed acceptance criteria for these clinic useful radiopharmaceuticals.The Food and Drug Administration (FDA) permits radiopharmaceuticals produced under well-controlled conditions in central commercial facilities to be distributed to local clinics where they are administered. In addition, radiopharmaceutical production process must adhere to Current Good Manufacturing Practice (CGMP) compliance to ensure the quality of drug product that meets acceptance criteria. The CGMP compliance covers manufacturing process and facility, quality guidelines, and personnel training. Y.-T. Chi et al. reported the design of CGMP production for in vitro and small animal models to validate the agent and require low levels of radioactivity. The use of manual synthesis for clinical imaging, however, is challenging for multiple reasons: (1) clinical agents must meet strict sterility and pyrogenicity requirements which are validated from batch to batch; (2) batch-to-batch reproducibility is required to demonstrate suitable radiochemical yield, radiochemical purity, and other quality control analyses; (3) synthesis time must be fast when dealing with radionuclides with a short half-life; (4) clinical studies require multiple patient doses and would expose radiochemists to much higher levels of radioactivity; and (5) production cost and availability of the technology may limit the viability of the agent in routine clinical practice. I.-H. Shih et al. reported the manufacturing of a cGMP grade of [18F]fluoropropoxytryptophan (18F-FTP) to assess tryptophan transporters. PET imaging studies were performed with 18F-FTP and 18F-FDG in prostate and small cell lung tumor-bearing animal models. They have reported that 18F-FTP could be synthesized with high radiochemical yield. They conclude that 18F-FTP may provide potential applications in differential diagnosis and prediction of early treatment response for carcinoids.Radiopharmaceutical chemistry requires intricate handling of radioactive materials, fast reaction times, ease of synthesis, and reproducible results. In the preclinical setting, radiopharmaceuticals are typically synthesized manually. Such applications use in vivo animal imaging using fluorescence, bioluminescence, and PET imaging modalities. Their findings may facilitate different fields of biomedical research and applications.Molecular imaging science has been focused on imaging guidance in the areas of targeting epigenetic abnormalities and disease microenvironment in overcoming resistance in diseases. Multimodality imaging using noncytotoxic triple fusion (TF) reporter genes is an important application for cell-based tracking, drug screening, and therapy. Y.-J. Hsieh et al. reported the rational design of a triple reporter gene for multimodality molecular imaging. They reported that an optimized triple fusion reporter constructed with DsRedm-fl-ttksr39 was developed and validated for more effective and sensitive18F-FDOPA and whole-body autoradiography. They used 18F-FDOPA PET imaging and autoradiographic techniques toassess the impact of recreational drugs such as ketamine, cocaine, and methamphetamine on dopamine neurons in peripheral organs. They have demonstrated that both dynamic 18F-FDOPA PET and autoradiography were useful crossing-validating tools to evaluate the alteration of dopaminergic neurons in peripheral tissues. D. Smith et al. reported the application of patched targeting peptides for imaging and treatment of hedgehog positive breast tumors. Hedgehog (Hh) signaling is involved in breast cancer growth and metastasis and high tumor Sonic Hedgehog (SHh) expression is correlated with poor prognosis in invasive ductal carcinoma. Peptides which bind the PTCH receptor have recently been reported to have a growth inhibitory effect in tumors with activated Hh signaling. These peptides may be used as molecular imaging probes to monitor changes in Hh expression after chemotherapy. Their studies showed that peptides which bind the SHh docking site in PTCH-1 correlate with PTCH-1 expression and can be used to image PTCH-1 in vivo. They conclude that radiolabeled peptides may enable examining the activity of the Hh signaling pathway and evaluating response to anticancer therapies.The use of image-guided technologies to select patient for personalized therapy and to monitor therapeutic outcomes is the focus of this special issue. S. H.-H. Yeh et al. reported the evaluation of inhibitory effect of recreational drugs on dopaminergic terminal neuron by In summary, this special issue covers advances in molecular imaging in drug manufacturing under CGMP environment, preclinical drug discovery, image-guided drug response, and target validation using PET/SPECT hybrid with CT.David J. YangLan PhamMei-Hsiu LiaoFan-Lin KongHiroji UemuraYen-Yu Ian Shih"} +{"text": "Cardiac MR (CMR) is considered the gold standard to assess right ventricular (RV) function in different scenarios, including cases of congenital heart disease. Moreover, an MR-compatible treadmill coupled with Real Time (RT) CMR has been developed for stress testing, and may be an optimal choice in this setting. The aims of this study were to determine the feasibility and accuracy of a RT CMR protocol to evaluate RV function at rest and after treadmill exercise in adults with history of repaired Tetralogy of Fallot (ToF).Ten young adults were prospectively enrolled, and imaging was performed using a 1.5T scanner and 32-channel phased array coil. RV cavity was covered by 10 to 12 contiguous 8 mm transverse slices. ECG-Gated SSFP cine was performed at rest , while non-triggered RT cine was executed both at rest and after stress . Patients underwent treadmill exercise with 12-lead ECG to achieve a goal of \u2265 85% age-predicted maximum heart rate (APMHR). RT cine imaging was performed immediately upon cessation of exercise. End-diastolic (EDV) and end-systolic (ESV) volumes were calculated by two different observers using Simpson's rule by manually tracing RV endocardial borders. Interobserver agreement was analyzed by the Pearson's correlation coefficient whereas differences were assessed with paired t-test .Both ECG-Gated and RT techniques demonstrated excellent interobserver agreements for EDV, ESV, and ejection fraction (EF) , indicating good reproducibility. Average results between the two observers are listed in Table The feasibility of RT CMR imaging coupled with treadmill exercise was demonstrated. The diagnostic value of this technique to assess RV function in patients with repaired ToF deserves further assessment in a larger patient cohort.Partially funded by NIH: R01 HL102450."} +{"text": "Familial Hemiplegic Migraine type 1 (FHM1) is a rare monogenic subtype of migraine with aura caused by mutations in the CACNA1A gene. In FHM1 knock-in mouse models these mutations increase the susceptibility for cortical spreading depression (CSD): the underlying mechanism of the migraine aura.To study the consequences of CSD in a migraine-relevant context, we measured cortical gene expression profiles in FHM1 and wild-type mice 24 hours after CSD induction.Expression profiles were generated using deep-Serial Analysis of Gene Expression (SAGE) sequencing, a tag-based next-generation sequencing method for gene expression profiling. Relevant expression changes were validated by qPCR experiments.Our data show that CSD induces differential expression of genes involved in inflammatory pathways in both the FHM1 and wild-type mice. However, we identified a gene set that is up-regulated upon CSD specifically in the FHM1 migraine mouse model. Genes from this gene set are involved in inflammatory and interferon-related signaling, and were often found up-regulated in immune-stimulated conditions.Differential expression of genes involved in inflammatory pathways in the brain of FHM1 migraine mice compared to wild-type mice upon CSD, indicates that CSD affects the brain differently in a genetically predisposed animal which may help increase our understanding of migraine pathophysiology.No conflict of interest"} +{"text": "Telomeres are specific nucleoprotein structures at the ends of eukaryotic chromosomes. Telomeres and telomere-associated proteins maintain genome stability by protecting the ends of chromosomes from fusion and degradation. In normal somatic cells, the length of the telomeres gradually becomes shortened with cell division. In tumor cells, the shortening of telomeres length is accelerated under the increased proliferation pressure. However, it will be maintained at an extremely short length as the result of activation of telomerase. Significantly shortened telomeres, activation of telomerase, and altered expression of telomere-associated proteins are common features of various hematologic malignancies and are related with progression or chemotherapy resistance in these diseases. In patients who have received hematopoietic stem cell transplantation (HSCT), the telomere length and the telomerase activity of the engrafted donor cells have a significant influence on HSCT outcomes. Transplantation-related factors should be taken into consideration because of their impacts on telomere homeostasis. As activation of telomerase is widespread in tumor cells, it has been employed as a target point in the treatment of neoplastic hematologic disorders. In this review, the characteristics and roles of telomeres and telomerase both in hematologic malignancies and in HSCT will be summarized. The current status of telomerase-targeted therapies utilized in the treatment of hematologic malignancies will also be reviewed. The telomeres are specific nucleoprotein structures at the ends of eukaryotic chromosomes which maintain genome stability by protecting chromosomes from end fusion and degradation. Human telomeres are composed of 10\u201315 kb of 5\u2032-TTAGGG-3\u2032 DNA sequence repeats and a telomere-associated protein complex, shelterin (reviewed by Blackburn) .In most somatic cells, telomeres gradually become shortened 20\u201359 bp/year) because of the end-replication problem during cell division ,4]. Onc. Onc4]. 9 bp/yearTelomerase is a reverse transcriptase which maintains telomere length by adding nucleotides to the single-stranded (ss) DNA of the telomere during cell division . TelomerShelterin is a protein complex which consists of 6 telomere-associated proteins: telomeric repeat-binding factors 1 and 2 (TRF1 and TRF2), TRF1-interacting nuclear factor 2 (TIN2), protection of telomeres (POT1), POT1 and TIN2-interacting protein 1 (TPP1), and TRF2-interacting protein 1 (Rap1) . As. As22]. survival . Telomersurvival .de novo acute leukemic cells. Shi et al. reported that the expression of TRF1, which is a negative regulator of telomerase activity, was lower in patients with AL than in normal volunteers . Th. Thet alelomeres .Shelterin alterations were also identified in CLL patients and were found to be involved in telomere instability. The expression levels of TRF1, RAP1 and POT1 were all reported to be reduced in B-CLL cells, while the expression of TPP1 was increased . In contet al. utilized bone marrow cells of telomerase knockout mice to establish a CML-like cell culture. They demonstrated the presence of shorted telomeres with an increase in the secretion of pro-inflammatory cytokines and growth factors associated with proliferation control in telomerase negative CML-like cells. Their work indicated that a telomerase-targeting strategy could induce senescence in CML-like cells and alleviate the tumor promoting/progressing effect of BCR-ABL ..42].The circular extra-chromosomal telomeric repeat (ECTR), one of the ALT hallmarks, was used to define ALT activation in CML patients in a recent study. In this study, 27% of CML patients in CP were reported to exhibit both high ALT activity and telomerase activities. As telomerase activity increases with disease progression, the dominating telomere maintenance mechanism might transition from ALT to telomerase .et al. reported that expression levels of TRF1 and TRF2 were increased in CML patients in the CP and in the accelerated phase (AP) but reduced to a level comparable to normal controls in the majority of patients in the BP. Increased expression of TRF1 may thus induce telomere shortening in CML in both the CP and AP . Si. Si51]. observed . In ordeobserved . Thus shobserved .HSCT is a potential curative therapy for many hematologic disorders and immunodeficiency diseases. The self-renewal capacity of hematopoietic stem cells (HSCs) is essential for reconstitution of the hematopoietic system. The proliferative potential of HSCs decreases with differentiation and age in line with the shortening of telomeres and increased telomerase activities in these cells. Mean telomere length is shorter in HSCs purified from adult bone marrow than from fetal liver or umbilical cord blood . Telomeret al. reported the loss of a 10 kb length of the telomere of leukocytes generated from hTERT knockout HSCs after 6 days of in vitro expansion and 3 months of regeneration in secondary-transplanted recipient mice [hTERT-deleted mice have been used as a telomerase-deficient model for the study of telomerase function in the hematopoietic system \u201359]. Se. Se59]. ent mice . Telomeret al. reported that the telomeres of transplanted cells became shortened by up to 1.9 kb in auto-HSCT recipients over an observation period of 5.3 years, the same frequency of telomere erosion as would occur over 15\u201320 years in normal individuals. Telomere erosions of up to 2.1 kb were observed in patients who received allo-HSCT . Th. Th61]. et al. compared telomere length in peripheral blood progenitor cells (PBSCs) collected after two tightly-spaced high-dose (hd) chemotherapy courses. Telomere length was significantly shorter in PBSCs collected after the second course (hd-Ara-C) compared to that collected after the first course (hd-CY) ..74].in vitro. The lysosome-associated membrane protein (LAMP-1) mRNA sequence is co-transduced into DCs to make the antigen easily degradable and to enhance the immune response ..in vitroin vitro study, GRN163L showed effective inhibition of telomerase and of cell growth in B-CLL cells and tumor initiating B cells of patients with multiple myeloma (MM) . GR. GRin vioma (MM) . That maoma (MM) .BIBR1532 is a synthetic non-nucleotidic small molecule which selectively inhibits the active site of telomerase. BIBR1532 leads to progressive telomere shortening and apoptotic cell death in a concentration-dependent manner in AML cell lines as well as in primary cells from patients with AML or CLL \u201384]. BI. BI84]. et al.), are more effective in reducing telomerase activity . IM. IM88]. activity ,90]..et al.),et al. reported a dose-dependent inhibition of telomerase activity of ATO and a reduction in telomere length in ATO-treated NB4 cells. The mRNA levels of Pin1, survivin, c-Myc, hTERT, and PinX1 were all reduced in a concentration-dependent manner after 2 days of ATO treatment . Gh. Gh92]. reatment .et al. reported that IFN-\u03b1 could significantly down-regulate the expression of hTERT and the activity of telomerase in many types of human hematologic malignant cell lines, primary leukemic cells and T-lymphocytes within 4 hours of treatment at a concentration of 5000 U/mL, through suppressing the hTERT promoter activity [et al. reported that IFN-\u03b3 could also induce a decrease of hTERT expression. hTERT mRNA levels were virtually abolished after 48 h of IFN-\u03b3 treatment at 5000 U/mL [Interferons (IFNs) are multi-functional cytokines produced by eukaryotic cells. Xu activity . Lindkvi000 U/mL .Telomeres are essential for the maintenance of chromosome stability in mammalian cells. Accelerated telomere shortening leads to activation of telomerase in stem cells and in the majority of tumor cells. In patients with hematologic malignancies, shortened telomeres and increased telomerase activity are usually observed and are associated with disease progression. In patients who have received HSCT the telomere length of engrafted stem cells is closely related to the outcomes of HSCT. Consequently the telomere characteristics should be taken into consideration during donor selection. It is also necessary to evaluate the effect of chemotherapy and conditioning courses on telomere length. Many promising telomerase targeting therapies have been confirmed to be tolerable and efficient to induce immune responeses in patients with hematological malignancies. However optimized strategies are still required to ensure their clinical efficiency. Further work will be needed to elucidate the complete story of telomere biology and to explore efficient telomerase-targeting therapies in hematologic malignances.ATM: Ataxia telangiectasia-mutated geneATR: Ataxia telangiectasia and Rad3ALT: Alternative lengthening of telomeresss DNA: Single-strand DNAds DNA: Double-strand DNATRF1: Telomeric repeat-binding factors 1TRF2: Telomeric repeat-binding factors 2TIN2: TRF1-interacting nuclear factor 2Rap1: TRF2-interacting protein 1POT1: Protection of telomeres protein 1TPP1: POT1 and TIN2-interacting protein 1AL: Acute leukemiaAML: Acute myeloid leukemiaALL: Acute lymphoblastic leukemiaLDH: Lactate dehydrogenaseCR: Complete remissionAPL: Acute promyelocytic leukemiaCLL: Chronic lymphocytic leukemiaUM-IGVH: Unmutated immunoglobulin variable regionPFS: Progression-free survivalOS: Overall survivalCML: Chronic myelocytic leukemiaCP: Chronic phaseBP: Blastic phaseCCR: Completely cytogenetic remissionIM: Imatinib MesylateECTR: Extra-chromosomal telomeric repeatAP: Accelerated phaseMDS: Myelodysplastic syndromesIPSS: International Prognostic Score System3D: Three-dimensionalHSCT: Hematopoietic stem cell transplantationHSCs: Hematopoietic stem cellsauto-HSCT: Autologous hematopoietic stem cell transplantationallo-HSCT: Allogeneic hematopoietic stem cell transplantationGVHD: Graft-versus-host diseasecGVHD: Chronic graft-versus-host diseaseaGVHD: Acute graft-versus-host diseaseTreg: Regulatory T cellsPBSCs: Peripheral blood progenitor cellst-MDS/AML: Therapy-related myelodysplasia or acute myelogenous leukemiaCTL: Cytotoxic T lymphocyteGM-CSF: Granulocyte-monocyte colony-stimulating factorTLR-7: Toll-like receptor-7DC: Dendritic cellMM: Multiple myelomaAPTT: Activated partial thromboplastin timeTKI: Tyrosine kinase inhibitorsPP2A: Protein phosphatase 2AATO: Arsenic trioxideThe authors declare no conflict of interest.LW participated in the design of this review, performed the selection and interpretation of data, and drafted the manuscript. HX participated in the design of this review, helped to draft and revise the manuscript. XZ performed the selection and interpretation of information about acute leukemia and helped to draft the manuscript. CW performed the selection and interpretation of information about the telomere biology and helped to draft the manuscript. HH conceived of the review, and participated in its design and coordination and revised the manuscript. All authors read and approved the final manuscript."} +{"text": "Demyelinating disorders have been reported in association with anti-tumor necrosis factor alpha treatment in adults. Few reports exist among children.We report a case of demyelination and optic neuritis in a child treated with eternacept to increase the awareness of the possible risk of demyelination during anti-TNF-alpha treatment in children.Case report.A 9 year old girl treated with methotrexate for 6 months and eternacept for 3 months because of polyarticular JIA developed loss of vision in both eyes. The weeks prior she had been extremely tired with periods of cough and fever. Bacterial- and Epstein-Barr-virus infection was absent. Her well-being improved spontaneously. Mild vitritis was diagnosed bilaterally and impaired vision was diagnosed. MR of the brain showed periventricular white matter lesions and lesions in hypothalamus. In addition signs of optic neuritis were seen. Visual evoked potential (VEP) showed delayed latency. Anti-aquaporin-4 antibodies were not present. Cerebrospinal fluid (CSF) examination was without pleocytosis and no infectious agent could be demonstrated. Oligoclonal bands in the CSF were present indicating production of gamma globulin in the central nervous system.The girl received high-dose intravenous steroid therapy followed by oral prednisone. The treatment with etanercept was stopped. Two months later her vision was almost normal and still improving. No further neurological symptoms have developed during prednisolone tapering.Development of cerebral demyelination might be the first attack of multiple sclerosis and may be triggered by anti-TNF-alpha treatment. The changes could also be due to an inflammatory disorder caused by infection or be of auto immune origin. The role of the TNF-alpha blockade is uncertain.None declared."} +{"text": "An ovine model can cast great insight in translational neuroscientific research due to its large brain volume and distinct regional neuroanatomical structures. The present study examined the applicability of brain functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) to sheep using a clinical MR scanner (3 tesla) with a head coil. The blood-oxygenation-level-dependent (BOLD) fMRI was performed on anesthetized sheep during the block-based presentation of external tactile and visual stimuli using gradient echo-planar-imaging (EPI) sequence.The individual as well as group-based data processing subsequently showed activation in the eloquent sensorimotor and visual areas. DTI was acquired using 26 differential magnetic gradient directions to derive directional fractional anisotropy (FA) and apparent diffusion coefficient (ADC) values from the brain. White matter tractography was also applied to reveal the macrostructure of the corticospinal tracts and optic radiations.Utilization of fMRI and DTI along with anatomical MRI in the sheep brain could shed light on a broader use of an ovine model in the field of translational neuroscientific research targeting the brain. Ovine models for neurological application targeting the brain have been gaining momentum for providing translational information on therapeutic applications to humans. Compared to small animal testing , the oviAnatomical and functional neuroimaging techniques are widely used to characterize functional-structural correlates or any morphological abnormalities in the brain that are implied in various pathological processes. Among various imaging modalities, magnetic resonance imaging (MRI) is advantageous in examining the brain anatomy compared to computerized tomography (CT) which provides limited signal contrasts for soft tissue. MRI, by utilizing a blood-oxygenation-level-dependent (BOLD) endogenous contrast mechanism associated with local brain activations, can also reveal spatiotemporal pattern of regional brain function in response to external stimulation in anesthetized animals .MRI also offers information on the white matter (WM) structures and their spatial orientations. Diffusion tensor MRI (DTI), introduced in the mid 90s , 9, useset al. in mm. After the motion-correction and smoothing, the task-related neuronal activity was estimated by a general linear model (GLM) for each individual sheep. The degree of voxel-wise statistic parametric map in t-value, with respect to the task-specific canonical hemodynamic response function (HRF), was obtained. To derive the group-averaged trend, random effect analysis (RFX) [www.restfmri.net; toolkit v1.8; 1000 Monte Carlo simulations were used). The time-course of BOLD signals from the region-of-interests (ROIs) for the sensorimotor and visual areas were averaged across the animals (n\u2009=\u20097).The fMRI time series from seven sheep were used for the data processing. Data from one sheep were excluded due to severe motion-related artifacts during the scan. The time series were processed by the SPM8 software package was usedis (RFX) in the sis (RFX) (www.resn\u2009=\u20096) was processed by the DTI Studio software , whereby diffusion tensor calculation was performed with diffusion-weighted image parameters . Fractional anisotropy (FA), apparent diffusion coefficient (ADC), trace, tensor, and color-coded directional FA maps were calculated as provided in the software. FA and ADC are one of the most frequently used quantitative parameters in humans. Circular region-of-interests (ROIs), having a size of 9\u00a0pixels, were delineated based on the directional FA maps. The ROIs were placed on the following anatomical locations (also shown in Fig.\u00a0Data from two animals, one due to motion effects and the other due to technical issues, were excluded. The acquired DTI sequence ("} +{"text": "In a clinical phase I trial feasibility, safety and tolerability of ex vivo TKD/IL-2 stimulated autologous NK cells has been demonstrated in patients with metastasised colorectal carcinoma and NSCLC. Based on these findings a proof-of-concept phase II randomised clinical trial was initiated (BMBF - Innovative therapies). NSCLC patients will be treated with ex vivo stimulated NK cells after RCT. Most patients are diagnosed in locally advanced disease stages IIIA and IIIIB. After conventional radiochemotherapy only part of the patients (less than 50%) show remission and despite improvements in standard therapies the mortality associated with this disease is very high . Therefore there is a strong medical need for innovative treatment strategies. Since an Hsp70 membrane-positive tumour phenotype is associated with a poor clinical outcome, only Hsp70 membrane-positive tumour patients are recruited into the trial. Leukapharesis products are generated centralised and cell processing is performed in a GMP-laboratory.Membrane-bound Hsp70 serves as a recognition structure for NK cells that were pre-stimulated with Hsp70 peptide TKD plus low dose IL-2 The aim of the study is to show the efficacy of the treatment with Hsp70-peptide TKD/IL-2 activated, autologous NK cells following completion of standard RCT by improvement of PFS."} +{"text": "The hyperintense acute reperfusion marker (HARM) has initially been described in acute ischemic stroke. The phenomenon is caused by blood-brain barrier disruption following acute reperfusion and consecutive delayed gadolinium enhancement in the subarachnoid space on fluid attenuated inversion recovery (FLAIR) images. Here we report the case of an 80-year-old man who presented with transient paresis and sensory loss in the right arm. Initial routine stroke MRI including diffusion- and perfusion-weighted imaging demonstrated no acute pathology. Follow-up MRI after three hours demonstrated subarachnoid gadolinium enhancement in the left middle cerebral artery territory consistent with HARM that completely resolved on follow-up MRI three days later. This case illustrates that even in transient ischemic attack patients disturbances of the blood-brain barrier may be present which significantly exceed the extent of acute ischemic lesions on diffusion-weighted imaging. Inclusion of FLAIR images with delayed acquisition after intravenous contrast agent application in MRI stroke protocols might facilitate the diagnosis of a recent acute ischemic stroke. In transient ischemic attack (TIA) acute stroke MRI including diffusion-weighted imaging (DWI) demonstrates small acute ischemic lesions in a subset of patients ranging from 9 to 67% . It has The hyperintense acute reperfusion marker (HARM) describes a hyperintense signal in the subarachnoid space on postcontrast fluid attenuated inversion recovery (FLAIR) images and has initially been described in acute ischemic stroke , 7. FLAIIn the present case report, we present a patient with left hemispheric TIA whose main finding on acute stroke MRI was HARM phenomenon in the left middle cerebral artery (MCA) territory.An 80-year-old, nonsmoking man was transferred to our emergency department with a right arm weakness and sensory loss on awakening at 5 a.m. The patient was last seen normal at half past ten p.m. On admission at 7 a.m. his symptoms had completely resolved and neurological examination was unremarkable. The patient's past medical history included arterial hypertension, diabetes mellitus type 2, previous right hemispheric transient ischemic attack (TIA) 18 months earlier, and previous left middle cerebral artery (MCA) stroke without residual deficits four months earlier.Routine stroke MRI at 1.5 Tesla was performed approximately 30 minutes after admission and revealed no acute pathology. The stroke MRI protocol included DWI, T1- and T2-weighted images, FLAIR images , perfusion-weighted images (PWI) following the first pass of contrast bolus through the brain, and time-of-flight MR angiography. Perfusion-weighted images were acquired using a gradient-echo echo planar imaging sequence . The contrast agent gadoteric acid was bolus injected by a power injector with a dose of 0.1\u2009mmol/kg of body weight at a rate of 4\u2009mL/sec.A follow-up MRI was performed three hours later in order to ascertain the ischemic pathogenesis of the clinical symptoms. Diffusion-weighted images demonstrated only a few small ischemic lesions, whereas FLAIR images showed subarachnoid contrast enhancement in the left MCA territory consisteThis case is of particular interest as it illustrates that even in TIA patients without or with only small ischemic lesions disturbances of the blood-brain barrier may be detectable by HARM on FLAIR images indicating transient vessel occlusion. A possible pathomechanism for the blood-brain barrier disruption after acute ischemia is the activation of inflammatory processes and several proteolytic enzymes . AlthougDiffusion-weighted imaging is able to demonstrate ischemic lesions as the final state of the pathophysiological process in TIA . WhetherHARM might be a valuable additional diagnostic tool in the assessment of patients with TIA in particular in those cases with unremarkable DWI. Consequently, we suggest the inclusion of delayed postcontrast FLAIR images in the MRI protocol in DWI-negative TIA as these might facilitate the diagnosis of a recent acute ischemic stroke. The consecutively longer MRI examination duration in these cases may be outweighed by the better diagnostic accuracy. However, this should be confirmed in a larger study with TIA patients."} +{"text": "Hepatocellular carcinoma (HCC) is the third leading cause of cancer worldwide. The incidence and mortality of HCC have increased three-fold in the United States over the past few years and the majority of patients present with advanced disease. Bavituximab is a novel chimeric IgG1 monoclonal antibody that selectively blocks phosphatidylserine (PS), a membrane phospholipid exposed on the tumor vasculature, tumor cells and tumor-derived exosomes. PS is tightly segregated to the inner leaflet of the plasma membrane, but becomes externalized on the outer surface of dying cells and vascular endothelium in response to oxidative stress, hypoxia, chemotherapy, radiation and other physiological stressors in the tumor microenvironment.Pre-clinical data demonstrate that Sorafenib increases PS exposure on vascular endothelium and HCC tumor cells. The combination of Sorafenib with a murine Bavituximab analogue potentially inhibited HCC tumor xenograft growth and induced an immunostimulatory macrophage phenotype. Following the preclinical efforts, a Phase I study was completed concluding that Sorafenib (400 mg) and Bavituximab (3 mg/kg) can be safely given in patients with advanced HCC.Patients in an ongoing open-label, single-center Phase II therapeutic study of Sorafenib and Bavituximab, patients consented to undergo two image guided core needle biopsies of a single site of HCC obtained at the time of diagnosis and following one cycle of treatment with Bavituximab and Sorafenib. Treatment cycles consisting of four weekly doses of Bavituximab (3 mg/kg I.V.) and four weeks of Sorafenib (400 mg P.O. BID) were repeated until progression or toxicity. Histologic analysis of immune and myeloid infiltrates in tumor tissues was performed.In 2 (33%) of the analyzed 6 patients, treatment of HCC patients with Bavituximab and Sorafenib increased infiltration of CD4+ (T-helper cells), and CD8+ (cytotoxic T-cells) \u2265 2-fold, with a corresponding decrease in FoxP3+ (regulatory T-cells) in the tumor microenvironment one cycle post- treatment as compared to baseline. Increased infiltration of tumor associated macrophages \u2265 2-fold was also observed post treatment in these two individuals.Immunohistochemical evaluation of HCC tumor tissues post combination treatment indicated an increase of immune infiltrates; raising the potential of a clinically meaningful anti-tumor immune response. The prevalence of such immune cells within the tumor microenvironment correlates with the pre-clinical experience with Bavituximab in combination with Sorafenib in murine models of HCC."} +{"text": "Caveolae are membrane micro-domains enriched in cholesterol, sphingolipids and caveolins, which are transmembrane proteins with a hairpin-like structure. Caveolae participate in receptor-mediated trafficking of cell surface receptors and receptor-mediated signaling. Furthermore, caveolae participate in clathrin-independent endocytosis of membrane receptors. On the one hand, caveolins are involved in vascular and cardiac dysfunction. Also, neurological abnormalities in caveolin-1 knockout mice and a link between caveolin-1 gene haplotypes and neurodegenerative diseases have been reported. The aim of this article is to present the rationale for considering caveolae as potential targets in cardiovascular and neurological diseases. The free cell surface between microvilli shows larger cave-like depressions, likewise representing caveolae intracellulares, containing a dense material.\u201d Twenty years later, Dulhunty and Franzini-Armstrong in caveolae. Since then several studies have confirmed a link between caveolins/caveolae and ion carriers. In cardiomyocytes the Na+/Ca2+ exchanger is very important for heart functionality. The exchanger may interact with caveolin-1 but may also form macromolecular complexes with caveolin-3 and annexin A5 whose current densities are affected by mutations in caveolin-3 processing of the amyloid precursor protein (APP), that leads to A\u00df peptide. The enzyme that cleaves APP to give A\u00df (BACE-1) physically associates to lipid-raft proteins than agonists (activators). Matters in the case of caveolins/caveolae are not as straightforward as caveolins have neither orthosteric binding sites for function regulation nor regulatory sites. To our knowledge, no small molecule targeting caveolins has been developed. Difficulties in targeting this type of membrane proteins likely underlie this lack of drug development and limit the use of caveolins as drug targets. One way to circumvent this issue is the use of anti-caveolin antibodies reductase inhibitors decrease caveolin-1 levels . Analogously, polymeric structures may target caveolae and interfere with caveolae-mediated physiological or pathological actions. As an example, polysorbitol-based transporter delivery of small interfering RNA use caveolae for cell entry superfamily are a relevant example. GPCRs are targets of approximately 40% of compounds used in human therapy. Agonist and/or antagonist modulation of their activity can lead to increases or decreases in the expression levels of caveolins. In addition, it seems possible that GPCRs can form heteroreceptor complexes with caveolins. Interactions may modify the pharmacological properties in turn making possible the design of compounds selective for GPCR protomers present in such complexes. Examples of the direct link between caveolae and GPCRs are given in the next section.Drosophila antennapedia homeodomain. By this approach platelet activating-factor-induced NO production and microvasculature permeability was reduced in tumor bearing animals contain putative caveolin binding domains or indirectly caveolin expression levels. Via activation of some GPCRs we could control or re-program caveolin expression levels to explore therapeutic outcomes in heart and brain.Cumulative evidence points to caveolae and caveolins as important regulators of GPCR traffic and function thus raising therapeutic potential in targeting caveolae or GPCRs in caveolae for the neurotransmitter dopamine of anion secretion in epithelial cells (Lam et al., 2A GPCRs are up-regulated in atrial fibrillation and their blockade results in restoring the abnormal calcium handling in cardiomyocytes from patients (Hove-Madsen et al., 2A GPCRs may also form homodimers or heteromers with other receptors. The complexes are unique entities with specific signaling properties (Hillion et al., 2A GPCR monomer/homomers/heteromers in membrane micro-domains is an interesting possibility for altered functional properties that should be further explored. Endothelin subtype B receptor in endothelial cells is mainly present in caveolae and its activation by endothelin leads to rapid caveolae-dependent internalization. It is likely that activation of such receptors present in caveolae leads to rapid caveolae-mediated trafficking (Oh et al., Specific G-protein-related signaling components are enriched in lipid rafts/caveolae meaning that these structures affect G-protein-coupling efficacy and signaling selectivity (see Chini and Parenti, e et al. reportedin vivo opioid-induced preconditioning (Tsutsumi et al., The selective advantage of reperfusion after ischemic injury to minimize the consequences of a second ischemic episode has been known for long (see Yellon et al., Future work will help on understanding how caveolin-protein and caveolin-GPCR interactions may help in combating cardiovascular and neurological diseases.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "High-resolution late gadolinium enhancement (LGE) MRI is used to assess fibrosis of the left atrium (LA) and visualize post-ablation scar in patients with atrial fibrillation (AF). Only few centers with advanced expertise in cardiac MR (CMR) have shown successful and good quality LGE-MRI of the LA. In this work, we assess the dependence of image quality of LGE images on the number of patients imaged in the centers participating in the multi-center trial DECAAF . Also, main causes of poor image quality were determined.Fifteen centers with different degrees of CMR expertise and typical MRI hardware participated in DECAAF. Customized sequences for LGE of LA were installed on 17 Siemens scanners in participating centers. Nine centers used 1.5T scanners, five used 3T scanners and one used both 1.5 and 3T scanners. Three hundred and twenty nine AF patients underwent LGE-MRI prior to ablation to estimate the extent of LA fibrosis. One center (8 patients) was excluded from analysis because of two-years of prior experience in LGE-MRI of LA. Two independent readers assessed the image quality as 1- poor, 2 - fair or 3 - good. Poor quality images were analyzed to identify the causes for scan failure.Figure The analysis of data from multi-center study DECAAF clearly shows a learning curve associated with LGE MRI of LA - imaging more patients improves image quality. Better training of MRI technologists may also further improve image quality.This study was supported by the CARMA Center at the University of Utah."} +{"text": "The Wnt signaling in the stably transfected cell line was proved to be very sensitive to (\u2212)-epigallocatechin-3-gallate (EGCG) and lithium chloride (LiCl) treatment, respectively. Natural compounds were screened and a couple of novel inhibitory modulators of the Wnt signaling pathway were obtained.Abnormal activation of canonical Wnt signaling has been associated with various types of cancer. Inhibitory reagents targeting the Wnt signaling have great potential to inhibit the growth of relevant tumors. Here we generated a cell-based screening strategy for identification of antagonists of the Wnt/\u03b2-catenin signaling pathway. Stable expression"} +{"text": "The possibility of healthcare exposure to Middle East Respiratory Syndrome Coronavirus (MERS-Cov) has been early described. Almost one-third of the confirmed MERS-Cov cases in Saudi Arabia were among healthcare workers (HCWs).To describe three-season experience of MERS-Cov exposure and outcome among HCWs in a tertiary care hospital in Saudi Arabia.Prospective surveillance was conducted in King Abdulaziz Medical City in Riyadh, Saudi Arabia for unprotected exposed HCWs, with every newly PCR-confirmed MERS-Cov case, between June 2013 and March 2015. HCWs exposed to confirmed MERS-Cov patients were examined for the presence of symptoms and nasopharyngeal (and rarely other) swab was obtained for MERS-Cov. Exposure was defined as caring of or being in close proximity (within 2 meters) of a confirmed patient, without proper personal protective equipment (PPE).During the duration covered, a total 32 patients with PCR-confirmed MERS-Cov were associated with exposure of 1361 HCWs. Only 328 (24.1%) of the exposed HCWs had symptoms suggestive of respiratory infection at the time of screening. MERS-Cov was confirmed in only 14 (1.03%) HCWs. MERS-Cov confirmation was roughly similar among symptomatic and asymptomatic HCWs. Only 2 (14.3%) of the 14 confirmed HCWs required hospitalization. While the mortality among the confirmed patients was very high , none of the 14 confirmed healthcare workers died.We are reporting high potential of healthcare exposure to MERS-Cov in the healthcare setting but a very low transmission rate. Proper compliance with PPEs is essential to further reduce unprotected exposure of the HCWS. In essence contact tracing and testing for all unprotected exposed HCWs to MERS CoV irrespective of symptoms remain critical measures to prevent or reduce the impact of MERS-Cov hospital outbreak till further understanding of MERS-Cov behavior is delineated.None declared."} +{"text": "Whole-genome sequencing revealed that MTB313 carried a nucleotide substitution within rocA, which generated an amber termination codon.Mucoid (MTB313) and nonmucoid (MTB314) strains of group A streptococcus We performed comparative genomics based on whole-genome sequencing of both GAS strains to comprehensively identify the naturally occurring nucleotide substitutions.We identified mucoid (MTB313) and nonmucoid (MTB314) strains of group A streptococcus (GAS) http://www.migap.org/). The sequences from MTB313 and MTB314 were analyzed for the detection of local and structural variations compared to those of MGAS5005 (a virulent type strain of emm1 GAS) . All operations were carried out according to the protocols provided by the manufacturer. A putative annotation of the genome sequence was made using the Microbial Genome Annotation Pipeline , which generated an amber chain-termination codon (UAG) at the 155th amino acid position (accession no. AB737848). In contrast, the same nucleotide sequences of rocA were detected in both MTB314 (accession no. AB737849) and MGAS5005 (gene ID 3571595).The genome sizes of MTB313 and MTB314 were smaller than the previously completed genomes (1.84 Mbp in average size) of four other covR-covS , a two-component regulatory system , influences the expression of chromosomal genes of GAS (rocA has been reported to be a positive regulator of covR (rocA of serotype M18 GAS exhibited structural homology to the catalytic domain of the Escherichia coli osmoregulator envZ. Although rocA was shown to positively enhance covR transcription, quantitative proteomics revealed that rocA was a metabolic regulator with activity beyond the covR-covS regulon. A naturally occurring truncation of rocA contributed to the hyperencapsulation phenotype, led to prolonged nasopharyngeal carriage of GAS in mice, and promoted bacterial airborne transmission (hasA expression through the suppression of covR expression by the depression of rocA.s of GAS \u20137. covR of covR . Recentl of covR demonstrsmission . These rAP014572 and AP014585, respectively.The complete whole-genome sequences of MTB313 and MTB314 were registered to the DDBJ/ENA/GenBank database under the genome project data accession numbers"} +{"text": "Petunia hybrida (line W115) was conducted. A microarray carrying 24,816 unique, non-redundant annotated sequences was hybridized to probes derived from different stages of AR formation. After exclusion of wound-responsive and root-regulated genes, 1,354 of them were identified which were significantly and specifically induced during various phases of AR formation. Based on a recent physiological model distinguishing three metabolic phases in AR formation, the present paper focuses on the response of genes related to particular metabolic pathways. Key genes involved in primary carbohydrate metabolism such as those mediating apoplastic sucrose unloading were induced at the early sink establishment phase of AR formation. Transcriptome changes also pointed to a possible role of trehalose metabolism and SnRK1 (sucrose non-fermenting 1- related protein kinase) in sugar sensing during this early step of AR formation. Symplastic sucrose unloading and nucleotide biosynthesis were the major processes induced during the later recovery and maintenance phases. Moreover, transcripts involved in peroxisomal beta-oxidation were up-regulated during different phases of AR formation. In addition to metabolic pathways, the analysis revealed the activation of cell division at the two later phases and in particular the induction of G1-specific genes in the maintenance phase. Furthermore, results point towards a specific demand for certain mineral nutrients starting in the recovery phase.To identify specific genes determining the initiation and formation of adventitious roots (AR), a microarray-based transcriptome analysis in the stem base of the cuttings of Adventitious root formation (AR formation) is the key developmental process for asexual propagation of most ornamental plants. Adventitious roots arise from tissues other than the root pericycle Focusing on physiological bottlenecks in the rooting zone of the stem base in relation to anatomical events, we defined three metabolic phases of AR formation: (1) the sink establishment phase (SEP), described by apoplastic unloading of sucrose as reflected by induced expression and high activity of cell wall invertase, (2) the recovery phase (RP), indicated by replenishment of resources and (3) the maintenance phase (MP), in which a steady state is maintained via symplastic unloading of sucrose Pinus contorta hypocotyls which were treated with the auxin indole-3-butyric acid. The respective gene products were involved in protein synthesis and degradation, auxin transport, photosynthesis, cell division or cell wall synthesis Arabidopsis led to the identification of eleven proteins including auxin-related and light-related proteins which positively or negatively correlated with adventitious root formation and could be suitable as molecular markers With respect to the wide range of sugars, enzymes and intermediates shown to influence AR formation or to correlate with root formation in stem cuttings, omics-approaches aiming at describing global changes are of particular advantage. Gas chromatography-mass spectroscopy (GC-MS) and liquid chromatography-mass spectroscopy (LC-MS) have been successfully used to detect changes in metabolite contents during AR formation P. hybrida as a model species to study molecular and physiological events in adventitious rooting of leafy stem cuttings Petunia hybrida and to describe the series of physiological processes during adventitious rooting, a microarray analysis was conducted. The microarray was described by Breuillin et al. The features of Petunia genus as an ornamental plant of high economic importance and its extensive uses as a model system Petunia hybrida cv. Mitchell were used for all experiments. The process for production of cuttings and growth conditions were performed as described 2 and stored at -80\u00b0C for further analyses. In order to determine early regulatory changes, materials were harvested at the eight most striking physiological time points of the cuttings at various developmental stages as described by Logemann et al. Total RNA from different developmental stages of cutting stem bases and control tissues (leaves and roots) were extracted using QIAGEN kit . After DNase treatment following the protocol of the DNase supplier (Qiagen), 20 \u00b5g of total RNA was used for probe synthesis and hybridization of the microarray . Normalized expression values of different time points (0 hpe - 192 hpe) were compared with 0 hpe. Significantly up- or down-regulated genes were recognized via Rank Product (RP) analysis The transcript levels of seven genes that were significantly induced during different developmental phases in the microarray experiments were confirmed by real-time PCR. RNA from three replicates of five different time points was isolated from stem bases of cuttings according to Logemann et al. http://pgrc.ipk-gatersleben.de/cr-est/index.php; In order to enrich the existing petunia databases by sequences from genes expressed during adventitious root formation a normalized cDNA library was generated based on pooled RNA extracted from cutting ends at particular time points . From 4700 EST's, 1,964 (42%) were singletons and 2,736 (58%) had a consensus sequence with an average sequence length of 561 bp. Annotation of sequences showed that 607 belonged to genes putatively encoding proteins which were clustered into different categories using the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway databases . The larhttp://pgrc.ipk-gatersleben.de/petunia_array). Besides, all sequences are provided under the following URL for download: http://pgrc.ipk-gatersleben.de/petunia_array/download/. Automatic BLAST runs showed 17,282 sequences being similar to entries in the NCBI NRPEP and/or the Arabidopsis TAIR8PEP databases. In order to enable convenient processing of the information derived from the screening of the microarrays, one specific gene function was assigned to each unigene by curating the BLAST results. These functions were subsequently grouped into thirteen major categories .Basis for the current study on AR formation in petunia was a database of 24,816 unigene sequences including the 4,700 ESTs from cuttings and a corresponding microarray which was previously used to analyse phosphate-regulation in mycorrhiza P values assigned to each effect based on the Rank Product (RP) analysis, were plotted against each other transcript which catalyzes the first step in proline catabolism in mitochondria was up-regulated about 3-fold in this phase, whereas transcripts encoding zinc/iron transporters and phosphate transporters were down regulated or remained unchanged during the first six hours after excision. Moreover, a transcript encoding ribonucleotide reductase was repressed, while a 3-hydroxyacyl-CoA dehyrogenase-encoding gene involved in \u03b2-oxidation was up-regulated in this phase. As components of signaling pathways, transcript abundances of sucrose non-fermenting 1- related protein kinase (SnRK1), transducin family protein/WD-40 repeat family protein and inositol-1,4,5-triphosphate-5-phosphatase were up-regulated up to two-fold only in this phase. Focusing on amino acid and N metabolism, the results showed an approximately 2-fold up-regulation in the expression of a transcript encoding S-adenosylmethionine synthase (SAMS) during SE phase.Among the genes specifically induced during AR formation, 544 genes were up-regulated and 71 genes down-regulated three days post excision. Transcripts involved in primary metabolism such as phosphoenolpyruvate (PEP) carboxylase, glutamine synthetase and enoyl-CoA hydratase were up-regulated at 72 hpe. However, transcripts encoding intermediates involved in trehalose metabolism were no longer induced in this phase as well as apoplastic invertase. Furthermore, genes involved in chromatin and DNA metabolism, cytoskeleton, cell cycle and mineral nutrient transport started to be highly up-regulated in this developmental stage. In particular, phosphate transporter (PT) and zinc/iron transporter-encoding (Zn/Fe-T) genes showed about up to five and seven-fold up-regulation, respectively . In addi. Furthermore, different types of peroxidases, P5CDH, UMP synthase, and cyclin family of cell cycle regulators accumulated at 72 hpe and continued to remain at an elevated level (about 2-fold) until 192 hpe. Interestingly, transcripts encoding various types of Cyclin D were induced up to approximately 1.5-fold only in M phase. In addition, transcripts encoding extensin and a plasma membrane proton ATPase were up-regulated in this phase, exclusively.A group of 459 genes were up-regulated and 81 genes down-regulated eight days after excision of the cuttings from the stock plant, but were not higher expressed in roots than in leaves. In general, most genes showed a similar expression pattern in the R and M phases. Likewise, transcripts encoding important mineral nutrient acquisition genes, such as transporters for metals, zinc/iron, phosphate or nitrate, were highly up-regulated up to 7-fold at 192 hpe . FurtherPetunia hybrida. These time points exemplified the three metabolic phases which have been identified before A cutting removed from the donor plant undergoes various anatomical changes accompanied by alterations in gene expression patterns during the wound response and subsequent rhizogenesis. To investigate the occurrence and temporal sequence of specific gene expression changes during AR formation, different time points after taking the cutting were analysed using the model plant A three-phase mechanism for the metabolic response involved in AR formation in petunia has been postulated Based on the data derived from gene functional classification of the current study, different genes were shown to be up- or down-regulated in three phases of AR formation in different metabolic pathways which interestingly supported our previous data and additionally revealed new findings.Approximately 17% of the known and functionally classified AR formation-regulated genes were related to primary metabolism. Except those involved in nucleotide metabolism, the majority was induced during the SE phase followed by a repression afterwards.Transcript levels of apoplastic invertase and monosaccharide transporters accumulated at 6 hpe followed by a reduction during the recovery and maintenance phases. This is a possible indication for a switch from apoplastic to symplastic phloem unloading of sucrose during AR formation and is in agreement with previous findings The transcript levels of three out of total ten enzymes involved in glycolysis were specifically induced during AR formation in petunia cuttings. This observation is in agreement with biochemical results regarding the enzymes involved in glycolysis Trehalose metabolism, a short side-branch of primary carbon metabolism which is controlled by a large gene family, is emerging as an important new regulatory pathway in plants The present transcriptome study suggests an active lipid metabolism in petunia cuttings especially during the SE phase. Transcript levels of two enzymes involved in plant peroxisomal fatty acid \u03b2-oxidation including 3-hydroxyacyl-CoA dehyrogenase and enoyl-CoA hydratase were induced during early and later stages of AR formation, respectively. Beyond its role in the breakdown of storage lipids, \u03b2-oxidation in plants has been shown to be active in a variety of other developmental processes, including the emergence of the radicle from the seed coat, embryo and flower development, production of jasmonic acid (JA) in the wound response or generation of the phytohormone indole-3-acetic acid (IAA) 2 during C4 photosynthesis and Crassulacean Acid Metabolism (CAM), PEP carboxylase (PEPC) functions anaplerotically in a variety of non-photosynthetic systems such as for C/N partitioning in C3 leaves, seed formation and germination, or ripening ArabidopsisBesides its cardinal roles in the initial fixation of atmospheric COThe degradation of proline is catalyzed by the sequential action of two mitochondrial enzymes, Pro-dehydrogenase (ProDH) and P5C-dehydrogenase (P5CDH). Transcript levels of ProDH, also known as proline oxidase (POX), which is catalyzing the rate-limiting oxidation/dehydrogenation of proline to pyrroline-5-carboxylate (P5C) Pinus contortaP. contortaA transcript encoding S-adenosylmethionine synthase (SAMS) was also induced in the SE phase, which is in agreement with earlier investigation showing that two SAMS-encoding genes were induced during adventitious root development in 4 were up-regulated in the R and M phases indicating an induction of the cell cycle during the late phases of AR formation. Similar observations were reported for AR formation in Pinus contortacyclin B1 gene showed a similar time-dependent pattern during AR formation 1 phase of the cell division cycle in response to extracellular signals such as auxin, cytokinin or sucrose cyclin D as a specific marker for the M phase of AR formation in petunia cuttings.In total, 29 genes specifically induced during AR formation in petunia cuttings are involved in chromatin and DNA metabolism. The number of up-regulated genes in this category was higher in the R and M phases of AR formation in comparison to the first six hours after excision, while no genes were down-regulated. The same expression pattern was observed for a total of 15 genes involved in the class of cytoskeleton-related functions. In addition, the number of up-regulated genes involved in cell cycle processes increased during AR formation, while the opposite trend was observed for down-regulated genes. These results indicate an increase in the induction of chromatin and DNA metabolism, cell cycle and cytoskeleton-related genes starting 72 hours after excision which coincided with the previous reports of formation of new meristematic cells at 72 hpe in the stem base of petunia cuttings Regarding ribonucleotide synthesis, a transcript encoding ribonucleotide reductase (RNR) was down-regulated in the sink establishment phase followed by an up-regulation in the recovery and maintenance phases. RNR catalyzes the rate-limiting step in the production of deoxyribonucleotides needed for DNA synthesis Nutrition is a key factor of root morphogenesis through effects on primary root length or lateral root formation Transcript levels of several nitrate transporters (NT) were induced during AR formation. Some transporter genes were induced in the SE phase (up to 5-fold) and also in the R and M phases . The indi) acquisition when Pi is limited. One of the main strategies is to increase the expression of high-affinity Pi transporters Plants have evolved sophisticated metabolic and developmental strategies to maximize inorganic phosphate , beta oxidation pathway, mineral nutrient acquisition, sucrose unloading process as well as SnRK1 or SAMS.Figure S1Anatomy of adventitious root formation in the stem base of the examined Petunia cuttings. Different magnifications of a cross section at 72 hpe showing the cortex (co), the pith parenchyma (pi) and a ring of vessels (r) with the outer phloem (oph), the cambium (ca), the xylem (xy), the inner phloem (iph) and the first meristematic cells (mc) of developing root meristems, i.e. small cells with a dense cytoplasm and large nuclei. (C\u2013F) Cross sections, revealing at 96 hpe (C) first developing root meristems (me), at 144 hpe (D) first differentiating root primordia with an organized meristem and a backward differentiation of cells of the root body (root cortex (ro) and vascular bundle (v)) and at 192 hpe first roots with vascular bundles (v) surrounded by elongated cells (ec) of the elongation zone and root hairs (rh). Indicated bars represent 500 \u00b5m for A and E, 200 \u00b5m for F and 100 \u00b5m for B, C and D.(TIF)Click here for additional data file.Table S1Gene-specific primers for Real-Time qPCR. Analysis was carried out using actin as housekeeping gene. All Real-Time qPCR reactions were repeated three times.(DOCX)Click here for additional data file.Table S2Annotations and categories. (S2a) Annotations: Based on BlastX searches in the NCBI and the TAIR peptide non redundant databases and on information of the Pfam protein family and the BRENDA enzyme database, one particular function was annotated to each sequence identifier and classified into functional categories. (S2b) Category abundance: Number of genes grouped in different functional categories are shown.(XLSX)Click here for additional data file.Table S3Expression values and ratios. (S3a) All expression and corresponding mean values. Arrays were hybridized to complex cDNA probes derived from stem bases 0 hours up to 192 hours post excision (hpe) of the cutting as well as from fresh leaves (FrL), from wounded leaves (WL) and from a root system (Root). Shown are means of expression values from 3 to 4 biological repetitions. (S3b) Expression ratios for all sequence identifiers. M-values (Log2 of expression ratios) are shown for comparisons of expression values of the Sink establishemnt phase (6 hpe), the Recovery Phase (72 hpe) and the Maintenance Phase (192 hpe) to the expression values at 0 hpe, as well as the comparison of fresh leaves (FrL) to wounded leaves (WL) and from root systems (Root) to cuttings at 192 hpe. M-values for putative genes being more than 2-times induced or repressed and where the differences are significant according to Rank Product Analysis are highlighted in red or in green, respectively . (S3c) Expression ratios for all AR formation-specifically regulated putative genes. M-values (Log2 of expression ratios) are shown for thos sequence identifiers belonging to putative genes induced or repressed during the Sink establishment phase (6 hpe) and not regulated by wounding, and during the Recovery Phase (72 hpe) or the Maintenance Phase (192 hpe) and not differentially expressed in the comparison roots versus shoot basis. M-values for putative genes being more than 2-times induced or repressed and where the differences are significant according to Rank Product Analysis are highlighted in red or in green, respectively . (S3d) Number of down- or up-regulated genes specifically induced during different phases of AR formation in petunia cuttings in each individual category. SEP: Sink Establishment Phase, RP: Recovery Phase, MP: Maintenance Phase.(XLSX)Click here for additional data file."} +{"text": "Personal exome and genome sequencing provides access to loss-of-function and rare deleterious alleles whose interpretation is expected to provide insight into individual disease burden. However, for each allele, accurate interpretation of its effect will depend on both its penetrance and the trait's expressivity. In this regard, an important factor that can modify the effect of a pathogenic coding allele is its level of expression; a factor which itself characteristically changes across tissues. To better inform the degree to which pathogenic alleles can be modified by expression level across multiple tissues, we have conducted exome, RNA and deep, targeted allele-specific expression (ASE) sequencing in ten tissues obtained from a single individual. By combining such data, we report the impact of rare and common loss-of-function variants on allelic expression exposing stronger allelic bias for rare stop-gain variants and informing the extent to which rare deleterious coding alleles are consistently expressed across tissues. This study demonstrates the potential importance of transcriptome data to the interpretation of pathogenic protein-coding variants. cis-acting regulatory variation. Distinguishing allelic activity is important for informing the abundance of altered mRNA and protein products. Advances in sequencing technologies allow us to quantify patterns of allele-specific expression (ASE) in different individuals and cell-types. Previous studies have identified patterns of ASE across human populations for single cell-types; however the degree of tissue-specificity of ASE has not been deeply characterized. In this study, we compare patterns of ASE across multiple tissues from a single individual using whole transcriptome sequencing (RNA-Seq) and a targeted, high-resolution assay (mmPCR-Seq). We detect patterns of ASE for rare deleterious and loss-of-function protein-coding variants, informing the frequency at which allelic expression could modify the functional impact of personal deleterious protein-coding across tissues. We demonstrate that these interactions occur for one third of such variants however large direction flips in allelic expression are infrequent.Gene expression is a fundamental cellular process that contributes to phenotypic diversity. Gene expression can vary between alleles of an individual through differences in genomic imprinting or Recent genome sequencing studies have highlighted that healthy individuals carry multiple loss-of-function and rare deleterious variants whose interpretation is expected to inform individual disease risk and facilitate precision medicine In this study we investigated patterns of gene expression and ASE for rare deleterious and loss-of-function variants across multiple tissues using both RNA-Seq and mmPCR-Seq, a targeted and high-resolution sequencing assay for measuring allelic ratios To map patterns of ASE for deleterious and loss-of-function coding variants, we sequenced the exome from two tissues and RNA from ten tissues from a single individual. From the exome data, we identified 51,875 SNPs, of which 45,058 had consistent genotypes across tissues and were defined as \u201chigh-confidence\u201d variants . We idenp is the empirical probability that a reference allele maps to the genome compared to a non-reference allele across all sites (http://montgomerylab.stanford.edu/resources.html.We performed RNA sequencing (RNA-Seq) for each tissue , S2, S3 ll sites . Qualityll sites . The detR>0.93). The tissue with the lowest reproducibility is the pancreas (R>0.70), which contains a high concentration of nucleases and other enzymes that can degrade RNA. The variability of effect size between the replicates was also quantified for each tissue at varying read depths . Likewise, the frontal lobe and cerebellum, which are both neural tissues derived from the ectoderm, have a high degree of shared gene expression (R\u200a=\u200a0.91). To test the degree of correlation of allelic expression across tissues, we measured concordance of allelic ratios between pairwise tissues using the high-depth mmPCR-Seq data. Here, allelic ratios are defined as the ratio of the non-reference allele to the sum of the non-reference allele and the reference allele. We observed that the concordance of ASE between tissues does not as strongly reflect the relationships seen for shared gene expression or shared embryonic origin (R\u200a=\u200a0.80). We also compared in detail the pairwise correlation coefficients for expression and allelic ratios for tissue pairs of highly similar embryonic origin that showed monoallelic expression across all testable tissues (N\u22655) in the RNA-Seq data. Two of these genes were mono-allelically expressed across all ten tissues: NDN, which is a known maternally imprinted gene We also investigated the sharing of monoallelic expression across tissues . We iden2<0.2) of the allelic ratios for all tissues tested. Variants were classified as shared ASE sites if they had a significant p-value (p<0.01), an imbalanced mean allelic ratio , and non-variable allelic ratios (\u03c32<0.2) across all tissues. Lastly, variants were classified as variable (tissue-specific) ASE sites if they had a significant p-value (p<0.01) and variable allelic ratios (\u03c32>0.2) across tissues. The reproducibility of the groups between replicates was tested at varying allelic ratio and variance cut-offs , which is associated with the Mendelian disease Muckle-Wells Syndrome (OMIM 191900) and associated with inflammasome function and immune responses. The single deleterious site that demonstrates variable ASE is a gene encoding a protocadherin (PCDHA13). In the skeletal muscle and heart, the deleterious allele exhibits greater expression than the normal allele, but in the liver and colon the deleterious alleles exhibits less expression. Of interest, PCDHA13, which is known to play a critical role in establishing specific cell-cell connections in the brain, shows no strong patterns of ASE in the two disease-relevant neural tissues, frontal lobe and cerebellum. While the consequences of allelic expression of this individual's deleterious alleles are unknown, different patterns of allelic expression across tissues highlight the potential importance of testing multiple tissues to better elucidate the functional context of rare, deleterious alleles.By focusing on patterns of ASE for rare deleterious variants in this individual, we identified 40 sites corresponding to 40 unique genes which were quantified by mmPCR-Seq across three or more tissues. Of these genes 28 exhibited no ASE across tissues, 11 exhibited shared patterns of ASE across tissues and 1 exhibited variable ASE . We nextp<0.05, student's t-test). This observation has been previously reported in a single cell-type, with a possible explanation for this phenomenon being that lowly-expressed alleles can better tolerate the fitness impact of deleterious protein-coding alleles Loss-of-function alleles that introduce premature stop codons have been identified to exhibit patterns of allelic expression indicating nonsense-mediated decay (NMD) In conclusion, despite the feasibility of sequencing individual genomes, the functional impact of potentially pathogenic protein-coding variants remains difficult to ascertain by DNA sequencing or computational prediction methods alone. The incorporation of transcriptome data can enhance the interpretation of such variants by providing insight into their patterns of ASE. We demonstrate the advantage of ASE for interpretation of pathogenic protein-coding allele by generated high resolution measurements of ASE for these variants across multiple tissues. Such data enables us to identify the extent to which these alleles are modified by regulatory effects and the extent to which this effect is detectable across tissues. We highlight as many as a 1/3 of all deleterious alleles are imbalanced and that nonsense alleles show characteristic and consistently lower expression across multiple tissues. Ultimately, by coupling interpretation of personal genomes with their corresponding transcriptomes, these results highlight that it may be possible to better understand the impact of pathogenic protein-coding variants within different tissues of an individual.In order to investigate the differential allelic effects of divergent tissues in a single individual, we obtained the genomic DNA and RNA for ten somatic tissues from Biochain Institute, Inc . The samples were collected post-mortem from a healthy 25-year-old male with no significant medical history.http://picard.sourceforge.net/) with base quality score recalibration and local realignment at known indels and BWA Genomic DNA from the frontal lobe and small intestine were prepared for exome sequencing. The enrichment of targeted regions was performed using the Agilent SureSelect Human All Exon 50\u2009Mb Kit following the manufacturer's recommended protocol. Paired-end libraries were constructed using the Illumina Paired End Sample Prep Kit following the manufacturer's instructions and sequencing was carried out using the Illumina HiSeq 2000 platform . Exome sequence data was processed through a pipeline based on Picard (Paired-end RNA-Seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation kit. PolyA+ RNA was isolated using Sera-Mag oligo(dT) beads (Thermo) and fragmented with the Ambion Fragmentation Reagents kit. Complementary DNA (cDNA) synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina's protocol. Each sample was barcoded and all samples were sequenced on one lane of the Illumina HiSeq 2000 platform (2\u00d7100-nt read length). In total, we obtained 13.3\u00b13.7 (mean \u00b1 SD) million paired end reads per sample. We assessed the sequence quality using the publicly available software FastQC. For each sample, we examined per-base quality scores across the length of the reads to ensure that >95% of the reads had >Q60 for bases 1\u2013100. Reads were mapped by TopHat (version 2.0.0) to the known transcriptome the human reference genome (hg19) using default parameters To quantify allele-specific expression at lowly expressed site, we applied a high-throughput method that couples microfluidics-based multiplex PCR and deep sequencing (mmPCR-Seq) http://montgomerylab.stanford.edu/resources.html). First, mapped reads were sorted using the Samtools (version 0.1.7) p to be the empirical probability of observing a reference versus non-reference allele across all sites. A significance cut-off of 0.05 and 0.01 were used for the RNA-Seq and mmPCR-Seq data, respectively.Allele-specific expression was determined on a per-heterozygote-site per-tissue basis using the pipeline depicted in http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE51769. The code for ASE detection pipeline can be found online (http://montgomerylab.stanford.edu/resources.html).The raw mmPCR-seq data has been submitted to the NCBI Gene Expression Omnibus (GEO) and read 2 (right). The y-axis is the average quality value, the x-axis is the base position, and each colored line represents a corresponding tissue sample as indicated by the legend (far right).(TIF)Click here for additional data file.Figure S2Mapping RNA-Seq reads. For all tissues except the stomach, \u223c90% of the reads mapped uniquely to the human genome. Reads under 20 bp were unmapped and reads that mapped to multiple regions of the genome (multi-mapping reads) were discarded for future analysis.(TIF)Click here for additional data file.Figure S3Reference mapping bias distributed by base quality scores. The reference to non-reference mapping bias for each tissue exhibits no distinct patterns with respect to specific tissue sample or base quality scores.(TIF)Click here for additional data file.Figure S4Pipeline for the detection of allele-specific expression.(TIF)Click here for additional data file.Figure S5Distribution of allele-specific expression for RNA-Seq. Density plots illustrate the distribution of the alternate allele ratio for each tissue for all heterozygous sites that are expressed. The alternate allele ratio was calculated from RNA-Seq reads as the fraction of alternate allele reads divided by the total reads. In ASE analyses using RNA-Seq reads, it is important to evaluate if mapping bias exists that results in the favoring of reads harboring the reference allele at heterozygous sites. In the absence of mapping bias, the average allelic ratio is expected to be 0.5, assuming that ASE is exhibiting in a minor fraction of heterozygous sites.(TIF)Click here for additional data file.Figure S6Quality control filtering of ASE sites. The identification of ASE sites from RNA-Seq data required quality control filter to identify high-confident sites. The x-axis shows the reference to non-reference mapping ratio for each sample and the y-axis shows the percentage of ASE sites remaining after each quality-control filter. The base quality and read depth filters resulted in a modest (\u223c10%) reduction in ASE sites. The p-value (p<0.05), bi-allelic expression, and intragenic location filters removed over 50% of the sites for each tissue. The proportion of sites removed after each filter shows no correlation with the reference to non-reference mapping bias for the RNA-Seq samples.(TIF)Click here for additional data file.Figure S7Selection of LoF sites for mmPCR-Seq testing. Rare and deleterious nonsynonymous SNPs were selected for testing by mmPCR-Seq. Rare and deleterious nsSNPs are defined as SNPs not observed in dbSNP, 1000Genomes, or ESP, and annotated as damaging and deleterious by SIFT and POLYPHEN. The nonsense variants selected for testing were identified as variants that affect every full transcript in the gene.(TIF)Click here for additional data file.Figure S8mmPCR-Seq reads by tissue. Two technical replicates of mmPCR-Seq were performed for each tissue. Since we have observed very high concordance of allelic ratios between technical replicates using mmPCR-Seq, the reads from each replicate were merged.(TIF)Click here for additional data file.Figure S9Mapping mmPCR-Seq reads. The total reads generated per tissue from the mmPCR-Seq experiments were mapped to the reference genome using the STAR aligner. For every tissue sample, approximately 98% of the reads mapped uniquely to the reference genome.(TIF)Click here for additional data file.Figure S10Correlation of effect size for mmPCR-Seq technical replicates. Two technical replicates of mmPCR-Seq were performed and the ASE effect size was quantified. For each tissue, the effect size for each technical replicate was plotted to demonstrate the correlation between technical replicates for mmPCR-Seq.(TIF)Click here for additional data file.Figure S11Variance of effect size for mmPCR-Seq technical replicates. The absolute difference in effect size between the two replicates for each tissue is plotted at varying read depth. At higher read depths, there is less variability between replicates. However, even at low read depths (<200), the variability is low for most tissues, except for the pancreas and frontal lobe, which are known to have low RNA quality post-mortem.(TIF)Click here for additional data file.Figure S12A) Comparison of read depth at heterozygous variants using RNA-Seq and mmPCR-Seq data. The tested heterozygous sites have consistently deeper coverage using mmPCR-Seq. (B) Comparison of ASE detection using RNA-Seq and mmPCR-Seq data. The comparison of p-values obtained from the ASE binomial test for matching heterozygous sites indicates increased enrichment for significant ASE effects using mmPCR-Seq.Comparison of coverage of LoF variants using different technologies. ((TIF)Click here for additional data file.Figure S13Distribution of alternate allele ratio and corresponding p-value for sites tested by mmPCR-Seq.(TIF)Click here for additional data file.Figure S14Pairwise correlation of expression and allelic effect for similar tissues. The Spearman correlation coefficient was determined for the pairwise comparisons of neural tissues and intestinal tissues for both expression and allelic effect. Independent of read depth, the correlation of expression for tissues of similar embryonic origin are consistently greater than the correlation of allelic effect.(TIF)Click here for additional data file.Figure S15Distribution of alternate allele ratio across tissues from mmPCR-Seq. The alternate allele ratio was calculated for each heterozygous site tested by mmPCR-Seq in all tissues. As expected, the majority of heterozygous sites have an alternate allele ratio of 0.5. For sites with ASE, there appears to be an equal distribution of expression bias towards both the alternate allele (upper left tail) and reference allele (lower right tail). Interestingly, we observed that some sites had measurably varied alternate allele ratios across tissues, while other tested sites had a consistent alternate allele ratio across tissues.(TIF)Click here for additional data file.Figure S16Reproducibility of ASE groups for mmPCR-Seq technical replicates. The reproducibility of the groups depicted in (TIF)Click here for additional data file.Figure S17Distribution of shared and variable ASE for RNA-Seq data. The distribution of mean values and standard deviations of the allelic ratios across tissues from the RNA-Seq data. Genomic loci with no ASE and low variance (red), ASE and low variance (blue), and ASE and high variance (green) were divided into three gene groups: no ASE, shared ASE, and variable ASE, respectively. The proportion of sites falling into each ASE group is similar to that found from the mmPCR-Seq data.(TIF)Click here for additional data file.Figure S18Distribution of effect size and direction of effect for ASE across different tissues. The minimum and maximum alternate allele ratio observed in any tissue for each mmPCR-Seq site tested in at least three tissues are plotted to demonstrate the range of allelic effects observed across tissues.(TIF)Click here for additional data file.Figure S19Relationship of ASE effect size and gene expression. The relationship between ASE effect size (measured by mmPCR-Seq) and gene expression level (measured by RNA-Seq) across all tissues was examined. There is no correlation between allelic effect size and gene expression level. Four lowly expressed sites had low allelic ratios (circled) but were not enriched in any class of variants or influenced calling of variable ASE within the study.(TIF)Click here for additional data file.Figure S20FMO3, which is associated with the rare Mendelian disorder trimethylaminuria (OMIM 602079), exhibits decreased expression of the deleterious allele across tissues. In contrast, gene NLRP3, which is associated with the Mendelian disease Muckle-Wells Syndrome (OMIM 191900), exhibited no ASE across tissues. The gene PCDHA13, which encodes a protocadherin, is an example of a gene with variable ASE across tissues; the deleterious allele is underexpressed in certain tissues and overexpressed in other tissues.Examples of genes with deleterious nsSNPs exhibiting shared, variable, and no ASE. The gene (TIF)Click here for additional data file.Table S1Identification of high-confidence heterozygous and homozygous variants.(PDF)Click here for additional data file.Table S2Identification of high-confidence common and rare variants.(PDF)Click here for additional data file.Table S3Identification of high-confident RNA-Seq ASE sites by quality-control filtering. To identify high-confident ASE sites, we implemented several quality control filters. We only kept ASE sites which met the following criteria: 1) base quality (BQ) greater than 10; 2) minimum sequencing depth of 10 reads; 3) calculated p-value less than 0.05 from the binomial test; 4) bi-allelic expression; and 5) intragenic location.(PDF)Click here for additional data file.Table S4OMIM genes associated with Mendelian disease phenotypes harboring rare deleterious nsSNP variants.(PDF)Click here for additional data file.Table S5Allelic imbalance of deleterious nsSNPs, nonsense variants, and control sites across tissues.(PDF)Click here for additional data file."} +{"text": "Image resolution is a crucial factor for myocardial scar quantification from late gadolinium enhanced (LGE) MR. The conventional usage of anisotropic short-axis LGE volumes may result in overestimation of the scar size, in particular at the gray zone, due to partial volume effect (PVE). This may impact the diagnostic accuracy of LGE in clinical applications.A group of 37 post-infarction patients with ventricular tachycardia (VT), who underwent both MRI and a VT catheter ablation procedure with electro-anatomical voltage mapping (EAVM), were included. LGE imaging was performed using a 3D breath-hold inversion recovery turbo-field echo sequence with full ventricular coverage in three views: short-axis (SA), two-chamber, and four-chamber. The three LGE sequences were combined as follows: 1) The inter-scan heart motion was compensated by a joint localized gradient-correlation-based volume registration scheme; 2) The registered volumes were combined into an isotropic volume by the super-resolution reconstruction (SRR) technique. The SRR reconstructed volumes were compared to conventional SA volume using the following measures: the full-width-half-maxima (FWHM)-identified myocardial scar size in terms of core zone and gray zone; the agreement between the scar zones and the gold-standard EAVM data. The agreement was evaluated by the voltage distribution of the mapping points which were back projected onto the normal myocardium, scar core zone and gray zone.The SRR volume achieved increased resolution in the through-plane direction Figure . CompareWe proposed a method to reconstruct a high-resolution isotropic LGE MR volume from three routinely acquired anisotropic views. Improving the through-plane resolution of LGE leads to more accurate myocardial scar assessment with reduced PVE, especially at the clinically significant gray zone.The work was financially supported by the Dutch Technology Foundation (STW) and EU ITEA2-09039."} +{"text": "Endomicrobium proavitum strain Rsa215, the first isolate of the class Endomicrobia (phylum Elusimicrobia). It is the closest free-living relative of the endosymbionts of termite gut flagellates and thereby provides an excellent model for studying the evolutionary processes during the establishment of an intracellular symbiosis.We sequenced the complete genome of Elusimicrobia phylum form a deep-branching clade of uncultivated bacteria in the a phylum , which i minutum . Members minutum \u20136. Howevminutum \u2013, 8. We itonensis .E.\u00a0proavitum was obtained with Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing. Genomic DNA of strain Rsa215 was prepared using cetyltrimethylammonium bromide (CTAB) extraction . Comparative genome analysis of the two strains will provide a better understanding of the evolutionary processes that started when their common free-living ancestor became associated with its flagellate host.Annotation on the MicroScope platform resultedn Rs-D17 , which in Rs-D17 . Althougn Rs-D17 . The samCP009498.The sequence data for the genome have been deposited in DDBJ/EMBL/GenBank under the accession no."} +{"text": "Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disease associated with a 10-fold increased risk of lung cancer (LC), independent of smoking-status. Together these diseases contribute tremendously to mortality worldwide. Based on the notion that chronic inflammation forms a specific cancer-promoting environment; we hypothesized that COPD and non-COPD related lung tumors are molecularly distinct, and that these differences may yield promising diagnostic and therapeutic targets. Since genes that sustain high-level DNA and RNA alterations are likely selectively altered in tumor systems, we applied an integrative multi-omics analysis to lung tumors from COPD and non-COPD patients. To assess the potential clinical application of these findings, we examined the methylation status of COPD+LC specific genes in non-malignant airways from COPD patients w/LC.Multi-omics profiling was performed on 76 tumor and non-malignant lung tissues using genome-wide array platforms. To identify genes/pathways which sustain high DNA and RNA level changes in tumors, we developed an algorithm to generate \u201cIntegrated Scores\u201d for each gene based on magnitude of concomitant DNA and mRNA alterations. Integrated Scores were applied to all downstream analyses. COPD+LC specific genes were further assessed at the level of DNA methylation in airways from 25 COPD patients w/ and w/out LC.PITX2 -a putative methylation biomarker in LC, previously associated with senescence gene networks in COPD.Gene set and pathway enrichment analyses of genes frequently and differentially disrupted at both DNA and RNA levels in COPD tumors revealed enrichment of transcription factor gene sets involved in inflammation-related cancer, oxidative stress and smoking response; the most significant being CCNDBP1, HPGD), genes associated with oxidative response and COPD progression (PPARGC1A) and biosynthesis of SAM (MAT2B).Pathways specifically disrupted in COPD tumors included those involved in inflammation , DNA damage and synthesis of the methyl-donor, S-Adenosyl-methionine (SAM) - a critical cofactor involved in DNA and histone methylation. Five COPD+LC specific genes were also altered at the DNA methylation level in non-cancerous airways of COPD patients w/LC, including putative cancer epigenetic diagnostic biomarkers (Genetic and epigenetic disruptions in lung tumors and small airways of patients with COPD and LC are distinct from those in corresponding tissues from patients w/COPD or LC alone. Genes altered in airways and involved in lung tumorigenesis in COPD patients may serve as clinically relevant markers for predicting LC or as targets for chemoprevention therapies."} +{"text": "Drosophila embryo results in defective hearts with missing hemisegments. This process is mediated by the Forkhead TFs regulating the fibroblast growth factor receptor Heartless (Htl) and the Wnt receptor Frizzled (Fz): CHES-1-like and jumu exhibit synergistic genetic interactions with htl and fz in CM specification, thereby implying that they function through the same genetic pathways, and transcriptionally activate the expression of both receptor-encoding genes. Furthermore, ectopic overexpression of either htl or fz in the mesoderm partially rescues the defective CM specification phenotype in embryos lacking both Forkhead genes. Together, these data emphasize the functional redundancy that leads to robustness in the cardiac progenitor specification process, and illustrate the pleiotropic functions of Forkhead TFs in different aspects of cardiogenesis.Cardiogenesis involves the coordinated regulation of multiple biological processes by a finite set of transcription factors (TFs). Here, we show that the Forkhead TFs Checkpoint suppressor homologue (CHES-1-like) and Jumeau (Jumu), which govern cardiac progenitor cell divisions by regulating Polo kinase activity, play an additional, mutually redundant role in specifying the cardiac mesoderm (CM) as eliminating the functions of both Forkhead genes in the same Summary: Checkpoint suppressor homologue and Jumeau, which are known to govern cardiac progenitor cell divisions, play additional, mutually redundant roles in specifying cardiac mesoderm in Drosophila. Drosophila exhibits remarkable similarities to the vertebrate heart at the primitive linear tube stage of development in terms of structure, morphogenetic origins and regulatory mechanisms and become determined as the cardiac mesoderm (CM), i.e. the cardiac progenitors that are the precursors of the embryonic heart. Subsequent refinement and modulation of these gene expression programs bring about the division and differentiation of these CM cells into distinct cardiac subtypes, such as the inner tube of Myocyte enhancer factor 2 (Mef2)-expressing contractile cardial cells (CCs) and the external sheath of Zn finger homeodomain 1 (zfh1)-expressing nephrocytic pericardial cells (PCs) in Drosophila.The rhythmically contracting heart of chanisms . In bothCardiogenesis thus requires the integration of multiple signaling pathways and transcription factor-mediated gene expression programs to orchestrate diverse developmental processes. This raises two intriguing questions: how are the numerous complex processes involved in cardiogenesis orchestrated by a finite set of regulators, and how is the requisite coordination between these distinct regulatory mechanisms achieved?Drosophila is the Forkhead (Fkh/Fox) domain family of proteins. At least four Fkh TFs are known to be required for proper cardiac development in mammals, and mutations in three Fkh genes have been linked to human congenital heart defects and Checkpoint suppressor homologue (CHES-1-like). Both genes are initially maternally expressed, with jumu and CHES-1-like showing subsequent zygotic expression in the cells fated to become the CM from embryonic Stages 11 to 13, and from Stages 11 to 12, respectively. Each of these two Fkh genes determines cardiac cell subtypes, numbers and positions by regulating a Polo kinase-dependent pathway to mediate three distinct categories of cardiac progenitor cell divisions (One family of transcription factors (TFs) that has been implicated in cardiogenesis in both vertebrates and defects . We haveivisions , 2012. Iivisions . Collectjumu and CHES-1-like also play a significant role in specifying the CM, and that this process is achieved by the Fkh TFs transcriptionally regulating Heartless (Htl), which is a fibroblast growth factor receptor (FGFR), and Frizzled (Fz), which is a receptor of the Wingless/Wnt signaling pathway.Here, we show that the Fkh genes jumu null deficiency Df(3R)Exel6157 or the CHES-1-like null mutation 1Df(1)CHES-1-like exhibit hemisegments with localized increases or decreases in CC number, occasional enlarged CC nuclei, or mispositioned CCs as a consequence of defective cardiac progenitor cell divisions when compared with wild-type embryos (P=0.0002) of embryos lacking both jumu and CHES-1-like functions exhibits a more severe phenotype that never occurs in embryos missing just one of these two Fkh genes: 16.25% of embryos that were doubly homozygous for both the jumu null deficiency and the CHES-1-like null mutation exhibit one or more hemisegments missing entire rows of cardial cells . The location of the hemisegments lacking all heart cells was random: no significant difference (P=0.83) was detected in the frequency of this \u2018missing cardiac hemisegments\u2019 (MCH) phenotype between the anterior aorta and the wider posterior section of the heart (Table\u00a0S1).Our previous study showed that embryos homozygous for either the embryos A-C , indicating that the requirement of both these Fkh genes for proper heart development is autonomous to the cells fated to become cardiac progenitors.Similar MCH phenotypes were also observed when both jumu or CHES-1-like for at least two reasons. First, because four of the six CCs in each hemisegment, the Tinman-expressing CCs (Tin-CCs), arise by two symmetric cell divisions from two cardiac progenitor cells of this MCH phenotype was detected when polo was ubiquitously expressed in embryos lacking both jumu and CHES-1-like functions: 19.44% of these embryos exhibited the phenotype . Althougobserved G.htl function phenocopies the MCH phenotype of CHES-1-like; jumu double mutants raised the possibility that htl and the Fkh genes could be acting together to specify the CM. In such a case, strong genetic interactions might occur between either of the Fkh genes and htl. To examine this possibility, we quantified and compared the MCH phenotypes in embryos heterozygous for a htl null mutation, in embryos homozygous for a CHES-1-like null mutation, in embryos homozyogous for a jumu null deficiency, in embryos both heterozygous for the htl mutation and homozygous for the CHES-1-like mutation, and in embryos heterozygous for the htl allele and homozygous for the jumu deficiency than the additive effects of the phenotypes in htl heterozygotes and the CHES-1-like homozygotes (htl mutation and homozygous for the jumu deficiency (P<0.0001) than the additive effects of the htl heterozygotes and jumu homozygotes drives reporter expression in virtually every cardiac hemisegment primarily in the four Tin-CCs . By contrast, mutating the Fkh binding site (resulting in the ChIPCRM2610Fkh enhancer) causes significant reduction (P<0.0001) of enhancer-driven reporter expression, with many hemisegments (11.90%) showing no cardiac reporter expression at all, and an overall decrease in the mean number of Tin-CCs per hemisegment in which the reporter is expressed from 3.79 to 2.52 .As the trans. Embryos lacking either CHES-1-like or jumu exhibited reporter expression driven by the wild-type ChIPCRM2610WT enhancer that was not significantly different from that in wild-type embryos in the number of cells with visible reporter expression, with expression being limited to a mean of 2.45 Tin-CCs per hemisegment, and 13.33% of the hemisegments examined showing no cardiac expression between these double homozygotes bearing the ChIPCRM2610WT enhancer and otherwise wild-type embryos bearing the ChIPCRM2610Fkh enhancer that the CHES-1-like and Jumu TFs activate htl expression in the precursors of the CM by directly binding to the ChIPCRM2610 enhancer, and (2) that either of these two Fkh TFs is sufficient by itself to activate expression in wild-type numbers of cells.Collectively, the convergence of results between these cis and trans analysis of htl expression suggest that CHES-1-like and jumu transcriptionally activate htl expression to bring about proper CM specification. To test this hypothesis, full length Htl . These numbers represent statistically significant over-representations of known cardiac genes among those for which expression is differentially regulated by the Fkh genes, thus confirming that the Fkh TFs do indeed regulate many heart genes.Consistent with the observation that Nidogen , our genhtl is not detected in the microarray data for either CHES-1-like or jumu null mutants alone . The most conservative explanation for this observation is that it reflects the functional redundancy already demonstrated between CHES-1-like and Jumu in regulating htl expression: either of these two Fkh TFs is sufficient by itself to activate wild-type levels of htl expression. Consistent with this explanation, microarray-based genome-wide expression profiling data from mesodermal cells ectopically overexpressing jumu compared with wild type (Table\u00a0S2F).Of note, significant reduction in the expression levels of ing jumu showed ejumu is indeed sufficient to activate htl, then ectopic overexpression of Jumu in the mesoderm would be expected to partially resemble the effects of ectopic overexpression of activated Htl. This result is indeed observed in our expression profiling data: there is significant overlap between genes with significantly elevated expression levels as a consequence of ectopic mesodermal overexpression of the constitutively activated form of Htl .If m of Htl and geneDrosophila and vertebrates also involves other signaling mechanisms besides FGF/FGFR, such as the Wingless/Wnt, Bone morphogenetic protein and Notch pathways (CHES-1-like and jumu null mutants.CM specification in both pathways . This rafrizzled (fz), which encodes a receptor of the Wnt signaling protein Wingless (Wg), had its expression levels significantly reduced in the mesoderm of embryos lacking either CHES-1-like or jumu function compared with wild type . These results indicate that both jumu and CHES-1-like activate fz expression in the mesoderm.We found that fz in the mesoderm would be expected to partially resemble the effects of inhibiting or reducing Wg signaling, such as with null mutations in wg. Expression profiling data on flow cytometry-purified mesodermal cells show that there is indeed significant overlap between genes downregulated in the mesoderm of embryos homozygous for a null mutation in wg or jumu null mutants, thus providing further evidence for the Fkh TF-mediated activation of fz .As Fz is one of the receptors of Wg, reductions in the expression levels of on in wg and genefz transcript at Stages 10-11 due to maternal expression , fail to develop cardiac progenitors significantly greater (P=0.00095) than the additive effects of the phenotypes in CHES-1-like homozygotes and the fz homozygotes (fz hypomorphic mutation and the jumu null deficiency was significantly greater (P=0.00062) than the additive effects of the single fz and jumu homozygotes . Given tan heart , it willCrucial developmental steps are frequently robust and interconnected in order to prevent damage to any one of their constituent genetic components resulting in the overall disruption of the process in which they are involved. This concept is demonstrated at multiple levels by the CM specification process examined in the present study.CHES-1-like and jumu, with either of these genes being able to compensate for defects in the function of the other to mediate normal heart formation. That is, each Fkh TF is individually sufficient to activate the expression of htl to bring about proper FGFR-mediated CM specification, with the absence of either the htl transcript or htl enhancer activity in a hemisegment, as well as the presence of the MCH phenotype, being detected only when both Fkh functions are eliminated in the same embryo.One elegant illustration of this regulatory design feature is the degree of mutual redundancy exhibited by htl enhancer and transcript is reduced but not completely abrogated in embryos lacking both Fkh functions. These observations indicate that additional redundant mechanisms must exist to at least partially maintain htl expression and CM specification in the absence of the Fkh TFs. A preliminary computational analysis we performed using the algorithm PhylCRM the subsequent cell divisions of these cardiac progenitors by regulating the activity of Polo kinase caro kinase . Such plDf(1)CHES-1-like1, Df(3R)Exel6157 and Ubi-polo assays targeted to CM precursors were performed as previously described . UAS-RNAr (VDRC) were expCHES-1-like and jumu cause defective cardiac progenitor cell divisions that result in certain hemisegments having atypical numbers of cells, only hemisegments with the correct number of Tin-CCs were examined and scored in 1Df(1)CHES-1-like embryos, Df(3R)Exel6157 embryos and 1; Df(3R)Exel6157Df(1)CHES-1-like embryos.Embryo fixation, probe synthesis and histochemical staining were carried out as previously described . For alltwi-GAL4 UAS-2EGFP embryos, 1; twi-GAL4 UAS-2EGFPDf(1)CHES-1-like embryos and twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos were obtained by Affymetrix microarray hybridization as described previously (affy Bioconductor package (limma (Microarray-based gene expression profiles for GFP-positive mesodermal cells isolated by fluorescence-activated sorting of single cell suspensions prepared from Stage 11-early Stage 12 eviously . Array d package and linee (limma . The miccis-trans enhancer assays and geneset enrichment is provided in the supplementary materials and methods.A description of the statistical analysis of genetic interaction assays, rescue assays,"} +{"text": "Stroke remains the major non-cardiac complication of coronary artery bypass surgery (CABG). Severe carotid artery disease is associated with a fourfold increase in the risk of post-operative stroke and this is the rationale for offering pre-operative carotid artery screening to these patients.We aim to assess the compliance with the ESC/EACTS guidelines for Myocardial Revascularisation (2014) regarding pre-operative carotid artery disease screening and estimate the clinical impact of adhering only to class-I evidence-based recommendations.The medical records of all the patients who underwent CABG in our unit between 1st November and 31st December 2014 were retrospectively reviewed.A total of 506 patients underwent CABG during the study period and 492 were included for analysis. 203 carotid artery Doppler ultrasound scans were performed. CAD screening was performed in 63/115 of the patients who met with class-I recommendations (history of stroke/transient ischaemic attack or carotid bruit) and 184/440 of the patients who met with class-IIa recommendations .There were 2 post-operative strokes, both in patients without CAD detected on pre-operative screening. Asynchronous carotid artery revascularisation was performed in 5 patients (4 prior to and 1 following CABG).Restricting carotid artery screening to class-I evidence-based recommendations criteria would have decrease the number of Doppler ultrasound scans from 203 to 115, without missing patients with CAD who actually required revascularisation.Adherence to class-I evidence-based recommendations for carotid artery screening would generate major efficiency savings and streamline pre-operative assessment of patients undergoing CABG."} +{"text": "The correlation of the inferior vena cava (IVC) diameter and the internal jugular vein (IJV) diameter with Central Venous Pressure (CVP) was already tested.Few reports compared IVC and IJV ultrasound measures in the same population. No data there are on the correlation of the internal jugular vein diameter and CVP in ventilated patients.To test and compare the correlation of CVP with IVC and IJV maximal diameters, collapsibility and distensibility indexes, IJV ratio in a population of ventilated and spontaneous breathing patients (SBP).This is a cross-sectional study conducted during 2015 in an Italian ICU. We included adult patients with a Central Venous catheter without cerebral ischemia or bradycardia.Ultrasound images of IJV and IVC diameters at end-expiration and at end-inspiration were obtained with the patient supine using a 5-10 MHz and a 1-5 MHz probe .At the same time: we performed a transthoracic echocardiography to evaluate the Left Ventricular Ejection Fraction and the Tricuspid annular plane systolic excursion (TAPSE) as index of Right Ventricular ejection fraction; we calculated the collapsibility index of IVC (IVCDmax - IVCDmin / IVCDmax X 100%) in SBP; the distensibility indexes (IVCDmax - IVCDmin / IVCDmin X 100%) in ventilated patients; the anteroposterior and transverse IJV diameters at end-expiration and the IJV ratio (AP-IJV divided by T-IJV); we collected clinical data . Analyses were performed using the Stata/SE Statistical Software 13.1. The Mann-Whitney test was used to compare variables between patient's groups. Correlations were calculated by means of Pearson or Spearman's rank correlation coefficients.55 patients (12 ventilated and 43 spontaneous breathing) were included. The overall median age was 79 years (range 69-83), SAPS II was 36 (32-48), shock was main admission diagnosis. There were significant differences between patients with CVP \u2264 8 mmHg and those with CVP > 8 mmHg regarding IVCDmax, AP-IJV, IJV ratio . There were no significant differences between ventilated and SBP patients regarding IVCDmax, AP-IJV, IJV ratio. We found a significant positive correlation between IVCDmax and IJV ratio and CVP in ventilated as in SBP . AP-IJV was correlated to CVP in SBP .If our results on the correlation of IVCDmax and IJV ratio with CVP in ventilated and spontaneous breathing patients will be confirmed in future studies, these measures could be use as alternative of CVP, in SBP could be used also AP-IJV. Limitation few ventilated patients."} +{"text": "Here I propose current and future strategies to develop immunoprevention approaches for cancer prevention. A major challenge in the development of effective immunopreventive agents is the recognized requirement for the simultaneous co-development of multiple agents. Infectious agents are linked to approximately 15% to 20% of all cancers worldwide. Viruses are the infectious agents most commonly associated with cancer causation but bacteria and parasites may also have a carcinogenic effect. Oncoviruses include human papillomavirus , Epstein-Barr virus , Kaposi's sarcoma-associated herpesvirus (Kaposi's sarcoma and primary effusion lymphomas), hepatitis B and hepatitis C viruses (hepatocellular carcinoma), and human T-lymphotropic virus-1 (adult T-cell leukemia/lymphoma). Current progress and our development of these areas include prophylactic vaccines and therapeutic vaccines ."} +{"text": "In the natural host (Bos taurus), infection with bovine leukemia virus (BLV) remains mostly asymptomatic, resulting in a benign lymphocytosis only in about one-third of infected animals and even less frequently in a B-cell leukemia/lymphoma (10% of cases). BLV can also be experimentally transmitted to sheep that almost invariably develop leukemia/lymphoma after shorter latency periods. Upon integration, the BLV provirus becomes transcriptionally silent except for the microRNAs that remain very abundantly expressed. We used reverse genetics to evaluate the role of the viral microRNAs in the natural and experimental hosts. A BLV lacking the microRNAs replicated at wild-type levels in sheep, indicating that these sequences were dispensable. Surprisingly, the microRNAs were required for efficient replication in cows, thereby underlining the importance of studying viral determinants in the natural host. To understand the mechanisms associated with the microRNAs, we performed high-throughput RNA-sequencing of transgenic B cell lines and peripheral blood mononuclear cells isolated from cows infected either by wild-type or by isogenic microRNA-deleted viruses. Bioinformatic analyses revealed that BLV microRNAs modulate a series of pathways that include B-cell signaling and immunity. Reporter assays showed that the microRNAs target granzyme A and c-FOS transcripts and downregulate indirectly Annexin A1 and phosphoinositide-3-kinase PIK3CG. Finally, expression of the microRNAs in B-lymphocytes was associated with a decrease in phagocytosis by primary bovine macrophages. These studies thus assign a functional relevance of the BLV microRNAs in viral evasion from the innate immune response in its natural host."} +{"text": "Patients presenting with chest pain, raised troponin but non-obstructive coronary arteries pose a clinical challenge in diagnosis, prognosis and management. We hypothesized that early, multiparametric cardiovascular magnetic resonance (CMR) imaging can localize areas of injury and provide a diagnosis these cases.We prospectively studied 120 patients presenting with chest pain, positive troponin I and non-obstructive coronaries. Early CMR at 1.5T included cine, dark-blood T2-weighted (STIR), native T1-mapping (ShMOLLI) and late gadolinium enhancement (LGE) imaging in patients presenting with troponin-positive chest pain but non-obstructive coronary arteries. Native T1-mapping detected additional areas of abnormality when conventional CMR was \"normal\", improving the detection rate to 98%. Early multiparametric CMR is able to localize areas of affected myocardium and may aid in the further management or diagnostic workup in this patient cohort.This study is funded by the Oxford National Institute for Health Research Biomedical Research Centre Programme. VMF received funding from the Alberta Innovates Health Solutions (AIHS) Clinical Fellowship and the University of Oxford Clarendon Fund Scholarship. RC is a Wellcome Trust Senior Research Fellow in Clinical Science. SN and RC acknowledge support from the British Heart Foundation Centre of Research Excellence, Oxford."} +{"text": "Migraine with visual aura (MA) is associated with distinct visual disturbances preceding migraine attacks, but shares other visual deficits in-between attacks with migraine without aura (MO). The dorsal extrastriate cortex in the occipital lobe (V3A) and middle temporal cortex were reported to be relevant neural substrate for MA and MO based on structural MRI studies.To determine if abnormalities specific to inter-ictal MA exist in functional brain connectivity of intrinsic cognitive networks. In particular, these networks are involved in top-down modulation of the visual system.Using resting-state functional magnetic resonance imaging, whole-brain functional connectivity maps were derived from seeds placed within the default mode (DMN), salience (SAL), and dorsal attention networks (DAN). Twenty-six inter-ictal MA patients were compared with 26 matched MO patients and 26 controls. Headache parameters were used for regression analyses.The major findings were: (1) Connectivity between the SAL and occipital visual areas was reduced in MA but not MO and was negatively correlated with headache severity. (2) The V3A region exhibited decreased connectivity with the SAL and increased connectivity with the posterior DMN in MA. (3) Connectivity between the DAN and visual regions in the inferior and middle temporal cortices were increased in both MA and MO.The unique pattern of connectivity changes found in inter-ictal MA patients involved area V3A which has been implicated in aura generation. Hyperconnectivity to temporal visual regions may reflect inter-ictal deficits in visual perceptions in both MA and MO.No conflict of interest."} +{"text": "Familial chilblain lupus is a monogenic form of cutaneous lupus erythematosus characterized by cold-induced cutaneous lesions at acral location. It is caused by loss-of-function mutations in the nucleic acid metabolizing enzymes TREX1 or SAMHD1. Gain-of-function mutations in STING (stimulator of Interferon genes) have been described in an infancy-onset autoinflammatory syndrome with fever, inflammatory cutaneous lesions and interstitial lung disease.Here we report on a family with dominant chilblain lupus over 4 generations. Affected family members presented with acral inflammatory and partially necrotizing lesions beginning in early childhood. In some cases, low-titered ANAs and immune complexes were detectable. The family tested negative for TREX1 or SAMHD1 mutations. Exome sequencing revealed a heterozygous STING mutation segregating with chilblain lupus in the family. The mutation affects a highly conserved residue within the STING dimer interface and is predicted to be pathogenic. Quantitative RT-PCR analysis showed an increased expression of IFN-stimulated genes in blood cells of affected family members suggesting that the identified mutation has an activating effect on type I IFN signaling. Taken together, our findings demonstrate that gain-of-function mutations in STING can cause familial chilblain lupus and expand the spectrum of type I interferonopathies."} +{"text": "The cyclic strain of lung tissue during mechanical ventilation compared with spontaneous breathing is associated with a largely increased mechanical load due to larger pressure amplitudes and higher acceleration forces. This additional load may change tissue mechanics and may lead to tissue damage. Although experimental mechanostimulation in vitro is a widely used method to analyse mechanical load on cells or tissue, in vitro experiments with ventilation-analogue stimulation are missing. In this work we compare for the first time the changes of monolayer lung cells after ventilation-analogue stimulation with spontaneous-breathing analogue mechanostimulation. The aim of the study was to show time- dependent differences in the induction of apoptosis due to mechanical overload, by fluorescence microscopic observations.Alveolar epithelial cells (A549) were grown on RGD-coated, highly flexible polydimethyl siloxane membranes. After becoming approximately 100% confluent, cells were stained with Hoechst 33342/TMRE/caspase-3 and caspase-7/PI and continuously observed by fluorescence microscopy. The cells were stimulated either with ventilation-analogue or spontaneous-breathing analogue profile [The analysis of fluorescence microscopic images showed the first evidence of apoptosis induction after 40 minutes of ventilation-analogue stimulation. In contrast, apoptosis induction after spontaneous-breathing analogue stimulation occurred after 90 minutes.The observation of cells during stimulation with continuous fluorescence microscopic imaging allowed us to analyse the time- dependent induction of apoptosis under the aspects of different stimuli. We could prove our hypothesis that ventilation-analogue stimulation was worse for the cellular viability then spontaneous- breathing analogue stimulation. In future, the direct optical tracking of cell damage should allow one to analyse other stimulation profiles as well, and thereby to improve the stimulation profiles and ultimately the ventilation profile as well."} +{"text": "The systemic right ventricle (RV) is at increased risk of developing heart failure. Combined MRI-catheterization (XMR) techniques offer a unique opportunity to study this condition. We assess pressure-volume relations in children with hypoplastic left heart syndrome (HLHS) post Fontan with stepwise increments of dobutamine stress.Prospective data from anesthetized patients with HLHS undergoing clinical XMR were analyzed. A fluid filled MR compatible catheter placed in the systemic RV recorded pressures at rest, with dobutamine infusion at 10 mcg/kg/min and at 20 mcg/kg/min. Simultaneous cine short axis stacks of the ventricle were performed. Pressure-volume loops were constructed. End-systolic pressure-volume relationship was derived at each state from a validated maximal pressure (Pmax) estimation method. Ventriculo-arterial coupling (Ees:Ea) was compared to myocardial power and overall global function.Five patients with HLHS and exercise intolerance, mean age 7.8 years (range 3.5-11.6 yrs), weight 26 Kg (range 16-46 Kg), time since Fontan completion (mean 3.2 years). No significant tricuspid regurgitation in any patient. Statistical analysis was performed using one-way ANOVA with post-hoc comparisons to assess subgroup variation where p < 0.05. There were significant increases in EF, indexed cardiac output, power and ventricular contractility (Ees) with increases limited to between rest and dobutamine 10 (p < 0.01) with no further significant increase at 20. iEDV fell significantly between rest and dobutamine 20 (p < 0.01). EDP and arterial elastance (Ea) did not change throughout. Ees:Ea increased between rest and dobutamine 10 only. dP/dtmin a measure of rate of relaxation fell with dobutamine 10 only.In the systemic RV, load independent indices of contraction in response to dobutamine are similar to those recorded in the healthy left ventricle (LV). The systemic RV at rest works neither at maximal mechanical efficiency (Ees:Ea = 2) nor maximal stroke work efficiency at a given EDV (Ees:Ea = 1). Increased coupling with dobutamine, mediated through increased myocardial contractility, indicates at higher heart rates the RV moves towards improved mechanical efficiency though at higher levels of overall energy expenditure. The relative increase in stroke work (37%) is comparable to data published on the healthy LV. The systemic RV has a limited cardiac reserve. Despite appropriate responses in contractility to low dose dobutamine, the heart is unable to further augment power and cardiac output with administration of dobutamine 20. Indeed, the plateauing of dP/dtmin - a measure of relaxation - indicates that in the presence of tachycardia there is failure to adequately fill the heart. Hence cardiac output and contractility may be limited by a ceiling of maximal flow through the Fontan circuit. This gives us valuable insights into the physiology of children with HLHS post-Fontan.The Division of Imaging Sciences receives support as the Centre of Excellence in Medical Engineering as well as the BHF Centre of Excellence (British Heart Foundation award RE/08/03). This work was also supported by the European Commission (FP7-ICT-224485:euHeart). The authors acknowledge financial support from the Department of Health via the National Institute for Health Research (NIHR) comprehensive Biomedical Research Centre award to Guy's & St Thomas' NHS Foundation Trust in partnership with King's College London and King's College Hospital NHS Foundation Trust."} +{"text": "Neoadjuvant chemotherapy is the state-of-the-art treatment in advanced breast cancer. A correct visualization of the post-therapeutic tumor size is of high prognostic relevance. X-ray phase-contrast computed tomography (PC-CT) has been shown to provide improved soft-tissue contrast at a resolution formerly restricted to histopathology, at low doses. This study aimed at assessing ex-vivo the potential use of PC-CT for visualizing the effects of neoadjuvant chemotherapy on breast carcinoma.The analysis was performed on two ex-vivo formalin-fixed mastectomy samples containing an invasive carcinoma removed from two patients treated with neoadjuvant chemotherapy. Images were matched with corresponding histological slices. The visibility of typical post-therapeutic tissue changes was assessed and compared to results obtained with conventional clinical imaging modalities.PC-CT depicted the different tissue types with an excellent correlation to histopathology. Post-therapeutic tissue changes were correctly visualized and the residual tumor mass could be detected. PC-CT outperformed clinical imaging modalities in the detection of chemotherapy-induced tissue alterations including post-therapeutic tumor size.PC-CT might become a unique diagnostic tool in the prediction of tumor response to neoadjuvant chemotherapy. PC-CT might be used to assist during histopathological diagnosis, offering a high-resolution and high-contrast virtual histological tool for the accurate delineation of tumor boundaries. Preoperative neoadjuvant chemotherapy (NAC) followed by surgery is currently the state-of-the-art therapy in locally advanced breast cancer. Additionally, NAC is increasingly applied to patients presenting an early-stage operable breast cancer \u20133. Due tThe pathological response rate of breast carcinomas undergoing NAC is assessed by histopathological analysis of the resected tumor and is an independent predictor for disease-free and overall survival of breast cancer patients compared with non-responders \u20133, 7, 8.X-ray phase-contrast imaging (PCI) has emerged within recent years as a new class of techniques for X-ray imaging with improved sensitivity as compared to conventional absorption-based radiography. PCI detects the phase shift that X-rays experience when passing through an object. The combination of X-ray PCI with computed tomography (CT) allows the three dimensional (3D) reconstruction of the refractive index distribution within an object, which can be converted into an accurate 3D map of the sample mass density. Several studies have shown that PCI allows for a superior observation of the breast architecture compared with conventional breast imaging \u201322. In tThe aims of this study were to 1) demonstrate that 3D index of refraction PC-CT is able to visualize typical changes within breast tumor tissue treated with NAC and 2) show that differential phase-contrast CT techniques are useful for studying the effect of neoadjuvant therapeutics and might have the potential to become a unique and highly accurate diagnostic tool to predict the response rate to NAC and with higher detail than conventional diagnostic techniques.Two formalin-fixated ex-vivo mastectomy specimens (sample A and sample B) from two women suffering from invasive breast cancer who had undergone preoperative NAC were imaged. The breast samples were acquired through the Institute of Gynaecology of the Ludwig-Maximilians-University (LMU), Munich, Germany. The study was conducted in accordance with the Declaration of Helsinki and was approved by the local ethics committee . Patients\u2019 written informed consent was obtained before inclusion after adequate explanation of the study protocol. The indication to breast surgery followed recommendations of the interdisciplinary tumor conference by the University of Munich breast center. Inclusion criteria were a histologically proven breast cancer in preoperative core biopsy, with a recommendation to mastectomy, according to gynecological guidelines as well as completed preoperative NAC and completed conventional breast imaging diagnostics .Preoperative diagnostics included clinical breast examination, clinical standard two-view digital mammography in craniocaudal (CC) and mediolateral-oblique (MLO) projections using a standard breast compression paddle, high resolution B-mode ultrasound and MRI using a dedicated sensitivity-encoding-enabled bilateral breast coil with a 1.5-Tesla system . The clinical diagnostics were perfomed by a specialized radiologist with seven years experience in breast diagnostics. The in-vivo measurements were performed using standard diagnostic software in all modalities that enables measurements directly on the imaging dataset.3) were resected for standard paraffin embedding and automatic staining. The samples were stored in a 4% formaldehyde-solution until imaging. For imaging purposes, the samples were manually recomposed and placed into a custom made PMMA cylindrical sample-holder shown in Within one hour after surgery, the mastectomy samples (sample A and B) were fixated in a 4% formaldehyde-solution. Clinical standard histopathological workup was completed before the PC-CT imaging session. In short, the formaldehyde-fixated samples were cut into 5-mm slices. The slices remained attached to the intact skin enabling later recomposition. Macroscopically suspicious and representative tissue sections (max. 3.0 x 2.0 x 0.5 cmX-ray phase-contrast imaging techniques enable acquisition of images (projections), whose intensity is proportional to the spatial derivative of the phase delays experienced by X-rays upon propagation in the sample. The phase delays are related to the index of refraction \u03b4 of various features and tissues composing the sample. The 3D distribution of the refractive index inside the object can be reconstructed from a tomographic set of differential phase projections by means of the filtered backprojection (FBP) algorithm for transvers gradient projections . Similar3. Detailed description of the setup, acquisition process, and data processing can be found in work [In this work the PC-CT experiment was performed at the biomedical beamline (ID17) of the European Synchrotron Radiation Facility, Grenoble, France (ESRF). Analyzer-based crystal setup was used to obtain raw phase-contrast images. in work .The dose deposited into the tissues during the image acquisition was about 100 mGy. The dose values have been calculated using the method published in the work of Mittone et al. . Such a 2). After solidification, the paraffin blocks were cut into 5 \u03bcm sections using a standard microtome and sections were stained with hematoxylin and eosin using standard protocols. Tumor diameters were calculated during the histopathological standard workup using standard rulers.After completion of the PCI representative tissue sections were dehydrated in an ascending alcohol series before embedding in hot paraffin wax. Since the sample size exceeded standard size, the procedure was performed manually by enwrapping the samples in a blotting-paper and using non-standard slides .The PC-CT images were interpreted by 2 radiologists experienced in clinical mammography in consensus. On the reconstructed PC-CT volume of the imaged breast, several slice orientations were investigated in order to find the best correlation with the produced histological cut. The best fitting slices were chosen and a visual co-registration between the different acquisition techniques was performed. The size calculations were performed by extrapolation from well-defined landmarks such as the diameter of the sample-holder.Information about patient A and B and sample A and B are shown in In order to reduce these artifacts more advanced post processing methods can be applied during the reconstructions of the images.3 lesion.3.Macroscopic examination of sample A showed a partly whitish, partly yellow, knotty configured tumor with a diameter of 6.2 x 5.8 x 4.2 cmHistology revealed a residual invasive carcinoma NST of 6.2 cm maximum diameter, in correlation with the pre-therapeutic MRI (maximum tumor diameter of 8.0 cm) reveals this a decrease of tumor size of approximately 2 cm. A representative hematoxylin-eosin-stained slice is shown in 3 in PC-CT versus 6.2 x 5.8 x 4.2 cm3 in histology). There are scattered brighter areas within the tumor and around the tumor, in correlation with histopathology conformable with sclerotic areas representing post-therapeutic tissue changes (regression grade 1 according to the Sinn classification = resorption and tumor sclerosis). PC-CT reveals that the tumor infiltrates close to the epidermis but shows a thin layer of fatty tissue (dark) between tumor and epidermis; this finding is in concordance with histopathology where the tumor infiltration is reported close to the epidermis without skin infiltration. The remaining breast parenchyma is displaced by the extensive tumor. Strands of fibrous tissue interspersing the adjacent fatty tissue are differentiable from the carcinoma in terms of different grey levels.Macroscopic examination of sample B showed a whitish tumor with a diameter of 6 x 4 x 2 cm with an irregular shape. The tumor was fibrous and compact with a microcystic surface.Histology revealed a residual ductal in situ carcinoma (DCIS) of 5.8 cm maximum diameter with extensive comedo necroses and microcalcifications. PC-CT enables A series of studies performed on tumor-bearing breast samples indicate that reconstructed hard X-ray index of refraction CT images provide an excellent soft-tissue contrast and an improved visualization of fine structures including collagen strands, microcalcifications and strands of lobular carcinoma , 31. SztTo our knowledge, this is the first study assessing the value of PC-CT as a method for therapy-response monitoring. The acquired PC-CT data provide correct visualization of histopathological structures in excellent correlation with histopathology and reflect the response to NAC correctly. In this work the ABI technique has been used for the investigation, however other differential PCI techniques can be employed as well. Some of these, while based on a similar contrast mechanism and providing similar sensitivity, are more suitable to be used with X-rays produced by other sources than synchrotron radiation machine. A very important step for a possible future application of the PCI techniques in clinics is linked to the development of compact sources and detectors. A combination of these new compact sources, advanced detectors and PCI techniques less stringent in terms of beam property may provide a new powerful diagnostic tool for routine examinations.Limitations of our study include the small number of samples and the necessity of data acquisition after formalin fixation with a consequent flattening of the image contrast. The effect of formalin fixation on breast cancer specimens complicates the comparison with preoperative in-vivo imaging. However, recent studies suggest that the tumor diameter does not substantially differ between non-fixated and fixated specimens , 34. The"} +{"text": "The National Institute of Standards and Technology (NIST) and The University of Maryland jointly hosted the Fiftieth Annual Conference on Physical Electronics, held at NIST in Gaithersburg, MD, June 11\u201313, 1990. This annual conference provides a forum where important new research results concerned with the physics and chemistry of solid surfaces presented in a 3-day conference with ample time for discussion.The 1990 meeting in Gaithersburg marked both the fiftieth anniversary of the conference and the first return to the NIST site since the 1971 conference. Approximately 125 participants registered for the meeting, representing a broad spectrum of the scientific community. Participants included representatives from industry , national laboratories , numerous American academic laboratories, and several international institutions .The competition to select the outstanding student paper saw an unusual number of highly qualified contestants. Their papers reflected the breadth of interests of the overall conference, covering topics from molecular beam probes of chemical processes at surfaces to the use of scanning tunneling microscopy (STM) to characterize the interaction of steps and defects. This year\u2019s Nottingham Prize was awarded to Yuan-Wo Mo, from The University of Wisconsin, Madison. His paper, \u201cScanning Tunneling Microscopy Studies of Surface Kinetic Processes at the Atomic Level,\u201d focused on the direct use of STM imaging of surface atoms to determine self-diffusion parameters.A variety of talks at this year\u2019s meeting continued the strong tradition of demonstrating the atomic-scale mechanisms underlying surface behavior. The increasing power of field ion microscopy to determine fundamental parameters was demonstrated in a number of talks . These experimental studies were nicely complemented by theoretical studies which utilized either first-principles techniques (P. Feibelman\u2014Sandia) or embedded atom calculations (M. Daw\u2014Sandia) to extract diffusion barriers, binding energies, and cluster geometries. The difficult problem of concerted surface diffusion was addressed in several experimental talks showing the use of Low Energy Electron Diffraction (LEED) studies of ordering (M. Tringides\u2014Iowa State), laser-induced desorption studies of filling (M. Arena\u2014Stanford), and Low Energy Electron Microscopy (LEEM) studies of step motion (R. Phaneuf\u2014Univ. of Maryland).The physical properties and growth properties of thin films were the focus of a group of talks, ranging from the growth of Au on Ag(110) (P. Fenter\u2014Rutgers) to the electronic properties of metal/semiconductor interfaces such as Cs-GaAs(110) (T. Wong\u2014Univ. of Penn.) and Cs-InSb(110) (L. Whitman\u2014NIST).6 (Z. Ying\u2014Cornell) to the influence of coadsorbates on excited state lifetimes (T. Orlando\u2014Sandia).A broad range of probes is now being applied to characterize the electronic structure of surfaces and interfaces. Of particular note was the emergence of laser-based three-wave mixing techniques which are now beginning to provide complementary data to that available from synchrotron-based photoemission . Several related papers reported on the role played by these excited surface electronic states in radiation-induced surface reactions, ranging from hot electron attachment to Mo(CO)With an eye toward future device developments, the layer-dependent properties and electronic excitations in cleaved high temperature superconductors were discussed (J. Demuth\u2014IBM) as were the kinetic and dynamic factors associated with ballistic electron emission across interfaces (M. Stiles\u2014 NIST).Recent refinements in both instrumentation and interpretation of x-ray photoelectron spectroscopy (XPS) lineshapes have led to the use of core-level shifts to follow both reconstructions (G. Wertheim\u2014AT&T) and the degree of charge transfer at interfaces (Y. Ma\u2014AT&T). Parallel advances in electron spectroscopies have permitted the clear identification of adsorbate symmetry at surfaces (F. Sette\u2014AT&T), measurement of substrate dielectric response (E. Jensen\u2014Univ. of Cambridge), and direct probing of adsorption/desorption kinetics at constant coverage . The elegant use of synchrotron-based angle-resolved photoemission to map out surface Fermi contours of O/W(011) and O/Mo(011) and to establish the relationship of these states to the surface reconstruction (S. Kevan\u2014Univ. of Oregon) was discussed. Results from an exciting new tool for the study of electronic state densities (Auger Coincidence Spectroscopy) were reported for the TaC(111) surface (R. Bartynski\u2014Rutgers).Studies of equilibrium statistical mechanics at surfaces were represented by direct STM imaging of step wandering (X. Wang\u2014Univ. Maryland) and related calculations (T. Einstein\u2014Univ. of Maryland), by a LEED search for the elusive surface roughening and/or melting transition (Y. Cao\u2014Univ. of Missouri), and by an x-ray study of soliton pinning in an epitaxial overlayer (K. Liang\u2014Exxon).Remarkable progress was noted in the frontier of molecular processes at surfaces. Several theoretical talks addressed the nature of molecular energy transfer at surfaces using techniques such as wavepacket dynamics to account for the redistribution of energy following molecular beam scattering , electron stimulated desorption (D. Jennison\u2014Sandia), and laser induced processing (H. Guo\u2014Northwestern Univ.). These theoretical reports were complemented by several timely experimental papers which included femtosecond probes of adsorbate energy transfer processes (J. Beckerle\u2014NIST), optical, electron and atom scattering probes of the vibrational dynamics of ideally H-terminated Si(111) , and state-resolved measurements of non-thermal desorption phenomena . In addition, there were several papers which reported on optically driven surface reactions where excited carriers in the substrate were identified as being responsible for the observed processes .Molecular beam scattering techniques were used in several experiments to clarify the adsorption/absorption process. Collision induced absorption in the H/Ni(111) system demonstrated the role of high-kinetic-energy collisions in driving adsorbates into the subsurface (A. Johnson\u2014MIT). This result is particularly significant in terms of accounting for reaction pathways which may only contribute at elevated pressure. Molecular beam scattering was also used to probe the surface/subsurface kinetics of H/D exchange on Pd surfaces (V. Shamamian\u2014 Sandia) and trapping-mediated chemisorption of ethane Characterizations of the magnetic properties of bulk metals and thin epitaxial films were presented in several papers. Bulk materials [Mo(110) and Cu(100)] were probed using spin-exchange electron scattering (G. Mulhollan\u2014Rice Univ.). Thin films of Co/Cu(111) and Fe/W(100) were examined using the surface magneto-optic Kerr effect (M. Kief\u2014Penn State) and spin-polarized angle-resolved photoemission (R. Fink\u2014Univ. of Texas), respectively.A healthy balance between theory and experiment was reflected in the papers at this year\u2019s meeting. The diversity of topics and the quality of the papers reflect the vitality of surface science."} +{"text": "Dissatisfaction with the intensive care unit may threaten medical care. Clarifying treatment preferences can be useful in these settings, where physician direction may influence decision making and therefore medical treatment. This study aimed to evaluate whether fast-track discharge from intensive care units affects the satisfaction of family members .Evaluate the satisfaction of the family members and to assess its determinants in Qatari intensive care related to fast- track discharge from theWe used a single-center non-randomized trial, with all eligible familymembers involved. To evaluate family satisfaction, we used the Society of Critical Care Family Needs Assessment questionnaire (SCCMFNAQ). We hypothesized that those discharged within 24 hours of intensive care unit admission and their families would have higher levels of satisfaction. Patients were scored using the therapeutic interventions scoring system (TISS) and additive EuroSCORE.Two-hundred fifty-five family members were enrolled. The mean patient age was 53 years, and 92% were male. The median satisfaction level among family member was 17.9 (range 14-31). Patients were divided into two groups, one receiving fast-track discharge (115 patients), and one whose members stayed longer (139 patients). The overall satisfaction was affected significantly by quality of the delivered care and dissatisfaction increased by lack of comfort in hospital settings, including the waiting room. No significant differences were seen between the two groups for overall satisfaction (p = 0.546) and individual components of the questionnaire. Higher satisfaction was linked to higher levels of education among family members (p = 0.045) and information being relayed by a senior physician p = 0.03 (two-tailed test).Fast-track discharge from intensive care did not influence family satisfaction as hypothesized. Satisfaction relied on family members\u00b4 level of education and the level of seniority of the physician relaying information.To all members of cardiothoracic surgery department and medical research center, Hamad medical corporation, Qatar"} +{"text": "To prospectively determine whether multi-parametric MRI (mpMRI) - contrast-enhanced ultrasound (CEUS) correlated, imaging-guided target biopsy (TB) method could improve the detection of prostate cancer in re-biopsy setting of patients with prior negative biopsy.From 2012 to 2014, a total of 42 Korean men with a negative result from previous systematic biopsy (SB) and elevated prostate-specific antigen underwent 3T mpMRI and real-time CEUS guided TB. Target lesions were determined by fusion of mpMRI and CEUS. Subsequently, 12-core SB was performed by a different radiologist. We compared core-based cancer detection rates (CaDR) using the generalized linear mixed model (GLIMMIX) for each biopsy method.Core-based CaDR was higher in TB than in SB . In the cancer-positive TB cores, CaDR with suspicious lesions by mpMRI was higher than that by CEUS and concordant rate between mpMRI and CEUS was significantly different with discordant rate .The mpMRI-CEUS correlated TB technique for the repeat prostate biopsy of patients with prior negative biopsy can improve CaDR based on the number of cores taken. Prostate cancer (PCa) is the second most common cancer and the sixth leading cause of cancer-related death in males worldwide , 2. The Although highly sensitive and specific, in-bore MR-guided prostate biopsy is performed selectively due to their procedure length, cost and discomfort to the patient. A potential solution to maximize the sensitivity is to acquire pre-biopsy diagnostic mpMRI and to correlate them to the real-time CEUS images acquired during the TRUS-guided TB procedure. With this protocol, the diagnostic power of prostate mpMRI could be fully coupled to the flexible and rapid US-guided procedure.The objective of our study is to evaluate prospectively the pre-acquired mpMRI-correlated, real-time CEUS guided TB technique for the repeat prostate biopsy of patients with elevated PSA levels. We hypothesized that the TB method will double the core-based detection rate of the conventional SB method..Patients who tested negative in a previous conventional 12-core TRUS-guided prostate biopsy and were scheduled for repeated biopsies due to persistent suspicion of PCa based on a continuously elevated serum PSA level (more than 4 ng/ml) were eligible for this study. Study enrollment started in October 2012 and finished July 2014. Fifty-three patients agreed to participate, but 5 were excluded for reasons stated in To identify suspected PCa lesions, patients underwent mpMRI using a 3T MR scanner without endorectal coil after injection of MR contrast media, Gadoterate meglumine . MR imagWithin one week after imaging by mpMRI, transrectal CEUS was performed on each patient. The contrast agent SonoVue was used in conjunction with a Siemens S2000 US system in a contrast-specific imaging mode called Cadence contrast pulse sequencing (CPS) technology . If therTB for PCa was performed as follows: first, correlated lesions on both mpMRI and CEUS were targeted .; secondThe prostate cancer detection rate (CaDR) based on core numbers was calculated in addition to the overall patient number-based CaDR. We compared the core-based detection rate of each biopsy method (TB versus SB) using GLIMMIX with correlated binary outcomes in this clustered data. To determine whether differences in the Gleason score between SB and TB were significant, the Wilcoxon\u2019s signed-rank test was performed. In the analysis of cancer-positive TB cores, we performed McNemar\u2019s test between mpMRI and CEUS findings in each cores. All reported P values are one-sided, and a significant level of 5% was used. All analyses were conducted using MedCalc software for Windows and SPSS 20.0 for GLIMMIX analysis.CaDR based on biopsy cores are summarized in We performed cognitive fusion between mpMRI and CEUS, which was simple, quick and required no additional equipment beyond the MRI and a CEUS facility. This method may overcome the disadvantage of simple cognitive fusion using conventional T2WI and ultrasound because perfusion mapping derived from DCE-MRI and real time CEUS images offers additional similar perfusion information in prostate tissues and is helpful in the detection and real-time registration of focal hypervascular lesions so that lesions can be targeted more precisely. The increase in microvessels in prostate cancer enables CEUS to improve vascular imaging and resolution . By addiThere was a technical limitation of CEUS. Because of a limited temporal window of CEUS for scanning entire prostate, biopsy had to be performed in very short time duration. As the prostate was larger, we had less of a chance to observe the enhancing pattern of the entire prostate. Follow up TB or SB will be planned in patients who were negative in this study. Since we carried out an extended biopsy (12 cores) in the control group instead of saturation biopsy, we could not perform a comparison between TB and saturation biopsy. Two of 5 patients who have missed PCa on TB cores were clinically significant.We initially hypothesized for detection rate to be twice by using this multi-modality-correlated, imaging-guided TB technique. We achieved the improvement in CaDR based on the number of cores taken. In conclusion, the mpMRI-CEUS-correlated imaging-guided TB technique for the repeat prostate biopsy of patients with suspected PCa can be used to improve diagnostic accuracy.S1 File(XLSX)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file."} +{"text": "There is no doubt that highly active antiretroviral therapy (ART) has decreased the total mortality of HIV-infected populations drastically, and HIV has become a chronic and manageable condition. However, complications after long-term treatment of ART tarnished the great efforts. We aimed to study the effects of add-on lipid-lowering agents on ART for patients who developed hyperlipidemia after HIV treatment. The risk factors for failure to normalize lipid profile were analyzed.HIV-infected patients who visited outpatient clinics of Taoyuan General Hospital between July 2013 and January 2014 were retrospectively reviewed. Subjects who needed the management of dyslipidemia were enrolled. Total cholesterol (TC), triglyceride (TG), high-density lipoprotein (HDL) and low-density lipoprotein (LDL) were regularly followed up for at least 6 months. ART modification and add-on lipid-lowering agents for dyslipidemia were analyzed.p<0.05 for baseline compared to 4\u201312 weeks and 1 year, respectively). No obvious changes in HDL were noted. In Cox proportional hazard model, patients who received lopinavir or efavirenz were less likely to achieve normalization of TC (<200 mg/dL) and TG (<200 mg/dL). Modification of ART did not change the outcome who needed management of dyslipidemia . Among t outcome .Efavirenz and lopinavir were independent factors for the persistence of dyslipidemia despite adding lipid-lowering agents. ART associated with a favourable lipid profile would be considered in the modern era, and this certainly leaves the question of cost versus benefit."} +{"text": "C. difficile infection (CDI) as a cause of hospital-acquired diarrhea, few studies have investigated the prevalence of asymptomatic C. difficile colonization in a broad cross-section of the general hospital patient population over multiple years and seasons.Despite the importance of C. difficile colonization of tertiary hospitals in different Australian States during six time-periods (late summer [Feb-Mar] and late winter [Aug-Sep]) 2012-2014 and to describe the diversity of PCR ribotypes isolated from asymptomatic patients.To estimate the prevalence of asymptomatic C. difficile and isolates were characterized by PCR ribotyping. Overall prevalence of asymptomatic C. difficile colonization, hospital and time-period specific prevalences were calculated and compared using logistic regression.A three-year repeated cross-sectional study with biannual surveys of randomly selected adult patients from all care wards in tertiary hospitals in Australia was conducted. Stool specimens were cultured for C. difficile colonization was identified in 112/1417 patients during the study period. Asymptomatic C. difficile colonization prevalence was at its highest in Feb-Mar 2012 , whereas the lowest prevalence was observed in Aug-Sep 2014 . A seasonal pattern characterized by lower prevalence in late winter was identified. The majority of the isolates (77.55%) were toxigenic C. difficile strains, PCR 014 and 018 were the most frequent toxigenic strains isolated.Asymptomatic C. difficile colonization prevalence was observed across seasons. The majority of the asymptomatic C. difficile infected patients were colonized by toxigenic strains.High variability of asymptomatic *The study was funded by a NHRMC project grant (APP1006243).None declared."} +{"text": "To investigate the moderating effect of timing and attitudes towards puberty on personality traits and severity of eating disorder (ED) symptomatology in a clinical ED sample and to assess whether differences existed between Anorexia Nervosa (AN) and Bulimia Nervosa (BN) patients.354 ED patients . Pubertal risk factors were assessed through the ORFI and the EATATE. ED symptom severity was assessed through the EDI-2 and personality through the TCI-R temperament scales: Novelty Seeking, Harm Avoidance, Reward Dependency and Persistence.A range of pubertal risk factors significantly moderated the relationship between temperaments and ED severity. In particular, the relationship between TCI-Novelty Seeking and ED severity was found to be positively moderated by a negative attitude toward menstruation (p<0.01) and negatively moderated by earlier breast development (p<0.05). Similarly, the relationships between TCI-Harm Avoidance, TCI-Reward Dependency and TCI-Persistence and ED severity were found to be positively moderated by an earlier age of menarche and negatively moderated by a negative attitude towards breast development (p<0.05). Regarding ED subtypes, the only significant findings were obtained for AN-R patients.These findings suggest that puberty moderates temperaments and consequent ED severity. The assessment of personality provides important insights into which girls struggle more with pubertal development and are at increased risk of EDs."} +{"text": "Histoplasma spp. (A 14-year-old Nepali male with a history of rheumatic heart disease complicated by severe mitral stenosis presented with a 2-week history of high-grade fever, dry cough, and hepatosplenomegaly on examination. He described chronic exposure to chickens but no other significant exposure history. Computerized tomography scan of the chest revealed a bilateral diffuse miliary pattern (Histoplasmosis has only been described twice in Nepal: once in an Indian national who traveled to Nepal for medical care"} +{"text": "Reduced representation libraries are being used as a preferred source of markers to address population genetic questions. However, libraries of RAD-Seq variants often suffer from significant percentage of missing data. In addition, algorithms used to mine SNPs from the raw data may also underscore biological variation. We investigate the effect of biological diversity in mining SNPs from the program STACKS and the effect of missing data on individual assignment implemented in STRUCTURE. We observed that changing diversity parameters in STACKS significantly alters the number of SNPs discovered and allowing for higher percentage of missing data retrieves more loci and possibly more power for individual assignment.The online version of this article (doi:10.1186/1756-0500-7-841) contains supplementary material, which is available to authorized users. Reduced representation genomic libraries are increasingly used to answer diverse questions in evolutionary biology, which remained unresolved otherwise. Various restriction-site based genome scans have become standard tools for both population genetic and phylogenetic analyses . AlthougRAD-Seq (restriction site-based reduced representation genomic libraries) generates tens of thousands of loci per individual, but overlapping loci across all individuals are much fewer, resulting in significant missing data. Since missing data could impact inference, it is important to test its effect on the analysis. While missing data may not significantly impact phylogenetic inference , other fCynopterus sphinx and C. brachyotis sites obtained from RAD-Seq for ten individuals of two Cynopterine fruit bat species As an ongoing project to estimate gene flow and understand its dynamics between these two bat species in sympatry, we used data from ten individuals from a pool of 387 genotyped individuals . For all these parameter sets we performed independent STRUCTURE runs considering two genotypic clusters (K =2) . Each ruC. brachyotis based on the SNP analysis , Ethical Clearance (EC), Biosafety and Animal Welfare committee approval to BC dated 21-11-2005 Madurai Kamaraj University and Institutional Animal Ethics Committee (IACE) to UR id UR-3/2009, National Centre for Biological Sciences).Raw sequence reads have been deposited in the Sequence Read Archive (SRA) (accession no. SRP042963).Supplementary information. Table S1. Details of samples used for RAD-Seq library preparation. Table S2. Number of locus per samples for each data set. Table S3: Number of SNPs obtained in stacks by varying different parameters in denovomap.pl program in STACKS. Table S4: Number of SNPs obtained in stacks by varying the level of missing data. The average level of missing data was calculated in PLINK 1.07 [7] (url: http://pngu.mgh.harvard.edu/purcell/plink/). (DOCX 115 KB)Additional file 1:Additional file 2: Figure S1: Bar plot of ancestry coefficient for individuals a) with increase in number of mismatches allowed to generate loci in Stacks and b) increase in proportion of missing data. (TIFF 554 KB)"} +{"text": "Although subthalamic nucleus deep brain stimulation (STN-DBS) is effective in patients with advanced Parkinson\u2019s disease (PD), its physiological mechanisms remain unclear. Because STN-DBS is effective in patients with PD whose motor symptoms are dramatically alleviated by L-3,4-dihydroxyphenylalanine (L-DOPA) treatment, the higher preoperative catecholamine levels might be related to the better clinical outcome after surgery. We aimed to examine the correlation between the preoperative catecholamine levels and postoperative clinical outcome after subthalamic nucleus deep brain stimulation. The effectiveness of STN-DBS in the patient who responded well to dopaminergic medication suggest the causal link between the dopaminergic system and STN-DBS. We also examined how catecholamine levels were modulated after subthalamic stimulation.In total 25 patients with PD were enrolled . Mean levodopa equivalent doses were 1032 \u00b1 34.6 mg before surgery. Cerebrospinal fluid and plasma catecholamine levels were measured an hour after oral administration of antiparkinsonian drugs before surgery. The mean Unified Parkinson\u2019s Disease Rating Scale scores (UPDRS) and the Parkinson\u2019s disease Questionnaire-39 (PDQ-39) were obtained before and after surgery. Of the 25 patients, postoperative cerebrospinal fluid and plasma were collected an hour after oral administration of antiparkinsonian drugs during on stimulation at follow up in 11 patients.Mean levodopa equivalent doses significantly decreased after surgery with improvement in motor functions and quality of life. The preoperative catecholamine levels had basically negative correlations with postoperative motor scores and quality of life, suggesting that higher preoperative catecholamine levels were related to better outcome after STN-DBS. The preoperative plasma levels of L-DOPA had significantly negative correlations with postoperative UPDRS- III score in off phase three months after STN-DBS. The preoperative cerebrospinal fluid (CSF) 3,4-dihydroxyphenylacetic acid (DOPAC) and 5-hydroxytryptamine (5-HT) levels had significantly negative correlations with postoperative UPDRS- III score in off phase one year after STN-DBS and the preoperative CSF homovanilic acid (HVA) levels had significant negative correlations with postoperative UPDRS- III score in on phase three months after STN-DBS. In PDQ-39 SI (summary index), preoperative plasma dopamine (DA) level had significantly negative correlations with postoperative PDQ-39 SI one year after STN-DBS suggesting that higher preoperative plasma DA level resulted in better quality of life (QOL) one year after STN-DBS. The stepwise multiple linear regression study revealed that higher preoperative plasma HVA levels had negative influence on the postoperative motor symptoms , whereas higher preoperative CSF L-DOPA levels had positive influence on the postoperative motor symptoms and QOL (decrease in the score of UPDRS and PDQ-39 SI) The catecholamine levels were not significantly reduced postoperatively in 11 patients despite the significant reduction in levodopa equivalent doses. Unexpectedly, CSF HVA levels significantly increased from 0.00089\u00b10.0003 ng/\u03bcl to 0.002\u00b10.0008 ng/\u03bcl after STN-DBS.The preoperative catecholamine levels might affect the postoperative motor symptoms and quality of life. The catecholamine levels were not significantly reduced postoperatively despite the significant reduction in levodopa equivalent doses. Subthalamic nucleus deep brain stimulation (STN-DBS) is the preferred surgical therapy in patients with advanced Parkinson\u2019s disease (PD) . However11C] raclopride uptake during STN-DBS failed to demonstrate any change in striatal DA in humans raclopride uptake during STN-DBS failed to demonstrate any change in striatal DA [The precise effects of STN-DBS on catecholamine levels remain unclear with studies finding STN-DBS to increase, decrease, or maintain striatal monoamine levels in normal and PD rat models ,11\u201314,17iatal DA .Although the present study revealed that CSF catecholamine levels tended to increase after STN-DBS despite the significant reduction in LED, it might be difficult to draw any conclusions due to small number of patients and large variability in SEM. We also do not know why plasma levels of DOPAC and HVA tended to decrease after STN-DBS. One of the advantage effects of the decreased plasma levels of DOPAC and HVA might be neuroprotection for PD. DOPAC and HVA are neurotoxic and induce apoptosis in cultured dopaminergic neuron by augmenting free radical-induced mitochondrial degeneration and eventually augmenting Charnoly Body (CB) formation implicated in apoptosis and progressive neurodegeneration. Metallothioneins (MTs) are low molecular weight (6-7kDa) cysteine-rich and antioxidant proteins that provide neuroprotection. In neurodegenerative disease, MTs inhibit CB formation by serving as free radical scavengers \u201322. MTs The correlations between preoperative catecholamine levels and postoperative clinical outcome have never been evaluated. However, because clinical outcome of STN-DBS depend on the responsiveness of preoperative L-DOPA treatment , preoperCSF levels of 5-HT had negative correlations with postoperative UPDRS- III scores. This result suggest that higher levels of CSF 5-HT might be correlated with better motor functions postoperatively. Although, there are a large number of studies examining the levels of 5-HT and 5-HIAA with relation to motor and psychiatric symptoms in animal model of PD and patients with PD , 23, theA stepwise multiple linear regression analysis revealed that higher preoperative plasma HVA levels had negative influence on the postoperative motor symptoms, whereas higher preoperative CSF L-DOPA levels had positive influence on the postoperative motor symptoms and QOL. The higher preoperative CSF DA levels also had positive influence on the QOL one year after STN-DBS. Although it seemed to be reasonable that higher preoperative CSF L-DOPA and DA levels had positive influence on the postoperative motor symptoms and QOL, it is hard to understand that higher preoperative plasma HVA levels had negative influence on the postoperative motor symptoms. Because plasma HVA are derived from extra-neuronal organs such as liver, kidney and mesenteric organs containing catechol-O-methyltransferase , it mighThere are some limitations to the present results. We could examine the postoperative CSF catecholamine levels in only 11 patients in this study. The small number of patients might have biased the results of postoperative CSF catecholamine levels in this study. The other limitation was that we did not measure the CSF catecholamine level during off stimulation, which might be important to confirm the effect of STN-DBS on CSF catecholamine levels. Stimulation should be turned off approximately 12 hours before lumbar puncture to evaluate the CSF catecholamine levels during stimulation off states. However, it is technically difficult to perform lumbar puncture during off stimulation due to the marked axial rigidity and bradykinesia. The patients might be suffering from keeping lateral position for more than 10 minutes during off stimulation. It seems to be unrealistic to perform lumbar puncture during off stimulation.Another limitation in this study was that plasma and CSF levels of catecholamine were only assessed at 1 point before and after STN-DBS; therefore we do not know the extent to which the present data reflect overall catecholamine levels.Although the AUC (Area under the curve) of CSF catecholamine may be more suitable for assessment than a 1-point evaluation of CSF catecholamine \u201328, it nThe preoperative catecholamine levels might affect the postoperative motor symptoms and quality of life. The catecholamine levels were not significantly reduced postoperatively despite the significant reduction in levodopa equivalent doses."} +{"text": "Plasmodium. However, most malaria deaths are caused by Plasmodium falciparum [Malaria is one of the most dangerous tropical diseases worldwide, resulting in approximately 1.5-2.7 million deaths per year [Plasmodium falciparum cGMP-dependent protein kinase (PfPKG) is one of the key regulators of the malaria parasite life cycle in both sexual and asexual blood-stages. Inhibition of PfPKG stops differentiation and transmission of the parasites, indicating that this kinase is a promising drug target for malaria [The malaria -5. Howev malaria . TherefoE. coli. For the cGMP binding studies we used fluorescence polarization (FP) assay and for the activation studies we used microfluidic mobility-shift assay (MSA).To investigate the role of the CNB-D in PfPKG activation, we generated a deletion mutant without the N-terminal 400 amino acid residues (\u0394400), which is missing a potential auto-inhibitory sequence. We expressed the deletion construct (PfPKG 401-853) containing the catalytic domain and the PfCNB-D in A about 240 nM) in comparison to the full length PfPKG (KA about 70 nM [The deletion construct showed similar affinity for cGMP (40 nM) like the isolated PfCNB-D. In activation, the \u0394400 mutant showed an approximately 3 fold increased activation constant for cGMP (Kut 70 nM ). UnexpeA for cGMP), suggesting that the cGMP binding at the CNB-D mainly triggers the activation of this mutant.In addition, disrupting cGMP binding through mutating the conserved arginine 492 to lysine (R492K) abolished the cGMP-dependent activation of the deletion mutant has a low basal activity and can be activated efficiently by cGMP. This suggests that controlling PfPKG activity may not depend on the interaction between the inhibitory sequence and the catalytic domain. Upon cGMP binding, conformational changes in the regulatory (R) domain, especially in the area that bridges the regulatory and catalytic domains, induce kinase activation."} +{"text": "Quantitative first pass cardiac magnetic resonance (CMR) perfusion imaging has shown excellent interobserver agreement at a sector level in healthy volunteers and patients. In this study, we compare the myocardial blood flow (MBF) estimates in sector-wise and pixel-wise analysis. We also study the interobserver variability in pixel-wise MBF estimates from patients with coronary artery disease (CAD).First pass CMR imaging was performed on 29 patients with known or suspected CAD . Twenty of the patients, defined as the normal group, had minimal or no stenosis ( < 30% by computed tomographic angiogram) and nine patients, defined as the CAD group, had significant CAD ( > 70% stenosis by invasive coronary angiography). All patients were scanned on a 1.5T scanner using a steady state free precession imaging sequence for regadenoson stress perfusion followed by rest perfusion 20 minutes later. Two observers independently traced the myocardial regions of interest in the mid-ventricular slice and quantified the MBF in sector-wise and pixel-wise analyses by a model-constrained deconvolution approach. Pixel-wise MBF estimates were averaged to six transmural sectors to compare with sector-wise analysis. Pearson correlation, Bland-Altman analysis, and paired student t-test were used to compare the results.There was excellent correlation between pixel-wise vs. sector-wise MBF quantification for the 20 normal and nine CAD patients Figure . In bothClinical first pass CMR perfusion can be quantified at the pixel level and the results agree well with sector-wise comparison. There is an excellent interobserver agreement in pixel-wise quantification of patients with CAD.This research was supported by the Intramural Research Program of the National Heart, Lung, and Blood Institute, National Institutes of Health."} +{"text": "RIG-I-like receptors detect viral RNA in infected cells and promote oligomerization of the outer mitochondrial membrane protein MAVS to induce innate immunity to viral infection through type I interferon production. Mitochondrial reactive oxygen species (mROS) have been shown to enhance anti-viral MAVS signalling, but the mechanisms have remained obscure. Using a biochemical oligomerization-reporter fused to the transmembrane domain of MAVS, we found that mROS inducers promoted lipid-dependent MAVS transmembrane domain oligomerization in the plane of the outer mitochondrial membrane. These events were mirrored by Sendai virus infection, which similarly induced lipid peroxidation and promoted lipid-dependent MAVS transmembrane domain oligomerization. Our observations point to a role for mROS-induced changes in lipid bilayer properties in modulating antiviral innate signalling by favouring the oligomerization of MAVS transmembrane domain in the outer-mitochondrial membrane. Detection of viruses by pathogen associated molecular pattern (PAMP) receptors leads to the secretion of type I interferons (IFN), which bind to IFN receptors and stimulate the expression of genes that inhibit virus replication and spread. Detection of viral nucleic acids by Toll-like receptors and RIG-I-like receptors (RLRs) initiates this antiviral innate immune response . RLRs coMAVS is a tail-anchored membrane protein inserted in the outer mitochondrial membrane (OMM), and is also found in the peroxisomal membrane and the mitochondrial associated membrane of the endoplasmic reticulum ,5. The lBecause of their link to inflammation ,12, mitoROS are extremely reactive towards double bonds of unsaturated fatty acids causing the addition of a peroxyl radical in the acyl chain and displacing the double bond; a process called lipid peroxidation . The incThe biophysical properties of membranes significantly influence the behaviour of transmembrane (TM) proteins within the lipid bilayer. Indeed, changes to the lipid bilayer biophysical properties have been shown to affect the oligomeric state of single pass TM proteins, independently of any ligand \u201324. OligMus musculus PERK\u2013Uniprot Q9Z2B5) (PERK-KD) fused to the C-terminal containing transmembrane domain of human MAVS (MAVS-TM) was synthesized by Genscript and cloned into the pCDNA5_FRT_TO plasmid (Invitrogen) to generate the FLAG_PERK-KD_MAVS-TM expression plasmid. A cDNA encoding the C-terminal containing transmembrane domain of the outer mitochondrial outer membrane protein 25 (OMP25-TM) was synthesized by Genscript and cloned into pCDNA5_FRT_TO_FLAG_PERK-KD_MAVS-TM to exchange the TM domain of MAVS with the TM domain of OMP25 and to generate FLAG_PERK-KD_OMP25-TM expression plasmid. These expression plasmids were co-transfected with the pOG44 plasmid (Invitrogen) into Flp-In T-Rex-293 cells (Invitrogen) to generate isogenic cells expressing the transgene under a doxycycline inducible promoter. Stable clones were selected by blasticidin selection. The cytosolic Fv2E-PERK construct and the generation of Fv2E-PERK expressing cells was previously described . TB. TB38]. To determine if rotenone and Sendai virus-induced TM oligomerization is restricted to the TM domain of MAVS, we fused Flag_PERK-KD to the TM domain of OMP25, an unrelated tail-anchored outer mitochondrial membrane resident protein . We intrMAVS-TM domain is shown here to oligomerize in response to changes in the outer mitochondrial lipid membrane properties caused by treatment with mROS inducers or by Sendai virus infection. As MAVS oligomerization regulates its function, these results call attention to the potential role of the outer mitochondrial lipid membrane properties as a modulator of MAVS-mediated antiviral innate immune signalling.The mROS inducer rotenone potentiated IFN-\u03b2 and CXCL10 mRNA induction in response to concomitant application of low concentrations of the RLR agonist poly(I:C)-LV. Interestingly, when applied alone rotenone was insufficient to activate type I IFNs transcription but was able to activate an oligomerization reporter construct (Flag_PERK-KD_MAVS-TM) localised to the outer mitochondrial membrane. Both events are dependent on oligomerization of their respective effector: Oligomerization of the cytosolic CARD domain of MAVS promotes downstream signalling to the IFNs genes, whereas oligomerization of PERK kinase domain is required for autophosphorylation in the chimeric reporter. The differences between the responses of the two are consistent with different thresholds of sensitivity to the oligomer-monomer equilibrium, with the MAVS requiring sustained oligomerization reinforced by concomitant RLR binding to trigger downstream signalling. Thus mROS inducers favour MAVS-TM oligomerization but at a level that is insufficient to cause the sustained MAVS CARD domain interaction needed for downstream signalling . NonetheThe endoplasmic reticulum lipid membrane properties have been shown to modulate signalling by the unfolded protein response (UPR) transducers, IRE1 and PERK ,40,41. LOligomerization was observed for the TM domain of MAVS and OMP25, which are two unrelated TM peptides that have a similar hydrophobicity profile, but that to our knowledge do not share any noticeable common peptide motif. As the amino acids constituting the TM domain seemed to have a minor role in conferring responsiveness to rotenone or Sendai virus induced lipid modifications, oligomerization is not likely to rely on specific peptide-lipid interactions, bur rather relies primarily on changes in the biophysical properties of the lipid membrane. Changes in the lipid bilayer biophysical properties known to modulate TM domain oligomerization include modifications of the thickness of the lipid bilayer, changes in membrane fluidity and acyl chain flexibility. These lipid bilayer biophysical properties affect the strength of the interaction between TM amino acid side chains and the surrounding lipids. When the strength of the peptide-lipid interaction decreases, polar amino acids embedded in the lipid bilayer are no longer solvated as efficiently by surrounding lipids, creating a thermodynamically unfavourable situation that can be relieved by the interaction between amino acid side chains from TM peptides . This geThe mitochondrial phospholipid composition has been extensively studied and reviewed \u201345. In aViruses rely on host cell metabolism for their replication. As a consequence, they are unlikely to develop resistance to or bypass the consequences of processes such as metabolism-induced ROS production that are linked to pathways needed for their replication. Thus, identifying ways to manipulate cellular metabolism to increase mROS production specifically in infected cells could be a promising approach to promote antiviral signalling. This could complement conventional PAMP detection mechanisms to strengthen the innate immune response by taking advantage of the specific metabolic requirements of a virus in a host cell.S1 FigHistogram of MitoSOX fluorescent signal from untreated Flp-In T-Rex-293 cells (blue curve) and cells treated for 90min with 10 \u03bcM rotenone (yellow curve), 40 \u03bcg/ml antimycin A (green curve), or infected with 16h with Sendai virus (orange curve). Cells were stained with MitoSOX and analysed by flow cytometry.(TIF)Click here for additional data file."} +{"text": "Parasites enter the eye through hematogenous spread. The interaction with host immune system may result in its destruction but not without collateral damage to the vital retinal structures. Currently, the accepted treatment for ocular parasitosis is surgical removal or direct laser photocoagulation. A 24-year-old Indian woman presented with abrupt painless loss of vision to 5/300. A large yellow-white lesion centered at macula was observed with associated retinal and subretinal hemorrhage and neurosensory retinal detachment. A parasite was seen protruding at the center of the lesion. Fluorescein angiography demonstrated disc leakage and vessel wall staining. Ultrasonography demonstrated a highly reflective subretinal lesion with aftershadowing. Serological test was positive for anti-cysticercus (IgM) antibody. Treatment with prednisolone and albendazole resulted in resolution of the lesion within 2 months with improvement of visual acuity to 20/400. A noncystic form of subretinal cysticercosis is likely with suggestive B-scan ultrasonography and serological investigations. Parasites transit the vascular tunic of eye prior to entering the subretinal or intraocular space. Host immune response triggered by the parasite antigens may incite inflammation of the ocular structures. According to Lech, \u201cto leave the parasite in the eye is to condemn the patient to blindness or total loss of the eye\u201d . The treWe report a case of submacular live parasite masquerading as posterior pole granuloma treated with systemic antihelminthics and corticosteroids. Toxoplasma and Toxocara but positive for anti-cysticercus (IgM) antibody.A 24-year-old Indian woman presented with abrupt loss of vision in the right eye of 1-week duration. Best-corrected visual acuity was 5/300 OD and 20/20 OS. The swinging flash light test demonstrated a positive relative afferent pupillary defect in the right eye. Slit lamp biomicroscopy revealed 3+ cells in the anterior vitreous. Intraocular pressure was in the normal range. A yellow-white subretinal lesion larger than 6-disc area size with adjacent satellite lesions, retinal and subretinal hemorrhage, and a serosanguineous detachment of neurosensory retina was observed in the posterior pole . There whttp://dx.doi.org/10.1155/2015/910383). A dense white (opaque) plaque-like lesion located at the site of motile parasite was observed with no activity indicating the response to albendazole therapy , 4 weeks (b) and 8 weeks (c) after initiation of medical therapy. Note the regression of the subretinal hemorrhage, perivascular sheathing, disc edema and consolidation of the posterior pole granuloma. Bright yellow-white center of the granuloma appeared calcified; the same was demonstrated on B-scan ultrasonography."} +{"text": "LV performance is coupled to loading conditions (i.e. preload and afterload) and myocardial contractility . Therefore load-independence is an important means to isolate and study LV contractility in preclinical studies of cardiovascular pharmaceuticals and devices (3). Precise and rapid assessment of LV pressure is achieved with high fidelity catheter-based pressure transducers but measurements of LV volume are more difficult and less reliable. Thus far, MRI has not demonstrated sufficient spatiotemporal resolution to measure beat-to-beat changes of the pressure-volume (PV) loop to measure left ventricular (LV) elasticity or preload-recruitable stroke work (PRSW). Our aim was to develop a real-time (rtMRI) approach to measure PV and Frank-Starling relationships in a preclinical model of heart disease under normal and stressed physiologic conditions.The University of Pennsylvania IACUC approved all experiments. Yorkshire swine (n = 8) were anesthetized and instrumented with expandable vascular occluders placed at the inferior (20 mm) and superior (24 mm) vena cavae and transiently inflated during simultaneous rtMRI and intraventricular pressure measurement. Images were reconstructed with non-Cartesian parallel SENSE and >10 k frames were segmented in < 5 min with semi-automatic active contours.The relationship between Te, Tr and ejection fraction is shown Figure . We founRtMRI can accurately assess LV volumes, elasticity and PRSW at baseline and elevated inotropic state, providing non-invasive into the Frank-Starling relationship of the intact heart.The authors gratefully acknowledge support from the National Institutes of Health through awards K99HL108157 and R01HL63904."} +{"text": "DNA methylation is a major epigenetic modification regulating several biological processes. A standard approach to measure DNA methylation is bisulfite sequencing (BS-Seq). BS-Seq couples bisulfite conversion of DNA with next-generation sequencing to profile genome-wide DNA methylation at single base resolution. The analysis of BS-Seq data involves the use of customized aligners for mapping bisulfite converted reads and the bioinformatic pipelines for downstream data analysis.Here we developed MethGo, a software tool designed for the analysis of data from whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS). MethGo provides both genomic and epigenomic analyses including: 1) coverage distribution of each cytosine; 2) global cytosine methylation level; 3) cytosine methylation level distribution; 4) cytosine methylation level of genomic elements; 5) chromosome-wide cytosine methylation level distribution; 6) Gene-centric cytosine methylation level; 7) cytosine methylation levels at transcription factor binding sites (TFBSs); 8) single nucleotide polymorphism (SNP) calling, and 9) copy number variation (CNV) calling.http://paoyangchen-laboratory.github.io/methgo/.MethGo is a simple and effective tool for the analysis of BS-Seq data including both WGBS and RRBS. It contains 9 analyses in 5 major modules to profile (epi)genome. It profiles genome-wide DNA methylation in global and in gene level scale. It can also analyze the methylation pattern around the transcription factor binding sites, and assess genetic variations such as SNPs and CNVs. MethGo is coded in Python and is publically available at Cytosine methylation is a crucial epigenetic modification involved in numerous biological processes, including transcriptional regulation, cell differentiation, and X-chromosome inactivation . It is vTo evaluate DNA methylation, bisulfite treatment of genomic DNA has been widely used to convert unmethylated cytosines (Cs) to uracils while methylated Cs remain unconverted . After PSodium bisulfite treatment coupling with high throughput sequencing (BS-seq) makes it possible to profile genome-wide DNA methylation in single base resolution ,6. The tThe first step to process BS-seq data is to align the BS reads to the reference genome. Aligners such as Bowtie2 and SOAPAfter alignment, further bioinformatics steps are required for extracting biologically meaningful information. Several tools for such post-alignment analysis including Kismeth , Bis-SNPIn this paper we present MethGo, a post-alignment tool consisting of 9 analyses in 5 functional modules for processing and analyzing BS-Seq alignments. MethGo provides coverage distribution across all methylation sites, global methylation states and methylation levels according to several defined regions, such as promoter, gene body or transcription factor binding sites (TFBSs). In addition to DNA methylation, MethGo also provides the information of genetic variations including CNV calling and SNP calling. MethGo produces high quality figures and tables for data presentation that are ready for scientific publication.MethGo is a Python software that takes the alignment file from both WGBS and RRBS as the input data. It consists of three modules for methylation analysis and two modules to detect genetic variations and generates reverse cumulative plot for methylation sites by the genomic contexts . For example, Figure The MET module takes methylation calls generated from the bisulfite aligner such as BS Seeker 2, and gene annotation file for analyses. Five analyses are carried out in MET module. First, global cytosine methylation level of CG/CHG/CHH are calculated and plotted Figure . Second,DNA methylation at the TFBSs can interfere with the binding of proteins and hence affects the activation of transcription . The TXNSince BS-seq is DNA-based sequencing, the coverage of the reads (i.e. depth) can be used as a proxy for assessing CNVs. The CNV module extracts the read coverage from the alignments and plots the coverage across the genome Figure . GenomicThe SNP module identifies both homozygous and heterozygous SNPs from the alignment. The homozygous SNPs are polymorphisms where the majority reads show one dominant allele, which is different from the allele on the reference genome. The heterozygous SNPs are the ones where reads show two major alleles, potentially reflecting the two parental alleles . C. Screenshot of homozygous SNP. There is one allele different from the reference genome (bottom).Click here for fileArabidopsisNon-CG methylation levels in different genomic elements in . A. wild-type. B. met1.Click here for fileHomozygous SNPs. This file contains homozygous SNP calling of WT Arabidopsis.Click here for fileHeterozygous SNPs. This file contains heterozygous SNP calling of WT Arabidopsis.Click here for fileSoftware installation guide and requirements. This file contains the MethGo installation guide and module requirements.Click here for file"} +{"text": "The surface composition and functionality of biomaterials and scaffolds are the most important factors for their applications in biomedical fields and tissue regeneration. Bulk and surface properties of biomaterials influence vital cell activities such as cell adhesion, proliferation, extracellular matrix secretion, and differentiation. Nano-/microstructural control is found to be another key factor in tailoring the bioactivity of material surfaces. The morphological/topographical designing of the grafts is also proved to be a strategic approach in improving the bioactivity and biological responses of the biomaterial. Furthermore, the nano-/microstructured grafts possess higher specific surface area, which will provide much more adsorption sites to adsorb bioactive molecules.In view of these specialties of the biomaterials, several investigators are invited to contribute original research findings that can stimulate continuing efforts to understand the dimensions of the polymers and bioceramics as well as their composites essentially with bioactive compositions along with 2D/3D nano-/microlevel surface structures. The special issue is divided into three categories based on the key words of nanoparticles, surface control, and 3D scaffolds. The published works are briefly addressed as follows. in vitro cell culture experiment, that keratin forming cancer cells (KB) were well proliferated in the presence of herceptin-conjugated QDs (QD-Her) while most of breast cancer cells (SK-BR3) were dead. The data from confocal laser scanning microscope showed that the QD-Her specifically bound to the membrane of SK-BR3 and almost saturated after 6 hours of incubation. This result suggested that growth signal of the breast cancer cell is completely inhibited by specific binding of the herceptin to the Her-2 receptor of SK-BR3 membrane, resulting in cell death. A. Takahashi et al. reported impact of core-forming segment structure on drug loading in biodegradable polymeric micelles using PEG-b-poly(lactide-co-depsipeptide) block copolymers. As a result, the drug loading increased with increase in the mole fraction of depsipeptide unit in the hydrophobic segments. Y. Huang et al. prepared reduction-triggered breakable polymeric micelles incorporated with methotrexate (MTX) using amphiphilic PAA-g-PEG copolymers having S\u2013S bonds in the backbone. The drug loading content and drug loading efficiency increased along with more hydrophobic segments in the copolymers. In reductive environments, the entire MTX payload could be quickly released due to the reduction-triggered breakage of the micelles.In the category of nanoparticles, S.-J. Han et al. prepared herceptin-immobilized CdSe/ZnS core-shell quantum dots (QDs). Mean size of the quantum dots (28\u2009nm) as determined by dynamic light scattering was increased up to 86\u2009nm after herceptin immobilization. It was found, fromIn the category of surface control, J. Kang et al. immobilized bone morphogenetic protein (BMP) on DOPA- or dopamine-treated titanium surfaces to enhance osseointegration. The immobilized BMP induced specific signal transduction and alkali phosphatase, a differentiation marker. J. O. Eniwumide et al. investigated the potential of a novel micropatterned substrate for neocartilage formation. In the comparison of flat and honeycomb-patterned surface, accumulation of DNA and keratin sulphate was higher on the honeycomb surface, suggesting potential usefulness of honeycomb-based scaffolds during early cultures of neocartilage and engineered soft tissue. T.-Y. Kwon et al. examined the polymerization shrinkage of five dental modeling resins as well as one temporary PMMA/MMA resin (control). They concluded, from the study of final volumetric shrinkage values for the modeling resins, that the optimal control of the polymerization kinetics seems to be more important for producing high-precision resin structures rather than using dental modeling resins. S. W. Hong et al. studied enhanced neural cell adhesion and neurite outgrowth on graphene-based biomimetic substrates. The result implied that graphene and CNTs, even though they were the same carbon-based nanomaterials, show differential influences on neural cells. Furthermore, graphene-coated or -patterned substrates were shown to substantially enhance the adhesion and neurite outgrowth of PC-12 cells. M. J. Kim et al. synthesized and evaluated biodegradable and elastomeric polyesters (poly(glycerol sebacate) (PGS)) using polycondensation between glycerol and sebacic acid to form a cross-linked network structure without using exogenous catalysts. They reported that synthesized materials possess good mechanical properties and elasticity and surface erosion biodegradation behavior and that the surface morphology and thickness of coating layer could be controlled by adjusting the electrospraying conditions and solution parameters.\u03b5-carprolactone). SEM observation showed that the cylinder-shaped sponges had evenly distributed bulk pore structures and the wall surfaces were less porous with a smaller pore size than the wall bulk pore structures. The porosity and pore size of the sponges could be controlled by the ratio and size of the porogen materials. They also studied collagen scaffolds with controlled insulin release and controlled pore structure for cartilage tissue engineering. Collagen-microbead hybrid scaffold was prepared by hybridization of insulin loaded PLGA microbeads with collagen using a freeze-drying technique. The pore structure of the hybrid scaffold was controlled by using preprepared ice particulates having a diameter range of 150\u2013250\u2009\u03bcm. Hybrid scaffold had a controlled pore structure with pore size equivalent to ice particulates and good interconnection. Culture of bovine articular chondrocytes in the hybrid scaffold demonstrated high bioactivity of the released insulin. The hybrid scaffold facilitated cell seeding and spatial cell distribution and promoted cell proliferation. H. H. Oh et al. fabricated and characterized thermoresponsive polystyrene nanofibrous mats for cultured cell recovery. Cultured cells were easily detached from the PIPAAm-grafted surfaces by reducing culture temperature to 20\u00b0C, while negligible cells were detached from ungrafted surfaces. Moreover, cells on PIPAAm-grafted PS nanofibrous mats were detached more rapidly than those on PIPAAm-grafted PS dishes. Y. I. Yoon et al. fabricated nano-/microfibrous scaffolds using melt and hybrid electrospinning and surface modification of poly(L-lactic acid) with plasticizer. The silk fibroin (SF)/PLA (20/80) scaffolds consisted of a randomly oriented structure of PLA microfibers (average fiber diameter = 8.9\u2009\u03bcm) and SF nanofibers (average fiber diameter = 820\u2009nm). The PLA nano-/microfiber (20/80) scaffolds were found to have pore parameters similar to the PLA microfiber scaffolds. The PLA scaffolds were treated with plasma in the presence of either oxygen or ammonia gas to modify the surface of the fibers. They claimed that the control of surface property and fiber diameter could be useful in the design and tailoring of novel scaffolds for tissue engineering.In the category of 3D scaffolds, X. He et al. prepared cylinder-shaped porous sponges of poly(L-lactic acid), poly(DL-lactic-co-glycolic acid), and poly(Inn-Kyu KangYoshihiro ItoOh Hyeong Kwon"} +{"text": "Quantification of spatial and temporal changes in forest cover is an essential component of forest monitoring programs. Due to its cloud free capability, Synthetic Aperture Radar (SAR) is an ideal source of information on forest dynamics in countries with near-constant cloud-cover. However, few studies have investigated the use of SAR for forest cover estimation in landscapes with highly sparse and fragmented forest cover. In this study, the potential use of L-band SAR for forest cover estimation in two regions (Longford and Sligo) in Ireland is investigated and compared to forest cover estimates derived from three national , one pan-European (Forest Map 2006) and one global forest cover product. Two machine-learning approaches (Random Forests and Extremely Randomised Trees) are evaluated. Both Random Forests and Extremely Randomised Trees classification accuracies were high (98.1\u201398.5%), with differences between the two classifiers being minimal (<0.5%). Increasing levels of post classification filtering led to a decrease in estimated forest area and an increase in overall accuracy of SAR-derived forest cover maps. All forest cover products were evaluated using an independent validation dataset. For the Longford region, the highest overall accuracy was recorded with the Forestry2010 dataset (97.42%) whereas in Sligo, highest overall accuracy was obtained for the Prime2 dataset (97.43%), although accuracies of SAR-derived forest maps were comparable. Our findings indicate that spaceborne radar could aid inventories in regions with low levels of forest cover in fragmented landscapes. The reduced accuracies observed for the global and pan-continental forest cover maps in comparison to national and SAR-derived forest maps indicate that caution should be exercised when applying these datasets for national reporting. Globally, forests cover 31% of the total land area ,3. Loss Recent research has focused on large-scale mapping of forest cover and change detection on continental \u201313 and gThis has particular importance for Ireland, given the past widespread transformation in the areal extent of forest cover. At the beginning of the twentieth century, forest cover in Ireland was < 1% following millennia of gradual deforestation . Over thA number of estimates for the extent of forest cover in the Republic of Ireland are available from both national and international sources . These eThe most common spaceborne microwave remote sensing instruments used for forest applications operate at X- (\u03bb~3cm), C- (\u03bb~5cm) and L-band (\u03bb~24cm). The shorter wavelength radar (X-band) interacts mainly with the tops of the canopy cover while longer wavelengths (L-band) are able to penetrate further into the canopy. L-band undergoes multiple scattering between the canopy, trunks and soil and is therefore significantly more useful in forest and vegetation studies as it is able to penetrate deeper into the canopy cover . HoweverIn this study, we investigate the potential use of L-band SAR for forest cover monitoring in fragmented forest landscapes. There are two specific objectives of the study. Firstly, the use of L-band SAR data for forest cover mapping in two study areas in Ireland is examined. Secondly, using independent accuracy assessment, a comparative analysis is carried out on radar-based forest cover estimates and three national, one pan-European and one global forest cover product. For the purposes of this analysis, the forest definition used for international forest reporting in Ireland has been adopted. The results of this study will help inform future forest extent estimation and monitoring approaches in Ireland.Picea sitchensis) is the main forest tree species in Sligo accounting for 59.3% of the stocked forest area, with native forest tree species accounting for only 24%. Although the non-native conifer species Sitka spruce and Norway spruce (Picea abies) are also the most common forest tree species in Longford (19.4% and 34.3% of the stocked forest area respectively), native species are more common (36.6% of the forest area) )Machine Learning techniques such as RF have been gaining more widespread use in forest cover and carbon mapping applications e.g. ,70,71) a,71 a70,7Random Forests (RF) builds an ensemble of individual decision-tree classifiers that are later combined using a majority voting scheme to improve predictive accuracy. The individual trees are constructed using a bootstrap sample of the training data, whereby the training is performed on two thirds of the data samples and the remaining one third of the data samples are omitted. These \u2018out-of-bag\u2019 (OOB) samples are used to test the classification during each iteration and estimate the OOB error. For this study, the RF algorithm was run using a 200-tree ensemble and a random sample of predictor variables at each node equal to the square root of the total number of predictor variables. RF can also provide the relative importance of each of the variables used in the model formulation which can provide valuable insight into the contribution of each variable to the classification accuracy see Tables.et al. )et. al. . Temporaland-cover mapping technique, whereas LULUCF reporting is based on land-use. In countries where the principal silvicultural method is clear-felling followed by replanting, a change in forest cover may be not associated with a change in land-use. Thus, for reporting land-use change events, SAR-based forest cover change identification should be used in combination with data from other sources such as ground surveys, ancillary data and other sensors [In countries with near constant cloud-cover, radar EO data has the potential to produce high-accuracy, high-resolution forest cover maps. Of particular note is the possible use of SAR data in Land-Use, Land-Use Change and Forestry (LULUCF) sector of UNFCCC inventory reports, whereby annual updates of forest area, afforestation and deforestation areas are required. SAR-derived forest cover maps for two Irish regions displayed high accuracies following independent accuracy assessment and were comparable with datasets currently used in national forest reporting. These findings indicate that dual-polarisation radar could aid forest inventories. However, SAR forest mapping is primarily a optical) . SAR-deroptical) which aroptical) .th May 2014. Furthermore, continuity of observations will be facilitated by the ever-increasing number of radar sensors being launched. This, in addition to free and open access policies for certain sensor data (e.g. Sentinel-1A/B\u2014launched 3rd April 2014) further constitute a basis for incorporating SAR-derived forest cover estimates into national reporting mechanisms. The reduced accuracies of global and pan-continental forest cover maps investigated in this study indicate that caution should be exercised when applying these datasets to nuanced local forest conditions.Although ALOS PALSAR is no longer operational, a follow-on mission, ALOS-2 was succS1 FigGreen dots refer to Forest samples and white dots depict Non-Forest samples.(TIF)Click here for additional data file.S2 FigGreen dots refer to Forest samples and white dots depict Non-Forest samples.(TIF)Click here for additional data file.S3 Fig(TIF)Click here for additional data file.S4 Fig(TIF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file."} +{"text": "Bloodstream Infection and Central Line-Associated Bloodstream Infection (BSI/CLABSI) in Intensive Care Units (ICUs) are associated with clinical and economic burden. Chlorhexidine gluconate body washing with washcloths (CHG-WC) has been described as potentially effective towards reducing the spread of infection. Current systematized evidence has not fully ascertained the impact of CHG-WC in bacteremia within the ICU. We have systematically assessed the evidence on the effectiveness of CHG-WC in reducing total HABSI/CLABSI in the ICU.To systematically review the effect of CHG-WC on total HABSI/CLABSI risk in the ICU.Medline, EMBASE, Cochrane library (CENTRAL) and Web of science databases were searched using variations of key terms Chlorhexidine washcloths, ICU, BSI and CLABSI. Eligible trials implemented CHG-WC in ICUs using a randomized crossover study design and reported total HABSI and CLABSI rates per patient days. Methodological quality of studies was assessed using Cochrane Risk of Bias assessment tool. Random effects meta-analysis calculated odds ratios (OR) and 95% confidence intervals (CI) for total HABSI and CLABSI rates between control (regular washcloth bathing) and treatment groups (CHG-WC). Results of 4 eligible studies were included in the final analysis.All 4 eligible studies were large randomized control trials encompassing 706 events in 22850 patients from 15 adult and 10 paediatric ICUs. Three studies describe a reduction in total HABSI/CLABSI on patients who received CHG-WC bathing. In one study this reduction is not significant.Current data suggests that the use of CHG-WC may be associated with an overall risk reduction of total HABSI and CLABSI, in adult/paediatric ICUs. However, conflicting data remains from the most recent randomized controlled trial, and even though this can be related to discrepancies in study design and outcome reporting, more trials are needed in order to ascertain the usefulness of CHG-WC bathing in the ICU."} +{"text": "Prevalence of respiratory distress syndrome (RDS) caused by primary surfactant deficiency reaches 50% in infants below 32 weeks of gestational age. Increased alveolar surface tension leads to atelectatic and/or dystelectatic lung areas followed by inflammation resulting in development of a bronchopulmonary dysplasia (BPD) in 8% of these children. Standard RDS treatment consists of administration of exogenous surfactant. With the introduction of less invasive application (LISA) of exogenous surfactant, the use of Surfactant has significantly increased. Pituitary adenylate cyclase-activating polypeptide (PACAP) and its receptors trigger inflammatory reactions as well as anti-inflammatory processes.Using cell cultures, FACS and ELISA methods we analyzed surfactant effects on inflammation and PACAP-regulation and of its receptors in vivo and ex vivo.We were able to show that lipopolysaccharide (LPS) in prestimulated cells (PBMC) after surfactant treatment resulted in a significant up-regulation of pro-inflammatory interleukin (IL)-8. In tracheal secretory cells of surfactant-treated neonates we found an up-regulation of pro-inflammatory receptor VPAC1. Furthermore, in cell cultures we identified changes in the proliferation rates. Amniotic infection syndrome (AIS) is one of the major causes for premature birth resulting in RDS requiring exogenous surfactant. After pre-stimulation of PBMCs and subsequent addition of surfactant, pro-inflammatory signals were fortified. These results were confirmed by analysis of tracheal secretions of preterms and newborns.Current findings may imply that safety and efficacy of routine surfactant administration should be reassessed as surfactant potentially triggers pulmonary inflammation and thus may contribute to BPD development."} +{"text": "The effect of dopamine medication (L-Dopa and Dopamine (DA) agonists) and Deep Brain Stimulation (DBS) of Sub Thalamic Nucleus (STN) on the cognition of Parkinson's disease (PD) patients has been of interest to neuroscientists, owing to their ability to produce impulsive behavior as a side effect. Interestingly, it has been found that the impulsive decision making in STN-DBS patients has been observed to be quite contrary. As an attempt to understand the aforementioned side effect, we built a spiking network model of basal ganglia (BG) and tested on a probabilistic learning task . BG nuclThe performance PD-OFF cases showed skewness towards punishment learning (avoiding 'B'), whereas the opposite was observed in PD-ON (L-Dopa) case fig. . These r"} +{"text": "The HAS-BLED score enables a risk estimate of major bleeds in patients with atrial fibrillation on vitamin K-antagonists (VKA) treatment, but has not been validated for patients with venous thromboembolism (VTE). We analyzed whether the HAS-BLED score accurately identifies patients at high risk of major bleeds during VKA treatment for acute VTE.Medical records of 537 patients with acute VTE starting VKA treatment between 2006-2007 were searched for items on the HAS-BLED score and the occurrence of major bleeds during the first 180 days of follow-up. The hazard ratio (HR) for the occurrence of major bleeds comparing non-high with high-risk patients as defined by a HAS-BLED score \u2265 3 points was calculated using Cox-regression analysis.Major bleeds occurred in 11/537 patients . Cumulative incidences of major bleeds were 1.3% (95% CI 0.1-2.5) in the non-high (HAS-BLED < 3) and 9.6% (95%CI 2.2-17.0) in the high-risk group (HAS-BLED \u2265 3), (p <0.0001 by Log-Rank test), with a HR of 8.7 (95% CI 2.7-28.4). Of the items in the HAS-BLED score, abnormal renal function and a history of bleeding events were independent predictors of major bleeds during follow-up.Acute VTE patients with a HAS-BLED score \u2265 3 points are at increased risk of major bleeding. These results warrant for correction of the potentially reversible risk factors for major bleeding and careful International Normalized Ratio monitoring in acute VTE patients with a high HAS-BLED score. Venous thromboembolism (VTE) is the third most common cardiovascular disease affecting 1\u20132 per 1000 adults annually \u20136 which Identifying patients at high risk of major bleeding events is therefore of importance and would help physicians targeting bleeding preventive strategies, such as adequate control of hypertension, discouraging the use of non-steroidal anti-inflammatory drugs or platelet-inhibitors, and frequent International Normalized Ratio (INR) monitoring. However, externally validated bleeding risk scores with adequate discriminative power are lacking for the VTE population , whereasThe aim of our study was to analyse whether the HAS-BLED score accurately identifies patients at high risk of major bleeds during VKA treatment for acute VTE.We identified all patients starting VKA treatment for acute VTE between January 2006 and March 2007 via records of the Leiden anticoagulation clinic. This timeframe was chosen to ensure sufficient follow-up time for included patients and treatment of acute VTE according to current clinical practice. Patients had to be treated for acute VTE by the affiliated academic or one of the two affiliated non-academic teaching hospitals of this anticoagulation clinic to be selected for inclusion for logistic reasons . VTE diagnosis was objectified by computed tomography-pulmonary angiography or ultrasound. Patients were managed according to clinical practice with initial low-molecular-weight-heparin followed by long-term VKA therapy (either phenprocoumon or acenocoumarol). The study was approved for all three participating centers by the ethics committee of the Leiden University Medical Center, Leiden, The Netherlands . Patient information was anonymized prior to analysis. The need for informed consent was waived by the ethics committee.Rosendaal method . Wh. Wh37]. Our study adds clinically relevant information to the research field as we analysed the discriminative value of a simple algorithm for the endpoint of major bleeds, of which the items are readily available in daily practice. However, some aspects of our study warrant comment. First, due to its retrospective design, 388 of 537 patients had missing information on one or more items of the HAS-BLED score, most frequently on alcohol use (lacking in 331 patients). These elements were analyzed as normal (i.e. zero points), as indicated by previous studies \u201318. ThisIn conclusion, patients with acute VTE and a HAS-BLED score of three points or higher are at high risk of major bleeding events during anticoagulant treatment. These results warrant for correction of the potentially reversible risk factors for major bleeding and careful INR monitoring in acute VTE patients with a high HAS-BLED score.S1 Database(SAV)Click here for additional data file."} +{"text": "Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection\u2013time-of-flight mass spectrometry analysis the metabolome of (i) nodules and roots from four different B. diazoefficiens host plants; (ii) soybean nodules harvested at different time points during nodule development; and (iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by independent transcriptomics data. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions. Bradyrhizobium diazoefficiens (previously named Bradyrhizobium japonicum) is an \u03b1-proteobacterium able to undergo nitrogen-fixing symbiosis in determinate root nodules of several legumes including Glycine max (soybean), Macroptilium atropurpureum (siratro), Vigna unguiculata (cowpea) and Vigna radiata (mungbean) \u2265 0.5 and q-value \u2264 0.01 were considered significant. To identify nodule-specific compounds, the metabolite levels measured in all nodules samples were compared with the level in all root samples .Ions were annotated based on their accurate mass and the KEGG ne 2015) allowingne 2015) . Unknowny et al. . ChangesnifH and nifA mutant B. diazoefficiens strains 110spc4, H1, and A9, respectively) was extracted and processed as described previously \u2265 1 when comparing two strains. The raw data files for the two mutant strains are accessible through the Gene Expression Omnibus (GEO) Series accession number GSE79811. For comparisons wild-type nodules data (GSM210242\u2013GSM210245) were used.RNA from nodules starvation in nifH nodules , nifA-induced soybean nodules showed signs of additional stress: they produced more phytoalexins and the bacteroids displayed elevated expression of genes involved in type III secretion (Another promising approach to dissect nodule metabolism into the respective bacterial and plant contribution is the use of nodules induced by ecretion . Indeed,B. diazoefficiens, will represent a very useful resource for the Rhizobium community and will stimulate further research of nodule metabolism.We believe that the wealth of data presented here, including the analysis of defined symbiotic mutants, as well as data covering metabolic differences for symbiosis with four different host plants of"} +{"text": "Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis.infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera\u2019s cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns.We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge.As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by A promising approach to address these problems relies on the characterization of cellular functionality in terms of a global description of the interwoven set of biochemical reactions that take place inside the cell. This systemic approach has received a lot of attention in recent years, fostered by the ever growing availability of massive amounts of data generated at In this context, the network metaphor has appeared as an appealing framework to organize and unveil global patterns of biological relevance from the deluge of available data. It provides a systematic description language based on pairwise relationships (i.e. network links or edges) between entities of interest (i.e. network nodes or vertices). This approach allowed to uncover the role of connectivity and interaction patterns in the emergence of biological functions ,2, to ascentral vertices according to network-based centrality indices, with the hope that meaningful biological entities could be recognized. Following this line of research several seminal studies have suggested, for instance, that hub proteins in the S. cerevisiae physical interaction network were more likely to be essential than other proteins, giving rise to the so called centrality-lethality-rule 19]. A scThe BHI figure-of-merit measures the degree a given partition embodies biologically meaningful clusters, using a reference set of functional classes . It basiA bootstrapping procedure was devised to control the node\u2019s degree distribution confounding factor for the role enrichment analysis. For each enrichment test, we considered an ensemble of 1000 control random gene-sets having the same degree distribution than the genes under study. A p-value level was assigned according to the number of random realizations displaying the same or larger effects (over/under representation significance) than the ones observed in the original data. Each random realization was built blindly selecting genes from pools of given degree levels in order to conform the degree distribution displayed by the original gene set node degree distribution for HIPPIE network (gray circles), and for the respective Erdos-Renyi random network (yelow triangles). Nodes of the HIPPIE network (gray circles), Rewired Network (red diamonds) and Erdos-Renyi network (yellow triangles) were displayed over the Degree-Betweenness and the Degree-Clustering Coefficient planes in panels (B) and (C) respectively.(TIF)Click here for additional data file.S2 Figint, as a function of cluster sizes. The dotted and dashed lines depict the expected relationships for fully connected cliques and linear structures respectively, and are included for reference purposes. (b) Fraction of internal CNM cluster\u2019s links that did not appear as internal links in the infomap modular description . Circle sizes are proportional to each CNM cluster log-size.(a) Number of internal links, l(TIF)Click here for additional data file.S3 FigCNM clusters with low internal-link density and more than ten nodes. infomap communities were depicted using different colors. Gray colored nodes belonged to infomap clusters not-totally included in the displayed CNM structure. Two scenarios can be recognized. For cases (a)-(d) a rather good agreement between the alternative modular descriptions was observed. However, for the cases illustrated in panels (e)-(j) internal structure not resolved by the CNM procedure was indeed highlighted by the infomap prescription.(TIF)Click here for additional data file.S4 FigCNM-based and infomap-based cartographical descriptions respectively. An overall increasing behavior in node participation levels can be observed when the infomap cluster recognition procedure was considered.Z-P planes for Batada yeast PPI network (panels A-B) and Bertin yeast PPI Network (panels C-D). Left and right panels correspond to (TIF)Click here for additional data file.S5 FigCNM and infomap modular descriptions are shown with dashed brown and continuous black lines respectively. The vertical dotted line represents the 90% specificity level. Statistically significant differences between total AUCs are observed , suggesting that the resolution level provided by infomap enhanced the detection of the topological bias displayed by ARG genes toward high-participation levels.Participation-based ROC curves estimated for ARG genes for (TIF)Click here for additional data file.S6 FigThe degree distribution of aging genes, and the whole HIPPIE network remaining nodes are shown in the left and right boxplots respectively. Significant differences were observed between both degree distributions.(TIF)Click here for additional data file.S7 FigDegree distributions for selected quantiles of 1000 control random realizations are displayed as boxplot. Blue circles depict ARG degree values for the respective quantiles. It can be observed that the top-10% of ARG with highest degree levels, lay outside the inter-quartile levels of their corresponding control random samples.(TIF)Click here for additional data file.S8 Fig(TIF)Click here for additional data file.S1 TableCNM algorithm resulted in a general tendency to assign lower participation coefficient values to network nodes. For instance 68% of infomap-connector vertices were assigned to lower participation roles when the CNM procedure was considered. More strikingly, the majority (94%) of the 635 infomap-kinless nodes were re-classified as: CNM-connectors (45%), CNM-peripheral (48%), and CNM-ultra-peripheral nodes (1%). Finally, it can also be observed that nodes originally assigned to hub-like roles when infomap procedure was employed were not only affected by this lowering effect in the participation, but in addition, almost 50% of them were also reassigned to non-hub roles when CNM was considered.Distribution of cartographic role assignments according to the Infomap and CNM descriptions. Cartographic role abbreviation: Ultra peripheral (R1), Peripheral (R2), Connector (R3), Kinless (R4), Provincial Hubs (R5), Connector Hubs (R6), Kinless Hubs (R7). The coarser resolution level achieved by the (DOCX)Click here for additional data file.S1 Text(DOCX)Click here for additional data file."} +{"text": "Campylobacter jejuni has been recognized as the leading cause of bacterial gastroenteritis worldwide. This facultative intracellular pathogen is a member of the Epsilonproteobacteria and requires microaerobic atmosphere and nutrient rich media for efficient proliferation in vitro. Its catabolic capacity is highly restricted in contrast to Salmonella Typhimurium and other enteropathogenic bacteria because several common pathways for carbohydrate utilization are either missing or incomplete. Despite these metabolic limitations, C. jejuni efficiently colonizes various animal hosts as a commensal intestinal inhabitant. Moreover, C. jejuni is tremendously successful in competing with the human intestinal microbiota; an infectious dose of few hundreds bacteria is sufficient to overcome the colonization resistance of humans and can lead to campylobacteriosis. Besides the importance and clear clinical manifestation of this disease, the pathogenesis mechanisms of C. jejuni infections are still poorly understood. In recent years comparative genome sequence, transcriptome and metabolome analyses as well as mutagenesis studies combined with animal infection models have provided a new understanding of how the specific metabolic capacity of C. jejuni drives its persistence in the intestinal habitat of various hosts. Furthermore, new insights into the metabolic requirements that support the intracellular survival of C. jejuni were obtained. Because C. jejuni harbors distinct properties in establishing an infection in comparison to pathogenic Enterobacteriaceae, it represents an excellent organism for elucidating new aspects of the dynamic interaction and metabolic cross talk between a bacterial pathogen, the microbiota and the host.During the last decade C. jejuni is associated with acute Campylobacter enteritis in humans causing more than 80% of the registered Campylobacter infections. Predominant sources of infections are contaminated meat , raw milk and water. The clinical manifestations of Campylobacter enteritis are indistinguishable from Salmonellosis and range from mild watery to severe, inflammatory and bloody diarrhea accompanied with abdominal pain and fever and can be isolated from various environmental sources or refrigerated foods. This life style implies that C. jejuni is able to resist varying temperatures, oxygen concentrations, pH values, osmotic environments and nutrient availabilities as reviewed comprehensively elsewhere pathway because they lack the glycolytic enzyme phosphofructokinase, which catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate. However, H. pylori possesses a complete pentose phosphate pathway and an Entner\u2013Doudoroff pathway and the 6-phosphogluconolactonase (EC 3.1.1.31) of the oxidative pentose phosphate pathway branch but harbors all enzymes of the reductive branch of the pentose phosphate pathway , the pyruvate kinase Pyk (Cj0392c) and the pyruvate carboxylase comprise a crucial metabolic junction between catabolism and anabolism in C. jejuni . In addition, other not yet identified transporter proteins are probably involved in the uptake of L- and D-lactate similar as described for H. pylori or Mueller-Hinton (MH) medium family TC 2.A.42.2. The sdaC gene (cj1625c) is organized in an operon with sdaA (cj1624c) encoding for a serine dehydratase that catalyzes the deamination of serine to pyruvate. SdaA harbors, like various respiratory enzymes of C. jejuni, an oxygen-labile [4Fe\u20134S] cluster that might contribute to the oxygen sensitivity of this pathogen of C. jejuni shows 75% identity to the PutP transporter (PutPHp) of the closely related H. pylori harboring genes for two permeases, one ATP-binding protein and one periplasmic substrate-binding protein Peb1A (Cj0921c). The latter has been first described as surface-bound antigen of C. jejuni with homology to amino acid-binding proteins like GlnH and HisJ , which is present in other representatives of the Campylobacteriaceae. Instead, glutamate might either be converted to glutamine by the type I glutamine synthetase GlnA (Cj0699c) or is substrate of the aspartate:glutamate transaminase AspB (Cj0762c) catalyzing the generation of aspartate and 2-oxoglutarate from oxaloacetate and glutamate catalyzing the deamination to fumarate facilitating the conversion of asparagine to aspartate and for a glutamate synthase (GltBD) catalyzing the generation of glutamate from glutamine and 2-oxoglutarate were able to utilize glutamine efficiently for growth resulted from differences in the sequence type (ST) / clonal complex (CC) composition of the analyzed C. jejuni collections as determined by multilocus sequence typing (MLST): The ggt gene was strongly associated with ST-45 CC and ST-22 strains is translocated to the periplasm where it catalyzes the deamination of asparagine to aspartate. Consequently, the growth of ansBs- and ggt-positive C. jejuni isolates with asparagine and glutamine relies on the conversion of both amino acids to aspartate and glutamate in the periplasm and the subsequent uptake of the deaminated amino acids branched-chain amino acid ABC transporter system of E. coli , the putative sodium/serine-threonine symporter, are conserved in C. jejuni and future studies are needed to elucidate their substrate specificity. Besides the aspartate/glutamate-binding protein Peb1A, C. jejuni harbors CjaA, CjaC and GlnH, three additional periplasmic proteins that belong to the family 3 of solute-binding proteins, which might also facilitate the uptake of amino acids. CjaA (Cj0982c) is an N-glycosylated 30 kDa lipoprotein attached to the inner membrane of E. coli, is involved in the catabolism of several tri- and dipeptides , a member of the Proton-dependent Oligopeptide Transporter (POT) family, has been described to promote the growth of C. jejuni 81\u2013176 with the dipeptides Cys-Gly, Arg-Trp and Arg-Ile C. jejuni colonizes preferentially the mucus layer and the intestinal crypt close to the epithelium and the 5\u2032-methylthioadenosine nucleosidase MTAN (Cj0117) exhibits low affinity for oxygen, whereas the cyanide-sensitive, cb-type cytochrome c oxidase CcoNOQP (Cj1490c-Cj1487c) shows high affinity to oxygen and might be crucial for respiration under oxygen-limited conditions and a periplasmic c-type cytochrome (Cj1153).Genome sequence analysis of C. jejuni is equipped with various enzymes facilitating oxygen-independent respiration, no growth can be observed under strictly anaerobic conditions and superoxide (O\u22122) radicals as well as hydrogen peroxide (H2O2). C. jejuni harbors a variety of ROS-detoxifying enzymes including the superoxide dismutase SodB -containing metabolic enzymes pyruvate:acceptor oxidoreductase POR and the oorDABC (cj0535-cj0538) encoded 2-oxoglutarate:acceptor oxidoreductase (OOR) to the oxygen sensitivity of C. jejuni and Cj0369c are no electron acceptors for OOR and flavin adenine dinucleotide (FADH) serve in many bacteria as major electron sources for the respiratory electron transport chain, which generates through the proton-translocating NADH:quinone oxidoreductase (Nuo/NDH-1) complex a proton gradient that drives the oxidative phosphorylation are required for assembling of the hydrogenase enzyme complex and insertion of the nickel cofactor. An ABC-transporter system (Cj1584c-Cj1580c) of C. jejuni NCTC 11168 has recently been identified as a high-affinity nickel uptake system and was named NikZYXWV , encoding for a periplasmic binding protein, led to an abolished hydrogenase activity of the mutant strain. This result demonstrated the importance of the Nik-transporter system for the acquisition of nickel as a cofactor for the enzyme. Yet hydrogenase activity of the nikZ mutant was observed in the presence of high nickel concentrations, indicating the presence of additional nickel transporters complex comprised of the selenocysteine-containing subunit FdhH (Cj1511c), the iron-sulfur subunit FdhB (Cj1510c) and the formate dehydrogenase cytochrome-b subunit FdhC (Cj1509c), which requires FdhD (Cj1508c) for its activity. The released electrons are directly transferred from the FDH complex to the menaquinone pool , FdhU (Cj1501) and a high-affinity TupABC-like tungstate transporter (Cj1538-Cj1540) indicating that tungstate might be incorporated into the FDH complex though inactivation of these genes in C. jejuni NCTC 11168 did not abolish the growth of respective mutants with lactate gene cluster encoding for an anaerobic dimethyl sulfoxide reductase complex in strains like C. jejuni 81\u2013176 SdhABC (Cj0437-Cj0439) of C. jejuni was misannotated and not involved in the conversion of succinate to fumarate system is conserved in C. jejuni and can also be found in C. lari but not in any other examined Campylobacter and Helicobacter species. The periplasmic proteins SorA (Cj0005c) and SorB (Cj0004c) with properties of a molybdopterin oxidoreductase and a monoheme cytochrome c552, respectively, catalyze the oxidation of sulfite to sulfate accompanied by an electron transfer to cytochrome c , MrfB (Cj0438) and MrfE (Cj0439), initially described as SdhABC complex system are additional electron acceptors of C. jejuni in vitro of C. jejuni 81\u2013176 is organized in a gene cluster together with three other gene genes encoding for the iron-sulfur containing DMSO reductase subunit DmsB (CJJ81176_1571), the DMSO reductase anchor subunit DmsC (CJJ81176_1572) and chaperon protein TorD (CJJ81176_1572) that are predicted to participate with DmsA at the electron transfer to DMSO / TMAO or other S- and N-oxides and trimethylamine C. jejuni encodes for the periplasmic located Nap-type nitrate reductase (Cj0780-Cj0785) catalyzing the reduction of nitrate to nitrite and the electron donor protein NrfH (Cj1358c) of the tetraheme NapC/NirT cytochrome C family in the detoxification of nitric oxide but possess like C. jejuni 81116 a less-active TsdA homolog (C8j_0040), which catalyzes the conversions between thiosulfate and tetrathionate at low levels , iron and phosphate transport. Elevated expression of the single-domain globin gene cbg and Cj0358 resulting in a mutant with significantly reduced colonization capability in chicken compared to the wild-type strain as well of a high-affinity zinc ABC transporter system (Cj0143c-Cj0141c) showed a caecum colonization defect in chickens with normal microbiota . To reduce the availability of Fe3+ for pathogens, specific iron-binding proteins like lactoferrin and transferrin sequester ferric iron in host organisms. To overcome this iron limitation commensal and pathogenic bacteria secret siderophores, specific iron chelators with higher affinity to Fe3+ than the iron-binding proteins of the host , which occurs in C. jejuni NCTC 11168 and other cfrA-positive strains as a pseudogene gene cluster is widespread in C. jejuni and encodes for an iron uptake system that facilitates the utilization of the host compounds like hemoglobin and hemin as iron sources iron. Some C. jejuni strains take up Fe2+ through the FeoB transport protein , the biosynthesis of amino acids , purines and fatty acids . In addition, several protein- and peptide-degrading proteins and transporters involved in the uptake of amino acids , phosphate (PstS) and metals like iron (Cj0175c), tungsten (TupA) or nickel (NikZ) showed lower levels 20 h post-infection exhibited decreased protein levels after 20 h inside cultured epithelial cells. Such a decreased level was also seen for the formate dehydrogenase (FdhAB), the nitrate (NapAB) and nitrite (NrfA) reductases. C. jejuni seems to adapt its respiration mode to the oxygen-restricted conditions inside the CCV , nitrate and TMAO or other N- and S-oxide respiration showed also no intracellular survival defect as being upregulated during the first 6 h post-infection of the cultured epithelial cells in C. jejuni 81\u2013176 comparable to a mutant strain lacking the polyphosphate kinase 1 (ppk1) mutant. PPK1 uses ATP for the generation of poly-P, which participates in the stress response of C. jejuni and enables the survival during osmotic shock and low-nutrient stress. It was demonstrated that PPK1 is required for extended survival in infected INT407 cells (Candon et al., ppk1 mutation results, similar to the mutation of spoT, in pleiotropic effects, it does not allow the identification of mechanisms solely required for the intracellular survival. Poly-P might not only be important as a metabolic regulator and protector against various stresses like hydrogen peroxide and osmotic stress, it might also serve as an energy and phosphate source (Kornberg, C. jejuni while residing in the nutrient restricted environment of the CCV.Additional insights into the intracellular lifestyle of C. jejuni to thrive in the gastrointestinal lumen of its hosts, how C. jejuni maintains its viability inside invaded epithelial cells and energizes its intracellular persistence remains ill-defined.Though progress has been made in recent years to describe the nutrient requirements that allow C. jejuni. Such short-term interactions prevent co-evolution and potential fine-tuning of Campylobacter virulence factors. Consequently, the evolutionary forces that shape the metabolic and pathogenic properties of C. jejuni occur during the interactions with the microbiota of its primary hosts rather than within the human gastrointestinal ecosystem. Still, the metabolic framework of C. jejuni is sufficient to overcome the colonization resistance in the human gastrointestinal tract and to efficiently promote its proliferation, leading consequently to the development of diarrhea. These findings illustrate the necessity for future comprehensive studies to investigate the extent to which metabolic factors mediate the long-term persistence of C. jejuni in its natural hosts like chicken and cattle. Specifically targeting such growth-promoting metabolic pathways for the development of drugs might not only lower the colonization burden in animal hosts with C. jejuni but will consequently lower the exposure doses for humans. Moreover, the restricted carbohydrate catabolism of C. jejuni in comparison with other enteropathogenic pathogens like S. Typhimurium (Becker et al., Campylobacter.Campylobacteriosis of humans in industrialized countries is assumed to be an accidental and transitory event in the life style of The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest."} +{"text": "Oocytes and early embryos contain minute amounts of DNA, RNA and proteins, making the study of early mammalian development highly challenging. The study of the embryo epigenome, in particular the DNA methylome, has been made accessible thanks to the possibility of amplifying specific sequences according to their initial methylation status. This paper describes a novel platform dedicated to the genome-wide study of bovine DNA methylation, including a complete pipeline for data analysis and visualization. The platform allows processing and integrating of DNA methylome and transcriptome data from the same sample. Procedures were optimized for genome-wide analysis of 10\u00a0ng of DNA (10 bovine blastocysts). Bovine sperm and blastocysts were compared as a test of platform capability.The hypermethylation of bovine sperm DNA compared to the embryo genome was confirmed. Differentially methylated regions were distributed across various classes of bovine sperm genomic feature including primarily promoter, intronic and exonic regions, non-CpG-island regions and CpG islands with low-to-intermediate CpG density. The blastocyst genome bore more methylation marks than sperm DNA only in CpG islands with high CpG density. Long-terminal-repeat retrotransposons (LTR), LINE and SINE were more methylated in sperm DNA, as were low-complexity repetitive elements in blastocysts.This is the first early embryo compatible genome-wide epigenetics platform for bovine. Such platforms should improve the study of the potential epigenetic risks of assisted reproductive technologies (ART), the establishment sequence of embryonic cell lines and potential deviations in both gene expression and DNA methylation capable of having long-term impact.The online version of this article (doi:10.1186/1471-2164-15-451) contains supplementary material, which is available to authorized users. The study of early embryonic development continues to pose formidable technical challenges due in large part to the limited amounts of sample material. However, high-throughput high-fidelity amplification of nucleic acid is making the macromolecular study of embryonic physiology more accessible. Microarray platforms, and more recently RNAseq, have made studying the early embryo transcriptome almost routine. Our group has been developing bovine and porcine microarrays based on transcriptomic platforms that include standardized sample preparation procedures and a complete user-friendly software suite for data normalization and analysis, allowing efficient processing of samples from extraction through to the generation of publishable graphs, 2. Tranin vivo/vitro culture, uterine conditions, or maternal nutritional regimen has represented a major challenge and continues to do so, due mainly to sample scarcity offering input DNA well below minimal recommendations.Among epigenomic effectors, DNA methylation is believed to be a strong primary molecular mark having a major impact on intergenerational gene silencing, 16. DNANumerous platforms already exist to study methylation of targeted loci or to obtain genome-wide methylation profiles. For the study of very small samples, determining DNA methylation at targeted loci has so far been more successful than genome-wide approaches. The maihttp://www.genomesize.com) and the expanded blastocyst of large mammalian species is composed of about 150 cells, a single bovine blastocyst contains approximately 1\u00a0ng of DNA. The current benchmark for minimal sample size is around 10\u00a0ng, therefore corresponding to a pool of 10 expanded blastocysts. The other criterion is ease of use, at both the sample handling and data processing steps. We thus sought to identify an existing methodological approach which would be best suited to analyze very small samples of DNA. The platform was tested and validated using experimental samples.The aim of the present work was to develop a technological platform that is complementary to existing platforms, in order to provide a whole-genome view of DNA methylation in bovine early embryos. Since a diploid mammalian nucleus contains about 6.8 picograms of DNA (http://embryogene.ca) DNA Methylation Analysis (EDMA) platform was designed for high-throughput methylation profiling of bovine genome using limited amounts of input material. It combines four independent methodological principles: i) restriction endonuclease-based (RE) (MseI) genomic DNA fragmentation; ii) targeting methylated regions using a cocktail of methyl-sensitive restriction endonucleases; iii) amplification of methylated (thus protected) fragments using ligation-mediated PCR; and iv) identification of the amplified methylated fragments using a microarray. The EDMA workflow is presented in Figure\u00a0The EmbryoGENE restriction sites, namely C/CGG (HpaII), GC/GC (HinP1I) and C/CGC (Aci1I). Distribution of common and unique MSRE sites within MseI fragments is shown in Additional fileMseI fragments containing MSRE sites within the genomic loci that we previously found to bear methylation or hydroxymethylation marks in early bovine embryos: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57709).The dataset of microarray results have been deposited in NCBI\u2019s Gene Expression Omnibus (GEO) and are accessible through GEO series accession number: GSE57709 The Venn diagram shows the overlaps between restriction sites of the HELP cocktail MSREs within the genomic MseI fragments targeted by EDMA probes. Figure S2. This figure shows the histogram number of (A) CpG dinucleotide per MseI restriction fragments and histograms number of MSREs ((B) HpaII; (C) HinP1I; (D) AciI) restriction sites per restriction fragments in EDMA. Figure S3. This figure clearly shows that there is not any correlation between the determined EDMA fold change and Pyrosequening results due to the enrichment-based nature of the applied protocol. (PDF 478 KB)Additional file 1: Figure S1: (A) This histogram shows the Table S2. Genomic and CpG coverage by MseI fragments targeted by EDMA probes as a function of the MSRE sites present within those fragments. Table S3. Gene and CpG Island coverage by EDMA probes. Table S4. Breakdown of the location of EDMA probes in relation to annotated features of the bovine genome. Table S5. The properties of the selected hypermethylated DMRs and their primers designed used for pyrosequencying. (PDF 497 KB)Additional file 2: Table S1: The designed Primers for the MSRE digestion quality control step."} +{"text": "However, direct visualization of cGMP in subcellular microdomains of adult cardiomyocytes has been challenging. Little is known also about changes in cardiomyocyte cGMP signalling at an early stage of the disease.We used a highly sensitive cytosolic and membrane-targeted F\u00f6rster resonance energy transfer (FRET)-based biosensors for cGMP and cAMP for real time measurements in freshly isolated sensor-trasngenic adult ventricular cardiomyocytes. Combined with single cell contractility measurements, biochemical techniques and whole-heart recording, the effect of atrial natriuretic peptide (ANP) on cardiomyocyte cGMP/cAMP and contractility in healthy and hypertrophied hearts (after transverse aortic constriction).Contractility measurements in hypertrophied hearts have unravelled ANP-induced augmentation of catecholamine stimulated increase in force and frequency of contraction which was present only in diseased hearts at the state of early compensated cardiac hypertrophy. Interestingly, this effect was not due to changes in cGMP content, membrane receptor densities or whole-cells phosphodiesterase (PDE) activity. Instead, physical redistribution of the cGMP-stimulated PDE2 and cGMP-inhibited PDE3 between distinct membrane domains led to a change of cAMP compartmentation towards an ANP/cGMP/PDE3-dependent increase of local cAMP levels in a microdomain regulating cardiac contractility . FRET-baANP/cGMP signalling can play distinct roles in cardiac disease, including a previously unrecognized contractility augmentation in early hypertrophy which might support heart function upon pressure overload. This can be achieved by PDE2/3 redistribution-dependent changes in cGMP/cAMP compartmentation."} +{"text": "The long-term outlook for regenerative medicine predicts an increased need for high quality materials that are compatible with the limited number of downstream processing steps required for cell-based therapies. Large scale manufacturing of adherent-dependent cell types necessitates movement away from planar culture and toward technologies such as stirred tank bioreactors where suspension culture using microcarriers is enabled . MicrocaTo evaluate different microcarriers, human adipose-derived MSCs (aMSCs) were grown on a panel of microcarriers in Petri dishes, 125 mL spinner flasks, or Mobius\u00ae 3 L bioreactors in DMEM supplemented with 10% FBS and 8 ng/mL bFGF (DMEM FBS). TrypLE was used to detach a MSCs from microcarriers to assess recovery.To evaluate different media formulations, human bone marrow-derived MSCs (bmMSCs) were grown on gelatin-coated T-flasks for planar culture or seeded onto collagen-coated microcarriers in 125 mL spinner flasks for suspension culture. Planar cultures were maintained in respective media from passage 4 to 8. Top performing media were further evaluated in microcarrier-based suspension culture for 7 days. Serum (DMEMFBS) control flasks were run in parallel.Cell were seeded at 3k cells / cm2 and 5.4 cm2 / mL of culture surface was provided in all microcarrier experiments. Nexcelom Cellometer\u00ae and NucleoCounter\u00ae devices were used for cell counting.Six commercially-available microcarriers were tested for their ability to support growth, detachment and viability of a MSCs expanded in DMEM FBS. The evaluation was conducted in both static culture (Petri dishes) and agitated culture (spinner flasks). Microcarriers were assigned a rank based on their overall performance in the two platforms Table . MicrocaA number of serum-free (SF), xeno-free (XF) and low serum (LS) media were evaluated for expansion of bmMSCs in both planar and microcarrier-based suspension culture. Human platelet lysate (PL), a serum alternative, was also tested in the microcarrier-based culture. Wide variation in the support of growth was observed when bmMSCs were cultured for multiple passages in planar culture in different media Figure . Only 4 The observation that some microcarriers and cell culture media that support robust MSC growth in static or planar culture do not perform in microcarrier-based suspension culture highlights the complex interaction between culture surface, media formulation and hydrodynamic forces introduced by agitation. Small scale platforms such as Petri dishes and spinner flasks are convenient tools for initial screening of many microcarriers or media, but a sufficient number of top performers need to be moved into bioreactor suspension culture for further evaluation. A better understanding of the underlying biological requirements of adherent-dependent cells in suspension culture will foster the development of high quality reagents that support expansion across platforms. The combination of serum-free systems with animal origin-free materials will be required to support the future implementation of large scale manufacturing solutions following clinical success of cell-based therapies."} +{"text": "Cow's milk Oral Immunotherapy (CM-OIT) is still an experimental treatment. The development of novel biomarkers to predict the safety and efficacy of CM-OIT is crucial to translate this treatment to common clinical practice.To analyze long-term changes in IgE and IgG4 epitope binding profile during CM-OIT to identify safety and efficacy biomarkers.We studied 25 CM-allergic children at baseline, after oral desensitization, and at 6, 12 and 24 months of follow-up. Seven patients who refused CM-OIT were used as controls. Patients were classified as low, moderate, and high risk according to the number of allergic reactions (safety), time required to achieve tolerance (efficacy), and requirement of premedication. IgE and IgG4 peptide microarray immunoassay was performed using a library of overlapping peptides of CM proteins.CM-OIT produced a rapid increase of IgG4-binding epitopes and slow decrease in IgE-binding epitopes. High risk patients recognized a higher number of IgE-positive peptides than low and moderate risk patients, with significant increases in caseins at all the times studied. Similar but less pronounced changes were observed for IgG4-positive peptides. Clustering analysis grouped together the high risk patients and we identified 13 regions of caseins significantly different between groups of patients. Bioinformatics analysis selected a set of 16 IgE-binding peptides at baseline that predicted safety and efficacy of CM-OIT.We developed a novel diagnostic approach based on a set of IgE-binding peptides that can be used as biomarkers to predict the safety and efficacy of CM-OIT before starting treatment."} +{"text": "Arabidopsis miRNAs have been predicted. Putative target mRNAs have been identified for most of the candidate genes.Using bioinformatic methods, 83 novel Arabidopsis thaliana microRNAs and their target mRNAs. This method uses characteristic features of known plant miRNAs as criteria to search for miRNAs conserved between Arabidopsis and Oryza sativa. Extensive sequence complementarity between miRNAs and their target mRNAs is used to predict miRNA-regulated Arabidopsis transcripts.A class of eukaryotic non-coding RNAs termed microRNAs (miRNAs) interact with target mRNAs by sequence complementarity to regulate their expression. The low abundance of some miRNAs and their time- and tissue-specific expression patterns make experimental miRNA identification difficult. We present here a computational method for genome-wide prediction of Arabidopsis miRNAs and identified 83 new miRNAs. Evidence for the expression of 25 predicted miRNAs came from northern blots, their presence in the Arabidopsis Small RNA Project database, and massively parallel signature sequencing (MPSS) data. Putative targets functionally conserved between Arabidopsis and O. sativa were identified for most newly identified miRNAs. Independent microarray data showed that the expression levels of some mRNA targets anti-correlated with the accumulation pattern of their corresponding regulatory miRNAs. The cleavage of three target mRNAs by miRNA binding was validated in 5' RACE experiments.Our prediction covered 63% of known Arabidopsis and O. sativa and report a wide range of transcripts as potential miRNA targets. Because MPSS data are generated from polyadenylated RNA molecules, our results suggest that at least some miRNA precursors are polyadenylated at certain stages. The broad range of putative miRNA targets indicates that miRNAs participate in the regulation of a variety of biological processes.We identified new plant miRNAs conserved between Arabidopsis thaliana and Caenorhabditis elegans to mouse and human are non-coding RNA molecules with important regulatory functions in eukaryotic gene expression. The majority of known mature miRNAs are about 21-23 nucleotides long and have been found in a wide range of eukaryotes, from iewed in . Experimd so far ,13,15-17C. elegans let-7 is sufficient for its specific expression at different developmental stages ATP and T4 polynucleotide kinase (New England Biolabs) to generate high specific activity probes. Hybridization was carried out using the ULTRAHyb-Oligo solution according to the manufacturer's directions (Ambion), and signals were detected by autoradiography.Two-day-old seedlings, 4-week-old adult plants, root-regenerated calluses and mixed-stage flowers of Arabidopsis miRNAs. If an intergenic region encoding a miRNA had fewer than 500 nucleotides on either side of the miRNA locus, sequences were extracted up to the neighboring gene.To obtain genomic regions corresponding to miRNA precursors, we extracted 500 nucleotides upstream and downstream of every genomic locus of all known and predicted Arabidopsis MPSS datasets were used in this study: a MPSS database from abscisic acid (ABA)-treated plants, and plants with elevated levels of endogenous cytokinin [Arabidopsis tissues at different developmental stages - around 10-week-old active growing calluses initiated from seedlings, mixed-stage buds and immature flowers, 14-day-old leaves, 14-day-old roots and 24- to 48-h post-fertilization siliques [Two ytokinin ,44 and asiliques .Arabidopsis miRNAs and their O. sativa orthologs were used as query datasets. mRNA sequences of the Arabidopsis and O. sativa annotated genes were used as target datasets. Gaps were allowed in the pairing of miRNA and their target mRNAs. Mismatches were preferred over gaps by assigning higher penalties to gaps in the alignment algorithm. Consecutive gaps were preferred over scattered individual gaps by assigning higher penalties to gap opening than to gap extension. The top 500 putative hits from Arabidopsis miRNA target list and their O. sativa ortholog target list were compared. For each mRNA hit of an Arabidopsis miRNA, if a rice ortholog from the same gene family was also found among the top 500 rice miRNA hits, the Arabidopsis mRNA hit was selected as a putative miRNA target.miRNA target gene prediction was performed by aligning miRNA sequences with target mRNA sequences using the TimeLogic implementation of the Smith-Waterman nucleotide-alignment algorithm. Sequences of known and predicted Tissue comparison (reference vs flower) microarray data used for target gene validation were downloaded from TAIR . mRNA saTo identify the products of miRNA-directed cleavage we used the First Choice RLM-RACE Kit (Ambion) in 5' RACE experiments, except that we used total RNA (2 \u03bcg) for direct ligation to the RNA adaptor without further processing of the RNA sample. Subsequent steps were according to manufacturer's directions. Oligonucleotide sequences for PCR amplification of At3g26810, At1g12820 and TIR1 (At3g62980) are available upon request.Arabidopsis miRNAs using the MEME motif-searching software and Smith-Waterman gapped local alignment to identify homologs of known miRNAs. Pairs of aligned sequences were grouped by transitive closure, and multiple alignments were generated with ClustalW [Predicted miRNAs were compared to known ClustalW -54. The We used mfold program to calculate the free energy (\u0394G) of predicted miRNA::mRNA pairs. For each miRNA::mRNA pair, the miRNA sequence was linked by 'LLL' to the target mRNA sequence. The 'LLL' linker sequence tells the mfold program to treat the miRNA and target sequence as two separate RNA sequences for energy calculation .Arabidopsis miRNAs, some of which are included among the predicted miRNAs in this work, confirming the validity of our approach.During revision of this manuscript, three groups -57 reporArabidopsis miRNA candidates and their rice orthologs (Additional data file Arabidopsis miRNAs (Additional data file The following additional data are available with the online version of this paper: the complete list of predicted miRNAs (Additional data file The complete list of predicted miRNAsClick here for additional data fileArabidopsis miRNA candidates and their rice orthologsA full list of the secondary structures of predicted precursors of Click here for additional data fileArabidopsis miRNAsMPSS evidence for known and predicted Click here for additional data filea complete list of predicted target mRNAs and their pairing with miRNA sequencesClick here for additional data file"} +{"text": "We previously reported that lifetime consumption of soy proteins or whey proteins reduced the incidence of azoxymethane (AOM)-induced colon tumors in rats. To obtain insights into these effects, global gene expression profiles of colons from rats with lifetime ingestion of casein , soy protein isolate (SPI), and whey protein hydrolysate (WPH) diets were determined.Male Sprague Dawley rats, fed one of the three purified diets, were studied at 40 weeks after AOM injection and when tumors had developed in some animals of each group. Total RNA, purified from non-tumor tissue within the proximal half of each colon, was used to prepare biotinylated probes, which were hybridized to Affymetrix RG_U34A rat microarrays containing probes sets for 8799 rat genes. Microarray data were analyzed using DMT (Affymetrix), SAM (Stanford) and pair-wise comparisons. Differentially expressed genes (SPI and/or WPH vs. CAS) were found. We identified 31 induced and 49 repressed genes in the proximal colons of the SPI-fed group and 44 induced and 119 repressed genes in the proximal colons of the WPH-fed group, relative to CAS. Hierarchical clustering identified the co-induction or co-repression of multiple genes by SPI and WPH. The differential expression of I-FABP , cyclin D1 , and the c-neu proto-oncogene mRNAs were confirmed by real-time quantitative RT-PCR. SPI and WPH affected colonic neuro-endocrine gene expression: peptide YY (PYY) and glucagon mRNAs were down-regulated in WPH fed rats, whereas somatostatin mRNA and corresponding circulating protein levels, were enhanced by SPI and WPH.The identification of transcripts co- or differentially-regulated by SPI and WPH diets suggests common as well as unique anti-tumorigenesis mechanisms of action which may involve growth factor, neuroendocrine and immune system genes. SPI and WPH induction of somatostatin, a known anti-proliferative agent for colon cancer cells, would inhibit tumorigenesis. Colorectal cancer (CRC) is the third most common cancer and the third leading cause of cancer-related mortality in the U.S. ,2. Estimet al., among others, reported that genistein inhibits colon cancer cell proliferation and stimulates apoptosis in vitro . A re24 primer and Superscript II . The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.Total RNA was isolated from rat proximal colons using TRIzol reagent , and further purified with the RNeasy Mini Kit . To remove contaminating DNA, on-column DNA digestion with RNase-Free DNase (QIAGEN) was performed. Integrity of isolated RNAs was confirmed using the RNA 6000 Nano LabChip kit with the Agilent 2100 Bioanalyzer System . To reduce errors due to biological variability, RNA samples were pooled as proposed by Bakay et al . Pooled Ten ug of cRNA was hybridized for 16 hours to an Affymetrix rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin. Following washing, GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software. Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes \u03b2-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target. To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.To validate the microarray procedure for our samples, unsupervised nearest-neighbor hierarchical clustering was performed on gene expression data. The inter-chip variability test also was performed as specified in the Affymetrix data analysis manual . To idenP < 0.05).One \u03bcg of total RNA from each of the 21 individual proximal colons was reverse-transcribed using random hexamers and MultiScribe Reverse Transcriptase in a two-step RT-PCR reaction . Primers Table were desRat serum Sst content was determined using the somatostatin-28 EIA kit purchased from Phoenix Pharmaceuticals Corporation .RX performed the microarray and real-time PCR experiments, conducted the data analysis, and participated in drafting the manuscript. TMB designed and oversaw the animal component of the study. FAS designed the analytical and overall approaches to the study, supervised the project, and drafted the manuscript. All authors read and approved the final manuscript."} +{"text": "The coronavirus disease 2019 (COVID-19) has a great impact on health care workers (HCWs) who are exposed to high levels of stress and trauma leading to negative mental health outcomes, including stress-related symptoms and depressive symptoms.The aim of this study was to investigate the prevalence of depressive symptoms, anxiety and post traumatic stress symptoms related to to the COVID 19 pandemic in Cyprus.In this cross-sectional study, we report on mental health outcomes among HCWs in Cyprus. Data were collected between May 3rd and May 27th, 2020, using an online questionnaire that included demographics, the 9-item Patient Health Questionnaire (PHQ-9), assessing depressive symptoms, the Impact of Events Scale Revised (IES-R) measuring PTSD symptoms and the 10 item Perceived Stress Scale (PSS) measuring stress.424 Health Care Workers (HCWs) participated in the study. 79 HCWs scored in PHQ-9 above the cut-off for depression while 62 HCWs scored high enough in IES-R indicating a diagnosis of post-traumatic stress disorder. The prevalence of depression and PTSD symptoms were significantly higher among nurses compared to doctors and other HCWs. , after adjustment for age and sex.Even in countries like Cyprus with minimum impact of the COVID-19 pandemic, the impact on the mental health of HCWs is substantial with nurses being more vulnerable."} +{"text": "Malaria is a devastating infectious disease that disproportionally threatens hundreds of millions of people in developing countries. In the history of anti-malaria campaign, chloroquine (CQ) has played an indispensable role, however, its mechanism of action (MoA) is not fully understood.We used the principle of photo-affinity labeling and click chemistry-based functionalization in the design of a CQ probe and developed a combined deconvolution strategy of activity-based protein profiling (ABPP) and mass spectrometry-coupled cellular thermal shift assay (MS-CETSA) that identified the protein targets of CQ in an unbiased manner in this study. The interactions between CQ and these identified potential protein hits were confirmed by biophysical and enzymatic assays.We developed a novel clickable, photo-affinity chloroquine analog probe (CQP) which retains the antimalarial activity in the nanomole range, and identified a total of 40 proteins that specifically interacted and photo-crosslinked with CQP which was inhibited in the presence of excess CQ. Using MS-CETSA, we identified 83 candidate interacting proteins out of a total of 3375 measured parasite proteins. At the same time, we identified 8 proteins as the most potential hits which were commonly identified by both methods.We found that CQ could disrupt glycolysis and energy metabolism of malarial parasites through direct binding with some of the key enzymes, a new mechanism that is different from its well-known inhibitory effect of hemozoin formation. This is the first report of identifying CQ antimalarial targets by a parallel usage of labeled (ABPP) and label-free (MS-CETSA) methods.The online version contains supplementary material available at 10.1186/s40779-022-00390-3. Plasmodium vivax (P. vivax), Plasmodium ovale, Plasmodium malariae, and Plasmodium knowlesi, but not Plasmodium falciparum in which CQ resistance unfortunately becomes a widespread phenomenon -N-ethylpentanamide. The click reaction of azide 5-Azido-N-(4-(7-chloroquinolin-4-ylamino) pentyl)-N-ethylpentanamide with diyne finally produced CQP and P. falciparum 3D7 parasite lysate was incubated with CQP or DMSO vehicle in the presence or absence of CQ, followed by UV irradiation and biotin moiety incorporation through click reaction. The CQP-binding targets were then retrieved by biotin-streptavidin affinity purification and identified by quantitative proteomics. The TMT-based multiplexing scheme was chosen for parallel analysis of samples from three different treatment conditions, in order to improve statistical power , PfOAT (PF3D7_0608800), PfPyrK (PF3D7_0626800), PfPGK (PF3D7_0922500) and PfTPI (PF3D7_1439900). To start with, we retrieved the structures of these 5 proteins from PDB database and modelled the binding poses of CQ to them through molecular docking simulation Fig.\u00a0a\u2013e. In sSubsequently, we conducted Gene Ontology enrichment analysis on the target proteins commonly identified in ABPP and MS-CETSA strategy, and the result also suggested that CQ could disrupt the glycolytic and energy metabolic processes of parasite to exert antimalarial effects . In our dataset, falcilysin as well as other hemoglobin proteolytic enzymes including plasmepsin II and plasmepsin IV also showed significant thermal shift. On the other hand, multidrug resistance protein 1 was identified as an interacting hit protein in our ABPP dataset, which has been demonstrated in previous study [To the best of our knowledge, this is the first report of identifying the CQ antimalarial targets by a parallel usage of labelled (ABPP) and label-free (MS-CETSA) methods. ABPP and MS-CETSA use different working principles for target deconvolution. ABPP is based on the affinity association between the drug and its target, whereas the readout of CETSA is thermal stabilization/destabilization of proteins upon drug binding . A distius study , 46. It us study . TherefoPfLDH, PfOAT, PfPyrK, PfPGK and PfTPI) we identified and verified are all important proteins related to glycolysis and energy metabolism of parasites, indicating that this is likely to be an important research direction related to antimalarial. In addition, this work established a new research strategy for the MoA study of other important but not-well-understood drugs.This work provides to a more complete understanding of the working mechanism of the antimalarial drug CQ. It is not our intention to challenge the classic view of CQ in inhibiting hemozoin formation. We instead attempted to unravel other overlooked mechanisms of CQ underlying its antimalarial activity. It is of great significance to alleviate the resistance of CQ in malaria treatment and expand the use of CQ for new indications. The 5 target proteins and Biotin-N3 (B) of CuAAC-based click chemistry reaction. Fig. S2 Heat map representation of the target proteins dataset identified by the CQP-based ABPP. The expression levels of all proteins are standardized to Z-score values. Fig. S3 Gene Ontology (GO) analysis of the enriched biological process (BP) (a), cellular component (CC) (b) and molecular function (MF) (c) for chloroquine targets identified by CQP-based ABPP. Fig. S4 GO enrichment analysis of biological process (BP) (a), cellular component (CC) (b) and molecular function (MF) (c) for chloroquine targets identified by MS-CETSA.Additional file 3: Table S1. Antibodies used for Western blotting validation. Table S2 Target proteins identified by CQP-based ABPP. Table S3 Potential hits identified by MS-CETSA."} +{"text": "In the last 3 years, COVID-19 pandemic has produced great impacts on global population in terms of health and social costs. Pneumonia represents only one of several pathologies associated to COVID-19 disease. Among these, the cerebral venous thrombosis (CVT), constitutes an important cause of stroke. Here, we report a case of CVT diagnosed approximately 2 weeks after first dose of Pfizer-BioNTech vaccination, in a patient affected by COVID-19 few months earlier. He presented with headache and severe asthenia. The laboratory tests put in evidence thrombocytopenia and D-dimer elevation. A brain magnetic resonance imaging (MRI) and a computed tomography (CT) demonstrated hemorrhagic and ischemic phenomena on the right ventral thalamic nuclei, left thalamus, hippocampal and parahippocampal regions and the splenium of the corpus callosum. The study revealed a poorly opacified vein of Galeno and straight sinus. Heparin administration improved his clinical status; platelets values also arose over time."} +{"text": "Background: The COVID-19 pandemic has made a significant impact on antimicrobial use patterns across health systems. We have described antibiotic use patterns at an academic medical center in Richmond, Virginia, before and after the onset of COVID-19. We also examined the impact on the proportional consumption of carbapenems (PoCC) metric. PoCC represents meropenem utilization relative to the narrower-spectrum antipseudomonal agents cefepime and piperacillin-tazobactam. Our institution practices antimicrobial restriction for meropenem. All other antibiotics included in the study data can be freely ordered by any provider. Methods: We evaluated antimicrobial use data from September 2018 through August 2021 using days of therapy (DOT) per 1,000 patient days. We included 18 months of data before and after the first recorded COVID-19 admission at our institution in March 2020. Mean comparisons were performed using the Welch 2-sample t test. The Bonferonni correction for multiple comparisons was utilized to determine significance with an initial baseline \u03b1 of 0.05. All data analyses were performed using R software . Results: Normality was evaluated with QQ-plots and all data demonstrated normality. Bonferroni correction produced an adjusted \u03b1 value of 0.007. We detected significant increases in the use of cefepime, piperacillin-tazobactam, ceftriaxone, and azithromycin following the onset of the COVID-19 pandemic. We noted a significant decrease in the PoCC metric during this period. No significant change was noted for levofloxacin or meropenem. Conclusions: The COVID-19 pandemic produced significant changes in antimicrobial use patterns at our institution. We noted statistically significant increases in bacterial community-acquired pneumonia-focused antibiotics (ceftriaxone and azithromycin). We observed significant increases for cefepime and piperacillin-tazobactam. Interestingly, relative utilization of carbapenems as measured by the PoCC metric continued to decrease during this time. This trend was primarily driven by increases in cefepime and piperacillin-tazobactam utilization while meropenem utilization remained relatively constant. This study highlights the importance of looking at normalized antibiotic consumption data and not relative-use data alone.Funding: NoneDisclosures: None"} +{"text": "Anxiety is a significant mental health problem among older adults and is commonly comorbid with personality disorders (PD). However, specific relationships between personality functioning (a proposed feature of PDs) and late-life anxiety remain unclear. This study examined relationships between two models of personality functioning with late life clinical anxiety and COVID-19 anxiety. Method: Older adults (n = 222) completed the Geriatric Anxiety Scale (GAS), Coronavirus Anxiety Scale (CAS), Levels of Personality Functioning Scale-Self-Report (LPFS-SR), and Severity Indices of Personality Problems-Short Form (SIPP-SF).The GAS and CAS were significantly correlated to all LPFS-SR and SIPP-SF domains with large effect sizes (> .78); higher clinical and COVID-19 anxiety was associated with increased personality dysfunction. In regressions, the LPFS-SR domains significantly accounted for 65% of variance in the GAS and 59% of variance in the CAS. Identity and Self-Direction were the strongest predictors of each anxiety scale, with Empathy also significantly related to coronavirus anxiety. The SIPP-SF domains significantly accounted for 65% of variance in the GAS and 58% of variance in the CAS. Responsibility and Social Concordance were the strongest predictors of each anxiety scale, with Self-Control also significantly related to clinical anxiety. Discussion: Results indicate theoretically-supported and meaningful overlap between clinical and COVID-19 anxiety with personality dysfunction according to two different models. This extensive overlap questions the extent to which personality functioning differentiates from affective distress. The two personality dysfunction models also differed somewhat in their relationships to anxiety, suggesting the need for further research especially among older adults."} +{"text": "This Special Issue comprises three original studies and five review articles. These publications highlight various aspects regarding the involvement of transcription factors in cancer. Two of the experimental papers address the functions of particular transcription factors in specific cancer types: SRY-box transcription factor 9 (SOX9) in chondrosarcoma and Yin Yang 1 (YY1) in B-cell non-Hodgkin lymphomas (B-NHLs) . In thesThe article by Vivarelli et al. focuses Cancers was devoted entirely to this topic: RKIP: A Pivotal Gene Product in the Pathogenesis of Cancer [RKIP promoter and negatively regulates the expression of the RKIP gene [The third experimental publication in this Special Issue is concerned with the Raf kinase inhibitory protein (RKIP), also known as a phosphatidylethanolamine-binding protein 1 (PEBP1), and metadherin (MTDH) . Technicf Cancer . In thisf Cancer investigKIP gene .The remaining five publications in this Special Issue are review articles. Kr\u00fcppel-associated box zinc finger proteins (KRAB-ZFPs) constitute a family of transcription factors that primarily perform co-repressor functions in mammalian cells. Sobocinska et al. explaineNRF2 and KEAP1 genes that induced HCC development and discussed their relevant molecular mechanisms.Kr\u00fcppel-like factor 4 (KLF4) acts as a tumor suppressor in many cancer types, but its functions and regulation are very complex. Taracha-Wisniewska et al. discusseEndoplasmic reticulum (ER) stress leads to the accumulation of misfolded proteins and triggers unfolded protein responses (UPRs) . This meIn summary, transcription factors constitute the largest functional class of proteins in all living organisms. They regulate the expression of all genes and are located at critical points in signaling pathways. Their activity is altered in numerous cancer types. Many of them act as essential tumor suppressors, while others are key oncogenic drivers and are considered to be very promising therapeutic targets ,16. For"} +{"text": "Megaptera novaeangliae), make capture and release health assessments unfeasible for conservation research. However, individual energetic condition or reproductive health may be assessed from the gene expression of remotely biopsied tissue. To do this, researchers must reliably extract RNA and interpret gene expression measurements within the context of an individual's sex. Here, we outline an RNA extraction protocol from blubber tissue and describe a novel mammalian RNA sex determination method. Our method consists of a duplex reverse transcription-quantitative polymerase chain reaction (RT-qPCR) with primer sets for a control gene (ACTB) and the X-chromosome inactivation gene (XIST). Products of each RT-qPCR had distinct melting temperature profiles based on the presence or absence of the XIST transcript. Using high-resolution melt analysis, reactions were sorted into one of two clusters based on their melting profiles. We validated the XIST method by comparing results with a standard DNA-based method. With adequate quantities of RNA (minimum of approx. 9 ng \u00b5l\u22121), the XIST sex determination method shows 100% agreement with traditional DNA sex determination. Using the XIST method, future cetacean health studies can interpret gene expression within the context of an individual's sex, all from a single extraction.The large size of free-ranging mysticetes, such as humpback whales ( The angliae, . MonitorTursiops truncatus, )"} +{"text": "We proceeded with fluid and blood products\u00b4 resuscitation and close monitoring of labor till delivery of 2100gm male baby with APGAR score 8. Active management of third stage of labor was done with oxytocics to prevent post-partum haemorrhage. After manually repositing the cervix and uterus inside for the time being, the woman was sent to post-natal ward. Daily dressing of prolapse with magnesium sulphate done. A supportive ring pessary with ideal fit for the lady was placed against symphysis pubis resting in the posterior fornix on post-partum day 8. We counseled the lady for interval sterilisation to prevent future pregnancies and telephonic follow-up was taken. Here, multiple vaginal deliveries, anaemia, poor nutritional status were significant contributing factors in both preterm labour pains and cervical prolapse. These etiological factors contribute to major health hazards in developing nations. Surveillance and correction of these comorbidities is of utmost importance in pre-conceptional and antepartum period itself.Cervical prolapse during pregnancy is extremely rare but can cause complications in antepartum or intrapartum period and can have long term sequelae-for mother and fetus. A 32-year-old grand multipara with moderate anaemia (Hb-7.6gm/dl) and poor nutritional status (BMI-17kg/m"} +{"text": "Borderline personality disorder (BPD) has been characterized by mood instability, impulsive behavior and eventual dissociative and psychotic symptoms. Around 70% of patients present repeated self-injury behavior which is associated with high risk of completed suicide.To investigate the effect of group psychotherapy on the annual incidence of self-harm behavior and suicide attempts in BPD.We carried out a retrospective longitudinal study by selecting BPD patients who received group psychotherapy during 2016. Systems Training for Emotional Predictability and Problem Solving (STEPPS) or Mentalization-Based Treatment (MBT) psychotherapies were applied. Patients without any self-harm/suicidal attempt before the intervention, those with comorbid diagnosis and those who did not engage at least half of total sessions were excluded for final analyses. Number of self-harm events, suicide attempts and other clinical events were recorded and compared one-year before and one-year post-intervention. SPSS software version 21.0 (IBM) was used for statistical analyses. Nonparametric tests and Survival tests were performed.Eight women out of 35 fulfilled our inclusion criteria. After group psychotherapy, a significant reduction in the number of self-harm events and suicidal attempts was found . Survival tests revealed significant differences in the occurrence of suicidal attempts. We did not find significant differences in the other clinical events.Our results show a clear effectiveness of group psychotherapy in reducing self-harm events and/or suicidal attempts in BPD patients. If these findings are confirmed in future studies including larger samples, group psychotherapy could be indicated for diminishing suicide risks in BPD.No significant relationships."} +{"text": "Neuroimaging findings have reported aberrant functional connectivity in brain regions involved reward system in individuals with anorexia nervosa (AN) altering hedonic processing over food. Likewise, endocannabinoids such as Anandamide (AEA) and 2-Arachidonoylglycerol (2-AG) have been involved in rewarding aspects of food intake.To identify nucleus accumbens (NAcc) functional connectivity with whole-brain comparing between individuals with AN and controls. Furthermore, in a sub-study, to explore the interaction between NAcc functional connectivity and peripheral AEA and 2-AG levels.A total of 60 adult women (18 to 56 years of age) took part in the present study. Twenty-six individuals belonged to the AN group (BMI<18) and 34 to the HC group (BMI=18-24.99). All participants underwent functional magnetic resonance in resting-state, and blood samples were obtained in fasting.Negative functional connectivity was observed in the AN group compared with the control group between the NAcc and the cerebellum (pFWE<.001), between the NAcc and the insula (pFWE<.001), between the NAcc and the supramarginal gyrus (pFWE=.019), and between the NAcc and the postcentral gyrus (pFWE=.010). Analyses exploring the association between NAcc functional connectivity and peripheral endocannabinoids levels displayed altered NAcc-cerebellum functional connectivity was negatively associated with peripheral 2-AG levels in the AN group .Understanding the interaction between the reward system and peripheral endocannabinoids in patients with AN could contribute to better elucidate the pathophysiology of this disorder. Future studies will need to further investigate the clinical and therapeutic implications of these findings in patients with AN.No significant relationships."} +{"text": "Inflammatory choroidal neovascularization (i-CNV) is an infrequent but sight-threatening complication of posterior uveitis. Although it can occur in a wide range of infectious and non-infectious uveitides, presence of simultaneous bilateral i-CNV is rare. In this report, we present a unique case of bilateral simultaneous i-CNV in a young patient of healed tubercular serpiginous-like choroiditis. A 20-year-old male presented with recent worsening of vision in the right eye for one month. Fundus examination revealed bilateral multifocal healed choroiditis lesions with right eye tiny subfoveal hemorrhage raising the suspicion of an underlying choroidal neovascularization. Fundus fluorescein angiography and optical coherence tomography confirmed presence of choroidal neovascular membrane in both eyes.Resolution of activity was noted in both eyes after bilateral sequential intravitreal bevacizumab injections.Inflammatory choroidal neovascularization may be seen in patients with healed tubercular serpiginous-like choroiditis, after a long period of quiescence. Simultaneous bilateral presentation is rare but possible, requiring mandatory multimodal imaging of both eyes under high index of suspicion. Early institution of anti-vascular endothelial growth factor may salvage optimum vision in such a scenario. Inflammatory choroidal neovascularization (i-CNV) is an uncommon complication of posterior uveitis, rarer with bilateral disease . DiagnosA 20-year-old Asian-Indian male presented with bilateral painless diminution of vision for five years with recent worsening in the right eye (OD) for last one month. Ocular examination revealed best-corrected visual acuity (BCVA) of 20/200 in OD and 20/120 in the left eye (OS). Intraocular pressures and anterior segments were unremarkable. Dilated fundus showed for nine months during that episode and also underwent ventriculoperitoneal shunt surgery.Based on the clinical findings and ancillary investigations, a diagnosis of bilateral i-CNV associated with healed tubercular serpiginous-like choroiditis (SLC) was made. The patient underwent bilateral intravitreal bevacizumab injection at two weeks interval (OD treated first). After a month, OD injection was repeated due to persistent i-CNV.The patient was followed up monthly thereafter and at six-months follow-up, his BCVA remained stable at 20/120 in both eyes. Fundus showed resolution of i-CNV , less commonly with anterior uveitis and rarely with intermediate uveitis . Eyes wiWhile extrafoveal i-CNV is mostly asymptomatic and incidentally detected on imaging, lesions close to the fovea may present with diminution of vision or new onset metamorphopsia. Diagnosis of such lesions are challenging and are often missed due to various factors like significant background scarring, intense pigmentation, poorly dilating pupil, cataract, vitreous haze and sunset glow of fundus , 3]. A . A 3]. AThe lesions of i-CNV need to be differentiated from active choroiditis patches because treatment differs. Both can present clinically as yellowish lesions at the posterior pole with ill-defined margins with or without overlying fluid. On OCT, i-CNV presents mostly as type 2 lesion; another distinctive feature is the \u2018pitchfork sign\u2019 in which there are hyperreflective projections from the membrane to the overlying retina . Active The majority of i-CNV present as classic lesion in FFA; focal breach in retinal pigment epithelium (RPE) due to infection and inflammation is responsible for growth and progression of the neovascular membrane in the outer retinal space , 8]. In. In8]. IOCT-angiography (OCTA) may be the only investigative modality that helps us differentiate between active choroiditis and i-CNV with certainity, especially in equivocal cases. OCTA helps in identifying the vascular network even in cases with inconclusive FFA , 10]. T. T10]. TInflammation and angiogenesis both need to be managed in a case of i-CNV . As compOccurrence of i-CNV following tubercular SLC is infrequently reported in literature despite tuberculosis being one of the leading causes of infectious uveitis in endemic regions like the Indian subcontinent. Invernizzi et al. have described five cases of i-CNV as a rare and unusual presenting sign of intraocular tuberculosis from a non-endemic country, which were initially misdiagnosed as exudative ARMD .This report is unique in depicting simultaneous bilateral presentation of i-CNV following healed tubercular SLC and emphasizes the importance of detailed examination of the fellow eye with appropriate ancillary imaging under high index of suspicion. Early treatment with anti-VEGF can be promising, although they may require long-term follow-up to look for any recurrences.The authors declare that they have no competing interests."} +{"text": "Vitamin D helps in the regulation of neurotransmission and neuroprotection. Therefore, vitamin D deficiency might lead to inactivated receptors and may result in depression.The study assessed the relation between serum level of vitamin D and severity, symptomatology and cognitive dysfunction of Major Depressive Disorder (MDD) in a sample of Egyptian patients.Serum levels of 25-hydroxy vitamin D were measured with electro-chemiluminescence binding assay technique in 75 patients with major depressive disorder. Patients were recruited from Psychiatry and Addiction Hospital, Kasr Al Ainy outpatient clinic. Patients were subjected to the Structured Clinical Interview for DSM-IV Axis I Disorders(SCID), Hamilton depression scale (HAM-D), Mini-mental status examination (MMSE), Wechsler memory subtests (story A and paired associate learning test (PALT) ), Benton visual retention test (BVRT) and Trail B test.94.6% of patients had vitamin D deficiency. There was no significant correlation between levels of vitamin D and severity of depression according to HAM-D. Regarding symptoms of depression, there was a statistically significant difference between levels of vitamin D, being more deficient with decreased concentration, decreased libido and menstrual disturbances. There was no statistically significant correlation between level of vitamin D and cognitive functions tests.Major depressive disorder was associated with vitamin D deficiency but no statistical significant correlation could be established neither between levels of vitamin D and severity of depression nor between levels of vitamin D and cognitive dysfunction. Vitamin D level was statistically correlated with decreased concentration, decreased libido and menstrual disturbances.No significant relationships."} +{"text": "Transsexuals are considered to be stable in their identity . Meanwhile, the stages of medical transition affect the mental state of transsexuals differently.The aim was to reveal relationships between salience of self-identification in transsexual people being on different stages of medical transition.151 transsexual people: 55 pre-operated Female-to-Male (FtM I), 25 FtM on a hormonal therapy (FtM II), 25 FtM after some surgical operations (FtM III); 12 pre-operated Male-to-Female-Transsexual (MtF I), 16 MtF on a hormonal therapy (MtF II), 18 MtF after some surgical operations (MtF III). The participants filled the modificated Kuhn\u2019s test \u201cWho am I?\u201d . The modification includes a Likert scale for evaluating one\u2019s self-identifications in terms of salience: \u201cHow often do You think or remember this answer?\u201d .There were differences between identity salience and stages of medical transition . Transsexuals before medical transition demonstrated higher levels of identity salience . Transsexuals on a hormonal therapy demonstrated sharply decreased level of identity salience . Transsexuals after surgical operations reported increased level of salience . There were no statistically significant differences between the groups by gender assigned at birth.Data suggest that medical transition could change the salience of self-identification. Hormone therapy is associated with a sharp revision of the salience of self-identifications for transsexuals."} +{"text": "Recent studies have found promising evidence of the benefits of cognitive-behavioral interventions (CBIs) in improving depression and health status of African-American dementia caregivers (CGs). However, limited information exists about the specific CB strategies used in these investigations and which CB strategies were most effective in reducing caregiver distress and distress-related health problems. To address these shortcomings, Glueckauf and colleagues developed the African-American Dementia Caregiver Strategies Inventory (DCSI-A) using data from two CBI interventions (Nf129). The primary objectives of the current study were: (a) to identify the most frequently used categories of CBI strategies deployed by African-American CGs and (b) to conduct an initial evaluation of the psychometric properties of the DCSI-A. Descriptive statistics were calculated to assess strategy category frequency and percent of total responses. The two most frequently used strategies were: (1) CG Health-Related Intervention Strategies with 19 endorsements, 16.10% of total strategies and (2) Strategies for CG Social, Recreational, Personal Enhancement and Other Community Activities with 18 endorsements, 15.25% of total responses. These findings suggested that health-related and social, recreational, and personal enhancement strategies were the most commonly used by African-American CBI participants. Intercoder agreement was assessed across two one-month coding intervals, each of which contained 5 coding sessions. Mean percent of agreement and Kappa were .94 and .93, respectively. Both reliability measures fell within the highly acceptable range. Coder drift was minimal across the two time intervals. Future research will evaluate the psychometric properties of the DCSI-A with a larger sample of African-American CGs undergoing CBI."} +{"text": "Neurovascular diseases, including stroke, atherosclerosis, aneurysm, cerebral small vessel disease (cSVD), vascular cognitive impairment and dementia (VCID), and others, are major causes of death and disabilities. The prevalence of these neurovascular diseases has been steadily increasing due to the global population aging. During the past few decades, the technical advances of medical imaging methods, including MRI, CT, PET, optical and ultrasound (US) imaging, as well as photoacoustic imaging, have given the opportunities to image the neurovascular system in great details from micro to macro scales, from the capillaries (<10 um), arterioles/venules (~100 um) to large vessels (mm) including lumen, vessel wall and perivascular space.While most of the vascular imaging methods focus on the flowing lumen, vessel wall MRI provides the ability to directly visualize the vessel wall, which is the source of pathology in atherosclerotic plaques, aneurysms and other vasculopathy. Most vessel MRI studies were performed at 3 Tesla due to its high signal to noise ratio (SNR) compared to 1.5 Tesla, and the use of ultra-high field 7 Tesla MRI scanners further increase the ability MRI sequence (T2IR-SPACE) which markedly suppressed the Cerebrospinal Fluid (CSF) signal without much SNR loss of the other tissues . Such sequence can be used in multi-contrast intracranial vessel wall imaging to achieve good CSF suppression and improve the vessel wall contrast. Kong et al. developed 3D inner-volume (IV) TSE (SPACE) sequence with optimized 2D spatially selective excitation (SSE) radio frequency (RF) pulses, and they achieved the highest resolution (0.3 mm isotropic) in vivo vessel wall MRI so far by using a 7T scanner. They found clearer delineation of lenticulostriate artery (LSA) than conventional SPACE images.In this Research Topic collection, Xu et al. developed automatic segmentation methods for carotid and intracranial plaques on vessel wall MRI in 124 patients using machine learning. Their method demonstrated satisfactory agreement with the manual method, with dice values of 93.8% for lumen contours and 86.0% for outer wall contours, which were higher than those obtained from the traditional U-Net, Attention U-Net, and Inception U-Net. Lindenholz et al. found an interrelationship between large vessel wall lesion burden and cerebral parenchymal manifestations often linked to small vessel disease (SVD). Li J. et al. studied 68 patients with vertebrobasilar atherosclerosis using vessel wall MRI, and found the vertebrobasilar junction (VBJ) angle over 90\u00b0 might aggravate the vessel wall condition of the atherosclerotic vertebrobasilar arteries, which might serve as a potential risk factor for vertebrobasilar atherosclerosis.Eisenmenger et al. presented 9 cases of arteriovenous malformation (AVM) and found Vessel wall \u201cenhancement\u201d occurs in AVMs with no prior clinical rupture. Xiao et al. presented a case of intracranial plaque with serial vessel wall MRI follow up and they found vessel wall MRI can directly visualize the morphology and signal change of plaques. The suggest early identification of patients who do not respond well to medication is critical to prevent the recurrence of cardiovascular events in these patients.Jann et al. applied 3D pseudo-continuous arterial spin labeling (pCASL) MRI in the cohort of elderly Latinx subjects and found cerebral blood flow (CBF) in the leptomeningeal and perforator middle cerebral artery (MCA) territories were the most likely candidate biomarker of Vascular Cognitive Impairment and Dementia (VCID). Shi et al. compared several software for CT perfusion measurements and found F-STROKE software had excellent agreement with the widely used analysis tool of RAPID in measuring ischemic core volume (ICV) and penumbra volume (PV). Shou et al. developed super-resolution perfusion imaging and achieved high spatial resolution (isotropic-2 mm) using 2D simultaneous multi-slice (SMS) pseudo-continuous arterial spin labeling (pCASL) and slice dithered enhanced resolution (SLIDER) technique. de Bortoli et al. used T2*-weighted imaging and ultra-small superparamagnetic iron oxide nanoparticles to obtain subtraction angiographies and steady-state cerebral blood volume (ss-CBV) maps. They found the maps agreed well with first pass dynamic susceptibility contrast MRI (DSC-MRI). They concluded that iron oxide nanoparticle-based ss-CBV could serve as a robust, non-invasive imaging surrogate marker for neocortical vessels, with the potential to reduce and refine preclinical models targeting the development and outgrowth of cerebral collateralization.Perfusion imaging plays an important role in the management of patients with neurovascular diseases. Zhai et al. performed CFD analysis in 20 unruptured and 12 ruptured pericallosal artery aneurysms (PAA) with 3D digital subtraction angiography (DSA), and found a high mean oscillatory shear index (OSI) was an independent risk factor for PAA rupture. Zhang G. et al. studied the Hemodynamics using 4D flow MRI and found increased WSS, especially during the diastolic period and in the axial direction, may be a signal of a high-risk plaque and may cause cerebrovascular events in patients with moderate carotid artery stenosis.Hemodynamics plays important roles in the development and progression of vascular diseases. The hemodynamics information could be either computed using computational fluid dynamics (CFD) by using image-derived geometry or directly acquired by flow imaging. Zhu et al. studied a total of 632 patients with 668 MCA aneurysms (423 ruptured aneurysms) from five hospitals and quantified their radiomics and morphological features from computed tomography angiography images. They concluded integrating radiomics features into conventional models might provide additional value in ruptured MCA aneurysms classification. Shou et al. applied deep learning methods in perfusion imaging, and Xu et al. applied deep learning in vessel wall imaging.Bretzner et al. analyzed a multi-site cohort of 4,163 acute ischemic strokes (AIS) patients with T2-FLAIR MR images with total brain and white matter hyperintensity (WMH) segmentations. They found Radiomics extracted from T2-FLAIR images of AIS patients capture microstructural damage of the cerebral parenchyma and correlate with clinical phenotypes, suggesting different radiographical textural abnormalities per cardiovascular risk profile. Li T. et al. found high-resolution flat-detector computed tomography (HR-FDCT) improves visualization of the fine structures of intracranial stents deployed for symptomatic intracranial atherosclerotic stenosis (ICAS) compared with that visualized using conventional flat-detector computed tomography (FDCT). The concluded HR-FDCT improves assessment of stent deployment and could reduce the risk of complications. Du et al. reviewed the histological and imaging features of intimal and medial calcification within the large intracranial arteries and highlighted its clinical relevance.Vessel wall imaging is a hot topic with increasing research and clinical translation interests grants R01HL162743 and R00HL136883. ZF was supported by NIH grant R01HL147355.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Homebound older adults rely on home-based clinical services and long-term services and supports to remain living at home, however patterns of service use are unknown. Using data from the 2015 National Health and Aging Trends Study linked to Medicare Claims Data, we identified a population of homebound older adults enrolled in fee-for-service Medicare (n=1066). Latent class analysis identified 3 distinct patterns of home-based service use: low (36%), medium (51%), and high (13%) service use. High family caregiving support was particularly prevalent in the medium service group (35% with over 40 hours of family care per week), but receipt of home-based medical care was minimal in this group. Additional support to connect family caregivers with other home-based services may improve care and outcomes for older adults living at home."} +{"text": "Ovarian cancer (OC) is the leading cause of death from gynecological malignancies. Despite great advances in treatment strategies, therapeutic resistance and the gap between preclinical data and actual clinical efficacy justify the necessity of developing novel models for investigating OC. Organoids represent revolutionary three-dimensional cell culture models, deriving from stem cells and reflecting the primary tissue\u2019s biology and pathology. The aim of the current review is to study the current status of mouse- and patient-derived organoids, as well as their potential to model carcinogenesis and perform drug screenings for OC. Herein, we describe the role of organoids in the assessment of high-grade serous OC (HGSOC) cells-of-origin, illustrate their use as promising preclinical OC models and highlight the advantages of organoid technology in terms of disease modelling and drug sensitivity testing. Ovarian cancer (OC) represents the most common cause of death from malignancies of the female genital tract and the fifth most common tumor-related cause of death in women in the United States . AccordiThe generation of reliable pre-clinical models for the study of OC is critical for the development of personalized therapies and is a quest of imperative importance. The ideal pre-clinical model should be reproducible and should fully recapitulate the biological and morphological characteristics of OC. Several pre-clinical OC experimental models have been developed up until now, including 2D cell lines, patient-derived xenografts (PDX), patient-derived explants (PDE), animal models and patient-derived organoids (PDO) ,9. OC ceThe principle of PDX development is the transplantation of fresh OC tissue into immunodeficient mice. The success rate of OC PDX implementation varies significantly between studies but it universally accepted that the xenografts faithfully recapitulate the histology and the genomic profile of the original cancer tissue . HoweverOrganoid technology was introduced in 2009 as a groundbreaking 3D primary tissue culture model and was quickly developed as a sophisticated and promising preclinical model for cancer research ,20. OrgaTumour-derived organoids are generated from tumour tissue that undergoes dissociation resulting in single cells or cell aggregates that are seeded in a saturated medium consisting of hormones, nutrients, appropriate growth factors for the desired organ and a fundamental extracellular matrix (ECM), sold by the brand name Matrigel . OvarianIn general, the establishment of ovary organoids follows a similar strategy to that of other organs. According to a common preparation strategy, tissue fragments are first collected from the patient, then shattered into constituent cells by mechanical or enzymatic digestion, which involves incubation in a collagenase solution at 37 \u00b0C with continuous stirring for 1\u20132 h, and finally the tumor cells are cultured in a specific medium containing 75% Matrigel/25% culturing medium . This cuHGSOC is inconclusively believed to arise from ovarian surface epithelial or fallopian tube secretory cells . SeveralThe role of organoids in the assessment of HGSOC origins is depicted in Tp53\u2212/\u2212; BRCA1\u2212/\u2212; MycOE and Tp53\u2212/\u2212; PTEN\u2212/\u2212; NF1\u2212/\u2212 fallopian-tube-epithelium-derived organoids cause HGSOC-like tumors. Moreover, AKT2 and/or KRAS were found to cooperate with Cyclin E1 (CCNE1) to give rise to HGSOC, whereas organoid genotype influenced genome stability, drug response and secretome, with RNA-sequencing analysis revealing distinct transcriptomes for OC with different genotypes. Of note, tumorigenic organoids evoked distinct immune microenvironments which could be regulated by neutralizing organoid-produced chemo-/cytokines [Organoid culture has become common for patient-derived samples in OC. Chan et al. employed cell viability and cancer organoid assays in order to investigate the effect of overexpression of short-form thymic stromal lymphopoietin (sfTSLP), an epithelial cell derived cytokine, on tumor growth in vitro, and showed significantly higher numbers of viable cells of sfTSLP-expressing ovarian A2780 and IGROV-1 cancer cells, thus confirming its upregulation in OC . Chen etytokines . Very reytokines . OC orgaytokines . CollectThe use of organoids as a preclinical model for OC is summarized in Systemic platinum-taxanes combination chemotherapy represents the standard first-line chemotherapy for OC patients . NeverthBi et al. performed drug sensitivity assays on 19 OC and endometrial cancer patient-derived organoids and concluded that taxanes seem to be the predominant driver of therapeutic effectiveness in the systemic platinum-taxanes combination chemotherapy. Moreover, second-line therapeutic regimens including bevacizumab, gemcitabine or topotecan were not superior to first-line chemotherapy, whereas drug response testing reflected resistance to different agents given in the neoadjuvant setting . Chen etD\u2019Amora et al. used ovarian- and uterine-adenocarcinoma-derived organoids for the measurement of individual patient platinum resistance, ex vivo. Two thirds of the 47 included patients achieved complete remission with a mean progression time of almost two years, disease-free survival (DFS) of 1.7 years and overall survival (OS) of 2.6 years. Mean cisplatin lethal concentration 50% (LC50) was associated with a non-significant decrease in complete remission, reduced DFS as well as biochemical signatures of numerous metabolites. Interestingly, receiver operating curves (ROC) of lipid ratios, branched chain amino acids and the tryptophan to kynurenine ratio represented highly sensitive and specific tools for the identification of patients at the highest risk of relapse and death . Gorski McCorkle et al. analyzed paclitaxel resistance in patient-derived OC organoids and found elevated ATP-binding cassette subfamily B, member 1 (ABCB1) expression to correlate with chemoresistance in the organoid lines . OrganoiIn order to assess HGSOC chemoresistance in a tissue-similar environment, ascites-derived HGSOC cells from women subjected to either primary debulking surgery or neoadjuvant chemotherapy treatment were grown into short-term organoids. Pietil\u00e4 et al. suggested that collagen-6 adhesion was upregulated by cisplatin, and that collagen-6 enhanced protection against cisplatin cytotoxicity, especially in relapsed HGSOC oganoids . Sun et An in vitro organoid drug assay, which was employed in order to test the efficacy of carboplatin-ReACp53 synergy in OVCAR3 organoids, indicated the presence of increased apoptosis of OVCAR3 cells upon combination of carboplatin with ReACp53 . A seconSingh et al. utilized a three-dimensional organoid bioassay to test the efficacy of the carboplatin-birinapant combination therapy and highlighted its synergistic effects on a subset of platinum-resistant OC, with birinapant representing a potent second mitochondrial activator of caspase (SMAC) mimetic targeting inhibitors of apoptosis .Wambecke et al. developed OC organoids from patients with incomplete response to carboplatin and suggested that inhibition of Ubiquitin Conjugating Enzyme E2 N (UBE2N) sensitized OC cells to platinum-based chemotherapy via proapoptotic B-cell lymphoma 2 (BCL2) family protein BCL-2 Interacting Mediator of cell death (BIM) upregulation .Hill et al. created a platform for functionally profiling DNA repair in short-term patient-derived HGSOC organoids and found a functional defect in homologous recombination to be associated with Poly (ADP-ribose) polymerase (PARP) inhibitor sensitivity, as well as a functional defect in replication fork protection to correlate with carboplatin, and Checkpoint Kinase 1 (CHK1) and Ataxia telangiectasia and Rad3-related protein (ATR) inhibitor sensitivity . By perfBy performing immunofluorescence imaging of a patient-derived, ovarian carcinosarcoma organoid culture, Bi et al. demonstrated the hyperstaining of p53 protein. Computational modeling highlighted the significance of this residue in terms of protein conformation maintenance, whereas drug sensitivity testing proved the combination of bortezomib with belinostat to represent the most effective treatment . The samTp53\u2212/\u2212; Ccne1OE; Akt2OE; KrasOE HGSOC tumors [Cao et al. employed short-term HGSOC organoids to validate the effect of tumor infiltrating mast cells on anti-PD1 therapy and described that organoids derived from stromal-tumor-infiltrating-mast-cells-low women were correlated with a better response to anti-PD-1 treatment . Wan et C tumors .In order to appreciate the cytotoxic effects of the Naftopidil combination with ABT-737 or Trametinib, Florent et al. established three HGSOC organoid lines and, after performing cell viability assays, confirmed that, even though Naftopidil, ABT-737 or Trametinib used alone did not show noticeable effects on organoid morphology, the combination of Naftopidil with ABT-737 disintegrated the organoid structure .Liu et al. investigated the antitumor effects of Stichoposide C and found that this triterpene glycoside succeeded in inhibiting the growth of two patient-derived OC organoids .The CDK4/6 inhibitor Palbociclib showed a synergistic lethal effect on promoting cell cycle arrest and inducing apoptosis in patient-derived OC organoids, once combined with the bromodomain protein 4 inhibitor AZD5153 that inhibits the cell cycle-related protein and mitogen-activated protein kinase (MAPK)/PI3K-protein kinase B (AKT) pathway .McDowell et al. utilized RNA-sequencing analysis to identify genes and the relevant genetic pathways which showed differential regulation in artesunate resistant vs. sensitive OC organoid models, and found G1/S-transition-related pathways to be upregulated in artesunate resistant OC organoids .3-Allyl 4c complex bearing N-trifluoromethyl N-heterocyclic carbenes was very active on patient-derived HGSOC organoids, with low activity on normal liver organoids [Unlike carboplatin, Palladium (II)-\u03b7rganoids .By culturing organoids directly from patients with clear cell OC, Shigeta et al. proved the synergistic effect of bromodomain and extra-terminal domain (BET) and PI3K-AKT-mTOR inhibitors on p53-independent apoptosis induction .Vernon et al. investigated the treatment effects of an epidermal growth factor receptor (EGFR) inhibitor in combination with a BH3-mimetic molecule in four patient-derived OC organoids, with cell viability assays revealing synergistic effects of the erlotinib-ABT-737-combination. Notably, these pharmacologic inhibitors mimic the antitumor effect of microRNA-3622b-5p, which inhibits BCL/XL in OC cell lines escaping BIM induction, hence sensitizing them to cisplatin .The use of organoids for disease modeling and drug sensitivity testing is summarized in OC organoids represent an experimental model that overcomes major limitations of other preclinical models such as 2D cell lines and PDX. OC organoids faithfully recapitulate the histology and pathophysiology of OC subtypes, can undergo expansion and manipulation and are ideal for high-throughput drug screening. Thus, they are considered as unique platforms that bridge the gap between in vitro and in vivo models and hold promise for providing meaningful data that will shed light to OC pathogenesis and drive clinical decisions .Despite the enormous potential, OC organoid technology has several drawbacks that impair a widespread adoption as the principal preclinical model for OC. The first limitation is technical. The OC organoids preparation is time-consuming and expensive (due to the cost of Matrigel) in comparison to cell lines. Moreover, there is no standard protocol for OC organoids establishment, resulting in differences to the efficiency of each method, passaging and timeline of culture as well as in the morphology and functionality of organoids. The second limitation concerns the absence of the tumor microenvironment (TME) since the OC organoids include the epithelial cells but not the stroma, the immune cells and the vasculature present in OC. This limitation partially impairs the functionality and the heterogeneity of the system and may alter the response of organoids to drug screening assays. These two major limitations of the organoid system lead to lack of technical, morphological and functional reproducibility of organoid-based studies and constitute a major bottleneck that we need to overcome .The first step that is required for a broader use of OC organoids is the standardization of the protocols for organoid generation and the extensive characterization and validation of the methods that are currently in use. OC organoids need integration of biochemical and biophysical cues from the ECM and TME to be fully representative of OC tissues. Co-culture systems of ovarian OC with elements of TME would allow for a better spatio-temporal resolution and the minimization of intra-organoid heterogeneity. In fact, this approach has been already implemented in pilot studies with promising results ,74. MoreEven though OC has long been the point of interest of numerous studies, many questions regarding the cells-of-origin, the pathophysiological pathways or the most appropriate therapeutic regimen still remain unanswered. Since the introduction of organoids as self-organizing organotypic structures grown from tissue-derived cells in cancer research, a new era of comprehensive and faithful studies allowing for functional testing, therapeutic sensitivity prediction, and biomarker interrogation has begun ,86. Pati"} +{"text": "To adapt the BCHSM population segmentation methodology to Ontario\u2019s health administrative data to identify mutually exclusive segments with similar health care needs to support integrated care efforts and population health management in Ontario, Canada. To compare health system related costs across derived segments to identify opportunities for better integrated care.We identified Ontarians alive with valid health card numbers as of April 1, 2020 and created a matrix of prior utilization, cost and diagnoses using linked health administrative databases. Using a hierarchical technique, we assigned individuals into one of 14 BCHSM segments based on the greatest health care needs. Segments of need range from non-users (low need) to end-of-life patients (greatest need). We report the distribution of individual characteristics, average monthly costs across segments and further stratified health care costs by quintile of material deprivation within segments.The largest segment was the healthy (low) users (43%) followed by low chronic conditions (28%) and non-users (10%). Five segments comprised <1% of the total population: end-of-life, frail in care, cancer, frail in the community and child and youth major. Average costs per month alive increased from $28 for the non-user segment to $5,100 for the end-of-life segment (0.5% of the population). Costs in the Frail with high chronic conditions segment were 3-times higher than costs in the high chronic conditions segment ($930/mo), 6-times higher than costs in the medium chronic conditions segment ($450/mo), and 14-times higher than costs in the low chronic conditions segment ($193/mo). Results were generally more favourable in areas of low (vs high) material deprivation overall and within population segments.Using Ontario\u2019s linkable health administrative data we have created an Ontario adaptation of the BCHSM needs-based population segmentation approach. Segmentation supports population health management as well as helping identify opportunities for improvement to strengthen integrated care and potential cost savings."} +{"text": "Dear Editor,1 which include atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma, and invasive adenocarcinoma (AD).2 Recent data indicate that up to 20% of GGN patients (3% of the screening population) are diagnosed with synchronous multiple ground-glass nodules (SM-GGNs).3 At present, neither auxiliary tests that could assist in differential diagnosis nor recommended strategy for the identification and treatment of GGNs exist in the clinical practice guidelines for lung cancer, although clinical evidence suggests that SM-GGNs are more complicated, making treatment decisions difficult.1 Recent studies using next generation sequencing suggest differences in the mutational landscape not only among inter-tumors but also intra-tumor.The persistent presence of ground-glass opacity nodules (GGN) on thin-section computed tomography (CT) usually suggests the presence of lung adenocarcinoma,In this study, we first performed whole-genome sequencing (WGS) on 15 samples from five patients with each having two GGNs and one normal control Fig. . Detaile4 for intra-tumor subclone analysis. The germline heterozygous SNP loci (HET) across the genome were detected and the CNV and loss of heterozygosity (LOH) segments were jointy inferred from read depth and digital allele ratios at the HETs of the tumor WGS data. The new CNV and LOH types were reassessed at the multi-clone state that might be different from the previous single clone detection , our discoveries include shared CNV patterns and clonal structures between SM-GGNs. Our data support CNV correlation and cellular subclone estimation being an alternative and potentially more accurate and specific route for lineage determination.In summary, SM-GGNs in lung tumors present clinical challenges in surgery setting, therapy decision, and prognosis prediction.SUPPLEMENTAL MATERIAL"} +{"text": "The associations of problematic social media use, the special use of image-based social media and mental health have been established . The links may be explained with the theory of social comparison and self-objectification.Testing theory-oriented hypotheses related to image-based social media use and body dissatisfaction, gender specifically, among adolescents and young adults.Three surveys have been conducted with convenience sampling: (1) 117 Hungarian university students in person , (2) 383 high school students in person ; (3) 124 Israeli adolescents online .(1): The tendency of modifying body image in social media mediates the association between body shame and problematic social media use. Physical appearance social comparison mediates the association between self-related negative emotions and attitude (low self-esteem+ineffectiveness) and problematic social media use. (2): The technology-based social comparison mediate the association between muscle checking and problematic Instagram use among boys. (3) Physical appearance social comparison mediates the association between the frequency of following celebrities and body dissatisfaction among girls, but not among boys.During the use of image based social media, social comparison and the exposure to the beauty standards may lead to poorer mental health, which could result in problematic social media use as maladaptive coping.No significant relationships."} +{"text": "Crop disease poses a significant threat to global food security as the world population continues to expand dramatically. Crops have evolved sophisticated strategies to ward off various invading phytopathogens. Accordingly, phytopathogens have evolved intricate virulent mechanisms to facilitate their infection processes. Steady progress has been achieved in understanding plant resistance to phytopathogens in the last two decades. An emerging field of studying the molecular basis of crop-pathogen interactions is gaining more attention.Fusarium head blight, soil-borne diseases, including Fusarium crown rot, Gibberella stalk rot, and sheath blight, have emerged as new threats to the global productions of wheat and maize.Wheat and maize are the main food crops cultivated worldwide. The dominant wheat-maize rotation in many areas has remarkably impacted the cultivation environments of these two crops. In addition to traditional fungal diseases such as wheat rust, powdery mildew, and This Research Topic aims to explore the application of multiple omics in understanding the molecular interactions between wheat/maize and phytopathogens; identification of novel genes or genetic loci of wheat/maize conferring resistance to phytopathogens; functional characterization of defense-related genes in wheat/maize; and discovery of pathogenicity-related factors in phytopathogens. In total, it collects nine intriguing articles from international experts in the field and covers a broad range of subjects, which allows us to divide these articles into the following two themes:Cheng et al. characterized a wheat glucan synthase-like gene TaGSL22 during plant resistance to powdery mildew pathogen . An avirulent Bgt pathotype significantly upregulated the expression level of TaGSL22. Knocking down of TaGSL22 by virus-induced gene silencing (VIGS) reduced callose deposition, which resulted in enhanced wheat susceptibility to Bgt.The plant cell wall serves as the first barrier against the invasion of phytopathogens. Glucan is involved in the formation of callose, which prevents the initial infection of pathogens at the cell wall. Guo et al. identified a maize gamma-aminobutyric acid transaminase (GABA-T) that directly interacted with a cellulase from corn sheath blight pathogen (Rhizoctonia solani). Furthermore, they demonstrated that the identified maize GABA-T gene and its rice homolog (OsGABA-T) were sufficient to suppress the cellulase-induced necrosis, while CRISPR/Cas9-mediated OsGABA-T knockout rice plants displayed enhanced susceptibility to R. solani.Necrotrophic phytopathogens destroy basal host defense with various cell wall-degrading enzymes (CWDEs) to facilitate their infections. In contrast, host plants evolve corresponding mechanisms to counteract the activities of CWDEs. Zhao J. et al. revealed that a wheat lipid transfer protein TaLTP3, also known as a homolog of PR14, was positively correlated with plant resistance to leaf rust. Overexpression of the TaLTP3 gene in the transgenic wheat lines resulted in enhanced rust resistance and higher expression of TaPR1a in response to the infection of the model bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Further investigation indicated that TaLTP3 directly interacted with TaPR1a in the apoplastic space to co-regulate the plant defense response.As key downstream of plant defense response, various pathogenesis-related (PR) proteins function in the apoplastic space during the onset of plant-pathogen interaction. Tang et al. profiled the regulatory network of a maize Gibberella stalk rot (GSR)-resistant gene ZmCCT at the early infection stage. The ZmCCT-mediated maize resistance to Gibberella stalk rot caused by Fusarium graminearum were associated with activations of pattern-triggered immunity (PTI), phytohormone pathways of salicylic acid (SA) and auxin, and accumulations of phenylalanine metabolites.Key regulators and components in early responses of plant resistance to phytopathogens may have great potential in interpreting the mechanism of plant defense responses. Using multiple omics techniques, Boamah et al. reported that a biocontrol fungus Trichoderma longibrachiatum (TG1) with positive effects on wheat tolerance to salt stress and resistance to Fusarium crown rot caused by F. pseudograminearum. Moreover, expression levels of PR genes were significantly increased in response to TG1.Systemic acquired resistance (SAR) was another critical add-on for plant defense response beyond the hypersensitive response (HR). The action of some biocontrol agents was intensively associated with SAR. R) genes in response to biotrophic phytopathogens often leads to hypersensitive responses (HR) at the infection site following the gene-for-gene theory. Many R genes derived from crop wild relatives are widely used in breeding practice. Jin et al. identified a stripe rust resistance gene YrM8664-3 in a wheat-Leymus mollis introgression line. YrM8664-3, located on wheat chromosome 4AL, encoded a protein with plastid lipid-associated proteins (PAP)_fibrillin domain (TaFBN). TaFBN conferred high resistance to stripe rust in transgenic wheat lines.Activation of plant major resistance . Conversely, silencing of TaMYB29 by VIGS significantly reduced the wheat resistance to stripe rust with reduced ROS accumulation.Myeloblastosis (MYB) transcription factors are vital components in plant development and resistance to various stresses. R genes that exhibited autoactivated HR are considered as valuable genetic resources to explore the mechanism of cell death in the plant. Ge et al. revealed the transcriptomic and metabolomic profiles of a maize auto-active HR mutant Rp1-D21. Further investigation indicated that two maize UDP-dependent glycosyltransferase (ZmUGTs) genes partially suppressed the HR triggered by Rp1-D21 in a protein interaction-independent manner.Specific mutations on plant Fusarium head blight (FHB) in resistant wheat cultivars. Zhao L. et al. investigated the HR-BNL response in the leaf samples of a resistant wheat cultivar Sumai 3 inoculated with four disinct F. graminearum isolates. Flavonoid metabolites were identified and proved to be involved in the formation of HR-BNL. SA signaling pathway associated with ROS burst positively regulated FHB resistance in wheat with HR-BNL.Interestingly, HR-like black necrotic lesions (HR-BNL) often occur around the leaf infection sites of Overall, this Research Topic presents a broad range of articles that describe the application of multi-omics approaches in different wheat/maize-fungus pathosystems and expand our knowledge toward understanding the molecular interactions between wheat/maize and phytopathogens. Notably, several collected articles focusing on the role of HR in crop resistance have provided new insights into the molecular mechanism of crop major resistance genes.All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.XiaodW was supported by the Provincial Natural Science Foundation of Hebei (C2022204010 and C2021204008) and State Key Laboratory of North China Crop Improvement and Regulation (NCCIR2021ZZ-4). XiaojW was supported by the Shaanxi Innovation Team Project (2018TD-004). X-RC was supported by the National Natural Science Foundation of China (31871907 and 31671971) and Jiangsu Agriculture Science and Technology Innovation Fund (JASTIF) [CX(20)3125]. JW was supported by the Key R&D Program of Shaanxi Province in China (2021ZDLNY0-01). J-YG was supported by the National Natural Science Foundation of China (31972350). MZ was supported by the National Natural Science Foundation of China (32072399 and 31672008) and the Fundamental Research Funds for the Central Universities (GK202201017). GL was supported by the National Natural Science Foundation of China (32172373). LM was supported by the Hundred Talents Program for the introduction of high-level overseas talents in Hebei Province (E2020100004).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher."} +{"text": "Regular testing for SARS-CoV-2 is an important strategy for controlling virus outbreaks on university campuses during the COVID-19 pandemic but testing participation can be low. The Residence-Based Testing Participation Pilot (RB-TPP) was a novel 4-week intervention implemented at two student residences on a UK university campus, aiming to increase asymptomatic testing frequency and normalise university life through relaxed social restrictions onsite.Mixed-methods process evaluation determined whether RB-TPP was implemented as planned and identified implementation barriers and facilitators. Data were collected from meeting records, university students , and staff . Barriers and facilitators to implementation were mapped to the \u2018Capability, Opportunity, Motivation-Behaviour\u2019 (COM-B) behaviour change framework.Uptake was high . Implementation was broadly as planned, with adjustments due to national escalation of the COVID-19 Delta variant. Majority engaged in testing (88%); 46% (52% of testers) were fully compliant with pre-determined testing frequency. Most felt positively towards relaxed social distancing (97.9%). Implementation was facilitated by convenience and efficiency of testing and reduced negative impacts of isolation through opportunities for students to socialise. Barriers to implementation were mixed-messages about the rules, ambivalent attitudes, and lack of adherence to COVID-19 protective measures in the minority.This is the first process evaluation of the implementation of asymptomatic SARS-CoV-2 testing in university residences. Testing participation increased and student mental wellbeing improved. Rapid adaptions to the changing pandemic context generated complexity and challenge. Findings have global relevance for outbreak prevention and management strategies in higher education settings.\u2022\u2002Delivery of asymptomatic SARS-CoV-2 testing and relaxation of social distancing within residences led to high rates of testing participation and benefits for student mental wellbeing.\u2022\u2002This is the first process evaluation of the implementation of asymptomatic SARS-CoV-2 testing in university residences with global relevance for outbreak prevention in higher education settings."} +{"text": "Gag drives viral assembly and facilitates specific recognition and packaging of the SIV genomic RNA (gRNA) into viral particles. While several studies have tried to elucidate the role of SIV Pr55Gag by expressing its different components independently, studies using full-length SIV Pr55Gag have not been conducted, primarily due to the unavailability of purified and biologically active full-length SIV Pr55Gag. We successfully expressed soluble, full-length SIV Pr55Gag with His6-tag in bacteria and purified it using affinity and gel filtration chromatography. In the process, we identified within Gag, a second in-frame start codon downstream of a putative Shine-Dalgarno-like sequence resulting in an additional truncated form of Gag. Synonymously mutating this sequence allowed expression of full-length Gag in its native form. The purified Gag assembled into virus-like particles (VLPs) in vitro in the presence of nucleic acids, revealing its biological functionality. In vivo experiments also confirmed formation of functional VLPs, and quantitative reverse transcriptase PCR demonstrated efficient packaging of SIV gRNA by these VLPs. The methodology we employed ensured the availability of >95% pure, biologically active, full-length SIV Pr55Gag which should facilitate future studies to understand protein structure and RNA-protein interactions involved during SIV gRNA packaging.The simian immunodeficiency virus (SIV) precursor polypeptide Pr55 Some in vitro systems and in cell culture , ASPIRE [21M150], Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University [UCBR-31R143].Prof Tahir A. Rizvi was supported by College of Medicine and Health Sciences, Data included in article/supp. material/referenced in article.The authors declare no competing interests."} +{"text": "GmPRRs exhibited obvious rhythmic expression under long-day (LD) and short-day (SD) conditions, and the expression of 12 GmPRRs was higher under LD in leaves. To evaluate the effects of natural variations in GmPRR alleles on soybean adaptation, we examined the sequences of GmPRRs among 207 varieties collected across China and the US, investigated the flowering phenotypes in six environments, and analyzed the geographical distributions of the major haplotypes. The results showed that a majority of non-synonymous mutations in the coding region were associated with flowering time, and we found that the nonsense mutations resulting in deletion of the CCT domain were related to early flowering. Haplotype analysis demonstrated that the haplotypes associated with early flowering were mostly distributed in Northeast China, while the haplotypes associated with late flowering were mostly cultivated in the lower latitudes of China. Our study of PRR family genes in soybean provides not only an important guide for characterizing the circadian clock-controlled flowering pathway but also a theoretical basis and opportunities to breed varieties with adaptation to specific regions and farming systems.Pseudo-response regulator (PRR) family members serve as key components of the core clock of the circadian clock, and play important roles in photoperiodic flowering, stress tolerance, growth, and the development of plants. In this study, 14 soybean PRR genes were identified, and classified into three groups according to phylogenetic analysis and structural characteristics. Real-time quantitative PCR analysis revealed that 13 Glycine max) is a typical short-day (SD) plant showing photoperiod sensitivity ..PRR famiGmPRRs have both the N-terminal response-regulator receiver domains and the C-terminal CCT domain, except for GmPRR9 and GmPRR10, whose proteins from reference genome W82 carry large effect mutations causing the loss of the CCT domain. This is consistent with previous studies . Th. Th58]. https://www.arabidopsis.org/) (accessed on 8 February 2020). Soybean genome annotation was downloaded from the Phytozome 13.0 database (https://phytozome-next.jgi.doe.gov/) (accessed on 8 February 2020). Soybean PRR members resulting from both searches with an E-value threshold of